PeakID (cmd=annotatePeaks.pl /analysisdata/dbtss_seq/data_integration/mm10/reftss.mm10.v2.new.ids.bed mm10)	Chr	Start	End	Strand	Peak Score	Focus Ratio/Region Size	Annotation	Detailed Annotation	Distance to TSS	Nearest PromoterID	Entrez ID	Nearest Unigene	Nearest Refseq	Nearest Ensembl	Gene Name	Gene Alias	Gene Description	Gene Type
mm_159857.1	chr5	138280472	138280472	+	1	NA	promoter-TSS (NM_016964)	promoter-TSS (NM_016964)	-37	NM_016964	50878	Mm.285609	NM_016964	ENSMUSG00000036928	Stag3	SA-2	stromal antigen 3	protein-coding
mm_45638.1	chr5	76858567	76858582	-	1	NA	exon (NM_001163793, exon 6 of 9)	exon (NM_001163793, exon 6 of 9)	17975	NM_001163793	320827	Mm.101504	NM_001163793	ENSMUSG00000036377	C530008M17Rik	2810489J07Rik|4930529A19Rik|4931405B09Rik|Kiaa1211|mKIAA1211	RIKEN cDNA C530008M17 gene	protein-coding
mm_37237.1	chr4	118091751	118091799	-	1	NA	intron (NM_009176, intron 2 of 11)	B3|SINE|B2	43171	NM_001285520	20441	Mm.251002	NM_009176	ENSMUSG00000028538	St3gal3	ST3GalIII|ST3N|Siat3|Siat6	ST3 beta-galactoside alpha-2,3-sialyltransferase 3	protein-coding
mm_4068.1	chr1	166130437	166130462	+	1	NA	promoter-TSS (NM_021610)	promoter-TSS (NM_021610)	-11	NM_021610	59290	Mm.46357	NM_021610	ENSMUSG00000000544	Gpa33	2010310L10Rik|2210401D16Rik|BB116197	glycoprotein A33 (transmembrane)	protein-coding
mm_154549.1	chrM	14907	14954	-	1	NA	NA	Intergenic	NA	NA								
mm_42590.1	chr5	117357275	117357355	+	1	NA	promoter-TSS (NM_021539)	promoter-TSS (NM_021539)	10	NM_021539	59043	Mm.28489	NM_021539	ENSMUSG00000029364	Wsb2	AA673511|Swip2|WSB-2	WD repeat and SOCS box-containing 2	protein-coding
mm_25508.1	chr3	109574020	109574026	+	1	NA	promoter-TSS (NM_146139)	promoter-TSS (NM_146139)	16	NM_146139	57257	Mm.282257	NM_020505	ENSMUSG00000033721	Vav3	A530094I06Rik|AA986410|Idd18.1	vav 3 oncogene	protein-coding
mm_130312.1	chr15	97055943	97055964	-	1	NA	promoter-TSS (NM_027052)	promoter-TSS (NM_027052)	3	NM_027052	69354	Mm.250980	NM_027052	ENSMUSG00000022464	Slc38a4	1110012E16Rik|1700012A18Rik|Ata3|mATA3|mNAT3	solute carrier family 38, member 4	protein-coding
mm_34499.1	chr4	148602528	148602583	+	1	NA	promoter-TSS (NM_010767)	promoter-TSS (NM_010767)	11	NM_001003893	17175	Mm.378962	NM_010767	ENSMUSG00000028979	Masp2	MASP-2|MAp19	mannan-binding lectin serine peptidase 2	protein-coding
mm_140290.1	chr17	85613227	85613238	+	1	NA	non-coding (NR_038082, exon 4 of 4)	non-coding (NR_038082, exon 4 of 4)	5164	NR_038084	100043902	Mm.150838	NR_015385	ENSMUSG00000093460	Six3os1	D17Mgi26|E130112H22Rik|Rncr1|Six3os	SIX homeobox 3, opposite strand 1	ncRNA
mm_73571.1	chr8	109705579	109705636	+	1	NA	promoter-TSS (NM_001286391)	promoter-TSS (NM_001286391)	61	NM_001167946	75871	Mm.180410	NM_029468	ENSMUSG00000031728	Zfp821	4930566A11Rik|Znf821	zinc finger protein 821	protein-coding
mm_123921.1	chr14	73364679	73364693	-	1	NA	exon (NM_008410, exon 5 of 6)	exon (NM_008410, exon 5 of 6)	20585	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_170516.1	chr19	29464757	29464762	-	1	NA	intron (NM_021396, intron 5 of 5)	RLTR9F|LTR|ERVK	53840	NM_021396	58205	Mm.116737	NM_021396	ENSMUSG00000016498	Pdcd1lg2	B7-DC|Btdc|F730015O22Rik|PD-L2	programmed cell death 1 ligand 2	protein-coding
mm_143736.1	chr17	81473544	81473552	-	1	NA	intron (NR_104580, intron 2 of 8)	intron (NR_104580, intron 2 of 8)	264839	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_120578.1	chr14	69244351	69244365	+	1	NA	3' UTR (NM_026331, exon 4 of 4)	3' UTR (NM_026331, exon 4 of 4)	40745	NM_026331	67712	Mm.293635	NM_026331	ENSMUSG00000034248	Slc25a37	1700020E22Rik|4930513O14Rik|4930526G11Rik|AI848481|C330015G08Rik|Mfrn|Mfrn1|Mscp|frascati|mitoferrin	solute carrier family 25, member 37	protein-coding
mm_75109.1	chr8	34147019	34147066	-	1	NA	promoter-TSS (NM_026609)	promoter-TSS (NM_026609)	-303	NM_026609	68192	Mm.34212	NM_026609	ENSMUSG00000031513	Leprotl1	1110067H13Rik|1520402O14Rik|AI854296	leptin receptor overlapping transcript-like 1	protein-coding
mm_50099.1	chr6	41533115	41533132	+	1	NA	Intergenic	Intergenic	11347	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_96574.1	chr11	69058509	69058535	+	1	NA	Intergenic	B1_Mur3|SINE|Alu	-1253	NM_028005	71923	Mm.340257	NM_028005	ENSMUSG00000045176	Borcs6	2310047M10Rik	BLOC-1 related complex subunit 6	protein-coding
mm_92870.1	chr10	82241272	82241290	-	1	NA	promoter-TSS (NM_001105557)	promoter-TSS (NM_001105557)	-6	NM_001105557	237411		NM_172789	ENSMUSG00000062931	Zfp938	B230315N10Rik	zinc finger protein 938	protein-coding
mm_86635.1	chr10	14048269	14048269	+	1	NA	intron (NM_010437, intron 1 of 8)	intron (NM_010437, intron 1 of 8)	81890	NM_010437	15273	Mm.42157	NM_010437	ENSMUSG00000015501	Hivep2	Gm20114|MIBP1|Schnurri-2|Shn-2	human immunodeficiency virus type I enhancer binding protein 2	protein-coding
mm_121459.1	chr14	120494603	120494603	+	1	NA	intron (NM_029519, intron 1 of 1)	intron (NM_029519, intron 1 of 1)	16142	NM_029519	76108	Mm.261448	NM_029519	ENSMUSG00000051615	Rap2a	5830461H18Rik	RAS related protein 2a	protein-coding
mm_15987.1	chr2	166906450	166906486	+	1	NA	intron (NM_023565, intron 1 of 24)	CpG	372	NM_023565	110750	Mm.22417	NM_023565	ENSMUSG00000002718	Cse1l	2610100P18Rik|AA407533|Capts|Cas|Xpo2	chromosome segregation 1-like (S. cerevisiae)	protein-coding
mm_58482.1	chr7	3617358	3617389	+	1	NA	promoter-TSS (NM_025348)	promoter-TSS (NM_025348)	0	NM_025348	66091	Mm.17851	NM_025348	ENSMUSG00000035674	Ndufa3	1010001M12Rik|1700022J01Rik	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 3	protein-coding
mm_38994.1	chr4	151129436	151129452	-	1	NA	intron (NM_001081557, intron 11 of 23)	CpG	39874	NM_001308446	105704528	Mm.415128	NM_001308446	ENSMUSG00000078491	Gm13090	OTTMUSG00000010356	predicted gene 13090	protein-coding
mm_159198.1	chr2	119618103	119618103	+	1	NA	promoter-TSS (NM_001042652)	promoter-TSS (NM_001042652)	-195	NM_133851	108907	Mm.290015	NM_133851	ENSMUSG00000027306	Nusap1	2610201A12Rik|AI481307|ANKT|AW547774|BB165529|BM037|LNP|NuSAP|Q0310|SAPL	nucleolar and spindle associated protein 1	protein-coding
mm_55050.1	chr6	49042903	49042909	-	1	NA	exon (NM_053110, exon 2 of 11)	exon (NM_053110, exon 2 of 11)	6388	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_115329.1	chr13	112466863	112466880	+	1	NA	intron (NM_010560, intron 1 of 16)	intron (NM_010560, intron 1 of 16)	2801	NM_010560	16195	Mm.4364	NM_010560	ENSMUSG00000021756	Il6st	5133400A03Rik|AA389424|BB405851|CD130|D13Ertd699e|gp130	interleukin 6 signal transducer	protein-coding
mm_98017.1	chr11	84880377	84880391	+	1	NA	promoter-TSS (NM_001077636)	promoter-TSS (NM_001077636)	-99	NM_001077636	70325	Mm.390414	NM_027388	ENSMUSG00000045140	Pigw	2610044A17Rik|Gwt1	phosphatidylinositol glycan anchor biosynthesis, class W	protein-coding
mm_42170.1	chr5	112261674	112261681	+	1	NA	intron (NM_023695, intron 3 of 5)	intron (NM_023695, intron 3 of 5)	5857	NM_001312893	12960	Mm.29488	NM_023695	ENSMUSG00000029343	Crybb1	3110006K12Rik|BB1CRY	crystallin, beta B1	protein-coding
mm_133298.1	chr16	77501275	77501295	+	1	NA	intron (NR_015543, intron 3 of 4)	intron (NR_015543, intron 3 of 4)	-97651	NR_029535	387229		NR_029535	ENSMUSG00000065530	Mir99a	Mirn99a|mir-99a|mmu-mir-99a	microRNA 99a	ncRNA
mm_86566.1	chr10	11286235	11286237	+	1	NA	intron (NM_001168297, intron 1 of 2)	intron (NM_001168297, intron 1 of 2)	4649	NM_001168297	71865	Mm.276229	NM_027968	ENSMUSG00000047648	Fbxo30	1700026A16Rik|MUSA1	F-box protein 30	protein-coding
mm_2076.1	chr1	87646611	87646645	+	1	NA	intron (NM_010566, intron 2 of 26)	RSINE1|SINE|B4	26316	NM_001110193	16331	Mm.15105	NM_010566	ENSMUSG00000026288	Inpp5d	SHIP|SHIP-1|SHIP1|SIP-145|p150Ship|s-SHIP	inositol polyphosphate-5-phosphatase D	protein-coding
mm_6909.1	chr1	84839281	84839289	-	1	NA	promoter-TSS (NM_025386)	promoter-TSS (NM_025386)	19	NM_133975	14897	Mm.209265	NM_133975	ENSMUSG00000026219	Trip12	1110036I07Rik|6720416K24Rik|AA410158|Gtl6|TRIP-12	thyroid hormone receptor interactor 12	protein-coding
mm_139572.1	chr17	57062261	57062315	+	1	NA	promoter-TSS (NM_177638)	promoter-TSS (NM_177638)	11	NM_177638	224912	Mm.284447	NM_177638	ENSMUSG00000044279	Crb3	5730439B18|AU015179|AU041752	crumbs family member 3	protein-coding
mm_5072.1	chr1	3377787	3377789	-	1	NA	intron (NM_001011874, intron 2 of 2)	intron (NM_001011874, intron 2 of 2)	293710	NM_001011874	497097	Mm.454496	NM_001011874	ENSMUSG00000051951	Xkr4	AY534250|Gm210|XRG4|mKIAA1889	X-linked Kx blood group related 4	protein-coding
mm_127681.1	chr15	102936817	102936834	+	1	NA	promoter-TSS (NM_010463)	promoter-TSS (NM_010463)	-28	NM_010463	15421	Mm.221179	NM_010463	ENSMUSG00000050328	Hoxc12	Hox-3.8	homeobox C12	protein-coding
mm_145208.1	chr18	50026295	50026297	+	1	NA	intron (NM_001177759, intron 1 of 1)	intron (NM_001177759, intron 1 of 1)	-26986	NM_134131	106869	Mm.27740	NM_134131	ENSMUSG00000062210	Tnfaip8	AA987150|E130304C20Rik|ENSMUSG00000073567|Gg2-1|Gm10539|Nded|Ssc-2|Tipe	tumor necrosis factor, alpha-induced protein 8	protein-coding
mm_135808.1	chr16	57353181	57353197	-	1	NA	promoter-TSS (NM_001040397)	promoter-TSS (NM_001040397)	-88	NM_001040397	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding
mm_39511.1	chr5	21251707	21251723	+	1	NA	intron (NM_175437, intron 16 of 30)	B1_Mus2|SINE|Alu	65448	NM_175437	212167	Mm.121705	NM_175437	ENSMUSG00000039934	Gsap	A530088I07Rik|Pion	gamma-secretase activating protein	protein-coding
mm_164404.1	chr16	35281474	35281477	-	1	NA	intron (NM_001012765, intron 11 of 20)	intron (NM_001012765, intron 11 of 20)	82443	NM_133704	317717	Mm.259164	NM_133704	ENSMUSG00000034473	Sec22a	1810005C06Rik|Sec22l2	SEC22 homolog A, vesicle trafficking protein	protein-coding
mm_169203.1	chr13	66401873	66401877	-	1	NA	Intergenic	Intergenic	39243	NM_183119	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
mm_20216.1	chr2	125723708	125723723	-	1	NA	5' UTR (NM_199022, exon 1 of 12)	5' UTR (NM_199022, exon 1 of 12)	433	NM_199022	271849	Mm.425101	NM_199022	ENSMUSG00000035109	Shc4	6230417E10Rik|9930029B02Rik|Gm685|RaLP	SHC (Src homology 2 domain containing) family, member 4	protein-coding
mm_128439.1	chr15	50715216	50715220	-	1	NA	intron (NM_001310481, intron 4 of 5)	intron (NM_001310481, intron 4 of 5)	173831	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_154215.1	chr19	59313956	59313957	-	1	NA	intron (NM_001033222, intron 3 of 4)	B1_Mur1|SINE|Alu	31824	NM_001033222	107368	Mm.27250	NM_001033222	ENSMUSG00000074746	Pdzd8	A630041P07Rik|AV329468|AW228944|Pdzk8	PDZ domain containing 8	protein-coding
mm_68474.1	chr7	110844377	110844451	-	1	NA	promoter-TSS (NM_025999)	promoter-TSS (NM_025999)	-33	NM_025999	67150	Mm.96867	NM_025999	ENSMUSG00000030788	Rnf141	2610110L04Rik|AA792898|AU022812|ZFP36|ZNF230	ring finger protein 141	protein-coding
mm_57680.1	chr6	128503527	128503539	-	1	NA	TTS (NR_028593)	TTS (NR_028593)	23187	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_94.1	chr1	7177672	7177679	+	1	NA	Intergenic	Intergenic	88755	NM_183028	319263	Mm.21539	NM_183028	ENSMUSG00000051285	Pcmtd1	8430411F12Rik|A030012M09Rik	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding
mm_104458.1	chr11	95065907	95065918	-	1	NA	exon (NM_001306162, exon 5 of 26)	exon (NM_001306162, exon 5 of 26)	3286	NM_001306071	16400	Mm.57035	NM_013565	ENSMUSG00000001507	Itga3	AA407068|CD49C|GAPB3	integrin alpha 3	protein-coding
mm_33225.1	chr4	126753871	126753880	+	1	NA	promoter-TSS (NM_011986)	promoter-TSS (NM_011986)	105	NM_001035526	100317	Mm.206206	NM_133886	ENSMUSG00000028830	AU040320	A730047D20Rik|AAVR|Kiaa0319l	expressed sequence AU040320	protein-coding
mm_90359.1	chr10	127165503	127165503	+	1	NA	promoter-TSS (NM_027739)	promoter-TSS (NM_027739)	-328	NM_027739	14421	Mm.386762	NM_008080	ENSMUSG00000006731	B4galnt1	4933429D13Rik|Gal-NAc-T|GalNAc-T|GalNAcT|Galgt1|Ggm-2|Ggm2	beta-1,4-N-acetyl-galactosaminyl transferase 1	protein-coding
mm_81975.1	chr9	121298747	121298757	+	1	NA	Intergenic	Intergenic	-21580	NM_177589	209012	Mm.371804	NM_177589	ENSMUSG00000040936	Ulk4	4932415A06Rik|A730098P15	unc-51-like kinase 4	protein-coding
mm_80180.1	chr9	72279159	72279163	+	1	NA	intron (NM_001311105, intron 1 of 20)	RMER10A|LTR|ERVL	4273	NM_001311105	235469	Mm.242791	NM_146224	ENSMUSG00000038535	Zfp280d	A930005F02Rik|BC027163|Suhw4|ZNF634|Znf280d	zinc finger protein 280D	protein-coding
mm_157371.1	chrX	37878487	37878498	-	1	NA	exon (NM_001004193, exon 2 of 4)	exon (NM_001004193, exon 2 of 4)	452	NM_001004193	434768	Mm.336025	NM_001004193	ENSMUSG00000064137	Rhox8	Tox	reproductive homeobox 8	protein-coding
mm_82033.1	chr9	121951048	121951087	+	1	NA	promoter-TSS (NM_001199927)	promoter-TSS (NM_001199927)	47	NM_001199927	245050	Mm.71062	NM_177743	ENSMUSG00000038233	Fam198a	C730027P07Rik	family with sequence similarity 198, member A	protein-coding
mm_19146.1	chr2	80524693	80524697	-	1	NA	intron (NM_016965, intron 18 of 30)	intron (NM_016965, intron 18 of 30)	56487	NM_001290745	50884	Mm.25203	NM_016965	ENSMUSG00000027002	Nckap1	C79304|H19|Hem-2|Hem2|Nap1|mKIAA0587|mh19|p125Nap1	NCK-associated protein 1	protein-coding
mm_79664.1	chr9	59658461	59658489	+	1	NA	intron (NM_001253883, intron 1 of 10)	intron (NM_001253883, intron 1 of 10)	2107	NM_001253883	18746	Mm.326167	NM_011099	ENSMUSG00000032294	Pkm	AA414905|AL024370|AL024424|Pk-2|Pk-3|Pk3|Pkm2	pyruvate kinase, muscle	protein-coding
mm_57868.1	chr6	129623972	129623978	-	1	NA	promoter-TSS (NM_001286018)	promoter-TSS (NM_001286018)	-111	NM_001286018	27007	Mm.8217	NM_033078	ENSMUSG00000030149	Klrk1	D6H12S2489E|NKG2-D|Nkg2d	killer cell lectin-like receptor subfamily K, member 1	protein-coding
mm_50944.1	chr6	58017482	58017483	+	1	NA	Intergenic	Intergenic	-8280	NM_134172	171190	Mm.377170	NM_134172	ENSMUSG00000048697	Vmn1r26	V1rc17	vomeronasal 1 receptor 26	protein-coding
mm_153190.1	chr19	34509831	34509850	-	1	NA	intron (NM_001111100, intron 4 of 9)	RMER17C|LTR|ERVK	17634	NM_001111100	16889	Mm.157545	NM_021460	ENSMUSG00000024781	Lipa	AA960673|Lal|Lip-1|Lip1	lysosomal acid lipase A	protein-coding
mm_10233.1	chr2	6472028	6472052	+	1	NA	Intergenic	MLT1B|LTR|ERVL-MaLR	119304	NM_181399	98910	Mm.40673	NM_181399	ENSMUSG00000039046	Usp6nl	AI316785|RNTRE|TRE2NL|mKIAA0019	USP6 N-terminal like	protein-coding
mm_12240.1	chr2	68861111	68861154	+	1	NA	promoter-TSS (NM_001347161)	promoter-TSS (NM_001347161)	-309	NM_172856	241447	Mm.222222	NM_172856	ENSMUSG00000027035	Cers6	4732462C07Rik|AW544719|Lass6|T1L	ceramide synthase 6	protein-coding
mm_134263.1	chr16	13750857	13750869	-	1	NA	Intergenic	B1_Mus2|SINE|Alu	-20379	NM_011987	26565	Mm.4214	NM_011987	ENSMUSG00000022683	Pla2g10	GX sPLA2|PLA2GX|sPLA2-X	phospholipase A2, group X	protein-coding
mm_128691.1	chr15	61989544	61989558	-	1	NA	exon (NM_001177354, exon 3 of 3)	exon (NM_001177354, exon 3 of 3)	4210	NM_001177352	17869	Mm.2444	NM_010849	ENSMUSG00000022346	Myc	AU016757|Myc2|Niard|Nird|bHLHe39	myelocytomatosis oncogene	protein-coding
mm_20117.1	chr2	121171078	121171093	-	1	NA	promoter-TSS (NR_110985)	promoter-TSS (NR_110985)	40	NM_001290819	99334	Mm.188422	NM_178889	ENSMUSG00000050619	Zscan29	AW125441|Zfp690	zinc finger SCAN domains 29	protein-coding
mm_13521.1	chr2	110013163	110013174	+	1	NA	3' UTR (NM_172671, exon 18 of 18)	3' UTR (NM_172671, exon 18 of 18)	-4649	NM_026613	68201	Mm.181767	NM_026613	ENSMUSG00000027160	Ccdc34	2810027O19Rik|4930522P10Rik|AI596202	coiled-coil domain containing 34	protein-coding
mm_88990.1	chr10	81565738	81565766	+	1	NA	non-coding (NR_074087, exon 7 of 7)	non-coding (NR_074087, exon 7 of 7)	6308	NM_001276288	14797	Mm.180013	NM_010347	ENSMUSG00000054452	Aes	AL024115|Esp1|Grg|Grg-5|Grg5|Tle5	amino-terminal enhancer of split	protein-coding
mm_134924.1	chr16	30550530	30550549	-	1	NA	promoter-TSS (NM_172614)	promoter-TSS (NM_172614)	39	NM_172614	224090	Mm.241459	NM_172614	ENSMUSG00000022537	Tmem44	1700007N03Rik|9330161C17Rik|B230220N21	transmembrane protein 44	protein-coding
mm_25248.1	chr3	103988338	103988386	+	1	NA	intron (NM_001163467, intron 7 of 18)	intron (NM_001163467, intron 7 of 18)	-20046	NR_030676	100125931	Mm.400392	NR_030676	ENSMUSG00000089998	Phtf1os	A130049A11Rik	putative homeodomain transcription factor 1, opposite strand	ncRNA
mm_147456.1	chr18	46574470	46574488	-	1	NA	promoter-TSS (NM_173394)	promoter-TSS (NM_173394)	54	NM_173394	225471	Mm.149280	NM_173394	ENSMUSG00000056130	Ticam2	B430113A10|TICAM-2|TRAM|Tirp|Trif	toll-like receptor adaptor molecule 2	protein-coding
mm_81079.1	chr9	106223923	106223934	+	1	NA	exon (NM_031178, exon 2 of 2)	exon (NM_031178, exon 2 of 2)	1330	NM_031178	81897	Mm.44889	NM_031178	ENSMUSG00000045322	Tlr9	-	toll-like receptor 9	protein-coding
mm_80647.1	chr9	89869825	89869843	+	1	NA	Intergenic	Intergenic	-39941	NM_011245	19417	Mm.44561	NM_011245	ENSMUSG00000032356	Rasgrf1	AI844718|CDC25|CDC25Mm|Gnrp|Grf1|Grfbeta|P190-A|Ras-GRF1|p190|p190RhoGEF	RAS protein-specific guanine nucleotide-releasing factor 1	protein-coding
mm_124287.1	chr14	103051479	103051494	-	1	NA	exon (NM_008392, exon 4 of 5)	exon (NM_008392, exon 4 of 5)	4474	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_145403.1	chr18	57405332	57405358	+	1	NA	Intergenic	Intergenic	50612	NM_028447	73137	Mm.29889	NM_028447	ENSMUSG00000024594	Prrc1	1190002C06Rik|2310058D16Rik|3110038B19Rik|9430085A19Rik	proline-rich coiled-coil 1	protein-coding
mm_98573.1	chr11	95569828	95569847	+	1	NA	3' UTR (NM_033217, exon 6 of 6)	3' UTR (NM_033217, exon 6 of 6)	17861	NM_033217	18053	Mm.283893	NM_033217	ENSMUSG00000000120	Ngfr	LNGFR|Tnfrsf16|p75|p75NGFR|p75NTR	nerve growth factor receptor (TNFR superfamily, member 16)	protein-coding
mm_101899.1	chr11	49187080	49187088	-	1	NA	promoter-TSS (NM_172793)	promoter-TSS (NM_172793)	5	NM_172793	237754	Mm.130787	NM_172793	ENSMUSG00000040283	Btnl9	B430208I01|Btn3|D330012D11Rik	butyrophilin-like 9	protein-coding
mm_139061.1	chr17	46433832	46433839	+	1	NA	intron (NM_144856, intron 7 of 9)	intron (NM_144856, intron 7 of 9)	4642	NM_144856	108114	Mm.387538	NM_144856	ENSMUSG00000067144	Slc22a7	NLT|OAT2	solute carrier family 22 (organic anion transporter), member 7	protein-coding
mm_47270.1	chr5	121859981	121859984	-	1	NA	TTS (NM_007804)	TTS (NM_007804)	10954	NM_175474	231717	Mm.12654	NM_175474	ENSMUSG00000044134	Fam109a	A230106M15Rik|AU017694|IPIP27A|Ses1	family with sequence similarity 109, member A	protein-coding
mm_91643.1	chr10	42276745	42276763	-	1	NA	promoter-TSS (NM_019740)	promoter-TSS (NM_019740)	-12	NM_019740	56484	Mm.338613	NM_019740	ENSMUSG00000048756	Foxo3	1110048B16Rik|2010203A17Rik|C76856|FKHRL1|Fkhr2|Foxo3a	forkhead box O3	protein-coding
mm_113698.1	chr13	43125931	43125938	+	1	NA	intron (NM_001005740, intron 9 of 12)	intron (NM_001005740, intron 9 of 12)	3095	NM_001005748	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding
mm_86147.1	chr9	117252127	117252183	-	1	NA	5' UTR (NM_001172126, exon 1 of 13)	5' UTR (NM_001172126, exon 1 of 13)	328	NM_001172123	207181	Mm.326411	NM_178660	ENSMUSG00000039607	Rbms3	6720477E09Rik|8430436O14Rik	RNA binding motif, single stranded interacting protein	protein-coding
mm_43507.1	chr5	136987585	136987642	+	1	NA	promoter-TSS (NM_001310748)	promoter-TSS (NM_001310748)	346	NM_027318	70103	Mm.273147	NM_027318	ENSMUSG00000059518	Znhit1	2700001K05Rik|ZNFN4A1	zinc finger, HIT domain containing 1	protein-coding
mm_153717.1	chr19	44403278	44403299	-	1	NA	exon (NM_009127, exon 3 of 6)	exon (NM_009127, exon 3 of 6)	4421	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_69229.1	chr7	127686827	127686840	-	1	NA	intron (NM_001347652, intron 5 of 5)	RMER17D2|LTR|ERVK	-21654	NR_030428	791073		NR_030428	ENSMUSG00000076454	Mir762	Mirn762|mir-762|mmu-mir-762	microRNA 762	ncRNA
mm_164869.1	chr18	56588339	56588339	+	1	NA	promoter-TSS (NM_026099)	promoter-TSS (NM_026099)	-9	NM_026099	67343	Mm.87057	NM_026099	ENSMUSG00000032900	Tex43	1700065I17Rik|Tseg7	testis expressed 43	protein-coding
mm_101833.1	chr11	47985153	47985176	-	1	NA	intron (NR_105801, intron 3 of 3)	intron (NR_105801, intron 3 of 3)	89419	NR_105801	102466638		NR_105801	ENSMUSG00000099011	Mir6380	Gm27356|mmu-mir-6380	microRNA 6380	ncRNA
mm_138216.1	chr17	34307548	34307550	+	1	NA	intron (NM_010382, intron 1 of 5)	intron (NM_010382, intron 1 of 5)	1682	NM_010382	14969	Mm.22564	NM_010382	ENSMUSG00000060586	H2-Eb1	Eb|H-2Eb|H2Eb|Ia-4|Ia4	histocompatibility 2, class II antigen E beta	protein-coding
mm_74625.1	chr8	13105486	13105508	-	1	NA	promoter-TSS (NM_178708)	promoter-TSS (NM_178708)	-154	NM_178708	234069	Mm.103427	NM_178708	ENSMUSG00000038542	Pcid2	A730042J05Rik	PCI domain containing 2	protein-coding
mm_49161.1	chr6	13682627	13682632	+	1	NA	Intergenic	RMER1B|Other|Other	-4663	NM_175312	101148	Mm.354863	NM_175312	ENSMUSG00000042742	Bmt2	AI666701|B630005N14Rik	base methyltransferase of 25S rRNA 2	protein-coding
mm_19858.1	chr2	113829613	113829639	-	1	NA	promoter-TSS (NM_009162)	promoter-TSS (NM_009162)	-535	NM_009162	20394	Mm.4836	NM_009162	ENSMUSG00000023236	Scg5	7B2|AI325031|Sgne-1|Sgne1	secretogranin V	protein-coding
mm_121659.1	chr14	12343731	12343749	-	1	NA	exon (NM_080433, exon 4 of 5)	exon (NM_080433, exon 4 of 5)	2125	NM_080433	54713	Mm.34644	NM_080433	ENSMUSG00000021743	Fezf2	AI451466|AI852056|Fez|Fezl|Zfp312	Fez family zinc finger 2	protein-coding
mm_135850.1	chr16	59557364	59557371	-	1	NA	Intergenic	Intergenic	-1615	NM_174848	224273	Mm.246424	NM_174848	ENSMUSG00000022723	Crybg3	5031404N19|AU022790|Gm9581	beta-gamma crystallin domain containing 3	protein-coding
mm_28207.1	chr3	88334429	88334466	-	1	NA	promoter-TSS (NM_024246)	promoter-TSS (NM_024246)	-14	NM_024246	71913	Mm.34256	NM_024246	ENSMUSG00000001420	Tmem79	2310042N02Rik|2310074C17Rik|Matt|ma	transmembrane protein 79	protein-coding
mm_69498.1	chr7	134225197	134225205	-	1	NA	promoter-TSS (NM_007400)	promoter-TSS (NM_007400)	-104	NM_007400	11489	Mm.439714	NM_007400	ENSMUSG00000054555	Adam12	Mltna	a disintegrin and metallopeptidase domain 12 (meltrin alpha)	protein-coding
mm_147495.1	chr18	47369069	47369089	-	1	NA	promoter-TSS (NM_018744)	promoter-TSS (NM_018744)	-209	NM_001311097	20358	Mm.40909	NM_018744	ENSMUSG00000019647	Sema6a	A730020P05Rik|AI851735|Sema6A-1|Semaq|VIa	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A	protein-coding
mm_61011.1	chr7	49364939	49364950	+	1	NA	intron (NM_175272, intron 2 of 37)	intron (NM_175272, intron 2 of 37)	118755	NM_175272	78286	Mm.333881	NM_175272	ENSMUSG00000052512	Nav2	5330421F07Rik|AU067780|BQ960892|HELAD1|POMFIL2|RAINB1|RAINB2|Unc53H2|mKIAA3015	neuron navigator 2	protein-coding
mm_116395.1	chr13	41220176	41220195	-	1	NA	promoter-TSS (NM_001311121)	promoter-TSS (NM_001311121)	-23	NM_001311121	54326	Mm.2567	NM_019423	ENSMUSG00000021364	Elovl2	AI317360|Ssc2	elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 2	protein-coding
mm_50686.1	chr6	51584488	51584507	+	1	NA	intron (NM_028035, intron 5 of 6)	ID_B1|SINE|B4	39974	NM_001127348	71982	Mm.294166	NM_028035	ENSMUSG00000038301	Snx10	2410004M09Rik	sorting nexin 10	protein-coding
mm_96708.1	chr11	69655712	69655733	+	1	NA	TTS (NR_125917)	TTS (NR_125917)	685	NM_009235	20670	Mm.347499	NM_009235	ENSMUSG00000041287	Sox15	-	SRY (sex determining region Y)-box 15	protein-coding
mm_79590.1	chr9	58276496	58276505	+	1	NA	Intergenic	Intergenic	23336	NM_026942	69106	Mm.216502	NM_026942	ENSMUSG00000032333	Stoml1	1810015E19Rik|AI847431|SLP1|STORP|UNC24|WPB72	stomatin-like 1	protein-coding
mm_33116.1	chr4	124742918	124742929	+	1	NA	promoter-TSS (NR_030480)	promoter-TSS (NR_030480)	-858	NR_030480	735263		NR_030480	ENSMUSG00000076119	Mir698	Mirn698|mir-698|mmu-mir-698	microRNA 698	ncRNA
mm_115274.1	chr13	111686200	111686210	+	1	NA	promoter-TSS (NM_172593)	promoter-TSS (NM_172593)	27	NM_172593	218613	Mm.31012	NM_172593	ENSMUSG00000032727	Mier3	5730509D14|AU015422|D130064H19Rik	MIER family member 3	protein-coding
mm_112458.1	chr13	5864851	5864861	+	1	NA	exon (NM_011803, exon 2 of 4)	exon (NM_011803, exon 2 of 4)	3367	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_79753.1	chr9	62373501	62373537	+	1	NA	exon (NM_009672, exon 4 of 7)	exon (NM_009672, exon 4 of 7)	32176	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	protein-coding
mm_64193.1	chr7	141464030	141464089	+	1	NA	intron (NM_001025103, intron 3 of 9)	intron (NM_001025103, intron 3 of 9)	2965	NM_001025103	213573	Mm.386851	NM_001025103	ENSMUSG00000048200	Cracr2b	6330520A15Rik|BC026645|Cracr2a|Efcab4|Efcab4a	calcium release activated channel regulator 2B	protein-coding
mm_108738.1	chr12	88360841	88360850	+	1	NA	promoter-TSS (NM_028105)	promoter-TSS (NM_028105)	63	NM_028105	72113	Mm.181387	NM_028105	ENSMUSG00000021044	Adck1	2610005A10Rik	aarF domain containing kinase 1	protein-coding
mm_60040.1	chr7	31037860	31037887	+	1	NA	exon (NM_001111073, exon 4 of 8)	exon (NM_001111073, exon 4 of 8)	2444	NR_106017	102465635		NR_106017	ENSMUSG00000098783	Mir7050	Gm27578|mmu-mir-7050	microRNA 7050	ncRNA
mm_151084.1	chr19	47622653	47622664	+	1	NA	exon (NM_001164639, exon 11 of 18)	exon (NM_001164639, exon 11 of 18)	42639	NM_001164639	20874	Mm.281011	NM_009289	ENSMUSG00000025060	Slk	9A2|AV021402|AW411554|Etk4|SMAK|Stk2|mKIAA0204|mSLK	STE20-like kinase	protein-coding
mm_117366.1	chr13	70841763	70841783	-	1	NA	promoter-TSS (NR_137640)	promoter-TSS (NR_137640)	38	NM_172053	271127	Mm.115970	NM_172053	ENSMUSG00000049538	Adamts16	-	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 16	protein-coding
mm_129658.1	chr15	81067023	81067037	-	1	NA	intron (NM_001082536, intron 2 of 13)	intron (NM_001082536, intron 2 of 13)	38017	NM_153049	223701	Mm.439814	NM_153049	ENSMUSG00000042292	Mkl1	AMKL|Bsac|Mal|Mrtf-A	MKL (megakaryoblastic leukemia)/myocardin-like 1	protein-coding
mm_29242.1	chr3	107216083	107216095	-	1	NA	exon (NM_001111143, exon 5 of 9)	exon (NM_001111143, exon 5 of 9)	5643	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_165711.1	chr3	98857915	98857915	-	1	NA	exon (NM_001304800, exon 2 of 4)	exon (NM_001304800, exon 2 of 4)	1879	NM_001304800	15492	Mm.140811	NM_008293	ENSMUSG00000027871	Hsd3b1	3-beta-HSD I|D3Ertd383e	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1	protein-coding
mm_31514.1	chr4	53826163	53826186	+	1	NA	exon (NM_028053, exon 1 of 6)	exon (NM_028053, exon 1 of 6)	129	NM_028053	52076	Mm.27184	NM_028053	ENSMUSG00000028420	Tmem38b	1600017F22Rik|AA437809|AV051057|D4Ertd89e|TRIC-B|mg33b	transmembrane protein 38B	protein-coding
mm_158862.1	chrY	2053271	2053273	+	1	NA	Intergenic	Intergenic	117137	NM_009571	22768	Mm.411381	NM_009571	ENSMUSG00000000103	Zfy2	Zfy-2	zinc finger protein 2, Y-linked	protein-coding
mm_122307.1	chr14	35812008	35812010	-	1	NA	promoter-TSS (NM_001033766)	promoter-TSS (NM_001033766)	-31	NM_001033766	239036	Mm.239970	NM_001033766	ENSMUSG00000041068	4930596D02Rik	-	RIKEN cDNA 4930596D02 gene	protein-coding
mm_166125.1	chr4	153697570	153697578	+	1	NA	Intergenic	Intergenic	-214744	NM_001099299	230959	Mm.318874	NM_001099299	ENSMUSG00000039546	Ajap1	Gm573	adherens junction associated protein 1	protein-coding
mm_118610.1	chr14	20929417	20929451	+	1	NA	promoter-TSS (NM_009502)	promoter-TSS (NM_009502)	1	NM_009502	22330	Mm.279361	NM_009502	ENSMUSG00000021823	Vcl	9430097D22|AA571387|AI462105|AW545629	vinculin	protein-coding
mm_117704.1	chr13	95049405	95049416	-	1	NA	intron (NM_001346782, intron 12 of 21)	intron (NM_001346782, intron 12 of 21)	73066	NM_172590	218460	Mm.33856	NM_172590	ENSMUSG00000042015	Wdr41	B830029I03Rik|MSTP048	WD repeat domain 41	protein-coding
mm_40065.1	chr5	34188058	34188119	+	1	NA	promoter-TSS (NM_010753)	promoter-TSS (NM_010753)	-378	NM_010753	17122	Mm.259260	NM_010753	ENSMUSG00000037235	Mxd4	2810410A03Rik|Mad4|bHLHc12	Max dimerization protein 4	protein-coding
mm_119158.1	chr14	31641019	31641029	+	1	NA	promoter-TSS (NM_019975)	promoter-TSS (NM_019975)	-33	NM_025295	26363	Mm.282679	NM_025295	ENSMUSG00000021900	Btd	-	biotinidase	protein-coding
mm_77752.1	chr8	128488472	128488482	-	1	NA	intron (NM_008737, intron 12 of 16)	intron (NM_008737, intron 12 of 16)	129236	NR_035436	100316680		NR_035436	ENSMUSG00000084523	Mir1903	Mirn1903|mmu-mir-1903	microRNA 1903	ncRNA
mm_35825.1	chr4	47302512	47302520	-	1	NA	intron (NM_009928, intron 33 of 39)	intron (NM_009928, intron 33 of 39)	-50706	NM_001312868	21812	Mm.197552	NM_009370	ENSMUSG00000007613	Tgfbr1	ALK5|AU017191|Alk-5|ESK2|TGFR-1|TbetaR-I|TbetaRI	transforming growth factor, beta receptor I	protein-coding
mm_116819.1	chr13	54565369	54565386	-	1	NA	promoter-TSS (NM_001252648)	promoter-TSS (NM_001252648)	5	NM_001252647	97820	Mm.24593	NM_133797	ENSMUSG00000025871	4833439L19Rik	4930558H15Rik|C81457|Kiaa1191|P33monox	RIKEN cDNA 4833439L19 gene	protein-coding
mm_110375.1	chr12	40201104	40201110	-	1	NA	Intergenic	(A)n|Simple_repeat|Simple_repeat	-1792	NM_001033437	380755	Mm.390463	NM_001033437	ENSMUSG00000071342	Lsmem1	Gm889	leucine-rich single-pass membrane protein 1	protein-coding
mm_130682.1	chr15	100678836	100678850	-	1	NA	intron (NM_033612, intron 6 of 7)	intron (NM_033612, intron 6 of 7)	9077	NM_033612	109901	Mm.2131	NM_033612	ENSMUSG00000023031	Cela1	1810009A17Rik|1810062B19Rik|Ela-1|Ela1|PC-TsF	chymotrypsin-like elastase family, member 1	protein-coding
mm_151014.1	chr19	46761579	46761618	+	1	NA	promoter-TSS (NM_001102471)	promoter-TSS (NM_001102471)	-11	NM_033569	94219	Mm.306903	NM_033569	ENSMUSG00000064105	Cnnm2	AU015877|AW048635|Acdp2|Clp2	cyclin M2	protein-coding
mm_84356.1	chr9	64704588	64704592	-	1	NA	intron (NM_001134399, intron 23 of 24)	intron (NM_001134399, intron 23 of 24)	33166	NM_017382	53869	Mm.1387	NM_017382	ENSMUSG00000004771	Rab11a	-	RAB11A, member RAS oncogene family	protein-coding
mm_41716.1	chr5	102070063	102070105	+	1	NA	promoter-TSS (NM_172882)	promoter-TSS (NM_172882)	-163	NM_172882	72145	Mm.332522	NM_172882	ENSMUSG00000043940	Wdfy3	2610509D04Rik|ALFY|AW319683|B930017C24|BWF1|Bchs|D5Ertd66e|Ggtb3|ZFYVE25|mKIAA0993	WD repeat and FYVE domain containing 3	protein-coding
mm_121662.1	chr14	12345634	12345671	-	1	NA	5' UTR (NM_080433, exon 1 of 5)	5' UTR (NM_080433, exon 1 of 5)	213	NM_080433	54713	Mm.34644	NM_080433	ENSMUSG00000021743	Fezf2	AI451466|AI852056|Fez|Fezl|Zfp312	Fez family zinc finger 2	protein-coding
mm_134974.1	chr16	32027075	32027107	-	1	NA	intron (NM_177326, intron 12 of 14)	intron (NM_177326, intron 12 of 14)	-23804	NM_177103	320213	Mm.152890	NM_023801	ENSMUSG00000022772	Senp5	6230429P13Rik|A730063F07Rik|AI851888|BB189556|SMT3IP3	SUMO/sentrin specific peptidase 5	protein-coding
mm_168965.1	chr12	80945552	80945553	+	1	NA	promoter-TSS (NM_001079694)	promoter-TSS (NM_001079694)	53	NM_001347415	20384	Mm.43331	NM_009159	ENSMUSG00000021134	Srsf5	Sfrs5	serine/arginine-rich splicing factor 5	protein-coding
mm_45820.1	chr5	87692739	87692742	-	1	NA	3' UTR (NM_001286023, exon 7 of 7)	3' UTR (NM_001286023, exon 7 of 7)	6685	NM_001286020	12991	Mm.268737	NM_009972	ENSMUSG00000063157	Csn2	Csnb	casein beta	protein-coding
mm_23586.1	chr3	63976138	63976211	+	1	NA	promoter-TSS (NM_001033300)	promoter-TSS (NM_001033300)	31	NM_001033300	229363	Mm.331051	NM_001033300	ENSMUSG00000027823	Gmps	670032|AA591640|AI047208|Gm9479	guanine monophosphate synthetase	protein-coding
mm_125358.1	chr15	39391937	39391947	+	1	NA	intron (NM_001256382, intron 3 of 26)	intron (NM_001256382, intron 3 of 26)	193656	NM_053271	116838	Mm.309296	NM_053271	ENSMUSG00000037386	Rims2	2810036I15Rik|AW048769|RIM2|Rab3ip2|Rim2(+40A)|Rim2(+44A)|Rim2(+4A)|Serg2|Syt3-rs|mKIAA0751	regulating synaptic membrane exocytosis 2	protein-coding
mm_118708.1	chr14	22178934	22178939	+	1	NA	intron (NM_028275, intron 2 of 6)	Lx3_Mus|LINE|L1	159224	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_75749.1	chr8	69901135	69901135	-	1	NA	intron (NM_023312, intron 2 of 4)	PB1D9|SINE|Alu	-1049	NM_032004	83984	Mm.432504	NM_032004	ENSMUSG00000047654	Tssk6	Sstk|TSK-6|TSSK-6	testis-specific serine kinase 6	protein-coding
mm_71474.1	chr8	46535644	46535656	+	1	NA	3' UTR (NM_007981, exon 21 of 21)	3' UTR (NM_007981, exon 21 of 21)	-16419	NM_027973	71876	Mm.22108	NM_027973	ENSMUSG00000031629	Cenpu	1700029A22Rik|Mlf1ip	centromere protein U	protein-coding
mm_8197.1	chr1	138121441	138121466	-	1	NA	intron (NM_001111316, intron 3 of 31)	intron (NM_001111316, intron 3 of 31)	53673	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_126083.1	chr15	77822474	77822482	+	1	NA	intron (NM_022410, intron 1 of 40)	intron (NM_022410, intron 1 of 40)	19697	NM_022410	17886	Mm.29677	NM_022410	ENSMUSG00000022443	Myh9	Fltn|Myhn-1|Myhn1|NMHCIIA|NMMHC-A|NMMHC-IIA|TU72.6	myosin, heavy polypeptide 9, non-muscle	protein-coding
mm_5285.1	chr1	20784267	20784271	-	1	NA	promoter-TSS (NM_145856)	promoter-TSS (NM_145856)	1	NM_145856	257630	Mm.222807	NM_145856	ENSMUSG00000041872	Il17f	C87042|IL-17F	interleukin 17F	protein-coding
mm_93456.1	chr10	110152269	110152273	-	1	NA	Intergenic	B4A|SINE|B4	-152052	NM_001081035	260315	Mm.225050	NM_177797	ENSMUSG00000020181	Nav3	4732483H20Rik|9630020C08Rik|POMFIL1|Pomfil1p|mKIAA0938|unc53H3	neuron navigator 3	protein-coding
mm_118690.1	chr14	22123302	22123320	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	103599	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_39836.1	chr5	30869599	30869620	+	1	NA	promoter-TSS (NM_144525)	promoter-TSS (NM_144525)	-38	NM_144525	68796	Mm.205169	NM_144525	ENSMUSG00000038828	Tmem214	1110039B18Rik|4921530J21Rik|AI841294|AU018742|C76280	transmembrane protein 214	protein-coding
mm_124429.1	chr14	118236962	118236970	-	1	NA	promoter-TSS (NM_177753)	promoter-TSS (NM_177753)	64	NM_177753	223227	Mm.70950	NM_177753	ENSMUSG00000061517	Sox21	Sox25	SRY (sex determining region Y)-box 21	protein-coding
mm_132624.1	chr16	38901241	38901289	+	1	NA	Intergenic	Intergenic	-1080	NM_170599	207683	Mm.245564	NM_170599	ENSMUSG00000022790	Igsf11	1700025L02Rik|BT-IgSF|Igsf13	immunoglobulin superfamily, member 11	protein-coding
mm_80208.1	chr9	72438844	72438846	+	1	NA	intron (NM_008613, intron 1 of 9)	intron (NM_008613, intron 1 of 9)	316	NM_008613	17427	Mm.387671	NM_008613	ENSMUSG00000032221	Mns1	AW546487	meiosis-specific nuclear structural protein 1	protein-coding
mm_17239.1	chr2	25607930	25607932	-	1	NA	TTS (NM_029859)	TTS (NM_029859)	515	NM_001024616	227624	Mm.29600	NM_001024616	ENSMUSG00000015087	Rabl6	B230208H17Rik|Rbel1|Rbel1a|Rbel1b|parf	RAB, member RAS oncogene family-like 6	protein-coding
mm_44424.1	chr5	20882033	20882051	-	1	NA	promoter-TSS (NM_177601)	promoter-TSS (NM_177601)	82	NM_172992	68770	Mm.86410	NM_172992	ENSMUSG00000039987	Phtf2	1110054G21Rik|9530062N20Rik|AI447096|C77923	putative homeodomain transcription factor 2	protein-coding
mm_144281.1	chr18	11839496	11839519	+	1	NA	promoter-TSS (NR_045421)	promoter-TSS (NR_045421)	-130	NR_045421	621998	Mm.353277	NR_045421		Gm6277	-	predicted gene 6277	ncRNA
mm_96187.1	chr11	61684425	61684454	+	1	NA	promoter-TSS (NM_178618)	promoter-TSS (NM_178618)	29	NM_178618	69640	Mm.458559	NM_178618	ENSMUSG00000042377	Fam83g	2310040C09Rik|AI506990|wly	family with sequence similarity 83, member G	protein-coding
mm_25692.1	chr3	122259495	122259496	+	1	NA	intron (NM_008129, intron 3 of 6)	B2_Mm2|SINE|B2	13938	NM_008129	14630	Mm.292676	NM_008129	ENSMUSG00000028124	Gclm	AI649393|Gcmc|Glclr	glutamate-cysteine ligase, modifier subunit	protein-coding
mm_33214.1	chr4	126609900	126609911	+	1	NA	promoter-TSS (NM_001145950)	promoter-TSS (NM_001145950)	51	NM_001145950	230757	Mm.296838	NM_001013755	ENSMUSG00000073755	5730409E04Rik	7530403E16Rik|AI849033	RIKEN cDNA 5730409E04Rik gene	protein-coding
mm_64519.1	chr7	143836624	143836631	+	1	NA	intron (NM_007856, intron 2 of 8)	intron (NM_007856, intron 2 of 8)	13460	NM_007856	13360	Mm.249342	NM_007856	ENSMUSG00000058454	Dhcr7	AA409147	7-dehydrocholesterol reductase	protein-coding
mm_99038.1	chr11	98960624	98960673	+	1	NA	5' UTR (NM_001176528, exon 1 of 8)	5' UTR (NM_001176528, exon 1 of 8)	177	NM_001176528	19401	Mm.439744	NM_009024	ENSMUSG00000037992	Rara	Nr1b1|RAR|RARalpha1	retinoic acid receptor, alpha	protein-coding
mm_31741.1	chr4	63215403	63215424	+	1	NA	promoter-TSS (NM_025685)	promoter-TSS (NM_025685)	1	NM_025685	373864	Mm.194116	NM_025685	ENSMUSG00000045672	Col27a1	5730512J02Rik|AI449266	collagen, type XXVII, alpha 1	protein-coding
mm_101489.1	chr11	31407869	31407869	-	1	NA	Intergenic	MLT1D|LTR|ERVL-MaLR	-37808	NM_011491	20856	Mm.32506	NM_011491	ENSMUSG00000020303	Stc2	AW125853|Stc2l|mustc2	stanniocalcin 2	protein-coding
mm_121698.1	chr14	14120905	14120963	-	1	NA	promoter-TSS (NM_025550)	promoter-TSS (NM_025550)	-30	NM_025550	66413	Mm.27591	NM_025550	ENSMUSG00000021737	Psmd6	2400006A19Rik	proteasome (prosome, macropain) 26S subunit, non-ATPase, 6	protein-coding
mm_28217.1	chr3	88410296	88410351	-	1	NA	promoter-TSS (NM_025928)	promoter-TSS (NM_025928)	74	NM_001310605	67037	Mm.36715	NM_025928	ENSMUSG00000028066	Pmf1	2600009M07Rik|AL033286|AW060657	polyamine-modulated factor 1	protein-coding
mm_128536.1	chr15	54893146	54893148	-	1	NA	intron (NM_001136077, intron 8 of 25)	intron (NM_001136077, intron 8 of 25)	26999	NM_015744	18606	Mm.250256	NM_015744	ENSMUSG00000022425	Enpp2	ATX|E-NPP 2|Npps2|PD-Ialpha|Pdnp2|lysoPLD	ectonucleotide pyrophosphatase/phosphodiesterase 2	protein-coding
mm_106906.1	chr12	8015501	8015513	+	1	NA	exon (NM_009693, exon 29 of 29)	exon (NM_009693, exon 29 of 29)	37830	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_48218.1	chr5	137611430	137611442	-	1	NA	promoter-TSS (NM_008788)	promoter-TSS (NM_008788)	-32	NM_008788	18542	Mm.262345	NM_008788	ENSMUSG00000029718	Pcolce	Astt-2|Astt2|P14|PCPE-1	procollagen C-endopeptidase enhancer protein	protein-coding
mm_88630.1	chr10	79886883	79886902	+	1	NA	intron (NM_015779, intron 2 of 4)	intron (NM_015779, intron 2 of 4)	580	NM_015779	50701	Mm.262194	NM_015779	ENSMUSG00000020125	Elane	Ela2|F430011M15Rik|NE	elastase, neutrophil expressed	protein-coding
mm_15675.1	chr2	163506823	163506860	+	1	NA	promoter-TSS (NM_001312906)	promoter-TSS (NM_001312906)	-16	NM_001312906	15378	Mm.202383	NM_008261	ENSMUSG00000017950	Hnf4a	HNF-4|Hnf4|Hnf4alpha|MODY1|Nr2a1|TCF-14|Tcf14	hepatic nuclear factor 4, alpha	protein-coding
mm_140981.1	chr17	24718052	24718062	-	1	NA	promoter-TSS (NM_026205)	promoter-TSS (NM_026205)	0	NM_026205	67504	Mm.46159	NM_026205	ENSMUSG00000008482	Rnf151	1700010O16Rik|AV047371	ring finger protein 151	protein-coding
mm_48675.1	chr5	146184295	146184317	-	1	NA	intron (NM_001008547, intron 2 of 4)	intron (NM_001008547, intron 2 of 4)	998	NM_001008547	69282	Mm.373573	NM_001008547	ENSMUSG00000095040	1700001J03Rik	-	RIKEN cDNA 1700001J03 gene	protein-coding
mm_44789.1	chr5	32195959	32195961	-	1	NA	Intergenic	L2b|LINE|L2	-36748	NM_030072	665270	Mm.160067	NM_030072	ENSMUSG00000029134	Plb1	4632413E21Rik|4930433E17Rik|4930539A06Rik|BC033606	phospholipase B1	protein-coding
mm_4636.1	chr1	179803475	179803477	+	1	NA	5' UTR (NM_026375, exon 1 of 36)	5' UTR (NM_026375, exon 1 of 36)	539	NM_026375	226747	Mm.128165	NM_026375	ENSMUSG00000026491	Ahctf1	6230412P20Rik|AV011447|Elys	AT hook containing transcription factor 1	protein-coding
mm_92036.1	chr10	62494729	62494750	-	1	NA	3' UTR (NM_011157, exon 3 of 3)	3' UTR (NM_011157, exon 3 of 3)	-7934	NM_133672	30930	Mm.260703	NM_133672	ENSMUSG00000020078	Vps26a	AA407240|HB58|Vps26	VPS26 retromer complex component A	protein-coding
mm_168771.1	chr12	17233589	17233607	+	1	NA	Intergenic	Intergenic	-32997	NM_027959	71853	Mm.222825	NM_027959	ENSMUSG00000020571	Pdia6	1700015E05Rik|AL023058|C77895|CaBP5|P5|Txndc7	protein disulfide isomerase associated 6	protein-coding
mm_137190.1	chr17	23822153	23822157	+	1	NA	intron (NM_175229, intron 10 of 13)	L3b|LINE|CR1	6954	NM_026305	67673	Mm.153758	NM_026305	ENSMUSG00000055839	Elob	0610040H15Rik|Tceb2	elongin B	protein-coding
mm_15574.1	chr2	158666691	158666740	+	1	NA	promoter-TSS (NM_001159662)	promoter-TSS (NM_001159662)	-18	NM_153089	228852	Mm.150540	NM_153089	ENSMUSG00000037754	Ppp1r16b	ANKRD4|C130078N17Rik|TIMAP|Wdt4	protein phosphatase 1, regulatory (inhibitor) subunit 16B	protein-coding
mm_99892.1	chr11	109613415	109613425	+	1	NA	Intergenic	Intergenic	-2031	NM_145940	52639	Mm.35817	NM_145940	ENSMUSG00000041895	Wipi1	4930533H01Rik|AW411817|D11Ertd498e	WD repeat domain, phosphoinositide interacting 1	protein-coding
mm_165496.1	chr2	166274498	166274498	+	1	NA	intron (NR_033467, intron 1 of 2)	MLT1G|LTR|ERVL-MaLR	590	NR_033467	670775	Mm.384326	NR_033467	ENSMUSG00000084840	Gm11468	OTTMUSG00000001131	predicted gene 11468	ncRNA
mm_65192.1	chr7	19696682	19696703	-	1	NA	exon (NM_009696, exon 4 of 4)	exon (NM_009696, exon 4 of 4)	1706	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_148978.1	chr19	7579133	7579146	+	1	NA	exon (NM_139269, exon 4 of 5)	exon (NM_139269, exon 4 of 5)	21680	NM_139269	225845	Mm.274810	NM_139269	ENSMUSG00000060675	Pla2g16	C78643|HRSL3|Hrasls3|Hrev107|MLP-3	phospholipase A2, group XVI	protein-coding
mm_12271.1	chr2	68979504	68979506	+	1	NA	intron (NM_172856, intron 3 of 9)	AT_rich|Low_complexity|Low_complexity	118064	NM_001347161	241447	Mm.222222	NM_172856	ENSMUSG00000027035	Cers6	4732462C07Rik|AW544719|Lass6|T1L	ceramide synthase 6	protein-coding
mm_79371.1	chr9	54698860	54698884	+	1	NA	promoter-TSS (NM_021422)	promoter-TSS (NM_021422)	-687	NM_021422	58233	Mm.489676	NM_021422	ENSMUSG00000032285	Dnaja4	1110021L12Rik|AV358213|Dj4|Hsj4|mmDjA4	DnaJ heat shock protein family (Hsp40) member A4	protein-coding
mm_104632.1	chr11	97440055	97440089	-	1	NA	Intergenic	CpG	-10088	NM_021493	58996	Mm.394118	NM_021493	ENSMUSG00000049807	Arhgap23	A330041B18Rik	Rho GTPase activating protein 23	protein-coding
mm_31812.1	chr4	66827679	66827697	+	1	NA	5' UTR (NM_021297, exon 1 of 3)	5' UTR (NM_021297, exon 1 of 3)	137	NM_021297	21898	Mm.38049	NM_021297	ENSMUSG00000039005	Tlr4	Lps|Ly87|Ran/M1|Rasl2-8	toll-like receptor 4	protein-coding
mm_1987.1	chr1	87124947	87124960	+	1	NA	promoter-TSS (NM_007432)	promoter-TSS (NM_007432)	-55	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_103879.1	chr11	83529222	83529247	-	1	NA	exon (NM_013653, exon 2 of 3)	exon (NM_013653, exon 2 of 3)	1284	NM_013653	20304	Mm.284248	NM_013653	ENSMUSG00000035042	Ccl5	MuRantes|RANTES|SISd|Scya5|TCP228	chemokine (C-C motif) ligand 5	protein-coding
mm_169566.1	chr15	16915124	16915124	-	1	NA	Intergenic	RLTR9E|LTR|ERVK	137023	NM_009869	12565	Mm.439758	NM_009869	ENSMUSG00000025370	Cdh9	-	cadherin 9	protein-coding
mm_158744.1	chrX	164258821	164258825	-	1	NA	promoter-TSS (NM_009759)	promoter-TSS (NM_009759)	-630	NM_009759	12169	Mm.504	NM_009759	ENSMUSG00000031377	Bmx	Etk|Etk/Bmx|Tyro8	BMX non-receptor tyrosine kinase	protein-coding
mm_24821.1	chr3	95650865	95650887	+	1	NA	Intergenic	PB1D11|SINE|Alu	-7845	NM_008562	17210	Mm.1639	NM_008562	ENSMUSG00000038612	Mcl1	AW556805|Mcl-1	myeloid cell leukemia sequence 1	protein-coding
mm_14812.1	chr2	146101648	146101654	+	1	NA	Intergenic	Intergenic	-120346	NM_016889	53626	Mm.379070	NM_016889	ENSMUSG00000068154	Insm1	IA-1	insulinoma-associated 1	protein-coding
mm_167871.1	chrX	36152052	36152089	+	1	NA	exon (NM_133990, exon 9 of 11)	exon (NM_133990, exon 9 of 11)	39962	NM_133990	16164	Mm.24208	NM_133990	ENSMUSG00000017057	Il13ra1	AI882074|CD213a1|IL-13R-alpha-1|IL-13r[a]|Il13ra|NR4	interleukin 13 receptor, alpha 1	protein-coding
mm_31181.1	chr4	43508851	43508899	+	1	NA	intron (NM_139305, intron 3 of 10)	intron (NM_139305, intron 3 of 10)	1849	NM_139305	230099	Mm.283682	NM_139305	ENSMUSG00000028463	Car9	CAIX|Ca9|MN/CA9	carbonic anhydrase 9	protein-coding
mm_119177.1	chr14	32165785	32165798	+	1	NA	promoter-TSS (NM_019744)	promoter-TSS (NM_019744)	2	NM_019744	27057	Mm.371598	NM_019744	ENSMUSG00000056234	Ncoa4	ARA70|Rfg	nuclear receptor coactivator 4	protein-coding
mm_35879.1	chr4	49538161	49538206	-	1	NA	exon (NM_144903, exon 8 of 9)	exon (NM_144903, exon 8 of 9)	11363	NM_144903	230163	Mm.482116	NM_144903	ENSMUSG00000028307	Aldob	Aldo-2|Aldo2|BC016435	aldolase B, fructose-bisphosphate	protein-coding
mm_29677.1	chr3	122899501	122899505	-	1	NA	TTS (NM_007980)	TTS (NM_007980)	4431	NM_007980	14079	Mm.28398	NM_007980	ENSMUSG00000023057	Fabp2	Fabpi|I-FABP	fatty acid binding protein 2, intestinal	protein-coding
mm_8156.1	chr1	136946200	136946205	-	1	NA	intron (NM_030676, intron 3 of 8)	intron (NM_030676, intron 3 of 8)	7428	NM_001159769	26424	Mm.16794	NM_030676	ENSMUSG00000026398	Nr5a2	AU020803|D1Ertd308e|Ftf|LRH-1|UF2-H3B	nuclear receptor subfamily 5, group A, member 2	protein-coding
mm_121464.1	chr14	120896854	120896877	+	1	NA	Intergenic	Intergenic	-14329	NM_023579	70572	Mm.221452	NM_023579	ENSMUSG00000030662	Ipo5	1110011C18Rik|5730478E03Rik|AA409333|C76941|IMB3|Kpnb3|Ranbp5	importin 5	protein-coding
mm_16252.1	chr2	173159020	173159043	+	1	NA	3' UTR (NM_011044, exon 10 of 10)	3' UTR (NM_011044, exon 10 of 10)	5958	NM_011044	18534	Mm.266867	NM_011044	ENSMUSG00000027513	Pck1	AI265463|PEPCK|Pck-1	phosphoenolpyruvate carboxykinase 1, cytosolic	protein-coding
mm_71803.1	chr8	68317712	68317717	+	1	NA	intron (NM_028182, intron 4 of 8)	intron (NM_028182, intron 4 of 8)	41186	NM_028182	72281	Mm.40974	NM_028182	ENSMUSG00000053886	Sh2d4a	2210402M20Rik|SH2A	SH2 domain containing 4A	protein-coding
mm_48167.1	chr5	137153070	137153080	-	1	NA	Intergenic	Intergenic	-36868	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_162970.1	chr11	11685907	11685907	+	1	NA	promoter-TSS (NM_009578)	promoter-TSS (NM_009578)	-18	NM_009578	22778	Mm.103545	NM_009578	ENSMUSG00000018654	Ikzf1	5832432G11Rik|Ikaros|LyF-1|Zfpn1a1|Znfn1a1|hlk-1|mKIAA4227	IKAROS family zinc finger 1	protein-coding
mm_1172.1	chr1	60921227	60921242	+	1	NA	Intergenic	(CACG)n|Simple_repeat|Simple_repeat	12209	NM_001281976	12477	Mm.390	NM_009843	ENSMUSG00000026011	Ctla4	Cd152|Ctla-4|Ly-56	cytotoxic T-lymphocyte-associated protein 4	protein-coding
mm_108507.1	chr12	83987685	83987725	+	1	NA	promoter-TSS (NM_134188)	promoter-TSS (NM_134188)	-156	NM_134188	171210	Mm.371675	NM_134188	ENSMUSG00000021226	Acot2	AA571646|MTE-I|Mte1	acyl-CoA thioesterase 2	protein-coding
mm_73326.1	chr8	105276439	105276482	+	1	NA	promoter-TSS (NM_030152)	promoter-TSS (NM_030152)	13	NM_030152	78688	Mm.475715	NM_030152	ENSMUSG00000014776	Nol3	ARC|B430311C09Rik|MYC|NOP|Nop30	nucleolar protein 3 (apoptosis repressor with CARD domain)	protein-coding
mm_51646.1	chr6	86028721	86028738	+	1	NA	promoter-TSS (NM_001271860)	promoter-TSS (NM_001271860)	48	NM_001271860	11519	Mm.104155	NM_013458	ENSMUSG00000030000	Add2	2900072M03Rik|add97	adducin 2 (beta)	protein-coding
mm_816.1	chr1	46066847	46066895	+	1	NA	intron (NM_001160386, intron 1 of 65)	intron (NM_001160386, intron 1 of 65)	133	NM_001160386	227058	Mm.296880	NM_001160386	ENSMUSG00000041144	Dnah7b	Dnahc7b|Gm107	dynein, axonemal, heavy chain 7B	protein-coding
mm_166190.1	chr5	33996784	33996790	+	1	NA	5' UTR (NM_001001985, exon 1 of 3)	5' UTR (NM_001001985, exon 1 of 3)	803	NM_001001985	269642	Mm.274610	NM_001001985	ENSMUSG00000048142	Nat8l	1110038O08Rik|Shati	N-acetyltransferase 8-like	protein-coding
mm_165371.1	chr2	128159265	128159269	+	1	NA	3' UTR (NM_009754, exon 4 of 4)	3' UTR (NM_009754, exon 4 of 4)	31692	NM_001284410	12125	Mm.141083	NM_009754	ENSMUSG00000027381	Bcl2l11	1500006F24Rik|Bim|Bod|bcl2-L-11	BCL2-like 11 (apoptosis facilitator)	protein-coding
mm_46783.1	chr5	112577187	112577204	-	1	NA	promoter-TSS (NM_001253916)	promoter-TSS (NM_001253916)	3	NM_001253917	56747	Mm.143742	NM_019982	ENSMUSG00000058153	Sez6l	AI843918|AIG1|AW539724|Acig1|BSRP-B|mKIAA0927	seizure related 6 homolog like	protein-coding
mm_78100.1	chr9	19622080	19622140	+	1	NA	promoter-TSS (NM_172918)	promoter-TSS (NM_172918)	19	NM_172918	244713	Mm.67366	NM_172918	ENSMUSG00000057551	Zfp317	4932416G03|D230022C05Rik|KRAB9|Zfp67|Zfp75|mszf40	zinc finger protein 317	protein-coding
mm_38193.1	chr4	135353626	135353628	-	1	NA	promoter-TSS (NM_001130477)	promoter-TSS (NM_001130477)	-413	NM_001130477	51796	Mm.1963	NM_016799	ENSMUSG00000028809	Srrm1	AA407769|POP101|Srm160	serine/arginine repetitive matrix 1	protein-coding
mm_25983.1	chr3	133320925	133320968	+	1	NA	exon (NM_001293641, exon 2 of 12)	exon (NM_001293641, exon 2 of 12)	10836	NM_146141	74776	Mm.210305	NM_146141	ENSMUSG00000028013	Ppa2	1110013G13Rik|Sid6306	pyrophosphatase (inorganic) 2	protein-coding
mm_1820.1	chr1	82534374	82534399	+	1	NA	intron (NM_007735, intron 9 of 47)	intron (NM_007735, intron 9 of 47)	52463	NM_007735	12829	Mm.40253	NM_007735	ENSMUSG00000067158	Col4a4	E130010M05Rik|[a]4(IV)	collagen, type IV, alpha 4	protein-coding
mm_93344.1	chr10	100444984	100444997	-	1	NA	3' UTR (NM_001110013, exon 14 of 14)	3' UTR (NM_001110013, exon 14 of 14)	42357	NM_001033332	237500	Mm.296805	NM_001033332	ENSMUSG00000036676	Tmtc3	9130014E20Rik|B130008E12Rik|mSmile	transmembrane and tetratricopeptide repeat containing 3	protein-coding
mm_144205.1	chr18	9494668	9494677	+	1	NA	Intergenic	Intergenic	-44522	NM_026484	67974	Mm.86523	NM_026484	ENSMUSG00000024286	Ccny	1700025H17Rik|3110050L10Rik|4631402G10Rik|5730405I09Rik	cyclin Y	protein-coding
mm_98185.1	chr11	87793433	87793445	+	1	NA	promoter-TSS (NM_010824)	promoter-TSS (NM_010824)	-345	NM_010824	17523	Mm.4668	NM_010824	ENSMUSG00000009350	Mpo	mKIAA4033	myeloperoxidase	protein-coding
mm_169826.1	chr16	24393454	24393461	+	1	NA	non-coding (NR_037954, exon 1 of 2)	non-coding (NR_037954, exon 1 of 2)	107	NM_178665	210126	Mm.209385	NM_178665	ENSMUSG00000033306	Lpp	9430020K16Rik|AA959454|AU024130|B130055L10Rik|C79715|D630048H16	LIM domain containing preferred translocation partner in lipoma	protein-coding
mm_84634.1	chr9	70952145	70952155	-	1	NA	promoter-TSS (NM_001324472)	promoter-TSS (NM_001324472)	71	NM_001324473	15450	Mm.390187	NM_008280	ENSMUSG00000032207	Lipc	AI256194|HL|Hpl	lipase, hepatic	protein-coding
mm_73824.1	chr8	117459342	117459362	+	1	NA	promoter-TSS (NR_106046)	promoter-TSS (NR_106046)	87	NR_106046	102465653		NR_106046	ENSMUSG00000098483	Mir7078	Gm27386|mmu-mir-7078	microRNA 7078	ncRNA
mm_133227.1	chr16	76500251	76500263	+	1	NA	Intergenic	Intergenic	-127208	NM_173440	268903	Mm.74711	NM_173440	ENSMUSG00000048490	Nrip1	6030458L20Rik|8430438I05Rik|9630050P12|AA959574|AW456757|RIP140	nuclear receptor interacting protein 1	protein-coding
mm_129243.1	chr15	76656906	76656934	-	1	NA	promoter-TSS (NM_001276321)	promoter-TSS (NM_001276321)	-19	NM_001276321	54151	Mm.247752	NM_019396	ENSMUSG00000053929	Cyhr1	1110031M01Rik|AU042374|Chrp	cysteine and histidine rich 1	protein-coding
mm_97138.1	chr11	75193869	75193877	+	1	NA	promoter-TSS (NM_177708)	promoter-TSS (NM_177708)	-120	NM_177708	237847	Mm.82661	NM_177708	ENSMUSG00000045287	Rtn4rl1	Ngr3|Ngrh2|Ngrl2	reticulon 4 receptor-like 1	protein-coding
mm_152422.1	chr19	10675074	10675080	-	1	NA	exon (NM_021453, exon 3 of 9)	exon (NM_021453, exon 3 of 9)	2994	NM_021453	58803	Mm.34037	NM_021453	ENSMUSG00000024738	Pga5	1110035E17Rik|Pepf	pepsinogen 5, group I	protein-coding
mm_170053.1	chr17	29319164	29319176	+	1	NA	5' UTR (NM_023734, exon 1 of 7)	5' UTR (NM_023734, exon 1 of 7)	288	NM_023734	74116	Mm.30950	NM_023734	ENSMUSG00000024011	Pi16	1200009H11Rik|Cripi|PI-16	peptidase inhibitor 16	protein-coding
mm_116988.1	chr13	56472421	56472426	-	1	NA	TTS (NM_177809)	TTS (NM_177809)	9823	NM_008373	16198	Mm.3006	NM_008373	ENSMUSG00000021538	Il9	Il-9|P40	interleukin 9	protein-coding
mm_106936.1	chr12	8674346	8674382	+	1	NA	promoter-TSS (NM_030723)	promoter-TSS (NM_030723)	105	NM_001160220	80913	Mm.341243	NM_030723	ENSMUSG00000020594	Pum2	5730503J23Rik|Pumm2	pumilio RNA-binding family member 2	protein-coding
mm_90933.1	chr10	12869145	12869222	-	1	NA	Intergenic	CpG	-7448	NM_011682	22288	Mm.331784	NM_011682	ENSMUSG00000019820	Utrn	AA589569|DRP|Dmdl	utrophin	protein-coding
mm_169835.1	chr16	25644820	25644821	-	1	NA	Intergenic	LTRIS2|LTR|ERV1	-38945	NM_001127259	22061	Mm.20894	NM_011641	ENSMUSG00000022510	Trp63	AI462811|Ket|P51/P63|P63|P73l|Tp63|Trp53rp1	transformation related protein 63	protein-coding
mm_77293.1	chr8	116944374	116944384	-	1	NA	intron (NM_177700, intron 1 of 3)	intron (NM_177700, intron 1 of 3)	986	NM_177700	234776	Mm.259736	NM_177700	ENSMUSG00000047388	Atmin	Asciz|gpg6|mKIAA0431	ATM interactor	protein-coding
mm_34482.1	chr4	148473115	148473119	+	1	NA	intron (NM_020009, intron 19 of 57)	intron (NM_020009, intron 19 of 57)	24535	NM_020009	56717	Mm.21158	NM_020009	ENSMUSG00000028991	Mtor	2610315D21Rik|AI327068|FRAP|FRAP2|Frap1|RAFT1|RAPT1|flat	mechanistic target of rapamycin (serine/threonine kinase)	protein-coding
mm_150529.1	chr19	39287089	39287104	+	1	NA	promoter-TSS (NM_007815)	promoter-TSS (NM_007815)	11	NM_007815	13095	Mm.20764	NM_007815	ENSMUSG00000003053	Cyp2c29	AHOH|AHOHase|AI159681|AI196010|Ah-2|Ahh-1|Cyp2c|P450-2C	cytochrome P450, family 2, subfamily c, polypeptide 29	protein-coding
mm_3253.1	chr1	136146550	136146551	+	1	NA	intron (NM_001039472, intron 3 of 34)	intron (NM_001039472, intron 3 of 34)	15149	NM_001039472	16565	Mm.276135	NM_019962	ENSMUSG00000041642	Kif21b	2610511N21Rik|mKIAA0449	kinesin family member 21B	protein-coding
mm_108105.1	chr12	75308309	75308317	+	1	NA	promoter-TSS (NM_023275)	promoter-TSS (NM_023275)	0	NM_023275	80837	Mm.27467	NM_023275	ENSMUSG00000046768	Rhoj	1110005O19Rik|AW210585|Arhj|TC10L|TCL	ras homolog family member J	protein-coding
mm_43829.1	chr5	142972116	142972133	+	1	NA	3' UTR (NM_007984, exon 5 of 5)	3' UTR (NM_007984, exon 5 of 5)	11769	NM_007984	14086	Mm.289707	NM_007984	ENSMUSG00000029581	Fscn1	AI663989|Fan1|fascin-1	fascin actin-bundling protein 1	protein-coding
mm_100289.1	chr11	117813659	117813679	+	1	NA	3' UTR (NM_009304, exon 4 of 4)	3' UTR (NM_009304, exon 4 of 4)	4002	NM_009304	20973	Mm.468228	NM_009304	ENSMUSG00000048277	Syngr2	Clast2|cellugyrin	synaptogyrin 2	protein-coding
mm_23085.1	chr3	36863149	36863164	+	1	NA	promoter-TSS (NM_172679)	promoter-TSS (NM_172679)	50	NM_172679	229227	Mm.207907	NM_172679	ENSMUSG00000037270	4932438A13Rik	4732443H21|B830039D19Rik|D630029K19Rik|FSA|Kiaa1109|Tweek	RIKEN cDNA 4932438A13 gene	protein-coding
mm_62679.1	chr7	109703673	109703759	+	1	NA	promoter-TSS (NM_020616)	promoter-TSS (NM_020616)	-21	NM_020616	57373	Mm.334138	NM_020616	ENSMUSG00000031023	Akip1	BCA3|C11orf17|D7H11orf17|D930014E17Rik|ICRFP703B1614Q5.6|ORF27	A kinase (PRKA) interacting protein 1	protein-coding
mm_6692.1	chr1	80715482	80715491	-	1	NA	intron (NM_175291, intron 1 of 55)	intron (NM_175291, intron 1 of 55)	43067	NM_175291	210293	Mm.133473	NM_175291	ENSMUSG00000038608	Dock10	9330153B10Rik|A630054M16Rik|Jr4|Jr5|R75174|ZIZ3|Zizimin3|mKIAA0694	dedicator of cytokinesis 10	protein-coding
mm_17230.1	chr2	25574846	25574878	-	1	NA	promoter-TSS (NM_029293)	promoter-TSS (NM_029293)	9	NM_029293	75454	Mm.458079	NM_029293	ENSMUSG00000036504	Phpt1	1700008C22Rik|PHP|Php14	phosphohistidine phosphatase 1	protein-coding
mm_61515.1	chr7	78913402	78913428	+	1	NA	promoter-TSS (NM_020583)	promoter-TSS (NM_020583)	-9	NM_001291221	57444	Mm.322843	NM_020583	ENSMUSG00000039236	Isg20	1600023I01Rik|2010107M23Rik|20kDa|DnaQL|HEM45	interferon-stimulated protein	protein-coding
mm_88657.1	chr10	79996480	79996505	+	1	NA	intron (NR_038088, intron 1 of 4)	intron (NR_038088, intron 1 of 4)	-1116	NM_001347081	27403	Mm.103351	NM_013850	ENSMUSG00000035722	Abca7	ABCX|Abc51	ATP-binding cassette, sub-family A (ABC1), member 7	protein-coding
mm_161830.1	chr17	80347355	80347355	+	1	NA	intron (NM_001145452, intron 4 of 17)	intron (NM_001145452, intron 4 of 17)	26187	NR_028385	791338	Mm.204722	NR_028385		Gm10190	ENSMUSG00000066938	predicted gene 10190	ncRNA
mm_80362.1	chr9	75232051	75232084	+	1	NA	promoter-TSS (NM_001081322)	promoter-TSS (NM_001081322)	53	NM_001081322	208943	Mm.41339	NM_001081322	ENSMUSG00000033590	Myo5c	9130003O20Rik|BB085560|C330029I24	myosin VC	protein-coding
mm_59076.1	chr7	19517895	19517916	+	1	NA	promoter-TSS (NM_027116)	promoter-TSS (NM_027116)	-826	NM_027116	69547	Mm.77325	NM_027116	ENSMUSG00000060621	Nkpd1	2310015G09Rik	NTPase, KAP family P-loop domain containing 1	protein-coding
mm_104839.1	chr11	99200088	99200119	-	1	NA	Intergenic	Intergenic	30914	NM_020618	57376	Mm.379086	NM_020618	ENSMUSG00000037935	Smarce1	2810417B20Rik|5830412H02Rik|9030408N19Rik|Baf27	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1	protein-coding
mm_21983.1	chr2	167492827	167492891	-	1	NA	promoter-TSS (NM_170756)	promoter-TSS (NM_170756)	15	NM_170756	263876	Mm.34342	NM_170756	ENSMUSG00000047030	Spata2	AI504642|mKIAA0757	spermatogenesis associated 2	protein-coding
mm_132918.1	chr16	49757365	49757369	+	1	NA	intron (NM_028680, intron 6 of 10)	intron (NM_028680, intron 6 of 10)	58073	NM_028680	73916	Mm.241276	NM_028680	ENSMUSG00000032965	Ift57	4833420A15Rik|Esrrbl1|Hippi|MHS4R2	intraflagellar transport 57	protein-coding
mm_51434.1	chr6	78911166	78911170	+	1	NA	Intergenic	U1|snRNA|snRNA	-120874	NR_040302	100504701	Mm.400420	NR_040301	ENSMUSG00000108072	Gm20362	-	predicted gene, 20362	ncRNA
mm_42915.1	chr5	122682892	122682911	+	1	NA	3' UTR (NM_011027, exon 13 of 13)	3' UTR (NM_011027, exon 13 of 13)	-24643	NM_001310720	18438	Mm.290884	NM_011026	ENSMUSG00000029470	P2rx4	AI504491|AW555605|D5Ertd444e|P2X4	purinergic receptor P2X, ligand-gated ion channel 4	protein-coding
mm_162686.1	chr10	17920029	17920031	-	1	NA	intron (NM_001033432, intron 1 of 3)	intron (NM_001033432, intron 1 of 3)	28037	NM_001033432	380629	Mm.276430	NM_001033432	ENSMUSG00000039879	Heca	Gm869|HDC|HDCL	hdc homolog, cell cycle regulator	protein-coding
mm_83677.1	chr9	50344983	50344984	-	1	NA	Intergenic	Intergenic	-111801	NR_131161	71873		NR_131161	ENSMUSG00000110916	2310003N18Rik	-	RIKEN cDNA 2310003N18 gene	ncRNA
mm_66345.1	chr7	43489968	43490016	-	1	NA	promoter-TSS (NM_001164518)	promoter-TSS (NM_001164518)	31	NM_001164518	210094	Mm.228087	NM_001164518	ENSMUSG00000013367	Iglon5	A230106M20Rik|Gm1431	IgLON family member 5	protein-coding
mm_115340.1	chr13	112504097	112504109	+	1	NA	exon (NM_010560, exon 17 of 17)	exon (NM_010560, exon 17 of 17)	40033	NM_010560	16195	Mm.4364	NM_010560	ENSMUSG00000021756	Il6st	5133400A03Rik|AA389424|BB405851|CD130|D13Ertd699e|gp130	interleukin 6 signal transducer	protein-coding
mm_33651.1	chr4	133055101	133055104	+	1	NA	5' UTR (NM_146155, exon 3 of 7)	5' UTR (NM_146155, exon 3 of 7)	43596	NM_146155	230793	Mm.31816	NM_146155	ENSMUSG00000037692	Ahdc1	D030015G18Rik	AT hook, DNA binding motif, containing 1	protein-coding
mm_52362.1	chr6	112696336	112696349	+	1	NA	intron (NM_001167730, intron 1 of 13)	CpG	328	NM_021385	58186	Mm.103812	NM_021385	ENSMUSG00000030254	Rad18	2810024C04Rik|Rad18sc	RAD18 E3 ubiquitin protein ligase	protein-coding
mm_88605.1	chr10	79807283	79807320	+	1	NA	intron (NM_023128, intron 3 of 8)	intron (NM_023128, intron 3 of 8)	-13720	NM_030218	78906	Mm.33087	NM_030218	ENSMUSG00000035852	Misp	9130017N09Rik	mitotic spindle positioning	protein-coding
mm_95485.1	chr11	51384179	51384189	+	1	NA	intron (NM_153393, intron 2 of 28)	intron (NM_153393, intron 2 of 28)	94264	NM_153393	237759	Mm.154093	NM_153393	ENSMUSG00000063564	Col23a1	2810458L13Rik|AI429655	collagen, type XXIII, alpha 1	protein-coding
mm_125630.1	chr15	61989557	61989567	+	1	NA	exon (NM_001177354, exon 3 of 3)	exon (NM_001177354, exon 3 of 3)	4221	NM_001177352	17869	Mm.2444	NM_010849	ENSMUSG00000022346	Myc	AU016757|Myc2|Niard|Nird|bHLHe39	myelocytomatosis oncogene	protein-coding
mm_84294.1	chr9	63322790	63322814	-	1	NA	intron (NM_011840, intron 7 of 21)	intron (NM_011840, intron 7 of 21)	55050	NM_011840	23938	Mm.325746	NM_011840	ENSMUSG00000058444	Map2k5	AI324775|AI428457|MEK5|Mapkk5|Prkmk5	mitogen-activated protein kinase kinase 5	protein-coding
mm_41654.1	chr5	98484046	98484048	+	1	NA	intron (NM_001024614, intron 2 of 5)	intron (NM_001024614, intron 2 of 5)	-8383	NR_030484	735265		NR_030484	ENSMUSG00000105814	Mir703	Mirn703|mir-703|mmu-mir-703	microRNA 703	ncRNA
mm_129603.1	chr15	79892354	79892364	-	1	NA	promoter-TSS (NM_001160415)	promoter-TSS (NM_001160415)	-49	NM_001160415	80287	Mm.284059	NM_030255	ENSMUSG00000009585	Apobec3	Apobec|Arp3|BC003314|Cem15|Rfv3	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 3	protein-coding
mm_64340.1	chr7	142377015	142377076	+	1	NA	exon (NM_009983, exon 7 of 9)	exon (NM_009983, exon 7 of 9)	-3299	NM_001347541	320802	Mm.154486	NM_177265	ENSMUSG00000045777	Ifitm10	6330512M04Rik|AI848576|DSPA3	interferon induced transmembrane protein 10	protein-coding
mm_104448.1	chr11	95032989	95032993	-	1	NA	intron (NM_133667, intron 2 of 10)	intron (NM_133667, intron 2 of 10)	8380	NM_133667	18604	Mm.29768	NM_133667	ENSMUSG00000038967	Pdk2	-	pyruvate dehydrogenase kinase, isoenzyme 2	protein-coding
mm_56712.1	chr6	115252264	115252299	-	1	NA	promoter-TSS (NM_080639)	promoter-TSS (NM_080639)	-432	NM_080639	110595	Mm.255607	NM_080639	ENSMUSG00000030317	Timp4	TIMP-4	tissue inhibitor of metalloproteinase 4	protein-coding
mm_35117.1	chr4	10989116	10989120	-	1	NA	3' UTR (NM_175175, exon 2 of 2)	3' UTR (NM_175175, exon 2 of 2)	18501	NM_175175	71801	Mm.34351	NM_175175	ENSMUSG00000049969	Plekhf2	1110070J07Rik|AA673237|ZFYVE18	pleckstrin homology domain containing, family F (with FYVE domain) member 2	protein-coding
mm_64020.1	chr7	140272496	140272509	+	1	NA	intron (NM_001128146, intron 5 of 15)	intron (NM_001128146, intron 5 of 15)	25121	NM_001128145	244234	Mm.85125	NM_175533	ENSMUSG00000054672	5830411N06Rik	Scart2	RIKEN cDNA 5830411N06 gene	protein-coding
mm_91995.1	chr10	62111062	62111072	-	1	NA	promoter-TSS (NM_027251)	promoter-TSS (NM_027251)	-54	NM_027251	69894	Mm.294126	NM_027251	ENSMUSG00000020083	2010107G23Rik	AA545165	RIKEN cDNA 2010107G23 gene	protein-coding
mm_162520.1	chr1	157072026	157072028	+	1	NA	Intergenic	MRLTR33|LTR|ERVK	36623	NM_001305059	73435	Mm.116705	NM_028540	ENSMUSG00000026592	Tex35	1700057K13Rik	testis expressed 35	protein-coding
mm_39711.1	chr5	27791724	27791753	+	1	NA	promoter-TSS (NM_018878)	promoter-TSS (NM_018878)	-188	NM_018878	55982	Mm.277190	NM_018878	ENSMUSG00000002221	Paxip1	D5Ertd149e|PTIP	PAX interacting (with transcription-activation domain) protein 1	protein-coding
mm_22322.1	chr2	180642307	180642315	-	1	NA	exon (NM_178254, exon 1 of 6)	exon (NM_178254, exon 1 of 6)	380	NM_178254	277353	Mm.473700	NM_178254	ENSMUSG00000038932	Tcfl5	AV260129|Figlb|Sosf1	transcription factor-like 5 (basic helix-loop-helix)	protein-coding
mm_29252.1	chr3	107219215	107219235	-	1	NA	intron (NM_001111143, intron 2 of 8)	intron (NM_001111143, intron 2 of 8)	2507	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_152376.1	chr19	10228772	10228793	-	1	NA	exon (NM_001033481, exon 3 of 26)	exon (NM_001033481, exon 3 of 26)	11966	NM_001033481	225908	Mm.329716	NM_001033481	ENSMUSG00000036098	Myrf	6030439E18|Gm1804|Gm98|Mrf	myelin regulatory factor	protein-coding
mm_13366.1	chr2	103456887	103456898	+	1	NA	exon (NM_009804, exon 11 of 13)	exon (NM_009804, exon 11 of 13)	28261	NM_009804	12359	Mm.4215	NM_009804	ENSMUSG00000027187	Cat	2210418N07|Cas-1|Cas1|Cs-1	catalase	protein-coding
mm_84772.1	chr9	75642311	75642326	-	1	NA	Intergenic	RMER6D|LTR|ERVK	16586	NM_027309	70082	Mm.19119	NM_027309	ENSMUSG00000032184	Lysmd2	2210402C18Rik|AV033872|AW538442	LysM, putative peptidoglycan-binding, domain containing 2	protein-coding
mm_9806.1	chr1	181927758	181927763	-	1	NA	intron (NM_001083121, intron 4 of 13)	intron (NM_001083121, intron 4 of 13)	-85359	NM_133815	98386	Mm.4538	NM_133815	ENSMUSG00000004880	Lbr	AI505894|ic	lamin B receptor	protein-coding
mm_28672.1	chr3	95293677	95293721	-	1	NA	exon (NM_133858, exon 7 of 10)	exon (NM_133858, exon 7 of 10)	10764	NM_199475	75007	Mm.279287	NM_133858	ENSMUSG00000038712	Fam63a	1810005H09Rik|4930504E06Rik|AA562754|AA960384|AW561904|cI-40|mKIAA1390|ni	family with sequence similarity 63, member A	protein-coding
mm_23033.1	chr3	34651072	34651082	+	1	NA	exon (NM_011443, exon 1 of 1)	exon (NM_011443, exon 1 of 1)	1082	NM_011443	20674	Mm.65396	NM_011443	ENSMUSG00000074637	Sox2	Sox-2|lcc|ysb	SRY (sex determining region Y)-box 2	protein-coding
mm_129561.1	chr15	79546271	79546273	-	1	NA	5' UTR (NM_001040187, exon 1 of 13)	5' UTR (NM_001040187, exon 1 of 13)	287	NM_199079	67040	Mm.29644	NM_152806	ENSMUSG00000055065	Ddx17	2610007K22Rik|A430025E01Rik|AI047725|C80929|Gm926|p72	DEAD (Asp-Glu-Ala-Asp) box polypeptide 17	protein-coding
mm_69092.1	chr7	127018473	127018523	-	1	NA	3' UTR (NM_001102563, exon 4 of 4)	3' UTR (NM_001102563, exon 4 of 4)	-1146	NM_030240	67278	Mm.345385	NM_030240	ENSMUSG00000030680	Pagr1a	2900092E17Rik|C77040|PA1|PAGR1	PAXIP1 associated glutamate rich protein 1A	protein-coding
mm_58645.1	chr7	6252790	6252796	+	1	NA	promoter-TSS (NM_001177416)	promoter-TSS (NM_001177416)	83	NM_001177416	627821	Mm.99441	NM_001177416	ENSMUSG00000053367	Gm6792	EG627821	predicted gene 6792	protein-coding
mm_58250.1	chr6	145048810	145048821	-	1	NA	promoter-TSS (NM_001024468)	promoter-TSS (NM_001024468)	-3	NM_001024468	12035	Mm.4606	NM_007532	ENSMUSG00000030268	Bcat1	BCATc|Eca39	branched chain aminotransferase 1, cytosolic	protein-coding
mm_80869.1	chr9	98563705	98563737	+	1	NA	promoter-TSS (NM_015827)	promoter-TSS (NM_015827)	-10	NM_015827	50797	Mm.400464	NM_015827	ENSMUSG00000032458	Copb2	AI256832	coatomer protein complex, subunit beta 2 (beta prime)	protein-coding
mm_117468.1	chr13	76018705	76018747	-	1	NA	promoter-TSS (NM_178916)	promoter-TSS (NM_178916)	-14	NM_001131069	218341	Mm.266515	NM_178916	ENSMUSG00000043190	Rfesd	AI256775|D030068K09	Rieske (Fe-S) domain containing	protein-coding
mm_87726.1	chr10	60106446	60106450	+	1	NA	5' UTR (NM_052994, exon 1 of 11)	5' UTR (NM_052994, exon 1 of 11)	191	NM_052994	94214	Mm.153429	NM_052994	ENSMUSG00000058297	Spock2	AA407235|Gcap26|mKIAA0275	sparc/osteonectin, cwcv and kazal-like domains proteoglycan 2	protein-coding
mm_66545.1	chr7	45204469	45204504	-	1	NA	intron (NM_201374, intron 1 of 19)	CpG	406	NM_201374	384619	Mm.214931	NM_201374	ENSMUSG00000038292	Ccdc155	Gm1434|KASH5	coiled-coil domain containing 155	protein-coding
mm_38747.1	chr4	145272810	145272836	-	1	NA	intron (NM_009401, intron 12 of 12)	intron (NM_009401, intron 12 of 12)	-25953	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_29015.1	chr3	101836182	101836210	-	1	NA	promoter-TSS (NM_172295)	promoter-TSS (NM_172295)	27	NM_172295	242125	Mm.32900	NM_172295	ENSMUSG00000044313	Mab21l3	-	mab-21-like 3 (C. elegans)	protein-coding
mm_24990.1	chr3	97158768	97158820	+	1	NA	promoter-TSS (NM_019800)	promoter-TSS (NM_019800)	17	NM_019800	66659	Mm.101368	NM_019800	ENSMUSG00000028093	Acp6	5730559A09Rik|ACPL1|AU022842|mPACPL1	acid phosphatase 6, lysophosphatidic	protein-coding
mm_75616.1	chr8	63828246	63828256	-	1	NA	Intergenic	Intergenic	123919	NM_001195687	244495	Mm.485331	NM_001195687	ENSMUSG00000094443	Sgol2b	EG244495|Gm4975|Sgo2B	shugoshin like 2b (S. pombe)	protein-coding
mm_21902.1	chr2	166158187	166158220	-	1	NA	Intergenic	Intergenic	-2520	NM_028072	72043	Mm.1011	NM_028072	ENSMUSG00000006800	Sulf2	2010004N24Rik|AU020235|MSulf-2|mKIAA1247	sulfatase 2	protein-coding
mm_133658.1	chr16	91820538	91820551	+	1	NA	exon (NM_001110276, exon 13 of 16)	exon (NM_001110276, exon 13 of 16)	91173	NM_010587	16443	Mm.40546	NM_010587	ENSMUSG00000022957	Itsn1	AA517634|AA545208|AI316805|AI839402|AI848451|Ehsh1|Ese1|Itsn|Sh3p17	intersectin 1 (SH3 domain protein 1A)	protein-coding
mm_19623.1	chr2	102812834	102812845	-	1	NA	3' UTR (NM_009851, exon 19 of 19)	3' UTR (NM_009851, exon 19 of 19)	88826	NM_001177785	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_45037.1	chr5	39643826	39643865	-	1	NA	intron (NM_010474, intron 1 of 1)	A-rich|Low_complexity|Low_complexity	786	NM_010474	15476	Mm.12559	NM_010474	ENSMUSG00000051022	Hs3st1	3-Ost|D5Wsu110e|Hsg3ost	heparan sulfate (glucosamine) 3-O-sulfotransferase 1	protein-coding
mm_47739.1	chr5	130250883	130250899	-	1	NA	exon (NM_023248, exon 3 of 5)	exon (NM_023248, exon 3 of 5)	4639	NM_023248	66711	Mm.280484	NM_023248	ENSMUSG00000025337	Sbds	4733401P19Rik|AI836084|CGI-97|SDS	Shwachman-Bodian-Diamond syndrome homolog (human)	protein-coding
mm_78944.1	chr9	45138529	45138537	+	1	NA	promoter-TSS (NM_001013390)	promoter-TSS (NM_001013390)	-509	NM_001013390	399548	Mm.335112	NM_001013390	ENSMUSG00000046480	Scn4b	Gm1471	sodium channel, type IV, beta	protein-coding
mm_148203.1	chr18	79109984	79110014	-	1	NA	promoter-TSS (NM_053099)	promoter-TSS (NM_053099)	-608	NM_053099	240427	Mm.312871	NM_053099	ENSMUSG00000024548	Setbp1	C130092E12|Seb|mKIAA0437	SET binding protein 1	protein-coding
mm_157233.1	chrX	16911467	16911478	-	1	NA	5' UTR (NM_010883, exon 1 of 3)	5' UTR (NM_010883, exon 1 of 3)	302	NM_010883	17986	Mm.5014	NM_010883	ENSMUSG00000040138	Ndp	ND|Ndph	Norrie disease (pseudoglioma) (human)	protein-coding
mm_92785.1	chr10	81291228	81291282	-	1	NA	promoter-TSS (NM_013769)	promoter-TSS (NM_013769)	12	NM_013769	27375	Mm.27984	NM_013769	ENSMUSG00000034917	Tjp3	-	tight junction protein 3	protein-coding
mm_112437.1	chr13	5786068	5786068	+	1	NA	Intergenic	MLT1F1|LTR|ERVL-MaLR	72024	NR_045891	71867	Mm.179181	NR_045891	ENSMUSG00000100625	1700016G22Rik	-	RIKEN cDNA 1700016G22 gene	ncRNA
mm_66542.1	chr7	45189648	45189650	-	1	NA	exon (NM_201374, exon 11 of 20)	exon (NM_201374, exon 11 of 20)	8654	NM_053256	114640	Mm.207078	NM_053256	ENSMUSG00000038300	Pth2	Tifp39|Tip39	parathyroid hormone 2	protein-coding
mm_108528.1	chr12	84132537	84132557	+	1	NA	intron (NM_001346528, intron 5 of 7)	intron (NM_001346528, intron 5 of 7)	15942	NM_027438	70481	Mm.444348	NM_027438	ENSMUSG00000054383	Pnma1	5730402C15Rik	paraneoplastic antigen MA1	protein-coding
mm_6416.1	chr1	73354383	73354385	-	1	NA	Intergenic	Intergenic	-44584	NR_040605	78718	Mm.244075	NR_040605	ENSMUSG00000101812	D530049I02Rik	-	RIKEN cDNA D530049I02 gene	ncRNA
mm_59197.1	chr7	24507015	24507024	+	1	NA	promoter-TSS (NM_001290461)	promoter-TSS (NM_001290461)	-68	NM_001290461	232969	Mm.181332	NM_146183	ENSMUSG00000064264	Zfp428	2410005H09Rik|AV271806|AW047854|Znf428	zinc finger protein 428	protein-coding
mm_159981.1	chr6	113600708	113600708	-	1	NA	promoter-TSS (NM_027633)	promoter-TSS (NM_027633)	7	NM_027633	70979	Mm.72959	NM_027633	ENSMUSG00000033963	Fancd2os	4931417G12Rik	Fancd2 opposite strand	protein-coding
mm_166149.1	chr5	5644795	5644795	+	1	NA	intron (NM_172447, intron 4 of 22)	intron (NM_172447, intron 4 of 22)	19437	NM_172447	207686	Mm.319007	NM_172447	ENSMUSG00000040473	Cfap69	4921525K03|A330021E22Rik|AI427898	cilia and flagella associated protein 69	protein-coding
mm_86571.1	chr10	11609257	11609269	+	1	NA	promoter-TSS (NM_013898)	promoter-TSS (NM_013898)	39	NM_013898	30058	Mm.214504	NM_013898	ENSMUSG00000048007	Timm8a1	DXHXS1274E|Ddp1|Fci-12|Tim8a|Timm8a	translocase of inner mitochondrial membrane 8A1	protein-coding
mm_42419.1	chr5	115312995	115313025	+	1	NA	intron (NR_131932, intron 1 of 1)	intron (NR_131932, intron 1 of 1)	11890	NR_131932	102639268	Mm.319998	NR_131932		Gm13830	OTTMUSG00000014646	predicted gene 13830	ncRNA
mm_85021.1	chr9	88436601	88436624	-	1	NA	intron (NM_172926, intron 1 of 27)	L1_Rod|LINE|L1	2339	NM_172926	244962	Mm.439873	NM_172926	ENSMUSG00000032422	Snx14	B830022K16|C330035N22Rik|YR-14	sorting nexin 14	protein-coding
mm_55733.1	chr6	77349623	77349647	-	1	NA	intron (NM_001109764, intron 8 of 19)	X8_LINE|LINE|CR1	32840	NR_045141	70753	Mm.490700	NR_045141	ENSMUSG00000108077	6330415B21Rik	-	RIKEN cDNA 6330415B21 gene	ncRNA
mm_8835.1	chr1	162571540	162571540	-	1	NA	intron (NM_001347125, intron 1 of 7)	CpG	712	NM_001347125	53330	Mm.10699	NM_016796	ENSMUSG00000026696	Vamp4	D1Ertd147e	vesicle-associated membrane protein 4	protein-coding
mm_158574.1	chrX	150589864	150589888	-	1	NA	promoter-TSS (NM_008824)	promoter-TSS (NM_008824)	-45	NM_008824	18639	Mm.249131	NM_008824	ENSMUSG00000025271	Pfkfb1	PFK/FBPase 1	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1	protein-coding
mm_133561.1	chr16	91393780	91393829	+	1	NA	exon (NM_010509, exon 7 of 9)	exon (NM_010509, exon 7 of 9)	-12431	NM_008349	16155	Mm.4154	NM_008349	ENSMUSG00000022969	Il10rb	6620401D04Rik|AI528744|CRF2-4|Crfb4|D16H21S58|D21S58h|IL-10R2|Il10r2	interleukin 10 receptor, beta	protein-coding
mm_169239.1	chr13	72455349	72455369	-	1	NA	Intergenic	ID_B1|SINE|B4	173205	NR_030701	328287	Mm.235072	NR_030701		Gm20554	D430050G20	predicted gene, 20554	ncRNA
mm_8443.1	chr1	152837502	152837518	-	1	NA	TTS (NM_010877)	TTS (NM_010877)	37357	NM_010877	17970	Mm.270307	NM_010877	ENSMUSG00000026480	Ncf2	NOXA2|Ncf-2|p67phox	neutrophil cytosolic factor 2	protein-coding
mm_82401.1	chr9	14770965	14770976	-	1	NA	promoter-TSS (NM_029306)	promoter-TSS (NM_029306)	60	NM_029306	69325	Mm.440453	NM_029306	ENSMUSG00000031927	1700012B09Rik	1700007P19Rik	RIKEN cDNA 1700012B09 gene	protein-coding
mm_83293.1	chr9	43200255	43200264	-	1	NA	intron (NM_011139, intron 1 of 12)	intron (NM_011139, intron 1 of 12)	5496	NM_011139	18988	Mm.436650	NM_011139	ENSMUSG00000032015	Pou2f3	Epoc-1|Oct-11a|Oct11|Otf-11|Otf11|Skin|Skin-1a|Skn-1a|Skn-li	POU domain, class 2, transcription factor 3	protein-coding
mm_48247.1	chr5	137786652	137786668	-	1	NA	promoter-TSS (NM_144913)	promoter-TSS (NM_144913)	41	NM_144913	231803	Mm.61193	NM_144913	ENSMUSG00000029726	Mepce	Bcdin3|D5Wsu46e	methylphosphate capping enzyme	protein-coding
mm_133740.1	chr16	93973764	93973797	+	1	NA	intron (NM_019500, intron 1 of 2)	intron (NM_019500, intron 1 of 2)	35057	NM_019500	56173	Mm.328716	NM_019500	ENSMUSG00000047109	Cldn14	AI851731	claudin 14	protein-coding
mm_161617.1	chr16	55838874	55838874	-	1	NA	promoter-TSS (NM_030612)	promoter-TSS (NM_030612)	-233	NM_001159395	80859	Mm.247272	NM_030612	ENSMUSG00000035356	Nfkbiz	AA408868|INAP|Mail	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, zeta	protein-coding
mm_58165.1	chr6	142571304	142571353	-	1	NA	5' UTR (NM_008428, exon 1 of 3)	5' UTR (NM_008428, exon 1 of 3)	286	NM_001330363	16523	Mm.1482	NM_008428	ENSMUSG00000030247	Kcnj8	AI448900|Kir6.1|gnite|slmbr|sltr|uKATP-1	potassium inwardly-rectifying channel, subfamily J, member 8	protein-coding
mm_35673.1	chr4	43578825	43578909	-	1	NA	promoter-TSS (NM_172692)	promoter-TSS (NM_172692)	-3	NM_172692	230101	Mm.229444	NM_172692	ENSMUSG00000028467	Gba2	F630034E04	glucosidase beta 2	protein-coding
mm_37446.1	chr4	123350985	123350998	-	1	NA	exon (NM_001199137, exon 93 of 93)	exon (NM_001199137, exon 93 of 93)	-7739	NM_007558	12163	Mm.439749	NM_007558	ENSMUSG00000032726	Bmp8a	Bmp7r1|OP-2|OP2	bone morphogenetic protein 8a	protein-coding
mm_101391.1	chr11	24926046	24926061	-	1	NA	Intergenic	Intergenic	-195331	NR_033491	100038617	Mm.387376	NR_033491	ENSMUSG00000073103	Gm10466	ENSMUSG00000073103	predicted gene 10466	ncRNA
mm_69012.1	chr7	126704705	126704711	-	1	NA	promoter-TSS (NM_001301374)	promoter-TSS (NM_001301374)	108	NM_009898	12721	Mm.290482	NM_009898	ENSMUSG00000030707	Coro1a	Clabp|Lmb3|TACO|p57	coronin, actin binding protein 1A	protein-coding
mm_4382.1	chr1	172198220	172198236	+	1	NA	3' UTR (NM_001329871, exon 4 of 4)	3' UTR (NM_001329871, exon 4 of 4)	8576	NM_001329871	18611	Mm.544	NM_011063	ENSMUSG00000013698	Pea15a	Mat1|PEA-15|Pea15|Pkcs15	phosphoprotein enriched in astrocytes 15A	protein-coding
mm_18861.1	chr2	75704471	75704533	-	1	NA	non-coding (NR_132727, exon 1 of 2)	non-coding (NR_132727, exon 1 of 2)	161	NR_132727	18024	Mm.1025	NM_010902	ENSMUSG00000015839	Nfe2l2	Nrf2	nuclear factor, erythroid derived 2, like 2	protein-coding
mm_137055.1	chr17	17928339	17928381	+	1	NA	Intergenic	RMER12|LTR|ERVK	40536	NM_008039	14289	Mm.378918	NM_008039	ENSMUSG00000052270	Fpr2	E330010I07Rik|Fpr-rs2	formyl peptide receptor 2	protein-coding
mm_112625.1	chr13	15848320	15848340	+	1	NA	Intergenic	Intergenic	41087	NR_046131	328190	Mm.446957	NR_046131		A530046M15Rik	A530046M15	RIKEN cDNA A530046M15 gene	ncRNA
mm_69006.1	chr7	126702470	126702486	-	1	NA	intron (NM_001301374, intron 2 of 10)	intron (NM_001301374, intron 2 of 10)	1742	NM_001301374	12721	Mm.290482	NM_009898	ENSMUSG00000030707	Coro1a	Clabp|Lmb3|TACO|p57	coronin, actin binding protein 1A	protein-coding
mm_135369.1	chr16	44061494	44061506	-	1	NA	Intergenic	Intergenic	-33555	NM_001172107	207798	Mm.19316	NM_153528	ENSMUSG00000036292	Gramd1c	4921521N14Rik	GRAM domain containing 1C	protein-coding
mm_163408.1	chr12	76795550	76795552	-	1	NA	promoter-TSS (NM_030677)	promoter-TSS (NM_030677)	3	NM_030677	14776	Mm.441856	NM_030677	ENSMUSG00000042808	Gpx2	GI-GPx|GPx-GI|GSHPx-2|GSHPx-GI	glutathione peroxidase 2	protein-coding
mm_70412.1	chr8	11448155	11448168	+	1	NA	exon (NM_009932, exon 48 of 48)	exon (NM_009932, exon 48 of 48)	-29768	NR_126558	102132	Mm.37632	NR_126558	ENSMUSG00000096957	E230013L22Rik	AI645545	RIKEN cDNA E230013L22 gene	ncRNA
mm_155857.1	chrX	101320170	101320184	+	1	NA	exon (NM_172932, exon 7 of 7)	exon (NM_172932, exon 7 of 7)	20998	NM_172932	245537	Mm.121508	NM_172932	ENSMUSG00000031302	Nlgn3	A230085M13Rik|HNL3|NL3	neuroligin 3	protein-coding
mm_6015.1	chr1	59014107	59014115	-	1	NA	Intergenic	Intergenic	40540	NM_172656	227154	Mm.286006	NM_172656	ENSMUSG00000026027	Stradb	AA792893|Als2cr2|B830008M19|D1Ucla2|ILPIP|ILPIPA|PRO1038|Papk|Syradb	STE20-related kinase adaptor beta	protein-coding
mm_26859.1	chr3	14871746	14871804	-	1	NA	3' UTR (NM_007606, exon 7 of 7)	3' UTR (NM_007606, exon 7 of 7)	8237	NM_007606	12350	Mm.300	NM_007606	ENSMUSG00000027559	Car3	BB219044|Ca3|Car-3	carbonic anhydrase 3	protein-coding
mm_11472.1	chr2	32374387	32374422	+	1	NA	exon (NM_001252538, exon 12 of 18)	exon (NM_001252538, exon 12 of 18)	7511	NM_198001	73737	Mm.27608	NM_198001	ENSMUSG00000039195	1110008P14Rik	C79326	RIKEN cDNA 1110008P14 gene	protein-coding
mm_140817.1	chr17	23193145	23193173	-	1	NA	promoter-TSS (NM_009555)	promoter-TSS (NM_009555)	69	NM_009555	22700	Mm.437934	NM_009555	ENSMUSG00000002617	Zfp40	CTfin12|NTfin12|Zfp-40	zinc finger protein 40	protein-coding
mm_91231.1	chr10	22302432	22302455	-	1	NA	intron (NM_009018, intron 5 of 5)	RMER15|LTR|ERVL	-4277	NR_015465	606736	Mm.387042	NR_015465	ENSMUSG00000097352	C920009B18Rik	-	RIKEN cDNA C920009B18 gene	ncRNA
mm_141783.1	chr17	34301146	34301163	-	1	NA	Intergenic	Intergenic	-4713	NM_010382	14969	Mm.22564	NM_010382	ENSMUSG00000060586	H2-Eb1	Eb|H-2Eb|H2Eb|Ia-4|Ia4	histocompatibility 2, class II antigen E beta	protein-coding
mm_74058.1	chr8	122342451	122342459	+	1	NA	Intergenic	RMER4A|LTR|ERVK	18291	NM_133202	170732	Mm.154808	NM_133202	ENSMUSG00000039079	Trhr2	TRH-R2	thyrotropin releasing hormone receptor 2	protein-coding
mm_58305.1	chr6	146212794	146212817	-	1	NA	intron (NM_010586, intron 44 of 55)	(TG)n|Simple_repeat|Simple_repeat	278658	NM_010656	16651	Mm.49689	NM_010656	ENSMUSG00000030255	Sspn	Krag	sarcospan	protein-coding
mm_116213.1	chr13	32783958	32783975	-	1	NA	Intergenic	Intergenic	-2187	NM_001166030	238564	Mm.60041	NM_001166030	ENSMUSG00000044951	Mylk4	EG238564	myosin light chain kinase family, member 4	protein-coding
mm_129601.1	chr15	79834336	79834344	-	1	NA	promoter-TSS (NM_001013360)	promoter-TSS (NM_001013360)	-7	NM_001013362	504193	Mm.38438	NM_029079	ENSMUSG00000089837	Npcd	Cbx6-Nptxr	neuronal pentraxin chromo domain	protein-coding
mm_166414.1	chr5	137151488	137151496	-	1	NA	Intergenic	Intergenic	-35285	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_137440.1	chr17	26508750	26508774	+	1	NA	promoter-TSS (NM_013642)	promoter-TSS (NM_013642)	-290	NM_013642	19252	Mm.239041	NM_013642	ENSMUSG00000024190	Dusp1	3CH134|MKP1|Ptpn16|U19515|erp|mkp-1	dual specificity phosphatase 1	protein-coding
mm_31231.1	chr4	44337823	44337826	+	1	NA	intron (NM_010790, intron 11 of 17)	intron (NM_010790, intron 11 of 17)	36907	NM_010790	17279	Mm.268668	NM_010790	ENSMUSG00000035683	Melk	AI327312|MPK38|mKIAA0175	maternal embryonic leucine zipper kinase	protein-coding
mm_155633.1	chrX	84772801	84772810	+	1	NA	intron (NM_007868, intron 55 of 78)	intron (NM_007868, intron 55 of 78)	-275490	NM_001314038	13405	Mm.275608	NM_007868	ENSMUSG00000045103	Dmd	DXSmh7|DXSmh9|Dp427|Dp71|dys|mdx|pke	dystrophin, muscular dystrophy	protein-coding
mm_143715.1	chr17	80801008	80801043	-	1	NA	Intergenic	Intergenic	-73000	NM_001290345	225028	Mm.311948	NM_001081357	ENSMUSG00000024242	Map4k3	4833416M01Rik|4833416M07Rik|9530052P13Rik|Glk|MAPKKKK3|MEKKK 3|MEKKK3|RAB8IPL1	mitogen-activated protein kinase kinase kinase kinase 3	protein-coding
mm_44863.1	chr5	34336135	34336161	-	1	NA	promoter-TSS (NM_011278)	promoter-TSS (NM_011278)	-102	NM_011278	19822	Mm.21281	NM_011278	ENSMUSG00000029110	Rnf4	AU018689|Gtrgeo8|SNURF	ring finger protein 4	protein-coding
mm_147446.1	chr18	46526023	46526027	-	1	NA	promoter-TSS (NM_173423)	promoter-TSS (NM_173423)	-54	NM_173423	240263	Mm.38249	NM_173423	ENSMUSG00000033319	Fem1c	2610312A07Rik|3632443A22Rik|AI646567	fem-1 homolog c (C.elegans)	protein-coding
mm_162268.1	chr1	10038209	10038228	+	1	NA	promoter-TSS (NM_013715)	promoter-TSS (NM_013715)	0	NM_026493	211660	Mm.244046	NM_026493	ENSMUSG00000056763	Cspp1	2310020J12Rik|4930413O22Rik|AA387550|BC055915|Cspp2|Cspp3	centrosome and spindle pole associated protein 1	protein-coding
mm_116522.1	chr13	45789201	45789215	-	1	NA	intron (NM_001199304, intron 4 of 6)	intron (NM_001199304, intron 4 of 6)	175783	NM_001199304	20238	Mm.342683	NM_009124	ENSMUSG00000046876	Atxn1	2900016G23Rik|Atx1|C85907|ENSMUSG00000074917|Gm10786|Sca1	ataxin 1	protein-coding
mm_82675.1	chr9	22131802	22131874	-	1	NA	promoter-TSS (NM_001102404)	promoter-TSS (NM_001102404)	27	NM_001102404	11433	Mm.46354	NM_007388	ENSMUSG00000001348	Acp5	TRACP|TRAP	acid phosphatase 5, tartrate resistant	protein-coding
mm_115076.1	chr13	101773501	101773501	+	1	NA	Intergenic	Intergenic	-5284	NM_001077495	18708	Mm.259333	NM_001024955	ENSMUSG00000041417	Pik3r1	PI3K|p50alpha|p55alpha|p85alpha	phosphatidylinositol 3-kinase, regulatory subunit, polypeptide 1 (p85 alpha)	protein-coding
mm_66923.1	chr7	61311641	61311655	-	1	NA	Intergenic	Intergenic	303679	NR_045727	319752	Mm.294476	NR_045727		B230209E15Rik	-	RIKEN cDNA B230209E15 gene	ncRNA
mm_108525.1	chr12	84114300	84114310	+	1	NA	promoter-TSS (NM_028821)	promoter-TSS (NM_028821)	-23	NM_028821	105000	Mm.101525	NM_028821	ENSMUSG00000042523	Dnal1	1700010H15Rik|AW121714|Dnalc1|E330027P08Rik	dynein, axonemal, light chain 1	protein-coding
mm_90166.1	chr10	119413456	119413475	+	1	NA	promoter-TSS (NR_040578)	promoter-TSS (NR_040578)	21	NR_040578	67081	Mm.72644	NR_040578	ENSMUSG00000100558	1700025F24Rik	-	RIKEN cDNA 1700025F24 gene	ncRNA
mm_141547.1	chr17	32034531	32034539	-	1	NA	promoter-TSS (NM_028902)	promoter-TSS (NM_028902)	-27	NM_028902	74377	Mm.75856	NM_028902	ENSMUSG00000002076	Hsf2bp	4932437G14Rik	heat shock transcription factor 2 binding protein	protein-coding
mm_50764.1	chr6	53592977	53592982	+	1	NA	intron (NM_172728, intron 1 of 6)	intron (NM_172728, intron 1 of 6)	19605	NM_172728	231991	Mm.227444	NM_172728	ENSMUSG00000053007	Creb5	9430076C15Rik|CRE-BPa|Crebpa|D430026C09Rik	cAMP responsive element binding protein 5	protein-coding
mm_145991.1	chr18	68319004	68319019	+	1	NA	intron (NM_001170953, intron 7 of 9)	intron (NM_001170953, intron 7 of 9)	-18592	NM_013596	17203	Mm.8003	NM_013596	ENSMUSG00000007480	Mc5r	-	melanocortin 5 receptor	protein-coding
mm_137042.1	chr17	17904039	17904047	+	1	NA	Intergenic	RSINE1|SINE|B4	16219	NM_008039	14289	Mm.378918	NM_008039	ENSMUSG00000052270	Fpr2	E330010I07Rik|Fpr-rs2	formyl peptide receptor 2	protein-coding
mm_108611.1	chr12	85476594	85476649	+	1	NA	3' UTR (NM_010234, exon 4 of 4)	3' UTR (NM_010234, exon 4 of 4)	2720	NM_010234	14281	Mm.246513	NM_010234	ENSMUSG00000021250	Fos	D12Rfj1|c-fos|cFos	FBJ osteosarcoma oncogene	protein-coding
mm_61699.1	chr7	81141905	81141921	+	1	NA	intron (NM_001004184, intron 9 of 17)	intron (NM_001004184, intron 9 of 17)	27114	NM_001004184	434203	Mm.389909	NM_001004184	ENSMUSG00000025726	Slc28a1	Cnt1	solute carrier family 28 (sodium-coupled nucleoside transporter), member 1	protein-coding
mm_116072.1	chr13	27642485	27642499	-	1	NA	promoter-TSS (NM_001164058)	promoter-TSS (NM_001164058)	1	NM_001164058	19113	Mm.196424	NM_008930	ENSMUSG00000006488	Prl7a1	AA407021|AA409971|AA410116|PLP-E|PLP-G|Prlpe|Prlpg	prolactin family 7, subfamily a, member 1	protein-coding
mm_172136.1	chr6	35395576	35395580	+	1	NA	Intergenic	L1Md_T|LINE|L1	64732	NR_040526	73409	Mm.69443	NR_040526	ENSMUSG00000107341	1700065J11Rik	-	RIKEN cDNA 1700065J11 gene	ncRNA
mm_164820.1	chr18	35438257	35438261	+	1	NA	intron (NM_030749, intron 2 of 9)	intron (NM_030749, intron 2 of 9)	60666	NM_030749	81500	Mm.291482	NM_030749	ENSMUSG00000024357	Sil1	1810057E01Rik|AI042831|wz	endoplasmic reticulum chaperone SIL1 homolog (S. cerevisiae)	protein-coding
mm_59430.1	chr7	27129788	27129799	+	1	NA	exon (NM_007817, exon 6 of 10)	exon (NM_007817, exon 6 of 10)	9838	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_111293.1	chr12	85472189	85472203	-	1	NA	Intergenic	CpG	-1705	NM_010234	14281	Mm.246513	NM_010234	ENSMUSG00000021250	Fos	D12Rfj1|c-fos|cFos	FBJ osteosarcoma oncogene	protein-coding
mm_17223.1	chr2	25501718	25501724	-	1	NA	promoter-TSS (NM_001271777)	promoter-TSS (NM_001271777)	-2	NM_001271777	69379	Mm.24596	NM_027062	ENSMUSG00000015083	C8g	-	complement component 8, gamma polypeptide	protein-coding
mm_143943.1	chr17	86444865	86444904	-	1	NA	intron (NM_011104, intron 2 of 14)	intron (NM_011104, intron 2 of 14)	-157706	NR_045435	72104	Mm.443401	NR_045435	ENSMUSG00000100738	2010106C02Rik	-	RIKEN cDNA 2010106C02 gene	ncRNA
mm_35400.1	chr4	34687313	34687342	-	1	NA	5' UTR (NM_011895, exon 1 of 8)	5' UTR (NM_011895, exon 1 of 8)	111	NM_011895	24060	Mm.281885	NM_011895	ENSMUSG00000028293	Slc35a1	AA408150|AI314851	solute carrier family 35 (CMP-sialic acid transporter), member 1	protein-coding
mm_142767.1	chr17	49529055	49529063	-	1	NA	intron (NM_001008231, intron 1 of 25)	intron (NM_001008231, intron 1 of 25)	35278	NM_001008231	76441	Mm.211275	NM_001008231	ENSMUSG00000040260	Daam2	2310016D11Rik|AI843643|AW557870	dishevelled associated activator of morphogenesis 2	protein-coding
mm_37847.1	chr4	132186583	132186602	-	1	NA	3' UTR (NM_145393, exon 5 of 5)	3' UTR (NM_145393, exon 5 of 5)	25664	NM_145393	213541	Mm.23998	NM_145393	ENSMUSG00000040025	Ythdf2	9430020E02Rik|HGRG8|NY-REN-2	YTH domain family 2	protein-coding
mm_28309.1	chr3	89239444	89239479	-	1	NA	exon (NM_183037, exon 6 of 10)	exon (NM_183037, exon 6 of 10)	5552	NR_121683	360213	Mm.331156	NM_183037	ENSMUSG00000042766	Trim46	TRIFIC	tripartite motif-containing 46	protein-coding
mm_117992.1	chr13	100437495	100437507	-	1	NA	intron (NM_008670, intron 4 of 15)	(A)n|Simple_repeat|Simple_repeat	15363	NM_008670	17940	Mm.6898	NM_008670	ENSMUSG00000021640	Naip1	AV364616|Birc1a|D13Lsd1|Naip|Naip-rs1	NLR family, apoptosis inhibitory protein 1	protein-coding
mm_37979.1	chr4	133601840	133601868	-	1	NA	5' UTR (NM_018754, exon 1 of 1)	5' UTR (NM_018754, exon 1 of 1)	314	NM_018754	55948	Mm.44482	NM_018754	ENSMUSG00000047281	Sfn	Er|Mme1|Ywhas	stratifin	protein-coding
mm_90451.1	chr10	127703524	127703552	+	1	NA	Intergenic	Intergenic	-1718	NM_001081219	432516	Mm.90450	NM_001081219	ENSMUSG00000025401	Myo1a	BBM-I|Myhl	myosin IA	protein-coding
mm_44514.1	chr5	24344551	24344567	-	1	NA	intron (NM_013569, intron 2 of 14)	intron (NM_013569, intron 2 of 14)	7045	NM_013569	16511	Mm.6539	NM_013569	ENSMUSG00000038319	Kcnh2	AI326795|ERG1|LQT|Lqt2|M-erg|Merg1|merg1a|merg1b	potassium voltage-gated channel, subfamily H (eag-related), member 2	protein-coding
mm_40304.1	chr5	43803630	43803632	+	1	NA	Intergenic	B3A|SINE|B2	-15262	NM_009763	12182	Mm.246332	NM_009763	ENSMUSG00000029082	Bst1	114/A10|A530073F09|BP-3|Bp3|Bsta1|CD157|Ly65	bone marrow stromal cell antigen 1	protein-coding
mm_81620.1	chr9	110813987	110814030	+	1	NA	promoter-TSS (NM_148940)	promoter-TSS (NM_148940)	14	NM_148940	73336	Mm.200587	NM_148940	ENSMUSG00000032493	Prss44	1700036D21Rik|79H19A|AU043574|AU043597|TESSP-4|Tessp4	protease, serine 44	protein-coding
mm_164331.1	chr16	10192877	10192883	+	1	NA	promoter-TSS (NM_029253)	promoter-TSS (NM_029253)	-26	NM_153123	75329	Mm.108729	NM_029253	ENSMUSG00000039200	Atf7ip2	4930558K11Rik|BC018510|Get-1|PSM2	activating transcription factor 7 interacting protein 2	protein-coding
mm_16735.1	chr2	9177874	9177895	-	1	NA	Intergenic	Intergenic	-11631	NR_038180	73438	Mm.23558	NR_038180	ENSMUSG00000085580	1700061F12Rik	-	RIKEN cDNA 1700061F12 gene	ncRNA
mm_91546.1	chr10	39731803	39731882	-	1	NA	promoter-TSS (NM_011264)	promoter-TSS (NM_011264)	165	NR_038037	327744	Mm.295265	NM_183198	ENSMUSG00000087177	E130307A14Rik	-	RIKEN cDNA E130307A14 gene	ncRNA
mm_54593.1	chr6	38254088	38254108	-	1	NA	promoter-TSS (NM_194061)	promoter-TSS (NM_194061)	-89	NM_194061	330286	Mm.277163	NM_194061	ENSMUSG00000063455	D630045J12Rik	Kiaa1549|mKIAA1549	RIKEN cDNA D630045J12 gene	protein-coding
mm_126378.1	chr15	80173189	80173204	+	1	NA	promoter-TSS (NM_010795)	promoter-TSS (NM_010795)	-525	NM_010795	17309	Mm.299693	NM_010795	ENSMUSG00000042428	Mgat3	1110038J12Rik|AI848272|GnT-III	mannoside acetylglucosaminyltransferase 3	protein-coding
mm_102501.1	chr11	60537308	60537337	-	1	NA	promoter-TSS (NM_172943)	promoter-TSS (NM_172943)	-361	NM_172943	268420	Mm.262056	NM_172943	ENSMUSG00000042650	Alkbh5	AW050020|AW215868|Abh5|E130207K11|Ofoxd	alkB homolog 5, RNA demethylase	protein-coding
mm_90575.1	chr10	128244829	128244831	+	1	NA	intron (NM_011589, intron 13 of 28)	intron (NM_011589, intron 13 of 28)	6764	NM_011589	21853	Mm.6458	NM_011589	ENSMUSG00000039994	Timeless	C77407|Debt69|tim	timeless circadian clock 1	protein-coding
mm_63228.1	chr7	126446050	126446058	+	1	NA	TTS (NM_030566)	TTS (NM_030566)	17019	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_24408.1	chr3	90450954	90450967	+	1	NA	3' UTR (NM_008727, exon 22 of 22)	3' UTR (NM_008727, exon 22 of 22)	14906	NM_008727	18160	Mm.4627	NM_008727	ENSMUSG00000027931	Npr1	AI893888|GC-A|NPR-A|NPRA|Pndr	natriuretic peptide receptor 1	protein-coding
mm_90921.1	chr10	12614688	12614700	-	1	NA	intron (NM_011682, intron 50 of 73)	intron (NM_011682, intron 50 of 73)	247041	NM_011682	22288	Mm.331784	NM_011682	ENSMUSG00000019820	Utrn	AA589569|DRP|Dmdl	utrophin	protein-coding
mm_76648.1	chr8	93130869	93130907	-	1	NA	exon (NM_007954, exon 2 of 13)	exon (NM_007954, exon 2 of 13)	395	NM_007954	13884	Mm.88078	NM_007954	ENSMUSG00000057400	Ces1c	Ces-N|Ee-1|Ee1|Es-4|Es-N|Es1|Es4|EsN|PESN	carboxylesterase 1C	protein-coding
mm_100242.1	chr11	117266217	117266266	+	1	NA	promoter-TSS (NM_001113487)	promoter-TSS (NM_001113487)	-5	NM_001113487	53860	Mm.38450	NM_017380	ENSMUSG00000059248	Sept9	MSF1|Msf|PNUTL4|Sint1	septin 9	protein-coding
mm_126351.1	chr15	79913008	79913013	+	1	NA	Intergenic	Intergenic	17987	NM_001347041	80287	Mm.284059	NM_030255	ENSMUSG00000009585	Apobec3	Apobec|Arp3|BC003314|Cem15|Rfv3	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 3	protein-coding
mm_157227.1	chrX	13846747	13846769	-	1	NA	promoter-TSS (NM_001284505)	promoter-TSS (NM_001284505)	-202	NM_009806	12361	Mm.327591	NM_009806	ENSMUSG00000031012	Cask	DXPri1|DXRib1|LIN-2|Pals3|mLin-2	calcium/calmodulin-dependent serine protein kinase (MAGUK family)	protein-coding
mm_143626.1	chr17	78882509	78882554	-	1	NA	promoter-TSS (NM_011163)	promoter-TSS (NM_011163)	41	NM_011163	19106	Mm.378990	NM_011163	ENSMUSG00000024079	Eif2ak2	2310047A08Rik|4732414G15Rik|AI467567|AI747578|Pkr|Prkr|Tik	eukaryotic translation initiation factor 2-alpha kinase 2	protein-coding
mm_121382.1	chr14	118952335	118952360	+	1	NA	intron (NM_008929, intron 1 of 11)	intron (NM_008929, intron 1 of 11)	14415	NM_008929	100037258	Mm.12616	NM_008929	ENSMUSG00000022136	Dnajc3	AA408985|AU067833|Dnajc3a|Dnajc3b|Prkri|mp58|p58|p58IPK	DnaJ heat shock protein family (Hsp40) member C3	protein-coding
mm_117477.1	chr13	76385239	76385248	-	1	NA	5' UTR (NM_030174, exon 1 of 21)	5' UTR (NM_030174, exon 1 of 21)	282	NM_030174	78771	Mm.316249	NM_030174	ENSMUSG00000021596	Mctp1	2810465F10Rik	multiple C2 domains, transmembrane 1	protein-coding
mm_1181.1	chr1	61662272	61662272	+	1	NA	intron (NM_001081050, intron 1 of 22)	intron (NM_001081050, intron 1 of 22)	23448	NM_001081050	72823	Mm.35153	NM_001081050	ENSMUSG00000052062	Pard3b	1810008K04Rik|2010002N16Rik|2810455B10Rik|Als2cr19|PAR3B|PAR3L|PAR3beta	par-3 family cell polarity regulator beta	protein-coding
mm_78198.1	chr9	21368048	21368061	+	1	NA	promoter-TSS (NM_001277322)	promoter-TSS (NM_001277322)	183	NM_001042709	16201	Mm.440026	NM_010561	ENSMUSG00000032178	Ilf3	MBII-26|MPHOSPH4|NF90|NFAR	interleukin enhancer binding factor 3	protein-coding
mm_38808.1	chr4	148214739	148214749	-	1	NA	Intergenic	Intergenic	54076	NM_176848	230904	Mm.262287	NM_176848	ENSMUSG00000041556	Fbxo2	FBG1|FBX2|Fbs1|Fbs2|NFB42|Prpl4	F-box protein 2	protein-coding
mm_144690.1	chr18	34840619	34840706	+	1	NA	promoter-TSS (NM_001204914)	promoter-TSS (NM_001204914)	73	NM_144865	225362	Mm.293588	NM_144865	ENSMUSG00000038555	Reep2	-	receptor accessory protein 2	protein-coding
mm_98974.1	chr11	98686005	98686018	+	1	NA	exon (NM_009439, exon 3 of 12)	exon (NM_009439, exon 3 of 12)	3457	NM_009439	22123	Mm.12194	NM_009439	ENSMUSG00000017221	Psmd3	AI255837|AntP91a|D11Bwg1349e|Psd3|Tstap91a	proteasome (prosome, macropain) 26S subunit, non-ATPase, 3	protein-coding
mm_77266.1	chr8	115707824	115707840	-	1	NA	promoter-TSS (NM_001025577)	promoter-TSS (NM_001025577)	-938	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_152444.1	chr19	10783976	10783992	-	1	NA	intron (NR_027805, intron 2 of 3)	intron (NR_027805, intron 2 of 3)	43037	NR_027805	403202	Mm.34482	NM_207529	ENSMUSG00000067577	A430093F15Rik	Gm674	RIKEN cDNA A430093F15 gene	ncRNA
mm_142999.1	chr17	56413078	56413123	-	1	NA	3' UTR (NM_001252453, exon 29 of 29)	3' UTR (NM_001252453, exon 29 of 29)	5809	NR_105943	102465590		NR_105943	ENSMUSG00000098339	Mir6977	Gm27922|mmu-mir-6977	microRNA 6977	ncRNA
mm_73670.1	chr8	111431268	111431278	+	1	NA	Intergenic	Intergenic	-18927	NR_105819	102466970		NR_105819	ENSMUSG00000098410	Mir1957b	Gm27725|mmu-mir-1957b	microRNA 1957b	ncRNA
mm_125652.1	chr15	62893881	62893890	+	1	NA	Intergenic	Intergenic	585723	NR_045279	432958	Mm.255105	NR_045279		Gm20740	-	predicted gene, 20740	ncRNA
mm_124089.1	chr14	78966557	78966594	-	1	NA	intron (NM_173758, intron 12 of 25)	intron (NM_173758, intron 12 of 25)	117397	NM_173758	219189	Mm.159651	NM_027906	ENSMUSG00000058997	Vwa8	1300010F03Rik|4932416F07Rik|AI957255|Kiaa0564|mKIAA0564	von Willebrand factor A domain containing 8	protein-coding
mm_84484.1	chr9	66845628	66845642	-	1	NA	3' UTR (NM_173413, exon 8 of 8)	3' UTR (NM_173413, exon 8 of 8)	-10929	NM_026674	68318	Mm.284229	NM_026674	ENSMUSG00000053040	Aph1c	0610008A10Rik|APH-1b|Aph1b	aph1 homolog C, gamma secretase subunit	protein-coding
mm_41844.1	chr5	104434706	104434739	+	1	NA	promoter-TSS (NM_001204203)	promoter-TSS (NM_001204203)	-389	NM_001204201	20750	Mm.288474	NM_009263	ENSMUSG00000029304	Spp1	2AR|Apl-1|BNSP|BSPI|Bsp|ETA-1|Eta|OP|Opn|Opnl|Ric|Spp-1	secreted phosphoprotein 1	protein-coding
mm_163451.1	chr12	89397993	89397996	+	1	NA	intron (NM_172544, intron 8 of 19)	RSINE1|SINE|B4	-414489	NM_001252074	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding
mm_51773.1	chr6	88084502	88084527	+	1	NA	promoter-TSS (NM_133933)	promoter-TSS (NM_133933)	41	NM_133933	103963	Mm.188544	NM_133933	ENSMUSG00000030062	Rpn1	AU018702|D6Wsu137e|Rpn-1	ribophorin I	protein-coding
mm_26745.1	chr3	7606506	7606519	-	1	NA	intron (NM_008371, intron 1 of 4)	intron (NM_008371, intron 1 of 4)	6381	NM_001313890	16196	Mm.3825	NM_008371	ENSMUSG00000040329	Il7	A630026I06Rik|Il-7|hlb368	interleukin 7	protein-coding
mm_97196.1	chr11	75577128	75577138	+	1	NA	3' UTR (NM_001199283, exon 14 of 14)	3' UTR (NM_001199283, exon 14 of 14)	-10946	NM_008850	18738	Mm.3128	NM_008850	ENSMUSG00000017781	Pitpna	Pitpn|vb|vibrator	phosphatidylinositol transfer protein, alpha	protein-coding
mm_69611.1	chr7	137196364	137196370	-	1	NA	3' UTR (NM_001113414, exon 16 of 16)	3' UTR (NM_001113414, exon 16 of 16)	-38316	NR_045885	100038555	Mm.444788	NR_045885	ENSMUSG00000109722	Gm10578	ENSMUSG00000073800	predicted gene 10578	ncRNA
mm_9212.1	chr1	171229935	171229946	-	1	NA	intron (NM_010185, intron 4 of 4)	intron (NM_010185, intron 4 of 4)	4409	NM_010185	14127	Mm.22673	NM_010185	ENSMUSG00000058715	Fcer1g	AI573376|CD23|FcR-gamma|FcR[g]|FcRgamma|Fce1g|FcepsilonRI|Ly-50	Fc receptor, IgE, high affinity I, gamma polypeptide	protein-coding
mm_69924.1	chr7	141884445	141884457	-	1	NA	exon (NM_023764, exon 6 of 6)	exon (NM_023764, exon 6 of 6)	17955	NM_023764	54473	Mm.103551	NM_023764	ENSMUSG00000025139	Tollip	4930403G24Rik|4931428G15Rik	toll interacting protein	protein-coding
mm_108252.1	chr12	78227560	78227562	+	1	NA	intron (NM_145965, intron 1 of 22)	intron (NM_145965, intron 1 of 22)	906	NM_145965	268566	Mm.341742	NM_145965	ENSMUSG00000047454	Gphn	5730552E08Rik|AI662856|BC027112|C230040D23|GPH|GPHRYN|geph	gephyrin	protein-coding
mm_80338.1	chr9	75071277	75071321	+	1	NA	promoter-TSS (NM_010864)	promoter-TSS (NM_010864)	93	NM_010864	17918	Mm.3645	NM_010864	ENSMUSG00000034593	Myo5a	9630007J19Rik|AI413174|AI661011|Dbv|MVa|Myo5|MyoVA|Sev-1|d|d-120J|flail|flr	myosin VA	protein-coding
mm_19652.1	chr2	102897964	102897992	-	1	NA	intron (NM_001039150, intron 1 of 13)	U6|snRNA|snRNA	3687	NM_001177785	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_93709.1	chr10	118796635	118796695	-	1	NA	Intergenic	MTEb|LTR|ERVL-MaLR	72238	NM_001014390	69181	Mm.45565	NM_001014390	ENSMUSG00000028630	Dyrk2	1810038L18Rik	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 2	protein-coding
mm_8662.1	chr1	156654351	156654377	-	1	NA	3' UTR (NM_023141, exon 6 of 6)	3' UTR (NM_023141, exon 6 of 6)	19975	NM_023141	30935	Mm.206737	NM_023141	ENSMUSG00000060519	Tor3a	Adir	torsin family 3, member A	protein-coding
mm_158948.1	chr1	85795363	85795363	+	1	NA	intron (NM_133781, intron 1 of 8)	intron (NM_133781, intron 1 of 8)	1916	NM_133781	12283	Mm.26135	NM_133781	ENSMUSG00000036707	Cab39	AA408805|AA960512|C78372|MO25|MO25alpha	calcium binding protein 39	protein-coding
mm_5308.1	chr1	22315873	22315881	-	1	NA	intron (NM_001012623, intron 10 of 14)	intron (NM_001012623, intron 10 of 14)	116966	NM_053270	116837	Mm.60061	NM_053270	ENSMUSG00000041670	Rims1	C030033M19Rik|RIM1|RIM1a|RIM1alpha|Rab3ip1|Rim|Serg1|mKIAA0340	regulating synaptic membrane exocytosis 1	protein-coding
mm_47142.1	chr5	120559754	120559756	-	1	NA	intron (NM_145853, intron 3 of 27)	PB1D9|SINE|Alu	28858	NM_145853	252972	Mm.114054	NM_145853	ENSMUSG00000032741	Tpcn1	5730403B01Rik|Tpc1|mKIAA1169	two pore channel 1	protein-coding
mm_119366.1	chr14	41121798	41121808	+	1	NA	exon (NM_133653, exon 9 of 10)	exon (NM_133653, exon 9 of 10)	-9985	NM_023134	20387	Mm.46062	NM_023134	ENSMUSG00000021789	Sftpa1	SP-A|Sftp-1|Sftp1	surfactant associated protein A1	protein-coding
mm_132402.1	chr16	35001429	35001444	+	1	NA	3' UTR (NM_139300, exon 32 of 32)	3' UTR (NM_139300, exon 32 of 32)	-20985	NM_023587	70757	Mm.27286	NM_023587	ENSMUSG00000035376	Hacd2	6330408J20Rik|AI255777|AI481689|Hcad2|Ptplb	3-hydroxyacyl-CoA dehydratase 2	protein-coding
mm_17143.1	chr2	25095153	25095169	-	1	NA	promoter-TSS (NM_001163626)	promoter-TSS (NM_001163626)	44	NM_001163626	241275	Mm.218774	NM_172204	ENSMUSG00000036805	Noxa1	NY-CO-31|SDCCAG31	NADPH oxidase activator 1	protein-coding
mm_5743.1	chr1	45873377	45873423	-	1	NA	Intergenic	Intergenic	52194	NM_016917	53945	Mm.28756	NM_016917	ENSMUSG00000025993	Slc40a1	Dusg|Fpn1|IREG1|MTP|MTP1|Ol5|Pcm|Slc11a3|Slc39a1	solute carrier family 40 (iron-regulated transporter), member 1	protein-coding
mm_154752.1	chrX	10596005	10596030	+	1	NA	3' UTR (NM_019634, exon 8 of 8)	3' UTR (NM_019634, exon 8 of 8)	110901	NM_019634	21912	Mm.18590	NM_019634	ENSMUSG00000058254	Tspan7	1200014P11Rik|A15|AI323365|Cd231|Mxs1|PE31|R74651|TALLA|Tm4sf2	tetraspanin 7	protein-coding
mm_11602.1	chr2	33794746	33794754	+	1	NA	intron (NM_175184, intron 7 of 9)	intron (NM_175184, intron 7 of 9)	-11066	NR_045729	320482	Mm.442057	NR_045729	ENSMUSG00000086484	Nron	A630071L07Rik|Gm24353	non-protein coding RNA, repressor of NFAT	ncRNA
mm_99132.1	chr11	100319921	100319951	+	1	NA	promoter-TSS (NM_011508)	promoter-TSS (NM_011508)	-13	NM_011508	20918	Mm.13886	NM_011508	ENSMUSG00000035530	Eif1	Sui1-rs1	eukaryotic translation initiation factor 1	protein-coding
mm_37361.1	chr4	120747396	120747404	-	1	NA	promoter-TSS (NM_001081142)	promoter-TSS (NM_001081142)	-224	NM_001081142	60613	Mm.249977	NM_001081142	ENSMUSG00000028631	Kcnq4	-	potassium voltage-gated channel, subfamily Q, member 4	protein-coding
mm_4109.1	chr1	167598590	167598618	+	1	NA	5' UTR (NM_009107, exon 1 of 10)	5' UTR (NM_009107, exon 1 of 10)	242	NM_009107	20183	Mm.3475	NM_009107	ENSMUSG00000015843	Rxrg	Nr2b3	retinoid X receptor gamma	protein-coding
mm_74767.1	chr8	20922060	20922086	-	1	NA	promoter-TSS (NM_001025353)	promoter-TSS (NM_001025353)	-2	NM_001025353	100503992	Mm.490240	NM_001025353	ENSMUSG00000071165	Gm6040	Defb51|EG574083	predicted gene 6040	protein-coding
mm_44906.1	chr5	35663224	35663240	-	1	NA	intron (NM_001042615, intron 6 of 6)	(TGGA)n|Simple_repeat|Simple_repeat	16548	NM_001042615	78558	Mm.274255	NM_030127	ENSMUSG00000029096	Htra3	2210021K23Rik|9530081K03Rik|Prsp|Tasp	HtrA serine peptidase 3	protein-coding
mm_100463.1	chr11	119876005	119876017	+	1	NA	intron (NM_028898, intron 24 of 33)	intron (NM_028898, intron 24 of 33)	-6278	NR_039557	100628577		NR_039557	ENSMUSG00000093061	Mir5098	mmu-mir-5098|mu-mir-5098	microRNA 5098	ncRNA
mm_160104.1	chr7	22871281	22871281	+	1	NA	promoter-TSS (NM_001166724)	promoter-TSS (NM_001166724)	57	NM_001166724	620758	Mm.480272	NM_001166724	ENSMUSG00000094931	Vmn1r160	Gm6178	vomeronasal 1 receptor 160	protein-coding
mm_132373.1	chr16	34883527	34883545	+	1	NA	intron (NM_139300, intron 9 of 31)	intron (NM_139300, intron 9 of 31)	55793	NR_040536	76649	Mm.420532	NR_040536	ENSMUSG00000100593	1700119H24Rik	-	RIKEN cDNA 1700119H24 gene	ncRNA
mm_164346.1	chr16	16869260	16869283	-	1	NA	promoter-TSS (NM_016982)	promoter-TSS (NM_016982)	-16	NM_016982	22362	Mm.57574	NM_016982	ENSMUSG00000059305	Vpreb1	CD179a|Vpreb-1	pre-B lymphocyte gene 1	protein-coding
mm_114543.1	chr13	73772897	73772916	+	1	NA	intron (NM_011390, intron 1 of 23)	intron (NM_011390, intron 1 of 23)	9209	NM_011390	20499	Mm.275800	NM_011390	ENSMUSG00000017756	Slc12a7	AA408796|D13Ertd261e|Kcc4	solute carrier family 12, member 7	protein-coding
mm_42636.1	chr5	118556485	118556510	+	1	NA	Intergenic	Intergenic	-4222	NM_001347445	76199	Mm.206238	NM_172424	ENSMUSG00000018076	Med13l	2210413I17Rik|6330591G05Rik|9030618F05Rik|Thrap2|Trap240L|mKIAA1025	mediator complex subunit 13-like	protein-coding
mm_95793.1	chr11	55097969	55097979	+	1	NA	promoter-TSS (NM_010299)	promoter-TSS (NM_010299)	-11	NM_010299	14667	Mm.287807	NM_010299	ENSMUSG00000000594	Gm2a	AA408702|AW215435|GM2-AP|SAP-3	GM2 ganglioside activator protein	protein-coding
mm_35216.1	chr4	19650380	19650401	-	1	NA	exon (NM_177327, exon 9 of 25)	exon (NM_177327, exon 9 of 25)	58614	NM_177327	107568	Mm.78312	NM_177327	ENSMUSG00000041058	Wwp1	8030445B08Rik|AIP5|SDRP1|Tiul1	WW domain containing E3 ubiquitin protein ligase 1	protein-coding
mm_21437.1	chr2	158610592	158610615	-	1	NA	promoter-TSS (NM_009508)	promoter-TSS (NM_009508)	120	NR_040358	100045469	Mm.143404	NR_040358	ENSMUSG00000086496	Gm14204	OTTMUSG00000015935	predicted gene 14204	ncRNA
mm_79673.1	chr9	59680172	59680184	+	1	NA	TTS (NM_011099)	TTS (NM_011099)	23810	NM_001253883	18746	Mm.326167	NM_011099	ENSMUSG00000032294	Pkm	AA414905|AL024370|AL024424|Pk-2|Pk-3|Pk3|Pkm2	pyruvate kinase, muscle	protein-coding
mm_133379.1	chr16	84714203	84714206	+	1	NA	promoter-TSS (NR_029565)	promoter-TSS (NR_029565)	64	NR_029565	387173		NR_029565	ENSMUSG00000065397	Mir155	Mirn155|mir-155|mmu-mir-155	microRNA 155	ncRNA
mm_15232.1	chr2	154551839	154551844	+	1	NA	promoter-TSS (NM_001171640)	promoter-TSS (NM_001171640)	65	NM_001171640	70362	Mm.479620	NM_001171640	ENSMUSG00000078129	Actl10	1700007I08Rik	actin-like 10	protein-coding
mm_144717.1	chr18	35118943	35118953	+	1	NA	promoter-TSS (NM_009818)	promoter-TSS (NM_009818)	36	NM_009818	12385	Mm.18962	NM_009818	ENSMUSG00000037815	Ctnna1	2010010M04Rik|AA517462|AI988031|Catna1	catenin (cadherin associated protein), alpha 1	protein-coding
mm_137647.1	chr17	28549487	28549502	+	1	NA	promoter-TSS (NM_001034871)	promoter-TSS (NM_001034871)	7	NM_001034871	328788	Mm.99400	NM_001034871	ENSMUSG00000024224	Clpsl2	Gm749	colipase-like 2	protein-coding
mm_107593.1	chr12	49377769	49377785	+	1	NA	Intergenic	Intergenic	-5106	NM_001160112	15228	Mm.4704	NM_008241	ENSMUSG00000020950	Foxg1	2900064B05Rik|BF-1|Bf1|Hfh9|Hfhbf1	forkhead box G1	protein-coding
mm_127323.1	chr15	100304199	100304210	+	1	NA	promoter-TSS (NM_027334)	promoter-TSS (NM_027334)	-613	NM_027334	70152	Mm.488086	NM_027334	ENSMUSG00000054619	Mettl7a1	2210414H16Rik|3300001H21Rik|Aam-B|Mettl7a|UbiE1	methyltransferase like 7A1	protein-coding
mm_51628.1	chr6	85459192	85459233	+	1	NA	exon (NM_007638, exon 2 of 12)	exon (NM_007638, exon 2 of 12)	-7242	NR_028081	73327	Mm.379221	NM_028505	ENSMUSG00000030008	Pradc1	1700040I03Rik|Pap21	protease-associated domain containing 1	protein-coding
mm_9738.1	chr1	180256239	180256258	-	1	NA	promoter-TSS (NM_001128605)	promoter-TSS (NM_001128605)	52	NM_001128605	19165	Mm.330850	NM_011183	ENSMUSG00000010609	Psen2	ALG-3|Ad4h|Alg3|PS-2|PS2|Psnl2|STM2	presenilin 2	protein-coding
mm_6621.1	chr1	75606504	75606530	-	1	NA	Intergenic	ORR1D2|LTR|ERVL-MaLR	60251	NM_009208	20536	Mm.5053	NM_009208	ENSMUSG00000006576	Slc4a3	A930038D23Rik|Ae3	solute carrier family 4 (anion exchanger), member 3	protein-coding
mm_33687.1	chr4	133412166	133412177	+	1	NA	exon (NM_016981, exon 2 of 12)	exon (NM_016981, exon 2 of 12)	42395	NR_039582	100628620		NR_039582	ENSMUSG00000092745	Mir5122	mmu-mir-5122|mu-mir-5122	microRNA 5122	ncRNA
mm_104655.1	chr11	97575273	97575275	-	1	NA	promoter-TSS (NM_018873)	promoter-TSS (NM_018873)	-148	NM_018873	56013	Mm.342665	NM_018873	ENSMUSG00000038453	Srcin1	P140|SNIP|mKIAA1684|p140Cap	SRC kinase signaling inhibitor 1	protein-coding
mm_51171.1	chr6	70726611	70726619	+	1	NA	Intergenic	Intergenic	65560	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_121271.1	chr14	103438678	103438683	+	1	NA	Intergenic	Intergenic	-74661	NM_022886	64929	Mm.244003	NM_022886	ENSMUSG00000022123	Scel	9230114I02Rik	sciellin	protein-coding
mm_12107.1	chr2	61587721	61587724	+	1	NA	intron (NM_011529, intron 1 of 7)	B1_Mur2|SINE|Alu	-5375	NM_001164072	21353	Mm.244393	NM_011529	ENSMUSG00000064289	Tank	C86182|E430026L09Rik|I-TRAF	TRAF family member-associated Nf-kappa B activator	protein-coding
mm_103795.1	chr11	82871134	82871183	-	1	NA	promoter-TSS (NM_001007465)	promoter-TSS (NM_001007465)	52	NM_001007465	67338	Mm.341608	NM_026097	ENSMUSG00000020696	Rffl	1700051E09Rik|4930516L10Rik|BG080975|Carp2	ring finger and FYVE like domain containing protein	protein-coding
mm_96992.1	chr11	70683829	70683854	+	1	NA	intron (NM_178116, intron 5 of 22)	intron (NM_178116, intron 5 of 22)	4264	NM_001190376	216874	Mm.473726	NM_178116	ENSMUSG00000040712	Camta2	Kiaa0909-hp|mKIAA0909	calmodulin binding transcription activator 2	protein-coding
mm_36989.1	chr4	109674249	109674254	-	1	NA	Intergenic	Intergenic	-2376	NM_007983	14084	Mm.318259	NM_007983	ENSMUSG00000010517	Faf1	AA408698|Dffrx|Fam	Fas-associated factor 1	protein-coding
mm_150979.1	chr19	46502291	46502325	+	1	NA	5' UTR (NM_053100, exon 1 of 6)	5' UTR (NM_053100, exon 1 of 6)	660	NM_053100	93679	Mm.392177	NM_053100	ENSMUSG00000025034	Trim8	AA408830|BB006755|GERP|Rnf27	tripartite motif-containing 8	protein-coding
mm_138773.1	chr17	37193921	37193940	+	1	NA	promoter-TSS (NM_023137)	promoter-TSS (NM_023137)	38	NM_023137	24108	Mm.140210	NM_023137	ENSMUSG00000035186	Ubd	FAT10	ubiquitin D	protein-coding
mm_97854.1	chr11	83069817	83069830	+	1	NA	exon (NM_011408, exon 2 of 2)	exon (NM_011408, exon 2 of 2)	4711	NM_011408	20556	Mm.278689	NM_011408	ENSMUSG00000072620	Slfn2	Shlf2	schlafen 2	protein-coding
mm_31920.1	chr4	85388096	85388106	+	1	NA	3' UTR (NM_019535, exon 9 of 9)	3' UTR (NM_019535, exon 9 of 9)	182645	NM_019535	20404	Mm.143603	NM_019535	ENSMUSG00000028488	Sh3gl2	9530001L19Rik|AI120490|AW555077|B930049H17Rik|EEN-B1|SH3PA|Sh3d2a	SH3-domain GRB2-like 2	protein-coding
mm_163990.1	chr14	62761113	62761121	-	1	NA	promoter-TSS (NM_008715)	promoter-TSS (NM_008715)	-5	NM_008715	18130	Mm.319684	NM_008715	ENSMUSG00000035161	Ints6	2900075H24Rik|AI480962|DICE1|Ddx26|HDB|Notch2l	integrator complex subunit 6	protein-coding
mm_81091.1	chr9	106368552	106368572	+	1	NA	promoter-TSS (NM_153459)	promoter-TSS (NM_153459)	-70	NM_153459	235584	Mm.275584	NM_153459	ENSMUSG00000053716	Dusp7	AU015694|Mkpx|Pyst2	dual specificity phosphatase 7	protein-coding
mm_55331.1	chr6	56311156	56311157	-	1	NA	intron (NM_001159956, intron 1 of 16)	ORR1D1-int|LTR|ERVL-MaLR	51236	NM_001159952	18575	Mm.5145	NM_011054	ENSMUSG00000004347	Pde1c	-	phosphodiesterase 1C	protein-coding
mm_161103.1	chr12	102283748	102283748	+	1	NA	5' UTR (NM_001161365, exon 1 of 10)	5' UTR (NM_001161365, exon 1 of 10)	107	NM_001161365	217835	Mm.24145	NM_177620	ENSMUSG00000044456	Rin3	6430500K07|C86933	Ras and Rab interactor 3	protein-coding
mm_155234.1	chrX	57200614	57200633	+	1	NA	promoter-TSS (NR_038463)	promoter-TSS (NR_038463)	-14	NR_038463	100502842	Mm.164733	NR_038463	ENSMUSG00000085808	Gm14718	OTTMUSG00000017790	predicted gene 14718	ncRNA
mm_73728.1	chr8	113635551	113635597	+	1	NA	promoter-TSS (NM_001048143)	promoter-TSS (NM_001048143)	-12	NM_001048143	270096	Mm.74689	NM_173015	ENSMUSG00000078908	Mon1b	5031407H10|5033413H12Rik	MON1 homolog B, secretory traffciking associated	protein-coding
mm_29316.1	chr3	108012671	108012709	-	1	NA	exon (NM_010358, exon 8 of 8)	exon (NM_010358, exon 8 of 8)	5283	NM_010358	14862	Mm.37199	NM_010358	ENSMUSG00000058135	Gstm1	Gstb-1|Gstb1	glutathione S-transferase, mu 1	protein-coding
mm_19412.1	chr2	91710361	91710396	-	1	NA	promoter-TSS (NM_178724)	promoter-TSS (NM_178724)	214	NM_145528	51897	Mm.28492	NM_145528	ENSMUSG00000027244	Atg13	1110053A20Rik|D2Ertd391e|Harbi1	autophagy related 13	protein-coding
mm_142936.1	chr17	56005567	56005597	-	1	NA	promoter-TSS (NR_102313)	promoter-TSS (NR_102313)	24	NM_145934	106766	Mm.204991	NM_145934	ENSMUSG00000038781	Stap2	AW049765|STAP-2	signal transducing adaptor family member 2	protein-coding
mm_132833.1	chr16	45535293	45535301	+	1	NA	promoter-TSS (NM_198106)	promoter-TSS (NM_198106)	31	NM_198106	208169	Mm.277437	NM_198106	ENSMUSG00000033210	Slc9c1	Gm610|NHE-10|Slc9a10|sNHE|spermNHE	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	protein-coding
mm_15556.1	chr2	158502538	158502552	+	1	NA	promoter-TSS (NM_145635)	promoter-TSS (NM_145635)	-67	NM_145635	246747	Mm.28800	NM_145635	ENSMUSG00000044405	Adig	SMAF-1|Smaf1	adipogenin	protein-coding
mm_97769.1	chr11	82045706	82045721	+	1	NA	promoter-TSS (NM_013654)	promoter-TSS (NM_013654)	1	NM_013654	20306	Mm.341574	NM_013654	ENSMUSG00000035373	Ccl7	MCP-3|Scya7|fic|marc|mcp3	chemokine (C-C motif) ligand 7	protein-coding
mm_83966.1	chr9	57148438	57148450	-	1	NA	Intergenic	Intergenic	-1410	NM_028347	72774	Mm.35749	NM_028347	ENSMUSG00000032298	Neil1	2810450N13Rik|Nei1	nei endonuclease VIII-like 1 (E. coli)	protein-coding
mm_170337.1	chr18	46597770	46597771	+	1	NA	promoter-TSS (NM_025698)	promoter-TSS (NM_025698)	66	NM_010120	13664	Mm.262037	NM_010120	ENSMUSG00000057561	Eif1a	C76390|Ef1a|Eftu|Eif4c|eIF-1A|eIF-4C	eukaryotic translation initiation factor 1A	protein-coding
mm_107460.1	chr12	37241669	37241683	+	1	NA	promoter-TSS (NM_178767)	promoter-TSS (NM_178767)	37	NM_178767	319660	Mm.485540	NM_178767	ENSMUSG00000050103	Agmo	A530016O06Rik|AI790538|Tmem195	alkylglycerol monooxygenase	protein-coding
mm_145745.1	chr18	64340226	64340241	+	1	NA	promoter-TSS (NM_194268)	promoter-TSS (NM_194268)	-131	NM_194268	225631	Mm.234723	NM_194268	ENSMUSG00000045991	Onecut2	C730009D12|OC-2|Oc2	one cut domain, family member 2	protein-coding
mm_5618.1	chr1	39805312	39805345	-	1	NA	promoter-TSS (NM_001177348)	promoter-TSS (NM_001177348)	4	NM_001177348	100042065	Mm.209678	NM_001177348	ENSMUSG00000091937	Gm3646	-	predicted gene 3646	protein-coding
mm_13461.1	chr2	105675430	105675449	+	1	NA	promoter-TSS (NM_013627)	promoter-TSS (NM_013627)	-305	NM_001244200	18508	Mm.3608	NM_013627	ENSMUSG00000027168	Pax6	1500038E17Rik|AEY11|Dey|Gsfaey11|Pax-6|Sey	paired box 6	protein-coding
mm_63197.1	chr7	125630614	125630627	+	1	NA	intron (NM_021887, intron 7 of 8)	intron (NM_021887, intron 7 of 8)	27191	NM_021887	60504	Mm.155643	NM_021887	ENSMUSG00000030745	Il21r	NILR	interleukin 21 receptor	protein-coding
mm_84954.1	chr9	83254441	83254455	-	1	NA	Intergenic	Intergenic	-107841	NM_026122	94353	Mm.244426	NM_026122	ENSMUSG00000066456	Hmgn3	1110002A15Rik|6330514M13Rik|BB071015|TRIP7	high mobility group nucleosomal binding domain 3	protein-coding
mm_134725.1	chr16	22898887	22898898	-	1	NA	exon (NM_001276450, exon 7 of 7)	exon (NM_001276450, exon 7 of 7)	-4506	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_100307.1	chr11	117976288	117976301	+	1	NA	Intergenic	Intergenic	-6928	NM_007707	12702	Mm.3468	NM_007707	ENSMUSG00000053113	Socs3	Cis3|Cish3|EF-10|Ef10|SSI-3|Ssi3	suppressor of cytokine signaling 3	protein-coding
mm_51306.1	chr6	72312867	72312918	+	1	NA	exon (NM_001282071, exon 10 of 11)	exon (NM_001282071, exon 10 of 11)	8282	NM_147779	20388	Mm.46033	NM_147779	ENSMUSG00000056370	Sftpb	AI562151|SF-B|SP-B|Sftp-3|Sftp3	surfactant associated protein B	protein-coding
mm_12623.1	chr2	74697970	74697982	+	1	NA	5' UTR (NM_013555, exon 1 of 2)	5' UTR (NM_013555, exon 1 of 2)	213	NM_013555	15438	Mm.26544	NM_013555	ENSMUSG00000043342	Hoxd9	Hox-4.4|Hox-5.2	homeobox D9	protein-coding
mm_43076.1	chr5	124446901	124446911	+	1	NA	5' UTR (NM_001310727, exon 1 of 7)	5' UTR (NM_001310727, exon 1 of 7)	202	NM_001310727	67956	Mm.137966	NM_030241	ENSMUSG00000049327	Kmt5a	2410195B05Rik|AA617402|AW536475|PR-SET7|PR/SET07|Setd8	lysine methyltransferase 5A	protein-coding
mm_13334.1	chr2	102785996	102786012	+	1	NA	3' UTR (NM_001077514, exon 11 of 11)	3' UTR (NM_001077514, exon 11 of 11)	79566	NM_001077515	20511	Mm.267547	NM_011393	ENSMUSG00000005089	Slc1a2	1700091C19Rik|2900019G14Rik|AI159670|Eaat2|GLT-1|GLT1|MGLT1	solute carrier family 1 (glial high affinity glutamate transporter), member 2	protein-coding
mm_112993.1	chr13	21735056	21735070	+	1	NA	promoter-TSS (NM_178210)	promoter-TSS (NM_178210)	29	NM_178210	319159		NM_178210	ENSMUSG00000067455	Hist1h4j	-	histone cluster 1, H4j	protein-coding
mm_113013.1	chr13	21936188	21936191	+	1	NA	Intergenic	Intergenic	-8905	NM_183014	193452	Mm.187446	NM_183014	ENSMUSG00000006720	Zfp184	4930500C15Rik	zinc finger protein 184 (Kruppel-like)	protein-coding
mm_76313.1	chr8	84662842	84662859	-	1	NA	promoter-TSS (NM_010499)	promoter-TSS (NM_010499)	2	NM_010499	15936	Mm.399	NM_010499	ENSMUSG00000053560	Ier2	AI317238|Ch1|Pip92	immediate early response 2	protein-coding
mm_56228.1	chr6	90599920	90599962	-	1	NA	TTS (NM_027406)	TTS (NM_027406)	-4939	NM_027868	71699	Mm.272633	NM_027868	ENSMUSG00000030089	Slc41a3	1010001P06Rik|AI480742|SLC41A1-L2	solute carrier family 41, member 3	protein-coding
mm_143142.1	chr17	57221059	57221073	-	1	NA	exon (NM_009778, exon 17 of 41)	exon (NM_009778, exon 17 of 41)	-3838	NR_105944	102465591		NR_105944	ENSMUSG00000099066	Mir6978	Gm27858|mmu-mir-6978	microRNA 6978	ncRNA
mm_49694.1	chr6	33650120	33650142	+	1	NA	intron (NM_009148, intron 10 of 17)	intron (NM_009148, intron 10 of 17)	-379317	NM_028886	74354	Mm.127952	NM_028886	ENSMUSG00000056215	Lrguk	4921528H16Rik	leucine-rich repeats and guanylate kinase domain containing	protein-coding
mm_26281.1	chr3	142505657	142505671	+	1	NA	intron (NM_153564, intron 7 of 10)	intron (NM_153564, intron 7 of 10)	8730	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_74856.1	chr8	24746763	24746776	-	1	NA	exon (NM_007401, exon 18 of 21)	exon (NM_007401, exon 18 of 21)	-20917	NM_001324489	11497	Mm.5168	NM_009619	ENSMUSG00000031553	Adam3	Cyrn1|Taz83|tMDC	a disintegrin and metallopeptidase domain 3 (cyritestin)	protein-coding
mm_87605.1	chr10	57782282	57782294	+	1	NA	Intergenic	Intergenic	-2635	NM_021272	12140	Mm.3644	NM_021272	ENSMUSG00000019874	Fabp7	B-FABP|BFABP|Blbp|MRG	fatty acid binding protein 7, brain	protein-coding
mm_149303.1	chr19	10713030	10713043	+	1	NA	exon (NM_181403, exon 5 of 5)	exon (NM_181403, exon 5 of 5)	24221	NM_181403	107305	Mm.19091	NM_181403	ENSMUSG00000048832	Vps37c	5730409F24Rik|AU042646	vacuolar protein sorting 37C	protein-coding
mm_128991.1	chr15	74836269	74836289	-	1	NA	exon (NM_001033229, exon 8 of 9)	exon (NM_001033229, exon 8 of 9)	5364	NM_001033229	110115	Mm.322606	NM_001033229	ENSMUSG00000075604	Cyp11b1	AA389061|CPN1|Cyp11b|Cyp11b-1|FHI	cytochrome P450, family 11, subfamily b, polypeptide 1	protein-coding
mm_5326.1	chr1	23383130	23383146	-	1	NA	promoter-TSS (NM_001081079)	promoter-TSS (NM_001081079)	37	NM_001081079	70155	Mm.28013	NM_001081079	ENSMUSG00000026158	Ogfrl1	2210417C17Rik	opioid growth factor receptor-like 1	protein-coding
mm_19012.1	chr2	76905653	76905665	-	1	NA	intron (NM_011652, intron 46 of 312)	intron (NM_011652, intron 46 of 312)	76888	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_52389.1	chr6	113282355	113282369	+	1	NA	promoter-TSS (NM_170673)	promoter-TSS (NM_170673)	55	NM_170673	211232	Mm.65597	NM_170673	ENSMUSG00000030270	Cpne9	A730016F12Rik|mKIAA4217	copine family member IX	protein-coding
mm_6964.1	chr1	86111997	86112031	-	1	NA	promoter-TSS (NM_008311)	promoter-TSS (NM_008311)	-44	NM_008311	15559	Mm.439747	NM_008311	ENSMUSG00000026228	Htr2b	5-HT2B|AJ012488|AV377389	5-hydroxytryptamine (serotonin) receptor 2B	protein-coding
mm_60852.1	chr7	45833306	45833320	+	1	NA	exon (NM_008172, exon 12 of 12)	exon (NM_008172, exon 12 of 12)	-2524	NM_153419	101612	Mm.274847	NM_153419	ENSMUSG00000053801	Grwd1	A301|AI504353|Grwd|Wdr28	glutamate-rich WD repeat containing 1	protein-coding
mm_151987.1	chr19	5846614	5846631	-	1	NA	Intergenic	Intergenic	-1142	NR_003513	66961	Mm.281895	NR_003513	ENSMUSG00000092274	Neat1	2310043N10Rik|VINC	nuclear paraspeckle assembly transcript 1 (non-protein coding)	ncRNA
mm_76116.1	chr8	80800358	80800380	-	1	NA	exon (NM_001301298, exon 2 of 11)	exon (NM_001301298, exon 2 of 11)	-60910	NM_053124	93762	Mm.246803	NM_053124	ENSMUSG00000031715	Smarca5	4933427E24Rik|D030040M08Rik|D330027N15Rik|MommeD4|Snf2h	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5	protein-coding
mm_46239.1	chr5	99223548	99223559	-	1	NA	intron (NM_145839, intron 10 of 13)	intron (NM_145839, intron 10 of 13)	29374	NM_181318	320292	Mm.259074	NM_145839	ENSMUSG00000089809	Rasgef1b	4732452O09Rik|GPIgamma4|Gpig4	RasGEF domain family, member 1B	protein-coding
mm_29548.1	chr3	116807707	116807711	-	1	NA	intron (NM_001081326, intron 1 of 33)	intron (NM_001081326, intron 1 of 33)	457	NM_001081326	77559	Mm.237099	NM_001081326	ENSMUSG00000033400	Agl	1110061O17Rik|9430004C13Rik|9630046L06Rik|AI850929|C77197	amylo-1,6-glucosidase, 4-alpha-glucanotransferase	protein-coding
mm_147428.1	chr18	46311812	46311834	-	1	NA	5' UTR (NM_001160399, exon 1 of 10)	5' UTR (NM_001160399, exon 1 of 10)	105	NM_001160399	240261	Mm.329416	NM_001160399	ENSMUSG00000071855	Ccdc112	8430438M01Rik|AW108467	coiled-coil domain containing 112	protein-coding
mm_101104.1	chr11	11931881	11931897	-	1	NA	3' UTR (NM_010345, exon 17 of 17)	3' UTR (NM_010345, exon 17 of 17)	-33745	NM_001190448	13195	Mm.12906	NM_016672	ENSMUSG00000020182	Ddc	Aadc	dopa decarboxylase	protein-coding
mm_112284.1	chr12	114435305	114435319	-	1	NA	Intergenic	Intergenic	34154	NR_106062	102465663		NR_106062	ENSMUSG00000105438	Mir7094-1	mmu-mir-7094-1	microRNA 7094-1	ncRNA
mm_38906.1	chr4	149955053	149955063	-	1	NA	promoter-TSS (NM_029035)	promoter-TSS (NM_029035)	-52	NM_029035	74646	Mm.30	NM_029035	ENSMUSG00000039911	Spsb1	1110014L01Rik|4930422J18Rik|AI596360|AI854583|SSB-1|SSB1	splA/ryanodine receptor domain and SOCS box containing 1	protein-coding
mm_3674.1	chr1	153665667	153665679	+	1	NA	promoter-TSS (NM_001347115)	promoter-TSS (NM_001347115)	0	NM_001347115	67792	Mm.379143	NM_026380	ENSMUSG00000042671	Rgs8	6530413N01Rik	regulator of G-protein signaling 8	protein-coding
mm_24389.1	chr3	90260962	90260975	+	1	NA	exon (NM_028881, exon 11 of 14)	exon (NM_028881, exon 11 of 14)	-5546	NM_201407	229541	Mm.30571	NM_201407	ENSMUSG00000042404	Dennd4b	-	DENN/MADD domain containing 4B	protein-coding
mm_50681.1	chr6	51575787	51575804	+	1	NA	intron (NM_028035, intron 2 of 6)	intron (NM_028035, intron 2 of 6)	31272	NM_001127348	71982	Mm.294166	NM_028035	ENSMUSG00000038301	Snx10	2410004M09Rik	sorting nexin 10	protein-coding
mm_94103.1	chr10	128566214	128566253	-	1	NA	promoter-TSS (NM_011119)	promoter-TSS (NM_011119)	-299	NM_011119	18813	Mm.4742	NM_011119	ENSMUSG00000025364	Pa2g4	38kDa|AA672939|Ebp1|Plfap	proliferation-associated 2G4	protein-coding
mm_126242.1	chr15	79002299	79002316	+	1	NA	promoter-TSS (NR_105921)	promoter-TSS (NR_105921)	84	NR_105921	102465577		NR_105921	ENSMUSG00000099180	Mir6956	Gm27880|mmu-mir-6956	microRNA 6956	ncRNA
mm_106358.1	chr11	118393706	118393744	-	1	NA	exon (NM_011150, exon 6 of 6)	exon (NM_011150, exon 6 of 6)	8206	NM_011150	19039	Mm.3152	NM_011150	ENSMUSG00000033880	Lgals3bp	90K|CyCAP|MAC-2BP|Ppicap|Tango10b	lectin, galactoside-binding, soluble, 3 binding protein	protein-coding
mm_157688.1	chrX	60178255	60178266	-	1	NA	intron (NM_001289731, intron 1 of 27)	intron (NM_001289731, intron 1 of 27)	829	NM_001289731	109904	Mm.93796	NM_133197	ENSMUSG00000031139	Mcf2	B230117G22Rik|Dbl|Mcf-2	mcf.2 transforming sequence	protein-coding
mm_38364.1	chr4	138250203	138250229	-	1	NA	promoter-TSS (NM_001099631)	promoter-TSS (NM_001099631)	-195	NM_001099631	230863	Mm.482408	NM_001099631	ENSMUSG00000045349	Sh2d5	BC036961	SH2 domain containing 5	protein-coding
mm_17621.1	chr2	30981858	30981947	-	1	NA	promoter-TSS (NM_028846)	promoter-TSS (NM_028846)	39	NM_144885	227707	Mm.235238	NM_144885	ENSMUSG00000026851	BC005624	-	cDNA sequence BC005624	protein-coding
mm_52682.1	chr6	117997078	117997100	+	1	NA	Intergenic	Intergenic	-14448	NM_001316749	70727	Mm.87660	NM_027526	ENSMUSG00000030134	Rasgef1a	6330404M18Rik|AI835194	RasGEF domain family, member 1A	protein-coding
mm_87872.1	chr10	61475783	61475834	+	1	NA	promoter-TSS (NM_153542)	promoter-TSS (NM_153542)	-25	NM_153542	216011	Mm.136116	NM_153542	ENSMUSG00000037151	Lrrc20	BC036304	leucine rich repeat containing 20	protein-coding
mm_53965.1	chr6	5819827	5819836	-	1	NA	intron (NM_001191027, intron 5 of 15)	intron (NM_001191027, intron 5 of 15)	94192	NM_001191026	13426	Mm.20893	NM_010063	ENSMUSG00000029757	Dync1i1	DH IC-1|DHIC-1|DIC|Dncic1|IC74	dynein cytoplasmic 1 intermediate chain 1	protein-coding
mm_11028.1	chr2	26910797	26910820	+	1	NA	promoter-TSS (NM_001033908)	promoter-TSS (NM_001033908)	1	NM_013721	27176	Mm.328601	NM_013721	ENSMUSG00000062647	Rpl7a	Surf3	ribosomal protein L7A	protein-coding
mm_7819.1	chr1	132007481	132007503	-	1	NA	promoter-TSS (NM_007923)	promoter-TSS (NM_007923)	-113	NM_007923	13714	Mm.254233	NM_007923	ENSMUSG00000026436	Elk4	2310011G17Rik|A130026I01Rik|BB162516|SAP-1|Sap1	ELK4, member of ETS oncogene family	protein-coding
mm_45419.1	chr5	66524642	66524660	-	1	NA	intron (NM_001310626, intron 2 of 15)	intron (NM_001310626, intron 2 of 15)	94166	NM_009686	11787	Mm.5159	NM_009686	ENSMUSG00000029207	Apbb2	2310007D03Rik|FE65L1|Rirl1|TR2L|Zfra	amyloid beta (A4) precursor protein-binding, family B, member 2	protein-coding
mm_132906.1	chr16	48872698	48872800	+	1	NA	intron (NM_181596, intron 1 of 3)	intron (NM_181596, intron 1 of 3)	141	NM_181596	245195	Mm.231288	NM_181596	ENSMUSG00000022651	Retnlg	Fizz3|Relmg|Xcp1	resistin like gamma	protein-coding
mm_63620.1	chr7	128252797	128252810	+	1	NA	exon (NM_001289552, exon 9 of 10)	exon (NM_001289552, exon 9 of 10)	5991	NM_001289552	21804	Mm.3248	NM_009365	ENSMUSG00000030782	Tgfb1i1	ARA55|Hic5|TSC-5|hic-5	transforming growth factor beta 1 induced transcript 1	protein-coding
mm_115167.1	chr13	107955599	107955617	+	1	NA	Intergenic	Intergenic	-65544	NM_145456	67263	Mm.490418	NM_145456	ENSMUSG00000032846	Zswim6	2900036G02Rik|mKIAA1577	zinc finger SWIM-type containing 6	protein-coding
mm_30043.1	chr3	135696872	135696878	-	1	NA	Intergenic	Intergenic	-5328	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_114336.1	chr13	60733826	60733842	+	1	NA	intron (NM_029653, intron 17 of 25)	intron (NM_029653, intron 17 of 25)	52530	NM_199148	218275	Mm.222427	NM_199148	ENSMUSG00000042243	BC051665	-	cDNA sequence BC051665	protein-coding
mm_10391.1	chr2	13411016	13411019	+	1	NA	intron (NM_001081084, intron 27 of 66)	intron (NM_001081084, intron 27 of 66)	80859	NM_001081084	65969	Mm.313915	NM_001081084	ENSMUSG00000026726	Cubn	AA408369|AL022750|D2Wsu88e	cubilin (intrinsic factor-cobalamin receptor)	protein-coding
mm_37867.1	chr4	132345716	132345718	-	1	NA	promoter-TSS (NM_133878)	promoter-TSS (NM_133878)	33	NM_001197082	100088	Mm.255045	NM_133878	ENSMUSG00000028896	Rcc1	4931417M11Rik|AI326872|Chc1	regulator of chromosome condensation 1	protein-coding
mm_1988.1	chr1	87125397	87125403	+	1	NA	exon (NM_007432, exon 3 of 11)	exon (NM_007432, exon 3 of 11)	392	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_39073.1	chr4	154289051	154289053	-	1	NA	intron (NM_001112744, intron 2 of 14)	intron (NM_001112744, intron 2 of 14)	10843	NM_001112744	230972	Mm.38481	NM_001112744	ENSMUSG00000029032	Arhgef16	-	Rho guanine nucleotide exchange factor (GEF) 16	protein-coding
mm_3827.1	chr1	159341987	159341989	+	1	NA	intron (NM_011931, intron 18 of 19)	Lx8b|LINE|L1	1630	NR_039543	100628622		NR_039543	ENSMUSG00000105399	Mir1843b	mir-1843b|mmu-mir-1843b	microRNA 1843b	ncRNA
mm_99688.1	chr11	106054885	106054918	+	1	NA	3' UTR (NM_027946, exon 7 of 7)	3' UTR (NM_027946, exon 7 of 7)	-11206	NM_027346	70207	Mm.343857	NM_027346	ENSMUSG00000001983	Taco1	2310066I18Rik|Ccdc44	translational activator of mitochondrially encoded cytochrome c oxidase I	protein-coding
mm_132629.1	chr16	38902439	38902462	+	1	NA	5' UTR (NM_170599, exon 1 of 7)	5' UTR (NM_170599, exon 1 of 7)	105	NM_170599	207683	Mm.245564	NM_170599	ENSMUSG00000022790	Igsf11	1700025L02Rik|BT-IgSF|Igsf13	immunoglobulin superfamily, member 11	protein-coding
mm_109467.1	chr12	111417452	111417467	+	1	NA	promoter-TSS (NM_001289489)	promoter-TSS (NM_001289489)	14	NM_001289488	74190	Mm.248640	NM_028807	ENSMUSG00000021280	Exoc3l4	1200009I06Rik|1600013K19Rik	exocyst complex component 3-like 4	protein-coding
mm_160513.1	chr9	21831722	21831722	-	1	NA	intron (NM_177030, intron 19 of 49)	intron (NM_177030, intron 19 of 49)	-3788	NM_001080940	624219	Mm.440264	NM_001080940	ENSMUSG00000047822	Angptl8	EG624219|Gm6484|Rifl	angiopoietin-like 8	protein-coding
mm_109893.1	chr12	7380375	7380377	-	1	NA	promoter-TSS (NR_045045)	promoter-TSS (NR_045045)	-46	NR_045045	73575	Mm.179463	NR_045045	ENSMUSG00000102096	1700101O22Rik	-	RIKEN cDNA 1700101O22 gene	ncRNA
mm_96807.1	chr11	69991062	69991074	+	1	NA	promoter-TSS (NM_019749)	promoter-TSS (NM_019749)	-302	NM_019749	56486	Mm.272460	NM_019749	ENSMUSG00000018567	Gabarap	-	gamma-aminobutyric acid receptor associated protein	protein-coding
mm_7042.1	chr1	87101716	87101719	-	1	NA	promoter-TSS (NM_001081082)	promoter-TSS (NM_001081082)	-111	NM_001081082	76768	Mm.58068	NM_001081082	ENSMUSG00000079440	Alpi	2010001C14Rik|Akp6|gIAP	alkaline phosphatase, intestinal	protein-coding
mm_139488.1	chr17	56081435	56081455	+	1	NA	intron (NM_001331053, intron 1 of 15)	intron (NM_001331053, intron 1 of 15)	1814	NM_001304785	15193	Mm.12966	NM_008233	ENSMUSG00000002833	Hdgfrp2	HRP-2	hepatoma-derived growth factor, related protein 2	protein-coding
mm_94082.1	chr10	128493473	128493489	-	1	NA	promoter-TSS (NM_001317220)	promoter-TSS (NM_001317220)	405	NM_001317218	17904	Mm.337074	NM_010860	ENSMUSG00000090841	Myl6	ESMLC|LC17|LC17-GI|MLC-3|MLC1SM|Myln	myosin, light polypeptide 6, alkali, smooth muscle and non-muscle	protein-coding
mm_59452.1	chr7	27179743	27179749	+	1	NA	promoter-TSS (NM_029391)	promoter-TSS (NM_029391)	-863	NM_029391	19342	Mm.482114	NM_029391	ENSMUSG00000053291	Rab4b	1500031G17Rik	RAB4B, member RAS oncogene family	protein-coding
mm_161555.1	chr16	13265200	13265200	+	1	NA	intron (NM_181860, intron 1 of 3)	intron (NM_181860, intron 1 of 3)	121	NM_181860	239719	Mm.270643	NM_153588	ENSMUSG00000009569	Mkl2	ENSMUSG00000075401|Gt4-1|MRTF-B|Mrtfb|mKIAA1243	MKL/myocardin-like 2	protein-coding
mm_33217.1	chr4	126613038	126613072	+	1	NA	3' UTR (NM_001145950, exon 2 of 2)	3' UTR (NM_001145950, exon 2 of 2)	3201	NM_001145950	230757	Mm.296838	NM_001013755	ENSMUSG00000073755	5730409E04Rik	7530403E16Rik|AI849033	RIKEN cDNA 5730409E04Rik gene	protein-coding
mm_98990.1	chr11	98763506	98763529	+	1	NA	intron (NM_178060, intron 7 of 8)	intron (NM_178060, intron 7 of 8)	11860	NM_145434	217166	Mm.390397	NM_145434	ENSMUSG00000020889	Nr1d1	A530070C09Rik|R75201	nuclear receptor subfamily 1, group D, member 1	protein-coding
mm_105161.1	chr11	101599230	101599255	-	1	NA	Intergenic	Intergenic	-11458	NM_001256318	666331	Mm.303457	NM_001256318		LOC666331	-	uncharacterized LOC666331	protein-coding
mm_79472.1	chr9	56865096	56865098	+	1	NA	promoter-TSS (NM_139001)	promoter-TSS (NM_139001)	-7	NM_139001	121021	Mm.41329	NM_139001	ENSMUSG00000032911	Cspg4	4732461B14Rik|AN2|NG2	chondroitin sulfate proteoglycan 4	protein-coding
mm_116684.1	chr13	49287730	49287746	-	1	NA	intron (NM_015759, intron 4 of 17)	(TG)n|Simple_repeat|Simple_repeat	21470	NM_015759	30938	Mm.291089	NM_015759	ENSMUSG00000037946	Fgd3	5830461L01Rik|ZFYVE5	FYVE, RhoGEF and PH domain containing 3	protein-coding
mm_67165.1	chr7	73550365	73550397	-	1	NA	intron (NR_037569, intron 3 of 4)	B3A|SINE|B2	8014	NR_037569	69170	Mm.34539	NR_037569	ENSMUSG00000101970	1810026B05Rik	-	RIKEN cDNA 1810026B05 gene	ncRNA
mm_20525.1	chr2	130840092	130840150	-	1	NA	promoter-TSS (NM_001311147)	promoter-TSS (NM_001311147)	24	NM_029432	228602	Mm.271990	NM_028367	ENSMUSG00000027309	4930402H24Rik	2810487F15Rik|AI413763|C78926	RIKEN cDNA 4930402H24 gene	protein-coding
mm_65626.1	chr7	27541801	27541835	-	1	NA	exon (NM_011116, exon 6 of 14)	exon (NM_011116, exon 6 of 14)	11400	NM_011116	18807	Mm.6483	NM_011116	ENSMUSG00000003363	Pld3	Sam-9	phospholipase D family, member 3	protein-coding
mm_89630.1	chr10	96371319	96371327	+	1	NA	Intergenic	Intergenic	145116	NR_110448	74881	Mm.410819	NR_110448		4930459C07Rik	-	RIKEN cDNA 4930459C07 gene	ncRNA
mm_144554.1	chr18	31634317	31634363	+	1	NA	promoter-TSS (NM_172965)	promoter-TSS (NM_172965)	-43	NM_172965	269003	Mm.194538	NM_172965	ENSMUSG00000024260	Sap130	2610304F09Rik|6720406D06	Sin3A associated protein	protein-coding
mm_141389.1	chr17	29099625	29099638	-	1	NA	3' UTR (NM_007669, exon 3 of 3)	3' UTR (NM_007669, exon 3 of 3)	5862	NM_007669	12575	Mm.195663	NM_007669	ENSMUSG00000023067	Cdkn1a	CAP20|CDKI|CIP1|Cdkn1|P21|SDI1|Waf1|mda6|p21Cip1|p21WAF	cyclin-dependent kinase inhibitor 1A (P21)	protein-coding
mm_10448.1	chr2	14273505	14273533	+	1	NA	intron (NM_008625, intron 9 of 29)	B4|SINE|B4	12516	NR_030609	100124488		NR_030609	ENSMUSG00000077897	Mir511	Mirn511|mir-511|mmu-mir-511	microRNA 511	ncRNA
mm_5395.1	chr1	33638005	33638020	-	1	NA	intron (NM_008922, intron 5 of 13)	intron (NM_008922, intron 5 of 13)	31782	NM_008922	19076	Mm.27705	NM_008922	ENSMUSG00000026134	Prim2	AI323589	DNA primase, p58 subunit	protein-coding
mm_146611.1	chr18	10029984	10029996	-	1	NA	5' UTR (NM_021522, exon 1 of 16)	5' UTR (NM_021522, exon 1 of 16)	159	NM_021522	59025	Mm.329277	NM_021522	ENSMUSG00000047879	Usp14	2610005K12Rik|2610037B11Rik|AW107924|C78769|ax|nmf375	ubiquitin specific peptidase 14	protein-coding
mm_444.1	chr1	34850313	34850363	+	1	NA	intron (NM_175421, intron 1 of 6)	intron (NM_175421, intron 1 of 6)	379	NM_145516	226971	Mm.292751	NM_145516	ENSMUSG00000026123	Plekhb2	2310009M15Rik|AU018239|Evt2|Phdc|evt-2	pleckstrin homology domain containing, family B (evectins) member 2	protein-coding
mm_170861.1	chr2	181917448	181917461	+	1	NA	Intergenic	B1_Mus1|SINE|Alu	53094	NM_025901	67005	Mm.271986	NM_025901	ENSMUSG00000038628	Polr3k	12.3kDa|1500004O14Rik|AI196849|AU014893|C11|RPC10|RPC11	polymerase (RNA) III (DNA directed) polypeptide K	protein-coding
mm_163194.1	chr11	95076593	95076616	-	1	NA	5' UTR (NM_001306162, exon 2 of 26)	5' UTR (NM_001306162, exon 2 of 26)	110	NM_013565	16400	Mm.57035	NM_013565	ENSMUSG00000001507	Itga3	AA407068|CD49C|GAPB3	integrin alpha 3	protein-coding
mm_38200.1	chr4	135494616	135494628	-	1	NA	promoter-TSS (NM_028995)	promoter-TSS (NM_028995)	-44	NM_001347220	74552	Mm.26548	NM_028995	ENSMUSG00000028803	Nipal3	9130020G22Rik|AI480660|Npal3	NIPA-like domain containing 3	protein-coding
mm_143700.1	chr17	80564713	80564717	-	1	NA	promoter-TSS (NM_001033443)	promoter-TSS (NM_001033443)	-881	NM_001033443	381113	Mm.329216	NM_001033443	ENSMUSG00000033966	Cdkl4	AU067824|Gm942	cyclin-dependent kinase-like 4	protein-coding
mm_7698.1	chr1	129680687	129680711	-	1	NA	intron (NM_172485, intron 7 of 27)	intron (NM_172485, intron 7 of 27)	407395	NM_172485	210417	Mm.380518	NM_172485	ENSMUSG00000042581	Thsd7b	1700074E13Rik|B930082A18|D130067I03Rik	thrombospondin, type I, domain containing 7B	protein-coding
mm_75462.1	chr8	47818180	47818184	-	1	NA	Intergenic	Intergenic	-3961	NM_001111318	100039801	Mm.471595	NM_001111318	ENSMUSG00000061974	Cldn24	ENSMUSG00000061974|Gm10107	claudin 24	protein-coding
mm_53962.1	chr6	5496286	5496290	-	1	NA	promoter-TSS (NM_013743)	promoter-TSS (NM_013743)	-10	NM_013743	27273	Mm.235547	NM_013743	ENSMUSG00000019577	Pdk4	AV005916	pyruvate dehydrogenase kinase, isoenzyme 4	protein-coding
mm_114636.1	chr13	76420569	76420575	+	1	NA	intron (NM_030174, intron 1 of 20)	intron (NM_030174, intron 1 of 20)	35611	NM_030174	78771	Mm.316249	NM_030174	ENSMUSG00000021596	Mctp1	2810465F10Rik	multiple C2 domains, transmembrane 1	protein-coding
mm_74855.1	chr8	24726020	24726030	-	1	NA	promoter-TSS (NM_001324489)	promoter-TSS (NM_001324489)	-173	NM_001324489	11497	Mm.5168	NM_009619	ENSMUSG00000031553	Adam3	Cyrn1|Taz83|tMDC	a disintegrin and metallopeptidase domain 3 (cyritestin)	protein-coding
mm_117062.1	chr13	58668687	58668707	-	1	NA	Intergenic	Intergenic	-57820	NM_022317	114304	Mm.18188	NM_022317	ENSMUSG00000021553	Slc28a3	Cnt3	solute carrier family 28 (sodium-coupled nucleoside transporter), member 3	protein-coding
mm_75368.1	chr8	45306173	45306183	-	1	NA	3' UTR (NM_133969, exon 11 of 11)	3' UTR (NM_133969, exon 11 of 11)	-11343	NM_008455	16621	Mm.482691	NM_008455	ENSMUSG00000109764	Klkb1	APS|Kal-3|Kal3|Klk3|PSA	kallikrein B, plasma 1	protein-coding
mm_143885.1	chr17	84313663	84313669	-	1	NA	intron (NM_183021, intron 28 of 37)	intron (NM_183021, intron 28 of 37)	-125719	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_142613.1	chr17	46857699	46857713	-	1	NA	Intergenic	RLTR20A4|LTR|ERVK	-26293	NM_001100452	210982	Mm.37642	NM_001100452	ENSMUSG00000036568	Gltscr1l	mKIAA0240	GLTSCR1-like	protein-coding
mm_94430.1	chr11	6292035	6292050	+	1	NA	promoter-TSS (NM_001252288)	promoter-TSS (NM_001252288)	445	NM_001252283	18293	Mm.276348	NM_010956	ENSMUSG00000020456	Ogdh	2210403E04Rik|2210412K19Rik|AA409584|d1401|mKIAA4192	oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)	protein-coding
mm_47773.1	chr5	131616560	131616570	-	1	NA	intron (NM_177047, intron 5 of 18)	CpG	-263704	NR_040704	75369	Mm.389696	NR_040704	ENSMUSG00000105773	4930563F08Rik	-	RIKEN cDNA 4930563F08 gene	ncRNA
mm_97672.1	chr11	79711289	79711311	+	1	NA	promoter-TSS (NR_029579)	promoter-TSS (NR_029579)	-669	NR_029579	387188		NR_029579	ENSMUSG00000065395	Mir193a	Mir193|Mirn193|mir-193a|mmu-mir-193|mmu-mir-193a	microRNA 193a	ncRNA
mm_68823.1	chr7	126160993	126161013	-	1	NA	exon (NM_028816, exon 5 of 24)	exon (NM_028816, exon 5 of 24)	39405	NM_028816	74204	Mm.235663	NM_028816	ENSMUSG00000000131	Xpo6	2610005L19Rik|AL022631|C230091E20Rik|R75304|Ranbp20|mKIAA0370	exportin 6	protein-coding
mm_33656.1	chr4	133104527	133104536	+	1	NA	Intergenic	L2c|LINE|L2	-26102	NM_153423	242687	Mm.23566	NM_153423	ENSMUSG00000028868	Wasf2	AW742646|D4Ertd13e|WAVE2	WAS protein family, member 2	protein-coding
mm_63637.1	chr7	128523763	128523782	+	1	NA	5' UTR (NM_013863, exon 1 of 4)	5' UTR (NM_013863, exon 1 of 4)	189	NM_013863	29810	Mm.84073	NM_013863	ENSMUSG00000030847	Bag3	AA407278|Bis|mg638	BCL2-associated athanogene 3	protein-coding
mm_105483.1	chr11	105940208	105940236	-	1	NA	intron (NM_007805, intron 1 of 5)	intron (NM_007805, intron 1 of 5)	3925	NM_007805	13056	Mm.149403	NM_007805	ENSMUSG00000019590	Cyb561	-	cytochrome b-561	protein-coding
mm_40272.1	chr5	40328649	40328682	+	1	NA	Intergenic	Intergenic	-684034	NM_010474	15476	Mm.12559	NM_010474	ENSMUSG00000051022	Hs3st1	3-Ost|D5Wsu110e|Hsg3ost	heparan sulfate (glucosamine) 3-O-sulfotransferase 1	protein-coding
mm_149845.1	chr19	25052430	25052448	+	1	NA	intron (NM_028785, intron 2 of 47)	intron (NM_028785, intron 2 of 47)	52910	NM_028785	76088	Mm.102485	NM_028785	ENSMUSG00000052085	Dock8	1200017A24Rik|5830472H07Rik|A130095G14Rik|AI461977	dedicator of cytokinesis 8	protein-coding
mm_95424.1	chr11	50147916	50147917	+	1	NA	intron (NM_001290760, intron 5 of 21)	intron (NM_001290760, intron 5 of 21)	16556	NM_029745	76795	Mm.290975	NM_029745	ENSMUSG00000036644	Tbc1d9b	-	TBC1 domain family, member 9B	protein-coding
mm_116403.1	chr13	41424980	41424993	-	1	NA	intron (NM_001111324, intron 2 of 7)	(TG)n|Simple_repeat|Simple_repeat	62374	NM_001111324	18003	Mm.288980	NM_017464	ENSMUSG00000021365	Nedd9	Cas-L|CasL|HEF1|MEF1|Nedd-9|p105	neural precursor cell expressed, developmentally down-regulated gene 9	protein-coding
mm_89389.1	chr10	89872960	89872973	+	1	NA	promoter-TSS (NM_001128086)	promoter-TSS (NM_001128086)	-543	NM_001128086	77531	Mm.440605	NM_181398	ENSMUSG00000058589	Anks1b	AIDA-1b|C030032C09Rik|E530015N03Rik|ENSMUSG00000078431|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding
mm_112086.1	chr12	112674344	112674367	-	1	NA	promoter-TSS (NM_001165894)	promoter-TSS (NM_001165894)	-79	NM_009652	11651	Mm.6645	NM_009652	ENSMUSG00000001729	Akt1	Akt|LTR-akt|PKB|PKB/Akt|PKBalpha|Rac	thymoma viral proto-oncogene 1	protein-coding
mm_31730.1	chr4	62970847	62970851	+	1	NA	intron (NM_028326, intron 1 of 14)	intron (NM_028326, intron 1 of 14)	5275	NM_028326	72701	Mm.26479	NM_028326	ENSMUSG00000028358	Zfp618	2810031P15Rik|2810040O04Rik|AI415580|AI505139|D430033D05Rik|Nedd10|Znf618|bM257P7.1	zinc finger protein 618	protein-coding
mm_67319.1	chr7	79617550	79617565	-	1	NA	promoter-TSS (NM_019799)	promoter-TSS (NM_019799)	100	NM_019799	56315	Mm.10909	NM_019799	ENSMUSG00000030549	Rhcg	BB065800	Rhesus blood group-associated C glycoprotein	protein-coding
mm_126337.1	chr15	79898348	79898350	+	1	NA	intron (NM_001347041, intron 4 of 7)	intron (NM_001347041, intron 4 of 7)	3326	NM_001347041	80287	Mm.284059	NM_030255	ENSMUSG00000009585	Apobec3	Apobec|Arp3|BC003314|Cem15|Rfv3	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 3	protein-coding
mm_94873.1	chr11	24098474	24098487	+	1	NA	intron (NM_016707, intron 2 of 4)	intron (NM_016707, intron 2 of 4)	17785	NM_001159290	14025	Mm.53687	NM_016707	ENSMUSG00000000861	Bcl11a	2810047E18Rik|BCL-11A|Ctip1|D930021L15Rik|Evi9|Evi9a|Evi9b|Evi9c|mKIAA1809	B cell CLL/lymphoma 11A (zinc finger protein)	protein-coding
mm_61672.1	chr7	80803507	80803526	+	1	NA	promoter-TSS (NM_016721)	promoter-TSS (NM_016721)	-185	NM_016721	29875	Mm.207619	NM_016721	ENSMUSG00000030536	Iqgap1	AA682088|D7Ertd237e|D7Ertd257e|mKIAA0051	IQ motif containing GTPase activating protein 1	protein-coding
mm_141722.1	chr17	34115221	34115264	-	1	NA	exon (NM_001204973, exon 7 of 13)	exon (NM_001204973, exon 7 of 13)	4658	NR_037970	14312	Mm.3444	NM_010238	ENSMUSG00000024335	Brd2	AW228947|D17H6S113E|Frg-1|Fsrg-1|Fsrg1|Nat|Ring3|Rnf3|mKIAA4005	bromodomain containing 2	protein-coding
mm_81748.1	chr9	113931309	113931317	+	1	NA	intron (NM_013699, intron 1 of 15)	G-rich|Low_complexity|Low_complexity	379	NM_013699	22221	Mm.28052	NM_013699	ENSMUSG00000009741	Ubp1	Cp2b|LBP-1a|LBP-1b|NF2d9	upstream binding protein 1	protein-coding
mm_65249.1	chr7	19861229	19861242	-	1	NA	promoter-TSS (NM_001033419)	promoter-TSS (NM_001033419)	64	NM_001033419	330483	Mm.260192	NM_001033419	ENSMUSG00000014686	Ceacam16	Gm769	carcinoembryonic antigen-related cell adhesion molecule 16	protein-coding
mm_136908.1	chr17	13016630	13016644	+	1	NA	3' UTR (NM_013671, exon 5 of 5)	3' UTR (NM_013671, exon 5 of 5)	8798	NM_013671	20656	Mm.290876	NM_013671	ENSMUSG00000006818	Sod2	MnSOD|Sod-2	superoxide dismutase 2, mitochondrial	protein-coding
mm_57789.1	chr6	129271452	129271466	-	1	NA	intron (NM_001033122, intron 1 of 4)	intron (NM_001033122, intron 1 of 4)	3910	NM_001033122	12515	Mm.74745	NM_001033122	ENSMUSG00000030156	Cd69	5830438K24Rik|AI452015|AIM|VEA	CD69 antigen	protein-coding
mm_9635.1	chr1	176836136	176836176	-	1	NA	promoter-TSS (NR_037996)	promoter-TSS (NR_037996)	-23	NR_037996	15365	Mm.441435	NR_037996		Hmga2-ps1	EG666235|Gm7996|Hmgic-ps1|[y]i-c	high mobility group AT-hook 2, pseudogene 1	pseudo
mm_141036.1	chr17	25273542	25273557	-	1	NA	promoter-TSS (NR_027452)	promoter-TSS (NR_027452)	-118	NM_001177610	22196	Mm.240044	NM_011665	ENSMUSG00000015120	Ube2i	5830467E05Rik|F830028O17Rik|UBC9|Ubce2i|Ubce9	ubiquitin-conjugating enzyme E2I	protein-coding
mm_92968.1	chr10	86123205	86123224	-	1	NA	intron (NM_013722, intron 7 of 13)	intron (NM_013722, intron 7 of 13)	27360	NR_038024	78170	Mm.444790	NR_038024		4930486F22Rik	-	RIKEN cDNA 4930486F22 gene	ncRNA
mm_83879.1	chr9	55283583	55283630	-	1	NA	promoter-TSS (NM_032002)	promoter-TSS (NM_032002)	19	NM_032002	83961	Mm.443874	NM_032002	ENSMUSG00000032311	Nrg4	AI552600	neuregulin 4	protein-coding
mm_170556.1	chr19	41525362	41525366	+	1	NA	exon (NM_001326287, exon 1 of 1)	exon (NM_001326287, exon 1 of 1)	112	NM_001326287	627352	Mm.395111	NM_001326287		Morf4l1b	EG627352|Gm6747	mortality factor 4 like 1B	protein-coding
mm_39828.1	chr5	30814572	30814617	+	1	NA	promoter-TSS (NM_133350)	promoter-TSS (NM_133350)	-47	NM_133350	100732	Mm.332295	NM_133350	ENSMUSG00000029166	Mapre3	AI790651|EB2|EB3|EBF3|RP3	microtubule-associated protein, RP/EB family, member 3	protein-coding
mm_129391.1	chr15	78204430	78204450	-	1	NA	promoter-TSS (NM_001330686)	promoter-TSS (NM_001330686)	-203	NM_001330686	19293	Mm.2766	NM_013645	ENSMUSG00000005716	Pvalb	PV|Parv|Pva	parvalbumin	protein-coding
mm_114549.1	chr13	73963845	73963847	+	1	NA	promoter-TSS (NM_027704)	promoter-TSS (NM_027704)	-16	NM_027704	71164	Mm.66995	NM_027704	ENSMUSG00000069189	Zdhhc11	4933421L13Rik|DHHC-11|Zdhhc20	zinc finger, DHHC domain containing 11	protein-coding
mm_7217.1	chr1	93160840	93160851	-	1	NA	promoter-TSS (NM_001159940)	promoter-TSS (NM_001159940)	25	NM_001159940	71874	Mm.158766	NM_172411	ENSMUSG00000034159	2310007B03Rik	-	RIKEN cDNA 2310007B03 gene	protein-coding
mm_76728.1	chr8	95020226	95020228	-	1	NA	intron (NM_173036, intron 1 of 11)	B1_Mur4|SINE|Alu	2535	NM_173036	54672	Mm.27995	NM_173036	ENSMUSG00000060470	Adgrg3	A030001G24Rik|AW214383|Gpr97|Pb1|Pb99	adhesion G protein-coupled receptor G3	protein-coding
mm_33381.1	chr4	129570265	129570306	+	1	NA	intron (NM_001162433, intron 1 of 12)	intron (NM_001162433, intron 1 of 12)	3356	NM_001162433	16818	Mm.293753	NM_010693	ENSMUSG00000000409	Lck	Hck-3|Lsk|Lskt|p56<lck>|p56Lck	lymphocyte protein tyrosine kinase	protein-coding
mm_41038.1	chr5	86085816	86085824	+	1	NA	intron (NM_001310639, intron 3 of 7)	intron (NM_001310639, intron 3 of 7)	14074	NM_001310639	56792	Mm.131237	NM_019992	ENSMUSG00000029254	Stap1	AI586015|Brdg1|STAP-1	signal transducing adaptor family member 1	protein-coding
mm_4678.1	chr1	180432149	180432172	+	1	NA	TTS (NM_001081227)	TTS (NM_001081227)	51344	NM_001081227	381310	Mm.44791	NM_001081227	ENSMUSG00000053963	Stum	6330403A02Rik|ENSMUSG00000056615|Gm10001|R75555	mechanosensory transduction mediator	protein-coding
mm_36059.1	chr4	57496552	57496596	-	1	NA	Intergenic	Intergenic	-71674	NM_001304544	677884	Mm.331630	NM_001304544	ENSMUSG00000089945	Pakap	AF064781|Gm20459|Palm2-Akap2|Palm2Akap2|Palm2akap2	paralemmin A kinase anchor protein	protein-coding
mm_115958.1	chr13	23762363	23762364	-	1	NA	promoter-TSS (NM_013550)	promoter-TSS (NM_013550)	23	NM_013550	360198	Mm.221301	NM_013550	ENSMUSG00000069265	Hist1h3a	-	histone cluster 1, H3a	protein-coding
mm_50765.1	chr6	53604532	53604546	+	1	NA	exon (NM_172728, exon 2 of 7)	exon (NM_172728, exon 2 of 7)	31165	NM_172728	231991	Mm.227444	NM_172728	ENSMUSG00000053007	Creb5	9430076C15Rik|CRE-BPa|Crebpa|D430026C09Rik	cAMP responsive element binding protein 5	protein-coding
mm_141831.1	chr17	34628159	34628171	-	1	NA	promoter-TSS (NM_001302396)	promoter-TSS (NM_001302396)	114	NM_001302393	54397	Mm.373627	NM_019441	ENSMUSG00000015474	Ppt2	0610007M19Rik|AA672937	palmitoyl-protein thioesterase 2	protein-coding
mm_68372.1	chr7	107952689	107952705	-	1	NA	Intergenic	Intergenic	-1946	NM_146495	258488	Mm.377530	NM_146495	ENSMUSG00000094197	Olfr474	MOR204-20	olfactory receptor 474	protein-coding
mm_155800.1	chrX	99003329	99003339	+	1	NA	Intergenic	Intergenic	-39247	NM_199018	236920	Mm.236928	NM_199018	ENSMUSG00000031216	Stard8	Dlc3|mKIAA0189	START domain containing 8	protein-coding
mm_132561.1	chr16	38089326	38089355	+	1	NA	promoter-TSS (NR_033221)	promoter-TSS (NR_033221)	-80	NR_033221	414072	Mm.483602	NR_033221		BC031361	-	cDNA sequence BC031361	ncRNA
mm_29258.1	chr3	107220410	107220414	-	1	NA	intron (NM_001111143, intron 1 of 8)	intron (NM_001111143, intron 1 of 8)	1320	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_116073.1	chr13	27642572	27642576	-	1	NA	promoter-TSS (NM_001164058)	promoter-TSS (NM_001164058)	-81	NM_008930	19113	Mm.196424	NM_008930	ENSMUSG00000006488	Prl7a1	AA407021|AA409971|AA410116|PLP-E|PLP-G|Prlpe|Prlpg	prolactin family 7, subfamily a, member 1	protein-coding
mm_162914.1	chr10	119827899	119827899	+	1	NA	intron (NR_131760, intron 4 of 4)	intron (NR_131760, intron 4 of 4)	8510	NM_028736	74053	Mm.196692	NM_028736	ENSMUSG00000034813	Grip1	4931400F03Rik|GRIP|eb	glutamate receptor interacting protein 1	protein-coding
mm_149129.1	chr19	9000686	9000699	+	1	NA	exon (NM_001286518, exon 4 of 7)	exon (NM_001286518, exon 4 of 7)	11408	NM_001286518	66395	Mm.203866	NM_009643	ENSMUSG00000069833	Ahnak	DY6	AHNAK nucleoprotein (desmoyokin)	protein-coding
mm_55501.1	chr6	69765010	69765051	-	1	NA	Intergenic	Intergenic	-437856	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_34977.1	chr4	156013836	156013849	+	1	NA	TTS (NM_011341)	TTS (NM_011341)	147	NM_011659	22163	Mm.13885	NM_011659	ENSMUSG00000029075	Tnfrsf4	ACT35|CD134|Ly-70|Ox40|TXGP1L|Txgp1	tumor necrosis factor receptor superfamily, member 4	protein-coding
mm_54588.1	chr6	38147381	38147407	-	1	NA	intron (NM_194061, intron 14 of 19)	intron (NM_194061, intron 14 of 19)	-22808	NM_080467	140494	Mm.462308	NM_080467	ENSMUSG00000038600	Atp6v0a4	Atp6n1b|a4	ATPase, H+ transporting, lysosomal V0 subunit A4	protein-coding
mm_122695.1	chr14	52079527	52079543	-	1	NA	intron (NM_016884, intron 5 of 8)	B2_Mm2|SINE|B2	10220	NR_028552	100217457		NR_028552	ENSMUSG00000064871	Snord58b	MBII-199	small nucleolar RNA, C/D box 58B	snoRNA
mm_50827.1	chr6	54679347	54679352	+	1	NA	Intergenic	RMER19C|LTR|ERVK	-2275	NM_001289741	68235	Mm.233860	NM_026629	ENSMUSG00000038065	Mturn	2410066E13Rik|AI448550|B230212L03Rik	maturin, neural progenitor differentiation regulator homolog (Xenopus)	protein-coding
mm_124767.1	chr15	6669516	6669556	+	1	NA	Intergenic	B3A|SINE|B2	-38845	NM_030168	78757	Mm.275811	NM_030168	ENSMUSG00000050310	Rictor	4921505C17Rik|6030405M08Rik|AVO3|AW492497|D530039E11Rik	RPTOR independent companion of MTOR, complex 2	protein-coding
mm_38306.1	chr4	136898811	136898823	-	1	NA	promoter-TSS (NM_007572)	promoter-TSS (NM_007572)	27	NM_007572	12259	Mm.439957	NM_007572	ENSMUSG00000036887	C1qa	AI255395|C1q	complement component 1, q subcomponent, alpha polypeptide	protein-coding
mm_66633.1	chr7	45523916	45523973	-	1	NA	exon (NM_008654, exon 2 of 3)	exon (NM_008654, exon 2 of 3)	2324	NM_008654	17872	Mm.4048	NM_008654	ENSMUSG00000040435	Ppp1r15a	9630030H21|Gadd34|Myd116	protein phosphatase 1, regulatory (inhibitor) subunit 15A	protein-coding
mm_134351.1	chr16	16600012	16600081	-	1	NA	promoter-TSS (NM_001301817)	promoter-TSS (NM_001301817)	-68	NM_001301817	224014	Mm.256131	NM_139232	ENSMUSG00000022788	Fgd4	9030023J02Rik|9330209B17Rik|Frabp|ZFYVE6	FYVE, RhoGEF and PH domain containing 4	protein-coding
mm_163024.1	chr11	48808460	48808465	-	1	NA	intron (NM_145377, intron 4 of 5)	intron (NM_145377, intron 4 of 5)	5323	NR_028564	100216540		NR_028564	ENSMUSG00000064780	Snord95	-	small nucleolar RNA, C/D box 95	snoRNA
mm_37265.1	chr4	118489762	118489777	-	1	NA	promoter-TSS (NM_011587)	promoter-TSS (NM_011587)	80	NM_011587	21846	Mm.4345	NM_011587	ENSMUSG00000033191	Tie1	D430008P04Rik|TIE|tie-1	tyrosine kinase with immunoglobulin-like and EGF-like domains 1	protein-coding
mm_8416.1	chr1	152090260	152090307	-	1	NA	promoter-TSS (NM_197990)	promoter-TSS (NM_197990)	37	NM_197990	69399	Mm.278031	NM_197990	ENSMUSG00000032666	1700025G04Rik	2610510E02Rik|2900042O04Rik|ENSMUSG00000073540	RIKEN cDNA 1700025G04 gene	protein-coding
mm_44459.1	chr5	22533277	22533297	-	1	NA	intron (NM_011959, intron 5 of 13)	intron (NM_011959, intron 5 of 13)	-4257	NR_004442	100042049	Mm.21724	NR_004442		Gm15421	OTTMUSG00000021442	ribosomal protein L22 like 1 pseudogene	pseudo
mm_25551.1	chr3	116007458	116007540	+	1	NA	promoter-TSS (NM_021388)	promoter-TSS (NM_021388)	50	NM_001163515	58193	Mm.41739	NM_021388	ENSMUSG00000027963	Extl2	3000001D04Rik|AW146439	exostoses (multiple)-like 2	protein-coding
mm_166996.1	chr7	46715630	46715665	-	1	NA	promoter-TSS (NM_011315)	promoter-TSS (NM_011315)	29	NM_011315	20210	Mm.14277	NM_011315	ENSMUSG00000040026	Saa3	AV098916|Saa-3|l7R3	serum amyloid A 3	protein-coding
mm_98675.1	chr11	96284137	96284203	+	1	NA	exon (NM_010461, exon 2 of 2)	exon (NM_010461, exon 2 of 2)	2265	NM_010461	15416	Mm.4822	NM_010461	ENSMUSG00000056648	Hoxb8	Hox-2.4	homeobox B8	protein-coding
mm_20121.1	chr2	121236057	121236102	-	1	NA	exon (NM_013735, exon 12 of 28)	exon (NM_013735, exon 12 of 28)	35328	NM_001290830	27223	Mm.215389	NM_013735	ENSMUSG00000043909	Trp53bp1	53BP1|Tp53bp1|m53BP1|p53BP1	transformation related protein 53 binding protein 1	protein-coding
mm_143416.1	chr17	70840865	70840879	-	1	NA	Intergenic	AT_rich|Low_complexity|Low_complexity	5905	NM_001164077	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_92777.1	chr10	81179747	81179779	-	1	NA	TTS (NR_028549)	TTS (NR_028549)	802	NR_028549	100217454		NR_028549	ENSMUSG00000064441	Snord37	MBII-376	small nucleolar RNA, C/D box 37	snoRNA
mm_118107.1	chr13	103921014	103921053	-	1	NA	promoter-TSS (NM_001289475)	promoter-TSS (NM_001289475)	-447	NM_001005868	59079	Mm.277354	NM_021563	ENSMUSG00000021709	Erbin	1700028E05Rik|Erbb2ip|mKIAA1225	Erbb2 interacting protein	protein-coding
mm_142118.1	chr17	35866494	35866511	-	1	NA	promoter-TSS (NM_175242)	promoter-TSS (NM_175242)	-113	NM_175242	76448	Mm.359982	NM_175242	ENSMUSG00000034595	Ppp1r18	2310014H01Rik|AA407849|AI450394	protein phosphatase 1, regulatory subunit 18	protein-coding
mm_138215.1	chr17	34306748	34306760	+	1	NA	intron (NM_010382, intron 1 of 5)	intron (NM_010382, intron 1 of 5)	887	NM_010382	14969	Mm.22564	NM_010382	ENSMUSG00000060586	H2-Eb1	Eb|H-2Eb|H2Eb|Ia-4|Ia4	histocompatibility 2, class II antigen E beta	protein-coding
mm_124651.1	chr15	5185520	5185552	+	1	NA	promoter-TSS (NM_026213)	promoter-TSS (NM_026213)	-24	NM_026213	67515	Mm.254979	NM_026213	ENSMUSG00000022151	Ttc33	2410099M07Rik|2900001O04Rik|AI507072|AW538342|Osrf	tetratricopeptide repeat domain 33	protein-coding
mm_109481.1	chr12	111429133	111429143	+	1	NA	intron (NM_001289487, intron 12 of 13)	intron (NM_001289487, intron 12 of 13)	11693	NM_001289488	74190	Mm.248640	NM_028807	ENSMUSG00000021280	Exoc3l4	1200009I06Rik|1600013K19Rik	exocyst complex component 3-like 4	protein-coding
mm_119120.1	chr14	31118785	31118788	+	1	NA	exon (NM_001081251, exon 33 of 33)	exon (NM_001081251, exon 33 of 33)	10144	NM_001308466	66487	Mm.379116	NM_001308091	ENSMUSG00000058351	Smim4	2010107H07Rik|Gm41122	small integral membrane protein 4	protein-coding
mm_85136.1	chr9	95754116	95754129	-	1	NA	3' UTR (NM_001033210, exon 16 of 16)	3' UTR (NM_001033210, exon 16 of 16)	-3764	NM_011643	22063	Mm.149633	NM_011643	ENSMUSG00000032839	Trpc1	Mtrp1|Trp1|Trrp1	transient receptor potential cation channel, subfamily C, member 1	protein-coding
mm_11048.1	chr2	27165644	27165683	+	1	NA	exon (NM_138942, exon 1 of 12)	exon (NM_138942, exon 1 of 12)	156	NM_138942	13166	Mm.167781	NM_138942	ENSMUSG00000000889	Dbh	-	dopamine beta hydroxylase	protein-coding
mm_156746.1	chrX	159973543	159973554	+	1	NA	non-coding (NR_110970, exon 17 of 17)	non-coding (NR_110970, exon 17 of 17)	-14885	NM_001163085	270672	Mm.386889	NM_001163085	ENSMUSG00000031303	Map3k15	BC031147|MEKK15	mitogen-activated protein kinase kinase kinase 15	protein-coding
mm_76657.1	chr8	93197800	93197809	-	1	NA	promoter-TSS (NM_053200)	promoter-TSS (NM_053200)	0	NM_053200	104158	Mm.292803	NM_053200	ENSMUSG00000056973	Ces1d	Ces3|TGH	carboxylesterase 1D	protein-coding
mm_51719.1	chr6	86850923	86850933	+	1	NA	intron (NM_001040106, intron 1 of 20)	intron (NM_001040106, intron 1 of 20)	1411	NM_001040106	269774	Mm.221038	NM_177762	ENSMUSG00000057230	Aak1	5530400K14Rik|9630042K20|AU067724|AU067726|BC028270|C79663|D6Ertd245e|R75501|mKIAA1048	AP2 associated kinase 1	protein-coding
mm_19522.1	chr2	94109244	94109269	-	1	NA	intron (NM_019657, intron 3 of 10)	intron (NM_019657, intron 3 of 10)	48653	NM_019657	56348	Mm.22505	NM_019657	ENSMUSG00000027195	Hsd17b12	2610510O05Rik|AI172963|KIK-I|Kik1	hydroxysteroid (17-beta) dehydrogenase 12	protein-coding
mm_81833.1	chr9	118478183	118478199	+	1	NA	promoter-TSS (NM_010136)	promoter-TSS (NM_010136)	2	NM_010136	13813	Mm.200692	NM_010136	ENSMUSG00000032446	Eomes	C77258|TBR-2|Tbr2	eomesodermin	protein-coding
mm_78851.1	chr9	44335290	44335372	+	1	NA	3' UTR (NM_010436, exon 1 of 1)	3' UTR (NM_010436, exon 1 of 1)	616	NM_010436	15270	Mm.245931	NM_010436	ENSMUSG00000049932	H2afx	AW228881|H2A.X|H2ax|Hist5-2ax|gammaH2ax	H2A histone family, member X	protein-coding
mm_23354.1	chr3	55112355	55112376	+	1	NA	5' UTR (NM_001144987, exon 1 of 9)	5' UTR (NM_001144987, exon 1 of 9)	199	NM_001144987	229285	Mm.235523	NM_144895	ENSMUSG00000036580	Spg20	AI840044|C79168|SPARTIN|TAHCCP1|mKIAA0610	spastic paraplegia 20, spartin (Troyer syndrome) homolog (human)	protein-coding
mm_91695.1	chr10	44003577	44003587	-	1	NA	exon (NM_172393, exon 1 of 20)	exon (NM_172393, exon 1 of 20)	1264	NM_172393	11630	Mm.292082	NM_172393	ENSMUSG00000019866	Aim1	AI462491|AI463325	absent in melanoma 1	protein-coding
mm_8394.1	chr1	151428404	151428414	-	1	NA	promoter-TSS (NM_025819)	promoter-TSS (NM_025819)	26	NM_025819	66875	Mm.290905	NM_025819	ENSMUSG00000052748	Swt1	1200016B10Rik|C1orf26	SWT1 RNA endoribonuclease homolog (S. cerevisiae)	protein-coding
mm_84744.1	chr9	75387991	75388001	-	1	NA	3' UTR (NM_015806, exon 6 of 6)	3' UTR (NM_015806, exon 6 of 6)	21363	NM_027418	50772	Mm.480076	NM_015806	ENSMUSG00000042688	Mapk6	2610021I23Rik|D130053K17Rik|Erk3|Mapk4|Mapk63|Prkm4|Prkm6	mitogen-activated protein kinase 6	protein-coding
mm_98607.1	chr11	95842249	95842270	+	1	NA	promoter-TSS (NM_001284397)	promoter-TSS (NM_001284397)	-36	NM_023121	14710	Mm.46299	NM_023121	ENSMUSG00000038811	Gngt2	AV096488	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 2	protein-coding
mm_76192.1	chr8	82402982	82402998	-	1	NA	promoter-TSS (NM_001254747)	promoter-TSS (NM_001254747)	-404	NM_008357	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_15489.1	chr2	157562295	157562320	+	1	NA	3' UTR (NM_010923, exon 3 of 3)	3' UTR (NM_010923, exon 3 of 3)	2229	NM_180960	18111	Mm.34330	NM_010923	ENSMUSG00000067786	Nnat	5730414I02Rik|AW107673|Peg5	neuronatin	protein-coding
mm_129019.1	chr15	74930829	74930837	-	1	NA	Intergenic	MurERV4-int|LTR|ERVK	-24218	NM_001164039	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_41391.1	chr5	90769694	90769704	+	1	NA	3' UTR (NM_023785, exon 3 of 3)	3' UTR (NM_023785, exon 3 of 3)	1181	NM_023785	57349	Mm.293614	NM_023785	ENSMUSG00000029372	Ppbp	2400003M24Rik|AI854500|CTAP3|CTAPIII|Cxcl7|LA-PF4|LDGF|MDGF|NAP-2|NAP-2-L1|Scyb7|TGB|TGB1|THBGB1|b-TG1|beta-TG	pro-platelet basic protein	protein-coding
mm_44363.1	chr5	17806252	17806273	-	1	NA	intron (NM_007643, intron 8 of 14)	ORR1C1-int|LTR|ERVL-MaLR	29634	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_75479.1	chr8	48555898	48555981	-	1	NA	intron (NM_011857, intron 2 of 28)	CpG	118751	NM_001145937	23965	Mm.42191	NM_011857	ENSMUSG00000031561	Tenm3	2610100B16Rik|Odz1|Odz3|Ten-m3|mKIAA1455	teneurin transmembrane protein 3	protein-coding
mm_31672.1	chr4	60006180	60006192	+	1	NA	TTS (NM_001081285)	TTS (NM_001081285)	2637	NM_001081285	620807	Mm.464562	NM_001081285	ENSMUSG00000078689	Mup6	Gm12544|Mup2|OTTMUSG00000007423	major urinary protein 6	protein-coding
mm_140585.1	chr17	10215213	10215245	-	1	NA	3' UTR (NM_021881, exon 7 of 7)	3' UTR (NM_021881, exon 7 of 7)	104132	NM_021881	19317	Mm.130694	NM_021881	ENSMUSG00000062078	Qk	1110003F05Rik|1500005P18|QkI|l(17)-1Wis|l17Wis1	quaking	protein-coding
mm_65251.1	chr7	19871303	19871315	-	1	NA	Intergenic	Intergenic	-10010	NM_001033419	330483	Mm.260192	NM_001033419	ENSMUSG00000014686	Ceacam16	Gm769	carcinoembryonic antigen-related cell adhesion molecule 16	protein-coding
mm_117424.1	chr13	74363972	74363986	-	1	NA	promoter-TSS (NM_001033042)	promoter-TSS (NM_001033042)	21	NM_001033042	432779	Mm.324679	NM_001033042	ENSMUSG00000021579	Lrrc14b	AI595366	leucine rich repeat containing 14B	protein-coding
mm_116764.1	chr13	52584126	52584174	-	1	NA	intron (NM_001198977, intron 1 of 13)	intron (NM_001198977, intron 1 of 13)	713	NM_001198977	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_156916.1	chrX	169091653	169091663	+	1	NA	intron (NR_109847, intron 1 of 14)	intron (NR_109847, intron 1 of 14)	-21220	NM_001287530	11856	Mm.441810	NM_009707	ENSMUSG00000031355	Arhgap6	AI504284|RhoGAPX-1	Rho GTPase activating protein 6	protein-coding
mm_154953.1	chrX	36743661	36743700	+	1	NA	promoter-TSS (NM_001085497)	promoter-TSS (NM_001085497)	48	NR_075096	194744	Mm.336014	NM_001085497	ENSMUSG00000037636	Slc25a43	Gm8	solute carrier family 25, member 43	protein-coding
mm_34277.1	chr4	141424542	141424548	+	1	NA	3' UTR (NM_013868, exon 3 of 3)	3' UTR (NM_013868, exon 3 of 3)	3766	NM_013868	29818	Mm.46181	NM_013868	ENSMUSG00000006221	Hspb7	27kDa|Hsp25-2|cvHsp	heat shock protein family, member 7 (cardiovascular)	protein-coding
mm_16903.1	chr2	13424769	13424785	-	1	NA	exon (NM_001081084, exon 27 of 67)	exon (NM_001081084, exon 27 of 67)	67099	NM_001081084	65969	Mm.313915	NM_001081084	ENSMUSG00000026726	Cubn	AA408369|AL022750|D2Wsu88e	cubilin (intrinsic factor-cobalamin receptor)	protein-coding
mm_113407.1	chr13	33964709	33964750	+	1	NA	promoter-TSS (NM_001163241)	promoter-TSS (NM_001163241)	70	NM_001163241	18105	Mm.264036	NM_020282	ENSMUSG00000046949	Nqo2	NMO2|Nmor2|Ox2	NAD(P)H dehydrogenase, quinone 2	protein-coding
mm_128695.1	chr15	62219447	62219452	-	1	NA	promoter-TSS (NR_003523)	promoter-TSS (NR_003523)	2	NR_003523	67552	Mm.484027	NM_026230		H2afy3	4933432H23Rik	H2A histone family, member Y3	pseudo
mm_22584.1	chr3	13471638	13471733	+	1	NA	promoter-TSS (NM_001163328)	promoter-TSS (NM_001163328)	30	NM_001163328	76897	Mm.422625	NM_178631	ENSMUSG00000039717	Ralyl	0710005M24Rik	RALY RNA binding protein-like	protein-coding
mm_140883.1	chr17	23829164	23829174	-	1	NA	promoter-TSS (NM_026305)	promoter-TSS (NM_026305)	-60	NM_026305	67673	Mm.153758	NM_026305	ENSMUSG00000055839	Elob	0610040H15Rik|Tceb2	elongin B	protein-coding
mm_133892.1	chr16	97489995	97489998	+	1	NA	intron (NM_020622, intron 2 of 7)	intron (NM_020622, intron 2 of 7)	14940	NM_020622	52793	Mm.327932	NM_020622	ENSMUSG00000022938	Fam3b	2-21|9030624C24Rik|D16Jhu19e|ORF9|Pander	family with sequence similarity 3, member B	protein-coding
mm_15551.1	chr2	158416713	158416721	+	1	NA	intron (NM_001291137, intron 1 of 30)	(T)n|Simple_repeat|Simple_repeat	6864	NM_001291138	228850	Mm.398185	NM_177227	ENSMUSG00000027652	Ralgapb	AI507211|B230339M05Rik|p170	Ral GTPase activating protein, beta subunit (non-catalytic)	protein-coding
mm_143691.1	chr17	80289805	80289820	-	1	NA	promoter-TSS (NM_194269)	promoter-TSS (NM_194269)	-400	NM_194269	378462	Mm.45208	NM_194269	ENSMUSG00000045257	Morn2	Mopt	MORN repeat containing 2	protein-coding
mm_98469.1	chr11	94950287	94950307	+	1	NA	exon (NM_007742, exon 48 of 51)	exon (NM_007742, exon 48 of 51)	14073	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_15682.1	chr2	163602332	163602359	+	1	NA	promoter-TSS (NM_029512)	promoter-TSS (NM_029512)	31	NR_131225	76080	Mm.89828	NM_029512	ENSMUSG00000017679	Ttpal	3110080A02Rik|5830472M02Rik	tocopherol (alpha) transfer protein-like	protein-coding
mm_148629.1	chr19	5454424	5454429	+	1	NA	exon (NM_010235, exon 3 of 4)	exon (NM_010235, exon 3 of 4)	3137	NM_198616	240514	Mm.329657	NM_198616	ENSMUSG00000095098	Ccdc85b	AI842788|BB115872	coiled-coil domain containing 85B	protein-coding
mm_145586.1	chr18	60985743	60985753	+	1	NA	3' UTR (NM_001286809, exon 6 of 6)	3' UTR (NM_001286809, exon 6 of 6)	22194	NM_001286809	12322	Mm.131530	NM_009792	ENSMUSG00000024617	Camk2a	CaMKII|R74975|mKIAA0968	calcium/calmodulin-dependent protein kinase II alpha	protein-coding
mm_72804.1	chr8	87472839	87472849	+	1	NA	promoter-TSS (NM_019626)	promoter-TSS (NM_019626)	32	NR_033430	100040294	Mm.213632	NR_033430	ENSMUSG00000097248	Gm2694	C230036H16Rik|linc1582	predicted gene 2694	ncRNA
mm_23672.1	chr3	68572509	68572515	+	1	NA	5' UTR (NM_013928, exon 1 of 7)	5' UTR (NM_013928, exon 1 of 7)	144	NM_013928	30953	Mm.331064	NM_013928	ENSMUSG00000027777	Schip1	Nf2ip|Schip-1	schwannomin interacting protein 1	protein-coding
mm_173135.1	chrX	20239404	20239417	+	1	NA	intron (NM_177353, intron 1 of 16)	intron (NM_177353, intron 1 of 16)	52354	NM_177353	236727	Mm.132983	NM_177353	ENSMUSG00000037341	Slc9a7	A530087D17Rik|NHE7	solute carrier family 9 (sodium/hydrogen exchanger), member 7	protein-coding
mm_16803.1	chr2	10119584	10119595	-	1	NA	exon (NM_010582, exon 6 of 21)	exon (NM_010582, exon 6 of 21)	11094	NM_010582	16425	Mm.182043	NM_010582	ENSMUSG00000037254	Itih2	AI747202|Intin2|Itih-2	inter-alpha trypsin inhibitor, heavy chain 2	protein-coding
mm_122022.1	chr14	28674815	28674819	-	1	NA	Intergenic	Intergenic	163412	NM_001256224	22418	Mm.287544	NM_009524	ENSMUSG00000021994	Wnt5a	8030457G12Rik|Wnt-5a	wingless-type MMTV integration site family, member 5A	protein-coding
mm_103811.1	chr11	83002554	83002564	-	1	NA	3' UTR (NM_001167743, exon 4 of 4)	3' UTR (NM_001167743, exon 4 of 4)	-10729	NM_172796	237886	Mm.270253	NM_172796	ENSMUSG00000069793	Slfn9	9830137M10Rik	schlafen 9	protein-coding
mm_85562.1	chr9	106891402	106891438	-	1	NA	intron (NM_029103, intron 1 of 3)	intron (NM_029103, intron 1 of 3)	518	NM_029103	74840	Mm.29778	NM_029103	ENSMUSG00000032575	Manf	3230402M22Rik|AA407711|AA408789|AA673178|Armet|D17914|D18Mgi17	mesencephalic astrocyte-derived neurotrophic factor	protein-coding
mm_104180.1	chr11	87751685	87751705	-	1	NA	Intergenic	Intergenic	-5169	NR_029555	387160		NR_029555	ENSMUSG00000105196	Mir142	Mirn142|miR-142|mir-142a|mmu-mir-142|mmu-mir-142a	microRNA 142	ncRNA
mm_101550.1	chr11	33578970	33578983	-	1	NA	promoter-TSS (NM_146017)	promoter-TSS (NM_146017)	-19	NM_146017	216643	Mm.99989	NM_146017	ENSMUSG00000020159	Gabrp	-	gamma-aminobutyric acid (GABA) A receptor, pi	protein-coding
mm_78796.1	chr9	44046839	44046849	+	1	NA	exon (NM_009382, exon 3 of 4)	exon (NM_009382, exon 3 of 4)	3460	NM_009382	21838	Mm.3951	NM_009382	ENSMUSG00000032011	Thy1	CD90|T25|Thy-1|Thy-1.2|Thy1.1|Thy1.2	thymus cell antigen 1, theta	protein-coding
mm_172323.1	chr7	106567927	106567931	-	1	NA	Intergenic	RLTR27|LTR|ERVK	76716	NM_001277179	434223	Mm.276443	NM_001277179		Gm1966	-	predicted gene 1966	protein-coding
mm_97348.1	chr11	77469881	77469889	+	1	NA	TTS (NM_139129)	TTS (NM_139129)	5972	NM_139130	216961	Mm.33477	NM_139128	ENSMUSG00000020836	Coro6	-	coronin 6	protein-coding
mm_92840.1	chr10	81499687	81499713	-	1	NA	5' UTR (NM_010102, exon 1 of 1)	5' UTR (NM_010102, exon 1 of 1)	437	NM_010102	13611	Mm.33065	NM_010102	ENSMUSG00000044199	S1pr4	Edg6|Lpc1|S1p4	sphingosine-1-phosphate receptor 4	protein-coding
mm_59534.1	chr7	27731446	27731456	+	1	NA	promoter-TSS (NM_029531)	promoter-TSS (NM_029531)	42	NM_009560	22718	Mm.66913	NM_009560	ENSMUSG00000037640	Zfp60	6330516O17Rik|AI426106|AI449354|Mfg-3|Mfg3	zinc finger protein 60	protein-coding
mm_30110.1	chr3	139002369	139002379	-	1	NA	intron (NM_001040690, intron 4 of 14)	L1_Mur3|LINE|L1	72827	NM_145544	229877	Mm.28893	NM_145544	ENSMUSG00000028149	Rap1gds1	BC011279|GDS1	RAP1, GTP-GDP dissociation stimulator 1	protein-coding
mm_88129.1	chr10	69328266	69328273	+	1	NA	Intergenic	Intergenic	24643	NM_007659	12534	Mm.281367	NM_007659	ENSMUSG00000019942	Cdk1	Cdc2|Cdc2a|p34<CDC2>	cyclin-dependent kinase 1	protein-coding
mm_141657.1	chr17	33718638	33718690	-	1	NA	promoter-TSS (NM_001252480)	promoter-TSS (NM_001252480)	13	NM_145486	224703	Mm.311439	NM_145486	ENSMUSG00000079557	March2	9530046H09Rik|MARCH-II	membrane-associated ring finger (C3HC4) 2	protein-coding
mm_117978.1	chr13	100104065	100104082	-	1	NA	promoter-TSS (NM_001081061)	promoter-TSS (NM_001081061)	-3	NM_001081061	544971	Mm.288546	NM_001081061	ENSMUSG00000049658	Bdp1	AI662220|AW049390|AW456745|B130055N23Rik|G630013P12Rik|TAF3B1|TFC5|TFIIIB150|TFIIIB90|Tfnr|mKIAA1241	B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB	protein-coding
mm_57230.1	chr6	123282746	123282774	-	1	NA	3' UTR (NM_019948, exon 6 of 6)	3' UTR (NM_019948, exon 6 of 6)	7111	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_161550.1	chr16	10395498	10395498	-	1	NA	promoter-TSS (NM_001099275)	promoter-TSS (NM_001099275)	-33	NM_001291001	70426	Mm.142181	NM_001099275	ENSMUSG00000039179	Tekt5	3300001K11Rik	tektin 5	protein-coding
mm_2783.1	chr1	130841693	130841704	+	1	NA	exon (NM_011082, exon 3 of 11)	exon (NM_011082, exon 3 of 11)	15014	NM_011082	18703	Mm.276414	NM_011082	ENSMUSG00000026417	Pigr	-	polymeric immunoglobulin receptor	protein-coding
mm_74989.1	chr8	27167087	27167090	-	1	NA	intron (NM_029423, intron 1 of 4)	intron (NM_029423, intron 1 of 4)	7558	NM_029423	75767	Mm.205335	NM_029423	ENSMUSG00000031488	Rab11fip1	2010200K21Rik|4833414G05Rik|Rcp	RAB11 family interacting protein 1 (class I)	protein-coding
mm_85850.1	chr9	110654170	110654212	-	1	NA	promoter-TSS (NM_183276)	promoter-TSS (NM_183276)	-30	NM_183276	235627	Mm.335481	NM_183276	ENSMUSG00000056724	Nbeal2	1110014F23Rik|BC042396|mKIAA0540	neurobeachin-like 2	protein-coding
mm_12024.1	chr2	58159909	58159912	+	1	NA	exon (NM_139200, exon 1 of 8)	exon (NM_139200, exon 1 of 8)	212	NM_139200	227929	Mm.273905	NM_139200	ENSMUSG00000026832	Cytip	A130053M09Rik|AI462064|C80816|Cbp|Cybr|Pscdbp	cytohesin 1 interacting protein	protein-coding
mm_22013.1	chr2	167777899	167777910	-	1	NA	Intergenic	Intergenic	86727	NR_015500	329562	Mm.123101	NM_177851	ENSMUSG00000006462	A530013C23Rik	-	RIKEN cDNA A530013C23 gene	ncRNA
mm_96799.1	chr11	69981256	69981260	+	1	NA	promoter-TSS (NM_026017)	promoter-TSS (NM_026017)	-23	NM_018740	54351	Mm.13430	NM_018740	ENSMUSG00000018565	Elp5	Derp6|Rai12	elongator acetyltransferase complex subunit 5	protein-coding
mm_79342.1	chr9	53384032	53384091	+	1	NA	promoter-TSS (NM_212445)	promoter-TSS (NM_212445)	38	NM_212445	68304	Mm.427519	NM_212445	ENSMUSG00000034487	Kdelc2	2010004J24Rik|4833410J10Rik|AW549401	KDEL (Lys-Asp-Glu-Leu) containing 2	protein-coding
mm_159358.1	chr3	84815371	84815371	+	1	NA	promoter-TSS (NM_001177773)	promoter-TSS (NM_001177773)	-206	NM_001177773	50754	Mm.196475	NM_080428	ENSMUSG00000028086	Fbxw7	1110001A17Rik|AGO|Cdc4|Fbw7|Fbwd6|Fbx30|Fbxo30|Fbxw6|SEL-10	F-box and WD-40 domain protein 7	protein-coding
mm_139026.1	chr17	46159566	46159611	+	1	NA	Intergenic	Intergenic	-1444	NM_019581	56055	Mm.22147	NM_019581	ENSMUSG00000023952	Gtpbp2	nmf205	GTP binding protein 2	protein-coding
mm_112605.1	chr13	14236938	14236944	+	1	NA	exon (NM_001081348, exon 27 of 29)	exon (NM_001081348, exon 27 of 29)	173157	NM_198122	94246	Mm.439784	NM_194262	ENSMUSG00000039219	Arid4b	BCAA|BRCAA1|RBBP1L1|Rbp1l1|SAP180	AT rich interactive domain 4B (RBP1-like)	protein-coding
mm_153895.1	chr19	46987810	46987820	-	1	NA	intron (NM_001164363, intron 1 of 17)	intron (NM_001164363, intron 1 of 17)	-18248	NM_001164365	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_9612.1	chr1	176213935	176213943	-	1	NA	promoter-TSS (NM_001195816)	promoter-TSS (NM_001195816)	3	NM_001195816	319455	Mm.338001	NM_176916	ENSMUSG00000055214	Pld5	B230365F16Rik	phospholipase D family, member 5	protein-coding
mm_19127.1	chr2	80129184	80129192	-	1	NA	promoter-TSS (NM_016744)	promoter-TSS (NM_016744)	-217	NM_016744	18573	Mm.40678	NM_016744	ENSMUSG00000059173	Pde1a	AI987702|AW125737	phosphodiesterase 1A, calmodulin-dependent	protein-coding
mm_170158.1	chr17	47196293	47196312	+	1	NA	intron (NM_001097623, intron 3 of 19)	ID4|SINE|ID	-33928	NM_172622	224829	Mm.260989	NM_172622		Trerf1	9430096I18Rik|AI429294|B830015H24|RAPA|Trep-132|Trep132	transcriptional regulating factor 1	protein-coding
mm_29765.1	chr3	127225319	127225322	-	1	NA	intron (NM_001327938, intron 1 of 47)	intron (NM_001327938, intron 1 of 47)	64015	NR_105029	100862268	Mm.444603	NR_105029	ENSMUSG00000097456	LOC100862268	-	uncharacterized LOC100862268	ncRNA
mm_131723.1	chr16	21693024	21693035	+	1	NA	intron (NM_001001881, intron 1 of 1)	intron (NM_001001881, intron 1 of 1)	1636	NM_001001881	72190	Mm.131606	NM_001001881	ENSMUSG00000043391	2510009E07Rik	AI194952	RIKEN cDNA 2510009E07 gene	protein-coding
mm_60687.1	chr7	45155819	45155838	+	1	NA	promoter-TSS (NM_001285904)	promoter-TSS (NM_001285904)	-118	NM_001285904	68845	Mm.181689	NM_029406	ENSMUSG00000003423	Pih1d1	1110061L23Rik|4933413A04Rik|Nop17	PIH1 domain containing 1	protein-coding
mm_64029.1	chr7	140769165	140769190	+	1	NA	exon (NM_021282, exon 3 of 9)	exon (NM_021282, exon 3 of 9)	5345	NM_021282	13106	Mm.21758	NM_021282	ENSMUSG00000025479	Cyp2e1	Cyp2e	cytochrome P450, family 2, subfamily e, polypeptide 1	protein-coding
mm_52409.1	chr6	113389110	113389113	+	1	NA	promoter-TSS (NM_001142732)	promoter-TSS (NM_001142732)	-149	NM_001142732	101100	Mm.388573	NM_133923	ENSMUSG00000030276	Ttll3	4833441J24Rik|AI450050	tubulin tyrosine ligase-like family, member 3	protein-coding
mm_62910.1	chr7	117485534	117485538	+	1	NA	intron (NM_175645, intron 2 of 11)	L2a|LINE|L2	104557	NM_175645	233781	Mm.461427	NM_175645	ENSMUSG00000030657	Xylt1	8030490L12	xylosyltransferase 1	protein-coding
mm_145918.1	chr18	67066578	67066593	+	1	NA	Intergenic	Intergenic	-21713	NM_177137	14680	Mm.440746	NM_010307	ENSMUSG00000024524	Gnal	2610011C15Rik|9630020G10Rik|Galphaolf|Gna10|Golf	guanine nucleotide binding protein, alpha stimulating, olfactory type	protein-coding
mm_96102.1	chr11	60536588	60536624	+	1	NA	Intergenic	Intergenic	-1077	NM_172943	268420	Mm.262056	NM_172943	ENSMUSG00000042650	Alkbh5	AW050020|AW215868|Abh5|E130207K11|Ofoxd	alkB homolog 5, RNA demethylase	protein-coding
mm_13977.1	chr2	121449363	121449393	+	1	NA	non-coding (NR_110986, exon 1 of 3)	non-coding (NR_110986, exon 1 of 3)	180	NR_110986	378702	Mm.262252	NM_011354	ENSMUSG00000074884	Serf2	C80083|Msmac1l|m4F5rel	small EDRK-rich factor 2	protein-coding
mm_80980.1	chr9	103215809	103215857	+	1	NA	exon (NM_133977, exon 13 of 17)	exon (NM_133977, exon 13 of 17)	-13768	NM_009275	20818	Mm.273053	NM_009275	ENSMUSG00000032553	Srprb	AA409543	signal recognition particle receptor, B subunit	protein-coding
mm_120783.1	chr14	74641981	74641991	+	1	NA	exon (NM_172812, exon 1 of 3)	exon (NM_172812, exon 1 of 3)	1146	NM_172812	15558	Mm.214351	NM_172812	ENSMUSG00000034997	Htr2a	E030013E04|Htr-2|Htr2	5-hydroxytryptamine (serotonin) receptor 2A	protein-coding
mm_114169.1	chr13	55471762	55471773	+	1	NA	intron (NM_001030296, intron 1 of 2)	CpG	6009	NR_105909	102465569		NR_105909	ENSMUSG00000098341	Mir6944	Gm27710|mmu-mir-6944	microRNA 6944	ncRNA
mm_94845.1	chr11	23754531	23754553	+	1	NA	intron (NM_009044, intron 3 of 9)	intron (NM_009044, intron 3 of 9)	16428	NM_009044	19696	Mm.4869	NM_009044	ENSMUSG00000020275	Rel	c-Rel	reticuloendotheliosis oncogene	protein-coding
mm_131717.1	chr16	21339956	21339959	+	1	NA	Intergenic	Intergenic	-6601	NR_131983	76222	Mm.86031	NR_131983		Magef1	6430590I03Rik	melanoma antigen family F, 1	pseudo
mm_116115.1	chr13	28950275	28950298	-	1	NA	TTS (NM_009238)	TTS (NM_009238)	3396	NM_009238	20677	Mm.240627	NM_009238	ENSMUSG00000076431	Sox4	AA682046|Sox-4	SRY (sex determining region Y)-box 4	protein-coding
mm_83340.1	chr9	44288042	44288079	-	1	NA	5' UTR (NM_138955, exon 1 of 15)	5' UTR (NM_138955, exon 1 of 15)	184	NM_138955	192663	Mm.101876	NM_138955	ENSMUSG00000032131	Abcg4	6430517O04Rik	ATP-binding cassette, sub-family G (WHITE), member 4	protein-coding
mm_131941.1	chr16	23988995	23989005	+	1	NA	promoter-TSS (NM_009744)	promoter-TSS (NM_009744)	-388	NM_009744	12053	Mm.347398	NM_009744	ENSMUSG00000022508	Bcl6	Bcl5	B cell leukemia/lymphoma 6	protein-coding
mm_69101.1	chr7	127020128	127020143	-	1	NA	exon (NM_001102563, exon 2 of 4)	exon (NM_001102563, exon 2 of 4)	1076	NM_001102563	69017	Mm.392047	NM_001102563	ENSMUSG00000045114	Prrt2	1500031I19Rik|AI195361|DSPB3	proline-rich transmembrane protein 2	protein-coding
mm_130194.1	chr15	94566027	94566035	-	1	NA	intron (NM_029926, intron 10 of 11)	ORR1D2|LTR|ERVL-MaLR	22371	NM_029926	266632	Mm.422858	NM_029926	ENSMUSG00000059883	Irak4	8430405M07Rik|9330209D03Rik|IRAK-4|NY-REN-64	interleukin-1 receptor-associated kinase 4	protein-coding
mm_57671.1	chr6	128488992	128489001	-	1	NA	exon (NM_007376, exon 29 of 36)	exon (NM_007376, exon 29 of 36)	37724	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_126762.1	chr15	85859690	85859744	+	1	NA	promoter-TSS (NM_013882)	promoter-TSS (NM_013882)	10	NM_001168672	29870	Mm.20858	NM_013882	ENSMUSG00000022385	Gtse1	B99|Gtse-1	G two S phase expressed protein 1	protein-coding
mm_27336.1	chr3	50406352	50406389	-	1	NA	intron (NM_011990, intron 6 of 11)	intron (NM_011990, intron 6 of 11)	37243	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_295.1	chr1	23271807	23271816	+	1	NA	promoter-TSS (NR_029533)	promoter-TSS (NR_029533)	-458	NR_029533	387225		NR_029533	ENSMUSG00000065405	Mir30a	Mirn30a|mir-30a|mmu-mir-30a	microRNA 30a	ncRNA
mm_26470.1	chr3	144570305	144570309	+	1	NA	promoter-TSS (NM_053102)	promoter-TSS (NM_053102)	-91	NM_011828	23908	Mm.12863	NM_011828	ENSMUSG00000040151	Hs2st1	AW214369|Hs2st|mKIAA0448	heparan sulfate 2-O-sulfotransferase 1	protein-coding
mm_10112.1	chr2	3713450	3713474	+	1	NA	promoter-TSS (NM_025626)	promoter-TSS (NM_025626)	4	NM_025626	66540	Mm.277864	NM_025626	ENSMUSG00000026655	Fam107b	3110001A13Rik|AA589595|AA959793|AI132312	family with sequence similarity 107, member B	protein-coding
mm_109998.1	chr12	15816031	15816059	-	1	NA	5' UTR (NM_144551, exon 1 of 3)	5' UTR (NM_144551, exon 1 of 3)	740	NM_144551	217410	Mm.491136	NM_144551	ENSMUSG00000020601	Trib2	AW319517|TRB-2|TRB2	tribbles pseudokinase 2	protein-coding
mm_158099.1	chrX	101734158	101734168	-	1	NA	promoter-TSS (NM_009910)	promoter-TSS (NM_009910)	-16	NM_009910	12766	Mm.12876	NM_009910	ENSMUSG00000050232	Cxcr3	Cd183|Cmkar3	chemokine (C-X-C motif) receptor 3	protein-coding
mm_154811.1	chrX	13632781	13632798	+	1	NA	promoter-TSS (NM_011823)	promoter-TSS (NM_011823)	20	NM_011823	23890	Mm.487326	NM_011823	ENSMUSG00000040229	Gpr34	Lypsr1	G protein-coupled receptor 34	protein-coding
mm_46961.1	chr5	115134908	115134968	-	1	NA	promoter-TSS (NM_175352)	promoter-TSS (NM_175352)	37	NM_175352	106840	Mm.29241	NM_175352	ENSMUSG00000046562	Unc119b	AA407659|AI414892	unc-119 lipid binding chaperone B	protein-coding
mm_125604.1	chr15	60142076	60142091	+	1	NA	Intergenic	MER92-int|LTR|ERV1	-125465	NM_027668	71088	Mm.425950	NM_027668	ENSMUSG00000071749	4933412E24Rik	-	RIKEN cDNA 4933412E24 gene	protein-coding
mm_3957.1	chr1	164115303	164115313	+	1	NA	promoter-TSS (NM_011347)	promoter-TSS (NM_011347)	44	NM_011347	20344	Mm.3337	NM_011347	ENSMUSG00000026580	Selp	CD62P|GMP-140|Grmp|LECAM3|PADGEM	selectin, platelet	protein-coding
mm_127797.1	chr15	3583465	3583542	-	1	NA	promoter-TSS (NM_010284)	promoter-TSS (NM_010284)	-151	NM_010284	14600	Mm.3986	NM_010284	ENSMUSG00000055737	Ghr	GHBP|GHR/BP	growth hormone receptor	protein-coding
mm_123442.1	chr14	64949731	64949751	-	1	NA	promoter-TSS (NM_001253731)	promoter-TSS (NM_001253731)	116	NM_177338	219150	Mm.344074	NM_177338	ENSMUSG00000021972	Hmbox1	AI451877|AI604847|F830020C16Rik	homeobox containing 1	protein-coding
mm_142611.1	chr17	46857491	46857538	-	1	NA	Intergenic	Intergenic	-26101	NM_001100452	210982	Mm.37642	NM_001100452	ENSMUSG00000036568	Gltscr1l	mKIAA0240	GLTSCR1-like	protein-coding
mm_69499.1	chr7	134225380	134225418	-	1	NA	promoter-TSS (NM_007400)	promoter-TSS (NM_007400)	-302	NM_007400	11489	Mm.439714	NM_007400	ENSMUSG00000054555	Adam12	Mltna	a disintegrin and metallopeptidase domain 12 (meltrin alpha)	protein-coding
mm_158537.1	chrX	143933024	143933055	-	1	NA	promoter-TSS (NM_001110222)	promoter-TSS (NM_001110222)	85	NM_001110222	13193	Mm.12871	NM_010025	ENSMUSG00000031285	Dcx	Dbct	doublecortin	protein-coding
mm_154869.1	chrX	20680792	20680818	+	1	NA	exon (NM_009457, exon 21 of 26)	exon (NM_009457, exon 21 of 26)	-7149	NM_001310456	18555	Mm.102574	NM_011049	ENSMUSG00000031065	Cdk16	Crk5|Pctaire1|Pctk1	cyclin-dependent kinase 16	protein-coding
mm_54889.1	chr6	44083308	44083316	-	1	NA	Intergenic	Intergenic	-417034	NM_013861	29807	Mm.320979	NM_013861	ENSMUSG00000029735	Tpk1	-	thiamine pyrophosphokinase	protein-coding
mm_9055.1	chr1	167331310	167331326	-	1	NA	3' UTR (NM_001039483, exon 7 of 7)	3' UTR (NM_001039483, exon 7 of 7)	-18673	NM_019993	56752	Mm.292539	NM_019993	ENSMUSG00000026687	Aldh9a1	AA139417|Abaldh|ESTM40|TMABA-DH|Tmabadh	aldehyde dehydrogenase 9, subfamily A1	protein-coding
mm_85327.1	chr9	101862658	101862666	-	1	NA	Intergenic	Intergenic	442313	NR_106163	102466241		NR_106163	ENSMUSG00000098521	Mir7243	Gm27363|mmu-mir-7243	microRNA 7243	ncRNA
mm_64858.1	chr7	13037660	13037667	-	1	NA	promoter-TSS (NM_001243968)	promoter-TSS (NM_001243968)	-36	NM_001243968	22192	Mm.196580	NM_145578	ENSMUSG00000005575	Ube2m	2510040H03Rik|UBC12|Ubc-rs2	ubiquitin-conjugating enzyme E2M	protein-coding
mm_124507.1	chr14	121915739	121915747	-	1	NA	promoter-TSS (NM_182806)	promoter-TSS (NM_182806)	31	NM_182806	110168	Mm.37405	NM_182806	ENSMUSG00000050350	Gpr18	-	G protein-coupled receptor 18	protein-coding
mm_74903.1	chr8	25202440	25202446	-	1	NA	promoter-TSS (NM_177089)	promoter-TSS (NM_177089)	-901	NM_177089	320165	Mm.308452	NM_177089	ENSMUSG00000065954	Tacc1	4833447E04Rik|AA960202|B230378H13Rik	transforming, acidic coiled-coil containing protein 1	protein-coding
mm_108598.1	chr12	85447569	85447588	+	1	NA	Intergenic	Intergenic	-26323	NM_010234	14281	Mm.246513	NM_010234	ENSMUSG00000021250	Fos	D12Rfj1|c-fos|cFos	FBJ osteosarcoma oncogene	protein-coding
mm_50125.1	chr6	41539070	41539080	+	1	NA	Intergenic	Intergenic	17299	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_19415.1	chr2	91710586	91710598	-	1	NA	promoter-TSS (NM_178724)	promoter-TSS (NM_178724)	0	NM_145528	51897	Mm.28492	NM_145528	ENSMUSG00000027244	Atg13	1110053A20Rik|D2Ertd391e|Harbi1	autophagy related 13	protein-coding
mm_14174.1	chr2	126707413	126707423	+	1	NA	promoter-TSS (NM_001252580)	promoter-TSS (NM_001252580)	90	NM_019729	84092	Mm.272629	NM_019729	ENSMUSG00000027363	Usp8	AI574262|AW557536|Ubpy|mKIAA0055	ubiquitin specific peptidase 8	protein-coding
mm_43342.1	chr5	135121749	135121782	+	1	NA	exon (NM_021455, exon 4 of 17)	exon (NM_021455, exon 4 of 17)	14874	NM_021455	58805	Mm.34213	NM_021455	ENSMUSG00000005373	Mlxipl	ChREBP|Mlx|WS-bHLH|Wbscr14|bHLHd14	MLX interacting protein-like	protein-coding
mm_158528.1	chrX	143861173	143861182	-	1	NA	3' UTR (NM_010025, exon 7 of 7)	3' UTR (NM_010025, exon 7 of 7)	-33765	NM_007603	12338	Mm.30290	NM_007603	ENSMUSG00000067276	Capn6	-	calpain 6	protein-coding
mm_88238.1	chr10	71478606	71478608	+	1	NA	Intergenic	MIR|SINE|MIR	130844	NM_027184	69718	Mm.245867	NM_027184	ENSMUSG00000060733	Ipmk	2410017C19Rik|AA408208|Impk	inositol polyphosphate multikinase	protein-coding
mm_162633.1	chr1	188654652	188654681	+	1	NA	exon (NM_021408, exon 36 of 71)	exon (NM_021408, exon 36 of 71)	353174	NM_172650	226823	Mm.209880	NM_172650	ENSMUSG00000026608	Kctd3	4930438A20Rik|9330185B06|E330032J19Rik|NY-REN-45	potassium channel tetramerisation domain containing 3	protein-coding
mm_156863.1	chrX	164436906	164436916	+	1	NA	promoter-TSS (NM_026853)	promoter-TSS (NM_026853)	-83	NM_026853	68854	Mm.33225	NM_026853	ENSMUSG00000031382	Asb11	1110067L12Rik|1600009D24Rik	ankyrin repeat and SOCS box-containing 11	protein-coding
mm_166850.1	chr7	19696832	19696864	+	1	NA	exon (NM_009696, exon 4 of 4)	exon (NM_009696, exon 4 of 4)	1550	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_63790.1	chr7	132610686	132610700	+	1	NA	promoter-TSS (NM_029609)	promoter-TSS (NM_029609)	50	NM_029609	76429	Mm.276721	NM_029609	ENSMUSG00000030946	Lhpp	2310007H09Rik	phospholysine phosphohistidine inorganic pyrophosphate phosphatase	protein-coding
mm_74679.1	chr8	14029552	14029564	-	1	NA	intron (NM_001034862, intron 5 of 5)	B4A|SINE|B4	30618	NR_131136	546036	Mm.31785	NR_131136	ENSMUSG00000110058	Gm5907	EG546036|Gm845	predicted gene 5907	ncRNA
mm_47545.1	chr5	124329945	124329957	-	1	NA	intron (NM_028310, intron 1 of 1)	intron (NM_028310, intron 1 of 1)	1862	NM_001134717	72650	Mm.121658	NM_028310	ENSMUSG00000047635	2810006K23Rik	-	RIKEN cDNA 2810006K23 gene	protein-coding
mm_51992.1	chr6	92092370	92092419	+	1	NA	promoter-TSS (NM_001347342)	promoter-TSS (NM_001347342)	-39	NM_001347342	22026	Mm.87062	NM_011630	ENSMUSG00000005893	Nr2c2	TAK1|Tr4|mKIAA4145	nuclear receptor subfamily 2, group C, member 2	protein-coding
mm_82920.1	chr9	35099063	35099078	-	1	NA	intron (NM_009178, intron 1 of 10)	intron (NM_009178, intron 1 of 10)	-17658	NR_029475	78934	Mm.391688	NR_029475	ENSMUSG00000070315	4930581F22Rik	-	RIKEN cDNA 4930581F22 gene	ncRNA
mm_160391.1	chr8	55940891	55940891	+	1	NA	promoter-TSS (NM_080438)	promoter-TSS (NM_080438)	66	NM_080438	110304	Mm.307061	NM_080438	ENSMUSG00000038257	Glra3	-	glycine receptor, alpha 3 subunit	protein-coding
mm_77028.1	chr8	109251396	109251407	-	1	NA	non-coding (NR_126329, exon 10 of 10)	non-coding (NR_126329, exon 10 of 10)	89507	NR_002928	384864	Mm.390083	NR_002928		Gm1943	-	WD repeat domain 70 pseudogene	pseudo
mm_87314.1	chr10	42806613	42806641	+	1	NA	exon (NM_153055, exon 13 of 21)	exon (NM_153055, exon 13 of 21)	45131	NM_153055	140740	Mm.214344	NM_153055	ENSMUSG00000019802	Sec63	5730478J10Rik|AI649014|AW319215	SEC63-like (S. cerevisiae)	protein-coding
mm_5933.1	chr1	55363341	55363364	-	1	NA	promoter-TSS (NM_001113367)	promoter-TSS (NM_001113367)	117	NM_029267	75388	Mm.483408	NM_029267	ENSMUSG00000025977	Boll	4930554P13Rik|4930597B14Rik	bol, boule-like (Drosophila)	protein-coding
mm_5428.1	chr1	34485949	34485967	-	1	NA	Intergenic	Intergenic	-12472	NM_009355	21755	Mm.10725	NM_009355	ENSMUSG00000026125	Prss39	Tesp1	protease, serine 39	protein-coding
mm_82943.1	chr9	35305456	35305491	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	24368	NR_040715	71133	Mm.158577	NR_040715	ENSMUSG00000111746	4933422A05Rik	-	RIKEN cDNA 4933422A05 gene	ncRNA
mm_62394.1	chr7	101092876	101092882	+	1	NA	Intergenic	Intergenic	-15896	NM_001146010	207278	Mm.263041	NM_199012	ENSMUSG00000030691	Fchsd2	BC034086|R74866|Sh3md3|mKIAA0769	FCH and double SH3 domains 2	protein-coding
mm_129925.1	chr15	84446538	84446581	-	1	NA	promoter-TSS (NM_001347543)	promoter-TSS (NM_001347543)	51	NM_001347543	72301	Mm.275387	NM_001163145	ENSMUSG00000062760	1810041L15Rik	Kiaa1644	RIKEN cDNA 1810041L15 gene	protein-coding
mm_129578.1	chr15	79739485	79739502	-	1	NA	intron (NM_001205346, intron 2 of 17)	intron (NM_001205346, intron 2 of 17)	3043	NM_194342	223697	Mm.202715	NM_194342	ENSMUSG00000042524	Sun2	B230369L08Rik|C030011B15|Unc84b	Sad1 and UNC84 domain containing 2	protein-coding
mm_115895.1	chr13	22041358	22041363	-	1	NA	promoter-TSS (NM_175656)	promoter-TSS (NM_175656)	2	NM_175656	319158	Mm.14775	NM_175656	ENSMUSG00000060639	Hist1h4i	-	histone cluster 1, H4i	protein-coding
mm_94871.1	chr11	24078354	24078379	+	1	NA	5' UTR (NM_001242934, exon 1 of 4)	5' UTR (NM_001242934, exon 1 of 4)	310	NM_001159289	14025	Mm.53687	NM_016707	ENSMUSG00000000861	Bcl11a	2810047E18Rik|BCL-11A|Ctip1|D930021L15Rik|Evi9|Evi9a|Evi9b|Evi9c|mKIAA1809	B cell CLL/lymphoma 11A (zinc finger protein)	protein-coding
mm_44562.1	chr5	24622660	24622680	-	1	NA	Intergenic	Intergenic	-20668	NM_025891	66993	Mm.436539	NM_025891	ENSMUSG00000028949	Smarcd3	1500001J14Rik|2210409C08Rik|BAF60C	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3	protein-coding
mm_7440.1	chr1	120074024	120074034	-	1	NA	promoter-TSS (NM_019432)	promoter-TSS (NM_019432)	-249	NM_019432	170706	Mm.24750	NM_019432	ENSMUSG00000050777	Tmem37	AI173373|AW540203|Pr|Pr1	transmembrane protein 37	protein-coding
mm_27090.1	chr3	30048208	30048219	-	1	NA	Intergenic	L2|LINE|L2	-35009	NM_007963	14013	Mm.56965	NM_007963	ENSMUSG00000027684	Mecom	D630039M04Rik|Evi-1|Evi1|Jbo|Mds|Mds1|Mds1-Evi1|Prdm3|Znfpr1b1	MDS1 and EVI1 complex locus	protein-coding
mm_149936.1	chr19	27217012	27217042	+	1	NA	promoter-TSS (NM_013703)	promoter-TSS (NM_013703)	7	NM_001161420	22359	Mm.4141	NM_013703	ENSMUSG00000024924	Vldlr	AA408956|AI451093|AW047288	very low density lipoprotein receptor	protein-coding
mm_137952.1	chr17	32902430	32902440	+	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-10832	NM_207245	240066	Mm.26636	NM_207245	ENSMUSG00000095325	Zfp870	AI173952	zinc finger protein 870	protein-coding
mm_123371.1	chr14	63191934	63191937	-	1	NA	intron (NM_201610, intron 1 of 4)	intron (NM_201610, intron 1 of 4)	1590	NM_201610	382913	Mm.239490	NM_201610	ENSMUSG00000035121	Neil2	Gm1212|NEH2	nei like 2 (E. coli)	protein-coding
mm_123125.1	chr14	56174605	56174611	-	1	NA	promoter-TSS (NM_001305808)	promoter-TSS (NM_001305808)	-9	NM_153052	245839	Mm.207063	NM_153052	ENSMUSG00000015443	Gzmn	GrN	granzyme N	protein-coding
mm_115826.1	chr13	21286468	21286472	-	1	NA	TTS (NM_010343)	TTS (NM_010343)	6216	NM_010343	14780	Mm.1332	NM_010343	ENSMUSG00000004344	Gpx5	AV379049|Arep	glutathione peroxidase 5	protein-coding
mm_164791.1	chr18	12744574	12744577	+	1	NA	exon (NM_001042420, exon 2 of 5)	exon (NM_001042420, exon 2 of 5)	3220	NM_027687	71132	Mm.179740	NM_027687	ENSMUSG00000024430	Cabyr	1700016C01Rik|4933421A18Rik|CBP86|FSP-2	calcium-binding tyrosine-(Y)-phosphorylation regulated (fibrousheathin 2)	protein-coding
mm_134417.1	chr16	17722942	17722954	-	1	NA	promoter-TSS (NM_001040683)	promoter-TSS (NM_001040683)	-1	NM_001040683	94112	Mm.208970	NM_033609	ENSMUSG00000012114	Med15	A230074L19Rik|AW536074|Pcqap|mPcqap	mediator complex subunit 15	protein-coding
mm_59083.1	chr7	19689555	19689572	+	1	NA	TTS (NM_001110009)	TTS (NM_001110009)	3096	NM_001110009	11812	Mm.182440	NM_007469	ENSMUSG00000040564	Apoc1	Apo-CIB|ApoC-IB|apo-CI|apoC-I	apolipoprotein C-I	protein-coding
mm_78970.1	chr9	45319073	45319086	+	1	NA	promoter-TSS (NM_001013373)	promoter-TSS (NM_001013373)	-21	NM_001013373	214531	Mm.394987	NM_001013373	ENSMUSG00000037129	Tmprss13	BC010843|Tpmrss13	transmembrane protease, serine 13	protein-coding
mm_150477.1	chr19	38930910	38930920	+	1	NA	promoter-TSS (NM_008234)	promoter-TSS (NM_008234)	-75	NM_008234	15201	Mm.57223	NM_008234	ENSMUSG00000025001	Hells	AI323785|E130115I21Rik|LSH|Lysh|PASG|YFK8	helicase, lymphoid specific	protein-coding
mm_56477.1	chr6	99087498	99087544	-	1	NA	intron (NM_001347345, intron 5 of 19)	intron (NM_001347345, intron 5 of 19)	-59223	NM_001197322	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_81707.1	chr9	111311540	111311551	+	1	NA	promoter-TSS (NM_001164659)	promoter-TSS (NM_001164659)	-194	NM_001164659	320429	Mm.270754	NM_001164659	ENSMUSG00000062296	Trank1	A230061D21Rik|C030048J01Rik|Gm187|Lba1	tetratricopeptide repeat and ankyrin repeat containing 1	protein-coding
mm_113920.1	chr13	49582542	49582578	+	1	NA	promoter-TSS (NM_012050)	promoter-TSS (NM_012050)	-187	NM_012050	27047	Mm.390589	NM_012050	ENSMUSG00000048368	Omd	OSAD|SLRR2C	osteomodulin	protein-coding
mm_110013.1	chr12	16604132	16604143	-	1	NA	Intergenic	Intergenic	-14367	NM_172950	14245	Mm.153625	NM_015763	ENSMUSG00000020593	Lpin1	4631420P06|Kiaa0188|Lipin1|fld|mKIAA0188	lipin 1	protein-coding
mm_167853.1	chrX	9747795	9747804	+	1	NA	Intergenic	Intergenic	-84816	NM_025975	67117	Mm.29150	NM_025975	ENSMUSG00000031176	Dynlt3	2310075M16Rik|AU042796|Tcte1l	dynein light chain Tctex-type 3	protein-coding
mm_85867.1	chr9	110879447	110879476	-	1	NA	promoter-TSS (NM_001146059)	promoter-TSS (NM_001146059)	622	NM_146260	20776	Mm.390229	NM_146260	ENSMUSG00000049555	Tmie	5131400L21Rik|Mm.87012|sr	transmembrane inner ear	protein-coding
mm_69944.1	chr7	142176002	142176007	-	1	NA	promoter-TSS (NM_027844)	promoter-TSS (NM_027844)	1	NM_027844	71623	Mm.293700	NM_027844	ENSMUSG00000054759	Krtap5-2	4833428E21Rik	keratin associated protein 5-2	protein-coding
mm_47371.1	chr5	122952193	122952202	-	1	NA	intron (NM_001003953, intron 6 of 22)	CpG	36902	NM_001003953	30841	Mm.86406	NM_013910	ENSMUSG00000029475	Kdm2b	Cxxc2|Fbl10|Fbxl10|Jhdm1b|PCCX2	lysine (K)-specific demethylase 2B	protein-coding
mm_27528.1	chr3	57387740	57387750	-	1	NA	Intergenic	Intergenic	-37665	NM_145539	229302	Mm.26618	NM_145539	ENSMUSG00000027801	Tm4sf4	Iltmp	transmembrane 4 superfamily member 4	protein-coding
mm_120790.1	chr14	74733427	74733436	+	1	NA	intron (NM_001285423, intron 1 of 8)	intron (NM_001285423, intron 1 of 8)	1134	NM_016903	13885	Mm.38055	NM_016903	ENSMUSG00000021996	Esd	Es-10|Es10|FGH|sid478	esterase D/formylglutathione hydrolase	protein-coding
mm_5193.1	chr1	13259527	13259530	-	1	NA	intron (NM_001302702, intron 2 of 21)	PB1D9|SINE|Alu	112901	NM_001302702	17978	Mm.2537	NM_008678	ENSMUSG00000005886	Ncoa2	D1Ertd433e|GRIP-1|Grip1|KAT13C|NCoA-2|SRC-2|TIF2|bHLHe75	nuclear receptor coactivator 2	protein-coding
mm_143507.1	chr17	71752902	71752917	-	1	NA	promoter-TSS (NM_146082)	promoter-TSS (NM_146082)	-24	NM_146082	225004	Mm.134151	NM_146082	ENSMUSG00000044375	BC027072	-	cDNA sequence BC027072	protein-coding
mm_78972.1	chr9	45346805	45346807	+	1	NA	3' UTR (NM_001013373, exon 13 of 13)	3' UTR (NM_001013373, exon 13 of 13)	-23379	NM_022004	59095	Mm.208287	NM_022004	ENSMUSG00000066705	Fxyd6	0610030I18Rik|Php	FXYD domain-containing ion transport regulator 6	protein-coding
mm_6254.1	chr1	68978721	68978724	-	1	NA	intron (NM_010154, intron 1 of 26)	intron (NM_010154, intron 1 of 26)	129337	NM_010154	13869	Mm.442420	NM_010154	ENSMUSG00000062209	Erbb4	Her4|c-erbB-4	erb-b2 receptor tyrosine kinase 4	protein-coding
mm_42598.1	chr5	117414808	117414823	+	1	NA	5' UTR (NM_001312914, exon 1 of 20)	5' UTR (NM_001312914, exon 1 of 20)	813	NM_001312914	333050	Mm.437947	NM_001034873	ENSMUSG00000061578	Ksr2	-	kinase suppressor of ras 2	protein-coding
mm_46934.1	chr5	114772651	114772665	-	1	NA	intron (NM_001347400, intron 1 of 19)	intron (NM_001347400, intron 1 of 19)	833	NM_019834	26431	Mm.195632	NM_019834	ENSMUSG00000041890	Git2	1500036H07Rik|5830420E16Rik|6430510B20Rik|9630056M03Rik|B230104M05Rik|CAT2|mKIAA0148	G protein-coupled receptor kinase-interactor 2	protein-coding
mm_107087.1	chr12	17371060	17371063	+	1	NA	intron (NM_001008421, intron 11 of 20)	intron (NM_001008421, intron 11 of 20)	15669	NR_037226	100526470		NR_037226	ENSMUSG00000093037	Mir3066	mir-3066|mmu-mir-3066	microRNA 3066	ncRNA
mm_41592.1	chr5	93270503	93270506	+	1	NA	intron (NM_007635, intron 3 of 7)	intron (NM_007635, intron 3 of 7)	2931	NM_007635	12452	Mm.3527	NM_007635	ENSMUSG00000029385	Ccng2	-	cyclin G2	protein-coding
mm_80583.1	chr9	84239306	84239309	+	1	NA	Intergenic	L1MC1|LINE|L1	290526	NM_199195	12040	Mm.12819	NM_199195	ENSMUSG00000032263	Bckdhb	BCKDE1B|BCKDH E1-beta	branched chain ketoacid dehydrogenase E1, beta polypeptide	protein-coding
mm_95803.1	chr11	55109706	55109716	+	1	NA	3' UTR (NM_010299, exon 4 of 4)	3' UTR (NM_010299, exon 4 of 4)	11726	NM_010299	14667	Mm.287807	NM_010299	ENSMUSG00000000594	Gm2a	AA408702|AW215435|GM2-AP|SAP-3	GM2 ganglioside activator protein	protein-coding
mm_23966.1	chr3	84952524	84952538	+	1	NA	exon (NM_080428, exon 1 of 11)	exon (NM_080428, exon 1 of 11)	320	NM_080428	50754	Mm.196475	NM_080428	ENSMUSG00000028086	Fbxw7	1110001A17Rik|AGO|Cdc4|Fbw7|Fbwd6|Fbx30|Fbxo30|Fbxw6|SEL-10	F-box and WD-40 domain protein 7	protein-coding
mm_64104.1	chr7	141025157	141025174	+	1	NA	Intergenic	RMER17C|LTR|ERVK	-8273	NM_001033632	213002	Mm.276440	NM_001033632	ENSMUSG00000059108	Ifitm6	A330075D07|Dspa2f|Fgls5|fragilis5	interferon induced transmembrane protein 6	protein-coding
mm_144377.1	chr18	20558278	20558280	+	1	NA	5' UTR (NM_007883, exon 1 of 15)	5' UTR (NM_007883, exon 1 of 15)	205	NM_007883	13511	Mm.345891	NM_007883	ENSMUSG00000044393	Dsg2	AA408168|D18Ertd293e	desmoglein 2	protein-coding
mm_70450.1	chr8	11779214	11779224	+	1	NA	intron (NM_001113517, intron 2 of 18)	intron (NM_001113517, intron 2 of 18)	20889	NM_001113518	54126	Mm.244068	NM_017402	ENSMUSG00000031511	Arhgef7	Cool|PIX|Pak3bp|betaPix|betaPix-b|betaPix-c|cool-1|mKIAA0142|p85Cool1|p85SPR	Rho guanine nucleotide exchange factor (GEF7)	protein-coding
mm_64836.1	chr7	12997417	12997453	-	1	NA	exon (NM_009512, exon 1 of 10)	exon (NM_009512, exon 1 of 10)	757	NM_009512	26459	Mm.10984	NM_009512	ENSMUSG00000030382	Slc27a5	FACVL3|FATP5|VLCS-H2|VLCSH2|Vlacsr	solute carrier family 27 (fatty acid transporter), member 5	protein-coding
mm_139417.1	chr17	53479213	53479237	+	1	NA	promoter-TSS (NM_025887)	promoter-TSS (NM_025887)	-9	NM_025887	271457	Mm.329123	NM_025887	ENSMUSG00000017831	Rab5a	2410015H04Rik|AI663973|AU021172|nnyRab5a	RAB5A, member RAS oncogene family	protein-coding
mm_80316.1	chr9	74861889	74861915	+	1	NA	promoter-TSS (NM_008262)	promoter-TSS (NM_008262)	-19	NM_008262	15379	Mm.303355	NM_008262	ENSMUSG00000043013	Onecut1	D9Ertd423e|HNF-6|Hfh12|Hnf6|Hnf6b|OC-1|Oc1	one cut domain, family member 1	protein-coding
mm_42195.1	chr5	112277457	112277481	+	1	NA	intron (NM_001326590, intron 1 of 5)	L1MB7|LINE|L1	778	NM_009419	22022	Mm.250631	NM_009419	ENSMUSG00000029344	Tpst2	AI448750|D5Ucla3|Tango13b|grm|grt	protein-tyrosine sulfotransferase 2	protein-coding
mm_41067.1	chr5	87666201	87666218	+	1	NA	promoter-TSS (NM_007784)	promoter-TSS (NM_007784)	1	NM_001286016	12990	Mm.427467	NM_007784	ENSMUSG00000070702	Csn1s1	AA959832|AW212882|Csna	casein alpha s1	protein-coding
mm_29092.1	chr3	104776250	104776251	-	1	NA	intron (NM_183224, intron 1 of 6)	intron (NM_183224, intron 1 of 6)	1297	NM_183224	329731	Mm.389494	NM_183224	ENSMUSG00000055865	Fam19a3	7530404M11Rik|TAFA3|Tafa-3	family with sequence similarity 19, member A3	protein-coding
mm_116480.1	chr13	43616068	43616086	-	1	NA	intron (NM_183204, intron 1 of 1)	CpG	280	NM_183204	328234	Mm.40588	NM_183204	ENSMUSG00000044164	Rnf182	C630023L15Rik	ring finger protein 182	protein-coding
mm_163450.1	chr12	88381724	88381728	+	1	NA	intron (NM_028105, intron 3 of 10)	intron (NM_028105, intron 3 of 10)	-4403	NR_045888	71818	Mm.490789	NR_045888		3200001D21Rik	-	RIKEN cDNA 3200001D21 gene	ncRNA
mm_55160.1	chr6	51848677	51848681	-	1	NA	Intergenic	Intergenic	163870	NM_018773	54353	Mm.221479	NM_018773	ENSMUSG00000059182	Skap2	2610021A10Rik|AA960083|BB137539|RA70|SKAP-HOM|Saps|Scap2|mSKAP55R	src family associated phosphoprotein 2	protein-coding
mm_130061.1	chr15	89187404	89187412	-	1	NA	exon (NM_027081, exon 10 of 20)	exon (NM_027081, exon 10 of 20)	-1871	NR_105923	102465578		NR_105923	ENSMUSG00000098663	Mir6958	Gm27581|mmu-mir-6958	microRNA 6958	ncRNA
mm_74766.1	chr8	20922043	20922049	-	1	NA	promoter-TSS (NM_001025353)	promoter-TSS (NM_001025353)	25	NM_001025353	100503992	Mm.490240	NM_001025353	ENSMUSG00000071165	Gm6040	Defb51|EG574083	predicted gene 6040	protein-coding
mm_157067.1	chrX	8192829	8192881	-	1	NA	TTS (NM_145907)	TTS (NM_145907)	657	NM_007898	13595	Mm.27183	NM_007898	ENSMUSG00000031168	Ebp	AI255399|Pabp|SI|Td|mSI	phenylalkylamine Ca2+ antagonist (emopamil) binding protein	protein-coding
mm_82963.1	chr9	35620805	35620807	-	1	NA	Intergenic	L1_Mur2|LINE|L1	-8921	NM_020264	56872	Mm.390143	NM_020264	ENSMUSG00000032099	Pate4	9530004K16Rik|Pate-B|Svs7	prostate and testis expressed 4	protein-coding
mm_44859.1	chr5	34288287	34288305	-	1	NA	promoter-TSS (NM_001015039)	promoter-TSS (NM_001015039)	28	NM_001015039	231125	Mm.113388	NM_001015039	ENSMUSG00000037224	Zfyve28	9630058O20Rik|Gm146|mKIAA1643	zinc finger, FYVE domain containing 28	protein-coding
mm_67654.1	chr7	84689935	84689939	-	1	NA	intron (NR_038175, intron 1 of 4)	CpG	297	NR_038175	72495	Mm.382914	NR_038175	ENSMUSG00000085236	2610206C17Rik	-	RIKEN cDNA 2610206C17 gene	ncRNA
mm_70101.1	chr7	142661227	142661238	-	1	NA	promoter-TSS (NM_001122736)	promoter-TSS (NM_001122736)	39	NM_001122736	16002	Mm.3862	NM_010514	ENSMUSG00000048583	Igf2	AL033362|Igf-2|Igf-II|M6pr|Mpr|Peg2	insulin-like growth factor 2	protein-coding
mm_67725.1	chr7	90108078	90108088	-	1	NA	Intergenic	Intergenic	21391	NR_046006	78329	Mm.389940	NR_046006	ENSMUSG00000097162	2310010J17Rik	-	RIKEN cDNA 2310010J17 gene	ncRNA
mm_68687.1	chr7	119472499	119472509	-	1	NA	exon (NM_001278605, exon 5 of 11)	exon (NM_001278605, exon 5 of 11)	6758	NM_009470	22242	Mm.10826	NM_009470	ENSMUSG00000030963	Umod	THP|Urehd1|urehr4	uromodulin	protein-coding
mm_107251.1	chr12	27342907	27342927	+	1	NA	promoter-TSS (NM_009234)	promoter-TSS (NM_009234)	-199	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding
mm_151789.1	chr19	5389925	5389942	-	1	NA	non-coding (NR_033224, exon 1 of 1)	non-coding (NR_033224, exon 1 of 1)	-1230	NM_016882	20227	Mm.34562	NM_016882	ENSMUSG00000039148	Sart1	U5-110K	squamous cell carcinoma antigen recognized by T cells 1	protein-coding
mm_13801.1	chr2	118997045	118997047	+	1	NA	Intergenic	Intergenic	32347	NM_199310	269336	Mm.292465	NM_199310	ENSMUSG00000039983	Ccdc32	Gm631	coiled-coil domain containing 32	protein-coding
mm_155821.1	chrX	100626073	100626158	+	1	NA	promoter-TSS (NM_008446)	promoter-TSS (NM_008446)	50	NM_008446	16571	Mm.383091	NM_008446	ENSMUSG00000034311	Kif4	AI323435|D330050K22Rik|Kns4	kinesin family member 4	protein-coding
mm_86101.1	chr9	115310101	115310157	-	1	NA	5' UTR (NM_024222, exon 1 of 16)	5' UTR (NM_024222, exon 1 of 16)	292	NM_024222	68292	Mm.296158	NM_024222	ENSMUSG00000032437	Stt3b	1300006C19Rik|Simp	STT3, subunit of the oligosaccharyltransferase complex, homolog B (S. cerevisiae)	protein-coding
mm_108062.1	chr12	73936201	73936223	+	1	NA	exon (NM_010431, exon 7 of 15)	exon (NM_010431, exon 7 of 15)	-28318	NM_178392	75627	Mm.25937	NM_178392	ENSMUSG00000021113	Snapc1	2700033G17Rik|AU015787	small nuclear RNA activating complex, polypeptide 1	protein-coding
mm_78083.1	chr9	16114590	16114609	+	1	NA	intron (NM_001080814, intron 2 of 24)	intron (NM_001080814, intron 2 of 24)	-240043	NM_145712	244701	Mm.222631	NM_145712	ENSMUSG00000050901	Mtnr1b	Mel-1B-R|Mel1b|Mt2	melatonin receptor 1B	protein-coding
mm_54236.1	chr6	28242334	28242345	-	1	NA	intron (NM_001081678, intron 5 of 5)	intron (NM_001081678, intron 5 of 5)	19262	NM_001081678	627049	Mm.84441	NM_001081678	ENSMUSG00000039841	Zfp800	AA407452|Znf800	zinc finger protein 800	protein-coding
mm_138561.1	chr17	35335850	35335890	+	1	NA	Intergenic	Intergenic	-6463	NM_010392	15013	Mm.427969	NM_010392	ENSMUSG00000091705	H2-Q2	BE136769|ENSMUSG00000079507|Gm11132|H-2Q2|gs14-2	histocompatibility 2, Q region locus 2	protein-coding
mm_136545.1	chr16	97962206	97962276	-	1	NA	intron (NM_175428, intron 1 of 2)	CpG	381	NM_001081685	114565	Mm.474489	NM_175428	ENSMUSG00000046962	Zbtb21	5430437K12Rik|B430213I24Rik|Zfp295|Znf295|mKIAA1227	zinc finger and BTB domain containing 21	protein-coding
mm_56637.1	chr6	113195327	113195362	-	1	NA	promoter-TSS (NM_177763)	promoter-TSS (NM_177763)	40	NM_177763	269788	Mm.37943	NM_177763	ENSMUSG00000042873	Lhfpl4	1190004M23Rik|AI604880|B230384L07|mKIAA4027	lipoma HMGIC fusion partner-like protein 4	protein-coding
mm_169338.1	chr14	123671265	123671279	+	1	NA	intron (NM_145467, intron 2 of 10)	L1Md_F3|LINE|L1	11132	NM_145467	223272	Mm.383176	NM_145467	ENSMUSG00000032925	Itgbl1	B930011D01Rik	integrin, beta-like 1	protein-coding
mm_26177.1	chr3	138289799	138289818	+	1	NA	exon (NM_007409, exon 8 of 9)	exon (NM_007409, exon 8 of 9)	12163	NM_007409	11522	Mm.2409	NM_007409	ENSMUSG00000074207	Adh1	ADH-AA|AI194826|Adh-1|Adh-1-t|Adh-1e|Adh-1t|Adh-3e|Adh1-e|Adh1-t|Adh1tl|Adh3-e	alcohol dehydrogenase 1 (class I)	protein-coding
mm_92001.1	chr10	62231250	62231252	-	1	NA	promoter-TSS (NM_197996)	promoter-TSS (NM_197996)	-33	NM_197996	70423	Mm.416781	NM_197996	ENSMUSG00000037031	Tspan15	1110036D12Rik|2700063A19Rik|AW048364|Tm4sf15	tetraspanin 15	protein-coding
mm_54123.1	chr6	18388161	18388164	-	1	NA	exon (NM_080285, exon 16 of 23)	exon (NM_080285, exon 16 of 23)	126663	NM_080285	30785	Mm.224189	NM_080285	ENSMUSG00000000416	Cttnbp2	3010022N24Rik|4732477G22Rik|6430526E05|9130022E09Rik|AU040881|Cortbp2|ORF4|mKIAA1758	cortactin binding protein 2	protein-coding
mm_127708.1	chr15	103009482	103009507	+	1	NA	promoter-TSS (NM_010465)	promoter-TSS (NM_010465)	-68	NM_010465	15425	Mm.4444	NM_010465	ENSMUSG00000001661	Hoxc6	Hox-3.3|Hox-6.1	homeobox C6	protein-coding
mm_19117.1	chr2	80005966	80005999	-	1	NA	intron (NM_001159582, intron 2 of 15)	intron (NM_001159582, intron 2 of 15)	-97583	NM_001009978	18573	Mm.40678	NM_016744	ENSMUSG00000059173	Pde1a	AI987702|AW125737	phosphodiesterase 1A, calmodulin-dependent	protein-coding
mm_100757.1	chr11	4427280	4427290	-	1	NA	exon (NM_029458, exon 3 of 11)	exon (NM_029458, exon 3 of 11)	13797	NM_029458	75828	Mm.159592	NM_029458	ENSMUSG00000020419	Hormad2	4930529M09Rik	HORMA domain containing 2	protein-coding
mm_168049.1	chrY	90811788	90811805	+	1	NA	intron (NM_133362, intron 2 of 3)	intron (NM_133362, intron 2 of 3)	26354	NM_133362	170942	Mm.76062	NM_133362	ENSMUSG00000096768	Erdr1	edr	erythroid differentiation regulator 1	protein-coding
mm_137703.1	chr17	29093764	29093781	+	1	NA	promoter-TSS (NM_007669)	promoter-TSS (NM_007669)	3	NM_007669	12575	Mm.195663	NM_007669	ENSMUSG00000023067	Cdkn1a	CAP20|CDKI|CIP1|Cdkn1|P21|SDI1|Waf1|mda6|p21Cip1|p21WAF	cyclin-dependent kinase inhibitor 1A (P21)	protein-coding
mm_120045.1	chr14	56575604	56575633	+	1	NA	promoter-TSS (NM_001145978)	promoter-TSS (NM_001145978)	-1	NM_001145978	328417	Mm.379357	NM_001145978	ENSMUSG00000054509	Parp4	Adprtl1|C030027K23Rik|E230037B21Rik|Gm743|PARPL|PH5P|VAULT3|VPARP|p193	poly (ADP-ribose) polymerase family, member 4	protein-coding
mm_110550.1	chr12	55489926	55489980	-	1	NA	exon (NM_010907, exon 6 of 6)	exon (NM_010907, exon 6 of 6)	2694	NM_010907	18035	Mm.170515	NM_010907	ENSMUSG00000021025	Nfkbia	AI462015|Nfkbi	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, alpha	protein-coding
mm_68310.1	chr7	105752194	105752234	-	1	NA	promoter-TSS (NM_009906)	promoter-TSS (NM_009906)	21	NM_009906	12751	Mm.20837	NM_009906	ENSMUSG00000030894	Tpp1	Cln2|LPIC|TPP-1|TPP-I	tripeptidyl peptidase I	protein-coding
mm_150230.1	chr19	33973021	33973066	+	1	NA	exon (NM_026334, exon 8 of 10)	exon (NM_026334, exon 8 of 10)	11795	NM_026334	67717	Mm.329816	NM_026334	ENSMUSG00000024768	Lipf	2310051B21Rik|AV082900	lipase, gastric	protein-coding
mm_5983.1	chr1	58420316	58420331	-	1	NA	non-coding (NR_027854, exon 3 of 11)	non-coding (NR_027854, exon 3 of 11)	3765	NR_027853	12747	Mm.1761	NM_009905	ENSMUSG00000026034	Clk1	STY	CDC-like kinase 1	protein-coding
mm_67664.1	chr7	86775861	86775872	-	1	NA	promoter-TSS (NM_001159706)	promoter-TSS (NM_001159706)	-2	NM_001159706	53320	Mm.269137	NM_016770	ENSMUSG00000001773	Folh1	GCP2|mopsm	folate hydrolase 1	protein-coding
mm_99072.1	chr11	99171114	99171124	+	1	NA	Intergenic	Intergenic	-16042	NM_007719	12775	Mm.2932	NM_007719	ENSMUSG00000037944	Ccr7	CC-CKR-7|CCR-7|CD197|Cdw197|Cmkbr7|EBI1|Ebi1h	chemokine (C-C motif) receptor 7	protein-coding
mm_122629.1	chr14	51145748	51145798	-	1	NA	exon (NM_011271, exon 2 of 2)	exon (NM_011271, exon 2 of 2)	994	NM_011271	19752	Mm.235538	NM_011271	ENSMUSG00000035896	Rnase1	AI574248|Rib-1|Rib1	ribonuclease, RNase A family, 1 (pancreatic)	protein-coding
mm_84368.1	chr9	64841797	64841799	-	1	NA	intron (NM_001162917, intron 5 of 34)	intron (NM_001162917, intron 5 of 34)	30787	NM_001162917	102442	Mm.222473	NM_176935	ENSMUSG00000053641	Dennd4a	AI115600|AI851943|F730015K02Rik	DENN/MADD domain containing 4A	protein-coding
mm_41728.1	chr5	102481691	102481714	+	1	NA	5' UTR (NM_029270, exon 1 of 10)	5' UTR (NM_029270, exon 1 of 10)	311	NM_029270	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding
mm_157015.1	chrX	7681035	7681045	-	1	NA	promoter-TSS (NM_018832)	promoter-TSS (NM_018832)	49	NM_018832	54634	Mm.67912	NM_018832	ENSMUSG00000031147	Magix	Pdzx|Sfc18	MAGI family member, X-linked	protein-coding
mm_97640.1	chr11	79087100	79087135	+	1	NA	intron (NM_013571, intron 1 of 17)	intron (NM_013571, intron 1 of 17)	59237	NM_013571	16706	Mm.4745	NM_013571	ENSMUSG00000018334	Ksr1	AW492498|B-KSR1|D11Bhm183e|D11Bhm184e|Ksr|RSU2|hb	kinase suppressor of ras 1	protein-coding
mm_146805.1	chr18	20745880	20745914	-	1	NA	5' UTR (NM_019737, exon 1 of 9)	5' UTR (NM_019737, exon 1 of 9)	507	NM_019737	56386	Mm.393827	NM_019737	ENSMUSG00000056124	B4galt6	AA536803|AU022389	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 6	protein-coding
mm_134124.1	chr16	10347570	10347613	-	1	NA	Intergenic	Intergenic	-16306	NR_126064	381033	Mm.263108	NR_126064		Gm1600	Gm1776	predicted gene 1600	ncRNA
mm_157179.1	chrX	9656014	9656048	-	1	NA	exon (NM_025975, exon 5 of 5)	exon (NM_025975, exon 5 of 5)	6952	NM_025975	67117	Mm.29150	NM_025975	ENSMUSG00000031176	Dynlt3	2310075M16Rik|AU042796|Tcte1l	dynein light chain Tctex-type 3	protein-coding
mm_50980.1	chr6	62109097	62109101	+	1	NA	intron (NM_001164316, intron 10 of 10)	intron (NM_001164316, intron 10 of 10)	-928289	NR_040287	100504262	Mm.438066	NR_040287		A730020E08Rik	-	RIKEN cDNA A730020E08 gene	ncRNA
mm_68406.1	chr7	109616549	109616616	-	1	NA	promoter-TSS (NR_037617)	promoter-TSS (NR_037617)	-14	NR_037617	76954	Mm.252009	NM_029811	ENSMUSG00000031024	St5	2010004M01Rik|2610305K15Rik	suppression of tumorigenicity 5	protein-coding
mm_37049.1	chr4	116017855	116017863	-	1	NA	promoter-TSS (NM_010173)	promoter-TSS (NM_010173)	43	NM_010173	14073	Mm.256025	NM_010173	ENSMUSG00000034171	Faah	AW412498	fatty acid amide hydrolase	protein-coding
mm_74511.1	chr8	8667129	8667136	-	1	NA	3' UTR (NM_176849, exon 4 of 4)	3' UTR (NM_176849, exon 4 of 4)	-6359	NM_010111	13642	Mm.209813	NM_010111	ENSMUSG00000001300	Efnb2	ELF-2|Epl5|Eplg5|Htk-L|LERK-5|Lerk5|NLERK-1	ephrin B2	protein-coding
mm_15490.1	chr2	157566621	157566641	+	1	NA	promoter-TSS (NM_016916)	promoter-TSS (NM_016916)	-270	NM_016916	53619	Mm.480461	NM_016916	ENSMUSG00000067787	Blcap	AI462828|Bc10	bladder cancer associated protein	protein-coding
mm_77776.1	chr9	3017526	3017543	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	21209	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_165694.1	chr3	93445124	93445126	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	2795	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_152841.1	chr19	23448333	23448350	-	1	NA	promoter-TSS (NM_174857)	promoter-TSS (NM_174857)	-19	NM_174857	71738	Mm.50841	NM_174857	ENSMUSG00000033207	Mamdc2	1200015L10Rik|AI591564|mamcan	MAM domain containing 2	protein-coding
mm_161370.1	chr14	64455962	64455962	-	1	NA	promoter-TSS (NM_026322)	promoter-TSS (NM_026322)	-59	NM_026322	110265	Mm.26713	NM_026322	ENSMUSG00000054733	Msra	2310045J23Rik|6530413P12Rik|MSR-A	methionine sulfoxide reductase A	protein-coding
mm_161071.1	chr12	76710545	76710545	-	1	NA	promoter-TSS (NM_013675)	promoter-TSS (NM_013675)	2	NM_013675	20741	Mm.32881	NM_013675	ENSMUSG00000021061	Sptb	AI842465|D330027P03Rik|Gm1301|Spnb-1|Spnb1|ja|jaundiced|mKIAA4219	spectrin beta, erythrocytic	protein-coding
mm_74231.1	chr8	124271889	124271917	+	1	NA	intron (NM_139272, intron 1 of 15)	intron (NM_139272, intron 1 of 15)	40509	NM_139272	108148	Mm.33808	NM_139272	ENSMUSG00000089704	Galnt2	AI480629	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2	protein-coding
mm_100489.1	chr11	120366463	120366504	+	1	NA	intron (NM_172802, intron 1 of 4)	intron (NM_172802, intron 1 of 4)	4949	NM_172802	238021	Mm.481403	NM_172802	ENSMUSG00000025380	Fscn2	A930022G03|Ahl8|C630046B20Rik	fascin actin-bundling protein 2	protein-coding
mm_29206.1	chr3	106788569	106788579	-	1	NA	intron (NM_007651, intron 1 of 7)	intron (NM_007651, intron 1 of 7)	1575	NM_007651	12508	Mm.316861	NM_007651	ENSMUSG00000040747	Cd53	AI323659|Ox-44|Tspan25	CD53 antigen	protein-coding
mm_73739.1	chr8	114133636	114133662	+	1	NA	promoter-TSS (NM_024446)	promoter-TSS (NM_024446)	75	NM_024437	67528	Mm.27889	NM_024437	ENSMUSG00000031767	Nudt7	1300007B24Rik|2210404C19Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 7	protein-coding
mm_53853.1	chr6	149167899	149167921	+	1	NA	intron (NM_001113424, intron 5 of 6)	MLTR12|LTR|ERV1	20802	NM_001113424	232566	Mm.209147	NM_001113424	ENSMUSG00000068250	Amn1	5830467E07Rik|A230083D09|C730024G19Rik	antagonist of mitotic exit network 1	protein-coding
mm_24357.1	chr3	90062782	90062836	+	1	NA	promoter-TSS (NM_028567)	promoter-TSS (NM_028567)	13	NM_028567	73545	Mm.482512	NM_028567	ENSMUSG00000027942	1700094D03Rik	-	RIKEN cDNA 1700094D03 gene	protein-coding
mm_91285.1	chr10	24787768	24787776	-	1	NA	exon (NM_134005, exon 18 of 25)	exon (NM_134005, exon 18 of 25)	48423	NM_134005	209558	Mm.338425	NM_134005	ENSMUSG00000019989	Enpp3	AI876438|CD203c	ectonucleotide pyrophosphatase/phosphodiesterase 3	protein-coding
mm_93605.1	chr10	117234056	117234058	-	1	NA	3' UTR (NM_029906, exon 4 of 4)	3' UTR (NM_029906, exon 4 of 4)	4624	NM_029906	77397	Mm.118350	NM_029906	ENSMUSG00000020177	9530003J23Rik	Lyzf1	RIKEN cDNA 9530003J23 gene	protein-coding
mm_82428.1	chr9	14904724	14904734	-	1	NA	promoter-TSS (NM_176807)	promoter-TSS (NM_176807)	-778	NM_022888	64931	Mm.86738	NM_022888	ENSMUSG00000031933	Izumo1r	0910001L11Rik|C86255|Folbp3|Folr4|Juno	IZUMO1 receptor, JUNO	protein-coding
mm_70194.1	chr7	144449768	144449785	-	1	NA	intron (NM_001252572, intron 10 of 16)	intron (NM_001252572, intron 10 of 16)	-6343	NR_037302	100499519		NR_037302	ENSMUSG00000093912	Mir3470b	mmu-mir-3470b	microRNA 3470b	ncRNA
mm_13891.1	chr2	120404717	120404746	+	1	NA	promoter-TSS (NM_173734)	promoter-TSS (NM_173734)	-615	NM_001110496	211499	Mm.260712	NM_173734	ENSMUSG00000033808	Tmem87a	A930025J12Rik	transmembrane protein 87A	protein-coding
mm_27186.1	chr3	34650715	34650720	-	1	NA	exon (NM_011443, exon 1 of 1)	exon (NM_011443, exon 1 of 1)	722	NM_011443	20674	Mm.65396	NM_011443	ENSMUSG00000074637	Sox2	Sox-2|lcc|ysb	SRY (sex determining region Y)-box 2	protein-coding
mm_161856.1	chr18	20376792	20376792	+	1	NA	promoter-TSS (NM_181682)	promoter-TSS (NM_181682)	63	NM_181682	225256	Mm.269128	NM_181682	ENSMUSG00000061928	Dsg1b	Dsg5|dsg1-beta	desmoglein 1 beta	protein-coding
mm_122644.1	chr14	51773579	51773596	-	1	NA	promoter-TSS (NM_177544)	promoter-TSS (NM_177544)	3	NM_177544	219033	Mm.343899	NM_177544	ENSMUSG00000060615	Ang4	Raa4|Rnase5d	angiogenin, ribonuclease A family, member 4	protein-coding
mm_60878.1	chr7	46099038	46099079	+	1	NA	exon (NM_001204411, exon 2 of 2)	exon (NM_001204411, exon 2 of 2)	1179	NM_010602	16514	Mm.333863	NM_010602	ENSMUSG00000096146	Kcnj11	Kir6.2|mBIR	potassium inwardly rectifying channel, subfamily J, member 11	protein-coding
mm_165235.1	chr2	60284228	60284235	-	1	NA	5' UTR (NM_025422, exon 1 of 5)	5' UTR (NM_025422, exon 1 of 5)	253	NM_025422	66205	Mm.227281	NM_025422	ENSMUSG00000060703	Cd302	1110055L24Rik|AI159627	CD302 antigen	protein-coding
mm_59570.1	chr7	28103936	28103946	+	1	NA	exon (NM_001122603, exon 13 of 20)	exon (NM_001122603, exon 13 of 20)	-25525	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_124883.1	chr15	10249593	10249606	+	1	NA	intron (NM_001253781, intron 1 of 9)	intron (NM_001253781, intron 1 of 9)	25693	NM_001253781	19116	Mm.10516	NM_011169	ENSMUSG00000005268	Prlr	AI987712|Pr-1|Pr-3|Prlr-rs1	prolactin receptor	protein-coding
mm_82374.1	chr9	14615419	14615425	-	1	NA	promoter-TSS (NM_001081395)	promoter-TSS (NM_001081395)	-422	NM_001081395	75723	Mm.159552	NM_001081395	ENSMUSG00000013076	Amotl1	2310010G08Rik|2310067L22Rik|4932416D09Rik|JEAP|mFLJ00155	angiomotin-like 1	protein-coding
mm_33671.1	chr4	133192089	133192117	+	1	NA	intron (NM_153423, intron 6 of 8)	intron (NM_153423, intron 6 of 8)	-3552	NR_105984	102466215		NR_105984	ENSMUSG00000099202	Mir7017	Gm27945|mmu-mir-7017	microRNA 7017	ncRNA
mm_116428.1	chr13	41847548	41847561	-	1	NA	promoter-TSS (NM_001145875)	promoter-TSS (NM_001145875)	62	NM_001145875	109254	Mm.25195	NM_175417	ENSMUSG00000058022	Adtrp	9530008L14Rik	androgen dependent TFPI regulating protein	protein-coding
mm_156279.1	chrX	136837051	136837064	+	1	NA	3' UTR (NM_011123, exon 7 of 7)	3' UTR (NM_011123, exon 7 of 7)	14311	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_122345.1	chr14	37581837	37581841	-	1	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	-446517	NM_078478	66092	Mm.182912	NM_078478	ENSMUSG00000041028	Ghitm	1010001P14Rik|C77840|MICS1|PTD010|Tmbim5	growth hormone inducible transmembrane protein	protein-coding
mm_70201.1	chr7	144582458	144582474	-	1	NA	promoter-TSS (NM_010175)	promoter-TSS (NM_010175)	-30	NM_010175	14082	Mm.5126	NM_010175	ENSMUSG00000031077	Fadd	Mort1/FADD	Fas (TNFRSF6)-associated via death domain	protein-coding
mm_32177.1	chr4	100776705	100776721	+	1	NA	promoter-TSS (NM_198037)	promoter-TSS (NM_198037)	34	NM_198037	320508	Mm.151962	NM_198037	ENSMUSG00000028532	Cachd1	1190007F10Rik|AI852726|B430218L07Rik|Vwcd1|mKIAA1573	cache domain containing 1	protein-coding
mm_61659.1	chr7	80628925	80628937	+	1	NA	intron (NM_173863, intron 3 of 14)	intron (NM_173863, intron 3 of 14)	-7086	NR_040343	100504375	Mm.322881	NR_040343	ENSMUSG00000084821	Gm15880	OTTMUSG00000027171	predicted gene 15880	ncRNA
mm_98393.1	chr11	94214828	94214838	+	1	NA	3' UTR (NM_009427, exon 2 of 2)	3' UTR (NM_009427, exon 2 of 2)	3379	NM_009427	22057	Mm.259673	NM_009427	ENSMUSG00000037573	Tob1	Tob|Trob	transducer of ErbB-2.1	protein-coding
mm_81502.1	chr9	110034581	110034597	+	1	NA	exon (NM_008633, exon 7 of 19)	exon (NM_008633, exon 7 of 19)	-17432	NM_001311163	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_160063.1	chr7	5013237	5013237	-	1	NA	promoter-TSS (NM_001110330)	promoter-TSS (NM_001110330)	5	NM_001110330	23877	Mm.38911	NM_011813	ENSMUSG00000061374	Fiz1	AI790204|mFLJ00416	Flt3 interacting zinc finger protein 1	protein-coding
mm_145253.1	chr18	52528646	52528664	+	1	NA	intron (NM_001286181, intron 2 of 7)	CpG	1066	NM_001286181	16948	Mm.172	NM_010728	ENSMUSG00000024529	Lox	AI893619|TSC-160|rrg	lysyl oxidase	protein-coding
mm_9591.1	chr1	174921722	174921724	-	1	NA	promoter-TSS (NM_011825)	promoter-TSS (NM_011825)	96	NM_011825	23893	Mm.25760	NM_011825	ENSMUSG00000050069	Grem2	Gremlin2|Prdc	gremlin 2, DAN family BMP antagonist	protein-coding
mm_128057.1	chr15	26402285	26402303	-	1	NA	intron (NM_177597, intron 3 of 3)	intron (NM_177597, intron 3 of 3)	93246	NM_001310774	211147	Mm.54257	NM_177597	ENSMUSG00000022269	March11	9630025C22	membrane-associated ring finger (C3HC4) 11	protein-coding
mm_41345.1	chr5	90501402	90501421	+	1	NA	exon (NM_007423, exon 8 of 15)	exon (NM_007423, exon 8 of 15)	10697	NM_007423	11576	Mm.358570	NM_007423	ENSMUSG00000054932	Afp	-	alpha fetoprotein	protein-coding
mm_99634.1	chr11	105181547	105181598	+	1	NA	promoter-TSS (NR_027956)	promoter-TSS (NR_027956)	45	NM_001294329	24086	Mm.126976	NM_011903	ENSMUSG00000020694	Tlk2	4933403M19Rik|PKU-alpha|PKUalpha|Tlk	tousled-like kinase 2 (Arabidopsis)	protein-coding
mm_171133.1	chr3	148901521	148901521	+	1	NA	intron (NM_001081298, intron 1 of 23)	intron (NM_001081298, intron 1 of 23)	53114	NM_001081298	99633	Mm.9776	NM_001081298	ENSMUSG00000028184	Adgrl2	AI450192|CIRL-2|Gm619|Lec1|Lphh1|Lphn2|mKIAA0786	adhesion G protein-coupled receptor L2	protein-coding
mm_127536.1	chr15	102104362	102104373	+	1	NA	intron (NM_153533, intron 1 of 28)	intron (NM_153533, intron 1 of 28)	1379	NM_153533	209039	Mm.29389	NM_153533	ENSMUSG00000037003	Tns2	C1-ten|Tenc1|nep|nph	tensin 2	protein-coding
mm_171562.1	chr4	147230365	147230372	+	1	NA	intron (NM_001039209, intron 1 of 2)	intron (NM_001039209, intron 1 of 2)	54502	NM_001039209	195531	Mm.270762	NM_001039209	ENSMUSG00000078496	Zfp982	Gm13152|OTTMUSG00000010671	zinc finger protein 982	protein-coding
mm_112045.1	chr12	111672084	111672089	-	1	NA	intron (NM_021273, intron 1 of 7)	CpG-3541	252	NM_021273	12709	Mm.16831	NM_021273	ENSMUSG00000001270	Ckb	B-CK|Bck|Ck-3|Ck3|Ckbb	creatine kinase, brain	protein-coding
mm_88665.1	chr10	80016762	80016768	+	1	NA	promoter-TSS (NM_001142701)	promoter-TSS (NM_001142701)	93	NM_001142701	70719	Mm.243954	NM_027521	ENSMUSG00000035697	Hmha1	6330406L22Rik|AW539505|Ha-1	histocompatibility (minor) HA-1	protein-coding
mm_82629.1	chr9	21927337	21927385	-	1	NA	promoter-TSS (NM_001253869)	promoter-TSS (NM_001253869)	-73	NM_001253869	235043	Mm.253329	NM_178577	ENSMUSG00000040883	Tmem205	-	transmembrane protein 205	protein-coding
mm_14333.1	chr2	129592671	129592681	+	1	NA	promoter-TSS (NM_001291022)	promoter-TSS (NM_001291022)	-163	NM_001291020	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_149803.1	chr19	23687708	23687724	+	1	NA	intron (NM_028208, intron 1 of 6)	CpG	316	NM_028208	72351	Mm.474795	NM_028208	ENSMUSG00000074925	Ptar1	1700084D09Rik|2010013L17Rik|4930428J16Rik|AI449677	protein prenyltransferase alpha subunit repeat containing 1	protein-coding
mm_97587.1	chr11	78945719	78945752	+	1	NA	exon (NM_010927, exon 14 of 27)	exon (NM_010927, exon 14 of 27)	20444	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_163143.1	chr11	80504688	80504691	+	1	NA	intron (NM_177390, intron 21 of 21)	intron (NM_177390, intron 21 of 21)	4417	NR_126552	77417	Mm.437510	NR_126552	ENSMUSG00000085078	C030013C21Rik	-	RIKEN cDNA C030013C21 gene	ncRNA
mm_1920.1	chr1	86026427	86026448	+	1	NA	exon (NM_001122732, exon 3 of 4)	exon (NM_001122732, exon 3 of 4)	4495	NM_027029	70060	Mm.196313	NM_027029	ENSMUSG00000026226	Spata3	1700011N12Rik|1700029H01Rik|4930424D10Rik|Mtsarg1|Tsarg1	spermatogenesis associated 3	protein-coding
mm_159982.1	chr6	113670021	113670021	+	1	NA	intron (NM_172161, intron 3 of 12)	intron (NM_172161, intron 3 of 12)	-27029	NM_001347356	381801	Mm.333322	NM_001033463	ENSMUSG00000056952	Tatdn2	AI646012|mKIAA0218	TatD DNase domain containing 2	protein-coding
mm_27163.1	chr3	33143172	33143186	-	1	NA	promoter-TSS (NM_001163516)	promoter-TSS (NM_001163516)	12	NM_001163516	58869	Mm.151332	NM_021483	ENSMUSG00000027674	Pex5l	1700016J08Rik|PXR2|Pex2|TRIP8b|pex5Rp	peroxisomal biogenesis factor 5-like	protein-coding
mm_164871.1	chr18	57405299	57405326	+	1	NA	Intergenic	Intergenic	50579	NM_028447	73137	Mm.29889	NM_028447	ENSMUSG00000024594	Prrc1	1190002C06Rik|2310058D16Rik|3110038B19Rik|9430085A19Rik	proline-rich coiled-coil 1	protein-coding
mm_7426.1	chr1	119837089	119837139	-	1	NA	promoter-TSS (NM_019933)	promoter-TSS (NM_019933)	-43	NM_019933	19258	Mm.458796	NM_019933	ENSMUSG00000026384	Ptpn4	PTPMEG|Ptn4|TEP|TEP/mPTPMEG|hPTP-MEG	protein tyrosine phosphatase, non-receptor type 4	protein-coding
mm_50987.1	chr6	63255936	63255954	+	1	NA	promoter-TSS (NM_008167)	promoter-TSS (NM_008167)	-912	NM_008167	14804	Mm.439651	NM_008167	ENSMUSG00000071424	Grid2	B230104L07Rik|GluD2|GluRdelta2|Lc|Lc<J>|MMS10-AC|Ms10ac|cpr|ho|nmf408|tpr	glutamate receptor, ionotropic, delta 2	protein-coding
mm_101782.1	chr11	45887509	45887531	-	1	NA	exon (NM_001045520, exon 5 of 12)	exon (NM_001045520, exon 5 of 12)	35556	NM_001045520	216705	Mm.169673	NM_001045520	ENSMUSG00000006169	Clint1	AI642036|AW537616|C530049I24Rik|Enth|Epn4|F630206G17Rik|mKIAA0171	clathrin interactor 1	protein-coding
mm_144165.1	chr18	6136421	6136427	+	1	NA	promoter-TSS (NM_001039692)	promoter-TSS (NM_001039692)	-326	NM_001039692	75415	Mm.239675	NM_029277	ENSMUSG00000041225	Arhgap12	2810011M08Rik	Rho GTPase activating protein 12	protein-coding
mm_74664.1	chr8	13594955	13594983	-	1	NA	intron (NM_009025, intron 7 of 23)	intron (NM_009025, intron 7 of 23)	-32508	NM_001080781	66501	Mm.46136	NM_025601	ENSMUSG00000031452	1700029H14Rik	-	RIKEN cDNA 1700029H14 gene	protein-coding
mm_35208.1	chr4	19570074	19570117	-	1	NA	promoter-TSS (NM_027769)	promoter-TSS (NM_027769)	9	NM_027769	70568	Mm.38390	NM_027769	ENSMUSG00000028228	Cpne3	5430428M23Rik|5730450C07Rik|C85108|CPN3	copine III	protein-coding
mm_167313.1	chr8	61902752	61902762	-	1	NA	promoter-TSS (NM_001293772)	promoter-TSS (NM_001293772)	-63	NM_001293772	72333	Mm.29933	NM_001081390	ENSMUSG00000058056	Palld	2410003B16Rik|6030492A02	palladin, cytoskeletal associated protein	protein-coding
mm_101077.1	chr11	11686706	11686736	-	1	NA	intron (NM_001025597, intron 1 of 7)	intron (NM_001025597, intron 1 of 7)	796	NM_001025597	22778	Mm.103545	NM_009578	ENSMUSG00000018654	Ikzf1	5832432G11Rik|Ikaros|LyF-1|Zfpn1a1|Znfn1a1|hlk-1|mKIAA4227	IKAROS family zinc finger 1	protein-coding
mm_165325.1	chr2	110422101	110422112	+	1	NA	Intergenic	(TTA)n|Simple_repeat|Simple_repeat	-59113	NM_026271	67606	Mm.291809	NM_026271	ENSMUSG00000074971	Fibin	1110018M03Rik	fin bud initiation factor homolog (zebrafish)	protein-coding
mm_122114.1	chr14	31001011	31001037	-	1	NA	promoter-TSS (NM_001165930)	promoter-TSS (NM_001165930)	-369	NM_001165930	76485	Mm.8766	NM_029626	ENSMUSG00000021916	Glt8d1	2410004H05Rik|5430414N14Rik|AI450005	glycosyltransferase 8 domain containing 1	protein-coding
mm_164330.1	chr16	9967490	9967501	-	1	NA	intron (NM_008170, intron 1 of 11)	ID4_|SINE|ID	25038	NM_008170	14811	Mm.2953	NM_008170	ENSMUSG00000059003	Grin2a	GluN2A|NMDAR2A|NR2A	glutamate receptor, ionotropic, NMDA2A (epsilon 1)	protein-coding
mm_15241.1	chr2	154657114	154657134	+	1	NA	promoter-TSS (NM_029362)	promoter-TSS (NM_029362)	98	NM_029362	75608	Mm.262480	NM_029362	ENSMUSG00000038467	Chmp4b	2010012F05Rik|C76846|Snf7-2	charged multivesicular body protein 4B	protein-coding
mm_80052.1	chr9	69314126	69314129	+	1	NA	intron (NM_001289916, intron 1 of 9)	intron (NM_001289916, intron 1 of 9)	24286	NM_001289916	19883	Mm.378450	NM_013646	ENSMUSG00000032238	Rora	9530021D13Rik|Nr1f1|ROR1|ROR2|ROR3|nmf267|sg|staggerer|tmgc26	RAR-related orphan receptor alpha	protein-coding
mm_125840.1	chr15	74958657	74958685	+	1	NA	exon (NM_001164036, exon 4 of 4)	exon (NM_001164036, exon 4 of 4)	3565	NM_001164040	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_105653.1	chr11	107212276	107212279	-	1	NA	3' UTR (NM_145823, exon 10 of 10)	3' UTR (NM_145823, exon 10 of 10)	-22896	NM_001161329	68979	Mm.294617	NM_133702	ENSMUSG00000018433	Nol11	1500002M01Rik|AU015220|AU019874	nucleolar protein 11	protein-coding
mm_172403.1	chr7	144939799	144939800	-	1	NA	5' UTR (NM_007631, exon 1 of 5)	5' UTR (NM_007631, exon 1 of 5)	126	NM_007631	12443	Mm.273049	NM_007631	ENSMUSG00000070348	Ccnd1	AI327039|CycD1|Cyl-1|PRAD1|bcl-1|cD1	cyclin D1	protein-coding
mm_94663.1	chr11	17200260	17200266	+	1	NA	3' UTR (NM_024459, exon 6 of 6)	3' UTR (NM_024459, exon 6 of 6)	11326	NM_025443	66249	Mm.27831	NM_025443	ENSMUSG00000020116	Pno1	1810003N24Rik|AA407421|AU015468|AU019495|AU042323|Emi3|Imi3	partner of NOB1 homolog	protein-coding
mm_47457.1	chr5	123637839	123637847	-	1	NA	intron (NM_001347468, intron 8 of 24)	intron (NM_001347468, intron 8 of 24)	46518	NM_019765	56430	Mm.241109	NM_019765	ENSMUSG00000049550	Clip1	1110007I12Rik|4631429H07Rik|AV017631|C81039|CLIP-170|CLIP170|CYLN1|Clip50|Rsn|mKIAA4046|restin	CAP-GLY domain containing linker protein 1	protein-coding
mm_116550.1	chr13	46696852	46696898	-	1	NA	intron (NM_175749, intron 14 of 21)	intron (NM_175749, intron 14 of 21)	27353	NM_001033192	97863	Mm.275934	NM_001033192	ENSMUSG00000069237	Fam8a1	C78339	family with sequence similarity 8, member A1	protein-coding
mm_1235.1	chr1	62795544	62795574	+	1	NA	promoter-TSS (NR_040601)	promoter-TSS (NR_040601)	-827	NR_040601	74992	Mm.401979	NR_040601		4930487H11Rik	-	RIKEN cDNA 4930487H11 gene	ncRNA
mm_113363.1	chr13	32965304	32965317	+	1	NA	promoter-TSS (NM_011454)	promoter-TSS (NM_011454)	-203	NM_011454	20708	Mm.36526	NM_011454	ENSMUSG00000042842	Serpinb6b	NK13|Spi12|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 6b	protein-coding
mm_160808.1	chr11	16508457	16508457	-	1	NA	promoter-TSS (NM_011343)	promoter-TSS (NM_011343)	27	NM_011343	20335	Mm.325350	NM_011343	ENSMUSG00000078974	Sec61g	-	SEC61, gamma subunit	protein-coding
mm_76115.1	chr8	80788936	80788947	-	1	NA	exon (NM_001301298, exon 4 of 11)	exon (NM_001301298, exon 4 of 11)	-49482	NM_053124	93762	Mm.246803	NM_053124	ENSMUSG00000031715	Smarca5	4933427E24Rik|D030040M08Rik|D330027N15Rik|MommeD4|Snf2h	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5	protein-coding
mm_154139.1	chr19	57360809	57360822	-	1	NA	promoter-TSS (NM_145505)	promoter-TSS (NM_145505)	84	NR_040316	320879	Mm.375089	NR_040316	ENSMUSG00000097785	B230217O12Rik	-	RIKEN cDNA B230217O12 gene	ncRNA
mm_87839.1	chr10	60399750	60399772	+	1	NA	promoter-TSS (NM_001164374)	promoter-TSS (NM_001164374)	35	NM_001164374	100302688	Mm.444135	NM_001164374	ENSMUSG00000090439	Gm17455	-	predicted gene, 17455	protein-coding
mm_88343.1	chr10	75835052	75835054	+	1	NA	promoter-TSS (NM_010361)	promoter-TSS (NM_010361)	-172	NM_010361	14872	Mm.24118	NM_010361	ENSMUSG00000033318	Gstt2	AI266894|Yrs|mGSTT2	glutathione S-transferase, theta 2	protein-coding
mm_42839.1	chr5	122105887	122105893	+	1	NA	intron (NM_010861, intron 6 of 6)	B1_Mur4|SINE|Alu	4910	NM_010861	17906	Mm.1529	NM_010861	ENSMUSG00000013936	Myl2	MLC-2|MLC-2s/v|MLC-2v|Mlc2v|Mylpc	myosin, light polypeptide 2, regulatory, cardiac, slow	protein-coding
mm_9872.1	chr1	185085930	185085942	-	1	NA	Intergenic	ORR1C2|LTR|ERVL-MaLR	-86387	NM_145515	226778	Mm.7445	NM_145515	ENSMUSG00000026620	Mark1	AW491150|B930025N23Rik|Emk3|Par-1c|mKIAA1477|mPar-1c	MAP/microtubule affinity regulating kinase 1	protein-coding
mm_23958.1	chr3	84952168	84952186	+	1	NA	promoter-TSS (NM_080428)	promoter-TSS (NM_080428)	-34	NM_080428	50754	Mm.196475	NM_080428	ENSMUSG00000028086	Fbxw7	1110001A17Rik|AGO|Cdc4|Fbw7|Fbwd6|Fbx30|Fbxo30|Fbxw6|SEL-10	F-box and WD-40 domain protein 7	protein-coding
mm_105417.1	chr11	103686761	103686770	-	1	NA	intron (NM_019650, intron 3 of 5)	intron (NM_019650, intron 3 of 5)	10945	NM_019650	56494	Mm.195451	NM_019650	ENSMUSG00000020946	Gosr2	2310032N09Rik|C76855|Gs27|SNARE|membrin	golgi SNAP receptor complex member 2	protein-coding
mm_160031.1	chr6	132210540	132210540	-	1	NA	promoter-TSS (NM_198669)	promoter-TSS (NM_198669)	-19	NM_198669	381833	Mm.7982	NM_198669	ENSMUSG00000067543	Prb1	BC011176|Prpg2	proline-rich protein BstNI subfamily 1	protein-coding
mm_30090.1	chr3	138186742	138186748	-	1	NA	promoter-TSS (NM_001163386)	promoter-TSS (NM_001163386)	-32	NM_001163386	67741	Mm.383221	NM_001163385	ENSMUSG00000012042	4930579F01Rik	-	RIKEN cDNA 4930579F01 gene	protein-coding
mm_145524.1	chr18	60560815	60560818	+	1	NA	promoter-TSS (NM_025776)	promoter-TSS (NM_025776)	30	NM_025776	66810	Mm.275106	NM_025776	ENSMUSG00000024604	Rbm22	8430430L24Rik	RNA binding motif protein 22	protein-coding
mm_161965.1	chr19	8819548	8819548	+	1	NA	promoter-TSS (NM_027412)	promoter-TSS (NM_027412)	147	NM_001081196	68693	Mm.476519	NM_001081196	ENSMUSG00000071659	Hnrnpul2	1110031M08Rik|AI465155|Hnrpul2	heterogeneous nuclear ribonucleoprotein U-like 2	protein-coding
mm_151880.1	chr19	5798506	5798516	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	-2530	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_88515.1	chr10	78049880	78049896	+	1	NA	promoter-TSS (NM_019448)	promoter-TSS (NM_019448)	46	NM_019448	54427	Mm.13433	NM_019448	ENSMUSG00000000730	Dnmt3l	D6Ertd14e|ecat7	DNA (cytosine-5-)-methyltransferase 3-like	protein-coding
mm_171605.1	chr4	149142590	149142602	-	1	NA	Intergenic	Intergenic	-4996	NM_027263	69928	Mm.260893	NM_027263	ENSMUSG00000073705	Apitd1	2610040C18Rik|2810407L01Rik|CENP-S	apoptosis-inducing, TAF9-like domain 1	protein-coding
mm_33566.1	chr4	131923428	131923431	+	1	NA	TTS (NM_001128607)	TTS (NM_001128607)	1658	NM_001201367	623230	Mm.421179	NM_001201367	ENSMUSG00000070720	Tmem200b	EG623230	transmembrane protein 200B	protein-coding
mm_165538.1	chr2	180589767	180589787	+	1	NA	intron (NM_031373, intron 1 of 6)	CpG	370	NM_031373	72075	Mm.250418	NM_031373	ENSMUSG00000049401	Ogfr	2010013E17Rik	opioid growth factor receptor	protein-coding
mm_157458.1	chrX	43429029	43429050	-	1	NA	Intergenic	Intergenic	-154255	NM_011855	23963	Mm.327698	NM_011855	ENSMUSG00000016150	Tenm1	Odz1|Odz2|TCAP-1|Ten-m1|ten-1	teneurin transmembrane protein 1	protein-coding
mm_16058.1	chr2	167778158	167778169	+	1	NA	Intergenic	Intergenic	86986	NR_015500	329562	Mm.123101	NM_177851	ENSMUSG00000006462	A530013C23Rik	-	RIKEN cDNA A530013C23 gene	ncRNA
mm_148519.1	chr19	4295624	4295629	+	1	NA	intron (NM_001290818, intron 1 of 20)	intron (NM_001290818, intron 1 of 20)	10596	NM_130863	110355	Mm.254144	NM_130863	ENSMUSG00000024858	Grk2	Adrbk-1|Adrbk1|Bark-1|beta ARK|betaARK1	G protein-coupled receptor kinase 2	protein-coding
mm_122025.1	chr14	28969467	28969476	-	1	NA	intron (NM_009785, intron 30 of 37)	intron (NM_009785, intron 30 of 37)	-48737	NM_176920	319476	Mm.95780	NM_176920	ENSMUSG00000045776	Lrtm1	A930016D02Rik	leucine-rich repeats and transmembrane domains 1	protein-coding
mm_24068.1	chr3	87919491	87919497	+	1	NA	promoter-TSS (NM_026591)	promoter-TSS (NM_026591)	-50	NM_026591	67707	Mm.393802	NM_026591	ENSMUSG00000019710	Mrpl24	2010005E08Rik|2810470K06Rik|6720473G22Rik|AA407670	mitochondrial ribosomal protein L24	protein-coding
mm_161274.1	chr14	11125677	11125677	-	1	NA	intron (NM_010210, intron 1 of 8)	intron (NM_010210, intron 1 of 8)	36358	NM_010210	14198	Mm.397619	NM_010210	ENSMUSG00000060579	Fhit	AW045638|Fra14A2	fragile histidine triad gene	protein-coding
mm_120284.1	chr14	63133302	63133312	+	1	NA	intron (NM_007798, intron 1 of 9)	intron (NM_007798, intron 1 of 9)	10845	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_108699.1	chr12	86948881	86948883	+	1	NA	intron (NM_001289432, intron 1 of 4)	intron (NM_001289432, intron 1 of 4)	1539	NM_001289432	217732	Mm.22337	NM_173735	ENSMUSG00000034157	Cipc	2310044G17Rik|AI842544|AI853744|Kiaa1737|mKIAA1737	CLOCK interacting protein, circadian	protein-coding
mm_159497.1	chr4	43584330	43584330	-	1	NA	5' UTR (NM_001099314, exon 1 of 3)	5' UTR (NM_001099314, exon 1 of 3)	164	NM_001099314	100039672	Mm.415110	NM_001099314	ENSMUSG00000078719	Msmp	OTTMUSG00000007017|Psmp	microseminoprotein, prostate associated	protein-coding
mm_70548.1	chr8	13055978	13055988	+	1	NA	3' UTR (NM_007972, exon 9 of 9)	3' UTR (NM_007972, exon 9 of 9)	-4925	NM_025834	66901	Mm.441140	NM_025834	ENSMUSG00000031445	Proz	1300015B06Rik	protein Z, vitamin K-dependent plasma glycoprotein	protein-coding
mm_36242.1	chr4	63172119	63172139	-	1	NA	promoter-TSS (NM_010616)	promoter-TSS (NM_010616)	2	NM_010616	16552	Mm.216057	NM_010616	ENSMUSG00000028357	Kif12	-	kinesin family member 12	protein-coding
mm_105407.1	chr11	103504956	103504966	-	1	NA	Intergenic	Intergenic	-92297	NM_183034	353047	Mm.18556	NM_183034	ENSMUSG00000034247	Plekhm1	AP162|B2|BC038943|D330036J23Rik	pleckstrin homology domain containing, family M (with RUN domain) member 1	protein-coding
mm_110488.1	chr12	51994093	51994093	-	1	NA	intron (NM_001347404, intron 3 of 3)	intron (NM_001347404, intron 3 of 3)	12414	NM_029545	328092	Mm.2821	NM_029545	ENSMUSG00000020956	Dtd2	4930578F06Rik|6530401N04Rik|B830049N13Rik	D-tyrosyl-tRNA deacylase 2	protein-coding
mm_44764.1	chr5	31647201	31647229	-	1	NA	intron (NM_153196, intron 7 of 7)	intron (NM_153196, intron 7 of 7)	20125	NR_105859	102466677		NR_105859	ENSMUSG00000099301	Mir3473e	Gm27422|mmu-mir-3473e	microRNA 3473e	ncRNA
mm_82243.1	chr9	4472211	4472228	-	1	NA	intron (NM_019691, intron 10 of 16)	intron (NM_019691, intron 10 of 16)	88682	NM_145609	78100	Mm.206549	NM_145609	ENSMUSG00000041124	Msantd4	8430410K20Rik|Mysantd4	Myb/SANT-like DNA-binding domain containing 4 with coiled-coils	protein-coding
mm_51581.1	chr6	83775639	83775651	+	1	NA	intron (NM_009357, intron 1 of 5)	CpG	167	NM_009357	21766	Mm.28371	NM_009357	ENSMUSG00000014748	Tex261	3110001O07Rik|AA409339|AI480706|AL033351|TEG-261	testis expressed gene 261	protein-coding
mm_50015.1	chr6	41113517	41113547	+	1	NA	Intergenic	Intergenic	-78023	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_95022.1	chr11	32001783	32001793	+	1	NA	exon (NM_008741, exon 2 of 5)	exon (NM_008741, exon 2 of 5)	511	NM_001290681	18197	Mm.3304	NM_008741	ENSMUSG00000020297	Nsg2	-	neuron specific gene family member 2	protein-coding
mm_53520.1	chr6	136501073	136501076	+	1	NA	Intergenic	MERV1_LTR|LTR|ERV1	-17777	NM_019426	54343	Mm.173271	NM_019426	ENSMUSG00000030213	Atf7ip	2610204M12Rik|AM|Mcaf1	activating transcription factor 7 interacting protein	protein-coding
mm_70083.1	chr7	142654043	142654053	-	1	NA	TTS (NR_030251)	TTS (NR_030251)	948	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_36475.1	chr4	82850699	82850706	-	1	NA	intron (NM_026647, intron 2 of 8)	intron (NM_026647, intron 2 of 8)	8959	NM_026647	68268	Mm.32047	NM_026647	ENSMUSG00000028403	Zdhhc21	9130404H11Rik|AL024349|D130004H04Rik|dep	zinc finger, DHHC domain containing 21	protein-coding
mm_130127.1	chr15	89841925	89841935	-	1	NA	promoter-TSS (NM_018803)	promoter-TSS (NM_018803)	-70	NM_018803	54526	Mm.261601	NM_018803	ENSMUSG00000063260	Syt10	-	synaptotagmin X	protein-coding
mm_76959.1	chr8	106059229	106059247	-	1	NA	promoter-TSS (NM_010901)	promoter-TSS (NM_010901)	-365	NM_010901	18021	Mm.383185	NM_010901	ENSMUSG00000031902	Nfatc3	C80703|D8Ertd281e|NFAT4|NFATx	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 3	protein-coding
mm_45299.1	chr5	65335582	65335592	-	1	NA	promoter-TSS (NM_011258)	promoter-TSS (NM_011258)	52	NM_011258	19687	Mm.148877	NM_011258	ENSMUSG00000029191	Rfc1	140kDa|Alp145|RFC140|Recc1	replication factor C (activator 1) 1	protein-coding
mm_98073.1	chr11	86212105	86212108	+	1	NA	TTS (NR_130958)	TTS (NR_130958)	10746	NR_130958	74038	Mm.171304	NR_130958	ENSMUSG00000085208	Brip1os	4632419I22Rik	BRCA1 interacting protein C-terminal helicase 1, opposite strand	ncRNA
mm_149917.1	chr19	26606737	26606809	+	1	NA	intron (NM_011416, intron 1 of 32)	CpG	1613	NM_011416	67155	Mm.342988	NM_011416	ENSMUSG00000024921	Smarca2	2610209L14Rik|SNF2alpha|Snf2l2|brahma|brm	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	protein-coding
mm_143399.1	chr17	70753272	70753293	-	1	NA	intron (NM_001347411, intron 9 of 14)	RMER10B|LTR|ERVL	93495	NM_001164077	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_155013.1	chrX	41414950	41414959	+	1	NA	intron (NR_104053, intron 2 of 16)	(TTTTTG)n|Simple_repeat|Simple_repeat	13425	NM_001290451	53623	Mm.327681	NM_016886	ENSMUSG00000001986	Gria3	2900064I19Rik|GluA3|GluR-C|GluR-K3|Glur-3|Glur3|Gluralpha3	glutamate receptor, ionotropic, AMPA3 (alpha 3)	protein-coding
mm_4911.1	chr1	190171086	190171087	+	1	NA	promoter-TSS (NM_008937)	promoter-TSS (NM_008937)	-406	NM_008937	19130	Mm.132579	NM_008937	ENSMUSG00000010175	Prox1	A230003G05Rik	prospero homeobox 1	protein-coding
mm_166944.1	chr7	43544419	43544437	-	1	NA	Intergenic	Lx4B|LINE|L1	-11257	NM_021293	12489	Mm.140157	NM_021293	ENSMUSG00000004609	Cd33	Siglec-3|gp67	CD33 antigen	protein-coding
mm_66454.1	chr7	44869773	44869783	-	1	NA	promoter-TSS (NM_133949)	promoter-TSS (NM_133949)	10	NM_133949	84113	Mm.42855	NM_133949	ENSMUSG00000038502	Ptov1	1110030G05Rik|AU041779|Gcap3	prostate tumor over expressed gene 1	protein-coding
mm_122128.1	chr14	31160036	31160074	-	1	NA	exon (NM_138672, exon 14 of 69)	exon (NM_138672, exon 14 of 69)	8586	NM_138672	192187	Mm.220821	NM_138672	ENSMUSG00000042286	Stab1	FEEL-1|FELE-1|MFEEL-1|MS-1|STAB-1|mKIAA0246	stabilin 1	protein-coding
mm_100637.1	chr11	121718577	121718601	+	1	NA	Intergenic	Intergenic	16162	NM_144797	210029	Mm.153566	NM_144797	ENSMUSG00000039208	Metrnl	9430048M07Rik|BC019776	meteorin, glial cell differentiation regulator-like	protein-coding
mm_93833.1	chr10	121586731	121586803	-	1	NA	promoter-TSS (NM_019786)	promoter-TSS (NM_019786)	27	NM_019786	56480	Mm.34580	NM_019786	ENSMUSG00000020115	Tbk1	1200008B05Rik|AI462036|AW048562	TANK-binding kinase 1	protein-coding
mm_171027.1	chr2	87906379	87906384	+	1	NA	Intergenic	Intergenic	-2707	NM_146647	258641	Mm.377608	NM_146647	ENSMUSG00000075146	Olfr1154	MOR173-2	olfactory receptor 1154	protein-coding
mm_144106.1	chr18	4165838	4165850	+	1	NA	promoter-TSS (NM_026092)	promoter-TSS (NM_026092)	12	NM_026092	67328	Mm.158148	NM_026092	ENSMUSG00000024233	Lyzl1	1700038F02Rik|Lyc2|Lyzd1	lysozyme-like 1	protein-coding
mm_66639.1	chr7	45575148	45575168	-	1	NA	promoter-TSS (NR_038166)	promoter-TSS (NR_038166)	18	NR_038166	71661	Mm.439894	NR_038165	ENSMUSG00000109644	0610005C13Rik	AI182092	RIKEN cDNA 0610005C13 gene	ncRNA
mm_47084.1	chr5	117115973	117116010	-	1	NA	promoter-TSS (NM_178622)	promoter-TSS (NM_178622)	2	NM_001122666	71954	Mm.34456	NM_178622	ENSMUSG00000066900	Suds3	2400003N08Rik|2410008L21Rik|AU067672|mSds3	suppressor of defective silencing 3 homolog (S. cerevisiae)	protein-coding
mm_46340.1	chr5	101851543	101851552	-	1	NA	intron (NM_172882, intron 59 of 66)	intron (NM_172882, intron 59 of 66)	86417	NM_173370	74596	Mm.46764	NM_173370	ENSMUSG00000029330	Cds1	4833409J18Rik|AI314024|AW125888	CDP-diacylglycerol synthase 1	protein-coding
mm_135493.1	chr16	46120192	46120211	-	1	NA	promoter-TSS (NM_032465)	promoter-TSS (NM_032465)	47	NM_032465	84544	Mm.29204	NM_032465	ENSMUSG00000022657	Cd96	1700109I12Rik|Tactile	CD96 antigen	protein-coding
mm_152973.1	chr19	29386951	29386961	-	1	NA	3' UTR (NM_021893, exon 7 of 7)	3' UTR (NM_021893, exon 7 of 7)	19518	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_81187.1	chr9	107539549	107539550	+	1	NA	TTS (NM_019704)	TTS (NM_019704)	2316	NM_019720	56368	Mm.24833	NM_019720	ENSMUSG00000037190	Cyb561d2	AW049681|Tsp10	cytochrome b-561 domain containing 2	protein-coding
mm_52748.1	chr6	120605718	120605727	+	1	NA	Intergenic	ID_B1|SINE|B4	50926	NR_045733	73505	Mm.416867	NR_045733		1700072O05Rik	-	RIKEN cDNA 1700072O05 gene	ncRNA
mm_995.1	chr1	58713205	58713217	+	1	NA	promoter-TSS (NM_207653)	promoter-TSS (NM_207653)	-75	NM_009805	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_139536.1	chr17	56709937	56709975	+	1	NA	intron (NR_045519, intron 14 of 16)	intron (NR_045519, intron 14 of 16)	6965	NM_178926	106639	Mm.37290	NM_178926	ENSMUSG00000054723	Vmac	AI662250	vimentin-type intermediate filament associated coiled-coil protein	protein-coding
mm_55255.1	chr6	52961724	52961739	-	1	NA	intron (NM_173406, intron 1 of 4)	intron (NM_173406, intron 1 of 4)	-52111	NM_001168277	231986	Mm.386865	NM_173406	ENSMUSG00000063568	Jazf1	AI591476|C820002C15|Jaz1|Tip27	JAZF zinc finger 1	protein-coding
mm_62065.1	chr7	92561485	92561537	+	1	NA	5' UTR (NM_025515, exon 1 of 9)	5' UTR (NM_025515, exon 1 of 9)	362	NM_001162918	66365	Mm.21173	NM_025515	ENSMUSG00000030613	Ccdc90b	2310015N07Rik|C86558	coiled-coil domain containing 90B	protein-coding
mm_47502.1	chr5	124034623	124034625	-	1	NA	Intergenic	Intergenic	-2364	NM_177876	330192	Mm.4079	NM_177876	ENSMUSG00000066278	Vps37b	2300007F24Rik|AI415429|BC026744	vacuolar protein sorting 37B	protein-coding
mm_28163.1	chr3	87832313	87832319	-	1	NA	Intergenic	MERVL_2A-int|LTR|ERVL	-14439	NM_001025571	27371	Mm.86361	NM_021309	ENSMUSG00000028071	Sh2d2a	Lad|Ribp|Tsad	SH2 domain containing 2A	protein-coding
mm_25305.1	chr3	105986156	105986162	+	1	NA	exon (NM_007696, exon 11 of 11)	exon (NM_007696, exon 11 of 11)	12357	NM_007696	12659	Mm.431947	NM_007696	ENSMUSG00000074340	Ovgp1	120kDa|AU016433|AU019448|Chit5|MOGP|OGP|muc9	oviductal glycoprotein 1	protein-coding
mm_115115.1	chr13	104157176	104157180	+	1	NA	intron (NM_001093760, intron 5 of 11)	RLTR13C2|LTR|ERVK	21288	NM_025879	66975	Mm.272541	NM_025879	ENSMUSG00000021711	Trappc13	2410002O22Rik|2610524F24Rik|AI451892|AU017229	trafficking protein particle complex 13	protein-coding
mm_22788.1	chr3	22081757	22081780	+	1	NA	intron (NM_030732, intron 1 of 15)	intron (NM_030732, intron 1 of 15)	5116	NM_030732	81004	Mm.202966	NM_030732	ENSMUSG00000027630	Tbl1xr1	8030499H02Rik|A630076E03Rik|AW539987|C21|C230089I12Rik|DC42|Ira1|TBLR1	transducin (beta)-like 1X-linked receptor 1	protein-coding
mm_19600.1	chr2	102400864	102400970	-	1	NA	promoter-TSS (NM_020267)	promoter-TSS (NM_020267)	-17	NM_020267	80985	Mm.315002	NM_020267	ENSMUSG00000027189	Trim44	Dipb|Mc7	tripartite motif-containing 44	protein-coding
mm_170208.1	chr17	70625959	70625959	-	1	NA	intron (NM_001347411, intron 6 of 14)	intron (NM_001347411, intron 6 of 14)	64212	NM_001128181	224997	Mm.311840	NM_027712	ENSMUSG00000003279	Dlgap1	4933422O14Rik|9630002F18|AI845682|AI848168|BB075781|D17Bwg0511e|GKAP/SAPAP|GKPA/SAPAP|Gkap|Sapap1|mKIAA4162	discs, large (Drosophila) homolog-associated protein 1	protein-coding
mm_29925.1	chr3	131490991	131491011	-	1	NA	Intergenic	Intergenic	-73767	NM_001289479	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_112016.1	chr12	111377439	111377502	-	1	NA	5' UTR (NM_183016, exon 1 of 37)	5' UTR (NM_183016, exon 1 of 37)	248	NM_183016	217866	Mm.27397	NM_183016	ENSMUSG00000021279	Cdc42bpb	MRCKb	CDC42 binding protein kinase beta	protein-coding
mm_88885.1	chr10	81135465	81135491	+	1	NA	promoter-TSS (NM_010731)	promoter-TSS (NM_010731)	-793	NM_010731	16969	Mm.20920	NM_010731	ENSMUSG00000035011	Zbtb7a	9030619K07Rik|9130006G12Rik|AI452336|FBI-1|Lrf|Pokemon|Zbtb7	zinc finger and BTB domain containing 7a	protein-coding
mm_21296.1	chr2	157017532	157017535	-	1	NA	3' UTR (NM_001164663, exon 15 of 15)	3' UTR (NM_001164663, exon 15 of 15)	-10458	NM_025853	66934	Mm.25410	NM_025853	ENSMUSG00000027635	Dsn1	1700022L09Rik|AW552447	DSN1 homolog, MIS12 kinetochore complex component	protein-coding
mm_39703.1	chr5	27262049	27262064	+	1	NA	5' UTR (NM_001136060, exon 1 of 26)	5' UTR (NM_001136060, exon 1 of 26)	121	NM_001136060	13483	Mm.42078	NM_010075	ENSMUSG00000061576	Dpp6	B930011P16Rik|D5Buc3|D5Buc4|D5Buc5|DPP VI|Dpp-6|Gm1377|In(5)6H-p|Peplb|Rw	dipeptidylpeptidase 6	protein-coding
mm_9782.1	chr1	181211945	181211968	-	1	NA	promoter-TSS (NM_145514)	promoter-TSS (NM_145514)	22	NM_145514	226757	Mm.289082	NM_145514	ENSMUSG00000038733	Wdr26	1600024A01Rik|AA693241|AI447817|AU044014|C77982|Gid7	WD repeat domain 26	protein-coding
mm_4513.1	chr1	174215426	174215434	+	1	NA	intron (NM_011465, intron 29 of 51)	intron (NM_011465, intron 29 of 51)	35546	NM_146715	258710	Mm.377647	NM_146715	ENSMUSG00000050788	Olfr419	MOR267-6	olfactory receptor 419	protein-coding
mm_39937.1	chr5	31699168	31699212	+	1	NA	intron (NM_181280, intron 1 of 12)	intron (NM_181280, intron 1 of 12)	1140	NM_144541	107976	Mm.482126	NM_144541	ENSMUSG00000052139	Bre	6030405P19Rik|AI429776|B830038C02Rik	brain and reproductive organ-expressed protein	protein-coding
mm_163563.1	chr13	25688405	25688407	+	1	NA	Intergenic	Intergenic	277910	NR_045062	100503530	Mm.86763	NR_045062	ENSMUSG00000086531	Gm11351	OTTMUSG00000000620	predicted gene 11351	ncRNA
mm_10510.1	chr2	16356295	16356316	+	1	NA	promoter-TSS (NM_026162)	promoter-TSS (NM_026162)	1	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding
mm_154025.1	chr19	53390590	53390622	-	1	NA	promoter-TSS (NM_172429)	promoter-TSS (NM_172429)	-33	NM_172429	76479	Mm.313687	NM_172429	ENSMUSG00000025024	Smndc1	2410004J23Rik|4933440I19Rik	survival motor neuron domain containing 1	protein-coding
mm_118285.1	chr13	112800578	112800588	-	1	NA	promoter-TSS (NM_008903)	promoter-TSS (NM_008903)	-194	NM_008903	19012	Mm.291029	NM_008247	ENSMUSG00000021759	Plpp1	Hic53|Hpic53|LPP-1|LPP1|PAP-2a|PAP2-alpha|PAP2a|Ppap2a|mPAP	phospholipid phosphatase 1	protein-coding
mm_127279.1	chr15	99875565	99875621	+	1	NA	promoter-TSS (NM_001113545)	promoter-TSS (NM_001113545)	-137	NM_001113545	65970	Mm.33207	NM_023063	ENSMUSG00000023022	Lima1	Eplin	LIM domain and actin binding 1	protein-coding
mm_75276.1	chr8	40904472	40904497	-	1	NA	exon (NM_001044740, exon 5 of 12)	exon (NM_001044740, exon 5 of 12)	-21749	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_119161.1	chr14	31671865	31671894	+	1	NA	Intergenic	Intergenic	30822	NM_025295	26363	Mm.282679	NM_025295	ENSMUSG00000021900	Btd	-	biotinidase	protein-coding
mm_109113.1	chr12	105475902	105475911	+	1	NA	intron (NM_001252508, intron 1 of 1)	intron (NM_001252508, intron 1 of 1)	22050	NM_001252508	268595	Mm.2388	NM_001252508	ENSMUSG00000094910	D430019H16Rik	AI852661	RIKEN cDNA D430019H16 gene	protein-coding
mm_149098.1	chr19	8941846	8941852	+	1	NA	promoter-TSS (NM_011842)	promoter-TSS (NM_011842)	-71	NM_011842	23942	Mm.25339	NM_011842	ENSMUSG00000071646	Mta2	AW550797|Mata1l1|Mta1l1|mmta2	metastasis-associated gene family, member 2	protein-coding
mm_108512.1	chr12	83993258	83993261	+	1	NA	3' UTR (NM_134188, exon 3 of 3)	3' UTR (NM_134188, exon 3 of 3)	5398	NM_134188	171210	Mm.371675	NM_134188	ENSMUSG00000021226	Acot2	AA571646|MTE-I|Mte1	acyl-CoA thioesterase 2	protein-coding
mm_17988.1	chr2	37914666	37914669	-	1	NA	intron (NM_146122, intron 13 of 21)	intron (NM_146122, intron 13 of 21)	138418	NM_001163566	241324	Mm.392369	NM_001163566	ENSMUSG00000035403	Crb2	5930402A21|BC043114	crumbs family member 2	protein-coding
mm_172338.1	chr7	110134255	110134255	+	1	NA	intron (NM_009516, intron 6 of 10)	RMER19A|LTR|ERVK	12196	NM_009516	22390	Mm.287173	NM_009516	ENSMUSG00000031016	Wee1	Wee1A	WEE 1 homolog 1 (S. pombe)	protein-coding
mm_62053.1	chr7	92447432	92447442	+	1	NA	3' UTR (NM_001243047, exon 11 of 11)	3' UTR (NM_001243047, exon 11 of 11)	-113712	NM_025515	66365	Mm.21173	NM_025515	ENSMUSG00000030613	Ccdc90b	2310015N07Rik|C86558	coiled-coil domain containing 90B	protein-coding
mm_59046.1	chr7	19359741	19359758	+	1	NA	promoter-TSS (NM_145822)	promoter-TSS (NM_145822)	-266	NM_145822	70333	Mm.171370	NM_145822	ENSMUSG00000047649	Cd3eap	1190028F09|2610103M17Rik|ASE-1|Ase1|CAST|PAF49	CD3E antigen, epsilon polypeptide associated protein	protein-coding
mm_161797.1	chr17	50292950	50292950	-	1	NA	intron (NM_001277863, intron 1 of 9)	CpG	670	NM_010021	13164	Mm.280641	NM_010021	ENSMUSG00000010592	Dazl	Daz-like|Dazh|Dazl1|Dazla|Tpx-2|Tpx2	deleted in azoospermia-like	protein-coding
mm_9128.1	chr1	170644329	170644340	-	1	NA	promoter-TSS (NM_177068)	promoter-TSS (NM_177068)	-198	NM_177068	320078	Mm.287131	NM_177068	ENSMUSG00000038463	Olfml2b	1110018N05Rik|4832415H08Rik|AI467542	olfactomedin-like 2B	protein-coding
mm_169532.1	chr14	92603061	92603069	-	1	NA	Intergenic	Intergenic	1285823	NM_001271800	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding
mm_156932.1	chrX	169685192	169685250	+	1	NA	promoter-TSS (NM_010797)	promoter-TSS (NM_010797)	22	NM_001290512	17318	Mm.34441	NM_010797	ENSMUSG00000035299	Mid1	61B3-R|DXHXS1141|Fxy|Trim18	midline 1	protein-coding
mm_17356.1	chr2	26617452	26617459	-	1	NA	Intergenic	RMER1C|Other|Other	-11002	NM_019833	56279	Mm.279863	NM_019833	ENSMUSG00000036186	Fam69b	AB030186|AW209000|B230317C12Rik|PIP49	family with sequence similarity 69, member B	protein-coding
mm_4196.1	chr1	171225754	171225767	+	1	NA	exon (NM_013474, exon 3 of 4)	exon (NM_013474, exon 3 of 4)	706	NM_013474	11807	Mm.389209	NM_013474	ENSMUSG00000005681	Apoa2	Alp-2|Apo-AII|ApoA-II|ApoAII|Apoa-2|Hdl-1	apolipoprotein A-II	protein-coding
mm_142000.1	chr17	35199392	35199405	-	1	NA	TTS (NM_013693)	TTS (NM_013693)	2609	NM_013693	21926	Mm.1293	NM_013693	ENSMUSG00000024401	Tnf	DIF|TNF-a|TNF-alpha|TNFSF2|TNFalpha|Tnfa|Tnfsf1a|Tnlg1f	tumor necrosis factor	protein-coding
mm_66850.1	chr7	50575935	50575943	-	1	NA	promoter-TSS (NR_045928)	promoter-TSS (NR_045928)	-55	NR_045928	73515	Mm.437440	NR_045928	ENSMUSG00000085265	Nell1os	1700081H22Rik	NEL-like 1, opposite strand	ncRNA
mm_75888.1	chr8	70863750	70863765	-	1	NA	Intergenic	Intergenic	-6749	NM_032397	84036	Mm.32074	NM_032397	ENSMUSG00000002908	Kcnn1	AI854248|KCa2.1|SK1	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 1	protein-coding
mm_146676.1	chr18	12819751	12819791	-	1	NA	non-coding (NR_045524, exon 1 of 12)	non-coding (NR_045524, exon 1 of 12)	136	NR_045524	64291	Mm.259470	NM_020573	ENSMUSG00000044252	Osbpl1a	G430090F17Rik|Gm753|ORP-1|Osbpl1b	oxysterol binding protein-like 1A	protein-coding
mm_106524.1	chr11	120563303	120563336	-	1	NA	exon (NM_011032, exon 7 of 11)	exon (NM_011032, exon 7 of 11)	9617	NM_011032	18453	Mm.16660	NM_011032	ENSMUSG00000025130	P4hb	ERp59|PDI|Pdia1|Thbp	prolyl 4-hydroxylase, beta polypeptide	protein-coding
mm_77231.1	chr8	115704285	115704317	-	1	NA	3' UTR (NM_001025577, exon 1 of 1)	3' UTR (NM_001025577, exon 1 of 1)	2593	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_78141.1	chr9	20945022	20945039	+	1	NA	intron (NM_001199432, intron 1 of 38)	ID|SINE|ID	7593	NM_001199433	13433	Mm.128580	NM_010066	ENSMUSG00000004099	Dnmt1	Cxxc9|Dnmt|Dnmt1o|MCMT|MTase|Met-1|Met1|MommeD2|m.MmuI	DNA methyltransferase (cytosine-5) 1	protein-coding
mm_121171.1	chr14	103017356	103017363	+	1	NA	intron (NR_045657, intron 2 of 2)	intron (NR_045657, intron 2 of 2)	16444	NR_045657	71264	Mm.399572	NR_045657		4933432I03Rik	-	RIKEN cDNA 4933432I03 gene	ncRNA
mm_149935.1	chr19	27216882	27216891	+	1	NA	promoter-TSS (NM_013703)	promoter-TSS (NM_013703)	-134	NM_013703	22359	Mm.4141	NM_013703	ENSMUSG00000024924	Vldlr	AA408956|AI451093|AW047288	very low density lipoprotein receptor	protein-coding
mm_94777.1	chr11	21283385	21283432	+	1	NA	intron (NM_139061, intron 7 of 22)	MIRb|SINE|MIR	44376	NM_001290628	245944	Mm.170103	NM_139061	ENSMUSG00000020128	Vps54	Hcc8|Vps54l|mSLP8|wr	VPS54 GARP complex subunit	protein-coding
mm_162890.1	chr10	109642452	109642456	+	1	NA	Intergenic	Intergenic	357765	NM_001081035	260315	Mm.225050	NM_177797	ENSMUSG00000020181	Nav3	4732483H20Rik|9630020C08Rik|POMFIL1|Pomfil1p|mKIAA0938|unc53H3	neuron navigator 3	protein-coding
mm_150930.1	chr19	46304831	46304839	+	1	NA	promoter-TSS (NM_019408)	promoter-TSS (NM_019408)	98	NM_001177369	18034	Mm.102365	NM_019408	ENSMUSG00000025225	Nfkb2	NF-kappaB2|lyt|p49|p49/p100|p50B|p52	nuclear factor of kappa light polypeptide gene enhancer in B cells 2, p49/p100	protein-coding
mm_106945.1	chr12	8771318	8771328	+	1	NA	promoter-TSS (NM_011519)	promoter-TSS (NM_011519)	-73	NM_011519	20969	Mm.2580	NM_011519	ENSMUSG00000020592	Sdc1	AA408134|AA409076|CD138|Sstn|Synd|Synd1|syn-1	syndecan 1	protein-coding
mm_15219.1	chr2	154427072	154427089	+	1	NA	Intergenic	Intergenic	-9404	NM_172860	12396	Mm.29914	NM_009823	ENSMUSG00000038533	Cbfa2t2	A430091M07|C330013D05Rik|Cbfa2t2h|MTGR1	core-binding factor, runt domain, alpha subunit 2, translocated to, 2 (human)	protein-coding
mm_170095.1	chr17	38759391	38759394	-	1	NA	Intergenic	B1_Mm|SINE|Alu	119945	NM_001177586	100126768	Mm.471528	NM_001177586	ENSMUSG00000092342	Esp31	Gm20516	exocrine gland secreted peptide 31	protein-coding
mm_64230.1	chr7	141692619	141692628	+	1	NA	intron (NM_023566, intron 2 of 45)	intron (NM_023566, intron 2 of 45)	2283	NM_023566	17831	Mm.2041	NM_023566		Muc2	2010015E03Rik|MCM|wnn	mucin 2	protein-coding
mm_154252.1	chr19	60766738	60766748	-	1	NA	exon (NM_010123, exon 19 of 22)	exon (NM_010123, exon 19 of 22)	7642	NR_034047	100217439		NR_034047		Snora19	MBI-51	small nucleolar RNA, H/ACA box 19	snoRNA
mm_168439.1	chr1	136698626	136698640	+	1	NA	intron (NR_037986, intron 1 of 4)	intron (NR_037986, intron 1 of 4)	2422	NR_037986	100503474	Mm.428276	NR_037986		Platr22	Gm16880	pluripotency associated transcript 22	ncRNA
mm_33123.1	chr4	124802544	124802588	+	1	NA	promoter-TSS (NM_008636)	promoter-TSS (NM_008636)	17	NM_008636	17764	Mm.272397	NM_008636	ENSMUSG00000028890	Mtf1	MTF-1|Thyls	metal response element binding transcription factor 1	protein-coding
mm_87181.1	chr10	39134051	39134066	+	1	NA	promoter-TSS (NM_028006)	promoter-TSS (NM_028006)	35	NM_028006	71924	Mm.297956	NM_028006	ENSMUSG00000019845	Tube1	2310061K05Rik|AI551343|Tube	epsilon-tubulin 1	protein-coding
mm_121323.1	chr14	113315025	113315056	+	1	NA	Intergenic	Intergenic	1293610	NR_030150	723922		NR_030150	ENSMUSG00000070099	Mir466	Mirn466|mmu-mir-466	microRNA 466	ncRNA
mm_58663.1	chr7	6734122	6734138	+	1	NA	intron (NM_021323, intron 1 of 7)	L1MD3|LINE|L1	3547	NM_001290994	57775	Mm.40752	NM_021323	ENSMUSG00000051527	Usp29	Ocat	ubiquitin specific peptidase 29	protein-coding
mm_161547.1	chr16	8738461	8738461	-	1	NA	promoter-TSS (NM_001003918)	promoter-TSS (NM_001003918)	-119	NM_001003918	252870	Mm.295330	NM_001003918	ENSMUSG00000022710	Usp7	2210010O09Rik|AA409944|AA617399|AU019296|AW548146|C80752|Hausp	ubiquitin specific peptidase 7	protein-coding
mm_57202.1	chr6	122850743	122850872	-	1	NA	exon (NM_009779, exon 2 of 2)	exon (NM_009779, exon 2 of 2)	5350	NM_009779	12267	Mm.2408	NM_009779	ENSMUSG00000040552	C3ar1	AZ3B|C3AR|HNFAG09	complement component 3a receptor 1	protein-coding
mm_167172.1	chr7	139224850	139224860	-	1	NA	intron (NM_001143755, intron 6 of 8)	intron (NM_001143755, intron 6 of 8)	-11548	NM_001162540	57740	Mm.65336	NM_021302	ENSMUSG00000015981	Stk32c	PKE|Pkek|YANK3	serine/threonine kinase 32C	protein-coding
mm_164013.1	chr14	70599559	70599569	-	1	NA	intron (NM_194345, intron 1 of 16)	CpG	271	NM_194345	239170	Mm.247582	NM_194345	ENSMUSG00000022095	Fam160b2	G430067P06Rik|Rai16	family with sequence similarity 160, member B2	protein-coding
mm_11463.1	chr2	32237298	32237340	+	1	NA	intron (NM_145145, intron 1 of 19)	intron (NM_145145, intron 1 of 19)	636	NM_145145	99011	Mm.31192	NM_145145	ENSMUSG00000039254	Pomt1	AI505244	protein-O-mannosyltransferase 1	protein-coding
mm_10894.1	chr2	25264271	25264290	+	1	NA	exon (NM_175286, exon 1 of 4)	exon (NM_175286, exon 1 of 4)	1682	NM_175286	97031	Mm.308539	NM_175286	ENSMUSG00000048707	Tprn	C430004E15Rik|C87750	taperin	protein-coding
mm_52660.1	chr6	117900312	117900349	+	1	NA	promoter-TSS (NM_001166432)	promoter-TSS (NM_001166432)	-10	NM_001166432	98758	Mm.422979	NM_133834	ENSMUSG00000042079	Hnrnpf	4833420I20Rik|AA407306|Hnrpf	heterogeneous nuclear ribonucleoprotein F	protein-coding
mm_14245.1	chr2	128055192	128055202	+	1	NA	intron (NM_028765, intron 14 of 17)	intron (NM_028765, intron 14 of 17)	-70841	NM_207681	12125	Mm.141083	NM_009754	ENSMUSG00000027381	Bcl2l11	1500006F24Rik|Bim|Bod|bcl2-L-11	BCL2-like 11 (apoptosis facilitator)	protein-coding
mm_118797.1	chr14	24490710	24490725	+	1	NA	promoter-TSS (NM_207634)	promoter-TSS (NM_207634)	36	NM_011297	20088	Mm.16775	NM_011297	ENSMUSG00000025290	Rps24	-	ribosomal protein S24	protein-coding
mm_71813.1	chr8	68884414	68884424	+	1	NA	intron (NM_008509, intron 1 of 9)	intron (NM_008509, intron 1 of 9)	3864	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_125671.1	chr15	66152703	66152709	+	1	NA	intron (NM_152923, intron 1 of 14)	intron (NM_152923, intron 1 of 14)	133518	NM_152923	110862	Mm.255585	NM_152923	ENSMUSG00000056258	Kcnq3	-	potassium voltage-gated channel, subfamily Q, member 3	protein-coding
mm_33658.1	chr4	133130535	133130590	+	1	NA	promoter-TSS (NM_153423)	promoter-TSS (NM_153423)	-71	NM_153423	242687	Mm.23566	NM_153423	ENSMUSG00000028868	Wasf2	AW742646|D4Ertd13e|WAVE2	WAS protein family, member 2	protein-coding
mm_103148.1	chr11	70322503	70322514	-	1	NA	promoter-TSS (NM_145684)	promoter-TSS (NM_145684)	10	NM_145684	11685	Mm.274093	NM_145684	ENSMUSG00000018907	Alox12e	8-LOX|AW259591|Alox12-ps1|Alox12-ps2|Aloxe|e-LOX1	arachidonate lipoxygenase, epidermal	protein-coding
mm_154877.1	chrX	20692864	20692908	+	1	NA	intron (NM_011049, intron 1 of 15)	intron (NM_011049, intron 1 of 15)	4460	NM_011049	18555	Mm.102574	NM_011049	ENSMUSG00000031065	Cdk16	Crk5|Pctaire1|Pctk1	cyclin-dependent kinase 16	protein-coding
mm_151517.1	chr19	58738273	58738282	+	1	NA	intron (NM_018874, intron 10 of 12)	intron (NM_018874, intron 10 of 12)	9390	NM_018874	18946	Mm.10753	NM_018874	ENSMUSG00000042179	Pnliprp1	Plrp1	pancreatic lipase related protein 1	protein-coding
mm_13027.1	chr2	91054026	91054038	+	1	NA	promoter-TSS (NM_008948)	promoter-TSS (NM_008948)	16	NM_008948	19182	Mm.289832	NM_008948	ENSMUSG00000002102	Psmc3	TBP-1	proteasome (prosome, macropain) 26S subunit, ATPase 3	protein-coding
mm_168866.1	chr12	33147681	33147688	+	1	NA	promoter-TSS (NM_028139)	promoter-TSS (NM_028139)	-2	NM_028139	380753	Mm.41540	NM_028139	ENSMUSG00000020564	Atxn7l1	2810423G08Rik|Atxn7l4	ataxin 7-like 1	protein-coding
mm_4965.1	chr1	191275953	191275959	+	1	NA	Intergenic	ID_B1|SINE|B4	42162	NM_025424	66208	Mm.46444	NM_025424	ENSMUSG00000037499	Nenf	1110060M21Rik|SCIRP10|Spuf	neuron derived neurotrophic factor	protein-coding
mm_130594.1	chr15	99706847	99706847	-	1	NA	intron (NM_031842, intron 6 of 12)	intron (NM_031842, intron 6 of 12)	4560	NM_031842	83797	Mm.273756	NM_031842	ENSMUSG00000023018	Smarcd1	AA407987|Baf60a|D15Kz1	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1	protein-coding
mm_60676.1	chr7	45077510	45077521	+	1	NA	3' UTR (NM_025533, exon 9 of 9)	3' UTR (NM_025533, exon 9 of 9)	14698	NM_026555	52377	Mm.29997	NM_026555	ENSMUSG00000019539	Rcn3	6030455P07Rik|D530026G20Rik|D7Ertd671e|RLP49	reticulocalbin 3, EF-hand calcium binding domain	protein-coding
mm_59307.1	chr7	25268441	25268454	+	1	NA	intron (NM_001302811, intron 1 of 20)	CpG	748	NM_001302811	71722	Mm.28833	NM_027882	ENSMUSG00000005442	Cic	1200010B10Rik|mKIAA0306	capicua transcriptional repressor	protein-coding
mm_162795.1	chr10	76442240	76442281	-	1	NA	intron (NM_008787, intron 1 of 41)	intron (NM_008787, intron 1 of 41)	652	NM_008787	18541	Mm.251794	NM_008787	ENSMUSG00000001151	Pcnt	AW476095|C86676|KEN|Pcnt2|kendrin|m239Asp|m275Asp	pericentrin (kendrin)	protein-coding
mm_150685.1	chr19	42090517	42090532	+	1	NA	promoter-TSS (NM_145501)	promoter-TSS (NM_145501)	89	NM_145501	84095	Mm.117037	NM_145501	ENSMUSG00000025178	Pi4k2a	Pi4k2	phosphatidylinositol 4-kinase type 2 alpha	protein-coding
mm_83372.1	chr9	44510182	44510190	-	1	NA	3' UTR (NM_030256, exon 9 of 9)	3' UTR (NM_030256, exon 9 of 9)	11050	NM_030256	80288	Mm.370270	NM_030256	ENSMUSG00000063382	Bcl9l	B9L|BC003321|BCL9-2|DLNB11	B cell CLL/lymphoma 9-like	protein-coding
mm_2850.1	chr1	131672263	131672277	+	1	NA	exon (NM_007799, exon 8 of 10)	exon (NM_007799, exon 8 of 10)	-16425	NM_145509	226421	Mm.44508	NM_145509	ENSMUSG00000052688	Rab7b	5430435G22Rik	RAB7B, member RAS oncogene family	protein-coding
mm_74842.1	chr8	24438938	24438952	-	1	NA	promoter-TSS (NM_026931)	promoter-TSS (NM_026931)	1	NM_026931	69068	Mm.25775	NM_026931	ENSMUSG00000056313	1810011O10Rik	1110065B09Rik|AW121743|AW321058	RIKEN cDNA 1810011O10 gene	protein-coding
mm_95911.1	chr11	58206939	58206949	+	1	NA	exon (NM_018738, exon 3 of 3)	exon (NM_018738, exon 3 of 3)	7388	NM_018738	16145	Mm.33902	NM_018738	ENSMUSG00000078853	Igtp	AW558444|Irgm3	interferon gamma induced GTPase	protein-coding
mm_1345.1	chr1	66290100	66290102	+	1	NA	intron (NM_001039934, intron 3 of 14)	intron (NM_001039934, intron 3 of 14)	-31623	NM_001310634	17756	Mm.256966	NM_008632	ENSMUSG00000015222	Map2	G1-397-34|MAP-2|Mtap-2|Mtap2|repro4	microtubule-associated protein 2	protein-coding
mm_166680.1	chr6	98697694	98697698	-	1	NA	Intergenic	Intergenic	330602	NM_001197322	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_20037.1	chr2	119897121	119897157	-	1	NA	promoter-TSS (NM_013720)	promoter-TSS (NM_013720)	-89	NM_001164274	29808	Mm.87532	NM_013720	ENSMUSG00000033943	Mga	AV312082|C130042M01Rik|C80739|D030062C11Rik|Mad5	MAX gene associated	protein-coding
mm_148556.1	chr19	4721061	4721165	+	1	NA	intron (NM_021287, intron 2 of 36)	intron (NM_021287, intron 2 of 36)	9890	NM_021287	20743	Mm.329668	NM_021287	ENSMUSG00000067889	Sptbn2	Spnb3|mKIAA0302	spectrin beta, non-erythrocytic 2	protein-coding
mm_2199.1	chr1	89463907	89463910	+	1	NA	intron (NM_001037136, intron 1 of 16)	Lx9|LINE|L1	9097	NM_001037136	347722	Mm.291135	NM_178119	ENSMUSG00000055013	Agap1	Centg2|Ggap1|R75364|mKIAA1099	ArfGAP with GTPase domain, ankyrin repeat and PH domain 1	protein-coding
mm_80972.1	chr9	103112073	103112093	+	1	NA	promoter-TSS (NM_173781)	promoter-TSS (NM_173781)	9	NM_173781	270192	Mm.490252	NM_173781	ENSMUSG00000032549	Rab6b	9630015C03|AI844641|C330006L04Rik|D9Bwg0185e	RAB6B, member RAS oncogene family	protein-coding
mm_148301.1	chr18	82787602	82787614	-	1	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	-28569	NR_045389	76961	Mm.396392	NR_045389	ENSMUSG00000101773	2210420H20Rik	-	RIKEN cDNA 2210420H20 gene	ncRNA
mm_126220.1	chr15	78914371	78914406	+	1	NA	exon (NM_020271, exon 1 of 2)	exon (NM_020271, exon 1 of 2)	469	NM_020271	57028	Mm.263169	NM_020271	ENSMUSG00000022436	Pdxp	1600027H05Rik|AB041662|PLPP	pyridoxal (pyridoxine, vitamin B6) phosphatase	protein-coding
mm_120466.1	chr14	65971727	65971791	+	1	NA	exon (NM_013492, exon 2 of 9)	exon (NM_013492, exon 2 of 9)	3276	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_140051.1	chr17	74528436	74528465	+	1	NA	5' UTR (NM_007566, exon 1 of 73)	5' UTR (NM_007566, exon 1 of 73)	155	NM_007566	12211	Mm.442564	NM_007566	ENSMUSG00000024073	Birc6	A430032G04Rik|A430040A19Rik|AA501170|Bruce|D630005A10Rik|mKIAA1289	baculoviral IAP repeat-containing 6	protein-coding
mm_34863.1	chr4	155555147	155555192	+	1	NA	exon (NM_008142, exon 10 of 12)	exon (NM_008142, exon 10 of 12)	-7223	NM_138671	192185	Mm.28347	NM_138671	ENSMUSG00000029063	Nadk	4432404C02Rik|BC004012	NAD kinase	protein-coding
mm_122504.1	chr14	46822172	46822222	-	1	NA	promoter-TSS (NM_022023)	promoter-TSS (NM_022023)	45	NM_022023	63985	Mm.87312	NM_022023	ENSMUSG00000062014	Gmfb	3110001H22Rik|3110001O16Rik|AI851627|C79176|D14Ertd630e	glia maturation factor, beta	protein-coding
mm_104921.1	chr11	99851628	99851632	-	1	NA	promoter-TSS (NM_001013823)	promoter-TSS (NM_001013823)	-25	NM_001013823	435285	Mm.351895	NM_001013823	ENSMUSG00000046474	Krtap4-16	OTTMUSG00000002196	keratin associated protein 4-16	protein-coding
mm_2844.1	chr1	131638389	131638404	+	1	NA	promoter-TSS (NM_007799)	promoter-TSS (NM_007799)	82	NM_007799	13034	Mm.230249	NM_007799	ENSMUSG00000004552	Ctse	A430072O03Rik|C920004C08Rik|CE|CatE	cathepsin E	protein-coding
mm_39738.1	chr5	29378605	29378607	+	1	NA	promoter-TSS (NM_020295)	promoter-TSS (NM_020295)	-216	NM_020295	56873	Mm.41572	NM_020295	ENSMUSG00000010721	Lmbr1	1110048D14Rik|AU017641	limb region 1	protein-coding
mm_166278.1	chr5	91770187	91770190	+	1	NA	Intergenic	Intergenic	-2888	NR_045383	73452	Mm.396233	NR_045383	ENSMUSG00000101978	1700063O14Rik	-	RIKEN cDNA 1700063O14 gene	ncRNA
mm_98613.1	chr11	95843143	95843158	+	1	NA	promoter-TSS (NM_001284397)	promoter-TSS (NM_001284397)	-95	NM_001284397	14710	Mm.46299	NM_023121	ENSMUSG00000038811	Gngt2	AV096488	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 2	protein-coding
mm_110002.1	chr12	15816737	15816747	-	1	NA	promoter-TSS (NM_144551)	promoter-TSS (NM_144551)	43	NM_144551	217410	Mm.491136	NM_144551	ENSMUSG00000020601	Trib2	AW319517|TRB-2|TRB2	tribbles pseudokinase 2	protein-coding
mm_169349.1	chr14	20640792	20640794	-	1	NA	Intergenic	CpG	15747	NM_021508	59011	Mm.439911	NM_021508	ENSMUSG00000068697	Myoz1	2310001N11Rik|AV090278|FATZ|Myoz	myozenin 1	protein-coding
mm_147425.1	chr18	46212814	46212821	-	1	NA	promoter-TSS (NM_178872)	promoter-TSS (NM_178872)	-210	NM_178872	28105	Mm.277382	NM_178872	ENSMUSG00000033949	Trim36	D18Wsu100e|haprin	tripartite motif-containing 36	protein-coding
mm_121968.1	chr14	25517352	25517362	-	1	NA	intron (NM_001310666, intron 2 of 23)	intron (NM_001310666, intron 2 of 23)	-17082	NR_037236	100526533		NR_037236	ENSMUSG00000093081	Mir3075	mir-3075|mmu-mir-3075	microRNA 3075	ncRNA
mm_36806.1	chr4	103173498	103173513	-	1	NA	3' UTR (NM_177732, exon 10 of 10)	3' UTR (NM_177732, exon 10 of 10)	41379	NM_177732	242585	Mm.281800	NM_177732	ENSMUSG00000028521	Slc35d1	AI834976|C330011J09|UGTREL7|mKIAA0260	solute carrier family 35 (UDP-glucuronic acid/UDP-N-acetylgalactosamine dual transporter), member D1	protein-coding
mm_32979.1	chr4	120134641	120134677	+	1	NA	3' UTR (NM_010657, exon 9 of 9)	3' UTR (NM_010657, exon 9 of 9)	-26547	NM_007902	13615	Mm.284855	NM_007902	ENSMUSG00000028635	Edn2	ET-2|PPET2|VIC	endothelin 2	protein-coding
mm_19971.1	chr2	118012375	118012385	-	1	NA	intron (NR_126479, intron 8 of 9)	Lx9|LINE|L1	98822	NR_126479	329496	Mm.235844	NR_126479	ENSMUSG00000087203	Gm13986	C230060E24|OTTMUSG00000015236	predicted gene 13986	ncRNA
mm_136317.1	chr16	91729382	91729392	-	1	NA	promoter-TSS (NM_001110276)	promoter-TSS (NM_001110276)	16	NM_010587	16443	Mm.40546	NM_010587	ENSMUSG00000022957	Itsn1	AA517634|AA545208|AI316805|AI839402|AI848451|Ehsh1|Ese1|Itsn|Sh3p17	intersectin 1 (SH3 domain protein 1A)	protein-coding
mm_32536.1	chr4	109000991	109001001	+	1	NA	exon (NM_146150, exon 1 of 31)	exon (NM_146150, exon 1 of 31)	191	NM_146150	230598	Mm.274950	NM_146150	ENSMUSG00000053510	Nrd1	2600011I06Rik|AI875733|NRD-C|Nrdc	nardilysin, N-arginine dibasic convertase, NRD convertase 1	protein-coding
mm_4762.1	chr1	182452709	182452718	+	1	NA	exon (NM_173378, exon 14 of 18)	exon (NM_173378, exon 14 of 18)	43546	NM_173378	209456	Mm.287450	NM_173378	ENSMUSG00000026510	Trp53bp2	53BP2|AI746547|ASPP2|PPP1R13A|Tp53bp2|X98550	transformation related protein 53 binding protein 2	protein-coding
mm_57466.1	chr6	125217333	125217341	-	1	NA	intron (NM_009496, intron 1 of 4)	U2|snRNA|snRNA	1756	NM_001080557	22317	Mm.32321	NM_009496	ENSMUSG00000030337	Vamp1	Syb-1|Syb1|VAMP-1|lew	vesicle-associated membrane protein 1	protein-coding
mm_42076.1	chr5	110135824	110135887	+	1	NA	promoter-TSS (NM_172717)	promoter-TSS (NM_172717)	25	NM_001289580	231600	Mm.30264	NM_172717	ENSMUSG00000014668	Chfr	5730484M20Rik|C230082M18|RNF116	checkpoint with forkhead and ring finger domains	protein-coding
mm_12334.1	chr2	69669846	69669857	+	1	NA	promoter-TSS (NM_001081087)	promoter-TSS (NM_001081087)	-269	NM_001081087	228003	Mm.178784	NM_001081087	ENSMUSG00000075307	Klhl41	Gm112|Kbtbd10|SARCOSIN	kelch-like 41	protein-coding
mm_17300.1	chr2	26294599	26294625	-	1	NA	promoter-TSS (NM_177841)	promoter-TSS (NM_177841)	-55	NM_177841	329366	Mm.77712	NM_177841	ENSMUSG00000048038	Ccdc187	4932418E24Rik	coiled-coil domain containing 187	protein-coding
mm_100448.1	chr11	119602982	119603034	+	1	NA	5' UTR (NM_001306081, exon 1 of 33)	5' UTR (NM_001306081, exon 1 of 33)	103	NM_028898	74370	Mm.209933	NM_028898	ENSMUSG00000025583	Rptor	4932417H02Rik|Rap|Raptor|mKIAA1303	regulatory associated protein of MTOR, complex 1	protein-coding
mm_99213.1	chr11	101024617	101024660	+	1	NA	intron (NM_001243050, intron 5 of 20)	B3|SINE|B2	-5702	NR_105893	102466767		NR_105893	ENSMUSG00000098415	Mir6928	Gm27728|mmu-mir-6928	microRNA 6928	ncRNA
mm_162373.1	chr1	67226575	67226576	+	1	NA	intron (NM_001080809, intron 34 of 37)	MIR|SINE|MIR	103548	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_147331.1	chr18	42867976	42867979	-	1	NA	intron (NM_028392, intron 1 of 8)	intron (NM_028392, intron 1 of 8)	31529	NR_073583	72930	Mm.26134	NM_027531	ENSMUSG00000024500	Ppp2r2b	2900026H06Rik|6330404L05Rik|E130009M08Rik|PP2A-PR55B|PR55-BETA|SCA12	protein phosphatase 2, regulatory subunit B, beta	protein-coding
mm_96408.1	chr11	67253998	67254007	+	1	NA	exon (NM_010855, exon 28 of 40)	exon (NM_010855, exon 28 of 40)	16190	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_171151.1	chr3	16059273	16059274	+	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	-52941	NM_001081687	381484	Mm.217376	NM_001081687	ENSMUSG00000078780	Gm5150	-	predicted gene 5150	protein-coding
mm_101172.1	chr11	16984042	16984068	-	1	NA	intron (NM_019549, intron 7 of 9)	RMER13B|LTR|ERVK	24663	NM_019549	56193	Mm.98232	NM_019549	ENSMUSG00000020120	Plek	2010300B13Rik	pleckstrin	protein-coding
mm_124003.1	chr14	76010618	76010631	-	1	NA	intron (NM_026816, intron 1 of 7)	CpG	241	NM_026816	68705	Mm.20415	NM_026816	ENSMUSG00000067995	Gtf2f2	1110031C13Rik|AI326315	general transcription factor IIF, polypeptide 2	protein-coding
mm_111608.1	chr12	102399979	102399998	-	1	NA	exon (NM_011175, exon 10 of 14)	exon (NM_011175, exon 10 of 14)	39825	NM_011175	19141	Mm.17185	NM_011175	ENSMUSG00000021190	Lgmn	AEP|AI746452|AU022324|Prsc1	legumain	protein-coding
mm_102349.1	chr11	58171997	58172005	-	1	NA	intron (NM_175001, intron 2 of 6)	CpG	347	NM_175001	216767	Mm.259907	NM_175001	ENSMUSG00000020514	Mrpl22	E030011D16Rik|HSPC158|MRP-L25|Rpml25	mitochondrial ribosomal protein L22	protein-coding
mm_158637.1	chrX	155214880	155214882	-	1	NA	intron (NM_009121, intron 3 of 5)	intron (NM_009121, intron 3 of 5)	1568	NM_009121	20229	Mm.2734	NM_009121	ENSMUSG00000025283	Sat1	AA617398|SSAT|Sat	spermidine/spermine N1-acetyl transferase 1	protein-coding
mm_113276.1	chr13	29757034	29757042	+	1	NA	intron (NR_131896, intron 5 of 16)	L1MCa|LINE|L1	98635	NR_131896	68916	Mm.212227	NM_144536	ENSMUSG00000006191	Cdkal1	1190005B03Rik|6620401C13Rik	CDK5 regulatory subunit associated protein 1-like 1	protein-coding
mm_75094.1	chr8	34097293	34097372	-	1	NA	intron (NM_001293758, intron 2 of 6)	intron (NM_001293758, intron 2 of 6)	10482	NM_001293758	22428	Mm.150373	NM_011722	ENSMUSG00000031516	Dctn6	AU044699|WS-3|p27	dynactin 6	protein-coding
mm_120657.1	chr14	70534410	70534421	+	1	NA	exon (NM_145219, exon 6 of 8)	exon (NM_145219, exon 6 of 8)	3594	NM_145219	213469	Mm.41708	NM_145219	ENSMUSG00000033595	Lgi3	AI841179|AW049851	leucine-rich repeat LGI family, member 3	protein-coding
mm_34517.1	chr4	148941068	148941081	+	1	NA	intron (NM_027195, intron 11 of 15)	intron (NM_027195, intron 11 of 15)	136682	NM_027195	69743	Mm.233879	NM_027195	ENSMUSG00000028977	Casz1	2410019P08Rik|AV096627|BC040081|Cst|D4Ertd432e	castor zinc finger 1	protein-coding
mm_22047.1	chr2	168231090	168231105	-	1	NA	promoter-TSS (NM_010072)	promoter-TSS (NM_010072)	475	NM_001160330	69372	Mm.482182	NM_001160330	ENSMUSG00000074576	Mocs3	1700020H17Rik|Uba4	molybdenum cofactor synthesis 3	protein-coding
mm_40379.1	chr5	52368550	52368577	+	1	NA	exon (NM_011435, exon 2 of 2)	exon (NM_011435, exon 2 of 2)	4759	NM_011435	20657	Mm.2407	NM_011435	ENSMUSG00000072941	Sod3	AI314465|EC-SOD	superoxide dismutase 3, extracellular	protein-coding
mm_2018.1	chr1	87128008	87128012	+	1	NA	TTS (NM_007432)	TTS (NM_007432)	3002	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_2868.1	chr1	131750382	131750386	+	1	NA	intron (NM_177243, intron 1 of 20)	intron (NM_177243, intron 1 of 20)	6362	NM_177243	320718	Mm.482704	NM_177243	ENSMUSG00000042268	Slc26a9	E030002L01Rik	solute carrier family 26, member 9	protein-coding
mm_68821.1	chr7	126108505	126108524	-	1	NA	exon (NM_028816, exon 20 of 24)	exon (NM_028816, exon 20 of 24)	-26103	NM_001101488	269994	Mm.39599	NM_001101488	ENSMUSG00000046182	Gsg1l	AI852434|C230098I05Rik|G630023A01Rik|Gm637|g1l	GSG1-like	protein-coding
mm_16382.1	chr2	178327603	178327613	+	1	NA	intron (NM_001177790, intron 8 of 12)	intron (NM_001177790, intron 8 of 12)	80050	NM_177191	320558	Mm.70781	NM_177191	ENSMUSG00000060445	Sycp2	3830402K23Rik|4930518F03Rik	synaptonemal complex protein 2	protein-coding
mm_101010.1	chr11	8503887	8503910	-	1	NA	intron (NM_001083587, intron 16 of 30)	intron (NM_001083587, intron 16 of 30)	160637	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_165798.1	chr3	141465262	141465269	+	1	NA	promoter-TSS (NM_009472)	promoter-TSS (NM_009472)	-299	NM_009472	22253	Mm.24430	NM_009472	ENSMUSG00000059921	Unc5c	B130051O18Rik|Unc5h3|rcm	unc-5 netrin receptor C	protein-coding
mm_161234.1	chr13	93304341	93304341	+	1	NA	5' UTR (NM_011982, exon 1 of 5)	5' UTR (NM_011982, exon 1 of 5)	584	NM_011982	26556	Mm.37533	NM_011982	ENSMUSG00000007617	Homer1	PSD-Zip45|SYN47|Ves-1|homer-1|vesl-1	homer scaffolding protein 1	protein-coding
mm_6380.1	chr1	72700559	72700584	-	1	NA	promoter-TSS (NM_176980)	promoter-TSS (NM_176980)	-7	NM_176980	319695	Mm.249056	NM_176980	ENSMUSG00000039342	Ankar	4932422E22Rik	ankyrin and armadillo repeat containing	protein-coding
mm_45068.1	chr5	43782087	43782143	-	1	NA	promoter-TSS (NM_178729)	promoter-TSS (NM_178729)	34	NM_001159963	242960	Mm.25794	NM_178729	ENSMUSG00000039753	Fbxl5	Fbl4|Fir4	F-box and leucine-rich repeat protein 5	protein-coding
mm_171769.1	chr5	108087941	108087951	+	1	NA	exon (NM_013827, exon 6 of 15)	exon (NM_013827, exon 6 of 15)	9781	NM_001253878	17765	Mm.257149	NM_013827	ENSMUSG00000029267	Mtf2	9230112N11Rik|AA537621|C76717|M96|Pcl2	metal response element binding transcription factor 2	protein-coding
mm_152558.1	chr19	11485719	11485728	-	1	NA	Intergenic	Intergenic	-6315	NM_001164202	666926	Mm.486382	NM_001164202	ENSMUSG00000058470	Gm8369	EG666926	predicted gene 8369	protein-coding
mm_163817.1	chr14	19416482	19416502	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	186095	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_96198.1	chr11	62005785	62005795	+	1	NA	intron (NM_001310526, intron 1 of 7)	intron (NM_001310526, intron 1 of 7)	49027	NM_001310526	432572	Mm.438022	NM_001029936	ENSMUSG00000042331	Specc1	2810012G08Rik|B230396K10Rik|Cytsb	sperm antigen with calponin homology and coiled-coil domains 1	protein-coding
mm_92287.1	chr10	71344796	71344881	-	1	NA	promoter-TSS (NM_134007)	promoter-TSS (NM_134007)	11	NM_134007	52637	Mm.254114	NM_134007	ENSMUSG00000037710	Cisd1	AU043990|AW743335|D10Ertd214e|Zcd1|mitoNEET	CDGSH iron sulfur domain 1	protein-coding
mm_160446.1	chr8	104541374	104541374	+	1	NA	promoter-TSS (NM_001301165)	promoter-TSS (NM_001301165)	65	NM_001301165	12354	Mm.129265	NM_053070	ENSMUSG00000031883	Car7	AV343731|Ca7	carbonic anhydrase 7	protein-coding
mm_19302.1	chr2	90479149	90479155	-	1	NA	promoter-TSS (NM_001135657)	promoter-TSS (NM_001135657)	22	NM_001135657	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_18912.1	chr2	76736143	76736154	-	1	NA	exon (NM_011652, exon 275 of 313)	exon (NM_011652, exon 275 of 313)	60833	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_10837.1	chr2	24925352	24925357	+	1	NA	TTS (NM_001162485)	TTS (NM_001162485)	-5745	NM_001109686	77683	Mm.24176	NM_172545	ENSMUSG00000036893	Ehmt1	9230102N17Rik|D330003E03|Eu-HMTase1|GLP|GLP1|KMT1D|mKIAA1876	euchromatic histone methyltransferase 1	protein-coding
mm_5389.1	chr1	31222605	31222620	-	1	NA	promoter-TSS (NM_029062)	promoter-TSS (NM_029062)	44	NR_033445	70988	Mm.161414	NM_027637	ENSMUSG00000086727	4931428L18Rik	4930563O14Rik	RIKEN cDNA 4931428L18 gene	ncRNA
mm_94282.1	chr11	3983641	3983695	+	1	NA	promoter-TSS (NM_001177703)	promoter-TSS (NM_001177703)	32	NM_016922	53897	Mm.103414	NM_016922	ENSMUSG00000049721	Gal3st1	Cst|Gcst	galactose-3-O-sulfotransferase 1	protein-coding
mm_7844.1	chr1	132360316	132360341	-	1	NA	exon (NM_178874, exon 3 of 5)	exon (NM_178874, exon 3 of 5)	7620	NM_001311108	68875	Mm.273785	NM_178874	ENSMUSG00000042066	Tmcc2	1110063G11Rik	transmembrane and coiled-coil domains 2	protein-coding
mm_139430.1	chr17	53567289	53567310	+	1	NA	5' UTR (NM_020005, exon 1 of 18)	5' UTR (NM_020005, exon 1 of 18)	328	NM_020005	18519	Mm.255025	NM_020005	ENSMUSG00000000708	Kat2b	A930006P13Rik|AI461839|AW536563|Pcaf|p/CAF	K(lysine) acetyltransferase 2B	protein-coding
mm_156924.1	chrX	169258666	169258668	+	1	NA	intron (NR_109847, intron 8 of 14)	intron (NR_109847, intron 8 of 14)	61705	NM_001331050	15159	Mm.284033	NM_008222	ENSMUSG00000031352	Hccs	-	holocytochrome c synthetase	protein-coding
mm_156631.1	chrX	155622680	155622698	+	1	NA	intron (NM_001093750, intron 1 of 2)	CpG	638	NM_001093750	211612	Mm.218811	NM_001093750	ENSMUSG00000041552	Ptchd1	9630036J22Rik|AI848149|Gm387	patched domain containing 1	protein-coding
mm_147713.1	chr18	60812473	60812490	-	1	NA	TTS (NR_039567)	TTS (NR_039567)	405	NR_039567	100628611		NR_039567	ENSMUSG00000093327	Mir5107	mir-5107|mmu-mir-5107|mu-mir-5107	microRNA 5107	ncRNA
mm_57179.1	chr6	122848430	122848440	-	1	NA	3' UTR (NM_009779, exon 2 of 2)	3' UTR (NM_009779, exon 2 of 2)	7722	NM_009779	12267	Mm.2408	NM_009779	ENSMUSG00000040552	C3ar1	AZ3B|C3AR|HNFAG09	complement component 3a receptor 1	protein-coding
mm_36750.1	chr4	101182779	101182779	-	1	NA	intron (NM_146145, intron 5 of 24)	intron (NM_146145, intron 5 of 24)	82503	NM_146145	16451	Mm.289657	NM_146145	ENSMUSG00000028530	Jak1	AA960307|BAP004|C130039L05Rik	Janus kinase 1	protein-coding
mm_57105.1	chr6	122591474	122591484	-	1	NA	intron (NM_031159, intron 3 of 7)	intron (NM_031159, intron 3 of 7)	10965	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_38053.1	chr4	134004121	134004138	-	1	NA	3' UTR (NM_145833, exon 4 of 4)	3' UTR (NM_145833, exon 4 of 4)	-3265	NM_026144	67422	Mm.100290	NM_026144	ENSMUSG00000012117	Dhdds	3222401G21Rik|CIT|DS|HDS|W91638	dehydrodolichyl diphosphate synthase	protein-coding
mm_15336.1	chr2	155974291	155974311	+	1	NA	exon (NM_008383, exon 16 of 34)	exon (NM_008383, exon 16 of 34)	17743	NM_177217	16328	Mm.288729	NM_008383	ENSMUSG00000038241	Cep250	AW490617|B230210E21Rik|Cep2|Inmp	centrosomal protein 250	protein-coding
mm_86755.1	chr10	19607259	19607286	+	1	NA	exon (NM_010511, exon 6 of 7)	exon (NM_010511, exon 6 of 7)	-14756	NM_178258	237310	Mm.331979	NM_178258	ENSMUSG00000039760	Il22ra2	CRF2-10|CRF2-s1|CRF2X|Il-22bp	interleukin 22 receptor, alpha 2	protein-coding
mm_152258.1	chr19	8786246	8786270	-	1	NA	promoter-TSS (NM_146092)	promoter-TSS (NM_146092)	58	NM_146092	225895	Mm.220886	NM_146092	ENSMUSG00000003680	Taf6l	2810417N14Rik|BB223262|C530024J06Rik|Paf65a	TATA-box binding protein associated factor 6 like	protein-coding
mm_52205.1	chr6	100834098	100834117	+	1	NA	intron (NM_182939, intron 1 of 8)	CpG	469	NM_182939	232314	Mm.27223	NM_182939	ENSMUSG00000052144	Ppp4r2	BE691708|C230060M08Rik	protein phosphatase 4, regulatory subunit 2	protein-coding
mm_77435.1	chr8	121570462	121570466	-	1	NA	intron (NM_133765, intron 1 of 8)	intron (NM_133765, intron 1 of 8)	8342	NM_133765	76454	Mm.24829	NM_133765	ENSMUSG00000052934	Fbxo31	1110003O08Rik|2310046N15Rik|Fbx14|Fbxo14	F-box protein 31	protein-coding
mm_114224.1	chr13	56441472	56441475	+	1	NA	intron (NM_177809, intron 1 of 7)	L1MB5|LINE|L1	3118	NM_177809	328258	Mm.482177	NM_177809	ENSMUSG00000021509	Slc25a48	AU042651|E230025K15	solute carrier family 25, member 48	protein-coding
mm_77608.1	chr8	123893282	123893315	-	1	NA	exon (NM_009606, exon 3 of 7)	exon (NM_009606, exon 3 of 7)	1477	NM_001272041	11459	Mm.214950	NM_009606	ENSMUSG00000031972	Acta1	AA959943|Acta-2|Acts|Actsk-1	actin, alpha 1, skeletal muscle	protein-coding
mm_142032.1	chr17	35235756	35235817	-	1	NA	promoter-TSS (NM_010909)	promoter-TSS (NM_010909)	29	NM_010909	18038	Mm.300795	NM_010909	ENSMUSG00000042419	Nfkbil1	Def-7|IKBL	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor like 1	protein-coding
mm_107381.1	chr12	33146957	33146994	+	1	NA	promoter-TSS (NM_028139)	promoter-TSS (NM_028139)	611	NR_015602	320046	Mm.208337	NR_015602	ENSMUSG00000052125	F730043M19Rik	-	RIKEN cDNA F730043M19 gene	ncRNA
mm_92673.1	chr10	80546659	80546672	-	1	NA	intron (NM_025852, intron 4 of 14)	intron (NM_025852, intron 4 of 14)	-7541	NM_026094	67331	Mm.52511	NM_026094	ENSMUSG00000003341	Atp8b3	1700042F02Rik|1700056N23Rik|ATPIK|SAPLT	ATPase, class I, type 8B, member 3	protein-coding
mm_122580.1	chr14	50835671	50835678	-	1	NA	intron (NM_009351, intron 41 of 54)	intron (NM_009351, intron 41 of 54)	27728	NM_009632	11546	Mm.281482	NM_009632	ENSMUSG00000036023	Parp2	ARTD2|Adprt2|Adprtl2|Aspartl2|C78626|PARP-2	poly (ADP-ribose) polymerase family, member 2	protein-coding
mm_10576.1	chr2	18073940	18073943	+	1	NA	intron (NR_045538, intron 3 of 22)	intron (NR_045538, intron 3 of 22)	9356	NM_001252561	17354	Mm.209175	NM_010804	ENSMUSG00000026743	Mllt10	Af10|B130021D15Rik|D630001B22Rik|mKIAA4140	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 10	protein-coding
mm_79696.1	chr9	60837581	60837599	+	1	NA	intron (NM_028283, intron 1 of 18)	intron (NM_028283, intron 1 of 18)	43042	NM_028283	72565	Mm.68819	NM_028283	ENSMUSG00000034485	Uaca	2700059D02Rik|nucling	uveal autoantigen with coiled-coil domains and ankyrin repeats	protein-coding
mm_147561.1	chr18	54988839	54988853	-	1	NA	intron (NM_175751, intron 1 of 9)	intron (NM_175751, intron 1 of 9)	1334	NM_175751	269023	Mm.192984	NM_175751	ENSMUSG00000052713	Zfp608	4932417D18Rik|D430007A19Rik|Znf608	zinc finger protein 608	protein-coding
mm_85975.1	chr9	112164297	112164309	-	1	NA	intron (NM_001177623, intron 9 of 9)	intron (NM_001177623, intron 9 of 9)	21646	NM_001177618	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_15437.1	chr2	157279279	157279317	+	1	NA	exon (NM_001039557, exon 1 of 25)	exon (NM_001039557, exon 1 of 25)	200	NM_019642	20014	Mm.22130	NM_019642	ENSMUSG00000027642	Rpn2	1300012C06Rik|AV261018|Rpn-2	ribophorin II	protein-coding
mm_67986.1	chr7	100855404	100855440	-	1	NA	intron (NM_177073, intron 1 of 10)	intron (NM_177073, intron 1 of 10)	7991	NM_177073	320100	Mm.40336	NM_177073	ENSMUSG00000008318	Relt	E430021K24Rik|Tnfrsf19l	RELT tumor necrosis factor receptor	protein-coding
mm_102531.1	chr11	61153137	61153144	-	1	NA	3' UTR (NM_001004143, exon 13 of 13)	3' UTR (NM_001004143, exon 13 of 13)	12305	NM_021349	57916	Mm.265915	NM_021349	ENSMUSG00000010142	Tnfrsf13b	1200009E08Rik|Taci	tumor necrosis factor receptor superfamily, member 13b	protein-coding
mm_61561.1	chr7	79535998	79536061	+	1	NA	Intergenic	CpG	20594	NR_040312	101694	Mm.41661	NR_040311	ENSMUSG00000097023	Mir9-3hg	AI854517	Mir9-3 host gene	ncRNA
mm_13530.1	chr2	110597299	110597316	+	1	NA	promoter-TSS (NM_001003915)	promoter-TSS (NM_001003915)	8	NM_001177624	241612	Mm.277148	NM_001003915	ENSMUSG00000041644	Slc5a12	AI315119|D630015G19|SMCT2	solute carrier family 5 (sodium/glucose cotransporter), member 12	protein-coding
mm_57244.1	chr6	123283200	123283215	-	1	NA	3' UTR (NM_019948, exon 6 of 6)	3' UTR (NM_019948, exon 6 of 6)	6664	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_153446.1	chr19	41011677	41011680	-	1	NA	Intergenic	Intergenic	-17143	NM_008528	17060	Mm.9749	NM_008528	ENSMUSG00000061132	Blnk	BASH|Bca|Ly-57|Ly57|Lyw-57|SLP-65	B cell linker	protein-coding
mm_92143.1	chr10	67011268	67011282	-	1	NA	3' UTR (NM_001204915, exon 9 of 9)	3' UTR (NM_001204915, exon 9 of 9)	6200	NR_110511	102634101	Mm.445258	NR_110511		Gm31763	-	predicted gene, 31763	ncRNA
mm_170393.1	chr1	86357288	86357291	-	1	NA	promoter-TSS (NR_002851)	promoter-TSS (NR_002851)	-962	NR_002851	80828		NR_002851	ENSMUSG00000064823	Snord82	Rnu82|U82|Z25	small nucleolar RNA, C/D box 82	snoRNA
mm_155849.1	chrX	101274064	101274088	+	1	NA	promoter-TSS (NM_021521)	promoter-TSS (NM_021521)	-15	NM_021521	59024	Mm.20873	NM_021521	ENSMUSG00000079487	Med12	230kDa|Mopa|OPA-1|Tnrc11|Trap230	mediator complex subunit 12	protein-coding
mm_27296.1	chr3	45776212	45776219	-	1	NA	Intergenic	Intergenic	-336906	NR_040594	72274	Mm.396202	NR_040594	ENSMUSG00000100799	1700027H10Rik	-	RIKEN cDNA 1700027H10 gene	ncRNA
mm_116210.1	chr13	32783904	32783914	-	1	NA	Intergenic	Intergenic	-2130	NM_001166030	238564	Mm.60041	NM_001166030	ENSMUSG00000044951	Mylk4	EG238564	myosin light chain kinase family, member 4	protein-coding
mm_58914.1	chr7	17672308	17672314	+	1	NA	promoter-TSS (NR_002857)	promoter-TSS (NR_002857)	-2	NR_002857	232919	Mm.153893	NR_002857	ENSMUSG00000108558	Psg-ps1	AV036018|Cea-6|Cea6	pregnancy specific glycoprotein pseudogene 1	pseudo
mm_27602.1	chr3	59153565	59153575	-	1	NA	promoter-TSS (NR_045641)	promoter-TSS (NR_045641)	58	NR_045641	320463	Mm.484506	NR_045641	ENSMUSG00000036381	F630111L10Rik	-	RIKEN cDNA F630111L10 gene	ncRNA
mm_2584.1	chr1	118628046	118628060	+	1	NA	exon (NM_023755, exon 1 of 15)	exon (NM_023755, exon 1 of 15)	108	NM_023755	81879	Mm.24621	NM_023755	ENSMUSG00000026380	Tfcp2l1	1810030F05Rik|4932442M07Rik|AA575098|Cp2l1|Crtr-1|D930018N21Rik|LBP-9|Tcfcp2l1	transcription factor CP2-like 1	protein-coding
mm_143617.1	chr17	78769078	78769101	-	1	NA	intron (NM_001081179, intron 27 of 35)	intron (NM_001081179, intron 27 of 35)	-32529	NM_011500	268980	Mm.311915	NM_011500	ENSMUSG00000024077	Strn	AU022939|D130055P19	striatin, calmodulin binding protein	protein-coding
mm_25599.1	chr3	116903698	116903715	+	1	NA	TTS (NM_001113478)	TTS (NM_001113478)	42026	NM_009146	20321	Mm.66293	NM_009146	ENSMUSG00000033386	Frrs1	AI131732|Sdfr2	ferric-chelate reductase 1	protein-coding
mm_49223.1	chr6	15793562	15793572	+	1	NA	intron (NM_175088, intron 4 of 4)	intron (NM_175088, intron 4 of 4)	72906	NM_175088	16543	Mm.1314	NM_175088	ENSMUSG00000041390	Mdfic	Kdt1|Mdfid	MyoD family inhibitor domain containing	protein-coding
mm_131055.1	chr16	4212813	4212819	+	1	NA	intron (NM_001025432, intron 1 of 30)	intron (NM_001025432, intron 1 of 30)	588	NM_001025432	12914	Mm.132238	NM_001025432	ENSMUSG00000022521	Crebbp	AW558298|CBP|CBP/p300|KAT3A|p300/CBP	CREB binding protein	protein-coding
mm_126131.1	chr15	78336342	78336348	+	1	NA	intron (NM_007780, intron 2 of 13)	intron (NM_007780, intron 2 of 13)	10355	NM_007780	12983	Mm.235324	NM_007780	ENSMUSG00000071713	Csf2rb	AI848964|AIC2B|Bc|CDw131|Csf2rb1|Csfgmrb|Il3r|Il3rb|Il3rb1|Il5rb	colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage)	protein-coding
mm_117022.1	chr13	58183236	58183258	-	1	NA	exon (NM_152234, exon 7 of 10)	exon (NM_152234, exon 7 of 10)	25598	NM_198004	75731	Mm.293919	NM_198004	ENSMUSG00000050002	Idnk	5133401N09Rik	idnK gluconokinase homolog (E. coli)	protein-coding
mm_26289.1	chr3	142506780	142506800	+	1	NA	exon (NM_153564, exon 8 of 11)	exon (NM_153564, exon 8 of 11)	9856	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_151432.1	chr19	57131700	57131735	+	1	NA	intron (NM_001290813, intron 6 of 20)	intron (NM_001290813, intron 6 of 20)	-12693	NM_001103178	226251	Mm.217161	NM_178688	ENSMUSG00000025085	Ablim1	2210411C18Rik|2610209L21Rik|4833406P10Rik|9330196J19Rik|AV079770|AW060987|AW215784|Limab1|mKIAA0059	actin-binding LIM protein 1	protein-coding
mm_52077.1	chr6	97827466	97827479	+	1	NA	intron (NM_001113198, intron 1 of 9)	intron (NM_001113198, intron 1 of 9)	20414	NM_001113198	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_12449.1	chr2	71211714	71211794	+	1	NA	promoter-TSS (NM_001198877)	promoter-TSS (NM_001198877)	48	NM_001198876	13427	Mm.249479	NM_010064	ENSMUSG00000027012	Dync1i2	3110079H08Rik|AW554389|Dncic2	dynein cytoplasmic 1 intermediate chain 2	protein-coding
mm_92964.1	chr10	86011834	86011896	-	1	NA	promoter-TSS (NM_177772)	promoter-TSS (NM_177772)	-5	NM_177772	270757	Mm.107214	NM_177772	ENSMUSG00000050108	Bpifc	4732454E24|Bpil2	BPI fold containing family C	protein-coding
mm_78032.1	chr9	13827709	13827781	+	1	NA	promoter-TSS (NM_001310721)	promoter-TSS (NM_001310721)	18	NM_176836	72826	Mm.246174	NM_176836	ENSMUSG00000037808	Fam76b	2810485I05Rik|C78303	family with sequence similarity 76, member B	protein-coding
mm_80523.1	chr9	80067453	80067465	+	1	NA	5' UTR (NM_146003, exon 1 of 23)	5' UTR (NM_146003, exon 1 of 23)	556	NM_146003	215351	Mm.28232	NM_146003	ENSMUSG00000034252	Senp6	2810017C20Rik|E130319N12Rik|Susp1|mKIAA0797	SUMO/sentrin specific peptidase 6	protein-coding
mm_10706.1	chr2	22774283	22774298	+	1	NA	promoter-TSS (NM_019456)	promoter-TSS (NM_019456)	-37	NM_019456	54519	Mm.14255	NM_019456	ENSMUSG00000026786	Apbb1ip	9930118P07Rik|Prp48	amyloid beta (A4) precursor protein-binding, family B, member 1 interacting protein	protein-coding
mm_51550.1	chr6	83277376	83277416	+	1	NA	intron (NM_001166067, intron 13 of 24)	intron (NM_001166067, intron 13 of 24)	40021	NM_001166067	232156	Mm.333189	NM_001166067	ENSMUSG00000068323	Slc4a5	C330006M16|C330016K18Rik	solute carrier family 4, sodium bicarbonate cotransporter, member 5	protein-coding
mm_44813.1	chr5	33535624	33535630	-	1	NA	Intergenic	Intergenic	94008	NM_178390	74504	Mm.294695	NM_178390	ENSMUSG00000037339	Fam53a	2410018C17Rik|5430419M09Rik|Dntnp	family with sequence similarity 53, member A	protein-coding
mm_114884.1	chr13	94224915	94224928	+	1	NA	exon (NM_029153, exon 6 of 9)	exon (NM_029153, exon 6 of 9)	60360	NM_029153	107767	Mm.201455	NM_029153	ENSMUSG00000021687	Scamp1	4930505M11Rik|AI415563|AW122395	secretory carrier membrane protein 1	protein-coding
mm_166912.1	chr7	29281901	29281904	-	1	NA	promoter-TSS (NM_001082548)	promoter-TSS (NM_001082548)	75	NM_001082548	20733	Mm.295230	NM_011464	ENSMUSG00000074227	Spint2	AL024025|C76321|HAI-2	serine protease inhibitor, Kunitz type 2	protein-coding
mm_41268.1	chr5	89085501	89085520	+	1	NA	intron (NM_001197147, intron 7 of 25)	B4A|SINE|B4	198250	NM_018760	54403	Mm.41044	NM_018760	ENSMUSG00000060961	Slc4a4	AI835705|NBC|NBC1	solute carrier family 4 (anion exchanger), member 4	protein-coding
mm_18112.1	chr2	44996100	44996115	-	1	NA	exon (NM_015753, exon 8 of 10)	exon (NM_015753, exon 8 of 10)	27070	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_99184.1	chr11	100860419	100860428	+	1	NA	promoter-TSS (NM_001164062)	promoter-TSS (NM_001164062)	-61	NM_001164062	20850	Mm.277403	NM_011488	ENSMUSG00000004043	Stat5a	AA959963|STAT5	signal transducer and activator of transcription 5A	protein-coding
mm_30456.1	chr3	153912967	153912990	-	1	NA	promoter-TSS (NR_028525)	promoter-TSS (NR_028525)	-12	NR_028094	19352	Mm.277831	NM_011231	ENSMUSG00000038975	Rabggtb	-	Rab geranylgeranyl transferase, b subunit	protein-coding
mm_14884.1	chr2	148835334	148835334	+	1	NA	exon (NM_009979, exon 1 of 3)	exon (NM_009979, exon 1 of 3)	187	NM_009979	13013	Mm.21005	NM_009979	ENSMUSG00000027445	Cst9	M12|cresp|testatin	cystatin 9	protein-coding
mm_94634.1	chr11	16870456	16870463	+	1	NA	intron (NM_207655, intron 7 of 27)	intron (NM_207655, intron 7 of 27)	80823	NR_110421	72735	Mm.268598	NR_015469		Eldr	2810442I21Rik|4930500E12Rik|Fabl	Egfr long non-coding downstream RNA	ncRNA
mm_93378.1	chr10	105558946	105558963	-	1	NA	intron (NM_177368, intron 1 of 11)	intron (NM_177368, intron 1 of 11)	15525	NM_177368	278279	Mm.25225	NM_177368	ENSMUSG00000036019	Tmtc2	8430438D04Rik|D330034A10Rik	transmembrane and tetratricopeptide repeat containing 2	protein-coding
mm_86824.1	chr10	21027078	21027091	+	1	NA	intron (NM_026203, intron 18 of 23)	L2|LINE|L2	-13736	NM_001177776	52906	Mm.253280	NM_026203	ENSMUSG00000019986	Ahi1	1700015F03Rik|Ahi-1|D10Bwg0629e	Abelson helper integration site 1	protein-coding
mm_171204.1	chr3	54538691	54538706	+	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	-154407	NM_019995	56790	Mm.486375	NM_019995	ENSMUSG00000027751	Supt20	AA667204|AI450544|D3Ertd300e|Fam48a|Supt20h|p38IP	suppressor of Ty 20	protein-coding
mm_74853.1	chr8	24674752	24674759	-	1	NA	promoter-TSS (NM_010084)	promoter-TSS (NM_010084)	0	NR_136908	13524	Mm.89943	NM_010084	ENSMUSG00000031552	Adam18	Adam27|Dtgn3|Tmdc3|tMDCIII	a disintegrin and metallopeptidase domain 18	protein-coding
mm_40843.1	chr5	73292822	73292846	+	1	NA	promoter-TSS (NM_001159889)	promoter-TSS (NM_001159889)	40	NM_001159888	68095	Mm.247039	NM_023429	ENSMUSG00000029152	Ociad1	6030432N09Rik|AI481327|AW557942|Asrij|B230209J16Rik|BB021357|Emi2|Imi2|OCIA|TPA018	OCIA domain containing 1	protein-coding
mm_126229.1	chr15	78947891	78947897	+	1	NA	5' UTR (NM_001039155, exon 1 of 8)	5' UTR (NM_001039155, exon 1 of 8)	170	NM_001039155	110253	Mm.123714	NM_138579	ENSMUSG00000033088	Triobp	AI428493|EST478828|Tara|mKIAA1662	TRIO and F-actin binding protein	protein-coding
mm_104301.1	chr11	90549439	90549446	-	1	NA	intron (NM_011505, intron 12 of 17)	intron (NM_011505, intron 12 of 17)	88666	NM_011505	20913	Mm.207203	NM_011505	ENSMUSG00000020546	Stxbp4	6030470M02Rik|Synip	syntaxin binding protein 4	protein-coding
mm_22887.1	chr3	30647924	30647934	+	1	NA	promoter-TSS (NM_001290510)	promoter-TSS (NM_001290510)	43	NM_001290510	68307	Mm.389425	NM_026668	ENSMUSG00000027703	Lrriq4	4930558O21Rik	leucine-rich repeats and IQ motif containing 4	protein-coding
mm_135378.1	chr16	44139056	44139077	-	1	NA	promoter-TSS (NM_007508)	promoter-TSS (NM_007508)	-47	NM_007508	11964	Mm.217787	NM_007508	ENSMUSG00000052459	Atp6v1a	AI647066|Atp6a1|Atp6a2|Atp6v1a1|VA68|VPP2	ATPase, H+ transporting, lysosomal V1 subunit A	protein-coding
mm_9647.1	chr1	177258830	177258857	-	1	NA	Intergenic	CpG	-10076	NM_011785	23797	Mm.235194	NM_011785	ENSMUSG00000019699	Akt3	AI851531|D930002M15Rik|Nmf350	thymoma viral proto-oncogene 3	protein-coding
mm_19703.1	chr2	103775955	103775972	-	1	NA	exon (NM_016739, exon 9 of 19)	exon (NM_016739, exon 9 of 19)	-14713	NM_153126	98956	Mm.288005	NM_153126	ENSMUSG00000027185	Nat10	AI429152	N-acetyltransferase 10	protein-coding
mm_54979.1	chr6	48740614	48740632	-	1	NA	intron (NM_175860, intron 1 of 2)	intron (NM_175860, intron 1 of 2)	1576	NM_008376	16205	Mm.252599	NM_008376	ENSMUSG00000090019	Gimap1	IAP38|Imap38|imap	GTPase, IMAP family member 1	protein-coding
mm_85420.1	chr9	103480337	103480348	-	1	NA	promoter-TSS (NM_001002896)	promoter-TSS (NM_001002896)	-14	NM_001002896	107993	Mm.335403	NM_001002896	ENSMUSG00000032556	Bfsp2	AI448593|CP49	beaded filament structural protein 2, phakinin	protein-coding
mm_28082.1	chr3	84582744	84582754	-	1	NA	promoter-TSS (NM_001293801)	promoter-TSS (NM_001293801)	-124	NM_001293801	99889	Mm.316536	NM_001081093	ENSMUSG00000074513	Arfip1	2310030I10Rik|Arfaptin|D3Ertd598e	ADP-ribosylation factor interacting protein 1	protein-coding
mm_153828.1	chr19	46317963	46317965	-	1	NA	intron (NM_028627, intron 11 of 17)	CpG	8902	NM_001347454	73728	Mm.268532	NM_028627	ENSMUSG00000037126	Psd	1110007H17Rik|A930015K15|Efa6|Efa6a|Psdl|mKIAA2011	pleckstrin and Sec7 domain containing	protein-coding
mm_136594.1	chr17	5012842	5012852	+	1	NA	intron (NM_001085355, intron 1 of 19)	intron (NM_001085355, intron 1 of 19)	17773	NM_001085355	239985	Mm.133401	NM_001085355	ENSMUSG00000069729	Arid1b	8030481M12|9330189K18Rik|AI836955|Ardi1b|B230217J03Rik|mKIAA1235	AT rich interactive domain 1B (SWI-like)	protein-coding
mm_132806.1	chr16	45158870	45158921	+	1	NA	promoter-TSS (NM_028756)	promoter-TSS (NM_028756)	66	NM_026402	67841	Mm.41775	NM_026402	ENSMUSG00000022663	Atg3	2610016C12Rik|APG3|Apg3l|Atg3l|PC3-96	autophagy related 3	protein-coding
mm_28759.1	chr3	95882032	95882047	-	1	NA	intron (NM_001033302, intron 1 of 5)	CpG	189	NM_001033302	229599	Mm.331218	NM_001033302	ENSMUSG00000038550	Ciart	Chrono|Gm129	circadian associated repressor of transcription	protein-coding
mm_68449.1	chr7	110059739	110059749	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-1958	NM_009281	20841	Mm.10815	NM_009281	ENSMUSG00000061079	Zfp143	AA959806|AU015869|D7Ertd805e|KRAB14|SBF|Staf|Zfp79|Zfp80-rs1|Znf143|pHZ-1	zinc finger protein 143	protein-coding
mm_39585.1	chr5	23482465	23482479	+	1	NA	exon (NM_026984, exon 12 of 26)	exon (NM_026984, exon 12 of 26)	48043	NM_026984	69188	Mm.205190	NM_026984	ENSMUSG00000029004	Kmt2e	1810033J14Rik|9530077A04Rik|D230038D11Rik|Mll5|NKp44L	lysine (K)-specific methyltransferase 2E	protein-coding
mm_16835.1	chr2	11498402	11498414	-	1	NA	intron (NM_001177758, intron 1 of 14)	intron (NM_001177758, intron 1 of 14)	3682	NM_001177754	170768	Mm.19669	NM_133232	ENSMUSG00000026773	Pfkfb3	E330010H22Rik|iPFK-2|uPFK-2	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	protein-coding
mm_168873.1	chr12	38075009	38075009	+	1	NA	intron (NM_178681, intron 2 of 24)	L1Md_T|LINE|L1	194304	NM_178681	217480	Mm.126525	NM_178681	ENSMUSG00000036095	Dgkb	6430574F24|90kda|C630029D13Rik|DAGK2|DGK|DGK-beta|mKIAA0718	diacylglycerol kinase, beta	protein-coding
mm_70953.1	chr8	26977303	26977344	+	1	NA	promoter-TSS (NM_001110508)	promoter-TSS (NM_001110508)	-13	NM_001101502	353310	Mm.212469	NM_001101502	ENSMUSG00000085795	Zfp703	1110032O19Rik|AI430822|AL022941|Csmn1|End2|Zeppo1|Znf703|Zpo1	zinc finger protein 703	protein-coding
mm_141664.1	chr17	33781536	33781550	-	1	NA	promoter-TSS (NM_020581)	promoter-TSS (NM_020581)	32	NM_020581	57875	Mm.196189	NM_020581	ENSMUSG00000002289	Angptl4	Arp4|Bk89|Fiaf|Hfarp|Ng27|Pgar|Pgarg|Pp1158	angiopoietin-like 4	protein-coding
mm_25962.1	chr3	132684107	132684145	+	1	NA	promoter-TSS (NM_007926)	promoter-TSS (NM_007926)	-18	NM_001163455	271981	Mm.257864	NM_173032	ENSMUSG00000028030	Tbck	1700120J03Rik|9430001M19|A630047E20Rik|C030007I09Rik|Tbckl	TBC1 domain containing kinase	protein-coding
mm_124300.1	chr14	103055714	103055727	-	1	NA	3' UTR (NM_008392, exon 5 of 5)	3' UTR (NM_008392, exon 5 of 5)	8708	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_100835.1	chr11	5542140	5542170	-	1	NA	promoter-TSS (NM_134033)	promoter-TSS (NM_134033)	62	NM_134033	104479	Mm.210403	NM_134033	ENSMUSG00000020482	Ccdc117	1110004K02Rik|1700026O03Rik|AU018638|AU042822|AV173073|BC018601	coiled-coil domain containing 117	protein-coding
mm_75597.1	chr8	61703174	61703187	-	1	NA	exon (NM_001293773, exon 6 of 20)	exon (NM_001293773, exon 6 of 20)	56918	NM_001293773	72333	Mm.29933	NM_001081390	ENSMUSG00000058056	Palld	2410003B16Rik|6030492A02	palladin, cytoskeletal associated protein	protein-coding
mm_76980.1	chr8	106886395	106886409	-	1	NA	exon (NM_145412, exon 4 of 4)	exon (NM_145412, exon 4 of 4)	7191	NM_145412	214987	Mm.490308	NM_145412	ENSMUSG00000046691	Chtf8	5830457O10Rik|Ctf8|Derpc	CTF8, chromosome transmission fidelity factor 8	protein-coding
mm_40229.1	chr5	37286431	37286441	+	1	NA	exon (NM_001136058, exon 12 of 14)	exon (NM_001136058, exon 12 of 14)	40672	NM_007765	12933	Mm.290995	NM_007765	ENSMUSG00000029121	Crmp1	CRMP-1|DRP-1|Dpysl1|ULIP-3|Ulip3	collapsin response mediator protein 1	protein-coding
mm_147742.1	chr18	61109741	61109796	-	1	NA	exon (NM_001037859, exon 3 of 22)	exon (NM_001037859, exon 3 of 22)	4196	NM_001037859	12978	Mm.22574	NM_007779	ENSMUSG00000024621	Csf1r	AI323359|CD115|CSF-1R|Csfmr|Fim-2|Fim2|Fms|M-CSF-R|M-CSFR	colony stimulating factor 1 receptor	protein-coding
mm_158176.1	chrX	103958259	103958304	-	1	NA	3' UTR (NM_011276, exon 5 of 5)	3' UTR (NM_011276, exon 5 of 5)	23003	NM_011276	19820	Mm.427762	NM_011276	ENSMUSG00000056537	Rlim	AL022832|AW743871|Ha1r|Rlim1|Rnf12	ring finger protein, LIM domain interacting	protein-coding
mm_133132.1	chr16	65839372	65839407	+	1	NA	exon (NM_028572, exon 3 of 4)	exon (NM_028572, exon 3 of 4)	23756	NM_028572	73569	Mm.25670	NM_028572	ENSMUSG00000091243	Vgll3	1700110N18Rik|4832416J22|C80713|Vgl-3|Vito-2	vestigial like family member 3	protein-coding
mm_124481.1	chr14	121624049	121624051	-	1	NA	intron (NM_001347596, intron 23 of 52)	MLT1A1|LTR|ERVL-MaLR	74367	NM_001347596	105445	Mm.378591	NM_134074	ENSMUSG00000025558	Dock9	AA959601|AW538057|B230309H04Rik|D14Wsu89e|Zizimin1|mKIAA1058	dedicator of cytokinesis 9	protein-coding
mm_172894.1	chr9	56223706	56223724	-	1	NA	intron (NM_172924, intron 6 of 6)	LSU-rRNA_Hsa|rRNA|rRNA	-62645	NM_019793	56434	Mm.28484	NM_019793	ENSMUSG00000032324	Tspan3	1700055K04Rik|TM4-A|Tm4sf8	tetraspanin 3	protein-coding
mm_107963.1	chr12	72735869	72735887	+	1	NA	Intergenic	MT2B|LTR|ERVL	-25333	NM_008910	19042	Mm.261045	NM_008910	ENSMUSG00000021096	Ppm1a	2310003C21Rik|2900017D14Rik|AI427932|AU017636|MMPa-2|MPPa-1	protein phosphatase 1A, magnesium dependent, alpha isoform	protein-coding
mm_160620.1	chr9	96478595	96478595	-	1	NA	promoter-TSS (NM_011279)	promoter-TSS (NM_011279)	80	NM_011279	19823	Mm.28235	NM_011279	ENSMUSG00000051234	Rnf7	Rbx2|SAG	ring finger protein 7	protein-coding
mm_112192.1	chr12	113425421	113425434	-	1	NA	Intergenic	(CAGCT)n|Simple_repeat|Simple_repeat	-64138	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_164951.1	chr19	5050448	5050466	+	1	NA	promoter-TSS (NM_145495)	promoter-TSS (NM_145495)	-351	NM_145495	225870	Mm.271922	NM_145495	ENSMUSG00000024883	Rin1	-	Ras and Rab interactor 1	protein-coding
mm_82072.1	chr9	122903294	122903308	+	1	NA	Intergenic	CpG	14830	NM_001177505	382118	Mm.86999	NM_001177505	ENSMUSG00000063488	Zkscan7	BC042569|Zfp167	zinc finger with KRAB and SCAN domains 7	protein-coding
mm_103234.1	chr11	70683619	70683640	-	1	NA	intron (NM_178116, intron 5 of 22)	intron (NM_178116, intron 5 of 22)	4476	NM_001190376	216874	Mm.473726	NM_178116	ENSMUSG00000040712	Camta2	Kiaa0909-hp|mKIAA0909	calmodulin binding transcription activator 2	protein-coding
mm_67657.1	chr7	84835037	84835037	-	1	NA	Intergenic	Intergenic	-18534	NM_146415	258410	Mm.484702	NM_146415	ENSMUSG00000070460	Olfr291	MOR254-2	olfactory receptor 291	protein-coding
mm_68312.1	chr7	105787507	105787523	-	1	NA	promoter-TSS (NM_001162943)	promoter-TSS (NM_001162943)	35	NM_001162943	233651	Mm.334108	NM_001162943	ENSMUSG00000036862	Dchs1	3110041P15Rik|C130033F22Rik|CDH25|FIB1|Gm165|PCDH16	dachsous 1 (Drosophila)	protein-coding
mm_31078.1	chr4	41517408	41517416	+	1	NA	promoter-TSS (NM_001048005)	promoter-TSS (NM_001048005)	-25	NR_045726	76992	Mm.440546	NR_045726	ENSMUSG00000036162	Fam219aos	1700066J24Rik	family with sequence similarity 219, member A, opposite strand	ncRNA
mm_71076.1	chr8	34216825	34216846	+	1	NA	Intergenic	ORR1B2|LTR|ERVL-MaLR	-50123	NR_105820	102465211		NR_105820	ENSMUSG00000098785	Mir6395	Gm27561|mmu-mir-6395	microRNA 6395	ncRNA
mm_47659.1	chr5	125393326	125393339	-	1	NA	Intergenic	Intergenic	-3315	NM_019639	22190	Mm.331	NM_019639	ENSMUSG00000008348	Ubc	2700054O04Rik|AI194771|Rps27a|TI-225|Uba52|Ubb	ubiquitin C	protein-coding
mm_79072.1	chr9	46241053	46241068	+	1	NA	5' UTR (NM_007468, exon 1 of 3)	5' UTR (NM_007468, exon 1 of 3)	216	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_161433.1	chr15	57985984	57985984	+	1	NA	promoter-TSS (NM_173862)	promoter-TSS (NM_173862)	81	NM_173862	239463	Mm.221241	NM_173862	ENSMUSG00000051225	Fam83a	-	family with sequence similarity 83, member A	protein-coding
mm_58441.1	chr7	3298205	3298232	+	1	NA	3' UTR (NM_016969, exon 3 of 3)	3' UTR (NM_016969, exon 3 of 3)	5190	NM_001093766	50918	Mm.29874	NM_016969	ENSMUSG00000068566	Myadm	D7Wsu62e	myeloid-associated differentiation marker	protein-coding
mm_28375.1	chr3	89959147	89959156	-	1	NA	intron (NM_001081182, intron 2 of 27)	intron (NM_001081182, intron 2 of 27)	4181	NM_001081182	54667	Mm.30455	NM_001081182	ENSMUSG00000060671	Atp8b2	Id	ATPase, class I, type 8B, member 2	protein-coding
mm_137772.1	chr17	29491344	29491357	+	1	NA	exon (NM_008842, exon 2 of 6)	exon (NM_008842, exon 2 of 6)	305	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_137178.1	chr17	23816198	23816208	+	1	NA	exon (NM_175229, exon 10 of 14)	exon (NM_175229, exon 10 of 14)	12906	NM_026305	67673	Mm.153758	NM_026305	ENSMUSG00000055839	Elob	0610040H15Rik|Tceb2	elongin B	protein-coding
mm_135698.1	chr16	52452614	52452677	-	1	NA	5' UTR (NM_001331110, exon 1 of 15)	5' UTR (NM_001331110, exon 1 of 15)	436	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_42206.1	chr5	112344701	112344738	+	1	NA	5' UTR (NM_138646, exon 2 of 14)	5' UTR (NM_138646, exon 2 of 14)	1624	NM_138646	192232	Mm.238043	NM_138646	ENSMUSG00000042328	Hps4	2010205O06Rik|AU040608|BLOC-3|C130020P05Rik|le|mKIAA1667	Hermansky-Pudlak syndrome 4	protein-coding
mm_90648.1	chr10	128745194	128745234	+	1	NA	Intergenic	Intergenic	-1158	NM_016811	13139	Mm.291235	NM_016811	ENSMUSG00000025357	Dgka	80kDa|AW146112|Dagk1	diacylglycerol kinase, alpha	protein-coding
mm_76827.1	chr8	104624267	104624306	-	1	NA	5' UTR (NM_001252627, exon 1 of 17)	5' UTR (NM_001252627, exon 1 of 17)	110	NM_007663	12556	Mm.19423	NM_007663	ENSMUSG00000031881	Cdh16	-	cadherin 16	protein-coding
mm_31108.1	chr4	42917235	42917333	+	1	NA	promoter-TSS (NM_172690)	promoter-TSS (NM_172690)	33	NM_172690	230085	Mm.240965	NM_172690	ENSMUSG00000036062	Phf24	GINIP|N28178	PHD finger protein 24	protein-coding
mm_158011.1	chrX	95658311	95658344	-	1	NA	5' UTR (NM_001003916, exon 1 of 5)	5' UTR (NM_001003916, exon 1 of 5)	182	NM_001289696	245522	Mm.336158	NM_001003916	ENSMUSG00000035062	Zc4h2	Gm372|mKIAA1166	zinc finger, C4H2 domain containing	protein-coding
mm_94052.1	chr10	128180230	128180254	-	1	NA	promoter-TSS (NM_001039080)	promoter-TSS (NM_001039080)	55	NM_001039080	56516	Mm.42247	NM_019711	ENSMUSG00000040043	Rbms2	2610315E04Rik|Scr3	RNA binding motif, single stranded interacting protein 2	protein-coding
mm_20342.1	chr2	127656246	127656256	-	1	NA	5' UTR (NM_001171187, exon 1 of 3)	5' UTR (NM_001171187, exon 1 of 3)	444	NM_010762	17153	Mm.39040	NM_010762	ENSMUSG00000027375	Mal	Mpv17|Vip17	myelin and lymphocyte protein, T cell differentiation protein	protein-coding
mm_18450.1	chr2	60962802	60962821	-	1	NA	5' UTR (NM_020296, exon 1 of 14)	5' UTR (NM_020296, exon 1 of 14)	393	NM_020296	56878	Mm.259667	NM_020296	ENSMUSG00000026970	Rbms1	2600014B10Rik|AI255215|MSSP-1|MSSP-2|MSSP-3|YC1	RNA binding motif, single stranded interacting protein 1	protein-coding
mm_171474.1	chr4	145781579	145781579	+	1	NA	promoter-TSS (NM_001083918)	promoter-TSS (NM_001083918)	36	NM_001083918	666532	Mm.392861	NM_001083918	ENSMUSG00000067916	Zfp991	Gm13139|OTTMUSG00000010657	zinc finger protein 991	protein-coding
mm_43014.1	chr5	123907200	123907210	+	1	NA	promoter-TSS (NM_026603)	promoter-TSS (NM_026603)	-70	NM_026603	68184	Mm.28549	NM_026603	ENSMUSG00000023106	Denr	1500003K04Rik	density-regulated protein	protein-coding
mm_152510.1	chr19	11266169	11266197	-	1	NA	promoter-TSS (NM_007641)	promoter-TSS (NM_007641)	-32	NM_007641	12482	Mm.4046	NM_007641	ENSMUSG00000024673	Ms4a1	AA960661|Cd20|Ly-44|Ms4a2	membrane-spanning 4-domains, subfamily A, member 1	protein-coding
mm_164354.1	chr16	20716140	20716147	-	1	NA	5' UTR (NM_009900, exon 1 of 24)	5' UTR (NM_009900, exon 1 of 24)	493	NM_009900	12724	Mm.177761	NM_009900	ENSMUSG00000022843	Clcn2	AL118368|ClC-2|Clc2|nmf240	chloride channel, voltage-sensitive 2	protein-coding
mm_61535.1	chr7	79084526	79084538	+	1	NA	exon (NM_007424, exon 3 of 17)	exon (NM_007424, exon 3 of 17)	31049	NM_007424	11595	Mm.358571	NM_007424	ENSMUSG00000030607	Acan	Agc|Agc1|Cspg1|b2b183Clo|cmd	aggrecan	protein-coding
mm_65126.1	chr7	19458749	19458776	-	1	NA	promoter-TSS (NM_172279)	promoter-TSS (NM_172279)	-268	NM_172279	232944	Mm.260504	NM_172279	ENSMUSG00000030397	Mark4	2410090P21Rik|C79806|Markl1	MAP/microtubule affinity regulating kinase 4	protein-coding
mm_172931.1	chr9	7723066	7723085	+	1	NA	Intergenic	Intergenic	-27444	NR_126562	102722	Mm.334941	NR_126562	ENSMUSG00000086381	AV064505	-	expressed sequence AV064505	ncRNA
mm_62203.1	chr7	97830920	97830930	+	1	NA	Intergenic	Intergenic	-12014	NM_011035	18479	Mm.260227	NM_011035	ENSMUSG00000030774	Pak1	AW045634|PAK-1|Paka	p21 protein (Cdc42/Rac)-activated kinase 1	protein-coding
mm_35502.1	chr4	41048152	41048162	-	1	NA	promoter-TSS (NM_007473)	promoter-TSS (NM_007473)	-21	NM_007473	11832	Mm.8728	NM_007473	ENSMUSG00000028427	Aqp7	AQP7L|AQPap	aquaporin 7	protein-coding
mm_11800.1	chr2	43659653	43659654	+	1	NA	intron (NM_027552, intron 10 of 13)	intron (NM_027552, intron 10 of 13)	-89171	NM_001301832	76117	Mm.217350	NM_153820	ENSMUSG00000049744	Arhgap15	5830480G12Rik	Rho GTPase activating protein 15	protein-coding
mm_167323.1	chr8	68533381	68533386	-	1	NA	intron (NM_172753, intron 3 of 9)	MTEa|LTR|ERVL-MaLR	164924	NR_038181	73609	Mm.443247	NR_038181	ENSMUSG00000085197	1700125H03Rik	4930510D22Rik	RIKEN cDNA 1700125H03 gene	ncRNA
mm_52504.1	chr6	115360891	115360912	+	1	NA	promoter-TSS (NM_001127330)	promoter-TSS (NM_001127330)	-50	NM_001127330	19016	Mm.3020	NM_011146	ENSMUSG00000000440	Pparg	Nr1c3|PPAR-gamma|PPAR-gamma2|PPARgamma|PPARgamma2	peroxisome proliferator activated receptor gamma	protein-coding
mm_136638.1	chr17	5726536	5726538	+	1	NA	intron (NM_146073, intron 6 of 8)	intron (NM_146073, intron 6 of 8)	-72120	NR_045081	78512	Mm.23696	NR_045079	ENSMUSG00000096965	3300005D01Rik	-	RIKEN cDNA 3300005D01 gene	ncRNA
mm_6489.1	chr1	74124483	74124495	-	1	NA	promoter-TSS (NM_001289895)	promoter-TSS (NM_001289895)	-40	NM_001289895	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_16933.1	chr2	14055891	14055917	-	1	NA	5' UTR (NM_013935, exon 1 of 7)	5' UTR (NM_013935, exon 1 of 7)	131	NM_001012396	30963	Mm.241205	NM_013935	ENSMUSG00000063275	Hacd1	Ptpla	3-hydroxyacyl-CoA dehydratase 1	protein-coding
mm_41896.1	chr5	105519083	105519095	+	1	NA	promoter-TSS (NM_133897)	promoter-TSS (NM_133897)	-382	NM_133897	100604	Mm.319847	NM_133897	ENSMUSG00000054720	Lrrc8c	AD158|AI326115|E430036I04Rik|fad158	leucine rich repeat containing 8 family, member C	protein-coding
mm_84080.1	chr9	58202162	58202190	-	1	NA	promoter-TSS (NM_001161540)	promoter-TSS (NM_001161540)	109	NM_177193	320563	Mm.186499	NM_177193	ENSMUSG00000051243	Islr2	B930052A04Rik|Linx|Mbu-3|mKIAA1465	immunoglobulin superfamily containing leucine-rich repeat 2	protein-coding
mm_166155.1	chr5	13587487	13587489	+	1	NA	intron (NM_001243073, intron 16 of 17)	intron (NM_001243073, intron 16 of 17)	188179	NM_009152	20346	Mm.372039	NM_009152	ENSMUSG00000028883	Sema3a	Hsema-I|SEMA1|SemD|Semad|coll-1	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	protein-coding
mm_96810.1	chr11	69991642	69991674	+	1	NA	5' UTR (NM_019749, exon 1 of 4)	5' UTR (NM_019749, exon 1 of 4)	288	NM_019749	56486	Mm.272460	NM_019749	ENSMUSG00000018567	Gabarap	-	gamma-aminobutyric acid receptor associated protein	protein-coding
mm_30248.1	chr3	146586382	146586384	-	1	NA	intron (NM_019957, intron 5 of 6)	AT_rich|Low_complexity|Low_complexity	-10766	NM_009474	22262	Mm.10865	NM_009474	ENSMUSG00000028186	Uox	AI663847	urate oxidase	protein-coding
mm_157037.1	chrX	7947849	7947857	-	1	NA	promoter-TSS (NM_010413)	promoter-TSS (NM_010413)	36	NM_001130416	15185	Mm.29854	NM_010413	ENSMUSG00000031161	Hdac6	Hd6|Hdac5|Sfc6|mHDA2	histone deacetylase 6	protein-coding
mm_137368.1	chr17	25471674	25471688	+	1	NA	promoter-TSS (NM_027951)	promoter-TSS (NM_027951)	91	NM_027951	71840	Mm.282330	NM_027951	ENSMUSG00000024175	Tekt4	1700010L19Rik	tektin 4	protein-coding
mm_102398.1	chr11	59002375	59002385	-	1	NA	intron (NM_001171512, intron 89 of 103)	intron (NM_001171512, intron 89 of 103)	24287	NM_053168	94091	Mm.248049	NM_053168	ENSMUSG00000020455	Trim11	-	tripartite motif-containing 11	protein-coding
mm_172196.1	chr6	51466335	51466343	-	1	NA	exon (NM_182650, exon 5 of 10)	exon (NM_182650, exon 5 of 10)	3555	NM_182650	53379	Mm.155896	NM_016806	ENSMUSG00000004980	Hnrnpa2b1	9130414A06Rik|Hnrpa2|Hnrpa2b1|hnrnp-A	heterogeneous nuclear ribonucleoprotein A2/B1	protein-coding
mm_137600.1	chr17	28207796	28207814	+	1	NA	promoter-TSS (NM_027185)	promoter-TSS (NM_027185)	27	NM_027185	23853	Mm.204731	NM_027185	ENSMUSG00000002257	Def6	2410003F05Rik|6430538D02Rik|AV094905|Ibp|Slat|Slat2|Slat6	differentially expressed in FDCP 6	protein-coding
mm_140575.1	chr17	9775856	9775858	-	1	NA	promoter-TSS (NR_045433)	promoter-TSS (NR_045433)	9	NR_045433	71092	Mm.243827	NR_045433		4930452A19Rik	4933424P20Rik	RIKEN cDNA 4930452A19 gene	ncRNA
mm_76209.1	chr8	83442479	83442507	-	1	NA	5' UTR (NM_019708, exon 1 of 4)	5' UTR (NM_019708, exon 1 of 4)	169	NM_001285992	56367	Mm.246911	NM_019708	ENSMUSG00000063253	Scoc	0610011C06Rik|2810002J11Rik|AA415030|SCOCO	short coiled-coil protein	protein-coding
mm_89877.1	chr10	108332113	108332159	+	1	NA	promoter-TSS (NM_054056)	promoter-TSS (NM_054056)	-53	NM_054056	114774	Mm.391419	NM_054056	ENSMUSG00000035873	Pawr	2310001G03Rik|PAR4|Par-4	PRKC, apoptosis, WT1, regulator	protein-coding
mm_165312.1	chr2	102968537	102968541	-	1	NA	Intergenic	Intergenic	-66874	NM_001039150	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_117263.1	chr13	64369051	64369179	-	1	NA	exon (NM_009984, exon 2 of 8)	exon (NM_009984, exon 2 of 8)	1405	NM_009984	13039	Mm.930	NM_009984	ENSMUSG00000021477	Ctsl	1190035F06Rik|CatL|Ctsl1|MEP|fs|nkt	cathepsin L	protein-coding
mm_85620.1	chr9	107614891	107614903	-	1	NA	3' UTR (NM_008138, exon 9 of 9)	3' UTR (NM_008138, exon 9 of 9)	-5656	NM_001291539	20347	Mm.4083	NM_009153	ENSMUSG00000057969	Sema3b	SemA|Semaa|sema5|semaV	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B	protein-coding
mm_63654.1	chr7	128748956	128748965	+	1	NA	intron (NM_001029982, intron 1 of 18)	intron (NM_001029982, intron 1 of 18)	4090	NM_001029982	207352	Mm.297105	NM_001029982	ENSMUSG00000055319	Sec23ip	D7Ertd373e|p125	Sec23 interacting protein	protein-coding
mm_78387.1	chr9	28403514	28403536	+	1	NA	intron (NM_177906, intron 1 of 7)	CpG	612256	NM_177906	330908	Mm.379474	NM_177906	ENSMUSG00000062257	Opcml	2900075O15Rik|3732419F12|AI844366|B930023M13Rik|C230027C17|Gm181|Obcam	opioid binding protein/cell adhesion molecule-like	protein-coding
mm_23579.1	chr3	63381325	63381354	+	1	NA	3' UTR (NM_008604, exon 23 of 23)	3' UTR (NM_008604, exon 23 of 23)	85244	NM_001289463	17380	Mm.296022	NM_008604	ENSMUSG00000027820	Mme	6030454K05Rik|C85356|CALLA|CD10|NEP|SFE	membrane metallo endopeptidase	protein-coding
mm_34776.1	chr4	153975164	153975247	+	1	NA	promoter-TSS (NM_177673)	promoter-TSS (NM_177673)	-124	NM_007859	13368	Mm.388918	NM_007859	ENSMUSG00000029027	Dffb	40kDa|5730477D02Rik|CAD|CPAN|DFF40|Didff	DNA fragmentation factor, beta subunit	protein-coding
mm_128773.1	chr15	66561090	66561100	-	1	NA	promoter-TSS (NM_172514)	promoter-TSS (NM_172514)	-49	NM_172514	213068	Mm.132299	NM_172514	ENSMUSG00000036944	Tmem71	AI661017|E430024D12	transmembrane protein 71	protein-coding
mm_149643.1	chr19	17400543	17400546	+	1	NA	3' UTR (NM_019437, exon 4 of 4)	3' UTR (NM_019437, exon 4 of 4)	6501	NM_019437	54391	Mm.7013	NM_019437	ENSMUSG00000024712	Rfk	0610038L10Rik|AF031381|KOI-4	riboflavin kinase	protein-coding
mm_124110.1	chr14	79467410	79467426	-	1	NA	exon (NM_018765, exon 8 of 10)	exon (NM_018765, exon 8 of 10)	-13776	NM_007920	13709	Mm.20938	NM_007920	ENSMUSG00000036461	Elf1	Elf-1|Sts1|mElf-1|p70	E74-like factor 1	protein-coding
mm_69973.1	chr7	142377085	142377092	-	1	NA	exon (NM_009983, exon 7 of 9)	exon (NM_009983, exon 7 of 9)	-3342	NM_001347541	320802	Mm.154486	NM_177265	ENSMUSG00000045777	Ifitm10	6330512M04Rik|AI848576|DSPA3	interferon induced transmembrane protein 10	protein-coding
mm_23838.1	chr3	82358168	82358185	+	1	NA	5' UTR (NM_001081230, exon 1 of 14)	5' UTR (NM_001081230, exon 1 of 14)	104	NM_001081230	213582	Mm.271269	NM_001081230	ENSMUSG00000033900	Map9	5033421J10Rik|5330427D05Rik|ASAP|Mtap9	microtubule-associated protein 9	protein-coding
mm_82259.1	chr9	5311472	5311479	-	1	NA	intron (NM_007609, intron 1 of 8)	RLTR17|LTR|ERVK	2626	NM_007609	12363	Mm.1569	NM_007609	ENSMUSG00000033538	Casp4	CASP-11|CASP-4|Casp11|Caspl|ich-3	caspase 4, apoptosis-related cysteine peptidase	protein-coding
mm_612.1	chr1	40009900	40009939	+	1	NA	intron (NM_001252200, intron 22 of 31)	intron (NM_001252200, intron 22 of 31)	-74849	NM_010555	16178	Mm.1349	NM_010555	ENSMUSG00000026073	Il1r2	CD121b|Il1r-2	interleukin 1 receptor, type II	protein-coding
mm_168648.1	chr11	8605329	8605338	-	1	NA	intron (NM_001083587, intron 2 of 30)	RLTR11A2|LTR|ERVK	59202	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_97305.1	chr11	76679643	76679647	+	1	NA	promoter-TSS (NM_177709)	promoter-TSS (NM_177709)	-228	NM_177709	237858	Mm.127006	NM_177709	ENSMUSG00000046275	Tusc5	C130069F04Rik|DSPB1|Lost1	tumor suppressor candidate 5	protein-coding
mm_79915.1	chr9	65541877	65541901	+	1	NA	Intergenic	Intergenic	38198	NM_153119	102595	Mm.247303	NM_153119	ENSMUSG00000050721	Plekho2	AI840980|Plekhq1	pleckstrin homology domain containing, family O member 2	protein-coding
mm_80638.1	chr9	89248509	89248527	+	1	NA	Intergenic	ORR1B2|LTR|ERVL-MaLR	37328	NM_026829	107885	Mm.486274	NM_026829	ENSMUSG00000066442	Mthfs	1110034I12Rik|2310020H23Rik|AI119695	5, 10-methenyltetrahydrofolate synthetase	protein-coding
mm_108795.1	chr12	91404023	91404053	+	1	NA	intron (NM_011648, intron 1 of 9)	ORR1B1|LTR|ERVL-MaLR	3045	NM_011648	22095	Mm.173847	NM_011648	ENSMUSG00000020963	Tshr	AI481368|hypothroid|hyt|pet	thyroid stimulating hormone receptor	protein-coding
mm_125070.1	chr15	25941145	25941155	+	1	NA	5' UTR (NM_001277315, exon 1 of 7)	5' UTR (NM_001277315, exon 1 of 7)	324	NM_025459	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_30247.1	chr3	146571883	146571886	-	1	NA	Intergenic	B1F|SINE|Alu	-25265	NM_009474	22262	Mm.10865	NM_009474	ENSMUSG00000028186	Uox	AI663847	urate oxidase	protein-coding
mm_26469.1	chr3	144570280	144570284	+	1	NA	promoter-TSS (NM_053102)	promoter-TSS (NM_053102)	-66	NM_011828	23908	Mm.12863	NM_011828	ENSMUSG00000040151	Hs2st1	AW214369|Hs2st|mKIAA0448	heparan sulfate 2-O-sulfotransferase 1	protein-coding
mm_2599.1	chr1	120007014	120007028	+	1	NA	promoter-TSS (NM_001012322)	promoter-TSS (NM_001012322)	41	NM_001311077	319229	Mm.189223	NM_001012322	ENSMUSG00000026387	Sctr	6530402O03Rik	secretin receptor	protein-coding
mm_136494.1	chr16	96128017	96128031	-	1	NA	promoter-TSS (NM_008251)	promoter-TSS (NM_008251)	-299	NM_008251	15312	Mm.2756	NM_008251	ENSMUSG00000040681	Hmgn1	HMG-14|Hmg14	high mobility group nucleosomal binding domain 1	protein-coding
mm_142453.1	chr17	45592913	45592952	-	1	NA	promoter-TSS (NM_022880)	promoter-TSS (NM_022880)	-539	NM_022880	63959	Mm.29744	NM_022880	ENSMUSG00000023942	Slc29a1	1200014D21Rik|AA407560|ENT1	solute carrier family 29 (nucleoside transporters), member 1	protein-coding
mm_40361.1	chr5	48022892	48022894	+	1	NA	intron (NR_111900, intron 4 of 35)	intron (NR_111900, intron 4 of 35)	39738	NM_001291228	20563	Mm.289739	NM_178804	ENSMUSG00000031558	Slit2	Drad-1|E030015M03Rik|E130320P19Rik|Slil3|mKIAA4141|slit-2	slit homolog 2 (Drosophila)	protein-coding
mm_56236.1	chr6	90662726	90662763	-	1	NA	exon (NM_001134384, exon 14 of 14)	exon (NM_001134384, exon 14 of 14)	43498	NM_001037493	71699	Mm.272633	NM_027868	ENSMUSG00000030089	Slc41a3	1010001P06Rik|AI480742|SLC41A1-L2	solute carrier family 41, member 3	protein-coding
mm_35461.1	chr4	40722308	40722333	-	1	NA	promoter-TSS (NM_001164672)	promoter-TSS (NM_001164672)	-3	NR_077221	622208	Mm.471544	NR_077221		Gm6297	-	predicted gene 6297	ncRNA
mm_116071.1	chr13	27642478	27642482	-	1	NA	promoter-TSS (NM_001164058)	promoter-TSS (NM_001164058)	13	NM_001164058	19113	Mm.196424	NM_008930	ENSMUSG00000006488	Prl7a1	AA407021|AA409971|AA410116|PLP-E|PLP-G|Prlpe|Prlpg	prolactin family 7, subfamily a, member 1	protein-coding
mm_130011.1	chr15	86706412	86706424	-	1	NA	Intergenic	Intergenic	491959	NM_145476	223754	Mm.28904	NM_145476	ENSMUSG00000051864	Tbc1d22a	BC023106|D15Ertd781e	TBC1 domain family, member 22a	protein-coding
mm_60575.1	chr7	44481649	44481659	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-2863	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_24502.1	chr3	92432579	92432585	+	1	NA	promoter-TSS (NM_011477)	promoter-TSS (NM_011477)	0	NM_011477	20765	Mm.57085	NM_011477	ENSMUSG00000054215	Sprr2k	-	small proline-rich protein 2K	protein-coding
mm_170352.1	chr1	85109651	85109654	-	1	NA	5' UTR (NM_213615, exon 1 of 7)	5' UTR (NM_213615, exon 1 of 7)	201	NM_213615	381287	Mm.487565	NM_213615	ENSMUSG00000089844	A530032D15Rik	Gm1888	RIKEN cDNA A530032D15Rik gene	protein-coding
mm_20195.1	chr2	122738346	122738365	-	1	NA	promoter-TSS (NM_019788)	promoter-TSS (NM_019788)	-150	NM_019788	18457	Mm.268921	NM_019788	ENSMUSG00000005804	Bloc1s6	BLOC-1|Pldn|Stx13bp1|pa	biogenesis of lysosomal organelles complex-1, subunit 6, pallidin	protein-coding
mm_62591.1	chr7	105640997	105641027	+	1	NA	promoter-TSS (NM_029802)	promoter-TSS (NM_029802)	472	NM_019502	14356	Mm.220330	NM_019502	ENSMUSG00000089847	Timm10b	Fxc1|Tim10b|Tim9b	translocase of inner mitochondrial membrane 10B	protein-coding
mm_67463.1	chr7	80404057	80404064	-	1	NA	intron (NM_001081454, intron 1 of 15)	intron (NM_001081454, intron 1 of 15)	-1248	NM_011046	18550	Mm.5241	NM_011046	ENSMUSG00000030530	Furin	9130404I01Rik|Fur|PACE|Pcsk3|SPC1	furin (paired basic amino acid cleaving enzyme)	protein-coding
mm_20823.1	chr2	146099203	146099221	-	1	NA	Intergenic	Intergenic	-122785	NM_016889	53626	Mm.379070	NM_016889	ENSMUSG00000068154	Insm1	IA-1	insulinoma-associated 1	protein-coding
mm_139357.1	chr17	50525303	50525309	+	1	NA	intron (NM_013880, intron 1 of 5)	Charlie24|DNA|hAT-Charlie	15759	NM_013880	224860	Mm.217362	NM_013880	ENSMUSG00000038910	Plcl2	PLC-L2|PRIP-2|Plce2|mKIAA1092	phospholipase C-like 2	protein-coding
mm_171848.1	chr5	16904254	16904256	+	1	NA	Intergenic	L1Md_T|LINE|L1	350354	NM_001289461	15234	Mm.267078	NM_010427	ENSMUSG00000028864	Hgf	C230052L06Rik|HGF/SF|NK1|NK2|SF|SF/HGF	hepatocyte growth factor	protein-coding
mm_108936.1	chr12	101975726	101975751	+	1	NA	promoter-TSS (NM_016856)	promoter-TSS (NM_016856)	-236	NM_016856	51786	Mm.716	NM_016856	ENSMUSG00000041781	Cpsf2	100kDa|2610024B04Rik|AI662483|Cpsf|MCPSF|mKIAA1367	cleavage and polyadenylation specific factor 2	protein-coding
mm_91687.1	chr10	43972014	43972036	-	1	NA	intron (NM_172393, intron 11 of 19)	intron (NM_172393, intron 11 of 19)	32821	NM_172393	11630	Mm.292082	NM_172393	ENSMUSG00000019866	Aim1	AI462491|AI463325	absent in melanoma 1	protein-coding
mm_90862.1	chr10	8885896	8885947	-	1	NA	5' UTR (NM_175155, exon 1 of 20)	5' UTR (NM_175155, exon 1 of 20)	149	NM_175155	70097	Mm.338275	NM_175155	ENSMUSG00000015305	Sash1	1100001C18Rik|2500002E12Rik|A330076K04Rik|mKIAA0790	SAM and SH3 domain containing 1	protein-coding
mm_114934.1	chr13	95893463	95893508	+	1	NA	Intergenic	Intergenic	-1563	NM_027711	544963	Mm.38878	NM_027711	ENSMUSG00000021676	Iqgap2	4933417J23Rik|A630053O10|AI788777	IQ motif containing GTPase activating protein 2	protein-coding
mm_33693.1	chr4	133518738	133518750	+	1	NA	promoter-TSS (NM_001083916)	promoter-TSS (NM_001083916)	-219	NM_001083916	69073	Mm.299081	NM_133707	ENSMUSG00000037600	Kdf1	1810019J16Rik	keratinocyte differentiation factor 1	protein-coding
mm_4369.1	chr1	172102100	172102111	+	1	NA	intron (NM_009938, intron 9 of 32)	intron (NM_009938, intron 9 of 32)	-19356	NM_021607	59287	Mm.218203	NM_021607	ENSMUSG00000003458	Ncstn	9430068N19Rik|AA727311|Aph2|D1Dau13e|Kiaa0253|Nct|mKIAA0253	nicastrin	protein-coding
mm_84362.1	chr9	64737685	64737763	-	1	NA	promoter-TSS (NM_017382)	promoter-TSS (NM_017382)	32	NM_017382	53869	Mm.1387	NM_017382	ENSMUSG00000004771	Rab11a	-	RAB11A, member RAS oncogene family	protein-coding
mm_41722.1	chr5	102481375	102481382	+	1	NA	promoter-TSS (NM_029270)	promoter-TSS (NM_029270)	-13	NM_146161	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding
mm_16249.1	chr2	173158773	173158781	+	1	NA	3' UTR (NM_011044, exon 10 of 10)	3' UTR (NM_011044, exon 10 of 10)	5704	NM_011044	18534	Mm.266867	NM_011044	ENSMUSG00000027513	Pck1	AI265463|PEPCK|Pck-1	phosphoenolpyruvate carboxykinase 1, cytosolic	protein-coding
mm_119878.1	chr14	54883431	54883489	+	1	NA	promoter-TSS (NM_007537)	promoter-TSS (NM_007537)	35	NM_007537	12050	Mm.6967	NM_007537	ENSMUSG00000089682	Bcl2l2	AW048834|Bcl-w|Gtrgal2|Gtrosa41|bclw|c98	BCL2-like 2	protein-coding
mm_49863.1	chr6	38551538	38551550	+	1	NA	5' UTR (NM_001170849, exon 1 of 8)	5' UTR (NM_001170849, exon 1 of 8)	210	NM_001170848	192196	Mm.276133	NM_138680	ENSMUSG00000029823	Luc7l2	4930471C18Rik|AA522013|AU015269|CGI59|Cgi74	LUC7-like 2 (S. cerevisiae)	protein-coding
mm_164855.1	chr18	49402439	49402439	-	1	NA	Intergenic	Intergenic	-120850	NR_033785	67321	Mm.245802	NR_033785	ENSMUSG00000100297	1700044K03Rik	-	RIKEN cDNA 1700044K03 gene	ncRNA
mm_40584.1	chr5	64159430	64159443	+	1	NA	promoter-TSS (NM_019636)	promoter-TSS (NM_019636)	-824	NM_019636	57915	Mm.286353	NM_019636	ENSMUSG00000029174	Tbc1d1	1110062G02Rik|AI385682|AW555803|Nob1|Nobq1|Tbc1|mKIAA1108	TBC1 domain family, member 1	protein-coding
mm_124325.1	chr14	103843059	103843072	-	1	NA	exon (NM_001136061, exon 2 of 8)	exon (NM_001136061, exon 2 of 8)	636	NM_007904	13618	Mm.229532	NM_007904	ENSMUSG00000022122	Ednrb	ET-B|ET-BR|ETR-b|ETb|Sox10m1	endothelin receptor type B	protein-coding
mm_76417.1	chr8	84969413	84969481	-	1	NA	promoter-TSS (NM_011563)	promoter-TSS (NM_011563)	-175	NM_001317385	21672	Mm.347009	NM_011563	ENSMUSG00000005161	Prdx2	AL022839|Band-8|NkefB|PRP|PrxII|TDX1|TPx|TPx-B|TR|TSA|Tdpx1|Torin	peroxiredoxin 2	protein-coding
mm_45024.1	chr5	38561788	38561792	-	1	NA	promoter-TSS (NM_011715)	promoter-TSS (NM_011715)	-195	NM_011715	22388	Mm.2654	NM_011715	ENSMUSG00000005103	Wdr1	Aip1|D5Wsu185e|rede	WD repeat domain 1	protein-coding
mm_114431.1	chr13	65240919	65240970	+	1	NA	Intergenic	CpG	-35228	NM_175290	97895	Mm.315815	NM_175290	ENSMUSG00000032999	Nlrp4f	C330026N02Rik|C86045|Nalp-kappa|Nalp4f	NLR family, pyrin domain containing 4F	protein-coding
mm_154214.1	chr19	59301414	59301456	-	1	NA	exon (NM_001033222, exon 5 of 5)	exon (NM_001033222, exon 5 of 5)	40557	NM_172523	214084	Mm.268797	NM_172523	ENSMUSG00000025094	Slc18a2	1110037L13Rik|9330105E13|Vmat2	solute carrier family 18 (vesicular monoamine), member 2	protein-coding
mm_125026.1	chr15	25749954	25749980	+	1	NA	intron (NM_019472, intron 19 of 40)	intron (NM_019472, intron 19 of 40)	-93331	NM_001034851	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_72326.1	chr8	78733532	78733534	+	1	NA	non-coding (NR_104094, exon 10 of 10)	non-coding (NR_104094, exon 10 of 10)	87619	NM_001191004	78651	Mm.28694	NM_030145	ENSMUSG00000031683	Lsm6	1500031N17Rik|2410088K19Rik|AI747288	LSM6 homolog, U6 small nuclear RNA and mRNA degradation associated	protein-coding
mm_127032.1	chr15	96370253	96370263	+	1	NA	exon (NM_175251, exon 15 of 21)	exon (NM_175251, exon 15 of 21)	82736	NM_175251	77044	Mm.17166	NM_175251	ENSMUSG00000033237	Arid2	1700124K17Rik|4432409D24Rik|zipzap/p200	AT rich interactive domain 2 (ARID, RFX-like)	protein-coding
mm_67469.1	chr7	80419391	80419401	-	1	NA	Intergenic	Intergenic	-13960	NM_001081454	18550	Mm.5241	NM_011046	ENSMUSG00000030530	Furin	9130404I01Rik|Fur|PACE|Pcsk3|SPC1	furin (paired basic amino acid cleaving enzyme)	protein-coding
mm_39693.1	chr5	27049370	27049424	+	1	NA	5' UTR (NM_207282, exon 1 of 26)	5' UTR (NM_207282, exon 1 of 26)	198	NM_207282	13483	Mm.42078	NM_010075	ENSMUSG00000061576	Dpp6	B930011P16Rik|D5Buc3|D5Buc4|D5Buc5|DPP VI|Dpp-6|Gm1377|In(5)6H-p|Peplb|Rw	dipeptidylpeptidase 6	protein-coding
mm_20829.1	chr2	146512027	146512083	-	1	NA	promoter-TSS (NM_001033348)	promoter-TSS (NM_001033348)	-51	NM_001033348	241694	Mm.222310	NM_001033348	ENSMUSG00000037110	Ralgapa2	A230067G21Rik|AS250|BC053994|RGC2|pp250	Ral GTPase activating protein, alpha subunit 2 (catalytic)	protein-coding
mm_93970.1	chr10	127290339	127290360	-	1	NA	promoter-TSS (NM_001290183)	promoter-TSS (NM_001290183)	-444	NM_007837	13198	Mm.110220	NM_007837	ENSMUSG00000025408	Ddit3	CHOP-10|CHOP10|chop|gadd153	DNA-damage inducible transcript 3	protein-coding
mm_113843.1	chr13	47194040	47194046	+	1	NA	promoter-TSS (NM_001170643)	promoter-TSS (NM_001170643)	40	NM_001170643	218215	Mm.287609	NM_146042	ENSMUSG00000038068	Rnf144b	BC025007|E130105P19Rik|Ibrdc2|Pir2	ring finger protein 144B	protein-coding
mm_17.1	chr1	5083106	5083160	+	1	NA	promoter-TSS (NM_133826)	promoter-TSS (NM_133826)	47	NM_001310442	108664	Mm.27082	NM_133826	ENSMUSG00000033793	Atp6v1h	0710001F19Rik|AU022349|CGI-11|SFD|SFDalpha|SFDbeta|VMA13	ATPase, H+ transporting, lysosomal V1 subunit H	protein-coding
mm_29732.1	chr3	126831423	126831430	-	1	NA	intron (NM_001346636, intron 16 of 20)	intron (NM_001346636, intron 16 of 20)	111960	NM_001034168	109676	Mm.220242	NM_178655	ENSMUSG00000032826	Ank2	100043364|AI835472|AW491075|Ank-2|Gm4392	ankyrin 2, brain	protein-coding
mm_158223.1	chrX	106011827	106011839	-	1	NA	promoter-TSS (NM_001190409)	promoter-TSS (NM_001190409)	66	NM_001190409	67075	Mm.275943	NM_025952	ENSMUSG00000031232	Magt1	2410001C15Rik|2610529C04Rik|2810482I07Rik|IAG2|IAP	magnesium transporter 1	protein-coding
mm_34245.1	chr4	141239635	141239657	+	1	NA	Intergenic	Intergenic	-3238	NM_172520	213649	Mm.134460	NM_172520	ENSMUSG00000028919	Arhgef19	6030432F23|6430573B13Rik|WGEF	Rho guanine nucleotide exchange factor (GEF) 19	protein-coding
mm_97095.1	chr11	73177237	73177261	+	1	NA	promoter-TSS (NM_025318)	promoter-TSS (NM_025318)	166	NM_029564	76281	Mm.371656	NM_029564	ENSMUSG00000040158	Tax1bp3	1300011C24Rik|TIP-1	Tax1 (human T cell leukemia virus type I) binding protein 3	protein-coding
mm_152915.1	chr19	27429808	27429870	-	1	NA	promoter-TSS (NR_027987)	promoter-TSS (NR_027987)	69	NM_177474	52874	Mm.261027	NM_177474	ENSMUSG00000041360	Pum3	1110069H02Rik|AA675048|D19Bwg1357e|Kiaa0020	pumilio RNA-binding family member 3	protein-coding
mm_50780.1	chr6	53698001	53698015	+	1	NA	3' UTR (NM_001327821, exon 11 of 11)	3' UTR (NM_001327821, exon 11 of 11)	122817	NM_025817	66873	Mm.422727	NM_025817	ENSMUSG00000043496	Tril	1200009O22Rik|AI316813|mKIAA0644	TLR4 interactor with leucine-rich repeats	protein-coding
mm_86483.1	chr10	4863446	4863457	+	1	NA	intron (NM_001302531, intron 5 of 8)	Lx2|LINE|L1	153293	NM_001302533	13982	Mm.9213	NM_007956	ENSMUSG00000019768	Esr1	ER|ER-alpha|ERa|ERalpha|ESR|Estr|Estra|Nr3a1	estrogen receptor 1 (alpha)	protein-coding
mm_30877.1	chr4	32238954	32238964	+	1	NA	Intergenic	CpG	-178476	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_11368.1	chr2	30982351	30982376	+	1	NA	promoter-TSS (NM_028846)	promoter-TSS (NM_028846)	84	NM_028846	74270	Mm.346654	NM_028846	ENSMUSG00000026854	Usp20	1700055M05Rik|AI467231|Vdu2	ubiquitin specific peptidase 20	protein-coding
mm_85414.1	chr9	103449154	103449168	-	1	NA	intron (NM_001002896, intron 3 of 6)	intron (NM_001002896, intron 3 of 6)	25583	NR_040466	100529079	Mm.437003	NR_040466	ENSMUSG00000086236	5830418P13Rik	-	RIKEN cDNA 5830418P13 gene	ncRNA
mm_148808.1	chr19	6276851	6276891	+	1	NA	promoter-TSS (NM_010119)	promoter-TSS (NM_010119)	-25	NM_010119	13660	Mm.30169	NM_010119	ENSMUSG00000024772	Ehd1	AA409636|Past1|RME-1	EH-domain containing 1	protein-coding
mm_76431.1	chr8	84978710	84978724	-	1	NA	promoter-TSS (NM_008416)	promoter-TSS (NM_008416)	31	NM_008416	16477	Mm.1167	NM_008416	ENSMUSG00000052837	Junb	-	jun B proto-oncogene	protein-coding
mm_141839.1	chr17	34722409	34722421	-	1	NA	Intergenic	Intergenic	21482	NM_009780	12268	Mm.477109	NM_009780	ENSMUSG00000073418	C4b	C4|Ss	complement component 4B (Chido blood group)	protein-coding
mm_172689.1	chr8	59741684	59741685	+	1	NA	Intergenic	L1Md_T|LINE|L1	-83965	NR_126087	75017	Mm.60775	NR_126087	ENSMUSG00000110406	4930470O06Rik	-	RIKEN cDNA 4930470O06 gene	ncRNA
mm_93258.1	chr10	95564022	95564028	-	1	NA	5' UTR (NM_027722, exon 1 of 5)	5' UTR (NM_027722, exon 1 of 5)	142	NM_027722	71207	Mm.24397	NM_027722	ENSMUSG00000020029	Nudt4	4933436C10Rik|DIPP2|DIPP2alpha|DIPP2beta|HDCMB47P	nudix (nucleoside diphosphate linked moiety X)-type motif 4	protein-coding
mm_65705.1	chr7	28378017	28378034	-	1	NA	exon (NM_011756, exon 2 of 2)	exon (NM_011756, exon 2 of 2)	1203	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_53277.1	chr6	128657977	128657989	+	1	NA	Intergenic	Intergenic	-4402	NM_053165	94071	Mm.197689	NM_053165	ENSMUSG00000030364	Clec2h	Clrf|clr-f	C-type lectin domain family 2, member h	protein-coding
mm_22551.1	chr3	9403112	9403130	+	1	NA	promoter-TSS (NR_015499)	promoter-TSS (NR_015499)	43	NR_015499	320088	Mm.212908	NR_015499	ENSMUSG00000097365	C030034L19Rik	A130044O20Rik	RIKEN cDNA C030034L19 gene	ncRNA
mm_20303.1	chr2	127141580	127141589	-	1	NA	exon (NM_001163528, exon 2 of 2)	exon (NM_001163528, exon 2 of 2)	1006	NM_001163528	73338	Mm.57559	NM_001163527	ENSMUSG00000074825	Itpripl1	1700041B20Rik	inositol 1,4,5-triphosphate receptor interacting protein-like 1	protein-coding
mm_164033.1	chr14	79301186	79301193	+	1	NA	intron (NM_025427, intron 1 of 4)	CpG	446	NM_025427	66214	Mm.29811	NM_025427	ENSMUSG00000022018	Rgcc	1190002H23Rik|Rgc-32|Rgc32	regulator of cell cycle	protein-coding
mm_94909.1	chr11	29374364	29374366	+	1	NA	exon (NM_176841, exon 1 of 32)	exon (NM_176841, exon 1 of 32)	193	NM_176841	108686	Mm.338284	NM_176841	ENSMUSG00000032740	Ccdc88a	A430106J12Rik|AI848406|Ape|C130096N06Rik|C330012F17Rik|D130005J21Rik|Girdin|Giv|Grdn|Hkrp1	coiled coil domain containing 88A	protein-coding
mm_119443.1	chr14	46832128	46832151	+	1	NA	promoter-TSS (NM_026832)	promoter-TSS (NM_026832)	-105	NM_026832	68755	Mm.343809	NM_026832	ENSMUSG00000055128	Cgrrf1	1110038G02Rik|1810009H17Rik|CGR19	cell growth regulator with ring finger domain 1	protein-coding
mm_158143.1	chrX	103438238	103438242	-	1	NA	intron (NR_002844, intron 1 of 3)	RMER10B|LTR|ERVL	6723	NR_002844	22097	Mm.472939	NR_002844	ENSMUSG00000085715	Tsix	-	X (inactive)-specific transcript, opposite strand	ncRNA
mm_27836.1	chr3	79142965	79142966	-	1	NA	intron (NM_001099624, intron 1 of 23)	intron (NM_001099624, intron 1 of 23)	1922	NM_001310536	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_80442.1	chr9	77960872	77960900	+	1	NA	exon (NM_134255, exon 3 of 8)	exon (NM_134255, exon 3 of 8)	43521	NM_134255	68801	Mm.430736	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	ELOVL family member 5, elongation of long chain fatty acids (yeast)	protein-coding
mm_81387.1	chr9	108982949	108982968	+	1	NA	intron (NM_007738, intron 113 of 117)	intron (NM_007738, intron 113 of 117)	-3205	NM_145077	171530	Mm.388865	NM_145077	ENSMUSG00000049699	Ucn2	Ucn II|Ucn-2|ucn-II	urocortin 2	protein-coding
mm_131463.1	chr16	17026354	17026371	+	1	NA	exon (NM_001038663, exon 6 of 8)	exon (NM_001038663, exon 6 of 8)	42980	NM_001038663	26413	Mm.196581	NM_011949	ENSMUSG00000063358	Mapk1	9030612K14Rik|AA407128|AU018647|C78273|ERK|Erk2|MAPK2|PRKM2|Prkm1|p41mapk|p42mapk	mitogen-activated protein kinase 1	protein-coding
mm_132066.1	chr16	30055716	30055720	+	1	NA	Intergenic	Intergenic	-9639	NM_008235	15205	Mm.390859	NM_008235	ENSMUSG00000022528	Hes1	Hry|bHLHb39	hairy and enhancer of split 1 (Drosophila)	protein-coding
mm_24189.1	chr3	88607439	88607468	+	1	NA	Intergenic	Intergenic	-8754	NM_001198911	16800	Mm.239329	NM_008487	ENSMUSG00000028059	Arhgef2	AA408978|GEF|GEF-H1|GEFH1|LFP40|Lbcl1|Lfc|P40|mKIAA0651	rho/rac guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_63658.1	chr7	129432468	129432470	+	1	NA	Intergenic	Intergenic	-159394	NM_172255	207425	Mm.229323	NM_172255	ENSMUSG00000042055	Wdr11	2900055P10Rik|AW489876|Brwd2|mKIAA1351	WD repeat domain 11	protein-coding
mm_93863.1	chr10	122986051	122986064	-	1	NA	promoter-TSS (NR_029527)	promoter-TSS (NR_029527)	-333	NR_029527	387251		NR_029527	ENSMUSG00000065406	Mirlet7i	Mirnlet7i|let-7i|mmu-let-7i	microRNA let7i	ncRNA
mm_144669.1	chr18	34542224	34542226	+	1	NA	promoter-TSS (NM_009290)	promoter-TSS (NM_009290)	-103	NM_009290	20890	Mm.558	NM_009290	ENSMUSG00000012282	Wnt8a	Stra11|Wnt-8A|Wnt-8D|Wnt8d	wingless-type MMTV integration site family, member 8A	protein-coding
mm_127547.1	chr15	102144497	102144514	+	1	NA	5' UTR (NM_008344, exon 1 of 4)	5' UTR (NM_008344, exon 1 of 4)	319	NM_008344	16012	Mm.358609	NM_008344	ENSMUSG00000023046	Igfbp6	IGFBP-6	insulin-like growth factor binding protein 6	protein-coding
mm_129470.1	chr15	78670549	78670549	-	1	NA	3' UTR (NM_183141, exon 2 of 2)	3' UTR (NM_183141, exon 2 of 2)	47564	NM_183141	207393	Mm.323188	NM_183141	ENSMUSG00000043460	Elfn2	6330514E13|AW048948|BC094219|Lrrc62|Ppp1r29	leucine rich repeat and fibronectin type III, extracellular 2	protein-coding
mm_7567.1	chr1	124783800	124783821	-	1	NA	Intergenic	Intergenic	651917	NM_023735	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding
mm_146220.1	chr18	77038879	77038895	+	1	NA	intron (NM_027721, intron 1 of 13)	B3A|SINE|B2	8409	NM_027721	71206	Mm.35803	NM_027721	ENSMUSG00000025420	Katnal2	3110023G01Rik|4933439B08Rik	katanin p60 subunit A-like 2	protein-coding
mm_80846.1	chr9	98296557	98296581	+	1	NA	promoter-TSS (NM_144533)	promoter-TSS (NM_144533)	-14	NM_144533	74080	Mm.294082	NM_144533	ENSMUSG00000032456	Nmnat3	4933408N02Rik|PNAT3	nicotinamide nucleotide adenylyltransferase 3	protein-coding
mm_87377.1	chr10	44475988	44475996	+	1	NA	Intergenic	RSINE1|SINE|B4	-17244	NM_007548	12142	Mm.4800	NM_007548	ENSMUSG00000038151	Prdm1	Blimp-1|Blimp1|PRDI-BF1|ZNFPR1A1|b2b1765Clo	PR domain containing 1, with ZNF domain	protein-coding
mm_144940.1	chr18	37755719	37755767	+	1	NA	promoter-TSS (NM_033594)	promoter-TSS (NM_033594)	-30	NM_033594	93723	Mm.247203	NM_033594	ENSMUSG00000102742	Pcdhga11	-	protocadherin gamma subfamily A, 11	protein-coding
mm_39901.1	chr5	31240949	31240959	+	1	NA	promoter-TSS (NM_147201)	promoter-TSS (NM_147201)	36	NM_147201	192292	Mm.292040	NM_147201	ENSMUSG00000029148	Nrbp1	B230344L17Rik|Nrbp	nuclear receptor binding protein 1	protein-coding
mm_119756.1	chr14	54166550	54166576	+	1	NA	Intergenic	Intergenic	87366	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_71247.1	chr8	40914912	40914995	+	1	NA	exon (NM_001044740, exon 11 of 12)	exon (NM_001044740, exon 11 of 12)	-11280	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_12784.1	chr2	79330948	79330967	+	1	NA	3' UTR (NM_010576, exon 28 of 28)	3' UTR (NM_010576, exon 28 of 28)	75531	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D|Itga4B	integrin alpha 4	protein-coding
mm_160518.1	chr9	24098080	24098080	+	1	NA	promoter-TSS (NM_175678)	promoter-TSS (NM_175678)	62	NM_175678	319239	Mm.130824	NM_175678	ENSMUSG00000043659	Npsr1	9330128H10Rik|GPRA|Gpr154|MVTR|PGR14|VRR1	neuropeptide S receptor 1	protein-coding
mm_48643.1	chr5	145584724	145584727	-	1	NA	promoter-TSS (NM_001105159)	promoter-TSS (NM_001105159)	5	NM_017396	53973	Mm.379071	NM_017396	ENSMUSG00000075551	Cyp3a41a	Cyp3a41	cytochrome P450, family 3, subfamily a, polypeptide 41A	protein-coding
mm_134643.1	chr16	21766548	21766574	-	1	NA	exon (NM_023737, exon 6 of 7)	exon (NM_023737, exon 6 of 7)	21273	NM_023737	74147	Mm.28100	NM_023737	ENSMUSG00000022853	Ehhadh	1300002P22Rik|HD|L-PBE|LBFP|LBP|MFP|MFP1|PBFE	enoyl-Coenzyme A, hydratase/3-hydroxyacyl Coenzyme A dehydrogenase	protein-coding
mm_144739.1	chr18	35564391	35564394	+	1	NA	intron (NM_010771, intron 1 of 14)	B1_Mur3|SINE|Alu	2234	NM_010771	17184	Mm.215034	NM_010771	ENSMUSG00000037236	Matr3	1110061A14Rik|2810017I02Rik|AI841759|AW555618|D030046F20Rik|mKIAA0723	matrin 3	protein-coding
mm_72862.1	chr8	88577546	88577549	+	1	NA	intron (NM_001163660, intron 2 of 7)	intron (NM_001163660, intron 2 of 7)	49914	NM_001163660	93960	Mm.30219	NM_027280	ENSMUSG00000031661	Nkd1	2810434J10Rik|9030215G15Rik|Nkd	naked cuticle 1 homolog (Drosophila)	protein-coding
mm_117227.1	chr13	64153195	64153207	-	1	NA	promoter-TSS (NM_175494)	promoter-TSS (NM_175494)	-2	NM_175494	238673	Mm.300065	NM_175494	ENSMUSG00000044934	Zfp367	8030486J21Rik|ZFF29a|ZFF29b|Znf367	zinc finger protein 367	protein-coding
mm_58560.1	chr7	4741821	4741835	+	1	NA	5' UTR (NM_001115018, exon 2 of 9)	5' UTR (NM_001115018, exon 2 of 9)	1701	NM_001115018	232811	Mm.247844	NM_146177	ENSMUSG00000059851	Kmt5c	BC024816|Suv4-20h2|Suv420h2	lysine methyltransferase 5C	protein-coding
mm_47133.1	chr5	120486098	120486124	-	1	NA	exon (NM_023625, exon 11 of 12)	exon (NM_023625, exon 11 of 12)	9564	NM_145565	231691	Mm.28685	NM_145565	ENSMUSG00000029597	Sds	4432411H13Rik|SDH	serine dehydratase	protein-coding
mm_110240.1	chr12	30911594	30911615	-	1	NA	promoter-TSS (NM_013709)	promoter-TSS (NM_013709)	8	NM_021330	11431	Mm.359831	NM_021330	ENSMUSG00000044573	Acp1	4632432E04Rik|AI427468|Acp-1|LMW-PTP|Lmptp	acid phosphatase 1, soluble	protein-coding
mm_37264.1	chr4	118457510	118457515	-	1	NA	promoter-TSS (NM_001122949)	promoter-TSS (NM_001122949)	1	NM_001285496	17480	Mm.4864	NM_010823	ENSMUSG00000006389	Mpl	CD110|TPO-R|c-mpl|hlb219	myeloproliferative leukemia virus oncogene	protein-coding
mm_42842.1	chr5	122131944	122131948	+	1	NA	intron (NM_001289809, intron 1 of 11)	intron (NM_001289809, intron 1 of 11)	2947	NM_001289811	330188	Mm.386907	NM_183307	ENSMUSG00000043036	Ccdc63	4921511C16Rik	coiled-coil domain containing 63	protein-coding
mm_27838.1	chr3	79145913	79145930	-	1	NA	promoter-TSS (NM_001099624)	promoter-TSS (NM_001099624)	-46	NM_001099624	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_87740.1	chr10	60261225	60261253	+	1	NA	Intergenic	ID_B1|SINE|B4	-16389	NM_001146123	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_20584.1	chr2	131158517	131158525	-	1	NA	intron (NM_001311138, intron 1 of 5)	intron (NM_001311138, intron 1 of 5)	1499	NM_026091	67326	Mm.27711	NM_026091	ENSMUSG00000027327	1700037H04Rik	-	RIKEN cDNA 1700037H04 gene	protein-coding
mm_58690.1	chr7	12897801	12897885	+	1	NA	promoter-TSS (NM_001290436)	promoter-TSS (NM_001290436)	34	NM_001290441	232878	Mm.40706	NM_001001447	ENSMUSG00000054715	Zscan22	AW227621|D530006B18Rik|Hkr2	zinc finger and SCAN domain containing 22	protein-coding
mm_111618.1	chr12	102404707	102404709	-	1	NA	intron (NM_011175, intron 4 of 13)	intron (NM_011175, intron 4 of 13)	35105	NM_011175	19141	Mm.17185	NM_011175	ENSMUSG00000021190	Lgmn	AEP|AI746452|AU022324|Prsc1	legumain	protein-coding
mm_126852.1	chr15	89196181	89196187	+	1	NA	intron (NM_027081, intron 1 of 19)	CpG	290	NM_027081	69440	Mm.482128	NM_027081	ENSMUSG00000015377	Dennd6b	1700027J05Rik|AI414881|Fam116b	DENN/MADD domain containing 6B	protein-coding
mm_59573.1	chr7	28115598	28115606	+	1	NA	intron (NM_001122603, intron 17 of 19)	intron (NM_001122603, intron 17 of 19)	-13864	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_124783.1	chr15	7497376	7497379	+	1	NA	Intergenic	Intergenic	-98982	NM_001289498	268780	Mm.203208	NM_178748	ENSMUSG00000042961	Egflam	5930412K08|AU040377	EGF-like, fibronectin type III and laminin G domains	protein-coding
mm_97269.1	chr11	75765339	75765349	+	1	NA	3' UTR (NM_009536, exon 6 of 6)	3' UTR (NM_009536, exon 6 of 6)	-30465	NR_136933	102641247	Mm.411386	NR_136932		Gm12339	OTTMUSG00000006218	predicted gene 12339	ncRNA
mm_102865.1	chr11	69405443	69405461	-	1	NA	exon (NM_001017426, exon 11 of 23)	exon (NM_001017426, exon 11 of 23)	-7218	NM_025915	67020	Mm.390406	NM_025915	ENSMUSG00000045377	Tmem88	2600017H02Rik	transmembrane protein 88	protein-coding
mm_150836.1	chr19	44837342	44837345	+	1	NA	3' UTR (NM_011037, exon 10 of 10)	3' UTR (NM_011037, exon 10 of 10)	-1405	NR_045315	73322	Mm.250457	NR_045315	ENSMUSG00000092369	1700039E22Rik	-	RIKEN cDNA 1700039E22 gene	ncRNA
mm_112788.1	chr13	20185288	20185301	+	1	NA	intron (NM_080288, intron 1 of 21)	intron (NM_080288, intron 1 of 21)	94787	NM_080288	140580	Mm.342392	NM_080288	ENSMUSG00000041112	Elmo1	6330578D22Rik|C230095H21Rik|CED-12	engulfment and cell motility 1	protein-coding
mm_82600.1	chr9	21320607	21320636	-	1	NA	promoter-TSS (NM_001199186)	promoter-TSS (NM_001199186)	-98	NM_001199186	68682	Mm.148425	NM_152808	ENSMUSG00000057193	Slc44a2	1110028E10Rik|CTL2	solute carrier family 44, member 2	protein-coding
mm_127980.1	chr15	12424796	12424799	-	1	NA	intron (NM_001081064, intron 5 of 23)	intron (NM_001081064, intron 5 of 23)	103301	NM_025673	66629	Mm.157655	NM_025673	ENSMUSG00000022200	Golph3	4733401N08Rik|5730410D03Rik|AW413496	golgi phosphoprotein 3	protein-coding
mm_152993.1	chr19	29806385	29806435	-	1	NA	promoter-TSS (NM_172836)	promoter-TSS (NM_172836)	-401	NM_172836	240613	Mm.313351	NM_172836	ENSMUSG00000046138	9930021J03Rik	ENSMUSG00000048936|Gm9832|mKIAA2026	RIKEN cDNA 9930021J03 gene	protein-coding
mm_143502.1	chr17	71598668	71598678	-	1	NA	promoter-TSS (NR_015549)	promoter-TSS (NR_015549)	88	NR_015549	68789	Mm.75202	NR_015549	ENSMUSG00000085492	Trmt61b	1110039F03Rik|623451|Gm6431	tRNA methyltransferase 61B	ncRNA
mm_98500.1	chr11	94951946	94951973	+	1	NA	3' UTR (NM_007742, exon 51 of 51)	3' UTR (NM_007742, exon 51 of 51)	-15634	NM_018792	54388	Mm.30482	NM_018792	ENSMUSG00000038994	Hils1	H1.9|TISP64	histone H1-like protein in spermatids 1	protein-coding
mm_31011.1	chr4	40269916	40269956	+	1	NA	promoter-TSS (NM_134097)	promoter-TSS (NM_134097)	-95	NM_134097	106021	Mm.251548	NM_134097	ENSMUSG00000036822	Topors	AW105885|LUN|TP53BPL|p53BP3/LUN	topoisomerase I binding, arginine/serine-rich	protein-coding
mm_1187.1	chr1	62660814	62660814	+	1	NA	Intergenic	Intergenic	-42503	NM_001077406	18187	Mm.266341	NM_010939	ENSMUSG00000025969	Nrp2	1110048P06Rik|Np-2|Np2|Npn-2|Npn2	neuropilin 2	protein-coding
mm_145758.1	chr18	64887840	64887853	+	1	NA	promoter-TSS (NM_001114386)	promoter-TSS (NM_001114386)	90	NM_001114386	83814	Mm.98668	NM_031881	ENSMUSG00000024589	Nedd4l	1300012C07Rik|Nedd4-2|Nedd4b	neural precursor cell expressed, developmentally down-regulated gene 4-like	protein-coding
mm_147229.1	chr18	38209734	38209747	-	1	NA	promoter-TSS (NM_029357)	promoter-TSS (NM_029357)	22	NM_029357	75599	Mm.36560	NM_029357	ENSMUSG00000051375	Pcdh1	2010005A06Rik|AI585920	protocadherin 1	protein-coding
mm_90449.1	chr10	127677065	127677099	+	1	NA	promoter-TSS (NM_001113211)	promoter-TSS (NM_001113211)	17	NM_001113211	210035	Mm.251075	NM_173732	ENSMUSG00000040195	Nemp1	Tmem194|Tmem194a	nuclear envelope integral membrane protein 1	protein-coding
mm_87343.1	chr10	43518567	43518581	+	1	NA	Intergenic	Intergenic	22420	NM_026411	67851	Mm.209953	NM_026411	ENSMUSG00000019797	1700021F05Rik	-	RIKEN cDNA 1700021F05 gene	protein-coding
mm_57944.1	chr6	134792597	134792682	-	1	NA	promoter-TSS (NM_130447)	promoter-TSS (NM_130447)	-11	NM_001048054	70686	Mm.491182	NM_130447	ENSMUSG00000030203	Dusp16	3830417M17Rik|AW558566|D6Ertd213e|MKP-7|MKP7|Mkpm	dual specificity phosphatase 16	protein-coding
mm_119640.1	chr14	51908089	51908099	+	1	NA	exon (NM_001145959, exon 9 of 15)	exon (NM_001145959, exon 9 of 15)	5394	NM_001145959	29811	Mm.26722	NM_013864	ENSMUSG00000004558	Ndrg2	AI182517|AU040374|Ndr2|SYLD	N-myc downstream regulated gene 2	protein-coding
mm_67823.1	chr7	98272071	98272075	-	1	NA	intron (NM_025408, intron 1 of 10)	intron (NM_025408, intron 1 of 10)	37454	NM_025408	66190	Mm.334041	NM_025408	ENSMUSG00000030760	Acer3	1110057L18Rik|5430429L08Rik|AV015045|Phca	alkaline ceramidase 3	protein-coding
mm_145674.1	chr18	61555707	61555751	+	1	NA	5' UTR (NM_146087, exon 1 of 10)	5' UTR (NM_146087, exon 1 of 10)	147	NM_146087	93687	Mm.26908	NM_146087	ENSMUSG00000024576	Csnk1a1	2610208K14Rik|4632404G05Rik|5430427P18Rik|CK1a|Csnk1a	casein kinase 1, alpha 1	protein-coding
mm_146871.1	chr18	25169014	25169048	-	1	NA	promoter-TSS (NM_001142698)	promoter-TSS (NM_001142698)	11	NM_001033532	225289	Mm.391081	NM_001033532	ENSMUSG00000033632	AW554918	4921538P22|AI461742|Kiaa1328|mKIAA1328	expressed sequence AW554918	protein-coding
mm_122757.1	chr14	54222487	54222499	-	1	NA	Intergenic	Intergenic	31436	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_63708.1	chr7	130674632	130674658	+	1	NA	exon (NM_206856, exon 4 of 21)	exon (NM_206856, exon 4 of 21)	-17911	NM_001347637	57752	Mm.86322	NM_021314	ENSMUSG00000030852	Tacc2	mKIAA4180	transforming, acidic coiled-coil containing protein 2	protein-coding
mm_62596.1	chr7	105650770	105650798	+	1	NA	Intergenic	Intergenic	10244	NM_019502	14356	Mm.220330	NM_019502	ENSMUSG00000089847	Timm10b	Fxc1|Tim10b|Tim9b	translocase of inner mitochondrial membrane 10B	protein-coding
mm_15899.1	chr2	164952424	164952434	+	1	NA	exon (NM_013599, exon 9 of 13)	exon (NM_013599, exon 9 of 13)	4210	NM_013599	17395	Mm.4406	NM_013599	ENSMUSG00000017737	Mmp9	AW743869|B/MMP9|Clg4b|Gel B|MMP-9|pro-MMP-9	matrix metallopeptidase 9	protein-coding
mm_3366.1	chr1	138304456	138304492	+	1	NA	Intergenic	Intergenic	30736	NM_177397	338375	Mm.114424	NM_177397	ENSMUSG00000026394	Atp6v1g3	-	ATPase, H+ transporting, lysosomal V1 subunit G3	protein-coding
mm_27851.1	chr3	79156732	79156743	-	1	NA	Intergenic	L1_Mur3|LINE|L1	-10862	NM_001099624	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_141148.1	chr17	26506173	26506188	-	1	NA	3' UTR (NM_013642, exon 4 of 4)	3' UTR (NM_013642, exon 4 of 4)	2292	NM_013642	19252	Mm.239041	NM_013642	ENSMUSG00000024190	Dusp1	3CH134|MKP1|Ptpn16|U19515|erp|mkp-1	dual specificity phosphatase 1	protein-coding
mm_93660.1	chr10	117690536	117690555	-	1	NA	exon (NM_010786, exon 12 of 12)	exon (NM_010786, exon 12 of 12)	20213	NM_010786	17246	Mm.22670	NM_010786	ENSMUSG00000020184	Mdm2	1700007J15Rik|AA415488|Mdm-2	transformed mouse 3T3 cell double minute 2	protein-coding
mm_15881.1	chr2	164839221	164839261	+	1	NA	TTS (NM_011125)	TTS (NM_011125)	5468	NM_008906	19025	Mm.359633	NM_008906	ENSMUSG00000017760	Ctsa	AU019505|PPCA|Ppgb	cathepsin A	protein-coding
mm_128453.1	chr15	50772791	50772805	-	1	NA	intron (NM_001310485, intron 5 of 7)	intron (NM_001310485, intron 5 of 7)	116251	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_26120.1	chr3	137864574	137864591	+	1	NA	promoter-TSS (NM_016750)	promoter-TSS (NM_016750)	95	NM_016750	51788	Mm.117541	NM_016750	ENSMUSG00000037894	H2afz	H2A.Z|H2a.z-1	H2A histone family, member Z	protein-coding
mm_6614.1	chr1	75505692	75505703	-	1	NA	exon (NM_178884, exon 1 of 20)	exon (NM_178884, exon 1 of 20)	755	NM_178884	98733	Mm.236454	NM_178884	ENSMUSG00000026211	Obsl1	AW822216	obscurin-like 1	protein-coding
mm_81520.1	chr9	110052126	110052136	+	1	NA	exon (NM_001311164, exon 1 of 10)	exon (NM_001311164, exon 1 of 10)	110	NM_001311164	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_57899.1	chr6	131385841	131385843	-	1	NA	intron (NM_139117, intron 1 of 9)	intron (NM_139117, intron 1 of 9)	2608	NM_139117	56449	Mm.458000	NM_011733	ENSMUSG00000030189	Ybx3	Csda|Dpba|MSY3|MSY4|Yb2|dbpA|oxyR	Y box protein 3	protein-coding
mm_132382.1	chr16	34922095	34922103	+	1	NA	exon (NM_139300, exon 16 of 32)	exon (NM_139300, exon 16 of 32)	17230	NR_040536	76649	Mm.420532	NR_040536	ENSMUSG00000100593	1700119H24Rik	-	RIKEN cDNA 1700119H24 gene	ncRNA
mm_140204.1	chr17	83775486	83775492	+	1	NA	intron (NM_001171053, intron 8 of 13)	intron (NM_001171053, intron 8 of 13)	69326	NM_001171052	116871	Mm.277668	NM_054082	ENSMUSG00000055817	Mta3	1110002J22Rik|mKIAA1266	metastasis associated 3	protein-coding
mm_93869.1	chr10	123147366	123147377	-	1	NA	intron (NM_001301628, intron 6 of 20)	intron (NM_001301628, intron 6 of 20)	49648	NM_027604	14479	Mm.244209	NM_027604	ENSMUSG00000020124	Usp15	4921514G19Rik|AI327321|E430033I05Rik|Gcap18	ubiquitin specific peptidase 15	protein-coding
mm_154845.1	chrX	20385167	20385182	+	1	NA	intron (NM_133669, intron 3 of 4)	intron (NM_133669, intron 3 of 4)	20693	NR_110967	19889	Mm.288141	NM_133669	ENSMUSG00000060090	Rp2	AI662636|Rp2h	retinitis pigmentosa 2 homolog	protein-coding
mm_38538.1	chr4	141576806	141576834	-	1	NA	3' UTR (NM_133754, exon 9 of 9)	3' UTR (NM_133754, exon 9 of 9)	23104	NM_001163256	74202	Mm.490327	NM_133754	ENSMUSG00000006219	Fblim1	2410043F08Rik|Cal|Fblp1|Gt10|migfilin|migfilin(s)	filamin binding LIM protein 1	protein-coding
mm_3250.1	chr1	136131444	136131494	+	1	NA	promoter-TSS (NM_001039472)	promoter-TSS (NM_001039472)	68	NM_001039472	16565	Mm.276135	NM_019962	ENSMUSG00000041642	Kif21b	2610511N21Rik|mKIAA0449	kinesin family member 21B	protein-coding
mm_2044.1	chr1	87326998	87327006	+	1	NA	promoter-TSS (NM_001110212)	promoter-TSS (NM_001110212)	4	NM_001110212	227331	Mm.23065	NM_146112	ENSMUSG00000048000	Gigyf2	2610016F01Rik|A830080H02Rik|AI852361|AW259676|BC006835|Tnrc15|mKIAA0642	GRB10 interacting GYF protein 2	protein-coding
mm_139611.1	chr17	57358573	57358591	+	1	NA	promoter-TSS (NM_010130)	promoter-TSS (NM_010130)	-104	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_85253.1	chr9	99304707	99304715	-	1	NA	Intergenic	Intergenic	53819	NM_177775	272636	Mm.490440	NM_177775	ENSMUSG00000037681	Esyt3	D930024E11|D9Ertd280e|Fam62c|mKIAA4186	extended synaptotagmin-like protein 3	protein-coding
mm_152937.1	chr19	28680166	28680183	-	1	NA	promoter-TSS (NM_175459)	promoter-TSS (NM_175459)	-97	NM_175459	226075	Mm.223508	NM_175459	ENSMUSG00000052942	Glis3	4833409N03Rik|E330013K21Rik	GLIS family zinc finger 3	protein-coding
mm_144491.1	chr18	24205608	24205632	+	1	NA	promoter-TSS (NM_001160404)	promoter-TSS (NM_001160404)	276	NM_013814	14423	Mm.30249	NM_013814	ENSMUSG00000000420	Galnt1	-	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 1	protein-coding
mm_165964.1	chr4	94740019	94740021	+	1	NA	intron (NM_001290549, intron 1 of 22)	intron (NM_001290549, intron 1 of 22)	731	NM_001290551	21687	Mm.14313	NM_013690	ENSMUSG00000006386	Tek	AA517024|Cd202b|Hyk|STK1|Tie-2|Tie2	endothelial-specific receptor tyrosine kinase	protein-coding
mm_135572.1	chr16	50330988	50331017	-	1	NA	intron (NM_001347240, intron 3 of 16)	intron (NM_001347240, intron 3 of 16)	101387	NM_027444	70508	Mm.28940	NM_027444	ENSMUSG00000022641	Bbx	5530401J07Rik|5730403O13Rik	bobby sox HMG box containing	protein-coding
mm_141927.1	chr17	35027666	35027673	-	1	NA	TTS (NR_130641)	TTS (NR_130641)	347	NR_028258	78376	Mm.390966	NM_023893	ENSMUSG00000036185	Sapcd1	2810436B06Rik|G7d|Ng23	suppressor APC domain containing 1	protein-coding
mm_126770.1	chr15	86058797	86058851	+	1	NA	promoter-TSS (NM_001205353)	promoter-TSS (NM_001205353)	97	NM_001205353	223752	Mm.24442	NM_172611	ENSMUSG00000035900	Gramd4	9930016O13	GRAM domain containing 4	protein-coding
mm_120245.1	chr14	62992378	62992392	+	1	NA	Intergenic	Intergenic	-5692	NM_001039125	654465	Mm.424929	NM_001039125	ENSMUSG00000075573	Defb47	Defb41|EG654465	defensin beta 47	protein-coding
mm_103771.1	chr11	82006847	82006857	-	1	NA	Intergenic	Intergenic	-28725	NM_011333	20296	Mm.290320	NM_011333	ENSMUSG00000035385	Ccl2	AI323594|HC11|JE|MCAF|MCP-1|MCP1|SMC-CF|Scya2|Sigje	chemokine (C-C motif) ligand 2	protein-coding
mm_172346.1	chr7	11345581	11345581	+	1	NA	Intergenic	IAPLTR4|LTR|ERVK	-52334	NM_001110316	665902	Mm.425380	NM_001110316	ENSMUSG00000070828	Zscan4f	C330039H09Rik	zinc finger and SCAN domain containing 4F	protein-coding
mm_167693.1	chr9	87740011	87740025	-	1	NA	Intergenic	CpG	-8758	NM_023814	76365	Mm.158789	NM_023814	ENSMUSG00000032419	Tbx18	2810012F10Rik|2810404D13Rik	T-box18	protein-coding
mm_125747.1	chr15	73727691	73727714	+	1	NA	intron (NM_001166388, intron 1 of 5)	intron (NM_001166388, intron 1 of 5)	2772	NM_001166388	19245	Mm.390807	NM_008975	ENSMUSG00000059895	Ptp4a3	AV088979|Prl-3|pPtp4a3	protein tyrosine phosphatase 4a3	protein-coding
mm_107566.1	chr12	44269146	44269227	+	1	NA	promoter-TSS (NM_026164)	promoter-TSS (NM_026164)	32	NM_026164	67452	Mm.54126	NM_026164	ENSMUSG00000036257	Pnpla8	1200006O19Rik|AI467579|Ipla2(gamma)	patatin-like phospholipase domain containing 8	protein-coding
mm_82688.1	chr9	22307642	22307694	-	1	NA	promoter-TSS (NM_145612)	promoter-TSS (NM_145612)	-30	NM_145612	235050	Mm.306038	NM_145612	ENSMUSG00000066829	Zfp810	BC005471	zinc finger protein 810	protein-coding
mm_90814.1	chr10	7906315	7906348	-	1	NA	3' UTR (NM_138667, exon 7 of 7)	3' UTR (NM_138667, exon 7 of 7)	49792	NM_138667	68652	Mm.193041	NM_138667	ENSMUSG00000015755	Tab2	1110030N06Rik|A530078N03Rik|Map3k7ip2|mKIAA0733	TGF-beta activated kinase 1/MAP3K7 binding protein 2	protein-coding
mm_74438.1	chr8	3754749	3754765	-	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	-5773	NM_133238	170786	Mm.32510	NM_133238	ENSMUSG00000031494	Cd209a	CD209|CDSIGN|CIRE|DC-SIGN|DC-SIGN1|Dcsign|SIGN-R1|SIGNR5	CD209a antigen	protein-coding
mm_494.1	chr1	36781096	36781112	+	1	NA	intron (NM_009539, intron 10 of 12)	intron (NM_009539, intron 10 of 12)	2120	NM_001289612	22637	Mm.8038	NM_009539	ENSMUSG00000026117	Zap70	Srk|ZAP-70|mrtle|mur	zeta-chain (TCR) associated protein kinase	protein-coding
mm_84071.1	chr9	58201628	58201638	-	1	NA	promoter-TSS (NM_001161537)	promoter-TSS (NM_001161537)	82	NM_001161535	320563	Mm.186499	NM_177193	ENSMUSG00000051243	Islr2	B930052A04Rik|Linx|Mbu-3|mKIAA1465	immunoglobulin superfamily containing leucine-rich repeat 2	protein-coding
mm_49032.1	chr6	4759808	4759819	+	1	NA	3' UTR (NM_130877, exon 2 of 2)	3' UTR (NM_130877, exon 2 of 2)	12507	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_172095.1	chr6	24196587	24196588	-	1	NA	Intergenic	MMERVK9C_I-int|LTR|ERVK	-28495	NM_019481	55961	Mm.19299	NM_019481	ENSMUSG00000029700	Slc13a1	AI314066|AI987826|NaSi-1|Nas1	solute carrier family 13 (sodium/sulfate symporters), member 1	protein-coding
mm_142037.1	chr17	35262846	35262854	-	1	NA	promoter-TSS (NM_001267808)	promoter-TSS (NM_001267808)	-244	NM_010380	14964	Mm.439675	NM_010380	ENSMUSG00000073411	H2-D1	H-2D|H2-D	histocompatibility 2, D region locus 1	protein-coding
mm_143911.1	chr17	85612332	85612377	-	1	NA	non-coding (NR_038083, exon 4 of 4)	non-coding (NR_038083, exon 4 of 4)	6042	NR_038084	100043902	Mm.150838	NR_015385	ENSMUSG00000093460	Six3os1	D17Mgi26|E130112H22Rik|Rncr1|Six3os	SIX homeobox 3, opposite strand 1	ncRNA
mm_140692.1	chr17	13760405	13760426	-	1	NA	promoter-TSS (NM_010806)	promoter-TSS (NM_010806)	-126	NM_010806	17356	Mm.59167	NM_010806	ENSMUSG00000068036	Afdn	5033403D15Rik|AF6|Af-6|Afadin|Gm314|I-afadin|Mllt4|S-afadin	afadin, adherens junction formation factor	protein-coding
mm_97893.1	chr11	83302818	83302822	+	1	NA	5' UTR (NM_001035854, exon 1 of 22)	5' UTR (NM_001035854, exon 1 of 22)	123	NM_001035854	71770	Mm.39053	NM_027915	ENSMUSG00000035152	Ap2b1	1300012O03Rik|AI788979	adaptor-related protein complex 2, beta 1 subunit	protein-coding
mm_110996.1	chr12	78299080	78299082	-	1	NA	intron (NM_145965, intron 1 of 22)	MERV1_LTR|LTR|ERV1	72426	NM_145965	268566	Mm.341742	NM_145965	ENSMUSG00000047454	Gphn	5730552E08Rik|AI662856|BC027112|C230040D23|GPH|GPHRYN|geph	gephyrin	protein-coding
mm_160355.1	chr8	21529030	21529030	+	1	NA	promoter-TSS (NM_001177521)	promoter-TSS (NM_001177521)	0	NM_001177521	100041890	Mm.423382	NM_001177521	ENSMUSG00000094818	Defa32	ENSMUSG00000065957|Gm15308|OTTMUSG00000019860	defensin, alpha, 32	protein-coding
mm_156868.1	chrX	164442166	164442176	+	1	NA	intron (NM_026853, intron 2 of 7)	intron (NM_026853, intron 2 of 7)	5177	NM_001313737	68854	Mm.33225	NM_026853	ENSMUSG00000031382	Asb11	1110067L12Rik|1600009D24Rik	ankyrin repeat and SOCS box-containing 11	protein-coding
mm_88739.1	chr10	80265088	80265154	+	1	NA	5' UTR (NM_133188, exon 1 of 12)	5' UTR (NM_133188, exon 1 of 12)	130	NM_133188	70248	Mm.148693	NM_133188	ENSMUSG00000069565	Dazap1	2410042M16Rik|mPrrp	DAZ associated protein 1	protein-coding
mm_135380.1	chr16	44139632	44139654	-	1	NA	promoter-TSS (NM_007508)	promoter-TSS (NM_007508)	-148	NM_001347239	72117	Mm.278726	NM_028108	ENSMUSG00000022698	Naa50	2600005K24Rik|2810441M03Rik|AW112078|Mak3|Mak3p|Nat13|Nat5|San	N(alpha)-acetyltransferase 50, NatE catalytic subunit	protein-coding
mm_121771.1	chr14	19875229	19875239	-	1	NA	3' UTR (NM_001285911, exon 4 of 4)	3' UTR (NM_001285911, exon 4 of 4)	36309	NR_105025	52512	Mm.483998	NR_105025		D14Ertd670e	-	DNA segment, Chr 14, ERATO Doi 670, expressed	ncRNA
mm_81228.1	chr9	107674858	107674878	+	1	NA	3' UTR (NM_008140, exon 9 of 9)	3' UTR (NM_008140, exon 9 of 9)	4724	NM_008140	14685	Mm.284853	NM_008140	ENSMUSG00000034837	Gnat1	Gnat-1|Ird1|Ird2|Tralpha|irdc|irdr|transducin	guanine nucleotide binding protein, alpha transducing 1	protein-coding
mm_81825.1	chr9	118050059	118050101	+	1	NA	intron (NM_001286508, intron 4 of 7)	intron (NM_001286508, intron 4 of 7)	9558	NM_013727	27215	Mm.92705	NM_013727	ENSMUSG00000039285	Azi2	AA410145|AZ2	5-azacytidine induced gene 2	protein-coding
mm_108072.1	chr12	73942049	73942065	+	1	NA	exon (NM_010431, exon 12 of 15)	exon (NM_010431, exon 12 of 15)	-22473	NM_178392	75627	Mm.25937	NM_178392	ENSMUSG00000021113	Snapc1	2700033G17Rik|AU015787	small nuclear RNA activating complex, polypeptide 1	protein-coding
mm_69696.1	chr7	140036334	140036350	-	1	NA	promoter-TSS (NM_001286011)	promoter-TSS (NM_001286011)	8	NM_133755	74237	Mm.40888	NM_133755	ENSMUSG00000025474	Tubgcp2	1700022B05Rik	tubulin, gamma complex associated protein 2	protein-coding
mm_34538.1	chr4	149497375	149497377	+	1	NA	TTS (NM_026963)	TTS (NM_026963)	12043	NM_026963	69151	Mm.464434	NM_026963	ENSMUSG00000028990	Lzic	1810030J04Rik|AW047580	leucine zipper and CTNNBIP1 domain containing	protein-coding
mm_152458.1	chr19	10871625	10871639	-	1	NA	3' UTR (NM_134142, exon 4 of 4)	3' UTR (NM_134142, exon 4 of 4)	-1853	NM_133804	98170	Mm.490254	NM_133804	ENSMUSG00000024736	Tmem132a	6720481D13Rik|Hspa5bp1|Orai1|R74613	transmembrane protein 132A	protein-coding
mm_161082.1	chr12	84396968	84396968	-	1	NA	intron (NM_007647, intron 2 of 14)	intron (NM_007647, intron 2 of 14)	3966	NM_001286058	12499	Mm.10211	NM_007647	ENSMUSG00000021236	Entpd5	AI196558|AI987697|Cd39l4|ER-UDPase|NTPDase-5|NTPDase5|Pcph|mNTPase	ectonucleoside triphosphate diphosphohydrolase 5	protein-coding
mm_92339.1	chr10	75834403	75834432	-	1	NA	5' UTR (NM_010361, exon 1 of 5)	5' UTR (NM_010361, exon 1 of 5)	464	NM_010361	14872	Mm.24118	NM_010361	ENSMUSG00000033318	Gstt2	AI266894|Yrs|mGSTT2	glutathione S-transferase, theta 2	protein-coding
mm_115524.1	chr13	5861264	5861281	-	1	NA	promoter-TSS (NM_011803)	promoter-TSS (NM_011803)	-217	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_36321.1	chr4	70307350	70307358	-	1	NA	intron (NM_145990, intron 14 of 36)	intron (NM_145990, intron 14 of 36)	103081	NM_001313762	214444	Mm.370777	NM_145990	ENSMUSG00000039298	Cdk5rap2	2900018K03Rik|an|mKIAA1633	CDK5 regulatory subunit associated protein 2	protein-coding
mm_114253.1	chr13	56703361	56703431	+	1	NA	promoter-TSS (NM_001164042)	promoter-TSS (NM_001164042)	-272	NM_001164042	17129	Mm.272920	NM_008541	ENSMUSG00000021540	Smad5	1110051M15Rik|AI451355|Dwf-C|Madh5|MusMLP	SMAD family member 5	protein-coding
mm_4801.1	chr1	185210707	185210732	+	1	NA	intron (NM_001163754, intron 1 of 34)	BC1_Mm|scRNA|scRNA	6551	NM_001163754	98732	Mm.275841	NM_172649	ENSMUSG00000039318	Rab3gap2	1110059F07Rik|2010002H18Rik|5830469C09|AI851069|AW743433|RAB3-GAP150|mKIAA0839	RAB3 GTPase activating protein subunit 2	protein-coding
mm_158491.1	chrX	142328055	142328066	-	1	NA	exon (NM_207625, exon 15 of 16)	exon (NM_207625, exon 15 of 16)	-21862	NM_021487	66240	Mm.58507	NM_021487	ENSMUSG00000090122	Kcne1l	1500015C14Rik|Kcne5|Mink	potassium voltage-gated channel, Isk-related family, member 1-like, pseudogene	protein-coding
mm_53357.1	chr6	129351453	129351481	+	1	NA	intron (NM_177686, intron 1 of 5)	PB1|SINE|Alu	1223	NM_177686	232413	Mm.90241	NM_177686	ENSMUSG00000053063	Clec12a	CLL-1|D230024O04|KLRL1|Micl	C-type lectin domain family 12, member a	protein-coding
mm_138272.1	chr17	34604885	34604921	+	1	NA	promoter-TSS (NM_001163379)	promoter-TSS (NM_001163379)	-958	NM_001163379	55979	Mm.8684	NM_018862	ENSMUSG00000034254	Agpat1	1-AGP|1-AGPAT|AW047140	1-acylglycerol-3-phosphate O-acyltransferase 1 (lysophosphatidic acid acyltransferase, alpha)	protein-coding
mm_168112.1	chr10	14802299	14802299	+	1	NA	Intergenic	(CAG)n|Simple_repeat|Simple_repeat	42010	NM_008703	18101	Mm.487342	NM_008703	ENSMUSG00000019865	Nmbr	BB182387	neuromedin B receptor	protein-coding
mm_84525.1	chr9	67043971	67043983	-	1	NA	promoter-TSS (NM_001164256)	promoter-TSS (NM_001164256)	-106	NM_001164253	22003	Mm.121878	NM_024427	ENSMUSG00000032366	Tpm1	AA986836|AI854628|TM2|Tm3|Tmpa|Tpm-1|alpha-TM	tropomyosin 1, alpha	protein-coding
mm_134217.1	chr16	11253983	11254045	-	1	NA	TTS (NR_035466)	TTS (NR_035466)	311	NM_001130008	14852	Mm.325827	NM_146066	ENSMUSG00000062203	Gspt1	AI314175|AI326449|AV307676|C79774|G1st|Gst-1	G1 to S phase transition 1	protein-coding
mm_90159.1	chr10	118866126	118866130	+	1	NA	intron (NM_001014390, intron 2 of 2)	intron (NM_001014390, intron 2 of 2)	2775	NM_001014390	69181	Mm.45565	NM_001014390	ENSMUSG00000028630	Dyrk2	1810038L18Rik	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 2	protein-coding
mm_107036.1	chr12	13501241	13501249	+	1	NA	intron (NM_027706, intron 44 of 51)	intron (NM_027706, intron 44 of 51)	126401	NR_136761	102639399	Mm.122052	NR_136761		Gm35725	-	predicted gene, 35725	ncRNA
mm_63752.1	chr7	131085373	131085388	+	1	NA	exon (NM_007769, exon 26 of 47)	exon (NM_007769, exon 26 of 47)	53304	NM_007769	12945	Mm.4138	NM_007769	ENSMUSG00000047517	Dmbt1	CRP|CRP-[a]|CRP-[b]|Crpd|DBMT1|gp300|p80	deleted in malignant brain tumors 1	protein-coding
mm_65730.1	chr7	28381879	28381899	-	1	NA	Intergenic	Intergenic	-2661	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_43980.1	chr5	146261256	146261295	+	1	NA	intron (NM_153599, intron 2 of 12)	LSU-rRNA_Hsa|rRNA|rRNA	29600	NM_153599	264064	Mm.260576	NM_153599	ENSMUSG00000029635	Cdk8	-	cyclin-dependent kinase 8	protein-coding
mm_16405.1	chr2	180034817	180034850	+	1	NA	3' UTR (NM_177727, exon 9 of 9)	3' UTR (NM_177727, exon 9 of 9)	7631	NM_001289476	26444	Mm.21728	NM_011969	ENSMUSG00000027566	Psma7	C6-I	proteasome (prosome, macropain) subunit, alpha type 7	protein-coding
mm_136177.1	chr16	88826140	88826151	-	1	NA	promoter-TSS (NM_013707)	promoter-TSS (NM_013707)	0	NM_013707	23927	Mm.3502	NM_013707	ENSMUSG00000074928	Krtap14	AA589630|Pmg1|mKAP13	keratin associated protein 14	protein-coding
mm_30835.1	chr4	22035613	22035615	+	1	NA	Intergenic	Intergenic	104288	NM_175234	76132	Mm.159689	NM_175234	ENSMUSG00000028246	Faxc	6230409E13Rik|AW742931	failed axon connections homolog	protein-coding
mm_92788.1	chr10	81302922	81302941	-	1	NA	intron (NM_008844, intron 1 of 17)	intron (NM_008844, intron 1 of 17)	9968	NM_001146687	18717	Mm.24222	NM_008844	ENSMUSG00000034902	Pip5k1c	AI115456|AI835305|Pip5kIgamma	phosphatidylinositol-4-phosphate 5-kinase, type 1 gamma	protein-coding
mm_83669.1	chr9	49718741	49718745	-	1	NA	intron (NM_001081445, intron 1 of 17)	intron (NM_001081445, intron 1 of 17)	80326	NM_001081445	17967	Mm.4974	NM_010875	ENSMUSG00000039542	Ncam1	CD56|E-NCAM|NCAM-1|Ncam	neural cell adhesion molecule 1	protein-coding
mm_48156.1	chr5	137152294	137152333	-	1	NA	Intergenic	Intergenic	-36106	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_10615.1	chr2	19300577	19300601	+	1	NA	exon (NM_001271565, exon 17 of 18)	exon (NM_001271565, exon 17 of 18)	-43728	NR_126563	108871	Mm.107666	NR_126563		4930447M23Rik	-	RIKEN cDNA 4930447M23 gene	ncRNA
mm_169821.1	chr16	22294998	22295000	+	1	NA	Intergenic	Intergenic	-28994	NM_001330555	20462	Mm.210352	NM_009186	ENSMUSG00000022858	Tra2b	5730405G21Rik|D16Ertd266e|SIG-41|Sfrs10|Silg41|TRA2beta	transformer 2 beta homolog (Drosophila)	protein-coding
mm_123649.1	chr14	69171801	69171823	-	1	NA	promoter-TSS (NM_010920)	promoter-TSS (NM_010920)	10	NM_010920	18092	Mm.390691	NM_010920	ENSMUSG00000044186	Nkx2-6	AV044928|Nkx-2.6|Nkx2.6|Tix|tinman	NK2 homeobox 6	protein-coding
mm_57367.1	chr6	124769549	124769570	-	1	NA	TTS (NM_001302555)	TTS (NM_001302555)	114	NM_001302642	13807	Mm.3913	NM_013509	ENSMUSG00000004267	Eno2	AI837106|D6Ertd375e|Eno-2|NSE	enolase 2, gamma neuronal	protein-coding
mm_41344.1	chr5	90500401	90500404	+	1	NA	intron (NM_007423, intron 7 of 14)	intron (NM_007423, intron 7 of 14)	9688	NM_007423	11576	Mm.358570	NM_007423	ENSMUSG00000054932	Afp	-	alpha fetoprotein	protein-coding
mm_80898.1	chr9	99856091	99856095	+	1	NA	Intergenic	Intergenic	20077	NM_011440	20669	Mm.261595	NM_011440	ENSMUSG00000053747	Sox14	-	SRY (sex determining region Y)-box 14	protein-coding
mm_67985.1	chr7	100706275	100706284	-	1	NA	promoter-TSS (NM_178764)	promoter-TSS (NM_178764)	-423	NM_178764	319604	Mm.260362	NM_178764	ENSMUSG00000029461	Fam168a	2610030B18Rik|B930006L02Rik|mKIAA0280	family with sequence similarity 168, member A	protein-coding
mm_142518.1	chr17	46270814	46270824	-	1	NA	intron (NM_001252475, intron 1 of 8)	intron (NM_001252475, intron 1 of 8)	12207	NM_001252475	74094	Mm.284594	NM_028751	ENSMUSG00000012296	Tjap1	0610041D19Rik|AI415281|AW121008|Pilt|Tjp4	tight junction associated protein 1	protein-coding
mm_81971.1	chr9	120970726	120970765	+	1	NA	intron (NM_177589, intron 35 of 36)	L1_Mur3|LINE|L1	15659	NR_106058	102465661		NR_106058	ENSMUSG00000106193	Mir7090	mmu-mir-7090	microRNA 7090	ncRNA
mm_154305.1	chr19	61226285	61226305	-	1	NA	exon (NM_009970, exon 6 of 12)	exon (NM_009970, exon 6 of 12)	2123	NM_009970	12982	Mm.287228	NM_009970	ENSMUSG00000059326	Csf2ra	CD116|Csfgmra|GM-CSF-Ra|GM-CSFR	colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)	protein-coding
mm_15322.1	chr2	155750806	155750819	+	1	NA	promoter-TSS (NM_011171)	promoter-TSS (NM_011171)	-405	NM_011171	19124	Mm.3243	NM_011171	ENSMUSG00000027611	Procr	AI325044|Ccca|Ccd41|Epcr	protein C receptor, endothelial	protein-coding
mm_77161.1	chr8	111687199	111687245	-	1	NA	exon (NM_025583, exon 6 of 7)	exon (NM_025583, exon 6 of 7)	2452	NR_106044	102466993		NR_106044	ENSMUSG00000099129	Mir7076	Gm27318|mmu-mir-7076	microRNA 7076	ncRNA
mm_116450.1	chr13	43171438	43171457	-	1	NA	promoter-TSS (NM_025935)	promoter-TSS (NM_025935)	54	NM_001252639	67046	Mm.269213	NM_025935	ENSMUSG00000021368	Tbc1d7	2610009C09Rik	TBC1 domain family, member 7	protein-coding
mm_78907.1	chr9	44773028	44773067	+	1	NA	promoter-TSS (NM_023831)	promoter-TSS (NM_023831)	38	NM_023831	76568	Mm.278597	NM_023831	ENSMUSG00000002031	Ift46	1500035H01Rik|AA408110|AI663846|R75047|c11orf2	intraflagellar transport 46	protein-coding
mm_59423.1	chr7	27124641	27124679	+	1	NA	intron (NM_007817, intron 3 of 9)	intron (NM_007817, intron 3 of 9)	4705	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_26675.1	chr3	154796283	154796289	+	1	NA	intron (NM_177066, intron 23 of 24)	intron (NM_177066, intron 23 of 24)	85153	NM_175176	209601	Mm.331454	NM_175176	ENSMUSG00000078161	Erich3	1700013E18Rik|4922501L14Rik|5031409G23Rik|AI596448|Gm133	glutamate rich 3	protein-coding
mm_679.1	chr1	40491053	40491055	+	1	NA	intron (NM_008365, intron 8 of 10)	intron (NM_008365, intron 8 of 10)	-24308	NM_010553	16174	Mm.20466	NM_010553	ENSMUSG00000026068	Il18rap	AcPL|IL-18R-beta|IL-18RAcP|IL-18Rbeta|IL-1RAcPL	interleukin 18 receptor accessory protein	protein-coding
mm_21270.1	chr2	156862831	156862855	-	1	NA	promoter-TSS (NM_026124)	promoter-TSS (NM_026124)	102	NR_015591	74487	Mm.490465	NR_015591	ENSMUSG00000085741	5430405H02Rik	2610307N17Rik	RIKEN cDNA 5430405H02 gene	ncRNA
mm_56842.1	chr6	117612563	117612579	-	1	NA	Intergenic	Intergenic	139198	NR_045731	72263	Mm.443289	NR_045731	ENSMUSG00000099869	1700030F04Rik	-	RIKEN cDNA 1700030F04 gene	ncRNA
mm_42473.1	chr5	115455334	115455365	+	1	NA	Intergenic	T-rich|Low_complexity|Low_complexity	-10917	NM_011107	18778	Mm.20190	NM_011107	ENSMUSG00000029522	Pla2g1b	Pla2a|sPLA2IB	phospholipase A2, group IB, pancreas	protein-coding
mm_161067.1	chr12	76031646	76031646	+	1	NA	exon (NM_001005510, exon 76 of 116)	exon (NM_001005510, exon 76 of 116)	122543	NR_039560	100628610		NR_039560	ENSMUSG00000092922	Mir5101	mmu-mir-5101|mu-mir-5101	microRNA 5101	ncRNA
mm_17270.1	chr2	26091777	26091791	-	1	NA	5' UTR (NM_001037098, exon 1 of 6)	5' UTR (NM_001037098, exon 1 of 6)	612	NM_001037098	67991	Mm.131074	NM_026495	ENSMUSG00000026932	Nacc2	0610020I02Rik|AI448087|Btbd14a|C030048H19Rik	nucleus accumbens associated 2, BEN and BTB (POZ) domain containing	protein-coding
mm_165981.1	chr4	103290899	103290906	-	1	NA	promoter-TSS (NM_001163494)	promoter-TSS (NM_001163494)	-39	NM_001163494	70941	Mm.158501	NM_027612	ENSMUSG00000028520	4921539E11Rik	-	RIKEN cDNA 4921539E11 gene	protein-coding
mm_128895.1	chr15	73243007	73243037	-	1	NA	intron (NM_001130409, intron 23 of 29)	intron (NM_001130409, intron 23 of 29)	11860	NR_029561	387169		NR_029561	ENSMUSG00000065612	Mir151	Mirn151|mir-151|mmu-mir-151	microRNA 151	ncRNA
mm_136092.1	chr16	85034399	85034401	-	1	NA	intron (NM_007471, intron 6 of 15)	intron (NM_007471, intron 6 of 15)	62189	NR_045889	100038614	Mm.441351	NR_045889		Gm10791	ENSMUSG00000074933	predicted gene 10791	ncRNA
mm_87603.1	chr10	57650991	57651010	+	1	NA	promoter-TSS (NM_001190402)	promoter-TSS (NM_001190402)	19	NM_001190402	18768	Mm.262135	NM_008863	ENSMUSG00000019876	Pkib	Pkibeta|Prkacn2	protein kinase inhibitor beta, cAMP dependent, testis specific	protein-coding
mm_51354.1	chr6	72558674	72558687	+	1	NA	intron (NM_001271395, intron 7 of 9)	intron (NM_001271395, intron 7 of 9)	9033	NM_001271395	12332	Mm.18626	NM_007599	ENSMUSG00000056737	Capg	gCap39|mbh1	capping protein (actin filament), gelsolin-like	protein-coding
mm_24656.1	chr3	94443316	94443345	+	1	NA	promoter-TSS (NM_030116)	promoter-TSS (NM_030116)	-6	NM_030116	78523	Mm.218515	NM_030116	ENSMUSG00000028140	Mrpl9	8030480E20Rik|AA409733|C330013D18Rik|L9mt	mitochondrial ribosomal protein L9	protein-coding
mm_34151.1	chr4	139376707	139376712	+	1	NA	3' UTR (NM_146157, exon 24 of 24)	3' UTR (NM_146157, exon 24 of 24)	-3950	NM_001160319	69116	Mm.271956	NM_001160319	ENSMUSG00000066036	Ubr4	1810009A16Rik|A930005E13Rik|D930005K06Rik|Gm1032|Gm1666|N28143|RBAF600|Zubr1|mKIAA0462|p600	ubiquitin protein ligase E3 component n-recognin 4	protein-coding
mm_110010.1	chr12	16583996	16583999	-	1	NA	intron (NM_172950, intron 1 of 19)	ID_B1|SINE|B4	5773	NM_015763	14245	Mm.153625	NM_015763	ENSMUSG00000020593	Lpin1	4631420P06|Kiaa0188|Lipin1|fld|mKIAA0188	lipin 1	protein-coding
mm_77473.1	chr8	122432895	122432923	-	1	NA	promoter-TSS (NM_007806)	promoter-TSS (NM_007806)	31	NM_001301284	13057	Mm.271671	NM_007806	ENSMUSG00000006519	Cyba	b558|nmf333|p22-phox|p22phox	cytochrome b-245, alpha polypeptide	protein-coding
mm_64759.1	chr7	4844996	4845011	-	1	NA	promoter-TSS (NM_172737)	promoter-TSS (NM_172737)	-307	NM_172737	232813	Mm.44666	NM_172737	ENSMUSG00000053550	Shisa7	ckamp59	shisa family member 7	protein-coding
mm_99680.1	chr11	105994636	105994678	+	1	NA	promoter-TSS (NM_001101453)	promoter-TSS (NM_001101453)	-18	NM_001101453	217246	Mm.296699	NM_001101453	ENSMUSG00000101605	Ace3	EG217246	angiotensin I converting enzyme (peptidyl-dipeptidase A) 3	protein-coding
mm_104691.1	chr11	97782410	97782420	-	1	NA	promoter-TSS (NR_028078)	promoter-TSS (NR_028078)	24	NM_022891	65019	Mm.140380	NM_022891	ENSMUSG00000071415	Rpl23	2810009A01Rik	ribosomal protein L23	protein-coding
mm_49326.1	chr6	21214822	21214859	+	1	NA	Intergenic	CpG	-1269	NM_019697	16508	Mm.425316	NM_019697	ENSMUSG00000060882	Kcnd2	AI839615|AW555701|Kv4.2|R75121|mKIAA1044	potassium voltage-gated channel, Shal-related family, member 2	protein-coding
mm_62105.1	chr7	96295943	96295947	+	1	NA	intron (NM_001310760, intron 1 of 32)	intron (NM_001310760, intron 1 of 32)	-9722	NR_105818	102465210		NR_105818	ENSMUSG00000099030	Mir6394	Gm27929|mmu-mir-6394	microRNA 6394	ncRNA
mm_21060.1	chr2	152728279	152728306	-	1	NA	Intergenic	Intergenic	-7959	NM_010495	15901	Mm.444	NM_010495	ENSMUSG00000042745	Id1	AI323524|D2Wsu140e|Idb1|bHLHb24	inhibitor of DNA binding 1	protein-coding
mm_101975.1	chr11	50326081	50326083	-	1	NA	promoter-TSS (NM_001110500)	promoter-TSS (NM_001110500)	-409	NM_001110500	12330	Mm.248827	NM_007597	ENSMUSG00000020368	Canx	1110069N15Rik|AI988026|Cnx|D11Ertd153e	calnexin	protein-coding
mm_156690.1	chrX	159414660	159414711	+	1	NA	5' UTR (NM_001081124, exon 1 of 17)	5' UTR (NM_001081124, exon 1 of 17)	113	NM_001313751	78283	Mm.160079	NM_001081124	ENSMUSG00000041020	Map7d2	1600028E09Rik|2900002G04Rik|5330432J06Rik|C030036K04Rik|Mtap7d2	MAP7 domain containing 2	protein-coding
mm_27850.1	chr3	79156708	79156730	-	1	NA	Intergenic	L1_Mur3|LINE|L1	-10844	NM_001099624	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_166866.1	chr7	24593858	24593858	+	1	NA	5' UTR (NM_023154, exon 2 of 8)	5' UTR (NM_023154, exon 2 of 8)	-6217	NM_001033205	101544	Mm.20117	NM_001033205	ENSMUSG00000066721	Zfp575	AI326876|Znf575	zinc finger protein 575	protein-coding
mm_12174.1	chr2	62686138	62686168	+	1	NA	intron (NM_145523, intron 4 of 7)	intron (NM_145523, intron 4 of 7)	21826	NM_145523	227960	Mm.219877	NM_145523	ENSMUSG00000026893	Gca	5133401E04Rik|AI573844	grancalcin	protein-coding
mm_107998.1	chr12	73336790	73336818	+	1	NA	intron (NM_001037717, intron 6 of 15)	intron (NM_001037717, intron 6 of 15)	49956	NM_001037717	625098	Mm.32075	NM_001037717	ENSMUSG00000044712	Slc38a6	AW322671|EG625098	solute carrier family 38, member 6	protein-coding
mm_134889.1	chr16	29541385	29541409	-	1	NA	promoter-TSS (NM_001164612)	promoter-TSS (NM_001164612)	86	NM_172613	224079	Mm.54954	NM_172613	ENSMUSG00000038094	Atp13a4	4631413J11Rik|4832416L12|9330174J19Rik	ATPase type 13A4	protein-coding
mm_162484.1	chr1	135155452	135155462	+	1	NA	3' UTR (NM_026823, exon 7 of 7)	3' UTR (NM_026823, exon 7 of 7)	8623	NM_026823	68724	Mm.174998	NM_026823	ENSMUSG00000026426	Arl8a	1110033P22Rik|Arl10b|gie2	ADP-ribosylation factor-like 8A	protein-coding
mm_117947.1	chr13	99435264	99435273	-	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-22442	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_82892.1	chr9	32541656	32541691	-	1	NA	promoter-TSS (NM_008026)	promoter-TSS (NM_008026)	-221	NM_008026	14247	Mm.258908	NM_008026	ENSMUSG00000016087	Fli1	EWSR2|Fli-1|SIC-1|Sic1	Friend leukemia integration 1	protein-coding
mm_163154.1	chr11	83604967	83604976	+	1	NA	intron (NR_036453, intron 2 of 8)	intron (NR_036453, intron 2 of 8)	-11884	NM_009139	20305	Mm.137	NM_009139	ENSMUSG00000018927	Ccl6	MRP-1|Scya6|c10	chemokine (C-C motif) ligand 6	protein-coding
mm_71299.1	chr8	41240984	41241019	+	1	NA	intron (NM_023662, intron 1 of 37)	intron (NM_023662, intron 1 of 37)	1242	NM_023662	18536	Mm.117896	NM_023662	ENSMUSG00000031592	Pcm1	2600002H09Rik|9430077F19Rik|C030044G17Rik	pericentriolar material 1	protein-coding
mm_100364.1	chr11	118988174	118988192	+	1	NA	promoter-TSS (NM_001030291)	promoter-TSS (NM_001030291)	-5	NM_001030291	238011	Mm.244114	NM_001030291	ENSMUSG00000046697	Enpp7	Alk-SMase|Gm254	ectonucleotide pyrophosphatase/phosphodiesterase 7	protein-coding
mm_154166.1	chr19	58673170	58673185	-	1	NA	exon (NM_026925, exon 4 of 13)	exon (NM_026925, exon 4 of 13)	2812	NM_026925	69060	Mm.20407	NM_026925	ENSMUSG00000046008	Pnlip	1810007A24Rik|PL|PTL	pancreatic lipase	protein-coding
mm_89076.1	chr10	83098088	83098090	+	1	NA	intron (NM_021439, intron 2 of 2)	intron (NM_021439, intron 2 of 2)	112592	NM_021439	58250	Mm.360747	NM_021439	ENSMUSG00000034612	Chst11	1110020P09Rik|C4ST|C4ST-1|C4ST1|C4s	carbohydrate sulfotransferase 11	protein-coding
mm_157939.1	chrX	85738708	85738744	-	1	NA	intron (NM_001294138, intron 9 of 19)	intron (NM_001294138, intron 9 of 19)	38093	NM_001294140	14933	Mm.246682	NM_008194	ENSMUSG00000025059	Gk	D930012N15Rik|Gyk	glycerol kinase	protein-coding
mm_54528.1	chr6	36715048	36715051	-	1	NA	TTS (NM_008973)	TTS (NM_008973)	96312	NM_008973	19242	Mm.279690	NM_008973	ENSMUSG00000029838	Ptn	HARP|HB-GAM|HBBN|HBGF-8|HBNF|OSF|Osf-1|Osf1	pleiotrophin	protein-coding
mm_27631.1	chr3	61363119	61363125	-	1	NA	Intergenic	Intergenic	-1385	NM_028712	74012	Mm.422674	NM_028712	ENSMUSG00000036894	Rap2b	4021402C18Rik|AA408554	RAP2B, member of RAS oncogene family	protein-coding
mm_168729.1	chr12	113381649	113381671	-	1	NA	Intergenic	Intergenic	-107905	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_14774.1	chr2	145820003	145820005	+	1	NA	intron (NM_028724, intron 2 of 12)	BC1_Mm|scRNA|scRNA	33888	NM_028724	74030	Mm.228799	NM_028724	ENSMUSG00000001768	Rin2	2010003K16Rik|4632403N06Rik|AW821980|RASSF4	Ras and Rab interactor 2	protein-coding
mm_168301.1	chr11	106252235	106252249	-	1	NA	exon (NM_025310, exon 13 of 21)	exon (NM_025310, exon 13 of 21)	3560	NM_025310	56095	Mm.29795	NM_025310	ENSMUSG00000020706	Ftsj3	AA537063|AU045295|C79843|D11Ertd400e|Epcs3	FtsJ RNA methyltransferase homolog 3 (E. coli)	protein-coding
mm_13292.1	chr2	101991946	101991953	+	1	NA	intron (NM_001290784, intron 4 of 5)	ORR1E|LTR|ERVL-MaLR	105687	NM_029635	76501	Mm.330424	NM_029635	ENSMUSG00000027163	Commd9	1810029F08Rik|AA409293	COMM domain containing 9	protein-coding
mm_57292.1	chr6	124433750	124433778	-	1	NA	intron (NM_001346656, intron 16 of 17)	intron (NM_001346656, intron 16 of 17)	-18697	NM_001277805	19305	Mm.22418	NM_008995	ENSMUSG00000005069	Pex5	AW212715|ESTM1|PTS1R|Pxr1|X83306	peroxisomal biogenesis factor 5	protein-coding
mm_62426.1	chr7	101345969	101345977	+	1	NA	exon (NM_019990, exon 7 of 7)	exon (NM_019990, exon 7 of 7)	-2096	NM_001040111	69710	Mm.277687	NM_027180	ENSMUSG00000032812	Arap1	2410002L19Rik|Centd2|mKIAA0782	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	protein-coding
mm_151211.1	chr19	53621827	53621861	+	1	NA	exon (NM_007790, exon 9 of 29)	exon (NM_007790, exon 9 of 29)	21448	NM_007790	13006	Mm.14910	NM_007790	ENSMUSG00000024974	Smc3	Bamacan|Cspg6|HCAP|Mmip1|SMC-3|SmcD	structural maintenance of chromosomes 3	protein-coding
mm_3628.1	chr1	152791896	152791904	+	1	NA	Intergenic	B3|SINE|B2	-8253	NM_010877	17970	Mm.270307	NM_010877	ENSMUSG00000026480	Ncf2	NOXA2|Ncf-2|p67phox	neutrophil cytosolic factor 2	protein-coding
mm_155557.1	chrX	75127120	75127131	+	1	NA	intron (NM_008621, intron 1 of 11)	intron (NM_008621, intron 1 of 11)	3891	NM_008621	17524	Mm.391267	NM_008621	ENSMUSG00000031402	Mpp1	55kDa|C130070C03Rik|p55	membrane protein, palmitoylated	protein-coding
mm_70038.1	chr7	142577488	142577492	-	1	NA	promoter-TSS (NR_030416)	promoter-TSS (NR_030416)	-343	NR_030416	735280		NR_030416	ENSMUSG00000076275	Mir675	Mirn675|mir-675|mmu-mir-675	microRNA 675	ncRNA
mm_41204.1	chr5	88520590	88520607	+	1	NA	3' UTR (NM_152839, exon 4 of 4)	3' UTR (NM_152839, exon 4 of 4)	7299	NM_152839	16069	Mm.1192	NM_152839	ENSMUSG00000067149	Jchain	9530090F24Rik|AI323815|Igj|Jch	immunoglobulin joining chain	protein-coding
mm_36857.1	chr4	106859378	106859389	-	1	NA	Intergenic	Intergenic	-52087	NM_198438	72475	Mm.195635	NM_023672	ENSMUSG00000061887	Ssbp3	2610021L12Rik|2610200M23Rik|5730488C10Rik|AI854733|AW551939|LAST|SSDP1	single-stranded DNA binding protein 3	protein-coding
mm_121370.1	chr14	117826879	117826911	+	1	NA	intron (NM_001079844, intron 4 of 9)	intron (NM_001079844, intron 4 of 9)	126952	NR_105747	102465148		NR_105747	ENSMUSG00000098648	Mir6239	Gm28025|mmu-mir-6239	microRNA 6239	ncRNA
mm_102791.1	chr11	68468271	68468282	-	1	NA	intron (NM_177320, intron 1 of 18)	intron (NM_177320, intron 1 of 18)	-34743	NM_001004435	104709	Mm.234573	NM_001004435	ENSMUSG00000046207	Pik3r6	BB220380|p84|p84 PIKAP|p87(PIKAP)|p87PIKAP	phosphoinositide-3-kinase, regulatory subunit 6	protein-coding
mm_78334.1	chr9	25253755	25253769	+	1	NA	intron (NM_001205367, intron 1 of 12)	intron (NM_001205367, intron 1 of 12)	1323	NM_001205367	235072	Mm.270259	NM_009859	ENSMUSG00000001833	Sept7	Cdc10|E430034N22	septin 7	protein-coding
mm_5363.1	chr1	25830027	25830041	-	1	NA	promoter-TSS (NM_175642)	promoter-TSS (NM_175642)	-327	NM_175642	210933	Mm.336569	NM_175642	ENSMUSG00000033569	Adgrb3	A830096D10Rik|Bai3	adhesion G protein-coupled receptor B3	protein-coding
mm_49935.1	chr6	39527536	39527550	+	1	NA	intron (NM_172477, intron 1 of 18)	intron (NM_172477, intron 1 of 18)	30291	NM_172477	209773	Mm.440021	NM_172477	ENSMUSG00000038456	Dennd2a	B930096L08Rik|C130031G22|mKIAA1277	DENN/MADD domain containing 2A	protein-coding
mm_150368.1	chr19	34649892	34649907	+	1	NA	3' UTR (NM_008331, exon 2 of 2)	3' UTR (NM_008331, exon 2 of 2)	9010	NM_008331	15957	Mm.439751	NM_008331	ENSMUSG00000034459	Ifit1	ISG56|Ifi56|P56	interferon-induced protein with tetratricopeptide repeats 1	protein-coding
mm_107423.1	chr12	35050994	35050999	+	1	NA	intron (NM_001014973, intron 1 of 25)	intron (NM_001014973, intron 1 of 25)	3807	NM_001014973	217463	Mm.213991	NM_001014973	ENSMUSG00000020590	Snx13	Rgs-px1|mKIAA0713	sorting nexin 13	protein-coding
mm_37422.1	chr4	122885835	122885897	-	1	NA	5' UTR (NM_007598, exon 1 of 13)	5' UTR (NM_007598, exon 1 of 13)	191	NM_007598	12331	Mm.8687	NM_007598	ENSMUSG00000028656	Cap1	-	CAP, adenylate cyclase-associated protein 1 (yeast)	protein-coding
mm_13524.1	chr2	110017880	110017890	+	1	NA	promoter-TSS (NM_026613)	promoter-TSS (NM_026613)	68	NM_026613	68201	Mm.181767	NM_026613	ENSMUSG00000027160	Ccdc34	2810027O19Rik|4930522P10Rik|AI596202	coiled-coil domain containing 34	protein-coding
mm_72807.1	chr8	87472897	87472910	+	1	NA	promoter-TSS (NM_019626)	promoter-TSS (NM_019626)	91	NR_033430	100040294	Mm.213632	NR_033430	ENSMUSG00000097248	Gm2694	C230036H16Rik|linc1582	predicted gene 2694	ncRNA
mm_131830.1	chr16	22957470	22957482	+	1	NA	exon (NM_053176, exon 5 of 7)	exon (NM_053176, exon 5 of 7)	6404	NM_053176	94175	Mm.358794	NM_053176	ENSMUSG00000022877	Hrg	AI265597|AW413091|D16jh2|D18020|Hprg|Hrgp	histidine-rich glycoprotein	protein-coding
mm_155333.1	chrX	66649377	66649394	+	1	NA	promoter-TSS (NM_001161431)	promoter-TSS (NM_001161431)	67	NM_001161431	245450	Mm.336081	NM_198863	ENSMUSG00000036790	Slitrk2	A930040J07	SLIT and NTRK-like family, member 2	protein-coding
mm_139010.1	chr17	45570509	45570536	+	1	NA	exon (NM_008302, exon 6 of 11)	exon (NM_008302, exon 6 of 11)	2739	NM_008302	15516	Mm.2180	NM_008302	ENSMUSG00000023944	Hsp90ab1	90kDa|AL022974|C81438|Hsp84|Hsp84-1|Hsp90|Hspcb	heat shock protein 90 alpha (cytosolic), class B member 1	protein-coding
mm_54939.1	chr6	48448666	48448685	-	1	NA	exon (NM_173428, exon 2 of 103)	exon (NM_173428, exon 2 of 103)	446	NM_173428	243369	Mm.25039	NM_173428	ENSMUSG00000029797	Sspo	C79529|Scospondin	SCO-spondin	protein-coding
mm_159732.1	chr5	54105348	54105348	+	1	NA	exon (NM_001081103, exon 7 of 12)	exon (NM_001081103, exon 7 of 12)	106825	NM_001081103	116873	Mm.265985	NM_054083	ENSMUSG00000039156	Stim2	-	stromal interaction molecule 2	protein-coding
mm_16545.1	chr2	181693784	181693784	+	1	NA	promoter-TSS (NM_001291208)	promoter-TSS (NM_001291208)	26	NM_001291206	56470	Mm.274366	NM_026446	ENSMUSG00000002458	Rgs19	2610042F04Rik|AI324841|AW547781|GAIP	regulator of G-protein signaling 19	protein-coding
mm_123803.1	chr14	70520657	70520682	-	1	NA	promoter-TSS (NM_009755)	promoter-TSS (NM_009755)	-409	NR_033241	12153	Mm.27757	NM_009755	ENSMUSG00000022098	Bmp1	Pcp|Tld	bone morphogenetic protein 1	protein-coding
mm_151663.1	chr19	4139626	4139630	-	1	NA	promoter-TSS (NM_206973)	promoter-TSS (NM_206973)	-19	NM_144532	73660	Mm.379226	NM_144532	ENSMUSG00000024842	Cabp4	2410038D05Rik	calcium binding protein 4	protein-coding
mm_42415.1	chr5	115238009	115238083	+	1	NA	5' UTR (NM_026398, exon 2 of 6)	5' UTR (NM_026398, exon 2 of 6)	2195	NM_026398	117109	Mm.24636	NM_026398	ENSMUSG00000060152	Pop5	1500019J17Rik|2700077E03Rik|AW049989|Rnasep3	processing of precursor 5, ribonuclease P/MRP family (S. cerevisiae)	protein-coding
mm_149362.1	chr19	11292409	11292421	+	1	NA	intron (NR_045317, intron 1 of 2)	RLTR9E|LTR|ERVK	-8602	NM_183190	269063	Mm.268940	NM_183190	ENSMUSG00000054523	Ms4a5	-	membrane-spanning 4-domains, subfamily A, member 5	protein-coding
mm_8575.1	chr1	155751720	155751738	-	1	NA	Intergenic	Intergenic	-9702	NM_010712	16872	Mm.103624	NM_010712	ENSMUSG00000026468	Lhx4	A330062J17Rik|Gsh-4|Gsh4	LIM homeobox protein 4	protein-coding
mm_37225.1	chr4	117929494	117929510	-	1	NA	5' UTR (NM_001284191, exon 1 of 6)	5' UTR (NM_001284191, exon 1 of 6)	261	NM_001284191	11876	Mm.56897	NM_009711	ENSMUSG00000028539	Artn	neublastin	artemin	protein-coding
mm_1178.1	chr1	61638870	61638891	+	1	NA	promoter-TSS (NM_001081050)	promoter-TSS (NM_001081050)	56	NM_001081050	72823	Mm.35153	NM_001081050	ENSMUSG00000052062	Pard3b	1810008K04Rik|2010002N16Rik|2810455B10Rik|Als2cr19|PAR3B|PAR3L|PAR3beta	par-3 family cell polarity regulator beta	protein-coding
mm_74666.1	chr8	13677513	13677519	-	1	NA	promoter-TSS (NM_009025)	promoter-TSS (NM_009025)	71	NM_009025	19414	Mm.18517	NM_009025	ENSMUSG00000031453	Rasa3	AI326412|C86362|E130011G04|GAPIII|hlb381|scat	RAS p21 protein activator 3	protein-coding
mm_2917.1	chr1	132014523	132014535	+	1	NA	exon (NM_007923, exon 2 of 5)	exon (NM_007923, exon 2 of 5)	6924	NM_007923	13714	Mm.254233	NM_007923	ENSMUSG00000026436	Elk4	2310011G17Rik|A130026I01Rik|BB162516|SAP-1|Sap1	ELK4, member of ETS oncogene family	protein-coding
mm_161195.1	chr13	54783966	54783966	+	1	NA	promoter-TSS (NR_104407)	promoter-TSS (NR_104407)	-32	NM_001286179	218268	Mm.425821	NM_001033269	ENSMUSG00000074895	Eif4e1b	Eif4eloo|Gm273	eukaryotic translation initiation factor 4E family member 1B	protein-coding
mm_155036.1	chrX	42075604	42075617	+	1	NA	intron (NM_001301641, intron 1 of 6)	intron (NM_001301641, intron 1 of 6)	4368	NM_001301641	11798	Mm.259879	NM_009688	ENSMUSG00000025860	Xiap	1110015C02Rik|Aipa|Api3|Birc4|IAP3|ILP-1|MIHA	X-linked inhibitor of apoptosis	protein-coding
mm_97071.1	chr11	72992639	72992649	+	1	NA	3' UTR (NM_001163337, exon 22 of 22)	3' UTR (NM_001163337, exon 22 of 22)	-6501	NM_008771	18436	Mm.25722	NM_008771	ENSMUSG00000020787	P2rx1	AI323649|BB122383|P2x|Pdcd3|RP-2	purinergic receptor P2X, ligand-gated ion channel, 1	protein-coding
mm_78251.1	chr9	21723625	21723657	+	1	NA	promoter-TSS (NM_001252659)	promoter-TSS (NM_001252659)	65	NM_010700	16835	Mm.3213	NM_010700	ENSMUSG00000032193	Ldlr	Hlb301	low density lipoprotein receptor	protein-coding
mm_97414.1	chr11	77982641	77982651	+	1	NA	promoter-TSS (NM_174852)	promoter-TSS (NM_174852)	-170	NM_174852	268448	Mm.274329	NM_174852	ENSMUSG00000037791	Phf12	2410142K10Rik|F630045O13|PF1|mKIAA1523	PHD finger protein 12	protein-coding
mm_93101.1	chr10	89745810	89745823	-	1	NA	intron (NM_029166, intron 1 of 20)	intron (NM_029166, intron 1 of 20)	825	NM_029166	75089	Mm.268922	NM_029166	ENSMUSG00000019951	Uhrf1bp1l	2010319N22Rik|4930506D01Rik|AA589495|C80672|E030041M21Rik|mKIAA0701	UHRF1 (ICBP90) binding protein 1-like	protein-coding
mm_124865.1	chr15	10177546	10177552	+	1	NA	5' UTR (NM_011169, exon 1 of 10)	5' UTR (NM_011169, exon 1 of 10)	311	NM_011169	19116	Mm.10516	NM_011169	ENSMUSG00000005268	Prlr	AI987712|Pr-1|Pr-3|Prlr-rs1	prolactin receptor	protein-coding
mm_73399.1	chr8	105855087	105855149	+	1	NA	promoter-TSS (NM_021513)	promoter-TSS (NM_021513)	15	NM_021513	59016	Mm.286598	NM_021513	ENSMUSG00000036442	Thap11	2810036E22Rik|AB041579|CTG-B43a|CTG-B45d|Ronin	THAP domain containing 11	protein-coding
mm_121258.1	chr14	103062271	103062274	+	1	NA	Intergenic	Lx9|LINE|L1	-7944	NM_001033242	211286	Mm.295289	NM_001033242	ENSMUSG00000022125	Cln5	A730075N08Rik	ceroid-lipofuscinosis, neuronal 5	protein-coding
mm_104133.1	chr11	86838723	86838726	-	1	NA	intron (NR_106195, intron 2 of 8)	intron (NR_106195, intron 2 of 8)	-31064	NM_026191	67487	Mm.260627	NM_026191	ENSMUSG00000018425	Dhx40	2410016C14Rik|ARG147|DDX40|PAD	DEAH (Asp-Glu-Ala-His) box polypeptide 40	protein-coding
mm_33452.1	chr4	130681246	130681247	+	1	NA	intron (NM_001159606, intron 2 of 17)	intron (NM_001159606, intron 2 of 17)	17887	NM_001159605	80912	Mm.440206	NM_030722	ENSMUSG00000028580	Pum1	AA517475|Pumm|mKIAA0099	pumilio RNA-binding family member 1	protein-coding
mm_6676.1	chr1	80385376	80385382	-	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-44689	NM_016716	26554	Mm.12665	NM_016716	ENSMUSG00000004364	Cul3	KIAA0617	cullin 3	protein-coding
mm_49842.1	chr6	38352522	38352534	+	1	NA	intron (NM_001347122, intron 1 of 12)	intron (NM_001347122, intron 1 of 12)	2075	NM_028864	78781	Mm.25243	NM_028421	ENSMUSG00000029826	Zc3hav1	1200014N16Rik|2900058M19Rik|9130009D18Rik|9830115L13Rik|ARTD13|D6Bwg1452e|ZAP	zinc finger CCCH type, antiviral 1	protein-coding
mm_19592.1	chr2	102076422	102076437	-	1	NA	intron (NM_001290784, intron 2 of 5)	intron (NM_001290784, intron 2 of 5)	110031	NM_178886	241576	Mm.489740	NM_178886	ENSMUSG00000048058	Ldlrad3	6430500P08|AI194318|Lrad3	low density lipoprotein receptor class A domain containing 3	protein-coding
mm_84182.1	chr9	60134712	60134728	-	1	NA	intron (NM_001040426, intron 7 of 17)	intron (NM_001040426, intron 7 of 17)	6500	NM_172444	207596	Mm.28791	NM_172444	ENSMUSG00000032289	Thsd4	ADAMTSL-6|ADAMTSL6|AI585901|Adamtsl4|B230114P05Rik	thrombospondin, type I, domain containing 4	protein-coding
mm_82092.1	chr9	123052736	123052749	+	1	NA	exon (NM_177911, exon 9 of 14)	exon (NM_177911, exon 9 of 14)	18001	NM_177911	331046	Mm.195309	NM_177911	ENSMUSG00000025787	Tgm4	9530008N10Rik|Eapa1|TGP	transglutaminase 4 (prostate)	protein-coding
mm_19847.1	chr2	113708548	113708552	-	1	NA	promoter-TSS (NR_040614)	promoter-TSS (NR_040614)	0	NR_040614	75166	Mm.410811	NR_040614	ENSMUSG00000084798	4930533B01Rik	-	RIKEN cDNA 4930533B01 gene	ncRNA
mm_97884.1	chr11	83291684	83291709	+	1	NA	promoter-TSS (NR_028363)	promoter-TSS (NR_028363)	-3	NR_028363	613254	Mm.383758	NR_028363	ENSMUSG00000093483	AA465934	-	expressed sequence AA465934	ncRNA
mm_116196.1	chr13	31674436	31674441	-	1	NA	Intergenic	L1_Mur3|LINE|L1	48622	NM_010225	14238	Mm.125548	NM_010225	ENSMUSG00000038402	Foxf2	FREAC2|Fkh20|LUN	forkhead box F2	protein-coding
mm_142633.1	chr17	47414686	47414691	-	1	NA	promoter-TSS (NM_001172091)	promoter-TSS (NM_001172091)	23	NM_001172091	75462	Mm.46129	NM_029296	ENSMUSG00000047150	1700001C19Rik	-	RIKEN cDNA 1700001C19 gene	protein-coding
mm_171039.1	chr2	93819143	93819146	+	1	NA	intron (NM_010163, intron 1 of 13)	RLTRETN_Mm|LTR|ERVK	3424	NM_010163	14043	Mm.4336	NM_010163	ENSMUSG00000027198	Ext2	AI893565	exostoses (multiple) 2	protein-coding
mm_76990.1	chr8	107063117	107063119	-	1	NA	intron (NM_025458, intron 3 of 3)	B1_Mur4|SINE|Alu	2526	NM_025458	66269	Mm.23032	NM_025458	ENSMUSG00000031919	Tmed6	1810015P03Rik|1810018I24Rik	transmembrane p24 trafficking protein 6	protein-coding
mm_76142.1	chr8	81854668	81854679	-	1	NA	intron (NM_001297591, intron 7 of 24)	intron (NM_001297591, intron 7 of 24)	512111	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_50329.1	chr6	48411588	48411599	+	1	NA	intron (NM_001347153, intron 11 of 17)	intron (NM_001347153, intron 11 of 17)	16007	NM_001347153	77827	Mm.107646	NM_133922	ENSMUSG00000042810	Krba1	A930040G15Rik|AI448780	KRAB-A domain containing 1	protein-coding
mm_143261.1	chr17	65613522	65613548	-	1	NA	promoter-TSS (NM_013933)	promoter-TSS (NM_013933)	20	NM_013933	30960	Mm.266767	NM_013933	ENSMUSG00000024091	Vapa	33kDa|VAP33	vesicle-associated membrane protein, associated protein A	protein-coding
mm_164100.1	chr15	18820750	18820752	+	1	NA	intron (NM_009865, intron 1 of 11)	intron (NM_009865, intron 1 of 11)	422	NM_009865	320873	Mm.117794	NM_009865	ENSMUSG00000022321	Cdh10	A830016G23Rik|C030003B10Rik|C030011H18Rik	cadherin 10	protein-coding
mm_6566.1	chr1	75180227	75180309	-	1	NA	TTS (NM_001288613)	TTS (NM_001288613)	124	NM_023732	74104	Mm.28663	NM_023732	ENSMUSG00000026198	Abcb6	1200005B17Rik	ATP-binding cassette, sub-family B (MDR/TAP), member 6	protein-coding
mm_83147.1	chr9	40456120	40456133	-	1	NA	promoter-TSS (NM_172768)	promoter-TSS (NM_172768)	-362	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_172871.1	chr9	4259590	4259595	+	1	NA	Intergenic	RLTR46A2|LTR|ERVK	49902	NR_136941	67618	Mm.33970	NM_026276	ENSMUSG00000025894	Aasdhppt	2010309J24Rik|2810407B07Rik|AASD-PPT|CGI-80|LYS2|LYS5	aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase	protein-coding
mm_57540.1	chr6	126644790	126644805	-	1	NA	5' UTR (NM_010595, exon 1 of 2)	5' UTR (NM_010595, exon 1 of 2)	1004	NM_010595	16485	Mm.40424	NM_010595	ENSMUSG00000047976	Kcna1	AI840627|Kca1-1|Kv1.1|MBK1|Mk-1|Shak|mceph	potassium voltage-gated channel, shaker-related subfamily, member 1	protein-coding
mm_3600.1	chr1	151571442	151571471	+	1	NA	promoter-TSS (NM_022018)	promoter-TSS (NM_022018)	83	NM_022018	63913	Mm.157700	NM_022018	ENSMUSG00000026483	Fam129a	AI256368|AU019833|Niban	family with sequence similarity 129, member A	protein-coding
mm_6316.1	chr1	71600416	71600457	-	1	NA	exon (NM_001276413, exon 34 of 44)	exon (NM_001276413, exon 34 of 44)	43280	NM_026195	108147	Mm.38010	NM_026195	ENSMUSG00000026192	Atic	2610509C24Rik|AA536954|AW212393	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	protein-coding
mm_161551.1	chr16	10788580	10788580	-	1	NA	promoter-TSS (NM_013694)	promoter-TSS (NM_013694)	75	NM_013694	21959	Mm.206798	NM_013694	ENSMUSG00000043050	Tnp2	TP2|Tp-2	transition protein 2	protein-coding
mm_119885.1	chr14	54898396	54898415	+	1	NA	3' UTR (NM_019402, exon 7 of 7)	3' UTR (NM_019402, exon 7 of 7)	4262	NM_019402	54196	Mm.7723	NM_019402	ENSMUSG00000022194	Pabpn1	PAB2|Pabp3|mPABII	poly(A) binding protein, nuclear 1	protein-coding
mm_150491.1	chr19	39011139	39011144	+	1	NA	exon (NM_028089, exon 2 of 9)	exon (NM_028089, exon 2 of 9)	4122	NM_028089	72082	Mm.142581	NM_028089	ENSMUSG00000025002	Cyp2c55	2010318C06Rik	cytochrome P450, family 2, subfamily c, polypeptide 55	protein-coding
mm_82032.1	chr9	121951009	121951044	+	1	NA	promoter-TSS (NM_001199927)	promoter-TSS (NM_001199927)	6	NM_001199927	245050	Mm.71062	NM_177743	ENSMUSG00000038233	Fam198a	C730027P07Rik	family with sequence similarity 198, member A	protein-coding
mm_143814.1	chr17	83831698	83831716	-	1	NA	exon (NM_025325, exon 10 of 10)	exon (NM_025325, exon 10 of 10)	15083	NM_025325	107766	Mm.30100	NM_025325	ENSMUSG00000000673	Haao	0610007K21Rik|0610012J07Rik|3-HAO|3-HAOxase|3HAO	3-hydroxyanthranilate 3,4-dioxygenase	protein-coding
mm_160041.1	chr6	137648342	137648342	-	1	NA	intron (NM_007945, intron 1 of 21)	intron (NM_007945, intron 1 of 21)	943	NM_001271588	13860	Mm.235346	NM_007945	ENSMUSG00000015766	Eps8	AW261790	epidermal growth factor receptor pathway substrate 8	protein-coding
mm_29032.1	chr3	102167548	102167572	-	1	NA	intron (NM_177545, intron 4 of 7)	intron (NM_177545, intron 4 of 7)	37133	NM_177545	229658	Mm.118004	NM_177545	ENSMUSG00000027860	Vangl1	Kitenin|Lpp2|Stb2|Stbm	vang-like 1 (van gogh, Drosophila)	protein-coding
mm_172705.1	chr8	65591595	65591597	+	1	NA	Intergenic	L1Md_T|LINE|L1	-26444	NM_001293784	72925	Mm.380457	NM_175188	ENSMUSG00000036469	March1	2900024D24Rik|BB085186	membrane-associated ring finger (C3HC4) 1	protein-coding
mm_18409.1	chr2	60553251	60553263	-	1	NA	promoter-TSS (NM_008867)	promoter-TSS (NM_008867)	51	NM_008867	18779	Mm.5092	NM_008867	ENSMUSG00000054580	Pla2r1	Pla2-r|Pla2g1br|Pla2r	phospholipase A2 receptor 1	protein-coding
mm_8491.1	chr1	153844131	153844158	-	1	NA	promoter-TSS (NM_001243223)	promoter-TSS (NM_001243223)	-3	NM_001243223	240816	Mm.329340	NM_001243223	ENSMUSG00000042641	Rgsl1	4930415K13Rik|Gm202|Rgsl2	regulator of G-protein signaling like 1	protein-coding
mm_10611.1	chr2	19050049	19050078	+	1	NA	Intergenic	RMER2|LTR|ERV1	51744	NR_024323	74629	Mm.117687	NR_024323	ENSMUSG00000026736	4930426L09Rik	-	RIKEN cDNA 4930426L09 gene	ncRNA
mm_112418.1	chr13	4049002	4049030	+	1	NA	Intergenic	Intergenic	-10575	NM_134072	105387	Mm.26838	NM_134072	ENSMUSG00000033715	Akr1c14	9030611N15Rik|AW557061	aldo-keto reductase family 1, member C14	protein-coding
mm_2101.1	chr1	87803864	87803880	+	1	NA	5' UTR (NM_009118, exon 1 of 16)	5' UTR (NM_009118, exon 1 of 16)	192	NM_009118	20215	Mm.1276	NM_009118	ENSMUSG00000056055	Sag	A930001K18Rik|Arr1|Irbp|arrestin	S-antigen, retina and pineal gland (arrestin)	protein-coding
mm_147068.1	chr18	35214944	35214969	-	1	NA	promoter-TSS (NM_178005)	promoter-TSS (NM_178005)	68	NM_178005	107065	Mm.39900	NM_178005	ENSMUSG00000071862	Lrrtm2	AI851755|BB129880|C630011A14Rik|mKIAA0416	leucine rich repeat transmembrane neuronal 2	protein-coding
mm_128894.1	chr15	73185322	73185351	-	1	NA	promoter-TSS (NM_153178)	promoter-TSS (NM_153178)	-389	NM_153178	239528	Mm.23095	NM_153178	ENSMUSG00000036698	Ago2	1110029L17Rik|2310051F07Rik|AI225898|AL022874|AW546247|ENSMUSG00000072493|Eif2c2|Gerp95|Gm10365|mKIAA4215	argonaute RISC catalytic subunit 2	protein-coding
mm_49646.1	chr6	30805740	30805758	+	1	NA	intron (NM_017478, intron 20 of 23)	intron (NM_017478, intron 20 of 23)	64450	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_84811.1	chr9	77347890	77347906	-	1	NA	promoter-TSS (NM_027150)	promoter-TSS (NM_027150)	-28	NM_027150	69642	Mm.35008	NM_027150	ENSMUSG00000032355	Mlip	2310046A06Rik|AI931782|CIP	muscular LMNA-interacting protein	protein-coding
mm_122833.1	chr14	54723270	54723281	-	1	NA	3' UTR (NM_016972, exon 11 of 11)	3' UTR (NM_016972, exon 11 of 11)	-11101	NM_207131	110794	Mm.236223	NM_207131	ENSMUSG00000052435	Cebpe	C/EBPe|CRP1|Gm294	CCAAT/enhancer binding protein (C/EBP), epsilon	protein-coding
mm_4823.1	chr1	185454914	185454931	+	1	NA	promoter-TSS (NM_001033286)	promoter-TSS (NM_001033286)	74	NM_001033286	226781	Mm.227117	NM_001033286	ENSMUSG00000026614	Slc30a10	E130106K10Rik|Gm212	solute carrier family 30, member 10	protein-coding
mm_100482.1	chr11	120232959	120232980	+	1	NA	promoter-TSS (NM_198423)	promoter-TSS (NM_198423)	22	NM_198423	268515	Mm.309498	NM_198423	ENSMUSG00000039741	Bahcc1	B930044J06|BC060615	BAH domain and coiled-coil containing 1	protein-coding
mm_66592.1	chr7	45422474	45422487	-	1	NA	TTS (NM_008497)	TTS (NM_008497)	1534	NM_008497	16866	Mm.57061	NM_008497	ENSMUSG00000100916	Lhb	Gm29035|LH|LH-B|LSH-B|LSH-beta	luteinizing hormone beta	protein-coding
mm_87295.1	chr10	42533144	42533166	+	1	NA	exon (NM_017472, exon 3 of 4)	exon (NM_017472, exon 3 of 4)	31101	NM_017472	54198	Mm.277870	NM_017472	ENSMUSG00000019804	Snx3	SDP3	sorting nexin 3	protein-coding
mm_140251.1	chr17	84187091	84187117	+	1	NA	exon (NM_001001806, exon 2 of 2)	exon (NM_001001806, exon 2 of 2)	843	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_108573.1	chr12	84970905	84970950	+	1	NA	promoter-TSS (NM_028632)	promoter-TSS (NM_028632)	-3	NM_028632	73736	Mm.341848	NM_028632	ENSMUSG00000021243	Fcf1	1110008B24Rik	FCF1 rRNA processing protein	protein-coding
mm_167403.1	chr8	103802115	103802137	-	1	NA	Intergenic	Intergenic	198327	NR_045730	71058	Mm.67707	NR_045730	ENSMUSG00000110336	4933400L20Rik	-	RIKEN cDNA 4933400L20 gene	ncRNA
mm_80816.1	chr9	96619174	96619203	+	1	NA	intron (NM_053268, intron 1 of 23)	intron (NM_053268, intron 1 of 23)	12315	NM_053268	114713	Mm.124502	NM_053268	ENSMUSG00000032413	Rasa2	5430433H21Rik|AA517451|AU023900|GAP1m	RAS p21 protein activator 2	protein-coding
mm_111998.1	chr12	110696435	110696447	-	1	NA	promoter-TSS (NM_010480)	promoter-TSS (NM_010480)	-46	NM_010480	15519	Mm.1843	NM_010480	ENSMUSG00000021270	Hsp90aa1	86kDa|89kDa|AL024080|AL024147|Hsp86-1|Hsp89|Hsp90|Hspca|hsp4	heat shock protein 90, alpha (cytosolic), class A member 1	protein-coding
mm_79470.1	chr9	56865052	56865072	+	1	NA	promoter-TSS (NM_139001)	promoter-TSS (NM_139001)	-42	NM_139001	121021	Mm.41329	NM_139001	ENSMUSG00000032911	Cspg4	4732461B14Rik|AN2|NG2	chondroitin sulfate proteoglycan 4	protein-coding
mm_108193.1	chr12	76773776	76773779	+	1	NA	intron (NM_206534, intron 2 of 3)	B1F|SINE|Alu	8204	NM_206534	211151	Mm.80970	NM_206534	ENSMUSG00000090258	Churc1	1700030P15Rik|My015|chch	churchill domain containing 1	protein-coding
mm_96122.1	chr11	60775181	60775205	+	1	NA	intron (NM_009410, intron 1 of 18)	intron (NM_009410, intron 1 of 18)	2172	NM_009410	21975	Mm.10708	NM_009410	ENSMUSG00000002814	Top3a	-	topoisomerase (DNA) III alpha	protein-coding
mm_21268.1	chr2	156857126	156857134	-	1	NA	intron (NR_015591, intron 1 of 2)	intron (NR_015591, intron 1 of 2)	5815	NR_015591	74487	Mm.490465	NR_015591	ENSMUSG00000085741	5430405H02Rik	2610307N17Rik	RIKEN cDNA 5430405H02 gene	ncRNA
mm_171383.1	chr4	119695388	119695403	+	1	NA	Intergenic	MTA_Mm|LTR|ERVL-MaLR	-36450	NM_008191	14916	Mm.278	NM_008191	ENSMUSG00000032978	Guca2b	AV066530|Gcap2|Ugn	guanylate cyclase activator 2b (retina)	protein-coding
mm_24072.1	chr3	87919661	87919677	+	1	NA	5' UTR (NM_026591, exon 1 of 6)	5' UTR (NM_026591, exon 1 of 6)	125	NM_026591	67707	Mm.393802	NM_026591	ENSMUSG00000019710	Mrpl24	2010005E08Rik|2810470K06Rik|6720473G22Rik|AA407670	mitochondrial ribosomal protein L24	protein-coding
mm_58777.1	chr7	16061811	16061820	+	1	NA	Intergenic	CpG	-10030	NM_001347559	666528	Mm.290718	NM_001099277	ENSMUSG00000078796	Zfp541	EG666528|Znf541	zinc finger protein 541	protein-coding
mm_158076.1	chrX	101264911	101264932	-	1	NA	promoter-TSS (NM_001317221)	promoter-TSS (NM_001317221)	-929	NM_001317221	245536	Mm.212463	NM_001033362	ENSMUSG00000090141	Gm614	-	predicted gene 614	protein-coding
mm_48283.1	chr5	138171814	138171816	-	1	NA	promoter-TSS (NM_008568)	promoter-TSS (NM_008568)	47	NM_008568	17220	Mm.378965	NM_008568	ENSMUSG00000029730	Mcm7	AI747533|Mcmd7|mCDC47	minichromosome maintenance complex component 7	protein-coding
mm_86812.1	chr10	20348358	20348385	+	1	NA	exon (NM_027930, exon 2 of 7)	exon (NM_027930, exon 2 of 7)	552	NM_027930	71804	Mm.262151	NM_027930	ENSMUSG00000019992	Mtfr2	2610016C23Rik|4933412C16Rik|Dufd1|Fam54a	mitochondrial fission regulator 2	protein-coding
mm_82611.1	chr9	21616452	21616471	-	1	NA	intron (NM_001174079, intron 1 of 33)	CpG	292	NM_001174078	20586	Mm.286593	NM_011417	ENSMUSG00000032187	Smarca4	Brg1|HP1-BP72|SNF2beta|SW1/SNF|b2b508.1Clo|b2b692Clo	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	protein-coding
mm_30295.1	chr3	148990520	148990561	-	1	NA	Intergenic	CpG	-35905	NM_001081298	99633	Mm.9776	NM_001081298	ENSMUSG00000028184	Adgrl2	AI450192|CIRL-2|Gm619|Lec1|Lphh1|Lphn2|mKIAA0786	adhesion G protein-coupled receptor L2	protein-coding
mm_135165.1	chr16	35872575	35872609	-	1	NA	Intergenic	Intergenic	-1210	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_113775.1	chr13	44896424	44896440	+	1	NA	exon (NM_001205043, exon 6 of 18)	exon (NM_001205043, exon 6 of 18)	105664	NM_025772	94245	Mm.352311	NM_025772	ENSMUSG00000057531	Dtnbp1	5430437B18Rik|AW048963|Bloc1s8|dysbindin|sdy	dystrobrevin binding protein 1	protein-coding
mm_91513.1	chr10	37138546	37138552	-	1	NA	5' UTR (NM_008538, exon 1 of 2)	5' UTR (NM_008538, exon 1 of 2)	377	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_87084.1	chr10	29535122	29535122	+	1	NA	intron (NM_028351, intron 1 of 4)	intron (NM_028351, intron 1 of 4)	745	NM_028351	72780	Mm.45191	NM_028351	ENSMUSG00000019880	Rspo3	2810459H04Rik|AW742308|Cristin1|Thsd2	R-spondin 3	protein-coding
mm_31415.1	chr4	48049927	48049966	+	1	NA	intron (NM_015743, intron 2 of 7)	intron (NM_015743, intron 2 of 7)	-1300	NM_001307989	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_105472.1	chr11	105936304	105936316	-	1	NA	intron (NM_007805, intron 3 of 5)	intron (NM_007805, intron 3 of 5)	7837	NM_007805	13056	Mm.149403	NM_007805	ENSMUSG00000019590	Cyb561	-	cytochrome b-561	protein-coding
mm_68685.1	chr7	119184599	119184619	-	1	NA	promoter-TSS (NM_001024138)	promoter-TSS (NM_001024138)	-235	NM_001024138	209776	Mm.300632	NM_001024138	ENSMUSG00000066197	Gpr139	GPRg1|Gm495|PGR3	G protein-coupled receptor 139	protein-coding
mm_147362.1	chr18	43393187	43393218	-	1	NA	5' UTR (NM_009468, exon 1 of 14)	5' UTR (NM_009468, exon 1 of 14)	175	NM_009468	22240	Mm.8180	NM_009468	ENSMUSG00000024501	Dpysl3	CRMP-4|DRP-3|TUC4|ULIP-1|Ulip|Ulip1	dihydropyrimidinase-like 3	protein-coding
mm_94915.1	chr11	29463677	29463691	+	1	NA	exon (NM_176841, exon 15 of 32)	exon (NM_176841, exon 15 of 32)	51349	NM_026465	67939	Mm.251087	NM_026465	ENSMUSG00000032673	Prorsd1	2010316F05Rik|Ncrna00117|Prdxdd1	prolyl-tRNA synthetase domain containing 1	protein-coding
mm_132291.1	chr16	33251416	33251456	+	1	NA	promoter-TSS (NM_080557)	promoter-TSS (NM_080557)	-20	NM_080557	69150	Mm.28196	NM_080557	ENSMUSG00000022808	Snx4	1810036H14Rik|AI037066	sorting nexin 4	protein-coding
mm_121256.1	chr14	103058276	103058282	+	1	NA	Intergenic	Intergenic	11267	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_95313.1	chr11	46389721	46389729	+	1	NA	promoter-TSS (NM_001281968)	promoter-TSS (NM_001281968)	-210	NM_001281965	16428	Mm.339927	NM_010583	ENSMUSG00000020395	Itk	Emt|Tcsk|Tsk	IL2 inducible T cell kinase	protein-coding
mm_88931.1	chr10	81257457	81257526	+	1	NA	5' UTR (NM_001285854, exon 1 of 13)	5' UTR (NM_001285854, exon 1 of 13)	192	NM_001285853	17179	Mm.2918	NM_010768	ENSMUSG00000004933	Matk	CHK|HYL|Ntk|p56ntk	megakaryocyte-associated tyrosine kinase	protein-coding
mm_82411.1	chr9	14780492	14780502	-	1	NA	3' UTR (NM_019683, exon 2 of 2)	3' UTR (NM_019683, exon 2 of 2)	2467	NM_019683	56503	Mm.395005	NM_019683	ENSMUSG00000031931	Ankrd49	AW060934|C86108|Gbif	ankyrin repeat domain 49	protein-coding
mm_10825.1	chr2	24385132	24385167	+	1	NA	promoter-TSS (NM_177611)	promoter-TSS (NM_177611)	-248	NM_177611	215632	Mm.490434	NM_177611	ENSMUSG00000026979	Psd4	BC046518|EFA6B	pleckstrin and Sec7 domain containing 4	protein-coding
mm_90046.1	chr10	115846318	115846329	+	1	NA	intron (NM_146010, intron 7 of 7)	intron (NM_146010, intron 7 of 7)	29039	NM_001168679	216350	Mm.22270	NM_146010	ENSMUSG00000034127	Tspan8	C76990|E330007O21Rik|Tm4sf3	tetraspanin 8	protein-coding
mm_117052.1	chr13	58392796	58392799	-	1	NA	promoter-TSS (NR_029825)	promoter-TSS (NR_029825)	89	NR_029825	723902		NR_029825	ENSMUSG00000065434	Mir7-1	Mir7a1|Mirn7-1|miR-7a1|mir-7a-1|mmu-miR-7a1|mmu-mir-7-1	microRNA 7-1	ncRNA
mm_67997.1	chr7	100930913	100930954	-	1	NA	exon (NM_001081116, exon 1 of 21)	exon (NM_001081116, exon 1 of 21)	1228	NM_001081116	207212	Mm.29954	NM_001081116	ENSMUSG00000032875	Arhgef17	8030463K16|AI428794|AW558066|BC035332|mKIAA0337	Rho guanine nucleotide exchange factor (GEF) 17	protein-coding
mm_119635.1	chr14	51884983	51884993	+	1	NA	exon (NM_001029990, exon 1 of 14)	exon (NM_001029990, exon 1 of 14)	146	NM_001029990	52535	Mm.5750	NM_001029990	ENSMUSG00000004561	Mettl17	2310032K15Rik|D14Ertd209e|Mett11d1	methyltransferase like 17	protein-coding
mm_25366.1	chr3	107101579	107101585	+	1	NA	promoter-TSS (NM_008417)	promoter-TSS (NM_008417)	15	NM_008417	16490	Mm.39285	NM_008417	ENSMUSG00000040724	Kcna2	Akr6a4|ENSMUSG00000074335|Gm10672|Kca1-2|Kv1.2|Mk-2	potassium voltage-gated channel, shaker-related subfamily, member 2	protein-coding
mm_69662.1	chr7	139979998	139980034	-	1	NA	exon (NM_001291066, exon 23 of 24)	exon (NM_001291066, exon 23 of 24)	-1261	NM_001347613	381933	Mm.440431	NM_001033465	ENSMUSG00000073795	6430531B16Rik	Gm1093	RIKEN cDNA 6430531B16 gene	protein-coding
mm_22256.1	chr2	177329844	177329863	-	1	NA	Intergenic	Intergenic	-134889	NM_001177568	628308	Mm.460436	NM_001177568	ENSMUSG00000078866	Zfp970	Gm14420|OTTMUSG00000016588	zinc finger protein 970	protein-coding
mm_3644.1	chr1	152902898	152902922	+	1	NA	promoter-TSS (NM_001160256)	promoter-TSS (NM_001160256)	-264	NM_001005507	226517	Mm.270775	NM_001005507	ENSMUSG00000042772	Smg7	9430023P16Rik|mKIAA0250	Smg-7 homolog, nonsense mediated mRNA decay factor (C. elegans)	protein-coding
mm_2852.1	chr1	131674861	131674876	+	1	NA	exon (NM_007799, exon 10 of 10)	exon (NM_007799, exon 10 of 10)	-13827	NM_145509	226421	Mm.44508	NM_145509	ENSMUSG00000052688	Rab7b	5430435G22Rik	RAB7B, member RAS oncogene family	protein-coding
mm_44161.1	chr5	150673753	150673817	+	1	NA	promoter-TSS (NM_175310)	promoter-TSS (NM_175310)	-42	NM_175310	100710	Mm.32959	NM_175310	ENSMUSG00000034021	Pds5b	AI646570|AS3|AW212954|Aprin|Tg(Wap-ERBB2)229Wzw|WAP-Her-2|mKIAA0979	PDS5 cohesin associated factor B	protein-coding
mm_155674.1	chrX	90744931	90744943	+	1	NA	Intergenic	Intergenic	-147205	NM_001101450	212952	Mm.477436	NM_001101450	ENSMUSG00000091497	Gm44	-	predicted gene 44	protein-coding
mm_161731.1	chr17	30005126	30005126	+	1	NA	promoter-TSS (NM_148926)	promoter-TSS (NM_148926)	39	NM_148926	21769	Mm.220972	NM_148926	ENSMUSG00000044477	Zfand3	AW539211|TEG-27|Tex27	zinc finger, AN1-type domain 3	protein-coding
mm_99431.1	chr11	102429354	102429373	+	1	NA	promoter-TSS (NM_008175)	promoter-TSS (NM_008175)	-959	NM_008175	14824	Mm.1568	NM_008175	ENSMUSG00000034708	Grn	Pgrn|epithelin	granulin	protein-coding
mm_40610.1	chr5	64576175	64576178	+	1	NA	Intergenic	Intergenic	34523	NR_045078	100042198	Mm.25191	NR_045078	ENSMUSG00000105402	Gm3716	Gm1683	predicted gene 3716	ncRNA
mm_110852.1	chr12	73284975	73284992	-	1	NA	exon (NM_029580, exon 2 of 5)	exon (NM_029580, exon 2 of 5)	1728	NM_029580	76357	Mm.311344	NM_029580	ENSMUSG00000034442	Trmt5	2610027O18Rik|mKIAA1393	TRM5 tRNA methyltransferase 5	protein-coding
mm_47267.1	chr5	121837614	121837689	-	1	NA	promoter-TSS (NM_001306128)	promoter-TSS (NM_001306128)	-792	NM_008507	16923	Mm.65493	NM_008507	ENSMUSG00000042594	Sh2b3	AI429800|Lnk	SH2B adaptor protein 3	protein-coding
mm_54834.1	chr6	42586146	42586172	-	1	NA	Intergenic	B4A|SINE|B4	11213	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_142195.1	chr17	36951637	36951718	-	1	NA	5' UTR (NM_029632, exon 1 of 3)	5' UTR (NM_029632, exon 1 of 3)	115	NM_029632	76497	Mm.46176	NM_029632	ENSMUSG00000036398	Ppp1r11	1500041B02Rik|AV117883|Hcgv|Tcte5|Tctex-5|Tctex5	protein phosphatase 1, regulatory (inhibitor) subunit 11	protein-coding
mm_91559.1	chr10	39986615	39986623	-	1	NA	promoter-TSS (NM_001113385)	promoter-TSS (NM_001113385)	27	NM_001113385	215928	Mm.31744	NM_001001489	ENSMUSG00000038528	Mfsd4b5	Naglt1c	major facilitator superfamily domain containing 4B5	protein-coding
mm_92385.1	chr10	76570434	76570455	-	1	NA	TTS (NM_029661)	TTS (NM_029661)	-5204	NM_080845	14317	Mm.36278	NM_080845	ENSMUSG00000001155	Ftcd	-	formiminotransferase cyclodeaminase	protein-coding
mm_72023.1	chr8	70754680	70754751	+	1	NA	promoter-TSS (NM_001166399)	promoter-TSS (NM_001166399)	36	NM_001166399	19339	Mm.5083	NM_009001	ENSMUSG00000031840	Rab3a	-	RAB3A, member RAS oncogene family	protein-coding
mm_45151.1	chr5	49291744	49291746	-	1	NA	Intergenic	Intergenic	-6086	NM_001199244	80334	Mm.160172	NM_030265	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding
mm_12917.1	chr2	84937370	84937389	+	1	NA	intron (NM_021398, intron 1 of 12)	intron (NM_021398, intron 1 of 12)	733	NM_021398	58207	Mm.290729	NM_021398	ENSMUSG00000027074	Slc43a3	Eeg1|SEEEG-1	solute carrier family 43, member 3	protein-coding
mm_137668.1	chr17	28747433	28747457	+	1	NA	3' UTR (NM_011951, exon 12 of 12)	3' UTR (NM_011951, exon 12 of 12)	-21872	NM_011950	26415	Mm.27970	NM_011950	ENSMUSG00000004864	Mapk13	SAPK4|Serk4	mitogen-activated protein kinase 13	protein-coding
mm_144630.1	chr18	32939229	32939239	+	1	NA	5' UTR (NM_009793, exon 1 of 11)	5' UTR (NM_009793, exon 1 of 11)	193	NM_009793	12326	Mm.222329	NM_009793	ENSMUSG00000038128	Camk4	A430110E23Rik|AI666733|CaMKIV|CaMKIV/Gr|D18Bwg0362e	calcium/calmodulin-dependent protein kinase IV	protein-coding
mm_89828.1	chr10	105842803	105842816	+	1	NA	exon (NM_025602, exon 2 of 4)	exon (NM_025602, exon 2 of 4)	1330	NM_025602	52713	Mm.339224	NM_025602	ENSMUSG00000019897	Ccdc59	2300004H16Rik|D10Ertd718e	coiled-coil domain containing 59	protein-coding
mm_103550.1	chr11	77718738	77718756	-	1	NA	TTS (NM_001024205)	TTS (NM_001024205)	6546	NM_001313933	12957	Mm.22830	NM_009965	ENSMUSG00000000724	Cryba1	BA3/A1|Cryb	crystallin, beta A1	protein-coding
mm_114701.1	chr13	83524272	83524289	+	1	NA	promoter-TSS (NM_001347567)	promoter-TSS (NM_001347567)	-463	NM_001347567	17260	Mm.24001	NM_025282	ENSMUSG00000005583	Mef2c	5430401D19Rik|9930028G15Rik|AV011172|Mef2	myocyte enhancer factor 2C	protein-coding
mm_147560.1	chr18	54988097	54988112	-	1	NA	exon (NM_175751, exon 2 of 10)	exon (NM_175751, exon 2 of 10)	2076	NM_175751	269023	Mm.192984	NM_175751	ENSMUSG00000052713	Zfp608	4932417D18Rik|D430007A19Rik|Znf608	zinc finger protein 608	protein-coding
mm_22947.1	chr3	32292343	32292343	+	1	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	-73146	NR_027966	67576	Mm.435324	NR_027966		4930429B21Rik	-	RIKEN cDNA 4930429B21 gene	ncRNA
mm_16005.1	chr2	167363585	167363588	+	1	NA	Intergenic	MLT-int|LTR|ERVL-MaLR	-14408	NM_019835	56336	Mm.200886	NM_019835	ENSMUSG00000017929	B4galt5	9430078I07Rik|AW049941|AW539721	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 5	protein-coding
mm_127611.1	chr15	102460059	102460065	+	1	NA	intron (NM_025385, intron 2 of 4)	intron (NM_025385, intron 2 of 4)	892	NM_025385	66151	Mm.393955	NM_025385	ENSMUSG00000023048	Prr13	1110020C13Rik|2010324E22Rik	proline rich 13	protein-coding
mm_65177.1	chr7	19692630	19692648	-	1	NA	promoter-TSS (NM_001110009)	promoter-TSS (NM_001110009)	20	NM_001110009	11812	Mm.182440	NM_007469	ENSMUSG00000040564	Apoc1	Apo-CIB|ApoC-IB|apo-CI|apoC-I	apolipoprotein C-I	protein-coding
mm_110269.1	chr12	31996882	31996882	-	1	NA	intron (NM_011158, intron 2 of 10)	MamRep605|LTR?|LTR?	-46347	NM_153198	73389	Mm.390461	NM_153198	ENSMUSG00000002996	Hbp1	1700058O05Rik|BE629963|C330012F01Rik|C86454	high mobility group box transcription factor 1	protein-coding
mm_45637.1	chr5	76658364	76658392	-	1	NA	Intergenic	CpG	66664	NM_199032	381644	Mm.332452	NM_199032	ENSMUSG00000036403	Cep135	BC062951|Cep4|Gm1044	centrosomal protein 135	protein-coding
mm_95667.1	chr11	53786818	53786821	+	1	NA	intron (NR_033332, intron 3 of 3)	intron (NR_033332, intron 3 of 3)	16346	NM_001159396	16362	Mm.105218	NM_008390	ENSMUSG00000018899	Irf1	AU020929|Irf-1	interferon regulatory factor 1	protein-coding
mm_158642.1	chrX	155338377	155338387	-	1	NA	promoter-TSS (NM_016764)	promoter-TSS (NM_016764)	78	NM_016764	53381	Mm.247542	NM_016764	ENSMUSG00000025289	Prdx4	AOE372|Prx-iv|Prx4|TRANK	peroxiredoxin 4	protein-coding
mm_62967.1	chr7	119794269	119794294	+	1	NA	promoter-TSS (NM_001004187)	promoter-TSS (NM_001004187)	94	NM_001004187	434234	Mm.38237	NM_028129	ENSMUSG00000030924	2610020H08Rik	-	RIKEN cDNA 2610020H08 gene	protein-coding
mm_154467.1	chrM	3663	3685	-	1	NA	NA	Intergenic	NA	NA								
mm_167848.1	chrX	7412745	7412747	-	1	NA	intron (NR_027924, intron 1 of 1)	intron (NR_027924, intron 1 of 1)	8301	NR_027925	68355	Mm.45111	NR_027924		2010204K13Rik	0610010M13Rik|Cip7	RIKEN cDNA 2010204K13 gene	ncRNA
mm_34595.1	chr4	150231140	150231146	+	1	NA	Intergenic	Intergenic	-6054	NM_023119	13806	Mm.70666	NM_023119	ENSMUSG00000063524	Eno1	0610008I15|AL022784|Eno-1|MBP-1	enolase 1, alpha non-neuron	protein-coding
mm_58179.1	chr6	142858506	142858509	-	1	NA	intron (NM_011374, intron 4 of 4)	intron (NM_011374, intron 4 of 4)	44276	NR_045707	665037	Mm.401493	NR_045707	ENSMUSG00000072683	Gm7457	EG665037|ENSMUSG00000072683	predicted gene 7457	ncRNA
mm_3623.1	chr1	152750555	152750564	+	1	NA	promoter-TSS (NM_001081197)	promoter-TSS (NM_001081197)	8	NM_001081197	71281	Mm.158650	NM_001081197	ENSMUSG00000055547	Apobec4	4933431M11Rik	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 4 (putative)	protein-coding
mm_111988.1	chr12	110591587	110591608	-	1	NA	non-coding (NR_033340, exon 1 of 1)	non-coding (NR_033340, exon 1 of 1)	223	NR_033340	319786	Mm.129691	NR_033340		B930059L03Rik	-	RIKEN cDNA B930059L03 gene	ncRNA
mm_130374.1	chr15	97823687	97823706	-	1	NA	intron (NM_001204275, intron 1 of 24)	intron (NM_001204275, intron 1 of 24)	8071	NM_019572	56233	Mm.384027	NM_019572	ENSMUSG00000022475	Hdac7	5830434K02Rik|HD7|HD7a|Hdac7a|mFLJ00062	histone deacetylase 7	protein-coding
mm_48055.1	chr5	136563322	136563325	-	1	NA	intron (NM_001291234, intron 1 of 22)	intron (NM_001291234, intron 1 of 22)	2658	NM_001291239	13047	Mm.320317	NM_009986	ENSMUSG00000029705	Cux1	CDP|Cutl1|Cux|Cux-1	cut-like homeobox 1	protein-coding
mm_146703.1	chr18	13849833	13849836	-	1	NA	intron (NM_145492, intron 3 of 7)	intron (NM_145492, intron 3 of 7)	122899	NM_145492	225207	Mm.40325	NM_145492	ENSMUSG00000024420	Zfp521	B930086A16Rik|Evi3|Znf521	zinc finger protein 521	protein-coding
mm_127750.1	chr15	103479118	103479125	+	1	NA	intron (NM_153505, intron 20 of 30)	ID_B1|SINE|B4	-23913	NM_008800	18574	Mm.390792	NM_008800	ENSMUSG00000022489	Pde1b	Pde1b1	phosphodiesterase 1B, Ca2+-calmodulin dependent	protein-coding
mm_150700.1	chr19	42255815	42255867	+	1	NA	5' UTR (NM_027694, exon 1 of 5)	5' UTR (NM_027694, exon 1 of 5)	102	NM_027694	71146	Mm.329851	NM_027694	ENSMUSG00000042532	Golga7b	4933417O08Rik|AI839934	golgi autoantigen, golgin subfamily a, 7B	protein-coding
mm_49110.1	chr6	8364594	8364607	+	1	NA	intron (NM_001302353, intron 2 of 4)	intron (NM_001302353, intron 2 of 4)	105312	NM_001302353	100036521	Mm.446106	NM_001302353	ENSMUSG00000089862	Umad1	Gm16039|OTTMUSG00000029336	UMAP1-MVP12 associated (UMA) domain containing 1	protein-coding
mm_101166.1	chr11	16974004	16974017	-	1	NA	3' UTR (NM_019549, exon 10 of 10)	3' UTR (NM_019549, exon 10 of 10)	22600	NM_176982	319701	Mm.120672	NM_176982	ENSMUSG00000044966	Fbxo48	A630050E13Rik	F-box protein 48	protein-coding
mm_47801.1	chr5	132542192	132542214	-	1	NA	5' UTR (NM_177047, exon 1 of 19)	5' UTR (NM_177047, exon 1 of 19)	140	NM_177047	319974	Mm.409595	NM_177047	ENSMUSG00000029673	Auts2	2700063G02Rik|A730011F23Rik|D830032G16Rik	autism susceptibility candidate 2	protein-coding
mm_77613.1	chr8	123893708	123893717	-	1	NA	intron (NM_009606, intron 1 of 6)	intron (NM_009606, intron 1 of 6)	1063	NM_001272041	11459	Mm.214950	NM_009606	ENSMUSG00000031972	Acta1	AA959943|Acta-2|Acts|Actsk-1	actin, alpha 1, skeletal muscle	protein-coding
mm_25965.1	chr3	132737420	132737426	+	1	NA	intron (NM_001163455, intron 18 of 25)	intron (NM_001163455, intron 18 of 25)	53279	NM_001163455	271981	Mm.257864	NM_173032	ENSMUSG00000028030	Tbck	1700120J03Rik|9430001M19|A630047E20Rik|C030007I09Rik|Tbckl	TBC1 domain containing kinase	protein-coding
mm_152475.1	chr19	11017934	11017980	-	1	NA	promoter-TSS (NM_001251849)	promoter-TSS (NM_001251849)	6	NM_001251849	76002	Mm.139320	NM_001251849	ENSMUSG00000094584	Ms4a18	5033428B15Rik	membrane-spanning 4-domains, subfamily A, member 18	protein-coding
mm_111716.1	chr12	103729372	103729391	-	1	NA	exon (NM_009244, exon 4 of 5)	exon (NM_009244, exon 4 of 5)	8808	NM_009244	20701	Mm.439692	NM_009244	ENSMUSG00000071178	Serpina1b	D12Ucla2|Dom2|PI2|Spi1-2	serine (or cysteine) preptidase inhibitor, clade A, member 1B	protein-coding
mm_140593.1	chr17	10274022	10274053	-	1	NA	exon (NM_001159517, exon 3 of 8)	exon (NM_001159517, exon 3 of 8)	45324	NM_021881	19317	Mm.130694	NM_021881	ENSMUSG00000062078	Qk	1110003F05Rik|1500005P18|QkI|l(17)-1Wis|l17Wis1	quaking	protein-coding
mm_124846.1	chr15	9463497	9463516	+	1	NA	intron (NM_029341, intron 4 of 4)	intron (NM_029341, intron 4 of 4)	27478	NM_029341	75568	Mm.82143	NM_029341	ENSMUSG00000039676	Capsl	1700028N11Rik|AW125205	calcyphosine-like	protein-coding
mm_2952.1	chr1	132417556	132417609	+	1	NA	5' UTR (NM_172516, exon 1 of 13)	5' UTR (NM_172516, exon 1 of 13)	129	NM_172516	213452	Mm.257120	NM_172516	ENSMUSG00000042046	Dstyk	A930019K20Rik|C430014H23Rik|C820013G01|Ripk5	dual serine/threonine and tyrosine protein kinase	protein-coding
mm_116709.1	chr13	51101510	51101530	-	1	NA	promoter-TSS (NR_029463)	promoter-TSS (NR_029463)	-27	NM_001283029	20729	Mm.188432	NM_011462	ENSMUSG00000021395	Spin1	Spin	spindlin 1	protein-coding
mm_70954.1	chr8	26977371	26977398	+	1	NA	promoter-TSS (NM_001110508)	promoter-TSS (NM_001110508)	48	NM_001110508	353310	Mm.212469	NM_001101502	ENSMUSG00000085795	Zfp703	1110032O19Rik|AI430822|AL022941|Csmn1|End2|Zeppo1|Znf703|Zpo1	zinc finger protein 703	protein-coding
mm_133428.1	chr16	87553314	87553342	+	1	NA	promoter-TSS (NM_144854)	promoter-TSS (NM_144854)	-2	NM_144854	224419	Mm.194466	NM_144854	ENSMUSG00000025610	Map3k7cl	C21orf7|ORF63|Tak1l	Map3k7 C-terminal like	protein-coding
mm_131794.1	chr16	22899016	22899042	+	1	NA	exon (NM_001276450, exon 7 of 7)	exon (NM_001276450, exon 7 of 7)	-4643	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_138791.1	chr17	37480771	37480845	+	1	NA	TTS (NM_008204)	TTS (NM_008204)	2721	NM_008204	14990	Mm.329041	NM_008204	ENSMUSG00000016283	H2-M2	H-2M2|Thy19.4	histocompatibility 2, M region locus 2	protein-coding
mm_71260.1	chr8	40917864	40917883	+	1	NA	3' UTR (NM_001044740, exon 12 of 12)	3' UTR (NM_001044740, exon 12 of 12)	-8360	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_63440.1	chr7	127480617	127480626	+	1	NA	Intergenic	L2c|LINE|L2	-4600	NM_010183	14123	Mm.323505	NM_010183	ENSMUSG00000042423	Fbrs	Fbs|Fbs1	fibrosin	protein-coding
mm_118615.1	chr14	21032508	21032522	+	1	NA	3' UTR (NM_009502, exon 21 of 21)	3' UTR (NM_009502, exon 21 of 21)	19927	NM_018829	55946	Mm.376269	NM_018829	ENSMUSG00000021824	Ap3m1	1200013D09Rik|C78982|R75378	adaptor-related protein complex 3, mu 1 subunit	protein-coding
mm_102702.1	chr11	66168506	66168518	-	1	NA	promoter-TSS (NM_001099633)	promoter-TSS (NM_001099633)	39	NM_001099633	237806	Mm.264210	NM_001099633	ENSMUSG00000056752	Dnah9	9030022M04|A230091C01|C230051G16|D11Ertd686e|Dnahc9|mKIAA0357	dynein, axonemal, heavy chain 9	protein-coding
mm_73955.1	chr8	120343856	120343893	+	1	NA	Intergenic	Intergenic	-115644	NR_110496	434353	Mm.411793	NR_110496	ENSMUSG00000097960	A330074K22Rik	-	RIKEN cDNA A330074K22 gene	ncRNA
mm_120708.1	chr14	71421007	71421017	+	1	NA	Intergenic	Intergenic	169739	NR_046076	100043132	Mm.399336	NR_046075		Gm4251	-	predicted gene 4251	ncRNA
mm_125420.1	chr15	41835115	41835125	+	1	NA	intron (NM_001130164, intron 1 of 5)	L1MEg|LINE|L1	4162	NM_001130164	170719	Mm.254267	NM_130885	ENSMUSG00000022307	Oxr1	2210416C20Rik|C7|C7B	oxidation resistance 1	protein-coding
mm_102337.1	chr11	57832005	57832021	-	1	NA	5' UTR (NM_008213, exon 1 of 2)	5' UTR (NM_008213, exon 1 of 2)	134	NM_008213	15110	Mm.4746	NM_008213	ENSMUSG00000037335	Hand1	Ehand1|Hxt|Th1|Thing1|bHLHa27|eHAND	heart and neural crest derivatives expressed transcript 1	protein-coding
mm_35970.1	chr4	53153717	53153743	-	1	NA	intron (NM_013454, intron 1 of 49)	intron (NM_013454, intron 1 of 49)	6165	NM_013454	11303	Mm.277376	NM_013454	ENSMUSG00000015243	Abca1	ABC-1|Abc1	ATP-binding cassette, sub-family A (ABC1), member 1	protein-coding
mm_132020.1	chr16	26463147	26463161	+	1	NA	promoter-TSS (NM_053241)	promoter-TSS (NM_053241)	19	NM_053241	114141	Mm.275205	NM_053241	ENSMUSG00000038148	Cldn16	PCLN1|claudin-16	claudin 16	protein-coding
mm_72693.1	chr8	84969825	84969862	+	1	NA	intron (NM_011563, intron 1 of 5)	intron (NM_011563, intron 1 of 5)	221	NM_011563	21672	Mm.347009	NM_011563	ENSMUSG00000005161	Prdx2	AL022839|Band-8|NkefB|PRP|PrxII|TDX1|TPx|TPx-B|TR|TSA|Tdpx1|Torin	peroxiredoxin 2	protein-coding
mm_61540.1	chr7	79297016	79297048	+	1	NA	exon (NM_018811, exon 3 of 11)	exon (NM_018811, exon 3 of 11)	23766	NM_018811	54608	Mm.365490	NM_018811	ENSMUSG00000039202	Abhd2	2210009N18Rik|LABH2|Labh-2	abhydrolase domain containing 2	protein-coding
mm_54060.1	chr6	13871168	13871176	-	1	NA	promoter-TSS (NR_045995)	promoter-TSS (NR_045995)	311	NR_024619	66520	Mm.29615	NM_183258		2610001J05Rik	C79299	RIKEN cDNA 2610001J05 gene	ncRNA
mm_15928.1	chr2	165068100	165068105	+	1	NA	intron (NM_170702, intron 6 of 7)	intron (NM_170702, intron 6 of 7)	12466	NM_011611	21939	Mm.271833	NM_011611	ENSMUSG00000017652	Cd40	AI326936|Bp50|GP39|HIGM1|IGM|IMD3|T-BAM|TRAP|Tnfrsf5|p50	CD40 antigen	protein-coding
mm_102911.1	chr11	69579125	69579140	-	1	NA	5' UTR (NM_144824, exon 1 of 10)	5' UTR (NM_144824, exon 1 of 10)	192	NM_144824	216853	Mm.31586	NM_144824	ENSMUSG00000041346	Wrap53	BC021790|Wdr79	WD repeat containing, antisense to Trp53	protein-coding
mm_167246.1	chr8	22625521	22625523	+	1	NA	intron (NM_145592, intron 2 of 3)	intron (NM_145592, intron 2 of 3)	1479	NM_145592	234130	Mm.157322	NM_145592	ENSMUSG00000031535	Dkk4	Dkk-4	dickkopf WNT signaling pathway inhibitor 4	protein-coding
mm_63111.1	chr7	122671188	122671198	+	1	NA	promoter-TSS (NM_019430)	promoter-TSS (NM_019430)	-551	NM_019430	54376	Mm.444212	NM_019430	ENSMUSG00000066189	Cacng3	-	calcium channel, voltage-dependent, gamma subunit 3	protein-coding
mm_64097.1	chr7	141008683	141008723	+	1	NA	TTS (NM_025378)	TTS (NM_025378)	2041	NM_025378	66141	Mm.141021	NM_025378	ENSMUSG00000025492	Ifitm3	1110004C05Rik|Cd225|Cdw217|DSPA2b|Fgls|IP15|mil-1	interferon induced transmembrane protein 3	protein-coding
mm_38215.1	chr4	135970074	135970089	-	1	NA	intron (NM_011942, intron 4 of 9)	intron (NM_011942, intron 4 of 9)	2513	NM_011942	26394	Mm.34302	NM_011942	ENSMUSG00000028670	Lypla2	LysoII	lysophospholipase 2	protein-coding
mm_54986.1	chr6	48747502	48747519	-	1	NA	intron (NM_175035, intron 1 of 2)	intron (NM_175035, intron 1 of 2)	1313	NM_175035	317757	Mm.455917	NM_175035	ENSMUSG00000043505	Gimap5	D630024P16|E230026N22Rik	GTPase, IMAP family member 5	protein-coding
mm_65784.1	chr7	28803860	28803863	-	1	NA	Intergenic	RLTR18B|LTR|ERVK	-7029	NM_177301	15388	Mm.9043	NM_177301	ENSMUSG00000015165	Hnrnpl	C79783|D830027H13Rik|Hnrpl	heterogeneous nuclear ribonucleoprotein L	protein-coding
mm_163919.1	chr14	37360571	37360572	+	1	NA	Intergenic	MLT1B|LTR|ERVL-MaLR	-225249	NM_078478	66092	Mm.182912	NM_078478	ENSMUSG00000041028	Ghitm	1010001P14Rik|C77840|MICS1|PTD010|Tmbim5	growth hormone inducible transmembrane protein	protein-coding
mm_124918.1	chr15	12117783	12117795	+	1	NA	promoter-TSS (NM_011767)	promoter-TSS (NM_011767)	-62	NM_011767	22763	Mm.273496	NM_011767	ENSMUSG00000022201	Zfr	C920030H05Rik	zinc finger RNA binding protein	protein-coding
mm_149315.1	chr19	10784413	10784450	+	1	NA	intron (NR_027805, intron 2 of 3)	intron (NR_027805, intron 2 of 3)	43484	NR_027805	403202	Mm.34482	NM_207529	ENSMUSG00000067577	A430093F15Rik	Gm674	RIKEN cDNA A430093F15 gene	ncRNA
mm_94690.1	chr11	19925970	19925974	+	1	NA	intron (NM_033523, intron 1 of 5)	intron (NM_033523, intron 1 of 5)	1530	NM_033523	114716	Mm.266627	NM_033523	ENSMUSG00000045671	Spred2	C79158	sprouty-related, EVH1 domain containing 2	protein-coding
mm_156862.1	chrX	164419856	164419865	+	1	NA	promoter-TSS (NM_011081)	promoter-TSS (NM_011081)	73	NM_011081	18700	Mm.3781	NM_011081	ENSMUSG00000031381	Piga	AI194334|Pig-a	phosphatidylinositol glycan anchor biosynthesis, class A	protein-coding
mm_110745.1	chr12	69893135	69893151	-	1	NA	promoter-TSS (NM_201519)	promoter-TSS (NM_201519)	20	NM_201519	399510	Mm.291936	NM_201519	ENSMUSG00000034761	Map4k5	4432415E19Rik|GCKR|KHS|MAPKKKK5	mitogen-activated protein kinase kinase kinase kinase 5	protein-coding
mm_97999.1	chr11	84173349	84173363	+	1	NA	Intergenic	Intergenic	-5880	NM_001037932	628813	Mm.390389	NM_001037932	ENSMUSG00000051452	Gm11437	AI463690|OTTMUSG00000000997	predicted gene 11437	protein-coding
mm_27848.1	chr3	79156641	79156651	-	1	NA	Intergenic	L1_Mur3|LINE|L1	-10771	NM_001099624	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_106041.1	chr11	116079322	116079335	-	1	NA	3' UTR (NM_016852, exon 8 of 8)	3' UTR (NM_016852, exon 8 of 8)	-1367	NM_001009573	70450	Mm.259460	NM_001009573	ENSMUSG00000057948	Unc13d	2610108D09Rik|Jinx|Munc13-4|mFLJ00067	unc-13 homolog D (C. elegans)	protein-coding
mm_63328.1	chr7	126945201	126945215	+	1	NA	TTS (NM_001039645)	TTS (NM_001039645)	4373	NM_001347657	233879	Mm.444143	NM_001039645	ENSMUSG00000046378	Asphd1	A830007L07Rik|Gm168	aspartate beta-hydroxylase domain containing 1	protein-coding
mm_28136.1	chr3	87174658	87174679	-	1	NA	promoter-TSS (NM_130867)	promoter-TSS (NM_130867)	79	NM_001170985	170643	Mm.89552	NM_130867	ENSMUSG00000041734	Kirrel	6720469N11Rik|Kirrel1|Neph1	kin of IRRE like (Drosophila)	protein-coding
mm_149318.1	chr19	10839856	10839867	+	1	NA	Intergenic	Intergenic	-2683	NM_023044	65221	Mm.27387	NM_023044	ENSMUSG00000024737	Slc15a3	Ci1|cI-1	solute carrier family 15, member 3	protein-coding
mm_85293.1	chr9	100466870	100466881	-	1	NA	intron (NM_001033543, intron 4 of 6)	intron (NM_001033543, intron 4 of 6)	19598	NM_001033543	213208	Mm.242896	NM_001033543	ENSMUSG00000044244	Il20rb	AV228068|Fndc6|Gm186|Il20R2	interleukin 20 receptor beta	protein-coding
mm_127362.1	chr15	100684610	100684622	+	1	NA	exon (NM_033612, exon 4 of 8)	exon (NM_033612, exon 4 of 8)	3304	NM_033612	109901	Mm.2131	NM_033612	ENSMUSG00000023031	Cela1	1810009A17Rik|1810062B19Rik|Ela-1|Ela1|PC-TsF	chymotrypsin-like elastase family, member 1	protein-coding
mm_107951.1	chr12	72434660	72434705	+	1	NA	Intergenic	MLT1A0|LTR|ERVL-MaLR	-7184	NM_001142728	78257	Mm.266280	NM_030070	ENSMUSG00000021090	Lrrc9	4921529O18Rik|4930432K16Rik	leucine rich repeat containing 9	protein-coding
mm_89464.1	chr10	93336221	93336239	+	1	NA	promoter-TSS (NR_038014)	promoter-TSS (NR_038014)	-2	NR_038014	432488	Mm.32833	NR_038014		Gm17745	-	predicted gene, 17745	ncRNA
mm_66326.1	chr7	42548588	42548588	-	1	NA	Intergenic	Lx|LINE|L1	-42835	NM_001309388	434178	Mm.333810	NM_001309388	ENSMUSG00000092416	Zfp141	-	zinc finger protein 141	protein-coding
mm_161520.1	chr15	100280894	100280894	+	1	NA	promoter-TSS (NM_183109)	promoter-TSS (NM_183109)	57	NM_183109	75002	Mm.261400	NM_183109	ENSMUSG00000045631	Tmprss12	4930478A21Rik	transmembrane (C-terminal) protease, serine 12	protein-coding
mm_113854.1	chr13	47225561	47225566	+	1	NA	intron (NM_001170643, intron 3 of 7)	intron (NM_001170643, intron 3 of 7)	31560	NM_001170643	218215	Mm.287609	NM_146042	ENSMUSG00000038068	Rnf144b	BC025007|E130105P19Rik|Ibrdc2|Pir2	ring finger protein 144B	protein-coding
mm_150760.1	chr19	44229630	44229632	+	1	NA	intron (NM_024450, intron 2 of 5)	RLTR19-int|LTR|ERVK	26343	NM_024450	30049	Mm.480594	NM_024450	ENSMUSG00000025202	Scd3	4930513N16Rik	stearoyl-coenzyme A desaturase 3	protein-coding
mm_127399.1	chr15	101134637	101134664	+	1	NA	exon (NM_001277255, exon 4 of 12)	exon (NM_001277255, exon 4 of 12)	6128	NM_001277257	11482	Mm.279542	NM_009612	ENSMUSG00000000530	Acvrl1	AI115505|AI427544|Acvrlk1|Alk1	activin A receptor, type II-like 1	protein-coding
mm_15643.1	chr2	163059397	163059418	+	1	NA	intron (NM_008652, intron 1 of 13)	intron (NM_008652, intron 1 of 13)	4772	NM_008652	17865	Mm.4594	NM_008652	ENSMUSG00000017861	Mybl2	B-Myb|Bmyb	myeloblastosis oncogene-like 2	protein-coding
mm_42906.1	chr5	122501782	122501810	+	1	NA	non-coding (NR_027838, exon 1 of 21)	non-coding (NR_027838, exon 1 of 21)	429	NM_001110140	11938	Mm.227583	NM_009722	ENSMUSG00000029467	Atp2a2	9530097L16Rik|D5Wsu150e|SERCA2|SERCA2B|Serca2a|mKIAA4195	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	protein-coding
mm_144249.1	chr18	10815726	10815729	+	1	NA	Intergenic	L1MB2|LINE|L1	-30175	NR_029781	723959		NR_029781	ENSMUSG00000106348	Mir1a-2	Mir1-2|Mirn1-2|mir-1a-2|mmu-mir-1-2|mmu-mir-1a-2	microRNA 1a-2	ncRNA
mm_116010.1	chr13	24634427	24634449	-	1	NA	intron (NM_178658, intron 1 of 13)	intron (NM_178658, intron 1 of 13)	-4210	NM_001080381	193385	Mm.217319	NM_029679	ENSMUSG00000036006	Fam65b	-	family with sequence similarity 65, member B	protein-coding
mm_143615.1	chr17	78769042	78769053	-	1	NA	intron (NM_001081179, intron 27 of 35)	intron (NM_001081179, intron 27 of 35)	-32487	NM_011500	268980	Mm.311915	NM_011500	ENSMUSG00000024077	Strn	AU022939|D130055P19	striatin, calmodulin binding protein	protein-coding
mm_18771.1	chr2	73486436	73486451	-	1	NA	promoter-TSS (NM_001289723)	promoter-TSS (NM_001289723)	-690	NM_001289723	215280	Mm.223504	NM_153138	ENSMUSG00000075284	Wipf1	AI115543|D2Ertd120e|WIP|Waspip	WAS/WASL interacting protein family, member 1	protein-coding
mm_16733.1	chr2	9176825	9176833	-	1	NA	Intergenic	Intergenic	-12686	NR_038180	73438	Mm.23558	NR_038180	ENSMUSG00000085580	1700061F12Rik	-	RIKEN cDNA 1700061F12 gene	ncRNA
mm_88251.1	chr10	73099155	73099177	+	1	NA	Intergenic	CpG	-12461	NR_040646	327768	Mm.417745	NR_040646		A330049N07Rik	-	RIKEN cDNA A330049N07 gene	ncRNA
mm_102930.1	chr11	69600835	69600841	-	1	NA	3' UTR (NM_013415, exon 7 of 7)	3' UTR (NM_013415, exon 7 of 7)	5122	NM_013415	11932	Mm.235204	NM_013415	ENSMUSG00000041329	Atp1b2	Amog|Atpb-2	ATPase, Na+/K+ transporting, beta 2 polypeptide	protein-coding
mm_10757.1	chr2	23207471	23207493	+	1	NA	promoter-TSS (NM_027635)	promoter-TSS (NM_027635)	6	NM_027635	70981	Mm.314026	NM_027635	ENSMUSG00000026774	4931423N10Rik	-	RIKEN cDNA 4931423N10 gene	protein-coding
mm_147027.1	chr18	34652492	34652509	-	1	NA	promoter-TSS (NM_178347)	promoter-TSS (NM_178347)	-764	NM_178347	52563	Mm.196638	NM_178347	ENSMUSG00000024370	Cdc23	6030435O18|D18Ertd243e	CDC23 cell division cycle 23	protein-coding
mm_113879.1	chr13	48968368	48968430	+	1	NA	promoter-TSS (NM_001033268)	promoter-TSS (NM_001033268)	287	NR_015601	68128	Mm.426304	NR_015601		Fam120aos	C030044B11Rik	family with sequence similarity 120A, opposite strand	ncRNA
mm_74745.1	chr8	18990993	18991001	-	1	NA	promoter-TSS (NM_181683)	promoter-TSS (NM_181683)	58	NM_181683	353320	Mm.270483	NM_181683	ENSMUSG00000053695	Defb37	BD-37	defensin beta 37	protein-coding
mm_112362.1	chr12	119159869	119159878	-	1	NA	Intergenic	Intergenic	78403	NM_177290	320910	Mm.217000	NM_177290	ENSMUSG00000025321	Itgb8	4832412O06Rik	integrin beta 8	protein-coding
mm_8403.1	chr1	151500988	151500994	-	1	NA	promoter-TSS (NM_011277)	promoter-TSS (NM_011277)	-168	NM_011277	19821	Mm.474038	NM_011277	ENSMUSG00000026484	Rnf2	AI326319|AI450156|AU019207|Ring1B|dinG	ring finger protein 2	protein-coding
mm_52306.1	chr6	108828527	108828542	+	1	NA	promoter-TSS (NM_138677)	promoter-TSS (NM_138677)	-107	NM_138677	192193	Mm.21596	NM_138677	ENSMUSG00000030104	Edem1	A130059K23Rik|EDEM|mKIAA0212	ER degradation enhancer, mannosidase alpha-like 1	protein-coding
mm_143769.1	chr17	81670124	81670134	-	1	NA	intron (NR_104580, intron 1 of 8)	CpG	68258	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_124004.1	chr14	76010836	76010862	-	1	NA	promoter-TSS (NM_026816)	promoter-TSS (NM_026816)	16	NM_026816	68705	Mm.20415	NM_026816	ENSMUSG00000067995	Gtf2f2	1110031C13Rik|AI326315	general transcription factor IIF, polypeptide 2	protein-coding
mm_20159.1	chr2	122146955	122146957	-	1	NA	promoter-TSS (NM_009735)	promoter-TSS (NM_009735)	-731	NM_009735	12010	Mm.163	NM_009735	ENSMUSG00000060802	B2m	Ly-m11|beta2-m|beta2m	beta-2 microglobulin	protein-coding
mm_167198.1	chr7	142661104	142661104	-	1	NA	5' UTR (NM_001122736, exon 1 of 4)	intron (NR_002855, intron 1 of 3)	167	NM_001122736	16002	Mm.3862	NM_010514	ENSMUSG00000048583	Igf2	AL033362|Igf-2|Igf-II|M6pr|Mpr|Peg2	insulin-like growth factor 2	protein-coding
mm_48071.1	chr5	136581753	136581771	-	1	NA	Intergenic	Intergenic	-14272	NM_001291238	13047	Mm.320317	NM_009986	ENSMUSG00000029705	Cux1	CDP|Cutl1|Cux|Cux-1	cut-like homeobox 1	protein-coding
mm_85191.1	chr9	96719810	96719889	-	1	NA	intron (NM_175537, intron 1 of 2)	CpG	11826	NM_175537	245007	Mm.485954	NM_175537	ENSMUSG00000040433	Zbtb38	A930014K01Rik|CIBZ	zinc finger and BTB domain containing 38	protein-coding
mm_117981.1	chr13	100109080	100109114	-	1	NA	exon (NM_011353, exon 2 of 3)	exon (NM_011353, exon 2 of 3)	1078	NM_011353	20365	Mm.286177	NM_011353	ENSMUSG00000021643	Serf1	4F5|Msmac1|m4F5	small EDRK-rich factor 1	protein-coding
mm_133219.1	chr16	76122608	76122629	+	1	NA	promoter-TSS (NR_040575)	promoter-TSS (NR_040575)	5	NR_040575	78215	Mm.243885	NR_040575		4930578N18Rik	-	RIKEN cDNA 4930578N18 gene	ncRNA
mm_133701.1	chr16	92995466	92995508	+	1	NA	Intergenic	Intergenic	-169413	NM_001111022	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_106803.1	chr12	5642999	5643001	+	1	NA	Intergenic	Intergenic	266498	NR_015579	72669	Mm.10434	NM_028318		2810032G03Rik	AI461720	RIKEN cDNA 2810032G03 gene	ncRNA
mm_160517.1	chr9	23223090	23223090	+	1	NA	promoter-TSS (NM_028472)	promoter-TSS (NM_028472)	14	NM_028472	73230	Mm.335020	NM_028472	ENSMUSG00000031963	Bmper	3110056H04Rik|CV-2|Crim3|Cv2	BMP-binding endothelial regulator	protein-coding
mm_43831.1	chr5	142972294	142972311	+	1	NA	3' UTR (NM_007984, exon 5 of 5)	3' UTR (NM_007984, exon 5 of 5)	11947	NM_007984	14086	Mm.289707	NM_007984	ENSMUSG00000029581	Fscn1	AI663989|Fan1|fascin-1	fascin actin-bundling protein 1	protein-coding
mm_141359.1	chr17	28770271	28770280	-	1	NA	intron (NM_011950, intron 2 of 11)	intron (NM_011950, intron 2 of 11)	958	NM_011950	26415	Mm.27970	NM_011950	ENSMUSG00000004864	Mapk13	SAPK4|Serk4	mitogen-activated protein kinase 13	protein-coding
mm_74484.1	chr8	4325321	4325328	-	1	NA	promoter-TSS (NM_010485)	promoter-TSS (NM_010485)	114	NR_033527	20300	Mm.7275	NM_009138	ENSMUSG00000023235	Ccl25	A130072A22Rik|AI852536|CKb15|Scya25|TECK	chemokine (C-C motif) ligand 25	protein-coding
mm_60911.1	chr7	46754266	46754272	+	1	NA	TTS (NM_011314)	TTS (NM_011314)	2436	NM_011314	20209	Mm.200941	NM_011314	ENSMUSG00000057465	Saa2	AW111173|Saa-2|Saa1	serum amyloid A 2	protein-coding
mm_26312.1	chr3	142519346	142519361	+	1	NA	intron (NM_153564, intron 10 of 10)	RMER2|LTR|ERV1	-10983	NM_001083312	229900	Mm.45740	NM_145545	ENSMUSG00000040253	Gbp7	9830147J24Rik	guanylate binding protein 7	protein-coding
mm_118601.1	chr14	20707549	20707555	+	1	NA	promoter-TSS (NM_001252082)	promoter-TSS (NM_001252082)	0	NM_001252081	268721	Mm.275082	NM_027996	ENSMUSG00000021819	Zswim8	2310021P13Rik|4832404P21Rik|Kiaa0913|mKIAA0913	zinc finger SWIM-type containing 8	protein-coding
mm_110283.1	chr12	32080833	32080863	-	1	NA	Intergenic	RLTR16|LTR|ERVK	-19569	NM_011158	19088	Mm.25594	NM_011158	ENSMUSG00000002997	Prkar2b	AI451071|AW061005|PKARIIbeta|Pkarb2|RII(beta)	protein kinase, cAMP dependent regulatory, type II beta	protein-coding
mm_29877.1	chr3	130978452	130978459	-	1	NA	Intergenic	Intergenic	-131842	NM_010703	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_60884.1	chr7	46396249	46396258	+	1	NA	promoter-TSS (NM_001112739)	promoter-TSS (NM_001112739)	-215	NM_008421	16502	Mm.249386	NM_008421	ENSMUSG00000058975	Kcnc1	C230009H10Rik|KShIIIB|KV4|Kcr2-1|Kv3.1|NGK2|Shaw	potassium voltage gated channel, Shaw-related subfamily, member 1	protein-coding
mm_140017.1	chr17	73804855	73804871	+	1	NA	promoter-TSS (NM_020578)	promoter-TSS (NM_020578)	22	NM_020578	57440	Mm.18526	NM_020578	ENSMUSG00000024065	Ehd3	Ehd2	EH-domain containing 3	protein-coding
mm_157416.1	chrX	38456408	38456458	-	1	NA	promoter-TSS (NM_001017959)	promoter-TSS (NM_001017959)	27	NM_010685	16784	Mm.486	NM_010685	ENSMUSG00000016534	Lamp2	CD107b|LGP-B|Lamp II|Lamp-2|Lamp-2a|Lamp-2b|Lamp-2c|Mac3	lysosomal-associated membrane protein 2	protein-coding
mm_127631.1	chr15	102470535	102470546	+	1	NA	promoter-TSS (NM_001174073)	promoter-TSS (NM_001174073)	-92	NM_011042	18521	Mm.236513	NM_011042	ENSMUSG00000056851	Pcbp2	AW412548|Hnrpx|alphaCP-2	poly(rC) binding protein 2	protein-coding
mm_105414.1	chr11	103638863	103638893	-	1	NA	promoter-TSS (NM_027083)	promoter-TSS (NM_027083)	-4	NM_027083	69444	Mm.275677	NM_027083	ENSMUSG00000020945	Lyzl6	1700023H08Rik|Lyc1|Lyzb	lysozyme-like 6	protein-coding
mm_6.1	chr1	4785773	4785802	+	1	NA	promoter-TSS (NM_001177658)	promoter-TSS (NM_001177658)	-61	NM_025300	27395	Mm.182927	NM_025300	ENSMUSG00000033845	Mrpl15	HSPC145|MRP-L7|Rpml7	mitochondrial ribosomal protein L15	protein-coding
mm_78642.1	chr9	40269431	40269441	+	1	NA	5' UTR (NM_001083917, exon 1 of 7)	5' UTR (NM_001083917, exon 1 of 7)	220	NM_178227	235281	Mm.290083	NM_153522	ENSMUSG00000049281	Scn3b	1110001K16Rik|4833414B02Rik|Scnb3	sodium channel, voltage-gated, type III, beta	protein-coding
mm_31579.1	chr4	57742042	57742054	+	1	NA	intron (NM_001304544, intron 5 of 8)	intron (NM_001304544, intron 5 of 8)	-103200	NM_009649	11641	Mm.467752	NM_009649	ENSMUSG00000038729	Akap2	AA959716|AI649048|Akap-2|Akap-kl|B230340M18Rik|Prka2	A kinase (PRKA) anchor protein 2	protein-coding
mm_91055.1	chr10	18831815	18831825	-	1	NA	non-coding (NR_102728, exon 1 of 4)	non-coding (NR_102728, exon 1 of 4)	110	NR_038035	73968	Mm.55591	NR_038034		4930444F02Rik	1700010L24Rik|mpiR	RIKEN cDNA 4930444F02 gene	ncRNA
mm_5756.1	chr1	46854053	46854079	-	1	NA	promoter-TSS (NM_172653)	promoter-TSS (NM_172653)	-557	NM_172653	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|mKIAA1265	solute carrier family 39 (zinc transporter), member 10	protein-coding
mm_35340.1	chr4	32167284	32167305	-	1	NA	Intergenic	Intergenic	203187	NM_172688	26409	Mm.258589	NM_009316	ENSMUSG00000028284	Map3k7	B430101B05|C87327|Tak1	mitogen-activated protein kinase kinase kinase 7	protein-coding
mm_140022.1	chr17	73830655	73830695	+	1	NA	3' UTR (NM_020578, exon 6 of 6)	3' UTR (NM_020578, exon 6 of 6)	25834	NM_020578	57440	Mm.18526	NM_020578	ENSMUSG00000024065	Ehd3	Ehd2	EH-domain containing 3	protein-coding
mm_103447.1	chr11	76161467	76161506	-	1	NA	intron (NM_026664, intron 4 of 21)	MTEa|LTR|ERVL-MaLR	18144	NM_026664	68299	Mm.46397	NM_026664	ENSMUSG00000017288	Vps53	2010002A08Rik|2310040I21Rik|3100002B05Rik|Hccs1	VPS53 GARP complex subunit	protein-coding
mm_71707.1	chr8	61933958	61933972	+	1	NA	intron (NM_001293783, intron 1 of 37)	(GGA)n|Simple_repeat|Simple_repeat	5878	NM_001293783	234311	Mm.275233	NM_144928	ENSMUSG00000037921	Ddx60	9830118M07	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	protein-coding
mm_27818.1	chr3	78888458	78888458	-	1	NA	Intergenic	Intergenic	256429	NM_001310536	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_18199.1	chr2	45117524	45117539	-	1	NA	Intergenic	Intergenic	-4252	NM_015753	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_75885.1	chr8	70805002	70805010	-	1	NA	Intergenic	CpG	-3443	NM_008353	16161	Mm.731	NM_008353	ENSMUSG00000000791	Il12rb1	CD212|IL-12R[b]	interleukin 12 receptor, beta 1	protein-coding
mm_8498.1	chr1	153875013	153875045	-	1	NA	exon (NM_001008426, exon 1 of 1)	exon (NM_001008426, exon 1 of 1)	684	NM_001008426	433365	Mm.229362	NM_001008426	ENSMUSG00000043282	Teddm1b	EG433365|Gm5531	transmembrane epididymal protein 1B	protein-coding
mm_6918.1	chr1	84840194	84840202	-	1	NA	promoter-TSS (NM_133975)	promoter-TSS (NM_133975)	357	NM_025386	66153	Mm.381192	NM_025386	ENSMUSG00000073633	Fbxo36	0610008D19Rik|1110020F21Rik|2410002G19Rik|D1Ertd757e	F-box protein 36	protein-coding
mm_144695.1	chr18	34862471	34862481	+	1	NA	exon (NM_007913, exon 2 of 2)	exon (NM_007913, exon 2 of 2)	1269	NM_007913	13653	Mm.181959	NM_007913	ENSMUSG00000038418	Egr1	A530045N19Rik|ETR103|Egr-1|Krox-1|Krox-24|Krox24|NGF1-A|NGFI-A|NGFIA|TIS8|Zenk|Zfp-6|Zif268|egr	early growth response 1	protein-coding
mm_48130.1	chr5	137149906	137149918	-	1	NA	Intergenic	Intergenic	-33705	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_125648.1	chr15	62328716	62328721	+	1	NA	Intergenic	Intergenic	-109267	NR_003523	67552	Mm.484027	NM_026230		H2afy3	4933432H23Rik	H2A histone family, member Y3	pseudo
mm_79092.1	chr9	46242776	46242786	+	1	NA	exon (NM_007468, exon 3 of 3)	exon (NM_007468, exon 3 of 3)	1937	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_15991.1	chr2	167058881	167058892	+	1	NA	intron (NM_001033196, intron 2 of 13)	B1_Mus1|SINE|Alu	-4048	NR_138563	68949	Mm.391959	NM_001081005		Zfas1	1500012F01Rik|Zfos1	zinc finger, NFX1-type containing 1, antisense RNA 1	ncRNA
mm_75157.1	chr8	36249293	36249368	-	1	NA	exon (NM_001081150, exon 1 of 12)	exon (NM_001081150, exon 1 of 12)	186	NM_001081150	244421	Mm.324032	NM_001081150	ENSMUSG00000039633	Lonrf1	-	LON peptidase N-terminal domain and ring finger 1	protein-coding
mm_152160.1	chr19	7275846	7275858	-	1	NA	TTS (NM_054048)	TTS (NM_054048)	7573	NM_001320554	104383	Mm.283859	NM_054048	ENSMUSG00000024968	Rcor2	1A13|AW122124|CoREST|Rcor|Rcor1	REST corepressor 2	protein-coding
mm_47123.1	chr5	119806405	119806419	-	1	NA	Intergenic	Intergenic	-28251	NM_011537	21388	Mm.103636	NM_011537	ENSMUSG00000018263	Tbx5	-	T-box 5	protein-coding
mm_33435.1	chr4	130104887	130104904	+	1	NA	Intergenic	Intergenic	-2661	NM_026441	67898	Mm.20818	NM_026441	ENSMUSG00000028779	Pef1	2600002E23Rik|Peflin	penta-EF hand domain containing 1	protein-coding
mm_67729.1	chr7	90129894	90129913	-	1	NA	promoter-TSS (NM_001252521)	promoter-TSS (NM_001252521)	33	NR_046007	78329	Mm.389940	NR_046006	ENSMUSG00000097162	2310010J17Rik	-	RIKEN cDNA 2310010J17 gene	ncRNA
mm_4257.1	chr1	171418965	171418969	+	1	NA	promoter-TSS (NM_001164525)	promoter-TSS (NM_001164525)	-66	NM_001164525	226654	Mm.46366	NM_001164525	ENSMUSG00000103711	Tstd1	AV065366|EG226654|Gm4848|KAT	thiosulfate sulfurtransferase (rhodanese)-like domain containing 1	protein-coding
mm_39277.1	chr5	3909291	3909299	+	1	NA	Intergenic	Intergenic	-15362	NM_172135	545725	Mm.99593	NM_172135	ENSMUSG00000040429	Mterf1a	4931431L11Rik|9230106K09Rik|Mterf|Mterf1|mTERF1b	mitochondrial transcription termination factor 1a	protein-coding
mm_112361.1	chr12	119107774	119107779	-	1	NA	Intergenic	L1_Mur3|LINE|L1	130500	NM_177290	320910	Mm.217000	NM_177290	ENSMUSG00000025321	Itgb8	4832412O06Rik	integrin beta 8	protein-coding
mm_98879.1	chr11	97806722	97806771	+	1	NA	intron (NM_010688, intron 1 of 6)	intron (NM_010688, intron 1 of 6)	7074	NM_010688	16796	Mm.271967	NM_010688	ENSMUSG00000038366	Lasp1	AA408629|Def-4|SH3P6|Tg(Col1a1-lacZ)1Ngma	LIM and SH3 protein 1	protein-coding
mm_100728.1	chr11	3931546	3931570	-	1	NA	5' UTR (NM_001130458, exon 2 of 10)	5' UTR (NM_001130458, exon 2 of 10)	403	NM_001130459	21452	Mm.20948	NM_015749	ENSMUSG00000020432	Tcn2	AW208754|Tcn-2	transcobalamin 2	protein-coding
mm_31793.1	chr4	63979862	63979870	+	1	NA	intron (NM_011607, intron 15 of 25)	intron (NM_011607, intron 15 of 25)	67149	NM_011607	21923	Mm.980	NM_011607	ENSMUSG00000028364	Tnc	AI528729|C130033P17Rik|Hxb|TN|TN-C|Ten|cytotactin|tenascin-C	tenascin C	protein-coding
mm_121854.1	chr14	20664481	20664551	-	1	NA	promoter-TSS (NM_001310432)	promoter-TSS (NM_001310432)	58	NM_001310432	68760	Mm.35789	NM_175132	ENSMUSG00000039376	Synpo2l	1110054M18Rik|Chap	synaptopodin 2-like	protein-coding
mm_159686.1	chr5	13791632	13791632	+	1	NA	promoter-TSS (NM_027650)	promoter-TSS (NM_027650)	13	NM_027650	71026	Mm.158536	NM_027650	ENSMUSG00000067855	Speer3	4933405P08Rik|SPEER-3	spermatogenesis associated glutamate (E)-rich protein 3	protein-coding
mm_97734.1	chr11	80403346	80403349	+	1	NA	intron (NR_045038, intron 14 of 16)	intron (NR_045038, intron 14 of 16)	20068	NM_001130171	22680	Mm.401332	NM_011751	ENSMUSG00000017421	Zfp207	8430401D15Rik|BuGZ|Zep|Znf207	zinc finger protein 207	protein-coding
mm_48395.1	chr5	139826838	139826891	-	1	NA	promoter-TSS (NM_025604)	promoter-TSS (NM_025604)	-21	NM_025604	66506	Mm.29070	NM_025604	ENSMUSG00000029551	Psmg3	1810042K04Rik|4930403H09Rik|AI303239	proteasome (prosome, macropain) assembly chaperone 3	protein-coding
mm_36355.1	chr4	74586375	74586376	-	1	NA	Intergenic	L1_Mur3|LINE|L1	334496	NM_144787	76804	Mm.209059	NM_144787	ENSMUSG00000028397	Kdm4c	2410141F18Rik|AA517467|Gasc1|Jmjd2c	lysine (K)-specific demethylase 4C	protein-coding
mm_162537.1	chr1	167308365	167308411	+	1	NA	promoter-TSS (NM_001039483)	promoter-TSS (NM_001039483)	-282	NM_001039483	68944	Mm.330045	NM_026881	ENSMUSG00000052428	Tmco1	1190006A08Rik|4930403O06Rik|AA109065|AU022572|ESTM39	transmembrane and coiled-coil domains 1	protein-coding
mm_75381.1	chr8	45382148	45382192	-	1	NA	5' UTR (NM_153535, exon 1 of 14)	5' UTR (NM_153535, exon 1 of 14)	121	NM_153535	212326	Mm.51259	NM_153535	ENSMUSG00000070044	Fam149a	AW213256|mKIAA4166	family with sequence similarity 149, member A	protein-coding
mm_117556.1	chr13	85126987	85127010	-	1	NA	Intergenic	Intergenic	-62387	NM_001347587	66671	Mm.18474	NM_023243	ENSMUSG00000021548	Ccnh	6330408H09Rik|AI661354|AV102684|AW538719	cyclin H	protein-coding
mm_83365.1	chr9	44432929	44432934	-	1	NA	Intergenic	RLTR53_Mm|LTR|ERVK	7937	NM_001033469	382074	Mm.335103	NM_001033469	ENSMUSG00000074397	Foxr1	Foxn5|Gm1115	forkhead box R1	protein-coding
mm_132472.1	chr16	36708290	36708304	+	1	NA	exon (NM_134109, exon 2 of 8)	exon (NM_134109, exon 2 of 8)	14319	NM_001285791	106347	Mm.17807	NM_134109	ENSMUSG00000022900	Ildr1	AU041483|AU044638	immunoglobulin-like domain containing receptor 1	protein-coding
mm_25113.1	chr3	101586245	101586271	+	1	NA	exon (NM_144900, exon 12 of 23)	exon (NM_144900, exon 12 of 23)	18449	NM_144900	11928	Mm.193670	NM_144900	ENSMUSG00000033161	Atp1a1	Atpa-1|BC010319	ATPase, Na+/K+ transporting, alpha 1 polypeptide	protein-coding
mm_164075.1	chr14	121063207	121063213	+	1	NA	intron (NM_134082, intron 1 of 26)	intron (NM_134082, intron 1 of 26)	27636	NM_134082	223254	Mm.223980	NM_134082	ENSMUSG00000025555	Farp1	AW228844|BC030329|Cdep	FERM, RhoGEF (Arhgef) and pleckstrin domain protein 1 (chondrocyte-derived)	protein-coding
mm_127011.1	chr15	95836943	95836946	+	1	NA	intron (NM_001253813, intron 2 of 20)	intron (NM_001253813, intron 2 of 20)	46101	NM_001253813	105722	Mm.38087	NM_175344	ENSMUSG00000064210	Ano6	2900059G15Rik|AA407480|AW554778|F730003B03Rik|Tmem16f	anoctamin 6	protein-coding
mm_7241.1	chr1	93635108	93635117	-	1	NA	intron (NM_021537, intron 2 of 11)	CpG	615	NM_021537	59041	Mm.28761	NM_021537	ENSMUSG00000026277	Stk25	1500019J11Rik|AU018434|C86992|Ste20-like|Ysk1	serine/threonine kinase 25 (yeast)	protein-coding
mm_93240.1	chr10	95415498	95415511	-	1	NA	promoter-TSS (NM_001168657)	promoter-TSS (NM_001168657)	-20	NM_001168656	216233	Mm.474283	NM_007706	ENSMUSG00000020027	Socs2	8030460M17|AI527257|AW108012|CIS2|Cish2|D130043N08Rik|JAB|SOCS-2|SSI-2|hg	suppressor of cytokine signaling 2	protein-coding
mm_53842.1	chr6	148831527	148831537	+	1	NA	promoter-TSS (NM_001081113)	promoter-TSS (NM_001081113)	-65	NM_001081113	320727	Mm.260105	NM_001081113	ENSMUSG00000040029	Ipo8	6230418K12Rik|Abcc10|C130009K11Rik|MRP7|OM-1|Om1|Ranbp8	importin 8	protein-coding
mm_150906.1	chr19	45782884	45782905	+	1	NA	intron (NM_023799, intron 1 of 15)	CpG	397	NM_023799	76055	Mm.122725	NM_023799	ENSMUSG00000025220	Mgea5	2810009A20Rik|4833427O07Rik|5830447M11Rik|AA408215|Hy5|Ncoat|OGA|mKIAA0679	meningioma expressed antigen 5 (hyaluronidase)	protein-coding
mm_107386.1	chr12	33207671	33207671	+	1	NA	intron (NM_028139, intron 2 of 3)	intron (NM_028139, intron 2 of 3)	59985	NM_028139	380753	Mm.41540	NM_028139	ENSMUSG00000020564	Atxn7l1	2810423G08Rik|Atxn7l4	ataxin 7-like 1	protein-coding
mm_89849.1	chr10	107271618	107271696	+	1	NA	promoter-TSS (NM_001039354)	promoter-TSS (NM_001039354)	-174	NM_001039354	108030	Mm.268025	NM_001033223	ENSMUSG00000019906	Lin7a	AI848705|LIN-7A|MALS-1|TIP-33|Veli|Veli1	lin-7 homolog A (C. elegans)	protein-coding
mm_4918.1	chr1	190911804	190911832	+	1	NA	promoter-TSS (NM_178775)	promoter-TSS (NM_178775)	-48	NM_178775	320119	Mm.220912	NM_178775	ENSMUSG00000089872	Rps6kc1	AA682037|B130003F20Rik|C80612|Rpk118	ribosomal protein S6 kinase polypeptide 1	protein-coding
mm_166362.1	chr5	123714045	123714046	+	1	NA	intron (NM_027494, intron 5 of 13)	intron (NM_027494, intron 5 of 13)	6999	NM_027494	70650	Mm.279427	NM_027494	ENSMUSG00000029427	Zcchc8	5730565F05Rik	zinc finger, CCHC domain containing 8	protein-coding
mm_118766.1	chr14	22466342	22466363	+	1	NA	intron (NM_028275, intron 2 of 6)	B4|SINE|B4	76446	NR_046307	74896	Mm.444661	NR_046307		4930405A10Rik	4930456G20Rik	RIKEN cDNA 4930405A10 gene	ncRNA
mm_87395.1	chr10	45335752	45335789	+	1	NA	promoter-TSS (NM_024285)	promoter-TSS (NM_024285)	8	NM_024285	23828	Mm.332793	NM_024285	ENSMUSG00000071317	Bves	Pop1|Popdc1|mBVES	blood vessel epicardial substance	protein-coding
mm_75005.1	chr8	27234425	27234458	-	1	NA	Intergenic	G-rich|Low_complexity|Low_complexity	-4853	NM_013462	11556	Mm.278475	NM_013462	ENSMUSG00000031489	Adrb3	Adrb-3	adrenergic receptor, beta 3	protein-coding
mm_63542.1	chr7	128062658	128062687	+	1	NA	promoter-TSS (NM_008401)	promoter-TSS (NM_008401)	32	NM_008401	16409	Mm.262106	NM_008401	ENSMUSG00000030786	Itgam	CD11b/CD18|CR3|CR3A|Cd11b|F730045J24Rik|Ly-40|MAC1|Mac-1|Mac-1a	integrin alpha M	protein-coding
mm_129246.1	chr15	76660088	76660098	-	1	NA	promoter-TSS (NM_001276335)	promoter-TSS (NM_001276335)	115	NM_001276322	54151	Mm.247752	NM_019396	ENSMUSG00000053929	Cyhr1	1110031M01Rik|AU042374|Chrp	cysteine and histidine rich 1	protein-coding
mm_41059.1	chr5	86804509	86804517	+	1	NA	promoter-TSS (NM_177680)	promoter-TSS (NM_177680)	23	NM_177680	231386	Mm.196325	NM_177680	ENSMUSG00000035851	Ythdc1	A730098D12Rik|C80342|mKIAA1966	YTH domain containing 1	protein-coding
mm_26152.1	chr3	138143823	138143843	+	1	NA	promoter-TSS (NM_001163457)	promoter-TSS (NM_001163457)	295	NM_175389	108943	Mm.471692	NM_175389	ENSMUSG00000004127	Trmt10a	3110023L08Rik|AA794508|Rg9mtd2|Rnmtd2	tRNA methyltransferase 10A	protein-coding
mm_83208.1	chr9	41985790	41985799	-	1	NA	intron (NM_011436, intron 38 of 47)	intron (NM_011436, intron 38 of 47)	138495	NM_011436	20660	Mm.121920	NM_011436	ENSMUSG00000049313	Sorl1	2900010L19Rik|AI596264|AW261561|LR11|SorLA|gp250|mSorLA	sortilin-related receptor, LDLR class A repeats-containing	protein-coding
mm_136774.1	chr17	10079249	10079258	+	1	NA	Intergenic	RMER10A|LTR|ERVL	240108	NM_021881	19317	Mm.130694	NM_021881	ENSMUSG00000062078	Qk	1110003F05Rik|1500005P18|QkI|l(17)-1Wis|l17Wis1	quaking	protein-coding
mm_146016.1	chr18	69404085	69404089	+	1	NA	intron (NM_013685, intron 3 of 19)	intron (NM_013685, intron 3 of 19)	58366	NM_001083967	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding
mm_111214.1	chr12	84400963	84400973	-	1	NA	promoter-TSS (NM_001286049)	promoter-TSS (NM_001286049)	-34	NM_001286049	12499	Mm.10211	NM_007647	ENSMUSG00000021236	Entpd5	AI196558|AI987697|Cd39l4|ER-UDPase|NTPDase-5|NTPDase5|Pcph|mNTPase	ectonucleoside triphosphate diphosphohydrolase 5	protein-coding
mm_88721.1	chr10	80168170	80168172	+	1	NA	intron (NM_007705, intron 1 of 6)	CpG	330	NM_007705	12696	Mm.17898	NM_007705	ENSMUSG00000045193	Cirbp	Cirp|R74941	cold inducible RNA binding protein	protein-coding
mm_16858.1	chr2	11646581	11646585	-	1	NA	intron (NM_008367, intron 1 of 7)	B4A|SINE|B4	3791	NM_008367	16184	Mm.915	NM_008367	ENSMUSG00000026770	Il2ra	CD25|Il2r|Ly-43	interleukin 2 receptor, alpha chain	protein-coding
mm_128320.1	chr15	38004691	38004694	-	1	NA	intron (NM_001112721, intron 28 of 58)	intron (NM_001112721, intron 28 of 58)	-43637	NM_199476	382985	Mm.24738	NM_199476	ENSMUSG00000022292	Rrm2b	p53R2	ribonucleotide reductase M2 B (TP53 inducible)	protein-coding
mm_147693.1	chr18	60748334	60748410	-	1	NA	Intergenic	GC_rich|Low_complexity|Low_complexity	-26224	NM_020600	20044	Mm.43778	NM_020600	ENSMUSG00000024608	Rps14	2600014J02Rik|AL023078	ribosomal protein S14	protein-coding
mm_15543.1	chr2	158385132	158385144	+	1	NA	3' UTR (NM_175692, exon 5 of 5)	3' UTR (NM_175692, exon 5 of 5)	9500	NM_175692	319317	Mm.294494	NM_175692	ENSMUSG00000044349	Snhg11	A930034L06Rik|AI854265|AL022637|AW319638|E130013N09Rik	small nucleolar RNA host gene 11	protein-coding
mm_14384.1	chr2	129631499	129631512	+	1	NA	3' UTR (NM_001291022, exon 5 of 5)	3' UTR (NM_001291022, exon 5 of 5)	38336	NM_001291022	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_54495.1	chr6	35510232	35510240	-	1	NA	3' UTR (NM_008098, exon 4 of 4)	3' UTR (NM_008098, exon 4 of 4)	29652	NM_008098	14489	Mm.182746	NM_008098	ENSMUSG00000029840	Mtpn	5033418D15Rik|Gcdp|V1	myotrophin	protein-coding
mm_155374.1	chrX	71556310	71556342	+	1	NA	intron (NM_001293623, intron 1 of 4)	CpG	409	NM_001293625	15354	Mm.336087	NM_008253	ENSMUSG00000015217	Hmgb3	Hmg2a|Hmg4	high mobility group box 3	protein-coding
mm_154998.1	chrX	38601210	38601274	+	1	NA	intron (NM_026902, intron 1 of 5)	intron (NM_026902, intron 1 of 5)	584	NM_026902	68995	Mm.262453	NM_026902	ENSMUSG00000000355	Mcts1	1500019M23Rik|MCT-1	malignant T cell amplified sequence 1	protein-coding
mm_131215.1	chr16	8830116	8830142	+	1	NA	promoter-TSS (NM_001081400)	promoter-TSS (NM_001081400)	29	NM_001081400	69053	Mm.390868	NM_001081400	ENSMUSG00000022507	1810013L24Rik	1110017P05Rik|3010002C02Rik|AA792997|AW124177|Gm19906|R74903	RIKEN cDNA 1810013L24 gene	protein-coding
mm_142680.1	chr17	47732499	47732506	-	1	NA	exon (NM_025973, exon 6 of 9)	exon (NM_025973, exon 6 of 9)	-4535	NM_001161722	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_42689.1	chr5	119835122	119835132	+	1	NA	5' UTR (NM_011537, exon 1 of 9)	5' UTR (NM_011537, exon 1 of 9)	464	NM_011537	21388	Mm.103636	NM_011537	ENSMUSG00000018263	Tbx5	-	T-box 5	protein-coding
mm_156178.1	chrX	130395393	130395418	+	1	NA	intron (NM_172493, intron 26 of 26)	(TTTTTG)n|Simple_repeat|Simple_repeat	645663	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diaph2	Dia3|Diap2|Drf2|E430022I22Rik	diaphanous related formin 2	protein-coding
mm_17880.1	chr2	34961752	34961788	-	1	NA	promoter-TSS (NM_001326601)	promoter-TSS (NM_001326601)	2	NM_009421	22029	Mm.239514	NM_009421	ENSMUSG00000026875	Traf1	4732496E14Rik	TNF receptor-associated factor 1	protein-coding
mm_51549.1	chr6	83277356	83277364	+	1	NA	intron (NM_001166067, intron 13 of 24)	intron (NM_001166067, intron 13 of 24)	39985	NM_001166067	232156	Mm.333189	NM_001166067	ENSMUSG00000068323	Slc4a5	C330006M16|C330016K18Rik	solute carrier family 4, sodium bicarbonate cotransporter, member 5	protein-coding
mm_2786.1	chr1	130847474	130847485	+	1	NA	exon (NM_011082, exon 6 of 11)	exon (NM_011082, exon 6 of 11)	-18298	NM_026976	69169	Mm.46042	NM_026976	ENSMUSG00000042474	Fcmr	1810037B05Rik|Faim3|FcmuR|Toso	Fc fragment of IgM receptor	protein-coding
mm_141494.1	chr17	31512254	31512324	-	1	NA	exon (NM_021322, exon 1 of 11)	exon (NM_021322, exon 1 of 11)	198	NM_021322	57773	Mm.143771	NM_021322	ENSMUSG00000024037	Wdr4	AI415180|AI448349|D530049K22Rik	WD repeat domain 4	protein-coding
mm_58343.1	chr6	147243785	147243793	-	1	NA	Intergenic	Lx8|LINE|L1	20224	NM_008970	19227	Mm.28440	NM_008970	ENSMUSG00000048776	Pthlh	PLP|PTH-like|Pthrp	parathyroid hormone-like peptide	protein-coding
mm_88539.1	chr10	78465201	78465216	+	1	NA	promoter-TSS (NM_172134)	promoter-TSS (NM_172134)	-260	NM_172134	216134	Mm.206159	NM_172134	ENSMUSG00000032788	Pdxk	2310036D04Rik|AA119688|C77999	pyridoxal (pyridoxine, vitamin B6) kinase	protein-coding
mm_23537.1	chr3	61002779	61002783	+	1	NA	promoter-TSS (NM_001282016)	promoter-TSS (NM_001282016)	-4	NM_008772	18441	Mm.281452	NM_008772	ENSMUSG00000027765	P2ry1	P2Y1	purinergic receptor P2Y, G-protein coupled 1	protein-coding
mm_58978.1	chr7	19054663	19054674	+	1	NA	promoter-TSS (NM_031255)	promoter-TSS (NM_031255)	-19	NM_031255	83434	Mm.84435	NM_031255	ENSMUSG00000040866	Rsph6a	RSP4|Rshl1	radial spoke head 6 homolog A (Chlamydomonas)	protein-coding
mm_164829.1	chr18	37806470	37806472	+	1	NA	promoter-TSS (NM_033581)	promoter-TSS (NM_033581)	61	NM_033581	93706	Mm.247203	NM_033581	ENSMUSG00000102918	Pcdhgc3	PC43|Pcdh2	protocadherin gamma subfamily C, 3	protein-coding
mm_111959.1	chr12	109561751	109561765	-	1	NA	non-coding (NR_003633, exon 5 of 5)	non-coding (NR_003633, exon 5 of 5)	-1934	NR_030427	791079		NR_030427	ENSMUSG00000076451	Mir770	Mirn770|mir-770|mmu-mir-770	microRNA 770	ncRNA
mm_36690.1	chr4	96591476	96591505	-	1	NA	promoter-TSS (NM_028979)	promoter-TSS (NM_028979)	-5	NM_028979	74519	Mm.458387	NM_028979	ENSMUSG00000015224	Cyp2j9	8430417E17Rik	cytochrome P450, family 2, subfamily j, polypeptide 9	protein-coding
mm_38222.1	chr4	135973639	135973683	-	1	NA	Intergenic	Intergenic	-1067	NM_011942	26394	Mm.34302	NM_011942	ENSMUSG00000028670	Lypla2	LysoII	lysophospholipase 2	protein-coding
mm_45708.1	chr5	84067042	84067068	-	1	NA	intron (NM_007937, intron 15 of 15)	intron (NM_007937, intron 15 of 15)	350327	NM_007937	13839	Mm.137991	NM_007937	ENSMUSG00000029245	Epha5	AI854630|AW125296|Cek7|Ehk1|Els1|Hek7|Rek7|bsk	Eph receptor A5	protein-coding
mm_130264.1	chr15	96643265	96643293	-	1	NA	promoter-TSS (NM_001166456)	promoter-TSS (NM_001166456)	-366	NM_001166458	105727	Mm.103568	NM_134086	ENSMUSG00000023169	Slc38a1	AA408026|AA409865|AL022800|AU015942|NAT2	solute carrier family 38, member 1	protein-coding
mm_153396.1	chr19	40450185	40450204	-	1	NA	intron (NM_001034963, intron 1 of 22)	Lx7|LINE|L1	1204	NM_001034962	20411	Mm.210815	NM_009166	ENSMUSG00000025006	Sorbs1	2310065E01Rik|9530001P15Rik|CAP|SH3P12|Sh3d5|mKIAA1296	sorbin and SH3 domain containing 1	protein-coding
mm_140732.1	chr17	15564300	15564313	-	1	NA	promoter-TSS (NM_144809)	promoter-TSS (NM_144809)	-983	NM_144809	213389	Mm.215162	NM_144809	ENSMUSG00000051977	Prdm9	BC012016|Dsbc1|G1-419-29|Meisetz|PRDM9-B|Rcr1|repro7	PR domain containing 9	protein-coding
mm_5880.1	chr1	53850922	53850962	-	1	NA	intron (NM_001001883, intron 21 of 28)	intron (NM_001001883, intron 21 of 28)	1518	NR_106149	102465783		NR_106149	ENSMUSG00000098443	Mir7681	Gm27806|mmu-mir-7681	microRNA 7681	ncRNA
mm_31950.1	chr4	86748584	86748598	+	1	NA	promoter-TSS (NM_184088)	promoter-TSS (NM_184088)	36	NM_184088	329877	Mm.273718	NM_184088	ENSMUSG00000038024	Dennd4c	1700065A05Rik|AA420392	DENN/MADD domain containing 4C	protein-coding
mm_87759.1	chr10	60284426	60284435	+	1	NA	promoter-TSS (NM_001146124)	promoter-TSS (NM_001146124)	-31	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_58861.1	chr7	16907025	16907033	+	1	NA	exon (NM_008967, exon 1 of 2)	exon (NM_008967, exon 1 of 2)	539	NM_008967	19222	Mm.287572	NM_008967	ENSMUSG00000043017	Ptgir	IP|PGI2	prostaglandin I receptor (IP)	protein-coding
mm_19961.1	chr2	117925440	117925458	-	1	NA	intron (NR_126479, intron 8 of 9)	intron (NR_126479, intron 8 of 9)	103521	NR_040631	73938	Mm.399107	NR_040631	ENSMUSG00000086221	4930412B13Rik	-	RIKEN cDNA 4930412B13 gene	ncRNA
mm_54204.1	chr6	24956107	24956131	-	1	NA	promoter-TSS (NM_177013)	promoter-TSS (NM_177013)	6	NM_177013	319832	Mm.127446	NM_177013	ENSMUSG00000048022	Tmem229a	6332401O19Rik	transmembrane protein 229A	protein-coding
mm_91765.1	chr10	51496492	51496502	-	1	NA	3' UTR (NM_013532, exon 9 of 9)	3' UTR (NM_013532, exon 9 of 9)	5599	NM_013532	14728	Mm.34408	NM_013532	ENSMUSG00000062593	Lilrb4a	CD85K|Gp49b|HM18|ILT3|LIR-5|Lilrb4|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4A	protein-coding
mm_123679.1	chr14	69503221	69503244	-	1	NA	Intergenic	CpG	9317	NM_173420	239167	Mm.259889	NM_173420	ENSMUSG00000047977	Synb	D930020E02Rik|syncytin-B	syncytin b	protein-coding
mm_107861.1	chr12	69843670	69843695	+	1	NA	promoter-TSS (NR_038173)	promoter-TSS (NR_038173)	-4	NR_038173	70934	Mm.440427	NR_038172		4931403G20Rik	-	RIKEN cDNA 4931403G20 gene	ncRNA
mm_52856.1	chr6	122078705	122078707	+	1	NA	exon (NM_008646, exon 27 of 35)	exon (NM_008646, exon 27 of 35)	-57922	NR_003624	381806	Mm.482418	NM_001013775	ENSMUSG00000071204	Gm10319	EG381806|ENSMUSG00000071204	murinoglobulin pseudogene	pseudo
mm_4766.1	chr1	182472184	182472186	+	1	NA	intron (NM_009794, intron 18 of 20)	(CA)n|Simple_repeat|Simple_repeat	45298	NM_009794	12334	Mm.19306	NM_009794	ENSMUSG00000026509	Capn2	AI326419|Capa-2|Capa2|m-calpain|m-calpin	calpain 2	protein-coding
mm_84896.1	chr9	79793546	79793571	-	1	NA	promoter-TSS (NR_040734)	promoter-TSS (NR_040734)	-83	NR_040734	74633	Mm.262175	NR_040734	ENSMUSG00000086918	4930429F24Rik	-	RIKEN cDNA 4930429F24 gene	ncRNA
mm_31815.1	chr4	66827773	66827793	+	1	NA	5' UTR (NM_021297, exon 1 of 3)	5' UTR (NM_021297, exon 1 of 3)	232	NM_021297	21898	Mm.38049	NM_021297	ENSMUSG00000039005	Tlr4	Lps|Ly87|Ran/M1|Rasl2-8	toll-like receptor 4	protein-coding
mm_60038.1	chr7	31037409	31037417	+	1	NA	intron (NM_008761, intron 5 of 8)	intron (NM_008761, intron 5 of 8)	2904	NR_106017	102465635		NR_106017	ENSMUSG00000098783	Mir7050	Gm27578|mmu-mir-7050	microRNA 7050	ncRNA
mm_128698.1	chr15	63270457	63270461	-	1	NA	Intergenic	Intergenic	209149	NR_045279	432958	Mm.255105	NR_045279		Gm20740	-	predicted gene, 20740	ncRNA
mm_79971.1	chr9	66512606	66512632	+	1	NA	intron (NM_175206, intron 1 of 1)	intron (NM_175206, intron 1 of 1)	1974	NM_175206	74165	Mm.297998	NM_175206	ENSMUSG00000050503	Fbxl22	1110004B15Rik	F-box and leucine-rich repeat protein 22	protein-coding
mm_130286.1	chr15	96997085	96997090	-	1	NA	exon (NM_027052, exon 16 of 16)	exon (NM_027052, exon 16 of 16)	58869	NM_027052	69354	Mm.250980	NM_027052	ENSMUSG00000022464	Slc38a4	1110012E16Rik|1700012A18Rik|Ata3|mATA3|mNAT3	solute carrier family 38, member 4	protein-coding
mm_19285.1	chr2	90395172	90395192	-	1	NA	Intergenic	L1Md_F3|LINE|L1	-5458	NM_146263	258330	Mm.330392	NM_146263	ENSMUSG00000082980	Olfr1274-ps	GA_x5J8B7W2BV0-3116-4045|MOR228-4|MOR228-5|Olfr1274	olfactory receptor 1274, pseudogene	protein-coding
mm_149436.1	chr19	11477748	11477760	+	1	NA	intron (NM_028595, intron 4 of 6)	intron (NM_028595, intron 4 of 6)	8386	NM_028595	73656	Mm.440719	NM_028595	ENSMUSG00000079419	Ms4a6c	2200009H22Rik|2210417N07Rik	membrane-spanning 4-domains, subfamily A, member 6C	protein-coding
mm_52447.1	chr6	113660670	113660690	+	1	NA	intron (NM_001113553, intron 2 of 11)	ORR1D2|LTR|ERVL-MaLR	22213	NM_001113553	108960	Mm.152142	NM_172161	ENSMUSG00000060477	Irak2	6330415L08Rik|AI649099|IRAK-2	interleukin-1 receptor-associated kinase 2	protein-coding
mm_29118.1	chr3	105019965	105019968	-	1	NA	intron (NM_001163332, intron 3 of 5)	intron (NM_001163332, intron 3 of 5)	32987	NM_001163333	80281	Mm.200327	NM_030249	ENSMUSG00000062127	Cttnbp2nl	AA552995|AA589392|AU018624|BC003236|mKIAA1433	CTTNBP2 N-terminal like	protein-coding
mm_11466.1	chr2	32288278	32288294	+	1	NA	promoter-TSS (NM_133852)	promoter-TSS (NM_133852)	33	NM_001080968	99412	Mm.106376	NM_133852	ENSMUSG00000002546	Golga2	AW555139|GM130|mKIAA4150	golgi autoantigen, golgin subfamily a, 2	protein-coding
mm_60433.1	chr7	44476877	44476887	+	1	NA	Intergenic	L1MEd|LINE|L1	6535	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_58991.1	chr7	19119854	19119913	+	1	NA	promoter-TSS (NM_175530)	promoter-TSS (NM_175530)	24	NM_175530	243867	Mm.230830	NM_175530	ENSMUSG00000050428	Fbxo46	20D7-FC4|4932704E22Rik|Fbxo34l	F-box protein 46	protein-coding
mm_21252.1	chr2	156312288	156312302	-	1	NA	promoter-TSS (NM_027585)	promoter-TSS (NM_027585)	-178	NM_027585	70873	Mm.475234	NM_027585	ENSMUSG00000038085	Cnbd2	4921517L17Rik|5430421B09Rik|Cris	cyclic nucleotide binding domain containing 2	protein-coding
mm_89529.1	chr10	94493213	94493223	+	1	NA	Intergenic	Intergenic	-21639	NM_172051	319880	Mm.23047	NM_172051	ENSMUSG00000020023	Tmcc3	AW488095|C630016B22Rik|C88213|Tmcc1	transmembrane and coiled coil domains 3	protein-coding
mm_73465.1	chr8	106663884	106663901	+	1	NA	exon (NM_009864, exon 12 of 16)	exon (NM_009864, exon 12 of 16)	-19176	NM_173037	272538	Mm.87151	NM_173037	ENSMUSG00000041949	Tango6	AW413431|E330010G16|Tmco7	transport and golgi organization 6	protein-coding
mm_113226.1	chr13	27065143	27065148	+	1	NA	TTS (NM_011164)	TTS (NM_011164)	7575	NM_011164	19109	Mm.1270	NM_011164	ENSMUSG00000021342	Prl	AV290867|Gha1|Prl1a1	prolactin	protein-coding
mm_123062.1	chr14	55671874	55671918	-	1	NA	promoter-TSS (NM_177992)	promoter-TSS (NM_177992)	10	NM_008683	18002	Mm.296566	NM_008683	ENSMUSG00000010376	Nedd8	Rub1	neural precursor cell expressed, developmentally down-regulated gene 8	protein-coding
mm_38206.1	chr4	135873547	135873606	-	1	NA	intron (NM_026383, intron 1 of 2)	CpG	270	NM_026383	52830	Mm.29159	NM_026383	ENSMUSG00000028675	Pnrc2	0610011E17Rik|D4Bwg0593e	proline-rich nuclear receptor coactivator 2	protein-coding
mm_150734.1	chr19	43731998	43732001	+	1	NA	3' UTR (NM_053103, exon 13 of 13)	3' UTR (NM_053103, exon 13 of 13)	21001	NM_144874	226139	Mm.248237	NM_144874	ENSMUSG00000040018	Cox15	2900026G05Rik	cytochrome c oxidase assembly protein 15	protein-coding
mm_10971.1	chr2	25706827	25706913	+	1	NA	promoter-TSS (NM_023326)	promoter-TSS (NM_023326)	-9	NM_023326	107771	Mm.330057	NM_023326	ENSMUSG00000049086	Bmyc	2900002K07Rik|AW060705|Mycb	brain expressed myelocytomatosis oncogene	protein-coding
mm_162642.1	chr1	191957907	191957910	+	1	NA	Intergenic	Intergenic	-19462	NM_001177900	74023	Mm.274393	NM_023727	ENSMUSG00000049353	Rd3	3322402L07Rik|rd-3|rd3	retinal degeneration 3	protein-coding
mm_9389.1	chr1	172215982	172215989	-	1	NA	exon (NM_009813, exon 4 of 11)	exon (NM_009813, exon 4 of 11)	3910	NM_009813	12372	Mm.12829	NM_009813	ENSMUSG00000007122	Casq1	CSQ|CSQ-1|CSQ1|sCSQ	calsequestrin 1	protein-coding
mm_161209.1	chr13	62383190	62383190	-	1	NA	promoter-TSS (NM_001162910)	promoter-TSS (NM_001162910)	-16	NM_001162910	100041979	Mm.445930	NM_001162910	ENSMUSG00000094942	Gm3604	-	predicted gene 3604	protein-coding
mm_66392.1	chr7	44236130	44236132	-	1	NA	promoter-TSS (NR_029436)	promoter-TSS (NR_029436)	-9	NR_029436	70004	Mm.158317	NR_029436	ENSMUSG00000038782	1700028J19Rik	-	RIKEN cDNA 1700028J19 gene	ncRNA
mm_104097.1	chr11	86694991	86695006	-	1	NA	3' UTR (NM_001003908, exon 32 of 32)	3' UTR (NM_001003908, exon 32 of 32)	10917	NM_001098810	217057	Mm.24868	NM_175004	ENSMUSG00000072582	Ptrh2	A230072I16Rik|Bit1|CGI-147	peptidyl-tRNA hydrolase 2	protein-coding
mm_66086.1	chr7	30966355	30966371	-	1	NA	intron (NM_001164184, intron 2 of 8)	B3|SINE|B2	7106	NM_001164185	54135	Mm.4067	NM_017405	ENSMUSG00000001247	Lsr	ILDR3|Lisch7	lipolysis stimulated lipoprotein receptor	protein-coding
mm_34529.1	chr4	149323984	149323992	+	1	NA	Intergenic	ID_B1|SINE|B4	-10651	NR_131918	74310	Mm.440455	NR_131918	ENSMUSG00000085286	Ube4bos3	1700121F15Rik	ubiquitination factor E4B, opposite strand 3	ncRNA
mm_106277.1	chr11	118130646	118130678	-	1	NA	Intergenic	Intergenic	-1443	NM_001167746	69926	Mm.473893	NM_001167746	ENSMUSG00000033987	Dnah17	2810003K23Rik|Dnahc17|Dnahcl1|Gm1178|mKIAA3028	dynein, axonemal, heavy chain 17	protein-coding
mm_88617.1	chr10	79854619	79854640	+	1	NA	non-coding (NR_029447, exon 1 of 1)	non-coding (NR_029447, exon 1 of 1)	197	NM_001283013	19205	Mm.265610	NM_008956	ENSMUSG00000006498	Ptbp1	AA407203|AL033359|HNRPI|PTB-1|PTB2|PTB3|PTB4|Ptb|pPTB	polypyrimidine tract binding protein 1	protein-coding
mm_18314.1	chr2	57106599	57106621	-	1	NA	TTS (NM_013613)	TTS (NM_013613)	8428	NM_013613	18227	Mm.3507	NM_013613	ENSMUSG00000026826	Nr4a2	HZF-3|NOT|Nurr1|RNR-1|TINOR|TINUR	nuclear receptor subfamily 4, group A, member 2	protein-coding
mm_3493.1	chr1	150106477	150106485	+	1	NA	3' UTR (NM_011198, exon 10 of 10)	3' UTR (NM_011198, exon 10 of 10)	6450	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_146255.1	chr18	77790527	77790531	+	1	NA	Intergenic	Intergenic	-4021	NM_013831	19201	Mm.57174	NM_013831	ENSMUSG00000025429	Pstpip2	MAYP|cmo	proline-serine-threonine phosphatase-interacting protein 2	protein-coding
mm_89018.1	chr10	82102186	82102194	+	1	NA	Intergenic	ORR1A4-int|LTR|ERVL-MaLR	-25823	NM_001163064	216177	Mm.482395	NM_001163064	ENSMUSG00000078435	AU041133	-	expressed sequence AU041133	protein-coding
mm_157762.1	chrX	73659836	73659877	-	1	NA	promoter-TSS (NM_012040)	promoter-TSS (NM_012040)	-2	NM_001199351	93843	Mm.89564	NM_012040	ENSMUSG00000002012	Pnck	Bstk3|CaMKIbeta2|CaMKlb2|Camk1b|Punc|caMKlb1	pregnancy upregulated non-ubiquitously expressed CaM kinase	protein-coding
mm_83676.1	chr9	50233181	50233184	-	1	NA	promoter-TSS (NR_131161)	promoter-TSS (NR_131161)	0	NR_131161	71873		NR_131161	ENSMUSG00000110916	2310003N18Rik	-	RIKEN cDNA 2310003N18 gene	ncRNA
mm_78501.1	chr9	32740035	32740038	+	1	NA	intron (NM_011808, intron 6 of 7)	intron (NM_011808, intron 6 of 7)	43994	NM_001038642	23871	Mm.292415	NM_011808	ENSMUSG00000032035	Ets1	AI196000|AI448617|D230050P06|Ets-1|Tpl1|vs	E26 avian leukemia oncogene 1, 5' domain	protein-coding
mm_66250.1	chr7	35585553	35585567	-	1	NA	promoter-TSS (NM_178263)	promoter-TSS (NM_178263)	22	NM_145840	243923	Mm.222680	NM_145840	ENSMUSG00000056043	Rgs9bp	R9AP|Rgs9-1bp	regulator of G-protein signalling 9 binding protein	protein-coding
mm_125915.1	chr15	76080648	76080656	+	1	NA	intron (NM_133691, intron 1 of 10)	CpG	218	NM_001164600	67959	Mm.29965	NM_028364	ENSMUSG00000002524	Puf60	2410104I19Rik|2810454F19Rik|SIAHBP1	poly-U binding splicing factor 60	protein-coding
mm_86612.1	chr10	13965015	13965043	+	1	NA	Intergenic	CpG	-1350	NM_010437	15273	Mm.42157	NM_010437	ENSMUSG00000015501	Hivep2	Gm20114|MIBP1|Schnurri-2|Shn-2	human immunodeficiency virus type I enhancer binding protein 2	protein-coding
mm_162241.1	chrX	155033307	155033307	-	1	NA	promoter-TSS (NM_020016)	promoter-TSS (NM_020016)	-15	NM_020016	17138	Mm.326653	NM_020016	ENSMUSG00000055746	Magea2	Mage-a2	melanoma antigen, family A, 2	protein-coding
mm_42765.1	chr5	121220248	121220274	+	1	NA	promoter-TSS (NM_181421)	promoter-TSS (NM_181421)	42	NM_181421	269700	Mm.184589	NM_181421	ENSMUSG00000042744	Gm15800	A130010L24|AU042671|BC019639|EG545802|OTTMUSG00000026283|mKIAA0614	predicted gene 15800	protein-coding
mm_42368.1	chr5	114923344	114923354	+	1	NA	intron (NM_145209, intron 1 of 6)	intron (NM_145209, intron 1 of 6)	109	NM_145209	231655	Mm.95479	NM_145209	ENSMUSG00000041827	Oasl1	7530414C13Rik|oasl9	2'-5' oligoadenylate synthetase-like 1	protein-coding
mm_117608.1	chr13	90905322	90905341	-	1	NA	promoter-TSS (NM_001145879)	promoter-TSS (NM_001145879)	24	NM_001145879	435376	Mm.292579	NM_001145879	ENSMUSG00000078958	Atp6ap1l	EG435376	ATPase, H+ transporting, lysosomal accessory protein 1-like	protein-coding
mm_119402.1	chr14	43925335	43925348	+	1	NA	Intergenic	IAPEY4_LTR|LTR|ERVK	-1973	NM_053112	93725	Mm.429087	NM_053112	ENSMUSG00000090166	Ear10	Raf2	eosinophil-associated, ribonuclease A family, member 10	protein-coding
mm_55225.1	chr6	52234227	52234237	-	1	NA	exon (NM_008263, exon 1 of 2)	exon (NM_008263, exon 1 of 2)	707	NM_008263	15395	Mm.5	NM_008263	ENSMUSG00000000938	Hoxa10	Hox-1.8|Hoxa-10	homeobox A10	protein-coding
mm_68194.1	chr7	104369885	104369896	-	1	NA	Intergenic	Intergenic	-11244	NM_175648	244183	Mm.347647	NM_175648	ENSMUSG00000052749	Trim30b	A530023O14Rik|Trim30-1	tripartite motif-containing 30B	protein-coding
mm_36528.1	chr4	86558311	86558332	-	1	NA	promoter-TSS (NM_001081096)	promoter-TSS (NM_001081096)	-18	NM_001081096	75811	Mm.56451	NM_001081096	ENSMUSG00000028492	Saxo1	4930500O09Rik|Fam154a	stabilizer of axonemal microtubules 1	protein-coding
mm_132367.1	chr16	34784918	34784935	+	1	NA	promoter-TSS (NM_139300)	promoter-TSS (NM_139300)	-24	NM_139300	107589	Mm.33360	NM_139300	ENSMUSG00000022836	Mylk	9530072E15Rik|A930019C19Rik|AW489456|KRP|MLCK108|MLCK210|Mlck|nmMlck|smMLCK	myosin, light polypeptide kinase	protein-coding
mm_127948.1	chr15	10720251	10720255	-	1	NA	intron (NR_045065, intron 3 of 3)	intron (NR_045065, intron 3 of 3)	5353	NR_045065	75259	Mm.33928	NR_045063	ENSMUSG00000097058	4930556M19Rik	1700009D01Rik|C130022M03Rik	RIKEN cDNA 4930556M19 gene	ncRNA
mm_18984.1	chr2	76854416	76854440	-	1	NA	exon (NM_011652, exon 125 of 313)	exon (NM_011652, exon 125 of 313)	128119	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_167179.1	chr7	141016115	141016126	-	1	NA	exon (NM_001033632, exon 2 of 2)	exon (NM_001033632, exon 2 of 2)	772	NM_001033632	213002	Mm.276440	NM_001033632	ENSMUSG00000059108	Ifitm6	A330075D07|Dspa2f|Fgls5|fragilis5	interferon induced transmembrane protein 6	protein-coding
mm_21483.1	chr2	163054408	163054420	-	1	NA	promoter-TSS (NM_008652)	promoter-TSS (NM_008652)	-221	NM_008652	17865	Mm.4594	NM_008652	ENSMUSG00000017861	Mybl2	B-Myb|Bmyb	myeloblastosis oncogene-like 2	protein-coding
mm_141216.1	chr17	27167760	27167777	-	1	NA	promoter-TSS (NM_173027)	promoter-TSS (NM_173027)	-4	NM_173027	271424	Mm.209679	NM_173027	ENSMUSG00000024210	Ip6k3	D830007E07Rik|Ihpk3	inositol hexaphosphate kinase 3	protein-coding
mm_53733.1	chr6	145121763	145121795	+	1	NA	promoter-TSS (NM_008511)	promoter-TSS (NM_008511)	40	NM_008511	16970	Mm.843	NM_008511	ENSMUSG00000030263	Lrmp	D6Int3|D6Int4|D6Int5|D6Int7|D6Int8|Jaw1	lymphoid-restricted membrane protein	protein-coding
mm_56699.1	chr6	114875076	114875127	-	1	NA	intron (NM_177683, intron 2 of 4)	intron (NM_177683, intron 2 of 4)	46651	NM_177683	232334	Mm.268357	NM_177683	ENSMUSG00000030315	Vgll4	BC048841|VGL-4	vestigial like family member 4	protein-coding
mm_32601.1	chr4	111972923	111972946	+	1	NA	promoter-TSS (NM_177818)	promoter-TSS (NM_177818)	7	NM_001142775	328505	Mm.226771	NM_177818	ENSMUSG00000049214	Skint7	C130057D23Rik	selection and upkeep of intraepithelial T cells 7	protein-coding
mm_32319.1	chr4	103619488	103619520	+	1	NA	Intergenic	MER45R|DNA|hAT-Tip100	237004	NR_040673	622167	Mm.244115	NR_040673	ENSMUSG00000086136	Gm12718	OTTMUSG00000008109	predicted gene 12718	ncRNA
mm_116485.1	chr13	44197459	44197469	-	1	NA	intron (NR_045088, intron 3 of 3)	RLTR15|LTR|ERVK	19023	NR_045088	100503592	Mm.184925	NR_045088		A330076C08Rik	-	RIKEN cDNA A330076C08 gene	ncRNA
mm_37424.1	chr4	122885944	122885985	-	1	NA	promoter-TSS (NM_007598)	promoter-TSS (NM_007598)	93	NM_007598	12331	Mm.8687	NM_007598	ENSMUSG00000028656	Cap1	-	CAP, adenylate cyclase-associated protein 1 (yeast)	protein-coding
mm_23652.1	chr3	67582738	67582768	+	1	NA	promoter-TSS (NM_025813)	promoter-TSS (NM_025813)	-15	NM_025813	66868	Mm.491153	NM_025813	ENSMUSG00000027775	Mfsd1	1200003O06Rik	major facilitator superfamily domain containing 1	protein-coding
mm_151166.1	chr19	53195470	53195485	+	1	NA	intron (NM_013758, intron 1 of 15)	intron (NM_013758, intron 1 of 15)	51480	NM_013758	27360	Mm.426080	NM_013758	ENSMUSG00000025026	Add3	AI463285|R75380	adducin 3 (gamma)	protein-coding
mm_63607.1	chr7	128173945	128173981	+	1	NA	promoter-TSS (NM_001029872)	promoter-TSS (NM_001029872)	17	NM_001029872	381924	Mm.334257	NM_001029872	ENSMUSG00000070369	Itgad	Cd11d	integrin, alpha D	protein-coding
mm_78455.1	chr9	32372436	32372446	+	1	NA	promoter-TSS (NM_019659)	promoter-TSS (NM_019659)	23	NM_019659	56379	Mm.390168	NM_019659	ENSMUSG00000041248	Kcnj1	Kir1.1|ROMK|Romk2	potassium inwardly-rectifying channel, subfamily J, member 1	protein-coding
mm_3344.1	chr1	137974632	137974639	+	1	NA	Intergenic	Intergenic	7996	NR_029820	723890		NR_029820	ENSMUSG00000065458	Mir181b-1	Mirn181b-1|mir-181b-1	microRNA 181b-1	ncRNA
mm_77979.1	chr9	7870960	7870989	+	1	NA	intron (NM_007464, intron 1 of 8)	intron (NM_007464, intron 1 of 8)	2196	NM_007464	11796	Mm.2026	NM_007464	ENSMUSG00000032000	Birc3	AW107670|Api1|Api2|Birc2|C-IAP2|HIAP2|IAP1|IAP2|MIAP1|MIAP2|MIHB|MIHC|RNF49|cIAP-1|cIAP-2|cIAP1|cIAP2	baculoviral IAP repeat-containing 3	protein-coding
mm_15447.1	chr2	157389296	157389301	+	1	NA	intron (NM_026968, intron 2 of 2)	B3|SINE|B2	21704	NM_026968	69161	Mm.228619	NM_026968	ENSMUSG00000063019	Manbal	1810024K12Rik|AI836500	mannosidase, beta A, lysosomal-like	protein-coding
mm_11500.1	chr2	32535316	32535347	+	1	NA	promoter-TSS (NM_153560)	promoter-TSS (NM_153560)	-28	NM_153560	98952	Mm.4065	NM_153560	ENSMUSG00000039157	Fam102a	AI426465|C230093N12Rik|Eeig1	family with sequence similarity 102, member A	protein-coding
mm_33849.1	chr4	135857887	135857890	+	1	NA	intron (NM_010178, intron 1 of 5)	PB1D9|SINE|Alu	1817	NM_010178	14105	Mm.10229	NM_010178	ENSMUSG00000028676	Srsf10	FUSIP2|Fusip1|NSSR1|NSSR2|Nssr|SRrp40|Sfrs13a|Srsf13a|TASR|TASR1|TASR2	serine/arginine-rich splicing factor 10	protein-coding
mm_31178.1	chr4	43507019	43507034	+	1	NA	promoter-TSS (NM_139305)	promoter-TSS (NM_139305)	0	NM_139305	230099	Mm.283682	NM_139305	ENSMUSG00000028463	Car9	CAIX|Ca9|MN/CA9	carbonic anhydrase 9	protein-coding
mm_54366.1	chr6	31126513	31126537	-	1	NA	intron (NR_110471, intron 3 of 3)	intron (NR_110471, intron 3 of 3)	-63432	NR_029532	387223		NR_029532	ENSMUSG00000065604	Mir29b-1	Mirn29b|Mirn29b-1|mir-29b-1	microRNA 29b-1	ncRNA
mm_40721.1	chr5	65966949	65966952	+	1	NA	promoter-TSS (NM_001081104)	promoter-TSS (NM_001081104)	-174	NM_001081104	231252	Mm.140015	NM_001081104	ENSMUSG00000029205	Chrna9	2410015I05Rik|Acra9|EG666827|Gm8311	cholinergic receptor, nicotinic, alpha polypeptide 9	protein-coding
mm_158298.1	chrX	116287134	116287157	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-161799	NM_001033471	382239	Mm.336224	NM_001033471	ENSMUSG00000072995	Cpxcr1	Gm1143	CPX chromosome region, candidate 1	protein-coding
mm_166396.1	chr5	135013178	135013204	-	1	NA	promoter-TSS (NR_026688)	promoter-TSS (NR_026688)	-34	NR_026688	69812	Mm.18422	NR_026688	ENSMUSG00000085042	Abhd11os	2010001M06Rik|AI462243|Wbscr26|Wnscr26	abhydrolase domain containing 11, opposite strand	ncRNA
mm_63248.1	chr7	126595135	126595187	+	1	NA	promoter-TSS (NM_145636)	promoter-TSS (NM_145636)	-251	NM_145636	246779	Mm.222632	NM_145636	ENSMUSG00000044701	Il27	IL-27|IL-27p28|Il30|p28	interleukin 27	protein-coding
mm_47311.1	chr5	122458484	122458501	-	1	NA	exon (NM_009722, exon 17 of 21)	exon (NM_009722, exon 17 of 21)	36048	NM_019805	56317	Mm.37341	NM_019805	ENSMUSG00000029466	Anapc7	APC7|AW545589	anaphase promoting complex subunit 7	protein-coding
mm_97384.1	chr11	77747006	77747007	+	1	NA	Intergenic	Intergenic	-21713	NM_009965	12957	Mm.22830	NM_009965	ENSMUSG00000000724	Cryba1	BA3/A1|Cryb	crystallin, beta A1	protein-coding
mm_107350.1	chr12	32820498	32820519	+	1	NA	5' UTR (NM_021524, exon 1 of 11)	5' UTR (NM_021524, exon 1 of 11)	173	NM_021524	59027	Mm.202727	NM_021524	ENSMUSG00000020572	Nampt	1110035O14Rik|AI314458|AI480535|NAmPRTase|Pbef|Pbef1|Visfatin	nicotinamide phosphoribosyltransferase	protein-coding
mm_117787.1	chr13	97034385	97034388	-	1	NA	promoter-TSS (NM_001284205)	promoter-TSS (NM_001284205)	-24	NM_001080777	66479	Mm.390629	NM_025585	ENSMUSG00000052075	1700029F12Rik	-	RIKEN cDNA 1700029F12 gene	protein-coding
mm_169969.1	chr17	13163444	13163463	+	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	-31662	NM_199252	381058	Mm.390935	NM_199252	ENSMUSG00000067049	Unc93a	Unc93l|unc-93A	unc-93 homolog A (C. elegans)	protein-coding
mm_26834.1	chr3	11211245	11211253	-	1	NA	Intergenic	RLTR9E|LTR|ERVK	633110	NR_040751	100038545	Mm.388494	NR_040751	ENSMUSG00000104015	Gm10745	ENSMUSG00000074696	predicted gene 10745	ncRNA
mm_52904.1	chr6	122761439	122761440	+	1	NA	Intergenic	Intergenic	-18694	NM_011401	20527	Mm.395108	NM_011401	ENSMUSG00000003153	Slc2a3	AA408729|AL023014|AL024341|AU040424|C78366|Glut-3|Glut3	solute carrier family 2 (facilitated glucose transporter), member 3	protein-coding
mm_25057.1	chr3	98684924	98684932	+	1	NA	Intergenic	AT_rich|Low_complexity|Low_complexity	-39394	NM_008295	15496	Mm.17910	NM_008295	ENSMUSG00000038092	Hsd3b5	-	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 5	protein-coding
mm_110755.1	chr12	70084159	70084162	-	1	NA	intron (NM_001081453, intron 2 of 28)	intron (NM_001081453, intron 2 of 28)	18694	NM_001081453	18080	Mm.244047	NM_008697	ENSMUSG00000021068	Nin	3110068G20Rik|AI385615|AU024711|mKIAA1565	ninein	protein-coding
mm_64791.1	chr7	6286300	6286318	-	1	NA	promoter-TSS (NM_001024928)	promoter-TSS (NM_001024928)	-271	NM_001024928	384763	Mm.276279	NM_001024928	ENSMUSG00000054893	Zfp667	A830025F02Rik|Mip1|ZNF667	zinc finger protein 667	protein-coding
mm_53740.1	chr6	145126632	145126643	+	1	NA	intron (NM_008511, intron 1 of 18)	B3A|SINE|B2	4898	NM_008511	16970	Mm.843	NM_008511	ENSMUSG00000030263	Lrmp	D6Int3|D6Int4|D6Int5|D6Int7|D6Int8|Jaw1	lymphoid-restricted membrane protein	protein-coding
mm_68056.1	chr7	101837736	101837768	-	1	NA	promoter-TSS (NM_001122739)	promoter-TSS (NM_001122739)	72	NM_001122739	16332	Mm.476000	NM_010567	ENSMUSG00000032737	Inppl1	51C|SHIP2	inositol polyphosphate phosphatase-like 1	protein-coding
mm_100460.1	chr11	119856238	119856253	+	1	NA	intron (NM_028898, intron 17 of 33)	intron (NM_028898, intron 17 of 33)	-21880	NR_045312	319454	Mm.442144	NR_045312	ENSMUSG00000085081	Rptoros	A430071A18Rik	regulatory associated protein of MTOR, complex 1, opposite strand	ncRNA
mm_58565.1	chr7	4782963	4782965	+	1	NA	promoter-TSS (NM_030028)	promoter-TSS (NM_030028)	24	NM_030028	78052	Mm.160043	NM_030028	ENSMUSG00000013091	Tmem190	4930572D21Rik	transmembrane protein 190	protein-coding
mm_44810.1	chr5	33518971	33518981	-	1	NA	Intergenic	Intergenic	-84886	NM_011320	672284		NM_011320	ENSMUSG00000029112	Nkx1-1	Nkx-1.1|Sax2	NK1 transcription factor related, locus 1 (Drosophila)	protein-coding
mm_15584.1	chr2	158768084	158768099	+	1	NA	promoter-TSS (NM_027975)	promoter-TSS (NM_027975)	-8	NM_027975	71878	Mm.85162	NM_027975	ENSMUSG00000027654	Fam83d	2310007D09Rik|BB104611	family with sequence similarity 83, member D	protein-coding
mm_126349.1	chr15	79907634	79907652	+	1	NA	3' UTR (NM_001160415, exon 9 of 9)	3' UTR (NM_001160415, exon 9 of 9)	12620	NM_001347041	80287	Mm.284059	NM_030255	ENSMUSG00000009585	Apobec3	Apobec|Arp3|BC003314|Cem15|Rfv3	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 3	protein-coding
mm_157824.1	chrX	74085657	74085672	-	1	NA	promoter-TSS (NM_010788)	promoter-TSS (NM_010788)	26	NM_010788	17257	Mm.131408	NM_010788	ENSMUSG00000031393	Mecp2	1500041B07Rik|D630021H01Rik|Mbd5|WBP10	methyl CpG binding protein 2	protein-coding
mm_19483.1	chr2	93046263	93046298	-	1	NA	promoter-TSS (NM_001177536)	promoter-TSS (NM_001177536)	-136	NM_001177536	100042784	Mm.102816	NM_001177536	ENSMUSG00000075028	Prdm11	8030443D09Rik|AA163972|Gm707	PR domain containing 11	protein-coding
mm_154711.1	chrX	8892377	8892423	+	1	NA	promoter-TSS (NR_045448)	promoter-TSS (NR_045448)	47	NR_045448	102941	Mm.41588	NM_175327	ENSMUSG00000052364	B630019K06Rik	AI843180	novel protein similar to F-box and leucine-rich repeat protein 17 (Fbxl17)	pseudo
mm_151437.1	chr19	57360941	57360952	+	1	NA	promoter-TSS (NM_145505)	promoter-TSS (NM_145505)	-47	NR_040316	320879	Mm.375089	NR_040316	ENSMUSG00000097785	B230217O12Rik	-	RIKEN cDNA B230217O12 gene	ncRNA
mm_79188.1	chr9	48418560	48418585	+	1	NA	Intergenic	Intergenic	-35772	NR_026561	667933	Mm.491076	NR_026561		Gm8884	EG667933	predicted gene 8884	ncRNA
mm_38426.1	chr4	139291100	139291107	-	1	NA	3' UTR (NM_001271405, exon 9 of 9)	3' UTR (NM_001271405, exon 9 of 9)	19597	NM_145384	212555	Mm.45131	NM_145384	ENSMUSG00000028744	Pqlc2	BC019216	PQ loop repeat containing 2	protein-coding
mm_13300.1	chr2	102550046	102550080	+	1	NA	promoter-TSS (NM_173749)	promoter-TSS (NM_173749)	42	NM_173749	210622	Mm.28649	NM_173749	ENSMUSG00000027188	Pamr1	5930437L24|E430002G05Rik|Ramp	peptidase domain containing associated with muscle regeneration 1	protein-coding
mm_153704.1	chr19	44397777	44397782	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	9930	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_44549.1	chr5	24598723	24598766	-	1	NA	exon (NM_025891, exon 2 of 13)	exon (NM_025891, exon 2 of 13)	3258	NM_025891	66993	Mm.436539	NM_025891	ENSMUSG00000028949	Smarcd3	1500001J14Rik|2210409C08Rik|BAF60C	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3	protein-coding
mm_51791.1	chr6	88220786	88220796	+	1	NA	Intergenic	Intergenic	-1477	NM_019964	56691	Mm.272871	NM_019964	ENSMUSG00000048206	Dnajb8	1700016F14Rik|1700031F10Rik|AI326313|mDj6	DnaJ heat shock protein family (Hsp40) member B8	protein-coding
mm_123839.1	chr14	70642157	70642188	-	1	NA	promoter-TSS (NM_008004)	promoter-TSS (NM_008004)	96	NM_008004	14171	Mm.12814	NM_008004	ENSMUSG00000022101	Fgf17	-	fibroblast growth factor 17	protein-coding
mm_65308.1	chr7	24760312	24760327	-	1	NA	promoter-TSS (NM_026862)	promoter-TSS (NM_026862)	-8	NM_026862	68891	Mm.292848	NM_026862	ENSMUSG00000052212	Cd177	1190003K14Rik|Pdp3	CD177 antigen	protein-coding
mm_136593.1	chr17	5012809	5012832	+	1	NA	intron (NM_001085355, intron 1 of 19)	intron (NM_001085355, intron 1 of 19)	17746	NM_001085355	239985	Mm.133401	NM_001085355	ENSMUSG00000069729	Arid1b	8030481M12|9330189K18Rik|AI836955|Ardi1b|B230217J03Rik|mKIAA1235	AT rich interactive domain 1B (SWI-like)	protein-coding
mm_157810.1	chrX	73950440	73950443	-	1	NA	exon (NM_008224, exon 17 of 26)	exon (NM_008224, exon 17 of 26)	15916	NM_008224	15161	Mm.491126	NM_008224	ENSMUSG00000031386	Hcfc1	AW060991|HCF|HCF1	host cell factor C1	protein-coding
mm_59352.1	chr7	25659425	25659446	+	1	NA	promoter-TSS (NM_007533)	promoter-TSS (NM_007533)	282	NR_104358	27998	Mm.27853	NM_138586	ENSMUSG00000061286	Exosc5	D7Wsu180e	exosome component 5	protein-coding
mm_121998.1	chr14	26591640	26591650	-	1	NA	intron (NM_001134465, intron 1 of 19)	intron (NM_001134465, intron 1 of 19)	12095	NM_145969	211922	Mm.260512	NM_145969	ENSMUSG00000040818	Dennd6a	Fam116a	DENN/MADD domain containing 6A	protein-coding
mm_125721.1	chr15	73090848	73090886	+	1	NA	intron (NM_053068, intron 1 of 2)	CpG	455	NM_053068	93696	Mm.23095	NM_053068	ENSMUSG00000068391	Chrac1	2410152E03Rik|2810406L04Rik|YCL1	chromatin accessibility complex 1	protein-coding
mm_2719.1	chr1	128155632	128155633	+	1	NA	intron (NM_181750, intron 3 of 26)	intron (NM_181750, intron 3 of 26)	-46729	NR_029543	387147		NR_029543	ENSMUSG00000065520	Mir128-1	Mirn128|Mirn128-1|Mirn128a|mir-128-1	microRNA 128-1	ncRNA
mm_168930.1	chr12	65742888	65742898	+	1	NA	Intergenic	RLTR9E|LTR|ERVK	517376	NM_027614	70948	Mm.219475	NM_027614	ENSMUSG00000035560	Wdr20rt	4921538B03Rik|4930427E19Rik|Wdr20|Wdr20b	WD repeat domain 20, retrogene	protein-coding
mm_101787.1	chr11	45955466	45955491	-	1	NA	promoter-TSS (NM_001290737)	promoter-TSS (NM_001290737)	25	NM_001080969	66628	Mm.269083	NM_001080969	ENSMUSG00000011254	Thg1l	-	tRNA-histidine guanylyltransferase 1-like (S. cerevisiae)	protein-coding
mm_126421.1	chr15	80572425	80572435	+	1	NA	promoter-TSS (NM_001289442)	promoter-TSS (NM_001289442)	-167	NM_001289442	17444	Mm.12947	NM_010815	ENSMUSG00000042351	Grap2	GRAP-2|GRB2L|GRBLG|GRID|Gads|GrbX|Grf40|GrpL|Mona|P38	GRB2-related adaptor protein 2	protein-coding
mm_120598.1	chr14	70077376	70077384	+	1	NA	promoter-TSS (NM_001289927)	promoter-TSS (NM_001289927)	-65	NM_018781	13655	Mm.103737	NM_018781	ENSMUSG00000033730	Egr3	Pilot	early growth response 3	protein-coding
mm_109938.1	chr12	11265769	11265816	-	1	NA	promoter-TSS (NM_177331)	promoter-TSS (NM_177331)	-5	NM_177331	209334	Mm.215295	NM_177331	ENSMUSG00000051235	Gen1	5830483C08Rik	GEN1, Holliday junction 5' flap endonuclease	protein-coding
mm_114598.1	chr13	75766167	75766170	+	1	NA	exon (NM_138953, exon 9 of 12)	exon (NM_138953, exon 9 of 12)	58684	NM_138953	192657	Mm.21288	NM_138953	ENSMUSG00000001542	Ell2	-	elongation factor RNA polymerase II 2	protein-coding
mm_118072.1	chr13	102958277	102958325	-	1	NA	intron (NM_175171, intron 4 of 28)	intron (NM_175171, intron 4 of 28)	198046	NR_130171	76624	Mm.426384	NR_130171	ENSMUSG00000091906	1700099I09Rik	-	RIKEN cDNA 1700099I09 gene	ncRNA
mm_90175.1	chr10	119692010	119692026	+	1	NA	intron (NM_133442, intron 1 of 21)	intron (NM_133442, intron 1 of 21)	69681	NR_045359	75321	Mm.402041	NR_045359	ENSMUSG00000084764	Grip1os2	4930564G21Rik	glutamate receptor interacting protein 1, opposite strand 2	ncRNA
mm_155986.1	chrX	106137087	106137097	+	1	NA	Intergenic	(T)n|Simple_repeat|Simple_repeat	-6183	NM_205820	279572	Mm.336203	NM_205820	ENSMUSG00000033777	Tlr13	AI666735|Gm713	toll-like receptor 13	protein-coding
mm_164125.1	chr15	38634713	38634721	+	1	NA	Intergenic	PB1|SINE|Alu	-27187	NM_025494	66335	Mm.276618	NM_025494	ENSMUSG00000022295	Atp6v1c1	1700025B18Rik|U13839	ATPase, H+ transporting, lysosomal V1 subunit C1	protein-coding
mm_157224.1	chrX	13846476	13846493	-	1	NA	promoter-TSS (NM_001284505)	promoter-TSS (NM_001284505)	72	NM_001284505	12361	Mm.327591	NM_009806	ENSMUSG00000031012	Cask	DXPri1|DXRib1|LIN-2|Pals3|mLin-2	calcium/calmodulin-dependent serine protein kinase (MAGUK family)	protein-coding
mm_57555.1	chr6	126877298	126877330	-	1	NA	exon (NM_207210, exon 14 of 15)	exon (NM_207210, exon 14 of 15)	24216	NM_009650	11642	Mm.87748	NM_009650	ENSMUSG00000030344	Akap3	Prka3	A kinase (PRKA) anchor protein 3	protein-coding
mm_65161.1	chr7	19671830	19671850	-	1	NA	exon (NM_001309795, exon 4 of 4)	exon (NM_001309795, exon 4 of 4)	2080	NM_001309795	11813	Mm.28394	NM_001277944	ENSMUSG00000002992	Apoc2	apo-CII|apoC-II	apolipoprotein C-II	protein-coding
mm_91516.1	chr10	37138584	37138588	-	1	NA	5' UTR (NM_008538, exon 1 of 2)	5' UTR (NM_008538, exon 1 of 2)	340	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_108987.1	chr12	102757937	102757954	+	1	NA	promoter-TSS (NM_001142939)	promoter-TSS (NM_001142939)	-30	NM_025666	66622	Mm.34261	NM_025666	ENSMUSG00000041712	Ubr7	5730410I19Rik|AA589405|AW557761	ubiquitin protein ligase E3 component n-recognin 7 (putative)	protein-coding
mm_97463.1	chr11	78262478	78262480	+	1	NA	intron (NM_001002004, intron 1 of 38)	intron (NM_001002004, intron 1 of 38)	725	NM_001002004	72503	Mm.237103	NM_001002004	ENSMUSG00000010277	2610507B11Rik	AU022687|D11Bhm178e|D11Bhm179e|E1|Kiaa0100|mKIAA0100	RIKEN cDNA 2610507B11 gene	protein-coding
mm_62526.1	chr7	102233075	102233085	+	1	NA	intron (NR_111937, intron 2 of 5)	intron (NR_111937, intron 2 of 5)	10052	NR_111937	233575	Mm.302013	NM_145583	ENSMUSG00000030990	Pgap2	1810006G21Rik|C76649|Frag1	post-GPI attachment to proteins 2	protein-coding
mm_13607.1	chr2	113327757	113327781	+	1	NA	promoter-TSS (NM_010230)	promoter-TSS (NM_010230)	33	NM_010230	14260	Mm.4938	NM_010230	ENSMUSG00000044042	Fmn1	Fmn|formin-1|ld	formin 1	protein-coding
mm_118373.1	chr13	116968705	116968706	-	1	NA	intron (NM_001081009, intron 3 of 26)	intron (NM_001081009, intron 3 of 26)	56811	NM_001081009	52552	Mm.274466	NM_027272	ENSMUSG00000021725	Parp8	2810430O08Rik|ARTD16|D13Ertd275e	poly (ADP-ribose) polymerase family, member 8	protein-coding
mm_82626.1	chr9	21852604	21852644	-	1	NA	promoter-TSS (NM_177030)	promoter-TSS (NM_177030)	11	NM_177030	319899	Mm.128153	NM_177030	ENSMUSG00000032198	Dock6	2410095B20Rik|4931431C02Rik|C330023D02Rik|mKIAA1395	dedicator of cytokinesis 6	protein-coding
mm_111853.1	chr12	107939147	107939153	-	1	NA	intron (NM_001286343, intron 1 of 1)	intron (NM_001286343, intron 1 of 1)	64264	NM_001079883	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_117034.1	chr13	58274462	58274495	-	1	NA	promoter-TSS (NM_019832)	promoter-TSS (NM_019832)	-290	NM_019832	56278	Mm.296625	NM_019832	ENSMUSG00000021552	Gkap1	42kDa|4933400B15Rik|D13Ertd340e|Gkap42	G kinase anchoring protein 1	protein-coding
mm_95170.1	chr11	40733878	40733931	+	1	NA	promoter-TSS (NM_013552)	promoter-TSS (NM_013552)	243	NM_001290697	52653	Mm.276504	NM_026023	ENSMUSG00000020328	Nudcd2	-	NudC domain containing 2	protein-coding
mm_32003.1	chr4	94614515	94614570	+	1	NA	promoter-TSS (NM_001290568)	promoter-TSS (NM_001290568)	51	NM_026319	67694	Mm.240619	NM_026319	ENSMUSG00000028576	Ift74	1700029H06Rik|Ccdc2|Cmg1|b2b796Clo	intraflagellar transport 74	protein-coding
mm_124449.1	chr14	118923071	118923105	-	1	NA	promoter-TSS (NR_130725)	promoter-TSS (NR_130725)	79	NR_130725	66573	Mm.87456	NM_025943	ENSMUSG00000042156	Dzip1	2510025K24Rik|2810422M04Rik	DAZ interacting protein 1	protein-coding
mm_82291.1	chr9	7763763	7763775	-	1	NA	promoter-TSS (NM_133739)	promoter-TSS (NM_133739)	-308	NM_133739	71929	Mm.283293	NM_133739	ENSMUSG00000050912	Tmem123	2310075C12Rik	transmembrane protein 123	protein-coding
mm_43373.1	chr5	135640809	135640812	+	1	NA	intron (NM_146002, intron 3 of 3)	intron (NM_146002, intron 3 of 3)	8156	NM_146002	215160	Mm.295438	NM_031398	ENSMUSG00000039917	Rhbdd2	0610011L13Rik|AI480532|Rhbdl7|Usmg1	rhomboid domain containing 2	protein-coding
mm_162705.1	chr10	22732021	22732036	+	1	NA	promoter-TSS (NM_011603)	promoter-TSS (NM_011603)	-581	NM_011603	237336	Mm.86670	NM_011603	ENSMUSG00000071359	Tbpl1	4732475G08|AW011832|AW491032|D18347|STD|TLF|TRF2|TRP|Tlp	TATA box binding protein-like 1	protein-coding
mm_67335.1	chr7	79743105	79743113	-	1	NA	promoter-TSS (NM_001037927)	promoter-TSS (NM_001037927)	-54	NM_001037927	626359	Mm.387216	NM_001037927	ENSMUSG00000039099	Wdr93	EG626359	WD repeat domain 93	protein-coding
mm_80636.1	chr9	89211634	89211640	+	1	NA	intron (NM_026829, intron 1 of 2)	intron (NM_026829, intron 1 of 2)	447	NM_026829	107885	Mm.486274	NM_026829	ENSMUSG00000066442	Mthfs	1110034I12Rik|2310020H23Rik|AI119695	5, 10-methenyltetrahydrofolate synthetase	protein-coding
mm_92259.1	chr10	70655935	70655972	-	1	NA	promoter-TSS (NR_045292)	promoter-TSS (NR_045292)	10	NR_045292	319646	Mm.483039	NR_045291	ENSMUSG00000037747	D630013N20Rik	-	RIKEN cDNA D630013N20 gene	ncRNA
mm_160566.1	chr9	55921350	55921350	-	1	NA	intron (NM_001081341, intron 1 of 32)	L1MB7|LINE|L1	16765	NM_001081341	244891	Mm.86588	NM_175536	ENSMUSG00000034007	Scaper	C430017I08|D530014O03Rik|Zfp291	S phase cyclin A-associated protein in the ER	protein-coding
mm_5382.1	chr1	30950018	30950038	-	1	NA	promoter-TSS (NR_002688)	promoter-TSS (NR_002688)	-273	NM_011200	19243	Mm.491181	NM_011200	ENSMUSG00000026064	Ptp4a1	AA415290|AU019864|C130021B01|Prl-1	protein tyrosine phosphatase 4a1	protein-coding
mm_168197.1	chr10	65389871	65389871	-	1	NA	Intergenic	Intergenic	734193	NR_038039	69433	Mm.23366	NR_038039	ENSMUSG00000100000	1700023F02Rik	AV205046	RIKEN cDNA 1700023F02 gene	ncRNA
mm_136293.1	chr16	91464816	91464828	-	1	NA	promoter-TSS (NR_077219)	promoter-TSS (NR_077219)	-282	NR_077219	100503120	Mm.387130	NR_077219	ENSMUSG00000084866	A930006K02Rik	-	RIKEN cDNA A930006K02 gene	ncRNA
mm_112296.1	chr12	114584035	114584063	-	1	NA	Intergenic	Intergenic	-70355	NR_106063	102465664		NR_106063	ENSMUSG00000098357	Mir7094-2	Gm27508|mmu-mir-7094-2	microRNA 7094-2	ncRNA
mm_69598.1	chr7	135716375	135716386	-	1	NA	promoter-TSS (NM_001081117)	promoter-TSS (NM_001081117)	-1	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_14024.1	chr2	122151036	122151085	+	1	NA	exon (NM_009735, exon 2 of 4)	exon (NM_009735, exon 2 of 4)	3373	NM_009735	12010	Mm.163	NM_009735	ENSMUSG00000060802	B2m	Ly-m11|beta2-m|beta2m	beta-2 microglobulin	protein-coding
mm_123142.1	chr14	56778302	56778352	-	1	NA	promoter-TSS (NM_025682)	promoter-TSS (NM_025682)	-11	NM_025682	66645	Mm.20129	NM_025682	ENSMUSG00000021938	Pspc1	5730470C09Rik|AI327109|AI449052|PSP1	paraspeckle protein 1	protein-coding
mm_22542.1	chr3	8881144	8881152	+	1	NA	intron (NM_025434, intron 2 of 2)	intron (NM_025434, intron 2 of 2)	42709	NM_025434	66230	Mm.38460	NM_025434	ENSMUSG00000040269	Mrps28	1500012D08Rik|AW061224	mitochondrial ribosomal protein S28	protein-coding
mm_63859.1	chr7	135675211	135675260	+	1	NA	intron (NM_001316681, intron 14 of 17)	L1MB7|LINE|L1	-22921	NR_015548	67765	Mm.445272	NR_015548	ENSMUSG00000097471	5830432E09Rik	-	RIKEN cDNA 5830432E09 gene	ncRNA
mm_152749.1	chr19	19111182	19111203	-	1	NA	promoter-TSS (NM_001043354)	promoter-TSS (NM_001043354)	4	NM_001043354	225998	Mm.234641	NM_146095	ENSMUSG00000036192	Rorb	Nr1f2|RZR-beta|RZRB|Rorbeta|hstp	RAR-related orphan receptor beta	protein-coding
mm_142027.1	chr17	35219597	35219611	-	1	NA	TTS (NM_010909)	TTS (NM_010909)	-14253	NM_010735	16992	Mm.87787	NM_010735	ENSMUSG00000024402	Lta	LT|LT-[a]|LT-alpha|LT[a]|LTalpha|Ltx|TNF-beta|TNFSF1|Tnfb|Tnfsf1b|Tnlg1e|hlb382	lymphotoxin A	protein-coding
mm_137861.1	chr17	31212107	31212121	+	1	NA	intron (NM_177823, intron 2 of 13)	ORR1C1|LTR|ERVL-MaLR	4048	NM_177823	328795	Mm.387930	NM_177823	ENSMUSG00000042345	Ubash3a	5830413C03Rik|C330001M22|Sts-2|TULA|TULA-1	ubiquitin associated and SH3 domain containing, A	protein-coding
mm_82793.1	chr9	29411781	29411811	-	1	NA	intron (NM_172290, intron 1 of 7)	CpG	551333	NM_172290	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding
mm_29962.1	chr3	133463908	133463910	-	1	NA	3' UTR (NM_001346736, exon 12 of 12)	3' UTR (NM_001346736, exon 12 of 12)	80481	NM_001346736	214133	Mm.347816	NM_145989	ENSMUSG00000040943	Tet2	Ayu17-449|E130014J05Rik|mKIAA1546	tet methylcytosine dioxygenase 2	protein-coding
mm_77346.1	chr8	119574841	119574851	-	1	NA	promoter-TSS (NM_026648)	promoter-TSS (NM_026648)	354	NM_175185	72552	Mm.36756	NM_175185	ENSMUSG00000034189	Hsdl1	2700067E09Rik	hydroxysteroid dehydrogenase like 1	protein-coding
mm_106776.1	chr12	4629904	4629921	+	1	NA	exon (NM_001198969, exon 7 of 17)	exon (NM_001198969, exon 7 of 17)	36904	NM_001198968	20403	Mm.341204	NM_011365	ENSMUSG00000020640	Itsn2	AI327390|Ese2|Sh3d1B|Sh3p18|mKIAA1256	intersectin 2	protein-coding
mm_101147.1	chr11	16591669	16591674	-	1	NA	Intergenic	Intergenic	-83187	NM_001109971	20335	Mm.325350	NM_011343	ENSMUSG00000078974	Sec61g	-	SEC61, gamma subunit	protein-coding
mm_49905.1	chr6	38980997	38981004	+	1	NA	intron (NM_011539, intron 3 of 12)	intron (NM_011539, intron 3 of 12)	62014	NM_011539	21391	Mm.4054	NM_011539	ENSMUSG00000029925	Tbxas1	CYP5|CYP5A1|THAS|TS|TXAS|TXS	thromboxane A synthase 1, platelet	protein-coding
mm_114654.1	chr13	77961327	77961328	+	1	NA	intron (NM_001163420, intron 6 of 8)	T-rich|Low_complexity|Low_complexity	-63575	NM_029315	75507	Mm.443255	NM_029315	ENSMUSG00000093668	Pou5f2	1700013G10Rik|SPRM-1|Sprm1	POU domain class 5, transcription factor 2	protein-coding
mm_153713.1	chr19	44400187	44400235	-	1	NA	exon (NM_009127, exon 5 of 6)	exon (NM_009127, exon 5 of 6)	7498	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_5439.1	chr1	34842978	34842984	-	1	NA	promoter-TSS (NM_001160236)	promoter-TSS (NM_001160236)	69	NM_001160235	214469	Mm.120151	NM_174997	ENSMUSG00000037503	Fam168b	mKIAA4042	family with sequence similarity 168, member B	protein-coding
mm_38188.1	chr4	135334214	135334218	-	1	NA	intron (NM_016799, intron 9 of 17)	intron (NM_016799, intron 9 of 17)	18998	NM_016799	51796	Mm.1963	NM_016799	ENSMUSG00000028809	Srrm1	AA407769|POP101|Srm160	serine/arginine repetitive matrix 1	protein-coding
mm_156310.1	chrX	136838129	136838144	+	1	NA	3' UTR (NM_011123, exon 7 of 7)	3' UTR (NM_011123, exon 7 of 7)	15390	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_78442.1	chr9	32116041	32116049	+	1	NA	promoter-TSS (NM_001195632)	promoter-TSS (NM_001195632)	-91	NM_001195632	330914	Mm.46683	NM_177379	ENSMUSG00000041444	Arhgap32	3426406O18Rik|Gc-gap|Grit|Px-rics|Rics|mKIAA0712|p200Rhogap|p250Gap	Rho GTPase activating protein 32	protein-coding
mm_86627.1	chr10	13967135	13967200	+	1	NA	intron (NM_010437, intron 1 of 8)	CpG-904	788	NM_010437	15273	Mm.42157	NM_010437	ENSMUSG00000015501	Hivep2	Gm20114|MIBP1|Schnurri-2|Shn-2	human immunodeficiency virus type I enhancer binding protein 2	protein-coding
mm_159730.1	chr5	45639723	45639723	-	1	NA	promoter-TSS (NM_021416)	promoter-TSS (NM_021416)	-222	NM_021416	58227	Mm.266466	NM_021416	ENSMUSG00000015879	Fam184b	9630031F12Rik|AB041544	family with sequence similarity 184, member B	protein-coding
mm_151821.1	chr19	5560571	5560582	-	1	NA	promoter-TSS (NM_019935)	promoter-TSS (NM_019935)	-1	NM_019935	18426	Mm.280225	NM_019935	ENSMUSG00000024922	Ovol1	BB147136|Ovo1|movo1	ovo like zinc finger 1	protein-coding
mm_52844.1	chr6	121838515	121838528	+	1	NA	promoter-TSS (NM_008645)	promoter-TSS (NM_008645)	-20	NM_008645	17836	Mm.1311	NM_008645	ENSMUSG00000059908	Mug1	-	murinoglobulin 1	protein-coding
mm_62622.1	chr7	107567425	107567440	+	1	NA	promoter-TSS (NM_172907)	promoter-TSS (NM_172907)	-1	NM_172907	244198	Mm.77425	NM_172907	ENSMUSG00000051041	Olfml1	6720478C22|AV321997|BC047207|MVAL564|ONT2|mONT2	olfactomedin-like 1	protein-coding
mm_57343.1	chr6	124747403	124747428	-	1	NA	exon (NM_007881, exon 5 of 10)	exon (NM_007881, exon 5 of 10)	-6336	NM_013535	14790	Mm.439877	NM_013535	ENSMUSG00000072772	Grcc10	2310033H05Rik|C10	gene rich cluster, C10 gene	protein-coding
mm_82512.1	chr9	20521361	20521371	-	1	NA	promoter-TSS (NM_001135019)	promoter-TSS (NM_001135019)	53	NM_001135019	77519	Mm.431849	NM_001082485	ENSMUSG00000060510	Zfp266	5330440G10Rik|5730601F06Rik|AW552317	zinc finger protein 266	protein-coding
mm_70081.1	chr7	142653935	142653946	-	1	NA	TTS (NR_030251)	TTS (NR_030251)	1056	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_64459.1	chr7	142660624	142660648	+	1	NA	non-coding (NR_002855, exon 1 of 4)	non-coding (NR_002855, exon 1 of 4)	635	NM_001122736	16002	Mm.3862	NM_010514	ENSMUSG00000048583	Igf2	AL033362|Igf-2|Igf-II|M6pr|Mpr|Peg2	insulin-like growth factor 2	protein-coding
mm_33304.1	chr4	129033435	129033447	+	1	NA	Intergenic	Intergenic	-24830	NM_029219	75234	Mm.259672	NM_029219	ENSMUSG00000028793	Rnf19b	4930534K13Rik|4930555L03Rik|Ibrdc3	ring finger protein 19B	protein-coding
mm_148805.1	chr19	6275922	6275928	+	1	NA	promoter-TSS (NM_010119)	promoter-TSS (NM_010119)	-971	NM_010119	13660	Mm.30169	NM_010119	ENSMUSG00000024772	Ehd1	AA409636|Past1|RME-1	EH-domain containing 1	protein-coding
mm_31331.1	chr4	46451147	46451157	+	1	NA	5' UTR (NM_130889, exon 1 of 7)	5' UTR (NM_130889, exon 1 of 7)	226	NM_130889	67628	Mm.263913	NM_130889	ENSMUSG00000028333	Anp32b	2410015B15Rik|PAL31|PHAPI2a|Ssp29	acidic (leucine-rich) nuclear phosphoprotein 32 family, member B	protein-coding
mm_30937.1	chr4	32983524	32983534	+	1	NA	exon (NM_027491, exon 1 of 7)	exon (NM_027491, exon 1 of 7)	531	NM_027491	52187	Mm.300814	NM_027491	ENSMUSG00000028278	Rragd	5730543C08Rik|AI467523|C030003H22Rik|D4Ertd174e	Ras-related GTP binding D	protein-coding
mm_134439.1	chr16	18247367	18247387	-	1	NA	exon (NM_011239, exon 2 of 6)	exon (NM_011239, exon 2 of 6)	1317	NM_011239	19385	Mm.235287	NM_011239	ENSMUSG00000005732	Ranbp1	Htf9a	RAN binding protein 1	protein-coding
mm_105222.1	chr11	102224774	102224821	-	1	NA	5' UTR (NM_001284249, exon 2 of 28)	5' UTR (NM_001284249, exon 2 of 28)	5353	NR_106179	102465892		NR_106179	ENSMUSG00000098863	Mir8101	Gm27705|mmu-mir-8101	microRNA 8101	ncRNA
mm_57968.1	chr6	135319556	135319567	-	1	NA	Intergenic	Intergenic	-9177	NM_029595	76400	Mm.293018	NM_029595	ENSMUSG00000047104	Pbp2	1700023A18Rik|AI326308|Pebp-2|Pebp2	phosphatidylethanolamine binding protein 2	protein-coding
mm_151416.1	chr19	56722141	56722153	+	1	NA	promoter-TSS (NM_007419)	promoter-TSS (NM_007419)	-225	NM_007419	11554	Mm.46797	NM_007419	ENSMUSG00000035283	Adrb1	Adrb-1|beta-AR	adrenergic receptor, beta 1	protein-coding
mm_33482.1	chr4	130818943	130818953	+	1	NA	exon (NM_011520, exon 3 of 5)	exon (NM_011520, exon 3 of 5)	26411	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_26260.1	chr3	142500608	142500619	+	1	NA	exon (NM_153564, exon 2 of 11)	exon (NM_153564, exon 2 of 11)	3679	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_148792.1	chr19	6165739	6165751	+	1	NA	intron (NM_028967, intron 1 of 2)	B3A|SINE|B2	1287	NM_028967	74481	Mm.159219	NM_028967	ENSMUSG00000039699	Batf2	4933430F08Rik	basic leucine zipper transcription factor, ATF-like 2	protein-coding
mm_122260.1	chr14	34274231	34274249	-	1	NA	intron (NM_029389, intron 2 of 10)	intron (NM_029389, intron 2 of 10)	36263	NM_029389	75698	Mm.45406	NM_029389	ENSMUSG00000041471	Fam35a	3110001K24Rik	family with sequence similarity 35, member A	protein-coding
mm_157848.1	chrX	74393212	74393267	-	1	NA	promoter-TSS (NM_001161424)	promoter-TSS (NM_001161424)	35	NM_025473	66294	Mm.166485	NM_025473	ENSMUSG00000031399	Fam3a	1810037C20Rik	family with sequence similarity 3, member A	protein-coding
mm_144107.1	chr18	4165857	4165868	+	1	NA	promoter-TSS (NM_026092)	promoter-TSS (NM_026092)	30	NM_026092	67328	Mm.158148	NM_026092	ENSMUSG00000024233	Lyzl1	1700038F02Rik|Lyc2|Lyzd1	lysozyme-like 1	protein-coding
mm_11733.1	chr2	37516593	37516606	+	1	NA	promoter-TSS (NM_177383)	promoter-TSS (NM_177383)	-27	NM_177383	338346	Mm.445325	NM_177383	ENSMUSG00000053164	Gpr21	C230004C13Rik	G protein-coupled receptor 21	protein-coding
mm_6008.1	chr1	58973451	58973461	-	1	NA	promoter-TSS (NM_172406)	promoter-TSS (NM_172406)	26	NM_172406	70827	Mm.222887	NM_172406	ENSMUSG00000026028	Trak2	2900022D04Rik|4733401O11Rik|AI480836|AW046271|Als2cr3|CALS-C|GRIF-1|GRIF1|OIP98|mKIAA0549	trafficking protein, kinesin binding 2	protein-coding
mm_18170.1	chr2	45106897	45106907	-	1	NA	intron (NM_001289521, intron 1 of 8)	AT_rich|Low_complexity|Low_complexity	3375	NM_001289521	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_156021.1	chrX	107148987	107149006	+	1	NA	promoter-TSS (NM_175442)	promoter-TSS (NM_175442)	69	NM_001122596	213438	Mm.265244	NM_175442	ENSMUSG00000054293	A630033H20Rik	AI662791|P2ry10	RIKEN cDNA A630033H20 gene	protein-coding
mm_57422.1	chr6	124913970	124913994	-	1	NA	3' UTR (NM_026988, exon 5 of 5)	3' UTR (NM_026988, exon 5 of 5)	-2277	NM_008479	16768	Mm.4528	NM_008479	ENSMUSG00000030124	Lag3	CD223|LAG-3|Ly66	lymphocyte-activation gene 3	protein-coding
mm_87763.1	chr10	60292501	60292514	+	1	NA	exon (NM_011179, exon 3 of 15)	exon (NM_011179, exon 3 of 15)	8046	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_156125.1	chrX	116659071	116659077	+	1	NA	Intergenic	U1|snRNA|snRNA	-22104	NM_001281530	624153		NM_001281530	ENSMUSG00000082482	H2afb2	EG624153|H2A.Bbd4|H2afb2-ps	H2A histone family, member B2	protein-coding
mm_43121.1	chr5	124862199	124862232	+	1	NA	promoter-TSS (NM_001081750)	promoter-TSS (NM_001081750)	6	NM_144819	215707	Mm.389693	NM_144819	ENSMUSG00000037979	Ccdc92	AW050178|D5Bwg0834e	coiled-coil domain containing 92	protein-coding
mm_41127.1	chr5	87786639	87786649	+	1	NA	exon (NM_001304768, exon 11 of 13)	exon (NM_001304768, exon 11 of 13)	12194	NM_007785	12993	Mm.4908	NM_007785	ENSMUSG00000061937	Csn1s2a	Csng|PP22	casein alpha s2-like A	protein-coding
mm_162673.1	chr10	7473554	7473598	-	1	NA	promoter-TSS (NM_029975)	promoter-TSS (NM_029975)	-99	NM_029975	77777	Mm.442442	NM_029975	ENSMUSG00000079685	Ulbp1	A430108B07Rik|MULT1	UL16 binding protein 1	protein-coding
mm_135506.1	chr16	46498558	46498571	-	1	NA	Intergenic	Intergenic	-1597	NM_021497	58998	Mm.40477	NM_021495	ENSMUSG00000022656	Nectin3	2610301B19Rik|3000002N23Rik|4921513D19Rik|AA407785|AU016832|AW538082|CD113|Pvrl3	nectin cell adhesion molecule 3	protein-coding
mm_82274.1	chr9	7353029	7353059	-	1	NA	exon (NM_008605, exon 5 of 10)	exon (NM_008605, exon 5 of 10)	5670	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_56224.1	chr6	90232806	90232846	-	1	NA	Intergenic	L1Md_F|LINE|L1	-8388	NM_053226	113853	Mm.434332	NM_053226	ENSMUSG00000057697	Vmn1r53	V1rb3|VN5	vomeronasal 1 receptor 53	protein-coding
mm_49934.1	chr6	39446908	39446913	+	1	NA	Intergenic	PB1D9|SINE|Alu	-26541	NM_018810	54484	Mm.270484	NM_018810	ENSMUSG00000029922	Mkrn1	RFP	makorin, ring finger protein, 1	protein-coding
mm_14215.1	chr2	127337555	127337557	+	1	NA	intron (NM_010090, intron 3 of 3)	intron (NM_010090, intron 3 of 3)	-1083	NM_172539	215095	Mm.31313	NM_172539	ENSMUSG00000050468	Astl	7420700F21|C87576|Sas1b	astacin-like metalloendopeptidase (M12 family)	protein-coding
mm_162538.1	chr1	168432574	168432578	+	1	NA	promoter-TSS (NM_001291509)	promoter-TSS (NM_001291509)	-407	NM_008783	18514	Mm.43358	NM_008783	ENSMUSG00000052534	Pbx1	2310056B04Rik|D230003C07Rik|Pbx-1	pre B cell leukemia homeobox 1	protein-coding
mm_94341.1	chr11	4729890	4729894	+	1	NA	intron (NM_026015, intron 3 of 5)	intron (NM_026015, intron 3 of 5)	16886	NM_138948	192650	Mm.207056	NM_138948	ENSMUSG00000009075	Cabp7	-	calcium binding protein 7	protein-coding
mm_21164.1	chr2	154613204	154613227	-	1	NA	promoter-TSS (NM_199304)	promoter-TSS (NM_199304)	-153	NM_199304	228807	Mm.103555	NM_199304	ENSMUSG00000059842	Zfp341	Znf341	zinc finger protein 341	protein-coding
mm_32685.1	chr4	115834968	115834977	+	1	NA	3' UTR (NM_175308, exon 4 of 4)	3' UTR (NM_175308, exon 4 of 4)	-4226	NM_001285488	17346	Mm.209327	NM_021461	ENSMUSG00000028708	Mknk1	2410048M24Rik|Mnk1	MAP kinase-interacting serine/threonine kinase 1	protein-coding
mm_58926.1	chr7	17972160	17972173	+	1	NA	promoter-TSS (NM_023289)	promoter-TSS (NM_023289)	-1	NM_023289	66996	Mm.36666	NM_023289	ENSMUSG00000030368	Ceacam11	1600015D01Rik	carcinoembryonic antigen-related cell adhesion molecule 11	protein-coding
mm_170875.1	chr2	20899933	20899944	+	1	NA	intron (NM_001128084, intron 3 of 24)	LSU-rRNA_Hsa|rRNA|rRNA	67783	NM_001081364	71435	Mm.28507	NM_001081364	ENSMUSG00000036591	Arhgap21	5530401C11Rik|AA416458|ARHGAP10	Rho GTPase activating protein 21	protein-coding
mm_144853.1	chr18	36664107	36664124	+	1	NA	promoter-TSS (NM_201256)	promoter-TSS (NM_201256)	55	NM_201256	108112	Mm.24790	NM_201256	ENSMUSG00000090264	Eif4ebp3	4e-bp3	eukaryotic translation initiation factor 4E binding protein 3	protein-coding
mm_60779.1	chr7	45565020	45565040	+	1	NA	intron (NM_025330, intron 6 of 8)	RLTR9A|LTR|ERVK	-5123	NM_009737	12036	Mm.24210	NM_009737	ENSMUSG00000030826	Bcat2	Bcat-2|Eca40	branched chain aminotransferase 2, mitochondrial	protein-coding
mm_125081.1	chr15	26309021	26309026	+	1	NA	promoter-TSS (NM_001310774)	promoter-TSS (NM_001310774)	-25	NM_177597	211147	Mm.54257	NM_177597	ENSMUSG00000022269	March11	9630025C22	membrane-associated ring finger (C3HC4) 11	protein-coding
mm_137223.1	chr17	24251661	24251679	+	1	NA	promoter-TSS (NM_007634)	promoter-TSS (NM_007634)	-261	NM_007634	12449	Mm.77695	NM_007634	ENSMUSG00000072082	Ccnf	CycF|Fbxo1	cyclin F	protein-coding
mm_97917.1	chr11	83526004	83526027	+	1	NA	exon (NM_013653, exon 3 of 3)	exon (NM_013653, exon 3 of 3)	-3916	NM_001045543	629303	Mm.390417	NM_001045543	ENSMUSG00000018925	Heatr9	Gm11435|OTTMUSG00000000990	HEAT repeat containing 9	protein-coding
mm_163497.1	chr12	111713326	111713340	+	1	NA	promoter-TSS (NM_026511)	promoter-TSS (NM_026511)	64	NM_026511	68020	Mm.425762	NM_026511	ENSMUSG00000037787	Apopt1	1700081D05Rik|2810002N01Rik|Apop-1|Apop1	apoptogenic, mitochondrial 1	protein-coding
mm_157051.1	chrX	8039006	8039019	-	1	NA	Intergenic	Intergenic	-20520	NM_027227	69824	Mm.279756	NM_027227	ENSMUSG00000031163	Glod5	2010001H14Rik|AV061890	glyoxalase domain containing 5	protein-coding
mm_133667.1	chr16	92060151	92060154	+	1	NA	intron (NM_080456, intron 1 of 2)	intron (NM_080456, intron 1 of 2)	1816	NM_080456	121022	Mm.217354	NM_080456	ENSMUSG00000039680	Mrps6	AW046321	mitochondrial ribosomal protein S6	protein-coding
mm_168319.1	chr11	114668541	114668543	+	1	NA	promoter-TSS (NM_001048058)	promoter-TSS (NM_001048058)	-1	NM_023372	67671	Mm.238817	NM_023372	ENSMUSG00000057322	Rpl38	0610025G13Rik|Rbt|Ts|Tss	ribosomal protein L38	protein-coding
mm_136978.1	chr17	15777569	15777571	+	1	NA	Intergenic	RLTR10C|LTR|ERVK	49016	NM_178615	68799	Mm.293466	NM_178615	ENSMUSG00000048027	Rgmb	1110059F19Rik|DRAGON	repulsive guidance molecule family member B	protein-coding
mm_126816.1	chr15	88708465	88708483	+	1	NA	intron (NM_001033274, intron 6 of 12)	ORR1A2|LTR|ERVL-MaLR	25745	NM_001033274	223770	Mm.254438	NM_001033274	ENSMUSG00000022387	Brd1	1110059H06Rik|AI316859|mKIAA4191	bromodomain containing 1	protein-coding
mm_87142.1	chr10	34483451	34483479	+	1	NA	promoter-TSS (NM_001159544)	promoter-TSS (NM_001159544)	65	NM_010237	14302	Mm.332432	NM_010237	ENSMUSG00000019779	Frk	BSK|BSK/IYK|C85044|GTK|RAK	fyn-related kinase	protein-coding
mm_43808.1	chr5	142904176	142904187	+	1	NA	exon (NM_007393, exon 5 of 6)	exon (NM_007393, exon 5 of 6)	2573	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_11120.1	chr2	28208156	28208167	+	1	NA	exon (NM_001038613, exon 2 of 6)	exon (NM_001038613, exon 2 of 6)	2472	NM_019498	56177	Mm.43278	NM_019498	ENSMUSG00000026833	Olfm1	AMY|AW742568|Noe1|OlfA|Pancortin|Pancortin3	olfactomedin 1	protein-coding
mm_150641.1	chr19	41831273	41831276	+	1	NA	3' UTR (NM_008043, exon 1 of 1)	3' UTR (NM_008043, exon 1 of 1)	1304	NM_008043	14296	Mm.4573	NM_008043	ENSMUSG00000067199	Frat1	AW060382	frequently rearranged in advanced T cell lymphomas	protein-coding
mm_132896.1	chr16	48844230	48844240	+	1	NA	exon (NM_020509, exon 4 of 4)	exon (NM_020509, exon 4 of 4)	1683	NM_020509	57262	Mm.441868	NM_020509	ENSMUSG00000061100	Retnla	1810019L16Rik|Fizz-1|Fizz1|HIMF|RELM-alpha|RELMa|RELMalpha|Xcp2	resistin like alpha	protein-coding
mm_42829.1	chr5	122101147	122101159	+	1	NA	intron (NM_010861, intron 1 of 6)	intron (NM_010861, intron 1 of 6)	173	NM_010861	17906	Mm.1529	NM_010861	ENSMUSG00000013936	Myl2	MLC-2|MLC-2s/v|MLC-2v|Mlc2v|Mylpc	myosin, light polypeptide 2, regulatory, cardiac, slow	protein-coding
mm_118298.1	chr13	113079174	113079184	-	1	NA	intron (NM_001281487, intron 7 of 11)	intron (NM_001281487, intron 7 of 11)	21802	NM_010370	14938	Mm.15510	NM_010370	ENSMUSG00000023132	Gzma	AW494114|Ctla-3|Ctla3|Hf|Hf1|SE1|TSP-1|TSP1	granzyme A	protein-coding
mm_117345.1	chr13	69611315	69611333	-	1	NA	promoter-TSS (NM_145354)	promoter-TSS (NM_145354)	139	NM_175283	78925	Mm.451912	NM_175283	ENSMUSG00000021594	Srd5a1	0610031P22Rik|4930435F02Rik|S5AR 1|Srd5a-1	steroid 5 alpha-reductase 1	protein-coding
mm_109571.1	chr12	112106842	112106887	+	1	NA	5' UTR (NM_001081169, exon 1 of 15)	5' UTR (NM_001081169, exon 1 of 15)	181	NM_001081169	104816	Mm.77133	NM_001081169	ENSMUSG00000037686	Aspg	A530050D06Rik|AI429460|Gm690	asparaginase	protein-coding
mm_115779.1	chr13	19311448	19311456	-	1	NA	Intergenic	Intergenic	84361	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_78758.1	chr9	43303215	43303225	+	1	NA	Intergenic	MIR|SINE|MIR	-7543	NM_023655	72169	Mm.273277	NM_023655	ENSMUSG00000032013	Trim29	1110047J21Rik|2810431N19Rik|4732461M22Rik|AI119726	tripartite motif-containing 29	protein-coding
mm_58317.1	chr6	146443028	146443031	-	1	NA	intron (NM_010586, intron 2 of 55)	intron (NM_010586, intron 2 of 55)	59194	NM_010586	16439	Mm.7800	NM_010586	ENSMUSG00000030287	Itpr2	AI649341|InsP3R-2|InsP3R-5|Ip3r2|Itpr5|insP3R2	inositol 1,4,5-triphosphate receptor 2	protein-coding
mm_24564.1	chr3	93443894	93443903	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	1568	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_13305.1	chr2	102658281	102658311	+	1	NA	promoter-TSS (NM_001077514)	promoter-TSS (NM_001077514)	-387	NM_001077514	20511	Mm.267547	NM_011393	ENSMUSG00000005089	Slc1a2	1700091C19Rik|2900019G14Rik|AI159670|Eaat2|GLT-1|GLT1|MGLT1	solute carrier family 1 (glial high affinity glutamate transporter), member 2	protein-coding
mm_153183.1	chr19	34499008	34499020	-	1	NA	intron (NM_001111100, intron 8 of 9)	RSINE1|SINE|B4	-23879	NM_009890	12642	Mm.30824	NM_009890	ENSMUSG00000050370	Ch25h	AI462618|m25OH	cholesterol 25-hydroxylase	protein-coding
mm_171795.1	chr5	118052609	118052610	+	1	NA	intron (NM_021344, intron 2 of 7)	intron (NM_021344, intron 2 of 7)	24785	NM_021344	57816	Mm.273285	NM_021344	ENSMUSG00000029359	Tesc	1010001A17Rik|2410011K10Rik|TE-1	tescalcin	protein-coding
mm_52766.1	chr6	120932874	120932890	+	1	NA	3' UTR (NM_001270475, exon 32 of 32)	3' UTR (NM_001270475, exon 32 of 32)	-16062	NM_007544	12122	Mm.235081	NM_007544	ENSMUSG00000004446	Bid	2700049M22Rik|AI875481|AU022477	BH3 interacting domain death agonist	protein-coding
mm_25418.1	chr3	107600434	107600441	+	1	NA	intron (NM_007441, intron 1 of 3)	intron (NM_007441, intron 1 of 3)	5406	NM_007441	11694	Mm.10112	NM_007441	ENSMUSG00000014603	Alx3	-	aristaless-like homeobox 3	protein-coding
mm_139904.1	chr17	70865692	70865708	+	1	NA	Intergenic	Intergenic	-12168	NM_001164074	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_13197.1	chr2	93315386	93315390	+	1	NA	intron (NM_183180, intron 1 of 9)	intron (NM_183180, intron 1 of 9)	19099	NM_183180	241556	Mm.274159	NM_183180	ENSMUSG00000027217	Tspan18	2610042G18Rik|6720430O15|BB226562	tetraspanin 18	protein-coding
mm_70523.1	chr8	12949513	12949533	+	1	NA	5' UTR (NM_001159485, exon 1 of 29)	5' UTR (NM_001159485, exon 1 of 29)	105	NM_001159485	17207	Mm.334413	NM_178076	ENSMUSG00000031442	Mcf2l	C130040G20Rik|Dbs|Ost|mKIAA0362	mcf.2 transforming sequence-like	protein-coding
mm_36332.1	chr4	72169547	72169549	-	1	NA	intron (NM_001285530, intron 5 of 17)	intron (NM_001285530, intron 5 of 17)	31345	NM_011599	21885	Mm.278444	NM_011599	ENSMUSG00000008305	Tle1	C230057C06Rik|Estm14|Grg-1|Grg1|Tle4l	transducin-like enhancer of split 1	protein-coding
mm_103210.1	chr11	70653033	70653047	-	1	NA	intron (NM_011072, intron 1 of 2)	intron (NM_011072, intron 1 of 2)	1610	NM_011072	18643	Mm.2647	NM_011072	ENSMUSG00000018293	Pfn1	Pfn	profilin 1	protein-coding
mm_68636.1	chr7	118243565	118243641	-	1	NA	promoter-TSS (NM_001031814)	promoter-TSS (NM_001031814)	34	NM_001031814	233789	Mm.309053	NM_177180	ENSMUSG00000030655	Smg1	2610207I05Rik|5430435M13Rik|C130002K18Rik|mKIAA0421	SMG1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)	protein-coding
mm_113947.1	chr13	50417875	50417912	+	1	NA	promoter-TSS (NM_175401)	promoter-TSS (NM_175401)	16	NM_175401	109082	Mm.18638	NM_175401	ENSMUSG00000037816	Fbxw17	1110064L07Rik|C85886	F-box and WD-40 domain protein 17	protein-coding
mm_108966.1	chr12	102439641	102439641	+	1	NA	5' UTR (NM_011175, exon 1 of 14)	5' UTR (NM_011175, exon 1 of 14)	172	NM_011175	19141	Mm.17185	NM_011175	ENSMUSG00000021190	Lgmn	AEP|AI746452|AU022324|Prsc1	legumain	protein-coding
mm_58014.1	chr6	136555614	136555626	-	1	NA	intron (NM_019426, intron 1 of 14)	intron (NM_019426, intron 1 of 14)	36769	NM_019426	54343	Mm.173271	NM_019426	ENSMUSG00000030213	Atf7ip	2610204M12Rik|AM|Mcaf1	activating transcription factor 7 interacting protein	protein-coding
mm_97012.1	chr11	71019571	71019579	+	1	NA	promoter-TSS (NM_001291148)	promoter-TSS (NM_001291148)	-36	NM_025993	67139	Mm.28227	NM_025993	ENSMUSG00000040599	Mis12	2510025F08Rik|AU044651|Misc12	MIS12 kinetochore complex component	protein-coding
mm_101226.1	chr11	20249361	20249433	-	1	NA	promoter-TSS (NM_172260)	promoter-TSS (NM_172260)	27	NM_172260	216543	Mm.260314	NM_172260	ENSMUSG00000044066	Cep68	6030463E10Rik|AI481761|BC027174|Kiaa0582	centrosomal protein 68	protein-coding
mm_66234.1	chr7	35275531	35275544	-	1	NA	Intergenic	Intergenic	42903	NM_026181	67471	Mm.358705	NM_026181	ENSMUSG00000063808	Gpatch1	1300003A17Rik|ECGP|Gpatc1	G patch domain containing 1	protein-coding
mm_54409.1	chr6	31563979	31563989	-	1	NA	promoter-TSS (NM_013723)	promoter-TSS (NM_013723)	-47	NM_013723	27205	Mm.89918	NM_013723	ENSMUSG00000025608	Podxl	AW121214|Ly102|PC|PCLP-1|Pclp1	podocalyxin-like	protein-coding
mm_122425.1	chr14	44859349	44859364	-	1	NA	promoter-TSS (NM_008962)	promoter-TSS (NM_008962)	19	NM_008962	19214	Mm.5105	NM_008962	ENSMUSG00000071489	Ptgdr	DP|PGD	prostaglandin D receptor	protein-coding
mm_160455.1	chr8	106870242	106870242	+	1	NA	promoter-TSS (NM_008217)	promoter-TSS (NM_008217)	0	NM_008217	15118	Mm.56986	NM_008217	ENSMUSG00000031910	Has3	-	hyaluronan synthase 3	protein-coding
mm_138268.1	chr17	34604287	34604304	+	1	NA	promoter-TSS (NM_019403)	promoter-TSS (NM_019403)	-734	NM_019403	54197	Mm.274542	NM_019403	ENSMUSG00000015478	Rnf5	2410131O05Rik|AA407576|NG2	ring finger protein 5	protein-coding
mm_119099.1	chr14	30896926	30896935	+	1	NA	intron (NM_001289632, intron 16 of 21)	intron (NM_001289632, intron 16 of 21)	10454	NM_001289632	16427	Mm.34819	NM_018746	ENSMUSG00000021922	Itih4	ITI-HC4|Itih-4|PK-120	inter alpha-trypsin inhibitor, heavy chain 4	protein-coding
mm_115737.1	chr13	17797377	17797381	-	1	NA	intron (NM_027118, intron 1 of 13)	intron (NM_027118, intron 1 of 13)	7718	NM_001081058	69562	Mm.193924	NM_027118	ENSMUSG00000041297	Cdk13	2310015O17Rik|Cdc2l5	cyclin-dependent kinase 13	protein-coding
mm_104735.1	chr11	98329642	98329654	-	1	NA	promoter-TSS (NM_010895)	promoter-TSS (NM_010895)	-3	NM_010895	18013	Mm.4814	NM_010895	ENSMUSG00000038255	Neurod2	Ndrf|bHLHa1	neurogenic differentiation 2	protein-coding
mm_90562.1	chr10	128194722	128194755	+	1	NA	exon (NM_001033264, exon 1 of 18)	exon (NM_001033264, exon 1 of 18)	103	NM_001285779	216456	Mm.30102	NM_001033264	ENSMUSG00000044005	Gls2	A330074B06Rik|AI195532|GA|GLS|Lga	glutaminase 2 (liver, mitochondrial)	protein-coding
mm_71019.1	chr8	33414608	33414610	+	1	NA	intron (NM_001098233, intron 1 of 1)	intron (NM_001098233, intron 1 of 1)	28284	NM_001098233	75029	Mm.159402	NM_152821	ENSMUSG00000049184	Purg	4930486B15Rik	purine-rich element binding protein G	protein-coding
mm_47427.1	chr5	123172247	123172265	-	1	NA	exon (NM_008277, exon 13 of 14)	exon (NM_008277, exon 13 of 14)	10430	NM_008277	15445	Mm.439709	NM_008277	ENSMUSG00000029445	Hpd	Fla|Flp|Hppd|Laf	4-hydroxyphenylpyruvic acid dioxygenase	protein-coding
mm_103150.1	chr11	70345703	70345723	-	1	NA	intron (NM_009660, intron 10 of 13)	intron (NM_009660, intron 10 of 13)	6318	NM_009660	11687	Mm.4584	NM_009660	ENSMUSG00000018924	Alox15	12-LO|12/15-LO|15-LOX|Alox12l|L-12LO	arachidonate 15-lipoxygenase	protein-coding
mm_928.1	chr1	55405882	55405967	+	1	NA	promoter-TSS (NM_001114663)	promoter-TSS (NM_001114663)	-22	NM_001114663	227120	Mm.194183	NM_001114663	ENSMUSG00000038349	Plcl1	C230017K02Rik|PLC-L|PLC-L1|PLCE|PLCL|PLDL1|PRIP|PRIP-1	phospholipase C-like 1	protein-coding
mm_25086.1	chr3	100685534	100685604	+	1	NA	promoter-TSS (NM_010763)	promoter-TSS (NM_010763)	-96	NM_010763	17156	Mm.271617	NM_010763	ENSMUSG00000008763	Man1a2	AI428775|AI528764|AI854422|Man1b|PCR2	mannosidase, alpha, class 1A, member 2	protein-coding
mm_120972.1	chr14	78384774	78384776	+	1	NA	Intergenic	Intergenic	-76732	NM_011613	21943	Mm.249221	NM_011613	ENSMUSG00000022015	Tnfsf11	Ly109l|ODF|OPGL|RANKL|Trance	tumor necrosis factor (ligand) superfamily, member 11	protein-coding
mm_81659.1	chr9	110992773	110992794	+	1	NA	Intergenic	Intergenic	-3070	NM_153100	235636	Mm.441138	NM_153100	ENSMUSG00000066319	Rtp3	Tmem7	receptor transporter protein 3	protein-coding
mm_157730.1	chrX	70477101	70477161	-	1	NA	promoter-TSS (NM_001033328)	promoter-TSS (NM_001033328)	-88	NM_001033328	236848	Mm.24569	NM_001033328	ENSMUSG00000073139	Tmem185a	-	transmembrane protein 185A	protein-coding
mm_165017.1	chr19	29806181	29806207	+	1	NA	promoter-TSS (NM_172836)	promoter-TSS (NM_172836)	-185	NM_172836	240613	Mm.313351	NM_172836	ENSMUSG00000046138	9930021J03Rik	ENSMUSG00000048936|Gm9832|mKIAA2026	RIKEN cDNA 9930021J03 gene	protein-coding
mm_84426.1	chr9	65827668	65827696	-	1	NA	promoter-TSS (NM_172536)	promoter-TSS (NM_172536)	-118	NM_172536	214812	Mm.139231	NM_172536	ENSMUSG00000040524	Zfp609	9830165N24|BC016271|Znf609|mKIAA0295	zinc finger protein 609	protein-coding
mm_56129.1	chr6	87590709	87590748	-	1	NA	promoter-TSS (NM_021381)	promoter-TSS (NM_021381)	-27	NM_021381	58182	Mm.333226	NM_021381	ENSMUSG00000049409	Prokr1	EG-VEGFR1|Gpr73|Pkr1	prokineticin receptor 1	protein-coding
mm_32858.1	chr4	118360072	118360082	+	1	NA	promoter-TSS (NM_026601)	promoter-TSS (NM_026601)	78	NR_003946	68180	Mm.193212	NM_026601	ENSMUSG00000006395	Hyi	2700033B16Rik|6430559E15Rik|HT036	hydroxypyruvate isomerase (putative)	protein-coding
mm_146704.1	chr18	13903449	13903452	-	1	NA	intron (NM_145492, intron 3 of 7)	intron (NM_145492, intron 3 of 7)	69283	NM_145492	225207	Mm.40325	NM_145492	ENSMUSG00000024420	Zfp521	B930086A16Rik|Evi3|Znf521	zinc finger protein 521	protein-coding
mm_63352.1	chr7	126976525	126976544	+	1	NA	5' UTR (NM_026638, exon 1 of 6)	5' UTR (NM_026638, exon 1 of 6)	620	NM_001347656	52858	Mm.28219	NM_026638	ENSMUSG00000030682	Cdipt	9530042F15Rik|D7Bwg0575e|Pis|Pis1	CDP-diacylglycerol--inositol 3-phosphatidyltransferase (phosphatidylinositol synthase)	protein-coding
mm_15330.1	chr2	155755056	155755068	+	1	NA	3' UTR (NM_011171, exon 4 of 4)	3' UTR (NM_011171, exon 4 of 4)	3845	NM_011171	19124	Mm.3243	NM_011171	ENSMUSG00000027611	Procr	AI325044|Ccca|Ccd41|Epcr	protein C receptor, endothelial	protein-coding
mm_164896.1	chr18	65459800	65459810	+	1	NA	intron (NM_172833, intron 9 of 15)	intron (NM_172833, intron 9 of 15)	28808	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_137617.1	chr17	28272192	28272205	+	1	NA	intron (NR_045427, intron 1 of 2)	intron (NR_045427, intron 1 of 2)	490	NR_045427	69050	Mm.486938	NR_045427	ENSMUSG00000002250	1810013A23Rik	-	RIKEN cDNA 1810013A23 gene	ncRNA
mm_130438.1	chr15	98296115	98296157	-	1	NA	promoter-TSS (NM_173769)	promoter-TSS (NM_173769)	-53	NM_173769	239652	Mm.207453	NM_173769	ENSMUSG00000022987	Zfp641	9930016F01Rik|Znf641	zinc finger protein 641	protein-coding
mm_59116.1	chr7	19824481	19824498	+	1	NA	Intergenic	Intergenic	-1734	NM_033601	12051	Mm.439658	NM_033601	ENSMUSG00000053175	Bcl3	AI528691|Bcl-3	B cell leukemia/lymphoma 3	protein-coding
mm_136446.1	chr16	94918386	94918389	-	1	NA	intron (NM_001025584, intron 2 of 4)	B4|SINE|B4	-61697	NM_001025590	16522	Mm.328720	NM_010606	ENSMUSG00000043301	Kcnj6	BIR1|GIRK2|KATP2|KCNJ7|Kir3.2|weaver|wv	potassium inwardly-rectifying channel, subfamily J, member 6	protein-coding
mm_977.1	chr1	58393484	58393496	+	1	NA	intron (NM_025824, intron 1 of 11)	CpG	354	NM_025824	66882	Mm.21848	NM_025824	ENSMUSG00000051223	Bzw1	1200015E15Rik|mKIAA0005	basic leucine zipper and W2 domains 1	protein-coding
mm_80796.1	chr9	96258715	96258726	+	1	NA	promoter-TSS (NM_001184710)	promoter-TSS (NM_001184710)	15	NM_001184709	211586	Mm.17977	NM_178667	ENSMUSG00000032411	Tfdp2	1110029I05Rik|A330080J22Rik|DP-3|DP3	transcription factor Dp 2	protein-coding
mm_58798.1	chr7	16175454	16175460	+	1	NA	promoter-TSS (NM_008627)	promoter-TSS (NM_008627)	62	NR_102730	17537	Mm.360516	NM_008627	ENSMUSG00000041420	Meis3	AI573393|Mrg2	Meis homeobox 3	protein-coding
mm_58390.1	chr7	3206920	3206933	+	1	NA	Intergenic	B1F2|SINE|Alu	-11700	NR_029640	100049710		NR_029640	ENSMUSG00000077815	Mir290a	Mir290|Mirn290|mir-290a|mmu-miR-290|mmu-mir-290a	microRNA 290a	ncRNA
mm_46399.1	chr5	104092889	104092902	-	1	NA	exon (NM_010097, exon 4 of 11)	exon (NM_010097, exon 4 of 11)	-15287	NM_001163772	100271704	Mm.366664	NM_001163772	ENSMUSG00000091034	Gm17660	Scpppq1	predicted gene, 17660	protein-coding
mm_824.1	chr1	47917439	47917443	+	1	NA	Intergenic	Intergenic	-450316	NR_105768	102466969		NR_105768	ENSMUSG00000098876	Mir6350	Gm27958|mmu-mir-6350	microRNA 6350	ncRNA
mm_59907.1	chr7	30360603	30360603	+	1	NA	exon (NM_175478, exon 2 of 3)	exon (NM_175478, exon 2 of 3)	2169	NM_175478	233067	Mm.23157	NM_175478	ENSMUSG00000036957	Lrfn3	A530045B06Rik|SALM4	leucine rich repeat and fibronectin type III domain containing 3	protein-coding
mm_52572.1	chr6	116338014	116338083	+	1	NA	promoter-TSS (NM_027920)	promoter-TSS (NM_027920)	26	NM_027920	71779	Mm.27064	NM_027920	ENSMUSG00000025702	March8	1300017E09Rik|MARCH-VIII|Mir	membrane-associated ring finger (C3HC4) 8	protein-coding
mm_10412.1	chr2	13579412	13579514	+	1	NA	exon (NM_011701, exon 5 of 9)	exon (NM_011701, exon 5 of 9)	5152	NM_011701	22352	Mm.268000	NM_011701	ENSMUSG00000026728	Vim	-	vimentin	protein-coding
mm_106290.1	chr11	118211850	118211870	-	1	NA	intron (NM_001112699, intron 1 of 12)	intron (NM_001112699, intron 1 of 12)	882	NM_001112700	19157	Mm.86413	NM_011180	ENSMUSG00000017132	Cyth1	CLM1|CTH-1|CYTIP|Pscd1	cytohesin 1	protein-coding
mm_163976.1	chr14	55758456	55758460	-	1	NA	promoter-TSS (NM_009894)	promoter-TSS (NM_009894)	-34	NM_009894	12684	Mm.466766	NM_009894	ENSMUSG00000022219	Cideb	1110030C18Rik|AI790179|CIDE-B	cell death-inducing DNA fragmentation factor, alpha subunit-like effector B	protein-coding
mm_147095.1	chr18	35649350	35649374	-	1	NA	promoter-TSS (NM_027222)	promoter-TSS (NM_027222)	5	NM_027222	69816	Mm.27252	NM_027222	ENSMUSG00000024353	Mzb1	2010001M09Rik|AV064572|PACAP|pERp1	marginal zone B and B1 cell-specific protein 1	protein-coding
mm_127188.1	chr15	99029929	99029949	+	1	NA	promoter-TSS (NM_009448)	promoter-TSS (NM_009448)	48	NM_009448	22146	Mm.88212	NM_009448	ENSMUSG00000043091	Tuba1c	M[a]6|Tuba6	tubulin, alpha 1C	protein-coding
mm_99531.1	chr11	103192398	103192435	+	1	NA	intron (NM_019679, intron 12 of 26)	intron (NM_019679, intron 12 of 26)	16132	NM_001254724	69441	Mm.380648	NM_027082	ENSMUSG00000020940	1700023F06Rik	-	RIKEN cDNA 1700023F06 gene	protein-coding
mm_84748.1	chr9	75409592	75409643	-	1	NA	promoter-TSS (NR_040719)	promoter-TSS (NR_040719)	-258	NM_027418	50772	Mm.480076	NM_015806	ENSMUSG00000042688	Mapk6	2610021I23Rik|D130053K17Rik|Erk3|Mapk4|Mapk63|Prkm4|Prkm6	mitogen-activated protein kinase 6	protein-coding
mm_79231.1	chr9	50494517	50494533	+	1	NA	promoter-TSS (NM_029639)	promoter-TSS (NM_029639)	0	NM_029639	76509	Mm.29959	NM_029639	ENSMUSG00000032068	Plet1	0610037B23Rik|1600029D21Rik|AA407923|AU043048	placenta expressed transcript 1	protein-coding
mm_70211.1	chr7	144914609	144914623	-	1	NA	promoter-TSS (NM_028184)	promoter-TSS (NM_028184)	-484	NM_001347536	72284	Mm.273049	NM_028184	ENSMUSG00000031072	Oraov1	2210010N10Rik|TAOS1	oral cancer overexpressed 1	protein-coding
mm_13762.1	chr2	118388652	118388669	+	1	NA	promoter-TSS (NM_013719)	promoter-TSS (NM_013719)	43	NM_013719	27103	Mm.217616	NM_013719	ENSMUSG00000005102	Eif2ak4	2610011M03|GCN2|MGCN2	eukaryotic translation initiation factor 2 alpha kinase 4	protein-coding
mm_123923.1	chr14	73365525	73365537	-	1	NA	intron (NM_008410, intron 4 of 5)	RSINE1|SINE|B4	19740	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_93086.1	chr10	89600693	89600719	-	1	NA	promoter-TSS (NM_001310710)	promoter-TSS (NM_001310710)	-891	NM_001310710	216227	Mm.233921	NM_182959	ENSMUSG00000019935	Slc17a8	BC042593|Vglut3	solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 8	protein-coding
mm_104993.1	chr11	100323044	100323049	-	1	NA	TTS (NM_011508)	TTS (NM_011508)	3097	NM_011508	20918	Mm.13886	NM_011508	ENSMUSG00000035530	Eif1	Sui1-rs1	eukaryotic translation initiation factor 1	protein-coding
mm_58075.1	chr6	136924318	136924334	-	1	NA	exon (NM_007486, exon 6 of 6)	exon (NM_007486, exon 6 of 6)	-2146	NM_026983	69187	Mm.33692	NM_026983	ENSMUSG00000030219	Erp27	1810033M07Rik|1810047B09Rik	endoplasmic reticulum protein 27	protein-coding
mm_149100.1	chr19	8942162	8942172	+	1	NA	TTS (NM_144872)	TTS (NM_144872)	247	NM_011842	23942	Mm.25339	NM_011842	ENSMUSG00000071646	Mta2	AW550797|Mata1l1|Mta1l1|mmta2	metastasis-associated gene family, member 2	protein-coding
mm_114159.1	chr13	55412039	55412050	+	1	NA	exon (NM_011392, exon 11 of 13)	exon (NM_011392, exon 11 of 13)	3188	NM_029303	75477	Mm.432537	NM_029303	ENSMUSG00000044444	Pfn3	1700012P12Rik	profilin 3	protein-coding
mm_117072.1	chr13	59242614	59242617	-	1	NA	Intergenic	Intergenic	301836	NM_001284221	67269	Mm.153008	NM_023328	ENSMUSG00000021557	Agtpbp1	1700020N17Rik|2310001G17Rik|2900054O13Rik|4930445M19Rik|5730402G09Rik|CCP1|Nna1|nmf243|pcd	ATP/GTP binding protein 1	protein-coding
mm_3917.1	chr1	162217904	162217906	+	1	NA	promoter-TSS (NR_029810)	promoter-TSS (NR_029810)	91	NR_029810	723821		NR_029810	ENSMUSG00000070126	Mir199a-2	Mirn199a-2|mir-199a-2	microRNA 199a-2	ncRNA
mm_161536.1	chr15	102921261	102921261	+	1	NA	exon (NM_010464, exon 1 of 2)	exon (NM_010464, exon 1 of 2)	130	NM_010464	15422	Mm.207062	NM_010464	ENSMUSG00000001655	Hoxc13	-	homeobox C13	protein-coding
mm_129124.1	chr15	76126539	76126550	-	1	NA	promoter-TSS (NM_001142968)	promoter-TSS (NM_001142968)	12	NM_001142968	271278	Mm.205253	NM_198172	ENSMUSG00000044361	BC024139	6230424I18Rik	cDNA sequence BC024139	protein-coding
mm_163561.1	chr13	24634658	24634667	+	1	NA	intron (NM_178658, intron 1 of 13)	intron (NM_178658, intron 1 of 13)	-3986	NM_001080381	193385	Mm.217319	NM_029679	ENSMUSG00000036006	Fam65b	-	family with sequence similarity 65, member B	protein-coding
mm_147400.1	chr18	44555923	44555937	-	1	NA	intron (NM_001085373, intron 3 of 18)	L2b|LINE|L2	-105735	NR_026853	626275	Mm.427116	NR_026853	ENSMUSG00000097610	A930012L18Rik	-	RIKEN cDNA A930012L18 gene	ncRNA
mm_35602.1	chr4	43040249	43040272	-	1	NA	promoter-TSS (NM_001253354)	promoter-TSS (NM_001253354)	41	NM_001253353	230088	Mm.260162	NM_172691	ENSMUSG00000036002	Fam214b	B230312A22Rik	family with sequence similarity 214, member B	protein-coding
mm_100545.1	chr11	120703988	120704002	+	1	NA	intron (NM_198223, intron 10 of 14)	intron (NM_198223, intron 10 of 14)	9772	NM_016665	20892	Mm.259716	NM_016665	ENSMUSG00000025144	Cenpx	Stra13	centromere protein X	protein-coding
mm_172937.1	chr9	78809568	78809568	-	1	NA	Intergenic	RLTR10E|LTR|ERVK	194022	NM_153098	235505	Mm.32955	NM_153098	ENSMUSG00000046186	Cd109	9930012E15Rik|AI480638|GARP	CD109 antigen	protein-coding
mm_54130.1	chr6	18848453	18848538	-	1	NA	promoter-TSS (NM_133939)	promoter-TSS (NM_133939)	-140	NM_133939	76522	Mm.275158	NM_133939	ENSMUSG00000044155	Lsm8	2010003I05Rik|AW214405|Naa38	LSM8 homolog, U6 small nuclear RNA associated	protein-coding
mm_76975.1	chr8	106337988	106337996	-	1	NA	promoter-TSS (NM_021491)	promoter-TSS (NM_021491)	-4	NM_021491	58994	Mm.23298	NM_021491	ENSMUSG00000031906	Smpd3	4631433G07Rik|AI427456|AW537966|fro|nSMase2	sphingomyelin phosphodiesterase 3, neutral	protein-coding
mm_6540.1	chr1	74968283	74968296	-	1	NA	intron (NM_029342, intron 3 of 4)	intron (NM_029342, intron 3 of 4)	-16617	NM_010544	16147	Mm.439736	NM_010544	ENSMUSG00000006538	Ihh	HHG-2	Indian hedgehog	protein-coding
mm_32158.1	chr4	99969681	99969689	+	1	NA	intron (NM_028132, intron 6 of 10)	intron (NM_028132, intron 6 of 10)	40234	NM_028132	72157	Mm.217764	NM_028132	ENSMUSG00000025791	Pgm2	2610020G18Rik|AA407108|AI098105|Pgm-2|Pgm1	phosphoglucomutase 2	protein-coding
mm_122989.1	chr14	54989101	54989112	-	1	NA	exon (NM_080728, exon 14 of 41)	exon (NM_080728, exon 14 of 41)	5443	NM_080728	140781	Mm.457983	NM_080728	ENSMUSG00000053093	Myh7	B-MHC|MyHC-I|Myhc-b|Myhcb|beta-MHC	myosin, heavy polypeptide 7, cardiac muscle, beta	protein-coding
mm_46863.1	chr5	113820100	113820120	-	1	NA	exon (NM_009151, exon 2 of 2)	exon (NM_009151, exon 2 of 2)	10391	NM_009151	20345	Mm.332590	NM_009151	ENSMUSG00000048163	Selplg	CD162|Psgl-1|Psgl1|Selp1|Selpl	selectin, platelet (p-selectin) ligand	protein-coding
mm_45718.1	chr5	84417396	84417400	-	1	NA	promoter-TSS (NM_007937)	promoter-TSS (NM_007937)	-16	NM_007937	13839	Mm.137991	NM_007937	ENSMUSG00000029245	Epha5	AI854630|AW125296|Cek7|Ehk1|Els1|Hek7|Rek7|bsk	Eph receptor A5	protein-coding
mm_52391.1	chr6	113301561	113301564	+	1	NA	intron (NM_170673, intron 17 of 19)	intron (NM_170673, intron 17 of 19)	-5575	NM_030178	78783	Mm.356059	NM_030178	ENSMUSG00000001632	Brpf1	4833438B11Rik|4930540D11Rik|Brpf2	bromodomain and PHD finger containing, 1	protein-coding
mm_155296.1	chrX	61185409	61185426	+	1	NA	exon (NM_001166658, exon 1 of 1)	exon (NM_001166658, exon 1 of 1)	141	NM_001166658	631990	Mm.401324	NM_001166658	ENSMUSG00000090546	Cdr1	100039759|Cdr|Cdr34|EG631990|Gm2409|Gm7077	cerebellar degeneration related antigen 1	protein-coding
mm_159834.1	chr5	129549040	129549040	+	1	NA	intron (NM_172276, intron 11 of 17)	RSINE1|SINE|B4	-35129	NM_011846	23948	Mm.42047	NM_011846	ENSMUSG00000029436	Mmp17	MT4-MMP|MT4MMP|MTMMP4	matrix metallopeptidase 17	protein-coding
mm_133096.1	chr16	64851992	64851996	+	1	NA	promoter-TSS (NM_178647)	promoter-TSS (NM_178647)	-91	NM_178647	106143	Mm.10160	NM_178647	ENSMUSG00000054604	Cggbp1	AA960172|AL023996|AW045841	CGG triplet repeat binding protein 1	protein-coding
mm_81127.1	chr9	106477280	106477352	+	1	NA	promoter-TSS (NM_145619)	promoter-TSS (NM_145619)	7	NM_145620	27966	Mm.239997	NM_145620	ENSMUSG00000041506	Rrp9	55kDa|D19435|D9Wsu10e|Rnu3ip2|U3-55k	RRP9, small subunit (SSU) processome component, homolog (yeast)	protein-coding
mm_73897.1	chr8	119425937	119425958	+	1	NA	Intergenic	Intergenic	-11215	NM_027950	71839	Mm.272357	NM_027950	ENSMUSG00000074063	Osgin1	1700012B18Rik|Okl38	oxidative stress induced growth inhibitor 1	protein-coding
mm_149902.1	chr19	25552073	25552118	+	1	NA	intron (NM_015826, intron 3 of 4)	intron (NM_015826, intron 3 of 4)	46389	NM_015826	50796	Mm.391208	NM_015826	ENSMUSG00000024837	Dmrt1	-	doublesex and mab-3 related transcription factor 1	protein-coding
mm_43040.1	chr5	124032545	124032572	+	1	NA	promoter-TSS (NM_177876)	promoter-TSS (NM_177876)	-298	NM_177876	330192	Mm.4079	NM_177876	ENSMUSG00000066278	Vps37b	2300007F24Rik|AI415429|BC026744	vacuolar protein sorting 37B	protein-coding
mm_117146.1	chr13	61040615	61040637	-	1	NA	promoter-TSS (NM_029636)	promoter-TSS (NM_029636)	-29	NM_029636	104002	Mm.46088	NM_029636	ENSMUSG00000021439	Ctsq	1600010J02Rik	cathepsin Q	protein-coding
mm_18560.1	chr2	65238594	65238609	-	1	NA	promoter-TSS (NM_177025)	promoter-TSS (NM_177025)	25	NM_177025	319876	Mm.34159	NM_027225	ENSMUSG00000034903	Cobll1	1810047P18Rik|Coblr1|D430044D16Rik	Cobl-like 1	protein-coding
mm_96496.1	chr11	67980493	67980496	+	1	NA	intron (NM_018768, intron 3 of 7)	intron (NM_018768, intron 3 of 7)	14011	NM_018768	55943	Mm.3973	NM_018768	ENSMUSG00000020903	Stx8	0610007H08Rik|1110002H11Rik|4930571E13Rik|CARB	syntaxin 8	protein-coding
mm_24588.1	chr3	93445045	93445047	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	2716	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_85411.1	chr9	103424973	103424994	-	1	NA	TTS (NM_001002896)	TTS (NM_001002896)	1405	NR_040466	100529079	Mm.437003	NR_040466	ENSMUSG00000086236	5830418P13Rik	-	RIKEN cDNA 5830418P13 gene	ncRNA
mm_130254.1	chr15	96642204	96642234	-	1	NA	promoter-TSS (NM_134086)	promoter-TSS (NM_134086)	124	NM_001166456	105727	Mm.103568	NM_134086	ENSMUSG00000023169	Slc38a1	AA408026|AA409865|AL022800|AU015942|NAT2	solute carrier family 38, member 1	protein-coding
mm_32452.1	chr4	107367758	107367813	+	1	NA	promoter-TSS (NM_028355)	promoter-TSS (NM_028355)	1	NM_028355	72787	Mm.28478	NM_028355	ENSMUSG00000028614	Ndc1	2810475A17Rik|AI450313|Tmem48|sks	NDC1 transmembrane nucleoporin	protein-coding
mm_165409.1	chr2	144116204	144116222	+	1	NA	Intergenic	Intergenic	73077	NR_136884	433481	Mm.330630	NR_136884	ENSMUSG00000074758	Gm5535	EG433481	predicted gene 5535	ncRNA
mm_122754.1	chr14	54206625	54206636	-	1	NA	Intergenic	Intergenic	47299	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_97114.1	chr11	74770823	74770876	+	1	NA	promoter-TSS (NM_026197)	promoter-TSS (NM_026197)	-14	NM_026197	67493	Mm.45748	NM_026197	ENSMUSG00000010554	Mettl16	2610100D03Rik|2810013M15Rik|A830095F14Rik|AI846133|Mett10d	methyltransferase like 16	protein-coding
mm_42193.1	chr5	112276695	112276756	+	1	NA	promoter-TSS (NM_009419)	promoter-TSS (NM_009419)	34	NM_009419	22022	Mm.250631	NM_009419	ENSMUSG00000029344	Tpst2	AI448750|D5Ucla3|Tango13b|grm|grt	protein-tyrosine sulfotransferase 2	protein-coding
mm_42223.1	chr5	113445713	113445716	+	1	NA	Intergenic	Intergenic	88420	NM_001012726	503692	Mm.348794	NM_001012726	ENSMUSG00000053873	Aym1	-	activator of yeast meiotic promoters 1	protein-coding
mm_160207.1	chr7	84963960	84963960	-	1	NA	promoter-TSS (NM_001105180)	promoter-TSS (NM_001105180)	49	NM_001105180	100009609	Mm.389926	NM_001105180	ENSMUSG00000066372	Vmn2r65	ENSMUSG00000070600|V2ro	vomeronasal 2, receptor 65	protein-coding
mm_108400.1	chr12	81152480	81152497	+	1	NA	intron (NM_022316, intron 6 of 12)	intron (NM_022316, intron 6 of 12)	-13663	NR_037227	100526532		NR_037227	ENSMUSG00000092673	Mir3067	mir-3067|mmu-mir-3067	microRNA 3067	ncRNA
mm_167694.1	chr9	88273582	88273602	+	1	NA	Intergenic	Intergenic	-54017	NM_011851	23959	Mm.244235	NM_011851	ENSMUSG00000032420	Nt5e	2210401F01Rik|5'-NT|AI447961|CD73|NT|Nt5|eNT	5' nucleotidase, ecto	protein-coding
mm_76157.1	chr8	82358531	82358567	-	1	NA	intron (NM_008357, intron 2 of 7)	intron (NM_008357, intron 2 of 7)	44037	NM_001254747	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_52131.1	chr6	97944545	97944555	+	1	NA	intron (NM_001113198, intron 2 of 9)	intron (NM_001113198, intron 2 of 9)	14733	NM_001178049	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_5245.1	chr1	16519285	16519336	-	1	NA	promoter-TSS (NM_025303)	promoter-TSS (NM_025303)	-8	NM_001111272	29819	Mm.216257	NM_025303	ENSMUSG00000025920	Stau2	-	staufen (RNA binding protein) homolog 2 (Drosophila)	protein-coding
mm_82713.1	chr9	24503334	24503343	-	1	NA	promoter-TSS (NM_172920)	promoter-TSS (NM_172920)	-198	NM_172920	244745	Mm.38526	NM_172920	ENSMUSG00000043067	Dpy19l1	1100001I19Rik|6030402K12|AI225861|AW558481	dpy-19-like 1 (C. elegans)	protein-coding
mm_19625.1	chr2	102813512	102813542	-	1	NA	3' UTR (NM_009851, exon 19 of 19)	3' UTR (NM_009851, exon 19 of 19)	88138	NM_001177785	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_110056.1	chr12	20921219	20921236	-	1	NA	Intergenic	CpG	-105448	NR_015521	69513	Mm.273972	NR_015521	ENSMUSG00000099759	1700030C10Rik	-	RIKEN cDNA 1700030C10 gene	ncRNA
mm_33705.1	chr4	133633086	133633106	+	1	NA	exon (NM_001017968, exon 1 of 8)	exon (NM_001017968, exon 1 of 8)	333	NM_001017968	503610	Mm.331948	NM_001017968	ENSMUSG00000037553	Zdhhc18	-	zinc finger, DHHC domain containing 18	protein-coding
mm_170093.1	chr17	36231561	36231561	-	1	NA	Intergenic	CpG	26285	NM_026308	67676	Mm.27131	NM_026308	ENSMUSG00000024446	Rpp21	0610037N01Rik	ribonuclease P 21 subunit	protein-coding
mm_58245.1	chr6	145048677	145048687	-	1	NA	exon (NM_001024468, exon 1 of 11)	exon (NM_001024468, exon 1 of 11)	130	NM_001024468	12035	Mm.4606	NM_007532	ENSMUSG00000030268	Bcat1	BCATc|Eca39	branched chain aminotransferase 1, cytosolic	protein-coding
mm_123204.1	chr14	59341326	59341358	-	1	NA	promoter-TSS (NM_001164327)	promoter-TSS (NM_001164327)	-12	NM_001164327	236451	Mm.247736	NM_001164327	ENSMUSG00000091649	Phf11b	EG236451|Gm4902	PHD finger protein 11B	protein-coding
mm_82537.1	chr9	20746385	20746401	-	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	-18179	NM_173777	244723	Mm.293552	NM_173777	ENSMUSG00000032172	Olfm2	A030009A06Rik	olfactomedin 2	protein-coding
mm_81082.1	chr9	106224314	106224325	+	1	NA	exon (NM_031178, exon 2 of 2)	exon (NM_031178, exon 2 of 2)	1721	NM_031178	81897	Mm.44889	NM_031178	ENSMUSG00000045322	Tlr9	-	toll-like receptor 9	protein-coding
mm_127481.1	chr15	101274439	101274447	+	1	NA	3' UTR (NM_010444, exon 7 of 7)	3' UTR (NM_010444, exon 7 of 7)	7597	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_146794.1	chr18	20549355	20549369	-	1	NA	Intergenic	Intergenic	-8712	NM_007883	13511	Mm.345891	NM_007883	ENSMUSG00000044393	Dsg2	AA408168|D18Ertd293e	desmoglein 2	protein-coding
mm_6992.1	chr1	86358212	86358232	-	1	NA	exon (NM_010880, exon 2 of 14)	exon (NM_010880, exon 2 of 14)	1233	NM_010880	17975	Mm.154378	NM_010880	ENSMUSG00000026234	Ncl	B530004O11Rik|C23|D0Nds28|D1Nds28|Nucl	nucleolin	protein-coding
mm_19381.1	chr2	91202644	91202694	-	1	NA	promoter-TSS (NM_007387)	promoter-TSS (NM_007387)	-243	NM_007387	11432	Mm.45570	NM_007387	ENSMUSG00000002103	Acp2	Acp-2|LAP	acid phosphatase 2, lysosomal	protein-coding
mm_48347.1	chr5	139325491	139325568	-	1	NA	promoter-TSS (NM_172723)	promoter-TSS (NM_172723)	-65	NM_172723	231821	Mm.297819	NM_172723	ENSMUSG00000056413	Adap1	4930431P11Rik|Centa1|GC1L|p42IP4	ArfGAP with dual PH domains 1	protein-coding
mm_150910.1	chr19	46056555	46056586	+	1	NA	promoter-TSS (NM_001081214)	promoter-TSS (NM_001081214)	31	NM_001081214	226169	Mm.2415	NM_145504	ENSMUSG00000055491	Pprc1	A930018M19|BC013720|PRC|mKIAA0595	peroxisome proliferative activated receptor, gamma, coactivator-related 1	protein-coding
mm_11328.1	chr2	30441832	30441836	+	1	NA	intron (NM_138748, intron 8 of 9)	intron (NM_138748, intron 8 of 9)	25784	NM_138748	110854	Mm.275393	NM_138748	ENSMUSG00000039515	Ptpa	2610042B21Rik|C77440|N28142|PR53|Ppp2r4	protein phosphatase 2 protein activator	protein-coding
mm_79246.1	chr9	50565338	50565376	+	1	NA	promoter-TSS (NM_008360)	promoter-TSS (NM_008360)	-11	NM_008360	16173	Mm.1410	NM_008360	ENSMUSG00000039217	Il18	Igif|Il-18	interleukin 18	protein-coding
mm_104841.1	chr11	99209994	99209999	-	1	NA	3' UTR (NM_020618, exon 11 of 11)	3' UTR (NM_020618, exon 11 of 11)	21021	NM_020618	57376	Mm.379086	NM_020618	ENSMUSG00000037935	Smarce1	2810417B20Rik|5830412H02Rik|9030408N19Rik|Baf27	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1	protein-coding
mm_48198.1	chr5	137531205	137531236	-	1	NA	intron (NM_010312, intron 1 of 9)	CpG	-1626	NR_105846	102465227		NR_105846	ENSMUSG00000098597	Mir6418	Gm27629|mir-6418|mmu-mir-6418	microRNA 6418	ncRNA
mm_40081.1	chr5	34462177	34462179	+	1	NA	exon (NM_001243123, exon 17 of 21)	exon (NM_001243123, exon 17 of 21)	51801	NM_139064	231130	Mm.28615	NM_139064	ENSMUSG00000059866	Tnip2	1810020H16Rik|ABIN-2|AI428870	TNFAIP3 interacting protein 2	protein-coding
mm_8046.1	chr1	135371885	135371888	-	1	NA	3' UTR (NM_175259, exon 5 of 5)	3' UTR (NM_175259, exon 5 of 5)	3177	NM_175259	77552	Mm.41407	NM_175259	ENSMUSG00000041889	Shisa4	9330132O05Rik|Tmem58|mShisa4	shisa family member 4	protein-coding
mm_118311.1	chr13	113101936	113101950	-	1	NA	promoter-TSS (NM_010370)	promoter-TSS (NM_010370)	-962	NM_010370	14938	Mm.15510	NM_010370	ENSMUSG00000023132	Gzma	AW494114|Ctla-3|Ctla3|Hf|Hf1|SE1|TSP-1|TSP1	granzyme A	protein-coding
mm_137521.1	chr17	27325195	27325198	+	1	NA	Intergenic	Intergenic	-3189	NR_106075	102466818		NR_106075	ENSMUSG00000099237	Mir7216	Gm27555|mmu-mir-7216	microRNA 7216	ncRNA
mm_86255.1	chr9	121495679	121495689	-	1	NA	promoter-TSS (NM_001284508)	promoter-TSS (NM_001284508)	10	NM_001284508	12424	Mm.2619	NM_031161	ENSMUSG00000032532	Cck	-	cholecystokinin	protein-coding
mm_43615.1	chr5	138085174	138085182	+	1	NA	promoter-TSS (NM_029869)	promoter-TSS (NM_029869)	94	NM_029869	74570	Mm.213114	NM_029869	ENSMUSG00000029729	Zkscan1	5930429A01Rik|9130423L19Rik|9230118B16Rik|AI646829|AI788588|C87323|KOX18|PHZ-37|ZNF139	zinc finger with KRAB and SCAN domains 1	protein-coding
mm_145729.1	chr18	64264611	64264639	+	1	NA	intron (NM_009182, intron 2 of 5)	intron (NM_009182, intron 2 of 5)	10266	NM_009182	20451	Mm.252110	NM_009182	ENSMUSG00000056812	St8sia3	AI847333|ST8SiaIII|Siat8c	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3	protein-coding
mm_170548.1	chr19	4064274	4064278	-	1	NA	Intergenic	MMVL30-int|LTR|ERV1	-4982	NM_144869	225884	Mm.440201	NM_144869	ENSMUSG00000058216	Gstp3	-	glutathione S-transferase pi 3	protein-coding
mm_136660.1	chr17	6007594	6007624	+	1	NA	promoter-TSS (NM_001290698)	promoter-TSS (NM_001290698)	29	NM_001290698	20975	Mm.236068	NM_011523	ENSMUSG00000023805	Synj2	AI481647|SJ2|mKIAA0348	synaptojanin 2	protein-coding
mm_146596.1	chr18	9449948	9450043	-	1	NA	5' UTR (NM_026484, exon 1 of 10)	5' UTR (NM_026484, exon 1 of 10)	155	NM_026484	67974	Mm.86523	NM_026484	ENSMUSG00000024286	Ccny	1700025H17Rik|3110050L10Rik|4631402G10Rik|5730405I09Rik	cyclin Y	protein-coding
mm_143685.1	chr17	80062334	80062363	-	1	NA	promoter-TSS (NM_144802)	promoter-TSS (NM_144802)	-80	NM_144802	72692	Mm.64579	NM_144802	ENSMUSG00000024095	Hnrnpll	2510028H02Rik|2810036L13Rik|AI256697|AI852082|Hnrpll	heterogeneous nuclear ribonucleoprotein L-like	protein-coding
mm_134146.1	chr16	10784838	10784849	-	1	NA	exon (NM_001271603, exon 2 of 2)	exon (NM_001271603, exon 2 of 2)	693	NM_009896	12703	Mm.130	NM_009896	ENSMUSG00000038037	Socs1	Cish1|Cish7|JAB|SOCS-1|SSI-1	suppressor of cytokine signaling 1	protein-coding
mm_166280.1	chr5	92817828	92817832	+	1	NA	intron (NM_001077595, intron 1 of 9)	B2_Mm2|SINE|B2	8448	NM_001077595	27428	Mm.46014	NM_015756	ENSMUSG00000029381	Shroom3	AL022960|D5Ertd287e|Shrm|Shrm3	shroom family member 3	protein-coding
mm_69693.1	chr7	139992545	139992545	-	1	NA	promoter-TSS (NM_001291066)	promoter-TSS (NM_001291066)	17	NM_007403	11501	Mm.15969	NM_007403	ENSMUSG00000025473	Adam8	ADAM 8|CD156|CD156a|E430039A18Rik|MS2	a disintegrin and metallopeptidase domain 8	protein-coding
mm_11025.1	chr2	26731718	26731725	+	1	NA	Intergenic	Intergenic	-60439	NM_010695	16821	Mm.123925	NM_010695	ENSMUSG00000026919	Lcn4	A630045M08Rik|Vnsp2	lipocalin 4	protein-coding
mm_104842.1	chr11	99230431	99230464	-	1	NA	5' UTR (NM_020618, exon 1 of 11)	5' UTR (NM_020618, exon 1 of 11)	570	NM_020618	57376	Mm.379086	NM_020618	ENSMUSG00000037935	Smarce1	2810417B20Rik|5830412H02Rik|9030408N19Rik|Baf27	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1	protein-coding
mm_143639.1	chr17	79020827	79020859	-	1	NA	promoter-TSS (NM_029239)	promoter-TSS (NM_029239)	-27	NM_029239	75292	Mm.252776	NM_029239	ENSMUSG00000024070	Prkd3	4930557O20Rik|5730497N19Rik|PKD3|Pkcnu|Prkcn	protein kinase D3	protein-coding
mm_128100.1	chr15	27876480	27876524	-	1	NA	intron (NM_001081302, intron 10 of 56)	intron (NM_001081302, intron 10 of 56)	149346	NM_001081302	223435	Mm.485422	NM_001081302	ENSMUSG00000022263	Trio	6720464I07Rik|AA408740|Solo	triple functional domain (PTPRF interacting)	protein-coding
mm_50940.1	chr6	57823713	57823723	+	1	NA	intron (NM_146168, intron 1 of 4)	intron (NM_146168, intron 1 of 4)	1407	NM_146168	232023	Mm.24642	NM_146168	ENSMUSG00000037788	Vopp1	AW146242|Ecop	vesicular, overexpressed in cancer, prosurvival protein 1	protein-coding
mm_95939.1	chr11	58382797	58382814	+	1	NA	exon (NM_001083884, exon 4 of 7)	exon (NM_001083884, exon 4 of 7)	2159	NM_001330197	70163	Mm.24119	NM_027339	ENSMUSG00000013643	Lypd8	2210415F13Rik	LY6/PLAUR domain containing 8	protein-coding
mm_48769.1	chr5	148399902	148399912	-	1	NA	promoter-TSS (NM_007513)	promoter-TSS (NM_007513)	-3	NM_007513	11987	Mm.275489	NM_007513	ENSMUSG00000041313	Slc7a1	4831426K01Rik|AI447493|Atrc-1|Atrc1|Cat1|Rec-1|Rev-1|mCAT-1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 1	protein-coding
mm_76367.1	chr8	84793301	84793315	-	1	NA	intron (NM_001081982, intron 1 of 9)	intron (NM_001081982, intron 1 of 9)	7030	NM_010906	18032	Mm.9394	NM_010906	ENSMUSG00000001911	Nfix	CTF|NF-I/X|NF1-X|NFI-X	nuclear factor I/X	protein-coding
mm_79085.1	chr9	46242524	46242543	+	1	NA	exon (NM_007468, exon 3 of 3)	exon (NM_007468, exon 3 of 3)	1689	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_77419.1	chr8	120716086	120716100	-	1	NA	Intergenic	ID_B1|SINE|B4	-20265	NM_008320	15900	Mm.334861	NM_008320	ENSMUSG00000041515	Irf8	AI893568|ICSBP|IRF-8|Icsbp1|Myls	interferon regulatory factor 8	protein-coding
mm_43156.1	chr5	125850003	125850008	+	1	NA	Intergenic	Intergenic	317587	NM_001190352	208151	Mm.40397	NM_001190352	ENSMUSG00000070498	Tmem132b	AK220418|mKIAA1786	transmembrane protein 132B	protein-coding
mm_92269.1	chr10	71159658	71159671	-	1	NA	promoter-TSS (NM_001347189)	promoter-TSS (NM_001347189)	26	NM_031397	83675	Mm.286834	NM_031397	ENSMUSG00000014329	Bicc1	Bic-C|bpk|jcpk	BicC family RNA binding protein 1	protein-coding
mm_109532.1	chr12	111539435	111539447	+	1	NA	5' UTR (NM_173363, exon 3 of 12)	5' UTR (NM_173363, exon 3 of 12)	1340	NM_173363	217869	Mm.271222	NM_173363	ENSMUSG00000021282	Eif5	2810011H21Rik|D12Ertd549e	eukaryotic translation initiation factor 5	protein-coding
mm_76794.1	chr8	102785345	102785395	-	1	NA	promoter-TSS (NM_009866)	promoter-TSS (NM_009866)	-259	NM_009866	12552	Mm.1571	NM_009866	ENSMUSG00000031673	Cdh11	Cad11|OSF-4	cadherin 11	protein-coding
mm_38674.1	chr4	144892478	144892485	-	1	NA	promoter-TSS (NM_001172424)	promoter-TSS (NM_001172424)	-346	NM_001172424	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding
mm_63394.1	chr7	127296230	127296232	+	1	NA	promoter-TSS (NM_001253873)	promoter-TSS (NM_001253873)	-29	NM_001253873	16408	Mm.1618	NM_008400	ENSMUSG00000030830	Itgal	(p180)|Cd11a|LFA-1|LFA-1A|Ly-15|Ly-21	integrin alpha L	protein-coding
mm_129050.1	chr15	75431746	75431774	-	1	NA	promoter-TSS (NR_108041)	promoter-TSS (NR_108041)	69	NR_108041	105892	Mm.38909	NM_001039720	ENSMUSG00000053168	9030619P08Rik	-	lymphocyte antigen 6 complex pseudogene	pseudo
mm_109758.1	chr12	117843695	117843740	+	1	NA	promoter-TSS (NM_146040)	promoter-TSS (NM_146040)	-144	NM_146040	217946	Mm.281149	NM_146040	ENSMUSG00000021175	Cdca7l	BC006933|JPO2	cell division cycle associated 7 like	protein-coding
mm_171391.1	chr4	122260042	122260048	+	1	NA	Intergenic	RMER16_Mm|LTR|ERVK	-429214	NM_023865	77432	Mm.491436	NM_023865	ENSMUSG00000023263	9530002B09Rik	Aump|Vpp1|Vppl	RIKEN cDNA 9530002B09 gene	protein-coding
mm_63054.1	chr7	121905649	121905662	+	1	NA	intron (NR_073548, intron 4 of 12)	B4A|SINE|B4	40617	NR_073548	20277	Mm.7709	NM_011325	ENSMUSG00000030873	Scnn1b	-	sodium channel, nonvoltage-gated 1 beta	protein-coding
mm_73730.1	chr8	113635788	113635842	+	1	NA	promoter-TSS (NM_173015)	promoter-TSS (NM_173015)	16	NM_173015	270096	Mm.74689	NM_173015	ENSMUSG00000078908	Mon1b	5031407H10|5033413H12Rik	MON1 homolog B, secretory traffciking associated	protein-coding
mm_118968.1	chr14	27768562	27768563	+	1	NA	intron (NM_177814, intron 2 of 15)	intron (NM_177814, intron 2 of 15)	146155	NM_177814	238988	Mm.318004	NM_177814	ENSMUSG00000040640	Erc2	6430531D06|CAST|CAST1/ERC2|D14Ertd171e|ELKS2alpha	ELKS/RAB6-interacting/CAST family member 2	protein-coding
mm_117815.1	chr13	97820521	97820530	-	1	NA	Intergenic	RLTR17|LTR|ERVK	260525	NR_046157	328314	Mm.138047	NR_046157	ENSMUSG00000110235	Gm5086	B230311A21|EG328314	predicted gene 5086	ncRNA
mm_144512.1	chr18	24709437	24709447	+	1	NA	5' UTR (NM_001289655, exon 1 of 26)	5' UTR (NM_001289655, exon 1 of 26)	819	NM_001289655	225288	Mm.329322	NM_175276	ENSMUSG00000034295	Fhod3	A930009H06Rik|FHOS2|mKIAA1695	formin homology 2 domain containing 3	protein-coding
mm_103224.1	chr11	70668653	70668677	-	1	NA	TTS (NM_001190378)	TTS (NM_001190378)	751	NM_172561	216873	Mm.432524	NM_172561	ENSMUSG00000018287	Spag7	5730443G10|ACRP|FSA-1|Fsa1l	sperm associated antigen 7	protein-coding
mm_104428.1	chr11	94950843	94950898	-	1	NA	exon (NM_007742, exon 49 of 51)	exon (NM_007742, exon 49 of 51)	14646	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_44826.1	chr5	33782811	33782826	-	1	NA	promoter-TSS (NM_019694)	promoter-TSS (NM_019694)	-114	NM_019694	56384	Mm.260538	NM_019694	ENSMUSG00000005299	Letm1	-	leucine zipper-EF-hand containing transmembrane protein 1	protein-coding
mm_135790.1	chr16	57167308	57167367	-	1	NA	promoter-TSS (NM_023175)	promoter-TSS (NM_023175)	-5	NM_023175	52633	Mm.383203	NM_023175	ENSMUSG00000022751	Nit2	1190017B19Rik|D16Ertd502e	nitrilase family, member 2	protein-coding
mm_56968.1	chr6	120187651	120187670	-	1	NA	intron (NM_016718, intron 1 of 3)	intron (NM_016718, intron 1 of 3)	-6163	NM_001347432	29862	Mm.103668	NM_016718	ENSMUSG00000041377	Ninj2	-	ninjurin 2	protein-coding
mm_48393.1	chr5	139819907	139819932	-	1	NA	Intergenic	Intergenic	-5636	NM_001161548	231832	Mm.482655	NM_144914	ENSMUSG00000036687	Tmem184a	Sdmg1	transmembrane protein 184a	protein-coding
mm_58911.1	chr7	17672236	17672259	+	1	NA	promoter-TSS (NR_002857)	promoter-TSS (NR_002857)	-66	NR_002857	232919	Mm.153893	NR_002857	ENSMUSG00000108558	Psg-ps1	AV036018|Cea-6|Cea6	pregnancy specific glycoprotein pseudogene 1	pseudo
mm_61198.1	chr7	63937772	63937811	+	1	NA	intron (NM_021366, intron 1 of 1)	CpG	1124	NM_021366	50794	Mm.240473	NM_021366	ENSMUSG00000052040	Klf13	0610043C13Rik|9430029L20Rik|Bteb3|FKLF-2|FKLF2|NSLP1|RFLAT-1|RFLAT1	Kruppel-like factor 13	protein-coding
mm_71130.1	chr8	36549382	36549386	+	1	NA	Intergenic	CpG	60193	NM_176952	319582	Mm.180924	NM_176952	ENSMUSG00000039620	6430573F11Rik	Kiaa1456|TRM9L	RIKEN cDNA 6430573F11 gene	protein-coding
mm_40970.1	chr5	77001464	77001470	+	1	NA	Intergenic	Intergenic	-2588	NM_206935	384185	Mm.451858	NM_206935	ENSMUSG00000063820	Arl9	1700110A09Rik	ADP-ribosylation factor-like 9	protein-coding
mm_65438.1	chr7	25388400	25388424	-	1	NA	exon (NM_010719, exon 2 of 10)	exon (NM_010719, exon 2 of 10)	1700	NM_001039507	16890	Mm.158548	NM_010719	ENSMUSG00000003123	Lipe	4933403G17Rik|HSL	lipase, hormone sensitive	protein-coding
mm_100764.1	chr11	4593806	4593809	-	1	NA	intron (NM_028860, intron 1 of 17)	intron (NM_028860, intron 1 of 17)	1008	NM_028860	74302	Mm.425669	NM_028860	ENSMUSG00000034354	Mtmr3	1700092A20Rik|AI255150|AW557713|FYVE-DSP1|ZFYVE10|mKIAA0371	myotubularin related protein 3	protein-coding
mm_36317.1	chr4	70252151	70252164	-	1	NA	intron (NM_145990, intron 27 of 36)	intron (NM_145990, intron 27 of 36)	158278	NM_001313762	214444	Mm.370777	NM_145990	ENSMUSG00000039298	Cdk5rap2	2900018K03Rik|an|mKIAA1633	CDK5 regulatory subunit associated protein 2	protein-coding
mm_72745.1	chr8	85087241	85087252	+	1	NA	exon (NM_010764, exon 6 of 24)	exon (NM_010764, exon 6 of 24)	3977	NM_010764	17159	Mm.4219	NM_010764	ENSMUSG00000005142	Man2b1	AW107687|LAMAN	mannosidase 2, alpha B1	protein-coding
mm_149225.1	chr19	10028465	10028477	+	1	NA	exon (NM_144538, exon 5 of 10)	exon (NM_144538, exon 5 of 10)	10243	NM_144538	74760	Mm.281969	NM_144538	ENSMUSG00000024663	Rab3il1	1200014K04Rik|AI115013|C76746|Rab3ail1	RAB3A interacting protein (rabin3)-like 1	protein-coding
mm_12897.1	chr2	84799421	84799443	+	1	NA	intron (NM_019949, intron 1 of 3)	intron (NM_019949, intron 1 of 3)	604	NM_019949	56791	Mm.38261	NM_019949	ENSMUSG00000027078	Ube2l6	2810489I21Rik|RIG-B|UBCH8|Ubce8|Ubcm8	ubiquitin-conjugating enzyme E2L 6	protein-coding
mm_86620.1	chr10	13966094	13966110	+	1	NA	promoter-TSS (NM_010437)	promoter-TSS (NM_010437)	-277	NM_010437	15273	Mm.42157	NM_010437	ENSMUSG00000015501	Hivep2	Gm20114|MIBP1|Schnurri-2|Shn-2	human immunodeficiency virus type I enhancer binding protein 2	protein-coding
mm_165557.1	chr3	14808410	14808421	-	1	NA	promoter-TSS (NM_009799)	promoter-TSS (NM_009799)	-50	NM_009799	12346	Mm.273195	NM_009799	ENSMUSG00000027556	Car1	AW555628|Ca1|Car-1	carbonic anhydrase 1	protein-coding
mm_28572.1	chr3	93445141	93445167	-	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	2824	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_128740.1	chr15	64312514	64312539	-	1	NA	5' UTR (NM_001276463, exon 1 of 28)	5' UTR (NM_001276463, exon 1 of 28)	147	NM_001276462	13196	Mm.277236	NM_010026	ENSMUSG00000022377	Asap1	AV239055|DEF-1|Ddef1|PAP|mKIAA1249|s19	ArfGAP with SH3 domain, ankyrin repeat and PH domain1	protein-coding
mm_12434.1	chr2	70661502	70661552	+	1	NA	promoter-TSS (NM_027352)	promoter-TSS (NM_027352)	18	NM_027352	70231	Mm.271950	NM_027352	ENSMUSG00000014959	Gorasp2	0610011A07Rik|2410043M02Rik|5730520M13Rik|9430094F20Rik|AW552058|ENSMUSG00000075299|GOLPH2|GRASP55|GRS2|p59	golgi reassembly stacking protein 2	protein-coding
mm_151812.1	chr19	5488942	5488950	-	1	NA	promoter-TSS (NM_027877)	promoter-TSS (NM_027877)	-610	NM_027877	71711	Mm.27697	NM_027877	ENSMUSG00000024906	Mus81	1200008A18Rik|AI182501|AW045863	MUS81 structure-specific endonuclease subunit	protein-coding
mm_25388.1	chr3	107218122	107218127	+	1	NA	exon (NM_001111143, exon 4 of 9)	exon (NM_001111143, exon 4 of 9)	3608	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_85167.1	chr9	96394956	96394971	-	1	NA	Intergenic	Intergenic	-30664	NM_007502	11933	Mm.424	NM_007502	ENSMUSG00000032412	Atp1b3	AA409958|AI664000|AW212096	ATPase, Na+/K+ transporting, beta 3 polypeptide	protein-coding
mm_58752.1	chr7	13324571	13324586	+	1	NA	Intergenic	MER54B|LTR|ERVL	-1089	NM_001168504	232889	Mm.223639	NM_001004762	ENSMUSG00000033847	Pla2g4c	D7Ertd445e	phospholipase A2, group IVC (cytosolic, calcium-independent)	protein-coding
mm_40116.1	chr5	34949436	34949504	+	1	NA	promoter-TSS (NM_173402)	promoter-TSS (NM_173402)	22	NM_173402	71729	Mm.196208	NM_173402	ENSMUSG00000029101	Rgs12	1200016K18Rik|4632412M04Rik|AI481290|E130309H11	regulator of G-protein signaling 12	protein-coding
mm_69880.1	chr7	141636800	141636806	-	1	NA	intron (NM_001330001, intron 31 of 33)	intron (NM_001330001, intron 31 of 33)	16102	NR_106030	102466798		NR_106030	ENSMUSG00000098759	Mir7063	Gm27654|mmu-mir-7063	microRNA 7063	ncRNA
mm_88777.1	chr10	80399823	80399848	+	1	NA	promoter-TSS (NM_013595)	promoter-TSS (NM_013595)	-304	NM_001306143	17192	Mm.7142	NM_013595	ENSMUSG00000035478	Mbd3	AI181826|AU019209	methyl-CpG binding domain protein 3	protein-coding
mm_54248.1	chr6	28260759	28260771	-	1	NA	exon (NM_001081678, exon 2 of 6)	exon (NM_001081678, exon 2 of 6)	836	NM_001081678	627049	Mm.84441	NM_001081678	ENSMUSG00000039841	Zfp800	AA407452|Znf800	zinc finger protein 800	protein-coding
mm_158033.1	chrX	97377191	97377195	-	1	NA	promoter-TSS (NM_001161432)	promoter-TSS (NM_001161432)	16	NM_001161432	245527	Mm.189270	NM_175540	ENSMUSG00000034457	Eda2r	9430060M22Rik|TNFRSF27|Xedar	ectodysplasin A2 receptor	protein-coding
mm_140462.1	chr17	91088213	91088215	+	1	NA	exon (NM_020252, exon 2 of 23)	exon (NM_020252, exon 2 of 23)	1391	NM_001346957	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_136670.1	chr17	6106851	6106875	+	1	NA	promoter-TSS (NM_001103181)	promoter-TSS (NM_001103181)	33	NM_001103181	68842	Mm.449307	NM_054040	ENSMUSG00000034377	Tulp4	1110057P05Rik|2210038L17Rik|Tusp	tubby like protein 4	protein-coding
mm_3518.1	chr1	150107491	150107505	+	1	NA	3' UTR (NM_011198, exon 10 of 10)	3' UTR (NM_011198, exon 10 of 10)	7467	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_155273.1	chrX	60050903	60050938	+	1	NA	Intergenic	Intergenic	51456	NM_001305797	14071	Mm.391283	NM_007979	ENSMUSG00000031138	F9	AW111646|Cf-9|Cf9	coagulation factor IX	protein-coding
mm_71734.1	chr8	62002103	62002107	+	1	NA	intron (NM_001293783, intron 28 of 37)	RLTR16C_MM|LTR|ERVK	74018	NM_001293783	234311	Mm.275233	NM_144928	ENSMUSG00000037921	Ddx60	9830118M07	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	protein-coding
mm_75764.1	chr8	69974236	69974257	-	1	NA	5' UTR (NM_001113346, exon 1 of 13)	5' UTR (NM_001113346, exon 1 of 13)	137	NM_001113346	234366	Mm.270044	NM_145596	ENSMUSG00000036180	Gatad2a	1110066C11Rik|BC031407|C80248	GATA zinc finger domain containing 2A	protein-coding
mm_91046.1	chr10	18653732	18653737	-	1	NA	intron (NM_001033258, intron 9 of 33)	intron (NM_001033258, intron 9 of 33)	90024	NM_001033258	215821	Mm.40491	NM_001033258	ENSMUSG00000019852	Arfgef3	9630004D11|B930094H20Rik|BIG3|D10Bwg1379e|mKIAA1244	ARFGEF family member 3	protein-coding
mm_159302.1	chr2	178078462	178078462	-	1	NA	promoter-TSS (NM_001162922)	promoter-TSS (NM_001162922)	-37	NM_001162922	353208	Mm.381194	NM_001162922	ENSMUSG00000078861	Zfp931	2810021G02Rik	zinc finger protein 931	protein-coding
mm_18594.1	chr2	66730192	66730193	-	1	NA	intron (NM_009135, intron 7 of 24)	intron (NM_009135, intron 7 of 24)	54718	NM_009135	20272	Mm.38127	NM_009135	ENSMUSG00000034810	Scn7a	1110034K09Rik|AI642000|NaG|Nav2|Nav2.3|Nax|Scn6a	sodium channel, voltage-gated, type VII, alpha	protein-coding
mm_115227.1	chr13	109837815	109837823	+	1	NA	intron (NM_011056, intron 7 of 16)	intron (NM_011056, intron 7 of 16)	-65990	NR_035442	100316683		NR_035442	ENSMUSG00000084651	Mir1904	Mirn1904|mmu-mir-1904	microRNA 1904	ncRNA
mm_148039.1	chr18	70244591	70244601	-	1	NA	promoter-TSS (NM_029346)	promoter-TSS (NM_029346)	-12	NM_029346	75577	Mm.58214	NM_029346	ENSMUSG00000024512	Dynap	2310002L13Rik	dynactin associated protein	protein-coding
mm_157743.1	chrX	73082412	73082434	-	1	NA	promoter-TSS (NM_001081642)	promoter-TSS (NM_001081642)	84	NM_001081642	434794	Mm.104764	NM_001081642	ENSMUSG00000079845	Xlr4a	-	X-linked lymphocyte-regulated 4A	protein-coding
mm_113586.1	chr13	40887182	40887199	+	1	NA	5' UTR (NM_008105, exon 1 of 3)	5' UTR (NM_008105, exon 1 of 3)	432	NM_008105	14538	Mm.314757	NM_008105	ENSMUSG00000021360	Gcnt2	5330430K10Rik|IGnT|IGnTA|IGnTB|IGnTC	glucosaminyl (N-acetyl) transferase 2, I-branching enzyme	protein-coding
mm_106870.1	chr12	8010312	8010326	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	32642	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_141559.1	chr17	32214733	32214755	-	1	NA	exon (NM_001286630, exon 9 of 20)	exon (NM_001286630, exon 9 of 20)	-25195	NM_001347341	71932	Mm.176240	NM_001033163	ENSMUSG00000037577	Ephx3	2310063B19Rik|Abhd9	epoxide hydrolase 3	protein-coding
mm_128218.1	chr15	36283106	36283150	-	1	NA	promoter-TSS (NM_013923)	promoter-TSS (NM_013923)	19	NM_013923	30945	Mm.5181	NM_013923	ENSMUSG00000022280	Rnf19a	AA032313|Dorfin|Rnf19|UIP117|Ubce7ip2|XYbp	ring finger protein 19A	protein-coding
mm_119133.1	chr14	31160759	31160765	+	1	NA	intron (NM_138672, intron 11 of 68)	intron (NM_138672, intron 11 of 68)	7879	NM_138672	192187	Mm.220821	NM_138672	ENSMUSG00000042286	Stab1	FEEL-1|FELE-1|MFEEL-1|MS-1|STAB-1|mKIAA0246	stabilin 1	protein-coding
mm_75499.1	chr8	52197135	52197144	-	1	NA	Intergenic	Intergenic	-1314563	NM_001205054	11593	Mm.334535	NM_001005847	ENSMUSG00000031521	Aga	AW060726	aspartylglucosaminidase	protein-coding
mm_75485.1	chr8	48843265	48843320	-	1	NA	Intergenic	CpG	-168602	NM_011857	23965	Mm.42191	NM_011857	ENSMUSG00000031561	Tenm3	2610100B16Rik|Odz1|Odz3|Ten-m3|mKIAA1455	teneurin transmembrane protein 3	protein-coding
mm_66522.1	chr7	45125892	45125915	-	1	NA	TTS (NR_000003)	TTS (NR_000003)	532	NR_000003	27211		NR_000003	ENSMUSG00000065818	Snord35a	Rnu35a|U35|U35A	small nucleolar RNA, C/D box 35A	snoRNA
mm_163181.1	chr11	91577504	91577512	-	1	NA	promoter-TSS (NM_028547)	promoter-TSS (NM_028547)	47	NM_028547	73470	Mm.67677	NM_028547	ENSMUSG00000046755	Kif2b	1700063D03Rik	kinesin family member 2B	protein-coding
mm_71674.1	chr8	60842343	60842354	+	1	NA	Intergenic	Intergenic	-48103	NM_028299	72612	Mm.25263	NM_028299	ENSMUSG00000038005	Hpf1	2700029M09Rik|C230006B22Rik|C4orf27	histone PARylation factor 1	protein-coding
mm_92352.1	chr10	75904452	75904456	-	1	NA	exon (NM_001161853, exon 7 of 9)	exon (NM_001161853, exon 7 of 9)	11056	NM_024440	70377	Mm.275878	NM_024440	ENSMUSG00000009092	Derl3	1810006I20Rik|1810063P04Rik|IZP6|derlin-3	Der1-like domain family, member 3	protein-coding
mm_155585.1	chrX	78737796	78737802	+	1	NA	promoter-TSS (NM_001164739)	promoter-TSS (NM_001164739)	36	NM_001164739	70864	Mm.66681	NM_001164739	ENSMUSG00000078315	Fam47c	4921509A18Rik|Fam47a|Fam47a-ps	family with sequence similarity 47, member C	protein-coding
mm_145507.1	chr18	60391594	60391604	+	1	NA	3' UTR (NM_001146275, exon 3 of 3)	3' UTR (NM_001146275, exon 3 of 3)	15570	NM_001146275	60440	Mm.261140	NM_021792	ENSMUSG00000054072	Iigp1	2900074L10Rik|AI046432|AW111922|Ifgga1|Iigp|Irga6	interferon inducible GTPase 1	protein-coding
mm_130973.1	chr15	103333811	103333836	-	1	NA	intron (NM_013866, intron 1 of 7)	intron (NM_013866, intron 1 of 7)	6263	NM_013866	29813	Mm.14099	NM_013866	ENSMUSG00000000552	Zfp385a	Hzf|Zfp385|Znf385a	zinc finger protein 385A	protein-coding
mm_60120.1	chr7	36171315	36171329	+	1	NA	Intergenic	Lx8b|LINE|L1	-368333	NM_177739	668501	Mm.286296	NM_177739	ENSMUSG00000044452	Zfp507	1810022O10Rik|A230056M16Rik|AL024009|AU021817|BB105092|Gm480|Znf507|mKIAA1084	zinc finger protein 507	protein-coding
mm_17197.1	chr2	25468147	25468162	-	1	NA	exon (NM_008963, exon 4 of 7)	exon (NM_008963, exon 4 of 7)	1595	NM_008963	19215	Mm.1008	NM_008963	ENSMUSG00000015090	Ptgds	21kDa|L-PGDS|PGD2|PGDS|PGDS2|Ptgs3	prostaglandin D2 synthase (brain)	protein-coding
mm_15095.1	chr2	153308606	153308655	+	1	NA	intron (NM_008444, intron 1 of 8)	intron (NM_008444, intron 1 of 8)	17214	NM_008444	16569	Mm.315560	NM_008444	ENSMUSG00000027475	Kif3b	AI854312|AW549267|mKIAA0359	kinesin family member 3B	protein-coding
mm_114002.1	chr13	52585950	52585963	+	1	NA	intron (NM_001198977, intron 1 of 13)	B3|SINE|B2	2519	NM_001198977	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_95678.1	chr11	54124417	54124420	+	1	NA	intron (NM_011031, intron 9 of 15)	intron (NM_011031, intron 9 of 15)	23494	NM_011031	18452	Mm.3705	NM_011031	ENSMUSG00000018906	P4ha2	AA407196|C76437|P4hl	procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha II polypeptide	protein-coding
mm_93027.1	chr10	88135780	88135786	-	1	NA	intron (NM_029249, intron 3 of 10)	intron (NM_029249, intron 3 of 10)	11158	NM_029249	75317	Mm.179378	NM_029249	ENSMUSG00000035365	Parpbp	4930547N16Rik|AI503644|PARI	PARP1 binding protein	protein-coding
mm_149927.1	chr19	26749839	26749877	+	1	NA	exon (NM_001347439, exon 2 of 8)	exon (NM_001347439, exon 2 of 8)	1455	NM_026003	67155	Mm.342988	NM_011416	ENSMUSG00000024921	Smarca2	2610209L14Rik|SNF2alpha|Snf2l2|brahma|brm	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	protein-coding
mm_38572.1	chr4	141814994	141815063	-	1	NA	TTS (NM_007919)	TTS (NM_007919)	10977	NM_007919	13706	Mm.45316	NM_007919	ENSMUSG00000058579	Cela2a	Ela-2|Ela2|Ela2a	chymotrypsin-like elastase family, member 2A	protein-coding
mm_126476.1	chr15	81523367	81523377	+	1	NA	Intergenic	CpG	57056	NM_019712	56438	Mm.29405	NM_019712	ENSMUSG00000022400	Rbx1	1500002P15Rik|AA517855|ROC1	ring-box 1	protein-coding
mm_165016.1	chr19	29101148	29101153	-	1	NA	promoter-TSS (NM_021525)	promoter-TSS (NM_021525)	-225	NM_021525	59028	Mm.28630	NM_021525	ENSMUSG00000024785	Rcl1	2310040A02Rik|AI789745|C76567|RPCL1|Rnac	RNA terminal phosphate cyclase-like 1	protein-coding
mm_94030.1	chr10	127884348	127884351	-	1	NA	3' UTR (NM_001150749, exon 4 of 4)	3' UTR (NM_001150749, exon 4 of 4)	4350	NM_017473	54150	Mm.6696	NM_017473	ENSMUSG00000040134	Rdh7	AI194929|CRAD2	retinol dehydrogenase 7	protein-coding
mm_84014.1	chr9	57646711	57646729	-	1	NA	intron (NM_001304761, intron 2 of 14)	intron (NM_001304761, intron 2 of 14)	-1067	NM_007783	12988	Mm.21974	NM_007783	ENSMUSG00000032312	Csk	AW212630|p50CSK	c-src tyrosine kinase	protein-coding
mm_40402.1	chr5	53003012	53003016	+	1	NA	Intergenic	Intergenic	-10722	NR_040413	75954	Mm.258937	NR_040413	ENSMUSG00000106352	5033403H07Rik	-	RIKEN cDNA 5033403H07 gene	ncRNA
mm_4884.1	chr1	188055007	188055010	+	1	NA	intron (NM_011935, intron 2 of 6)	intron (NM_011935, intron 2 of 6)	-46018	NR_038007	320272	Mm.446274	NR_038007	ENSMUSG00000103577	9330162B11Rik	-	RIKEN cDNA 9330162B11 gene	ncRNA
mm_81003.1	chr9	103426638	103426647	+	1	NA	non-coding (NR_040466, exon 2 of 6)	non-coding (NR_040466, exon 2 of 6)	3064	NR_040466	100529079	Mm.437003	NR_040466	ENSMUSG00000086236	5830418P13Rik	-	RIKEN cDNA 5830418P13 gene	ncRNA
mm_83327.1	chr9	44233476	44233527	-	1	NA	intron (NM_007619, intron 1 of 15)	intron (NM_007619, intron 1 of 15)	545	NM_007619	12402	Mm.266871	NM_007619	ENSMUSG00000034342	Cbl	4732447J05Rik|Cbl-2|c-Cbl|cbl	Casitas B-lineage lymphoma	protein-coding
mm_39796.1	chr5	30596007	30596024	+	1	NA	intron (NM_010608, intron 1 of 1)	intron (NM_010608, intron 1 of 1)	-7396	NR_040427	100502829	Mm.39944	NR_040427	ENSMUSG00000053214	Gm9899	ENSMUSG00000053214	predicted gene 9899	ncRNA
mm_154250.1	chr19	60766658	60766685	-	1	NA	exon (NM_010123, exon 19 of 22)	exon (NM_010123, exon 19 of 22)	7714	NR_034047	100217439		NR_034047		Snora19	MBI-51	small nucleolar RNA, H/ACA box 19	snoRNA
mm_92827.1	chr10	81472860	81472868	-	1	NA	intron (NM_001311124, intron 2 of 11)	intron (NM_001311124, intron 2 of 11)	267	NM_001311127	319586	Mm.152689	NM_176954	ENSMUSG00000034818	Celf5	4930565A21Rik|Brunol5	CUGBP, Elav-like family member 5	protein-coding
mm_166415.1	chr5	137151577	137151586	-	1	NA	Intergenic	Intergenic	-35374	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_42028.1	chr5	108279510	108279521	+	1	NA	3' UTR (NM_026106, exon 3 of 3)	3' UTR (NM_026106, exon 3 of 3)	10618	NM_026106	13486	Mm.303534	NM_026106	ENSMUSG00000029265	Dr1	1700121L09Rik|Dr1l|NC2|NC2beta	down-regulator of transcription 1	protein-coding
mm_124684.1	chr15	6435162	6435190	+	1	NA	exon (NM_001102400, exon 10 of 13)	exon (NM_001102400, exon 10 of 13)	-10157	NM_013485	12279	Mm.29095	NM_013485	ENSMUSG00000022149	C9	-	complement component 9	protein-coding
mm_39926.1	chr5	31596977	31596994	+	1	NA	Intergenic	Intergenic	-16966	NM_025796	66845	Mm.120763	NM_025796	ENSMUSG00000106918	Mrpl33	0610009M10Rik|L33mt|MRP-L33	mitochondrial ribosomal protein L33	protein-coding
mm_158053.1	chrX	100625884	100625900	-	1	NA	promoter-TSS (NM_008446)	promoter-TSS (NM_008446)	15	NM_028303	72621	Mm.291607	NM_028303	ENSMUSG00000015668	Pdzd11	1810012H22Rik|2310079D11Rik|2700099C19Rik|AI854765|Pdzk11	PDZ domain containing 11	protein-coding
mm_119286.1	chr14	34378783	34378795	+	1	NA	intron (NM_153127, intron 1 of 6)	intron (NM_153127, intron 1 of 6)	3285	NM_153127	105450	Mm.272673	NM_153127	ENSMUSG00000041445	Mmrn2	AA986839|ENDOGLYX1|Emilin3|EndoGlyx-1	multimerin 2	protein-coding
mm_28452.1	chr3	90614412	90614415	-	1	NA	TTS (NM_011313)	TTS (NM_011313)	1519	NM_011313	20200	Mm.100144	NM_011313	ENSMUSG00000001025	S100a6	2A9|5B10|CALCYCLIN|Cacy|PRA	S100 calcium binding protein A6 (calcyclin)	protein-coding
mm_125699.1	chr15	66909256	66909272	+	1	NA	intron (NM_018865, intron 2 of 4)	intron (NM_018865, intron 2 of 4)	17871	NM_018865	22402	Mm.10222	NM_018865	ENSMUSG00000005124	Wisp1	AW146261|CCN4|Elm1	WNT1 inducible signaling pathway protein 1	protein-coding
mm_77594.1	chr8	123892144	123892160	-	1	NA	exon (NM_009606, exon 7 of 7)	exon (NM_009606, exon 7 of 7)	2623	NM_001272041	11459	Mm.214950	NM_009606	ENSMUSG00000031972	Acta1	AA959943|Acta-2|Acts|Actsk-1	actin, alpha 1, skeletal muscle	protein-coding
mm_116761.1	chr13	52568091	52568098	-	1	NA	Intergenic	L1M5|LINE|L1	5131	NR_046069	100040572	Mm.278873	NR_046069		Gm2848	-	predicted gene 2848	ncRNA
mm_42936.1	chr5	122989243	122989252	+	1	NA	promoter-TSS (NM_001003953)	promoter-TSS (NM_001003953)	-107	NR_045820	109202	Mm.30769	NM_175405	ENSMUSG00000056735	A930024E05Rik	-	RIKEN cDNA A930024E05 gene	ncRNA
mm_133967.1	chr16	4214035	4214070	-	1	NA	promoter-TSS (NM_001025432)	promoter-TSS (NM_001025432)	-648	NM_001025432	12914	Mm.132238	NM_001025432	ENSMUSG00000022521	Crebbp	AW558298|CBP|CBP/p300|KAT3A|p300/CBP	CREB binding protein	protein-coding
mm_6283.1	chr1	69685781	69685828	-	1	NA	5' UTR (NM_011770, exon 1 of 8)	5' UTR (NM_011770, exon 1 of 8)	156	NM_011770	22779	Mm.106343	NM_011770	ENSMUSG00000025997	Ikzf2	A730095J18Rik|Helios|Zfpn1a2|Znfn1a2	IKAROS family zinc finger 2	protein-coding
mm_11829.1	chr2	45075436	45075439	+	1	NA	intron (NM_001289521, intron 1 of 8)	intron (NM_001289521, intron 1 of 8)	34840	NM_001289521	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_12122.1	chr2	61617175	61617190	+	1	NA	intron (NM_001164072, intron 2 of 7)	L2a|LINE|L2	24085	NM_001164071	21353	Mm.244393	NM_011529	ENSMUSG00000064289	Tank	C86182|E430026L09Rik|I-TRAF	TRAF family member-associated Nf-kappa B activator	protein-coding
mm_98933.1	chr11	98356728	98356738	+	1	NA	intron (NM_144828, intron 5 of 6)	intron (NM_144828, intron 5 of 6)	1550	NR_045477	69338	Mm.398308	NR_045477	ENSMUSG00000085944	1700003D09Rik	-	RIKEN cDNA 1700003D09 gene	ncRNA
mm_147242.1	chr18	38338998	38339007	-	1	NA	promoter-TSS (NM_011937)	promoter-TSS (NM_011937)	-9	NM_011937	26384	Mm.22374	NM_011937	ENSMUSG00000052102	Gnpda1	GNPDA|Gnp1|Gnpi|oscillin	glucosamine-6-phosphate deaminase 1	protein-coding
mm_71235.1	chr8	40906874	40906885	+	1	NA	intron (NM_007514, intron 6 of 11)	intron (NM_007514, intron 6 of 11)	-19354	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_64796.1	chr7	6685455	6685513	-	1	NA	intron (NM_011769, intron 5 of 7)	intron (NM_011769, intron 5 of 7)	10948	NM_011769	22776	Mm.89976	NM_011769	ENSMUSG00000002266	Zim1	-	zinc finger, imprinted 1	protein-coding
mm_12673.1	chr2	75773805	75773809	+	1	NA	Intergenic	Intergenic	-58370	NM_172666	228061	Mm.31227	NM_172666	ENSMUSG00000042410	Agps	5832437L22|9930035G10Rik|AW123847|Adaps|Adas|Adhaps|Adps|Aldhpsy|bs2	alkylglycerone phosphate synthase	protein-coding
mm_69366.1	chr7	130547390	130547410	-	1	NA	promoter-TSS (NM_001162855)	promoter-TSS (NM_001162855)	-19	NM_001162855	67872	Mm.21714	NM_001162855	ENSMUSG00000040331	Nsmce4a	2410003A14Rik	NSE4 homolog A, SMC5-SMC6 complex component	protein-coding
mm_16823.1	chr2	11473986	11473996	-	1	NA	3' UTR (NM_001177754, exon 16 of 16)	3' UTR (NM_001177754, exon 16 of 16)	28099	NM_001177754	170768	Mm.19669	NM_133232	ENSMUSG00000026773	Pfkfb3	E330010H22Rik|iPFK-2|uPFK-2	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	protein-coding
mm_97354.1	chr11	77493409	77493487	+	1	NA	promoter-TSS (NM_001004144)	promoter-TSS (NM_001004144)	36	NM_001004144	216963	Mm.290182	NM_001004144	ENSMUSG00000011877	Git1	Cat-1|p95Cat	G protein-coupled receptor kinase-interactor 1	protein-coding
mm_24853.1	chr3	95871520	95871580	+	1	NA	promoter-TSS (NR_040446)	promoter-TSS (NR_040446)	28	NR_040446	100042889	Mm.440109	NR_040446	ENSMUSG00000080727	C920021L13Rik	-	RIKEN cDNA C920021L13 gene	ncRNA
mm_92760.1	chr10	81089334	81089342	-	1	NA	exon (NM_145365, exon 7 of 12)	exon (NM_145365, exon 7 of 12)	9534	NM_145365	208677	Mm.294693	NM_145365	ENSMUSG00000035041	Creb3l3	BC010786|CREB-H|D10Bur1e	cAMP responsive element binding protein 3-like 3	protein-coding
mm_78997.1	chr9	45406067	45406109	+	1	NA	promoter-TSS (NM_007503)	promoter-TSS (NM_007503)	11	NM_007503	11936	Mm.22742	NM_007503	ENSMUSG00000059412	Fxyd2	Atp1g1	FXYD domain-containing ion transport regulator 2	protein-coding
mm_20403.1	chr2	129297206	129297216	-	1	NA	promoter-TSS (NM_181589)	promoter-TSS (NM_181589)	1	NM_181589	70466	Mm.45785	NM_181589	ENSMUSG00000048327	Ckap2l	2010016H04Rik|2610318C08Rik|AV070319|radmis|rdm	cytoskeleton associated protein 2-like	protein-coding
mm_115192.1	chr13	108775282	108775302	+	1	NA	intron (NM_011056, intron 1 of 16)	intron (NM_011056, intron 1 of 16)	121115	NM_011056	238871	Mm.434429	NM_011056	ENSMUSG00000021699	Pde4d	9630011N22Rik|Dpde3	phosphodiesterase 4D, cAMP specific	protein-coding
mm_116015.1	chr13	24761876	24761950	-	1	NA	promoter-TSS (NM_020567)	promoter-TSS (NM_020567)	24	NM_020567	57441	Mm.12239	NM_020567	ENSMUSG00000006715	Gmnn	AW546347|Gem	geminin	protein-coding
mm_90889.1	chr10	10234874	10234882	-	1	NA	Intergenic	Intergenic	237436	NM_001127353	215772	Mm.246573	NM_172547	ENSMUSG00000050994	Adgb	9130014G24Rik	androglobin	protein-coding
mm_137326.1	chr17	25016344	25016423	+	1	NA	5' UTR (NM_134126, exon 1 of 30)	5' UTR (NM_134126, exon 1 of 30)	297	NM_134126	106633	Mm.32802	NM_134126	ENSMUSG00000024169	Ift140	AI661311|Tce5|Wdtc2|mKIAA0590	intraflagellar transport 140	protein-coding
mm_107890.1	chr12	70459825	70459835	+	1	NA	intron (NM_028339, intron 4 of 7)	intron (NM_028339, intron 4 of 7)	6676	NM_028339	72736	Mm.204670	NM_028339	ENSMUSG00000021072	Tmx1	2810425A04Rik|AI465319|Txndc1	thioredoxin-related transmembrane protein 1	protein-coding
mm_20497.1	chr2	130393246	130393254	-	1	NA	intron (NM_019696, intron 11 of 13)	intron (NM_019696, intron 11 of 13)	4379	NM_019696	56264	Mm.112701	NM_019696	ENSMUSG00000027408	Cpxm1	AA986902|Cpx-1|Cpx1|Cpxm	carboxypeptidase X 1 (M14 family)	protein-coding
mm_125347.1	chr15	39198062	39198075	+	1	NA	promoter-TSS (NM_053271)	promoter-TSS (NM_053271)	-218	NM_001256382	116838	Mm.309296	NM_053271	ENSMUSG00000037386	Rims2	2810036I15Rik|AW048769|RIM2|Rab3ip2|Rim2(+40A)|Rim2(+44A)|Rim2(+4A)|Serg2|Syt3-rs|mKIAA0751	regulating synaptic membrane exocytosis 2	protein-coding
mm_131955.1	chr16	24486742	24486763	+	1	NA	intron (NM_001145952, intron 2 of 11)	intron (NM_001145952, intron 2 of 11)	38661	NM_001145952	210126	Mm.209385	NM_178665	ENSMUSG00000033306	Lpp	9430020K16Rik|AA959454|AU024130|B130055L10Rik|C79715|D630048H16	LIM domain containing preferred translocation partner in lipoma	protein-coding
mm_75560.1	chr8	58700982	58701000	-	1	NA	promoter-TSS (NM_001177534)	promoter-TSS (NM_001177534)	-195	NM_001177534	100271928	Mm.484123	NM_001177534		Gm15881	OTTMUSG00000027193	predicted gene 15881	protein-coding
mm_164756.1	chr17	84117839	84117852	-	1	NA	Intergenic	Intergenic	39185	NR_045458	74473	Mm.399575	NR_045458		4933433H22Rik	-	RIKEN cDNA 4933433H22 gene	ncRNA
mm_91892.1	chr10	59951732	59951742	-	1	NA	promoter-TSS (NM_029083)	promoter-TSS (NM_029083)	33	NM_029083	74747	Mm.21697	NM_029083	ENSMUSG00000020108	Ddit4	5830413E08Rik|AA415483|REDD1|Rtp801|dig2	DNA-damage-inducible transcript 4	protein-coding
mm_102540.1	chr11	61267103	61267134	-	1	NA	promoter-TSS (NM_007437)	promoter-TSS (NM_007437)	68	NM_001331114	11671	Mm.398221	NM_007437	ENSMUSG00000010025	Aldh3a2	AI194803|Ahd-3|Ahd-3r|Ahd3|Ahd3-r|Aldh4|Aldh4-r|FALDH	aldehyde dehydrogenase family 3, subfamily A2	protein-coding
mm_36890.1	chr4	107679381	107679395	-	1	NA	exon (NM_019872, exon 3 of 4)	exon (NM_019872, exon 3 of 4)	4774	NM_019872	56296	Mm.141324	NM_019872	ENSMUSG00000028610	Dmrtb1	Dmrt6|Prp13	DMRT-like family B with proline-rich C-terminal, 1	protein-coding
mm_65337.1	chr7	24978544	24978554	-	1	NA	exon (NM_001290469, exon 23 of 23)	exon (NM_001290469, exon 23 of 23)	-5821	NM_010261	14470	Mm.22473	NM_010261	ENSMUSG00000003380	Rabac1	2310040I06Rik|Gbpap1|PRA1|prenylin	Rab acceptor 1 (prenylated)	protein-coding
mm_62970.1	chr7	119896381	119896394	+	1	NA	promoter-TSS (NM_001163703)	promoter-TSS (NM_001163703)	95	NM_029610	73919	Mm.46381	NM_029610	ENSMUSG00000030922	Lyrm1	1110065L10Rik|2310004B22Rik|4930404J24Rik	LYR motif containing 1	protein-coding
mm_78258.1	chr9	21835636	21835646	+	1	NA	exon (NM_001080940, exon 1 of 4)	exon (NM_001080940, exon 1 of 4)	131	NM_001080940	624219	Mm.440264	NM_001080940	ENSMUSG00000047822	Angptl8	EG624219|Gm6484|Rifl	angiopoietin-like 8	protein-coding
mm_87970.1	chr10	63457506	63457539	+	1	NA	promoter-TSS (NM_001164376)	promoter-TSS (NM_001164376)	11	NM_001164376	216033	Mm.444692	NM_177612	ENSMUSG00000060843	Ctnna3	4930429L08Rik|4933408A16|Catna3|Vr22	catenin (cadherin associated protein), alpha 3	protein-coding
mm_115878.1	chr13	21753662	21753699	-	1	NA	promoter-TSS (NM_178201)	promoter-TSS (NM_178201)	232	NM_178183	319169	Mm.370338	NM_178183	ENSMUSG00000063021	Hist1h2ak	-	histone cluster 1, H2ak	protein-coding
mm_49834.1	chr6	37870963	37870973	+	1	NA	5' UTR (NM_145076, exon 1 of 19)	5' UTR (NM_145076, exon 1 of 19)	157	NM_145076	21848	Mm.41063	NM_145076	ENSMUSG00000029833	Trim24	A130082H20Rik|AI447469|D430004I05Rik|TIF1|TIF1-alpha|TIF1alpha|Tif1a	tripartite motif-containing 24	protein-coding
mm_11410.1	chr2	31572668	31572678	+	1	NA	promoter-TSS (NM_001290548)	promoter-TSS (NM_001290548)	22	NM_001290548	320267	Mm.207261	NM_001033389	ENSMUSG00000026843	Fubp3	A330051M14Rik|AV006371|FBP3|Marta2	far upstream element (FUSE) binding protein 3	protein-coding
mm_15645.1	chr2	163062436	163062455	+	1	NA	intron (NM_008652, intron 3 of 13)	intron (NM_008652, intron 3 of 13)	-5645	NR_105970	102465607		NR_105970	ENSMUSG00000099091	Mir7003	Gm27340|mmu-mir-7003	microRNA 7003	ncRNA
mm_167310.1	chr8	61700319	61700333	-	1	NA	intron (NM_001081390, intron 8 of 19)	intron (NM_001081390, intron 8 of 19)	59772	NM_001293773	72333	Mm.29933	NM_001081390	ENSMUSG00000058056	Palld	2410003B16Rik|6030492A02	palladin, cytoskeletal associated protein	protein-coding
mm_63257.1	chr7	126649411	126649432	+	1	NA	5' UTR (NM_029339, exon 1 of 10)	5' UTR (NM_029339, exon 1 of 10)	112	NM_029339	75565	Mm.45686	NM_029339	ENSMUSG00000030714	Sgf29	1700023O11Rik|9530025I05Rik|Ccdc101	SAGA complex associated factor 29	protein-coding
mm_115881.1	chr13	21780617	21780632	-	1	NA	promoter-TSS (NM_020034)	promoter-TSS (NM_020034)	1	NM_020034	56702	Mm.221314	NM_020034	ENSMUSG00000058773	Hist1h1b	H1.5|H1B|H1f5|H1s-3	histone cluster 1, H1b	protein-coding
mm_143176.1	chr17	57247304	57247316	-	1	NA	5' UTR (NM_001308074, exon 1 of 17)	5' UTR (NM_001308074, exon 1 of 17)	160	NM_001308074	78308	Mm.28468	NM_030084	ENSMUSG00000005823	Gpr108	1810015L19Rik|AA589464|C79132|Lustr2	G protein-coupled receptor 108	protein-coding
mm_160563.1	chr9	54193341	54193341	-	1	NA	exon (NM_007810, exon 1 of 9)	exon (NM_007810, exon 1 of 9)	101	NM_007810	13075	Mm.5199	NM_007810	ENSMUSG00000032274	Cyp19a1	Ar|ArKO|Cyp19|Int-5|Int5|p450arom	cytochrome P450, family 19, subfamily a, polypeptide 1	protein-coding
mm_44507.1	chr5	24030627	24030646	-	1	NA	promoter-TSS (NM_053090)	promoter-TSS (NM_053090)	54	NM_053090	84652	Mm.304976	NM_053090	ENSMUSG00000028995	Fam126a	AB030242|Drctnnb1a	family with sequence similarity 126, member A	protein-coding
mm_68715.1	chr7	119896286	119896305	-	1	NA	promoter-TSS (NM_001163703)	promoter-TSS (NM_001163703)	3	NM_029610	73919	Mm.46381	NM_029610	ENSMUSG00000030922	Lyrm1	1110065L10Rik|2310004B22Rik|4930404J24Rik	LYR motif containing 1	protein-coding
mm_128172.1	chr15	34443162	34443166	-	1	NA	promoter-TSS (NR_028101)	promoter-TSS (NR_028101)	61	NM_009083	19946	Mm.358632	NM_009083	ENSMUSG00000058600	Rpl30	-	ribosomal protein L30	protein-coding
mm_124131.1	chr14	84443363	84443412	-	1	NA	promoter-TSS (NM_001013753)	promoter-TSS (NM_001013753)	-176	NM_001013753	219228	Mm.153643	NM_001013753	ENSMUSG00000035566	Pcdh17	C030033F14Rik|Gm78	protocadherin 17	protein-coding
mm_79045.1	chr9	46228348	46228374	+	1	NA	promoter-TSS (NM_009692)	promoter-TSS (NM_009692)	-269	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2|apo-AI|apoA-I	apolipoprotein A-I	protein-coding
mm_109453.1	chr12	111076508	111076511	+	1	NA	intron (NM_198023, intron 2 of 11)	intron (NM_198023, intron 2 of 11)	36711	NM_198023	217864	Mm.23808	NM_198023	ENSMUSG00000037896	Rcor1	5730409O11|6720480E22Rik|AU042633|D12Wsu95e|Rocr1|mKIAA0071	REST corepressor 1	protein-coding
mm_17258.1	chr2	25945827	25945832	-	1	NA	intron (NM_001276359, intron 5 of 16)	B1_Mur4|SINE|Alu	37453	NM_001276360	227634	Mm.36834	NM_001115076	ENSMUSG00000026933	Camsap1	9530003A05Rik|C77823|PRO2405	calmodulin regulated spectrin-associated protein 1	protein-coding
mm_45089.1	chr5	44101543	44101560	-	1	NA	intron (NM_001163577, intron 1 of 27)	intron (NM_001163577, intron 1 of 27)	185	NM_008935	19126	Mm.6250	NM_008935	ENSMUSG00000029086	Prom1	4932416E19Rik|AC133|CD133|Prom|Prom-1|Proml1	prominin 1	protein-coding
mm_105375.1	chr11	103239869	103239875	-	1	NA	intron (NM_016896, intron 3 of 15)	intron (NM_016896, intron 3 of 15)	-21440	NM_177801	328019	Mm.189646	NM_177801	ENSMUSG00000044787	Spata32	4933400C05Rik|VAD1.2	spermatogenesis associated 32	protein-coding
mm_7849.1	chr1	132384777	132384780	-	1	NA	intron (NM_178874, intron 1 of 4)	intron (NM_178874, intron 1 of 4)	5540	NM_001311107	68875	Mm.273785	NM_178874	ENSMUSG00000042066	Tmcc2	1110063G11Rik	transmembrane and coiled-coil domains 2	protein-coding
mm_81148.1	chr9	106890182	106890211	+	1	NA	exon (NM_029103, exon 3 of 4)	exon (NM_029103, exon 3 of 4)	1742	NM_029103	74840	Mm.29778	NM_029103	ENSMUSG00000032575	Manf	3230402M22Rik|AA407711|AA408789|AA673178|Armet|D17914|D18Mgi17	mesencephalic astrocyte-derived neurotrophic factor	protein-coding
mm_131401.1	chr16	14370978	14370992	+	1	NA	intron (NM_008576, intron 1 of 30)	intron (NM_008576, intron 1 of 30)	9427	NM_008576	17250	Mm.196634	NM_008576	ENSMUSG00000023088	Abcc1	Abcc1a|Abcc1b|MRP|Mdrap|Mrp1	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	protein-coding
mm_5542.1	chr1	38472451	38472453	-	1	NA	intron (NM_001290814, intron 4 of 21)	intron (NM_001290814, intron 4 of 21)	154792	NM_001290814	16764	Mm.336679	NM_010678	ENSMUSG00000037138	Aff3	3222402O04Rik|A730046J16|LAF-4|Laf4	AF4/FMR2 family, member 3	protein-coding
mm_7521.1	chr1	124046004	124046085	-	1	NA	promoter-TSS (NM_199021)	promoter-TSS (NM_199021)	-485	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_54659.1	chr6	39118183	39118207	-	1	NA	promoter-TSS (NR_045813)	promoter-TSS (NR_045813)	154	NM_172893	243771	Mm.268462	NM_172893	ENSMUSG00000038507	Parp12	9930021O16|AA409132|AA536654|ARTD12|PARP-12|Zc3hdc1	poly (ADP-ribose) polymerase family, member 12	protein-coding
mm_32012.1	chr4	94739494	94739513	+	1	NA	5' UTR (NM_001290551, exon 1 of 22)	5' UTR (NM_001290551, exon 1 of 22)	214	NM_001290551	21687	Mm.14313	NM_013690	ENSMUSG00000006386	Tek	AA517024|Cd202b|Hyk|STK1|Tie-2|Tie2	endothelial-specific receptor tyrosine kinase	protein-coding
mm_133505.1	chr16	90738223	90738238	+	1	NA	promoter-TSS (NM_029844)	promoter-TSS (NM_029844)	-94	NM_029844	77037	Mm.22455	NM_029844	ENSMUSG00000039956	Mrap	1110025G12Rik|Falp|ORF61	melanocortin 2 receptor accessory protein	protein-coding
mm_82979.1	chr9	35849973	35849997	-	1	NA	promoter-TSS (NR_030730)	promoter-TSS (NR_030730)	-105	NR_030730	100041605	Mm.99350	NR_030730	ENSMUSG00000098705	Gm3428	-	predicted gene 3428	ncRNA
mm_127746.1	chr15	103462734	103462791	+	1	NA	exon (NM_153505, exon 7 of 31)	exon (NM_153505, exon 7 of 31)	8937	NM_153505	105855	Mm.30805	NM_153505	ENSMUSG00000022488	Nckap1l	4930568P13Rik|AI463083|Hem1|Hemp1	NCK associated protein 1 like	protein-coding
mm_42296.1	chr5	114444455	114444470	+	1	NA	promoter-TSS (NM_029956)	promoter-TSS (NM_029956)	193	NM_023556	17855	Mm.28088	NM_023556	ENSMUSG00000041939	Mvk	2310010A05Rik|AI256848|AI414037|MK	mevalonate kinase	protein-coding
mm_88321.1	chr10	75564199	75564217	+	1	NA	Intergenic	Intergenic	-3878	NM_198860	192734	Mm.259320	NM_198860	ENSMUSG00000046807	Lrrc75b	AI646023|Fam211b	leucine rich repeat containing 75B	protein-coding
mm_83932.1	chr9	56635963	56635977	-	1	NA	promoter-TSS (NM_001311076)	promoter-TSS (NM_001311076)	-322	NM_001311076	235402	Mm.246605	NM_181074	ENSMUSG00000049556	Lingo1	4930471K13Rik|AV148400|LERN1|LINGO-1|Lrrn6a|UNQ201	leucine rich repeat and Ig domain containing 1	protein-coding
mm_70036.1	chr7	142577395	142577405	-	1	NA	promoter-TSS (NR_030416)	promoter-TSS (NR_030416)	-253	NR_030416	735280		NR_030416	ENSMUSG00000076275	Mir675	Mirn675|mir-675|mmu-mir-675	microRNA 675	ncRNA
mm_118412.1	chr14	7791429	7791433	+	1	NA	Intergenic	CpG	-26526	NM_001081427	286940	Mm.489652	NM_134080	ENSMUSG00000025278	Flnb	AL024016|Fln-b	filamin, beta	protein-coding
mm_121679.1	chr14	12822995	12823012	-	1	NA	promoter-TSS (NM_001042617)	promoter-TSS (NM_001042617)	76	NM_001042617	27062	Mm.260881	NM_012061	ENSMUSG00000054423	Cadps	AU067781|CAPS|CAPS1|mKIAA1121	Ca2+-dependent secretion activator	protein-coding
mm_142280.1	chr17	40208590	40208616	-	1	NA	promoter-TSS (NM_031190)	promoter-TSS (NM_031190)	6	NM_031190	18663	Mm.717	NM_031190	ENSMUSG00000031233	Pgk2	Pgk-2|Tcp-2	phosphoglycerate kinase 2	protein-coding
mm_58764.1	chr7	15881647	15881668	+	1	NA	promoter-TSS (NR_038092)	promoter-TSS (NR_038092)	-960	NR_038092	546024	Mm.259041	NM_001033638	ENSMUSG00000074365	Crxos	AA606869|AY590891|Crxos1|Egam1	cone-rod homeobox, opposite strand	protein-coding
mm_138330.1	chr17	34894516	34894573	+	1	NA	promoter-TSS (NM_198886)	promoter-TSS (NM_198886)	-15	NM_198886	193736	Mm.161119	NM_198886	ENSMUSG00000049823	Zbtb12	BC020447|Bat-9|Bat9|G10|NG35	zinc finger and BTB domain containing 12	protein-coding
mm_47179.1	chr5	120749811	120749845	-	1	NA	promoter-TSS (NM_145227)	promoter-TSS (NM_145227)	20	NM_145227	246728	Mm.260926	NM_145227	ENSMUSG00000032690	Oas2	Oasl11	2'-5' oligoadenylate synthetase 2	protein-coding
mm_117489.1	chr13	78183183	78183197	-	1	NA	Intergenic	Intergenic	13259	NM_001347538	13865	Mm.439653	NM_010151	ENSMUSG00000069171	Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR-3|EAR3|Erbal3|SVP44|Tcfcoup1	nuclear receptor subfamily 2, group F, member 1	protein-coding
mm_38607.1	chr4	141861993	141862031	-	1	NA	intron (NM_025994, intron 1 of 3)	intron (NM_025994, intron 1 of 3)	12908	NM_025994	27984	Mm.395598	NM_025994	ENSMUSG00000040659	Efhd2	2600015J22Rik|AA408606|D4Wsu27e	EF hand domain containing 2	protein-coding
mm_152203.1	chr19	7607141	7607203	-	1	NA	promoter-TSS (NM_019516)	promoter-TSS (NM_019516)	4	NM_019516	56072	Mm.298242	NM_019516	ENSMUSG00000024972	Lgals12	AW987437|Grip1	lectin, galactose binding, soluble 12	protein-coding
mm_20170.1	chr2	122305707	122305715	-	1	NA	intron (NM_001305262, intron 6 of 9)	intron (NM_001305262, intron 6 of 9)	6811	NM_025777	66811	Mm.171333	NM_025777	ENSMUSG00000027225	Duoxa2	9030623N16Rik|Nip2	dual oxidase maturation factor 2	protein-coding
mm_50599.1	chr6	49218282	49218304	+	1	NA	Intergenic	CpG	-3339	NM_023670	140488	Mm.281018	NM_023670	ENSMUSG00000029814	Igf2bp3	2610101N11Rik|AA522010|AL022933|AU045931|IMP-3|IMP3|Koc13|Neilsen|mimp3	insulin-like growth factor 2 mRNA binding protein 3	protein-coding
mm_22802.1	chr3	25731183	25731216	+	1	NA	intron (NM_001163387, intron 3 of 5)	intron (NM_001163387, intron 3 of 5)	422108	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_61496.1	chr7	75752719	75752749	+	1	NA	3' UTR (NM_029332, exon 37 of 37)	3' UTR (NM_029332, exon 37 of 37)	-95604	NM_001122780	207952	Mm.206223	NM_029652	ENSMUSG00000055652	Klhl25	2810402K13Rik|BC027373|Enc-1	kelch-like 25	protein-coding
mm_52574.1	chr6	116338374	116338392	+	1	NA	5' UTR (NM_027920, exon 1 of 7)	5' UTR (NM_027920, exon 1 of 7)	361	NM_027920	71779	Mm.27064	NM_027920	ENSMUSG00000025702	March8	1300017E09Rik|MARCH-VIII|Mir	membrane-associated ring finger (C3HC4) 8	protein-coding
mm_90560.1	chr10	128194632	128194667	+	1	NA	promoter-TSS (NM_001285779)	promoter-TSS (NM_001285779)	14	NM_001285779	216456	Mm.30102	NM_001033264	ENSMUSG00000044005	Gls2	A330074B06Rik|AI195532|GA|GLS|Lga	glutaminase 2 (liver, mitochondrial)	protein-coding
mm_108518.1	chr12	84052115	84052145	+	1	NA	promoter-TSS (NM_134246)	promoter-TSS (NM_134246)	-14	NM_001346701	171281	Mm.202331	NM_134246	ENSMUSG00000021228	Acot3	AW108394|PTE-Ia|Pte2a	acyl-CoA thioesterase 3	protein-coding
mm_156505.1	chrX	146962477	146962485	+	1	NA	promoter-TSS (NM_008312)	promoter-TSS (NM_008312)	-32	NM_008312	15560	Mm.439670	NM_008312	ENSMUSG00000041380	Htr2c	5-HT2C|5-HT2cR|5-HTR2C|5HT1c|Htr1c|SR1	5-hydroxytryptamine (serotonin) receptor 2C	protein-coding
mm_58508.1	chr7	4119526	4119555	+	1	NA	promoter-TSS (NM_001109765)	promoter-TSS (NM_001109765)	10	NM_001001454	57776	Mm.29729	NM_021324	ENSMUSG00000030428	Ttyh1	4930459B04Rik|6330408P11Rik|TTY1|mTTY1|tty	tweety family member 1	protein-coding
mm_31668.1	chr4	60004769	60004793	+	1	NA	intron (NM_001081285, intron 2 of 5)	intron (NM_001081285, intron 2 of 5)	1232	NM_001081285	620807	Mm.464562	NM_001081285	ENSMUSG00000078689	Mup6	Gm12544|Mup2|OTTMUSG00000007423	major urinary protein 6	protein-coding
mm_113415.1	chr13	34021451	34021466	+	1	NA	intron (NM_009068, intron 7 of 10)	intron (NM_009068, intron 7 of 10)	-16183	NM_026512	68021	Mm.140243	NM_026512	ENSMUSG00000038286	Bphl	2010012D11Rik|5730533B08Rik|AI115341	biphenyl hydrolase-like (serine hydrolase, breast epithelial mucin-associated antigen)	protein-coding
mm_55035.1	chr6	48987427	48987435	-	1	NA	exon (NM_172888, exon 1 of 5)	exon (NM_172888, exon 1 of 5)	570	NM_172888	243377	Mm.446302	NM_172888	ENSMUSG00000039215	Svs1	9530003A11	seminal vesicle secretory protein 1	protein-coding
mm_155624.1	chrX	83593892	83593896	+	1	NA	intron (NM_007868, intron 7 of 78)	(CAGA)n|Simple_repeat|Simple_repeat	-105970	NM_021898	100502723	Mm.383210	NM_021898	ENSMUSG00000035522	Tsga8	Halap-X|Halapx	testis specific gene A8	protein-coding
mm_121926.1	chr14	23641713	23641735	-	1	NA	intron (NM_001253366, intron 3 of 29)	intron (NM_001253366, intron 3 of 29)	362481	NM_001253375	16531	Mm.343607	NM_010610	ENSMUSG00000063142	Kcnma1	5730414M22Rik|BKCa|MaxiK|Slo|Slo1|mSlo|mSlo1	potassium large conductance calcium-activated channel, subfamily M, alpha member 1	protein-coding
mm_52618.1	chr6	117173984	117173990	+	1	NA	3' UTR (NM_021704, exon 3 of 3)	3' UTR (NM_021704, exon 3 of 3)	5452	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_156343.1	chrX	139010120	139010144	+	1	NA	Intergenic	B4|SINE|B4	75104	NM_177920	331535	Mm.211704	NM_177920	ENSMUSG00000031271	Serpina7	C730040N12Rik|Tbg	serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 7	protein-coding
mm_95826.1	chr11	55406547	55406558	+	1	NA	exon (NM_009242, exon 4 of 10)	exon (NM_009242, exon 4 of 10)	13528	NM_009242	20692	Mm.291442	NM_009242	ENSMUSG00000018593	Sparc	BM-40|ON	secreted acidic cysteine rich glycoprotein	protein-coding
mm_80513.1	chr9	79793628	79793670	+	1	NA	promoter-TSS (NR_040734)	promoter-TSS (NR_040734)	8	NR_040734	74633	Mm.262175	NR_040734	ENSMUSG00000086918	4930429F24Rik	-	RIKEN cDNA 4930429F24 gene	ncRNA
mm_27357.1	chr3	50417980	50417992	-	1	NA	intron (NM_011990, intron 6 of 11)	intron (NM_011990, intron 6 of 11)	25627	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_12934.1	chr2	85060938	85060960	+	1	NA	intron (NM_001081260, intron 5 of 11)	intron (NM_001081260, intron 5 of 11)	10489	NM_001081260	228140	Mm.23606	NM_001081260	ENSMUSG00000033955	Tnks1bp1	Tab182|mKIAA1741	tankyrase 1 binding protein 1	protein-coding
mm_61170.1	chr7	59276915	59276924	+	1	NA	exon (NM_001033962, exon 4 of 11)	exon (NM_001033962, exon 4 of 11)	47230	NR_015479	330544	Mm.9002	NR_015479	ENSMUSG00000100826	C230091D08Rik	-	RIKEN cDNA C230091D08 gene	ncRNA
mm_40312.1	chr5	43856118	43856154	+	1	NA	Intergenic	B1_Mur3|SINE|Alu	-12673	NM_007646	12494	Mm.249873	NM_007646	ENSMUSG00000029084	Cd38	ADPRC 1|Cd38-rs1|I-19	CD38 antigen	protein-coding
mm_4914.1	chr1	190596536	190596554	+	1	NA	Intergenic	Intergenic	315225	NM_178775	320119	Mm.220912	NM_178775	ENSMUSG00000089872	Rps6kc1	AA682037|B130003F20Rik|C80612|Rpk118	ribosomal protein S6 kinase polypeptide 1	protein-coding
mm_81386.1	chr9	108953598	108953609	+	1	NA	promoter-TSS (NM_007738)	promoter-TSS (NM_007738)	-142	NM_007738	12836	Mm.6200	NM_007738	ENSMUSG00000025650	Col7a1	AW209154	collagen, type VII, alpha 1	protein-coding
mm_171832.1	chr5	146662026	146662036	+	1	NA	Intergenic	RLTR17|LTR|ERVK	-76792	NM_001010941	14738	Mm.153539	NM_008151	ENSMUSG00000041468	Gpr12	Gpcr01|Gpcr12|Gpcr20|Gpcr21	G-protein coupled receptor 12	protein-coding
mm_9980.1	chr1	191230397	191230424	-	1	NA	Intergenic	Intergenic	-47077	NM_007498	11910	Mm.2706	NM_007498	ENSMUSG00000026628	Atf3	LRG-21	activating transcription factor 3	protein-coding
mm_588.1	chr1	39493347	39493357	+	1	NA	Intergenic	HAL1|LINE|L1	-14605	NM_018775	54610	Mm.387293	NM_018775	ENSMUSG00000003134	Tbc1d8	AD3|HBLP1|VRP	TBC1 domain family, member 8	protein-coding
mm_140459.1	chr17	90048081	90048084	+	1	NA	intron (NM_001346962, intron 2 of 2)	intron (NM_001346962, intron 2 of 2)	40286	NM_001346962	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_73683.1	chr8	111550346	111550352	+	1	NA	intron (NM_001168623, intron 1 of 4)	(T)n|Simple_repeat|Simple_repeat	12006	NM_001168623	170737	Mm.271578	NM_133206	ENSMUSG00000033545	Znrf1	B830022L21Rik|Rnf42|Zrfp1|nin283	zinc and ring finger 1	protein-coding
mm_76109.1	chr8	80395238	80395240	-	1	NA	Intergenic	Intergenic	-98806	NM_010369	14934	Mm.13123	NM_010369	ENSMUSG00000051839	Gypa	AI853584|CD235a|GPA	glycophorin A	protein-coding
mm_95245.1	chr11	44617868	44617887	+	1	NA	promoter-TSS (NM_001290711)	promoter-TSS (NM_001290711)	-223	NM_001290711	13591	Mm.439662	NM_007897	ENSMUSG00000057098	Ebf1	Ebf|O/E-1|OE-1|Olf-1|Olf1	early B cell factor 1	protein-coding
mm_11157.1	chr2	28545067	28545104	+	1	NA	exon (NM_009058, exon 7 of 18)	exon (NM_009058, exon 7 of 18)	11621	NM_001145836	19730	Mm.5236	NM_009058	ENSMUSG00000026821	Ralgds	Gnds|Rgds|mKIAA1308	ral guanine nucleotide dissociation stimulator	protein-coding
mm_145271.1	chr18	52768337	52768387	+	1	NA	5' UTR (NM_001199154, exon 1 of 11)	5' UTR (NM_001199154, exon 1 of 11)	218	NM_001199154	67847	Mm.292168	NM_026408	ENSMUSG00000024534	Sncaip	2810407O15Rik|4933427B05Rik|BB104594|SYPH1	synuclein, alpha interacting protein (synphilin)	protein-coding
mm_46361.1	chr5	103309704	103309739	-	1	NA	Intergenic	Intergenic	-10692	NR_040699	74624	Mm.389662	NR_040699	ENSMUSG00000104956	4930429D17Rik	-	RIKEN cDNA 4930429D17 gene	ncRNA
mm_50687.1	chr6	51584526	51584543	+	1	NA	intron (NM_028035, intron 5 of 6)	ID_B1|SINE|B4	40011	NM_001127348	71982	Mm.294166	NM_028035	ENSMUSG00000038301	Snx10	2410004M09Rik	sorting nexin 10	protein-coding
mm_109885.1	chr12	5334638	5334641	-	1	NA	intron (NM_001164493, intron 1 of 13)	B1_Mur4|SINE|Alu	41043	NM_001164493	208439	Mm.388281	NM_001164493	ENSMUSG00000020627	Klhl29	A230106N14Rik|Gm68|Kbtbd9|mKIAA1921	kelch-like 29	protein-coding
mm_42626.1	chr5	118245384	118245443	+	1	NA	promoter-TSS (NM_001109902)	promoter-TSS (NM_001109902)	186	NM_001081236	76792	Mm.103428	NM_001081236	ENSMUSG00000032840	2410131K14Rik	-	RIKEN cDNA 2410131K14 gene	protein-coding
mm_161947.1	chr19	4398306	4398306	-	1	NA	Intergenic	CpG	-1229	NM_001001984	225876	Mm.31941	NM_001001984	ENSMUSG00000054611	Kdm2a	100043628|5530401A10Rik|AA589516|AW536790|Cxxc8|Fbl11|Fbl7|Fbxl11|Gm4560|Jhdm1|Jhdm1a|lalina	lysine (K)-specific demethylase 2A	protein-coding
mm_14895.1	chr2	149405316	149405332	+	1	NA	promoter-TSS (NM_021405)	promoter-TSS (NM_021405)	75	NM_021405	58214	Mm.117117	NM_021405	ENSMUSG00000033156	Cst10	DD72	cystatin 10 (chondrocytes)	protein-coding
mm_82780.1	chr9	27187005	27187012	-	1	NA	Intergenic	RMER17C|LTR|ERVK	-31587	NM_023277	83964	Mm.28770	NM_023277	ENSMUSG00000031990	Jam3	1110002N23Rik|JAM-3|JAM-C|Jcam3	junction adhesion molecule 3	protein-coding
mm_99269.1	chr11	101246961	101246981	+	1	NA	intron (NM_019444, intron 1 of 3)	intron (NM_019444, intron 1 of 3)	637	NM_019444	54409	Mm.260698	NM_019444	ENSMUSG00000001240	Ramp2	-	receptor (calcitonin) activity modifying protein 2	protein-coding
mm_146288.1	chr18	78476873	78476883	+	1	NA	intron (NM_030683, intron 2 of 11)	intron (NM_030683, intron 2 of 11)	120072	NM_207651	27411	Mm.44158	NM_030683	ENSMUSG00000024552	Slc14a2	UT-A1|UT-A3	solute carrier family 14 (urea transporter), member 2	protein-coding
mm_2353.1	chr1	92912046	92912063	+	1	NA	intron (NM_181405, intron 1 of 10)	intron (NM_181405, intron 1 of 10)	1229	NM_181405	108657	Mm.200971	NM_181405	ENSMUSG00000026269	Rnpepl1	1110014H17Rik|AI894167	arginyl aminopeptidase (aminopeptidase B)-like 1	protein-coding
mm_95729.1	chr11	54626370	54626417	+	1	NA	intron (NM_175258, intron 10 of 27)	intron (NM_175258, intron 10 of 27)	30247	NM_001252497	192786	Mm.254404	NM_175258	ENSMUSG00000037533	Rapgef6	A530068K01|AI844632|BB085664|C030018K18Rik|PDZ-GEF2|Pdzgef2|RA-GEF-2|Ragef2|mKIAA4052	Rap guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_120115.1	chr14	59491249	59491263	+	1	NA	intron (NM_026908, intron 3 of 10)	intron (NM_026908, intron 3 of 10)	50275	NM_026908	69008	Mm.179091	NM_026908	ENSMUSG00000021981	Cab39l	1500031K13Rik|2810425O13Rik|4930520C08Rik|AA589432|MO2L	calcium binding protein 39-like	protein-coding
mm_313.1	chr1	24230808	24230830	+	1	NA	intron (NM_007740, intron 29 of 37)	intron (NM_007740, intron 29 of 37)	35616	NM_001290691	12839	Mm.154662	NM_007740	ENSMUSG00000026147	Col9a1	Col9a-1	collagen, type IX, alpha 1	protein-coding
mm_145747.1	chr18	64386590	64386605	+	1	NA	exon (NM_194268, exon 2 of 2)	exon (NM_194268, exon 2 of 2)	46233	NM_194268	225631	Mm.234723	NM_194268	ENSMUSG00000045991	Onecut2	C730009D12|OC-2|Oc2	one cut domain, family member 2	protein-coding
mm_150083.1	chr19	29387441	29387453	+	1	NA	3' UTR (NM_021893, exon 7 of 7)	3' UTR (NM_021893, exon 7 of 7)	20009	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_7694.1	chr1	128766892	128766895	-	1	NA	Intergenic	Intergenic	-174594	NM_009911	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding
mm_70150.1	chr7	143460237	143460266	-	1	NA	exon (NM_001161624, exon 2 of 4)	exon (NM_001161624, exon 2 of 4)	799	NM_009876	12577	Mm.168789	NM_009876	ENSMUSG00000037664	Cdkn1c	AL024410|CDKI|Kip2|p57(kip2)|p57Kip2	cyclin-dependent kinase inhibitor 1C (P57)	protein-coding
mm_96205.1	chr11	62248978	62249011	+	1	NA	promoter-TSS (NM_007413)	promoter-TSS (NM_007413)	10	NM_007413	11541	Mm.40740	NM_007413	ENSMUSG00000018500	Adora2b	A2BAR|A2BR|A2b|AA2BR|AI480866|AI605384	adenosine A2b receptor	protein-coding
mm_30779.1	chr4	19280911	19280919	+	1	NA	promoter-TSS (NM_013927)	promoter-TSS (NM_013927)	65	NM_013927	30952	Mm.445778	NM_013927	ENSMUSG00000056494	Cngb3	CCNC2|CNG6|Cngbeta2	cyclic nucleotide gated channel beta 3	protein-coding
mm_145684.1	chr18	61632941	61632982	+	1	NA	Intergenic	Intergenic	-6692	NR_045420	545261	Mm.426593	NR_045420	ENSMUSG00000098098	Bvht	Braveheart|Gm20748	braveheart long non-coding RNA	ncRNA
mm_105366.1	chr11	103199479	103199503	-	1	NA	TTS (NM_001077698)	TTS (NM_001077698)	9057	NM_001254724	69441	Mm.380648	NM_027082	ENSMUSG00000020940	1700023F06Rik	-	RIKEN cDNA 1700023F06 gene	protein-coding
mm_147926.1	chr18	65939049	65939088	-	1	NA	promoter-TSS (NM_013833)	promoter-TSS (NM_013833)	21	NM_013833	19434	Mm.431047	NM_013833	ENSMUSG00000024518	Rax	7530406A22Rik|E130303K03Rik|Rx|ey-1|ey1	retina and anterior neural fold homeobox	protein-coding
mm_47568.1	chr5	124478272	124478282	-	1	NA	promoter-TSS (NM_030259)	promoter-TSS (NM_030259)	-42	NM_030259	80291	Mm.425280	NM_030259	ENSMUSG00000029401	Rilpl2	-	Rab interacting lysosomal protein-like 2	protein-coding
mm_1318.1	chr1	65100394	65100398	+	1	NA	TTS (NM_007774)	TTS (NM_007774)	2967	NM_007774	12964	Mm.26904	NM_007774	ENSMUSG00000044429	Cryga	Cryg-4|DGcry-4	crystallin, gamma A	protein-coding
mm_117937.1	chr13	99434562	99434570	-	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-21740	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_160593.1	chr9	71162866	71162866	-	1	NA	promoter-TSS (NM_001271843)	promoter-TSS (NM_001271843)	-233	NM_001271843	64008	Mm.449427	NM_022026	ENSMUSG00000032204	Aqp9	1700020I22Rik|AI266899|AQP-9	aquaporin 9	protein-coding
mm_141861.1	chr17	34804117	34804127	-	1	NA	exon (NM_009995, exon 2 of 10)	exon (NM_009995, exon 2 of 10)	304	NM_009995	13079	Mm.440407	NM_009995	ENSMUSG00000024365	Cyp21a1	21-OH|21OH|21OHA|21OHB|CYP21OH-A|Cyp21|Cyp21-ps1|Cyp21B|Cyp21a2-ps|Cyp21a2ps|Oh21-1|Oh21-2	cytochrome P450, family 21, subfamily a, polypeptide 1	protein-coding
mm_138360.1	chr17	34982155	34982168	+	1	NA	promoter-TSS (NM_030597)	promoter-TSS (NM_030597)	31	NM_030597	27756	Mm.165735	NM_030597	ENSMUSG00000007050	Lsm2	D17H6S56E-2|D17H6S56E2|Dmapl|Dmpkap|G7b|Sm-X5|SmX5|snRNP	LSM2 homolog, U6 small nuclear RNA and mRNA degradation associated	protein-coding
mm_144031.1	chr17	90037210	90037231	-	1	NA	exon (NM_001347419, exon 3 of 3)	exon (NM_001347419, exon 3 of 3)	51148	NM_001346962	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_161598.1	chr16	36561944	36561944	-	1	NA	5' UTR (NM_013803, exon 1 of 7)	5' UTR (NM_013803, exon 1 of 7)	190	NM_013803	12374	Mm.103619	NM_013803	ENSMUSG00000051980	Casr	CaR|Gprc2a	calcium-sensing receptor	protein-coding
mm_45154.1	chr5	49341488	49341491	-	1	NA	Intergenic	Intergenic	-55830	NM_001199244	80334	Mm.160172	NM_030265	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding
mm_120861.1	chr14	75229422	75229433	+	1	NA	3' UTR (NM_001247984, exon 16 of 16)	3' UTR (NM_001247984, exon 16 of 16)	-12860	NM_019775	56373	Mm.24242	NM_019775	ENSMUSG00000021999	Cpb2	1110032P04Rik|4930405E17Rik|AI255929|CPR|Cpu|TAFI	carboxypeptidase B2 (plasma)	protein-coding
mm_29979.1	chr3	133791516	133791523	-	1	NA	Intergenic	Intergenic	-247129	NM_001040400	214133	Mm.347816	NM_145989	ENSMUSG00000040943	Tet2	Ayu17-449|E130014J05Rik|mKIAA1546	tet methylcytosine dioxygenase 2	protein-coding
mm_88208.1	chr10	70191193	70191197	+	1	NA	3' UTR (NM_001111121, exon 9 of 9)	3' UTR (NM_001111121, exon 9 of 9)	-13469	NM_001304739	69563	Mm.64672	NM_001304739	ENSMUSG00000019933	Mrln	2310015B20Rik|Mln	myoregulin	protein-coding
mm_6250.1	chr1	68780834	68780834	-	1	NA	intron (NM_010154, intron 1 of 26)	intron (NM_010154, intron 1 of 26)	327225	NM_010154	13869	Mm.442420	NM_010154	ENSMUSG00000062209	Erbb4	Her4|c-erbB-4	erb-b2 receptor tyrosine kinase 4	protein-coding
mm_161806.1	chr17	57769359	57769359	+	1	NA	promoter-TSS (NM_001081653)	promoter-TSS (NM_001081653)	-211	NM_001081653	620292	Mm.391030	NM_001081653	ENSMUSG00000038048	Cntnap5c	Caspr5-3|EG620292|Gm325	contactin associated protein-like 5C	protein-coding
mm_103816.1	chr11	83003529	83003548	-	1	NA	exon (NM_181545, exon 6 of 6)	exon (NM_181545, exon 6 of 6)	-11708	NM_172796	237886	Mm.270253	NM_172796	ENSMUSG00000069793	Slfn9	9830137M10Rik	schlafen 9	protein-coding
mm_26350.1	chr3	142548211	142548225	+	1	NA	3' UTR (NM_001083312, exon 11 of 11)	3' UTR (NM_001083312, exon 11 of 11)	-11834	NM_018734	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_64870.1	chr7	14123073	14123075	-	1	NA	promoter-TSS (NM_001101586)	promoter-TSS (NM_001101586)	-81	NM_001101586	629203	Mm.482066	NM_001101586	ENSMUSG00000074375	Sult2a3	EG629203|Gm6955	sulfotransferase family 2A, dehydroepiandrosterone (DHEA)-preferring, member 3	protein-coding
mm_56536.1	chr6	99666763	99666786	-	1	NA	promoter-TSS (NM_025829)	promoter-TSS (NM_025829)	-3	NM_025829	66892	Mm.32889	NM_025829	ENSMUSG00000093661	Eif4e3	1300018P11Rik|AI451927|eIF4E-3	eukaryotic translation initiation factor 4E member 3	protein-coding
mm_145433.1	chr18	58836322	58836339	+	1	NA	promoter-TSS (NM_175506)	promoter-TSS (NM_175506)	-33	NM_175506	240322	Mm.71963	NM_175506	ENSMUSG00000053441	Adamts19	4831407I23Rik|AU015154|D230034E10Rik	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 19	protein-coding
mm_129595.1	chr15	79804718	79804732	-	1	NA	promoter-TSS (NM_030689)	promoter-TSS (NM_030689)	-16	NM_030689	73340	Mm.38438	NM_030689	ENSMUSG00000022421	Nptxr	1200009K17Rik|1700036C17Rik|5730406O18Rik|AI452369|AI785356|D15Bwg0580e|NPR|Npcd	neuronal pentraxin receptor	protein-coding
mm_52395.1	chr6	113306951	113306977	+	1	NA	promoter-TSS (NM_001282127)	promoter-TSS (NM_001282127)	-173	NM_030178	78783	Mm.356059	NM_030178	ENSMUSG00000001632	Brpf1	4833438B11Rik|4930540D11Rik|Brpf2	bromodomain and PHD finger containing, 1	protein-coding
mm_17874.1	chr2	34958103	34958113	-	1	NA	intron (NM_009421, intron 4 of 10)	intron (NM_009421, intron 4 of 10)	3664	NM_009421	22029	Mm.239514	NM_009421	ENSMUSG00000026875	Traf1	4732496E14Rik	TNF receptor-associated factor 1	protein-coding
mm_135618.1	chr16	52271519	52271530	-	1	NA	intron (NM_009655, intron 11 of 15)	L1_Mur3|LINE|L1	181557	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_62842.1	chr7	114181376	114181407	+	1	NA	Intergenic	MIRb|SINE|MIR	-63610	NM_025846	66922	Mm.276572	NM_025846	ENSMUSG00000055723	Rras2	2610016H24Rik|C86394|TC21	related RAS viral (r-ras) oncogene 2	protein-coding
mm_160289.1	chr7	127052011	127052011	-	1	NA	promoter-TSS (NM_026918)	promoter-TSS (NM_026918)	-34	NM_026918	69036	Mm.21835	NM_026918	ENSMUSG00000049350	Zg16	1810010M01Rik|AI593689|ZG16p	zymogen granule protein 16	protein-coding
mm_11109.1	chr2	28193070	28193076	+	1	NA	promoter-TSS (NM_001038613)	promoter-TSS (NM_001038613)	-20	NM_001038613	56177	Mm.43278	NM_019498	ENSMUSG00000026833	Olfm1	AMY|AW742568|Noe1|OlfA|Pancortin|Pancortin3	olfactomedin 1	protein-coding
mm_172408.1	chr7	17026940	17026961	-	1	NA	intron (NM_011155, intron 1 of 12)	intron (NM_011155, intron 1 of 12)	964	NM_011155	19060	Mm.3294	NM_011155	ENSMUSG00000003099	Ppp5c	AU020526|PP5	protein phosphatase 5, catalytic subunit	protein-coding
mm_9125.1	chr1	170540815	170540818	-	1	NA	intron (NM_001109985, intron 1 of 9)	intron (NM_001109985, intron 1 of 9)	16294	NM_027528	70729	Mm.487078	NM_027528	ENSMUSG00000038473	Nos1ap	6330408P19Rik|Capon	nitric oxide synthase 1 (neuronal) adaptor protein	protein-coding
mm_38995.1	chr4	151139522	151139577	-	1	NA	intron (NM_001081557, intron 9 of 23)	intron (NM_001081557, intron 9 of 23)	49979	NM_001308446	105704528	Mm.415128	NM_001308446	ENSMUSG00000078491	Gm13090	OTTMUSG00000010356	predicted gene 13090	protein-coding
mm_170774.1	chr2	164770047	164770054	+	1	NA	exon (NM_026785, exon 1 of 6)	exon (NM_026785, exon 1 of 6)	121	NM_026785	68612	Mm.89830	NM_026785	ENSMUSG00000001403	Ube2c	1110015A16Rik|D2Ertd695e	ubiquitin-conjugating enzyme E2C	protein-coding
mm_96136.1	chr11	60931144	60931167	+	1	NA	promoter-TSS (NM_008928)	promoter-TSS (NM_008928)	712	NR_027800	24082	Mm.46270	NM_025293	ENSMUSG00000042549	Map2k3os	F3-1|Gm16516|Gtlf3a	mitogen-activated protein kinase kinase 3, opposite strand	ncRNA
mm_163871.1	chr14	19419152	19419183	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	183420	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_110907.1	chr12	75818182	75818225	-	1	NA	promoter-TSS (NM_001005510)	promoter-TSS (NM_001005510)	-115	NM_001005510	319565	Mm.26652	NM_001005510	ENSMUSG00000063450	Syne2	6820443O06Rik|AW546258|Cpfl8|D12Ertd777e|NUA|Nesp2g|dice|mKIAA1011	spectrin repeat containing, nuclear envelope 2	protein-coding
mm_163509.1	chr12	113145463	113145474	+	1	NA	TTS (NM_024223)	TTS (NM_024223)	4863	NM_001347443	68337	Mm.133825	NM_024223	ENSMUSG00000006356	Crip2	0610010I23Rik|AW743261|C77570|CRP2|CRP4|Crp|ESP1|Hlp	cysteine rich protein 2	protein-coding
mm_105411.1	chr11	103627658	103627669	-	1	NA	Intergenic	Intergenic	11211	NM_027083	69444	Mm.275677	NM_027083	ENSMUSG00000020945	Lyzl6	1700023H08Rik|Lyc1|Lyzb	lysozyme-like 6	protein-coding
mm_50930.1	chr6	57663258	57663273	+	1	NA	3' UTR (NM_025992, exon 23 of 23)	3' UTR (NM_025992, exon 23 of 23)	28813	NM_025574	66459	Mm.44201	NM_025574	ENSMUSG00000043162	Pyurf	2610022G08Rik|AI847956|Prey	Pigy upstream reading frame	protein-coding
mm_55814.1	chr6	83033399	83033409	-	1	NA	promoter-TSS (NM_013586)	promoter-TSS (NM_013586)	67	NM_010070	13448	Mm.156	NM_010070	ENSMUSG00000068335	Dok1	AW557123|p62DOK	docking protein 1	protein-coding
mm_14889.1	chr2	148875225	148875256	+	1	NA	exon (NM_009976, exon 1 of 3)	exon (NM_009976, exon 1 of 3)	272	NM_009976	13010	Mm.4263	NM_009976	ENSMUSG00000027447	Cst3	CysC	cystatin C	protein-coding
mm_39494.1	chr5	20951961	20951992	+	1	NA	promoter-TSS (NM_001080977)	promoter-TSS (NM_001080977)	-154	NM_001080977	242860	Mm.254286	NM_001080977	ENSMUSG00000039968	Rsbn1l	8430412F05Rik|AI447441|C330002G24Rik	round spermatid basic protein 1-like	protein-coding
mm_116564.1	chr13	46930207	46930217	-	1	NA	promoter-TSS (NM_010617)	promoter-TSS (NM_010617)	-494	NM_010617	16553	Mm.342703	NM_010617	ENSMUSG00000021375	Kif13a	4930505I07Rik|mKIAA4109	kinesin family member 13A	protein-coding
mm_26658.1	chr3	154597220	154597244	+	1	NA	promoter-TSS (NM_172474)	promoter-TSS (NM_172474)	-134	NM_172474	209584	Mm.347513	NM_172474	ENSMUSG00000047583	Tyw3	5230400J09Rik	tRNA-yW synthesizing protein 3 homolog (S. cerevisiae)	protein-coding
mm_100208.1	chr11	116853255	116853272	+	1	NA	promoter-TSS (NM_178620)	promoter-TSS (NM_178620)	-169	NM_011358	20382	Mm.21841	NM_011358	ENSMUSG00000034120	Srsf2	D11Wsu175e|MRF-1|Pr264|SC35|Sfrs10|Sfrs2	serine/arginine-rich splicing factor 2	protein-coding
mm_91432.1	chr10	33256345	33256362	-	1	NA	promoter-TSS (NR_040657)	promoter-TSS (NR_040657)	4	NR_040657	442820	Mm.490725	NR_040657		D830005E20Rik	-	RIKEN cDNA D830005E20 gene	ncRNA
mm_165625.1	chr3	65390982	65390986	-	1	NA	intron (NM_026155, intron 2 of 4)	AT_rich|Low_complexity|Low_complexity	1569	NM_026155	67437	Mm.232728	NM_026155	ENSMUSG00000027828	Ssr3	0610038P07Rik|AL022999|AU022074|AW553833|TRAPG	signal sequence receptor, gamma	protein-coding
mm_161301.1	chr14	30715160	30715160	+	1	NA	promoter-TSS (NM_001166532)	promoter-TSS (NM_001166532)	-7	NM_001166531	54650	Mm.294662	NM_019460	ENSMUSG00000006527	Sfmbt1	4930442N21Rik|9330180L21Rik|AA536974|Sfmbt|Smr	Scm-like with four mbt domains 1	protein-coding
mm_68510.1	chr7	111122669	111122709	-	1	NA	promoter-TSS (NR_015573)	promoter-TSS (NR_015573)	-14	NR_015573	75479	Mm.381620	NR_015573	ENSMUSG00000110424	1700012D14Rik	-	RIKEN cDNA 1700012D14 gene	ncRNA
mm_120855.1	chr14	75226963	75227011	+	1	NA	exon (NM_001247984, exon 15 of 16)	exon (NM_001247984, exon 15 of 16)	-15300	NM_019775	56373	Mm.24242	NM_019775	ENSMUSG00000021999	Cpb2	1110032P04Rik|4930405E17Rik|AI255929|CPR|Cpu|TAFI	carboxypeptidase B2 (plasma)	protein-coding
mm_123502.1	chr14	66232257	66232269	-	1	NA	intron (NM_001162365, intron 1 of 30)	intron (NM_001162365, intron 1 of 30)	-18711	NM_001162366	19229	Mm.21613	NM_172498	ENSMUSG00000059456	Ptk2b	CADTK|CAKB|CAKbeta|E430023O05Rik|FADK2|FAK2|PYK2|Raftk	PTK2 protein tyrosine kinase 2 beta	protein-coding
mm_17615.1	chr2	30929895	30929908	-	1	NA	Intergenic	Intergenic	-23100	NM_133673	30934	Mm.249164	NM_133673	ENSMUSG00000026848	Tor1b	2610016F05Rik|DQ1|torsinB	torsin family 1, member B	protein-coding
mm_118294.1	chr13	113071157	113071180	-	1	NA	intron (NM_001281487, intron 5 of 11)	intron (NM_001281487, intron 5 of 11)	-24780	NM_027127	69590	Mm.12715	NM_027127	ENSMUSG00000021760	Gpx8	2310016C16Rik|AU017063	glutathione peroxidase 8 (putative)	protein-coding
mm_81995.1	chr9	121586995	121587005	+	1	NA	promoter-TSS (NR_040740)	promoter-TSS (NR_040740)	-20	NR_040740	75384	Mm.445955	NR_040740	ENSMUSG00000084995	Lyzl4os	4930589B17Rik|4930596M17Rik	lysozyme-like 4, opposite strand	ncRNA
mm_117922.1	chr13	99433597	99433607	-	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-20776	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_27803.1	chr3	75956388	75956456	-	1	NA	5' UTR (NM_175193, exon 1 of 15)	5' UTR (NM_175193, exon 1 of 15)	527	NM_175193	73124	Mm.249232	NM_175193	ENSMUSG00000034109	Golim4	3110027H23Rik|GIMPC|GPP130|Golph4|P138	golgi integral membrane protein 4	protein-coding
mm_113385.1	chr13	33027533	33027547	+	1	NA	5' UTR (NM_011452, exon 1 of 7)	5' UTR (NM_011452, exon 1 of 7)	126	NM_011452	20706	Mm.45371	NM_011452	ENSMUSG00000021403	Serpinb9b	1600019A21Rik|R86|SPI-CI|Spi10|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 9b	protein-coding
mm_32811.1	chr4	117126801	117126818	+	1	NA	promoter-TSS (NM_175030)	promoter-TSS (NM_175030)	-4	NM_175030	242646	Mm.358914	NM_175030	ENSMUSG00000047671	Tctex1d4	4833401D15Rik	Tctex1 domain containing 4	protein-coding
mm_121231.1	chr14	103055799	103055801	+	1	NA	3' UTR (NM_008392, exon 5 of 5)	3' UTR (NM_008392, exon 5 of 5)	8788	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_95906.1	chr11	58205063	58205095	+	1	NA	intron (NM_018738, intron 2 of 2)	B3|SINE|B2	5523	NM_018738	16145	Mm.33902	NM_018738	ENSMUSG00000078853	Igtp	AW558444|Irgm3	interferon gamma induced GTPase	protein-coding
mm_143557.1	chr17	74173906	74173915	-	1	NA	Intergenic	Intergenic	120953	NM_133771	76890	Mm.311874	NM_133771	ENSMUSG00000058704	Memo1	0610016J10Rik|D930048L02Rik	mediator of cell motility 1	protein-coding
mm_52835.1	chr6	121636219	121636237	+	1	NA	promoter-TSS (NM_175628)	promoter-TSS (NM_175628)	55	NM_175628	232345	Mm.30151	NM_175628	ENSMUSG00000030111	A2m	A2mp	alpha-2-macroglobulin	protein-coding
mm_35344.1	chr4	32241243	32241253	-	1	NA	Intergenic	Intergenic	-176187	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_118148.1	chr13	105054896	105054906	-	1	NA	promoter-TSS (NM_029879)	promoter-TSS (NM_029879)	29	NM_029879	52882	Mm.100348	NM_029879	ENSMUSG00000021719	Rgs7bp	A930030I01Rik|AI842293|D13Bwg1146e|R7bp	regulator of G-protein signalling 7 binding protein	protein-coding
mm_132035.1	chr16	27417173	27417193	+	1	NA	intron (NM_001025615, intron 4 of 9)	intron (NM_001025615, intron 4 of 9)	28227	NM_001289436	67501	Mm.258985	NM_026202	ENSMUSG00000038127	Ccdc50	C3orf6	coiled-coil domain containing 50	protein-coding
mm_79113.1	chr9	46270309	46270332	+	1	NA	exon (NM_080434, exon 4 of 4)	exon (NM_080434, exon 4 of 4)	1712	NM_080434	66113	Mm.29738	NM_080434	ENSMUSG00000032079	Apoa5	1300007O05Rik|Apoav|RAP3	apolipoprotein A-V	protein-coding
mm_61543.1	chr7	79308016	79308023	+	1	NA	intron (NM_018811, intron 3 of 10)	intron (NM_018811, intron 3 of 10)	34753	NM_018811	54608	Mm.365490	NM_018811	ENSMUSG00000039202	Abhd2	2210009N18Rik|LABH2|Labh-2	abhydrolase domain containing 2	protein-coding
mm_37823.1	chr4	131921020	131921022	-	1	NA	promoter-TSS (NM_001201367)	promoter-TSS (NM_001201367)	-750	NM_001201367	623230	Mm.421179	NM_001201367	ENSMUSG00000070720	Tmem200b	EG623230	transmembrane protein 200B	protein-coding
mm_136806.1	chr17	12382118	12382129	+	1	NA	exon (NM_008877, exon 2 of 19)	exon (NM_008877, exon 2 of 19)	3514	NM_008877	18815	Mm.971	NM_008877	ENSMUSG00000059481	Plg	AI649309|Pg	plasminogen	protein-coding
mm_48125.1	chr5	137149639	137149648	-	1	NA	Intergenic	Intergenic	-33436	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_33762.1	chr4	134344003	134344024	+	1	NA	exon (NM_001039677, exon 2 of 8)	exon (NM_001039677, exon 2 of 8)	547	NM_001346578	230810	Mm.358876	NM_001039677	ENSMUSG00000028836	Slc30a2	ZnT-2|Znt2	solute carrier family 30 (zinc transporter), member 2	protein-coding
mm_38147.1	chr4	134896330	134896340	-	1	NA	TTS (NM_011270)	TTS (NM_011270)	18581	NM_027935	71817	Mm.88349	NM_027935	ENSMUSG00000028822	Tmem50a	3200001F09Rik|CAM|Smp1	transmembrane protein 50A	protein-coding
mm_104810.1	chr11	98939611	98939623	-	1	NA	promoter-TSS (NM_001177303)	promoter-TSS (NM_001177303)	-94	NM_001177303	19401	Mm.439744	NM_009024	ENSMUSG00000037992	Rara	Nr1b1|RAR|RARalpha1	retinoic acid receptor, alpha	protein-coding
mm_26585.1	chr3	150588812	150588822	+	1	NA	Intergenic	Intergenic	-849065	NM_133222	170757	Mm.317261	NM_133222	ENSMUSG00000039167	Adgrl4	1110033N21Rik|ETL1|Eltd1|Etl	adhesion G protein-coupled receptor L4	protein-coding
mm_141925.1	chr17	35027635	35027647	-	1	NA	TTS (NR_130641)	TTS (NR_130641)	375	NR_028258	78376	Mm.390966	NM_023893	ENSMUSG00000036185	Sapcd1	2810436B06Rik|G7d|Ng23	suppressor APC domain containing 1	protein-coding
mm_113092.1	chr13	24104365	24104373	+	1	NA	intron (NM_026825, intron 17 of 37)	intron (NM_026825, intron 17 of 37)	-113155	NM_145399	214189	Mm.255667	NM_145399	ENSMUSG00000021337	Scgn	-	secretagogin, EF-hand calcium binding protein	protein-coding
mm_6256.1	chr1	69097006	69097006	-	1	NA	intron (NM_010154, intron 1 of 26)	intron (NM_010154, intron 1 of 26)	11053	NM_010154	13869	Mm.442420	NM_010154	ENSMUSG00000062209	Erbb4	Her4|c-erbB-4	erb-b2 receptor tyrosine kinase 4	protein-coding
mm_158687.1	chrX	160751265	160751274	-	1	NA	Intergenic	Intergenic	-16744	NM_011302	20147	Mm.41982	NM_011302	ENSMUSG00000031293	Rs1	Rs1h|Xlrs1|tmgc1	retinoschisis (X-linked, juvenile) 1 (human)	protein-coding
mm_125127.1	chr15	30173084	30173114	+	1	NA	5' UTR (NM_008729, exon 1 of 23)	5' UTR (NM_008729, exon 1 of 23)	506	NM_008729	18163	Mm.321648	NM_008729	ENSMUSG00000022240	Ctnnd2	Catnd2|Nprap|neurojugin	catenin (cadherin associated protein), delta 2	protein-coding
mm_163660.1	chr13	75690110	75690113	+	1	NA	Intergenic	Intergenic	-17373	NM_138953	192657	Mm.21288	NM_138953	ENSMUSG00000001542	Ell2	-	elongation factor RNA polymerase II 2	protein-coding
mm_33782.1	chr4	134873643	134873647	+	1	NA	intron (NM_011270, intron 1 of 9)	intron (NM_011270, intron 1 of 9)	9109	NM_011270	19746	Mm.195461	NM_011270	ENSMUSG00000028825	Rhd	Rh|Rhced|Rhl1	Rh blood group, D antigen	protein-coding
mm_38338.1	chr4	137742426	137742434	-	1	NA	3' UTR (NM_007431, exon 12 of 12)	3' UTR (NM_007431, exon 12 of 12)	17969	NR_138592	110351	Mm.180763	NM_029563	ENSMUSG00000041351	Rap1gap	1300019I11Rik|2310004O14Rik|AI427470|ARPP-90|Gap|Rap1GAP1|Rap1ga1	Rap1 GTPase-activating protein	protein-coding
mm_45305.1	chr5	65422885	65422895	-	1	NA	intron (NM_009466, intron 5 of 11)	intron (NM_009466, intron 5 of 11)	12952	NM_009466	22235	Mm.344831	NM_009466	ENSMUSG00000029201	Ugdh	Udpgdh	UDP-glucose dehydrogenase	protein-coding
mm_4377.1	chr1	172148059	172148094	+	1	NA	promoter-TSS (NM_153555)	promoter-TSS (NM_153555)	61	NM_153555	98193	Mm.159915	NM_153555	ENSMUSG00000026554	Dcaf8	AA408877|AA433120|AA792214|AU018973|C76055|D1Dau35e|D1Ucla4|H326|Wdr42a	DDB1 and CUL4 associated factor 8	protein-coding
mm_110737.1	chr12	69790661	69790735	-	1	NA	promoter-TSS (NM_183294)	promoter-TSS (NM_183294)	9	NM_183294	71091	Mm.132325	NM_183294	ENSMUSG00000020990	Cdkl1	4933411O17Rik	cyclin-dependent kinase-like 1 (CDC2-related kinase)	protein-coding
mm_145328.1	chr18	55539755	55539766	+	1	NA	Intergenic	Intergenic	-549580	NM_175751	269023	Mm.192984	NM_175751	ENSMUSG00000052713	Zfp608	4932417D18Rik|D430007A19Rik|Znf608	zinc finger protein 608	protein-coding
mm_124372.1	chr14	105897733	105897778	-	1	NA	promoter-TSS (NM_011897)	promoter-TSS (NM_011897)	-936	NM_011897	24064	Mm.89982	NM_011897	ENSMUSG00000022114	Spry2	sprouty2	sprouty homolog 2 (Drosophila)	protein-coding
mm_71872.1	chr8	69209096	69209106	+	1	NA	promoter-TSS (NM_001013379)	promoter-TSS (NM_001013379)	55	NM_001013379	234358	Mm.334577	NM_001013379	ENSMUSG00000059897	Zfp930	-	zinc finger protein 930	protein-coding
mm_4123.1	chr1	169693828	169693847	+	1	NA	3' UTR (NM_009063, exon 5 of 5)	3' UTR (NM_009063, exon 5 of 5)	38336	NM_009063	19737	Mm.20954	NM_009063	ENSMUSG00000026678	Rgs5	1110070A02Rik	regulator of G-protein signaling 5	protein-coding
mm_35191.1	chr4	16013836	16013856	-	1	NA	promoter-TSS (NM_145950)	promoter-TSS (NM_145950)	31	NM_145950	209212	Mm.46455	NM_145950	ENSMUSG00000041153	Osgin2	BC010311|C230027H09Rik	oxidative stress induced growth inhibitor family member 2	protein-coding
mm_155089.1	chrX	48138176	48138179	+	1	NA	Intergenic	Intergenic	-8259	NM_001313749	74131	Mm.276131	NM_028773	ENSMUSG00000031101	Sash3	1200013B08Rik|AW413946|SLY1	SAM and SH3 domain containing 3	protein-coding
mm_78119.1	chr9	20643405	20643411	+	1	NA	promoter-TSS (NM_013911)	promoter-TSS (NM_013911)	90	NM_025401	66177	Mm.390165	NM_025401	ENSMUSG00000084786	Ubl5	1110030M22Rik|beacon	ubiquitin-like 5	protein-coding
mm_47886.1	chr5	134703422	134703439	-	1	NA	3' UTR (NM_007925, exon 37 of 37)	3' UTR (NM_007925, exon 37 of 37)	-14840	NM_010717	16885	Mm.15409	NM_010717	ENSMUSG00000029674	Limk1	KIZ-1|LIMK-1|Limk	LIM-domain containing, protein kinase	protein-coding
mm_38442.1	chr4	139868652	139868652	-	1	NA	Intergenic	RMER1B|Other|Other	-35684	NM_011039	18509	Mm.218760	NM_011039	ENSMUSG00000028736	Pax7	Pax-7	paired box 7	protein-coding
mm_40942.1	chr5	76809965	76810010	+	1	NA	Intergenic	Intergenic	-30612	NM_001163793	320827	Mm.101504	NM_001163793	ENSMUSG00000036377	C530008M17Rik	2810489J07Rik|4930529A19Rik|4931405B09Rik|Kiaa1211|mKIAA1211	RIKEN cDNA C530008M17 gene	protein-coding
mm_148280.1	chr18	82477109	82477117	-	1	NA	intron (NM_001025245, intron 1 of 3)	intron (NM_001025245, intron 1 of 3)	1990	NM_001025245	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_152887.1	chr19	24678759	24678771	-	1	NA	3' UTR (NM_183160, exon 2 of 2)	3' UTR (NM_183160, exon 2 of 2)	4757	NM_183160	226040	Mm.391170	NM_183160	ENSMUSG00000048572	Tmem252	E030010A14Rik	transmembrane protein 252	protein-coding
mm_66899.1	chr7	59962000	59962014	-	1	NA	Intergenic	L1M4|LINE|L1	12424	NR_015456	52480	Mm.482346	NR_015456	ENSMUSG00000100826	Snhg14	AU018661|D7Ertd715e|Lncat	small nucleolar RNA host gene 14	ncRNA
mm_40613.1	chr5	64797946	64797948	+	1	NA	Intergenic	ORR1A3|LTR|ERVL-MaLR	-5576	NM_008453	16599	Mm.392759	NM_008453	ENSMUSG00000029178	Klf3	9930027G08Rik|AL024007|Bklf|Tef-2	Kruppel-like factor 3 (basic)	protein-coding
mm_164409.1	chr16	36367725	36367766	-	1	NA	promoter-TSS (NM_001082546)	promoter-TSS (NM_001082546)	-175	NM_001082546	100034684	Mm.383561	NM_001082546	ENSMUSG00000071561	BC100530	-	cDNA sequence BC100530	protein-coding
mm_49020.1	chr6	4759472	4759474	+	1	NA	3' UTR (NM_130877, exon 2 of 2)	3' UTR (NM_130877, exon 2 of 2)	12167	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_116398.1	chr13	41220396	41220412	-	1	NA	promoter-TSS (NM_019423)	promoter-TSS (NM_019423)	-1	NM_019423	54326	Mm.2567	NM_019423	ENSMUSG00000021364	Elovl2	AI317360|Ssc2	elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 2	protein-coding
mm_13331.1	chr2	102785813	102785824	+	1	NA	3' UTR (NM_001077514, exon 11 of 11)	3' UTR (NM_001077514, exon 11 of 11)	79380	NM_001077515	20511	Mm.267547	NM_011393	ENSMUSG00000005089	Slc1a2	1700091C19Rik|2900019G14Rik|AI159670|Eaat2|GLT-1|GLT1|MGLT1	solute carrier family 1 (glial high affinity glutamate transporter), member 2	protein-coding
mm_94036.1	chr10	128007590	128007628	-	1	NA	promoter-TSS (NM_013786)	promoter-TSS (NM_013786)	-101	NM_013786	27400	Mm.26719	NM_013786	ENSMUSG00000025396	Hsd17b6	17betaHSD9|Hsd17b9|Rdh8	hydroxysteroid (17-beta) dehydrogenase 6	protein-coding
mm_65775.1	chr7	28766192	28766225	-	1	NA	promoter-TSS (NM_001122766)	promoter-TSS (NM_001122766)	436	NM_001306222	18036	Mm.220333	NM_010908	ENSMUSG00000030595	Nfkbib	I(Kappa)B(beta)|I-kappa-B-beta|IKB-beta|IKappaBbeta|IkB|IkBb|NF-kappa-BIB|ikB-B	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, beta	protein-coding
mm_139211.1	chr17	47728761	47728763	+	1	NA	exon (NM_025973, exon 2 of 9)	exon (NM_025973, exon 2 of 9)	1920	NM_025973	109820	Mm.22957	NM_025973	ENSMUSG00000023987	Pgc	2210410L06Rik|Upg-1|Upg1	progastricsin (pepsinogen C)	protein-coding
mm_72966.1	chr8	92840433	92840457	+	1	NA	exon (NM_008610, exon 9 of 13)	exon (NM_008610, exon 9 of 13)	13148	NM_008610	17390	Mm.29564	NM_008610	ENSMUSG00000031740	Mmp2	Clg4a|GelA|MMP-2	matrix metallopeptidase 2	protein-coding
mm_48847.1	chr5	149618788	149618805	-	1	NA	exon (NM_013559, exon 16 of 18)	exon (NM_013559, exon 16 of 18)	17519	NM_013559	15505	Mm.270681	NM_013559	ENSMUSG00000029657	Hsph1	105kDa|AI790491|Hsp105|Hsp110|hsp-E7I|hsp110/105	heat shock 105kDa/110kDa protein 1	protein-coding
mm_153159.1	chr19	34492719	34492734	-	1	NA	3' UTR (NM_021460, exon 10 of 10)	3' UTR (NM_021460, exon 10 of 10)	-17591	NM_009890	12642	Mm.30824	NM_009890	ENSMUSG00000050370	Ch25h	AI462618|m25OH	cholesterol 25-hydroxylase	protein-coding
mm_107649.1	chr12	52529443	52529446	+	1	NA	intron (NM_009706, intron 1 of 5)	PB1D11|SINE|Alu	13367	NM_009706	11855	Mm.35059	NM_009706	ENSMUSG00000035133	Arhgap5	p190-B|p190B	Rho GTPase activating protein 5	protein-coding
mm_164602.1	chr17	29327101	29327110	+	1	NA	exon (NM_023734, exon 5 of 7)	exon (NM_023734, exon 5 of 7)	8223	NM_023734	74116	Mm.30950	NM_023734	ENSMUSG00000024011	Pi16	1200009H11Rik|Cripi|PI-16	peptidase inhibitor 16	protein-coding
mm_161994.1	chr19	36057465	36057465	-	1	NA	promoter-TSS (NM_008315)	promoter-TSS (NM_008315)	-105	NM_008315	15566	Mm.254266	NM_008315	ENSMUSG00000024798	Htr7	5-HT7	5-hydroxytryptamine (serotonin) receptor 7	protein-coding
mm_83856.1	chr9	54642700	54642723	-	1	NA	intron (NM_053178, intron 1 of 13)	intron (NM_053178, intron 1 of 13)	19174	NM_053178	94180	Mm.20592	NM_053178	ENSMUSG00000032281	Acsbg1	BG1|Bgm|E230019G03Rik|GR-LACS|Lpd|R75185	acyl-CoA synthetase bubblegum family member 1	protein-coding
mm_19960.1	chr2	117418721	117418728	-	1	NA	Intergenic	Intergenic	-75847	NM_011246	19419	Mm.42150	NM_011246	ENSMUSG00000027347	Rasgrp1	Rasgrp	RAS guanyl releasing protein 1	protein-coding
mm_143017.1	chr17	56476487	56476493	-	1	NA	promoter-TSS (NM_001252453)	promoter-TSS (NM_001252453)	-10	NM_011218	19280	Mm.258771	NM_011218	ENSMUSG00000013236	Ptprs	AL022616|PTP|PTP-NU3|PTPNU-3|PTPsigma|Ptpt9|R-PTP-S|RPTPsigma	protein tyrosine phosphatase, receptor type, S	protein-coding
mm_168641.1	chr11	85072441	85072452	+	1	NA	intron (NM_001029934, intron 5 of 33)	intron (NM_001029934, intron 5 of 33)	67509	NM_001029934	237898	Mm.178524	NM_001029934	ENSMUSG00000000804	Usp32	2900074J03Rik|6430526O11Rik|AW045245	ubiquitin specific peptidase 32	protein-coding
mm_107860.1	chr12	69724988	69725004	+	1	NA	promoter-TSS (NM_026536)	promoter-TSS (NM_026536)	34	NM_026536	68055	Mm.27844	NM_026536	ENSMUSG00000054894	Atp5s	1110015E18Rik|ATPW	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit S	protein-coding
mm_99669.1	chr11	105967939	105967956	+	1	NA	promoter-TSS (NM_001281819)	promoter-TSS (NM_001281819)	2	NM_207624	11421	Mm.754	NM_009598	ENSMUSG00000020681	Ace	AW208573|CD143	angiotensin I converting enzyme (peptidyl-dipeptidase A) 1	protein-coding
mm_2011.1	chr1	87127695	87127695	+	1	NA	exon (NM_007432, exon 11 of 11)	exon (NM_007432, exon 11 of 11)	2687	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_75999.1	chr8	72475094	72475102	-	1	NA	5' UTR (NM_138585, exon 1 of 18)	5' UTR (NM_138585, exon 1 of 18)	135	NM_138585	27967	Mm.30136	NM_138585	ENSMUSG00000052488	Cherp	5730408I11Rik|D8Wsu96e|DAN16|Scaf6	calcium homeostasis endoplasmic reticulum protein	protein-coding
mm_131417.1	chr16	14705833	14705858	+	1	NA	promoter-TSS (NM_011415)	promoter-TSS (NM_011415)	-14	NM_011415	20583	Mm.4272	NM_011415	ENSMUSG00000022676	Snai2	Slug|Slugh|Snail2	snail family zinc finger 2	protein-coding
mm_53309.1	chr6	129181853	129181863	+	1	NA	intron (NM_053109, intron 1 of 4)	intron (NM_053109, intron 1 of 4)	1243	NM_053109	93694	Mm.197536	NM_053109	ENSMUSG00000030157	Clec2d	Clr-b|Clrb|Ocil	C-type lectin domain family 2, member d	protein-coding
mm_108927.1	chr12	100992971	100992973	+	1	NA	intron (NM_026681, intron 3 of 29)	ORR1G|LTR|ERVL-MaLR	28796	NR_035421	100316805		NR_035421	ENSMUSG00000080575	Mir1190	Mirn1190|mmu-mir-1190	microRNA 1190	ncRNA
mm_77790.1	chr9	3026738	3026769	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	11990	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_84590.1	chr9	70036706	70036711	-	1	NA	5' UTR (NM_028087, exon 2 of 3)	5' UTR (NM_028087, exon 2 of 3)	1380	NM_028087	72077	Mm.195555	NM_028087	ENSMUSG00000032226	Gcnt3	2010013H22Rik|2210021I22Rik|2210401J11Rik	glucosaminyl (N-acetyl) transferase 3, mucin type	protein-coding
mm_41950.1	chr5	105741590	105741598	+	1	NA	intron (NM_001122768, intron 2 of 2)	AT_rich|Low_complexity|Low_complexity	40784	NM_178701	231549	Mm.23837	NM_178701	ENSMUSG00000046079	Lrrc8d	2810473G09Rik|4930525N13Rik|A930019F03|Lrrc5	leucine rich repeat containing 8D	protein-coding
mm_151593.1	chr19	3389189	3389244	-	1	NA	promoter-TSS (NM_001286558)	promoter-TSS (NM_001286558)	-162	NM_001286557	17771	Mm.209941	NM_010841	ENSMUSG00000024905	Mtl5	tesmin	metallothionein-like 5, testis-specific (tesmin)	protein-coding
mm_7568.1	chr1	124791545	124791591	-	1	NA	Intergenic	B4|SINE|B4	644159	NM_023735	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding
mm_147629.1	chr18	58210409	58210419	-	1	NA	promoter-TSS (NM_010181)	promoter-TSS (NM_010181)	-488	NM_010181	14119	Mm.20271	NM_010181	ENSMUSG00000024598	Fbn2	BC063774|Fib-2|mKIAA4226|sne|sy	fibrillin 2	protein-coding
mm_122019.1	chr14	27429302	27429346	-	1	NA	exon (NM_001114879, exon 1 of 24)	exon (NM_001114879, exon 1 of 24)	477	NM_001114879	218850	Mm.247767	NM_028945	ENSMUSG00000040651	Fam208a	4732418E12|4933409E02Rik|D14Abb1e|MommeD6	family with sequence similarity 208, member A	protein-coding
mm_98825.1	chr11	97362397	97362464	+	1	NA	promoter-TSS (NM_138657)	promoter-TSS (NM_138657)	-121	NM_138657	192157	Mm.34339	NM_138657	ENSMUSG00000038485	Socs7	2310063P06Rik|C85125|Nap4	suppressor of cytokine signaling 7	protein-coding
mm_13226.1	chr2	97467687	97467699	+	1	NA	promoter-TSS (NM_178725)	promoter-TSS (NM_178725)	36	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_83648.1	chr9	49505487	49505511	-	1	NA	exon (NM_001311065, exon 18 of 18)	exon (NM_001311065, exon 18 of 18)	-12789	NR_029465	100036537	Mm.437541	NR_029465	ENSMUSG00000079564	Gm11149	ENSMUSG00000060603|ENSMUSG00000079564	predicted gene 11149	ncRNA
mm_25549.1	chr3	115888243	115888250	+	1	NA	promoter-TSS (NR_027895)	promoter-TSS (NR_027895)	63	NM_027193	69740	Mm.5915	NM_027193	ENSMUSG00000033554	Dph5	2410012M04Rik|AU045680|C80186	diphthamide biosynthesis 5	protein-coding
mm_59681.1	chr7	28436364	28436370	+	1	NA	promoter-TSS (NM_175021)	promoter-TSS (NM_175021)	-176	NM_175021	233033	Mm.54120	NM_175021	ENSMUSG00000109336	Samd4b	BC042901	sterile alpha motif domain containing 4B	protein-coding
mm_21534.1	chr2	163690599	163690608	-	1	NA	intron (NM_001039390, intron 2 of 4)	intron (NM_001039390, intron 2 of 4)	-3434	NM_011106	18769	Mm.10091	NM_011106	ENSMUSG00000035268	Pkig	PKIgamma	protein kinase inhibitor, gamma	protein-coding
mm_109829.1	chr12	3960440	3960482	-	1	NA	exon (NM_008895, exon 3 of 3)	exon (NM_008895, exon 3 of 3)	5516	NM_001278583	18976	Mm.277996	NM_008895	ENSMUSG00000020660	Pomc	ACTH|BE|Beta-LPH|Clip|Gamma-LPH|Npp|Pomc-1|Pomc1|alpha-MSH|alphaMSH|beta-MSH|gamma-MSH	pro-opiomelanocortin-alpha	protein-coding
mm_87484.1	chr10	51493979	51493989	+	1	NA	intron (NM_001291894, intron 5 of 8)	intron (NM_001291894, intron 5 of 8)	3086	NM_013532	14728	Mm.34408	NM_013532	ENSMUSG00000062593	Lilrb4a	CD85K|Gp49b|HM18|ILT3|LIR-5|Lilrb4|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4A	protein-coding
mm_64174.1	chr7	141457033	141457066	+	1	NA	intron (NR_028142, intron 2 of 9)	intron (NR_028142, intron 2 of 9)	1861	NM_001163689	66853	Mm.29998	NM_025802	ENSMUSG00000025509	Pnpla2	0610039C21Rik|1110001C14Rik|Atgl|TTS-2.2	patatin-like phospholipase domain containing 2	protein-coding
mm_167948.1	chrX	138920338	138920338	+	1	NA	intron (NM_013724, intron 1 of 27)	intron (NM_013724, intron 1 of 27)	5908	NM_013724	27206	Mm.482319	NM_013724	ENSMUSG00000052854	Nrk	AA407323|AA409510|AI225895|AV168563|AW538185|Nesk	Nik related kinase	protein-coding
mm_165331.1	chr2	114013693	114013727	+	1	NA	promoter-TSS (NM_010290)	promoter-TSS (NM_010290)	-91	NM_010290	14617	Mm.389394	NM_010290	ENSMUSG00000068615	Gjd2	Gja9|connexin36|cx36	gap junction protein, delta 2	protein-coding
mm_75605.1	chr8	61869654	61869656	-	1	NA	intron (NM_001081390, intron 2 of 19)	intron (NM_001081390, intron 2 of 19)	33035	NM_001081390	72333	Mm.29933	NM_001081390	ENSMUSG00000058056	Palld	2410003B16Rik|6030492A02	palladin, cytoskeletal associated protein	protein-coding
mm_38004.1	chr4	133720865	133720881	-	1	NA	exon (NM_001080819, exon 3 of 20)	exon (NM_001080819, exon 3 of 20)	-3765	NR_106086	102465707		NR_106086	ENSMUSG00000104566	Mir7227	mmu-mir-7227	microRNA 7227	ncRNA
mm_104875.1	chr11	99428893	99428897	-	1	NA	3' UTR (NM_023256, exon 8 of 8)	3' UTR (NM_023256, exon 8 of 8)	-6636	NM_010661	268482	Mm.436651	NM_010661	ENSMUSG00000020912	Krt12	AI835216|K12|Krt-12|Krt1-12	keratin 12	protein-coding
mm_105558.1	chr11	106487834	106487880	-	1	NA	promoter-TSS (NM_023913)	promoter-TSS (NM_023913)	-61	NM_023913	78943	Mm.340943	NM_023913	ENSMUSG00000020715	Ern1	9030414B18Rik|AI225830|C85377|Ire1a|Ire1alpha|Ire1p	endoplasmic reticulum (ER) to nucleus signalling 1	protein-coding
mm_100954.1	chr11	6625786	6625796	-	1	NA	intron (NM_001130457, intron 1 of 12)	CpG	276	NM_001130457	21379	Mm.247761	NM_134011	ENSMUSG00000000384	Tbrg4	2310042P22Rik|AA120735|AA408001|AI527316|Cpr2|R74877|Tb-12|mKIAA0948	transforming growth factor beta regulated gene 4	protein-coding
mm_83316.1	chr9	44134514	44134533	-	1	NA	promoter-TSS (NM_023061)	promoter-TSS (NM_023061)	-135	NM_023061	84004	Mm.275003	NM_023061	ENSMUSG00000032135	Mcam	1-gicerin|AV025631|CD146|CD149|Muc18|s-endo|s-gicerin	melanoma cell adhesion molecule	protein-coding
mm_129221.1	chr15	76576808	76576814	-	1	NA	intron (NR_073123, intron 1 of 14)	intron (NR_073123, intron 1 of 14)	452	NR_073123	268822	Mm.181624	NM_172960	ENSMUSG00000022550	Adck5	A230108P17	aarF domain containing kinase 5	protein-coding
mm_128249.1	chr15	36609569	36609620	-	1	NA	promoter-TSS (NM_008774)	promoter-TSS (NM_008774)	-621	NM_008774	18458	Mm.371570	NM_008774	ENSMUSG00000022283	Pabpc1	PABP|Pabp1|PabpI|Pabpl1|ePAB	poly(A) binding protein, cytoplasmic 1	protein-coding
mm_44330.1	chr5	14723667	14723679	-	1	NA	intron (NM_001110796, intron 9 of 19)	intron (NM_001110796, intron 9 of 19)	191216	NM_198666	381714	Mm.368256	NM_198666	ENSMUSG00000033219	Gm9758	ENSMUSG00000033219	predicted gene 9758	protein-coding
mm_27053.1	chr3	27258710	27258736	-	1	NA	Intergenic	MuRRS-int|LTR|ERV1	-58354	NM_009425	22035	Mm.1062	NM_009425	ENSMUSG00000039304	Tnfsf10	A330042I21Rik|AI448571|APO-2L|Ly81|TL2|Tnlg6a|Trail	tumor necrosis factor (ligand) superfamily, member 10	protein-coding
mm_85755.1	chr9	108649292	108649306	-	1	NA	promoter-TSS (NM_011790)	promoter-TSS (NM_011790)	81	NM_011790	23807	Mm.290447	NM_011790	ENSMUSG00000064145	Arih2	AI843547|ARI2|TRIAD1|UIP48	ariadne RBR E3 ubiquitin protein ligase 2	protein-coding
mm_475.1	chr1	36492710	36492736	+	1	NA	intron (NM_033570, intron 1 of 6)	intron (NM_033570, intron 1 of 6)	-19144	NM_001331209	94218	Mm.256323	NM_053186	ENSMUSG00000001138	Cnnm3	Acdp3|Clp3|mACDP3	cyclin M3	protein-coding
mm_13436.1	chr2	105126506	105126516	+	1	NA	promoter-TSS (NM_144783)	promoter-TSS (NM_144783)	-1	NR_015462	329480	Mm.246679	NR_015462	ENSMUSG00000074987	Wt1os	6030498F17|AI314831|Wt1-as	Wilms tumor 1 homolog, opposite strand	ncRNA
mm_115639.1	chr13	12258136	12258185	-	1	NA	promoter-TSS (NM_001081128)	promoter-TSS (NM_001081128)	-47	NM_001081128	238505	Mm.40335	NM_001081128	ENSMUSG00000021311	Mtr	AI894170|D830038K18Rik|MS	5-methyltetrahydrofolate-homocysteine methyltransferase	protein-coding
mm_106300.1	chr11	118248508	118248571	-	1	NA	promoter-TSS (NM_011180)	promoter-TSS (NM_011180)	53	NM_001112699	19157	Mm.86413	NM_011180	ENSMUSG00000017132	Cyth1	CLM1|CTH-1|CYTIP|Pscd1	cytohesin 1	protein-coding
mm_48232.1	chr5	137707045	137707055	-	1	NA	Intergenic	MLT1F|LTR|ERVL-MaLR	-22297	NM_001303266	231801	Mm.260869	NM_145566	ENSMUSG00000029722	Agfg2	A630095P14Rik|Hrbl|RAB-R|RABR	ArfGAP with FG repeats 2	protein-coding
mm_661.1	chr1	40439768	40439788	+	1	NA	5' UTR (NM_010743, exon 1 of 8)	5' UTR (NM_010743, exon 1 of 8)	149	NM_010743	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_49945.1	chr6	39876865	39876867	+	1	NA	Intergenic	Intergenic	-65930	NM_001010930	14548	Mm.377071	NM_010270	ENSMUSG00000029918	Mrps33	AI841153|CGI-139|Gdap3|MRP-S33|PTD003	mitochondrial ribosomal protein S33	protein-coding
mm_41513.1	chr5	92386880	92386895	+	1	NA	intron (NM_001310664, intron 2 of 10)	intron (NM_001310664, intron 2 of 10)	-1247	NM_181728	109979	Mm.263514	NM_181728	ENSMUSG00000034842	Art3	4930569O04Rik|ARTC3	ADP-ribosyltransferase 3	protein-coding
mm_11177.1	chr2	28700156	28700187	+	1	NA	promoter-TSS (NM_027283)	promoter-TSS (NM_027283)	10	NM_001033874	68870	Mm.273318	NM_001033874	ENSMUSG00000026807	Ak8	1190002A17Rik|AK 8	adenylate kinase 8	protein-coding
mm_42492.1	chr5	115474579	115474581	+	1	NA	exon (NM_011107, exon 4 of 4)	exon (NM_011107, exon 4 of 4)	8314	NM_011107	18778	Mm.20190	NM_011107	ENSMUSG00000029522	Pla2g1b	Pla2a|sPLA2IB	phospholipase A2, group IB, pancreas	protein-coding
mm_70525.1	chr8	12984247	12984330	+	1	NA	intron (NM_001159486, intron 3 of 29)	intron (NM_001159486, intron 3 of 29)	34870	NM_001159485	17207	Mm.334413	NM_178076	ENSMUSG00000031442	Mcf2l	C130040G20Rik|Dbs|Ost|mKIAA0362	mcf.2 transforming sequence-like	protein-coding
mm_100725.1	chr11	3923516	3923526	-	1	NA	exon (NM_001130458, exon 7 of 10)	exon (NM_001130458, exon 7 of 10)	8440	NM_001130459	21452	Mm.20948	NM_015749	ENSMUSG00000020432	Tcn2	AW208754|Tcn-2	transcobalamin 2	protein-coding
mm_137154.1	chr17	23681796	23681810	+	1	NA	TTS (NM_020293)	TTS (NM_020293)	2223	NM_020293	56863	Mm.491368	NM_020293	ENSMUSG00000066720	Cldn9	nmf329	claudin 9	protein-coding
mm_101471.1	chr11	30649454	30649470	-	1	NA	promoter-TSS (NM_029344)	promoter-TSS (NM_029344)	-66	NM_029344	75572	Mm.390319	NM_029344	ENSMUSG00000060923	Acyp2	2310004B09Rik	acylphosphatase 2, muscle type	protein-coding
mm_127471.1	chr15	101273027	101273039	+	1	NA	exon (NM_010444, exon 6 of 7)	exon (NM_010444, exon 6 of 7)	6187	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_114383.1	chr13	63241038	63241040	+	1	NA	intron (NR_110520, intron 2 of 5)	intron (NR_110520, intron 2 of 5)	1010	NR_110521	72061	Mm.188105	NM_028079	ENSMUSG00000021458	2010111I01Rik	2300006M17Rik|AP-O|AW742919|Aopep|ApO|mir-23b|mir-24-1|mir-27b	RIKEN cDNA 2010111I01 gene	protein-coding
mm_74189.1	chr8	123653824	123653834	+	1	NA	promoter-TSS (NM_133955)	promoter-TSS (NM_133955)	-100	NM_133955	69581	Mm.168257	NM_133955	ENSMUSG00000039960	Rhou	2310026M05Rik|AI182090|Arhu|CDC42L1|G28K|WRCH-1|WRCH1|mG28K	ras homolog family member U	protein-coding
mm_110624.1	chr12	57197167	57197192	-	1	NA	5' UTR (NM_172577, exon 1 of 10)	5' UTR (NM_172577, exon 1 of 10)	293	NM_172577	217593	Mm.32835	NM_172577	ENSMUSG00000035472	Slc25a21	9930033G19Rik|A630030I10|BB158148	solute carrier family 25 (mitochondrial oxodicarboxylate carrier), member 21	protein-coding
mm_3837.1	chr1	160044375	160044452	+	1	NA	promoter-TSS (NR_028111)	promoter-TSS (NR_028111)	33	NM_001162896	67647	Mm.171518	NM_001024470	ENSMUSG00000090394	4930523C07Rik	-	RIKEN cDNA 4930523C07 gene	protein-coding
mm_144927.1	chr18	37694408	37694423	+	1	NA	promoter-TSS (NM_033588)	promoter-TSS (NM_033588)	-86	NM_033588	93713	Mm.247203	NM_033588	ENSMUSG00000103567	Pcdhga5	-	protocadherin gamma subfamily A, 5	protein-coding
mm_27843.1	chr3	79156189	79156203	-	1	NA	Intergenic	B4|SINE|B4	-10321	NM_001099624	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_65060.1	chr7	18798520	18798526	-	1	NA	promoter-TSS (NM_011964)	promoter-TSS (NM_011964)	-13	NM_011964	26439	Mm.36878	NM_011964	ENSMUSG00000004542	Psg19	CGM7|Cea-4|Cea4	pregnancy specific glycoprotein 19	protein-coding
mm_130868.1	chr15	102204275	102204290	-	1	NA	promoter-TSS (NM_001289690)	promoter-TSS (NM_001289690)	-289	NM_001289690	68744	Mm.352945	NM_153194	ENSMUSG00000046897	Zfp740	1110034O07Rik|AW548228|Znf740	zinc finger protein 740	protein-coding
mm_20979.1	chr2	151974079	151974101	-	1	NA	promoter-TSS (NM_001289151)	promoter-TSS (NM_001289151)	-109	NM_028666	73847	Mm.272444	NM_028666	ENSMUSG00000027459	Fam110a	1700008J10Rik|5430432M24Rik|AI747080	family with sequence similarity 110, member A	protein-coding
mm_40800.1	chr5	67639884	67639893	+	1	NA	intron (NM_001284345, intron 33 of 36)	intron (NM_001284345, intron 33 of 36)	32005	NM_001033415	330096	Mm.442747	NM_001033415	ENSMUSG00000050010	Shisa3	D830007B15Rik	shisa family member 3	protein-coding
mm_14354.1	chr2	129609002	129609055	+	1	NA	exon (NM_001177647, exon 2 of 6)	exon (NM_001177647, exon 2 of 6)	15859	NM_001291022	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_93568.1	chr10	116559265	116559290	-	1	NA	intron (NM_001037846, intron 1 of 15)	intron (NM_001037846, intron 1 of 15)	22234	NM_001037848	72068	Mm.351553	NM_028082	ENSMUSG00000020166	Cnot2	2600016M12Rik|2810470K03Rik|AA537049|AA959607|AW557563|C79650	CCR4-NOT transcription complex, subunit 2	protein-coding
mm_55954.1	chr6	85374575	85374579	-	1	NA	promoter-TSS (NM_177466)	promoter-TSS (NM_177466)	57	NM_177466	52055	Mm.220334	NM_177466	ENSMUSG00000051343	Rab11fip5	9130206P09Rik|C75969|D6Ertd32e|GAF1|RIP11	RAB11 family interacting protein 5 (class I)	protein-coding
mm_21647.1	chr2	164333554	164333556	-	1	NA	exon (NM_009301, exon 2 of 3)	exon (NM_009301, exon 2 of 3)	790	NM_009301	20944	Mm.140154	NM_009301	ENSMUSG00000017004	Svs5	BB115186|Semg1|Svp-1|Svp1|Svp5	seminal vesicle secretory protein 5	protein-coding
mm_69238.1	chr7	127746071	127746095	-	1	NA	promoter-TSS (NM_172748)	promoter-TSS (NM_172748)	-692	NM_172748	233902	Mm.259353	NM_172748	ENSMUSG00000030811	Fbxl19	6030430O11|BC059812|Fbl19	F-box and leucine-rich repeat protein 19	protein-coding
mm_88549.1	chr10	78591696	78591712	+	1	NA	intron (NM_027875, intron 1 of 7)	intron (NM_027875, intron 1 of 7)	260	NM_027875	71709	Mm.86439	NM_027875	ENSMUSG00000032714	Syde1	1200008N06Rik|BB043000|mSYD1A	synapse defective 1, Rho GTPase, homolog 1 (C. elegans)	protein-coding
mm_106510.1	chr11	120467415	120467479	-	1	NA	promoter-TSS (NM_008244)	promoter-TSS (NM_008244)	153	NM_197995	70317	Mm.485046	NM_197995	ENSMUSG00000057594	Arl16	2600005N12Rik	ADP-ribosylation factor-like 16	protein-coding
mm_62290.1	chr7	99906533	99906536	+	1	NA	exon (NM_001164258, exon 12 of 19)	exon (NM_001164258, exon 12 of 19)	47316	NM_001164258	446101	Mm.440757	NM_001164258	ENSMUSG00000035211	Xrra1	AI449753	X-ray radiation resistance associated 1	protein-coding
mm_73588.1	chr8	109991558	109991568	+	1	NA	exon (NM_146214, exon 2 of 12)	exon (NM_146214, exon 2 of 12)	1127	NM_146214	234724	Mm.28110	NM_146214	ENSMUSG00000001670	Tat	-	tyrosine aminotransferase	protein-coding
mm_59472.1	chr7	27447996	27448046	+	1	NA	promoter-TSS (NM_144923)	promoter-TSS (NM_144923)	43	NM_144923	233016	Mm.24021	NM_144923	ENSMUSG00000040466	Blvrb	-	biliverdin reductase B (flavin reductase (NADPH))	protein-coding
mm_124589.1	chr15	3274655	3274671	+	1	NA	5' UTR (NM_009155, exon 2 of 5)	5' UTR (NM_009155, exon 2 of 5)	3686	NM_009155	20363	Mm.392203	NM_009155	ENSMUSG00000064373	Selenop	AU018766|D15Ucla1|Se-P|Sepp1|selp	selenoprotein P	protein-coding
mm_64620.1	chr7	3629875	3629924	-	1	NA	promoter-TSS (NM_001290381)	promoter-TSS (NM_001290381)	30	NM_023524	69714	Mm.358730	NM_023524	ENSMUSG00000006335	Tfpt	2400004F01Rik|AI450389|Amida|FB1	TCF3 (E2A) fusion partner	protein-coding
mm_6005.1	chr1	58973356	58973381	-	1	NA	promoter-TSS (NM_172656)	promoter-TSS (NM_172656)	114	NM_172406	70827	Mm.222887	NM_172406	ENSMUSG00000026028	Trak2	2900022D04Rik|4733401O11Rik|AI480836|AW046271|Als2cr3|CALS-C|GRIF-1|GRIF1|OIP98|mKIAA0549	trafficking protein, kinesin binding 2	protein-coding
mm_92280.1	chr10	71285207	71285229	-	1	NA	promoter-TSS (NM_145420)	promoter-TSS (NM_145420)	44	NM_145420	216080	Mm.270530	NM_145420	ENSMUSG00000019927	Ube2d1	UBCH5	ubiquitin-conjugating enzyme E2D 1	protein-coding
mm_91690.1	chr10	43997316	43997320	-	1	NA	exon (NM_172393, exon 2 of 20)	exon (NM_172393, exon 2 of 20)	7528	NM_172393	11630	Mm.292082	NM_172393	ENSMUSG00000019866	Aim1	AI462491|AI463325	absent in melanoma 1	protein-coding
mm_80401.1	chr9	77636495	77636528	+	1	NA	promoter-TSS (NM_172925)	promoter-TSS (NM_172925)	-221	NM_172925	244923	Mm.138238	NM_172925	ENSMUSG00000044938	Klhl31	9830147P19Rik|D930047P17Rik|Kbtbd1	kelch-like 31	protein-coding
mm_12313.1	chr2	69135864	69135887	+	1	NA	promoter-TSS (NM_181547)	promoter-TSS (NM_181547)	75	NM_181547	329416	Mm.90047	NM_181547	ENSMUSG00000034738	Nostrin	Daip2|mDaIP2	nitric oxide synthase trafficker	protein-coding
mm_124601.1	chr15	3277153	3277195	+	1	NA	exon (NM_009155, exon 4 of 5)	exon (NM_009155, exon 4 of 5)	6197	NM_009155	20363	Mm.392203	NM_009155	ENSMUSG00000064373	Selenop	AU018766|D15Ucla1|Se-P|Sepp1|selp	selenoprotein P	protein-coding
mm_161140.1	chr13	21440603	21440603	-	1	NA	5' UTR (NM_001162919, exon 1 of 5)	5' UTR (NM_001162919, exon 1 of 5)	107	NM_001162919	319207	Mm.434384	NM_001012311	ENSMUSG00000055313	Pgbd1	4921509E05Rik	piggyBac transposable element derived 1	protein-coding
mm_36935.1	chr4	108579110	108579151	-	1	NA	promoter-TSS (NM_011015)	promoter-TSS (NM_011015)	206	NM_172697	230596	Mm.157534	NM_172697	ENSMUSG00000063800	Prpf38a	2410002M20Rik	PRP38 pre-mRNA processing factor 38 (yeast) domain containing A	protein-coding
mm_8071.1	chr1	135510376	135510388	-	1	NA	intron (NM_173437, intron 3 of 28)	intron (NM_173437, intron 3 of 28)	-55699	NR_049188	100885827		NR_049188	ENSMUSG00000093515	Mir1231	Gm23720|mir-1231|mmu-mir-1231	microRNA 1231	ncRNA
mm_102944.1	chr11	69605954	69605971	-	1	NA	promoter-TSS (NM_013415)	promoter-TSS (NM_013415)	-2	NM_013415	11932	Mm.235204	NM_013415	ENSMUSG00000041329	Atp1b2	Amog|Atpb-2	ATPase, Na+/K+ transporting, beta 2 polypeptide	protein-coding
mm_40735.1	chr5	66259864	66259887	+	1	NA	promoter-TSS (NM_027602)	promoter-TSS (NM_027602)	-23	NM_001302833	70918	Mm.23166	NM_027602	ENSMUSG00000029206	Nsun7	4921525L17Rik	NOL1/NOP2/Sun domain family, member 7	protein-coding
mm_148697.1	chr19	5741960	5742015	+	1	NA	5' UTR (NM_008520, exon 2 of 28)	5' UTR (NM_008520, exon 2 of 28)	1083	NM_008520	16998	Mm.182396	NM_008520	ENSMUSG00000024940	Ltbp3	Ltbp2|mFLJ00070	latent transforming growth factor beta binding protein 3	protein-coding
mm_56187.1	chr6	88515409	88515426	-	1	NA	exon (NM_016906, exon 4 of 12)	exon (NM_016906, exon 4 of 12)	3383	NM_016906	53421	Mm.28375	NM_016906	ENSMUSG00000030082	Sec61a1	AA408394|AA410007|Sec61a	Sec61 alpha 1 subunit (S. cerevisiae)	protein-coding
mm_13636.1	chr2	114047380	114047407	+	1	NA	3' UTR (NM_009608, exon 7 of 7)	3' UTR (NM_009608, exon 7 of 7)	5482	NM_009608	11464	Mm.686	NM_009608	ENSMUSG00000068614	Actc1	Actc-1	actin, alpha, cardiac muscle 1	protein-coding
mm_140243.1	chr17	84180950	84180985	+	1	NA	Intergenic	Intergenic	6980	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_35484.1	chr4	40876017	40876030	-	1	NA	Intergenic	Intergenic	-21486	NM_022305	14595	Mm.15622	NM_022305	ENSMUSG00000028413	B4galt1	B-1,4-GalT|B-1,4-GalT1|GalT|Ggtb|Ggtb2|b4Gal-T1|beta-1,4-GalT|beta-1,4-GalT1|beta4Gal-T1	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1	protein-coding
mm_145394.1	chr18	57142739	57142755	+	1	NA	intron (NM_001001979, intron 1 of 24)	intron (NM_001001979, intron 1 of 24)	9657	NM_001001979	70417	Mm.297863	NM_001001979	ENSMUSG00000024593	Megf10	3000002B06Rik|Gm331	multiple EGF-like-domains 10	protein-coding
mm_143822.1	chr17	83846890	83846905	-	1	NA	promoter-TSS (NM_025325)	promoter-TSS (NM_025325)	-107	NM_025325	107766	Mm.30100	NM_025325	ENSMUSG00000000673	Haao	0610007K21Rik|0610012J07Rik|3-HAO|3-HAOxase|3HAO	3-hydroxyanthranilate 3,4-dioxygenase	protein-coding
mm_91507.1	chr10	37136797	37136808	-	1	NA	exon (NM_008538, exon 2 of 2)	exon (NM_008538, exon 2 of 2)	2124	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_136825.1	chr17	12584216	12584236	+	1	NA	promoter-TSS (NM_013667)	promoter-TSS (NM_013667)	37	NM_013667	20518	Mm.17322	NM_013667	ENSMUSG00000040966	Slc22a2	Oct2|Orct2	solute carrier family 22 (organic cation transporter), member 2	protein-coding
mm_111189.1	chr12	84174935	84174943	-	1	NA	intron (NM_001163501, intron 1 of 12)	intron (NM_001163501, intron 1 of 12)	19076	NM_001163502	238317	Mm.31256	NM_001163501	ENSMUSG00000042507	Elmsan1	9430029N19Rik|C130039O16Rik|Gm260	ELM2 and Myb/SANT-like domain containing 1	protein-coding
mm_145031.1	chr18	39291447	39291451	+	1	NA	intron (NM_175164, intron 18 of 22)	intron (NM_175164, intron 18 of 22)	195796	NM_008173	14815	Mm.129481	NM_008173	ENSMUSG00000024431	Nr3c1	GR|Grl-1|Grl1	nuclear receptor subfamily 3, group C, member 1	protein-coding
mm_134782.1	chr16	23988234	23988235	-	1	NA	intron (NM_009744, intron 1 of 9)	intron (NM_009744, intron 1 of 9)	378	NM_009744	12053	Mm.347398	NM_009744	ENSMUSG00000022508	Bcl6	Bcl5	B cell leukemia/lymphoma 6	protein-coding
mm_42498.1	chr5	115489311	115489322	+	1	NA	Intergenic	Intergenic	-4832	NM_133760	75387	Mm.332616	NM_133760	ENSMUSG00000029524	Sirt4	4930596O17Rik	sirtuin 4	protein-coding
mm_51290.1	chr6	72305644	72305660	+	1	NA	exon (NM_001282071, exon 3 of 11)	exon (NM_001282071, exon 3 of 11)	1042	NM_147779	20388	Mm.46033	NM_147779	ENSMUSG00000056370	Sftpb	AI562151|SF-B|SP-B|Sftp-3|Sftp3	surfactant associated protein B	protein-coding
mm_166426.1	chr5	137152243	137152273	-	1	NA	Intergenic	Intergenic	-36051	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_108712.1	chr12	87147150	87147201	+	1	NA	promoter-TSS (NM_001252556)	promoter-TSS (NM_001252556)	10	NM_001252555	14874	Mm.29652	NM_010363	ENSMUSG00000021033	Gstz1	MAAI	glutathione transferase zeta 1 (maleylacetoacetate isomerase)	protein-coding
mm_29027.1	chr3	102165918	102165946	-	1	NA	intron (NM_177545, intron 5 of 7)	intron (NM_177545, intron 5 of 7)	38761	NM_177545	229658	Mm.118004	NM_177545	ENSMUSG00000027860	Vangl1	Kitenin|Lpp2|Stb2|Stbm	vang-like 1 (van gogh, Drosophila)	protein-coding
mm_32566.1	chr4	109676778	109676800	+	1	NA	5' UTR (NM_007983, exon 1 of 19)	5' UTR (NM_007983, exon 1 of 19)	162	NM_007983	14084	Mm.318259	NM_007983	ENSMUSG00000010517	Faf1	AA408698|Dffrx|Fam	Fas-associated factor 1	protein-coding
mm_35157.1	chr4	12171814	12171851	-	1	NA	exon (NM_001310743, exon 1 of 8)	exon (NM_001310743, exon 1 of 8)	183	NM_001310743	68099	Mm.25340	NM_026558	ENSMUSG00000028218	Fam92a	6720467C03Rik|Fam92a1	family with sequence similarity 92, member A	protein-coding
mm_11314.1	chr2	30322486	30322506	+	1	NA	exon (NM_198304, exon 18 of 44)	exon (NM_198304, exon 18 of 44)	36063	NM_198304	227699	Mm.330119	NM_198304	ENSMUSG00000052533	Nup188	BC025526|U89435|mKIAA0169	nucleoporin 188	protein-coding
mm_9985.1	chr1	191269317	191269318	-	1	NA	Intergenic	Intergenic	48801	NM_025424	66208	Mm.46444	NM_025424	ENSMUSG00000037499	Nenf	1110060M21Rik|SCIRP10|Spuf	neuron derived neurotrophic factor	protein-coding
mm_29854.1	chr3	130041032	130041063	-	1	NA	exon (NM_207209, exon 2 of 24)	exon (NM_207209, exon 2 of 24)	19860	NM_207209	99683	Mm.192303	NM_207209	ENSMUSG00000001052	Sec24b	AI605202|SEC24	Sec24 related gene family, member B (S. cerevisiae)	protein-coding
mm_99542.1	chr11	103266199	103266204	+	1	NA	intron (NM_016896, intron 1 of 15)	intron (NM_016896, intron 1 of 15)	1200	NM_016896	53859	Mm.158981	NM_016896	ENSMUSG00000020941	Map3k14	Nik|aly	mitogen-activated protein kinase kinase kinase 14	protein-coding
mm_131486.1	chr16	17222308	17222321	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-11273	NM_178922	58180	Mm.261602	NM_178922	ENSMUSG00000050240	Hic2	AA409108|HRG22|mKIAA1020	hypermethylated in cancer 2	protein-coding
mm_158287.1	chrX	112407054	112407072	-	1	NA	promoter-TSS (NM_028655)	promoter-TSS (NM_028655)	-284	NM_028655	73809	Mm.50508	NM_028655	ENSMUSG00000025527	Satl1	4930404K22Rik	spermidine/spermine N1-acetyl transferase-like 1	protein-coding
mm_49372.1	chr6	24528187	24528200	+	1	NA	promoter-TSS (NM_001311068)	promoter-TSS (NM_001311068)	49	NM_080847	78910	Mm.160150	NM_080847	ENSMUSG00000029685	Asb15	4930400E23Rik|Asb-15	ankyrin repeat and SOCS box-containing 15	protein-coding
mm_169901.1	chr16	52083792	52083796	+	1	NA	intron (NM_001033238, intron 3 of 17)	intron (NM_001033238, intron 3 of 17)	52245	NM_001033238	208650	Mm.328206	NM_001033238	ENSMUSG00000022637	Cblb	AI429560|AI851073|Cbl-b	Casitas B-lineage lymphoma b	protein-coding
mm_97359.1	chr11	77503857	77503869	+	1	NA	intron (NM_001004144, intron 10 of 19)	intron (NM_001004144, intron 10 of 19)	9410	NM_001024920	216964	Mm.341211	NM_001024920	ENSMUSG00000044328	Trp53i13	2410019G02Rik|Tp53i13	transformation related protein 53 inducible protein 13	protein-coding
mm_109883.1	chr12	5201122	5201123	-	1	NA	intron (NM_001164493, intron 3 of 13)	intron (NM_001164493, intron 3 of 13)	174560	NM_001164493	208439	Mm.388281	NM_001164493	ENSMUSG00000020627	Klhl29	A230106N14Rik|Gm68|Kbtbd9|mKIAA1921	kelch-like 29	protein-coding
mm_76186.1	chr8	82402495	82402504	-	1	NA	promoter-TSS (NM_001254747)	promoter-TSS (NM_001254747)	87	NM_001254747	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_127366.1	chr15	100747406	100747409	+	1	NA	Intergenic	Intergenic	-14340	NM_021530	59033	Mm.209856	NM_021530	ENSMUSG00000023032	Slc4a8	AW493845|C230026C11|NDCBE|kNBC-3	solute carrier family 4 (anion exchanger), member 8	protein-coding
mm_93190.1	chr10	93891142	93891194	-	1	NA	promoter-TSS (NM_019648)	promoter-TSS (NM_019648)	34	NM_019648	56307	Mm.289329	NM_019648	ENSMUSG00000036112	Metap2	4930584B20Rik|A930035J23Rik|AI047573|AL024412|AU014659|Amp2|Mnpep|p67|p67eIF2	methionine aminopeptidase 2	protein-coding
mm_108891.1	chr12	100010756	100010769	+	1	NA	intron (NM_146037, intron 2 of 2)	intron (NM_146037, intron 2 of 2)	46263	NM_001164427	217826	Mm.312335	NM_146037	ENSMUSG00000045404	Kcnk13	BB085247|F730021E22Rik|Gm1570|Gm1685	potassium channel, subfamily K, member 13	protein-coding
mm_115521.1	chr13	5860799	5860816	-	1	NA	promoter-TSS (NM_011803)	promoter-TSS (NM_011803)	-682	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_89242.1	chr10	87858603	87858620	+	1	NA	promoter-TSS (NM_010512)	promoter-TSS (NM_010512)	346	NM_001314010	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_3842.1	chr1	160044605	160044621	+	1	NA	non-coding (NR_028111, exon 1 of 3)	non-coding (NR_028111, exon 1 of 3)	233	NM_001162896	67647	Mm.171518	NM_001024470	ENSMUSG00000090394	4930523C07Rik	-	RIKEN cDNA 4930523C07 gene	protein-coding
mm_98615.1	chr11	95843594	95843629	+	1	NA	intron (NM_001284397, intron 1 of 3)	intron (NM_001284397, intron 1 of 3)	366	NM_001284397	14710	Mm.46299	NM_023121	ENSMUSG00000038811	Gngt2	AV096488	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 2	protein-coding
mm_33047.1	chr4	122998836	122998847	+	1	NA	intron (NM_001303121, intron 2 of 2)	intron (NM_001303121, intron 2 of 2)	2910	NM_008506	16918	Mm.1055	NM_008506	ENSMUSG00000028654	Mycl	AW536278|L-myc|Lmyc-1|Lmyc1|Mycl1|bHLHe38	v-myc avian myelocytomatosis viral oncogene lung carcinoma derived	protein-coding
mm_166587.1	chr6	55336054	55336079	+	1	NA	promoter-TSS (NM_007472)	promoter-TSS (NM_007472)	-233	NM_007472	11826	Mm.18625	NM_007472	ENSMUSG00000004655	Aqp1	CHIP28	aquaporin 1	protein-coding
mm_142203.1	chr17	36972919	36972932	-	1	NA	Intergenic	Intergenic	8312	NM_029747	76797	Mm.159787	NM_029747	ENSMUSG00000064308	2410137M14Rik	-	RIKEN cDNA 2410137M14 gene	protein-coding
mm_138716.1	chr17	36271433	36271483	+	1	NA	promoter-TSS (NM_178281)	promoter-TSS (NM_178281)	-25	NM_178281	79263	Mm.40624	NM_024468	ENSMUSG00000045409	Trim39	1100001D15Rik|E130103K13Rik|RBCC-B30.2|Rnf23|mKIAA4179|tfp	tripartite motif-containing 39	protein-coding
mm_7286.1	chr1	97761596	97761609	-	1	NA	5' UTR (NM_173760, exon 2 of 28)	5' UTR (NM_173760, exon 2 of 28)	8490	NM_173760	227399	Mm.220817	NM_173760	ENSMUSG00000040648	Ppip5k2	AW555814|Cfap160|D330021B20|Hisppd1|Vip2|mKIAA0433	diphosphoinositol pentakisphosphate kinase 2	protein-coding
mm_84418.1	chr9	65580044	65580061	-	1	NA	promoter-TSS (NM_153119)	promoter-TSS (NM_153119)	35	NM_153119	102595	Mm.247303	NM_153119	ENSMUSG00000050721	Plekho2	AI840980|Plekhq1	pleckstrin homology domain containing, family O member 2	protein-coding
mm_77209.1	chr8	114013805	114013816	-	1	NA	Intergenic	Intergenic	-119764	NM_024446	67528	Mm.27889	NM_024437	ENSMUSG00000031767	Nudt7	1300007B24Rik|2210404C19Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 7	protein-coding
mm_160753.1	chr10	81771161	81771161	-	1	NA	promoter-TSS (NM_199062)	promoter-TSS (NM_199062)	13	NM_001346707	100040944		NM_001346707		Gm3055	-	predicted gene 3055	protein-coding
mm_10987.1	chr2	26278705	26278709	+	1	NA	intron (NM_177841, intron 6 of 9)	intron (NM_177841, intron 6 of 9)	15850	NM_177841	329366	Mm.77712	NM_177841	ENSMUSG00000048038	Ccdc187	4932418E24Rik	coiled-coil domain containing 187	protein-coding
mm_141794.1	chr17	34343011	34343034	-	1	NA	exon (NM_010381, exon 3 of 4)	exon (NM_010381, exon 3 of 4)	1623	NM_010381	100504404	Mm.15680	NM_010381		H2-Ea-ps	AI323765|E-alpha-f|H-2Ea|H2-Ea|I-Ealpha|Ia-3|Ia3|MHC-H2-Ea	histocompatibility 2, class II antigen E alpha, pseudogene	protein-coding
mm_115550.1	chr13	8871697	8871749	-	1	NA	promoter-TSS (NM_172445)	promoter-TSS (NM_172445)	13	NM_001039388	207615	Mm.284654	NM_172445	ENSMUSG00000021147	Wdr37	-	WD repeat domain 37	protein-coding
mm_94941.1	chr11	29712814	29712819	+	1	NA	intron (NM_194054, intron 3 of 8)	B1_Mur4|SINE|Alu	-5747	NM_024226	68585	Mm.192580	NM_024226	ENSMUSG00000020458	Rtn4	1110020G17Rik|AA407876|AA409940|AA960376|ASY|C130026I10Rik|NOGO|NSP-CL|NgA|Nogo-A|Nogo-B|Nogo-C|mKIAA0886|mKIAA4153	reticulon 4	protein-coding
mm_166134.1	chr4	155630549	155630559	+	1	NA	intron (NM_001347308, intron 6 of 20)	MTEb|LTR|ERVL-MaLR	5685	NM_007661	12537	Mm.267410	NM_007661	ENSMUSG00000029062	Cdk11b	AA989746|CDK11-p110|CDK11-p46|CDK11-p58|Cdc11b|Cdc2l1|Cdc2l2|Cdk11|p58	cyclin-dependent kinase 11B	protein-coding
mm_69623.1	chr7	137314275	137314289	-	1	NA	5' UTR (NM_001113414, exon 1 of 16)	5' UTR (NM_001113414, exon 1 of 16)	163	NM_001113415	13593	Mm.258708	NM_010096	ENSMUSG00000010476	Ebf3	3110018A08Rik|O/E-2|mKIAA4201	early B cell factor 3	protein-coding
mm_87989.1	chr10	64314524	64314527	+	1	NA	intron (NM_177612, intron 9 of 17)	intron (NM_177612, intron 9 of 17)	-224270	NM_178678	216028	Mm.431318	NM_178678	ENSMUSG00000042846	Lrrtm3	9630044H04Rik	leucine rich repeat transmembrane neuronal 3	protein-coding
mm_103686.1	chr11	79483455	79483473	-	1	NA	non-coding (NR_045305, exon 3 of 4)	non-coding (NR_045305, exon 3 of 4)	567	NR_045305	104522	Mm.436987	NR_045305	ENSMUSG00000091523	AU040972	AU040954	expressed sequence AU040972	ncRNA
mm_46943.1	chr5	114826333	114826339	-	1	NA	Intergenic	Intergenic	-2868	NM_181075	330173	Mm.482205	NM_181075	ENSMUSG00000092486	2610524H06Rik	-	RIKEN cDNA 2610524H06 gene	protein-coding
mm_124034.1	chr14	77032454	77032465	-	1	NA	intron (NM_172488, intron 5 of 7)	L1MB3|LINE|L1	4158	NM_172488	210808	Mm.89278	NM_172488	ENSMUSG00000044350	Lacc1	9030625A04Rik	laccase (multicopper oxidoreductase) domain containing 1	protein-coding
mm_70494.1	chr8	12589198	12589201	+	1	NA	intron (NM_024279, intron 4 of 6)	intron (NM_024279, intron 4 of 6)	16150	NM_024279	78634	Mm.116871	NM_024279	ENSMUSG00000010435	Spaca7	1700094C09Rik	sperm acrosome associated 7	protein-coding
mm_143099.1	chr17	57081171	57081182	-	1	NA	exon (NM_009451, exon 4 of 4)	exon (NM_009451, exon 4 of 4)	-2666	NM_153551	70785	Mm.284447	NM_153551	ENSMUSG00000002668	Dennd1c	4432409M07Rik	DENN/MADD domain containing 1C	protein-coding
mm_132681.1	chr16	42947906	42947908	+	1	NA	intron (NM_001285805, intron 1 of 10)	intron (NM_001285805, intron 1 of 10)	-7673	NR_002445	170658	Mm.375824	NR_002445		BC002163	-	NADH dehydrogenase Fe-S protein 5 pseudogene	pseudo
mm_14097.1	chr2	125229442	125229453	+	1	NA	3' UTR (NM_001079690, exon 28 of 28)	3' UTR (NM_001079690, exon 28 of 28)	-17801	NM_001159646	110074	Mm.282499	NM_023595	ENSMUSG00000027203	Dut	5031412I06Rik|5133400F09Rik|D2Bwg0749e|Dutp|dUTPase	deoxyuridine triphosphatase	protein-coding
mm_135588.1	chr16	50591073	50591119	-	1	NA	promoter-TSS (NM_027046)	promoter-TSS (NM_027046)	58	NM_027046	69339	Mm.422869	NM_027046	ENSMUSG00000050685	Ccdc54	1700007N18Rik|AI644412|BB013989|NYD-SP17	coiled-coil domain containing 54	protein-coding
mm_158693.1	chrX	160994642	160994661	-	1	NA	promoter-TSS (NM_001024624)	promoter-TSS (NM_001024624)	30	NM_001024624	382253	Mm.443717	NM_001024624	ENSMUSG00000031292	Cdkl5	BC038161|Stk9	cyclin-dependent kinase-like 5	protein-coding
mm_25634.1	chr3	119987533	119987533	+	1	NA	Intergenic	L2a|LINE|L2	-204145	NM_019550	56195	Mm.29966	NM_019550	ENSMUSG00000028134	Ptbp2	Ptb2|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding
mm_163309.1	chr12	4593799	4593832	+	1	NA	intron (NM_011365, intron 1 of 38)	intron (NM_011365, intron 1 of 38)	807	NM_001198968	20403	Mm.341204	NM_011365	ENSMUSG00000020640	Itsn2	AI327390|Ese2|Sh3d1B|Sh3p18|mKIAA1256	intersectin 2	protein-coding
mm_55095.1	chr6	49338689	49338695	-	1	NA	intron (NM_175098, intron 2 of 2)	RLTR20C2_MM|LTR|ERVK	19418	NM_001311112	57895	Mm.32416	NM_175098	ENSMUSG00000050786	Ccdc126	6330407D12Rik|AA675040|AI465320|AL022711	coiled-coil domain containing 126	protein-coding
mm_42326.1	chr5	114901413	114901419	+	1	NA	intron (NM_011854, intron 3 of 5)	intron (NM_011854, intron 3 of 5)	4482	NM_011854	23962	Mm.228363	NM_011854	ENSMUSG00000029561	Oasl2	M1204|Mmu-OASL|Oasl	2'-5' oligoadenylate synthetase-like 2	protein-coding
mm_29773.1	chr3	127282347	127282355	-	1	NA	intron (NM_001327938, intron 1 of 47)	intron (NM_001327938, intron 1 of 47)	121046	NR_105029	100862268	Mm.444603	NR_105029	ENSMUSG00000097456	LOC100862268	-	uncharacterized LOC100862268	ncRNA
mm_128326.1	chr15	38078823	38078836	-	1	NA	promoter-TSS (NM_001081359)	promoter-TSS (NM_001081359)	25	NM_001112721	70790	Mm.476840	NM_027553	ENSMUSG00000037487	Ubr5	Edd|Edd1	ubiquitin protein ligase E3 component n-recognin 5	protein-coding
mm_165800.1	chr3	141495200	141495204	+	1	NA	intron (NM_001293561, intron 1 of 16)	L1MEf|LINE|L1	29638	NM_001293561	22253	Mm.24430	NM_009472	ENSMUSG00000059921	Unc5c	B130051O18Rik|Unc5h3|rcm	unc-5 netrin receptor C	protein-coding
mm_101616.1	chr11	35836028	35836028	-	1	NA	Intergenic	Intergenic	-1500	NM_025936	104458	Mm.284906	NM_025936	ENSMUSG00000018848	Rars	2610011N19Rik|2610037E21Rik|AL033339|AW985894	arginyl-tRNA synthetase	protein-coding
mm_146233.1	chr18	77144311	77144321	+	1	NA	intron (NM_008602, intron 11 of 13)	B1_Mur2|SINE|Alu	-41531	NM_153124	225742	Mm.365178	NM_013666	ENSMUSG00000025425	St8sia5	ST8SiaV|Siat8e	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 5	protein-coding
mm_129990.1	chr15	86160427	86160437	-	1	NA	intron (NM_145475, intron 3 of 12)	MT2B2|LTR|ERVL	25709	NM_145475	223753	Mm.222685	NM_145475	ENSMUSG00000035891	Cerk	AI848610|D330016D08Rik|mKIAA1646	ceramide kinase	protein-coding
mm_129315.1	chr15	77760952	77760963	-	1	NA	3' UTR (NM_022410, exon 41 of 41)	3' UTR (NM_022410, exon 41 of 41)	-5728	NM_001081970	239552	Mm.125650	NM_001081970	ENSMUSG00000056656	Apol8	9830006J20Rik|APOL-II|Apol2	apolipoprotein L 8	protein-coding
mm_147781.1	chr18	61575480	61575488	-	1	NA	exon (NM_146087, exon 5 of 10)	exon (NM_146087, exon 5 of 10)	19902	NM_146087	93687	Mm.26908	NM_146087	ENSMUSG00000024576	Csnk1a1	2610208K14Rik|4632404G05Rik|5430427P18Rik|CK1a|Csnk1a	casein kinase 1, alpha 1	protein-coding
mm_120153.1	chr14	60635879	60635882	+	1	NA	intron (NM_001033272, intron 1 of 12)	T-rich|Low_complexity|Low_complexity	1175	NM_001033272	219140	Mm.149776	NM_001033272	ENSMUSG00000021990	Spata13	C79050|ESTM11|X83327|mFLJ00298	spermatogenesis associated 13	protein-coding
mm_125873.1	chr15	75615161	75615166	+	1	NA	Intergenic	Intergenic	-1521	NM_001044718	22701	Mm.87210	NM_011759	ENSMUSG00000047003	Zfp41	CTfin92|Zfp-41	zinc finger protein 41	protein-coding
mm_141017.1	chr17	25115734	25115783	-	1	NA	5' UTR (NM_001163661, exon 1 of 21)	5' UTR (NM_001163661, exon 1 of 21)	147	NM_027880	71718	Mm.288702	NM_027880	ENSMUSG00000024170	Telo2	1200003M09Rik|AI415602|Tel2|mKIAA0683	telomere maintenance 2	protein-coding
mm_76638.1	chr8	92356104	92356119	-	1	NA	promoter-TSS (NR_033641)	promoter-TSS (NR_033641)	9	NR_110452	71296	Mm.86664	NR_033641	ENSMUSG00000031736	Crnde	4933436C20Rik	colorectal neoplasia differentially expressed (non-protein coding)	ncRNA
mm_23226.1	chr3	49113958	49113961	+	1	NA	Intergenic	Intergenic	-504859	NR_003617	66332	Mm.46124	NM_025493		1700018B24Rik	-	enhancer of rudimentary homolog pseudogene	pseudo
mm_12816.1	chr2	80315704	80315744	+	1	NA	5' UTR (NM_024181, exon 1 of 23)	5' UTR (NM_024181, exon 1 of 23)	258	NM_024181	66861	Mm.21762	NM_024181	ENSMUSG00000027006	Dnajc10	1200006L06Rik|D2Ertd706e|ERdj5|JPDI	DnaJ heat shock protein family (Hsp40) member C10	protein-coding
mm_49671.1	chr6	31327264	31327266	+	1	NA	intron (NR_040261, intron 3 of 4)	intron (NR_040261, intron 3 of 4)	71508	NR_040300	100503869	Mm.370532	NR_040300	ENSMUSG00000086212	Mkln1os	Gm13845|OTTMUSG00000014733	muskelin 1, intracellular mediator containing kelch motifs, opposite strand	ncRNA
mm_136981.1	chr17	16951523	16951553	+	1	NA	Intergenic	Intergenic	-112565	NM_001005358	449000	Mm.483718	NM_001005358	ENSMUSG00000096696	Zfp960	-	zinc finger protein 960	protein-coding
mm_95191.1	chr11	42630436	42630439	+	1	NA	3' UTR (NM_008070, exon 10 of 10)	3' UTR (NM_008070, exon 10 of 10)	209087	NM_001347314	14401	Mm.338723	NM_008070	ENSMUSG00000007653	Gabrb2	AI834970|C030002O17Rik|C030021G16Rik|Gabrab2|Gabrb-2	gamma-aminobutyric acid (GABA) A receptor, subunit beta 2	protein-coding
mm_107117.1	chr12	18390908	18390910	+	1	NA	Intergenic	IAPLTR2_Mm|LTR|ERVK	-123601	NM_001033157	236366	Mm.352227	NM_001033157	ENSMUSG00000073197	5730507C01Rik	-	RIKEN cDNA 5730507C01 gene	protein-coding
mm_117520.1	chr13	81253096	81253098	-	1	NA	intron (NM_054053, intron 85 of 89)	intron (NM_054053, intron 85 of 89)	289023	NR_015587	319983	Mm.343027	NR_015587	ENSMUSG00000097098	9330111N05Rik	-	RIKEN cDNA 9330111N05 gene	ncRNA
mm_124182.1	chr14	93890675	93890689	-	1	NA	promoter-TSS (NM_001271798)	promoter-TSS (NM_001271798)	-3	NM_001346722	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding
mm_103746.1	chr11	80142999	80143013	-	1	NA	promoter-TSS (NM_183275)	promoter-TSS (NM_183275)	-853	NM_183275	68550	Mm.18466	NM_183275	ENSMUSG00000046909	Tefm	1110002N22Rik	transcription elongation factor, mitochondrial	protein-coding
mm_129813.1	chr15	82998932	82998953	-	1	NA	3' UTR (NM_028728, exon 6 of 6)	3' UTR (NM_028728, exon 6 of 6)	24196	NM_028728	74039	Mm.32584	NM_028728	ENSMUSG00000058099	Nfam1	4921501M20Rik|Cnaip	Nfat activating molecule with ITAM motif 1	protein-coding
mm_169527.1	chr1	49150242	49150255	+	1	NA	Intergenic	RLTR9E|LTR|ERVK	-1683123	NR_105768	102466969		NR_105768	ENSMUSG00000098876	Mir6350	Gm27958|mmu-mir-6350	microRNA 6350	ncRNA
mm_172178.1	chr6	48686371	48686377	+	1	NA	intron (NM_174990, intron 1 of 2)	intron (NM_174990, intron 1 of 2)	1796	NM_174990	107526	Mm.333048	NM_174990	ENSMUSG00000054435	Gimap4	AU019574|E430007K16Rik|Ian-1|Ian1|Imap4	GTPase, IMAP family member 4	protein-coding
mm_102515.1	chr11	60811025	60811027	-	1	NA	5' UTR (NM_009171, exon 1 of 12)	5' UTR (NM_009171, exon 1 of 12)	239	NM_009171	20425	Mm.364956	NM_009171	ENSMUSG00000020534	Shmt1	AI324848|AI385541|C81125|Shmt|mshmt|mshmt1|mshmt2	serine hydroxymethyltransferase 1 (soluble)	protein-coding
mm_123874.1	chr14	72603010	72603022	-	1	NA	intron (NM_207636, intron 3 of 25)	intron (NM_207636, intron 3 of 25)	106987	NM_207636	319448	Mm.205421	NM_207636	ENSMUSG00000033487	Fndc3a	1700094E19Rik|D14Ertd453e|F730017H24Rik|Fndc3|sys	fibronectin type III domain containing 3A	protein-coding
mm_61283.1	chr7	67222575	67222635	+	1	NA	promoter-TSS (NM_175215)	promoter-TSS (NM_175215)	-11	NM_001191051	75099	Mm.121691	NM_175215	ENSMUSG00000043831	Lysmd4	4930506D23Rik	LysM, putative peptidoglycan-binding, domain containing 4	protein-coding
mm_25567.1	chr3	116598188	116598204	+	1	NA	intron (NM_030016, intron 1 of 11)	intron (NM_030016, intron 1 of 11)	3238	NM_001289571	72776	Mm.440836	NM_028349	ENSMUSG00000027959	Sass6	2810453L12Rik	SAS-6 centriolar assembly protein	protein-coding
mm_85561.1	chr9	106891395	106891397	-	1	NA	intron (NM_029103, intron 1 of 3)	intron (NM_029103, intron 1 of 3)	542	NM_029103	74840	Mm.29778	NM_029103	ENSMUSG00000032575	Manf	3230402M22Rik|AA407711|AA408789|AA673178|Armet|D17914|D18Mgi17	mesencephalic astrocyte-derived neurotrophic factor	protein-coding
mm_48394.1	chr5	139819934	139819973	-	1	NA	Intergenic	Intergenic	-5670	NM_001161548	231832	Mm.482655	NM_144914	ENSMUSG00000036687	Tmem184a	Sdmg1	transmembrane protein 184a	protein-coding
mm_171839.1	chr5	149661264	149661282	-	1	NA	Intergenic	Intergenic	-16984	NM_001081204	381694	Mm.45060	NM_001081204	ENSMUSG00000051950	B3glct	B3galtl|Gm1057	beta-3-glucosyltransferase	protein-coding
mm_150838.1	chr19	44918540	44918553	+	1	NA	Intergenic	Intergenic	-12573	NM_001081225	226151	Mm.212609	NM_172638	ENSMUSG00000036097	Fam178a	3632432H19|6030443O07Rik|AU014917|Slf2	family with sequence similarity 178, member A	protein-coding
mm_135057.1	chr16	33966996	33967010	-	1	NA	promoter-TSS (NM_009471)	promoter-TSS (NM_009471)	0	NM_009471	22247	Mm.13145	NM_009471	ENSMUSG00000022814	Umps	1700095D23Rik|AA408257|AL033308|BB164745	uridine monophosphate synthetase	protein-coding
mm_143271.1	chr17	65643938	65643967	-	1	NA	Intergenic	Intergenic	-1748	NM_001146002	213272	Mm.255732	NM_153519	ENSMUSG00000050612	Txndc2	AU021712|Sptrx-1|Sptrx1|Trx4	thioredoxin domain containing 2 (spermatozoa)	protein-coding
mm_128985.1	chr15	74834537	74834551	-	1	NA	TTS (NM_001033229)	TTS (NM_001033229)	7099	NM_001033229	110115	Mm.322606	NM_001033229	ENSMUSG00000075604	Cyp11b1	AA389061|CPN1|Cyp11b|Cyp11b-1|FHI	cytochrome P450, family 11, subfamily b, polypeptide 1	protein-coding
mm_42442.1	chr5	115429945	115429992	+	1	NA	intron (NM_008629, intron 1 of 14)	CpG	283	NM_008629	17690	Mm.5077	NM_008629	ENSMUSG00000054256	Msi1	Msi1h|Musahi1|m-Msi-1	musashi RNA-binding protein 1	protein-coding
mm_18546.1	chr2	64975726	64975758	-	1	NA	intron (NM_016719, intron 2 of 13)	intron (NM_016719, intron 2 of 13)	47024	NM_016719	50915	Mm.214554	NM_016719	ENSMUSG00000026888	Grb14	AI505286	growth factor receptor bound protein 14	protein-coding
mm_172362.1	chr7	120326277	120326288	+	1	NA	TTS (NM_026458)	TTS (NM_026458)	-2402	NM_177213	320631	Mm.78330	NM_177213	ENSMUSG00000054746	Abca15	4930500I12Rik	ATP-binding cassette, sub-family A (ABC1), member 15	protein-coding
mm_82434.1	chr9	15112101	15112119	-	1	NA	promoter-TSS (NM_001164797)	promoter-TSS (NM_001164797)	-2	NM_001164797	244698	Mm.325134	NM_001164797	ENSMUSG00000031936	Hephl1	Gm509|Zp|zyklopen	hephaestin-like 1	protein-coding
mm_69926.1	chr7	141902362	141902448	-	1	NA	promoter-TSS (NM_023764)	promoter-TSS (NM_023764)	1	NM_023764	54473	Mm.103551	NM_023764	ENSMUSG00000025139	Tollip	4930403G24Rik|4931428G15Rik	toll interacting protein	protein-coding
mm_40857.1	chr5	73557280	73557290	+	1	NA	exon (NM_001190734, exon 11 of 12)	exon (NM_001190734, exon 11 of 12)	66259	NM_178896	100737	Mm.220312	NM_178896	ENSMUSG00000051674	Dcun1d4	AI836376	DCN1, defective in cullin neddylation 1, domain containing 4 (S. cerevisiae)	protein-coding
mm_169463.1	chr14	65666373	65666374	+	1	NA	promoter-TSS (NM_001168318)	promoter-TSS (NM_001168318)	-30	NM_028903	71145	Mm.83840	NM_028903	ENSMUSG00000022032	Scara5	4932433F15Rik|4933425F03Rik|AV278087|Tesr	scavenger receptor class A, member 5	protein-coding
mm_84186.1	chr9	60141225	60141246	-	1	NA	promoter-TSS (NM_172444)	promoter-TSS (NM_172444)	-15	NM_172444	207596	Mm.28791	NM_172444	ENSMUSG00000032289	Thsd4	ADAMTSL-6|ADAMTSL6|AI585901|Adamtsl4|B230114P05Rik	thrombospondin, type I, domain containing 4	protein-coding
mm_48669.1	chr5	145997276	145997281	-	1	NA	intron (NR_030782, intron 4 of 11)	intron (NR_030782, intron 4 of 11)	12339	NM_019792	56388	Mm.301900	NM_019792	ENSMUSG00000029630	Cyp3a25	AI327008	cytochrome P450, family 3, subfamily a, polypeptide 25	protein-coding
mm_133872.1	chr16	96372840	96372853	+	1	NA	exon (NM_028078, exon 3 of 8)	exon (NM_028078, exon 3 of 8)	11082	NM_028078	72058	Mm.119714	NM_028078	ENSMUSG00000000159	Igsf5	2010003D20Rik|JCAM|Jam4	immunoglobulin superfamily, member 5	protein-coding
mm_85121.1	chr9	95472093	95472120	-	1	NA	exon (NM_001114977, exon 24 of 28)	exon (NM_001114977, exon 24 of 28)	39890	NM_026476	67958	Mm.292742	NM_026476	ENSMUSG00000032407	U2surp	2610101N10Rik|AU023006|Sr140	U2 snRNP-associated SURP domain containing	protein-coding
mm_162708.1	chr10	24223443	24223445	+	1	NA	promoter-TSS (NM_021509)	promoter-TSS (NM_021509)	-73	NM_021509	59012	Mm.285934	NM_021509	ENSMUSG00000020000	Moxd1	3230402N08Rik|MNCb-5203	monooxygenase, DBH-like 1	protein-coding
mm_35147.1	chr4	11958945	11958946	-	1	NA	3' UTR (NM_001290387, exon 2 of 2)	3' UTR (NM_001290387, exon 2 of 2)	6768	NM_001098231	381511	Mm.331489	NM_001033453	ENSMUSG00000049225	Pdp1	Gm1024|Ppm2c	pyruvate dehyrogenase phosphatase catalytic subunit 1	protein-coding
mm_154140.1	chr19	57418589	57418597	-	1	NA	Intergenic	Intergenic	-34313	NM_029839	72133	Mm.258404	NM_028115	ENSMUSG00000025086	Trub1	2610009I02Rik|9030425C13Rik|AI448235|BB118943|C76870	TruB pseudouridine (psi) synthase family member 1	protein-coding
mm_44690.1	chr5	30155484	30155530	-	1	NA	promoter-TSS (NM_178878)	promoter-TSS (NM_178878)	254	NM_001289798	231086	Mm.291463	NM_145558	ENSMUSG00000059447	Hadhb	4930479F15Rik|Mtpb|TP-beta	hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), beta subunit	protein-coding
mm_8373.1	chr1	150993141	150993155	-	1	NA	5' UTR (NM_001024720, exon 1 of 107)	5' UTR (NM_001024720, exon 1 of 107)	287	NM_001024720	545370	Mm.379425	NM_001024720	ENSMUSG00000066842	Hmcn1	EG545370|FIBL-6|Gm201	hemicentin 1	protein-coding
mm_168097.1	chr10	128909874	128909874	+	1	NA	promoter-TSS (NM_007653)	promoter-TSS (NM_007653)	8	NM_007653	12512	Mm.371552	NM_007653	ENSMUSG00000025351	Cd63	C75951|ME491|Tspan30	CD63 antigen	protein-coding
mm_8992.1	chr1	165708089	165708099	-	1	NA	promoter-TSS (NM_001038846)	promoter-TSS (NM_001038846)	0	NM_178593	226594	Mm.265552	NM_178593	ENSMUSG00000040723	Rcsd1	A430105K13Rik|BC025872|CapZIP	RCSD domain containing 1	protein-coding
mm_39397.1	chr5	14025475	14025488	+	1	NA	5' UTR (NM_011348, exon 1 of 17)	5' UTR (NM_011348, exon 1 of 17)	205	NM_011348	20349	Mm.134093	NM_011348	ENSMUSG00000063531	Sema3e	6430702L12|AA408817|Semah|mKIAA0331	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	protein-coding
mm_123445.1	chr14	65098032	65098100	-	1	NA	promoter-TSS (NM_018788)	promoter-TSS (NM_018788)	40	NM_018788	54616	Mm.103748	NM_018788	ENSMUSG00000021978	Extl3	2900009G18Rik|AU040105|Ext1l|mKIAA0519	exostoses (multiple)-like 3	protein-coding
mm_20579.1	chr2	131146572	131146580	-	1	NA	TTS (NM_028306)	TTS (NM_028306)	13444	NM_026091	67326	Mm.27711	NM_026091	ENSMUSG00000027327	1700037H04Rik	-	RIKEN cDNA 1700037H04 gene	protein-coding
mm_152848.1	chr19	24031007	24031028	-	1	NA	promoter-TSS (NM_001114174)	promoter-TSS (NM_001114174)	2	NM_001114174	381217	Mm.426078	NM_001114174	ENSMUSG00000071604	Fam189a2	AI414343|AI666772|Gm967	family with sequence similarity 189, member A2	protein-coding
mm_142629.1	chr17	47400550	47400571	-	1	NA	promoter-TSS (NM_008189)	promoter-TSS (NM_008189)	46	NM_008189	14913	Mm.16224	NM_008189	ENSMUSG00000023982	Guca1a	GC-A|Gcap1|Guca1|mGCAP1	guanylate cyclase activator 1a (retina)	protein-coding
mm_138822.1	chr17	39847717	39847785	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	4754	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_121830.1	chr14	20496711	20496724	-	1	NA	5' UTR (NM_029104, exon 1 of 7)	5' UTR (NM_029104, exon 1 of 7)	184	NM_029104	74843	Mm.295241	NM_029104	ENSMUSG00000021815	Mss51	4833444M15Rik|Zmynd17	MSS51 mitochondrial translational activator	protein-coding
mm_107850.1	chr12	69374598	69374621	+	1	NA	3' UTR (NM_007481, exon 2 of 2)	3' UTR (NM_007481, exon 2 of 2)	2459	NM_007481	11845	Mm.27308	NM_007481	ENSMUSG00000044147	Arf6	AI788669|AW496366	ADP-ribosylation factor 6	protein-coding
mm_75137.1	chr8	35250688	35250704	-	1	NA	Intergenic	LTR78B|LTR|ERV1	-125045	NM_177741	244416	Mm.247126	NM_177741	ENSMUSG00000046794	Ppp1r3b	6430576E21|AW821953|GL|PTG	protein phosphatase 1, regulatory (inhibitor) subunit 3B	protein-coding
mm_62162.1	chr7	97210209	97210223	+	1	NA	intron (NM_001162477, intron 1 of 9)	intron (NM_001162477, intron 1 of 9)	115748	NM_001177412	244144	Mm.297541	NM_001177412	ENSMUSG00000035713	Usp35	Gm1088|Gm493	ubiquitin specific peptidase 35	protein-coding
mm_64591.1	chr7	3169094	3169112	-	1	NA	promoter-TSS (NM_001004153)	promoter-TSS (NM_001004153)	100	NM_001004153	245128	Mm.268551	NM_001004153	ENSMUSG00000054753	AU018091	-	expressed sequence AU018091	protein-coding
mm_76333.1	chr8	84708506	84708516	-	1	NA	3' UTR (NM_010906, exon 9 of 9)	3' UTR (NM_010906, exon 9 of 9)	7054	NM_008535	17095	Mm.4925	NM_008535	ENSMUSG00000034041	Lyl1	Lyl-1|bHLHa18	lymphoblastomic leukemia 1	protein-coding
mm_110422.1	chr12	46818342	46818357	-	1	NA	intron (NM_021361, intron 1 of 4)	intron (NM_021361, intron 1 of 4)	426	NM_021361	664883	Mm.247195	NM_021361	ENSMUSG00000021047	Nova1	9430099M15Rik|G630039L02|Nova-1	neuro-oncological ventral antigen 1	protein-coding
mm_57623.1	chr6	128243479	128243503	-	1	NA	exon (NM_001080979, exon 7 of 11)	exon (NM_001080979, exon 7 of 11)	57322	NM_001080979	21679	Mm.14774	NM_011567	ENSMUSG00000030353	Tead4	ETFR-2|Etfr2|FR-19|Rtef1|TEAD-4|TEF-3|Tcf13r1|Tef3|Tefr|Tefr1|Tefr1a	TEA domain family member 4	protein-coding
mm_104253.1	chr11	88924269	88924276	-	1	NA	3' UTR (NM_029023, exon 13 of 13)	3' UTR (NM_029023, exon 13 of 13)	18344	NR_045955	73921	Mm.439148	NR_045955	ENSMUSG00000087338	Scpep1os	4930405P13Rik	serine carboxypeptidase 1, opposite strand	ncRNA
mm_7891.1	chr1	133258541	133258553	-	1	NA	non-coding (NR_037984, exon 2 of 4)	non-coding (NR_037984, exon 2 of 4)	11261	NR_037984	100502933	Mm.487491	NR_037984	ENSMUSG00000101693	Gm19461	-	predicted gene, 19461	ncRNA
mm_165417.1	chr2	148022053	148022055	-	1	NA	Intergenic	Intergenic	23410	NM_001291067	15376	Mm.938	NM_010446	ENSMUSG00000037025	Foxa2	HNF3-beta|HNF3beta|Hnf-3b|Hnf3b|Tcf-3b|Tcf3b	forkhead box A2	protein-coding
mm_110658.1	chr12	59070199	59070234	-	1	NA	exon (NM_008891, exon 7 of 9)	exon (NM_008891, exon 7 of 9)	3297	NM_008891	18949	Mm.22347	NM_008891	ENSMUSG00000020994	Pnn	AU045199|D12Ertd512e	pinin	protein-coding
mm_124815.1	chr15	8968390	8968392	+	1	NA	5' UTR (NM_198024, exon 1 of 14)	5' UTR (NM_198024, exon 1 of 14)	442	NM_198024	223332	Mm.321371	NM_198024	ENSMUSG00000048424	Ranbp3l	C130037N17Rik	RAN binding protein 3-like	protein-coding
mm_108061.1	chr12	73931561	73931571	+	1	NA	intron (NM_001313920, intron 5 of 14)	B2_Mm2|SINE|B2	23699	NM_001313919	15251	Mm.3879	NM_010431	ENSMUSG00000021109	Hif1a	AA959795|HIF-1-alpha|HIF1-alpha|HIF1alpha|MOP1|bHLHe78	hypoxia inducible factor 1, alpha subunit	protein-coding
mm_61024.1	chr7	49516875	49516875	+	1	NA	intron (NM_175272, intron 11 of 37)	intron (NM_175272, intron 11 of 37)	119960	NM_001005232	13172	Mm.307176	NM_001005232	ENSMUSG00000030507	Dbx1	AI426026|Dbx	developing brain homeobox 1	protein-coding
mm_34345.1	chr4	144520224	144520233	+	1	NA	intron (NM_198662, intron 1 of 3)	intron (NM_198662, intron 1 of 3)	406	NM_198662	381572	Mm.184290	NM_198662	ENSMUSG00000028593	9430007A20Rik	Aadacl4|Gm1034	RIKEN cDNA 9430007A20 gene	protein-coding
mm_115272.1	chr13	111686089	111686100	+	1	NA	promoter-TSS (NM_172593)	promoter-TSS (NM_172593)	-84	NM_172593	218613	Mm.31012	NM_172593	ENSMUSG00000032727	Mier3	5730509D14|AU015422|D130064H19Rik	MIER family member 3	protein-coding
mm_166325.1	chr5	112292112	112292114	+	1	NA	intron (NM_001326590, intron 1 of 5)	intron (NM_001326590, intron 1 of 5)	15422	NM_009419	22022	Mm.250631	NM_009419	ENSMUSG00000029344	Tpst2	AI448750|D5Ucla3|Tango13b|grm|grt	protein-tyrosine sulfotransferase 2	protein-coding
mm_50134.1	chr6	41542645	41542663	+	1	NA	Intergenic	Intergenic	20878	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_54992.1	chr6	48770807	48770822	-	1	NA	promoter-TSS (NM_031247)	promoter-TSS (NM_031247)	37	NM_031247	83408	Mm.333050	NM_031247	ENSMUSG00000039264	Gimap3	2010110D23Rik|Gimap5|Ian4	GTPase, IMAP family member 3	protein-coding
mm_148078.1	chr18	72351091	72351108	-	1	NA	promoter-TSS (NM_007831)	promoter-TSS (NM_007831)	-30	NM_007831	13176	Mm.167882	NM_007831	ENSMUSG00000060534	Dcc	C030036D22Rik|Igdcc1	deleted in colorectal carcinoma	protein-coding
mm_161326.1	chr14	50084522	50084522	-	1	NA	exon (NM_146316, exon 1 of 1)	exon (NM_146316, exon 1 of 1)	157	NM_146316	258313	Mm.463727	NM_146316	ENSMUSG00000060523	Olfr726	MOR246-4	olfactory receptor 726	protein-coding
mm_6720.1	chr1	82482735	82482736	-	1	NA	intron (NM_007735, intron 35 of 47)	intron (NM_007735, intron 35 of 47)	104114	NM_007735	12829	Mm.40253	NM_007735	ENSMUSG00000067158	Col4a4	E130010M05Rik|[a]4(IV)	collagen, type IV, alpha 4	protein-coding
mm_105140.1	chr11	101459735	101459749	-	1	NA	3' UTR (NM_012037, exon 6 of 6)	3' UTR (NM_012037, exon 6 of 6)	6457	NM_012037	26949	Mm.29210	NM_012037	ENSMUSG00000034993	Vat1	VAT-1	vesicle amine transport 1	protein-coding
mm_172203.1	chr6	54098607	54098615	+	1	NA	intron (NM_001163640, intron 1 of 12)	RLTR31D_MM|LTR|ERVK	58679	NM_001163640	69993	Mm.321147	NM_023543	ENSMUSG00000004633	Chn2	1700026N20Rik|4930557O16Rik|ARHGAP3|Bch	chimerin 2	protein-coding
mm_70015.1	chr7	142512072	142512110	-	1	NA	exon (NM_001163669, exon 13 of 17)	exon (NM_001163669, exon 13 of 17)	-5320	NR_033261	677289	Mm.350054	NR_033261	ENSMUSG00000043795	Prr33	ENSMUSG00000043795|Gm14492|OTTMUSG00000016823	proline rich 33	ncRNA
mm_27106.1	chr3	30647780	30647782	-	1	NA	promoter-TSS (NM_001290510)	promoter-TSS (NM_001290510)	37	NM_027941	71827	Mm.45373	NM_027941	ENSMUSG00000027702	Lrrc34	1700007J06Rik|SPATA34	leucine rich repeat containing 34	protein-coding
mm_53059.1	chr6	124829583	124829587	+	1	NA	promoter-TSS (NM_013538)	promoter-TSS (NM_013538)	-101	NM_013700	22225	Mm.3571	NM_013700	ENSMUSG00000038429	Usp5	AA407472|ISOT|ISOT-1|Ucht	ubiquitin specific peptidase 5 (isopeptidase T)	protein-coding
mm_21097.1	chr2	153231655	153231687	-	1	NA	exon (NM_018807, exon 3 of 3)	exon (NM_018807, exon 3 of 3)	-6230	NM_198617	241732	Mm.277243	NM_198617	ENSMUSG00000074671	Tspyl3	AW212607|Gm36	TSPY-like 3	protein-coding
mm_78205.1	chr9	21424985	21425021	+	1	NA	promoter-TSS (NM_001039520)	promoter-TSS (NM_001039520)	95	NM_001039520	13430	Mm.433257	NM_007871	ENSMUSG00000033335	Dnm2	Dyn2|Udnm|b2b2159Clo	dynamin 2	protein-coding
mm_19774.1	chr2	105959566	105959568	-	1	NA	intron (NM_028260, intron 5 of 6)	L1MA5A|LINE|L1	43982	NM_026992	99349	Mm.25661	NM_026992	ENSMUSG00000027166	Dnajc24	1700030A21Rik|2610027M02Rik|AV066965|AW240712|Dph4|MmDjC7|Zcsl3	DnaJ heat shock protein family (Hsp40) member C24	protein-coding
mm_135297.1	chr16	38622348	38622363	-	1	NA	intron (NM_020260, intron 6 of 11)	B3A|SINE|B2	59541	NM_026407	67846	Mm.310476	NM_026407	ENSMUSG00000002845	Tmem39a	2610033C09Rik	transmembrane protein 39a	protein-coding
mm_87773.1	chr10	60294595	60294603	+	1	NA	exon (NM_011179, exon 5 of 15)	exon (NM_011179, exon 5 of 15)	10138	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_155057.1	chrX	42374621	42374625	+	1	NA	Intergenic	Lx8|LINE|L1	-127942	NM_011364	20400	Mm.441197	NM_011364	ENSMUSG00000005696	Sh2d1a	Gm686|SAP	SH2 domain containing 1A	protein-coding
mm_10094.1	chr2	3333159	3333163	+	1	NA	promoter-TSS (NM_001013376)	promoter-TSS (NM_001013376)	-533	NM_001013376	227522	Mm.293948	NM_001013376	ENSMUSG00000049950	Rpp38	C330006A15Rik	ribonuclease P/MRP 38 subunit	protein-coding
mm_102815.1	chr11	68973279	68973292	-	1	NA	TTS (NM_028048)	TTS (NM_028048)	570	NM_021329	57785	Mm.143774	NM_021329	ENSMUSG00000032892	Rangrf	2400006H24Rik|Mog1|Rangnrf	RAN guanine nucleotide release factor	protein-coding
mm_170064.1	chr17	30626989	30626990	+	1	NA	promoter-TSS (NR_045287)	promoter-TSS (NR_045287)	53	NM_013811	13417	Mm.426017	NM_013811	ENSMUSG00000033826	Dnah8	ATPase|Dnahc8|Hst6.7b|P1-Loop	dynein, axonemal, heavy chain 8	protein-coding
mm_157599.1	chrX	53269787	53269858	-	1	NA	promoter-TSS (NM_030167)	promoter-TSS (NM_030167)	-17	NM_001166583	78755	Mm.28559	NM_030167	ENSMUSG00000036022	Fam122b	4632404H22Rik|AI256344|SPACIA2	family with sequence similarity 122, member B	protein-coding
mm_22833.1	chr3	27317107	27317117	+	1	NA	promoter-TSS (NM_009425)	promoter-TSS (NM_009425)	35	NM_009425	22035	Mm.1062	NM_009425	ENSMUSG00000039304	Tnfsf10	A330042I21Rik|AI448571|APO-2L|Ly81|TL2|Tnlg6a|Trail	tumor necrosis factor (ligand) superfamily, member 10	protein-coding
mm_131903.1	chr16	23268464	23268479	+	1	NA	intron (NM_001252505, intron 2 of 7)	intron (NM_001252505, intron 2 of 7)	-21999	NM_001252506	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_10943.1	chr2	25501844	25501850	+	1	NA	promoter-TSS (NM_001271777)	promoter-TSS (NM_001271777)	-128	NM_001271777	69379	Mm.24596	NM_027062	ENSMUSG00000015083	C8g	-	complement component 8, gamma polypeptide	protein-coding
mm_88004.1	chr10	67096368	67096378	+	1	NA	intron (NM_178606, intron 1 of 7)	CpG	615	NM_001204915	28193	Mm.41272	NM_178606	ENSMUSG00000019873	Reep3	D10Ucla1	receptor accessory protein 3	protein-coding
mm_84667.1	chr9	71996638	71996641	-	1	NA	intron (NM_001253862, intron 5 of 19)	intron (NM_001253862, intron 5 of 19)	33198	NR_029879	723889		NR_029879	ENSMUSG00000105200	Mir378a	Mir378|Mirn378|mmu-mir-378|mmu-mir-378a	microRNA 378a	ncRNA
mm_111252.1	chr12	84946922	84946923	-	1	NA	intron (NM_178065, intron 2 of 19)	ORR1A4|LTR|ERVL-MaLR	23964	NM_178065	68497	Mm.24446	NM_178065	ENSMUSG00000042350	Arel1	1110018G07Rik|AI649076|AW610792|Kiaa0317|mKIAA0317	apoptosis resistant E3 ubiquitin protein ligase 1	protein-coding
mm_116572.1	chr13	47100206	47100216	-	1	NA	exon (NM_025900, exon 5 of 11)	exon (NM_025900, exon 5 of 11)	6010	NM_025900	110052	Mm.131150	NM_025900	ENSMUSG00000021377	Dek	1810019E15Rik|D13H6S231E	DEK oncogene (DNA binding)	protein-coding
mm_169096.1	chr1	34109761	34109764	+	1	NA	intron (NM_001276764, intron 5 of 102)	intron (NM_001276764, intron 5 of 102)	-7597	NR_105861	102466987		NR_105861	ENSMUSG00000105982	Mir6896	mmu-mir-6896	microRNA 6896	ncRNA
mm_58644.1	chr7	6252733	6252755	+	1	NA	promoter-TSS (NM_001177416)	promoter-TSS (NM_001177416)	34	NM_001177416	627821	Mm.99441	NM_001177416	ENSMUSG00000053367	Gm6792	EG627821	predicted gene 6792	protein-coding
mm_86396.1	chr9	123968606	123968632	-	1	NA	promoter-TSS (NM_009912)	promoter-TSS (NM_009912)	73	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_43756.1	chr5	140505621	140505666	+	1	NA	promoter-TSS (NM_021528)	promoter-TSS (NM_021528)	34	NM_021528	59031	Mm.28934	NM_021528	ENSMUSG00000036599	Chst12	AI595374|C4S-2|C4ST2	carbohydrate sulfotransferase 12	protein-coding
mm_38688.1	chr4	145194968	145194993	-	1	NA	promoter-TSS (NM_001276465)	promoter-TSS (NM_001276465)	25	NM_001276465	230895	Mm.240310	NM_001033190	ENSMUSG00000020220	Vps13d	-	vacuolar protein sorting 13D	protein-coding
mm_137242.1	chr17	24470822	24470835	+	1	NA	exon (NM_025954, exon 1 of 2)	exon (NM_025954, exon 1 of 2)	355	NM_025954	67078	Mm.28541	NM_025954	ENSMUSG00000043445	Pgp	1700012G19Rik|AI481330|AUM|G3PP	phosphoglycolate phosphatase	protein-coding
mm_40036.1	chr5	33721770	33721800	+	1	NA	promoter-TSS (NM_001163215)	promoter-TSS (NM_001163215)	61	NM_001163215	14184	Mm.6904	NM_008010	ENSMUSG00000054252	Fgfr3	CD333|FR3|Fgfr-3|Flg-2|HBGFR|Mfr3|sam3	fibroblast growth factor receptor 3	protein-coding
mm_118461.1	chr14	9885960	9885996	+	1	NA	non-coding (NR_030680, exon 1 of 1)	non-coding (NR_030680, exon 1 of 1)	1883	NR_030680	100042415	Mm.235938	NR_030680		Mnd1-ps	Gm3833	Mnd1 retrotransposed pseudogene	pseudo
mm_148790.1	chr19	6164451	6164461	+	1	NA	promoter-TSS (NM_028967)	promoter-TSS (NM_028967)	-2	NM_028967	74481	Mm.159219	NM_028967	ENSMUSG00000039699	Batf2	4933430F08Rik	basic leucine zipper transcription factor, ATF-like 2	protein-coding
mm_105314.1	chr11	102880982	102880992	-	1	NA	promoter-TSS (NM_001109995)	promoter-TSS (NM_001109995)	-12	NM_001109995	20624	Mm.873	NM_011431	ENSMUSG00000020929	Eftud2	116kDa|Snrp116|U5-116kD	elongation factor Tu GTP binding domain containing 2	protein-coding
mm_94900.1	chr11	29178417	29178424	+	1	NA	intron (NM_134034, intron 2 of 15)	AT_rich|Low_complexity|Low_complexity	5513	NM_134034	104570	Mm.276386	NM_134034	ENSMUSG00000020463	Smek2	AW011752|AW557776|Ppp4r3b|mKIAA1387	SMEK homolog 2, suppressor of mek1 (Dictyostelium)	protein-coding
mm_9186.1	chr1	171113946	171113954	-	1	NA	Intergenic	Intergenic	-7711	NM_001081275	75472	Mm.32760	NM_029301	ENSMUSG00000026649	Cfap126	1700009P17Rik|AV282292|Flattop|Fltp	cilia and flagella associated protein 126	protein-coding
mm_91.1	chr1	7098127	7098131	+	1	NA	intron (NM_183028, intron 1 of 5)	intron (NM_183028, intron 1 of 5)	9209	NM_183028	319263	Mm.21539	NM_183028	ENSMUSG00000051285	Pcmtd1	8430411F12Rik|A030012M09Rik	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding
mm_68378.1	chr7	109170530	109170557	-	1	NA	promoter-TSS (NM_001302206)	promoter-TSS (NM_001302206)	-24	NM_057173	109594	Mm.360145	NM_057173	ENSMUSG00000036111	Lmo1	Rbtn-1|Rbtn1|Ttg1	LIM domain only 1	protein-coding
mm_11093.1	chr2	27911890	27911892	+	1	NA	intron (NM_015734, intron 1 of 65)	intron (NM_015734, intron 1 of 65)	25466	NM_015734	12831	Mm.7281	NM_015734	ENSMUSG00000026837	Col5a1	AI413331	collagen, type V, alpha 1	protein-coding
mm_72644.1	chr8	84701908	84701910	+	1	NA	5' UTR (NM_008535, exon 1 of 4)	5' UTR (NM_008535, exon 1 of 4)	452	NM_008535	17095	Mm.4925	NM_008535	ENSMUSG00000034041	Lyl1	Lyl-1|bHLHa18	lymphoblastomic leukemia 1	protein-coding
mm_127033.1	chr15	96402994	96403023	+	1	NA	3' UTR (NM_175251, exon 21 of 21)	3' UTR (NM_175251, exon 21 of 21)	57835	NM_028148	72193	Mm.324474	NM_028148	ENSMUSG00000033228	Scaf11	1110061H03Rik|2610510E10Rik|AI462454|CASP11|SIP1|SRRP129|Sfrs2ip|Srsf2ip|mKIAA3013	SR-related CTD-associated factor 11	protein-coding
mm_114839.1	chr13	92611079	92611117	+	1	NA	promoter-TSS (NM_172588)	promoter-TSS (NM_172588)	-40	NM_172588	218442	Mm.297970	NM_172588	ENSMUSG00000021703	Serinc5	A130038L21Rik|AIGP3|C86123|TPO1	serine incorporator 5	protein-coding
mm_70528.1	chr8	13012413	13012413	+	1	NA	intron (NM_001159486, intron 23 of 29)	intron (NM_001159486, intron 23 of 29)	-13621	NM_010172	14068	Mm.4827	NM_010172	ENSMUSG00000031443	F7	AI132620|Cf7|FVII	coagulation factor VII	protein-coding
mm_29574.1	chr3	116968929	116968938	-	1	NA	promoter-TSS (NM_023245)	promoter-TSS (NM_023245)	19	NM_023245	114301	Mm.253736	NM_023245	ENSMUSG00000033377	Palmd	4631423C22Rik|PALML	palmdelphin	protein-coding
mm_108263.1	chr12	78691517	78691540	+	1	NA	promoter-TSS (NM_029069)	promoter-TSS (NM_029069)	-7	NM_027597	70897	Mm.56514	NM_027597	ENSMUSG00000056987	Fam71d	4921509E07Rik|4930516C23Rik|GARI-L2	family with sequence similarity 71, member D	protein-coding
mm_142093.1	chr17	35834477	35834494	-	1	NA	3' UTR (NM_011655, exon 4 of 4)	3' UTR (NM_011655, exon 4 of 4)	3816	NM_011655	22154	Mm.273538	NM_011655	ENSMUSG00000001525	Tubb5	AA408537|AI596182|B130022C14Rik|M(beta)5	tubulin, beta 5 class I	protein-coding
mm_152482.1	chr19	11048304	11048379	-	1	NA	non-coding (NR_102366, exon 2 of 3)	non-coding (NR_102366, exon 2 of 3)	2225	NR_102366	107350	Mm.6381	NM_001177351	ENSMUSG00000075010	AW112010	-	expressed sequence AW112010	ncRNA
mm_93896.1	chr10	125389352	125389383	-	1	NA	Intergenic	Intergenic	-60832	NM_011391	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|Mct2	solute carrier family 16 (monocarboxylic acid transporters), member 7	protein-coding
mm_88859.1	chr10	80930858	80930862	+	1	NA	intron (NM_008655, intron 2 of 3)	intron (NM_008655, intron 2 of 3)	769	NM_008655	17873	Mm.1360	NM_008655	ENSMUSG00000015312	Gadd45b	AI323528|Myd118	growth arrest and DNA-damage-inducible 45 beta	protein-coding
mm_48333.1	chr5	139039154	139039154	-	1	NA	intron (NM_008923, intron 8 of 10)	intron (NM_008923, intron 8 of 10)	-44201	NM_008808	18590	Mm.2675	NM_008808	ENSMUSG00000025856	Pdgfa	-	platelet derived growth factor, alpha	protein-coding
mm_114834.1	chr13	92425958	92426031	+	1	NA	promoter-TSS (NM_175455)	promoter-TSS (NM_175455)	25	NM_175455	218440	Mm.213623	NM_175455	ENSMUSG00000045034	Ankrd34b	6430502M16Rik|DP58	ankyrin repeat domain 34B	protein-coding
mm_111497.1	chr12	99376948	99376954	-	1	NA	intron (NM_183186, intron 2 of 5)	intron (NM_183186, intron 2 of 5)	73123	NM_183186	71375	Mm.341972	NM_183186	ENSMUSG00000033713	Foxn3	5430426H20Rik|AA589593|AW556347|Ches1|Ches1l|HTLFL1	forkhead box N3	protein-coding
mm_10677.1	chr2	21367599	21367617	+	1	NA	promoter-TSS (NM_001004761)	promoter-TSS (NM_001004761)	41	NM_001004761	241263	Mm.166647	NM_175706	ENSMUSG00000045967	Gpr158	5330427M13Rik|mKIAA1136	G protein-coupled receptor 158	protein-coding
mm_149391.1	chr19	11386822	11386834	+	1	NA	intron (NM_001310331, intron 4 of 6)	intron (NM_001310331, intron 4 of 6)	11340	NM_001310331	666907		NM_001310331	ENSMUSG00000101389	Ms4a4a	EG666907	membrane-spanning 4-domains, subfamily A, member 4A	protein-coding
mm_91561.1	chr10	40025155	40025171	-	1	NA	5' UTR (NM_144821, exon 1 of 4)	5' UTR (NM_144821, exon 1 of 4)	105	NM_144821	215929	Mm.55513	NM_144821	ENSMUSG00000038522	Mfsd4b1	AI317395|AI482555|Naglt1a	major facilitator superfamily domain containing 4B1	protein-coding
mm_2872.1	chr1	131761558	131761563	+	1	NA	intron (NM_177243, intron 12 of 20)	intron (NM_177243, intron 12 of 20)	17538	NM_177243	320718	Mm.482704	NM_177243	ENSMUSG00000042268	Slc26a9	E030002L01Rik	solute carrier family 26, member 9	protein-coding
mm_58687.1	chr7	12835249	12835261	+	1	NA	intron (NM_022981, intron 1 of 7)	intron (NM_022981, intron 1 of 7)	445	NM_022981	65020	Mm.292297	NM_022981	ENSMUSG00000058638	Zfp110	2900024E01Rik|N28112|NRIF|Nrif1	zinc finger protein 110	protein-coding
mm_171785.1	chr5	110118718	110118734	-	1	NA	intron (NM_001163996, intron 2 of 4)	intron (NM_001163996, intron 2 of 4)	8634	NM_001163996	675812	Mm.442122	NM_001163996	ENSMUSG00000023284	Zfp605	A830023I12Rik	zinc finger protein 605	protein-coding
mm_36456.1	chr4	82505275	82505358	-	1	NA	5' UTR (NM_001113209, exon 1 of 12)	5' UTR (NM_001113209, exon 1 of 12)	463	NM_001286127	18028	Mm.317947	NM_008687	ENSMUSG00000008575	Nfib	6720429L07Rik|CTF|E030026I10Rik|NF-I/B|NF1-B|NFI-B	nuclear factor I/B	protein-coding
mm_80191.1	chr9	72394349	72394351	+	1	NA	Intergenic	Intergenic	-44179	NM_008613	17427	Mm.387671	NM_008613	ENSMUSG00000032221	Mns1	AW546487	meiosis-specific nuclear structural protein 1	protein-coding
mm_79280.1	chr9	50803510	50803521	+	1	NA	intron (NR_045601, intron 9 of 13)	RMER1B|Other|Other	28290	NR_045601	102580	Mm.160035	NM_133981	ENSMUSG00000032059	Alg9	8230402H15Rik|AI747665|B430313H07Rik|Dibd1	asparagine-linked glycosylation 9 (alpha 1,2 mannosyltransferase)	protein-coding
mm_102608.1	chr11	62456524	62456527	-	1	NA	intron (NM_177229, intron 1 of 8)	intron (NM_177229, intron 1 of 8)	807	NM_177229	20185	Mm.271814	NM_011308	ENSMUSG00000018501	Ncor1	5730405M06Rik|A230020K14Rik|N-CoR|RIP13|Rxrip13|mKIAA1047	nuclear receptor co-repressor 1	protein-coding
mm_7944.1	chr1	133914920	133914924	-	1	NA	exon (NM_054077, exon 2 of 3)	exon (NM_054077, exon 2 of 3)	6479	NM_054077	116847	Mm.214514	NM_054077	ENSMUSG00000041577	Prelp	7330409J17Rik|SLRR2A	proline arginine-rich end leucine-rich repeat	protein-coding
mm_73285.1	chr8	104847062	104847079	+	1	NA	promoter-TSS (NM_145603)	promoter-TSS (NM_145603)	2	NM_145603	234671	Mm.28191	NM_145603	ENSMUSG00000061825	Ces2c	ACH M1|CES 2|Ces2|ces2A3	carboxylesterase 2C	protein-coding
mm_25385.1	chr3	107215981	107215992	+	1	NA	exon (NM_001111143, exon 5 of 9)	exon (NM_001111143, exon 5 of 9)	5746	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_115088.1	chr13	102706081	102706089	+	1	NA	exon (NM_008533, exon 3 of 3)	exon (NM_008533, exon 3 of 3)	12527	NM_008533	17079	Mm.373974	NM_008533	ENSMUSG00000021624	Cd180	F630107B15|Ly78|RP105	CD180 antigen	protein-coding
mm_92425.1	chr10	77085390	77085398	-	1	NA	exon (NM_001109991, exon 5 of 41)	exon (NM_001109991, exon 5 of 41)	28311	NM_001109991	12822	Mm.4352	NM_009929	ENSMUSG00000001435	Col18a1	-	collagen, type XVIII, alpha 1	protein-coding
mm_127885.1	chr15	8710445	8710498	-	1	NA	5' UTR (NM_148938, exon 1 of 10)	5' UTR (NM_148938, exon 1 of 10)	336	NM_148938	20512	Mm.204834	NM_148938	ENSMUSG00000005360	Slc1a3	AI504299|B430115D02Rik|Eaat1|GLAST|GLAST-1|GLU-T|GluT-1|Gmt1|MGluT1	solute carrier family 1 (glial high affinity glutamate transporter), member 3	protein-coding
mm_14507.1	chr2	132253392	132253435	+	1	NA	promoter-TSS (NM_011045)	promoter-TSS (NM_011045)	-233	NM_011045	18538	Mm.7141	NM_011045	ENSMUSG00000027342	Pcna	-	proliferating cell nuclear antigen	protein-coding
mm_49554.1	chr6	30544023	30544030	+	1	NA	intron (NM_001024698, intron 1 of 10)	intron (NM_001024698, intron 1 of 10)	2384	NM_001024698	232680	Mm.268855	NM_001024698	ENSMUSG00000071553	Cpa2	-	carboxypeptidase A2, pancreatic	protein-coding
mm_141303.1	chr17	28177642	28177682	-	1	NA	intron (NM_172617, intron 1 of 14)	CpG	244	NM_172617	224656	Mm.267359	NM_172617	ENSMUSG00000024220	Zfp523	2810027J07|BC025615|Znf76	zinc finger protein 523	protein-coding
mm_124947.1	chr15	12350179	12350191	+	1	NA	3' UTR (NM_025673, exon 4 of 4)	3' UTR (NM_025673, exon 4 of 4)	28689	NM_025673	66629	Mm.157655	NM_025673	ENSMUSG00000022200	Golph3	4733401N08Rik|5730410D03Rik|AW413496	golgi phosphoprotein 3	protein-coding
mm_155082.1	chrX	47912470	47912481	+	1	NA	promoter-TSS (NM_177215)	promoter-TSS (NM_177215)	19	NM_177215	320634	Mm.210343	NM_177215	ENSMUSG00000001173	Ocrl	9530014D17Rik|BB143339|OCRL1	oculocerebrorenal syndrome of Lowe	protein-coding
mm_25960.1	chr3	132629923	132629935	+	1	NA	promoter-TSS (NM_001270430)	promoter-TSS (NM_001270430)	-262	NM_001270430	433653		NM_001270430	ENSMUSG00000091721	Gimd1	EG433653|Gm5549	GIMAP family P-loop NTPase domain containing 1	protein-coding
mm_52486.1	chr6	114643177	114643187	+	1	NA	promoter-TSS (NM_028835)	promoter-TSS (NM_028835)	85	NM_001253717	74244	Mm.275332	NM_028835	ENSMUSG00000030314	Atg7	1810013K23Rik|Agp7|Apg7l|Atg7l|Gm21553	autophagy related 7	protein-coding
mm_25473.1	chr3	108774922	108774930	+	1	NA	intron (NM_177859, intron 7 of 11)	intron (NM_177859, intron 7 of 11)	35268	NM_177859	329738	Mm.72322	NM_177859	ENSMUSG00000049565	Aknad1	4921525H12Rik	AKNA domain containing 1	protein-coding
mm_21084.1	chr2	152951663	152951675	-	1	NA	promoter-TSS (NM_001159376)	promoter-TSS (NM_001159376)	-87	NM_001159376	252864	Mm.330671	NM_145744	ENSMUSG00000042662	Dusp15	AI851682|LMW-DSP10|T-DSP10	dual specificity phosphatase-like 15	protein-coding
mm_115425.1	chr13	117220738	117220754	+	1	NA	5' UTR (NM_010330, exon 1 of 9)	5' UTR (NM_010330, exon 1 of 9)	173	NM_010330	13723	Mm.274926	NM_010330	ENSMUSG00000021728	Emb	AL022799|Gp70	embigin	protein-coding
mm_19727.1	chr2	104493572	104493591	-	1	NA	intron (NM_010434, intron 1 of 15)	CpG	908	NM_010434	15259	Mm.257925	NM_010434	ENSMUSG00000027177	Hipk3	DYRK6|FIST3|PKY|mir-1902	homeodomain interacting protein kinase 3	protein-coding
mm_69424.1	chr7	132776856	132776911	-	1	NA	promoter-TSS (NM_001347630)	promoter-TSS (NM_001347630)	33	NM_001347630	77938	Mm.225649	NM_175268	ENSMUSG00000030956	Fam53b	A930008G19Rik|mKIAA0140	family with sequence similarity 53, member B	protein-coding
mm_172644.1	chr8	26054209	26054209	+	1	NA	intron (NM_207659, intron 15 of 21)	LTRIS2|LTR|ERV1	-28400	NR_110583	76604	Mm.437190	NR_110583	ENSMUSG00000085437	1700047A11Rik	4930554C15Rik	RIKEN cDNA 1700047A11 gene	ncRNA
mm_170647.1	chr19	9861327	9861329	+	1	NA	Intergenic	L1Md_T|LINE|L1	38205	NM_016692	16319	Mm.29755	NM_016692	ENSMUSG00000024660	Incenp	2700067E22Rik|AU019509|C130081E20|C77457	inner centromere protein	protein-coding
mm_166319.1	chr5	110808575	110808585	+	1	NA	intron (NM_001347394, intron 3 of 27)	intron (NM_001347394, intron 3 of 27)	1501	NM_009469	22241	Mm.271898	NM_009469	ENSMUSG00000029512	Ulk1	AU041434|Unc51.1|mKIAA0722	unc-51 like kinase 1	protein-coding
mm_152320.1	chr19	9931174	9931189	-	1	NA	Intergenic	Intergenic	-31648	NM_016692	16319	Mm.29755	NM_016692	ENSMUSG00000024660	Incenp	2700067E22Rik|AU019509|C130081E20|C77457	inner centromere protein	protein-coding
mm_28971.1	chr3	101012149	101012162	-	1	NA	exon (NM_001167906, exon 6 of 9)	exon (NM_001167906, exon 6 of 9)	17340	NM_001167906	630146	Mm.190915	NM_001099332	ENSMUSG00000086564	Cd101	EWI-101|Gm1016|Gm734|Igsf2	CD101 antigen	protein-coding
mm_88308.1	chr10	75406968	75406974	+	1	NA	promoter-TSS (NM_133995)	promoter-TSS (NM_133995)	60	NM_133995	103149	Mm.441195	NM_133995	ENSMUSG00000033427	Upb1	AI195023	ureidopropionase, beta	protein-coding
mm_18534.1	chr2	64097887	64097912	-	1	NA	5' UTR (NM_021716, exon 1 of 3)	5' UTR (NM_021716, exon 1 of 3)	139	NM_001267846	60344	Mm.130769	NM_021716	ENSMUSG00000075324	Fign	fi|fidget	fidgetin	protein-coding
mm_168595.1	chr1	173942278	173942279	-	1	NA	5' UTR (NM_001302650, exon 2 of 9)	5' UTR (NM_001302650, exon 2 of 9)	214	NM_001302649	15950	Mm.463437	NM_008328	ENSMUSG00000039997	Ifi203	Mndal	interferon activated gene 203	protein-coding
mm_15547.1	chr2	158409868	158409906	+	1	NA	promoter-TSS (NM_001291138)	promoter-TSS (NM_001291138)	34	NM_001291138	228850	Mm.398185	NM_177227	ENSMUSG00000027652	Ralgapb	AI507211|B230339M05Rik|p170	Ral GTPase activating protein, beta subunit (non-catalytic)	protein-coding
mm_116153.1	chr13	29986049	29986059	-	1	NA	promoter-TSS (NM_010093)	promoter-TSS (NM_010093)	9	NM_010093	13557	Mm.268356	NM_010093	ENSMUSG00000016477	E2f3	E2F3b|E2f3a	E2F transcription factor 3	protein-coding
mm_50542.1	chr6	49046208	49046218	+	1	NA	intron (NM_053110, intron 4 of 10)	intron (NM_053110, intron 4 of 10)	9695	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_80329.1	chr9	75037745	75037755	+	1	NA	promoter-TSS (NM_021548)	promoter-TSS (NM_021548)	18	NM_021548	59046	Mm.247837	NM_021548	ENSMUSG00000007656	Arpp19	19kDa|2700024H10Rik|ARPP-19|AW559096|Arpp12	cAMP-regulated phosphoprotein 19	protein-coding
mm_157397.1	chrX	38420390	38420403	-	1	NA	3' UTR (NM_010685, exon 9 of 9)	3' UTR (NM_010685, exon 9 of 9)	36064	NM_010685	16784	Mm.486	NM_010685	ENSMUSG00000016534	Lamp2	CD107b|LGP-B|Lamp II|Lamp-2|Lamp-2a|Lamp-2b|Lamp-2c|Mac3	lysosomal-associated membrane protein 2	protein-coding
mm_153376.1	chr19	40365044	40365060	-	1	NA	exon (NM_001034964, exon 7 of 22)	exon (NM_001034964, exon 7 of 22)	37258	NM_001034964	20411	Mm.210815	NM_009166	ENSMUSG00000025006	Sorbs1	2310065E01Rik|9530001P15Rik|CAP|SH3P12|Sh3d5|mKIAA1296	sorbin and SH3 domain containing 1	protein-coding
mm_96435.1	chr11	67301717	67301728	+	1	NA	exon (NM_177369, exon 32 of 40)	exon (NM_177369, exon 32 of 40)	24598	NM_177369	17885	Mm.340163	NM_177369	ENSMUSG00000055775	Myh8	4832426G23Rik|AI327267|MHCp|MyHC-pn|Myhs-p|Myhsp	myosin, heavy polypeptide 8, skeletal muscle, perinatal	protein-coding
mm_83631.1	chr9	49148128	49148141	-	1	NA	Intergenic	Intergenic	45355	NM_030709	80893	Mm.72799	NM_030709	ENSMUSG00000032268	Tmprss5	spinesin	transmembrane protease, serine 5 (spinesin)	protein-coding
mm_13631.1	chr2	113685084	113685096	+	1	NA	promoter-TSS (NM_001287818)	promoter-TSS (NM_001287818)	0	NM_001287818	14260	Mm.4938	NM_010230	ENSMUSG00000044042	Fmn1	Fmn|formin-1|ld	formin 1	protein-coding
mm_109073.1	chr12	104345532	104345540	+	1	NA	3' UTR (NM_011458, exon 5 of 5)	3' UTR (NM_011458, exon 5 of 5)	7050	NM_011458	20714	Mm.291569	NM_011458	ENSMUSG00000058207	Serpina3k	1300001I07Rik|D12Rp54|MMCM2|MMSpi2|RP54|Spi-2|Spi2|contrapsin	serine (or cysteine) peptidase inhibitor, clade A, member 3K	protein-coding
mm_122764.1	chr14	54253760	54253770	-	1	NA	promoter-TSS (NM_001205181)	promoter-TSS (NM_001205181)	164	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_150324.1	chr19	34574195	34574205	+	1	NA	exon (NM_008332, exon 3 of 3)	exon (NM_008332, exon 3 of 3)	-9329	NM_010501	15959	Mm.426079	NM_010501	ENSMUSG00000074896	Ifit3	Ifi49|P49	interferon-induced protein with tetratricopeptide repeats 3	protein-coding
mm_44146.1	chr5	150259899	150259911	+	1	NA	promoter-TSS (NM_172887)	promoter-TSS (NM_172887)	-25	NM_172887	320365	Mm.216590	NM_172887	ENSMUSG00000056602	Fry	13CDNA73|9330186A19Rik|AF346502|AI462658|C87180|D930046M03|cg003|mKIAA4143	FRY microtubule binding protein	protein-coding
mm_130865.1	chr15	102203854	102203909	-	1	NA	promoter-TSS (NM_001289690)	promoter-TSS (NM_001289690)	236	NM_001289691	68744	Mm.352945	NM_153194	ENSMUSG00000046897	Zfp740	1110034O07Rik|AW548228|Znf740	zinc finger protein 740	protein-coding
mm_137394.1	chr17	25820654	25820675	+	1	NA	3' UTR (NM_001164225, exon 6 of 6)	3' UTR (NM_001164225, exon 6 of 6)	-2963	NM_173741	268933	Mm.95512	NM_173741	ENSMUSG00000025737	Wdr24	BC037651	WD repeat domain 24	protein-coding
mm_7742.1	chr1	131021650	131021652	-	1	NA	intron (NM_010548, intron 3 of 4)	intron (NM_010548, intron 3 of 4)	1806	NM_010548	16153	Mm.874	NM_010548	ENSMUSG00000016529	Il10	CSIF|Il-10	interleukin 10	protein-coding
mm_65162.1	chr7	19673589	19673600	-	1	NA	exon (NM_001309795, exon 2 of 4)	exon (NM_001309795, exon 2 of 4)	326	NM_001309795	11813	Mm.28394	NM_001277944	ENSMUSG00000002992	Apoc2	apo-CII|apoC-II	apolipoprotein C-II	protein-coding
mm_172612.1	chr8	19180014	19180014	-	1	NA	Intergenic	L1Md_T|LINE|L1	-14314	NM_183026	244332	Mm.358923	NM_183026	ENSMUSG00000046354	Defb14	BD-14	defensin beta 14	protein-coding
mm_40144.1	chr5	35200329	35200331	+	1	NA	Intergenic	Intergenic	-78236	NM_007418	11553	Mm.57205	NM_007418	ENSMUSG00000045318	Adra2c	Adra-2c|[a]2C|alpha2-C4|alpha2C	adrenergic receptor, alpha 2c	protein-coding
mm_164201.1	chr15	79935621	79935623	+	1	NA	Intergenic	Intergenic	-2976	NM_144811	52609	Mm.323442	NM_144811	ENSMUSG00000053411	Cbx7	1600014J01Rik|AI851678|D15Ertd417e	chromobox 7	protein-coding
mm_28471.1	chr3	92080302	92080347	-	1	NA	TTS (NM_008508)	TTS (NM_008508)	2818	NM_008508	16939	Mm.1121	NM_008508	ENSMUSG00000043165	Lor	AI036317|S77319	loricrin	protein-coding
mm_90849.1	chr10	8762350	8762370	-	1	NA	intron (NM_175155, intron 8 of 19)	intron (NM_175155, intron 8 of 19)	123710	NM_175155	70097	Mm.338275	NM_175155	ENSMUSG00000015305	Sash1	1100001C18Rik|2500002E12Rik|A330076K04Rik|mKIAA0790	SAM and SH3 domain containing 1	protein-coding
mm_113853.1	chr13	47211351	47211353	+	1	NA	intron (NM_001170643, intron 2 of 7)	intron (NM_001170643, intron 2 of 7)	17349	NM_001170643	218215	Mm.287609	NM_146042	ENSMUSG00000038068	Rnf144b	BC025007|E130105P19Rik|Ibrdc2|Pir2	ring finger protein 144B	protein-coding
mm_42016.1	chr5	108161101	108161126	+	1	NA	intron (NM_028481, intron 8 of 28)	B1F|SINE|Alu	28199	NM_028481	73254	Mm.441231	NM_028481	ENSMUSG00000056531	Ccdc18	1700021E15Rik|4932411G06Rik|NY-SAR-41	coiled-coil domain containing 18	protein-coding
mm_161828.1	chr17	80206716	80206716	-	1	NA	intron (NR_036615, intron 1 of 8)	CpG	589	NM_001195486	225027	Mm.292016	NM_146083	ENSMUSG00000024097	Srsf7	35kDa|9430065L19Rik|9G8|NX-96|Sfrs7	serine/arginine-rich splicing factor 7	protein-coding
mm_112158.1	chr12	113329296	113329296	-	1	NA	Intergenic	Intergenic	143393	NM_153776	69195	Mm.313244	NM_153776	ENSMUSG00000049036	Tmem121	2410008J05Rik|Hole	transmembrane protein 121	protein-coding
mm_118158.1	chr13	105291915	105291938	-	1	NA	intron (NM_027934, intron 1 of 7)	MMVL30-int|LTR|ERV1	1088	NM_027934	71816	Mm.317015	NM_027934	ENSMUSG00000021720	Rnf180	3110001E11Rik|Rines	ring finger protein 180	protein-coding
mm_124616.1	chr15	3279591	3279610	+	1	NA	exon (NM_009155, exon 5 of 5)	exon (NM_009155, exon 5 of 5)	8623	NM_009155	20363	Mm.392203	NM_009155	ENSMUSG00000064373	Selenop	AU018766|D15Ucla1|Se-P|Sepp1|selp	selenoprotein P	protein-coding
mm_49513.1	chr6	29870264	29870270	+	1	NA	intron (NM_001347084, intron 3 of 17)	intron (NM_001347084, intron 3 of 17)	10671	NM_001171001	74340	Mm.210899	NM_021414	ENSMUSG00000029772	Ahcyl2	4631427C17Rik|AI227036|Adohcyase3|mKIAA0828	S-adenosylhomocysteine hydrolase-like 2	protein-coding
mm_78482.1	chr9	32696866	32696876	+	1	NA	intron (NM_011808, intron 1 of 7)	intron (NM_011808, intron 1 of 7)	829	NM_001038642	23871	Mm.292415	NM_011808	ENSMUSG00000032035	Ets1	AI196000|AI448617|D230050P06|Ets-1|Tpl1|vs	E26 avian leukemia oncogene 1, 5' domain	protein-coding
mm_23284.1	chr3	51765550	51765560	+	1	NA	intron (NM_001004176, intron 2 of 4)	intron (NM_001004176, intron 2 of 4)	104376	NM_001310482	211666	Mm.24679	NM_174995	ENSMUSG00000074604	Mgst2	GST2|MGST-II	microsomal glutathione S-transferase 2	protein-coding
mm_18214.1	chr2	49452862	49452874	-	1	NA	intron (NM_172663, intron 1 of 13)	intron (NM_172663, intron 1 of 13)	1382	NM_172663	227867	Mm.29167	NM_172663	ENSMUSG00000069495	Epc2	5830499L14|D2Ertd694e	enhancer of polycomb homolog 2 (Drosophila)	protein-coding
mm_170071.1	chr17	33255127	33255145	-	1	NA	promoter-TSS (NM_029952)	promoter-TSS (NM_029952)	9	NM_029952	77652	Mm.460572	NM_029952	ENSMUSG00000094441	Zfp955a	AI842447|Zfp883a	zinc finger protein 955A	protein-coding
mm_126883.1	chr15	89454020	89454095	+	1	NA	5' UTR (NM_021921, exon 1 of 12)	5' UTR (NM_021921, exon 1 of 12)	146	NM_021921	60597	Mm.173337	NM_021921	ENSMUSG00000022619	Mapk8ip2	3230402N03Rik|AI847694|AW049958|IB2|Jip2|R75148	mitogen-activated protein kinase 8 interacting protein 2	protein-coding
mm_115334.1	chr13	112480072	112480097	+	1	NA	exon (NM_010560, exon 4 of 17)	exon (NM_010560, exon 4 of 17)	16014	NM_010560	16195	Mm.4364	NM_010560	ENSMUSG00000021756	Il6st	5133400A03Rik|AA389424|BB405851|CD130|D13Ertd699e|gp130	interleukin 6 signal transducer	protein-coding
mm_101499.1	chr11	31871613	31871640	-	1	NA	5' UTR (NM_026252, exon 1 of 10)	5' UTR (NM_026252, exon 1 of 10)	686	NM_026252	67579	Mm.339792	NM_026252	ENSMUSG00000020300	Cpeb4	Cpe-bp4|Cpeb-4|mCPEB-4	cytoplasmic polyadenylation element binding protein 4	protein-coding
mm_71037.1	chr8	33654130	33654160	+	1	NA	intron (NM_010344, intron 1 of 12)	intron (NM_010344, intron 1 of 12)	907	NM_010344	14782	Mm.283573	NM_010344	ENSMUSG00000031584	Gsr	AI325518|D8Ertd238e|Gr-1|Gr1	glutathione reductase	protein-coding
mm_167473.1	chr8	127379107	127379114	+	1	NA	intron (NM_001309391, intron 11 of 24)	intron (NM_001309391, intron 11 of 24)	79458	NM_001013580	93742	Mm.299254	NM_033620	ENSMUSG00000025812	Pard3	AA960621|AI256638|Asip|D8Ertd580e|Par-3|Par3|Pard-3|Pard3a|Phip	par-3 family cell polarity regulator	protein-coding
mm_120874.1	chr14	75260695	75260735	+	1	NA	exon (NM_019775, exon 4 of 11)	exon (NM_019775, exon 4 of 11)	18428	NM_019775	56373	Mm.24242	NM_019775	ENSMUSG00000021999	Cpb2	1110032P04Rik|4930405E17Rik|AI255929|CPR|Cpu|TAFI	carboxypeptidase B2 (plasma)	protein-coding
mm_67334.1	chr7	79743035	79743088	-	1	NA	promoter-TSS (NM_001037927)	promoter-TSS (NM_001037927)	-36	NM_011068	18631	Mm.20615	NM_011068	ENSMUSG00000030545	Pex11a	PEX11alpha	peroxisomal biogenesis factor 11 alpha	protein-coding
mm_166706.1	chr6	115935512	115935516	+	1	NA	exon (NM_145383, exon 4 of 5)	exon (NM_145383, exon 4 of 5)	3587	NM_145383	212541	Mm.2965	NM_145383	ENSMUSG00000030324	Rho	Noerg1|Opn2|Ops|RP4	rhodopsin	protein-coding
mm_21704.1	chr2	164573331	164573332	-	1	NA	5' UTR (NM_001177401, exon 1 of 2)	5' UTR (NM_001177401, exon 1 of 2)	125	NM_001177401	629747	Mm.234248	NM_001177401	ENSMUSG00000074596	Spint3	Gm14315|OTTMUSG00000016288	serine peptidase inhibitor, Kunitz type, 3	protein-coding
mm_7857.1	chr1	132465911	132465914	-	1	NA	3' UTR (NM_172516, exon 13 of 13)	3' UTR (NM_172516, exon 13 of 13)	-11455	NM_172517	213464	Mm.132868	NM_172517	ENSMUSG00000026439	Rbbp5	4933411J24Rik|C330016J05	retinoblastoma binding protein 5	protein-coding
mm_46205.1	chr5	98031411	98031421	-	1	NA	promoter-TSS (NM_133738)	promoter-TSS (NM_133738)	-454	NM_133738	71914	Mm.24842	NM_133738	ENSMUSG00000029338	Antxr2	2310046B19Rik|AW561899|CMG-2|CMG2|cI-35	anthrax toxin receptor 2	protein-coding
mm_16338.1	chr2	174330187	174330197	+	1	NA	5' UTR (NM_001077510, exon 1 of 11)	5' UTR (NM_001077510, exon 1 of 11)	103	NM_001077510	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_23637.1	chr3	66985701	66985740	+	1	NA	promoter-TSS (NM_025822)	promoter-TSS (NM_025822)	48	NM_025822	66880	Mm.316418	NM_025822	ENSMUSG00000034544	Rsrc1	1200013F24Rik|SRrp53	arginine/serine-rich coiled-coil 1	protein-coding
mm_147113.1	chr18	35722312	35722327	-	1	NA	promoter-TSS (NM_001033141)	promoter-TSS (NM_001033141)	-828	NM_001033141	68545	Mm.329362	NM_001033141	ENSMUSG00000073599	Ecscr	1110006O17Rik|ARIA	endothelial cell surface expressed chemotaxis and apoptosis regulator	protein-coding
mm_105477.1	chr11	105936916	105936933	-	1	NA	intron (NM_007805, intron 2 of 5)	intron (NM_007805, intron 2 of 5)	7223	NM_007805	13056	Mm.149403	NM_007805	ENSMUSG00000019590	Cyb561	-	cytochrome b-561	protein-coding
mm_125697.1	chr15	66891478	66891495	+	1	NA	promoter-TSS (NM_018865)	promoter-TSS (NM_018865)	93	NM_018865	22402	Mm.10222	NM_018865	ENSMUSG00000005124	Wisp1	AW146261|CCN4|Elm1	WNT1 inducible signaling pathway protein 1	protein-coding
mm_101335.1	chr11	23498026	23498044	-	1	NA	promoter-TSS (NM_172391)	promoter-TSS (NM_172391)	4	NM_001290655	268390	Mm.13148	NM_172391	ENSMUSG00000020288	Ahsa2	-	AHA1, activator of heat shock protein ATPase 2	protein-coding
mm_84885.1	chr9	79759678	79759745	-	1	NA	5' UTR (NM_009945, exon 1 of 4)	5' UTR (NM_009945, exon 1 of 4)	142	NM_009945	12866	Mm.152627	NM_009945	ENSMUSG00000032330	Cox7a2	COX7AL|Cox7a3|CoxVIIa-L	cytochrome c oxidase subunit VIIa 2	protein-coding
mm_47911.1	chr5	134946918	134946945	-	1	NA	promoter-TSS (NM_009903)	promoter-TSS (NM_009903)	3	NM_009903	12740	Mm.7339	NM_009903	ENSMUSG00000047501	Cldn4	Cep-r|Cpetr|Cpetr1	claudin 4	protein-coding
mm_120181.1	chr14	61309807	61309813	+	1	NA	promoter-TSS (NM_177337)	promoter-TSS (NM_177337)	57	NM_177337	219144	Mm.206566	NM_177337	ENSMUSG00000043157	Arl11	ARLTS1|C730007L20Rik	ADP-ribosylation factor-like 11	protein-coding
mm_59282.1	chr7	24907670	24907732	+	1	NA	intron (NM_001130152, intron 1 of 28)	intron (NM_001130152, intron 1 of 28)	3355	NM_001130152	16801	Mm.3181	NM_008488	ENSMUSG00000040940	Arhgef1	Lbcl2|Lsc	Rho guanine nucleotide exchange factor (GEF) 1	protein-coding
mm_55430.1	chr6	65779698	65779706	-	1	NA	intron (NM_029549, intron 1 of 10)	intron (NM_029549, intron 1 of 10)	740	NM_029549	70779	Mm.263355	NM_027547	ENSMUSG00000029913	Prdm5	4432417F03Rik|6530401I24Rik|AI197291|E130112L17Rik|PFM2	PR domain containing 5	protein-coding
mm_82999.1	chr9	36693159	36693164	-	1	NA	promoter-TSS (NM_007391)	promoter-TSS (NM_007391)	28	NR_040741	75567	Mm.426883	NR_040741	ENSMUSG00000098304	1700027I24Rik	-	RIKEN cDNA 1700027I24 gene	ncRNA
mm_166566.1	chr6	48988073	48988084	+	1	NA	exon (NM_172888, exon 1 of 5)	exon (NM_172888, exon 1 of 5)	1217	NM_172888	243377	Mm.446302	NM_172888	ENSMUSG00000039215	Svs1	9530003A11	seminal vesicle secretory protein 1	protein-coding
mm_86237.1	chr9	120789806	120789810	-	1	NA	Intergenic	MTB_Mm|LTR|ERVL-MaLR	125442	NR_040742	76402	Mm.436588	NR_040742	ENSMUSG00000100146	1700020M21Rik	-	RIKEN cDNA 1700020M21 gene	ncRNA
mm_85672.1	chr9	107679625	107679640	-	1	NA	promoter-TSS (NM_008140)	promoter-TSS (NM_008140)	-40	NM_008140	14685	Mm.284853	NM_008140	ENSMUSG00000034837	Gnat1	Gnat-1|Ird1|Ird2|Tralpha|irdc|irdr|transducin	guanine nucleotide binding protein, alpha transducing 1	protein-coding
mm_35836.1	chr4	48043190	48043240	-	1	NA	Intergenic	CpG	-2090	NM_015743	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_29220.1	chr3	107211344	107211384	-	1	NA	TTS (NM_001111143)	TTS (NM_001111143)	10368	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_23029.1	chr3	34650025	34650050	+	1	NA	promoter-TSS (NM_011443)	promoter-TSS (NM_011443)	42	NM_011443	20674	Mm.65396	NM_011443	ENSMUSG00000074637	Sox2	Sox-2|lcc|ysb	SRY (sex determining region Y)-box 2	protein-coding
mm_117575.1	chr13	86046773	86046800	-	1	NA	promoter-TSS (NM_007749)	promoter-TSS (NM_007749)	9	NM_007749	12867	Mm.378898	NM_007749	ENSMUSG00000017778	Cox7c	COXVIIc|Cox7c1	cytochrome c oxidase subunit VIIc	protein-coding
mm_103237.1	chr11	70686136	70686153	-	1	NA	exon (NM_001190378, exon 3 of 22)	exon (NM_001190378, exon 3 of 22)	1961	NM_001190376	216874	Mm.473726	NM_178116	ENSMUSG00000040712	Camta2	Kiaa0909-hp|mKIAA0909	calmodulin binding transcription activator 2	protein-coding
mm_27409.1	chr3	51340629	51340681	-	1	NA	promoter-TSS (NM_001291059)	promoter-TSS (NM_001291059)	-11	NM_023502	69257	Mm.131038	NM_023502	ENSMUSG00000037174	Elf2	2610036A20Rik|A230104O07Rik|AW111824|BB183398|EU32|NERF|NERF-1A|NERF-1B|NERF-2	E74-like factor 2	protein-coding
mm_133542.1	chr16	91221079	91221080	+	1	NA	Intergenic	Intergenic	-4471	NM_016967	50913	Mm.37289	NM_016967	ENSMUSG00000039830	Olig2	AI604895|Bhlhb1|Olg-2|Oligo2|RK17|bHLHe19	oligodendrocyte transcription factor 2	protein-coding
mm_103607.1	chr11	78497694	78497730	-	1	NA	promoter-TSS (NM_001168521)	promoter-TSS (NM_001168521)	42	NM_001168521	237868	Mm.210332	NM_172795	ENSMUSG00000050132	Sarm1	A830091I15Rik|C78606|MyD885|Sarm	sterile alpha and HEAT/Armadillo motif containing 1	protein-coding
mm_94738.1	chr11	21091372	21091401	+	1	NA	promoter-TSS (NM_023324)	promoter-TSS (NM_023324)	62	NM_023324	67245	Mm.28957	NM_023324	ENSMUSG00000020134	Peli1	2810468L03Rik|A930031K15Rik|AA409794|AI586297|D11Ertd676e	pellino 1	protein-coding
mm_44340.1	chr5	17571665	17571685	-	1	NA	Intergenic	Intergenic	-3141	NM_013657	20348	Mm.5071	NM_013657	ENSMUSG00000028780	Sema3c	1110036B02Rik|SemE|Semae	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	protein-coding
mm_164065.1	chr14	118253964	118253969	+	1	NA	intron (NR_131969, intron 1 of 2)	L1MB8|LINE|L1	-4668	NR_105749	102465149		NR_105749	ENSMUSG00000098612	Mir6241	Gm27302|mmu-mir-6241	microRNA 6241	ncRNA
mm_135997.1	chr16	75304389	75304391	-	1	NA	Intergenic	MLTR18A_MM|LTR|ERVK	281671	NM_001252513	320355	Mm.99517	NM_177142	ENSMUSG00000032948	Lipi	D930038D03Rik|lpd1	lipase, member I	protein-coding
mm_128577.1	chr15	57892337	57892347	-	1	NA	promoter-TSS (NM_024207)	promoter-TSS (NM_024207)	76	NM_024207	67819	Mm.289387	NM_024207	ENSMUSG00000022365	Derl1	1110021N07Rik|AI195141|AW551338|Derlin-1	Der1-like domain family, member 1	protein-coding
mm_43399.1	chr5	135783366	135783409	+	1	NA	exon (NM_008617, exon 2 of 9)	exon (NM_008617, exon 2 of 9)	4738	NM_008617	17448	Mm.297096	NM_008617	ENSMUSG00000019179	Mdh2	MDH|Mdh-2|Mor-1|Mor1	malate dehydrogenase 2, NAD (mitochondrial)	protein-coding
mm_27269.1	chr3	39533911	39533921	-	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	646976	NM_183221	329628	Mm.316210	NM_183221	ENSMUSG00000046743	Fat4	6030410K14Rik|9430004M15	FAT atypical cadherin 4	protein-coding
mm_79507.1	chr9	57428180	57428190	+	1	NA	intron (NM_176831, intron 3 of 6)	intron (NM_176831, intron 3 of 6)	11929	NM_176831	66812	Mm.250508	NM_176831	ENSMUSG00000063849	Ppcdc	1810057I13Rik|8430432M10Rik	phosphopantothenoylcysteine decarboxylase	protein-coding
mm_39733.1	chr5	29196034	29196063	+	1	NA	promoter-TSS (NM_021470)	promoter-TSS (NM_021470)	55	NR_110371	56874	Mm.87352	NM_021470	ENSMUSG00000029130	Rnf32	1700009J01Rik|2700025B22Rik|4930542N22Rik|Lmbr2	ring finger protein 32	protein-coding
mm_109680.1	chr12	113133470	113133480	+	1	NA	intron (NM_001346696, intron 17 of 19)	intron (NM_001346696, intron 17 of 19)	-6761	NM_024223	68337	Mm.133825	NM_024223	ENSMUSG00000006356	Crip2	0610010I23Rik|AW743261|C77570|CRP2|CRP4|Crp|ESP1|Hlp	cysteine rich protein 2	protein-coding
mm_6826.1	chr1	84200478	84200487	-	1	NA	intron (NM_001003948, intron 1 of 2)	intron (NM_001003948, intron 1 of 2)	18479	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_50728.1	chr6	52313631	52313641	+	1	NA	5' UTR (NM_007966, exon 1 of 3)	5' UTR (NM_007966, exon 1 of 3)	138	NM_007966	14028	Mm.389754	NM_007966	ENSMUSG00000005503	Evx1	Evx-1	even-skipped homeobox 1	protein-coding
mm_49371.1	chr6	24125668	24125669	+	1	NA	intron (NM_019481, intron 6 of 14)	L1MEd|LINE|L1	42424	NM_019481	55961	Mm.19299	NM_019481	ENSMUSG00000029700	Slc13a1	AI314066|AI987826|NaSi-1|Nas1	solute carrier family 13 (sodium/sulfate symporters), member 1	protein-coding
mm_89607.1	chr10	96012121	96012129	+	1	NA	exon (NM_001001932, exon 12 of 29)	exon (NM_001001932, exon 12 of 29)	71462	NM_001001932	216238	Mm.210035	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding
mm_127671.1	chr15	102671926	102671948	+	1	NA	promoter-TSS (NR_030460)	promoter-TSS (NR_030460)	-71	NR_030460	751542		NR_030460	ENSMUSG00000076009	Mir688	Mirn688|mmu-mir-688	microRNA 688	ncRNA
mm_28144.1	chr3	87263704	87263714	-	1	NA	promoter-TSS (NM_030707)	promoter-TSS (NM_030707)	-185	NM_030707	80891	Mm.45173	NM_030707	ENSMUSG00000015852	Fcrls	2810439C17Rik|9330158F12|FcRH2sc|Fcrh2|IFGP2|IgSR|MMAN-g|Msr2|moFcRH2sc	Fc receptor-like S, scavenger receptor	protein-coding
mm_48615.1	chr5	144736543	144736553	-	1	NA	3' UTR (NM_177735, exon 8 of 8)	3' UTR (NM_177735, exon 8 of 8)	25030	NM_177735	243339	Mm.126793	NM_177735	ENSMUSG00000043388	Tmem130	BC067004|C130036G08	transmembrane protein 130	protein-coding
mm_105919.1	chr11	115004093	115004105	-	1	NA	Intergenic	Intergenic	-2219	NM_134158	140497	Mm.2699	NM_134158	ENSMUSG00000044811	Cd300c2	CLM4|Cd300c|Cd300d|DIgR1|Igsf7|Lmir2|MAIR-II	CD300C molecule 2	protein-coding
mm_10454.1	chr2	14282143	14282190	+	1	NA	intron (NM_008625, intron 11 of 29)	intron (NM_008625, intron 11 of 29)	21163	NR_030609	100124488		NR_030609	ENSMUSG00000077897	Mir511	Mirn511|mir-511|mmu-mir-511	microRNA 511	ncRNA
mm_169260.1	chr13	81699833	81699845	-	1	NA	exon (NM_001081176, exon 2 of 8)	exon (NM_001081176, exon 2 of 8)	11174	NM_001081176	67486	Mm.279781	NM_001081176	ENSMUSG00000035834	Polr3g	2310047G20Rik|AV275904|RPC32|RPC7	polymerase (RNA) III (DNA directed) polypeptide G	protein-coding
mm_7092.1	chr1	88698686	88698715	-	1	NA	3' UTR (NM_177305, exon 1 of 1)	3' UTR (NM_177305, exon 1 of 1)	3491	NM_177305	320982	Mm.27968	NM_177305	ENSMUSG00000049866	Arl4c	A630084M22Rik|Arl7|LAK	ADP-ribosylation factor-like 4C	protein-coding
mm_160918.1	chr11	83489006	83489006	+	1	NA	exon (NM_027427, exon 7 of 16)	exon (NM_027427, exon 7 of 16)	15898	NM_027427	70439	Mm.181050	NM_027427	ENSMUSG00000020680	Taf15	2610111C21Rik|68kDa|TAFII68|Taf2n	TATA-box binding protein associated factor 15	protein-coding
mm_41058.1	chr5	86804383	86804393	+	1	NA	promoter-TSS (NM_177680)	promoter-TSS (NM_177680)	-102	NM_177680	231386	Mm.196325	NM_177680	ENSMUSG00000035851	Ythdc1	A730098D12Rik|C80342|mKIAA1966	YTH domain containing 1	protein-coding
mm_117974.1	chr13	100066011	100066033	-	1	NA	exon (NM_001081061, exon 15 of 39)	exon (NM_001081061, exon 15 of 39)	38048	NM_001081061	544971	Mm.288546	NM_001081061	ENSMUSG00000049658	Bdp1	AI662220|AW049390|AW456745|B130055N23Rik|G630013P12Rik|TAF3B1|TFC5|TFIIIB150|TFIIIB90|Tfnr|mKIAA1241	B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB	protein-coding
mm_123953.1	chr14	74689681	74689700	-	1	NA	intron (NM_172812, intron 2 of 2)	intron (NM_172812, intron 2 of 2)	-42607	NM_001285423	13885	Mm.38055	NM_016903	ENSMUSG00000021996	Esd	Es-10|Es10|FGH|sid478	esterase D/formylglutathione hydrolase	protein-coding
mm_100290.1	chr11	117813702	117813736	+	1	NA	3' UTR (NM_009304, exon 4 of 4)	3' UTR (NM_009304, exon 4 of 4)	4052	NM_009304	20973	Mm.468228	NM_009304	ENSMUSG00000048277	Syngr2	Clast2|cellugyrin	synaptogyrin 2	protein-coding
mm_27085.1	chr3	30013248	30013260	-	1	NA	promoter-TSS (NM_007963)	promoter-TSS (NM_007963)	-50	NM_007963	14013	Mm.56965	NM_007963	ENSMUSG00000027684	Mecom	D630039M04Rik|Evi-1|Evi1|Jbo|Mds|Mds1|Mds1-Evi1|Prdm3|Znfpr1b1	MDS1 and EVI1 complex locus	protein-coding
mm_34091.1	chr4	138833002	138833010	+	1	NA	non-coding (NR_002926, exon 3 of 5)	non-coding (NR_002926, exon 3 of 5)	1130	NM_001082531	18780	Mm.4675	NM_011108	ENSMUSG00000058908	Pla2g2a	EF|Mom1|Pla2|sPLA2|sPla2-IIA	phospholipase A2, group IIA (platelets, synovial fluid)	protein-coding
mm_53108.1	chr6	125083174	125083184	+	1	NA	TTS (NM_001163269)	TTS (NM_001163269)	11902	NM_001163268	381810	Mm.333386	NM_001163268	ENSMUSG00000067714	Lpar5	GPR93|Gm1072|Gpr92|LPA5	lysophosphatidic acid receptor 5	protein-coding
mm_144757.1	chr18	35771358	35771368	+	1	NA	promoter-TSS (NM_019912)	promoter-TSS (NM_019912)	-196	NM_019912	56550	Mm.180052	NM_019912	ENSMUSG00000091896	Ube2d2a	1500034D03Rik|Ubc2e|Ube2d2|ubc4	ubiquitin-conjugating enzyme E2D 2A	protein-coding
mm_139444.1	chr17	55445485	55445499	+	1	NA	promoter-TSS (NM_172829)	promoter-TSS (NM_172829)	110	NM_001347403	240119	Mm.311687	NM_172829	ENSMUSG00000024172	St6gal2	C230064G14Rik|St6galII|mKIAA1877	beta galactoside alpha 2,6 sialyltransferase 2	protein-coding
mm_78464.1	chr9	32508402	32508432	+	1	NA	intron (NM_008026, intron 1 of 8)	intron (NM_008026, intron 1 of 8)	33035	NM_008026	14247	Mm.258908	NM_008026	ENSMUSG00000016087	Fli1	EWSR2|Fli-1|SIC-1|Sic1	Friend leukemia integration 1	protein-coding
mm_50278.1	chr6	47044595	47044619	+	1	NA	intron (NM_001004357, intron 17 of 23)	intron (NM_001004357, intron 17 of 23)	-199789	NM_025771	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding
mm_168375.1	chr11	21370828	21370831	-	1	NA	promoter-TSS (NM_139297)	promoter-TSS (NM_139297)	-200	NM_139297	216558	Mm.28877	NM_139297	ENSMUSG00000001891	Ugp2	UDPGP|UGPase	UDP-glucose pyrophosphorylase 2	protein-coding
mm_23335.1	chr3	54383412	54383426	+	1	NA	exon (NM_015784, exon 17 of 22)	exon (NM_015784, exon 17 of 22)	22312	NM_015784	50706	Mm.236067	NM_015784	ENSMUSG00000027750	Postn	A630052E07Rik|AI747096|OSF-2|Osf2|PLF|PN	periostin, osteoblast specific factor	protein-coding
mm_110778.1	chr12	70968687	70968701	-	1	NA	Intergenic	Intergenic	-5929	NM_001310595	19167	Mm.296338	NM_011184	ENSMUSG00000060073	Psma3	Lmpc8	proteasome (prosome, macropain) subunit, alpha type 3	protein-coding
mm_42313.1	chr5	114865510	114865518	+	1	NA	intron (NM_026263, intron 5 of 11)	intron (NM_026263, intron 5 of 11)	11800	NM_026263	67593	Mm.251409	NM_026263	ENSMUSG00000029564	4930519G04Rik	1700014B12Rik	RIKEN cDNA 4930519G04 gene	protein-coding
mm_14840.1	chr2	147374036	147374048	+	1	NA	3' UTR (NM_008780, exon 5 of 5)	3' UTR (NM_008780, exon 5 of 5)	9048	NM_008780	18503	Mm.315502	NM_008780	ENSMUSG00000037034	Pax1	Pax-1|hbs|hunchback|un|undulated|wt	paired box 1	protein-coding
mm_73261.1	chr8	104340730	104340751	+	1	NA	5' UTR (NM_024217, exon 1 of 5)	5' UTR (NM_024217, exon 1 of 5)	146	NM_024217	68119	Mm.390108	NM_024217	ENSMUSG00000031875	Cmtm3	9430096L06Rik|AI413895|BNAS2|Cklfsf3	CKLF-like MARVEL transmembrane domain containing 3	protein-coding
mm_30929.1	chr4	32964768	32964818	+	1	NA	Intergenic	Intergenic	-13967	NM_001012451	140577	Mm.214766	NM_080471	ENSMUSG00000040183	Ankrd6	-	ankyrin repeat domain 6	protein-coding
mm_156433.1	chrX	141475601	141475612	+	1	NA	5' UTR (NM_001163155, exon 1 of 51)	5' UTR (NM_001163155, exon 1 of 51)	187	NM_001163155	12830	Mm.286892	NM_007736	ENSMUSG00000031274	Col4a5	-	collagen, type IV, alpha 5	protein-coding
mm_88341.1	chr10	75589462	75589483	+	1	NA	promoter-TSS (NM_011820)	promoter-TSS (NM_011820)	91	NM_011820	23887	Mm.257927	NM_011820	ENSMUSG00000006344	Ggt5	AI551243|GGL|GGT-REL|Ggtla1	gamma-glutamyltransferase 5	protein-coding
mm_152279.1	chr19	8839151	8839161	-	1	NA	promoter-TSS (NM_008144)	promoter-TSS (NM_008144)	90	NM_010316	14704	Mm.329700	NM_010316	ENSMUSG00000071658	Gng3	-	guanine nucleotide binding protein (G protein), gamma 3	protein-coding
mm_48246.1	chr5	137786421	137786430	-	1	NA	5' UTR (NM_144913, exon 1 of 4)	5' UTR (NM_144913, exon 1 of 4)	276	NM_144913	231803	Mm.61193	NM_144913	ENSMUSG00000029726	Mepce	Bcdin3|D5Wsu46e	methylphosphate capping enzyme	protein-coding
mm_144231.1	chr18	10326125	10326130	+	1	NA	intron (NM_001083628, intron 1 of 32)	intron (NM_001083628, intron 1 of 32)	948	NM_001083628	381157	Mm.261535	NM_001083628	ENSMUSG00000042942	Greb1l	mKIAA4095	growth regulation by estrogen in breast cancer-like	protein-coding
mm_67151.1	chr7	73519515	73519568	-	1	NA	exon (NM_001081345, exon 3 of 39)	exon (NM_001081345, exon 3 of 39)	22205	NM_001081345	244059	Mm.34539	NM_001081345	ENSMUSG00000078671	Chd2	2810013C04Rik|2810040A01Rik|5630401D06Rik|AI851092|BC029703|CHD-2	chromodomain helicase DNA binding protein 2	protein-coding
mm_20511.1	chr2	130638328	130638339	-	1	NA	intron (NM_197945, intron 1 of 4)	intron (NM_197945, intron 1 of 4)	4511	NM_197945	241638	Mm.440130	NM_197945	ENSMUSG00000037703	Lzts3	Prosapip1	leucine zipper, putative tumor suppressor family member 3	protein-coding
mm_126151.1	chr15	78406778	78406796	+	1	NA	promoter-TSS (NM_138670)	promoter-TSS (NM_138670)	-14	NM_001162492	246221	Mm.294215	NM_138670	ENSMUSG00000071711	Mpst	Mst	mercaptopyruvate sulfurtransferase	protein-coding
mm_156402.1	chrX	139953853	139953853	+	1	NA	intron (NM_153586, intron 6 of 6)	B4A|SINE|B4	44742	NM_153586	237073	Mm.256670	NM_153586	ENSMUSG00000031433	Rbm41	BB131279|D330023I21Rik	RNA binding motif protein 41	protein-coding
mm_82636.1	chr9	21963596	21963604	-	1	NA	promoter-TSS (NM_010149)	promoter-TSS (NM_010149)	-24	NM_010149	13857	Mm.2653	NM_010149	ENSMUSG00000006235	Epor	-	erythropoietin receptor	protein-coding
mm_30957.1	chr4	33350714	33350718	+	1	NA	intron (NM_011884, intron 8 of 15)	intron (NM_011884, intron 8 of 15)	40405	NM_001305273	24018	Mm.240024	NM_011884	ENSMUSG00000028274	Rngtt	AU020997|HCE|MCE1	RNA guanylyltransferase and 5'-phosphatase	protein-coding
mm_123369.1	chr14	63177805	63177889	-	1	NA	5' UTR (NM_010191, exon 3 of 10)	5' UTR (NM_010191, exon 3 of 10)	1731	NM_010191	14137	Mm.474432	NM_010191	ENSMUSG00000021273	Fdft1	SQS|SS	farnesyl diphosphate farnesyl transferase 1	protein-coding
mm_122225.1	chr14	32685456	32685470	-	1	NA	promoter-TSS (NM_001195097)	promoter-TSS (NM_001195097)	-191	NM_001195097	100504518	Mm.318319	NM_001195097	ENSMUSG00000071540	3425401B19Rik	-	RIKEN cDNA 3425401B19 gene	protein-coding
mm_94597.1	chr11	11809806	11809808	+	1	NA	promoter-TSS (NM_021891)	promoter-TSS (NM_021891)	-845	NM_001163360	60530	Mm.236114	NM_021891	ENSMUSG00000035455	Fignl1	-	fidgetin-like 1	protein-coding
mm_6700.1	chr1	80758663	80758680	-	1	NA	promoter-TSS (NM_175291)	promoter-TSS (NM_175291)	-118	NM_175291	210293	Mm.133473	NM_175291	ENSMUSG00000038608	Dock10	9330153B10Rik|A630054M16Rik|Jr4|Jr5|R75174|ZIZ3|Zizimin3|mKIAA0694	dedicator of cytokinesis 10	protein-coding
mm_47405.1	chr5	123132303	123132317	-	1	NA	exon (NM_175092, exon 1 of 5)	exon (NM_175092, exon 1 of 5)	319	NM_175092	23912	Mm.253876	NM_175092	ENSMUSG00000029449	Rhof	AI845056|AV026554|Arhf|Ifld1|Rif	ras homolog family member F (in filopodia)	protein-coding
mm_19048.1	chr2	77184485	77184487	-	1	NA	3' UTR (NM_175465, exon 18 of 18)	3' UTR (NM_175465, exon 18 of 18)	-13851	NM_001025576	545428	Mm.26579	NM_001025576	ENSMUSG00000044033	Ccdc141	2610301F02Rik|CAMDI|ENSMUSG00000075261	coiled-coil domain containing 141	protein-coding
mm_77067.1	chr8	109962085	109962126	-	1	NA	promoter-TSS (NM_028584)	promoter-TSS (NM_028584)	100	NM_212447	73608	Mm.86833	NM_028584	ENSMUSG00000001672	Marveld3	1810006A16Rik|AI642133|Marvd3|Mrvldc3	MARVEL (membrane-associating) domain containing 3	protein-coding
mm_103000.1	chr11	69687310	69687327	-	1	NA	exon (NM_001159503, exon 6 of 13)	exon (NM_001159503, exon 6 of 13)	-1764	NM_023517	69583	Mm.8983	NM_023517	ENSMUSG00000089669	Tnfsf13	2310026N09Rik|April|Tall2|Tnlg7b|Trdl1	tumor necrosis factor (ligand) superfamily, member 13	protein-coding
mm_21216.1	chr2	155818867	155818895	-	1	NA	TTS (NM_010808)	TTS (NM_010808)	322	NR_015528	613262	Mm.330707	NR_015528	ENSMUSG00000074649	BC029722	-	cDNA sequence BC029722	ncRNA
mm_139110.1	chr17	47369173	47369212	+	1	NA	promoter-TSS (NM_183086)	promoter-TSS (NM_183086)	-5	NM_183086	64657	Mm.216250	NM_183086	ENSMUSG00000034729	Mrps10	1110038B19Rik|AW743084|Rpms10	mitochondrial ribosomal protein S10	protein-coding
mm_35448.1	chr4	40261681	40261691	-	1	NA	exon (NM_134097, exon 3 of 3)	exon (NM_134097, exon 3 of 3)	-7893	NR_045265	100504309	Mm.392019	NR_045265		Toporsos	2010003O02Rik	topoisomerase I binding, arginine/serine-rich, opposite strand	ncRNA
mm_100505.1	chr11	120491896	120491921	+	1	NA	promoter-TSS (NM_013770)	promoter-TSS (NM_013770)	71	NM_013770	27376	Mm.3991	NM_013770	ENSMUSG00000025792	Slc25a10	Dic	solute carrier family 25 (mitochondrial carrier, dicarboxylate transporter), member 10	protein-coding
mm_103463.1	chr11	76422256	76422268	-	1	NA	intron (NM_001346670, intron 19 of 21)	intron (NM_001346670, intron 19 of 21)	15119	NM_019818	56322	Mm.18803	NM_019818	ENSMUSG00000020843	Timm22	Tim22	translocase of inner mitochondrial membrane 22	protein-coding
mm_91477.1	chr10	34208295	34208321	-	1	NA	promoter-TSS (NM_172508)	promoter-TSS (NM_172508)	-757	NM_172508	212898	Mm.34557	NM_172508	ENSMUSG00000039497	Dse	6030499O08|AI480506|B130024B19Rik|DS-epi1|Sart2	dermatan sulfate epimerase	protein-coding
mm_162639.1	chr1	191397209	191397234	-	1	NA	promoter-TSS (NM_144880)	promoter-TSS (NM_144880)	-180	NM_144880	226849	Mm.205569	NM_144880	ENSMUSG00000026626	Ppp2r5a	PR61alpha	protein phosphatase 2, regulatory subunit B', alpha	protein-coding
mm_124392.1	chr14	111513833	111513852	-	1	NA	Intergenic	B3A|SINE|B2	-161273	NM_198865	75409	Mm.235097	NM_029273	ENSMUSG00000033214	Slitrk5	2610019D03Rik	SLIT and NTRK-like family, member 5	protein-coding
mm_96859.1	chr11	70092647	70092651	+	1	NA	promoter-TSS (NM_007493)	promoter-TSS (NM_007493)	5	NM_001313927	11890	Mm.1357	NM_007493	ENSMUSG00000040963	Asgr2	ASGPR2|Asgr|Asgr-2|HL-2	asialoglycoprotein receptor 2	protein-coding
mm_11637.1	chr2	34826279	34826299	+	1	NA	promoter-TSS (NM_013890)	promoter-TSS (NM_013890)	-54	NM_001164772	30050	Mm.4465	NM_013890	ENSMUSG00000035949	Fbxw2	2700071L08Rik|FBW2|Fwd2|MD6	F-box and WD-40 domain protein 2	protein-coding
mm_93064.1	chr10	88826773	88826837	-	1	NA	promoter-TSS (NM_175158)	promoter-TSS (NM_175158)	9	NM_175158	70683	Mm.29631	NM_175158	ENSMUSG00000004356	Utp20	3830408P06Rik|AA617408|Drim|mDRIM|mDRIN	UTP20 small subunit processome component	protein-coding
mm_65012.1	chr7	17090486	17090525	-	1	NA	5' UTR (NM_007676, exon 2 of 5)	5' UTR (NM_007676, exon 2 of 5)	16465	NM_007676	26436	Mm.143686	NM_007676	ENSMUSG00000066760	Psg16	Cea11|PSG|bCEA	pregnancy specific glycoprotein 16	protein-coding
mm_42564.1	chr5	117142160	117142175	+	1	NA	intron (NM_001081308, intron 1 of 19)	intron (NM_001081308, intron 1 of 19)	8579	NM_183306	330177	Mm.24343	NM_183306	ENSMUSG00000061288	Taok3	2900006A08Rik|A130052D22|A430105I05Rik	TAO kinase 3	protein-coding
mm_151751.1	chr19	5093249	5093266	-	1	NA	TTS (NM_026553)	TTS (NM_026553)	4719	NM_026553	68090	Mm.44202	NM_026553	ENSMUSG00000024875	Yif1a	5330422J23Rik|54TM|Yif1|Yif1p	Yip1 interacting factor homolog A (S. cerevisiae)	protein-coding
mm_144769.1	chr18	35780788	35780791	+	1	NA	intron (NM_019912, intron 1 of 6)	intron (NM_019912, intron 1 of 6)	9230	NM_019912	56550	Mm.180052	NM_019912	ENSMUSG00000091896	Ube2d2a	1500034D03Rik|Ubc2e|Ube2d2|ubc4	ubiquitin-conjugating enzyme E2D 2A	protein-coding
mm_29112.1	chr3	104864965	104865045	-	1	NA	promoter-TSS (NM_009797)	promoter-TSS (NM_009797)	499	NM_153091	229681	Mm.206379	NM_153091	ENSMUSG00000045576	St7l	St7r	suppression of tumorigenicity 7-like	protein-coding
mm_34753.1	chr4	152325832	152325876	+	1	NA	non-coding (NR_102292, exon 1 of 5)	non-coding (NR_102292, exon 1 of 5)	128	NR_102291	19934	Mm.307846	NM_009079	ENSMUSG00000028936	Rpl22	2700038K18Rik	ribosomal protein L22	protein-coding
mm_160099.1	chr7	18532193	18532193	-	1	NA	promoter-TSS (NM_054060)	promoter-TSS (NM_054060)	34	NM_054060	114868	Mm.389809	NM_054060	ENSMUSG00000070798	Psg25	cea13	pregnancy-specific glycoprotein 25	protein-coding
mm_16113.1	chr2	169699397	169699403	+	1	NA	intron (NM_080455, intron 1 of 1)	intron (NM_080455, intron 1 of 1)	65754	NM_080455	228911	Mm.315789	NM_080455	ENSMUSG00000047907	Tshz2	2900073F20Rik|B830045G17|Mtsh2|Sdccag33l|Tsh2|Zfp218|mKIAA4248|teashirt2	teashirt zinc finger family member 2	protein-coding
mm_112336.1	chr12	116000507	116000516	-	1	NA	Intergenic	Intergenic	-47213	NM_001004066	56220	Mm.254997	NM_019565	ENSMUSG00000042063	Zfp386	Kzf1|mKIAA4205	zinc finger protein 386 (Kruppel-like)	protein-coding
mm_150211.1	chr19	32817968	32817982	+	1	NA	exon (NM_008960, exon 8 of 9)	exon (NM_008960, exon 8 of 9)	60398	NM_008960	19211	Mm.245395	NM_008960	ENSMUSG00000013663	Pten	2310035O07Rik|A130070J02Rik|AI463227|B430203M17Rik|MMAC1|TEP1	phosphatase and tensin homolog	protein-coding
mm_130568.1	chr15	99457721	99457736	-	1	NA	promoter-TSS (NM_001001884)	promoter-TSS (NM_001001884)	20	NM_001001884	380969	Mm.22915	NM_001001884	ENSMUSG00000023009	Nckap5l	C230021P08Rik|Cep169	NCK-associated protein 5-like	protein-coding
mm_65578.1	chr7	27196139	27196174	-	1	NA	promoter-TSS (NM_001046637)	promoter-TSS (NM_001046637)	115	NM_015782	53607	Mm.386890	NM_015782	ENSMUSG00000061479	Snrpa	C430021M15Rik|Rnu1a-1|Rnu1a1|U1-A|U1A	small nuclear ribonucleoprotein polypeptide A	protein-coding
mm_85341.1	chr9	103197590	103197620	-	1	NA	exon (NM_009275, exon 4 of 7)	exon (NM_009275, exon 4 of 7)	4460	NM_009275	20818	Mm.273053	NM_009275	ENSMUSG00000032553	Srprb	AA409543	signal recognition particle receptor, B subunit	protein-coding
mm_80033.1	chr9	68803106	68803108	+	1	NA	intron (NM_013646, intron 1 of 10)	intron (NM_013646, intron 1 of 10)	37761	NR_033299	320440	Mm.483129	NM_177159		9530091C08Rik	-	RIKEN cDNA 9530091C08 gene	ncRNA
mm_35590.1	chr4	43000452	43000485	-	1	NA	promoter-TSS (NM_009503)	promoter-TSS (NM_009503)	39	NM_009503	269523	Mm.245976	NM_009503	ENSMUSG00000028452	Vcp	3110001E05|CDC48|p97|p97/VCP	valosin containing protein	protein-coding
mm_104978.1	chr11	100247630	100247663	-	1	NA	exon (NM_008470, exon 3 of 8)	exon (NM_008470, exon 3 of 8)	1256	NM_001313958	16666	Mm.422799	NM_008470	ENSMUSG00000053797	Krt16	AI324768|CK-16|K16|Krt1-16	keratin 16	protein-coding
mm_83502.1	chr9	45955197	45955212	-	1	NA	promoter-TSS (NM_001289668)	promoter-TSS (NM_001289668)	45	NM_172257	214597	Mm.379345	NM_172257	ENSMUSG00000034908	Sidt2	B930096O19|BC023957|CGI-40	SID1 transmembrane family, member 2	protein-coding
mm_116408.1	chr13	41425367	41425379	-	1	NA	intron (NM_001111324, intron 2 of 7)	B1F1|SINE|Alu	61987	NM_001111324	18003	Mm.288980	NM_017464	ENSMUSG00000021365	Nedd9	Cas-L|CasL|HEF1|MEF1|Nedd-9|p105	neural precursor cell expressed, developmentally down-regulated gene 9	protein-coding
mm_3584.1	chr1	151344449	151344458	+	1	NA	promoter-TSS (NM_001039512)	promoter-TSS (NM_001039512)	-45	NM_001039512	117198	Mm.33764	NM_028582	ENSMUSG00000023150	Ivns1abp	1190004M08Rik|1700126I16Rik|AA960440|HSPC068|ND1|NS-1|NS1-BP|Nd1-L|Nd1-S|mKIAA0850	influenza virus NS1A binding protein	protein-coding
mm_121575.1	chr14	122912986	122913014	+	1	NA	intron (NM_145466, intron 1 of 2)	CpG	165	NM_145466	223267	Mm.379358	NM_145466	ENSMUSG00000041625	Ggact	A2ld1	gamma-glutamylamine cyclotransferase	protein-coding
mm_123975.1	chr14	75176581	75176603	-	1	NA	intron (NM_008879, intron 1 of 16)	intron (NM_008879, intron 1 of 16)	40167	NM_008879	18826	Mm.153911	NM_008879	ENSMUSG00000021998	Lcp1	AW536232|D14Ertd310e|LCP-1|Pls2|pp65	lymphocyte cytosolic protein 1	protein-coding
mm_136267.1	chr16	91044077	91044087	-	1	NA	exon (NM_026110, exon 1 of 18)	exon (NM_026110, exon 1 of 18)	297	NM_026110	67367	Mm.347	NM_026110	ENSMUSG00000022974	Paxbp1	1810007M14Rik|C21orf66|Gcfc|Gcfc1|Pax3/7bp	PAX3 and PAX7 binding protein 1	protein-coding
mm_98599.1	chr11	95825222	95825240	+	1	NA	intron (NM_153104, intron 1 of 2)	intron (NM_153104, intron 1 of 2)	731	NM_153104	237928	Mm.133075	NM_153104	ENSMUSG00000050860	Phospho1	D11Moh36|Phospo1	phosphatase, orphan 1	protein-coding
mm_166323.1	chr5	111630460	111630460	+	1	NA	Intergenic	Intergenic	48899	NR_015546	330164	Mm.193276	NM_177875	ENSMUSG00000052848	C130026L21Rik	-	RIKEN cDNA C130026L21 gene	ncRNA
mm_146557.1	chr18	6225345	6225362	-	1	NA	exon (NM_008448, exon 8 of 26)	exon (NM_008448, exon 8 of 26)	16171	NM_008448	16573	Mm.223744	NM_008448	ENSMUSG00000006740	Kif5b	AL022807|Khc|Khcs|Kns1|Ukhc	kinesin family member 5B	protein-coding
mm_120014.1	chr14	55745879	55745891	+	1	NA	promoter-TSS (NM_026819)	promoter-TSS (NM_026819)	192	NM_026403	67842	Mm.180338	NM_026403	ENSMUSG00000019297	Nop9	2610027L16Rik	NOP9 nucleolar protein	protein-coding
mm_115235.1	chr13	109903389	109903406	+	1	NA	promoter-TSS (NR_035442)	promoter-TSS (NR_035442)	-412	NR_035442	100316683		NR_035442	ENSMUSG00000084651	Mir1904	Mirn1904|mmu-mir-1904	microRNA 1904	ncRNA
mm_100066.1	chr11	115394637	115394642	+	1	NA	3' UTR (NM_001080929, exon 5 of 5)	3' UTR (NM_001080929, exon 5 of 5)	-9113	NM_001347645	68572	Mm.271062	NM_026729	ENSMUSG00000018858	Mrpl58	1110001A02Rik|1110002E03Rik|Ict1|MRP-L58	mitochondrial ribosomal protein L58	protein-coding
mm_144313.1	chr18	12643414	12643424	+	1	NA	promoter-TSS (NM_028341)	promoter-TSS (NM_028341)	-114	NM_028341	72747	Mm.52526	NM_028341	ENSMUSG00000024424	Ttc39c	1700008N02Rik|2810439F02Rik	tetratricopeptide repeat domain 39C	protein-coding
mm_38791.1	chr4	148130639	148130649	-	1	NA	promoter-TSS (NM_027426)	promoter-TSS (NM_027426)	54	NM_027426	70433	Mm.275288	NM_027426	ENSMUSG00000029005	Draxin	2610109H07Rik|neucrin	dorsal inhibitory axon guidance protein	protein-coding
mm_90312.1	chr10	127041932	127041972	+	1	NA	promoter-TSS (NM_010792)	promoter-TSS (NM_010792)	20	NM_010792	17299	Mm.251593	NM_010792	ENSMUSG00000006732	Mettl1	2810012D02Rik	methyltransferase like 1	protein-coding
mm_144932.1	chr18	37720364	37720411	+	1	NA	promoter-TSS (NM_033576)	promoter-TSS (NM_033576)	-167	NM_033576	93701	Mm.247203	NM_033576	ENSMUSG00000103585	Pcdhgb4	-	protocadherin gamma subfamily B, 4	protein-coding
mm_170246.1	chr17	93321704	93321708	+	1	NA	Intergenic	RLTR17|LTR|ERVK	122538	NM_009625	11516	Mm.3407	NM_009625	ENSMUSG00000024256	Adcyap1	PACAP	adenylate cyclase activating polypeptide 1	protein-coding
mm_151896.1	chr19	5799004	5799008	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	-3025	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_150954.1	chr19	46356898	46356942	+	1	NA	promoter-TSS (NM_029186)	promoter-TSS (NM_029186)	40	NM_029186	75146	Mm.159290	NM_029186	ENSMUSG00000025227	Mfsd13a	4930449A08Rik|4930538D17Rik|Tmem180	major facilitator superfamily domain containing 13a	protein-coding
mm_89548.1	chr10	94688620	94688641	+	1	NA	promoter-TSS (NM_029852)	promoter-TSS (NM_029852)	-17	NR_015524	67723	Mm.116284	NR_015524	ENSMUSG00000097164	Cep83os	4932415G12Rik|Ccdc41os1	centrosomal protein 83, opposite strand	ncRNA
mm_158428.1	chrX	139834739	139834744	-	1	NA	intron (NM_029413, intron 13 of 15)	intron (NM_029413, intron 13 of 15)	33933	NM_016675	12738	Mm.117068	NM_016675	ENSMUSG00000047230	Cldn2	AL022813	claudin 2	protein-coding
mm_155329.1	chrX	65047672	65047683	+	1	NA	promoter-TSS (NM_027302)	promoter-TSS (NM_027302)	33	NM_027302	70062	Mm.45791	NM_027302	ENSMUSG00000031181	Ctag2	1700030B21Rik	cancer/testis antigen 2	protein-coding
mm_68999.1	chr7	126676429	126676439	-	1	NA	promoter-TSS (NM_133670)	promoter-TSS (NM_133670)	-77	NM_133670	20887	Mm.368982	NM_133670	ENSMUSG00000030711	Sult1a1	AI266890|PST|ST1A1|Stp|Stp1	sulfotransferase family 1A, phenol-preferring, member 1	protein-coding
mm_143440.1	chr17	70853176	70853184	-	1	NA	intron (NM_001164074, intron 1 of 2)	CpG	352	NM_001164074	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_147364.1	chr18	43393279	43393298	-	1	NA	promoter-TSS (NM_009468)	promoter-TSS (NM_009468)	89	NM_009468	22240	Mm.8180	NM_009468	ENSMUSG00000024501	Dpysl3	CRMP-4|DRP-3|TUC4|ULIP-1|Ulip|Ulip1	dihydropyrimidinase-like 3	protein-coding
mm_129761.1	chr15	82404536	82404545	-	1	NA	exon (NM_010005, exon 5 of 9)	exon (NM_010005, exon 5 of 9)	2654	NM_010005	13101	Mm.174372	NM_010005	ENSMUSG00000094806	Cyp2d10	AI303445|Cyp2d|P450-2D	cytochrome P450, family 2, subfamily d, polypeptide 10	protein-coding
mm_172271.1	chr6	81333647	81333647	+	1	NA	Intergenic	L1Md_F|LINE|L1	562016	NR_106091	102465711		NR_106091	ENSMUSG00000106154	Mir7232	mmu-mir-7232	microRNA 7232	ncRNA
mm_12196.1	chr2	65668754	65668769	+	1	NA	promoter-TSS (NM_001346680)	promoter-TSS (NM_001346680)	75	NM_001346680	110876	Mm.220329	NM_001099298	ENSMUSG00000075318	Scn2a	6430408L10|A230052E19Rik|Nav1.2|Scn2a1	sodium channel, voltage-gated, type II, alpha	protein-coding
mm_164197.1	chr15	79414832	79414857	+	1	NA	Intergenic	Intergenic	-11541	NM_172608	223693	Mm.323358	NM_172608	ENSMUSG00000009035	Tmem184b	2610507A11|4732495E13Rik	transmembrane protein 184b	protein-coding
mm_146182.1	chr18	75488406	75488454	+	1	NA	intron (NM_201354, intron 9 of 11)	ORR1B2|LTR|ERVL-MaLR	-26215	NR_045879	100038353	Mm.440724	NR_045879	ENSMUSG00000097712	Gm10532	ENSMUSG00000073534	predicted gene 10532	ncRNA
mm_49389.1	chr6	24863871	24863919	+	1	NA	intron (NM_028957, intron 1 of 3)	intron (NM_028957, intron 1 of 3)	5898	NM_028957	74468	Mm.251601	NM_028957	ENSMUSG00000029678	Hyal5	4933439A12Rik	hyaluronoglucosaminidase 5	protein-coding
mm_122413.1	chr14	41030984	41030996	-	1	NA	Intergenic	L1MC|LINE|L1	-17157	NM_001316737	70564	Mm.27227	NM_027464	ENSMUSG00000021792	Fam213a	5730469M10Rik|AU040822|Adrx|Pamm	family with sequence similarity 213, member A	protein-coding
mm_103395.1	chr11	75432529	75432538	-	1	NA	exon (NM_008878, exon 10 of 10)	exon (NM_008878, exon 10 of 10)	6968	NM_008878	18816	Mm.279733	NM_008878	ENSMUSG00000038224	Serpinf2	AI747498|Pli|Serpimf2	serine (or cysteine) peptidase inhibitor, clade F, member 2	protein-coding
mm_78159.1	chr9	21027951	21027964	+	1	NA	3' UTR (NM_010493, exon 7 of 7)	3' UTR (NM_010493, exon 7 of 7)	-1416	NM_023892	78369	Mm.30220	NM_023892	ENSMUSG00000001014	Icam4	1810015M19Rik|Cd242|ICAM-4	intercellular adhesion molecule 4, Landsteiner-Wiener blood group	protein-coding
mm_154316.1	chrM	2133	2143	+	1	NA	NA	LSU-rRNA_Hsa|rRNA|rRNA	NA	NA								
mm_26645.1	chr3	153944852	153944866	+	1	NA	promoter-TSS (NM_007382)	promoter-TSS (NM_007382)	-216	NM_007382	11364	Mm.10530	NM_007382	ENSMUSG00000062908	Acadm	AU018656|MCAD	acyl-Coenzyme A dehydrogenase, medium chain	protein-coding
mm_124897.1	chr15	10470677	10470726	+	1	NA	promoter-TSS (NM_030046)	promoter-TSS (NM_030046)	-185	NM_030046	78244	Mm.297862	NM_030046	ENSMUSG00000044224	Dnajc21	4930461P20Rik|9930116P15Rik	DnaJ heat shock protein family (Hsp40) member C21	protein-coding
mm_80631.1	chr9	89211163	89211196	+	1	NA	promoter-TSS (NM_026829)	promoter-TSS (NM_026829)	-11	NM_026829	107885	Mm.486274	NM_026829	ENSMUSG00000066442	Mthfs	1110034I12Rik|2310020H23Rik|AI119695	5, 10-methenyltetrahydrofolate synthetase	protein-coding
mm_59368.1	chr7	25688130	25688148	+	1	NA	exon (NM_011577, exon 1 of 7)	exon (NM_011577, exon 1 of 7)	1137	NM_011577	21803	Mm.248380	NM_011577	ENSMUSG00000002603	Tgfb1	TGF-beta1|TGFbeta1|Tgfb|Tgfb-1	transforming growth factor, beta 1	protein-coding
mm_157027.1	chrX	7899197	7899206	-	1	NA	promoter-TSS (NM_001252528)	promoter-TSS (NM_001252528)	68	NM_001252529	54633	Mm.14616	NM_019478	ENSMUSG00000031157	Pqbp1	PQBP-1|Sfc2|npw38	polyglutamine binding protein 1	protein-coding
mm_127831.1	chr15	6581080	6581094	-	1	NA	intron (NM_011815, intron 1 of 17)	intron (NM_011815, intron 1 of 17)	1240	NM_011815	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_62304.1	chr7	100176703	100176711	+	1	NA	promoter-TSS (NM_001190869)	promoter-TSS (NM_001190869)	37	NM_001190869	57442	Mm.282386	NM_020574	ENSMUSG00000035165	Kcne3	2210017H05Rik|MiRP2	potassium voltage-gated channel, Isk-related subfamily, gene 3	protein-coding
mm_96147.1	chr11	61065799	61065816	+	1	NA	promoter-TSS (NM_010603)	promoter-TSS (NM_010603)	3	NM_010603	16515	Mm.4970	NM_010603	ENSMUSG00000042529	Kcnj12	IRK-2|IRK2|Kir2.2|MB-IRK2	potassium inwardly-rectifying channel, subfamily J, member 12	protein-coding
mm_57208.1	chr6	122852849	122852868	-	1	NA	intron (NM_009779, intron 1 of 1)	MTD|LTR|ERVL-MaLR	3299	NM_009779	12267	Mm.2408	NM_009779	ENSMUSG00000040552	C3ar1	AZ3B|C3AR|HNFAG09	complement component 3a receptor 1	protein-coding
mm_125816.1	chr15	74954190	74954197	+	1	NA	promoter-TSS (NM_001164036)	promoter-TSS (NM_001164036)	-858	NM_001164039	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_123706.1	chr14	69805445	69805458	-	1	NA	promoter-TSS (NM_153514)	promoter-TSS (NM_153514)	94	NM_153514	246710	Mm.102367	NM_153514	ENSMUSG00000022075	Rhobtb2	Dbc2|E130206H14Rik|mKIAA0717	Rho-related BTB domain containing 2	protein-coding
mm_102195.1	chr11	54353459	54353478	-	1	NA	intron (NM_001033597, intron 20 of 20)	intron (NM_001033597, intron 20 of 20)	-17184	NM_029105	74847	Mm.486538	NM_029105	ENSMUSG00000020332	Meikin	4930404A10Rik	meiotic kinetochore factor	protein-coding
mm_119552.1	chr14	48654827	48654851	+	1	NA	Intergenic	Intergenic	8033	NM_144841	18424	Mm.134516	NM_144841	ENSMUSG00000021848	Otx2	E130306E05Rik	orthodenticle homeobox 2	protein-coding
mm_133196.1	chr16	72982945	72982945	+	1	NA	intron (NM_019413, intron 15 of 28)	intron (NM_019413, intron 15 of 28)	319796	NM_019413	19876	Mm.310772	NM_019413	ENSMUSG00000022883	Robo1	AW494633|AW742721|DUTT1|Gm310	roundabout guidance receptor 1	protein-coding
mm_99058.1	chr11	99052313	99052338	+	1	NA	3' UTR (NM_010517, exon 4 of 4)	3' UTR (NM_010517, exon 4 of 4)	11065	NM_010517	16010	Mm.233799	NM_010517	ENSMUSG00000017493	Igfbp4	AI875747|Deb2|IGFBP-4	insulin-like growth factor binding protein 4	protein-coding
mm_36130.1	chr4	59254275	59254286	-	1	NA	Intergenic	RMER17D2|LTR|ERVK	-5771	NR_105031	101055769	Mm.421401	NR_105031		Gm12596	OTTMUSG00000007649	predicted gene 12596	ncRNA
mm_142950.1	chr17	56109776	56109794	-	1	NA	promoter-TSS (NM_020568)	promoter-TSS (NM_020568)	17	NM_020568	57435	Mm.12966	NM_020568	ENSMUSG00000002831	Plin4	S3-12|mKIAA1881	perilipin 4	protein-coding
mm_158416.1	chrX	137119806	137119819	-	1	NA	intron (NM_007957, intron 1 of 4)	intron (NM_007957, intron 1 of 4)	514	NM_007957	13984	Mm.8017	NM_007957	ENSMUSG00000023443	Esx1	Spx1	extraembryonic, spermatogenesis, homeobox 1	protein-coding
mm_75704.1	chr8	68887488	68887525	-	1	NA	exon (NM_008509, exon 2 of 10)	exon (NM_008509, exon 2 of 10)	6951	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_137270.1	chr17	24698350	24698371	+	1	NA	exon (NM_027988, exon 2 of 9)	exon (NM_027988, exon 2 of 9)	2126	NM_027988	71893	Mm.390971	NM_027988	ENSMUSG00000019320	Noxo1	2310034C04Rik|P41NOX|P41NOXA|P41NOXB|P41NOXC|Snx28|hslt	NADPH oxidase organizer 1	protein-coding
mm_47219.1	chr5	121157079	121157083	-	1	NA	intron (NM_011202, intron 6 of 15)	intron (NM_011202, intron 6 of 15)	34316	NM_001109992	19247	Mm.8681	NM_011202	ENSMUSG00000043733	Ptpn11	2700084A17Rik|AW536184|PTP1D|PTP2C|SAP-2|SH-PTP2|SH-PTP3|SHP-2|Shp2|Syp	protein tyrosine phosphatase, non-receptor type 11	protein-coding
mm_34117.1	chr4	139207454	139207459	+	1	NA	intron (NM_001271405, intron 1 of 8)	intron (NM_001271405, intron 1 of 8)	13345	NM_001271405	12345	Mm.2945	NM_009798	ENSMUSG00000028745	Capzb	1700120C01Rik|AI325129|CPB1|CPB2|CPbeat2|CPbeta1|CPbeta2|Cappb1	capping protein (actin filament) muscle Z-line, beta	protein-coding
mm_40212.1	chr5	37047465	37047488	+	1	NA	Intergenic	Intergenic	-3381	NM_178394	76071	Mm.85280	NM_178394	ENSMUSG00000063646	Jakmip1	5830437M04Rik|C330021K24Rik|Gababrbp|Marlin-1	janus kinase and microtubule interacting protein 1	protein-coding
mm_118068.1	chr13	102906016	102906038	-	1	NA	intron (NM_175171, intron 4 of 28)	intron (NM_175171, intron 4 of 28)	145772	NR_130171	76624	Mm.426384	NR_130171	ENSMUSG00000091906	1700099I09Rik	-	RIKEN cDNA 1700099I09 gene	ncRNA
mm_148627.1	chr19	5447887	5447905	+	1	NA	5' UTR (NM_010235, exon 1 of 4)	5' UTR (NM_010235, exon 1 of 4)	198	NM_010235	14283	Mm.6215	NM_010235	ENSMUSG00000024912	Fosl1	AW538199|Fra1|fra-1	fos-like antigen 1	protein-coding
mm_129983.1	chr15	86034044	86034106	-	1	NA	promoter-TSS (NM_009886)	promoter-TSS (NM_009886)	-298	NM_009886	12614	Mm.22680	NM_009886	ENSMUSG00000016028	Celsr1	Adgrc1|Crsh|Scy|crash	cadherin, EGF LAG seven-pass G-type receptor 1	protein-coding
mm_92440.1	chr10	77418208	77418228	-	1	NA	promoter-TSS (NR_004429)	promoter-TSS (NR_004429)	55	NM_130895	110532	Mm.276815	NM_130895	ENSMUSG00000020262	Adarb1	1700057H01Rik|AW124433|AW558573|Adar2|BB220382|D10Bwg0447e|Red1	adenosine deaminase, RNA-specific, B1	protein-coding
mm_15142.1	chr2	153974845	153974855	+	1	NA	promoter-TSS (NM_001080811)	promoter-TSS (NM_001080811)	-95	NM_001080811	545477	Mm.379973	NM_001080811	ENSMUSG00000078998	Bpifa6	EG545477|Gm5840|Splunc6	BPI fold containing family A, member 6	protein-coding
mm_36050.1	chr4	57300752	57300839	-	1	NA	intron (NM_011207, intron 1 of 25)	intron (NM_011207, intron 1 of 25)	1042	NM_011207	545622	Mm.246552	NM_011207	ENSMUSG00000038764	Ptpn3	9530011I20Rik|PTP-H1|PTPCL	protein tyrosine phosphatase, non-receptor type 3	protein-coding
mm_55443.1	chr6	67186569	67186601	-	1	NA	Intergenic	Intergenic	-80394	NM_001113564	66870	Mm.240490	NM_025814	ENSMUSG00000036371	Serbp1	1200009K13Rik|9330147J08Rik|AL022786|Pairbp1	serpine1 mRNA binding protein 1	protein-coding
mm_74846.1	chr8	24576298	24576368	-	1	NA	promoter-TSS (NM_145949)	promoter-TSS (NM_145949)	0	NM_145949	209176	Mm.219580	NM_145949	ENSMUSG00000031549	Ido2	AI265623|C230043N17Rik|Ido-2|Indol1	indoleamine 2,3-dioxygenase 2	protein-coding
mm_111795.1	chr12	104865151	104865163	-	1	NA	promoter-TSS (NR_104437)	promoter-TSS (NR_104437)	-81	NR_104435	94040	Mm.244078	NM_053155	ENSMUSG00000021097	Clmn	9330188N17Rik|AI428889|AI788815|mKIAA1188	calmin	protein-coding
mm_88585.1	chr10	79710256	79710267	+	1	NA	exon (NM_001077184, exon 4 of 7)	exon (NM_001077184, exon 4 of 7)	5903	NM_009768	12215	Mm.726	NM_009768	ENSMUSG00000023175	Bsg	AI115436|AI325119|CD147|EMMPRIN|HT-7	basigin	protein-coding
mm_168336.1	chr1	111881317	111881334	-	1	NA	Intergenic	Intergenic	-16407	NM_001081316	319901	Mm.103468	NM_001081316	ENSMUSG00000038702	Dsel	9330132E09Rik|DS-epi2	dermatan sulfate epimerase-like	protein-coding
mm_61783.1	chr7	83755913	83755956	+	1	NA	Intergenic	Intergenic	-20444	NM_010551	16170	Mm.10137	NM_010551	ENSMUSG00000001741	Il16	mKIAA4048	interleukin 16	protein-coding
mm_87587.1	chr10	57486355	57486414	+	1	NA	promoter-TSS (NM_008297)	promoter-TSS (NM_008297)	-1	NM_008297	15500	Mm.261395	NM_008297	ENSMUSG00000019878	Hsf2	AI661205	heat shock factor 2	protein-coding
mm_80957.1	chr9	103008480	103008497	+	1	NA	promoter-TSS (NM_033314)	promoter-TSS (NM_033314)	-1	NM_033314	24059	Mm.207106	NM_033314	ENSMUSG00000032548	Slco2a1	2310021C19Rik|Pgt|Slc21a2|mPgt	solute carrier organic anion transporter family, member 2a1	protein-coding
mm_116357.1	chr13	40725827	40725831	-	1	NA	intron (NM_001301674, intron 3 of 7)	intron (NM_001301674, intron 3 of 7)	-1979	NR_125899	102633805		NR_125899	ENSMUSG00000097752	Gm26688	Tfap2a-as1	predicted gene, 26688	ncRNA
mm_60237.1	chr7	43712506	43712527	+	1	NA	promoter-TSS (NM_001039042)	promoter-TSS (NM_001039042)	-51	NM_001039042	626834	Mm.389891	NM_001039042	ENSMUSG00000054046	Klk13	Egfbp-2|mGk-13	kallikrein related-peptidase 13	protein-coding
mm_85522.1	chr9	106453038	106453070	-	1	NA	promoter-TSS (NM_021567)	promoter-TSS (NM_021567)	-784	NM_021567	59092	Mm.286394	NM_021567	ENSMUSG00000023495	Pcbp4	1200003L19Rik|AlphaCP-4	poly(rC) binding protein 4	protein-coding
mm_37919.1	chr4	132785470	132785478	-	1	NA	exon (NM_001033308, exon 4 of 6)	exon (NM_001033308, exon 4 of 6)	10890	NM_001033308	230787	Mm.290912	NM_001033308	ENSMUSG00000037731	Themis2	ICB-1	thymocyte selection associated family member 2	protein-coding
mm_75263.1	chr8	40634730	40634744	-	1	NA	promoter-TSS (NM_001040699)	promoter-TSS (NM_001040699)	55	NM_001040699	54384	Mm.294871	NM_019433	ENSMUSG00000039431	Mtmr7	-	myotubularin related protein 7	protein-coding
mm_30286.1	chr3	148989379	148989389	-	1	NA	Intergenic	CpG	-34749	NM_001081298	99633	Mm.9776	NM_001081298	ENSMUSG00000028184	Adgrl2	AI450192|CIRL-2|Gm619|Lec1|Lphh1|Lphn2|mKIAA0786	adhesion G protein-coupled receptor L2	protein-coding
mm_19432.1	chr2	91950289	91950359	-	1	NA	promoter-TSS (NM_001166597)	promoter-TSS (NM_001166597)	24	NM_001166597	104418	Mm.314923	NM_138306	ENSMUSG00000040479	Dgkz	E130307B02Rik|ENSMUSG00000075035|F730209L11Rik|mDGK[z]	diacylglycerol kinase zeta	protein-coding
mm_32266.1	chr4	102605430	102605441	+	1	NA	3' UTR (NM_001177980, exon 10 of 10)	3' UTR (NM_001177980, exon 10 of 10)	15592	NM_001177981	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_109502.1	chr12	111452094	111452104	+	1	NA	intron (NM_009396, intron 11 of 11)	(TCTA)n|Simple_repeat|Simple_repeat	9438	NM_009396	21928	Mm.255332	NM_009396	ENSMUSG00000021281	Tnfaip2	B94|Exoc3l3|M-sec|Tnfip2|tnfb94	tumor necrosis factor, alpha-induced protein 2	protein-coding
mm_39032.1	chr4	152291656	152291659	-	1	NA	promoter-TSS (NM_008237)	promoter-TSS (NM_008237)	5	NM_008237	15207	Mm.3516	NM_008237	ENSMUSG00000028946	Hes3	Hes-3|bHLHb43	hairy and enhancer of split 3 (Drosophila)	protein-coding
mm_142033.1	chr17	35236495	35236531	-	1	NA	promoter-TSS (NM_010909)	promoter-TSS (NM_010909)	-83	NM_023179	66237	Mm.396107	NM_023179	ENSMUSG00000024403	Atp6v1g2	1500002D01Rik|Atp6g2|NG38|VAG2	ATPase, H+ transporting, lysosomal V1 subunit G2	protein-coding
mm_22110.1	chr2	170131157	170131184	-	1	NA	promoter-TSS (NM_001033299)	promoter-TSS (NM_001033299)	50	NM_001033299	228913	Mm.22858	NM_001033299	ENSMUSG00000052056	Zfp217	4933431C08Rik|AW987152|Gm562|ZABC1|Znf217	zinc finger protein 217	protein-coding
mm_67666.1	chr7	86775954	86775962	-	1	NA	promoter-TSS (NM_001159706)	promoter-TSS (NM_001159706)	-94	NM_001159706	53320	Mm.269137	NM_016770	ENSMUSG00000001773	Folh1	GCP2|mopsm	folate hydrolase 1	protein-coding
mm_142920.1	chr17	53823794	53823795	-	1	NA	Intergenic	Intergenic	22164	NM_026935	69083	Mm.19320	NM_026935	ENSMUSG00000023122	Sult1c2	1810008N17Rik|ST1C1|ST1C2|Sult1c1	sulfotransferase family, cytosolic, 1C, member 2	protein-coding
mm_64166.1	chr7	141401869	141401882	+	1	NA	exon (NM_011528, exon 6 of 8)	exon (NM_011528, exon 6 of 8)	9715	NM_011528	21351	Mm.29182	NM_011528	ENSMUSG00000025503	Taldo1	-	transaldolase 1	protein-coding
mm_39141.1	chr4	155328647	155328690	-	1	NA	intron (NM_008860, intron 4 of 17)	intron (NM_008860, intron 4 of 17)	17121	NM_001039079	18762	Mm.28561	NM_008860	ENSMUSG00000029053	Prkcz	AI098070|C80388|Pkcz|R74924|aPKCzeta|nPKC-zeta|zetaPKC	protein kinase C, zeta	protein-coding
mm_167418.1	chr8	110738560	110738577	+	1	NA	exon (NM_198625, exon 14 of 14)	exon (NM_198625, exon 14 of 14)	12842	NM_001310591	244654	Mm.490385	NM_198625	ENSMUSG00000033763	Mtss1l	ABBA	metastasis suppressor 1-like	protein-coding
mm_70891.1	chr8	25574063	25574074	+	1	NA	3' UTR (NM_010206, exon 18 of 18)	3' UTR (NM_010206, exon 18 of 18)	-17985	NR_110510	102633315	Mm.437828	NR_110510	ENSMUSG00000086134	Gm16159	OTTMUSG00000031030	predicted gene 16159	ncRNA
mm_49125.1	chr6	8527261	8527268	+	1	NA	intron (NM_001286728, intron 1 of 7)	Lx8|LINE|L1	7206	NM_001286729	170772	Mm.210787	NM_133236	ENSMUSG00000029638	Glcci1	2310047L21Rik|A130036A18Rik|Fam117c|Gig18|Tssn1	glucocorticoid induced transcript 1	protein-coding
mm_6564.1	chr1	75142361	75142424	-	1	NA	promoter-TSS (NM_026977)	promoter-TSS (NM_026977)	-24	NM_026977	69171	Mm.28193	NM_026977	ENSMUSG00000033159	Cnppd1	1810031K17Rik|AU043960	cyclin Pas1/PHO80 domain containing 1	protein-coding
mm_108804.1	chr12	91757269	91757274	+	1	NA	intron (NM_175367, intron 1 of 6)	PB1D10|SINE|Alu	29165	NM_175367	108800	Mm.23125	NM_175367	ENSMUSG00000020961	Ston2	4933401N24Rik|AI425999|AW544599	stonin 2	protein-coding
mm_104742.1	chr11	98438709	98438776	-	1	NA	exon (NM_025559, exon 2 of 4)	exon (NM_025559, exon 2 of 4)	246	NM_025559	103742	Mm.259614	NM_025559	ENSMUSG00000002580	Mien1	1810046J19Rik|AI463380|Rdx12	migration and invasion enhancer 1	protein-coding
mm_3413.1	chr1	144317892	144317894	+	1	NA	Intergenic	Intergenic	-68789	NM_015811	50778	Mm.103701	NM_015811	ENSMUSG00000026358	Rgs1	BL34	regulator of G-protein signaling 1	protein-coding
mm_49399.1	chr6	28426234	28426265	+	1	NA	3' UTR (NM_007480, exon 6 of 6)	3' UTR (NM_007480, exon 6 of 6)	-1652	NM_019569	56223	Mm.31708	NM_019569	ENSMUSG00000029707	Fscn3	-	fascin actin-bundling protein 3	protein-coding
mm_83802.1	chr9	53248052	53248062	-	1	NA	promoter-TSS (NM_029936)	promoter-TSS (NM_029936)	55	NM_029936	77591	Mm.133560	NM_029936	ENSMUSG00000053289	Ddx10	4632415A01Rik|AI646054	DEAD (Asp-Glu-Ala-Asp) box polypeptide 10	protein-coding
mm_16698.1	chr2	6885256	6885268	-	1	NA	promoter-TSS (NM_001110228)	promoter-TSS (NM_001110228)	-266	NM_001160293	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_14992.1	chr2	152293864	152293884	+	1	NA	promoter-TSS (NM_024196)	promoter-TSS (NM_024196)	2	NM_024196	67231	Mm.288733	NM_024196	ENSMUSG00000027465	Tbc1d20	1110028I04Rik|2810442O16Rik|AI414693|bs	TBC1 domain family, member 20	protein-coding
mm_126171.1	chr15	78561413	78561436	+	1	NA	3' UTR (NM_009008, exon 7 of 7)	3' UTR (NM_009008, exon 7 of 7)	11359	NM_009008	19354	Mm.1972	NM_009008	ENSMUSG00000033220	Rac2	AI323801|AI452260	RAS-related C3 botulinum substrate 2	protein-coding
mm_138111.1	chr17	34122816	34122883	+	1	NA	promoter-TSS (NM_001204973)	promoter-TSS (NM_001204973)	17	NM_010386	14998	Mm.16373	NM_010386	ENSMUSG00000037649	H2-DMa	H-2Ma|H2-Ma	histocompatibility 2, class II, locus DMa	protein-coding
mm_97260.1	chr11	75759340	75759397	+	1	NA	exon (NM_009536, exon 5 of 6)	exon (NM_009536, exon 5 of 6)	26481	NM_009536	22627	Mm.234700	NM_009536	ENSMUSG00000020849	Ywhae	AU019196	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide	protein-coding
mm_135800.1	chr16	57231365	57231405	-	1	NA	promoter-TSS (NM_026254)	promoter-TSS (NM_026254)	81	NM_026254	67581	Mm.257819	NM_026254	ENSMUSG00000022749	Tbc1d23	4930451A13Rik|AU015720|AU043671|AU043778|D030022P07Rik|W51689	TBC1 domain family, member 23	protein-coding
mm_56954.1	chr6	120002312	120002324	-	1	NA	exon (NM_001185020, exon 2 of 26)	exon (NM_001185020, exon 2 of 26)	31993	NR_030487	735290		NR_030487	ENSMUSG00000076217	Mir706	Mirn706|mir-706|mmu-mir-706	microRNA 706	ncRNA
mm_34833.1	chr4	155249961	155250010	+	1	NA	promoter-TSS (NM_001190445)	promoter-TSS (NM_001190445)	19	NR_033802	67513	Mm.10374	NM_001190445	ENSMUSG00000073684	Faap20	2610002J02Rik	Fanconi anemia core complex associated protein 20	protein-coding
mm_149248.1	chr19	10389069	10389084	+	1	NA	promoter-TSS (NM_018801)	promoter-TSS (NM_018801)	-14	NM_018801	54525	Mm.182654	NM_018801	ENSMUSG00000024743	Syt7	AI851541|B230112P13Rik	synaptotagmin VII	protein-coding
mm_76872.1	chr8	105549622	105549640	-	1	NA	intron (NM_013477, intron 1 of 7)	intron (NM_013477, intron 1 of 7)	16409	NM_013477	11972	Mm.17708	NM_013477	ENSMUSG00000013160	Atp6v0d1	AI267038|Ac39|Atp6d|P39|VATX|Vma6	ATPase, H+ transporting, lysosomal V0 subunit D1	protein-coding
mm_25604.1	chr3	117575229	117575239	+	1	NA	promoter-TSS (NM_029425)	promoter-TSS (NM_029425)	7	NM_001305451	75769	Mm.72187	NM_029425	ENSMUSG00000033342	Plppr5	4833424O15Rik|Lppr5|PRG-5|Pap2d	phospholipid phosphatase related 5	protein-coding
mm_168060.1	chr10	100212603	100212607	+	1	NA	Intergenic	Intergenic	-123071	NM_001166636	100043247	Mm.478257	NM_001166636	ENSMUSG00000096640	Gm4312	-	predicted gene 4312	protein-coding
mm_86596.1	chr10	13130594	13130639	+	1	NA	3' UTR (NM_009538, exon 6 of 6)	3' UTR (NM_009538, exon 6 of 6)	39771	NR_131912	338438		NR_131912		Hymai	-	hydatidiform mole associated and imprinted transcript	ncRNA
mm_122584.1	chr14	50851141	50851157	-	1	NA	intron (NM_009351, intron 15 of 54)	B1_Mur2|SINE|Alu	19405	NM_009351	21745	Mm.318736	NM_009351	ENSMUSG00000006281	Tep1	Tp1	telomerase associated protein 1	protein-coding
mm_168029.1	chrY	90738464	90738496	+	1	NA	Intergenic	IMPB_01|Satellite|Satellite	16570	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_164508.1	chr16	93730115	93730145	+	1	NA	intron (NM_027293, intron 2 of 36)	intron (NM_027293, intron 2 of 36)	18223	NM_027293	70028	Mm.23230	NM_026700	ENSMUSG00000022946	Dopey2	0610038M01Rik|2610510B01Rik|AI503246|C21orf5|mKIAA0933	dopey family member 2	protein-coding
mm_111539.1	chr12	100887926	100887936	-	1	NA	5' UTR (NM_175493, exon 2 of 3)	5' UTR (NM_175493, exon 2 of 3)	11593	NM_001177674	238377	Mm.32160	NM_175493	ENSMUSG00000047415	Gpr68	BB131428|Ogr1	G protein-coupled receptor 68	protein-coding
mm_164258.1	chr15	100084212	100084248	+	1	NA	intron (NR_037311, intron 3 of 3)	intron (NR_037311, intron 3 of 3)	45566	NM_001159361	239667	Mm.243658	NM_172819	ENSMUSG00000023026	Dip2b	4932422C22|AI317237|AI854602|mKIAA1463	disco interacting protein 2 homolog B	protein-coding
mm_32863.1	chr4	118426896	118426898	+	1	NA	Intergenic	Intergenic	-1196	NM_001039175	54325	Mm.282096	NM_019422	ENSMUSG00000006390	Elovl1	AA407424|BB151133|Ssc1	elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 1	protein-coding
mm_81191.1	chr9	107551420	107551440	+	1	NA	promoter-TSS (NM_001243748)	promoter-TSS (NM_001243748)	-125	NM_001243748	56289	Mm.12091	NM_019713	ENSMUSG00000010067	Rassf1	123F2|AA536941|AU044980|NORE2A|RDA32|REH3P21|Rassf1A|Rassf1B|Rassf1C	Ras association (RalGDS/AF-6) domain family member 1	protein-coding
mm_169112.1	chr13	44870000	44870003	-	1	NA	intron (NM_001205044, intron 4 of 18)	LSU-rRNA_Hsa|rRNA|rRNA	132095	NM_025772	94245	Mm.352311	NM_025772	ENSMUSG00000057531	Dtnbp1	5430437B18Rik|AW048963|Bloc1s8|dysbindin|sdy	dystrobrevin binding protein 1	protein-coding
mm_152349.1	chr19	9984933	9984959	-	1	NA	TTS (NM_011913)	TTS (NM_011913)	2300	NM_010239	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
mm_161931.1	chr18	80986671	80986671	-	1	NA	promoter-TSS (NM_178280)	promoter-TSS (NM_178280)	-93	NM_178280	20689	Mm.215917	NM_178280	ENSMUSG00000024565	Sall3	B130022O04Rik|Msal|Msal-1|Sal|Salt|Spalt	sal-like 3 (Drosophila)	protein-coding
mm_42853.1	chr5	122210078	122210124	+	1	NA	promoter-TSS (NM_028752)	promoter-TSS (NM_028752)	-186	NM_028752	74096	Mm.28804	NM_028752	ENSMUSG00000064267	Hvcn1	0610039P13Rik|AI450555|BTS|HV1|Vsop.|mVSOP	hydrogen voltage-gated channel 1	protein-coding
mm_128629.1	chr15	59075974	59075978	-	1	NA	intron (NM_001146180, intron 1 of 13)	intron (NM_001146180, intron 1 of 13)	6050	NM_001146180	211401	Mm.215481	NM_144800	ENSMUSG00000022353	Mtss1	2310003N14Rik|BC024131|D130001D01Rik|Mim|mKIAA0429	metastasis suppressor 1	protein-coding
mm_128834.1	chr15	68337428	68337432	-	1	NA	promoter-TSS (NR_029534)	promoter-TSS (NR_029534)	80	NR_029534	387226		NR_029534	ENSMUSG00000065476	Mir30b	Mirn30b|mir-30b|mmu-mir-30b	microRNA 30b	ncRNA
mm_119294.1	chr14	34674153	34674205	+	1	NA	5' UTR (NM_001301330, exon 1 of 19)	5' UTR (NM_001301330, exon 1 of 19)	251	NM_001301330	218914	Mm.27957	NM_001004436	ENSMUSG00000041408	Wapl	A530089A20Rik|BC037674|DIF-2|FOE|Wapal	WAPL cohesin release factor	protein-coding
mm_38003.1	chr4	133720784	133720828	-	1	NA	exon (NM_001080819, exon 3 of 20)	exon (NM_001080819, exon 3 of 20)	-3698	NR_106086	102465707		NR_106086	ENSMUSG00000104566	Mir7227	mmu-mir-7227	microRNA 7227	ncRNA
mm_23859.1	chr3	83011347	83011364	+	1	NA	exon (NM_133862, exon 7 of 10)	exon (NM_133862, exon 7 of 10)	3631	NM_001317105	99571	Mm.16422	NM_133862	ENSMUSG00000033860	Fgg	3010002H13Rik|AI256424	fibrinogen gamma chain	protein-coding
mm_80772.1	chr9	95560434	95560448	+	1	NA	exon (NM_198414, exon 1 of 1)	exon (NM_198414, exon 1 of 1)	624	NM_198414	75552	Mm.151485	NM_198414	ENSMUSG00000064225	Paqr9	1700020G04Rik	progestin and adipoQ receptor family member IX	protein-coding
mm_160695.1	chr10	31414201	31414201	-	1	NA	5' UTR (NM_011509, exon 1 of 1)	5' UTR (NM_011509, exon 1 of 1)	234	NM_011509	100041294	Mm.7821	NM_011509		Supt4b	Gm3258|Supt4h1b|Supt4h2	suppressor of Ty 4B	protein-coding
mm_72215.1	chr8	72646729	72646781	+	1	NA	promoter-TSS (NM_176940)	promoter-TSS (NM_176940)	44	NM_176940	319555	Mm.212927	NM_176940	ENSMUSG00000048148	Nwd1	A230063L24Rik	NACHT and WD repeat domain containing 1	protein-coding
mm_35765.1	chr4	46138668	46138730	-	1	NA	promoter-TSS (NM_173033)	promoter-TSS (NM_173033)	188	NM_001033201	433702	Mm.389536	NM_001033201	ENSMUSG00000028330	Ncbp1	AU014645|AW538051|CBP80	nuclear cap binding protein subunit 1	protein-coding
mm_165124.1	chr2	5063619	5063626	+	1	NA	intron (NM_181848, intron 1 of 14)	intron (NM_181848, intron 1 of 14)	316	NM_181848	71648	Mm.116942	NM_181848	ENSMUSG00000026672	Optn	4930441O07Rik|FIP2|HYPL|NRP	optineurin	protein-coding
mm_120494.1	chr14	65980902	65980930	+	1	NA	exon (NM_013492, exon 8 of 9)	exon (NM_013492, exon 8 of 9)	12433	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_16935.1	chr2	14055964	14056022	-	1	NA	promoter-TSS (NM_013935)	promoter-TSS (NM_013935)	42	NM_001012396	30963	Mm.241205	NM_013935	ENSMUSG00000063275	Hacd1	Ptpla	3-hydroxyacyl-CoA dehydratase 1	protein-coding
mm_105583.1	chr11	106715060	106715073	-	1	NA	5' UTR (NM_008816, exon 1 of 15)	5' UTR (NM_008816, exon 1 of 15)	215	NM_001305158	18613	Mm.343951	NM_008816	ENSMUSG00000020717	Pecam1	C85791|Cd31|PECAM-1|Pecam	platelet/endothelial cell adhesion molecule 1	protein-coding
mm_17297.1	chr2	26294526	26294534	-	1	NA	promoter-TSS (NM_177841)	promoter-TSS (NM_177841)	27	NM_177841	329366	Mm.77712	NM_177841	ENSMUSG00000048038	Ccdc187	4932418E24Rik	coiled-coil domain containing 187	protein-coding
mm_58572.1	chr7	4793174	4793185	+	1	NA	intron (NM_009081, intron 1 of 4)	CpG	214	NM_009081	19943	Mm.379002	NM_009081	ENSMUSG00000030432	Rpl28	D7Wsu21e	ribosomal protein L28	protein-coding
mm_36038.1	chr4	57241123	57241139	-	1	NA	intron (NM_011207, intron 10 of 25)	intron (NM_011207, intron 10 of 25)	60706	NM_011207	545622	Mm.246552	NM_011207	ENSMUSG00000038764	Ptpn3	9530011I20Rik|PTP-H1|PTPCL	protein tyrosine phosphatase, non-receptor type 3	protein-coding
mm_28861.1	chr3	97242530	97242532	-	1	NA	Intergenic	Intergenic	-15167	NM_029933	77578	Mm.226175	NM_029933	ENSMUSG00000038256	Bcl9	2610202E01Rik|8030475K17Rik|A330041G23Rik|Gm130	B cell CLL/lymphoma 9	protein-coding
mm_69751.1	chr7	140956004	140956014	-	1	NA	promoter-TSS (NM_030694)	promoter-TSS (NM_030694)	-48	NM_030694	80876	Mm.379266	NM_030694	ENSMUSG00000060591	Ifitm2	DSPA2c|Ifitm3l|fragilis3|mil-3	interferon induced transmembrane protein 2	protein-coding
mm_1142.1	chr1	60705288	60705295	+	1	NA	Intergenic	(TTTTTG)n|Simple_repeat|Simple_repeat	-41097	NM_007642	12487	Mm.255003	NM_007642	ENSMUSG00000026012	Cd28	-	CD28 antigen	protein-coding
mm_78935.1	chr9	45117814	45117876	+	1	NA	promoter-TSS (NM_001014761)	promoter-TSS (NM_001014761)	-31	NM_001014761	72821	Mm.229373	NM_001014761	ENSMUSG00000070304	Scn2b	2810451E09Rik|AI840361|Gm183	sodium channel, voltage-gated, type II, beta	protein-coding
mm_135879.1	chr16	63864064	63864072	-	1	NA	promoter-TSS (NM_010140)	promoter-TSS (NM_010140)	89	NM_010140	13837	Mm.1977	NM_010140	ENSMUSG00000052504	Epha3	AW492086|Cek4|ETK1|End3|Hek|Hek4|Mek4|Tyro4	Eph receptor A3	protein-coding
mm_125789.1	chr15	74721239	74721260	+	1	NA	promoter-TSS (NM_198607)	promoter-TSS (NM_198607)	15	NM_198607	223626	Mm.268603	NM_198607	ENSMUSG00000056665	Them6	4930572J05Rik	thioesterase superfamily member 6	protein-coding
mm_95326.1	chr11	46727783	46727792	+	1	NA	Intergenic	Intergenic	-12436	NM_001166632	171283	Mm.17771	NM_134248	ENSMUSG00000040405	Havcr1	AI503787|KIM-1|TIM-1|Tim1|Timd1	hepatitis A virus cellular receptor 1	protein-coding
mm_34792.1	chr4	154506910	154506918	+	1	NA	intron (NM_001177995, intron 2 of 15)	intron (NM_001177995, intron 2 of 15)	129453	NR_045643	320939	Mm.436738	NR_045643		5930403L14Rik	-	RIKEN cDNA 5930403L14 gene	ncRNA
mm_125965.1	chr15	76274134	76274140	+	1	NA	intron (NM_028852, intron 1 of 4)	intron (NM_028852, intron 1 of 4)	-4298	NR_045747	100038659	Mm.448549	NR_045747		Mirt2	ENSMUSG00000075583|Gm10872|Gm24562	myocardial infraction associated transcript 2	ncRNA
mm_76482.1	chr8	85555262	85555315	-	1	NA	promoter-TSS (NM_019794)	promoter-TSS (NM_019794)	-17	NM_019794	56445	Mm.475573	NM_019794	ENSMUSG00000031701	Dnaja2	1500017M13Rik|2010206B19Rik|DNAJ|DNJ3|Dnaj3|HIRIP4|PRO3015|mDj3	DnaJ heat shock protein family (Hsp40) member A2	protein-coding
mm_155935.1	chrX	103630576	103630597	+	1	NA	promoter-TSS (NM_029158)	promoter-TSS (NM_029158)	0	NM_029158	75064	Mm.159414	NM_029158	ENSMUSG00000031330	Zcchc13	4930513O09Rik|Cnbp2	zinc finger, CCHC domain containing 13	protein-coding
mm_126037.1	chr15	76899963	76899973	+	1	NA	promoter-TSS (NM_025536)	promoter-TSS (NM_025536)	27	NM_025536	66398	Mm.291716	NM_025536	ENSMUSG00000055041	Commd5	2310065H03Rik|AI854466|D15Ertd81e|Hcarg	COMM domain containing 5	protein-coding
mm_162828.1	chr10	81378355	81378361	-	1	NA	promoter-TSS (NM_019757)	promoter-TSS (NM_019757)	12	NM_019757	56371	Mm.24202	NM_019757	ENSMUSG00000020235	Fzr1	AW108046|Cdh1|FZR|FZR2|Fyr|HCDH|HCDH1	fizzy/cell division cycle 20 related 1 (Drosophila)	protein-coding
mm_92050.1	chr10	62497908	62497931	-	1	NA	exon (NM_011157, exon 2 of 3)	exon (NM_011157, exon 2 of 3)	9836	NM_011157	19073	Mm.338790	NM_011157	ENSMUSG00000020077	Srgn	Prg|Prg1|Sgc	serglycin	protein-coding
mm_45661.1	chr5	77134531	77134534	-	1	NA	Intergenic	Intergenic	-19409	NM_175606	74318	Mm.181852	NM_175606	ENSMUSG00000059325	Hopx	1110018K11Rik|1200015P04Rik|2300002F06Rik|AI848177|AW490897|Cameo|Hdop|Hod|Hop|Ob1|Obl|Toto	HOP homeobox	protein-coding
mm_70243.1	chr8	3354658	3354668	+	1	NA	intron (NM_001033378, intron 1 of 10)	intron (NM_001033378, intron 1 of 10)	1248	NM_001033378	319493	Mm.234565	NM_001033378	ENSMUSG00000074497	A430078G23Rik	-	RIKEN cDNA A430078G23 gene	protein-coding
mm_148589.1	chr19	5068118	5068122	+	1	NA	promoter-TSS (NM_054042)	promoter-TSS (NM_054042)	42	NM_054042	70445	Mm.29597	NM_054042	ENSMUSG00000056481	Cd248	2610111G01Rik|AI842296|Cd164l1|Tem1	CD248 antigen, endosialin	protein-coding
mm_11603.1	chr2	33805808	33805819	+	1	NA	promoter-TSS (NR_045729)	promoter-TSS (NR_045729)	-3	NR_045729	320482	Mm.442057	NR_045729	ENSMUSG00000086484	Nron	A630071L07Rik|Gm24353	non-protein coding RNA, repressor of NFAT	ncRNA
mm_152864.1	chr19	24224949	24224966	-	1	NA	promoter-TSS (NM_011597)	promoter-TSS (NM_011597)	69	NM_011597	21873	Mm.104744	NM_011597	ENSMUSG00000024812	Tjp2	ZO-2	tight junction protein 2	protein-coding
mm_45526.1	chr5	72642726	72642749	-	1	NA	promoter-TSS (NM_007723)	promoter-TSS (NM_007723)	15	NM_007723	12788	Mm.436652	NM_007723	ENSMUSG00000067220	Cnga1	Cncg	cyclic nucleotide gated channel alpha 1	protein-coding
mm_149438.1	chr19	11478245	11478260	+	1	NA	exon (NM_028595, exon 5 of 7)	exon (NM_028595, exon 5 of 7)	8884	NM_028595	73656	Mm.440719	NM_028595	ENSMUSG00000079419	Ms4a6c	2200009H22Rik|2210417N07Rik	membrane-spanning 4-domains, subfamily A, member 6C	protein-coding
mm_45410.1	chr5	66323729	66323748	-	1	NA	intron (NM_001310626, intron 10 of 15)	intron (NM_001310626, intron 10 of 15)	13927	NM_001201416	11787	Mm.5159	NM_009686	ENSMUSG00000029207	Apbb2	2310007D03Rik|FE65L1|Rirl1|TR2L|Zfra	amyloid beta (A4) precursor protein-binding, family B, member 2	protein-coding
mm_126553.1	chr15	82146277	82146282	+	1	NA	promoter-TSS (NM_033218)	promoter-TSS (NM_033218)	-990	NM_033218	20788	Mm.9002	NM_033218	ENSMUSG00000022463	Srebf2	AI608257|SREBP-2|SREBP2|SREBP2gc|bHLHd2|lop13|nuc	sterol regulatory element binding factor 2	protein-coding
mm_158148.1	chrX	103468914	103468927	-	1	NA	non-coding (NR_001570, exon 6 of 8)	non-coding (NR_001570, exon 6 of 8)	14313	NR_001570	213742	Mm.274770	NR_001463	ENSMUSG00000086503	Xist	A430022B11|AI314753	inactive X specific transcripts	ncRNA
mm_141279.1	chr17	27826925	27826958	-	1	NA	Intergenic	PB1D9|SINE|Alu	-6399	NM_001271511	224647	Mm.196577	NM_001033279	ENSMUSG00000056692	D17Wsu92e	AU020189|C030010A15|C80239	DNA segment, Chr 17, Wayne State University 92, expressed	protein-coding
mm_5514.1	chr1	37540981	37540992	-	1	NA	promoter-TSS (NM_173870)	promoter-TSS (NM_173870)	30	NM_173870	269181	Mm.25861	NM_173870	ENSMUSG00000026110	Mgat4a	9530018I07Rik|GnT-IVa|glcNAc-T-IVa	mannoside acetylglucosaminyltransferase 4, isoenzyme A	protein-coding
mm_80057.1	chr9	69364370	69364393	+	1	NA	promoter-TSS (NR_136934)	promoter-TSS (NR_136934)	-134	NR_136934	102642202	Mm.415363	NR_136934	ENSMUSG00000086648	Gm15511	OTTMUSG00000023029	predicted gene 15511	ncRNA
mm_68069.1	chr7	101868673	101868700	-	1	NA	intron (NM_001252552, intron 2 of 6)	intron (NM_001252552, intron 2 of 6)	2102	NM_001252554	14275	Mm.2135	NM_008034	ENSMUSG00000001827	Folr1	FBP1|Folbp-1|Folbp1	folate receptor 1 (adult)	protein-coding
mm_60361.1	chr7	44428939	44428979	+	1	NA	Intergenic	CpG	-13528	NM_198250	272381	Mm.44173	NM_198250	ENSMUSG00000047085	Lrrc4b	A830007M12|Lrig4	leucine rich repeat containing 4B	protein-coding
mm_92855.1	chr10	81524409	81524409	-	1	NA	promoter-TSS (NM_010304)	promoter-TSS (NM_010304)	-184	NM_010304	14676	Mm.1546	NM_010304	ENSMUSG00000034792	Gna15	G[a]15|Galpha15	guanine nucleotide binding protein, alpha 15	protein-coding
mm_86113.1	chr9	115458293	115458297	-	1	NA	Intergenic	Intergenic	76476	NR_130329	100316675		NR_130329	ENSMUSG00000080409	Mir467h	Mirn467h|mmu-mir-467h	microRNA 467h	ncRNA
mm_95523.1	chr11	52224316	52224356	+	1	NA	Intergenic	RLTR26C_MM|LTR|ERVK	-7659	NM_011543	21402	Mm.42944	NM_011543	ENSMUSG00000036309	Skp1a	15kDa|2610043E24Rik|2610206H23Rik|EMC19|OCP-II|OCP2|SKP1|Tceb1l|p19A|p19Skp1	S-phase kinase-associated protein 1A	protein-coding
mm_140245.1	chr17	84181617	84181654	+	1	NA	Intergenic	Intergenic	6312	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_143744.1	chr17	81513059	81513071	-	1	NA	intron (NR_104580, intron 2 of 8)	intron (NR_104580, intron 2 of 8)	225322	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_118671.1	chr14	22019810	22019832	+	1	NA	5' UTR (NM_028275, exon 1 of 7)	5' UTR (NM_028275, exon 1 of 7)	109	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_145802.1	chr18	65375671	65375710	+	1	NA	intron (NM_001037294, intron 2 of 12)	intron (NM_001037294, intron 2 of 12)	18198	NM_001037294	225638	Mm.296528	NM_001037294	ENSMUSG00000032845	Alpk2	Gm549|Hak	alpha-kinase 2	protein-coding
mm_96547.1	chr11	68853396	68853402	+	1	NA	promoter-TSS (NM_023668)	promoter-TSS (NM_023668)	-268	NM_023668	83431	Mm.31979	NM_023668	ENSMUSG00000018736	Ndel1	2600006O07Rik|MITAP1|NUDEL|mNudel	nudE neurodevelopment protein 1 like 1	protein-coding
mm_36593.1	chr4	88522843	88522847	-	1	NA	promoter-TSS (NM_010510)	promoter-TSS (NM_010510)	-51	NM_010510	15977	Mm.1245	NM_010510	ENSMUSG00000048806	Ifnb1	IFN-beta|IFNB|Ifb	interferon beta 1, fibroblast	protein-coding
mm_15028.1	chr2	152687179	152687200	+	1	NA	promoter-TSS (NM_025543)	promoter-TSS (NM_025543)	41	NM_025543	66405	Mm.440291	NM_025543	ENSMUSG00000042814	Mcts2	2400002F11Rik|MCT-2	malignant T cell amplified sequence 2	protein-coding
mm_126514.1	chr15	81815104	81815132	+	1	NA	exon (NM_153484, exon 2 of 4)	exon (NM_153484, exon 2 of 4)	3704	NM_017376	21685	Mm.270278	NM_017376	ENSMUSG00000022389	Tef	2310028D20Rik	thyrotroph embryonic factor	protein-coding
mm_92268.1	chr10	71159575	71159581	-	1	NA	exon (NM_001347189, exon 1 of 22)	exon (NM_001347189, exon 1 of 22)	112	NM_031397	83675	Mm.286834	NM_031397	ENSMUSG00000014329	Bicc1	Bic-C|bpk|jcpk	BicC family RNA binding protein 1	protein-coding
mm_79869.1	chr9	65101305	65101342	+	1	NA	promoter-TSS (NM_020043)	promoter-TSS (NM_020043)	-163	NM_001290315	56741	Mm.209041	NM_020043	ENSMUSG00000032816	Igdcc4	DDM36|Nope	immunoglobulin superfamily, DCC subclass, member 4	protein-coding
mm_162126.1	chrX	72916864	72916864	-	1	NA	intron (NM_019405, intron 1 of 4)	intron (NM_019405, intron 1 of 4)	1480	NM_019405	26370	Mm.24643	NM_019405	ENSMUSG00000031347	Cetn2	1110034A02Rik|AI326150|Calt|caltractin	centrin 2	protein-coding
mm_33708.1	chr4	133751838	133751848	+	1	NA	intron (NM_001080819, intron 1 of 19)	intron (NM_001080819, intron 1 of 19)	1768	NM_001080819	93760	Mm.22478	NM_001080819	ENSMUSG00000007880	Arid1a	1110030E03Rik|BAF250a|Osa1|Smarcf1	AT rich interactive domain 1A (SWI-like)	protein-coding
mm_126180.1	chr15	78602771	78602787	+	1	NA	intron (NM_028195, intron 2 of 12)	intron (NM_028195, intron 2 of 12)	5732	NM_028195	72318	Mm.32911	NM_028195	ENSMUSG00000018008	Cyth4	2510004M07Rik|5830469K17Rik|AI467541|Pscd4|mFLJ00017	cytohesin 4	protein-coding
mm_85770.1	chr9	109039151	109039178	-	1	NA	intron (NM_025858, intron 1 of 5)	intron (NM_025858, intron 1 of 5)	597	NM_001284332	66940	Mm.196533	NM_025858	ENSMUSG00000025647	Shisa5	2310008D10Rik|6430628I05Rik|Scotin|mShisa5	shisa family member 5	protein-coding
mm_85352.1	chr9	103211864	103211870	-	1	NA	exon (NM_133977, exon 15 of 17)	exon (NM_133977, exon 15 of 17)	-9802	NM_009275	20818	Mm.273053	NM_009275	ENSMUSG00000032553	Srprb	AA409543	signal recognition particle receptor, B subunit	protein-coding
mm_121457.1	chr14	120480858	120480860	+	1	NA	intron (NM_029519, intron 1 of 1)	B1_Mur4|SINE|Alu	2398	NM_029519	76108	Mm.261448	NM_029519	ENSMUSG00000051615	Rap2a	5830461H18Rik	RAS related protein 2a	protein-coding
mm_60818.1	chr7	45705186	45705292	+	1	NA	promoter-TSS (NM_016974)	promoter-TSS (NM_016974)	-8	NM_016974	13170	Mm.24222	NM_016974	ENSMUSG00000059824	Dbp	-	D site albumin promoter binding protein	protein-coding
mm_29861.1	chr3	130060811	130060826	-	1	NA	promoter-TSS (NM_207209)	promoter-TSS (NM_207209)	89	NM_207209	99683	Mm.192303	NM_207209	ENSMUSG00000001052	Sec24b	AI605202|SEC24	Sec24 related gene family, member B (S. cerevisiae)	protein-coding
mm_129575.1	chr15	79734366	79734401	-	1	NA	intron (NM_001205346, intron 7 of 17)	intron (NM_001205346, intron 7 of 17)	8153	NM_194342	223697	Mm.202715	NM_194342	ENSMUSG00000042524	Sun2	B230369L08Rik|C030011B15|Unc84b	Sad1 and UNC84 domain containing 2	protein-coding
mm_2591.1	chr1	119305587	119305632	+	1	NA	Intergenic	Intergenic	116639	NM_008381	16324	Mm.3092	NM_008381	ENSMUSG00000037035	Inhbb	-	inhibin beta-B	protein-coding
mm_155914.1	chrX	102004869	102004879	+	1	NA	intron (NM_001163610, intron 1 of 7)	RLTR51A_Mm|LTR|ERVK?	66433	NM_001278534	331474	Mm.23297	NM_183318	ENSMUSG00000049191	Rgag4	6430402L03Rik|Mar5|Mart5|mKIAA2001	retrotransposon gag domain containing 4	protein-coding
mm_125917.1	chr15	76150279	76150279	+	1	NA	Intergenic	L1MB7|LINE|L1	-23723	NM_001142968	271278	Mm.205253	NM_198172	ENSMUSG00000044361	BC024139	6230424I18Rik	cDNA sequence BC024139	protein-coding
mm_172360.1	chr7	11805515	11805526	-	1	NA	Intergenic	IAP1-MM_LTR|LTR|ERVK	-41255	NM_134206	171240	Mm.377196	NM_134206	ENSMUSG00000047655	Vmn1r74	V1rg5	vomeronasal 1 receptor 74	protein-coding
mm_51242.1	chr6	71545234	71545240	+	1	NA	intron (NM_025783, intron 1 of 5)	intron (NM_025783, intron 1 of 5)	1383	NM_025783	66700	Mm.181278	NM_025783	ENSMUSG00000053119	Chmp3	25.1|4921505F14Rik|9130011K15Rik|CGI-49|D6Ertd286e|NEDF|Vps24	charged multivesicular body protein 3	protein-coding
mm_41985.1	chr5	107597761	107597784	+	1	NA	promoter-TSS (NM_133248)	promoter-TSS (NM_133248)	76	NM_001289569	231571	Mm.482420	NM_144911	ENSMUSG00000033773	Rpap2	AW060207	RNA polymerase II associated protein 2	protein-coding
mm_30629.1	chr4	8785544	8785550	+	1	NA	exon (NM_001277149, exon 3 of 38)	exon (NM_001277149, exon 3 of 38)	95141	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_854.1	chr1	52119897	52119935	+	1	NA	5' UTR (NM_001205314, exon 2 of 25)	5' UTR (NM_001205314, exon 2 of 25)	294	NM_001205313	20846	Mm.277406	NM_009283	ENSMUSG00000026104	Stat1	2010005J02Rik|AA408197	signal transducer and activator of transcription 1	protein-coding
mm_151354.1	chr19	55898597	55898606	+	1	NA	intron (NM_001142924, intron 1 of 11)	intron (NM_001142924, intron 1 of 11)	3280	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_35219.1	chr4	19656198	19656207	-	1	NA	intron (NR_074090, intron 8 of 24)	intron (NR_074090, intron 8 of 24)	52802	NM_177327	107568	Mm.78312	NM_177327	ENSMUSG00000041058	Wwp1	8030445B08Rik|AIP5|SDRP1|Tiul1	WW domain containing E3 ubiquitin protein ligase 1	protein-coding
mm_146984.1	chr18	33891629	33891666	-	1	NA	intron (NM_013512, intron 3 of 23)	intron (NM_013512, intron 3 of 23)	96755	NR_038151	69749	Mm.248787	NR_038151	ENSMUSG00000087590	Epb41l4aos	2410004N09Rik|Epb4.1l4aos	erythrocyte membrane protein band 4.1 like 4a, opposite strand	ncRNA
mm_162262.1	chrY	2720728	2720728	-	1	NA	promoter-TSS (NM_001113395)	promoter-TSS (NM_001113395)	-54	NM_001177569	547210	Mm.472681	NM_001177569	ENSMUSG00000094881	H2al2c	Gm6026|H2al2y	H2A histone family member L2C	protein-coding
mm_31746.1	chr4	63344520	63344533	+	1	NA	promoter-TSS (NM_008768)	promoter-TSS (NM_008768)	-30	NM_008768	18405	Mm.4777	NM_008768	ENSMUSG00000039196	Orm1	Agp-1|Agp-2|Orm-1	orosomucoid 1	protein-coding
mm_60254.1	chr7	43791942	43791949	+	1	NA	promoter-TSS (NM_028660)	promoter-TSS (NM_028660)	54	NM_028660	101533	Mm.19942	NM_028660	ENSMUSG00000047884	Klk9	1200016C12Rik|AI324041	kallikrein related-peptidase 9	protein-coding
mm_171823.1	chr5	142694063	142694076	+	1	NA	Intergenic	(T)n|Simple_repeat|Simple_repeat	-8032	NM_146257	243328	Mm.125942	NM_146257	ENSMUSG00000050822	Slc29a4	ENT4|mPMAT	solute carrier family 29 (nucleoside transporters), member 4	protein-coding
mm_117143.1	chr13	61005919	61005930	-	1	NA	promoter-TSS (NM_012007)	promoter-TSS (NM_012007)	-13	NM_012007	26898	Mm.31948	NM_012007	ENSMUSG00000055298	Ctsj	CATP|CatRLP|Ctsp	cathepsin J	protein-coding
mm_165125.1	chr2	5137736	5137740	+	1	NA	promoter-TSS (NM_028804)	promoter-TSS (NM_028804)	-38	NM_028804	74186	Mm.274715	NM_028804	ENSMUSG00000026676	Ccdc3	2310045O21Rik	coiled-coil domain containing 3	protein-coding
mm_137951.1	chr17	32891782	32891797	+	1	NA	promoter-TSS (NM_207245)	promoter-TSS (NM_207245)	-186	NM_207245	240066	Mm.26636	NM_207245	ENSMUSG00000095325	Zfp870	AI173952	zinc finger protein 870	protein-coding
mm_80340.1	chr9	75071528	75071569	+	1	NA	5' UTR (NM_010864, exon 1 of 41)	5' UTR (NM_010864, exon 1 of 41)	342	NM_010864	17918	Mm.3645	NM_010864	ENSMUSG00000034593	Myo5a	9630007J19Rik|AI413174|AI661011|Dbv|MVa|Myo5|MyoVA|Sev-1|d|d-120J|flail|flr	myosin VA	protein-coding
mm_149774.1	chr19	23090939	23090945	+	1	NA	Intergenic	B1F2|SINE|Alu	-50284	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_7901.1	chr1	133655160	133655169	-	1	NA	TTS (NM_001166552)	TTS (NM_001166552)	5721	NM_001166552	667118	Mm.245357	NM_001166552	ENSMUSG00000094410	Zbed6	Gm8466|MGR	zinc finger, BED type containing 6	protein-coding
mm_83598.1	chr9	48494436	48494457	-	1	NA	promoter-TSS (NM_001004191)	promoter-TSS (NM_001004191)	884	NM_001326355	67010	Mm.76911	NM_144948	ENSMUSG00000042396	Rbm7	1200007M24Rik|1500011D06Rik|AU041934|AW554393	RNA binding motif protein 7	protein-coding
mm_14647.1	chr2	136910178	136910188	+	1	NA	intron (NM_001038641, intron 2 of 7)	intron (NM_001038641, intron 2 of 7)	10832	NM_001038641	74243	Mm.330612	NM_028201	ENSMUSG00000027281	Slx4ip	2210009G21Rik|2410004I22Rik|C85661|Slxip	SLX4 interacting protein	protein-coding
mm_100419.1	chr11	119436730	119436749	+	1	NA	Intergenic	Intergenic	46267	NR_035453	100316690		NR_035453	ENSMUSG00000088015	Mir1932	mir-1932|mmu-mir-1932	microRNA 1932	ncRNA
mm_64848.1	chr7	13033953	13033965	-	1	NA	exon (NM_026885, exon 2 of 6)	exon (NM_026885, exon 2 of 6)	818	NM_026885	68953	Mm.295670	NM_026885	ENSMUSG00000033916	Chmp2a	1500016L11Rik	charged multivesicular body protein 2A	protein-coding
mm_81562.1	chr9	110415510	110415532	+	1	NA	Intergenic	Intergenic	-4287	NM_008694	18054	Mm.236225	NM_008694	ENSMUSG00000032484	Ngp	bectenecin	neutrophilic granule protein	protein-coding
mm_123852.1	chr14	70777854	70777860	-	1	NA	exon (NM_010071, exon 5 of 5)	exon (NM_010071, exon 5 of 5)	3476	NM_010071	13449	Mm.243323	NM_010071	ENSMUSG00000022102	Dok2	DokR|Frip	docking protein 2	protein-coding
mm_89337.1	chr10	87934008	87934045	+	1	NA	3' UTR (NM_010512, exon 5 of 5)	3' UTR (NM_010512, exon 5 of 5)	-32645	NR_000040	22172	Mm.391420	NR_000040		Tyms-ps	-	thymidylate synthase, pseudogene	pseudo
mm_53993.1	chr6	6881929	6881949	-	1	NA	5' UTR (NM_010056, exon 1 of 3)	5' UTR (NM_010056, exon 1 of 3)	129	NM_198854	13395	Mm.4873	NM_010056	ENSMUSG00000029755	Dlx5	AI385752	distal-less homeobox 5	protein-coding
mm_101021.1	chr11	8575656	8575666	-	1	NA	intron (NM_001083587, intron 4 of 30)	intron (NM_001083587, intron 4 of 30)	88874	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_168619.1	chr11	78094666	78094666	+	1	NA	promoter-TSS (NM_145430)	promoter-TSS (NM_145430)	-1	NM_001346762	216971	Mm.119387	NM_145430	ENSMUSG00000037750	Fam222b	9630020I17Rik	family with sequence similarity 222, member B	protein-coding
mm_33633.1	chr4	132918147	132918151	+	1	NA	intron (NM_001163792, intron 2 of 7)	intron (NM_001163792, intron 2 of 7)	4402	NM_145553	230789	Mm.11473	NM_145553	ENSMUSG00000028878	Fam76a	-	family with sequence similarity 76, member A	protein-coding
mm_154976.1	chrX	37826956	37826962	+	1	NA	promoter-TSS (NM_008955)	promoter-TSS (NM_008955)	-96	NM_008955	19202	Mm.10105	NM_008955	ENSMUSG00000006200	Rhox6	AV213605|AW548842|Psx1	reproductive homeobox 6	protein-coding
mm_84632.1	chr9	70934599	70934624	-	1	NA	5' UTR (NM_008280, exon 1 of 9)	5' UTR (NM_008280, exon 1 of 9)	197	NM_008280	15450	Mm.390187	NM_008280	ENSMUSG00000032207	Lipc	AI256194|HL|Hpl	lipase, hepatic	protein-coding
mm_78130.1	chr9	20867113	20867135	+	1	NA	Intergenic	L1MA5|LINE|L1	-1518	NM_175687	319278	Mm.249932	NM_175687	ENSMUSG00000038884	A230050P20Rik	RyDEN	RIKEN cDNA A230050P20 gene	protein-coding
mm_118898.1	chr14	26638238	26638249	+	1	NA	promoter-TSS (NM_007479)	promoter-TSS (NM_007479)	46	NM_007479	11843	Mm.297768	NM_007479	ENSMUSG00000021877	Arf4	AA407803	ADP-ribosylation factor 4	protein-coding
mm_14876.1	chr2	148799950	148799967	+	1	NA	5' UTR (NM_009978, exon 2 of 4)	5' UTR (NM_009978, exon 2 of 4)	1119	NM_009978	13012	Mm.20435	NM_009978	ENSMUSG00000027442	Cst8	Cres|Cst-rs1	cystatin 8 (cystatin-related epididymal spermatogenic)	protein-coding
mm_153812.1	chr19	46045390	46045400	-	1	NA	promoter-TSS (NM_001113408)	promoter-TSS (NM_001113408)	-184	NM_001113408	16825	Mm.327442	NM_010697	ENSMUSG00000025223	Ldb1	CLIM2|NLI	LIM domain binding 1	protein-coding
mm_106252.1	chr11	117825785	117825872	-	1	NA	promoter-TSS (NM_027827)	promoter-TSS (NM_027827)	-91	NM_027827	71562	Mm.273958	NM_027827	ENSMUSG00000017718	Afmid	9030621K19Rik|Ammd|FKF|KFA|Kf|formylase	arylformamidase	protein-coding
mm_53650.1	chr6	140776867	140776870	+	1	NA	Intergenic	Intergenic	149983	NM_001309436	11569	Mm.86453	NM_009637	ENSMUSG00000030232	Aebp2	AU023766|B230313N05Rik	AE binding protein 2	protein-coding
mm_100588.1	chr11	120949517	120949519	+	1	NA	intron (NM_001038654, intron 1 of 4)	CpG	451	NM_001038654	80879	Mm.28632	NM_030696	ENSMUSG00000025161	Slc16a3	Mct3|Mct4	solute carrier family 16 (monocarboxylic acid transporters), member 3	protein-coding
mm_114053.1	chr13	54346642	54346645	+	1	NA	Intergenic	Intergenic	-24706	NM_009946	12890	Mm.268902	NM_009946	ENSMUSG00000025867	Cplx2	921-L|AI413745|AW492120	complexin 2	protein-coding
mm_76698.1	chr8	94194806	94194811	-	1	NA	Intergenic	Intergenic	15719	NM_013602	17748	Mm.192991	NM_013602	ENSMUSG00000031765	Mt1	MT-I|Mt-1	metallothionein 1	protein-coding
mm_98860.1	chr11	97685904	97685966	+	1	NA	promoter-TSS (NM_001085500)	promoter-TSS (NM_001085500)	-17	NM_001085500	217149	Mm.29659	NM_001085500	ENSMUSG00000078695	Cisd3	Mel-13|Mel13	CDGSH iron sulfur domain 3	protein-coding
mm_98147.1	chr11	87592146	87592229	+	1	NA	promoter-TSS (NM_133215)	promoter-TSS (NM_133215)	-30	NM_133215	170749	Mm.399376	NM_133215	ENSMUSG00000018401	Mtmr4	AA596759|ESTM44|FYVE-DSP2|ZFYVE11|mKIAA0647	myotubularin related protein 4	protein-coding
mm_39760.1	chr5	29936388	29936395	+	1	NA	intron (NR_105781, intron 1 of 2)	RLTR48A|LTR|ERV1	-76723	NM_001314054	16193	Mm.1019	NM_031168	ENSMUSG00000025746	Il6	Il-6	interleukin 6	protein-coding
mm_74980.1	chr8	27141607	27141623	-	1	NA	3' UTR (NM_001080813, exon 6 of 6)	3' UTR (NM_001080813, exon 6 of 6)	-1295	NR_045840	71082	Mm.395259	NR_045840		4933416M07Rik	-	RIKEN cDNA 4933416M07 gene	ncRNA
mm_141692.1	chr17	33975518	33975537	-	1	NA	non-coding (NR_004446, exon 5 of 6)	non-coding (NR_004446, exon 5 of 6)	3264	NR_004446	630499	Mm.440940	NM_001081015		H2-K2	EG630499|Gm7035|H-2K1|H-2K1K|H-2K2|H2-K1	histocompatibility 2, K region locus 2	pseudo
mm_100715.1	chr11	3863870	3863886	-	1	NA	promoter-TSS (NM_152818)	promoter-TSS (NM_152818)	25	NM_152818	74309	Mm.61022	NM_152818	ENSMUSG00000020435	Osbp2	1700095P05Rik|C630001G20Rik|Gm244|ORP-4|OSBPL1	oxysterol binding protein 2	protein-coding
mm_168624.1	chr1	179971750	179971750	+	1	NA	intron (NM_001346805, intron 1 of 34)	B1F1|SINE|Alu	10661	NM_001033285	226751	Mm.259655	NM_001033285	ENSMUSG00000026490	Cdc42bpa	A930014J19Rik|DMPK-like	CDC42 binding protein kinase alpha	protein-coding
mm_166523.1	chr6	24597905	24597915	+	1	NA	exon (NM_053098, exon 1 of 3)	exon (NM_053098, exon 1 of 3)	139	NM_053098	93677	Mm.332941	NM_053098	ENSMUSG00000029683	Lmod2	C-Lmod	leiomodin 2 (cardiac)	protein-coding
mm_15736.1	chr2	164237215	164237218	+	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	1125	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_126896.1	chr15	89500070	89500108	+	1	NA	intron (NM_021423, intron 1 of 21)	CpG-5250	232	NM_021423	58234	Mm.146855	NM_021423	ENSMUSG00000022623	Shank3	AI841104|SHANK3c-3|SHANK3c-4|Shank3b	SH3/ankyrin domain gene 3	protein-coding
mm_169232.1	chr13	68235815	68235831	-	1	NA	Intergenic	Intergenic	346281	NM_001308475	210009	Mm.205514	NM_172480	ENSMUSG00000034617	Mtrr	4732420G08|MSR	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	protein-coding
mm_70974.1	chr8	27143148	27143158	+	1	NA	non-coding (NR_045840, exon 1 of 4)	non-coding (NR_045840, exon 1 of 4)	243	NR_045840	71082	Mm.395259	NR_045840		4933416M07Rik	-	RIKEN cDNA 4933416M07 gene	ncRNA
mm_131624.1	chr16	20097604	20097615	+	1	NA	promoter-TSS (NM_029436)	promoter-TSS (NM_029436)	55	NM_029436	75785	Mm.392450	NM_029436	ENSMUSG00000062901	Klhl24	1110046J11Rik|4930429H24Rik|6530402O20Rik|C85082	kelch-like 24	protein-coding
mm_87508.1	chr10	52417533	52417580	+	1	NA	promoter-TSS (NM_030250)	promoter-TSS (NM_030250)	9	NM_030250	52014	Mm.199964	NM_030250	ENSMUSG00000023068	Nus1	1600027K07Rik|AU019165|AW538011|BC003223|D10Ertd438e	NUS1 dehydrodolichyl diphosphate synthase subunit	protein-coding
mm_125497.1	chr15	55208726	55208732	+	1	NA	intron (NM_001037937, intron 4 of 8)	intron (NM_001037937, intron 4 of 8)	75293	NM_001037937	97998	Mm.295397	NM_145470	ENSMUSG00000022419	Deptor	Depdc6	DEP domain containing MTOR-interacting protein	protein-coding
mm_73050.1	chr8	94358138	94358155	+	1	NA	intron (NM_019415, intron 23 of 24)	MIRb|SINE|MIR	-28354	NM_022331	64209	Mm.29151	NM_022331	ENSMUSG00000031770	Herpud1	Herp|Mifl|SUP	homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1	protein-coding
mm_54247.1	chr6	28260033	28260034	-	1	NA	intron (NM_001081678, intron 2 of 5)	intron (NM_001081678, intron 2 of 5)	1568	NM_001081678	627049	Mm.84441	NM_001081678	ENSMUSG00000039841	Zfp800	AA407452|Znf800	zinc finger protein 800	protein-coding
mm_17257.1	chr2	25847325	25847339	-	1	NA	promoter-TSS (NM_001001714)	promoter-TSS (NM_001001714)	-84	NM_001001714	227631	Mm.301632	NM_001001714	ENSMUSG00000059625	Sohlh1	Gm110|Nohlh	spermatogenesis and oogenesis specific basic helix-loop-helix 1	protein-coding
mm_90739.1	chr10	5367707	5367723	-	1	NA	intron (NM_001347732, intron 14 of 145)	intron (NM_001347732, intron 14 of 145)	120599	NM_001347711	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_42140.1	chr5	111417264	111417306	+	1	NA	promoter-TSS (NM_001081235)	promoter-TSS (NM_001081235)	-881	NM_001081235	433938	Mm.332576	NM_001081235	ENSMUSG00000070576	Mn1	AA003644|AA009236	meningioma 1	protein-coding
mm_132435.1	chr16	35919397	35919409	+	1	NA	Intergenic	Intergenic	-19067	NM_030253	80285	Mm.49074	NM_030253	ENSMUSG00000022906	Parp9	ARTD9|AW214463|BC003281|Bagl|Bal|PARP-9	poly (ADP-ribose) polymerase family, member 9	protein-coding
mm_15023.1	chr2	152685331	152685335	+	1	NA	TTS (NM_001159553)	TTS (NM_001159553)	-1815	NM_025543	66405	Mm.440291	NM_025543	ENSMUSG00000042814	Mcts2	2400002F11Rik|MCT-2	malignant T cell amplified sequence 2	protein-coding
mm_61342.1	chr7	68282907	68282931	+	1	NA	intron (NM_001013811, intron 1 of 8)	intron (NM_001013811, intron 1 of 8)	-6325	NR_040340	100504026	Mm.426764	NR_040340	ENSMUSG00000086628	Gm16157	OTTMUSG00000031023	predicted gene 16157	ncRNA
mm_22315.1	chr2	180439870	180439904	-	1	NA	Intergenic	Intergenic	-21091	NM_148933	108115	Mm.133687	NM_148933	ENSMUSG00000038963	Slco4a1	OATP-E|Slc21a12	solute carrier organic anion transporter family, member 4a1	protein-coding
mm_15524.1	chr2	158382171	158382174	+	1	NA	3' UTR (NM_175692, exon 5 of 5)	3' UTR (NM_175692, exon 5 of 5)	6534	NM_175692	319317	Mm.294494	NM_175692	ENSMUSG00000044349	Snhg11	A930034L06Rik|AI854265|AL022637|AW319638|E130013N09Rik	small nucleolar RNA host gene 11	protein-coding
mm_33747.1	chr4	134244193	134244204	+	1	NA	3' UTR (NM_024215, exon 3 of 3)	3' UTR (NM_024215, exon 3 of 3)	435	NR_040436	77490	Mm.426238	NR_040435	ENSMUSG00000086322	E130218I03Rik	E130106C14Rik	RIKEN cDNA E130218I03 gene	ncRNA
mm_1825.1	chr1	82587228	82587236	+	1	NA	promoter-TSS (NM_007735)	promoter-TSS (NM_007735)	311	NM_007734	12828	Mm.389135	NM_007734	ENSMUSG00000079465	Col4a3	[a]3(IV)|alpha3(IV)	collagen, type IV, alpha 3	protein-coding
mm_137691.1	chr17	28905230	28905248	+	1	NA	promoter-TSS (NR_045457)	promoter-TSS (NR_045457)	-26	NR_045457	74179	Mm.248931	NR_045457	ENSMUSG00000085333	1700030A11Rik	-	RIKEN cDNA 1700030A11 gene	ncRNA
mm_29556.1	chr3	116807934	116807961	-	1	NA	intron (NM_001081326, intron 1 of 33)	CpG	219	NM_001081326	77559	Mm.237099	NM_001081326	ENSMUSG00000033400	Agl	1110061O17Rik|9430004C13Rik|9630046L06Rik|AI850929|C77197	amylo-1,6-glucosidase, 4-alpha-glucanotransferase	protein-coding
mm_173186.1	chrX	60183716	60183731	-	1	NA	Intergenic	MTA_Mm|LTR|ERVL-MaLR	-4634	NM_001289731	109904	Mm.93796	NM_133197	ENSMUSG00000031139	Mcf2	B230117G22Rik|Dbl|Mcf-2	mcf.2 transforming sequence	protein-coding
mm_140165.1	chr17	80254695	80254706	+	1	NA	intron (NM_198942, intron 13 of 22)	ORR1B1|LTR|ERVL-MaLR	30211	NM_026053	67242	Mm.279985	NM_026053	ENSMUSG00000055760	Gemin6	2610019B15Rik|2810470M17Rik	gem (nuclear organelle) associated protein 6	protein-coding
mm_117919.1	chr13	99433460	99433468	-	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-20638	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_92483.1	chr10	78297853	78297863	-	1	NA	intron (NM_053014, intron 2 of 9)	intron (NM_053014, intron 2 of 9)	42349	NR_106119	102465765		NR_106119	ENSMUSG00000098885	Mir7659	Gm27433|mmu-mir-7659	microRNA 7659	ncRNA
mm_111188.1	chr12	84173452	84173476	-	1	NA	exon (NM_001163501, exon 2 of 13)	exon (NM_001163501, exon 2 of 13)	20551	NM_001163502	238317	Mm.31256	NM_001163501	ENSMUSG00000042507	Elmsan1	9430029N19Rik|C130039O16Rik|Gm260	ELM2 and Myb/SANT-like domain containing 1	protein-coding
mm_160221.1	chr7	101372919	101372919	+	1	NA	intron (NM_001040111, intron 2 of 33)	intron (NM_001040111, intron 2 of 33)	-5203	NM_001040112	69710	Mm.277687	NM_027180	ENSMUSG00000032812	Arap1	2410002L19Rik|Centd2|mKIAA0782	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	protein-coding
mm_87182.1	chr10	39136938	39136963	+	1	NA	intron (NM_028006, intron 3 of 11)	intron (NM_028006, intron 3 of 11)	2927	NM_028006	71924	Mm.297956	NM_028006	ENSMUSG00000019845	Tube1	2310061K05Rik|AI551343|Tube	epsilon-tubulin 1	protein-coding
mm_35325.1	chr4	25800435	25800465	-	1	NA	promoter-TSS (NM_010243)	promoter-TSS (NM_010243)	-447	NM_010243	14348	Mm.39101	NM_010243	ENSMUSG00000055373	Fut9	AI746471|AU067636|mFUT9|mFuc-TIX	fucosyltransferase 9	protein-coding
mm_30259.1	chr3	146731249	146731258	-	1	NA	3' UTR (NM_001164199, exon 10 of 10)	3' UTR (NM_001164199, exon 10 of 10)	38985	NM_001164198	18749	Mm.16766	NM_011100	ENSMUSG00000005034	Prkacb	CbPKA|Pkacb	protein kinase, cAMP dependent, catalytic, beta	protein-coding
mm_83408.1	chr9	44801804	44801818	-	1	NA	intron (NM_138951, intron 1 of 2)	intron (NM_138951, intron 1 of 2)	1140	NM_138951	192653	Mm.325487	NM_138951	ENSMUSG00000039438	Ttc36	-	tetratricopeptide repeat domain 36	protein-coding
mm_121372.1	chr14	118098456	118098460	+	1	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	34307	NM_029578	76355	Mm.251537	NM_029578	ENSMUSG00000022130	Tgds	2610017J16Rik|2610025M23Rik|AI648925	TDP-glucose 4,6-dehydratase	protein-coding
mm_84358.1	chr9	64704611	64704621	-	1	NA	intron (NM_001134399, intron 23 of 24)	intron (NM_001134399, intron 23 of 24)	33140	NM_017382	53869	Mm.1387	NM_017382	ENSMUSG00000004771	Rab11a	-	RAB11A, member RAS oncogene family	protein-coding
mm_61107.1	chr7	52015809	52015850	+	1	NA	promoter-TSS (NM_001195601)	promoter-TSS (NM_001195601)	-113	NM_001195601	100503036	Mm.279725	NM_001195601	ENSMUSG00000094445	1700015G11Rik	Ccdc179	RIKEN cDNA 1700015G11 gene	protein-coding
mm_41718.1	chr5	102175310	102175318	+	1	NA	Intergenic	L1VL2|LINE|L1	-105393	NM_172882	72145	Mm.332522	NM_172882	ENSMUSG00000043940	Wdfy3	2610509D04Rik|ALFY|AW319683|B930017C24|BWF1|Bchs|D5Ertd66e|Ggtb3|ZFYVE25|mKIAA0993	WD repeat and FYVE domain containing 3	protein-coding
mm_87416.1	chr10	50356595	50356598	+	1	NA	Intergenic	Intergenic	-236073	NM_198007	77987	Mm.222497	NM_198007	ENSMUSG00000038774	Ascc3	ASC1p200|B630009I04Rik|BC023451|D430001L07Rik|D630041L21|Helic1|RNAH	activating signal cointegrator 1 complex subunit 3	protein-coding
mm_129441.1	chr15	78529610	78529612	-	1	NA	promoter-TSS (NM_001204153)	promoter-TSS (NM_001204153)	40	NM_001204153	72709	Mm.34776	NM_028331	ENSMUSG00000022440	C1qtnf6	2810036M19Rik|CTRP6	C1q and tumor necrosis factor related protein 6	protein-coding
mm_80715.1	chr9	92275752	92275767	+	1	NA	5' UTR (NM_001195084, exon 1 of 8)	5' UTR (NM_001195084, exon 1 of 8)	157	NM_001195084	18828	Mm.10306	NM_008880	ENSMUSG00000032372	Plscr2	-	phospholipid scramblase 2	protein-coding
mm_78766.1	chr9	43310788	43310806	+	1	NA	promoter-TSS (NM_023655)	promoter-TSS (NM_023655)	34	NM_023655	72169	Mm.273277	NM_023655	ENSMUSG00000032013	Trim29	1110047J21Rik|2810431N19Rik|4732461M22Rik|AI119726	tripartite motif-containing 29	protein-coding
mm_49350.1	chr6	21986352	21986362	+	1	NA	5' UTR (NM_001081351, exon 1 of 22)	5' UTR (NM_001081351, exon 1 of 22)	447	NM_001081351	214642	Mm.221404	NM_001081351	ENSMUSG00000062980	Cped1	6720481P07|A430107O13Rik|AI552584	cadherin-like and PC-esterase domain containing 1	protein-coding
mm_80650.1	chr9	89909892	89909924	+	1	NA	5' UTR (NM_001039655, exon 1 of 3)	5' UTR (NM_001039655, exon 1 of 3)	133	NM_001039655	19417	Mm.44561	NM_011245	ENSMUSG00000032356	Rasgrf1	AI844718|CDC25|CDC25Mm|Gnrp|Grf1|Grfbeta|P190-A|Ras-GRF1|p190|p190RhoGEF	RAS protein-specific guanine nucleotide-releasing factor 1	protein-coding
mm_51806.1	chr6	88733551	88733580	+	1	NA	intron (NM_011844, intron 2 of 7)	intron (NM_011844, intron 2 of 7)	8861	NM_001166251	23945	Mm.272197	NM_011844	ENSMUSG00000033174	Mgll	AA589436|Magl|Mgl	monoglyceride lipase	protein-coding
mm_160005.1	chr6	124636199	124636199	-	1	NA	promoter-TSS (NM_173864)	promoter-TSS (NM_173864)	-114	NM_173864	317677	Mm.483270	NM_173864	ENSMUSG00000079343	C1s2	C1sb|EG317677|Gm5077	complement component 1, s subcomponent 2	protein-coding
mm_74341.1	chr8	127179036	127179039	+	1	NA	intron (NM_001309391, intron 2 of 24)	intron (NM_001309391, intron 2 of 24)	114981	NM_001309391	93742	Mm.299254	NM_033620	ENSMUSG00000025812	Pard3	AA960621|AI256638|Asip|D8Ertd580e|Par-3|Par3|Pard-3|Pard3a|Phip	par-3 family cell polarity regulator	protein-coding
mm_112037.1	chr12	111574385	111574405	-	1	NA	promoter-TSS (NM_021516)	promoter-TSS (NM_021516)	7	NR_045295	100504687	Mm.26072	NR_045295	ENSMUSG00000096995	2810029C07Rik	AU017849	RIKEN cDNA 2810029C07 gene	ncRNA
mm_55127.1	chr6	50596565	50596573	-	1	NA	promoter-TSS (NM_027564)	promoter-TSS (NM_027564)	21	NM_027564	70821	Mm.157323	NM_027564	ENSMUSG00000029828	4921507P07Rik	TISP74	RIKEN cDNA 4921507P07 gene	protein-coding
mm_159477.1	chr4	33209195	33209195	+	1	NA	exon (NM_177774, exon 1 of 3)	exon (NM_177774, exon 1 of 3)	204	NM_177774	272009	Mm.156636	NM_177774	ENSMUSG00000054679	Srsf12	B830039L16|Sfrs13b|Srrp|Srsf13b	serine/arginine-rich splicing factor 12	protein-coding
mm_173213.1	chrX	73214387	73214391	+	1	NA	promoter-TSS (NM_021365)	promoter-TSS (NM_021365)	56	NM_001293679	27083	Mm.104764	NM_021365	ENSMUSG00000067768	Xlr4b	Xlr4	X-linked lymphocyte-regulated 4B	protein-coding
mm_97481.1	chr11	78324304	78324395	+	1	NA	5' UTR (NM_009657, exon 1 of 8)	5' UTR (NM_009657, exon 1 of 8)	151	NM_009657	11676	Mm.7729	NM_009657	ENSMUSG00000017390	Aldoc	AI847350|AU040929|Aldo3|Scrg2	aldolase C, fructose-bisphosphate	protein-coding
mm_1175.1	chr1	60998188	60998192	+	1	NA	3' UTR (NM_017480, exon 5 of 5)	3' UTR (NM_017480, exon 5 of 5)	20276	NM_017480	54167	Mm.42044	NM_017480	ENSMUSG00000026009	Icos	AILIM|CCLP|CRP-1|H4|Ly115	inducible T cell co-stimulator	protein-coding
mm_167116.1	chr7	118761457	118761463	-	1	NA	intron (NM_027815, intron 8 of 30)	RMER19B|LTR|ERVK	21189	NM_027815	71517	Mm.213298	NM_027815	ENSMUSG00000030982	9030624J02Rik	2610029J22Rik	RIKEN cDNA 9030624J02 gene	protein-coding
mm_57430.1	chr6	124914207	124914213	-	1	NA	exon (NM_026988, exon 5 of 5)	exon (NM_026988, exon 5 of 5)	-2505	NM_008479	16768	Mm.4528	NM_008479	ENSMUSG00000030124	Lag3	CD223|LAG-3|Ly66	lymphocyte-activation gene 3	protein-coding
mm_93449.1	chr10	109986533	109986581	-	1	NA	intron (NM_001081035, intron 1 of 38)	intron (NM_001081035, intron 1 of 38)	13662	NM_001081035	260315	Mm.225050	NM_177797	ENSMUSG00000020181	Nav3	4732483H20Rik|9630020C08Rik|POMFIL1|Pomfil1p|mKIAA0938|unc53H3	neuron navigator 3	protein-coding
mm_62338.1	chr7	100496728	100496797	+	1	NA	5' UTR (NM_011671, exon 3 of 8)	5' UTR (NM_011671, exon 3 of 8)	3404	NM_011671	22228	Mm.171378	NM_011671	ENSMUSG00000033685	Ucp2	Slc25a8	uncoupling protein 2 (mitochondrial, proton carrier)	protein-coding
mm_126362.1	chr15	80091199	80091207	+	1	NA	promoter-TSS (NM_009303)	promoter-TSS (NM_009303)	-131	NM_009303	20972	Mm.230301	NM_009303	ENSMUSG00000022415	Syngr1	R75468|Syngr1b|p29	synaptogyrin 1	protein-coding
mm_142261.1	chr17	39844376	39844410	-	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	1396	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_25543.1	chr3	115815845	115815891	+	1	NA	Intergenic	Intergenic	72191	NR_027894	68161	Mm.392043	NR_015487	ENSMUSG00000054426	A930005H10Rik	-	RIKEN cDNA A930005H10 gene	ncRNA
mm_113177.1	chr13	24831701	24831721	+	1	NA	promoter-TSS (NM_019551)	promoter-TSS (NM_019551)	52	NM_019551	56196	Mm.427162	NM_019551	ENSMUSG00000035958	Tdp2	D13Ertd656e|Ttrap	tyrosyl-DNA phosphodiesterase 2	protein-coding
mm_104539.1	chr11	96467119	96467123	-	1	NA	intron (NM_001033186, intron 1 of 12)	intron (NM_001033186, intron 1 of 12)	2530	NM_001177898	78473	Mm.395840	NM_001033186	ENSMUSG00000057058	Skap1	1700091G21Rik|Scap1|Skap-55	src family associated phosphoprotein 1	protein-coding
mm_23336.1	chr3	54569898	54569917	+	1	NA	Intergenic	Intergenic	-123198	NM_019995	56790	Mm.486375	NM_019995	ENSMUSG00000027751	Supt20	AA667204|AI450544|D3Ertd300e|Fam48a|Supt20h|p38IP	suppressor of Ty 20	protein-coding
mm_96941.1	chr11	70540261	70540315	+	1	NA	promoter-TSS (NM_001302476)	promoter-TSS (NM_001302476)	16	NM_001302476	18806	Mm.260177	NM_008876	ENSMUSG00000020828	Pld2	PLD1C	phospholipase D2	protein-coding
mm_159218.1	chr2	127338775	127338775	+	1	NA	TTS (NM_010090)	TTS (NM_010090)	136	NM_172539	215095	Mm.31313	NM_172539	ENSMUSG00000050468	Astl	7420700F21|C87576|Sas1b	astacin-like metalloendopeptidase (M12 family)	protein-coding
mm_65712.1	chr7	28378207	28378213	-	1	NA	exon (NM_011756, exon 2 of 2)	exon (NM_011756, exon 2 of 2)	1018	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_86948.1	chr10	24869983	24869989	+	1	NA	promoter-TSS (NM_001166416)	promoter-TSS (NM_001166416)	0	NM_001166416	70208	Mm.28020	NM_027347	ENSMUSG00000019984	Med23	130kDa|3000002A17Rik|Crsp3|ESTM7|Sur2|X83317|mKIAA1216	mediator complex subunit 23	protein-coding
mm_139224.1	chr17	47730611	47730611	+	1	NA	exon (NM_025973, exon 5 of 9)	exon (NM_025973, exon 5 of 9)	3769	NM_025973	109820	Mm.22957	NM_025973	ENSMUSG00000023987	Pgc	2210410L06Rik|Upg-1|Upg1	progastricsin (pepsinogen C)	protein-coding
mm_123569.1	chr14	66911061	66911061	-	1	NA	promoter-TSS (NM_175498)	promoter-TSS (NM_175498)	-147	NM_175498	239157	Mm.44358	NM_175498	ENSMUSG00000046204	Pnma2	A830049P17Rik|mKIAA0883	paraneoplastic antigen MA2	protein-coding
mm_14867.1	chr2	148799488	148799498	+	1	NA	intron (NM_009978, intron 1 of 3)	intron (NM_009978, intron 1 of 3)	654	NM_009978	13012	Mm.20435	NM_009978	ENSMUSG00000027442	Cst8	Cres|Cst-rs1	cystatin 8 (cystatin-related epididymal spermatogenic)	protein-coding
mm_81955.1	chr9	120571477	120571487	+	1	NA	promoter-TSS (NM_025974)	promoter-TSS (NM_025974)	-35	NM_025974	67115	Mm.289810	NM_025974	ENSMUSG00000025794	Rpl14	3100001N19Rik|AA407502|AL022816|CAG-ISL-7|CTG-B33|L14	ribosomal protein L14	protein-coding
mm_133921.1	chr16	97734924	97734934	+	1	NA	Intergenic	Intergenic	28826	NM_023663	72388	Mm.35290	NM_023663	ENSMUSG00000005251	Ripk4	2310069J12Rik|AI552420|ANKK2|Ankrd3|DIk|PKK|RIP4	receptor-interacting serine-threonine kinase 4	protein-coding
mm_704.1	chr1	40681609	40681644	+	1	NA	promoter-TSS (NM_001033289)	promoter-TSS (NM_001033289)	-86	NM_001033289	226999	Mm.256414	NM_001033289	ENSMUSG00000026062	Slc9a2	2210416H12Rik|4932415O19Rik|AV333884|NHE2	solute carrier family 9 (sodium/hydrogen exchanger), member 2	protein-coding
mm_157441.1	chrX	40137585	40137592	-	1	NA	Intergenic	Intergenic	-273984	NM_001191032	100504400	Mm.373409	NM_001191032	ENSMUSG00000095240	Cypt14	-	cysteine-rich perinuclear theca 14	protein-coding
mm_97377.1	chr11	77710965	77710975	+	1	NA	3' UTR (NM_001024205, exon 4 of 4)	3' UTR (NM_001024205, exon 4 of 4)	14323	NM_001313933	12957	Mm.22830	NM_009965	ENSMUSG00000000724	Cryba1	BA3/A1|Cryb	crystallin, beta A1	protein-coding
mm_119400.1	chr14	43713730	43713737	+	1	NA	Intergenic	Intergenic	-105720	NM_001098269	100042342	Mm.429750	NM_001098269	ENSMUSG00000095528	Gm10375	ENSMUSG00000072602	predicted gene 10375	protein-coding
mm_77859.1	chr9	5312884	5312898	+	1	NA	intron (NM_007609, intron 1 of 8)	L1M2|LINE|L1	4042	NM_007609	12363	Mm.1569	NM_007609	ENSMUSG00000033538	Casp4	CASP-11|CASP-4|Casp11|Caspl|ich-3	caspase 4, apoptosis-related cysteine peptidase	protein-coding
mm_52194.1	chr6	99877961	99877979	+	1	NA	Intergenic	Intergenic	-151578	NM_001170419	50501	Mm.87365	NM_015768	ENSMUSG00000030069	Prok2	Bv8|PK2|Prok1	prokineticin 2	protein-coding
mm_115556.1	chr13	8996058	8996068	-	1	NA	promoter-TSS (NM_027000)	promoter-TSS (NM_027000)	-51	NM_027000	69237	Mm.41800	NM_027000	ENSMUSG00000021149	Gtpbp4	2610028C09Rik|Crfg|Gtpbp3|NGB|Nog1	GTP binding protein 4	protein-coding
mm_72595.1	chr8	84414384	84414475	+	1	NA	promoter-TSS (NM_001252060)	promoter-TSS (NM_001252060)	-935	NM_001252060	12286	Mm.334658	NM_007578	ENSMUSG00000034656	Cacna1a	APCA|BI|Caca1a|Cacnl1a4|Cav2.1|Ccha1a|EA2|FHM|HPCA|MHP|MHP1|SCA6|alpha1A|la|nmf352|rkr|smrl|tg	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	protein-coding
mm_35330.1	chr4	26346842	26346874	-	1	NA	promoter-TSS (NM_172865)	promoter-TSS (NM_172865)	-206	NM_172865	242362	Mm.245602	NM_172865	ENSMUSG00000040520	Manea	4932703L02Rik	mannosidase, endo-alpha	protein-coding
mm_20397.1	chr2	129198549	129198564	-	1	NA	promoter-TSS (NM_015747)	promoter-TSS (NM_015747)	-217	NM_015747	20515	Mm.272675	NM_015747	ENSMUSG00000027397	Slc20a1	AI607883|Glvr-1|Glvr1	solute carrier family 20, member 1	protein-coding
mm_166269.1	chr5	90460787	90460791	+	1	NA	promoter-TSS (NM_009654)	promoter-TSS (NM_009654)	-81	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_153025.1	chr19	31624503	31624503	-	1	NA	intron (NM_001013833, intron 1 of 17)	intron (NM_001013833, intron 1 of 17)	39867	NM_011160	19091	Mm.381170	NM_011160	ENSMUSG00000052920	Prkg1	AW125416|CGKI|Gm19690|Prkg1b|Prkgr1b	protein kinase, cGMP-dependent, type I	protein-coding
mm_45117.1	chr5	45639516	45639525	-	1	NA	promoter-TSS (NM_021416)	promoter-TSS (NM_021416)	-19	NM_021416	58227	Mm.266466	NM_021416	ENSMUSG00000015879	Fam184b	9630031F12Rik|AB041544	family with sequence similarity 184, member B	protein-coding
mm_84167.1	chr9	59750617	59750644	-	1	NA	promoter-TSS (NM_001172071)	promoter-TSS (NM_001172071)	19	NM_001172069	71599	Mm.279070	NM_027838	ENSMUSG00000051705	Senp8	9130010J17Rik|AU020827|Den1|Nedp1|Prsc2	SUMO/sentrin specific peptidase 8	protein-coding
mm_106210.1	chr11	116851445	116851475	-	1	NA	intron (NM_011358, intron 2 of 2)	intron (NM_011358, intron 2 of 2)	1634	NM_011358	20382	Mm.21841	NM_011358	ENSMUSG00000034120	Srsf2	D11Wsu175e|MRF-1|Pr264|SC35|Sfrs10|Sfrs2	serine/arginine-rich splicing factor 2	protein-coding
mm_96822.1	chr11	69994676	69994724	+	1	NA	3' UTR (NM_019749, exon 4 of 4)	3' UTR (NM_019749, exon 4 of 4)	-1066	NM_001291125	78246	Mm.20805	NM_030064	ENSMUSG00000018572	Phf23	JUNE-1	PHD finger protein 23	protein-coding
mm_94302.1	chr11	4160349	4160404	+	1	NA	promoter-TSS (NM_177616)	promoter-TSS (NM_177616)	22	NM_026175	67465	Mm.156914	NM_026175	ENSMUSG00000002129	Sf3a1	1200014H24Rik|5930416L09Rik|AI159724	splicing factor 3a, subunit 1	protein-coding
mm_113151.1	chr13	24773101	24773104	+	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	-11165	NM_020567	57441	Mm.12239	NM_020567	ENSMUSG00000006715	Gmnn	AW546347|Gem	geminin	protein-coding
mm_99063.1	chr11	99155271	99155284	+	1	NA	promoter-TSS (NM_007719)	promoter-TSS (NM_007719)	-200	NM_007719	12775	Mm.2932	NM_007719	ENSMUSG00000037944	Ccr7	CC-CKR-7|CCR-7|CD197|Cdw197|Cmkbr7|EBI1|Ebi1h	chemokine (C-C motif) receptor 7	protein-coding
mm_168756.1	chr12	116048078	116048078	+	1	NA	intron (NM_001004066, intron 1 of 2)	intron (NM_001004066, intron 1 of 2)	354	NM_019565	56220	Mm.254997	NM_019565	ENSMUSG00000042063	Zfp386	Kzf1|mKIAA4205	zinc finger protein 386 (Kruppel-like)	protein-coding
mm_53767.1	chr6	145862751	145862764	+	1	NA	3' UTR (NM_001271768, exon 5 of 5)	3' UTR (NM_001271768, exon 5 of 5)	2663	NM_001271768	79362	Mm.154529	NM_024469	ENSMUSG00000030256	Bhlhe41	6430520M22Rik|Bhlhb2l|Bhlhb3|DEC2|Sharp1	basic helix-loop-helix family, member e41	protein-coding
mm_86276.1	chr9	121792479	121792490	-	1	NA	promoter-TSS (NM_029095)	promoter-TSS (NM_029095)	23	NM_029095	74770	Mm.44195	NM_029095	ENSMUSG00000032523	Hhatl	1110011D13Rik|Gup1|Mg56	hedgehog acyltransferase-like	protein-coding
mm_43636.1	chr5	138229787	138229795	+	1	NA	5' UTR (NM_001013773, exon 2 of 6)	5' UTR (NM_001013773, exon 2 of 6)	3887	NM_001013773	381680	Mm.156846	NM_001013773	ENSMUSG00000047592	Nxpe5	-	neurexophilin and PC-esterase domain family, member 5	protein-coding
mm_139593.1	chr17	57226257	57226294	+	1	NA	exon (NM_009778, exon 3 of 41)	exon (NM_009778, exon 3 of 41)	1861	NM_009778	12266	Mm.19131	NM_009778	ENSMUSG00000024164	C3	AI255234|ASP|HSE-MSF|Plp	complement component 3	protein-coding
mm_61225.1	chr7	64501728	64501738	+	1	NA	promoter-TSS (NM_001291167)	promoter-TSS (NM_001291167)	27	NM_007461	11784	Mm.4657	NM_007461	ENSMUSG00000030519	Apba2	X11-like|X11L|XllL|mXllL	amyloid beta (A4) precursor protein-binding, family A, member 2	protein-coding
mm_160067.1	chr7	5116721	5116721	-	1	NA	5' UTR (NM_138954, exon 1 of 3)	5' UTR (NM_138954, exon 1 of 3)	190	NM_001145013	192658	Mm.28764	NM_138954	ENSMUSG00000035191	Rfpl4	D7Ertd486e|Rfpl4a	ret finger protein-like 4	protein-coding
mm_57672.1	chr6	128491549	128491569	-	1	NA	exon (NM_007376, exon 24 of 36)	exon (NM_007376, exon 24 of 36)	35161	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_65382.1	chr7	25091180	25091186	-	1	NA	TTS (NM_001163556)	TTS (NM_001163556)	5992	NR_105855	102465968		NR_105855	ENSMUSG00000098441	Mir6537	Gm27808|mmu-mir-6537	microRNA 6537	ncRNA
mm_38078.1	chr4	134128030	134128050	-	1	NA	exon (NM_080559, exon 2 of 3)	exon (NM_080559, exon 2 of 3)	713	NM_080559	73723	Mm.22240	NM_080559	ENSMUSG00000028843	Sh3bgrl3	1110004L05Rik|AU022188	SH3 domain binding glutamic acid-rich protein-like 3	protein-coding
mm_134850.1	chr16	27444571	27444616	-	1	NA	exon (NM_001289436, exon 11 of 12)	exon (NM_001289436, exon 11 of 12)	55637	NM_001289436	67501	Mm.258985	NM_026202	ENSMUSG00000038127	Ccdc50	C3orf6	coiled-coil domain containing 50	protein-coding
mm_102534.1	chr11	61174968	61174978	-	1	NA	promoter-TSS (NM_001004143)	promoter-TSS (NM_001004143)	86	NM_001004143	216825	Mm.30602	NM_001004143	ENSMUSG00000042506	Usp22	AI427806	ubiquitin specific peptidase 22	protein-coding
mm_45675.1	chr5	77246228	77246237	-	1	NA	Intergenic	Intergenic	-19262	NM_011263	19712	Mm.28840	NM_011263	ENSMUSG00000029249	Rest	2610008J04Rik|AA407358|NRSF|REST4	RE1-silencing transcription factor	protein-coding
mm_17348.1	chr2	26607815	26607825	-	1	NA	Intergenic	Intergenic	-3403	NM_026212	67512	Mm.24244	NM_026212	ENSMUSG00000026922	Agpat2	2510002J07Rik|AV000834|BSCL|BSCL1|LPAAB|LPAAT-beta	1-acylglycerol-3-phosphate O-acyltransferase 2 (lysophosphatidic acid acyltransferase, beta)	protein-coding
mm_64572.1	chr7	144914448	144914458	+	1	NA	promoter-TSS (NM_028184)	promoter-TSS (NM_028184)	-647	NM_001347536	72284	Mm.273049	NM_028184	ENSMUSG00000031072	Oraov1	2210010N10Rik|TAOS1	oral cancer overexpressed 1	protein-coding
mm_147841.1	chr18	62615743	62615747	-	1	NA	intron (NM_001168423, intron 1 of 4)	intron (NM_001168423, intron 1 of 4)	-19481	NM_001001803	408198	Mm.478742	NM_001001803	ENSMUSG00000060201	Spink7	EG408198|Ecg2	serine peptidase inhibitor, Kazal type 7 (putative)	protein-coding
mm_82070.1	chr9	122886803	122886859	+	1	NA	Intergenic	CpG	-1640	NM_001177505	382118	Mm.86999	NM_001177505	ENSMUSG00000063488	Zkscan7	BC042569|Zfp167	zinc finger with KRAB and SCAN domains 7	protein-coding
mm_124137.1	chr14	86749069	86749088	-	1	NA	intron (NM_019670, intron 27 of 27)	intron (NM_019670, intron 27 of 27)	392036	NM_019670	56419	Mm.440585	NM_019670	ENSMUSG00000022021	Diaph3	4930417P13Rik|Dia2|Diap3|Drf3|mDia2|mKIAA4117|p134MDia2	diaphanous related formin 3	protein-coding
mm_85517.1	chr9	106438208	106438227	-	1	NA	promoter-TSS (NM_001276442)	promoter-TSS (NM_001276442)	19	NM_025371	109652	Mm.7165	NM_025371	ENSMUSG00000023262	Acy1	1110014J22Rik|Acy-1	aminoacylase 1	protein-coding
mm_105899.1	chr11	114982766	114982782	-	1	NA	3' UTR (NM_145437, exon 4 of 4)	3' UTR (NM_145437, exon 4 of 4)	7112	NM_145437	217305	Mm.275986	NM_145437	ENSMUSG00000034641	Cd300ld	4732429D16Rik|CLM5|Cd300ld1|LMIR4|MAIR-IV|clm-5	CD300 molecule like family member d	protein-coding
mm_125100.1	chr15	27641472	27641482	+	1	NA	Intergenic	Intergenic	-10784	NM_001013792	432940	Mm.309164	NM_001013792	ENSMUSG00000046034	Otulin	C79097|Fam105b|m3Sapc|m7-1Sapc	OTU deubiquitinase with linear linkage specificity	protein-coding
mm_9491.1	chr1	173729493	173729540	-	1	NA	exon (NM_001204910, exon 5 of 8)	exon (NM_001204910, exon 5 of 8)	12293	NM_001204910	226691	Mm.440876	NM_001204910	ENSMUSG00000073490	Ifi207	AI607873|Pyhin-A	interferon activated gene 207	protein-coding
mm_74101.1	chr8	122709504	122709528	+	1	NA	Intergenic	Intergenic	-10407	NM_009824	12398	Mm.194339	NM_009824	ENSMUSG00000006362	Cbfa2t3	A630044F12Rik|AI465270|AW229127|Cbfa2t3h|ETO-2|Eto2|MTGR2	core-binding factor, runt domain, alpha subunit 2, translocated to, 3 (human)	protein-coding
mm_57577.1	chr6	127149613	127149627	-	1	NA	promoter-TSS (NR_040275)	promoter-TSS (NR_040275)	-6	NR_040275	77558	Mm.358918	NR_040273	ENSMUSG00000097166	9330179D12Rik	-	RIKEN cDNA 9330179D12 gene	ncRNA
mm_46933.1	chr5	114761946	114761975	-	1	NA	intron (NM_001347400, intron 6 of 19)	intron (NM_001347400, intron 6 of 19)	11531	NM_019834	26431	Mm.195632	NM_019834	ENSMUSG00000041890	Git2	1500036H07Rik|5830420E16Rik|6430510B20Rik|9630056M03Rik|B230104M05Rik|CAT2|mKIAA0148	G protein-coupled receptor kinase-interactor 2	protein-coding
mm_149279.1	chr19	10606274	10606288	+	1	NA	intron (NM_015735, intron 1 of 26)	intron (NM_015735, intron 1 of 26)	656	NM_015735	13194	Mm.289915	NM_015735	ENSMUSG00000024740	Ddb1	127kDa|AA408517|p127-Ddb1	damage specific DNA binding protein 1	protein-coding
mm_80701.1	chr9	92249679	92249689	+	1	NA	promoter-TSS (NM_011636)	promoter-TSS (NM_011636)	-510	NM_011636	22038	Mm.421956	NM_011636	ENSMUSG00000032369	Plscr1	MmTRA1a|MmTRA1b|Nor1|Tra1|Tra1a|Tra1b|Tras1|Tras2	phospholipid scramblase 1	protein-coding
mm_95080.1	chr11	32696852	32696854	+	1	NA	intron (NM_001271347, intron 2 of 12)	L1MD|LINE|L1	54298	NM_001271347	103583	Mm.28017	NM_134015	ENSMUSG00000020271	Fbxw11	2310065A07Rik|AA536858|BTRC2|BTRCP2|Fbxw1b|HOS	F-box and WD-40 domain protein 11	protein-coding
mm_41889.1	chr5	105495600	105495608	+	1	NA	Intergenic	Intergenic	-23867	NM_133897	100604	Mm.319847	NM_133897	ENSMUSG00000054720	Lrrc8c	AD158|AI326115|E430036I04Rik|fad158	leucine rich repeat containing 8 family, member C	protein-coding
mm_123682.1	chr14	69515484	69515497	-	1	NA	Intergenic	Intergenic	-2941	NM_173420	239167	Mm.259889	NM_173420	ENSMUSG00000047977	Synb	D930020E02Rik|syncytin-B	syncytin b	protein-coding
mm_84760.1	chr9	75597718	75597738	-	1	NA	intron (NM_016711, intron 1 of 9)	intron (NM_016711, intron 1 of 9)	1405	NM_001038710	50876	Mm.291880	NM_016711	ENSMUSG00000032186	Tmod2	N-Tmod|NTMOD	tropomodulin 2	protein-coding
mm_35835.1	chr4	48042854	48042871	-	1	NA	Intergenic	Intergenic	-2443	NM_015743	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_80761.1	chr9	95559150	95559161	+	1	NA	promoter-TSS (NM_198414)	promoter-TSS (NM_198414)	-662	NM_198414	75552	Mm.151485	NM_198414	ENSMUSG00000064225	Paqr9	1700020G04Rik	progestin and adipoQ receptor family member IX	protein-coding
mm_59985.1	chr7	30552533	30552564	+	1	NA	promoter-TSS (NM_183321)	promoter-TSS (NM_183321)	-276	NM_183321	333193	Mm.34885	NM_183321	ENSMUSG00000036864	Proser3	-	proline and serine rich 3	protein-coding
mm_93728.1	chr10	119240491	119240536	-	1	NA	promoter-TSS (NM_027994)	promoter-TSS (NM_027994)	-458	NM_027994	71902	Mm.203965	NM_027994	ENSMUSG00000020114	Cand1	2310038O07Rik|6330512O03Rik|AI195005|AI846556|D10Ertd516e|Tp120a|mKIAA0829	cullin associated and neddylation disassociated 1	protein-coding
mm_171476.1	chr4	145798105	145798113	+	1	NA	intron (NR_040355, intron 1 of 4)	intron (NR_040355, intron 1 of 4)	8594	NR_040355	70005	Mm.276881	NM_027285		Znf41-ps	1700029I01Rik	ZNF41, pseudogene	pseudo
mm_115275.1	chr13	111686226	111686240	+	1	NA	promoter-TSS (NM_172593)	promoter-TSS (NM_172593)	55	NM_172593	218613	Mm.31012	NM_172593	ENSMUSG00000032727	Mier3	5730509D14|AU015422|D130064H19Rik	MIER family member 3	protein-coding
mm_111532.1	chr12	100724994	100725002	-	1	NA	5' UTR (NM_001330702, exon 1 of 17)	5' UTR (NM_001330702, exon 1 of 17)	122	NM_001330702	73086	Mm.220417	NM_153587	ENSMUSG00000021180	Rps6ka5	3110005L17Rik|6330404E13Rik|AI854034|MSK1|MSPK1|RLPK|RLSK|S6K-alpha-5	ribosomal protein S6 kinase, polypeptide 5	protein-coding
mm_120066.1	chr14	56924915	56924918	+	1	NA	intron (NM_029498, intron 8 of 23)	B1_Mur4|SINE|Alu	37121	NM_029498	76007	Mm.31417	NM_029498	ENSMUSG00000021945	Zmym2	5830413P05Rik|FIM|MYM|RAMP|SCLL|Zfp198|Znf198	zinc finger, MYM-type 2	protein-coding
mm_54443.1	chr6	34423021	34423038	-	1	NA	3' UTR (NM_009731, exon 10 of 10)	3' UTR (NM_009731, exon 10 of 10)	10667	NM_009731	11997	Mm.482073	NM_009731	ENSMUSG00000052131	Akr1b7	AR|Avdp|MVDP	aldo-keto reductase family 1, member B7	protein-coding
mm_132766.1	chr16	44748305	44748313	+	1	NA	Intergenic	Intergenic	-1946	NM_025332	66067	Mm.34520	NM_025332	ENSMUSG00000022668	Gtpbp8	0610037H22Rik	GTP-binding protein 8 (putative)	protein-coding
mm_73589.1	chr8	109991681	109991687	+	1	NA	exon (NM_146214, exon 2 of 12)	exon (NM_146214, exon 2 of 12)	1248	NM_146214	234724	Mm.28110	NM_146214	ENSMUSG00000001670	Tat	-	tyrosine aminotransferase	protein-coding
mm_115405.1	chr13	114111175	114111176	+	1	NA	intron (NM_172595, intron 4 of 4)	intron (NM_172595, intron 4 of 4)	40417	NR_045836	319803	Mm.386896	NM_177004		A430090L17Rik	-	RIKEN cDNA A430090L17 gene	ncRNA
mm_146799.1	chr18	20694737	20694749	-	1	NA	intron (NM_019737, intron 5 of 8)	B1_Mus2|SINE|Alu	29493	NM_013697	22139	Mm.2108	NM_013697	ENSMUSG00000061808	Ttr	AA408768|AI787086|D17860|prealbumin	transthyretin	protein-coding
mm_143340.1	chr17	66518050	66518053	-	1	NA	intron (NM_024448, intron 1 of 5)	intron (NM_024448, intron 1 of 5)	1619	NM_024448	19328	Mm.248313	NM_024448	ENSMUSG00000023460	Rab12	2900054P15Rik|AW555448|C77700	RAB12, member RAS oncogene family	protein-coding
mm_63494.1	chr7	127777096	127777152	+	1	NA	promoter-TSS (NM_178029)	promoter-TSS (NM_178029)	-265	NM_178029	233904	Mm.435494	NM_010940	ENSMUSG00000042308	Setd1a	BC010250|KMT2F|Nsccn1|mKIAA0339|mNSC1	SET domain containing 1A	protein-coding
mm_45302.1	chr5	65391409	65391451	-	1	NA	promoter-TSS (NM_024471)	promoter-TSS (NM_024471)	1	NM_011292	20005	Mm.300271	NM_011292	ENSMUSG00000047215	Rpl9	-	ribosomal protein L9	protein-coding
mm_158400.1	chrX	136743676	136743692	-	1	NA	promoter-TSS (NM_001168230)	promoter-TSS (NM_001168230)	2	NM_001168230	56397	Mm.27218	NM_019768	ENSMUSG00000031422	Morf4l2	2410017O14Rik|Mrgx|Sid393p|mKIAA0026	mortality factor 4 like 2	protein-coding
mm_803.1	chr1	45348716	45348756	+	1	NA	exon (NM_009930, exon 51 of 51)	exon (NM_009930, exon 51 of 51)	37198	NM_009930	12825	Mm.249555	NM_009930	ENSMUSG00000026043	Col3a1	AW550625|Col3a-1|Tsk-2|Tsk2	collagen, type III, alpha 1	protein-coding
mm_32552.1	chr4	109407095	109407119	+	1	NA	promoter-TSS (NM_153392)	promoter-TSS (NM_153392)	7	NM_153392	230603	Mm.33091	NM_153392	ENSMUSG00000028555	Ttc39a	4922503N01Rik	tetratricopeptide repeat domain 39A	protein-coding
mm_112757.1	chr13	19344201	19344233	+	1	NA	Intergenic	Intergenic	51596	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_140835.1	chr17	23669970	23670004	-	1	NA	intron (NM_001008425, intron 7 of 12)	intron (NM_001008425, intron 7 of 12)	-3621	NM_181821	353502	Mm.359030	NM_181821	ENSMUSG00000023904	Hcfc1r1	HPIP	host cell factor C1 regulator 1 (XPO1-dependent)	protein-coding
mm_162322.1	chr1	39482437	39482438	-	1	NA	Intergenic	Intergenic	-3690	NM_018775	54610	Mm.387293	NM_018775	ENSMUSG00000003134	Tbc1d8	AD3|HBLP1|VRP	TBC1 domain family, member 8	protein-coding
mm_116967.1	chr13	56178583	56178593	-	1	NA	5' UTR (NM_001168615, exon 1 of 3)	5' UTR (NM_001168615, exon 1 of 3)	297	NM_145976	212937	Mm.116697	NM_145976	ENSMUSG00000049625	Tifab	-	TRAF-interacting protein with forkhead-associated domain, family member B	protein-coding
mm_52730.1	chr6	120364394	120364448	+	1	NA	promoter-TSS (NR_045558)	promoter-TSS (NR_045558)	-52	NR_045558	67200	Mm.45767	NM_026028	ENSMUSG00000030177	Ccdc77	2400002C23Rik|2700091N06Rik|AV168274	coiled-coil domain containing 77	protein-coding
mm_131122.1	chr16	5431476	5431486	+	1	NA	Intergenic	Intergenic	-175525	NM_027446	70511	Mm.45780	NM_027446	ENSMUSG00000022544	Eef2kmt	5730409G15Rik|Fam86|Fam86a|eEF2-KMT	eukaryotic elongation factor 2 lysine methyltransferase	protein-coding
mm_141183.1	chr17	26939199	26939213	-	1	NA	intron (NM_026948, intron 1 of 5)	intron (NM_026948, intron 1 of 5)	252	NR_104458	67675	Mm.439919	NM_026307	ENSMUSG00000024194	Cuta	0610039D01Rik|1810022E02Rik|1810060C03Rik|2700094G22Rik|AI326454	cutA divalent cation tolerance homolog	protein-coding
mm_104637.1	chr11	97523906	97523915	-	1	NA	intron (NM_018873, intron 16 of 19)	intron (NM_018873, intron 16 of 19)	-23570	NM_001289118	100141474	Mm.482426	NM_001289118	ENSMUSG00000047988	4933428G20Rik	-	RIKEN cDNA 4933428G20 gene	protein-coding
mm_39253.1	chr5	3515190	3515238	+	1	NA	intron (NM_009873, intron 5 of 7)	intron (NM_009873, intron 5 of 7)	-28619	NM_001042501	68152	Mm.240265	NM_026583	ENSMUSG00000058503	Fam133b	2900022K02Rik|5830415L20Rik	family with sequence similarity 133, member B	protein-coding
mm_61704.1	chr7	81213495	81213496	+	1	NA	promoter-TSS (NM_008803)	promoter-TSS (NM_008803)	-309	NM_008803	18584	Mm.371577	NM_008803	ENSMUSG00000025584	Pde8a	AI551852|Pde8	phosphodiesterase 8A	protein-coding
mm_13978.1	chr2	121450307	121450313	+	1	NA	TTS (NM_001025371)	TTS (NM_001025371)	1112	NR_110986	378702	Mm.262252	NM_011354	ENSMUSG00000074884	Serf2	C80083|Msmac1l|m4F5rel	small EDRK-rich factor 2	protein-coding
mm_172255.1	chr6	70341471	70341477	-	1	NA	Intergenic	Intergenic	450701	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_165265.1	chr2	74715974	74715976	-	1	NA	non-coding (NR_027899, exon 1 of 3)	non-coding (NR_027899, exon 1 of 3)	155	NR_027899	73429	Mm.443313	NR_027899		Hoxd3os1	1700064D17Rik|1700109F18Rik	homeobox D3, opposite strand 1	ncRNA
mm_93208.1	chr10	94943874	94943887	-	1	NA	exon (NM_018797, exon 1 of 31)	exon (NM_018797, exon 1 of 31)	698	NM_018797	54712	Mm.256712	NM_018797	ENSMUSG00000074785	Plxnc1	2510048K12Rik|AW742158|CD232|Vespr	plexin C1	protein-coding
mm_167433.1	chr8	119415988	119415990	+	1	NA	Intergenic	Intergenic	21097	NM_019966	56690	Mm.423037	NM_019966	ENSMUSG00000074064	Mlycd	AI324784|Mcd	malonyl-CoA decarboxylase	protein-coding
mm_104283.1	chr11	89841267	89841279	-	1	NA	Intergenic	Intergenic	-144337	NM_001327810	382543	Mm.60997	NM_172534	ENSMUSG00000047773	Ankfn1	4932411E22Rik|Gm1175|nmf9	ankyrin-repeat and fibronectin type III domain containing 1	protein-coding
mm_58538.1	chr7	4480779	4480789	+	1	NA	TTS (NM_001290416)	TTS (NM_001290416)	-9900	NR_028416	320749	Mm.396688	NR_028416		D630041G03Rik	-	RIKEN cDNA D630041G03 gene	ncRNA
mm_74653.1	chr8	13471511	13471535	-	1	NA	exon (NM_019521, exon 11 of 15)	exon (NM_019521, exon 11 of 15)	23012	NM_019521	14456	Mm.3982	NM_019521	ENSMUSG00000031451	Gas6	Gas-6	growth arrest specific 6	protein-coding
mm_39417.1	chr5	15934686	15934696	+	1	NA	promoter-TSS (NM_001110843)	promoter-TSS (NM_001110843)	0	NM_001110843	12293	Mm.159842	NM_009784	ENSMUSG00000040118	Cacna2d1	Ca(v)alpha2delta1|Cacna2|Cchl2a	calcium channel, voltage-dependent, alpha2/delta subunit 1	protein-coding
mm_54359.1	chr6	31088543	31088552	-	1	NA	Intergenic	Intergenic	-25454	NR_029532	387223		NR_029532	ENSMUSG00000065604	Mir29b-1	Mirn29b|Mirn29b-1|mir-29b-1	microRNA 29b-1	ncRNA
mm_54003.1	chr6	7693154	7693169	-	1	NA	promoter-TSS (NM_012055)	promoter-TSS (NM_012055)	21	NM_012055	27053	Mm.2942	NM_012055	ENSMUSG00000029752	Asns	-	asparagine synthetase	protein-coding
mm_165618.1	chr3	58525733	58525737	-	1	NA	promoter-TSS (NM_001005509)	promoter-TSS (NM_001005509)	-86	NM_001005509	229317	Mm.21617	NM_001005509	ENSMUSG00000027810	Eif2a	D030048D22|D3Ertd194e	eukaryotic translation initiation factor 2A	protein-coding
mm_148317.1	chr18	83768166	83768172	-	1	NA	Intergenic	Intergenic	318393	NM_001081300	110796	Mm.102136	NM_001081300	ENSMUSG00000046982	Tshz1	5730407I04Rik|D18Bwg1409e|Mtsh1|NY-CO-33|Sdccag33|Tsh1|mKIAA4206|teashirt1	teashirt zinc finger family member 1	protein-coding
mm_44933.1	chr5	36321636	36321648	-	1	NA	intron (NM_030889, intron 1 of 26)	intron (NM_030889, intron 1 of 26)	20072	NR_106162	102465792		NR_106162	ENSMUSG00000098884	Mir7689	Gm27434|mmu-mir-7689	microRNA 7689	ncRNA
mm_125685.1	chr15	66798745	66798751	+	1	NA	intron (NM_009192, intron 3 of 8)	intron (NM_009192, intron 3 of 8)	33081	NM_001029841	20491	Mm.7601	NM_009192	ENSMUSG00000022372	Sla	Slap|Slap-1	src-like adaptor	protein-coding
mm_141784.1	chr17	34301193	34301206	-	1	NA	Intergenic	Intergenic	-4668	NM_010382	14969	Mm.22564	NM_010382	ENSMUSG00000060586	H2-Eb1	Eb|H-2Eb|H2Eb|Ia-4|Ia4	histocompatibility 2, class II antigen E beta	protein-coding
mm_9997.1	chr1	191397045	191397061	-	1	NA	promoter-TSS (NM_144880)	promoter-TSS (NM_144880)	-12	NM_144880	226849	Mm.205569	NM_144880	ENSMUSG00000026626	Ppp2r5a	PR61alpha	protein phosphatase 2, regulatory subunit B', alpha	protein-coding
mm_115165.1	chr13	107891086	107891100	+	1	NA	Intergenic	CpG-4160	-1029	NM_145456	67263	Mm.490418	NM_145456	ENSMUSG00000032846	Zswim6	2900036G02Rik|mKIAA1577	zinc finger SWIM-type containing 6	protein-coding
mm_88799.1	chr10	80696406	80696408	+	1	NA	intron (NM_172457, intron 1 of 3)	B4A|SINE|B4	5413	NM_172457	208228	Mm.49309	NM_172457	ENSMUSG00000003348	Mob3a	5330417K06Rik|A630029F06|AV218468|Mobkl2a	MOB kinase activator 3A	protein-coding
mm_148099.1	chr18	73970848	73970865	-	1	NA	5' UTR (NM_172632, exon 2 of 6)	5' UTR (NM_172632, exon 2 of 6)	-47051	NR_045390	77855	Mm.410760	NR_045390	ENSMUSG00000090263	D730045A05Rik	-	RIKEN cDNA D730045A05 gene	ncRNA
mm_123357.1	chr14	63142685	63142711	-	1	NA	3' UTR (NM_007798, exon 10 of 10)	3' UTR (NM_007798, exon 10 of 10)	20236	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_84913.1	chr9	79977839	79977861	-	1	NA	promoter-TSS (NM_001081243)	promoter-TSS (NM_001081243)	32	NM_001081243	70598	Mm.23049	NM_001081243	ENSMUSG00000034898	Filip1	5730485H21Rik|AI843021	filamin A interacting protein 1	protein-coding
mm_89760.1	chr10	100019285	100019289	+	1	NA	intron (NM_001347156, intron 1 of 8)	intron (NM_001347156, intron 1 of 8)	3466	NM_013598	17311	Mm.45124	NM_013598	ENSMUSG00000019966	Kitl	Clo|Con|Gb|Kitlg|Mgf|SCF|SF|SLF|Sl|blz|contrasted	kit ligand	protein-coding
mm_74112.1	chr8	123042415	123042436	+	1	NA	promoter-TSS (NR_045268)	promoter-TSS (NR_045268)	-141	NM_001081379	77087	Mm.31567	NM_001081379	ENSMUSG00000035569	Ankrd11	2410104C19Rik|3010027A04Rik|6330578C09Rik|9530048I21Rik|AA930108|Gm176|Yod	ankyrin repeat domain 11	protein-coding
mm_66769.1	chr7	46732582	46732611	-	1	NA	promoter-TSS (NM_011316)	promoter-TSS (NM_011316)	7	NM_011316	20211	Mm.3489	NM_011316	ENSMUSG00000040017	Saa4	Saa-4|Saa-5	serum amyloid A 4	protein-coding
mm_141219.1	chr17	27204358	27204447	-	1	NA	promoter-TSS (NM_146075)	promoter-TSS (NM_146075)	36	NM_146075	224640	Mm.29689	NM_146075	ENSMUSG00000044857	Lemd2	BC026588|Lem2|NET25	LEM domain containing 2	protein-coding
mm_48899.1	chr6	3201267	3201304	+	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	-87234	NR_036696	667335	Mm.380219	NR_036696	ENSMUSG00000106779	Gm8579	EG667335	spermatogenesis associated glutamate (E)-rich protein 4a pseudogene	pseudo
mm_104329.1	chr11	93988835	93988843	-	1	NA	Intergenic	Intergenic	-7252	NM_001199203	70834	Mm.260737	NM_027569	ENSMUSG00000020859	Spag9	3110018C07Rik|4733401I23Rik|4831406C20Rik|AW552012|JLP|JSAP2|JSAP2a|Jip4|Mapk8ip4|syd1	sperm associated antigen 9	protein-coding
mm_48227.1	chr5	137650564	137650565	-	1	NA	TTS (NM_178162)	TTS (NM_178162)	-4850	NM_010571	16369	Mm.24486	NM_010571	ENSMUSG00000047182	Irs3	AA408304	insulin receptor substrate 3	protein-coding
mm_45257.1	chr5	63827817	63827824	-	1	NA	intron (NM_029554, intron 1 of 3)	RMER17C|LTR|ERVK	15325	NM_029554	76261	Mm.38143	NM_029554	ENSMUSG00000060512	0610040J01Rik	AI662686	RIKEN cDNA 0610040J01 gene	protein-coding
mm_39779.1	chr5	30155316	30155336	+	1	NA	promoter-TSS (NM_001289798)	promoter-TSS (NM_001289798)	73	NM_001289798	231086	Mm.291463	NM_145558	ENSMUSG00000059447	Hadhb	4930479F15Rik|Mtpb|TP-beta	hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), beta subunit	protein-coding
mm_71589.1	chr8	54954935	54954949	+	1	NA	5' UTR (NM_153581, exon 1 of 7)	5' UTR (NM_153581, exon 1 of 7)	214	NM_001253756	234267	Mm.241700	NM_153581	ENSMUSG00000031517	Gpm6a	Gpm6|M6A	glycoprotein m6a	protein-coding
mm_44799.1	chr5	32820691	32820707	-	1	NA	exon (NM_194340, exon 8 of 11)	exon (NM_194340, exon 8 of 11)	33531	NM_194340	215476	Mm.248721	NM_194340	ENSMUSG00000054280	Prr14l	6030436E02Rik|C330019G07Rik|Prl14l	proline rich 14-like	protein-coding
mm_150771.1	chr19	44294143	44294149	+	1	NA	5' UTR (NM_009128, exon 1 of 6)	5' UTR (NM_009128, exon 1 of 6)	470	NM_009128	20250	Mm.487021	NM_009128	ENSMUSG00000025203	Scd2	Mir5114|Scd-2|mir-5114|swty	stearoyl-Coenzyme A desaturase 2	protein-coding
mm_114653.1	chr13	77876426	77876435	+	1	NA	intron (NM_001163419, intron 5 of 9)	B4|SINE|B4	-148472	NM_029315	75507	Mm.443255	NM_029315	ENSMUSG00000093668	Pou5f2	1700013G10Rik|SPRM-1|Sprm1	POU domain class 5, transcription factor 2	protein-coding
mm_49158.1	chr6	13069880	13069895	+	1	NA	5' UTR (NM_027992, exon 1 of 9)	5' UTR (NM_027992, exon 1 of 9)	128	NM_027992	71900	Mm.27742	NM_027992	ENSMUSG00000029571	Tmem106b	2310036D22Rik|5830455K21Rik|6430519M21Rik|AI428776|AI661344	transmembrane protein 106B	protein-coding
mm_144791.1	chr18	35942370	35942409	+	1	NA	Intergenic	Intergenic	-22441	NM_028707	74002	Mm.196944	NM_028707	ENSMUSG00000024347	Psd2	6330404E20Rik|AW125584|EFA6C	pleckstrin and Sec7 domain containing 2	protein-coding
mm_70984.1	chr8	27260396	27260418	+	1	NA	promoter-TSS (NM_007918)	promoter-TSS (NM_007918)	80	NM_007918	13685	Mm.6700	NM_007918	ENSMUSG00000031490	Eif4ebp1	4e-bp1|AA959816|PHAS-I	eukaryotic translation initiation factor 4E binding protein 1	protein-coding
mm_50828.1	chr6	54679400	54679410	+	1	NA	Intergenic	RMER19C|LTR|ERVK	-2219	NM_001289741	68235	Mm.233860	NM_026629	ENSMUSG00000038065	Mturn	2410066E13Rik|AI448550|B230212L03Rik	maturin, neural progenitor differentiation regulator homolog (Xenopus)	protein-coding
mm_88526.1	chr10	78069352	78069371	+	1	NA	promoter-TSS (NM_015790)	promoter-TSS (NM_015790)	-7	NM_015790	50723	Mm.17819	NM_015790	ENSMUSG00000000732	Icosl	AU044799|B7-H2|B7RP-1|B7h|BG071784|GI50|GL50|GL50-B|ICOS-L|Icoslg|LICOS|Ly115l|mKIAA0653	icos ligand	protein-coding
mm_72440.1	chr8	83155796	83155818	+	1	NA	Intergenic	Intergenic	-9545	NM_001111304	71310	Mm.24031	NM_027758	ENSMUSG00000031709	Tbc1d9	4933431N12Rik|AI847101|AW490653|C76116	TBC1 domain family, member 9	protein-coding
mm_43571.1	chr5	137705344	137705390	+	1	NA	Intergenic	Intergenic	-20614	NM_001303266	231801	Mm.260869	NM_145566	ENSMUSG00000029722	Agfg2	A630095P14Rik|Hrbl|RAB-R|RABR	ArfGAP with FG repeats 2	protein-coding
mm_138405.1	chr17	35065340	35065366	+	1	NA	non-coding (NR_001462, exon 1 of 1)	non-coding (NR_001462, exon 1 of 1)	831	NM_001033221	106722	Mm.390956	NM_001033221	ENSMUSG00000073414	G6b	AU023871|C6orf25|Ng31	immunoreceptor tyrosine-based inhibitory motif (ITIM) containing platelet receptor	protein-coding
mm_127042.1	chr15	96641630	96641640	+	1	NA	5' UTR (NM_134086, exon 1 of 16)	5' UTR (NM_134086, exon 1 of 16)	327	NM_134086	105727	Mm.103568	NM_134086	ENSMUSG00000023169	Slc38a1	AA408026|AA409865|AL022800|AU015942|NAT2	solute carrier family 38, member 1	protein-coding
mm_129274.1	chr15	77022633	77022648	-	1	NA	promoter-TSS (NM_001164048)	promoter-TSS (NM_001164048)	87	NM_001164048	17189	Mm.404074	NM_013593	ENSMUSG00000018893	Mb	AI325109	myoglobin	protein-coding
mm_37110.1	chr4	116641041	116641053	-	1	NA	exon (NM_021473, exon 4 of 9)	exon (NM_021473, exon 4 of 9)	10627	NM_021473	58810	Mm.30085	NM_021473	ENSMUSG00000028692	Akr1a1	2610201A18Rik|Akr1a4	aldo-keto reductase family 1, member A1 (aldehyde reductase)	protein-coding
mm_147906.1	chr18	65393845	65393922	-	1	NA	promoter-TSS (NM_001037294)	promoter-TSS (NM_001037294)	5	NM_001037294	225638	Mm.296528	NM_001037294	ENSMUSG00000032845	Alpk2	Gm549|Hak	alpha-kinase 2	protein-coding
mm_143371.1	chr17	67632485	67632527	-	1	NA	exon (NM_001033340, exon 1 of 1)	exon (NM_001033340, exon 1 of 1)	217	NM_001033340	240131	Mm.295736	NM_001033340	ENSMUSG00000073375	Lrrc30	Gm326	leucine rich repeat containing 30	protein-coding
mm_114875.1	chr13	94167192	94167192	+	1	NA	intron (NM_172589, intron 2 of 3)	intron (NM_172589, intron 2 of 3)	109396	NM_172589	218454	Mm.316553	NM_172589	ENSMUSG00000045312	Lhfpl2	6030465B15|AI447312|AW050335|mKIAA0206|vgim	lipoma HMGIC fusion partner-like 2	protein-coding
mm_9960.1	chr1	191096233	191096275	-	1	NA	Intergenic	B3|SINE|B2	-2160	NM_030060	381319	Mm.6922	NM_030060	ENSMUSG00000026630	Batf3	9130211I03Rik|Snft	basic leucine zipper transcription factor, ATF-like 3	protein-coding
mm_9227.1	chr1	171240108	171240116	-	1	NA	intron (NM_153064, intron 3 of 12)	intron (NM_153064, intron 3 of 12)	-5763	NM_010185	14127	Mm.22673	NM_010185	ENSMUSG00000058715	Fcer1g	AI573376|CD23|FcR-gamma|FcR[g]|FcRgamma|Fce1g|FcepsilonRI|Ly-50	Fc receptor, IgE, high affinity I, gamma polypeptide	protein-coding
mm_73276.1	chr8	104624512	104624518	+	1	NA	promoter-TSS (NM_001252627)	promoter-TSS (NM_001252627)	-119	NM_001252628	12556	Mm.19423	NM_007663	ENSMUSG00000031881	Cdh16	-	cadherin 16	protein-coding
mm_121388.1	chr14	118971898	118971900	+	1	NA	intron (NM_008929, intron 7 of 11)	intron (NM_008929, intron 7 of 11)	33967	NM_008929	100037258	Mm.12616	NM_008929	ENSMUSG00000022136	Dnajc3	AA408985|AU067833|Dnajc3a|Dnajc3b|Prkri|mp58|p58|p58IPK	DnaJ heat shock protein family (Hsp40) member C3	protein-coding
mm_143912.1	chr17	85613055	85613064	-	1	NA	non-coding (NR_038082, exon 4 of 4)	non-coding (NR_038082, exon 4 of 4)	5337	NR_038084	100043902	Mm.150838	NR_015385	ENSMUSG00000093460	Six3os1	D17Mgi26|E130112H22Rik|Rncr1|Six3os	SIX homeobox 3, opposite strand 1	ncRNA
mm_78735.1	chr9	41584412	41584415	+	1	NA	intron (NR_015483, intron 1 of 1)	intron (NR_015483, intron 1 of 1)	2487	NR_029822	387236		NR_029822	ENSMUSG00000093354	Mir125b-1	Mirn125b|Mirn125b-1|mir-125b-1	microRNA 125b-1	ncRNA
mm_50579.1	chr6	49053041	49053082	+	1	NA	intron (NM_053110, intron 9 of 10)	B4|SINE|B4	16543	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_78649.1	chr9	40327256	40327258	+	1	NA	intron (NM_172768, intron 4 of 19)	intron (NM_172768, intron 4 of 19)	-6215	NR_040728	73558	Mm.398307	NR_040728		1700110K17Rik	-	RIKEN cDNA 1700110K17 gene	ncRNA
mm_50617.1	chr6	49827538	49827546	+	1	NA	exon (NM_023456, exon 3 of 4)	exon (NM_023456, exon 3 of 4)	4832	NM_023456	109648	Mm.154796	NM_023456	ENSMUSG00000029819	Npy	0710005A05Rik	neuropeptide Y	protein-coding
mm_256.1	chr1	20669880	20669884	+	1	NA	promoter-TSS (NR_131249)	promoter-TSS (NR_131249)	0	NR_131249	105661730	Mm.137893	NR_131249		Linc-md1	-	long intergenic non-coding RNA muscle differentiation 1	ncRNA
mm_45771.1	chr5	87091151	87091178	-	1	NA	intron (NM_001029867, intron 1 of 5)	intron (NM_001029867, intron 1 of 5)	1391	NM_001029867	231396	Mm.439851	NM_001029867	ENSMUSG00000070704	Ugt2b36	-	UDP glucuronosyltransferase 2 family, polypeptide B36	protein-coding
mm_7469.1	chr1	120485879	120485923	-	1	NA	exon (NM_010766, exon 9 of 17)	exon (NM_010766, exon 9 of 17)	19183	NM_010766	17167	Mm.1856	NM_010766	ENSMUSG00000026390	Marco	AI323439|Ly112|Scara2	macrophage receptor with collagenous structure	protein-coding
mm_107534.1	chr12	40556243	40556255	+	1	NA	intron (NM_172803, intron 1 of 52)	intron (NM_172803, intron 1 of 52)	110196	NM_172803	238130	Mm.341423	NM_172803	ENSMUSG00000035954	Dock4	5330406C03|6330411N01Rik|AF263288|C030023J22|mKIAA0716	dedicator of cytokinesis 4	protein-coding
mm_52095.1	chr6	97850673	97850700	+	1	NA	intron (NM_001113198, intron 1 of 9)	intron (NM_001113198, intron 1 of 9)	43628	NM_001113198	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_144983.1	chr18	38228549	38228561	+	1	NA	Intergenic	RMER19B|LTR|ERVK	-18793	NM_029357	75599	Mm.36560	NM_029357	ENSMUSG00000051375	Pcdh1	2010005A06Rik|AI585920	protocadherin 1	protein-coding
mm_62536.1	chr7	102250221	102250255	+	1	NA	promoter-TSS (NM_019566)	promoter-TSS (NM_019566)	-120	NM_019566	56212	Mm.259795	NM_019566	ENSMUSG00000073982	Rhog	2810426G09Rik|Arhg|Sid10750	ras homolog family member G	protein-coding
mm_21491.1	chr2	163375413	163375427	-	1	NA	intron (NM_021566, intron 2 of 5)	intron (NM_021566, intron 2 of 5)	22553	NM_021566	59091	Mm.34459	NM_021566	ENSMUSG00000017817	Jph2	1110002E14Rik|JP-2|Jp2	junctophilin 2	protein-coding
mm_82205.1	chr9	124102458	124102462	+	1	NA	intron (NM_009915, intron 1 of 2)	intron (NM_009915, intron 1 of 2)	277	NM_009915	12772	Mm.6272	NM_009915	ENSMUSG00000049103	Ccr2	Cc-ckr-2|Ccr2a|Ccr2b|Ckr2|Ckr2a|Ckr2b|Cmkbr2|mJe-r	chemokine (C-C motif) receptor 2	protein-coding
mm_482.1	chr1	36761756	36761773	+	1	NA	promoter-TSS (NM_009539)	promoter-TSS (NM_009539)	-34	NM_009539	22637	Mm.8038	NM_009539	ENSMUSG00000026117	Zap70	Srk|ZAP-70|mrtle|mur	zeta-chain (TCR) associated protein kinase	protein-coding
mm_85976.1	chr9	112164352	112164365	-	1	NA	intron (NM_001177623, intron 9 of 9)	intron (NM_001177623, intron 9 of 9)	21591	NM_001177618	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_33240.1	chr4	127023479	127023509	+	1	NA	exon (NM_023603, exon 3 of 10)	exon (NM_023603, exon 3 of 10)	2193	NM_023603	71514	Mm.257276	NM_023603	ENSMUSG00000028820	Sfpq	1110004P21Rik|2810416M14Rik|5730453G22Rik|9030402K04Rik|AU021830|D4Ertd314e|Gm12940|OTTMUSG00000009329|PSF|REP1	splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)	protein-coding
mm_30030.1	chr3	135689779	135689782	-	1	NA	intron (NM_008689, intron 1 of 24)	intron (NM_008689, intron 1 of 24)	1767	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_170105.1	chr17	39844715	39844732	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	1726	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_100164.1	chr11	116434233	116434254	+	1	NA	promoter-TSS (NR_003376)	promoter-TSS (NR_003376)	30	NR_003376	664849	Mm.258466	NR_003376		Gm7367	EG664849	1110014K08Rik pseudogene	pseudo
mm_114551.1	chr13	74009431	74009453	+	1	NA	promoter-TSS (NM_182839)	promoter-TSS (NM_182839)	23	NM_182839	72948	Mm.39752	NM_182839	ENSMUSG00000021573	Tppp	2900041A09Rik|AI849835	tubulin polymerization promoting protein	protein-coding
mm_47282.1	chr5	122103875	122103899	-	1	NA	exon (NM_010861, exon 4 of 7)	exon (NM_010861, exon 4 of 7)	2907	NM_010861	17906	Mm.1529	NM_010861	ENSMUSG00000013936	Myl2	MLC-2|MLC-2s/v|MLC-2v|Mlc2v|Mylpc	myosin, light polypeptide 2, regulatory, cardiac, slow	protein-coding
mm_128441.1	chr15	50722557	50722584	-	1	NA	intron (NM_001310481, intron 4 of 5)	intron (NM_001310481, intron 4 of 5)	166479	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_137556.1	chr17	27655546	27655568	+	1	NA	promoter-TSS (NM_001286743)	promoter-TSS (NM_001286743)	-34	NM_011861	23969	Mm.4926	NM_011861	ENSMUSG00000040276	Pacsin1	A830061D09Rik|H74|mKIAA1379|syndapin	protein kinase C and casein kinase substrate in neurons 1	protein-coding
mm_69568.1	chr7	135700756	135700767	-	1	NA	exon (NM_001081117, exon 12 of 14)	exon (NM_001081117, exon 12 of 14)	15618	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_65236.1	chr7	19760086	19760111	-	1	NA	exon (NM_020486, exon 10 of 15)	exon (NM_020486, exon 10 of 15)	10434	NM_020486	57278	Mm.29236	NM_020486	ENSMUSG00000002980	Bcam	1200005K12Rik|B-CAM|Gplu|Lu	basal cell adhesion molecule	protein-coding
mm_170670.1	chr2	119803058	119803072	+	1	NA	intron (NM_001290800, intron 4 of 19)	intron (NM_001290800, intron 4 of 19)	3551	NM_019392	22174	Mm.2901	NM_019392	ENSMUSG00000027298	Tyro3	AI323366|Brt|Dtk|Etk-2|Rse|Sky|TK19-2|Tif|etk2/tyro3|tk19-1	TYRO3 protein tyrosine kinase 3	protein-coding
mm_140466.1	chr17	93199009	93199033	+	1	NA	promoter-TSS (NM_009625)	promoter-TSS (NM_009625)	4	NM_001315503	11516	Mm.3407	NM_009625	ENSMUSG00000024256	Adcyap1	PACAP	adenylate cyclase activating polypeptide 1	protein-coding
mm_45100.1	chr5	44648378	44648388	-	1	NA	intron (NM_001347349, intron 2 of 7)	intron (NM_001347349, intron 2 of 7)	151363	NM_001347349	16826	Mm.25785	NM_010698	ENSMUSG00000039706	Ldb2	AI035351|AW146358|CLIM1|CLP-36|Ldb3	LIM domain binding 2	protein-coding
mm_26815.1	chr3	10301170	10301202	-	1	NA	promoter-TSS (NM_029310)	promoter-TSS (NM_029310)	-3	NM_029310	75497	Mm.47052	NM_029310	ENSMUSG00000027530	Fabp12	1700008G05Rik	fatty acid binding protein 12	protein-coding
mm_4147.1	chr1	170998566	170998594	+	1	NA	Intergenic	MLT1L|LTR|ERVL-MaLR	-20346	NM_144559	246256	Mm.251254	NM_144559	ENSMUSG00000059089	Fcgr4	4833442P21Rik|CD16-2|FcgRIV|FcgammaRIV|Fcgr3a|Fcrl3	Fc receptor, IgG, low affinity IV	protein-coding
mm_63743.1	chr7	130936173	130936254	+	1	NA	promoter-TSS (NM_019564)	promoter-TSS (NM_019564)	10	NM_019564	56213	Mm.30156	NM_019564	ENSMUSG00000006205	Htra1	AI429470|HTRA|L56|Prss11|RSPP11	HtrA serine peptidase 1	protein-coding
mm_129582.1	chr15	79741354	79741361	-	1	NA	intron (NM_001205346, intron 1 of 17)	intron (NM_001205346, intron 1 of 17)	1179	NM_194342	223697	Mm.202715	NM_194342	ENSMUSG00000042524	Sun2	B230369L08Rik|C030011B15|Unc84b	Sad1 and UNC84 domain containing 2	protein-coding
mm_50751.1	chr6	53287294	53287310	+	1	NA	promoter-TSS (NM_001327821)	promoter-TSS (NM_001327821)	-1	NM_001327821	231991	Mm.227444	NM_172728	ENSMUSG00000053007	Creb5	9430076C15Rik|CRE-BPa|Crebpa|D430026C09Rik	cAMP responsive element binding protein 5	protein-coding
mm_166928.1	chr7	33606065	33606074	-	1	NA	Intergenic	Intergenic	47212	NR_045685	353109	Mm.63867	NR_045685	ENSMUSG00000083896	Scgb2b23-ps	1700028O08Rik|Abpbg23-ps|C2y|Scgb2b1|Scgb2b1-ps	secretoglobin, family 2B, member 23, pseudogene	pseudo
mm_166776.1	chr6	136828458	136828480	+	1	NA	promoter-TSS (NM_021714)	promoter-TSS (NM_021714)	-253	NM_021714	60321	Mm.141197	NM_021714	ENSMUSG00000030216	Wbp11	2510026P17Rik|D6Wsu113e|Npwbp|SIPP1	WW domain binding protein 11	protein-coding
mm_46328.1	chr5	100845737	100845743	-	1	NA	promoter-TSS (NM_172715)	promoter-TSS (NM_172715)	-489	NM_172715	231510	Mm.271911	NM_172715	ENSMUSG00000029314	Agpat9	1-AGPAT|1-AGPAT 9|4933407I02Rik|4933408F15|A230097K15Rik|GPAT-3|Gpat3|mGPAT3	1-acylglycerol-3-phosphate O-acyltransferase 9	protein-coding
mm_33597.1	chr4	132568410	132568433	+	1	NA	intron (NM_001081211, intron 1 of 1)	B4|SINE|B4	4354	NM_001081211	19204	Mm.89389	NM_001081211	ENSMUSG00000056529	Ptafr	PAFR	platelet-activating factor receptor	protein-coding
mm_99281.1	chr11	101316201	101316275	+	1	NA	promoter-TSS (NM_011192)	promoter-TSS (NM_011192)	-13	NM_011192	19192	Mm.288477	NM_011192	ENSMUSG00000078652	Psme3	AA410043|AU020960|Ki|PA28gamma|REGgamma|pa28g	proteaseome (prosome, macropain) activator subunit 3 (PA28 gamma, Ki)	protein-coding
mm_83649.1	chr9	49505515	49505533	-	1	NA	exon (NM_001311065, exon 18 of 18)	exon (NM_001311065, exon 18 of 18)	-12764	NR_029465	100036537	Mm.437541	NR_029465	ENSMUSG00000079564	Gm11149	ENSMUSG00000060603|ENSMUSG00000079564	predicted gene 11149	ncRNA
mm_62530.1	chr7	102239432	102239463	+	1	NA	TTS (NM_145583)	TTS (NM_145583)	10671	NM_019566	56212	Mm.259795	NM_019566	ENSMUSG00000073982	Rhog	2810426G09Rik|Arhg|Sid10750	ras homolog family member G	protein-coding
mm_137808.1	chr17	30004779	30004846	+	1	NA	promoter-TSS (NM_148926)	promoter-TSS (NM_148926)	-275	NM_148926	21769	Mm.220972	NM_148926	ENSMUSG00000044477	Zfand3	AW539211|TEG-27|Tex27	zinc finger, AN1-type domain 3	protein-coding
mm_5603.1	chr1	39571158	39571164	-	1	NA	intron (NM_001033135, intron 1 of 6)	intron (NM_001033135, intron 1 of 6)	6186	NM_001033135	67702	Mm.28614	NM_001033135	ENSMUSG00000048234	Rnf149	1600023E10Rik|AV037261|C76763|Gm15832|Greul4|OTTMUSG00000026591	ring finger protein 149	protein-coding
mm_66580.1	chr7	45340712	45340742	-	1	NA	exon (NM_029741, exon 28 of 30)	exon (NM_029741, exon 28 of 30)	5458	NM_010473	15464	Mm.39968	NM_010473	ENSMUSG00000038239	Hrc	-	histidine rich calcium binding protein	protein-coding
mm_34611.1	chr4	150286513	150286516	+	1	NA	intron (NM_001085492, intron 1 of 22)	PB1D7|SINE|Alu	4598	NM_001085492	68703	Mm.291274	NM_001085492	ENSMUSG00000039852	Rere	1110033A15Rik|AI414665|ARG|ARP|ATN1L|AW742570|Atr2|DNB1|eye<m03Jus>|eyes3|mKIAA0458	arginine glutamic acid dipeptide (RE) repeats	protein-coding
mm_119710.1	chr14	53845308	53845321	+	1	NA	Intergenic	Intergenic	408615	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_162632.1	chr1	188262900	188262903	+	1	NA	promoter-TSS (NM_021408)	promoter-TSS (NM_021408)	63	NM_021408	22283	Mm.331238	NM_021408	ENSMUSG00000026609	Ush2a	A930011D15Rik|A930037M10Rik|Gm676|Gm983|Mush2a|Usherin|Ushrn	Usher syndrome 2A	protein-coding
mm_78544.1	chr9	35305376	35305390	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	24278	NR_040715	71133	Mm.158577	NR_040715	ENSMUSG00000111746	4933422A05Rik	-	RIKEN cDNA 4933422A05 gene	ncRNA
mm_98831.1	chr11	97415578	97415597	+	1	NA	Intergenic	CpG	-34573	NM_021493	58996	Mm.394118	NM_021493	ENSMUSG00000049807	Arhgap23	A330041B18Rik	Rho GTPase activating protein 23	protein-coding
mm_90271.1	chr10	122681163	122681169	+	1	NA	intron (NM_176919, intron 1 of 8)	(GGGA)n|Simple_repeat|Simple_repeat	1851	NR_106182	102466884		NR_106182	ENSMUSG00000099225	Mir8104	Gm27380|mmu-mir-8104	microRNA 8104	ncRNA
mm_47425.1	chr5	123172020	123172026	-	1	NA	exon (NM_008277, exon 14 of 14)	exon (NM_008277, exon 14 of 14)	10663	NM_008277	15445	Mm.439709	NM_008277	ENSMUSG00000029445	Hpd	Fla|Flp|Hppd|Laf	4-hydroxyphenylpyruvic acid dioxygenase	protein-coding
mm_156161.1	chrX	129994456	129994505	+	1	NA	intron (NM_172493, intron 17 of 26)	L1_Mus3|LINE|L1	244738	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diaph2	Dia3|Diap2|Drf2|E430022I22Rik	diaphanous related formin 2	protein-coding
mm_108023.1	chr12	73618644	73618645	+	1	NA	intron (NM_001313977, intron 2 of 14)	L1MEg|LINE|L1	33848	NM_008856	18755	Mm.341677	NM_008856	ENSMUSG00000021108	Prkch	Pkch	protein kinase C, eta	protein-coding
mm_64890.1	chr7	15922362	15922378	-	1	NA	promoter-TSS (NM_009156)	promoter-TSS (NM_009156)	1	NM_009156	20364	Mm.42829	NM_009156	ENSMUSG00000041571	Selenow	Sepw1|selW	selenoprotein W	protein-coding
mm_127504.1	chr15	101447763	101447804	+	1	NA	promoter-TSS (NM_025487)	promoter-TSS (NM_025487)	38	NM_025487	66322	Mm.158111	NM_025487	ENSMUSG00000063971	Krt88	1700011A15Rik	keratin 88	protein-coding
mm_32636.1	chr4	115000235	115000244	+	1	NA	5' UTR (NM_009185, exon 1 of 17)	5' UTR (NM_009185, exon 1 of 17)	121	NM_001304555	20460	Mm.3988	NM_009185	ENSMUSG00000028718	Stil	Sil	Scl/Tal1 interrupting locus	protein-coding
mm_15106.1	chr2	153368811	153368814	+	1	NA	intron (NM_001039939, intron 3 of 11)	intron (NM_001039939, intron 3 of 11)	22673	NM_001039939	228790	Mm.330677	NM_001039939	ENSMUSG00000042548	Asxl1	mKIAA0978	additional sex combs like 1	protein-coding
mm_62794.1	chr7	112687223	112687225	+	1	NA	intron (NM_009346, intron 1 of 12)	ID_B1|SINE|B4	7904	NM_009346	21676	Mm.24685	NM_009346	ENSMUSG00000055320	Tead1	2610024B07Rik|B230114H05Rik|Gtrgeo5|TEAD-1|TEF-1|Tcf13|mTEF-1	TEA domain family member 1	protein-coding
mm_161077.1	chr12	81421910	81421910	-	1	NA	5' UTR (NM_009620, exon 1 of 1)	5' UTR (NM_009620, exon 1 of 1)	129	NM_009620	11498	Mm.408462	NM_009620	ENSMUSG00000072972	Adam4	AV274654|tMDCV	a disintegrin and metallopeptidase domain 4	protein-coding
mm_46253.1	chr5	99252811	99252824	-	1	NA	5' UTR (NM_181318, exon 1 of 14)	5' UTR (NM_181318, exon 1 of 14)	110	NM_181318	320292	Mm.259074	NM_145839	ENSMUSG00000089809	Rasgef1b	4732452O09Rik|GPIgamma4|Gpig4	RasGEF domain family, member 1B	protein-coding
mm_20130.1	chr2	121314732	121314734	-	1	NA	intron (NM_178795, intron 29 of 29)	PB1D9|SINE|Alu	19279	NM_001173506	17754	Mm.36501	NM_032393	ENSMUSG00000027254	Map1a	6330416M19Rik|AI853608|Mtap-1|Mtap1|Mtap1a|moth1	microtubule-associated protein 1 A	protein-coding
mm_103053.1	chr11	69817734	69817768	-	1	NA	exon (NM_175368, exon 3 of 3)	exon (NM_175368, exon 3 of 3)	689	NM_175368	108803	Mm.73263	NM_175368	ENSMUSG00000044084	4933402P03Rik	-	RIKEN cDNA 4933402P03 gene	protein-coding
mm_104987.1	chr11	100265932	100265950	-	1	NA	intron (NM_212483, intron 3 of 7)	intron (NM_212483, intron 3 of 7)	3930	NM_212483	68239	Mm.158190	NM_212483	ENSMUSG00000053654	Krt42	2410039E07Rik|K17n|Ka22|ecat6	keratin 42	protein-coding
mm_45311.1	chr5	65434886	65434889	-	1	NA	intron (NM_009466, intron 1 of 11)	intron (NM_009466, intron 1 of 11)	955	NM_009466	22235	Mm.344831	NM_009466	ENSMUSG00000029201	Ugdh	Udpgdh	UDP-glucose dehydrogenase	protein-coding
mm_34840.1	chr4	155397084	155397090	+	1	NA	intron (NM_008072, intron 1 of 8)	intron (NM_008072, intron 1 of 8)	982	NM_008072	14403	Mm.388925	NM_008072	ENSMUSG00000029054	Gabrd	AI853201	gamma-aminobutyric acid (GABA) A receptor, subunit delta	protein-coding
mm_25805.1	chr3	127789803	127789809	+	1	NA	promoter-TSS (NM_145133)	promoter-TSS (NM_145133)	-107	NM_145133	211550	Mm.31852	NM_145133	ENSMUSG00000046688	Tifa	T2bp	TRAF-interacting protein with forkhead-associated domain	protein-coding
mm_53338.1	chr6	129237293	129237314	+	1	NA	intron (NR_040265, intron 1 of 2)	intron (NR_040265, intron 1 of 2)	742	NR_040265	76432	Mm.261738	NR_040265	ENSMUSG00000097354	2310001H17Rik	AI646108	RIKEN cDNA 2310001H17 gene	ncRNA
mm_81840.1	chr9	118485146	118485170	+	1	NA	3' UTR (NM_010136, exon 6 of 6)	3' UTR (NM_010136, exon 6 of 6)	6969	NM_010136	13813	Mm.200692	NM_010136	ENSMUSG00000032446	Eomes	C77258|TBR-2|Tbr2	eomesodermin	protein-coding
mm_88088.1	chr10	68277465	68277514	+	1	NA	intron (NM_023598, intron 2 of 9)	intron (NM_023598, intron 2 of 9)	1237	NM_023598	71371	Mm.440357	NM_023598	ENSMUSG00000019947	Arid5b	4930580B11|5430435G07Rik|AI467247|Desrt|Mrf2|Mrf2alpha|Mrf2beta	AT rich interactive domain 5B (MRF1-like)	protein-coding
mm_52640.1	chr6	117175170	117175187	+	1	NA	TTS (NM_021704)	TTS (NM_021704)	6643	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_172974.1	chr9	9299122	9299126	-	1	NA	Intergenic	MMERVK10C-int|LTR|ERVK	-60111	NM_027823	71544	Mm.334955	NM_027823	ENSMUSG00000050730	Arhgap42	9030420J04Rik|BE136619	Rho GTPase activating protein 42	protein-coding
mm_1458.1	chr1	67230899	67230901	+	1	NA	3' UTR (NM_001080809, exon 38 of 38)	3' UTR (NM_001080809, exon 38 of 38)	107873	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_171106.1	chr3	133545076	133545093	+	1	NA	promoter-TSS (NM_001346736)	promoter-TSS (NM_001346736)	-694	NM_001040400	214133	Mm.347816	NM_145989	ENSMUSG00000040943	Tet2	Ayu17-449|E130014J05Rik|mKIAA1546	tet methylcytosine dioxygenase 2	protein-coding
mm_77900.1	chr9	7348717	7348731	+	1	NA	exon (NM_008605, exon 2 of 10)	exon (NM_008605, exon 2 of 10)	1350	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_137738.1	chr17	29360924	29360940	+	1	NA	promoter-TSS (NM_013710)	promoter-TSS (NM_013710)	18	NM_001159538	26382	Mm.279187	NM_013710	ENSMUSG00000024013	Fgd2	Tcd-2|Tcd2|ZFYVE4|tcs-2|tcs2	FYVE, RhoGEF and PH domain containing 2	protein-coding
mm_43848.1	chr5	143270045	143270084	+	1	NA	promoter-TSS (NM_017467)	promoter-TSS (NM_017467)	-42	NM_017467	54201	Mm.6666	NM_017467	ENSMUSG00000046658	Zfp316	Emzf1|Mzf3|Znf316	zinc finger protein 316	protein-coding
mm_29537.1	chr3	116711776	116711784	-	1	NA	intron (NM_144902, intron 1 of 7)	CpG	500	NM_144902	229782	Mm.190758	NM_144902	ENSMUSG00000027957	Slc35a3	2310050P13Rik	solute carrier family 35 (UDP-N-acetylglucosamine (UDP-GlcNAc) transporter), member 3	protein-coding
mm_157200.1	chrX	12160493	12160523	-	1	NA	promoter-TSS (NM_001168321)	promoter-TSS (NM_001168321)	-153	NM_001168321	71458	Mm.196328	NM_029510	ENSMUSG00000040363	Bcor	2900008C10Rik|5830466J11Rik|8430401K06Rik|BcorR|D930024N20Rik|mKIAA1575	BCL6 interacting corepressor	protein-coding
mm_44620.1	chr5	25533290	25533292	-	1	NA	Intergenic	(CAAAA)n|Simple_repeat|Simple_repeat	3273	NR_027388	73571	Mm.105263	NR_027388	ENSMUSG00000101856	1700096K18Rik	-	RIKEN cDNA 1700096K18 gene	ncRNA
mm_76516.1	chr8	87470297	87470302	-	1	NA	exon (NM_019626, exon 3 of 3)	exon (NM_019626, exon 3 of 3)	2293	NM_019626	12404	Mm.4880	NM_019626	ENSMUSG00000031654	Cbln1	AI323299	cerebellin 1 precursor protein	protein-coding
mm_74934.1	chr8	25785155	25785215	-	1	NA	promoter-TSS (NM_026032)	promoter-TSS (NM_026032)	24	NM_026121	67384	Mm.118400	NM_026121	ENSMUSG00000037316	Bag4	2410112I15Rik|SODD	BCL2-associated athanogene 4	protein-coding
mm_54165.1	chr6	23132907	23132913	-	1	NA	promoter-TSS (NM_013930)	promoter-TSS (NM_013930)	76	NM_013930	30956	Mm.18651	NM_013930	ENSMUSG00000029695	Aass	LKR|LKR/SDH|LOR|LOR/SDH|Lorsdh|SDH	aminoadipate-semialdehyde synthase	protein-coding
mm_71419.1	chr8	46490920	46490930	+	1	NA	promoter-TSS (NM_001302163)	promoter-TSS (NM_001302163)	-41	NM_001302163	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_31835.1	chr4	70625208	70625220	+	1	NA	Intergenic	RMER1C|Other|Other	-90286	NM_172694	230316	Mm.251188	NM_172694	ENSMUSG00000039270	Megf9	4933405H16Rik|9630025C07|Egfl5|mKIAA0818	multiple EGF-like-domains 9	protein-coding
mm_33499.1	chr4	130825867	130825878	+	1	NA	3' UTR (NM_011520, exon 5 of 5)	3' UTR (NM_011520, exon 5 of 5)	33335	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_132529.1	chr16	37834597	37834607	+	1	NA	3' UTR (NM_008047, exon 11 of 11)	3' UTR (NM_008047, exon 11 of 11)	-33798	NM_177093	320184	Mm.390882	NM_177093	ENSMUSG00000034158	Lrrc58	1810012N18Rik|C330018J07Rik	leucine rich repeat containing 58	protein-coding
mm_131270.1	chr16	10960856	10960866	+	1	NA	3' UTR (NM_019980, exon 4 of 4)	3' UTR (NM_019980, exon 4 of 4)	32260	NM_019980	56722	Mm.294753	NM_019980	ENSMUSG00000022500	Litaf	3222402J11Rik|C85531|N4WBP3|TBX1	LPS-induced TN factor	protein-coding
mm_84082.1	chr9	58202282	58202295	-	1	NA	promoter-TSS (NM_177193)	promoter-TSS (NM_177193)	-3	NM_001161536	320563	Mm.186499	NM_177193	ENSMUSG00000051243	Islr2	B930052A04Rik|Linx|Mbu-3|mKIAA1465	immunoglobulin superfamily containing leucine-rich repeat 2	protein-coding
mm_137059.1	chr17	17939584	17939603	+	1	NA	Intergenic	L1_Mus1|LINE|L1	-30865	NM_008042	14294	Mm.378918	NM_008042	ENSMUSG00000079700	Fpr3	ALX|Fpr-rs1|Fpr-s1|Fprl1|LXA4-R|Lxa4r	formyl peptide receptor 3	protein-coding
mm_82098.1	chr9	123060568	123060571	+	1	NA	intron (NM_177911, intron 10 of 13)	MTD-int|LTR|ERVL-MaLR	25828	NM_177911	331046	Mm.195309	NM_177911	ENSMUSG00000025787	Tgm4	9530008N10Rik|Eapa1|TGP	transglutaminase 4 (prostate)	protein-coding
mm_19341.1	chr2	90745208	90745249	-	1	NA	promoter-TSS (NM_018828)	promoter-TSS (NM_018828)	-142	NM_018828	55935	Mm.489638	NM_018828	ENSMUSG00000008200	Fnbp4	FBP30|Fnbp30|mKIAA1014	formin binding protein 4	protein-coding
mm_40079.1	chr5	34369895	34369905	+	1	NA	promoter-TSS (NM_001243123)	promoter-TSS (NM_001243123)	-33	NM_001243123	231128	Mm.286885	NM_001030306	ENSMUSG00000037210	Fam193a	-	family with sequence similarity 193, member A	protein-coding
mm_46012.1	chr5	90890472	90890478	-	1	NA	promoter-TSS (NM_008176)	promoter-TSS (NM_008176)	-770	NM_008176	14825	Mm.21013	NM_008176	ENSMUSG00000029380	Cxcl1	Fsp|Gro1|KC|Mgsa|N51|Scyb1|gro	chemokine (C-X-C motif) ligand 1	protein-coding
mm_18533.1	chr2	64096715	64096719	-	1	NA	intron (NM_001267847, intron 1 of 3)	intron (NM_001267847, intron 1 of 3)	1321	NM_001267846	60344	Mm.130769	NM_021716	ENSMUSG00000075324	Fign	fi|fidget	fidgetin	protein-coding
mm_22826.1	chr3	27241548	27241564	+	1	NA	exon (NM_178772, exon 5 of 5)	exon (NM_178772, exon 5 of 5)	58552	NM_178772	320024	Mm.24576	NM_178772	ENSMUSG00000027698	Nceh1	Aadacl1|B230106I24Rik|CPO-BP|Nceh	neutral cholesterol ester hydrolase 1	protein-coding
mm_11049.1	chr2	27170530	27170546	+	1	NA	exon (NM_138942, exon 3 of 12)	exon (NM_138942, exon 3 of 12)	5031	NM_138942	13166	Mm.167781	NM_138942	ENSMUSG00000000889	Dbh	-	dopamine beta hydroxylase	protein-coding
mm_172106.1	chr6	3200773	3200779	+	1	NA	Intergenic	B3A|SINE|B2	-87743	NR_036696	667335	Mm.380219	NR_036696	ENSMUSG00000106779	Gm8579	EG667335	spermatogenesis associated glutamate (E)-rich protein 4a pseudogene	pseudo
mm_104044.1	chr11	86352118	86352118	-	1	NA	intron (NM_001080931, intron 2 of 29)	intron (NM_001080931, intron 2 of 29)	5407	NM_001080931	327987	Mm.341886	NM_001080931	ENSMUSG00000034297	Med13	1110067M05Rik|D030023K18|Thrap1|Trap240	mediator complex subunit 13	protein-coding
mm_115206.1	chr13	109142778	109142794	+	1	NA	intron (NM_011056, intron 3 of 16)	L1M2|LINE|L1	-181958	NR_030644	100124489		NR_030644	ENSMUSG00000076946	Mir582	Mirn582|mir-582|mmu-mir-582	microRNA 582	ncRNA
mm_1377.1	chr1	66700863	66700875	+	1	NA	promoter-TSS (NM_001310644)	promoter-TSS (NM_001310644)	38	NM_001310644	66646	Mm.240912	NM_025683	ENSMUSG00000026005	Rpe	2810429B02Rik|5730518J08Rik	ribulose-5-phosphate-3-epimerase	protein-coding
mm_111282.1	chr12	85351126	85351157	-	1	NA	intron (NM_026775, intron 2 of 4)	intron (NM_026775, intron 2 of 4)	-11779	NM_145138	217718	Mm.29071	NM_145138	ENSMUSG00000034290	Nek9	C130021H08Rik	NIMA (never in mitosis gene a)-related expressed kinase 9	protein-coding
mm_61679.1	chr7	80993659	80993698	+	1	NA	promoter-TSS (NM_178707)	promoter-TSS (NM_178707)	-6	NM_178707	233410	Mm.29525	NM_178707	ENSMUSG00000005621	Zfp592	8430405N24|A730014M16Rik|Znf592|mKIAA0211	zinc finger protein 592	protein-coding
mm_118572.1	chr14	19277973	19277991	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	324605	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_43989.1	chr5	146706637	146706645	+	1	NA	Intergenic	Intergenic	88315	NM_011669	22217	Mm.167971	NM_011669	ENSMUSG00000029640	Usp12	Ubh1	ubiquitin specific peptidase 12	protein-coding
mm_103187.1	chr11	70615573	70615591	-	1	NA	promoter-TSS (NM_001145537)	promoter-TSS (NM_001145537)	-312	NM_001145537	668433	Mm.425687	NM_001145537	ENSMUSG00000087279	4930544D05Rik	-	RIKEN cDNA 4930544D05 gene	protein-coding
mm_121868.1	chr14	20734517	20734547	-	1	NA	promoter-TSS (NM_010811)	promoter-TSS (NM_010811)	30	NM_010811	17423	Mm.4084	NM_010811	ENSMUSG00000039308	Ndst2	Mndns|NDST-2	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 2	protein-coding
mm_140497.1	chr17	3557814	3557824	-	1	NA	promoter-TSS (NR_045303)	promoter-TSS (NR_045303)	-5	NR_045303	68230	Mm.431352	NR_045302		1700102H20Rik	-	RIKEN cDNA 1700102H20 gene	ncRNA
mm_126274.1	chr15	79144622	79144636	+	1	NA	exon (NM_027231, exon 2 of 5)	exon (NM_027231, exon 2 of 5)	3304	NM_027231	69833	Mm.279861	NM_027231	ENSMUSG00000033020	Polr2f	1810060D16Rik|RPB6	polymerase (RNA) II (DNA directed) polypeptide F	protein-coding
mm_13750.1	chr2	118125724	118125745	+	1	NA	3' UTR (NM_011580, exon 22 of 22)	3' UTR (NM_011580, exon 22 of 22)	13858	NM_001313914	21825	Mm.4159	NM_011580	ENSMUSG00000040152	Thbs1	TSP-1|TSP1|Thbs-1|tbsp1	thrombospondin 1	protein-coding
mm_86754.1	chr10	19606227	19606278	+	1	NA	exon (NM_010511, exon 5 of 7)	exon (NM_010511, exon 5 of 7)	14303	NM_010511	15979	Mm.549	NM_010511	ENSMUSG00000020009	Ifngr1	CD119|IFN-gammaR|Ifgr|Ifngr|Nktar	interferon gamma receptor 1	protein-coding
mm_164471.1	chr16	67620636	67620671	-	1	NA	5' UTR (NM_178721, exon 1 of 10)	5' UTR (NM_178721, exon 1 of 10)	255	NM_001347247	239857	Mm.394300	NM_178721	ENSMUSG00000064115	Cadm2	2900078E11Rik|9330131D06|A830029E02Rik|Igdf4d|Igsf4d|NECL3|SynCAM 2|SynCAM2	cell adhesion molecule 2	protein-coding
mm_130018.1	chr15	88708346	88708362	-	1	NA	intron (NM_001033274, intron 6 of 12)	intron (NM_001033274, intron 6 of 12)	25865	NM_001033274	223770	Mm.254438	NM_001033274	ENSMUSG00000022387	Brd1	1110059H06Rik|AI316859|mKIAA4191	bromodomain containing 1	protein-coding
mm_117111.1	chr13	60177393	60177399	-	1	NA	5' UTR (NM_008086, exon 1 of 1)	5' UTR (NM_008086, exon 1 of 1)	139	NM_008086	14451	Mm.22701	NM_008086	ENSMUSG00000052957	Gas1	AW554192|Gas-1	growth arrest specific 1	protein-coding
mm_158466.1	chrX	140956645	140956657	-	1	NA	promoter-TSS (NM_001164177)	promoter-TSS (NM_001164177)	60	NM_016883	53380	Mm.17640	NM_016883	ENSMUSG00000031429	Psmd10	AW554874	proteasome (prosome, macropain) 26S subunit, non-ATPase, 10	protein-coding
mm_162030.1	chr19	53390000	53390000	-	1	NA	intron (NM_172429, intron 1 of 5)	CpG	573	NM_172429	76479	Mm.313687	NM_172429	ENSMUSG00000025024	Smndc1	2410004J23Rik|4933440I19Rik	survival motor neuron domain containing 1	protein-coding
mm_14730.1	chr2	144270575	144270591	+	1	NA	promoter-TSS (NM_024225)	promoter-TSS (NM_024225)	-11	NM_024225	69178	Mm.273379	NM_024225	ENSMUSG00000027423	Snx5	0910001N05Rik|1810032P22Rik|AU019504|D2Ertd52e	sorting nexin 5	protein-coding
mm_172693.1	chr8	60736514	60736521	-	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	80960	NM_001177882	71306	Mm.23242	NM_027756	ENSMUSG00000031647	Mfap3l	4933428A15Rik|5430405D20Rik|AI461995|AW125052|NYD-sp9|mKIAA0626	microfibrillar-associated protein 3-like	protein-coding
mm_35010.1	chr4	3454357	3454361	-	1	NA	Intergenic	RMER19B|LTR|ERVK	-82731	NR_037306	100499523		NR_037306	ENSMUSG00000094253	Mir3471-2	mmu-mir-3471-2	microRNA 3471-2	ncRNA
mm_35946.1	chr4	53113337	53113411	-	1	NA	intron (NM_013454, intron 5 of 49)	intron (NM_013454, intron 5 of 49)	46521	NM_013454	11303	Mm.277376	NM_013454	ENSMUSG00000015243	Abca1	ABC-1|Abc1	ATP-binding cassette, sub-family A (ABC1), member 1	protein-coding
mm_70025.1	chr7	142576222	142576263	-	1	NA	TTS (NR_030416)	TTS (NR_030416)	905	NR_030416	735280		NR_030416	ENSMUSG00000076275	Mir675	Mirn675|mir-675|mmu-mir-675	microRNA 675	ncRNA
mm_76925.1	chr8	105936837	105936848	-	1	NA	intron (NM_013640, intron 5 of 7)	intron (NM_013640, intron 5 of 7)	1550	NM_013640	19171	Mm.787	NM_013640	ENSMUSG00000031897	Psmb10	Mecl-1|Mecl1	proteasome (prosome, macropain) subunit, beta type 10	protein-coding
mm_35530.1	chr4	41313430	41313437	-	1	NA	exon (NM_026893, exon 2 of 9)	exon (NM_026893, exon 2 of 9)	1468	NM_026893	68970	Mm.28891	NM_026893	ENSMUSG00000028436	Dcaf12	1500001L20Rik|5830424K06Rik|AA420338|AI851081|Wdr40a	DDB1 and CUL4 associated factor 12	protein-coding
mm_157103.1	chrX	9437679	9437693	-	1	NA	3' UTR (NM_007807, exon 13 of 13)	3' UTR (NM_007807, exon 13 of 13)	31638	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_78985.1	chr9	45390794	45390808	+	1	NA	exon (NM_022004, exon 4 of 8)	exon (NM_022004, exon 4 of 8)	-8908	NR_028499	11936	Mm.22742	NM_007503	ENSMUSG00000059412	Fxyd2	Atp1g1	FXYD domain-containing ion transport regulator 2	protein-coding
mm_60148.1	chr7	38186255	38186262	+	1	NA	intron (NM_028166, intron 1 of 3)	PB1D10|SINE|Alu	2471	NM_028166	72244	Mm.187554	NM_028166		1600014C10Rik	AI428873	RIKEN cDNA 1600014C10 gene	protein-coding
mm_48020.1	chr5	136171597	136171629	-	1	NA	promoter-TSS (NM_178751)	promoter-TSS (NM_178751)	-957	NM_178751	269717	Mm.308396	NM_178751	ENSMUSG00000039747	Orai2	A730041O15Rik|Tmem142b	ORAI calcium release-activated calcium modulator 2	protein-coding
mm_56133.1	chr6	87690820	87690852	-	1	NA	promoter-TSS (NR_045482)	promoter-TSS (NR_045482)	11	NR_045482	613264	Mm.480195	NR_045482	ENSMUSG00000089997	1810020O05Rik	-	Riken cDNA 1810020O05 gene	ncRNA
mm_3432.1	chr1	150101185	150101195	+	1	NA	intron (NM_011198, intron 2 of 9)	intron (NM_011198, intron 2 of 9)	1159	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_57652.1	chr6	128438639	128438667	-	1	NA	promoter-TSS (NM_010219)	promoter-TSS (NM_010219)	-22	NM_010219	14228	Mm.12758	NM_010219	ENSMUSG00000030357	Fkbp4	59kDa|AL022792|AW208983|FKBP-4|FKBP-52|FKBP52|FKPB52|p59	FK506 binding protein 4	protein-coding
mm_101827.1	chr11	47240706	47240718	-	1	NA	intron (NM_011891, intron 2 of 7)	intron (NM_011891, intron 2 of 7)	138590	NM_011891	24052	Mm.338890	NM_011891	ENSMUSG00000020354	Sgcd	35kDa|delta-SG	sarcoglycan, delta (dystrophin-associated glycoprotein)	protein-coding
mm_67493.1	chr7	80748869	80748895	-	1	NA	exon (NM_016721, exon 15 of 38)	exon (NM_016721, exon 15 of 38)	54449	NM_016721	29875	Mm.207619	NM_016721	ENSMUSG00000030536	Iqgap1	AA682088|D7Ertd237e|D7Ertd257e|mKIAA0051	IQ motif containing GTPase activating protein 1	protein-coding
mm_20853.1	chr2	148397022	148397036	-	1	NA	TTS (NM_009219)	TTS (NM_009219)	1652	NM_009219	20608	Mm.35324	NM_009219	ENSMUSG00000037014	Sstr4	Smstr4|sst4	somatostatin receptor 4	protein-coding
mm_26046.1	chr3	135607386	135607395	+	1	NA	intron (NM_008689, intron 13 of 24)	intron (NM_008689, intron 13 of 24)	84157	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_140379.1	chr17	87078256	87078267	+	1	NA	Intergenic	Intergenic	-29418	NM_019654	56468	Mm.126885	NM_019654	ENSMUSG00000037104	Socs5	1810018L08Rik|Cish5|mKIAA0671	suppressor of cytokine signaling 5	protein-coding
mm_106239.1	chr11	117779606	117779631	-	1	NA	intron (NM_145439, intron 1 of 19)	intron (NM_145439, intron 1 of 19)	1003	NM_181321	217353	Mm.286963	NM_145439	ENSMUSG00000025572	Tmc6	D11Ertd204e|EVER1	transmembrane channel-like gene family 6	protein-coding
mm_110049.1	chr12	17737238	17737265	-	1	NA	intron (NM_016677, intron 1 of 3)	intron (NM_016677, intron 1 of 3)	46437	NM_016677	53602	Mm.313619	NM_016677	ENSMUSG00000071379	Hpcal1	NVP-3|Nvp3|VILIP3|Vnsl3|Vsnl3	hippocalcin-like 1	protein-coding
mm_76139.1	chr8	81491882	81491886	-	1	NA	intron (NM_001297591, intron 2 of 24)	intron (NM_001297591, intron 2 of 24)	149322	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_15300.1	chr2	155385926	155385949	+	1	NA	exon (NM_178111, exon 3 of 4)	exon (NM_178111, exon 3 of 4)	4081	NM_178111	68728	Mm.293605	NM_178111	ENSMUSG00000038375	Trp53inp2	1110029F20Rik|Tp53inp2	transformation related protein 53 inducible nuclear protein 2	protein-coding
mm_12206.1	chr2	66440857	66440905	+	1	NA	promoter-TSS (NR_033495)	promoter-TSS (NR_033495)	1	NR_033495	100038743	Mm.330264	NR_033495		Gm13629	OTTMUSG00000013098	predicted gene 13629	ncRNA
mm_35870.1	chr4	49536608	49536621	-	1	NA	3' UTR (NM_144903, exon 9 of 9)	3' UTR (NM_144903, exon 9 of 9)	12932	NM_144903	230163	Mm.482116	NM_144903	ENSMUSG00000028307	Aldob	Aldo-2|Aldo2|BC016435	aldolase B, fructose-bisphosphate	protein-coding
mm_123344.1	chr14	63138482	63138500	-	1	NA	exon (NM_007798, exon 7 of 10)	exon (NM_007798, exon 7 of 10)	16029	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_153176.1	chr19	34493874	34493884	-	1	NA	3' UTR (NM_021460, exon 10 of 10)	3' UTR (NM_021460, exon 10 of 10)	-18744	NM_009890	12642	Mm.30824	NM_009890	ENSMUSG00000050370	Ch25h	AI462618|m25OH	cholesterol 25-hydroxylase	protein-coding
mm_125322.1	chr15	38301193	38301220	+	1	NA	promoter-TSS (NM_013692)	promoter-TSS (NM_013692)	-495	NM_001289471	21847	Mm.4292	NM_013692	ENSMUSG00000037465	Klf10	AI115143|EGR[a]|Egral|Gdnfif|TIEG-1|Tieg|Tieg1|mGIF	Kruppel-like factor 10	protein-coding
mm_64158.1	chr7	141356116	141356129	+	1	NA	exon (NM_133191, exon 8 of 21)	exon (NM_133191, exon 8 of 21)	8988	NR_033532	320871	Mm.475463	NM_177280	ENSMUSG00000086844	B230206H07Rik	-	RIKEN cDNA B230206H07 gene	ncRNA
mm_53626.1	chr6	140491065	140491073	+	1	NA	intron (NM_144920, intron 3 of 30)	intron (NM_144920, intron 3 of 30)	66970	NM_144920	109135	Mm.247670	NM_144920	ENSMUSG00000030231	Plekha5	2810431N21Rik|AI428202|AK129423|AMH-Cre|Ayu21-9|Gt(pU21)9Imeg|Pepp2|Tg(AMH-cre)1Flor	pleckstrin homology domain containing, family A member 5	protein-coding
mm_32939.1	chr4	119294176	119294191	+	1	NA	intron (NM_011732, intron 1 of 7)	CpG-10232	330	NM_011732	22608	Mm.258204	NM_011732	ENSMUSG00000028639	Ybx1	1700102N10Rik|C79409|EF1A|MSY1|Nsep1|YB-1|dbpB|mYB-1a	Y box protein 1	protein-coding
mm_165706.1	chr3	97651890	97651920	+	1	NA	3' UTR (NM_001161763, exon 9 of 9)	3' UTR (NM_001161763, exon 9 of 9)	-6307	NM_182997	108097	Mm.31175	NM_182997	ENSMUSG00000038205	Prkab2	5730553K21Rik|AW049591|BB124140	protein kinase, AMP-activated, beta 2 non-catalytic subunit	protein-coding
mm_22981.1	chr3	32818346	32818346	+	1	NA	intron (NM_001013024, intron 1 of 20)	intron (NM_001013024, intron 1 of 20)	720	NM_001013024	72607	Mm.316153	NM_001013024	ENSMUSG00000056900	Usp13	2700071E21Rik|AI848077|ISOT3|IsoT-3	ubiquitin specific peptidase 13 (isopeptidase T-3)	protein-coding
mm_46672.1	chr5	109015680	109015710	-	1	NA	Intergenic	Intergenic	-9259	NM_009491	22307	Mm.261598	NM_009491	ENSMUSG00000067010	Vmn2r10	V2r16|VR16	vomeronasal 2, receptor 10	protein-coding
mm_106886.1	chr12	8012095	8012101	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	34421	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_36412.1	chr4	78078435	78078454	-	1	NA	intron (NM_011211, intron 1 of 39)	MIRc|SINE|MIR	133451	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding
mm_89424.1	chr10	90918162	90918166	+	1	NA	intron (NM_001177396, intron 6 of 11)	intron (NM_001177396, intron 6 of 11)	88321	NM_001347053	77531	Mm.440605	NM_181398	ENSMUSG00000058589	Anks1b	AIDA-1b|C030032C09Rik|E530015N03Rik|ENSMUSG00000078431|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding
mm_76018.1	chr8	74994266	74994283	-	1	NA	intron (NM_178017, intron 1 of 10)	CpG	624	NM_178017	70823	Mm.261739	NM_178017	ENSMUSG00000034518	Hmgxb4	4733401K04Rik|AI316803|Hmgb2l1	HMG box domain containing 4	protein-coding
mm_125151.1	chr15	30646848	30646911	+	1	NA	exon (NM_008729, exon 7 of 23)	exon (NM_008729, exon 7 of 23)	-392247	NR_045186	73784	Mm.66947	NR_045186		4930430F21Rik	-	RIKEN cDNA 4930430F21 gene	ncRNA
mm_56530.1	chr6	99523324	99523338	-	1	NA	Intergenic	Intergenic	-2338	NM_001347345	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_27561.1	chr3	58576553	58576582	-	1	NA	promoter-TSS (NM_001040396)	promoter-TSS (NM_001040396)	-91	NM_001040396	69227	Mm.270950	NM_001040396	ENSMUSG00000075700	Selenot	2810407C02Rik|5730408P04Rik|Selt	selenoprotein T	protein-coding
mm_117832.1	chr13	98316976	98317003	-	1	NA	promoter-TSS (NR_137279)	promoter-TSS (NR_137279)	17	NM_001170540	218490	Mm.371688	NM_145455	ENSMUSG00000021660	Btf3	1700054E11Rik	basic transcription factor 3	protein-coding
mm_163397.1	chr12	70219438	70219452	+	1	NA	intron (NM_133198, intron 3 of 19)	intron (NM_133198, intron 3 of 19)	8238	NM_133198	110095	Mm.256926	NM_133198	ENSMUSG00000021069	Pygl	-	liver glycogen phosphorylase	protein-coding
mm_152080.1	chr19	6858174	6858178	-	1	NA	promoter-TSS (NM_001081291)	promoter-TSS (NM_001081291)	35	NM_001081291	78317	Mm.329596	NM_198008	ENSMUSG00000047810	Ccdc88b	2610041P08Rik|Ccdc88	coiled-coil domain containing 88B	protein-coding
mm_9280.1	chr1	171634492	171634509	-	1	NA	3' UTR (NM_144539, exon 8 of 8)	3' UTR (NM_144539, exon 8 of 8)	7400	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_10088.1	chr2	3118524	3118542	+	1	NA	promoter-TSS (NM_001347067)	promoter-TSS (NM_001347067)	145	NM_001081161	269233	Mm.23044	NM_001081161	ENSMUSG00000050530	Fam171a1	9630050M13Rik|AA409679	family with sequence similarity 171, member A1	protein-coding
mm_139112.1	chr17	47385387	47385395	+	1	NA	promoter-TSS (NM_146079)	promoter-TSS (NM_146079)	-2	NM_146079	107477	Mm.59151	NM_146079	ENSMUSG00000023979	Guca1b	BC018258|GCAP2	guanylate cyclase activator 1B	protein-coding
mm_9846.1	chr1	184732130	184732149	-	1	NA	exon (NM_008250, exon 1 of 4)	exon (NM_008250, exon 1 of 4)	354	NM_008250	15284	Mm.1347	NM_008250	ENSMUSG00000039377	Hlx	Hlx1	H2.0-like homeobox	protein-coding
mm_45201.1	chr5	52566265	52566312	-	1	NA	promoter-TSS (NM_144945)	promoter-TSS (NM_144945)	18	NM_001310604	246316	Mm.44721	NM_144945	ENSMUSG00000039252	Lgi2	mKIAA1916	leucine-rich repeat LGI family, member 2	protein-coding
mm_42846.1	chr5	122171508	122171528	+	1	NA	intron (NM_013636, intron 3 of 6)	intron (NM_013636, intron 3 of 6)	13239	NM_013636	19047	Mm.280784	NM_013636	ENSMUSG00000004455	Ppp1cc	PP-1G|PP1|dis2m1	protein phosphatase 1, catalytic subunit, gamma isoform	protein-coding
mm_108333.1	chr12	80113395	80113405	+	1	NA	promoter-TSS (NM_007564)	promoter-TSS (NM_007564)	-387	NM_007564	12192	Mm.235132	NM_007564	ENSMUSG00000021127	Zfp36l1	AW742437|AW743212|Berg36|Brf1|D530020L18Rik|ERF1|TIS11b|cMG1	zinc finger protein 36, C3H type-like 1	protein-coding
mm_135230.1	chr16	36874807	36874862	-	1	NA	promoter-TSS (NM_134111)	promoter-TSS (NM_134111)	-8	NM_134111	106389	Mm.432078	NM_134111	ENSMUSG00000022838	Eaf2	AW048865|FESTA-L|FESTA-S|Festa|Traits|U19	ELL associated factor 2	protein-coding
mm_92017.1	chr10	62342737	62342751	-	1	NA	intron (NR_038038, intron 1 of 1)	intron (NR_038038, intron 1 of 1)	2137	NR_038038	70162	Mm.441212	NR_038038		Hk1os	2210417K05Rik	hexokinase 1, opposite strand	ncRNA
mm_150229.1	chr19	33970819	33970830	+	1	NA	exon (NM_026334, exon 7 of 10)	exon (NM_026334, exon 7 of 10)	9576	NM_026334	67717	Mm.329816	NM_026334	ENSMUSG00000024768	Lipf	2310051B21Rik|AV082900	lipase, gastric	protein-coding
mm_146680.1	chr18	12819870	12819874	-	1	NA	promoter-TSS (NR_045524)	promoter-TSS (NR_045524)	35	NR_045524	64291	Mm.259470	NM_020573	ENSMUSG00000044252	Osbpl1a	G430090F17Rik|Gm753|ORP-1|Osbpl1b	oxysterol binding protein-like 1A	protein-coding
mm_21514.1	chr2	163627951	163627971	-	1	NA	exon (NM_012032, exon 8 of 10)	exon (NM_012032, exon 8 of 10)	-16889	NR_028113	68386	Mm.410649	NR_028113	ENSMUSG00000058812	0610039K10Rik	-	RIKEN cDNA 0610039K10 gene	ncRNA
mm_37448.1	chr4	123387351	123387363	-	1	NA	exon (NM_001199137, exon 63 of 93)	exon (NM_001199137, exon 63 of 93)	24554	NM_001167918	442834	Mm.483803	NM_001167918		D830031N03Rik	Kiaa0754|mKIAA0754	RIKEN cDNA D830031N03 gene	protein-coding
mm_6762.1	chr1	84105595	84105629	-	1	NA	intron (NM_001003948, intron 2 of 2)	ORR1F|LTR|ERVL-MaLR	113349	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_39415.1	chr5	15934374	15934397	+	1	NA	promoter-TSS (NM_001110843)	promoter-TSS (NM_001110843)	-306	NM_001110843	12293	Mm.159842	NM_009784	ENSMUSG00000040118	Cacna2d1	Ca(v)alpha2delta1|Cacna2|Cchl2a	calcium channel, voltage-dependent, alpha2/delta subunit 1	protein-coding
mm_32763.1	chr4	116690674	116690697	+	1	NA	intron (NM_011034, intron 2 of 5)	B2_Mm1t|SINE|B2	-4663	NR_040442	100502959	Mm.395400	NR_040442		AV051173	-	expressed sequence AV051173	ncRNA
mm_48521.1	chr5	142903290	142903309	-	1	NA	3' UTR (NM_007393, exon 6 of 6)	3' UTR (NM_007393, exon 6 of 6)	3455	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_24875.1	chr3	95982810	95982815	+	1	NA	Intergenic	Intergenic	-2698	NR_045872	668224	Mm.357766	NR_045872		Gm9054	EG668224	predicted gene 9054	ncRNA
mm_44005.1	chr5	146948756	146948760	+	1	NA	5' UTR (NM_025652, exon 1 of 9)	5' UTR (NM_025652, exon 1 of 9)	101	NM_025652	66596	Mm.196528	NM_025652	ENSMUSG00000016503	Gtf3a	2010015D03Rik|2610111I01Rik|5330403M05Rik	general transcription factor III A	protein-coding
mm_9110.1	chr1	170111178	170111214	-	1	NA	Intergenic	Intergenic	-22252	NM_022563	18214	Mm.229249	NM_022563	ENSMUSG00000026674	Ddr2	AW495251|Ntrkr3|tyro10	discoidin domain receptor family, member 2	protein-coding
mm_138180.1	chr17	34267470	34267484	+	1	NA	exon (NM_207105, exon 3 of 6)	exon (NM_207105, exon 3 of 6)	4250	NM_207105	14961	Mm.254067	NM_207105	ENSMUSG00000073421	H2-Ab1	AI845868|Abeta|H-2Ab|H2-Ab|I-Abeta|IAb|Ia-2|Ia2|Rmcs1	histocompatibility 2, class II antigen A, beta 1	protein-coding
mm_160734.1	chr10	78847962	78847962	-	1	NA	promoter-TSS (NM_146308)	promoter-TSS (NM_146308)	-49	NM_146308	258305	Mm.377425	NM_146308	ENSMUSG00000051190	Olfr1356	MOR142-1|MOR142-2_p	olfactory receptor 1356	protein-coding
mm_8852.1	chr1	162710459	162710482	-	1	NA	exon (NM_001081290, exon 12 of 35)	exon (NM_001081290, exon 12 of 35)	30086	NM_001081290	226562	Mm.245446	NM_001081290	ENSMUSG00000040225	Prrc2c	1810043M20Rik|9630039I18Rik|A630006J20|Bat2d|Bat2d1|Bat2l2|E130112L15Rik|Prrc3|mKIAA1096	proline-rich coiled-coil 2C	protein-coding
mm_75956.1	chr8	71701763	71701784	-	1	NA	promoter-TSS (NM_028189)	promoter-TSS (NM_028189)	27	NM_028189	72297	Mm.290837	NM_028189	ENSMUSG00000031803	B3gnt3	2210008L19Rik	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 3	protein-coding
mm_38964.1	chr4	150879591	150879600	-	1	NA	Intergenic	Intergenic	24504	NM_133753	74155	Mm.318841	NM_133753	ENSMUSG00000028967	Errfi1	1300002F13Rik|AI788755|Mig-6|Mig6|RALT	ERBB receptor feedback inhibitor 1	protein-coding
mm_138596.1	chr17	35517262	35517271	+	1	NA	promoter-TSS (NM_001163763)	promoter-TSS (NM_001163763)	150	NM_146248	240084	Mm.49544	NM_146248	ENSMUSG00000040312	Cchcr1	Hcr	coiled-coil alpha-helical rod protein 1	protein-coding
mm_93337.1	chr10	99759476	99759492	-	1	NA	5' UTR (NM_027945, exon 1 of 1)	5' UTR (NM_027945, exon 1 of 1)	174	NM_027945	71832	Mm.483162	NM_027945	ENSMUSG00000046934	Csl	1700007H16Rik	citrate synthase like	protein-coding
mm_172876.1	chr9	44407723	44407739	+	1	NA	promoter-TSS (NM_021789)	promoter-TSS (NM_021789)	17	NM_024266	75617	Mm.292027	NM_024266	ENSMUSG00000009927	Rps25	2810009D21Rik	ribosomal protein S25	protein-coding
mm_105825.1	chr11	113171858	113171872	-	1	NA	intron (NR_015556, intron 1 of 2)	RLTR20C1_MM|LTR|ERVK	29973	NR_015556	72386	Mm.266961	NR_015556	ENSMUSG00000087259	2610035D17Rik	-	RIKEN cDNA 2610035D17 gene	ncRNA
mm_9774.1	chr1	181093746	181093749	-	1	NA	3' UTR (NM_026171, exon 23 of 23)	3' UTR (NM_026171, exon 23 of 23)	42510	NM_001033819	619326	Mm.355174	NM_001033819	ENSMUSG00000038768	9130409I23Rik	-	RIKEN cDNA 9130409I23 gene	protein-coding
mm_147327.1	chr18	42275170	42275212	-	1	NA	promoter-TSS (NM_172626)	promoter-TSS (NM_172626)	6	NR_033452	100042757	Mm.100172	NR_033452		Gm4013	-	predicted gene 4013	ncRNA
mm_127401.1	chr15	101186363	101186404	+	1	NA	intron (NM_007395, intron 1 of 8)	intron (NM_007395, intron 1 of 8)	-7486	NR_105927	102466774		NR_105927	ENSMUSG00000106563	Mir6962	mmu-mir-6962	microRNA 6962	ncRNA
mm_13496.1	chr2	107010885	107010893	+	1	NA	Intergenic	Intergenic	-36492	NM_001025102	212772	Mm.381231	NM_173750	ENSMUSG00000027122	Arl14ep	2700007P21Rik|4930448O08Rik|ARF7EP	ADP-ribosylation factor-like 14 effector protein	protein-coding
mm_94294.1	chr11	4064910	4064927	+	1	NA	promoter-TSS (NM_001029937)	promoter-TSS (NM_001029937)	65	NM_001029937	380683	Mm.296806	NM_001029937	ENSMUSG00000054986	Sec14l3	1110069O07Rik	SEC14-like lipid binding 3	protein-coding
mm_78057.1	chr9	14900521	14900545	+	1	NA	exon (NM_022888, exon 5 of 5)	exon (NM_022888, exon 5 of 5)	3418	NM_176807	64931	Mm.86738	NM_022888	ENSMUSG00000031933	Izumo1r	0910001L11Rik|C86255|Folbp3|Folr4|Juno	IZUMO1 receptor, JUNO	protein-coding
mm_80966.1	chr9	103111876	103111892	+	1	NA	promoter-TSS (NM_173781)	promoter-TSS (NM_173781)	-190	NM_173781	270192	Mm.490252	NM_173781	ENSMUSG00000032549	Rab6b	9630015C03|AI844641|C330006L04Rik|D9Bwg0185e	RAB6B, member RAS oncogene family	protein-coding
mm_126464.1	chr15	81039640	81039646	+	1	NA	intron (NM_001082536, intron 3 of 13)	U4|snRNA|snRNA	61878	NM_134091	105835	Mm.274943	NM_134091	ENSMUSG00000042303	Sgsm3	1810012I01Rik|AI428557|BB175482|Cip85|R75178|RUSC3|Rutbc3	small G protein signaling modulator 3	protein-coding
mm_157247.1	chrX	19146299	19146312	-	1	NA	promoter-TSS (NR_029806)	promoter-TSS (NR_029806)	83	NR_029806	723827		NR_029806	ENSMUSG00000065422	Mir221	Mirn221|mir-221|mmu-mir-221	microRNA 221	ncRNA
mm_125601.1	chr15	59695819	59695819	+	1	NA	Intergenic	B4|SINE|B4	47165	NM_144549	211770	Mm.40298	NM_144549	ENSMUSG00000032501	Trib1	A530090O15Rik|TRB-1|Trb1	tribbles pseudokinase 1	protein-coding
mm_70364.1	chr8	8666574	8666579	+	1	NA	TTS (NM_176849)	TTS (NM_176849)	-5803	NM_010111	13642	Mm.209813	NM_010111	ENSMUSG00000001300	Efnb2	ELF-2|Epl5|Eplg5|Htk-L|LERK-5|Lerk5|NLERK-1	ephrin B2	protein-coding
mm_171833.1	chr5	146666615	146666628	+	1	NA	Intergenic	(TTAGGG)n|Simple_repeat|Simple_repeat	-81382	NM_001010941	14738	Mm.153539	NM_008151	ENSMUSG00000041468	Gpr12	Gpcr01|Gpcr12|Gpcr20|Gpcr21	G-protein coupled receptor 12	protein-coding
mm_90205.1	chr10	120461999	120462007	+	1	NA	intron (NM_001347170, intron 3 of 5)	intron (NM_001347170, intron 3 of 5)	-13893	NR_030434	791076		NR_030434	ENSMUSG00000076448	Mir763	Mirn763|mir-763|mmu-mir-763	microRNA 763	ncRNA
mm_4799.1	chr1	185204233	185204243	+	1	NA	promoter-TSS (NM_001163754)	promoter-TSS (NM_001163754)	70	NM_001163754	98732	Mm.275841	NM_172649	ENSMUSG00000039318	Rab3gap2	1110059F07Rik|2010002H18Rik|5830469C09|AI851069|AW743433|RAB3-GAP150|mKIAA0839	RAB3 GTPase activating protein subunit 2	protein-coding
mm_162738.1	chr10	56388510	56388529	+	1	NA	exon (NM_010288, exon 2 of 2)	exon (NM_010288, exon 2 of 2)	11219	NM_010288	14609	Mm.378921	NM_010288	ENSMUSG00000050953	Gja1	AU042049|AW546267|Cnx43|Cx43|Cx43alpha1|Gja-1|Npm1|connexin43	gap junction protein, alpha 1	protein-coding
mm_46167.1	chr5	96164148	96164201	-	1	NA	Intergenic	Intergenic	-2184	NM_144910	231464	Mm.28374	NM_144910	ENSMUSG00000034724	Cnot6l	4932442K20Rik	CCR4-NOT transcription complex, subunit 6-like	protein-coding
mm_132298.1	chr16	33518190	33518207	+	1	NA	promoter-TSS (NM_134251)	promoter-TSS (NM_134251)	-131	NM_134251	171286	Mm.35253	NM_134251	ENSMUSG00000035506	Slc12a8	CCC9|E330020C02Rik	solute carrier family 12 (potassium/chloride transporters), member 8	protein-coding
mm_134071.1	chr16	8666505	8666520	-	1	NA	intron (NM_025821, intron 1 of 3)	intron (NM_025821, intron 1 of 3)	5641	NM_025821	52502	Mm.142095	NM_025821	ENSMUSG00000008393	Carhsp1	1200011K09Rik|Crhsp-24|D16Ertd465e	calcium regulated heat stable protein 1	protein-coding
mm_84685.1	chr9	72111702	72111712	-	1	NA	promoter-TSS (NM_001253862)	promoter-TSS (NM_001253862)	112	NM_011544	21406	Mm.171615	NM_011544	ENSMUSG00000032228	Tcf12	A130037E08Rik|ALF1|HEB|HEBAlt|HTF-4|HTF4|ME1|REB|bHLHb20	transcription factor 12	protein-coding
mm_17100.1	chr2	23521986	23522000	-	1	NA	intron (NM_001165998, intron 7 of 10)	L1_Mur3|LINE|L1	50111	NM_029773	76857	Mm.276415	NM_029773	ENSMUSG00000026771	Spopl	4921517N04Rik|AU014935|BB233739|E430033K04Rik	speckle-type POZ protein-like	protein-coding
mm_42613.1	chr5	117976762	117976803	+	1	NA	promoter-TSS (NM_001346588)	promoter-TSS (NM_001346588)	12	NM_001346588	231670	Mm.21912	NM_145564	ENSMUSG00000032898	Fbxo21	2810425J22Rik|AU016673	F-box protein 21	protein-coding
mm_68911.1	chr7	126458892	126458902	-	1	NA	intron (NM_007504, intron 5 of 22)	intron (NM_007504, intron 5 of 22)	4176	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_149152.1	chr19	9013413	9013433	+	1	NA	exon (NM_009643, exon 5 of 5)	exon (NM_009643, exon 5 of 5)	-4481	NR_105786	102465190		NR_105786	ENSMUSG00000099308	Mir6367	Gm27467|mmu-mir-6367	microRNA 6367	ncRNA
mm_47170.1	chr5	120744140	120744175	-	1	NA	intron (NM_001347448, intron 3 of 11)	intron (NM_001347448, intron 3 of 11)	5691	NM_145227	246728	Mm.260926	NM_145227	ENSMUSG00000032690	Oas2	Oasl11	2'-5' oligoadenylate synthetase 2	protein-coding
mm_46726.1	chr5	110770203	110770211	-	1	NA	intron (NM_173066, intron 1 of 50)	CpG	510	NM_029337	75560	Mm.270487	NM_029337	ENSMUSG00000029505	Ep400	1700020J09Rik|AU023439|mDomino|mKIAA1498|p400	E1A binding protein p400	protein-coding
mm_104509.1	chr11	95982603	95982627	-	1	NA	intron (NM_009951, intron 2 of 14)	intron (NM_009951, intron 2 of 14)	-19232	NR_037223	100526468		NR_037223	ENSMUSG00000093358	Mir3063	mmu-mir-3063	microRNA 3063	ncRNA
mm_127697.1	chr15	102990864	102990882	+	1	NA	exon (NM_010466, exon 1 of 2)	exon (NM_010466, exon 1 of 2)	334	NM_010466	15426	Mm.6167	NM_010466	ENSMUSG00000001657	Hoxc8	D130011F21Rik|Hox-3.1	homeobox C8	protein-coding
mm_140784.1	chr17	17910196	17910219	-	1	NA	Intergenic	CpG	22383	NM_008039	14289	Mm.378918	NM_008039	ENSMUSG00000052270	Fpr2	E330010I07Rik|Fpr-rs2	formyl peptide receptor 2	protein-coding
mm_111372.1	chr12	87238757	87238771	-	1	NA	promoter-TSS (NM_027744)	promoter-TSS (NM_027744)	-163	NM_027744	71275	Mm.79198	NM_027744	ENSMUSG00000072919	Noxred1	4933437F05Rik	NADP+ dependent oxidoreductase domain containing 1	protein-coding
mm_75744.1	chr8	69882163	69882176	-	1	NA	exon (NM_026818, exon 8 of 8)	exon (NM_026818, exon 8 of 8)	5223	NM_026818	68709	Mm.334584	NM_026818	ENSMUSG00000044006	Cilp2	1110031K21Rik|AA407300|CLIP-2	cartilage intermediate layer protein 2	protein-coding
mm_56101.1	chr6	87459332	87459340	-	1	NA	non-coding (NR_104483, exon 11 of 11)	non-coding (NR_104483, exon 11 of 11)	30342	NM_009756	12154	Mm.483321	NM_009756	ENSMUSG00000030046	Bmp10	-	bone morphogenetic protein 10	protein-coding
mm_124126.1	chr14	79662149	79662173	-	1	NA	promoter-TSS (NM_001310655)	promoter-TSS (NM_001310655)	22	NM_001310655	16840	Mm.46561	NM_010701	ENSMUSG00000022025	Cnmd	Bricd3|ChM-I|Chmd|Lect1	chondromodulin	protein-coding
mm_11885.1	chr2	49698873	49698889	+	1	NA	intron (NM_008449, intron 8 of 25)	intron (NM_008449, intron 8 of 25)	79567	NM_008449	16574	Mm.256342	NM_008449	ENSMUSG00000026764	Kif5c	KINN|Khc|NKHC|NKHC2	kinesin family member 5C	protein-coding
mm_99018.1	chr11	98907811	98907824	+	1	NA	promoter-TSS (NM_011799)	promoter-TSS (NM_011799)	-72	NM_001025779	23834	Mm.20912	NM_011799	ENSMUSG00000017499	Cdc6	CDC18L	cell division cycle 6	protein-coding
mm_156410.1	chrX	140664297	140664326	+	1	NA	Intergenic	Intergenic	-13717	NM_011845	23947	Mm.131097	NM_011845	ENSMUSG00000000266	Mid2	FXY2|Trim1	midline 2	protein-coding
mm_47745.1	chr5	130255395	130255399	-	1	NA	promoter-TSS (NM_178897)	promoter-TSS (NM_178897)	133	NM_023248	66711	Mm.280484	NM_023248	ENSMUSG00000025337	Sbds	4733401P19Rik|AI836084|CGI-97|SDS	Shwachman-Bodian-Diamond syndrome homolog (human)	protein-coding
mm_66038.1	chr7	30650124	30650182	-	1	NA	promoter-TSS (NM_133693)	promoter-TSS (NM_133693)	75	NM_133693	68035	Mm.401747	NM_133693	ENSMUSG00000036733	Rbm42	1700003D06Rik|3100004P22Rik	RNA binding motif protein 42	protein-coding
mm_77088.1	chr8	110790381	110790390	-	1	NA	intron (NM_029646, intron 1 of 7)	intron (NM_029646, intron 1 of 7)	15539	NM_029646	76527	Mm.77697	NM_029646	ENSMUSG00000031750	Il34	2010004A03Rik|AI593503	interleukin 34	protein-coding
mm_14209.1	chr2	127270209	127270271	+	1	NA	promoter-TSS (NM_139308)	promoter-TSS (NM_139308)	11	NM_139308	99138	Mm.41271	NM_139308	ENSMUSG00000027367	Stard7	AI852671|AL022671|AW544915	START domain containing 7	protein-coding
mm_23.1	chr1	5105327	5105334	+	1	NA	intron (NM_133826, intron 7 of 13)	B1_Mus2|SINE|Alu	22244	NM_001310442	108664	Mm.27082	NM_133826	ENSMUSG00000033793	Atp6v1h	0710001F19Rik|AU022349|CGI-11|SFD|SFDalpha|SFDbeta|VMA13	ATPase, H+ transporting, lysosomal V1 subunit H	protein-coding
mm_15488.1	chr2	157562281	157562291	+	1	NA	3' UTR (NM_010923, exon 3 of 3)	3' UTR (NM_010923, exon 3 of 3)	2208	NM_180960	18111	Mm.34330	NM_010923	ENSMUSG00000067786	Nnat	5730414I02Rik|AW107673|Peg5	neuronatin	protein-coding
mm_169433.1	chr14	54314708	54314708	-	1	NA	Intergenic	IAPEY_LTR|LTR|ERVK	-31783	NM_010991	18348	Mm.436623	NM_010991	ENSMUSG00000048153	Olfr49	IC6|MOR1181	olfactory receptor 49	protein-coding
mm_25582.1	chr3	116866166	116866202	+	1	NA	intron (NM_009146, intron 1 of 16)	ID_B1|SINE|B4	4504	NM_009146	20321	Mm.66293	NM_009146	ENSMUSG00000033386	Frrs1	AI131732|Sdfr2	ferric-chelate reductase 1	protein-coding
mm_161755.1	chr17	35127084	35127084	+	1	NA	5' UTR (NM_033477, exon 3 of 3)	5' UTR (NM_033477, exon 3 of 3)	682	NM_033477	114585	Mm.42070	NM_033477	ENSMUSG00000043311	D17H6S53E	G4|NG34	DNA segment, Chr 17, human D6S53E	protein-coding
mm_118749.1	chr14	22349757	22349777	+	1	NA	intron (NM_028275, intron 2 of 6)	L1MEf|LINE|L1	193031	NR_046307	74896	Mm.444661	NR_046307		4930405A10Rik	4930456G20Rik	RIKEN cDNA 4930405A10 gene	ncRNA
mm_71442.1	chr8	46513310	46513342	+	1	NA	exon (NM_007981, exon 6 of 21)	exon (NM_007981, exon 6 of 21)	22360	NM_001302163	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_6606.1	chr1	75370449	75370485	-	1	NA	intron (NR_037976, intron 2 of 3)	intron (NR_037976, intron 2 of 3)	4548	NR_037976	100503248	Mm.403916	NR_037976	ENSMUSG00000085653	Gm15179	OTTMUSG00000019417	predicted gene 15179	ncRNA
mm_24919.1	chr3	96402097	96402110	+	1	NA	Intergenic	CpG	12730	NR_001579	21748		NR_001579	ENSMUSG00000064796	Terc	mTER|mTR	telomerase RNA component	ncRNA
mm_149445.1	chr19	11484369	11484373	+	1	NA	Intergenic	Intergenic	-7667	NM_001164202	666926	Mm.486382	NM_001164202	ENSMUSG00000058470	Gm8369	EG666926	predicted gene 8369	protein-coding
mm_163773.1	chr13	120018209	120018268	+	1	NA	Intergenic	Intergenic	33966	NM_001302966	100861753	Mm.165042	NM_001302966	ENSMUSG00000095609	Gm21188	-	predicted gene, 21188	protein-coding
mm_5833.1	chr1	52817696	52817736	-	1	NA	promoter-TSS (NM_008384)	promoter-TSS (NM_008384)	-28	NM_008384	16329	Mm.917	NM_008384	ENSMUSG00000026102	Inpp1	2300002C06Rik|AV137389	inositol polyphosphate-1-phosphatase	protein-coding
mm_142762.1	chr17	49113527	49113533	-	1	NA	promoter-TSS (NR_038142)	promoter-TSS (NR_038142)	3	NR_038141	69311	Mm.46140	NR_038141	ENSMUSG00000101012	1700008K24Rik	-	RIKEN cDNA 1700008K24 gene	ncRNA
mm_127420.1	chr15	101266840	101266859	+	1	NA	promoter-TSS (NM_010444)	promoter-TSS (NM_010444)	3	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_7239.1	chr1	93478863	93478868	-	1	NA	promoter-TSS (NM_010891)	promoter-TSS (NM_010891)	52	NM_133808	110611	Mm.30012	NM_133808	ENSMUSG00000034088	Hdlbp	1110005P14Rik|AA960365|AI118566|D1Ertd101e	high density lipoprotein (HDL) binding protein	protein-coding
mm_129581.1	chr15	79741329	79741341	-	1	NA	intron (NM_001205346, intron 1 of 17)	intron (NM_001205346, intron 1 of 17)	1201	NM_194342	223697	Mm.202715	NM_194342	ENSMUSG00000042524	Sun2	B230369L08Rik|C030011B15|Unc84b	Sad1 and UNC84 domain containing 2	protein-coding
mm_64510.1	chr7	143628221	143628230	+	1	NA	promoter-TSS (NM_175649)	promoter-TSS (NM_175649)	-380	NM_175649	244237	Mm.247498	NM_175649	ENSMUSG00000045362	Tnfrsf26	Tnfrh3|Tnfrsf24	tumor necrosis factor receptor superfamily, member 26	protein-coding
mm_62247.1	chr7	99202403	99202426	+	1	NA	Intergenic	MIR|SINE|MIR	-19701	NM_026384	67800	Mm.180189	NM_026384	ENSMUSG00000030747	Dgat2	0610010B06Rik|ARAT|DGAT-2	diacylglycerol O-acyltransferase 2	protein-coding
mm_64005.1	chr7	140193425	140193441	+	1	NA	Intergenic	Intergenic	9335	NM_001011814	258055	Mm.377339	NM_001011814	ENSMUSG00000050366	Olfr524	MOR103-14P	olfactory receptor 524	protein-coding
mm_55940.1	chr6	85001001	85001006	-	1	NA	intron (NM_177077, intron 5 of 21)	intron (NM_177077, intron 5 of 21)	68510	NM_177077	75914	Mm.159621	NM_177077	ENSMUSG00000033769	Exoc6b	4930569O18Rik|G430127E12Rik|Sec15b|Sec15l2|mKIAA0919	exocyst complex component 6B	protein-coding
mm_57101.1	chr6	122591066	122591087	-	1	NA	intron (NM_001134391, intron 4 of 7)	intron (NM_001134391, intron 4 of 7)	11368	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_131050.1	chr16	4037093	4037103	+	1	NA	promoter-TSS (NM_010061)	promoter-TSS (NM_010061)	-47	NM_010061	13419	Mm.291048	NM_010061	ENSMUSG00000005980	Dnase1	AI788650|DNaseI|Dnl1	deoxyribonuclease I	protein-coding
mm_110905.1	chr12	75735829	75735831	-	1	NA	promoter-TSS (NM_030750)	promoter-TSS (NM_030750)	-101	NM_030750	81535	Mm.280199	NM_030750	ENSMUSG00000021054	Sgpp1	AI463453|SPP|SPP1|Spph1	sphingosine-1-phosphate phosphatase 1	protein-coding
mm_161295.1	chr14	27460923	27460923	+	1	NA	intron (NM_028945, intron 13 of 23)	intron (NM_028945, intron 13 of 23)	32076	NM_001114879	218850	Mm.247767	NM_028945	ENSMUSG00000040651	Fam208a	4732418E12|4933409E02Rik|D14Abb1e|MommeD6	family with sequence similarity 208, member A	protein-coding
mm_33086.1	chr4	124657652	124657656	+	1	NA	promoter-TSS (NM_011141)	promoter-TSS (NM_011141)	8	NM_011141	18991	Mm.297371	NM_011141	ENSMUSG00000090125	Pou3f1	Oct-6|Oct6|Otf-6|Otf6|Scip|Test1|Tst-1|Tst1	POU domain, class 3, transcription factor 1	protein-coding
mm_157395.1	chrX	38406842	38406862	-	1	NA	intron (NM_001017959, intron 8 of 8)	L1M3|LINE|L1	49608	NM_010685	16784	Mm.486	NM_010685	ENSMUSG00000016534	Lamp2	CD107b|LGP-B|Lamp II|Lamp-2|Lamp-2a|Lamp-2b|Lamp-2c|Mac3	lysosomal-associated membrane protein 2	protein-coding
mm_29921.1	chr3	131490511	131490531	-	1	NA	Intergenic	CpG	-74247	NM_001289479	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_76622.1	chr8	91800282	91800294	-	1	NA	exon (NM_001253822, exon 2 of 4)	exon (NM_001253822, exon 2 of 4)	1366	NM_001253822	16373	Mm.238044	NM_008393	ENSMUSG00000031734	Irx3	AI894186	Iroquois related homeobox 3	protein-coding
mm_133449.1	chr16	88608717	88608724	+	1	NA	Intergenic	Intergenic	3559	NM_001163141	239932	Mm.120273	NM_001163141	ENSMUSG00000050239	Krtap24-1	Gm312	keratin associated protein 24-1	protein-coding
mm_155509.1	chrX	73966486	73966506	+	1	NA	promoter-TSS (NM_008224)	promoter-TSS (NM_008224)	-139	NM_008224	15161	Mm.491126	NM_008224	ENSMUSG00000031386	Hcfc1	AW060991|HCF|HCF1	host cell factor C1	protein-coding
mm_52830.1	chr6	121363227	121363238	+	1	NA	exon (NM_133661, exon 13 of 15)	exon (NM_133661, exon 13 of 15)	16535	NM_133661	14411	Mm.274506	NM_133661	ENSMUSG00000030109	Slc6a12	BGT1|GAT-2|GAT2|Gabt2	solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12	protein-coding
mm_143726.1	chr17	81378943	81378954	-	1	NA	non-coding (NR_104580, exon 9 of 9)	non-coding (NR_104580, exon 9 of 9)	-313863	NM_028138	72167	Mm.273257	NM_028138	ENSMUSG00000024246	Thumpd2	2810025A12Rik	THUMP domain containing 2	protein-coding
mm_58313.1	chr6	146290063	146290065	-	1	NA	intron (NM_010586, intron 36 of 55)	intron (NM_010586, intron 36 of 55)	212159	NM_010586	16439	Mm.7800	NM_010586	ENSMUSG00000030287	Itpr2	AI649341|InsP3R-2|InsP3R-5|Ip3r2|Itpr5|insP3R2	inositol 1,4,5-triphosphate receptor 2	protein-coding
mm_151994.1	chr19	5875211	5875264	-	1	NA	promoter-TSS (NM_026169)	promoter-TSS (NM_026169)	-29	NM_026169	67457	Mm.202092	NM_026169	ENSMUSG00000024816	Frmd8	1200004M23Rik|2310035N23Rik|4931429L16Rik|AU018809	FERM domain containing 8	protein-coding
mm_121843.1	chr14	20615515	20615520	-	1	NA	intron (NM_030180, intron 1 of 20)	intron (NM_030180, intron 1 of 20)	2837	NM_030180	78787	Mm.301173	NM_030180	ENSMUSG00000034235	Usp54	4930429G18Rik|AI115571|C030002J06Rik	ubiquitin specific peptidase 54	protein-coding
mm_60661.1	chr7	44986882	44986945	+	1	NA	promoter-TSS (NR_045266)	promoter-TSS (NR_045266)	13	NR_045266	100502630	Mm.490013	NR_045266	ENSMUSG00000087138	Gm15545	OTTMUSG00000023473	predicted gene 15545	ncRNA
mm_127548.1	chr15	102144690	102144698	+	1	NA	exon (NM_008344, exon 1 of 4)	exon (NM_008344, exon 1 of 4)	508	NM_008344	16012	Mm.358609	NM_008344	ENSMUSG00000023046	Igfbp6	IGFBP-6	insulin-like growth factor binding protein 6	protein-coding
mm_157579.1	chrX	52744584	52744598	-	1	NA	promoter-TSS (NR_003188)	promoter-TSS (NR_003188)	2	NR_003188	751866	Mm.381916	NR_003188		Kis2	Kis2-T1|Kis2-T2|Kis2-T3|Kis2-T4|Kis2-T5|Platr24|Xpcl1	Kaplan integration site 2	ncRNA
mm_100806.1	chr11	5065277	5065329	-	1	NA	promoter-TSS (NM_001190408)	promoter-TSS (NM_001190408)	24	NM_144560	78926	Mm.44591	NM_030228	ENSMUSG00000034201	Gas2l1	4930500E24Rik|D0Jmb1|Gar22|TU-71.1	growth arrest-specific 2 like 1	protein-coding
mm_173027.1	chrX	104413760	104413765	-	1	NA	promoter-TSS (NM_009592)	promoter-TSS (NM_009592)	84	NM_009592	11306	Mm.426128	NM_009592	ENSMUSG00000031333	Abcb7	AA517758|AU019072|Abc7	ATP-binding cassette, sub-family B (MDR/TAP), member 7	protein-coding
mm_96212.1	chr11	62456598	62456614	+	1	NA	intron (NM_177229, intron 1 of 8)	intron (NM_177229, intron 1 of 8)	726	NM_177229	20185	Mm.271814	NM_011308	ENSMUSG00000018501	Ncor1	5730405M06Rik|A230020K14Rik|N-CoR|RIP13|Rxrip13|mKIAA1047	nuclear receptor co-repressor 1	protein-coding
mm_8278.1	chr1	139982135	139982135	-	1	NA	Intergenic	Lx3A|LINE|L1	-123436	NM_001025575	545366	Mm.439660	NM_001025575	ENSMUSG00000033898	Cfhr2	Cfhrb_4/2	complement factor H-related 2	protein-coding
mm_114730.1	chr13	83721358	83721384	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-6735	NR_015561	320203	Mm.245636	NM_177100	ENSMUSG00000050334	C130071C03Rik	2810449C10Rik	RIKEN cDNA C130071C03 gene	ncRNA
mm_18090.1	chr2	44984607	44984617	-	1	NA	3' UTR (NM_015753, exon 10 of 10)	3' UTR (NM_015753, exon 10 of 10)	38565	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_144827.1	chr18	36348795	36348803	+	1	NA	5' UTR (NM_001081365, exon 1 of 3)	5' UTR (NM_001081365, exon 1 of 3)	175	NM_001081365	66060	Mm.272527	NM_001081365	ENSMUSG00000046727	Cystm1	0610010O12Rik	cysteine-rich transmembrane module containing 1	protein-coding
mm_169360.1	chr14	29968481	29968483	+	1	NA	5' UTR (NM_019979, exon 1 of 5)	5' UTR (NM_019979, exon 1 of 5)	102	NM_019979	80795	Mm.104491	NM_019979	ENSMUSG00000042682	Selenok	1110001C03Rik|AA673253|HSPC030|Hsp30|Selk	selenoprotein K	protein-coding
mm_28208.1	chr3	88334483	88334495	-	1	NA	promoter-TSS (NM_024246)	promoter-TSS (NM_024246)	-56	NM_024246	71913	Mm.34256	NM_024246	ENSMUSG00000001420	Tmem79	2310042N02Rik|2310074C17Rik|Matt|ma	transmembrane protein 79	protein-coding
mm_155506.1	chrX	73787204	73787230	+	1	NA	promoter-TSS (NM_008323)	promoter-TSS (NM_008323)	74	NM_009279	20832	Mm.831	NM_009279	ENSMUSG00000002014	Ssr4	AW743063|C78062|Trap	signal sequence receptor, delta	protein-coding
mm_122522.1	chr14	47277189	47277211	-	1	NA	promoter-TSS (NM_080843)	promoter-TSS (NM_080843)	57	NM_080843	67296	Mm.23957	NM_080843	ENSMUSG00000048379	Socs4	3110032M18Rik|A730004F22Rik|AI427843|AU015727|AU015859|Socs7	suppressor of cytokine signaling 4	protein-coding
mm_57494.1	chr6	125313699	125313723	-	1	NA	5' UTR (NM_010736, exon 1 of 10)	5' UTR (NM_010736, exon 1 of 10)	159	NM_010736	17000	Mm.3122	NM_010736	ENSMUSG00000030339	Ltbr	AI256028|CD18|LTbetaR|Ltar|TNF-R-III|TNFCR|TNFR-RP|TNFR2-RP|TNFRrp|Tnfbr|Tnfrsf3	lymphotoxin B receptor	protein-coding
mm_44284.1	chr5	8162156	8162159	-	1	NA	intron (NM_001310440, intron 5 of 30)	L2a|LINE|L2	105615	NM_001080974	109552	Mm.96211	NM_025618	ENSMUSG00000003161	Sri	2210417O06Rik|2900070H08Rik|Sor	sorcin	protein-coding
mm_69610.1	chr7	137195799	137195803	-	1	NA	3' UTR (NM_001113414, exon 16 of 16)	3' UTR (NM_001113414, exon 16 of 16)	-38882	NR_045885	100038555	Mm.444788	NR_045885	ENSMUSG00000109722	Gm10578	ENSMUSG00000073800	predicted gene 10578	ncRNA
mm_136941.1	chr17	14261054	14261054	+	1	NA	Intergenic	Intergenic	-18452	NM_022315	64074	Mm.30162	NM_022315	ENSMUSG00000023886	Smoc2	1700056C05Rik|5430426J21Rik|Smoc2l	SPARC related modular calcium binding 2	protein-coding
mm_22883.1	chr3	29891009	29891031	+	1	NA	promoter-TSS (NR_110437)	promoter-TSS (NR_110437)	3	NR_110437	102636083		NR_110437	ENSMUSG00000102590	Mannr	Manr	Mecom adjacent non-protein coding RNA	ncRNA
mm_47299.1	chr5	122323915	122323917	-	1	NA	3' UTR (NM_177242, exon 6 of 6)	3' UTR (NM_177242, exon 6 of 6)	30279	NM_144912	231724	Mm.255587	NM_144912	ENSMUSG00000038569	Rad9b	A630082N15Rik|BC021784	RAD9 checkpoint clamp component B	protein-coding
mm_77895.1	chr9	7348569	7348591	+	1	NA	5' UTR (NM_001320076, exon 2 of 10)	5' UTR (NM_001320076, exon 2 of 10)	1206	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_138537.1	chr17	35249082	35249129	+	1	NA	intron (NM_019693, intron 6 of 10)	CT-rich|Low_complexity|Low_complexity	-2184	NR_106169	102465886		NR_106169	ENSMUSG00000098269	Mir8094	Gm27513|mmu-mir-8094	microRNA 8094	ncRNA
mm_50703.1	chr6	52103964	52103974	+	1	NA	intron (NR_110440, intron 1 of 2)	intron (NR_110440, intron 1 of 2)	1020	NR_110440	102635415	Mm.333063	NR_110440	ENSMUSG00000085412	Halr1	Gm15055|Haunt|Linchoxa1|OTTMUSG00000018881|linc-Evx1|linc-Hoxa1|linc1547	Hoxa adjacent long noncoding RNA 1	ncRNA
mm_7364.1	chr1	106712430	106712456	-	1	NA	exon (NM_177410, exon 1 of 1)	exon (NM_177410, exon 1 of 1)	1847	NM_009741	12043	Mm.257460	NM_009741	ENSMUSG00000057329	Bcl2	AW986256|Bcl-2|C430015F12Rik|D630044D05Rik|D830018M01Rik	B cell leukemia/lymphoma 2	protein-coding
mm_2180.1	chr1	88551526	88551547	+	1	NA	promoter-TSS (NR_037971)	promoter-TSS (NR_037971)	19	NR_037971	100503197	Mm.99352	NR_037971	ENSMUSG00000100798	Gm19589	-	predicted gene, 19589	ncRNA
mm_104737.1	chr11	98359466	98359476	-	1	NA	intron (NM_021547, intron 1 of 14)	intron (NM_021547, intron 1 of 14)	1103	NM_021547	59045	Mm.265546	NM_021547	ENSMUSG00000018167	Stard3	Mln64|es64	START domain containing 3	protein-coding
mm_122401.1	chr14	41004374	41004384	-	1	NA	intron (NM_001316735, intron 1 of 5)	intron (NM_001316735, intron 1 of 5)	2541	NM_001316739	70564	Mm.27227	NM_027464	ENSMUSG00000021792	Fam213a	5730469M10Rik|AU040822|Adrx|Pamm	family with sequence similarity 213, member A	protein-coding
mm_17345.1	chr2	26604268	26604309	-	1	NA	5' UTR (NM_026212, exon 1 of 6)	5' UTR (NM_026212, exon 1 of 6)	129	NM_026212	67512	Mm.24244	NM_026212	ENSMUSG00000026922	Agpat2	2510002J07Rik|AV000834|BSCL|BSCL1|LPAAB|LPAAT-beta	1-acylglycerol-3-phosphate O-acyltransferase 2 (lysophosphatidic acid acyltransferase, beta)	protein-coding
mm_55813.1	chr6	83033368	83033378	-	1	NA	promoter-TSS (NM_013586)	promoter-TSS (NM_013586)	98	NM_010070	13448	Mm.156	NM_010070	ENSMUSG00000068335	Dok1	AW557123|p62DOK	docking protein 1	protein-coding
mm_22173.1	chr2	173159076	173159081	-	1	NA	3' UTR (NM_011044, exon 10 of 10)	3' UTR (NM_011044, exon 10 of 10)	6005	NM_011044	18534	Mm.266867	NM_011044	ENSMUSG00000027513	Pck1	AI265463|PEPCK|Pck-1	phosphoenolpyruvate carboxykinase 1, cytosolic	protein-coding
mm_12197.1	chr2	65765283	65765289	+	1	NA	3' UTR (NM_001346679, exon 27 of 27)	3' UTR (NM_001346679, exon 27 of 27)	-80481	NM_001290666	77771	Mm.102025	NM_153409	ENSMUSG00000044647	Csrnp3	A330102K23Rik|CSRNP-3|Csnrp3|Mbu1|taip-2	cysteine-serine-rich nuclear protein 3	protein-coding
mm_68874.1	chr7	126447167	126447204	-	1	NA	exon (NM_007504, exon 20 of 23)	exon (NM_007504, exon 20 of 23)	15888	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_143367.1	chr17	67354525	67354537	-	1	NA	promoter-TSS (NM_008984)	promoter-TSS (NM_008984)	-72	NM_008984	19274	Mm.311809	NM_008984	ENSMUSG00000033278	Ptprm	RPTPmu|mKIAA4044	protein tyrosine phosphatase, receptor type, M	protein-coding
mm_19135.1	chr2	80304612	80304626	-	1	NA	Intergenic	MERV1_LTR|LTR|ERV1	-10847	NM_024181	66861	Mm.21762	NM_024181	ENSMUSG00000027006	Dnajc10	1200006L06Rik|D2Ertd706e|ERdj5|JPDI	DnaJ heat shock protein family (Hsp40) member C10	protein-coding
mm_89608.1	chr10	96019862	96019872	+	1	NA	exon (NM_001001932, exon 15 of 29)	exon (NM_001001932, exon 15 of 29)	79204	NM_001001932	216238	Mm.210035	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding
mm_40399.1	chr5	52834169	52834183	+	1	NA	promoter-TSS (NM_024213)	promoter-TSS (NM_024213)	41	NM_024213	52206	Mm.272568	NM_024213	ENSMUSG00000029176	Anapc4	2610306D21Rik|APC4|D5Ertd249e	anaphase promoting complex subunit 4	protein-coding
mm_137299.1	chr17	24850485	24850495	+	1	NA	promoter-TSS (NM_024284)	promoter-TSS (NM_024284)	0	NM_024284	14651	Mm.43784	NM_024284	ENSMUSG00000024158	Hagh	BC019817|Glo-2|Glo2|Rsp29	hydroxyacyl glutathione hydrolase	protein-coding
mm_7942.1	chr1	133914830	133914838	-	1	NA	exon (NM_054077, exon 2 of 3)	exon (NM_054077, exon 2 of 3)	6567	NM_054077	116847	Mm.214514	NM_054077	ENSMUSG00000041577	Prelp	7330409J17Rik|SLRR2A	proline arginine-rich end leucine-rich repeat	protein-coding
mm_68716.1	chr7	119896320	119896342	-	1	NA	promoter-TSS (NM_001163703)	promoter-TSS (NM_001163703)	39	NM_029610	73919	Mm.46381	NM_029610	ENSMUSG00000030922	Lyrm1	1110065L10Rik|2310004B22Rik|4930404J24Rik	LYR motif containing 1	protein-coding
mm_172818.1	chr9	124480741	124480741	-	1	NA	Intergenic	Intergenic	-3879	NR_102716	19054	Mm.271249	NM_011154	ENSMUSG00000093803	Ppp2r3d	PP2A B''-PR59|PP2A PR59|PR59|Ppp2r3|Ppp2r3a	protein phosphatase 2 (formerly 2A), regulatory subunit B'', delta	protein-coding
mm_23663.1	chr3	68493246	68493270	+	1	NA	promoter-TSS (NM_001282044)	promoter-TSS (NM_001282044)	-923	NM_001282044	30953	Mm.331064	NM_013928	ENSMUSG00000027777	Schip1	Nf2ip|Schip-1	schwannomin interacting protein 1	protein-coding
mm_126322.1	chr15	79739541	79739558	+	1	NA	intron (NM_001205346, intron 2 of 17)	intron (NM_001205346, intron 2 of 17)	2987	NM_194342	223697	Mm.202715	NM_194342	ENSMUSG00000042524	Sun2	B230369L08Rik|C030011B15|Unc84b	Sad1 and UNC84 domain containing 2	protein-coding
mm_7573.1	chr1	124846007	124846021	-	1	NA	Intergenic	Intergenic	589713	NM_023735	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding
mm_145193.1	chr18	49840743	49840747	+	1	NA	intron (NM_001081371, intron 2 of 42)	B3|SINE|B2	7748	NM_001081371	240283	Mm.257790	NM_001081371	ENSMUSG00000037416	Dmxl1	C630007L23Rik|D030030C22	Dmx-like 1	protein-coding
mm_45933.1	chr5	89883298	89883309	-	1	NA	promoter-TSS (NM_177872)	promoter-TSS (NM_177872)	31	NM_177872	330119	Mm.133062	NM_177872	ENSMUSG00000043635	Adamts3	1100001H14Rik|6330442E02Rik	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 3	protein-coding
mm_59328.1	chr7	25317068	25317131	+	1	NA	promoter-TSS (NM_001160400)	promoter-TSS (NM_001160400)	-65	NM_001160400	269878	Mm.38527	NM_001160400	ENSMUSG00000045039	Megf8	AW049492|Egfl4|b2b1702.2Clo|b2b1702Clo|b2b288Clo|m687Ddg|mKIAA0817	multiple EGF-like-domains 8	protein-coding
mm_118954.1	chr14	27379623	27379635	+	1	NA	exon (NM_027871, exon 4 of 11)	exon (NM_027871, exon 4 of 11)	18240	NM_001289688	71704	Mm.248606	NM_027871	ENSMUSG00000021895	Arhgef3	1200004I24Rik|9830169H03Rik|C76747|Xpln	Rho guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_173216.1	chrX	73716682	73716687	+	1	NA	promoter-TSS (NM_012060)	promoter-TSS (NM_012060)	87	NM_007435	11666	Mm.365	NM_007435	ENSMUSG00000031378	Abcd1	ALDP|Ald|Aldgh	ATP-binding cassette, sub-family D (ALD), member 1	protein-coding
mm_18567.1	chr2	65363926	65363936	-	1	NA	promoter-TSS (NM_177074)	promoter-TSS (NM_177074)	95	NM_177074	320106	Mm.227703	NM_177074	ENSMUSG00000061171	Slc38a11	9330158F14Rik	solute carrier family 38, member 11	protein-coding
mm_133717.1	chr16	93676422	93676424	+	1	NA	Intergenic	Intergenic	-6796	NM_173047	109857	Mm.4512	NM_173047	ENSMUSG00000022947	Cbr3	1110001J05Rik|C81353	carbonyl reductase 3	protein-coding
mm_25952.1	chr3	132007480	132007492	+	1	NA	Intergenic	L4_B_Mam|LINE|RTE-X	-77806	NM_020265	56811	Mm.103593	NM_020265	ENSMUSG00000028031	Dkk2	-	dickkopf WNT signaling pathway inhibitor 2	protein-coding
mm_79608.1	chr9	58607483	58607484	+	1	NA	intron (NM_001293673, intron 1 of 7)	B4|SINE|B4	25243	NM_009145	20320	Mm.15125	NM_009145	ENSMUSG00000032336	Nptn	AW554172|SDR-1|Sdfr1	neuroplastin	protein-coding
mm_136869.1	chr17	12916427	12916447	+	1	NA	promoter-TSS (NM_026310)	promoter-TSS (NM_026310)	108	NM_013686	21454	Mm.229342	NM_013686	ENSMUSG00000068039	Tcp1	AI528772|CCT|Cct1|Ccta|TRic|Tcp-1|Tp63|c-cpn|p63	t-complex protein 1	protein-coding
mm_51933.1	chr6	91683595	91683644	+	1	NA	promoter-TSS (NM_009320)	promoter-TSS (NM_009320)	-448	NM_009320	21366	Mm.395650	NM_009320	ENSMUSG00000030096	Slc6a6	AA589629|C80501|Taut	solute carrier family 6 (neurotransmitter transporter, taurine), member 6	protein-coding
mm_79543.1	chr9	57911040	57911050	+	1	NA	promoter-TSS (NM_027086)	promoter-TSS (NM_027086)	59	NM_001122873	69459	Mm.41735	NM_027086	ENSMUSG00000055720	Ubl7	2300004C15Rik	ubiquitin-like 7 (bone marrow stromal cell-derived)	protein-coding
mm_30745.1	chr4	14864092	14864150	+	1	NA	promoter-TSS (NM_028264)	promoter-TSS (NM_028264)	-98	NM_028264	72519	Mm.279158	NM_028264	ENSMUSG00000028221	Tmem55a	2610319K07Rik|AI315591|AV001360	transmembrane protein 55A	protein-coding
mm_14082.1	chr2	125018894	125018895	+	1	NA	Intergenic	Intergenic	-49233	NM_175034	317750	Mm.330538	NM_175034	ENSMUSG00000035183	Slc24a5	F630045L20Rik|JSX|NCKX5|NCX5|Oca6	solute carrier family 24, member 5	protein-coding
mm_32515.1	chr4	108633086	108633094	+	1	NA	intron (NM_177045, intron 23 of 24)	intron (NM_177045, intron 23 of 24)	13134	NM_177045	319965	Mm.151129	NM_177045	ENSMUSG00000028582	Cc2d1b	A830039B04Rik|Freud2	coiled-coil and C2 domain containing 1B	protein-coding
mm_138500.1	chr17	35210453	35210463	+	1	NA	Intergenic	Intergenic	-5107	NM_010735	16992	Mm.87787	NM_010735	ENSMUSG00000024402	Lta	LT|LT-[a]|LT-alpha|LT[a]|LTalpha|Ltx|TNF-beta|TNFSF1|Tnfb|Tnfsf1b|Tnlg1e|hlb382	lymphotoxin A	protein-coding
mm_141886.1	chr17	34860888	34860895	-	1	NA	exon (NM_008198, exon 4 of 18)	exon (NM_008198, exon 4 of 18)	1623	NM_001142706	14962	Mm.653	NM_008198	ENSMUSG00000090231	Cfb	AI195813|AI255840|B|Bf|C2|Fb|H2-Bf	complement factor B	protein-coding
mm_68032.1	chr7	101301658	101301671	-	1	NA	intron (NM_001111111, intron 1 of 17)	intron (NM_001111111, intron 1 of 17)	424	NM_001111111	73683	Mm.275744	NM_001111111	ENSMUSG00000047767	Atg16l2	2410118P20Rik	autophagy related 16-like 2 (S. cerevisiae)	protein-coding
mm_167446.1	chr8	121796668	121796678	+	1	NA	exon (NM_145605, exon 12 of 12)	exon (NM_145605, exon 12 of 12)	32896	NM_145605	234825	Mm.209329	NM_145605	ENSMUSG00000040263	Klhdc4	AA408426|AV352552|BC012312|G430025P05Rik	kelch domain containing 4	protein-coding
mm_22476.1	chr3	5218820	5218830	+	1	NA	5' UTR (NM_030708, exon 1 of 11)	5' UTR (NM_030708, exon 1 of 11)	271	NM_030708	80892	Mm.41522	NM_030708	ENSMUSG00000025255	Zfhx4	A930021B15|C130041O22Rik|Zfh-4|Zfh4	zinc finger homeodomain 4	protein-coding
mm_140138.1	chr17	79737409	79737419	+	1	NA	Intergenic	Intergenic	-22373	NM_009994	13078	Mm.214016	NM_009994	ENSMUSG00000024087	Cyp1b1	CP1B|P4501b1	cytochrome P450, family 1, subfamily b, polypeptide 1	protein-coding
mm_1555.1	chr1	73001566	73001567	+	1	NA	Intergenic	Intergenic	14333	NM_009407	21958	Mm.425024	NM_009407	ENSMUSG00000026182	Tnp1	Stp-1|TP1|Tp-1	transition protein 1	protein-coding
mm_73215.1	chr8	96105102	96105106	+	1	NA	Intergenic	Chap1_Mam|DNA|hAT-Charlie	-216739	NM_010325	14719	Mm.230169	NM_010325	ENSMUSG00000031672	Got2	AL022787|FABP-pm|Got-2|Kyat4|mAspAT	glutamatic-oxaloacetic transaminase 2, mitochondrial	protein-coding
mm_50466.1	chr6	48977143	48977148	+	1	NA	intron (NM_001029987, intron 1 of 3)	intron (NM_001029987, intron 1 of 3)	2002	NM_001029987	243376	Mm.244112	NM_001029987	ENSMUSG00000068536	Doxl2	-	diamine oxidase-like protein 2	protein-coding
mm_47947.1	chr5	135404843	135404854	-	1	NA	Intergenic	Intergenic	-10302	NM_148932	107939	Mm.28399	NM_148932	ENSMUSG00000053293	Pom121	2610027A18Rik|C80273|mKIAA0618	nuclear pore membrane protein 121	protein-coding
mm_4629.1	chr1	179668025	179668034	+	1	NA	promoter-TSS (NM_178653)	promoter-TSS (NM_178653)	-202	NM_178653	109232	Mm.136458	NM_178653	ENSMUSG00000038936	Sccpdh	AW214504|C330023F11Rik	saccharopine dehydrogenase (putative)	protein-coding
mm_66210.1	chr7	34313509	34313528	-	1	NA	Intergenic	CpG	-27909	NM_172741	233103	Mm.491097	NM_172741	ENSMUSG00000066571	4931406P16Rik	AA553327|mKIAA0355	RIKEN cDNA 4931406P16 gene	protein-coding
mm_24545.1	chr3	93293327	93293333	+	1	NA	Intergenic	Intergenic	-26419	NM_133698	68723	Mm.208047	NM_133698	ENSMUSG00000041991	Hrnr	1110033K19Rik|A530063N20Rik|S100a18	hornerin	protein-coding
mm_66187.1	chr7	34196140	34196157	-	1	NA	intron (NM_026549, intron 2 of 6)	intron (NM_026549, intron 2 of 6)	499	NM_026549	68079	Mm.38173	NM_026549	ENSMUSG00000002635	Pdcd2l	6030457N17Rik	programmed cell death 2-like	protein-coding
mm_29638.1	chr3	121815138	121815153	-	1	NA	promoter-TSS (NM_008991)	promoter-TSS (NM_008991)	70	NM_008991	19299	Mm.399042	NM_008991	ENSMUSG00000028127	Abcd3	AI313901|AU018866|AW146054|PMP68|PMP70|Pxmp1	ATP-binding cassette, sub-family D (ALD), member 3	protein-coding
mm_99971.1	chr11	113700201	113700206	+	1	NA	intron (NM_029794, intron 5 of 6)	intron (NM_029794, intron 5 of 6)	9323	NM_026682	52670	Mm.229207	NM_026682	ENSMUSG00000018727	Cpsf4l	0610010C04Rik|1500000C01Rik|D11Ertd636e	cleavage and polyadenylation specific factor 4-like	protein-coding
mm_82536.1	chr9	20746348	20746368	-	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	-18144	NM_173777	244723	Mm.293552	NM_173777	ENSMUSG00000032172	Olfm2	A030009A06Rik	olfactomedin 2	protein-coding
mm_76405.1	chr8	84846861	84846872	-	1	NA	promoter-TSS (NM_007591)	promoter-TSS (NM_007591)	65	NM_007591	12317	Mm.1971	NM_007591	ENSMUSG00000003814	Calr	CRT|Calregulin	calreticulin	protein-coding
mm_150023.1	chr19	29372458	29372498	+	1	NA	exon (NM_021893, exon 2 of 7)	exon (NM_021893, exon 2 of 7)	5040	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_77830.1	chr9	4309761	4309779	+	1	NA	promoter-TSS (NM_026962)	promoter-TSS (NM_026962)	27	NM_001164574	69149	Mm.25946	NM_026962	ENSMUSG00000025893	Kbtbd3	2200003A07Rik|Bklhd3	kelch repeat and BTB (POZ) domain containing 3	protein-coding
mm_18920.1	chr2	76742256	76742266	-	1	NA	exon (NM_011652, exon 275 of 313)	exon (NM_011652, exon 275 of 313)	66946	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_172476.1	chr7	45460066	45460075	+	1	NA	promoter-TSS (NM_010240)	promoter-TSS (NM_010240)	-184	NM_010240	14325	Mm.30357	NM_010240	ENSMUSG00000050708	Ftl1	Ftl|Ftl-1|L-ferritin	ferritin light polypeptide 1	protein-coding
mm_9127.1	chr1	170589792	170589854	-	1	NA	promoter-TSS (NM_001109985)	promoter-TSS (NM_001109985)	26	NM_001109985	70729	Mm.487078	NM_027528	ENSMUSG00000038473	Nos1ap	6330408P19Rik|Capon	nitric oxide synthase 1 (neuronal) adaptor protein	protein-coding
mm_6108.1	chr1	64035743	64035767	-	1	NA	TTS (NM_033563)	TTS (NM_033563)	6746	NR_105864	102466760		NR_105864	ENSMUSG00000098487	Mir6899	Gm27384|mmu-mir-6899	microRNA 6899	ncRNA
mm_71510.1	chr8	46844807	46844847	+	1	NA	exon (NM_008391, exon 8 of 9)	exon (NM_008391, exon 8 of 9)	105082	NM_008391	16363	Mm.1149	NM_008391	ENSMUSG00000031627	Irf2	9830146E22Rik|AI646973|Irf-2	interferon regulatory factor 2	protein-coding
mm_79289.1	chr9	51213684	51213697	+	1	NA	promoter-TSS (NM_011136)	promoter-TSS (NM_011136)	0	NM_011136	18985	Mm.897	NM_011136	ENSMUSG00000032053	Pou2af1	BOB.1|Bob-1|Bob1|OBF-1|OBF.1|OCA-B|OCAB	POU domain, class 2, associating factor 1	protein-coding
mm_50039.1	chr6	41141283	41141293	+	1	NA	Intergenic	Intergenic	-105779	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_59566.1	chr7	28091797	28091817	+	1	NA	exon (NM_001122603, exon 7 of 20)	exon (NM_001122603, exon 7 of 20)	20571	NM_001122603	215384	Mm.292276	NM_175444	ENSMUSG00000047730	Fcgbp	A430096B05Rik	Fc fragment of IgG binding protein	protein-coding
mm_48690.1	chr5	146790489	146790499	-	1	NA	intron (NM_011669, intron 1 of 8)	(GAAA)n|Simple_repeat|Simple_repeat	4462	NM_011669	22217	Mm.167971	NM_011669	ENSMUSG00000029640	Usp12	Ubh1	ubiquitin specific peptidase 12	protein-coding
mm_141355.1	chr17	28689784	28689831	-	1	NA	5' UTR (NM_001290320, exon 1 of 20)	5' UTR (NM_001290320, exon 1 of 20)	180	NM_001290320	224661		NM_146076	ENSMUSG00000036196	Slc26a8	-	solute carrier family 26, member 8	protein-coding
mm_75908.1	chr8	71381908	71381977	-	1	NA	promoter-TSS (NM_010150)	promoter-TSS (NM_010150)	10	NM_010150	13864	Mm.28989	NM_010150	ENSMUSG00000002393	Nr2f6	AV090102|COUP-TF3|EAR2|Erbal2	nuclear receptor subfamily 2, group F, member 6	protein-coding
mm_52986.1	chr6	123264144	123264168	+	1	NA	intron (NM_001163161, intron 1 of 5)	(CA)n|Simple_repeat|Simple_repeat	2049	NM_010819	17474	Mm.441101	NM_010819	ENSMUSG00000030144	Clec4d	Clecsf8|Mpcl|mcl	C-type lectin domain family 4, member d	protein-coding
mm_82193.1	chr9	123965049	123965063	+	1	NA	intron (NM_009912, intron 1 of 1)	intron (NM_009912, intron 1 of 1)	3636	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_30022.1	chr3	135665416	135665427	-	1	NA	intron (NM_008689, intron 3 of 24)	intron (NM_008689, intron 3 of 24)	26126	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_43262.1	chr5	130257030	130257072	+	1	NA	promoter-TSS (NM_001015876)	promoter-TSS (NM_001015876)	14	NM_001015876	100929	Mm.271296	NM_178897	ENSMUSG00000056310	Tyw1	AW125391|Rsafd1	tRNA-yW synthesizing protein 1 homolog (S. cerevisiae)	protein-coding
mm_146494.1	chr18	3280814	3280824	-	1	NA	intron (NM_001311067, intron 1 of 3)	intron (NM_001311067, intron 1 of 3)	313	NM_001311066	12916	Mm.5244	NM_013498	ENSMUSG00000063889	Crem	ICER|ICERI	cAMP responsive element modulator	protein-coding
mm_124218.1	chr14	100284220	100284222	-	1	NA	Intergenic	Intergenic	-134425	NM_010636	16597	Mm.396499	NM_010636	ENSMUSG00000072294	Klf12	2700063E05Rik|AI225908|AI315654|AP-2rep|B130052C06Rik|D530033K05Rik	Kruppel-like factor 12	protein-coding
mm_44317.1	chr5	9480934	9480945	-	1	NA	TTS (NM_172706)	TTS (NM_172706)	105235	NR_030537	100124492		NR_030537	ENSMUSG00000077896	Mir879	Mirn879|mir-879|mmu-mir-879	microRNA 879	ncRNA
mm_36019.1	chr4	56960437	56960440	-	1	NA	3' UTR (NM_001142965, exon 5 of 5)	3' UTR (NM_001142965, exon 5 of 5)	-13009	NM_175518	242474	Mm.296632	NM_175518	ENSMUSG00000055296	Tmem245	A630051L19Rik|AI957324|D730040F13Rik	transmembrane protein 245	protein-coding
mm_138072.1	chr17	33949255	33949296	+	1	NA	TTS (NM_019420)	TTS (NM_019420)	2213	NM_019420	54218	Mm.11132	NM_019420	ENSMUSG00000067370	B3galt4	Gal-T2|Galt2	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 4	protein-coding
mm_94930.1	chr11	29692938	29692997	+	1	NA	promoter-TSS (NM_194051)	promoter-TSS (NM_194051)	69	NM_194052	68585	Mm.192580	NM_024226	ENSMUSG00000020458	Rtn4	1110020G17Rik|AA407876|AA409940|AA960376|ASY|C130026I10Rik|NOGO|NSP-CL|NgA|Nogo-A|Nogo-B|Nogo-C|mKIAA0886|mKIAA4153	reticulon 4	protein-coding
mm_17455.1	chr2	28556288	28556298	-	1	NA	exon (NM_009885, exon 11 of 11)	exon (NM_009885, exon 11 of 11)	7110	NM_009885	12613	Mm.236017	NM_009885	ENSMUSG00000026818	Cel	1810036E18Rik|BAL	carboxyl ester lipase	protein-coding
mm_29332.1	chr3	108121181	108121189	-	1	NA	intron (NM_010306, intron 3 of 8)	intron (NM_010306, intron 3 of 8)	24967	NM_010306	14679	Mm.271703	NM_010306	ENSMUSG00000000001	Gnai3	AI158965|AW537698|Galphai3|Gnai-3	guanine nucleotide binding protein (G protein), alpha inhibiting 3	protein-coding
mm_146094.1	chr18	73863195	73863215	+	1	NA	5' UTR (NM_001305882, exon 2 of 9)	5' UTR (NM_001305882, exon 2 of 9)	3820	NM_001305882	71263	Mm.126220	NM_027741	ENSMUSG00000064036	Mro	4930507C04Rik|4933435E20Rik	maestro	protein-coding
mm_76468.1	chr8	85386227	85386240	-	1	NA	Intergenic	Intergenic	-5192	NM_001297612	213435	Mm.32804	NM_175441	ENSMUSG00000031698	Mylk3	D830007F02Rik|MLCK	myosin light chain kinase 3	protein-coding
mm_171508.1	chr4	146270527	146270539	+	1	NA	intron (NM_001083918, intron 1 of 6).2	intron (NM_001083918, intron 1 of 6).2	148	NM_001083918	666532	Mm.392861	NM_001083918	ENSMUSG00000067916	Zfp991	Gm13139|OTTMUSG00000010657	zinc finger protein 991	protein-coding
mm_18836.1	chr2	74753456	74753463	-	1	NA	non-coding (NR_110447, exon 2 of 2)	non-coding (NR_110447, exon 2 of 2)	775	NR_110447	102634401	Mm.235021	NR_110447	ENSMUSG00000085015	LOC102634401	-	uncharacterized LOC102634401	ncRNA
mm_136699.1	chr17	7170138	7170163	+	1	NA	promoter-TSS (NM_011299)	promoter-TSS (NM_011299)	35	NM_011299	20112	Mm.268383	NM_011299	ENSMUSG00000023809	Rps6ka2	90kDa|D17Wsu134e|Rps6ka-rs1|Rsk3|p90rsk|pp90rsk	ribosomal protein S6 kinase, polypeptide 2	protein-coding
mm_9861.1	chr1	184811305	184811314	-	1	NA	promoter-TSS (NM_001290273)	promoter-TSS (NM_001290273)	-9	NM_001290273	66112	Mm.272457	NM_001081361	ENSMUSG00000026621	Marc1	1300013F15Rik|Mosc1	mitochondrial amidoxime reducing component 1	protein-coding
mm_6151.1	chr1	64956712	64956725	-	1	NA	5' UTR (NM_001039493, exon 1 of 8)	5' UTR (NM_001039493, exon 1 of 8)	106	NM_001039493	241075	Mm.239534	NM_175509	ENSMUSG00000051344	Plekhm3	9430067K14Rik|A230102O09Rik|AI449570|DAPR|Plekhm1l	pleckstrin homology domain containing, family M, member 3	protein-coding
mm_67149.1	chr7	73515769	73515788	-	1	NA	exon (NM_001081345, exon 4 of 39)	exon (NM_001081345, exon 4 of 39)	25968	NM_001081345	244059	Mm.34539	NM_001081345	ENSMUSG00000078671	Chd2	2810013C04Rik|2810040A01Rik|5630401D06Rik|AI851092|BC029703|CHD-2	chromodomain helicase DNA binding protein 2	protein-coding
mm_20509.1	chr2	130629995	130630032	-	1	NA	promoter-TSS (NM_001255994)	promoter-TSS (NM_001255994)	14	NM_198176	380601	Mm.27090	NM_198176	ENSMUSG00000079043	Fastkd5	C78212|mKIAA1792	FAST kinase domains 5	protein-coding
mm_66787.1	chr7	47015782	47015785	-	1	NA	Intergenic	LTR41|LTR|ERVL	-7369	NM_175318	101685	Mm.155687	NM_175318	ENSMUSG00000049516	Spty2d1	5830435K17Rik|AI852426|P16H6	SPT2, Suppressor of Ty, domain containing 1 (S. cerevisiae)	protein-coding
mm_103417.1	chr11	75533064	75533082	-	1	NA	intron (NM_173388, intron 2 of 13)	intron (NM_173388, intron 2 of 13)	961	NM_001199283	215113	Mm.11186	NM_173388	ENSMUSG00000038178	Slc43a2	7630402D21Rik|BC042513|Lat4	solute carrier family 43, member 2	protein-coding
mm_79372.1	chr9	54698891	54698896	+	1	NA	promoter-TSS (NM_021422)	promoter-TSS (NM_021422)	-666	NM_021422	58233	Mm.489676	NM_021422	ENSMUSG00000032285	Dnaja4	1110021L12Rik|AV358213|Dj4|Hsj4|mmDjA4	DnaJ heat shock protein family (Hsp40) member A4	protein-coding
mm_172843.1	chr9	33118748	33118760	-	1	NA	Intergenic	L1_Mur3|LINE|L1	-189788	NR_131058	330917	Mm.488283	NR_131058		Gm27162	A430016B06	predicted gene 27162	ncRNA
mm_81051.1	chr9	105658387	105658391	+	1	NA	intron (NM_001081309, intron 6 of 19)	intron (NM_001081309, intron 6 of 19)	15394	NM_001081309	75669	Mm.274830	NM_029380	ENSMUSG00000032571	Pik3r4	2210010O15Rik|C730038E05Rik|C85833|D9Ertd418e	phosphatidylinositol 3 kinase, regulatory subunit, polypeptide 4, p150	protein-coding
mm_87347.1	chr10	43579162	43579178	+	1	NA	promoter-TSS (NM_009846)	promoter-TSS (NM_009846)	1	NM_009846	12484	Mm.29742	NM_009846	ENSMUSG00000047139	Cd24a	Cd24|HSA|Ly-52|nectadrin	CD24a antigen	protein-coding
mm_119980.1	chr14	55575620	55575660	+	1	NA	promoter-TSS (NM_026808)	promoter-TSS (NM_026808)	-34	NM_026808	68680	Mm.36758	NM_026808	ENSMUSG00000022215	Fitm1	1110028A07Rik|AV010547|Cg10671|Fit1	fat storage-inducing transmembrane protein 1	protein-coding
mm_126312.1	chr15	79670857	79670888	+	1	NA	promoter-TSS (NM_172609)	promoter-TSS (NM_172609)	4	NM_172609	223696	Mm.246435	NM_172609	ENSMUSG00000022427	Tomm22	2310047D01|Tom22	translocase of outer mitochondrial membrane 22 homolog (yeast)	protein-coding
mm_148719.1	chr19	5845113	5845140	+	1	NA	non-coding (NR_003513, exon 1 of 1)	non-coding (NR_003513, exon 1 of 1)	352	NR_131212	66961	Mm.281895	NR_003513	ENSMUSG00000092274	Neat1	2310043N10Rik|VINC	nuclear paraspeckle assembly transcript 1 (non-protein coding)	ncRNA
mm_65050.1	chr7	18647094	18647108	-	1	NA	3' UTR (NM_027403, exon 5 of 5)	3' UTR (NM_027403, exon 5 of 5)	9624	NM_027403	72242	Mm.326858	NM_027403	ENSMUSG00000070796	Psg21	1600019C01Rik|1600025N01Rik|1600026N13Rik|cea8	pregnancy-specific glycoprotein 21	protein-coding
mm_58804.1	chr7	16308746	16308761	+	1	NA	promoter-TSS (NM_133234)	promoter-TSS (NM_133234)	-830	NM_133234	170770	Mm.7660	NM_133234	ENSMUSG00000002083	Bbc3	PUMA|PUMA/JFY1	BCL2 binding component 3	protein-coding
mm_21300.1	chr2	157057918	157057957	-	1	NA	intron (NM_001164663, intron 2 of 14)	intron (NM_001164663, intron 2 of 14)	21328	NM_001164663	320706	Mm.79466	NM_001164663	ENSMUSG00000055485	Soga1	9830001H06Rik|AI426038|D430036N24Rik|Soga	suppressor of glucose, autophagy associated 1	protein-coding
mm_60608.1	chr7	44585039	44585065	+	1	NA	exon (NM_008437, exon 6 of 9)	exon (NM_008437, exon 6 of 9)	-5834	NM_008422	16504	Mm.40312	NM_008422	ENSMUSG00000062785	Kcnc3	KShIIID|Kcr2-3|Kv3.3	potassium voltage gated channel, Shaw-related subfamily, member 3	protein-coding
mm_41152.1	chr5	87929801	87929803	+	1	NA	exon (NM_007786, exon 4 of 5)	exon (NM_007786, exon 4 of 5)	4169	NM_007786	12994	Mm.296303	NM_007786	ENSMUSG00000001622	Csn3	AW208918|CSN10|Csnk	casein kappa	protein-coding
mm_55790.1	chr6	82705329	82705338	-	1	NA	Intergenic	Intergenic	-52468	NM_025882	66979	Mm.195753	NM_025882	ENSMUSG00000030042	Pole4	2400007P05Rik|5830430F06Rik	polymerase (DNA-directed), epsilon 4 (p12 subunit)	protein-coding
mm_31594.1	chr4	57877484	57877486	+	1	NA	intron (NM_009649, intron 2 of 2)	U6|snRNA|snRNA	22923	NM_001035533	11641	Mm.467752	NM_009649	ENSMUSG00000038729	Akap2	AA959716|AI649048|Akap-2|Akap-kl|B230340M18Rik|Prka2	A kinase (PRKA) anchor protein 2	protein-coding
mm_79694.1	chr9	60794469	60794577	+	1	NA	promoter-TSS (NM_028283)	promoter-TSS (NM_028283)	-25	NM_028283	72565	Mm.68819	NM_028283	ENSMUSG00000034485	Uaca	2700059D02Rik|nucling	uveal autoantigen with coiled-coil domains and ankyrin repeats	protein-coding
mm_92623.1	chr10	80260960	80260975	-	1	NA	promoter-TSS (NM_001347119)	promoter-TSS (NM_001347119)	45	NM_001347119	14431	Mm.7329	NM_010255	ENSMUSG00000020150	Gamt	AA571402|Spintz1	guanidinoacetate methyltransferase	protein-coding
mm_56791.1	chr6	116645225	116645247	-	1	NA	TTS (NR_106010)	TTS (NR_106010)	811	NR_106010	102466793		NR_106010	ENSMUSG00000098334	Mir7043	Gm27776|mmu-mir-7043	microRNA 7043	ncRNA
mm_154199.1	chr19	58987985	58987999	-	1	NA	intron (NM_175172, intron 14 of 14)	intron (NM_175172, intron 14 of 14)	-44320	NM_001327998	73442	Mm.39739	NM_175199	ENSMUSG00000025092	Hspa12a	1700063D12Rik|AI118035|AI840429|AW048913|AW556406|D5Mgi40|Gm19925|mKIAA0417	heat shock protein 12A	protein-coding
mm_167679.1	chr9	78378582	78378582	-	1	NA	promoter-TSS (NM_026480)	promoter-TSS (NM_026480)	6	NM_026480	67968	Mm.26883	NM_026480	ENSMUSG00000032346	Ooep	2410146L05Rik|Floped|Moep19|Sddr	oocyte expressed protein	protein-coding
mm_79407.1	chr9	55149435	55149448	+	1	NA	promoter-TSS (NM_180600)	promoter-TSS (NM_180600)	72	NM_001346657	109161	Mm.207894	NM_180600	ENSMUSG00000032307	Ube2q2	3010021M21Rik	ubiquitin-conjugating enzyme E2Q family member 2	protein-coding
mm_123392.1	chr14	63416818	63416845	-	1	NA	5' UTR (NM_007549, exon 1 of 13)	5' UTR (NM_007549, exon 1 of 13)	356	NM_007549	12143	Mm.3962	NM_007549	ENSMUSG00000014453	Blk	-	B lymphoid kinase	protein-coding
mm_79281.1	chr9	50835303	50835329	+	1	NA	intron (NR_045601, intron 13 of 13)	intron (NR_045601, intron 13 of 13)	-21608	NM_001034085	73699	Mm.7726	NM_028614	ENSMUSG00000032058	Ppp2r1b	2410091N08Rik|AI790395	protein phosphatase 2, regulatory subunit A, beta	protein-coding
mm_13488.1	chr2	106693186	106693278	+	1	NA	promoter-TSS (NM_001143683)	promoter-TSS (NM_001143683)	-227	NM_001143683	77015	Mm.45628	NM_029837	ENSMUSG00000016386	Mpped2	239Fb|2700082O15Rik|AV354767|AW060960	metallophosphoesterase domain containing 2	protein-coding
mm_13412.1	chr2	104096929	104096956	+	1	NA	intron (NM_007652, intron 1 of 3)	intron (NM_007652, intron 1 of 3)	1141	NM_001111060	12509	Mm.247265	NM_007652	ENSMUSG00000032679	Cd59a	AA987121|Cd59|protectin	CD59a antigen	protein-coding
mm_11535.1	chr2	32629774	32629803	+	1	NA	intron (NM_021515, intron 1 of 5)	intron (NM_021515, intron 1 of 5)	288	NM_021515	11636	Mm.29189	NM_021515	ENSMUSG00000026817	Ak1	Ak-1|B430205N08Rik	adenylate kinase 1	protein-coding
mm_128083.1	chr15	27681574	27681584	-	1	NA	promoter-TSS (NM_198301)	promoter-TSS (NM_198301)	-37	NM_001242423	223433	Mm.266485	NM_198301	ENSMUSG00000056069	Fam105a	9830126M18	family with sequence similarity 105, member A	protein-coding
mm_97383.1	chr11	77722606	77722644	+	1	NA	exon (NM_009965, exon 3 of 6)	exon (NM_009965, exon 3 of 6)	2668	NM_001313933	12957	Mm.22830	NM_009965	ENSMUSG00000000724	Cryba1	BA3/A1|Cryb	crystallin, beta A1	protein-coding
mm_54447.1	chr6	34741820	34741840	-	1	NA	exon (NM_145575, exon 2 of 12)	exon (NM_145575, exon 2 of 12)	32386	NM_145575	109624	Mm.308134	NM_145575	ENSMUSG00000029761	Cald1	4833423D12Rik|AI195384|AV071549|AW536160|C920027I18Rik	caldesmon 1	protein-coding
mm_5566.1	chr1	38897981	38897992	-	1	NA	5' UTR (NM_145142, exon 1 of 7)	5' UTR (NM_145142, exon 1 of 7)	174	NM_145142	98388	Mm.260054	NM_145142	ENSMUSG00000026080	Chst10	AI507003|AU041319|Hnk-1st|ST	carbohydrate sulfotransferase 10	protein-coding
mm_118646.1	chr14	21556001	21556003	+	1	NA	intron (NM_017479, intron 2 of 16)	intron (NM_017479, intron 2 of 16)	56217	NM_017479	54169	Mm.248967	NM_017479	ENSMUSG00000021767	Kat6b	AI507552|B130044K16Rik|MYST-4|Morf|Myst4|mKIAA0383|qkf|querkopf	K(lysine) acetyltransferase 6B	protein-coding
mm_115879.1	chr13	21753852	21753868	-	1	NA	promoter-TSS (NM_178201)	promoter-TSS (NM_178201)	52	NM_178183	319169	Mm.370338	NM_178183	ENSMUSG00000063021	Hist1h2ak	-	histone cluster 1, H2ak	protein-coding
mm_56823.1	chr6	117173557	117173576	-	1	NA	exon (NM_021704, exon 3 of 3)	exon (NM_021704, exon 3 of 3)	5031	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_43560.1	chr5	137629150	137629160	+	1	NA	promoter-TSS (NM_146164)	promoter-TSS (NM_146164)	32	NR_033148	100316903	Mm.200763	NR_033148		Gm20605	Lrch4-sap25	predicted gene 20605	ncRNA
mm_37312.1	chr4	119294745	119294753	-	1	NA	promoter-TSS (NM_011732)	promoter-TSS (NM_011732)	-236	NM_011732	22608	Mm.258204	NM_011732	ENSMUSG00000028639	Ybx1	1700102N10Rik|C79409|EF1A|MSY1|Nsep1|YB-1|dbpB|mYB-1a	Y box protein 1	protein-coding
mm_153512.1	chr19	41371908	41371922	-	1	NA	intron (NM_031376, intron 2 of 16)	intron (NM_031376, intron 2 of 16)	13155	NM_031376	83490	Mm.222266	NM_031376	ENSMUSG00000025017	Pik3ap1	1810044J04Rik|BCAP	phosphoinositide-3-kinase adaptor protein 1	protein-coding
mm_118689.1	chr14	22123229	22123240	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	103522	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_105760.1	chr11	109549829	109549835	-	1	NA	intron (NM_028710, intron 11 of 13)	intron (NM_028710, intron 11 of 13)	6121	NM_001166177	74008	Mm.482224	NM_028710	ENSMUSG00000020604	Arsg	6330406P08Rik|AI846872	arylsulfatase G	protein-coding
mm_94234.1	chr11	3291739	3291766	+	1	NA	exon (NM_001253691, exon 1 of 5)	exon (NM_001253691, exon 1 of 5)	1295	NM_019574	56218	Mm.275563	NM_019574	ENSMUSG00000020453	Patz1	8430401L15Rik|AI447519|Mazr|Patz|Zfp278	POZ (BTB) and AT hook containing zinc finger 1	protein-coding
mm_69989.1	chr7	142382617	142382720	-	1	NA	exon (NM_009983, exon 4 of 9)	exon (NM_009983, exon 4 of 9)	5202	NM_009983	13033	Mm.231395	NM_009983	ENSMUSG00000007891	Ctsd	CD|CatD	cathepsin D	protein-coding
mm_170649.1	chr2	10064222	10064237	-	1	NA	exon (NM_001112738, exon 4 of 10)	exon (NM_001112738, exon 4 of 10)	-15620	NM_027748	209361	Mm.86343	NM_027748	ENSMUSG00000025782	Taf3	140kDa|4933439M23Rik|AW539625|TAF140|TAFII-140|TAFII140|mTAFII140	TATA-box binding protein associated factor 3	protein-coding
mm_28267.1	chr3	88748879	88748889	-	1	NA	exon (NM_018804, exon 3 of 4)	exon (NM_018804, exon 3 of 4)	23715	NM_018804	229521	Mm.379376	NM_018804	ENSMUSG00000068923	Syt11	1500004A13Rik|3632445O20Rik|5430404N14Rik|6530420C11Rik|AI851970	synaptotagmin XI	protein-coding
mm_23569.1	chr3	63295993	63296016	+	1	NA	promoter-TSS (NM_001289463)	promoter-TSS (NM_001289463)	-91	NM_001289463	17380	Mm.296022	NM_008604	ENSMUSG00000027820	Mme	6030454K05Rik|C85356|CALLA|CD10|NEP|SFE	membrane metallo endopeptidase	protein-coding
mm_118131.1	chr13	104623337	104623352	-	1	NA	Intergenic	Intergenic	193609	NM_026072	67285	Mm.235398	NM_026072	ENSMUSG00000021715	Cwc27	3110009E13Rik|NY-CO-10|Sdccag10	CWC27 spliceosome-associated protein	protein-coding
mm_58038.1	chr6	136808057	136808070	-	1	NA	promoter-TSS (NM_177688)	promoter-TSS (NM_177688)	-185	NM_177688	232440	Mm.154564	NM_177688	ENSMUSG00000060032	H2afj	E130307C13	H2A histone family, member J	protein-coding
mm_66267.1	chr7	35855265	35855275	-	1	NA	Intergenic	Intergenic	-52281	NM_177739	668501	Mm.286296	NM_177739	ENSMUSG00000044452	Zfp507	1810022O10Rik|A230056M16Rik|AL024009|AU021817|BB105092|Gm480|Znf507|mKIAA1084	zinc finger protein 507	protein-coding
mm_47224.1	chr5	121330313	121330313	-	1	NA	intron (NM_181421, intron 49 of 75)	IAPLTR2a|LTR|ERVK	55302	NM_001163470	231712	Mm.20488	NM_172275	ENSMUSG00000042726	Trafd1	1110008K06Rik|Fln29	TRAF type zinc finger domain containing 1	protein-coding
mm_11232.1	chr2	29802807	29802819	+	1	NA	5' UTR (NM_011989, exon 1 of 13)	5' UTR (NM_011989, exon 1 of 13)	133	NM_011989	26569	Mm.330113	NM_011989	ENSMUSG00000059316	Slc27a4	BB144259|FATP4	solute carrier family 27 (fatty acid transporter), member 4	protein-coding
mm_127961.1	chr15	11906185	11906202	-	1	NA	promoter-TSS (NM_001039181)	promoter-TSS (NM_001039181)	-332	NR_131059	381002	Mm.441967	NR_131059		Gm5144	-	predicted gene 5144	ncRNA
mm_5572.1	chr1	39455734	39455739	-	1	NA	intron (NM_018775, intron 1 of 19)	intron (NM_018775, intron 1 of 19)	23011	NM_018775	54610	Mm.387293	NM_018775	ENSMUSG00000003134	Tbc1d8	AD3|HBLP1|VRP	TBC1 domain family, member 8	protein-coding
mm_102259.1	chr11	55312144	55312191	-	1	NA	promoter-TSS (NM_001029988)	promoter-TSS (NM_001029988)	90	NM_001029988	245827	Mm.339363	NM_001029988	ENSMUSG00000055333	Fat2	EMI2|Fath2|Gm523|mKIAA0811	FAT atypical cadherin 2	protein-coding
mm_61462.1	chr7	75609660	75609686	+	1	NA	exon (NM_029332, exon 7 of 37)	exon (NM_029332, exon 7 of 37)	154139	NM_029332	75547	Mm.216107	NM_029332	ENSMUSG00000066406	Akap13	1700026G02Rik|5730522G15Rik|5830460E08Rik|AKAP-13|AKAP-Lbc|BRX|Ht31|LBC|PROTO-LB|PROTO-LBC	A kinase (PRKA) anchor protein 13	protein-coding
mm_42595.1	chr5	117413767	117413785	+	1	NA	promoter-TSS (NM_001312914)	promoter-TSS (NM_001312914)	-226	NM_001312914	333050	Mm.437947	NM_001034873	ENSMUSG00000061578	Ksr2	-	kinase suppressor of ras 2	protein-coding
mm_123138.1	chr14	56620505	56620527	-	1	NA	exon (NM_001145978, exon 22 of 35)	exon (NM_001145978, exon 22 of 35)	44897	NM_001145978	328417	Mm.379357	NM_001145978	ENSMUSG00000054509	Parp4	Adprtl1|C030027K23Rik|E230037B21Rik|Gm743|PARPL|PH5P|VAULT3|VPARP|p193	poly (ADP-ribose) polymerase family, member 4	protein-coding
mm_144189.1	chr18	7869215	7869226	+	1	NA	promoter-TSS (NM_001146298)	promoter-TSS (NM_001146298)	23	NM_153085	225131	Mm.204524	NM_153085	ENSMUSG00000024283	Wac	1110067P07Rik|A230035H12Rik|AI256735|AI256776|Wwp4	WW domain containing adaptor with coiled-coil	protein-coding
mm_65537.1	chr7	25816617	25816628	-	1	NA	promoter-TSS (NM_028775)	promoter-TSS (NM_028775)	-92	NM_028775	74134	Mm.275188	NM_028775	ENSMUSG00000040703	Cyp2s1	1200011C15Rik|AU041727|C79779	cytochrome P450, family 2, subfamily s, polypeptide 1	protein-coding
mm_21253.1	chr2	156312312	156312323	-	1	NA	promoter-TSS (NM_027585)	promoter-TSS (NM_027585)	-156	NM_027585	70873	Mm.475234	NM_027585	ENSMUSG00000038085	Cnbd2	4921517L17Rik|5430421B09Rik|Cris	cyclic nucleotide binding domain containing 2	protein-coding
mm_6413.1	chr1	72874878	72874891	-	1	NA	promoter-TSS (NM_010518)	promoter-TSS (NM_010518)	-19	NM_010518	16011	Mm.405761	NM_010518	ENSMUSG00000026185	Igfbp5	AI256729|AW208790|IGFBP-5|IGFBP-5P	insulin-like growth factor binding protein 5	protein-coding
mm_84499.1	chr9	66916602	66916610	-	1	NA	intron (NM_173413, intron 1 of 7)	AmnSINE1|SINE|Deu	3099	NM_173413	235442	Mm.260376	NM_173413	ENSMUSG00000036943	Rab8b	5930437D16|D330025I23Rik	RAB8B, member RAS oncogene family	protein-coding
mm_41859.1	chr5	104440572	104440576	+	1	NA	exon (NM_001204203, exon 7 of 7)	exon (NM_001204203, exon 7 of 7)	4382	NM_001204233	20750	Mm.288474	NM_009263	ENSMUSG00000029304	Spp1	2AR|Apl-1|BNSP|BSPI|Bsp|ETA-1|Eta|OP|Opn|Opnl|Ric|Spp-1	secreted phosphoprotein 1	protein-coding
mm_169640.1	chr15	5023901	5023911	+	1	NA	intron (NM_001243837, intron 8 of 17)	RLTR9E|LTR|ERVK	39867	NM_001243837	109828	Mm.208034	NM_001243837	ENSMUSG00000079105	C7	A530026G17|Gm1238	complement component 7	protein-coding
mm_29320.1	chr3	108017461	108017470	-	1	NA	intron (NM_010358, intron 1 of 7)	intron (NM_010358, intron 1 of 7)	508	NM_010358	14862	Mm.37199	NM_010358	ENSMUSG00000058135	Gstm1	Gstb-1|Gstb1	glutathione S-transferase, mu 1	protein-coding
mm_11215.1	chr2	29643699	29643712	+	1	NA	intron (NM_001039087, intron 1 of 25)	intron (NM_001039087, intron 1 of 25)	23985	NM_001039086	107746	Mm.298274	NM_054050	ENSMUSG00000039844	Rapgef1	4932418O06Rik|C3G|Grf2	Rap guanine nucleotide exchange factor (GEF) 1	protein-coding
mm_81923.1	chr9	120168387	120168394	+	1	NA	exon (NM_001039365, exon 4 of 4)	exon (NM_001039365, exon 4 of 4)	18648	NM_001039364	17433	Mm.486167	NM_008614	ENSMUSG00000032517	Mobp	AI835053|AI839848|MOBP155|MOBP170|MOBP69|MOBP73|MOBP81|R74645	myelin-associated oligodendrocytic basic protein	protein-coding
mm_26971.1	chr3	24783609	24783621	-	1	NA	5' UTR (NM_001326288, exon 1 of 14)	5' UTR (NM_001326288, exon 1 of 14)	391	NM_001326288	635702	Mm.448351	NM_001326288	ENSMUSG00000102758	Naaladl2	2810043G22Rik|EG635702|Gm1021	N-acetylated alpha-linked acidic dipeptidase-like 2	protein-coding
mm_114239.1	chr13	56613826	56613844	+	1	NA	intron (NM_009369, intron 1 of 16)	intron (NM_009369, intron 1 of 16)	4232	NM_009369	21810	Mm.14455	NM_009369	ENSMUSG00000035493	Tgfbi	68kDa|AI181842|AI747162|Beta-ig|big-h3	transforming growth factor, beta induced	protein-coding
mm_155283.1	chrX	61183244	61183259	+	1	NA	TTS (NM_001166658)	TTS (NM_001166658)	2307	NM_001166658	631990	Mm.401324	NM_001166658	ENSMUSG00000090546	Cdr1	100039759|Cdr|Cdr34|EG631990|Gm2409|Gm7077	cerebellar degeneration related antigen 1	protein-coding
mm_72442.1	chr8	83165362	83165399	+	1	NA	promoter-TSS (NM_001111304)	promoter-TSS (NM_001111304)	28	NM_027758	71310	Mm.24031	NM_027758	ENSMUSG00000031709	Tbc1d9	4933431N12Rik|AI847101|AW490653|C76116	TBC1 domain family, member 9	protein-coding
mm_156345.1	chrX	139086227	139086250	+	1	NA	promoter-TSS (NM_029174)	promoter-TSS (NM_029174)	-5	NM_029174	75125	Mm.179221	NM_029174	ENSMUSG00000031270	4930513O06Rik	-	RIKEN cDNA 4930513O06 gene	protein-coding
mm_98710.1	chr11	96307118	96307128	+	1	NA	promoter-TSS (NR_131758)	promoter-TSS (NR_131758)	-213	NR_131758	75395	Mm.440014	NR_131758	ENSMUSG00000085645	Hoxb5os	0610040B09Rik|AV302770|Hoxb5/6as	homeobox B5 and homeobox B6, opposite strand	ncRNA
mm_127513.1	chr15	101850124	101850134	+	1	NA	exon (NM_008473, exon 1 of 9)	exon (NM_008473, exon 1 of 9)	657	NM_008473	16678	Mm.183137	NM_008473	ENSMUSG00000046834	Krt1	Krt-2.1|Krt2-1|Krt86	keratin 1	protein-coding
mm_126709.1	chr15	85238501	85238529	+	1	NA	exon (NM_010180, exon 10 of 17)	exon (NM_010180, exon 10 of 17)	32507	NM_010180	14114	Mm.297992	NM_010180	ENSMUSG00000006369	Fbln1	-	fibulin 1	protein-coding
mm_115676.1	chr13	12912997	12912998	-	1	NA	Intergenic	MERVL_2A-int|LTR|ERVL	92333	NM_031191	18811	Mm.88796	NM_031191	ENSMUSG00000079092	Prl2c2	Ghd2|MRP-1|PLF-1|Plf|Plf1	prolactin family 2, subfamily c, member 2	protein-coding
mm_109778.1	chr12	119238309	119238313	+	1	NA	promoter-TSS (NM_177290)	promoter-TSS (NM_177290)	-35	NM_177290	320910	Mm.217000	NM_177290	ENSMUSG00000025321	Itgb8	4832412O06Rik	integrin beta 8	protein-coding
mm_5742.1	chr1	45503057	45503071	-	1	NA	5' UTR (NM_007737, exon 1 of 54)	5' UTR (NM_007737, exon 1 of 54)	218	NM_007737	12832	Mm.10299	NM_007737	ENSMUSG00000026042	Col5a2	1110014L14Rik	collagen, type V, alpha 2	protein-coding
mm_25.1	chr1	5139384	5139388	+	1	NA	intron (NM_001310442, intron 10 of 12)	intron (NM_001310442, intron 10 of 12)	56300	NM_001310442	108664	Mm.27082	NM_133826	ENSMUSG00000033793	Atp6v1h	0710001F19Rik|AU022349|CGI-11|SFD|SFDalpha|SFDbeta|VMA13	ATPase, H+ transporting, lysosomal V1 subunit H	protein-coding
mm_109055.1	chr12	104340511	104340521	+	1	NA	exon (NM_011458, exon 2 of 5)	exon (NM_011458, exon 2 of 5)	2030	NM_011458	20714	Mm.291569	NM_011458	ENSMUSG00000058207	Serpina3k	1300001I07Rik|D12Rp54|MMCM2|MMSpi2|RP54|Spi-2|Spi2|contrapsin	serine (or cysteine) peptidase inhibitor, clade A, member 3K	protein-coding
mm_48299.1	chr5	138264014	138264060	-	1	NA	promoter-TSS (NM_153161)	promoter-TSS (NM_153161)	-8	NR_045821	69004	Mm.439868	NR_045821	ENSMUSG00000085227	6330418K02Rik	-	RIKEN cDNA 6330418K02 gene	ncRNA
mm_39452.1	chr5	17574586	17574605	+	1	NA	promoter-TSS (NM_013657)	promoter-TSS (NM_013657)	-221	NM_013657	20348	Mm.5071	NM_013657	ENSMUSG00000028780	Sema3c	1110036B02Rik|SemE|Semae	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	protein-coding
mm_15830.1	chr2	164653896	164653900	+	1	NA	intron (NM_001160414, intron 1 of 3)	intron (NM_001160414, intron 1 of 3)	1068	NM_001160414	629754	Mm.190489	NM_001160414	ENSMUSG00000074594	Wfdc9	OTTMUSG00000001088	WAP four-disulfide core domain 9	protein-coding
mm_144035.1	chr17	90088323	90088341	-	1	NA	promoter-TSS (NM_001347419)	promoter-TSS (NM_001347419)	36	NM_001346962	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_54514.1	chr6	35512006	35512041	-	1	NA	3' UTR (NM_008098, exon 4 of 4)	3' UTR (NM_008098, exon 4 of 4)	27865	NM_008098	14489	Mm.182746	NM_008098	ENSMUSG00000029840	Mtpn	5033418D15Rik|Gcdp|V1	myotrophin	protein-coding
mm_82962.1	chr9	35611988	35611995	-	1	NA	promoter-TSS (NM_020264)	promoter-TSS (NM_020264)	-106	NM_020264	56872	Mm.390143	NM_020264	ENSMUSG00000032099	Pate4	9530004K16Rik|Pate-B|Svs7	prostate and testis expressed 4	protein-coding
mm_150007.1	chr19	29289619	29289634	+	1	NA	intron (NM_001048177, intron 11 of 23)	intron (NM_001048177, intron 11 of 23)	35692	NM_013754	27356	Mm.306511	NM_013754	ENSMUSG00000050957	Insl6	RIF1	insulin-like 6	protein-coding
mm_168352.1	chr1	113904149	113904154	-	1	NA	Intergenic	L1Md_F3|LINE|L1	-1780986	NM_001077425	636808	Mm.101576	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding
mm_100791.1	chr11	4939681	4939694	-	1	NA	exon (NM_010904, exon 4 of 4)	exon (NM_010904, exon 4 of 4)	-7834	NM_001243043	11764	Mm.274816	NM_007454	ENSMUSG00000009090	Ap1b1	Adtb1|b2b1660Clo	adaptor protein complex AP-1, beta 1 subunit	protein-coding
mm_36607.1	chr4	88982592	88982624	-	1	NA	Intergenic	Intergenic	-40566	NR_132735	106557447	Mm.484668	NR_132734		LOC106557447	-	uncharacterized LOC106557447	ncRNA
mm_18988.1	chr2	76863318	76863344	-	1	NA	exon (NM_011652, exon 111 of 313)	exon (NM_011652, exon 111 of 313)	119216	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_160737.1	chr10	79613865	79613865	-	1	NA	5' UTR (NM_198614, exon 1 of 2)	5' UTR (NM_198614, exon 1 of 2)	153	NM_198614	237397	Mm.334207	NM_198614	ENSMUSG00000045912	C2cd4c	4932409I22Rik|Fam148c|Gm238	C2 calcium-dependent domain containing 4C	protein-coding
mm_158391.1	chrX	136203817	136203926	-	1	NA	promoter-TSS (NM_177919)	promoter-TSS (NM_177919)	-20	NM_177919	331532	Mm.41605	NM_177919	ENSMUSG00000054034	Tceal5	6430401A05Rik	transcription elongation factor A (SII)-like 5	protein-coding
mm_21100.1	chr2	153237918	153237934	-	1	NA	intron (NM_018807, intron 1 of 2)	intron (NM_018807, intron 1 of 2)	3432	NM_018807	54711	Mm.103199	NM_018807	ENSMUSG00000051413	Plagl2	AU018672|AW552839|mKIAA0198	pleiomorphic adenoma gene-like 2	protein-coding
mm_137508.1	chr17	27037811	27037827	+	1	NA	Intergenic	Intergenic	8560	NM_027544	70772	Mm.440437	NM_027544	ENSMUSG00000048731	Ggnbp1	0610031G08Rik|mdf	gametogenetin binding protein 1	protein-coding
mm_67258.1	chr7	75772892	75772929	-	1	NA	Intergenic	B1_Mur4|SINE|Alu	-75428	NM_001122780	207952	Mm.206223	NM_029652	ENSMUSG00000055652	Klhl25	2810402K13Rik|BC027373|Enc-1	kelch-like 25	protein-coding
mm_27935.1	chr3	79572404	79572451	-	1	NA	Intergenic	Intergenic	-4748	NM_001162999	329679	Mm.244005	NM_001162999	ENSMUSG00000061175	Fnip2	D630023B12Rik|mKIAA1450	folliculin interacting protein 2	protein-coding
mm_20618.1	chr2	131855532	131855544	-	1	NA	3' UTR (NM_001166206, exon 2 of 2)	3' UTR (NM_001166206, exon 2 of 2)	4209	NM_001166206	71995	Mm.22	NM_028045	ENSMUSG00000037482	Erv3	1600014E20Rik|AA389086|AI426069|AI448024|D19349	endogenous retroviral sequence 3	protein-coding
mm_170005.1	chr1	71653199	71653200	-	1	NA	promoter-TSS (NM_001276413)	promoter-TSS (NM_001276413)	35	NM_010233	14268	Mm.193099	NM_010233	ENSMUSG00000026193	Fn1	E330027I09|Fn|Fn-1	fibronectin 1	protein-coding
mm_97724.1	chr11	80383399	80383415	+	1	NA	non-coding (NR_045038, exon 1 of 17)	non-coding (NR_045038, exon 1 of 17)	128	NM_001130171	22680	Mm.401332	NM_011751	ENSMUSG00000017421	Zfp207	8430401D15Rik|BuGZ|Zep|Znf207	zinc finger protein 207	protein-coding
mm_81598.1	chr9	110532502	110532600	+	1	NA	promoter-TSS (NM_001081340)	promoter-TSS (NM_001081340)	-46	NM_001081340	235626	Mm.288949	NM_001081340	ENSMUSG00000044791	Setd2	4921524K10Rik|BC031601|KMT3A	SET domain containing 2	protein-coding
mm_56005.1	chr6	86488186	86488214	-	1	NA	promoter-TSS (NR_040293)	promoter-TSS (NR_040293)	27	NR_040293	381792	Mm.333223	NR_040292	ENSMUSG00000101655	2310040G24Rik	-	RIKEN cDNA 2310040G24 gene	ncRNA
mm_128624.1	chr15	59019264	59019285	-	1	NA	intron (NM_001146180, intron 3 of 13)	intron (NM_001146180, intron 3 of 13)	62752	NM_001146180	211401	Mm.215481	NM_144800	ENSMUSG00000022353	Mtss1	2310003N14Rik|BC024131|D130001D01Rik|Mim|mKIAA0429	metastasis suppressor 1	protein-coding
mm_163714.1	chr13	110415168	110415168	+	1	NA	Intergenic	Intergenic	20124	NM_152804	20620	Mm.380	NM_152804	ENSMUSG00000021701	Plk2	Snk	polo-like kinase 2	protein-coding
mm_57142.1	chr6	122610047	122610081	-	1	NA	promoter-TSS (NM_008108)	promoter-TSS (NM_008108)	23	NM_008108	14562	Mm.299742	NM_008108	ENSMUSG00000030117	Gdf3	C78318|Gdf-3|Vgr-2|Vgr2|ecat9	growth differentiation factor 3	protein-coding
mm_63706.1	chr7	130646299	130646317	+	1	NA	intron (NM_001004468, intron 3 of 21)	CpG	-46248	NM_001347637	57752	Mm.86322	NM_021314	ENSMUSG00000030852	Tacc2	mKIAA4180	transforming, acidic coiled-coil containing protein 2	protein-coding
mm_140728.1	chr17	15499895	15499909	-	1	NA	promoter-TSS (NM_013684)	promoter-TSS (NM_013684)	14	NM_013684	21374	Mm.244820	NM_013684	ENSMUSG00000014767	Tbp	GTF2D1|Gtf2d|SCA17|TFIID	TATA box binding protein	protein-coding
mm_100590.1	chr11	120956536	120956547	+	1	NA	exon (NM_001038654, exon 4 of 5)	exon (NM_001038654, exon 4 of 5)	7474	NM_001038654	80879	Mm.28632	NM_030696	ENSMUSG00000025161	Slc16a3	Mct3|Mct4	solute carrier family 16 (monocarboxylic acid transporters), member 3	protein-coding
mm_23787.1	chr3	79418474	79418475	+	1	NA	intron (NM_001142953, intron 2 of 4)	intron (NM_001142953, intron 2 of 4)	73098	NM_001142953	100233207	Mm.373801	NM_001142953	ENSMUSG00000091685	Gm17359	-	predicted gene, 17359	protein-coding
mm_77782.1	chr9	3022871	3022899	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	15858	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_173215.1	chrX	73483661	73483661	+	1	NA	promoter-TSS (NM_007542)	promoter-TSS (NM_007542)	60	NM_007542	12111	Mm.2608	NM_007542	ENSMUSG00000031375	Bgn	BG|DSPG1|PG-S1|PGI|SLRR1A	biglycan	protein-coding
mm_74567.1	chr8	11008942	11008973	-	1	NA	promoter-TSS (NM_001081212)	promoter-TSS (NM_001081212)	-527	NM_001081212	384783	Mm.407207	NM_001081212	ENSMUSG00000038894	Irs2	Irs-2	insulin receptor substrate 2	protein-coding
mm_171641.1	chr4	29096071	29096079	-	1	NA	Intergenic	(CCA)n|Simple_repeat|Simple_repeat	282930	NM_001122889	13841	Mm.257266	NM_010141	ENSMUSG00000028289	Epha7	Cek11|Ebk|Ehk3|Hek11|Mdk1	Eph receptor A7	protein-coding
mm_77834.1	chr9	4313102	4313105	+	1	NA	intron (NM_001164574, intron 1 of 2)	intron (NM_001164574, intron 1 of 2)	3287	NM_026962	69149	Mm.25946	NM_026962	ENSMUSG00000025893	Kbtbd3	2200003A07Rik|Bklhd3	kelch repeat and BTB (POZ) domain containing 3	protein-coding
mm_139449.1	chr17	55510263	55510265	+	1	NA	exon (NM_001347403, exon 6 of 6)	exon (NM_001347403, exon 6 of 6)	64547	NM_172829	240119	Mm.311687	NM_172829	ENSMUSG00000024172	St6gal2	C230064G14Rik|St6galII|mKIAA1877	beta galactoside alpha 2,6 sialyltransferase 2	protein-coding
mm_17553.1	chr2	30093643	30093679	-	1	NA	promoter-TSS (NM_025428)	promoter-TSS (NM_025428)	-26	NM_001037762	66220	Mm.22538	NM_025428	ENSMUSG00000015335	Zdhhc12	1190004A01Rik	zinc finger, DHHC domain containing 12	protein-coding
mm_165882.1	chr4	42705971	42705975	+	1	NA	Intergenic	MTC|LTR|ERVL-MaLR	-40210	NM_001100596	100038993	Mm.458019	NM_001100596	ENSMUSG00000095623	Gm2002	-	predicted gene 2002	protein-coding
mm_19743.1	chr2	104785745	104785746	-	1	NA	intron (NM_001123327, intron 3 of 11)	intron (NM_001123327, intron 3 of 11)	30951	NM_001123327	99003	Mm.274314	NM_001123327	ENSMUSG00000074994	Qser1	4732486I23Rik|AI502974	glutamine and serine rich 1	protein-coding
mm_122153.1	chr14	31323885	31323929	-	1	NA	promoter-TSS (NM_001033668)	promoter-TSS (NM_001033668)	-11	NM_001033668	110084	Mm.101811	NM_001033668	ENSMUSG00000019027	Dnah1	B230373P09Rik|Dnahc1|E030034C22Rik|MDHC7	dynein, axonemal, heavy chain 1	protein-coding
mm_50378.1	chr6	48684590	48684598	+	1	NA	promoter-TSS (NM_001243199)	promoter-TSS (NM_001243199)	16	NM_174990	107526	Mm.333048	NM_174990	ENSMUSG00000054435	Gimap4	AU019574|E430007K16Rik|Ian-1|Ian1|Imap4	GTPase, IMAP family member 4	protein-coding
mm_139225.1	chr17	47730642	47730642	+	1	NA	exon (NM_025973, exon 5 of 9)	exon (NM_025973, exon 5 of 9)	3800	NM_025973	109820	Mm.22957	NM_025973	ENSMUSG00000023987	Pgc	2210410L06Rik|Upg-1|Upg1	progastricsin (pepsinogen C)	protein-coding
mm_7787.1	chr1	131427170	131427173	-	1	NA	intron (NM_001081011, intron 3 of 22)	PB1D10|SINE|Alu	100190	NM_001081011	14270	Mm.276259	NM_019520	ENSMUSG00000026425	Srgap2	9930124L22Rik|AI448945|FBP2|Fnbp2|srGAP3	SLIT-ROBO Rho GTPase activating protein 2	protein-coding
mm_63427.1	chr7	127478208	127478256	+	1	NA	Intergenic	Intergenic	6618	NM_145589	233895	Mm.44183	NM_145589	ENSMUSG00000030822	Prr14	BC006909	proline rich 14	protein-coding
mm_29850.1	chr3	129970136	129970150	-	1	NA	promoter-TSS (NM_025779)	promoter-TSS (NM_025779)	63	NM_025779	66815	Mm.31056	NM_025779	ENSMUSG00000027994	Ccdc109b	9030408N13Rik|MCUb	coiled-coil domain containing 109B	protein-coding
mm_110338.1	chr12	36020563	36020596	-	1	NA	exon (NM_025359, exon 5 of 6)	exon (NM_025359, exon 5 of 6)	21899	NM_025359	66109	Mm.254663	NM_025359	ENSMUSG00000020577	Tspan13	1100001I23Rik|NET-6|Tm4sf13	tetraspanin 13	protein-coding
mm_28287.1	chr3	89089700	89089716	-	1	NA	exon (NM_001083808, exon 2 of 9)	exon (NM_001083808, exon 2 of 9)	323	NM_001083808	72296	Mm.27687	NM_028188	ENSMUSG00000041263	Rusc1	2210403N08Rik|AA408288|NESCA	RUN and SH3 domain containing 1	protein-coding
mm_86044.1	chr9	114496597	114496605	-	1	NA	promoter-TSS (NM_009916)	promoter-TSS (NM_009916)	-57	NM_009916	12773	Mm.1337	NM_009916	ENSMUSG00000047898	Ccr4	C-C CKR-4|CHEMR1|Cmkbr4|LESTR|Sdf1r	chemokine (C-C motif) receptor 4	protein-coding
mm_43404.1	chr5	135863021	135863032	+	1	NA	intron (NM_021403, intron 11 of 14)	B4|SINE|B4	-24893	NM_013560	15507	Mm.13849	NM_013560	ENSMUSG00000004951	Hspb1	27kDa|Hsp25	heat shock protein 1	protein-coding
mm_164349.1	chr16	19883825	19883831	-	1	NA	non-coding (NR_015488, exon 1 of 2)	non-coding (NR_015488, exon 1 of 2)	446	NR_027896	68162	Mm.35159	NR_015488		A930003A15Rik	AI853191	RIKEN cDNA A930003A15 gene	ncRNA
mm_24510.1	chr3	92584407	92584416	+	1	NA	exon (NM_008574, exon 2 of 2)	exon (NM_008574, exon 2 of 2)	4613	NM_008574	17235	Mm.331192	NM_008574		Smcp	Mcs|Mcsp	sperm mitochondria-associated cysteine-rich protein	protein-coding
mm_133866.1	chr16	96361750	96361801	+	1	NA	promoter-TSS (NM_028078)	promoter-TSS (NM_028078)	11	NM_028078	72058	Mm.119714	NM_028078	ENSMUSG00000000159	Igsf5	2010003D20Rik|JCAM|Jam4	immunoglobulin superfamily, member 5	protein-coding
mm_15536.1	chr2	158383109	158383184	+	1	NA	3' UTR (NM_175692, exon 5 of 5)	3' UTR (NM_175692, exon 5 of 5)	7508	NM_175692	319317	Mm.294494	NM_175692	ENSMUSG00000044349	Snhg11	A930034L06Rik|AI854265|AL022637|AW319638|E130013N09Rik	small nucleolar RNA host gene 11	protein-coding
mm_19442.1	chr2	91965722	91965738	-	1	NA	Intergenic	Intergenic	-2167	NM_138306	104418	Mm.314923	NM_138306	ENSMUSG00000040479	Dgkz	E130307B02Rik|ENSMUSG00000075035|F730209L11Rik|mDGK[z]	diacylglycerol kinase zeta	protein-coding
mm_162145.1	chrX	74481516	74481516	-	1	NA	promoter-TSS (NM_001099305)	promoter-TSS (NM_001099305)	-117	NM_001099305	628456	Mm.455664	NM_001099305	ENSMUSG00000079536	Gm6880	EG628456	predicted gene 6880	protein-coding
mm_169194.1	chr13	66108844	66108846	+	1	NA	Intergenic	Intergenic	-4608	NM_001177832	628709	Mm.390595	NM_001177832	ENSMUSG00000095909	Gm10324	ENSMUSG00000071302	predicted gene 10324	protein-coding
mm_115193.1	chr13	108775308	108775344	+	1	NA	intron (NM_011056, intron 1 of 16)	intron (NM_011056, intron 1 of 16)	121149	NM_011056	238871	Mm.434429	NM_011056	ENSMUSG00000021699	Pde4d	9630011N22Rik|Dpde3	phosphodiesterase 4D, cAMP specific	protein-coding
mm_18877.1	chr2	76360375	76360391	-	1	NA	promoter-TSS (NM_009989)	promoter-TSS (NM_009989)	70	NM_009989	13067	Mm.4872	NM_009989	ENSMUSG00000056436	Cyct	T-Cc	cytochrome c, testis	protein-coding
mm_81590.1	chr9	110477035	110477045	+	1	NA	promoter-TSS (NM_001163569)	promoter-TSS (NM_001163569)	46	NM_001163569	16578	Mm.42170	NM_010628	ENSMUSG00000032489	Kif9	-	kinesin family member 9	protein-coding
mm_27912.1	chr3	79531678	79531688	-	1	NA	intron (NM_001162999, intron 1 of 16)	intron (NM_001162999, intron 1 of 16)	35996	NM_001162999	329679	Mm.244005	NM_001162999	ENSMUSG00000061175	Fnip2	D630023B12Rik|mKIAA1450	folliculin interacting protein 2	protein-coding
mm_57229.1	chr6	123282643	123282676	-	1	NA	3' UTR (NM_019948, exon 6 of 6)	3' UTR (NM_019948, exon 6 of 6)	7212	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_111253.1	chr12	84951142	84951146	-	1	NA	5' UTR (NM_178065, exon 2 of 20)	5' UTR (NM_178065, exon 2 of 20)	19742	NM_178065	68497	Mm.24446	NM_178065	ENSMUSG00000042350	Arel1	1110018G07Rik|AI649076|AW610792|Kiaa0317|mKIAA0317	apoptosis resistant E3 ubiquitin protein ligase 1	protein-coding
mm_19290.1	chr2	90453307	90453344	-	1	NA	exon (NM_008982, exon 12 of 24)	exon (NM_008982, exon 12 of 24)	25849	NM_001135657	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_56516.1	chr6	99435372	99435382	-	1	NA	promoter-TSS (NM_053202)	promoter-TSS (NM_053202)	-32	NM_053202	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_148914.1	chr19	6975112	6975118	+	1	NA	promoter-TSS (NM_008889)	promoter-TSS (NM_008889)	67	NM_008889	18938	Mm.140	NM_008889	ENSMUSG00000056612	Ppp1r14b	AOM172|PHI-1|PLCB3N|Png	protein phosphatase 1, regulatory (inhibitor) subunit 14B	protein-coding
mm_132610.1	chr16	38585381	38585391	+	1	NA	exon (NM_026407, exon 6 of 9)	exon (NM_026407, exon 6 of 9)	22572	NM_026407	67846	Mm.310476	NM_026407	ENSMUSG00000002845	Tmem39a	2610033C09Rik	transmembrane protein 39a	protein-coding
mm_131845.1	chr16	23058327	23058351	+	1	NA	promoter-TSS (NM_001102411)	promoter-TSS (NM_001102411)	39	NM_001102412	16644	Mm.2160	NM_023125	ENSMUSG00000022875	Kng1	Kng	kininogen 1	protein-coding
mm_73707.1	chr8	111687139	111687179	+	1	NA	exon (NM_025583, exon 6 of 7)	exon (NM_025583, exon 6 of 7)	2515	NR_106044	102466993		NR_106044	ENSMUSG00000099129	Mir7076	Gm27318|mmu-mir-7076	microRNA 7076	ncRNA
mm_109656.1	chr12	112976746	112976752	+	1	NA	exon (NM_201646, exon 1 of 4)	exon (NM_201646, exon 1 of 4)	186	NM_201646	399566	Mm.440140	NM_201646	ENSMUSG00000002803	Btbd6	-	BTB (POZ) domain containing 6	protein-coding
mm_24641.1	chr3	94377455	94377481	+	1	NA	promoter-TSS (NM_001293734)	promoter-TSS (NM_001293734)	36	NR_121656	19885	Mm.4372	NM_011281	ENSMUSG00000028150	Rorc	Nr1f3|RORgamma|TOR|Thor	RAR-related orphan receptor gamma	protein-coding
mm_163763.1	chr13	120012245	120012257	+	1	NA	Intergenic	Intergenic	39953	NM_001302966	100861753	Mm.165042	NM_001302966	ENSMUSG00000095609	Gm21188	-	predicted gene, 21188	protein-coding
mm_58132.1	chr6	140625413	140625416	-	1	NA	intron (NM_001309437, intron 1 of 8)	intron (NM_001309437, intron 1 of 8)	505	NM_001309437	11569	Mm.86453	NM_009637	ENSMUSG00000030232	Aebp2	AU023766|B230313N05Rik	AE binding protein 2	protein-coding
mm_2791.1	chr1	130850734	130850742	+	1	NA	intron (NM_011082, intron 10 of 10)	intron (NM_011082, intron 10 of 10)	-15039	NM_026976	69169	Mm.46042	NM_026976	ENSMUSG00000042474	Fcmr	1810037B05Rik|Faim3|FcmuR|Toso	Fc fragment of IgM receptor	protein-coding
mm_28650.1	chr3	95228637	95228719	-	1	NA	promoter-TSS (NM_019914)	promoter-TSS (NM_019914)	-1	NM_019914	56772	Mm.331208	NM_019914	ENSMUSG00000053192	Mllt11	AI839562|Af1q|Zfp692	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 11	protein-coding
mm_32652.1	chr4	115088735	115088769	+	1	NA	promoter-TSS (NM_001164557)	promoter-TSS (NM_001164557)	44	NM_001164557	67182	Mm.30181	NM_026018	ENSMUSG00000028716	Pdzk1ip1	0610007F13Rik|2700030M23Rik|AU046042|Map17	PDZK1 interacting protein 1	protein-coding
mm_7927.1	chr1	133899216	133899250	-	1	NA	intron (NM_054076, intron 5 of 6)	intron (NM_054076, intron 5 of 6)	7940	NM_054076	269120	Mm.59985	NM_054076	ENSMUSG00000010311	Optc	-	opticin	protein-coding
mm_125116.1	chr15	28325851	28325853	+	1	NA	intron (NM_133365, intron 35 of 78)	intron (NM_133365, intron 35 of 78)	122086	NM_133365	110082	Mm.248464	NM_133365	ENSMUSG00000022262	Dnah5	AU022615|Dnahc5|Mdnah5|b2b1134Clo|b2b1154Clo|b2b1537Clo|b2b1565Clo|b2b601Clo|mKIAA1603	dynein, axonemal, heavy chain 5	protein-coding
mm_29170.1	chr3	106511463	106511467	-	1	NA	intron (NM_001293694, intron 5 of 8)	intron (NM_001293694, intron 5 of 8)	25425	NM_028110	72121	Mm.14816	NM_028110	ENSMUSG00000027901	Dennd2d	2010308M01Rik|AI451421	DENN/MADD domain containing 2D	protein-coding
mm_124442.1	chr14	118735144	118735160	-	1	NA	Intergenic	Intergenic	-28933	NM_001033336	239273	Mm.40537	NM_001033336	ENSMUSG00000032849	Abcc4	ABCC4-N1|D630049P08Rik|MOATB|MRP4	ATP-binding cassette, sub-family C (CFTR/MRP), member 4	protein-coding
mm_48621.1	chr5	144965794	144965877	-	1	NA	promoter-TSS (NM_029438)	promoter-TSS (NM_029438)	-5	NM_029438	75788	Mm.27735	NM_029438	ENSMUSG00000038780	Smurf1	4930431E10Rik|mKIAA1625	SMAD specific E3 ubiquitin protein ligase 1	protein-coding
mm_135844.1	chr16	58638392	58638410	-	1	NA	promoter-TSS (NM_175011)	promoter-TSS (NM_175011)	2	NM_175011	224247	Mm.26145	NM_175011	ENSMUSG00000055789	E330017A01Rik	-	RIKEN cDNA E330017A01 gene	protein-coding
mm_73387.1	chr8	105693827	105693880	+	1	NA	intron (NM_001033320, intron 8 of 16)	CpG	2947	NM_001033320	234695	Mm.471640	NM_001033320	ENSMUSG00000050357	Carmil2	CG1399-PB|D130029J02Rik|Gm585|Rltpr	capping protein regulator and myosin 1 linker 2	protein-coding
mm_83298.1	chr9	43239884	43239892	-	1	NA	promoter-TSS (NM_178644)	promoter-TSS (NM_178644)	-72	NM_178644	102644	Mm.246479	NM_178644	ENSMUSG00000032014	Oaf	AL024221|D130038B21Rik|D9Ucla1	out at first homolog	protein-coding
mm_99252.1	chr11	101120108	101120157	+	1	NA	promoter-TSS (NM_134024)	promoter-TSS (NM_134024)	1	NM_134024	103733	Mm.479145	NM_134024	ENSMUSG00000035198	Tubg1	1500010O08Rik|AI451582|AI503389|Tubg	tubulin, gamma 1	protein-coding
mm_4615.1	chr1	178636897	178636904	+	1	NA	intron (NM_001161665, intron 2 of 14)	intron (NM_001161665, intron 2 of 14)	107775	NM_001161665	269152	Mm.129727	NM_177724	ENSMUSG00000026494	Kif26b	4832420M10|BC056349|D230039L06Rik	kinesin family member 26B	protein-coding
mm_132897.1	chr16	48844267	48844293	+	1	NA	exon (NM_020509, exon 4 of 4)	exon (NM_020509, exon 4 of 4)	1728	NM_020509	57262	Mm.441868	NM_020509	ENSMUSG00000061100	Retnla	1810019L16Rik|Fizz-1|Fizz1|HIMF|RELM-alpha|RELMa|RELMalpha|Xcp2	resistin like alpha	protein-coding
mm_46864.1	chr5	113820160	113820171	-	1	NA	exon (NM_009151, exon 2 of 2)	exon (NM_009151, exon 2 of 2)	10336	NM_009151	20345	Mm.332590	NM_009151	ENSMUSG00000048163	Selplg	CD162|Psgl-1|Psgl1|Selp1|Selpl	selectin, platelet (p-selectin) ligand	protein-coding
mm_26500.1	chr3	145757260	145757267	+	1	NA	Intergenic	Intergenic	-1429	NM_026993	69219	Mm.234247	NM_026993	ENSMUSG00000028194	Ddah1	2410006N07Rik|2510015N06Rik|AI987801|AW050362	dimethylarginine dimethylaminohydrolase 1	protein-coding
mm_53681.1	chr6	142314077	142314096	+	1	NA	intron (NM_130861, intron 1 of 14)	intron (NM_130861, intron 1 of 14)	8895	NM_130861	108096	Mm.206599	NM_130861	ENSMUSG00000063975	Slco1a5	Oatp-3|Oatp3|Slc21a7	solute carrier organic anion transporter family, member 1a5	protein-coding
mm_117939.1	chr13	99434609	99434618	-	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-21787	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_165429.1	chr2	153345503	153345506	+	1	NA	promoter-TSS (NM_001039939)	promoter-TSS (NM_001039939)	306	NR_040318	72326	Mm.400102	NR_040318	ENSMUSG00000073236	2500004C02Rik	-	RIKEN cDNA 2500004C02 gene	ncRNA
mm_5695.1	chr1	43186468	43186470	-	1	NA	intron (NM_001289533, intron 1 of 5)	intron (NM_001289533, intron 1 of 5)	10292	NM_001289533	14200	Mm.6799	NM_010212	ENSMUSG00000008136	Fhl2	FHL-2|SLIM-3|SLIM3	four and a half LIM domains 2	protein-coding
mm_48171.1	chr5	137153194	137153202	-	1	NA	Intergenic	Intergenic	-36991	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_81337.1	chr9	108517713	108517724	+	1	NA	intron (NM_175143, intron 1 of 9)	CpG	631	NM_175143	69232	Mm.335449	NM_175143	ENSMUSG00000006673	Qrich1	2610028H07Rik	glutamine-rich 1	protein-coding
mm_20261.1	chr2	126618656	126618671	-	1	NA	promoter-TSS (NM_008230)	promoter-TSS (NM_008230)	15	NM_008230	15186	Mm.18603	NM_008230	ENSMUSG00000027360	Hdc	AW108189|Hdc-a|Hdc-c|Hdc-e|Hdc-s	histidine decarboxylase	protein-coding
mm_111688.1	chr12	103457196	103457270	-	1	NA	promoter-TSS (NM_145449)	promoter-TSS (NM_145449)	-10	NM_145449	217845	Mm.298416	NM_145449	ENSMUSG00000021208	Ifi27l2b	1810023F06Rik|ISG12(b2)	interferon, alpha-inducible protein 27 like 2B	protein-coding
mm_63587.1	chr7	128132952	128133010	+	1	NA	intron (NM_021334, intron 5 of 29)	intron (NM_021334, intron 5 of 29)	3413	NM_021334	16411	Mm.22378	NM_021334	ENSMUSG00000030789	Itgax	AI449405|Cd11c|Cr4|N418	integrin alpha X	protein-coding
mm_158674.1	chrX	157598657	157598694	-	1	NA	promoter-TSS (NM_172307)	promoter-TSS (NM_172307)	40	NM_172307	270669	Mm.37577	NM_172307	ENSMUSG00000046873	Mbtps2	9630032G22Rik|AI662535	membrane-bound transcription factor peptidase, site 2	protein-coding
mm_85333.1	chr9	102603572	102603573	-	1	NA	intron (NM_001301689, intron 8 of 14)	intron (NM_001301689, intron 8 of 14)	22552	NM_001301689	28135	Mm.38910	NM_001081122	ENSMUSG00000032534	Cep63	4921501M07|AL450317.13gm1|AW107703|CD20R|D9Mgc41|D9Mgc48e|ET2	centrosomal protein 63	protein-coding
mm_36794.1	chr4	103114358	103114366	-	1	NA	promoter-TSS (NM_027696)	promoter-TSS (NM_027696)	-28	NM_027696	71148	Mm.288721	NM_027696	ENSMUSG00000028522	Mier1	4933425I22Rik|5830411K19Rik|er1	MEIR1 treanscription regulator	protein-coding
mm_27428.1	chr3	51554073	51554083	-	1	NA	intron (NM_080793, intron 1 of 7)	intron (NM_080793, intron 1 of 7)	-5679	NR_033624	100039684	Mm.387178	NR_033624		5031434O11Rik	AI481280|Gm2370	RIKEN cDNA 5031434O11 gene	ncRNA
mm_92232.1	chr10	69125083	69125097	-	1	NA	Intergenic	Intergenic	-83462	NM_001252636	69288	Mm.26659	NM_001081347	ENSMUSG00000019944	Rhobtb1	1700008H16Rik|3110048G13Rik|AI173445|AI573858|AV350930	Rho-related BTB domain containing 1	protein-coding
mm_154937.1	chrX	36111808	36111836	+	1	NA	promoter-TSS (NM_133990)	promoter-TSS (NM_133990)	-286	NM_133990	16164	Mm.24208	NM_133990	ENSMUSG00000017057	Il13ra1	AI882074|CD213a1|IL-13R-alpha-1|IL-13r[a]|Il13ra|NR4	interleukin 13 receptor, alpha 1	protein-coding
mm_122941.1	chr14	54965361	54965402	-	1	NA	exon (NM_010856, exon 3 of 39)	exon (NM_010856, exon 3 of 39)	1226	NM_001164171	17888	Mm.290003	NM_010856	ENSMUSG00000040752	Myh6	A830009F23Rik|AA517445|Myhc-a|Myhca|alpha-MHC	myosin, heavy polypeptide 6, cardiac muscle, alpha	protein-coding
mm_72041.1	chr8	70905971	70906017	+	1	NA	promoter-TSS (NM_173013)	promoter-TSS (NM_173013)	20	NM_173013	270058	Mm.248559	NM_173013	ENSMUSG00000019261	Map1s	6430517J16Rik|Bpy2ip1|Map8|Mtap1s|VCY2IP1	microtubule-associated protein 1S	protein-coding
mm_94053.1	chr10	128180266	128180307	-	1	NA	promoter-TSS (NM_001039080)	promoter-TSS (NM_001039080)	11	NM_001039080	56516	Mm.42247	NM_019711	ENSMUSG00000040043	Rbms2	2610315E04Rik|Scr3	RNA binding motif, single stranded interacting protein 2	protein-coding
mm_109260.1	chr12	109460529	109460584	+	1	NA	non-coding (NR_033813, exon 6 of 6)	non-coding (NR_033813, exon 6 of 6)	7101	NM_010052	13386	Mm.157069	NM_010052	ENSMUSG00000040856	Dlk1	AW742678|DLK-1|DlkI|FA1|Ly107|Peg9|SCP1|ZOG|pG2|pref-1	delta-like 1 homolog (Drosophila)	protein-coding
mm_106352.1	chr11	118393558	118393575	-	1	NA	exon (NM_011150, exon 6 of 6)	exon (NM_011150, exon 6 of 6)	8365	NM_011150	19039	Mm.3152	NM_011150	ENSMUSG00000033880	Lgals3bp	90K|CyCAP|MAC-2BP|Ppicap|Tango10b	lectin, galactoside-binding, soluble, 3 binding protein	protein-coding
mm_45704.1	chr5	83355073	83355092	-	1	NA	5' UTR (NM_153801, exon 1 of 12)	5' UTR (NM_153801, exon 1 of 12)	113	NM_153801	243078	Mm.126783	NM_153801	ENSMUSG00000049537	Tecrl	D330017N19Rik|Srd5a2l2	trans-2,3-enoyl-CoA reductase-like	protein-coding
mm_172544.1	chr7	98119465	98119469	-	1	NA	promoter-TSS (NM_008663)	promoter-TSS (NM_008663)	26	NM_001256081	17921	Mm.1403	NM_008663	ENSMUSG00000030761	Myo7a	Hdb|Myo7|USH1B|nmf371|polka|sh-1|sh1	myosin VIIA	protein-coding
mm_3271.1	chr1	136466384	136466405	+	1	NA	Intergenic	CpG	-1454	NM_001287179	381293	Mm.458468	NM_001081258	ENSMUSG00000041498	Kif14	D1Ertd367e|E130203M01	kinesin family member 14	protein-coding
mm_152511.1	chr19	11277945	11277953	-	1	NA	intron (NM_183190, intron 2 of 4)	intron (NM_183190, intron 2 of 4)	5864	NM_183190	269063	Mm.268940	NM_183190	ENSMUSG00000054523	Ms4a5	-	membrane-spanning 4-domains, subfamily A, member 5	protein-coding
mm_85810.1	chr9	110387642	110387661	-	1	NA	exon (NM_001081043, exon 20 of 25)	exon (NM_001081043, exon 20 of 25)	20559	NM_001081043	104831	Mm.335477	NM_001081043	ENSMUSG00000036057	Ptpn23	AI462446|PTP-TD14	protein tyrosine phosphatase, non-receptor type 23	protein-coding
mm_113318.1	chr13	30764829	30764841	+	1	NA	3' UTR (NM_013674, exon 9 of 9)	3' UTR (NM_013674, exon 9 of 9)	15602	NM_013674	16364	Mm.4677	NM_013674	ENSMUSG00000021356	Irf4	AI385587|IRF-4|LSIRF|NF-EM5|Spip	interferon regulatory factor 4	protein-coding
mm_127846.1	chr15	7398104	7398115	-	1	NA	5' UTR (NM_001289498, exon 1 of 23)	5' UTR (NM_001289498, exon 1 of 23)	281	NM_001289496	268780	Mm.203208	NM_178748	ENSMUSG00000042961	Egflam	5930412K08|AU040377	EGF-like, fibronectin type III and laminin G domains	protein-coding
mm_99099.1	chr11	99948421	99948429	+	1	NA	promoter-TSS (NM_001085527)	promoter-TSS (NM_001085527)	-50	NM_001085527	435286	Mm.457964	NM_001085527	ENSMUSG00000078255	Krtap9-5	-	keratin associated protein 9-5	protein-coding
mm_62327.1	chr7	100472986	100472998	+	1	NA	promoter-TSS (NM_009464)	promoter-TSS (NM_009464)	1	NM_009464	22229	Mm.6254	NM_009464	ENSMUSG00000032942	Ucp3	AI645527|Slc25a9|UCP-3	uncoupling protein 3 (mitochondrial, proton carrier)	protein-coding
mm_83957.1	chr9	56950785	56950804	-	1	NA	promoter-TSS (NM_178374)	promoter-TSS (NM_178374)	-130	NM_178374	66069	Mm.220984	NM_178374	ENSMUSG00000055334	Snupn	0610031A09Rik|Rnut1|Snupn1	snurportin 1	protein-coding
mm_172539.1	chr7	96203642	96203642	-	1	NA	intron (NM_001310762, intron 1 of 32)	intron (NM_001310762, intron 1 of 32)	-6995	NM_011858	23966	Mm.254610	NM_011858	ENSMUSG00000048078	Tenm4	Doc4|ELM2|Odz4|R75022|Ten-m4|l(7)-3Rn|l7Rn3|mKIAA1302	teneurin transmembrane protein 4	protein-coding
mm_129437.1	chr15	78511606	78511616	-	1	NA	Intergenic	Intergenic	-16545	NM_008368	16185	Mm.35287	NM_008368	ENSMUSG00000068227	Il2rb	CD122|IL-15Rbeta|IL15Rbeta|Il-2/15Rbeta|Il-2Rbeta|p70	interleukin 2 receptor, beta chain	protein-coding
mm_83651.1	chr9	49506902	49506931	-	1	NA	exon (NM_001113204, exon 18 of 19)	exon (NM_001113204, exon 18 of 19)	-11372	NR_029465	100036537	Mm.437541	NR_029465	ENSMUSG00000079564	Gm11149	ENSMUSG00000060603|ENSMUSG00000079564	predicted gene 11149	ncRNA
mm_138953.1	chr17	44172544	44172547	+	1	NA	Intergenic	Intergenic	-16027	NM_172621	224796	Mm.37666	NM_172621	ENSMUSG00000023959	Clic5	5730531E12Rik|B330005L24|Gm322|jbg	chloride intracellular channel 5	protein-coding
mm_130482.1	chr15	98741376	98741387	-	1	NA	exon (NM_007478, exon 3 of 5)	exon (NM_007478, exon 3 of 5)	-13183	NM_024169	66120	Mm.30729	NM_024169	ENSMUSG00000003355	Fkbp11	1110002O23Rik|FKBP-11	FK506 binding protein 11	protein-coding
mm_70396.1	chr8	11098966	11098983	+	1	NA	Intergenic	Intergenic	-90544	NM_001081212	384783	Mm.407207	NM_001081212	ENSMUSG00000038894	Irs2	Irs-2	insulin receptor substrate 2	protein-coding
mm_42903.1	chr5	122500727	122500735	+	1	NA	exon (NM_009722, exon 3 of 21)	exon (NM_009722, exon 3 of 21)	1494	NM_001110140	11938	Mm.227583	NM_009722	ENSMUSG00000029467	Atp2a2	9530097L16Rik|D5Wsu150e|SERCA2|SERCA2B|Serca2a|mKIAA4195	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	protein-coding
mm_79169.1	chr9	47852404	47852420	+	1	NA	3' UTR (NM_018770, exon 10 of 10)	3' UTR (NM_018770, exon 10 of 10)	-34204	NR_046048	100038460	Mm.447649	NR_046048		Gm10677	ENSMUSG00000074363	predicted gene 10677	ncRNA
mm_111144.1	chr12	81790902	81790940	-	1	NA	Intergenic	Intergenic	-9751	NM_001174107	338372	Mm.35284	NM_177395	ENSMUSG00000042724	Map3k9	E130314H24Rik|Mlk1|Prke1	mitogen-activated protein kinase kinase kinase 9	protein-coding
mm_12903.1	chr2	84809500	84809523	+	1	NA	3' UTR (NM_019949, exon 4 of 4)	3' UTR (NM_019949, exon 4 of 4)	10683	NM_019949	56791	Mm.38261	NM_019949	ENSMUSG00000027078	Ube2l6	2810489I21Rik|RIG-B|UBCH8|Ubce8|Ubcm8	ubiquitin-conjugating enzyme E2L 6	protein-coding
mm_10546.1	chr2	16568521	16568550	+	1	NA	intron (NM_026162, intron 4 of 13)	intron (NM_026162, intron 4 of 13)	212231	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding
mm_37563.1	chr4	126202336	126202401	-	1	NA	intron (NM_146153, intron 1 of 10)	CpG	342	NM_146153	230753	Mm.29813	NM_146153	ENSMUSG00000043962	Thrap3	9330151F09Rik|B230333E16Rik|Trap150	thyroid hormone receptor associated protein 3	protein-coding
mm_17981.1	chr2	37703846	37703885	-	1	NA	Intergenic	CpG	-56580	NM_009261	20744	Mm.237095	NM_009261	ENSMUSG00000026915	Strbp	6430510M02Rik|AI852513|C230082I21Rik|C86322|Spnr	spermatid perinuclear RNA binding protein	protein-coding
mm_56258.1	chr6	90810026	90810073	-	1	NA	promoter-TSS (NM_001134384)	promoter-TSS (NM_001134384)	74	NM_001134384	232227	Mm.196943	NM_182784	ENSMUSG00000034312	Iqsec1	AW561907|BC026481|BRAG2|D6Ertd349e|cI-43	IQ motif and Sec7 domain 1	protein-coding
mm_167387.1	chr8	94802471	94802473	-	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	-7981	NM_011332	20295	Mm.41988	NM_011332	ENSMUSG00000031780	Ccl17	Abcd-2|Scya17|Scya17l|Tarc	chemokine (C-C motif) ligand 17	protein-coding
mm_77952.1	chr9	7560611	7560621	+	1	NA	exon (NM_008611, exon 2 of 10)	exon (NM_008611, exon 2 of 10)	2187	NM_008611	17394	Mm.16415	NM_008611	ENSMUSG00000005800	Mmp8	BB138268	matrix metallopeptidase 8	protein-coding
mm_118281.1	chr13	112746078	112746080	-	1	NA	Intergenic	Intergenic	-54698	NM_008903	19012	Mm.291029	NM_008247	ENSMUSG00000021759	Plpp1	Hic53|Hpic53|LPP-1|LPP1|PAP-2a|PAP2-alpha|PAP2a|Ppap2a|mPAP	phospholipid phosphatase 1	protein-coding
mm_135981.1	chr16	75092428	75092430	-	1	NA	Intergenic	Intergenic	493632	NM_001252513	320355	Mm.99517	NM_177142	ENSMUSG00000032948	Lipi	D930038D03Rik|lpd1	lipase, member I	protein-coding
mm_74136.1	chr8	123212914	123212924	+	1	NA	promoter-TSS (NM_145606)	promoter-TSS (NM_145606)	61	NM_177279	320869	Mm.258354	NM_177279	ENSMUSG00000048478	Spata33	4732415M23Rik|AI847264	spermatogenesis associated 33	protein-coding
mm_166036.1	chr4	129033784	129033798	-	1	NA	Intergenic	Intergenic	-24480	NM_029219	75234	Mm.259672	NM_029219	ENSMUSG00000028793	Rnf19b	4930534K13Rik|4930555L03Rik|Ibrdc3	ring finger protein 19B	protein-coding
mm_15182.1	chr2	154191269	154191273	+	1	NA	intron (NM_001012392, intron 1 of 15)	intron (NM_001012392, intron 1 of 15)	453	NM_001012392	228801	Mm.3783	NM_153418	ENSMUSG00000027485	Bpifb1	Lplunc1	BPI fold containing family B, member 1	protein-coding
mm_113856.1	chr13	47239989	47239993	+	1	NA	intron (NM_001170643, intron 6 of 7)	intron (NM_001170643, intron 6 of 7)	45988	NM_001170643	218215	Mm.287609	NM_146042	ENSMUSG00000038068	Rnf144b	BC025007|E130105P19Rik|Ibrdc2|Pir2	ring finger protein 144B	protein-coding
mm_41054.1	chr5	86804282	86804297	+	1	NA	promoter-TSS (NM_177680)	promoter-TSS (NM_177680)	23	NM_001347376	231386	Mm.196325	NM_177680	ENSMUSG00000035851	Ythdc1	A730098D12Rik|C80342|mKIAA1966	YTH domain containing 1	protein-coding
mm_148855.1	chr19	6396555	6396556	+	1	NA	intron (NM_011224, intron 17 of 19)	intron (NM_011224, intron 17 of 19)	-4028	NM_011242	19395	Mm.77017	NM_011242	ENSMUSG00000032946	Rasgrp2	CDC25L|Caldaggef1	RAS, guanyl releasing protein 2	protein-coding
mm_1193.1	chr1	62703668	62703702	+	1	NA	5' UTR (NM_001077407, exon 1 of 16)	5' UTR (NM_001077407, exon 1 of 16)	368	NM_001077405	18187	Mm.266341	NM_010939	ENSMUSG00000025969	Nrp2	1110048P06Rik|Np-2|Np2|Npn-2|Npn2	neuropilin 2	protein-coding
mm_10628.1	chr2	19660046	19660079	+	1	NA	3' UTR (NM_027715, exon 1 of 1)	3' UTR (NM_027715, exon 1 of 1)	2000	NM_027715	71198	Mm.83981	NM_027715	ENSMUSG00000043415	Otud1	4933428L19Rik	OTU domain containing 1	protein-coding
mm_137731.1	chr17	29294040	29294060	+	1	NA	exon (NM_030561, exon 5 of 9)	exon (NM_030561, exon 5 of 9)	-24832	NM_023734	74116	Mm.30950	NM_023734	ENSMUSG00000024011	Pi16	1200009H11Rik|Cripi|PI-16	peptidase inhibitor 16	protein-coding
mm_122005.1	chr14	26939918	26939926	-	1	NA	intron (NM_145221, intron 16 of 21)	B2_Mm2|SINE|B2	30629	NM_145221	72993	Mm.202322	NM_145221	ENSMUSG00000040760	Appl1	2900057D21Rik|7330406P05Rik|AI585782|AW209077|BB022931|C88264|DIP13	adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 1	protein-coding
mm_10979.1	chr2	25823466	25823513	+	1	NA	intron (NM_029959, intron 1 of 6)	intron (NM_029959, intron 1 of 6)	336	NM_029959	77704	Mm.159974	NM_029959	ENSMUSG00000023210	Lcn9	9230102I19Rik	lipocalin 9	protein-coding
mm_58226.1	chr6	144270901	144270902	-	1	NA	Intergenic	B3|SINE|B2	-61333	NM_001243163	20678	Mm.1752	NM_011444	ENSMUSG00000041540	Sox5	A730017D01Rik|AI528773	SRY (sex determining region Y)-box 5	protein-coding
mm_32551.1	chr4	109406748	109406763	+	1	NA	promoter-TSS (NM_153392)	promoter-TSS (NM_153392)	-345	NM_153392	230603	Mm.33091	NM_153392	ENSMUSG00000028555	Ttc39a	4922503N01Rik	tetratricopeptide repeat domain 39A	protein-coding
mm_18363.1	chr2	59154713	59154718	-	1	NA	Intergenic	Intergenic	-6135	NM_026361	227937	Mm.260938	NM_026361	ENSMUSG00000026991	Pkp4	5031422I09Rik|9430019K17Rik|Armrp|p0071	plakophilin 4	protein-coding
mm_116546.1	chr13	45964965	45965001	-	1	NA	promoter-TSS (NM_009124)	promoter-TSS (NM_009124)	8	NM_001199304	20238	Mm.342683	NM_009124	ENSMUSG00000046876	Atxn1	2900016G23Rik|Atx1|C85907|ENSMUSG00000074917|Gm10786|Sca1	ataxin 1	protein-coding
mm_106425.1	chr11	119300040	119300064	-	1	NA	promoter-TSS (NM_138669)	promoter-TSS (NM_138669)	-9	NM_138669	192170	Mm.197555	NM_138669	ENSMUSG00000025580	Eif4a3	2400003O03Rik|Ddx48|eIF4A-III|mKIAA0111	eukaryotic translation initiation factor 4A3	protein-coding
mm_173363.1	chrY	90819748	90819762	+	1	NA	Intergenic	Intergenic	19651	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_107966.1	chr12	72760522	72760529	+	1	NA	promoter-TSS (NM_008910)	promoter-TSS (NM_008910)	-686	NM_008910	19042	Mm.261045	NM_008910	ENSMUSG00000021096	Ppm1a	2310003C21Rik|2900017D14Rik|AI427932|AU017636|MMPa-2|MPPa-1	protein phosphatase 1A, magnesium dependent, alpha isoform	protein-coding
mm_1902.1	chr1	85801894	85801897	+	1	NA	intron (NM_133781, intron 1 of 8)	B1F2|SINE|Alu	8448	NM_133781	12283	Mm.26135	NM_133781	ENSMUSG00000036707	Cab39	AA408805|AA960512|C78372|MO25|MO25alpha	calcium binding protein 39	protein-coding
mm_8275.1	chr1	139781255	139781282	-	1	NA	promoter-TSS (NM_001160304)	promoter-TSS (NM_001160304)	-29	NM_001160303	214403	Mm.337613	NM_001029977	ENSMUSG00000070594	Gm4788	Cfhrc|EG214403	predicted gene 4788	protein-coding
mm_112412.1	chr13	3634035	3634108	+	1	NA	promoter-TSS (NM_001267724)	promoter-TSS (NM_001267724)	39	NM_001267724	142688	Mm.253061	NM_178283	ENSMUSG00000033781	Asb13	2210015B19Rik|6430573K02Rik|Asb-13|C85285	ankyrin repeat and SOCS box-containing 13	protein-coding
mm_103902.1	chr11	83576948	83576954	-	1	NA	intron (NM_011338, intron 1 of 3)	ORSL-2a|DNA|hAT-Tip100	1685	NM_011338	20308	Mm.416125	NM_011338	ENSMUSG00000019122	Ccl9	CCF18|MRP-2|Scya10|Scya9	chemokine (C-C motif) ligand 9	protein-coding
mm_160260.1	chr7	109493705	109493705	-	1	NA	promoter-TSS (NM_001170913)	promoter-TSS (NM_001170913)	33	NM_001170913	330627	Mm.183528	NM_181853	ENSMUSG00000031026	Trim66	Kiaa0298-hp|Tif1d	tripartite motif-containing 66	protein-coding
mm_24603.1	chr3	93445470	93445478	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	3144	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_41546.1	chr5	92898054	92898075	+	1	NA	promoter-TSS (NM_001077596)	promoter-TSS (NM_001077596)	71	NM_001077596	27428	Mm.46014	NM_015756	ENSMUSG00000029381	Shroom3	AL022960|D5Ertd287e|Shrm|Shrm3	shroom family member 3	protein-coding
mm_29013.1	chr3	101605169	101605190	-	1	NA	promoter-TSS (NM_144900)	promoter-TSS (NM_144900)	-472	NM_144900	11928	Mm.193670	NM_144900	ENSMUSG00000033161	Atp1a1	Atpa-1|BC010319	ATPase, Na+/K+ transporting, alpha 1 polypeptide	protein-coding
mm_121872.1	chr14	21011340	21011355	-	1	NA	intron (NM_009502, intron 13 of 20)	intron (NM_009502, intron 13 of 20)	41095	NM_018829	55946	Mm.376269	NM_018829	ENSMUSG00000021824	Ap3m1	1200013D09Rik|C78982|R75378	adaptor-related protein complex 3, mu 1 subunit	protein-coding
mm_163360.1	chr12	31536557	31536566	-	1	NA	intron (NM_011867, intron 10 of 20)	intron (NM_011867, intron 10 of 20)	23408	NM_011867	23985	Mm.100187	NM_011867	ENSMUSG00000020651	Slc26a4	Pds|pendrin	solute carrier family 26, member 4	protein-coding
mm_28872.1	chr3	97702867	97702903	-	1	NA	intron (NM_001039376, intron 36 of 46)	intron (NM_001039376, intron 36 of 46)	-12323	NR_106084	102466229		NR_106084	ENSMUSG00000098381	Mir7225	Gm27499|mmu-mir-7225	microRNA 7225	ncRNA
mm_151745.1	chr19	5023927	5023979	-	1	NA	promoter-TSS (NM_007854)	promoter-TSS (NM_007854)	-53	NM_007854	13340	Mm.4930	NM_007854	ENSMUSG00000024891	Slc29a2	Der12|Ent2|Hnp36	solute carrier family 29 (nucleoside transporters), member 2	protein-coding
mm_19969.1	chr2	118011777	118011808	-	1	NA	intron (NR_126479, intron 8 of 9)	intron (NR_126479, intron 8 of 9)	99410	NR_126479	329496	Mm.235844	NR_126479	ENSMUSG00000087203	Gm13986	C230060E24|OTTMUSG00000015236	predicted gene 13986	ncRNA
mm_2870.1	chr1	131750507	131750519	+	1	NA	intron (NM_177243, intron 1 of 20)	intron (NM_177243, intron 1 of 20)	6491	NM_177243	320718	Mm.482704	NM_177243	ENSMUSG00000042268	Slc26a9	E030002L01Rik	solute carrier family 26, member 9	protein-coding
mm_48738.1	chr5	147637461	147637467	-	1	NA	intron (NM_010228, intron 13 of 29)	intron (NM_010228, intron 13 of 29)	88524	NM_010228	14254	Mm.389712	NM_010228	ENSMUSG00000029648	Flt1	AI323757|Flt-1|VEGFR-1|VEGFR1|sFlt1	FMS-like tyrosine kinase 1	protein-coding
mm_127213.1	chr15	99249469	99249504	+	1	NA	exon (NM_016766, exon 4 of 15)	exon (NM_016766, exon 4 of 15)	-2302	NR_045627	73600	Mm.475134	NR_045627	ENSMUSG00000100599	1700120C14Rik	-	RIKEN cDNA 1700120C14 gene	ncRNA
mm_109994.1	chr12	15815573	15815583	-	1	NA	5' UTR (NM_144551, exon 1 of 3)	5' UTR (NM_144551, exon 1 of 3)	1207	NM_144551	217410	Mm.491136	NM_144551	ENSMUSG00000020601	Trib2	AW319517|TRB-2|TRB2	tribbles pseudokinase 2	protein-coding
mm_77127.1	chr8	111337762	111337827	-	1	NA	intron (NM_029005, intron 1 of 10)	intron (NM_029005, intron 1 of 10)	411	NM_001310613	74568	Mm.207971	NM_029005	ENSMUSG00000012519	Mlkl	9130019I15Rik	mixed lineage kinase domain-like	protein-coding
mm_36063.1	chr4	57916162	57916175	-	1	NA	promoter-TSS (NM_178727)	promoter-TSS (NM_178727)	96	NM_178727	242484	Mm.23214	NM_178727	ENSMUSG00000052117	D630039A03Rik	-	RIKEN cDNA D630039A03 gene	protein-coding
mm_122566.1	chr14	50781215	50781219	-	1	NA	intron (NM_177625, intron 2 of 3)	B1F2|SINE|Alu	4303	NM_177625	219022	Mm.276362	NM_177625	ENSMUSG00000006288	Ttc5	-	tetratricopeptide repeat domain 5	protein-coding
mm_106862.1	chr12	8009324	8009335	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	31652	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_896.1	chr1	53313623	53313635	+	1	NA	promoter-TSS (NM_001285839)	promoter-TSS (NM_001285839)	5	NR_104360	72085	Mm.482256	NM_028091	ENSMUSG00000026096	Osgepl1	2610001M19Rik|AA416452	O-sialoglycoprotein endopeptidase-like 1	protein-coding
mm_6301.1	chr1	71414804	71414815	-	1	NA	5' UTR (NM_175210, exon 1 of 53)	5' UTR (NM_175210, exon 1 of 53)	101	NM_175210	74591	Mm.159251	NM_175210	ENSMUSG00000050296	Abca12	4832428G11Rik|4833417A11Rik	ATP-binding cassette, sub-family A (ABC1), member 12	protein-coding
mm_95956.1	chr11	58782957	58782969	+	1	NA	Intergenic	Intergenic	-3176	NM_001011760	257917	Mm.377302	NM_001011760	ENSMUSG00000059504	Olfr314	MOR278-2	olfactory receptor 314	protein-coding
mm_140932.1	chr17	24351073	24351108	-	1	NA	promoter-TSS (NM_001039581)	promoter-TSS (NM_001039581)	-933	NM_013855	27410	Mm.239470	NM_013855	ENSMUSG00000024130	Abca3	1810036E22Rik|ABC-C|Abc3	ATP-binding cassette, sub-family A (ABC1), member 3	protein-coding
mm_76994.1	chr8	107080666	107080667	-	1	NA	intron (NR_104410, intron 5 of 10)	B3|SINE|B2	-15022	NM_025458	66269	Mm.23032	NM_025458	ENSMUSG00000031919	Tmed6	1810015P03Rik|1810018I24Rik	transmembrane p24 trafficking protein 6	protein-coding
mm_58681.1	chr7	12512514	12512520	+	1	NA	promoter-TSS (NM_028434)	promoter-TSS (NM_028434)	-34	NM_028434	73090	Mm.84622	NM_028434	ENSMUSG00000030385	2900092C05Rik	-	RIKEN cDNA 2900092C05 gene	protein-coding
mm_43016.1	chr5	123907295	123907315	+	1	NA	promoter-TSS (NM_026603)	promoter-TSS (NM_026603)	30	NM_026603	68184	Mm.28549	NM_026603	ENSMUSG00000023106	Denr	1500003K04Rik	density-regulated protein	protein-coding
mm_100082.1	chr11	115466746	115466756	+	1	NA	intron (NM_001080934, intron 2 of 3)	B4|SINE|B4	4278	NM_001080934	217316	Mm.25773	NM_001080934	ENSMUSG00000045775	Slc16a5	A130015N09Rik|MCT 5|MCT 6|MCT5	solute carrier family 16 (monocarboxylic acid transporters), member 5	protein-coding
mm_156759.1	chrX	160502509	160502524	+	1	NA	promoter-TSS (NM_001177878)	promoter-TSS (NM_001177878)	82	NM_001177878	110094	Mm.350712	NM_172783	ENSMUSG00000031295	Phka2	6330505C01Rik|D330034O08|Phk	phosphorylase kinase alpha 2	protein-coding
mm_131613.1	chr16	19760233	19760247	+	1	NA	promoter-TSS (NM_001159407)	promoter-TSS (NM_001159407)	6	NM_001159407	108105	Mm.33935	NM_054052	ENSMUSG00000022686	B3gnt5	beta3GnT5	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5	protein-coding
mm_102017.1	chr11	51635849	51635859	-	1	NA	promoter-TSS (NM_025346)	promoter-TSS (NM_025346)	42	NM_025346	66089	Mm.288183	NM_025346	ENSMUSG00000001054	Rmnd5b	0610039K22Rik|Gid2	required for meiotic nuclear division 5 homolog B	protein-coding
mm_32839.1	chr4	117835305	117835333	+	1	NA	promoter-TSS (NM_008135)	promoter-TSS (NM_008135)	61	NM_008135	14664	Mm.244549	NM_008135	ENSMUSG00000028542	Slc6a9	Glyt-1|Glyt1	solute carrier family 6 (neurotransmitter transporter, glycine), member 9	protein-coding
mm_21889.1	chr2	166155376	166155380	-	1	NA	promoter-TSS (NM_001252578)	promoter-TSS (NM_001252578)	-93	NM_001252578	72043	Mm.1011	NM_028072	ENSMUSG00000006800	Sulf2	2010004N24Rik|AU020235|MSulf-2|mKIAA1247	sulfatase 2	protein-coding
mm_6603.1	chr1	75317591	75317612	-	1	NA	promoter-TSS (NM_016878)	promoter-TSS (NM_016878)	36	NM_001110831	13437	Mm.24680	NM_016878	ENSMUSG00000026209	Dnpep	AA407814	aspartyl aminopeptidase	protein-coding
mm_1269.1	chr1	63273204	63273230	+	1	NA	promoter-TSS (NM_028673)	promoter-TSS (NM_028673)	-52	NM_028673	73884	Mm.86986	NM_028673	ENSMUSG00000027520	Zdbf2	4930431J08Rik|9330107J05Rik	zinc finger, DBF-type containing 2	protein-coding
mm_56590.1	chr6	108185553	108185587	-	1	NA	promoter-TSS (NM_145937)	promoter-TSS (NM_145937)	13	NM_145937	58911	Mm.439876	NM_145937	ENSMUSG00000030101	Sumf1	AA543204|AI463102|AI851573|FGE	sulfatase modifying factor 1	protein-coding
mm_25303.1	chr3	105977787	105977791	+	1	NA	exon (NM_007696, exon 5 of 11)	exon (NM_007696, exon 5 of 11)	3987	NM_007696	12659	Mm.431947	NM_007696	ENSMUSG00000074340	Ovgp1	120kDa|AU016433|AU019448|Chit5|MOGP|OGP|muc9	oviductal glycoprotein 1	protein-coding
mm_53337.1	chr6	129237260	129237270	+	1	NA	intron (NR_040265, intron 1 of 2)	intron (NR_040265, intron 1 of 2)	780	NR_040265	76432	Mm.261738	NR_040265	ENSMUSG00000097354	2310001H17Rik	AI646108	RIKEN cDNA 2310001H17 gene	ncRNA
mm_141032.1	chr17	25273290	25273301	-	1	NA	promoter-TSS (NR_027452)	promoter-TSS (NR_027452)	136	NM_001177610	22196	Mm.240044	NM_011665	ENSMUSG00000015120	Ube2i	5830467E05Rik|F830028O17Rik|UBC9|Ubce2i|Ubce9	ubiquitin-conjugating enzyme E2I	protein-coding
mm_4258.1	chr1	171419028	171419052	+	1	NA	promoter-TSS (NM_001164525)	promoter-TSS (NM_001164525)	7	NM_001164525	226654	Mm.46366	NM_001164525	ENSMUSG00000103711	Tstd1	AV065366|EG226654|Gm4848|KAT	thiosulfate sulfurtransferase (rhodanese)-like domain containing 1	protein-coding
mm_5456.1	chr1	36274471	36274496	-	1	NA	Intergenic	Intergenic	-1058	NM_153408	214854	Mm.389110	NM_153408	ENSMUSG00000047180	Neurl3	2010300P06Rik|Lincr	neuralized E3 ubiquitin protein ligase 3	protein-coding
mm_165246.1	chr2	69766141	69766145	+	1	NA	intron (NM_001077684, intron 7 of 8)	intron (NM_001077684, intron 7 of 8)	23343	NM_001077684	75051	Mm.195726	NM_001077684	ENSMUSG00000070883	Ccdc173	4930525K21Rik|4930578N16Rik	coiled-coil domain containing 173	protein-coding
mm_93392.1	chr10	107486078	107486090	-	1	NA	promoter-TSS (NM_008656)	promoter-TSS (NM_008656)	50	NM_008656	17877	Mm.4984	NM_008656	ENSMUSG00000000435	Myf5	B130010J22Rik|Myf-5|bHLHc2	myogenic factor 5	protein-coding
mm_30410.1	chr3	152255356	152255373	-	1	NA	5' UTR (NM_199465, exon 2 of 13)	5' UTR (NM_199465, exon 2 of 13)	10956	NM_199465	68810	Mm.200188	NM_199465	ENSMUSG00000039103	Nexn	1110046H09Rik|AA553326|NELIN	nexilin	protein-coding
mm_148423.1	chr19	3938162	3938201	+	1	NA	intron (NM_001161428, intron 3 of 9)	ID_B1|SINE|B4	2995	NM_001161428	54445	Mm.262094	NM_019449	ENSMUSG00000036908	Unc93b1	Unc-93B1|Unc93b	unc-93 homolog B1 (C. elegans)	protein-coding
mm_29820.1	chr3	129225523	129225542	-	1	NA	Intergenic	Intergenic	11600	NM_001287048	18741	Mm.246804	NM_011098	ENSMUSG00000028023	Pitx2	9430085M16Rik|Brx1|Brx1b|Munc30|Otlx2|Ptx2|Rieg	paired-like homeodomain transcription factor 2	protein-coding
mm_11221.1	chr2	29761556	29761567	+	1	NA	promoter-TSS (NM_001177392)	promoter-TSS (NM_001177392)	33	NM_001177392	433416	Mm.330112	NM_001034887	ENSMUSG00000075425	Gm13547	OTTMUSG00000012686	predicted gene 13547	protein-coding
mm_100501.1	chr11	120484652	120484696	+	1	NA	promoter-TSS (NM_027204)	promoter-TSS (NM_027204)	5	NM_027204	56282	Mm.133851	NM_027204	ENSMUSG00000039640	Mrpl12	0610034O11Rik|1500031N16Rik|MRP-L12|Rpml12	mitochondrial ribosomal protein L12	protein-coding
mm_164682.1	chr17	47509477	47509491	+	1	NA	intron (NM_001081635, intron 1 of 6)	intron (NM_001081635, intron 1 of 6)	4433	NM_001081635	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_17477.1	chr2	28561181	28561192	-	1	NA	exon (NM_009885, exon 2 of 11)	exon (NM_009885, exon 2 of 11)	2217	NM_009885	12613	Mm.236017	NM_009885	ENSMUSG00000026818	Cel	1810036E18Rik|BAL	carboxyl ester lipase	protein-coding
mm_85546.1	chr9	106685326	106685363	-	1	NA	5' UTR (NM_011573, exon 1 of 6)	5' UTR (NM_011573, exon 1 of 6)	472	NM_011573	21767	Mm.22266	NM_011573	ENSMUSG00000040813	Tex264	TEG-264	testis expressed gene 264	protein-coding
mm_106320.1	chr11	118303490	118303524	-	1	NA	3' UTR (NM_011594, exon 5 of 5)	3' UTR (NM_011594, exon 5 of 5)	-13263	NM_001033528	72344	Mm.232293	NM_001033528	ENSMUSG00000033909	Usp36	2700002L06Rik|mKIAA1453	ubiquitin specific peptidase 36	protein-coding
mm_91991.1	chr10	62071621	62071668	-	1	NA	Intergenic	Intergenic	39369	NM_027251	69894	Mm.294126	NM_027251	ENSMUSG00000020083	2010107G23Rik	AA545165	RIKEN cDNA 2010107G23 gene	protein-coding
mm_150373.1	chr19	34922352	34922404	+	1	NA	promoter-TSS (NM_183046)	promoter-TSS (NM_183046)	20	NM_183046	240641	Mm.278471	NM_183046	ENSMUSG00000024795	Kif20b	33cex|B130024C23|C330014J10Rik|Mphosph1|magoo	kinesin family member 20B	protein-coding
mm_105690.1	chr11	107763148	107763172	-	1	NA	intron (NM_019431, intron 1 of 3)	intron (NM_019431, intron 1 of 3)	31304	NM_019431	54377	Mm.103724	NM_019431	ENSMUSG00000020723	Cacng4	AI413107|AW491861	calcium channel, voltage-dependent, gamma subunit 4	protein-coding
mm_11927.1	chr2	52120982	52120988	+	1	NA	intron (NM_175238, intron 35 of 35)	intron (NM_175238, intron 35 of 35)	48148	NM_175238	51869	Mm.254530	NM_175238	ENSMUSG00000036202	Rif1	5730435J01Rik|6530403D07Rik|AU016181|AW549474|D2Ertd145e	replication timing regulatory factor 1	protein-coding
mm_165070.1	chr19	44407545	44407548	-	1	NA	5' UTR (NM_009127, exon 1 of 6)	5' UTR (NM_009127, exon 1 of 6)	163	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_76258.1	chr8	83741174	83741190	-	1	NA	5' UTR (NM_001163029, exon 1 of 18)	5' UTR (NM_001163029, exon 1 of 18)	129	NM_001163029	26364	Mm.334648	NM_011925	ENSMUSG00000002885	Adgre5	AA409984|Cd97|TM7LN1	adhesion G protein-coupled receptor E5	protein-coding
mm_133817.1	chr16	95718987	95718992	+	1	NA	exon (NM_011809, exon 10 of 10)	exon (NM_011809, exon 10 of 10)	16582	NM_011809	23872	Mm.290207	NM_011809	ENSMUSG00000022895	Ets2	AU022856|Ets-2	E26 avian leukemia oncogene 2, 3' domain	protein-coding
mm_155766.1	chrX	96168458	96168470	+	1	NA	TTS (NM_010833)	TTS (NM_010833)	-71462	NR_030718	100038363	Mm.30815	NR_030718	ENSMUSG00000078122	F630028O10Rik	ENSMUSG00000065522|Gm14924|OTTMUSG00000018496|mir-223	RIKEN cDNA F630028O10 gene	ncRNA
mm_166979.1	chr7	45212098	45212109	-	1	NA	promoter-TSS (NM_015789)	promoter-TSS (NM_015789)	-220	NM_015789	50722	Mm.27287	NM_015789	ENSMUSG00000030792	Dkkl1	AI414495|SGY|SGY-1|SGY1|Soggy|mSgy	dickkopf-like 1	protein-coding
mm_164872.1	chr18	57468697	57468716	+	1	NA	5' UTR (NM_001134697, exon 1 of 2)	5' UTR (NM_001134697, exon 1 of 2)	220	NM_001134697	629147	Mm.57415	NM_001134697	ENSMUSG00000069372	Ctxn3	ENSMUSG00000069372	cortexin 3	protein-coding
mm_117744.1	chr13	95891715	95891733	-	1	NA	5' UTR (NM_027711, exon 1 of 36)	5' UTR (NM_027711, exon 1 of 36)	198	NM_027711	544963	Mm.38878	NM_027711	ENSMUSG00000021676	Iqgap2	4933417J23Rik|A630053O10|AI788777	IQ motif containing GTPase activating protein 2	protein-coding
mm_159608.1	chr4	131921738	131921738	+	1	NA	promoter-TSS (NM_001201367)	promoter-TSS (NM_001201367)	-33	NM_001201367	623230	Mm.421179	NM_001201367	ENSMUSG00000070720	Tmem200b	EG623230	transmembrane protein 200B	protein-coding
mm_55198.1	chr6	52204252	52204262	-	1	NA	exon (NM_010453, exon 1 of 2)	exon (NM_010453, exon 1 of 2)	330	NM_010453	15402	Mm.173	NM_010453	ENSMUSG00000038253	Hoxa5	Hox-1.3	homeobox A5	protein-coding
mm_160984.1	chr11	103774384	103774384	+	1	NA	intron (NM_009521, intron 1 of 4)	CpG	209	NM_009521	22415	Mm.159091	NM_009521	ENSMUSG00000000125	Wnt3	Int-4|Wnt-3	wingless-type MMTV integration site family, member 3	protein-coding
mm_141058.1	chr17	25754226	25754240	-	1	NA	promoter-TSS (NM_018857)	promoter-TSS (NM_018857)	94	NM_018857	56047	Mm.17510	NM_018857	ENSMUSG00000063011	Msln	MPF	mesothelin	protein-coding
mm_85721.1	chr9	108305942	108305958	-	1	NA	promoter-TSS (NM_016802)	promoter-TSS (NM_016802)	209	NM_133986	102791	Mm.24670	NM_133986	ENSMUSG00000039461	Tcta	9130410M22Rik|AW553637|C85065|Tctal	T cell leukemia translocation altered gene	protein-coding
mm_120010.1	chr14	55672309	55672315	+	1	NA	promoter-TSS (NM_177992)	promoter-TSS (NM_177992)	77	NM_177992	105446	Mm.390685	NM_177992	ENSMUSG00000002326	Gmpr2	1810008P16Rik|5730544D12Rik|AA959850|GMPR 2	guanosine monophosphate reductase 2	protein-coding
mm_122420.1	chr14	41185206	41185212	-	1	NA	promoter-TSS (NM_009160)	promoter-TSS (NM_009160)	-11	NM_009160	20390	Mm.1321	NM_009160	ENSMUSG00000021795	Sftpd	AI573415|SP-D|Sfpd|Sftp4	surfactant associated protein D	protein-coding
mm_81297.1	chr9	108339074	108339098	+	1	NA	promoter-TSS (NM_008160)	promoter-TSS (NM_008160)	6	NM_001329528	14775	Mm.1090	NM_008160	ENSMUSG00000063856	Gpx1	AI195024|AL033363|CGPx|GPx-1|GSHPx-1|Gpx	glutathione peroxidase 1	protein-coding
mm_40657.1	chr5	65135215	65135225	+	1	NA	intron (NM_175174, intron 1 of 10)	B3|SINE|B2	3989	NM_175174	71778	Mm.10281	NM_175174	ENSMUSG00000054920	Klhl5	1300013C10Rik	kelch-like 5	protein-coding
mm_39813.1	chr5	30674159	30674173	+	1	NA	non-coding (NR_126074, exon 5 of 5)	non-coding (NR_126074, exon 5 of 5)	7280	NR_126074	12615	Mm.290563	NM_007681	ENSMUSG00000029177	Cenpa	Cenp-A	centromere protein A	protein-coding
mm_122506.1	chr14	46831985	46832057	-	1	NA	promoter-TSS (NM_026832)	promoter-TSS (NM_026832)	-223	NM_026832	68755	Mm.343809	NM_026832	ENSMUSG00000055128	Cgrrf1	1110038G02Rik|1810009H17Rik|CGR19	cell growth regulator with ring finger domain 1	protein-coding
mm_75881.1	chr8	70776721	70776731	-	1	NA	promoter-TSS (NR_029440)	promoter-TSS (NR_029440)	-14	NM_008841	18709	Mm.12945	NM_008841	ENSMUSG00000031834	Pik3r2	p85beta	phosphatidylinositol 3-kinase, regulatory subunit, polypeptide 2 (p85 beta)	protein-coding
mm_90564.1	chr10	128225944	128225961	+	1	NA	exon (NM_008600, exon 1 of 4)	exon (NM_008600, exon 1 of 4)	142	NM_008600	17339	Mm.31625	NM_008600	ENSMUSG00000025389	Mip	Aqp0|Cat|Cts|Hfi|Lop|MIP26|MP26|Svl|shrivelled	major intrinsic protein of lens fiber	protein-coding
mm_85380.1	chr9	103226076	103226098	-	1	NA	exon (NM_133977, exon 4 of 17)	exon (NM_133977, exon 4 of 17)	4199	NM_133977	22041	Mm.37214	NM_133977	ENSMUSG00000032554	Trf	AI266983|Cd176|HP|Tf|Tfn|hpx	transferrin	protein-coding
mm_19576.1	chr2	101643913	101643919	-	1	NA	exon (NM_009019, exon 2 of 2)	exon (NM_009019, exon 2 of 2)	5616	NM_009019	19373	Mm.828	NM_009019	ENSMUSG00000061311	Rag1	Rag-1	recombination activating gene 1	protein-coding
mm_47533.1	chr5	124204220	124204253	-	1	NA	intron (NM_011256, intron 2 of 24)	intron (NM_011256, intron 2 of 24)	-17054	NM_001289472	19679	Mm.44261	NM_011256	ENSMUSG00000029406	Pitpnm2	NIR3|RDGBA2|Rdgb2|mKIAA1457	phosphatidylinositol transfer protein, membrane-associated 2	protein-coding
mm_115864.1	chr13	21453670	21453700	-	1	NA	promoter-TSS (NM_001347491)	promoter-TSS (NM_001347491)	42	NM_001013786	432731	Mm.390557	NM_001013786	ENSMUSG00000022228	Zscan26	BC068174|Zfp187|Znf187	zinc finger and SCAN domain containing 26	protein-coding
mm_100344.1	chr11	118402048	118402063	+	1	NA	promoter-TSS (NM_011150)	promoter-TSS (NM_011150)	-124	NM_011150	19039	Mm.3152	NM_011150	ENSMUSG00000033880	Lgals3bp	90K|CyCAP|MAC-2BP|Ppicap|Tango10b	lectin, galactoside-binding, soluble, 3 binding protein	protein-coding
mm_47481.1	chr5	123749394	123749418	-	1	NA	promoter-TSS (NM_001042421)	promoter-TSS (NM_001042421)	8	NM_001005525	208606	Mm.276341	NM_025438	ENSMUSG00000029422	Rsrc2	1500011J06Rik	arginine/serine-rich coiled-coil 2	protein-coding
mm_77225.1	chr8	115703546	115703564	-	1	NA	3' UTR (NM_001025577, exon 1 of 1)	3' UTR (NM_001025577, exon 1 of 1)	3339	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_71670.1	chr8	60674501	60674513	+	1	NA	3' UTR (NM_001177882, exon 3 of 3)	3' UTR (NM_001177882, exon 3 of 3)	18950	NM_001177882	71306	Mm.23242	NM_027756	ENSMUSG00000031647	Mfap3l	4933428A15Rik|5430405D20Rik|AI461995|AW125052|NYD-sp9|mKIAA0626	microfibrillar-associated protein 3-like	protein-coding
mm_101145.1	chr11	16508488	16508507	-	1	NA	promoter-TSS (NM_011343)	promoter-TSS (NM_011343)	-13	NM_001109971	20335	Mm.325350	NM_011343	ENSMUSG00000078974	Sec61g	-	SEC61, gamma subunit	protein-coding
mm_49265.1	chr6	17464172	17464174	+	1	NA	5' UTR (NM_008591, exon 1 of 22)	5' UTR (NM_008591, exon 1 of 22)	216	NM_008591	17295	Mm.86844	NM_008591	ENSMUSG00000009376	Met	AI838057|HGF|HGFR|Par4|c-Met	met proto-oncogene	protein-coding
mm_83668.1	chr9	49716059	49716079	-	1	NA	intron (NM_001081445, intron 1 of 17)	intron (NM_001081445, intron 1 of 17)	83000	NM_001081445	17967	Mm.4974	NM_010875	ENSMUSG00000039542	Ncam1	CD56|E-NCAM|NCAM-1|Ncam	neural cell adhesion molecule 1	protein-coding
mm_70692.1	chr8	15027168	15027176	+	1	NA	5' UTR (NM_029116, exon 2 of 2)	5' UTR (NM_029116, exon 2 of 2)	16147	NM_029116	74901	Mm.46675	NM_029116	ENSMUSG00000055675	Kbtbd11	2900016B01Rik|4930465M17Rik|mKIAA0711	kelch repeat and BTB (POZ) domain containing 11	protein-coding
mm_2499.1	chr1	106171774	106171879	+	1	NA	promoter-TSS (NM_133821)	promoter-TSS (NM_133821)	-43	NM_133821	98432	Mm.24115	NM_133821	ENSMUSG00000044340	Phlpp1	AI836256|Phlpp|Plekhe1|SCOP|mKIAA0606	PH domain and leucine rich repeat protein phosphatase 1	protein-coding
mm_107024.1	chr12	12909413	12909431	+	1	NA	Intergenic	Intergenic	32414	NM_008709	18109	Mm.16469	NM_008709	ENSMUSG00000037169	Mycn	N-myc|Nmyc|Nmyc-1|Nmyc1|bHLHe37|c-nmyc	v-myc avian myelocytomatosis viral related oncogene, neuroblastoma derived	protein-coding
mm_64111.1	chr7	141061316	141061330	+	1	NA	promoter-TSS (NM_177897)	promoter-TSS (NM_177897)	49	NM_177897	330671	Mm.133741	NM_177897	ENSMUSG00000055629	B4galnt4	BC038881|Gm1095|beta4GalNAcT4	beta-1,4-N-acetyl-galactosaminyl transferase 4	protein-coding
mm_15233.1	chr2	154603964	154603968	+	1	NA	promoter-TSS (NM_021534)	promoter-TSS (NM_021534)	-293	NM_021534	59038	Mm.24673	NM_021534	ENSMUSG00000000876	Pxmp4	3010018P03Rik|Pmp24	peroxisomal membrane protein 4	protein-coding
mm_610.1	chr1	39986625	39986633	+	1	NA	exon (NM_001252202, exon 10 of 30)	exon (NM_001252202, exon 10 of 30)	85716	NM_008696	26921	Mm.491139	NM_008696	ENSMUSG00000026074	Map4k4	9430080K19Rik|AU043147|AU045934|AW046177|HGK|Nik	mitogen-activated protein kinase kinase kinase kinase 4	protein-coding
mm_72185.1	chr8	72351502	72351505	+	1	NA	intron (NM_007944, intron 22 of 23)	PB1D7|SINE|Alu	32441	NM_008452	16598	Mm.26938	NM_008452	ENSMUSG00000055148	Klf2	Lklf	Kruppel-like factor 2 (lung)	protein-coding
mm_120464.1	chr14	65971114	65971153	+	1	NA	intron (NM_013492, intron 1 of 8)	intron (NM_013492, intron 1 of 8)	2650	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_8665.1	chr1	156655728	156655765	-	1	NA	exon (NM_023141, exon 6 of 6)	exon (NM_023141, exon 6 of 6)	18593	NM_023141	30935	Mm.206737	NM_023141	ENSMUSG00000060519	Tor3a	Adir	torsin family 3, member A	protein-coding
mm_93278.1	chr10	96077742	96077747	-	1	NA	Intergenic	Intergenic	137081	NM_001001932	216238	Mm.210035	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding
mm_78321.1	chr9	24542072	24542097	+	1	NA	Intergenic	SYNREP_MM|Satellite|Satellite	-38944	NM_172920	244745	Mm.38526	NM_172920	ENSMUSG00000043067	Dpy19l1	1100001I19Rik|6030402K12|AI225861|AW558481	dpy-19-like 1 (C. elegans)	protein-coding
mm_22745.1	chr3	19957171	19957179	+	1	NA	5' UTR (NM_007752, exon 1 of 19)	5' UTR (NM_007752, exon 1 of 19)	121	NM_007752	12870	Mm.13787	NM_007752	ENSMUSG00000003617	Cp	D3Ertd555e	ceruloplasmin	protein-coding
mm_80758.1	chr9	95557240	95557252	+	1	NA	Intergenic	Intergenic	-2571	NM_198414	75552	Mm.151485	NM_198414	ENSMUSG00000064225	Paqr9	1700020G04Rik	progestin and adipoQ receptor family member IX	protein-coding
mm_56080.1	chr6	87255852	87255889	-	1	NA	exon (NM_054041, exon 10 of 18)	exon (NM_054041, exon 10 of 18)	79905	NM_054041	69538	Mm.232525	NM_054041	ENSMUSG00000033420	Antxr1	2310008J16Rik|2810405N18Rik|Antrx1|Tem8	anthrax toxin receptor 1	protein-coding
mm_93732.1	chr10	120092697	120092744	-	1	NA	intron (NM_080446, intron 9 of 12)	intron (NM_080446, intron 9 of 12)	20245	NM_080446	117599	Mm.214703	NM_080446	ENSMUSG00000020228	Helb	AI447783|D10Ertd664e	helicase (DNA) B	protein-coding
mm_139082.1	chr17	46682036	46682040	+	1	NA	TTS (NM_009358)	TTS (NM_009358)	858	NM_001277312	17256	Mm.329083	NM_010787	ENSMUSG00000002768	Mea1	Mea-1	male enhanced antigen 1	protein-coding
mm_27898.1	chr3	79458372	79458406	-	1	NA	3' UTR (NM_001162999, exon 17 of 17)	3' UTR (NM_001162999, exon 17 of 17)	109290	NM_001162999	329679	Mm.244005	NM_001162999	ENSMUSG00000061175	Fnip2	D630023B12Rik|mKIAA1450	folliculin interacting protein 2	protein-coding
mm_147490.1	chr18	47368482	47368486	-	1	NA	5' UTR (NM_018744, exon 1 of 19)	5' UTR (NM_018744, exon 1 of 19)	384	NM_018744	20358	Mm.40909	NM_018744	ENSMUSG00000019647	Sema6a	A730020P05Rik|AI851735|Sema6A-1|Semaq|VIa	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A	protein-coding
mm_139438.1	chr17	53769830	53769848	+	1	NA	Intergenic	Intergenic	53330	NR_073205	211496	Mm.251553	NM_177599	ENSMUSG00000062036	4932415M13Rik	-	RIKEN cDNA 4932415M13 gene	ncRNA
mm_56752.1	chr6	115994940	115994945	-	1	NA	promoter-TSS (NM_026376)	promoter-TSS (NM_026376)	63	NM_026376	67784	Mm.3085	NM_026376	ENSMUSG00000030123	Plxnd1	6230425C21Rik|b2b1863Clo|b2b553Clo	plexin D1	protein-coding
mm_2003.1	chr1	87127058	87127063	+	1	NA	exon (NM_007432, exon 9 of 11)	exon (NM_007432, exon 9 of 11)	2052	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_87655.1	chr10	58476323	58476337	+	1	NA	exon (NM_011240, exon 20 of 29)	exon (NM_011240, exon 20 of 29)	-21607	NM_001162956	76138	Mm.211744	NM_001162956	ENSMUSG00000038010	Ccdc138	6230424H07Rik|BC042726	coiled-coil domain containing 138	protein-coding
mm_48745.1	chr5	147875607	147875651	-	1	NA	3' UTR (NM_025624, exon 6 of 6)	3' UTR (NM_025624, exon 6 of 6)	15001	NM_025624	66537	Mm.332855	NM_025624	ENSMUSG00000029649	Pomp	2510048O06Rik|Ump1	proteasome maturation protein	protein-coding
mm_36895.1	chr4	107680904	107680942	-	1	NA	intron (NM_019872, intron 1 of 3)	intron (NM_019872, intron 1 of 3)	3239	NM_019872	56296	Mm.141324	NM_019872	ENSMUSG00000028610	Dmrtb1	Dmrt6|Prp13	DMRT-like family B with proline-rich C-terminal, 1	protein-coding
mm_155468.1	chrX	73639399	73639410	+	1	NA	promoter-TSS (NM_029352)	promoter-TSS (NM_029352)	-37	NM_029352	75590	Mm.16479	NM_029352	ENSMUSG00000031383	Dusp9	Dusp4|Mpk4|Pyst3	dual specificity phosphatase 9	protein-coding
mm_91077.1	chr10	19011813	19011823	-	1	NA	exon (NM_001166402, exon 1 of 8)	exon (NM_001166402, exon 1 of 8)	145	NM_001166402	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_60468.1	chr7	44478049	44478051	+	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	-6467	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_18184.1	chr2	45111709	45111721	-	1	NA	promoter-TSS (NR_110571)	promoter-TSS (NR_110571)	-545	NR_110571	433424	Mm.441408	NR_110571	ENSMUSG00000052248	Zeb2os	Gm13476|OTTMUSG00000012358|Zeb2nat	zinc finger E-box binding homeobox 2, opposite strand	ncRNA
mm_155056.1	chrX	42360692	42360763	+	1	NA	Intergenic	Intergenic	-141838	NM_011364	20400	Mm.441197	NM_011364	ENSMUSG00000005696	Sh2d1a	Gm686|SAP	SH2 domain containing 1A	protein-coding
mm_116019.1	chr13	24831338	24831348	-	1	NA	promoter-TSS (NM_019551)	promoter-TSS (NM_019551)	146	NM_025790	66834	Mm.2125	NM_025790	ENSMUSG00000006717	Acot13	0610006O17Rik|Them2	acyl-CoA thioesterase 13	protein-coding
mm_26082.1	chr3	136670868	136670874	+	1	NA	exon (NM_001293622, exon 1 of 13)	exon (NM_001293622, exon 1 of 13)	805	NM_001293622	19055	Mm.331389	NM_008913	ENSMUSG00000028161	Ppp3ca	2900074D19Rik|CN|Caln|Calna|CnA	protein phosphatase 3, catalytic subunit, alpha isoform	protein-coding
mm_34295.1	chr4	141614585	141614593	+	1	NA	exon (NM_145987, exon 6 of 6)	exon (NM_145987, exon 6 of 6)	219	NR_033566	100165	Mm.439819	NR_033566	ENSMUSG00000073731	AI507597	-	expressed sequence AI507597	ncRNA
mm_27031.1	chr3	26153958	26153994	-	1	NA	promoter-TSS (NM_001163387)	promoter-TSS (NM_001163387)	-669	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_154884.1	chrX	20703923	20703951	+	1	NA	promoter-TSS (NM_145628)	promoter-TSS (NM_145628)	28	NM_145628	236733	Mm.34489	NM_145628	ENSMUSG00000031066	Usp11	6230415D12Rik|mKIAA4085	ubiquitin specific peptidase 11	protein-coding
mm_137172.1	chr17	23815197	23815238	+	1	NA	exon (NM_175229, exon 10 of 14)	exon (NM_175229, exon 10 of 14)	12030	NM_175229	75956	Mm.5222	NM_175229	ENSMUSG00000039218	Srrm2	5033413A03Rik|AA410130|SRm300|mKIAA0324	serine/arginine repetitive matrix 2	protein-coding
mm_3276.1	chr1	136570639	136570649	+	1	NA	Intergenic	Intergenic	-54257	NM_177643	226442	Mm.62521	NM_177643	ENSMUSG00000041483	Zfp281	Znf281	zinc finger protein 281	protein-coding
mm_173146.1	chrX	22534467	22534480	-	1	NA	Intergenic	Lx3C|LINE|L1	72877	NR_033731	76705	Mm.399727	NM_029707		Ppp1r2-ps7	1700023I07Rik	protein phosphatase 1, regulatory (inhibitor) subunit 2, pseudogene 7	pseudo
mm_19182.1	chr2	84393353	84393354	-	1	NA	intron (NM_018782, intron 2 of 15)	intron (NM_018782, intron 2 of 15)	31913	NM_018782	54598	Mm.75467	NM_018782	ENSMUSG00000059588	Calcrl	AV071593|CRLR	calcitonin receptor-like	protein-coding
mm_26630.1	chr3	152912346	152912403	+	1	NA	intron (NM_012028, intron 2 of 4)	intron (NM_012028, intron 2 of 4)	69833	NM_012028	26938	Mm.40915	NM_012028	ENSMUSG00000039037	St6galnac5	AI851940|Siat7e	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 5	protein-coding
mm_114424.1	chr13	64432480	64432557	+	1	NA	promoter-TSS (NM_053180)	promoter-TSS (NM_053180)	-35	NM_053180	105278	Mm.74982	NM_053180	ENSMUSG00000021483	Cdk20	4932702G04Rik|AU019450|AW558027|CDCH|Ccrk|PNQLARE|p42	cyclin-dependent kinase 20	protein-coding
mm_155778.1	chrX	96455497	96455497	+	1	NA	promoter-TSS (NM_010417)	promoter-TSS (NM_010417)	61	NM_010417	15203	Mm.277092	NM_010417	ENSMUSG00000031209	Heph	C130006F04Rik|Cpl|mKIAA0698|sla	hephaestin	protein-coding
mm_77381.1	chr8	119840581	119840584	-	1	NA	promoter-TSS (NM_028071)	promoter-TSS (NM_028071)	-3	NM_028071	72042	Mm.393405	NM_028071	ENSMUSG00000031827	Cotl1	1810074P22Rik|2010004C08Rik|Clp	coactosin-like 1 (Dictyostelium)	protein-coding
mm_88432.1	chr10	77530343	77530412	+	1	NA	promoter-TSS (NM_008404)	promoter-TSS (NM_008404)	29	NM_008404	16414	Mm.1137	NM_008404	ENSMUSG00000000290	Itgb2	2E6|AI528527|Cd18|LAD|LCAMB|Lfa1|MF17	integrin beta 2	protein-coding
mm_4975.1	chr1	191325986	191325998	+	1	NA	promoter-TSS (NM_025864)	promoter-TSS (NM_025864)	27	NM_025864	66950	Mm.236300	NM_025864	ENSMUSG00000026627	Tmem206	2310028N02Rik|AI118576	transmembrane protein 206	protein-coding
mm_98496.1	chr11	94951714	94951720	+	1	NA	3' UTR (NM_007742, exon 51 of 51)	3' UTR (NM_007742, exon 51 of 51)	15493	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_16796.1	chr2	10098006	10098023	-	1	NA	exon (NM_010582, exon 18 of 21)	exon (NM_010582, exon 18 of 21)	17402	NM_025280	16588	Mm.35498	NM_025280	ENSMUSG00000037262	Kin	Kin17	Kin17 DNA and RNA binding protein	protein-coding
mm_65330.1	chr7	24978316	24978342	-	1	NA	3' UTR (NM_001290469, exon 23 of 23)	3' UTR (NM_001290469, exon 23 of 23)	-5601	NM_010261	14470	Mm.22473	NM_010261	ENSMUSG00000003380	Rabac1	2310040I06Rik|Gbpap1|PRA1|prenylin	Rab acceptor 1 (prenylated)	protein-coding
mm_26540.1	chr3	146149830	146149843	+	1	NA	promoter-TSS (NM_026656)	promoter-TSS (NM_026656)	3	NM_026656	68279	Mm.116862	NM_026656	ENSMUSG00000011008	Mcoln2	3300002C04Rik|AI549968|C86638|TRPML2	mucolipin 2	protein-coding
mm_45440.1	chr5	67394356	67394359	-	1	NA	3' UTR (NM_001164806, exon 5 of 5)	3' UTR (NM_001164806, exon 5 of 5)	33442	NM_001164806	666938	Mm.101339	NM_001164806	ENSMUSG00000092060	Bend4	D330027G24Rik|EG666938	BEN domain containing 4	protein-coding
mm_34012.1	chr4	137993479	137993504	+	1	NA	promoter-TSS (NM_001256198)	promoter-TSS (NM_001256198)	35	NM_172703	230861	Mm.268903	NM_172703	ENSMUSG00000028760	Eif4g3	1500002J22Rik|4930523M17Rik|G1-419-52|eIF4GII|repro8	eukaryotic translation initiation factor 4 gamma, 3	protein-coding
mm_1241.1	chr1	62796290	62796294	+	1	NA	3' UTR (NM_001077407, exon 16 of 16)	3' UTR (NM_001077407, exon 16 of 16)	-1560	NR_040601	74992	Mm.401979	NR_040601		4930487H11Rik	-	RIKEN cDNA 4930487H11 gene	ncRNA
mm_156388.1	chrX	139800731	139800741	+	1	NA	promoter-TSS (NM_016675)	promoter-TSS (NM_016675)	-72	NM_016675	12738	Mm.117068	NM_016675	ENSMUSG00000047230	Cldn2	AL022813	claudin 2	protein-coding
mm_155069.1	chrX	43590927	43590933	+	1	NA	promoter-TSS (NM_001195271)	promoter-TSS (NM_001195271)	-59	NM_001195271	637093	Mm.368463	NM_001195271	ENSMUSG00000078320	Tex13c1	Gm362|Tex13c	TEX13 family member C1	protein-coding
mm_46907.1	chr5	114274246	114274269	-	1	NA	promoter-TSS (NM_148935)	promoter-TSS (NM_148935)	-496	NM_148935	116810	Mm.17709	NM_148935	ENSMUSG00000042002	Foxn4	-	forkhead box N4	protein-coding
mm_54620.1	chr6	38533641	38533669	-	1	NA	Intergenic	Intergenic	-1206	NM_025363	66117	Mm.158971	NM_025363	ENSMUSG00000019689	Fmc1	1110001J03Rik	formation of mitochondrial complex V assembly factor 1	protein-coding
mm_105104.1	chr11	100957983	100957993	-	1	NA	3' UTR (NM_008986, exon 2 of 2)	3' UTR (NM_008986, exon 2 of 2)	12629	NM_008986	19285	Mm.21864	NM_008986	ENSMUSG00000004044	Ptrf	2310075E07Rik|AW546441|Cav-p60|Cavin	polymerase I and transcript release factor	protein-coding
mm_156401.1	chrX	139809107	139809124	+	1	NA	exon (NM_016675, exon 2 of 2)	exon (NM_016675, exon 2 of 2)	8307	NM_016675	12738	Mm.117068	NM_016675	ENSMUSG00000047230	Cldn2	AL022813	claudin 2	protein-coding
mm_140705.1	chr17	14690148	14690162	-	1	NA	exon (NM_011581, exon 3 of 22)	exon (NM_011581, exon 3 of 22)	4107	NM_011581	21826	Mm.26688	NM_011581	ENSMUSG00000023885	Thbs2	TSP2|Thbs-2	thrombospondin 2	protein-coding
mm_69323.1	chr7	128499832	128499834	-	1	NA	Intergenic	B1_Mur1|SINE|Alu	-23750	NM_013863	29810	Mm.84073	NM_013863	ENSMUSG00000030847	Bag3	AA407278|Bis|mg638	BCL2-associated athanogene 3	protein-coding
mm_39402.1	chr5	14144447	14144450	+	1	NA	intron (NM_011348, intron 2 of 16)	intron (NM_011348, intron 2 of 16)	119172	NM_011348	20349	Mm.134093	NM_011348	ENSMUSG00000063531	Sema3e	6430702L12|AA408817|Semah|mKIAA0331	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	protein-coding
mm_20447.1	chr2	129364743	129364778	-	1	NA	3' UTR (NM_008361, exon 7 of 7)	3' UTR (NM_008361, exon 7 of 7)	-5142	NR_015474	329514	Mm.207315	NM_177848	ENSMUSG00000074805	Il1bos	9430083I22|Gm14047|OTTMUSG00000015529	interleukin 1 beta, opposite strand	ncRNA
mm_121257.1	chr14	103059337	103059344	+	1	NA	Intergenic	Intergenic	-10876	NM_001033242	211286	Mm.295289	NM_001033242	ENSMUSG00000022125	Cln5	A730075N08Rik	ceroid-lipofuscinosis, neuronal 5	protein-coding
mm_53594.1	chr6	138140299	138140320	+	1	NA	promoter-TSS (NM_019946)	promoter-TSS (NM_019946)	-228	NM_019946	56615	Mm.14796	NM_019946	ENSMUSG00000008540	Mgst1	1500002K10Rik|Gst	microsomal glutathione S-transferase 1	protein-coding
mm_127370.1	chr15	100761850	100761864	+	1	NA	5' UTR (NM_021530, exon 1 of 25)	5' UTR (NM_021530, exon 1 of 25)	110	NM_021530	59033	Mm.209856	NM_021530	ENSMUSG00000023032	Slc4a8	AW493845|C230026C11|NDCBE|kNBC-3	solute carrier family 4 (anion exchanger), member 8	protein-coding
mm_161328.1	chr14	50320616	50320616	-	1	NA	exon (NM_146664, exon 1 of 1)	exon (NM_146664, exon 1 of 1)	217	NM_146664	258658	Mm.377621	NM_146664	ENSMUSG00000045306	Olfr734	MOR242-1	olfactory receptor 734	protein-coding
mm_148542.1	chr19	4621136	4621148	+	1	NA	exon (NM_001162946, exon 21 of 21)	exon (NM_001162946, exon 21 of 21)	2813	NR_105952	102466780		NR_105952	ENSMUSG00000098346	Mir6986	Gm27709|mmu-mir-6986	microRNA 6986	ncRNA
mm_31418.1	chr4	48051278	48051297	+	1	NA	promoter-TSS (NM_001307989)	promoter-TSS (NM_001307989)	41	NM_001307989	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_134101.1	chr16	9995045	9995088	-	1	NA	Intergenic	CpG	-2533	NM_008170	14811	Mm.2953	NM_008170	ENSMUSG00000059003	Grin2a	GluN2A|NMDAR2A|NR2A	glutamate receptor, ionotropic, NMDA2A (epsilon 1)	protein-coding
mm_57346.1	chr6	124754015	124754017	-	1	NA	intron (NM_007881, intron 1 of 9)	ID_B1|SINE|B4	2471	NM_007881	13498	Mm.333380	NM_007881	ENSMUSG00000004263	Atn1	Atr1|Drpla|atrophin-1	atrophin 1	protein-coding
mm_149694.1	chr19	21272517	21272542	+	1	NA	5' UTR (NM_009551, exon 1 of 6)	5' UTR (NM_009551, exon 1 of 6)	251	NM_009551	22682	Mm.292405	NM_009551	ENSMUSG00000024750	Zfand5	2310057A04Rik|5830475F03Rik|AA415485|Za20d2|Zfp216	zinc finger, AN1-type domain 5	protein-coding
mm_36123.1	chr4	58912679	58912776	-	1	NA	promoter-TSS (NM_172381)	promoter-TSS (NM_172381)	-2	NM_172381	230249	Mm.234801	NM_172381	ENSMUSG00000050812	AI314180	AW558785|BB181316|mKIAA0368	expressed sequence AI314180	protein-coding
mm_169046.1	chr1	3156050	3156054	+	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	515446	NM_001011874	497097	Mm.454496	NM_001011874	ENSMUSG00000051951	Xkr4	AY534250|Gm210|XRG4|mKIAA1889	X-linked Kx blood group related 4	protein-coding
mm_93316.1	chr10	98914156	98914168	-	1	NA	promoter-TSS (NM_026482)	promoter-TSS (NM_026482)	-990	NM_026482	67972	Mm.166944	NM_026482	ENSMUSG00000019943	Atp2b1	2810442I22Rik|E130111D10Rik|Pmca1	ATPase, Ca++ transporting, plasma membrane 1	protein-coding
mm_71902.1	chr8	70064828	70064835	+	1	NA	intron (NM_027481, intron 7 of 13)	(T)n|Simple_repeat|Simple_repeat	-8093	NM_001293795	107770	Mm.37974	NM_181540	ENSMUSG00000036151	Tm6sf2	-	transmembrane 6 superfamily member 2	protein-coding
mm_78836.1	chr9	44240733	44240743	+	1	NA	promoter-TSS (NM_001081369)	promoter-TSS (NM_001081369)	61	NM_001081369	270150	Mm.347681	NM_001081369	ENSMUSG00000070306	Ccdc153	-	coiled-coil domain containing 153	protein-coding
mm_82155.1	chr9	123780348	123780355	+	1	NA	exon (NM_001166625, exon 4 of 4)	exon (NM_001166625, exon 4 of 4)	13140	NM_001166625	12769	Mm.440604	NM_009913	ENSMUSG00000029530	Ccr9	A130091K22Rik|Cmkbr10|GPR-9-6	chemokine (C-C motif) receptor 9	protein-coding
mm_113379.1	chr13	33015925	33015937	+	1	NA	3' UTR (NM_009256, exon 7 of 7)	3' UTR (NM_009256, exon 7 of 7)	11390	NM_009256	20723	Mm.245041	NM_009256	ENSMUSG00000045827	Serpinb9	BB283241|CAP-3|CAP3|PI-9|PI9|Spi6|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 9	protein-coding
mm_100074.1	chr11	115462374	115462380	+	1	NA	promoter-TSS (NM_001080934)	promoter-TSS (NM_001080934)	-96	NM_001080934	217316	Mm.25773	NM_001080934	ENSMUSG00000045775	Slc16a5	A130015N09Rik|MCT 5|MCT 6|MCT5	solute carrier family 16 (monocarboxylic acid transporters), member 5	protein-coding
mm_101519.1	chr11	32542721	32542767	-	1	NA	intron (NM_009288, intron 1 of 18)	intron (NM_009288, intron 1 of 18)	9478	NM_009288	20868	Mm.8235	NM_009288	ENSMUSG00000020272	Stk10	Gek1|Lok|mKIAA4026	serine/threonine kinase 10	protein-coding
mm_172659.1	chr8	40883635	40883637	+	1	NA	intron (NM_007514, intron 1 of 11)	RLTR10|LTR|ERVK	21269	NM_001044740	11988	Mm.4676	NM_007514	ENSMUSG00000031596	Slc7a2	20.5|AI158848|Atrc2|CAT-2|Cat2|Tea	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	protein-coding
mm_64944.1	chr7	16314054	16314063	-	1	NA	intron (NM_133234, intron 3 of 3)	CpG	4475	NM_133234	170770	Mm.7660	NM_133234	ENSMUSG00000002083	Bbc3	PUMA|PUMA/JFY1	BCL2 binding component 3	protein-coding
mm_114394.1	chr13	63274400	63274402	+	1	NA	intron (NR_110520, intron 2 of 5)	intron (NR_110520, intron 2 of 5)	22746	NR_045794	100504114	Mm.437070	NR_045794	ENSMUSG00000097242	Gm16907	-	predicted gene, 16907	ncRNA
mm_9975.1	chr1	191217933	191217959	-	1	NA	Intergenic	Intergenic	-34613	NM_007498	11910	Mm.2706	NM_007498	ENSMUSG00000026628	Atf3	LRG-21	activating transcription factor 3	protein-coding
mm_162083.1	chrX	33702358	33702358	-	1	NA	promoter-TSS (NM_001145038).2	promoter-TSS (NM_001145038).2	-9	NM_001145038	100040732	Mm.465135	NM_001145038	ENSMUSG00000078324	Btbd35f14	Gm2933	BTB domain containing 35, family member 14	protein-coding
mm_39935.1	chr5	31698732	31698752	+	1	NA	intron (NM_181280, intron 1 of 12)	intron (NM_181280, intron 1 of 12)	692	NM_144541	107976	Mm.482126	NM_144541	ENSMUSG00000052139	Bre	6030405P19Rik|AI429776|B830038C02Rik	brain and reproductive organ-expressed protein	protein-coding
mm_126707.1	chr15	85231479	85231496	+	1	NA	exon (NM_010180, exon 7 of 17)	exon (NM_010180, exon 7 of 17)	25479	NM_010180	14114	Mm.297992	NM_010180	ENSMUSG00000006369	Fbln1	-	fibulin 1	protein-coding
mm_112282.1	chr12	114392232	114392247	-	1	NA	Intergenic	Intergenic	77227	NR_106062	102465663		NR_106062	ENSMUSG00000105438	Mir7094-1	mmu-mir-7094-1	microRNA 7094-1	ncRNA
mm_106981.1	chr12	9580799	9580810	+	1	NA	3' UTR (NM_011859, exon 3 of 3)	3' UTR (NM_011859, exon 3 of 3)	6362	NM_011859	23967	Mm.45055	NM_011859	ENSMUSG00000048387	Osr1	Odd1|Osr	odd-skipped related 1 (Drosophila)	protein-coding
mm_109731.1	chr12	116485715	116485784	+	1	NA	promoter-TSS (NM_011215)	promoter-TSS (NM_011215)	29	NM_011215	19276	Mm.206054	NM_011215	ENSMUSG00000056553	Ptprn2	4930425H11Rik|IA2beta|PTP-NP|Phol|mKIAA0387|phogrin	protein tyrosine phosphatase, receptor type, N polypeptide 2	protein-coding
mm_104439.1	chr11	94976178	94976179	-	1	NA	5' UTR (NM_009161, exon 1 of 11)	5' UTR (NM_009161, exon 1 of 11)	149	NM_009161	20391	Mm.18709	NM_009161	ENSMUSG00000001508	Sgca	50DAG|Asg	sarcoglycan, alpha (dystrophin-associated glycoprotein)	protein-coding
mm_112200.1	chr12	113426692	113426701	-	1	NA	Intergenic	Intergenic	-62869	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_86312.1	chr9	122844015	122844027	-	1	NA	Intergenic	Intergenic	21985	NM_173364	235682	Mm.326477	NM_173364	ENSMUSG00000047036	Zfp445	AW610627|ZNF168|Znf445|mszf29|mszf50	zinc finger protein 445	protein-coding
mm_52380.1	chr6	113124331	113124347	+	1	NA	intron (NM_173005, intron 14 of 20)	B3A|SINE|B2	19404	NM_173005	72895	Mm.367159	NM_028385	ENSMUSG00000034269	Setd5	2900045N06Rik|C330007C20|C85544|mKIAA1757	SET domain containing 5	protein-coding
mm_96867.1	chr11	70166767	70166784	+	1	NA	5' UTR (NM_010796, exon 1 of 10)	5' UTR (NM_010796, exon 1 of 10)	152	NM_010796	17312	Mm.252405	NM_010796	ENSMUSG00000000318	Clec10a	CD301a|M-ASGP-BP-1|Mgl|Mgl1	C-type lectin domain family 10, member A	protein-coding
mm_45579.1	chr5	73651800	73651836	-	1	NA	intron (NM_178387, intron 1 of 12)	intron (NM_178387, intron 1 of 12)	438	NM_178387	73472	Mm.87067	NM_178387	ENSMUSG00000029155	Spata18	1700067I02Rik	spermatogenesis associated 18	protein-coding
mm_114277.1	chr13	58263977	58263989	+	1	NA	exon (NM_019832, exon 2 of 12)	exon (NM_019832, exon 2 of 12)	10205	NM_019832	56278	Mm.296625	NM_019832	ENSMUSG00000021552	Gkap1	42kDa|4933400B15Rik|D13Ertd340e|Gkap42	G kinase anchoring protein 1	protein-coding
mm_135260.1	chr16	37856427	37856429	-	1	NA	Intergenic	Intergenic	-11972	NM_177093	320184	Mm.390882	NM_177093	ENSMUSG00000034158	Lrrc58	1810012N18Rik|C330018J07Rik	leucine rich repeat containing 58	protein-coding
mm_162173.1	chrX	101420866	101420866	-	1	NA	promoter-TSS (NM_019831)	promoter-TSS (NM_019831)	-181	NM_001177987	56364	Mm.23458	NM_019831	ENSMUSG00000031310	Zmym3	9030216B10Rik|AW122925|DXS6673El|Zfp261	zinc finger, MYM-type 3	protein-coding
mm_166371.1	chr5	125532532	125532538	+	1	NA	5' UTR (NM_001190352, exon 1 of 9)	5' UTR (NM_001190352, exon 1 of 9)	117	NM_001190352	208151	Mm.40397	NM_001190352	ENSMUSG00000070498	Tmem132b	AK220418|mKIAA1786	transmembrane protein 132B	protein-coding
mm_136042.1	chr16	78357308	78357325	-	1	NA	intron (NM_009988, intron 7 of 7)	intron (NM_009988, intron 7 of 7)	19441	NR_002700	654432	Mm.458574	NR_002700	ENSMUSG00000044645	Gm7334	EG654432	B-cell translocation gene 3 pseudogene	pseudo
mm_106477.1	chr11	120139496	120139496	-	1	NA	intron (NM_024249, intron 4 of 16)	intron (NM_024249, intron 4 of 16)	11855	NM_001164799	72055	Mm.253403	NM_024249	ENSMUSG00000061306	Slc38a10	1810073N04Rik	solute carrier family 38, member 10	protein-coding
mm_125103.1	chr15	27770970	27770978	+	1	NA	intron (NM_001081302, intron 36 of 56)	intron (NM_001081302, intron 36 of 56)	-89432	NM_001242423	223433	Mm.266485	NM_198301	ENSMUSG00000056069	Fam105a	9830126M18	family with sequence similarity 105, member A	protein-coding
mm_25921.1	chr3	131159716	131159730	+	1	NA	intron (NM_001276403, intron 3 of 11)	intron (NM_001276403, intron 3 of 11)	46932	NM_001276403	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_52201.1	chr6	100704744	100704760	+	1	NA	promoter-TSS (NM_198612)	promoter-TSS (NM_198612)	18	NM_198612	232313	Mm.272037	NM_198612	ENSMUSG00000030074	Gxylt2	Glt8d4|Gm152	glucoside xylosyltransferase 2	protein-coding
mm_58321.1	chr6	146476002	146476044	-	1	NA	intron (NM_010586, intron 2 of 55)	MTD|LTR|ERVL-MaLR	26200	NM_010586	16439	Mm.7800	NM_010586	ENSMUSG00000030287	Itpr2	AI649341|InsP3R-2|InsP3R-5|Ip3r2|Itpr5|insP3R2	inositol 1,4,5-triphosphate receptor 2	protein-coding
mm_138005.1	chr17	33824563	33824598	+	1	NA	promoter-TSS (NM_023202)	promoter-TSS (NM_023202)	8	NR_103516	66416	Mm.29513	NM_023202	ENSMUSG00000041881	Ndufa7	14.5kDa|2400007M02Rik|CI-B14.5a	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 7 (B14.5a)	protein-coding
mm_132426.1	chr16	35612381	35612382	+	1	NA	intron (NM_013661, intron 1 of 21)	intron (NM_013661, intron 1 of 21)	71019	NM_013661	20357	Mm.42015	NM_013661	ENSMUSG00000052133	Sema5b	AI893641|SemG|Semag|mKIAA1445	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B	protein-coding
mm_11474.1	chr2	32381965	32382007	+	1	NA	promoter-TSS (NM_198001)	promoter-TSS (NM_198001)	-71	NM_198001	73737	Mm.27608	NM_198001	ENSMUSG00000039195	1110008P14Rik	C79326	RIKEN cDNA 1110008P14 gene	protein-coding
mm_149145.1	chr19	9005705	9005708	+	1	NA	exon (NM_009643, exon 5 of 5)	exon (NM_009643, exon 5 of 5)	-12198	NR_105786	102465190		NR_105786	ENSMUSG00000099308	Mir6367	Gm27467|mmu-mir-6367	microRNA 6367	ncRNA
mm_163262.1	chr11	113094298	113094310	+	1	NA	intron (NR_015556, intron 1 of 2)	intron (NR_015556, intron 1 of 2)	107534	NR_015556	72386	Mm.266961	NR_015556	ENSMUSG00000087259	2610035D17Rik	-	RIKEN cDNA 2610035D17 gene	ncRNA
mm_133106.1	chr16	65473721	65473736	+	1	NA	Intergenic	(CAG)n|Simple_repeat|Simple_repeat	-46901	NM_008849	18736	Mm.355440	NM_008849	ENSMUSG00000004842	Pou1f1	GHF-1|Hmp1|Pit-1|Pit1|Pit1-rs1|dw|dwarf	POU domain, class 1, transcription factor 1	protein-coding
mm_74680.1	chr8	14090281	14090304	-	1	NA	promoter-TSS (NM_001034862)	promoter-TSS (NM_001034862)	35	NM_001034862	234086	Mm.268896	NM_001034862	ENSMUSG00000051978	Erich1	-	glutamate rich 1	protein-coding
mm_12317.1	chr2	69380469	69380478	+	1	NA	promoter-TSS (NM_175512)	promoter-TSS (NM_175512)	11	NM_175512	241452	Mm.211655	NM_175512	ENSMUSG00000027068	Dhrs9	C730025I08Rik|Rdh15	dehydrogenase/reductase (SDR family) member 9	protein-coding
mm_83717.1	chr9	50756453	50756502	-	1	NA	exon (NM_001289784, exon 4 of 4)	exon (NM_001289784, exon 4 of 4)	3506	NM_009964	12955	Mm.178	NM_009964	ENSMUSG00000032060	Cryab	Crya-2|Crya2|HspB5|P23	crystallin, alpha B	protein-coding
mm_82753.1	chr9	26860624	26860639	-	1	NA	5' UTR (NM_001113323, exon 1 of 20)	5' UTR (NM_001113323, exon 1 of 20)	192	NM_001113323	70893	Mm.78118	NM_001113323	ENSMUSG00000031966	Glb1l3	4921509F24Rik	galactosidase, beta 1 like 3	protein-coding
mm_49114.1	chr6	8509445	8509449	+	1	NA	promoter-TSS (NR_040452)	promoter-TSS (NR_040452)	-153	NM_133236	170772	Mm.210787	NM_133236	ENSMUSG00000029638	Glcci1	2310047L21Rik|A130036A18Rik|Fam117c|Gig18|Tssn1	glucocorticoid induced transcript 1	protein-coding
mm_171794.1	chr5	117287564	117287569	-	1	NA	promoter-TSS (NM_018858)	promoter-TSS (NM_018858)	-2	NM_018858	23980	Mm.195898	NM_018858	ENSMUSG00000032959	Pebp1	HCNP|Pbp|Pbp1|Pbpr|Rkip	phosphatidylethanolamine binding protein 1	protein-coding
mm_47013.1	chr5	115484352	115484387	-	1	NA	promoter-TSS (NM_001167691)	promoter-TSS (NM_001167691)	-72	NM_001167691	75387	Mm.332616	NM_133760	ENSMUSG00000029524	Sirt4	4930596O17Rik	sirtuin 4	protein-coding
mm_138206.1	chr17	34301465	34301482	+	1	NA	Intergenic	Intergenic	-4394	NM_010382	14969	Mm.22564	NM_010382	ENSMUSG00000060586	H2-Eb1	Eb|H-2Eb|H2Eb|Ia-4|Ia4	histocompatibility 2, class II antigen E beta	protein-coding
mm_134537.1	chr16	19706294	19706297	-	1	NA	promoter-TSS (NM_177356)	promoter-TSS (NM_177356)	70	NM_177356	239739	Mm.258059	NM_177356	ENSMUSG00000041247	Lamp3	1200002D17Rik|Cd208|DC-LAMP|DCLAMP|LAMP|TSC403	lysosomal-associated membrane protein 3	protein-coding
mm_81074.1	chr9	106222599	106222629	+	1	NA	promoter-TSS (NM_031178)	promoter-TSS (NM_031178)	16	NM_031178	81897	Mm.44889	NM_031178	ENSMUSG00000045322	Tlr9	-	toll-like receptor 9	protein-coding
mm_29768.1	chr3	127226017	127226021	-	1	NA	intron (NM_001327938, intron 1 of 47)	intron (NM_001327938, intron 1 of 47)	64714	NR_105029	100862268	Mm.444603	NR_105029	ENSMUSG00000097456	LOC100862268	-	uncharacterized LOC100862268	ncRNA
mm_123276.1	chr14	61370758	61370772	-	1	NA	exon (NM_008466, exon 14 of 17)	exon (NM_008466, exon 14 of 17)	-10320	NM_026598	68177	Mm.22758	NM_026598	ENSMUSG00000021928	Ebpl	5730442K12Rik|EBRP	emopamil binding protein-like	protein-coding
mm_121825.1	chr14	20479908	20479914	-	1	NA	5' UTR (NM_001110794, exon 1 of 13)	5' UTR (NM_001110794, exon 1 of 13)	222	NM_001110794	11750	Mm.280231	NM_009674	ENSMUSG00000021814	Anxa7	AI265384|AI316497|Anx7|synexin	annexin A7	protein-coding
mm_12881.1	chr2	84678566	84678620	+	1	NA	promoter-TSS (NM_001290751)	promoter-TSS (NM_001290751)	191	NM_025885	381379	Mm.219643	NM_025885	ENSMUSG00000027080	Med19	2410018M14Rik|3110040A13Rik|LCMR1	mediator complex subunit 19	protein-coding
mm_22914.1	chr3	31094667	31094688	+	1	NA	promoter-TSS (NM_001039090)	promoter-TSS (NM_001039090)	-381	NM_011386	20482	Mm.15406	NM_011386	ENSMUSG00000027660	Skil	Skir|SnoN|sno	SKI-like	protein-coding
mm_131191.1	chr16	7224409	7224417	+	1	NA	exon (NM_183188, exon 2 of 13)	exon (NM_183188, exon 2 of 13)	154578	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_98678.1	chr11	96285228	96285230	+	1	NA	TTS (NM_010461)	TTS (NM_010461)	-1417	NM_010460	15415	Mm.390366	NM_010460	ENSMUSG00000038721	Hoxb7	AI325018|Hox-2.3	homeobox B7	protein-coding
mm_155158.1	chrX	52927023	52927034	+	1	NA	intron (NM_027642, intron 3 of 10)	intron (NM_027642, intron 3 of 10)	14814	NM_001290546	70998	Mm.26870	NM_027642	ENSMUSG00000025626	Phf6	2700007B13Rik|4931428F02Rik|mKIAA1823	PHD finger protein 6	protein-coding
mm_8268.1	chr1	139377095	139377110	-	1	NA	promoter-TSS (NM_133239)	promoter-TSS (NM_133239)	-26	NM_133239	170788	Mm.95700	NM_133239	ENSMUSG00000063681	Crb1	7530426H14Rik|A930008G09Rik	crumbs family member 1, photoreceptor morphogenesis associated	protein-coding
mm_69316.1	chr7	128461169	128461177	-	1	NA	5' UTR (NM_009383, exon 1 of 12)	5' UTR (NM_009383, exon 1 of 12)	340	NM_009383	21843	Mm.242072	NM_009383	ENSMUSG00000030846	Tial1	5330433G13Rik|AL033329|TIAR|mTIAR	Tia1 cytotoxic granule-associated RNA binding protein-like 1	protein-coding
mm_144480.1	chr18	23954707	23954717	+	1	NA	promoter-TSS (NM_027007)	promoter-TSS (NM_027007)	24	NM_027007	69256	Mm.218343	NM_027007	ENSMUSG00000024276	Zfp397	2810411K16Rik|6720480F11Rik|AI461664	zinc finger protein 397	protein-coding
mm_123523.1	chr14	66713635	66713647	-	1	NA	intron (NM_001271761, intron 2 of 2)	B4A|SINE|B4	78390	NM_001271760	11549	Mm.57064	NM_013461	ENSMUSG00000045875	Adra1a	Adra1c	adrenergic receptor, alpha 1a	protein-coding
mm_8412.1	chr1	152055271	152055313	-	1	NA	intron (NM_197990, intron 1 of 5)	ORR1F|LTR|ERVL-MaLR	35028	NM_197990	69399	Mm.278031	NM_197990	ENSMUSG00000032666	1700025G04Rik	2610510E02Rik|2900042O04Rik|ENSMUSG00000073540	RIKEN cDNA 1700025G04 gene	protein-coding
mm_141883.1	chr17	34860565	34860596	-	1	NA	exon (NM_008198, exon 5 of 18)	exon (NM_008198, exon 5 of 18)	1934	NM_001142706	14962	Mm.653	NM_008198	ENSMUSG00000090231	Cfb	AI195813|AI255840|B|Bf|C2|Fb|H2-Bf	complement factor B	protein-coding
mm_58955.1	chr7	18839955	18840006	+	1	NA	promoter-TSS (NM_153761)	promoter-TSS (NM_153761)	14	NM_153760	243864	Mm.233503	NM_153760	ENSMUSG00000040987	Mill2	Micb	MHC I like leukocyte 2	protein-coding
mm_151021.1	chr19	46846849	46846860	+	1	NA	intron (NM_033569, intron 1 of 7)	intron (NM_033569, intron 1 of 7)	85245	NM_001102471	94219	Mm.306903	NM_033569	ENSMUSG00000064105	Cnnm2	AU015877|AW048635|Acdp2|Clp2	cyclin M2	protein-coding
mm_144980.1	chr18	37955686	37955694	+	1	NA	promoter-TSS (NM_010411)	promoter-TSS (NM_010411)	131	NM_153793	225392	Mm.233516	NM_153793	ENSMUSG00000044024	Rell2	4631403P03Rik|ependolin	RELT-like 2	protein-coding
mm_101400.1	chr11	26593709	26593748	-	1	NA	5' UTR (NM_027260, exon 1 of 13)	5' UTR (NM_027260, exon 1 of 13)	192	NM_027260	69922	Mm.285351	NM_027260	ENSMUSG00000064090	Vrk2	2810003O05Rik|AI447698	vaccinia related kinase 2	protein-coding
mm_127853.1	chr15	7923594	7923595	-	1	NA	intron (NM_001081402, intron 11 of 17)	intron (NM_001081402, intron 11 of 17)	108044	NM_001301357	14573	Mm.4679	NM_010275	ENSMUSG00000022144	Gdnf	AI385739|ATF	glial cell line derived neurotrophic factor	protein-coding
mm_158249.1	chrX	107816239	107816337	-	1	NA	promoter-TSS (NM_025921)	promoter-TSS (NM_025921)	46	NM_025921	67028	Mm.37274	NM_025921	ENSMUSG00000031242	2610002M06Rik	8430408J07Rik|AI876413|Chmp1b2	RIKEN cDNA 2610002M06 gene	protein-coding
mm_48879.1	chr5	151127554	151127567	-	1	NA	intron (NM_146258, intron 1 of 13)	intron (NM_146258, intron 1 of 13)	62633	NM_001163493	243362	Mm.209272	NM_146258	ENSMUSG00000016128	Stard13	DLC2|GT650	StAR-related lipid transfer (START) domain containing 13	protein-coding
mm_121553.1	chr14	122477223	122477227	+	1	NA	intron (NM_009574, intron 1 of 2)	intron (NM_009574, intron 1 of 2)	1841	NM_009574	22772	Mm.308936	NM_009574	ENSMUSG00000061524	Zic2	HPE5|Ku	zinc finger protein of the cerebellum 2	protein-coding
mm_19675.1	chr2	103454450	103454466	-	1	NA	3' UTR (NM_009804, exon 13 of 13)	3' UTR (NM_009804, exon 13 of 13)	30390	NM_010125	13711	Mm.20888	NM_010125	ENSMUSG00000027186	Elf5	ESE-2|ESE-5|ESE-5.	E74-like factor 5	protein-coding
mm_3144.1	chr1	135144608	135144664	+	1	NA	3' UTR (NM_177081, exon 10 of 10)	3' UTR (NM_177081, exon 10 of 10)	-2198	NM_026823	68724	Mm.174998	NM_026823	ENSMUSG00000026426	Arl8a	1110033P22Rik|Arl10b|gie2	ADP-ribosylation factor-like 8A	protein-coding
mm_156899.1	chrX	167207485	167207514	+	1	NA	3' UTR (NM_021278, exon 3 of 3)	3' UTR (NM_021278, exon 3 of 3)	1719	NM_021278	19241	Mm.142729	NM_021278	ENSMUSG00000049775	Tmsb4x	Ptmb4|Tb4	thymosin, beta 4, X chromosome	protein-coding
mm_75229.1	chr8	39619234	39619243	-	1	NA	intron (NM_001113326, intron 5 of 9)	intron (NM_001113326, intron 5 of 9)	23440	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_52685.1	chr6	118054832	118054839	+	1	NA	intron (NM_001316749, intron 1 of 12)	intron (NM_001316749, intron 1 of 12)	-11550	NM_027526	70727	Mm.87660	NM_027526	ENSMUSG00000030134	Rasgef1a	6330404M18Rik|AI835194	RasGEF domain family, member 1A	protein-coding
mm_70614.1	chr8	13435174	13435186	+	1	NA	promoter-TSS (NM_001143672)	promoter-TSS (NM_001143672)	-279	NM_001143671	272465	Mm.250502	NM_001143671	ENSMUSG00000038457	Tmem255b	Fam70b|Gm687	transmembrane protein 255B	protein-coding
mm_103852.1	chr11	83126625	83126632	-	1	NA	Intergenic	Intergenic	9783	NM_011407	20555	Mm.10948	NM_011407	ENSMUSG00000078763	Slfn1	AV316259	schlafen 1	protein-coding
mm_10577.1	chr2	18086274	18086275	+	1	NA	intron (NR_045538, intron 3 of 22)	intron (NR_045538, intron 3 of 22)	21689	NM_001252561	17354	Mm.209175	NM_010804	ENSMUSG00000026743	Mllt10	Af10|B130021D15Rik|D630001B22Rik|mKIAA4140	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 10	protein-coding
mm_159238.1	chr2	146863660	146863660	+	1	NA	intron (NM_001033298, intron 2 of 13)	intron (NM_001033298, intron 2 of 13)	7771	NM_001033298	228730	Mm.292352	NM_001033298	ENSMUSG00000074749	Kiz	Gm114|Ncrna00153|Plk1s1	kizuna centrosomal protein	protein-coding
mm_55668.1	chr6	72521694	72521707	-	1	NA	Intergenic	Intergenic	-22691	NM_007599	12332	Mm.18626	NM_007599	ENSMUSG00000056737	Capg	gCap39|mbh1	capping protein (actin filament), gelsolin-like	protein-coding
mm_109987.1	chr12	14148598	14148601	-	1	NA	3' UTR (NM_029007, exon 2 of 2)	3' UTR (NM_029007, exon 2 of 2)	3439	NM_029007	105005	Mm.227253	NM_029007	ENSMUSG00000020607	Fam84a	2310003N02Rik|4731402F03Rik|AW125753|Nse1	family with sequence similarity 84, member A	protein-coding
mm_139320.1	chr17	48410207	48410262	+	1	NA	promoter-TSS (NM_010913)	promoter-TSS (NM_010913)	234	NM_207219	106821	Mm.203943	NM_207219	ENSMUSG00000040771	Oard1	AI314976|AW558560	O-acyl-ADP-ribose deacylase 1	protein-coding
mm_82239.1	chr9	3259232	3259247	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-59426	NR_027988	114673	Mm.422774	NM_053265	ENSMUSG00000042360	4930433N12Rik	-	RIKEN cDNA 4930433N12 gene	ncRNA
mm_140368.1	chr17	86963280	86963303	+	1	NA	5' UTR (NM_145491, exon 1 of 5)	5' UTR (NM_145491, exon 1 of 5)	180	NM_145491	104215	Mm.826	NM_145491	ENSMUSG00000024143	Rhoq	Arhq|TC10A|Tc10	ras homolog family member Q	protein-coding
mm_10473.1	chr2	14331497	14331518	+	1	NA	3' UTR (NM_008625, exon 30 of 30)	3' UTR (NM_008625, exon 30 of 30)	-56891	NM_001012305	277468	Mm.44662	NM_001012305	ENSMUSG00000036949	Slc39a12	AW046938|Gm731	solute carrier family 39 (zinc transporter), member 12	protein-coding
mm_97116.1	chr11	74770909	74770920	+	1	NA	promoter-TSS (NM_026197)	promoter-TSS (NM_026197)	51	NM_026197	67493	Mm.45748	NM_026197	ENSMUSG00000010554	Mettl16	2610100D03Rik|2810013M15Rik|A830095F14Rik|AI846133|Mett10d	methyltransferase like 16	protein-coding
mm_102230.1	chr11	54916952	54916966	-	1	NA	exon (NM_021327, exon 16 of 18)	exon (NM_021327, exon 16 of 18)	14105	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_147955.1	chr18	67048190	67048192	-	1	NA	Intergenic	Intergenic	-40107	NM_177137	14680	Mm.440746	NM_010307	ENSMUSG00000024524	Gnal	2610011C15Rik|9630020G10Rik|Galphaolf|Gna10|Golf	guanine nucleotide binding protein, alpha stimulating, olfactory type	protein-coding
mm_156507.1	chrX	147703009	147703033	+	1	NA	Intergenic	Intergenic	-148940	NM_001081173	210297	Mm.30506	NM_001081173	ENSMUSG00000031290	Lrch2	AI316885|mKIAA1495	leucine-rich repeats and calponin homology (CH) domain containing 2	protein-coding
mm_125753.1	chr15	73750779	73750783	+	1	NA	intron (NM_008975, intron 1 of 5)	intron (NM_008975, intron 1 of 5)	2755	NM_008975	19245	Mm.390807	NM_008975	ENSMUSG00000059895	Ptp4a3	AV088979|Prl-3|pPtp4a3	protein tyrosine phosphatase 4a3	protein-coding
mm_37417.1	chr4	122862956	122863013	-	1	NA	exon (NM_007598, exon 9 of 13)	exon (NM_007598, exon 9 of 13)	23073	NM_007598	12331	Mm.8687	NM_007598	ENSMUSG00000028656	Cap1	-	CAP, adenylate cyclase-associated protein 1 (yeast)	protein-coding
mm_15277.1	chr2	155247863	155247894	+	1	NA	exon (NM_025947, exon 3 of 4)	exon (NM_025947, exon 3 of 4)	11270	NM_001291108	67068	Mm.23693	NM_025947	ENSMUSG00000047459	Dynlrb1	2010012N15Rik|2010320M17Rik|9430076K19Rik|AV124457|DNLC2A|Dncl2a|km23-1	dynein light chain roadblock-type 1	protein-coding
mm_87522.1	chr10	53280265	53280271	+	1	NA	promoter-TSS (NR_038015)	promoter-TSS (NR_038015)	-2	NR_038015	100502820	Mm.55827	NR_038015		Gm19395	-	predicted gene, 19395	ncRNA
mm_52592.1	chr6	116671795	116671838	+	1	NA	intron (NM_178045, intron 1 of 10)	intron (NM_178045, intron 1 of 10)	2020	NM_178045	213391	Mm.257931	NM_178045	ENSMUSG00000042129	Rassf4	3830411C14Rik|AD037|AI586137	Ras association (RalGDS/AF-6) domain family member 4	protein-coding
mm_83702.1	chr9	50659791	50659801	-	1	NA	promoter-TSS (NM_145614)	promoter-TSS (NM_145614)	-16	NM_145614	235339	Mm.285076	NM_145614	ENSMUSG00000000168	Dlat	6332404G05Rik|DLTA|PDC-E2	dihydrolipoamide S-acetyltransferase (E2 component of pyruvate dehydrogenase complex)	protein-coding
mm_160483.1	chr8	124433897	124433897	-	1	NA	promoter-TSS (NM_171824)	promoter-TSS (NM_171824)	39	NM_171824	209966	Mm.234233	NM_171824	ENSMUSG00000050751	Pgbd5	2900019M05Rik|AI854313	piggyBac transposable element derived 5	protein-coding
mm_149583.1	chr19	15985052	15985105	+	1	NA	promoter-TSS (NM_198019)	promoter-TSS (NM_198019)	3	NR_045355	100502653	Mm.149980	NR_045355	ENSMUSG00000097557	C130060C02Rik	-	RIKEN cDNA C130060C02 gene	ncRNA
mm_79172.1	chr9	47852596	47852612	+	1	NA	3' UTR (NM_018770, exon 10 of 10)	3' UTR (NM_018770, exon 10 of 10)	-34396	NR_046048	100038460	Mm.447649	NR_046048		Gm10677	ENSMUSG00000074363	predicted gene 10677	ncRNA
mm_145044.1	chr18	39773579	39773594	+	1	NA	promoter-TSS (NM_011033)	promoter-TSS (NM_011033)	89	NM_011033	18459	Mm.9493	NM_011033	ENSMUSG00000051732	Pabpc2	Pabp|Pabp+|Pabp2	poly(A) binding protein, cytoplasmic 2	protein-coding
mm_116528.1	chr13	45819464	45819467	-	1	NA	intron (NM_001199304, intron 3 of 6)	intron (NM_001199304, intron 3 of 6)	145526	NM_001199304	20238	Mm.342683	NM_009124	ENSMUSG00000046876	Atxn1	2900016G23Rik|Atx1|C85907|ENSMUSG00000074917|Gm10786|Sca1	ataxin 1	protein-coding
mm_104773.1	chr11	98545897	98545907	-	1	NA	5' UTR (NM_011771, exon 1 of 8)	5' UTR (NM_011771, exon 1 of 8)	129	NM_011771	22780	Mm.133367	NM_011771	ENSMUSG00000018168	Ikzf3	5830411O07Rik|Aiolos|Zfpn1a3|Znfn1a3	IKAROS family zinc finger 3	protein-coding
mm_53294.1	chr6	129036673	129036682	+	1	NA	Intergenic	RMER19A|LTR|ERVK	-9224	NR_024262	232408	Mm.259262	NM_153094	ENSMUSG00000030154	Klrb1f	A630024B12Rik|Nkr-p1f|Nkrp1-f|Nkrp1f	killer cell lectin-like receptor subfamily B member 1F	protein-coding
mm_47063.1	chr5	116422645	116422686	-	1	NA	5' UTR (NM_030704, exon 1 of 3)	5' UTR (NM_030704, exon 1 of 3)	199	NM_030704	80888	Mm.21549	NM_030704	ENSMUSG00000041548	Hspb8	AU018630|AW413033|Cryac|D5Ucla4|E2IG1|H11|H11K|HSP20-like|HSP22	heat shock protein 8	protein-coding
mm_122133.1	chr14	31160652	31160664	-	1	NA	intron (NM_138672, intron 11 of 68)	intron (NM_138672, intron 11 of 68)	7983	NM_138672	192187	Mm.220821	NM_138672	ENSMUSG00000042286	Stab1	FEEL-1|FELE-1|MFEEL-1|MS-1|STAB-1|mKIAA0246	stabilin 1	protein-coding
mm_105419.1	chr11	103692446	103692453	-	1	NA	intron (NM_019650, intron 1 of 5)	intron (NM_019650, intron 1 of 5)	5261	NM_019650	56494	Mm.195451	NM_019650	ENSMUSG00000020946	Gosr2	2310032N09Rik|C76855|Gs27|SNARE|membrin	golgi SNAP receptor complex member 2	protein-coding
mm_148414.1	chr19	3935472	3935483	+	1	NA	intron (NM_001161428, intron 1 of 9)	intron (NM_001161428, intron 1 of 9)	291	NM_001161428	54445	Mm.262094	NM_019449	ENSMUSG00000036908	Unc93b1	Unc-93B1|Unc93b	unc-93 homolog B1 (C. elegans)	protein-coding
mm_76968.1	chr8	106281013	106281031	-	1	NA	intron (NM_021491, intron 2 of 8)	intron (NM_021491, intron 2 of 8)	-1207	NR_126091	75044	Mm.445896	NR_126090		4930506A18Rik	-	RIKEN cDNA 4930506A18 gene	ncRNA
mm_16119.1	chr2	169970791	169970802	+	1	NA	Intergenic	MTE2b|LTR|ERVL-MaLR	-7609	NR_131974	446211	Mm.266854	NR_131974	ENSMUSG00000103935	AY702102	STDP1	cDNA sequence AY702102	ncRNA
mm_110555.1	chr12	55491448	55491467	-	1	NA	TTS (NR_035430)	TTS (NR_035430)	1190	NM_010907	18035	Mm.170515	NM_010907	ENSMUSG00000021025	Nfkbia	AI462015|Nfkbi	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, alpha	protein-coding
mm_100858.1	chr11	5866969	5866990	-	1	NA	exon (NM_009636, exon 8 of 21)	exon (NM_009636, exon 8 of 21)	5113	NM_001291857	11568	Mm.3317	NM_009636	ENSMUSG00000020473	Aebp1	ACLP	AE binding protein 1	protein-coding
mm_99744.1	chr11	106516370	106516379	+	1	NA	intron (NM_198292, intron 8 of 11)	intron (NM_198292, intron 8 of 11)	15383	NR_030703	100216537		NR_030703	ENSMUSG00000065126	Snord104	-	small nucleolar RNA, C/D box 104	snoRNA
mm_45185.1	chr5	52015482	52015485	-	1	NA	Intergenic	Intergenic	120534	NR_105845	102466648		NR_105845	ENSMUSG00000098726	Mir6417	Gm27334|mmu-mir-6417	microRNA 6417	ncRNA
mm_73699.1	chr8	111651580	111651598	+	1	NA	intron (NM_001037665, intron 1 of 3)	intron (NM_001037665, intron 1 of 3)	8146	NM_011742	22640	Mm.4184	NM_011742	ENSMUSG00000055835	Zfp1	Fnp-1|Zfp-1|mkr-1	zinc finger protein 1	protein-coding
mm_16399.1	chr2	179976873	179976889	+	1	NA	promoter-TSS (NM_001081092)	promoter-TSS (NM_001081092)	28	NR_033782	66730	Mm.31773	NR_033782	ENSMUSG00000085704	4921531C22Rik	-	RIKEN cDNA 4921531C22 gene	ncRNA
mm_108277.1	chr12	78887712	78887736	+	1	NA	TTS (NM_026114)	TTS (NM_026114)	19214	NM_013738	27260	Mm.103380	NM_013738	ENSMUSG00000021118	Plek2	-	pleckstrin 2	protein-coding
mm_1492.1	chr1	71887975	71888003	+	1	NA	promoter-TSS (NR_027659)	promoter-TSS (NR_027659)	-123	NR_027658	667931	Mm.214128	NR_027658	ENSMUSG00000099707	Gm8883	EG667931|Gm554	predicted gene 8883	ncRNA
mm_135229.1	chr16	36873429	36873435	-	1	NA	TTS (NM_177128)	TTS (NM_177128)	1394	NM_134111	106389	Mm.432078	NM_134111	ENSMUSG00000022838	Eaf2	AW048865|FESTA-L|FESTA-S|Festa|Traits|U19	ELL associated factor 2	protein-coding
mm_154843.1	chrX	20364642	20364666	+	1	NA	non-coding (NR_110966, exon 1 of 8)	non-coding (NR_110966, exon 1 of 8)	173	NR_110967	19889	Mm.288141	NM_133669	ENSMUSG00000060090	Rp2	AI662636|Rp2h	retinitis pigmentosa 2 homolog	protein-coding
mm_79551.1	chr9	57959996	57959998	+	1	NA	intron (NM_011352, intron 10 of 13)	intron (NM_011352, intron 10 of 13)	19862	NM_011352	20361	Mm.335187	NM_011352	ENSMUSG00000038264	Sema7a	2900057C09Rik|CDw108|H-Sema-L|M-Sema-L|Semal	sema domain, immunoglobulin domain (Ig), and GPI membrane anchor, (semaphorin) 7A	protein-coding
mm_155238.1	chrX	57212111	57212141	+	1	NA	promoter-TSS (NM_011616)	promoter-TSS (NM_011616)	-17	NM_011616	21947	Mm.4861	NM_011616	ENSMUSG00000031132	Cd40lg	CD154|CD40-L|Cd40l|HIGM1|IGM|IMD3|Ly-62|Ly62|T-BAM|TRAP|Tnfsf5|Tnlg8b|gp39	CD40 ligand	protein-coding
mm_37983.1	chr4	133620736	133620762	-	1	NA	intron (NM_001017968, intron 2 of 7)	intron (NM_001017968, intron 2 of 7)	12680	NM_001017968	503610	Mm.331948	NM_001017968	ENSMUSG00000037553	Zdhhc18	-	zinc finger, DHHC domain containing 18	protein-coding
mm_13387.1	chr2	103969548	103969567	+	1	NA	promoter-TSS (NM_008505)	promoter-TSS (NM_008505)	0	NM_001142336	16909	Mm.29266	NM_008505	ENSMUSG00000032698	Lmo2	Rbtn-2|Rbtn2|Rhom-2|Ttg2	LIM domain only 2	protein-coding
mm_172020.1	chr6	115003040	115003052	+	1	NA	Intergenic	Intergenic	34828	NM_026894	68971	Mm.24937	NM_026894	ENSMUSG00000030316	Tamm41	1500001M20Rik|TAM41	TAM41 mitochondrial translocator assembly and maintenance homolog	protein-coding
mm_49047.1	chr6	4903058	4903068	+	1	NA	promoter-TSS (NM_181595)	promoter-TSS (NM_181595)	-257	NM_181595	243725	Mm.332901	NM_181595	ENSMUSG00000032827	Ppp1r9a	2810430P21Rik|4930518N04Rik|5330407E15|A230094E16Rik|BB181831|NRB|mKIAA1222|neurabin-I	protein phosphatase 1, regulatory (inhibitor) subunit 9A	protein-coding
mm_138192.1	chr17	34269257	34269261	+	1	NA	3' UTR (NM_207105, exon 6 of 6)	3' UTR (NM_207105, exon 6 of 6)	6032	NM_207105	14961	Mm.254067	NM_207105	ENSMUSG00000073421	H2-Ab1	AI845868|Abeta|H-2Ab|H2-Ab|I-Abeta|IAb|Ia-2|Ia2|Rmcs1	histocompatibility 2, class II antigen A, beta 1	protein-coding
mm_5908.1	chr1	55001108	55001110	-	1	NA	intron (NM_031179, intron 12 of 24)	intron (NM_031179, intron 12 of 24)	26369	NM_031179	81898	Mm.279736	NM_031179	ENSMUSG00000025982	Sf3b1	155kDa|2810001M05Rik|AA409119|Prp10|SAP155|SF3b155|TA-8|Targ4	splicing factor 3b, subunit 1	protein-coding
mm_38274.1	chr4	136886112	136886155	-	1	NA	promoter-TSS (NM_009777)	promoter-TSS (NM_009777)	44	NM_009777	12260	Mm.2570	NM_009777	ENSMUSG00000036905	C1qb	-	complement component 1, q subcomponent, beta polypeptide	protein-coding
mm_19249.1	chr2	84773258	84773267	-	1	NA	exon (NM_009776, exon 3 of 8)	exon (NM_009776, exon 3 of 8)	2167	NM_009776	12258	Mm.38888	NM_009776	ENSMUSG00000023224	Serping1	C1INH|C1nh	serine (or cysteine) peptidase inhibitor, clade G, member 1	protein-coding
mm_151832.1	chr19	5688541	5688590	-	1	NA	promoter-TSS (NM_022012)	promoter-TSS (NM_022012)	343	NM_144868	104401	Mm.329650	NM_144868	ENSMUSG00000054874	Pcnx3	Pcnxl3|mKIAA4073	pecanex homolog 3	protein-coding
mm_61613.1	chr7	80082311	80082331	+	1	NA	exon (NM_175433, exon 2 of 5)	exon (NM_175433, exon 2 of 5)	-7064	NR_045695	100859962	Mm.392575	NR_045695	ENSMUSG00000108714	Gm21057	-	predicted gene, 21057	ncRNA
mm_42212.1	chr5	112793332	112793338	+	1	NA	promoter-TSS (NR_040676)	promoter-TSS (NR_040676)	43	NR_040676	67360	Mm.59218	NR_040675	ENSMUSG00000098230	1700095B10Rik	-	RIKEN cDNA 1700095B10 gene	ncRNA
mm_134653.1	chr16	21995540	21995548	-	1	NA	promoter-TSS (NM_153404)	promoter-TSS (NM_153404)	-2	NM_001289581	239759	Mm.33192	NM_153404	ENSMUSG00000044626	Liph	C130037N08Rik|D16Wsu119e|H06|Lpdlr|P3|PLA1B|lpd1|lpd2|mPA-PLA1	lipase, member H	protein-coding
mm_69795.1	chr7	141167871	141167909	-	1	NA	intron (NM_001172100, intron 1 of 9)	intron (NM_001172100, intron 1 of 9)	796	NM_001172101	107702	Mm.197493	NM_145135	ENSMUSG00000038650	Rnh1	AW546468|C80305|RNH	ribonuclease/angiogenin inhibitor 1	protein-coding
mm_153578.1	chr19	43388339	43388349	-	1	NA	promoter-TSS (NM_001081257)	promoter-TSS (NM_001081257)	11	NM_001081257	545291	Mm.442200	NM_001081257	ENSMUSG00000074852	Hpse2	Gm968|Hpa2	heparanase 2	protein-coding
mm_20056.1	chr2	120314142	120314172	-	1	NA	promoter-TSS (NM_001024145)	promoter-TSS (NM_001024145)	8	NM_001024145	271844	Mm.24880	NM_001024145	ENSMUSG00000046971	Pla2g4f	4732472I07Rik|Gm647|Pla2zeta	phospholipase A2, group IVF	protein-coding
mm_3083.1	chr1	134405769	134405792	+	1	NA	promoter-TSS (NM_028057)	promoter-TSS (NM_028057)	-210	NM_028057	72017	Mm.280230	NM_028057	ENSMUSG00000026456	Cyb5r1	1500005G05Rik|B5R.1|C80155|Nqo3a2	cytochrome b5 reductase 1	protein-coding
mm_76359.1	chr8	84772327	84772360	-	1	NA	intron (NM_001081982, intron 1 of 9)	G-rich|Low_complexity|Low_complexity	2026	NM_001081981	18032	Mm.9394	NM_010906	ENSMUSG00000001911	Nfix	CTF|NF-I/X|NF1-X|NFI-X	nuclear factor I/X	protein-coding
mm_163441.1	chr12	85476725	85476764	-	1	NA	3' UTR (NM_010234, exon 4 of 4)	3' UTR (NM_010234, exon 4 of 4)	2843	NM_010234	14281	Mm.246513	NM_010234	ENSMUSG00000021250	Fos	D12Rfj1|c-fos|cFos	FBJ osteosarcoma oncogene	protein-coding
mm_169154.1	chr13	63240153	63240157	+	1	NA	exon (NM_001289924, exon 12 of 17)	exon (NM_001289924, exon 12 of 17)	126	NR_110521	72061	Mm.188105	NM_028079	ENSMUSG00000021458	2010111I01Rik	2300006M17Rik|AP-O|AW742919|Aopep|ApO|mir-23b|mir-24-1|mir-27b	RIKEN cDNA 2010111I01 gene	protein-coding
mm_94674.1	chr11	17325076	17325081	+	1	NA	Intergenic	Intergenic	67390	NM_001330649	57316	Mm.287982	NM_020558	ENSMUSG00000000581	C1d	1110036E10Rik|AI875855|SUN-CoR	C1D nuclear receptor co-repressor	protein-coding
mm_162721.1	chr10	37135642	37135646	-	1	NA	3' UTR (NM_008538, exon 2 of 2)	3' UTR (NM_008538, exon 2 of 2)	3282	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_120737.1	chr14	73172894	73172909	+	1	NA	intron (NR_033185, intron 11 of 15)	intron (NR_033185, intron 11 of 15)	30116	NR_033185	105670	Mm.280068	NM_134083	ENSMUSG00000022106	Rcbtb2	2610028E02Rik|2810420M18Rik|AI448345|AW240694|Chc1l|RC/BTB2	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 2	protein-coding
mm_65070.1	chr7	19001185	19001239	-	1	NA	3' UTR (NM_145579, exon 3 of 3)	3' UTR (NM_145579, exon 3 of 3)	-2853	NM_178757	272359	Mm.274237	NM_178757	ENSMUSG00000044030	Irf2bp1	6330414O09Rik|C530033F24	interferon regulatory factor 2 binding protein 1	protein-coding
mm_162175.1	chrX	102119512	102119512	+	1	NA	promoter-TSS (NM_027181)	promoter-TSS (NM_027181)	47	NM_027181	69713	Mm.371635	NM_027181	ENSMUSG00000079480	Pin4	2410002I22Rik|EPVH|Par14	protein (peptidyl-prolyl cis/trans isomerase) NIMA-interacting, 4 (parvulin)	protein-coding
mm_94207.1	chr11	3105171	3105179	+	1	NA	Intergenic	IAPLTR3-int|LTR|ERVK	-18846	NR_003517	236604	Mm.247625	NM_001004146		Pisd-ps1	-	phosphatidylserine decarboxylase, pseudogene 1	pseudo
mm_4935.1	chr1	191121037	191121047	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	22628	NM_030060	381319	Mm.6922	NM_030060	ENSMUSG00000026630	Batf3	9130211I03Rik|Snft	basic leucine zipper transcription factor, ATF-like 3	protein-coding
mm_2187.1	chr1	89016136	89016147	+	1	NA	promoter-TSS (NR_040471)	promoter-TSS (NR_040471)	28	NR_040471	73475	Mm.491040	NR_040471	ENSMUSG00000099378	1700067G17Rik	-	RIKEN cDNA 1700067G17 gene	ncRNA
mm_32630.1	chr4	114987260	114987306	+	1	NA	promoter-TSS (NM_025647)	promoter-TSS (NM_025647)	-55	NM_025647	66588	Mm.294159	NM_025647	ENSMUSG00000028719	Cmpk1	0610011D08Rik|CK|Cmpk|UMP-CMPk	cytidine monophosphate (UMP-CMP) kinase 1	protein-coding
mm_25105.1	chr3	101297524	101297536	+	1	NA	Intergenic	MLT1G1|LTR|ERVL-MaLR	-9591	NM_013486	12481	Mm.22842	NM_013486	ENSMUSG00000027863	Cd2	LFA-2|Ly-37|Ly37	CD2 antigen	protein-coding
mm_48367.1	chr5	139473139	139473182	-	1	NA	3' UTR (NM_001159908, exon 7 of 7)	3' UTR (NM_001159908, exon 7 of 7)	11331	NM_133349	100494	Mm.24521	NM_133349	ENSMUSG00000053581	Zfand2a	AA407930|AU016206|Airap	zinc finger, AN1-type domain 2A	protein-coding
mm_11464.1	chr2	32278812	32278820	+	1	NA	TTS (NR_110965)	TTS (NR_110965)	9253	NR_110965	72931	Mm.27344	NM_175190	ENSMUSG00000044627	Swi5	1500019F05Rik|2900010J23Rik|AI046671	SWI5 recombination repair homolog (yeast)	protein-coding
mm_142694.1	chr17	47833257	47833279	-	1	NA	promoter-TSS (NM_010783)	promoter-TSS (NM_010783)	23	NM_001276391	17240	Mm.329100	NM_010783	ENSMUSG00000032717	Mdfi	I-mf|I-mfa	MyoD family inhibitor	protein-coding
mm_89574.1	chr10	95523185	95523191	+	1	NA	intron (NM_080560, intron 1 of 3)	B1_Mus1|SINE|Alu	8026	NM_080560	93765	Mm.371667	NM_080560	ENSMUSG00000074781	Ube2n	1500026J17Rik|AL022654|BB101821|UBC13	ubiquitin-conjugating enzyme E2N	protein-coding
mm_92169.1	chr10	67571939	67571944	-	1	NA	Intergenic	Intergenic	-22986	NM_001005419	211488	Mm.297250	NM_001005419	ENSMUSG00000057134	Ado	Gm237	2-aminoethanethiol (cysteamine) dioxygenase	protein-coding
mm_151260.1	chr19	53950391	53950435	+	1	NA	intron (NM_019658, intron 1 of 8)	intron (NM_019658, intron 1 of 8)	5537	NM_019658	56392	Mm.228669	NM_019658	ENSMUSG00000024976	Shoc2	AU017287|Sur8|mKIAA0862	soc-2 (suppressor of clear) homolog (C. elegans)	protein-coding
mm_131718.1	chr16	21423146	21423214	+	1	NA	promoter-TSS (NM_001285894)	promoter-TSS (NM_001285894)	62	NM_001285894	209018	Mm.235683	NM_145948	ENSMUSG00000033653	Vps8	AI315068|AU040738|mKIAA0804	VPS8 CORVET complex subunit	protein-coding
mm_16997.1	chr2	18390834	18390861	-	1	NA	intron (NM_007869, intron 1 of 11)	(A)n|Simple_repeat|Simple_repeat	1983	NM_001190817	13418	Mm.246674	NM_007869	ENSMUSG00000026740	Dnajc1	4733401K02Rik|AA960110|D230036H06Rik|Dnajl1|ERdj1|ERj1p|MTJ1	DnaJ heat shock protein family (Hsp40) member C1	protein-coding
mm_73517.1	chr8	107454135	107454160	+	1	NA	intron (NM_025830, intron 2 of 23)	ID_B1|SINE|B4	17749	NM_025830	66894	Mm.390058	NM_025830	ENSMUSG00000031930	Wwp2	1300010O06Rik|AA690238|AIP2|AW554328	WW domain containing E3 ubiquitin protein ligase 2	protein-coding
mm_69030.1	chr7	126797480	126797505	-	1	NA	exon (NM_001177307, exon 4 of 10)	exon (NM_001177307, exon 4 of 10)	1686	NM_001177307	11674	Mm.275831	NM_007438	ENSMUSG00000030695	Aldoa	Aldo-1|Aldo1	aldolase A, fructose-bisphosphate	protein-coding
mm_44983.1	chr5	37336871	37336899	-	1	NA	promoter-TSS (NM_021292)	promoter-TSS (NM_021292)	-4	NM_021292	59056	Mm.479678	NM_021292	ENSMUSG00000029122	Evc	-	Ellis van Creveld gene syndrome	protein-coding
mm_34409.1	chr4	145245712	145245722	+	1	NA	intron (NM_011610, intron 1 of 9)	intron (NM_011610, intron 1 of 9)	1153	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_18939.1	chr2	76755959	76755964	-	1	NA	exon (NM_011652, exon 269 of 313)	exon (NM_011652, exon 269 of 313)	80646	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_78942.1	chr9	45138391	45138403	+	1	NA	promoter-TSS (NM_001013390)	promoter-TSS (NM_001013390)	-645	NM_001013390	399548	Mm.335112	NM_001013390	ENSMUSG00000046480	Scn4b	Gm1471	sodium channel, type IV, beta	protein-coding
mm_25632.1	chr3	119782860	119782880	+	1	NA	intron (NM_001310711, intron 1 of 13)	CpG	518	NM_001310711	56195	Mm.29966	NM_019550	ENSMUSG00000028134	Ptbp2	Ptb2|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding
mm_115782.1	chr13	19311552	19311566	-	1	NA	Intergenic	Intergenic	84254	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_82583.1	chr9	21168321	21168378	-	1	NA	TTS (NR_106127)	TTS (NR_106127)	2635	NM_183408	18577	Mm.191749	NM_019798	ENSMUSG00000032177	Pde4a	D9Ertd60e|Dpde2	phosphodiesterase 4A, cAMP specific	protein-coding
mm_125179.1	chr15	31602107	31602132	+	1	NA	promoter-TSS (NM_007637)	promoter-TSS (NM_007637)	3	NM_026546	68073	Mm.119185	NM_026546	ENSMUSG00000039065	Fam173b	A930016P21Rik|AA987072	family with sequence similarity 173, member B	protein-coding
mm_144709.1	chr18	34932161	34932179	+	1	NA	promoter-TSS (NM_144866)	promoter-TSS (NM_144866)	-167	NM_144866	225363	Mm.329353	NM_144866	ENSMUSG00000024360	Etf1	AI463371|D6Ertd109e|ERF|ERF1|SUP45L1|TB3-1	eukaryotic translation termination factor 1	protein-coding
mm_102243.1	chr11	55033399	55033461	-	1	NA	promoter-TSS (NM_013472)	promoter-TSS (NM_013472)	41	NR_138556	11749	Mm.265347	NM_013472	ENSMUSG00000018340	Anxa6	AW107198|Anx6|AnxVI|Cabm|Camb	annexin A6	protein-coding
mm_64660.1	chr7	4164662	4164675	-	1	NA	promoter-TSS (NM_021454)	promoter-TSS (NM_021454)	31	NM_021454	58804	Mm.34268	NM_021454	ENSMUSG00000063838	Cdc42ep5	1700027J19Rik|2010007O02Rik|Borg3|C85526|CEP5	CDC42 effector protein (Rho GTPase binding) 5	protein-coding
mm_19224.1	chr2	84670590	84670600	-	1	NA	TTS (NM_001290751)	TTS (NM_001290751)	113	NM_001033166	72657	Mm.259293	NM_001033166	ENSMUSG00000076437	Selenoh	2700094K13Rik|Selh	selenoprotein H	protein-coding
mm_154847.1	chrX	20425744	20425762	+	1	NA	promoter-TSS (NM_001289684)	promoter-TSS (NM_001289684)	65	NM_001289684	382207	Mm.281517	NM_199317	ENSMUSG00000037315	Jade3	5730598B06|AI851988|AW544806|Phf16|mKIAA0215	jade family PHD finger 3	protein-coding
mm_159910.1	chr6	48047943	48047943	-	1	NA	promoter-TSS (NM_001347139)	promoter-TSS (NM_001347139)	-149	NM_001347139	72306	Mm.381553	NM_001081382	ENSMUSG00000071477	Zfp777	2500002G23Rik	zinc finger protein 777	protein-coding
mm_80610.1	chr9	87144286	87144317	+	1	NA	promoter-TSS (NM_001101482)	promoter-TSS (NM_001101482)	-5	NM_001177731	244958	Mm.335337	NM_001101482	ENSMUSG00000042761	Mrap2	BB633055	melanocortin 2 receptor accessory protein 2	protein-coding
mm_42534.1	chr5	115866484	115866488	+	1	NA	intron (NM_007708, intron 4 of 46)	intron (NM_007708, intron 4 of 46)	20830	NM_007708	12704	Mm.8321	NM_007708	ENSMUSG00000029516	Cit	C030025P15Rik|CRIK|CRIK-SK|Cit-k	citron	protein-coding
mm_78828.1	chr9	44107673	44107718	+	1	NA	5' UTR (NM_001190313, exon 13 of 14)	5' UTR (NM_001190313, exon 13 of 14)	386	NM_001190319	235312	Mm.227110	NM_145613	ENSMUSG00000079592	C1qtnf5	Ctrp5	C1q and tumor necrosis factor related protein 5	protein-coding
mm_42558.1	chr5	117126263	117126324	+	1	NA	intron (NM_001199685, intron 1 of 20)	Lx8|LINE|L1	6164	NM_001199685	330177	Mm.24343	NM_183306	ENSMUSG00000061288	Taok3	2900006A08Rik|A130052D22|A430105I05Rik	TAO kinase 3	protein-coding
mm_52196.1	chr6	100451047	100451057	+	1	NA	Intergenic	Intergenic	-76348	NR_040525	73395	Mm.69413	NR_040525	ENSMUSG00000101553	1700049E22Rik	-	RIKEN cDNA 1700049E22 gene	ncRNA
mm_69970.1	chr7	142376929	142376940	-	1	NA	intron (NM_009983, intron 7 of 8)	intron (NM_009983, intron 7 of 8)	-3188	NM_001347541	320802	Mm.154486	NM_177265	ENSMUSG00000045777	Ifitm10	6330512M04Rik|AI848576|DSPA3	interferon induced transmembrane protein 10	protein-coding
mm_147762.1	chr18	61375062	61375169	-	1	NA	intron (NM_133249, intron 1 of 11)	(TG)n|Simple_repeat|Simple_repeat	25316	NM_133249	170826	Mm.415302	NM_133249	ENSMUSG00000033871	Ppargc1b	4631412G21Rik|Perc	peroxisome proliferative activated receptor, gamma, coactivator 1 beta	protein-coding
mm_68379.1	chr7	109175116	109175126	-	1	NA	promoter-TSS (NM_001302205)	promoter-TSS (NM_001302205)	86	NM_001302205	109594	Mm.360145	NM_057173	ENSMUSG00000036111	Lmo1	Rbtn-1|Rbtn1|Ttg1	LIM domain only 1	protein-coding
mm_28187.1	chr3	88072040	88072042	-	1	NA	intron (NM_172526, intron 6 of 9)	intron (NM_172526, intron 6 of 9)	6263	NM_172526	214191	Mm.229191	NM_172526	ENSMUSG00000051036	Ttc24	A430025D11Rik	tetratricopeptide repeat domain 24	protein-coding
mm_86902.1	chr10	22306775	22306790	+	1	NA	promoter-TSS (NR_015465)	promoter-TSS (NR_015465)	62	NR_015465	606736	Mm.387042	NR_015465	ENSMUSG00000097352	C920009B18Rik	-	RIKEN cDNA C920009B18 gene	ncRNA
mm_113102.1	chr13	24395257	24395279	+	1	NA	5' UTR (NM_001111110, exon 2 of 17)	5' UTR (NM_001111110, exon 2 of 17)	-19854	NM_007717	12763	Mm.8396	NM_007717	ENSMUSG00000016756	Cmah	-	cytidine monophospho-N-acetylneuraminic acid hydroxylase	protein-coding
mm_39784.1	chr5	30166101	30166104	+	1	NA	intron (NM_001289799, intron 3 of 15)	intron (NM_001289799, intron 3 of 15)	-4637	NR_035486	100316709		NR_035486	ENSMUSG00000088113	Mir1960	mir-1960|mmu-mir-1960	microRNA 1960	ncRNA
mm_21292.1	chr2	156992022	156992119	-	1	NA	promoter-TSS (NM_180956)	promoter-TSS (NM_180956)	41	NM_013865	29812	Mm.279256	NM_013865	ENSMUSG00000027634	Ndrg3	4833415O14Rik|AI747193|Ndr3	N-myc downstream regulated gene 3	protein-coding
mm_10390.1	chr2	13271580	13271630	+	1	NA	promoter-TSS (NM_009105)	promoter-TSS (NM_009105)	-190	NM_009105	20163	Mm.905	NM_009105	ENSMUSG00000026727	Rsu1	RsuI|rsp-1	Ras suppressor protein 1	protein-coding
mm_113210.1	chr13	25074749	25074756	+	1	NA	intron (NM_001195617, intron 2 of 7)	B1_Mus1|SINE|Alu	18748	NM_177577	195208	Mm.284719	NM_177577	ENSMUSG00000035910	Dcdc2a	AW492955|Dcdc2|RU2	doublecortin domain containing 2a	protein-coding
mm_55948.1	chr6	85137799	85137807	-	1	NA	promoter-TSS (NM_011467)	promoter-TSS (NM_011467)	-39	NM_011467	20751	Mm.28393	NM_011467	ENSMUSG00000033735	Spr	AA409688|ENSMUSG00000071345|Gm10328	sepiapterin reductase	protein-coding
mm_26067.1	chr3	135887074	135887093	+	1	NA	3' UTR (NM_001135150, exon 9 of 9)	3' UTR (NM_001135150, exon 9 of 9)	-46814	NR_040540	71038	Mm.410798	NR_040540	ENSMUSG00000106306	4933401H06Rik	-	RIKEN cDNA 4933401H06 gene	ncRNA
mm_83847.1	chr9	54501566	54501644	-	1	NA	promoter-TSS (NM_172771)	promoter-TSS (NM_172771)	21	NM_172771	235380	Mm.93636	NM_172771	ENSMUSG00000041268	Dmxl2	6330586A12|6430411K14Rik|E130119P06Rik|mKIAA0856	Dmx-like 2	protein-coding
mm_87510.1	chr10	52417702	52417712	+	1	NA	5' UTR (NM_030250, exon 1 of 5)	5' UTR (NM_030250, exon 1 of 5)	160	NM_030250	52014	Mm.199964	NM_030250	ENSMUSG00000023068	Nus1	1600027K07Rik|AU019165|AW538011|BC003223|D10Ertd438e	NUS1 dehydrodolichyl diphosphate synthase subunit	protein-coding
mm_162490.1	chr1	135848007	135848010	-	1	NA	exon (NM_001130176, exon 7 of 13)	exon (NM_001130176, exon 7 of 13)	7147	NM_001130176	21956	Mm.247470	NM_011619	ENSMUSG00000026414	Tnnt2	Tnt|cTnT	troponin T2, cardiac	protein-coding
mm_151046.1	chr19	47024728	47024738	+	1	NA	TTS (NM_146100)	TTS (NM_146100)	-9544	NM_001164363	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_68185.1	chr7	104143258	104143306	-	1	NA	promoter-TSS (NM_198623)	promoter-TSS (NM_198623)	-10	NM_198623	244178	Mm.334092	NM_198623	ENSMUSG00000051618	Ubqln3	4933400K24Rik	ubiquilin 3	protein-coding
mm_66918.1	chr7	60047974	60047984	-	1	NA	intron (NM_001082962, intron 2 of 10)	intron (NM_001082962, intron 2 of 10)	-42823	NM_033174	84704	Mm.274995	NM_033174	ENSMUSG00000000948	Snurf	2410045I01Rik|Snrpn	SNRPN upstream reading frame	protein-coding
mm_166619.1	chr6	72355774	72355785	+	1	NA	intron (NM_144916, intron 1 of 7)	CpG	296	NM_144916	232086	Mm.491165	NM_144916	ENSMUSG00000055912	Tmem150a	BC014685|Tmem150	transmembrane protein 150A	protein-coding
mm_42969.1	chr5	123138656	123138710	+	1	NA	Intergenic	Intergenic	-3510	NM_001040398	208043	Mm.250391	NM_177581	ENSMUSG00000038384	Setd1b	AA516740|BC035291|KMT2G|mKIAA1076	SET domain containing 1B	protein-coding
mm_24354.1	chr3	90051631	90051636	+	1	NA	promoter-TSS (NM_001287087)	promoter-TSS (NM_001287087)	-3	NM_001287087	99650	Mm.300083	NM_025762	ENSMUSG00000027942	4933434E20Rik	5730552F22Rik|AI462154|NICE-3|NS5ATP4	RIKEN cDNA 4933434E20 gene	protein-coding
mm_23167.1	chr3	40745322	40745324	+	1	NA	promoter-TSS (NM_011020)	promoter-TSS (NM_011020)	-290	NM_011020	18415	Mm.39330	NM_011020	ENSMUSG00000025757	Hspa4l	94kDa|AI461691|APG-1|Osp94	heat shock protein 4 like	protein-coding
mm_33061.1	chr4	123201504	123201529	+	1	NA	promoter-TSS (NM_001085502)	promoter-TSS (NM_001085502)	-37	NM_001085502	230718	Mm.354635	NM_001085502	ENSMUSG00000054958	Nt5c1a	Cn1a|Gm49	5'-nucleotidase, cytosolic IA	protein-coding
mm_76800.1	chr8	104239624	104239628	-	1	NA	intron (NM_021028, intron 4 of 9)	intron (NM_021028, intron 4 of 9)	8932	NR_045642	57813	Mm.183110	NM_021028	ENSMUSG00000035824	Tk2	AU024611|mt-TK	thymidine kinase 2, mitochondrial	protein-coding
mm_33743.1	chr4	134127909	134127966	+	1	NA	exon (NM_080559, exon 2 of 3)	exon (NM_080559, exon 2 of 3)	816	NM_080559	73723	Mm.22240	NM_080559	ENSMUSG00000028843	Sh3bgrl3	1110004L05Rik|AU022188	SH3 domain binding glutamic acid-rich protein-like 3	protein-coding
mm_78357.1	chr9	25515269	25515272	+	1	NA	intron (NM_026189, intron 2 of 7)	intron (NM_026189, intron 2 of 7)	33673	NM_026189	67484	Mm.112977	NM_026189	ENSMUSG00000036611	Eepd1	2310005P05Rik|AI481005	endonuclease/exonuclease/phosphatase family domain containing 1	protein-coding
mm_87426.1	chr10	50792269	50792283	+	1	NA	intron (NM_198007, intron 36 of 41)	B1_Mus2|SINE|Alu	-103375	NM_011376	20464	Mm.4774	NM_011376	ENSMUSG00000019913	Sim1	bHLHe14|mSIM1	single-minded homolog 1 (Drosophila)	protein-coding
mm_65327.1	chr7	24972659	24972684	-	1	NA	promoter-TSS (NM_010261)	promoter-TSS (NM_010261)	57	NM_010261	14470	Mm.22473	NM_010261	ENSMUSG00000003380	Rabac1	2310040I06Rik|Gbpap1|PRA1|prenylin	Rab acceptor 1 (prenylated)	protein-coding
mm_33746.1	chr4	134244110	134244146	+	1	NA	3' UTR (NM_024215, exon 3 of 3)	3' UTR (NM_024215, exon 3 of 3)	365	NR_040436	77490	Mm.426238	NR_040435	ENSMUSG00000086322	E130218I03Rik	E130106C14Rik	RIKEN cDNA E130218I03 gene	ncRNA
mm_80283.1	chr9	73044834	73044864	+	1	NA	promoter-TSS (NM_023635)	promoter-TSS (NM_023635)	39	NM_001301230	11891	Mm.34867	NM_023635	ENSMUSG00000032202	Rab27a	2210402C08Rik|2410003M20Rik|4933437C11Rik|ash	RAB27A, member RAS oncogene family	protein-coding
mm_39690.1	chr5	26904683	26904710	+	1	NA	promoter-TSS (NM_001198886)	promoter-TSS (NM_001198886)	-82	NM_001198886	13483	Mm.42078	NM_010075	ENSMUSG00000061576	Dpp6	B930011P16Rik|D5Buc3|D5Buc4|D5Buc5|DPP VI|Dpp-6|Gm1377|In(5)6H-p|Peplb|Rw	dipeptidylpeptidase 6	protein-coding
mm_21144.1	chr2	154354237	154354288	-	1	NA	intron (NM_025876, intron 6 of 13)	intron (NM_025876, intron 6 of 13)	18457	NM_025876	66971	Mm.289427	NM_025876	ENSMUSG00000027487	Cdk5rap1	2310066P17Rik	CDK5 regulatory subunit associated protein 1	protein-coding
mm_48364.1	chr5	139460491	139460500	-	1	NA	promoter-TSS (NM_028469)	promoter-TSS (NM_028469)	39	NM_028469	73212	Mm.84294	NM_028469	ENSMUSG00000053553	3110082I17Rik	AW411904	RIKEN cDNA 3110082I17 gene	protein-coding
mm_28261.1	chr3	88571889	88571899	-	1	NA	Intergenic	RLTR12E|LTR|ERVK	-7777	NM_025448	66256	Mm.7091	NM_025448	ENSMUSG00000041355	Ssr2	1500032E05Rik|AI315033|AU020133|TLAP|TRAPB|TRAPbeta	signal sequence receptor, beta	protein-coding
mm_139882.1	chr17	70756043	70756053	+	1	NA	intron (NM_001347411, intron 9 of 14)	intron (NM_001347411, intron 9 of 14)	90729	NM_001164077	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_115584.1	chr13	11790086	11790089	-	1	NA	intron (NM_023868, intron 23 of 104)	intron (NM_023868, intron 23 of 104)	268035	NR_027813	664793	Mm.410565	NR_027813		Zp4-ps	EG664793|Zp4|Zpb	zona pellucida glycoprotein 4, pseudogene	pseudo
mm_99241.1	chr11	101078414	101078422	+	1	NA	promoter-TSS (NM_010475)	promoter-TSS (NM_010475)	7	NM_010475	15485	Mm.188939	NM_010475	ENSMUSG00000019301	Hsd17b1	17HSDB1|17beta-HSD|E2DH|Hsd17ba	hydroxysteroid (17-beta) dehydrogenase 1	protein-coding
mm_68804.1	chr7	125491476	125491486	-	1	NA	promoter-TSS (NM_026330)	promoter-TSS (NM_026330)	61	NM_026330	67711	Mm.4467	NM_026330	ENSMUSG00000030750	Nsmce1	2510027N19Rik	NSE1 homolog, SMC5-SMC6 complex component	protein-coding
mm_79427.1	chr9	55541191	55541209	+	1	NA	promoter-TSS (NM_027397)	promoter-TSS (NM_027397)	51	NM_027397	104360	Mm.273996	NM_027397	ENSMUSG00000032318	Isl2	3110001N10Rik	insulin related protein 2 (islet 2)	protein-coding
mm_124436.1	chr14	118594876	118594896	-	1	NA	exon (NM_001163676, exon 18 of 30)	exon (NM_001163676, exon 18 of 30)	-2414	NR_105815	102465208		NR_105815	ENSMUSG00000098433	Mir6391	Gm27914|mmu-mir-6391	microRNA 6391	ncRNA
mm_54354.1	chr6	31087626	31087645	-	1	NA	Intergenic	Intergenic	-24542	NR_029532	387223		NR_029532	ENSMUSG00000065604	Mir29b-1	Mirn29b|Mirn29b-1|mir-29b-1	microRNA 29b-1	ncRNA
mm_112480.1	chr13	5869019	5869089	+	1	NA	3' UTR (NM_011803, exon 4 of 4)	3' UTR (NM_011803, exon 4 of 4)	7565	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_44683.1	chr5	30119795	30119810	-	1	NA	3' UTR (NM_178878, exon 20 of 20)	3' UTR (NM_178878, exon 20 of 20)	-13716	NM_001256263	433868	Mm.450696	NM_001256263	ENSMUSG00000086815	3110082J24Rik	ENSMUSG00000073106	RIKEN cDNA 3110082J24 gene	protein-coding
mm_58395.1	chr7	3210784	3210792	+	1	NA	Intergenic	MER31B|LTR|ERV1	-7838	NR_029640	100049710		NR_029640	ENSMUSG00000077815	Mir290a	Mir290|Mirn290|mir-290a|mmu-miR-290|mmu-mir-290a	microRNA 290a	ncRNA
mm_51730.1	chr6	87022997	87023009	+	1	NA	intron (NM_001170591, intron 5 of 7)	B1_Mur1|SINE|Alu	13167	NM_020045	56748	Mm.23809	NM_020045	ENSMUSG00000029993	Nfu1	0610006G17Rik|CGI-33|Hirip5	NFU1 iron-sulfur cluster scaffold	protein-coding
mm_19057.1	chr2	77280766	77280848	-	1	NA	promoter-TSS (NM_175465)	promoter-TSS (NM_175465)	-215	NM_175465	228071	Mm.27120	NM_175465	ENSMUSG00000042272	Sestd1	1500031J16Rik|A930010O20|Solo/Trio8	SEC14 and spectrin domains 1	protein-coding
mm_54931.1	chr6	48396742	48396767	-	1	NA	intron (NM_001347152, intron 1 of 17)	intron (NM_001347152, intron 1 of 17)	1168	NM_001347153	77827	Mm.107646	NM_133922	ENSMUSG00000042810	Krba1	A930040G15Rik|AI448780	KRAB-A domain containing 1	protein-coding
mm_3145.1	chr1	135144685	135144706	+	1	NA	3' UTR (NM_177081, exon 10 of 10)	3' UTR (NM_177081, exon 10 of 10)	-2139	NM_026823	68724	Mm.174998	NM_026823	ENSMUSG00000026426	Arl8a	1110033P22Rik|Arl10b|gie2	ADP-ribosylation factor-like 8A	protein-coding
mm_73292.1	chr8	104961714	104961786	+	1	NA	promoter-TSS (NM_197999)	promoter-TSS (NM_197999)	32	NM_197999	72361	Mm.26580	NM_197999	ENSMUSG00000031877	Ces2g	2210023G05Rik|Ces2l	carboxylesterase 2G	protein-coding
mm_38834.1	chr4	149153947	149153984	-	1	NA	exon (NM_001081274, exon 10 of 13)	exon (NM_001081274, exon 10 of 13)	12742	NM_001081274	110208	Mm.252080	NM_025801	ENSMUSG00000028961	Pgd	0610042A05Rik|AU019875|C78335	phosphogluconate dehydrogenase	protein-coding
mm_16785.1	chr2	9951813	9951833	-	1	NA	exon (NM_027748, exon 3 of 7)	exon (NM_027748, exon 3 of 7)	-62283	NR_040511	77682	Mm.488621	NR_040511	ENSMUSG00000079602	9230102O04Rik	-	RIKEN cDNA 9230102O04 gene	ncRNA
mm_146001.1	chr18	68398932	68398935	+	1	NA	Intergenic	RLTR34D_MM|LTR|ERVK	28907	NM_001271717	17200	Mm.426053	NM_008560	ENSMUSG00000045569	Mc2r	ACTH-R|ACTHR|MC2-R	melanocortin 2 receptor	protein-coding
mm_135537.1	chr16	49770819	49770836	-	1	NA	Intergenic	MER63A|DNA|hAT-Blackjack	71533	NM_028680	73916	Mm.241276	NM_028680	ENSMUSG00000032965	Ift57	4833420A15Rik|Esrrbl1|Hippi|MHS4R2	intraflagellar transport 57	protein-coding
mm_118092.1	chr13	103845547	103845564	-	1	NA	exon (NM_001289475, exon 16 of 26)	exon (NM_001289475, exon 16 of 26)	75031	NM_001289473	59079	Mm.277354	NM_021563	ENSMUSG00000021709	Erbin	1700028E05Rik|Erbb2ip|mKIAA1225	Erbb2 interacting protein	protein-coding
mm_141346.1	chr17	28558886	28558892	-	1	NA	promoter-TSS (NR_105935)	promoter-TSS (NR_105935)	-388	NR_105935	102465585		NR_105935	ENSMUSG00000099152	Mir6969	Gm27305|mmu-mir-6969	microRNA 6969	ncRNA
mm_123407.1	chr14	63543932	63543991	-	1	NA	promoter-TSS (NM_177594)	promoter-TSS (NM_177594)	-8	NM_177594	210376	Mm.441613	NM_177594	ENSMUSG00000035078	Mtmr9	9430075G12Rik|AA516943|AF073881|LIP-STYX|MTMR8|mMTMH3	myotubularin related protein 9	protein-coding
mm_106739.1	chr12	3905353	3905353	+	1	NA	intron (NM_007872, intron 20 of 22)	intron (NM_007872, intron 20 of 22)	13609	NM_153743	13435	Mm.5001	NM_007872	ENSMUSG00000020661	Dnmt3a	MmuIIIA	DNA methyltransferase 3A	protein-coding
mm_46114.1	chr5	92363256	92363258	-	1	NA	promoter-TSS (NM_019494)	promoter-TSS (NM_019494)	20	NM_019494	56066	Mm.131723	NM_019494	ENSMUSG00000060183	Cxcl11	Cxc11|H174|I-tac|Ip9|Itac|Scyb11|Scyb9b|b-R1|betaR1	chemokine (C-X-C motif) ligand 11	protein-coding
mm_54995.1	chr6	48770887	48770892	-	1	NA	promoter-TSS (NM_031247)	promoter-TSS (NM_031247)	-38	NM_031247	83408	Mm.333050	NM_031247	ENSMUSG00000039264	Gimap3	2010110D23Rik|Gimap5|Ian4	GTPase, IMAP family member 3	protein-coding
mm_4070.1	chr1	166130518	166130528	+	1	NA	promoter-TSS (NM_021610)	promoter-TSS (NM_021610)	63	NM_021610	59290	Mm.46357	NM_021610	ENSMUSG00000000544	Gpa33	2010310L10Rik|2210401D16Rik|BB116197	glycoprotein A33 (transmembrane)	protein-coding
mm_155685.1	chrX	93701092	93701102	+	1	NA	intron (NM_211138, intron 1 of 7)	intron (NM_211138, intron 1 of 7)	25985	NM_211138	236899	Mm.166467	NM_177546	ENSMUSG00000035246	Pcyt1b	AW045697|CTTbeta	phosphate cytidylyltransferase 1, choline, beta isoform	protein-coding
mm_140313.1	chr17	86168425	86168439	+	1	NA	5' UTR (NM_011104, exon 1 of 15)	5' UTR (NM_011104, exon 1 of 15)	647	NM_011104	18754	Mm.24614	NM_011104	ENSMUSG00000045038	Prkce	5830406C15Rik|PKC[e]|PKCepsilon|Pkce|R75156	protein kinase C, epsilon	protein-coding
mm_166015.1	chr4	121055314	121055324	-	1	NA	TTS (NM_007741)	TTS (NM_007741)	15753	NM_007741	12840	Mm.269384	NM_007741	ENSMUSG00000028626	Col9a2	AI427499|Col9a-2	collagen, type IX, alpha 2	protein-coding
mm_78515.1	chr9	32926401	32926420	+	1	NA	intron (NR_131058, intron 1 of 3)	intron (NR_131058, intron 1 of 3)	2556	NR_131058	330917	Mm.488283	NR_131058		Gm27162	A430016B06	predicted gene 27162	ncRNA
mm_76371.1	chr8	84800345	84800378	-	1	NA	promoter-TSS (NM_010906)	promoter-TSS (NM_010906)	-23	NM_001081982	18032	Mm.9394	NM_010906	ENSMUSG00000001911	Nfix	CTF|NF-I/X|NF1-X|NFI-X	nuclear factor I/X	protein-coding
mm_97371.1	chr11	77686133	77686146	+	1	NA	promoter-TSS (NM_001024205)	promoter-TSS (NM_001024205)	0	NM_001024205	68564	Mm.428996	NM_001024205	ENSMUSG00000037857	Nufip2	1110001M19Rik|9530056D24Rik|AI256692|AI461731|PIG1|mKIAA1321	nuclear fragile X mental retardation protein interacting protein 2	protein-coding
mm_770.1	chr1	44147874	44147934	+	1	NA	5' UTR (NM_011729, exon 1 of 15)	5' UTR (NM_011729, exon 1 of 15)	160	NM_011729	22592	Mm.2213	NM_011729	ENSMUSG00000026048	Ercc5	Xpg	excision repair cross-complementing rodent repair deficiency, complementation group 5	protein-coding
mm_1092.1	chr1	59689545	59689548	+	1	NA	intron (NM_018868, intron 1 of 14)	intron (NM_018868, intron 1 of 14)	-2412	NR_028554	100217459		NR_028554		Snord70	MBII-234|snoRNA234	small nucleolar RNA, C/D box 70	snoRNA
mm_67314.1	chr7	79504755	79504763	-	1	NA	promoter-TSS (NR_029818)	promoter-TSS (NR_029818)	-505	NR_029818	723968		NR_029818	ENSMUSG00000093238	Mir9-3	Mirn9-3|mir-9-3|mmu-mir-9-3	microRNA 9-3	ncRNA
mm_93787.1	chr10	120624288	120624320	-	1	NA	Intergenic	Intergenic	-141428	NR_038000	70874	Mm.427286	NR_038000	ENSMUSG00000044544	4921513I03Rik	-	RIKEN cDNA 4921513I03 gene	ncRNA
mm_39945.1	chr5	31876661	31876697	+	1	NA	intron (NM_144541, intron 6 of 11)	intron (NM_144541, intron 6 of 11)	178629	NM_144541	107976	Mm.482126	NM_144541	ENSMUSG00000052139	Bre	6030405P19Rik|AI429776|B830038C02Rik	brain and reproductive organ-expressed protein	protein-coding
mm_158503.1	chrX	142390492	142390520	-	1	NA	promoter-TSS (NM_207625)	promoter-TSS (NM_207625)	29	NM_001033600	50790	Mm.391337	NM_019477	ENSMUSG00000031278	Acsl4	9430020A05Rik|ACS4|AU018108|Facl4|Lacs4	acyl-CoA synthetase long-chain family member 4	protein-coding
mm_137100.1	chr17	21567420	21567424	+	1	NA	intron (NM_001002008, intron 1 of 5)	intron (NM_001002008, intron 1 of 5)	376	NM_001002008	381066	Mm.441097	NM_001002008	ENSMUSG00000067931	Zfp948	-	zinc finger protein 948	protein-coding
mm_75105.1	chr8	34146733	34146752	-	1	NA	promoter-TSS (NM_026609)	promoter-TSS (NM_026609)	-3	NM_026609	68192	Mm.34212	NM_026609	ENSMUSG00000031513	Leprotl1	1110067H13Rik|1520402O14Rik|AI854296	leptin receptor overlapping transcript-like 1	protein-coding
mm_39424.1	chr5	16008811	16008811	+	1	NA	intron (NM_001110846, intron 1 of 37)	intron (NM_001110846, intron 1 of 37)	74120	NM_001110844	12293	Mm.159842	NM_009784	ENSMUSG00000040118	Cacna2d1	Ca(v)alpha2delta1|Cacna2|Cchl2a	calcium channel, voltage-dependent, alpha2/delta subunit 1	protein-coding
mm_108556.1	chr12	84569822	84569835	+	1	NA	promoter-TSS (NM_007701)	promoter-TSS (NM_007701)	0	NM_007701	12677	Mm.4405	NM_007701	ENSMUSG00000021239	Vsx2	Chx10|Hox-10|Hox10|or	visual system homeobox 2	protein-coding
mm_40817.1	chr5	72259495	72259513	+	1	NA	intron (NM_153389, intron 10 of 22)	intron (NM_153389, intron 10 of 22)	56161	NM_153389	231287	Mm.32775	NM_153389	ENSMUSG00000046808	Atp10d	9830145H18Rik|ATPVD|D5Buc24e	ATPase, class V, type 10D	protein-coding
mm_2502.1	chr1	106178535	106178548	+	1	NA	intron (NM_133821, intron 1 of 16)	intron (NM_133821, intron 1 of 16)	6672	NM_133821	98432	Mm.24115	NM_133821	ENSMUSG00000044340	Phlpp1	AI836256|Phlpp|Plekhe1|SCOP|mKIAA0606	PH domain and leucine rich repeat protein phosphatase 1	protein-coding
mm_154203.1	chr19	59041919	59041935	-	1	NA	exon (NM_001114312, exon 4 of 17)	exon (NM_001114312, exon 4 of 17)	34142	NM_175172	71653	Mm.37338	NM_175172	ENSMUSG00000041362	Shtn1	4930506M07Rik|Kiaa1598|Shootin1|mKIAA1598	shootin 1	protein-coding
mm_119639.1	chr14	51908064	51908080	+	1	NA	exon (NM_001145959, exon 9 of 15)	exon (NM_001145959, exon 9 of 15)	5416	NM_001145959	29811	Mm.26722	NM_013864	ENSMUSG00000004558	Ndrg2	AI182517|AU040374|Ndr2|SYLD	N-myc downstream regulated gene 2	protein-coding
mm_108913.1	chr12	100206712	100206766	+	1	NA	3' UTR (NM_009790, exon 6 of 6)	3' UTR (NM_009790, exon 6 of 6)	6595	NM_001313934	12313	Mm.285993	NM_009790	ENSMUSG00000001175	Calm1	AI256814|AI327027|AI461935|AL024000|CaM|Calm	calmodulin 1	protein-coding
mm_26485.1	chr3	144947779	144947816	+	1	NA	Intergenic	RLTR9F|LTR|ERVK	-15268	NM_001033199	99709	Mm.440040	NM_001033199	ENSMUSG00000074195	Clca4b	AI747448|Clca7	chloride channel accessory 4B	protein-coding
mm_161434.1	chr15	59040408	59040408	-	1	NA	intron (NM_001146180, intron 3 of 13)	intron (NM_001146180, intron 3 of 13)	41618	NM_001146180	211401	Mm.215481	NM_144800	ENSMUSG00000022353	Mtss1	2310003N14Rik|BC024131|D130001D01Rik|Mim|mKIAA0429	metastasis suppressor 1	protein-coding
mm_78322.1	chr9	24583987	24583991	+	1	NA	intron (NM_001166207, intron 19 of 21)	intron (NM_001166207, intron 19 of 21)	-41196	NM_173412	235067	Mm.437189	NM_173412	ENSMUSG00000047995	Cypt4	1700009B20Rik|Ckt1r2	cysteine-rich perinuclear theca 4	protein-coding
mm_21289.1	chr2	156991807	156991835	-	1	NA	intron (NM_013865, intron 1 of 15)	CpG	290	NM_013865	29812	Mm.279256	NM_013865	ENSMUSG00000027634	Ndrg3	4833415O14Rik|AI747193|Ndr3	N-myc downstream regulated gene 3	protein-coding
mm_170480.1	chr19	12273377	12273379	+	1	NA	intron (NR_030566, intron 2 of 3)	intron (NR_030566, intron 2 of 3)	5146	NM_146686	258681	Mm.271522	NM_146686	ENSMUSG00000060049	Olfr235	MOR214-3|Olfr232|Olfr232-ps1|Olfr235-ps1|Olfr245|Olfr245-ps1	olfactory receptor 235	protein-coding
mm_110930.1	chr12	76369732	76369765	-	1	NA	promoter-TSS (NM_001172104)	promoter-TSS (NM_001172104)	-188	NM_028356	109929	Mm.41880	NM_028356	ENSMUSG00000056459	Zbtb25	2810462M08Rik|2900064P18Rik|AI842128|Kup|Zfp-50|Zfp50	zinc finger and BTB domain containing 25	protein-coding
mm_94961.1	chr11	30771834	30771842	+	1	NA	promoter-TSS (NM_134013)	promoter-TSS (NM_134013)	63	NM_134013	103554	Mm.240066	NM_134013	ENSMUSG00000040850	Psme4	AA409398|AU041366|TEMO|mKIAA0077	proteasome (prosome, macropain) activator subunit 4	protein-coding
mm_108086.1	chr12	74093217	74093225	+	1	NA	intron (NM_172804, intron 1 of 6)	intron (NM_172804, intron 1 of 6)	95460	NM_172804	238266	Mm.311393	NM_172804	ENSMUSG00000044912	Syt16	6430703N11|Strep14|Syt14l|syt14r	synaptotagmin XVI	protein-coding
mm_133922.1	chr16	97745790	97745816	+	1	NA	intron (NM_023663, intron 7 of 7)	intron (NM_023663, intron 7 of 7)	17952	NM_023663	72388	Mm.35290	NM_023663	ENSMUSG00000005251	Ripk4	2310069J12Rik|AI552420|ANKK2|Ankrd3|DIk|PKK|RIP4	receptor-interacting serine-threonine kinase 4	protein-coding
mm_44154.1	chr5	150457731	150457752	+	1	NA	intron (NM_172887, intron 50 of 60)	intron (NM_172887, intron 50 of 60)	44478	NR_024513	194292	Mm.300184	NR_024513		Gm5	Gm1812	predicted gene 5	ncRNA
mm_140658.1	chr17	12769703	12769727	-	1	NA	promoter-TSS (NM_010515)	promoter-TSS (NM_010515)	-9	NM_010515	16004	Mm.26553	NM_010515	ENSMUSG00000023830	Igf2r	AI661837|CD222|CI-MPR|M6P/IGF2R|Mpr300	insulin-like growth factor 2 receptor	protein-coding
mm_44882.1	chr5	34637204	34637216	-	1	NA	promoter-TSS (NM_026660)	promoter-TSS (NM_026660)	-96	NM_026660	68294	Mm.34564	NM_026660	ENSMUSG00000001082	Mfsd10	0610009O03Rik|Tetran	major facilitator superfamily domain containing 10	protein-coding
mm_106978.1	chr12	9574457	9574476	+	1	NA	promoter-TSS (NM_011859)	promoter-TSS (NM_011859)	24	NM_011859	23967	Mm.45055	NM_011859	ENSMUSG00000048387	Osr1	Odd1|Osr	odd-skipped related 1 (Drosophila)	protein-coding
mm_8311.1	chr1	144200561	144200571	-	1	NA	Intergenic	Intergenic	-23194	NM_153171	246709	Mm.38271	NM_153171	ENSMUSG00000051079	Rgs13	-	regulator of G-protein signaling 13	protein-coding
mm_95066.1	chr11	32535983	32535997	+	1	NA	intron (NM_009288, intron 1 of 18)	intron (NM_009288, intron 1 of 18)	2724	NM_009288	20868	Mm.8235	NM_009288	ENSMUSG00000020272	Stk10	Gek1|Lok|mKIAA4026	serine/threonine kinase 10	protein-coding
mm_82087.1	chr9	123045038	123045052	+	1	NA	exon (NM_177911, exon 4 of 14)	exon (NM_177911, exon 4 of 14)	10304	NM_177911	331046	Mm.195309	NM_177911	ENSMUSG00000025787	Tgm4	9530008N10Rik|Eapa1|TGP	transglutaminase 4 (prostate)	protein-coding
mm_122583.1	chr14	50840523	50840525	-	1	NA	intron (NM_009351, intron 33 of 54)	intron (NM_009351, intron 33 of 54)	30030	NM_009351	21745	Mm.318736	NM_009351	ENSMUSG00000006281	Tep1	Tp1	telomerase associated protein 1	protein-coding
mm_138637.1	chr17	35865788	35865843	+	1	NA	promoter-TSS (NM_001146710)	promoter-TSS (NM_001146710)	220	NM_001146711	76448	Mm.359982	NM_175242	ENSMUSG00000034595	Ppp1r18	2310014H01Rik|AA407849|AI450394	protein phosphatase 1, regulatory subunit 18	protein-coding
mm_45325.1	chr5	65492400	65492435	-	1	NA	intron (NM_133697, intron 1 of 4)	intron (NM_133697, intron 1 of 4)	418	NM_133697	68552	Mm.10709	NM_133697	ENSMUSG00000037822	Smim14	1110003E01Rik|1700127H04Rik|5430439C17Rik|MAd4	small integral membrane protein 14	protein-coding
mm_37242.1	chr4	118139010	118139020	-	1	NA	intron (NM_001161823, intron 19 of 21)	intron (NM_001161823, intron 19 of 21)	-4069	NM_001161774	20441	Mm.251002	NM_009176	ENSMUSG00000028538	St3gal3	ST3GalIII|ST3N|Siat3|Siat6	ST3 beta-galactoside alpha-2,3-sialyltransferase 3	protein-coding
mm_46354.1	chr5	102978481	102978483	-	1	NA	intron (NM_001318131, intron 6 of 11)	intron (NM_001318131, intron 6 of 11)	79910	NM_001310686	26414	Mm.39253	NM_009158	ENSMUSG00000046709	Mapk10	C230008H04Rik|JNK3|JNK3B1|JNK3B2|SAPK(beta)|Serk2|p493F12|p54bSAPK	mitogen-activated protein kinase 10	protein-coding
mm_139382.1	chr17	51882692	51882706	+	1	NA	promoter-TSS (NR_045095)	promoter-TSS (NR_045095)	-28	NR_045095	100504169	Mm.417731	NR_045095		Gm20098	-	predicted gene, 20098	ncRNA
mm_25754.1	chr3	123355554	123355586	+	1	NA	intron (NM_027135, intron 18 of 22)	intron (NM_027135, intron 18 of 22)	30420	NM_201638	210529	Mm.260039	NM_201638	ENSMUSG00000028114	Mettl14	G430022H21Rik|mKIAA1627	methyltransferase like 14	protein-coding
mm_53706.1	chr6	143167272	143167300	+	1	NA	promoter-TSS (NM_029250)	promoter-TSS (NM_029250)	56	NM_029250	75320	Mm.272548	NM_029250	ENSMUSG00000030275	Etnk1	1110061E11Rik|4930555L11Rik|AI195356|AI841245|C80956|D6Ertd3e|EKI1	ethanolamine kinase 1	protein-coding
mm_52747.1	chr6	120554785	120554793	+	1	NA	promoter-TSS (NR_045733)	promoter-TSS (NR_045733)	-7	NR_045733	73505	Mm.416867	NR_045733		1700072O05Rik	-	RIKEN cDNA 1700072O05 gene	ncRNA
mm_22326.1	chr2	180642652	180642664	-	1	NA	promoter-TSS (NM_178254)	promoter-TSS (NM_178254)	33	NM_178254	277353	Mm.473700	NM_178254	ENSMUSG00000038932	Tcfl5	AV260129|Figlb|Sosf1	transcription factor-like 5 (basic helix-loop-helix)	protein-coding
mm_113055.1	chr13	23695792	23695817	+	1	NA	promoter-TSS (NM_010377)	promoter-TSS (NM_010377)	-7	NM_010377	107970	Mm.8048	NM_010377	ENSMUSG00000036211	Hist1h1t	H1.6|H1ft|H1t	histone cluster 1, H1t	protein-coding
mm_55022.1	chr6	48841374	48841412	-	1	NA	promoter-TSS (NM_001164209)	promoter-TSS (NM_001164209)	-19	NM_001164208	65963	Mm.28385	NM_023056	ENSMUSG00000029810	Tmem176b	1810009M01Rik|Clast1|Lr8	transmembrane protein 176B	protein-coding
mm_9954.1	chr1	191020394	191020405	-	1	NA	intron (NM_001313747, intron 1 of 8)	intron (NM_001313747, intron 1 of 8)	-4952	NR_027298	100125339	Mm.472263	NR_027298	ENSMUSG00000097845	A230020J21Rik	ENSMUSG00000066596	RIKEN cDNA A230020J21 gene	ncRNA
mm_24097.1	chr3	88043132	88043150	+	1	NA	promoter-TSS (NM_001110809)	promoter-TSS (NM_001110809)	35	NM_025663	66614	Mm.46029	NM_025663	ENSMUSG00000028069	Gpatch4	2610029K21Rik|Gpatc4	G patch domain containing 4	protein-coding
mm_22208.1	chr2	174047351	174047381	-	1	NA	Intergenic	Intergenic	-29685	NM_172675	228960	Mm.277977	NM_172675	ENSMUSG00000027522	Stx16	4930401D03|5430410K23Rik|6330500A18Rik|AI648908|AW553605|Syn16	syntaxin 16	protein-coding
mm_42574.1	chr5	117240496	117240500	+	1	NA	intron (NM_001081308, intron 12 of 19)	intron (NM_001081308, intron 12 of 19)	47066	NM_018858	23980	Mm.195898	NM_018858	ENSMUSG00000032959	Pebp1	HCNP|Pbp|Pbp1|Pbpr|Rkip	phosphatidylethanolamine binding protein 1	protein-coding
mm_79799.1	chr9	64117255	64117267	+	1	NA	5' UTR (NM_145835, exon 1 of 14)	5' UTR (NM_145835, exon 1 of 14)	114	NM_145835	235435	Mm.436581	NM_145835	ENSMUSG00000032401	Lctl	E130104I05Rik|KLPH	lactase-like	protein-coding
mm_172157.1	chr6	42966284	42966291	+	1	NA	Intergenic	Intergenic	10787	NM_146656	258650	Mm.377613	NM_146656	ENSMUSG00000073110	Olfr444	MOR261-2	olfactory receptor 444	protein-coding
mm_141507.1	chr17	31637136	31637185	-	1	NA	promoter-TSS (NM_144855)	promoter-TSS (NM_144855)	45	NM_144855	12411	Mm.206417	NM_144855	ENSMUSG00000024039	Cbs	AI047524|AI303044|HIP4	cystathionine beta-synthase	protein-coding
mm_129926.1	chr15	84447020	84447034	-	1	NA	promoter-TSS (NM_001163145)	promoter-TSS (NM_001163145)	70	NM_001163145	72301	Mm.275387	NM_001163145	ENSMUSG00000062760	1810041L15Rik	Kiaa1644	RIKEN cDNA 1810041L15 gene	protein-coding
mm_145284.1	chr18	53210330	53210349	+	1	NA	exon (NM_026386, exon 9 of 15)	exon (NM_026386, exon 9 of 15)	33974	NM_026386	67804	Mm.252171	NM_026386	ENSMUSG00000034484	Snx2	0610030A03Rik	sorting nexin 2	protein-coding
mm_163963.1	chr14	54966418	54966421	-	1	NA	intron (NM_001164171, intron 1 of 38)	intron (NM_001164171, intron 1 of 38)	188	NM_001164171	17888	Mm.290003	NM_010856	ENSMUSG00000040752	Myh6	A830009F23Rik|AA517445|Myhc-a|Myhca|alpha-MHC	myosin, heavy polypeptide 6, cardiac muscle, alpha	protein-coding
mm_10608.1	chr2	18998389	18998395	+	1	NA	promoter-TSS (NR_024323)	promoter-TSS (NR_024323)	73	NR_024323	74629	Mm.117687	NR_024323	ENSMUSG00000026736	4930426L09Rik	-	RIKEN cDNA 4930426L09 gene	ncRNA
mm_32499.1	chr4	108459390	108459451	+	1	NA	promoter-TSS (NM_175472)	promoter-TSS (NM_175472)	-6	NM_175472	230594	Mm.25181	NM_175472	ENSMUSG00000034610	Zcchc11	6030404K05Rik|9230115F04Rik|PPAPD3|mKIAA0191	zinc finger, CCHC domain containing 11	protein-coding
mm_25950.1	chr3	131638364	131638368	+	1	NA	intron (NM_001289477, intron 12 of 12)	intron (NM_001289477, intron 12 of 12)	72334	NM_001289477	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_19177.1	chr2	84387190	84387192	-	1	NA	intron (NM_018782, intron 2 of 15)	(A)n|Simple_repeat|Simple_repeat	38075	NM_018782	54598	Mm.75467	NM_018782	ENSMUSG00000059588	Calcrl	AV071593|CRLR	calcitonin receptor-like	protein-coding
mm_94480.1	chr11	6561179	6561181	+	1	NA	5' UTR (NM_001190344, exon 2 of 10)	5' UTR (NM_001190344, exon 2 of 10)	997	NM_001190344	216527	Mm.221271	NM_146014	ENSMUSG00000000378	Ccm2	BC029157	cerebral cavernous malformation 2	protein-coding
mm_132108.1	chr16	31450230	31450238	+	1	NA	intron (NM_175177, intron 5 of 6)	L2a|LINE|L2	21481	NM_001122683	71911	Mm.293470	NM_175177	ENSMUSG00000046598	Bdh1	2310032J20Rik|AI327223|Bdh	3-hydroxybutyrate dehydrogenase, type 1	protein-coding
mm_19761.1	chr2	105399250	105399275	-	1	NA	promoter-TSS (NM_009037)	promoter-TSS (NM_009037)	57	NM_009037	19672	Mm.4876	NM_009037	ENSMUSG00000005973	Rcn1	Rcn	reticulocalbin 1	protein-coding
mm_163252.1	chr11	108936695	108936695	+	1	NA	intron (NM_015732, intron 3 of 10)	intron (NM_015732, intron 3 of 10)	16346	NM_015732	12006	Mm.71710	NM_015732	ENSMUSG00000000142	Axin2	Axi1|Axil|Conductin	axin 2	protein-coding
mm_64076.1	chr7	140920919	140920929	+	1	NA	promoter-TSS (NM_133946)	promoter-TSS (NM_133946)	22	NM_133946	101613	Mm.386833	NM_133946	ENSMUSG00000038745	Nlrp6	AI504961|Avr|Nalp6|Navr|Navr/Avr|Non-AVR|Pypaf5	NLR family, pyrin domain containing 6	protein-coding
mm_113297.1	chr13	30660045	30660116	+	1	NA	promoter-TSS (NM_134068)	promoter-TSS (NM_134068)	21	NM_134068	105352	Mm.289646	NM_134068	ENSMUSG00000069255	Dusp22	JKAP|JSP1|LMW-DSP2|MKPX	dual specificity phosphatase 22	protein-coding
mm_55149.1	chr6	51466930	51466945	-	1	NA	exon (NM_182650, exon 3 of 10)	exon (NM_182650, exon 3 of 10)	2957	NM_182650	53379	Mm.155896	NM_016806	ENSMUSG00000004980	Hnrnpa2b1	9130414A06Rik|Hnrpa2|Hnrpa2b1|hnrnp-A	heterogeneous nuclear ribonucleoprotein A2/B1	protein-coding
mm_133202.1	chr16	73072370	73072382	+	1	NA	Intergenic	MTC-int|LTR|ERVL-MaLR	409227	NM_019413	19876	Mm.310772	NM_019413	ENSMUSG00000022883	Robo1	AW494633|AW742721|DUTT1|Gm310	roundabout guidance receptor 1	protein-coding
mm_166710.1	chr6	116650633	116650641	+	1	NA	promoter-TSS (NM_001166580)	promoter-TSS (NM_001166580)	-47	NM_145980	213393	Mm.38231	NM_145980	ENSMUSG00000048489	8430408G22Rik	Depp|Fseg	RIKEN cDNA 8430408G22 gene	protein-coding
mm_125373.1	chr15	39964106	39964162	+	1	NA	non-coding (NR_045719, exon 2 of 3)	non-coding (NR_045719, exon 2 of 3)	1485	NR_045719	105976	Mm.394885	NR_045719		AU022793	-	expressed sequence AU022793	ncRNA
mm_157509.1	chrX	49273656	49273667	-	1	NA	intron (NM_001271450, intron 2 of 15)	intron (NM_001271450, intron 2 of 15)	14581	NM_001271449	209224	Mm.327730	NM_145951	ENSMUSG00000031109	Enox2	APK1|Cova1|tNOX	ecto-NOX disulfide-thiol exchanger 2	protein-coding
mm_168150.1	chr10	39198688	39198691	+	1	NA	Intergenic	Intergenic	-34895	NM_001127376	327743	Mm.208111	NM_001127376	ENSMUSG00000062074	Wisp3	CCN6|ENSMUSG00000062074|Gm735|WISP-3	WNT1 inducible signaling pathway protein 3	protein-coding
mm_150851.1	chr19	44992326	44992344	+	1	NA	5' UTR (NM_011976, exon 2 of 15)	5' UTR (NM_011976, exon 2 of 15)	2991	NM_011976	26456	Mm.34404	NM_011976	ENSMUSG00000025207	Sema4g	AI507908|AW554132	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4G	protein-coding
mm_1086.1	chr1	59551029	59551040	+	1	NA	intron (NM_001013771, intron 5 of 19)	intron (NM_001013771, intron 5 of 19)	34770	NM_001013771	381260	Mm.486706	NM_001013771	ENSMUSG00000047361	Gm973	AW554518	predicted gene 973	protein-coding
mm_38047.1	chr4	133968115	133968126	-	1	NA	promoter-TSS (NM_016957)	promoter-TSS (NM_016957)	-129	NM_016957	15331	Mm.319660	NM_016957	ENSMUSG00000003038	Hmgn2	HMG-17|Hmg17	high mobility group nucleosomal binding domain 2	protein-coding
mm_124053.1	chr14	77874867	77874877	-	1	NA	promoter-TSS (NM_025384)	promoter-TSS (NM_025384)	45	NM_025384	66148	Mm.248046	NM_025384	ENSMUSG00000022013	Dnajc15	1110003P16Rik|Dnajd1	DnaJ heat shock protein family (Hsp40) member C15	protein-coding
mm_32023.1	chr4	95093526	95093536	+	1	NA	Intergenic	Intergenic	-41309	NM_010591	16476	Mm.275071	NM_010591	ENSMUSG00000052684	Jun	AP-1|Junc|c-jun	jun proto-oncogene	protein-coding
mm_11677.1	chr2	35444701	35444721	+	1	NA	intron (NM_001308300, intron 1 of 6)	intron (NM_001308300, intron 1 of 6)	16738	NM_001308299	14594	Mm.281124	NM_010283	ENSMUSG00000035778	Ggta1	AW108479|GALT|Gal|Ggta|Ggta-1|alpha Gal|alpha3GalT	glycoprotein galactosyltransferase alpha 1, 3	protein-coding
mm_23952.1	chr3	84905897	84905908	+	1	NA	intron (NM_001177773, intron 4 of 13)	intron (NM_001177773, intron 4 of 13)	41757	NM_001177774	50754	Mm.196475	NM_080428	ENSMUSG00000028086	Fbxw7	1110001A17Rik|AGO|Cdc4|Fbw7|Fbwd6|Fbx30|Fbxo30|Fbxw6|SEL-10	F-box and WD-40 domain protein 7	protein-coding
mm_104731.1	chr11	98326965	98327011	-	1	NA	3' UTR (NM_010895, exon 2 of 2)	3' UTR (NM_010895, exon 2 of 2)	2657	NM_010895	18013	Mm.4814	NM_010895	ENSMUSG00000038255	Neurod2	Ndrf|bHLHa1	neurogenic differentiation 2	protein-coding
mm_171308.1	chr3	94178188	94178195	-	1	NA	promoter-TSS (NM_001146107)	promoter-TSS (NM_001146107)	2	NM_001146107	100043188	Mm.304029	NM_001146107	ENSMUSG00000074424	Gm10696	ENSMUSG00000074424	predicted gene 10696	protein-coding
mm_36420.1	chr4	81348723	81348736	-	1	NA	exon (NM_001305286, exon 21 of 46)	exon (NM_001305286, exon 21 of 46)	94086	NM_010820	17475	Mm.153039	NM_010820	ENSMUSG00000028402	Mpdz	AI225843|B930003D11Rik|MUPP1	multiple PDZ domain protein	protein-coding
mm_70794.1	chr8	22624020	22624023	+	1	NA	promoter-TSS (NM_145592)	promoter-TSS (NM_145592)	-22	NM_145592	234130	Mm.157322	NM_145592	ENSMUSG00000031535	Dkk4	Dkk-4	dickkopf WNT signaling pathway inhibitor 4	protein-coding
mm_50997.1	chr6	63336735	63336737	+	1	NA	intron (NM_008167, intron 1 of 15)	L1MA5|LINE|L1	79879	NM_008167	14804	Mm.439651	NM_008167	ENSMUSG00000071424	Grid2	B230104L07Rik|GluD2|GluRdelta2|Lc|Lc<J>|MMS10-AC|Ms10ac|cpr|ho|nmf408|tpr	glutamate receptor, ionotropic, delta 2	protein-coding
mm_125160.1	chr15	31225118	31225138	+	1	NA	intron (NM_146057, intron 1 of 3)	intron (NM_146057, intron 1 of 3)	743	NM_146057	223453	Mm.222867	NM_146057	ENSMUSG00000039168	Dap	4921531N22Rik|AI789753|AU040360	death-associated protein	protein-coding
mm_18375.1	chr2	59953741	59953751	-	1	NA	intron (NM_001001182, intron 12 of 35)	intron (NM_001001182, intron 12 of 35)	-71140	NM_028118	72137	Mm.288734	NM_028118	ENSMUSG00000026988	Wdsub1	1700048E19Rik|2610014F08Rik	WD repeat, SAM and U-box domain containing 1	protein-coding
mm_30741.1	chr4	14433843	14433848	+	1	NA	Intergenic	Intergenic	-142536	NR_131155	100040030	Mm.366499	NR_131155		Gm2560	-	predicted gene 2560	ncRNA
mm_113576.1	chr13	40717138	40717147	+	1	NA	exon (NM_011547, exon 7 of 7)	exon (NM_011547, exon 7 of 7)	-10666	NR_125899	102633805		NR_125899	ENSMUSG00000097752	Gm26688	Tfap2a-as1	predicted gene, 26688	ncRNA
mm_107287.1	chr12	29840208	29840250	+	1	NA	intron (NM_001093778, intron 13 of 24)	intron (NM_001093778, intron 13 of 24)	-97807	NM_181395	69675	Mm.251774	NM_181395	ENSMUSG00000020674	Pxdn	2310075M15Rik|C85409|E330004E07|VPO1|mKIAA0230	peroxidasin	protein-coding
mm_68913.1	chr7	126459718	126459729	-	1	NA	intron (NM_007504, intron 4 of 22)	intron (NM_007504, intron 4 of 22)	3350	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_115290.1	chr13	111977961	111977990	+	1	NA	Intergenic	CpG	110039	NR_130345	102636620	Mm.402328	NR_130345	ENSMUSG00000086111	Gm15326	OTTMUSG00000020187	predicted gene 15326	ncRNA
mm_164388.1	chr16	32487597	32487602	-	1	NA	5' UTR (NM_145932, exon 1 of 9)	5' UTR (NM_145932, exon 1 of 9)	280	NM_145932	106407	Mm.476915	NM_145932	ENSMUSG00000035699	Slc51a	AV001382|AW261577|D630035O19Rik|OSTalpha|Osta	solute carrier family 51, alpha subunit	protein-coding
mm_66911.1	chr7	60003165	60003186	-	1	NA	intron (NM_001082962, intron 2 of 10)	intron (NM_001082962, intron 2 of 10)	1981	NM_013670	20646	Mm.274995	NM_013670	ENSMUSG00000102252	Snrpn	2410045I01Rik|HCERN3|Peg4|Pwcr1|SMN	small nuclear ribonucleoprotein N	protein-coding
mm_59717.1	chr7	28767234	28767244	+	1	NA	promoter-TSS (NM_010908)	promoter-TSS (NM_010908)	487	NM_001122766	64383	Mm.272443	NM_022432	ENSMUSG00000015149	Sirt2	5730427M03Rik|SIR2L2|Sir2l	sirtuin 2	protein-coding
mm_92094.1	chr10	62865439	62865471	-	1	NA	intron (NM_027384, intron 1 of 10)	intron (NM_027384, intron 1 of 10)	14559	NM_027384	52463	Mm.17774	NM_027384	ENSMUSG00000047146	Tet1	2510010B09Rik|AA517754|BB001228|Cxxc6|D10Ertd17e|LCX|mKIAA1676	tet methylcytosine dioxygenase 1	protein-coding
mm_90468.1	chr10	127801146	127801189	+	1	NA	promoter-TSS (NM_009040)	promoter-TSS (NM_009040)	14	NM_009040	19683	Mm.100276	NM_009040	ENSMUSG00000069456	Rdh16	CRAD|CRAD1|Rdh6	retinol dehydrogenase 16	protein-coding
mm_95476.1	chr11	51059232	51059307	+	1	NA	promoter-TSS (NM_001347495)	promoter-TSS (NM_001347495)	12	NM_001347495	21408	Mm.4792	NM_009329	ENSMUSG00000020364	Zfp354a	AW488485|Tcf17|Znf354a|kid1	zinc finger protein 354A	protein-coding
mm_64344.1	chr7	142380832	142380846	+	1	NA	exon (NM_009983, exon 5 of 9)	exon (NM_009983, exon 5 of 9)	7031	NM_009983	13033	Mm.231395	NM_009983	ENSMUSG00000007891	Ctsd	CD|CatD	cathepsin D	protein-coding
mm_149515.1	chr19	12435196	12435215	+	1	NA	Intergenic	Intergenic	7300	NM_019540	56093	Mm.285849	NM_019540	ENSMUSG00000040065	Pfpl	Epcs5|Epcs50	pore forming protein-like	protein-coding
mm_170466.1	chr18	9707592	9707597	+	1	NA	promoter-TSS (NM_130449)	promoter-TSS (NM_130449)	-54	NM_130449	140792	Mm.218571	NM_130449	ENSMUSG00000036103	Colec12	CL-P1|SRCL|Scara4	collectin sub-family member 12	protein-coding
mm_141053.1	chr17	25727365	25727426	-	1	NA	promoter-TSS (NM_145409)	promoter-TSS (NM_145409)	20	NM_145409	214901	Mm.102540	NM_145409	ENSMUSG00000019214	Chtf18	6030457M03Rik|CTF18|Chl12	CTF18, chromosome transmission fidelity factor 18	protein-coding
mm_89275.1	chr10	87861078	87861109	+	1	NA	promoter-TSS (NM_001111276)	promoter-TSS (NM_001111276)	-18	NM_001111274	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_172070.1	chr6	136875760	136875762	-	1	NA	promoter-TSS (NM_008597)	promoter-TSS (NM_008597)	62	NM_008597	17313	Mm.243085	NM_008597	ENSMUSG00000030218	Mgp	Mglap	matrix Gla protein	protein-coding
mm_109088.1	chr12	104414081	104414101	+	1	NA	3' UTR (NM_009252, exon 5 of 5)	3' UTR (NM_009252, exon 5 of 5)	7383	NM_009252	20716	Mm.482074	NM_009252	ENSMUSG00000021091	Serpina3n	Spi2-2|Spi2.2|Spi2/eb.4	serine (or cysteine) peptidase inhibitor, clade A, member 3N	protein-coding
mm_50860.1	chr6	55336083	55336094	+	1	NA	promoter-TSS (NM_007472)	promoter-TSS (NM_007472)	-211	NM_007472	11826	Mm.18625	NM_007472	ENSMUSG00000004655	Aqp1	CHIP28	aquaporin 1	protein-coding
mm_102346.1	chr11	58139521	58139534	-	1	NA	exon (NM_001166670, exon 17 of 28)	exon (NM_001166670, exon 17 of 28)	29012	NM_172558	216766	Mm.275349	NM_172558	ENSMUSG00000037275	Gemin5	AA407055|AA407208|AI451603|BB194447|C330013N08	gem (nuclear organelle) associated protein 5	protein-coding
mm_155699.1	chrX	94636067	94636086	+	1	NA	promoter-TSS (NM_008179)	promoter-TSS (NM_008179)	7	NM_008179	14853	Mm.20826	NM_008179	ENSMUSG00000071723	Gspt2	-	G1 to S phase transition 2	protein-coding
mm_81695.1	chr9	111182321	111182336	+	1	NA	intron (NM_001164838, intron 5 of 14)	intron (NM_001164838, intron 5 of 14)	64217	NM_001164838	71268	Mm.302287	NM_027742	ENSMUSG00000032497	Lrrfip2	5133400F20Rik|AI850587	leucine rich repeat (in FLII) interacting protein 2	protein-coding
mm_57536.1	chr6	126641717	126641730	-	1	NA	3' UTR (NM_010595, exon 2 of 2)	3' UTR (NM_010595, exon 2 of 2)	4078	NM_010595	16485	Mm.40424	NM_010595	ENSMUSG00000047976	Kcna1	AI840627|Kca1-1|Kv1.1|MBK1|Mk-1|Shak|mceph	potassium voltage-gated channel, shaker-related subfamily, member 1	protein-coding
mm_158447.1	chrX	140543070	140543080	-	1	NA	promoter-TSS (NR_122039)	promoter-TSS (NR_122039)	112	NM_010286	14605	Mm.22216	NM_010286	ENSMUSG00000031431	Tsc22d3	DIP|Dsip1|Gilz|TSC-22R|Tilz3	TSC22 domain family, member 3	protein-coding
mm_65887.1	chr7	29906525	29906567	-	1	NA	promoter-TSS (NM_001285797)	promoter-TSS (NM_001285797)	-14	NM_001285798	22689	Mm.86747	NM_011754	ENSMUSG00000062040	Zfp27	Zfp-27|mkr-4|mszf76	zinc finger protein 27	protein-coding
mm_120136.1	chr14	60277148	60277165	+	1	NA	exon (NM_144843, exon 2 of 14)	exon (NM_144843, exon 2 of 14)	11951	NM_144843	219135	Mm.247007	NM_144843	ENSMUSG00000021987	Mtmr6	4022440C11Rik|AI428804|AU041072	myotubularin related protein 6	protein-coding
mm_147809.1	chr18	61707584	61707658	-	1	NA	promoter-TSS (NM_172832)	promoter-TSS (NM_172832)	14	NM_172832	240334	Mm.234457	NM_172832	ENSMUSG00000024579	Pcyox1l	BC060677|C630049M13	prenylcysteine oxidase 1 like	protein-coding
mm_87156.1	chr10	36507014	36507024	+	1	NA	5' UTR (NM_001253356, exon 1 of 5)	5' UTR (NM_001253356, exon 1 of 5)	212	NM_001253356	319415	Mm.332442	NM_001081208	ENSMUSG00000044499	Hs3st5	D930005L05Rik|Gm1151|Hs3ost5	heparan sulfate (glucosamine) 3-O-sulfotransferase 5	protein-coding
mm_117312.1	chr13	67526137	67526179	-	1	NA	promoter-TSS (NM_133228)	promoter-TSS (NM_133228)	73	NM_133228	170763	Mm.491205	NM_133228	ENSMUSG00000097333	Zfp87	2210039O17Rik|4631412O18Rik|KRAB4|Mzf22|Zfp72	zinc finger protein 87	protein-coding
mm_121173.1	chr14	103033754	103033762	+	1	NA	promoter-TSS (NR_045657)	promoter-TSS (NR_045657)	45	NR_045657	71264	Mm.399572	NR_045657		4933432I03Rik	-	RIKEN cDNA 4933432I03 gene	ncRNA
mm_106146.1	chr11	116549369	116549409	-	1	NA	intron (NM_173755, intron 1 of 17)	intron (NM_173755, intron 1 of 17)	14649	NM_011451	20698	Mm.20944	NM_011451	ENSMUSG00000061878	Sphk1	1110006G24Rik|Sk1|Spk1	sphingosine kinase 1	protein-coding
mm_12147.1	chr2	61804888	61804906	+	1	NA	exon (NM_009322, exon 1 of 6)	exon (NM_009322, exon 1 of 6)	444	NM_009322	21375	Mm.308525	NM_009322	ENSMUSG00000035033	Tbr1	-	T-box brain gene 1	protein-coding
mm_63070.1	chr7	122159423	122159501	+	1	NA	promoter-TSS (NM_011121)	promoter-TSS (NM_011121)	27	NM_011121	18817	Mm.16525	NM_011121	ENSMUSG00000030867	Plk1	Plk|STPK13	polo-like kinase 1	protein-coding
mm_96431.1	chr11	67292930	67292946	+	1	NA	exon (NM_177369, exon 21 of 40)	exon (NM_177369, exon 21 of 40)	15814	NM_177369	17885	Mm.340163	NM_177369	ENSMUSG00000055775	Myh8	4832426G23Rik|AI327267|MHCp|MyHC-pn|Myhs-p|Myhsp	myosin, heavy polypeptide 8, skeletal muscle, perinatal	protein-coding
mm_132287.1	chr16	33179127	33179143	+	1	NA	Intergenic	Intergenic	-5936	NM_176840	106326	Mm.486405	NM_176840	ENSMUSG00000022807	Osbpl11	9430097N02Rik|AI132306|AU019795|ORP-11	oxysterol binding protein-like 11	protein-coding
mm_158047.1	chrX	99030581	99030589	-	1	NA	Intergenic	Intergenic	-11996	NM_199018	236920	Mm.236928	NM_199018	ENSMUSG00000031216	Stard8	Dlc3|mKIAA0189	START domain containing 8	protein-coding
mm_76511.1	chr8	86888080	86888096	-	1	NA	Intergenic	Intergenic	-2830	NM_030563	80750	Mm.25117	NM_030563	ENSMUSG00000031652	N4bp1	AI481586|C81621	NEDD4 binding protein 1	protein-coding
mm_142119.1	chr17	35866949	35866960	-	1	NA	5' UTR (NM_175242, exon 1 of 3)	5' UTR (NM_175242, exon 1 of 3)	339	NM_175242	76448	Mm.359982	NM_175242	ENSMUSG00000034595	Ppp1r18	2310014H01Rik|AA407849|AI450394	protein phosphatase 1, regulatory subunit 18	protein-coding
mm_79841.1	chr9	64811314	64811337	+	1	NA	intron (NM_001162917, intron 1 of 34)	CpG	314	NM_001162917	102442	Mm.222473	NM_176935	ENSMUSG00000053641	Dennd4a	AI115600|AI851943|F730015K02Rik	DENN/MADD domain containing 4A	protein-coding
mm_55231.1	chr6	52240670	52240683	-	1	NA	5' UTR (NM_001122950, exon 1 of 2)	5' UTR (NM_001122950, exon 1 of 2)	178	NM_001122950	15395	Mm.5	NM_008263	ENSMUSG00000000938	Hoxa10	Hox-1.8|Hoxa-10	homeobox A10	protein-coding
mm_102325.1	chr11	57657806	57657839	-	1	NA	intron (NM_134189, intron 1 of 11)	intron (NM_134189, intron 1 of 11)	12380	NM_134189	171212	Mm.271670	NM_134189	ENSMUSG00000020520	Galnt10	AU018154|C330012K04Rik|GalNAc-T10|GalNAc-T9|Galnt9|ppGaNTase	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 10	protein-coding
mm_149841.1	chr19	25027991	25028003	+	1	NA	intron (NM_028785, intron 1 of 47)	ORR1E|LTR|ERVL-MaLR	28468	NM_028785	76088	Mm.102485	NM_028785	ENSMUSG00000052085	Dock8	1200017A24Rik|5830472H07Rik|A130095G14Rik|AI461977	dedicator of cytokinesis 8	protein-coding
mm_6017.1	chr1	59042565	59042569	-	1	NA	Intergenic	Intergenic	52333	NM_175200	73463	Mm.252811	NM_175200	ENSMUSG00000072295	Als2cr11	1700052H20Rik|4930408G06Rik	amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 11 (human)	protein-coding
mm_156378.1	chrX	139672031	139672051	+	1	NA	3' UTR (NM_023270, exon 7 of 7)	3' UTR (NM_023270, exon 7 of 7)	-12955	NM_001081499	245638	Mm.275869	NM_001081499	ENSMUSG00000042473	Tbc1d8b	4921505D17Rik|9030605E16Rik	TBC1 domain family, member 8B	protein-coding
mm_161954.1	chr19	6245506	6245506	+	1	NA	exon (NM_194348, exon 5 of 40)	exon (NM_194348, exon 5 of 40)	3838	NM_194348	329015	Mm.277384	NM_194348	ENSMUSG00000024773	Atg2a	1810013C15Rik|A830054M12|BC023754|mKIAA0404	autophagy related 2A	protein-coding
mm_125593.1	chr15	59648504	59648537	+	1	NA	promoter-TSS (NM_144549)	promoter-TSS (NM_144549)	-134	NM_144549	211770	Mm.40298	NM_144549	ENSMUSG00000032501	Trib1	A530090O15Rik|TRB-1|Trb1	tribbles pseudokinase 1	protein-coding
mm_24190.1	chr3	88607474	88607479	+	1	NA	Intergenic	Intergenic	-8731	NM_001198911	16800	Mm.239329	NM_008487	ENSMUSG00000028059	Arhgef2	AA408978|GEF|GEF-H1|GEFH1|LFP40|Lbcl1|Lfc|P40|mKIAA0651	rho/rac guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_6081.1	chr1	62798603	62798627	-	1	NA	intron (NM_010939, intron 15 of 15)	intron (NM_010939, intron 15 of 15)	-3883	NR_040601	74992	Mm.401979	NR_040601		4930487H11Rik	-	RIKEN cDNA 4930487H11 gene	ncRNA
mm_60526.1	chr7	44480118	44480128	+	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	-4394	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_88874.1	chr10	81070236	81070246	+	1	NA	5' UTR (NM_022653, exon 1 of 13)	5' UTR (NM_022653, exon 1 of 13)	158	NM_022653	50492	Mm.26995	NM_022653	ENSMUSG00000004929	Thop1	AI131655|AI327041|EP24.15	thimet oligopeptidase 1	protein-coding
mm_169607.1	chr15	36793568	36793574	-	1	NA	5' UTR (NM_011740, exon 2 of 7)	5' UTR (NM_011740, exon 2 of 7)	967	NM_011740	22631	Mm.3360	NM_011740	ENSMUSG00000022285	Ywhaz	1110013I11Rik|14-3-3zeta|AI596267|AL022924|AU020854	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide	protein-coding
mm_148986.1	chr19	8594052	8594069	+	1	NA	exon (NM_001164634, exon 2 of 11)	exon (NM_001164634, exon 2 of 11)	878	NM_001164635	19879	Mm.285294	NM_031194	ENSMUSG00000063796	Slc22a8	Oat3|Roct	solute carrier family 22 (organic anion transporter), member 8	protein-coding
mm_8695.1	chr1	157412259	157412302	-	1	NA	promoter-TSS (NR_027984)	promoter-TSS (NR_027984)	-72	NR_027984	69953	Mm.286863	NM_027274	ENSMUSG00000049881	2810025M15Rik	AI429618	RIKEN cDNA 2810025M15 gene	ncRNA
mm_21464.1	chr2	160912293	160912344	-	1	NA	promoter-TSS (NM_001291145)	promoter-TSS (NM_001291145)	21	NM_001291145	280635	Mm.330747	NM_182840	ENSMUSG00000050700	Emilin3	1110013O17Rik|EMILIN-3|EMILIN-5|EMILIN-T|Emilin5	elastin microfibril interfacer 3	protein-coding
mm_3487.1	chr1	150105806	150105815	+	1	NA	3' UTR (NM_011198, exon 10 of 10)	3' UTR (NM_011198, exon 10 of 10)	5779	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_152912.1	chr19	27262318	27262328	-	1	NA	Intergenic	Intergenic	45303	NM_001161420	22359	Mm.4141	NM_013703	ENSMUSG00000024924	Vldlr	AA408956|AI451093|AW047288	very low density lipoprotein receptor	protein-coding
mm_122986.1	chr14	54984801	54984817	-	1	NA	intron (NM_080728, intron 22 of 40)	intron (NM_080728, intron 22 of 40)	-9033	NR_030607	100124433		NR_030607	ENSMUSG00000077928	Mir208b	Mirn208b|mir-208b	microRNA 208b	ncRNA
mm_111871.1	chr12	108003202	108003212	-	1	NA	5' UTR (NM_021399, exon 1 of 3)	5' UTR (NM_021399, exon 1 of 3)	207	NM_001079883	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_58423.1	chr7	3293140	3293181	+	1	NA	5' UTR (NM_001093766, exon 1 of 2)	5' UTR (NM_001093766, exon 1 of 2)	132	NM_001093766	50918	Mm.29874	NM_016969	ENSMUSG00000068566	Myadm	D7Wsu62e	myeloid-associated differentiation marker	protein-coding
mm_166751.1	chr6	125337860	125337868	+	1	NA	exon (NM_011324, exon 4 of 12)	exon (NM_011324, exon 4 of 12)	-11859	NM_011609	21937	Mm.1258	NM_011609	ENSMUSG00000030341	Tnfrsf1a	CD120a|FPF|TNF-R|TNF-R-I|TNF-R1|TNF-R55|TNF-alphaR1|TNFAR|TNFR60|TNFRI|TNFRp55|TNFalpha-R1|Tnfr-2|Tnfr1|p55|p55-R	tumor necrosis factor receptor superfamily, member 1a	protein-coding
mm_52251.1	chr6	106791799	106791803	+	1	NA	intron (NM_175357, intron 4 of 10)	intron (NM_175357, intron 4 of 10)	8286	NM_021449	58799	Mm.290085	NM_021449	ENSMUSG00000005362	Crbn	2610203G15Rik|2900045O07Rik|AF229032|AW108261|piL	cereblon	protein-coding
mm_26111.1	chr3	137623770	137623789	+	1	NA	5' UTR (NM_030143, exon 1 of 3)	5' UTR (NM_030143, exon 1 of 3)	107	NM_030143	73284	Mm.250841	NM_030143	ENSMUSG00000046818	Ddit4l	1700037B15Rik|1700108M02Rik|REDD2|RTP801L|Smhs1	DNA-damage-inducible transcript 4-like	protein-coding
mm_4522.1	chr1	175632045	175632057	+	1	NA	promoter-TSS (NM_133809)	promoter-TSS (NM_133809)	-142	NM_133809	98256	Mm.27217	NM_133809	ENSMUSG00000039783	Kmo	AI046660	kynurenine 3-monooxygenase (kynurenine 3-hydroxylase)	protein-coding
mm_38526.1	chr4	141445430	141445440	-	1	NA	intron (NM_009541, intron 1 of 15)	MIRb|SINE|MIR	762	NM_009541	22642	Mm.389590	NM_009541	ENSMUSG00000006215	Zbtb17	AA589413|Lp-1|Miz1|Zfp100|mZ13	zinc finger and BTB domain containing 17	protein-coding
mm_123404.1	chr14	63543686	63543747	-	1	NA	5' UTR (NM_177594, exon 1 of 10)	5' UTR (NM_177594, exon 1 of 10)	237	NM_177594	210376	Mm.441613	NM_177594	ENSMUSG00000035078	Mtmr9	9430075G12Rik|AA516943|AF073881|LIP-STYX|MTMR8|mMTMH3	myotubularin related protein 9	protein-coding
mm_171007.1	chr2	81990336	81990346	+	1	NA	Intergenic	MMVL30-int|LTR|ERV1	-63317	NM_175513	241514	Mm.119383	NM_175513	ENSMUSG00000070866	Zfp804a	C630007C17Rik|Znf804a	zinc finger protein 804A	protein-coding
mm_48223.1	chr5	137644706	137644711	-	1	NA	exon (NM_010571, exon 2 of 2)	exon (NM_010571, exon 2 of 2)	1006	NM_010571	16369	Mm.24486	NM_010571	ENSMUSG00000047182	Irs3	AA408304	insulin receptor substrate 3	protein-coding
mm_125426.1	chr15	43184428	43184435	+	1	NA	Intergenic	Tigger17a|DNA|TcMar-Tigger	-13613	NM_172815	239405	Mm.193274	NM_172815	ENSMUSG00000051920	Rspo2	2610028F08Rik|AA673245|D430027K22|ftls	R-spondin 2	protein-coding
mm_166865.1	chr7	24530936	24530942	+	1	NA	intron (NM_153134, intron 1 of 2)	intron (NM_153134, intron 1 of 2)	291	NM_153134	210146	Mm.41108	NM_153134	ENSMUSG00000041037	Irgq	AF322649|FKSG27|Irgq1	immunity-related GTPase family, Q	protein-coding
mm_147778.1	chr18	61536571	61536583	-	1	NA	promoter-TSS (NM_177828)	promoter-TSS (NM_177828)	-41	NM_177828	328967	Mm.488098	NM_177828	ENSMUSG00000045094	Arhgef37	4933429F08Rik	Rho guanine nucleotide exchange factor (GEF) 37	protein-coding
mm_122749.1	chr14	54176658	54176662	-	1	NA	Intergenic	Intergenic	77269	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_57141.1	chr6	122610013	122610039	-	1	NA	promoter-TSS (NM_008108)	promoter-TSS (NM_008108)	61	NM_008108	14562	Mm.299742	NM_008108	ENSMUSG00000030117	Gdf3	C78318|Gdf-3|Vgr-2|Vgr2|ecat9	growth differentiation factor 3	protein-coding
mm_90830.1	chr10	7956453	7956488	-	1	NA	promoter-TSS (NM_138667)	promoter-TSS (NM_138667)	-347	NM_138667	68652	Mm.193041	NM_138667	ENSMUSG00000015755	Tab2	1110030N06Rik|A530078N03Rik|Map3k7ip2|mKIAA0733	TGF-beta activated kinase 1/MAP3K7 binding protein 2	protein-coding
mm_151916.1	chr19	5799763	5799774	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	2904	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_19334.1	chr2	90580316	90580326	-	1	NA	exon (NM_008982, exon 1 of 24)	exon (NM_008982, exon 1 of 24)	326	NM_008982	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_167110.1	chr7	114152269	114152271	+	1	NA	Intergenic	LFSINE_Vert|SINE|tRNA	-34489	NM_025846	66922	Mm.276572	NM_025846	ENSMUSG00000055723	Rras2	2610016H24Rik|C86394|TC21	related RAS viral (r-ras) oncogene 2	protein-coding
mm_119883.1	chr14	54894579	54894627	+	1	NA	intron (NM_019402, intron 1 of 6)	CpG	460	NM_019402	54196	Mm.7723	NM_019402	ENSMUSG00000022194	Pabpn1	PAB2|Pabp3|mPABII	poly(A) binding protein, nuclear 1	protein-coding
mm_35756.1	chr4	45816313	45816318	-	1	NA	exon (NM_018741, exon 2 of 5)	exon (NM_018741, exon 2 of 5)	10512	NM_018741	75426	Mm.3919	NM_018741	ENSMUSG00000035551	Igfbpl1	2810011G06Rik|2810453O06Rik|IGFBPL	insulin-like growth factor binding protein-like 1	protein-coding
mm_94481.1	chr11	6564349	6564361	+	1	NA	intron (NM_001190344, intron 2 of 9)	intron (NM_001190344, intron 2 of 9)	4172	NM_001190344	216527	Mm.221271	NM_146014	ENSMUSG00000000378	Ccm2	BC029157	cerebral cavernous malformation 2	protein-coding
mm_70175.1	chr7	143649615	143649671	-	1	NA	promoter-TSS (NM_001311145)	promoter-TSS (NM_001311145)	21	NM_001311145	79202	Mm.261384	NM_023680	ENSMUSG00000010751	Tnfrsf22	2810028K06Rik|C130035G06Rik|SOBa|Tnfrh2|Tnfrsf1al2|mDcTrailr2	tumor necrosis factor receptor superfamily, member 22	protein-coding
mm_116849.1	chr13	54759306	54759313	-	1	NA	3' UTR (NM_033610, exon 6 of 6)	3' UTR (NM_033610, exon 6 of 6)	7131	NM_033610	104069	Mm.200843	NM_033610	ENSMUSG00000034891	Sncb	AI838531|betaSYN	synuclein, beta	protein-coding
mm_67946.1	chr7	100467150	100467171	-	1	NA	intron (NM_001017985, intron 32 of 32)	intron (NM_001017985, intron 32 of 32)	-5831	NM_009464	22229	Mm.6254	NM_009464	ENSMUSG00000032942	Ucp3	AI645527|Slc25a9|UCP-3	uncoupling protein 3 (mitochondrial, proton carrier)	protein-coding
mm_92073.1	chr10	62616414	62616416	-	1	NA	exon (NM_053183, exon 15 of 15)	exon (NM_053183, exon 15 of 15)	-14117	NM_019553	56200	Mm.413275	NM_019553	ENSMUSG00000020075	Ddx21	AI255159|AL022742|D10Ertd645e|D10Wsu42e	DEAD (Asp-Glu-Ala-Asp) box polypeptide 21	protein-coding
mm_41549.1	chr5	92925401	92925448	+	1	NA	intron (NM_001077595, intron 2 of 9)	intron (NM_001077595, intron 2 of 9)	27431	NM_001077596	27428	Mm.46014	NM_015756	ENSMUSG00000029381	Shroom3	AL022960|D5Ertd287e|Shrm|Shrm3	shroom family member 3	protein-coding
mm_129191.1	chr15	76351009	76351131	-	1	NA	promoter-TSS (NM_026859)	promoter-TSS (NM_026859)	40	NM_025340	106025	Mm.41463	NM_025340	ENSMUSG00000022552	Sharpin	0610041B22Rik|AW121341|RBCKL1|SIPL1|cpdm	SHANK-associated RH domain interacting protein	protein-coding
mm_99037.1	chr11	98960604	98960620	+	1	NA	5' UTR (NM_001176528, exon 1 of 8)	5' UTR (NM_001176528, exon 1 of 8)	141	NM_001176528	19401	Mm.439744	NM_009024	ENSMUSG00000037992	Rara	Nr1b1|RAR|RARalpha1	retinoic acid receptor, alpha	protein-coding
mm_135549.1	chr16	49839827	49839848	-	1	NA	Intergenic	Intergenic	-15817	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_88986.1	chr10	81564659	81564690	+	1	NA	exon (NM_010347, exon 4 of 7)	exon (NM_010347, exon 4 of 7)	5230	NM_001276288	14797	Mm.180013	NM_010347	ENSMUSG00000054452	Aes	AL024115|Esp1|Grg|Grg-5|Grg5|Tle5	amino-terminal enhancer of split	protein-coding
mm_36294.1	chr4	66159779	66159786	-	1	NA	intron (NM_207109, intron 3 of 22)	intron (NM_207109, intron 3 of 22)	244701	NM_019514	56079	Mm.445312	NM_019514	ENSMUSG00000028373	Astn2	1d8|Astnl|bM452J22.1	astrotactin 2	protein-coding
mm_45762.1	chr5	86906349	86906359	-	1	NA	exon (NM_153598, exon 1 of 6)	exon (NM_153598, exon 1 of 6)	583	NM_153598	100727	Mm.281844	NM_153598	ENSMUSG00000029260	Ugt2b34	AI788959	UDP glucuronosyltransferase 2 family, polypeptide B34	protein-coding
mm_163692.1	chr13	99434213	99434264	+	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-21412	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_158228.1	chrX	106219683	106219693	-	1	NA	exon (NM_001167988, exon 2 of 8)	exon (NM_001167988, exon 2 of 8)	154	NM_001001176	407786	Mm.19440	NM_001001176	ENSMUSG00000047242	Taf9b	BC066223|Taf9l	TATA-box binding protein associated factor 9B	protein-coding
mm_29615.1	chr3	121283018	121283030	-	1	NA	Intergenic	Intergenic	-8793	NM_024178	66789	Mm.269881	NM_024178	ENSMUSG00000039887	Alg14	5430428G01Rik|AI854024	asparagine-linked glycosylation 14	protein-coding
mm_62043.1	chr7	92236169	92236173	+	1	NA	intron (NM_001243047, intron 1 of 10)	intron (NM_001243047, intron 1 of 10)	1201	NM_001243047	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_52570.1	chr6	116337901	116337911	+	1	NA	promoter-TSS (NM_027920)	promoter-TSS (NM_027920)	-116	NM_001302385	71779	Mm.27064	NM_027920	ENSMUSG00000025702	March8	1300017E09Rik|MARCH-VIII|Mir	membrane-associated ring finger (C3HC4) 8	protein-coding
mm_126490.1	chr15	81626433	81626448	+	1	NA	exon (NM_177821, exon 13 of 31)	exon (NM_177821, exon 13 of 31)	-37449	NM_001289712	214669	Mm.280768	NM_145993	ENSMUSG00000022394	L3mbtl2	4732493N06Rik|M4mbt	l(3)mbt-like 2 (Drosophila)	protein-coding
mm_128595.1	chr15	58135002	58135012	-	1	NA	promoter-TSS (NM_027435)	promoter-TSS (NM_027435)	75	NM_027435	70472	Mm.221758	NM_027435	ENSMUSG00000022360	Atad2	2610509G12Rik	ATPase family, AAA domain containing 2	protein-coding
mm_145446.1	chr18	60211971	60212033	+	1	NA	promoter-TSS (NM_001033767)	promoter-TSS (NM_001033767)	-75	NM_001033767	240327	Mm.357104	NM_001033767	ENSMUSG00000073555	Gm4951	EG240327|Ifgga2	predicted gene 4951	protein-coding
mm_134409.1	chr16	17673313	17673335	-	1	NA	exon (NM_001040683, exon 7 of 17)	exon (NM_001040683, exon 7 of 17)	26854	NM_001166164	72315	Mm.297777	NM_001166164	ENSMUSG00000041617	Ccdc74a	2310015A05Rik	coiled-coil domain containing 74A	protein-coding
mm_94292.1	chr11	4048622	4048633	+	1	NA	TTS (NM_146013)	TTS (NM_146013)	-16226	NM_001029937	380683	Mm.296806	NM_001029937	ENSMUSG00000054986	Sec14l3	1110069O07Rik	SEC14-like lipid binding 3	protein-coding
mm_35198.1	chr4	16163612	16163625	-	1	NA	promoter-TSS (NR_045765)	promoter-TSS (NR_045765)	25	NM_138952	192656	Mm.112765	NM_138952	ENSMUSG00000041135	Ripk2	2210420D18Rik|CARD3|CARDIAK|CCK|D4Bwg0615e|RICK|RIP2	receptor (TNFRSF)-interacting serine-threonine kinase 2	protein-coding
mm_3329.1	chr1	137931786	137931796	+	1	NA	Intergenic	Intergenic	-34664	NR_029795	735252		NR_029795	ENSMUSG00000065565	Mir181a-1	Mirn181a-1|Mirn213|miR-213|mir-181a-1|mmu-mir-213	microRNA 181a-1	ncRNA
mm_8817.1	chr1	161985702	161985704	-	1	NA	Intergenic	Intergenic	-6067	NM_001204904	75368	Mm.108728	NM_001204904	ENSMUSG00000086277	4930558K02Rik	-	RIKEN cDNA 4930558K02 gene	protein-coding
mm_147780.1	chr18	61555036	61555083	-	1	NA	promoter-TSS (NM_146087)	promoter-TSS (NM_146087)	-523	NM_146087	93687	Mm.26908	NM_146087	ENSMUSG00000024576	Csnk1a1	2610208K14Rik|4632404G05Rik|5430427P18Rik|CK1a|Csnk1a	casein kinase 1, alpha 1	protein-coding
mm_164826.1	chr18	36997808	36997825	+	1	NA	promoter-TSS (NM_138661)	promoter-TSS (NM_138661)	-64	NM_138661	192161	Mm.308500	NM_138661	ENSMUSG00000103770	Pcdha9	-	protocadherin alpha 9	protein-coding
mm_153877.1	chr19	46901468	46901471	-	1	NA	intron (NM_001164365, intron 5 of 17)	intron (NM_001164365, intron 5 of 17)	60882	NM_029810	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_135498.1	chr16	46481341	46481344	-	1	NA	intron (NM_021496, intron 1 of 8)	intron (NM_021496, intron 1 of 8)	15625	NM_021496	58998	Mm.40477	NM_021495	ENSMUSG00000022656	Nectin3	2610301B19Rik|3000002N23Rik|4921513D19Rik|AA407785|AU016832|AW538082|CD113|Pvrl3	nectin cell adhesion molecule 3	protein-coding
mm_146528.1	chr18	5273279	5273299	-	1	NA	intron (NM_178722, intron 2 of 4)	intron (NM_178722, intron 2 of 4)	61150	NM_178722	240186	Mm.118257	NM_178722	ENSMUSG00000050945	Zfp438	9430031G09|9430091M14Rik|B830013J05Rik	zinc finger protein 438	protein-coding
mm_55653.1	chr6	72374681	72374683	-	1	NA	intron (NM_016872, intron 1 of 2)	L1MEd|LINE|L1	5786	NM_016872	53620	Mm.440321	NM_016872	ENSMUSG00000073002	Vamp5	AF119384|Camp	vesicle-associated membrane protein 5	protein-coding
mm_63899.1	chr7	139085985	139086048	+	1	NA	promoter-TSS (NM_011993)	promoter-TSS (NM_011993)	15	NM_011993	26757	Mm.250414	NM_011993	ENSMUSG00000025478	Dpysl4	AI173505|CRMP-3|Crmp3|DPY4|Drp-4|Ulip4	dihydropyrimidinase-like 4	protein-coding
mm_19049.1	chr2	77259524	77259556	-	1	NA	intron (NM_175465, intron 1 of 17)	intron (NM_175465, intron 1 of 17)	21052	NM_175465	228071	Mm.27120	NM_175465	ENSMUSG00000042272	Sestd1	1500031J16Rik|A930010O20|Solo/Trio8	SEC14 and spectrin domains 1	protein-coding
mm_89598.1	chr10	95973990	95974002	+	1	NA	exon (NM_001001932, exon 2 of 29)	exon (NM_001001932, exon 2 of 29)	33333	NM_001001932	216238	Mm.210035	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding
mm_54492.1	chr6	35510045	35510055	-	1	NA	3' UTR (NM_008098, exon 4 of 4)	3' UTR (NM_008098, exon 4 of 4)	29838	NM_008098	14489	Mm.182746	NM_008098	ENSMUSG00000029840	Mtpn	5033418D15Rik|Gcdp|V1	myotrophin	protein-coding
mm_119863.1	chr14	54469329	54469351	+	1	NA	exon (NM_022993, exon 7 of 7)	exon (NM_022993, exon 7 of 7)	5193	NM_022993	65107	Mm.472719	NM_022993	ENSMUSG00000022175	Lrp10	Lrp9	low-density lipoprotein receptor-related protein 10	protein-coding
mm_155208.1	chrX	56779652	56779656	+	1	NA	promoter-TSS (NM_001077362)	promoter-TSS (NM_001077362)	-29	NM_001077362	14199	Mm.3126	NM_010211	ENSMUSG00000023092	Fhl1	FHL-1|KyoT|RAM14-1|SLIM|SLIM-1	four and a half LIM domains 1	protein-coding
mm_3463.1	chr1	150104302	150104321	+	1	NA	exon (NM_011198, exon 8 of 10)	exon (NM_011198, exon 8 of 10)	4280	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_143356.1	chr17	67176351	67176354	-	1	NA	intron (NM_008984, intron 2 of 30)	intron (NM_008984, intron 2 of 30)	-150117	NR_049205	100885844		NR_049205	ENSMUSG00000093508	Mir5709	Gm22041|mir-5709|mmu-mir-5709	microRNA 5709	ncRNA
mm_83442.1	chr9	45001103	45001132	-	1	NA	exon (NM_007648, exon 6 of 8)	exon (NM_007648, exon 6 of 8)	8473	NM_007648	12501	Mm.210361	NM_007648	ENSMUSG00000032093	Cd3e	AI504783|CD3|CD3epsilon|T3e	CD3 antigen, epsilon polypeptide	protein-coding
mm_155071.1	chrX	43590953	43590955	+	1	NA	promoter-TSS (NM_001195271)	promoter-TSS (NM_001195271)	-35	NM_001195271	637093	Mm.368463	NM_001195271	ENSMUSG00000078320	Tex13c1	Gm362|Tex13c	TEX13 family member C1	protein-coding
mm_75170.1	chr8	36732101	36732116	-	1	NA	intron (NM_001194940, intron 5 of 17)	intron (NM_001194940, intron 5 of 17)	946	NM_001194941	50768	Mm.125155	NM_015802	ENSMUSG00000031523	Dlc1	A730069N07Rik|Arhgap7|HP|STARD12|dlc-1	deleted in liver cancer 1	protein-coding
mm_94503.1	chr11	7197833	7197839	+	1	NA	promoter-TSS (NM_008341)	promoter-TSS (NM_008341)	49	NM_008341	16006	Mm.21300	NM_008341	ENSMUSG00000020429	Igfbp1	-	insulin-like growth factor binding protein 1	protein-coding
mm_8885.1	chr1	162875384	162875393	-	1	NA	3' UTR (NM_018881, exon 9 of 9)	3' UTR (NM_018881, exon 9 of 9)	-8778	NM_010231	14261	Mm.976	NM_010231	ENSMUSG00000040181	Fmo1	-	flavin containing monooxygenase 1	protein-coding
mm_9342.1	chr1	172052658	172052698	-	1	NA	3' UTR (NM_010916, exon 2 of 2)	3' UTR (NM_010916, exon 2 of 2)	4918	NM_010916	18071	Mm.2474	NM_010916	ENSMUSG00000051251	Nhlh1	Hen1|Nscl|Tal2|bHLHa35	nescient helix loop helix 1	protein-coding
mm_26226.1	chr3	138903176	138903187	+	1	NA	non-coding (NR_121195, exon 8 of 8)	non-coding (NR_121195, exon 8 of 8)	160973	NM_019571	56224	Mm.31927	NM_019571	ENSMUSG00000028152	Tspan5	2810455A09Rik|4930505M03Rik|NET-4|Tm4sf9	tetraspanin 5	protein-coding
mm_93384.1	chr10	105574467	105574469	-	1	NA	promoter-TSS (NM_177368)	promoter-TSS (NM_177368)	11	NM_177368	278279	Mm.25225	NM_177368	ENSMUSG00000036019	Tmtc2	8430438D04Rik|D330034A10Rik	transmembrane and tetratricopeptide repeat containing 2	protein-coding
mm_60324.1	chr7	44227623	44227631	+	1	NA	exon (NM_010639, exon 2 of 5)	exon (NM_010639, exon 2 of 5)	2267	NM_001320331	16612	Mm.142722	NM_010639	ENSMUSG00000063903	Klk1	0610007D04Rik|KAL-B|Kal|Klk1b6|Klk6|mGk-6	kallikrein 1	protein-coding
mm_138274.1	chr17	34605444	34605476	+	1	NA	promoter-TSS (NM_001163379)	promoter-TSS (NM_001163379)	-401	NM_001163379	55979	Mm.8684	NM_018862	ENSMUSG00000034254	Agpat1	1-AGP|1-AGPAT|AW047140	1-acylglycerol-3-phosphate O-acyltransferase 1 (lysophosphatidic acid acyltransferase, alpha)	protein-coding
mm_81262.1	chr9	108002616	108002680	+	1	NA	promoter-TSS (NM_013785)	promoter-TSS (NM_013785)	0	NM_013785	27399	Mm.276155	NM_013785	ENSMUSG00000032594	Ip6k1	1200016D08Rik|AU022776|Ihpk1|InsP6|InsP6k1|Itpk6	inositol hexaphosphate kinase 1	protein-coding
mm_55404.1	chr6	60829706	60829752	-	1	NA	promoter-TSS (NM_001042451)	promoter-TSS (NM_001042451)	126	NM_009221	20617	Mm.17484	NM_009221	ENSMUSG00000025889	Snca	NACP|alphaSYN	synuclein, alpha	protein-coding
mm_127281.1	chr15	99931680	99931695	+	1	NA	promoter-TSS (NM_028180)	promoter-TSS (NM_028180)	-29	NM_028180	72277	Mm.272766	NM_028180	ENSMUSG00000045350	1700030F18Rik	FAM186A	RIKEN cDNA 1700030F18 gene	protein-coding
mm_51898.1	chr6	90619352	90619363	+	1	NA	5' UTR (NM_001037493, exon 1 of 10)	5' UTR (NM_001037493, exon 1 of 10)	111	NM_001037493	71699	Mm.272633	NM_027868	ENSMUSG00000030089	Slc41a3	1010001P06Rik|AI480742|SLC41A1-L2	solute carrier family 41, member 3	protein-coding
mm_48158.1	chr5	137152420	137152486	-	1	NA	Intergenic	Intergenic	-36246	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_100210.1	chr11	116853753	116853836	+	1	NA	promoter-TSS (NM_178620)	promoter-TSS (NM_178620)	-221	NM_178620	69900	Mm.348004	NM_178620	ENSMUSG00000020818	Mfsd11	2600014M03Rik	major facilitator superfamily domain containing 11	protein-coding
mm_152730.1	chr19	18936378	18936384	-	1	NA	3' UTR (NM_001289921, exon 11 of 11)	3' UTR (NM_001289921, exon 11 of 11)	64736	NM_146095	225998	Mm.234641	NM_146095	ENSMUSG00000036192	Rorb	Nr1f2|RZR-beta|RZRB|Rorbeta|hstp	RAR-related orphan receptor beta	protein-coding
mm_52950.1	chr6	122990296	122990308	+	1	NA	promoter-TSS (NM_001005860)	promoter-TSS (NM_001005860)	-65	NM_001005860	474145	Mm.263483	NM_001005860	ENSMUSG00000059639	Clec4a4	Dcir2	C-type lectin domain family 4, member a4	protein-coding
mm_9007.1	chr1	165935019	165935036	-	1	NA	promoter-TSS (NM_198933)	promoter-TSS (NM_198933)	-79	NM_198934	18986	Mm.245261	NM_011137	ENSMUSG00000026565	Pou2f1	2810482H01Rik|NF-A1|Oct-1|Oct1|Otf-1|Otf1	POU domain, class 2, transcription factor 1	protein-coding
mm_97169.1	chr11	75513531	75513541	+	1	NA	promoter-TSS (NM_001004157)	promoter-TSS (NM_001004157)	-5	NM_001004157	380713	Mm.10486	NM_001004157	ENSMUSG00000038188	Scarf1	AA986099|SREC|SREC-I|mKIAA0149	scavenger receptor class F, member 1	protein-coding
mm_120971.1	chr14	77940382	77940383	+	1	NA	intron (NM_178825, intron 6 of 6)	intron (NM_178825, intron 6 of 6)	36143	NM_029495	108670	Mm.68134	NM_029495	ENSMUSG00000022014	Epsti1	2310046K10Rik|5033415K03Rik|BRESI1	epithelial stromal interaction 1 (breast)	protein-coding
mm_44720.1	chr5	30960199	30960209	-	1	NA	5' UTR (NM_001294302, exon 1 of 8)	5' UTR (NM_001294302, exon 1 of 8)	123	NM_001294302	50907	Mm.272414	NM_016703	ENSMUSG00000045302	Preb	C85705	prolactin regulatory element binding	protein-coding
mm_113748.1	chr13	44731020	44731036	+	1	NA	promoter-TSS (NM_001205043)	promoter-TSS (NM_001205043)	-243	NM_001205043	16468	Mm.25059	NM_021878	ENSMUSG00000038518	Jarid2	Jmj|jumonji	jumonji, AT rich interactive domain 2	protein-coding
mm_1546.1	chr1	72852305	72852316	+	1	NA	3' UTR (NM_008342, exon 4 of 4)	3' UTR (NM_008342, exon 4 of 4)	22555	NM_010518	16011	Mm.405761	NM_010518	ENSMUSG00000026185	Igfbp5	AI256729|AW208790|IGFBP-5|IGFBP-5P	insulin-like growth factor binding protein 5	protein-coding
mm_139743.1	chr17	63044787	63044787	+	1	NA	Intergenic	Intergenic	-163470	NM_010109	13640	Mm.7978	NM_010109	ENSMUSG00000048915	Efna5	AL-1|AV158822|EFL-5|Ephrin-A5|Epl7|LERK-7|RAGS	ephrin A5	protein-coding
mm_137212.1	chr17	24162821	24162846	+	1	NA	intron (NM_172935, intron 3 of 10)	intron (NM_172935, intron 3 of 10)	900	NM_172935	245847	Mm.87319	NM_172935	ENSMUSG00000036820	Amdhd2	5730457F11Rik	amidohydrolase domain containing 2	protein-coding
mm_127599.1	chr15	102401365	102401370	+	1	NA	Intergenic	Intergenic	-4949	NM_013672	20683	Mm.4618	NM_013672	ENSMUSG00000001280	Sp1	1110003E12Rik|AA450830|AI845540|Sp1-1	trans-acting transcription factor 1	protein-coding
mm_24938.1	chr3	96560322	96560343	+	1	NA	exon (NM_023719, exon 7 of 8)	exon (NM_023719, exon 7 of 8)	2375	NM_023719	56338	Mm.410189	NM_023719	ENSMUSG00000038393	Txnip	1200008J08Rik|AA682105|Hyplip1|THIF|Tbp-2|VDUP1	thioredoxin interacting protein	protein-coding
mm_1927.1	chr1	86064650	86064681	+	1	NA	promoter-TSS (NM_027357)	promoter-TSS (NM_027357)	46	NM_027357	70247	Mm.280013	NM_027357	ENSMUSG00000026229	Psmd1	2410026J11Rik|P112|S1	proteasome (prosome, macropain) 26S subunit, non-ATPase, 1	protein-coding
mm_35536.1	chr4	41314815	41314859	-	1	NA	promoter-TSS (NM_026893)	promoter-TSS (NM_026893)	64	NM_026893	68970	Mm.28891	NM_026893	ENSMUSG00000028436	Dcaf12	1500001L20Rik|5830424K06Rik|AA420338|AI851081|Wdr40a	DDB1 and CUL4 associated factor 12	protein-coding
mm_54080.1	chr6	15728148	15728149	-	1	NA	intron (NM_175088, intron 2 of 4)	intron (NM_175088, intron 2 of 4)	7487	NM_175088	16543	Mm.1314	NM_175088	ENSMUSG00000041390	Mdfic	Kdt1|Mdfid	MyoD family inhibitor domain containing	protein-coding
mm_156951.1	chrX	169986685	169986697	+	1	NA	intron (NM_001290512, intron 8 of 9)	intron (NM_001290512, intron 8 of 9)	-7774	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_22435.1	chr2	181689290	181689302	-	1	NA	intron (NM_001291206, intron 5 of 5)	intron (NM_001291206, intron 5 of 5)	2521	NM_001291205	56470	Mm.274366	NM_026446	ENSMUSG00000002458	Rgs19	2610042F04Rik|AI324841|AW547781|GAIP	regulator of G-protein signaling 19	protein-coding
mm_128137.1	chr15	31467939	31467952	-	1	NA	intron (NM_172606, intron 22 of 25)	Lx8b|LINE|L1	-14256	NM_145852	252967	Mm.436668	NM_145852	ENSMUSG00000022236	Ropn1l	ASP|AV047578|Akapasp	ropporin 1-like	protein-coding
mm_165073.1	chr19	45017633	45017674	+	1	NA	promoter-TSS (NM_001130526)	promoter-TSS (NM_001130526)	-482	NM_001130526	226154	Mm.28204	NM_145503	ENSMUSG00000035342	Lzts2	BC014695|LAPSER1|mKIAA1813	leucine zipper, putative tumor suppressor 2	protein-coding
mm_113437.1	chr13	34883226	34883250	+	1	NA	exon (NM_013830, exon 2 of 15)	exon (NM_013830, exon 2 of 15)	7744	NM_013830	19134	Mm.10027	NM_013830	ENSMUSG00000021413	Prpf4b	2610037H07|Prp4|Prp4k|Prpk|cbp143	pre-mRNA processing factor 4B	protein-coding
mm_145847.1	chr18	65449906	65449927	+	1	NA	intron (NM_172833, intron 6 of 15)	B2_Mm1t|SINE|B2	18919	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_86249.1	chr9	121454660	121454678	-	1	NA	intron (NM_175114, intron 13 of 15)	intron (NM_175114, intron 13 of 15)	41025	NM_001284508	12424	Mm.2619	NM_031161	ENSMUSG00000032532	Cck	-	cholecystokinin	protein-coding
mm_43609.1	chr5	137981513	137981556	+	1	NA	promoter-TSS (NM_013478)	promoter-TSS (NM_013478)	13	NM_013478	12007	Mm.30061	NM_013478	ENSMUSG00000037053	Azgp1	Zag	alpha-2-glycoprotein 1, zinc	protein-coding
mm_13942.1	chr2	121187441	121187471	+	1	NA	intron (NR_077245, intron 9 of 18)	(T)n|Simple_repeat|Simple_repeat	16288	NM_001290824	51885	Mm.383499	NM_153387	ENSMUSG00000027263	Tubgcp4	4932441P04Rik|76p|D2Ertd435e|GCP-4	tubulin, gamma complex associated protein 4	protein-coding
mm_152454.1	chr19	10842864	10842945	-	1	NA	5' UTR (NM_023044, exon 1 of 8)	5' UTR (NM_023044, exon 1 of 8)	360	NM_023044	65221	Mm.27387	NM_023044	ENSMUSG00000024737	Slc15a3	Ci1|cI-1	solute carrier family 15, member 3	protein-coding
mm_167288.1	chr8	44629766	44629767	+	1	NA	Intergenic	Lx5b|LINE|L1	-320442	NM_001081286	14107	Mm.27365	NM_001081286	ENSMUSG00000070047	Fat1	2310038E12Rik|AU023433|Fath|mFat1	FAT atypical cadherin 1	protein-coding
mm_29328.1	chr3	108082393	108082424	-	1	NA	intron (NM_001289719, intron 2 of 18)	intron (NM_001289719, intron 2 of 18)	2994	NM_001346665	109674	Mm.274335	NM_028779	ENSMUSG00000027889	Ampd2	1200014F01Rik|AI552571|Ampd-2|m4521Dajl	adenosine monophosphate deaminase 2	protein-coding
mm_64200.1	chr7	141468810	141468845	+	1	NA	promoter-TSS (NM_001111050)	promoter-TSS (NM_001111050)	38	NM_001111050	12476	Mm.30246	NM_009842	ENSMUSG00000025510	Cd151	PETA-3|SFA-1|Tspan24	CD151 antigen	protein-coding
mm_126781.1	chr15	86194877	86194895	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-8745	NM_145475	223753	Mm.222685	NM_145475	ENSMUSG00000035891	Cerk	AI848610|D330016D08Rik|mKIAA1646	ceramide kinase	protein-coding
mm_40619.1	chr5	64803572	64803580	+	1	NA	promoter-TSS (NM_008453)	promoter-TSS (NM_008453)	53	NM_008453	16599	Mm.392759	NM_008453	ENSMUSG00000029178	Klf3	9930027G08Rik|AL024007|Bklf|Tef-2	Kruppel-like factor 3 (basic)	protein-coding
mm_24155.1	chr3	88441106	88441136	+	1	NA	promoter-TSS (NR_105978)	promoter-TSS (NR_105978)	-170	NR_105978	102465611		NR_105978	ENSMUSG00000098655	Mir7011	Gm27677|mmu-mir-7011	microRNA 7011	ncRNA
mm_17165.1	chr2	25272381	25272421	-	1	NA	promoter-TSS (NM_175300)	promoter-TSS (NM_175300)	17	NM_023464	68475	Mm.21444	NM_023464	ENSMUSG00000026966	Ssna1	1110003H09Rik|1190004J23Rik|AA934184|N14|NA14	SS nuclear autoantigen 1	protein-coding
mm_87511.1	chr10	52417872	52417918	+	1	NA	exon (NM_030250, exon 1 of 5)	exon (NM_030250, exon 1 of 5)	348	NM_030250	52014	Mm.199964	NM_030250	ENSMUSG00000023068	Nus1	1600027K07Rik|AU019165|AW538011|BC003223|D10Ertd438e	NUS1 dehydrodolichyl diphosphate synthase subunit	protein-coding
mm_112483.1	chr13	5869503	5869532	+	1	NA	3' UTR (NM_011803, exon 4 of 4)	3' UTR (NM_011803, exon 4 of 4)	8028	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_104659.1	chr11	97628635	97628647	-	1	NA	exon (NM_175332, exon 1 of 1)	exon (NM_175332, exon 1 of 1)	1075	NM_175332	103551	Mm.24506	NM_175332	ENSMUSG00000043439	Epop	AA409164|AI413509|AW539173|E13|E130012A19Rik|esPRC2p48	elongin BC and polycomb repressive complex 2 associated protein	protein-coding
mm_67432.1	chr7	80371406	80371416	-	1	NA	promoter-TSS (NM_172903)	promoter-TSS (NM_172903)	-36	NM_172903	140481	Mm.269245	NM_172903	ENSMUSG00000038886	Man2a2	1700052O22Rik|4931438M07Rik|AI480988|MX|Man IIx	mannosidase 2, alpha 2	protein-coding
mm_36534.1	chr4	86648204	86648214	-	1	NA	Intergenic	Intergenic	21850	NM_007408	11520	Mm.381	NM_007408	ENSMUSG00000028494	Plin2	AA407157|ADPH|Adfp|Adrp	perilipin 2	protein-coding
mm_153670.1	chr19	44396096	44396111	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	11606	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_156655.1	chrX	157702888	157702914	+	1	NA	intron (NR_045569, intron 1 of 6)	intron (NR_045569, intron 1 of 6)	3928	NR_103722	66106	Mm.140340	NM_025357	ENSMUSG00000041476	Smpx	1010001C09Rik|Csl	small muscle protein, X-linked	protein-coding
mm_38240.1	chr4	136180549	136180571	-	1	NA	promoter-TSS (NM_001305399)	promoter-TSS (NM_001305399)	-222	NM_001305399	242705	Mm.307932	NM_177733	ENSMUSG00000018983	E2f2	E2F-2	E2F transcription factor 2	protein-coding
mm_166240.1	chr5	73292865	73292875	+	1	NA	promoter-TSS (NM_001159889)	promoter-TSS (NM_001159889)	76	NM_001159888	68095	Mm.247039	NM_023429	ENSMUSG00000029152	Ociad1	6030432N09Rik|AI481327|AW557942|Asrij|B230209J16Rik|BB021357|Emi2|Imi2|OCIA|TPA018	OCIA domain containing 1	protein-coding
mm_152184.1	chr19	7427674	7427700	-	1	NA	3' UTR (NM_053076, exon 7 of 7)	3' UTR (NM_053076, exon 7 of 7)	5114	NR_105957	102466781		NR_105957	ENSMUSG00000098293	Mir6991	Gm27966|mmu-mir-6991	microRNA 6991	ncRNA
mm_66798.1	chr7	47132726	47132750	-	1	NA	promoter-TSS (NM_001163565)	promoter-TSS (NM_001163565)	-140	NM_001163565	19259	Mm.4654	NM_013643	ENSMUSG00000030854	Ptpn5	Step	protein tyrosine phosphatase, non-receptor type 5	protein-coding
mm_41254.1	chr5	88815832	88815840	+	1	NA	Intergenic	Intergenic	50823	NM_007832	13178	Mm.298892	NM_007832	ENSMUSG00000029366	Dck	-	deoxycytidine kinase	protein-coding
mm_100368.1	chr11	119081725	119081743	+	1	NA	exon (NM_007625, exon 5 of 5)	exon (NM_007625, exon 5 of 5)	4503	NM_007625	12418	Mm.268070	NM_007625	ENSMUSG00000039989	Cbx4	MPc2|PC2	chromobox 4	protein-coding
mm_44827.1	chr5	33933233	33933233	-	1	NA	intron (NM_011914, intron 1 of 10)	intron (NM_011914, intron 1 of 10)	3025	NM_011914	24116	Mm.332320	NM_011914	ENSMUSG00000029111	Nelfa	Whsc2|Whsc2h	negative elongation factor complex member A, Whsc2	protein-coding
mm_149008.1	chr19	8724114	8724143	+	1	NA	promoter-TSS (NM_001161413)	promoter-TSS (NM_001161413)	641	NR_002896	83673	Mm.292489	NR_002896	ENSMUSG00000108414	Snhg1	-	small nucleolar RNA host gene 1	ncRNA
mm_47129.1	chr5	120431758	120431771	-	1	NA	promoter-TSS (NM_008499)	promoter-TSS (NM_008499)	-122	NM_008499	16873	Mm.5151	NM_008499	ENSMUSG00000029595	Lhx5	Lim2	LIM homeobox protein 5	protein-coding
mm_119233.1	chr14	33319742	33319744	+	1	NA	intron (NM_153800, intron 4 of 10)	CpG	91281	NM_001310452	26419	Mm.21495	NM_016700	ENSMUSG00000021936	Mapk8	AI849689|JNK|JNK1|Prkm8|SAPK1	mitogen-activated protein kinase 8	protein-coding
mm_16052.1	chr2	167760349	167760352	+	1	NA	Intergenic	Intergenic	69173	NR_015500	329562	Mm.123101	NM_177851	ENSMUSG00000006462	A530013C23Rik	-	RIKEN cDNA A530013C23 gene	ncRNA
mm_121755.1	chr14	19627170	19627216	-	1	NA	Intergenic	Intergenic	-24606	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_90152.1	chr10	118156109	118156112	+	1	NA	intron (NM_148922, intron 7 of 13)	(T)n|Simple_repeat|Simple_repeat	14323	NM_010785	17245	Mm.101191	NM_010785	ENSMUSG00000020212	Mdm1	Arrd2|Mdm-1	transformed mouse 3T3 cell double minute 1	protein-coding
mm_92164.1	chr10	67548945	67549001	-	1	NA	promoter-TSS (NM_001005419)	promoter-TSS (NM_001005419)	-18	NM_001005419	211488	Mm.297250	NM_001005419	ENSMUSG00000057134	Ado	Gm237	2-aminoethanethiol (cysteamine) dioxygenase	protein-coding
mm_133536.1	chr16	91056577	91056579	+	1	NA	intron (NM_001163695, intron 1 of 1)	intron (NM_001163695, intron 1 of 1)	-12199	NM_026110	67367	Mm.347	NM_026110	ENSMUSG00000022974	Paxbp1	1810007M14Rik|C21orf66|Gcfc|Gcfc1|Pax3/7bp	PAX3 and PAX7 binding protein 1	protein-coding
mm_128020.1	chr15	24724816	24724831	-	1	NA	Intergenic	Intergenic	688941	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	brain abundant, membrane attached signal protein 1	protein-coding
mm_92857.1	chr10	81530524	81530547	-	1	NA	3' UTR (NM_010301, exon 7 of 7)	3' UTR (NM_010301, exon 7 of 7)	-6310	NM_010304	14676	Mm.1546	NM_010304	ENSMUSG00000034792	Gna15	G[a]15|Galpha15	guanine nucleotide binding protein, alpha 15	protein-coding
mm_5679.1	chr1	43162002	43162012	-	1	NA	intron (NM_001289533, intron 1 of 5)	intron (NM_001289533, intron 1 of 5)	1954	NM_010212	14200	Mm.6799	NM_010212	ENSMUSG00000008136	Fhl2	FHL-2|SLIM-3|SLIM3	four and a half LIM domains 2	protein-coding
mm_35865.1	chr4	49481274	49481309	-	1	NA	Intergenic	Intergenic	25267	NM_007519	12012	Mm.2859	NM_007519	ENSMUSG00000039653	Baat	AI118337|AI158864|BAT	bile acid-Coenzyme A: amino acid N-acyltransferase	protein-coding
mm_157353.1	chrX	37048650	37048659	-	1	NA	promoter-TSS (NM_173779)	promoter-TSS (NM_173779)	-191	NM_173779	245381	Mm.123697	NM_173779	ENSMUSG00000044400	Sowahd	A630014H24Rik|Ankrd58	sosondowah ankyrin repeat domain family member D	protein-coding
mm_108671.1	chr12	86520027	86520064	+	1	NA	3' UTR (NM_011934, exon 7 of 7)	3' UTR (NM_011934, exon 7 of 7)	98401	NM_011934	26380	Mm.235550	NM_011934	ENSMUSG00000021255	Esrrb	Err2|Errb|Estrrb|Nr3b2	estrogen related receptor, beta	protein-coding
mm_96811.1	chr11	69991676	69991684	+	1	NA	5' UTR (NM_019749, exon 1 of 4)	5' UTR (NM_019749, exon 1 of 4)	310	NM_019749	56486	Mm.272460	NM_019749	ENSMUSG00000018567	Gabarap	-	gamma-aminobutyric acid receptor associated protein	protein-coding
mm_87387.1	chr10	45067168	45067279	+	1	NA	promoter-TSS (NM_011156)	promoter-TSS (NM_011156)	9	NM_011156	19072	Mm.10281	NM_011156	ENSMUSG00000019849	Prep	AI047692|AI450383|D10Wsu136e|PEP|Pop	prolyl endopeptidase	protein-coding
mm_141262.1	chr17	27623392	27623416	-	1	NA	promoter-TSS (NM_001291046)	promoter-TSS (NM_001291046)	48	NM_019837	56409	Mm.144699	NM_019837	ENSMUSG00000024213	Nudt3	1110011B09Rik|AA960325|Dipp|Dipp1	nudix (nucleotide diphosphate linked moiety X)-type motif 3	protein-coding
mm_95756.1	chr11	54904002	54904006	+	1	NA	intron (NM_001329860, intron 1 of 5)	intron (NM_001329860, intron 1 of 5)	1150	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_71818.1	chr8	68886942	68886963	+	1	NA	intron (NM_008509, intron 1 of 9)	intron (NM_008509, intron 1 of 9)	6397	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_157683.1	chrX	60045156	60045176	-	1	NA	Intergenic	Intergenic	45702	NM_001305797	14071	Mm.391283	NM_007979	ENSMUSG00000031138	F9	AW111646|Cf-9|Cf9	coagulation factor IX	protein-coding
mm_38737.1	chr4	145245717	145245730	-	1	NA	intron (NM_011610, intron 1 of 9)	intron (NM_011610, intron 1 of 9)	1147	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_21670.1	chr2	164425606	164425616	-	1	NA	3' UTR (NM_011521, exon 5 of 5)	3' UTR (NM_011521, exon 5 of 5)	17577	NM_011521	20971	Mm.3815	NM_011521	ENSMUSG00000017009	Sdc4	AA959608|AW108331|S4|Synd4|ryudocan|syndecan-4	syndecan 4	protein-coding
mm_3096.1	chr1	134423996	134424027	+	1	NA	exon (NM_001306069, exon 3 of 8)	exon (NM_001306069, exon 3 of 8)	8347	NM_001306069	72674	Mm.259976	NM_028320	ENSMUSG00000026457	Adipor1	2810031L11Rik|ACDCR1|CGI-45|Paqr1	adiponectin receptor 1	protein-coding
mm_77571.1	chr8	123432433	123432439	-	1	NA	Intergenic	MuLV-int|LTR|ERV1	-10520	NM_001253784	23854	Mm.275127	NM_054046	ENSMUSG00000001482	Def8	AI449518|D8Ertd713e|DEF-8	differentially expressed in FDCP 8	protein-coding
mm_78951.1	chr9	45138763	45138769	+	1	NA	promoter-TSS (NM_001013390)	promoter-TSS (NM_001013390)	-276	NM_001013390	399548	Mm.335112	NM_001013390	ENSMUSG00000046480	Scn4b	Gm1471	sodium channel, type IV, beta	protein-coding
mm_68978.1	chr7	126589239	126589249	-	1	NA	TTS (NM_138310)	TTS (NM_138310)	-3427	NM_001146311	12752	Mm.268930	NM_009907	ENSMUSG00000030720	Cln3	AI323623	ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease)	protein-coding
mm_135363.1	chr16	44016388	44016399	-	1	NA	promoter-TSS (NM_153528)	promoter-TSS (NM_153528)	43	NM_153528	207798	Mm.19316	NM_153528	ENSMUSG00000036292	Gramd1c	4921521N14Rik	GRAM domain containing 1C	protein-coding
mm_87396.1	chr10	45335887	45335897	+	1	NA	intron (NM_024285, intron 1 of 7)	CpG	130	NM_024285	23828	Mm.332793	NM_024285	ENSMUSG00000071317	Bves	Pop1|Popdc1|mBVES	blood vessel epicardial substance	protein-coding
mm_103843.1	chr11	83045628	83045645	-	1	NA	Intergenic	Intergenic	-5103	NR_073524	237887	Mm.341645	NM_181542	ENSMUSG00000072621	Slfn10-ps	Slfn10|mFLJ00257	schlafen 10, pseudogene	pseudo
mm_149644.1	chr19	17401119	17401122	+	1	NA	3' UTR (NM_019437, exon 4 of 4)	3' UTR (NM_019437, exon 4 of 4)	7077	NM_019437	54391	Mm.7013	NM_019437	ENSMUSG00000024712	Rfk	0610038L10Rik|AF031381|KOI-4	riboflavin kinase	protein-coding
mm_107637.1	chr12	52265735	52265760	+	1	NA	intron (NM_029760, intron 6 of 10)	RMER13B|LTR|ERVK	168001	NM_029760	76826	Mm.244781	NM_029760	ENSMUSG00000035142	Nubpl	2410170E07Rik	nucleotide binding protein-like	protein-coding
mm_6221.1	chr1	66863318	66863335	-	1	NA	promoter-TSS (NM_007381)	promoter-TSS (NM_007381)	-17	NM_007381	11363	Mm.2445	NM_007381	ENSMUSG00000026003	Acadl	AA960361|AU018452|C79855|LCAD	acyl-Coenzyme A dehydrogenase, long-chain	protein-coding
mm_10101.1	chr2	3461603	3461649	+	1	NA	TTS (NM_175683)	TTS (NM_175683)	13360	NM_022724	64707	Mm.23483	NM_022724	ENSMUSG00000026646	Suv39h2	4930507K23Rik|AA536750|D030054H19Rik|D2Ertd544e|KMT1B	suppressor of variegation 3-9 homolog 2 (Drosophila)	protein-coding
mm_128023.1	chr15	24857567	24857579	-	1	NA	Intergenic	Intergenic	556191	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	brain abundant, membrane attached signal protein 1	protein-coding
mm_82404.1	chr9	14771142	14771150	-	1	NA	promoter-TSS (NM_029306)	promoter-TSS (NM_029306)	-116	NM_029306	69325	Mm.440453	NM_029306	ENSMUSG00000031927	1700012B09Rik	1700007P19Rik	RIKEN cDNA 1700012B09 gene	protein-coding
mm_87757.1	chr10	60278670	60278680	+	1	NA	intron (NM_001146120, intron 1 of 13)	intron (NM_001146120, intron 1 of 13)	1047	NM_001146121	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_5292.1	chr1	20997608	20997611	-	1	NA	Intergenic	Intergenic	45983	NM_027974	71877	Mm.29178	NM_027974	ENSMUSG00000041809	Efhc1	1700029F22Rik|mRib72-1|myoclonin1	EF-hand domain (C-terminal) containing 1	protein-coding
mm_104622.1	chr11	97301733	97301736	-	1	NA	Intergenic	Intergenic	-13982	NM_025927	67036	Mm.5381	NM_025927	ENSMUSG00000018882	Mrpl45	2600005P05Rik|AU043542|R75241	mitochondrial ribosomal protein L45	protein-coding
mm_58398.1	chr7	3217797	3217801	+	1	NA	promoter-TSS (NR_029640)	promoter-TSS (NR_029640)	-827	NR_029640	100049710		NR_029640	ENSMUSG00000077815	Mir290a	Mir290|Mirn290|mir-290a|mmu-miR-290|mmu-mir-290a	microRNA 290a	ncRNA
mm_52261.1	chr6	108213312	108213323	+	1	NA	5' UTR (NM_010585, exon 1 of 62)	5' UTR (NM_010585, exon 1 of 62)	221	NM_010585	16438	Mm.227912	NM_010585	ENSMUSG00000030102	Itpr1	D6Pas2|ENSMUSG00000072853|Gm10429|IP3R 1|IP3R1|InsP3R|Ip3r|Itpr-1|P400|Pcp-1|Pcp1|insP3R1|opt|wblo	inositol 1,4,5-trisphosphate receptor 1	protein-coding
mm_141884.1	chr17	34860834	34860844	-	1	NA	exon (NM_008198, exon 4 of 18)	exon (NM_008198, exon 4 of 18)	1675	NM_001142706	14962	Mm.653	NM_008198	ENSMUSG00000090231	Cfb	AI195813|AI255840|B|Bf|C2|Fb|H2-Bf	complement factor B	protein-coding
mm_122249.1	chr14	33978802	33978812	-	1	NA	promoter-TSS (NM_001013777)	promoter-TSS (NM_001013777)	-43	NM_001013777	382867	Mm.343728	NM_001013777	ENSMUSG00000044519	Zfp488	Gm1206|Znf488	zinc finger protein 488	protein-coding
mm_63439.1	chr7	127480069	127480081	+	1	NA	Intergenic	Intergenic	-5146	NM_010183	14123	Mm.323505	NM_010183	ENSMUSG00000042423	Fbrs	Fbs|Fbs1	fibrosin	protein-coding
mm_29245.1	chr3	107218165	107218172	-	1	NA	exon (NM_001111143, exon 4 of 9)	exon (NM_001111143, exon 4 of 9)	3564	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_38005.1	chr4	133720887	133720976	-	1	NA	exon (NM_001080819, exon 3 of 20)	exon (NM_001080819, exon 3 of 20)	-3823	NR_106086	102465707		NR_106086	ENSMUSG00000104566	Mir7227	mmu-mir-7227	microRNA 7227	ncRNA
mm_21964.1	chr2	167252120	167252141	-	1	NA	Intergenic	Intergenic	-11593	NM_008968	19223	Mm.2339	NM_008968	ENSMUSG00000017969	Ptgis	Cyp8|Cyp8a1|Pgis	prostaglandin I2 (prostacyclin) synthase	protein-coding
mm_72859.1	chr8	88428877	88428901	+	1	NA	Intergenic	MLT1G|LTR|ERVL-MaLR	-66698	NM_012047	26992	Mm.5400	NM_012047	ENSMUSG00000031660	Brd7	BP75|CELTIX1|Ptpn13ip	bromodomain containing 7	protein-coding
mm_123480.1	chr14	65980987	65981024	-	1	NA	exon (NM_013492, exon 8 of 9)	exon (NM_013492, exon 8 of 9)	12522	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_153965.1	chr19	47837379	47837424	-	1	NA	promoter-TSS (NM_027559)	promoter-TSS (NM_027559)	-40	NM_027559	100048534	Mm.29457	NM_027559	ENSMUSG00000044948	Cfap43	4632415N18Rik|4930428C11Rik|4930463G05Rik|AI429486|D19Ertd652e|Wdr96	cilia and flagella associated protein 43	protein-coding
mm_124927.1	chr15	12149313	12149315	+	1	NA	intron (NM_011767, intron 6 of 19)	B1_Mur1|SINE|Alu	-22178	NR_035443	100316684		NR_035443	ENSMUSG00000084592	Mir1898	Mirn1898|mmu-mir-1898	microRNA 1898	ncRNA
mm_111007.1	chr12	78980570	78980587	-	1	NA	intron (NM_178745, intron 1 of 2)	intron (NM_178745, intron 1 of 2)	2900	NM_001170401	268567	Mm.341747	NM_178745	ENSMUSG00000046157	Tmem229b	6330442E10Rik|9830138K24|AU019070	transmembrane protein 229B	protein-coding
mm_48542.1	chr5	142905380	142905401	-	1	NA	exon (NM_007393, exon 3 of 6)	exon (NM_007393, exon 3 of 6)	1364	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_8871.1	chr1	162859832	162859842	-	1	NA	5' UTR (NM_001330291, exon 1 of 9)	5' UTR (NM_001330291, exon 1 of 9)	163	NM_001330291	14261	Mm.976	NM_010231	ENSMUSG00000040181	Fmo1	-	flavin containing monooxygenase 1	protein-coding
mm_33537.1	chr4	130932618	130932644	+	1	NA	intron (NM_010686, intron 7 of 7)	(TCCA)n|Simple_repeat|Simple_repeat	-11754	NM_010769	17180	Mm.271796	NM_010769	ENSMUSG00000040533	Matn1	CMP|Crtm|Mat1|matrilin-1	matrilin 1, cartilage matrix protein	protein-coding
mm_172564.1	chr8	110606990	110607006	-	1	NA	intron (NM_172916, intron 85 of 86)	ORR1A2|LTR|ERVL-MaLR	-11640	NM_146216	234729	Mm.274894	NM_146216	ENSMUSG00000010936	Vac14	AA959718|BC032215|D8Wsu151e|Tax1bp2|Trx|ingls	Vac14 homolog (S. cerevisiae)	protein-coding
mm_123095.1	chr14	55788737	55788749	-	1	NA	5' UTR (NM_019955, exon 1 of 10)	5' UTR (NM_019955, exon 1 of 10)	114	NM_001164107	56532	Mm.46612	NM_019955	ENSMUSG00000022221	Ripk3	2610528K09Rik|AW107945|Rip3	receptor-interacting serine-threonine kinase 3	protein-coding
mm_56266.1	chr6	90988406	90988448	-	1	NA	Intergenic	CpG	128399	NM_018815	54563	Mm.28162	NM_018815	ENSMUSG00000030091	Nup210	9830001L10|AI836801|Pom210|gp190|gp210	nucleoporin 210	protein-coding
mm_112342.1	chr12	116405158	116405185	-	1	NA	promoter-TSS (NR_028421)	promoter-TSS (NR_028421)	-10	NR_028421	319545	Mm.390543	NR_028421		D430020J02Rik	-	RIKEN cDNA D430020J02 gene	ncRNA
mm_10804.1	chr2	24349763	24349784	+	1	NA	3' UTR (NM_031167, exon 5 of 5)	3' UTR (NM_031167, exon 5 of 5)	4402	NM_001039701	16181	Mm.882	NM_031167	ENSMUSG00000026981	Il1rn	F630041P17Rik|IL-1ra	interleukin 1 receptor antagonist	protein-coding
mm_169508.1	chr14	8088422	8088424	-	1	NA	intron (NM_025938, intron 4 of 5)	ERVB7_1-LTR_MM|LTR|ERVK	8110	NM_025938	67053	Mm.210048	NM_025938	ENSMUSG00000023156	Rpp14	2610511E03Rik|AA682089	ribonuclease P 14 subunit	protein-coding
mm_94012.1	chr10	127621652	127621682	-	1	NA	promoter-TSS (NM_008512)	promoter-TSS (NM_008512)	-519	NM_008512	16971	Mm.271854	NM_008512	ENSMUSG00000040249	Lrp1	A2mr|AI316852|CD91|Lrp|b2b1554Clo	low density lipoprotein receptor-related protein 1	protein-coding
mm_4687.1	chr1	180640692	180640706	+	1	NA	promoter-TSS (NR_120498)	promoter-TSS (NR_120498)	-451	NM_001103182	72568	Mm.275044	NM_175186	ENSMUSG00000058729	Lin9	2700022J23Rik|Bara|Lin-9|TGS|TGS1|mLin-9	lin-9 homolog (C. elegans)	protein-coding
mm_134075.1	chr16	8672146	8672161	-	1	NA	promoter-TSS (NM_025821)	promoter-TSS (NM_025821)	0	NM_025821	52502	Mm.142095	NM_025821	ENSMUSG00000008393	Carhsp1	1200011K09Rik|Crhsp-24|D16Ertd465e	calcium regulated heat stable protein 1	protein-coding
mm_84721.1	chr9	73969059	73969072	-	1	NA	Intergenic	Intergenic	-35498	NM_001081153	208898	Mm.41035	NM_001081153	ENSMUSG00000062151	Unc13c	1500037O19Rik|AU019458|D9Ertd414e|Munc13-3|Unc13h3	unc-13 homolog C (C. elegans)	protein-coding
mm_51608.1	chr6	84154749	84154759	+	1	NA	intron (NM_001077694, intron 40 of 54)	intron (NM_001077694, intron 40 of 54)	135368	NM_021469	26903	Mm.220982	NM_021469	ENSMUSG00000033788	Dysf	2310004N10Rik|AI604795|D6Pas3	dysferlin	protein-coding
mm_39710.1	chr5	27709423	27709443	+	1	NA	intron (NM_010075, intron 17 of 25)	intron (NM_010075, intron 17 of 25)	82117	NM_018878	55982	Mm.277190	NM_018878	ENSMUSG00000002221	Paxip1	D5Ertd149e|PTIP	PAX interacting (with transcription-activation domain) protein 1	protein-coding
mm_172314.1	chr7	105953993	105953993	-	1	NA	promoter-TSS (NM_001243039)	promoter-TSS (NM_001243039)	-23	NM_029000	74558	Mm.458429	NM_029000	ENSMUSG00000045868	Gvin1	9130002C22Rik|9830104F22Rik|Iigs1|VLIG|VLIG-1	GTPase, very large interferon inducible 1	protein-coding
mm_14526.1	chr2	132692023	132692047	+	1	NA	exon (NM_028637, exon 2 of 3)	exon (NM_028637, exon 2 of 3)	1752	NM_028637	73747	Mm.284114	NM_028637	ENSMUSG00000044991	1110034G24Rik	-	RIKEN cDNA 1110034G24 gene	protein-coding
mm_4769.1	chr1	182490022	182490035	+	1	NA	exon (NM_009794, exon 6 of 21)	exon (NM_009794, exon 6 of 21)	27455	NM_009794	12334	Mm.19306	NM_009794	ENSMUSG00000026509	Capn2	AI326419|Capa-2|Capa2|m-calpain|m-calpin	calpain 2	protein-coding
mm_71968.1	chr8	70534272	70534289	+	1	NA	intron (NM_010223, intron 7 of 8)	intron (NM_010223, intron 7 of 8)	-5395	NM_007924	13716	Mm.271973	NM_007924	ENSMUSG00000070002	Ell	Ell1|Men	elongation factor RNA polymerase II	protein-coding
mm_77038.1	chr8	109575187	109575199	-	1	NA	TTS (NM_017370)	TTS (NM_017370)	3979	NM_017370	15439	Mm.26730	NM_017370	ENSMUSG00000031722	Hp	HP-1|preHP2	haptoglobin	protein-coding
mm_67237.1	chr7	75308374	75308384	-	1	NA	promoter-TSS (NM_001109753)	promoter-TSS (NM_001109753)	7	NM_001109753	64176	Mm.273082	NM_153579	ENSMUSG00000053025	Sv2b	A830038F04Rik|AI850768|mKIAA0735	synaptic vesicle glycoprotein 2 b	protein-coding
mm_9285.1	chr1	171634716	171634732	-	1	NA	3' UTR (NM_144539, exon 8 of 8)	3' UTR (NM_144539, exon 8 of 8)	7176	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_48080.1	chr5	136883116	136883168	-	1	NA	promoter-TSS (NM_024474)	promoter-TSS (NM_024474)	-35	NM_024474	140709	Mm.295020	NM_024474	ENSMUSG00000004415	Col26a1	9430032K24Rik|BC002218|Col26a|Emid2|Emu2	collagen, type XXVI, alpha 1	protein-coding
mm_17737.1	chr2	32694121	32694176	-	1	NA	promoter-TSS (NM_010236)	promoter-TSS (NM_010236)	27	NM_010236	14287	Mm.3830	NM_010236	ENSMUSG00000009566	Fpgs	AA408187	folylpolyglutamyl synthetase	protein-coding
mm_75636.1	chr8	64838308	64838324	-	1	NA	intron (NM_178633, intron 1 of 14)	B4A|SINE|B4	11608	NM_178633	77113	Mm.350347	NM_178633	ENSMUSG00000031605	Klhl2	6030411N21Rik|ABP-KELCH|AU020744|Mav	kelch-like 2, Mayven	protein-coding
mm_87595.1	chr10	57632063	57632101	+	1	NA	5' UTR (NM_008863, exon 1 of 6)	5' UTR (NM_008863, exon 1 of 6)	101	NM_001039051	18768	Mm.262135	NM_008863	ENSMUSG00000019876	Pkib	Pkibeta|Prkacn2	protein kinase inhibitor beta, cAMP dependent, testis specific	protein-coding
mm_14244.1	chr2	128055172	128055184	+	1	NA	intron (NM_028765, intron 14 of 17)	intron (NM_028765, intron 14 of 17)	-70860	NM_207681	12125	Mm.141083	NM_009754	ENSMUSG00000027381	Bcl2l11	1500006F24Rik|Bim|Bod|bcl2-L-11	BCL2-like 11 (apoptosis facilitator)	protein-coding
mm_40757.1	chr5	66898478	66898494	+	1	NA	intron (NM_001001980, intron 3 of 25)	intron (NM_001001980, intron 3 of 25)	-69930	NM_001256122	77569	Mm.374778	NM_001001980	ENSMUSG00000037736	Limch1	3732412D22Rik|mKIAA1102	LIM and calponin homology domains 1	protein-coding
mm_152903.1	chr19	25672228	25672240	-	1	NA	promoter-TSS (NM_145831)	promoter-TSS (NM_145831)	5	NR_045347	100503074	Mm.140012	NR_045347	ENSMUSG00000101089	2610016A17Rik	2610317C19Rik	RIKEN cDNA 2610016A17 gene	ncRNA
mm_13622.1	chr2	113441043	113441058	+	1	NA	promoter-TSS (NM_001285459)	promoter-TSS (NM_001285459)	-14	NM_001285459	14260	Mm.4938	NM_010230	ENSMUSG00000044042	Fmn1	Fmn|formin-1|ld	formin 1	protein-coding
mm_137930.1	chr17	32538351	32538371	+	1	NA	intron (NM_024442, intron 2 of 12)	intron (NM_024442, intron 2 of 12)	1732	NM_024442	70101	Mm.30504	NM_024442	ENSMUSG00000048440	Cyp4f16	2310021J05Rik|AI746515	cytochrome P450, family 4, subfamily f, polypeptide 16	protein-coding
mm_114129.1	chr13	55211679	55211730	+	1	NA	intron (NM_008739, intron 1 of 22)	CpG	1922	NM_008739	18193	Mm.12964	NM_008739	ENSMUSG00000021488	Nsd1	AI528500|KMT3B	nuclear receptor-binding SET-domain protein 1	protein-coding
mm_46219.1	chr5	98936656	98936658	-	1	NA	intron (NM_008926, intron 17 of 18)	intron (NM_008926, intron 17 of 18)	82242	NM_001310677	110075	Mm.136461	NM_173404	ENSMUSG00000029335	Bmp3	9530029I04Rik	bone morphogenetic protein 3	protein-coding
mm_126136.1	chr15	78344878	78344911	+	1	NA	intron (NM_007780, intron 9 of 13)	intron (NM_007780, intron 9 of 13)	-3705	NR_106137	102465776		NR_106137	ENSMUSG00000098996	Mir7676-1	Gm27600|mmu-mir-7676-1	microRNA 7676-1	ncRNA
mm_129334.1	chr15	77829456	77829458	-	1	NA	intron (NM_022410, intron 1 of 40)	intron (NM_022410, intron 1 of 40)	12718	NM_022410	17886	Mm.29677	NM_022410	ENSMUSG00000022443	Myh9	Fltn|Myhn-1|Myhn1|NMHCIIA|NMMHC-A|NMMHC-IIA|TU72.6	myosin, heavy polypeptide 9, non-muscle	protein-coding
mm_40341.1	chr5	45493386	45493437	+	1	NA	promoter-TSS (NM_024434)	promoter-TSS (NM_024434)	37	NM_024434	66988	Mm.286830	NM_024434	ENSMUSG00000039682	Lap3	2410015L10Rik|AA410100|LAP-3|Lap|Lapep|Pep-7|Pep-S|Pep7|Peps	leucine aminopeptidase 3	protein-coding
mm_18522.1	chr2	63088260	63088265	-	1	NA	intron (NM_133207, intron 2 of 15)	intron (NM_133207, intron 2 of 15)	96025	NM_133207	170738	Mm.242532	NM_133207	ENSMUSG00000059742	Kcnh7	9330137I11Rik|Kv11.3|erg3	potassium voltage-gated channel, subfamily H (eag-related), member 7	protein-coding
mm_157432.1	chrX	38576190	38576204	-	1	NA	promoter-TSS (NM_028288)	promoter-TSS (NM_028288)	-1	NM_001110142	72584	Mm.327675	NM_028288	ENSMUSG00000031095	Cul4b	2700050M05Rik|AA409770|CUL-4B|mKIAA0695	cullin 4B	protein-coding
mm_50748.1	chr6	52825841	52825859	+	1	NA	intron (NM_173406, intron 2 of 4)	B3A|SINE|B2	83770	NM_001168277	231986	Mm.386865	NM_173406	ENSMUSG00000063568	Jazf1	AI591476|C820002C15|Jaz1|Tip27	JAZF zinc finger 1	protein-coding
mm_10599.1	chr2	18677134	18677214	+	1	NA	TTS (NM_147778)	TTS (NM_147778)	156	NM_007552	12151	Mm.289584	NM_007552	ENSMUSG00000026739	Bmi1	AW546694|Bmi-1|Pcgf4	Bmi1 polycomb ring finger oncogene	protein-coding
mm_124550.1	chr14	122905109	122905120	-	1	NA	intron (NM_145466, intron 1 of 2)	B1_Mus1|SINE|Alu	8051	NM_145466	223267	Mm.379358	NM_145466	ENSMUSG00000041625	Ggact	A2ld1	gamma-glutamylamine cyclotransferase	protein-coding
mm_7536.1	chr1	124423677	124423685	-	1	NA	Intergenic	MLT1G3|LTR|ERVL-MaLR	-378122	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_152589.1	chr19	11604769	11604793	-	1	NA	promoter-TSS (NM_026835)	promoter-TSS (NM_026835)	23	NM_026835	68774	Mm.290390	NM_026835	ENSMUSG00000024679	Ms4a6d	1110058E16Rik|AI447446|Ms4a11	membrane-spanning 4-domains, subfamily A, member 6D	protein-coding
mm_128438.1	chr15	50709220	50709223	-	1	NA	intron (NM_001310481, intron 4 of 5)	intron (NM_001310481, intron 4 of 5)	179828	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_117516.1	chr13	80886003	80886040	-	1	NA	intron (NM_001042591, intron 1 of 7)	CpG	2599	NM_001042591	105171	Mm.423137	NM_001042591	ENSMUSG00000074794	Arrdc3	AI450344|mKIAA1376	arrestin domain containing 3	protein-coding
mm_106482.1	chr11	120216632	120216642	-	1	NA	Intergenic	Intergenic	-16310	NM_001347621	268515	Mm.309498	NM_198423	ENSMUSG00000039741	Bahcc1	B930044J06|BC060615	BAH domain and coiled-coil containing 1	protein-coding
mm_35696.1	chr4	44149063	44149128	-	1	NA	exon (NM_175201, exon 3 of 11)	exon (NM_175201, exon 3 of 11)	18443	NM_175201	73469	Mm.262859	NM_175201	ENSMUSG00000035696	Rnf38	1700065B19Rik|2610202O07Rik|AA673263|Oip1	ring finger protein 38	protein-coding
mm_126610.1	chr15	82899061	82899082	+	1	NA	promoter-TSS (NR_027799)	promoter-TSS (NR_027799)	-9	NR_045068	100504637	Mm.440928	NR_045068	ENSMUSG00000100199	Gm20324	-	predicted gene, 20324	ncRNA
mm_50038.1	chr6	41141187	41141199	+	1	NA	Intergenic	Intergenic	-105684	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_51037.1	chr6	65596127	65596146	+	1	NA	exon (NM_001001495, exon 3 of 8)	exon (NM_001001495, exon 3 of 8)	5738	NM_001001495	414084	Mm.117558	NM_001001495	ENSMUSG00000044162	Tnip3	9030611K07Rik|ABIN-3|LIND	TNFAIP3 interacting protein 3	protein-coding
mm_128481.1	chr15	50889999	50890012	-	1	NA	promoter-TSS (NR_035444)	promoter-TSS (NR_035444)	36	NM_032000	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_16432.1	chr2	180394319	180394329	+	1	NA	intron (NR_045331, intron 3 of 3)	intron (NR_045331, intron 3 of 3)	-4055	NR_029901	723954		NR_029901	ENSMUSG00000065460	Mir133a-2	Mirn133a-2|mir-133a-2	microRNA 133a-2	ncRNA
mm_37373.1	chr4	120968826	120968857	-	1	NA	3' UTR (NM_133716, exon 10 of 10)	3' UTR (NM_133716, exon 10 of 10)	4481	NR_105982	102465614		NR_105982	ENSMUSG00000106436	Mir7015	mmu-mir-7015	microRNA 7015	ncRNA
mm_38095.1	chr4	134245504	134245510	-	1	NA	promoter-TSS (NM_024215)	promoter-TSS (NM_024215)	84	NM_024215	68040	Mm.300404	NM_024215	ENSMUSG00000028840	Zfp593	3110024A21Rik|AV062409|E130106C14Rik|ZNF593	zinc finger protein 593	protein-coding
mm_136964.1	chr17	15705003	15705033	+	1	NA	promoter-TSS (NM_007690)	promoter-TSS (NM_007690)	51	NM_007690	12648	Mm.8137	NM_007690	ENSMUSG00000023852	Chd1	4930525N21Rik|AI851787|AW555109	chromodomain helicase DNA binding protein 1	protein-coding
mm_91259.1	chr10	23203831	23203835	-	1	NA	intron (NM_010167, intron 3 of 18)	intron (NM_010167, intron 3 of 18)	146057	NM_001347372	14051	Mm.332128	NM_010167	ENSMUSG00000010461	Eya4	B130023L16Rik	EYA transcriptional coactivator and phosphatase 4	protein-coding
mm_53145.1	chr6	125236105	125236110	+	1	NA	intron (NM_001033126, intron 2 of 5)	PB1|SINE|Alu	920	NM_001033126	21940	Mm.367714	NM_001033126	ENSMUSG00000030336	Cd27	S152|Tnfrsf7|Tp55	CD27 antigen	protein-coding
mm_39844.1	chr5	30889329	30889406	+	1	NA	promoter-TSS (NM_001294262)	promoter-TSS (NM_001294262)	33	NM_001294262	231093	Mm.440364	NM_174849	ENSMUSG00000029165	Agbl5	9430057O19Rik|CCP5	ATP/GTP binding protein-like 5	protein-coding
mm_170714.1	chr2	144158382	144158399	-	1	NA	Intergenic	MamTip3|DNA|hAT-Tip100	30900	NR_136884	433481	Mm.330630	NR_136884	ENSMUSG00000074758	Gm5535	EG433481	predicted gene 5535	ncRNA
mm_145378.1	chr18	56925734	56925752	+	1	NA	promoter-TSS (NM_177115)	promoter-TSS (NM_177115)	-195	NM_177115	320253	Mm.312623	NM_177115	ENSMUSG00000032656	March3	6330411I15Rik|A530081L18Rik|AI843639|MARCH-III	membrane-associated ring finger (C3HC4) 3	protein-coding
mm_126095.1	chr15	77966674	77966696	+	1	NA	exon (NM_018749, exon 5 of 15)	exon (NM_018749, exon 5 of 15)	4139	NM_018749	55944	Mm.3955	NM_018749	ENSMUSG00000016554	Eif3d	66/67kDa|AA407891|Eif3s7|eIF3p66	eukaryotic translation initiation factor 3, subunit D	protein-coding
mm_119647.1	chr14	51984858	51984908	+	1	NA	promoter-TSS (NM_001145922)	promoter-TSS (NM_001145922)	50	NM_198249	268739	Mm.9239	NM_198249	ENSMUSG00000004562	Arhgef40	E130112L23Rik|Gm669|Solo	Rho guanine nucleotide exchange factor (GEF) 40	protein-coding
mm_83725.1	chr9	50775227	50775257	-	1	NA	promoter-TSS (NM_133981)	promoter-TSS (NM_133981)	17	NR_045601	102580	Mm.160035	NM_133981	ENSMUSG00000032059	Alg9	8230402H15Rik|AI747665|B430313H07Rik|Dibd1	asparagine-linked glycosylation 9 (alpha 1,2 mannosyltransferase)	protein-coding
mm_13080.1	chr2	91206458	91206475	+	1	NA	intron (NM_007387, intron 6 of 10)	intron (NM_007387, intron 6 of 10)	3554	NM_007387	11432	Mm.45570	NM_007387	ENSMUSG00000002103	Acp2	Acp-2|LAP	acid phosphatase 2, lysosomal	protein-coding
mm_35949.1	chr4	53113498	53113509	-	1	NA	intron (NM_013454, intron 5 of 49)	intron (NM_013454, intron 5 of 49)	46392	NM_013454	11303	Mm.277376	NM_013454	ENSMUSG00000015243	Abca1	ABC-1|Abc1	ATP-binding cassette, sub-family A (ABC1), member 1	protein-coding
mm_30446.1	chr3	153725105	153725179	-	1	NA	promoter-TSS (NM_011372)	promoter-TSS (NM_011372)	-9	NM_011372	20447	Mm.296453	NM_011372	ENSMUSG00000052544	St6galnac3	Siat7c	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 3	protein-coding
mm_10238.1	chr2	6871532	6871538	+	1	NA	intron (NM_001110229, intron 2 of 14)	intron (NM_001110229, intron 2 of 14)	500	NM_001347094	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_22030.1	chr2	168051947	168051952	-	1	NA	Intergenic	Intergenic	-29055	NM_021409	58220	Mm.292834	NM_021409	ENSMUSG00000044641	Pard6b	AV025615|Par6b	par-6 family cell polarity regulator beta	protein-coding
mm_132997.1	chr16	55818555	55818558	+	1	NA	intron (NM_001159395, intron 5 of 12)	intron (NM_001159395, intron 5 of 12)	3582	NM_001159394	80859	Mm.247272	NM_030612	ENSMUSG00000035356	Nfkbiz	AA408868|INAP|Mail	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, zeta	protein-coding
mm_84657.1	chr9	71663395	71663398	-	1	NA	intron (NM_001304362, intron 8 of 18)	intron (NM_001304362, intron 8 of 18)	-71036	NM_001033208	102371	Mm.27585	NM_001033208	ENSMUSG00000041361	Myzap	AA407270|AV006038|Gcom1|Gm640|Grinl1a7|Myozap	myocardial zonula adherens protein	protein-coding
mm_83834.1	chr9	54218045	54218047	-	1	NA	Intergenic	Intergenic	-24604	NM_007810	13075	Mm.5199	NM_007810	ENSMUSG00000032274	Cyp19a1	Ar|ArKO|Cyp19|Int-5|Int5|p450arom	cytochrome P450, family 19, subfamily a, polypeptide 1	protein-coding
mm_83599.1	chr9	48494983	48494989	-	1	NA	promoter-TSS (NM_001004191)	promoter-TSS (NM_001004191)	344	NM_001326355	67010	Mm.76911	NM_144948	ENSMUSG00000042396	Rbm7	1200007M24Rik|1500011D06Rik|AU041934|AW554393	RNA binding motif protein 7	protein-coding
mm_22539.1	chr3	8743643	8743692	+	1	NA	Intergenic	Intergenic	-76629	NM_010423	15213	Mm.29581	NM_010423	ENSMUSG00000040289	Hey1	AI316788|AI414254|CHF2|HRT1|Herp2|Hesr1|bHLHb31|hesr-1	hairy/enhancer-of-split related with YRPW motif 1	protein-coding
mm_84823.1	chr9	77917145	77917164	-	1	NA	promoter-TSS (NM_134255)	promoter-TSS (NM_134255)	-211	NM_134255	68801	Mm.430736	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	ELOVL family member 5, elongation of long chain fatty acids (yeast)	protein-coding
mm_117547.1	chr13	83729682	83729711	-	1	NA	intron (NR_015561, intron 1 of 3)	intron (NR_015561, intron 1 of 3)	1590	NR_015561	320203	Mm.245636	NM_177100	ENSMUSG00000050334	C130071C03Rik	2810449C10Rik	RIKEN cDNA C130071C03 gene	ncRNA
mm_91876.1	chr10	59583282	59583294	-	1	NA	intron (NM_001033259, intron 1 of 7)	(TG)n|Simple_repeat|Simple_repeat	33404	NM_001033259	215999	Mm.296470	NM_001033259	ENSMUSG00000009647	Mcu	2010012O16Rik|AV064928|C10orf42|Ccdc109a|D130073L02Rik|Gm64	mitochondrial calcium uniporter	protein-coding
mm_112524.1	chr13	9276478	9276620	+	1	NA	promoter-TSS (NM_001081426)	promoter-TSS (NM_001081426)	24	NM_001081426	208440	Mm.217326	NM_172459	ENSMUSG00000048264	Dip2c	2900024P20Rik|9630044M06|mKIAA0934	disco interacting protein 2 homolog C	protein-coding
mm_162078.1	chrX	24775164	24775164	-	1	NA	promoter-TSS (NM_001081657)	promoter-TSS (NM_001081657)	0	NM_001081657	546282	Mm.391219	NM_001081657	ENSMUSG00000093923	Gm5935	EG546282	predicted gene 5935	protein-coding
mm_85594.1	chr9	107337996	107337999	-	1	NA	intron (NM_133984, intron 1 of 10)	MIRb|SINE|MIR	353	NM_133984	69536	Mm.259467	NM_133984	ENSMUSG00000032579	Hemk1	2310008M14Rik|AW049265	HemK methyltransferase family member 1	protein-coding
mm_33431.1	chr4	130056174	130056218	+	1	NA	intron (NM_028266, intron 11 of 69)	intron (NM_028266, intron 11 of 69)	8356	NM_028266	107581	Mm.41860	NM_028266	ENSMUSG00000040690	Col16a1	2700007F12Rik|A530052M23Rik|AI838662|CA1F	collagen, type XVI, alpha 1	protein-coding
mm_14596.1	chr2	136058225	136058237	+	1	NA	5' UTR (NM_029530, exon 1 of 6)	5' UTR (NM_029530, exon 1 of 6)	304	NM_029530	76161	Mm.41638	NM_029530	ENSMUSG00000027270	Lamp5	3110035N03Rik|6330527O06Rik|BAD-LAMP|LAMP-5	lysosomal-associated membrane protein family, member 5	protein-coding
mm_149999.1	chr19	29275062	29275080	+	1	NA	exon (NM_008413, exon 5 of 25)	exon (NM_008413, exon 5 of 25)	23268	NM_008413	16452	Mm.275839	NM_008413	ENSMUSG00000024789	Jak2	Fd17	Janus kinase 2	protein-coding
mm_30116.1	chr3	139075310	139075319	-	1	NA	promoter-TSS (NM_001286759)	promoter-TSS (NM_001286759)	-113	NM_001040690	229877	Mm.28893	NM_145544	ENSMUSG00000028149	Rap1gds1	BC011279|GDS1	RAP1, GTP-GDP dissociation stimulator 1	protein-coding
mm_60980.1	chr7	48975808	48975828	+	1	NA	intron (NM_001111016, intron 2 of 38)	PB1D10|SINE|Alu	16745	NM_001111016	78286	Mm.333881	NM_175272	ENSMUSG00000052512	Nav2	5330421F07Rik|AU067780|BQ960892|HELAD1|POMFIL2|RAINB1|RAINB2|Unc53H2|mKIAA3015	neuron navigator 2	protein-coding
mm_126126.1	chr15	78331865	78331893	+	1	NA	intron (NM_007780, intron 1 of 13)	PB1|SINE|Alu	5889	NM_007780	12983	Mm.235324	NM_007780	ENSMUSG00000071713	Csf2rb	AI848964|AIC2B|Bc|CDw131|Csf2rb1|Csfgmrb|Il3r|Il3rb|Il3rb1|Il5rb	colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage)	protein-coding
mm_82190.1	chr9	123940569	123940572	+	1	NA	Intergenic	RMER20B|LTR|ERVK	28122	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_40276.1	chr5	41707171	41707178	+	1	NA	intron (NR_132325, intron 1 of 5)	intron (NR_132325, intron 1 of 5)	517	NM_001310592	100972	Mm.41555	NM_027295	ENSMUSG00000029128	Rab28	2700023P08Rik|AW496496	RAB28, member RAS oncogene family	protein-coding
mm_99599.1	chr11	104527075	104527081	+	1	NA	intron (NM_001285988, intron 7 of 18)	intron (NM_001285988, intron 7 of 18)	23542	NM_001285990	217232	Mm.89845	NM_145436	ENSMUSG00000020687	Cdc27	AI452358|APC3|BC023187	cell division cycle 27	protein-coding
mm_12762.1	chr2	79255938	79255952	+	1	NA	intron (NM_010576, intron 1 of 27)	intron (NM_010576, intron 1 of 27)	519	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D|Itga4B	integrin alpha 4	protein-coding
mm_145133.1	chr18	44828453	44828470	+	1	NA	promoter-TSS (NM_001163013)	promoter-TSS (NM_001163013)	-204	NM_001163013	240255	Mm.244482	NM_001163013	ENSMUSG00000034653	Ythdc2	3010002F02Rik|BC037178	YTH domain containing 2	protein-coding
mm_89491.1	chr10	93819977	93819985	+	1	NA	Intergenic	Intergenic	-11574	NM_183199	327799	Mm.491598	NM_183199	ENSMUSG00000020020	Usp44	E430004F17Rik	ubiquitin specific peptidase 44	protein-coding
mm_130549.1	chr15	98957148	98957171	-	1	NA	Intergenic	Intergenic	-3658	NM_011653	22142	Mm.405359	NM_011653	ENSMUSG00000072235	Tuba1a	Tuba-1|Tuba1	tubulin, alpha 1A	protein-coding
mm_129227.1	chr15	76612966	76612972	-	1	NA	intron (NM_028064, intron 10 of 11)	intron (NM_028064, intron 10 of 11)	3883	NM_028064	72027	Mm.276829	NM_028064	ENSMUSG00000063354	Slc39a4	1600025H15Rik|AU041686|AWMS2|ZIP4	solute carrier family 39 (zinc transporter), member 4	protein-coding
mm_114485.1	chr13	69612265	69612276	+	1	NA	promoter-TSS (NM_175283)	promoter-TSS (NM_175283)	254	NM_145354	28114	Mm.260009	NM_145354	ENSMUSG00000021595	Nsun2	D13Wsu123e|Misu	NOL1/NOP2/Sun domain family member 2	protein-coding
mm_131789.1	chr16	22898871	22898875	+	1	NA	exon (NM_001276450, exon 7 of 7)	exon (NM_001276450, exon 7 of 7)	-4487	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_157669.1	chrX	59134362	59134375	-	1	NA	promoter-TSS (NM_010200)	promoter-TSS (NM_010200)	68	NM_010200	14168	Mm.7995	NM_010200	ENSMUSG00000031137	Fgf13	Fhf2	fibroblast growth factor 13	protein-coding
mm_160012.1	chr6	125603763	125603763	+	1	NA	intron (NM_011708, intron 14 of 51)	intron (NM_011708, intron 14 of 51)	50815	NM_011708	22371	Mm.22339	NM_011708	ENSMUSG00000001930	Vwf	6820430P06Rik|AI551257|B130011O06Rik|C630030D09|F8VWF|VWD	Von Willebrand factor	protein-coding
mm_38697.1	chr4	145214366	145214395	-	1	NA	3' UTR (NM_011610, exon 10 of 10)	3' UTR (NM_011610, exon 10 of 10)	-19375	NM_001276465	230895	Mm.240310	NM_001033190	ENSMUSG00000020220	Vps13d	-	vacuolar protein sorting 13D	protein-coding
mm_103438.1	chr11	75926492	75926499	-	1	NA	promoter-TSS (NM_001291159)	promoter-TSS (NM_001291159)	-604	NM_001291159	380714	Mm.425697	NM_029548	ENSMUSG00000020847	Rph3al	Gm1753|Noc2	rabphilin 3A-like (without C2 domains)	protein-coding
mm_147382.1	chr18	43737307	43737333	-	1	NA	promoter-TSS (NM_009258)	promoter-TSS (NM_009258)	-83	NM_009258	20730	Mm.272	NM_009258	ENSMUSG00000024503	Spink1	Spink3|p12	serine peptidase inhibitor, Kazal type 1	protein-coding
mm_70190.1	chr7	143780513	143780515	-	1	NA	3' UTR (NM_175534, exon 2 of 2)	3' UTR (NM_175534, exon 2 of 2)	3986	NM_175534	244238	Mm.183561	NM_175534	ENSMUSG00000048965	Mrgpre	C130069N09Rik|Ebrt3|Mgrf|MrgE	MAS-related GPR, member E	protein-coding
mm_126078.1	chr15	77775207	77775209	+	1	NA	exon (NM_022410, exon 22 of 41)	exon (NM_022410, exon 22 of 41)	-19979	NM_001081970	239552	Mm.125650	NM_001081970	ENSMUSG00000056656	Apol8	9830006J20Rik|APOL-II|Apol2	apolipoprotein L 8	protein-coding
mm_114039.1	chr13	53393683	53393694	+	1	NA	promoter-TSS (NR_037991)	promoter-TSS (NR_037991)	-1	NR_037991	100040421	Mm.83967	NR_037991	ENSMUSG00000107008	Gm2762	1700025I17Rik	predicted gene 2762	ncRNA
mm_129128.1	chr15	76190174	76190182	-	1	NA	exon (NM_201393, exon 12 of 32)	exon (NM_201393, exon 12 of 32)	5532	NM_201394	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
mm_97425.1	chr11	78069955	78069982	+	1	NA	Intergenic	Intergenic	-3037	NR_029556	387162		NR_029556	ENSMUSG00000065401	Mir144	Mirn144|mir-144|mmu-mir-144	microRNA 144	ncRNA
mm_95852.1	chr11	57831687	57831689	+	1	NA	exon (NM_008213, exon 1 of 2)	exon (NM_008213, exon 1 of 2)	459	NM_008213	15110	Mm.4746	NM_008213	ENSMUSG00000037335	Hand1	Ehand1|Hxt|Th1|Thing1|bHLHa27|eHAND	heart and neural crest derivatives expressed transcript 1	protein-coding
mm_86729.1	chr10	19065493	19065503	+	1	NA	Intergenic	Intergenic	-50088	NM_009397	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_76308.1	chr8	84638884	84638901	-	1	NA	intron (NM_001252061, intron 46 of 46)	intron (NM_001252061, intron 46 of 46)	23960	NM_010499	15936	Mm.399	NM_010499	ENSMUSG00000053560	Ier2	AI317238|Ch1|Pip92	immediate early response 2	protein-coding
mm_25719.1	chr3	122729199	122729233	+	1	NA	promoter-TSS (NM_153422)	promoter-TSS (NM_153422)	58	NM_153422	242202	Mm.134911	NM_153422	ENSMUSG00000053965	Pde5a	Cgbpde|Cn5n|PDE5a2|Pde5|Pde5a1	phosphodiesterase 5A, cGMP-specific	protein-coding
mm_117269.1	chr13	64432463	64432495	-	1	NA	promoter-TSS (NM_053180)	promoter-TSS (NM_053180)	-74	NM_053180	105278	Mm.74982	NM_053180	ENSMUSG00000021483	Cdk20	4932702G04Rik|AU019450|AW558027|CDCH|Ccrk|PNQLARE|p42	cyclin-dependent kinase 20	protein-coding
mm_78656.1	chr9	40455892	40455910	+	1	NA	promoter-TSS (NM_172768)	promoter-TSS (NM_172768)	-137	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_78871.1	chr9	44419326	44419337	+	1	NA	Intergenic	RMER21A|LTR|ERV1	-1324	NM_201372	382073	Mm.259573	NM_201372	ENSMUSG00000043923	Ccdc84	D630044F24Rik|Gm1114	coiled-coil domain containing 84	protein-coding
mm_87154.1	chr10	36506908	36506921	+	1	NA	5' UTR (NM_001253356, exon 1 of 5)	5' UTR (NM_001253356, exon 1 of 5)	107	NM_001253356	319415	Mm.332442	NM_001081208	ENSMUSG00000044499	Hs3st5	D930005L05Rik|Gm1151|Hs3ost5	heparan sulfate (glucosamine) 3-O-sulfotransferase 5	protein-coding
mm_85097.1	chr9	94533123	94533129	-	1	NA	intron (NM_001033145, intron 1 of 2)	intron (NM_001033145, intron 1 of 2)	4955	NM_001033145	68861	Mm.258746	NM_001033145	ENSMUSG00000045414	1190002N15Rik	GoPro49|HASF	RIKEN cDNA 1190002N15 gene	protein-coding
mm_144425.1	chr18	21001293	21001335	+	1	NA	promoter-TSS (NM_207623)	promoter-TSS (NM_207623)	14	NM_001303005	56515	Mm.253542	NM_019706	ENSMUSG00000024317	Rnf138	2410015A17Rik|2810480D20Rik|STRIN|Trif|Trif-d	ring finger protein 138	protein-coding
mm_36236.1	chr4	63154281	63154297	-	1	NA	promoter-TSS (NM_007443)	promoter-TSS (NM_007443)	-117	NM_007443	11699	Mm.2197	NM_007443	ENSMUSG00000028356	Ambp	AI194774|ASPI|HI-30|Intin4|Itil|UTI	alpha 1 microglobulin/bikunin	protein-coding
mm_65983.1	chr7	30457031	30457070	-	1	NA	5' UTR (NM_172898, exon 1 of 15)	5' UTR (NM_172898, exon 1 of 15)	465	NM_172898	243911	Mm.113908	NM_172898	ENSMUSG00000036915	Kirrel2	C330019F22Rik|NEPH3|NLG1	kin of IRRE like 2 (Drosophila)	protein-coding
mm_24834.1	chr3	95659051	95659082	+	1	NA	exon (NM_008562, exon 1 of 3)	exon (NM_008562, exon 1 of 3)	345	NM_008562	17210	Mm.1639	NM_008562	ENSMUSG00000038612	Mcl1	AW556805|Mcl-1	myeloid cell leukemia sequence 1	protein-coding
mm_36680.1	chr4	96507446	96507452	-	1	NA	promoter-TSS (NM_001104927)	promoter-TSS (NM_001104927)	-63	NM_001104927	665095	Mm.331717	NM_001104927	ENSMUSG00000082932	Cyp2j8	Cyp2j8-ps|OTTMUSG00000007938	cytochrome P450, family 2, subfamily j, polypeptide 8	protein-coding
mm_63736.1	chr7	130895049	130895056	+	1	NA	intron (NM_001346515, intron 5 of 12)	intron (NM_001346515, intron 5 of 12)	-13216	NR_106028	102466219		NR_106028	ENSMUSG00000104914	Mir7061	mmu-mir-7061	microRNA 7061	ncRNA
mm_81670.1	chr9	111027359	111027372	+	1	NA	exon (NM_008522, exon 10 of 17)	exon (NM_008522, exon 10 of 17)	8073	NM_008522	17002	Mm.282359	NM_008522	ENSMUSG00000032496	Ltf	Csp82|Lf|MMS10R|Ms10r	lactotransferrin	protein-coding
mm_26293.1	chr3	142507677	142507709	+	1	NA	exon (NM_153564, exon 9 of 11)	exon (NM_153564, exon 9 of 11)	10759	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_82613.1	chr9	21760276	21760294	-	1	NA	promoter-TSS (NM_026282)	promoter-TSS (NM_026282)	1	NM_026282	67629	Mm.295642	NM_026282	ENSMUSG00000074476	Spc24	2410030K01Rik|AV109292|Spbc24	SPC24, NDC80 kinetochore complex component, homolog (S. cerevisiae)	protein-coding
mm_27597.1	chr3	59131228	59131239	-	1	NA	promoter-TSS (NM_001287124)	promoter-TSS (NM_001287124)	95	NM_001287121	140795	Mm.439021	NM_133200	ENSMUSG00000036381	P2ry14	A330108O13Rik|Gpr105|P2Y14	purinergic receptor P2Y, G-protein coupled, 14	protein-coding
mm_123702.1	chr14	69732511	69732581	-	1	NA	promoter-TSS (NM_134078)	promoter-TSS (NM_134078)	24	NM_134078	105513	Mm.159637	NM_134078	ENSMUSG00000034190	Chmp7	4930596K11Rik|6330407G04Rik|AI450338|AW550775	charged multivesicular body protein 7	protein-coding
mm_7931.1	chr1	133911036	133911049	-	1	NA	3' UTR (NM_054077, exon 3 of 3)	3' UTR (NM_054077, exon 3 of 3)	-3043	NM_001160420	269120	Mm.59985	NM_054076	ENSMUSG00000010311	Optc	-	opticin	protein-coding
mm_145905.1	chr18	65800608	65800618	+	1	NA	promoter-TSS (NM_025468)	promoter-TSS (NM_025468)	35	NM_025468	66286	Mm.27800	NM_025468	ENSMUSG00000024516	Sec11c	1810029G24Rik|Sec11l3	SEC11 homolog C, signal peptidase complex subunit	protein-coding
mm_15544.1	chr2	158385699	158385717	+	1	NA	3' UTR (NM_175692, exon 5 of 5)	3' UTR (NM_175692, exon 5 of 5)	10070	NM_175692	319317	Mm.294494	NM_175692	ENSMUSG00000044349	Snhg11	A930034L06Rik|AI854265|AL022637|AW319638|E130013N09Rik	small nucleolar RNA host gene 11	protein-coding
mm_126152.1	chr15	78409714	78409728	+	1	NA	intron (NM_138670, intron 1 of 2)	intron (NM_138670, intron 1 of 2)	2617	NM_138670	246221	Mm.294215	NM_138670	ENSMUSG00000071711	Mpst	Mst	mercaptopyruvate sulfurtransferase	protein-coding
mm_38789.1	chr4	148089210	148089218	-	1	NA	Intergenic	Intergenic	-1150	NM_001301281	11610	Mm.46247	NM_009642	ENSMUSG00000029007	Agtrap	3300002E14Rik|AT1R|Atrap|D4Wsu124e	angiotensin II, type I receptor-associated protein	protein-coding
mm_102918.1	chr11	69600008	69600018	-	1	NA	3' UTR (NM_013415, exon 7 of 7)	3' UTR (NM_013415, exon 7 of 7)	5947	NM_013415	11932	Mm.235204	NM_013415	ENSMUSG00000041329	Atp1b2	Amog|Atpb-2	ATPase, Na+/K+ transporting, beta 2 polypeptide	protein-coding
mm_10294.1	chr2	10372427	10372497	+	1	NA	promoter-TSS (NM_177386)	promoter-TSS (NM_177386)	26	NM_177386	353282	Mm.329991	NM_177386	ENSMUSG00000061186	Sfmbt2	D2Wsu23e|D330030P06Rik	Scm-like with four mbt domains 2	protein-coding
mm_60327.1	chr7	44236150	44236183	+	1	NA	promoter-TSS (NR_029436)	promoter-TSS (NR_029436)	-44	NR_029436	70004	Mm.158317	NR_029436	ENSMUSG00000038782	1700028J19Rik	-	RIKEN cDNA 1700028J19 gene	ncRNA
mm_130190.1	chr15	93927044	93927053	-	1	NA	promoter-TSS (NR_045737)	promoter-TSS (NR_045737)	63	NR_045737	77248	Mm.410768	NR_045737		9430014N10Rik	-	RIKEN cDNA 9430014N10 gene	ncRNA
mm_96666.1	chr11	69409728	69409745	+	1	NA	intron (NM_001017426, intron 1 of 22)	intron (NM_001017426, intron 1 of 22)	3939	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_87403.1	chr10	45634575	45634596	+	1	NA	intron (NM_172473, intron 6 of 23)	intron (NM_172473, intron 6 of 23)	56756	NM_172473	209462	Mm.458633	NM_172473	ENSMUSG00000038822	Hace1	1700042J16Rik|A730034A22Rik|BC025474	HECT domain and ankyrin repeat containing, E3 ubiquitin protein ligase 1	protein-coding
mm_65099.1	chr7	19280033	19280056	-	1	NA	promoter-TSS (NM_177691)	promoter-TSS (NM_177691)	5	NM_177691	232941	Mm.134068	NM_177691	ENSMUSG00000030402	Ppm1n	A930002H20|C79127	protein phosphatase, Mg2+/Mn2+ dependent, 1N (putative)	protein-coding
mm_14264.1	chr2	128591206	128591223	+	1	NA	Intergenic	Intergenic	-1127	NM_001310641	241634	Mm.297682	NM_001310641	ENSMUSG00000074812	Spdye4c	Gm355|SpeedyB3|SpyB3	speedy/RINGO cell cycle regulator family, member E4C	protein-coding
mm_13537.1	chr2	110654922	110654928	+	1	NA	TTS (NM_001128103)	TTS (NM_001128103)	57626	NM_001177624	241612	Mm.277148	NM_001003915	ENSMUSG00000041644	Slc5a12	AI315119|D630015G19|SMCT2	solute carrier family 5 (sodium/glucose cotransporter), member 12	protein-coding
mm_173224.1	chrX	75104440	75104444	+	1	NA	exon (NM_001030307, exon 10 of 15)	exon (NM_001030307, exon 10 of 15)	8588	NM_001030307	245474	Mm.291062	NM_001030307	ENSMUSG00000031403	Dkc1	BC068171	dyskeratosis congenita 1, dyskerin	protein-coding
mm_30464.1	chr3	154094091	154094100	-	1	NA	intron (NM_001081263, intron 1 of 21)	intron (NM_001081263, intron 1 of 21)	120659	NM_001081263	242259	Mm.239962	NM_001081263	ENSMUSG00000028360	Slc44a5	AA117069|Gm422	solute carrier family 44, member 5	protein-coding
mm_19481.1	chr2	93037237	93037259	-	1	NA	intron (NM_001177536, intron 1 of 6)	intron (NM_001177536, intron 1 of 6)	7900	NR_110333	433456	Mm.235231	NM_001002794	ENSMUSG00000075027	4631405J19Rik	-	RIKEN cDNA 4631405J19 gene	ncRNA
mm_102440.1	chr11	59526692	59526711	-	1	NA	Intergenic	Intergenic	-15985	NM_145827	216799	Mm.54174	NM_145827	ENSMUSG00000032691	Nlrp3	AGTAVPRL|AII/AVP|Cias1|FCAS|FCU|MWS|Mmig1|NALP3|Pypaf1	NLR family, pyrin domain containing 3	protein-coding
mm_75547.1	chr8	57529111	57529130	-	1	NA	intron (NM_001167981, intron 11 of 11)	intron (NM_001167981, intron 11 of 11)	17277	NM_008252	97165	Mm.276881	NM_008252	ENSMUSG00000054717	Hmgb2	C80539|HMG-2|Hmg2	high mobility group box 2	protein-coding
mm_93242.1	chr10	95416008	95416035	-	1	NA	promoter-TSS (NM_001168657)	promoter-TSS (NM_001168657)	191	NM_001168655	216233	Mm.474283	NM_007706	ENSMUSG00000020027	Socs2	8030460M17|AI527257|AW108012|CIS2|Cish2|D130043N08Rik|JAB|SOCS-2|SSI-2|hg	suppressor of cytokine signaling 2	protein-coding
mm_23882.1	chr3	83031031	83031039	+	1	NA	exon (NM_010196, exon 5 of 5)	exon (NM_010196, exon 5 of 5)	4882	NM_001111048	14161	Mm.88793	NM_010196	ENSMUSG00000028001	Fga	ENSMUSG00000059807|Fib	fibrinogen alpha chain	protein-coding
mm_144258.1	chr18	11047622	11047639	+	1	NA	non-coding (NR_105023, exon 4 of 6)	non-coding (NR_105023, exon 4 of 6)	-4880	NM_010258	14465	Mm.329287	NM_010258	ENSMUSG00000005836	Gata6	AA410133|GATA-6	GATA binding protein 6	protein-coding
mm_122608.1	chr14	51057481	51057487	-	1	NA	promoter-TSS (NM_001011875)	promoter-TSS (NM_001011875)	-242	NM_001011875	497106	Mm.379740	NM_001011875	ENSMUSG00000068407	Rnase12	Rai1	ribonuclease, RNase A family, 12 (non-active)	protein-coding
mm_131544.1	chr16	17807308	17807316	+	1	NA	exon (NM_153790, exon 11 of 11)	exon (NM_153790, exon 11 of 11)	10030	NM_153790	224024	Mm.194950	NM_153790	ENSMUSG00000012017	Scarf2	NSR1|SREC-II|SRECRP-1|Scatf1|Srec2|SrecII	scavenger receptor class F, member 2	protein-coding
mm_87410.1	chr10	45868747	45868762	+	1	NA	Intergenic	Intergenic	61050	NR_040624	320363	Mm.123343	NR_040624	ENSMUSG00000110874	D030045P18Rik	-	RIKEN cDNA D030045P18 gene	ncRNA
mm_112260.1	chr12	113932425	113932432	-	1	NA	Intergenic	Intergenic	388520	NM_174885	238406	Mm.188683	NM_174885	ENSMUSG00000043945	Adam6a	Adam6|tMDCIV	a disintegrin and metallopeptidase domain 6A	protein-coding
mm_27878.1	chr3	79173051	79173057	-	1	NA	Intergenic	Intergenic	-27179	NM_001099624	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_146273.1	chr18	77882221	77882232	+	1	NA	3' UTR (NM_013831, exon 15 of 15)	3' UTR (NM_013831, exon 15 of 15)	-56241	NM_001195633	100502841	Mm.297782	NM_001195633	ENSMUSG00000039840	Epg5	4732475F16|5430411K18Rik|AI661957|AW456499|mKIAA1632	ectopic P-granules autophagy protein 5 homolog (C. elegans)	protein-coding
mm_139298.1	chr17	48324216	48324223	+	1	NA	3' UTR (NM_177083, exon 6 of 6)	3' UTR (NM_177083, exon 6 of 6)	8057	NM_177083	320148	Mm.123455	NM_177083	ENSMUSG00000043740	B430306N03Rik	Treml6	RIKEN cDNA B430306N03 gene	protein-coding
mm_114140.1	chr13	55272945	55272948	+	1	NA	intron (NM_008739, intron 9 of 22)	B3|SINE|B2	49034	NM_009000	19336	Mm.220923	NM_009000	ENSMUSG00000034789	Rab24	6530406O07Rik	RAB24, member RAS oncogene family	protein-coding
mm_159411.1	chr3	103576216	103576216	+	1	NA	promoter-TSS (NM_001276680)	promoter-TSS (NM_001276680)	90	NM_001276681	54524	Mm.88818	NM_018800	ENSMUSG00000027849	Syt6	3110037A08Rik|AW048930|sytVI	synaptotagmin VI	protein-coding
mm_134991.1	chr16	32145687	32145690	-	1	NA	intron (NM_001347182, intron 1 of 1)	B1_Mur1|SINE|Alu	19788	NM_146069	224109	Mm.33498	NM_146069	ENSMUSG00000052384	Nrros	E430025L02Rik|Lrcc33|Lrrc33	negative regulator of reactive oxygen species	protein-coding
mm_112270.1	chr12	114176910	114176918	-	1	NA	Intergenic	Intergenic	292552	NR_106062	102465663		NR_106062	ENSMUSG00000105438	Mir7094-1	mmu-mir-7094-1	microRNA 7094-1	ncRNA
mm_85593.1	chr9	107334606	107334618	-	1	NA	intron (NM_133984, intron 4 of 10)	intron (NM_133984, intron 4 of 10)	3738	NM_133984	69536	Mm.259467	NM_133984	ENSMUSG00000032579	Hemk1	2310008M14Rik|AW049265	HemK methyltransferase family member 1	protein-coding
mm_91225.1	chr10	22067663	22067665	-	1	NA	exon (NM_053264, exon 1 of 1)	exon (NM_053264, exon 1 of 1)	415	NM_053264	114671	Mm.288194	NM_053264	ENSMUSG00000069712	4930444G20Rik	-	RIKEN cDNA 4930444G20 gene	protein-coding
mm_166583.1	chr6	53452912	53452928	-	1	NA	intron (NM_001327821, intron 5 of 10)	intron (NM_001327821, intron 5 of 10)	-120454	NM_172728	231991	Mm.227444	NM_172728	ENSMUSG00000053007	Creb5	9430076C15Rik|CRE-BPa|Crebpa|D430026C09Rik	cAMP responsive element binding protein 5	protein-coding
mm_126021.1	chr15	76690585	76690610	+	1	NA	5' UTR (NM_033371, exon 2 of 11)	5' UTR (NM_033371, exon 2 of 11)	-6129	NM_182805	76282	Mm.30130	NM_182805	ENSMUSG00000022546	Gpt	1300007J06Rik|2310022B03Rik|ALT|ALT1|Gpt-1|Gpt1	glutamic pyruvic transaminase, soluble	protein-coding
mm_78991.1	chr9	45403143	45403158	+	1	NA	promoter-TSS (NM_052823)	promoter-TSS (NM_052823)	12	NM_052823	11936	Mm.22742	NM_007503	ENSMUSG00000059412	Fxyd2	Atp1g1	FXYD domain-containing ion transport regulator 2	protein-coding
mm_169842.1	chr16	3115508	3115524	-	1	NA	Intergenic	Intergenic	-476882	NM_146860	258859	Mm.377723	NM_146860	ENSMUSG00000051003	Olfr161	MOR131-1|OR912-47M6	olfactory receptor 161	protein-coding
mm_160779.1	chr10	127341470	127341470	-	1	NA	intron (NM_010296, intron 1 of 12)	intron (NM_010296, intron 1 of 12)	109	NM_010296	14632	Mm.391450	NM_010296	ENSMUSG00000025407	Gli1	AV235269|Zfp-5|Zfp5	GLI-Kruppel family member GLI1	protein-coding
mm_138541.1	chr17	35262803	35262823	+	1	NA	promoter-TSS (NM_001267808)	promoter-TSS (NM_001267808)	-281	NM_010380	14964	Mm.439675	NM_010380	ENSMUSG00000073411	H2-D1	H-2D|H2-D	histocompatibility 2, D region locus 1	protein-coding
mm_98402.1	chr11	94328147	94328176	+	1	NA	5' UTR (NM_027799, exon 1 of 5)	5' UTR (NM_027799, exon 1 of 5)	160	NM_146024	71452	Mm.141054	NM_027799	ENSMUSG00000020864	Ankrd40	1110011C06Rik|5530600A18Rik|Gcap15	ankyrin repeat domain 40	protein-coding
mm_18178.1	chr2	45110269	45110295	-	1	NA	promoter-TSS (NM_001289521)	promoter-TSS (NM_001289521)	-5	NM_001289521	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_119328.1	chr14	38626748	38626750	+	1	NA	intron (NM_001190188, intron 3 of 8)	intron (NM_001190188, intron 3 of 8)	-271553	NR_045713	75170	Mm.372967	NR_045713	ENSMUSG00000093528	Nrg3os	4930529F24Rik	neuregulin 3, opposite strand	ncRNA
mm_70410.1	chr8	11406822	11406825	+	1	NA	exon (NM_009932, exon 12 of 48)	exon (NM_009932, exon 12 of 48)	-71106	NR_126558	102132	Mm.37632	NR_126558	ENSMUSG00000096957	E230013L22Rik	AI645545	RIKEN cDNA E230013L22 gene	ncRNA
mm_173078.1	chrX	137427711	137427715	+	1	NA	Intergenic	L1Md_T|LINE|L1	-143041	NM_030688	60367	Mm.328321	NM_030688	ENSMUSG00000059203	Il1rapl2	-	interleukin 1 receptor accessory protein-like 2	protein-coding
mm_6263.1	chr1	69537201	69537209	-	1	NA	3' UTR (NM_011770, exon 8 of 8)	3' UTR (NM_011770, exon 8 of 8)	148755	NM_011770	22779	Mm.106343	NM_011770	ENSMUSG00000025997	Ikzf2	A730095J18Rik|Helios|Zfpn1a2|Znfn1a2	IKAROS family zinc finger 2	protein-coding
mm_22648.1	chr3	14869217	14869224	+	1	NA	intron (NM_007606, intron 4 of 6)	intron (NM_007606, intron 4 of 6)	5682	NM_007606	12350	Mm.300	NM_007606	ENSMUSG00000027559	Car3	BB219044|Ca3|Car-3	carbonic anhydrase 3	protein-coding
mm_96058.1	chr11	59566379	59566391	+	1	NA	3' UTR (NM_145827, exon 10 of 10)	3' UTR (NM_145827, exon 10 of 10)	5353	NM_001011789	257962	Mm.377316	NM_001011789	ENSMUSG00000059610	Olfr222	MOR256-45P	olfactory receptor 222	protein-coding
mm_44305.1	chr5	8996999	8997038	-	1	NA	intron (NM_023733, intron 1 of 17)	CpG	128	NM_023733	74114	Mm.28197	NM_023733	ENSMUSG00000003623	Crot	1200003H03Rik	carnitine O-octanoyltransferase	protein-coding
mm_172590.1	chr8	126422087	126422095	-	1	NA	promoter-TSS (NM_174987)	promoter-TSS (NM_174987)	-410	NM_174987	67892	Mm.31946	NM_174987	ENSMUSG00000051671	Coa6	1810063B05Rik|AI447995	cytochrome c oxidase assembly factor 6	protein-coding
mm_35018.1	chr4	3875169	3875179	-	1	NA	Intergenic	CpG	-3069	NM_020021	17451	Mm.459300	NM_020021	ENSMUSG00000078365	Mos	c-mos	Moloney sarcoma oncogene	protein-coding
mm_151015.1	chr19	46761628	46761638	+	1	NA	promoter-TSS (NM_001102471)	promoter-TSS (NM_001102471)	24	NM_001102471	94219	Mm.306903	NM_033569	ENSMUSG00000064105	Cnnm2	AU015877|AW048635|Acdp2|Clp2	cyclin M2	protein-coding
mm_151976.1	chr19	5826920	5826929	-	1	NA	non-coding (NR_131212, exon 1 of 1)	non-coding (NR_131212, exon 1 of 1)	18554	NR_131212	66961	Mm.281895	NR_003513	ENSMUSG00000092274	Neat1	2310043N10Rik|VINC	nuclear paraspeckle assembly transcript 1 (non-protein coding)	ncRNA
mm_121138.1	chr14	101887470	101887480	+	1	NA	exon (NM_201529, exon 10 of 31)	exon (NM_201529, exon 10 of 31)	46852	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_117565.1	chr13	85285460	85285464	-	1	NA	intron (NM_145452, intron 1 of 24)	PB1|SINE|Alu	4024	NM_145452	218397	Mm.259653	NM_145452	ENSMUSG00000021549	Rasa1	Gap|RasGAP|Rasa	RAS p21 protein activator 1	protein-coding
mm_87066.1	chr10	29143650	29143720	+	1	NA	promoter-TSS (NM_026138)	promoter-TSS (NM_026138)	-311	NM_026138	67412	Mm.390264	NM_026138	ENSMUSG00000038916	Soga3	6330407J23Rik	SOGA family member 3	protein-coding
mm_122449.1	chr14	45299957	45299969	-	1	NA	intron (NM_015774, intron 6 of 15)	intron (NM_015774, intron 6 of 15)	18609	NM_015774	50527	Mm.387108	NM_015774	ENSMUSG00000021831	Ero1l	ERO1-L|Ero1a	ERO1-like (S. cerevisiae)	protein-coding
mm_111830.1	chr12	107146787	107146792	-	1	NA	Intergenic	MIRc|SINE|MIR	-430465	NR_015512	71033	Mm.159404	NR_015512	ENSMUSG00000085820	4933406K04Rik	4930426M03Rik|4930485I22Rik|4933427G14Rik	RIKEN cDNA 4933406K04 gene	ncRNA
mm_114842.1	chr13	92642228	92642236	+	1	NA	intron (NM_172588, intron 1 of 11)	intron (NM_172588, intron 1 of 11)	31094	NM_172588	218442	Mm.297970	NM_172588	ENSMUSG00000021703	Serinc5	A130038L21Rik|AIGP3|C86123|TPO1	serine incorporator 5	protein-coding
mm_72552.1	chr8	84026150	84026169	+	1	NA	intron (NM_028877, intron 2 of 6)	CpG	4685	NM_028877	74337	Mm.250943	NM_028877	ENSMUSG00000047986	Palm3	4432412L15Rik|AL024300	paralemmin 3	protein-coding
mm_161181.1	chr13	47014602	47014602	-	1	NA	exon (NM_175340, exon 1 of 1)	exon (NM_175340, exon 1 of 1)	248	NM_175340	105193	Mm.25593	NM_175340	ENSMUSG00000044231	Nhlrc1	AI505271|B230309E09Rik|EPM2B	NHL repeat containing 1	protein-coding
mm_130255.1	chr15	96642237	96642271	-	1	NA	promoter-TSS (NM_001166456)	promoter-TSS (NM_001166456)	89	NM_001166456	105727	Mm.103568	NM_134086	ENSMUSG00000023169	Slc38a1	AA408026|AA409865|AL022800|AU015942|NAT2	solute carrier family 38, member 1	protein-coding
mm_107481.1	chr12	37880914	37880924	+	1	NA	5' UTR (NM_178681, exon 1 of 25)	5' UTR (NM_178681, exon 1 of 25)	214	NM_178681	217480	Mm.126525	NM_178681	ENSMUSG00000036095	Dgkb	6430574F24|90kda|C630029D13Rik|DAGK2|DGK|DGK-beta|mKIAA0718	diacylglycerol kinase, beta	protein-coding
mm_33545.1	chr4	130934640	130934673	+	1	NA	3' UTR (NM_010686, exon 8 of 8)	3' UTR (NM_010686, exon 8 of 8)	-9729	NM_010769	17180	Mm.271796	NM_010769	ENSMUSG00000040533	Matn1	CMP|Crtm|Mat1|matrilin-1	matrilin 1, cartilage matrix protein	protein-coding
mm_50624.1	chr6	50144728	50144748	+	1	NA	intron (NM_019939, intron 2 of 12)	ORR1F|LTR|ERVL-MaLR	34497	NM_001164733	56524	Mm.41288	NM_008016	ENSMUSG00000038388	Mpp6	P55t|Pals2	membrane protein, palmitoylated 6 (MAGUK p55 subfamily member 6)	protein-coding
mm_151457.1	chr19	58144044	58144056	+	1	NA	Intergenic	Intergenic	92883	NR_049196	100885835		NR_049196	ENSMUSG00000093757	Mir5623	Gm26068|mir-5623|mmu-mir-5623	microRNA 5623	ncRNA
mm_156085.1	chrX	110814264	110814276	+	1	NA	promoter-TSS (NM_008901)	promoter-TSS (NM_008901)	-109	NM_008901	18994	Mm.56946	NM_008901	ENSMUSG00000056854	Pou3f4	Brn-4|Brn4|OTF-9|Otf9|Slf|oct-9	POU domain, class 3, transcription factor 4	protein-coding
mm_116303.1	chr13	36734267	36734275	-	1	NA	exon (NM_153529, exon 1 of 3)	exon (NM_153529, exon 1 of 3)	206	NM_153529	68404	Mm.232930	NM_153529	ENSMUSG00000039114	Nrn1	0710008J23Rik|Cpg15|Nrn	neuritin 1	protein-coding
mm_13253.1	chr2	98663886	98663890	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	1196231	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_106447.1	chr11	119937428	119937444	-	1	NA	Intergenic	Intergenic	-5656	NM_001037754	108100	Mm.197534	NM_130862	ENSMUSG00000025372	Baiap2	IRSp53|R75030	brain-specific angiogenesis inhibitor 1-associated protein 2	protein-coding
mm_45584.1	chr5	74065737	74065758	-	1	NA	intron (NM_177561, intron 1 of 8)	intron (NM_177561, intron 1 of 8)	2664	NM_177561	69727	Mm.48795	NM_177561	ENSMUSG00000054814	Usp46	1190009E20Rik|2410018I08Rik|AI451644	ubiquitin specific peptidase 46	protein-coding
mm_96065.1	chr11	59662700	59662759	+	1	NA	5' UTR (NM_201245, exon 1 of 23)	5' UTR (NM_201245, exon 1 of 23)	234	NM_012027	26936	Mm.2402	NM_012027	ENSMUSG00000005417	Mprip	9530046C02|AA536749|AI647711|C76423|RIP3|Rhoip3|mKIAA0864|p116Rip	myosin phosphatase Rho interacting protein	protein-coding
mm_3999.1	chr1	164569739	164569765	+	1	NA	Intergenic	RLTR42-int|LTR|ERVK	-111397	NM_009721	11931	Mm.4550	NM_009721	ENSMUSG00000026576	Atp1b1	Atp4b|Atpb|Atpb-1|NKbeta1	ATPase, Na+/K+ transporting, beta 1 polypeptide	protein-coding
mm_87039.1	chr10	28730814	28730819	+	1	NA	intron (NM_178666, intron 2 of 5)	intron (NM_178666, intron 2 of 5)	62456	NM_178666	210757	Mm.123021	NM_178666	ENSMUSG00000049109	Themis	E430004N04Rik|Gasp|Spot|Tsepa|thylex	thymocyte selection associated	protein-coding
mm_6106.1	chr1	64033533	64033552	-	1	NA	Intergenic	Intergenic	8959	NR_105864	102466760		NR_105864	ENSMUSG00000098487	Mir6899	Gm27384|mmu-mir-6899	microRNA 6899	ncRNA
mm_78396.1	chr9	28920421	28920454	+	1	NA	3' UTR (NM_177906, exon 8 of 8)	3' UTR (NM_177906, exon 8 of 8)	1042692	NM_172290	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding
mm_104275.1	chr11	89403511	89403519	-	1	NA	intron (NM_001327810, intron 19 of 19)	intron (NM_001327810, intron 19 of 19)	15433	NM_172534	382543	Mm.60997	NM_172534	ENSMUSG00000047773	Ankfn1	4932411E22Rik|Gm1175|nmf9	ankyrin-repeat and fibronectin type III domain containing 1	protein-coding
mm_107206.1	chr12	26443913	26443919	+	1	NA	3' UTR (NM_021384, exon 6 of 6)	3' UTR (NM_021384, exon 6 of 6)	12536	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_106525.1	chr11	120567995	120568027	-	1	NA	exon (NM_011032, exon 4 of 11)	exon (NM_011032, exon 4 of 11)	4925	NM_011032	18453	Mm.16660	NM_011032	ENSMUSG00000025130	P4hb	ERp59|PDI|Pdia1|Thbp	prolyl 4-hydroxylase, beta polypeptide	protein-coding
mm_97154.1	chr11	75463927	75463943	+	1	NA	TTS (NR_029739)	TTS (NR_029739)	219	NR_029739	387141		NR_029739	ENSMUSG00000065529	Mir22	Mirn22|mmu-mir-22	microRNA 22	ncRNA
mm_47946.1	chr5	135404770	135404813	-	1	NA	Intergenic	Intergenic	-10245	NM_148932	107939	Mm.28399	NM_148932	ENSMUSG00000053293	Pom121	2610027A18Rik|C80273|mKIAA0618	nuclear pore membrane protein 121	protein-coding
mm_139638.1	chr17	57377119	57377135	+	1	NA	intron (NM_010130, intron 2 of 21)	Lx5b|LINE|L1	18441	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_115399.1	chr13	113818167	113818181	+	1	NA	intron (NM_172595, intron 1 of 4)	intron (NM_172595, intron 1 of 4)	23666	NM_172595	218639	Mm.79837	NM_172595	ENSMUSG00000042348	Arl15	A430036I03|Arfrp2|C230032K13Rik	ADP-ribosylation factor-like 15	protein-coding
mm_112914.1	chr13	20923070	20923080	+	1	NA	intron (NM_012054, intron 11 of 20)	Lx8b|LINE|L1	128962	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_101593.1	chr11	34682227	34682251	-	1	NA	intron (NM_033374, intron 22 of 51)	RLTR44-int|LTR|ERVK	101666	NM_033374	94176	Mm.380679	NM_033374	ENSMUSG00000020143	Dock2	AI662014|AW122239|CED-5|Hch|MBC	dedicator of cyto-kinesis 2	protein-coding
mm_12634.1	chr2	74705179	74705189	+	1	NA	promoter-TSS (NM_001290730)	promoter-TSS (NM_001290730)	-305	NM_001290730	15437	Mm.280673	NM_008276	ENSMUSG00000027102	Hoxd8	4921540P06Rik|AI047735|Hox-4.3|Hox-5.4	homeobox D8	protein-coding
mm_68088.1	chr7	101903749	101903777	-	1	NA	promoter-TSS (NM_001282088)	promoter-TSS (NM_001282088)	22	NM_001282088	791260	Mm.475469	NM_001081679	ENSMUSG00000078630	Tomt	Comt2|F930017I19Rik	transmembrane O-methyltransferase	protein-coding
mm_125197.1	chr15	32920783	32920826	+	1	NA	promoter-TSS (NM_008304)	promoter-TSS (NM_008304)	81	NM_008304	15529	Mm.234266	NM_008304	ENSMUSG00000022261	Sdc2	4833414L08Rik|AA960457|Hspg1|Synd2|syndecan-2	syndecan 2	protein-coding
mm_78142.1	chr9	20972961	20972974	+	1	NA	intron (NM_010333, intron 1 of 1)	intron (NM_010333, intron 1 of 1)	3826	NM_010333	14739	Mm.46493	NM_010333	ENSMUSG00000043895	S1pr2	1100001A16Rik|Edg5|Gpcr13|H218|LPb2|S1P2	sphingosine-1-phosphate receptor 2	protein-coding
mm_157253.1	chrX	19150774	19150790	-	1	NA	Intergenic	Intergenic	-3811	NR_029807	723828		NR_029807	ENSMUSG00000065471	Mir222	Mirn222|mir-222|mmu-mir-222	microRNA 222	ncRNA
mm_131082.1	chr16	4741595	4741630	+	1	NA	promoter-TSS (NM_010443)	promoter-TSS (NM_010443)	-1	NM_010443	15369	Mm.272866	NM_010443	ENSMUSG00000004070	Hmox2	HO-2|HO2	heme oxygenase 2	protein-coding
mm_126575.1	chr15	82256327	82256333	+	1	NA	non-coding (NR_037698, exon 1 of 2)	non-coding (NR_037698, exon 1 of 2)	307	NR_037698	76505	Mm.23023	NR_037697	ENSMUSG00000068099	1500009C09Rik	-	RIKEN cDNA 1500009C09 gene	ncRNA
mm_83791.1	chr9	52172603	52172654	-	1	NA	Intergenic	Intergenic	-4517	NM_001162921	244871	Mm.295686	NM_001162921	ENSMUSG00000035164	Zc3h12c	A230108E06|C230027N18Rik|mKIAA1726	zinc finger CCCH type containing 12C	protein-coding
mm_41015.1	chr5	81043225	81043269	+	1	NA	intron (NM_198702, intron 1 of 27)	intron (NM_198702, intron 1 of 27)	21654	NM_198702	319387	Mm.273631	NM_198702	ENSMUSG00000037605	Adgrl3	5430402I23Rik|CIRL-3|D130075K09Rik|Gm1379|LEC3|Lphn3|mKIAA0768	adhesion G protein-coupled receptor L3	protein-coding
mm_158925.1	chr1	59764487	59764487	+	1	NA	5' UTR (NM_007561, exon 1 of 13)	5' UTR (NM_007561, exon 1 of 13)	208	NM_007561	12168	Mm.7106	NM_007561	ENSMUSG00000067336	Bmpr2	2610024H22Rik|AL117858|AW546137|BB189135|BMP-2|BMPR-2|BMPR-II|BMPRII|BRK-3|Gm20272	bone morphogenetic protein receptor, type II (serine/threonine kinase)	protein-coding
mm_43674.1	chr5	138789283	138789317	+	1	NA	intron (NM_030565, intron 3 of 9)	intron (NM_030565, intron 3 of 9)	-30780	NM_001195128	384244	Mm.485002	NM_001195128	ENSMUSG00000094504	Gm5294	EG384244	predicted gene 5294	protein-coding
mm_72609.1	chr8	84597114	84597150	+	1	NA	intron (NM_001252059, intron 30 of 45)	intron (NM_001252059, intron 30 of 45)	65720	NM_010499	15936	Mm.399	NM_010499	ENSMUSG00000053560	Ier2	AI317238|Ch1|Pip92	immediate early response 2	protein-coding
mm_4014.1	chr1	165461336	165461346	+	1	NA	promoter-TSS (NM_028759)	promoter-TSS (NM_028759)	133	NM_027430	70456	Mm.195625	NM_027430	ENSMUSG00000026568	Mpc2	0610006C01Rik|2010002I07Rik|2610205H19Rik|AA108335|Brp44|ESTM43	mitochondrial pyruvate carrier 2	protein-coding
mm_143628.1	chr17	78895092	78895107	-	1	NA	intron (NM_001163625, intron 3 of 6)	intron (NM_001163625, intron 3 of 6)	11893	NM_001163625	73671	Mm.45514	NM_001163625	ENSMUSG00000038045	Sult6b1	2410078J06Rik|AV101767|ST6B1	sulfotransferase family, cytosolic, 6B, member 1	protein-coding
mm_98290.1	chr11	89066362	89066406	+	1	NA	intron (NR_110336, intron 2 of 3)	intron (NR_110336, intron 2 of 3)	5633	NR_110336	414094	Mm.124287	NM_001001497		Dgkeos	A930013B10Rik	diacylglycerol kinase, epsilon, opposite strand	ncRNA
mm_123288.1	chr14	61440064	61440102	-	1	NA	promoter-TSS (NM_008466)	promoter-TSS (NM_008466)	-136	NM_008466	16648	Mm.25548	NM_008466	ENSMUSG00000021929	Kpna3	IPOA4	karyopherin (importin) alpha 3	protein-coding
mm_71347.1	chr8	45628081	45628093	+	1	NA	5' UTR (NM_001310707, exon 1 of 24)	5' UTR (NM_001310707, exon 1 of 24)	336	NM_001310707	234214	Mm.211096	NM_172752	ENSMUSG00000031626	Sorbs2	2010203O03Rik|9430041O17Rik|A530071H08|Argbp2|mKIAA0777|nArgBP2	sorbin and SH3 domain containing 2	protein-coding
mm_133103.1	chr16	65219385	65219408	+	1	NA	Intergenic	Intergenic	-113612	NM_008310	15557	Mm.5040	NM_008310	ENSMUSG00000050783	Htr1f	Htr1eb	5-hydroxytryptamine (serotonin) receptor 1F	protein-coding
mm_154248.1	chr19	60766596	60766607	-	1	NA	exon (NM_010123, exon 19 of 22)	exon (NM_010123, exon 19 of 22)	7784	NR_034047	100217439		NR_034047		Snora19	MBI-51	small nucleolar RNA, H/ACA box 19	snoRNA
mm_156287.1	chrX	136837423	136837433	+	1	NA	3' UTR (NM_011123, exon 7 of 7)	3' UTR (NM_011123, exon 7 of 7)	14682	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_148483.1	chr19	4140291	4140321	+	1	NA	promoter-TSS (NM_144532)	promoter-TSS (NM_144532)	507	NM_206973	269053	Mm.131677	NM_206973	ENSMUSG00000044724	Gpr152	A930009H15Rik|Gm673	G protein-coupled receptor 152	protein-coding
mm_117087.1	chr13	59746930	59746940	-	1	NA	Intergenic	Intergenic	13285	NR_045977	75223	Mm.444771	NR_045977	ENSMUSG00000097502	4930528D03Rik	-	RIKEN cDNA 4930528D03 gene	ncRNA
mm_129111.1	chr15	76069761	76069777	-	1	NA	promoter-TSS (NM_134089)	promoter-TSS (NM_134089)	15	NM_134089	105782	Mm.25568	NM_134089	ENSMUSG00000022568	Scrib	AI118201|CRIB|Crc|SCRIB1|Scrb1|mKIAA0147|vartul	scribbled planar cell polarity	protein-coding
mm_24036.1	chr3	87796890	87796894	+	1	NA	promoter-TSS (NM_011832)	promoter-TSS (NM_011832)	-59	NM_011832	23920	Mm.42041	NM_011832	ENSMUSG00000005640	Insrr	Irr	insulin receptor-related receptor	protein-coding
mm_130432.1	chr15	98165607	98165609	-	1	NA	promoter-TSS (NM_001170711)	promoter-TSS (NM_001170711)	-30	NM_001170711	78541	Mm.200766	NM_030121	ENSMUSG00000048175	Asb8	4930539L19Rik|AI788835|C430011H06Rik	ankyrin repeat and SOCS box-containing 8	protein-coding
mm_11557.1	chr2	32751568	32751583	+	1	NA	exon (NM_013781, exon 9 of 12)	exon (NM_013781, exon 9 of 12)	-5659	NR_045485	30933	Mm.200695	NM_152800	ENSMUSG00000009563	Tor2a	Prosalusin	torsin family 2, member A	protein-coding
mm_91221.1	chr10	22048531	22048537	-	1	NA	Intergenic	Intergenic	19545	NM_053264	114671	Mm.288194	NM_053264	ENSMUSG00000069712	4930444G20Rik	-	RIKEN cDNA 4930444G20 gene	protein-coding
mm_4555.1	chr1	177444654	177444669	+	1	NA	promoter-TSS (NM_001012330)	promoter-TSS (NM_001012330)	0	NM_001012330	30928	Mm.330700	NM_013915	ENSMUSG00000063659	Zbtb18	RP58|Zfp238|Znf238	zinc finger and BTB domain containing 18	protein-coding
mm_155188.1	chrX	56374551	56374617	+	1	NA	promoter-TSS (NR_028086)	promoter-TSS (NR_028086)	-2	NR_028086	320237	Mm.233168	NM_183030		Smim10l2a	6330419J24Rik|Ncrna00086	small integral membrane protein 10 like 2A	ncRNA
mm_8531.1	chr1	155050281	155050286	-	1	NA	Intergenic	Intergenic	49353	NM_010500	15939	Mm.12246	NM_010500	ENSMUSG00000056708	Ier5	-	immediate early response 5	protein-coding
mm_161758.1	chr17	35425291	35425291	+	1	NA	exon (NM_207648, exon 2 of 5)	exon (NM_207648, exon 2 of 5)	414	NM_207648	110557	Mm.439827	NM_207648	ENSMUSG00000073409	H2-Q6	0610037M15Rik|H-2Q6|Qa-6|Qa6	histocompatibility 2, Q region locus 6	protein-coding
mm_5521.1	chr1	37755424	37755426	-	1	NA	3' UTR (NM_207228, exon 20 of 20)	3' UTR (NM_207228, exon 20 of 20)	-35614	NM_028096	72097	Mm.142607	NM_028096	ENSMUSG00000026090	2010300C02Rik	-	RIKEN cDNA 2010300C02 gene	protein-coding
mm_157187.1	chrX	10717452	10717456	-	1	NA	promoter-TSS (NM_001166635)	promoter-TSS (NM_001166635)	89	NM_001166635	68041	Mm.29429	NM_026524	ENSMUSG00000008035	Mid1ip1	3110038L01Rik|Mig12|S14R	Mid1 interacting protein 1 (gastrulation specific G12-like (zebrafish))	protein-coding
mm_92564.1	chr10	79874234	79874439	-	1	NA	non-coding (NR_033210, exon 1 of 6)	non-coding (NR_033210, exon 1 of 6)	298	NM_181681	216152	Mm.29678	NM_181681	ENSMUSG00000035835	Plppr3	Lppr3|Prg2	phospholipid phosphatase related 3	protein-coding
mm_119347.1	chr14	41105360	41105378	+	1	NA	5' UTR (NM_133653, exon 2 of 10)	5' UTR (NM_133653, exon 2 of 10)	336	NM_133653	11720	Mm.14064	NM_133653	ENSMUSG00000037798	Mat1a	AI046368|AdoMet|Ams|MAT|MATA1|SAMS|SAMS1	methionine adenosyltransferase I, alpha	protein-coding
mm_108630.1	chr12	85639542	85639560	+	1	NA	3' UTR (NM_001205053, exon 4 of 4)	3' UTR (NM_001205053, exon 4 of 4)	39533	NM_001205053	81703	Mm.103560	NM_030887	ENSMUSG00000034271	Jdp2	Jundm2|Jundp2|TIF	Jun dimerization protein 2	protein-coding
mm_13691.1	chr2	117120922	117120933	+	1	NA	promoter-TSS (NM_001277256)	promoter-TSS (NM_001277256)	-144	NM_001277256	114715	Mm.245890	NM_033524	ENSMUSG00000027351	Spred1	5730461F13Rik|AL024345|AW047647	sprouty protein with EVH-1 domain 1, related sequence	protein-coding
mm_82335.1	chr9	9239108	9239124	-	1	NA	promoter-TSS (NM_027823)	promoter-TSS (NM_027823)	-103	NM_027823	71544	Mm.334955	NM_027823	ENSMUSG00000050730	Arhgap42	9030420J04Rik|BE136619	Rho GTPase activating protein 42	protein-coding
mm_158128.1	chrX	102644211	102644254	-	1	NA	promoter-TSS (NM_008832)	promoter-TSS (NM_008832)	14	NM_008832	18679	Mm.212889	NM_008832	ENSMUSG00000034055	Phka1	5330411D17|9830108K24Rik|Phka	phosphorylase kinase alpha 1	protein-coding
mm_38035.1	chr4	133887745	133887762	-	1	NA	promoter-TSS (NM_009097)	promoter-TSS (NM_009097)	44	NM_001285505	20111	Mm.301827	NM_009097	ENSMUSG00000003644	Rps6ka1	Mapkapk-1a|Rsk|Rsk-1|Rsk1|S6K-alpha-1|p90-Rsk1|p90Rsk1|p90S6K|p90rsk	ribosomal protein S6 kinase polypeptide 1	protein-coding
mm_157928.1	chrX	79671435	79671438	-	1	NA	promoter-TSS (NM_028025)	promoter-TSS (NM_028025)	-1	NM_028025	71967	Mm.379207	NM_028025	ENSMUSG00000046942	Mageb16	2410003J06Rik	melanoma antigen family B, 16	protein-coding
mm_82548.1	chr9	20938100	20938114	-	1	NA	exon (NM_001199431, exon 6 of 39)	exon (NM_001199431, exon 6 of 39)	14516	NM_001199433	13433	Mm.128580	NM_010066	ENSMUSG00000004099	Dnmt1	Cxxc9|Dnmt|Dnmt1o|MCMT|MTase|Met-1|Met1|MommeD2|m.MmuI	DNA methyltransferase (cytosine-5) 1	protein-coding
mm_49598.1	chr6	30723492	30723503	+	1	NA	Intergenic	Intergenic	-10009	NM_001252293	17294	Mm.335639	NM_008590	ENSMUSG00000051855	Mest	AA408879|AI256745|Peg1	mesoderm specific transcript	protein-coding
mm_104442.1	chr11	94976369	94976399	-	1	NA	promoter-TSS (NM_009161)	promoter-TSS (NM_009161)	-57	NM_009161	20391	Mm.18709	NM_009161	ENSMUSG00000001508	Sgca	50DAG|Asg	sarcoglycan, alpha (dystrophin-associated glycoprotein)	protein-coding
mm_70337.1	chr8	4524717	4524729	+	1	NA	3' UTR (NM_026058, exon 11 of 11)	3' UTR (NM_026058, exon 11 of 11)	31318	NM_026058	67260	Mm.35511	NM_026058	ENSMUSG00000008206	Cers4	2900019C14Rik|Lass4|Trh1	ceramide synthase 4	protein-coding
mm_111938.1	chr12	108893414	108893493	-	1	NA	promoter-TSS (NM_177602)	promoter-TSS (NM_177602)	-242	NM_011710	22375	Mm.38433	NM_011710	ENSMUSG00000021266	Wars	TrpRS|WRS	tryptophanyl-tRNA synthetase	protein-coding
mm_64854.1	chr7	13034723	13034782	-	1	NA	promoter-TSS (NM_026885)	promoter-TSS (NM_026885)	25	NM_026885	68953	Mm.295670	NM_026885	ENSMUSG00000033916	Chmp2a	1500016L11Rik	charged multivesicular body protein 2A	protein-coding
mm_50685.1	chr6	51584323	51584333	+	1	NA	intron (NM_028035, intron 5 of 6)	intron (NM_028035, intron 5 of 6)	39805	NM_001127348	71982	Mm.294166	NM_028035	ENSMUSG00000038301	Snx10	2410004M09Rik	sorting nexin 10	protein-coding
mm_103907.1	chr11	83578530	83578534	-	1	NA	5' UTR (NM_011338, exon 1 of 4)	5' UTR (NM_011338, exon 1 of 4)	104	NM_011338	20308	Mm.416125	NM_011338	ENSMUSG00000019122	Ccl9	CCF18|MRP-2|Scya10|Scya9	chemokine (C-C motif) ligand 9	protein-coding
mm_91613.1	chr10	41519078	41519103	-	1	NA	promoter-TSS (NM_016898)	promoter-TSS (NM_016898)	-410	NM_016898	53599	Mm.269815	NM_016898	ENSMUSG00000019818	Cd164	A115|A24|AA589639|AW540279|MGC-24|MSSP	CD164 antigen	protein-coding
mm_36556.1	chr4	86857366	86857415	-	1	NA	promoter-TSS (NM_009096)	promoter-TSS (NM_009096)	-23	NM_009096	20104	Mm.379007	NM_009096	ENSMUSG00000028495	Rps6	S6R	ribosomal protein S6	protein-coding
mm_145563.1	chr18	60812408	60812418	+	1	NA	TTS (NR_039567)	TTS (NR_039567)	337	NR_039567	100628611		NR_039567	ENSMUSG00000093327	Mir5107	mir-5107|mmu-mir-5107|mu-mir-5107	microRNA 5107	ncRNA
mm_11182.1	chr2	28840683	28840752	+	1	NA	promoter-TSS (NM_001166033)	promoter-TSS (NM_001166033)	311	NM_001033294	227674	Mm.44179	NM_001033294	ENSMUSG00000026806	Ddx31	5830444G11Rik|Gm997	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 31	protein-coding
mm_171607.1	chr4	149436823	149436839	-	1	NA	Intergenic	MMVL30-int|LTR|ERV1	-10200	NM_022022	63958	Mm.415260	NM_022022	ENSMUSG00000028960	Ube4b	4930551I19Rik|4933406G05Rik|AU014668|D4Bwg0973e|UFD2|UFD2a|Ufd2p|mKIAA0684	ubiquitination factor E4B	protein-coding
mm_17283.1	chr2	26138895	26138916	-	1	NA	5' UTR (NM_001256522, exon 2 of 2)	5' UTR (NM_001256522, exon 2 of 2)	638	NM_001256522	109299	Mm.389259	NM_001256521		C330006A16Rik	AI551216	RIKEN cDNA C330006A16 gene	protein-coding
mm_41969.1	chr5	107359544	107359586	+	1	NA	intron (NM_054054, intron 11 of 18)	intron (NM_054054, intron 11 of 18)	28371	NM_054054	114642	Mm.182836	NM_054054	ENSMUSG00000029279	Brdt	7420412D09Rik|Brd6|Fsrg3	bromodomain, testis-specific	protein-coding
mm_149388.1	chr19	11386612	11386623	+	1	NA	intron (NM_001310331, intron 4 of 6)	intron (NM_001310331, intron 4 of 6)	11129	NM_001310331	666907		NM_001310331	ENSMUSG00000101389	Ms4a4a	EG666907	membrane-spanning 4-domains, subfamily A, member 4A	protein-coding
mm_129527.1	chr15	79265784	79265792	-	1	NA	intron (NM_177580, intron 7 of 13)	intron (NM_177580, intron 7 of 13)	-11040	NM_020516	57274	Mm.441697	NM_020516	ENSMUSG00000032988	Slc16a8	Mct3	solute carrier family 16 (monocarboxylic acid transporters), member 8	protein-coding
mm_60118.1	chr7	35754568	35754579	+	1	NA	promoter-TSS (NM_178704)	promoter-TSS (NM_178704)	-119	NM_178704	233115	Mm.257808	NM_178704	ENSMUSG00000043671	Dpy19l3	6030410G08|9330164H19Rik	dpy-19-like 3 (C. elegans)	protein-coding
mm_152782.1	chr19	21384043	21384051	-	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	88614	NM_010266	14544	Mm.45054	NM_010266	ENSMUSG00000058624	Gda	AU015411|AW047581|GAH	guanine deaminase	protein-coding
mm_25441.1	chr3	108186333	108186407	+	1	NA	promoter-TSS (NM_001287093)	promoter-TSS (NM_001287093)	81	NM_001287093	229715	Mm.275752	NM_146137	ENSMUSG00000050947	Amigo1	Amigo|ali2	adhesion molecule with Ig like domain 1	protein-coding
mm_75293.1	chr8	41054611	41054642	-	1	NA	exon (NM_001005864, exon 1 of 12)	exon (NM_001005864, exon 1 of 12)	170	NM_001005864	102103	Mm.149438	NM_001005863	ENSMUSG00000045636	Mtus1	AI481402|ATBP135|Atip1|B430010I23Rik|B430305I03Rik|C85752|Cctsg1-440|MD44|MTSG1|mKIAA1288	mitochondrial tumor suppressor 1	protein-coding
mm_37117.1	chr4	116651436	116651446	-	1	NA	5' UTR (NM_021473, exon 1 of 9)	5' UTR (NM_021473, exon 1 of 9)	233	NM_021473	58810	Mm.30085	NM_021473	ENSMUSG00000028692	Akr1a1	2610201A18Rik|Akr1a4	aldo-keto reductase family 1, member A1 (aldehyde reductase)	protein-coding
mm_4550.1	chr1	177442384	177442394	+	1	NA	Intergenic	CpG	-2272	NM_001012330	30928	Mm.330700	NM_013915	ENSMUSG00000063659	Zbtb18	RP58|Zfp238|Znf238	zinc finger and BTB domain containing 18	protein-coding
mm_130024.1	chr15	88862015	88862028	-	1	NA	promoter-TSS (NM_145478)	promoter-TSS (NM_145478)	-173	NM_145478	223775	Mm.400129	NM_145478	ENSMUSG00000035828	Pim3	BC026639|Kid1	proviral integration site 3	protein-coding
mm_34197.1	chr4	140714295	140714305	+	1	NA	intron (NM_173867, intron 7 of 12)	intron (NM_173867, intron 7 of 12)	12827	NM_173867	108911	Mm.253	NM_173867	ENSMUSG00000040945	Rcc2	2610510H01Rik|2610529N02Rik|AA536646|AA675016|Td60|mKIAA1470	regulator of chromosome condensation 2	protein-coding
mm_171702.1	chr4	72354582	72354588	+	1	NA	Intergenic	L1Md_T|LINE|L1	153341	NR_027923	68285	Mm.37541	NR_027923		C630043F03Rik	AI851307	RIKEN cDNA C630043F03 gene	ncRNA
mm_153222.1	chr19	34856127	34856138	-	1	NA	intron (NM_001114339, intron 1 of 6)	intron (NM_001114339, intron 1 of 6)	21785	NM_023792	75735	Mm.24742	NM_023792	ENSMUSG00000033610	Pank1	Pank|Pank1b	pantothenate kinase 1	protein-coding
mm_69322.1	chr7	128461631	128461662	-	1	NA	promoter-TSS (NM_009383)	promoter-TSS (NM_009383)	27	NM_001347641	21843	Mm.242072	NM_009383	ENSMUSG00000030846	Tial1	5330433G13Rik|AL033329|TIAR|mTIAR	Tia1 cytotoxic granule-associated RNA binding protein-like 1	protein-coding
mm_122190.1	chr14	31653274	31653279	-	1	NA	intron (NM_025295, intron 1 of 3)	RLTR14_RN|LTR|ERV1	12219	NM_025295	26363	Mm.282679	NM_025295	ENSMUSG00000021900	Btd	-	biotinidase	protein-coding
mm_62863.1	chr7	114717430	114717448	+	1	NA	Intergenic	Intergenic	-1204	NM_054084	116903	Mm.273838	NM_054084	ENSMUSG00000030666	Calcb	CGRP2|Calc2	calcitonin-related polypeptide, beta	protein-coding
mm_46113.1	chr5	92363232	92363241	-	1	NA	promoter-TSS (NM_019494)	promoter-TSS (NM_019494)	41	NM_019494	56066	Mm.131723	NM_019494	ENSMUSG00000060183	Cxcl11	Cxc11|H174|I-tac|Ip9|Itac|Scyb11|Scyb9b|b-R1|betaR1	chemokine (C-X-C motif) ligand 11	protein-coding
mm_34462.1	chr4	148140683	148140698	+	1	NA	5' UTR (NM_027985, exon 1 of 8)	5' UTR (NM_027985, exon 1 of 8)	200	NM_027985	71890	Mm.9648	NM_027985	ENSMUSG00000029003	Mad2l2	2310033C13Rik|G1-453-4|MAD2B|REV7|repro22	MAD2 mitotic arrest deficient-like 2	protein-coding
mm_11893.1	chr2	49787712	49787725	+	1	NA	promoter-TSS (NM_027990)	promoter-TSS (NM_027990)	32	NM_027990	71897	Mm.41381	NM_027990	ENSMUSG00000026765	Lypd6b	2310010M24Rik|AW049525	LY6/PLAUR domain containing 6B	protein-coding
mm_168348.1	chr1	112440225	112440225	-	1	NA	Intergenic	IAPEY_LTR|LTR|ERVK	-575307	NM_001081316	319901	Mm.103468	NM_001081316	ENSMUSG00000038702	Dsel	9330132E09Rik|DS-epi2	dermatan sulfate epimerase-like	protein-coding
mm_169539.1	chr15	100334897	100334907	+	1	NA	promoter-TSS (NM_001081471)	promoter-TSS (NM_001081471)	-27	NM_001081471	668178	Mm.425943	NM_001081471	ENSMUSG00000058057	Mettl7a3	ENSMUSG00000058057|Gm10035|Ubie3	methyltransferase like 7A3	protein-coding
mm_128000.1	chr15	12739949	12739961	-	1	NA	Intergenic	CpG	84702	NM_029998	77877	Mm.207311	NM_029998	ENSMUSG00000022195	6030458C11Rik	-	RIKEN cDNA 6030458C11 gene	protein-coding
mm_88969.1	chr10	81409512	81409528	+	1	NA	intron (NM_026756, intron 3 of 8)	ZP3AR|Satellite|Satellite	6777	NR_106141	102465778		NR_106141	ENSMUSG00000105379	Mir1191b	mmu-mir-1191b	microRNA 1191b	ncRNA
mm_137108.1	chr17	21963590	21963596	+	1	NA	intron (NM_001025373, intron 1 of 3)	intron (NM_001025373, intron 1 of 3)	1034	NM_001025373	74670	Mm.26540	NM_001025373	ENSMUSG00000053347	Zfp943	4930432O21Rik	zinc finger prtoein 943	protein-coding
mm_133837.1	chr16	96145392	96145448	+	1	NA	promoter-TSS (NM_207301)	promoter-TSS (NM_207301)	1	NM_207301	71446	Mm.255063	NM_207301	ENSMUSG00000023147	Wrb	5530402J05Rik|C030018G21Rik|Chd5	tryptophan rich basic protein	protein-coding
mm_5092.1	chr1	4608983	4609021	-	1	NA	Intergenic	Intergenic	-111648	NM_001289465	20671	Mm.279103	NM_011441	ENSMUSG00000025902	Sox17	-	SRY (sex determining region Y)-box 17	protein-coding
mm_88645.1	chr10	79952300	79952316	+	1	NA	3' UTR (NM_001288626, exon 9 of 9)	3' UTR (NM_001288626, exon 9 of 9)	-7844	NM_175450	216156	Mm.35828	NM_175450	ENSMUSG00000035754	Wdr18	2310012I10Rik|AU044733|AW122032	WD repeat domain 18	protein-coding
mm_81377.1	chr9	108855615	108855648	+	1	NA	intron (NM_134420, intron 1 of 17)	intron (NM_134420, intron 1 of 17)	1588	NM_134420	171429	Mm.45201	NM_134420	ENSMUSG00000023259	Slc26a6	B930010B04Rik|CFEX|Pat-1|Pat1	solute carrier family 26, member 6	protein-coding
mm_167364.1	chr8	85060421	85060437	-	1	NA	promoter-TSS (NR_110582)	promoter-TSS (NR_110582)	31	NR_110582	320466	Mm.401371	NR_110581	ENSMUSG00000087026	A230103J11Rik	-	RIKEN cDNA A230103J11 gene	ncRNA
mm_39304.1	chr5	7304129	7304152	+	1	NA	promoter-TSS (NM_027603)	promoter-TSS (NM_027603)	-24	NM_027603	70920	Mm.158494	NM_027603	ENSMUSG00000040514	4921511H03Rik	-	RIKEN cDNA 4921511H03 gene	protein-coding
mm_21444.1	chr2	160364586	160364628	-	1	NA	3' UTR (NM_010658, exon 1 of 1)	3' UTR (NM_010658, exon 1 of 1)	2458	NM_010658	16658	Mm.330745	NM_010658	ENSMUSG00000074622	Mafb	Kreisler|Krml|Krml1|kr	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein B (avian)	protein-coding
mm_60806.1	chr7	45639885	45639897	+	1	NA	promoter-TSS (NM_172418)	promoter-TSS (NM_172418)	-86	NM_172418	74490	Mm.107442	NM_172418	ENSMUSG00000042918	Mamstr	2810022D01Rik|5430432N15Rik|AW743872|Mastr	MEF2 activating motif and SAP domain containing transcriptional regulator	protein-coding
mm_64991.1	chr7	16917185	16917212	-	1	NA	exon (NM_007590, exon 5 of 6)	exon (NM_007590, exon 5 of 6)	6834	NM_007590	12315	Mm.288630	NM_007590	ENSMUSG00000019370	Calm3	CaMA|R75142	calmodulin 3	protein-coding
mm_146942.1	chr18	32405460	32405467	-	1	NA	intron (NM_001083334, intron 1 of 14)	ORR1F|LTR|ERVL-MaLR	-27179	NR_045403	402767	Mm.385109	NR_045403	ENSMUSG00000097413	A830052D11Rik	-	RIKEN cDNA A830052D11 gene	ncRNA
mm_19949.1	chr2	117305773	117305777	-	1	NA	intron (NM_011246, intron 3 of 16)	intron (NM_011246, intron 3 of 16)	37102	NM_011246	19419	Mm.42150	NM_011246	ENSMUSG00000027347	Rasgrp1	Rasgrp	RAS guanyl releasing protein 1	protein-coding
mm_140866.1	chr17	23771544	23771595	-	1	NA	promoter-TSS (NM_153791)	promoter-TSS (NM_153791)	22	NM_153791	224613	Mm.328835	NM_153791	ENSMUSG00000040097	Flywch1	E030034P13Rik|mKIAA1552	FLYWCH-type zinc finger 1	protein-coding
mm_82395.1	chr9	14740619	14740624	-	1	NA	exon (NM_177905, exon 1 of 19)	exon (NM_177905, exon 1 of 19)	112	NM_177905	330890	Mm.334969	NM_177905	ENSMUSG00000036912	Piwil4	9230101H05Rik|Miwi2	piwi-like RNA-mediated gene silencing 4	protein-coding
mm_159051.1	chr1	189343776	189343776	-	1	NA	promoter-TSS (NM_010607)	promoter-TSS (NM_010607)	-69	NM_010607	16526	Mm.33304	NM_010607	ENSMUSG00000037624	Kcnk2	A430027H14Rik|AI848635|TREK-1	potassium channel, subfamily K, member 2	protein-coding
mm_113761.1	chr13	44757929	44757932	+	1	NA	intron (NM_001205044, intron 2 of 18)	intron (NM_001205044, intron 2 of 18)	26659	NM_001205043	16468	Mm.25059	NM_021878	ENSMUSG00000038518	Jarid2	Jmj|jumonji	jumonji, AT rich interactive domain 2	protein-coding
mm_7430.1	chr1	119837467	119837555	-	1	NA	promoter-TSS (NM_019933)	promoter-TSS (NM_019933)	-440	NM_019933	19258	Mm.458796	NM_019933	ENSMUSG00000026384	Ptpn4	PTPMEG|Ptn4|TEP|TEP/mPTPMEG|hPTP-MEG	protein tyrosine phosphatase, non-receptor type 4	protein-coding
mm_172542.1	chr7	97595463	97595478	-	1	NA	intron (NM_001081267, intron 1 of 15)	intron (NM_001081267, intron 1 of 15)	15574	NM_001081267	233532	Mm.43977	NM_001081267	ENSMUSG00000035623	Rsf1	4832420A03Rik|C030033M12Rik|Gm164|Hbxap|XAP8|p325	remodeling and spacing factor 1	protein-coding
mm_134542.1	chr16	19758207	19758213	-	1	NA	Intergenic	Intergenic	-2024	NM_001159408	108105	Mm.33935	NM_054052	ENSMUSG00000022686	B3gnt5	beta3GnT5	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5	protein-coding
mm_148328.1	chr18	84086380	84086403	-	1	NA	5' UTR (NM_001081300, exon 1 of 2)	5' UTR (NM_001081300, exon 1 of 2)	171	NM_001081300	110796	Mm.102136	NM_001081300	ENSMUSG00000046982	Tshz1	5730407I04Rik|D18Bwg1409e|Mtsh1|NY-CO-33|Sdccag33|Tsh1|mKIAA4206|teashirt1	teashirt zinc finger family member 1	protein-coding
mm_110022.1	chr12	16753312	16753318	-	1	NA	intron (NM_001252071, intron 1 of 32)	intron (NM_001252071, intron 1 of 32)	3924	NM_001252071	268527	Mm.428062	NM_015764	ENSMUSG00000036523	Greb1	5730583K22Rik|9130004E13|AF180470|AU023194|mKIAA0575	gene regulated by estrogen in breast cancer protein	protein-coding
mm_94856.1	chr11	24076613	24076628	+	1	NA	Intergenic	CpG	-1436	NM_016707	14025	Mm.53687	NM_016707	ENSMUSG00000000861	Bcl11a	2810047E18Rik|BCL-11A|Ctip1|D930021L15Rik|Evi9|Evi9a|Evi9b|Evi9c|mKIAA1809	B cell CLL/lymphoma 11A (zinc finger protein)	protein-coding
mm_139892.1	chr17	70850696	70850720	+	1	NA	promoter-TSS (NM_001164076)	promoter-TSS (NM_001164076)	502	NM_009372	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_60168.1	chr7	40898933	40898943	+	1	NA	promoter-TSS (NM_021387)	promoter-TSS (NM_021387)	-340	NM_021387	58188	Mm.150675	NM_021387	ENSMUSG00000039257	Vstm2b	2900093B09Rik|AB030198	V-set and transmembrane domain containing 2B	protein-coding
mm_146737.1	chr18	15403505	15403531	-	1	NA	promoter-TSS (NM_001308647)	promoter-TSS (NM_001308647)	240	NM_001317729	11829	Mm.250786	NM_009700	ENSMUSG00000024411	Aqp4	WCH4	aquaporin 4	protein-coding
mm_169075.1	chr13	30947744	30947745	-	1	NA	promoter-TSS (NM_153072)	promoter-TSS (NM_153072)	17	NM_153072	210554	Mm.450571	NM_153072	ENSMUSG00000076430	Hus1b	-	HUS1 checkpoint clamp component B	protein-coding
mm_165540.1	chr2	180710287	180710287	+	1	NA	promoter-TSS (NM_001291432)	promoter-TSS (NM_001291432)	-41	NM_001289651	76425	Mm.41464	NM_029607	ENSMUSG00000027573	Gid8	2310003C23Rik|4833420G11Rik|AI451474|Twa1	GID complex subunit 8	protein-coding
mm_157755.1	chrX	73494802	73494815	-	1	NA	3' UTR (NM_007542, exon 8 of 8)	3' UTR (NM_007542, exon 8 of 8)	-8278	NM_001310537	320707	Mm.210095	NM_177236	ENSMUSG00000031376	Atp2b3	6430519O13Rik|Pmca3	ATPase, Ca++ transporting, plasma membrane 3	protein-coding
mm_36791.1	chr4	103114239	103114298	-	1	NA	promoter-TSS (NM_027696)	promoter-TSS (NM_027696)	31	NM_146254	242584	Mm.374877	NM_146254	ENSMUSG00000035126	Wdr78	BC028975	WD repeat domain 78	protein-coding
mm_150330.1	chr19	34574971	34574986	+	1	NA	3' UTR (NM_008332, exon 3 of 3)	3' UTR (NM_008332, exon 3 of 3)	-8551	NM_010501	15959	Mm.426079	NM_010501	ENSMUSG00000074896	Ifit3	Ifi49|P49	interferon-induced protein with tetratricopeptide repeats 3	protein-coding
mm_134198.1	chr16	11021517	11021556	-	1	NA	Intergenic	Intergenic	12638	NR_040518	100043147	Mm.489001	NR_040518	ENSMUSG00000097056	Gm4262	-	predicted gene 4262	ncRNA
mm_84189.1	chr9	60449671	60449689	-	1	NA	intron (NM_001040426, intron 3 of 17)	intron (NM_001040426, intron 3 of 17)	61355	NM_001040426	207596	Mm.28791	NM_172444	ENSMUSG00000032289	Thsd4	ADAMTSL-6|ADAMTSL6|AI585901|Adamtsl4|B230114P05Rik	thrombospondin, type I, domain containing 4	protein-coding
mm_63680.1	chr7	130552933	130552946	+	1	NA	Intergenic	Intergenic	-5558	NM_001162855	67872	Mm.21714	NM_001162855	ENSMUSG00000040331	Nsmce4a	2410003A14Rik	NSE4 homolog A, SMC5-SMC6 complex component	protein-coding
mm_18724.1	chr2	72948195	72948199	-	1	NA	intron (NM_001018042, intron 4 of 6)	intron (NM_001018042, intron 4 of 6)	31084	NM_001098425	20687	Mm.124328	NM_011450	ENSMUSG00000027109	Sp3	D130027J01Rik	trans-acting transcription factor 3	protein-coding
mm_75694.1	chr8	68212055	68212065	-	1	NA	Intergenic	Intergenic	-64468	NM_028182	72281	Mm.40974	NM_028182	ENSMUSG00000053886	Sh2d4a	2210402M20Rik|SH2A	SH2 domain containing 4A	protein-coding
mm_107169.1	chr12	24708553	24708565	+	1	NA	intron (NM_009104, intron 1 of 9)	CpG	305	NM_009104	20135	Mm.99	NM_009104	ENSMUSG00000020649	Rrm2	AA407299|R2	ribonucleotide reductase M2	protein-coding
mm_84105.1	chr9	58312962	58312973	-	1	NA	5' UTR (NM_010729, exon 1 of 7)	5' UTR (NM_010729, exon 1 of 7)	245	NM_010729	16949	Mm.250492	NM_010729	ENSMUSG00000032334	Loxl1	Loxl	lysyl oxidase-like 1	protein-coding
mm_14662.1	chr2	138256618	138256677	+	1	NA	promoter-TSS (NM_001025431)	promoter-TSS (NM_001025431)	63	NM_001025431	228662	Mm.153405	NM_145534	ENSMUSG00000062098	Btbd3	mKIAA0952	BTB (POZ) domain containing 3	protein-coding
mm_88498.1	chr10	77837618	77837624	+	1	NA	TTS (NM_001024709)	TTS (NM_001024709)	1674	NM_001024709	544710	Mm.441890	NM_001024709		Krtap10-10	EG544710	keratin associated protein 10-10	protein-coding
mm_116926.1	chr13	55571088	55571108	-	1	NA	promoter-TSS (NM_145382)	promoter-TSS (NM_145382)	22	NM_145382	212483	Mm.35661	NM_145382	ENSMUSG00000021495	Fam193b	IRIZIO|Kiaa1931	family with sequence similarity 193, member B	protein-coding
mm_162379.1	chr1	72284289	72284293	-	1	NA	promoter-TSS (NM_175564)	promoter-TSS (NM_175564)	23	NM_023523	111175	Mm.281738	NM_023523	ENSMUSG00000026189	Pecr	2400003B18Rik|TERP	peroxisomal trans-2-enoyl-CoA reductase	protein-coding
mm_136573.1	chr17	3454239	3454253	+	1	NA	exon (NM_011878, exon 14 of 27)	exon (NM_011878, exon 14 of 27)	-28069	NM_001286758	24001	Mm.137134	NM_011878	ENSMUSG00000023800	Tiam2	3000002F19Rik|STEF|mKIAA2016	T cell lymphoma invasion and metastasis 2	protein-coding
mm_3470.1	chr1	150104535	150104547	+	1	NA	exon (NM_011198, exon 8 of 10)	exon (NM_011198, exon 8 of 10)	4510	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_84440.1	chr9	66124762	66124805	-	1	NA	5' UTR (NM_019727, exon 1 of 15)	5' UTR (NM_019727, exon 1 of 15)	103	NM_019727	56440	Mm.271891	NM_019727	ENSMUSG00000032382	Snx1	-	sorting nexin 1	protein-coding
mm_41800.1	chr5	103753910	103753923	+	1	NA	promoter-TSS (NM_133919)	promoter-TSS (NM_133919)	-246	NM_133919	17355	Mm.6949	NM_133919	ENSMUSG00000029313	Aff1	9630032B01Rik|AW319193|Af4|Mllt2h|Rob	AF4/FMR2 family, member 1	protein-coding
mm_124682.1	chr15	6429796	6429813	+	1	NA	exon (NM_023118, exon 10 of 15)	exon (NM_023118, exon 10 of 15)	-15529	NM_013485	12279	Mm.29095	NM_013485	ENSMUSG00000022149	C9	-	complement component 9	protein-coding
mm_2465.1	chr1	105455968	105455976	+	1	NA	Intergenic	Intergenic	-99262	NM_001160368	320311	Mm.389162	NM_178779	ENSMUSG00000047496	Rnf152	A930029B02Rik	ring finger protein 152	protein-coding
mm_104171.1	chr11	87591557	87591560	-	1	NA	promoter-TSS (NM_133215)	promoter-TSS (NM_133215)	-659	NM_133215	170749	Mm.399376	NM_133215	ENSMUSG00000018401	Mtmr4	AA596759|ESTM44|FYVE-DSP2|ZFYVE11|mKIAA0647	myotubularin related protein 4	protein-coding
mm_136376.1	chr16	92825772	92825782	-	1	NA	intron (NM_001111022, intron 1 of 6)	intron (NM_001111022, intron 1 of 6)	297	NM_001111021	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_150227.1	chr19	33970757	33970761	+	1	NA	exon (NM_026334, exon 7 of 10)	exon (NM_026334, exon 7 of 10)	9511	NM_026334	67717	Mm.329816	NM_026334	ENSMUSG00000024768	Lipf	2310051B21Rik|AV082900	lipase, gastric	protein-coding
mm_152779.1	chr19	21174873	21174883	-	1	NA	Intergenic	Intergenic	70168	NR_126458	75354	Mm.243873	NR_126458		4930554I06Rik	-	RIKEN cDNA 4930554I06 gene	ncRNA
mm_157360.1	chrX	37102102	37102117	-	1	NA	exon (NM_026573, exon 5 of 10)	exon (NM_026573, exon 5 of 10)	8213	NM_026573	68134	Mm.271160	NM_026573	ENSMUSG00000036572	Upf3b	5730594O13Rik|AI317193|AW541158|RENT3B|UPF3X	UPF3 regulator of nonsense transcripts homolog B (yeast)	protein-coding
mm_165871.1	chr4	40260465	40260467	+	1	NA	exon (NM_134097, exon 3 of 3)	exon (NM_134097, exon 3 of 3)	-9113	NR_045265	100504309	Mm.392019	NR_045265		Toporsos	2010003O02Rik	topoisomerase I binding, arginine/serine-rich, opposite strand	ncRNA
mm_50182.1	chr6	41605497	41605569	+	1	NA	promoter-TSS (NM_001146351)	promoter-TSS (NM_001146351)	51	NM_007680	13848	Mm.271976	NM_007680	ENSMUSG00000029869	Ephb6	Cekl|Mep	Eph receptor B6	protein-coding
mm_89992.1	chr10	112060211	112060230	+	1	NA	promoter-TSS (NM_027018)	promoter-TSS (NM_027018)	31	NM_027018	69286	Mm.47058	NM_027018	ENSMUSG00000020213	Glipr1l1	1700011E04Rik	GLI pathogenesis-related 1 like 1	protein-coding
mm_18048.1	chr2	39133088	39133090	-	1	NA	intron (NM_178778, intron 2 of 17)	intron (NM_178778, intron 2 of 17)	29146	NR_033526	100042584	Mm.451696	NR_033526	ENSMUSG00000082315	Gm16523	A130054J05Rik	mitochondrial ribosomal protein L40 pseudogene	pseudo
mm_66819.1	chr7	48456291	48456319	-	1	NA	promoter-TSS (NM_205810)	promoter-TSS (NM_205810)	37	NM_205810	233231	Mm.297430	NM_205810	ENSMUSG00000070547	Mrgprb1	MrgB1	MAS-related GPR, member B1	protein-coding
mm_27265.1	chr3	38484832	38484864	-	1	NA	promoter-TSS (NM_001167883)	promoter-TSS (NM_001167883)	-32	NM_001167883	99696	Mm.290937	NM_001033198	ENSMUSG00000044864	Ankrd50	AI662170|E430012K20Rik|mKIAA1223|mKIAA3019	ankyrin repeat domain 50	protein-coding
mm_164740.1	chr17	72913018	72913033	-	1	NA	Intergenic	B1_Mur2|SINE|Alu	-5280	NM_029999	77889	Mm.154109	NM_029999	ENSMUSG00000024063	Lbh	1810009F10Rik|6720416L16Rik	limb-bud and heart	protein-coding
mm_150706.1	chr19	42518796	42518830	+	1	NA	promoter-TSS (NM_177464)	promoter-TSS (NM_177464)	8	NM_177464	52013	Mm.254169	NM_177464	ENSMUSG00000025184	R3hcc1l	1700036B12Rik|AI450607|C10orf28|D19Ertd386e|GIDRP86|Gidrp88	R3H domain and coiled-coil containing 1 like	protein-coding
mm_82935.1	chr9	35210900	35210960	-	1	NA	promoter-TSS (NM_026130)	promoter-TSS (NM_026130)	125	NM_172291	235169	Mm.138512	NM_172291	ENSMUSG00000039048	Foxred1	BC024806|TEG-23|Tex23	FAD-dependent oxidoreductase domain containing 1	protein-coding
mm_33717.1	chr4	134052686	134052696	+	1	NA	Intergenic	Intergenic	-15761	NM_001162970	230806	Mm.240080	NM_001162970	ENSMUSG00000012123	Aim1l	-	absent in melanoma 1-like	protein-coding
mm_165780.1	chr3	130647530	130647534	+	1	NA	Intergenic	ID_B1|SINE|B4	29957	NM_027907	71760	Mm.29125	NM_027907	ENSMUSG00000019232	Etnppl	1300019H02Rik|AI195447|Agxt2l1	ethanolamine phosphate phospholyase	protein-coding
mm_95547.1	chr11	52307627	52307639	+	1	NA	Intergenic	Intergenic	-24619	NM_001313981	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_50839.1	chr6	54816870	54816889	+	1	NA	promoter-TSS (NM_199143)	promoter-TSS (NM_199143)	-37	NM_199143	387524	Mm.286149	NM_199143	ENSMUSG00000058446	Znrf2	1190002C14Rik|AU044205|D6Ertd365e	zinc and ring finger 2	protein-coding
mm_49926.1	chr6	39381103	39381117	+	1	NA	promoter-TSS (NM_011226)	promoter-TSS (NM_011226)	-318	NM_011226	19331	Mm.123866	NM_011226	ENSMUSG00000029923	Rab19	-	RAB19, member RAS oncogene family	protein-coding
mm_13126.1	chr2	91710901	91710970	+	1	NA	promoter-TSS (NM_178724)	promoter-TSS (NM_178724)	-15	NM_178724	241547	Mm.130331	NM_178724	ENSMUSG00000027243	Harbi1	D230010M03Rik	harbinger transposase derived 1	protein-coding
mm_113371.1	chr13	33003223	33003257	+	1	NA	Intergenic	Intergenic	-1301	NM_009256	20723	Mm.245041	NM_009256	ENSMUSG00000045827	Serpinb9	BB283241|CAP-3|CAP3|PI-9|PI9|Spi6|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 9	protein-coding
mm_25206.1	chr3	103809649	103809667	+	1	NA	promoter-TSS (NM_133865)	promoter-TSS (NM_133865)	141	NM_001163553	67489	Mm.197568	NM_026193	ENSMUSG00000032952	Ap4b1	1810038H16Rik|AV004952|Ap4b4	adaptor-related protein complex AP-4, beta 1	protein-coding
mm_82983.1	chr9	36493296	36493309	-	1	NA	Intergenic	L1_Mur2|LINE|L1	17664	NM_001128510	671003	Mm.475847	NM_001128510	ENSMUSG00000090710	Gm9513	Pate-P|Pate11	predicted gene 9513	protein-coding
mm_81871.1	chr9	119063430	119063467	+	1	NA	intron (NM_001164567, intron 10 of 19)	intron (NM_001164567, intron 10 of 19)	10670	NM_001164567	22351	Mm.83817	NM_011700	ENSMUSG00000038775	Vill	Villp	villin-like	protein-coding
mm_138893.1	chr17	43568153	43568157	+	1	NA	promoter-TSS (NM_013737)	promoter-TSS (NM_013737)	-296	NM_013737	27226	Mm.9277	NM_013737	ENSMUSG00000023913	Pla2g7	PAF-AH|R75400	phospholipase A2, group VII (platelet-activating factor acetylhydrolase, plasma)	protein-coding
mm_1666.1	chr1	74771887	74771911	+	1	NA	promoter-TSS (NM_009526)	promoter-TSS (NM_009526)	7	NM_009526	22420	Mm.268282	NM_009526	ENSMUSG00000033227	Wnt6	AA409270|Wnt-6	wingless-type MMTV integration site family, member 6	protein-coding
mm_69892.1	chr7	141637385	141637389	-	1	NA	intron (NM_001330001, intron 31 of 33)	intron (NM_001330001, intron 31 of 33)	16686	NR_106030	102466798		NR_106030	ENSMUSG00000098759	Mir7063	Gm27654|mmu-mir-7063	microRNA 7063	ncRNA
mm_61832.1	chr7	88280583	88280592	+	1	NA	intron (NM_001311790, intron 1 of 3)	(T)n|Simple_repeat|Simple_repeat	2502	NM_001311790	13032	Mm.89295	NM_009982	ENSMUSG00000030560	Ctsc	AI047818|CatC|DPP1|DPPI	cathepsin C	protein-coding
mm_60782.1	chr7	45565324	45565338	+	1	NA	intron (NM_025330, intron 6 of 8)	intron (NM_025330, intron 6 of 8)	-4822	NM_009737	12036	Mm.24210	NM_009737	ENSMUSG00000030826	Bcat2	Bcat-2|Eca40	branched chain aminotransferase 2, mitochondrial	protein-coding
mm_83785.1	chr9	52167380	52167382	-	1	NA	intron (NM_001162921, intron 1 of 5)	B4|SINE|B4	730	NM_001162921	244871	Mm.295686	NM_001162921	ENSMUSG00000035164	Zc3h12c	A230108E06|C230027N18Rik|mKIAA1726	zinc finger CCCH type containing 12C	protein-coding
mm_137523.1	chr17	27325382	27325386	+	1	NA	Intergenic	Intergenic	-3001	NR_106075	102466818		NR_106075	ENSMUSG00000099237	Mir7216	Gm27555|mmu-mir-7216	microRNA 7216	ncRNA
mm_122792.1	chr14	54417814	54417835	-	1	NA	promoter-TSS (NM_011405)	promoter-TSS (NM_011405)	-122	NM_011405	20540	Mm.142455	NM_011405	ENSMUSG00000000958	Slc7a7	AI790233|my+lat1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 7	protein-coding
mm_21577.1	chr2	164237171	164237179	-	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	1166	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_170372.1	chr18	54699259	54699264	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	87517	NR_045400	328957	Mm.402781	NR_045400		9330117O12Rik	9330117O12	RIKEN cDNA 9330117O12 gene	ncRNA
mm_23866.1	chr3	83026148	83026162	+	1	NA	promoter-TSS (NM_010196)	promoter-TSS (NM_010196)	2	NM_001111048	14161	Mm.88793	NM_010196	ENSMUSG00000028001	Fga	ENSMUSG00000059807|Fib	fibrinogen alpha chain	protein-coding
mm_140046.1	chr17	74499304	74499306	+	1	NA	3' UTR (NM_026417, exon 6 of 6)	3' UTR (NM_026417, exon 6 of 6)	9812	NM_026417	67864	Mm.41891	NM_026417	ENSMUSG00000024072	Yipf4	2310034L04Rik	Yip1 domain family, member 4	protein-coding
mm_105466.1	chr11	105291489	105291492	-	1	NA	Intergenic	Intergenic	-1156	NM_008626	17534	Mm.235616	NM_008626	ENSMUSG00000020695	Mrc2	Endo180|mKIAA0709|uPARAP	mannose receptor, C type 2	protein-coding
mm_97765.1	chr11	82035570	82035585	+	1	NA	promoter-TSS (NM_011333)	promoter-TSS (NM_011333)	0	NM_011333	20296	Mm.290320	NM_011333	ENSMUSG00000035385	Ccl2	AI323594|HC11|JE|MCAF|MCP-1|MCP1|SMC-CF|Scya2|Sigje	chemokine (C-C motif) ligand 2	protein-coding
mm_66782.1	chr7	46975904	46975913	-	1	NA	promoter-TSS (NR_033461)	promoter-TSS (NR_033461)	3	NR_015609	97402	Mm.22314	NR_015609	ENSMUSG00000110001	C86187	-	expressed sequence C86187	ncRNA
mm_29727.1	chr3	125978640	125978650	-	1	NA	Intergenic	Intergenic	-40095	NM_011674	22239	Mm.306021	NM_011674	ENSMUSG00000032854	Ugt8a	AI850488|AW455908|Cgt|Ugt8|mCerGT	UDP galactosyltransferase 8A	protein-coding
mm_92693.1	chr10	80668667	80668675	-	1	NA	exon (NM_021462, exon 11 of 14)	exon (NM_021462, exon 11 of 14)	7622	NM_021462	17347	Mm.42126	NM_021462	ENSMUSG00000020190	Mknk2	2010016G11Rik|Gprk7|Mnk2	MAP kinase-interacting serine/threonine kinase 2	protein-coding
mm_78076.1	chr9	15627926	15627970	+	1	NA	promoter-TSS (NM_181816)	promoter-TSS (NM_181816)	-15	NM_181816	234964	Mm.32237	NM_181816	ENSMUSG00000039977	Ccdc67	4933401K09Rik|Deup1	coiled-coil domain containing 67	protein-coding
mm_36316.1	chr4	70249441	70249446	-	1	NA	intron (NM_145990, intron 28 of 36)	intron (NM_145990, intron 28 of 36)	160992	NM_001313762	214444	Mm.370777	NM_145990	ENSMUSG00000039298	Cdk5rap2	2900018K03Rik|an|mKIAA1633	CDK5 regulatory subunit associated protein 2	protein-coding
mm_132881.1	chr16	48790239	48790255	+	1	NA	Intergenic	Intergenic	-18291	NM_198297	77647	Mm.167298	NM_198297	ENSMUSG00000030775	Trat1	C030046M14Rik|Tcrim|Trim	T cell receptor associated transmembrane adaptor 1	protein-coding
mm_44868.1	chr5	34500833	34500835	-	1	NA	intron (NM_139064, intron 3 of 5)	intron (NM_139064, intron 3 of 5)	13145	NM_139064	231130	Mm.28615	NM_139064	ENSMUSG00000059866	Tnip2	1810020H16Rik|ABIN-2|AI428870	TNFAIP3 interacting protein 2	protein-coding
mm_67429.1	chr7	80370816	80370828	-	1	NA	5' UTR (NM_172903, exon 2 of 24)	5' UTR (NM_172903, exon 2 of 24)	553	NM_172903	140481	Mm.269245	NM_172903	ENSMUSG00000038886	Man2a2	1700052O22Rik|4931438M07Rik|AI480988|MX|Man IIx	mannosidase 2, alpha 2	protein-coding
mm_15924.1	chr2	165066893	165066908	+	1	NA	intron (NM_170702, intron 6 of 7)	intron (NM_170702, intron 6 of 7)	11264	NM_011611	21939	Mm.271833	NM_011611	ENSMUSG00000017652	Cd40	AI326936|Bp50|GP39|HIGM1|IGM|IMD3|T-BAM|TRAP|Tnfrsf5|p50	CD40 antigen	protein-coding
mm_126005.1	chr15	76538878	76538903	+	1	NA	promoter-TSS (NM_013909)	promoter-TSS (NM_013909)	-53	NM_029643	52710	Mm.28597	NM_029643	ENSMUSG00000022560	Slc52a2	2010003P03Rik|D15Ertd747e|GPCR42|Gpr172b|PAR2|mRFT1	solute carrier protein 52, member 2	protein-coding
mm_138259.1	chr17	34592216	34592226	+	1	NA	promoter-TSS (NM_017463)	promoter-TSS (NM_017463)	-250	NM_017463	18515	Mm.390957	NM_017463	ENSMUSG00000034673	Pbx2	AU043397|G17	pre B cell leukemia homeobox 2	protein-coding
mm_154567.1	chrX	6416942	6416955	+	1	NA	intron (NM_001313764, intron 1 of 8)	(T)n|Simple_repeat|Simple_repeat	1206	NM_001313764	208431	Mm.23208	NM_001040459	ENSMUSG00000068270	Shroom4	D430043L16Rik|Gm724|Shrm4	shroom family member 4	protein-coding
mm_86123.1	chr9	116175141	116175153	-	1	NA	5' UTR (NM_029575, exon 1 of 7)	5' UTR (NM_029575, exon 1 of 7)	216	NM_029575	21813	Mm.172346	NM_009371	ENSMUSG00000032440	Tgfbr2	1110020H15Rik|AU042018|DNIIR|RIIDN|TBR-II|TbetaR-II|TbetaRII	transforming growth factor, beta receptor II	protein-coding
mm_120177.1	chr14	61173024	61173081	+	1	NA	intron (NM_172809, intron 2 of 9)	CpG	34595	NM_172809	50720	Mm.440703	NM_015788	ENSMUSG00000048279	Sacs	A230052M14|DNAJC29|E130115J16Rik|mKIAA0730	sacsin	protein-coding
mm_98498.1	chr11	94951761	94951832	+	1	NA	3' UTR (NM_007742, exon 51 of 51)	3' UTR (NM_007742, exon 51 of 51)	15572	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_96955.1	chr11	70615837	70615841	+	1	NA	promoter-TSS (NM_001145537)	promoter-TSS (NM_001145537)	-55	NM_001145537	668433	Mm.425687	NM_001145537	ENSMUSG00000087279	4930544D05Rik	-	RIKEN cDNA 4930544D05 gene	protein-coding
mm_134627.1	chr16	21650166	21650177	-	1	NA	3' UTR (NM_001001881, exon 2 of 2)	3' UTR (NM_001001881, exon 2 of 2)	44494	NM_001001881	72190	Mm.131606	NM_001001881	ENSMUSG00000043391	2510009E07Rik	AI194952	RIKEN cDNA 2510009E07 gene	protein-coding
mm_61887.1	chr7	89671033	89671037	+	1	NA	intron (NM_181407, intron 1 of 13)	intron (NM_181407, intron 1 of 13)	38217	NM_181407	109264	Mm.334011	NM_181407	ENSMUSG00000030621	Me3	1700020C08Rik|B230207H15Rik	malic enzyme 3, NADP(+)-dependent, mitochondrial	protein-coding
mm_131562.1	chr16	18127656	18127662	+	1	NA	promoter-TSS (NM_022982)	promoter-TSS (NM_022982)	-47	NM_022982	65079	Mm.40149	NM_022982	ENSMUSG00000043811	Rtn4r	NOGOR|NgR|NgR1	reticulon 4 receptor	protein-coding
mm_169664.1	chr15	60398096	60398097	+	1	NA	Intergenic	L1Md_T|LINE|L1	-381478	NM_027668	71088	Mm.425950	NM_027668	ENSMUSG00000071749	4933412E24Rik	-	RIKEN cDNA 4933412E24 gene	protein-coding
mm_53426.1	chr6	134036025	134036034	+	1	NA	5' UTR (NM_007961, exon 1 of 8)	5' UTR (NM_007961, exon 1 of 8)	329	NM_007961	14011	Mm.269995	NM_007961	ENSMUSG00000030199	Etv6	AW123102|AW557856|Tel	ets variant 6	protein-coding
mm_40975.1	chr5	77016024	77016054	+	1	NA	promoter-TSS (NM_027970)	promoter-TSS (NM_027970)	16	NM_027970	71868	Mm.151092	NM_027970	ENSMUSG00000029248	Thegl	1700023E05Rik	theg spermatid protein like	protein-coding
mm_123991.1	chr14	75761148	75761163	-	1	NA	TTS (NM_026232)	TTS (NM_026232)	-6662	NM_177381	338337	Mm.86507	NM_177381	ENSMUSG00000034893	Cog3	E430004N23	component of oligomeric golgi complex 3	protein-coding
mm_154968.1	chrX	37126804	37126836	+	1	NA	promoter-TSS (NM_025937)	promoter-TSS (NM_025937)	57	NM_025937	67050	Mm.55422	NM_025937	ENSMUSG00000016409	Nkap	2610020O08Rik|AA987160|AI849147|AL024236	NFKB activating protein	protein-coding
mm_51365.1	chr6	72636328	72636332	+	1	NA	non-coding (NR_040422, exon 4 of 5)	non-coding (NR_040422, exon 4 of 5)	6499	NR_040421	100038714	Mm.321330	NR_040421		Gm15401	ENSMUSG00000072999|OTTMUSG00000021199	predicted gene 15401	ncRNA
mm_35229.1	chr4	19705160	19705163	-	1	NA	intron (NR_074089, intron 1 of 23)	B1_Mur1|SINE|Alu	3843	NM_177327	107568	Mm.78312	NM_177327	ENSMUSG00000041058	Wwp1	8030445B08Rik|AIP5|SDRP1|Tiul1	WW domain containing E3 ubiquitin protein ligase 1	protein-coding
mm_159562.1	chr4	109016786	109016786	+	1	NA	promoter-TSS (NR_030432)	promoter-TSS (NR_030432)	-869	NR_030432	791075		NR_030432	ENSMUSG00000076444	Mir761	Mirn761|mir-761|mmu-mir-761	microRNA 761	ncRNA
mm_24619.1	chr3	93511276	93511296	+	1	NA	Intergenic	Intergenic	-9210	NM_016740	20195	Mm.280038	NM_016740	ENSMUSG00000027907	S100a11	EMAPI|Emap1|S100a14|S100c|cal	S100 calcium binding protein A11	protein-coding
mm_22709.1	chr3	19187367	19187373	+	1	NA	promoter-TSS (NM_001253391)	promoter-TSS (NM_001253391)	41	NM_001253391	67472	Mm.45125	NM_026182	ENSMUSG00000027601	Mtfr1	1300002C08Rik|1700080D04Rik|2810026O10Rik|4930579E05Rik|Chppr|Fam54a2	mitochondrial fission regulator 1	protein-coding
mm_130738.1	chr15	101253777	101253808	-	1	NA	Intergenic	MIRc|SINE|MIR	-13054	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_112038.1	chr12	111670486	111670506	-	1	NA	intron (NM_021273, intron 5 of 7)	intron (NM_021273, intron 5 of 7)	1842	NM_021273	12709	Mm.16831	NM_021273	ENSMUSG00000001270	Ckb	B-CK|Bck|Ck-3|Ck3|Ckbb	creatine kinase, brain	protein-coding
mm_101762.1	chr11	43598714	43598717	-	1	NA	exon (NM_008375, exon 2 of 4)	exon (NM_008375, exon 2 of 4)	2847	NM_008375	16204	Mm.142716	NM_008375	ENSMUSG00000020405	Fabp6	GT|I-15P|I-BABP|ILBP|ILBP3|Illbp	fatty acid binding protein 6, ileal (gastrotropin)	protein-coding
mm_1844.1	chr1	82913323	82913329	+	1	NA	Intergenic	Intergenic	73866	NM_001347077	15463	Mm.392569	NM_010472	ENSMUSG00000026159	Agfg1	AU045498|C130049H11Rik|C85612|D730048C23Rik|Hrb|RAB|Rip	ArfGAP with FG repeats 1	protein-coding
mm_53118.1	chr6	125097078	125097109	+	1	NA	promoter-TSS (NR_106012)	promoter-TSS (NR_106012)	69	NR_106012	102466272		NR_106012	ENSMUSG00000098762	Mir7045	Gm27758|mmu-mir-7045	microRNA 7045	ncRNA
mm_150471.1	chr19	38481153	38481212	+	1	NA	Intergenic	CpG	-43015	NM_019588	74055	Mm.34031	NM_019588	ENSMUSG00000024998	Plce1	4933403A21Rik|PLCepsilon|Plce|mKIAA1516	phospholipase C, epsilon 1	protein-coding
mm_130202.1	chr15	95527960	95527973	-	1	NA	intron (NM_001289653, intron 1 of 20)	CpG-5276	286	NM_001289653	54003	Mm.3959	NM_016743	ENSMUSG00000022454	Nell2	A330108N19Rik|R75516|mel91	NEL-like 2	protein-coding
mm_85296.1	chr9	100481244	100481247	-	1	NA	intron (NM_001033543, intron 1 of 6)	L1MD|LINE|L1	5228	NM_001033543	213208	Mm.242896	NM_001033543	ENSMUSG00000044244	Il20rb	AV228068|Fndc6|Gm186|Il20R2	interleukin 20 receptor beta	protein-coding
mm_136078.1	chr16	84834980	84835015	-	1	NA	promoter-TSS (NM_001302216)	promoter-TSS (NM_001302216)	1	NM_001302216	11957	Mm.353	NM_016755	ENSMUSG00000022890	Atp5j	CF6	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit F	protein-coding
mm_168524.1	chr11	59505690	59505690	+	1	NA	promoter-TSS (NR_135273)	promoter-TSS (NR_135273)	37	NR_015585	74476	Mm.440257	NR_015585	ENSMUSG00000072893	4933439C10Rik	2610028M21Rik	RIKEN cDNA 4933439C10 gene	ncRNA
mm_151068.1	chr19	47510628	47510649	+	1	NA	intron (NM_175360, intron 7 of 9)	intron (NM_175360, intron 7 of 9)	-2344	NR_045322	100503104	Mm.442735	NR_045322	ENSMUSG00000097990	Gm19557	-	predicted gene, 19557	ncRNA
mm_106060.1	chr11	116131054	116131062	-	1	NA	promoter-TSS (NM_178802)	promoter-TSS (NM_178802)	70	NM_178802	338364	Mm.439976	NM_178802	ENSMUSG00000054517	Trim65	4732463G12Rik	tripartite motif-containing 65	protein-coding
mm_147247.1	chr18	38381182	38381191	-	1	NA	Intergenic	Intergenic	-37789	NM_022996	65113	Mm.102496	NM_022996	ENSMUSG00000024425	Ndfip1	0610010M22Rik|N4wbp5	Nedd4 family interacting protein 1	protein-coding
mm_71569.1	chr8	54077203	54077240	+	1	NA	promoter-TSS (NM_009506)	promoter-TSS (NM_009506)	-311	NM_009506	22341	Mm.1402	NM_009506	ENSMUSG00000031520	Vegfc	AW228853|VEGF-C	vascular endothelial growth factor C	protein-coding
mm_20424.1	chr2	129304714	129304727	-	1	NA	exon (NM_010554, exon 5 of 7)	exon (NM_010554, exon 5 of 7)	5252	NM_010554	16175	Mm.15534	NM_010554	ENSMUSG00000027399	Il1a	Il-1a	interleukin 1 alpha	protein-coding
mm_157035.1	chrX	7947780	7947815	-	1	NA	promoter-TSS (NM_010413)	promoter-TSS (NM_010413)	92	NM_001130416	15185	Mm.29854	NM_010413	ENSMUSG00000031161	Hdac6	Hd6|Hdac5|Sfc6|mHDA2	histone deacetylase 6	protein-coding
mm_109610.1	chr12	112722796	112722821	+	1	NA	intron (NM_001024602, intron 1 of 18)	C-rich|Low_complexity|Low_complexity	634	NM_001024602	217882	Mm.23689	NM_001024602	ENSMUSG00000072825	Cep170b	AI466840|AW555464|Kiaa0284|mKIAA0284	centrosomal protein 170B	protein-coding
mm_166853.1	chr7	19696936	19696940	+	1	NA	exon (NM_009696, exon 4 of 4)	exon (NM_009696, exon 4 of 4)	1460	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_151733.1	chr19	4879215	4879242	-	1	NA	intron (NM_027476, intron 1 of 2)	L2a|LINE|L2	538	NM_001168517	70605	Mm.36885	NM_027476	ENSMUSG00000006463	Zdhhc24	5730496N17Rik|Leng4	zinc finger, DHHC domain containing 24	protein-coding
mm_23695.1	chr3	68693694	68693704	+	1	NA	intron (NM_001159424, intron 3 of 7)	intron (NM_001159424, intron 3 of 7)	2275	NM_008351	16159	Mm.103783	NM_008351	ENSMUSG00000027776	Il12a	IL-12p35|Il-12a|Ll12a|p35	interleukin 12a	protein-coding
mm_143362.1	chr17	67346478	67346483	-	1	NA	intron (NM_008984, intron 1 of 30)	intron (NM_008984, intron 1 of 30)	7979	NM_008984	19274	Mm.311809	NM_008984	ENSMUSG00000033278	Ptprm	RPTPmu|mKIAA4044	protein tyrosine phosphatase, receptor type, M	protein-coding
mm_158504.1	chrX	142390575	142390581	-	1	NA	promoter-TSS (NM_207625)	promoter-TSS (NM_207625)	-43	NM_019477	50790	Mm.391337	NM_019477	ENSMUSG00000031278	Acsl4	9430020A05Rik|ACS4|AU018108|Facl4|Lacs4	acyl-CoA synthetase long-chain family member 4	protein-coding
mm_79596.1	chr9	58455157	58455185	+	1	NA	promoter-TSS (NR_040736)	promoter-TSS (NR_040736)	-2	NR_040736	74879	Mm.416924	NR_040736	ENSMUSG00000097651	4930461G14Rik	-	RIKEN cDNA 4930461G14 gene	ncRNA
mm_31016.1	chr4	40722526	40722547	+	1	NA	promoter-TSS (NM_001164672)	promoter-TSS (NM_001164672)	68	NM_008298	15502	Mm.27897	NM_008298	ENSMUSG00000028410	Dnaja1	HSJ-2|Hsj2|Nedd7	DnaJ heat shock protein family (Hsp40) member A1	protein-coding
mm_149017.1	chr19	8741474	8741503	+	1	NA	promoter-TSS (NM_001167799)	promoter-TSS (NM_001167799)	64	NM_001167799	56389	Mm.153061	NM_019829	ENSMUSG00000010110	Stx5a	0610031F24Rik|D19Ertd627e|Stx5	syntaxin 5A	protein-coding
mm_146981.1	chr18	33832853	33832861	-	1	NA	intron (NM_013512, intron 13 of 23)	B4|SINE|B4	37965	NR_038151	69749	Mm.248787	NR_038151	ENSMUSG00000087590	Epb41l4aos	2410004N09Rik|Epb4.1l4aos	erythrocyte membrane protein band 4.1 like 4a, opposite strand	ncRNA
mm_96718.1	chr11	69665602	69665636	+	1	NA	exon (NM_001291058, exon 2 of 6)	exon (NM_001291058, exon 2 of 6)	551	NM_001291058	12514	Mm.15819	NM_009853	ENSMUSG00000018774	Cd68	Lamp4|Scard1|gp110	CD68 antigen	protein-coding
mm_88423.1	chr10	77225710	77225717	+	1	NA	Intergenic	Intergenic	33510	NR_026944	100169878	Mm.420901	NR_026944	ENSMUSG00000078444	Gm10941	ENSMUSG00000078444	predicted gene 10941	ncRNA
mm_33993.1	chr4	137903256	137903267	+	1	NA	intron (NM_199307, intron 1 of 19)	intron (NM_199307, intron 1 of 19)	41024	NM_199307	230857	Mm.401062	NM_199307	ENSMUSG00000057530	Ece1	AW322500|ECE-1|ECE-1a|ECE-1b|ECE-1d	endothelin converting enzyme 1	protein-coding
mm_112378.1	chr12	119236871	119236873	-	1	NA	intron (NM_177290, intron 1 of 13)	intron (NM_177290, intron 1 of 13)	1404	NM_177290	320910	Mm.217000	NM_177290	ENSMUSG00000025321	Itgb8	4832412O06Rik	integrin beta 8	protein-coding
mm_94298.1	chr11	4096854	4096905	+	1	NA	TTS (NM_144520)	TTS (NM_144520)	-1448	NM_026443	67900	Mm.41719	NM_026443	ENSMUSG00000004748	Mtfp1	1700020C11Rik|2610507A21Rik|AV005788|Mtp18	mitochondrial fission process 1	protein-coding
mm_141407.1	chr17	29368846	29368851	-	1	NA	intron (NM_001159538, intron 8 of 15)	RMER17C|LTR|ERVK	7934	NM_001159538	26382	Mm.279187	NM_013710	ENSMUSG00000024013	Fgd2	Tcd-2|Tcd2|ZFYVE4|tcs-2|tcs2	FYVE, RhoGEF and PH domain containing 2	protein-coding
mm_144743.1	chr18	35584739	35584767	+	1	NA	exon (NM_010771, exon 12 of 15)	exon (NM_010771, exon 12 of 15)	-13914	NM_026420	67869	Mm.126534	NM_026420	ENSMUSG00000037058	Paip2	2310050K10Rik|AU045972	polyadenylate-binding protein-interacting protein 2	protein-coding
mm_53028.1	chr6	124480524	124480528	+	1	NA	Intergenic	Intergenic	-12587	NM_181344	232371	Mm.132974	NM_181344	ENSMUSG00000038527	C1rl	C1r-LP|C1rl1|C1rlp	complement component 1, r subcomponent-like	protein-coding
mm_138787.1	chr17	37271036	37271075	+	1	NA	exon (NM_013819, exon 3 of 8)	exon (NM_013819, exon 3 of 8)	821	NM_013819	14991	Mm.14437	NM_013819	ENSMUSG00000016206	H2-M3	H-2M3|Hmt|M3a|MuprM3|MuprM301|MuprM302|R4B2	histocompatibility 2, M region locus 3	protein-coding
mm_122739.1	chr14	54123585	54123630	-	1	NA	Intergenic	Intergenic	130322	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_24561.1	chr3	93443668	93443676	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	1342	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_63259.1	chr7	126663917	126663924	+	1	NA	intron (NM_029339, intron 2 of 9)	intron (NM_029339, intron 2 of 9)	12437	NM_133670	20887	Mm.368982	NM_133670	ENSMUSG00000030711	Sult1a1	AI266890|PST|ST1A1|Stp|Stp1	sulfotransferase family 1A, phenol-preferring, member 1	protein-coding
mm_43251.1	chr5	130188424	130188425	+	1	NA	intron (NM_001199059, intron 2 of 8)	intron (NM_001199059, intron 2 of 8)	1244	NM_019983	56715	Mm.288639	NM_019983	ENSMUSG00000025340	Rabgef1	Rab5ef|Rabex5|Rin2	RAB guanine nucleotide exchange factor (GEF) 1	protein-coding
mm_168158.1	chr10	4253934	4253945	+	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-12390	NM_031185	83397	Mm.27481	NM_031185	ENSMUSG00000038587	Akap12	AI317366|SSeCKS|Srcs5|Tsga12	A kinase (PRKA) anchor protein (gravin) 12	protein-coding
mm_86815.1	chr10	20534151	20534175	+	1	NA	intron (NM_013875, intron 2 of 12)	UCON26|Unknown|Unknown	14165	NM_001347366	29863	Mm.425617	NM_013875	ENSMUSG00000019990	Pde7b	-	phosphodiesterase 7B	protein-coding
mm_12047.1	chr2	59160885	59160896	+	1	NA	promoter-TSS (NM_026361)	promoter-TSS (NM_026361)	40	NM_175464	227937	Mm.260938	NM_026361	ENSMUSG00000026991	Pkp4	5031422I09Rik|9430019K17Rik|Armrp|p0071	plakophilin 4	protein-coding
mm_170339.1	chr18	46914418	46914424	-	1	NA	Intergenic	RMER16_Mm|LTR|ERVK	-7394	NM_001033446	381142	Mm.329423	NM_001033446	ENSMUSG00000073568	Arl14epl	Gm949	ADP-ribosylation factor-like 14 effector protein-like	protein-coding
mm_78817.1	chr9	44084945	44084957	+	1	NA	promoter-TSS (NM_198091)	promoter-TSS (NM_198091)	31	NM_198091	53376	Mm.272770	NM_016808	ENSMUSG00000032010	Usp2	B930035K21Rik|Ubp41	ubiquitin specific peptidase 2	protein-coding
mm_53021.1	chr6	124272529	124272538	+	1	NA	Intergenic	Intergenic	-32118	NM_001170395	93671	Mm.37426	NM_053094	ENSMUSG00000008845	Cd163	CD163v2|CD163v3	CD163 antigen	protein-coding
mm_132107.1	chr16	31450198	31450210	+	1	NA	intron (NM_175177, intron 5 of 6)	L2a|LINE|L2	21451	NM_001122683	71911	Mm.293470	NM_175177	ENSMUSG00000046598	Bdh1	2310032J20Rik|AI327223|Bdh	3-hydroxybutyrate dehydrogenase, type 1	protein-coding
mm_54824.1	chr6	42373239	42373253	-	1	NA	promoter-TSS (NM_023580)	promoter-TSS (NM_023580)	22	NM_023580	13835	Mm.133330	NM_023580	ENSMUSG00000029859	Epha1	5730453L17Rik|AL033318|Eph|Esk	Eph receptor A1	protein-coding
mm_128259.1	chr15	36771314	36771324	-	1	NA	3' UTR (NM_001253807, exon 5 of 5)	3' UTR (NM_001253807, exon 5 of 5)	19613	NM_001253807	22631	Mm.3360	NM_011740	ENSMUSG00000022285	Ywhaz	1110013I11Rik|14-3-3zeta|AI596267|AL022924|AU020854	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide	protein-coding
mm_53558.1	chr6	136943644	136943652	+	1	NA	Intergenic	MTC|LTR|ERVL-MaLR	-1749	NM_001301309	11857	Mm.2241	NM_007486	ENSMUSG00000030220	Arhgdib	D4|Gdid4|Ly-GDI	Rho, GDP dissociation inhibitor (GDI) beta	protein-coding
mm_94356.1	chr11	4947474	4947511	+	1	NA	promoter-TSS (NM_001243043)	promoter-TSS (NM_001243043)	-29	NM_001243043	11764	Mm.274816	NM_007454	ENSMUSG00000009090	Ap1b1	Adtb1|b2b1660Clo	adaptor protein complex AP-1, beta 1 subunit	protein-coding
mm_20406.1	chr2	129299849	129299868	-	1	NA	3' UTR (NM_010554, exon 7 of 7)	3' UTR (NM_010554, exon 7 of 7)	2488	NR_040371	100503468	Mm.446943	NR_040371	ENSMUSG00000085498	Gm14023	OTTMUSG00000015408	predicted gene 14023	ncRNA
mm_171831.1	chr5	146231198	146231200	+	1	NA	promoter-TSS (NM_153599)	promoter-TSS (NM_153599)	-476	NM_153599	264064	Mm.260576	NM_153599	ENSMUSG00000029635	Cdk8	-	cyclin-dependent kinase 8	protein-coding
mm_168750.1	chr12	115803120	115803136	-	1	NA	Intergenic	Intergenic	-107334	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
mm_53417.1	chr6	133699966	133699972	+	1	NA	Intergenic	Intergenic	67439	NM_001177652	545886	Mm.449716	NM_001177652	ENSMUSG00000108106	Gm5886	EG545886|smarp	predicted gene 5886	protein-coding
mm_37479.1	chr4	123565628	123565634	-	1	NA	intron (NM_001199136, intron 1 of 97)	intron (NM_001199136, intron 1 of 97)	-50789	NR_105824	102465214		NR_105824	ENSMUSG00000099005	Mir6398	Gm27657|mmu-mir-6398	microRNA 6398	ncRNA
mm_75281.1	chr8	41016584	41016614	-	1	NA	promoter-TSS (NR_015457)	promoter-TSS (NR_015457)	-869	NR_015457	78849	Mm.440930	NR_015457	ENSMUSG00000084960	B430010I23Rik	-	RIKEN cDNA B430010I23 gene	ncRNA
mm_2878.1	chr1	131828058	131828066	+	1	NA	promoter-TSS (NM_173865)	promoter-TSS (NM_173865)	50	NM_173865	98396	Mm.389181	NM_173865	ENSMUSG00000013275	Slc41a1	AI573938|B230315F01Rik	solute carrier family 41, member 1	protein-coding
mm_76502.1	chr8	86786741	86786742	-	1	NA	Intergenic	Intergenic	-40735	NM_009172	20437	Mm.324553	NM_009172	ENSMUSG00000036840	Siah1a	AA982064|AI853500|Sinh1a	seven in absentia 1A	protein-coding
mm_65224.1	chr7	19700446	19700458	-	1	NA	TTS (NM_001109748)	TTS (NM_001109748)	-1264	NM_009696	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_181.1	chr1	14864999	14865008	+	1	NA	Intergenic	Intergenic	53859	NM_177781	277328	Mm.186329	NM_177781	ENSMUSG00000032769	Trpa1	Anktm1|TRPA1b	transient receptor potential cation channel, subfamily A, member 1	protein-coding
mm_153834.1	chr19	46326190	46326211	-	1	NA	5' UTR (NM_001347454, exon 2 of 18)	5' UTR (NM_001347454, exon 2 of 18)	666	NM_001347454	73728	Mm.268532	NM_028627	ENSMUSG00000037126	Psd	1110007H17Rik|A930015K15|Efa6|Efa6a|Psdl|mKIAA2011	pleckstrin and Sec7 domain containing	protein-coding
mm_80960.1	chr9	103050239	103050260	+	1	NA	exon (NM_033314, exon 3 of 14)	exon (NM_033314, exon 3 of 14)	41760	NM_033314	24059	Mm.207106	NM_033314	ENSMUSG00000032548	Slco2a1	2310021C19Rik|Pgt|Slc21a2|mPgt	solute carrier organic anion transporter family, member 2a1	protein-coding
mm_140648.1	chr17	12691982	12691986	-	1	NA	exon (NM_010515, exon 40 of 48)	exon (NM_010515, exon 40 of 48)	-16146	NM_009202	20517	Mm.594	NM_009202	ENSMUSG00000023829	Slc22a1	Lx1|Oct1|Orct|Orct1	solute carrier family 22 (organic cation transporter), member 1	protein-coding
mm_105707.1	chr11	108273785	108273789	-	1	NA	intron (NM_011101, intron 2 of 16)	intron (NM_011101, intron 2 of 16)	70101	NM_011101	18750	Mm.222178	NM_011101	ENSMUSG00000050965	Prkca	AI875142|Pkca	protein kinase C, alpha	protein-coding
mm_162249.1	chrX	162902171	162902171	+	1	NA	promoter-TSS (NR_033143)	promoter-TSS (NR_033143)	0	NR_033143	55936	Mm.2065	NM_018737	ENSMUSG00000031360	Ctps2	A830031M15Rik|AI326475|Ctpsh	cytidine 5'-triphosphate synthase 2	protein-coding
mm_139936.1	chr17	71101552	71101554	+	1	NA	intron (NM_010867, intron 25 of 37)	intron (NM_010867, intron 25 of 37)	81996	NM_001083934	17929	Mm.4103	NM_010867	ENSMUSG00000024049	Myom1	D430047A17Rik	myomesin 1	protein-coding
mm_78059.1	chr9	14903196	14903204	+	1	NA	intron (NM_022888, intron 1 of 4)	intron (NM_022888, intron 1 of 4)	751	NM_176807	64931	Mm.86738	NM_022888	ENSMUSG00000031933	Izumo1r	0910001L11Rik|C86255|Folbp3|Folr4|Juno	IZUMO1 receptor, JUNO	protein-coding
mm_130814.1	chr15	101742919	101742929	-	1	NA	exon (NM_019956, exon 1 of 9)	exon (NM_019956, exon 1 of 9)	173	NM_019956	56735	Mm.358677	NM_019956	ENSMUSG00000051879	Krt71	AA589543|Ca|Cal4|Cu|Krt2-6g|mK6irs|mK6irs1	keratin 71	protein-coding
mm_145841.1	chr18	65447606	65447637	+	1	NA	exon (NM_172833, exon 4 of 16)	exon (NM_172833, exon 4 of 16)	16624	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_84324.1	chr9	64015034	64015035	-	1	NA	intron (NM_008542, intron 1 of 3)	intron (NM_008542, intron 1 of 3)	7025	NM_008542	17130	Mm.325757	NM_008542	ENSMUSG00000036867	Smad6	Madh6|b2b390Clo	SMAD family member 6	protein-coding
mm_128166.1	chr15	34082576	34082593	-	1	NA	promoter-TSS (NM_026002)	promoter-TSS (NM_026002)	-135	NM_026002	67154	Mm.130883	NM_026002	ENSMUSG00000022255	Mtdh	2610103J23Rik|3D3|3D3/Lyric|AEG-1|AV353288|D8Bwg1112e|Lyric	metadherin	protein-coding
mm_83560.1	chr9	46243318	46243340	-	1	NA	3' UTR (NM_007468, exon 3 of 3)	3' UTR (NM_007468, exon 3 of 3)	2485	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_24319.1	chr3	89430537	89430543	+	1	NA	promoter-TSS (NM_026869)	promoter-TSS (NM_026869)	-200	NM_001293767	68911	Mm.22521	NM_026869	ENSMUSG00000047824	Pygo2	1190004M21Rik	pygopus 2	protein-coding
mm_92244.1	chr10	70288157	70288166	-	1	NA	Intergenic	Intergenic	42885	NM_025807	66859	Mm.19325	NM_025807	ENSMUSG00000037762	Slc16a9	1200003C15Rik|4930425B13Rik|AI552636	solute carrier family 16 (monocarboxylic acid transporters), member 9	protein-coding
mm_164421.1	chr16	43973955	43973957	-	1	NA	exon (NM_001007460, exon 2 of 4)	exon (NM_001007460, exon 2 of 4)	5094	NM_001007460	332175	Mm.327852	NM_001007460	ENSMUSG00000036304	Zdhhc23	Gm1751|Gm779|nidd	zinc finger, DHHC domain containing 23	protein-coding
mm_105034.1	chr11	100527897	100527916	-	1	NA	promoter-TSS (NM_134037)	promoter-TSS (NM_134037)	94	NM_134037	104112	Mm.282039	NM_134037	ENSMUSG00000020917	Acly	A730098H14Rik|AW538652	ATP citrate lyase	protein-coding
mm_61739.1	chr7	82175188	82175199	+	1	NA	Intergenic	CpG	-84715	NM_001277955	20408	Mm.736	NM_017400	ENSMUSG00000030638	Sh3gl3	EEN-B2|SH3P13|Sh3d2c|Sh3d2c2	SH3-domain GRB2-like 3	protein-coding
mm_152702.1	chr19	17339543	17339562	-	1	NA	promoter-TSS (NM_001136484)	promoter-TSS (NM_001136484)	-47	NM_001136484	14537	Mm.244825	NM_010265	ENSMUSG00000038843	Gcnt1	5630400D21Rik|B130048E03|C2 GlcNAcT|C2GNT|IGnT	glucosaminyl (N-acetyl) transferase 1, core 2	protein-coding
mm_97445.1	chr11	78188738	78188787	+	1	NA	promoter-TSS (NM_033475)	promoter-TSS (NM_033475)	14	NM_033475	19376	Mm.275864	NM_033475	ENSMUSG00000002059	Rab34	AI326479|Narr|Rah|Rah1	RAB34, member RAS oncogene family	protein-coding
mm_5610.1	chr1	39629451	39629456	-	1	NA	intron (NM_170597, intron 2 of 3)	intron (NM_170597, intron 2 of 3)	21729	NM_170597	263764	Mm.122091	NM_170597	ENSMUSG00000050967	Creg2	A830098L22Rik	cellular repressor of E1A-stimulated genes 2	protein-coding
mm_51567.1	chr6	83711233	83711288	+	1	NA	promoter-TSS (NR_002873)	promoter-TSS (NR_002873)	-4	NM_011912	24113	Mm.307165	NM_011912	ENSMUSG00000034777	Vax2	Dres93	ventral anterior homeobox 2	protein-coding
mm_159919.1	chr6	52212903	52212903	-	1	NA	intron (NR_015611, intron 2 of 2)	intron (NR_015611, intron 2 of 2)	164	NM_010452	15400	Mm.71533	NM_010452	ENSMUSG00000079560	Hoxa3	Hox-1.5|Mo-10	homeobox A3	protein-coding
mm_21516.1	chr2	163628006	163628056	-	1	NA	exon (NM_012032, exon 8 of 10)	exon (NM_012032, exon 8 of 10)	-16819	NR_028113	68386	Mm.410649	NR_028113	ENSMUSG00000058812	0610039K10Rik	-	RIKEN cDNA 0610039K10 gene	ncRNA
mm_43187.1	chr5	128600831	128600848	+	1	NA	promoter-TSS (NM_175284)	promoter-TSS (NM_175284)	-152	NR_015517	319616	Mm.387738	NR_015517	ENSMUSG00000072591	5930412G12Rik	-	RIKEN cDNA 5930412G12 gene	ncRNA
mm_66125.1	chr7	31053847	31053862	-	1	NA	intron (NM_052991, intron 3 of 7)	intron (NM_052991, intron 3 of 7)	999	NM_052991	56188	Mm.1491	NM_019503	ENSMUSG00000036570	Fxyd1	0610012C17Rik|1110006M24Rik|Plm|Pml	FXYD domain-containing ion transport regulator 1	protein-coding
mm_29843.1	chr3	129831290	129831341	-	1	NA	promoter-TSS (NM_026578)	promoter-TSS (NM_026578)	81	NM_026578	68147	Mm.24873	NM_026578	ENSMUSG00000028010	Gar1	AA409823|AI326794|C430047J18Rik|Nola1	GAR1 ribonucleoprotein	protein-coding
mm_70673.1	chr8	14911669	14911677	+	1	NA	promoter-TSS (NM_001037736)	promoter-TSS (NM_001037736)	10	NM_001037736	234094	Mm.240298	NM_172751	ENSMUSG00000071176	Arhgef10	6430549H08Rik|mKIAA0294	Rho guanine nucleotide exchange factor (GEF) 10	protein-coding
mm_142814.1	chr17	51739679	51739695	-	1	NA	3' UTR (NM_001163632, exon 11 of 11)	3' UTR (NM_001163632, exon 11 of 11)	72367	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_152179.1	chr19	7383030	7383063	-	1	NA	promoter-TSS (NM_001033139)	promoter-TSS (NM_001033139)	-20	NM_001167831	68229	Mm.34766	NM_001033139	ENSMUSG00000024970	AI846148	1700105P06Rik	expressed sequence AI846148	protein-coding
mm_53533.1	chr6	136587562	136587582	+	1	NA	exon (NM_019426, exon 9 of 15)	exon (NM_019426, exon 9 of 15)	68721	NM_019426	54343	Mm.173271	NM_019426	ENSMUSG00000030213	Atf7ip	2610204M12Rik|AM|Mcaf1	activating transcription factor 7 interacting protein	protein-coding
mm_115213.1	chr13	109441113	109441132	+	1	NA	intron (NM_011056, intron 3 of 16)	intron (NM_011056, intron 3 of 16)	116378	NR_030644	100124489		NR_030644	ENSMUSG00000076946	Mir582	Mirn582|mir-582|mmu-mir-582	microRNA 582	ncRNA
mm_45748.1	chr5	86676311	86676320	-	1	NA	promoter-TSS (NM_177024)	promoter-TSS (NM_177024)	-17	NM_177024	319875	Mm.253994	NM_177024	ENSMUSG00000035861	Tmprss11b	9930019B18Rik|Tmprss11bnl	transmembrane protease, serine 11B	protein-coding
mm_156751.1	chrX	160390561	160390616	+	1	NA	promoter-TSS (NM_178712)	promoter-TSS (NM_178712)	-102	NM_001079847	237175	Mm.213016	NM_178712	ENSMUSG00000031298	Adgrg2	AW212196|B830041D06Rik|Gpr64|Me6	adhesion G protein-coupled receptor G2	protein-coding
mm_132537.1	chr16	37868736	37868763	+	1	NA	exon (NM_177093, exon 1 of 4)	exon (NM_177093, exon 1 of 4)	349	NM_177093	320184	Mm.390882	NM_177093	ENSMUSG00000034158	Lrrc58	1810012N18Rik|C330018J07Rik	leucine rich repeat containing 58	protein-coding
mm_48700.1	chr5	146963743	146963805	-	1	NA	promoter-TSS (NM_001256102)	promoter-TSS (NM_001256102)	23	NM_001256101	76366	Mm.486234	NM_029581	ENSMUSG00000016510	Mtif3	2810012L14Rik|AI414549	mitochondrial translational initiation factor 3	protein-coding
mm_46417.1	chr5	104113421	104113435	-	1	NA	5' UTR (NM_010097, exon 1 of 11)	5' UTR (NM_010097, exon 1 of 11)	660	NM_010097	13602	Mm.29027	NM_010097	ENSMUSG00000029309	Sparcl1	Ecm2|Sc1|hevin|mast9	SPARC-like 1	protein-coding
mm_144198.1	chr18	7916115	7916130	+	1	NA	exon (NM_001146298, exon 7 of 13)	exon (NM_001146298, exon 7 of 13)	46925	NM_153085	225131	Mm.204524	NM_153085	ENSMUSG00000024283	Wac	1110067P07Rik|A230035H12Rik|AI256735|AI256776|Wwp4	WW domain containing adaptor with coiled-coil	protein-coding
mm_308.1	chr1	24100039	24100073	+	1	NA	intron (NM_026604, intron 1 of 20)	CpG	285	NM_026604	68187	Mm.87130	NM_026604	ENSMUSG00000026153	Fam135a	4921533L14Rik|AI256732|AI835491	family with sequence similarity 135, member A	protein-coding
mm_127596.1	chr15	102394087	102394114	+	1	NA	Intergenic	Intergenic	-12216	NM_013672	20683	Mm.4618	NM_013672	ENSMUSG00000001280	Sp1	1110003E12Rik|AA450830|AI845540|Sp1-1	trans-acting transcription factor 1	protein-coding
mm_142082.1	chr17	35704001	35704091	-	1	NA	promoter-TSS (NM_172962)	promoter-TSS (NM_172962)	93	NM_007584	12305	Mm.5021	NM_007584	ENSMUSG00000003534	Ddr1	6030432F18|AI323681|CD167a|Cak|Nep|PTK3A	discoidin domain receptor family, member 1	protein-coding
mm_54380.1	chr6	31211144	31211171	-	1	NA	intron (NR_110469, intron 1 of 3)	MER5A|DNA|hAT-Charlie	7317	NR_110470	232685	Mm.443019	NM_144555	ENSMUSG00000044471	Lncpint	Lincpint|MNCb-1768|Pint|linc-Pint	long non-protein coding RNA, Trp53 induced transcript	ncRNA
mm_24673.1	chr3	94787654	94787664	+	1	NA	Intergenic	Intergenic	-1144	NM_001037711	70737	Mm.87634	NM_001037711	ENSMUSG00000068876	Cgn	6330408J11Rik	cingulin	protein-coding
mm_14787.1	chr2	145860354	145860368	+	1	NA	exon (NM_028724, exon 9 of 13)	exon (NM_028724, exon 9 of 13)	-42880	NM_026425	67877	Mm.151168	NM_026425	ENSMUSG00000002728	Naa20	1500004D14Rik|2900026I01Rik|AU041458|D2Ertd186e|Nat5	N(alpha)-acetyltransferase 20, NatB catalytic subunit	protein-coding
mm_153963.1	chr19	47837263	47837275	-	1	NA	promoter-TSS (NM_027559)	promoter-TSS (NM_027559)	92	NM_027559	100048534	Mm.29457	NM_027559	ENSMUSG00000044948	Cfap43	4632415N18Rik|4930428C11Rik|4930463G05Rik|AI429486|D19Ertd652e|Wdr96	cilia and flagella associated protein 43	protein-coding
mm_173200.1	chrX	67474483	67474487	+	1	NA	Intergenic	MT2_Mm|LTR|ERVL	219077	NM_001126317	382217	Mm.422933	NM_001126317	ENSMUSG00000079578	Gm1140	-	predicted gene 1140	protein-coding
mm_113234.1	chr13	27247833	27247891	+	1	NA	exon (NM_008865, exon 4 of 5)	exon (NM_008865, exon 4 of 5)	5432	NM_008865	18776	Mm.37203	NM_008865	ENSMUSG00000038891	Prl3b1	Csh2|Ghd8|PL|Pl-2|Pl2|mPL-II|mplII	prolactin family 3, subfamily b, member 1	protein-coding
mm_134732.1	chr16	22899116	22899116	-	1	NA	non-coding (NR_075099, exon 6 of 6)	non-coding (NR_075099, exon 6 of 6)	-4730	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_106267.1	chr11	117969285	117969297	-	1	NA	promoter-TSS (NM_007707)	promoter-TSS (NM_007707)	75	NM_007707	12702	Mm.3468	NM_007707	ENSMUSG00000053113	Socs3	Cis3|Cish3|EF-10|Ef10|SSI-3|Ssi3	suppressor of cytokine signaling 3	protein-coding
mm_131239.1	chr16	10488214	10488253	+	1	NA	promoter-TSS (NM_007575)	promoter-TSS (NM_007575)	55	NM_007575	12265	Mm.249560	NM_007575	ENSMUSG00000022504	Ciita	C2ta|EG669998|Gm9475|Mhc2ta	class II transactivator	protein-coding
mm_58502.1	chr7	3712598	3712611	+	1	NA	TTS (NM_011095)	TTS (NM_011095)	7778	NM_011095	18733	Mm.326531	NM_011095	ENSMUSG00000058818	Pirb	Gp91|LIR-3|Lilrb3|PIR-B	paired Ig-like receptor B	protein-coding
mm_73630.1	chr8	110721452	110721456	+	1	NA	promoter-TSS (NM_198625)	promoter-TSS (NM_198625)	-22	NM_198625	244654	Mm.490385	NM_198625	ENSMUSG00000033763	Mtss1l	ABBA	metastasis suppressor 1-like	protein-coding
mm_156500.1	chrX	144455917	144455924	+	1	NA	promoter-TSS (NM_001195579)	promoter-TSS (NM_001195579)	-662	NM_001195579	100503240	Mm.387258	NM_001195579	ENSMUSG00000072934	Trpc5os	ENSMUSG00000072934|Gm15070|OTTMUSG00000018931	transient receptor potential cation channel, subfamily C, member 5, opposite strand	protein-coding
mm_19123.1	chr2	80128941	80128996	-	1	NA	promoter-TSS (NM_016744)	promoter-TSS (NM_016744)	3	NM_016744	18573	Mm.40678	NM_016744	ENSMUSG00000059173	Pde1a	AI987702|AW125737	phosphodiesterase 1A, calmodulin-dependent	protein-coding
mm_88173.1	chr10	69787392	69787402	+	1	NA	intron (NM_170730, intron 1 of 17)	intron (NM_170730, intron 1 of 17)	-138135	NM_170687	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_123056.1	chr14	55643801	55643822	-	1	NA	promoter-TSS (NM_028780)	promoter-TSS (NM_028780)	-5	NM_028780	74140	Mm.132857	NM_028780	ENSMUSG00000002320	Tm9sf1	1200014D02Rik|AI893436|MP70	transmembrane 9 superfamily member 1	protein-coding
mm_133532.1	chr16	91043482	91043503	+	1	NA	intron (NM_026110, intron 1 of 17)	intron (NM_026110, intron 1 of 17)	887	NM_026110	67367	Mm.347	NM_026110	ENSMUSG00000022974	Paxbp1	1810007M14Rik|C21orf66|Gcfc|Gcfc1|Pax3/7bp	PAX3 and PAX7 binding protein 1	protein-coding
mm_29940.1	chr3	132791230	132791235	-	1	NA	intron (NM_001163455, intron 23 of 25)	intron (NM_001163455, intron 23 of 25)	87364	NR_102297	101243624	Mm.306256	NR_102297	ENSMUSG00000106230	Gm29811	-	predicted gene, 29811	ncRNA
mm_173262.1	chrX	94882793	94882810	+	1	NA	Intergenic	Intergenic	-84512	NR_003292	668171	Mm.426134	NR_003292		Zxda	4933406P09Rik|AW413531	zinc finger, X-linked, duplicated A	pseudo
mm_106608.1	chr11	120784253	120784261	-	1	NA	promoter-TSS (NM_145370)	promoter-TSS (NM_145370)	-15	NM_001346709	209318	Mm.30195	NM_145370	ENSMUSG00000025156	Gps1	Cops1|Csn1|R75577|Sgn1	G protein pathway suppressor 1	protein-coding
mm_165508.1	chr2	169949469	169949472	+	1	NA	Intergenic	B4A|SINE|B4	13717	NR_131974	446211	Mm.266854	NR_131974	ENSMUSG00000103935	AY702102	STDP1	cDNA sequence AY702102	ncRNA
mm_79335.1	chr9	53341255	53341298	+	1	NA	intron (NM_176846, intron 3 of 5)	intron (NM_176846, intron 3 of 5)	39606	NM_176846	320051	Mm.277540	NM_176846	ENSMUSG00000034584	Exph5	AC079869.22gm5|B130009M24Rik|E030050P12|Kiaa0624|Slac2b|slac2-b	exophilin 5	protein-coding
mm_43877.1	chr5	143732634	143732643	+	1	NA	promoter-TSS (NM_029749)	promoter-TSS (NM_029749)	-358	NM_029749	76800	Mm.259620	NM_029749	ENSMUSG00000051306	Usp42	2410140K03Rik|3110031A07Rik|A630018G05Rik|D5Ertd591e	ubiquitin specific peptidase 42	protein-coding
mm_73076.1	chr8	94460472	94460475	+	1	NA	Intergenic	LTR78|LTR|ERV1	-12290	NM_001033207	434341	Mm.334720	NM_001033207	ENSMUSG00000074151	Nlrc5	AI451557|AK220210|NOD27	NLR family, CARD domain containing 5	protein-coding
mm_135449.1	chr16	45693728	45693743	-	1	NA	promoter-TSS (NM_172455)	promoter-TSS (NM_172455)	-77	NM_172455	208171	Mm.186306	NM_172455	ENSMUSG00000033177	Tmprss7	B230219I23Rik|Gm1748	transmembrane serine protease 7	protein-coding
mm_42617.1	chr5	118027841	118027849	+	1	NA	promoter-TSS (NM_021344)	promoter-TSS (NM_021344)	21	NM_021344	57816	Mm.273285	NM_021344	ENSMUSG00000029359	Tesc	1010001A17Rik|2410011K10Rik|TE-1	tescalcin	protein-coding
mm_111659.1	chr12	103242144	103242148	-	1	NA	promoter-TSS (NM_133364)	promoter-TSS (NM_133364)	0	NM_133364	170952	Mm.217019	NM_133364	ENSMUSG00000041669	Prima1	B230212M13Rik|BB120497|PRiMA	proline rich membrane anchor 1	protein-coding
mm_27673.1	chr3	65639279	65639303	-	1	NA	Intergenic	Intergenic	-19997	NR_106200	102465905		NR_106200	ENSMUSG00000098944	Mir8120	Gm27637|mmu-mir-8120	microRNA 8120	ncRNA
mm_2858.1	chr1	131688745	131688753	+	1	NA	promoter-TSS (NM_145509)	promoter-TSS (NM_145509)	54	NM_001311096	226421	Mm.44508	NM_145509	ENSMUSG00000052688	Rab7b	5430435G22Rik	RAB7B, member RAS oncogene family	protein-coding
mm_42578.1	chr5	117256806	117256809	+	1	NA	intron (NM_001081308, intron 16 of 19)	PB1D11|SINE|Alu	30757	NM_018858	23980	Mm.195898	NM_018858	ENSMUSG00000032959	Pebp1	HCNP|Pbp|Pbp1|Pbpr|Rkip	phosphatidylethanolamine binding protein 1	protein-coding
mm_85130.1	chr9	95606665	95606665	-	1	NA	Intergenic	RCHARR1|DNA|hAT-Charlie	-30963	NM_029620	76477	Mm.46016	NM_029620	ENSMUSG00000015354	Pcolce2	2400001O18Rik|Pcpe2	procollagen C-endopeptidase enhancer 2	protein-coding
mm_53873.1	chr6	149408974	149409038	+	1	NA	promoter-TSS (NM_001112796)	promoter-TSS (NM_001112796)	22	NM_009753	12121	Mm.177181	NM_009753	ENSMUSG00000003452	Bicd1	B830009D06Rik|bic-D 1	bicaudal D homolog 1 (Drosophila)	protein-coding
mm_82775.1	chr9	27029989	27030004	-	1	NA	promoter-TSS (NM_178113)	promoter-TSS (NM_178113)	98	NM_178027	69091	Mm.218717	NM_178027	ENSMUSG00000031988	Vps26b	1810012I05Rik|2310075A12Rik|AI848392	VPS26 retromer complex component B	protein-coding
mm_82673.1	chr9	22131636	22131665	-	1	NA	intron (NM_001102405, intron 1 of 4)	intron (NM_001102405, intron 1 of 4)	215	NM_001102404	11433	Mm.46354	NM_007388	ENSMUSG00000001348	Acp5	TRACP|TRAP	acid phosphatase 5, tartrate resistant	protein-coding
mm_106765.1	chr12	4592794	4592836	+	1	NA	promoter-TSS (NM_001198969)	promoter-TSS (NM_001198969)	-193	NM_001198969	20403	Mm.341204	NM_011365	ENSMUSG00000020640	Itsn2	AI327390|Ese2|Sh3d1B|Sh3p18|mKIAA1256	intersectin 2	protein-coding
mm_31726.1	chr4	62879699	62879699	+	1	NA	Intergenic	Intergenic	-85875	NM_028326	72701	Mm.26479	NM_028326	ENSMUSG00000028358	Zfp618	2810031P15Rik|2810040O04Rik|AI415580|AI505139|D430033D05Rik|Nedd10|Znf618|bM257P7.1	zinc finger protein 618	protein-coding
mm_80368.1	chr9	75338136	75338163	+	1	NA	intron (NR_073186, intron 8 of 11)	intron (NR_073186, intron 8 of 11)	-9609	NM_013479	12049	Mm.25988	NM_013479	ENSMUSG00000032191	Bcl2l10	AA420380|AU023065|Boo|C85687|Diva	Bcl2-like 10	protein-coding
mm_164841.1	chr18	42196744	42196747	-	1	NA	promoter-TSS (NM_027072)	promoter-TSS (NM_027072)	-36	NM_027072	69401	Mm.34841	NM_027072	ENSMUSG00000059455	Plac8l1	1700009N18Rik|1700015M15Rik	PLAC8-like 1	protein-coding
mm_39977.1	chr5	32353591	32353622	+	1	NA	promoter-TSS (NM_172147)	promoter-TSS (NM_172147)	26	NM_172147	665270	Mm.160067	NM_030072	ENSMUSG00000029134	Plb1	4632413E21Rik|4930433E17Rik|4930539A06Rik|BC033606	phospholipase B1	protein-coding
mm_143813.1	chr17	83777985	83777989	-	1	NA	intron (NM_001171053, intron 9 of 13)	RLTR31C_MM|LTR|ERVK	68803	NM_025325	107766	Mm.30100	NM_025325	ENSMUSG00000000673	Haao	0610007K21Rik|0610012J07Rik|3-HAO|3-HAOxase|3HAO	3-hydroxyanthranilate 3,4-dioxygenase	protein-coding
mm_89075.1	chr10	83094628	83094628	+	1	NA	intron (NM_021439, intron 2 of 2)	intron (NM_021439, intron 2 of 2)	109131	NM_021439	58250	Mm.360747	NM_021439	ENSMUSG00000034612	Chst11	1110020P09Rik|C4ST|C4ST-1|C4ST1|C4s	carbohydrate sulfotransferase 11	protein-coding
mm_19900.1	chr2	114146974	114146994	-	1	NA	exon (NM_009702, exon 13 of 35)	exon (NM_009702, exon 13 of 35)	3586	NR_105968	102465982		NR_105968	ENSMUSG00000098464	Mir7002	Gm27429|mmu-mir-7002	microRNA 7002	ncRNA
mm_27184.1	chr3	34649757	34649769	-	1	NA	promoter-TSS (NM_011443)	promoter-TSS (NM_011443)	-232	NM_011443	20674	Mm.65396	NM_011443	ENSMUSG00000074637	Sox2	Sox-2|lcc|ysb	SRY (sex determining region Y)-box 2	protein-coding
mm_9022.1	chr1	166238687	166238719	-	1	NA	promoter-TSS (NM_175296)	promoter-TSS (NM_175296)	41	NM_175296	98558	Mm.26189	NM_175296	ENSMUSG00000040629	Mael	4933405K18Rik|AU019877	maelstrom spermatogenic transposon silencer	protein-coding
mm_59119.1	chr7	19852025	19852045	+	1	NA	promoter-TSS (NM_001270489)	promoter-TSS (NM_001270489)	32	NM_001270489	100502736	Mm.445354	NM_001270489	ENSMUSG00000092216	Gm19345	-	predicted gene, 19345	protein-coding
mm_52371.1	chr6	113065408	113065431	+	1	NA	intron (NM_008188, intron 6 of 9)	intron (NM_008188, intron 6 of 9)	11825	NR_027010	14910	Mm.280950	NR_027008	ENSMUSG00000086429	Gt(ROSA)26Sor	AV258896|Gtrgeo26|Gtrosa26|R26|ROSA26|Thumpd3as1	gene trap ROSA 26, Philippe Soriano	ncRNA
mm_31018.1	chr4	40723018	40723031	+	1	NA	promoter-TSS (NM_001164672)	promoter-TSS (NM_001164672)	94	NM_001164672	15502	Mm.27897	NM_008298	ENSMUSG00000028410	Dnaja1	HSJ-2|Hsj2|Nedd7	DnaJ heat shock protein family (Hsp40) member A1	protein-coding
mm_113538.1	chr13	37856873	37856876	+	1	NA	intron (NM_001039188, intron 1 of 9)	intron (NM_001039188, intron 1 of 9)	29481	NM_001039188	68750	Mm.491109	NM_026830	ENSMUSG00000039087	Rreb1	1110037N09Rik|AA414966|B930013M22Rik	ras responsive element binding protein 1	protein-coding
mm_28930.1	chr3	98859775	98859800	-	1	NA	promoter-TSS (NM_001304800)	promoter-TSS (NM_001304800)	7	NM_001304800	15492	Mm.140811	NM_008293	ENSMUSG00000027871	Hsd3b1	3-beta-HSD I|D3Ertd383e	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1	protein-coding
mm_103181.1	chr11	70489860	70489863	-	1	NA	Intergenic	Intergenic	-15413	NM_029360	75604	Mm.24400	NM_029360	ENSMUSG00000018919	Tm4sf5	2010003F10Rik|AI323987	transmembrane 4 superfamily member 5	protein-coding
mm_90649.1	chr10	128746458	128746474	+	1	NA	Intergenic	Intergenic	-1413	NM_030100	78428	Mm.27358	NM_030100	ENSMUSG00000064030	Pym1	A030010B05Rik|Pym|Wibg	PYM homolog 1, exon junction complex associated factor	protein-coding
mm_133798.1	chr16	95293102	95293110	+	1	NA	intron (NM_001039056, intron 3 of 3)	intron (NM_001039056, intron 3 of 3)	35548	NM_001271690	16516	Mm.272239	NM_019664	ENSMUSG00000062609	Kcnj15	4930414N08Rik|AI182284|AI267127|IRKK|Kir4.2	potassium inwardly-rectifying channel, subfamily J, member 15	protein-coding
mm_39232.1	chr4	156254508	156254534	-	1	NA	exon (NM_001110516, exon 2 of 11)	exon (NM_001110516, exon 2 of 11)	817	NM_001110516	231004	Mm.406833	NM_173736	ENSMUSG00000096351	Samd11	BC026991|mr-s	sterile alpha motif domain containing 11	protein-coding
mm_100692.1	chr11	3529557	3529592	-	1	NA	exon (NM_001284429, exon 12 of 22)	exon (NM_001284429, exon 12 of 22)	9718	NM_013870	29856	Mm.188516	NM_013870	ENSMUSG00000020439	Smtn	smsmo	smoothelin	protein-coding
mm_139738.1	chr17	59424720	59424721	+	1	NA	Intergenic	B3|SINE|B2	-411398	NM_026497	67993	Mm.36507	NM_026497	ENSMUSG00000024228	Nudt12	0610016O18Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 12	protein-coding
mm_50096.1	chr6	41533018	41533037	+	1	NA	Intergenic	Intergenic	11251	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_47580.1	chr5	124557086	124557095	-	1	NA	intron (NM_026409, intron 5 of 13)	intron (NM_026409, intron 5 of 13)	4226	NM_026409	67848	Mm.281601	NM_026409	ENSMUSG00000029389	Ddx55	2810021H22Rik|mKIAA1595	DEAD (Asp-Glu-Ala-Asp) box polypeptide 55	protein-coding
mm_118718.1	chr14	22202211	22202224	+	1	NA	intron (NM_028275, intron 2 of 6)	Lx7|LINE|L1	182505	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_141034.1	chr17	25273391	25273443	-	1	NA	promoter-TSS (NR_027452)	promoter-TSS (NR_027452)	14	NM_001177610	22196	Mm.240044	NM_011665	ENSMUSG00000015120	Ube2i	5830467E05Rik|F830028O17Rik|UBC9|Ubce2i|Ubce9	ubiquitin-conjugating enzyme E2I	protein-coding
mm_44344.1	chr5	17782653	17782663	-	1	NA	3' UTR (NM_001159558, exon 16 of 16)	3' UTR (NM_001159558, exon 16 of 16)	53238	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_125534.1	chr15	58002108	58002118	+	1	NA	intron (NM_173862, intron 3 of 3)	intron (NM_173862, intron 3 of 3)	16210	NM_173862	239463	Mm.221241	NM_173862	ENSMUSG00000051225	Fam83a	-	family with sequence similarity 83, member A	protein-coding
mm_80522.1	chr9	80067154	80067165	+	1	NA	5' UTR (NM_146003, exon 1 of 23)	5' UTR (NM_146003, exon 1 of 23)	256	NM_146003	215351	Mm.28232	NM_146003	ENSMUSG00000034252	Senp6	2810017C20Rik|E130319N12Rik|Susp1|mKIAA0797	SUMO/sentrin specific peptidase 6	protein-coding
mm_51624.1	chr6	85451489	85451502	+	1	NA	promoter-TSS (NM_001163427)	promoter-TSS (NM_001163427)	-10	NM_007638	12468	Mm.289900	NM_007638	ENSMUSG00000030007	Cct7	AA408524|AL022769|Ccth|Cctz	chaperonin containing Tcp1, subunit 7 (eta)	protein-coding
mm_35937.1	chr4	53033119	53033130	-	1	NA	3' UTR (NM_013454, exon 50 of 50)	3' UTR (NM_013454, exon 50 of 50)	21244	NM_025623	66536	Mm.38244	NM_025623	ENSMUSG00000015247	Nipsnap3b	2700063N13Rik|Nipsnap3a	nipsnap homolog 3B (C. elegans)	protein-coding
mm_103421.1	chr11	75594744	75594760	-	1	NA	intron (NM_008850, intron 2 of 11)	intron (NM_008850, intron 2 of 11)	5479	NR_110477	654359	Mm.439961	NR_110477		Gm12338	OTTMUSG00000006216	cytochrome c oxidase, subunit VIIc pseudogene	pseudo
mm_84061.1	chr9	58199734	58199756	-	1	NA	exon (NM_177193, exon 3 of 3)	exon (NM_177193, exon 3 of 3)	1970	NM_001161535	320563	Mm.186499	NM_177193	ENSMUSG00000051243	Islr2	B930052A04Rik|Linx|Mbu-3|mKIAA1465	immunoglobulin superfamily containing leucine-rich repeat 2	protein-coding
mm_129689.1	chr15	81514261	81514281	-	1	NA	Intergenic	Intergenic	47955	NM_019712	56438	Mm.29405	NM_019712	ENSMUSG00000022400	Rbx1	1500002P15Rik|AA517855|ROC1	ring-box 1	protein-coding
mm_115791.1	chr13	19338745	19338755	-	1	NA	Intergenic	L1M2|LINE|L1	57063	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_72002.1	chr8	70673365	70673428	+	1	NA	5' UTR (NM_015816, exon 1 of 5)	5' UTR (NM_015816, exon 1 of 5)	165	NM_015816	50783	Mm.248188	NM_015816	ENSMUSG00000031848	Lsm4	-	LSM4 homolog, U6 small nuclear RNA and mRNA degradation associated	protein-coding
mm_3280.1	chr1	136624934	136624949	+	1	NA	promoter-TSS (NM_001160251)	promoter-TSS (NM_001160251)	40	NM_001160251	226442	Mm.62521	NM_177643	ENSMUSG00000041483	Zfp281	Znf281	zinc finger protein 281	protein-coding
mm_143442.1	chr17	70853483	70853537	-	1	NA	promoter-TSS (NM_001164074)	promoter-TSS (NM_001164074)	22	NM_001164074	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_49775.1	chr6	34907526	34907537	+	1	NA	intron (NM_001013366, intron 3 of 14)	intron (NM_001013366, intron 3 of 14)	3300	NM_001013366	101240	Mm.152120	NM_001013366	ENSMUSG00000058486	Wdr91	9530020G05Rik|AI987683|AU018665	WD repeat domain 91	protein-coding
mm_45694.1	chr5	82123367	82123373	-	1	NA	intron (NR_138557, intron 1 of 1)	intron (NR_138557, intron 1 of 1)	1343	NR_138557	67327	Mm.87058	NR_138557		1700031L13Rik	-	RIKEN cDNA 1700031L13 gene	ncRNA
mm_5699.1	chr1	43187335	43187340	-	1	NA	intron (NM_001289533, intron 1 of 5)	intron (NM_001289533, intron 1 of 5)	9424	NM_001289533	14200	Mm.6799	NM_010212	ENSMUSG00000008136	Fhl2	FHL-2|SLIM-3|SLIM3	four and a half LIM domains 2	protein-coding
mm_148392.1	chr19	3708288	3708395	+	1	NA	promoter-TSS (NM_028077)	promoter-TSS (NM_028077)	8	NM_028077	72056	Mm.23780	NM_028077	ENSMUSG00000035372	1810055G02Rik	AI256204	RIKEN cDNA 1810055G02 gene	protein-coding
mm_98918.1	chr11	98294257	98294261	+	1	NA	Intergenic	Intergenic	31653	NR_039579	100628613		NR_039579	ENSMUSG00000093176	Mir5119	mmu-mir-5119|mu-mir-5119	microRNA 5119	ncRNA
mm_13071.1	chr2	91119202	91119217	+	1	NA	exon (NM_008653, exon 2 of 32)	exon (NM_008653, exon 2 of 32)	1065	NM_008653	17868	Mm.10728	NM_008653	ENSMUSG00000002100	Mybpc3	-	myosin binding protein C, cardiac	protein-coding
mm_104478.1	chr11	95569862	95569886	-	1	NA	3' UTR (NM_033217, exon 6 of 6)	3' UTR (NM_033217, exon 6 of 6)	17824	NM_033217	18053	Mm.283893	NM_033217	ENSMUSG00000000120	Ngfr	LNGFR|Tnfrsf16|p75|p75NGFR|p75NTR	nerve growth factor receptor (TNFR superfamily, member 16)	protein-coding
mm_91429.1	chr10	33206633	33206635	-	1	NA	intron (NM_029726, intron 9 of 37)	L1VL4|LINE|L1	49723	NR_040657	442820	Mm.490725	NR_040657		D830005E20Rik	-	RIKEN cDNA D830005E20 gene	ncRNA
mm_61419.1	chr7	73617971	73618001	+	1	NA	Intergenic	Intergenic	-59591	NR_037569	69170	Mm.34539	NR_037569	ENSMUSG00000101970	1810026B05Rik	-	RIKEN cDNA 1810026B05 gene	ncRNA
mm_36725.1	chr4	99030816	99030826	-	1	NA	promoter-TSS (NM_013913)	promoter-TSS (NM_013913)	-133	NM_013913	30924	Mm.28341	NM_013913	ENSMUSG00000028553	Angptl3	hypl	angiopoietin-like 3	protein-coding
mm_23463.1	chr3	60472823	60472837	+	1	NA	promoter-TSS (NM_001253713)	promoter-TSS (NM_001253713)	0	NM_001253713	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_50650.1	chr6	51470184	51470217	+	1	NA	promoter-TSS (NM_007624)	promoter-TSS (NM_007624)	-306	NM_016806	53379	Mm.155896	NM_016806	ENSMUSG00000004980	Hnrnpa2b1	9130414A06Rik|Hnrpa2|Hnrpa2b1|hnrnp-A	heterogeneous nuclear ribonucleoprotein A2/B1	protein-coding
mm_120097.1	chr14	58036665	58036669	+	1	NA	Intergenic	Intergenic	-36019	NM_013518	14180	Mm.8846	NM_013518	ENSMUSG00000021974	Fgf9	Eks	fibroblast growth factor 9	protein-coding
mm_61713.1	chr7	81523532	81523554	+	1	NA	promoter-TSS (NR_045299)	promoter-TSS (NR_045299)	-7	NR_045299	100504421	Mm.217071	NR_045299	ENSMUSG00000097277	2900076A07Rik	WI1-1616M8.2	RIKEN cDNA 2900076A07 gene	ncRNA
mm_140824.1	chr17	23620432	23620446	-	1	NA	Intergenic	Intergenic	19613	NM_001289482	332221	Mm.270315	NM_001033425	ENSMUSG00000023902	Zscan10	BC068284|Zfp206|Zkscan10|Znf206	zinc finger and SCAN domain containing 10	protein-coding
mm_42347.1	chr5	114911255	114911273	+	1	NA	exon (NM_011854, exon 6 of 6)	exon (NM_011854, exon 6 of 6)	-11976	NM_145209	231655	Mm.95479	NM_145209	ENSMUSG00000041827	Oasl1	7530414C13Rik|oasl9	2'-5' oligoadenylate synthetase-like 1	protein-coding
mm_167195.1	chr7	142653845	142653853	-	1	NA	exon (NM_010514, exon 4 of 4)	exon (NM_010514, exon 4 of 4)	1147	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_64787.1	chr7	6155940	6155970	-	1	NA	promoter-TSS (NM_001013012)	promoter-TSS (NM_001013012)	16	NM_001013012	67109	Mm.3254	NM_001013012	ENSMUSG00000046792	Zfp787	2210018M03Rik|Znf787	zinc finger protein 787	protein-coding
mm_70772.1	chr8	22060713	22060732	+	1	NA	promoter-TSS (NM_001243161)	promoter-TSS (NM_001243161)	1	NM_183142	207958	Mm.267439	NM_183142	ENSMUSG00000063362	Alg11	AI849156|AW492253|B230397C21|Mmat-4(5)	asparagine-linked glycosylation 11 (alpha-1,2-mannosyltransferase)	protein-coding
mm_108505.1	chr12	83950814	83950844	+	1	NA	exon (NM_023633, exon 1 of 1)	exon (NM_023633, exon 1 of 1)	221	NM_023633	71952	Mm.251483	NM_023633	ENSMUSG00000046791	2410016O06Rik	MAPJD|NO66	RIKEN cDNA 2410016O06 gene	protein-coding
mm_121417.1	chr14	119722368	119722371	+	1	NA	intron (NM_015820, intron 1 of 1)	Lx5c|LINE|L1	-26858	NR_045621	75432	Mm.443277	NR_045621	ENSMUSG00000100274	1700006F04Rik	-	RIKEN cDNA 1700006F04 gene	ncRNA
mm_154794.1	chrX	13202543	13202546	+	1	NA	Intergenic	Intergenic	33739	NR_045430	72122	Mm.75434	NR_045429	ENSMUSG00000100714	2010308F09Rik	-	RIKEN cDNA 2010308F09 gene	ncRNA
mm_116452.1	chr13	43226908	43226908	-	1	NA	intron (NM_001033399, intron 1 of 1)	L1MB7|LINE|L1	-55407	NM_001252640	67046	Mm.269213	NM_025935	ENSMUSG00000021368	Tbc1d7	2610009C09Rik	TBC1 domain family, member 7	protein-coding
mm_97768.1	chr11	82045538	82045558	+	1	NA	promoter-TSS (NM_013654)	promoter-TSS (NM_013654)	-164	NM_013654	20306	Mm.341574	NM_013654	ENSMUSG00000035373	Ccl7	MCP-3|Scya7|fic|marc|mcp3	chemokine (C-C motif) ligand 7	protein-coding
mm_13350.1	chr2	102998594	102998604	+	1	NA	Intergenic	Intergenic	74914	NM_175094	27402	Mm.315011	NM_175094	ENSMUSG00000010914	Pdhx	AI481367|E3bp|Pdx1	pyruvate dehydrogenase complex, component X	protein-coding
mm_148734.1	chr19	5878623	5878644	+	1	NA	5' UTR (NM_134154, exon 1 of 6)	5' UTR (NM_134154, exon 1 of 6)	167	NM_134154	107375	Mm.5323	NM_134154	ENSMUSG00000024818	Slc25a45	AW491445	solute carrier family 25, member 45	protein-coding
mm_73873.1	chr8	119086562	119086562	+	1	NA	intron (NM_019707, intron 6 of 13)	B4A|SINE|B4	-257976	NM_024219	68196	Mm.358714	NM_024219	ENSMUSG00000031839	Hsbp1	0610007A03Rik|AA408769|Hsp25	heat shock factor binding protein 1	protein-coding
mm_28419.1	chr3	90433524	90433534	-	1	NA	5' UTR (NM_178876, exon 1 of 31)	5' UTR (NM_178876, exon 1 of 31)	107	NM_145540	229543	Mm.268564	NM_145540	ENSMUSG00000027933	Ints3	C77668	integrator complex subunit 3	protein-coding
mm_117182.1	chr13	63431699	63431733	-	1	NA	promoter-TSS (NM_007985)	promoter-TSS (NM_007985)	29	NM_001347515	14088	Mm.126106	NM_007985	ENSMUSG00000021461	Fancc	Facc	Fanconi anemia, complementation group C	protein-coding
mm_46380.1	chr5	103970843	103970848	-	1	NA	exon (NM_001163486, exon 3 of 7)	exon (NM_001163486, exon 3 of 7)	6543	NM_198030	243168	Mm.284944	NM_198030	ENSMUSG00000034528	Hsd17b13	AI047820|PAN1B-like|Pan1b	hydroxysteroid (17-beta) dehydrogenase 13	protein-coding
mm_125239.1	chr15	34238736	34238746	+	1	NA	intron (NM_033521, intron 1 of 6)	CpG	715	NM_033521	114128	Mm.197518	NM_033521	ENSMUSG00000022257	Laptm4b	C330023P13Rik|LAPTM4beta	lysosomal-associated protein transmembrane 4B	protein-coding
mm_146338.1	chr18	82475158	82475170	+	1	NA	promoter-TSS (NM_010777)	promoter-TSS (NM_010777)	41	NM_001025245	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_154098.1	chr19	57008188	57008223	-	1	NA	5' UTR (NM_001177797, exon 1 of 19)	5' UTR (NM_001177797, exon 1 of 19)	370	NM_146102	226250	Mm.226284	NM_146102	ENSMUSG00000025083	Afap1l2	AU041783|C86904|mKIAA1914	actin filament associated protein 1-like 2	protein-coding
mm_116618.1	chr13	48872467	48872491	-	1	NA	Intergenic	MIRb|SINE|MIR	-1594	NM_011078	18676	Mm.486213	NM_011078	ENSMUSG00000038025	Phf2	GRC5	PHD finger protein 2	protein-coding
mm_77351.1	chr8	119575144	119575205	-	1	NA	promoter-TSS (NM_026648)	promoter-TSS (NM_026648)	26	NM_175185	72552	Mm.36756	NM_175185	ENSMUSG00000034189	Hsdl1	2700067E09Rik	hydroxysteroid dehydrogenase like 1	protein-coding
mm_53466.1	chr6	134920652	134920675	+	1	NA	5' UTR (NM_009875, exon 1 of 3)	5' UTR (NM_009875, exon 1 of 3)	262	NM_009875	12576	Mm.2958	NM_009875	ENSMUSG00000003031	Cdkn1b	AA408329|AI843786|Kip1|p27|p27Kip1	cyclin-dependent kinase inhibitor 1B	protein-coding
mm_129611.1	chr15	79958392	79958406	-	1	NA	Intergenic	Intergenic	-25753	NM_144811	52609	Mm.323442	NM_144811	ENSMUSG00000053411	Cbx7	1600014J01Rik|AI851678|D15Ertd417e	chromobox 7	protein-coding
mm_51396.1	chr6	78371223	78371227	+	1	NA	exon (NM_011036, exon 2 of 6)	exon (NM_011036, exon 2 of 6)	340	NM_011036	18489	Mm.2553	NM_011036	ENSMUSG00000071356	Reg3b	HIP|PAP1|Pap|REG-III	regenerating islet-derived 3 beta	protein-coding
mm_134728.1	chr16	22898971	22898975	-	1	NA	exon (NM_001276450, exon 7 of 7)	exon (NM_001276450, exon 7 of 7)	-4587	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_131685.1	chr16	20678211	20678256	+	1	NA	intron (NM_001304432, intron 6 of 31)	intron (NM_001304432, intron 6 of 31)	5506	NM_001304432	208643	Mm.260256	NM_145941	ENSMUSG00000045983	Eif4g1	E030015G23Rik|eIF-4-gamma 1|eIF-4G 1|eIF-4G1|eIF4GI	eukaryotic translation initiation factor 4, gamma 1	protein-coding
mm_77807.1	chr9	3036316	3036343	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	2414	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_47828.1	chr5	134269218	134269221	-	1	NA	intron (NM_001080747, intron 11 of 33)	intron (NM_001080747, intron 11 of 33)	-39594	NR_104383	17969	Mm.425296	NM_010876	ENSMUSG00000015950	Ncf1	NCF-47K|NOXO2|Ncf-1|p47-phox|p47<phox>|p47phox	neutrophil cytosolic factor 1	protein-coding
mm_16127.1	chr2	170201978	170201999	+	1	NA	Intergenic	Intergenic	-59313	NM_001159683	228913	Mm.22858	NM_001033299	ENSMUSG00000052056	Zfp217	4933431C08Rik|AW987152|Gm562|ZABC1|Znf217	zinc finger protein 217	protein-coding
mm_18905.1	chr2	76719961	76719971	-	1	NA	exon (NM_011652, exon 298 of 313)	exon (NM_011652, exon 298 of 313)	44651	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_107148.1	chr12	23163422	23163433	+	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	-153184	NR_015504	69732	Mm.391403	NM_028362	ENSMUSG00000073164	2410018L13Rik	2810480C08Rik	RIKEN cDNA 2410018L13 gene	ncRNA
mm_124093.1	chr14	79199144	79199160	-	1	NA	intron (NM_027906, intron 44 of 44)	ORR1C2|LTR|ERVL-MaLR	48215	NM_001033215	105590	Mm.486536	NM_001033215	ENSMUSG00000071262	Zfp957	AU017455	zinc finger protein 957	protein-coding
mm_64330.1	chr7	142283209	142283213	+	1	NA	Intergenic	ERVB4_1C-LTR_Mm|LTR|ERVK	-8848	NM_001199309	100043627	Mm.388589	NM_001199309	ENSMUSG00000056885	Gm4559	-	predicted gene 4559	protein-coding
mm_46878.1	chr5	113844019	113844039	-	1	NA	3' UTR (NM_011779, exon 11 of 11)	3' UTR (NM_011779, exon 11 of 11)	-13528	NM_009151	20345	Mm.332590	NM_009151	ENSMUSG00000048163	Selplg	CD162|Psgl-1|Psgl1|Selp1|Selpl	selectin, platelet (p-selectin) ligand	protein-coding
mm_100230.1	chr11	117199679	117199692	+	1	NA	promoter-TSS (NM_001113486)	promoter-TSS (NM_001113486)	24	NM_001113486	53860	Mm.38450	NM_017380	ENSMUSG00000059248	Sept9	MSF1|Msf|PNUTL4|Sint1	septin 9	protein-coding
mm_151903.1	chr19	5799353	5799366	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	3313	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_56370.1	chr6	93913648	93913658	-	1	NA	promoter-TSS (NR_104594)	promoter-TSS (NR_104594)	37	NM_001286788	14924	Mm.217216	NM_010367	ENSMUSG00000045095	Magi1	AIP3|BAP1|Baiap1|Gukmi1|MAGI1c|Magi-1|TNRC19|WWP3|mKIAA4129	membrane associated guanylate kinase, WW and PDZ domain containing 1	protein-coding
mm_64506.1	chr7	143479710	143479757	+	1	NA	exon (NM_008767, exon 4 of 11)	exon (NM_008767, exon 4 of 11)	4617	NM_001042760	18400	Mm.271740	NM_008767	ENSMUSG00000000154	Slc22a18	AW260131|BWR1A|BWSCR1A|HET|ITM|Impt1|Orctl2|Slc22a1l|TSSC5|p45-BWR1A	solute carrier family 22 (organic cation transporter), member 18	protein-coding
mm_105540.1	chr11	106301802	106301816	-	1	NA	promoter-TSS (NM_008117)	promoter-TSS (NM_008117)	87	NM_008117	14599	Mm.343934	NM_008117	ENSMUSG00000020713	Gh	Gh1|Ghb1	growth hormone	protein-coding
mm_16831.1	chr2	11492653	11492663	-	1	NA	intron (NM_001177756, intron 2 of 16)	intron (NM_001177756, intron 2 of 16)	9432	NM_001177754	170768	Mm.19669	NM_133232	ENSMUSG00000026773	Pfkfb3	E330010H22Rik|iPFK-2|uPFK-2	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	protein-coding
mm_88130.1	chr10	69398725	69398740	+	1	NA	Intergenic	CpG	-45820	NM_007659	12534	Mm.281367	NM_007659	ENSMUSG00000019942	Cdk1	Cdc2|Cdc2a|p34<CDC2>	cyclin-dependent kinase 1	protein-coding
mm_120845.1	chr14	75199411	75199416	+	1	NA	exon (NM_001247984, exon 3 of 16)	exon (NM_001247984, exon 3 of 16)	-42874	NM_019775	56373	Mm.24242	NM_019775	ENSMUSG00000021999	Cpb2	1110032P04Rik|4930405E17Rik|AI255929|CPR|Cpu|TAFI	carboxypeptidase B2 (plasma)	protein-coding
mm_167986.1	chrX	170009266	170009276	+	1	NA	Intergenic	Intergenic	-30354	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_140266.1	chr17	84683091	84683104	+	1	NA	promoter-TSS (NM_031884)	promoter-TSS (NM_031884)	-24	NM_001347418	67470	Mm.26581	NM_026180	ENSMUSG00000024254	Abcg8	1300003C16Rik|AI114946|sterolin-2	ATP-binding cassette, sub-family G (WHITE), member 8	protein-coding
mm_90195.1	chr10	120208815	120208842	+	1	NA	promoter-TSS (NM_026617)	promoter-TSS (NM_026617)	2	NM_026617	68212	Mm.157426	NM_026617	ENSMUSG00000020225	Tmbim4	0610007H07Rik|AU022431	transmembrane BAX inhibitor motif containing 4	protein-coding
mm_170929.1	chr2	40523033	40523050	-	1	NA	Intergenic	RLTR9E|LTR|ERVK	-1296703	NM_024209	67857	Mm.389242	NM_024209	ENSMUSG00000026753	Ppp6c	2310003C10Rik	protein phosphatase 6, catalytic subunit	protein-coding
mm_138032.1	chr17	33919598	33919617	+	1	NA	TTS (NM_020625)	TTS (NM_020625)	129	NM_009318	21356	Mm.154457	NM_009318	ENSMUSG00000024308	Tapbp	D17Wsu91e|TPN	TAP binding protein	protein-coding
mm_150104.1	chr19	29499335	29499347	+	1	NA	Intergenic	Intergenic	22646	NR_015567	77779	Mm.458738	NR_015567	ENSMUSG00000097855	A930007I19Rik	-	RIKEN cDNA A930007I19 gene	ncRNA
mm_7613.1	chr1	126626303	126626306	-	1	NA	intron (NM_001081756, intron 2 of 16)	ID_B1|SINE|B4	-133377	NM_172484	210356	Mm.377234	NM_172484	ENSMUSG00000049690	Nckap5	8430408F21|D130011D22Rik|E030049G20Rik|Erih1|Erih2|Gm1548|Nap5	NCK-associated protein 5	protein-coding
mm_46989.1	chr5	115334030	115334064	-	1	NA	TTS (NM_025573)	TTS (NM_025573)	6870	NR_036616	108014	Mm.287826	NM_025573	ENSMUSG00000029538	Srsf9	25kDa|2610029M16Rik|SRp30c|Sfrs9	serine/arginine-rich splicing factor 9	protein-coding
mm_36300.1	chr4	68762069	68762087	-	1	NA	exon (NM_019967, exon 8 of 8)	exon (NM_019967, exon 8 of 8)	192319	NM_019967	56710	Mm.248788	NM_019967	ENSMUSG00000028351	Brinp1	BRINP|Dbc1|Dbccr1|Fam5a	bone morphogenic protein/retinoic acid inducible neural specific 1	protein-coding
mm_52108.1	chr6	97888259	97888269	+	1	NA	intron (NM_001113198, intron 1 of 9)	intron (NM_001113198, intron 1 of 9)	-41553	NM_001178049	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_32381.1	chr4	106464229	106464232	+	1	NA	promoter-TSS (NM_153565)	promoter-TSS (NM_153565)	95	NM_153565	100102	Mm.133268	NM_153565	ENSMUSG00000044254	Pcsk9	AI415265|AI747682|FH3|HCHOLA3|Narc1|PC9	proprotein convertase subtilisin/kexin type 9	protein-coding
mm_34461.1	chr4	148140512	148140552	+	1	NA	promoter-TSS (NM_027985)	promoter-TSS (NM_027985)	42	NM_027985	71890	Mm.9648	NM_027985	ENSMUSG00000029003	Mad2l2	2310033C13Rik|G1-453-4|MAD2B|REV7|repro22	MAD2 mitotic arrest deficient-like 2	protein-coding
mm_169470.1	chr14	67893910	67893921	-	1	NA	intron (NM_177780, intron 1 of 51)	ORR1D1|LTR|ERVL-MaLR	-34170	NR_105857	102465310		NR_105857	ENSMUSG00000098866	Mir6539	Gm27464|mir-6539|mmu-mir-6539	microRNA 6539	ncRNA
mm_46694.1	chr5	110094402	110094443	-	1	NA	Intergenic	Intergenic	-5547	NM_207279	403178	Mm.297057	NM_207279	ENSMUSG00000064247	Plcxd1	A330045H12Rik|Gm576	phosphatidylinositol-specific phospholipase C, X domain containing 1	protein-coding
mm_3274.1	chr1	136570602	136570610	+	1	NA	Intergenic	Intergenic	-54295	NM_177643	226442	Mm.62521	NM_177643	ENSMUSG00000041483	Zfp281	Znf281	zinc finger protein 281	protein-coding
mm_76566.1	chr8	88636153	88636163	-	1	NA	promoter-TSS (NM_027840)	promoter-TSS (NM_027840)	-30	NM_027840	71607	Mm.270607	NM_027840	ENSMUSG00000031662	Snx20	9130017C17Rik	sorting nexin 20	protein-coding
mm_70935.1	chr8	25849639	25849650	+	1	NA	promoter-TSS (NM_008432)	promoter-TSS (NM_008432)	21	NM_008432	16532	Mm.289679	NM_008432	ENSMUSG00000031576	Kcnu1	Kcnma3|Slo3|mSlo3	potassium channel, subfamily U, member 1	protein-coding
mm_61548.1	chr7	79364126	79364135	+	1	NA	Intergenic	Intergenic	22897	NM_020599	19771	Mm.41653	NM_020599	ENSMUSG00000039194	Rlbp1	3110056M11Rik|CRALBP	retinaldehyde binding protein 1	protein-coding
mm_137276.1	chr17	24720103	24720118	+	1	NA	promoter-TSS (NR_028515)	promoter-TSS (NR_028515)	47	NM_008503	16898	Mm.157452	NM_008503	ENSMUSG00000044533	Rps2	Llrep3|S4	ribosomal protein S2	protein-coding
mm_159047.1	chr1	184999792	184999792	-	1	NA	promoter-TSS (NM_145515)	promoter-TSS (NM_145515)	-243	NM_145515	226778	Mm.7445	NM_145515	ENSMUSG00000026620	Mark1	AW491150|B930025N23Rik|Emk3|Par-1c|mKIAA1477|mPar-1c	MAP/microtubule affinity regulating kinase 1	protein-coding
mm_52954.1	chr6	123050000	123050021	+	1	NA	promoter-TSS (NM_027218)	promoter-TSS (NM_027218)	48	NM_001190310	69810	Mm.333374	NM_027218	ENSMUSG00000030147	Clec4b1	1810046I24Rik|Aplra2|Clec4b|DCAR|DCARbeta|Dcar2	C-type lectin domain family 4, member b1	protein-coding
mm_62360.1	chr7	100523986	100523997	+	1	NA	Intergenic	ORR1D1|LTR|ERVL-MaLR	-9176	NM_153527	69387	Mm.278554	NM_153527	ENSMUSG00000030708	Dnajb13	1700014P03Rik|Tsarg	DnaJ heat shock protein family (Hsp40) member B13	protein-coding
mm_106175.1	chr11	116680597	116680601	-	1	NA	intron (NM_009180, intron 6 of 8)	intron (NM_009180, intron 6 of 8)	6002	NR_028570	100216538		NR_028570	ENSMUSG00000065094	Snord1a	snR38	small nucleolar RNA, C/D box 1A	snoRNA
mm_86880.1	chr10	21997170	21997181	+	1	NA	intron (NM_001161848, intron 8 of 11)	intron (NM_001161848, intron 8 of 11)	2509	NM_011361	20393	Mm.28405	NM_011361	ENSMUSG00000019970	Sgk1	Sgk	serum/glucocorticoid regulated kinase 1	protein-coding
mm_80950.1	chr9	102900204	102900210	+	1	NA	intron (NM_001284258, intron 12 of 13)	RLTR11A2|LTR|ERVK	65287	NM_001042607	20187	Mm.335391	NM_013649	ENSMUSG00000032547	Ryk	AW536699|ERK-3|Vik	receptor-like tyrosine kinase	protein-coding
mm_100248.1	chr11	117308163	117308184	+	1	NA	intron (NM_001113487, intron 2 of 10)	intron (NM_001113487, intron 2 of 10)	-23542	NM_017380	53860	Mm.38450	NM_017380	ENSMUSG00000059248	Sept9	MSF1|Msf|PNUTL4|Sint1	septin 9	protein-coding
mm_67122.1	chr7	70361724	70361748	-	1	NA	intron (NM_183261, intron 1 of 2)	intron (NM_183261, intron 1 of 2)	-1143	NM_009697	11819	Mm.158143	NM_009697	ENSMUSG00000030551	Nr2f2	2700033K02Rik|9430015G03Rik|ARP-1|Aporp1|COUP-TF2|COUP-TFII|COUPTFB|EAR3|SVP40|Tcfcoup2	nuclear receptor subfamily 2, group F, member 2	protein-coding
mm_167394.1	chr8	95294075	95294101	-	1	NA	intron (NM_001195413, intron 11 of 32)	intron (NM_001195413, intron 11 of 32)	12497	NM_145601	333329	Mm.484049	NM_145601	ENSMUSG00000031789	Cngb1	Cngb1b|Garp2|Gm1959	cyclic nucleotide gated channel beta 1	protein-coding
mm_57427.1	chr6	124914092	124914107	-	1	NA	3' UTR (NM_026988, exon 5 of 5)	3' UTR (NM_026988, exon 5 of 5)	-2394	NM_008479	16768	Mm.4528	NM_008479	ENSMUSG00000030124	Lag3	CD223|LAG-3|Ly66	lymphocyte-activation gene 3	protein-coding
mm_12899.1	chr2	84809213	84809235	+	1	NA	3' UTR (NM_019949, exon 4 of 4)	3' UTR (NM_019949, exon 4 of 4)	10396	NM_019949	56791	Mm.38261	NM_019949	ENSMUSG00000027078	Ube2l6	2810489I21Rik|RIG-B|UBCH8|Ubce8|Ubcm8	ubiquitin-conjugating enzyme E2L 6	protein-coding
mm_67742.1	chr7	90353894	90353931	-	1	NA	intron (NR_110348, intron 2 of 8)	intron (NR_110348, intron 2 of 8)	-33069	NM_001040087	83671	Mm.26751	NM_031394	ENSMUSG00000030616	Sytl2	AI266830|Slp2|mKIAA1597	synaptotagmin-like 2	protein-coding
mm_168305.1	chr11	106787050	106787050	-	1	NA	exon (NM_007840, exon 2 of 13)	exon (NM_007840, exon 2 of 13)	1444	NM_007840	13207	Mm.491096	NM_007840	ENSMUSG00000020719	Ddx5	2600009A06Rik|G17P1|HUMP68|Hlr1|p68	DEAD (Asp-Glu-Ala-Asp) box polypeptide 5	protein-coding
mm_77523.1	chr8	122946522	122946524	-	1	NA	intron (NM_001081379, intron 2 of 12)	intron (NM_001081379, intron 2 of 12)	95761	NR_037865	77087	Mm.31567	NM_001081379	ENSMUSG00000035569	Ankrd11	2410104C19Rik|3010027A04Rik|6330578C09Rik|9530048I21Rik|AA930108|Gm176|Yod	ankyrin repeat domain 11	protein-coding
mm_36557.1	chr4	86984198	86984208	-	1	NA	3' UTR (NM_001110240, exon 10 of 10)	3' UTR (NM_001110240, exon 10 of 10)	109789	NM_139306	230379	Mm.45019	NM_139306	ENSMUSG00000038007	Acer2	2410116I05Rik|Asah3l|CRG-L1|maCER2	alkaline ceramidase 2	protein-coding
mm_126290.1	chr15	79347535	79347556	+	1	NA	promoter-TSS (NM_010755)	promoter-TSS (NM_010755)	25	NM_010755	17133	Mm.86646	NM_010755	ENSMUSG00000042622	Maff	-	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein F (avian)	protein-coding
mm_109083.1	chr12	104413675	104413702	+	1	NA	3' UTR (NM_009252, exon 5 of 5)	3' UTR (NM_009252, exon 5 of 5)	6980	NM_009252	20716	Mm.482074	NM_009252	ENSMUSG00000021091	Serpina3n	Spi2-2|Spi2.2|Spi2/eb.4	serine (or cysteine) peptidase inhibitor, clade A, member 3N	protein-coding
mm_100976.1	chr11	7152395	7152404	-	1	NA	intron (NM_009622, intron 14 of 19)	intron (NM_009622, intron 14 of 19)	36170	NR_045101	100041347	Mm.300962	NR_045101	ENSMUSG00000087512	Gm11985	OTTMUSG00000005133	predicted gene 11985	ncRNA
mm_40961.1	chr5	76951800	76951811	+	1	NA	promoter-TSS (NM_172146)	promoter-TSS (NM_172146)	-227	NM_172146	231327	Mm.202337	NM_172146	ENSMUSG00000029246	Ppat	5730454C12Rik|AA408689|AA675351|AI507113|C79945	phosphoribosyl pyrophosphate amidotransferase	protein-coding
mm_7050.1	chr1	87127578	87127596	-	1	NA	exon (NM_007432, exon 11 of 11)	exon (NM_007432, exon 11 of 11)	2579	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_7252.1	chr1	93731962	93731972	-	1	NA	promoter-TSS (NM_001310761)	promoter-TSS (NM_001310761)	-41	NM_001310761	67026	Mm.272356	NM_025920	ENSMUSG00000026279	Thap4	2010320B01Rik	THAP domain containing 4	protein-coding
mm_54138.1	chr6	21856339	21856339	-	1	NA	Intergenic	Intergenic	-3824	NM_173007	269831	Mm.21950	NM_173007	ENSMUSG00000029669	Tspan12	9030619E17|AI426782|AI663988|AW111457|Tm4sf12	tetraspanin 12	protein-coding
mm_152489.1	chr19	11052015	11052016	-	1	NA	Intergenic	Charlie1a|DNA|hAT-Charlie	-1449	NR_102366	107350	Mm.6381	NM_001177351	ENSMUSG00000075010	AW112010	-	expressed sequence AW112010	ncRNA
mm_90078.1	chr10	116474022	116474032	+	1	NA	promoter-TSS (NM_021452)	promoter-TSS (NM_021452)	-504	NM_021452	58802	Mm.440652	NM_021452	ENSMUSG00000054934	Kcnmb4	1700058G18Rik|2900045G12Rik	potassium large conductance calcium-activated channel, subfamily M, beta member 4	protein-coding
mm_46439.1	chr5	105030700	105030711	-	1	NA	intron (NM_029509, intron 5 of 9)	intron (NM_029509, intron 5 of 9)	22856	NM_029509	76074	Mm.458519	NM_029509	ENSMUSG00000034438	Gbp8	5830443L24Rik|mGBP8	guanylate-binding protein 8	protein-coding
mm_67120.1	chr7	70361635	70361684	-	1	NA	intron (NM_183261, intron 1 of 2)	intron (NM_183261, intron 1 of 2)	-1066	NM_009697	11819	Mm.158143	NM_009697	ENSMUSG00000030551	Nr2f2	2700033K02Rik|9430015G03Rik|ARP-1|Aporp1|COUP-TF2|COUP-TFII|COUPTFB|EAR3|SVP40|Tcfcoup2	nuclear receptor subfamily 2, group F, member 2	protein-coding
mm_152401.1	chr19	10577054	10577095	-	1	NA	promoter-TSS (NM_201351)	promoter-TSS (NM_201351)	12	NM_001302218	72982	Mm.391194	NM_028411	ENSMUSG00000024666	Tmem138	1700113I01Rik|2900055D14Rik	transmembrane protein 138	protein-coding
mm_105473.1	chr11	105936328	105936342	-	1	NA	intron (NM_007805, intron 3 of 5)	intron (NM_007805, intron 3 of 5)	7812	NM_007805	13056	Mm.149403	NM_007805	ENSMUSG00000019590	Cyb561	-	cytochrome b-561	protein-coding
mm_93649.1	chr10	117376907	117376917	-	1	NA	promoter-TSS (NM_001013391)	promoter-TSS (NM_001013391)	61	NM_001013391	432508	Mm.478881	NM_001013391	ENSMUSG00000055531	Cpsf6	4733401N12Rik|AI256641|CFIM|CFIM68|HPBRII-4|HPBRII-7	cleavage and polyadenylation specific factor 6	protein-coding
mm_22506.1	chr3	7501523	7501535	+	1	NA	Intergenic	RMER1B|Other|Other	-1897	NM_173181	67306	Mm.332366	NM_173181	ENSMUSG00000043542	Zc2hc1a	3110050N22Rik|AI790358|AU023959|Fam164a	zinc finger, C2HC-type containing 1A	protein-coding
mm_119472.1	chr14	47298619	47298647	+	1	NA	intron (NM_178684, intron 1 of 3)	CpG	319	NM_178684	218975	Mm.212297	NM_178684	ENSMUSG00000021840	Mapk1ip1l	9130202B12|C130032J12Rik	mitogen-activated protein kinase 1 interacting protein 1-like	protein-coding
mm_75523.1	chr8	56550792	56550881	-	1	NA	promoter-TSS (NM_015791)	promoter-TSS (NM_015791)	-270	NM_001009951	382010	Mm.425534	NM_001009951	ENSMUSG00000038215	Cep44	4933440G23Rik|mKIAA1712	centrosomal protein 44	protein-coding
mm_97701.1	chr11	80177445	80177448	+	1	NA	intron (NM_172133, intron 10 of 10)	intron (NM_172133, intron 10 of 10)	-6426	NM_028019	71956	Mm.22985	NM_028019	ENSMUSG00000020707	Rnf135	0610037N03Rik|2410006N06Rik	ring finger protein 135	protein-coding
mm_8162.1	chr1	136949580	136949584	-	1	NA	intron (NM_030676, intron 2 of 8)	intron (NM_030676, intron 2 of 8)	4048	NM_001159769	26424	Mm.16794	NM_030676	ENSMUSG00000026398	Nr5a2	AU020803|D1Ertd308e|Ftf|LRH-1|UF2-H3B	nuclear receptor subfamily 5, group A, member 2	protein-coding
mm_140548.1	chr17	6948722	6948745	-	1	NA	promoter-TSS (NM_001083945)	promoter-TSS (NM_001083945)	-377	NM_001083945	100037282	Mm.29830	NM_001083945	ENSMUSG00000023806	Rsph3b	Rshl2b	radial spoke 3B homolog (Chlamydomonas)	protein-coding
mm_121753.1	chr14	19626872	19626880	-	1	NA	Intergenic	Intergenic	-24289	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_85838.1	chr9	110532781	110532801	-	1	NA	intron (NM_001081340, intron 1 of 20)	CpG	194	NM_001081340	235626	Mm.288949	NM_001081340	ENSMUSG00000044791	Setd2	4921524K10Rik|BC031601|KMT3A	SET domain containing 2	protein-coding
mm_70196.1	chr7	144520672	144520688	-	1	NA	exon (NM_001195086, exon 4 of 32)	exon (NM_001195086, exon 4 of 32)	33049	NM_001033319	233977	Mm.490347	NM_001033319	ENSMUSG00000037519	Ppfia1	C030014K08Rik|C87158|LIP.1|LIP1	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1	protein-coding
mm_26185.1	chr3	138342793	138342811	+	1	NA	Intergenic	Intergenic	29516	NM_026945	69117	Mm.46265	NM_026945	ENSMUSG00000053054	Adh6a	1810009C16Rik|Adh5a	alcohol dehydrogenase 6A (class V)	protein-coding
mm_81681.1	chr9	111058232	111058240	+	1	NA	promoter-TSS (NM_017466)	promoter-TSS (NM_017466)	-718	NM_001302376	54199	Mm.7336	NM_017466	ENSMUSG00000043953	Ccrl2	1810047I05Rik|Ackr5|CCR11|Cmkbr1l2|E01|L-CCR	chemokine (C-C motif) receptor-like 2	protein-coding
mm_95785.1	chr11	54955818	54955839	+	1	NA	intron (NM_001271455, intron 1 of 17)	CpG	7112	NM_021327	57783	Mm.259671	NM_021327	ENSMUSG00000020400	Tnip1	ABIN|ABIN-1|ABIN1|AU018810|Naf1|Nef|VAN	TNFAIP3 interacting protein 1	protein-coding
mm_54586.1	chr6	38128228	38128248	-	1	NA	3' UTR (NM_194061, exon 20 of 20)	3' UTR (NM_194061, exon 20 of 20)	-3652	NM_080467	140494	Mm.462308	NM_080467	ENSMUSG00000038600	Atp6v0a4	Atp6n1b|a4	ATPase, H+ transporting, lysosomal V0 subunit A4	protein-coding
mm_60642.1	chr7	44849217	44849295	+	1	NA	promoter-TSS (NM_001290695)	promoter-TSS (NM_001290695)	32	NM_026270	67605	Mm.148007	NM_026270	ENSMUSG00000011096	Akt1s1	1110012J22Rik|AI227026|Lobe|Lobel|PRAS40	AKT1 substrate 1 (proline-rich)	protein-coding
mm_73926.1	chr8	119830773	119830784	+	1	NA	intron (NM_028071, intron 2 of 3)	intron (NM_028071, intron 2 of 3)	9801	NM_028071	72042	Mm.393405	NM_028071	ENSMUSG00000031827	Cotl1	1810074P22Rik|2010004C08Rik|Clp	coactosin-like 1 (Dictyostelium)	protein-coding
mm_47231.1	chr5	121385388	121385455	-	1	NA	intron (NM_172275, intron 1 of 11)	CpG	194	NM_001163470	231712	Mm.20488	NM_172275	ENSMUSG00000042726	Trafd1	1110008K06Rik|Fln29	TRAF type zinc finger domain containing 1	protein-coding
mm_35014.1	chr4	3574845	3574850	-	1	NA	promoter-TSS (NM_028097)	promoter-TSS (NM_028097)	-32	NM_054089	116940	Mm.171323	NM_054089	ENSMUSG00000028233	Tgs1	D4Ertd800e|Ncoa6ip|Pimt	trimethylguanosine synthase 1	protein-coding
mm_27446.1	chr3	51930030	51930032	-	1	NA	intron (NM_001004176, intron 1 of 4)	intron (NM_001004176, intron 1 of 4)	174975	NM_001004176	433586	Mm.234972	NM_001004176	ENSMUSG00000061143	Maml3	AV234550|BC049812|Mam-2|mKIAA1816	mastermind like 3 (Drosophila)	protein-coding
mm_40888.1	chr5	75075591	75075597	+	1	NA	promoter-TSS (NM_133256)	promoter-TSS (NM_133256)	-7	NM_133256	14843	Mm.218752	NM_133256	ENSMUSG00000035946	Gsx2	Gsh-2|Gsh2	GS homeobox 2	protein-coding
mm_74201.1	chr8	123892044	123892051	+	1	NA	exon (NM_009606, exon 7 of 7)	exon (NM_009606, exon 7 of 7)	2728	NM_001272041	11459	Mm.214950	NM_009606	ENSMUSG00000031972	Acta1	AA959943|Acta-2|Acts|Actsk-1	actin, alpha 1, skeletal muscle	protein-coding
mm_147197.1	chr18	37830091	37830102	-	1	NA	intron (NM_001301259, intron 2 of 3)	intron (NM_001301259, intron 2 of 3)	10550	NM_033583	93708	Mm.247203	NM_033583	ENSMUSG00000102543	Pcdhgc5	-	protocadherin gamma subfamily C, 5	protein-coding
mm_170231.1	chr17	83064454	83064467	-	1	NA	intron (NR_045094, intron 2 of 3)	ERVB7_1-LTR_MM|LTR|ERVK	13765	NR_045094	100503434	Mm.187281	NR_045094		Gm19689	-	predicted gene, 19689	ncRNA
mm_169530.1	chr14	91832415	91832415	-	1	NA	Intergenic	Lx7|LINE|L1	1705524	NR_045712	74967	Mm.390704	NR_045712		4930474H20Rik	-	RIKEN cDNA 4930474H20 gene	ncRNA
mm_132982.1	chr16	52146585	52146589	+	1	NA	intron (NM_001033238, intron 9 of 17)	intron (NM_001033238, intron 9 of 17)	115038	NM_001033238	208650	Mm.328206	NM_001033238	ENSMUSG00000022637	Cblb	AI429560|AI851073|Cbl-b	Casitas B-lineage lymphoma b	protein-coding
mm_110632.1	chr12	57544110	57544126	-	1	NA	intron (NM_008259, intron 1 of 1)	AT_rich|Low_complexity|Low_complexity	2003	NM_008259	15375	Mm.4578	NM_008259	ENSMUSG00000035451	Foxa1	Hnf-3a|Hnf3a|Tcf-3a|Tcf3a	forkhead box A1	protein-coding
mm_103813.1	chr11	83002643	83002686	-	1	NA	3' UTR (NM_001167743, exon 4 of 4)	3' UTR (NM_001167743, exon 4 of 4)	-10834	NM_172796	237886	Mm.270253	NM_172796	ENSMUSG00000069793	Slfn9	9830137M10Rik	schlafen 9	protein-coding
mm_13928.1	chr2	120977082	120977107	+	1	NA	promoter-TSS (NM_175285)	promoter-TSS (NM_175285)	32	NM_175285	96957	Mm.315212	NM_175285	ENSMUSG00000054484	Tmem62	B830009D23Rik|C77355	transmembrane protein 62	protein-coding
mm_147748.1	chr18	61196199	61196231	-	1	NA	TTS (NM_007885)	TTS (NM_007885)	15381	NM_007885	13521	Mm.24803	NM_007885	ENSMUSG00000034320	Slc26a2	Dtd|ST-OB	solute carrier family 26 (sulfate transporter), member 2	protein-coding
mm_106560.1	chr11	120630517	120630537	-	1	NA	intron (NM_010756, intron 1 of 2)	intron (NM_010756, intron 1 of 2)	3020	NM_010756	17134	Mm.268010	NM_010756	ENSMUSG00000051510	Mafg	AA545192|C630022N07Rik	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein G (avian)	protein-coding
mm_95540.1	chr11	52280002	52280033	+	1	NA	intron (NM_001313981, intron 3 of 10)	intron (NM_001313981, intron 3 of 10)	2578	NM_009331	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_62481.1	chr7	101879593	101879605	+	1	NA	Intergenic	MT2B|LTR|ERVL	-1726	NM_001291353	75430	Mm.284491	NM_027532	ENSMUSG00000030649	Anapc15	3200002M19Rik|6330414C15Rik|APC15	anaphase prompoting complex C subunit 15	protein-coding
mm_94894.1	chr11	28921465	28921496	+	1	NA	exon (NM_146015, exon 9 of 11)	exon (NM_146015, exon 9 of 11)	68275	NM_146015	216616	Mm.44176	NM_146015	ENSMUSG00000020467	Efemp1	-	epidermal growth factor-containing fibulin-like extracellular matrix protein 1	protein-coding
mm_83076.1	chr9	37669171	37669226	-	1	NA	promoter-TSS (NM_172454)	promoter-TSS (NM_172454)	24	NM_172454	208098	Mm.217159	NM_172454	ENSMUSG00000011118	Panx3	3230401P04|4833413G11Rik	pannexin 3	protein-coding
mm_82660.1	chr9	22085392	22085443	-	1	NA	promoter-TSS (NM_012029)	promoter-TSS (NM_012029)	10	NM_001253897	26940	Mm.425568	NM_012029	ENSMUSG00000066839	Ecsit	Sitpec	ECSIT signalling integrator	protein-coding
mm_141469.1	chr17	30604172	30604182	-	1	NA	intron (NM_025374, intron 1 of 5)	intron (NM_025374, intron 1 of 5)	8482	NM_025374	109801	Mm.261984	NM_025374	ENSMUSG00000024026	Glo1	0610009E22Rik|1110008E19Rik|2510049H23Rik|AW550643|GLY1|Glo-1|Glo-1r|Glo-1s|Glo1-r|Glo1-s|Qglo	glyoxalase 1	protein-coding
mm_30123.1	chr3	141814706	141814707	-	1	NA	intron (NM_001293561, intron 13 of 16)	intron (NM_001293561, intron 13 of 16)	116882	NM_001277218	12167	Mm.39089	NM_007560	ENSMUSG00000052430	Bmpr1b	AI385617|ALK-6|AV355320|Acvrlk6|Alk6|BMPR-1B|BMPR-IB|CFK-43a|SKR6	bone morphogenetic protein receptor, type 1B	protein-coding
mm_117376.1	chr13	72628486	72628505	-	1	NA	promoter-TSS (NR_030701)	promoter-TSS (NR_030701)	69	NR_030701	328287	Mm.235072	NR_030701		Gm20554	D430050G20	predicted gene, 20554	ncRNA
mm_129900.1	chr15	83919365	83919387	-	1	NA	promoter-TSS (NM_001161629)	promoter-TSS (NM_001161629)	-3	NM_001161629	77627	Mm.196288	NM_029946	ENSMUSG00000022441	Efcab6	4931407K02Rik|4932408N08Rik|bM150J22.2|mKIAA1672	EF-hand calcium binding domain 6	protein-coding
mm_155553.1	chrX	74448513	74448517	+	1	NA	3' UTR (NM_178590, exon 10 of 10)	3' UTR (NM_178590, exon 10 of 10)	18834	NM_010547	16151	Mm.12967	NM_010547	ENSMUSG00000004221	Ikbkg	1110037D23Rik|AI848108|AI851264|AW124339|IKK[g]|NEMO	inhibitor of kappaB kinase gamma	protein-coding
mm_35600.1	chr4	43038654	43038656	-	1	NA	intron (NR_045567, intron 1 of 7)	intron (NR_045567, intron 1 of 7)	1646	NM_001253353	230088	Mm.260162	NM_172691	ENSMUSG00000036002	Fam214b	B230312A22Rik	family with sequence similarity 214, member B	protein-coding
mm_24851.1	chr3	95736171	95736182	+	1	NA	exon (NM_007899, exon 8 of 11)	exon (NM_007899, exon 8 of 11)	-1203	NR_105981	102466787		NR_105981	ENSMUSG00000098737	Mir7014	Gm27837|mmu-mir-7014	microRNA 7014	ncRNA
mm_132657.1	chr16	41640002	41640013	+	1	NA	intron (NM_001347236, intron 1 of 6)	B1_Mus1|SINE|Alu	106665	NM_175548	268890	Mm.310524	NM_175548	ENSMUSG00000061080	Lsamp	5430428I19|AW046674|B130007O04Rik|D930023J12Rik|Lam|Lamp	limbic system-associated membrane protein	protein-coding
mm_117511.1	chr13	78954847	78954866	-	1	NA	Intergenic	Intergenic	-755983	NM_010151	13865	Mm.439653	NM_010151	ENSMUSG00000069171	Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR-3|EAR3|Erbal3|SVP44|Tcfcoup1	nuclear receptor subfamily 2, group F, member 1	protein-coding
mm_152473.1	chr19	10993177	10993186	-	1	NA	promoter-TSS (NM_001034898)	promoter-TSS (NM_001034898)	69	NM_001034898	545279	Mm.329729	NM_001034898	ENSMUSG00000067571	Ms4a15	E530011F12Rik|Gm1286	membrane-spanning 4-domains, subfamily A, member 15	protein-coding
mm_115427.1	chr13	117234622	117234625	+	1	NA	intron (NM_010330, intron 2 of 8)	intron (NM_010330, intron 2 of 8)	14050	NM_010330	13723	Mm.274926	NM_010330	ENSMUSG00000021728	Emb	AL022799|Gp70	embigin	protein-coding
mm_77580.1	chr8	123655566	123655578	-	1	NA	intron (NM_133955, intron 2 of 2)	intron (NM_133955, intron 2 of 2)	1643	NM_133955	69581	Mm.168257	NM_133955	ENSMUSG00000039960	Rhou	2310026M05Rik|AI182090|Arhu|CDC42L1|G28K|WRCH-1|WRCH1|mG28K	ras homolog family member U	protein-coding
mm_23764.1	chr3	73121865	73121868	+	1	NA	intron (NR_040557, intron 1 of 4)	U4|snRNA|snRNA	55515	NR_040557	626082	Mm.428099	NR_040557	ENSMUSG00000103428	Gm20754	-	predicted gene, 20754	ncRNA
mm_9631.1	chr1	176814042	176814064	-	1	NA	promoter-TSS (NM_029756)	promoter-TSS (NM_029756)	-607	NM_029756	76816	Mm.171399	NM_029756	ENSMUSG00000026504	Sdccag8	2700048G21Rik|5730470G24Rik|Cccap	serologically defined colon cancer antigen 8	protein-coding
mm_139696.1	chr17	57445061	57445076	+	1	NA	exon (NM_010130, exon 15 of 22)	exon (NM_010130, exon 15 of 22)	86382	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_131680.1	chr16	20675358	20675376	+	1	NA	exon (NM_145941, exon 5 of 33)	exon (NM_145941, exon 5 of 33)	2640	NM_001304432	208643	Mm.260256	NM_145941	ENSMUSG00000045983	Eif4g1	E030015G23Rik|eIF-4-gamma 1|eIF-4G 1|eIF-4G1|eIF4GI	eukaryotic translation initiation factor 4, gamma 1	protein-coding
mm_67770.1	chr7	95596121	95596145	-	1	NA	Intergenic	Intergenic	-575111	NM_001310762	23966	Mm.254610	NM_011858	ENSMUSG00000048078	Tenm4	Doc4|ELM2|Odz4|R75022|Ten-m4|l(7)-3Rn|l7Rn3|mKIAA1302	teneurin transmembrane protein 4	protein-coding
mm_120037.1	chr14	56364859	56364865	+	1	NA	promoter-TSS (NM_138652)	promoter-TSS (NM_138652)	-206	NM_138652	192113	Mm.273271	NM_138652	ENSMUSG00000022229	Atp12a	Atp1al1|HKalpha2|cHKA	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	protein-coding
mm_75710.1	chr8	68904551	68904580	-	1	NA	3' UTR (NM_008509, exon 10 of 10)	3' UTR (NM_008509, exon 10 of 10)	24010	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_125867.1	chr15	75498719	75498725	+	1	NA	Intergenic	Intergenic	49270	NM_001347049	102637705		NM_001347049	ENSMUSG00000093626	Ly6l	Gm20654	lymphocyte antigen 6 complex, locus L	protein-coding
mm_10730.1	chr2	22895584	22895629	+	1	NA	promoter-TSS (NM_019501)	promoter-TSS (NM_019501)	84	NM_019501	56075	Mm.249752	NM_019501	ENSMUSG00000026784	Pdss1	2610203G20Rik|2700031G06Rik|TPT|TPT 1|Tprt|mDLP1|mSPS1	prenyl (solanesyl) diphosphate synthase, subunit 1	protein-coding
mm_85585.1	chr9	107306164	107306190	-	1	NA	Intergenic	Intergenic	9518	NM_009895	12700	Mm.4592	NM_009895	ENSMUSG00000032578	Cish	CIS-1|CIS1|Cis|F17|F23|SOCS	cytokine inducible SH2-containing protein	protein-coding
mm_155308.1	chrX	61186131	61186146	+	1	NA	promoter-TSS (NM_001166658)	promoter-TSS (NM_001166658)	-580	NM_001166658	631990	Mm.401324	NM_001166658	ENSMUSG00000090546	Cdr1	100039759|Cdr|Cdr34|EG631990|Gm2409|Gm7077	cerebellar degeneration related antigen 1	protein-coding
mm_76441.1	chr8	85019872	85019893	-	1	NA	exon (NM_019652, exon 3 of 7)	exon (NM_019652, exon 3 of 7)	-5351	NR_052011	212989	Mm.215154	NM_001130194	ENSMUSG00000052819	Best2	Vmd2l1	bestrophin 2	protein-coding
mm_123692.1	chr14	69654468	69654470	-	1	NA	intron (NM_033325, intron 3 of 13)	B4A|SINE|B4	-37779	NR_105915	102465573		NR_105915	ENSMUSG00000098666	Mir6950	Gm27586|mmu-mir-6950	microRNA 6950	ncRNA
mm_168114.1	chr10	15263248	15263251	-	1	NA	Intergenic	RLTR13D6|LTR|ERVK	502960	NM_008703	18101	Mm.487342	NM_008703	ENSMUSG00000019865	Nmbr	BB182387	neuromedin B receptor	protein-coding
mm_37317.1	chr4	119359883	119359897	-	1	NA	promoter-TSS (NM_001270446)	promoter-TSS (NM_001270446)	4	NM_001270446	73332	Mm.425204	NM_028506	ENSMUSG00000028637	Ccdc30	1700001O02Rik|1700041C02Rik|1700111D19Rik|4930445I03Rik	coiled-coil domain containing 30	protein-coding
mm_93804.1	chr10	120899052	120899062	-	1	NA	promoter-TSS (NM_177092)	promoter-TSS (NM_177092)	-86	NM_177092	320183	Mm.169755	NM_177092	ENSMUSG00000051236	Msrb3	D430026P16Rik|I-8-23|MsrB2	methionine sulfoxide reductase B3	protein-coding
mm_163671.1	chr13	80941114	80941124	+	1	NA	intron (NR_103550, intron 1 of 4)	AmnSINE1|SINE|Deu	716	NR_103550	71416	Mm.415500	NR_103550		5430425K12Rik	-	RIKEN cDNA 5430425K12 gene	ncRNA
mm_82026.1	chr9	121857762	121857768	+	1	NA	5' UTR (NM_019814, exon 1 of 4)	5' UTR (NM_019814, exon 1 of 4)	235	NM_019814	56295	Mm.347915	NM_019814	ENSMUSG00000038412	Higd1a	2210020B17Rik|7420700H20Rik|AI303276|AW049839|HIMP1|Hig1	HIG1 domain family, member 1A	protein-coding
mm_96434.1	chr11	67299328	67299365	+	1	NA	exon (NM_177369, exon 28 of 40)	exon (NM_177369, exon 28 of 40)	22222	NM_177369	17885	Mm.340163	NM_177369	ENSMUSG00000055775	Myh8	4832426G23Rik|AI327267|MHCp|MyHC-pn|Myhs-p|Myhsp	myosin, heavy polypeptide 8, skeletal muscle, perinatal	protein-coding
mm_74199.1	chr8	123853792	123853794	+	1	NA	intron (NM_028536, intron 2 of 3)	intron (NM_028536, intron 2 of 3)	6416	NM_028536	73420	Mm.157746	NM_028536	ENSMUSG00000031971	Ccsap	1700054N08Rik|AI853424	centriole, cilia and spindle associated protein	protein-coding
mm_5964.1	chr1	56974501	56974520	-	1	NA	non-coding (NR_024325, exon 1 of 1)	non-coding (NR_024325, exon 1 of 1)	3041	NR_024325	329160	Mm.419039	NR_024325	ENSMUSG00000087022	9130024F11Rik	B530002L08|EG329160	RIKEN cDNA 9130024F11 gene	ncRNA
mm_65557.1	chr7	27166383	27166393	-	1	NA	intron (NM_053208, intron 1 of 5)	CpG	414	NM_053208	112406	Mm.29978	NM_053208	ENSMUSG00000058709	Egln2	0610011A13Rik|C85656|Hif-p4h-1|Ier4|Phd1|SM-20	egl-9 family hypoxia-inducible factor 2	protein-coding
mm_130570.1	chr15	99457759	99457777	-	1	NA	promoter-TSS (NM_001001884)	promoter-TSS (NM_001001884)	-20	NM_001001884	380969	Mm.22915	NM_001001884	ENSMUSG00000023009	Nckap5l	C230021P08Rik|Cep169	NCK-associated protein 5-like	protein-coding
mm_67630.1	chr7	84152067	84152118	-	1	NA	promoter-TSS (NM_133722)	promoter-TSS (NM_133722)	-199	NM_133722	70178	Mm.23914	NM_133722	ENSMUSG00000038459	Abhd17c	2210412D01Rik|AL023007|Fam108c|Fam108c1	abhydrolase domain containing 17C	protein-coding
mm_35324.1	chr4	25800419	25800427	-	1	NA	promoter-TSS (NM_010243)	promoter-TSS (NM_010243)	-420	NM_010243	14348	Mm.39101	NM_010243	ENSMUSG00000055373	Fut9	AI746471|AU067636|mFUT9|mFuc-TIX	fucosyltransferase 9	protein-coding
mm_77090.1	chr8	110793586	110793597	-	1	NA	intron (NM_029646, intron 1 of 7)	intron (NM_029646, intron 1 of 7)	12333	NM_029646	76527	Mm.77697	NM_029646	ENSMUSG00000031750	Il34	2010004A03Rik|AI593503	interleukin 34	protein-coding
mm_166674.1	chr6	96978271	96978274	+	1	NA	intron (NM_177233, intron 3 of 5)	intron (NM_177233, intron 3 of 5)	82139	NM_177233	320701	Mm.131700	NM_177233	ENSMUSG00000046500	Fam19a4	C130034I18Rik|Fam19a4 Tafa-4|Tafa-4	family with sequence similarity 19, member A4	protein-coding
mm_33896.1	chr4	136206412	136206454	+	1	NA	promoter-TSS (NM_001008232)	promoter-TSS (NM_001008232)	68	NM_001008232	230837	Mm.77788	NM_001008232	ENSMUSG00000036995	Asap3	9430088F20Rik|Ddefl1|Gm140|UPLC1	ArfGAP with SH3 domain, ankyrin repeat and PH domain 3	protein-coding
mm_111597.1	chr12	101976283	101976301	-	1	NA	intron (NM_016856, intron 1 of 14)	CpG	318	NM_016856	51786	Mm.716	NM_016856	ENSMUSG00000041781	Cpsf2	100kDa|2610024B04Rik|AI662483|Cpsf|MCPSF|mKIAA1367	cleavage and polyadenylation specific factor 2	protein-coding
mm_100283.1	chr11	117798393	117798422	+	1	NA	intron (NM_029964, intron 1 of 5)	intron (NM_029964, intron 1 of 5)	747	NM_029964	77727	Mm.159981	NM_029964	ENSMUSG00000025573	6030468B19Rik	-	RIKEN cDNA 6030468B19 gene	protein-coding
mm_37680.1	chr4	129189647	129189697	-	1	NA	promoter-TSS (NM_029036)	promoter-TSS (NM_029036)	55	NM_001347203	74648	Mm.172064	NM_029036	ENSMUSG00000040928	S100pbp	4930429A08Rik|AI851343|S100pbpr	S100P binding protein	protein-coding
mm_70095.1	chr7	142659483	142659497	-	1	NA	promoter-TSS (NM_010514)	promoter-TSS (NM_010514)	-190	NR_002855	111975	Mm.440180	NR_002855	ENSMUSG00000086266	Igf2os	Igf2as|Peg8	insulin-like growth factor 2, opposite strand	ncRNA
mm_152291.1	chr19	9001781	9001802	-	1	NA	exon (NM_009643, exon 5 of 5)	exon (NM_009643, exon 5 of 5)	12507	NM_001286518	66395	Mm.203866	NM_009643	ENSMUSG00000069833	Ahnak	DY6	AHNAK nucleoprotein (desmoyokin)	protein-coding
mm_137522.1	chr17	27325356	27325360	+	1	NA	Intergenic	Intergenic	-3027	NR_106075	102466818		NR_106075	ENSMUSG00000099237	Mir7216	Gm27555|mmu-mir-7216	microRNA 7216	ncRNA
mm_12523.1	chr2	72173240	72173242	+	1	NA	intron (NM_019688, intron 6 of 29)	MLT1D|LTR|ERVL-MaLR	-112396	NM_023057	65964	Mm.304143	NM_023057	ENSMUSG00000004085	Map3k20	AV006891|B230120H23Rik|MLTK|MLTKalpha|MLTKbeta|Zak	mitogen-activated protein kinase kinase kinase 20	protein-coding
mm_148967.1	chr19	7536860	7536870	+	1	NA	3' UTR (NM_001163505, exon 13 of 13)	3' UTR (NM_001163505, exon 13 of 13)	-20594	NM_139269	225845	Mm.274810	NM_139269	ENSMUSG00000060675	Pla2g16	C78643|HRSL3|Hrasls3|Hrev107|MLP-3	phospholipase A2, group XVI	protein-coding
mm_56985.1	chr6	120493925	120493935	-	1	NA	promoter-TSS (NM_033567)	promoter-TSS (NM_033567)	-123	NM_033567	94047	Mm.23088	NM_033567	ENSMUSG00000094626	Cecr6	AW048664	cat eye syndrome chromosome region, candidate 6	protein-coding
mm_71207.1	chr8	40890466	40890475	+	1	NA	intron (NM_007514, intron 1 of 11)	MLT1B|LTR|ERVL-MaLR	28103	NM_001044740	11988	Mm.4676	NM_007514	ENSMUSG00000031596	Slc7a2	20.5|AI158848|Atrc2|CAT-2|Cat2|Tea	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	protein-coding
mm_132908.1	chr16	48872840	48872846	+	1	NA	intron (NM_181596, intron 1 of 3)	intron (NM_181596, intron 1 of 3)	235	NM_181596	245195	Mm.231288	NM_181596	ENSMUSG00000022651	Retnlg	Fizz3|Relmg|Xcp1	resistin like gamma	protein-coding
mm_125272.1	chr15	36176174	36176178	+	1	NA	intron (NM_023127, intron 3 of 3)	intron (NM_023127, intron 3 of 3)	2166	NM_001039368	17749	Mm.27375	NM_023127	ENSMUSG00000045996	Polr2k	ABC10-alpha|MafY|Mt1a|RPABC4|RPB10alpha|RPB12|RPB7.0	polymerase (RNA) II (DNA directed) polypeptide K	protein-coding
mm_95408.1	chr11	49901804	49901895	+	1	NA	promoter-TSS (NM_029004)	promoter-TSS (NM_029004)	14	NM_029004	74563	Mm.258798	NM_029004	ENSMUSG00000020374	Rasgef1c	9130006A14Rik	RasGEF domain family, member 1C	protein-coding
mm_84401.1	chr9	65554756	65554806	-	1	NA	3' UTR (NM_153119, exon 6 of 6)	3' UTR (NM_153119, exon 6 of 6)	25306	NM_153119	102595	Mm.247303	NM_153119	ENSMUSG00000050721	Plekho2	AI840980|Plekhq1	pleckstrin homology domain containing, family O member 2	protein-coding
mm_151326.1	chr19	55893314	55893344	+	1	NA	intron (NR_138565, intron 4 of 15)	intron (NR_138565, intron 4 of 15)	-1992	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_162008.1	chr19	41549783	41549783	+	1	NA	5' UTR (NM_172154, exon 1 of 3)	5' UTR (NM_172154, exon 1 of 3)	144	NM_172154	212391	Mm.422910	NM_172154	ENSMUSG00000025019	Lcor	3110023F06Rik|A630025C20Rik|Mlr2|mKIAA1795	ligand dependent nuclear receptor corepressor	protein-coding
mm_111885.1	chr12	108211577	108211590	-	1	NA	exon (NM_001159910, exon 3 of 6)	exon (NM_001159910, exon 3 of 6)	31845	NM_009832	12454	Mm.474441	NM_009832	ENSMUSG00000021258	Ccnk	AW123198|AW413594|CPR4|CycK	cyclin K	protein-coding
mm_38354.1	chr4	137785669	137785677	-	1	NA	intron (NM_007431, intron 1 of 11)	intron (NM_007431, intron 1 of 11)	10711	NM_007431	11647	Mm.288186	NM_007431	ENSMUSG00000028766	Alpl	ALP|APTNAP|Akp-2|Akp2|TNAP|TNSALP	alkaline phosphatase, liver/bone/kidney	protein-coding
mm_102287.1	chr11	55404509	55404533	-	1	NA	intron (NM_001290817, intron 5 of 9)	MIRb|SINE|MIR	15559	NM_009242	20692	Mm.291442	NM_009242	ENSMUSG00000018593	Sparc	BM-40|ON	secreted acidic cysteine rich glycoprotein	protein-coding
mm_126189.1	chr15	78616296	78616483	+	1	NA	intron (NM_028195, intron 9 of 12)	(TCCA)n|Simple_repeat|Simple_repeat	19342	NM_028195	72318	Mm.32911	NM_028195	ENSMUSG00000018008	Cyth4	2510004M07Rik|5830469K17Rik|AI467541|Pscd4|mFLJ00017	cytohesin 4	protein-coding
mm_80848.1	chr9	98296855	98296874	+	1	NA	5' UTR (NM_144533, exon 1 of 5)	5' UTR (NM_144533, exon 1 of 5)	281	NM_144533	74080	Mm.294082	NM_144533	ENSMUSG00000032456	Nmnat3	4933408N02Rik|PNAT3	nicotinamide nucleotide adenylyltransferase 3	protein-coding
mm_47560.1	chr5	124425549	124425566	-	1	NA	intron (NM_001081203, intron 1 of 31)	CpG	357	NM_001081203	243272	Mm.23879	NM_001081203	ENSMUSG00000038095	Sbno1	9330180L10Rik|AI849128|AW557836|BC021875|Sbno|mSno1|sno	strawberry notch homolog 1 (Drosophila)	protein-coding
mm_172823.1	chr9	15434621	15434633	+	1	NA	Intergenic	RLTR46B|LTR|ERVK	-70868	NM_133214	170748	Mm.86572	NM_133214	ENSMUSG00000058173	Smco4	Fn5	single-pass membrane protein with coiled-coil domains 4	protein-coding
mm_114476.1	chr13	68597410	68597420	+	1	NA	promoter-TSS (NM_027035)	promoter-TSS (NM_027035)	-24	NM_027035	69315	Mm.272795	NM_027035	ENSMUSG00000021534	1700001L19Rik	-	RIKEN cDNA 1700001L19 gene	protein-coding
mm_114280.1	chr13	58281187	58281196	+	1	NA	Intergenic	Intergenic	-7003	NM_019832	56278	Mm.296625	NM_019832	ENSMUSG00000021552	Gkap1	42kDa|4933400B15Rik|D13Ertd340e|Gkap42	G kinase anchoring protein 1	protein-coding
mm_75902.1	chr8	71272420	71272435	-	1	NA	promoter-TSS (NM_001142322)	promoter-TSS (NM_001142322)	163	NM_001163042	76478	Mm.27355	NM_029621	ENSMUSG00000035439	Haus8	2410004L22Rik|Hice1	4HAUS augmin-like complex, subunit 8	protein-coding
mm_9122.1	chr1	170255722	170255761	-	1	NA	Intergenic	CpG	-21583	NM_012009	26904	Mm.57009	NM_012009	ENSMUSG00000102418	Sh2d1b1	EAT-2|EAT-2A|Eat2|Eat2a|Sh2d1b	SH2 domain containing 1B1	protein-coding
mm_148438.1	chr19	3947069	3947093	+	1	NA	exon (NM_019449, exon 10 of 11)	exon (NM_019449, exon 10 of 11)	-11727	NM_028545	73458	Mm.482922	NM_028545	ENSMUSG00000037263	Aldh3b3	1700055N04Rik	aldehyde dehydrogenase 3 family, member B3	protein-coding
mm_711.1	chr1	41743730	41743741	+	1	NA	Intergenic	Intergenic	-562483	NR_040475	74897	Mm.243822	NR_040475	ENSMUSG00000104072	4930448I06Rik	-	RIKEN cDNA 4930448I06 gene	ncRNA
mm_88826.1	chr10	80804101	80804118	+	1	NA	exon (NM_013651, exon 9 of 9)	exon (NM_013651, exon 9 of 9)	-1139	NM_007445	11705	Mm.376094	NM_007445	ENSMUSG00000035262	Amh	MIS	anti-Mullerian hormone	protein-coding
mm_45873.1	chr5	88008290	88008326	-	1	NA	exon (NM_011422, exon 3 of 3)	exon (NM_011422, exon 3 of 3)	5783	NM_011422	20599	Mm.261199	NM_011422	ENSMUSG00000029280	Smr3a	AA589601|MSG1|MSG3|Smr1|Smr3	submaxillary gland androgen regulated protein 3A	protein-coding
mm_30044.1	chr3	135719239	135719249	-	1	NA	Intergenic	Intergenic	-27697	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_111407.1	chr12	91215769	91215772	-	1	NA	intron (NM_181815, intron 19 of 25)	intron (NM_181815, intron 19 of 25)	105541	NR_030473	735273		NR_030473	ENSMUSG00000076118	Mir669c	Mirn669c|Mirn669c-1	microRNA 669c	ncRNA
mm_127136.1	chr15	98168230	98168268	+	1	NA	5' UTR (NM_177716, exon 1 of 1)	5' UTR (NM_177716, exon 1 of 1)	443	NM_177716	239650	Mm.54140	NM_177716	ENSMUSG00000029875	Ccdc184	5630400A08|AI836003	coiled-coil domain containing 184	protein-coding
mm_102335.1	chr11	57829447	57829460	-	1	NA	3' UTR (NM_008213, exon 2 of 2)	3' UTR (NM_008213, exon 2 of 2)	2694	NM_008213	15110	Mm.4746	NM_008213	ENSMUSG00000037335	Hand1	Ehand1|Hxt|Th1|Thing1|bHLHa27|eHAND	heart and neural crest derivatives expressed transcript 1	protein-coding
mm_27004.1	chr3	25847332	25847346	-	1	NA	intron (NM_001163387, intron 3 of 5)	intron (NM_001163387, intron 3 of 5)	305968	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_135556.1	chr16	49855833	49855843	-	1	NA	intron (NM_010581, intron 1 of 9)	CpG	184	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_136087.1	chr16	84955313	84955349	-	1	NA	exon (NM_001198823, exon 18 of 18)	exon (NM_001198823, exon 18 of 18)	-16880	NR_045889	100038614	Mm.441351	NR_045889		Gm10791	ENSMUSG00000074933	predicted gene 10791	ncRNA
mm_125301.1	chr15	37233080	37233094	+	1	NA	promoter-TSS (NM_026496)	promoter-TSS (NM_026496)	51	NM_026496	252973	Mm.244612	NM_026496	ENSMUSG00000022286	Grhl2	0610015A08Rik|BOM|Tcfcp2l3|clft3	grainyhead-like 2 (Drosophila)	protein-coding
mm_171293.1	chr3	90293402	90293402	+	1	NA	Intergenic	Intergenic	23253	NR_105979	102465612		NR_105979	ENSMUSG00000099199	Mir7012	Gm27370|mmu-mir-7012	microRNA 7012	ncRNA
mm_48339.1	chr5	139130077	139130079	-	1	NA	promoter-TSS (NM_008923)	promoter-TSS (NM_008923)	308	NM_001253890	19085	Mm.306163	NM_008923	ENSMUSG00000025855	Prkar1b	AI385716|RIbeta	protein kinase, cAMP dependent regulatory, type I beta	protein-coding
mm_8829.1	chr1	162571350	162571365	-	1	NA	intron (NM_001347125, intron 1 of 7)	CpG	529	NM_001347125	53330	Mm.10699	NM_016796	ENSMUSG00000026696	Vamp4	D1Ertd147e	vesicle-associated membrane protein 4	protein-coding
mm_45479.1	chr5	69592312	69592318	-	1	NA	promoter-TSS (NM_001038015)	promoter-TSS (NM_001038015)	-11	NM_001347363	67980	Mm.33830	NM_027681	ENSMUSG00000029209	Gnpda2	4921523I18Rik|4933412A11Rik|BB189630|GNPDA|Gnp2|Sb52|mKIAA4008	glucosamine-6-phosphate deaminase 2	protein-coding
mm_141348.1	chr17	28603560	28603561	-	1	NA	intron (NM_016795, intron 6 of 15)	intron (NM_016795, intron 6 of 15)	18894	NM_016795	20815	Mm.15252	NM_016795	ENSMUSG00000004865	Srpk1	AU017960	serine/arginine-rich protein specific kinase 1	protein-coding
mm_135933.1	chr16	73958409	73958411	-	1	NA	exon (NM_175549, exon 15 of 28)	exon (NM_175549, exon 15 of 28)	383657	NR_030464	751561		NR_030464	ENSMUSG00000104758	Mir691	Mirn691|mir-691|mmu-mir-691	microRNA 691	ncRNA
mm_74179.1	chr8	123477850	123477856	+	1	NA	promoter-TSS (NR_028260)	promoter-TSS (NR_028260)	-9	NM_054070	114896	Mm.287475	NM_054070	ENSMUSG00000031967	Afg3l1	1700047G05Rik|3110061K15Rik	AFG3-like AAA ATPase 1	protein-coding
mm_19662.1	chr2	103263610	103263613	-	1	NA	3' UTR (NM_007914, exon 9 of 9)	3' UTR (NM_007914, exon 9 of 9)	39585	NM_007914	13661	Mm.10724	NM_007914	ENSMUSG00000012350	Ehf	9030625L19Rik|AU019492	ets homologous factor	protein-coding
mm_59505.1	chr7	27560471	27560496	+	1	NA	promoter-TSS (NM_001122767)	promoter-TSS (NM_001122767)	7	NM_001122767	66367	Mm.29831	NM_175107	ENSMUSG00000049643	2310022A10Rik	-	RIKEN cDNA 2310022A10 gene	protein-coding
mm_137879.1	chr17	31564856	31564873	+	1	NA	promoter-TSS (NM_016670)	promoter-TSS (NM_016670)	91	NM_016670	18771	Mm.259295	NM_016670	ENSMUSG00000006705	Pknox1	D17Wsu76e|PREP1	Pbx/knotted 1 homeobox	protein-coding
mm_76862.1	chr8	105471448	105471458	-	1	NA	promoter-TSS (NM_026481)	promoter-TSS (NM_026481)	-31	NM_026481	67971	Mm.29358	NM_026481	ENSMUSG00000014846	Tppp3	2700055K07Rik|CGI-38|Ceacam9|mmCGM8	tubulin polymerization-promoting protein family member 3	protein-coding
mm_169594.1	chr15	30754112	30754116	-	1	NA	intron (NM_008729, intron 9 of 22)	L1Md_T|LINE|L1	-285012	NR_045186	73784	Mm.66947	NR_045186		4930430F21Rik	-	RIKEN cDNA 4930430F21 gene	ncRNA
mm_149003.1	chr19	8702826	8702839	+	1	NA	Intergenic	Intergenic	11065	NM_008577	17254	Mm.4114	NM_008577	ENSMUSG00000010095	Slc3a2	4F2|4F2HC|AI314110|Cd98|Ly-10|Ly-m10|Ly10|Mdu1|Mgp-2hc|NACAE	solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2	protein-coding
mm_41558.1	chr5	93093474	93093483	+	1	NA	promoter-TSS (NM_001310669)	promoter-TSS (NM_001310669)	62	NM_001347377	52398	Mm.394184	NM_001009818	ENSMUSG00000058013	Sept11	6230410I01Rik|AW548875|D5Ertd606e	septin 11	protein-coding
mm_20978.1	chr2	151973841	151973858	-	1	NA	promoter-TSS (NM_001289151)	promoter-TSS (NM_001289151)	132	NM_001289150	73847	Mm.272444	NM_028666	ENSMUSG00000027459	Fam110a	1700008J10Rik|5430432M24Rik|AI747080	family with sequence similarity 110, member A	protein-coding
mm_151161.1	chr19	53194336	53194346	+	1	NA	intron (NM_013758, intron 1 of 15)	intron (NM_013758, intron 1 of 15)	50344	NM_013758	27360	Mm.426080	NM_013758	ENSMUSG00000025026	Add3	AI463285|R75380	adducin 3 (gamma)	protein-coding
mm_93999.1	chr10	127589607	127589614	-	1	NA	exon (NM_008512, exon 13 of 89)	exon (NM_008512, exon 13 of 89)	31538	NM_008512	16971	Mm.271854	NM_008512	ENSMUSG00000040249	Lrp1	A2mr|AI316852|CD91|Lrp|b2b1554Clo	low density lipoprotein receptor-related protein 1	protein-coding
mm_54371.1	chr6	31131825	31131846	-	1	NA	intron (NR_110471, intron 3 of 3)	intron (NR_110471, intron 3 of 3)	-68742	NR_029532	387223		NR_029532	ENSMUSG00000065604	Mir29b-1	Mirn29b|Mirn29b-1|mir-29b-1	microRNA 29b-1	ncRNA
mm_108718.1	chr12	87157877	87157890	+	1	NA	intron (NM_001252555, intron 2 of 9)	intron (NM_001252555, intron 2 of 9)	-2398	NR_136901	625237	Mm.390529	NR_136901		Gm6566	EG625237	predicted gene 6566	ncRNA
mm_28399.1	chr3	90213637	90213670	-	1	NA	promoter-TSS (NM_001293741)	promoter-TSS (NM_001293741)	-5	NM_027015	57294	Mm.270283	NM_027015	ENSMUSG00000090733	Rps27	3200001M24Rik	ribosomal protein S27	protein-coding
mm_21091.1	chr2	153191487	153191497	-	1	NA	intron (NM_133847, intron 8 of 17)	intron (NM_133847, intron 8 of 17)	30191	NM_133847	99237	Mm.330674	NM_133847	ENSMUSG00000068040	Tm9sf4	AA986553|AU045326|B930079E06|mKIAA0255	transmembrane 9 superfamily protein member 4	protein-coding
mm_169170.1	chr13	65613907	65613908	+	1	NA	Intergenic	Intergenic	335053	NM_178364	170936	Mm.151546	NM_178364	ENSMUSG00000021514	Zfp369	B930030B22Rik|D230020H11Rik|NRIF2	zinc finger protein 369	protein-coding
mm_119804.1	chr14	54219031	54219039	+	1	NA	Intergenic	Intergenic	34894	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_129210.1	chr15	76522248	76522307	-	1	NA	promoter-TSS (NM_130893)	promoter-TSS (NM_130893)	-148	NM_130893	170729	Mm.218747	NM_130893	ENSMUSG00000048385	Scrt1	-	scratch family zinc finger 1	protein-coding
mm_71360.1	chr8	45689983	45690000	+	1	NA	intron (NM_001310708, intron 1 of 19)	intron (NM_001310708, intron 1 of 19)	27998	NM_001310708	234214	Mm.211096	NM_172752	ENSMUSG00000031626	Sorbs2	2010203O03Rik|9430041O17Rik|A530071H08|Argbp2|mKIAA0777|nArgBP2	sorbin and SH3 domain containing 2	protein-coding
mm_133816.1	chr16	95715139	95715150	+	1	NA	exon (NM_011809, exon 7 of 10)	exon (NM_011809, exon 7 of 10)	12737	NM_011809	23872	Mm.290207	NM_011809	ENSMUSG00000022895	Ets2	AU022856|Ets-2	E26 avian leukemia oncogene 2, 3' domain	protein-coding
mm_134192.1	chr16	10992145	10992190	-	1	NA	intron (NM_019980, intron 1 of 3)	ID_B1|SINE|B4	954	NM_019980	56722	Mm.294753	NM_019980	ENSMUSG00000022500	Litaf	3222402J11Rik|C85531|N4WBP3|TBX1	LPS-induced TN factor	protein-coding
mm_146098.1	chr18	73878235	73878242	+	1	NA	3' UTR (NM_001305882, exon 9 of 9)	3' UTR (NM_001305882, exon 9 of 9)	18853	NM_001305882	71263	Mm.126220	NM_027741	ENSMUSG00000064036	Mro	4930507C04Rik|4933435E20Rik	maestro	protein-coding
mm_159223.1	chr2	129199503	129199503	+	1	NA	5' UTR (NM_015747, exon 2 of 11)	5' UTR (NM_015747, exon 2 of 11)	730	NM_001159593	20515	Mm.272675	NM_015747	ENSMUSG00000027397	Slc20a1	AI607883|Glvr-1|Glvr1	solute carrier family 20, member 1	protein-coding
mm_59949.1	chr7	30425773	30425775	+	1	NA	exon (NM_172142, exon 6 of 11)	exon (NM_172142, exon 6 of 11)	2470	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_132636.1	chr16	39777714	39777715	+	1	NA	Intergenic	Lx7|LINE|L1	875369	NM_170599	207683	Mm.245564	NM_170599	ENSMUSG00000022790	Igsf11	1700025L02Rik|BT-IgSF|Igsf13	immunoglobulin superfamily, member 11	protein-coding
mm_4062.1	chr1	165864643	165864660	+	1	NA	TTS (NM_198933)	TTS (NM_198933)	70297	NM_198933	18986	Mm.245261	NM_011137	ENSMUSG00000026565	Pou2f1	2810482H01Rik|NF-A1|Oct-1|Oct1|Otf-1|Otf1	POU domain, class 2, transcription factor 1	protein-coding
mm_155232.1	chrX	57200533	57200546	+	1	NA	promoter-TSS (NR_038463)	promoter-TSS (NR_038463)	-98	NR_038463	100502842	Mm.164733	NR_038463	ENSMUSG00000085808	Gm14718	OTTMUSG00000017790	predicted gene 14718	ncRNA
mm_85381.1	chr9	103226125	103226143	-	1	NA	exon (NM_133977, exon 4 of 17)	exon (NM_133977, exon 4 of 17)	4152	NM_133977	22041	Mm.37214	NM_133977	ENSMUSG00000032554	Trf	AI266983|Cd176|HP|Tf|Tfn|hpx	transferrin	protein-coding
mm_68653.1	chr7	118533299	118533333	-	1	NA	promoter-TSS (NM_009940)	promoter-TSS (NM_009940)	40	NM_001304758	12850	Mm.20634	NM_009940	ENSMUSG00000030652	Coq7	clk-1	demethyl-Q 7	protein-coding
mm_139749.1	chr17	63863042	63863080	+	1	NA	promoter-TSS (NM_001037997)	promoter-TSS (NM_001037997)	-920	NM_001037997	14158	Mm.23039	NM_008000	ENSMUSG00000000127	Fer	AV082135|C330004K01Rik|Fert|Fert2	fer (fms/fps related) protein kinase	protein-coding
mm_71739.1	chr8	62951392	62951498	+	1	NA	promoter-TSS (NM_023689)	promoter-TSS (NM_023689)	100	NM_023689	72902	Mm.334552	NM_023689	ENSMUSG00000054162	Spock3	2900045C01Rik|AI428471|mKIAA4039	sparc/osteonectin, cwcv and kazal-like domains proteoglycan 3	protein-coding
mm_25506.1	chr3	109573970	109573990	+	1	NA	promoter-TSS (NM_146139)	promoter-TSS (NM_146139)	-27	NM_146139	57257	Mm.282257	NM_020505	ENSMUSG00000033721	Vav3	A530094I06Rik|AA986410|Idd18.1	vav 3 oncogene	protein-coding
mm_139586.1	chr17	57223223	57223255	+	1	NA	exon (NM_009778, exon 12 of 41)	exon (NM_009778, exon 12 of 41)	4897	NM_009778	12266	Mm.19131	NM_009778	ENSMUSG00000024164	C3	AI255234|ASP|HSE-MSF|Plp	complement component 3	protein-coding
mm_115618.1	chr13	12068363	12068364	-	1	NA	intron (NM_023868, intron 1 of 104)	MTB_Mm|LTR|ERVL-MaLR	38582	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding
mm_86744.1	chr10	19356389	19356391	+	1	NA	promoter-TSS (NM_053008)	promoter-TSS (NM_053008)	-149	NM_053008	94222	Mm.156946	NM_053008	ENSMUSG00000045591	Olig3	Bhlhb7|bHLHe20|oligo3	oligodendrocyte transcription factor 3	protein-coding
mm_92149.1	chr10	67096907	67096923	-	1	NA	promoter-TSS (NM_001204915)	promoter-TSS (NM_001204915)	73	NM_001204915	28193	Mm.41272	NM_178606	ENSMUSG00000019873	Reep3	D10Ucla1	receptor accessory protein 3	protein-coding
mm_4403.1	chr1	172435300	172435312	+	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-40054	NM_029612	98365	Mm.150050	NM_029612	ENSMUSG00000026548	Slamf9	2310026I04Rik|AI462096|CD2F-10|CD84-H1|Cd2f10|SF2001	SLAM family member 9	protein-coding
mm_83456.1	chr9	45246175	45246178	-	1	NA	intron (NM_001198971, intron 4 of 4)	intron (NM_001198971, intron 4 of 4)	20531	NR_106054	102466803		NR_106054	ENSMUSG00000098361	Mir7086	Gm27643|mmu-mir-7086	microRNA 7086	ncRNA
mm_79397.1	chr9	54917331	54917339	+	1	NA	promoter-TSS (NM_177351)	promoter-TSS (NM_177351)	45	NM_177351	235386	Mm.259334	NM_177351	ENSMUSG00000035878	Hykk	Agphd1|C630028N24Rik	hydroxylysine kinase 1	protein-coding
mm_141514.1	chr17	31678499	31678540	-	1	NA	exon (NM_001278569, exon 2 of 4)	exon (NM_001278569, exon 2 of 4)	588	NM_001278570	12954	Mm.1228	NM_013501	ENSMUSG00000024041	Cryaa	Acry-1|Crya-1|Crya1|DAcry-1|lop18	crystallin, alpha A	protein-coding
mm_79554.1	chr9	57998069	57998093	+	1	NA	promoter-TSS (NM_001346787)	promoter-TSS (NM_001346787)	57	NM_001346787	13070	Mm.302865	NM_019779	ENSMUSG00000032323	Cyp11a1	Cyp11a|Cypxia1|D9Ertd411e|P450scc|Scc|cscc	cytochrome P450, family 11, subfamily a, polypeptide 1	protein-coding
mm_118225.1	chr13	110601908	110601911	-	1	NA	Intergenic	Intergenic	206865	NM_152804	20620	Mm.380	NM_152804	ENSMUSG00000021701	Plk2	Snk	polo-like kinase 2	protein-coding
mm_72242.1	chr8	75016298	75016308	+	1	NA	promoter-TSS (NM_001316754)	promoter-TSS (NM_001316754)	81	NM_001316754	70823	Mm.261739	NM_178017	ENSMUSG00000034518	Hmgxb4	4733401K04Rik|AI316803|Hmgb2l1	HMG box domain containing 4	protein-coding
mm_116894.1	chr13	55362811	55362821	-	1	NA	promoter-TSS (NM_025828)	promoter-TSS (NM_025828)	-33	NM_025828	66890	Mm.38868	NM_025828	ENSMUSG00000021484	Lman2	1110003H06Rik|1300009F09Rik|AA408240|AL023023|AU040819|GP36B|VIP36	lectin, mannose-binding 2	protein-coding
mm_18871.1	chr2	75981739	75981797	-	1	NA	5' UTR (NM_030188, exon 1 of 1)	5' UTR (NM_030188, exon 1 of 1)	199	NM_030188	78802	Mm.282339	NM_030188	ENSMUSG00000075271	Ttc30a1	4930506L13Rik	tetratricopeptide repeat domain 30A1	protein-coding
mm_50710.1	chr6	52172811	52172825	+	1	NA	intron (NM_010452, intron 3 of 4)	intron (NM_010452, intron 3 of 4)	7144	NR_131182	105242657	Mm.490651	NR_131182	ENSMUSG00000056445	Hoxaas2	2810043O09Rik|5730446D14Rik	Hoxa cluster antisense RNA 2	ncRNA
mm_73154.1	chr8	94994746	94994789	+	1	NA	intron (NM_018882, intron 1 of 13)	intron (NM_018882, intron 1 of 13)	10368	NM_018882	14766	Mm.290834	NM_018882	ENSMUSG00000031785	Adgrg1	Cyt28|Gpr56|TM7LN4|TM7XN1	adhesion G protein-coupled receptor G1	protein-coding
mm_12458.1	chr2	71319731	71319743	+	1	NA	intron (NM_172436, intron 5 of 17)	intron (NM_172436, intron 5 of 17)	47817	NM_172436	78830	Mm.30928	NM_172436	ENSMUSG00000027010	Slc25a12	2610002D09Rik|AI839531|B230107K20Rik|BB129864	solute carrier family 25 (mitochondrial carrier, Aralar), member 12	protein-coding
mm_66339.1	chr7	43443921	43443937	-	1	NA	promoter-TSS (NM_026695)	promoter-TSS (NM_026695)	-143	NM_026695	110826	Mm.30200	NM_026695	ENSMUSG00000004610	Etfb	0610009I16Rik|2810441H06Rik	electron transferring flavoprotein, beta polypeptide	protein-coding
mm_135861.1	chr16	60605227	60605229	-	1	NA	exon (NM_007938, exon 1 of 18)	exon (NM_007938, exon 1 of 18)	303	NM_007938	13840	Mm.455790	NM_007938	ENSMUSG00000055540	Epha6	Ehk2|Hek12|m-ehk2	Eph receptor A6	protein-coding
mm_173129.1	chrX	170009937	170009949	+	1	NA	Intergenic	CpG	-31026	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_87899.1	chr10	62071660	62071686	+	1	NA	Intergenic	Intergenic	39340	NM_027251	69894	Mm.294126	NM_027251	ENSMUSG00000020083	2010107G23Rik	AA545165	RIKEN cDNA 2010107G23 gene	protein-coding
mm_47855.1	chr5	134552415	134552444	-	1	NA	promoter-TSS (NM_001039162)	promoter-TSS (NM_001039162)	5	NM_001039162	269713	Mm.255138	NM_009990	ENSMUSG00000063146	Clip2	B230327O20|CLIP-115|Clip1|Cyln2|WSCR4|mKIAA0291|wbscr4	CAP-GLY domain containing linker protein 2	protein-coding
mm_60581.1	chr7	44482638	44482647	+	1	NA	Intergenic	Intergenic	-1875	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_31783.1	chr4	63580561	63580568	+	1	NA	intron (NM_144905, intron 9 of 9)	intron (NM_144905, intron 9 of 9)	20200	NR_028584	670833	Mm.32213	NR_028583	ENSMUSG00000084782	Gm11213	OTTMUSG00000000252	predicted gene 11213	ncRNA
mm_117344.1	chr13	69611292	69611312	-	1	NA	promoter-TSS (NM_145354)	promoter-TSS (NM_145354)	161	NM_175283	78925	Mm.451912	NM_175283	ENSMUSG00000021594	Srd5a1	0610031P22Rik|4930435F02Rik|S5AR 1|Srd5a-1	steroid 5 alpha-reductase 1	protein-coding
mm_18810.1	chr2	74307696	74307725	-	1	NA	promoter-TSS (NR_040501)	promoter-TSS (NR_040501)	7	NR_040501	73962	Mm.50289	NR_040501	ENSMUSG00000085405	4930441J16Rik	Astx1a|Astx1b|Astx1c	RIKEN cDNA 4930441J16 gene	ncRNA
mm_9454.1	chr1	172632816	172632869	-	1	NA	exon (NM_026725, exon 1 of 2)	exon (NM_026725, exon 1 of 2)	132	NM_026725	68440	Mm.33024	NM_026725	ENSMUSG00000026544	Dusp23	1300005N15Rik|LDP-3	dual specificity phosphatase 23	protein-coding
mm_142183.1	chr17	36642662	36642664	-	1	NA	promoter-TSS (NM_008205)	promoter-TSS (NM_008205)	-19	NM_008205	14997	Mm.57004	NM_008205	ENSMUSG00000067201	H2-M9	M9	histocompatibility 2, M region locus 9	protein-coding
mm_71336.1	chr8	45507769	45507807	+	1	NA	promoter-TSS (NM_001205219)	promoter-TSS (NM_001205219)	0	NM_172752	234214	Mm.211096	NM_172752	ENSMUSG00000031626	Sorbs2	2010203O03Rik|9430041O17Rik|A530071H08|Argbp2|mKIAA0777|nArgBP2	sorbin and SH3 domain containing 2	protein-coding
mm_2165.1	chr1	88259133	88259145	+	1	NA	exon (NM_001281466, exon 40 of 42)	exon (NM_001281466, exon 40 of 42)	10269	NR_040291	78605	Mm.384762	NR_040291		6430706D22Rik	-	RIKEN cDNA 6430706D22 gene	ncRNA
mm_153555.1	chr19	42128983	42129041	-	1	NA	promoter-TSS (NM_027106)	promoter-TSS (NM_027106)	-19	NM_027106	69534	Mm.30060	NM_027106	ENSMUSG00000018821	Avpi1	2310008N12Rik|AA410041|VIT32|esu|mVIT32	arginine vasopressin-induced 1	protein-coding
mm_108056.1	chr12	73923240	73923250	+	1	NA	intron (NM_010431, intron 1 of 14)	B2_Mm2|SINE|B2	15378	NM_001313919	15251	Mm.3879	NM_010431	ENSMUSG00000021109	Hif1a	AA959795|HIF-1-alpha|HIF1-alpha|HIF1alpha|MOP1|bHLHe78	hypoxia inducible factor 1, alpha subunit	protein-coding
mm_125292.1	chr15	36771401	36771438	+	1	NA	3' UTR (NM_001253807, exon 5 of 5)	3' UTR (NM_001253807, exon 5 of 5)	19513	NM_001253807	22631	Mm.3360	NM_011740	ENSMUSG00000022285	Ywhaz	1110013I11Rik|14-3-3zeta|AI596267|AL022924|AU020854	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide	protein-coding
mm_44946.1	chr5	36566563	36566567	-	1	NA	intron (NM_133910, intron 2 of 13)	intron (NM_133910, intron 2 of 13)	15832	NM_133910	100855	Mm.486203	NM_133910	ENSMUSG00000029192	Tbc1d14	2810413P16Rik|AU043625|C86258|D5Ertd110e|mKIAA1322	TBC1 domain family, member 14	protein-coding
mm_110882.1	chr12	75176777	75176808	-	1	NA	5' UTR (NM_172805, exon 1 of 11)	5' UTR (NM_172805, exon 1 of 11)	540	NM_172805	238271	Mm.44465	NM_172805	ENSMUSG00000034402	Kcnh5	Eag2	potassium voltage-gated channel, subfamily H (eag-related), member 5	protein-coding
mm_136286.1	chr16	91367115	91367167	-	1	NA	Intergenic	Intergenic	-5642	NM_010509	15976	Mm.6834	NM_010509	ENSMUSG00000022971	Ifnar2	AI747302|Ifnar-2	interferon (alpha and beta) receptor 2	protein-coding
mm_100895.1	chr11	6066111	6066120	-	1	NA	promoter-TSS (NM_001174054)	promoter-TSS (NM_001174054)	-367	NM_007595	12323	Mm.439733	NM_007595	ENSMUSG00000057897	Camk2b	CaMKII	calcium/calmodulin-dependent protein kinase II, beta	protein-coding
mm_2195.1	chr1	89454770	89454885	+	1	NA	promoter-TSS (NM_178119)	promoter-TSS (NM_178119)	16	NM_001037136	347722	Mm.291135	NM_178119	ENSMUSG00000055013	Agap1	Centg2|Ggap1|R75364|mKIAA1099	ArfGAP with GTPase domain, ankyrin repeat and PH domain 1	protein-coding
mm_9506.1	chr1	173737942	173737953	-	1	NA	intron (NM_001204910, intron 1 of 7)	Lx8|LINE|L1	3862	NM_001204910	226691	Mm.440876	NM_001204910	ENSMUSG00000073490	Ifi207	AI607873|Pyhin-A	interferon activated gene 207	protein-coding
mm_65076.1	chr7	19118358	19118404	-	1	NA	Intergenic	CpG	-1478	NM_175530	243867	Mm.230830	NM_175530	ENSMUSG00000050428	Fbxo46	20D7-FC4|4932704E22Rik|Fbxo34l	F-box protein 46	protein-coding
mm_4929.1	chr1	191069194	191069199	+	1	NA	intron (NM_198654, intron 2 of 5)	intron (NM_198654, intron 2 of 5)	6175	NM_198654	381318	Mm.32504	NM_198654	ENSMUSG00000062510	Nsl1	4833432M17Rik|AI451597|Gm105|Gm984	NSL1, MIS12 kinetochore complex component	protein-coding
mm_172792.1	chr9	110281274	110281277	+	1	NA	promoter-TSS (NR_105744)	promoter-TSS (NR_105744)	-12	NR_105744	102465959		NR_105744	ENSMUSG00000098973	Mir6236	Gm27547|mmu-mir-6236	microRNA 6236	ncRNA
mm_70419.1	chr8	11461229	11461244	+	1	NA	intron (NM_011227, intron 1 of 1)	intron (NM_011227, intron 1 of 1)	-16693	NR_126558	102132	Mm.37632	NR_126558	ENSMUSG00000096957	E230013L22Rik	AI645545	RIKEN cDNA E230013L22 gene	ncRNA
mm_98353.1	chr11	93597184	93597197	+	1	NA	exon (NM_028296, exon 7 of 9)	exon (NM_028296, exon 7 of 9)	288576	NM_001013375	217109	Mm.379350	NM_001013375	ENSMUSG00000054079	Utp18	6230425C22Rik|6430513M13|Wdr50	UTP18 small subunit processome component	protein-coding
mm_163205.1	chr11	97780799	97780801	+	1	NA	TTS (NR_028078)	TTS (NR_028078)	966	NR_028078	100302498	Mm.453536	NR_028078	ENSMUSG00000064901	Snora21	MBI-3	small nucleolar RNA, H/ACA box 21	snoRNA
mm_129339.1	chr15	77836832	77836832	-	1	NA	intron (NM_022410, intron 1 of 40)	intron (NM_022410, intron 1 of 40)	5343	NM_022410	17886	Mm.29677	NM_022410	ENSMUSG00000022443	Myh9	Fltn|Myhn-1|Myhn1|NMHCIIA|NMMHC-A|NMMHC-IIA|TU72.6	myosin, heavy polypeptide 9, non-muscle	protein-coding
mm_108526.1	chr12	84114322	84114383	+	1	NA	promoter-TSS (NM_028821)	promoter-TSS (NM_028821)	24	NM_001346528	105000	Mm.101525	NM_028821	ENSMUSG00000042523	Dnal1	1700010H15Rik|AW121714|Dnalc1|E330027P08Rik	dynein, axonemal, light chain 1	protein-coding
mm_165245.1	chr2	69381910	69381922	-	1	NA	intron (NM_175512, intron 1 of 4)	intron (NM_175512, intron 1 of 4)	1454	NM_175512	241452	Mm.211655	NM_175512	ENSMUSG00000027068	Dhrs9	C730025I08Rik|Rdh15	dehydrogenase/reductase (SDR family) member 9	protein-coding
mm_64965.1	chr7	16614882	16614891	-	1	NA	5' UTR (NM_172739, exon 1 of 7)	5' UTR (NM_172739, exon 1 of 7)	107	NM_172739	232906	Mm.28646	NM_172739	ENSMUSG00000058230	Arhgap35	6430596G11Rik|AI841135|Grlf1|mKIAA1722|p190A|p190RhoGAP	Rho GTPase activating protein 35	protein-coding
mm_85858.1	chr9	110743654	110743673	-	1	NA	promoter-TSS (NM_001083935)	promoter-TSS (NM_001083935)	23	NM_001083935	19228	Mm.3542	NM_011199	ENSMUSG00000032492	Pth1r	PPR|Pthr|Pthr1	parathyroid hormone 1 receptor	protein-coding
mm_165099.1	chr19	55196302	55196315	-	1	NA	TTS (NM_009348)	TTS (NM_009348)	3630	NR_106146	102465990		NR_106146	ENSMUSG00000098289	Mir6715	Gm27474|mmu-mir-6715	microRNA 6715	ncRNA
mm_168574.1	chr1	171252346	171252351	-	1	NA	intron (NM_172845, intron 1 of 8)	intron (NM_172845, intron 1 of 8)	2219	NM_172845	240913	Mm.491147	NM_172845	ENSMUSG00000006403	Adamts4	ADAM-TS4|ADAMTS-2|ADMP-1	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 4	protein-coding
mm_34518.1	chr4	148941144	148941155	+	1	NA	intron (NM_027195, intron 11 of 15)	intron (NM_027195, intron 11 of 15)	136757	NM_027195	69743	Mm.233879	NM_027195	ENSMUSG00000028977	Casz1	2410019P08Rik|AV096627|BC040081|Cst|D4Ertd432e	castor zinc finger 1	protein-coding
mm_155923.1	chrX	103356465	103356488	+	1	NA	promoter-TSS (NM_009767)	promoter-TSS (NM_009767)	0	NM_009767	12212	Mm.42223	NM_009767	ENSMUSG00000031327	Chic1	Brx|ENSMUSG00000073019|Gm10454	cysteine-rich hydrophobic domain 1	protein-coding
mm_136465.1	chr16	95459060	95459098	-	1	NA	intron (NM_001302152, intron 3 of 10)	intron (NM_001302152, intron 3 of 10)	269	NM_001302154	13876	Mm.164531	NM_133659	ENSMUSG00000040732	Erg	D030036I24Rik	avian erythroblastosis virus E-26 (v-ets) oncogene related	protein-coding
mm_106954.1	chr12	8792179	8792192	+	1	NA	3' UTR (NM_011519, exon 5 of 5)	3' UTR (NM_011519, exon 5 of 5)	20789	NM_011519	20969	Mm.2580	NM_011519	ENSMUSG00000020592	Sdc1	AA408134|AA409076|CD138|Sstn|Synd|Synd1|syn-1	syndecan 1	protein-coding
mm_8232.1	chr1	138175672	138175688	-	1	NA	promoter-TSS (NM_001268286)	promoter-TSS (NM_001268286)	-375	NM_001268286	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_112843.1	chr13	20831125	20831134	+	1	NA	intron (NM_012054, intron 2 of 20)	MER57D|LTR|ERV1	37016	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_78782.1	chr9	43869404	43869405	+	1	NA	Intergenic	Intergenic	124828	NM_021424	58235	Mm.335096	NM_021424	ENSMUSG00000032012	Nectin1	AI835281|AW549174|Cd111|HIgR|HveC|PRR|PRR1|Pvrl1|nectin-1	nectin cell adhesion molecule 1	protein-coding
mm_28212.1	chr3	88372741	88372745	-	1	NA	promoter-TSS (NM_001305449)	promoter-TSS (NM_001305449)	-2	NM_001305448	12095	Mm.482191	NM_031368	ENSMUSG00000074489	Bglap3	AI461847|Bglap-rs1|OC-X|ORG|mOC-X	bone gamma-carboxyglutamate protein 3	protein-coding
mm_12845.1	chr2	83293200	83293200	+	1	NA	Intergenic	L1MCa|LINE|L1	-351378	NM_026934	69082	Mm.27804	NM_026934	ENSMUSG00000027091	Zc3h15	1700006A17Rik|1810012H02Rik|2610312B22Rik|FM22|Ierepo4	zinc finger CCCH-type containing 15	protein-coding
mm_66383.1	chr7	43979429	43979434	-	1	NA	exon (NM_010116, exon 3 of 5)	exon (NM_010116, exon 3 of 5)	3370	NM_010116	13648	Mm.440884	NM_010116	ENSMUSG00000059042	Klk1b9	EGF-BP C|Egfbp-3|Egfbp3|KAL|Klk9|kallikrein|mGk-9	kallikrein 1-related peptidase b9	protein-coding
mm_58042.1	chr6	136827715	136827744	-	1	NA	intron (NM_021714, intron 1 of 11)	CpG	487	NM_021714	60321	Mm.141197	NM_021714	ENSMUSG00000030216	Wbp11	2510026P17Rik|D6Wsu113e|Npwbp|SIPP1	WW domain binding protein 11	protein-coding
mm_161151.1	chr13	23488833	23488833	-	1	NA	promoter-TSS (NM_001289615)	promoter-TSS (NM_001289615)	24	NM_001289615	238555	Mm.129668	NM_175938	ENSMUSG00000053216	Btn2a2	Btn2|D030063K05	butyrophilin, subfamily 2, member A2	protein-coding
mm_115904.1	chr13	23423799	23423808	-	1	NA	promoter-TSS (NM_013924)	promoter-TSS (NM_013924)	63	NM_013924	30946	Mm.292094	NM_013924	ENSMUSG00000036376	Abt1	-	activator of basal transcription 1	protein-coding
mm_129485.1	chr15	78773395	78773405	-	1	NA	promoter-TSS (NM_008595)	promoter-TSS (NM_008595)	45	NM_008595	17305	Mm.149235	NM_008595	ENSMUSG00000018169	Mfng	AW546563	MFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	protein-coding
mm_62698.1	chr7	110164316	110164321	+	1	NA	Intergenic	Intergenic	42259	NM_009516	22390	Mm.287173	NM_009516	ENSMUSG00000031016	Wee1	Wee1A	WEE 1 homolog 1 (S. pombe)	protein-coding
mm_118227.1	chr13	111449224	111449272	-	1	NA	intron (NM_001122963, intron 5 of 11)	ID4_|SINE|ID	40793	NM_028487	73274	Mm.57286	NM_028487	ENSMUSG00000032745	Gpbp1	1700034P14Rik|AU019836|D230035M11Rik|Gpbp|mGPBP	GC-rich promoter binding protein 1	protein-coding
mm_110735.1	chr12	69790282	69790298	-	1	NA	promoter-TSS (NR_033573)	promoter-TSS (NR_033573)	-54	NR_033573	74724	Mm.399254	NR_033573		4930512B01Rik	4930472D12Rik	RIKEN cDNA 4930512B01 gene	ncRNA
mm_67100.1	chr7	69909558	69909563	-	1	NA	Intergenic	Intergenic	413466	NR_045940	73796	Mm.410832	NR_045940	ENSMUSG00000108885	4930402F11Rik	-	RIKEN cDNA 4930402F11 gene	ncRNA
mm_164776.1	chr17	94774460	94774505	+	1	NA	intron (NR_024720, intron 9 of 9)	RLTR13D6|LTR|ERVK	24382	NR_024720	77022	Mm.440259	NR_024720	ENSMUSG00000098090	2700099C18Rik	9430041D22Rik	NDC80 homolog, kinetochore complex component pseudogene	pseudo
mm_151293.1	chr19	55412491	55412538	+	1	NA	intron (NM_001293685, intron 6 of 8)	intron (NM_001293685, intron 6 of 8)	96457	NM_001293686	53611	Mm.258637	NM_016862	ENSMUSG00000024983	Vti1a	1110014F16Rik|1110018K19Rik|4921537J05Rik|MVti1|MVti1a|Vti1|Vti1-rp2	vesicle transport through interaction with t-SNAREs 1A	protein-coding
mm_156348.1	chrX	139210032	139210046	+	1	NA	promoter-TSS (NM_175541)	promoter-TSS (NM_175541)	-5	NM_175541	245631	Mm.131001	NM_175541	ENSMUSG00000042515	Mum1l1	9430086K21Rik	melanoma associated antigen (mutated) 1-like 1	protein-coding
mm_56479.1	chr6	99095604	99095613	-	1	NA	intron (NM_001347345, intron 5 of 19)	intron (NM_001347345, intron 5 of 19)	-67310	NM_001197322	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_102539.1	chr11	61267088	61267101	-	1	NA	promoter-TSS (NM_007437)	promoter-TSS (NM_007437)	92	NM_001331114	11671	Mm.398221	NM_007437	ENSMUSG00000010025	Aldh3a2	AI194803|Ahd-3|Ahd-3r|Ahd3|Ahd3-r|Aldh4|Aldh4-r|FALDH	aldehyde dehydrogenase family 3, subfamily A2	protein-coding
mm_23402.1	chr3	58062101	58062104	+	1	NA	Intergenic	ORR1B2|LTR|ERVL-MaLR	101705	NR_040538	67850	Mm.416968	NR_040538	ENSMUSG00000100666	1700007F19Rik	-	RIKEN cDNA 1700007F19 gene	ncRNA
mm_39606.1	chr5	24100696	24100698	+	1	NA	5' UTR (NM_026448, exon 1 of 11)	5' UTR (NM_026448, exon 1 of 11)	107	NM_001161800	52323	Mm.273768	NM_026448	ENSMUSG00000028986	Klhl7	2700038B03Rik|D5Ertd363e|SBBI26	kelch-like 7	protein-coding
mm_107176.1	chr12	24864151	24864154	+	1	NA	intron (NM_001083341, intron 1 of 11)	intron (NM_001083341, intron 1 of 11)	32553	NM_001083341	67216	Mm.167671	NM_026037	ENSMUSG00000020646	Mboat2	2810049G06Rik|AU022889|AW547221|LPCAT4|Moact2|Oact2	membrane bound O-acyltransferase domain containing 2	protein-coding
mm_51603.1	chr6	84008937	84008946	+	1	NA	exon (NM_001077694, exon 1 of 55)	exon (NM_001077694, exon 1 of 55)	343	NM_001077694	26903	Mm.220982	NM_021469	ENSMUSG00000033788	Dysf	2310004N10Rik|AI604795|D6Pas3	dysferlin	protein-coding
mm_84862.1	chr9	78585126	78585135	-	1	NA	intron (NM_001276452, intron 1 of 10)	RLTR18B|LTR|ERVK	2915	NM_172773	235504	Mm.46932	NM_172773	ENSMUSG00000049624	Slc17a5	4631416G20Rik|4732491M05|AST|ISSD|NSD|SD|SIALIN|SIASD|SLD	solute carrier family 17 (anion/sugar transporter), member 5	protein-coding
mm_128860.1	chr15	72806715	72806726	-	1	NA	non-coding (NR_002864, exon 1 of 1)	non-coding (NR_002864, exon 1 of 1)	3604	NR_002864	353342	Mm.440245	NR_002864	ENSMUSG00000106847	Peg13	-	paternally expressed 13	ncRNA
mm_64885.1	chr7	15920100	15920114	-	1	NA	exon (NM_009156, exon 4 of 6)	exon (NM_009156, exon 4 of 6)	2264	NM_009156	20364	Mm.42829	NM_009156	ENSMUSG00000041571	Selenow	Sepw1|selW	selenoprotein W	protein-coding
mm_29951.1	chr3	133091765	133091783	-	1	NA	promoter-TSS (NM_026231)	promoter-TSS (NM_026231)	-34	NM_026231	67553	Mm.304899	NM_026231	ENSMUSG00000028018	Gstcd	4933434L15Rik	glutathione S-transferase, C-terminal domain containing	protein-coding
mm_92190.1	chr10	68106738	68106743	-	1	NA	intron (NM_023598, intron 8 of 9)	intron (NM_023598, intron 8 of 9)	127142	NM_001081346	170799	Mm.209844	NM_133244	ENSMUSG00000037846	Rtkn2	B130039D23Rik|Mbf|Plekhk1	rhotekin 2	protein-coding
mm_62052.1	chr7	92447380	92447391	+	1	NA	3' UTR (NM_001243047, exon 11 of 11)	3' UTR (NM_001243047, exon 11 of 11)	-113764	NM_025515	66365	Mm.21173	NM_025515	ENSMUSG00000030613	Ccdc90b	2310015N07Rik|C86558	coiled-coil domain containing 90B	protein-coding
mm_140588.1	chr17	10216386	10216412	-	1	NA	exon (NM_001159517, exon 6 of 8)	exon (NM_001159517, exon 6 of 8)	102962	NM_021881	19317	Mm.130694	NM_021881	ENSMUSG00000062078	Qk	1110003F05Rik|1500005P18|QkI|l(17)-1Wis|l17Wis1	quaking	protein-coding
mm_128898.1	chr15	73284762	73284771	-	1	NA	intron (NM_001130409, intron 15 of 29)	PB1D10|SINE|Alu	-29884	NR_029561	387169		NR_029561	ENSMUSG00000065612	Mir151	Mirn151|mir-151|mmu-mir-151	microRNA 151	ncRNA
mm_45565.1	chr5	73212607	73212622	-	1	NA	intron (NM_028194, intron 2 of 62)	intron (NM_028194, intron 2 of 62)	44004	NM_028194	72313	Mm.260594	NM_028194	ENSMUSG00000070733	Fryl	2010313D22Rik|2310004H21Rik|2510002A14Rik|9030227G01Rik|mKIAA0826	FRY like transcription coactivator	protein-coding
mm_65187.1	chr7	19696520	19696529	-	1	NA	exon (NM_009696, exon 4 of 4)	exon (NM_009696, exon 4 of 4)	1874	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_19138.1	chr2	80447088	80447090	-	1	NA	5' UTR (NM_011356, exon 1 of 6)	5' UTR (NM_011356, exon 1 of 6)	307	NM_011356	20378	Mm.427436	NM_011356	ENSMUSG00000027004	Frzb	Frp|Sfrp3|frezzled|fritz|frzb-1	frizzled-related protein	protein-coding
mm_14569.1	chr2	135262424	135262427	+	1	NA	intron (NM_019677, intron 9 of 32)	intron (NM_019677, intron 9 of 32)	-46809	NR_040517	78805	Mm.78702	NR_040517	ENSMUSG00000085247	4930545L23Rik	-	RIKEN cDNA 4930545L23 gene	ncRNA
mm_27013.1	chr3	26027088	26027099	-	1	NA	intron (NM_138666, intron 3 of 7)	(TG)n|Simple_repeat|Simple_repeat	126214	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_147325.1	chr18	42262143	42262153	-	1	NA	promoter-TSS (NM_134137)	promoter-TSS (NM_134137)	-77	NM_134137	107045	Mm.312170	NM_134137	ENSMUSG00000024493	Lars	2310045K21Rik|3110009L02Rik|AW536573|mKIAA1352	leucyl-tRNA synthetase	protein-coding
mm_43210.1	chr5	129235035	129235038	+	1	NA	Intergenic	Intergenic	138286	NM_001347486	243277	Mm.440501	NM_177734	ENSMUSG00000044017	Adgrd1	E230012M21Rik|Gpr133	adhesion G protein-coupled receptor D1	protein-coding
mm_142218.1	chr17	37185460	37185460	-	1	NA	Intergenic	Intergenic	-8432	NM_023137	24108	Mm.140210	NM_023137	ENSMUSG00000035186	Ubd	FAT10	ubiquitin D	protein-coding
mm_108356.1	chr12	80644503	80644525	+	1	NA	promoter-TSS (NM_007951)	promoter-TSS (NM_007951)	299	NM_026244	328133	Mm.238279	NM_026244	ENSMUSG00000048833	Slc39a9	2010002A02Rik|2610511I23Rik|4833420E20Rik|AW209151	solute carrier family 39 (zinc transporter), member 9	protein-coding
mm_44836.1	chr5	34165030	34165034	-	1	NA	intron (NM_146159, intron 3 of 4)	B4A|SINE|B4	4392	NM_146159	231123	Mm.319286	NM_146159	ENSMUSG00000079555	Haus3	D4S43h|D5H4S43|D5H4S43E	HAUS augmin-like complex, subunit 3	protein-coding
mm_34727.1	chr4	152178127	152178166	+	1	NA	promoter-TSS (NM_133348)	promoter-TSS (NM_133348)	46	NM_133348	70025	Mm.296191	NM_133348	ENSMUSG00000028937	Acot7	2410041A17Rik|Ach1|Act|Bach|CTE-IIa|Cte-II|Lach1	acyl-CoA thioesterase 7	protein-coding
mm_62142.1	chr7	97101258	97101272	+	1	NA	intron (NM_001162477, intron 1 of 9)	intron (NM_001162477, intron 1 of 9)	19514	NM_010248	14389	Mm.42033	NM_010248	ENSMUSG00000004508	Gab2	AI463667|D130058I17Rik|p97	growth factor receptor bound protein 2-associated protein 2	protein-coding
mm_169735.1	chr15	83406201	83406209	-	1	NA	intron (NM_001159509, intron 1 of 10)	(CCG)n|Simple_repeat|Simple_repeat	26645	NM_011862	23970	Mm.23978	NM_011862	ENSMUSG00000016664	Pacsin2	AI197433	protein kinase C and casein kinase substrate in neurons 2	protein-coding
mm_40355.1	chr5	47983148	47983162	+	1	NA	promoter-TSS (NM_001291227)	promoter-TSS (NM_001291227)	0	NR_111900	20563	Mm.289739	NM_178804	ENSMUSG00000031558	Slit2	Drad-1|E030015M03Rik|E130320P19Rik|Slil3|mKIAA4141|slit-2	slit homolog 2 (Drosophila)	protein-coding
mm_143248.1	chr17	64331966	64331977	-	1	NA	promoter-TSS (NM_001025309)	promoter-TSS (NM_001025309)	-88	NM_001025309	224938	Mm.489681	NM_144859	ENSMUSG00000024083	Pja2	AI447901|AL022700|Neurodap1|mKIAA0438	praja 2, RING-H2 motif containing	protein-coding
mm_46123.1	chr5	92470867	92470880	-	1	NA	intron (NM_007644, intron 2 of 11)	B4A|SINE|B4	12316	NR_105843	102466159		NR_105843	ENSMUSG00000099160	Mir6415	Gm27714|mmu-mir-6415	microRNA 6415	ncRNA
mm_84917.1	chr9	80067675	80067698	-	1	NA	intron (NM_001311110, intron 1 of 23)	CpG	783	NM_146003	215351	Mm.28232	NM_146003	ENSMUSG00000034252	Senp6	2810017C20Rik|E130319N12Rik|Susp1|mKIAA0797	SUMO/sentrin specific peptidase 6	protein-coding
mm_49753.1	chr6	34746545	34746557	+	1	NA	intron (NM_001347100, intron 5 of 13)	intron (NM_001347100, intron 5 of 13)	-33881	NM_001289657	76223	Mm.150047	NM_178630	ENSMUSG00000038836	Agbl3	2900053G10Rik|4930431N21Rik|6530406M24Rik|CCP3	ATP/GTP binding protein-like 3	protein-coding
mm_45210.1	chr5	52992324	52992351	-	1	NA	promoter-TSS (NR_040413)	promoter-TSS (NR_040413)	-45	NR_040413	75954	Mm.258937	NR_040413	ENSMUSG00000106352	5033403H07Rik	-	RIKEN cDNA 5033403H07 gene	ncRNA
mm_109493.1	chr12	111446022	111446036	+	1	NA	exon (NM_009396, exon 3 of 12)	exon (NM_009396, exon 3 of 12)	3368	NM_009396	21928	Mm.255332	NM_009396	ENSMUSG00000021281	Tnfaip2	B94|Exoc3l3|M-sec|Tnfip2|tnfb94	tumor necrosis factor, alpha-induced protein 2	protein-coding
mm_88764.1	chr10	80335103	80335115	+	1	NA	intron (NM_139292, intron 5 of 5)	intron (NM_139292, intron 5 of 5)	4964	NM_139292	70335	Mm.28147	NM_139292	ENSMUSG00000035504	Reep6	0610011M24Rik|Dp1l1	receptor accessory protein 6	protein-coding
mm_9135.1	chr1	170857454	170857463	-	1	NA	intron (NM_001081304, intron 1 of 15)	intron (NM_001081304, intron 1 of 15)	10313	NM_001081304	226641	Mm.377046	NM_001081304	ENSMUSG00000026663	Atf6	9130025P16Rik|9630036G24|AA789574|Atf6alpha|ESTM49	activating transcription factor 6	protein-coding
mm_69020.1	chr7	126792144	126792172	-	1	NA	exon (NM_019674, exon 2 of 9)	exon (NM_019674, exon 2 of 9)	313	NM_019674	56420	Mm.41998	NM_019674	ENSMUSG00000030697	Ppp4c	1110002D08Rik|AU016079|Ppx	protein phosphatase 4, catalytic subunit	protein-coding
mm_102.1	chr1	9545490	9545495	+	1	NA	promoter-TSS (NM_021511)	promoter-TSS (NM_021511)	84	NM_021511	59014	Mm.29061	NM_021511	ENSMUSG00000061024	Rrs1	5730466A07Rik|AA415037|D1Ertd701e|Rrr	ribosome biogenesis regulator 1	protein-coding
mm_7919.1	chr1	133800965	133800973	-	1	NA	Intergenic	Intergenic	-47222	NM_213616	381290	Mm.188617	NM_213616	ENSMUSG00000026463	Atp2b4	Pmca4	ATPase, Ca++ transporting, plasma membrane 4	protein-coding
mm_469.1	chr1	36372211	36372220	+	1	NA	promoter-TSS (NM_001277076)	promoter-TSS (NM_001277076)	-76	NM_001277076	100534273	Mm.389112	NM_001277076	ENSMUSG00000037432	Fer1l5	4930533C12Rik	fer-1-like 5 (C. elegans)	protein-coding
mm_95747.1	chr11	54866375	54866392	+	1	NA	promoter-TSS (NM_008248)	promoter-TSS (NM_008248)	-55	NM_008248	15254	Mm.425	NM_008248	ENSMUSG00000020267	Hint1	AA673479|Hint|Ipk1|PKCI-1|PRKCNH1	histidine triad nucleotide binding protein 1	protein-coding
mm_61572.1	chr7	79761374	79761377	+	1	NA	intron (NM_001037927, intron 6 of 17)	intron (NM_001037927, intron 6 of 17)	18212	NM_001037927	626359	Mm.387216	NM_001037927	ENSMUSG00000039099	Wdr93	EG626359	WD repeat domain 93	protein-coding
mm_28019.1	chr3	83045006	83045059	-	1	NA	exon (NM_181849, exon 4 of 8)	exon (NM_181849, exon 4 of 8)	4831	NM_181849	110135	Mm.30063	NM_181849	ENSMUSG00000033831	Fgb	2510049G14Rik	fibrinogen beta chain	protein-coding
mm_159269.1	chr2	163853786	163853786	+	1	NA	promoter-TSS (NM_001030292)	promoter-TSS (NM_001030292)	36	NM_001030292	241769	Mm.295337	NM_001030292	ENSMUSG00000035238	Kcnk15	KCNK11|KCNK14|KT3.3|TASK5	potassium channel, subfamily K, member 15	protein-coding
mm_47847.1	chr5	134434367	134434370	-	1	NA	intron (NM_001347488, intron 1 of 27)	intron (NM_001347488, intron 1 of 27)	21894	NM_001081465	57080	Mm.332735	NM_020331	ENSMUSG00000023079	Gtf2ird1	1700012P16Rik|BEN|Cream1|ESTM9|GTF3|Gtf2il|MusTRD1|Tg(Alb1-Myc)166.8Sst|WBSCR11|X83320	general transcription factor II I repeat domain-containing 1	protein-coding
mm_50604.1	chr6	49319291	49319367	+	1	NA	promoter-TSS (NM_175098)	promoter-TSS (NM_175098)	55	NM_001311112	57895	Mm.32416	NM_175098	ENSMUSG00000050786	Ccdc126	6330407D12Rik|AA675040|AI465320|AL022711	coiled-coil domain containing 126	protein-coding
mm_147901.1	chr18	65375402	65375416	-	1	NA	intron (NM_001037294, intron 2 of 12)	intron (NM_001037294, intron 2 of 12)	18479	NM_001037294	225638	Mm.296528	NM_001037294	ENSMUSG00000032845	Alpk2	Gm549|Hak	alpha-kinase 2	protein-coding
mm_54918.1	chr6	47800994	47801015	-	1	NA	exon (NM_009787, exon 7 of 10)	exon (NM_009787, exon 7 of 10)	2648	NR_030485	735289		NR_030485	ENSMUSG00000076060	Mir704	Mirn704|mir-704|mmu-mir-704	microRNA 704	ncRNA
mm_136037.1	chr16	77421787	77421797	-	1	NA	intron (NR_015543, intron 2 of 4)	intron (NR_015543, intron 2 of 4)	92464	NR_015543	77994	Mm.394688	NR_015543	ENSMUSG00000090386	Mir99ahg	2810055G20Rik|D730043B02Rik	Mir99a and Mirlet7c-1 host gene (non-protein coding)	ncRNA
mm_126665.1	chr15	84324441	84324463	+	1	NA	promoter-TSS (NM_022321)	promoter-TSS (NM_022321)	-268	NM_022321	64099	Mm.251356	NM_022321	ENSMUSG00000022439	Parvg	AI413459	parvin, gamma	protein-coding
mm_34811.1	chr4	154936141	154936150	+	1	NA	Intergenic	Intergenic	-8068	NM_178931	230979	Mm.215147	NM_178931	ENSMUSG00000042333	Tnfrsf14	Atar|HveA|Hvem|Tnfrs14	tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)	protein-coding
mm_112732.1	chr13	19213652	19213673	+	1	NA	Intergenic	Intergenic	182151	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_60797.1	chr7	45620809	45620837	+	1	NA	promoter-TSS (NM_001018013)	promoter-TSS (NM_001018013)	-988	NM_001018013	73456	Mm.380445	NM_001018013	ENSMUSG00000064158	Izumo1	1700058F15Rik|Izumo	izumo sperm-egg fusion 1	protein-coding
mm_49185.1	chr6	15185371	15185393	+	1	NA	promoter-TSS (NM_001286607)	promoter-TSS (NM_001286607)	-124	NM_212435	114142	Mm.332919	NM_053242	ENSMUSG00000029563	Foxp2	2810043D05Rik|AI449000|CAG-16|D0Kist7	forkhead box P2	protein-coding
mm_9714.1	chr1	179803165	179803170	-	1	NA	intron (NM_026375, intron 1 of 35)	CpG	848	NM_026375	226747	Mm.128165	NM_026375	ENSMUSG00000026491	Ahctf1	6230412P20Rik|AV011447|Elys	AT hook containing transcription factor 1	protein-coding
mm_168517.1	chr11	58199595	58199596	+	1	NA	promoter-TSS (NM_018738)	promoter-TSS (NM_018738)	39	NM_018738	16145	Mm.33902	NM_018738	ENSMUSG00000078853	Igtp	AW558444|Irgm3	interferon gamma induced GTPase	protein-coding
mm_5299.1	chr1	21291680	21291682	-	1	NA	intron (NR_002858, intron 3 of 5)	PB1D10|SINE|Alu	6631	NR_002858	241041	Mm.290634	NR_002858	ENSMUSG00000025936	Gm4956	EG241041	predicted gene 4956	pseudo
mm_132910.1	chr16	48872951	48872961	+	1	NA	exon (NM_181596, exon 2 of 4)	exon (NM_181596, exon 2 of 4)	348	NM_181596	245195	Mm.231288	NM_181596	ENSMUSG00000022651	Retnlg	Fizz3|Relmg|Xcp1	resistin like gamma	protein-coding
mm_150101.1	chr19	29485740	29485753	+	1	NA	Intergenic	Intergenic	36241	NR_015567	77779	Mm.458738	NR_015567	ENSMUSG00000097855	A930007I19Rik	-	RIKEN cDNA A930007I19 gene	ncRNA
mm_74620.1	chr8	13090132	13090135	-	1	NA	intron (NM_178708, intron 7 of 13)	B1_Mus1|SINE|Alu	15210	NM_178708	234069	Mm.103427	NM_178708	ENSMUSG00000038542	Pcid2	A730042J05Rik	PCI domain containing 2	protein-coding
mm_62763.1	chr7	112225858	112225900	+	1	NA	promoter-TSS (NM_177282)	promoter-TSS (NM_177282)	43	NM_001193305	320878	Mm.52312	NM_177282	ENSMUSG00000038244	Mical2	5330438E18Rik|9530064J02|MICAL-2|mKIAA0750	microtubule associated monooxygenase, calponin and LIM domain containing 2	protein-coding
mm_44438.1	chr5	21424642	21424659	-	1	NA	promoter-TSS (NM_177869)	promoter-TSS (NM_177869)	27	NM_029195	75172	Mm.426695	NM_029195	ENSMUSG00000064280	Ccdc146	4930528G09Rik|mKIAA1505	coiled-coil domain containing 146	protein-coding
mm_42901.1	chr5	122491734	122491740	+	1	NA	exon (NM_009722, exon 4 of 21)	exon (NM_009722, exon 4 of 21)	10488	NM_001110140	11938	Mm.227583	NM_009722	ENSMUSG00000029467	Atp2a2	9530097L16Rik|D5Wsu150e|SERCA2|SERCA2B|Serca2a|mKIAA4195	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	protein-coding
mm_171487.1	chr4	146097307	146097325	+	1	NA	promoter-TSS (NM_001037926)	promoter-TSS (NM_001037926)	4	NM_001037926	626316	Mm.270762	NM_001037926	ENSMUSG00000066009	Zfp987	Gm13051|OTTMUSG00000010104|OTTMUSG00000010173	zinc finger protein 987	protein-coding
mm_55587.1	chr6	71440466	71440523	-	1	NA	5' UTR (NM_024288, exon 1 of 9)	5' UTR (NM_024288, exon 1 of 9)	143	NM_024288	68477	Mm.28474	NM_024288	ENSMUSG00000002222	Rmnd5a	1110007A06Rik|AJ237586|AW125795|Gid2|MTA.D02.090	required for meiotic nuclear division 5 homolog A	protein-coding
mm_129310.1	chr15	77659845	77659849	-	1	NA	Intergenic	Intergenic	-16561	NM_001143686	328563	Mm.17957	NM_001143686	ENSMUSG00000091694	Apol11b	A330102K04Rik	apolipoprotein L 11b	protein-coding
mm_70017.1	chr7	142512282	142512304	-	1	NA	exon (NM_001163669, exon 14 of 17)	exon (NM_001163669, exon 14 of 17)	-5522	NR_033261	677289	Mm.350054	NR_033261	ENSMUSG00000043795	Prr33	ENSMUSG00000043795|Gm14492|OTTMUSG00000016823	proline rich 33	ncRNA
mm_112455.1	chr13	5864692	5864702	+	1	NA	intron (NM_011803, intron 1 of 3)	intron (NM_011803, intron 1 of 3)	3208	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_86166.1	chr9	118887217	118887229	-	1	NA	intron (NM_001113514, intron 12 of 13)	ORR1B2|LTR|ERVL-MaLR	-39313	NM_133710	69274	Mm.439928	NM_133710	ENSMUSG00000047409	Ctdspl	2810418J22Rik|AI426263|HYA22|SCP3	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase-like	protein-coding
mm_43526.1	chr5	137152868	137152877	+	1	NA	Intergenic	Intergenic	-36665	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_168470.1	chr1	14865277	14865286	+	1	NA	Intergenic	Intergenic	53581	NM_177781	277328	Mm.186329	NM_177781	ENSMUSG00000032769	Trpa1	Anktm1|TRPA1b	transient receptor potential cation channel, subfamily A, member 1	protein-coding
mm_106497.1	chr11	120348514	120348559	-	1	NA	promoter-TSS (NM_009609)	promoter-TSS (NM_009609)	-41	NM_009609	11465	Mm.196173	NM_009609	ENSMUSG00000062825	Actg1	AL023024|Actg|Actl|E51	actin, gamma, cytoplasmic 1	protein-coding
mm_155777.1	chrX	96455413	96455450	+	1	NA	promoter-TSS (NM_010417)	promoter-TSS (NM_010417)	-5	NM_001159628	15203	Mm.277092	NM_010417	ENSMUSG00000031209	Heph	C130006F04Rik|Cpl|mKIAA0698|sla	hephaestin	protein-coding
mm_148416.1	chr19	3935794	3935838	+	1	NA	exon (NM_019449, exon 2 of 11)	exon (NM_019449, exon 2 of 11)	630	NM_001161428	54445	Mm.262094	NM_019449	ENSMUSG00000036908	Unc93b1	Unc-93B1|Unc93b	unc-93 homolog B1 (C. elegans)	protein-coding
mm_23334.1	chr3	54367600	54367619	+	1	NA	exon (NM_015784, exon 4 of 22)	exon (NM_015784, exon 4 of 22)	6502	NM_015784	50706	Mm.236067	NM_015784	ENSMUSG00000027750	Postn	A630052E07Rik|AI747096|OSF-2|Osf2|PLF|PN	periostin, osteoblast specific factor	protein-coding
mm_581.1	chr1	39367817	39367848	+	1	NA	promoter-TSS (NM_053257)	promoter-TSS (NM_053257)	-19	NM_053257	114641	Mm.379302	NM_053257	ENSMUSG00000073702	Rpl31	Dts	ribosomal protein L31	protein-coding
mm_45315.1	chr5	65435807	65435829	-	1	NA	promoter-TSS (NM_009466)	promoter-TSS (NM_009466)	24	NM_009466	22235	Mm.344831	NM_009466	ENSMUSG00000029201	Ugdh	Udpgdh	UDP-glucose dehydrogenase	protein-coding
mm_156013.1	chrX	107089343	107089383	+	1	NA	promoter-TSS (NM_172435)	promoter-TSS (NM_172435)	28	NM_172435	78826	Mm.74639	NM_172435	ENSMUSG00000050921	P2ry10	5830408N17Rik|Lypsr2|P2Y10	purinergic receptor P2Y, G-protein coupled 10	protein-coding
mm_60576.1	chr7	44481691	44481701	+	1	NA	Intergenic	Intergenic	-2821	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_114674.1	chr13	80883404	80883422	+	1	NA	promoter-TSS (NM_001042591)	promoter-TSS (NM_001042591)	-9	NM_001042591	105171	Mm.423137	NM_001042591	ENSMUSG00000074794	Arrdc3	AI450344|mKIAA1376	arrestin domain containing 3	protein-coding
mm_91754.1	chr10	50589601	50589623	-	1	NA	Intergenic	RMER6A|LTR|ERVK	-3057	NM_198007	77987	Mm.222497	NM_198007	ENSMUSG00000038774	Ascc3	ASC1p200|B630009I04Rik|BC023451|D430001L07Rik|D630041L21|Helic1|RNAH	activating signal cointegrator 1 complex subunit 3	protein-coding
mm_70363.1	chr8	8661820	8661826	+	1	NA	Intergenic	CpG-13817	-1050	NM_010111	13642	Mm.209813	NM_010111	ENSMUSG00000001300	Efnb2	ELF-2|Epl5|Eplg5|Htk-L|LERK-5|Lerk5|NLERK-1	ephrin B2	protein-coding
mm_60810.1	chr7	45643954	45643966	+	1	NA	intron (NM_172418, intron 7 of 9)	intron (NM_172418, intron 7 of 9)	3983	NM_172418	74490	Mm.107442	NM_172418	ENSMUSG00000042918	Mamstr	2810022D01Rik|5430432N15Rik|AW743872|Mastr	MEF2 activating motif and SAP domain containing transcriptional regulator	protein-coding
mm_143853.1	chr17	84161229	84161245	-	1	NA	Intergenic	Intergenic	26710	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_108521.1	chr12	84053350	84053383	+	1	NA	5' UTR (NM_134246, exon 2 of 4)	5' UTR (NM_134246, exon 2 of 4)	1215	NM_134246	171281	Mm.202331	NM_134246	ENSMUSG00000021228	Acot3	AW108394|PTE-Ia|Pte2a	acyl-CoA thioesterase 3	protein-coding
mm_9080.1	chr1	168431647	168431666	-	1	NA	5' UTR (NM_001291509, exon 1 of 7)	5' UTR (NM_001291509, exon 1 of 7)	513	NM_001291508	18514	Mm.43358	NM_008783	ENSMUSG00000052534	Pbx1	2310056B04Rik|D230003C07Rik|Pbx-1	pre B cell leukemia homeobox 1	protein-coding
mm_71149.1	chr8	39298791	39298804	+	1	NA	intron (NR_044988, intron 1 of 3)	intron (NR_044988, intron 1 of 3)	817	NR_044988	621335	Mm.208080	NR_044988	ENSMUSG00000109827	Gm6213	EG621335	predicted gene 6213	ncRNA
mm_160910.1	chr11	82897564	82897564	+	1	NA	exon (NM_030224, exon 2 of 4)	exon (NM_030224, exon 2 of 4)	5419	NM_030224	78919	Mm.286733	NM_030224	ENSMUSG00000018844	Fndc8	4930466G16Rik	fibronectin type III domain containing 8	protein-coding
mm_62204.1	chr7	97830944	97830967	+	1	NA	Intergenic	Intergenic	-11984	NM_011035	18479	Mm.260227	NM_011035	ENSMUSG00000030774	Pak1	AW045634|PAK-1|Paka	p21 protein (Cdc42/Rac)-activated kinase 1	protein-coding
mm_64048.1	chr7	140835304	140835316	+	1	NA	promoter-TSS (NM_029821)	promoter-TSS (NM_029821)	172	NM_001347605	76974	Mm.272359	NM_029821	ENSMUSG00000025481	Urah	1190003J15Rik|2810420C16Rik	urate (5-hydroxyiso-) hydrolase	protein-coding
mm_89936.1	chr10	111254213	111254217	+	1	NA	intron (NM_175489, intron 4 of 23)	intron (NM_175489, intron 4 of 23)	-44464	NM_027914	71769	Mm.45256	NM_027914	ENSMUSG00000035759	Bbs10	1300007O09Rik|AI452285	Bardet-Biedl syndrome 10 (human)	protein-coding
mm_136497.1	chr16	96220530	96220559	-	1	NA	exon (NM_015825, exon 5 of 8)	exon (NM_015825, exon 5 of 8)	-15257	NM_001122993	93961	Mm.154783	NM_033149	ENSMUSG00000074892	B3galt5	1190002B21Rik|AU045265|b3Galt-V	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 5	protein-coding
mm_143333.1	chr17	66481475	66481487	-	1	NA	Intergenic	RMER17C|LTR|ERVK	-31731	NM_001114098	68617	Mm.33421	NM_172963	ENSMUSG00000052105	Mtcl1	1110012J17Rik|Ccdc165|D130071O13|Kiaa0802|Soga2|mKIAA0802|t8219b25	microtubule crosslinking factor 1	protein-coding
mm_132823.1	chr16	45224326	45224346	+	1	NA	promoter-TSS (NM_001037719)	promoter-TSS (NM_001037719)	-1	NM_001037719	208154	Mm.38199	NM_177584	ENSMUSG00000052013	Btla	A630002H24	B and T lymphocyte associated	protein-coding
mm_149482.1	chr19	11770419	11770440	+	1	NA	promoter-TSS (NM_025606)	promoter-TSS (NM_025606)	14	NM_025606	94063	Mm.203928	NM_025606	ENSMUSG00000024683	Mrpl16	2310039D06Rik	mitochondrial ribosomal protein L16	protein-coding
mm_172246.1	chr6	69305415	69305419	-	1	NA	Intergenic	Intergenic	21757	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_63069.1	chr7	122148288	122148296	+	1	NA	3' UTR (NM_021608, exon 6 of 6)	3' UTR (NM_021608, exon 6 of 6)	-11143	NM_011121	18817	Mm.16525	NM_011121	ENSMUSG00000030867	Plk1	Plk|STPK13	polo-like kinase 1	protein-coding
mm_15709.1	chr2	164017588	164017604	+	1	NA	3' UTR (NM_018753, exon 6 of 6)	3' UTR (NM_018753, exon 6 of 6)	-7628	NM_001114079	381404	Mm.82301	NM_001114079	ENSMUSG00000054582	Pabpc1l	1810053B01Rik|Epab	poly(A) binding protein, cytoplasmic 1-like	protein-coding
mm_125397.1	chr15	41447384	41447414	+	1	NA	promoter-TSS (NM_001130166)	promoter-TSS (NM_001130166)	-83	NM_001130166	170719	Mm.254267	NM_130885	ENSMUSG00000022307	Oxr1	2210416C20Rik|C7|C7B	oxidation resistance 1	protein-coding
mm_89566.1	chr10	95417236	95417267	+	1	NA	promoter-TSS (NM_007706)	promoter-TSS (NM_007706)	-124	NR_045339	70523	Mm.158398	NR_045338	ENSMUSG00000097766	5730420D15Rik	-	RIKEN cDNA 5730420D15 gene	ncRNA
mm_46524.1	chr5	105346520	105346548	-	1	NA	promoter-TSS (NM_001039647)	promoter-TSS (NM_001039647)	-58	NR_132129	634650	Mm.458435	NM_001039647	ENSMUSG00000092021	Gbp11	EG634650|Gm7141	guanylate binding protein 11	protein-coding
mm_137008.1	chr17	17827135	17827163	+	1	NA	Intergenic	CpG	-3039	NR_029536	387230		NR_029536	ENSMUSG00000065396	Mir99b	Mirn99b|mmu-mir-99b	microRNA 99b	ncRNA
mm_36923.1	chr4	108144987	108145020	-	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-20434	NM_026728	52430	Mm.270783	NM_026728	ENSMUSG00000028601	Echdc2	1300017C12Rik|2610009M20Rik|D4Ertd765e	enoyl Coenzyme A hydratase domain containing 2	protein-coding
mm_30129.1	chr3	141982207	141982221	-	1	NA	promoter-TSS (NM_007560)	promoter-TSS (NM_007560)	50	NM_007560	12167	Mm.39089	NM_007560	ENSMUSG00000052430	Bmpr1b	AI385617|ALK-6|AV355320|Acvrlk6|Alk6|BMPR-1B|BMPR-IB|CFK-43a|SKR6	bone morphogenetic protein receptor, type 1B	protein-coding
mm_103635.1	chr11	78950127	78950141	-	1	NA	exon (NM_010927, exon 20 of 27)	exon (NM_010927, exon 20 of 27)	24843	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_8543.1	chr1	155099471	155099481	-	1	NA	5' UTR (NM_010500, exon 1 of 1)	5' UTR (NM_010500, exon 1 of 1)	160	NM_010500	15939	Mm.12246	NM_010500	ENSMUSG00000056708	Ier5	-	immediate early response 5	protein-coding
mm_60652.1	chr7	44859747	44859747	+	1	NA	exon (NM_021549, exon 4 of 16)	exon (NM_021549, exon 4 of 16)	2344	NM_001290767	59047	Mm.238254	NM_021549	ENSMUSG00000002963	Pnkp	1810009G08Rik|PNK	polynucleotide kinase 3'- phosphatase	protein-coding
mm_30115.1	chr3	139075179	139075253	-	1	NA	promoter-TSS (NM_001286759)	promoter-TSS (NM_001286759)	-15	NM_001040690	229877	Mm.28893	NM_145544	ENSMUSG00000028149	Rap1gds1	BC011279|GDS1	RAP1, GTP-GDP dissociation stimulator 1	protein-coding
mm_86877.1	chr10	21997098	21997112	+	1	NA	intron (NM_001161848, intron 8 of 11)	intron (NM_001161848, intron 8 of 11)	2439	NM_011361	20393	Mm.28405	NM_011361	ENSMUSG00000019970	Sgk1	Sgk	serum/glucocorticoid regulated kinase 1	protein-coding
mm_70312.1	chr8	4238816	4238886	+	1	NA	5' UTR (NM_001164172, exon 1 of 12)	5' UTR (NM_001164172, exon 1 of 12)	111	NM_001164172	26400	Mm.3906	NM_011944	ENSMUSG00000002948	Map2k7	5930412N11Rik|JNKK 2|Jnkk2|MAPKK 7|MEK 7|Mapkk7|Mek7|Mkk7|Prkmk7|sek2	mitogen-activated protein kinase kinase 7	protein-coding
mm_59005.1	chr7	19181294	19181325	+	1	NA	promoter-TSS (NR_029763)	promoter-TSS (NR_029763)	139	NM_028153	72205	Mm.154121	NM_028153	ENSMUSG00000040811	Eml2	1600029N02Rik|EMAP-2	echinoderm microtubule associated protein like 2	protein-coding
mm_18776.1	chr2	73529709	73529721	-	1	NA	promoter-TSS (NM_153138)	promoter-TSS (NM_153138)	-228	NM_153138	215280	Mm.223504	NM_153138	ENSMUSG00000075284	Wipf1	AI115543|D2Ertd120e|WIP|Waspip	WAS/WASL interacting protein family, member 1	protein-coding
mm_128782.1	chr15	66801622	66801637	-	1	NA	intron (NM_001029841, intron 1 of 7)	intron (NM_001029841, intron 1 of 7)	30200	NM_001029841	20491	Mm.7601	NM_009192	ENSMUSG00000022372	Sla	Slap|Slap-1	src-like adaptor	protein-coding
mm_82774.1	chr9	26999492	26999557	-	1	NA	promoter-TSS (NM_144543)	promoter-TSS (NM_144543)	25	NM_025862	66948	Mm.289244	NM_025862	ENSMUSG00000031969	Acad8	2310016C19Rik|AI786953	acyl-Coenzyme A dehydrogenase family, member 8	protein-coding
mm_107610.1	chr12	49384962	49384972	+	1	NA	exon (NM_008241, exon 2 of 2)	exon (NM_008241, exon 2 of 2)	1960	NM_008241	15228	Mm.4704	NM_008241	ENSMUSG00000020950	Foxg1	2900064B05Rik|BF-1|Bf1|Hfh9|Hfhbf1	forkhead box G1	protein-coding
mm_65893.1	chr7	30090400	30090435	-	1	NA	promoter-TSS (NM_152814)	promoter-TSS (NM_152814)	93	NM_152814	72556	Mm.441512	NM_152814	ENSMUSG00000078768	Zfp566	2700043M03Rik|mszf4	zinc finger protein 566	protein-coding
mm_53153.1	chr6	125265588	125265598	+	1	NA	promoter-TSS (NR_015527)	promoter-TSS (NR_015527)	68	NR_015527	73870	Mm.440681	NR_015527	ENSMUSG00000108129	4930417O13Rik	-	RIKEN cDNA 4930417O13 gene	ncRNA
mm_36154.1	chr4	59581428	59581438	-	1	NA	promoter-TSS (NM_024255)	promoter-TSS (NM_024255)	-130	NM_001301367	72479	Mm.272905	NM_024255	ENSMUSG00000028383	Hsdl2	2610207I16Rik	hydroxysteroid dehydrogenase like 2	protein-coding
mm_96372.1	chr11	67237765	67237776	+	1	NA	promoter-TSS (NM_010855)	promoter-TSS (NM_010855)	-42	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_52915.1	chr6	122847970	122847976	+	1	NA	3' UTR (NM_009779, exon 2 of 2)	3' UTR (NM_009779, exon 2 of 2)	8184	NM_009779	12267	Mm.2408	NM_009779	ENSMUSG00000040552	C3ar1	AZ3B|C3AR|HNFAG09	complement component 3a receptor 1	protein-coding
mm_150422.1	chr19	37388128	37388132	+	1	NA	intron (NM_010615, intron 6 of 21)	intron (NM_010615, intron 6 of 21)	11727	NM_010615	16551	Mm.42203	NM_010615	ENSMUSG00000012443	Kif11	Eg5|Kif8|Kifl1|Knsl1	kinesin family member 11	protein-coding
mm_47140.1	chr5	120548330	120548340	-	1	NA	intron (NM_145853, intron 12 of 27)	intron (NM_145853, intron 12 of 27)	37143	NM_001177594	170756	Mm.291070	NM_133221	ENSMUSG00000032754	Slc8b1	AF261233|NCKX6|NCLX|Slc24a6	solute carrier family 8 (sodium/lithium/calcium exchanger), member B1	protein-coding
mm_104874.1	chr11	99422253	99422260	-	1	NA	promoter-TSS (NM_010661)	promoter-TSS (NM_010661)	3	NM_010661	268482	Mm.436651	NM_010661	ENSMUSG00000020912	Krt12	AI835216|K12|Krt-12|Krt1-12	keratin 12	protein-coding
mm_79046.1	chr9	46228702	46228714	+	1	NA	promoter-TSS (NM_009692)	promoter-TSS (NM_009692)	78	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2|apo-AI|apoA-I	apolipoprotein A-I	protein-coding
mm_125037.1	chr15	25773986	25774042	+	1	NA	intron (NM_019472, intron 19 of 40)	intron (NM_019472, intron 19 of 40)	-69284	NM_001034851	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_163949.1	chr14	52610357	52610364	+	1	NA	Intergenic	ORR1A1|LTR|ERVL-MaLR	-114665	NM_001170918	57269	Mm.88822	NM_020512	ENSMUSG00000059887	Olfr1507	MOR244-1|Mor28|Or28	olfactory receptor 1507	protein-coding
mm_4310.1	chr1	171844974	171844989	+	1	NA	intron (NM_001289470, intron 2 of 8)	intron (NM_001289470, intron 2 of 8)	5284	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_25603.1	chr3	117574883	117574905	+	1	NA	promoter-TSS (NM_029425)	promoter-TSS (NM_029425)	-333	NM_029425	75769	Mm.72187	NM_029425	ENSMUSG00000033342	Plppr5	4833424O15Rik|Lppr5|PRG-5|Pap2d	phospholipid phosphatase related 5	protein-coding
mm_57100.1	chr6	122590825	122590839	-	1	NA	intron (NM_001134391, intron 4 of 7)	intron (NM_001134391, intron 4 of 7)	11612	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_138726.1	chr17	36942911	36942924	+	1	NA	promoter-TSS (NM_001099632)	promoter-TSS (NM_001099632)	-134	NM_001099632	386454	Mm.105324	NM_001099632	ENSMUSG00000036492	Rnf39	BC038661|Gm1786|Gm1787|Gm320|LIRF	ring finger protein 39	protein-coding
mm_168770.1	chr12	14675942	14675947	+	1	NA	Intergenic	L1Md_T|LINE|L1	374445	NR_045960	73972	Mm.107680	NR_045960		4930448C13Rik	-	RIKEN cDNA 4930448C13 gene	ncRNA
mm_36239.1	chr4	63172018	63172024	-	1	NA	5' UTR (NM_010616, exon 1 of 19)	5' UTR (NM_010616, exon 1 of 19)	110	NM_010616	16552	Mm.216057	NM_010616	ENSMUSG00000028357	Kif12	-	kinesin family member 12	protein-coding
mm_73645.1	chr8	110847144	110847150	+	1	NA	promoter-TSS (NM_133953)	promoter-TSS (NM_133953)	123	NM_133973	102339	Mm.272930	NM_133973	ENSMUSG00000031753	Cog4	AW554810|D8Ertd515e	component of oligomeric golgi complex 4	protein-coding
mm_31981.1	chr4	89123315	89123325	+	1	NA	Intergenic	Intergenic	-14050	NM_024433	66902	Mm.28500	NM_024433	ENSMUSG00000062937	Mtap	1300019I21Rik|MSAP	methylthioadenosine phosphorylase	protein-coding
mm_17334.1	chr2	26556340	26556388	-	1	NA	Intergenic	Intergenic	-24692	NM_178444	353156	Mm.268933	NM_178444	ENSMUSG00000026921	Egfl7	VE-statin|Zneu1	EGF-like domain 7	protein-coding
mm_154699.1	chrX	8271386	8271453	+	1	NA	promoter-TSS (NM_172479)	promoter-TSS (NM_172479)	38	NM_172479	209837	Mm.6055	NM_172479	ENSMUSG00000031170	Slc38a5	C81234|E330031E14|JM24|SN2	solute carrier family 38, member 5	protein-coding
mm_161913.1	chr18	67392693	67392693	+	1	NA	intron (NM_026473, intron 2 of 3)	intron (NM_026473, intron 2 of 3)	1962	NM_026473	67951	Mm.181860	NM_026473	ENSMUSG00000001473	Tubb6	2310057H16Rik|BB220206	tubulin, beta 6 class V	protein-coding
mm_75129.1	chr8	34918551	34918579	-	1	NA	intron (NM_175091, intron 2 of 26)	intron (NM_175091, intron 2 of 26)	47125	NM_175091	21951	Mm.88364	NM_175091	ENSMUSG00000031529	Tnks	4930554K12Rik|AI662855|ARTD5|C86528|D130072O21Rik|TANK1|mTNKS1	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase	protein-coding
mm_66773.1	chr7	46827585	46827614	-	1	NA	Intergenic	Intergenic	-18205	NM_010699	16828	Mm.29324	NM_010699	ENSMUSG00000063229	Ldha	Ldh1|Ldhm|l7R2	lactate dehydrogenase A	protein-coding
mm_58263.1	chr6	145288244	145288260	-	1	NA	Intergenic	7SK|RNA|RNA	37700	NR_045598	100039495	Mm.121014	NR_045598	ENSMUSG00000086013	Gm15706	OTTMUSG00000025463	predicted gene 15706	ncRNA
mm_167703.1	chr9	90245302	90245350	-	1	NA	intron (NM_194334, intron 2 of 12)	intron (NM_194334, intron 2 of 12)	25443	NM_194334	67016	Mm.335347	NM_194334	ENSMUSG00000037410	Tbc1d2b	1810061M12Rik|AI480956|AV021536|AV023399|AW491493|mKIAA1055	TBC1 domain family, member 2B	protein-coding
mm_32578.1	chr4	110397765	110397808	+	1	NA	promoter-TSS (NM_001284190)	promoter-TSS (NM_001284190)	88	NM_030231	78933	Mm.435620	NM_030231	ENSMUSG00000061298	Agbl4	4930578N11Rik|4931433A01Rik	ATP/GTP binding protein-like 4	protein-coding
mm_83091.1	chr9	40321127	40321137	-	1	NA	intron (NM_172768, intron 4 of 19)	intron (NM_172768, intron 4 of 19)	-12340	NR_040728	73558	Mm.398307	NR_040728		1700110K17Rik	-	RIKEN cDNA 1700110K17 gene	ncRNA
mm_10121.1	chr2	3749250	3749260	+	1	NA	intron (NM_025626, intron 1 of 3)	intron (NM_025626, intron 1 of 3)	35797	NM_025626	66540	Mm.277864	NM_025626	ENSMUSG00000026655	Fam107b	3110001A13Rik|AA589595|AA959793|AI132312	family with sequence similarity 107, member B	protein-coding
mm_140386.1	chr17	87240945	87240947	+	1	NA	Intergenic	B4A|SINE|B4	25001	NM_176808	193813	Mm.30251	NM_139295	ENSMUSG00000024150	Mcfd2	1810021C21Rik|F5f8d|Lman1ip|Sdnsf	multiple coagulation factor deficiency 2	protein-coding
mm_168452.1	chr1	141189691	141189701	+	1	NA	Intergenic	L1Md_T|LINE|L1	-533294	NR_040604	75910	Mm.483845	NR_040604	ENSMUSG00000102368	4930590L20Rik	-	RIKEN cDNA 4930590L20 gene	ncRNA
mm_5089.1	chr1	4497367	4497391	-	1	NA	promoter-TSS (NM_001289467)	promoter-TSS (NM_001289467)	-25	NM_001289465	20671	Mm.279103	NM_011441	ENSMUSG00000025902	Sox17	-	SRY (sex determining region Y)-box 17	protein-coding
mm_115498.1	chr13	3893557	3893589	-	1	NA	promoter-TSS (NM_001047159)	promoter-TSS (NM_001047159)	8	NM_001047159	56349	Mm.22261	NM_019671	ENSMUSG00000021215	Net1	Net1a|mNET1	neuroepithelial cell transforming gene 1	protein-coding
mm_111057.1	chr12	80110319	80110325	-	1	NA	exon (NM_007564, exon 2 of 2)	exon (NM_007564, exon 2 of 2)	2691	NM_007564	12192	Mm.235132	NM_007564	ENSMUSG00000021127	Zfp36l1	AW742437|AW743212|Berg36|Brf1|D530020L18Rik|ERF1|TIS11b|cMG1	zinc finger protein 36, C3H type-like 1	protein-coding
mm_125238.1	chr15	34238179	34238189	+	1	NA	5' UTR (NM_033521, exon 1 of 7)	5' UTR (NM_033521, exon 1 of 7)	158	NM_033521	114128	Mm.197518	NM_033521	ENSMUSG00000022257	Laptm4b	C330023P13Rik|LAPTM4beta	lysosomal-associated protein transmembrane 4B	protein-coding
mm_132080.1	chr16	30190724	30190729	+	1	NA	Intergenic	Intergenic	76806	NM_027904	71756	Mm.290614	NM_027904	ENSMUSG00000023176	Cpn2	1300018K11Rik	carboxypeptidase N, polypeptide 2	protein-coding
mm_29386.1	chr3	108889800	108889808	-	1	NA	5' UTR (NM_177091, exon 1 of 13)	5' UTR (NM_177091, exon 1 of 13)	204	NM_177091	320181	Mm.244233	NM_177091	ENSMUSG00000045326	Fndc7	E230011A21Rik	fibronectin type III domain containing 7	protein-coding
mm_163629.1	chr13	58263230	58263243	+	1	NA	exon (NM_019832, exon 3 of 12)	exon (NM_019832, exon 3 of 12)	10952	NM_019832	56278	Mm.296625	NM_019832	ENSMUSG00000021552	Gkap1	42kDa|4933400B15Rik|D13Ertd340e|Gkap42	G kinase anchoring protein 1	protein-coding
mm_102832.1	chr11	69099914	69099931	-	1	NA	promoter-TSS (NM_001159367)	promoter-TSS (NM_001159367)	-236	NM_001159367	18626	Mm.7373	NM_011065	ENSMUSG00000020893	Per1	Hftm|Per|m-rigui|mPer1	period circadian clock 1	protein-coding
mm_166210.1	chr5	48766432	48766432	-	1	NA	intron (NM_001199244, intron 1 of 7)	intron (NM_001199244, intron 1 of 7)	123125	NM_030265	80334	Mm.160172	NM_030265	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding
mm_95327.1	chr11	46739784	46739798	+	1	NA	promoter-TSS (NM_001166632)	promoter-TSS (NM_001166632)	-432	NM_001166632	171283	Mm.17771	NM_134248	ENSMUSG00000040405	Havcr1	AI503787|KIM-1|TIM-1|Tim1|Timd1	hepatitis A virus cellular receptor 1	protein-coding
mm_46198.1	chr5	98030798	98030820	-	1	NA	5' UTR (NM_133738, exon 1 of 17)	5' UTR (NM_133738, exon 1 of 17)	153	NM_133738	71914	Mm.24842	NM_133738	ENSMUSG00000029338	Antxr2	2310046B19Rik|AW561899|CMG-2|CMG2|cI-35	anthrax toxin receptor 2	protein-coding
mm_37341.1	chr4	119658089	119658108	-	1	NA	intron (NM_008191, intron 1 of 2)	intron (NM_008191, intron 1 of 2)	847	NM_008191	14916	Mm.278	NM_008191	ENSMUSG00000032978	Guca2b	AV066530|Gcap2|Ugn	guanylate cyclase activator 2b (retina)	protein-coding
mm_98606.1	chr11	95842231	95842241	+	1	NA	promoter-TSS (NM_001284393)	promoter-TSS (NM_001284393)	-59	NM_023121	14710	Mm.46299	NM_023121	ENSMUSG00000038811	Gngt2	AV096488	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 2	protein-coding
mm_36444.1	chr4	82386762	82386775	-	1	NA	intron (NM_001113210, intron 2 of 11)	MIRb|SINE|MIR	119011	NM_001286127	18028	Mm.317947	NM_008687	ENSMUSG00000008575	Nfib	6720429L07Rik|CTF|E030026I10Rik|NF-I/B|NF1-B|NFI-B	nuclear factor I/B	protein-coding
mm_86368.1	chr9	123794826	123794843	-	1	NA	exon (NM_001110253, exon 17 of 18)	exon (NM_001110253, exon 17 of 18)	-11643	NM_030712	80901	Mm.124289	NM_030712	ENSMUSG00000048521	Cxcr6	BB217514|BONZO|STRL33	chemokine (C-X-C motif) receptor 6	protein-coding
mm_43728.1	chr5	139547996	139548004	+	1	NA	3' UTR (NM_013702, exon 3 of 3)	3' UTR (NM_013702, exon 3 of 3)	4102	NM_013702	22255	Mm.42190	NM_013702	ENSMUSG00000029546	Uncx	Chx4|Uncx4.1	UNC homeobox	protein-coding
mm_58164.1	chr6	142571292	142571297	-	1	NA	5' UTR (NM_008428, exon 1 of 3)	5' UTR (NM_008428, exon 1 of 3)	320	NM_001330363	16523	Mm.1482	NM_008428	ENSMUSG00000030247	Kcnj8	AI448900|Kir6.1|gnite|slmbr|sltr|uKATP-1	potassium inwardly-rectifying channel, subfamily J, member 8	protein-coding
mm_71983.1	chr8	70610391	70610412	+	1	NA	Intergenic	Intergenic	-2087	NM_133772	76900	Mm.6667	NM_133772	ENSMUSG00000070003	Ssbp4	1210002E11Rik|AW743380|Sspb4	single stranded DNA binding protein 4	protein-coding
mm_59652.1	chr7	28169771	28169781	+	1	NA	promoter-TSS (NM_007991)	promoter-TSS (NM_007991)	28	NM_007991	14113	Mm.4595	NM_007991	ENSMUSG00000046865	Fbl	AL022665|FIB|FLRN|RNU3IP1	fibrillarin	protein-coding
mm_45515.1	chr5	72504501	72504520	-	1	NA	promoter-TSS (NM_001122756)	promoter-TSS (NM_001122756)	30	NM_001122756	53419	Mm.332425	NM_016869	ENSMUSG00000005220	Corin	AV273130|Lrp4	corin	protein-coding
mm_53945.1	chr6	5193758	5193809	-	1	NA	5' UTR (NM_011134, exon 1 of 9)	5' UTR (NM_011134, exon 1 of 9)	163	NM_011134	18979	Mm.237657	NM_011134	ENSMUSG00000002588	Pon1	Pon	paraoxonase 1	protein-coding
mm_102833.1	chr11	69197446	69197491	-	1	NA	exon (NM_009661, exon 2 of 14)	exon (NM_009661, exon 2 of 14)	375	NM_009661	11688	Mm.289672	NM_009661	ENSMUSG00000020891	Alox8	15-LOX-2|15-LOX-B|8-LOX|8S-LOX|Alox15b	arachidonate 8-lipoxygenase	protein-coding
mm_149323.1	chr19	10842579	10842589	+	1	NA	promoter-TSS (NM_023044)	promoter-TSS (NM_023044)	40	NM_023044	65221	Mm.27387	NM_023044	ENSMUSG00000024737	Slc15a3	Ci1|cI-1	solute carrier family 15, member 3	protein-coding
mm_17588.1	chr2	30473475	30473521	-	1	NA	exon (NM_030244, exon 1 of 1)	exon (NM_030244, exon 1 of 1)	701	NM_030244	72500	Mm.295464	NM_030244	ENSMUSG00000089762	Ier5l	2610524G09Rik	immediate early response 5-like	protein-coding
mm_146884.1	chr18	25684794	25684797	-	1	NA	intron (NM_001146292, intron 1 of 12)	intron (NM_001146292, intron 1 of 12)	69188	NM_133195	108013	Mm.266435	NM_133195	ENSMUSG00000024268	Celf4	A230070D14Rik|BRUNOL-4|Brul4|Brunol4|C130060B05Rik	CUGBP, Elav-like family member 4	protein-coding
mm_86710.1	chr10	18845125	18845139	+	1	NA	promoter-TSS (NM_022032)	promoter-TSS (NM_022032)	61	NM_022032	64058	Mm.28209	NM_022032	ENSMUSG00000019851	Perp	1110017A08Rik|KCP1|KRTCAP1|PIGPC1|THW	PERP, TP53 apoptosis effector	protein-coding
mm_104626.1	chr11	97310291	97310307	-	1	NA	Intergenic	Intergenic	-5417	NM_025927	67036	Mm.5381	NM_025927	ENSMUSG00000018882	Mrpl45	2600005P05Rik|AU043542|R75241	mitochondrial ribosomal protein L45	protein-coding
mm_9059.1	chr1	167373522	167373525	-	1	NA	intron (NM_025569, intron 5 of 5)	B1_Mur4|SINE|Alu	20274	NM_025569	66447	Mm.218286	NM_025569	ENSMUSG00000026688	Mgst3	2010012L10Rik|2010306B17Rik|2700004G04Rik|AA516734|GST-III	microsomal glutathione S-transferase 3	protein-coding
mm_152563.1	chr19	11586758	11586823	-	1	NA	3' UTR (NM_026835, exon 7 of 7)	3' UTR (NM_026835, exon 7 of 7)	18014	NM_026835	68774	Mm.290390	NM_026835	ENSMUSG00000024679	Ms4a6d	1110058E16Rik|AI447446|Ms4a11	membrane-spanning 4-domains, subfamily A, member 6D	protein-coding
mm_64418.1	chr7	142575531	142575534	+	1	NA	TTS (NR_130974)	TTS (NR_130974)	1615	NR_030416	735280		NR_030416	ENSMUSG00000076275	Mir675	Mirn675|mir-675|mmu-mir-675	microRNA 675	ncRNA
mm_128049.1	chr15	25754007	25754016	-	1	NA	intron (NM_019472, intron 19 of 40)	intron (NM_019472, intron 19 of 40)	-89287	NM_001034851	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_147162.1	chr18	36725098	36725127	-	1	NA	TTS (NM_009841)	TTS (NM_009841)	1703	NM_009841	12475	Mm.3460	NM_009841	ENSMUSG00000051439	Cd14	-	CD14 antigen	protein-coding
mm_70728.1	chr8	18606896	18606902	+	1	NA	intron (NM_173189, intron 2 of 13)	intron (NM_173189, intron 2 of 13)	11726	NM_173189	244329	Mm.235296	NM_173189	ENSMUSG00000039842	Mcph1	5430437K10Rik|BRIT1|D030046N04Rik|MCT	microcephaly, primary autosomal recessive 1	protein-coding
mm_110278.1	chr12	32058411	32058420	-	1	NA	intron (NM_011158, intron 1 of 10)	intron (NM_011158, intron 1 of 10)	2864	NM_011158	19088	Mm.25594	NM_011158	ENSMUSG00000002997	Prkar2b	AI451071|AW061005|PKARIIbeta|Pkarb2|RII(beta)	protein kinase, cAMP dependent regulatory, type II beta	protein-coding
mm_152990.1	chr19	29648356	29648425	-	1	NA	promoter-TSS (NM_001081213)	promoter-TSS (NM_001081213)	30	NM_001081213	226090	Mm.267131	NM_146098	ENSMUSG00000046324	Ermp1	D19Ertd410e|D19Wsu12e|Fxna|mKIAA1815	endoplasmic reticulum metallopeptidase 1	protein-coding
mm_140321.1	chr17	86439018	86439030	+	1	NA	intron (NM_011104, intron 2 of 14)	intron (NM_011104, intron 2 of 14)	-151846	NR_045435	72104	Mm.443401	NR_045435	ENSMUSG00000100738	2010106C02Rik	-	RIKEN cDNA 2010106C02 gene	ncRNA
mm_10585.1	chr2	18186537	18186541	+	1	NA	intron (NR_045539, intron 16 of 24)	intron (NR_045539, intron 16 of 24)	121954	NM_001252561	17354	Mm.209175	NM_010804	ENSMUSG00000026743	Mllt10	Af10|B130021D15Rik|D630001B22Rik|mKIAA4140	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 10	protein-coding
mm_58081.1	chr6	136941834	136941842	-	1	NA	promoter-TSS (NM_007486)	promoter-TSS (NM_007486)	61	NM_001301301	11857	Mm.2241	NM_007486	ENSMUSG00000030220	Arhgdib	D4|Gdid4|Ly-GDI	Rho, GDP dissociation inhibitor (GDI) beta	protein-coding
mm_49622.1	chr6	30803375	30803390	+	1	NA	intron (NM_017478, intron 20 of 23)	intron (NM_017478, intron 20 of 23)	62083	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_47517.1	chr5	124083464	124083487	-	1	NA	intron (NM_019875, intron 3 of 11)	intron (NM_019875, intron 3 of 11)	12323	NM_019875	56325	Mm.254839	NM_019875	ENSMUSG00000029408	Abcb9	TAPL|mKIAA1520	ATP-binding cassette, sub-family B (MDR/TAP), member 9	protein-coding
mm_151702.1	chr19	4477568	4477592	-	1	NA	promoter-TSS (NM_134164)	promoter-TSS (NM_134164)	-437	NM_134164	171180	Mm.262270	NM_134164	ENSMUSG00000049303	Syt12	-	synaptotagmin XII	protein-coding
mm_112229.1	chr12	113430787	113430795	-	1	NA	Intergenic	Intergenic	-58774	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_73526.1	chr8	107545084	107545107	+	1	NA	intron (NM_025830, intron 10 of 23)	intron (NM_025830, intron 10 of 23)	-6149	NR_029553	387158		NR_029553	ENSMUSG00000065439	Mir140	Mirn140|mir-140|mmu-mir-140	microRNA 140	ncRNA
mm_171849.1	chr5	16904466	16904468	+	1	NA	Intergenic	L1Md_T|LINE|L1	350566	NM_001289461	15234	Mm.267078	NM_010427	ENSMUSG00000028864	Hgf	C230052L06Rik|HGF/SF|NK1|NK2|SF|SF/HGF	hepatocyte growth factor	protein-coding
mm_150745.1	chr19	43786951	43786964	+	1	NA	intron (NM_013806, intron 2 of 31)	intron (NM_013806, intron 2 of 31)	4649	NM_013806	12780	Mm.39054	NM_013806	ENSMUSG00000025194	Abcc2	AI173996|Abc30|Cmoat|Mrp2|cMRP	ATP-binding cassette, sub-family C (CFTR/MRP), member 2	protein-coding
mm_10874.1	chr2	25225417	25225431	+	1	NA	promoter-TSS (NM_146116)	promoter-TSS (NM_146116)	-722	NM_146116	227613	Mm.227260	NM_146116	ENSMUSG00000036752	Tubb4b	4930542G03Rik|Tubb2c|Tubb2c1	tubulin, beta 4B class IVB	protein-coding
mm_88414.1	chr10	77033291	77033301	+	1	NA	promoter-TSS (NM_031196)	promoter-TSS (NM_031196)	84	NM_031196	20509	Mm.265060	NM_031196	ENSMUSG00000001436	Slc19a1	AI323572|RFC|RFC-1|RFC1	solute carrier family 19 (folate transporter), member 1	protein-coding
mm_116985.1	chr13	56296374	56296399	-	1	NA	5' UTR (NM_019568, exon 1 of 4)	5' UTR (NM_019568, exon 1 of 4)	165	NM_019568	57266	Mm.30211	NM_019568	ENSMUSG00000021508	Cxcl14	1110031L23Rik|1200006I23Rik|AI414372|BMAC|BRAK|KS1|Kec|MIP-2g|MIP2gamma|NJAC|Scyb14|bolekine	chemokine (C-X-C motif) ligand 14	protein-coding
mm_163056.1	chr11	60704111	60704111	+	1	NA	intron (NM_001159404, intron 2 of 20)	intron (NM_001159404, intron 2 of 20)	4421	NM_008502	16897	Mm.285453	NM_008502	ENSMUSG00000020536	Llgl1	AI325176|Lgl1|Llglh|Mgl1	lethal giant larvae homolog 1 (Drosophila)	protein-coding
mm_90099.1	chr10	116964833	116964842	+	1	NA	promoter-TSS (NR_027847)	promoter-TSS (NR_027847)	97	NR_027847	103175	Mm.27138	NR_027846	ENSMUSG00000031294	D630029K05Rik	AI314111|AI875589	RIKEN cDNA D630029K05 gene	ncRNA
mm_34605.1	chr4	150237724	150237737	+	1	NA	intron (NM_023119, intron 1 of 11)	intron (NM_023119, intron 1 of 11)	406	NM_001025388	433182	Mm.70666	NM_001025388	ENSMUSG00000059040	Eno1b	EG433182|Eno1|Gm5506	enolase 1B, retrotransposed	protein-coding
mm_6729.1	chr1	82768450	82768465	-	1	NA	promoter-TSS (NM_025453)	promoter-TSS (NM_025453)	-1	NM_025453	66261	Mm.46325	NM_025453	ENSMUSG00000026149	Tm4sf20	1810018L02Rik	transmembrane 4 L six family member 20	protein-coding
mm_2065.1	chr1	87607810	87607822	+	1	NA	Intergenic	Intergenic	-12496	NM_001110192	16331	Mm.15105	NM_010566	ENSMUSG00000026288	Inpp5d	SHIP|SHIP-1|SHIP1|SIP-145|p150Ship|s-SHIP	inositol polyphosphate-5-phosphatase D	protein-coding
mm_11267.1	chr2	30021059	30021062	+	1	NA	intron (NM_001309460, intron 43 of 57)	ID4_|SINE|ID	25110	NR_105963	102465603		NR_105963	ENSMUSG00000098453	Mir6997	Gm27310|mmu-mir-6997	microRNA 6997	ncRNA
mm_143231.1	chr17	63472735	63472738	-	1	NA	intron (NM_015794, intron 3 of 8)	Lx8b|LINE|L1	27844	NM_015794	50758	Mm.136366	NM_015794	ENSMUSG00000023965	Fbxl17	6330576B01Rik|AI452053|BB073797|C130023C01Rik|Fbx13|Fbxo13	F-box and leucine-rich repeat protein 17	protein-coding
mm_136996.1	chr17	17402917	17402921	+	1	NA	5' UTR (NM_025681, exon 1 of 6)	5' UTR (NM_025681, exon 1 of 6)	233	NM_025681	66643	Mm.268018	NM_025681	ENSMUSG00000047786	Lix1	5730466L18Rik	limb and CNS expressed 1	protein-coding
mm_16213.1	chr2	173073207	173073218	+	1	NA	Intergenic	Intergenic	46313	NM_001081387	664799	Mm.389396	NM_001081387	ENSMUSG00000070495	Ctcfl	Boris|OTTMUSG00000016680	CCCTC-binding factor (zinc finger protein)-like	protein-coding
mm_145343.1	chr18	56469526	56469541	+	1	NA	exon (NM_026240, exon 2 of 14)	exon (NM_026240, exon 2 of 14)	37401	NM_026240	107022	Mm.24356	NM_026240	ENSMUSG00000001700	Gramd3	9030613F08Rik|9130427A09Rik|AW061306|NS3TP2	GRAM domain containing 3	protein-coding
mm_107034.1	chr12	13487113	13487139	+	1	NA	intron (NM_027706, intron 44 of 51)	RMER15|LTR|ERVL	140520	NR_136761	102639399	Mm.122052	NR_136761		Gm35725	-	predicted gene, 35725	ncRNA
mm_153020.1	chr19	31119934	31119942	-	1	NA	intron (NM_011160, intron 3 of 17)	intron (NM_011160, intron 3 of 17)	37097	NM_031249	83410	Mm.22031	NM_031249	ENSMUSG00000053536	Cstf2t	64kDa|C77975|tCstF-64|tauCstF-64	cleavage stimulation factor, 3' pre-RNA subunit 2, tau	protein-coding
mm_130134.1	chr15	90898395	90898409	-	1	NA	promoter-TSS (NR_033583)	promoter-TSS (NR_033583)	74	NR_033583	20738	Mm.431547	NR_033583		Spn-ps	Cd43-ps	sialophorin, pseudogene	pseudo
mm_17992.1	chr2	38078378	38078378	-	1	NA	intron (NM_146122, intron 5 of 21)	intron (NM_146122, intron 5 of 21)	209006	NM_146122	227801	Mm.314245	NM_146122	ENSMUSG00000035392	Dennd1a	6030446I19Rik|connecdenn	DENN/MADD domain containing 1A	protein-coding
mm_90311.1	chr10	127000733	127000747	+	1	NA	promoter-TSS (NM_009635)	promoter-TSS (NM_009635)	31	NM_009635	11567	Mm.10739	NM_009635	ENSMUSG00000025432	Avil	Advil|DOC6	advillin	protein-coding
mm_122096.1	chr14	30890690	30890733	-	1	NA	exon (NM_001289633, exon 6 of 22)	exon (NM_001289633, exon 6 of 22)	4235	NM_001289632	16427	Mm.34819	NM_018746	ENSMUSG00000021922	Itih4	ITI-HC4|Itih-4|PK-120	inter alpha-trypsin inhibitor, heavy chain 4	protein-coding
mm_159861.1	chr5	140724098	140724098	+	1	NA	promoter-TSS (NM_173405)	promoter-TSS (NM_173405)	-29	NM_173405	231842	Mm.491298	NM_173405	ENSMUSG00000050022	Amz1	5330426I05|6530401C20Rik	archaelysin family metallopeptidase 1	protein-coding
mm_164352.1	chr16	20174732	20174753	+	1	NA	intron (NM_001033237, intron 8 of 29)	PB1D7|SINE|Alu	1492	NR_030454	735274		NR_030454	ENSMUSG00000106252	Mir684-1	Mirn684-1	microRNA 684-1	ncRNA
mm_86946.1	chr10	24842292	24842308	+	1	NA	Intergenic	MTD-int|LTR|ERVL-MaLR	-6105	NM_134005	209558	Mm.338425	NM_134005	ENSMUSG00000019989	Enpp3	AI876438|CD203c	ectonucleotide pyrophosphatase/phosphodiesterase 3	protein-coding
mm_165093.1	chr19	53874819	53874825	-	1	NA	Intergenic	Intergenic	-17409	NM_011050	18569	Mm.1605	NM_011050	ENSMUSG00000024975	Pdcd4	D19Ucla1|Ma3|Tis	programmed cell death 4	protein-coding
mm_142469.1	chr17	45602097	45602108	-	1	NA	promoter-TSS (NM_001177468)	promoter-TSS (NM_001177468)	0	NM_001177469	653016	Mm.45676	NM_001177468	ENSMUSG00000079471	Gm7325	EG653016|Esgp	predicted gene 7325	protein-coding
mm_39396.1	chr5	14025417	14025472	+	1	NA	5' UTR (NM_011348, exon 1 of 17)	5' UTR (NM_011348, exon 1 of 17)	168	NM_011348	20349	Mm.134093	NM_011348	ENSMUSG00000063531	Sema3e	6430702L12|AA408817|Semah|mKIAA0331	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	protein-coding
mm_33581.1	chr4	132532710	132532724	+	1	NA	intron (NM_007512, intron 3 of 3)	intron (NM_007512, intron 3 of 3)	2697	NM_007512	11983	Mm.2171	NM_007512	ENSMUSG00000054428	Atpif1	Atpi|IF(1)|If1	ATPase inhibitory factor 1	protein-coding
mm_162514.1	chr1	156036464	156036468	-	1	NA	promoter-TSS (NM_144791)	promoter-TSS (NM_144791)	14	NM_144791	208263	Mm.211654	NM_144791	ENSMUSG00000026466	Tor1aip1	LAP1|Lap1B	torsin A interacting protein 1	protein-coding
mm_145560.1	chr18	60812341	60812353	+	1	NA	TTS (NR_039567)	TTS (NR_039567)	271	NR_039567	100628611		NR_039567	ENSMUSG00000093327	Mir5107	mir-5107|mmu-mir-5107|mu-mir-5107	microRNA 5107	ncRNA
mm_31031.1	chr4	40920048	40920063	+	1	NA	promoter-TSS (NM_011463)	promoter-TSS (NM_011463)	-1	NM_011463	20731	Mm.25246	NM_011463	ENSMUSG00000028415	Spink4	MPGC60	serine peptidase inhibitor, Kazal type 4	protein-coding
mm_125926.1	chr15	76246748	76246806	+	1	NA	promoter-TSS (NM_023168)	promoter-TSS (NM_023168)	-30	NM_023168	66168	Mm.41665	NM_023168	ENSMUSG00000022564	Grina	1110025J15Rik|Lag|Tmbim3	glutamate receptor, ionotropic, N-methyl D-aspartate-associated protein 1 (glutamate binding)	protein-coding
mm_53419.1	chr6	134035017	134035038	+	1	NA	promoter-TSS (NM_007961)	promoter-TSS (NM_007961)	-673	NM_001303102	14011	Mm.269995	NM_007961	ENSMUSG00000030199	Etv6	AW123102|AW557856|Tel	ets variant 6	protein-coding
mm_161629.1	chr16	87472127	87472127	+	1	NA	exon (NM_024258, exon 9 of 18)	exon (NM_024258, exon 9 of 18)	17142	NM_024258	74112	Mm.152941	NM_024258	ENSMUSG00000025616	Usp16	1200004E02Rik|2810483I07Rik|6330514E22Rik|UBPM	ubiquitin specific peptidase 16	protein-coding
mm_55576.1	chr6	71396232	71396242	-	1	NA	intron (NM_024288, intron 7 of 8)	intron (NM_024288, intron 7 of 8)	22810	NM_001081110	12525	Mm.1858	NM_009857	ENSMUSG00000053977	Cd8a	BB154331|Ly-2|Ly-35|Ly-B|Lyt-2	CD8 antigen, alpha chain	protein-coding
mm_75019.1	chr8	31149967	31149970	-	1	NA	promoter-TSS (NM_144927)	promoter-TSS (NM_144927)	-348	NM_144927	234138	Mm.349800	NM_144927	ENSMUSG00000031577	Tti2	-	TELO2 interacting protein 2	protein-coding
mm_110892.1	chr12	75596109	75596113	-	1	NA	promoter-TSS (NM_012024)	promoter-TSS (NM_012024)	89	NM_012024	26932	Mm.259626	NM_012024	ENSMUSG00000021051	Ppp2r5e	4633401M22Rik|AI449017|B56beta	protein phosphatase 2, regulatory subunit B', epsilon	protein-coding
mm_102159.1	chr11	53724510	53724528	-	1	NA	3' UTR (NM_010558, exon 4 of 4)	3' UTR (NM_010558, exon 4 of 4)	3725	NM_010558	16191	Mm.4461	NM_010558	ENSMUSG00000036117	Il5	Il-5	interleukin 5	protein-coding
mm_83948.1	chr9	56925784	56925797	-	1	NA	exon (NM_175483, exon 1 of 2)	exon (NM_175483, exon 1 of 2)	2581	NM_175483	235406	Mm.191459	NM_175483	ENSMUSG00000032733	Snx33	E130307J07Rik|Sh3px3	sorting nexin 33	protein-coding
mm_57159.1	chr6	122758827	122758858	-	1	NA	Intergenic	Intergenic	-16097	NM_011401	20527	Mm.395108	NM_011401	ENSMUSG00000003153	Slc2a3	AA408729|AL023014|AL024341|AU040424|C78366|Glut-3|Glut3	solute carrier family 2 (facilitated glucose transporter), member 3	protein-coding
mm_46127.1	chr5	92501792	92501796	-	1	NA	intron (NM_007644, intron 1 of 11)	PB1D9|SINE|Alu	3863	NM_007644	12492	Mm.297964	NM_007644	ENSMUSG00000029426	Scarb2	9330185J12Rik|Cd36l2|LGP85|LIMP II|LIMP-2|MLGP85	scavenger receptor class B, member 2	protein-coding
mm_101849.1	chr11	48838529	48838542	-	1	NA	intron (NM_001347446, intron 1 of 6)	intron (NM_001347446, intron 1 of 6)	530	NM_001347436	94089	Mm.390335	NM_053166	ENSMUSG00000040350	Trim7	AI790312	tripartite motif-containing 7	protein-coding
mm_145121.1	chr18	44380560	44380577	+	1	NA	promoter-TSS (NM_027490)	promoter-TSS (NM_027490)	68	NM_027490	70640	Mm.87629	NM_027490	ENSMUSG00000024472	Dcp2	2410015D23Rik|5730537H01Rik|AL118268	decapping mRNA 2	protein-coding
mm_135820.1	chr16	58479175	58479186	-	1	NA	intron (NM_018784, intron 6 of 10)	intron (NM_018784, intron 6 of 10)	44132	NM_018784	54613	Mm.212742	NM_018784	ENSMUSG00000022747	St3gal6	1700023B24Rik|AI930218|AW552396|Siat10|St3galVI	ST3 beta-galactoside alpha-2,3-sialyltransferase 6	protein-coding
mm_118192.1	chr13	107794813	107794820	-	1	NA	intron (NM_145456, intron 2 of 14)	L1MA5|LINE|L1	-33729	NR_029759	723929		NR_029759	ENSMUSG00000065425	Mir325	Mirn325|mmu-mir-325	microRNA 325	ncRNA
mm_29381.1	chr3	108840478	108840509	-	1	NA	promoter-TSS (NM_011504)	promoter-TSS (NM_011504)	9	NM_011504	20912	Mm.316894	NM_011504	ENSMUSG00000027882	Stxbp3	Munc-18c|Stxbp3a|Sxtbp3|Unc18-3	syntaxin binding protein 3	protein-coding
mm_131527.1	chr16	17646447	17646458	+	1	NA	promoter-TSS (NM_001166164)	promoter-TSS (NM_001166164)	-18	NM_001166164	72315	Mm.297777	NM_001166164	ENSMUSG00000041617	Ccdc74a	2310015A05Rik	coiled-coil domain containing 74A	protein-coding
mm_120612.1	chr14	70205245	70205255	+	1	NA	promoter-TSS (NM_001271408)	promoter-TSS (NM_001271408)	-627	NM_001271408	20410	Mm.5068	NM_011366	ENSMUSG00000022091	Sorbs3	SCAM-1|SH3P3|Sh3d4|vinexin-g	sorbin and SH3 domain containing 3	protein-coding
mm_83038.1	chr9	37348313	37348321	-	1	NA	promoter-TSS (NM_001081429)	promoter-TSS (NM_001081429)	75	NM_001081429	245902	Mm.390150	NM_001081429	ENSMUSG00000034303	Ccdc15	A630039F14Rik|D030074L19	coiled-coil domain containing 15	protein-coding
mm_2441.1	chr1	98131471	98131499	+	1	NA	promoter-TSS (NR_040439)	promoter-TSS (NR_040439)	18	NR_040439	69030	Mm.402692	NR_040439	ENSMUSG00000100182	1810006J02Rik	-	RIKEN cDNA 1810006J02 gene	ncRNA
mm_104865.1	chr11	99387125	99387135	-	1	NA	intron (NM_010660, intron 4 of 7)	intron (NM_010660, intron 4 of 7)	2234	NM_010660	16661	Mm.22662	NM_010660	ENSMUSG00000019761	Krt10	D130054E02Rik|K10|K1C1|Krt-1.10|Krt1-10	keratin 10	protein-coding
mm_50727.1	chr6	52313431	52313445	+	1	NA	promoter-TSS (NM_007966)	promoter-TSS (NM_007966)	-60	NM_007966	14028	Mm.389754	NM_007966	ENSMUSG00000005503	Evx1	Evx-1	even-skipped homeobox 1	protein-coding
mm_159866.1	chr5	145032751	145032751	-	1	NA	promoter-TSS (NM_001101463)	promoter-TSS (NM_001101463)	13	NM_001101463	231885	Mm.443311	NM_001101463	ENSMUSG00000061707	Gm4871	EG231885	predicted gene 4871	protein-coding
mm_13286.1	chr2	101649698	101649728	+	1	NA	promoter-TSS (NM_009019)	promoter-TSS (NM_009019)	-181	NM_009019	19373	Mm.828	NM_009019	ENSMUSG00000061311	Rag1	Rag-1	recombination activating gene 1	protein-coding
mm_152188.1	chr19	7439659	7439668	-	1	NA	intron (NM_053076, intron 1 of 6)	B2_Mm2|SINE|B2	17090	NR_105957	102466781		NR_105957	ENSMUSG00000098293	Mir6991	Gm27966|mmu-mir-6991	microRNA 6991	ncRNA
mm_138384.1	chr17	35048568	35048587	+	1	NA	Intergenic	Intergenic	-1666	NM_033444	114584	Mm.29524	NM_033444	ENSMUSG00000007041	Clic1	Clcp|G6	chloride intracellular channel 1	protein-coding
mm_150441.1	chr19	37697864	37697870	+	1	NA	promoter-TSS (NM_007811)	promoter-TSS (NM_007811)	59	NM_007811	13082	Mm.42230	NM_007811	ENSMUSG00000024987	Cyp26a1	Cyp26|P450RA|P450RAI|RAH	cytochrome P450, family 26, subfamily a, polypeptide 1	protein-coding
mm_79370.1	chr9	54595105	54595133	+	1	NA	intron (NM_029573, intron 3 of 10)	intron (NM_029573, intron 3 of 10)	8608	NM_029573	67834	Mm.279195	NM_029573	ENSMUSG00000032279	Idh3a	1110003P10Rik|1500012E04Rik|AA407078|AI316514	isocitrate dehydrogenase 3 (NAD+) alpha	protein-coding
mm_136429.1	chr16	94313557	94313577	-	1	NA	Intergenic	CpG	-14855	NM_133229	170765	Mm.42604	NM_133229	ENSMUSG00000022941	Ripply3	Dscr6	ripply transcriptional repressor 3	protein-coding
mm_161121.1	chr12	108676096	108676096	+	1	NA	intron (NM_001163394, intron 6 of 13)	intron (NM_001163394, intron 6 of 13)	17476	NR_029771	723909		NR_029771	ENSMUSG00000065436	Mir342	Mirn342|mmu-mir-342	microRNA 342	ncRNA
mm_171312.1	chr3	95042542	95042542	-	1	NA	promoter-TSS (NM_008951)	promoter-TSS (NM_008951)	72	NM_001282017	19185	Mm.2261	NM_008951	ENSMUSG00000005625	Psmd4	Af1|Mcb1|angiocidin	proteasome (prosome, macropain) 26S subunit, non-ATPase, 4	protein-coding
mm_11950.1	chr2	52952670	52952704	+	1	NA	intron (NM_172409, intron 1 of 26)	intron (NM_172409, intron 1 of 26)	94819	NM_172409	71409	Mm.394427	NM_172409	ENSMUSG00000036053	Fmnl2	5430425K04Rik|Man	formin-like 2	protein-coding
mm_84512.1	chr9	67032843	67032871	-	1	NA	exon (NM_001164251, exon 5 of 10)	exon (NM_001164251, exon 5 of 10)	11014	NM_001164252	22003	Mm.121878	NM_024427	ENSMUSG00000032366	Tpm1	AA986836|AI854628|TM2|Tm3|Tmpa|Tpm-1|alpha-TM	tropomyosin 1, alpha	protein-coding
mm_64581.1	chr7	145300637	145300665	+	1	NA	promoter-TSS (NM_145379)	promoter-TSS (NM_145379)	-258	NM_145379	211577	Mm.215151	NM_145379	ENSMUSG00000031070	Mrgprf	BC019711|Mgrc|MrgF	MAS-related GPR, member F	protein-coding
mm_105010.1	chr11	100397741	100397792	-	1	NA	promoter-TSS (NM_010593)	promoter-TSS (NM_010593)	24	NM_010593	16480	Mm.299774	NM_010593	ENSMUSG00000001552	Jup	Ctnng|D930025P04Rik|PG	junction plakoglobin	protein-coding
mm_139114.1	chr17	47410248	47410253	+	1	NA	Intergenic	CpG	4461	NM_001172091	75462	Mm.46129	NM_029296	ENSMUSG00000047150	1700001C19Rik	-	RIKEN cDNA 1700001C19 gene	protein-coding
mm_28307.1	chr3	89237928	89237940	-	1	NA	intron (NM_001039466, intron 7 of 8)	intron (NM_001039466, intron 7 of 8)	7079	NR_121683	360213	Mm.331156	NM_183037	ENSMUSG00000042766	Trim46	TRIFIC	tripartite motif-containing 46	protein-coding
mm_5624.1	chr1	40381070	40381099	-	1	NA	Intergenic	Intergenic	-48486	NM_001294171	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_108921.1	chr12	100779106	100779137	+	1	NA	promoter-TSS (NM_145448)	promoter-TSS (NM_145448)	-2	NM_145448	217830	Mm.218590	NM_145448	ENSMUSG00000021185	9030617O03Rik	-	RIKEN cDNA 9030617O03 gene	protein-coding
mm_71187.1	chr8	40864295	40864309	+	1	NA	intron (NM_007514, intron 1 of 11)	intron (NM_007514, intron 1 of 11)	1935	NM_001044740	11988	Mm.4676	NM_007514	ENSMUSG00000031596	Slc7a2	20.5|AI158848|Atrc2|CAT-2|Cat2|Tea	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	protein-coding
mm_125506.1	chr15	55457721	55457742	+	1	NA	intron (NM_181277, intron 34 of 47)	intron (NM_181277, intron 34 of 47)	99581	NM_026759	68537	Mm.236795	NM_026759	ENSMUSG00000022370	Mrpl13	1110002D09Rik	mitochondrial ribosomal protein L13	protein-coding
mm_91887.1	chr10	59908165	59908206	-	1	NA	Intergenic	Intergenic	28594	NM_019965	56709	Mm.103610	NM_019965	ENSMUSG00000020109	Dnajb12	Dj10|mDj10	DnaJ heat shock protein family (Hsp40) member B12	protein-coding
mm_154903.1	chrX	20961851	20961856	+	1	NA	promoter-TSS (NR_027446)	promoter-TSS (NR_027446)	125	NM_013840	22294	Mm.34779	NM_013840	ENSMUSG00000001134	Uxt	0910002B17Rik	ubiquitously expressed transcript	protein-coding
mm_12961.1	chr2	90487742	90487749	+	1	NA	intron (NM_008982, intron 1 of 23)	intron (NM_008982, intron 1 of 23)	-8571	NM_001135657	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_101098.1	chr11	11898063	11898080	-	1	NA	promoter-TSS (NM_001190448)	promoter-TSS (NM_001190448)	73	NM_001190448	13195	Mm.12906	NM_016672	ENSMUSG00000020182	Ddc	Aadc	dopa decarboxylase	protein-coding
mm_131466.1	chr16	17043698	17043736	+	1	NA	3' UTR (NM_011949, exon 9 of 9)	3' UTR (NM_011949, exon 9 of 9)	-26422	NM_023249	106369	Mm.237941	NM_023249	ENSMUSG00000022773	Ypel1	0610009L05Rik|1700016N17Rik|1700019O22Rik|4921520K19Rik|4930511F14Rik|AV118478|DGL-1|Dgl1|Ppil2|mdgl-1	yippee-like 1 (Drosophila)	protein-coding
mm_90978.1	chr10	13553000	13553061	-	1	NA	5' UTR (NM_019961, exon 1 of 12)	5' UTR (NM_019961, exon 1 of 12)	112	NM_019961	56535	Mm.282711	NM_019961	ENSMUSG00000019809	Pex3	1700014F15Rik|2810027F19Rik|2900010N04Rik	peroxisomal biogenesis factor 3	protein-coding
mm_25558.1	chr3	116513095	116513144	+	1	NA	promoter-TSS (NM_010022)	promoter-TSS (NM_010022)	40	NM_010022	13171	Mm.3636	NM_010022	ENSMUSG00000000340	Dbt	D3Wsu60e	dihydrolipoamide branched chain transacylase E2	protein-coding
mm_153319.1	chr19	38116868	38116916	-	1	NA	exon (NM_011255, exon 6 of 6)	exon (NM_011255, exon 6 of 6)	7919	NM_011255	19662	Mm.2605	NM_011255	ENSMUSG00000024990	Rbp4	Rbp-4	retinol binding protein 4, plasma	protein-coding
mm_81705.1	chr9	111275750	111275770	+	1	NA	3' UTR (NM_175266, exon 1 of 1)	3' UTR (NM_175266, exon 1 of 1)	3915	NM_175266	77781	Mm.209005	NM_175266	ENSMUSG00000046785	Epm2aip1	A930003G21Rik|mKIAA0766	EPM2A (laforin) interacting protein 1	protein-coding
mm_161044.1	chr12	36218301	36218301	-	1	NA	promoter-TSS (NM_027699)	promoter-TSS (NM_027699)	-99	NM_027699	71156	Mm.250837	NM_027699	ENSMUSG00000020545	Lrrc72	1700108M19Rik|4933421E18Rik	leucine rich repeat containing 72	protein-coding
mm_112126.1	chr12	112929416	112929419	-	1	NA	promoter-TSS (NM_010588)	promoter-TSS (NM_010588)	78	NM_010588	16450	Mm.186146	NM_010588	ENSMUSG00000002799	Jag2	D12Ggc2e|Serh|mJagged2-1|sm	jagged 2	protein-coding
mm_91265.1	chr10	23787051	23787074	-	1	NA	intron (NM_011295, intron 1 of 5)	CpG-941	147	NM_011295	20042	Mm.371846	NM_011295	ENSMUSG00000061983	Rps12	-	ribosomal protein S12	protein-coding
mm_128167.1	chr15	34082610	34082637	-	1	NA	promoter-TSS (NM_026002)	promoter-TSS (NM_026002)	-96	NM_026002	67154	Mm.130883	NM_026002	ENSMUSG00000022255	Mtdh	2610103J23Rik|3D3|3D3/Lyric|AEG-1|AV353288|D8Bwg1112e|Lyric	metadherin	protein-coding
mm_38044.1	chr4	133967297	133967308	-	1	NA	intron (NM_016957, intron 1 of 5)	CpG	689	NM_016957	15331	Mm.319660	NM_016957	ENSMUSG00000003038	Hmgn2	HMG-17|Hmg17	high mobility group nucleosomal binding domain 2	protein-coding
mm_33020.1	chr4	121039702	121039712	+	1	NA	5' UTR (NM_007741, exon 1 of 32)	5' UTR (NM_007741, exon 1 of 32)	141	NM_007741	12840	Mm.269384	NM_007741	ENSMUSG00000028626	Col9a2	AI427499|Col9a-2	collagen, type IX, alpha 2	protein-coding
mm_41019.1	chr5	81420069	81420070	+	1	NA	intron (NM_001347371, intron 4 of 23)	Lx7|LINE|L1	398476	NM_198702	319387	Mm.273631	NM_198702	ENSMUSG00000037605	Adgrl3	5430402I23Rik|CIRL-3|D130075K09Rik|Gm1379|LEC3|Lphn3|mKIAA0768	adhesion G protein-coupled receptor L3	protein-coding
mm_11214.1	chr2	29643666	29643681	+	1	NA	intron (NM_001039087, intron 1 of 25)	intron (NM_001039087, intron 1 of 25)	23953	NM_001039086	107746	Mm.298274	NM_054050	ENSMUSG00000039844	Rapgef1	4932418O06Rik|C3G|Grf2	Rap guanine nucleotide exchange factor (GEF) 1	protein-coding
mm_34049.1	chr4	138239600	138239618	+	1	NA	exon (NM_001122896, exon 10 of 12)	exon (NM_001122896, exon 10 of 12)	-10802	NM_001099631	230863	Mm.482408	NM_001099631	ENSMUSG00000045349	Sh2d5	BC036961	SH2 domain containing 5	protein-coding
mm_28270.1	chr3	88762140	88762152	-	1	NA	exon (NM_018804, exon 2 of 4)	exon (NM_018804, exon 2 of 4)	10453	NM_018804	229521	Mm.379376	NM_018804	ENSMUSG00000068923	Syt11	1500004A13Rik|3632445O20Rik|5430404N14Rik|6530420C11Rik|AI851970	synaptotagmin XI	protein-coding
mm_140536.1	chr17	6756944	6756951	-	1	NA	intron (NM_009510, intron 2 of 12)	intron (NM_009510, intron 2 of 12)	25833	NM_009510	22350	Mm.277812	NM_009510	ENSMUSG00000052397	Ezr	AW146364|R75297|Vil2|p81	ezrin	protein-coding
mm_106570.1	chr11	120660532	120660557	-	1	NA	intron (NM_175263, intron 1 of 11)	CpG-2953	293	NM_175263	77583	Mm.32839	NM_175263	ENSMUSG00000042988	Notum	5730593N15Rik	notum pectinacetylesterase homolog (Drosophila)	protein-coding
mm_170822.1	chr2	176670511	176670527	+	1	NA	promoter-TSS (NM_001242943).2	promoter-TSS (NM_001242943).2	-3	NM_001242943	545490	Mm.484023	NM_001242943	ENSMUSG00000078879	Zfp973	6230416C02Rik|Gm14306|Gm14436|OTTMUSG00000016614	zinc finger protein 973	protein-coding
mm_89866.1	chr10	108162359	108162408	+	1	NA	promoter-TSS (NM_027892)	promoter-TSS (NM_027892)	-17	NM_027892	17931	Mm.422959	NM_027892	ENSMUSG00000019907	Ppp1r12a	1200015F06Rik|5730577I22Rik|AA792106|AV099298|D10Ertd625e|Mypt1	protein phosphatase 1, regulatory (inhibitor) subunit 12A	protein-coding
mm_45836.1	chr5	87694926	87694972	-	1	NA	exon (NM_001286023, exon 5 of 7)	exon (NM_001286023, exon 5 of 7)	4476	NM_001286020	12991	Mm.268737	NM_009972	ENSMUSG00000063157	Csn2	Csnb	casein beta	protein-coding
mm_59719.1	chr7	28769775	28769782	+	1	NA	intron (NM_022432, intron 2 of 15)	B3|SINE|B2	3026	NM_001122766	64383	Mm.272443	NM_022432	ENSMUSG00000015149	Sirt2	5730427M03Rik|SIR2L2|Sir2l	sirtuin 2	protein-coding
mm_111834.1	chr12	107912035	107912047	-	1	NA	3' UTR (NM_021399, exon 3 of 3)	3' UTR (NM_021399, exon 3 of 3)	91373	NM_001079883	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_150827.1	chr19	44746592	44746622	+	1	NA	Intergenic	Intergenic	-10787	NM_011037	18504	Mm.192158	NM_011037	ENSMUSG00000004231	Pax2	Opdc|Pax-2	paired box 2	protein-coding
mm_85349.1	chr9	103210526	103210615	-	1	NA	exon (NM_133977, exon 16 of 17)	exon (NM_133977, exon 16 of 17)	-8505	NM_009275	20818	Mm.273053	NM_009275	ENSMUSG00000032553	Srprb	AA409543	signal recognition particle receptor, B subunit	protein-coding
mm_37664.1	chr4	129111840	129111852	-	1	NA	TTS (NM_001290706)	TTS (NM_001290706)	6298	NM_001290706	66260	Mm.25295	NM_025452	ENSMUSG00000028786	Tmem54	1810017F10Rik|AI507302	transmembrane protein 54	protein-coding
mm_56276.1	chr6	91116762	91116775	-	1	NA	promoter-TSS (NM_018815)	promoter-TSS (NM_018815)	58	NM_018815	54563	Mm.28162	NM_018815	ENSMUSG00000030091	Nup210	9830001L10|AI836801|Pom210|gp190|gp210	nucleoporin 210	protein-coding
mm_5201.1	chr1	13374221	13374263	-	1	NA	promoter-TSS (NM_008678)	promoter-TSS (NM_008678)	-159	NM_008678	17978	Mm.2537	NM_008678	ENSMUSG00000005886	Ncoa2	D1Ertd433e|GRIP-1|Grip1|KAT13C|NCoA-2|SRC-2|TIF2|bHLHe75	nuclear receptor coactivator 2	protein-coding
mm_10691.1	chr2	22622385	22622397	+	1	NA	promoter-TSS (NM_008078)	promoter-TSS (NM_008078)	64	NM_008078	14417	Mm.4784	NM_008078	ENSMUSG00000026787	Gad2	6330404F12Rik|GAD(65)|GAD65|Gad-2	glutamic acid decarboxylase 2	protein-coding
mm_138712.1	chr17	36121758	36121763	+	1	NA	promoter-TSS (NM_010395)	promoter-TSS (NM_010395)	-316	NR_046286	15024	Mm.426031	NM_010395	ENSMUSG00000079491	H2-T10	H-2T10	histocompatibility 2, T region locus 10	protein-coding
mm_171461.1	chr4	145670686	145670718	+	1	NA	promoter-TSS (NM_001103158)	promoter-TSS (NM_001103158)	5	NM_001103158	100041379	Mm.276881	NM_001103158	ENSMUSG00000058186	Zfp980	Gm13242|OTTMUSG00000011070	zinc finger protein 980	protein-coding
mm_100596.1	chr11	120991413	120991439	+	1	NA	promoter-TSS (NM_139059)	promoter-TSS (NM_139059)	-93	NM_027874	104318	Mm.216227	NM_027874	ENSMUSG00000025162	Csnk1d	1200006A05Rik|AA409348|D930010H05Rik	casein kinase 1, delta	protein-coding
mm_79368.1	chr9	54587029	54587050	+	1	NA	intron (NM_029573, intron 1 of 10)	intron (NM_029573, intron 1 of 10)	528	NM_029573	67834	Mm.279195	NM_029573	ENSMUSG00000032279	Idh3a	1110003P10Rik|1500012E04Rik|AA407078|AI316514	isocitrate dehydrogenase 3 (NAD+) alpha	protein-coding
mm_4806.1	chr1	185312186	185312200	+	1	NA	intron (NM_198653, intron 12 of 22)	intron (NM_198653, intron 12 of 22)	-1126	NR_029580	387189		NR_029580	ENSMUSG00000065581	Mir194-1	Mirn194|Mirn194-1|miR-194|mir-194-1	microRNA 194-1	ncRNA
mm_153257.1	chr19	36918249	36918287	-	1	NA	3' UTR (NM_028263, exon 2 of 2)	3' UTR (NM_028263, exon 2 of 2)	1331	NM_028263	72514	Mm.41674	NM_028263	ENSMUSG00000047632	Fgfbp3	2610306H15Rik|Fgf-bp3	fibroblast growth factor binding protein 3	protein-coding
mm_161752.1	chr17	34972777	34972777	+	1	NA	promoter-TSS (NM_013558)	promoter-TSS (NM_013558)	74	NM_013558	15482	Mm.14287	NM_013558	ENSMUSG00000007033	Hspa1l	Hsc70t|Msh5	heat shock protein 1-like	protein-coding
mm_118366.1	chr13	115101910	115101984	-	1	NA	promoter-TSS (NM_001033228)	promoter-TSS (NM_001033228)	17	NM_001033228	109700	Mm.317280	NM_001033228	ENSMUSG00000042284	Itga1	CD49A|E130012M19Rik|Vla1	integrin alpha 1	protein-coding
mm_53304.1	chr6	129180918	129180939	+	1	NA	intron (NM_053109, intron 1 of 4)	intron (NM_053109, intron 1 of 4)	313	NM_053109	93694	Mm.197536	NM_053109	ENSMUSG00000030157	Clec2d	Clr-b|Clrb|Ocil	C-type lectin domain family 2, member d	protein-coding
mm_31604.1	chr4	58285931	58285975	+	1	NA	promoter-TSS (NM_010944)	promoter-TSS (NM_010944)	-9	NM_001165996	18198	Mm.16148	NM_010944	ENSMUSG00000057280	Musk	Mdk4|Mlk|Nsk1|Nsk2|Nsk3	muscle, skeletal, receptor tyrosine kinase	protein-coding
mm_39051.1	chr4	153482940	153482972	-	1	NA	promoter-TSS (NM_001099299)	promoter-TSS (NM_001099299)	-126	NM_001099299	230959	Mm.318874	NM_001099299	ENSMUSG00000039546	Ajap1	Gm573	adherens junction associated protein 1	protein-coding
mm_62620.1	chr7	107370746	107370848	+	1	NA	promoter-TSS (NM_021889)	promoter-TSS (NM_021889)	7	NM_021889	60510	Mm.302793	NM_021889	ENSMUSG00000062542	Syt9	-	synaptotagmin IX	protein-coding
mm_95595.1	chr11	53332486	53332515	+	1	NA	exon (NM_026479, exon 4 of 4)	exon (NM_026479, exon 4 of 4)	7811	NM_026479	67966	Mm.288072	NM_026479	ENSMUSG00000018239	Zcchc10	2410141K03Rik|AA675321|D11Ertd416e	zinc finger, CCHC domain containing 10	protein-coding
mm_59469.1	chr7	27308915	27308951	+	1	NA	exon (NM_175641, exon 29 of 33)	exon (NM_175641, exon 29 of 33)	24715	NM_001113549	108075	Mm.272251	NM_175641	ENSMUSG00000040488	Ltbp4	2310046A13Rik	latent transforming growth factor beta binding protein 4	protein-coding
mm_172683.1	chr8	55567058	55567069	-	1	NA	Intergenic	MMVL30-int|LTR|ERV1	339901	NM_175939	244486	Mm.67684	NM_175939	ENSMUSG00000046258	Adam29	-	a disintegrin and metallopeptidase domain 29	protein-coding
mm_54937.1	chr6	48445745	48445821	-	1	NA	promoter-TSS (NM_001085417)	promoter-TSS (NM_001085417)	42	NM_020589	68910	Mm.2464	NM_020589	ENSMUSG00000068551	Zfp467	1190001I08Rik|AB041616|AI426952|AV017623|EZI|MNCb-3350|Znf467	zinc finger protein 467	protein-coding
mm_81464.1	chr9	109861647	109861656	+	1	NA	Intergenic	Intergenic	-12195	NM_009921	12796	Mm.3834	NM_009921	ENSMUSG00000038357	Camp	CAP18|Cnlp|Cramp|FALL39|MCLP	cathelicidin antimicrobial peptide	protein-coding
mm_57861.1	chr6	129533279	129533289	-	1	NA	promoter-TSS (NR_045270)	promoter-TSS (NR_045270)	0	NR_045270	100504641	Mm.398286	NR_045270	ENSMUSG00000097675	1700101I11Rik	-	RIKEN cDNA 1700101I11 gene	ncRNA
mm_132300.1	chr16	33518529	33518542	+	1	NA	promoter-TSS (NM_001083902)	promoter-TSS (NM_001083902)	-60	NM_001083902	171286	Mm.35253	NM_134251	ENSMUSG00000035506	Slc12a8	CCC9|E330020C02Rik	solute carrier family 12 (potassium/chloride transporters), member 8	protein-coding
mm_163558.1	chr13	24376051	24376061	+	1	NA	intron (NM_001284519, intron 2 of 17)	intron (NM_001284519, intron 2 of 17)	-39066	NM_007717	12763	Mm.8396	NM_007717	ENSMUSG00000016756	Cmah	-	cytidine monophospho-N-acetylneuraminic acid hydroxylase	protein-coding
mm_1229.1	chr1	62764594	62764597	+	1	NA	intron (NM_001077405, intron 9 of 15)	intron (NM_001077405, intron 9 of 15)	30137	NR_040601	74992	Mm.401979	NR_040601		4930487H11Rik	-	RIKEN cDNA 4930487H11 gene	ncRNA
mm_43660.1	chr5	138707602	138707616	+	1	NA	Intergenic	RMER15|LTR|ERVL	-47472	NM_030565	80752	Mm.320355	NM_030565	ENSMUSG00000025854	Fam20c	C76981|DMP-4|DMP4|GEF-CK|mKIAA4081	family with sequence similarity 20, member C	protein-coding
mm_117865.1	chr13	98842993	98843014	-	1	NA	3' UTR (NM_178716, exon 24 of 24)	3' UTR (NM_178716, exon 24 of 24)	-27554	NM_172591	218503	Mm.23928	NM_172591	ENSMUSG00000041685	Fcho2	5832424M12Rik|AA387320	FCH domain only 2	protein-coding
mm_131344.1	chr16	13447973	13447994	+	1	NA	Intergenic	Intergenic	-1540	NR_030549	100124432		NR_030549	ENSMUSG00000076972	Mir193b	Mir193|Mirn193b|mir-193b	microRNA 193b	ncRNA
mm_144572.1	chr18	31857041	31857049	+	1	NA	intron (NM_028866, intron 7 of 21)	intron (NM_028866, intron 7 of 21)	52988	NM_001170966	74320	Mm.277705	NM_028866	ENSMUSG00000024400	Wdr33	1110001N06Rik|2310011G05Rik|2810021O11Rik|8430413N20Rik|WDC146	WD repeat domain 33	protein-coding
mm_61803.1	chr7	84528965	84528981	+	1	NA	promoter-TSS (NR_045098)	promoter-TSS (NR_045098)	19	NR_045098	100039239	Mm.44882	NR_045098		Gm2115	C77713	predicted gene 2115	ncRNA
mm_110156.1	chr12	26455727	26455737	-	1	NA	intron (NM_021384, intron 1 of 5)	intron (NM_021384, intron 1 of 5)	720	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_19990.1	chr2	118709718	118709728	-	1	NA	intron (NM_001290790, intron 29 of 30)	MIRb|SINE|MIR	-5760	NM_001081971	383787	Mm.35758	NM_001081971	ENSMUSG00000078137	Ankrd63	Gm1337	ankyrin repeat domain 63	protein-coding
mm_146248.1	chr18	77775789	77775805	+	1	NA	exon (NM_007505, exon 2 of 12)	exon (NM_007505, exon 2 of 12)	2029	NM_007505	11946	Mm.276137	NM_007505	ENSMUSG00000025428	Atp5a1	AI035633|AL022851|AL023067|Atpm|D18Ertd206e|Mom2	ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1	protein-coding
mm_142360.1	chr17	43744559	43744569	-	1	NA	intron (NM_018887, intron 10 of 11)	intron (NM_018887, intron 10 of 11)	-57287	NM_207649	53901	Mm.251242	NM_030598	ENSMUSG00000039601	Rcan2	Csp2|Dscr1l1|MCIP2|ZAKI-4	regulator of calcineurin 2	protein-coding
mm_129763.1	chr15	82456384	82456400	-	1	NA	exon (NM_010006, exon 8 of 9)	exon (NM_010006, exon 8 of 9)	4015	NM_010006	13105	Mm.226708	NM_010006	ENSMUSG00000068086	Cyp2d9	Cyp2d|P450-2D	cytochrome P450, family 2, subfamily d, polypeptide 9	protein-coding
mm_101951.1	chr11	50278681	50278683	-	1	NA	intron (NM_175334, intron 1 of 4)	intron (NM_175334, intron 1 of 4)	13654	NM_175334	103806	Mm.51116	NM_175334	ENSMUSG00000050567	Maml1	AI644666|AW743257|D930008C07Rik|Mam-1|Mam1|mKIAA0200	mastermind like 1 (Drosophila)	protein-coding
mm_44584.1	chr5	24908431	24908482	-	1	NA	promoter-TSS (NM_001170556)	promoter-TSS (NM_001170556)	53	NM_001170556	108099	Mm.33649	NM_145401	ENSMUSG00000028944	Prkag2	2410051C13Rik|AAKG|AAKG2|AI854673|H91620p|WPWS	protein kinase, AMP-activated, gamma 2 non-catalytic subunit	protein-coding
mm_10165.1	chr2	4401540	4401556	+	1	NA	5' UTR (NM_001177843, exon 1 of 24)	5' UTR (NM_001177843, exon 1 of 24)	572	NM_001177843	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding
mm_84223.1	chr9	61946694	61946698	-	1	NA	5' UTR (NM_024245, exon 1 of 23)	5' UTR (NM_024245, exon 1 of 23)	103	NM_024245	71819	Mm.259374	NM_024245	ENSMUSG00000032254	Kif23	3110001D19Rik|C87313|CHO1|Knsl5|MKLP-1|MKLP1	kinesin family member 23	protein-coding
mm_58708.1	chr7	12966231	12966261	+	1	NA	exon (NM_178732, exon 1 of 4)	exon (NM_178732, exon 1 of 4)	382	NM_178732	243834	Mm.133086	NM_178732	ENSMUSG00000004500	Zfp324	A930002M05|D430030K24Rik|ZF5128	zinc finger protein 324	protein-coding
mm_51338.1	chr6	72414324	72414352	+	1	NA	promoter-TSS (NM_019802)	promoter-TSS (NM_019802)	30	NM_019802	56316	Mm.19937	NM_019802	ENSMUSG00000053460	Ggcx	-	gamma-glutamyl carboxylase	protein-coding
mm_26215.1	chr3	138758435	138758460	+	1	NA	intron (NM_019571, intron 1 of 7)	(CCAA)n|Simple_repeat|Simple_repeat	16239	NM_019571	56224	Mm.31927	NM_019571	ENSMUSG00000028152	Tspan5	2810455A09Rik|4930505M03Rik|NET-4|Tm4sf9	tetraspanin 5	protein-coding
mm_26922.1	chr3	20249557	20249581	-	1	NA	TTS (NM_029706)	TTS (NM_029706)	-7388	NM_007753	12873	Mm.1135	NM_007753	ENSMUSG00000001865	Cpa3	MC-CPA	carboxypeptidase A3, mast cell	protein-coding
mm_73239.1	chr8	104143236	104143249	+	1	NA	3' UTR (NM_009868, exon 12 of 12)	3' UTR (NM_009868, exon 12 of 12)	-27271	NM_001141924	65115	Mm.41849	NM_001141922	ENSMUSG00000031872	Bean1	Bean	brain expressed, associated with Nedd4, 1	protein-coding
mm_26000.1	chr3	135212558	135212585	+	1	NA	promoter-TSS (NM_173762)	promoter-TSS (NM_173762)	8	NM_173762	229841	Mm.161470	NM_173762	ENSMUSG00000045328	Cenpe	312kDa|AU019344|BC049989|C530022J18|CENP-E|Kif10	centromere protein E	protein-coding
mm_140160.1	chr17	80224448	80224493	+	1	NA	promoter-TSS (NM_026053)	promoter-TSS (NM_026053)	-19	NM_026053	67242	Mm.279985	NM_026053	ENSMUSG00000055760	Gemin6	2610019B15Rik|2810470M17Rik	gem (nuclear organelle) associated protein 6	protein-coding
mm_97754.1	chr11	80505314	80505331	+	1	NA	intron (NM_177390, intron 21 of 21)	intron (NM_177390, intron 21 of 21)	3784	NR_126552	77417	Mm.437510	NR_126552	ENSMUSG00000085078	C030013C21Rik	-	RIKEN cDNA C030013C21 gene	ncRNA
mm_67198.1	chr7	74284267	74284281	-	1	NA	3' UTR (NM_023908, exon 10 of 10)	3' UTR (NM_023908, exon 10 of 10)	270506	NM_023908	108116	Mm.425467	NM_023908	ENSMUSG00000025790	Slco3a1	5830414C08Rik|Anr1|MJAM|OATP-D|R75096|Slc21a11	solute carrier organic anion transporter family, member 3a1	protein-coding
mm_20558.1	chr2	131074304	131074317	-	1	NA	exon (NM_011426, exon 14 of 21)	exon (NM_011426, exon 14 of 21)	-10496	NM_001163529	110751	Mm.108550	NM_033615	ENSMUSG00000027318	Adam33	Adaml	a disintegrin and metallopeptidase domain 33	protein-coding
mm_56162.1	chr6	87981612	87981622	-	1	NA	promoter-TSS (NR_026990)	promoter-TSS (NR_026990)	-66	NR_026990	434064	Mm.371796	NR_026990	ENSMUSG00000084950	Gm5577	EG434064	predicted gene 5577	ncRNA
mm_112811.1	chr13	20794299	20794307	+	1	NA	5' UTR (NM_001281854, exon 1 of 5)	5' UTR (NM_001281854, exon 1 of 5)	190	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_45677.1	chr5	77310050	77310094	-	1	NA	promoter-TSS (NM_019836)	promoter-TSS (NM_019836)	14	NM_019836	56412	Mm.129136	NM_019836	ENSMUSG00000036285	Noa1	2610024G14Rik|AU022345|AtNOS1|mAtNOS1	nitric oxide associated 1	protein-coding
mm_113527.1	chr13	37826618	37826706	+	1	NA	promoter-TSS (NM_001039188)	promoter-TSS (NM_001039188)	-250	NM_001177868	68750	Mm.491109	NM_026830	ENSMUSG00000039087	Rreb1	1110037N09Rik|AA414966|B930013M22Rik	ras responsive element binding protein 1	protein-coding
mm_104269.1	chr11	89060529	89060588	-	1	NA	promoter-TSS (NR_110336)	promoter-TSS (NR_110336)	190	NM_019505	56077	Mm.153695	NM_019505	ENSMUSG00000000276	Dgke	C87606|DAGK6|DGK	diacylglycerol kinase, epsilon	protein-coding
mm_93481.1	chr10	111995868	111995878	-	1	NA	intron (NM_028608, intron 1 of 5)	intron (NM_028608, intron 1 of 5)	1391	NM_028608	73690	Mm.173790	NM_028608	ENSMUSG00000056888	Glipr1	2410114O14Rik|RTVP-1|RTVP1|mRTVP-1	GLI pathogenesis-related 1 (glioma)	protein-coding
mm_155383.1	chrX	71816121	71816129	+	1	NA	promoter-TSS (NM_001081356)	promoter-TSS (NM_001081356)	45	NM_001290781	67048	Mm.41102	NM_001081356	ENSMUSG00000073131	Vma21	2610030H06Rik|AI840175	VMA21 vacuolar H+-ATPase homolog (S. cerevisiae)	protein-coding
mm_24241.1	chr3	89116708	89116711	+	1	NA	Intergenic	Intergenic	-14742	NM_001253751	110196	Mm.39472	NM_134469	ENSMUSG00000059743	Fdps	6030492I17Rik|AI256750|Fdpsl1|mKIAA1293	farnesyl diphosphate synthetase	protein-coding
mm_125342.1	chr15	39112869	39112915	+	1	NA	promoter-TSS (NM_198606)	promoter-TSS (NM_198606)	18	NM_198606	223499	Mm.321937	NM_198606	ENSMUSG00000022300	Dcaf13	Gm83|Wdsof1	DDB1 and CUL4 associated factor 13	protein-coding
mm_99602.1	chr11	104550689	104550699	+	1	NA	promoter-TSS (NM_010858)	promoter-TSS (NM_010858)	31	NM_010858	17896	Mm.390355	NM_010858	ENSMUSG00000061086	Myl4	ALC1|AMLC|ELC|ELC1a|GT1|MLC1a|Myla	myosin, light polypeptide 4	protein-coding
mm_172610.1	chr8	18607364	18607364	+	1	NA	exon (NM_173189, exon 3 of 14)	exon (NM_173189, exon 3 of 14)	12191	NM_173189	244329	Mm.235296	NM_173189	ENSMUSG00000039842	Mcph1	5430437K10Rik|BRIT1|D030046N04Rik|MCT	microcephaly, primary autosomal recessive 1	protein-coding
mm_15012.1	chr2	152604325	152604350	+	1	NA	promoter-TSS (NM_001037247)	promoter-TSS (NM_001037247)	10	NM_001037247	266620	Mm.330669	NM_001037247	ENSMUSG00000044863	Defb36	BD-36|Defb123|mBD-36	defensin beta 36	protein-coding
mm_140652.1	chr17	12692048	12692067	-	1	NA	exon (NM_010515, exon 40 of 48)	exon (NM_010515, exon 40 of 48)	-16219	NM_009202	20517	Mm.594	NM_009202	ENSMUSG00000023829	Slc22a1	Lx1|Oct1|Orct|Orct1	solute carrier family 22 (organic cation transporter), member 1	protein-coding
mm_168665.1	chr1	191120946	191120958	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	22538	NM_030060	381319	Mm.6922	NM_030060	ENSMUSG00000026630	Batf3	9130211I03Rik|Snft	basic leucine zipper transcription factor, ATF-like 3	protein-coding
mm_118506.1	chr14	13976148	13976156	+	1	NA	Intergenic	Intergenic	-14839	NM_025435	66231	Mm.295875	NM_025435	ENSMUSG00000053453	Thoc7	Nif3l1bp1	THO complex 7	protein-coding
mm_92713.1	chr10	80797862	80797891	-	1	NA	promoter-TSS (NM_013651)	promoter-TSS (NM_013651)	750	NM_023900	78670	Mm.41479	NM_023900	ENSMUSG00000035278	Plekhj1	9530063M10Rik	pleckstrin homology domain containing, family J member 1	protein-coding
mm_113202.1	chr13	24990367	24990409	+	1	NA	3' UTR (NM_008156, exon 26 of 26)	3' UTR (NM_008156, exon 26 of 26)	29929	NM_001013389	380836	Mm.387097	NM_001013389	ENSMUSG00000021339	Mrs2	Gm902|HPT|Mrs2l|RPT	MRS2 magnesium transporter	protein-coding
mm_14449.1	chr2	131103467	131103471	+	1	NA	Intergenic	Intergenic	-16704	NM_011426	20612	Mm.1374	NM_011426	ENSMUSG00000027322	Siglec1	Cd169|Siglec-1|Sn	sialic acid binding Ig-like lectin 1, sialoadhesin	protein-coding
mm_14352.1	chr2	129603731	129603744	+	1	NA	intron (NM_001291022, intron 1 of 4)	intron (NM_001291022, intron 1 of 4)	10568	NM_001291022	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_150332.1	chr19	34575072	34575117	+	1	NA	3' UTR (NM_008332, exon 3 of 3)	3' UTR (NM_008332, exon 3 of 3)	-8435	NM_010501	15959	Mm.426079	NM_010501	ENSMUSG00000074896	Ifit3	Ifi49|P49	interferon-induced protein with tetratricopeptide repeats 3	protein-coding
mm_41398.1	chr5	90773188	90773200	+	1	NA	exon (NM_019932, exon 3 of 3)	exon (NM_019932, exon 3 of 3)	759	NM_019932	56744	Mm.332490	NM_019932	ENSMUSG00000029373	Pf4	Cxcl4|Scyb4	platelet factor 4	protein-coding
mm_21367.1	chr2	157135113	157135134	-	1	NA	promoter-TSS (NM_001139520)	promoter-TSS (NM_001139520)	99	NM_001139520	56045	Mm.248478	NM_018851	ENSMUSG00000027639	Samhd1	E330031J07Rik|Mg11	SAM domain and HD domain, 1	protein-coding
mm_71439.1	chr8	46511760	46511771	+	1	NA	intron (NM_001302163, intron 5 of 20)	intron (NM_001302163, intron 5 of 20)	20799	NM_001302163	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_154782.1	chrX	13041839	13041852	+	1	NA	promoter-TSS (NR_038158)	promoter-TSS (NR_038158)	-170	NR_038158	70489	Mm.383563	NR_038158	ENSMUSG00000087424	5730405O15Rik	-	RIKEN cDNA 5730405O15 gene	ncRNA
mm_142584.1	chr17	46726328	46726342	-	1	NA	TTS (NM_145488)	TTS (NM_145488)	2830	NM_010321	14711	Mm.29395	NM_010321	ENSMUSG00000002769	Gnmt	-	glycine N-methyltransferase	protein-coding
mm_79661.1	chr9	59657201	59657252	+	1	NA	intron (NM_001253883, intron 1 of 10)	CpG	858	NM_001253883	18746	Mm.326167	NM_011099	ENSMUSG00000032294	Pkm	AA414905|AL024370|AL024424|Pk-2|Pk-3|Pk3|Pkm2	pyruvate kinase, muscle	protein-coding
mm_83961.1	chr9	57148102	57148151	-	1	NA	Intergenic	Intergenic	-1092	NM_028347	72774	Mm.35749	NM_028347	ENSMUSG00000032298	Neil1	2810450N13Rik|Nei1	nei endonuclease VIII-like 1 (E. coli)	protein-coding
mm_116595.1	chr13	48545744	48545758	-	1	NA	Intergenic	CpG	-7479	NR_029725	387244		NR_029725	ENSMUSG00000065421	Mirlet7a-1	Let-7a|Mirnlet7a|Mirnlet7a-1|let-7a-1	microRNA let7a-1	ncRNA
mm_103125.1	chr11	70220777	70220790	-	1	NA	5' UTR (NM_172371, exon 1 of 4)	5' UTR (NM_172371, exon 1 of 4)	211	NM_172371	69309	Mm.93266	NM_172371	ENSMUSG00000044367	Slc16a13	1700007D07Rik	solute carrier family 16 (monocarboxylic acid transporters), member 13	protein-coding
mm_94588.1	chr11	11741844	11741858	+	1	NA	intron (NM_001301866, intron 3 of 5)	intron (NM_001301866, intron 3 of 5)	51674	NM_001301863	22778	Mm.103545	NM_009578	ENSMUSG00000018654	Ikzf1	5832432G11Rik|Ikaros|LyF-1|Zfpn1a1|Znfn1a1|hlk-1|mKIAA4227	IKAROS family zinc finger 1	protein-coding
mm_27942.1	chr3	79628753	79628763	-	1	NA	promoter-TSS (NM_025794)	promoter-TSS (NM_025794)	9	NM_025794	66841	Mm.28336	NM_025794	ENSMUSG00000027809	Etfdh	0610010I20Rik|AV001013	electron transferring flavoprotein, dehydrogenase	protein-coding
mm_57011.1	chr6	121131071	121131079	-	1	NA	promoter-TSS (NM_001270475)	promoter-TSS (NM_001270475)	-53	NM_001270475	194401	Mm.122399	NM_153396	ENSMUSG00000051586	Mical3	C130040D16Rik|Mical-3|mKIAA1364	microtubule associated monooxygenase, calponin and LIM domain containing 3	protein-coding
mm_121434.1	chr14	120413046	120413079	+	1	NA	intron (NM_175341, intron 8 of 8)	ORR1F|LTR|ERVL-MaLR	-65399	NM_029519	76108	Mm.261448	NM_029519	ENSMUSG00000051615	Rap2a	5830461H18Rik	RAS related protein 2a	protein-coding
mm_66323.1	chr7	42448080	42448112	-	1	NA	promoter-TSS (NM_027702)	promoter-TSS (NM_027702)	-16	NM_027702	71162	Mm.158598	NM_027702	ENSMUSG00000030463	4933421I07Rik	-	RIKEN cDNA 4933421I07 gene	protein-coding
mm_2459.1	chr1	104780924	104780926	+	1	NA	intron (NM_011800, intron 1 of 11)	PB1D10|SINE|Alu	12106	NM_011800	23836	Mm.103640	NM_011800	ENSMUSG00000050840	Cdh20	Cdh7	cadherin 20	protein-coding
mm_151127.1	chr19	47937649	47937696	+	1	NA	promoter-TSS (NM_001163267)	promoter-TSS (NM_001163267)	-40	NM_001163267	381229	Mm.300553	NM_001163267	ENSMUSG00000046585	Cfap58	Ccdc147|Gm969	cilia and flagella associated protein 58	protein-coding
mm_124794.1	chr15	8169032	8169066	+	1	NA	promoter-TSS (NM_001162906)	promoter-TSS (NM_001162906)	-57	NM_001162906	73692	Mm.164436	NM_001162906	ENSMUSG00000039801	2410089E03Rik	4732468D17Rik|Hug|Jbts17|b2b012Clo	RIKEN cDNA 2410089E03 gene	protein-coding
mm_135178.1	chr16	35939709	35939731	-	1	NA	promoter-TSS (NM_001013371)	promoter-TSS (NM_001013371)	-693	NM_001013371	209200	Mm.390852	NM_001013371	ENSMUSG00000049502	Dtx3l	AU042200|BC023741	deltex 3-like, E3 ubiquitin ligase	protein-coding
mm_111101.1	chr12	80791180	80791196	-	1	NA	intron (NM_001242419, intron 1 of 6)	CpG	656	NM_001242419	217684	Mm.341776	NM_178682	ENSMUSG00000021133	Susd6	4933426M11Rik|mKIAA0247	sushi domain containing 6	protein-coding
mm_3568.1	chr1	150448826	150448834	+	1	NA	TTS (NM_021400)	TTS (NM_021400)	17335	NM_021400	96875	Mm.174256	NM_021400	ENSMUSG00000006014	Prg4	CACP|DOL54|JCAP|MSF|SZP|lubricin	proteoglycan 4 (megakaryocyte stimulating factor, articular superficial zone protein)	protein-coding
mm_30348.1	chr3	151745954	151745974	-	1	NA	exon (NM_133871, exon 4 of 8)	exon (NM_133871, exon 4 of 8)	3995	NM_133871	99899	Mm.30756	NM_133871	ENSMUSG00000028037	Ifi44	A430056A10Rik|AW261460|MTAP44|p44	interferon-induced protein 44	protein-coding
mm_84592.1	chr9	70036796	70036802	-	1	NA	5' UTR (NM_028087, exon 2 of 3)	5' UTR (NM_028087, exon 2 of 3)	1289	NM_028087	72077	Mm.195555	NM_028087	ENSMUSG00000032226	Gcnt3	2010013H22Rik|2210021I22Rik|2210401J11Rik	glucosaminyl (N-acetyl) transferase 3, mucin type	protein-coding
mm_41952.1	chr5	105763897	105763911	+	1	NA	intron (NM_001122768, intron 2 of 2)	intron (NM_001122768, intron 2 of 2)	63094	NM_178701	231549	Mm.23837	NM_178701	ENSMUSG00000046079	Lrrc8d	2810473G09Rik|4930525N13Rik|A930019F03|Lrrc5	leucine rich repeat containing 8D	protein-coding
mm_15090.1	chr2	153241608	153241618	+	1	NA	promoter-TSS (NM_080463)	promoter-TSS (NM_080463)	81	NM_080463	140484	Mm.293761	NM_080463	ENSMUSG00000046020	Pofut1	O-FucT-1|mKIAA0180	protein O-fucosyltransferase 1	protein-coding
mm_4186.1	chr1	171160424	171160434	+	1	NA	3' UTR (NM_008623, exon 8 of 8)	3' UTR (NM_008623, exon 8 of 8)	4911	NM_001315500	17528	Mm.9986	NM_008623	ENSMUSG00000056569	Mpz	Mpp|P-zero|P0	myelin protein zero	protein-coding
mm_15565.1	chr2	158610965	158610971	+	1	NA	promoter-TSS (NR_040359)	promoter-TSS (NR_040359)	210	NM_009508	22348	Mm.143404	NM_009508	ENSMUSG00000037771	Slc32a1	R75019|VGAT|Viaat	solute carrier family 32 (GABA vesicular transporter), member 1	protein-coding
mm_168776.1	chr12	17547992	17547993	+	1	NA	exon (NM_013614, exon 5 of 12)	exon (NM_013614, exon 5 of 12)	3119	NM_013614	18263	Mm.34102	NM_013614	ENSMUSG00000011179	Odc1	ODC	ornithine decarboxylase, structural 1	protein-coding
mm_152596.1	chr19	11640773	11640773	-	1	NA	promoter-TSS (NM_133246)	promoter-TSS (NM_133246)	78	NM_133246	170813	Mm.240438	NM_133246	ENSMUSG00000024681	Ms4a3	HTm4	membrane-spanning 4-domains, subfamily A, member 3	protein-coding
mm_13738.1	chr2	118113092	118113105	+	1	NA	exon (NM_011580, exon 3 of 22)	exon (NM_011580, exon 3 of 22)	1222	NM_001313914	21825	Mm.4159	NM_011580	ENSMUSG00000040152	Thbs1	TSP-1|TSP1|Thbs-1|tbsp1	thrombospondin 1	protein-coding
mm_27751.1	chr3	69588070	69588080	-	1	NA	intron (NM_020026, intron 1 of 2)	intron (NM_020026, intron 1 of 2)	10885	NM_020026	26879	Mm.153710	NM_020026	ENSMUSG00000043300	B3galnt1	B3galt3|b3GT3	UDP-GalNAc:betaGlcNAc beta 1,3-galactosaminyltransferase, polypeptide 1	protein-coding
mm_85514.1	chr9	106314339	106314342	-	1	NA	intron (NM_027354, intron 9 of 10)	MLT1A0|LTR|ERVL-MaLR	33279	NM_027354	70235	Mm.23054	NM_027354	ENSMUSG00000023345	Poc1a	2510040D07Rik|Wdr51a|cha	POC1 centriolar protein A	protein-coding
mm_66716.1	chr7	46098430	46098443	-	1	NA	3' UTR (NM_001204411, exon 2 of 2)	3' UTR (NM_001204411, exon 2 of 2)	1801	NM_010602	16514	Mm.333863	NM_010602	ENSMUSG00000096146	Kcnj11	Kir6.2|mBIR	potassium inwardly rectifying channel, subfamily J, member 11	protein-coding
mm_96151.1	chr11	61142689	61142696	+	1	NA	intron (NM_021349, intron 2 of 3)	intron (NM_021349, intron 2 of 3)	1857	NM_021349	57916	Mm.265915	NM_021349	ENSMUSG00000010142	Tnfrsf13b	1200009E08Rik|Taci	tumor necrosis factor receptor superfamily, member 13b	protein-coding
mm_100229.1	chr11	117199642	117199663	+	1	NA	promoter-TSS (NM_001113486)	promoter-TSS (NM_001113486)	-9	NM_001113486	53860	Mm.38450	NM_017380	ENSMUSG00000059248	Sept9	MSF1|Msf|PNUTL4|Sint1	septin 9	protein-coding
mm_150601.1	chr19	40739399	40739421	+	1	NA	3' UTR (NM_009848, exon 10 of 10)	3' UTR (NM_009848, exon 10 of 10)	79640	NM_009848	12495	Mm.2824	NM_009848	ENSMUSG00000048120	Entpd1	2610206B08Rik|AA408691|Cd39|NTPDase-1	ectonucleoside triphosphate diphosphohydrolase 1	protein-coding
mm_164463.1	chr16	59471864	59471875	+	1	NA	promoter-TSS (NM_025910)	promoter-TSS (NM_025910)	94	NM_025910	67014	Mm.289150	NM_025910	ENSMUSG00000022724	Mina	1810047J07Rik|2410057H13Rik|3830408E23Rik|AI449204	myc induced nuclear antigen	protein-coding
mm_76007.1	chr8	72548346	72548354	-	1	NA	promoter-TSS (NM_027485)	promoter-TSS (NM_027485)	-40	NM_027485	70625	Mm.235885	NM_027485	ENSMUSG00000045248	Med26	5730493L18Rik|AI414941|AW495270|Crsp7	mediator complex subunit 26	protein-coding
mm_150993.1	chr19	46599153	46599178	+	1	NA	promoter-TSS (NM_001177812)	promoter-TSS (NM_001177812)	59	NM_146099	226178	Mm.329895	NM_146099	ENSMUSG00000047731	Wbp1l	D19Wsu162e|Opal1	WW domain binding protein 1 like	protein-coding
mm_72121.1	chr8	71687224	71687241	+	1	NA	intron (NM_010589, intron 22 of 24)	intron (NM_010589, intron 22 of 24)	-2020	NM_013564	16336	Mm.476857	NM_013564	ENSMUSG00000079019	Insl3	Rlf|Rlnl	insulin-like 3	protein-coding
mm_46919.1	chr5	114658383	114658413	-	1	NA	promoter-TSS (NM_022017)	promoter-TSS (NM_022017)	23	NM_022017	63873	Mm.266450	NM_022017	ENSMUSG00000014158	Trpv4	0610033B08Rik|OTRPC4|Trp12|VR-OAC|VRL-2|VROAC	transient receptor potential cation channel, subfamily V, member 4	protein-coding
mm_137534.1	chr17	27555852	27555865	+	1	NA	promoter-TSS (NM_001166545)	promoter-TSS (NM_001166545)	-716	NM_001166536	15361	Mm.4438	NM_016660	ENSMUSG00000046711	Hmga1	AL023995|Hmga1a|Hmga1b|Hmgi|Hmgiy|Hmgy	high mobility group AT-hook 1	protein-coding
mm_154510.1	chrM	12187	12202	-	1	NA	NA	Intergenic	NA	NA								
mm_1766.1	chr1	75549732	75549748	+	1	NA	intron (NM_009208, intron 6 of 22)	intron (NM_009208, intron 6 of 22)	3474	NM_009208	20536	Mm.5053	NM_009208	ENSMUSG00000006576	Slc4a3	A930038D23Rik|Ae3	solute carrier family 4 (anion exchanger), member 3	protein-coding
mm_50108.1	chr6	41533729	41533752	+	1	NA	Intergenic	Intergenic	11964	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_128110.1	chr15	28025895	28025924	-	1	NA	promoter-TSS (NM_001081302)	promoter-TSS (NM_001081302)	-61	NM_001081302	223435	Mm.485422	NM_001081302	ENSMUSG00000022263	Trio	6720464I07Rik|AA408740|Solo	triple functional domain (PTPRF interacting)	protein-coding
mm_50311.1	chr6	47835799	47835824	+	1	NA	5' UTR (NM_027477, exon 1 of 6)	5' UTR (NM_027477, exon 1 of 6)	150	NM_027477	272347	Mm.169059	NM_027477	ENSMUSG00000062519	Zfp398	5730513I23Rik	zinc finger protein 398	protein-coding
mm_153658.1	chr19	44395233	44395245	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	12470	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_28549.1	chr3	93100671	93100674	-	1	NA	Intergenic	Intergenic	27151	NM_001177694	229571	Mm.331194	NM_001034860	ENSMUSG00000096879	Gm4858	EG229571	predicted gene 4858	protein-coding
mm_15114.1	chr2	153649646	153649683	+	1	NA	5' UTR (NM_010068, exon 1 of 21)	5' UTR (NM_010068, exon 1 of 21)	215	NM_001271747	13436	Mm.89772	NM_010068	ENSMUSG00000027478	Dnmt3b	MmuIIIB	DNA methyltransferase 3B	protein-coding
mm_146084.1	chr18	72033054	72033054	+	1	NA	intron (NM_007831, intron 1 of 28)	intron (NM_007831, intron 1 of 28)	318015	NM_007831	13176	Mm.167882	NM_007831	ENSMUSG00000060534	Dcc	C030036D22Rik|Igdcc1	deleted in colorectal carcinoma	protein-coding
mm_90240.1	chr10	121395837	121395871	+	1	NA	3' UTR (NM_029364, exon 14 of 14)	3' UTR (NM_029364, exon 14 of 14)	30764	NM_029364	75612	Mm.207683	NM_029364	ENSMUSG00000034707	Gns	2610016K11Rik|AU042285|C87209|G6S|N28088	glucosamine (N-acetyl)-6-sulfatase	protein-coding
mm_23326.1	chr3	53488678	53488714	+	1	NA	promoter-TSS (NM_153156)	promoter-TSS (NM_153156)	-97	NM_153156	229277	Mm.222810	NM_153156	ENSMUSG00000027744	Stoml3	Epb7.2l|SLP3|sro	stomatin (Epb7.2)-like 3	protein-coding
mm_121183.1	chr14	103049305	103049324	+	1	NA	exon (NM_008392, exon 2 of 5)	exon (NM_008392, exon 2 of 5)	2302	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_91927.1	chr10	60358048	60358100	-	1	NA	exon (NM_001159572, exon 2 of 7)	exon (NM_001159572, exon 2 of 7)	11223	NM_028732	74048	Mm.273584	NM_028732	ENSMUSG00000020101	Vsir	4632428N05Rik|Dies1|PD-1H|VISTA	V-set immunoregulatory receptor	protein-coding
mm_75965.1	chr8	71725651	71725684	-	1	NA	promoter-TSS (NM_028715)	promoter-TSS (NM_028715)	14	NR_131256	74015	Mm.22025	NM_028715	ENSMUSG00000070000	Fcho1	3322402E17Rik|N28152	FCH domain only 1	protein-coding
mm_71887.1	chr8	69822598	69822635	+	1	NA	promoter-TSS (NM_020028)	promoter-TSS (NM_020028)	51	NM_020028	53978	Mm.23253	NM_020028	ENSMUSG00000031861	Lpar2	Edg4|IPA2|LPA2	lysophosphatidic acid receptor 2	protein-coding
mm_57958.1	chr6	135237644	135237648	-	1	NA	exon (NM_010352, exon 7 of 7)	exon (NM_010352, exon 7 of 7)	10238	NM_001080552	14840	Mm.272306	NM_010352	ENSMUSG00000030206	Gsg1	-	germ cell associated 1	protein-coding
mm_172287.1	chr6	93648426	93648429	-	1	NA	Intergenic	MTB_Mm|LTR|ERVL-MaLR	264536	NR_104594	14924	Mm.217216	NM_010367	ENSMUSG00000045095	Magi1	AIP3|BAP1|Baiap1|Gukmi1|MAGI1c|Magi-1|TNRC19|WWP3|mKIAA4129	membrane associated guanylate kinase, WW and PDZ domain containing 1	protein-coding
mm_52600.1	chr6	117171509	117171546	+	1	NA	exon (NM_021704, exon 2 of 3)	exon (NM_021704, exon 2 of 3)	2992	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_128944.1	chr15	74734761	74734776	-	1	NA	promoter-TSS (NM_026671)	promoter-TSS (NM_026671)	-455	NM_026671	68311	Mm.306880	NM_026671	ENSMUSG00000022595	Lypd2	0610005K03Rik|Lypdc2|VLL	Ly6/Plaur domain containing 2	protein-coding
mm_121354.1	chr14	116925559	116925571	+	1	NA	5' UTR (NM_011821, exon 1 of 9)	5' UTR (NM_011821, exon 1 of 9)	268	NM_011821	23888	Mm.440025	NM_011821	ENSMUSG00000058571	Gpc6	-	glypican 6	protein-coding
mm_98270.1	chr11	89004772	89004783	+	1	NA	exon (NM_009546, exon 2 of 9)	exon (NM_009546, exon 2 of 9)	5374	NM_009546	217069	Mm.248445	NM_009546	ENSMUSG00000000275	Trim25	AA960166|AL022677|EFP|Zfp147	tripartite motif-containing 25	protein-coding
mm_64524.1	chr7	143977656	143977684	+	1	NA	intron (NR_037302, intron 5 of 5)	intron (NR_037302, intron 5 of 5)	-31584	NR_037292	100526562		NR_037292	ENSMUSG00000093221	Mir3105	mmu-mir-3105	microRNA 3105	ncRNA
mm_116132.1	chr13	28953406	28953424	-	1	NA	5' UTR (NM_009238, exon 1 of 1)	5' UTR (NM_009238, exon 1 of 1)	267	NM_009238	20677	Mm.240627	NM_009238	ENSMUSG00000076431	Sox4	AA682046|Sox-4	SRY (sex determining region Y)-box 4	protein-coding
mm_130196.1	chr15	94586511	94586531	-	1	NA	exon (NM_008971, exon 3 of 9)	exon (NM_008971, exon 3 of 9)	3303	NM_008971	19230	Mm.490250	NM_008971	ENSMUSG00000022451	Twf1	A6|Ptk9|twinfilin	twinfilin actin binding protein 1	protein-coding
mm_122243.1	chr14	33447121	33447133	-	1	NA	promoter-TSS (NM_001310453)	promoter-TSS (NM_001310453)	31	NM_001310453	26419	Mm.21495	NM_016700	ENSMUSG00000021936	Mapk8	AI849689|JNK|JNK1|Prkm8|SAPK1	mitogen-activated protein kinase 8	protein-coding
mm_7068.1	chr1	87659796	87659808	-	1	NA	intron (NM_010566, intron 2 of 26)	intron (NM_010566, intron 2 of 26)	39490	NM_001110193	16331	Mm.15105	NM_010566	ENSMUSG00000026288	Inpp5d	SHIP|SHIP-1|SHIP1|SIP-145|p150Ship|s-SHIP	inositol polyphosphate-5-phosphatase D	protein-coding
mm_101527.1	chr11	33151288	33151291	-	1	NA	Intergenic	B1_Mus1|SINE|Alu	-3889	NR_102395	14172	Mm.339812	NM_008005	ENSMUSG00000057967	Fgf18	D130055P09Rik|FGF-18	fibroblast growth factor 18	protein-coding
mm_20457.1	chr2	129365227	129365242	-	1	NA	exon (NM_008361, exon 7 of 7)	exon (NM_008361, exon 7 of 7)	-4668	NR_015474	329514	Mm.207315	NM_177848	ENSMUSG00000074805	Il1bos	9430083I22|Gm14047|OTTMUSG00000015529	interleukin 1 beta, opposite strand	ncRNA
mm_89355.1	chr10	88201159	88201218	+	1	NA	promoter-TSS (NM_001122960)	promoter-TSS (NM_001122960)	91	NM_027487	67282	Mm.208465	NM_026070	ENSMUSG00000020056	Washc3	2900091E11Rik|5730495F03Rik|Ccdc53	WASH complex subunit 3	protein-coding
mm_148926.1	chr19	6996144	6996207	+	1	NA	promoter-TSS (NM_153597)	promoter-TSS (NM_153597)	44	NR_027351	107328	Mm.391161	NM_153597	ENSMUSG00000047656	Trpt1	AU079016|AW045591|Tpt1|Tpt1h	tRNA phosphotransferase 1	protein-coding
mm_125286.1	chr15	36726362	36726379	+	1	NA	Intergenic	Intergenic	64562	NM_001253807	22631	Mm.3360	NM_011740	ENSMUSG00000022285	Ywhaz	1110013I11Rik|14-3-3zeta|AI596267|AL022924|AU020854	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide	protein-coding
mm_110233.1	chr12	29915154	29915162	-	1	NA	intron (NM_001093778, intron 23 of 24)	intron (NM_001093778, intron 23 of 24)	-22878	NM_181395	69675	Mm.251774	NM_181395	ENSMUSG00000020674	Pxdn	2310075M15Rik|C85409|E330004E07|VPO1|mKIAA0230	peroxidasin	protein-coding
mm_159247.1	chr2	151668586	151668586	-	1	NA	promoter-TSS (NM_001276400)	promoter-TSS (NM_001276400)	-53	NM_001276400	668929	Mm.473683	NM_001114677	ENSMUSG00000074704	Rad21l	Gm14160|MeiRAD21L|Rad21l1	RAD21-like (S. pombe)	protein-coding
mm_116068.1	chr13	27640748	27640754	-	1	NA	exon (NM_001164058, exon 2 of 7)	exon (NM_001164058, exon 2 of 7)	1742	NM_001164058	19113	Mm.196424	NM_008930	ENSMUSG00000006488	Prl7a1	AA407021|AA409971|AA410116|PLP-E|PLP-G|Prlpe|Prlpg	prolactin family 7, subfamily a, member 1	protein-coding
mm_79314.1	chr9	52068211	52068249	+	1	NA	exon (NM_009041, exon 7 of 14)	exon (NM_009041, exon 7 of 14)	-19525	NR_023357	629557	Mm.422775	NR_023357		Gm6981	EG629557	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_124742.1	chr15	6599374	6599407	+	1	NA	intron (NM_011815, intron 1 of 17)	B1_Mur1|SINE|Alu	19543	NM_011815	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_131905.1	chr16	23269311	23269328	+	1	NA	intron (NM_001252505, intron 2 of 7)	RMER13A2|LTR|ERVK	-21151	NM_001252506	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_10162.1	chr2	4401292	4401332	+	1	NA	5' UTR (NM_001177843, exon 1 of 24)	5' UTR (NM_001177843, exon 1 of 24)	336	NM_001177843	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding
mm_156769.1	chrX	160768127	160768129	+	1	NA	5' UTR (NM_011302, exon 1 of 6)	5' UTR (NM_011302, exon 1 of 6)	115	NM_011302	20147	Mm.41982	NM_011302	ENSMUSG00000031293	Rs1	Rs1h|Xlrs1|tmgc1	retinoschisis (X-linked, juvenile) 1 (human)	protein-coding
mm_25340.1	chr3	106721810	106721822	+	1	NA	5' UTR (NM_001039488, exon 1 of 4)	5' UTR (NM_001039488, exon 1 of 4)	134	NM_001286685	321000	Mm.259638	NM_028081	ENSMUSG00000056260	Lrif1	2010012G17Rik|4933421E11Rik|AI450568	ligand dependent nuclear receptor interacting factor 1	protein-coding
mm_63012.1	chr7	120982497	120982514	+	1	NA	promoter-TSS (NM_007672)	promoter-TSS (NM_007672)	-4	NM_028955	74466	Mm.189707	NM_028955	ENSMUSG00000030877	Mfsd13b	4933427G17Rik	major facilitator superfamily domain containing 13B	protein-coding
mm_159997.1	chr6	119052763	119052763	-	1	NA	intron (NM_001256002, intron 2 of 47)	intron (NM_001256002, intron 2 of 47)	55732	NM_001159534	12288	Mm.41628	NM_009781	ENSMUSG00000051331	Cacna1c	Cav1.2|Cchl1a1|D930026N18Rik|MBC|MELC-CC	calcium channel, voltage-dependent, L type, alpha 1C subunit	protein-coding
mm_42355.1	chr5	114911672	114911680	+	1	NA	3' UTR (NM_011854, exon 6 of 6)	3' UTR (NM_011854, exon 6 of 6)	-11564	NM_145209	231655	Mm.95479	NM_145209	ENSMUSG00000041827	Oasl1	7530414C13Rik|oasl9	2'-5' oligoadenylate synthetase-like 1	protein-coding
mm_132012.1	chr16	25865777	25865785	+	1	NA	intron (NM_001127259, intron 7 of 13)	intron (NM_001127259, intron 7 of 13)	63865	NM_001127264	22061	Mm.20894	NM_011641	ENSMUSG00000022510	Trp63	AI462811|Ket|P51/P63|P63|P73l|Tp63|Trp53rp1	transformation related protein 63	protein-coding
mm_93670.1	chr10	117710104	117710128	-	1	NA	intron (NM_001288586, intron 1 of 10)	CpG-1528	642	NM_010786	17246	Mm.22670	NM_010786	ENSMUSG00000020184	Mdm2	1700007J15Rik|AA415488|Mdm-2	transformed mouse 3T3 cell double minute 2	protein-coding
mm_37723.1	chr4	129558356	129558378	-	1	NA	promoter-TSS (NM_010693)	promoter-TSS (NM_010693)	5	NM_001162432	16818	Mm.293753	NM_010693	ENSMUSG00000000409	Lck	Hck-3|Lsk|Lskt|p56<lck>|p56Lck	lymphocyte protein tyrosine kinase	protein-coding
mm_2128.1	chr1	88055378	88055449	+	1	NA	promoter-TSS (NM_201641)	promoter-TSS (NM_201641)	2	NM_201641	394430	Mm.300095	NM_201641	ENSMUSG00000090165	Ugt1a10	A13|Ugt1a13	UDP glycosyltransferase 1 family, polypeptide A10	protein-coding
mm_82172.1	chr9	123850322	123850333	+	1	NA	intron (NM_148925, intron 1 of 18)	intron (NM_148925, intron 1 of 18)	1334	NM_148925	17281	Mm.252941	NM_148925	ENSMUSG00000025241	Fyco1	2810409M01Rik|Mem2|RUFY3|ZFYVE7	FYVE and coiled-coil domain containing 1	protein-coding
mm_82399.1	chr9	14751959	14751973	-	1	NA	exon (NM_010242, exon 1 of 1)	exon (NM_010242, exon 1 of 1)	156	NM_010242	14345	Mm.63450	NM_010242	ENSMUSG00000049307	Fut4	AI451562|CD15|FAL|FucT-IV|LeX|SSEA-1|Ssea1	fucosyltransferase 4	protein-coding
mm_58635.1	chr7	5097242	5097291	+	1	NA	exon (NM_001252454, exon 10 of 11)	exon (NM_001252454, exon 10 of 11)	17031	NM_001252454	13854	Mm.3091	NM_010147	ENSMUSG00000035203	Epn1	AA269831|Ibp1	epsin 1	protein-coding
mm_103977.1	chr11	84823589	84823610	-	1	NA	intron (NM_177564, intron 2 of 6)	intron (NM_177564, intron 2 of 6)	-4084	NM_145433	217038	Mm.280825	NM_145433	ENSMUSG00000018405	Mrm1	A530065E19Rik|ENSMUSG00000054212	mitochondrial rRNA methyltransferase 1	protein-coding
mm_76043.1	chr8	77517899	77517938	-	1	NA	promoter-TSS (NM_030113)	promoter-TSS (NM_030113)	-11	NM_030113	78514	Mm.165974	NM_030113	ENSMUSG00000037148	Arhgap10	A930033B01Rik|PSGAP-m|PSGAP-s	Rho GTPase activating protein 10	protein-coding
mm_67501.1	chr7	80778842	80778858	-	1	NA	intron (NM_016721, intron 2 of 37)	B1_Mus1|SINE|Alu	24481	NM_016721	29875	Mm.207619	NM_016721	ENSMUSG00000030536	Iqgap1	AA682088|D7Ertd237e|D7Ertd257e|mKIAA0051	IQ motif containing GTPase activating protein 1	protein-coding
mm_45321.1	chr5	65479817	65479844	-	1	NA	intron (NM_133697, intron 1 of 4)	intron (NM_133697, intron 1 of 4)	13005	NM_133697	68552	Mm.10709	NM_133697	ENSMUSG00000037822	Smim14	1110003E01Rik|1700127H04Rik|5430439C17Rik|MAd4	small integral membrane protein 14	protein-coding
mm_63304.1	chr7	126824114	126824135	+	1	NA	promoter-TSS (NM_001146347)	promoter-TSS (NM_001146347)	-529	NM_001146347	68952	Mm.440393	NM_026884	ENSMUSG00000058966	Fam57b	1500016O10Rik|A330104J06Rik|AI413816|AW060769	family with sequence similarity 57, member B	protein-coding
mm_23916.1	chr3	83046643	83046659	+	1	NA	intron (NM_181849, intron 2 of 7)	intron (NM_181849, intron 2 of 7)	3212	NM_181849	110135	Mm.30063	NM_181849	ENSMUSG00000033831	Fgb	2510049G14Rik	fibrinogen beta chain	protein-coding
mm_87195.1	chr10	39531846	39531884	+	1	NA	intron (NM_001122892, intron 8 of 12)	intron (NM_001122892, intron 8 of 12)	-81069	NM_134000	103213	Mm.436686	NM_134000	ENSMUSG00000019842	Traf3ip2	AI429613|Act1|CIKS	TRAF3 interacting protein 2	protein-coding
mm_15401.1	chr2	156730648	156730690	+	1	NA	intron (NM_001042487, intron 1 of 6)	intron (NM_001042487, intron 1 of 6)	9390	NM_001042487	228836	Mm.22094	NM_146128	ENSMUSG00000061689	Dlgap4	AI225853|BC024558|DAP-4|DAP4|SAPAP-4|Sapap4|WBP16	discs, large homolog-associated protein 4 (Drosophila)	protein-coding
mm_171482.1	chr4	145868882	145868886	+	1	NA	Intergenic	Intergenic	31665	NR_033612	236069	Mm.276881	NR_033612	ENSMUSG00000096233	Gm13238	OTTMUSG00000011065	carnitine deficiency-associated gene expressed in ventricle 3 pseudogene	pseudo
mm_170622.1	chr19	6855286	6855295	-	1	NA	intron (NM_001081291, intron 10 of 26)	intron (NM_001081291, intron 10 of 26)	2921	NM_001081291	78317	Mm.329596	NM_198008	ENSMUSG00000047810	Ccdc88b	2610041P08Rik|Ccdc88	coiled-coil domain containing 88B	protein-coding
mm_170108.1	chr17	39844798	39844802	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	1803	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_94358.1	chr11	4986899	4986949	+	1	NA	promoter-TSS (NM_001243044)	promoter-TSS (NM_001243044)	100	NM_007454	11764	Mm.274816	NM_007454	ENSMUSG00000009090	Ap1b1	Adtb1|b2b1660Clo	adaptor protein complex AP-1, beta 1 subunit	protein-coding
mm_122112.1	chr14	30951256	30951289	-	1	NA	promoter-TSS (NM_001308328)	promoter-TSS (NM_001308328)	-105	NM_001308328	23955	Mm.251494	NM_011849	ENSMUSG00000021918	Nek4	Stk2	NIMA (never in mitosis gene a)-related expressed kinase 4	protein-coding
mm_145123.1	chr18	44380813	44380825	+	1	NA	intron (NM_027490, intron 1 of 10)	CpG	319	NM_027490	70640	Mm.87629	NM_027490	ENSMUSG00000024472	Dcp2	2410015D23Rik|5730537H01Rik|AL118268	decapping mRNA 2	protein-coding
mm_76309.1	chr8	84642841	84642848	-	1	NA	Intergenic	Intergenic	20008	NM_010499	15936	Mm.399	NM_010499	ENSMUSG00000053560	Ier2	AI317238|Ch1|Pip92	immediate early response 2	protein-coding
mm_80106.1	chr9	70398853	70398871	+	1	NA	3' UTR (NM_181072, exon 28 of 28)	3' UTR (NM_181072, exon 28 of 28)	6891	NR_049200	100885839		NR_049200	ENSMUSG00000093763	Mir5626	Gm25590|mir-5626|mmu-mir-5626	microRNA 5626	ncRNA
mm_98014.1	chr11	84870862	84870921	+	1	NA	promoter-TSS (NM_153144)	promoter-TSS (NM_153144)	-32	NR_131197	102635561	Mm.341797	NR_131197		Ggnbp2os	-	gametogenetin binding protein 2, opposite strand	ncRNA
mm_136420.1	chr16	93971113	93971118	-	1	NA	intron (NM_019500, intron 1 of 2)	intron (NM_019500, intron 1 of 2)	37722	NM_019500	56173	Mm.328716	NM_019500	ENSMUSG00000047109	Cldn14	AI851731	claudin 14	protein-coding
mm_143881.1	chr17	84273109	84273140	-	1	NA	intron (NM_183021, intron 29 of 37)	intron (NM_183021, intron 29 of 37)	-85177	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_29491.1	chr3	115887880	115887891	-	1	NA	promoter-TSS (NM_027193)	promoter-TSS (NM_027193)	174	NR_027894	68161	Mm.392043	NR_015487	ENSMUSG00000054426	A930005H10Rik	-	RIKEN cDNA A930005H10 gene	ncRNA
mm_26878.1	chr3	17785306	17785316	-	1	NA	Intergenic	Intergenic	-4610	NR_033490	70441	Mm.458192	NR_033490	ENSMUSG00000100252	Mir124-2hg	100040120|2610100L16Rik|6430547I21Rik|A930005K07Rik|AW125202|Gm2612	Mir124-2 host gene (non-protein coding)	ncRNA
mm_18502.1	chr2	62610601	62610618	-	1	NA	exon (NM_027835, exon 7 of 16)	exon (NM_027835, exon 7 of 16)	35646	NM_027835	71586	Mm.136224	NM_027835	ENSMUSG00000026896	Ifih1	9130009C22Rik|Helicard|Hlcd|MDA5|RLR-2	interferon induced with helicase C domain 1	protein-coding
mm_77153.1	chr8	111686606	111686612	-	1	NA	TTS (NM_025583)	TTS (NM_025583)	3065	NR_106044	102466993		NR_106044	ENSMUSG00000099129	Mir7076	Gm27318|mmu-mir-7076	microRNA 7076	ncRNA
mm_32702.1	chr4	116075438	116075461	+	1	NA	promoter-TSS (NM_025641)	promoter-TSS (NM_025641)	180	NM_153521	230654	Mm.3655	NM_153521	ENSMUSG00000028703	Lrrc41	AA409966|AW555107|D630045E04Rik|D730026A16Rik|MUF1	leucine rich repeat containing 41	protein-coding
mm_115430.1	chr13	117249435	117249446	+	1	NA	exon (NM_010330, exon 3 of 9)	exon (NM_010330, exon 3 of 9)	28867	NM_010330	13723	Mm.274926	NM_010330	ENSMUSG00000021728	Emb	AL022799|Gp70	embigin	protein-coding
mm_8192.1	chr1	138102836	138102857	-	1	NA	intron (NM_001111316, intron 11 of 31)	intron (NM_001111316, intron 11 of 31)	72280	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_25254.1	chr3	104657091	104657094	+	1	NA	3' UTR (NM_009196, exon 5 of 5)	3' UTR (NM_009196, exon 5 of 5)	18428	NM_009196	20501	Mm.9086	NM_009196	ENSMUSG00000032902	Slc16a1	AL022710|Mct1	solute carrier family 16 (monocarboxylic acid transporters), member 1	protein-coding
mm_30442.1	chr3	153650255	153650268	-	1	NA	intron (NM_011372, intron 1 of 4)	Lx9|LINE|L1	74872	NM_011372	20447	Mm.296453	NM_011372	ENSMUSG00000052544	St6galnac3	Siat7c	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 3	protein-coding
mm_50502.1	chr6	49036498	49036514	+	1	NA	promoter-TSS (NM_053110)	promoter-TSS (NM_053110)	-12	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_127753.1	chr15	103502952	103503030	+	1	NA	promoter-TSS (NM_008800)	promoter-TSS (NM_008800)	-43	NM_008800	18574	Mm.390792	NM_008800	ENSMUSG00000022489	Pde1b	Pde1b1	phosphodiesterase 1B, Ca2+-calmodulin dependent	protein-coding
mm_102483.1	chr11	60199420	60199453	-	1	NA	TTS (NM_009021)	TTS (NM_009021)	1181	NR_105886	102465555		NR_105886	ENSMUSG00000098547	Mir6921	Gm27352|mmu-mir-6921	microRNA 6921	ncRNA
mm_77187.1	chr8	111854279	111854356	-	1	NA	promoter-TSS (NM_011801)	promoter-TSS (NM_011801)	-7	NM_011801	23837	Mm.279437	NM_011801	ENSMUSG00000031954	Cfdp1	AA408409|Bcnt|Bucentaur|Cfdp|cp27	craniofacial development protein 1	protein-coding
mm_45494.1	chr5	72159787	72159801	-	1	NA	3' UTR (NM_178599, exon 5 of 5)	3' UTR (NM_178599, exon 5 of 5)	8389	NM_178599	27784	Mm.44223	NM_178599	ENSMUSG00000029213	Commd8	C77770|D5Buc26e	COMM domain containing 8	protein-coding
mm_45619.1	chr5	75933664	75933667	-	1	NA	3' UTR (NM_010612, exon 30 of 30)	3' UTR (NM_010612, exon 30 of 30)	44763	NM_010612	16542	Mm.285	NM_010612	ENSMUSG00000062960	Kdr	6130401C07|Flk-1|Flk1|Krd-1|Ly73|VEGFR-2|VEGFR2|sVEGFR-2	kinase insert domain protein receptor	protein-coding
mm_144732.1	chr18	35562168	35562174	+	1	NA	promoter-TSS (NM_010771)	promoter-TSS (NM_010771)	13	NM_010771	17184	Mm.215034	NM_010771	ENSMUSG00000037236	Matr3	1110061A14Rik|2810017I02Rik|AI841759|AW555618|D030046F20Rik|mKIAA0723	matrin 3	protein-coding
mm_52170.1	chr6	99095721	99095731	+	1	NA	intron (NM_001347345, intron 5 of 19)	intron (NM_001347345, intron 5 of 19)	-67428	NM_001197322	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_112933.1	chr13	20966663	20966678	+	1	NA	intron (NM_012054, intron 12 of 20)	intron (NM_012054, intron 12 of 20)	106629	NM_146535	258528	Mm.377554	NM_146535	ENSMUSG00000042869	Olfr1370	MOR256-14	olfactory receptor 1370	protein-coding
mm_129410.1	chr15	78305639	78305670	-	1	NA	promoter-TSS (NM_007781)	promoter-TSS (NM_007781)	67	NM_007781	12984	Mm.1940	NM_007781	ENSMUSG00000071714	Csf2rb2	AIC2A|BetaIl3|Bil3|Csfgmrb|Il3r|Il3rb|Il3rb2	colony stimulating factor 2 receptor, beta 2, low-affinity (granulocyte-macrophage)	protein-coding
mm_29710.1	chr3	123672381	123672400	-	1	NA	promoter-TSS (NM_031186)	promoter-TSS (NM_031186)	87	NM_031186	83398	Mm.443908	NM_031186	ENSMUSG00000027977	Ndst3	4921531K01Rik|4930511P15Rik|N-HSST 3|NDST-3	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 3	protein-coding
mm_162522.1	chr1	157363100	157363101	+	1	NA	intron (NM_177644, intron 1 of 17)	intron (NM_177644, intron 1 of 17)	-49252	NR_027984	69953	Mm.286863	NM_027274	ENSMUSG00000049881	2810025M15Rik	AI429618	RIKEN cDNA 2810025M15 gene	ncRNA
mm_84587.1	chr9	70032635	70032637	-	1	NA	3' UTR (NM_028087, exon 3 of 3)	3' UTR (NM_028087, exon 3 of 3)	5452	NM_028087	72077	Mm.195555	NM_028087	ENSMUSG00000032226	Gcnt3	2010013H22Rik|2210021I22Rik|2210401J11Rik	glucosaminyl (N-acetyl) transferase 3, mucin type	protein-coding
mm_41947.1	chr5	105732083	105732111	+	1	NA	intron (NM_178701, intron 1 of 2)	CpG	31287	NM_178701	231549	Mm.23837	NM_178701	ENSMUSG00000046079	Lrrc8d	2810473G09Rik|4930525N13Rik|A930019F03|Lrrc5	leucine rich repeat containing 8D	protein-coding
mm_84785.1	chr9	76567127	76567131	-	1	NA	Intergenic	CpG	-21325	NM_001045518	208994	Mm.256929	NM_001045518	ENSMUSG00000032358	Fam83b	C530008M07Rik|Gm516	family with sequence similarity 83, member B	protein-coding
mm_102744.1	chr11	67254559	67254585	-	1	NA	exon (NM_010855, exon 29 of 40)	exon (NM_010855, exon 29 of 40)	16760	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_149484.1	chr19	11810014	11810022	+	1	NA	intron (NM_001025307, intron 1 of 10)	intron (NM_001025307, intron 1 of 10)	9385	NM_001286543	20908	Mm.272264	NM_011502	ENSMUSG00000041488	Stx3	Syn-3	syntaxin 3	protein-coding
mm_164689.1	chr17	47728751	47728751	+	1	NA	exon (NM_025973, exon 2 of 9)	exon (NM_025973, exon 2 of 9)	1909	NM_025973	109820	Mm.22957	NM_025973	ENSMUSG00000023987	Pgc	2210410L06Rik|Upg-1|Upg1	progastricsin (pepsinogen C)	protein-coding
mm_112714.1	chr13	19185006	19185022	+	1	NA	Intergenic	Intergenic	210799	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_15801.1	chr2	164461064	164461074	+	1	NA	promoter-TSS (NM_025575)	promoter-TSS (NM_025575)	98	NM_025575	66460	Mm.44218	NM_025575	ENSMUSG00000045503	Sys1	2610042O14Rik|AI266964|C87389	SYS1 Golgi-localized integral membrane protein homolog (S. cerevisiae)	protein-coding
mm_51516.1	chr6	83142388	83142429	+	1	NA	intron (NM_009106, intron 2 of 12)	CpG	5324	NM_009106	20166	Mm.4139	NM_009106	ENSMUSG00000034930	Rtkn	-	rhotekin	protein-coding
mm_5075.1	chr1	3667835	3667838	-	1	NA	intron (NM_001011874, intron 1 of 2)	AT_rich|Low_complexity|Low_complexity	3662	NM_001011874	497097	Mm.454496	NM_001011874	ENSMUSG00000051951	Xkr4	AY534250|Gm210|XRG4|mKIAA1889	X-linked Kx blood group related 4	protein-coding
mm_43590.1	chr5	137758112	137758118	+	1	NA	intron (NM_029805, intron 3 of 5)	intron (NM_029805, intron 3 of 5)	12146	NM_029805	78829	Mm.286399	NM_023910	ENSMUSG00000029723	Tsc22d4	0610009M14Rik|1700023B23Rik|AI415410|Thg-1pit|Tilz2	TSC22 domain family, member 4	protein-coding
mm_71759.1	chr8	66386293	66386308	+	1	NA	promoter-TSS (NM_001166375)	promoter-TSS (NM_001166375)	-1	NM_001166375	72925	Mm.380457	NM_175188	ENSMUSG00000036469	March1	2900024D24Rik|BB085186	membrane-associated ring finger (C3HC4) 1	protein-coding
mm_34157.1	chr4	139431087	139431107	+	1	NA	intron (NM_001160319, intron 48 of 105)	ID_B1|SINE|B4	50438	NM_001160319	69116	Mm.271956	NM_001160319	ENSMUSG00000066036	Ubr4	1810009A16Rik|A930005E13Rik|D930005K06Rik|Gm1032|Gm1666|N28143|RBAF600|Zubr1|mKIAA0462|p600	ubiquitin protein ligase E3 component n-recognin 4	protein-coding
mm_155109.1	chrX	48519246	48519281	+	1	NA	promoter-TSS (NM_011228)	promoter-TSS (NM_011228)	-22	NM_011228	19337	Mm.2015	NM_011228	ENSMUSG00000031104	Rab33a	Rabs10	RAB33A, member RAS oncogene family	protein-coding
mm_86139.1	chr9	116860114	116860117	-	1	NA	intron (NM_001172122, intron 4 of 13)	intron (NM_001172122, intron 4 of 13)	392368	NM_001172123	207181	Mm.326411	NM_178660	ENSMUSG00000039607	Rbms3	6720477E09Rik|8430436O14Rik	RNA binding motif, single stranded interacting protein	protein-coding
mm_85686.1	chr9	107985908	107985924	-	1	NA	promoter-TSS (NM_026597)	promoter-TSS (NM_026597)	0	NM_026597	68176	Mm.76166	NM_026597	ENSMUSG00000042106	Fam212a	6230427J02Rik|Inka1	family with sequence similarity 212, member A	protein-coding
mm_91572.1	chr10	40128222	40128260	-	1	NA	intron (NM_001114332, intron 1 of 5)	(TG)n|Simple_repeat|Simple_repeat	14013	NM_028247	72472	Mm.186778	NM_028247	ENSMUSG00000019838	Slc16a10	2610103N14Rik|9830169E08|Mct10|PRO0813|TAT1	solute carrier family 16 (monocarboxylic acid transporters), member 10	protein-coding
mm_136000.1	chr16	75399738	75399746	-	1	NA	Intergenic	Lx2B|LINE|L1	186319	NM_001252513	320355	Mm.99517	NM_177142	ENSMUSG00000032948	Lipi	D930038D03Rik|lpd1	lipase, member I	protein-coding
mm_113268.1	chr13	28953915	28953920	+	1	NA	promoter-TSS (NM_009238)	promoter-TSS (NM_009238)	-235	NM_009238	20677	Mm.240627	NM_009238	ENSMUSG00000076431	Sox4	AA682046|Sox-4	SRY (sex determining region Y)-box 4	protein-coding
mm_142163.1	chr17	36145762	36145769	-	1	NA	intron (NR_033517, intron 1 of 3)	CpG	747	NR_033517	675325	Mm.75890	NR_033517	ENSMUSG00000038311	2410017I17Rik	-	RIKEN cDNA 2410017I17 gene	ncRNA
mm_83377.1	chr9	44526505	44526515	-	1	NA	promoter-TSS (NM_007551)	promoter-TSS (NM_007551)	-89	NM_007551	12145	Mm.6246	NM_007551	ENSMUSG00000047880	Cxcr5	Blr1|CXC-R5|CXCR-5|Gpcr6|MDR15	chemokine (C-X-C motif) receptor 5	protein-coding
mm_101381.1	chr11	23818862	23818886	-	1	NA	Intergenic	Intergenic	-47904	NM_009044	19696	Mm.4869	NM_009044	ENSMUSG00000020275	Rel	c-Rel	reticuloendotheliosis oncogene	protein-coding
mm_9838.1	chr1	184034258	184034268	-	1	NA	promoter-TSS (NM_028516)	promoter-TSS (NM_028516)	-198	NM_022019	63953	Mm.404024	NM_022019	ENSMUSG00000039384	Dusp10	2610306G15Rik|AI158871|MKP-5|MKP5	dual specificity phosphatase 10	protein-coding
mm_145511.1	chr18	60392260	60392275	+	1	NA	3' UTR (NM_001146275, exon 3 of 3)	3' UTR (NM_001146275, exon 3 of 3)	16238	NM_001146275	60440	Mm.261140	NM_021792	ENSMUSG00000054072	Iigp1	2900074L10Rik|AI046432|AW111922|Ifgga1|Iigp|Irga6	interferon inducible GTPase 1	protein-coding
mm_148728.1	chr19	5877795	5877840	+	1	NA	promoter-TSS (NM_134154)	promoter-TSS (NM_134154)	-649	NM_134154	107375	Mm.5323	NM_134154	ENSMUSG00000024818	Slc25a45	AW491445	solute carrier family 25, member 45	protein-coding
mm_4789.1	chr1	184372244	184372248	+	1	NA	Intergenic	Intergenic	185445	NR_040472	73590	Mm.82792	NR_040472	ENSMUSG00000101574	1700112H15Rik	-	RIKEN cDNA 1700112H15 gene	ncRNA
mm_37721.1	chr4	129558254	129558258	-	1	NA	promoter-TSS (NR_106199)	promoter-TSS (NR_106199)	116	NM_001162432	16818	Mm.293753	NM_010693	ENSMUSG00000000409	Lck	Hck-3|Lsk|Lskt|p56<lck>|p56Lck	lymphocyte protein tyrosine kinase	protein-coding
mm_29421.1	chr3	108976568	108976586	-	1	NA	intron (NM_001163567, intron 10 of 10)	intron (NM_001163567, intron 10 of 10)	36020	NM_001078646	66715	Mm.158124	NM_025723	ENSMUSG00000045662	Henmt1	4921515J06Rik|Hen1|mHEN1	HEN1 methyltransferase homolog 1 (Arabidopsis)	protein-coding
mm_10736.1	chr2	23068262	23068284	+	1	NA	promoter-TSS (NM_001102438)	promoter-TSS (NM_001102438)	72	NM_001102436	74159	Mm.181973	NM_028793	ENSMUSG00000026781	Acbd5	1300014E15Rik	acyl-Coenzyme A binding domain containing 5	protein-coding
mm_1384.1	chr1	66944817	66944825	+	1	NA	exon (NM_021285, exon 1 of 7)	exon (NM_021285, exon 1 of 7)	235	NM_021285	17901	Mm.1000	NM_021285	ENSMUSG00000061816	Myl1	AI325107|MLC1f|MLC3f|Mylf	myosin, light polypeptide 1	protein-coding
mm_119706.1	chr14	53800816	53800834	+	1	NA	Intergenic	Intergenic	453104	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_67670.1	chr7	88299468	88299485	-	1	NA	exon (NM_009982, exon 4 of 7)	exon (NM_009982, exon 4 of 7)	21391	NM_001311790	13032	Mm.89295	NM_009982	ENSMUSG00000030560	Ctsc	AI047818|CatC|DPP1|DPPI	cathepsin C	protein-coding
mm_78181.1	chr9	21200706	21200761	+	1	NA	intron (NM_001310750, intron 7 of 14)	intron (NM_001310750, intron 7 of 14)	4028	NM_019798	18577	Mm.191749	NM_019798	ENSMUSG00000032177	Pde4a	D9Ertd60e|Dpde2	phosphodiesterase 4A, cAMP specific	protein-coding
mm_87630.1	chr10	58323527	58323533	+	1	NA	promoter-TSS (NM_026148)	promoter-TSS (NM_026148)	64	NM_026148	110829	Mm.57734	NM_026148	ENSMUSG00000019920	Lims1	2310016J22Rik|4921524A02Rik|AI507642|AU021743|AW551584|C430041B13Rik|Lims1l|PINCH|PINCH1	LIM and senescent cell antigen-like domains 1	protein-coding
mm_173017.1	chrX	100865916	100865917	-	1	NA	intron (NM_031384, intron 25 of 29)	L1Md_T|LINE|L1	88645	NM_001177780	53310	Mm.4615	NM_016747	ENSMUSG00000000881	Dlg3	Dlgh3|SAP102|mKIAA1232	discs, large homolog 3 (Drosophila)	protein-coding
mm_120427.1	chr14	65666431	65666443	+	1	NA	promoter-TSS (NM_001168318)	promoter-TSS (NM_001168318)	34	NM_001168318	71145	Mm.83840	NM_028903	ENSMUSG00000022032	Scara5	4932433F15Rik|4933425F03Rik|AV278087|Tesr	scavenger receptor class A, member 5	protein-coding
mm_42132.1	chr5	111116382	111116384	+	1	NA	intron (NM_001267622, intron 5 of 22)	L1MEg|LINE|L1	112239	NR_030482	735278		NR_030482	ENSMUSG00000076163	Mir701	Mirn701|mir-701|mmu-mir-701	microRNA 701	ncRNA
mm_38249.1	chr4	136676138	136676140	-	1	NA	intron (NM_001290753, intron 6 of 15)	ID_B1|SINE|B4	53518	NM_001243262	242707	Mm.448979	NM_001243262	ENSMUSG00000070683	Lactbl1	-	lactamase, beta-like 1	protein-coding
mm_82055.1	chr9	122681894	122681896	+	1	NA	promoter-TSS (NR_029819)	promoter-TSS (NR_029819)	-981	NR_029819	387156		NR_029819	ENSMUSG00000065414	Mir138-1	Mirn138|Mirn138-1|mir-138-1	microRNA 138-1	ncRNA
mm_136600.1	chr17	5134935	5134938	+	1	NA	intron (NM_001085355, intron 4 of 19)	intron (NM_001085355, intron 4 of 19)	139862	NM_001085355	239985	Mm.133401	NM_001085355	ENSMUSG00000069729	Arid1b	8030481M12|9330189K18Rik|AI836955|Ardi1b|B230217J03Rik|mKIAA1235	AT rich interactive domain 1B (SWI-like)	protein-coding
mm_33709.1	chr4	133813403	133813405	+	1	NA	Intergenic	CpG	-59793	NM_001080819	93760	Mm.22478	NM_001080819	ENSMUSG00000007880	Arid1a	1110030E03Rik|BAF250a|Osa1|Smarcf1	AT rich interactive domain 1A (SWI-like)	protein-coding
mm_11964.1	chr2	53192068	53192100	+	1	NA	promoter-TSS (NM_018785)	promoter-TSS (NM_018785)	0	NM_022989	65103	Mm.37623	NM_022989	ENSMUSG00000026960	Arl6ip6	2310057C01Rik|2610529A11Rik|Aip-6	ADP-ribosylation factor-like 6 interacting protein 6	protein-coding
mm_164962.1	chr19	5800181	5800187	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	2488	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_43084.1	chr5	124450165	124450173	+	1	NA	intron (NM_001310725, intron 2 of 6)	intron (NM_001310725, intron 2 of 6)	3465	NM_001310727	67956	Mm.137966	NM_030241	ENSMUSG00000049327	Kmt5a	2410195B05Rik|AA617402|AW536475|PR-SET7|PR/SET07|Setd8	lysine methyltransferase 5A	protein-coding
mm_137264.1	chr17	24669685	24669727	+	1	NA	promoter-TSS (NM_183149)	promoter-TSS (NM_183149)	-46	NM_183149	213753	Mm.219581	NM_183149	ENSMUSG00000041130	Zfp598	BC023040|Ntrap|Znf598	zinc finger protein 598	protein-coding
mm_100756.1	chr11	4346914	4346922	-	1	NA	intron (NM_029458, intron 10 of 10)	intron (NM_029458, intron 10 of 10)	80122	NM_001039537	16878	Mm.4964	NM_008501	ENSMUSG00000034394	Lif	-	leukemia inhibitory factor	protein-coding
mm_78061.1	chr9	14903508	14903520	+	1	NA	intron (NM_022888, intron 1 of 4)	intron (NM_022888, intron 1 of 4)	437	NM_176807	64931	Mm.86738	NM_022888	ENSMUSG00000031933	Izumo1r	0910001L11Rik|C86255|Folbp3|Folr4|Juno	IZUMO1 receptor, JUNO	protein-coding
mm_112660.1	chr13	16026980	16027002	+	1	NA	exon (NM_008380, exon 5 of 5)	exon (NM_008380, exon 5 of 5)	15140	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_134840.1	chr16	26371805	26371821	-	1	NA	promoter-TSS (NM_016674)	promoter-TSS (NM_016674)	26	NM_016674	12737	Mm.289441	NM_016674	ENSMUSG00000022512	Cldn1	AI596271	claudin 1	protein-coding
mm_98923.1	chr11	98348663	98348742	+	1	NA	5' UTR (NM_144828, exon 1 of 7)	5' UTR (NM_144828, exon 1 of 7)	296	NM_144828	19049	Mm.45372	NM_144828	ENSMUSG00000061718	Ppp1r1b	AU040756|DARPP-32|Darpp32	protein phosphatase 1, regulatory (inhibitor) subunit 1B	protein-coding
mm_9124.1	chr1	170434263	170434291	-	1	NA	intron (NM_027528, intron 2 of 7)	Tigger13a|DNA|TcMar-Tigger	122833	NM_027528	70729	Mm.487078	NM_027528	ENSMUSG00000038473	Nos1ap	6330408P19Rik|Capon	nitric oxide synthase 1 (neuronal) adaptor protein	protein-coding
mm_104649.1	chr11	97574025	97574039	-	1	NA	intron (NM_018873, intron 1 of 19)	intron (NM_018873, intron 1 of 19)	1094	NM_018873	56013	Mm.342665	NM_018873	ENSMUSG00000038453	Srcin1	P140|SNIP|mKIAA1684|p140Cap	SRC kinase signaling inhibitor 1	protein-coding
mm_46029.1	chr5	91403003	91403024	-	1	NA	promoter-TSS (NM_007568)	promoter-TSS (NM_007568)	-19	NM_007568	12223	Mm.2024	NM_007568	ENSMUSG00000082361	Btc	Bcn	betacellulin, epidermal growth factor family member	protein-coding
mm_9225.1	chr1	171237599	171237606	-	1	NA	intron (NM_153064, intron 8 of 12)	intron (NM_153064, intron 8 of 12)	-3253	NM_010185	14127	Mm.22673	NM_010185	ENSMUSG00000058715	Fcer1g	AI573376|CD23|FcR-gamma|FcR[g]|FcRgamma|Fce1g|FcepsilonRI|Ly-50	Fc receptor, IgE, high affinity I, gamma polypeptide	protein-coding
mm_170457.1	chr18	89952242	89952255	-	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	-183112	NM_001039173	623279	Mm.447164	NM_001039173	ENSMUSG00000073514	Dok6	Dok-6	docking protein 6	protein-coding
mm_62839.1	chr7	114041031	114041062	+	1	NA	3' UTR (NM_145584, exon 16 of 16)	3' UTR (NM_145584, exon 16 of 16)	76735	NM_025846	66922	Mm.276572	NM_025846	ENSMUSG00000055723	Rras2	2610016H24Rik|C86394|TC21	related RAS viral (r-ras) oncogene 2	protein-coding
mm_26439.1	chr3	142623730	142623801	+	1	NA	TTS (NR_105802)	TTS (NR_105802)	181	NR_105802	102465200		NR_105802	ENSMUSG00000098871	Mir6381	Gm27963|mmu-mir-6381	microRNA 6381	ncRNA
mm_112647.1	chr13	16017374	16017413	+	1	NA	exon (NM_008380, exon 4 of 5)	exon (NM_008380, exon 4 of 5)	5542	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_143964.1	chr17	87203367	87203368	-	1	NA	Intergenic	Intergenic	-8425	NR_046016	399626	Mm.396062	NR_046016		C330024C12Rik	-	RIKEN cDNA C330024C12 gene	ncRNA
mm_137237.1	chr17	24426677	24426701	+	1	NA	promoter-TSS (NM_010023)	promoter-TSS (NM_010023)	6	NM_010023	13177	Mm.291743	NM_010023	ENSMUSG00000024132	Eci1	Dci|eci	enoyl-Coenzyme A delta isomerase 1	protein-coding
mm_18008.1	chr2	38281991	38281998	-	1	NA	intron (NM_146122, intron 1 of 21)	L1MB7|LINE|L1	5390	NM_146122	227801	Mm.314245	NM_146122	ENSMUSG00000035392	Dennd1a	6030446I19Rik|connecdenn	DENN/MADD domain containing 1A	protein-coding
mm_119703.1	chr14	53776931	53776957	+	1	NA	Intergenic	Intergenic	476985	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_162394.1	chr1	80412771	80412791	+	1	NA	Intergenic	Intergenic	-33151	NR_040460	72208	Mm.396181	NR_040460	ENSMUSG00000101483	1700016L21Rik	Jr3	RIKEN cDNA 1700016L21 gene	ncRNA
mm_26840.1	chr3	14611202	14611212	-	1	NA	promoter-TSS (NM_001347206)	promoter-TSS (NM_001347206)	14	NM_001347206	69126	Mm.389020	NM_001099674	ENSMUSG00000078784	1810022K09Rik	AI746582|AL023036	RIKEN cDNA 1810022K09 gene	protein-coding
mm_153756.1	chr19	45338315	45338324	-	1	NA	Intergenic	Intergenic	-25415	NM_001286466	12234	Mm.119717	NM_009771	ENSMUSG00000025217	Btrc	Beta-Trcp1|E3RS-IkappaB|E3RSIkappaB|FWD1|Fbw1a|HOS|Slimb|b-TrCP|beta-TrCP	beta-transducin repeat containing protein	protein-coding
mm_42058.1	chr5	108694260	108694270	+	1	NA	promoter-TSS (NM_001164259)	promoter-TSS (NM_001164259)	36	NM_054071	116701	Mm.35691	NM_054071	ENSMUSG00000008090	Fgfrl1	FGFR5|FGFR5beta|FGFR5gamma	fibroblast growth factor receptor-like 1	protein-coding
mm_111975.1	chr12	110023846	110023877	-	1	NA	Intergenic	Intergenic	134212	NR_045466	67280	Mm.390495	NR_045466		3110009F21Rik	-	RIKEN cDNA 3110009F21 gene	ncRNA
mm_23451.1	chr3	60031774	60031802	+	1	NA	promoter-TSS (NM_023383)	promoter-TSS (NM_023383)	0	NM_023383	67758	Mm.24547	NM_023383	ENSMUSG00000027761	Aadac	5033417E09Rik|AI265437|Aada	arylacetamide deacetylase (esterase)	protein-coding
mm_119966.1	chr14	55478925	55478941	+	1	NA	exon (NM_030686, exon 1 of 5)	exon (NM_030686, exon 1 of 5)	175	NM_030686	28200	Mm.27427	NM_030686	ENSMUSG00000022210	Dhrs4	AI043103|AI790593|CR|D14Ucla2|NDRD|PHCR|PSCD|RRD|mouNRDR	dehydrogenase/reductase (SDR family) member 4	protein-coding
mm_75555.1	chr8	57778348	57778358	-	1	NA	intron (NM_175032, intron 11 of 11)	intron (NM_175032, intron 11 of 11)	-125298	NM_144731	108150	Mm.62886	NM_144731	ENSMUSG00000031608	Galnt7	AI225872	UDP-N-acetyl-alpha-D-galactosamine: polypeptide N-acetylgalactosaminyltransferase 7	protein-coding
mm_168491.1	chr1	150232795	150232813	+	1	NA	Intergenic	L1Md_T|LINE|L1	-67856	NR_110420	102639566	Mm.417208	NR_110420	ENSMUSG00000097754	Ptgs2os2	Gm26687|Linc-cox2|Lincrna-cox2	prostaglandin-endoperoxide synthase 2, opposite strand 2	ncRNA
mm_144818.1	chr18	36290023	36290036	+	1	NA	Intergenic	Intergenic	8867	NM_008989	19290	Mm.231802	NM_008989	ENSMUSG00000043991	Pura	CAGER-1|Pur-alpha|ssCRE-BP	purine rich element binding protein A	protein-coding
mm_41089.1	chr5	87694502	87694511	+	1	NA	exon (NM_001286023, exon 5 of 7)	exon (NM_001286023, exon 5 of 7)	4919	NM_001286020	12991	Mm.268737	NM_009972	ENSMUSG00000063157	Csn2	Csnb	casein beta	protein-coding
mm_93580.1	chr10	116918926	116918931	-	1	NA	exon (NM_001003950, exon 5 of 10)	exon (NM_001003950, exon 5 of 10)	-22049	NM_001033333	237558	Mm.336386	NM_001033333	ENSMUSG00000034057	Myrfl	Gm239	myelin regulatory factor-like	protein-coding
mm_3601.1	chr1	151571482	151571492	+	1	NA	5' UTR (NM_022018, exon 1 of 14)	5' UTR (NM_022018, exon 1 of 14)	114	NM_022018	63913	Mm.157700	NM_022018	ENSMUSG00000026483	Fam129a	AI256368|AU019833|Niban	family with sequence similarity 129, member A	protein-coding
mm_2936.1	chr1	132299033	132299070	+	1	NA	5' UTR (NM_144810, exon 1 of 5)	5' UTR (NM_144810, exon 1 of 5)	425	NM_144810	213417	Mm.39723	NM_144810	ENSMUSG00000042115	Klhdc8a	A630065K24Rik	kelch domain containing 8A	protein-coding
mm_85277.1	chr9	99499483	99499514	-	1	NA	intron (NM_028768, intron 15 of 21)	intron (NM_028768, intron 15 of 21)	29077	NR_028123	69797	Mm.307159	NR_028123	ENSMUSG00000046242	1600029I14Rik	-	RIKEN cDNA 1600029I14 gene	ncRNA
mm_117241.1	chr13	64320387	64320391	-	1	NA	Intergenic	RMER19B2|LTR|ERVK	-7679	NM_025370	66129	Mm.491110	NM_025370	ENSMUSG00000021482	Aaed1	1110018J18Rik|AI849003	AhpC/TSA antioxidant enzyme domain containing 1	protein-coding
mm_71886.1	chr8	69822563	69822592	+	1	NA	promoter-TSS (NM_020028)	promoter-TSS (NM_020028)	12	NM_020028	53978	Mm.23253	NM_020028	ENSMUSG00000031861	Lpar2	Edg4|IPA2|LPA2	lysophosphatidic acid receptor 2	protein-coding
mm_138369.1	chr17	35001099	35001161	+	1	NA	promoter-TSS (NM_033075)	promoter-TSS (NM_033075)	223	NM_011690	22321	Mm.28420	NM_011690	ENSMUSG00000007029	Vars	Bat6|D17H6S56E|G7a|Vars2	valyl-tRNA synthetase	protein-coding
mm_72435.1	chr8	83085163	83085170	+	1	NA	3' UTR (NM_177378, exon 7 of 7)	3' UTR (NM_177378, exon 7 of 7)	-80186	NM_001111304	71310	Mm.24031	NM_027758	ENSMUSG00000031709	Tbc1d9	4933431N12Rik|AI847101|AW490653|C76116	TBC1 domain family, member 9	protein-coding
mm_84872.1	chr9	79698730	79698730	-	1	NA	intron (NM_001290308, intron 10 of 65)	intron (NM_001290308, intron 10 of 65)	19992	NM_001290308	12816	Mm.3819	NM_007730	ENSMUSG00000032332	Col12a1	-	collagen, type XII, alpha 1	protein-coding
mm_107249.1	chr12	27336370	27336373	+	1	NA	3' UTR (NM_009234, exon 1 of 1)	3' UTR (NM_009234, exon 1 of 1)	6347	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding
mm_84730.1	chr9	75038629	75038677	-	1	NA	intron (NM_021548, intron 1 of 2)	intron (NM_021548, intron 1 of 2)	921	NM_021548	59046	Mm.247837	NM_021548	ENSMUSG00000007656	Arpp19	19kDa|2700024H10Rik|ARPP-19|AW559096|Arpp12	cAMP-regulated phosphoprotein 19	protein-coding
mm_56301.1	chr6	91758327	91758352	-	1	NA	3' UTR (NM_009320, exon 15 of 15)	3' UTR (NM_009320, exon 15 of 15)	49054	NM_001159507	243547	Mm.333264	NM_001033353	ENSMUSG00000030098	Grip2	-	glutamate receptor interacting protein 2	protein-coding
mm_128517.1	chr15	53346176	53346206	-	1	NA	promoter-TSS (NM_010162)	promoter-TSS (NM_010162)	-8	NM_010162	14042	Mm.309395	NM_010162	ENSMUSG00000061731	Ext1	AA409028	exostoses (multiple) 1	protein-coding
mm_5473.1	chr1	36565612	36565613	-	1	NA	intron (NM_001126046, intron 12 of 14)	PB1D11|SINE|Alu	-7231	NM_001126047	20353	Mm.29558	NM_001126047	ENSMUSG00000026121	Sema4c	AI426163|M-Sema F|Semacl1|Semaf|Semai|sema I	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4C	protein-coding
mm_160477.1	chr8	120566435	120566435	+	1	NA	exon (NM_198671, exon 4 of 16)	exon (NM_198671, exon 4 of 16)	22640	NM_178856	272551	Mm.275910	NM_178856	ENSMUSG00000031821	Gins2	2210013I18Rik|4833427B12Rik|AI323585|Pfs2	GINS complex subunit 2 (Psf2 homolog)	protein-coding
mm_41046.1	chr5	86093242	86093258	+	1	NA	intron (NM_001310639, intron 5 of 7)	intron (NM_001310639, intron 5 of 7)	21504	NM_001310639	56792	Mm.131237	NM_019992	ENSMUSG00000029254	Stap1	AI586015|Brdg1|STAP-1	signal transducing adaptor family member 1	protein-coding
mm_25728.1	chr3	122730253	122730261	+	1	NA	intron (NM_153422, intron 1 of 20)	CpG	1099	NM_153422	242202	Mm.134911	NM_153422	ENSMUSG00000053965	Pde5a	Cgbpde|Cn5n|PDE5a2|Pde5|Pde5a1	phosphodiesterase 5A, cGMP-specific	protein-coding
mm_25291.1	chr3	105870886	105870895	+	1	NA	promoter-TSS (NM_001174169)	promoter-TSS (NM_001174169)	32	NM_001174169	69296	Mm.235024	NM_027025	ENSMUSG00000000562	Tmigd3	1700001d09rik|4930578J19Rik	transmembrane and immunoglobulin domain containing 3	protein-coding
mm_76045.1	chr8	77597020	77597054	-	1	NA	exon (NM_145599, exon 10 of 10)	exon (NM_145599, exon 10 of 10)	13616	NM_145599	234463	Mm.273578	NM_145599	ENSMUSG00000031617	Tmem184c	8430433H16Rik|AI645453|AL033298|BC004056|Tmem34	transmembrane protein 184C	protein-coding
mm_165063.1	chr19	42307126	42307134	-	1	NA	intron (NM_145123, intron 6 of 14)	intron (NM_145123, intron 6 of 14)	-26960	NR_037246	100526549		NR_037246	ENSMUSG00000093234	Mir3085	mir-3085|mmu-mir-3085	microRNA 3085	ncRNA
mm_102212.1	chr11	54907234	54907285	-	1	NA	exon (NM_008161, exon 2 of 5)	exon (NM_008161, exon 2 of 5)	4405	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_47766.1	chr5	131538156	131538237	-	1	NA	intron (NM_177047, intron 5 of 18)	CpG	-230674	NM_145218	212996	Mm.299204	NM_145218	ENSMUSG00000034040	Wbscr17	AA388321|E330012B09Rik	Williams-Beuren syndrome chromosome region 17 homolog (human)	protein-coding
mm_114601.1	chr13	75770979	75771020	+	1	NA	3' UTR (NM_138953, exon 12 of 12)	3' UTR (NM_138953, exon 12 of 12)	63515	NM_138953	192657	Mm.21288	NM_138953	ENSMUSG00000001542	Ell2	-	elongation factor RNA polymerase II 2	protein-coding
mm_130311.1	chr15	97055887	97055907	-	1	NA	promoter-TSS (NM_027052)	promoter-TSS (NM_027052)	59	NM_027052	69354	Mm.250980	NM_027052	ENSMUSG00000022464	Slc38a4	1110012E16Rik|1700012A18Rik|Ata3|mATA3|mNAT3	solute carrier family 38, member 4	protein-coding
mm_103077.1	chr11	69895499	69895520	-	1	NA	promoter-TSS (NM_153788)	promoter-TSS (NM_153788)	30	NM_153788	216859	Mm.288671	NM_153788	ENSMUSG00000001588	Acap1	Centb1	ArfGAP with coiled-coil, ankyrin repeat and PH domains 1	protein-coding
mm_121347.1	chr14	116925206	116925218	+	1	NA	promoter-TSS (NM_011821)	promoter-TSS (NM_011821)	-85	NM_001079844	23888	Mm.440025	NM_011821	ENSMUSG00000058571	Gpc6	-	glypican 6	protein-coding
mm_165661.1	chr3	87906158	87906170	+	1	NA	promoter-TSS (NM_008231)	promoter-TSS (NM_008231)	-157	NM_008231	15191	Mm.292208	NM_008231	ENSMUSG00000004897	Hdgf	AI118077|D3Ertd299e	hepatoma-derived growth factor	protein-coding
mm_84698.1	chr9	72491951	72491989	-	1	NA	promoter-TSS (NM_009359)	promoter-TSS (NM_009359)	-11	NM_009359	21778	Mm.14485	NM_009359	ENSMUSG00000090626	Tex9	Gm19407|tsec-1	testis expressed gene 9	protein-coding
mm_169262.1	chr13	83524888	83524891	+	1	NA	5' UTR (NM_001347567, exon 1 of 11)	5' UTR (NM_001347567, exon 1 of 11)	146	NM_001347580	17260	Mm.24001	NM_025282	ENSMUSG00000005583	Mef2c	5430401D19Rik|9930028G15Rik|AV011172|Mef2	myocyte enhancer factor 2C	protein-coding
mm_135136.1	chr16	35845396	35845412	-	1	NA	exon (NM_001039530, exon 10 of 17)	exon (NM_001039530, exon 10 of 17)	25978	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_18948.1	chr2	76778516	76778533	-	1	NA	exon (NM_011652, exon 236 of 313)	exon (NM_011652, exon 236 of 313)	103209	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_150901.1	chr19	45575112	45575119	+	1	NA	intron (NM_172639, intron 4 of 5)	intron (NM_172639, intron 4 of 5)	14500	NM_172639	226162	Mm.21978	NM_172639	ENSMUSG00000041035	Dpcd	5330431N19Rik|Ndac	deleted in primary ciliary dyskinesia	protein-coding
mm_96556.1	chr11	68901644	68901657	+	1	NA	promoter-TSS (NM_009080)	promoter-TSS (NM_009080)	61	NR_003373	100034726	Mm.3229	NR_003373	ENSMUSG00000062353	Gm15772	ENSMUSG00000062353|OTTMUSG00000026108	ribosomal protein L26 pseudogene	pseudo
mm_31743.1	chr4	63215558	63215568	+	1	NA	5' UTR (NM_025685, exon 1 of 61)	5' UTR (NM_025685, exon 1 of 61)	151	NM_025685	373864	Mm.194116	NM_025685	ENSMUSG00000045672	Col27a1	5730512J02Rik|AI449266	collagen, type XXVII, alpha 1	protein-coding
mm_58937.1	chr7	18067172	18067190	+	1	NA	exon (NM_001162524, exon 2 of 3)	exon (NM_001162524, exon 2 of 3)	1252	NM_001162523	67315	Mm.46089	NM_026087	ENSMUSG00000030366	Ceacam12	1600031J20Rik|Ceacam12-C1|Ceacam12-C3|Ceacam12C1|Ceacam12C3	carcinoembryonic antigen-related cell adhesion molecule 12	protein-coding
mm_100887.1	chr11	6029217	6029249	-	1	NA	intron (NM_007595, intron 1 of 20)	intron (NM_007595, intron 1 of 20)	36515	NM_001174054	12323	Mm.439733	NM_007595	ENSMUSG00000057897	Camk2b	CaMKII	calcium/calmodulin-dependent protein kinase II, beta	protein-coding
mm_148486.1	chr19	4150481	4150527	+	1	NA	exon (NM_011778, exon 5 of 11)	exon (NM_011778, exon 5 of 11)	1841	NM_011778	23789	Mm.276859	NM_011778	ENSMUSG00000024835	Coro1b	-	coronin, actin binding protein 1B	protein-coding
mm_143296.1	chr17	65923513	65923515	-	1	NA	3' UTR (NM_023053, exon 5 of 5)	3' UTR (NM_023053, exon 5 of 5)	27673	NM_023053	65960	Mm.10153	NM_023053	ENSMUSG00000024098	Twsg1	1810013J15Rik|9030422N06Rik|AW552143|D17Ertd403e|Tsg|Twg	twisted gastrulation BMP signaling modulator 1	protein-coding
mm_67720.1	chr7	90046978	90047012	-	1	NA	intron (NR_110364, intron 5 of 5)	intron (NR_110364, intron 5 of 5)	17836	NR_110364	319711	Mm.31753	NR_015614	ENSMUSG00000097585	E230029C05Rik	AI452102|B230337J15	RIKEN cDNA E230029C05 gene	ncRNA
mm_172260.1	chr6	73641988	73641995	-	1	NA	Intergenic	RLTR9C|LTR|ERVK	-170970	NR_108032	73408	Mm.233629	NR_108032	ENSMUSG00000107408	1700065L07Rik	-	RIKEN cDNA 1700065L07 gene	ncRNA
mm_171277.1	chr3	88832486	88832486	-	1	NA	promoter-TSS (NR_015498)	promoter-TSS (NR_015498)	1	NR_015498	319830	Mm.400394	NR_015498		1500004A13Rik	5430404N14Rik|BB132176	RIKEN cDNA 1500004A13 gene	ncRNA
mm_47089.1	chr5	117388974	117389027	-	1	NA	promoter-TSS (NM_028128)	promoter-TSS (NM_028128)	23	NM_028128	72151	Mm.27997	NM_028128	ENSMUSG00000029363	Rfc5	2610020K06Rik|2610209F07Rik|36.5kDa|36kDa|Recc5	replication factor C (activator 1) 5	protein-coding
mm_100607.1	chr11	121287971	121287995	+	1	NA	exon (NM_001080932, exon 3 of 9)	exon (NM_001080932, exon 3 of 9)	27996	NM_001080932	68837	Mm.209750	NM_001080932	ENSMUSG00000039275	Foxk2	1110054H05Rik|5730434B08Rik|6230415M23Rik|ILF|Ilf1	forkhead box K2	protein-coding
mm_140169.1	chr17	80307384	80307394	+	1	NA	promoter-TSS (NM_001145452)	promoter-TSS (NM_001145452)	-18	NM_001145452	381112	Mm.360004	NM_001145452	ENSMUSG00000054901	Arhgef33	Gm941	Rho guanine nucleotide exchange factor (GEF) 33	protein-coding
mm_159902.1	chr6	39489142	39489142	-	1	NA	intron (NM_172477, intron 8 of 18)	intron (NM_172477, intron 8 of 18)	68692	NM_172477	209773	Mm.440021	NM_172477	ENSMUSG00000038456	Dennd2a	B930096L08Rik|C130031G22|mKIAA1277	DENN/MADD domain containing 2A	protein-coding
mm_151853.1	chr19	5796546	5796570	-	1	NA	promoter-TSS (NR_144621)	promoter-TSS (NR_144621)	-577	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_76069.1	chr8	78508877	78508909	-	1	NA	promoter-TSS (NM_001282108)	promoter-TSS (NM_001282108)	35	NM_001252089	19656	Mm.24718	NM_009033	ENSMUSG00000037070	Rbmxl1	Hnrpg|Rbmx|Rbmxrt	RNA binding motif protein, X-linked like-1	protein-coding
mm_69769.1	chr7	141011359	141011369	-	1	NA	promoter-TSS (NM_025378)	promoter-TSS (NM_025378)	-620	NM_025378	66141	Mm.141021	NM_025378	ENSMUSG00000025492	Ifitm3	1110004C05Rik|Cd225|Cdw217|DSPA2b|Fgls|IP15|mil-1	interferon induced transmembrane protein 3	protein-coding
mm_118914.1	chr14	26693255	26693262	+	1	NA	Intergenic	MIR3|SINE|MIR	-23412	NM_178668	211948	Mm.290758	NM_178668	ENSMUSG00000043702	Pde12	2'-PDE|E430028B21Rik	phosphodiesterase 12	protein-coding
mm_96081.1	chr11	60105016	60105035	+	1	NA	promoter-TSS (NM_009021)	promoter-TSS (NM_009021)	12	NM_009021	19377	Mm.296366	NM_009021	ENSMUSG00000062115	Rai1	Gt1	retinoic acid induced 1	protein-coding
mm_91601.1	chr10	41072293	41072308	-	1	NA	promoter-TSS (NM_199058)	promoter-TSS (NM_199058)	-716	NM_199058	140741	Mm.290693	NM_199058	ENSMUSG00000046922	Gpr6	AI852874|Gm233	G protein-coupled receptor 6	protein-coding
mm_28851.1	chr3	96832050	96832081	-	1	NA	promoter-TSS (NM_001146001)	promoter-TSS (NM_001146001)	5	NR_015596	67583	Mm.444284	NR_015596	ENSMUSG00000087223	4930442L01Rik	-	RIKEN cDNA 4930442L01 gene	ncRNA
mm_27208.1	chr3	35754734	35754749	-	1	NA	intron (NM_029570, intron 1 of 29)	intron (NM_029570, intron 1 of 29)	603	NM_029570	76295	Mm.239416	NM_029570	ENSMUSG00000037400	Atp11b	1110019I14Rik|ATPIF|ATPIR|mKIAA0956	ATPase, class VI, type 11B	protein-coding
mm_129517.1	chr15	79108605	79108625	-	1	NA	promoter-TSS (NM_177461)	promoter-TSS (NM_177461)	-368	NM_177461	27008	Mm.196480	NM_177461	ENSMUSG00000033039	Micall1	AI448246|D15Mit260|D15N2e|EST573322|EST820961|MIRab13|mKIAA1668	microtubule associated monooxygenase, calponin and LIM domain containing -like 1	protein-coding
mm_35648.1	chr4	43523768	43523789	-	1	NA	promoter-TSS (NM_009416)	promoter-TSS (NM_009416)	-224	NM_001277875	22004	Mm.646	NM_009416	ENSMUSG00000028464	Tpm2	Tpm-2|Trop-2	tropomyosin 2, beta	protein-coding
mm_132022.1	chr16	26581726	26581763	+	1	NA	promoter-TSS (NM_008364)	promoter-TSS (NM_008364)	39	NM_008364	16180	Mm.253424	NM_008364	ENSMUSG00000022514	Il1rap	6430709H04Rik|AI255955|AV239853|IL-1RAcP	interleukin 1 receptor accessory protein	protein-coding
mm_147945.1	chr18	66292083	66292097	-	1	NA	promoter-TSS (NM_178793)	promoter-TSS (NM_178793)	-252	NM_178793	320924	Mm.442049	NM_178793	ENSMUSG00000046318	Ccbe1	4933426F18Rik|9430093N24Rik|mKIAA1983	collagen and calcium binding EGF domains 1	protein-coding
mm_6858.1	chr1	84262756	84262787	-	1	NA	intron (NM_001003948, intron 1 of 2)	L1MA10|LINE|L1	21874	NM_001003948	98496	Mm.187470	NM_001003948	ENSMUSG00000045658	Pid1	5033414K04Rik|NYGGF4	phosphotyrosine interaction domain containing 1	protein-coding
mm_103414.1	chr11	75470775	75470777	-	1	NA	3' UTR (NM_001291156, exon 5 of 5)	3' UTR (NM_001291156, exon 5 of 5)	2726	NM_027249	380712	Mm.41393	NM_027249	ENSMUSG00000038217	Tlcd2	-	TLC domain containing 2	protein-coding
mm_33640.1	chr4	132974203	132974217	+	1	NA	5' UTR (NM_010208, exon 1 of 13)	5' UTR (NM_010208, exon 1 of 13)	115	NM_010208	14191	Mm.271665	NM_010208	ENSMUSG00000028874	Fgr	-	FGR proto-oncogene, Src family tyrosine kinase	protein-coding
mm_172089.1	chr6	18157190	18157207	-	1	NA	Intergenic	Intergenic	-13489	NM_021050	12638	Mm.15621	NM_021050	ENSMUSG00000041301	Cftr	AW495489|Abcc7	cystic fibrosis transmembrane conductance regulator	protein-coding
mm_143535.1	chr17	73950173	73950189	-	1	NA	promoter-TSS (NM_011723)	promoter-TSS (NM_011723)	15	NM_011723	22436	Mm.11223	NM_011723	ENSMUSG00000024066	Xdh	XO|Xor|Xox-1|Xox1	xanthine dehydrogenase	protein-coding
mm_157627.1	chrX	56598016	56598025	-	1	NA	promoter-TSS (NM_146234)	promoter-TSS (NM_146234)	-101	NM_146234	236792	Mm.291824	NM_146234	ENSMUSG00000061273	Mmgt1	9630048L06Rik|BC032271|Emc5|Mir5116|Tmem32|mir-5116	membrane magnesium transporter 1	protein-coding
mm_73072.1	chr8	94446333	94446334	+	1	NA	Intergenic	B1F|SINE|Alu	-11230	NR_015514	320377	Mm.486022	NR_015514		9330175E14Rik	A630085K21	RIKEN cDNA 9330175E14 gene	ncRNA
mm_79492.1	chr9	57076344	57076387	+	1	NA	promoter-TSS (NM_011378)	promoter-TSS (NM_011378)	-11	NM_001110350	20466	Mm.15755	NM_011378	ENSMUSG00000042557	Sin3a	AW553200|Sin3|mKIAA4126|mSin3A	transcriptional regulator, SIN3A (yeast)	protein-coding
mm_49929.1	chr6	39419822	39419842	+	1	NA	promoter-TSS (NM_001311109)	promoter-TSS (NM_001311109)	-56	NM_001311109	54484	Mm.270484	NM_018810	ENSMUSG00000029922	Mkrn1	RFP	makorin, ring finger protein, 1	protein-coding
mm_137624.1	chr17	28313514	28313580	+	1	NA	promoter-TSS (NM_001163820)	promoter-TSS (NM_001163820)	17	NM_001163820	72775	Mm.201859	NM_028348	ENSMUSG00000007570	Fance	2810451D06Rik|AI415634|AW209126	Fanconi anemia, complementation group E	protein-coding
mm_68763.1	chr7	121707385	121707460	-	1	NA	promoter-TSS (NM_001033173)	promoter-TSS (NM_001033173)	-169	NM_001033173	76179	Mm.122538	NM_001033173	ENSMUSG00000063317	Usp31	6330567E21Rik|mKIAA1203	ubiquitin specific peptidase 31	protein-coding
mm_120842.1	chr14	75195890	75195897	+	1	NA	intron (NM_008879, intron 2 of 16)	intron (NM_008879, intron 2 of 16)	-46394	NM_019775	56373	Mm.24242	NM_019775	ENSMUSG00000021999	Cpb2	1110032P04Rik|4930405E17Rik|AI255929|CPR|Cpu|TAFI	carboxypeptidase B2 (plasma)	protein-coding
mm_129559.1	chr15	79534364	79534382	-	1	NA	TTS (NM_199079)	TTS (NM_199079)	-1456	NM_152806	67040	Mm.29644	NM_152806	ENSMUSG00000055065	Ddx17	2610007K22Rik|A430025E01Rik|AI047725|C80929|Gm926|p72	DEAD (Asp-Glu-Ala-Asp) box polypeptide 17	protein-coding
mm_93363.1	chr10	103236281	103236327	-	1	NA	promoter-TSS (NM_001163559)	promoter-TSS (NM_001163559)	18	NM_001163559	74978	Mm.483817	NM_029134	ENSMUSG00000019892	Lrriq1	4930503E15Rik|Gm1557	leucine-rich repeats and IQ motif containing 1	protein-coding
mm_71177.1	chr8	40752228	40752245	+	1	NA	promoter-TSS (NM_011781)	promoter-TSS (NM_011781)	28	NM_011781	23793	Mm.483208	NM_011781	ENSMUSG00000071937	Adam25	-	a disintegrin and metallopeptidase domain 25 (testase 2)	protein-coding
mm_33365.1	chr4	129512552	129512567	+	1	NA	Intergenic	Intergenic	-1022	NM_010807	17357	Mm.424974	NM_010807	ENSMUSG00000047945	Marcksl1	AL022768|AW215397|AW536807|D4Bc1|F52|MacMARCKS|Macs2|Macs3|Mlp|Mrp	MARCKS-like 1	protein-coding
mm_125093.1	chr15	27570374	27570376	+	1	NA	intron (NM_020332, intron 7 of 11)	intron (NM_020332, intron 7 of 11)	-1119	NR_106065	102466808		NR_106065	ENSMUSG00000098416	Mir7117	Gm27729|mmu-mir-7117	microRNA 7117	ncRNA
mm_122599.1	chr14	50987654	50987656	-	1	NA	Intergenic	RMER21B|LTR|ERV1	-20096	NM_001162863	75019	Mm.318775	NM_029145	ENSMUSG00000021872	Rnase10	4930474F22Rik|Rah1	ribonuclease, RNase A family, 10 (non-active)	protein-coding
mm_170678.1	chr2	121956421	121956422	+	1	NA	promoter-TSS (NM_008545)	promoter-TSS (NM_008545)	-329	NM_008545	17147	Mm.389349	NM_008545	ENSMUSG00000074881	Mageb3	Mage-b3|Mage-ps1|Mage-rs3|Smage3	melanoma antigen, family B, 3	protein-coding
mm_49102.1	chr6	8209217	8209263	+	1	NA	promoter-TSS (NM_145374)	promoter-TSS (NM_145374)	13	NM_145374	252875	Mm.257151	NM_145374	ENSMUSG00000042447	Mios	C81488	missing oocyte, meiosis regulator, homolog (Drosophila)	protein-coding
mm_33878.1	chr4	136172397	136172427	+	1	NA	5' UTR (NM_177733, exon 1 of 7)	5' UTR (NM_177733, exon 1 of 7)	138	NM_177733	242705	Mm.307932	NM_177733	ENSMUSG00000018983	E2f2	E2F-2	E2F transcription factor 2	protein-coding
mm_91419.1	chr10	32552515	32552517	-	1	NA	intron (NM_001013411, intron 1 of 6)	Lx3A|LINE|L1	337399	NM_001013411	432450	Mm.49665	NM_001013411	ENSMUSG00000069670	Nkain2	6330571D19Rik|AW455467|Tcba1	Na+/K+ transporting ATPase interacting 2	protein-coding
mm_120142.1	chr14	60378243	60378292	+	1	NA	promoter-TSS (NM_001164705)	promoter-TSS (NM_001164705)	-19	NM_028113	72125	Mm.275499	NM_028113	ENSMUSG00000021986	Amer2	2600011E07Rik|Fam123a	APC membrane recruitment 2	protein-coding
mm_106904.1	chr12	8015368	8015386	+	1	NA	exon (NM_009693, exon 29 of 29)	exon (NM_009693, exon 29 of 29)	37700	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_63965.1	chr7	139944547	139944554	+	1	NA	exon (NM_009482, exon 2 of 2)	exon (NM_009482, exon 2 of 2)	694	NM_009482	22286	Mm.10205	NM_009482	ENSMUSG00000047751	Utf1	AI505934	undifferentiated embryonic cell transcription factor 1	protein-coding
mm_138925.1	chr17	43801295	43801322	+	1	NA	promoter-TSS (NM_207649)	promoter-TSS (NM_207649)	-543	NM_207649	53901	Mm.251242	NM_030598	ENSMUSG00000039601	Rcan2	Csp2|Dscr1l1|MCIP2|ZAKI-4	regulator of calcineurin 2	protein-coding
mm_71063.1	chr8	33990259	33990278	+	1	NA	Intergenic	ORR1D2|LTR|ERVL-MaLR	-60405	NM_001042675	19663	Mm.323997	NM_019733	ENSMUSG00000031586	Rbpms	2010300K22Rik|2700019M19Rik|AU017537|RBP-MS|hermes	RNA binding protein gene with multiple splicing	protein-coding
mm_43662.1	chr5	138754460	138754522	+	1	NA	promoter-TSS (NM_030565)	promoter-TSS (NM_030565)	-590	NM_030565	80752	Mm.320355	NM_030565	ENSMUSG00000025854	Fam20c	C76981|DMP-4|DMP4|GEF-CK|mKIAA4081	family with sequence similarity 20, member C	protein-coding
mm_99432.1	chr11	102430369	102430399	+	1	NA	promoter-TSS (NM_008175)	promoter-TSS (NM_008175)	62	NM_008175	14824	Mm.1568	NM_008175	ENSMUSG00000034708	Grn	Pgrn|epithelin	granulin	protein-coding
mm_145935.1	chr18	67289206	67289225	+	1	NA	promoter-TSS (NM_053261)	promoter-TSS (NM_053261)	-8	NM_053261	114663	Mm.34079	NM_053261	ENSMUSG00000024525	Impa2	2210415D20Rik|AI326924|AW259601	inositol (myo)-1(or 4)-monophosphatase 2	protein-coding
mm_81168.1	chr9	107299946	107299955	+	1	NA	exon (NM_009895, exon 2 of 3)	exon (NM_009895, exon 2 of 3)	3291	NM_009895	12700	Mm.4592	NM_009895	ENSMUSG00000032578	Cish	CIS-1|CIS1|Cis|F17|F23|SOCS	cytokine inducible SH2-containing protein	protein-coding
mm_115959.1	chr13	23762379	23762391	-	1	NA	promoter-TSS (NM_013550)	promoter-TSS (NM_013550)	1	NM_013550	360198	Mm.221301	NM_013550	ENSMUSG00000069265	Hist1h3a	-	histone cluster 1, H3a	protein-coding
mm_22718.1	chr3	19311441	19311473	+	1	NA	promoter-TSS (NM_001122759)	promoter-TSS (NM_001122759)	-135	NM_001122759	18583	Mm.355614	NM_008802	ENSMUSG00000069094	Pde7a	AU015378|AW047537	phosphodiesterase 7A	protein-coding
mm_12783.1	chr2	79330850	79330858	+	1	NA	3' UTR (NM_010576, exon 28 of 28)	3' UTR (NM_010576, exon 28 of 28)	75428	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D|Itga4B	integrin alpha 4	protein-coding
mm_120648.1	chr14	70530661	70530691	+	1	NA	promoter-TSS (NM_145219)	promoter-TSS (NM_145219)	-145	NM_145219	213469	Mm.41708	NM_145219	ENSMUSG00000033595	Lgi3	AI841179|AW049851	leucine-rich repeat LGI family, member 3	protein-coding
mm_168673.1	chr1	19372283	19372287	+	1	NA	Intergenic	L1Md_F3|LINE|L1	160231	NM_001025305	21419	Mm.137021	NM_009334	ENSMUSG00000025927	Tfap2b	AI606113|AP-2(beta)|E130018K07Rik|Tcfap2b	transcription factor AP-2 beta	protein-coding
mm_68004.1	chr7	100938432	100938445	-	1	NA	exon (NM_183168, exon 3 of 3)	exon (NM_183168, exon 3 of 3)	-6277	NM_001081116	207212	Mm.29954	NM_001081116	ENSMUSG00000032875	Arhgef17	8030463K16|AI428794|AW558066|BC035332|mKIAA0337	Rho guanine nucleotide exchange factor (GEF) 17	protein-coding
mm_133086.1	chr16	62814721	62814731	+	1	NA	promoter-TSS (NM_026588)	promoter-TSS (NM_026588)	50	NM_026588	68159	Mm.386793	NM_026588	ENSMUSG00000047854	Stx19	A030009B12Rik	syntaxin 19	protein-coding
mm_98977.1	chr11	98700333	98700370	+	1	NA	promoter-TSS (NM_009971)	promoter-TSS (NM_009971)	-962	NM_009971	12985	Mm.1238	NM_009971	ENSMUSG00000038067	Csf3	Csfg|G-CSF|MGI-IG	colony stimulating factor 3 (granulocyte)	protein-coding
mm_109751.1	chr12	117688718	117688727	+	1	NA	intron (NM_175930, intron 12 of 27)	C-rich|Low_complexity|Low_complexity	-155139	NM_146040	217946	Mm.281149	NM_146040	ENSMUSG00000021175	Cdca7l	BC006933|JPO2	cell division cycle associated 7 like	protein-coding
mm_122426.1	chr14	44859371	44859381	-	1	NA	promoter-TSS (NM_008962)	promoter-TSS (NM_008962)	-1	NM_008962	19214	Mm.5105	NM_008962	ENSMUSG00000071489	Ptgdr	DP|PGD	prostaglandin D receptor	protein-coding
mm_153638.1	chr19	44069737	44069787	-	1	NA	promoter-TSS (NM_001164360)	promoter-TSS (NM_001164360)	13	NM_001164359	226144	Mm.279865	NM_145502	ENSMUSG00000025198	Erlin1	2810439N09Rik|C80197|Keo4|Spfh1	ER lipid raft associated 1	protein-coding
mm_140232.1	chr17	84100837	84100863	+	1	NA	Intergenic	Intergenic	22190	NR_045458	74473	Mm.399575	NR_045458		4933433H22Rik	-	RIKEN cDNA 4933433H22 gene	ncRNA
mm_168496.1	chr1	151571418	151571418	+	1	NA	promoter-TSS (NM_022018)	promoter-TSS (NM_022018)	45	NM_022018	63913	Mm.157700	NM_022018	ENSMUSG00000026483	Fam129a	AI256368|AU019833|Niban	family with sequence similarity 129, member A	protein-coding
mm_6358.1	chr1	71938616	71938619	-	1	NA	Intergenic	GA-rich|Low_complexity|Low_complexity	50505	NR_027659	667931	Mm.214128	NR_027658	ENSMUSG00000099707	Gm8883	EG667931|Gm554	predicted gene 8883	ncRNA
mm_168951.1	chr12	77553741	77553760	+	1	NA	Intergenic	L1Md_T|LINE|L1	143609	NM_001252616	53618	Mm.35628	NM_016893	ENSMUSG00000021065	Fut8	-	fucosyltransferase 8	protein-coding
mm_34589.1	chr4	150187458	150187468	+	1	NA	exon (NM_009802, exon 8 of 8)	exon (NM_009802, exon 8 of 8)	13672	NM_009802	12353	Mm.232523	NM_009802	ENSMUSG00000028972	Car6	Ca6|DOC1	carbonic anhydrase 6	protein-coding
mm_52499.1	chr6	115138515	115138518	+	1	NA	intron (NM_001111015, intron 1 of 12)	intron (NM_001111015, intron 1 of 12)	3614	NM_001111015	20965	Mm.441431	NM_013681	ENSMUSG00000009394	Syn2	2900074L19Rik|AI836018|AI841723	synapsin II	protein-coding
mm_30166.1	chr3	144193994	144194033	-	1	NA	exon (NM_010723, exon 4 of 5)	exon (NM_010723, exon 4 of 5)	8319	NM_001161770	16911	Mm.29187	NM_010723	ENSMUSG00000028266	Lmo4	A730077C12Rik|Crp3|Etohi4	LIM domain only 4	protein-coding
mm_112107.1	chr12	112785885	112785895	-	1	NA	Intergenic	Intergenic	-23085	NM_145450	217887	Mm.186678	NM_145450	ENSMUSG00000037594	BC022687	AW050009|C130001I08Rik|Flj20080	cDNA sequence BC022687	protein-coding
mm_111700.1	chr12	103659890	103659910	-	1	NA	Intergenic	Intergenic	-2682	NM_007618	12401	Mm.290079	NM_007618	ENSMUSG00000060807	Serpina6	Cbg	serine (or cysteine) peptidase inhibitor, clade A, member 6	protein-coding
mm_127015.1	chr15	95959154	95959161	+	1	NA	intron (NM_175344, intron 16 of 19)	intron (NM_175344, intron 16 of 19)	120396	NR_126493	402773	Mm.210567	NM_001033483	ENSMUSG00000078925	D030018L15Rik	-	nuclear receptor coactivator 2 pseudogene	pseudo
mm_152242.1	chr19	8713863	8713881	-	1	NA	promoter-TSS (NM_008577)	promoter-TSS (NM_008577)	25	NM_008577	17254	Mm.4114	NM_008577	ENSMUSG00000010095	Slc3a2	4F2|4F2HC|AI314110|Cd98|Ly-10|Ly-m10|Ly10|Mdu1|Mgp-2hc|NACAE	solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2	protein-coding
mm_64577.1	chr7	144934095	144934131	+	1	NA	exon (NM_007631, exon 4 of 5)	exon (NM_007631, exon 4 of 5)	-1978	NR_039539	100628615		NR_039539	ENSMUSG00000092633	Mir3962	mmu-mir-3962|mu-mir-3962	microRNA 3962	ncRNA
mm_171045.1	chr2	99909727	99909729	-	1	NA	Intergenic	L1Md_T|LINE|L1	-1715020	NM_009020	19374	Mm.4988	NM_009020	ENSMUSG00000032864	Rag2	Rag-2	recombination activating gene 2	protein-coding
mm_33610.1	chr4	132588787	132588794	+	1	NA	Intergenic	Intergenic	24723	NM_001081211	19204	Mm.89389	NM_001081211	ENSMUSG00000056529	Ptafr	PAFR	platelet-activating factor receptor	protein-coding
mm_127972.1	chr15	12136664	12136684	-	1	NA	exon (NM_011767, exon 3 of 20)	exon (NM_011767, exon 3 of 20)	18823	NM_011767	22763	Mm.273496	NM_011767	ENSMUSG00000022201	Zfr	C920030H05Rik	zinc finger RNA binding protein	protein-coding
mm_115048.1	chr13	100108157	100108167	+	1	NA	5' UTR (NM_011353, exon 1 of 3)	5' UTR (NM_011353, exon 1 of 3)	143	NM_011353	20365	Mm.286177	NM_011353	ENSMUSG00000021643	Serf1	4F5|Msmac1|m4F5	small EDRK-rich factor 1	protein-coding
mm_11038.1	chr2	27006593	27006604	+	1	NA	intron (NM_001001322, intron 26 of 28)	intron (NM_001001322, intron 26 of 28)	-3328	NM_001243240	381356	Mm.150270	NM_029862	ENSMUSG00000015488	Cacfd1	5930434B04Rik|mFwe	calcium channel flower domain containing 1	protein-coding
mm_117592.1	chr13	89742342	89742365	-	1	NA	5' UTR (NM_001134474, exon 1 of 14)	5' UTR (NM_001134474, exon 1 of 14)	159	NM_001081249	13003	Mm.158700	NM_019389	ENSMUSG00000021614	Vcan	5430420N07Rik|9430051N09|Cspg2|DPEAAE|NG2|PG-M|PG-M(V0)|PG-M(V1)|hdf	versican	protein-coding
mm_40922.1	chr5	75830551	75830587	+	1	NA	Intergenic	Intergenic	147859	NM_010612	16542	Mm.285	NM_010612	ENSMUSG00000062960	Kdr	6130401C07|Flk-1|Flk1|Krd-1|Ly73|VEGFR-2|VEGFR2|sVEGFR-2	kinase insert domain protein receptor	protein-coding
mm_20019.1	chr2	119325566	119325588	-	1	NA	promoter-TSS (NM_019454)	promoter-TSS (NM_019454)	-207	NM_019454	54485	Mm.143719	NM_019454	ENSMUSG00000027314	Dll4	Delta4	delta-like 4 (Drosophila)	protein-coding
mm_162986.1	chr11	22990379	22990390	+	1	NA	promoter-TSS (NM_009837)	promoter-TSS (NM_009837)	-209	NM_009837	12464	Mm.296985	NM_009837	ENSMUSG00000007739	Cct4	2610204B21Rik|A45|C78323|Cctd	chaperonin containing Tcp1, subunit 4 (delta)	protein-coding
mm_68660.1	chr7	118740572	118740613	-	1	NA	5' UTR (NM_027815, exon 1 of 31)	5' UTR (NM_027815, exon 1 of 31)	321	NM_027815	71517	Mm.213298	NM_027815	ENSMUSG00000030982	9030624J02Rik	2610029J22Rik	RIKEN cDNA 9030624J02 gene	protein-coding
mm_112844.1	chr13	20835685	20835695	+	1	NA	intron (NM_012054, intron 2 of 20)	L1M4|LINE|L1	41577	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_70048.1	chr7	142578080	142578085	-	1	NA	promoter-TSS (NR_130974)	promoter-TSS (NR_130974)	64	NR_130974	14955	Mm.14802	NR_001592	ENSMUSG00000000031	H19	AI747191	H19, imprinted maternally expressed transcript	ncRNA
mm_148062.1	chr18	72227933	72227950	-	1	NA	intron (NM_007831, intron 1 of 28)	intron (NM_007831, intron 1 of 28)	123128	NM_007831	13176	Mm.167882	NM_007831	ENSMUSG00000060534	Dcc	C030036D22Rik|Igdcc1	deleted in colorectal carcinoma	protein-coding
mm_116538.1	chr13	45922548	45922553	-	1	NA	intron (NM_001199304, intron 2 of 6)	intron (NM_001199304, intron 2 of 6)	42441	NM_001199304	20238	Mm.342683	NM_009124	ENSMUSG00000046876	Atxn1	2900016G23Rik|Atx1|C85907|ENSMUSG00000074917|Gm10786|Sca1	ataxin 1	protein-coding
mm_106394.1	chr11	118797714	118797724	-	1	NA	intron (NM_001039168, intron 2 of 14)	intron (NM_001039168, intron 2 of 14)	-36678	NM_001285438	52897	Mm.341103	NM_001024931	ENSMUSG00000025576	Rbfox3	Fox-3|Hrnbp3|NeuN|Neuna60	RNA binding protein, fox-1 homolog (C. elegans) 3	protein-coding
mm_173244.1	chrX	89338871	89338872	+	1	NA	Intergenic	RLTR10A|LTR|ERVK	70818	NM_008821	18630	Mm.3086	NM_008821	ENSMUSG00000035395	Pet2	PC231|PC326|Pex3	plasmacytoma expressed transcript 2	protein-coding
mm_124631.1	chr15	4026613	4026695	+	1	NA	non-coding (NR_028266, exon 1 of 2)	non-coding (NR_028266, exon 1 of 2)	226	NM_024188	67041	Mm.13445	NM_024188	ENSMUSG00000022186	Oxct1	2610008O03Rik|Oxct|Oxct2a|Scot-s	3-oxoacid CoA transferase 1	protein-coding
mm_145837.1	chr18	65442590	65442605	+	1	NA	intron (NM_172833, intron 2 of 15)	intron (NM_172833, intron 2 of 15)	11600	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_107896.1	chr12	70650076	70650088	+	1	NA	intron (NR_037248, intron 4 of 4)	intron (NR_037248, intron 4 of 4)	-175432	NM_028127	319710	Mm.2962	NM_028127	ENSMUSG00000048285	Frmd6	2610019M19Rik|4930488L10Rik|AW212977|Willin	FERM domain containing 6	protein-coding
mm_15866.1	chr2	164833782	164833812	+	1	NA	promoter-TSS (NM_001082974)	promoter-TSS (NM_001082974)	24	NM_008906	19025	Mm.359633	NM_008906	ENSMUSG00000017760	Ctsa	AU019505|PPCA|Ppgb	cathepsin A	protein-coding
mm_154302.1	chr19	61225409	61225446	-	1	NA	intron (NM_009970, intron 9 of 11)	CpG-7695	2991	NM_009970	12982	Mm.287228	NM_009970	ENSMUSG00000059326	Csf2ra	CD116|Csfgmra|GM-CSF-Ra|GM-CSFR	colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)	protein-coding
mm_135134.1	chr16	35844383	35844397	-	1	NA	exon (NM_001039530, exon 12 of 17)	exon (NM_001039530, exon 12 of 17)	26992	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_90999.1	chr10	14545179	14545193	-	1	NA	promoter-TSS (NM_001002268)	promoter-TSS (NM_001002268)	-150	NM_001002268	215798	Mm.440142	NM_001002268	ENSMUSG00000039116	Adgrg6	1190004A11Rik|AI449247|AW045736|DREG|Gm222|Gpr126	adhesion G protein-coupled receptor G6	protein-coding
mm_56664.1	chr6	113531576	113531667	-	1	NA	promoter-TSS (NM_001033244)	promoter-TSS (NM_001033244)	17	NM_175101	66087	Mm.275989	NM_175101	ENSMUSG00000030286	Emc3	0610039A15Rik|AI225901|AW260416|Pob|Tmem111	ER membrane protein complex subunit 3	protein-coding
mm_78524.1	chr9	34488822	34488835	+	1	NA	promoter-TSS (NM_001190912)	promoter-TSS (NM_001190912)	97	NM_001190911	67703	Mm.220710	NM_026324	ENSMUSG00000032036	Kirrel3	1500010O20Rik|2900036G11Rik|NEPH2|SST4|mKIAA1867	kin of IRRE like 3 (Drosophila)	protein-coding
mm_29668.1	chr3	122619713	122619723	-	1	NA	promoter-TSS (NM_001114665)	promoter-TSS (NM_001114665)	-4	NM_153118	214459	Mm.209491	NM_153118	ENSMUSG00000039735	Fnbp1l	2610318I01Rik|AW548221|TOCA1|toca-1	formin binding protein 1-like	protein-coding
mm_121046.1	chr14	80022561	80022567	+	1	NA	TTS (NM_001030294)	TTS (NM_001030294)	22262	NM_001030294	380924	Mm.26456	NM_001030294	ENSMUSG00000022026	Olfm4	GC1|GW112|Gm296|Gm913|OlfD|pPD4	olfactomedin 4	protein-coding
mm_82729.1	chr9	25151688	25151704	-	1	NA	promoter-TSS (NM_020586)	promoter-TSS (NM_020586)	85	NM_020586	80517	Mm.142843	NM_020586	ENSMUSG00000008429	Herpud2	5031400M07Rik|AB041580	HERPUD family member 2	protein-coding
mm_44965.1	chr5	36720814	36720818	-	1	NA	Intergenic	Intergenic	-24795	NM_001081232	320661	Mm.26480	NM_177221	ENSMUSG00000029190	D5Ertd579e	9030221A05Rik|A930018H20Rik|Kiaa0232	DNA segment, Chr 5, ERATO Doi 579, expressed	protein-coding
mm_3614.1	chr1	152399803	152399809	+	1	NA	promoter-TSS (NM_177756)	promoter-TSS (NM_177756)	-61	NM_177756	269132	Mm.23782	NM_177756	ENSMUSG00000032649	Colgalt2	AI427652|D730024P12|Glt25d2	collagen beta(1-O)galactosyltransferase 2	protein-coding
mm_170162.1	chr1	75209482	75209493	-	1	NA	5' UTR (NM_029010, exon 2 of 17)	5' UTR (NM_029010, exon 2 of 17)	1291	NM_029010	74577	Mm.458319	NM_029010	ENSMUSG00000026200	Glb1l	4833408P15Rik	galactosidase, beta 1-like	protein-coding
mm_138025.1	chr17	33912723	33912726	+	1	NA	exon (NM_001199733, exon 5 of 8)	exon (NM_001199733, exon 5 of 8)	3123	NM_001199733	13163	Mm.271809	NM_007829	ENSMUSG00000002307	Daxx	-	Fas death domain-associated protein	protein-coding
mm_137814.1	chr17	30011169	30011176	+	1	NA	intron (NM_148926, intron 1 of 4)	(T)n|Simple_repeat|Simple_repeat	6085	NM_148926	21769	Mm.220972	NM_148926	ENSMUSG00000044477	Zfand3	AW539211|TEG-27|Tex27	zinc finger, AN1-type domain 3	protein-coding
mm_167053.1	chr7	84410011	84410021	-	1	NA	promoter-TSS (NM_007488)	promoter-TSS (NM_007488)	22	NM_007488	11864	Mm.38594	NM_007488	ENSMUSG00000015709	Arnt2	Hif-2b|bHLHe1|mKIAA0307	aryl hydrocarbon receptor nuclear translocator 2	protein-coding
mm_145533.1	chr18	60803858	60803868	+	1	NA	promoter-TSS (NM_010545)	promoter-TSS (NM_010545)	14	NM_010545	16149	Mm.439737	NM_010545	ENSMUSG00000024610	Cd74	CLIP|DHLAG|HLADG|Ia-GAMMA|Ii	CD74 antigen (invariant polypeptide of major histocompatibility complex, class II antigen-associated)	protein-coding
mm_105327.1	chr11	102897124	102897139	-	1	NA	promoter-TSS (NM_010277)	promoter-TSS (NM_010277)	69	NM_001131020	14580	Mm.1239	NM_010277	ENSMUSG00000020932	Gfap	AI836096	glial fibrillary acidic protein	protein-coding
mm_79730.1	chr9	62342060	62342082	+	1	NA	intron (NM_009672, intron 1 of 6)	CpG	728	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	protein-coding
mm_120031.1	chr14	55853998	55854033	+	1	NA	promoter-TSS (NM_001040072)	promoter-TSS (NM_001040072)	-100	NM_001040072	277154	Mm.319347	NM_001040072	ENSMUSG00000075592	Nynrin	AA409373|C80530|mKIAA1305	NYN domain and retroviral integrase containing	protein-coding
mm_148236.1	chr18	80502497	80502499	-	1	NA	Intergenic	Intergenic	-32831	NM_026295	67655	Mm.312893	NM_026295	ENSMUSG00000033323	Ctdp1	4930563P03Rik|AW553592	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) phosphatase, subunit 1	protein-coding
mm_74268.1	chr8	124898505	124898524	+	1	NA	promoter-TSS (NM_198103)	promoter-TSS (NM_198103)	628	NM_001111141	244666	Mm.482915	NM_001111141	ENSMUSG00000031986	Sprtn	Gm505	SprT-like N-terminal domain	protein-coding
mm_51497.1	chr6	83087279	83087328	+	1	NA	intron (NM_010692, intron 1 of 1)	intron (NM_010692, intron 1 of 1)	938	NM_010692	16815	Mm.20359	NM_010692	ENSMUSG00000034968	Lbx2	Lbx2h	ladybird homeobox homolog 2 (Drosophila)	protein-coding
mm_36753.1	chr4	101264857	101264878	-	1	NA	intron (NM_146145, intron 1 of 24)	CpG	415	NM_146145	16451	Mm.289657	NM_146145	ENSMUSG00000028530	Jak1	AA960307|BAP004|C130039L05Rik	Janus kinase 1	protein-coding
mm_174.1	chr1	13593596	13593611	+	1	NA	Intergenic	ORR1D2|LTR|ERVL-MaLR	-3693	NM_028173	72265	Mm.28765	NM_028173	ENSMUSG00000025935	Tram1	1810049E02Rik|TRAMP	translocating chain-associating membrane protein 1	protein-coding
mm_73077.1	chr8	94460526	94460534	+	1	NA	Intergenic	LTR78|LTR|ERV1	-12233	NM_001033207	434341	Mm.334720	NM_001033207	ENSMUSG00000074151	Nlrc5	AI451557|AK220210|NOD27	NLR family, CARD domain containing 5	protein-coding
mm_16726.1	chr2	7395969	7396011	-	1	NA	promoter-TSS (NM_001110232)	promoter-TSS (NM_001110232)	10	NM_001110232	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_2875.1	chr1	131827521	131827537	+	1	NA	promoter-TSS (NM_173865)	promoter-TSS (NM_173865)	-483	NM_173865	98396	Mm.389181	NM_173865	ENSMUSG00000013275	Slc41a1	AI573938|B230315F01Rik	solute carrier family 41, member 1	protein-coding
mm_119851.1	chr14	54440994	54441010	+	1	NA	3' UTR (NM_008608, exon 10 of 10)	3' UTR (NM_008608, exon 10 of 10)	9404	NM_008608	17387	Mm.280175	NM_008608	ENSMUSG00000000957	Mmp14	AI325305|MMP-X1|MT-MMP-1|MT1-MMP|sabe	matrix metallopeptidase 14 (membrane-inserted)	protein-coding
mm_35474.1	chr4	40839282	40839291	-	1	NA	intron (NM_022305, intron 1 of 5)	L1MD|LINE|L1	10852	NR_039584	100628614		NR_039584	ENSMUSG00000096377	Mir5123	mmu-mir-5123|mu-mir-5123	microRNA 5123	ncRNA
mm_25910.1	chr3	131113852	131113865	+	1	NA	exon (NM_001276402, exon 2 of 10)	exon (NM_001276402, exon 2 of 10)	1067	NM_001276403	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_168066.1	chr10	104545661	104545666	-	1	NA	Intergenic	L1Md_T|LINE|L1	258394	NR_105838	102465222		NR_105838	ENSMUSG00000099264	Mir6411	Gm27767|mmu-mir-6411	microRNA 6411	ncRNA
mm_172238.1	chr6	68270473	68270488	+	1	NA	Intergenic	Intergenic	-704781	NR_003100	75070	Mm.463364	NR_003100		4930515G16Rik	-	myc induced nuclear antigen pseudogene	pseudo
mm_164118.1	chr15	34609893	34609897	+	1	NA	intron (NM_145469, intron 4 of 10)	intron (NM_145469, intron 4 of 10)	-65178	NR_045883	71637	Mm.410827	NR_045883		4930413F20Rik	-	RIKEN cDNA 4930413F20 gene	ncRNA
mm_8583.1	chr1	155973174	155973204	-	1	NA	promoter-TSS (NM_001039184)	promoter-TSS (NM_001039184)	66	NM_001039184	74081	Mm.260247	NM_001039184	ENSMUSG00000033671	Cep350	4933409L06Rik|6430546F08Rik	centrosomal protein 350	protein-coding
mm_34076.1	chr4	138457939	138457946	+	1	NA	3' UTR (NM_025451, exon 2 of 2)	3' UTR (NM_025451, exon 2 of 2)	2794	NM_025451	66259	Mm.41603	NM_025451	ENSMUSG00000046447	Camk2n1	1810006K23Rik|AI848599|AI891706	calcium/calmodulin-dependent protein kinase II inhibitor 1	protein-coding
mm_89893.1	chr10	110878094	110878109	+	1	NA	intron (NR_045979, intron 2 of 2)	intron (NR_045979, intron 2 of 2)	18406	NR_045979	75630	Mm.392786	NR_045979	ENSMUSG00000101801	1700020G17Rik	4930480D05Rik	RIKEN cDNA 1700020G17 gene	ncRNA
mm_47426.1	chr5	123172083	123172089	-	1	NA	exon (NM_008277, exon 14 of 14)	exon (NM_008277, exon 14 of 14)	10600	NM_008277	15445	Mm.439709	NM_008277	ENSMUSG00000029445	Hpd	Fla|Flp|Hppd|Laf	4-hydroxyphenylpyruvic acid dioxygenase	protein-coding
mm_165395.1	chr2	132599505	132599525	+	1	NA	intron (NR_033469, intron 1 of 3)	intron (NR_033469, intron 1 of 3)	1319	NR_033469	767814	Mm.371752	NR_033468	ENSMUSG00000074783	AU019990	-	expressed sequence AU019990	ncRNA
mm_22185.1	chr2	173218880	173218931	-	1	NA	promoter-TSS (NM_021394)	promoter-TSS (NM_021394)	17	NM_021394	58203	Mm.116687	NM_021394	ENSMUSG00000027514	Zbp1	2010010H03Rik|Dai|Dlm1|mZaDLM	Z-DNA binding protein 1	protein-coding
mm_38262.1	chr4	136880380	136880397	-	1	NA	exon (NM_009777, exon 3 of 3)	exon (NM_009777, exon 3 of 3)	5789	NM_009777	12260	Mm.2570	NM_009777	ENSMUSG00000036905	C1qb	-	complement component 1, q subcomponent, beta polypeptide	protein-coding
mm_40427.1	chr5	53532321	53532329	+	1	NA	Intergenic	MTE2b|LTR|ERVL-MaLR	-23454	NM_001080928	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_113400.1	chr13	33661403	33661406	+	1	NA	promoter-TSS (NM_001300892)	promoter-TSS (NM_001300892)	-1	NM_001076790	238568	Mm.249698	NM_001076790	ENSMUSG00000047889	Serpinb6d	Gm11390|OTTMUSG00000000712|SPI3D	serine (or cysteine) peptidase inhibitor, clade B, member 6d	protein-coding
mm_110559.1	chr12	55491782	55491801	-	1	NA	TTS (NR_035430)	TTS (NR_035430)	856	NM_010907	18035	Mm.170515	NM_010907	ENSMUSG00000021025	Nfkbia	AI462015|Nfkbi	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, alpha	protein-coding
mm_98449.1	chr11	94944747	94944782	+	1	NA	exon (NM_007742, exon 28 of 51)	exon (NM_007742, exon 28 of 51)	8540	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_58692.1	chr7	12922955	12922972	+	1	NA	intron (NM_009095, intron 1 of 5)	intron (NM_009095, intron 1 of 5)	652	NM_009095	20103	Mm.5291	NM_009095	ENSMUSG00000012848	Rps5	AA617411	ribosomal protein S5	protein-coding
mm_57349.1	chr6	124756700	124756768	-	1	NA	promoter-TSS (NM_007881)	promoter-TSS (NM_007881)	-247	NM_007881	13498	Mm.333380	NM_007881	ENSMUSG00000004263	Atn1	Atr1|Drpla|atrophin-1	atrophin 1	protein-coding
mm_66718.1	chr7	46100559	46100591	-	1	NA	promoter-TSS (NM_010602)	promoter-TSS (NM_010602)	189	NM_001204411	16514	Mm.333863	NM_010602	ENSMUSG00000096146	Kcnj11	Kir6.2|mBIR	potassium inwardly rectifying channel, subfamily J, member 11	protein-coding
mm_40228.1	chr5	37286388	37286410	+	1	NA	exon (NM_001136058, exon 12 of 14)	exon (NM_001136058, exon 12 of 14)	40635	NM_007765	12933	Mm.290995	NM_007765	ENSMUSG00000029121	Crmp1	CRMP-1|DRP-1|Dpysl1|ULIP-3|Ulip3	collapsin response mediator protein 1	protein-coding
mm_131279.1	chr16	11066293	11066381	+	1	NA	promoter-TSS (NM_009223)	promoter-TSS (NM_009223)	39	NM_009223	20621	Mm.325800	NM_009223	ENSMUSG00000037972	Snn	2810407J07Rik|AI848521|AW547286	stannin	protein-coding
mm_50148.1	chr6	41543671	41543703	+	1	NA	Intergenic	Intergenic	21911	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_41670.1	chr5	99508374	99508392	+	1	NA	intron (NR_030692, intron 2 of 3)	intron (NR_030692, intron 2 of 3)	220677	NR_030692	319818	Mm.295233	NR_030692	ENSMUSG00000089809	A930011G23Rik	-	RIKEN cDNA A930011G23 gene	ncRNA
mm_93233.1	chr10	95324073	95324114	-	1	NA	promoter-TSS (NM_001330175)	promoter-TSS (NM_001330175)	44	NM_001330141	12905	Mm.473739	NM_009950	ENSMUSG00000045867	Cradd	RAIDD	CASP2 and RIPK1 domain containing adaptor with death domain	protein-coding
mm_86131.1	chr9	116218973	116218977	-	1	NA	Intergenic	Intergenic	-43612	NM_009371	21813	Mm.172346	NM_009371	ENSMUSG00000032440	Tgfbr2	1110020H15Rik|AU042018|DNIIR|RIIDN|TBR-II|TbetaR-II|TbetaRII	transforming growth factor, beta receptor II	protein-coding
mm_46402.1	chr5	104093014	104093033	-	1	NA	exon (NM_010097, exon 4 of 11)	exon (NM_010097, exon 4 of 11)	-15415	NM_001163772	100271704	Mm.366664	NM_001163772	ENSMUSG00000091034	Gm17660	Scpppq1	predicted gene, 17660	protein-coding
mm_84980.1	chr9	85350385	85350387	-	1	NA	Intergenic	RMER15|LTR|ERVL	-23236	NM_001160379	212943	Mm.74610	NM_001160378	ENSMUSG00000032265	Fam46a	BAP014|D930050G01Rik	family with sequence similarity 46, member A	protein-coding
mm_53914.1	chr6	3988968	3988987	-	1	NA	promoter-TSS (NR_138566)	promoter-TSS (NR_138566)	-119	NR_138566	21789	Mm.25612	NM_009364	ENSMUSG00000029664	Tfpi2	AV000670|PP5/TFPI-2	tissue factor pathway inhibitor 2	protein-coding
mm_168785.1	chr12	18853557	18853580	+	1	NA	Intergenic	CpG	339058	NM_001201330	236366	Mm.352227	NM_001033157	ENSMUSG00000073197	5730507C01Rik	-	RIKEN cDNA 5730507C01 gene	protein-coding
mm_105319.1	chr11	102887989	102888001	-	1	NA	3' UTR (NM_010277, exon 9 of 9)	3' UTR (NM_010277, exon 9 of 9)	2826	NM_025766	66784	Mm.483216	NM_025766	ENSMUSG00000075510	Fam187a	4933439F11Rik	family with sequence similarity 187, member A	protein-coding
mm_111059.1	chr12	80110443	80110453	-	1	NA	exon (NM_007564, exon 2 of 2)	exon (NM_007564, exon 2 of 2)	2565	NM_007564	12192	Mm.235132	NM_007564	ENSMUSG00000021127	Zfp36l1	AW742437|AW743212|Berg36|Brf1|D530020L18Rik|ERF1|TIS11b|cMG1	zinc finger protein 36, C3H type-like 1	protein-coding
mm_126531.1	chr15	82016421	82016459	+	1	NA	promoter-TSS (NM_010247)	promoter-TSS (NM_010247)	71	NM_010247	14375	Mm.288809	NM_010247	ENSMUSG00000022471	Xrcc6	70kDa|G22p1|Ku70	X-ray repair complementing defective repair in Chinese hamster cells 6	protein-coding
mm_162644.1	chr1	193360040	193360043	+	1	NA	intron (NM_144817, intron 2 of 12)	intron (NM_144817, intron 2 of 12)	10241	NM_144817	215303	Mm.40329	NM_144817	ENSMUSG00000016179	Camk1g	CLICK-III|CaMKIgamma	calcium/calmodulin-dependent protein kinase I gamma	protein-coding
mm_5604.1	chr1	39577289	39577312	-	1	NA	promoter-TSS (NM_001033135)	promoter-TSS (NM_001033135)	47	NM_001033135	67702	Mm.28614	NM_001033135	ENSMUSG00000048234	Rnf149	1600023E10Rik|AV037261|C76763|Gm15832|Greul4|OTTMUSG00000026591	ring finger protein 149	protein-coding
mm_35299.1	chr4	22488144	22488160	-	1	NA	5' UTR (NM_008899, exon 1 of 1)	5' UTR (NM_008899, exon 1 of 1)	214	NM_008899	18992	Mm.129387	NM_008899	ENSMUSG00000095139	Pou3f2	9430075J19Rik|A230098E07Rik|Brn-2|Brn2|OTF-7|Otf7|oct-7	POU domain, class 3, transcription factor 2	protein-coding
mm_57361.1	chr6	124762723	124762736	-	1	NA	exon (NM_013509, exon 10 of 12)	exon (NM_013509, exon 10 of 12)	-6242	NM_007881	13498	Mm.333380	NM_007881	ENSMUSG00000004263	Atn1	Atr1|Drpla|atrophin-1	atrophin 1	protein-coding
mm_43369.1	chr5	135463681	135463681	+	1	NA	intron (NM_146001, intron 1 of 30)	intron (NM_146001, intron 1 of 30)	-69135	NM_148932	107939	Mm.28399	NM_148932	ENSMUSG00000053293	Pom121	2610027A18Rik|C80273|mKIAA0618	nuclear pore membrane protein 121	protein-coding
mm_65597.1	chr7	27339693	27339709	-	1	NA	Intergenic	Intergenic	-2089	NM_175641	108075	Mm.272251	NM_175641	ENSMUSG00000040488	Ltbp4	2310046A13Rik	latent transforming growth factor beta binding protein 4	protein-coding
mm_165178.1	chr2	27950635	27950651	+	1	NA	exon (NM_015734, exon 6 of 66)	exon (NM_015734, exon 6 of 66)	64218	NM_015734	12831	Mm.7281	NM_015734	ENSMUSG00000026837	Col5a1	AI413331	collagen, type V, alpha 1	protein-coding
mm_153187.1	chr19	34507031	34507101	-	1	NA	exon (NM_021460, exon 6 of 10)	exon (NM_021460, exon 6 of 10)	20408	NM_001111100	16889	Mm.157545	NM_021460	ENSMUSG00000024781	Lipa	AA960673|Lal|Lip-1|Lip1	lysosomal acid lipase A	protein-coding
mm_139216.1	chr17	47729251	47729255	+	1	NA	exon (NM_025973, exon 3 of 9)	exon (NM_025973, exon 3 of 9)	2411	NM_025973	109820	Mm.22957	NM_025973	ENSMUSG00000023987	Pgc	2210410L06Rik|Upg-1|Upg1	progastricsin (pepsinogen C)	protein-coding
mm_133450.1	chr16	88728829	88728845	+	1	NA	promoter-TSS (NM_183189)	promoter-TSS (NM_183189)	-25	NM_183189	268905	Mm.206668	NM_183189	ENSMUSG00000056350	Krtap13-1	AA589563|KAP13.1	keratin associated protein 13-1	protein-coding
mm_168689.1	chr11	96248603	96248621	+	1	NA	Intergenic	B4A|SINE|B4	-3048	NR_037977	193022	Mm.169508	NR_037977		Gm53	-	predicted gene 53	ncRNA
mm_114638.1	chr13	76456551	76456575	+	1	NA	intron (NM_030174, intron 1 of 20)	intron (NM_030174, intron 1 of 20)	71602	NM_030174	78771	Mm.316249	NM_030174	ENSMUSG00000021596	Mctp1	2810465F10Rik	multiple C2 domains, transmembrane 1	protein-coding
mm_108255.1	chr12	78303641	78303659	+	1	NA	intron (NM_145965, intron 1 of 22)	L1_Mus1|LINE|L1	76995	NM_145965	268566	Mm.341742	NM_145965	ENSMUSG00000047454	Gphn	5730552E08Rik|AI662856|BC027112|C230040D23|GPH|GPHRYN|geph	gephyrin	protein-coding
mm_169459.1	chr1	46415992	46416007	+	1	NA	Intergenic	Intergenic	-9519	NM_001310335	100101919	Mm.383402	NM_001310335	ENSMUSG00000101337	Dnah7c	Dnahc7c	dynein, axonemal, heavy chain 7C	protein-coding
mm_126335.1	chr15	79896697	79896719	+	1	NA	intron (NM_001347041, intron 2 of 7)	intron (NM_001347041, intron 2 of 7)	1685	NM_001347041	80287	Mm.284059	NM_030255	ENSMUSG00000009585	Apobec3	Apobec|Arp3|BC003314|Cem15|Rfv3	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 3	protein-coding
mm_154528.1	chrM	13539	13561	-	1	NA	NA	Intergenic	NA	NA								
mm_16011.1	chr2	167384085	167384096	+	1	NA	Intergenic	MER44D|DNA|TcMar-Tigger	-34912	NM_019835	56336	Mm.200886	NM_019835	ENSMUSG00000017929	B4galt5	9430078I07Rik|AW049941|AW539721	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 5	protein-coding
mm_154368.1	chrM	8963	8969	+	1	NA	NA	Intergenic	NA	NA								
mm_75160.1	chr8	36547834	36547835	-	1	NA	Intergenic	Intergenic	58643	NM_176952	319582	Mm.180924	NM_176952	ENSMUSG00000039620	6430573F11Rik	Kiaa1456|TRM9L	RIKEN cDNA 6430573F11 gene	protein-coding
mm_75095.1	chr8	34107763	34107789	-	1	NA	promoter-TSS (NM_001293758)	promoter-TSS (NM_001293758)	38	NM_001293758	22428	Mm.150373	NM_011722	ENSMUSG00000031516	Dctn6	AU044699|WS-3|p27	dynactin 6	protein-coding
mm_15404.1	chr2	156735320	156735337	+	1	NA	intron (NM_001042487, intron 1 of 6)	intron (NM_001042487, intron 1 of 6)	14049	NM_001042487	228836	Mm.22094	NM_146128	ENSMUSG00000061689	Dlgap4	AI225853|BC024558|DAP-4|DAP4|SAPAP-4|Sapap4|WBP16	discs, large homolog-associated protein 4 (Drosophila)	protein-coding
mm_156566.1	chrX	151902108	151902109	+	1	NA	intron (NM_021523, intron 48 of 82)	intron (NM_021523, intron 48 of 82)	-10238	NR_029732	387253		NR_029732	ENSMUSG00000065602	Mirlet7f-2	Mirlet7f2|Mirnlet7f2|let-7f-2	microRNA let7f-2	ncRNA
mm_38358.1	chr4	137881383	137881418	-	1	NA	intron (NM_199307, intron 1 of 19)	ID4_|SINE|ID	19163	NM_199307	230857	Mm.401062	NM_199307	ENSMUSG00000057530	Ece1	AW322500|ECE-1|ECE-1a|ECE-1b|ECE-1d	endothelin converting enzyme 1	protein-coding
mm_97171.1	chr11	75516372	75516378	+	1	NA	intron (NM_001004157, intron 4 of 10)	B1_Mur2|SINE|Alu	2834	NM_001004157	380713	Mm.10486	NM_001004157	ENSMUSG00000038188	Scarf1	AA986099|SREC|SREC-I|mKIAA0149	scavenger receptor class F, member 1	protein-coding
mm_102776.1	chr11	68386872	68386889	-	1	NA	promoter-TSS (NM_008744)	promoter-TSS (NM_008744)	-54	NM_008744	18208	Mm.39095	NM_008744	ENSMUSG00000020902	Ntn1	AI561871|BC019633|Netrin-1	netrin 1	protein-coding
mm_133677.1	chr16	92292399	92292411	+	1	NA	promoter-TSS (NM_134110)	promoter-TSS (NM_134110)	16	NM_134110	246133	Mm.156736	NM_134110	ENSMUSG00000039672	Kcne2	2200002I16Rik|AW048273|MiRP1	potassium voltage-gated channel, Isk-related subfamily, gene 2	protein-coding
mm_45871.1	chr5	88008251	88008279	-	1	NA	exon (NM_011422, exon 3 of 3)	exon (NM_011422, exon 3 of 3)	5740	NM_011422	20599	Mm.261199	NM_011422	ENSMUSG00000029280	Smr3a	AA589601|MSG1|MSG3|Smr1|Smr3	submaxillary gland androgen regulated protein 3A	protein-coding
mm_152091.1	chr19	6908105	6908117	-	1	NA	exon (NM_012021, exon 2 of 6)	exon (NM_012021, exon 2 of 6)	1534	NM_012021	54683	Mm.279782	NM_012021	ENSMUSG00000024953	Prdx5	AOEB166|AOPP|Pmp20|Prdx6|PrxV	peroxiredoxin 5	protein-coding
mm_25913.1	chr3	131133264	131133267	+	1	NA	intron (NM_001276403, intron 3 of 11)	intron (NM_001276403, intron 3 of 11)	20474	NM_001276403	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_47389.1	chr5	123014841	123014863	-	1	NA	promoter-TSS (NM_175423)	promoter-TSS (NM_175423)	-222	NM_175423	109305	Mm.218582	NM_175423	ENSMUSG00000049686	Orai1	D730049H07Rik|Tmem142a|orai-1	ORAI calcium release-activated calcium modulator 1	protein-coding
mm_118654.1	chr14	21750614	21750624	+	1	NA	promoter-TSS (NM_026283)	promoter-TSS (NM_026283)	88	NM_026283	67630	Mm.102765	NM_026283	ENSMUSG00000021770	Samd8	1110053F04Rik|1700010P07Rik|SMSr	sterile alpha motif domain containing 8	protein-coding
mm_128394.1	chr15	43171182	43171199	-	1	NA	promoter-TSS (NM_172815)	promoter-TSS (NM_172815)	-372	NM_172815	239405	Mm.193274	NM_172815	ENSMUSG00000051920	Rspo2	2610028F08Rik|AA673245|D430027K22|ftls	R-spondin 2	protein-coding
mm_145200.1	chr18	49979478	49979507	+	1	NA	promoter-TSS (NM_001177760)	promoter-TSS (NM_001177760)	65	NM_001177759	106869	Mm.27740	NM_134131	ENSMUSG00000062210	Tnfaip8	AA987150|E130304C20Rik|ENSMUSG00000073567|Gg2-1|Gm10539|Nded|Ssc-2|Tipe	tumor necrosis factor, alpha-induced protein 8	protein-coding
mm_164355.1	chr16	20841640	20841643	+	1	NA	Intergenic	RLTR42-int|LTR|ERVK	-107130	NM_009379	21832	Mm.3943	NM_009379	ENSMUSG00000022847	Thpo	Mgdf|Ml|Mpllg|Tpo	thrombopoietin	protein-coding
mm_79871.1	chr9	65136999	65137011	+	1	NA	3' UTR (NM_020043, exon 20 of 20)	3' UTR (NM_020043, exon 20 of 20)	-4184	NM_008988	19289	Mm.41529	NM_008988	ENSMUSG00000032394	Igdcc3	2810401C09Rik|AI851425|Punc|WI-14920	immunoglobulin superfamily, DCC subclass, member 3	protein-coding
mm_53046.1	chr6	124713100	124713117	+	1	NA	promoter-TSS (NM_013536)	promoter-TSS (NM_013536)	819	NM_007531	12034	Mm.36241	NM_007531	ENSMUSG00000004264	Phb2	AU044498|BAP|Bap37|Bcap37|REA	prohibitin 2	protein-coding
mm_122790.1	chr14	54417740	54417750	-	1	NA	promoter-TSS (NM_011405)	promoter-TSS (NM_011405)	-43	NM_011405	20540	Mm.142455	NM_011405	ENSMUSG00000000958	Slc7a7	AI790233|my+lat1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 7	protein-coding
mm_100018.1	chr11	114890273	114890370	+	1	NA	5' UTR (NM_170758, exon 1 of 7)	5' UTR (NM_170758, exon 1 of 7)	280	NM_170758	217303	Mm.294439	NM_170758	ENSMUSG00000034652	Cd300a	B230315M08Rik|Clm8|LMIR1|MAIR-I|MAIR-Ia|MMAC8|Pigr4|mcpir1	CD300A molecule	protein-coding
mm_36293.1	chr4	65381347	65381358	-	1	NA	3' UTR (NM_207109, exon 23 of 23)	3' UTR (NM_207109, exon 23 of 23)	-223634	NM_053084	69807	Mm.22786	NM_053084	ENSMUSG00000051675	Trim32	1810045E12Rik|3f3|BBS11|Zfp117	tripartite motif-containing 32	protein-coding
mm_50752.1	chr6	53287312	53287324	+	1	NA	promoter-TSS (NM_001327821)	promoter-TSS (NM_001327821)	15	NM_001327821	231991	Mm.227444	NM_172728	ENSMUSG00000053007	Creb5	9430076C15Rik|CRE-BPa|Crebpa|D430026C09Rik	cAMP responsive element binding protein 5	protein-coding
mm_27470.1	chr3	52856374	52856385	-	1	NA	Intergenic	Intergenic	71287	NR_040555	622124	Mm.389434	NR_040555	ENSMUSG00000104401	Gm20750	-	predicted gene, 20750	ncRNA
mm_130512.1	chr15	98846296	98846309	-	1	NA	exon (NM_001033276, exon 40 of 55)	exon (NM_001033276, exon 40 of 55)	-14794	NM_016781	19082	Mm.6670	NM_016781	ENSMUSG00000067713	Prkag1	AA571379|BB036179|Prkaac	protein kinase, AMP-activated, gamma 1 non-catalytic subunit	protein-coding
mm_125180.1	chr15	31602139	31602158	+	1	NA	promoter-TSS (NM_007637)	promoter-TSS (NM_007637)	32	NM_026546	68073	Mm.119185	NM_026546	ENSMUSG00000039065	Fam173b	A930016P21Rik|AA987072	family with sequence similarity 173, member B	protein-coding
mm_53132.1	chr6	125145401	125145413	+	1	NA	TTS (NM_138747)	TTS (NM_138747)	183	NM_001302779	320678	Mm.129415	NM_178787	ENSMUSG00000038271	Iffo1	4733401N06Rik|A930037G23Rik|HOM-TES-103|Iffo	intermediate filament family orphan 1	protein-coding
mm_164297.1	chr15	103896015	103896026	+	1	NA	exon (NM_009267, exon 4 of 4)	exon (NM_009267, exon 4 of 4)	3280	NM_009268	20771	Mm.30276	NM_009268		Mucl1	Spt-2|Spt2	mucin-like 1	protein-coding
mm_33552.1	chr4	130934947	130934959	+	1	NA	3' UTR (NM_010686, exon 8 of 8)	3' UTR (NM_010686, exon 8 of 8)	-9432	NM_010769	17180	Mm.271796	NM_010769	ENSMUSG00000040533	Matn1	CMP|Crtm|Mat1|matrilin-1	matrilin 1, cartilage matrix protein	protein-coding
mm_170275.1	chr18	25304031	25304032	+	1	NA	intron (NM_001033532, intron 6 of 10)	B1_Mus1|SINE|Alu	135011	NM_001033532	225289	Mm.391081	NM_001033532	ENSMUSG00000033632	AW554918	4921538P22|AI461742|Kiaa1328|mKIAA1328	expressed sequence AW554918	protein-coding
mm_98594.1	chr11	95824470	95824512	+	1	NA	promoter-TSS (NM_153104)	promoter-TSS (NM_153104)	-9	NM_153104	237928	Mm.133075	NM_153104	ENSMUSG00000050860	Phospho1	D11Moh36|Phospo1	phosphatase, orphan 1	protein-coding
mm_114177.1	chr13	55609932	55609935	+	1	NA	3' UTR (NM_146045, exon 6 of 6)	3' UTR (NM_146045, exon 6 of 6)	10037	NM_001311137	218271	Mm.139825	NM_146045	ENSMUSG00000021504	B4galt7	-	xylosylprotein beta1,4-galactosyltransferase, polypeptide 7 (galactosyltransferase I)	protein-coding
mm_94956.1	chr11	30221641	30221646	+	1	NA	Intergenic	RMER2|LTR|ERV1	-1871	NM_175836	20742	Mm.123110	NM_009260	ENSMUSG00000020315	Sptbn1	9930031C03Rik|AL033301|SPTB2|Spnb-2|Spnb2|elf1|elf3|mKIAA4049	spectrin beta, non-erythrocytic 1	protein-coding
mm_144448.1	chr18	23217123	23217125	+	1	NA	promoter-TSS (NR_110491)	promoter-TSS (NR_110491)	-472	NR_110491	665797	Mm.328158	NR_110491		Gm7788	EG665797	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_117726.1	chr13	95525286	95525292	-	1	NA	promoter-TSS (NM_007974)	promoter-TSS (NM_007974)	-49	NM_007974	14063	Mm.1614	NM_007974	ENSMUSG00000021678	F2rl1	Gpcr11|PAR-2|Par2	coagulation factor II (thrombin) receptor-like 1	protein-coding
mm_19064.1	chr2	77519566	77519647	-	1	NA	promoter-TSS (NM_001113400)	promoter-TSS (NM_001113400)	60	NM_001113400	241494	Mm.490320	NM_178723	ENSMUSG00000027016	Zfp385b	B830010L13Rik|C130013B13Rik|Zfp533|Znf385b	zinc finger protein 385B	protein-coding
mm_135831.1	chr16	58523497	58523502	-	1	NA	promoter-TSS (NM_018784)	promoter-TSS (NM_018784)	-187	NM_018784	54613	Mm.212742	NM_018784	ENSMUSG00000022747	St3gal6	1700023B24Rik|AI930218|AW552396|Siat10|St3galVI	ST3 beta-galactoside alpha-2,3-sialyltransferase 6	protein-coding
mm_95132.1	chr11	34506975	34506984	+	1	NA	intron (NM_033374, intron 23 of 51)	intron (NM_033374, intron 23 of 51)	192157	NM_001025382	574403	Mm.444796	NM_001025382	ENSMUSG00000069911	Fam196b	EG574403|Gm6041	family with sequence similarity 196, member B	protein-coding
mm_55305.1	chr6	54967231	54967232	-	1	NA	intron (NM_172729, intron 1 of 11)	intron (NM_172729, intron 1 of 11)	4430	NM_001171007	107607	Mm.28498	NM_172729	ENSMUSG00000038058	Nod1	C230079P11|Card4|F830007N14Rik|Nlrc1	nucleotide-binding oligomerization domain containing 1	protein-coding
mm_144112.1	chr18	4353582	4353592	+	1	NA	promoter-TSS (NM_007746)	promoter-TSS (NM_007746)	40	NR_040328	73915	Mm.482777	NR_040328		4833419F23Rik	-	RIKEN cDNA 4833419F23 gene	ncRNA
mm_134254.1	chr16	13730458	13730470	-	1	NA	promoter-TSS (NM_011987)	promoter-TSS (NM_011987)	20	NR_110990	26565	Mm.4214	NM_011987	ENSMUSG00000022683	Pla2g10	GX sPLA2|PLA2GX|sPLA2-X	phospholipase A2, group X	protein-coding
mm_15231.1	chr2	154551789	154551798	+	1	NA	promoter-TSS (NM_001171640)	promoter-TSS (NM_001171640)	17	NM_001171640	70362	Mm.479620	NM_001171640	ENSMUSG00000078129	Actl10	1700007I08Rik	actin-like 10	protein-coding
mm_153399.1	chr19	40496999	40497005	-	1	NA	intron (NM_178362, intron 1 of 28)	intron (NM_178362, intron 1 of 28)	16734	NM_178362	20411	Mm.210815	NM_009166	ENSMUSG00000025006	Sorbs1	2310065E01Rik|9530001P15Rik|CAP|SH3P12|Sh3d5|mKIAA1296	sorbin and SH3 domain containing 1	protein-coding
mm_97039.1	chr11	72305460	72305474	+	1	NA	intron (NM_001037713, intron 3 of 5)	ORR1E|LTR|ERVL-MaLR	3838	NM_001037713	327959	Mm.291131	NM_001037713	ENSMUSG00000040483	Xaf1	Fbox39	XIAP associated factor 1	protein-coding
mm_105057.1	chr11	100712347	100712355	-	1	NA	exon (NM_020004, exon 1 of 18)	exon (NM_020004, exon 1 of 18)	116	NM_001038010	14534	Mm.218837	NM_020004	ENSMUSG00000020918	Kat2a	1110051E14Rik|AW212720|Gcn5|Gcn5l2|mmGCN5	K(lysine) acetyltransferase 2A	protein-coding
mm_61379.1	chr7	70871133	70871152	+	1	NA	Intergenic	Intergenic	-504396	NM_183261	11819	Mm.158143	NM_009697	ENSMUSG00000030551	Nr2f2	2700033K02Rik|9430015G03Rik|ARP-1|Aporp1|COUP-TF2|COUP-TFII|COUPTFB|EAR3|SVP40|Tcfcoup2	nuclear receptor subfamily 2, group F, member 2	protein-coding
mm_15620.1	chr2	161004622	161004634	+	1	NA	intron (NR_126509, intron 16 of 35)	intron (NR_126509, intron 16 of 35)	-92289	NM_182840	280635	Mm.330747	NM_182840	ENSMUSG00000050700	Emilin3	1110013O17Rik|EMILIN-3|EMILIN-5|EMILIN-T|Emilin5	elastin microfibril interfacer 3	protein-coding
mm_112380.1	chr12	119238007	119238018	-	1	NA	5' UTR (NM_177290, exon 1 of 14)	5' UTR (NM_177290, exon 1 of 14)	264	NM_177290	320910	Mm.217000	NM_177290	ENSMUSG00000025321	Itgb8	4832412O06Rik	integrin beta 8	protein-coding
mm_138973.1	chr17	45298571	45298595	+	1	NA	Intergenic	Intergenic	135124	NM_152810	71702	Mm.28270	NM_152810	ENSMUSG00000023932	Cdc5l	1200002I02Rik|AA408004|PCDC5RP	cell division cycle 5-like (S. pombe)	protein-coding
mm_97561.1	chr11	78935395	78935419	+	1	NA	exon (NM_010927, exon 6 of 27)	exon (NM_010927, exon 6 of 27)	10116	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_172298.1	chr7	101155128	101155135	-	1	NA	intron (NM_199012, intron 3 of 20)	intron (NM_199012, intron 3 of 20)	46356	NM_199012	207278	Mm.263041	NM_199012	ENSMUSG00000030691	Fchsd2	BC034086|R74866|Sh3md3|mKIAA0769	FCH and double SH3 domains 2	protein-coding
mm_60674.1	chr7	45062464	45062500	+	1	NA	promoter-TSS (NM_025533)	promoter-TSS (NM_025533)	53	NM_025533	66394	Mm.272139	NM_025533	ENSMUSG00000003421	Nosip	2310061K06Rik|CGI-25	nitric oxide synthase interacting protein	protein-coding
mm_78974.1	chr9	45370093	45370109	+	1	NA	promoter-TSS (NM_022004)	promoter-TSS (NM_022004)	-84	NM_022004	59095	Mm.208287	NM_022004	ENSMUSG00000066705	Fxyd6	0610030I18Rik|Php	FXYD domain-containing ion transport regulator 6	protein-coding
mm_40711.1	chr5	65868257	65868270	+	1	NA	intron (NM_001081105, intron 1 of 2)	B3|SINE|B2	4694	NM_001081105	74734	Mm.20323	NM_001081105	ENSMUSG00000029204	Rhoh	5830400A04Rik|AU019774|Arhh	ras homolog family member H	protein-coding
mm_77128.1	chr8	111337884	111337914	-	1	NA	5' UTR (NM_001310613, exon 1 of 11)	5' UTR (NM_001310613, exon 1 of 11)	306	NM_001310613	74568	Mm.207971	NM_029005	ENSMUSG00000012519	Mlkl	9130019I15Rik	mixed lineage kinase domain-like	protein-coding
mm_165939.1	chr4	76864181	76864186	-	1	NA	intron (NM_011211, intron 8 of 39)	L1MC1|LINE|L1	1347712	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding
mm_35261.1	chr4	19892343	19892352	-	1	NA	intron (NM_175406, intron 2 of 7)	intron (NM_175406, intron 2 of 7)	30219	NM_175406	242341	Mm.19298	NM_175406	ENSMUSG00000028238	Atp6v0d2	1620401A02Rik|AI324824|V-ATPase	ATPase, H+ transporting, lysosomal V0 subunit D2	protein-coding
mm_19086.1	chr2	79132372	79132379	-	1	NA	Intergenic	Intergenic	-123051	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D|Itga4B	integrin alpha 4	protein-coding
mm_134212.1	chr16	11176271	11176365	-	1	NA	promoter-TSS (NR_027502)	promoter-TSS (NR_027502)	75	NR_027502	106205	Mm.226860	NM_145931	ENSMUSG00000037965	Zc3h7a	A430104C18Rik|AI447294|AW556219|HSPC055|Zc3h7|Zc3hdc7	zinc finger CCCH type containing 7 A	protein-coding
mm_14121.1	chr2	125912670	125912680	+	1	NA	intron (NM_175154, intron 5 of 9)	ID_B1|SINE|B4	46452	NM_001291002	69976	Mm.20216	NM_175154	ENSMUSG00000027207	Galk2	2810017M24Rik|AI327030|Gk2	galactokinase 2	protein-coding
mm_10808.1	chr2	24349897	24349910	+	1	NA	3' UTR (NM_031167, exon 5 of 5)	3' UTR (NM_031167, exon 5 of 5)	4532	NM_001039701	16181	Mm.882	NM_031167	ENSMUSG00000026981	Il1rn	F630041P17Rik|IL-1ra	interleukin 1 receptor antagonist	protein-coding
mm_143473.1	chr17	71127618	71127643	-	1	NA	TTS (NM_001083934)	TTS (NM_001083934)	-56348	NM_022882	64898	Mm.227924	NM_022882	ENSMUSG00000024052	Lpin2	2610511G02Rik|AI481352|AW742896	lipin 2	protein-coding
mm_127438.1	chr15	101270318	101270337	+	1	NA	exon (NM_010444, exon 2 of 7)	exon (NM_010444, exon 2 of 7)	3481	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_64355.1	chr7	142388227	142388239	+	1	NA	promoter-TSS (NM_009983)	promoter-TSS (NM_009983)	-363	NM_009983	13033	Mm.231395	NM_009983	ENSMUSG00000007891	Ctsd	CD|CatD	cathepsin D	protein-coding
mm_105858.1	chr11	113751814	113751849	-	1	NA	promoter-TSS (NM_001163346)	promoter-TSS (NM_001163346)	-16	NM_001163346	56699	Mm.293378	NM_020006	ENSMUSG00000041598	Cdc42ep4	1500041M20Rik|Borg4|CEP4	CDC42 effector protein (Rho GTPase binding) 4	protein-coding
mm_145055.1	chr18	40271675	40271677	+	1	NA	intron (NM_026135, intron 1 of 1)	MTD|LTR|ERVL-MaLR	13315	NM_026135	383348	Mm.76366	NM_026135	ENSMUSG00000051401	Kctd16	4930434H12Rik|Gm1267	potassium channel tetramerisation domain containing 16	protein-coding
mm_53703.1	chr6	142917820	142917827	+	1	NA	intron (NM_011374, intron 1 of 4)	L1MA5|LINE|L1	46629	NM_011374	20449	Mm.260838	NM_011374	ENSMUSG00000030283	St8sia1	9330109E03Rik|GD3S|Sia-T|Siat8|Siat8a	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 1	protein-coding
mm_131113.1	chr16	5233616	5233653	+	1	NA	promoter-TSS (NM_145362)	promoter-TSS (NM_145362)	13	NM_145362	208211	Mm.34581	NM_145362	ENSMUSG00000039427	Alg1	HMAT1|HMT1	asparagine-linked glycosylation 1 (beta-1,4-mannosyltransferase)	protein-coding
mm_128935.1	chr15	74651838	74651842	-	1	NA	Intergenic	Intergenic	-15522	NM_001177437	69439	Mm.263708	NM_001177437	ENSMUSG00000022603	Mroh4	1700016M24Rik	maestro heat-like repeat family member 4	protein-coding
mm_81084.1	chr9	106270963	106270970	+	1	NA	Intergenic	ID4|SINE|ID	-10095	NM_027354	70235	Mm.23054	NM_027354	ENSMUSG00000023345	Poc1a	2510040D07Rik|Wdr51a|cha	POC1 centriolar protein A	protein-coding
mm_16539.1	chr2	181628703	181628705	+	1	NA	intron (NM_133701, intron 6 of 20)	ID_B1|SINE|B4	27385	NM_133701	68879	Mm.292001	NM_133701	ENSMUSG00000002455	Prpf6	1190003A07Rik|2610031L17Rik|ANT-1|U5-102K	pre-mRNA splicing factor 6	protein-coding
mm_67062.1	chr7	67620017	67620028	-	1	NA	intron (NR_028144, intron 2 of 8)	intron (NR_028144, intron 2 of 8)	25214	NM_175124	67867	Mm.31247	NM_027413	ENSMUSG00000030556	Lrrc28	1300004K21Rik|2210012C09Rik|2310058O11Rik	leucine rich repeat containing 28	protein-coding
mm_54786.1	chr6	41554411	41554423	-	1	NA	Intergenic	Intergenic	32641	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_86052.1	chr9	114563288	114563303	-	1	NA	5' UTR (NM_001042503, exon 1 of 4)	5' UTR (NM_001042503, exon 1 of 4)	1074	NM_001042503	636931	Mm.17857	NM_001042503	ENSMUSG00000079259	Trim71	2610206G21Rik|AL022943|Gm1127|Lin41|lin-41|mLin41|mlin-41	tripartite motif-containing 71	protein-coding
mm_43412.1	chr5	135958104	135958107	+	1	NA	Intergenic	Intergenic	16371	NM_001160366	109267	Mm.332750	NM_001160366	ENSMUSG00000029699	Ssc4d	C330016E03Rik|S4D-SRCRB|SRCRB-S4D|Srcrb4d	scavenger receptor cysteine rich family, 4 domains	protein-coding
mm_146890.1	chr18	25754117	25754176	-	1	NA	promoter-TSS (NM_001146295)	promoter-TSS (NM_001146295)	-163	NM_001174074	108013	Mm.266435	NM_133195	ENSMUSG00000024268	Celf4	A230070D14Rik|BRUNOL-4|Brul4|Brunol4|C130060B05Rik	CUGBP, Elav-like family member 4	protein-coding
mm_94032.1	chr10	127888645	127888662	-	1	NA	promoter-TSS (NM_001150749)	promoter-TSS (NM_001150749)	46	NM_017473	54150	Mm.6696	NM_017473	ENSMUSG00000040134	Rdh7	AI194929|CRAD2	retinol dehydrogenase 7	protein-coding
mm_77478.1	chr8	122460667	122460695	-	1	NA	promoter-TSS (NM_013914)	promoter-TSS (NM_013914)	11	NM_013914	30927	Mm.103673	NM_013914	ENSMUSG00000006587	Snai3	AI643946|Smuc|Zfp293	snail family zinc finger 3	protein-coding
mm_140086.1	chr17	75442453	75442456	+	1	NA	intron (NM_001166493, intron 1 of 16)	B4A|SINE|B4	6549	NM_001166493	240168	Mm.329203	NM_207246	ENSMUSG00000071042	Rasgrp3	BC066069|Gm327	RAS, guanyl releasing protein 3	protein-coding
mm_130224.1	chr15	96210865	96210876	-	1	NA	Intergenic	RLTR17|LTR|ERVK	-12896	NR_040423	70040	Mm.437832	NR_040423		2610037D02Rik	AU024679	RIKEN cDNA 2610037D02 gene	ncRNA
mm_62348.1	chr7	100498732	100498743	+	1	NA	exon (NM_011671, exon 7 of 8)	exon (NM_011671, exon 7 of 8)	5379	NM_011671	22228	Mm.171378	NM_011671	ENSMUSG00000033685	Ucp2	Slc25a8	uncoupling protein 2 (mitochondrial, proton carrier)	protein-coding
mm_61997.1	chr7	91156853	91156855	+	1	NA	intron (NM_011807, intron 1 of 22)	intron (NM_011807, intron 1 of 22)	66068	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_110592.1	chr12	56532992	56533013	-	1	NA	3' UTR (NM_009385, exon 3 of 3)	3' UTR (NM_009385, exon 3 of 3)	-3582	NR_045082	104798	Mm.310950	NR_045082		E030019B13Rik	AI413669	RIKEN cDNA E030019B13 gene	ncRNA
mm_168812.1	chr12	21778878	21778883	-	1	NA	Intergenic	CpG	-361444	NM_011739	22630	Mm.289630	NM_011739	ENSMUSG00000076432	Ywhaq	2700028P07Rik|AA409740|AU021156|R74690	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide	protein-coding
mm_8537.1	chr1	155059535	155059545	-	1	NA	Intergenic	Intergenic	40096	NM_010500	15939	Mm.12246	NM_010500	ENSMUSG00000056708	Ier5	-	immediate early response 5	protein-coding
mm_45323.1	chr5	65484039	65484076	-	1	NA	intron (NM_133697, intron 1 of 4)	intron (NM_133697, intron 1 of 4)	8778	NM_133697	68552	Mm.10709	NM_133697	ENSMUSG00000037822	Smim14	1110003E01Rik|1700127H04Rik|5430439C17Rik|MAd4	small integral membrane protein 14	protein-coding
mm_51118.1	chr6	67896152	67896152	+	1	NA	Intergenic	Intergenic	-330453	NR_003100	75070	Mm.463364	NR_003100		4930515G16Rik	-	myc induced nuclear antigen pseudogene	pseudo
mm_100751.1	chr11	4232622	4232637	-	1	NA	Intergenic	Intergenic	-4156	NM_001013365	18413	Mm.131422	NM_001013365	ENSMUSG00000058755	Osm	OncoM	oncostatin M	protein-coding
mm_158475.1	chrX	141473881	141473894	-	1	NA	5' UTR (NM_053185, exon 1 of 45)	5' UTR (NM_053185, exon 1 of 45)	189	NM_053185	94216	Mm.155586	NM_053185	ENSMUSG00000031273	Col4a6	BB116301	collagen, type IV, alpha 6	protein-coding
mm_133661.1	chr16	91848865	91848881	+	1	NA	exon (NM_010587, exon 20 of 39)	exon (NM_010587, exon 20 of 39)	82757	NM_138597	28080	Mm.41	NM_138597	ENSMUSG00000022956	Atp5o	ATPO|D12Wsu28e|OSCP	ATP synthase, H+ transporting, mitochondrial F1 complex, O subunit	protein-coding
mm_66101.1	chr7	31037895	31037919	-	1	NA	exon (NM_001111073, exon 4 of 8)	exon (NM_001111073, exon 4 of 8)	2410	NR_106017	102465635		NR_106017	ENSMUSG00000098783	Mir7050	Gm27578|mmu-mir-7050	microRNA 7050	ncRNA
mm_68402.1	chr7	109609226	109609229	-	1	NA	intron (NM_001001326, intron 1 of 19)	intron (NM_001001326, intron 1 of 19)	7341	NR_037617	76954	Mm.252009	NM_029811	ENSMUSG00000031024	St5	2010004M01Rik|2610305K15Rik	suppression of tumorigenicity 5	protein-coding
mm_145575.1	chr18	60925645	60925655	+	1	NA	promoter-TSS (NM_177407)	promoter-TSS (NM_177407)	18	NM_177407	12322	Mm.131530	NM_009792	ENSMUSG00000024617	Camk2a	CaMKII|R74975|mKIAA0968	calcium/calmodulin-dependent protein kinase II alpha	protein-coding
mm_160011.1	chr6	124998677	124998677	+	1	NA	promoter-TSS (NM_001145926)	promoter-TSS (NM_001145926)	67	NM_001145926	319352	Mm.295327	NM_175696	ENSMUSG00000030329	Pianp	AI255183|AU067746|C530028O21Rik|Panp	PILR alpha associated neural protein	protein-coding
mm_5717.1	chr1	44101638	44101649	-	1	NA	intron (NM_029368, intron 2 of 7)	intron (NM_029368, intron 2 of 7)	745	NM_029368	75623	Mm.348017	NM_029368	ENSMUSG00000026049	Tex30	1700029F09Rik|3110030D08Rik	testis expressed 30	protein-coding
mm_28469.1	chr3	90695789	90695796	-	1	NA	promoter-TSS (NM_001281852)	promoter-TSS (NM_001281852)	-71	NM_009114	20202	Mm.2128	NM_009114	ENSMUSG00000056071	S100a9	60B8Ag|AW546964|BEE22|Cagb|GAGB|L1Ag|MRP14|p14	S100 calcium binding protein A9 (calgranulin B)	protein-coding
mm_67325.1	chr7	79732164	79732177	-	1	NA	intron (NM_001113471, intron 1 of 8)	intron (NM_001113471, intron 1 of 8)	606	NM_175640	103968	Mm.254917	NM_175640	ENSMUSG00000030546	Plin1	6030432J05Rik|Peri|Plin	perilipin 1	protein-coding
mm_146734.1	chr18	15346196	15346200	-	1	NA	Intergenic	RLTR41|LTR|ERV1	56801	NM_001308647	11829	Mm.250786	NM_009700	ENSMUSG00000024411	Aqp4	WCH4	aquaporin 4	protein-coding
mm_139383.1	chr17	51904206	51904222	+	1	NA	intron (NR_045095, intron 1 of 2)	intron (NR_045095, intron 1 of 2)	21487	NR_045095	100504169	Mm.417731	NR_045095		Gm20098	-	predicted gene, 20098	ncRNA
mm_51740.1	chr6	87277739	87277750	+	1	NA	intron (NM_054041, intron 8 of 17)	intron (NM_054041, intron 8 of 17)	58031	NM_054041	69538	Mm.232525	NM_054041	ENSMUSG00000033420	Antxr1	2310008J16Rik|2810405N18Rik|Antrx1|Tem8	anthrax toxin receptor 1	protein-coding
mm_120620.1	chr14	70456993	70457014	+	1	NA	promoter-TSS (NM_145981)	promoter-TSS (NM_145981)	-514	NM_145981	105653	Mm.192598	NM_145981	ENSMUSG00000003469	Phyhip	AW049870|C630010D02Rik|Lnap1ip|PAHX-AP#1|PAHX-AP1	phytanoyl-CoA hydroxylase interacting protein	protein-coding
mm_118459.1	chr14	8666370	8666413	+	1	NA	promoter-TSS (NM_028934)	promoter-TSS (NM_028934)	1	NR_045968	74859	Mm.84041	NR_045968	ENSMUSG00000097898	4930455B14Rik	1700027C12Rik	RIKEN cDNA 4930455B14 gene	ncRNA
mm_97191.1	chr11	75576773	75576786	+	1	NA	3' UTR (NM_001199283, exon 14 of 14)	3' UTR (NM_001199283, exon 14 of 14)	-11300	NM_008850	18738	Mm.3128	NM_008850	ENSMUSG00000017781	Pitpna	Pitpn|vb|vibrator	phosphatidylinositol transfer protein, alpha	protein-coding
mm_151783.1	chr19	5366286	5366378	-	1	NA	promoter-TSS (NM_027236)	promoter-TSS (NM_027236)	31	NM_001038231	23825	Mm.358649	NM_011793	ENSMUSG00000024844	Banf1	Baf|Bcrp1|L2bp1/Baf	barrier to autointegration factor 1	protein-coding
mm_41193.1	chr5	88328029	88328042	+	1	NA	exon (NM_008644, exon 3 of 3)	exon (NM_008644, exon 3 of 3)	10723	NM_008644	17830	Mm.200411	NM_008644	ENSMUSG00000064156	Prol1	Muc10	proline rich, lacrimal 1	protein-coding
mm_115660.1	chr13	12461411	12461417	-	1	NA	5' UTR (NM_001199043, exon 1 of 10)	5' UTR (NM_001199043, exon 1 of 10)	324	NM_001291060	56048	Mm.474138	NM_018886	ENSMUSG00000057554	Lgals8	1200015E08Rik|AI326142|D13Ertd524e|Lgals-8	lectin, galactose binding, soluble 8	protein-coding
mm_122742.1	chr14	54149222	54149240	-	1	NA	Intergenic	Intergenic	104698	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_47324.1	chr5	122479567	122479570	-	1	NA	intron (NM_001110140, intron 5 of 19)	intron (NM_001110140, intron 5 of 19)	22657	NM_001110140	11938	Mm.227583	NM_009722	ENSMUSG00000029467	Atp2a2	9530097L16Rik|D5Wsu150e|SERCA2|SERCA2B|Serca2a|mKIAA4195	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	protein-coding
mm_13679.1	chr2	116899745	116899751	+	1	NA	promoter-TSS (NR_040336)	promoter-TSS (NR_040336)	-404	NR_040336	320975	Mm.132509	NR_040335	ENSMUSG00000085316	D330050G23Rik	-	RIKEN cDNA D330050G23 gene	ncRNA
mm_167517.1	chr9	14903784	14903786	-	1	NA	5' UTR (NM_176807, exon 1 of 5)	5' UTR (NM_176807, exon 1 of 5)	166	NM_176807	64931	Mm.86738	NM_022888	ENSMUSG00000031933	Izumo1r	0910001L11Rik|C86255|Folbp3|Folr4|Juno	IZUMO1 receptor, JUNO	protein-coding
mm_113122.1	chr13	24562942	24562942	+	1	NA	Intergenic	MLT1J|LTR|ERVL-MaLR	-19247	NM_001286100	193385	Mm.217319	NM_029679	ENSMUSG00000036006	Fam65b	-	family with sequence similarity 65, member B	protein-coding
mm_46630.1	chr5	108449113	108449129	-	1	NA	promoter-TSS (NM_172883)	promoter-TSS (NM_172883)	-230	NM_172883	243197	Mm.106818	NM_172883	ENSMUSG00000029490	Mfsd7a	4732482E20Rik|Mfsd7	major facilitator superfamily domain containing 7A	protein-coding
mm_157110.1	chrX	9438134	9438144	-	1	NA	3' UTR (NM_007807, exon 13 of 13)	3' UTR (NM_007807, exon 13 of 13)	31185	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_80357.1	chr9	75193387	75193404	+	1	NA	intron (NM_010864, intron 30 of 40)	intron (NM_010864, intron 30 of 40)	-38619	NM_001081322	208943	Mm.41339	NM_001081322	ENSMUSG00000033590	Myo5c	9130003O20Rik|BB085560|C330029I24	myosin VC	protein-coding
mm_56666.1	chr6	113600646	113600653	-	1	NA	promoter-TSS (NM_027633)	promoter-TSS (NM_027633)	66	NM_027633	70979	Mm.72959	NM_027633	ENSMUSG00000033963	Fancd2os	4931417G12Rik	Fancd2 opposite strand	protein-coding
mm_99731.1	chr11	106301384	106301409	+	1	NA	exon (NM_008117, exon 2 of 5)	exon (NM_008117, exon 2 of 5)	500	NM_008117	14599	Mm.343934	NM_008117	ENSMUSG00000020713	Gh	Gh1|Ghb1	growth hormone	protein-coding
mm_107569.1	chr12	44328561	44328573	+	1	NA	promoter-TSS (NM_176930)	promoter-TSS (NM_176930)	-318	NM_176930	319504	Mm.208439	NM_176930	ENSMUSG00000020598	Nrcam	Bravo|C030017F07Rik|C130076O07Rik|mKIAA0343	neuronal cell adhesion molecule	protein-coding
mm_107773.1	chr12	59133828	59133839	+	1	NA	intron (NM_001165253, intron 1 of 22)	intron (NM_001165253, intron 1 of 22)	2380	NM_001165253	338320	Mm.213215	NM_146034	ENSMUSG00000021000	Mia2	Ctage5|D12Bwg0579e|Mea6|Mgea|Mgea6	melanoma inhibitory activity 2	protein-coding
mm_7284.1	chr1	97706969	97706973	-	1	NA	3' UTR (NM_173760, exon 28 of 28)	3' UTR (NM_173760, exon 28 of 28)	-44953	NM_133825	52392	Mm.12309	NM_133825	ENSMUSG00000044768	D1Ertd622e	AI987691|AW047450	DNA segment, Chr 1, ERATO Doi 622, expressed	protein-coding
mm_110265.1	chr12	31948770	31948774	-	1	NA	intron (NM_177993, intron 1 of 8)	intron (NM_177993, intron 1 of 8)	1763	NM_177993	73389	Mm.390461	NM_153198	ENSMUSG00000002996	Hbp1	1700058O05Rik|BE629963|C330012F01Rik|C86454	high mobility group box transcription factor 1	protein-coding
mm_80041.1	chr9	69094579	69094583	+	1	NA	intron (NM_013646, intron 1 of 10)	intron (NM_013646, intron 1 of 10)	-195260	NM_001289916	19883	Mm.378450	NM_013646	ENSMUSG00000032238	Rora	9530021D13Rik|Nr1f1|ROR1|ROR2|ROR3|nmf267|sg|staggerer|tmgc26	RAR-related orphan receptor alpha	protein-coding
mm_17251.1	chr2	25712773	25712780	-	1	NA	Intergenic	RMER15|LTR|ERVL	5897	NM_023326	107771	Mm.330057	NM_023326	ENSMUSG00000049086	Bmyc	2900002K07Rik|AW060705|Mycb	brain expressed myelocytomatosis oncogene	protein-coding
mm_117381.1	chr13	73328443	73328467	-	1	NA	promoter-TSS (NM_010888)	promoter-TSS (NM_010888)	27	NR_033306	407785	Mm.29897	NM_010888	ENSMUSG00000021606	Ndufs6	BC059730|IP13	NADH dehydrogenase (ubiquinone) Fe-S protein 6	protein-coding
mm_91197.1	chr10	21157295	21157297	-	1	NA	intron (NM_010848, intron 1 of 14)	intron (NM_010848, intron 1 of 14)	3688	NM_001198914	17863	Mm.52109	NM_010848	ENSMUSG00000019982	Myb	AI550390|M16449|c-myb	myeloblastosis oncogene	protein-coding
mm_108825.1	chr12	95728331	95728342	+	1	NA	intron (NM_201518, intron 1 of 1)	intron (NM_201518, intron 1 of 1)	36110	NM_201518	399558	Mm.341948	NM_201518	ENSMUSG00000047414	Flrt2	-	fibronectin leucine rich transmembrane protein 2	protein-coding
mm_69763.1	chr7	141009757	141009793	-	1	NA	exon (NM_025378, exon 2 of 2)	exon (NM_025378, exon 2 of 2)	969	NM_025378	66141	Mm.141021	NM_025378	ENSMUSG00000025492	Ifitm3	1110004C05Rik|Cd225|Cdw217|DSPA2b|Fgls|IP15|mil-1	interferon induced transmembrane protein 3	protein-coding
mm_48442.1	chr5	140636061	140636065	-	1	NA	exon (NM_175274, exon 2 of 14)	exon (NM_175274, exon 2 of 14)	12968	NM_001308040	78339	Mm.28947	NM_175274	ENSMUSG00000036565	Ttyh3	2900029G13Rik|AI414930|TTY3|mTTY3	tweety family member 3	protein-coding
mm_107359.1	chr12	32834354	32834392	+	1	NA	intron (NM_021524, intron 3 of 10)	intron (NM_021524, intron 3 of 10)	10257	NR_045032	100504486	Mm.440246	NR_045032		Gdap10	Gdap-ps	ganglioside-induced differentiation-associated-protein 10	ncRNA
mm_141642.1	chr17	33358833	33358886	-	1	NA	promoter-TSS (NM_207541)	promoter-TSS (NM_207541)	19	NM_207541	224694	Mm.170029	NM_207541	ENSMUSG00000003929	Zfp81	AA409460|AA409461|C330034P10Rik|D330034E10Rik|Hszfp36|KRAB13|Zfp78	zinc finger protein 81	protein-coding
mm_171485.1	chr4	146097277	146097278	+	1	NA	promoter-TSS (NM_001037926)	promoter-TSS (NM_001037926)	-35	NM_001037926	626316	Mm.270762	NM_001037926	ENSMUSG00000066009	Zfp987	Gm13051|OTTMUSG00000010104|OTTMUSG00000010173	zinc finger protein 987	protein-coding
mm_19999.1	chr2	118762608	118762666	-	1	NA	promoter-TSS (NM_001001982)	promoter-TSS (NM_001001982)	24	NM_001001982	214239	Mm.379342	NM_001001982	ENSMUSG00000045838	A430105I19Rik	Gm353	RIKEN cDNA A430105I19 gene	protein-coding
mm_84099.1	chr9	58274044	58274060	-	1	NA	Intergenic	MTC|LTR|ERVL-MaLR	20888	NM_026942	69106	Mm.216502	NM_026942	ENSMUSG00000032333	Stoml1	1810015E19Rik|AI847431|SLP1|STORP|UNC24|WPB72	stomatin-like 1	protein-coding
mm_71640.1	chr8	57511894	57511930	+	1	NA	promoter-TSS (NM_008252)	promoter-TSS (NM_008252)	69	NM_008252	97165	Mm.276881	NM_008252	ENSMUSG00000054717	Hmgb2	C80539|HMG-2|Hmg2	high mobility group box 2	protein-coding
mm_71251.1	chr8	40915861	40915881	+	1	NA	intron (NM_007514, intron 11 of 11)	intron (NM_007514, intron 11 of 11)	-10362	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_59660.1	chr7	28267798	28267808	+	1	NA	promoter-TSS (NM_198425)	promoter-TSS (NM_198425)	-78	NM_198425	386655	Mm.258201	NM_198425	ENSMUSG00000046058	Eid2	Cri2|EID-2	EP300 interacting inhibitor of differentiation 2	protein-coding
mm_4497.1	chr1	173647827	173647846	+	1	NA	TTS (NM_175026)	TTS (NM_175026)	16977	NM_175026	236312	Mm.447	NM_175026	ENSMUSG00000043263	Ifi209	4930422C14|AI447904|Ifix|Pyhin-1|Pyhin1	interferon activated gene 209	protein-coding
mm_4731.1	chr1	181428136	181428141	+	1	NA	intron (NM_028408, intron 3 of 5)	intron (NM_028408, intron 3 of 5)	75510	NM_001160211	72978	Mm.338083	NM_028408	ENSMUSG00000026514	Cnih3	2900075G08Rik|CNIH-3	cornichon family AMPA receptor auxiliary protein 3	protein-coding
mm_70911.1	chr8	25716573	25716584	+	1	NA	3' UTR (NM_001081269, exon 23 of 23)	3' UTR (NM_001081269, exon 23 of 23)	-3470	NR_121642	71910	Mm.385055	NM_028000	ENSMUSG00000031570	Plpp5	1810019D05Rik|2310022A04Rik|AW045471|Ppapdc1|Ppapdc1b	phospholipid phosphatase 5	protein-coding
mm_46759.1	chr5	112251138	112251177	-	1	NA	intron (NM_001312884, intron 1 of 4)	intron (NM_001312884, intron 1 of 4)	1361	NM_001312884	12959	Mm.40324	NM_021351	ENSMUSG00000066975	Cryba4	-	crystallin, beta A4	protein-coding
mm_53398.1	chr6	129591714	129591723	+	1	NA	promoter-TSS (NM_010654)	promoter-TSS (NM_010654)	-93	NM_010654	16643	Mm.391515	NM_010654	ENSMUSG00000030165	Klrd1	CD94	killer cell lectin-like receptor, subfamily D, member 1	protein-coding
mm_41436.1	chr5	90904165	90904183	+	1	NA	exon (NM_009140, exon 2 of 4)	exon (NM_009140, exon 2 of 4)	275	NM_009140	20310	Mm.4979	NM_009140	ENSMUSG00000058427	Cxcl2	CINC-2a|GROb|Gro2|MIP-2|MIP-2a|Mgsa-b|Mip2|Scyb|Scyb2	chemokine (C-X-C motif) ligand 2	protein-coding
mm_6169.1	chr1	65071610	65071616	-	1	NA	TTS (NM_007775)	TTS (NM_007775)	1919	NM_007775	12966	Mm.491115	NM_007775	ENSMUSG00000025952	Crygc	Cryg-5	crystallin, gamma C	protein-coding
mm_42209.1	chr5	112576436	112576443	+	1	NA	intron (NM_001253917, intron 1 of 15)	intron (NM_001253917, intron 1 of 15)	759	NM_001253917	56747	Mm.143742	NM_019982	ENSMUSG00000058153	Sez6l	AI843918|AIG1|AW539724|Acig1|BSRP-B|mKIAA0927	seizure related 6 homolog like	protein-coding
mm_89414.1	chr10	90829836	90829848	+	1	NA	promoter-TSS (NM_001347053)	promoter-TSS (NM_001347053)	-1	NM_001347053	77531	Mm.440605	NM_181398	ENSMUSG00000058589	Anks1b	AIDA-1b|C030032C09Rik|E530015N03Rik|ENSMUSG00000078431|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding
mm_996.1	chr1	58713242	58713314	+	1	NA	promoter-TSS (NM_207653)	promoter-TSS (NM_207653)	-8	NM_009805	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_41681.1	chr5	100039991	100040069	+	1	NA	promoter-TSS (NM_016690)	promoter-TSS (NM_016690)	36	NR_027990	67870	Mm.11311	NM_026421	ENSMUSG00000029326	Enoph1	2310057D15Rik|BB183658|C81437	enolase-phosphatase 1	protein-coding
mm_85803.1	chr9	110132367	110132396	-	1	NA	intron (NM_009211, intron 1 of 27)	CpG	357	NM_009211	20588	Mm.85410	NM_009211	ENSMUSG00000032481	Smarcc1	AI115498|BAF155|Rsc8|SRG3|msp3	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 1	protein-coding
mm_1355.1	chr1	66321992	66322012	+	1	NA	5' UTR (NM_001310634, exon 1 of 15)	5' UTR (NM_001310634, exon 1 of 15)	278	NM_001310634	17756	Mm.256966	NM_008632	ENSMUSG00000015222	Map2	G1-397-34|MAP-2|Mtap-2|Mtap2|repro4	microtubule-associated protein 2	protein-coding
mm_167097.1	chr7	109457994	109457996	+	1	NA	intron (NM_001170913, intron 14 of 19)	intron (NM_001170913, intron 14 of 19)	-18942	NM_054103	117229	Mm.389950	NM_054103	ENSMUSG00000031027	Stk33	4921505G21Rik|AW061264	serine/threonine kinase 33	protein-coding
mm_48598.1	chr5	144050630	144050646	-	1	NA	promoter-TSS (NM_033039)	promoter-TSS (NM_033039)	-29	NM_033039	18261	Mm.270533	NM_033039	ENSMUSG00000029618	Ocm	-	oncomodulin	protein-coding
mm_171295.1	chr3	91126813	91126820	+	1	NA	Intergenic	L1Md_T|LINE|L1	-36011	NM_001101461	229550	Mm.98335	NM_001101461	ENSMUSG00000091175	9130204L05Rik	Gm127	RIKEN cDNA 9130204L05 gene	protein-coding
mm_127054.1	chr15	96710017	96710028	+	1	NA	Intergenic	CpG	-10324	NM_175121	67760	Mm.46754	NM_175121	ENSMUSG00000022462	Slc38a2	5033402L14Rik|AI316867|ATA2|SAT2|mKIAA1382	solute carrier family 38, member 2	protein-coding
mm_65899.1	chr7	30187479	30187516	-	1	NA	3' UTR (NM_009795, exon 11 of 11)	3' UTR (NM_009795, exon 11 of 11)	3326	NM_009944	12865	Mm.423030	NM_009944	ENSMUSG00000074218	Cox7a1	COX7A|COX7AH|COX7AM	cytochrome c oxidase subunit VIIa 1	protein-coding
mm_170693.1	chr2	132285082	132285092	+	1	NA	promoter-TSS (NM_001291039)	promoter-TSS (NM_001291039)	-852	NM_001291039	110911	Mm.284503	NM_138651	ENSMUSG00000058793	Cds2	5730450N06Rik|5730460C18Rik|AI854580|D2Wsu127e	CDP-diacylglycerol synthase (phosphatidate cytidylyltransferase) 2	protein-coding
mm_118640.1	chr14	21481429	21481439	+	1	NA	Intergenic	ORR1B2|LTR|ERVL-MaLR	-18336	NM_001205241	54169	Mm.248967	NM_017479	ENSMUSG00000021767	Kat6b	AI507552|B130044K16Rik|MYST-4|Morf|Myst4|mKIAA0383|qkf|querkopf	K(lysine) acetyltransferase 6B	protein-coding
mm_18761.1	chr2	73453889	73453900	-	1	NA	promoter-TSS (NM_001289722)	promoter-TSS (NM_001289722)	-5	NM_001289722	215280	Mm.223504	NM_153138	ENSMUSG00000075284	Wipf1	AI115543|D2Ertd120e|WIP|Waspip	WAS/WASL interacting protein family, member 1	protein-coding
mm_23518.1	chr3	60595631	60595657	+	1	NA	exon (NM_001253708, exon 3 of 9)	exon (NM_001253708, exon 3 of 9)	94465	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_86551.1	chr10	10234999	10235023	+	1	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	237303	NM_001127353	215772	Mm.246573	NM_172547	ENSMUSG00000050994	Adgb	9130014G24Rik	androglobin	protein-coding
mm_11575.1	chr2	32916532	32916538	+	1	NA	intron (NM_146119, intron 5 of 13)	B3|SINE|B2	40401	NM_146119	227737	Mm.301646	NM_146119	ENSMUSG00000026796	Fam129b	9130404D14Rik	family with sequence similarity 129, member B	protein-coding
mm_129286.1	chr15	77163071	77163086	-	1	NA	intron (NM_053104, intron 2 of 13)	intron (NM_053104, intron 2 of 13)	-9266	NM_001286418	93686	Mm.202774	NM_053104	ENSMUSG00000033565	Rbfox2	Fbm2|Fxh|Hrnbp2|Rbm9	RNA binding protein, fox-1 homolog (C. elegans) 2	protein-coding
mm_148827.1	chr19	6335094	6335113	+	1	NA	promoter-TSS (NM_001168489)	promoter-TSS (NM_001168489)	64	NM_008583	17283	Mm.12917	NM_008583	ENSMUSG00000024947	Men1	AW045611	multiple endocrine neoplasia 1	protein-coding
mm_24448.1	chr3	90612273	90612296	+	1	NA	promoter-TSS (NM_011313)	promoter-TSS (NM_011313)	-610	NM_011313	20200	Mm.100144	NM_011313	ENSMUSG00000001025	S100a6	2A9|5B10|CALCYCLIN|Cacy|PRA	S100 calcium binding protein A6 (calcyclin)	protein-coding
mm_132753.1	chr16	44161353	44161399	+	1	NA	3' UTR (NM_028108, exon 5 of 5)	3' UTR (NM_028108, exon 5 of 5)	-12021	NM_001029889	207806	Mm.310566	NM_001029889	ENSMUSG00000068284	Usf3	5530400K22Rik|Gm1779|Gm608|mKIAA2018	upstream transcription factor family member 3	protein-coding
mm_9345.1	chr1	172066551	172066566	-	1	NA	3' UTR (NM_021607, exon 17 of 17)	3' UTR (NM_021607, exon 17 of 17)	-8962	NM_010916	18071	Mm.2474	NM_010916	ENSMUSG00000051251	Nhlh1	Hen1|Nscl|Tal2|bHLHa35	nescient helix loop helix 1	protein-coding
mm_63873.1	chr7	136048066	136048070	+	1	NA	Intergenic	Intergenic	-220256	NR_102277	77383	Mm.227745	NR_102277	ENSMUSG00000110027	C030029H02Rik	-	RIKEN cDNA C030029H02 gene	ncRNA
mm_56765.1	chr6	116133897	116133908	-	1	NA	exon (NM_177412, exon 3 of 6)	exon (NM_177412, exon 3 of 6)	59472	NM_177412	330401	Mm.425352	NM_177412	ENSMUSG00000030126	Tmcc1	3632431M01Rik|mKIAA0779	transmembrane and coiled coil domains 1	protein-coding
mm_119507.1	chr14	47381623	47381635	+	1	NA	exon (NM_010705, exon 4 of 6)	exon (NM_010705, exon 4 of 6)	7769	NM_001145953	16854	Mm.248615	NM_010705	ENSMUSG00000050335	Lgals3	GBP|L-34|Mac-2|gal3	lectin, galactose binding, soluble 3	protein-coding
mm_43812.1	chr5	142904701	142904750	+	1	NA	exon (NM_007393, exon 4 of 6)	exon (NM_007393, exon 4 of 6)	2029	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_54240.1	chr6	28244222	28244262	-	1	NA	exon (NM_001081678, exon 5 of 6)	exon (NM_001081678, exon 5 of 6)	17359	NM_001081678	627049	Mm.84441	NM_001081678	ENSMUSG00000039841	Zfp800	AA407452|Znf800	zinc finger protein 800	protein-coding
mm_95218.1	chr11	44014054	44014064	+	1	NA	Intergenic	Intergenic	-112822	NM_001284381	11548	Mm.39086	NM_007416	ENSMUSG00000050541	Adra1b	[a]1b	adrenergic receptor, alpha 1b	protein-coding
mm_60805.1	chr7	45632344	45632358	+	1	NA	exon (NM_028544, exon 5 of 12)	exon (NM_028544, exon 5 of 12)	4814	NM_028544	69903	Mm.181396	NM_028544	ENSMUSG00000044562	Rasip1	1110025D03Rik|2610025P08Rik|AI853551|Rain	Ras interacting protein 1	protein-coding
mm_48371.1	chr5	139478935	139478948	-	1	NA	intron (NM_133349, intron 3 of 6)	intron (NM_133349, intron 3 of 6)	5550	NM_133349	100494	Mm.24521	NM_133349	ENSMUSG00000053581	Zfand2a	AA407930|AU016206|Airap	zinc finger, AN1-type domain 2A	protein-coding
mm_9934.1	chr1	189922406	189922416	-	1	NA	promoter-TSS (NM_026796)	promoter-TSS (NM_026796)	-123	NM_026796	226830	Mm.156895	NM_026796	ENSMUSG00000026603	Smyd2	1110020E07Rik|4930402C15|KMT3C|Zmynd14	SET and MYND domain containing 2	protein-coding
mm_150379.1	chr19	36115242	36115252	+	1	NA	exon (NM_013468, exon 7 of 9)	exon (NM_013468, exon 7 of 9)	4597	NM_013468	107765	Mm.10279	NM_013468	ENSMUSG00000024803	Ankrd1	Alrp|CARP|Crap|MARP1	ankyrin repeat domain 1 (cardiac muscle)	protein-coding
mm_149952.1	chr19	27906335	27906338	+	1	NA	intron (NM_011265, intron 1 of 16)	intron (NM_011265, intron 1 of 16)	76612	NM_001166414	19726	Mm.313321	NM_011265	ENSMUSG00000040929	Rfx3	C230093O12Rik|MRFX3	regulatory factor X, 3 (influences HLA class II expression)	protein-coding
mm_152847.1	chr19	24030918	24030995	-	1	NA	promoter-TSS (NM_001114174)	promoter-TSS (NM_001114174)	63	NM_001114174	381217	Mm.426078	NM_001114174	ENSMUSG00000071604	Fam189a2	AI414343|AI666772|Gm967	family with sequence similarity 189, member A2	protein-coding
mm_109948.1	chr12	11332033	11332055	-	1	NA	exon (NM_012038, exon 3 of 4)	exon (NM_012038, exon 3 of 4)	32157	NR_106136	102465775		NR_106136	ENSMUSG00000098879	Mir7675	Gm27965|mmu-mir-7675	microRNA 7675	ncRNA
mm_96281.1	chr11	62951192	62951195	+	1	NA	promoter-TSS (NM_025496)	promoter-TSS (NM_025496)	0	NM_025496	66338	Mm.46166	NM_025496	ENSMUSG00000042200	Cdrt4	1700019I23Rik	CMT1A duplicated region transcript 4	protein-coding
mm_17231.1	chr2	25574891	25574897	-	1	NA	promoter-TSS (NM_029293)	promoter-TSS (NM_029293)	-23	NM_029293	75454	Mm.458079	NM_029293	ENSMUSG00000036504	Phpt1	1700008C22Rik|PHP|Php14	phosphohistidine phosphatase 1	protein-coding
mm_58837.1	chr7	16830863	16830871	+	1	NA	intron (NM_133789, intron 7 of 17)	intron (NM_133789, intron 7 of 17)	-12035	NM_001252458	101540	Mm.1881	NM_178900	ENSMUSG00000041187	Prkd2	AI325941|PKD2	protein kinase D2	protein-coding
mm_74841.1	chr8	23648517	23648544	-	1	NA	Intergenic	Intergenic	-21131	NM_001277239	320158	Mm.121274	NM_177086	ENSMUSG00000037492	Zmat4	9630048M01Rik	zinc finger, matrin type 4	protein-coding
mm_59647.1	chr7	28162865	28162875	+	1	NA	exon (NM_001164655, exon 18 of 20)	exon (NM_001164655, exon 18 of 20)	-6878	NM_007991	14113	Mm.4595	NM_007991	ENSMUSG00000046865	Fbl	AL022665|FIB|FLRN|RNU3IP1	fibrillarin	protein-coding
mm_78356.1	chr9	25504431	25504451	+	1	NA	intron (NM_026189, intron 2 of 7)	intron (NM_026189, intron 2 of 7)	22844	NM_026189	67484	Mm.112977	NM_026189	ENSMUSG00000036611	Eepd1	2310005P05Rik|AI481005	endonuclease/exonuclease/phosphatase family domain containing 1	protein-coding
mm_106166.1	chr11	116654246	116654325	-	1	NA	promoter-TSS (NM_030206)	promoter-TSS (NM_030206)	28	NM_030206	114886	Mm.34598	NM_030206	ENSMUSG00000020810	Cygb	3110001K20Rik|HGb|Staap	cytoglobin	protein-coding
mm_48829.1	chr5	149127724	149127734	-	1	NA	non-coding (NR_015478, exon 2 of 3)	non-coding (NR_015478, exon 2 of 3)	-16534	NR_137278	105242579	Mm.445929	NR_137278	ENSMUSG00000107388	Gm42788	-	predicted gene 42788	ncRNA
mm_4752.1	chr1	182287926	182287969	+	1	NA	Intergenic	LTR33A_|LTR|ERVL	-5188	NM_007853	13244	Mm.29648	NM_007853	ENSMUSG00000038633	Degs1	AA536663|Degs|Des1|Mdes	delta(4)-desaturase, sphingolipid 1	protein-coding
mm_157133.1	chrX	9453628	9453671	-	1	NA	exon (NM_007807, exon 6 of 13)	exon (NM_007807, exon 6 of 13)	15675	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_3904.1	chr1	161864462	161864462	+	1	NA	intron (NM_172645, intron 1 of 23)	intron (NM_172645, intron 1 of 23)	12199	NM_172645	226551	Mm.170002	NM_172645	ENSMUSG00000040297	Suco	4732491B11|AI848100|AU016931|Opt	SUN domain containing ossification factor	protein-coding
mm_115211.1	chr13	109260482	109260518	+	1	NA	intron (NM_011056, intron 3 of 16)	intron (NM_011056, intron 3 of 16)	-64244	NR_030644	100124489		NR_030644	ENSMUSG00000076946	Mir582	Mirn582|mir-582|mmu-mir-582	microRNA 582	ncRNA
mm_107699.1	chr12	55410427	55410431	+	1	NA	intron (NM_011968, intron 4 of 6)	AT_rich|Low_complexity|Low_complexity	11604	NM_011968	26443	Mm.30210	NM_011968	ENSMUSG00000021024	Psma6	IOTA	proteasome (prosome, macropain) subunit, alpha type 6	protein-coding
mm_23691.1	chr3	68691925	68691935	+	1	NA	intron (NM_001159424, intron 2 of 7)	intron (NM_001159424, intron 2 of 7)	506	NM_008351	16159	Mm.103783	NM_008351	ENSMUSG00000027776	Il12a	IL-12p35|Il-12a|Ll12a|p35	interleukin 12a	protein-coding
mm_151194.1	chr19	53533825	53533839	+	1	NA	exon (NM_001085390, exon 2 of 4)	exon (NM_001085390, exon 2 of 4)	4514	NM_001085390	240672	Mm.482424	NM_001085390	ENSMUSG00000034765	Dusp5	Gm337	dual specificity phosphatase 5	protein-coding
mm_66057.1	chr7	30743766	30743776	-	1	NA	promoter-TSS (NM_001290631)	promoter-TSS (NM_001290631)	-90	NM_001290631	14447	Mm.436562	NM_008085	ENSMUSG00000061099	Gapdhs	Gapd-s|Gapds	glyceraldehyde-3-phosphate dehydrogenase, spermatogenic	protein-coding
mm_5633.1	chr1	40432079	40432101	-	1	NA	intron (NM_001294171, intron 1 of 7)	intron (NM_001294171, intron 1 of 7)	2520	NM_001294171	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_52124.1	chr6	97941228	97941229	+	1	NA	exon (NM_001178049, exon 2 of 10)	exon (NM_001178049, exon 2 of 10)	11411	NM_001178049	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_34521.1	chr4	148960355	148960365	+	1	NA	TTS (NM_019781)	TTS (NM_019781)	139452	NM_019781	56273	Mm.184172	NM_019781	ENSMUSG00000028975	Pex14	Pex14p|R75137	peroxisomal biogenesis factor 14	protein-coding
mm_2150.1	chr1	88165985	88165991	+	1	NA	promoter-TSS (NM_201643)	promoter-TSS (NM_201643)	-24	NM_201643	394433	Mm.300095	NM_201643	ENSMUSG00000089943	Ugt1a5	-	UDP glucuronosyltransferase 1 family, polypeptide A5	protein-coding
mm_62221.1	chr7	98489984	98490001	+	1	NA	Intergenic	CpG	-4230	NM_001113379	434215	Mm.323057	NM_001113379	ENSMUSG00000090958	Lrrc32	AI426318|D11S833Eh|D7H11S833E|EG434215|Garp	leucine rich repeat containing 32	protein-coding
mm_116028.1	chr13	25269899	25269907	-	1	NA	promoter-TSS (NM_009513)	promoter-TSS (NM_009513)	93	NM_009513	22360	Mm.4766	NM_009513	ENSMUSG00000048978	Nrsn1	Neurensin-1|Neuro-p24|Vmp	neurensin 1	protein-coding
mm_1561.1	chr1	74154012	74154035	+	1	NA	promoter-TSS (NM_009909)	promoter-TSS (NM_009909)	29	NM_009909	12765	Mm.234466	NM_009909	ENSMUSG00000026180	Cxcr2	CD128|CDw128|Cmkar2|Gpcr16|IL-8Rh|IL-8rb|IL8RA|Il8rb|mIL-8RH	chemokine (C-X-C motif) receptor 2	protein-coding
mm_34000.1	chr4	137920745	137920761	+	1	NA	intron (NM_199307, intron 3 of 19)	intron (NM_199307, intron 3 of 19)	58516	NM_199307	230857	Mm.401062	NM_199307	ENSMUSG00000057530	Ece1	AW322500|ECE-1|ECE-1a|ECE-1b|ECE-1d	endothelin converting enzyme 1	protein-coding
mm_31255.1	chr4	45012796	45012844	+	1	NA	promoter-TSS (NM_001163284)	promoter-TSS (NM_001163284)	-408	NM_173399	230119	Mm.44222	NM_173399	ENSMUSG00000049657	Zbtb5	5930421I10|9430083K24Rik|AI646847|mKIAA0354	zinc finger and BTB domain containing 5	protein-coding
mm_63759.1	chr7	131111081	131111097	+	1	NA	exon (NM_007769, exon 43 of 47)	exon (NM_007769, exon 43 of 47)	35194	NM_173409	233918	Mm.78341	NM_173409	ENSMUSG00000013668	4933402N03Rik	4930412O05	RIKEN cDNA 4933402N03 gene	protein-coding
mm_52925.1	chr6	122922553	122922577	+	1	NA	intron (NM_199311, intron 1 of 5)	intron (NM_199311, intron 1 of 5)	717	NM_199311	269799	Mm.297275	NM_199311	ENSMUSG00000049037	Clec4a1	BC049354|Dcir4	C-type lectin domain family 4, member a1	protein-coding
mm_145708.1	chr18	62922318	62922339	+	1	NA	promoter-TSS (NM_133237)	promoter-TSS (NM_133237)	1	NM_133237	494504	Mm.391102	NM_133237	ENSMUSG00000071847	Apcdd1	AB023957|AU041258|Drapc1|EIG180	adenomatosis polyposis coli down-regulated 1	protein-coding
mm_20370.1	chr2	128429142	128429146	-	1	NA	non-coding (NR_028591, exon 1 of 2)	non-coding (NR_028591, exon 1 of 2)	207	NR_028591	100043424	Mm.297222	NR_028589		Gm14005	OTTMUSG00000015351	predicted gene 14005	ncRNA
mm_24437.1	chr3	90588537	90588550	+	1	NA	Intergenic	Intergenic	-1704	NM_001195760	628324	Mm.33816	NM_001195760	ENSMUSG00000094018	S100a2	CaN19|EG628324|S100L	S100 calcium binding protein A2	protein-coding
mm_1765.1	chr1	75549582	75549626	+	1	NA	intron (NM_009208, intron 6 of 22)	intron (NM_009208, intron 6 of 22)	3338	NM_009208	20536	Mm.5053	NM_009208	ENSMUSG00000006576	Slc4a3	A930038D23Rik|Ae3	solute carrier family 4 (anion exchanger), member 3	protein-coding
mm_33338.1	chr4	129231821	129231853	+	1	NA	intron (NM_001285867, intron 1 of 6)	intron (NM_001285867, intron 1 of 6)	-3926	NM_001285866	97130	Mm.331907	NM_001033189	ENSMUSG00000050390	C77080	Kiaa1522|mKIAA1522	expressed sequence C77080	protein-coding
mm_138066.1	chr17	33935200	33935213	+	1	NA	exon (NM_009059, exon 13 of 18)	exon (NM_009059, exon 13 of 18)	5124	NM_001185182	14976	Mm.2948	NM_010385	ENSMUSG00000024309	Pfdn6	H-2Ke2|H2-Ke2|Ke-2	prefoldin subunit 6	protein-coding
mm_13861.1	chr2	119733448	119733449	+	1	NA	3' UTR (NM_030112, exon 18 of 18)	3' UTR (NM_030112, exon 18 of 18)	-8889	NM_146125	228550	Mm.65337	NM_146125	ENSMUSG00000027296	Itpka	-	inositol 1,4,5-trisphosphate 3-kinase A	protein-coding
mm_135279.1	chr16	38445941	38445969	-	1	NA	exon (NM_007414, exon 4 of 4)	exon (NM_007414, exon 4 of 4)	6734	NM_007414	11544	Mm.20047	NM_007414	ENSMUSG00000002844	Adprh	Arh1	ADP-ribosylarginine hydrolase	protein-coding
mm_31494.1	chr4	53128819	53128835	+	1	NA	exon (NM_013454, exon 4 of 50)	exon (NM_013454, exon 4 of 50)	31068	NM_013454	11303	Mm.277376	NM_013454	ENSMUSG00000015243	Abca1	ABC-1|Abc1	ATP-binding cassette, sub-family A (ABC1), member 1	protein-coding
mm_100530.1	chr11	120598681	120598693	+	1	NA	promoter-TSS (NM_011568)	promoter-TSS (NM_011568)	155	NM_001038230	66156	Mm.21645	NM_025389	ENSMUSG00000025135	Anapc11	1110011I19Rik|R75218	anaphase promoting complex subunit 11	protein-coding
mm_33853.1	chr4	135868626	135868638	+	1	NA	3' UTR (NM_001284196, exon 6 of 6)	3' UTR (NM_001284196, exon 6 of 6)	5214	NM_026383	52830	Mm.29159	NM_026383	ENSMUSG00000028675	Pnrc2	0610011E17Rik|D4Bwg0593e	proline-rich nuclear receptor coactivator 2	protein-coding
mm_29648.1	chr3	122239793	122239803	-	1	NA	Intergenic	Lx5|LINE|L1	-5759	NM_008129	14630	Mm.292676	NM_008129	ENSMUSG00000028124	Gclm	AI649393|Gcmc|Glclr	glutamate-cysteine ligase, modifier subunit	protein-coding
mm_91122.1	chr10	19583096	19583109	-	1	NA	Intergenic	Intergenic	-8847	NM_010511	15979	Mm.549	NM_010511	ENSMUSG00000020009	Ifngr1	CD119|IFN-gammaR|Ifgr|Ifngr|Nktar	interferon gamma receptor 1	protein-coding
mm_22891.1	chr3	30746211	30746235	+	1	NA	promoter-TSS (NM_029489)	promoter-TSS (NM_029489)	-70	NM_029489	75953	Mm.308084	NM_029489	ENSMUSG00000051860	Samd7	4930597A01Rik	sterile alpha motif domain containing 7	protein-coding
mm_86479.1	chr10	4710194	4710204	+	1	NA	promoter-TSS (NM_001302533)	promoter-TSS (NM_001302533)	41	NM_001302533	13982	Mm.9213	NM_007956	ENSMUSG00000019768	Esr1	ER|ER-alpha|ERa|ERalpha|ESR|Estr|Estra|Nr3a1	estrogen receptor 1 (alpha)	protein-coding
mm_141906.1	chr17	34959114	34959150	-	1	NA	5' UTR (NM_010478, exon 1 of 1)	5' UTR (NM_010478, exon 1 of 1)	106	NM_010478	15511	Mm.372314	NM_010478	ENSMUSG00000090877	Hspa1b	Hsp70|Hsp70-1|Hsp70.1|hsp68	heat shock protein 1B	protein-coding
mm_38402.1	chr4	138969016	138969026	-	1	NA	TTS (NM_025786)	TTS (NM_025786)	1909	NM_025786	66825	Mm.252312	NM_025786	ENSMUSG00000070661	Rnf186	9130020G10Rik	ring finger protein 186	protein-coding
mm_121566.1	chr14	122557718	122557740	+	1	NA	exon (NM_144844, exon 2 of 24)	exon (NM_144844, exon 2 of 24)	23401	NM_144844	110821	Mm.23876	NM_144844	ENSMUSG00000041650	Pcca	C79630	propionyl-Coenzyme A carboxylase, alpha polypeptide	protein-coding
mm_61751.1	chr7	82771017	82771056	+	1	NA	intron (NM_175317, intron 18 of 19)	(TCTCTG)n|Simple_repeat|Simple_repeat	-15392	NR_046004	77800	Mm.444811	NR_046004	ENSMUSG00000086690	4933406J10Rik	A930009F24Rik	RIKEN cDNA 4933406J10 gene	ncRNA
mm_161470.1	chr15	79125027	79125027	+	1	NA	intron (NM_177461, intron 7 of 15)	intron (NM_177461, intron 7 of 15)	16044	NM_177461	27008	Mm.196480	NM_177461	ENSMUSG00000033039	Micall1	AI448246|D15Mit260|D15N2e|EST573322|EST820961|MIRab13|mKIAA1668	microtubule associated monooxygenase, calponin and LIM domain containing -like 1	protein-coding
mm_100551.1	chr11	120721544	120721564	+	1	NA	promoter-TSS (NM_133223)	promoter-TSS (NM_133223)	86	NM_133223	170758	Mm.34008	NM_133223	ENSMUSG00000018012	Rac3	Rac1B	RAS-related C3 botulinum substrate 3	protein-coding
mm_66423.1	chr7	44548751	44548833	-	1	NA	promoter-TSS (NM_011131)	promoter-TSS (NM_011131)	23	NM_011131	18971	Mm.16549	NM_011131	ENSMUSG00000038644	Pold1	125kDa	polymerase (DNA directed), delta 1, catalytic subunit	protein-coding
mm_30131.1	chr3	142108451	142108465	-	1	NA	intron (NM_001277216, intron 1 of 11)	intron (NM_001277216, intron 1 of 11)	60770	NM_001277217	12167	Mm.39089	NM_007560	ENSMUSG00000052430	Bmpr1b	AI385617|ALK-6|AV355320|Acvrlk6|Alk6|BMPR-1B|BMPR-IB|CFK-43a|SKR6	bone morphogenetic protein receptor, type 1B	protein-coding
mm_163535.1	chr13	10947420	10947420	-	1	NA	Intergenic	Intergenic	-574632	NR_027813	664793	Mm.410565	NR_027813		Zp4-ps	EG664793|Zp4|Zpb	zona pellucida glycoprotein 4, pseudogene	pseudo
mm_85706.1	chr9	108135397	108135409	-	1	NA	intron (NR_126078, intron 1 of 2)	RSINE1|SINE|B4	-1452	NR_126077	76873	Mm.436935	NR_126077	ENSMUSG00000102224	4930447F24Rik	-	RIKEN cDNA 4930447F24 gene	ncRNA
mm_167942.1	chrX	118799097	118799097	+	1	NA	Intergenic	BGLII_B2|LTR|ERVK	-318360	NM_001142750	100039551	Mm.272850	NM_001142750	ENSMUSG00000100194	Tgif2lx2	-	TGFB-induced factor homeobox 2-like, X-linked 2	protein-coding
mm_16540.1	chr2	181650462	181650466	+	1	NA	intron (NM_133701, intron 17 of 20)	intron (NM_133701, intron 17 of 20)	21176	NM_009236	20672	Mm.264904	NM_009236	ENSMUSG00000046470	Sox18	AI385749|Ra|Ragl	SRY (sex determining region Y)-box 18	protein-coding
mm_88497.1	chr10	77837585	77837593	+	1	NA	TTS (NM_001024709)	TTS (NM_001024709)	1642	NM_001024709	544710	Mm.441890	NM_001024709		Krtap10-10	EG544710	keratin associated protein 10-10	protein-coding
mm_134959.1	chr16	31314538	31314548	-	1	NA	intron (NM_007470, intron 1 of 5)	intron (NM_007470, intron 1 of 5)	265	NM_001301353	11815	Mm.2082	NM_007470	ENSMUSG00000022548	Apod	-	apolipoprotein D	protein-coding
mm_91683.1	chr10	43901671	43901702	-	1	NA	promoter-TSS (NM_130892)	promoter-TSS (NM_130892)	50	NM_001081054	76563	Mm.5904	NM_001081054	ENSMUSG00000019863	Qrsl1	2700038P16Rik|C80053|GatA	glutaminyl-tRNA synthase (glutamine-hydrolyzing)-like 1	protein-coding
mm_5263.1	chr1	17015453	17015456	-	1	NA	intron (NM_020604, intron 3 of 4)	Lx9|LINE|L1	82435	NM_020604	57339	Mm.143761	NM_020604	ENSMUSG00000042686	Jph1	ENSMUSG00000054314|JP-1|Jp1	junctophilin 1	protein-coding
mm_116896.1	chr13	55375790	55375793	-	1	NA	intron (NM_016758, intron 1 of 14)	intron (NM_016758, intron 1 of 14)	6059	NM_016758	51791	Mm.1426	NM_016758	ENSMUSG00000052087	Rgs14	RPIP1	regulator of G-protein signaling 14	protein-coding
mm_137962.1	chr17	33432217	33432236	+	1	NA	promoter-TSS (NM_183282)	promoter-TSS (NM_183282)	-673	NM_183282	69481	Mm.154333	NM_183282	ENSMUSG00000092519	Actl9	1700029I08Rik|AV259599	actin-like 9	protein-coding
mm_161314.1	chr14	43608065	43608065	-	1	NA	promoter-TSS (NM_001098269)	promoter-TSS (NM_001098269)	-52	NM_001098269	100042342	Mm.429750	NM_001098269	ENSMUSG00000095528	Gm10375	ENSMUSG00000072602	predicted gene 10375	protein-coding
mm_105807.1	chr11	110251737	110251754	-	1	NA	promoter-TSS (NM_147218)	promoter-TSS (NM_147218)	31	NM_147218	76184	Mm.159704	NM_147218	ENSMUSG00000044749	Abca6	6330565N06Rik	ATP-binding cassette, sub-family A (ABC1), member 6	protein-coding
mm_95548.1	chr11	52307775	52307792	+	1	NA	Intergenic	Intergenic	-24769	NM_001313981	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_58025.1	chr6	136661872	136661894	-	1	NA	promoter-TSS (NM_025806)	promoter-TSS (NM_025806)	10	NM_025806	66857	Mm.3311	NM_025806	ENSMUSG00000030214	Plbd1	1100001H23Rik	phospholipase B domain containing 1	protein-coding
mm_33939.1	chr4	136945641	136945666	+	1	NA	exon (NM_007939, exon 3 of 17)	exon (NM_007939, exon 3 of 17)	11163	NM_007939	13842	Mm.1390	NM_007939	ENSMUSG00000028661	Epha8	AW047546|Eek|Hek3|mKIAA1459	Eph receptor A8	protein-coding
mm_122496.1	chr14	46673813	46673818	-	1	NA	promoter-TSS (NR_131909)	promoter-TSS (NR_131909)	-40	NR_131909	328385	Mm.271545	NR_131909		D330046F09Rik	Gm808	RIKEN cDNA D330046F09 gene	ncRNA
mm_127124.1	chr15	98108483	98108499	+	1	NA	promoter-TSS (NM_001163487)	promoter-TSS (NM_001163487)	20	NM_001163487	18642	Mm.272582	NM_021514	ENSMUSG00000033065	Pfkm	AI131669|ATP-PFK|PFK-A|PFK-M|Pfk-4|Pfk4|Pfka|Pfkx	phosphofructokinase, muscle	protein-coding
mm_60647.1	chr7	44852777	44852823	+	1	NA	exon (NM_001290694, exon 2 of 5)	exon (NM_001290694, exon 2 of 5)	2793	NM_001253920	67605	Mm.148007	NM_026270	ENSMUSG00000011096	Akt1s1	1110012J22Rik|AI227026|Lobe|Lobel|PRAS40	AKT1 substrate 1 (proline-rich)	protein-coding
mm_26386.1	chr3	142570484	142570499	+	1	NA	intron (NM_001289493, intron 8 of 10)	intron (NM_001289493, intron 8 of 10)	9995	NM_001289493	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_136212.1	chr16	89888708	89888724	-	1	NA	intron (NM_009384, intron 4 of 27)	intron (NM_009384, intron 4 of 27)	-70364	NM_001145887	21844	Mm.310902	NM_009384	ENSMUSG00000002489	Tiam1	AI847750|D16Ium10|D16Ium10e	T cell lymphoma invasion and metastasis 1	protein-coding
mm_74204.1	chr8	123892870	123892884	+	1	NA	exon (NM_009606, exon 4 of 7)	exon (NM_009606, exon 4 of 7)	1898	NM_001272041	11459	Mm.214950	NM_009606	ENSMUSG00000031972	Acta1	AA959943|Acta-2|Acts|Actsk-1	actin, alpha 1, skeletal muscle	protein-coding
mm_108869.1	chr12	99562816	99562819	+	1	NA	Intergenic	Intergenic	-1024	NR_136760	102639404	Mm.396324	NR_136760	ENSMUSG00000097917	Gm26839	-	predicted gene, 26839	ncRNA
mm_103567.1	chr11	77884546	77884564	-	1	NA	intron (NM_008952, intron 2 of 7)	B3A|SINE|B2	9317	NM_008952	19193	Mm.8543	NM_008952	ENSMUSG00000017453	Pipox	LPIPOX|Pso	pipecolic acid oxidase	protein-coding
mm_44569.1	chr5	24730636	24730655	-	1	NA	promoter-TSS (NM_001081441)	promoter-TSS (NM_001081441)	35	NM_001081441	269633	Mm.392539	NM_026621	ENSMUSG00000055235	Wdr86	2810046M22Rik|BC059069	WD repeat domain 86	protein-coding
mm_143916.1	chr17	85615137	85615152	-	1	NA	intron (NR_038084, intron 2 of 3)	CpG	3252	NR_038084	100043902	Mm.150838	NR_015385	ENSMUSG00000093460	Six3os1	D17Mgi26|E130112H22Rik|Rncr1|Six3os	SIX homeobox 3, opposite strand 1	ncRNA
mm_172315.1	chr7	105954004	105954004	-	1	NA	promoter-TSS (NM_001243039)	promoter-TSS (NM_001243039)	-34	NM_029000	74558	Mm.458429	NM_029000	ENSMUSG00000045868	Gvin1	9130002C22Rik|9830104F22Rik|Iigs1|VLIG|VLIG-1	GTPase, very large interferon inducible 1	protein-coding
mm_76624.1	chr8	91801423	91801467	-	1	NA	5' UTR (NM_001253822, exon 1 of 4)	5' UTR (NM_001253822, exon 1 of 4)	209	NM_001253822	16373	Mm.238044	NM_008393	ENSMUSG00000031734	Irx3	AI894186	Iroquois related homeobox 3	protein-coding
mm_40668.1	chr5	65391594	65391594	+	1	NA	promoter-TSS (NM_024471)	promoter-TSS (NM_024471)	97	NM_001310612	79464	Mm.195776	NM_024471	ENSMUSG00000029199	Lias	2900022L22Rik|4933425M12Rik|7a5ex|C77512|LS|lip-syn	lipoic acid synthetase	protein-coding
mm_150147.1	chr19	31910761	31910772	+	1	NA	intron (NM_001081074, intron 3 of 11)	intron (NM_001081074, intron 3 of 11)	42005	NM_001081074	69865	Mm.87538	NM_001081074	ENSMUSG00000052595	A1cf	1810073H04Rik|ACF64|ACF65|ASP|Acf|MCM|MerCreMer|Tg(Myh6-cre/Esr1*)1Jmk|mer	APOBEC1 complementation factor	protein-coding
mm_117309.1	chr13	67484226	67484269	-	1	NA	promoter-TSS (NM_001076791)	promoter-TSS (NM_001076791)	6	NM_001076791	408067	Mm.315879	NM_001076791	ENSMUSG00000059839	Zfp874b	9630025I21Rik|Rslcan16	zinc finger protein 874b	protein-coding
mm_57816.1	chr6	129462655	129462674	-	1	NA	non-coding (NR_132130, exon 6 of 6)	non-coding (NR_132130, exon 6 of 6)	10115	NM_001309637	56644	Mm.239516	NM_020008	ENSMUSG00000079293	Clec7a	BGR|Clecsf12|beta-GR	C-type lectin domain family 7, member a	protein-coding
mm_38360.1	chr4	137993285	137993304	-	1	NA	promoter-TSS (NM_001256198)	promoter-TSS (NM_001256198)	-162	NM_001256198	230861	Mm.268903	NM_172703	ENSMUSG00000028760	Eif4g3	1500002J22Rik|4930523M17Rik|G1-419-52|eIF4GII|repro8	eukaryotic translation initiation factor 4 gamma, 3	protein-coding
mm_146269.1	chr18	77875400	77875408	+	1	NA	intron (NM_013831, intron 11 of 14)	ORR1F|LTR|ERVL-MaLR	-63063	NM_001195633	100502841	Mm.297782	NM_001195633	ENSMUSG00000039840	Epg5	4732475F16|5430411K18Rik|AI661957|AW456499|mKIAA1632	ectopic P-granules autophagy protein 5 homolog (C. elegans)	protein-coding
mm_99418.1	chr11	102309290	102309309	+	1	NA	intron (NM_001302955, intron 12 of 19)	CpG	7988	NM_001044383	21429	Mm.2845	NM_011551	ENSMUSG00000020923	Ubtf	A930005G04Rik|NOR-90|Tcfubf|UBF|UBF-1|UBF1	upstream binding transcription factor, RNA polymerase I	protein-coding
mm_81066.1	chr9	106178924	106178926	+	1	NA	promoter-TSS (NR_029526)	promoter-TSS (NR_029526)	85	NR_029526	387249		NR_029526	ENSMUSG00000065440	Mirlet7g	Mirnlet7g|let-7g|mmu-let-7g	microRNA let7g	ncRNA
mm_46498.1	chr5	105133408	105133419	-	1	NA	intron (NM_008620, intron 3 of 10)	intron (NM_008620, intron 3 of 10)	6139	NM_008620	17472	Mm.440525	NM_008620	ENSMUSG00000079363	Gbp4	AW228052|Mag-2|Mpa-2|Mpa2	guanylate binding protein 4	protein-coding
mm_98452.1	chr11	94945560	94945579	+	1	NA	exon (NM_007742, exon 31 of 51)	exon (NM_007742, exon 31 of 51)	9345	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_11244.1	chr2	29890067	29890081	+	1	NA	promoter-TSS (NM_013615)	promoter-TSS (NM_013615)	11	NM_013615	18286	Mm.330116	NM_013615	ENSMUSG00000026790	Odf2	AI848335|MMTEST29	outer dense fiber of sperm tails 2	protein-coding
mm_58394.1	chr7	3207089	3207097	+	1	NA	Intergenic	Intergenic	-11533	NR_029640	100049710		NR_029640	ENSMUSG00000077815	Mir290a	Mir290|Mirn290|mir-290a|mmu-miR-290|mmu-mir-290a	microRNA 290a	ncRNA
mm_164658.1	chr17	37410544	37410544	+	1	NA	Intergenic	RLTR53_Mm|LTR|ERVK	5067	NM_146511	258504	Mm.377541	NM_146511	ENSMUSG00000063188	Olfr107	MOR156-3	olfactory receptor 107	protein-coding
mm_122671.1	chr14	51923157	51923161	-	1	NA	promoter-TSS (NM_001011687)	promoter-TSS (NM_001011687)	-386	NM_001011687	497071	Mm.378602	NM_001011687	ENSMUSG00000068392	Rnase13	-	ribonuclease, RNase A family, 13 (non-active)	protein-coding
mm_166421.1	chr5	137151728	137151757	+	1	NA	Intergenic	Intergenic	-35535	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_84878.1	chr9	79718757	79718763	-	1	NA	promoter-TSS (NM_001290308)	promoter-TSS (NM_001290308)	-38	NM_001290308	12816	Mm.3819	NM_007730	ENSMUSG00000032332	Col12a1	-	collagen, type XII, alpha 1	protein-coding
mm_88081.1	chr10	68042243	68042246	+	1	NA	3' UTR (NM_001081346, exon 13 of 13)	3' UTR (NM_001081346, exon 13 of 13)	62646	NM_001081346	170799	Mm.209844	NM_133244	ENSMUSG00000037846	Rtkn2	B130039D23Rik|Mbf|Plekhk1	rhotekin 2	protein-coding
mm_94022.1	chr10	127666895	127666937	-	1	NA	promoter-TSS (NM_008668)	promoter-TSS (NM_008668)	-207	NR_045171	72243	Mm.482902	NR_045171	ENSMUSG00000040195	1700012D01Rik	-	RIKEN cDNA 1700012D01 gene	ncRNA
mm_804.1	chr1	45348785	45348829	+	1	NA	3' UTR (NM_009930, exon 51 of 51)	3' UTR (NM_009930, exon 51 of 51)	37269	NM_009930	12825	Mm.249555	NM_009930	ENSMUSG00000026043	Col3a1	AW550625|Col3a-1|Tsk-2|Tsk2	collagen, type III, alpha 1	protein-coding
mm_167028.1	chr7	68282697	68282705	-	1	NA	intron (NM_001013811, intron 1 of 8)	intron (NM_001013811, intron 1 of 8)	-6107	NR_040340	100504026	Mm.426764	NR_040340	ENSMUSG00000086628	Gm16157	OTTMUSG00000031023	predicted gene 16157	ncRNA
mm_162313.1	chr1	37997988	37997994	+	1	NA	promoter-TSS (NM_172054)	promoter-TSS (NM_172054)	-19	NM_198303	226982	Mm.260943	NM_198303	ENSMUSG00000026083	Eif5b	A030003E17Rik|BC018347|IF2	eukaryotic translation initiation factor 5B	protein-coding
mm_73529.1	chr8	108612214	108612231	+	1	NA	Intergenic	Intergenic	-27545	NR_077224	109215	Mm.65282	NR_077224	ENSMUSG00000110613	Lncbate1	3010033K07Rik|Lnc-BATE1	brown adipose tissue enriched long non-coding RNA 1	ncRNA
mm_40516.1	chr5	57821914	57821918	+	1	NA	intron (NM_001310608, intron 1 of 3)	intron (NM_001310608, intron 1 of 3)	103835	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_141481.1	chr17	31198959	31198976	-	1	NA	promoter-TSS (NM_001163776)	promoter-TSS (NM_001163776)	7	NM_001163776	140765	Mm.214638	NM_080727	ENSMUSG00000024034	Tmprss3	-	transmembrane protease, serine 3	protein-coding
mm_123924.1	chr14	73365669	73365679	-	1	NA	intron (NM_008410, intron 4 of 5)	intron (NM_008410, intron 4 of 5)	19597	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_105988.1	chr11	115627744	115627759	-	1	NA	5' UTR (NM_001252384, exon 2 of 8)	5' UTR (NM_001252384, exon 2 of 8)	544	NM_001252394	67283	Mm.383426	NM_026071	ENSMUSG00000020744	Slc25a19	2900089E13Rik|DNC|MUP1|TPC	solute carrier family 25 (mitochondrial thiamine pyrophosphate carrier), member 19	protein-coding
mm_53968.1	chr6	6056248	6056251	-	1	NA	intron (NM_015829, intron 14 of 17)	intron (NM_015829, intron 14 of 17)	-78856	NR_040255	72249	Mm.443268	NR_040255	ENSMUSG00000085416	1700019G24Rik	-	RIKEN cDNA 1700019G24 gene	ncRNA
mm_51156.1	chr6	70722492	70722545	+	1	NA	Intergenic	Intergenic	69657	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_159441.1	chr3	126363872	126363872	+	1	NA	promoter-TSS (NM_173451)	promoter-TSS (NM_173451)	20	NM_173451	271970	Mm.317021	NM_173451	ENSMUSG00000046561	Arsj	9330196J05Rik|D830047F08	arylsulfatase J	protein-coding
mm_24678.1	chr3	94837683	94837693	+	1	NA	5' UTR (NM_172683, exon 1 of 19)	5' UTR (NM_172683, exon 1 of 19)	121	NM_172683	229584	Mm.274787	NM_172683	ENSMUSG00000038902	Pogz	9530006B08Rik	pogo transposable element with ZNF domain	protein-coding
mm_142402.1	chr17	45433712	45433745	-	1	NA	promoter-TSS (NM_152810)	promoter-TSS (NM_152810)	-21	NM_152810	71702	Mm.28270	NM_152810	ENSMUSG00000023932	Cdc5l	1200002I02Rik|AA408004|PCDC5RP	cell division cycle 5-like (S. pombe)	protein-coding
mm_98664.1	chr11	96282232	96282242	+	1	NA	5' UTR (NM_010461, exon 1 of 2)	5' UTR (NM_010461, exon 1 of 2)	332	NM_010461	15416	Mm.4822	NM_010461	ENSMUSG00000056648	Hoxb8	Hox-2.4	homeobox B8	protein-coding
mm_136783.1	chr17	10496415	10496428	+	1	NA	intron (NM_027032, intron 4 of 4)	intron (NM_027032, intron 4 of 4)	40205	NR_077238	319750	Mm.383485	NR_077237	ENSMUSG00000089633	A230009B12Rik	-	RIKEN cDNA A230009B12 gene	ncRNA
mm_159553.1	chr4	103115549	103115549	+	1	NA	promoter-TSS (NM_001286223)	promoter-TSS (NM_001286223)	-11	NM_001286221	71148	Mm.288721	NM_027696	ENSMUSG00000028522	Mier1	4933425I22Rik|5830411K19Rik|er1	MEIR1 treanscription regulator	protein-coding
mm_19060.1	chr2	77316884	77316901	-	1	NA	Intergenic	Intergenic	-36300	NM_175465	228071	Mm.27120	NM_175465	ENSMUSG00000042272	Sestd1	1500031J16Rik|A930010O20|Solo/Trio8	SEC14 and spectrin domains 1	protein-coding
mm_78574.1	chr9	36693248	36693256	+	1	NA	promoter-TSS (NM_007391)	promoter-TSS (NM_007391)	32	NM_007391	11451	Mm.4776	NM_007391	ENSMUSG00000032110	Acrv1	Msa63|SP-10	acrosomal vesicle protein 1	protein-coding
mm_104556.1	chr11	96823988	96824024	-	1	NA	promoter-TSS (NM_001130453)	promoter-TSS (NM_001130453)	7	NM_001130453	18023	Mm.6743	NM_008686	ENSMUSG00000038615	Nfe2l1	AA408798|AW212678|LCR-F1|Lcrf1|NRF1|TCF-11|TCF11	nuclear factor, erythroid derived 2,-like 1	protein-coding
mm_61534.1	chr7	79053289	79053301	+	1	NA	promoter-TSS (NM_007424)	promoter-TSS (NM_007424)	28	NR_132432	102633600	Mm.382916	NR_132432	ENSMUSG00000097441	Gm26633	-	predicted gene, 26633	ncRNA
mm_86979.1	chr10	25436920	25436930	+	1	NA	intron (NM_013511, intron 1 of 19)	intron (NM_013511, intron 1 of 19)	28557	NM_013511	13822	Mm.306026	NM_013511	ENSMUSG00000019978	Epb41l2	4.1G|AW555191|D10Ertd398e|Epb4.1l2|NBL2	erythrocyte membrane protein band 4.1 like 2	protein-coding
mm_116577.1	chr13	47105609	47105622	-	1	NA	exon (NM_025900, exon 2 of 11)	exon (NM_025900, exon 2 of 11)	606	NM_025900	110052	Mm.131150	NM_025900	ENSMUSG00000021377	Dek	1810019E15Rik|D13H6S231E	DEK oncogene (DNA binding)	protein-coding
mm_153731.1	chr19	44408735	44408757	-	1	NA	Intergenic	B1_Mur2|SINE|Alu	-1037	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_103826.1	chr11	83012449	83012465	-	1	NA	intron (NM_181545, intron 4 of 5)	intron (NM_181545, intron 4 of 5)	8265	NM_001167743	276950	Mm.491599	NM_181545	ENSMUSG00000035208	Slfn8	-	schlafen 8	protein-coding
mm_99067.1	chr11	99168305	99168327	+	1	NA	Intergenic	Intergenic	-13239	NM_007719	12775	Mm.2932	NM_007719	ENSMUSG00000037944	Ccr7	CC-CKR-7|CCR-7|CD197|Cdw197|Cmkbr7|EBI1|Ebi1h	chemokine (C-C motif) receptor 7	protein-coding
mm_156398.1	chrX	139808518	139808576	+	1	NA	5' UTR (NM_016675, exon 2 of 2)	5' UTR (NM_016675, exon 2 of 2)	7739	NM_016675	12738	Mm.117068	NM_016675	ENSMUSG00000047230	Cldn2	AL022813	claudin 2	protein-coding
mm_73301.1	chr8	105131824	105131830	+	1	NA	promoter-TSS (NM_146213)	promoter-TSS (NM_146213)	27	NM_146213	234677	Mm.120297	NM_146213	ENSMUSG00000060560	Ces4a	Ces8	carboxylesterase 4A	protein-coding
mm_110576.1	chr12	56497551	56497560	-	1	NA	intron (NR_045082, intron 5 of 6)	intron (NR_045082, intron 5 of 6)	31865	NR_045082	104798	Mm.310950	NR_045082		E030019B13Rik	AI413669	RIKEN cDNA E030019B13 gene	ncRNA
mm_98104.1	chr11	86757918	86757928	+	1	NA	promoter-TSS (NM_001003908)	promoter-TSS (NM_001003908)	-431	NM_001003908	67300	Mm.254588	NM_001003908	ENSMUSG00000047126	Cltc	3110065L21Rik|CHC|R74732	clathrin, heavy polypeptide (Hc)	protein-coding
mm_162690.1	chr10	19589687	19589698	+	1	NA	Intergenic	ID_B1|SINE|B4	-2257	NM_010511	15979	Mm.549	NM_010511	ENSMUSG00000020009	Ifngr1	CD119|IFN-gammaR|Ifgr|Ifngr|Nktar	interferon gamma receptor 1	protein-coding
mm_49737.1	chr6	34745754	34745771	+	1	NA	exon (NM_145575, exon 3 of 12)	exon (NM_145575, exon 3 of 12)	-34670	NM_001289657	76223	Mm.150047	NM_178630	ENSMUSG00000038836	Agbl3	2900053G10Rik|4930431N21Rik|6530406M24Rik|CCP3	ATP/GTP binding protein-like 3	protein-coding
mm_164763.1	chr17	85621032	85621041	+	1	NA	5' UTR (NM_011381, exon 1 of 2)	5' UTR (NM_011381, exon 1 of 2)	202	NM_011381	20473	Mm.370208	NM_011381	ENSMUSG00000038805	Six3	E130112M24Rik|Six3a|Six3alpha|Six3b|Six3beta	sine oculis-related homeobox 3	protein-coding
mm_62765.1	chr7	112238503	112238513	+	1	NA	intron (NM_001193305, intron 2 of 25)	intron (NM_001193305, intron 2 of 25)	12672	NM_001193305	320878	Mm.52312	NM_177282	ENSMUSG00000038244	Mical2	5330438E18Rik|9530064J02|MICAL-2|mKIAA0750	microtubule associated monooxygenase, calponin and LIM domain containing 2	protein-coding
mm_90798.1	chr10	7212635	7212672	-	1	NA	promoter-TSS (NM_172546)	promoter-TSS (NM_172546)	-416	NM_172546	215748	Mm.37984	NM_172546	ENSMUSG00000015202	Cnksr3	6820402C05|BC024086|Magi1	Cnksr family member 3	protein-coding
mm_131058.1	chr16	4276400	4276410	+	1	NA	Intergenic	Intergenic	47176	NR_003628	436332	Mm.478141	NM_001013830	ENSMUSG00000089645	Gm5766	EG436332	ribosomal protein L7a pseudogene	pseudo
mm_139825.1	chr17	68187932	68187949	+	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	-85857	NM_177278	320858	Mm.137356	NM_177278	ENSMUSG00000041565	L3mbtl4	A730037L19Rik|D930040M24Rik	l(3)mbt-like 4 (Drosophila)	protein-coding
mm_22836.1	chr3	27482529	27482533	+	1	NA	intron (NM_173182, intron 11 of 25)	intron (NM_173182, intron 11 of 25)	102464	NR_037275	100526525		NR_037275	ENSMUSG00000092695	Mir3092	mir-3092|mmu-mir-3092	microRNA 3092	ncRNA
mm_10725.1	chr2	22860742	22860749	+	1	NA	intron (NM_019456, intron 10 of 13)	intron (NM_019456, intron 10 of 13)	-34777	NM_019501	56075	Mm.249752	NM_019501	ENSMUSG00000026784	Pdss1	2610203G20Rik|2700031G06Rik|TPT|TPT 1|Tprt|mDLP1|mSPS1	prenyl (solanesyl) diphosphate synthase, subunit 1	protein-coding
mm_76983.1	chr8	106928446	106928456	-	1	NA	Intergenic	Intergenic	-7299	NM_009229	20650	Mm.30228	NM_009229	ENSMUSG00000041308	Sntb2	Snt2	syntrophin, basic 2	protein-coding
mm_13658.1	chr2	114055219	114055227	+	1	NA	non-coding (NR_028422, exon 1 of 3)	non-coding (NR_028422, exon 1 of 3)	827	NR_028422	100303644	Mm.330469	NR_028422	ENSMUSG00000092397	C130080G10Rik	-	RIKEN cDNA C130080G10 gene	ncRNA
mm_21618.1	chr2	164276077	164276078	-	1	NA	3' UTR (NM_009300, exon 3 of 3)	3' UTR (NM_009300, exon 3 of 3)	2230	NM_009300	20941	Mm.1286	NM_009300	ENSMUSG00000016998	Svs4	SVS-IV|Svp-2|Svp-4|Svp2|Svp4	seminal vesicle secretory protein 4	protein-coding
mm_117722.1	chr13	95444887	95444898	-	1	NA	promoter-TSS (NM_198408)	promoter-TSS (NM_198408)	-61	NM_198408	12919	Mm.316614	NM_198408	ENSMUSG00000021680	Crhbp	CRH-BP	corticotropin releasing hormone binding protein	protein-coding
mm_97008.1	chr11	70929794	70929805	+	1	NA	intron (NM_001291143, intron 14 of 18)	B1_Mur2|SINE|Alu	40174	NM_172394	19069	Mm.288962	NM_172394	ENSMUSG00000040667	Nup88	Nup84|Prei2	nucleoporin 88	protein-coding
mm_9353.1	chr1	172082758	172082770	-	1	NA	promoter-TSS (NM_021607)	promoter-TSS (NM_021607)	-15	NM_021607	59287	Mm.218203	NM_021607	ENSMUSG00000003458	Ncstn	9430068N19Rik|AA727311|Aph2|D1Dau13e|Kiaa0253|Nct|mKIAA0253	nicastrin	protein-coding
mm_38099.1	chr4	134254077	134254128	-	1	NA	promoter-TSS (NM_001099296)	promoter-TSS (NM_001099296)	4	NM_001099296	72690	Mm.100168	NM_001099296	ENSMUSG00000050105	Grrp1	2810043G13Rik|Fam110d	glycine/arginine rich protein 1	protein-coding
mm_21535.1	chr2	163690681	163690695	-	1	NA	intron (NM_001039390, intron 2 of 4)	intron (NM_001039390, intron 2 of 4)	-3349	NM_011106	18769	Mm.10091	NM_011106	ENSMUSG00000035268	Pkig	PKIgamma	protein kinase inhibitor, gamma	protein-coding
mm_53220.1	chr6	126921921	126921958	+	1	NA	promoter-TSS (NM_207210)	promoter-TSS (NM_207210)	-100	NM_207210	101320	Mm.44896	NM_207210	ENSMUSG00000030345	Dyrk4	AW049118|Dyrk4a|Dyrk4b	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 4	protein-coding
mm_129891.1	chr15	83518946	83518949	-	1	NA	Intergenic	Intergenic	-7915	NM_007546	12124	Mm.267006	NM_007546	ENSMUSG00000016758	Bik	Biklk|Blk|Nbk	BCL2-interacting killer	protein-coding
mm_135417.1	chr16	45158593	45158612	-	1	NA	promoter-TSS (NM_028756)	promoter-TSS (NM_028756)	71	NM_028756	74102	Mm.264984	NM_028756	ENSMUSG00000022664	Slc35a5	1010001J06Rik|AU021179|BB097433|D16Ertd450e|D730043G07Rik	solute carrier family 35, member A5	protein-coding
mm_125382.1	chr15	40655260	40655266	+	1	NA	5' UTR (NM_011766, exon 1 of 8)	5' UTR (NM_011766, exon 1 of 8)	221	NM_011766	22762	Mm.39496	NM_011766	ENSMUSG00000022306	Zfpm2	B330005D23Rik|FOG-2|FOG2	zinc finger protein, multitype 2	protein-coding
mm_148485.1	chr19	4148685	4148697	+	1	NA	promoter-TSS (NM_011778)	promoter-TSS (NM_011778)	28	NM_011778	23789	Mm.276859	NM_011778	ENSMUSG00000024835	Coro1b	-	coronin, actin binding protein 1B	protein-coding
mm_105445.1	chr11	104441805	104441870	-	1	NA	5' UTR (NM_001081045, exon 1 of 14)	5' UTR (NM_001081045, exon 1 of 14)	454	NM_001081045	76719	Mm.136418	NM_001081045	ENSMUSG00000018412	Kansl1	1700081L11Rik|9430041J06Rik|mKIAA1267	KAT8 regulatory NSL complex subunit 1	protein-coding
mm_135694.1	chr16	52438330	52438330	-	1	NA	intron (NM_009655, intron 1 of 15)	intron (NM_009655, intron 1 of 15)	14751	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_81207.1	chr9	107576916	107576976	+	1	NA	promoter-TSS (NM_008317)	promoter-TSS (NM_008317)	19	NM_001331161	15586	Mm.475658	NM_008317	ENSMUSG00000010051	Hyal1	Hya1|Hyal-1	hyaluronoglucosaminidase 1	protein-coding
mm_140510.1	chr17	5493976	5493997	-	1	NA	intron (NM_146073, intron 1 of 8)	intron (NM_146073, intron 1 of 8)	1386	NM_146073	224454	Mm.487663	NM_146073	ENSMUSG00000034265	Zdhhc14	B530001K09Rik|New1cp	zinc finger, DHHC domain containing 14	protein-coding
mm_67289.1	chr7	78738004	78738029	-	1	NA	Intergenic	L1ME1|LINE|L1	-19796	NR_015542	414121	Mm.482537	NR_015542	ENSMUSG00000059146	E430016F16Rik	-	RIKEN cDNA E430016F16 gene	ncRNA
mm_20649.1	chr2	132053290	132053302	-	1	NA	3' UTR (NM_018824, exon 16 of 16)	3' UTR (NM_018824, exon 16 of 16)	-23308	NM_175445	215653	Mm.204737	NM_175445	ENSMUSG00000027339	Rassf2	3830431H01Rik|9030412M04Rik|AI852669|AW495050	Ras association (RalGDS/AF-6) domain family member 2	protein-coding
mm_46250.1	chr5	99249814	99249828	-	1	NA	intron (NM_145839, intron 1 of 13)	intron (NM_145839, intron 1 of 13)	3106	NM_181318	320292	Mm.259074	NM_145839	ENSMUSG00000089809	Rasgef1b	4732452O09Rik|GPIgamma4|Gpig4	RasGEF domain family, member 1B	protein-coding
mm_33468.1	chr4	130812592	130812601	+	1	NA	intron (NM_011520, intron 1 of 4)	intron (NM_011520, intron 1 of 4)	20059	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_86337.1	chr9	123113313	123113329	-	1	NA	promoter-TSS (NM_026917)	promoter-TSS (NM_026917)	90	NM_001081188	66446	Mm.41562	NM_001081188	ENSMUSG00000025785	Exosc7	2610002K22Rik|AV212732|mKIAA0116	exosome component 7	protein-coding
mm_173204.1	chrX	69606107	69606114	-	1	NA	intron (NM_008032, intron 3 of 19)	intron (NM_008032, intron 3 of 19)	245779	NM_008032	14266	Mm.466576	NM_008032	ENSMUSG00000031189	Aff2	FMR2P|Fmr2|Ox19|Oxh	AF4/FMR2 family, member 2	protein-coding
mm_23957.1	chr3	84925477	84925488	+	1	NA	intron (NM_001177773, intron 4 of 13)	intron (NM_001177773, intron 4 of 13)	-26729	NM_080428	50754	Mm.196475	NM_080428	ENSMUSG00000028086	Fbxw7	1110001A17Rik|AGO|Cdc4|Fbw7|Fbwd6|Fbx30|Fbxo30|Fbxw6|SEL-10	F-box and WD-40 domain protein 7	protein-coding
mm_100044.1	chr11	115154140	115154194	+	1	NA	promoter-TSS (NM_021411)	promoter-TSS (NM_021411)	-11	NM_021411	58222	Mm.143789	NM_021411	ENSMUSG00000020732	Rab37	B230331O03Rik|B230354I04Rik	RAB37, member RAS oncogene family	protein-coding
mm_80794.1	chr9	96196289	96196353	+	1	NA	promoter-TSS (NM_178667)	promoter-TSS (NM_178667)	46	NM_001184706	211586	Mm.17977	NM_178667	ENSMUSG00000032411	Tfdp2	1110029I05Rik|A330080J22Rik|DP-3|DP3	transcription factor Dp 2	protein-coding
mm_42596.1	chr5	117413811	117413822	+	1	NA	promoter-TSS (NM_001312914)	promoter-TSS (NM_001312914)	-186	NM_001312914	333050	Mm.437947	NM_001034873	ENSMUSG00000061578	Ksr2	-	kinase suppressor of ras 2	protein-coding
mm_27118.1	chr3	31208067	31208076	-	1	NA	3' UTR (NM_172861, exon 8 of 8)	3' UTR (NM_172861, exon 8 of 8)	58151	NM_008770	18417	Mm.4425	NM_008770	ENSMUSG00000037625	Cldn11	Claudin-11|Claudin11|Osp|Otm	claudin 11	protein-coding
mm_25015.1	chr3	97992466	97992469	+	1	NA	Intergenic	Intergenic	-21071	NM_010928	18129	Mm.485843	NM_010928	ENSMUSG00000027878	Notch2	AI853703|N2	notch 2	protein-coding
mm_77512.1	chr8	122893943	122893970	-	1	NA	non-coding (NR_037865, exon 10 of 14)	non-coding (NR_037865, exon 10 of 14)	45582	NM_007662	12555	Mm.1976	NM_007662	ENSMUSG00000031962	Cdh15	AI323380|Cdh14|Mcad	cadherin 15	protein-coding
mm_54903.1	chr6	47563266	47563280	-	1	NA	intron (NM_001146689, intron 3 of 19)	MT2B1|LTR|ERVL	31757	NM_007971	14056	Mm.246688	NM_007971	ENSMUSG00000029687	Ezh2	Enx-1|Enx1h|KMT6|mKIAA4065	enhancer of zeste 2 polycomb repressive complex 2 subunit	protein-coding
mm_54894.1	chr6	47044579	47044585	-	1	NA	intron (NM_001004357, intron 17 of 23)	intron (NM_001004357, intron 17 of 23)	-199814	NM_025771	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding
mm_93271.1	chr10	95778946	95778982	-	1	NA	Intergenic	Intergenic	-161699	NM_001001932	216238	Mm.210035	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding
mm_78688.1	chr9	40801906	40801913	+	1	NA	intron (NM_031165, intron 1 of 8)	intron (NM_031165, intron 1 of 8)	636	NM_031165	15481	Mm.290774	NM_031165	ENSMUSG00000015656	Hspa8	2410008N15Rik|Hsc70|Hsc71|Hsc73|Hsp73|Hspa10	heat shock protein 8	protein-coding
mm_130296.1	chr15	97013586	97013608	-	1	NA	intron (NM_027052, intron 4 of 15)	intron (NM_027052, intron 4 of 15)	42359	NM_027052	69354	Mm.250980	NM_027052	ENSMUSG00000022464	Slc38a4	1110012E16Rik|1700012A18Rik|Ata3|mATA3|mNAT3	solute carrier family 38, member 4	protein-coding
mm_134460.1	chr16	18426373	18426389	-	1	NA	promoter-TSS (NM_013711)	promoter-TSS (NM_013711)	-36	NM_013711	26462	Mm.390906	NM_013711	ENSMUSG00000075704	Txnrd2	AA118373|ESTM573010|TGR|Tr3|Trxr2|Trxrd2	thioredoxin reductase 2	protein-coding
mm_35050.1	chr4	6352880	6352890	-	1	NA	Intergenic	ORR1A1-int|LTR|ERVL-MaLR	-12795	NM_016807	53378	Mm.247473	NM_016807	ENSMUSG00000028249	Sdcbp	MDA-9|Sycl|syntenin-1	syndecan binding protein	protein-coding
mm_74694.1	chr8	15027621	15027663	-	1	NA	exon (NM_029116, exon 2 of 2)	exon (NM_029116, exon 2 of 2)	16617	NM_029116	74901	Mm.46675	NM_029116	ENSMUSG00000055675	Kbtbd11	2900016B01Rik|4930465M17Rik|mKIAA0711	kelch repeat and BTB (POZ) domain containing 11	protein-coding
mm_13796.1	chr2	118901590	118901617	+	1	NA	promoter-TSS (NM_001045523)	promoter-TSS (NM_001045523)	-12	NM_001045523	228536	Mm.330487	NM_001045523	ENSMUSG00000040007	Bahd1	AL022997|AW541238|Gm117|mKIAA0945	bromo adjacent homology domain containing 1	protein-coding
mm_131409.1	chr16	14458615	14458624	+	1	NA	intron (NM_008576, intron 20 of 30)	ID_B1|SINE|B4	97061	NM_008576	17250	Mm.196634	NM_008576	ENSMUSG00000023088	Abcc1	Abcc1a|Abcc1b|MRP|Mdrap|Mrp1	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	protein-coding
mm_110504.1	chr12	54649872	54649877	-	1	NA	intron (NM_134054, intron 1 of 1)	intron (NM_134054, intron 1 of 1)	-3862	NR_035439	100316682		NR_035439	ENSMUSG00000106344	Mir1892	Mirn1892|mir-1892|mmu-mir-1892	microRNA 1892	ncRNA
mm_39235.1	chr4	156254822	156254839	-	1	NA	intron (NM_001110516, intron 1 of 10)	intron (NM_001110516, intron 1 of 10)	508	NM_001110516	231004	Mm.406833	NM_173736	ENSMUSG00000096351	Samd11	BC026991|mr-s	sterile alpha motif domain containing 11	protein-coding
mm_101189.1	chr11	17211577	17211590	-	1	NA	promoter-TSS (NM_178909)	promoter-TSS (NM_178909)	6	NM_025443	66249	Mm.27831	NM_025443	ENSMUSG00000020116	Pno1	1810003N24Rik|AA407421|AU015468|AU019495|AU042323|Emi3|Imi3	partner of NOB1 homolog	protein-coding
mm_60056.1	chr7	31150069	31150075	+	1	NA	intron (NM_027898, intron 1 of 18)	intron (NM_027898, intron 1 of 18)	978	NM_027898	52857	Mm.27366	NM_027898	ENSMUSG00000001248	Gramd1a	1300003M23Rik|AI415002|AW547240|D7Bwg0611e	GRAM domain containing 1A	protein-coding
mm_45423.1	chr5	66618637	66618711	-	1	NA	5' UTR (NM_009686, exon 1 of 18)	5' UTR (NM_009686, exon 1 of 18)	143	NM_009686	11787	Mm.5159	NM_009686	ENSMUSG00000029207	Apbb2	2310007D03Rik|FE65L1|Rirl1|TR2L|Zfra	amyloid beta (A4) precursor protein-binding, family B, member 2	protein-coding
mm_42320.1	chr5	114897605	114897615	+	1	NA	5' UTR (NM_011854, exon 1 of 6)	5' UTR (NM_011854, exon 1 of 6)	676	NM_011854	23962	Mm.228363	NM_011854	ENSMUSG00000029561	Oasl2	M1204|Mmu-OASL|Oasl	2'-5' oligoadenylate synthetase-like 2	protein-coding
mm_165986.1	chr4	107981688	107981692	+	1	NA	intron (NM_146255, intron 2 of 10)	L2b|LINE|L2	13356	NM_146255	242607	Mm.192040	NM_146255	ENSMUSG00000008932	Slc1a7	A930031E15Rik|Eaat5	solute carrier family 1 (glutamate transporter), member 7	protein-coding
mm_10889.1	chr2	25263213	25263219	+	1	NA	exon (NM_175286, exon 1 of 4)	exon (NM_175286, exon 1 of 4)	618	NM_175286	97031	Mm.308539	NM_175286	ENSMUSG00000048707	Tprn	C430004E15Rik|C87750	taperin	protein-coding
mm_113509.1	chr13	37701000	37701000	+	1	NA	Intergenic	Intergenic	-125038	NM_026830	68750	Mm.491109	NM_026830	ENSMUSG00000039087	Rreb1	1110037N09Rik|AA414966|B930013M22Rik	ras responsive element binding protein 1	protein-coding
mm_169505.1	chr14	78997398	78997411	+	1	NA	intron (NM_173758, intron 16 of 25)	L1Md_Gf|LINE|L1	148226	NM_173758	219189	Mm.159651	NM_027906	ENSMUSG00000058997	Vwa8	1300010F03Rik|4932416F07Rik|AI957255|Kiaa0564|mKIAA0564	von Willebrand factor A domain containing 8	protein-coding
mm_6783.1	chr1	84139317	84139350	-	1	NA	intron (NM_001003948, intron 2 of 2)	L1_Mur3|LINE|L1	79628	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_18950.1	chr2	76784510	76784527	-	1	NA	exon (NM_011652, exon 226 of 313)	exon (NM_011652, exon 226 of 313)	109203	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_12171.1	chr2	62664280	62664300	+	1	NA	promoter-TSS (NM_145523)	promoter-TSS (NM_145523)	-37	NM_145523	227960	Mm.219877	NM_145523	ENSMUSG00000026893	Gca	5133401E04Rik|AI573844	grancalcin	protein-coding
mm_159852.1	chr5	137485634	137485634	-	1	NA	intron (NM_001312875, intron 1 of 4)	intron (NM_001312875, intron 1 of 4)	182	NM_007942	13856	Mm.349116	NM_007942	ENSMUSG00000029711	Epo	-	erythropoietin	protein-coding
mm_51614.1	chr6	85105440	85105449	+	1	NA	Intergenic	RLTR17|LTR|ERVK	20650	NM_001034902	545861	Mm.321419	NM_001034902	ENSMUSG00000072952	Gm5878	EG545861	predicted gene 5878	protein-coding
mm_98253.1	chr11	88619702	88619711	+	1	NA	non-coding (NR_131025, exon 1 of 3)	non-coding (NR_131025, exon 1 of 3)	455	NR_131025	68397	Mm.426889	NR_131025		0610039H22Rik	-	RIKEN cDNA 0610039H22 gene	ncRNA
mm_132172.1	chr16	32324322	32324330	+	1	NA	Intergenic	RMER17C|LTR|ERVK	-7926	NM_177633	224111	Mm.31275	NM_177633	ENSMUSG00000053774	Ubxn7	A630090P18|AI196514|Ubxd7|mKIAA0794	UBX domain protein 7	protein-coding
mm_145274.1	chr18	52801083	52801086	+	1	NA	intron (NM_001199154, intron 1 of 10)	intron (NM_001199154, intron 1 of 10)	32940	NM_001199154	67847	Mm.292168	NM_026408	ENSMUSG00000024534	Sncaip	2810407O15Rik|4933427B05Rik|BB104594|SYPH1	synuclein, alpha interacting protein (synphilin)	protein-coding
mm_129639.1	chr15	80255846	80255864	-	1	NA	intron (NM_001287180, intron 2 of 3)	CpG	671	NM_009716	11911	Mm.641	NM_009716	ENSMUSG00000042406	Atf4	Atf-4|C/ATF|CREB2|TAXREB67	activating transcription factor 4	protein-coding
mm_43178.1	chr5	127700620	127700630	+	1	NA	intron (NM_177005, intron 11 of 11)	(T)n|Simple_repeat|Simple_repeat	68363	NM_177005	319804	Mm.237888	NM_177005	ENSMUSG00000049971	Glt1d1	5730455A04Rik	glycosyltransferase 1 domain containing 1	protein-coding
mm_61373.1	chr7	70365082	70365102	+	1	NA	promoter-TSS (NR_045850)	promoter-TSS (NR_045850)	-291	NR_045850	434198	Mm.389911	NR_045850	ENSMUSG00000100005	B130024G19Rik	-	RIKEN cDNA B130024G19 gene	ncRNA
mm_144587.1	chr18	31958015	31958039	+	1	NA	3' UTR (NM_144862, exon 10 of 10)	3' UTR (NM_144862, exon 10 of 10)	-8391	NM_001025381	574402	Mm.391108	NM_001025381	ENSMUSG00000052229	Gpr17	AI853548	G protein-coupled receptor 17	protein-coding
mm_140105.1	chr17	78560994	78561037	+	1	NA	intron (NM_028813, intron 3 of 13)	intron (NM_028813, intron 3 of 13)	52952	NM_028813	74199	Mm.292983	NM_028813	ENSMUSG00000024076	Vit	1700052E02Rik|1700110E08Rik|2810429K11Rik	vitrin	protein-coding
mm_51061.1	chr6	65790009	65790009	+	1	NA	intron (NM_029549, intron 1 of 10)	intron (NM_029549, intron 1 of 10)	11047	NM_029549	70779	Mm.263355	NM_027547	ENSMUSG00000029913	Prdm5	4432417F03Rik|6530401I24Rik|AI197291|E130112L17Rik|PFM2	PR domain containing 5	protein-coding
mm_27012.1	chr3	25936741	25936744	-	1	NA	intron (NM_138666, intron 3 of 7)	intron (NM_138666, intron 3 of 7)	216565	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_1887.1	chr1	85681072	85681109	+	1	NA	exon (NM_013673, exon 11 of 20)	exon (NM_013673, exon 11 of 20)	31102	NM_001313714	20684	Mm.290906	NM_013673	ENSMUSG00000026222	Sp100	A430075G10Rik	nuclear antigen Sp100	protein-coding
mm_32296.1	chr4	103119372	103119403	+	1	NA	promoter-TSS (NM_001039081)	promoter-TSS (NM_001039081)	-3	NM_001039081	71148	Mm.288721	NM_027696	ENSMUSG00000028522	Mier1	4933425I22Rik|5830411K19Rik|er1	MEIR1 treanscription regulator	protein-coding
mm_123468.1	chr14	65973401	65973411	-	1	NA	exon (NM_013492, exon 3 of 9)	exon (NM_013492, exon 3 of 9)	4923	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_53571.1	chr6	137376545	137376577	+	1	NA	intron (NM_001164401, intron 2 of 25)	intron (NM_001164401, intron 2 of 25)	-34160	NM_001164402	19277	Mm.186361	NM_011216	ENSMUSG00000030223	Ptpro	D28|GLEPP1|PTPBK|PTPROt|PTPU2|PTPoc|PTPphi|Ptpn15|R-PTP-O	protein tyrosine phosphatase, receptor type, O	protein-coding
mm_100451.1	chr11	119671294	119671304	+	1	NA	exon (NM_028898, exon 3 of 34)	exon (NM_028898, exon 3 of 34)	68394	NM_028898	74370	Mm.209933	NM_028898	ENSMUSG00000025583	Rptor	4932417H02Rik|Rap|Raptor|mKIAA1303	regulatory associated protein of MTOR, complex 1	protein-coding
mm_170000.1	chr1	71651548	71651558	-	1	NA	exon (NM_001276413, exon 2 of 44)	exon (NM_001276413, exon 2 of 44)	1681	NM_010233	14268	Mm.193099	NM_010233	ENSMUSG00000026193	Fn1	E330027I09|Fn|Fn-1	fibronectin 1	protein-coding
mm_155694.1	chrX	94274776	94274786	+	1	NA	TTS (NR_106133)	TTS (NR_106133)	207	NR_106133	102466238		NR_106133	ENSMUSG00000099072	Mir7673	Gm27569|mmu-mir-7673	microRNA 7673	ncRNA
mm_51816.1	chr6	88902455	88902535	+	1	NA	5' UTR (NM_011906, exon 1 of 12)	5' UTR (NM_011906, exon 1 of 12)	244	NM_011906	24100	Mm.284480	NM_011906	ENSMUSG00000002871	Tpra1	40kDa|Gpr175|Tpra40	transmembrane protein, adipocyte asscociated 1	protein-coding
mm_22810.1	chr3	27182995	27183017	+	1	NA	promoter-TSS (NM_178772)	promoter-TSS (NM_178772)	2	NM_178772	320024	Mm.24576	NM_178772	ENSMUSG00000027698	Nceh1	Aadacl1|B230106I24Rik|CPO-BP|Nceh	neutral cholesterol ester hydrolase 1	protein-coding
mm_80287.1	chr9	73064166	73064181	+	1	NA	promoter-TSS (NM_001301232)	promoter-TSS (NM_001301232)	25	NM_001301232	11891	Mm.34867	NM_023635	ENSMUSG00000032202	Rab27a	2210402C08Rik|2410003M20Rik|4933437C11Rik|ash	RAB27A, member RAS oncogene family	protein-coding
mm_58403.1	chr7	3218698	3218731	+	1	NA	promoter-TSS (NR_029640)	promoter-TSS (NR_029640)	-19	NR_106158	102465789		NR_106158	ENSMUSG00000106340	Mir290b	mmu-mir-290b	microRNA 290b	ncRNA
mm_172786.1	chr9	103849341	103849342	+	1	NA	Intergenic	(T)n|Simple_repeat|Simple_repeat	-87504	NM_178638	81907	Mm.384704	NM_178638	ENSMUSG00000042757	Tmem108	AI462967|B130017P16Rik|R74726	transmembrane protein 108	protein-coding
mm_134010.1	chr16	4875829	4875846	-	1	NA	exon (NM_145359, exon 3 of 3)	exon (NM_145359, exon 3 of 3)	4014	NM_145359	207740	Mm.268895	NM_145359	ENSMUSG00000039568	Ubald1	1500031H01Rik|BC013706|Fam100a	UBA-like domain containing 1	protein-coding
mm_40772.1	chr5	67260672	67260692	+	1	NA	5' UTR (NM_030108, exon 1 of 9)	5' UTR (NM_030108, exon 1 of 9)	117	NM_030108	67878	Mm.23217	NM_028975	ENSMUSG00000037720	Tmem33	1110006G02Rik|1600019D15Rik|2410089A21Rik|2700052H22Rik|5430406L04Rik|AA388285|AI314185|AI426615|db83	transmembrane protein 33	protein-coding
mm_89702.1	chr10	97647085	97647113	+	1	NA	intron (NM_007884, intron 1 of 7)	intron (NM_007884, intron 1 of 7)	3031	NM_007884	13516	Mm.148886	NM_007884	ENSMUSG00000019936	Epyc	Dspg3|PG-Lb|SLRR3B	epiphycan	protein-coding
mm_140181.1	chr17	80944612	80944644	+	1	NA	promoter-TSS (NM_026516)	promoter-TSS (NM_026516)	-4	NM_026516	68027	Mm.357108	NM_026516	ENSMUSG00000024245	Tmem178	2810417M05Rik|Tmem178a	transmembrane protein 178	protein-coding
mm_126508.1	chr15	81802736	81802758	+	1	NA	promoter-TSS (NM_153484)	promoter-TSS (NM_153484)	74	NM_153484	21685	Mm.270278	NM_017376	ENSMUSG00000022389	Tef	2310028D20Rik	thyrotroph embryonic factor	protein-coding
mm_74440.1	chr8	3803353	3803362	-	1	NA	promoter-TSS (NR_024198)	promoter-TSS (NR_024198)	4	NR_024198	19785		NR_024198		Rprl3	RPRH4|Rmrp4	ribonuclease P RNA-like 3	ncRNA
mm_150360.1	chr19	34649170	34649180	+	1	NA	3' UTR (NM_008331, exon 2 of 2)	3' UTR (NM_008331, exon 2 of 2)	8286	NM_008331	15957	Mm.439751	NM_008331	ENSMUSG00000034459	Ifit1	ISG56|Ifi56|P56	interferon-induced protein with tetratricopeptide repeats 1	protein-coding
mm_119458.1	chr14	47068939	47068948	+	1	NA	promoter-TSS (NM_001310544)	promoter-TSS (NM_001310544)	-34	NM_001310544	74480	Mm.214454	NM_028966	ENSMUSG00000021838	Samd4	1700024G08Rik|1700111L17Rik|4933436G17Rik|Samd4a|Smaug|Smaug1|sunk	sterile alpha motif domain containing 4	protein-coding
mm_98958.1	chr11	98551106	98551165	+	1	NA	promoter-TSS (NM_001166494)	promoter-TSS (NM_001166494)	38	NM_001166494	69376	Mm.55996	NM_027061	ENSMUSG00000017195	Zpbp2	1700017D11Rik|2610022C02Rik|ZPBPL	zona pellucida binding protein 2	protein-coding
mm_165480.1	chr2	164333418	164333422	+	1	NA	exon (NM_009301, exon 2 of 3)	exon (NM_009301, exon 2 of 3)	655	NM_009301	20944	Mm.140154	NM_009301	ENSMUSG00000017004	Svs5	BB115186|Semg1|Svp-1|Svp1|Svp5	seminal vesicle secretory protein 5	protein-coding
mm_75468.1	chr8	47990362	47990400	-	1	NA	5' UTR (NM_133791, exon 1 of 23)	5' UTR (NM_133791, exon 1 of 23)	170	NM_133791	52357	Mm.235074	NM_133791	ENSMUSG00000031563	Wwc2	5330431C14Rik|AU022508|C85457|D8Ertd594e	WW, C2 and coiled-coil domain containing 2	protein-coding
mm_38838.1	chr4	149165169	149165179	-	1	NA	exon (NM_001081274, exon 3 of 13)	exon (NM_001081274, exon 3 of 13)	1533	NM_001081274	110208	Mm.252080	NM_025801	ENSMUSG00000028961	Pgd	0610042A05Rik|AU019875|C78335	phosphogluconate dehydrogenase	protein-coding
mm_67450.1	chr7	80398768	80398791	-	1	NA	5' UTR (NM_001081454, exon 2 of 16)	5' UTR (NM_001081454, exon 2 of 16)	4033	NM_011046	18550	Mm.5241	NM_011046	ENSMUSG00000030530	Furin	9130404I01Rik|Fur|PACE|Pcsk3|SPC1	furin (paired basic amino acid cleaving enzyme)	protein-coding
mm_20810.1	chr2	144365682	144365686	-	1	NA	Intergenic	Intergenic	-3299	NM_001164813	100048644	Mm.227925	NM_001164813	ENSMUSG00000098387	Pet117	Gm20571	PET117 homolog	protein-coding
mm_37354.1	chr4	120287671	120287683	-	1	NA	promoter-TSS (NM_194060)	promoter-TSS (NM_194060)	-416	NM_194060	329934	Mm.277090	NM_194060	ENSMUSG00000052135	Foxo6	-	forkhead box O6	protein-coding
mm_113837.1	chr13	47193834	47193838	+	1	NA	promoter-TSS (NM_001170643)	promoter-TSS (NM_001170643)	-167	NM_001170643	218215	Mm.287609	NM_146042	ENSMUSG00000038068	Rnf144b	BC025007|E130105P19Rik|Ibrdc2|Pir2	ring finger protein 144B	protein-coding
mm_115497.1	chr13	3893507	3893553	-	1	NA	promoter-TSS (NM_001047159)	promoter-TSS (NM_001047159)	51	NM_001047159	56349	Mm.22261	NM_019671	ENSMUSG00000021215	Net1	Net1a|mNET1	neuroepithelial cell transforming gene 1	protein-coding
mm_1228.1	chr1	62762950	62762962	+	1	NA	exon (NM_001077407, exon 9 of 16)	exon (NM_001077407, exon 9 of 16)	31776	NR_040601	74992	Mm.401979	NR_040601		4930487H11Rik	-	RIKEN cDNA 4930487H11 gene	ncRNA
mm_103610.1	chr11	78536108	78536215	-	1	NA	promoter-TSS (NM_018854)	promoter-TSS (NM_018854)	99	NM_001159392	21927	Mm.386774	NM_009395	ENSMUSG00000017615	Tnfaip1	Bacurd2|Edp-1|Edp1|Tnfip1	tumor necrosis factor, alpha-induced protein 1 (endothelial)	protein-coding
mm_18045.1	chr2	39007987	39008015	-	1	NA	promoter-TSS (NM_028809)	promoter-TSS (NM_028809)	-138	NM_028809	74192	Mm.38155	NM_028809	ENSMUSG00000026755	Arpc5l	2010015J01Rik|AI852867|ARC16-2|AW555592|AW742746	actin related protein 2/3 complex, subunit 5-like	protein-coding
mm_157264.1	chrX	19168306	19168317	-	1	NA	Intergenic	Intergenic	-21340	NR_029807	723828		NR_029807	ENSMUSG00000065471	Mir222	Mirn222|mir-222|mmu-mir-222	microRNA 222	ncRNA
mm_28426.1	chr3	90464540	90464613	-	1	NA	intron (NM_008727, intron 1 of 21)	intron (NM_008727, intron 1 of 21)	1290	NM_008727	18160	Mm.4627	NM_008727	ENSMUSG00000027931	Npr1	AI893888|GC-A|NPR-A|NPRA|Pndr	natriuretic peptide receptor 1	protein-coding
mm_3608.1	chr1	151755340	151755393	+	1	NA	promoter-TSS (NM_001039644)	promoter-TSS (NM_001039644)	-8	NM_001311165	66967	Mm.337691	NM_001039644	ENSMUSG00000043019	Edem3	2310050N11Rik	ER degradation enhancer, mannosidase alpha-like 3	protein-coding
mm_142494.1	chr17	46018671	46018682	-	1	NA	3' UTR (NM_001025250, exon 8 of 8)	3' UTR (NM_001025250, exon 8 of 8)	6487	NM_001110267	22339	Mm.282184	NM_009505	ENSMUSG00000023951	Vegfa	Vegf|Vpf	vascular endothelial growth factor A	protein-coding
mm_12844.1	chr2	82943628	82943640	+	1	NA	Intergenic	Intergenic	-700944	NM_026934	69082	Mm.27804	NM_026934	ENSMUSG00000027091	Zc3h15	1700006A17Rik|1810012H02Rik|2610312B22Rik|FM22|Ierepo4	zinc finger CCCH-type containing 15	protein-coding
mm_22428.1	chr2	181599129	181599235	-	1	NA	promoter-TSS (NM_172676)	promoter-TSS (NM_172676)	-35	NM_172676	229011	Mm.205422	NM_172676	ENSMUSG00000038605	Samd10	D930033N23Rik|E130318E08	sterile alpha motif domain containing 10	protein-coding
mm_41481.1	chr5	91963318	91963327	+	1	NA	promoter-TSS (NM_001271797)	promoter-TSS (NM_001271797)	-254	NM_001271797	68098	Mm.159453	NM_026557	ENSMUSG00000029397	Rchy1	ARNIP|CHIMP|Pirh2|Zfp363|Znf363	ring finger and CHY zinc finger domain containing 1	protein-coding
mm_18419.1	chr2	60722637	60722657	-	1	NA	promoter-TSS (NM_001159564)	promoter-TSS (NM_001159564)	-44	NM_001159564	16420	Mm.98193	NM_021359	ENSMUSG00000026971	Itgb6	2210409C20Rik|4831415H04Rik	integrin beta 6	protein-coding
mm_120567.1	chr14	68765606	68765608	+	1	NA	Intergenic	ORR1A3|LTR|ERVL-MaLR	-109765	NM_183366	13522	Mm.117450	NM_010082	ENSMUSG00000014725	Adam28	C130072N01Rik|D430033C21Rik|Dtgn1|MDC-L|MDCL|TECADAM|eMDCII	a disintegrin and metallopeptidase domain 28	protein-coding
mm_156565.1	chrX	151883484	151883492	+	1	NA	intron (NM_021523, intron 32 of 82)	intron (NM_021523, intron 32 of 82)	23926	NR_130340	100526542		NR_130340	ENSMUSG00000093219	Mir3113	mmu-mir-3113	microRNA 3113	ncRNA
mm_118200.1	chr13	107890076	107890084	-	1	NA	promoter-TSS (NM_145456)	promoter-TSS (NM_145456)	-16	NM_145456	67263	Mm.490418	NM_145456	ENSMUSG00000032846	Zswim6	2900036G02Rik|mKIAA1577	zinc finger SWIM-type containing 6	protein-coding
mm_164367.1	chr16	23981189	23981192	-	1	NA	intron (NM_009744, intron 1 of 9)	intron (NM_009744, intron 1 of 9)	7422	NM_009744	12053	Mm.347398	NM_009744	ENSMUSG00000022508	Bcl6	Bcl5	B cell leukemia/lymphoma 6	protein-coding
mm_53253.1	chr6	127796443	127796453	+	1	NA	Intergenic	Intergenic	-8305	NR_106092	102466996		NR_106092	ENSMUSG00000104804	Mir7233	mmu-mir-7233	microRNA 7233	ncRNA
mm_46214.1	chr5	98186065	98186081	-	1	NA	exon (NM_029947, exon 4 of 4)	exon (NM_029947, exon 4 of 4)	5204	NM_029947	77630	Mm.332511	NM_029947	ENSMUSG00000035456	Prdm8	4930565F05Rik|PFM5	PR domain containing 8	protein-coding
mm_340.1	chr1	30722087	30722087	+	1	NA	Intergenic	Intergenic	141169	NM_001081080	213109	Mm.194486	NM_025871	ENSMUSG00000048874	Phf3	2310061N19Rik|mKIAA0244	PHD finger protein 3	protein-coding
mm_27458.1	chr3	52104985	52105032	-	1	NA	promoter-TSS (NM_001004176)	promoter-TSS (NM_001004176)	-2	NM_001004176	433586	Mm.234972	NM_001004176	ENSMUSG00000061143	Maml3	AV234550|BC049812|Mam-2|mKIAA1816	mastermind like 3 (Drosophila)	protein-coding
mm_45530.1	chr5	72736541	72736575	-	1	NA	promoter-TSS (NM_013698)	promoter-TSS (NM_013698)	44	NM_013698	22165	Mm.3264	NM_013698	ENSMUSG00000054892	Txk	A130089B16Rik|Btkl|PTK-RL-18|PTK4|Rlk	TXK tyrosine kinase	protein-coding
mm_31585.1	chr4	57813261	57813261	+	1	NA	intron (NM_001304544, intron 6 of 8)	intron (NM_001304544, intron 6 of 8)	-31987	NM_009649	11641	Mm.467752	NM_009649	ENSMUSG00000038729	Akap2	AA959716|AI649048|Akap-2|Akap-kl|B230340M18Rik|Prka2	A kinase (PRKA) anchor protein 2	protein-coding
mm_1247.1	chr1	62809845	62809860	+	1	NA	intron (NM_010939, intron 15 of 15)	intron (NM_010939, intron 15 of 15)	-15120	NR_040601	74992	Mm.401979	NR_040601		4930487H11Rik	-	RIKEN cDNA 4930487H11 gene	ncRNA
mm_29047.1	chr3	103384980	103384984	-	1	NA	Intergenic	Intergenic	105689	NM_001079830	94093	Mm.195036	NM_053170	ENSMUSG00000033014	Trim33	8030451N04Rik|AI413936|Ecto|Tif1g	tripartite motif-containing 33	protein-coding
mm_98874.1	chr11	97799761	97799771	+	1	NA	promoter-TSS (NM_010688)	promoter-TSS (NM_010688)	94	NM_010688	16796	Mm.271967	NM_010688	ENSMUSG00000038366	Lasp1	AA408629|Def-4|SH3P6|Tg(Col1a1-lacZ)1Ngma	LIM and SH3 protein 1	protein-coding
mm_56381.1	chr6	94283801	94283820	-	1	NA	5' UTR (NM_010367, exon 1 of 22)	5' UTR (NM_010367, exon 1 of 22)	107	NM_001286786	14924	Mm.217216	NM_010367	ENSMUSG00000045095	Magi1	AIP3|BAP1|Baiap1|Gukmi1|MAGI1c|Magi-1|TNRC19|WWP3|mKIAA4129	membrane associated guanylate kinase, WW and PDZ domain containing 1	protein-coding
mm_41118.1	chr5	87781782	87781805	+	1	NA	exon (NM_001304768, exon 8 of 13)	exon (NM_001304768, exon 8 of 13)	7343	NM_007785	12993	Mm.4908	NM_007785	ENSMUSG00000061937	Csn1s2a	Csng|PP22	casein alpha s2-like A	protein-coding
mm_160873.1	chr11	68556173	68556173	+	1	NA	promoter-TSS (NM_146004)	promoter-TSS (NM_146004)	-13	NM_146004	215723	Mm.131205	NM_146004	ENSMUSG00000048329	Mfsd6l	-	major facilitator superfamily domain containing 6-like	protein-coding
mm_156734.1	chrX	159942845	159942870	+	1	NA	5' UTR (NM_001290664, exon 1 of 6)	5' UTR (NM_001290664, exon 1 of 6)	164	NM_001290664	58194	Mm.286495	NM_021389	ENSMUSG00000040990	Sh3kbp1	1200007H22Rik|1700125L08Rik|5830464D22Rik|AI447724|Cin85|IN85|Ruk|Seta	SH3-domain kinase binding protein 1	protein-coding
mm_98539.1	chr11	95009967	95010029	+	1	NA	5' UTR (NM_146025, exon 1 of 10)	5' UTR (NM_146025, exon 1 of 10)	119	NM_146025	217125	Mm.297199	NM_146025	ENSMUSG00000047181	Samd14	AI839049|AI854782|BC034054	sterile alpha motif domain containing 14	protein-coding
mm_96417.1	chr11	67255655	67255670	+	1	NA	exon (NM_010855, exon 32 of 40)	exon (NM_010855, exon 32 of 40)	17850	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_126797.1	chr15	86469000	86469000	+	1	NA	intron (NM_145476, intron 12 of 12)	ORR1C2|LTR|ERVL-MaLR	254541	NM_145476	223754	Mm.28904	NM_145476	ENSMUSG00000051864	Tbc1d22a	BC023106|D15Ertd781e	TBC1 domain family, member 22a	protein-coding
mm_115605.1	chr13	11991457	11991473	-	1	NA	intron (NM_023868, intron 1 of 104)	RLTR17B_Mm|LTR|ERVK	115480	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding
mm_158177.1	chrX	103960861	103960864	-	1	NA	3' UTR (NM_011276, exon 5 of 5)	3' UTR (NM_011276, exon 5 of 5)	20422	NM_011276	19820	Mm.427762	NM_011276	ENSMUSG00000056537	Rlim	AL022832|AW743871|Ha1r|Rlim1|Rnf12	ring finger protein, LIM domain interacting	protein-coding
mm_65475.1	chr7	25539805	25539815	-	1	NA	5' UTR (NM_001113369, exon 1 of 7)	5' UTR (NM_001113369, exon 1 of 7)	194	NM_001113368	26367	Mm.439731	NM_007543	ENSMUSG00000054385	Ceacam2	AI267129|Bgp2|Ceacam2-L	carcinoembryonic antigen-related cell adhesion molecule 2	protein-coding
mm_8569.1	chr1	155527084	155527091	-	1	NA	promoter-TSS (NR_132128)	promoter-TSS (NR_132128)	24	NR_132128	433367	Mm.359304	NR_132128	ENSMUSG00000073535	Gm5532	EG433367	predicted gene 5532	ncRNA
mm_171727.1	chr4	89617886	89617886	+	1	NA	Intergenic	L1Md_T|LINE|L1	-70312	NM_175647	242523	Mm.130167	NM_175647	ENSMUSG00000043753	Dmrta1	Dmrt4	doublesex and mab-3 related transcription factor like family A1	protein-coding
mm_75009.1	chr8	27296301	27296314	-	1	NA	non-coding (NR_003107, exon 1 of 1)	non-coding (NR_003107, exon 1 of 1)	262	NR_003107	732482	Mm.463248	NR_003107		Gm9731	-	Fam58a pseudogene	pseudo
mm_173218.1	chrX	74243053	74243062	-	1	NA	exon (NM_010227, exon 2 of 46)	exon (NM_010227, exon 2 of 46)	3477	NM_010227	192176	Mm.295533	NM_010227	ENSMUSG00000031328	Flna	ABP-280|Dilp2|F730004A14Rik|Fln1|GENA 379|filamin-1	filamin, alpha	protein-coding
mm_100099.1	chr11	115699594	115699642	+	1	NA	promoter-TSS (NM_001313937)	promoter-TSS (NM_001313937)	-84	NM_001313937	14784	Mm.439649	NM_008163	ENSMUSG00000059923	Grb2	AA408164|Ash	growth factor receptor bound protein 2	protein-coding
mm_4086.1	chr1	167001420	167001431	+	1	NA	promoter-TSS (NM_175461)	promoter-TSS (NM_175461)	8	NM_001160261	226610	Mm.389217	NM_175461	ENSMUSG00000060568	Fam78b	C030014K22Rik|C030020L09Rik	family with sequence similarity 78, member B	protein-coding
mm_26434.1	chr3	142620648	142620665	+	1	NA	promoter-TSS (NM_010260)	promoter-TSS (NM_010260)	-7	NM_010260	14469	Mm.24038	NM_010260	ENSMUSG00000028270	Gbp2	-	guanylate binding protein 2	protein-coding
mm_163895.1	chr14	27351689	27351708	-	1	NA	intron (NM_001289687, intron 1 of 9)	intron (NM_001289687, intron 1 of 9)	-9691	NM_001289688	71704	Mm.248606	NM_027871	ENSMUSG00000021895	Arhgef3	1200004I24Rik|9830169H03Rik|C76747|Xpln	Rho guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_103642.1	chr11	78965716	78965729	-	1	NA	exon (NM_010708, exon 10 of 11)	exon (NM_010708, exon 10 of 11)	19202	NM_001159301	16859	Mm.341434	NM_010708	ENSMUSG00000001123	Lgals9	AA407335|AI194909|AI265545|LGALS35|Lgals5|gal-9|galectin-9	lectin, galactose binding, soluble 9	protein-coding
mm_9425.1	chr1	172475166	172475200	-	1	NA	promoter-TSS (NM_029612)	promoter-TSS (NM_029612)	-177	NM_029612	98365	Mm.150050	NM_029612	ENSMUSG00000026548	Slamf9	2310026I04Rik|AI462096|CD2F-10|CD84-H1|Cd2f10|SF2001	SLAM family member 9	protein-coding
mm_27585.1	chr3	59116465	59116477	-	1	NA	intron (NM_001287119, intron 1 of 2)	intron (NM_001287119, intron 1 of 2)	14291	NM_001008497	140795	Mm.439021	NM_133200	ENSMUSG00000036381	P2ry14	A330108O13Rik|Gpr105|P2Y14	purinergic receptor P2Y, G-protein coupled, 14	protein-coding
mm_169748.1	chr15	88333926	88333929	+	1	NA	intron (NR_045281, intron 1 of 2)	BGLII|LTR|ERVK	19053	NR_045281	328579	Mm.146839	NR_045281		B230214G05Rik	B230214G05	RIKEN cDNA B230214G05 gene	ncRNA
mm_126629.1	chr15	83464815	83464817	+	1	NA	promoter-TSS (NM_001159509)	promoter-TSS (NM_001159509)	-210	NM_001159509	23970	Mm.23978	NM_011862	ENSMUSG00000016664	Pacsin2	AI197433	protein kinase C and casein kinase substrate in neurons 2	protein-coding
mm_12747.1	chr2	79231262	79231270	+	1	NA	Intergenic	Intergenic	-24160	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D|Itga4B	integrin alpha 4	protein-coding
mm_171706.1	chr4	74675612	74675617	+	1	NA	Intergenic	L1VL1|LINE|L1	423735	NM_144787	76804	Mm.209059	NM_144787	ENSMUSG00000028397	Kdm4c	2410141F18Rik|AA517467|Gasc1|Jmjd2c	lysine (K)-specific demethylase 4C	protein-coding
mm_72272.1	chr8	75100007	75100016	+	1	NA	exon (NM_010442, exon 5 of 5)	exon (NM_010442, exon 5 of 5)	6393	NM_010442	15368	Mm.276389	NM_010442	ENSMUSG00000005413	Hmox1	D8Wsu38e|HO-1|HO1|Hemox|Hmox|Hsp32	heme oxygenase 1	protein-coding
mm_4928.1	chr1	191063002	191063038	+	1	NA	promoter-TSS (NM_001163422)	promoter-TSS (NM_001163422)	-1	NM_198654	381318	Mm.32504	NM_198654	ENSMUSG00000062510	Nsl1	4833432M17Rik|AI451597|Gm105|Gm984	NSL1, MIS12 kinetochore complex component	protein-coding
mm_81237.1	chr9	107928439	107928439	+	1	NA	promoter-TSS (NM_026338)	promoter-TSS (NM_026338)	-30	NM_026338	67722	Mm.390222	NM_026338	ENSMUSG00000066368	Actl11	4921517D21Rik	actin-like 11	protein-coding
mm_78199.1	chr9	21368496	21368505	+	1	NA	promoter-TSS (NM_001277322)	promoter-TSS (NM_001277322)	-32	NM_001277322	16201	Mm.440026	NM_010561	ENSMUSG00000032178	Ilf3	MBII-26|MPHOSPH4|NF90|NFAR	interleukin enhancer binding factor 3	protein-coding
mm_77080.1	chr8	110503049	110503067	-	1	NA	promoter-TSS (NR_105058)	promoter-TSS (NR_105058)	-702	NR_105058	100861869	Mm.84499	NR_105058		Gm21283	-	predicted gene, 21283	ncRNA
mm_115740.1	chr13	17805094	17805189	-	1	NA	promoter-TSS (NM_001081058)	promoter-TSS (NM_001081058)	-44	NM_027118	69562	Mm.193924	NM_027118	ENSMUSG00000041297	Cdk13	2310015O17Rik|Cdc2l5	cyclin-dependent kinase 13	protein-coding
mm_100532.1	chr11	120608470	120608487	+	1	NA	promoter-TSS (NM_153288)	promoter-TSS (NM_153288)	1	NM_001347616	208990	Mm.29444	NM_153288	ENSMUSG00000044034	Npb	-	neuropeptide B	protein-coding
mm_7650.1	chr1	128319221	128319238	-	1	NA	intron (NM_001081078, intron 1 of 16)	intron (NM_001081078, intron 1 of 16)	9089	NM_001081078	226413	Mm.26930	NM_001081078	ENSMUSG00000026354	Lct	Gm100|LAC|LPH|Lphl	lactase	protein-coding
mm_61716.1	chr7	81588872	81588888	+	1	NA	intron (NM_001004185, intron 5 of 9)	intron (NM_001004185, intron 5 of 9)	17588	NM_001004185	434204	Mm.181641	NM_001004185	ENSMUSG00000045795	Whamm	BB081391|Whdc1|mKIAA1971	WAS protein homolog associated with actin, golgi membranes and microtubules	protein-coding
mm_8761.1	chr1	160784105	160784108	-	1	NA	intron (NM_013862, intron 1 of 20)	intron (NM_013862, intron 1 of 20)	8832	NM_013862	29809	Mm.25833	NM_013862	ENSMUSG00000026721	Rabgap1l	5830411O09Rik|8430421H08Rik|9630005B12Rik|AW049894|HHL|Hh1|mKIAA0471	RAB GTPase activating protein 1-like	protein-coding
mm_28363.1	chr3	89870229	89870244	-	1	NA	3' UTR (NM_010559, exon 10 of 10)	3' UTR (NM_010559, exon 10 of 10)	38866	NM_172530	214547	Mm.225	NM_172530	ENSMUSG00000046280	She	9430022A14	src homology 2 domain-containing transforming protein E	protein-coding
mm_151823.1	chr19	5610039	5610066	-	1	NA	promoter-TSS (NM_178637)	promoter-TSS (NM_178637)	42	NM_001199249	81601	Mm.228930	NM_178637	ENSMUSG00000024926	Kat5	AI839539|CPLA2|Htatip|Htatip1|PLIP|Tip55|Tip60	K(lysine) acetyltransferase 5	protein-coding
mm_140473.1	chr17	94750096	94750121	+	1	NA	promoter-TSS (NM_176917)	promoter-TSS (NM_176917)	8	NR_024720	77022	Mm.440259	NR_024720	ENSMUSG00000098090	2700099C18Rik	9430041D22Rik	NDC80 homolog, kinetochore complex component pseudogene	pseudo
mm_35443.1	chr4	40220579	40220605	-	1	NA	intron (NM_172689, intron 9 of 17)	intron (NM_172689, intron 9 of 17)	19233	NM_172689	230073	Mm.86382	NM_172689	ENSMUSG00000040296	Ddx58	6430573D20Rik|C330021E21|RIG-I|RLR-1	DEAD (Asp-Glu-Ala-Asp) box polypeptide 58	protein-coding
mm_34199.1	chr4	140720541	140720567	+	1	NA	exon (NM_173867, exon 12 of 13)	exon (NM_173867, exon 12 of 13)	19081	NM_173867	108911	Mm.253	NM_173867	ENSMUSG00000040945	Rcc2	2610510H01Rik|2610529N02Rik|AA536646|AA675016|Td60|mKIAA1470	regulator of chromosome condensation 2	protein-coding
mm_65791.1	chr7	28894146	28894183	-	1	NA	TTS (NM_001110807)	TTS (NM_001110807)	12508	NM_001110807	60594	Mm.476990	NM_021894	ENSMUSG00000054083	Capn12	CANP 12	calpain 12	protein-coding
mm_144894.1	chr18	36967620	36967650	+	1	NA	promoter-TSS (NM_007767)	promoter-TSS (NM_007767)	4	NM_001301256	103611158		NM_001301256		Gm38666	Pcdha6-g	predicted gene, 38666	protein-coding
mm_90617.1	chr10	128411624	128411676	+	1	NA	promoter-TSS (NM_026259)	promoter-TSS (NM_026259)	34	NM_026259	67588	Mm.294120	NM_026259	ENSMUSG00000025373	Rnf41	2210404G21Rik|4930511A05Rik|4933415P08Rik|D10Ertd722e|FLRF|Nrdp1	ring finger protein 41	protein-coding
mm_44527.1	chr5	24423517	24423538	-	1	NA	promoter-TSS (NM_007668)	promoter-TSS (NM_007668)	3	NM_007668	12568	Mm.298798	NM_007668	ENSMUSG00000028969	Cdk5	AW048668|Crk6	cyclin-dependent kinase 5	protein-coding
mm_120297.1	chr14	63138445	63138469	+	1	NA	exon (NM_007798, exon 7 of 10)	exon (NM_007798, exon 7 of 10)	15995	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_71331.1	chr8	45051501	45051550	+	1	NA	3' UTR (NM_001081286, exon 26 of 26)	3' UTR (NM_001081286, exon 26 of 26)	13893	NR_033588	434310	Mm.334512	NR_033588	ENSMUSG00000066158	AY512931	-	cDNA sequence AY512931	ncRNA
mm_36940.1	chr4	108638624	108638636	-	1	NA	TTS (NM_183300)	TTS (NM_183300)	18674	NM_177045	319965	Mm.151129	NM_177045	ENSMUSG00000028582	Cc2d1b	A830039B04Rik|Freud2	coiled-coil and C2 domain containing 1B	protein-coding
mm_617.1	chr1	40084734	40084749	+	1	NA	promoter-TSS (NM_010555)	promoter-TSS (NM_010555)	-27	NM_010555	16178	Mm.1349	NM_010555	ENSMUSG00000026073	Il1r2	CD121b|Il1r-2	interleukin 1 receptor, type II	protein-coding
mm_19.1	chr1	5083207	5083217	+	1	NA	5' UTR (NM_133826, exon 1 of 14)	5' UTR (NM_133826, exon 1 of 14)	126	NM_001310442	108664	Mm.27082	NM_133826	ENSMUSG00000033793	Atp6v1h	0710001F19Rik|AU022349|CGI-11|SFD|SFDalpha|SFDbeta|VMA13	ATPase, H+ transporting, lysosomal V1 subunit H	protein-coding
mm_162973.1	chr11	14703491	14703492	+	1	NA	Intergenic	Intergenic	104251	NM_001164166	432536	Mm.33646	NM_001164166	ENSMUSG00000084135	Pom121l12	1700054H16Rik	POM121 membrane glycoprotein-like 12	protein-coding
mm_6580.1	chr1	75219246	75219262	-	1	NA	promoter-TSS (NM_001313724)	promoter-TSS (NM_001313724)	40	NM_001313723	22145	Mm.1155	NM_009447	ENSMUSG00000026202	Tuba4a	M[a]4|Tuba4	tubulin, alpha 4A	protein-coding
mm_64547.1	chr7	144321384	144321437	+	1	NA	intron (NM_001113373, intron 7 of 15)	intron (NM_001113373, intron 7 of 15)	37025	NM_001081370	210274	Mm.483624	NM_001081370	ENSMUSG00000037541	Shank2	ProSAP1|mKIAA1022	SH3/ankyrin domain gene 2	protein-coding
mm_51943.1	chr6	91721719	91721740	+	1	NA	intron (NM_009320, intron 2 of 14)	intron (NM_009320, intron 2 of 14)	37662	NM_009320	21366	Mm.395650	NM_009320	ENSMUSG00000030096	Slc6a6	AA589629|C80501|Taut	solute carrier family 6 (neurotransmitter transporter, taurine), member 6	protein-coding
mm_49801.1	chr6	35997012	35997034	+	1	NA	Intergenic	MT2A|LTR|ERVL	-391061	NM_203491	243764	Mm.448632	NM_203491	ENSMUSG00000045613	Chrm2	AChR-M2|Chrm-2|M2	cholinergic receptor, muscarinic 2, cardiac	protein-coding
mm_83406.1	chr9	44799180	44799255	-	1	NA	promoter-TSS (NM_027865)	promoter-TSS (NM_027865)	-1	NM_027865	71687	Mm.41409	NM_027865	ENSMUSG00000002032	Tmem25	0610039J01Rik|AI429491	transmembrane protein 25	protein-coding
mm_159936.1	chr6	72306511	72306511	+	1	NA	intron (NM_147779, intron 4 of 11)	intron (NM_147779, intron 4 of 11)	1901	NM_147779	20388	Mm.46033	NM_147779	ENSMUSG00000056370	Sftpb	AI562151|SF-B|SP-B|Sftp-3|Sftp3	surfactant associated protein B	protein-coding
mm_118236.1	chr13	111509346	111509363	-	1	NA	Intergenic	B3A|SINE|B2	-19313	NM_001122963	73274	Mm.57286	NM_028487	ENSMUSG00000032745	Gpbp1	1700034P14Rik|AU019836|D230035M11Rik|Gpbp|mGPBP	GC-rich promoter binding protein 1	protein-coding
mm_88393.1	chr10	76531638	76531657	+	1	NA	promoter-TSS (NM_146006)	promoter-TSS (NM_146006)	42	NM_146006	16987	Mm.55075	NM_146006	ENSMUSG00000033105	Lss	2810025N20Rik|D10Ertd116e|Osc	lanosterol synthase	protein-coding
mm_70948.1	chr8	26847054	26847058	+	1	NA	Intergenic	Intergenic	-22633	NR_045904	72316	Mm.490534	NR_045904	ENSMUSG00000100335	2310008N11Rik	-	RIKEN cDNA 2310008N11 gene	ncRNA
mm_71018.1	chr8	33385827	33385894	+	1	NA	promoter-TSS (NM_001122822)	promoter-TSS (NM_001122822)	-333	NM_011721	22427	Mm.228805	NM_011721	ENSMUSG00000031583	Wrn	AI846146	Werner syndrome homolog (human)	protein-coding
mm_60082.1	chr7	34168637	34168648	+	1	NA	promoter-TSS (NM_016682)	promoter-TSS (NM_016682)	-113	NM_016682	50995	Mm.27560	NM_016682	ENSMUSG00000052997	Uba2	AA986091|Arx|Sae2|UBA1|Ubl1a2|Uble1b	ubiquitin-like modifier activating enzyme 2	protein-coding
mm_108312.1	chr12	79559045	79559052	+	1	NA	intron (NM_009014, intron 7 of 10)	intron (NM_009014, intron 7 of 10)	261697	NM_001252562	19363	Mm.341756	NM_009014	ENSMUSG00000059060	Rad51b	AI553500|R51H2|Rad51l1|mREC2	RAD51 paralog B	protein-coding
mm_5394.1	chr1	33621417	33621423	-	1	NA	intron (NM_008922, intron 7 of 13)	intron (NM_008922, intron 7 of 13)	48374	NM_008922	19076	Mm.27705	NM_008922	ENSMUSG00000026134	Prim2	AI323589	DNA primase, p58 subunit	protein-coding
mm_117158.1	chr13	61570112	61570135	-	1	NA	promoter-TSS (NM_054092)	promoter-TSS (NM_054092)	4	NM_026906	117066	Mm.485905	NM_026906	ENSMUSG00000074870	Cts3	1600000I23Rik	cathepsin 3	protein-coding
mm_34541.1	chr4	149518196	149518209	+	1	NA	promoter-TSS (NM_023465)	promoter-TSS (NM_023465)	-39	NM_023465	67087	Mm.299735	NM_023465	ENSMUSG00000028988	Ctnnbip1	1110008O09Rik|2310001I19Rik|AW457332|Catnbip1|Icat	catenin beta interacting protein 1	protein-coding
mm_79350.1	chr9	53771500	53771535	+	1	NA	promoter-TSS (NM_028060)	promoter-TSS (NM_028060)	-18	NM_028060	72022	Mm.26159	NM_028060	ENSMUSG00000042195	Slc35f2	1500009K05Rik|AU019213	solute carrier family 35, member F2	protein-coding
mm_54542.1	chr6	36743405	36743419	-	1	NA	exon (NM_008973, exon 3 of 5)	exon (NM_008973, exon 3 of 5)	67949	NM_008973	19242	Mm.279690	NM_008973	ENSMUSG00000029838	Ptn	HARP|HB-GAM|HBBN|HBGF-8|HBNF|OSF|Osf-1|Osf1	pleiotrophin	protein-coding
mm_147782.1	chr18	61624061	61624094	-	1	NA	Intergenic	Intergenic	-15576	NR_045420	545261	Mm.426593	NR_045420	ENSMUSG00000098098	Bvht	Braveheart|Gm20748	braveheart long non-coding RNA	ncRNA
mm_155706.1	chrX	95711687	95711712	+	1	NA	promoter-TSS (NM_001034907)	promoter-TSS (NM_001034907)	21	NM_001034907	547176	Mm.302708	NM_001034907	ENSMUSG00000035045	Zc3h12b	A130028J20Rik|CXorf32|Gm373	zinc finger CCCH-type containing 12B	protein-coding
mm_49942.1	chr6	39871510	39871520	+	1	NA	Intergenic	CpG	-60579	NM_001010930	14548	Mm.377071	NM_010270	ENSMUSG00000029918	Mrps33	AI841153|CGI-139|Gdap3|MRP-S33|PTD003	mitochondrial ribosomal protein S33	protein-coding
mm_148777.1	chr19	6108449	6108458	+	1	NA	intron (NM_001009546, intron 4 of 17)	intron (NM_001009546, intron 4 of 17)	2655	NM_001009546	381204	Mm.359041	NM_001009546	ENSMUSG00000054999	Naaladl1	Gm964|Naaladasel	N-acetylated alpha-linked acidic dipeptidase-like 1	protein-coding
mm_128090.1	chr15	27788248	27788258	-	1	NA	intron (NM_001081302, intron 34 of 56)	intron (NM_001081302, intron 34 of 56)	-106711	NM_001242423	223433	Mm.266485	NM_198301	ENSMUSG00000056069	Fam105a	9830126M18	family with sequence similarity 105, member A	protein-coding
mm_7878.1	chr1	133019411	133019419	-	1	NA	5' UTR (NM_008575, exon 2 of 12)	5' UTR (NM_008575, exon 2 of 12)	6001	NR_126506	17248	Mm.426531	NM_008575	ENSMUSG00000054387	Mdm4	4933417N07Rik|AA414968|AL023055|AU018793|AU021806|C85810|Mdmx	transformed mouse 3T3 cell double minute 4	protein-coding
mm_4484.1	chr1	173630848	173630882	+	1	NA	promoter-TSS (NM_175026)	promoter-TSS (NM_175026)	6	NM_175026	236312	Mm.447	NM_175026	ENSMUSG00000043263	Ifi209	4930422C14|AI447904|Ifix|Pyhin-1|Pyhin1	interferon activated gene 209	protein-coding
mm_40016.1	chr5	33112107	33112113	+	1	NA	intron (NM_019810, intron 1 of 14)	RLTR31D_MM|LTR|ERVK	7891	NM_019810	20537	Mm.25237	NM_019810	ENSMUSG00000011034	Slc5a1	Sglt1	solute carrier family 5 (sodium/glucose cotransporter), member 1	protein-coding
mm_38731.1	chr4	145240779	145240790	-	1	NA	intron (NM_011610, intron 1 of 9)	intron (NM_011610, intron 1 of 9)	6086	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_93707.1	chr10	118633486	118633508	-	1	NA	Intergenic	Intergenic	-76972	NR_104123	103214	Mm.30529	NR_104123		Tmevpg1	AI447422	Theiler's murine encephalomyelitis virus persistence candidate gene 1	ncRNA
mm_76259.1	chr8	83748176	83748180	-	1	NA	Intergenic	Intergenic	-6867	NM_001163031	26364	Mm.334648	NM_011925	ENSMUSG00000002885	Adgre5	AA409984|Cd97|TM7LN1	adhesion G protein-coupled receptor E5	protein-coding
mm_89595.1	chr10	95943439	95943443	+	1	NA	intron (NM_001001932, intron 1 of 28)	intron (NM_001001932, intron 1 of 28)	2778	NM_001001932	216238	Mm.210035	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding
mm_102836.1	chr11	69323737	69323765	-	1	NA	promoter-TSS (NM_001024206)	promoter-TSS (NM_001024206)	122	NM_172560	216846	Mm.28774	NM_172560	ENSMUSG00000032782	Cntrob	9830165K03Rik|Lip8|Nip2	centrobin, centrosomal BRCA2 interacting protein	protein-coding
mm_127078.1	chr15	97424557	97424572	+	1	NA	Intergenic	Intergenic	-177277	NM_001164602	105827	Mm.24005	NM_178114	ENSMUSG00000048218	Amigo2	AI415330|AMIGO-2|AW208913|Ali1	adhesion molecule with Ig like domain 2	protein-coding
mm_124357.1	chr14	105138376	105138383	-	1	NA	intron (NM_134077, intron 13 of 20)	intron (NM_134077, intron 13 of 20)	-23703	NR_040628	100502987	Mm.124957	NR_040628		Gm17066	-	predicted gene 17066	ncRNA
mm_123593.1	chr14	67708536	67708548	-	1	NA	intron (NM_001110162, intron 4 of 14)	intron (NM_001110162, intron 4 of 14)	7068	NM_001110162	108912	Mm.33831	NM_175384	ENSMUSG00000048922	Cdca2	2610311M19Rik|AI586158	cell division cycle associated 2	protein-coding
mm_85419.1	chr9	103480305	103480315	-	1	NA	promoter-TSS (NM_001002896)	promoter-TSS (NM_001002896)	18	NM_001002896	107993	Mm.335403	NM_001002896	ENSMUSG00000032556	Bfsp2	AI448593|CP49	beaded filament structural protein 2, phakinin	protein-coding
mm_153402.1	chr19	40509047	40509059	-	1	NA	intron (NM_009166, intron 1 of 23)	intron (NM_009166, intron 1 of 23)	4683	NM_178362	20411	Mm.210815	NM_009166	ENSMUSG00000025006	Sorbs1	2310065E01Rik|9530001P15Rik|CAP|SH3P12|Sh3d5|mKIAA1296	sorbin and SH3 domain containing 1	protein-coding
mm_136546.1	chr16	97962582	97962636	-	1	NA	promoter-TSS (NM_001081684)	promoter-TSS (NM_001081684)	13	NM_001081685	114565	Mm.474489	NM_175428	ENSMUSG00000046962	Zbtb21	5430437K12Rik|B430213I24Rik|Zfp295|Znf295|mKIAA1227	zinc finger and BTB domain containing 21	protein-coding
mm_78298.1	chr9	22421964	22421965	+	1	NA	intron (NM_026739, intron 1 of 6)	(T)n|Simple_repeat|Simple_repeat	10387	NM_026739	68283	Mm.280669	NM_026739	ENSMUSG00000036411	9530077C05Rik	1110003N12Rik|Kiaa0895|mKIAA0895	RIKEN cDNA 9530077C05 gene	protein-coding
mm_149639.1	chr19	17395030	17395037	+	1	NA	intron (NM_019437, intron 1 of 3)	intron (NM_019437, intron 1 of 3)	990	NM_019437	54391	Mm.7013	NM_019437	ENSMUSG00000024712	Rfk	0610038L10Rik|AF031381|KOI-4	riboflavin kinase	protein-coding
mm_20683.1	chr2	132578129	132578153	-	1	NA	5' UTR (NM_027096, exon 1 of 18)	5' UTR (NM_027096, exon 1 of 18)	107	NM_001291050	74182	Mm.211211	NM_027096	ENSMUSG00000027346	Gpcpd1	2310004G06Rik|2310032D16Rik|AU015213|Gde5|Prei4|mKIAA1434	glycerophosphocholine phosphodiesterase 1	protein-coding
mm_30816.1	chr4	21767156	21767201	+	1	NA	promoter-TSS (NM_029840)	promoter-TSS (NM_029840)	33	NM_029840	77032	Mm.87238	NM_029840	ENSMUSG00000028251	Tstd3	2610029I01Rik	thiosulfate sulfurtransferase (rhodanese)-like domain containing 3	protein-coding
mm_119459.1	chr14	47068963	47068983	+	1	NA	promoter-TSS (NM_001310544)	promoter-TSS (NM_001310544)	-4	NM_001310544	74480	Mm.214454	NM_028966	ENSMUSG00000021838	Samd4	1700024G08Rik|1700111L17Rik|4933436G17Rik|Samd4a|Smaug|Smaug1|sunk	sterile alpha motif domain containing 4	protein-coding
mm_74733.1	chr8	18741343	18741359	-	1	NA	5' UTR (NM_007426, exon 1 of 9)	5' UTR (NM_007426, exon 1 of 9)	211	NM_007426	11601	Mm.439874	NM_007426	ENSMUSG00000031465	Angpt2	Agpt2|Ang-2|Ang2	angiopoietin 2	protein-coding
mm_87975.1	chr10	63528385	63528387	+	1	NA	intron (NM_177612, intron 2 of 17)	intron (NM_177612, intron 2 of 17)	70875	NM_001164376	216033	Mm.444692	NM_177612	ENSMUSG00000060843	Ctnna3	4930429L08Rik|4933408A16|Catna3|Vr22	catenin (cadherin associated protein), alpha 3	protein-coding
mm_167782.1	chr9	119119661	119119666	+	1	NA	exon (NM_177117, exon 7 of 37)	exon (NM_177117, exon 7 of 37)	17185	NM_177117	320256	Mm.110648	NM_177117	ENSMUSG00000038060	Dlec1	D630005C06Rik	deleted in lung and esophageal cancer 1	protein-coding
mm_36785.1	chr4	103012154	103012165	-	1	NA	promoter-TSS (NR_028391)	promoter-TSS (NR_028391)	-194	NR_028391	100473	Mm.393171	NR_028391	ENSMUSG00000085041	BB031773	-	expressed sequence BB031773	ncRNA
mm_30611.1	chr4	6702139	6702145	+	1	NA	intron (NM_145711, intron 6 of 8)	Lx8|LINE|L1	-247871	NM_010945	18201	Mm.3059	NM_010945	ENSMUSG00000028245	Nsmaf	AA959567|C630007J05|Fan	neutral sphingomyelinase (N-SMase) activation associated factor	protein-coding
mm_37792.1	chr4	130519834	130519844	-	1	NA	Intergenic	Intergenic	54197	NM_025998	67149	Mm.423029	NM_025998	ENSMUSG00000078532	Nkain1	2610200G18Rik|2810426C15Rik	Na+/K+ transporting ATPase interacting 1	protein-coding
mm_33290.1	chr4	128884099	128884114	+	1	NA	promoter-TSS (NM_178110)	promoter-TSS (NM_178110)	-34	NM_178110	67525	Mm.30653	NM_178110	ENSMUSG00000041000	Trim62	6330414G21Rik|AI450348|Dear1	tripartite motif-containing 62	protein-coding
mm_22269.1	chr2	178416630	178416639	-	1	NA	5' UTR (NM_001081289, exon 2 of 4)	5' UTR (NM_001081289, exon 2 of 4)	2100	NM_001081289	71532	Mm.40216	NM_001081289	ENSMUSG00000070476	Fam217b	9030418K01Rik|AI851938	family with sequence similarity 217, member B	protein-coding
mm_56738.1	chr6	115762323	115762344	-	1	NA	5' UTR (NM_001168257, exon 1 of 11)	5' UTR (NM_001168257, exon 1 of 11)	133	NM_001168256	94346	Mm.29739	NM_144805	ENSMUSG00000059900	Tmem40	9030407H20Rik|AV091463|W64236	transmembrane protein 40	protein-coding
mm_56755.1	chr6	116073122	116073148	-	1	NA	intron (NM_177412, intron 3 of 5)	intron (NM_177412, intron 3 of 5)	-78130	NM_026376	67784	Mm.3085	NM_026376	ENSMUSG00000030123	Plxnd1	6230425C21Rik|b2b1863Clo|b2b553Clo	plexin D1	protein-coding
mm_93388.1	chr10	107123586	107123673	-	1	NA	promoter-TSS (NM_001142804)	promoter-TSS (NM_001142804)	35	NM_001142804	380660	Mm.336072	NM_198636	ENSMUSG00000035948	Acss3	8430416H19Rik|Gm874	acyl-CoA synthetase short-chain family member 3	protein-coding
mm_89534.1	chr10	94514951	94514964	+	1	NA	promoter-TSS (NM_172051)	promoter-TSS (NM_172051)	100	NM_172051	319880	Mm.23047	NM_172051	ENSMUSG00000020023	Tmcc3	AW488095|C630016B22Rik|C88213|Tmcc1	transmembrane and coiled coil domains 3	protein-coding
mm_108304.1	chr12	79327240	79327250	+	1	NA	exon (NM_009014, exon 7 of 11)	exon (NM_009014, exon 7 of 11)	29894	NM_001252562	19363	Mm.341756	NM_009014	ENSMUSG00000059060	Rad51b	AI553500|R51H2|Rad51l1|mREC2	RAD51 paralog B	protein-coding
mm_96768.1	chr11	69921997	69922006	+	1	NA	promoter-TSS (NM_001166595)	promoter-TSS (NM_001166595)	-43	NM_001166593	276770	Mm.18026	NM_181582	ENSMUSG00000078812	Eif5a	AA410058|D19Wsu54e|Eif4d|Eif5a1|eIF-4D|eIF-5A|eIF-5A-1|eIF-5A1	eukaryotic translation initiation factor 5A	protein-coding
mm_9084.1	chr1	168431910	168431982	-	1	NA	5' UTR (NM_001291509, exon 1 of 7)	5' UTR (NM_001291509, exon 1 of 7)	223	NM_001291508	18514	Mm.43358	NM_008783	ENSMUSG00000052534	Pbx1	2310056B04Rik|D230003C07Rik|Pbx-1	pre B cell leukemia homeobox 1	protein-coding
mm_66723.1	chr7	46115985	46115995	-	1	NA	intron (NM_011510, intron 26 of 38)	intron (NM_011510, intron 26 of 38)	-15226	NM_001204411	16514	Mm.333863	NM_010602	ENSMUSG00000096146	Kcnj11	Kir6.2|mBIR	potassium inwardly rectifying channel, subfamily J, member 11	protein-coding
mm_11247.1	chr2	29890521	29890531	+	1	NA	intron (NM_013615, intron 1 of 16)	CpG	463	NM_013615	18286	Mm.330116	NM_013615	ENSMUSG00000026790	Odf2	AI848335|MMTEST29	outer dense fiber of sperm tails 2	protein-coding
mm_95746.1	chr11	54861016	54861026	+	1	NA	promoter-TSS (NM_029327)	promoter-TSS (NM_029327)	-430	NM_029327	75530	Mm.83578	NM_029327	ENSMUSG00000020268	Lyrm7	1700024C24Rik|9330147L21Rik	LYR motif containing 7	protein-coding
mm_25939.1	chr3	131473068	131473071	+	1	NA	Intergenic	Intergenic	-91699	NM_001289479	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_45949.1	chr5	90365231	90365253	-	1	NA	intron (NM_198010, intron 1 of 32)	CpG	943	NM_030886	81702	Mm.245522	NM_030886	ENSMUSG00000055204	Ankrd17	4933425K22Rik|A130069E23Rik|A930008M01|AA407558|AA516750|AU040470|Foe|Gtar|Mask|mKIAA0697	ankyrin repeat domain 17	protein-coding
mm_94422.1	chr11	5878369	5878377	+	1	NA	promoter-TSS (NM_008894)	promoter-TSS (NM_008894)	-117	NM_008894	18972	Mm.35788	NM_008894	ENSMUSG00000020471	Pold2	50kDa|p50|po1D2	polymerase (DNA directed), delta 2, regulatory subunit	protein-coding
mm_65410.1	chr7	25245001	25245015	-	1	NA	exon (NM_010155, exon 4 of 4)	exon (NM_010155, exon 4 of 4)	5750	NM_010155	13875	Mm.8068	NM_010155	ENSMUSG00000040857	Erf	-	Ets2 repressor factor	protein-coding
mm_26195.1	chr3	138526175	138526178	+	1	NA	promoter-TSS (NM_007917)	promoter-TSS (NM_007917)	-15	NM_007917	13684	Mm.3941	NM_007917	ENSMUSG00000028156	Eif4e	EG668879|Eif4e-ps|If4e|eIF-4E	eukaryotic translation initiation factor 4E	protein-coding
mm_171557.1	chr4	147132129	147132129	+	1	NA	Intergenic	Intergenic	-43737	NM_001039209	195531	Mm.270762	NM_001039209	ENSMUSG00000078496	Zfp982	Gm13152|OTTMUSG00000010671	zinc finger protein 982	protein-coding
mm_28738.1	chr3	95737657	95737681	-	1	NA	exon (NM_007899, exon 5 of 11)	exon (NM_007899, exon 5 of 11)	1900	NM_007899	13601	Mm.3433	NM_007899	ENSMUSG00000028108	Ecm1	AI663821|p85	extracellular matrix protein 1	protein-coding
mm_91853.1	chr10	59221470	59221518	-	1	NA	promoter-TSS (NM_172939)	promoter-TSS (NM_172939)	353	NM_001024911	103080	Mm.346842	NM_001024910	ENSMUSG00000019917	Sept10	4921515A04Rik|9430099J10Rik|AA408298|AI874685	septin 10	protein-coding
mm_99293.1	chr11	101330833	101330858	+	1	NA	5' UTR (NM_009675, exon 1 of 4)	5' UTR (NM_009675, exon 1 of 4)	239	NM_009675	11754	Mm.67281	NM_009675	ENSMUSG00000019326	Aoc3	SSAO|VAP1	amine oxidase, copper containing 3	protein-coding
mm_157539.1	chrX	51205617	51205638	-	1	NA	intron (NM_134163, intron 1 of 7)	CpG	363	NM_001310515	171170	Mm.295324	NM_134163	ENSMUSG00000036109	Mbnl3	A530038J18Rik|AI661274|CHCR|E430034C16Rik|MBLX|MBLX39|MBXL	muscleblind-like 3 (Drosophila)	protein-coding
mm_3868.1	chr1	160989495	160989512	+	1	NA	exon (NM_080844, exon 3 of 8)	exon (NM_080844, exon 3 of 8)	10897	NM_080844	11905	Mm.260770	NM_080844	ENSMUSG00000026715	Serpinc1	AI114908|ATIII|At-3|At3	serine (or cysteine) peptidase inhibitor, clade C (antithrombin), member 1	protein-coding
mm_159194.1	chr2	119167723	119167723	+	1	NA	promoter-TSS (NM_177157)	promoter-TSS (NM_177157)	-65	NM_177157	320415	Mm.86373	NM_177157	ENSMUSG00000046814	Gchfr	2010323F13Rik|GFRP|P35	GTP cyclohydrolase I feedback regulator	protein-coding
mm_154609.1	chrX	7651883	7651901	+	1	NA	3' UTR (NM_009305, exon 7 of 7)	3' UTR (NM_009305, exon 7 of 7)	-5487	NM_001290624	54630	Mm.232232	NM_175097	ENSMUSG00000031145	Prickle3	Lmo6|Sfc16	prickle planar cell polarity protein 3	protein-coding
mm_81057.1	chr9	106147968	106147983	+	1	NA	Intergenic	Intergenic	-6149	NR_029549	387153		NR_029549	ENSMUSG00000065407	Mir135a-1	Mir135a01|Mirn135|Mirn135a-1|mir-135a-1	microRNA 135a-1	ncRNA
mm_85234.1	chr9	98033216	98033225	-	1	NA	promoter-TSS (NM_022319)	promoter-TSS (NM_022319)	-53	NM_022319	64085	Mm.440903	NM_022319	ENSMUSG00000032452	Clstn2	2900042C18Rik|AI448973|CSTN2|Cs2|Cst-2|mKIAA4134	calsyntenin 2	protein-coding
mm_50559.1	chr6	49047888	49047900	+	1	NA	exon (NM_053110, exon 6 of 11)	exon (NM_053110, exon 6 of 11)	11376	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_128400.1	chr15	44422671	44422671	-	1	NA	intron (NM_001113554, intron 1 of 9)	intron (NM_001113554, intron 1 of 9)	-5440	NM_175009	223527	Mm.291828	NM_175009	ENSMUSG00000022338	Eny2	1810057B09Rik|6720481I12|DC6|Ey2	enhancer of yellow 2 homolog (Drosophila)	protein-coding
mm_34669.1	chr4	150920155	150920197	+	1	NA	promoter-TSS (NM_001077508)	promoter-TSS (NM_001077508)	21	NM_001077508	21942	Mm.244187	NM_011612	ENSMUSG00000028965	Tnfrsf9	4-1BB|A930040I11Rik|AA408498|AI325004|CDw137|Cd137|ILA|Ly63	tumor necrosis factor receptor superfamily, member 9	protein-coding
mm_130120.1	chr15	89523691	89523710	-	1	NA	intron (NM_021423, intron 10 of 21)	intron (NM_021423, intron 10 of 21)	23843	NM_021423	58234	Mm.146855	NM_021423	ENSMUSG00000022623	Shank3	AI841104|SHANK3c-3|SHANK3c-4|Shank3b	SH3/ankyrin domain gene 3	protein-coding
mm_102278.1	chr11	55395558	55395566	-	1	NA	3' UTR (NM_009242, exon 10 of 10)	3' UTR (NM_009242, exon 10 of 10)	24518	NM_009242	20692	Mm.291442	NM_009242	ENSMUSG00000018593	Sparc	BM-40|ON	secreted acidic cysteine rich glycoprotein	protein-coding
mm_58528.1	chr7	4149323	4149357	+	1	NA	exon (NM_175529, exon 1 of 1)	exon (NM_175529, exon 1 of 1)	532	NM_175529	243813	Mm.347643	NM_175529	ENSMUSG00000043432	Leng9	9530024C23Rik|F630035L11Rik	leukocyte receptor cluster (LRC) member 9	protein-coding
mm_131272.1	chr16	11008465	11008493	+	1	NA	promoter-TSS (NR_040518)	promoter-TSS (NR_040518)	-419	NR_040518	100043147	Mm.489001	NR_040518	ENSMUSG00000097056	Gm4262	-	predicted gene 4262	ncRNA
mm_168813.1	chr12	21778894	21778902	-	1	NA	Intergenic	CpG	-361462	NM_011739	22630	Mm.289630	NM_011739	ENSMUSG00000076432	Ywhaq	2700028P07Rik|AA409740|AU021156|R74690	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide	protein-coding
mm_74258.1	chr8	124892333	124892337	+	1	NA	3' UTR (NM_198103, exon 1 of 1)	3' UTR (NM_198103, exon 1 of 1)	5370	NM_198103	102058	Mm.347360	NM_198103	ENSMUSG00000074030	Exoc8	AI414418|EXO84|Exo84p|R74783|SEC84	exocyst complex component 8	protein-coding
mm_164685.1	chr17	47580718	47580732	+	1	NA	intron (NM_001081635, intron 2 of 6)	B1_Mus2|SINE|Alu	-12742	NM_007632	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_121496.1	chr14	121878742	121878750	+	1	NA	promoter-TSS (NR_131002)	promoter-TSS (NR_131002)	140	NM_026861	68889	Mm.441151	NM_026861	ENSMUSG00000041765	Ubac2	1190008A14Rik|AW554959|Phgdhl1	ubiquitin associated domain containing 2	protein-coding
mm_165426.1	chr2	152518237	152518243	+	1	NA	promoter-TSS (NM_001037502)	promoter-TSS (NM_001037502)	-15	NM_001037502	545475	Mm.389378	NM_001037502	ENSMUSG00000074679	Defb28	Gm1635|OTTMUSG00000015852	defensin beta 28	protein-coding
mm_105266.1	chr11	102361446	102361457	-	1	NA	5' UTR (NM_011403, exon 2 of 20)	5' UTR (NM_011403, exon 2 of 20)	3830	NM_011403	20533	Mm.7248	NM_011403	ENSMUSG00000006574	Slc4a1	Ae1|CD233|Empb3|l11Jus51	solute carrier family 4 (anion exchanger), member 1	protein-coding
mm_86717.1	chr10	19009657	19009677	+	1	NA	intron (NM_001166402, intron 1 of 7)	intron (NM_001166402, intron 1 of 7)	2296	NM_001166402	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_52648.1	chr6	117179656	117179661	+	1	NA	3' UTR (NM_001012477, exon 4 of 4)	3' UTR (NM_001012477, exon 4 of 4)	11123	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_13146.1	chr2	92189775	92189817	+	1	NA	intron (NM_001109691, intron 2 of 18)	BC1_Mm|scRNA|scRNA	-2181	NR_035480	100316756		NR_035480	ENSMUSG00000088639	Mir1955	mir-1955|mmu-mir-1955	microRNA 1955	ncRNA
mm_96448.1	chr11	67532449	67532476	+	1	NA	promoter-TSS (NM_008088)	promoter-TSS (NM_008088)	-536	NM_008088	14457	Mm.40338	NM_008088	ENSMUSG00000033066	Gas7	AW124766|B230343A10Rik|Gas7-cb	growth arrest specific 7	protein-coding
mm_78905.1	chr9	44772976	44772980	+	1	NA	promoter-TSS (NM_023831)	promoter-TSS (NM_023831)	-31	NM_023831	76568	Mm.278597	NM_023831	ENSMUSG00000002031	Ift46	1500035H01Rik|AA408110|AI663846|R75047|c11orf2	intraflagellar transport 46	protein-coding
mm_82126.1	chr9	123509261	123509287	+	1	NA	intron (NM_013860, intron 2 of 7)	intron (NM_013860, intron 2 of 7)	-20608	NM_030692	83493	Mm.273671	NM_030692	ENSMUSG00000025240	Sacm1l	SAC1|Sac1p|mKIAA0851	SAC1 suppressor of actin mutations 1-like (yeast)	protein-coding
mm_47318.1	chr5	122460112	122460148	-	1	NA	exon (NM_009722, exon 15 of 21)	exon (NM_009722, exon 15 of 21)	37686	NM_019805	56317	Mm.37341	NM_019805	ENSMUSG00000029466	Anapc7	APC7|AW545589	anaphase promoting complex subunit 7	protein-coding
mm_110899.1	chr12	75631372	75631380	-	1	NA	non-coding (NR_038063, exon 1 of 1)	non-coding (NR_038063, exon 1 of 1)	373	NR_038063	665931	Mm.341719	NR_038063		Rplp2-ps1	Gm7852	ribosomal protein, large P2, pseudogene 1	pseudo
mm_41582.1	chr5	93175353	93175355	+	1	NA	TTS (NM_001009818)	TTS (NM_001009818)	31141	NM_017367	12453	Mm.250419	NM_017367	ENSMUSG00000063015	Ccni	-	cyclin I	protein-coding
mm_171905.1	chr5	45658639	45658650	+	1	NA	Intergenic	RLTR10D2|LTR|ERVK	11064	NR_073433	69788	Mm.381492	NR_073433	ENSMUSG00000104986	1600023N17Rik	AV119442	RIKEN cDNA 1600023N17 gene	ncRNA
mm_90866.1	chr10	8886117	8886125	-	1	NA	promoter-TSS (NM_175155)	promoter-TSS (NM_175155)	-51	NM_175155	70097	Mm.338275	NM_175155	ENSMUSG00000015305	Sash1	1100001C18Rik|2500002E12Rik|A330076K04Rik|mKIAA0790	SAM and SH3 domain containing 1	protein-coding
mm_33533.1	chr4	130932396	130932410	+	1	NA	intron (NM_010686, intron 7 of 7)	RMER1C|Other|Other	-11982	NM_010769	17180	Mm.271796	NM_010769	ENSMUSG00000040533	Matn1	CMP|Crtm|Mat1|matrilin-1	matrilin 1, cartilage matrix protein	protein-coding
mm_127473.1	chr15	101273093	101273100	+	1	NA	exon (NM_010444, exon 6 of 7)	exon (NM_010444, exon 6 of 7)	6250	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_76652.1	chr8	93191871	93191882	-	1	NA	intron (NM_053200, intron 3 of 13)	(GA)n|Simple_repeat|Simple_repeat	5928	NM_053200	104158	Mm.292803	NM_053200	ENSMUSG00000056973	Ces1d	Ces3|TGH	carboxylesterase 1D	protein-coding
mm_111661.1	chr12	103326927	103326929	-	1	NA	intron (NM_023049, intron 7 of 9)	intron (NM_023049, intron 7 of 9)	11969	NM_001195726	100504156	Mm.425749	NM_001195726	ENSMUSG00000096753	Fam181a	EG544888	family with sequence similarity 181, member A	protein-coding
mm_38965.1	chr4	150902074	150902086	-	1	NA	intron (NM_020569, intron 5 of 6)	intron (NM_020569, intron 5 of 6)	7841	NM_020569	57320	Mm.277349	NM_020569	ENSMUSG00000028964	Park7	DJ-1|Dj1	Parkinson disease (autosomal recessive, early onset) 7	protein-coding
mm_137638.1	chr17	28412476	28412477	+	1	NA	intron (NM_010220, intron 6 of 10)	intron (NM_010220, intron 6 of 10)	-47333	NM_021478	22157	Mm.42102	NM_021478	ENSMUSG00000037446	Tulp1	Tulp1l	tubby like protein 1	protein-coding
mm_34579.1	chr4	150119339	150119349	+	1	NA	promoter-TSS (NM_019741)	promoter-TSS (NM_019741)	0	NM_019741	56485	Mm.260220	NM_019741	ENSMUSG00000028976	Slc2a5	AI526984|Glut5|Slc5a	solute carrier family 2 (facilitated glucose transporter), member 5	protein-coding
mm_127757.1	chr15	103503251	103503259	+	1	NA	5' UTR (NM_008800, exon 1 of 16)	5' UTR (NM_008800, exon 1 of 16)	221	NM_008800	18574	Mm.390792	NM_008800	ENSMUSG00000022489	Pde1b	Pde1b1	phosphodiesterase 1B, Ca2+-calmodulin dependent	protein-coding
mm_88264.1	chr10	73947027	73947071	+	1	NA	5' UTR (NM_001142743, exon 2 of 35)	5' UTR (NM_001142743, exon 2 of 35)	125182	NM_001142735	11994	Mm.338933	NM_023115	ENSMUSG00000052613	Pcdh15	BB078305|ENSMUSG00000046980|Gm9815|Ush1f|av|nmf19|roda	protocadherin 15	protein-coding
mm_77557.1	chr8	123318554	123318579	-	1	NA	promoter-TSS (NM_016925)	promoter-TSS (NM_016925)	10	NM_016925	14087	Mm.6536	NM_016925	ENSMUSG00000032815	Fanca	AW208693|FACA	Fanconi anemia, complementation group A	protein-coding
mm_3958.1	chr1	164115320	164115330	+	1	NA	promoter-TSS (NM_011347)	promoter-TSS (NM_011347)	61	NM_011347	20344	Mm.3337	NM_011347	ENSMUSG00000026580	Selp	CD62P|GMP-140|Grmp|LECAM3|PADGEM	selectin, platelet	protein-coding
mm_143136.1	chr17	57218193	57218197	-	1	NA	promoter-TSS (NR_105944)	promoter-TSS (NR_105944)	-967	NR_105944	102465591		NR_105944	ENSMUSG00000099066	Mir6978	Gm27858|mmu-mir-6978	microRNA 6978	ncRNA
mm_155900.1	chrX	101655551	101655560	+	1	NA	intron (NM_139144, intron 4 of 21)	intron (NM_139144, intron 4 of 21)	15337	NM_001290535	108155	Mm.487332	NM_139144	ENSMUSG00000034160	Ogt	1110038P24Rik|4831420N21Rik|AI115525|Ogtl	O-linked N-acetylglucosamine (GlcNAc) transferase (UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase)	protein-coding
mm_64542.1	chr7	144264106	144264112	+	1	NA	intron (NM_001113373, intron 5 of 15)	MIRc|SINE|MIR	-20276	NM_001081370	210274	Mm.483624	NM_001081370	ENSMUSG00000037541	Shank2	ProSAP1|mKIAA1022	SH3/ankyrin domain gene 2	protein-coding
mm_161062.1	chr12	70871501	70871501	+	1	NA	intron (NM_028127, intron 2 of 13)	L1MA8|LINE|L1	45987	NM_028127	319710	Mm.2962	NM_028127	ENSMUSG00000048285	Frmd6	2610019M19Rik|4930488L10Rik|AW212977|Willin	FERM domain containing 6	protein-coding
mm_131554.1	chr16	18028668	18028696	+	1	NA	Intergenic	Intergenic	-24178	NM_010047	13353	Mm.27155	NM_010047	ENSMUSG00000003531	Dgcr6	-	DiGeorge syndrome critical region gene 6	protein-coding
mm_108747.1	chr12	88794996	88795007	+	1	NA	5' UTR (NM_001198587, exon 1 of 20)	5' UTR (NM_001198587, exon 1 of 20)	497	NM_001198587	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding
mm_5555.1	chr1	38665006	38665012	-	1	NA	Intergenic	Intergenic	-37765	NM_001290814	16764	Mm.336679	NM_010678	ENSMUSG00000037138	Aff3	3222402O04Rik|A730046J16|LAF-4|Laf4	AF4/FMR2 family, member 3	protein-coding
mm_116382.1	chr13	41079547	41079557	-	1	NA	intron (NM_001145802, intron 1 of 11)	CpG	154	NM_001145803	17152	Mm.8149	NM_008547	ENSMUSG00000021363	Mak	A930010O05Rik	male germ cell-associated kinase	protein-coding
mm_18705.1	chr2	71867552	71867584	-	1	NA	intron (NR_039557, intron 3 of 3).2	intron (NR_039557, intron 3 of 3).2	-5656	NM_172665	228026	Mm.34411	NM_172665	ENSMUSG00000006494	Pdk1	B830012B01|D530020C15Rik	pyruvate dehydrogenase kinase, isoenzyme 1	protein-coding
mm_78999.1	chr9	45407120	45407129	+	1	NA	intron (NM_007503, intron 1 of 5)	intron (NM_007503, intron 1 of 5)	1047	NM_007503	11936	Mm.22742	NM_007503	ENSMUSG00000059412	Fxyd2	Atp1g1	FXYD domain-containing ion transport regulator 2	protein-coding
mm_68880.1	chr7	126447672	126447679	-	1	NA	exon (NM_007504, exon 18 of 23)	exon (NM_007504, exon 18 of 23)	15398	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_74586.1	chr8	11354302	11354323	-	1	NA	exon (NM_009932, exon 4 of 48)	exon (NM_009932, exon 4 of 48)	-41486	NM_009931	12826	Mm.738	NM_009931	ENSMUSG00000031502	Col4a1	Bru|Col4a-1|Raw|Svc	collagen, type IV, alpha 1	protein-coding
mm_92982.1	chr10	86694010	86694024	-	1	NA	exon (NM_011631, exon 13 of 18)	exon (NM_011631, exon 13 of 18)	8490	NR_015572	66263	Mm.392261	NR_015572		1810014B01Rik	-	RIKEN cDNA 1810014B01 gene	pseudo
mm_160510.1	chr9	20727967	20727967	-	1	NA	intron (NM_173777, intron 1 of 5)	CpG	247	NM_173777	244723	Mm.293552	NM_173777	ENSMUSG00000032172	Olfm2	A030009A06Rik	olfactomedin 2	protein-coding
mm_100388.1	chr11	119375862	119375890	+	1	NA	intron (NM_178743, intron 12 of 16)	intron (NM_178743, intron 12 of 16)	-14596	NR_035453	100316690		NR_035453	ENSMUSG00000088015	Mir1932	mir-1932|mmu-mir-1932	microRNA 1932	ncRNA
mm_12869.1	chr2	83848754	83848765	+	1	NA	intron (NM_175514, intron 1 of 7)	intron (NM_175514, intron 1 of 7)	36031	NM_175514	241520	Mm.330351	NM_175514	ENSMUSG00000048388	Fam171b	D430039N05Rik	family with sequence similarity 171, member B	protein-coding
mm_137464.1	chr17	26624179	26624188	+	1	NA	intron (NM_026170, intron 3 of 9)	intron (NM_026170, intron 3 of 9)	-52213	NM_025272	11974	Mm.22602	NM_025272	ENSMUSG00000015575	Atp6v0e	Atp6k|Atp6v0e1|M9.2	ATPase, H+ transporting, lysosomal V0 subunit E	protein-coding
mm_144611.1	chr18	32558471	32558476	+	1	NA	intron (NM_001048207, intron 1 of 2)	intron (NM_001048207, intron 1 of 2)	1561	NM_001347610	71683	Mm.292145	NM_027863	ENSMUSG00000090523	Gypc	0610037F22Rik|Cd236r	glycophorin C	protein-coding
mm_38724.1	chr4	145234917	145234925	-	1	NA	intron (NM_011610, intron 1 of 9)	intron (NM_011610, intron 1 of 9)	11949	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_78488.1	chr9	32699891	32699897	+	1	NA	intron (NM_011808, intron 1 of 7)	MIR|SINE|MIR	3852	NM_001038642	23871	Mm.292415	NM_011808	ENSMUSG00000032035	Ets1	AI196000|AI448617|D230050P06|Ets-1|Tpl1|vs	E26 avian leukemia oncogene 1, 5' domain	protein-coding
mm_117188.1	chr13	63563068	63563084	-	1	NA	intron (NM_001328514, intron 2 of 23)	intron (NM_001328514, intron 2 of 23)	2659	NM_008957	19206	Mm.228798	NM_008957	ENSMUSG00000021466	Ptch1	A230106A15Rik|Ptc|Ptc1|Ptch|mes	patched 1	protein-coding
mm_15752.1	chr2	164237804	164237812	+	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	533	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_112487.1	chr13	6009617	6009621	+	1	NA	Intergenic	Intergenic	148130	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_23902.1	chr3	83031837	83031855	+	1	NA	exon (NM_010196, exon 5 of 5)	exon (NM_010196, exon 5 of 5)	5693	NM_001111048	14161	Mm.88793	NM_010196	ENSMUSG00000028001	Fga	ENSMUSG00000059807|Fib	fibrinogen alpha chain	protein-coding
mm_13813.1	chr2	119174553	119174563	+	1	NA	promoter-TSS (NM_001039223)	promoter-TSS (NM_001039223)	49	NM_001039223	623781	Mm.389344	NM_001039223	ENSMUSG00000055926	Gm14137	OTTMUSG00000015762	predicted gene 14137	protein-coding
mm_144036.1	chr17	90088344	90088373	-	1	NA	promoter-TSS (NM_001347419)	promoter-TSS (NM_001347419)	10	NM_001346962	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_54103.1	chr6	16898310	16898318	-	1	NA	5' UTR (NM_031198, exon 1 of 7)	5' UTR (NM_031198, exon 1 of 7)	127	NM_031198	21426	Mm.36217	NM_031198	ENSMUSG00000029553	Tfec	BB107417|Tcfec|bHLHe34	transcription factor EC	protein-coding
mm_68192.1	chr7	104369827	104369837	-	1	NA	Intergenic	Intergenic	-11186	NM_175648	244183	Mm.347647	NM_175648	ENSMUSG00000052749	Trim30b	A530023O14Rik|Trim30-1	tripartite motif-containing 30B	protein-coding
mm_173046.1	chrX	118584347	118584358	-	1	NA	Intergenic	RLTR9D|LTR|ERVK	-103615	NM_001142750	100039551	Mm.272850	NM_001142750	ENSMUSG00000100194	Tgif2lx2	-	TGFB-induced factor homeobox 2-like, X-linked 2	protein-coding
mm_144061.1	chr17	90789919	90789921	-	1	NA	intron (NM_001346957, intron 3 of 18)	MIR|SINE|MIR	3556	NR_136930	102634634		NR_136930		Gm20491	-	enolase 1, alpha non-neuron pseudogene	pseudo
mm_110774.1	chr12	70347499	70347513	-	1	NA	5' UTR (NM_001110203, exon 1 of 9)	5' UTR (NM_001110203, exon 1 of 9)	108	NM_001286386	94090	Mm.184012	NM_053167	ENSMUSG00000021071	Trim9	-	tripartite motif-containing 9	protein-coding
mm_88248.1	chr10	72671375	72671387	+	1	NA	intron (NM_001293683, intron 7 of 7)	intron (NM_001293683, intron 7 of 7)	16535	NM_001293683	52696	Mm.62876	NM_025635	ENSMUSG00000019923	Zwint	2010007E07Rik|2600001N01Rik|D10Ertd749e|Zwint-1	ZW10 interactor	protein-coding
mm_9835.1	chr1	184034003	184034016	-	1	NA	promoter-TSS (NM_028516)	promoter-TSS (NM_028516)	-11	NM_028516	73363	Mm.50115	NM_028516	ENSMUSG00000044854	1700056E22Rik	-	RIKEN cDNA 1700056E22 gene	protein-coding
mm_71397.1	chr8	46163785	46163800	+	1	NA	Intergenic	CpG	-5764	NM_025747	66756	Mm.133623	NM_025747	ENSMUSG00000031631	Cfap97	1110068E21Rik|4933411K20Rik|AW049273|Kiaa1430|mKIAA1430	cilia and flagella associated protein 97	protein-coding
mm_63217.1	chr7	126272848	126272858	+	1	NA	5' UTR (NM_145587, exon 1 of 4)	5' UTR (NM_145587, exon 1 of 4)	234	NM_145587	104175	Mm.29660	NM_145587	ENSMUSG00000042978	Sbk1	Sbk	SH3-binding kinase 1	protein-coding
mm_17861.1	chr2	34821619	34821630	-	1	NA	intron (NM_001164768, intron 1 of 5)	RMER1A|Other|Other	1557	NM_001164768	30050	Mm.4465	NM_013890	ENSMUSG00000035949	Fbxw2	2700071L08Rik|FBW2|Fwd2|MD6	F-box and WD-40 domain protein 2	protein-coding
mm_90953.1	chr10	13193070	13193076	-	1	NA	promoter-TSS (NM_181470)	promoter-TSS (NM_181470)	64	NM_181470	353258	Mm.117581	NM_181470	ENSMUSG00000019814	Ltv1	2610020N02Rik	LTV1 ribosome biogenesis factor	protein-coding
mm_86508.1	chr10	7629322	7629335	+	1	NA	TTS (NM_008786)	TTS (NM_008786)	-34043	NR_030698	320642	Mm.398806	NR_030698		A630066F11Rik	-	RIKEN cDNA A630066F11 gene	ncRNA
mm_73809.1	chr8	117340536	117340550	+	1	NA	intron (NM_001163262, intron 1 of 20)	intron (NM_001163262, intron 1 of 20)	-8627	NM_028941	74440	Mm.233181	NM_028941	ENSMUSG00000034390	Cmip	4933407C03Rik|5830471E12Rik|AI314065|AI464126	c-Maf inducing protein	protein-coding
mm_8409.1	chr1	151947321	151947325	-	1	NA	intron (NM_197990, intron 3 of 5)	intron (NM_197990, intron 3 of 5)	142997	NM_197990	69399	Mm.278031	NM_197990	ENSMUSG00000032666	1700025G04Rik	2610510E02Rik|2900042O04Rik|ENSMUSG00000073540	RIKEN cDNA 1700025G04 gene	protein-coding
mm_151981.1	chr19	5831254	5831420	-	1	NA	non-coding (NR_131212, exon 1 of 1)	non-coding (NR_131212, exon 1 of 1)	14141	NR_131212	66961	Mm.281895	NR_003513	ENSMUSG00000092274	Neat1	2310043N10Rik|VINC	nuclear paraspeckle assembly transcript 1 (non-protein coding)	ncRNA
mm_28765.1	chr3	95892829	95892845	-	1	NA	promoter-TSS (NM_153513)	promoter-TSS (NM_153513)	-832	NM_153513	229600	Mm.89556	NM_153513	ENSMUSG00000038543	BC028528	L259	cDNA sequence BC028528	protein-coding
mm_107027.1	chr12	12993309	12993341	+	1	NA	Intergenic	Intergenic	-51489	NM_008709	18109	Mm.16469	NM_008709	ENSMUSG00000037169	Mycn	N-myc|Nmyc|Nmyc-1|Nmyc1|bHLHe37|c-nmyc	v-myc avian myelocytomatosis viral related oncogene, neuroblastoma derived	protein-coding
mm_126044.1	chr15	76904861	76904871	+	1	NA	exon (NM_012053, exon 4 of 6)	exon (NM_012053, exon 4 of 6)	795	NM_012053	26961	Mm.30066	NM_012053	ENSMUSG00000003970	Rpl8	-	ribosomal protein L8	protein-coding
mm_48175.1	chr5	137300008	137300026	-	1	NA	exon (NM_031405, exon 7 of 20)	exon (NM_031405, exon 7 of 20)	-3329	NR_106003	102465627		NR_106003	ENSMUSG00000098624	Mir7036	Gm27973|mmu-mir-7036|mmu-mir-7036a	microRNA 7036	ncRNA
mm_52071.1	chr6	97807899	97807914	+	1	NA	intron (NM_001113198, intron 1 of 9)	intron (NM_001113198, intron 1 of 9)	848	NM_001113198	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_58048.1	chr6	136828187	136828197	-	1	NA	promoter-TSS (NM_021714)	promoter-TSS (NM_021714)	24	NM_021714	60321	Mm.141197	NM_021714	ENSMUSG00000030216	Wbp11	2510026P17Rik|D6Wsu113e|Npwbp|SIPP1	WW domain binding protein 11	protein-coding
mm_151710.1	chr19	4615519	4615539	-	1	NA	5' UTR (NM_153388, exon 1 of 3)	5' UTR (NM_153388, exon 1 of 3)	138	NM_153388	225875	Mm.329675	NM_153388	ENSMUSG00000045045	Lrfn4	BC023156|Salm3	leucine rich repeat and fibronectin type III domain containing 4	protein-coding
mm_12029.1	chr2	58163952	58163996	+	1	NA	promoter-TSS (NR_045895)	promoter-TSS (NR_045895)	0	NR_045896	100042926	Mm.446515	NR_045895	ENSMUSG00000086862	Gm13546	OTTMUSG00000012675	predicted gene 13546	ncRNA
mm_101900.1	chr11	49187093	49187105	-	1	NA	promoter-TSS (NM_172793)	promoter-TSS (NM_172793)	-10	NM_172793	237754	Mm.130787	NM_172793	ENSMUSG00000040283	Btnl9	B430208I01|Btn3|D330012D11Rik	butyrophilin-like 9	protein-coding
mm_79622.1	chr9	59288328	59288340	+	1	NA	Intergenic	Intergenic	-3238	NM_028121	72141	Mm.22456	NM_028121	ENSMUSG00000025236	Adpgk	2610017G09Rik|Adp-gk|C77577	ADP-dependent glucokinase	protein-coding
mm_28628.1	chr3	95139843	95139865	-	1	NA	promoter-TSS (NR_106175)	promoter-TSS (NR_106175)	-668	NR_106175	102465890		NR_106175	ENSMUSG00000098498	Mir8099-1	Gm27917|mmu-mir-8099-1	microRNA 8099-1	ncRNA
mm_122224.1	chr14	32685247	32685312	-	1	NA	promoter-TSS (NM_001195097)	promoter-TSS (NM_001195097)	-7	NM_001195097	100504518	Mm.318319	NM_001195097	ENSMUSG00000071540	3425401B19Rik	-	RIKEN cDNA 3425401B19 gene	protein-coding
mm_155996.1	chrX	106156850	106156876	+	1	NA	exon (NM_205820, exon 3 of 3)	exon (NM_205820, exon 3 of 3)	13588	NM_205820	279572	Mm.336203	NM_205820	ENSMUSG00000033777	Tlr13	AI666735|Gm713	toll-like receptor 13	protein-coding
mm_42902.1	chr5	122491742	122491763	+	1	NA	exon (NM_009722, exon 4 of 21)	exon (NM_009722, exon 4 of 21)	10473	NM_001110140	11938	Mm.227583	NM_009722	ENSMUSG00000029467	Atp2a2	9530097L16Rik|D5Wsu150e|SERCA2|SERCA2B|Serca2a|mKIAA4195	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	protein-coding
mm_45727.1	chr5	86172748	86172793	-	1	NA	promoter-TSS (NM_172712)	promoter-TSS (NM_172712)	-27	NM_172712	231380	Mm.34012	NM_172712	ENSMUSG00000035898	Uba6	4930542H01|5730469D23Rik|AU021846|AW124799|E1-L2|Ube1l2	ubiquitin-like modifier activating enzyme 6	protein-coding
mm_105997.1	chr11	115686179	115686194	-	1	NA	intron (NM_001313937, intron 1 of 4)	intron (NM_001313937, intron 1 of 4)	13348	NM_001313937	14784	Mm.439649	NM_008163	ENSMUSG00000059923	Grb2	AA408164|Ash	growth factor receptor bound protein 2	protein-coding
mm_139162.1	chr17	47557520	47557525	+	1	NA	intron (NM_001081635, intron 1 of 6)	intron (NM_001081635, intron 1 of 6)	-35945	NM_007632	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_3219.1	chr1	135845894	135845904	+	1	NA	exon (NM_001130176, exon 4 of 13)	exon (NM_001130176, exon 4 of 13)	5038	NM_001130176	21956	Mm.247470	NM_011619	ENSMUSG00000026414	Tnnt2	Tnt|cTnT	troponin T2, cardiac	protein-coding
mm_35999.1	chr4	56433058	56433064	-	1	NA	Intergenic	MTB_Mm|LTR|ERVL-MaLR	308364	NM_025271	11471	Mm.251434	NM_025271	ENSMUSG00000070980	Actl7b	Tact1	actin-like 7b	protein-coding
mm_21150.1	chr2	154408079	154408116	-	1	NA	promoter-TSS (NM_009228)	promoter-TSS (NM_009228)	-13	NM_009228	20648	Mm.1541	NM_009228	ENSMUSG00000027488	Snta1	AW228934|Snt1	syntrophin, acidic 1	protein-coding
mm_73705.1	chr8	111687104	111687112	+	1	NA	exon (NM_025583, exon 6 of 7)	exon (NM_025583, exon 6 of 7)	2566	NR_106044	102466993		NR_106044	ENSMUSG00000099129	Mir7076	Gm27318|mmu-mir-7076	microRNA 7076	ncRNA
mm_143595.1	chr17	74819925	74819941	-	1	NA	intron (NM_152817, intron 13 of 19)	RMER19C|LTR|ERVK	102183	NM_152817	74196	Mm.209503	NM_152817	ENSMUSG00000024078	Ttc27	2610511O17Rik	tetratricopeptide repeat domain 27	protein-coding
mm_83387.1	chr9	44603495	44603515	-	1	NA	Intergenic	MER89|LTR|ERV1	-1387	NM_001110826	13209	Mm.267061	NM_007841	ENSMUSG00000032097	Ddx6	1110001P04Rik|E230023J21Rik|HLR2|mRCK/P54|p54|rck	DEAD (Asp-Glu-Ala-Asp) box polypeptide 6	protein-coding
mm_66791.1	chr7	47091715	47091725	-	1	NA	intron (NM_013643, intron 2 of 13)	intron (NM_013643, intron 2 of 13)	-8496	NR_106023	102465639		NR_106023	ENSMUSG00000098960	Mir7056	Gm27696|mmu-mir-7056	microRNA 7056	ncRNA
mm_116815.1	chr13	54468806	54468862	-	1	NA	promoter-TSS (NM_028597)	promoter-TSS (NM_028597)	6	NM_028597	73666	Mm.292487	NM_028597	ENSMUSG00000025872	Thoc3	2410044K02Rik|AL033344	THO complex 3	protein-coding
mm_138138.1	chr17	34198343	34198384	+	1	NA	5' UTR (NM_010724, exon 1 of 6)	5' UTR (NM_010724, exon 1 of 6)	168	NM_010724	16913	Mm.180191	NM_010724	ENSMUSG00000024338	Psmb8	Lmp-7|Lmp7	proteasome (prosome, macropain) subunit, beta type 8 (large multifunctional peptidase 7)	protein-coding
mm_6776.1	chr1	84134307	84134330	-	1	NA	intron (NM_001003948, intron 2 of 2)	B4A|SINE|B4	84643	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_66130.1	chr7	31055368	31055397	-	1	NA	promoter-TSS (NM_194321)	promoter-TSS (NM_194321)	274	NM_052992	56188	Mm.1491	NM_019503	ENSMUSG00000036570	Fxyd1	0610012C17Rik|1110006M24Rik|Plm|Pml	FXYD domain-containing ion transport regulator 1	protein-coding
mm_98426.1	chr11	94645271	94645272	+	1	NA	TTS (NM_133807)	TTS (NM_133807)	8483	NM_177752	268465	Mm.358937	NM_177752	ENSMUSG00000039055	Eme1	6820428D13	essential meiotic structure-specific endonuclease 1	protein-coding
mm_49025.1	chr6	4759598	4759606	+	1	NA	3' UTR (NM_130877, exon 2 of 2)	3' UTR (NM_130877, exon 2 of 2)	12296	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_116111.1	chr13	28950125	28950135	-	1	NA	TTS (NM_009238)	TTS (NM_009238)	3552	NM_009238	20677	Mm.240627	NM_009238	ENSMUSG00000076431	Sox4	AA682046|Sox-4	SRY (sex determining region Y)-box 4	protein-coding
mm_87437.1	chr10	51459931	51459934	+	1	NA	Intergenic	Intergenic	-20680	NM_008147	14727	Mm.439661	NM_008147	ENSMUSG00000062593	Lilr4b	Gp49a|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4B	protein-coding
mm_86071.1	chr9	114775489	114775502	-	1	NA	intron (NM_001252479, intron 1 of 3)	intron (NM_001252479, intron 1 of 3)	6498	NM_133978	102545	Mm.35600	NM_133978	ENSMUSG00000032436	Cmtm7	AI481279|Cklfsf7|LNV	CKLF-like MARVEL transmembrane domain containing 7	protein-coding
mm_43431.1	chr5	136083912	136083920	+	1	NA	promoter-TSS (NM_133914)	promoter-TSS (NM_133914)	0	NM_133914	54153	Mm.290655	NM_133914	ENSMUSG00000004952	Rasa4	AA793972|AW112107|BB079060|CAPRI|GAPL	RAS p21 protein activator 4	protein-coding
mm_153191.1	chr19	34510785	34510795	-	1	NA	intron (NM_001111100, intron 4 of 9)	intron (NM_001111100, intron 4 of 9)	16684	NM_001111100	16889	Mm.157545	NM_021460	ENSMUSG00000024781	Lipa	AA960673|Lal|Lip-1|Lip1	lysosomal acid lipase A	protein-coding
mm_132487.1	chr16	36916413	36916437	+	1	NA	exon (NM_030035, exon 13 of 22)	exon (NM_030035, exon 13 of 22)	-18558	NM_008225	15163	Mm.4091	NM_008225	ENSMUSG00000022831	Hcls1	AW213261|HS1	hematopoietic cell specific Lyn substrate 1	protein-coding
mm_99396.1	chr11	102163853	102163855	+	1	NA	3' UTR (NM_172947, exon 5 of 5)	3' UTR (NM_172947, exon 5 of 5)	-7447	NM_029649	76547	Mm.46529	NM_029649	ENSMUSG00000020921	Tmem101	2610511E22Rik	transmembrane protein 101	protein-coding
mm_76286.1	chr8	84198369	84198394	-	1	NA	Intergenic	Intergenic	-10137	NR_029740	387216		NR_029740	ENSMUSG00000065611	Mir23a	Mirn23a|mir-23a|mmu-mir-23a	microRNA 23a	ncRNA
mm_25726.1	chr3	122730137	122730153	+	1	NA	intron (NM_153422, intron 1 of 20)	CpG	987	NM_153422	242202	Mm.134911	NM_153422	ENSMUSG00000053965	Pde5a	Cgbpde|Cn5n|PDE5a2|Pde5|Pde5a1	phosphodiesterase 5A, cGMP-specific	protein-coding
mm_63957.1	chr7	139914655	139914665	+	1	NA	intron (NM_177261, intron 9 of 30)	intron (NM_177261, intron 9 of 30)	19964	NM_177261	76484	Mm.44442	NM_177261	ENSMUSG00000066129	Kndc1	2410012C07Rik|B830014K08Rik|VKIND|very-kind	kinase non-catalytic C-lobe domain (KIND) containing 1	protein-coding
mm_21297.1	chr2	157026034	157026037	-	1	NA	intron (NM_001164663, intron 11 of 14)	B1_Mur4|SINE|Alu	-18960	NM_025853	66934	Mm.25410	NM_025853	ENSMUSG00000027635	Dsn1	1700022L09Rik|AW552447	DSN1 homolog, MIS12 kinetochore complex component	protein-coding
mm_11688.1	chr2	35661269	35661290	+	1	NA	intron (NM_001290641, intron 2 of 15)	CpG	-30715	NM_001001602	69601	Mm.29629	NM_001001602	ENSMUSG00000026883	Dab2ip	2310011D08Rik|AI480459|Aip1|mKIAA1743	disabled 2 interacting protein	protein-coding
mm_122414.1	chr14	41031016	41031019	-	1	NA	Intergenic	L1MC|LINE|L1	-17184	NM_001316737	70564	Mm.27227	NM_027464	ENSMUSG00000021792	Fam213a	5730469M10Rik|AU040822|Adrx|Pamm	family with sequence similarity 213, member A	protein-coding
mm_70186.1	chr7	143780223	143780233	-	1	NA	3' UTR (NM_175534, exon 2 of 2)	3' UTR (NM_175534, exon 2 of 2)	4272	NM_175534	244238	Mm.183561	NM_175534	ENSMUSG00000048965	Mrgpre	C130069N09Rik|Ebrt3|Mgrf|MrgE	MAS-related GPR, member E	protein-coding
mm_126697.1	chr15	85037182	85037231	+	1	NA	5' UTR (NM_133750, exon 1 of 9)	5' UTR (NM_133750, exon 1 of 9)	144	NM_133750	73225	Mm.247535	NM_133750	ENSMUSG00000022434	Fam118a	-	family with sequence similarity 118, member A	protein-coding
mm_121929.1	chr14	23835847	23835855	-	1	NA	intron (NM_001253366, intron 1 of 29)	MIRb|SINE|MIR	168354	NM_001253375	16531	Mm.343607	NM_010610	ENSMUSG00000063142	Kcnma1	5730414M22Rik|BKCa|MaxiK|Slo|Slo1|mSlo|mSlo1	potassium large conductance calcium-activated channel, subfamily M, alpha member 1	protein-coding
mm_112007.1	chr12	110889120	110889144	-	1	NA	promoter-TSS (NM_026048)	promoter-TSS (NM_026048)	13	NM_027223	67236	Mm.287157	NM_026048	ENSMUSG00000021276	Cinp	1810047K05Rik|2810452K22Rik	cyclin-dependent kinase 2 interacting protein	protein-coding
mm_147719.1	chr18	60822952	60822962	-	1	NA	exon (NM_011552, exon 17 of 25)	exon (NM_011552, exon 17 of 25)	10881	NR_039567	100628611		NR_039567	ENSMUSG00000093327	Mir5107	mir-5107|mmu-mir-5107|mu-mir-5107	microRNA 5107	ncRNA
mm_33097.1	chr4	124700372	124700384	+	1	NA	promoter-TSS (NM_010213)	promoter-TSS (NM_010213)	-321	NM_010213	14201	Mm.331856	NM_010213	ENSMUSG00000032643	Fhl3	SLIM2	four and a half LIM domains 3	protein-coding
mm_116135.1	chr13	28953453	28953468	-	1	NA	5' UTR (NM_009238, exon 1 of 1)	5' UTR (NM_009238, exon 1 of 1)	222	NM_009238	20677	Mm.240627	NM_009238	ENSMUSG00000076431	Sox4	AA682046|Sox-4	SRY (sex determining region Y)-box 4	protein-coding
mm_77724.1	chr8	126844906	126844916	-	1	NA	Intergenic	Intergenic	101010	NM_024214	67952	Mm.6932	NM_024214	ENSMUSG00000093904	Tomm20	1810060K07Rik|BB284719|Gm19268|MAS20|MOM19|TOM20|mKIAA0016	translocase of outer mitochondrial membrane 20 homolog (yeast)	protein-coding
mm_116421.1	chr13	41828315	41828325	-	1	NA	exon (NM_175417, exon 2 of 7)	exon (NM_175417, exon 2 of 7)	19168	NM_175417	109254	Mm.25195	NM_175417	ENSMUSG00000058022	Adtrp	9530008L14Rik	androgen dependent TFPI regulating protein	protein-coding
mm_127232.1	chr15	99406147	99406157	+	1	NA	exon (NM_026669, exon 7 of 10)	exon (NM_026669, exon 7 of 10)	12933	NM_001171035	110213	Mm.16769	NM_026669	ENSMUSG00000023010	Tmbim6	5031406P05Rik|Bi1|Tegt	transmembrane BAX inhibitor motif containing 6	protein-coding
mm_67140.1	chr7	73238646	73238662	-	1	NA	Intergenic	Intergenic	-71726	NR_105062	100505025	Mm.445959	NR_105062	ENSMUSG00000108530	LOC100505025	-	uncharacterized LOC100505025	ncRNA
mm_20500.1	chr2	130423749	130423812	-	1	NA	promoter-TSS (NM_030559)	promoter-TSS (NM_030559)	508	NM_178762	319513	Mm.482539	NM_178762	ENSMUSG00000037773	Pced1a	A930025D01Rik|AI480484|Fam113a	PC-esterase domain containing 1A	protein-coding
mm_126072.1	chr15	77508269	77508270	+	1	NA	promoter-TSS (NM_001177533)	promoter-TSS (NM_001177533)	-2	NM_001177533	626615	Mm.390820	NM_001177533	ENSMUSG00000091650	Apol11a	EG626615	apolipoprotein L 11a	protein-coding
mm_102612.1	chr11	62457773	62457835	-	1	NA	promoter-TSS (NM_177229)	promoter-TSS (NM_177229)	-472	NM_177229	20185	Mm.271814	NM_011308	ENSMUSG00000018501	Ncor1	5730405M06Rik|A230020K14Rik|N-CoR|RIP13|Rxrip13|mKIAA1047	nuclear receptor co-repressor 1	protein-coding
mm_93688.1	chr10	117815979	117815985	-	1	NA	intron (NM_024457, intron 7 of 7)	intron (NM_024457, intron 7 of 7)	-23277	NM_134010	103468	Mm.12568	NM_134010	ENSMUSG00000052798	Nup107	AW541137|C76801	nucleoporin 107	protein-coding
mm_162186.1	chrX	103630657	103630657	+	1	NA	promoter-TSS (NM_029158)	promoter-TSS (NM_029158)	71	NM_029158	75064	Mm.159414	NM_029158	ENSMUSG00000031330	Zcchc13	4930513O09Rik|Cnbp2	zinc finger, CCHC domain containing 13	protein-coding
mm_103097.1	chr11	69935757	69935765	-	1	NA	promoter-TSS (NM_016875)	promoter-TSS (NM_016875)	-138	NM_016875	53422	Mm.29286	NM_016875	ENSMUSG00000018554	Ybx2	Msy2	Y box protein 2	protein-coding
mm_88179.1	chr10	69925801	69925824	+	1	NA	5' UTR (NM_009670, exon 1 of 20)	5' UTR (NM_009670, exon 1 of 20)	280	NM_009670	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_87381.1	chr10	44612002	44612012	+	1	NA	Intergenic	Intergenic	-153259	NM_007548	12142	Mm.4800	NM_007548	ENSMUSG00000038151	Prdm1	Blimp-1|Blimp1|PRDI-BF1|ZNFPR1A1|b2b1765Clo	PR domain containing 1, with ZNF domain	protein-coding
mm_82761.1	chr9	26889086	26889087	-	1	NA	intron (NM_001281475, intron 14 of 20)	intron (NM_001281475, intron 14 of 20)	-28263	NM_001113323	70893	Mm.78118	NM_001113323	ENSMUSG00000031966	Glb1l3	4921509F24Rik	galactosidase, beta 1 like 3	protein-coding
mm_50149.1	chr6	41543803	41543827	+	1	NA	Intergenic	Intergenic	22039	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_32394.1	chr4	106651088	106651120	+	1	NA	promoter-TSS (NM_001285784)	promoter-TSS (NM_001285784)	35	NM_001083887	230577	Mm.134029	NM_172272	ENSMUSG00000043572	Pars2	BC027073	prolyl-tRNA synthetase (mitochondrial)(putative)	protein-coding
mm_123458.1	chr14	65593017	65593074	-	1	NA	promoter-TSS (NM_028811)	promoter-TSS (NM_028811)	67	NM_001253812	74195	Mm.29719	NM_028811	ENSMUSG00000022031	Elp3	2610507P14Rik|KAT9	elongator acetyltransferase complex subunit 3	protein-coding
mm_82658.1	chr9	22085057	22085085	-	1	NA	non-coding (NR_040407, exon 3 of 3)	non-coding (NR_040407, exon 3 of 3)	356	NM_001253897	26940	Mm.425568	NM_012029	ENSMUSG00000066839	Ecsit	Sitpec	ECSIT signalling integrator	protein-coding
mm_122776.1	chr14	54409968	54409984	-	1	NA	promoter-TSS (NM_001253680)	promoter-TSS (NM_001253680)	-504	NM_001253680	20540	Mm.142455	NM_011405	ENSMUSG00000000958	Slc7a7	AI790233|my+lat1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 7	protein-coding
mm_159712.1	chr5	32146692	32146692	+	1	NA	intron (NM_008037, intron 1 of 3)	intron (NM_008037, intron 1 of 3)	10220	NM_008037	14284	Mm.24684	NM_008037	ENSMUSG00000029135	Fosl2	Fra-2	fos-like antigen 2	protein-coding
mm_132572.1	chr16	38143314	38143358	+	1	NA	intron (NM_001347232, intron 1 of 11)	intron (NM_001347232, intron 1 of 11)	-54076	NR_033221	414072	Mm.483602	NR_033221		BC031361	-	cDNA sequence BC031361	ncRNA
mm_170273.1	chr18	24869805	24869810	+	1	NA	intron (NM_175276, intron 3 of 26)	intron (NM_175276, intron 3 of 26)	161184	NM_001289655	225288	Mm.329322	NM_175276	ENSMUSG00000034295	Fhod3	A930009H06Rik|FHOS2|mKIAA1695	formin homology 2 domain containing 3	protein-coding
mm_81101.1	chr9	106429538	106429548	+	1	NA	5' UTR (NM_001324533, exon 1 of 4)	5' UTR (NM_001324533, exon 1 of 4)	132	NM_009082	19944	Mm.288696	NM_009082	ENSMUSG00000048758	Rpl29	Rpl43	ribosomal protein L29	protein-coding
mm_116658.1	chr13	49190794	49190803	-	1	NA	intron (NM_013610, intron 1 of 3)	intron (NM_013610, intron 1 of 3)	3251	NM_013610	18081	Mm.18503	NM_013610	ENSMUSG00000037966	Ninj1	AU024536	ninjurin 1	protein-coding
mm_100244.1	chr11	117266411	117266472	+	1	NA	5' UTR (NM_001113487, exon 1 of 11)	5' UTR (NM_001113487, exon 1 of 11)	195	NM_001113487	53860	Mm.38450	NM_017380	ENSMUSG00000059248	Sept9	MSF1|Msf|PNUTL4|Sint1	septin 9	protein-coding
mm_97484.1	chr11	78324637	78324648	+	1	NA	exon (NM_009657, exon 2 of 8)	exon (NM_009657, exon 2 of 8)	444	NM_009657	11676	Mm.7729	NM_009657	ENSMUSG00000017390	Aldoc	AI847350|AU040929|Aldo3|Scrg2	aldolase C, fructose-bisphosphate	protein-coding
mm_164136.1	chr15	51040922	51040924	+	1	NA	Intergenic	Intergenic	-150882	NM_032000	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_49881.1	chr6	38609016	38609023	+	1	NA	3' UTR (NM_001170848, exon 9 of 9)	3' UTR (NM_001170848, exon 9 of 9)	28220	NM_001033171	74253	Mm.121859	NM_001033171	ENSMUSG00000071537	Klrg2	2310020F24Rik	killer cell lectin-like receptor subfamily G, member 2	protein-coding
mm_86771.1	chr10	20010359	20010361	+	1	NA	intron (NM_008580, intron 2 of 29)	intron (NM_008580, intron 2 of 29)	75834	NM_008580	26408	Mm.6595	NM_008580	ENSMUSG00000071369	Map3k5	7420452D20Rik|ASK|ASK1|MAPKKK5|Mekk5	mitogen-activated protein kinase kinase kinase 5	protein-coding
mm_31733.1	chr4	63086969	63086973	+	1	NA	intron (NM_028326, intron 3 of 14)	intron (NM_028326, intron 3 of 14)	67201	NM_007443	11699	Mm.2197	NM_007443	ENSMUSG00000028356	Ambp	AI194774|ASPI|HI-30|Intin4|Itil|UTI	alpha 1 microglobulin/bikunin	protein-coding
mm_62003.1	chr7	91250749	91250768	+	1	NA	intron (NM_011807, intron 1 of 22)	MTE2a|LTR|ERVL-MaLR	159972	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_26360.1	chr3	142549472	142549490	+	1	NA	3' UTR (NM_001083312, exon 11 of 11)	3' UTR (NM_001083312, exon 11 of 11)	-10571	NM_018734	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_19997.1	chr2	118728527	118728544	-	1	NA	promoter-TSS (NM_177568)	promoter-TSS (NM_177568)	-97	NM_001290790	18796	Mm.215156	NM_177568	ENSMUSG00000040061	Plcb2	AI550384|B230205M18Rik|B230399N12	phospholipase C, beta 2	protein-coding
mm_32692.1	chr4	115884368	115884374	+	1	NA	promoter-TSS (NM_001039124)	promoter-TSS (NM_001039124)	-29	NM_001039124	654462	Mm.388913	NM_001039124	ENSMUSG00000073774	Kncn	Kino|L5	kinocilin	protein-coding
mm_9097.1	chr1	169531344	169531437	-	1	NA	promoter-TSS (NM_023284)	promoter-TSS (NM_023284)	74	NM_023284	66977	Mm.151315	NM_023284	ENSMUSG00000026683	Nuf2	2410003C07Rik|AU044112|C85691|Cdca1|NUF2R	NUF2, NDC80 kinetochore complex component	protein-coding
mm_172184.1	chr6	4924096	4924103	-	1	NA	intron (NM_181595, intron 2 of 15)	(CCCTAA)n|Simple_repeat|Simple_repeat	20779	NM_181595	243725	Mm.332901	NM_181595	ENSMUSG00000032827	Ppp1r9a	2810430P21Rik|4930518N04Rik|5330407E15|A230094E16Rik|BB181831|NRB|mKIAA1222|neurabin-I	protein phosphatase 1, regulatory (inhibitor) subunit 9A	protein-coding
mm_156728.1	chrX	159913984	159914004	+	1	NA	exon (NM_021389, exon 9 of 17)	exon (NM_021389, exon 9 of 17)	-28699	NM_001290661	58194	Mm.286495	NM_021389	ENSMUSG00000040990	Sh3kbp1	1200007H22Rik|1700125L08Rik|5830464D22Rik|AI447724|Cin85|IN85|Ruk|Seta	SH3-domain kinase binding protein 1	protein-coding
mm_103519.1	chr11	76809041	76809044	-	1	NA	intron (NM_007754, intron 6 of 20)	intron (NM_007754, intron 6 of 20)	37966	NM_007754	12874	Mm.276736	NM_007754	ENSMUSG00000020841	Cpd	AA960140|AW322530|D830034L15Rik	carboxypeptidase D	protein-coding
mm_45741.1	chr5	86518579	86518610	-	1	NA	promoter-TSS (NM_177162)	promoter-TSS (NM_177162)	6	NM_177162	320454	Mm.184522	NM_177162	ENSMUSG00000079451	Tmprss11g	9930032O22Rik|Desc4	transmembrane protease, serine 11g	protein-coding
mm_73776.1	chr8	116873707	116873717	+	1	NA	Intergenic	Intergenic	47724	NM_026844	66531	Mm.4011	NM_026844	ENSMUSG00000014633	Cmc2	1110046L09Rik|2310061C15Rik|DC13	COX assembly mitochondrial protein 2	protein-coding
mm_12193.1	chr2	65620935	65620945	+	1	NA	5' UTR (NM_001346679, exon 1 of 27)	5' UTR (NM_001346679, exon 1 of 27)	171	NM_001346679	110876	Mm.220329	NM_001099298	ENSMUSG00000075318	Scn2a	6430408L10|A230052E19Rik|Nav1.2|Scn2a1	sodium channel, voltage-gated, type II, alpha	protein-coding
mm_112698.1	chr13	17695439	17695454	+	1	NA	promoter-TSS (NM_138654)	promoter-TSS (NM_138654)	33	NM_025479	66308	Mm.291109	NM_025479	ENSMUSG00000012429	Mplkip	2810021B07Rik|C330007M08Rik|Ttdn1	M-phase specific PLK1 intereacting protein	protein-coding
mm_7708.1	chr1	130449268	130449279	-	1	NA	intron (NM_010016, intron 7 of 9)	intron (NM_010016, intron 7 of 9)	13471	NM_010016	13136	Mm.101591	NM_010016	ENSMUSG00000026399	Cd55	Daf|Daf-GPI|Daf1|GPI-DAF	CD55 molecule, decay accelerating factor for complement	protein-coding
mm_159930.1	chr6	66897005	66897005	+	1	NA	intron (NM_001177558, intron 1 of 4)	intron (NM_001177558, intron 1 of 4)	114	NM_001177558	14701	Mm.234342	NM_025278	ENSMUSG00000036402	Gng12	2010305F15Rik|AA536815|AI115529|AI314170|AI842738	guanine nucleotide binding protein (G protein), gamma 12	protein-coding
mm_46357.1	chr5	103211075	103211101	-	1	NA	5' UTR (NM_001081567, exon 1 of 14)	5' UTR (NM_001081567, exon 1 of 14)	246	NM_001081567	26414	Mm.39253	NM_009158	ENSMUSG00000046709	Mapk10	C230008H04Rik|JNK3|JNK3B1|JNK3B2|SAPK(beta)|Serk2|p493F12|p54bSAPK	mitogen-activated protein kinase 10	protein-coding
mm_47320.1	chr5	122460939	122460954	-	1	NA	exon (NM_009722, exon 14 of 21)	exon (NM_009722, exon 14 of 21)	38502	NM_019805	56317	Mm.37341	NM_019805	ENSMUSG00000029466	Anapc7	APC7|AW545589	anaphase promoting complex subunit 7	protein-coding
mm_74584.1	chr8	11312732	11312758	-	1	NA	promoter-TSS (NM_009932)	promoter-TSS (NM_009932)	-60	NM_009932	12827	Mm.181021	NM_009932	ENSMUSG00000031503	Col4a2	Col4a-2	collagen, type IV, alpha 2	protein-coding
mm_21715.1	chr2	164608847	164608853	-	1	NA	exon (NM_001080550, exon 2 of 8)	exon (NM_001080550, exon 2 of 8)	4536	NM_001276432	277343	Mm.383292	NM_001080550	ENSMUSG00000070533	Wfdc8	Gm706	WAP four-disulfide core domain 8	protein-coding
mm_164200.1	chr15	79768356	79768359	+	1	NA	intron (NM_017470, intron 1 of 3)	intron (NM_017470, intron 1 of 3)	6110	NM_017470	54152	Mm.288159	NM_017470	ENSMUSG00000022420	Dnal4	D15Ertd424e|Dnalc4	dynein, axonemal, light chain 4	protein-coding
mm_19944.1	chr2	116397349	116397357	-	1	NA	Intergenic	Intergenic	-321257	NR_033447	69974	Mm.440293	NR_033447		2810405F15Rik	-	RIKEN cDNA 2810405F15 gene	ncRNA
mm_48648.1	chr5	145855082	145855094	-	1	NA	exon (NM_007818, exon 13 of 13)	exon (NM_007818, exon 13 of 13)	24766	NM_007818	13112	Mm.332844	NM_007818	ENSMUSG00000056035	Cyp3a11	AI256190|Cyp3a|IIIAm1|Pcn	cytochrome P450, family 3, subfamily a, polypeptide 11	protein-coding
mm_65940.1	chr7	30394523	30394552	-	1	NA	Intergenic	LTR33A|LTR|ERVL	-19251	NM_011662	22177	Mm.46301	NM_011662	ENSMUSG00000030579	Tyrobp	DAP12|KARAP|Ly83	TYRO protein tyrosine kinase binding protein	protein-coding
mm_49832.1	chr6	37870894	37870927	+	1	NA	promoter-TSS (NM_145076)	promoter-TSS (NM_145076)	99	NM_145076	21848	Mm.41063	NM_145076	ENSMUSG00000029833	Trim24	A130082H20Rik|AI447469|D430004I05Rik|TIF1|TIF1-alpha|TIF1alpha|Tif1a	tripartite motif-containing 24	protein-coding
mm_50047.1	chr6	41151703	41151735	+	1	NA	Intergenic	Intergenic	-116210	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_159709.1	chr5	31048562	31048562	-	1	NA	promoter-TSS (NM_177870)	promoter-TSS (NM_177870)	0	NM_001177621	330064	Mm.205463	NM_177870	ENSMUSG00000006641	Slc5a6	E430023I20	solute carrier family 5 (sodium-dependent vitamin transporter), member 6	protein-coding
mm_41253.1	chr5	88793943	88793945	+	1	NA	Intergenic	Intergenic	28931	NM_007832	13178	Mm.298892	NM_007832	ENSMUSG00000029366	Dck	-	deoxycytidine kinase	protein-coding
mm_139332.1	chr17	49292741	49292750	+	1	NA	Intergenic	U1|snRNA|snRNA	20215	NR_033486	100415784	Mm.400421	NR_033486		Gm17830	-	predicted gene, 17830	ncRNA
mm_78126.1	chr9	20652091	20652104	+	1	NA	promoter-TSS (NM_023371)	promoter-TSS (NM_023371)	-33	NM_023371	23988	Mm.7906	NM_023371	ENSMUSG00000032171	Pin1	0610025L01Rik|D9Bwg1161e	protein (peptidyl-prolyl cis/trans isomerase) NIMA-interacting 1	protein-coding
mm_39853.1	chr5	30913688	30913792	+	1	NA	promoter-TSS (NM_133918)	promoter-TSS (NM_133918)	-46	NM_133918	100952	Mm.286375	NM_133918	ENSMUSG00000029163	Emilin1	5830419M17Rik|AW229038|BB105748|EMILIN-1|gp115	elastin microfibril interfacer 1	protein-coding
mm_161116.1	chr12	105191288	105191288	+	1	NA	intron (NM_013772, intron 1 of 3)	intron (NM_013772, intron 1 of 3)	243	NM_013772	27378	Mm.485527	NM_013772	ENSMUSG00000068940	Tcl1b3	-	T cell leukemia/lymphoma 1B, 3	protein-coding
mm_94602.1	chr11	12314510	12314529	+	1	NA	intron (NM_172496, intron 7 of 14)	intron (NM_172496, intron 7 of 14)	97621	NM_001282994	12808	Mm.22847	NM_172496	ENSMUSG00000020173	Cobl	-	cordon-bleu WH2 repeat	protein-coding
mm_75994.1	chr8	72435044	72435057	-	1	NA	5' UTR (NM_029782, exon 1 of 7)	5' UTR (NM_029782, exon 1 of 7)	106	NM_029782	73316	Mm.196315	NM_028500	ENSMUSG00000019732	Calr3	1700031L01Rik|6330586I20Rik|Crt2|cspn	calreticulin 3	protein-coding
mm_58905.1	chr7	17163957	17163961	+	1	NA	TTS (NM_054059)	TTS (NM_054059)	13559	NM_054059	384557	Mm.486145	NM_054059	ENSMUSG00000053228	Ceacam3	EG384557|Psg24|cea12	carcinoembryonic antigen-related cell adhesion molecule 3	protein-coding
mm_90815.1	chr10	7906971	7906989	-	1	NA	3' UTR (NM_138667, exon 7 of 7)	3' UTR (NM_138667, exon 7 of 7)	49143	NM_138667	68652	Mm.193041	NM_138667	ENSMUSG00000015755	Tab2	1110030N06Rik|A530078N03Rik|Map3k7ip2|mKIAA0733	TGF-beta activated kinase 1/MAP3K7 binding protein 2	protein-coding
mm_76194.1	chr8	82403153	82403163	-	1	NA	promoter-TSS (NM_001254747)	promoter-TSS (NM_001254747)	-572	NM_008357	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_109717.1	chr12	116048008	116048070	+	1	NA	intron (NM_001004066, intron 1 of 2)	intron (NM_001004066, intron 1 of 2)	315	NM_019565	56220	Mm.254997	NM_019565	ENSMUSG00000042063	Zfp386	Kzf1|mKIAA4205	zinc finger protein 386 (Kruppel-like)	protein-coding
mm_57.1	chr1	6539789	6539805	+	1	NA	intron (NM_001244693, intron 2 of 22)	intron (NM_001244693, intron 2 of 22)	52566	NM_001244692	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding
mm_104074.1	chr11	86586671	86586689	-	1	NA	intron (NM_029478, intron 10 of 11)	intron (NM_029478, intron 10 of 11)	-2522	NR_029738	387140		NR_029738	ENSMUSG00000065455	Mir21a	Mir21|Mirn21|mmu-mir-21|mmu-mir-21a	microRNA 21a	ncRNA
mm_25798.1	chr3	127633198	127633212	+	1	NA	promoter-TSS (NM_009718)	promoter-TSS (NM_009718)	60	NM_009718	11924	Mm.42017	NM_009718	ENSMUSG00000027967	Neurog2	Atoh4|Math4A|bHLHa8|ngn-2|ngn2	neurogenin 2	protein-coding
mm_1543.1	chr1	72852176	72852189	+	1	NA	3' UTR (NM_008342, exon 4 of 4)	3' UTR (NM_008342, exon 4 of 4)	22683	NM_010518	16011	Mm.405761	NM_010518	ENSMUSG00000026185	Igfbp5	AI256729|AW208790|IGFBP-5|IGFBP-5P	insulin-like growth factor binding protein 5	protein-coding
mm_48108.1	chr5	137109087	137109097	-	1	NA	Intergenic	ID_B1|SINE|B4	7115	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_42516.1	chr5	115544342	115544378	+	1	NA	exon (NM_011223, exon 2 of 11)	exon (NM_011223, exon 2 of 11)	-15107	NM_007475	11837	Mm.5286	NM_007475	ENSMUSG00000067274	Rplp0	36B4|Arbp|L10E	ribosomal protein, large, P0	protein-coding
mm_148940.1	chr19	7056782	7056809	+	1	NA	promoter-TSS (NM_134147)	promoter-TSS (NM_134147)	27	NM_134147	107227	Mm.439977	NM_134147	ENSMUSG00000036278	Macrod1	AI604841|AW743046|D930010J01Rik|Lrp16	MACRO domain containing 1	protein-coding
mm_140962.1	chr17	24645020	24645028	-	1	NA	promoter-TSS (NM_023449)	promoter-TSS (NM_023449)	-67	NM_023449	65962	Mm.21587	NM_023055	ENSMUSG00000002504	Slc9a3r2	0610011L07Rik|1200011K07Rik|2010007A20Rik|E3karp|NHERF-2|Nherf2|Octs2|Sip-1|Sip1|Sryip1|Tka-1	solute carrier family 9 (sodium/hydrogen exchanger), member 3 regulator 2	protein-coding
mm_148354.1	chr18	84720706	84720718	-	1	NA	intron (NM_173770, intron 1 of 4)	intron (NM_173770, intron 1 of 4)	470	NM_173770	240479	Mm.472378	NM_173770	ENSMUSG00000047992	Fam69c	B230399E16Rik	family with sequence similarity 69, member C	protein-coding
mm_14588.1	chr2	136052181	136052199	+	1	NA	Intergenic	Intergenic	-5737	NM_029530	76161	Mm.41638	NM_029530	ENSMUSG00000027270	Lamp5	3110035N03Rik|6330527O06Rik|BAD-LAMP|LAMP-5	lysosomal-associated membrane protein family, member 5	protein-coding
mm_14719.1	chr2	143936254	143936257	+	1	NA	intron (NM_019771, intron 1 of 3)	L1MB7|LINE|L1	20924	NM_019771	56431	Mm.28919	NM_019771	ENSMUSG00000015932	Dstn	2610043P17Rik|ADF|AU042046|Dsn|corn1|sid23p	destrin	protein-coding
mm_100655.1	chr11	3173320	3173329	-	1	NA	intron (NM_030207, intron 6 of 32)	B1_Mur2|SINE|Alu	20139	NM_030207	78887	Mm.394071	NM_030207	ENSMUSG00000023764	Sfi1	-	Sfi1 homolog, spindle assembly associated (yeast)	protein-coding
mm_78280.1	chr9	22101191	22101206	+	1	NA	exon (NM_009922, exon 2 of 7)	exon (NM_009922, exon 2 of 7)	1945	NM_009922	12797	Mm.4356	NM_009922	ENSMUSG00000001349	Cnn1	CN|CnnI	calponin 1	protein-coding
mm_121543.1	chr14	122474473	122474488	+	1	NA	promoter-TSS (NM_009574)	promoter-TSS (NM_009574)	719	NR_045046	69248	Mm.235369	NR_045046	ENSMUSG00000085555	2610035F20Rik	-	RIKEN cDNA 2610035F20 gene	ncRNA
mm_55260.1	chr6	53592319	53592329	-	1	NA	intron (NM_172728, intron 1 of 6)	intron (NM_172728, intron 1 of 6)	18950	NM_172728	231991	Mm.227444	NM_172728	ENSMUSG00000053007	Creb5	9430076C15Rik|CRE-BPa|Crebpa|D430026C09Rik	cAMP responsive element binding protein 5	protein-coding
mm_139460.1	chr17	55952822	55952838	+	1	NA	5' UTR (NM_015766, exon 1 of 5)	5' UTR (NM_015766, exon 1 of 5)	207	NM_015766	50498	Mm.256798	NM_015766	ENSMUSG00000003206	Ebi3	EBI-3|IL-27	Epstein-Barr virus induced gene 3	protein-coding
mm_173274.1	chrX	98583641	98583658	+	1	NA	intron (NM_001313755, intron 19 of 23)	L1VL1|LINE|L1	307376	NM_052976	94190	Mm.33536	NM_052976	ENSMUSG00000031214	Ophn1	C130037N19Rik|Wtgr	oligophrenin 1	protein-coding
mm_127307.1	chr15	100227908	100227916	+	1	NA	promoter-TSS (NM_007497)	promoter-TSS (NM_007497)	53	NM_007497	11908	Mm.676	NM_007497	ENSMUSG00000023027	Atf1	-	activating transcription factor 1	protein-coding
mm_5991.1	chr1	58581974	58581978	-	1	NA	intron (NM_001310598, intron 1 of 12)	PB1D9|SINE|Alu	4178	NM_001310599	213056	Mm.26272	NM_172513	ENSMUSG00000038174	Fam126b	C130065N10Rik|D1Ertd53e|D630010C10	family with sequence similarity 126, member B	protein-coding
mm_66510.1	chr7	45102658	45102680	-	1	NA	exon (NM_010189, exon 3 of 7)	exon (NM_010189, exon 3 of 7)	1153	NM_010189	14132	Mm.3303	NM_010189	ENSMUSG00000003420	Fcgrt	FcRn	Fc receptor, IgG, alpha chain transporter	protein-coding
mm_157927.1	chrX	79643594	79643614	-	1	NA	intron (NM_028025, intron 1 of 3)	intron (NM_028025, intron 1 of 3)	-8022	NM_001113734	71967	Mm.379207	NM_028025	ENSMUSG00000046942	Mageb16	2410003J06Rik	melanoma antigen family B, 16	protein-coding
mm_67828.1	chr7	98321182	98321207	-	1	NA	Intergenic	Intergenic	-11667	NM_025408	66190	Mm.334041	NM_025408	ENSMUSG00000030760	Acer3	1110057L18Rik|5430429L08Rik|AV015045|Phca	alkaline ceramidase 3	protein-coding
mm_149764.1	chr19	22913626	22913632	+	1	NA	intron (NM_001035243, intron 17 of 23)	intron (NM_001035243, intron 17 of 23)	163024	NR_029591	387200		NR_029591	ENSMUSG00000065507	Mir204	Mirn204|mir-204|mmu-mir-204	microRNA 204	ncRNA
mm_21107.1	chr2	153346073	153346116	-	1	NA	promoter-TSS (NM_001039939)	promoter-TSS (NM_001039939)	-45	NM_001039939	228790	Mm.330677	NM_001039939	ENSMUSG00000042548	Asxl1	mKIAA0978	additional sex combs like 1	protein-coding
mm_10859.1	chr2	25054498	25054529	+	1	NA	TTS (NM_146251)	TTS (NM_146251)	134	NM_001177655	56876	Mm.42956	NM_020276	ENSMUSG00000006476	Nsmf	Jacob|Nelf	NMDA receptor synaptonuclear signaling and neuronal migration factor	protein-coding
mm_157119.1	chrX	9444454	9444466	-	1	NA	intron (NM_007807, intron 10 of 12)	intron (NM_007807, intron 10 of 12)	24864	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_107075.1	chr12	16958690	16958703	+	1	NA	exon (NM_009072, exon 16 of 33)	exon (NM_009072, exon 16 of 33)	41422	NM_172574	217430	Mm.379451	NM_172574	ENSMUSG00000045679	Pqlc3	C78076|E030024M05Rik	PQ loop repeat containing	protein-coding
mm_167961.1	chrX	143685093	143685100	+	1	NA	intron (NM_001195049, intron 4 of 17)	intron (NM_001195049, intron 4 of 17)	-8191	NM_001195047	18481	Mm.40035	NM_008778	ENSMUSG00000031284	Pak3	PAK-3|Pak65alpha|Pak65beta|Stk4	p21 protein (Cdc42/Rac)-activated kinase 3	protein-coding
mm_83272.1	chr9	43051351	43051361	-	1	NA	intron (NM_027144, intron 1 of 40)	L1M5|LINE|L1	54362	NM_027144	69632	Mm.275266	NM_027144	ENSMUSG00000059495	Arhgef12	2310014B11Rik|AU019857|Larg|mKIAA0382	Rho guanine nucleotide exchange factor (GEF) 12	protein-coding
mm_117928.1	chr13	99434282	99434294	-	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-21462	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_60189.1	chr7	43351419	43351456	+	1	NA	promoter-TSS (NM_145581)	promoter-TSS (NM_145581)	96	NM_145581	233186	Mm.290569	NM_145581	ENSMUSG00000039013	Siglecf	Siglec5|mSiglec-F	sialic acid binding Ig-like lectin F	protein-coding
mm_18078.1	chr2	42653318	42653329	-	1	NA	5' UTR (NM_053011, exon 1 of 91)	5' UTR (NM_053011, exon 1 of 91)	275	NM_053011	94217	Mm.441398	NM_053011	ENSMUSG00000049252	Lrp1b	9630004P12Rik|LRP-DIT	low density lipoprotein-related protein 1B (deleted in tumors)	protein-coding
mm_100011.1	chr11	114872381	114872391	+	1	NA	3' UTR (NM_001110337, exon 5 of 5)	3' UTR (NM_001110337, exon 5 of 5)	-17655	NM_001347654	217303	Mm.294439	NM_170758	ENSMUSG00000034652	Cd300a	B230315M08Rik|Clm8|LMIR1|MAIR-I|MAIR-Ia|MMAC8|Pigr4|mcpir1	CD300A molecule	protein-coding
mm_80185.1	chr9	72352367	72352370	+	1	NA	intron (NM_146224, intron 20 of 21)	intron (NM_146224, intron 20 of 21)	77480	NM_001311105	235469	Mm.242791	NM_146224	ENSMUSG00000038535	Zfp280d	A930005F02Rik|BC027163|Suhw4|ZNF634|Znf280d	zinc finger protein 280D	protein-coding
mm_10240.1	chr2	8797047	8797059	+	1	NA	Intergenic	Intergenic	-392462	NR_038180	73438	Mm.23558	NR_038180	ENSMUSG00000085580	1700061F12Rik	-	RIKEN cDNA 1700061F12 gene	ncRNA
mm_81422.1	chr9	109056314	109056347	+	1	NA	exon (NM_026381, exon 3 of 4)	exon (NM_026381, exon 3 of 4)	1464	NM_026381	66940	Mm.196533	NM_025858	ENSMUSG00000025647	Shisa5	2310008D10Rik|6430628I05Rik|Scotin|mShisa5	shisa family member 5	protein-coding
mm_136237.1	chr16	90749646	90749681	-	1	NA	3' UTR (NM_029844, exon 3 of 3)	3' UTR (NM_029844, exon 3 of 3)	11339	NM_029844	77037	Mm.22455	NM_029844	ENSMUSG00000039956	Mrap	1110025G12Rik|Falp|ORF61	melanocortin 2 receptor accessory protein	protein-coding
mm_158460.1	chrX	140599504	140599518	-	1	NA	intron (NM_001077364, intron 1 of 3)	CpG	1011	NM_001077364	14605	Mm.22216	NM_010286	ENSMUSG00000031431	Tsc22d3	DIP|Dsip1|Gilz|TSC-22R|Tilz3	TSC22 domain family, member 3	protein-coding
mm_53652.1	chr6	141249162	141249175	+	1	NA	promoter-TSS (NM_018779)	promoter-TSS (NM_018779)	-101	NM_018779	54611	Mm.103728	NM_018779	ENSMUSG00000041741	Pde3a	A930022O17Rik|C87899	phosphodiesterase 3A, cGMP inhibited	protein-coding
mm_137243.1	chr17	24473896	24473922	+	1	NA	promoter-TSS (NM_175682)	promoter-TSS (NM_175682)	25	NM_175682	319259	Mm.258355	NM_175682	ENSMUSG00000045744	Bricd5	9930021D14Rik	BRICHOS domain containing 5	protein-coding
mm_77370.1	chr8	119822704	119822724	-	1	NA	exon (NM_028071, exon 3 of 4)	exon (NM_028071, exon 3 of 4)	17865	NM_028071	72042	Mm.393405	NM_028071	ENSMUSG00000031827	Cotl1	1810074P22Rik|2010004C08Rik|Clp	coactosin-like 1 (Dictyostelium)	protein-coding
mm_26313.1	chr3	142519409	142519440	+	1	NA	intron (NM_153564, intron 10 of 10)	RMER2|LTR|ERV1	-10912	NM_001083312	229900	Mm.45740	NM_145545	ENSMUSG00000040253	Gbp7	9830147J24Rik	guanylate binding protein 7	protein-coding
mm_125224.1	chr15	34123679	34123689	+	1	NA	exon (NM_026002, exon 7 of 12)	exon (NM_026002, exon 7 of 12)	40965	NM_026002	67154	Mm.130883	NM_026002	ENSMUSG00000022255	Mtdh	2610103J23Rik|3D3|3D3/Lyric|AEG-1|AV353288|D8Bwg1112e|Lyric	metadherin	protein-coding
mm_10504.1	chr2	16355638	16355656	+	1	NA	promoter-TSS (NM_026162)	promoter-TSS (NM_026162)	-657	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding
mm_41124.1	chr5	87785276	87785289	+	1	NA	intron (NM_007785, intron 10 of 13)	intron (NM_007785, intron 10 of 13)	10832	NM_007785	12993	Mm.4908	NM_007785	ENSMUSG00000061937	Csn1s2a	Csng|PP22	casein alpha s2-like A	protein-coding
mm_77221.1	chr8	115695965	115695967	-	1	NA	Intergenic	Intergenic	10928	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_69263.1	chr7	127894637	127894664	-	1	NA	intron (NM_178600, intron 1 of 2)	intron (NM_178600, intron 1 of 2)	967	NM_178600	27973	Mm.29703	NM_178600	ENSMUSG00000096145	Vkorc1	D7Wsu86e	vitamin K epoxide reductase complex, subunit 1	protein-coding
mm_84691.1	chr9	72393871	72393879	-	1	NA	Intergenic	Intergenic	-44654	NM_008613	17427	Mm.387671	NM_008613	ENSMUSG00000032221	Mns1	AW546487	meiosis-specific nuclear structural protein 1	protein-coding
mm_155730.1	chrX	96163765	96163781	+	1	NA	exon (NM_010833, exon 10 of 13)	exon (NM_010833, exon 10 of 13)	67728	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_142599.1	chr17	46763728	46763741	-	1	NA	promoter-TSS (NM_011195)	promoter-TSS (NM_011195)	-22	NM_011195	19208	Mm.215173	NM_011195	ENSMUSG00000036858	Ptcra	gp33|pT-alpha|pT-alpha-TCR|pT[a]|pTa|pTalpha	pre T cell antigen receptor alpha	protein-coding
mm_75972.1	chr8	72009620	72009634	-	1	NA	promoter-TSS (NM_024444)	promoter-TSS (NM_024444)	-1	NM_024444	72054	Mm.160020	NM_024444	ENSMUSG00000003484	Cyp4f18	1810054N16Rik|Cyp4f3|Cypf18	cytochrome P450, family 4, subfamily f, polypeptide 18	protein-coding
mm_27698.1	chr3	66981260	66981277	-	1	NA	promoter-TSS (NM_001302359)	promoter-TSS (NM_001302359)	-127	NM_001302359	20429	Mm.39093	NM_013665	ENSMUSG00000027833	Shox2	6330543G17Rik|OG12|Og12x|Prx3|SHOT	short stature homeobox 2	protein-coding
mm_166242.1	chr5	74029211	74029221	-	1	NA	exon (NM_177561, exon 4 of 9)	exon (NM_177561, exon 4 of 9)	39195	NM_177561	69727	Mm.48795	NM_177561	ENSMUSG00000054814	Usp46	1190009E20Rik|2410018I08Rik|AI451644	ubiquitin specific peptidase 46	protein-coding
mm_64298.1	chr7	141861567	141861576	+	1	NA	exon (NM_028801, exon 31 of 49)	exon (NM_028801, exon 31 of 49)	22499	NM_028801	74180	Mm.200752	NM_028801	ENSMUSG00000066108	Muc5b	2300002I04Rik|A130042M24|AV085033|MUC5|MUC9|mucin 5b	mucin 5, subtype B, tracheobronchial	protein-coding
mm_80889.1	chr9	99451438	99451453	+	1	NA	Intergenic	Intergenic	-4798	NM_001165957	623534	Mm.484967	NM_001165957		Nme9	Txndc6	NME/NM23 family member 9	protein-coding
mm_18589.1	chr2	66441150	66441162	-	1	NA	promoter-TSS (NM_001313997)	promoter-TSS (NM_001313997)	276	NR_033495	100038743	Mm.330264	NR_033495		Gm13629	OTTMUSG00000013098	predicted gene 13629	ncRNA
mm_62520.1	chr7	102230130	102230145	+	1	NA	intron (NR_111937, intron 2 of 5)	intron (NR_111937, intron 2 of 5)	7109	NR_111937	233575	Mm.302013	NM_145583	ENSMUSG00000030990	Pgap2	1810006G21Rik|C76649|Frag1	post-GPI attachment to proteins 2	protein-coding
mm_94530.1	chr11	9118071	9118091	+	1	NA	promoter-TSS (NM_009477)	promoter-TSS (NM_009477)	-22	NM_009477	22271	Mm.4610	NM_009477	ENSMUSG00000020407	Upp1	AI325217|UPase|UdRPase|Up|Upp	uridine phosphorylase 1	protein-coding
mm_42575.1	chr5	117240874	117240891	+	1	NA	intron (NM_001081308, intron 12 of 19)	intron (NM_001081308, intron 12 of 19)	46682	NM_018858	23980	Mm.195898	NM_018858	ENSMUSG00000032959	Pebp1	HCNP|Pbp|Pbp1|Pbpr|Rkip	phosphatidylethanolamine binding protein 1	protein-coding
mm_125815.1	chr15	74932295	74932306	+	1	NA	Intergenic	RLTR6-int|LTR|ERV1	-22751	NM_001164039	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_4419.1	chr1	172500254	172500255	+	1	NA	promoter-TSS (NM_178598)	promoter-TSS (NM_178598)	8	NM_178598	21346	Mm.271711	NM_178598	ENSMUSG00000026547	Tagln2	2700094C18Rik|SM22beta|Sm22B|Sm22a	transgelin 2	protein-coding
mm_7339.1	chr1	105880864	105880868	-	1	NA	Intergenic	Intergenic	100143	NM_009399	21934	Mm.6251	NM_009399	ENSMUSG00000026321	Tnfrsf11a	Ly109|ODFR|OFE|Rank|TRANCE-R|mRANK	tumor necrosis factor receptor superfamily, member 11a, NFKB activator	protein-coding
mm_64673.1	chr7	4500803	4500807	-	1	NA	intron (NM_029834, intron 1 of 21)	intron (NM_029834, intron 1 of 21)	875	NM_029834	232807	Mm.360391	NM_029834	ENSMUSG00000019254	Ppp1r12c	2410197A17Rik|AI839747|B430101M08|Mbs85	protein phosphatase 1, regulatory (inhibitor) subunit 12C	protein-coding
mm_76327.1	chr8	84705815	84705827	-	1	NA	3' UTR (NM_010906, exon 9 of 9)	3' UTR (NM_010906, exon 9 of 9)	4364	NM_008535	17095	Mm.4925	NM_008535	ENSMUSG00000034041	Lyl1	Lyl-1|bHLHa18	lymphoblastomic leukemia 1	protein-coding
mm_16241.1	chr2	173156439	173156449	+	1	NA	intron (NM_011044, intron 6 of 9)	RSINE1|SINE|B4	3371	NM_011044	18534	Mm.266867	NM_011044	ENSMUSG00000027513	Pck1	AI265463|PEPCK|Pck-1	phosphoenolpyruvate carboxykinase 1, cytosolic	protein-coding
mm_108140.1	chr12	76255210	76255239	+	1	NA	promoter-TSS (NM_138745)	promoter-TSS (NM_138745)	-8	NM_138745	108156	Mm.29584	NM_138745	ENSMUSG00000021048	Mthfd1	Dcs|E430024A07Rik|Mthfd	methylenetetrahydrofolate dehydrogenase (NADP+ dependent), methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthase	protein-coding
mm_27271.1	chr3	40509738	40509782	-	1	NA	intron (NR_040445, intron 3 of 5)	intron (NR_040445, intron 3 of 5)	13152	NR_040445	100040882	Mm.272869	NR_040445	ENSMUSG00000037884	1700017G19Rik	-	RIKEN cDNA 1700017G19 gene	ncRNA
mm_97002.1	chr11	70844928	70844959	+	1	NA	5' UTR (NM_019400, exon 1 of 18)	5' UTR (NM_019400, exon 1 of 18)	182	NM_001291142	54189	Mm.7087	NM_019400	ENSMUSG00000020817	Rabep1	Rab5ep|rabaptin-5|rabaptin-5alpha	rabaptin, RAB GTPase binding effector protein 1	protein-coding
mm_163128.1	chr11	78149461	78149485	-	1	NA	intron (NM_001346762, intron 2 of 2)	intron (NM_001346762, intron 2 of 2)	16077	NM_009423	22032	Mm.390418	NM_009423	ENSMUSG00000017386	Traf4	A530032M13Rik|CART1|msp2	TNF receptor associated factor 4	protein-coding
mm_129824.1	chr15	83122734	83122746	-	1	NA	promoter-TSS (NM_029101)	promoter-TSS (NM_029101)	61	NM_029101	74778	Mm.30056	NM_029101	ENSMUSG00000018040	Rrp7a	1110014J01Rik|AA408146|Kheg1	ribosomal RNA processing 7 homolog A (S. cerevisiae)	protein-coding
mm_10471.1	chr2	14331430	14331451	+	1	NA	3' UTR (NM_008625, exon 30 of 30)	3' UTR (NM_008625, exon 30 of 30)	-56958	NM_001012305	277468	Mm.44662	NM_001012305	ENSMUSG00000036949	Slc39a12	AW046938|Gm731	solute carrier family 39 (zinc transporter), member 12	protein-coding
mm_72101.1	chr8	71592546	71592594	+	1	NA	5' UTR (NM_001294269, exon 1 of 5)	5' UTR (NM_001294269, exon 1 of 5)	386	NM_001294269	66171	Mm.282284	NM_025396	ENSMUSG00000031807	Pgls	1110030K05Rik|AI447866|Plgs	6-phosphogluconolactonase	protein-coding
mm_113511.1	chr13	37778413	37778424	+	1	NA	Intergenic	CpG	-47620	NM_026830	68750	Mm.491109	NM_026830	ENSMUSG00000039087	Rreb1	1110037N09Rik|AA414966|B930013M22Rik	ras responsive element binding protein 1	protein-coding
mm_163229.1	chr11	102916186	102916189	-	1	NA	intron (NM_197959, intron 2 of 15)	intron (NM_197959, intron 2 of 15)	8937	NM_197959	70218	Mm.32084	NM_197959	ENSMUSG00000051378	Kif18b	3000004C01Rik	kinesin family member 18B	protein-coding
mm_90237.1	chr10	121395167	121395212	+	1	NA	3' UTR (NM_029364, exon 14 of 14)	3' UTR (NM_029364, exon 14 of 14)	30099	NM_029364	75612	Mm.207683	NM_029364	ENSMUSG00000034707	Gns	2610016K11Rik|AU042285|C87209|G6S|N28088	glucosamine (N-acetyl)-6-sulfatase	protein-coding
mm_55681.1	chr6	72610593	72610600	-	1	NA	TTS (NM_009444)	TTS (NM_009444)	6152	NM_009444	22135	Mm.246563	NM_009444		Tgoln2	TGN38B|TGN41|TGN46|Ttgn2	trans-golgi network protein 2	protein-coding
mm_16314.1	chr2	174304110	174304112	+	1	NA	intron (NM_001310085, intron 2 of 12)	intron (NM_001310085, intron 2 of 12)	6252	NM_001310085	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_110436.1	chr12	47834082	47834091	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	467376	NR_039586	100628593		NR_039586	ENSMUSG00000092981	Mir5125	mmu-mir-5125|mu-mir-5125	microRNA 5125	ncRNA
mm_68627.1	chr7	118128665	118128670	-	1	NA	intron (NM_019419, intron 1 of 5)	intron (NM_019419, intron 1 of 5)	958	NM_019419	54208	Mm.29924	NM_019419	ENSMUSG00000030654	Arl6ip1	AIP-6|AL022945|ARMER|AU042858|Aip-1|Arl6ip|C85138|mKIAA0069	ADP-ribosylation factor-like 6 interacting protein 1	protein-coding
mm_17226.1	chr2	25546873	25546915	-	1	NA	promoter-TSS (NM_001290413)	promoter-TSS (NM_001290413)	46	NM_001290413	22030	Mm.3399	NM_009422	ENSMUSG00000026942	Traf2	AI325259	TNF receptor-associated factor 2	protein-coding
mm_117252.1	chr13	64366509	64366596	-	1	NA	exon (NM_009984, exon 6 of 8)	exon (NM_009984, exon 6 of 8)	3968	NM_009984	13039	Mm.930	NM_009984	ENSMUSG00000021477	Ctsl	1190035F06Rik|CatL|Ctsl1|MEP|fs|nkt	cathepsin L	protein-coding
mm_164074.1	chr14	120637003	120637045	+	1	NA	Intergenic	URR1B|DNA|hAT-Charlie	158563	NM_029519	76108	Mm.261448	NM_029519	ENSMUSG00000051615	Rap2a	5830461H18Rik	RAS related protein 2a	protein-coding
mm_169534.1	chr14	92603534	92603536	-	1	NA	Intergenic	Intergenic	1285353	NM_001271800	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding
mm_166394.1	chr5	135012728	135012737	-	1	NA	TTS (NM_001190437)	TTS (NM_001190437)	425	NR_026688	69812	Mm.18422	NR_026688	ENSMUSG00000085042	Abhd11os	2010001M06Rik|AI462243|Wbscr26|Wnscr26	abhydrolase domain containing 11, opposite strand	ncRNA
mm_166425.1	chr5	137152205	137152226	+	1	NA	Intergenic	Intergenic	-36008	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_37122.1	chr4	116651678	116651682	-	1	NA	promoter-TSS (NM_021473)	promoter-TSS (NM_021473)	-6	NM_021473	58810	Mm.30085	NM_021473	ENSMUSG00000028692	Akr1a1	2610201A18Rik|Akr1a4	aldo-keto reductase family 1, member A1 (aldehyde reductase)	protein-coding
mm_10722.1	chr2	22834303	22834342	+	1	NA	exon (NM_019456, exon 6 of 14)	exon (NM_019456, exon 6 of 14)	59995	NM_019456	54519	Mm.14255	NM_019456	ENSMUSG00000026786	Apbb1ip	9930118P07Rik|Prp48	amyloid beta (A4) precursor protein-binding, family B, member 1 interacting protein	protein-coding
mm_127839.1	chr15	6874261	6874285	-	1	NA	promoter-TSS (NM_011019)	promoter-TSS (NM_011019)	40	NM_011019	18414	Mm.10760	NM_011019	ENSMUSG00000022146	Osmr	OSMRB	oncostatin M receptor	protein-coding
mm_14383.1	chr2	129631269	129631279	+	1	NA	3' UTR (NM_001291022, exon 5 of 5)	3' UTR (NM_001291022, exon 5 of 5)	38105	NM_001291022	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_153350.1	chr19	39886668	39886695	-	1	NA	promoter-TSS (NM_001104525)	promoter-TSS (NM_001104525)	88	NM_001104525	100043108	Mm.482331	NM_001104525	ENSMUSG00000092008	Cyp2c69	AI098658	cytochrome P450, family 2, subfamily c, polypeptide 69	protein-coding
mm_153946.1	chr19	47545828	47545845	-	1	NA	Intergenic	Intergenic	-8816	NM_175360	108689	Mm.218048	NM_175360	ENSMUSG00000042694	Obfc1	0610009H20Rik|2310057J23Rik|AAF-44|AAF44|AI413458|RPA-32	oligonucleotide/oligosaccharide-binding fold containing 1	protein-coding
mm_148930.1	chr19	7017962	7017972	+	1	NA	intron (NM_153795, intron 2 of 14)	intron (NM_153795, intron 2 of 14)	1502	NM_153795	108101	Mm.157591	NM_153795	ENSMUSG00000024965	Fermt3	C79673|Kindlin3	fermitin family member 3	protein-coding
mm_162666.1	chr10	6986532	6986552	+	1	NA	intron (NM_001304955, intron 5 of 6)	intron (NM_001304955, intron 5 of 6)	-6077	NM_001170801	320495	Mm.331674	NM_001033391	ENSMUSG00000064065	Ipcef1	A130090K04Rik	interaction protein for cytohesin exchange factors 1	protein-coding
mm_170272.1	chr18	24576822	24576840	-	1	NA	Intergenic	Intergenic	26986	NM_139143	106957	Mm.21688	NM_139143	ENSMUSG00000024270	Slc39a6	Ermelin	solute carrier family 39 (metal ion transporter), member 6	protein-coding
mm_61876.1	chr7	89510067	89510071	+	1	NA	exon (NM_029614, exon 2 of 2)	exon (NM_029614, exon 2 of 2)	7517	NM_029614	76453	Mm.250438	NM_029614	ENSMUSG00000039405	Prss23	2310046G15Rik|4930479H08Rik|AI790574|Spuve	protease, serine 23	protein-coding
mm_36517.1	chr4	84518565	84518569	-	1	NA	intron (NM_172870, intron 2 of 5)	intron (NM_172870, intron 2 of 5)	156519	NM_172870	242509	Mm.190774	NM_172870	ENSMUSG00000028487	Bnc2	5031434M05Rik|8430420F16Rik	basonuclin 2	protein-coding
mm_88216.1	chr10	70245261	70245318	+	1	NA	promoter-TSS (NM_025807)	promoter-TSS (NM_025807)	13	NM_025807	66859	Mm.19325	NM_025807	ENSMUSG00000037762	Slc16a9	1200003C15Rik|4930425B13Rik|AI552636	solute carrier family 16 (monocarboxylic acid transporters), member 9	protein-coding
mm_89717.1	chr10	98880391	98880402	+	1	NA	Intergenic	Intergenic	-34756	NM_026482	67972	Mm.166944	NM_026482	ENSMUSG00000019943	Atp2b1	2810442I22Rik|E130111D10Rik|Pmca1	ATPase, Ca++ transporting, plasma membrane 1	protein-coding
mm_47710.1	chr5	129995489	129995510	-	1	NA	exon (NM_010368, exon 9 of 12)	exon (NM_010368, exon 9 of 12)	7329	NM_010368	110006	Mm.3317	NM_010368	ENSMUSG00000025534	Gusb	AI747421|Gur|Gus|Gus-r|Gus-s|Gus-t|Gus-u|Gut|asd|g	glucuronidase, beta	protein-coding
mm_104274.1	chr11	89302546	89302567	-	1	NA	promoter-TSS (NM_008711)	promoter-TSS (NM_008711)	3	NM_008711	18121	Mm.135266	NM_008711	ENSMUSG00000048616	Nog	-	noggin	protein-coding
mm_92124.1	chr10	64037903	64037934	-	1	NA	intron (NM_178678, intron 2 of 2)	intron (NM_178678, intron 2 of 2)	52337	NM_178678	216028	Mm.431318	NM_178678	ENSMUSG00000042846	Lrrtm3	9630044H04Rik	leucine rich repeat transmembrane neuronal 3	protein-coding
mm_116138.1	chr13	29357675	29357695	-	1	NA	intron (NR_131896, intron 13 of 16)	intron (NR_131896, intron 13 of 16)	341430	NR_045075	77920	Mm.197051	NR_045073	ENSMUSG00000086363	A330102I10Rik	-	RIKEN cDNA A330102I10 gene	ncRNA
mm_65711.1	chr7	28378188	28378199	-	1	NA	exon (NM_011756, exon 2 of 2)	exon (NM_011756, exon 2 of 2)	1035	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_9629.1	chr1	176813944	176813960	-	1	NA	promoter-TSS (NM_029756)	promoter-TSS (NM_029756)	-708	NM_029756	76816	Mm.171399	NM_029756	ENSMUSG00000026504	Sdccag8	2700048G21Rik|5730470G24Rik|Cccap	serologically defined colon cancer antigen 8	protein-coding
mm_124046.1	chr14	77252328	77252328	-	1	NA	intron (NM_001253759, intron 1 of 19)	intron (NM_001253759, intron 1 of 19)	95565	NM_172813	239188	Mm.441158	NM_172813	ENSMUSG00000022012	Enox1	B230207J08|D230005D02Rik	ecto-NOX disulfide-thiol exchanger 1	protein-coding
mm_97373.1	chr11	77686230	77686240	+	1	NA	promoter-TSS (NM_001024205)	promoter-TSS (NM_001024205)	96	NM_001024205	68564	Mm.428996	NM_001024205	ENSMUSG00000037857	Nufip2	1110001M19Rik|9530056D24Rik|AI256692|AI461731|PIG1|mKIAA1321	nuclear fragile X mental retardation protein interacting protein 2	protein-coding
mm_93674.1	chr10	117710675	117710736	-	1	NA	promoter-TSS (NM_010786)	promoter-TSS (NM_010786)	53	NM_010786	17246	Mm.22670	NM_010786	ENSMUSG00000020184	Mdm2	1700007J15Rik|AA415488|Mdm-2	transformed mouse 3T3 cell double minute 2	protein-coding
mm_162442.1	chr1	115684955	115684958	+	1	NA	promoter-TSS (NM_001077425)	promoter-TSS (NM_001077425)	-181	NM_001077425	636808	Mm.101576	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding
mm_139195.1	chr17	47629787	47629799	+	1	NA	promoter-TSS (NM_198421)	promoter-TSS (NM_198421)	-897	NM_198421	224836	Mm.59393	NM_198421	ENSMUSG00000090115	Usp49	C330046L10Rik|Gm545	ubiquitin specific peptidase 49	protein-coding
mm_94444.1	chr11	6346534	6346558	+	1	NA	exon (NM_001252282, exon 12 of 24)	exon (NM_001252282, exon 12 of 24)	-48579	NM_001005867	52915	Mm.1144	NM_028601	ENSMUSG00000041164	Zmiz2	Zimp7	zinc finger, MIZ-type containing 2	protein-coding
mm_92019.1	chr10	62379902	62379917	-	1	NA	promoter-TSS (NM_010438)	promoter-TSS (NM_010438)	-1	NM_010438	15275	Mm.196605	NM_010438	ENSMUSG00000037012	Hk1	BB404130|Hk-1|Hk1-s|dea|mHk1-s	hexokinase 1	protein-coding
mm_48846.1	chr5	149368168	149368185	-	1	NA	Intergenic	Intergenic	-43630	NM_027519	70717	Mm.252139	NM_027519	ENSMUSG00000029659	Medag	6330406I15Rik|Awms3|MEDA-4|Meda4|mAWMS3	mesenteric estrogen dependent adipogenesis	protein-coding
mm_93491.1	chr10	112002613	112002636	-	1	NA	Intergenic	Intergenic	-5360	NM_028608	73690	Mm.173790	NM_028608	ENSMUSG00000056888	Glipr1	2410114O14Rik|RTVP-1|RTVP1|mRTVP-1	GLI pathogenesis-related 1 (glioma)	protein-coding
mm_66154.1	chr7	31149706	31149717	-	1	NA	intron (NM_027898, intron 1 of 18)	intron (NM_027898, intron 1 of 18)	1339	NM_027898	52857	Mm.27366	NM_027898	ENSMUSG00000001248	Gramd1a	1300003M23Rik|AI415002|AW547240|D7Bwg0611e	GRAM domain containing 1A	protein-coding
mm_70750.1	chr8	19535427	19535463	+	1	NA	Intergenic	CpG	40348	NM_139220	246080	Mm.207067	NM_139220	ENSMUSG00000037790	Defb7	BD-7|Defb15	defensin beta 7	protein-coding
mm_47254.1	chr5	121618866	121618925	-	1	NA	promoter-TSS (NM_178799)	promoter-TSS (NM_178799)	43	NM_178799	338350	Mm.482918	NM_178799	ENSMUSG00000042647	Acad12	9330129D05Rik	acyl-Coenzyme A dehydrogenase family, member 12	protein-coding
mm_64913.1	chr7	16222014	16222050	-	1	NA	promoter-TSS (NM_027883)	promoter-TSS (NM_027883)	0	NM_027883	71723	Mm.75259	NM_027883	ENSMUSG00000006019	Dhx34	1200013B07Rik|1810012L18Rik|Ddx34|mKIAA0134	DEAH (Asp-Glu-Ala-His) box polypeptide 34	protein-coding
mm_9178.1	chr1	171058079	171058079	-	1	NA	intron (NM_010188, intron 2 of 4)	intron (NM_010188, intron 2 of 4)	1324	NM_010188	14131	Mm.22119	NM_010188	ENSMUSG00000059498	Fcgr3	CD16	Fc receptor, IgG, low affinity III	protein-coding
mm_138858.1	chr17	42435805	42435808	+	1	NA	intron (NM_028474, intron 3 of 3)	intron (NM_028474, intron 3 of 3)	119859	NM_028474	627626	Mm.390999	NM_028474	ENSMUSG00000042256	Ptchd4	3110082D06Rik|Gm321	patched domain containing 4	protein-coding
mm_172776.1	chr8	95271989	95271993	-	1	NA	intron (NM_001195413, intron 16 of 32)	intron (NM_001195413, intron 16 of 32)	34594	NM_145601	333329	Mm.484049	NM_145601	ENSMUSG00000031789	Cngb1	Cngb1b|Garp2|Gm1959	cyclic nucleotide gated channel beta 1	protein-coding
mm_14524.1	chr2	132691998	132692008	+	1	NA	exon (NM_028637, exon 2 of 3)	exon (NM_028637, exon 2 of 3)	1720	NM_028637	73747	Mm.284114	NM_028637	ENSMUSG00000044991	1110034G24Rik	-	RIKEN cDNA 1110034G24 gene	protein-coding
mm_78744.1	chr9	42095001	42095027	+	1	NA	intron (NM_011436, intron 3 of 47)	intron (NM_011436, intron 3 of 47)	29275	NM_011436	20660	Mm.121920	NM_011436	ENSMUSG00000049313	Sorl1	2900010L19Rik|AI596264|AW261561|LR11|SorLA|gp250|mSorLA	sortilin-related receptor, LDLR class A repeats-containing	protein-coding
mm_58935.1	chr7	18065973	18065987	+	1	NA	promoter-TSS (NM_001162524)	promoter-TSS (NM_001162524)	51	NM_001162523	67315	Mm.46089	NM_026087	ENSMUSG00000030366	Ceacam12	1600031J20Rik|Ceacam12-C1|Ceacam12-C3|Ceacam12C1|Ceacam12C3	carcinoembryonic antigen-related cell adhesion molecule 12	protein-coding
mm_50172.1	chr6	41558503	41558522	+	1	NA	Intergenic	Intergenic	36736	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_6228.1	chr1	66937489	66937512	-	1	NA	intron (NM_021285, intron 1 of 6)	intron (NM_021285, intron 1 of 6)	-2134	NM_001113387	17901	Mm.1000	NM_021285	ENSMUSG00000061816	Myl1	AI325107|MLC1f|MLC3f|Mylf	myosin, light polypeptide 1	protein-coding
mm_159964.1	chr6	90301394	90301394	+	1	NA	intron (NM_177738, intron 1 of 4)	intron (NM_177738, intron 1 of 4)	124	NM_177738	243535	Mm.233854	NM_177738	ENSMUSG00000049694	BC048671	-	cDNA sequence BC048671	protein-coding
mm_18453.1	chr2	60963122	60963132	-	1	NA	promoter-TSS (NM_020296)	promoter-TSS (NM_020296)	77	NM_020296	56878	Mm.259667	NM_020296	ENSMUSG00000026970	Rbms1	2600014B10Rik|AI255215|MSSP-1|MSSP-2|MSSP-3|YC1	RNA binding motif, single stranded interacting protein 1	protein-coding
mm_53436.1	chr6	134115227	134115257	+	1	NA	intron (NM_001303102, intron 2 of 8)	intron (NM_001303102, intron 2 of 8)	79542	NM_007961	14011	Mm.269995	NM_007961	ENSMUSG00000030199	Etv6	AW123102|AW557856|Tel	ets variant 6	protein-coding
mm_37085.1	chr4	116406109	116406120	-	1	NA	intron (NM_008641, intron 3 of 28)	intron (NM_008641, intron 3 of 28)	58067	NM_001042743	17776	Mm.9287	NM_008641	ENSMUSG00000003810	Mast2	MAST205|Mtssk	microtubule associated serine/threonine kinase 2	protein-coding
mm_30677.1	chr4	11169914	11169942	+	1	NA	exon (NM_021897, exon 4 of 4)	exon (NM_021897, exon 4 of 4)	13487	NM_021897	60599	Mm.393018	NM_021897	ENSMUSG00000028211	Trp53inp1	2700057G22Rik|SIP|SIP18|SIP27|Stinp|Teap	transformation related protein 53 inducible nuclear protein 1	protein-coding
mm_85481.1	chr9	106066499	106066515	-	1	NA	intron (NM_026763, intron 8 of 37)	intron (NM_026763, intron 8 of 37)	30184	NM_026763	68553	Mm.28854	NM_026763	ENSMUSG00000032572	Col6a4	1110001D15Rik|AI413310|AU023415|Dvwa|EG235580|Vwa6	collagen, type VI, alpha 4	protein-coding
mm_66729.1	chr7	46238549	46238557	-	1	NA	promoter-TSS (NM_153677)	promoter-TSS (NM_153677)	-63	NM_153677	72088	Mm.119709	NM_023649	ENSMUSG00000030838	Ush1c	2010016F01Rik|harmonin	Usher syndrome 1C	protein-coding
mm_83329.1	chr9	44233928	44233967	-	1	NA	promoter-TSS (NM_007619)	promoter-TSS (NM_007619)	99	NM_007619	12402	Mm.266871	NM_007619	ENSMUSG00000034342	Cbl	4732447J05Rik|Cbl-2|c-Cbl|cbl	Casitas B-lineage lymphoma	protein-coding
mm_119972.1	chr14	55540468	55540478	+	1	NA	exon (NM_028994, exon 1 of 10)	exon (NM_028994, exon 1 of 10)	207	NM_028994	74551	Mm.29856	NM_028994	ENSMUSG00000040618	Pck2	1810010O14Rik|9130022B02Rik|PEPCK-M	phosphoenolpyruvate carboxykinase 2 (mitochondrial)	protein-coding
mm_81203.1	chr9	107569113	107569135	+	1	NA	promoter-TSS (NM_010489)	promoter-TSS (NM_010489)	-39	NM_010489	15587	Mm.4834	NM_010489	ENSMUSG00000010047	Hyal2	AI256841|AU020858|AW555733	hyaluronoglucosaminidase 2	protein-coding
mm_48319.1	chr5	138977137	138977152	-	1	NA	3' UTR (NM_008808, exon 6 of 6)	3' UTR (NM_008808, exon 6 of 6)	17809	NM_008808	18590	Mm.2675	NM_008808	ENSMUSG00000025856	Pdgfa	-	platelet derived growth factor, alpha	protein-coding
mm_40889.1	chr5	75110305	75110351	+	1	NA	promoter-TSS (NR_045792)	promoter-TSS (NR_045792)	7	NR_045792	100503184	Mm.386273	NR_045792	ENSMUSG00000107192	Gm19583	-	predicted gene, 19583	ncRNA
mm_104160.1	chr11	87294048	87294061	-	1	NA	intron (NR_106195, intron 6 of 8)	intron (NR_106195, intron 6 of 8)	64940	NM_177167	320472	Mm.341988	NM_177167	ENSMUSG00000046442	Ppm1e	AW049266|B930008A12Rik|POPX1|PP2CH|mKIAA1072	protein phosphatase 1E (PP2C domain containing)	protein-coding
mm_67768.1	chr7	93179670	93179678	-	1	NA	Intergenic	MusHAL1|LINE|L1	99795	NM_021427	58238	Mm.113787	NM_021427	ENSMUSG00000051515	Fam181b	A830059I20Rik|AB041569	family with sequence similarity 181, member B	protein-coding
mm_42615.1	chr5	118027794	118027800	+	1	NA	promoter-TSS (NM_021344)	promoter-TSS (NM_021344)	-27	NM_021344	57816	Mm.273285	NM_021344	ENSMUSG00000029359	Tesc	1010001A17Rik|2410011K10Rik|TE-1	tescalcin	protein-coding
mm_156902.1	chrX	168874762	168874770	+	1	NA	intron (NM_009707, intron 1 of 12)	intron (NM_009707, intron 1 of 12)	79667	NM_009707	11856	Mm.441810	NM_009707	ENSMUSG00000031355	Arhgap6	AI504284|RhoGAPX-1	Rho GTPase activating protein 6	protein-coding
mm_161989.1	chr19	32349301	32349301	-	1	NA	promoter-TSS (NM_001168525)	promoter-TSS (NM_001168525)	15	NM_001168525	208449	Mm.329810	NM_144792	ENSMUSG00000040451	Sgms1	9530058O11Rik|AI841905|C80702|Mob|Sms1|Sor1|Tmem23	sphingomyelin synthase 1	protein-coding
mm_9925.1	chr1	189729657	189729671	-	1	NA	intron (NM_008976, intron 1 of 18)	intron (NM_008976, intron 1 of 18)	1396	NM_008976	19250	Mm.4498	NM_008976	ENSMUSG00000026604	Ptpn14	C130080N23Rik|OTTMUSG00000022087|PTP36	protein tyrosine phosphatase, non-receptor type 14	protein-coding
mm_101695.1	chr11	40750709	40750728	-	1	NA	3' UTR (NM_009831, exon 6 of 6)	3' UTR (NM_009831, exon 6 of 6)	4568	NM_009831	12450	Mm.2103	NM_009831	ENSMUSG00000020326	Ccng1	AI314029	cyclin G1	protein-coding
mm_35637.1	chr4	43515788	43515801	-	1	NA	3' UTR (NM_009416, exon 9 of 9)	3' UTR (NM_009416, exon 9 of 9)	7760	NM_009416	22004	Mm.646	NM_009416	ENSMUSG00000028464	Tpm2	Tpm-2|Trop-2	tropomyosin 2, beta	protein-coding
mm_138873.1	chr17	43087990	43088002	+	1	NA	3' UTR (NM_178589, exon 6 of 6)	3' UTR (NM_178589, exon 6 of 6)	70295	NR_045155	545207	Mm.329050	NR_045153		E130008D07Rik	-	RIKEN cDNA E130008D07 gene	ncRNA
mm_152585.1	chr19	11603876	11603888	-	1	NA	intron (NM_026835, intron 1 of 6)	intron (NM_026835, intron 1 of 6)	922	NM_026835	68774	Mm.290390	NM_026835	ENSMUSG00000024679	Ms4a6d	1110058E16Rik|AI447446|Ms4a11	membrane-spanning 4-domains, subfamily A, member 6D	protein-coding
mm_11145.1	chr2	28513106	28513126	+	1	NA	promoter-TSS (NM_009058)	promoter-TSS (NM_009058)	-51	NM_009058	19730	Mm.5236	NM_009058	ENSMUSG00000026821	Ralgds	Gnds|Rgds|mKIAA1308	ral guanine nucleotide dissociation stimulator	protein-coding
mm_124170.1	chr14	93766059	93766066	-	1	NA	intron (NM_001346722, intron 2 of 4)	intron (NM_001346722, intron 2 of 4)	122826	NM_001271800	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding
mm_148349.1	chr18	84679098	84679106	-	1	NA	intron (NM_023149, intron 3 of 11)	intron (NM_023149, intron 3 of 11)	2957	NM_001289531	66054	Mm.29646	NM_023149	ENSMUSG00000024644	Cndp2	0610010E05Rik|C76600|Cn2|Dip-2|Pep-1|Pep1	CNDP dipeptidase 2 (metallopeptidase M20 family)	protein-coding
mm_27845.1	chr3	79156342	79156364	-	1	NA	Intergenic	Intergenic	-10478	NM_001099624	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_140378.1	chr17	87025557	87025635	+	1	NA	promoter-TSS (NM_008838)	promoter-TSS (NM_008838)	35	NM_019936	56724	Mm.109329	NM_019936	ENSMUSG00000024146	Cript	1200020A08Rik|AA589469	cysteine-rich PDZ-binding protein	protein-coding
mm_320.1	chr1	24678614	24678627	+	1	NA	promoter-TSS (NM_026719)	promoter-TSS (NM_026719)	76	NM_026719	68421	Mm.336563	NM_026719	ENSMUSG00000073725	Lmbrd1	0910001K20Rik|AV347960	LMBR1 domain containing 1	protein-coding
mm_2904.1	chr1	131970556	131970572	+	1	NA	promoter-TSS (NM_145977)	promoter-TSS (NM_145977)	-45	NM_145977	212980	Mm.200307	NM_145977	ENSMUSG00000026435	Slc45a3	2210413P12Rik|AU023994|AU043764|IPCA-6|PRST|Pcanap6	solute carrier family 45, member 3	protein-coding
mm_39158.1	chr4	155491219	155491234	-	1	NA	promoter-TSS (NM_008142)	promoter-TSS (NM_008142)	-135	NM_001160017	14688	Mm.2344	NM_008142	ENSMUSG00000029064	Gnb1	AA409223|C77571|Gnb-1	guanine nucleotide binding protein (G protein), beta 1	protein-coding
mm_134088.1	chr16	8792332	8792348	-	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	-37760	NM_001081400	69053	Mm.390868	NM_001081400	ENSMUSG00000022507	1810013L24Rik	1110017P05Rik|3010002C02Rik|AA792997|AW124177|Gm19906|R74903	RIKEN cDNA 1810013L24 gene	protein-coding
mm_68203.1	chr7	104381144	104381154	-	1	NA	Intergenic	MIRb|SINE|MIR	-22503	NM_175648	244183	Mm.347647	NM_175648	ENSMUSG00000052749	Trim30b	A530023O14Rik|Trim30-1	tripartite motif-containing 30B	protein-coding
mm_150088.1	chr19	29414769	29414798	+	1	NA	intron (NM_021396, intron 1 of 5)	intron (NM_021396, intron 1 of 5)	3864	NM_021396	58205	Mm.116737	NM_021396	ENSMUSG00000016498	Pdcd1lg2	B7-DC|Btdc|F730015O22Rik|PD-L2	programmed cell death 1 ligand 2	protein-coding
mm_13400.1	chr2	103970332	103970340	+	1	NA	promoter-TSS (NM_008505)	promoter-TSS (NM_008505)	49	NM_001142335	16909	Mm.29266	NM_008505	ENSMUSG00000032698	Lmo2	Rbtn-2|Rbtn2|Rhom-2|Ttg2	LIM domain only 2	protein-coding
mm_145627.1	chr18	61109737	61109759	+	1	NA	exon (NM_001037859, exon 3 of 22)	exon (NM_001037859, exon 3 of 22)	4176	NM_001037859	12978	Mm.22574	NM_007779	ENSMUSG00000024621	Csf1r	AI323359|CD115|CSF-1R|Csfmr|Fim-2|Fim2|Fms|M-CSF-R|M-CSFR	colony stimulating factor 1 receptor	protein-coding
mm_142207.1	chr17	36988732	36988743	-	1	NA	exon (NM_001115075, exon 3 of 6)	exon (NM_001115075, exon 3 of 6)	767	NM_001115075	240095	Mm.246609	NM_001115075	ENSMUSG00000024459	H2-M5	CRW2|D130003B22Rik|H-2M5	histocompatibility 2, M region locus 5	protein-coding
mm_126358.1	chr15	80012322	80012348	+	1	NA	intron (NM_011057, intron 1 of 6)	CpG	2473	NM_011057	18591	Mm.144089	NM_011057	ENSMUSG00000000489	Pdgfb	PDGF-B|Sis	platelet derived growth factor, B polypeptide	protein-coding
mm_168701.1	chr11	97781867	97781871	-	1	NA	promoter-TSS (NR_028078)	promoter-TSS (NR_028078)	-103	NR_028078	100302498	Mm.453536	NR_028078	ENSMUSG00000064901	Snora21	MBI-3	small nucleolar RNA, H/ACA box 21	snoRNA
mm_94366.1	chr11	5012676	5012705	+	1	NA	intron (NM_007454, intron 2 of 20)	intron (NM_007454, intron 2 of 20)	25866	NM_007454	11764	Mm.274816	NM_007454	ENSMUSG00000009090	Ap1b1	Adtb1|b2b1660Clo	adaptor protein complex AP-1, beta 1 subunit	protein-coding
mm_70928.1	chr8	25813089	25813099	+	1	NA	3' UTR (NM_011485, exon 7 of 7)	3' UTR (NM_011485, exon 7 of 7)	4620	NM_011485	20845	Mm.293314	NM_011485	ENSMUSG00000031574	Star	AV363654|D8Ertd419e|stARD1	steroidogenic acute regulatory protein	protein-coding
mm_49452.1	chr6	29366118	29366134	+	1	NA	exon (NM_184053, exon 4 of 7)	exon (NM_184053, exon 4 of 7)	14387	NM_007538	12057	Mm.56987	NM_007538	ENSMUSG00000058831	Opn1sw	AW551857|Bcp	opsin 1 (cone pigments), short-wave-sensitive (color blindness, tritan)	protein-coding
mm_25787.1	chr3	126780409	126780416	+	1	NA	exon (NM_001293663, exon 7 of 20)	exon (NM_001293663, exon 7 of 20)	162974	NM_001034168	109676	Mm.220242	NM_178655	ENSMUSG00000032826	Ank2	100043364|AI835472|AW491075|Ank-2|Gm4392	ankyrin 2, brain	protein-coding
mm_25477.1	chr3	108912414	108912422	+	1	NA	promoter-TSS (NM_025845)	promoter-TSS (NM_025845)	-714	NM_025845	66921	Mm.51049	NM_025845	ENSMUSG00000027881	Prpf38b	1110021E09Rik|AU018955	PRP38 pre-mRNA processing factor 38 (yeast) domain containing B	protein-coding
mm_142477.1	chr17	45686215	45686265	-	1	NA	promoter-TSS (NM_026732)	promoter-TSS (NM_026732)	-22	NM_198167	224807	Mm.157904	NM_198167	ENSMUSG00000036026	Tmem63b	BC026370	transmembrane protein 63b	protein-coding
mm_4213.1	chr1	171281308	171281319	+	1	NA	promoter-TSS (NM_008911)	promoter-TSS (NM_008911)	-127	NM_008911	19044	Mm.266888	NM_008911	ENSMUSG00000062729	Ppox	Ppo	protoporphyrinogen oxidase	protein-coding
mm_103023.1	chr11	69735045	69735053	-	1	NA	exon (NM_001291068, exon 29 of 29)	exon (NM_001291068, exon 29 of 29)	23584	NM_001291068	20020	Mm.16533	NM_009089	ENSMUSG00000005198	Polr2a	220kDa|Rpb1|Rpo2-1	polymerase (RNA) II (DNA directed) polypeptide A	protein-coding
mm_152332.1	chr19	9964631	9964638	-	1	NA	Intergenic	Intergenic	-15966	NR_073181	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
mm_112426.1	chr13	4228683	4228727	+	1	NA	Intergenic	Intergenic	-5035	NM_001013785	432720	Mm.22832	NM_001013785	ENSMUSG00000071551	Akr1c19	1810010N06Rik	aldo-keto reductase family 1, member C19	protein-coding
mm_141997.1	chr17	35190235	35190258	-	1	NA	Intergenic	Intergenic	-1806	NM_010734	16988	Mm.19379	NM_010734	ENSMUSG00000073412	Lst1	B144	leukocyte specific transcript 1	protein-coding
mm_166544.1	chr6	34438608	34438610	+	1	NA	Intergenic	RMER15|LTR|ERVL	26247	NM_009731	11997	Mm.482073	NM_009731	ENSMUSG00000052131	Akr1b7	AR|Avdp|MVDP	aldo-keto reductase family 1, member B7	protein-coding
mm_24980.1	chr3	96830070	96830115	+	1	NA	promoter-TSS (NM_001163497)	promoter-TSS (NM_001163497)	27	NM_021517	59020	Mm.489677	NM_021517	ENSMUSG00000038298	Pdzk1	1700023D20Rik|2610507N21Rik|4921513F16Rik|AI267131|AI314638|AL022680|D3Ertd537e|Pdzd1|mPDZK1	PDZ domain containing 1	protein-coding
mm_137183.1	chr17	23816359	23816375	+	1	NA	exon (NM_175229, exon 10 of 14)	exon (NM_175229, exon 10 of 14)	12742	NM_026305	67673	Mm.153758	NM_026305	ENSMUSG00000055839	Elob	0610040H15Rik|Tceb2	elongin B	protein-coding
mm_97441.1	chr11	78178959	78178986	+	1	NA	TTS (NR_106113)	TTS (NR_106113)	145	NR_106113	102465761		NR_106113	ENSMUSG00000099101	Mir7653	Gm27900|mmu-mir-7653	microRNA 7653	ncRNA
mm_131321.1	chr16	11984390	11984422	+	1	NA	5' UTR (NM_028277, exon 1 of 5)	5' UTR (NM_028277, exon 1 of 5)	293	NM_001174086	72555	Mm.310139	NM_028277	ENSMUSG00000022494	Shisa9	2700045P11Rik|Ckamp44	shisa family member 9	protein-coding
mm_114172.1	chr13	55478657	55478659	+	1	NA	promoter-TSS (NR_105909)	promoter-TSS (NR_105909)	-882	NR_105909	102465569		NR_105909	ENSMUSG00000098341	Mir6944	Gm27710|mmu-mir-6944	microRNA 6944	ncRNA
mm_89290.1	chr10	87892586	87892614	+	1	NA	intron (NM_001314010, intron 3 of 4)	B4A|SINE|B4	31489	NM_001111276	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_107915.1	chr12	71015967	71016063	+	1	NA	promoter-TSS (NR_045056)	promoter-TSS (NR_045056)	48	NM_001081195	238247	Mm.241601	NM_001081195	ENSMUSG00000048118	Arid4a	A630009N03|A630067N03Rik|MmRBBP1|Rbbp1	AT rich interactive domain 4A (RBP1-like)	protein-coding
mm_50016.1	chr6	41113553	41113581	+	1	NA	Intergenic	Intergenic	-78058	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_130489.1	chr15	98778529	98778541	-	1	NA	promoter-TSS (NM_011718)	promoter-TSS (NM_011718)	-385	NM_011718	22410	Mm.4709	NM_011718	ENSMUSG00000022996	Wnt10b	Wnt12	wingless-type MMTV integration site family, member 10B	protein-coding
mm_101522.1	chr11	32824549	32824551	-	1	NA	promoter-TSS (NM_027050)	promoter-TSS (NM_027050)	44	NM_027050	69351	Mm.65488	NM_027050	ENSMUSG00000020270	Smim23	1700008A04Rik	small integral membrane protein 23	protein-coding
mm_75466.1	chr8	47948386	47948407	-	1	NA	intron (NM_133791, intron 1 of 22)	intron (NM_133791, intron 1 of 22)	42155	NM_133791	52357	Mm.235074	NM_133791	ENSMUSG00000031563	Wwc2	5330431C14Rik|AU022508|C85457|D8Ertd594e	WW, C2 and coiled-coil domain containing 2	protein-coding
mm_157624.1	chrX	56553145	56553179	-	1	NA	Intergenic	Intergenic	-3556	NM_001033372	270599	Mm.424438	NM_001033372	ENSMUSG00000064016	Gm648	-	predicted gene 648	protein-coding
mm_153229.1	chr19	34879289	34879313	-	1	NA	5' UTR (NM_001114339, exon 1 of 7)	5' UTR (NM_001114339, exon 1 of 7)	154	NM_001114339	75735	Mm.24742	NM_023792	ENSMUSG00000033610	Pank1	Pank|Pank1b	pantothenate kinase 1	protein-coding
mm_104992.1	chr11	100320379	100320383	-	1	NA	intron (NM_011508, intron 1 of 3)	CpG	432	NM_011508	20918	Mm.13886	NM_011508	ENSMUSG00000035530	Eif1	Sui1-rs1	eukaryotic translation initiation factor 1	protein-coding
mm_87458.1	chr10	51484452	51484472	+	1	NA	intron (NM_001291892, intron 6 of 8)	intron (NM_001291892, intron 6 of 8)	3850	NM_001291892	14727	Mm.439661	NM_008147	ENSMUSG00000062593	Lilr4b	Gp49a|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4B	protein-coding
mm_53664.1	chr6	141524590	141524629	+	1	NA	5' UTR (NM_001177772, exon 1 of 15)	5' UTR (NM_001177772, exon 1 of 15)	223	NM_021471	58807	Mm.284495	NM_021471	ENSMUSG00000030235	Slco1c1	OATP-14|OATP-F|Oatp2|Oatpf|Slc21a14	solute carrier organic anion transporter family, member 1c1	protein-coding
mm_103557.1	chr11	77720996	77721002	-	1	NA	exon (NM_009965, exon 4 of 6)	exon (NM_009965, exon 4 of 6)	4294	NM_001313933	12957	Mm.22830	NM_009965	ENSMUSG00000000724	Cryba1	BA3/A1|Cryb	crystallin, beta A1	protein-coding
mm_60039.1	chr7	31037806	31037856	+	1	NA	exon (NM_001111073, exon 4 of 8)	exon (NM_001111073, exon 4 of 8)	2486	NR_106017	102465635		NR_106017	ENSMUSG00000098783	Mir7050	Gm27578|mmu-mir-7050	microRNA 7050	ncRNA
mm_169026.1	chr13	113794500	113794512	+	1	NA	promoter-TSS (NM_172595)	promoter-TSS (NM_172595)	-2	NM_172595	218639	Mm.79837	NM_172595	ENSMUSG00000042348	Arl15	A430036I03|Arfrp2|C230032K13Rik	ADP-ribosylation factor-like 15	protein-coding
mm_117066.1	chr13	58827012	58827014	-	1	NA	intron (NM_001025074, intron 2 of 17)	L4_C_Mam|LINE|RTE-X	19316	NM_001025074	18212	Mm.130054	NM_008745	ENSMUSG00000055254	Ntrk2	GP145-TrkB/GP95-TrkB|Tkrb|trk-B|trkB	neurotrophic tyrosine kinase, receptor, type 2	protein-coding
mm_112159.1	chr12	113329467	113329475	-	1	NA	Intergenic	Intergenic	143568	NM_153776	69195	Mm.313244	NM_153776	ENSMUSG00000049036	Tmem121	2410008J05Rik|Hole	transmembrane protein 121	protein-coding
mm_9570.1	chr1	173979831	173979841	-	1	NA	intron (NM_008327, intron 1 of 6)	Lx9|LINE|L1	3008	NM_008327	26388	Mm.218770	NM_008327	ENSMUSG00000026535	Ifi202b	Ifbip-1|Ifi202|Ifi202a|p202	interferon activated gene 202B	protein-coding
mm_97690.1	chr11	80154072	80154082	+	1	NA	promoter-TSS (NM_172133)	promoter-TSS (NM_172133)	-85	NM_172133	216991	Mm.341520	NM_172133	ENSMUSG00000020709	Adap2	Centa2	ArfGAP with dual PH domains 2	protein-coding
mm_71753.1	chr8	65820595	65820599	+	1	NA	intron (NM_175188, intron 1 of 7)	intron (NM_175188, intron 1 of 7)	202072	NM_175188	72925	Mm.380457	NM_175188	ENSMUSG00000036469	March1	2900024D24Rik|BB085186	membrane-associated ring finger (C3HC4) 1	protein-coding
mm_125328.1	chr15	38644406	38644411	+	1	NA	Intergenic	Intergenic	-17496	NM_025494	66335	Mm.276618	NM_025494	ENSMUSG00000022295	Atp6v1c1	1700025B18Rik|U13839	ATPase, H+ transporting, lysosomal V1 subunit C1	protein-coding
mm_9691.1	chr1	178337160	178337172	-	1	NA	exon (NM_016805, exon 1 of 14)	exon (NM_016805, exon 1 of 14)	618	NM_016805	51810	Mm.86589	NM_016805	ENSMUSG00000039630	Hnrnpu	AA408410|AI256620|AL024194|AL024437|AW557595|C86794|Hnrpu|SAFA|Sp120|hnRNP U	heterogeneous nuclear ribonucleoprotein U	protein-coding
mm_148761.1	chr19	6061385	6061395	+	1	NA	exon (NM_013859, exon 1 of 1)	exon (NM_013859, exon 1 of 1)	183	NM_013859	29805	Mm.2310	NM_013859	ENSMUSG00000075227	Znhit2	C11orf5|Fon|ORF6|Znhit2-ps	zinc finger, HIT domain containing 2	protein-coding
mm_93216.1	chr10	94950786	94950786	-	1	NA	Intergenic	Intergenic	-6208	NM_018797	54712	Mm.256712	NM_018797	ENSMUSG00000074785	Plxnc1	2510048K12Rik|AW742158|CD232|Vespr	plexin C1	protein-coding
mm_71532.1	chr8	46921855	46921880	+	1	NA	Intergenic	Intergenic	-65020	NM_177304	320981	Mm.211429	NM_177304	ENSMUSG00000038173	Enpp6	4833421B01Rik|B830047L21Rik|D8Ertd514e|E-NPP 6|GPC-Cpde|Npp6	ectonucleotide pyrophosphatase/phosphodiesterase 6	protein-coding
mm_16900.1	chr2	13410801	13410805	-	1	NA	intron (NM_001081084, intron 27 of 66)	intron (NM_001081084, intron 27 of 66)	81073	NM_001081084	65969	Mm.313915	NM_001081084	ENSMUSG00000026726	Cubn	AA408369|AL022750|D2Wsu88e	cubilin (intrinsic factor-cobalamin receptor)	protein-coding
mm_157553.1	chrX	51840615	51840617	-	1	NA	Intergenic	Intergenic	-39383	NM_031388	83563	Mm.242827	NM_031388	ENSMUSG00000055780	Usp26	-	ubiquitin specific peptidase 26	protein-coding
mm_165822.1	chr3	147064431	147064433	+	1	NA	Intergenic	Intergenic	212065	NM_001302958	70892	Mm.187793	NM_027594	ENSMUSG00000036745	Ttll7	1110049N09Rik|4921517B04Rik|C630030B20|mTTLL7	tubulin tyrosine ligase-like family, member 7	protein-coding
mm_127102.1	chr15	97791543	97791576	+	1	NA	3' UTR (NM_026353, exon 3 of 3)	3' UTR (NM_026353, exon 3 of 3)	7194	NM_026353	67739	Mm.28955	NM_026353	ENSMUSG00000081534	Slc48a1	4930570C03Rik	solute carrier family 48 (heme transporter), member 1	protein-coding
mm_7907.1	chr1	133670446	133670464	-	1	NA	Intergenic	Intergenic	-9056	NM_144530	70579	Mm.245357	NM_144530	ENSMUSG00000102976	Zc3h11a	1110003F06Rik|5730454B08Rik|G630041M05Rik|Zc3hdc11a|Zc3hh11a|mKIAA0663	zinc finger CCCH type containing 11A	protein-coding
mm_18658.1	chr2	70089715	70089736	-	1	NA	intron (NM_177376, intron 2 of 34)	intron (NM_177376, intron 2 of 34)	50599	NM_177376	329421	Mm.99648	NM_177376	ENSMUSG00000042064	Myo3b	A430065P19Rik	myosin IIIB	protein-coding
mm_12860.1	chr2	83765497	83765499	+	1	NA	intron (NM_008402, intron 6 of 29)	intron (NM_008402, intron 6 of 29)	41101	NM_008402	16410	Mm.227	NM_008402	ENSMUSG00000027087	Itgav	1110004F14Rik|2610028E01Rik|CD51|D430040G12Rik	integrin alpha V	protein-coding
mm_156446.1	chrX	142681852	142681871	+	1	NA	5' UTR (NM_001199360, exon 1 of 7)	5' UTR (NM_001199360, exon 1 of 7)	135	NM_001199360	209497	Mm.249648	NM_177592	ENSMUSG00000047045	Tmem164	AI316850|AI852450|AW547186|F730011B02	transmembrane protein 164	protein-coding
mm_95347.1	chr11	48800865	48800868	+	1	NA	intron (NM_008143, intron 1 of 7)	intron (NM_008143, intron 1 of 7)	506	NM_008143	14694	Mm.5305	NM_008143	ENSMUSG00000020372	Rack1	AL033335|GB-like|Gnb2-rs1|Gnb2l1|p205	receptor for activated C kinase 1	protein-coding
mm_160230.1	chr7	102604427	102604427	+	1	NA	promoter-TSS (NM_147102)	promoter-TSS (NM_147102)	71	NM_147102	259106	Mm.377848	NM_147102	ENSMUSG00000073973	Olfr552	MOR28-1	olfactory receptor 552	protein-coding
mm_100119.1	chr11	115887611	115887651	+	1	NA	Intergenic	Intergenic	-12508	NM_183259	66528	Mm.275740	NM_183259	ENSMUSG00000048442	Smim5	2210020M01Rik	small integral membrane protein 5	protein-coding
mm_45982.1	chr5	90476487	90476511	-	1	NA	3' UTR (NM_009654, exon 15 of 15)	3' UTR (NM_009654, exon 15 of 15)	-14215	NM_007423	11576	Mm.358570	NM_007423	ENSMUSG00000054932	Afp	-	alpha fetoprotein	protein-coding
mm_106328.1	chr11	118318719	118318736	-	1	NA	intron (NM_011594, intron 2 of 4)	B3A|SINE|B2	23807	NM_021440	58251	Mm.439815	NM_021440	ENSMUSG00000076433	BC100451	Cep295nl|Ddc8|FS39|Kiaa1731nl	cDNA sequence BC100451	protein-coding
mm_131548.1	chr16	17894198	17894232	+	1	NA	promoter-TSS (NM_009435)	promoter-TSS (NM_009435)	12	NM_009435	22114	Mm.439725	NM_009435	ENSMUSG00000041566	Tssk1	Stk22a|TSK-1|Tsk1|Tssk|Tssk1b	testis-specific serine kinase 1	protein-coding
mm_150381.1	chr19	36347787	36347827	+	1	NA	Intergenic	Intergenic	-31260	NM_029508	76073	Mm.259180	NM_029508	ENSMUSG00000024805	Pcgf5	0610009F02Rik|1110054A01Rik|5830406C17Rik|5830443C21Rik|9530023M17Rik|AI324127	polycomb group ring finger 5	protein-coding
mm_20456.1	chr2	129365181	129365200	-	1	NA	exon (NM_008361, exon 7 of 7)	exon (NM_008361, exon 7 of 7)	-4712	NR_015474	329514	Mm.207315	NM_177848	ENSMUSG00000074805	Il1bos	9430083I22|Gm14047|OTTMUSG00000015529	interleukin 1 beta, opposite strand	ncRNA
mm_138115.1	chr17	34138003	34138024	+	1	NA	exon (NM_010386, exon 4 of 6)	exon (NM_010386, exon 4 of 6)	-7403	NM_010388	15000	Mm.195060	NM_010388	ENSMUSG00000037548	H2-DMb2	H-2Mb2|H2-Mb2	histocompatibility 2, class II, locus Mb2	protein-coding
mm_69033.1	chr7	126798247	126798262	-	1	NA	intron (NM_001177307, intron 1 of 9)	intron (NM_001177307, intron 1 of 9)	924	NM_001177307	11674	Mm.275831	NM_007438	ENSMUSG00000030695	Aldoa	Aldo-1|Aldo1	aldolase A, fructose-bisphosphate	protein-coding
mm_49587.1	chr6	30642965	30643018	+	1	NA	exon (NM_025350, exon 8 of 10)	exon (NM_025350, exon 8 of 10)	3773	NM_025350	109697	Mm.25377	NM_025350	ENSMUSG00000054446	Cpa1	0910001L12Rik|Cpa	carboxypeptidase A1, pancreatic	protein-coding
mm_96573.1	chr11	69045900	69045919	+	1	NA	5' UTR (NM_011496, exon 1 of 8)	5' UTR (NM_011496, exon 1 of 8)	272	NM_011496	20877	Mm.3488	NM_011496	ENSMUSG00000020897	Aurkb	AIM-1|AIRK2|AL022959|Aik2|Aim1|Ark2|AurB|IPL1|STK-1|Stk12|Stk5	aurora kinase B	protein-coding
mm_163035.1	chr11	52253872	52253885	+	1	NA	3' UTR (NM_009331, exon 10 of 10)	3' UTR (NM_009331, exon 10 of 10)	21883	NM_011543	21402	Mm.42944	NM_011543	ENSMUSG00000036309	Skp1a	15kDa|2610043E24Rik|2610206H23Rik|EMC19|OCP-II|OCP2|SKP1|Tceb1l|p19A|p19Skp1	S-phase kinase-associated protein 1A	protein-coding
mm_9610.1	chr1	176213741	176213747	-	1	NA	5' UTR (NM_001195816, exon 1 of 10)	5' UTR (NM_001195816, exon 1 of 10)	198	NM_001195816	319455	Mm.338001	NM_176916	ENSMUSG00000055214	Pld5	B230365F16Rik	phospholipase D family, member 5	protein-coding
mm_25156.1	chr3	103028984	103029068	+	1	NA	5' UTR (NM_001310693, exon 2 of 18)	5' UTR (NM_001310693, exon 2 of 18)	8480	NM_144901	229663	Mm.277713	NM_144901	ENSMUSG00000068823	Csde1	AA960392|BC016898|D3Jfr1|mKIAA0885|unr	cold shock domain containing E1, RNA binding	protein-coding
mm_5831.1	chr1	52817504	52817583	-	1	NA	5' UTR (NM_008384, exon 1 of 6)	5' UTR (NM_008384, exon 1 of 6)	145	NM_008384	16329	Mm.917	NM_008384	ENSMUSG00000026102	Inpp1	2300002C06Rik|AV137389	inositol polyphosphate-1-phosphatase	protein-coding
mm_159516.1	chr4	60222663	60222663	-	1	NA	promoter-TSS (NM_001134676)	promoter-TSS (NM_001134676)	-64	NM_001134676	100041687	Mm.457982	NM_001134676	ENSMUSG00000078687	Mup8	Gm12809|Mup5|OTTMUSG00000008509	major urinary protein 8	protein-coding
mm_97355.1	chr11	77496334	77496340	+	1	NA	intron (NM_001004144, intron 1 of 19)	PB1D9|SINE|Alu	2925	NM_001004144	216963	Mm.290182	NM_001004144	ENSMUSG00000011877	Git1	Cat-1|p95Cat	G protein-coupled receptor kinase-interactor 1	protein-coding
mm_144531.1	chr18	25168617	25168627	+	1	NA	promoter-TSS (NM_001033532)	promoter-TSS (NM_001033532)	255	NM_001142698	66648	Mm.263189	NM_001004361	ENSMUSG00000024269	Tpgs2	5730437P09Rik|5730494M16Rik|AI666318|Pgs2	tubulin polyglutamylase complex subunit 2	protein-coding
mm_115255.1	chr13	110399794	110399813	+	1	NA	exon (NM_152804, exon 13 of 14)	exon (NM_152804, exon 13 of 14)	4759	NM_152804	20620	Mm.380	NM_152804	ENSMUSG00000021701	Plk2	Snk	polo-like kinase 2	protein-coding
mm_66964.1	chr7	62464485	62464498	-	1	NA	promoter-TSS (NM_013788)	promoter-TSS (NM_013788)	19	NM_013788	27412	Mm.422745	NM_013788	ENSMUSG00000070526	Peg12	Frat3	paternally expressed 12	protein-coding
mm_33965.1	chr4	137563944	137563963	+	1	NA	intron (NM_008305, intron 85 of 96)	intron (NM_008305, intron 85 of 96)	11227	NM_001033979	435811	Mm.359646	NM_001033979	ENSMUSG00000094035	Ldlrad2	-	low density lipoprotein receptor A domain containing 2	protein-coding
mm_147741.1	chr18	61109715	61109725	-	1	NA	exon (NM_001037859, exon 3 of 22)	exon (NM_001037859, exon 3 of 22)	4148	NM_001037859	12978	Mm.22574	NM_007779	ENSMUSG00000024621	Csf1r	AI323359|CD115|CSF-1R|Csfmr|Fim-2|Fim2|Fms|M-CSF-R|M-CSFR	colony stimulating factor 1 receptor	protein-coding
mm_46667.1	chr5	108750958	108750995	-	1	NA	Intergenic	Lx|LINE|L1	-12866	NR_040691	73295	Mm.416858	NR_040691	ENSMUSG00000101762	1700047L14Rik	-	RIKEN cDNA 1700047L14 gene	ncRNA
mm_15648.1	chr2	163074632	163074654	+	1	NA	exon (NM_008652, exon 8 of 14)	exon (NM_008652, exon 8 of 14)	6553	NR_105970	102465607		NR_105970	ENSMUSG00000099091	Mir7003	Gm27340|mmu-mir-7003	microRNA 7003	ncRNA
mm_89853.1	chr10	107271891	107271901	+	1	NA	promoter-TSS (NM_001039354)	promoter-TSS (NM_001039354)	65	NM_001033223	108030	Mm.268025	NM_001033223	ENSMUSG00000019906	Lin7a	AI848705|LIN-7A|MALS-1|TIP-33|Veli|Veli1	lin-7 homolog A (C. elegans)	protein-coding
mm_38785.1	chr4	148087962	148088027	-	1	NA	promoter-TSS (NM_001301281)	promoter-TSS (NM_001301281)	70	NM_009642	11610	Mm.46247	NM_009642	ENSMUSG00000029007	Agtrap	3300002E14Rik|AT1R|Atrap|D4Wsu124e	angiotensin II, type I receptor-associated protein	protein-coding
mm_60409.1	chr7	44476041	44476051	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	5699	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_14616.1	chr2	136756072	136756142	+	1	NA	5' UTR (NM_001291056, exon 2 of 8)	5' UTR (NM_001291056, exon 2 of 8)	42657	NM_001291056	20614	Mm.45953	NM_011428	ENSMUSG00000027273	Snap25	Bdr|GENA70|SNAP-25|SUP|sp	synaptosomal-associated protein 25	protein-coding
mm_47182.1	chr5	120753892	120753902	-	1	NA	3' UTR (NM_145226, exon 16 of 16)	3' UTR (NM_145226, exon 16 of 16)	-4049	NM_001347448	246728	Mm.260926	NM_145227	ENSMUSG00000032690	Oas2	Oasl11	2'-5' oligoadenylate synthetase 2	protein-coding
mm_32148.1	chr4	99715641	99715682	+	1	NA	promoter-TSS (NM_001081264)	promoter-TSS (NM_001081264)	31	NM_001081264	320438	Mm.32408	NM_001081264	ENSMUSG00000073792	Alg6	E230028F23Rik	asparagine-linked glycosylation 6 (alpha-1,3,-glucosyltransferase)	protein-coding
mm_138045.1	chr17	33925470	33925491	+	1	NA	exon (NM_009318, exon 4 of 8)	exon (NM_009318, exon 4 of 8)	-4414	NM_009059	19732	Mm.43777	NM_009059	ENSMUSG00000041354	Rgl2	KE1.5|Rab2l|Rgt2|Rlf	ral guanine nucleotide dissociation stimulator-like 2	protein-coding
mm_133197.1	chr16	73011593	73011605	+	1	NA	intron (NM_019413, intron 23 of 28)	intron (NM_019413, intron 23 of 28)	348450	NM_019413	19876	Mm.310772	NM_019413	ENSMUSG00000022883	Robo1	AW494633|AW742721|DUTT1|Gm310	roundabout guidance receptor 1	protein-coding
mm_106382.1	chr11	118495277	118495280	-	1	NA	exon (NM_001039167, exon 13 of 15)	exon (NM_001039167, exon 13 of 15)	18318	NM_172573	217364	Mm.473963	NM_172573	ENSMUSG00000033857	Engase	C130099A03|D230014K01Rik	endo-beta-N-acetylglucosaminidase	protein-coding
mm_94275.1	chr11	3895319	3895329	+	1	NA	promoter-TSS (NM_026150)	promoter-TSS (NM_026150)	84	NM_173745	75219	Mm.32588	NM_173745	ENSMUSG00000047205	Dusp18	4930527G07Rik|AI430870|BB028064|DSP18|DUSP20|LMWDSP20	dual specificity phosphatase 18	protein-coding
mm_105813.1	chr11	111427999	111428019	-	1	NA	Intergenic	Intergenic	361845	NM_008425	16518	Mm.4951	NM_008425	ENSMUSG00000041695	Kcnj2	IRK1|Kcnf1|Kir2.1	potassium inwardly-rectifying channel, subfamily J, member 2	protein-coding
mm_41316.1	chr5	90470734	90470809	+	1	NA	exon (NM_009654, exon 10 of 15)	exon (NM_009654, exon 10 of 15)	9901	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_41560.1	chr5	93104823	93104846	+	1	NA	intron (NM_001347377, intron 1 of 10)	intron (NM_001347377, intron 1 of 10)	11418	NM_001347377	52398	Mm.394184	NM_001009818	ENSMUSG00000058013	Sept11	6230410I01Rik|AW548875|D5Ertd606e	septin 11	protein-coding
mm_22673.1	chr3	14886816	14886859	+	1	NA	intron (NM_009801, intron 1 of 6)	CpG	411	NM_009801	12349	Mm.1186	NM_009801	ENSMUSG00000027562	Car2	AI131712|CAII|Ca2|Car-2|Ltw-5|Lvtw-5	carbonic anhydrase 2	protein-coding
mm_122784.1	chr14	54410653	54410674	-	1	NA	intron (NM_001253679, intron 2 of 10)	intron (NM_001253679, intron 2 of 10)	-1191	NM_001253680	20540	Mm.142455	NM_011405	ENSMUSG00000000958	Slc7a7	AI790233|my+lat1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 7	protein-coding
mm_105916.1	chr11	114999260	114999282	-	1	NA	intron (NM_134158, intron 2 of 3)	intron (NM_134158, intron 2 of 3)	2609	NM_134158	140497	Mm.2699	NM_134158	ENSMUSG00000044811	Cd300c2	CLM4|Cd300c|Cd300d|DIgR1|Igsf7|Lmir2|MAIR-II	CD300C molecule 2	protein-coding
mm_61176.1	chr7	60037012	60037018	+	1	NA	intron (NM_001082962, intron 2 of 10)	ORR1B1-int|LTR|ERVL-MaLR	-31859	NM_033174	84704	Mm.274995	NM_033174	ENSMUSG00000000948	Snurf	2410045I01Rik|Snrpn	SNRPN upstream reading frame	protein-coding
mm_55389.1	chr6	59024471	59024511	-	1	NA	promoter-TSS (NM_153574)	promoter-TSS (NM_153574)	11	NM_153574	58909	Mm.28813	NM_153574	ENSMUSG00000037709	Fam13a	AI462012|D430015B01Rik|FAM13A1|Precm1	family with sequence similarity 13, member A	protein-coding
mm_104429.1	chr11	94951212	94951257	-	1	NA	exon (NM_007742, exon 50 of 51)	exon (NM_007742, exon 50 of 51)	15010	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_28502.1	chr3	92485887	92485901	-	1	NA	promoter-TSS (NM_009264)	promoter-TSS (NM_009264)	-13	NM_009264	20753	Mm.331191	NM_009264	ENSMUSG00000050359	Sprr1a	AI528815|SPR1a|mSPRR1A	small proline-rich protein 1A	protein-coding
mm_82594.1	chr9	21248411	21248422	-	1	NA	promoter-TSS (NM_053190)	promoter-TSS (NM_053190)	27	NM_053190	94226	Mm.190619	NM_053190	ENSMUSG00000045087	S1pr5	Edg8|S1P5|lpB4	sphingosine-1-phosphate receptor 5	protein-coding
mm_1823.1	chr1	82587144	82587156	+	1	NA	promoter-TSS (NM_007735)	promoter-TSS (NM_007735)	229	NM_007734	12828	Mm.389135	NM_007734	ENSMUSG00000079465	Col4a3	[a]3(IV)|alpha3(IV)	collagen, type IV, alpha 3	protein-coding
mm_79555.1	chr9	58014473	58014507	+	1	NA	promoter-TSS (NM_019779)	promoter-TSS (NM_019779)	-462	NM_019779	13070	Mm.302865	NM_019779	ENSMUSG00000032323	Cyp11a1	Cyp11a|Cypxia1|D9Ertd411e|P450scc|Scc|cscc	cytochrome P450, family 11, subfamily a, polypeptide 1	protein-coding
mm_12539.1	chr2	72297836	72297860	+	1	NA	intron (NM_023057, intron 1 of 19)	intron (NM_023057, intron 1 of 19)	12147	NM_178084	65964	Mm.304143	NM_023057	ENSMUSG00000004085	Map3k20	AV006891|B230120H23Rik|MLTK|MLTKalpha|MLTKbeta|Zak	mitogen-activated protein kinase kinase kinase 20	protein-coding
mm_66181.1	chr7	34133216	34133297	-	1	NA	promoter-TSS (NM_207212)	promoter-TSS (NM_207212)	12	NM_207212	101543	Mm.422738	NM_207212	ENSMUSG00000036459	Wtip	-	WT1-interacting protein	protein-coding
mm_14292.1	chr2	128845578	128845583	+	1	NA	intron (NM_028248, intron 15 of 18)	intron (NM_028248, intron 15 of 18)	-18352	NM_024237	70370	Mm.5107	NM_024237	ENSMUSG00000027386	Fbln7	1600015H20Rik|AI464334|TM14	fibulin 7	protein-coding
mm_119845.1	chr14	54439897	54439908	+	1	NA	intron (NM_008608, intron 8 of 9)	intron (NM_008608, intron 8 of 9)	8304	NM_008608	17387	Mm.280175	NM_008608	ENSMUSG00000000957	Mmp14	AI325305|MMP-X1|MT-MMP-1|MT1-MMP|sabe	matrix metallopeptidase 14 (membrane-inserted)	protein-coding
mm_45247.1	chr5	59948275	59948277	-	1	NA	Intergenic	Lx3A|LINE|L1	37726	NR_040683	71057	Mm.50817	NR_040682	ENSMUSG00000106013	4933402J10Rik	-	RIKEN cDNA 4933402J10 gene	ncRNA
mm_116570.1	chr13	47099373	47099387	-	1	NA	exon (NM_025900, exon 6 of 11)	exon (NM_025900, exon 6 of 11)	6841	NM_025900	110052	Mm.131150	NM_025900	ENSMUSG00000021377	Dek	1810019E15Rik|D13H6S231E	DEK oncogene (DNA binding)	protein-coding
mm_36466.1	chr4	82561691	82561692	-	1	NA	Intergenic	Intergenic	53702	NR_137202	102635783	Mm.41666	NR_137202		Gm11266	OTTMUSG00000000396	predicted gene 11266	ncRNA
mm_93272.1	chr10	95779705	95779715	-	1	NA	Intergenic	Intergenic	-160953	NM_001001932	216238	Mm.210035	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding
mm_62489.1	chr7	101905911	101905992	+	1	NA	5' UTR (NM_025605, exon 1 of 5)	5' UTR (NM_025605, exon 1 of 5)	114	NM_025605	66508	Mm.30003	NM_025605	ENSMUSG00000030842	Lamtor1	2400001E08Rik|Pdro|p18	late endosomal/lysosomal adaptor, MAPK and MTOR activator 1	protein-coding
mm_11465.1	chr2	32288245	32288256	+	1	NA	promoter-TSS (NM_133852)	promoter-TSS (NM_133852)	-3	NM_133852	99412	Mm.106376	NM_133852	ENSMUSG00000002546	Golga2	AW555139|GM130|mKIAA4150	golgi autoantigen, golgin subfamily a, 2	protein-coding
mm_171030.1	chr2	88711582	88711585	-	1	NA	Intergenic	Intergenic	-10256	NM_146464	258456	Mm.377510	NM_146464	ENSMUSG00000075120	Olfr1196	MOR225-5	olfactory receptor 1196	protein-coding
mm_144854.1	chr18	36664133	36664157	+	1	NA	promoter-TSS (NM_201256)	promoter-TSS (NM_201256)	85	NM_201256	108112	Mm.24790	NM_201256	ENSMUSG00000090264	Eif4ebp3	4e-bp3	eukaryotic translation initiation factor 4E binding protein 3	protein-coding
mm_80591.1	chr9	85842863	85842880	+	1	NA	promoter-TSS (NM_001164792)	promoter-TSS (NM_001164792)	19	NM_001164792	21983	Mm.20864	NM_011627	ENSMUSG00000035274	Tpbg	5T4|AW495680|WAIF1	trophoblast glycoprotein	protein-coding
mm_72453.1	chr8	83168655	83168663	+	1	NA	intron (NM_027758, intron 1 of 17)	intron (NM_027758, intron 1 of 17)	3307	NM_027758	71310	Mm.24031	NM_027758	ENSMUSG00000031709	Tbc1d9	4933431N12Rik|AI847101|AW490653|C76116	TBC1 domain family, member 9	protein-coding
mm_84953.1	chr9	83250222	83250238	-	1	NA	Intergenic	MER5A|DNA|hAT-Charlie	-103623	NM_026122	94353	Mm.244426	NM_026122	ENSMUSG00000066456	Hmgn3	1110002A15Rik|6330514M13Rik|BB071015|TRIP7	high mobility group nucleosomal binding domain 3	protein-coding
mm_69943.1	chr7	142165750	142165753	-	1	NA	Intergenic	Intergenic	10254	NM_027844	71623	Mm.293700	NM_027844	ENSMUSG00000054759	Krtap5-2	4833428E21Rik	keratin associated protein 5-2	protein-coding
mm_138903.1	chr17	43569397	43569434	+	1	NA	intron (NM_013737, intron 1 of 11)	intron (NM_013737, intron 1 of 11)	964	NM_013737	27226	Mm.9277	NM_013737	ENSMUSG00000023913	Pla2g7	PAF-AH|R75400	phospholipase A2, group VII (platelet-activating factor acetylhydrolase, plasma)	protein-coding
mm_25951.1	chr3	131638427	131638443	+	1	NA	intron (NM_001289477, intron 12 of 12)	intron (NM_001289477, intron 12 of 12)	72403	NM_001289477	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_130869.1	chr15	102215783	102215786	-	1	NA	TTS (NM_001289690)	TTS (NM_001289690)	11213	NM_001289695	68744	Mm.352945	NM_153194	ENSMUSG00000046897	Zfp740	1110034O07Rik|AW548228|Znf740	zinc finger protein 740	protein-coding
mm_4723.1	chr1	181210826	181210832	+	1	NA	intron (NM_145514, intron 1 of 13)	CpG	1149	NM_145514	226757	Mm.289082	NM_145514	ENSMUSG00000038733	Wdr26	1600024A01Rik|AA693241|AI447817|AU044014|C77982|Gid7	WD repeat domain 26	protein-coding
mm_144772.1	chr18	35828799	35828815	+	1	NA	Intergenic	Intergenic	-1011	NM_133687	67393	Mm.94560	NM_133687	ENSMUSG00000046668	Cxxc5	4930415K17Rik	CXXC finger 5	protein-coding
mm_117980.1	chr13	100108179	100108183	-	1	NA	5' UTR (NM_011353, exon 1 of 3)	5' UTR (NM_011353, exon 1 of 3)	162	NM_011353	20365	Mm.286177	NM_011353	ENSMUSG00000021643	Serf1	4F5|Msmac1|m4F5	small EDRK-rich factor 1	protein-coding
mm_24335.1	chr3	89662682	89662716	+	1	NA	intron (NM_080466, intron 6 of 7)	intron (NM_080466, intron 6 of 7)	-52323	NM_001038587	56417	Mm.316628	NM_019655	ENSMUSG00000027951	Adar	AV242451|Adar1|Adar1p110|Adar1p150|mZaADAR	adenosine deaminase, RNA-specific	protein-coding
mm_155670.1	chrX	90744721	90744730	+	1	NA	Intergenic	Intergenic	-147417	NM_001101450	212952	Mm.477436	NM_001101450	ENSMUSG00000091497	Gm44	-	predicted gene 44	protein-coding
mm_124596.1	chr15	3275212	3275222	+	1	NA	intron (NM_001042613, intron 2 of 4)	intron (NM_001042613, intron 2 of 4)	4240	NM_009155	20363	Mm.392203	NM_009155	ENSMUSG00000064373	Selenop	AU018766|D15Ucla1|Se-P|Sepp1|selp	selenoprotein P	protein-coding
mm_148198.1	chr18	79109420	79109510	-	1	NA	promoter-TSS (NM_053099)	promoter-TSS (NM_053099)	-74	NM_053099	240427	Mm.312871	NM_053099	ENSMUSG00000024548	Setbp1	C130092E12|Seb|mKIAA0437	SET binding protein 1	protein-coding
mm_106638.1	chr11	120991079	120991095	-	1	NA	5' UTR (NM_139059, exon 1 of 9)	5' UTR (NM_139059, exon 1 of 9)	246	NM_139059	104318	Mm.216227	NM_027874	ENSMUSG00000025162	Csnk1d	1200006A05Rik|AA409348|D930010H05Rik	casein kinase 1, delta	protein-coding
mm_155473.1	chrX	73640179	73640186	+	1	NA	intron (NM_029352, intron 1 of 3)	CpG	741	NM_029352	75590	Mm.16479	NM_029352	ENSMUSG00000031383	Dusp9	Dusp4|Mpk4|Pyst3	dual specificity phosphatase 9	protein-coding
mm_157457.1	chrX	43428987	43429013	-	1	NA	Intergenic	Intergenic	-154216	NM_011855	23963	Mm.327698	NM_011855	ENSMUSG00000016150	Tenm1	Odz1|Odz2|TCAP-1|Ten-m1|ten-1	teneurin transmembrane protein 1	protein-coding
mm_63034.1	chr7	121074686	121074713	+	1	NA	promoter-TSS (NM_030691)	promoter-TSS (NM_030691)	-169	NM_030691	80719	Mm.160384	NM_030691	ENSMUSG00000035004	Igsf6	-	immunoglobulin superfamily, member 6	protein-coding
mm_23818.1	chr3	79936465	79936470	+	1	NA	intron (NM_133187, intron 2 of 3)	intron (NM_133187, intron 2 of 3)	50537	NM_133187	68659	Mm.427274	NM_133187	ENSMUSG00000027955	Fam198b	1110032E23Rik|2210419I08Rik|AV011458|Ened	family with sequence similarity 198, member B	protein-coding
mm_132564.1	chr16	38089793	38089808	+	1	NA	promoter-TSS (NR_033221)	promoter-TSS (NR_033221)	-540	NR_033221	414072	Mm.483602	NR_033221		BC031361	-	cDNA sequence BC031361	ncRNA
mm_64077.1	chr7	140920941	140920941	+	1	NA	promoter-TSS (NM_133946)	promoter-TSS (NM_133946)	39	NM_133946	101613	Mm.386833	NM_133946	ENSMUSG00000038745	Nlrp6	AI504961|Avr|Nalp6|Navr|Navr/Avr|Non-AVR|Pypaf5	NLR family, pyrin domain containing 6	protein-coding
mm_106487.1	chr11	120235074	120235080	-	1	NA	intron (NM_001347621, intron 1 of 27)	CpG	2130	NM_198423	268515	Mm.309498	NM_198423	ENSMUSG00000039741	Bahcc1	B930044J06|BC060615	BAH domain and coiled-coil containing 1	protein-coding
mm_74677.1	chr8	13974954	13974969	-	1	NA	promoter-TSS (NM_173744)	promoter-TSS (NM_173744)	-184	NM_173744	72148	Mm.5727	NM_173744	ENSMUSG00000050052	Tdrp	2610019F03Rik	testis development related protein	protein-coding
mm_96248.1	chr11	62575878	62575890	+	1	NA	intron (NM_011706, intron 1 of 15)	intron (NM_011706, intron 1 of 15)	1398	NM_011706	22368	Mm.288064	NM_011706	ENSMUSG00000018507	Trpv2	GRC|OTRPC2|VRL-1|Vrl1	transient receptor potential cation channel, subfamily V, member 2	protein-coding
mm_90479.1	chr10	127879314	127879324	+	1	NA	Intergenic	Intergenic	9380	NM_017473	54150	Mm.6696	NM_017473	ENSMUSG00000040134	Rdh7	AI194929|CRAD2	retinol dehydrogenase 7	protein-coding
mm_82914.1	chr9	35053741	35053744	-	1	NA	intron (NM_009178, intron 6 of 10)	B1F|SINE|Alu	-62986	NR_029475	78934	Mm.391688	NR_029475	ENSMUSG00000070315	4930581F22Rik	-	RIKEN cDNA 4930581F22 gene	ncRNA
mm_64740.1	chr7	4752764	4752775	-	1	NA	TTS (NM_172895)	TTS (NM_172895)	133	NM_183406	333182	Mm.29625	NM_183405	ENSMUSG00000051811	Cox6b2	1700067P11Rik|BC048670|COXVIB2	cytochrome c oxidase subunit VIb polypeptide 2	protein-coding
mm_9956.1	chr1	191026182	191026197	-	1	NA	promoter-TSS (NM_001081259)	promoter-TSS (NM_001081259)	1	NM_001081259	226844	Mm.134053	NM_198025	ENSMUSG00000066595	Mfsd7b	9630055N22Rik|FLVCR|Flvcr1	major facilitator superfamily domain containing 7B	protein-coding
mm_59979.1	chr7	30465327	30465364	+	1	NA	intron (NM_019459, intron 11 of 29)	intron (NM_019459, intron 11 of 29)	246	NR_004443	445267	Mm.398140	NR_004443	ENSMUSG00000087009	Nphs1os	Nphs1as	nephrosis 1 homolog, nephrin, opposite strand	ncRNA
mm_10858.1	chr2	25054473	25054483	+	1	NA	promoter-TSS (NM_020276)	promoter-TSS (NM_020276)	99	NM_001177655	56876	Mm.42956	NM_020276	ENSMUSG00000006476	Nsmf	Jacob|Nelf	NMDA receptor synaptonuclear signaling and neuronal migration factor	protein-coding
mm_163952.1	chr14	54463916	54463926	+	1	NA	promoter-TSS (NM_022993)	promoter-TSS (NM_022993)	-226	NM_022993	65107	Mm.472719	NM_022993	ENSMUSG00000022175	Lrp10	Lrp9	low-density lipoprotein receptor-related protein 10	protein-coding
mm_238.1	chr1	19208999	19209011	+	1	NA	promoter-TSS (NM_009334)	promoter-TSS (NM_009334)	91	NM_001286340	21419	Mm.137021	NM_009334	ENSMUSG00000025927	Tfap2b	AI606113|AP-2(beta)|E130018K07Rik|Tcfap2b	transcription factor AP-2 beta	protein-coding
mm_81392.1	chr9	108987891	108987902	+	1	NA	TTS (NM_145077)	TTS (NM_145077)	1733	NM_145077	171530	Mm.388865	NM_145077	ENSMUSG00000049699	Ucn2	Ucn II|Ucn-2|ucn-II	urocortin 2	protein-coding
mm_154293.1	chr19	61140773	61140823	-	1	NA	promoter-TSS (NM_001309216)	promoter-TSS (NM_001309216)	42	NR_131956	414758	Mm.100056	NM_001001737	ENSMUSG00000074733	Zfp950	5830428H23Rik|AU016073|BC055757|Gm34518|Zfp826|mszf84	zinc finger protein 950	protein-coding
mm_118921.1	chr14	26894607	26894627	+	1	NA	promoter-TSS (NM_080856)	promoter-TSS (NM_080856)	13	NM_080856	142687	Mm.138259	NM_080856	ENSMUSG00000021898	Asb14	Asb-14	ankyrin repeat and SOCS box-containing 14	protein-coding
mm_158514.1	chrX	143393851	143393861	-	1	NA	5' UTR (NM_031258, exon 1 of 9)	5' UTR (NM_031258, exon 1 of 9)	406	NM_031258	83453	Mm.157697	NM_031258	ENSMUSG00000031283	Chrdl1	CHL|CHL1|Nrln1|VOPT	chordin-like 1	protein-coding
mm_71062.1	chr8	33964211	33964258	+	1	NA	Intergenic	Intergenic	-34371	NM_001042675	19663	Mm.323997	NM_019733	ENSMUSG00000031586	Rbpms	2010300K22Rik|2700019M19Rik|AU017537|RBP-MS|hermes	RNA binding protein gene with multiple splicing	protein-coding
mm_151869.1	chr19	5797904	5797914	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	-1928	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_61768.1	chr7	82867328	82867357	+	1	NA	promoter-TSS (NM_175366)	promoter-TSS (NM_175366)	9	NM_175366	108797	Mm.306789	NM_175366	ENSMUSG00000057706	Mex3b	4931439A04Rik|M-04814|Rkhd3|mKIAA2009	mex3 RNA binding family member B	protein-coding
mm_104029.1	chr11	86201613	86201623	-	1	NA	promoter-TSS (NM_178309)	promoter-TSS (NM_178309)	258	NR_130958	74038	Mm.171304	NR_130958	ENSMUSG00000085208	Brip1os	4632419I22Rik	BRCA1 interacting protein C-terminal helicase 1, opposite strand	ncRNA
mm_2542.1	chr1	107511464	107511468	+	1	NA	promoter-TSS (NM_001174170)	promoter-TSS (NM_001174170)	43	NM_001174170	18788	Mm.271870	NM_011111	ENSMUSG00000062345	Serpinb2	PAI-2|Planh2|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 2	protein-coding
mm_170635.1	chr1	98594778	98594789	+	1	NA	Intergenic	IAP1-MM_LTR|LTR|ERVK	173659	NM_027584	70866	Mm.389164	NM_027584	ENSMUSG00000026336	Slco6d1	4921511I05Rik	solute carrier organic anion transporter family, member 6d1	protein-coding
mm_66529.1	chr7	45136083	45136100	-	1	NA	intron (NR_102725, intron 1 of 7)	intron (NR_102725, intron 1 of 7)	341	NM_013520	14256	Mm.1658	NM_013520	ENSMUSG00000110206	Flt3l	Flt3lg|Ly72L	FMS-like tyrosine kinase 3 ligand	protein-coding
mm_36350.1	chr4	73950780	73950790	-	1	NA	promoter-TSS (NM_027104)	promoter-TSS (NM_027104)	61	NM_027981	71886	Mm.158769	NM_027104	ENSMUSG00000028396	2310002L09Rik	2310003M01Rik|AV083437	RIKEN cDNA 2310002L09 gene	protein-coding
mm_13822.1	chr2	119237635	119237645	+	1	NA	intron (NM_016907, intron 1 of 10)	CpG	280	NM_016907	20732	Mm.104955	NM_016907	ENSMUSG00000027315	Spint1	HAI-1	serine protease inhibitor, Kunitz type 1	protein-coding
mm_143875.1	chr17	84187205	84187252	-	1	NA	intron (NM_001001806, intron 1 of 1)	CpG	719	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_51249.1	chr6	71809411	71809434	+	1	NA	3' UTR (NM_178608, exon 7 of 7)	3' UTR (NM_178608, exon 7 of 7)	14362	NM_025430	66223	Mm.28579	NM_025430	ENSMUSG00000052962	Mrpl35	1110066C01Rik	mitochondrial ribosomal protein L35	protein-coding
mm_132326.1	chr16	33794482	33794496	+	1	NA	5' UTR (NM_010739, exon 2 of 13)	5' UTR (NM_010739, exon 2 of 13)	452	NM_010739	17063	Mm.3177	NM_010739	ENSMUSG00000022824	Muc13	114/A10|14/A10|AI159736|Lrrp|Ly64|NJ-1	mucin 13, epithelial transmembrane	protein-coding
mm_144841.1	chr18	36560631	36560657	+	1	NA	promoter-TSS (NM_175375)	promoter-TSS (NM_175375)	41	NM_175375	108857	Mm.482287	NM_175375	ENSMUSG00000024483	Ankhd1	1110004O12Rik|4933432B13Rik|9130019P20Rik|A530027J04Rik|A630021B20Rik|AA571404|Mask|mFLJ00246|mKIAA1085	ankyrin repeat and KH domain containing 1	protein-coding
mm_69215.1	chr7	127512407	127512417	-	1	NA	non-coding (NR_024331, exon 1 of 1)	non-coding (NR_024331, exon 1 of 1)	429	NM_001304266	100043597	Mm.428042	NM_175144	ENSMUSG00000053877	Srcap	B930091H02Rik|D030022P06Rik|F630004O05Rik	Snf2-related CREBBP activator protein	protein-coding
mm_16890.1	chr2	13156695	13156727	-	1	NA	intron (NM_009105, intron 8 of 8)	intron (NM_009105, intron 8 of 8)	114704	NM_009105	20163	Mm.905	NM_009105	ENSMUSG00000026727	Rsu1	RsuI|rsp-1	Ras suppressor protein 1	protein-coding
mm_159986.1	chr6	114403820	114403820	+	1	NA	5' UTR (NM_001252642, exon 1 of 2)	5' UTR (NM_001252642, exon 1 of 2)	154	NM_001252643	15465	Mm.333327	NM_008285	ENSMUSG00000053004	Hrh1	Bphs|H1R|HH1R|Hir	histamine receptor H1	protein-coding
mm_41084.1	chr5	87680016	87680054	+	1	NA	intron (NM_001286015, intron 29 of 32)	intron (NM_001286015, intron 29 of 32)	13827	NM_001286016	12990	Mm.427467	NM_007784	ENSMUSG00000070702	Csn1s1	AA959832|AW212882|Csna	casein alpha s1	protein-coding
mm_170496.1	chr19	23140932	23140940	+	1	NA	promoter-TSS (NM_010638)	promoter-TSS (NM_010638)	-290	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_123632.1	chr14	68525253	68525262	-	1	NA	exon (NM_007402, exon 6 of 23)	exon (NM_007402, exon 6 of 23)	8432	NM_007402	11500	Mm.261495	NM_007402	ENSMUSG00000022056	Adam7	ADAM 7|EAP1|EAPI	a disintegrin and metallopeptidase domain 7	protein-coding
mm_51490.1	chr6	83056769	83056784	+	1	NA	non-coding (NR_125891, exon 9 of 12)	non-coding (NR_125891, exon 9 of 12)	-1068	NM_033606	93838	Mm.140332	NM_033606	ENSMUSG00000009145	Dqx1	2310066E11Rik	DEAQ RNA-dependent ATPase	protein-coding
mm_41293.1	chr5	90464081	90464085	+	1	NA	exon (NM_009654, exon 4 of 15)	exon (NM_009654, exon 4 of 15)	3213	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_109234.1	chr12	108853478	108853508	+	1	NA	intron (NM_001012310, intron 2 of 5)	intron (NM_001012310, intron 2 of 5)	2364	NM_001012310	104910	Mm.202653	NM_001012310	ENSMUSG00000048856	Slc25a47	AI132487|AI876593|HDMCP	solute carrier family 25, member 47	protein-coding
mm_97770.1	chr11	82046519	82046529	+	1	NA	exon (NM_013654, exon 2 of 3)	exon (NM_013654, exon 2 of 3)	812	NM_013654	20306	Mm.341574	NM_013654	ENSMUSG00000035373	Ccl7	MCP-3|Scya7|fic|marc|mcp3	chemokine (C-C motif) ligand 7	protein-coding
mm_114761.1	chr13	85197245	85197252	+	1	NA	intron (NM_001347588, intron 3 of 8)	intron (NM_001347588, intron 3 of 8)	7863	NM_023243	66671	Mm.18474	NM_023243	ENSMUSG00000021548	Ccnh	6330408H09Rik|AI661354|AV102684|AW538719	cyclin H	protein-coding
mm_122488.1	chr14	46390502	46390529	-	1	NA	5' UTR (NM_007554, exon 1 of 4)	5' UTR (NM_007554, exon 1 of 4)	154	NM_001316360	12159	Mm.6813	NM_007554	ENSMUSG00000021835	Bmp4	Bmp-4|Bmp2b|Bmp2b-1|Bmp2b1	bone morphogenetic protein 4	protein-coding
mm_169450.1	chr1	46076111	46076111	-	1	NA	intron (NM_001160386, intron 2 of 65)	L1Md_F2|LINE|L1	9373	NM_001160386	227058	Mm.296880	NM_001160386	ENSMUSG00000041144	Dnah7b	Dnahc7b|Gm107	dynein, axonemal, heavy chain 7B	protein-coding
mm_148561.1	chr19	4756437	4756443	+	1	NA	promoter-TSS (NM_025717)	promoter-TSS (NM_025717)	-85	NM_025717	66704	Mm.396734	NM_025717	ENSMUSG00000033760	Rbm4b	4921506I22Rik|AI504630|AI506404|Lark2|Neosin	RNA binding motif protein 4B	protein-coding
mm_55140.1	chr6	51346753	51346774	-	1	NA	Intergenic	Intergenic	-32947	NR_110455	625167	Mm.389772	NR_110455	ENSMUSG00000107660	Gm6559	EG625167	predicted gene 6559	ncRNA
mm_159510.1	chr4	56802295	56802295	+	1	NA	promoter-TSS (NM_026079)	promoter-TSS (NM_026079)	-34	NM_001081420	230234	Mm.268148	NM_001081420	ENSMUSG00000038827	Fam206a	simiate	family with sequence similarity 206, member A	protein-coding
mm_137348.1	chr17	25184565	25184602	+	1	NA	promoter-TSS (NM_183150)	promoter-TSS (NM_183150)	22	NM_183150	214489	Mm.274433	NM_183150	ENSMUSG00000067722	BC003965	Ccsmst1	cDNA sequence BC003965	protein-coding
mm_31124.1	chr4	42969954	42969965	+	1	NA	promoter-TSS (NM_026088)	promoter-TSS (NM_026088)	13	NM_026088	67317	Mm.478018	NM_026088	ENSMUSG00000028451	1700022I11Rik	-	RIKEN cDNA 1700022I11 gene	protein-coding
mm_21863.1	chr2	165885552	165885574	-	1	NA	promoter-TSS (NM_001252584)	promoter-TSS (NM_001252584)	-725	NM_001252587	228880	Mm.227598	NM_027230	ENSMUSG00000039671	Zmynd8	1110013E22Rik|2010005I16Rik|3632413B07Rik|AI316811|AL024039|Prkcbp1|RACK7	zinc finger, MYND-type containing 8	protein-coding
mm_140253.1	chr17	84226579	84226579	+	1	NA	intron (NM_183021, intron 34 of 37)	intron (NM_183021, intron 34 of 37)	-38632	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_106253.1	chr11	117827398	117827406	-	1	NA	intron (NM_027827, intron 1 of 10)	ID4|SINE|ID	-1388	NM_009387	21877	Mm.2661	NM_009387	ENSMUSG00000025574	Tk1	D530002A18Rik|Tk-1|Tk1a|Tk1b	thymidine kinase 1	protein-coding
mm_39917.1	chr5	31485882	31485891	+	1	NA	promoter-TSS (NM_026296)	promoter-TSS (NM_026296)	27	NM_026296	67656	Mm.23355	NM_026296	ENSMUSG00000029138	4930548H24Rik	AI427865	RIKEN cDNA 4930548H24 gene	protein-coding
mm_112276.1	chr12	114300419	114300453	-	1	NA	Intergenic	Intergenic	169030	NR_106062	102465663		NR_106062	ENSMUSG00000105438	Mir7094-1	mmu-mir-7094-1	microRNA 7094-1	ncRNA
mm_38884.1	chr4	149702839	149702858	-	1	NA	Intergenic	Intergenic	-1219	NM_001029837	18707	Mm.229108	NM_008840	ENSMUSG00000039936	Pik3cd	2410099E07Rik|2610208K16Rik|AW545373|p110delta	phosphatidylinositol 3-kinase catalytic delta polypeptide	protein-coding
mm_121853.1	chr14	20663688	20663696	-	1	NA	intron (NM_001310431, intron 3 of 3)	intron (NM_001310431, intron 3 of 3)	882	NM_001310432	68760	Mm.35789	NM_175132	ENSMUSG00000039376	Synpo2l	1110054M18Rik|Chap	synaptopodin 2-like	protein-coding
mm_167096.1	chr7	109384868	109384869	+	1	NA	intron (NM_054103, intron 1 of 13)	RMER13A|LTR|ERVK	54185	NM_054103	117229	Mm.389950	NM_054103	ENSMUSG00000031027	Stk33	4921505G21Rik|AW061264	serine/threonine kinase 33	protein-coding
mm_16396.1	chr2	179442428	179442442	+	1	NA	promoter-TSS (NM_009867)	promoter-TSS (NM_009867)	4	NM_009867	12561	Mm.184711	NM_009867	ENSMUSG00000000305	Cdh4	AW120700|R-CAD|R-Cadh|Rcad	cadherin 4	protein-coding
mm_145538.1	chr18	60806998	60807024	+	1	NA	intron (NM_001042605, intron 1 of 8)	B1_Mm|SINE|Alu	3162	NM_010545	16149	Mm.439737	NM_010545	ENSMUSG00000024610	Cd74	CLIP|DHLAG|HLADG|Ia-GAMMA|Ii	CD74 antigen (invariant polypeptide of major histocompatibility complex, class II antigen-associated)	protein-coding
mm_169439.1	chr14	56415553	56415560	+	1	NA	intron (NM_001033043, intron 2 of 36)	intron (NM_001033043, intron 2 of 36)	12859	NM_001033043	30054	Mm.287783	NM_001033043	ENSMUSG00000000365	Rnf17	MMIP-2|Mmip2|TDRD4	ring finger protein 17	protein-coding
mm_24446.1	chr3	90608498	90608501	+	1	NA	promoter-TSS (NM_011312)	promoter-TSS (NM_011312)	-23	NM_011312	20199	Mm.19946	NM_011312	ENSMUSG00000001023	S100a5	S100D9	S100 calcium binding protein A5	protein-coding
mm_54210.1	chr6	25689548	25689561	-	1	NA	5' UTR (NM_010338, exon 1 of 2)	5' UTR (NM_010338, exon 1 of 2)	426	NM_010338	14763	Mm.409670	NM_010338	ENSMUSG00000039904	Gpr37	AI848630|Pael-R	G protein-coupled receptor 37	protein-coding
mm_114618.1	chr13	75943258	75943273	+	1	NA	exon (NM_028493, exon 2 of 12)	exon (NM_028493, exon 2 of 12)	559	NM_028493	73296	Mm.276200	NM_028493	ENSMUSG00000021589	Rhobtb3	1700040C17Rik|2610033K01Rik|4930503C18Rik|AI317148|AW208826|mKIAA0878	Rho-related BTB domain containing 3	protein-coding
mm_16719.1	chr2	7301862	7301874	-	1	NA	intron (NM_001110231, intron 2 of 15)	intron (NM_001110231, intron 2 of 15)	94132	NM_001110232	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_166689.1	chr6	108688530	108688537	+	1	NA	Intergenic	Intergenic	-27599	NR_104577	75394	Mm.395061	NR_040757	ENSMUSG00000087341	0610040F04Rik	-	RIKEN cDNA 0610040F04 gene	ncRNA
mm_68280.1	chr7	105599354	105599380	-	1	NA	exon (NM_017371, exon 4 of 10)	exon (NM_017371, exon 4 of 10)	749	NM_017371	15458	Mm.3485	NM_017371	ENSMUSG00000030895	Hpx	Hpxn|hx	hemopexin	protein-coding
mm_68111.1	chr7	102065127	102065159	-	1	NA	promoter-TSS (NR_104582)	promoter-TSS (NR_104582)	-11	NM_029211	75212	Mm.101141	NM_029211	ENSMUSG00000070426	Rnf121	4930544L10Rik	ring finger protein 121	protein-coding
mm_57085.1	chr6	122583933	122583948	-	1	NA	intron (NM_001134391, intron 5 of 7)	B1_Mus2|SINE|Alu	18504	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_49567.1	chr6	30640440	30640450	+	1	NA	intron (NM_025350, intron 2 of 9)	intron (NM_025350, intron 2 of 9)	1227	NM_025350	109697	Mm.25377	NM_025350	ENSMUSG00000054446	Cpa1	0910001L12Rik|Cpa	carboxypeptidase A1, pancreatic	protein-coding
mm_98654.1	chr11	96264269	96264284	+	1	NA	promoter-TSS (NR_029721)	promoter-TSS (NR_029721)	-888	NR_029721	387191		NR_029721	ENSMUSG00000065546	Mir196a-1	Mirn196|Mirn196a-1|miR-196|mir-196a-1	microRNA 196a-1	ncRNA
mm_86896.1	chr10	22303002	22303013	+	1	NA	intron (NM_009018, intron 5 of 5)	intron (NM_009018, intron 5 of 5)	-3713	NR_015465	606736	Mm.387042	NR_015465	ENSMUSG00000097352	C920009B18Rik	-	RIKEN cDNA C920009B18 gene	ncRNA
mm_59416.1	chr7	27121666	27121677	+	1	NA	exon (NM_007817, exon 2 of 10)	exon (NM_007817, exon 2 of 10)	1716	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_114362.1	chr13	61827503	61827505	+	1	NA	Intergenic	Intergenic	55924	NR_028430	432812	Mm.317358	NR_028430		BC052688	-	cDNA sequence BC052688	pseudo
mm_114101.1	chr13	54730244	54730246	+	1	NA	intron (NM_001033364, intron 21 of 31)	intron (NM_001033364, intron 21 of 31)	19629	NM_001316710	26913	Mm.41812	NM_012014	ENSMUSG00000069227	Gprin1	GRIN1|Z16	G protein-regulated inducer of neurite outgrowth 1	protein-coding
mm_66711.1	chr7	46015913	46015916	-	1	NA	intron (NM_018795, intron 7 of 30)	intron (NM_018795, intron 7 of 30)	14372	NM_018795	27421	Mm.63514	NM_018795	ENSMUSG00000030834	Abcc6	Abcc1b|DCC|Dyscalc1|Mrp6|dyscalc	ATP-binding cassette, sub-family C (CFTR/MRP), member 6	protein-coding
mm_7591.1	chr1	125435662	125435688	-	1	NA	promoter-TSS (NM_023735)	promoter-TSS (NM_023735)	52	NM_023735	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding
mm_70179.1	chr7	143740317	143740368	-	1	NA	promoter-TSS (NM_001199227)	promoter-TSS (NM_001199227)	18	NM_001199227	79196	Mm.21199	NM_024289	ENSMUSG00000037606	Osbpl5	1110006M06Rik|AI462538|ORP5|Obph1|Osbp2	oxysterol binding protein-like 5	protein-coding
mm_128736.1	chr15	64303183	64303187	-	1	NA	intron (NM_010026, intron 3 of 30)	intron (NM_010026, intron 3 of 30)	9488	NM_001276462	13196	Mm.277236	NM_010026	ENSMUSG00000022377	Asap1	AV239055|DEF-1|Ddef1|PAP|mKIAA1249|s19	ArfGAP with SH3 domain, ankyrin repeat and PH domain1	protein-coding
mm_103212.1	chr11	70653935	70654070	-	1	NA	intron (NM_011072, intron 1 of 2)	CpG	648	NM_011072	18643	Mm.2647	NM_011072	ENSMUSG00000018293	Pfn1	Pfn	profilin 1	protein-coding
mm_84471.1	chr9	66782280	66782283	-	1	NA	intron (NM_177583, intron 5 of 5)	intron (NM_177583, intron 5 of 5)	13142	NM_177583	208117	Mm.41291	NM_177583	ENSMUSG00000032375	Aph1b	2310057K14Rik|Aph1c	aph1 homolog B, gamma secretase subunit	protein-coding
mm_41831.1	chr5	104170677	104170699	+	1	NA	promoter-TSS (NM_010080)	promoter-TSS (NM_010080)	-15	NM_010080	666279	Mm.319832	NM_010080	ENSMUSG00000053268	Dspp	Dmp2|Dmp3|Dpp|Dsp	dentin sialophosphoprotein	protein-coding
mm_165305.1	chr2	98474927	98474931	+	1	NA	Intergenic	Intergenic	1007272	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_48782.1	chr5	148552618	148552688	-	1	NA	5' UTR (NM_011908, exon 1 of 5)	5' UTR (NM_011908, exon 1 of 5)	135	NM_011908	24109	Mm.21846	NM_011908	ENSMUSG00000001687	Ubl3	AW108023|HCG	ubiquitin-like 3	protein-coding
mm_68689.1	chr7	119476812	119476819	-	1	NA	exon (NM_001278605, exon 3 of 11)	exon (NM_001278605, exon 3 of 11)	2447	NM_009470	22242	Mm.10826	NM_009470	ENSMUSG00000030963	Umod	THP|Urehd1|urehr4	uromodulin	protein-coding
mm_126343.1	chr15	79900376	79900385	+	1	NA	intron (NM_001160415, intron 5 of 8)	intron (NM_001160415, intron 5 of 8)	5357	NM_001347041	80287	Mm.284059	NM_030255	ENSMUSG00000009585	Apobec3	Apobec|Arp3|BC003314|Cem15|Rfv3	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 3	protein-coding
mm_62274.1	chr7	99579628	99579644	+	1	NA	intron (NM_177231, intron 1 of 15)	MLT1O|LTR|ERVL-MaLR	27367	NR_029760	723840		NR_029760	ENSMUSG00000065571	Mir326	Mirn326|mir-326|mmu-mir-326	microRNA 326	ncRNA
mm_38105.1	chr4	134517579	134517587	-	1	NA	intron (NM_001081099, intron 1 of 2)	intron (NM_001081099, intron 1 of 2)	6584	NM_001081099	69885	Mm.141592	NM_001081099	ENSMUSG00000078521	Aunip	2610002D18Rik|Clhc1	aurora kinase A and ninein interacting protein	protein-coding
mm_24887.1	chr3	96108522	96108531	+	1	NA	intron (NM_001025614, intron 1 of 11)	intron (NM_001025614, intron 1 of 11)	3999	NM_001025614	229603	Mm.272336	NM_001025613	ENSMUSG00000038495	Otud7b	2900060B22Rik|4930463P07Rik|AI462125|CEZANNE|Trabid2|Za20d1	OTU domain containing 7B	protein-coding
mm_23075.1	chr3	36467763	36467773	+	1	NA	intron (NM_009673, intron 2 of 12)	intron (NM_009673, intron 2 of 12)	7756	NR_105976	102466786		NR_105976	ENSMUSG00000098808	Mir7009	Gm27472|mmu-mir-7009	microRNA 7009	ncRNA
mm_123312.1	chr14	62411814	62411817	-	1	NA	exon (NM_001204340, exon 11 of 17)	exon (NM_001204340, exon 11 of 17)	44474	NM_001204340	239134	Mm.236557	NM_172810	ENSMUSG00000021933	Gucy1b2	B930025B03|GC-SB2	guanylate cyclase 1, soluble, beta 2	protein-coding
mm_172347.1	chr7	113484686	113484689	-	1	NA	Intergenic	L1Md_T|LINE|L1	-29147	NM_001285831	67420	Mm.206919	NM_026143	ENSMUSG00000030759	Far1	2600011M19Rik|2900034E22Rik|3732409C05Rik|AI850429|Mlstd2	fatty acyl CoA reductase 1	protein-coding
mm_144589.1	chr18	32067974	32068013	+	1	NA	5' UTR (NM_173441, exon 1 of 14)	5' UTR (NM_173441, exon 1 of 14)	259	NM_173441	73473	Mm.66853	NM_173441	ENSMUSG00000024384	Iws1	1700069O15Rik|3000008H23|AL117927|AW214353	IWS1, SUPT6 interacting protein	protein-coding
mm_73878.1	chr8	119344473	119344483	+	1	NA	promoter-TSS (NM_024219)	promoter-TSS (NM_024219)	-60	NM_024219	68196	Mm.358714	NM_024219	ENSMUSG00000031839	Hsbp1	0610007A03Rik|AA408769|Hsp25	heat shock factor binding protein 1	protein-coding
mm_160381.1	chr8	43528135	43528135	-	1	NA	promoter-TSS (NM_001009547)	promoter-TSS (NM_001009547)	2	NM_001009547	382007	Mm.55952	NM_001009547	ENSMUSG00000063900	Adam26b	-	a disintegrin and metallopeptidase domain 26B	protein-coding
mm_69220.1	chr7	127588195	127588218	-	1	NA	promoter-TSS (NM_172281)	promoter-TSS (NM_172281)	389	NM_001033040	233899	Mm.25220	NM_001033040	ENSMUSG00000057176	Ccdc189	Gm166	coiled-coil domain containing 189	protein-coding
mm_127593.1	chr15	102392803	102392815	+	1	NA	Intergenic	ID_B1|SINE|B4	-13507	NM_013672	20683	Mm.4618	NM_013672	ENSMUSG00000001280	Sp1	1110003E12Rik|AA450830|AI845540|Sp1-1	trans-acting transcription factor 1	protein-coding
mm_106213.1	chr11	116852203	116852258	-	1	NA	exon (NM_011358, exon 2 of 3)	exon (NM_011358, exon 2 of 3)	864	NM_011358	20382	Mm.21841	NM_011358	ENSMUSG00000034120	Srsf2	D11Wsu175e|MRF-1|Pr264|SC35|Sfrs10|Sfrs2	serine/arginine-rich splicing factor 2	protein-coding
mm_94846.1	chr11	23769794	23769804	+	1	NA	intron (NM_009044, intron 1 of 9)	intron (NM_009044, intron 1 of 9)	1171	NM_009044	19696	Mm.4869	NM_009044	ENSMUSG00000020275	Rel	c-Rel	reticuloendotheliosis oncogene	protein-coding
mm_92933.1	chr10	84527705	84527719	-	1	NA	exon (NM_175451, exon 2 of 2)	exon (NM_175451, exon 2 of 2)	6176	NM_175451	216197	Mm.334999	NM_175451	ENSMUSG00000046841	Ckap4	5630400A09Rik|CLIMP-63|P63	cytoskeleton-associated protein 4	protein-coding
mm_139185.1	chr17	47594630	47594645	+	1	NA	intron (NM_001081635, intron 3 of 6)	intron (NM_001081635, intron 3 of 6)	1170	NM_007632	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_49750.1	chr6	34746369	34746393	+	1	NA	intron (NM_001347100, intron 5 of 13)	GA-rich|Low_complexity|Low_complexity	-34051	NM_001289657	76223	Mm.150047	NM_178630	ENSMUSG00000038836	Agbl3	2900053G10Rik|4930431N21Rik|6530406M24Rik|CCP3	ATP/GTP binding protein-like 3	protein-coding
mm_10761.1	chr2	24186314	24186322	+	1	NA	promoter-TSS (NM_153511)	promoter-TSS (NM_153511)	-158	NM_153511	215257	Mm.249379	NM_153511	ENSMUSG00000044103	Il1f9	Il36g	interleukin 1 family, member 9	protein-coding
mm_145582.1	chr18	60984310	60984332	+	1	NA	intron (NM_177407, intron 16 of 17)	C-rich|Low_complexity|Low_complexity	20767	NM_001286809	12322	Mm.131530	NM_009792	ENSMUSG00000024617	Camk2a	CaMKII|R74975|mKIAA0968	calcium/calmodulin-dependent protein kinase II alpha	protein-coding
mm_62137.1	chr7	97090595	97090618	+	1	NA	intron (NM_001162477, intron 1 of 9)	intron (NM_001162477, intron 1 of 9)	8855	NM_010248	14389	Mm.42033	NM_010248	ENSMUSG00000004508	Gab2	AI463667|D130058I17Rik|p97	growth factor receptor bound protein 2-associated protein 2	protein-coding
mm_3050.1	chr1	134040930	134040940	+	1	NA	exon (NM_021355, exon 2 of 3)	exon (NM_021355, exon 2 of 3)	3420	NM_021355	14264	Mm.287146	NM_021355	ENSMUSG00000041559	Fmod	AI131919|AU041740|SLRR2E	fibromodulin	protein-coding
mm_96219.1	chr11	62509086	62509106	+	1	NA	intron (NM_001039536, intron 4 of 6)	LTRIS3|LTR|ERV1	30165	NM_028448	73139	Mm.390409	NM_028448	ENSMUSG00000018509	Cenpv	3110013H01Rik|AA671303|Prr6	centromere protein V	protein-coding
mm_104333.1	chr11	93996767	93996790	-	1	NA	intron (NM_001199203, intron 1 of 29)	intron (NM_001199203, intron 1 of 29)	687	NM_027569	70834	Mm.260737	NM_027569	ENSMUSG00000020859	Spag9	3110018C07Rik|4733401I23Rik|4831406C20Rik|AW552012|JLP|JSAP2|JSAP2a|Jip4|Mapk8ip4|syd1	sperm associated antigen 9	protein-coding
mm_76229.1	chr8	83573223	83573271	-	1	NA	exon (NM_027179, exon 4 of 12)	exon (NM_027179, exon 4 of 12)	6489	NM_025843	66916	Mm.29683	NM_025843	ENSMUSG00000033938	Ndufb7	1110002H15Rik	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 7	protein-coding
mm_162837.1	chr10	84517772	84517787	+	1	NA	Intergenic	MIR|SINE|MIR	16109	NM_175451	216197	Mm.334999	NM_175451	ENSMUSG00000046841	Ckap4	5630400A09Rik|CLIMP-63|P63	cytoskeleton-associated protein 4	protein-coding
mm_55180.1	chr6	52158293	52158324	-	1	NA	promoter-TSS (NM_010449)	promoter-TSS (NM_010449)	9	NM_010449	15394	Mm.197	NM_010449	ENSMUSG00000029844	Hoxa1	ERA1|Hox-1.6	homeobox A1	protein-coding
mm_24525.1	chr3	93188583	93188600	+	1	NA	Intergenic	Lx8b|LINE|L1	-8682	NM_001013804	229574	Mm.10755	NM_001013804		Flg2	EG229574	filaggrin family member 2	protein-coding
mm_18305.1	chr2	53190814	53190845	-	1	NA	intron (NM_018785, intron 1 of 25)	intron (NM_018785, intron 1 of 25)	358	NM_018785	56194	Mm.257474	NM_018785	ENSMUSG00000061136	Prpf40a	2810012K09Rik|FBP-11|FBP11|Fnbp11|Fnbp3	pre-mRNA processing factor 40A	protein-coding
mm_66749.1	chr7	46712192	46712199	-	1	NA	exon (NM_011315, exon 4 of 4)	exon (NM_011315, exon 4 of 4)	-1544	NM_030233	78935	Mm.289866	NM_030233	ENSMUSG00000006763	Saal1	5031425D22Rik|SPACIA1	serum amyloid A-like 1	protein-coding
mm_142547.1	chr17	46587083	46587088	-	1	NA	intron (NM_175168, intron 5 of 19)	B3|SINE|B2	-30923	NM_020493	20807	Mm.45044	NM_020493	ENSMUSG00000015605	Srf	AW049942|AW240594	serum response factor	protein-coding
mm_87276.1	chr10	41887458	41887498	+	1	NA	promoter-TSS (NM_001013370)	promoter-TSS (NM_001013370)	39	NM_001013370	140742	Mm.139418	NM_001013370	ENSMUSG00000038332	Sesn1	1110002G11Rik|AU044290|Pa26|Sest1	sestrin 1	protein-coding
mm_50289.1	chr6	47454341	47454423	+	1	NA	promoter-TSS (NM_012042)	promoter-TSS (NM_012042)	58	NM_012042	26965	Mm.87611	NM_012042	ENSMUSG00000029686	Cul1	-	cullin 1	protein-coding
mm_49629.1	chr6	30804820	30804824	+	1	NA	intron (NM_017478, intron 20 of 23)	intron (NM_017478, intron 20 of 23)	63523	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_172993.1	chrM	13986	13990	-	1	NA	NA	Intergenic	NA	NA								
mm_102169.1	chr11	53891639	53891656	-	1	NA	promoter-TSS (NM_011396)	promoter-TSS (NM_011396)	56	NM_011396	20520	Mm.42253	NM_011396	ENSMUSG00000018900	Slc22a5	Lstpl|Octn2|jvs	solute carrier family 22 (organic cation transporter), member 5	protein-coding
mm_4464.1	chr1	173333557	173333580	+	1	NA	promoter-TSS (NM_010045)	promoter-TSS (NM_010045)	-65	NM_010045	13349	Mm.6393	NM_010045	ENSMUSG00000037872	Ackr1	AA162249|CCBP1|CD234|Darc|Dfy|ESTM35|FY|GPD	atypical chemokine receptor 1 (Duffy blood group)	protein-coding
mm_65048.1	chr7	18647024	18647030	-	1	NA	3' UTR (NM_027403, exon 5 of 5)	3' UTR (NM_027403, exon 5 of 5)	9698	NM_027403	72242	Mm.326858	NM_027403	ENSMUSG00000070796	Psg21	1600019C01Rik|1600025N01Rik|1600026N13Rik|cea8	pregnancy-specific glycoprotein 21	protein-coding
mm_34608.1	chr4	150279221	150279228	+	1	NA	Intergenic	AT_rich|Low_complexity|Low_complexity	-2692	NM_001085492	68703	Mm.291274	NM_001085492	ENSMUSG00000039852	Rere	1110033A15Rik|AI414665|ARG|ARP|ATN1L|AW742570|Atr2|DNB1|eye<m03Jus>|eyes3|mKIAA0458	arginine glutamic acid dipeptide (RE) repeats	protein-coding
mm_68767.1	chr7	121946357	121946369	-	1	NA	intron (NM_001033318, intron 9 of 16)	intron (NM_001033318, intron 9 of 16)	35330	NM_001033318	233824	Mm.442015	NM_001033318	ENSMUSG00000034951	Cog7	5630400E24Rik|Gm167	component of oligomeric golgi complex 7	protein-coding
mm_121192.1	chr14	103051035	103051050	+	1	NA	intron (NM_008392, intron 3 of 4)	Lx7|LINE|L1	4030	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_115935.1	chr13	23621890	23621931	-	1	NA	promoter-TSS (NM_178194)	promoter-TSS (NM_178194)	648	NM_015787	50709	Mm.170587	NM_015787	ENSMUSG00000051627	Hist1h1e	H1-4|H1.4|H1e|H1f4|H1s-4|H1var2	histone cluster 1, H1e	protein-coding
mm_15443.1	chr2	157367146	157367171	+	1	NA	promoter-TSS (NM_026968)	promoter-TSS (NM_026968)	-436	NM_026968	69161	Mm.228619	NM_026968	ENSMUSG00000063019	Manbal	1810024K12Rik|AI836500	mannosidase, beta A, lysosomal-like	protein-coding
mm_104883.1	chr11	99521604	99521606	-	1	NA	promoter-TSS (NM_213730)	promoter-TSS (NM_213730)	-347	NM_213730	237934	Mm.484091	NM_213730	ENSMUSG00000064165	Krt39	4732494G06Rik|Ka35	keratin 39	protein-coding
mm_166200.1	chr5	37983709	37983720	+	1	NA	Intergenic	Intergenic	-55516	NM_001289536	71116	Mm.18959	NM_026959	ENSMUSG00000029125	Stx18	1810035L21Rik|4933425D03Rik|AU041562	syntaxin 18	protein-coding
mm_13289.1	chr2	101678404	101678469	+	1	NA	promoter-TSS (NM_009424)	promoter-TSS (NM_009424)	16	NM_001303273	22034	Mm.292729	NM_009424	ENSMUSG00000027164	Traf6	2310003F17Rik|AI851288|C630032O20Rik	TNF receptor-associated factor 6	protein-coding
mm_151027.1	chr19	46987926	46987956	+	1	NA	intron (NM_001164363, intron 1 of 17)	intron (NM_001164363, intron 1 of 17)	-18374	NM_001164365	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_120000.1	chr14	55618127	55618137	+	1	NA	promoter-TSS (NM_020002)	promoter-TSS (NM_020002)	-34	NM_020002	56739	Mm.23149	NM_020002	ENSMUSG00000002324	Rec8	Rec8L1|mrec	REC8 meiotic recombination protein	protein-coding
mm_135716.1	chr16	55812236	55812248	-	1	NA	3' UTR (NM_030612, exon 14 of 14)	3' UTR (NM_030612, exon 14 of 14)	9896	NM_001159394	80859	Mm.247272	NM_030612	ENSMUSG00000035356	Nfkbiz	AA408868|INAP|Mail	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, zeta	protein-coding
mm_119226.1	chr14	33250437	33250475	+	1	NA	intron (NM_153800, intron 2 of 10)	intron (NM_153800, intron 2 of 10)	33633	NM_153800	239027	Mm.318350	NM_153800	ENSMUSG00000063506	Arhgap22	B230341L19Rik|RHOGAP2|p68RacGAP	Rho GTPase activating protein 22	protein-coding
mm_19032.1	chr2	76969709	76969721	-	1	NA	exon (NM_011652, exon 7 of 313)	exon (NM_011652, exon 7 of 313)	12832	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_60799.1	chr7	45621806	45621825	+	1	NA	promoter-TSS (NM_001018013)	promoter-TSS (NM_001018013)	4	NM_001018013	73456	Mm.380445	NM_001018013	ENSMUSG00000064158	Izumo1	1700058F15Rik|Izumo	izumo sperm-egg fusion 1	protein-coding
mm_75148.1	chr8	35826436	35826485	-	1	NA	promoter-TSS (NM_027998)	promoter-TSS (NM_027998)	99	NM_027998	71908	Mm.37817	NM_027998	ENSMUSG00000055976	Cldn23	2310014B08Rik	claudin 23	protein-coding
mm_67968.1	chr7	100608230	100608268	-	1	NA	promoter-TSS (NR_003559)	promoter-TSS (NR_003559)	-253	NR_003559	52443	Mm.473730	NM_198831	ENSMUSG00000030706	Mrpl48	1810030E20Rik|2610028L11Rik|CGI-118|D4Ertd786e	mitochondrial ribosomal protein L48	protein-coding
mm_908.1	chr1	54250814	54250844	+	1	NA	exon (NM_030025, exon 1 of 28)	exon (NM_030025, exon 1 of 28)	146	NM_030025	78016	Mm.67455	NM_030025	ENSMUSG00000025983	Ccdc150	4930511H11Rik	coiled-coil domain containing 150	protein-coding
mm_21076.1	chr2	152830616	152830680	-	1	NA	promoter-TSS (NM_001289716)	promoter-TSS (NM_001289716)	69	NM_001289716	12048	Mm.238213	NM_009743	ENSMUSG00000007659	Bcl2l1	Bcl(X)L|Bcl-XL|Bcl2l|BclX|bcl-x|bcl2-L-1	BCL2-like 1	protein-coding
mm_18535.1	chr2	64097918	64097938	-	1	NA	5' UTR (NM_021716, exon 1 of 3)	5' UTR (NM_021716, exon 1 of 3)	110	NM_001267846	60344	Mm.130769	NM_021716	ENSMUSG00000075324	Fign	fi|fidget	fidgetin	protein-coding
mm_147405.1	chr18	44652166	44652169	-	1	NA	intron (NM_001085373, intron 3 of 18)	intron (NM_001085373, intron 3 of 18)	-9498	NR_026853	626275	Mm.427116	NR_026853	ENSMUSG00000097610	A930012L18Rik	-	RIKEN cDNA A930012L18 gene	ncRNA
mm_96294.1	chr11	63133069	63133075	+	1	NA	intron (NM_001302260, intron 1 of 4)	CpG	269	NM_001302260	18858	Mm.1237	NM_008885	ENSMUSG00000018217	Pmp22	22kDa|Gas-3|HNPP|Tr|trembler	peripheral myelin protein 22	protein-coding
mm_55583.1	chr6	71399339	71399348	-	1	NA	intron (NM_024288, intron 4 of 8)	intron (NM_024288, intron 4 of 8)	25916	NM_001081110	12525	Mm.1858	NM_009857	ENSMUSG00000053977	Cd8a	BB154331|Ly-2|Ly-35|Ly-B|Lyt-2	CD8 antigen, alpha chain	protein-coding
mm_99158.1	chr11	100619730	100619760	+	1	NA	5' UTR (NM_019795, exon 1 of 14)	5' UTR (NM_019795, exon 1 of 14)	423	NM_019795	56354	Mm.402409	NM_019795	ENSMUSG00000014195	Dnajc7	2010003F24Rik|2010004G07Rik|CCRP|Ttc2|mDj11|mTpr2	DnaJ heat shock protein family (Hsp40) member C7	protein-coding
mm_11572.1	chr2	32912479	32912518	+	1	NA	exon (NM_146119, exon 5 of 14)	exon (NM_146119, exon 5 of 14)	36364	NM_146119	227737	Mm.301646	NM_146119	ENSMUSG00000026796	Fam129b	9130404D14Rik	family with sequence similarity 129, member B	protein-coding
mm_126112.1	chr15	78254865	78254894	+	1	NA	exon (NM_008677, exon 5 of 10)	exon (NM_008677, exon 5 of 10)	10068	NM_008677	17972	Mm.2068	NM_008677	ENSMUSG00000071715	Ncf4	AI451400|p40phox	neutrophil cytosolic factor 4	protein-coding
mm_112744.1	chr13	19340548	19340578	+	1	NA	Intergenic	Intergenic	55250	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_36091.1	chr4	58483622	58483642	-	1	NA	intron (NM_001290486, intron 2 of 2)	intron (NM_001290486, intron 2 of 2)	15771	NM_001290486	14745	Mm.4772	NM_010336	ENSMUSG00000038668	Lpar1	AI326300|Edg2|Gpcr26|Kdt2|lpA1|vzg-1	lysophosphatidic acid receptor 1	protein-coding
mm_96761.1	chr11	69914237	69914266	+	1	NA	promoter-TSS (NM_019726)	promoter-TSS (NM_019726)	59	NM_019726	56310	Mm.477738	NM_019726	ENSMUSG00000023170	Gps2	AI505953	G protein pathway suppressor 2	protein-coding
mm_76749.1	chr8	95434644	95434654	-	1	NA	5' UTR (NM_008187, exon 1 of 6)	5' UTR (NM_008187, exon 1 of 6)	220	NM_008187	14894	Mm.2080	NM_008187	ENSMUSG00000031796	Cfap20	2600014O15Rik|AL024127|Gtl3|T10-2A2	cilia and flagella associated protein 20	protein-coding
mm_74722.1	chr8	17459526	17459540	-	1	NA	intron (NM_053171, intron 1 of 69)	L1MCb|LINE|L1	75852	NM_053171	94109	Mm.436988	NM_053171	ENSMUSG00000060924	Csmd1	B930082H09|mKIAA1890	CUB and Sushi multiple domains 1	protein-coding
mm_115000.1	chr13	98263106	98263177	+	1	NA	promoter-TSS (NM_178918)	promoter-TSS (NM_178918)	65	NM_001271388	68558	Mm.209642	NM_023472	ENSMUSG00000021661	Ankra2	1110004M18Rik|Ankra	ankyrin repeat, family A (RFXANK-like), 2	protein-coding
mm_161812.1	chr17	63938148	63938148	+	1	NA	intron (NM_008000, intron 1 of 13)	intron (NM_008000, intron 1 of 13)	176	NM_008000	14158	Mm.23039	NM_008000	ENSMUSG00000000127	Fer	AV082135|C330004K01Rik|Fert|Fert2	fer (fms/fps related) protein kinase	protein-coding
mm_50595.1	chr6	49071256	49071271	+	1	NA	Intergenic	Intergenic	-2532	NM_029353	75593	Mm.439947	NM_029353	ENSMUSG00000029815	Malsu1	2410003K15Rik|Matsu1	mitochondrial assembly of ribosomal large subunit 1	protein-coding
mm_162770.1	chr10	67549011	67549022	-	1	NA	promoter-TSS (NM_001005419)	promoter-TSS (NM_001005419)	-61	NM_001005419	211488	Mm.297250	NM_001005419	ENSMUSG00000057134	Ado	Gm237	2-aminoethanethiol (cysteamine) dioxygenase	protein-coding
mm_130754.1	chr15	101270508	101270523	-	1	NA	exon (NM_010444, exon 2 of 7)	exon (NM_010444, exon 2 of 7)	3669	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_118537.1	chr14	16253881	16253882	+	1	NA	intron (NM_021504, intron 1 of 11)	ORR1A1|LTR|ERVL-MaLR	-4073	NM_027695	71147	Mm.197960	NM_027695	ENSMUSG00000021786	Oxsm	4933425A18Rik|C80494	3-oxoacyl-ACP synthase, mitochondrial	protein-coding
mm_126760.1	chr15	85832320	85832351	+	1	NA	promoter-TSS (NM_001033337)	promoter-TSS (NM_001033337)	31	NM_001033337	239570	Mm.151748	NM_001033337	ENSMUSG00000035944	Ttc38	9030019H09	tetratricopeptide repeat domain 38	protein-coding
mm_68048.1	chr7	101538256	101538260	-	1	NA	Intergenic	Intergenic	17544	NM_007490	11871	Mm.439746	NM_007490	ENSMUSG00000092517	Art2a-ps	ARTC2|Art2a|Ly92a|Rt-6|Rt6|Rt6-1	ADP-ribosyltransferase 2a, pseudogene	protein-coding
mm_43890.1	chr5	143933060	143933077	+	1	NA	Intergenic	Intergenic	23067	NM_008886	18861	Mm.2950	NM_008886	ENSMUSG00000075569	Pms2	AW555130|Pmsl2	postmeiotic segregation increased 2 (S. cerevisiae)	protein-coding
mm_64341.1	chr7	142377092	142377131	+	1	NA	exon (NM_009983, exon 7 of 9)	exon (NM_009983, exon 7 of 9)	-3365	NM_001347541	320802	Mm.154486	NM_177265	ENSMUSG00000045777	Ifitm10	6330512M04Rik|AI848576|DSPA3	interferon induced transmembrane protein 10	protein-coding
mm_173342.1	chrY	90812261	90812267	+	1	NA	intron (NM_133362, intron 2 of 3)	IMPB_01|Satellite|Satellite	26822	NM_133362	170942	Mm.76062	NM_133362	ENSMUSG00000096768	Erdr1	edr	erythroid differentiation regulator 1	protein-coding
mm_62001.1	chr7	91176912	91176928	+	1	NA	intron (NM_011807, intron 1 of 22)	intron (NM_011807, intron 1 of 22)	86134	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_88461.1	chr10	77561069	77561091	+	1	NA	exon (NM_008404, exon 14 of 16)	exon (NM_008404, exon 14 of 16)	-20687	NM_145925	108705	Mm.28853	NM_145925	ENSMUSG00000009291	Pttg1ip	1810010L20Rik|AI314311|AU018448|C79540	pituitary tumor-transforming 1 interacting protein	protein-coding
mm_35416.1	chr4	35020016	35020026	-	1	NA	intron (NM_178061, intron 2 of 3)	intron (NM_178061, intron 2 of 3)	-108540	NR_040652	73696	Mm.1361	NR_040652	ENSMUSG00000085824	Platr9	2410114N07Rik	pluripotency associated transcript 9	ncRNA
mm_44260.1	chr5	5514837	5514858	-	1	NA	promoter-TSS (NM_001193660)	promoter-TSS (NM_001193660)	2	NM_001193661	64945	Mm.40132	NM_022890	ENSMUSG00000046798	Cldn12	-	claudin 12	protein-coding
mm_118769.1	chr14	22616378	22616395	+	1	NA	intron (NM_028275, intron 5 of 6)	intron (NM_028275, intron 5 of 6)	-73588	NR_046307	74896	Mm.444661	NR_046307		4930405A10Rik	4930456G20Rik	RIKEN cDNA 4930405A10 gene	ncRNA
mm_10277.1	chr2	9884458	9884475	+	1	NA	non-coding (NR_024257, exon 5 of 5)	non-coding (NR_024257, exon 5 of 5)	3220	NR_024257	381347	Mm.441450	NR_024257		4930412O13Rik	ENSMUSG00000075535|Gm10853	RIKEN cDNA 4930412O13 gene	ncRNA
mm_37489.1	chr4	123613702	123613751	-	1	NA	intron (NM_001199136, intron 1 of 97)	intron (NM_001199136, intron 1 of 97)	-2694	NR_105824	102465214		NR_105824	ENSMUSG00000099005	Mir6398	Gm27657|mmu-mir-6398	microRNA 6398	ncRNA
mm_106555.1	chr11	120617888	120617941	-	1	NA	promoter-TSS (NM_024229)	promoter-TSS (NM_024229)	-24	NM_024229	68671	Mm.21439	NM_024229	ENSMUSG00000025137	Pcyt2	1110033E03Rik|ET	phosphate cytidylyltransferase 2, ethanolamine	protein-coding
mm_29758.1	chr3	127162196	127162259	-	1	NA	intron (NR_105029, intron 2 of 3)	intron (NR_105029, intron 2 of 3)	922	NR_105029	100862268	Mm.444603	NR_105029	ENSMUSG00000097456	LOC100862268	-	uncharacterized LOC100862268	ncRNA
mm_108767.1	chr12	89601992	89601995	+	1	NA	intron (NM_172544, intron 14 of 19)	intron (NM_172544, intron 14 of 19)	-210490	NM_001252074	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding
mm_34037.1	chr4	138172985	138172988	+	1	NA	intron (NM_172703, intron 21 of 34)	B1_Mus2|SINE|Alu	9777	NR_105825	102466907		NR_105825	ENSMUSG00000098513	Mir6399	Gm27667|mir-6399|mmu-mir-6399	microRNA 6399	ncRNA
mm_24662.1	chr3	94484370	94484408	+	1	NA	intron (NR_110353, intron 1 of 11)	intron (NR_110353, intron 1 of 11)	1667	NR_110353	78784	Mm.44292	NM_172434	ENSMUSG00000028137	Celf3	4930415M08Rik|BRUNOL1|CAGH4|ERDA4|Tnrc4	CUGBP, Elav-like family member 3	protein-coding
mm_78233.1	chr9	21616153	21616163	+	1	NA	promoter-TSS (NM_001174078)	promoter-TSS (NM_001174078)	-11	NM_011417	20586	Mm.286593	NM_011417	ENSMUSG00000032187	Smarca4	Brg1|HP1-BP72|SNF2beta|SW1/SNF|b2b508.1Clo|b2b692Clo	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	protein-coding
mm_88994.1	chr10	81574700	81574738	+	1	NA	promoter-TSS (NM_019725)	promoter-TSS (NM_019725)	-568	NM_019725	21886	Mm.38608	NM_019725	ENSMUSG00000034771	Tle2	Grg2|mKIAA4188	transducin-like enhancer of split 2	protein-coding
mm_44373.1	chr5	17814222	17814232	-	1	NA	exon (NM_001159558, exon 7 of 16)	exon (NM_001159558, exon 7 of 16)	21669	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_160719.1	chr10	63382418	63382418	+	1	NA	promoter-TSS (NM_001253685)	promoter-TSS (NM_001253685)	-25	NM_001253685	30045	Mm.32550	NM_013888	ENSMUSG00000036764	Dnajc12	Jdp1|mJDP1	DnaJ heat shock protein family (Hsp40) member C12	protein-coding
mm_86470.1	chr10	4611814	4611823	+	1	NA	promoter-TSS (NR_126357)	promoter-TSS (NR_126357)	-171	NM_001302532	13982	Mm.9213	NM_007956	ENSMUSG00000019768	Esr1	ER|ER-alpha|ERa|ERalpha|ESR|Estr|Estra|Nr3a1	estrogen receptor 1 (alpha)	protein-coding
mm_171657.1	chr4	43000398	43000402	-	1	NA	5' UTR (NM_009503, exon 1 of 17)	5' UTR (NM_009503, exon 1 of 17)	107	NM_009503	269523	Mm.245976	NM_009503	ENSMUSG00000028452	Vcp	3110001E05|CDC48|p97|p97/VCP	valosin containing protein	protein-coding
mm_130679.1	chr15	100678085	100678093	-	1	NA	intron (NM_033612, intron 6 of 7)	intron (NM_033612, intron 6 of 7)	-8589	NM_001270537	668218	Mm.451225	NM_001270537	ENSMUSG00000098112	Bin2	-	bridging integrator 2	protein-coding
mm_67835.1	chr7	98361394	98361401	-	1	NA	promoter-TSS (NM_001168539)	promoter-TSS (NM_001168539)	-69	NM_001168539	244152	Mm.25317	NM_001024619	ENSMUSG00000049580	Tsku	9530051K01Rik|E2ig4|Lrrc54|Tsk	tsukushi, small leucine rich proteoglycan	protein-coding
mm_150417.1	chr19	37212437	37212452	+	1	NA	intron (NM_001164336, intron 2 of 4)	B1_Mm|SINE|Alu	4899	NM_001164336	69104	Mm.175989	NM_027314	ENSMUSG00000023307	March5	1810015H18Rik|2310008I22Rik|2700055A20Rik|5730499H23Rik|E130202O05Rik|MARCH-V|MITOL|Marchv|Rnf153	membrane-associated ring finger (C3HC4) 5	protein-coding
mm_21170.1	chr2	154658042	154658050	-	1	NA	intron (NM_029362, intron 1 of 4)	intron (NM_029362, intron 1 of 4)	1020	NM_029362	75608	Mm.262480	NM_029362	ENSMUSG00000038467	Chmp4b	2010012F05Rik|C76846|Snf7-2	charged multivesicular body protein 4B	protein-coding
mm_122070.1	chr14	30595710	30595727	-	1	NA	3' UTR (NM_001310682, exon 17 of 17)	3' UTR (NM_001310682, exon 17 of 17)	14592	NM_001310682	18753	Mm.2314	NM_011103	ENSMUSG00000021948	Prkcd	AI385711|D14Ertd420e|PKC[d]|PKCdelta|Pkcd	protein kinase C, delta	protein-coding
mm_62587.1	chr7	105596279	105596306	+	1	NA	exon (NM_017371, exon 5 of 10)	exon (NM_017371, exon 5 of 10)	3824	NM_017371	15458	Mm.3485	NM_017371	ENSMUSG00000030895	Hpx	Hpxn|hx	hemopexin	protein-coding
mm_8193.1	chr1	138107821	138107851	-	1	NA	exon (NM_001268286, exon 8 of 29)	exon (NM_001268286, exon 8 of 29)	67290	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_58658.1	chr7	6415213	6415219	+	1	NA	promoter-TSS (NM_001134752)	promoter-TSS (NM_001134752)	41	NM_001134752	100042450	Mm.416919	NM_001134752	ENSMUSG00000093536	Smim17	Gm16532	small integral membrane protein 17	protein-coding
mm_69729.1	chr7	140822125	140822193	-	1	NA	promoter-TSS (NM_001001180)	promoter-TSS (NM_001001180)	19	NM_001001180	407812	Mm.359154	NM_001001180	ENSMUSG00000060314	Zfp941	-	zinc finger protein 941	protein-coding
mm_124932.1	chr15	12205069	12205119	+	1	NA	promoter-TSS (NM_172958)	promoter-TSS (NM_172958)	0	NM_172958	268783	Mm.54460	NM_172958	ENSMUSG00000039458	Mtmr12	3Pap|4932703C11|C730015A02Rik|Pip3ap|mKIAA1682	myotubularin related protein 12	protein-coding
mm_111033.1	chr12	79185709	79185735	-	1	NA	intron (NM_021557, intron 4 of 6)	intron (NM_021557, intron 4 of 6)	6097	NM_021557	17252	Mm.291799	NM_021557	ENSMUSG00000066441	Rdh11	2610319N22Rik|AI428145|AU045252|Arsdr1|C85936|CGI-82|HCBP12|M42C60|Mdt1|Psdr1|SCALD|UBE-1c1|Ube-1c	retinol dehydrogenase 11	protein-coding
mm_78581.1	chr9	37208292	37208360	+	1	NA	promoter-TSS (NM_001310096)	promoter-TSS (NM_001310096)	10	NM_001310096	66279	Mm.41451	NM_025464	ENSMUSG00000032121	Tmem218	1810021J13Rik|AV004931	transmembrane protein 218	protein-coding
mm_59607.1	chr7	28142263	28142270	+	1	NA	exon (NM_001164655, exon 6 of 20)	exon (NM_001164655, exon 6 of 20)	12800	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_9810.1	chr1	181956533	181956547	-	1	NA	exon (NM_010135, exon 3 of 15)	exon (NM_010135, exon 3 of 15)	63440	NM_008680	13800	Mm.87759	NM_008680	ENSMUSG00000022995	Enah	Mena|NDPP-1|Ndpp1|WBP8	enabled homolog (Drosophila)	protein-coding
mm_158721.1	chrX	162888413	162888423	-	1	NA	promoter-TSS (NM_025932)	promoter-TSS (NM_025932)	44	NM_025932	67043	Mm.44207	NM_025932	ENSMUSG00000031357	Syap1	2010110O17Rik|AW011796	synapse associated protein 1	protein-coding
mm_72754.1	chr8	85299893	85299928	+	1	NA	promoter-TSS (NM_022997)	promoter-TSS (NM_022997)	278	NR_028268	56452	Mm.29709	NM_019716	ENSMUSG00000031697	Orc6	6720420I10Rik|Orc6l	origin recognition complex, subunit 6	protein-coding
mm_18945.1	chr2	76768979	76768989	-	1	NA	exon (NM_011652, exon 252 of 313)	exon (NM_011652, exon 252 of 313)	93669	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_112736.1	chr13	19256989	19257004	+	1	NA	Intergenic	Intergenic	138817	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_129129.1	chr15	76190300	76190315	-	1	NA	intron (NM_011117, intron 11 of 31)	intron (NM_011117, intron 11 of 31)	5403	NM_201394	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
mm_74573.1	chr8	11201785	11201806	-	1	NA	exon (NM_009931, exon 51 of 52)	exon (NM_009931, exon 51 of 52)	-111010	NM_009932	12827	Mm.181021	NM_009932	ENSMUSG00000031503	Col4a2	Col4a-2	collagen, type IV, alpha 2	protein-coding
mm_45964.1	chr5	90465893	90465913	-	1	NA	exon (NM_009654, exon 6 of 15)	exon (NM_009654, exon 6 of 15)	5033	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_57120.1	chr6	122596859	122596882	-	1	NA	intron (NM_001134391, intron 2 of 7)	intron (NM_001134391, intron 2 of 7)	5574	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_28315.1	chr3	89270490	89270551	-	1	NA	promoter-TSS (NM_009057)	promoter-TSS (NM_009057)	50	NM_009057	19729	Mm.17958	NM_009057	ENSMUSG00000027953	Slc50a1	MmSWEET1|Rag1ap1|Rga	solute carrier family 50 (sugar transporter), member 1	protein-coding
mm_154149.1	chr19	58454491	58454512	-	1	NA	non-coding (NR_104342, exon 2 of 12)	non-coding (NR_104342, exon 2 of 12)	897	NM_001285457	14585	Mm.88367	NM_010279	ENSMUSG00000025089	Gfra1	AU042498	glial cell line derived neurotrophic factor family receptor alpha 1	protein-coding
mm_47218.1	chr5	121122172	121122185	-	1	NA	Intergenic	Intergenic	69219	NM_001109992	19247	Mm.8681	NM_011202	ENSMUSG00000043733	Ptpn11	2700084A17Rik|AW536184|PTP1D|PTP2C|SAP-2|SH-PTP2|SH-PTP3|SHP-2|Shp2|Syp	protein tyrosine phosphatase, non-receptor type 11	protein-coding
mm_42136.1	chr5	111287366	111287376	+	1	NA	3' UTR (NM_001267622, exon 23 of 23)	3' UTR (NM_001267622, exon 23 of 23)	-43326	NM_001301644	56305	Mm.200516	NM_019640	ENSMUSG00000050017	Pitpnb	PI-TP-beta	phosphatidylinositol transfer protein, beta	protein-coding
mm_9027.1	chr1	166464904	166464930	-	1	NA	Intergenic	RMER1B|Other|Other	32671	NM_001164306	226601	Mm.475593	NM_001164306	ENSMUSG00000086056	Gm4846	EG226601|Fmo13	predicted gene 4846	protein-coding
mm_36071.1	chr4	57953521	57953533	-	1	NA	intron (NM_011660, intron 1 of 4)	B3|SINE|B2	2884	NM_011660	22166	Mm.260618	NM_011660	ENSMUSG00000028367	Txn1	ADF|AW550880|Trx1|Txn	thioredoxin 1	protein-coding
mm_124724.1	chr15	6580157	6580167	+	1	NA	exon (NM_001278269, exon 1 of 17)	exon (NM_001278269, exon 1 of 17)	315	NM_011815	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_123868.1	chr14	72584601	72584618	-	1	NA	exon (NM_207636, exon 6 of 26)	exon (NM_207636, exon 6 of 26)	125394	NM_207636	319448	Mm.205421	NM_207636	ENSMUSG00000033487	Fndc3a	1700094E19Rik|D14Ertd453e|F730017H24Rik|Fndc3|sys	fibronectin type III domain containing 3A	protein-coding
mm_155099.1	chrX	48274931	48274941	+	1	NA	exon (NM_028276, exon 11 of 15)	exon (NM_028276, exon 11 of 15)	10490	NR_045916	100500713	Mm.396609	NR_045916	ENSMUSG00000097197	9530027J09Rik	-	RIKEN cDNA 9530027J09 gene	ncRNA
mm_3232.1	chr1	135849948	135849954	+	1	NA	intron (NM_001130174, intron 10 of 13)	B1_Mur2|SINE|Alu	9090	NM_001130176	21956	Mm.247470	NM_011619	ENSMUSG00000026414	Tnnt2	Tnt|cTnT	troponin T2, cardiac	protein-coding
mm_30406.1	chr3	152253720	152253750	-	1	NA	intron (NM_199465, intron 2 of 12)	intron (NM_199465, intron 2 of 12)	12585	NM_199465	68810	Mm.200188	NM_199465	ENSMUSG00000039103	Nexn	1110046H09Rik|AA553326|NELIN	nexilin	protein-coding
mm_164038.1	chr14	86749106	86749118	-	1	NA	intron (NM_019670, intron 27 of 27)	intron (NM_019670, intron 27 of 27)	392002	NM_019670	56419	Mm.440585	NM_019670	ENSMUSG00000022021	Diaph3	4930417P13Rik|Dia2|Diap3|Drf3|mDia2|mKIAA4117|p134MDia2	diaphanous related formin 3	protein-coding
mm_109866.1	chr12	4907567	4907584	-	1	NA	promoter-TSS (NM_145441)	promoter-TSS (NM_145441)	-55	NM_145441	217379	Mm.259170	NM_145441	ENSMUSG00000020634	Ubxn2a	6330407P03Rik|Ubxd4	UBX domain protein 2A	protein-coding
mm_50412.1	chr6	48740013	48740024	+	1	NA	intron (NM_175860, intron 1 of 2)	intron (NM_175860, intron 1 of 2)	971	NM_008376	16205	Mm.252599	NM_008376	ENSMUSG00000090019	Gimap1	IAP38|Imap38|imap	GTPase, IMAP family member 1	protein-coding
mm_124277.1	chr14	103037070	103037077	-	1	NA	Intergenic	Intergenic	-3270	NR_045657	71264	Mm.399572	NR_045657		4933432I03Rik	-	RIKEN cDNA 4933432I03 gene	ncRNA
mm_149693.1	chr19	21272277	21272296	+	1	NA	promoter-TSS (NM_009551)	promoter-TSS (NM_009551)	8	NM_009551	22682	Mm.292405	NM_009551	ENSMUSG00000024750	Zfand5	2310057A04Rik|5830475F03Rik|AA415485|Za20d2|Zfp216	zinc finger, AN1-type domain 5	protein-coding
mm_105136.1	chr11	101459285	101459302	-	1	NA	TTS (NM_027320)	TTS (NM_027320)	6906	NM_012037	26949	Mm.29210	NM_012037	ENSMUSG00000034993	Vat1	VAT-1	vesicle amine transport 1	protein-coding
mm_5830.1	chr1	52817442	52817477	-	1	NA	5' UTR (NM_008384, exon 1 of 6)	5' UTR (NM_008384, exon 1 of 6)	229	NM_008384	16329	Mm.917	NM_008384	ENSMUSG00000026102	Inpp1	2300002C06Rik|AV137389	inositol polyphosphate-1-phosphatase	protein-coding
mm_58453.1	chr7	3330554	3330566	+	1	NA	3' UTR (NM_011102, exon 18 of 18)	3' UTR (NM_011102, exon 18 of 18)	-6025	NM_133189	81904	Mm.214994	NM_133189	ENSMUSG00000069806	Cacng7	-	calcium channel, voltage-dependent, gamma subunit 7	protein-coding
mm_89562.1	chr10	95411763	95411776	+	1	NA	3' UTR (NM_007706, exon 3 of 3)	3' UTR (NM_007706, exon 3 of 3)	3514	NM_001168657	216233	Mm.474283	NM_007706	ENSMUSG00000020027	Socs2	8030460M17|AI527257|AW108012|CIS2|Cish2|D130043N08Rik|JAB|SOCS-2|SSI-2|hg	suppressor of cytokine signaling 2	protein-coding
mm_148535.1	chr19	4594399	4594422	+	1	NA	promoter-TSS (NM_008797)	promoter-TSS (NM_008797)	91	NM_008797	18563	Mm.1845	NM_008797	ENSMUSG00000024892	Pcx	Pc|Pcb	pyruvate carboxylase	protein-coding
mm_125507.1	chr15	55557400	55557436	+	1	NA	promoter-TSS (NM_026759)	promoter-TSS (NM_026759)	10	NM_001168250	105837	Mm.390829	NM_134092	ENSMUSG00000022369	Mtbp	AI429604|MDM2BP	Mdm2, transformed 3T3 cell double minute p53 binding protein	protein-coding
mm_3963.1	chr1	164151567	164151591	+	1	NA	promoter-TSS (NM_007976)	promoter-TSS (NM_007976)	-256	NM_007976	14067	Mm.12900	NM_007976	ENSMUSG00000026579	F5	AI173222|Cf-5|Cf5	coagulation factor V	protein-coding
mm_134197.1	chr16	11006071	11006109	-	1	NA	Intergenic	MIR|SINE|MIR	-2808	NR_040518	100043147	Mm.489001	NR_040518	ENSMUSG00000097056	Gm4262	-	predicted gene 4262	ncRNA
mm_89047.1	chr10	82860490	82860550	+	1	NA	5' UTR (NM_001042514, exon 1 of 14)	5' UTR (NM_001042514, exon 1 of 14)	179	NM_001042514	50493	Mm.210155	NM_015762	ENSMUSG00000020250	Txnrd1	TR|TR1|TrxR1	thioredoxin reductase 1	protein-coding
mm_39934.1	chr5	31698051	31698067	+	1	NA	promoter-TSS (NM_181282)	promoter-TSS (NM_181282)	9	NM_144541	107976	Mm.482126	NM_144541	ENSMUSG00000052139	Bre	6030405P19Rik|AI429776|B830038C02Rik	brain and reproductive organ-expressed protein	protein-coding
mm_44917.1	chr5	35729008	35729016	-	1	NA	5' UTR (NM_194344, exon 1 of 18)	5' UTR (NM_194344, exon 1 of 18)	264	NM_194344	231147	Mm.290429	NM_194344	ENSMUSG00000036553	Sh3tc1	4631428G15|BC024909	SH3 domain and tetratricopeptide repeats 1	protein-coding
mm_145285.1	chr18	53213884	53213898	+	1	NA	intron (NM_026386, intron 11 of 14)	B1_Mur2|SINE|Alu	-31771	NM_029394	69226	Mm.32414	NM_029394	ENSMUSG00000024535	Snx24	2810011K15Rik|5730433I16Rik|AI451341	sorting nexing 24	protein-coding
mm_13780.1	chr2	118779691	118779701	+	1	NA	promoter-TSS (NM_170593)	promoter-TSS (NM_170593)	-23	NM_170593	214240	Mm.221499	NM_170593	ENSMUSG00000040035	Disp2	AI840597|B230210L08Rik|DispB|mKIAA1742	dispatched RND tramsporter family member 2	protein-coding
mm_109622.1	chr12	112765062	112765082	+	1	NA	exon (NM_178911, exon 6 of 11)	exon (NM_178911, exon 6 of 11)	4417	NM_178911	104759	Mm.203915	NM_178911	ENSMUSG00000052160	Pld4	AI132321|thss	phospholipase D family, member 4	protein-coding
mm_85779.1	chr9	109058394	109058405	-	1	NA	TTS (NM_026381)	TTS (NM_026381)	852	NM_001012236	22040	Mm.439964	NM_011637	ENSMUSG00000049734	Trex1	AU041952	three prime repair exonuclease 1	protein-coding
mm_56139.1	chr6	87745037	87745047	-	1	NA	intron (NM_001159697, intron 2 of 7)	MER20B|DNA|hAT-Charlie	14173	NM_001159697	58229	Mm.333229	NM_021418	ENSMUSG00000068263	Efcc1	Ccdc48	EF hand and coiled-coil domain containing 1	protein-coding
mm_119269.1	chr14	34085979	34086004	+	1	NA	promoter-TSS (NM_001281845)	promoter-TSS (NM_001281845)	12	NM_013473	11752	Mm.3267	NM_013473	ENSMUSG00000021950	Anxa8	AI466995|Anx8	annexin A8	protein-coding
mm_25245.1	chr3	103967946	103967972	+	1	NA	promoter-TSS (NM_001163469)	promoter-TSS (NM_001163469)	-151	NM_001163467	18685	Mm.385178	NM_013629	ENSMUSG00000058388	Phtf1	AU041898|AW049785|Phft|Phtf	putative homeodomain transcription factor 1	protein-coding
mm_167836.1	chr9	124424547	124424587	-	1	NA	non-coding (NR_015516, exon 1 of 1)	non-coding (NR_015516, exon 1 of 1)	780	NR_015516	75135	Mm.476814	NR_015516		4930526I15Rik	1600027J15Rik	RIKEN cDNA 4930526I15 gene	ncRNA
mm_112611.1	chr13	15463203	15463240	+	1	NA	promoter-TSS (NM_008130)	promoter-TSS (NM_008130)	-502	NM_008130	14634	Mm.5098	NM_008130	ENSMUSG00000021318	Gli3	AI854843|AU023367|Bph|GLI3-190|GLI3FL|Pdn|Xt|add	GLI-Kruppel family member GLI3	protein-coding
mm_151860.1	chr19	5797222	5797242	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	-1251	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_129056.1	chr15	75566812	75566896	-	1	NA	promoter-TSS (NM_001135689)	promoter-TSS (NM_001135689)	2	NM_001135688	23934	Mm.22154	NM_011837	ENSMUSG00000022577	Ly6h	-	lymphocyte antigen 6 complex, locus H	protein-coding
mm_137983.1	chr17	33594542	33594548	+	1	NA	intron (NM_053214, intron 19 of 27)	RSINE1|SINE|B4	-34547	NR_034153	328801	Mm.181488	NM_026712	ENSMUSG00000073423	Zfp414	0610030H11Rik|Znf414	zinc finger protein 414	protein-coding
mm_29799.1	chr3	127780227	127780238	-	1	NA	5' UTR (NM_027808, exon 1 of 14)	5' UTR (NM_027808, exon 1 of 14)	295	NM_027808	71481	Mm.158704	NM_027808	ENSMUSG00000028028	Alpk1	8430410J10Rik|LAK	alpha-kinase 1	protein-coding
mm_114437.1	chr13	65897158	65897171	+	1	NA	Intergenic	Intergenic	-216289	NM_001177832	628709	Mm.390595	NM_001177832	ENSMUSG00000095909	Gm10324	ENSMUSG00000071302	predicted gene 10324	protein-coding
mm_41376.1	chr5	90719168	90719204	+	1	NA	Intergenic	Lx8|LINE|L1	-40112	NM_009141	20311	Mm.4660	NM_009141	ENSMUSG00000029371	Cxcl5	AMCF-II|Cxcl6|ENA-78|GCP-2|LIX|Scyb5|Scyb6	chemokine (C-X-C motif) ligand 5	protein-coding
mm_161936.1	chr19	3323288	3323288	+	1	NA	promoter-TSS (NM_013495)	promoter-TSS (NM_013495)	-13	NM_013495	12894	Mm.18522	NM_013495	ENSMUSG00000024900	Cpt1a	C730027G07|CPTI|Cpt1	carnitine palmitoyltransferase 1a, liver	protein-coding
mm_89924.1	chr10	111229386	111229417	+	1	NA	intron (NM_175489, intron 3 of 23)	MT2B|LTR|ERVL	64599	NM_175489	237542	Mm.220204	NM_175489	ENSMUSG00000020189	Osbpl8	AA536976|AA536995|C730029P18Rik|D330025H14Rik|ORP-8	oxysterol binding protein-like 8	protein-coding
mm_155596.1	chrX	82310963	82310973	+	1	NA	Intergenic	Intergenic	-637902	NM_007868	13405	Mm.275608	NM_007868	ENSMUSG00000045103	Dmd	DXSmh7|DXSmh9|Dp427|Dp71|dys|mdx|pke	dystrophin, muscular dystrophy	protein-coding
mm_71737.1	chr8	62025047	62025057	+	1	NA	intron (NM_001293783, intron 35 of 37)	intron (NM_001293783, intron 35 of 37)	96965	NM_001293783	234311	Mm.275233	NM_144928	ENSMUSG00000037921	Ddx60	9830118M07	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	protein-coding
mm_14141.1	chr2	126499976	126499996	+	1	NA	Intergenic	Intergenic	-8433	NM_001080944	241633	Mm.222235	NM_001080944	ENSMUSG00000060131	Atp8b4	A530043E15|Im	ATPase, class I, type 8B, member 4	protein-coding
mm_166614.1	chr6	71360953	71360962	+	1	NA	Intergenic	Intergenic	-12470	NM_009857	12525	Mm.1858	NM_009857	ENSMUSG00000053977	Cd8a	BB154331|Ly-2|Ly-35|Ly-B|Lyt-2	CD8 antigen, alpha chain	protein-coding
mm_55705.1	chr6	72958079	72958089	-	1	NA	5' UTR (NM_001039392, exon 1 of 2)	5' UTR (NM_001039392, exon 1 of 2)	148	NM_001039392	19240	Mm.3532	NM_025284	ENSMUSG00000079523	Tmsb10	Ptmb10|Tb10	thymosin, beta 10	protein-coding
mm_84790.1	chr9	77045728	77045742	-	1	NA	promoter-TSS (NM_012033)	promoter-TSS (NM_012033)	46	NR_136923	26944	Mm.23199	NM_012033	ENSMUSG00000032357	Tinag	AI452335|TIN-ag	tubulointerstitial nephritis antigen	protein-coding
mm_156975.1	chrX	6320718	6320726	-	1	NA	promoter-TSS (NM_009757)	promoter-TSS (NM_009757)	2	NM_009757	12155	Mm.42160	NM_009757	ENSMUSG00000023279	Bmp15	AU015375|AU018861|AU021453|Bmp-15|C86824|C87336|GDF-9B	bone morphogenetic protein 15	protein-coding
mm_116610.1	chr13	48863655	48863679	-	1	NA	intron (NM_011078, intron 1 of 21)	L1MB5|LINE|L1	7218	NM_011078	18676	Mm.486213	NM_011078	ENSMUSG00000038025	Phf2	GRC5	PHD finger protein 2	protein-coding
mm_103994.1	chr11	84860602	84860630	-	1	NA	exon (NM_153144, exon 4 of 14)	exon (NM_153144, exon 4 of 14)	-9389	NR_131201	102635561	Mm.341797	NR_131197		Ggnbp2os	-	gametogenetin binding protein 2, opposite strand	ncRNA
mm_81746.1	chr9	113930991	113931066	+	1	NA	promoter-TSS (NM_001083319)	promoter-TSS (NM_001083319)	94	NM_013699	22221	Mm.28052	NM_013699	ENSMUSG00000009741	Ubp1	Cp2b|LBP-1a|LBP-1b|NF2d9	upstream binding protein 1	protein-coding
mm_137514.1	chr17	27057426	27057436	+	1	NA	5' UTR (NM_080553, exon 1 of 58)	5' UTR (NM_080553, exon 1 of 58)	127	NM_080553	16440	Mm.458106	NM_080553	ENSMUSG00000042644	Itpr3	IP3R 3|Ip3r3|Itpr-3|tf	inositol 1,4,5-triphosphate receptor 3	protein-coding
mm_32823.1	chr4	117550327	117550409	+	1	NA	promoter-TSS (NM_080469)	promoter-TSS (NM_080469)	3	NM_080469	140546	Mm.235891	NM_080469	ENSMUSG00000033423	Eri3	PINT1|Prnpip1	exoribonuclease 3	protein-coding
mm_94875.1	chr11	24102588	24102591	+	1	NA	intron (NM_016707, intron 2 of 4)	(T)n|Simple_repeat|Simple_repeat	21894	NM_001159290	14025	Mm.53687	NM_016707	ENSMUSG00000000861	Bcl11a	2810047E18Rik|BCL-11A|Ctip1|D930021L15Rik|Evi9|Evi9a|Evi9b|Evi9c|mKIAA1809	B cell CLL/lymphoma 11A (zinc finger protein)	protein-coding
mm_161609.1	chr16	44867113	44867113	+	1	NA	promoter-TSS (NM_206535)	promoter-TSS (NM_206535)	16	NM_206535	271375	Mm.441535	NM_206535	ENSMUSG00000090176	Cd200r2	AY230198|Cd200r1l	Cd200 receptor 2	protein-coding
mm_108613.1	chr12	85486272	85486290	+	1	NA	Intergenic	CpG	12380	NM_010234	14281	Mm.246513	NM_010234	ENSMUSG00000021250	Fos	D12Rfj1|c-fos|cFos	FBJ osteosarcoma oncogene	protein-coding
mm_37426.1	chr4	122886030	122886040	-	1	NA	promoter-TSS (NM_007598)	promoter-TSS (NM_007598)	22	NM_007598	12331	Mm.8687	NM_007598	ENSMUSG00000028656	Cap1	-	CAP, adenylate cyclase-associated protein 1 (yeast)	protein-coding
mm_103498.1	chr11	76571605	76571620	-	1	NA	promoter-TSS (NM_198895)	promoter-TSS (NM_198895)	-228	NM_198895	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_112541.1	chr13	11345600	11345603	+	1	NA	Intergenic	PB1D9|SINE|Alu	-176451	NR_027813	664793	Mm.410565	NR_027813		Zp4-ps	EG664793|Zp4|Zpb	zona pellucida glycoprotein 4, pseudogene	pseudo
mm_76159.1	chr8	82367713	82367743	-	1	NA	intron (NM_008357, intron 2 of 7)	intron (NM_008357, intron 2 of 7)	34858	NM_001254747	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_108532.1	chr12	84206968	84206980	+	1	NA	intron (NM_001163501, intron 1 of 12)	intron (NM_001163501, intron 1 of 12)	11907	NM_001163501	238317	Mm.31256	NM_001163501	ENSMUSG00000042507	Elmsan1	9430029N19Rik|C130039O16Rik|Gm260	ELM2 and Myb/SANT-like domain containing 1	protein-coding
mm_6504.1	chr1	74303938	74303978	-	1	NA	intron (NM_027154, intron 1 of 11)	CpG	378	NM_027154	69660	Mm.261182	NM_027154	ENSMUSG00000006301	Tmbim1	2310061B02Rik|AA960455|AU024746|C78899|RECS1|Tmbib1|mKIAA4161	transmembrane BAX inhibitor motif containing 1	protein-coding
mm_93519.1	chr10	115288049	115288131	-	1	NA	Intergenic	Intergenic	27501	NM_024454	216344	Mm.21936	NM_024454	ENSMUSG00000020132	Rab21	9630024B22	RAB21, member RAS oncogene family	protein-coding
mm_164203.1	chr15	80743021	80743027	-	1	NA	intron (NM_144812, intron 1 of 24)	ORR1C1|LTR|ERVL-MaLR	31711	NM_144812	213988	Mm.131328	NM_144812	ENSMUSG00000047888	Tnrc6b	2700090M07Rik|A730065C02Rik|AI848765|D230019K20Rik	trinucleotide repeat containing 6b	protein-coding
mm_59951.1	chr7	30426112	30426126	+	1	NA	exon (NM_172142, exon 8 of 11)	exon (NM_172142, exon 8 of 11)	2815	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_156091.1	chrX	111110412	111110424	+	1	NA	promoter-TSS (NM_026134)	promoter-TSS (NM_026134)	0	NM_026134	67407	Mm.426142	NM_026134	ENSMUSG00000073001	Cylc1	4930401M13Rik	cylicin, basic protein of sperm head cytoskeleton 1	protein-coding
mm_162852.1	chr10	88459621	88459639	+	1	NA	promoter-TSS (NM_011517)	promoter-TSS (NM_011517)	43	NM_011517	20962	Mm.297977	NM_011517	ENSMUSG00000020059	Sycp3	Cor1|Scp3	synaptonemal complex protein 3	protein-coding
mm_94443.1	chr11	6334449	6334452	+	1	NA	intron (NM_001252283, intron 5 of 23)	intron (NM_001252283, intron 5 of 23)	41892	NM_001252288	18293	Mm.276348	NM_010956	ENSMUSG00000020456	Ogdh	2210403E04Rik|2210412K19Rik|AA409584|d1401|mKIAA4192	oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)	protein-coding
mm_129107.1	chr15	76050777	76050795	-	1	NA	intron (NM_001310543, intron 27 of 35)	intron (NM_001310543, intron 27 of 35)	14102	NR_105917	102466772		NR_105917	ENSMUSG00000098451	Mir6952	Gm27948|mmu-mir-6952	microRNA 6952	ncRNA
mm_39361.1	chr5	9113265	9113282	+	1	NA	intron (NM_001081029, intron 2 of 4)	intron (NM_001081029, intron 2 of 4)	12536	NM_001081029	652925	Mm.439954	NM_001081029	ENSMUSG00000079659	Tmem243	4930420K17Rik|E030031F02Rik	transmembrane protein 243, mitochondrial	protein-coding
mm_132163.1	chr16	32271474	32271523	+	1	NA	promoter-TSS (NM_183283)	promoter-TSS (NM_183283)	-111	NM_183283	69576	Mm.432545	NM_183283	ENSMUSG00000046345	Smco1	2310010M20Rik	single-pass membrane protein with coiled-coil domains 1	protein-coding
mm_158546.1	chrX	145480665	145480673	-	1	NA	intron (NM_001290274, intron 1 of 8)	intron (NM_001290274, intron 1 of 8)	6970	NM_001290274	27494	Mm.100068	NM_153319	ENSMUSG00000041688	Amot	CAG-2|D0Kist1|Sii6	angiomotin	protein-coding
mm_146576.1	chr18	7297065	7297072	-	1	NA	intron (NM_001081393, intron 1 of 20)	intron (NM_001081393, intron 1 of 20)	833	NM_001081393	74934	Mm.107918	NM_001081393	ENSMUSG00000061802	Armc4	4930463I21Rik|b2b227.1Clo|b2b643Clo	armadillo repeat containing 4	protein-coding
mm_61110.1	chr7	52887590	52887612	+	1	NA	Intergenic	RLTR15|LTR|ERVK	-871885	NM_001195601	100503036	Mm.279725	NM_001195601	ENSMUSG00000094445	1700015G11Rik	Ccdc179	RIKEN cDNA 1700015G11 gene	protein-coding
mm_134539.1	chr16	19706341	19706352	-	1	NA	promoter-TSS (NM_177356)	promoter-TSS (NM_177356)	19	NM_177356	239739	Mm.258059	NM_177356	ENSMUSG00000041247	Lamp3	1200002D17Rik|Cd208|DC-LAMP|DCLAMP|LAMP|TSC403	lysosomal-associated membrane protein 3	protein-coding
mm_26321.1	chr3	142522263	142522273	+	1	NA	TTS (NM_153564)	TTS (NM_153564)	-8068	NM_001083312	229900	Mm.45740	NM_145545	ENSMUSG00000040253	Gbp7	9830147J24Rik	guanylate binding protein 7	protein-coding
mm_18374.1	chr2	59952856	59952866	-	1	NA	intron (NM_001001182, intron 12 of 35)	MIR3|SINE|MIR	-70255	NM_028118	72137	Mm.288734	NM_028118	ENSMUSG00000026988	Wdsub1	1700048E19Rik|2610014F08Rik	WD repeat, SAM and U-box domain containing 1	protein-coding
mm_144385.1	chr18	20667402	20667406	+	1	NA	intron (NM_013697, intron 2 of 3)	intron (NM_013697, intron 2 of 3)	2154	NM_013697	22139	Mm.2108	NM_013697	ENSMUSG00000061808	Ttr	AA408768|AI787086|D17860|prealbumin	transthyretin	protein-coding
mm_104285.1	chr11	90002882	90002898	-	1	NA	promoter-TSS (NM_001316372)	promoter-TSS (NM_001316372)	4	NM_008796	18559	Mm.5062	NM_008796	ENSMUSG00000020553	Pctp	PC-TP|StarD2	phosphatidylcholine transfer protein	protein-coding
mm_12298.1	chr2	69092641	69092659	+	1	NA	intron (NM_172856, intron 8 of 9)	RCHARR1|DNA|hAT-Charlie	-43150	NM_181547	329416	Mm.90047	NM_181547	ENSMUSG00000034738	Nostrin	Daip2|mDaIP2	nitric oxide synthase trafficker	protein-coding
mm_81149.1	chr9	106892115	106892123	+	1	NA	promoter-TSS (NM_029103)	promoter-TSS (NM_029103)	-181	NM_029103	74840	Mm.29778	NM_029103	ENSMUSG00000032575	Manf	3230402M22Rik|AA407711|AA408789|AA673178|Armet|D17914|D18Mgi17	mesencephalic astrocyte-derived neurotrophic factor	protein-coding
mm_127100.1	chr15	97791302	97791331	+	1	NA	3' UTR (NM_026353, exon 3 of 3)	3' UTR (NM_026353, exon 3 of 3)	6951	NM_026353	67739	Mm.28955	NM_026353	ENSMUSG00000081534	Slc48a1	4930570C03Rik	solute carrier family 48 (heme transporter), member 1	protein-coding
mm_21802.1	chr2	164911561	164911583	-	1	NA	5' UTR (NM_199027, exon 1 of 28)	5' UTR (NM_199027, exon 1 of 28)	178	NM_199027	329559	Mm.330776	NM_199027	ENSMUSG00000039834	Zfp335	1810045J01Rik|NIF-1|Nif1|Znf335	zinc finger protein 335	protein-coding
mm_37683.1	chr4	129223139	129223153	-	1	NA	exon (NM_001285867, exon 6 of 7)	exon (NM_001285867, exon 6 of 7)	4765	NM_001285866	97130	Mm.331907	NM_001033189	ENSMUSG00000050390	C77080	Kiaa1522|mKIAA1522	expressed sequence C77080	protein-coding
mm_92015.1	chr10	62342675	62342718	-	1	NA	intron (NR_038038, intron 1 of 1)	MIRc|SINE|MIR	2089	NR_038038	70162	Mm.441212	NR_038038		Hk1os	2210417K05Rik	hexokinase 1, opposite strand	ncRNA
mm_59373.1	chr7	25704810	25704833	+	1	NA	exon (NM_011577, exon 7 of 7)	exon (NM_011577, exon 7 of 7)	14232	NM_028771	52132	Mm.278798	NM_028771	ENSMUSG00000002608	Ccdc97	1200014H14Rik|2810446P04Rik|AA545218|D7Ertd462e	coiled-coil domain containing 97	protein-coding
mm_115797.1	chr13	19345190	19345231	-	1	NA	Intergenic	Intergenic	50603	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_110046.1	chr12	17507217	17507225	-	1	NA	Intergenic	Intergenic	-37652	NM_013614	18263	Mm.34102	NM_013614	ENSMUSG00000011179	Odc1	ODC	ornithine decarboxylase, structural 1	protein-coding
mm_90103.1	chr10	116986623	116986635	+	1	NA	5' UTR (NM_001007583, exon 1 of 10)	5' UTR (NM_001007583, exon 1 of 10)	315	NM_001007583	382427	Mm.339322	NM_001007583	ENSMUSG00000020169	Best3	Vmd2l3|mBest4	bestrophin 3	protein-coding
mm_1036.1	chr1	58756346	58756401	+	1	NA	3' UTR (NM_207653, exon 10 of 10)	3' UTR (NM_207653, exon 10 of 10)	25821	NM_001293805	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_74344.1	chr8	127268981	127268984	+	1	NA	intron (NM_001309391, intron 2 of 24)	intron (NM_001309391, intron 2 of 24)	-30630	NM_001013581	93742	Mm.299254	NM_033620	ENSMUSG00000025812	Pard3	AA960621|AI256638|Asip|D8Ertd580e|Par-3|Par3|Pard-3|Pard3a|Phip	par-3 family cell polarity regulator	protein-coding
mm_51002.1	chr6	63599419	63599423	+	1	NA	intron (NM_008167, intron 2 of 15)	intron (NM_008167, intron 2 of 15)	342564	NM_008167	14804	Mm.439651	NM_008167	ENSMUSG00000071424	Grid2	B230104L07Rik|GluD2|GluRdelta2|Lc|Lc<J>|MMS10-AC|Ms10ac|cpr|ho|nmf408|tpr	glutamate receptor, ionotropic, delta 2	protein-coding
mm_56747.1	chr6	115967484	115967489	-	1	NA	exon (NM_026376, exon 16 of 36)	exon (NM_026376, exon 16 of 36)	22555	NM_138311	171506	Mm.21899	NM_138311	ENSMUSG00000042279	H1foo	C86609|H1.8|H1fo|H1oo	H1 histone family, member O, oocyte-specific	protein-coding
mm_20699.1	chr2	132945470	132945570	-	1	NA	5' UTR (NM_198029, exon 1 of 15)	5' UTR (NM_198029, exon 1 of 15)	516	NM_198029	241639	Mm.209784	NM_198029	ENSMUSG00000027356	Fermt1	5830467P10Rik|Kindlin-1	fermitin family member 1	protein-coding
mm_156886.1	chrX	166357655	166357658	+	1	NA	intron (NM_001177956, intron 2 of 7)	intron (NM_001177956, intron 2 of 7)	13103	NM_001177960	14758	Mm.222320	NM_023122	ENSMUSG00000031342	Gpm6b	AI593561|Gpm6|M6B	glycoprotein m6b	protein-coding
mm_90042.1	chr10	115817461	115817489	+	1	NA	5' UTR (NM_146010, exon 1 of 8)	5' UTR (NM_146010, exon 1 of 8)	191	NM_001168679	216350	Mm.22270	NM_146010	ENSMUSG00000034127	Tspan8	C76990|E330007O21Rik|Tm4sf3	tetraspanin 8	protein-coding
mm_80405.1	chr9	77636622	77636635	+	1	NA	promoter-TSS (NM_172925)	promoter-TSS (NM_172925)	-104	NM_172925	244923	Mm.138238	NM_172925	ENSMUSG00000044938	Klhl31	9830147P19Rik|D930047P17Rik|Kbtbd1	kelch-like 31	protein-coding
mm_155946.1	chrX	104508904	104508917	+	1	NA	Intergenic	Intergenic	26128	NM_001081189	331487	Mm.438275	NM_001081189	ENSMUSG00000073016	Uprt	Gm774	uracil phosphoribosyltransferase	protein-coding
mm_87997.1	chr10	66865275	66865294	+	1	NA	Intergenic	Intergenic	55100	NR_138560	68488	Mm.338835	NR_138560		1110002J07Rik	-	RIKEN cDNA 1110002J07 gene	ncRNA
mm_16742.1	chr2	9593809	9593828	-	1	NA	Intergenic	Intergenic	284782	NM_008091	14462	Mm.313866	NM_008091	ENSMUSG00000015619	Gata3	Gata-3|jal	GATA binding protein 3	protein-coding
mm_164492.1	chr16	89488236	89488242	+	1	NA	promoter-TSS (NM_010675)	promoter-TSS (NM_010675)	-287	NM_010675	16703	Mm.13979	NM_010675	ENSMUSG00000059632	Krtap8-1	AI326176	keratin associated protein 8-1	protein-coding
mm_56092.1	chr6	87350905	87350921	-	1	NA	promoter-TSS (NM_025466)	promoter-TSS (NM_025466)	2	NM_025466	66283	Mm.46414	NM_025466	ENSMUSG00000030050	Gkn1	2200002K21Rik|AMP-18|BRICD1|Fov	gastrokine 1	protein-coding
mm_85998.1	chr9	112227206	112227217	-	1	NA	promoter-TSS (NR_131053)	promoter-TSS (NR_131053)	-245	NR_131053	70194	Mm.452769	NR_131053		2310075C17Rik	-	RIKEN cDNA 2310075C17 gene	ncRNA
mm_111933.1	chr12	108889307	108889309	-	1	NA	intron (NM_001164314, intron 1 of 9)	intron (NM_001164314, intron 1 of 9)	3890	NM_001164488	22375	Mm.38433	NM_011710	ENSMUSG00000021266	Wars	TrpRS|WRS	tryptophanyl-tRNA synthetase	protein-coding
mm_171845.1	chr5	16903640	16903642	+	1	NA	Intergenic	L1Md_T|LINE|L1	349740	NM_001289461	15234	Mm.267078	NM_010427	ENSMUSG00000028864	Hgf	C230052L06Rik|HGF/SF|NK1|NK2|SF|SF/HGF	hepatocyte growth factor	protein-coding
mm_134671.1	chr16	22265951	22265961	-	1	NA	promoter-TSS (NM_001330554)	promoter-TSS (NM_001330554)	49	NM_001330554	20462	Mm.210352	NM_009186	ENSMUSG00000022858	Tra2b	5730405G21Rik|D16Ertd266e|SIG-41|Sfrs10|Silg41|TRA2beta	transformer 2 beta homolog (Drosophila)	protein-coding
mm_4698.1	chr1	180848306	180848337	+	1	NA	Intergenic	Intergenic	-2830	NM_145943	208768	Mm.272625	NM_145943	ENSMUSG00000038806	Sde2	-	SDE2 telomere maintenance homolog (S. pombe)	protein-coding
mm_58795.1	chr7	16175086	16175104	+	1	NA	promoter-TSS (NM_008627)	promoter-TSS (NM_008627)	-300	NM_001277988	17537	Mm.360516	NM_008627	ENSMUSG00000041420	Meis3	AI573393|Mrg2	Meis homeobox 3	protein-coding
mm_104212.1	chr11	88341917	88341918	-	1	NA	3' UTR (NM_054043, exon 14 of 14)	3' UTR (NM_054043, exon 14 of 14)	-10856	NR_039545	100628571		NR_039545	ENSMUSG00000092985	Mir378b	mir-378b|mmu-mir-378b	microRNA 378b	ncRNA
mm_165297.1	chr2	91526834	91526840	+	1	NA	Intergenic	CpG	-19485	NM_001165989	75786	Mm.168478	NM_029437	ENSMUSG00000040549	Ckap5	3110043H24Rik|4930432B04Rik|D730027C18Rik|T25636|mKIAA0097	cytoskeleton associated protein 5	protein-coding
mm_116164.1	chr13	30753477	30753496	-	1	NA	exon (NM_013674, exon 5 of 9)	exon (NM_013674, exon 5 of 9)	4253	NM_013674	16364	Mm.4677	NM_013674	ENSMUSG00000021356	Irf4	AI385587|IRF-4|LSIRF|NF-EM5|Spip	interferon regulatory factor 4	protein-coding
mm_62671.1	chr7	109010851	109010930	+	1	NA	promoter-TSS (NM_021885)	promoter-TSS (NM_021885)	10	NM_021885	22141	Mm.439722	NM_021885	ENSMUSG00000031028	Tub	rd5|tub	tubby candidate gene	protein-coding
mm_110074.1	chr12	21417592	21417605	-	1	NA	promoter-TSS (NM_011739)	promoter-TSS (NM_011739)	-162	NM_011739	22630	Mm.289630	NM_011739	ENSMUSG00000076432	Ywhaq	2700028P07Rik|AA409740|AU021156|R74690	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide	protein-coding
mm_140124.1	chr17	79611839	79611858	+	1	NA	Intergenic	Intergenic	-3052	NM_201361	381110	Mm.209801	NM_201361	ENSMUSG00000036368	Rmdn2	AW061290|Fam82a1|RMD-2|mRMD-2	regulator of microtubule dynamics 2	protein-coding
mm_43968.1	chr5	145404969	145404973	+	1	NA	Intergenic	Intergenic	59701	NM_001100180	622127	Mm.359379	NM_001100180	ENSMUSG00000070419	Cyp3a57	EG622127	cytochrome P450, family 3, subfamily a, polypeptide 57	protein-coding
mm_21032.1	chr2	152464613	152464640	-	1	NA	promoter-TSS (NM_001037933)	promoter-TSS (NM_001037933)	-6	NM_001037933	629114	Mm.389372	NM_001037933	ENSMUSG00000074681	Defb23	EG629114	defensin beta 23	protein-coding
mm_85376.1	chr9	103225075	103225162	-	1	NA	exon (NM_133977, exon 5 of 17)	exon (NM_133977, exon 5 of 17)	5168	NM_133977	22041	Mm.37214	NM_133977	ENSMUSG00000032554	Trf	AI266983|Cd176|HP|Tf|Tfn|hpx	transferrin	protein-coding
mm_73437.1	chr8	106150471	106150481	+	1	NA	promoter-TSS (NM_133792)	promoter-TSS (NM_133792)	77	NM_133792	192654	Mm.284770	NM_133792	ENSMUSG00000031903	Pla2g15	ACS|C87498|LLPL|Lpla2|Lypla3	phospholipase A2, group XV	protein-coding
mm_46342.1	chr5	102018390	102018393	-	1	NA	intron (NM_172882, intron 2 of 66)	intron (NM_172882, intron 2 of 66)	51530	NM_172882	72145	Mm.332522	NM_172882	ENSMUSG00000043940	Wdfy3	2610509D04Rik|ALFY|AW319683|B930017C24|BWF1|Bchs|D5Ertd66e|Ggtb3|ZFYVE25|mKIAA0993	WD repeat and FYVE domain containing 3	protein-coding
mm_137900.1	chr17	31808463	31808467	+	1	NA	Intergenic	Intergenic	47327	NM_010831	17691	Mm.290941	NM_010831	ENSMUSG00000024042	Sik1	Msk|Sik|Snf1lk	salt inducible kinase 1	protein-coding
mm_105922.1	chr11	115048373	115048399	-	1	NA	promoter-TSS (NM_199201)	promoter-TSS (NM_199201)	-91	NM_199201	382551	Mm.424732	NM_199201	ENSMUSG00000069607	Cd300ld3	AY457049|Cd300lh|Clm3|Lmir7|clm-3	CD300 molecule like family member D3	protein-coding
mm_150719.1	chr19	43528326	43528332	+	1	NA	Intergenic	Intergenic	-3724	NM_010324	14718	Mm.19039	NM_010324	ENSMUSG00000025190	Got1	AI789014|Got-1|cAspAT|cCAT	glutamic-oxaloacetic transaminase 1, soluble	protein-coding
mm_107116.1	chr12	18387486	18387496	+	1	NA	Intergenic	CpG	-127019	NM_001033157	236366	Mm.352227	NM_001033157	ENSMUSG00000073197	5730507C01Rik	-	RIKEN cDNA 5730507C01 gene	protein-coding
mm_90423.1	chr10	127487812	127487831	+	1	NA	exon (NM_001168293, exon 19 of 24)	exon (NM_001168293, exon 19 of 24)	-13896	NM_177707	237611	Mm.32087	NM_177707	ENSMUSG00000040287	Stac3	9830125E18	SH3 and cysteine rich domain 3	protein-coding
mm_17943.1	chr2	36104808	36104818	-	1	NA	promoter-TSS (NM_001083127)	promoter-TSS (NM_001083127)	595	NM_001083125	16874	Mm.12881	NM_008500	ENSMUSG00000026890	Lhx6	Lhx6.1	LIM homeobox protein 6	protein-coding
mm_68746.1	chr7	121064481	121064497	-	1	NA	3' UTR (NM_030691, exon 6 of 6)	3' UTR (NM_030691, exon 6 of 6)	10041	NM_030691	80719	Mm.160384	NM_030691	ENSMUSG00000035004	Igsf6	-	immunoglobulin superfamily, member 6	protein-coding
mm_144254.1	chr18	10921069	10921089	+	1	NA	Intergenic	Intergenic	-131431	NM_010258	14465	Mm.329287	NM_010258	ENSMUSG00000005836	Gata6	AA410133|GATA-6	GATA binding protein 6	protein-coding
mm_57528.1	chr6	126534998	126535034	-	1	NA	exon (NM_145983, exon 1 of 1)	exon (NM_145983, exon 1 of 1)	539	NM_145983	16493	Mm.222831	NM_145983	ENSMUSG00000045534	Kcna5	Kv1.5	potassium voltage-gated channel, shaker-related subfamily, member 5	protein-coding
mm_119307.1	chr14	34820096	34820153	+	1	NA	promoter-TSS (NM_008166)	promoter-TSS (NM_008166)	-12	NM_008166	14803	Mm.121569	NM_008166	ENSMUSG00000041078	Grid1	GluD1|GluRdelta1	glutamate receptor, ionotropic, delta 1	protein-coding
mm_94067.1	chr10	128400498	128400537	-	1	NA	promoter-TSS (NM_028092)	promoter-TSS (NM_028092)	0	NM_028092	72002	Mm.22983	NM_028051	ENSMUSG00000039878	Slc39a5	1810013D05Rik|2010205A06Rik|Zip5	solute carrier family 39 (metal ion transporter), member 5	protein-coding
mm_97840.1	chr11	83065210	83065215	+	1	NA	promoter-TSS (NM_011408)	promoter-TSS (NM_011408)	100	NM_011408	20556	Mm.278689	NM_011408	ENSMUSG00000072620	Slfn2	Shlf2	schlafen 2	protein-coding
mm_134199.1	chr16	11066078	11066109	-	1	NA	promoter-TSS (NM_009223)	promoter-TSS (NM_009223)	-205	NM_009223	20621	Mm.325800	NM_009223	ENSMUSG00000037972	Snn	2810407J07Rik|AI848521|AW547286	stannin	protein-coding
mm_25845.1	chr3	129221519	129221559	+	1	NA	Intergenic	Intergenic	7607	NM_001287048	18741	Mm.246804	NM_011098	ENSMUSG00000028023	Pitx2	9430085M16Rik|Brx1|Brx1b|Munc30|Otlx2|Ptx2|Rieg	paired-like homeodomain transcription factor 2	protein-coding
mm_20452.1	chr2	129364979	129364992	-	1	NA	3' UTR (NM_008361, exon 7 of 7)	3' UTR (NM_008361, exon 7 of 7)	-4917	NR_015474	329514	Mm.207315	NM_177848	ENSMUSG00000074805	Il1bos	9430083I22|Gm14047|OTTMUSG00000015529	interleukin 1 beta, opposite strand	ncRNA
mm_163174.1	chr11	87795263	87795268	+	1	NA	exon (NM_010824, exon 4 of 14)	exon (NM_010824, exon 4 of 14)	1481	NM_010824	17523	Mm.4668	NM_010824	ENSMUSG00000009350	Mpo	mKIAA4033	myeloperoxidase	protein-coding
mm_153285.1	chr19	37264061	37264113	-	1	NA	promoter-TSS (NR_040299)	promoter-TSS (NR_040299)	8	NR_040299	77059	Mm.251476	NR_040298		4931408D14Rik	-	RIKEN cDNA 4931408D14 gene	ncRNA
mm_95573.1	chr11	52402912	52402932	+	1	NA	intron (NM_153117, intron 1 of 2)	intron (NM_153117, intron 1 of 2)	6494	NM_153117	213673	Mm.291979	NM_153117	ENSMUSG00000036275	9530068E07Rik	C85061|Kct2	RIKEN cDNA 9530068E07 gene	protein-coding
mm_82438.1	chr9	15279848	15279856	-	1	NA	promoter-TSS (NM_144933)	promoter-TSS (NM_144933)	15	NM_144933	234959	Mm.44151	NM_144933	ENSMUSG00000031935	Med17	77kDa|C330002H14Rik|Crsp6|Trap80	mediator complex subunit 17	protein-coding
mm_17408.1	chr2	27246786	27246803	-	1	NA	5' UTR (NM_138665, exon 1 of 21)	5' UTR (NM_138665, exon 1 of 21)	509	NM_138665	192166	Mm.278467	NM_138665	ENSMUSG00000009614	Sardh	-	sarcosine dehydrogenase	protein-coding
mm_129596.1	chr15	79834209	79834219	-	1	NA	5' UTR (NM_001013360, exon 1 of 8)	5' UTR (NM_001013360, exon 1 of 8)	119	NM_001013360	504193	Mm.38438	NM_029079	ENSMUSG00000089837	Npcd	Cbx6-Nptxr	neuronal pentraxin chromo domain	protein-coding
mm_86825.1	chr10	21055011	21055021	+	1	NA	exon (NM_026203, exon 20 of 24)	exon (NM_026203, exon 20 of 24)	14196	NM_001177776	52906	Mm.253280	NM_026203	ENSMUSG00000019986	Ahi1	1700015F03Rik|Ahi-1|D10Bwg0629e	Abelson helper integration site 1	protein-coding
mm_78911.1	chr9	44981780	44981798	+	1	NA	promoter-TSS (NM_013487)	promoter-TSS (NM_013487)	3	NM_013487	12500	Mm.4527	NM_013487	ENSMUSG00000032094	Cd3d	T3d	CD3 antigen, delta polypeptide	protein-coding
mm_49821.1	chr6	37530185	37530198	+	1	NA	promoter-TSS (NM_145364)	promoter-TSS (NM_145364)	18	NM_145364	208665	Mm.262635	NM_145364	ENSMUSG00000038641	Akr1d1	-	aldo-keto reductase family 1, member D1	protein-coding
mm_15475.1	chr2	157560574	157560604	+	1	NA	intron (NM_001291128, intron 2 of 2)	intron (NM_001291128, intron 2 of 2)	511	NM_180960	18111	Mm.34330	NM_010923	ENSMUSG00000067786	Nnat	5730414I02Rik|AW107673|Peg5	neuronatin	protein-coding
mm_164438.1	chr16	48874379	48874411	-	1	NA	3' UTR (NM_181596, exon 4 of 4)	3' UTR (NM_181596, exon 4 of 4)	1787	NM_181596	245195	Mm.231288	NM_181596	ENSMUSG00000022651	Retnlg	Fizz3|Relmg|Xcp1	resistin like gamma	protein-coding
mm_37147.1	chr4	116994375	116994385	-	1	NA	promoter-TSS (NM_009478)	promoter-TSS (NM_009478)	33	NM_009478	22275	Mm.46484	NM_009478	ENSMUSG00000028684	Urod	AI323803|UPD|Uro-d	uroporphyrinogen decarboxylase	protein-coding
mm_62070.1	chr7	92698912	92698922	+	1	NA	Intergenic	Intergenic	-29005	NM_029078	74737	Mm.288645	NM_029078	ENSMUSG00000041328	Pcf11	2500001H09Rik|5730417B17Rik|C77803	PCF11 cleavage and polyadenylation factor subunit	protein-coding
mm_46750.1	chr5	112120888	112120915	-	1	NA	Intergenic	Intergenic	-85862	NR_045377	75569	Mm.243721	NR_045377	ENSMUSG00000101683	1700028D13Rik	-	RIKEN cDNA 1700028D13 gene	ncRNA
mm_145942.1	chr18	67343784	67343802	+	1	NA	5' UTR (NM_007702, exon 1 of 5)	5' UTR (NM_007702, exon 1 of 5)	229	NM_007702	12683	Mm.449	NM_007702	ENSMUSG00000024526	Cidea	AW212747	cell death-inducing DNA fragmentation factor, alpha subunit-like effector A	protein-coding
mm_110809.1	chr12	72219281	72219304	-	1	NA	exon (NM_001286448, exon 3 of 7)	exon (NM_001286448, exon 3 of 7)	16454	NR_104446	104001	Mm.221275	NM_153457	ENSMUSG00000021087	Rtn1	Nsp	reticulon 1	protein-coding
mm_148047.1	chr18	70530314	70530326	-	1	NA	promoter-TSS (NM_001136090)	promoter-TSS (NM_001136090)	1	NM_001136090	26447	Mm.244352	NM_011972	ENSMUSG00000038425	Poli	Rad30b	polymerase (DNA directed), iota	protein-coding
mm_63958.1	chr7	139938052	139938099	+	1	NA	exon (NM_177261, exon 30 of 31)	exon (NM_177261, exon 30 of 31)	-5781	NM_009482	22286	Mm.10205	NM_009482	ENSMUSG00000047751	Utf1	AI505934	undifferentiated embryonic cell transcription factor 1	protein-coding
mm_4740.1	chr1	181853761	181853784	+	1	NA	Intergenic	Intergenic	-11371	NM_133815	98386	Mm.4538	NM_133815	ENSMUSG00000004880	Lbr	AI505894|ic	lamin B receptor	protein-coding
mm_17023.1	chr2	19388908	19388925	-	1	NA	intron (NM_029619, intron 3 of 4)	intron (NM_029619, intron 3 of 4)	17280	NM_029619	76467	Mm.27166	NM_029619	ENSMUSG00000023094	Msrb2	2310050L06Rik|Mrsb|Msrb|Pilb	methionine sulfoxide reductase B2	protein-coding
mm_125387.1	chr15	40735376	40735378	+	1	NA	intron (NM_011766, intron 1 of 7)	Lx5c|LINE|L1	80335	NM_011766	22762	Mm.39496	NM_011766	ENSMUSG00000022306	Zfpm2	B330005D23Rik|FOG-2|FOG2	zinc finger protein, multitype 2	protein-coding
mm_150712.1	chr19	43034946	43034956	+	1	NA	intron (NM_001081257, intron 3 of 11)	intron (NM_001081257, intron 3 of 11)	-254975	NM_019424	192236	Mm.218381	NM_019424	ENSMUSG00000025188	Hps1	6030422N11Rik|BB405864|Gm21361|Hps|ep	Hermansky-Pudlak syndrome 1	protein-coding
mm_23295.1	chr3	52268375	52268388	+	1	NA	promoter-TSS (NM_019739)	promoter-TSS (NM_019739)	44	NM_019739	56458	Mm.29891	NM_019739	ENSMUSG00000044167	Foxo1	AI876417|Afxh|FKHR|Fkhr1|Foxo1a	forkhead box O1	protein-coding
mm_97733.1	chr11	80399629	80399634	+	1	NA	intron (NR_045038, intron 13 of 16)	intron (NR_045038, intron 13 of 16)	16352	NM_001130171	22680	Mm.401332	NM_011751	ENSMUSG00000017421	Zfp207	8430401D15Rik|BuGZ|Zep|Znf207	zinc finger protein 207	protein-coding
mm_152121.1	chr19	6987592	6987618	-	1	NA	promoter-TSS (NM_011697)	promoter-TSS (NM_011697)	46	NM_001185164	22340	Mm.15607	NM_011697	ENSMUSG00000024962	Vegfb	VEGF-B|Vrf	vascular endothelial growth factor B	protein-coding
mm_141798.1	chr17	34347660	34347678	-	1	NA	Intergenic	Intergenic	-3024	NM_010381	100504404	Mm.15680	NM_010381		H2-Ea-ps	AI323765|E-alpha-f|H-2Ea|H2-Ea|I-Ealpha|Ia-3|Ia3|MHC-H2-Ea	histocompatibility 2, class II antigen E alpha, pseudogene	protein-coding
mm_20282.1	chr2	126892384	126892408	-	1	NA	3' UTR (NM_023220, exon 15 of 15)	3' UTR (NM_023220, exon 15 of 15)	9989	NR_106202	102466258		NR_106202	ENSMUSG00000098896	Mir3473g	Gm27751|mmu-mir-3473g	microRNA 3473g	ncRNA
mm_130170.1	chr15	93275155	93275178	-	1	NA	promoter-TSS (NM_001033275)	promoter-TSS (NM_001033275)	13	NM_001346785	223827	Mm.22819	NM_001033275	ENSMUSG00000036197	Gxylt1	Glt8d3|Gm1228|Gm87	glucoside xylosyltransferase 1	protein-coding
mm_69196.1	chr7	127345406	127345416	-	1	NA	promoter-TSS (NM_146202)	promoter-TSS (NM_146202)	-97	NM_146202	233890	Mm.23031	NM_146202	ENSMUSG00000047371	Zfp768	BC026432|Znf768	zinc finger protein 768	protein-coding
mm_127115.1	chr15	97969815	97969833	+	1	NA	3' UTR (NM_201359, exon 8 of 8)	3' UTR (NM_201359, exon 8 of 8)	5595	NM_001252153	380967	Mm.196630	NM_201359	ENSMUSG00000052369	Tmem106c	AI046681|BC046621|D15Ertd405e	transmembrane protein 106C	protein-coding
mm_130914.1	chr15	102624964	102624996	-	1	NA	intron (NM_001310067, intron 1 of 11)	intron (NM_001310067, intron 1 of 11)	484	NM_001310070	223922	Mm.208714	NM_146065	ENSMUSG00000052414	Atf7	1110012F10Rik|9430065F09Rik|AI549878|C130020M04Rik	activating transcription factor 7	protein-coding
mm_168003.1	chrY	903849	903855	+	1	NA	intron (NM_011419, intron 5 of 25)	Lx5c|LINE|L1	6064	NM_011419	20592	Mm.262676	NM_011419	ENSMUSG00000056673	Kdm5d	HY|Jarid1d|Smcy	lysine (K)-specific demethylase 5D	protein-coding
mm_140416.1	chr17	87650566	87650580	+	1	NA	3' UTR (NM_008532, exon 10 of 10)	3' UTR (NM_008532, exon 10 of 10)	14594	NM_008532	17075	Mm.4259	NM_008532	ENSMUSG00000045394	Epcam	CD326|EGP|EGP-2|Egp314|Ep-CAM|EpCAM1|GA733-2|Ly74|TROP1|Tacsd1|Tacstd1|gp40	epithelial cell adhesion molecule	protein-coding
mm_8848.1	chr1	162706178	162706191	-	1	NA	exon (NM_001081290, exon 16 of 35)	exon (NM_001081290, exon 16 of 35)	34372	NM_001081290	226562	Mm.245446	NM_001081290	ENSMUSG00000040225	Prrc2c	1810043M20Rik|9630039I18Rik|A630006J20|Bat2d|Bat2d1|Bat2l2|E130112L15Rik|Prrc3|mKIAA1096	proline-rich coiled-coil 2C	protein-coding
mm_49163.1	chr6	13838729	13838742	+	1	NA	5' UTR (NM_001330667, exon 2 of 3)	5' UTR (NM_001330667, exon 2 of 3)	1207	NM_001330666	64450	Mm.167625	NM_145066	ENSMUSG00000048216	Gpr85	2900026B03Rik	G protein-coupled receptor 85	protein-coding
mm_29484.1	chr3	115714781	115714797	-	1	NA	5' UTR (NM_007901, exon 1 of 2)	5' UTR (NM_007901, exon 1 of 2)	266	NM_007901	13609	Mm.982	NM_007901	ENSMUSG00000045092	S1pr1	AI849002|Edg1|Lpb1|S1p|S1p1	sphingosine-1-phosphate receptor 1	protein-coding
mm_39668.1	chr5	25247371	25247381	+	1	NA	intron (NM_144908, intron 1 of 11)	intron (NM_144908, intron 1 of 11)	24483	NM_144908	231050	Mm.21814	NM_144908	ENSMUSG00000038072	Galnt11	A430075I06Rik|AI648252|E430002F06Rik	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 11	protein-coding
mm_146743.1	chr18	15760110	15760122	-	1	NA	Intergenic	CpG	-42070	NM_199055	71367	Mm.329304	NM_199055	ENSMUSG00000047161	Chst9	5430438D01Rik	carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 9	protein-coding
mm_96162.1	chr11	61487953	61487963	+	1	NA	TTS (NM_001291037)	TTS (NM_001291037)	2514	NM_029568	76293	Mm.272278	NM_029568	ENSMUSG00000042436	Mfap4	1110007F23Rik	microfibrillar-associated protein 4	protein-coding
mm_22082.1	chr2	168765371	168765441	-	1	NA	intron (NM_201395, intron 1 of 3)	intron (NM_201395, intron 1 of 3)	1795	NM_201395	99377	Mm.434054	NM_175303	ENSMUSG00000027547	Sall4	5730441M18Rik|AA407717|AL022809|AW536104|C330011P20Rik|C78083|C78563|Tex20	sal-like 4 (Drosophila)	protein-coding
mm_72794.1	chr8	86915184	86915211	+	1	NA	Intergenic	Intergenic	-29939	NM_030563	80750	Mm.25117	NM_030563	ENSMUSG00000031652	N4bp1	AI481586|C81621	NEDD4 binding protein 1	protein-coding
mm_131797.1	chr16	22899131	22899158	+	1	NA	non-coding (NR_075099, exon 6 of 6)	non-coding (NR_075099, exon 6 of 6)	-4758	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_88641.1	chr10	79930395	79930409	+	1	NA	intron (NM_001288625, intron 1 of 8)	intron (NM_001288625, intron 1 of 8)	3061	NM_001288625	13496	Mm.301282	NM_007880	ENSMUSG00000019564	Arid3a	Bright|Dri1|Dril1	AT rich interactive domain 3A (BRIGHT-like)	protein-coding
mm_48113.1	chr5	137116222	137116241	-	1	NA	promoter-TSS (NM_201373)	promoter-TSS (NM_201373)	-24	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_115729.1	chr13	17742758	17742760	-	1	NA	intron (NM_027118, intron 7 of 13)	intron (NM_027118, intron 7 of 13)	-4714	NR_035412	100316665		NR_035412	ENSMUSG00000080574	Mir466i	Mirn466i|mmu-mir-466i	microRNA 466i	ncRNA
mm_74150.1	chr8	123332743	123332770	+	1	NA	promoter-TSS (NM_172287)	promoter-TSS (NM_172287)	43	NM_172287	234857	Mm.150200	NM_172287	ENSMUSG00000010154	Spire2	BC026502|Spir-2|Spir2	spire homolog 2 (Drosophila)	protein-coding
mm_108789.1	chr12	90969895	90969904	+	1	NA	Intergenic	RMER1C|Other|Other	-75949	NR_045858	71349	Mm.442093	NR_045858		5430427M07Rik	-	RIKEN cDNA 5430427M07 gene	ncRNA
mm_79162.1	chr9	47813904	47813923	+	1	NA	exon (NM_018770, exon 7 of 10)	exon (NM_018770, exon 7 of 10)	4295	NR_046048	100038460	Mm.447649	NR_046048		Gm10677	ENSMUSG00000074363	predicted gene 10677	ncRNA
mm_32836.1	chr4	117787291	117787301	+	1	NA	Intergenic	Intergenic	-21630	NM_029416	75753	Mm.3848	NM_029416	ENSMUSG00000048626	Klf17	7420700M05Rik|AA420409|AU043468|C85123|D4Ertd561e|Gzf|Zfp393	Kruppel-like factor 17	protein-coding
mm_102829.1	chr11	69098169	69098207	-	1	NA	promoter-TSS (NM_011065)	promoter-TSS (NM_011065)	-768	NM_011065	18626	Mm.7373	NM_011065	ENSMUSG00000020893	Per1	Hftm|Per|m-rigui|mPer1	period circadian clock 1	protein-coding
mm_49346.1	chr6	21985979	21985992	+	1	NA	promoter-TSS (NM_001081351)	promoter-TSS (NM_001081351)	75	NM_001081351	214642	Mm.221404	NM_001081351	ENSMUSG00000062980	Cped1	6720481P07|A430107O13Rik|AI552584	cadherin-like and PC-esterase domain containing 1	protein-coding
mm_127539.1	chr15	102104507	102104520	+	1	NA	intron (NM_153533, intron 1 of 28)	intron (NM_153533, intron 1 of 28)	1525	NM_153533	209039	Mm.29389	NM_153533	ENSMUSG00000037003	Tns2	C1-ten|Tenc1|nep|nph	tensin 2	protein-coding
mm_168690.1	chr11	97062595	97062595	+	1	NA	intron (NM_001310509, intron 16 of 22)	(CAGAGA)n|Simple_repeat|Simple_repeat	-1173	NR_106181	102465893		NR_106181	ENSMUSG00000098769	Mir8103	Gm27841|mmu-mir-8103	microRNA 8103	ncRNA
mm_41499.1	chr5	92326766	92326777	+	1	NA	exon (NM_008599, exon 2 of 4)	exon (NM_008599, exon 2 of 4)	1308	NM_008599	17329	Mm.766	NM_008599	ENSMUSG00000029417	Cxcl9	BB139920|CMK|Mig|MuMIG|Scyb9|crg-10	chemokine (C-X-C motif) ligand 9	protein-coding
mm_21082.1	chr2	152951528	152951540	-	1	NA	promoter-TSS (NM_001159376)	promoter-TSS (NM_001159376)	48	NM_001159376	252864	Mm.330671	NM_145744	ENSMUSG00000042662	Dusp15	AI851682|LMW-DSP10|T-DSP10	dual specificity phosphatase-like 15	protein-coding
mm_99452.1	chr11	102434180	102434190	+	1	NA	exon (NM_008175, exon 6 of 13)	exon (NM_008175, exon 6 of 13)	3863	NM_008175	14824	Mm.1568	NM_008175	ENSMUSG00000034708	Grn	Pgrn|epithelin	granulin	protein-coding
mm_69980.1	chr7	142380791	142380809	-	1	NA	exon (NM_009983, exon 5 of 9)	exon (NM_009983, exon 5 of 9)	-7054	NM_001347541	320802	Mm.154486	NM_177265	ENSMUSG00000045777	Ifitm10	6330512M04Rik|AI848576|DSPA3	interferon induced transmembrane protein 10	protein-coding
mm_59973.1	chr7	30458244	30458254	+	1	NA	promoter-TSS (NM_172898)	promoter-TSS (NM_172898)	-734	NM_172898	243911	Mm.113908	NM_172898	ENSMUSG00000036915	Kirrel2	C330019F22Rik|NEPH3|NLG1	kin of IRRE like 2 (Drosophila)	protein-coding
mm_4527.1	chr1	175632142	175632151	+	1	NA	promoter-TSS (NM_133809)	promoter-TSS (NM_133809)	-47	NM_133809	98256	Mm.27217	NM_133809	ENSMUSG00000039783	Kmo	AI046660	kynurenine 3-monooxygenase (kynurenine 3-hydroxylase)	protein-coding
mm_136608.1	chr17	5278503	5278507	+	1	NA	intron (NM_001085355, intron 6 of 19)	intron (NM_001085355, intron 6 of 19)	140262	NM_175349	106557	Mm.432764	NM_175349	ENSMUSG00000101959	Ldhal6b	4933402O15Rik|AI326310|LDHL|Ldhal	lactate dehydrogenase A-like 6B	protein-coding
mm_144135.1	chr18	4980601	4980627	+	1	NA	Intergenic	Intergenic	-65975	NM_153153	225115	Mm.136791	NM_153153	ENSMUSG00000024236	Svil	AU024053|B430302E16Rik	supervillin	protein-coding
mm_117633.1	chr13	92131878	92131886	-	1	NA	Intergenic	CpG	-143840	NM_009027	19418	Mm.248630	NM_009027	ENSMUSG00000021708	Rasgrf2	6330417G04Rik|AW048350|Grf2|Ras-GRF2	RAS protein-specific guanine nucleotide-releasing factor 2	protein-coding
mm_151160.1	chr19	53194309	53194319	+	1	NA	intron (NM_013758, intron 1 of 15)	intron (NM_013758, intron 1 of 15)	50317	NM_013758	27360	Mm.426080	NM_013758	ENSMUSG00000025026	Add3	AI463285|R75380	adducin 3 (gamma)	protein-coding
mm_57262.1	chr6	123285533	123285547	-	1	NA	exon (NM_019948, exon 5 of 6)	exon (NM_019948, exon 5 of 6)	4331	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_39354.1	chr5	9100682	9100778	+	1	NA	promoter-TSS (NM_001081029)	promoter-TSS (NM_001081029)	-7	NM_001081029	652925	Mm.439954	NM_001081029	ENSMUSG00000079659	Tmem243	4930420K17Rik|E030031F02Rik	transmembrane protein 243, mitochondrial	protein-coding
mm_154314.1	chrM	593	603	+	1	NA	NA	Intergenic	NA	NA								
mm_24839.1	chr3	95661000	95661052	+	1	NA	3' UTR (NM_008562, exon 3 of 3)	3' UTR (NM_008562, exon 3 of 3)	2305	NM_008562	17210	Mm.1639	NM_008562	ENSMUSG00000038612	Mcl1	AW556805|Mcl-1	myeloid cell leukemia sequence 1	protein-coding
mm_112937.1	chr13	20986205	20986213	+	1	NA	intron (NM_012054, intron 13 of 20)	MT2B|LTR|ERVL	87090	NM_146535	258528	Mm.377554	NM_146535	ENSMUSG00000042869	Olfr1370	MOR256-14	olfactory receptor 1370	protein-coding
mm_122904.1	chr14	54953348	54953393	-	1	NA	exon (NM_010856, exon 22 of 39)	exon (NM_010856, exon 22 of 39)	-4228	NR_029724	387204		NR_029724	ENSMUSG00000065432	Mir208a	Mirn208|Mirn208a|mir-208|mir-208a|mmu-mir-208	microRNA 208a	ncRNA
mm_97538.1	chr11	78826576	78826618	+	1	NA	promoter-TSS (NM_001076681)	promoter-TSS (NM_001076681)	2	NM_001076681	66274	Mm.258932	NM_001076681	ENSMUSG00000072640	Lyrm9	1810012P15Rik	LYR motif containing 9	protein-coding
mm_151835.1	chr19	5720298	5720311	-	1	NA	exon (NM_001114597, exon 9 of 19)	exon (NM_001114597, exon 9 of 19)	6013	NM_001114595	114601	Mm.210447	NM_053252	ENSMUSG00000024937	Ehbp1l1	G430002G23Rik	EH domain binding protein 1-like 1	protein-coding
mm_142421.1	chr17	45568963	45568976	-	1	NA	exon (NM_008302, exon 9 of 11)	exon (NM_008302, exon 9 of 11)	4292	NM_008302	15516	Mm.2180	NM_008302	ENSMUSG00000023944	Hsp90ab1	90kDa|AL022974|C81438|Hsp84|Hsp84-1|Hsp90|Hspcb	heat shock protein 90 alpha (cytosolic), class B member 1	protein-coding
mm_19962.1	chr2	117931237	117931250	-	1	NA	intron (NR_126479, intron 8 of 9)	intron (NR_126479, intron 8 of 9)	109315	NR_040631	73938	Mm.399107	NR_040631	ENSMUSG00000086221	4930412B13Rik	-	RIKEN cDNA 4930412B13 gene	ncRNA
mm_36820.1	chr4	104876431	104876439	-	1	NA	promoter-TSS (NM_146148)	promoter-TSS (NM_146148)	-37	NM_001316667	230558	Mm.197638	NM_146148	ENSMUSG00000035031	C8a	-	complement component 8, alpha polypeptide	protein-coding
mm_22241.1	chr2	174472879	174472936	-	1	NA	promoter-TSS (NM_025531)	promoter-TSS (NM_025531)	34	NM_025531	66390	Mm.182294	NM_025531	ENSMUSG00000016257	Slmo2	2310042G06Rik|AA407013|Prelid3b	slowmo homolog 2 (Drosophila)	protein-coding
mm_80066.1	chr9	69460140	69460151	+	1	NA	intron (NM_007585, intron 1 of 12)	MTEa|LTR|ERVL-MaLR	3201	NR_037296	100526560		NR_037296	ENSMUSG00000093042	Mir3109	mir-3109|mmu-mir-3109	microRNA 3109	ncRNA
mm_98187.1	chr11	87793723	87793805	+	1	NA	promoter-TSS (NM_010824)	promoter-TSS (NM_010824)	-20	NM_010824	17523	Mm.4668	NM_010824	ENSMUSG00000009350	Mpo	mKIAA4033	myeloperoxidase	protein-coding
mm_170553.1	chr1	94151502	94151502	+	1	NA	Intergenic	L1Md_T|LINE|L1	-98949	NM_008798	18566	Mm.5024	NM_008798	ENSMUSG00000026285	Pdcd1	Ly101|PD-1|Pdc1	programmed cell death 1	protein-coding
mm_26644.1	chr3	153849866	153849893	+	1	NA	TTS (NR_040373)	TTS (NR_040373)	2545	NR_040373	72317	Mm.440147	NR_040373	ENSMUSG00000086438	Asb17os	2510003D18Rik	ankyrin repeat and SOCS box-containing 17, opposite strand	ncRNA
mm_81636.1	chr9	110880287	110880315	+	1	NA	promoter-TSS (NM_001146060)	promoter-TSS (NM_001146060)	-21	NM_001146060	235633	Mm.86338	NM_146228	ENSMUSG00000044037	Als2cl	79H19D|79H19E|BC022645|D930044G19Rik|mRn.49018	ALS2 C-terminal like	protein-coding
mm_50605.1	chr6	49367790	49367866	+	1	NA	promoter-TSS (NM_172727)	promoter-TSS (NM_172727)	89	NM_172727	231946	Mm.35199	NM_172727	ENSMUSG00000047115	Fam221a	D330028D13Rik	family with sequence similarity 221, member A	protein-coding
mm_148903.1	chr19	6941876	6941890	+	1	NA	promoter-TSS (NM_001177360)	promoter-TSS (NM_001177360)	22	NM_007522	12015	Mm.4387	NM_007522	ENSMUSG00000024959	Bad	AI325008|Bbc2	BCL2-associated agonist of cell death	protein-coding
mm_141868.1	chr17	34810677	34810710	-	1	NA	intron (NM_011413, intron 35 of 40)	intron (NM_011413, intron 35 of 40)	-6267	NM_009995	13079	Mm.440407	NM_009995	ENSMUSG00000024365	Cyp21a1	21-OH|21OH|21OHA|21OHB|CYP21OH-A|Cyp21|Cyp21-ps1|Cyp21B|Cyp21a2-ps|Cyp21a2ps|Oh21-1|Oh21-2	cytochrome P450, family 21, subfamily a, polypeptide 1	protein-coding
mm_161111.1	chr12	104314720	104314720	+	1	NA	exon (NM_001101472, exon 1 of 4)	exon (NM_001101472, exon 1 of 4)	150	NM_001101472	238395	Mm.436975	NM_001101472	ENSMUSG00000079013	Serpina3j	AI506554|EG238395|Gm4931	serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3J	protein-coding
mm_156582.1	chrX	152027718	152027730	+	1	NA	exon (NM_019710, exon 6 of 25)	exon (NM_019710, exon 6 of 25)	11296	NM_019710	24061	Mm.482095	NM_019710	ENSMUSG00000041133	Smc1a	5830426I24Rik|SMC-1A|Sb1.8|Smc1|Smc1alpha|Smc1l1|Smcb|mKIAA0178	structural maintenance of chromosomes 1A	protein-coding
mm_167156.1	chr7	132088764	132088776	+	1	NA	intron (NM_018867, intron 4 of 13)	intron (NM_018867, intron 4 of 13)	65971	NM_018867	55987	Mm.471654	NM_018867	ENSMUSG00000030862	Cpxm2	4632435C11Rik|CPX-2|Cpx2	carboxypeptidase X 2 (M14 family)	protein-coding
mm_170216.1	chr17	74717799	74717800	+	1	NA	promoter-TSS (NM_152817)	promoter-TSS (NM_152817)	49	NM_152817	74196	Mm.209503	NM_152817	ENSMUSG00000024078	Ttc27	2610511O17Rik	tetratricopeptide repeat domain 27	protein-coding
mm_49560.1	chr6	30564399	30564416	+	1	NA	TTS (NM_001024698)	TTS (NM_001024698)	-3962	NM_027926	71791	Mm.105759	NM_027926	ENSMUSG00000039070	Cpa4	1110019K20Rik|AV009555	carboxypeptidase A4	protein-coding
mm_82297.1	chr9	7836962	7836974	-	1	NA	promoter-TSS (NM_007465)	promoter-TSS (NM_007465)	89	NM_007465	11797	Mm.335659	NM_007465	ENSMUSG00000057367	Birc2	AW146227|Api1|Api2|Birc3|C-IAP1|C330006D17Rik|HIAP1|HIAP2|IAP1|IAP2|MIAP1|MIAP2|MIHB|MIHC|RNF48|cIAP1|cIAP2|mcIAP1	baculoviral IAP repeat-containing 2	protein-coding
mm_23467.1	chr3	60475930	60475950	+	1	NA	intron (NM_001253713, intron 2 of 9)	intron (NM_001253713, intron 2 of 9)	3110	NM_001253713	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_162360.1	chr1	62931169	62931171	+	1	NA	Intergenic	Intergenic	-136438	NR_040601	74992	Mm.401979	NR_040601		4930487H11Rik	-	RIKEN cDNA 4930487H11 gene	ncRNA
mm_47591.1	chr5	124862161	124862204	-	1	NA	promoter-TSS (NM_001081750)	promoter-TSS (NM_001081750)	39	NM_144819	215707	Mm.389693	NM_144819	ENSMUSG00000037979	Ccdc92	AW050178|D5Bwg0834e	coiled-coil domain containing 92	protein-coding
mm_29673.1	chr3	122802013	122802018	-	1	NA	promoter-TSS (NR_045168)	promoter-TSS (NR_045168)	-35	NR_045168	71647	Mm.449992	NR_045168	ENSMUSG00000106583	4930447N08Rik	-	RIKEN cDNA 4930447N08 gene	ncRNA
mm_134250.1	chr16	13668123	13668181	-	1	NA	promoter-TSS (NM_028761)	promoter-TSS (NM_028761)	18	NM_028761	74108	Mm.182350	NM_028761	ENSMUSG00000022685	Parn	1200003I18Rik|DAN	poly(A)-specific ribonuclease (deadenylation nuclease)	protein-coding
mm_13989.1	chr2	121793637	121793638	+	1	NA	intron (NM_172673, intron 1 of 14)	intron (NM_172673, intron 1 of 14)	13420	NM_172673	228564	Mm.121514	NM_172673	ENSMUSG00000027238	Frmd5	1500032A09Rik|5830442F04|A930004K21Rik|R75430	FERM domain containing 5	protein-coding
mm_152664.1	chr19	14494197	14494200	-	1	NA	intron (NM_001302947, intron 8 of 19)	intron (NM_001302947, intron 8 of 19)	-55692	NR_003027	19862		NR_003027	ENSMUSG00000095132	Rnu6	-	U6 small nuclear RNA	snRNA
mm_89408.1	chr10	90828898	90828926	+	1	NA	promoter-TSS (NM_001347054)	promoter-TSS (NM_001347054)	-742	NM_001347054	77531	Mm.440605	NM_181398	ENSMUSG00000058589	Anks1b	AIDA-1b|C030032C09Rik|E530015N03Rik|ENSMUSG00000078431|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding
mm_149963.1	chr19	28990477	28990497	+	1	NA	5' UTR (NM_025950, exon 1 of 7)	5' UTR (NM_025950, exon 1 of 7)	135	NM_025950	67072	Mm.78875	NM_025950	ENSMUSG00000024780	Cdc37l1	2700033A15Rik|BB159850|Cdc37l|Harc	cell division cycle 37-like 1	protein-coding
mm_24342.1	chr3	89773563	89773642	+	1	NA	promoter-TSS (NR_130957)	promoter-TSS (NR_130957)	-7	NM_027315	70093	Mm.41438	NM_027315	ENSMUSG00000042572	Ube2q1	1110002C01Rik|2310012M18Rik|AI854014|Gtap|NICE-5|PRO3094|Ube2q	ubiquitin-conjugating enzyme E2Q family member 1	protein-coding
mm_53266.1	chr6	128362920	128363058	+	1	NA	promoter-TSS (NM_008021)	promoter-TSS (NM_008021)	-5	NM_008021	14235	Mm.42148	NM_008021	ENSMUSG00000001517	Foxm1	AA408308|AW554517|BB238854|Fkh16|Foxm1b|HFH-11B|MPHOSPH2|Mpm2|WIN	forkhead box M1	protein-coding
mm_15753.1	chr2	164240974	164240978	+	1	NA	Intergenic	MLTR11B|LTR|ERVK	-2635	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_169853.1	chr16	32408422	32408426	+	1	NA	TTS (NM_001160402)	TTS (NM_001160402)	7918	NM_001160402	277203	Mm.484240	NM_001160402	ENSMUSG00000079625	Tm4sf19	EG277203	transmembrane 4 L six family member 19	protein-coding
mm_59268.1	chr7	24899153	24899166	+	1	NA	exon (NM_007655, exon 2 of 5)	exon (NM_007655, exon 2 of 5)	1648	NM_007655	12518	Mm.1355	NM_007655	ENSMUSG00000003379	Cd79a	Ig-alpha|Iga|Igalpha|Ly-54|Ly54|mb-1	CD79A antigen (immunoglobulin-associated alpha)	protein-coding
mm_102210.1	chr11	54850526	54850536	-	1	NA	intron (NM_029327, intron 2 of 4)	intron (NM_029327, intron 2 of 4)	10060	NM_029327	75530	Mm.83578	NM_029327	ENSMUSG00000020268	Lyrm7	1700024C24Rik|9330147L21Rik	LYR motif containing 7	protein-coding
mm_56963.1	chr6	120038547	120038555	-	1	NA	5' UTR (NM_001185020, exon 1 of 26)	5' UTR (NM_001185020, exon 1 of 26)	104	NM_001199083	232341	Mm.333349	NM_198703	ENSMUSG00000045962	Wnk1	6430573H23Rik|EG406236|Hsn2|Prkwnk1|mKIAA0344	WNK lysine deficient protein kinase 1	protein-coding
mm_91171.1	chr10	20721278	20721339	-	1	NA	intron (NM_013875, intron 1 of 12)	B4A|SINE|B4	3770	NM_013875	29863	Mm.425617	NM_013875	ENSMUSG00000019990	Pde7b	-	phosphodiesterase 7B	protein-coding
mm_41446.1	chr5	90905336	90905345	+	1	NA	3' UTR (NM_009140, exon 4 of 4)	3' UTR (NM_009140, exon 4 of 4)	1441	NM_009140	20310	Mm.4979	NM_009140	ENSMUSG00000058427	Cxcl2	CINC-2a|GROb|Gro2|MIP-2|MIP-2a|Mgsa-b|Mip2|Scyb|Scyb2	chemokine (C-X-C motif) ligand 2	protein-coding
mm_126995.1	chr15	94996883	94996887	+	1	NA	intron (NM_178789, intron 5 of 7)	intron (NM_178789, intron 5 of 7)	152433	NR_015482	100043315	Mm.159041	NR_015482	ENSMUSG00000100603	LOC100043315	-	uncharacterized LOC100043315	ncRNA
mm_136371.1	chr16	92824477	92824507	-	1	NA	intron (NM_001111022, intron 2 of 6)	intron (NM_001111022, intron 2 of 6)	1582	NM_001111021	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_29497.1	chr3	115974332	115974336	-	1	NA	intron (NM_023214, intron 8 of 10)	L2|LINE|L2	-5568	NR_130332	100316705		NR_130332	ENSMUSG00000089261	Mir669n	mmu-mir-669n	microRNA 669n	ncRNA
mm_165728.1	chr3	105635692	105635693	+	1	NA	intron (NM_001039347, intron 2 of 6)	intron (NM_001039347, intron 2 of 6)	51879	NM_017397	53975	Mm.272826	NM_017397	ENSMUSG00000027905	Ddx20	GEMIN3|dp103	DEAD (Asp-Glu-Ala-Asp) box polypeptide 20	protein-coding
mm_103263.1	chr11	71144751	71144794	-	1	NA	promoter-TSS (NM_001004142)	promoter-TSS (NM_001004142)	-68	NM_001004142	195046	Mm.240227	NM_001004142	ENSMUSG00000069830	Nlrp1a	CARD7|DEFCAP|Gm14|Gm15|NAC|Nalp1|Nalp1a|Nlrp1|PP1044	NLR family, pyrin domain containing 1A	protein-coding
mm_71821.1	chr8	68895660	68895726	+	1	NA	exon (NM_008509, exon 5 of 10)	exon (NM_008509, exon 5 of 10)	15138	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_102090.1	chr11	52282804	52282826	-	1	NA	promoter-TSS (NM_009331)	promoter-TSS (NM_009331)	199	NM_001313981	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_113875.1	chr13	48870051	48870066	+	1	NA	intron (NM_011078, intron 1 of 21)	intron (NM_011078, intron 1 of 21)	827	NM_011078	18676	Mm.486213	NM_011078	ENSMUSG00000038025	Phf2	GRC5	PHD finger protein 2	protein-coding
mm_82331.1	chr9	9238951	9238964	-	1	NA	promoter-TSS (NM_027823)	promoter-TSS (NM_027823)	56	NM_027823	71544	Mm.334955	NM_027823	ENSMUSG00000050730	Arhgap42	9030420J04Rik|BE136619	Rho GTPase activating protein 42	protein-coding
mm_67564.1	chr7	81885336	81885351	-	1	NA	3' UTR (NM_013886, exon 6 of 6)	3' UTR (NM_013886, exon 6 of 6)	22656	NM_001291282	107769	Mm.221412	NM_145375	ENSMUSG00000038623	Tm6sf1	AI428514|BC023123|C630016D09Rik	transmembrane 6 superfamily member 1	protein-coding
mm_20924.1	chr2	150842399	150842409	-	1	NA	intron (NM_024465, intron 5 of 12)	intron (NM_024465, intron 5 of 12)	55608	NM_153781	110078	Mm.222584	NM_153781	ENSMUSG00000033059	Pygb	-	brain glycogen phosphorylase	protein-coding
mm_80929.1	chr9	102506073	102506092	+	1	NA	promoter-TSS (NM_024291)	promoter-TSS (NM_024291)	-56	NM_024291	16716	Mm.101692	NM_024291	ENSMUSG00000035606	Ky	CD1|D9Mgc44e|ky	kyphoscoliosis peptidase	protein-coding
mm_109258.1	chr12	109459968	109459980	+	1	NA	exon (NM_010052, exon 5 of 5)	exon (NM_010052, exon 5 of 5)	6519	NM_010052	13386	Mm.157069	NM_010052	ENSMUSG00000040856	Dlk1	AW742678|DLK-1|DlkI|FA1|Ly107|Peg9|SCP1|ZOG|pG2|pref-1	delta-like 1 homolog (Drosophila)	protein-coding
mm_26520.1	chr3	145924381	145924391	+	1	NA	5' UTR (NM_009740, exon 1 of 3)	5' UTR (NM_009740, exon 1 of 3)	124	NM_009740	12042	Mm.239141	NM_009740	ENSMUSG00000028191	Bcl10	AI132454|BCL-10|C81403|CARMEN|CIPER|CLAP|ME10|cE10	B cell leukemia/lymphoma 10	protein-coding
mm_10641.1	chr2	20547498	20547514	+	1	NA	intron (NM_029895, intron 3 of 18)	intron (NM_029895, intron 3 of 18)	27993	NM_001177631	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding
mm_110595.1	chr12	56535048	56535100	-	1	NA	intron (NM_009385, intron 1 of 2)	CpG-3195	1834	NM_009385	21869	Mm.89972	NM_009385	ENSMUSG00000001496	Nkx2-1	AV026640|Nkx2.1|T/EBP|Titf1|Ttf-1	NK2 homeobox 1	protein-coding
mm_15807.1	chr2	164488104	164488127	+	1	NA	promoter-TSS (NM_001048229)	promoter-TSS (NM_001048229)	4	NM_001048229	52840	Mm.256927	NM_026797	ENSMUSG00000017734	Dbndd2	1110017A21Rik|2900022J10Rik|AU041050|AW048677|D2Bwg0891e|Nkip|R74724	dysbindin (dystrobrevin binding protein 1) domain containing 2	protein-coding
mm_138324.1	chr17	34850426	34850445	+	1	NA	promoter-TSS (NM_021337)	promoter-TSS (NM_021337)	44	NM_001045864	27632	Mm.653	NM_138580	ENSMUSG00000024369	Nelfe	D17H6S45|NELF-E|RD|Rdbp	negative elongation factor complex member E, Rdbp	protein-coding
mm_40462.1	chr5	53629968	53629974	+	1	NA	intron (NM_001080928, intron 2 of 10)	(GGGA)n|Simple_repeat|Simple_repeat	39485	NM_001080927	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_26664.1	chr3	154711086	154711096	+	1	NA	promoter-TSS (NM_175176)	promoter-TSS (NM_175176)	-42	NM_175176	209601	Mm.331454	NM_175176	ENSMUSG00000078161	Erich3	1700013E18Rik|4922501L14Rik|5031409G23Rik|AI596448|Gm133	glutamate rich 3	protein-coding
mm_27273.1	chr3	40682549	40682582	-	1	NA	intron (NM_175515, intron 7 of 15)	L2a|LINE|L2	-26306	NM_178386	73333	Mm.78691	NM_178386	ENSMUSG00000069041	Slc25a31	1700034J06Rik|Ant4|Sfec	solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 31	protein-coding
mm_52802.1	chr6	121341989	121342011	+	1	NA	Intergenic	Intergenic	-1076	NM_001347433	14411	Mm.274506	NM_133661	ENSMUSG00000030109	Slc6a12	BGT1|GAT-2|GAT2|Gabt2	solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12	protein-coding
mm_20685.1	chr2	132578245	132578255	-	1	NA	promoter-TSS (NM_027096)	promoter-TSS (NM_027096)	-2	NM_028802	74182	Mm.211211	NM_027096	ENSMUSG00000027346	Gpcpd1	2310004G06Rik|2310032D16Rik|AU015213|Gde5|Prei4|mKIAA1434	glycerophosphocholine phosphodiesterase 1	protein-coding
mm_13741.1	chr2	118118677	118118688	+	1	NA	exon (NM_011580, exon 10 of 22)	exon (NM_011580, exon 10 of 22)	6806	NM_001313914	21825	Mm.4159	NM_011580	ENSMUSG00000040152	Thbs1	TSP-1|TSP1|Thbs-1|tbsp1	thrombospondin 1	protein-coding
mm_114011.1	chr13	52607269	52607291	+	1	NA	intron (NM_011518, intron 1 of 13)	RLTR17D_Mm|LTR|ERVK	10398	NM_011518	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_164242.1	chr15	94715347	94715350	+	1	NA	intron (NM_178789, intron 3 of 7)	intron (NM_178789, intron 3 of 7)	86163	NM_178789	320709	Mm.74873	NM_178789	ENSMUSG00000063296	Tmem117	B930062P21Rik	transmembrane protein 117	protein-coding
mm_169918.1	chr16	57391191	57391191	-	1	NA	intron (NM_001040397, intron 1 of 4)	LSU-rRNA_Hsa|rRNA|rRNA	37914	NM_001040397	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding
mm_47319.1	chr5	122460697	122460713	-	1	NA	exon (NM_009722, exon 14 of 21)	exon (NM_009722, exon 14 of 21)	38261	NM_019805	56317	Mm.37341	NM_019805	ENSMUSG00000029466	Anapc7	APC7|AW545589	anaphase promoting complex subunit 7	protein-coding
mm_139116.1	chr17	47410853	47410884	+	1	NA	Intergenic	T-rich|Low_complexity|Low_complexity	3843	NM_001172091	75462	Mm.46129	NM_029296	ENSMUSG00000047150	1700001C19Rik	-	RIKEN cDNA 1700001C19 gene	protein-coding
mm_69001.1	chr7	126695732	126695788	-	1	NA	promoter-TSS (NM_029420)	promoter-TSS (NM_029420)	23	NM_029420	75764	Mm.280573	NM_029420	ENSMUSG00000059772	Slx1b	1110030E23Rik|2410170E21Rik|4833422P03Rik|AI853643|Giyd1|Giyd2	SLX1 structure-specific endonuclease subunit homolog B (S. cerevisiae)	protein-coding
mm_12707.1	chr2	76675266	76675287	+	1	NA	promoter-TSS (NM_031256)	promoter-TSS (NM_031256)	-39	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_152572.1	chr19	11590153	11590208	-	1	NA	exon (NM_026835, exon 5 of 7)	exon (NM_026835, exon 5 of 7)	14624	NM_026835	68774	Mm.290390	NM_026835	ENSMUSG00000024679	Ms4a6d	1110058E16Rik|AI447446|Ms4a11	membrane-spanning 4-domains, subfamily A, member 6D	protein-coding
mm_127928.1	chr15	10461991	10461998	-	1	NA	exon (NM_030046, exon 4 of 12)	exon (NM_030046, exon 4 of 12)	8522	NM_030046	78244	Mm.297862	NM_030046	ENSMUSG00000044224	Dnajc21	4930461P20Rik|9930116P15Rik	DnaJ heat shock protein family (Hsp40) member C21	protein-coding
mm_94126.1	chr10	128672300	128672309	-	1	NA	intron (NM_173733, intron 2 of 3)	intron (NM_173733, intron 2 of 3)	1614	NM_173733	211389	Mm.23352	NM_173733	ENSMUSG00000049858	Suox	SO	sulfite oxidase	protein-coding
mm_137113.1	chr17	22424249	22424260	+	1	NA	promoter-TSS (NM_001331197)	promoter-TSS (NM_001331197)	52	NM_001331198	74149	Mm.30767	NM_198003	ENSMUSG00000071266	Zfp946	1300003B13Rik	zinc finger protein 946	protein-coding
mm_129702.1	chr15	81712556	81712574	-	1	NA	intron (NM_001146174, intron 7 of 15)	intron (NM_001146174, intron 7 of 15)	-15278	NM_001164320	214685	Mm.393287	NM_001164320	ENSMUSG00000063765	Chadl	AY100452|D930017K21Rik	chondroadherin-like	protein-coding
mm_120727.1	chr14	73142592	73142602	+	1	NA	promoter-TSS (NM_001170694)	promoter-TSS (NM_001170694)	87	NM_134083	105670	Mm.280068	NM_134083	ENSMUSG00000022106	Rcbtb2	2610028E02Rik|2810420M18Rik|AI448345|AW240694|Chc1l|RC/BTB2	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 2	protein-coding
mm_109031.1	chr12	104084221	104084231	+	1	NA	intron (NR_002861, intron 3 of 3)	intron (NR_002861, intron 3 of 3)	6267	NR_002861	321018	Mm.297023	NR_002861		Serpina4-ps1	KALps|Klst	serine (or cysteine) peptidase inhibitor, clade A, member 4, pseudogene 1	pseudo
mm_171412.1	chr4	129898953	129898958	+	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-7271	NR_045190	319894	Mm.59196	NR_045190	ENSMUSG00000086369	E330017L17Rik	-	RIKEN cDNA E330017L17 gene	ncRNA
mm_88773.1	chr10	80336142	80336162	+	1	NA	3' UTR (NM_139292, exon 6 of 6)	3' UTR (NM_139292, exon 6 of 6)	6007	NM_139292	70335	Mm.28147	NM_139292	ENSMUSG00000035504	Reep6	0610011M24Rik|Dp1l1	receptor accessory protein 6	protein-coding
mm_62625.1	chr7	107567719	107567746	+	1	NA	5' UTR (NM_172907, exon 1 of 3)	5' UTR (NM_172907, exon 1 of 3)	299	NM_172907	244198	Mm.77425	NM_172907	ENSMUSG00000051041	Olfml1	6720478C22|AV321997|BC047207|MVAL564|ONT2|mONT2	olfactomedin-like 1	protein-coding
mm_153775.1	chr19	45749379	45749418	-	1	NA	TTS (NM_023799)	TTS (NM_023799)	165	NM_008723	18150	Mm.1406	NM_008723	ENSMUSG00000056209	Npm3	Nub1	nucleoplasmin 3	protein-coding
mm_158512.1	chrX	142966782	142966790	-	1	NA	promoter-TSS (NM_019496)	promoter-TSS (NM_019496)	-58	NM_019496	56068	Mm.143724	NM_019496	ENSMUSG00000042225	Ammecr1	6230420G18Rik	Alport syndrome, mental retardation, midface hypoplasia and elliptocytosis chromosomal region gene 1	protein-coding
mm_111125.1	chr12	81373293	81373293	-	1	NA	intron (NM_001309848, intron 5 of 5)	MTD-int|LTR|ERVL-MaLR	6193	NM_001038995	214321	Mm.444671	NM_001038995	ENSMUSG00000072974	Gm4787	Adam4b|EG214321	predicted gene 4787	protein-coding
mm_104981.1	chr11	100258113	100258118	-	1	NA	intron (NM_010663, intron 4 of 7)	intron (NM_010663, intron 4 of 7)	2914	NM_010663	16667	Mm.14046	NM_010663	ENSMUSG00000035557	Krt17	K17|Krt1-17	keratin 17	protein-coding
mm_89107.1	chr10	84608549	84608587	+	1	NA	exon (NM_146008, exon 9 of 10)	exon (NM_146008, exon 9 of 10)	-13869	NM_027423	70428	Mm.335007	NM_027423	ENSMUSG00000034453	Polr3b	2700078H01Rik|A330032P03Rik|C85372|RPC2	polymerase (RNA) III (DNA directed) polypeptide B	protein-coding
mm_30397.1	chr3	152249679	152249724	-	1	NA	exon (NM_199465, exon 5 of 13)	exon (NM_199465, exon 5 of 13)	16619	NM_199465	68810	Mm.200188	NM_199465	ENSMUSG00000039103	Nexn	1110046H09Rik|AA553326|NELIN	nexilin	protein-coding
mm_73621.1	chr8	110266961	110266982	+	1	NA	promoter-TSS (NM_172916)	promoter-TSS (NM_172916)	-6	NM_172916	244653	Mm.444803	NM_172916	ENSMUSG00000059854	Hydin	1700034M11Rik|4930545D19Rik|4932703P14|A830061H17|AC069308.21gm4|hy-3|hy3|hyrh	HYDIN, axonemal central pair apparatus protein	protein-coding
mm_87859.1	chr10	61175592	61175601	+	1	NA	intron (NM_001017409, intron 1 of 3)	intron (NM_001017409, intron 1 of 3)	334	NM_023064	65971	Mm.30227	NM_023064	ENSMUSG00000020096	Tbata	1700021K02Rik|AI428928|Spatial|Titest	thymus, brain and testes associated	protein-coding
mm_41433.1	chr5	90904070	90904074	+	1	NA	intron (NM_009140, intron 1 of 3)	intron (NM_009140, intron 1 of 3)	173	NM_009140	20310	Mm.4979	NM_009140	ENSMUSG00000058427	Cxcl2	CINC-2a|GROb|Gro2|MIP-2|MIP-2a|Mgsa-b|Mip2|Scyb|Scyb2	chemokine (C-X-C motif) ligand 2	protein-coding
mm_98995.1	chr11	98795172	98795209	+	1	NA	promoter-TSS (NM_028722)	promoter-TSS (NM_028722)	-579	NM_028722	74026	Mm.258352	NM_028722	ENSMUSG00000052915	Msl1	2810017F12Rik|4121402D02Rik|4930463F05Rik|AA682082|Msl-1	male-specific lethal 1 homolog (Drosophila)	protein-coding
mm_112360.1	chr12	119101543	119101551	-	1	NA	Intergenic	Intergenic	-135126	NM_029961	77706	Mm.261496	NM_029961	ENSMUSG00000072791	Abcb5	9230106F14Rik	ATP-binding cassette, sub-family B (MDR/TAP), member 5	protein-coding
mm_48606.1	chr5	144255903	144255959	-	1	NA	intron (NM_018772, intron 2 of 2)	CpG-11782	706	NM_018772	55950	Mm.38011	NM_018772	ENSMUSG00000047843	Bri3	I3	brain protein I3	protein-coding
mm_85823.1	chr9	110420877	110420899	-	1	NA	exon (NM_008694, exon 2 of 4)	exon (NM_008694, exon 2 of 4)	1080	NM_008694	18054	Mm.236225	NM_008694	ENSMUSG00000032484	Ngp	bectenecin	neutrophilic granule protein	protein-coding
mm_135324.1	chr16	38784263	38784283	-	1	NA	exon (NM_178924, exon 5 of 8)	exon (NM_178924, exon 5 of 8)	15930	NM_178924	22268	Mm.130793	NM_178924	ENSMUSG00000049436	Upk1b	AI413235|Tspan20|UPIb|Upk1	uroplakin 1B	protein-coding
mm_80926.1	chr9	102051717	102051717	+	1	NA	intron (NM_001168296, intron 4 of 14)	intron (NM_001168296, intron 4 of 14)	253258	NR_106163	102466241		NR_106163	ENSMUSG00000098521	Mir7243	Gm27363|mmu-mir-7243	microRNA 7243	ncRNA
mm_11626.1	chr2	34775116	34775136	+	1	NA	exon (NM_001163434, exon 8 of 9)	exon (NM_001163434, exon 8 of 9)	3036	NM_022310	14828	Mm.330160	NM_022310	ENSMUSG00000026864	Hspa5	AL022860|AU019543|Bip|D2Wsu141e|D2Wsu17e|Grp78|Hsce70|SEZ-7|Sez7|baffled|mBiP	heat shock protein 5	protein-coding
mm_147671.1	chr18	60648265	60648289	-	1	NA	Intergenic	Intergenic	-15133	NR_045401	328963	Mm.417203	NR_045401		G630071F17Rik	G630071F17	RIKEN cDNA G630071F17 gene	ncRNA
mm_103008.1	chr11	69695989	69696011	-	1	NA	promoter-TSS (NM_001159503)	promoter-TSS (NM_001159503)	98	NM_011614	21944	Mm.8983	NM_011614	ENSMUSG00000097328	Tnfsf12	Apo3l|Dr3l|Dr3lg|Tweak	tumor necrosis factor (ligand) superfamily, member 12	protein-coding
mm_99443.1	chr11	102433240	102433315	+	1	NA	exon (NM_008175, exon 3 of 13)	exon (NM_008175, exon 3 of 13)	2955	NM_008175	14824	Mm.1568	NM_008175	ENSMUSG00000034708	Grn	Pgrn|epithelin	granulin	protein-coding
mm_65077.1	chr7	19140171	19140187	-	1	NA	TTS (NM_026111)	TTS (NM_026111)	9017	NM_026111	67369	Mm.234876	NM_026111	ENSMUSG00000030407	Qpctl	1810019P04Rik|BB101812|gQC	glutaminyl-peptide cyclotransferase-like	protein-coding
mm_57812.1	chr6	129462428	129462444	-	1	NA	non-coding (NR_132130, exon 6 of 6)	non-coding (NR_132130, exon 6 of 6)	10343	NM_001309637	56644	Mm.239516	NM_020008	ENSMUSG00000079293	Clec7a	BGR|Clecsf12|beta-GR	C-type lectin domain family 7, member a	protein-coding
mm_43196.1	chr5	129020194	129020253	+	1	NA	promoter-TSS (NM_009391)	promoter-TSS (NM_009391)	67	NM_009391	19384	Mm.297440	NM_009391	ENSMUSG00000029430	Ran	-	RAN, member RAS oncogene family	protein-coding
mm_3159.1	chr1	135155566	135155577	+	1	NA	3' UTR (NM_026823, exon 7 of 7)	3' UTR (NM_026823, exon 7 of 7)	8737	NM_026823	68724	Mm.174998	NM_026823	ENSMUSG00000026426	Arl8a	1110033P22Rik|Arl10b|gie2	ADP-ribosylation factor-like 8A	protein-coding
mm_141527.1	chr17	31819306	31819312	-	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	36483	NM_010831	17691	Mm.290941	NM_010831	ENSMUSG00000024042	Sik1	Msk|Sik|Snf1lk	salt inducible kinase 1	protein-coding
mm_14546.1	chr2	132846906	132846951	+	1	NA	promoter-TSS (NM_025646)	promoter-TSS (NM_025646)	262	NM_001024385	66586	Mm.357342	NM_025646	ENSMUSG00000027357	Crls1	0610009I22Rik|4930557M15Rik|5730490M08Rik	cardiolipin synthase 1	protein-coding
mm_17614.1	chr2	30929831	30929893	-	1	NA	Intergenic	Intergenic	-23139	NM_133673	30934	Mm.249164	NM_133673	ENSMUSG00000026848	Tor1b	2610016F05Rik|DQ1|torsinB	torsin family 1, member B	protein-coding
mm_165502.1	chr2	167773128	167773134	+	1	NA	Intergenic	Intergenic	81954	NR_015500	329562	Mm.123101	NM_177851	ENSMUSG00000006462	A530013C23Rik	-	RIKEN cDNA A530013C23 gene	ncRNA
mm_136211.1	chr16	89888673	89888679	-	1	NA	intron (NM_009384, intron 4 of 27)	intron (NM_009384, intron 4 of 27)	-70324	NM_001145887	21844	Mm.310902	NM_009384	ENSMUSG00000002489	Tiam1	AI847750|D16Ium10|D16Ium10e	T cell lymphoma invasion and metastasis 1	protein-coding
mm_58927.1	chr7	17972222	17972232	+	1	NA	promoter-TSS (NM_023289)	promoter-TSS (NM_023289)	60	NM_023289	66996	Mm.36666	NM_023289	ENSMUSG00000030368	Ceacam11	1600015D01Rik	carcinoembryonic antigen-related cell adhesion molecule 11	protein-coding
mm_170829.1	chr2	176871680	176871693	+	1	NA	Intergenic	Intergenic	-7249	NR_040256	626877	Mm.490744	NR_040256		Gm14405	OTTMUSG00000016573	predicted gene 14405	pseudo
mm_115151.1	chr13	105444262	105444271	+	1	NA	exon (NM_008308, exon 1 of 1)	exon (NM_008308, exon 1 of 1)	573	NM_008308	15550	Mm.4716	NM_008308	ENSMUSG00000021721	Htr1a	Gpcr18	5-hydroxytryptamine (serotonin) receptor 1A	protein-coding
mm_93188.1	chr10	93889970	93889987	-	1	NA	5' UTR (NM_019648, exon 2 of 12)	5' UTR (NM_019648, exon 2 of 12)	1224	NM_019648	56307	Mm.289329	NM_019648	ENSMUSG00000036112	Metap2	4930584B20Rik|A930035J23Rik|AI047573|AL024412|AU014659|Amp2|Mnpep|p67|p67eIF2	methionine aminopeptidase 2	protein-coding
mm_67567.1	chr7	81934167	81934177	-	1	NA	5' UTR (NM_013886, exon 1 of 6)	5' UTR (NM_013886, exon 1 of 6)	287	NM_013886	29877	Mm.392934	NM_013886	ENSMUSG00000025104	Hdgfrp3	2700022B06Rik|HRP-3	hepatoma-derived growth factor, related protein 3	protein-coding
mm_52942.1	chr6	122952451	122952505	+	1	NA	promoter-TSS (NM_153197)	promoter-TSS (NM_153197)	-37	NM_001204241	73149	Mm.25684	NM_153197	ENSMUSG00000043832	Clec4a3	3110037K17Rik|Dcir3	C-type lectin domain family 4, member a3	protein-coding
mm_20927.1	chr2	150855729	150855774	-	1	NA	intron (NM_024465, intron 2 of 12)	(TG)n|Simple_repeat|Simple_repeat	48980	NM_024465	76192	Mm.112632	NM_024465	ENSMUSG00000032046	Abhd12	1500011G07Rik|6330583M11Rik|AI431047|AW547313	abhydrolase domain containing 12	protein-coding
mm_39346.1	chr5	8893914	8893916	+	1	NA	intron (NM_008830, intron 1 of 27)	CpG	194	NM_008830	18670	Mm.297825	NM_008830	ENSMUSG00000042476	Abcb4	Mdr2|Pgy-2|Pgy2|mdr-2	ATP-binding cassette, sub-family B (MDR/TAP), member 4	protein-coding
mm_32827.1	chr4	117563831	117563834	+	1	NA	intron (NM_001285899, intron 2 of 8)	intron (NM_001285899, intron 2 of 8)	13467	NM_080469	140546	Mm.235891	NM_080469	ENSMUSG00000033423	Eri3	PINT1|Prnpip1	exoribonuclease 3	protein-coding
mm_15515.1	chr2	158306626	158306653	+	1	NA	5' UTR (NM_008489, exon 1 of 15)	5' UTR (NM_008489, exon 1 of 15)	146	NM_008489	16803	Mm.218846	NM_008489	ENSMUSG00000016024	Lbp	Bpifd2|Ly88	lipopolysaccharide binding protein	protein-coding
mm_80262.1	chr9	72872433	72872433	+	1	NA	intron (NM_175485, intron 11 of 19)	intron (NM_175485, intron 11 of 19)	-53217	NM_028116	72135	Mm.273605	NM_028116	ENSMUSG00000034910	Pygo1	2600014C22Rik	pygopus 1	protein-coding
mm_145106.1	chr18	44104549	44104559	+	1	NA	promoter-TSS (NM_030061)	promoter-TSS (NM_030061)	31	NM_030061	78242	Mm.99782	NM_030061	ENSMUSG00000061144	Spink12	9230117E20Rik	serine peptidase inhibitor, Kazal type 12	protein-coding
mm_153152.1	chr19	34252470	34252494	-	1	NA	exon (NM_007392, exon 2 of 9)	exon (NM_007392, exon 2 of 9)	2891	NM_007392	11475	Mm.213025	NM_007392	ENSMUSG00000035783	Acta2	0610041G09Rik|Actvs|SMalphaA|a-SMA|alphaSMA	actin, alpha 2, smooth muscle, aorta	protein-coding
mm_165473.1	chr2	164289754	164289762	+	1	NA	exon (NM_021363, exon 2 of 3)	exon (NM_021363, exon 2 of 3)	490	NM_021363	64335	Mm.389393	NM_021363	ENSMUSG00000017003	Svs3a	9530026M05Rik|BB121242|Semg2|Svp-3|Svp3|Svs3	seminal vesicle secretory protein 3A	protein-coding
mm_109347.1	chr12	109603916	109603920	+	1	NA	promoter-TSS (NR_028261)	promoter-TSS (NR_028261)	-27	NR_028261	75745	Mm.293263	NR_028261		Rian	5530401N18Rik|C130089L09Rik|Meg8	RNA imprinted and accumulated in nucleus	ncRNA
mm_94696.1	chr11	20112487	20112498	+	1	NA	intron (NM_146243, intron 1 of 8)	CpG	459	NM_146243	66713	Mm.259045	NM_146243	ENSMUSG00000020152	Actr2	4921510D23Rik|AA409782|Arp2|D6Ertd746e	ARP2 actin-related protein 2	protein-coding
mm_100730.1	chr11	3931792	3931816	-	1	NA	intron (NM_001130458, intron 1 of 9)	intron (NM_001130458, intron 1 of 9)	157	NM_001130459	21452	Mm.20948	NM_015749	ENSMUSG00000020432	Tcn2	AW208754|Tcn-2	transcobalamin 2	protein-coding
mm_11458.1	chr2	32193942	32193964	+	1	NA	exon (NM_001159634, exon 7 of 32)	exon (NM_001159634, exon 7 of 32)	-42730	NM_145145	99011	Mm.31192	NM_145145	ENSMUSG00000039254	Pomt1	AI505244	protein-O-mannosyltransferase 1	protein-coding
mm_128207.1	chr15	36055115	36055128	-	1	NA	intron (NM_001195748, intron 14 of 27)	ID4_|SINE|ID	85279	NM_001195748	626596	Mm.321798	NM_001195748	ENSMUSG00000037627	Rgs22	-	regulator of G-protein signalling 22	protein-coding
mm_155307.1	chrX	61186059	61186066	+	1	NA	promoter-TSS (NM_001166658)	promoter-TSS (NM_001166658)	-504	NM_001166658	631990	Mm.401324	NM_001166658	ENSMUSG00000090546	Cdr1	100039759|Cdr|Cdr34|EG631990|Gm2409|Gm7077	cerebellar degeneration related antigen 1	protein-coding
mm_146137.1	chr18	74733693	74733703	+	1	NA	intron (NM_201600, intron 30 of 38)	intron (NM_201600, intron 30 of 38)	44757	NR_028560	100217466		NR_028560		Scarna17	MBII-119	small Cajal body-specific RNA 17	ncRNA
mm_160304.1	chr7	140202794	140202794	-	1	NA	promoter-TSS (NM_001011814)	promoter-TSS (NM_001011814)	-26	NM_001011814	258055	Mm.377339	NM_001011814	ENSMUSG00000050366	Olfr524	MOR103-14P	olfactory receptor 524	protein-coding
mm_67502.1	chr7	80779238	80779256	-	1	NA	intron (NM_016721, intron 2 of 37)	intron (NM_016721, intron 2 of 37)	24084	NM_016721	29875	Mm.207619	NM_016721	ENSMUSG00000030536	Iqgap1	AA682088|D7Ertd237e|D7Ertd257e|mKIAA0051	IQ motif containing GTPase activating protein 1	protein-coding
mm_125204.1	chr15	33083155	33083166	+	1	NA	promoter-TSS (NM_018755)	promoter-TSS (NM_018755)	31	NM_176073	54381	Mm.158251	NM_018755	ENSMUSG00000039007	Cpq	1190003P12Rik|2610034C17Rik|Hls2|Lal-1|Pgcp	carboxypeptidase Q	protein-coding
mm_112792.1	chr13	20204425	20204434	+	1	NA	intron (NM_080288, intron 2 of 21)	intron (NM_080288, intron 2 of 21)	113922	NM_080288	140580	Mm.342392	NM_080288	ENSMUSG00000041112	Elmo1	6330578D22Rik|C230095H21Rik|CED-12	engulfment and cell motility 1	protein-coding
mm_41511.1	chr5	92375592	92375602	+	1	NA	intron (NM_001310664, intron 2 of 10)	intron (NM_001310664, intron 2 of 10)	-12301	NR_038116	56066	Mm.131723	NM_019494	ENSMUSG00000060183	Cxcl11	Cxc11|H174|I-tac|Ip9|Itac|Scyb11|Scyb9b|b-R1|betaR1	chemokine (C-X-C motif) ligand 11	protein-coding
mm_96560.1	chr11	68968180	68968186	+	1	NA	promoter-TSS (NM_028048)	promoter-TSS (NM_028048)	52	NM_028048	71998	Mm.298622	NM_028048	ENSMUSG00000018740	Slc25a35	1810012H11Rik	solute carrier family 25, member 35	protein-coding
mm_91072.1	chr10	19009235	19009249	-	1	NA	intron (NM_001166402, intron 1 of 7)	intron (NM_001166402, intron 1 of 7)	2721	NM_001166402	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_131650.1	chr16	20535476	20535546	+	1	NA	promoter-TSS (NM_009679)	promoter-TSS (NM_009679)	31	NM_009679	11773	Mm.18946	NM_009679	ENSMUSG00000022841	Ap2m1	-	adaptor-related protein complex 2, mu 1 subunit	protein-coding
mm_118553.1	chr14	17660967	17660980	+	1	NA	promoter-TSS (NM_001113417)	promoter-TSS (NM_001113417)	13	NM_001113417	21834	Mm.32563	NM_009380	ENSMUSG00000021779	Thrb	Nr1a2|T3R[b]|T3Rbeta|Thrb1|Thrb2|c-erbAbeta	thyroid hormone receptor beta	protein-coding
mm_47508.1	chr5	124052047	124052074	-	1	NA	Intergenic	Intergenic	-19800	NM_177876	330192	Mm.4079	NM_177876	ENSMUSG00000066278	Vps37b	2300007F24Rik|AI415429|BC026744	vacuolar protein sorting 37B	protein-coding
mm_83998.1	chr9	57467986	57468074	-	1	NA	promoter-TSS (NM_020270)	promoter-TSS (NM_020270)	30	NM_020270	56807	Mm.102278	NM_020270	ENSMUSG00000040722	Scamp5	Sc5	secretory carrier membrane protein 5	protein-coding
mm_38907.1	chr4	149974986	149974989	-	1	NA	Intergenic	Intergenic	-19981	NM_029035	74646	Mm.30	NM_029035	ENSMUSG00000039911	Spsb1	1110014L01Rik|4930422J18Rik|AI596360|AI854583|SSB-1|SSB1	splA/ryanodine receptor domain and SOCS box containing 1	protein-coding
mm_49269.1	chr6	17492875	17492891	+	1	NA	intron (NM_008591, intron 3 of 21)	B4|SINE|B4	28926	NM_008591	17295	Mm.86844	NM_008591	ENSMUSG00000009376	Met	AI838057|HGF|HGFR|Par4|c-Met	met proto-oncogene	protein-coding
mm_74565.1	chr8	11008895	11008905	-	1	NA	promoter-TSS (NM_001081212)	promoter-TSS (NM_001081212)	-470	NM_001081212	384783	Mm.407207	NM_001081212	ENSMUSG00000038894	Irs2	Irs-2	insulin receptor substrate 2	protein-coding
mm_47200.1	chr5	120887599	120887612	-	1	NA	promoter-TSS (NR_126529)	promoter-TSS (NR_126529)	8	NM_011852	23960	Mm.389688	NM_011852	ENSMUSG00000066861	Oas1g	AI449562|L2|Mmu-L|Mmu-L2|Oas1b|Oias-1|Oias1	2'-5' oligoadenylate synthetase 1G	protein-coding
mm_68641.1	chr7	118443550	118443571	-	1	NA	promoter-TSS (NM_138649)	promoter-TSS (NM_138649)	-8	NM_138649	110058	Mm.156558	NM_138649	ENSMUSG00000058420	Syt17	Bk	synaptotagmin XVII	protein-coding
mm_16676.1	chr2	6872255	6872282	-	1	NA	promoter-TSS (NM_001347094)	promoter-TSS (NM_001347094)	-233	NM_001347094	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_150989.1	chr19	46573363	46573421	+	1	NA	promoter-TSS (NM_053196)	promoter-TSS (NM_053196)	27	NM_053196	94279	Mm.296837	NM_053196	ENSMUSG00000025036	Sfxn2	C79732|F630107H02Rik	sideroflexin 2	protein-coding
mm_24830.1	chr3	95656174	95656178	+	1	NA	Intergenic	B3A|SINE|B2	-2545	NM_008562	17210	Mm.1639	NM_008562	ENSMUSG00000038612	Mcl1	AW556805|Mcl-1	myeloid cell leukemia sequence 1	protein-coding
mm_90032.1	chr10	115430938	115430946	+	1	NA	intron (NM_001033261, intron 32 of 34)	intron (NM_001033261, intron 32 of 34)	45983	NM_001033261	216345	Mm.207621	NM_001033261	ENSMUSG00000034163	Zfc3h1	BC033596|Ccdc131|Psrc2	zinc finger, C3H1-type containing	protein-coding
mm_106650.1	chr11	121063544	121063574	-	1	NA	promoter-TSS (NM_026907)	promoter-TSS (NM_026907)	10	NM_026907	58210	Mm.116986	NM_026907	ENSMUSG00000039364	Sectm1b	1810003C24Rik|K12|Sectm1	secreted and transmembrane 1B	protein-coding
mm_151920.1	chr19	5799897	5799912	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	2768	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_50392.1	chr6	48708307	48708332	+	1	NA	promoter-TSS (NM_153175)	promoter-TSS (NM_153175)	-75	NM_153175	231931	Mm.321047	NM_153175	ENSMUSG00000047867	Gimap6	4833419H03Rik|Ian6|mFLJ00102	GTPase, IMAP family member 6	protein-coding
mm_61661.1	chr7	80766426	80766460	+	1	NA	intron (NM_016721, intron 4 of 37)	intron (NM_016721, intron 4 of 37)	36888	NM_016721	29875	Mm.207619	NM_016721	ENSMUSG00000030536	Iqgap1	AA682088|D7Ertd237e|D7Ertd257e|mKIAA0051	IQ motif containing GTPase activating protein 1	protein-coding
mm_61111.1	chr7	54661003	54661016	+	1	NA	Intergenic	Intergenic	-174236	NM_178705	233271	Mm.387344	NM_178705	ENSMUSG00000063297	Luzp2	9330154K17Rik|D130073E01	leucine zipper protein 2	protein-coding
mm_96935.1	chr11	70525910	70525931	+	1	NA	exon (NM_008946, exon 2 of 6)	exon (NM_008946, exon 2 of 6)	563	NM_008946	19175	Mm.98	NM_008946	ENSMUSG00000018286	Psmb6	Lmp19|Mpnd	proteasome (prosome, macropain) subunit, beta type 6	protein-coding
mm_151850.1	chr19	5771619	5771640	-	1	NA	promoter-TSS (NM_023912)	promoter-TSS (NM_023912)	-228	NM_023912	78891	Mm.276063	NM_023912	ENSMUSG00000024941	Scyl1	2810011O19Rik|C85140|Ntkl|mdf|mfd|p105	SCY1-like 1 (S. cerevisiae)	protein-coding
mm_106082.1	chr11	116175160	116175169	-	1	NA	intron (NM_001271898, intron 10 of 13)	intron (NM_001271898, intron 10 of 13)	-6986	NM_172571	217335	Mm.35241	NM_172571	ENSMUSG00000020776	Fbf1	1110033G01Rik|5930413D20|mKIAA1863	Fas (TNFRSF6) binding factor 1	protein-coding
mm_5527.1	chr1	37916413	37916426	-	1	NA	promoter-TSS (NM_001033427)	promoter-TSS (NM_001033427)	74	NM_001033427	332427	Mm.332981	NM_001033427	ENSMUSG00000061584	Lyg2	Gm776	lysozyme G-like 2	protein-coding
mm_164171.1	chr15	74785390	74785438	+	1	NA	Intergenic	Intergenic	-6555	NR_027837	78725	Mm.171357	NM_172433	ENSMUSG00000101026	D730001G18Rik	Ly6g6g	RIKEN cDNA D730001G18 gene	ncRNA
mm_97363.1	chr11	77507159	77507171	+	1	NA	TTS (NM_001024920)	TTS (NM_001024920)	6108	NM_001024920	216964	Mm.341211	NM_001024920	ENSMUSG00000044328	Trp53i13	2410019G02Rik|Tp53i13	transformation related protein 53 inducible protein 13	protein-coding
mm_33525.1	chr4	130932162	130932177	+	1	NA	intron (NM_010686, intron 7 of 7)	MIRb|SINE|MIR	-12216	NM_010769	17180	Mm.271796	NM_010769	ENSMUSG00000040533	Matn1	CMP|Crtm|Mat1|matrilin-1	matrilin 1, cartilage matrix protein	protein-coding
mm_71447.1	chr8	46521495	46521504	+	1	NA	intron (NM_001302163, intron 11 of 20)	intron (NM_001302163, intron 11 of 20)	30533	NM_001302163	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_33356.1	chr4	129464539	129464550	+	1	NA	intron (NM_133889, intron 2 of 10)	intron (NM_133889, intron 2 of 10)	2865	NM_133889	100383	Mm.17918	NM_133889	ENSMUSG00000040859	Bsdc1	1110063F24Rik|AW011758	BSD domain containing 1	protein-coding
mm_102115.1	chr11	53300188	53300198	-	1	NA	5' UTR (NM_008300, exon 1 of 19)	5' UTR (NM_008300, exon 1 of 19)	286	NM_008300	15525	Mm.239865	NM_008300	ENSMUSG00000020361	Hspa4	70kDa|AI317151|APG-2|Hsp110|Hsp70RY|mKIAA4025	heat shock protein 4	protein-coding
mm_41498.1	chr5	92325118	92325127	+	1	NA	exon (NM_008599, exon 3 of 4)	exon (NM_008599, exon 3 of 4)	2957	NM_008599	17329	Mm.766	NM_008599	ENSMUSG00000029417	Cxcl9	BB139920|CMK|Mig|MuMIG|Scyb9|crg-10	chemokine (C-X-C motif) ligand 9	protein-coding
mm_33542.1	chr4	130934560	130934566	+	1	NA	3' UTR (NM_010686, exon 8 of 8)	3' UTR (NM_010686, exon 8 of 8)	-9822	NM_010769	17180	Mm.271796	NM_010769	ENSMUSG00000040533	Matn1	CMP|Crtm|Mat1|matrilin-1	matrilin 1, cartilage matrix protein	protein-coding
mm_167410.1	chr8	105877389	105877405	+	1	NA	intron (NR_033574, intron 4 of 4)	intron (NR_033574, intron 4 of 4)	-3484	NM_001301100	234699	Mm.28979	NM_181594	ENSMUSG00000036270	Edc4	BC022641	enhancer of mRNA decapping 4	protein-coding
mm_103342.1	chr11	74724030	74724091	-	1	NA	promoter-TSS (NR_037610)	promoter-TSS (NR_037610)	-202	NR_037610	18472	Mm.397111	NM_013625	ENSMUSG00000020745	Pafah1b1	LIS-1|Lis1|MMS10-U|Mdsh|Ms10u|Pafaha	platelet-activating factor acetylhydrolase, isoform 1b, subunit 1	protein-coding
mm_163554.1	chr13	23839724	23839732	+	1	NA	intron (NM_001164743, intron 1 of 11)	intron (NM_001164743, intron 1 of 11)	294	NM_134069	105355	Mm.27038	NM_134069	ENSMUSG00000036083	Slc17a3	AW261723|Npt4	solute carrier family 17 (sodium phosphate), member 3	protein-coding
mm_168842.1	chr12	23634715	23634718	-	1	NA	Intergenic	CpG	462553	NM_001256489	66808	Mm.379124	NM_001256489	ENSMUSG00000073158	9030624G23Rik	-	RIKEN cDNA 9030624G23 gene	protein-coding
mm_75222.1	chr8	39608153	39608163	-	1	NA	intron (NM_001113326, intron 7 of 9)	intron (NM_001113326, intron 7 of 9)	34520	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_52200.1	chr6	100704710	100704742	+	1	NA	promoter-TSS (NM_198612)	promoter-TSS (NM_198612)	-8	NM_198612	232313	Mm.272037	NM_198612	ENSMUSG00000030074	Gxylt2	Glt8d4|Gm152	glucoside xylosyltransferase 2	protein-coding
mm_168252.1	chr10	8551661	8551671	-	1	NA	Intergenic	RLTR9E|LTR|ERVK	-32841	NM_177387	338362	Mm.41163	NM_177387	ENSMUSG00000047712	Ust	D930010O20Rik|UA2OST	uronyl-2-sulfotransferase	protein-coding
mm_14138.1	chr2	126152166	126152212	+	1	NA	promoter-TSS (NM_026981)	promoter-TSS (NM_026981)	48	NM_026981	69185	Mm.29019	NM_026981	ENSMUSG00000023330	Dtwd1	1810033A06Rik	DTW domain containing 1	protein-coding
mm_169807.1	chr16	18533292	18533293	-	1	NA	intron (NR_104347, intron 2 of 8)	SSU-rRNA_Hsa|rRNA|rRNA	34421	NR_104347	13972	Mm.236139	NM_023120	ENSMUSG00000000884	Gnb1l	ESTM55|Gm16314|Me49f07|OTTMUSG00000033458|Wdr14|Wdvcf	guanine nucleotide binding protein (G protein), beta polypeptide 1-like	protein-coding
mm_172645.1	chr8	26118977	26118995	-	1	NA	promoter-TSS (NM_029965)	promoter-TSS (NM_029965)	238	NM_207659	320191	Mm.334464	NM_207659	ENSMUSG00000037234	Hook3	5830454D03Rik|AI317159|E330005F07Rik	hook microtubule tethering protein 3	protein-coding
mm_160687.1	chr10	21296014	21296014	+	1	NA	promoter-TSS (NM_001145209)	promoter-TSS (NM_001145209)	35	NM_001145209	56422	Mm.25527	NM_019702	ENSMUSG00000019977	Hbs1l	2810035F15Rik|AI326327|eRFS	Hbs1-like (S. cerevisiae)	protein-coding
mm_23245.1	chr3	51223900	51223912	+	1	NA	promoter-TSS (NM_009834)	promoter-TSS (NM_009834)	-541	NM_009834	12457	Mm.86541	NM_009834	ENSMUSG00000023087	Noct	AU043840|Ccr4|Ccrn4l	nocturnin	protein-coding
mm_60511.1	chr7	44479607	44479638	+	1	NA	Intergenic	L1MC4|LINE|L1	-4895	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_74003.1	chr8	121083331	121083340	+	1	NA	promoter-TSS (NR_045471)	promoter-TSS (NR_045471)	-225	NR_130109	68790	Mm.246916	NR_045471	ENSMUSG00000097336	Fendrr	1110050K14Rik|LL66|linc-Foxf1a|lincFoxf1	Foxf1 adjacent non-coding developmental regulatory RNA	ncRNA
mm_135471.1	chr16	45880713	45880713	-	1	NA	Intergenic	Intergenic	-36335	NM_001252442	208177	Mm.211477	NM_153412	ENSMUSG00000033149	Phldb2	AV253284|C820004H04Rik|LL5b|LL5beta	pleckstrin homology like domain, family B, member 2	protein-coding
mm_123003.1	chr14	54993358	54993382	-	1	NA	intron (NM_080728, intron 2 of 40)	intron (NM_080728, intron 2 of 40)	1179	NM_080728	140781	Mm.457983	NM_080728	ENSMUSG00000053093	Myh7	B-MHC|MyHC-I|Myhc-b|Myhcb|beta-MHC	myosin, heavy polypeptide 7, cardiac muscle, beta	protein-coding
mm_20220.1	chr2	125773413	125773470	-	1	NA	exon (NM_177608, exon 3 of 18)	exon (NM_177608, exon 3 of 18)	9429	NM_177608	70354	Mm.138091	NM_133725	ENSMUSG00000035093	Secisbp2l	3110001I20Rik|AI504340|C630011I23	SECIS binding protein 2-like	protein-coding
mm_137654.1	chr17	28575726	28575743	+	1	NA	promoter-TSS (NM_026571)	promoter-TSS (NM_026571)	15	NM_026571	328789	Mm.284760	NM_026571	ENSMUSG00000062252	Lhfpl5	9330179O15Rik|Tmhs|hscy	lipoma HMGIC fusion partner-like 5	protein-coding
mm_1791.1	chr1	78738127	78738158	+	1	NA	Intergenic	Intergenic	-78807	NM_021342	57814	Mm.24386	NM_021342	ENSMUSG00000047330	Kcne4	AW487937|MiRP3	potassium voltage-gated channel, Isk-related subfamily, gene 4	protein-coding
mm_84192.1	chr9	60521990	60522005	-	1	NA	Intergenic	CpG	-10962	NM_001040426	207596	Mm.28791	NM_172444	ENSMUSG00000032289	Thsd4	ADAMTSL-6|ADAMTSL6|AI585901|Adamtsl4|B230114P05Rik	thrombospondin, type I, domain containing 4	protein-coding
mm_127342.1	chr15	100599773	100599793	+	1	NA	5' UTR (NM_001304965, exon 1 of 11)	5' UTR (NM_001304965, exon 1 of 11)	201	NM_001304965	19009	Mm.28825	NM_010127	ENSMUSG00000009739	Pou6f1	2310038G18Rik|C79593|Emb|cns-1	POU domain, class 6, transcription factor 1	protein-coding
mm_2678.1	chr1	127300005	127300013	+	1	NA	intron (NM_145128, intron 2 of 17)	Lx8|LINE|L1	95023	NM_145128	107895	Mm.214682	NM_145128	ENSMUSG00000036155	Mgat5	4930471A21Rik|5330407H02Rik|AI480971|GlcNAc-TV	mannoside acetylglucosaminyltransferase 5	protein-coding
mm_54054.1	chr6	13839425	13839438	-	1	NA	intron (NM_145066, intron 1 of 3)	intron (NM_145066, intron 1 of 3)	511	NM_001330666	64450	Mm.167625	NM_145066	ENSMUSG00000048216	Gpr85	2900026B03Rik	G protein-coupled receptor 85	protein-coding
mm_151262.1	chr19	54045066	54045082	+	1	NA	promoter-TSS (NM_007417)	promoter-TSS (NM_007417)	-108	NM_007417	11551	Mm.235195	NM_007417	ENSMUSG00000033717	Adra2a	AW122659|Adra-2|Adra-2a|alpha(2A)AR|alpha2-C10|alpha2A|alpha2A-AR	adrenergic receptor, alpha 2a	protein-coding
mm_62240.1	chr7	98703240	98703292	+	1	NA	promoter-TSS (NM_028410)	promoter-TSS (NM_028410)	-97	NM_028410	72981	Mm.4428	NM_028410	ENSMUSG00000030753	Thap12	2900052B10Rik|Dap4|Prkrir|Rpkrir	THAP domain containing 12	protein-coding
mm_112507.1	chr13	8885664	8885674	+	1	NA	promoter-TSS (NM_145360)	promoter-TSS (NM_145360)	63	NM_145360	319554	Mm.29847	NM_145360	ENSMUSG00000058258	Idi1	4832416K17Rik	isopentenyl-diphosphate delta isomerase	protein-coding
mm_137715.1	chr17	29100069	29100112	+	1	NA	3' UTR (NM_007669, exon 3 of 3)	3' UTR (NM_007669, exon 3 of 3)	6321	NM_007669	12575	Mm.195663	NM_007669	ENSMUSG00000023067	Cdkn1a	CAP20|CDKI|CIP1|Cdkn1|P21|SDI1|Waf1|mda6|p21Cip1|p21WAF	cyclin-dependent kinase inhibitor 1A (P21)	protein-coding
mm_108350.1	chr12	80507205	80507207	+	1	NA	promoter-TSS (NR_045490)	promoter-TSS (NR_045490)	0	NR_045490	69522	Mm.390530	NR_045490		2310002D06Rik	-	RIKEN cDNA 2310002D06 gene	ncRNA
mm_120952.1	chr14	76780850	76780857	+	1	NA	Intergenic	Intergenic	103285	NR_015485	73272	Mm.116804	NR_015485	ENSMUSG00000101009	1700108F19Rik	1700020I02Rik|BB065030	RIKEN cDNA 1700108F19 gene	ncRNA
mm_32167.1	chr4	100227731	100227731	+	1	NA	intron (NM_001312690, intron 1 of 3)	intron (NM_001312690, intron 1 of 3)	131940	NM_001312690	26563	Mm.57252	NM_013845	ENSMUSG00000035305	Ror1	2810404D04Rik|Ntrkr1	receptor tyrosine kinase-like orphan receptor 1	protein-coding
mm_75505.1	chr8	54078001	54078023	-	1	NA	intron (NM_009506, intron 1 of 6)	intron (NM_009506, intron 1 of 6)	480	NM_009506	22341	Mm.1402	NM_009506	ENSMUSG00000031520	Vegfc	AW228853|VEGF-C	vascular endothelial growth factor C	protein-coding
mm_65268.1	chr7	19950730	19950748	-	1	NA	promoter-TSS (NM_027308)	promoter-TSS (NM_027308)	4	NM_027308	70080	Mm.98583	NM_027308	ENSMUSG00000040498	Igsf23	2210010C17Rik	immunoglobulin superfamily, member 23	protein-coding
mm_7089.1	chr1	88584649	88584661	-	1	NA	Intergenic	Intergenic	33138	NR_037971	100503197	Mm.99352	NR_037971	ENSMUSG00000100798	Gm19589	-	predicted gene, 19589	ncRNA
mm_61293.1	chr7	67655147	67655181	+	1	NA	intron (NM_001168476, intron 1 of 9)	intron (NM_001168476, intron 1 of 9)	7754	NM_025905	67009	Mm.249356	NM_025905	ENSMUSG00000030555	Ttc23	1600012K10Rik	tetratricopeptide repeat domain 23	protein-coding
mm_87958.1	chr10	63243889	63243964	+	1	NA	5' UTR (NM_026101, exon 1 of 25)	5' UTR (NM_026101, exon 1 of 25)	129	NM_026101	67345	Mm.234437	NM_026101	ENSMUSG00000020064	Herc4	1700056O17Rik|4921531D01Rik|9530080M15Rik|mKIAA1593	hect domain and RLD 4	protein-coding
mm_116055.1	chr13	27438616	27438626	-	1	NA	promoter-TSS (NM_011167)	promoter-TSS (NM_011167)	67	NM_001271379	19112	Mm.142728	NM_011167	ENSMUSG00000021345	Prl8a6	Ghd13|PLP-C1|PLP-Ca|PLP-calpha|Prlpc|Prlpc1	prolactin family 8, subfamily a, member 6	protein-coding
mm_38422.1	chr4	139192642	139192658	-	1	NA	promoter-TSS (NM_009798)	promoter-TSS (NM_009798)	-249	NM_009798	12345	Mm.2945	NM_009798	ENSMUSG00000028745	Capzb	1700120C01Rik|AI325129|CPB1|CPB2|CPbeat2|CPbeta1|CPbeta2|Cappb1	capping protein (actin filament) muscle Z-line, beta	protein-coding
mm_10816.1	chr2	24350377	24350383	+	1	NA	3' UTR (NM_031167, exon 5 of 5)	3' UTR (NM_031167, exon 5 of 5)	5009	NM_001039701	16181	Mm.882	NM_031167	ENSMUSG00000026981	Il1rn	F630041P17Rik|IL-1ra	interleukin 1 receptor antagonist	protein-coding
mm_83822.1	chr9	53936091	53936097	-	1	NA	intron (NM_177769, intron 2 of 10)	intron (NM_177769, intron 2 of 10)	39207	NM_177769	270162	Mm.259791	NM_177769	ENSMUSG00000041986	Elmod1	4831417L10|AI428506|AI834991	ELMO/CED-12 domain containing 1	protein-coding
mm_112680.1	chr13	16028552	16028567	+	1	NA	3' UTR (NM_008380, exon 5 of 5)	3' UTR (NM_008380, exon 5 of 5)	16708	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_138410.1	chr17	35068695	35068712	+	1	NA	intron (NM_023463, intron 1 of 2)	intron (NM_023463, intron 1 of 2)	1378	NM_023463	68468	Mm.215096	NM_023463	ENSMUSG00000092586	Ly6g6c	1110003M04Rik|AU016360|G6c|NG24	lymphocyte antigen 6 complex, locus G6C	protein-coding
mm_116381.1	chr13	41078039	41078074	-	1	NA	intron (NM_001145802, intron 1 of 11)	intron (NM_001145802, intron 1 of 11)	1650	NM_001145803	17152	Mm.8149	NM_008547	ENSMUSG00000021363	Mak	A930010O05Rik	male germ cell-associated kinase	protein-coding
mm_110621.1	chr12	57151129	57151132	-	1	NA	intron (NM_172577, intron 1 of 9)	intron (NM_172577, intron 1 of 9)	9513	NM_001167976	217593	Mm.32835	NM_172577	ENSMUSG00000035472	Slc25a21	9930033G19Rik|A630030I10|BB158148	solute carrier family 25 (mitochondrial oxodicarboxylate carrier), member 21	protein-coding
mm_119917.1	chr14	54953475	54953501	+	1	NA	exon (NM_010856, exon 22 of 39)	exon (NM_010856, exon 22 of 39)	-4346	NR_029724	387204		NR_029724	ENSMUSG00000065432	Mir208a	Mirn208|Mirn208a|mir-208|mir-208a|mmu-mir-208	microRNA 208a	ncRNA
mm_122820.1	chr14	54641348	54641374	-	1	NA	promoter-TSS (NM_199470)	promoter-TSS (NM_199470)	3	NM_199470	239096	Mm.386871	NM_199470	ENSMUSG00000059674	Cdh24	1700040A22Rik|ENSMUSG00000022188	cadherin-like 24	protein-coding
mm_34329.1	chr4	142078279	142078290	+	1	NA	intron (NM_145402, intron 1 of 2)	intron (NM_145402, intron 1 of 2)	-6014	NR_027137	100038693	Mm.402714	NR_027137	ENSMUSG00000073728	Tmem51os1	ENSMUSG00000073728|Gm10565|Tmem51as1	Tmem51 opposite strand 1	ncRNA
mm_168214.1	chr10	75860243	75860246	-	1	NA	promoter-TSS (NM_010798)	promoter-TSS (NM_010798)	6	NM_010798	17319	Mm.2326	NM_010798	ENSMUSG00000033307	Mif	GIF|Glif	macrophage migration inhibitory factor	protein-coding
mm_74707.1	chr8	17106662	17106664	-	1	NA	intron (NM_053171, intron 2 of 69)	intron (NM_053171, intron 2 of 69)	428722	NM_053171	94109	Mm.436988	NM_053171	ENSMUSG00000060924	Csmd1	B930082H09|mKIAA1890	CUB and Sushi multiple domains 1	protein-coding
mm_56741.1	chr6	115808766	115808779	-	1	NA	promoter-TSS (NR_028546)	promoter-TSS (NR_028546)	-29	NM_172086	19951	Mm.104368	NM_172086	ENSMUSG00000057841	Rpl32	AU020185|rpL32-3A	ribosomal protein L32	protein-coding
mm_15639.1	chr2	163054652	163054677	+	1	NA	promoter-TSS (NM_008652)	promoter-TSS (NM_008652)	29	NM_008652	17865	Mm.4594	NM_008652	ENSMUSG00000017861	Mybl2	B-Myb|Bmyb	myeloblastosis oncogene-like 2	protein-coding
mm_102852.1	chr11	69395433	69395478	-	1	NA	promoter-TSS (NM_030083)	promoter-TSS (NM_030083)	-109	NM_001045525	327951	Mm.415669	NM_001045525	ENSMUSG00000044795	Cyb5d1	Gm740	cytochrome b5 domain containing 1	protein-coding
mm_93309.1	chr10	98744306	98744314	-	1	NA	Intergenic	Intergenic	-170842	NM_026482	67972	Mm.166944	NM_026482	ENSMUSG00000019943	Atp2b1	2810442I22Rik|E130111D10Rik|Pmca1	ATPase, Ca++ transporting, plasma membrane 1	protein-coding
mm_162727.1	chr10	41239866	41239866	+	1	NA	intron (NM_133999, intron 16 of 22)	B1F|SINE|Alu	63375	NM_133999	103199	Mm.277242	NM_133999	ENSMUSG00000038417	Fig4	A530089I17Rik|AI326867|Sac3	FIG4 phosphoinositide 5-phosphatase	protein-coding
mm_3519.1	chr1	150107511	150107513	+	1	NA	3' UTR (NM_011198, exon 10 of 10)	3' UTR (NM_011198, exon 10 of 10)	7481	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_22568.1	chr3	10014511	10014513	+	1	NA	intron (NM_001272098, intron 1 of 2)	intron (NM_001272098, intron 1 of 2)	1927	NM_001272098	16592	Mm.741	NM_010634	ENSMUSG00000027533	Fabp5	E-FABP|Fabpe|Klbp|PA-FABP|mal1	fatty acid binding protein 5, epidermal	protein-coding
mm_1837.1	chr1	82824946	82824953	+	1	NA	Intergenic	Intergenic	-14511	NM_001310713	15463	Mm.392569	NM_010472	ENSMUSG00000026159	Agfg1	AU045498|C130049H11Rik|C85612|D730048C23Rik|Hrb|RAB|Rip	ArfGAP with FG repeats 1	protein-coding
mm_112464.1	chr13	5867738	5867757	+	1	NA	3' UTR (NM_011803, exon 4 of 4)	3' UTR (NM_011803, exon 4 of 4)	6258	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_44886.1	chr5	34660069	34660138	-	1	NA	promoter-TSS (NM_019497)	promoter-TSS (NM_019497)	45	NM_029278	75416	Mm.40292	NM_029278	ENSMUSG00000036693	Nop14	2610033H07Rik|Nol14	NOP14 nucleolar protein	protein-coding
mm_56960.1	chr6	120038024	120038050	-	1	NA	5' UTR (NM_001185020, exon 1 of 26)	5' UTR (NM_001185020, exon 1 of 26)	618	NM_001199083	232341	Mm.333349	NM_198703	ENSMUSG00000045962	Wnk1	6430573H23Rik|EG406236|Hsn2|Prkwnk1|mKIAA0344	WNK lysine deficient protein kinase 1	protein-coding
mm_99965.1	chr11	113684511	113684514	+	1	NA	promoter-TSS (NM_138598)	promoter-TSS (NM_138598)	100	NM_177777	276852	Mm.239566	NM_177777	ENSMUSG00000041623	D11Wsu47e	-	DNA segment, Chr 11, Wayne State University 47, expressed	protein-coding
mm_37665.1	chr4	129111865	129111881	-	1	NA	TTS (NM_001290706)	TTS (NM_001290706)	6325	NM_001290706	66260	Mm.25295	NM_025452	ENSMUSG00000028786	Tmem54	1810017F10Rik|AI507302	transmembrane protein 54	protein-coding
mm_160247.1	chr7	105337855	105337855	-	1	NA	promoter-TSS (NM_147061)	promoter-TSS (NM_147061)	-141	NM_147061	259063	Mm.377817	NM_147061	ENSMUSG00000043948	Olfr691	MOR31-6	olfactory receptor 691	protein-coding
mm_144486.1	chr18	24121615	24121645	+	1	NA	intron (NM_172625, intron 1 of 4)	CpG	189	NM_172625	225280	Mm.258973	NM_172625	ENSMUSG00000047989	Ino80c	D030070L09Rik	INO80 complex subunit C	protein-coding
mm_137770.1	chr17	29490847	29490862	+	1	NA	promoter-TSS (NM_008842)	promoter-TSS (NM_008842)	-191	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_118802.1	chr14	25178805	25178805	+	1	NA	Intergenic	Intergenic	-35564	NR_045718	75862	Mm.109191	NR_045718		4930572O13Rik	-	RIKEN cDNA 4930572O13 gene	ncRNA
mm_65902.1	chr7	30192907	30192930	-	1	NA	intron (NM_009795, intron 2 of 10)	intron (NM_009795, intron 2 of 10)	2130	NM_009795	12336	Mm.439782	NM_009795	ENSMUSG00000001794	Capns1	Capa-4|Capa4|Capn4|D7Ertd146e	calpain, small subunit 1	protein-coding
mm_161982.1	chr19	22915985	22915985	+	1	NA	intron (NM_001035243, intron 18 of 23)	intron (NM_001035243, intron 18 of 23)	165380	NR_029591	387200		NR_029591	ENSMUSG00000065507	Mir204	Mirn204|mir-204|mmu-mir-204	microRNA 204	ncRNA
mm_139812.1	chr17	66485248	66485306	+	1	NA	Intergenic	RLTR23|LTR|ERV1	34393	NM_024448	19328	Mm.248313	NM_024448	ENSMUSG00000023460	Rab12	2900054P15Rik|AW555448|C77700	RAB12, member RAS oncogene family	protein-coding
mm_86701.1	chr10	18526337	18526339	+	1	NA	exon (NM_001163592, exon 6 of 8)	exon (NM_001163592, exon 6 of 8)	19738	NM_019487	56016	Mm.35551	NM_019487	ENSMUSG00000019853	Hebp2	SOUL	heme binding protein 2	protein-coding
mm_22553.1	chr3	9608827	9608841	+	1	NA	intron (NM_133218, intron 1 of 8)	intron (NM_133218, intron 1 of 8)	1251	NM_133218	170753	Mm.212908	NM_133218	ENSMUSG00000040209	Zfp704	C030026M03|C030034L19Rik|Gig1|Znf704	zinc finger protein 704	protein-coding
mm_29116.1	chr3	104961696	104961728	-	1	NA	promoter-TSS (NM_009520)	promoter-TSS (NM_009520)	-3	NM_009520	22414	Mm.10740	NM_009520	ENSMUSG00000027840	Wnt2b	Wnt13	wingless-type MMTV integration site family, member 2B	protein-coding
mm_159419.1	chr3	107183164	107183164	+	1	NA	promoter-TSS (NM_001081140)	promoter-TSS (NM_001081140)	21	NM_001081140	242151	Mm.245155	NM_001081140	ENSMUSG00000042861	Kcna10	Gm1962|Kcna8|Kv1.8	potassium voltage-gated channel, shaker-related subfamily, member 10	protein-coding
mm_110732.1	chr12	69769734	69769742	-	1	NA	intron (NM_183294, intron 2 of 9)	intron (NM_183294, intron 2 of 9)	-5794	NR_030450	751538		NR_030450	ENSMUSG00000076065	Mir681	Mirn681|mmu-mir-681	microRNA 681	ncRNA
mm_6048.1	chr1	60042932	60042975	-	1	NA	5' UTR (NM_027407, exon 1 of 11)	5' UTR (NM_027407, exon 1 of 11)	169	NM_001316694	70375	Mm.17834	NM_027407	ENSMUSG00000026018	Ica1l	1700030B17Rik|Als2cr15	islet cell autoantigen 1-like	protein-coding
mm_101935.1	chr11	50207250	50207262	-	1	NA	exon (NM_011018, exon 4 of 8)	exon (NM_011018, exon 4 of 8)	3564	NM_001290769	18412	Mm.40828	NM_011018	ENSMUSG00000015837	Sqstm1	A170|OSF-6|Osi|STAP|STONE14|p62	sequestosome 1	protein-coding
mm_133125.1	chr16	65815848	65815860	+	1	NA	intron (NM_028572, intron 1 of 3)	intron (NM_028572, intron 1 of 3)	221	NM_028572	73569	Mm.25670	NM_028572	ENSMUSG00000091243	Vgll3	1700110N18Rik|4832416J22|C80713|Vgl-3|Vito-2	vestigial like family member 3	protein-coding
mm_70514.1	chr8	12947866	12947931	+	1	NA	promoter-TSS (NR_128567)	promoter-TSS (NR_128567)	-43	NR_128567	104797311		NR_128567	ENSMUSG00000105030	Gm38671	Mir9768|mmu-mir-9768	predicted gene, 38671	ncRNA
mm_124587.1	chr15	3271391	3271410	+	1	NA	intron (NM_009155, intron 1 of 4)	intron (NM_009155, intron 1 of 4)	423	NM_009155	20363	Mm.392203	NM_009155	ENSMUSG00000064373	Selenop	AU018766|D15Ucla1|Se-P|Sepp1|selp	selenoprotein P	protein-coding
mm_5273.1	chr1	18223604	18223608	-	1	NA	promoter-TSS (NR_002879)	promoter-TSS (NR_002879)	-42	NR_002879	654454	Mm.383637	NR_002879	ENSMUSG00000070977	Defb44-ps	Defb44|Defb49|Defb49-ps|EG574082	defensin beta 44, pseudogene	pseudo
mm_35533.1	chr4	41314728	41314758	-	1	NA	5' UTR (NM_026893, exon 1 of 9)	5' UTR (NM_026893, exon 1 of 9)	158	NM_026893	68970	Mm.28891	NM_026893	ENSMUSG00000028436	Dcaf12	1500001L20Rik|5830424K06Rik|AA420338|AI851081|Wdr40a	DDB1 and CUL4 associated factor 12	protein-coding
mm_142800.1	chr17	50293593	50293606	-	1	NA	promoter-TSS (NM_010021)	promoter-TSS (NM_010021)	21	NM_010021	13164	Mm.280641	NM_010021	ENSMUSG00000010592	Dazl	Daz-like|Dazh|Dazl1|Dazla|Tpx-2|Tpx2	deleted in azoospermia-like	protein-coding
mm_91398.1	chr10	30802855	30802865	-	1	NA	5' UTR (NM_172495, exon 1 of 16)	5' UTR (NM_172495, exon 1 of 16)	247	NM_172495	211329	Mm.297903	NM_172495	ENSMUSG00000039697	Ncoa7	9030406N13Rik	nuclear receptor coactivator 7	protein-coding
mm_149532.1	chr19	12464808	12464818	+	1	NA	3' UTR (NM_010821, exon 2 of 2)	3' UTR (NM_010821, exon 2 of 2)	4034	NM_010821	17476	Mm.3999	NM_010821	ENSMUSG00000046805	Mpeg1	MPS1|Mpg-1	macrophage expressed gene 1	protein-coding
mm_100761.1	chr11	4497557	4497585	-	1	NA	intron (NM_028860, intron 10 of 17)	intron (NM_028860, intron 10 of 17)	-56489	NM_029458	75828	Mm.159592	NM_029458	ENSMUSG00000020419	Hormad2	4930529M09Rik	HORMA domain containing 2	protein-coding
mm_3357.1	chr1	138172305	138172315	+	1	NA	intron (NM_001111316, intron 1 of 31)	intron (NM_001111316, intron 1 of 31)	2816	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_89062.1	chr10	82896869	82896880	+	1	NA	3' UTR (NM_001042523, exon 15 of 15)	3' UTR (NM_001042523, exon 15 of 15)	30248	NM_025499	66341	Mm.443284	NM_025499	ENSMUSG00000109864	Eid3	1700027M21Rik|NS4EB	EP300 interacting inhibitor of differentiation 3	protein-coding
mm_127869.1	chr15	8436657	8436660	-	1	NA	intron (NM_201232, intron 1 of 45)	RCHARR1|DNA|hAT-Charlie	7805	NM_027707	71175	Mm.240329	NM_027707	ENSMUSG00000022141	Nipbl	Idn3	Nipped-B homolog (Drosophila)	protein-coding
mm_168195.1	chr10	64400020	64400025	-	1	NA	intron (NM_177612, intron 9 of 17)	(A)n|Simple_repeat|Simple_repeat	-309767	NM_178678	216028	Mm.431318	NM_178678	ENSMUSG00000042846	Lrrtm3	9630044H04Rik	leucine rich repeat transmembrane neuronal 3	protein-coding
mm_81390.1	chr9	108984883	108984899	+	1	NA	TTS (NM_007738)	TTS (NM_007738)	-1272	NM_145077	171530	Mm.388865	NM_145077	ENSMUSG00000049699	Ucn2	Ucn II|Ucn-2|ucn-II	urocortin 2	protein-coding
mm_143693.1	chr17	80373222	80373232	-	1	NA	non-coding (NR_028385, exon 1 of 1)	non-coding (NR_028385, exon 1 of 1)	315	NR_028385	791338	Mm.204722	NR_028385		Gm10190	ENSMUSG00000066938	predicted gene 10190	ncRNA
mm_20578.1	chr2	131141719	131141721	-	1	NA	TTS (NR_037281)	TTS (NR_037281)	14308	NM_028306	72630	Mm.277465	NM_028306	ENSMUSG00000074793	Hspa12b	2700081N06Rik	heat shock protein 12B	protein-coding
mm_85071.1	chr9	91350912	91350965	-	1	NA	Intergenic	Intergenic	14861	NM_009573	22771	Mm.335350	NM_009573	ENSMUSG00000032368	Zic1	ZIC|ZNF201	zinc finger protein of the cerebellum 1	protein-coding
mm_71773.1	chr8	66469164	66469195	+	1	NA	3' UTR (NM_001293784, exon 9 of 9)	3' UTR (NM_001293784, exon 9 of 9)	17328	NM_025465	66282	Mm.294985	NM_025465	ENSMUSG00000025591	Tma16	1810029B16Rik	translation machinery associated 16	protein-coding
mm_23727.1	chr3	69019252	69019263	+	1	NA	exon (NM_133786, exon 9 of 24)	exon (NM_133786, exon 9 of 24)	9355	NR_029735	723949		NR_029735	ENSMUSG00000065606	Mir16-2	Mirn16-2|mir-16-2	microRNA 16-2	ncRNA
mm_22567.1	chr3	10013216	10013263	+	1	NA	intron (NM_001272098, intron 1 of 2)	intron (NM_001272098, intron 1 of 2)	654	NM_001272098	16592	Mm.741	NM_010634	ENSMUSG00000027533	Fabp5	E-FABP|Fabpe|Klbp|PA-FABP|mal1	fatty acid binding protein 5, epidermal	protein-coding
mm_59592.1	chr7	28137105	28137111	+	1	NA	exon (NM_001164655, exon 4 of 20)	exon (NM_001164655, exon 4 of 20)	7642	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_16179.1	chr2	172588760	172588768	+	1	NA	Intergenic	Intergenic	37773	NM_001159696	21420	Mm.3629	NM_009335	ENSMUSG00000028640	Tfap2c	AA409384|AP2gamma|Ap-2.2|Stra2|Tcfap2c	transcription factor AP-2, gamma	protein-coding
mm_144307.1	chr18	12504179	12504207	+	1	NA	promoter-TSS (NM_001347461)	promoter-TSS (NM_001347461)	-6	NM_001347461	16774	Mm.42012	NM_010680	ENSMUSG00000024421	Lama3	Lama3B|[a]3B	laminin, alpha 3	protein-coding
mm_122199.1	chr14	31781489	31781501	-	1	NA	intron (NM_001024604, intron 1 of 27)	intron (NM_001024604, intron 1 of 27)	48920	NM_001024604	105522	Mm.37660	NM_001024604	ENSMUSG00000014496	Ankrd28	AI465466|AI604979|E430019N21Rik|mKIAA0379	ankyrin repeat domain 28	protein-coding
mm_159148.1	chr2	87711687	87711687	-	1	NA	exon (NM_001011833, exon 1 of 1)	exon (NM_001011833, exon 1 of 1)	217	NM_001011833	258101	Mm.377350	NM_001011833	ENSMUSG00000075150	Olfr1137	MOR177-20|MOR40-9P	olfactory receptor 1137	protein-coding
mm_47579.1	chr5	124552805	124552834	-	1	NA	promoter-TSS (NM_001190795)	promoter-TSS (NM_001190795)	-45	NM_001190795	67848	Mm.281601	NM_026409	ENSMUSG00000029389	Ddx55	2810021H22Rik|mKIAA1595	DEAD (Asp-Glu-Ala-Asp) box polypeptide 55	protein-coding
mm_63523.1	chr7	127904355	127904367	+	1	NA	intron (NM_009739, intron 1 of 11)	intron (NM_009739, intron 1 of 11)	288	NM_009739	12041	Mm.425495	NM_009739	ENSMUSG00000030802	Bckdk	AI327402	branched chain ketoacid dehydrogenase kinase	protein-coding
mm_28687.1	chr3	95511736	95511740	-	1	NA	Intergenic	B1_Mur2|SINE|Alu	12528	NM_007802	13038	Mm.272085	NM_007802	ENSMUSG00000028111	Ctsk	AI323530|MMS10-Q|Ms10q|catK	cathepsin K	protein-coding
mm_60656.1	chr7	44929719	44929725	+	1	NA	promoter-TSS (NM_001077264)	promoter-TSS (NM_001077264)	-232	NM_001077264	11771	Mm.6877	NM_007458	ENSMUSG00000060279	Ap2a1	Adtaa	adaptor-related protein complex 2, alpha 1 subunit	protein-coding
mm_37335.1	chr4	119656740	119656762	-	1	NA	3' UTR (NM_008191, exon 3 of 3)	3' UTR (NM_008191, exon 3 of 3)	2194	NM_008191	14916	Mm.278	NM_008191	ENSMUSG00000032978	Guca2b	AV066530|Gcap2|Ugn	guanylate cyclase activator 2b (retina)	protein-coding
mm_56623.1	chr6	112721767	112721778	-	1	NA	3' UTR (NM_080448, exon 22 of 22)	3' UTR (NM_080448, exon 22 of 22)	-25102	NM_001167730	58186	Mm.103812	NM_021385	ENSMUSG00000030254	Rad18	2810024C04Rik|Rad18sc	RAD18 E3 ubiquitin protein ligase	protein-coding
mm_137496.1	chr17	26970988	26970994	+	1	NA	TTS (NM_001281491)	TTS (NM_001281491)	-2188	NM_001005916	474156	Mm.328890	NM_001005916	ENSMUSG00000079605	Zbtb9	3930402F13Rik	zinc finger and BTB domain containing 9	protein-coding
mm_57321.1	chr6	124733068	124733120	-	1	NA	promoter-TSS (NM_013545)	promoter-TSS (NM_013545)	60	NM_013545	15170	Mm.271799	NM_013545	ENSMUSG00000004266	Ptpn6	70Z-SHP|Hcph|PTPTY-42|Ptp1C|SH-PTP1|SHP-1|hcp|me	protein tyrosine phosphatase, non-receptor type 6	protein-coding
mm_20224.1	chr2	125782735	125782772	-	1	NA	5' UTR (NM_177608, exon 1 of 18)	5' UTR (NM_177608, exon 1 of 18)	117	NM_177608	70354	Mm.138091	NM_133725	ENSMUSG00000035093	Secisbp2l	3110001I20Rik|AI504340|C630011I23	SECIS binding protein 2-like	protein-coding
mm_102106.1	chr11	53257708	53257715	-	1	NA	Intergenic	Intergenic	42768	NM_008300	15525	Mm.239865	NM_008300	ENSMUSG00000020361	Hspa4	70kDa|AI317151|APG-2|Hsp110|Hsp70RY|mKIAA4025	heat shock protein 4	protein-coding
mm_169596.1	chr15	32856736	32856741	+	1	NA	Intergenic	Lx7|LINE|L1	-63985	NM_008304	15529	Mm.234266	NM_008304	ENSMUSG00000022261	Sdc2	4833414L08Rik|AA960457|Hspg1|Synd2|syndecan-2	syndecan 2	protein-coding
mm_80224.1	chr9	72661982	72662012	+	1	NA	promoter-TSS (NM_010890)	promoter-TSS (NM_010890)	-350	NM_010890	17999	Mm.279923	NM_010890	ENSMUSG00000032216	Nedd4	AA959633|AL023035|AU019897|E430025J12Rik|Nedd4-1|Nedd4a|mKIAA0093	neural precursor cell expressed, developmentally down-regulated 4	protein-coding
mm_49701.1	chr6	34179302	34179309	+	1	NA	Intergenic	(CCAA)n|Simple_repeat|Simple_repeat	-2251	NM_021435	58246	Mm.245527	NM_021435	ENSMUSG00000018999	Slc35b4	4930474D06Rik|AB041549|AW494345	solute carrier family 35, member B4	protein-coding
mm_13899.1	chr2	120463567	120463594	+	1	NA	promoter-TSS (NM_007601)	promoter-TSS (NM_007601)	-13	NM_001177799	12335	Mm.458021	NM_007601	ENSMUSG00000079110	Capn3	AI323605|Capa-3|Capa3|Lp82|p94	calpain 3	protein-coding
mm_109403.1	chr12	110444687	110444697	+	1	NA	Intergenic	RMER15|LTR|ERVL	-2487	NM_001135001	26931	Mm.240396	NM_012023	ENSMUSG00000017843	Ppp2r5c	2610043M05Rik|2700063L20Rik|AI060890|AW545884|C85228|D12Bwg0916e|mKIAA0044	protein phosphatase 2, regulatory subunit B', gamma	protein-coding
mm_154475.1	chrM	4089	4126	-	1	NA	NA	Intergenic	NA	NA								
mm_98523.1	chr11	94967623	94967639	+	1	NA	promoter-TSS (NM_018792)	promoter-TSS (NM_018792)	38	NM_018792	54388	Mm.30482	NM_018792	ENSMUSG00000038994	Hils1	H1.9|TISP64	histone H1-like protein in spermatids 1	protein-coding
mm_52639.1	chr6	117174732	117174740	+	1	NA	3' UTR (NM_021704, exon 3 of 3)	3' UTR (NM_021704, exon 3 of 3)	6201	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_49359.1	chr6	22440129	22440142	+	1	NA	Intergenic	Intergenic	-84054	NM_138587	27999	Mm.490307	NM_138587	ENSMUSG00000029672	Fam3c	D6Wsu176e|Ilei	family with sequence similarity 3, member C	protein-coding
mm_162387.1	chr1	75210718	75210730	-	1	NA	promoter-TSS (NM_011494)	promoter-TSS (NM_011494)	54	NM_029010	74577	Mm.458319	NM_029010	ENSMUSG00000026200	Glb1l	4833408P15Rik	galactosidase, beta 1-like	protein-coding
mm_165120.1	chr2	3779888	3779917	+	1	NA	3' UTR (NM_025626, exon 4 of 4)	3' UTR (NM_025626, exon 4 of 4)	66444	NM_025626	66540	Mm.277864	NM_025626	ENSMUSG00000026655	Fam107b	3110001A13Rik|AA589595|AA959793|AI132312	family with sequence similarity 107, member B	protein-coding
mm_129080.1	chr15	75841938	75841954	-	1	NA	promoter-TSS (NM_172121)	promoter-TSS (NM_172121)	-38	NM_172121	223642	Mm.209800	NM_172121	ENSMUSG00000075600	Zc3h3	BC049953|Kiaa0150|Smicl|Zc3hdc3	zinc finger CCCH type containing 3	protein-coding
mm_83485.1	chr9	45935888	45935903	-	1	NA	5' UTR (NM_011526, exon 1 of 5)	5' UTR (NM_011526, exon 1 of 5)	163	NM_011526	21345	Mm.283283	NM_011526	ENSMUSG00000032085	Tagln	Sm22|Sm22a|Ws310	transgelin	protein-coding
mm_51872.1	chr6	90552250	90552262	+	1	NA	intron (NM_027406, intron 1 of 22)	(CA)n|Simple_repeat|Simple_repeat	1408	NM_027406	107747	Mm.30035	NM_027406	ENSMUSG00000030088	Aldh1l1	1810048F20Rik|FDH|Fthfd|Neut2	aldehyde dehydrogenase 1 family, member L1	protein-coding
mm_85616.1	chr9	107614616	107614679	-	1	NA	3' UTR (NM_008138, exon 9 of 9)	3' UTR (NM_008138, exon 9 of 9)	-5406	NM_001291539	20347	Mm.4083	NM_009153	ENSMUSG00000057969	Sema3b	SemA|Semaa|sema5|semaV	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B	protein-coding
mm_144117.1	chr18	4484718	4484727	+	1	NA	Intergenic	Intergenic	109130	NM_026157	67440	Mm.49826	NM_026157	ENSMUSG00000024234	Mtpap	0610027A18Rik|AW551379|Papd1	mitochondrial poly(A) polymerase	protein-coding
mm_138943.1	chr17	44038976	44038987	+	1	NA	3' UTR (NM_207649, exon 5 of 5)	3' UTR (NM_207649, exon 5 of 5)	-39821	NM_001168620	83965	Mm.30145	NM_032003	ENSMUSG00000023960	Enpp5	AW061004|D17Abb1e|E-NPP 5	ectonucleotide pyrophosphatase/phosphodiesterase 5	protein-coding
mm_121644.1	chr14	8666237	8666279	-	1	NA	promoter-TSS (NM_028934)	promoter-TSS (NM_028934)	32	NM_028934	74430	Mm.271901	NM_028934	ENSMUSG00000021747	4930452B06Rik	4933406L09Rik|AI854000	RIKEN cDNA 4930452B06 gene	protein-coding
mm_116508.1	chr13	45553119	45553127	-	1	NA	3' UTR (NM_009124, exon 8 of 8)	3' UTR (NM_009124, exon 8 of 8)	45679	NM_025508	66355	Mm.290802	NM_025508	ENSMUSG00000000253	Gmpr	2310004P21Rik|AV028449|GMPR 1	guanosine monophosphate reductase	protein-coding
mm_86135.1	chr9	116618491	116618503	-	1	NA	intron (NM_001172122, intron 11 of 13)	intron (NM_001172122, intron 11 of 13)	-443134	NM_009371	21813	Mm.172346	NM_009371	ENSMUSG00000032440	Tgfbr2	1110020H15Rik|AU042018|DNIIR|RIIDN|TBR-II|TbetaR-II|TbetaRII	transforming growth factor, beta receptor II	protein-coding
mm_129460.1	chr15	78572755	78572790	-	1	NA	promoter-TSS (NM_009008)	promoter-TSS (NM_009008)	11	NM_009008	19354	Mm.1972	NM_009008	ENSMUSG00000033220	Rac2	AI323801|AI452260	RAS-related C3 botulinum substrate 2	protein-coding
mm_31572.1	chr4	57595082	57595098	+	1	NA	intron (NM_001304544, intron 1 of 8)	intron (NM_001304544, intron 1 of 8)	26842	NM_172868	242481	Mm.331630	NM_172868	ENSMUSG00000090053	Palm2	53-H12|B130066I24|R75368|pEN70	paralemmin 2	protein-coding
mm_83874.1	chr9	55048562	55048593	-	1	NA	promoter-TSS (NM_148944)	promoter-TSS (NM_148944)	-33	NM_148944	108015	Mm.32694	NM_148944	ENSMUSG00000035200	Chrnb4	Acrb-4|Acrb4	cholinergic receptor, nicotinic, beta polypeptide 4	protein-coding
mm_57823.1	chr6	129462884	129462894	-	1	NA	non-coding (NR_132130, exon 6 of 6)	non-coding (NR_132130, exon 6 of 6)	9890	NM_001309637	56644	Mm.239516	NM_020008	ENSMUSG00000079293	Clec7a	BGR|Clecsf12|beta-GR	C-type lectin domain family 7, member a	protein-coding
mm_31774.1	chr4	63558749	63558859	+	1	NA	Intergenic	CpG	-1556	NM_144905	230279	Mm.41523	NM_144905	ENSMUSG00000045917	Tmem268	6330416G13Rik|AW492431|bM230C2.2	transmembrane protein 268	protein-coding
mm_11847.1	chr2	45197780	45197790	+	1	NA	Intergenic	Intergenic	-84506	NM_015753	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_165190.1	chr2	30469221	30469222	-	1	NA	Intergenic	Intergenic	4978	NM_030244	72500	Mm.295464	NM_030244	ENSMUSG00000089762	Ier5l	2610524G09Rik	immediate early response 5-like	protein-coding
mm_75656.1	chr8	65129582	65129599	-	1	NA	promoter-TSS (NR_033217)	promoter-TSS (NR_033217)	-53	NR_033217	407795	Mm.387876	NR_033217	ENSMUSG00000074300	BC030870	-	cDNA sequence BC030870	ncRNA
mm_34042.1	chr4	138216412	138216464	+	1	NA	promoter-TSS (NM_001122896)	promoter-TSS (NM_001122896)	-174	NM_001122896	15441	Mm.348429	NM_010470	ENSMUSG00000028759	Hp1bp3	Hp1bp74	heterochromatin protein 1, binding protein 3	protein-coding
mm_38019.1	chr4	133754323	133754378	-	1	NA	promoter-TSS (NM_001080819)	promoter-TSS (NM_001080819)	-739	NM_001080819	93760	Mm.22478	NM_001080819	ENSMUSG00000007880	Arid1a	1110030E03Rik|BAF250a|Osa1|Smarcf1	AT rich interactive domain 1A (SWI-like)	protein-coding
mm_138393.1	chr17	35050628	35050647	+	1	NA	intron (NM_033444, intron 1 of 5)	intron (NM_033444, intron 1 of 5)	394	NM_033444	114584	Mm.29524	NM_033444	ENSMUSG00000007041	Clic1	Clcp|G6	chloride intracellular channel 1	protein-coding
mm_124870.1	chr15	10177739	10177745	+	1	NA	5' UTR (NM_011169, exon 1 of 10)	5' UTR (NM_011169, exon 1 of 10)	504	NM_011169	19116	Mm.10516	NM_011169	ENSMUSG00000005268	Prlr	AI987712|Pr-1|Pr-3|Prlr-rs1	prolactin receptor	protein-coding
mm_82735.1	chr9	25252023	25252084	-	1	NA	promoter-TSS (NM_001205367)	promoter-TSS (NM_001205367)	-386	NM_009859	235072	Mm.270259	NM_009859	ENSMUSG00000001833	Sept7	Cdc10|E430034N22	septin 7	protein-coding
mm_74683.1	chr8	14095660	14095671	-	1	NA	promoter-TSS (NM_001145965)	promoter-TSS (NM_001145965)	-210	NM_001145965	244310	Mm.404697	NM_172910	ENSMUSG00000047495	Dlgap2	6430596N04Rik|Dap-2|Dap2|Sapap2	discs, large (Drosophila) homolog-associated protein 2	protein-coding
mm_105153.1	chr11	101465928	101465959	-	1	NA	exon (NM_012037, exon 1 of 6)	exon (NM_012037, exon 1 of 6)	256	NM_012037	26949	Mm.29210	NM_012037	ENSMUSG00000034993	Vat1	VAT-1	vesicle amine transport 1	protein-coding
mm_31220.1	chr4	44012662	44012694	+	1	NA	promoter-TSS (NM_001080385)	promoter-TSS (NM_001080385)	28	NM_001290470	12757	Mm.298875	NM_016760	ENSMUSG00000028478	Clta	AV026556|Lca	clathrin, light polypeptide (Lca)	protein-coding
mm_153378.1	chr19	40371449	40371454	-	1	NA	intron (NM_001034962, intron 7 of 22)	intron (NM_001034962, intron 7 of 22)	30859	NM_001034964	20411	Mm.210815	NM_009166	ENSMUSG00000025006	Sorbs1	2310065E01Rik|9530001P15Rik|CAP|SH3P12|Sh3d5|mKIAA1296	sorbin and SH3 domain containing 1	protein-coding
mm_92029.1	chr10	62468320	62468345	-	1	NA	exon (NM_001113355, exon 5 of 9)	exon (NM_001113355, exon 5 of 9)	18266	NM_001113355	30930	Mm.260703	NM_133672	ENSMUSG00000020078	Vps26a	AA407240|HB58|Vps26	VPS26 retromer complex component A	protein-coding
mm_166341.1	chr5	114897627	114897633	+	1	NA	5' UTR (NM_011854, exon 1 of 6)	5' UTR (NM_011854, exon 1 of 6)	696	NM_011854	23962	Mm.228363	NM_011854	ENSMUSG00000029561	Oasl2	M1204|Mmu-OASL|Oasl	2'-5' oligoadenylate synthetase-like 2	protein-coding
mm_37323.1	chr4	119415444	119415459	-	1	NA	promoter-TSS (NM_001270435)	promoter-TSS (NM_001270435)	70	NM_001270435	73332	Mm.425204	NM_028506	ENSMUSG00000028637	Ccdc30	1700001O02Rik|1700041C02Rik|1700111D19Rik|4930445I03Rik	coiled-coil domain containing 30	protein-coding
mm_65647.1	chr7	28055201	28055209	-	1	NA	Intergenic	Intergenic	-5113	NM_011874	23996	Mm.29582	NM_011874	ENSMUSG00000030603	Psmc4	CIP21|MIP224	proteasome (prosome, macropain) 26S subunit, ATPase, 4	protein-coding
mm_140435.1	chr17	88440743	88440787	+	1	NA	promoter-TSS (NM_180974)	promoter-TSS (NM_180974)	53	NM_180974	14236	Mm.112824	NM_180974	ENSMUSG00000034998	Foxn2	3230402J05Rik|6030465J18Rik|Fkh19|Foxn1|HTLF	forkhead box N2	protein-coding
mm_4930.1	chr1	191085854	191085881	+	1	NA	Intergenic	Intergenic	-12547	NM_030060	381319	Mm.6922	NM_030060	ENSMUSG00000026630	Batf3	9130211I03Rik|Snft	basic leucine zipper transcription factor, ATF-like 3	protein-coding
mm_43266.1	chr5	130369421	130369474	+	1	NA	promoter-TSS (NM_181045)	promoter-TSS (NM_181045)	-11	NM_181045	140904	Mm.40875	NM_021371	ENSMUSG00000060371	Caln1	9630012C17Rik|Cabp8|MNCb-0849	calneuron 1	protein-coding
mm_118902.1	chr14	26652237	26652241	+	1	NA	intron (NM_007479, intron 3 of 5)	MTC|LTR|ERVL-MaLR	14042	NM_007479	11843	Mm.297768	NM_007479	ENSMUSG00000021877	Arf4	AA407803	ADP-ribosylation factor 4	protein-coding
mm_33844.1	chr4	135855708	135855744	+	1	NA	promoter-TSS (NM_001284196)	promoter-TSS (NM_001284196)	-345	NM_001284196	14105	Mm.10229	NM_010178	ENSMUSG00000028676	Srsf10	FUSIP2|Fusip1|NSSR1|NSSR2|Nssr|SRrp40|Sfrs13a|Srsf13a|TASR|TASR1|TASR2	serine/arginine-rich splicing factor 10	protein-coding
mm_19491.1	chr2	93334468	93334515	-	1	NA	promoter-TSS (NM_183180)	promoter-TSS (NM_183180)	-4	NM_183180	241556	Mm.274159	NM_183180	ENSMUSG00000027217	Tspan18	2610042G18Rik|6720430O15|BB226562	tetraspanin 18	protein-coding
mm_167035.1	chr7	73558925	73558927	+	1	NA	promoter-TSS (NR_037569)	promoter-TSS (NR_037569)	-531	NR_037569	69170	Mm.34539	NR_037569	ENSMUSG00000101970	1810026B05Rik	-	RIKEN cDNA 1810026B05 gene	ncRNA
mm_5551.1	chr1	38638632	38638633	-	1	NA	Intergenic	Intergenic	-11388	NM_001290814	16764	Mm.336679	NM_010678	ENSMUSG00000037138	Aff3	3222402O04Rik|A730046J16|LAF-4|Laf4	AF4/FMR2 family, member 3	protein-coding
mm_43228.1	chr5	129895747	129895800	+	1	NA	promoter-TSS (NM_183088)	promoter-TSS (NM_183088)	50	NM_183088	71970	Mm.422716	NM_183088	ENSMUSG00000034173	Zbed5	2410018M08Rik|Scand3	zinc finger, BED type containing 5	protein-coding
mm_45747.1	chr5	86632461	86632471	-	1	NA	promoter-TSS (NM_178730)	promoter-TSS (NM_178730)	-42	NM_178730	243083	Mm.106867	NM_178730	ENSMUSG00000048764	Tmprss11f	4631408C20|4732406D01Rik	transmembrane protease, serine 11f	protein-coding
mm_107218.1	chr12	26456117	26456127	+	1	NA	exon (NM_021384, exon 1 of 6)	exon (NM_021384, exon 1 of 6)	330	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_156749.1	chrX	160126017	160126025	+	1	NA	intron (NM_008810, intron 9 of 10)	intron (NM_008810, intron 9 of 10)	12409	NM_008810	18597	Mm.34775	NM_008810	ENSMUSG00000031299	Pdha1	Pdha-1	pyruvate dehydrogenase E1 alpha 1	protein-coding
mm_81409.1	chr9	109051999	109052003	+	1	NA	intron (NM_025858, intron 3 of 5)	intron (NM_025858, intron 3 of 5)	-2865	NM_026381	66940	Mm.196533	NM_025858	ENSMUSG00000025647	Shisa5	2310008D10Rik|6430628I05Rik|Scotin|mShisa5	shisa family member 5	protein-coding
mm_95311.1	chr11	46386741	46386753	+	1	NA	intron (NM_010583, intron 1 of 16)	intron (NM_010583, intron 1 of 16)	2768	NM_001281968	16428	Mm.339927	NM_010583	ENSMUSG00000020395	Itk	Emt|Tcsk|Tsk	IL2 inducible T cell kinase	protein-coding
mm_80557.1	chr9	83431524	83431530	+	1	NA	promoter-TSS (NR_102437)	promoter-TSS (NR_102437)	-20	NR_102437	100039186	Mm.212721	NR_102437	ENSMUSG00000099718	Gm2087	-	predicted gene 2087	ncRNA
mm_114722.1	chr13	83715245	83715255	+	1	NA	Intergenic	Intergenic	-12856	NR_015561	320203	Mm.245636	NM_177100	ENSMUSG00000050334	C130071C03Rik	2810449C10Rik	RIKEN cDNA C130071C03 gene	ncRNA
mm_280.1	chr1	21257142	21257154	+	1	NA	intron (NM_001288617, intron 3 of 7)	RLTR41|LTR|ERV1	16563	NM_010356	14859	Mm.394593	NM_010356	ENSMUSG00000025934	Gsta3	Gst2-3	glutathione S-transferase, alpha 3	protein-coding
mm_88013.1	chr10	67145172	67145173	+	1	NA	intron (NM_207221, intron 1 of 25)	B1_Mur3|SINE|Alu	17914	NM_207221	108829	Mm.23846	NM_207221	ENSMUSG00000037876	Jmjd1c	5430433L24Rik|D630035I23Rik|Jmjdic|TRIP8	jumonji domain containing 1C	protein-coding
mm_78467.1	chr9	32616263	32616290	+	1	NA	Intergenic	Intergenic	-74824	NM_008026	14247	Mm.258908	NM_008026	ENSMUSG00000016087	Fli1	EWSR2|Fli-1|SIC-1|Sic1	Friend leukemia integration 1	protein-coding
mm_121932.1	chr14	23967149	23967160	-	1	NA	intron (NM_001253366, intron 1 of 29)	intron (NM_001253366, intron 1 of 29)	37051	NM_001253375	16531	Mm.343607	NM_010610	ENSMUSG00000063142	Kcnma1	5730414M22Rik|BKCa|MaxiK|Slo|Slo1|mSlo|mSlo1	potassium large conductance calcium-activated channel, subfamily M, alpha member 1	protein-coding
mm_3053.1	chr1	134061096	134061107	+	1	NA	Intergenic	Intergenic	18054	NM_007570	12227	Mm.392646	NM_007570	ENSMUSG00000020423	Btg2	AA959598|APRO1|Pc3|TIS21	B cell translocation gene 2, anti-proliferative	protein-coding
mm_355.1	chr1	33669862	33669880	+	1	NA	promoter-TSS (NR_033199)	promoter-TSS (NR_033199)	47	NR_033199	67503	Mm.87069	NM_026204	ENSMUSG00000103746	1700001G17Rik	-	RIKEN cDNA 1700001G17 gene	ncRNA
mm_171911.1	chr5	53555770	53555772	+	1	NA	promoter-TSS (NM_001080928)	promoter-TSS (NM_001080928)	-8	NM_001080928	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_140147.1	chr17	80062533	80062555	+	1	NA	promoter-TSS (NM_144802)	promoter-TSS (NM_144802)	-276	NM_144802	72692	Mm.64579	NM_144802	ENSMUSG00000024095	Hnrnpll	2510028H02Rik|2810036L13Rik|AI256697|AI852082|Hnrpll	heterogeneous nuclear ribonucleoprotein L-like	protein-coding
mm_150920.1	chr19	46083110	46083122	+	1	NA	exon (NM_001039352, exon 10 of 13)	exon (NM_001039352, exon 10 of 13)	7269	NM_001039351	70769	Mm.402190	NM_053086	ENSMUSG00000015176	Nolc1	NOPP130|NOPP140|P130	nucleolar and coiled-body phosphoprotein 1	protein-coding
mm_46744.1	chr5	111178659	111178670	-	1	NA	intron (NM_001267622, intron 5 of 22)	ORR1E|LTR|ERVL-MaLR	-152033	NM_001301644	56305	Mm.200516	NM_019640	ENSMUSG00000050017	Pitpnb	PI-TP-beta	phosphatidylinositol transfer protein, beta	protein-coding
mm_19888.1	chr2	114050488	114050488	-	1	NA	exon (NM_009608, exon 3 of 7)	exon (NM_009608, exon 3 of 7)	2387	NM_009608	11464	Mm.686	NM_009608	ENSMUSG00000068614	Actc1	Actc-1	actin, alpha, cardiac muscle 1	protein-coding
mm_151338.1	chr19	55895157	55895175	+	1	NA	promoter-TSS (NM_001142924)	promoter-TSS (NM_001142924)	-155	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_95376.1	chr11	49090180	49090212	+	1	NA	intron (NM_010999, intron 2 of 5)	L1_Mus2|LINE|L1	3179	NM_008330	15953	Mm.24769	NM_008330	ENSMUSG00000078920	Ifi47	47kDa|IRG-47|Ifggc1|Igrd|Iigp4|Iipg4|Irgd	interferon gamma inducible protein 47	protein-coding
mm_170006.1	chr1	71653217	71653223	-	1	NA	promoter-TSS (NM_001276413)	promoter-TSS (NM_001276413)	14	NM_010233	14268	Mm.193099	NM_010233	ENSMUSG00000026193	Fn1	E330027I09|Fn|Fn-1	fibronectin 1	protein-coding
mm_162942.1	chr10	128704181	128704186	+	1	NA	intron (NM_183417, intron 1 of 7)	intron (NM_183417, intron 1 of 7)	868	NM_183417	12566	Mm.111326	NM_016756	ENSMUSG00000025358	Cdk2	A630093N05Rik	cyclin-dependent kinase 2	protein-coding
mm_14542.1	chr2	132816149	132816168	+	1	NA	promoter-TSS (NM_025676)	promoter-TSS (NM_025676)	17	NM_001291054	66634	Mm.157070	NM_025676	ENSMUSG00000027353	Mcm8	5730432L01Rik	minichromosome maintenance 8 homologous recombination repair factor	protein-coding
mm_168585.1	chr1	173491283	173491300	-	1	NA	Intergenic	Intergenic	44666	NM_001024721	545384	Mm.371698	NM_001024721	ENSMUSG00000070501	Ifi214	Pyhin-B|p214	interferon activated gene 214	protein-coding
mm_118391.1	chr13	118658679	118658726	-	1	NA	promoter-TSS (NR_131153)	promoter-TSS (NR_131153)	41	NR_131153	100038690	Mm.384983	NR_131153		Gm10732	ENSMUSG00000074638	predicted gene 10732	ncRNA
mm_58389.1	chr7	3206867	3206879	+	1	NA	Intergenic	B4A|SINE|B4	-11753	NR_029640	100049710		NR_029640	ENSMUSG00000077815	Mir290a	Mir290|Mirn290|mir-290a|mmu-miR-290|mmu-mir-290a	microRNA 290a	ncRNA
mm_3331.1	chr1	137937026	137937030	+	1	NA	Intergenic	Intergenic	-29427	NR_029795	735252		NR_029795	ENSMUSG00000065565	Mir181a-1	Mirn181a-1|Mirn213|miR-213|mir-181a-1|mmu-mir-213	microRNA 181a-1	ncRNA
mm_13716.1	chr2	117179487	117179513	+	1	NA	3' UTR (NM_033524, exon 7 of 7)	3' UTR (NM_033524, exon 7 of 7)	-5627	NR_030440	732489		NR_030440	ENSMUSG00000076376	Mir674	Mirn674|mir-674|mmu-mir-674	microRNA 674	ncRNA
mm_165003.1	chr19	22448546	22448584	-	1	NA	intron (NM_177341, intron 1 of 26)	intron (NM_177341, intron 1 of 26)	357	NM_177341	226025	Mm.131943	NM_177341	ENSMUSG00000052387	Trpm3	6330504P12Rik|9330180E14|AU018608|B930001P07Rik|LTRPC3|MLSN2	transient receptor potential cation channel, subfamily M, member 3	protein-coding
mm_152202.1	chr19	7606955	7606965	-	1	NA	5' UTR (NM_019516, exon 1 of 9)	5' UTR (NM_019516, exon 1 of 9)	216	NM_019516	56072	Mm.298242	NM_019516	ENSMUSG00000024972	Lgals12	AW987437|Grip1	lectin, galactose binding, soluble 12	protein-coding
mm_80047.1	chr9	69289866	69289895	+	1	NA	promoter-TSS (NM_001289916)	promoter-TSS (NM_001289916)	39	NM_001289916	19883	Mm.378450	NM_013646	ENSMUSG00000032238	Rora	9530021D13Rik|Nr1f1|ROR1|ROR2|ROR3|nmf267|sg|staggerer|tmgc26	RAR-related orphan receptor alpha	protein-coding
mm_26338.1	chr3	142547155	142547166	+	1	NA	3' UTR (NM_001083312, exon 11 of 11)	3' UTR (NM_001083312, exon 11 of 11)	-12892	NM_018734	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_157315.1	chrX	21061982	21062062	-	1	NA	promoter-TSS (NM_001111076)	promoter-TSS (NM_001111076)	16	NM_001013387	319535	Mm.170163	NM_001013387	ENSMUSG00000054737	Zfp182	6330583I20Rik|Znf182	zinc finger protein 182	protein-coding
mm_119452.1	chr14	46899427	46899445	+	1	NA	intron (NM_001037221, intron 2 of 12)	intron (NM_001037221, intron 2 of 12)	16471	NM_001037221	74480	Mm.214454	NM_028966	ENSMUSG00000021838	Samd4	1700024G08Rik|1700111L17Rik|4933436G17Rik|Samd4a|Smaug|Smaug1|sunk	sterile alpha motif domain containing 4	protein-coding
mm_31229.1	chr4	44300904	44300936	+	1	NA	promoter-TSS (NM_010790)	promoter-TSS (NM_010790)	3	NM_010790	17279	Mm.268668	NM_010790	ENSMUSG00000035683	Melk	AI327312|MPK38|mKIAA0175	maternal embryonic leucine zipper kinase	protein-coding
mm_121269.1	chr14	103346875	103346946	+	1	NA	promoter-TSS (NM_207215)	promoter-TSS (NM_207215)	-110	NM_207215	105689	Mm.6478	NM_207215	ENSMUSG00000033004	Mycbp2	AU023734|AW107953|AW546647|C130061D10Rik|Pam|Phr1|R75243	MYC binding protein 2	protein-coding
mm_20231.1	chr2	125839467	125839493	-	1	NA	exon (NM_001285513, exon 7 of 12)	exon (NM_001285513, exon 7 of 12)	19602	NM_009939	12848	Mm.3596	NM_009939	ENSMUSG00000027206	Cops2	AI315723|C85265|Csn2|Sgn2|TRIP-15|Trip15	COP9 signalosome subunit 2	protein-coding
mm_99391.1	chr11	102097846	102097849	+	1	NA	Intergenic	Intergenic	3453	NM_008918	19064	Mm.1269	NM_008918	ENSMUSG00000017316	Ppy	AV061413|IGSPP|PP	pancreatic polypeptide	protein-coding
mm_143660.1	chr17	79714713	79714747	-	1	NA	5' UTR (NM_009994, exon 1 of 3)	5' UTR (NM_009994, exon 1 of 3)	311	NM_009994	13078	Mm.214016	NM_009994	ENSMUSG00000024087	Cyp1b1	CP1B|P4501b1	cytochrome P450, family 1, subfamily b, polypeptide 1	protein-coding
mm_67286.1	chr7	78721332	78721336	-	1	NA	Intergenic	Intergenic	-3114	NR_015542	414121	Mm.482537	NR_015542	ENSMUSG00000059146	E430016F16Rik	-	RIKEN cDNA E430016F16 gene	ncRNA
mm_20646.1	chr2	132029816	132029822	-	1	NA	5' UTR (NM_175445, exon 1 of 11)	5' UTR (NM_175445, exon 1 of 11)	169	NM_175445	215653	Mm.204737	NM_175445	ENSMUSG00000027339	Rassf2	3830431H01Rik|9030412M04Rik|AI852669|AW495050	Ras association (RalGDS/AF-6) domain family member 2	protein-coding
mm_146696.1	chr18	12941687	12941697	-	1	NA	5' UTR (NM_207530, exon 1 of 28)	5' UTR (NM_207530, exon 1 of 28)	149	NM_207530	64291	Mm.259470	NM_020573	ENSMUSG00000044252	Osbpl1a	G430090F17Rik|Gm753|ORP-1|Osbpl1b	oxysterol binding protein-like 1A	protein-coding
mm_86301.1	chr9	122310946	122310955	-	1	NA	Intergenic	MLT1F1|LTR|ERVL-MaLR	-16527	NM_133979	102566	Mm.87676	NM_133979	ENSMUSG00000037949	Ano10	AI604832|Tmem16k	anoctamin 10	protein-coding
mm_118846.1	chr14	25663896	25663912	+	1	NA	3' UTR (NM_183208, exon 24 of 24)	3' UTR (NM_183208, exon 24 of 24)	-30266	NM_134084	105675	Mm.41656	NM_134084	ENSMUSG00000021868	Ppif	AW457192|CyP-D|CyP-F|CypD|PPIase	peptidylprolyl isomerase F (cyclophilin F)	protein-coding
mm_125275.1	chr15	36210469	36210489	+	1	NA	intron (NM_012031, intron 10 of 18)	CpG	29685	NR_106173	102465888		NR_106173	ENSMUSG00000098457	Mir8097	Gm27497|mmu-mir-8097	microRNA 8097	ncRNA
mm_116728.1	chr13	51717814	51717833	-	1	NA	intron (NM_013660, intron 6 of 15)	intron (NM_013660, intron 6 of 15)	66115	NM_029279	75420	Mm.275981	NM_029279	ENSMUSG00000035139	Secisbp2	2210413N07Rik|2810012K13Rik|SBP2	SECIS binding protein 2	protein-coding
mm_69987.1	chr7	142380959	142380968	-	1	NA	exon (NM_009983, exon 5 of 9)	exon (NM_009983, exon 5 of 9)	6907	NM_009983	13033	Mm.231395	NM_009983	ENSMUSG00000007891	Ctsd	CD|CatD	cathepsin D	protein-coding
mm_135292.1	chr16	38550143	38550168	-	1	NA	exon (NM_172380, exon 1 of 11)	exon (NM_172380, exon 1 of 11)	101	NM_172380	224143	Mm.284366	NM_172380	ENSMUSG00000034064	Poglut1	9630046K23Rik|Clp46|Ktelc1|Rumi	protein O-glucosyltransferase 1	protein-coding
mm_123508.1	chr14	66235588	66235609	-	1	NA	intron (NM_001162365, intron 1 of 30)	intron (NM_001162365, intron 1 of 30)	-22046	NM_001162366	19229	Mm.21613	NM_172498	ENSMUSG00000059456	Ptk2b	CADTK|CAKB|CAKbeta|E430023O05Rik|FADK2|FAK2|PYK2|Raftk	PTK2 protein tyrosine kinase 2 beta	protein-coding
mm_157912.1	chrX	78545277	78545286	-	1	NA	intron (NM_027322, intron 1 of 3)	intron (NM_027322, intron 1 of 3)	38524	NM_001164275	546336	Mm.211712	NM_027322	ENSMUSG00000047996	Prrg1	2010007L08Rik	proline rich Gla (G-carboxyglutamic acid) 1	protein-coding
mm_130795.1	chr15	101690501	101690501	-	1	NA	exon (NM_008476, exon 9 of 9)	exon (NM_008476, exon 9 of 9)	3804	NM_008476	16687	Mm.302399	NM_008476	ENSMUSG00000058354	Krt6a	2310016L08Rik|Krt2-6a|Krt2-6c|MK6a|mK6[a]	keratin 6A	protein-coding
mm_3328.1	chr1	137931748	137931764	+	1	NA	Intergenic	Intergenic	-34699	NR_029795	735252		NR_029795	ENSMUSG00000065565	Mir181a-1	Mirn181a-1|Mirn213|miR-213|mir-181a-1|mmu-mir-213	microRNA 181a-1	ncRNA
mm_81166.1	chr9	107299412	107299425	+	1	NA	intron (NM_001317354, intron 1 of 1)	intron (NM_001317354, intron 1 of 1)	2759	NM_009895	12700	Mm.4592	NM_009895	ENSMUSG00000032578	Cish	CIS-1|CIS1|Cis|F17|F23|SOCS	cytokine inducible SH2-containing protein	protein-coding
mm_3371.1	chr1	138963418	138963472	+	1	NA	promoter-TSS (NM_001166501)	promoter-TSS (NM_001166501)	-264	NM_001166501	329260	Mm.337604	NM_181347	ENSMUSG00000056268	Dennd1b	4632404N19Rik|4930467M19Rik|6820401H01Rik|F730008N07Rik	DENN/MADD domain containing 1B	protein-coding
mm_132638.1	chr16	39984350	39984380	+	1	NA	Intergenic	Intergenic	1082020	NM_170599	207683	Mm.245564	NM_170599	ENSMUSG00000022790	Igsf11	1700025L02Rik|BT-IgSF|Igsf13	immunoglobulin superfamily, member 11	protein-coding
mm_124368.1	chr14	105892828	105892848	-	1	NA	exon (NM_011897, exon 2 of 2)	exon (NM_011897, exon 2 of 2)	3981	NM_011897	24064	Mm.89982	NM_011897	ENSMUSG00000022114	Spry2	sprouty2	sprouty homolog 2 (Drosophila)	protein-coding
mm_104380.1	chr11	94473929	94473968	-	1	NA	5' UTR (NM_001177890, exon 1 of 35)	5' UTR (NM_001177890, exon 1 of 35)	250	NM_001177888	12291	Mm.29585	NM_009783	ENSMUSG00000020866	Cacna1g	Cav3.1d|[a]1G|a1G|alpha-1G|mKIAA1123	calcium channel, voltage-dependent, T type, alpha 1G subunit	protein-coding
mm_124386.1	chr14	108914060	108914139	-	1	NA	5' UTR (NM_199065, exon 1 of 1)	5' UTR (NM_199065, exon 1 of 1)	140	NM_199065	76965	Mm.257268	NM_199065	ENSMUSG00000075478	Slitrk1	3200001I04Rik	SLIT and NTRK-like family, member 1	protein-coding
mm_11200.1	chr2	29125244	29125254	+	1	NA	5' UTR (NM_198033, exon 1 of 26)	5' UTR (NM_198033, exon 1 of 26)	257	NM_198033	269254	Mm.41867	NM_198033	ENSMUSG00000043535	Setx	A130090N03|A930037J23Rik|AOA2|AW060766|Als4|SCAR1|Sen1|mKIAA0625	senataxin	protein-coding
mm_153146.1	chr19	34249332	34249359	-	1	NA	intron (NM_007392, intron 3 of 8)	intron (NM_007392, intron 3 of 8)	6028	NM_007392	11475	Mm.213025	NM_007392	ENSMUSG00000035783	Acta2	0610041G09Rik|Actvs|SMalphaA|a-SMA|alphaSMA	actin, alpha 2, smooth muscle, aorta	protein-coding
mm_158147.1	chrX	103468013	103468036	-	1	NA	non-coding (NR_001570, exon 7 of 8)	non-coding (NR_001570, exon 7 of 8)	15209	NR_001570	213742	Mm.274770	NR_001463	ENSMUSG00000086503	Xist	A430022B11|AI314753	inactive X specific transcripts	ncRNA
mm_109429.1	chr12	110609345	110609361	+	1	NA	intron (NM_030238, intron 1 of 76)	B1_Mur3|SINE|Alu	7958	NM_030238	13424	Mm.181430	NM_030238	ENSMUSG00000018707	Dync1h1	9930018I23Rik|AI894280|DHC1|DHC1a|DNCL|Dnchc1|Dnec1|Dnecl|Loa|MAP1C|P22|Swl|mKIAA0325	dynein cytoplasmic 1 heavy chain 1	protein-coding
mm_41367.1	chr5	90508808	90508824	+	1	NA	TTS (NM_007423)	TTS (NM_007423)	-10133	NM_145146	280662	Mm.348786	NM_145146	ENSMUSG00000029369	Afm	Alf|alpha-Alb	afamin	protein-coding
mm_36883.1	chr4	107253328	107253356	-	1	NA	promoter-TSS (NM_028394)	promoter-TSS (NM_028394)	191	NM_029985	77809	Mm.29681	NM_029985	ENSMUSG00000028617	Lrrc42	A930011F22Rik|AA536996	leucine rich repeat containing 42	protein-coding
mm_145276.1	chr18	53109283	53109332	+	1	NA	Intergenic	Lx8|LINE|L1	-67058	NM_026386	67804	Mm.252171	NM_026386	ENSMUSG00000034484	Snx2	0610030A03Rik	sorting nexin 2	protein-coding
mm_157575.1	chrX	52613937	52613979	-	1	NA	promoter-TSS (NM_016697)	promoter-TSS (NM_016697)	16	NM_016697	14734	Mm.22515	NM_016697	ENSMUSG00000055653	Gpc3	OCI-5	glypican 3	protein-coding
mm_43581.1	chr5	137746691	137746701	+	1	NA	intron (NM_029805, intron 1 of 5)	intron (NM_029805, intron 1 of 5)	727	NM_029805	78829	Mm.286399	NM_023910	ENSMUSG00000029723	Tsc22d4	0610009M14Rik|1700023B23Rik|AI415410|Thg-1pit|Tilz2	TSC22 domain family, member 4	protein-coding
mm_170282.1	chr18	27599268	27599276	+	1	NA	Intergenic	(TGG)n|Simple_repeat|Simple_repeat	-960892	NR_045398	320624	Mm.50107	NR_045398		4930474G06Rik	-	RIKEN cDNA 4930474G06 gene	ncRNA
mm_124597.1	chr15	3275557	3275591	+	1	NA	exon (NM_009155, exon 3 of 5)	exon (NM_009155, exon 3 of 5)	4597	NM_009155	20363	Mm.392203	NM_009155	ENSMUSG00000064373	Selenop	AU018766|D15Ucla1|Se-P|Sepp1|selp	selenoprotein P	protein-coding
mm_88555.1	chr10	78780349	78780392	+	1	NA	promoter-TSS (NM_009200)	promoter-TSS (NM_009200)	-126	NM_009200	20513	Mm.6257	NM_009200	ENSMUSG00000005357	Slc1a6	EAAT4	solute carrier family 1 (high affinity aspartate/glutamate transporter), member 6	protein-coding
mm_107039.1	chr12	13566156	13566168	+	1	NA	exon (NM_027706, exon 51 of 52)	exon (NM_027706, exon 51 of 52)	61484	NR_136761	102639399	Mm.122052	NR_136761		Gm35725	-	predicted gene, 35725	ncRNA
mm_52416.1	chr6	113393063	113393082	+	1	NA	intron (NM_133923, intron 1 of 12)	intron (NM_133923, intron 1 of 12)	575	NM_133923	101100	Mm.388573	NM_133923	ENSMUSG00000030276	Ttll3	4833441J24Rik|AI450050	tubulin tyrosine ligase-like family, member 3	protein-coding
mm_133243.1	chr16	77093615	77093628	+	1	NA	exon (NM_013918, exon 18 of 24)	exon (NM_013918, exon 18 of 24)	79552	NM_013918	30940	Mm.40986	NM_013918	ENSMUSG00000022867	Usp25	-	ubiquitin specific peptidase 25	protein-coding
mm_108459.1	chr12	83028218	83028221	+	1	NA	intron (NM_001310478, intron 3 of 17)	intron (NM_001310478, intron 3 of 17)	-89064	NR_046045	74283	Mm.398247	NR_046045	ENSMUSG00000100890	1700085C21Rik	-	RIKEN cDNA 1700085C21 gene	ncRNA
mm_120357.1	chr14	64093683	64093712	+	1	NA	promoter-TSS (NM_001193631)	promoter-TSS (NM_001193631)	1	NM_001193631	100504162	Mm.72752	NM_001193631	ENSMUSG00000052099	Prss51	1700007N14Rik	protease, serine 51	protein-coding
mm_64672.1	chr7	4471229	4471290	-	1	NA	promoter-TSS (NR_028416)	promoter-TSS (NR_028416)	-375	NR_028416	320749	Mm.396688	NR_028416		D630041G03Rik	-	RIKEN cDNA D630041G03 gene	ncRNA
mm_162794.1	chr10	76253818	76253822	+	1	NA	promoter-TSS (NM_009115)	promoter-TSS (NM_009115)	-16	NM_009115	20203	Mm.235998	NM_009115	ENSMUSG00000033208	S100b	AI850290|Bpb	S100 protein, beta polypeptide, neural	protein-coding
mm_34659.1	chr4	150866554	150866573	+	1	NA	exon (NM_133753, exon 4 of 4)	exon (NM_133753, exon 4 of 4)	11472	NM_133753	74155	Mm.318841	NM_133753	ENSMUSG00000028967	Errfi1	1300002F13Rik|AI788755|Mig-6|Mig6|RALT	ERBB receptor feedback inhibitor 1	protein-coding
mm_160155.1	chr7	43976055	43976055	+	1	NA	promoter-TSS (NM_010116)	promoter-TSS (NM_010116)	-6	NM_010116	13648	Mm.440884	NM_010116	ENSMUSG00000059042	Klk1b9	EGF-BP C|Egfbp-3|Egfbp3|KAL|Klk9|kallikrein|mGk-9	kallikrein 1-related peptidase b9	protein-coding
mm_32271.1	chr4	102625331	102625342	+	1	NA	Intergenic	Intergenic	35493	NM_001177981	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_44812.1	chr5	33535456	33535487	-	1	NA	Intergenic	Intergenic	94164	NM_178390	74504	Mm.294695	NM_178390	ENSMUSG00000037339	Fam53a	2410018C17Rik|5430419M09Rik|Dntnp	family with sequence similarity 53, member A	protein-coding
mm_163597.1	chr13	41569560	41569580	+	1	NA	Intergenic	B4A|SINE|B4	-36646	NM_001163572	621976	Mm.259830	NM_001163572	ENSMUSG00000087370	Tmem170b	EG621976	transmembrane protein 170B	protein-coding
mm_42188.1	chr5	112269475	112269482	+	1	NA	exon (NM_001312894, exon 6 of 6)	exon (NM_001312894, exon 6 of 6)	-7213	NM_001326590	22022	Mm.250631	NM_009419	ENSMUSG00000029344	Tpst2	AI448750|D5Ucla3|Tango13b|grm|grt	protein-tyrosine sulfotransferase 2	protein-coding
mm_46640.1	chr5	108548559	108548570	-	1	NA	5' UTR (NM_007756, exon 2 of 4)	5' UTR (NM_007756, exon 2 of 4)	1463	NM_007756	12889	Mm.5195	NM_007756	ENSMUSG00000033615	Cplx1	921-S	complexin 1	protein-coding
mm_39868.1	chr5	31056527	31056542	+	1	NA	intron (NM_023525, intron 2 of 43)	T-rich|Low_complexity|Low_complexity	1754	NM_001289522	69719	Mm.305535	NM_023525	ENSMUSG00000013629	Cad	2410008J01Rik|AU018859|Cpad	carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase	protein-coding
mm_135750.1	chr16	55934846	55934868	-	1	NA	promoter-TSS (NM_001159365)	promoter-TSS (NM_001159365)	-9	NM_001159365	74201	Mm.178427	NM_028815	ENSMUSG00000022604	Cep97	2810403B08Rik|4932439K18Rik|AA437768|E130116N02Rik|Lrriq2	centrosomal protein 97	protein-coding
mm_28926.1	chr3	98858311	98858312	-	1	NA	5' UTR (NM_008293, exon 2 of 5)	5' UTR (NM_008293, exon 2 of 5)	1483	NM_001304800	15492	Mm.140811	NM_008293	ENSMUSG00000027871	Hsd3b1	3-beta-HSD I|D3Ertd383e	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1	protein-coding
mm_94307.1	chr11	4186808	4186865	+	1	NA	promoter-TSS (NM_134023)	promoter-TSS (NM_134023)	3	NM_134023	103724	Mm.28140	NM_134023	ENSMUSG00000034412	Tbc1d10a	AI447804|EPI64|Tbc1d10|mFLJ00288	TBC1 domain family, member 10a	protein-coding
mm_4836.1	chr1	186587504	186587515	+	1	NA	Intergenic	Intergenic	-28828	NR_131158	320449	Mm.404477	NR_131124	ENSMUSG00000103690	A730004F24Rik	-	RIKEN cDNA A730004F24 gene	ncRNA
mm_84700.1	chr9	72510958	72510969	-	1	NA	Intergenic	L1MCa|LINE|L1	-19004	NM_009359	21778	Mm.14485	NM_009359	ENSMUSG00000090626	Tex9	Gm19407|tsec-1	testis expressed gene 9	protein-coding
mm_164087.1	chr15	7406592	7406592	+	1	NA	Intergenic	Intergenic	-8197	NM_001289498	268780	Mm.203208	NM_178748	ENSMUSG00000042961	Egflam	5930412K08|AU040377	EGF-like, fibronectin type III and laminin G domains	protein-coding
mm_171110.1	chr3	135774963	135774965	-	1	NA	Intergenic	ERVB7_1-LTR_MM|LTR|ERVK	-50315	NM_026228	67547	Mm.30239	NM_026228	ENSMUSG00000053897	Slc39a8	4933419D20Rik|AA986696|BIGM103|ZIP-8|Zip8	solute carrier family 39 (metal ion transporter), member 8	protein-coding
mm_150117.1	chr19	29925108	29925122	+	1	NA	promoter-TSS (NM_133775)	promoter-TSS (NM_133775)	1	NM_133775	77125	Mm.182359	NM_133775	ENSMUSG00000024810	Il33	9230117N10Rik|Il-33|Il1f11|NF-HEV	interleukin 33	protein-coding
mm_143740.1	chr17	81498764	81498811	-	1	NA	intron (NR_104580, intron 2 of 8)	intron (NR_104580, intron 2 of 8)	239600	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_132568.1	chr16	38128541	38128548	+	1	NA	intron (NM_001347232, intron 1 of 11)	intron (NM_001347232, intron 1 of 11)	-39284	NR_033221	414072	Mm.483602	NR_033221		BC031361	-	cDNA sequence BC031361	ncRNA
mm_94590.1	chr11	11765078	11765082	+	1	NA	intron (NM_001025597, intron 7 of 7)	intron (NM_001025597, intron 7 of 7)	43882	NM_021891	60530	Mm.236114	NM_021891	ENSMUSG00000035455	Fignl1	-	fidgetin-like 1	protein-coding
mm_143483.1	chr17	71268621	71268631	-	1	NA	intron (NM_145158, intron 4 of 7)	intron (NM_145158, intron 4 of 7)	42339	NM_145158	246707	Mm.23462	NM_145158	ENSMUSG00000024053	Emilin2	FOAP-10	elastin microfibril interfacer 2	protein-coding
mm_58166.1	chr6	142571499	142571527	-	1	NA	5' UTR (NM_008428, exon 1 of 3)	5' UTR (NM_008428, exon 1 of 3)	101	NM_001330363	16523	Mm.1482	NM_008428	ENSMUSG00000030247	Kcnj8	AI448900|Kir6.1|gnite|slmbr|sltr|uKATP-1	potassium inwardly-rectifying channel, subfamily J, member 8	protein-coding
mm_10076.1	chr1	195131343	195131407	-	1	NA	5' UTR (NM_013499, exon 1 of 10)	5' UTR (NM_013499, exon 1 of 10)	195	NM_013499	12946	Mm.301652	NM_013499	ENSMUSG00000016481	Cr1l	Crry|Mcp|mCRY	complement component (3b/4b) receptor 1-like	protein-coding
mm_65845.1	chr7	29248376	29248424	-	1	NA	promoter-TSS (NM_028179)	promoter-TSS (NM_028179)	67	NM_028179	72275	Mm.441142	NM_028179	ENSMUSG00000030587	2200002D01Rik	2010005J02Rik|H2RSP|IMUP|IMUP-1|IMUP-2	RIKEN cDNA 2200002D01 gene	protein-coding
mm_122291.1	chr14	34555467	34555493	-	1	NA	exon (NM_001039074, exon 9 of 15)	exon (NM_001039074, exon 9 of 15)	-32679	NM_030062	78243	Mm.117483	NM_030062	ENSMUSG00000021797	9230112D13Rik	-	RIKEN cDNA 9230112D13 gene	protein-coding
mm_150307.1	chr19	34570682	34570692	+	1	NA	intron (NM_008332, intron 2 of 2)	(TC)n|Simple_repeat|Simple_repeat	-12842	NM_010501	15959	Mm.426079	NM_010501	ENSMUSG00000074896	Ifit3	Ifi49|P49	interferon-induced protein with tetratricopeptide repeats 3	protein-coding
mm_12840.1	chr2	82053379	82053391	+	1	NA	promoter-TSS (NM_175513)	promoter-TSS (NM_175513)	-273	NM_175513	241514	Mm.119383	NM_175513	ENSMUSG00000070866	Zfp804a	C630007C17Rik|Znf804a	zinc finger protein 804A	protein-coding
mm_26843.1	chr3	14766493	14766507	-	1	NA	3' UTR (NM_001083957, exon 7 of 7)	3' UTR (NM_001083957, exon 7 of 7)	11960	NM_001083957	12346	Mm.273195	NM_009799	ENSMUSG00000027556	Car1	AW555628|Ca1|Car-1	carbonic anhydrase 1	protein-coding
mm_161432.1	chr15	57477562	57477562	-	1	NA	promoter-TSS (NM_172378)	promoter-TSS (NM_172378)	63	NM_172378	210463	Mm.26555	NM_172378	ENSMUSG00000022366	Slc22a22	oat-pg	solute carrier family 22 (organic cation transporter), member 22	protein-coding
mm_125516.1	chr15	57694652	57694686	+	1	NA	promoter-TSS (NM_199449)	promoter-TSS (NM_199449)	2	NM_199449	387609	Mm.36557	NM_199449	ENSMUSG00000071757	Zhx2	Afr-1|Afr1|Raf|mKIAA0854	zinc fingers and homeoboxes 2	protein-coding
mm_87789.1	chr10	60297696	60297699	+	1	NA	intron (NM_011179, intron 8 of 14)	L1MEc|LINE|L1	13236	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_14112.1	chr2	125838444	125838463	+	1	NA	intron (NM_009939, intron 9 of 12)	(T)n|Simple_repeat|Simple_repeat	20629	NM_009939	12848	Mm.3596	NM_009939	ENSMUSG00000027206	Cops2	AI315723|C85265|Csn2|Sgn2|TRIP-15|Trip15	COP9 signalosome subunit 2	protein-coding
mm_158384.1	chrX	136085197	136085204	-	1	NA	promoter-TSS (NM_001024141)	promoter-TSS (NM_001024141)	55	NM_001024141	245610	Mm.336244	NM_001024141	ENSMUSG00000057000	Nxf3	Gm384	nuclear RNA export factor 3	protein-coding
mm_44430.1	chr5	20991987	20991995	-	1	NA	intron (NM_011203, intron 15 of 17)	intron (NM_011203, intron 15 of 17)	-40169	NM_001080977	242860	Mm.254286	NM_001080977	ENSMUSG00000039968	Rsbn1l	8430412F05Rik|AI447441|C330002G24Rik	round spermatid basic protein 1-like	protein-coding
mm_154209.1	chr19	59076265	59076281	-	1	NA	promoter-TSS (NM_001114312)	promoter-TSS (NM_001114312)	-204	NM_001114312	71653	Mm.37338	NM_175172	ENSMUSG00000041362	Shtn1	4930506M07Rik|Kiaa1598|Shootin1|mKIAA1598	shootin 1	protein-coding
mm_102936.1	chr11	69601139	69601147	-	1	NA	3' UTR (NM_013415, exon 7 of 7)	3' UTR (NM_013415, exon 7 of 7)	4817	NM_013415	11932	Mm.235204	NM_013415	ENSMUSG00000041329	Atp1b2	Amog|Atpb-2	ATPase, Na+/K+ transporting, beta 2 polypeptide	protein-coding
mm_119326.1	chr14	38117697	38117698	+	1	NA	Intergenic	RLTR6C_Mm|LTR|ERV1	-780605	NR_045713	75170	Mm.372967	NR_045713	ENSMUSG00000093528	Nrg3os	4930529F24Rik	neuregulin 3, opposite strand	ncRNA
mm_97702.1	chr11	80177933	80177943	+	1	NA	intron (NM_172133, intron 10 of 10)	B1_Mur2|SINE|Alu	-5934	NM_028019	71956	Mm.22985	NM_028019	ENSMUSG00000020707	Rnf135	0610037N03Rik|2410006N06Rik	ring finger protein 135	protein-coding
mm_68080.1	chr7	101870632	101870646	-	1	NA	5' UTR (NM_008034, exon 1 of 7)	5' UTR (NM_008034, exon 1 of 7)	149	NM_001252554	14275	Mm.2135	NM_008034	ENSMUSG00000001827	Folr1	FBP1|Folbp-1|Folbp1	folate receptor 1 (adult)	protein-coding
mm_11171.1	chr2	28562510	28562527	+	1	NA	intron (NM_009885, intron 1 of 10)	intron (NM_009885, intron 1 of 10)	885	NM_009885	12613	Mm.236017	NM_009885	ENSMUSG00000026818	Cel	1810036E18Rik|BAL	carboxyl ester lipase	protein-coding
mm_59805.1	chr7	29155644	29155668	+	1	NA	intron (NM_001146023, intron 3 of 7)	CpG	554	NM_001146023	73833	Mm.260890	NM_028661	ENSMUSG00000030590	Fam98c	1110006G06Rik|AI836081|AV026483|B230110F21Rik	family with sequence similarity 98, member C	protein-coding
mm_41082.1	chr5	87677854	87677856	+	1	NA	intron (NM_001286015, intron 27 of 32)	intron (NM_001286015, intron 27 of 32)	11647	NM_001286016	12990	Mm.427467	NM_007784	ENSMUSG00000070702	Csn1s1	AA959832|AW212882|Csna	casein alpha s1	protein-coding
mm_140740.1	chr17	15826522	15826590	-	1	NA	promoter-TSS (NM_178615)	promoter-TSS (NM_178615)	30	NM_178615	68799	Mm.293466	NM_178615	ENSMUSG00000048027	Rgmb	1110059F19Rik|DRAGON	repulsive guidance molecule family member B	protein-coding
mm_164753.1	chr17	81738417	81738462	-	1	NA	promoter-TSS (NM_001112798)	promoter-TSS (NM_001112798)	-52	NM_011406	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_115664.1	chr13	12464926	12464949	-	1	NA	Intergenic	Intergenic	-3199	NM_001291057	56048	Mm.474138	NM_018886	ENSMUSG00000057554	Lgals8	1200015E08Rik|AI326142|D13Ertd524e|Lgals-8	lectin, galactose binding, soluble 8	protein-coding
mm_76688.1	chr8	94098491	94098534	-	1	NA	5' UTR (NM_026116, exon 1 of 17)	5' UTR (NM_026116, exon 1 of 17)	299	NM_026116	67378	Mm.292107	NM_026116	ENSMUSG00000031755	Bbs2	2410125H22Rik|AI447581	Bardet-Biedl syndrome 2 (human)	protein-coding
mm_60743.1	chr7	45448895	45448913	+	1	NA	intron (NM_030678, intron 12 of 15)	intron (NM_030678, intron 12 of 15)	10982	NM_010240	14325	Mm.30357	NM_010240	ENSMUSG00000050708	Ftl1	Ftl|Ftl-1|L-ferritin	ferritin light polypeptide 1	protein-coding
mm_165842.1	chr3	159495478	159495488	+	1	NA	promoter-TSS (NM_001172093)	promoter-TSS (NM_001172093)	50	NM_001172093	76131	Mm.371655	NM_029523	ENSMUSG00000028175	Depdc1a	5830484J08Rik|Depdc1	DEP domain containing 1a	protein-coding
mm_110923.1	chr12	76369172	76369181	-	1	NA	intron (NM_028356, intron 1 of 2)	CpG	288	NM_001172104	109929	Mm.41880	NM_028356	ENSMUSG00000056459	Zbtb25	2810462M08Rik|2900064P18Rik|AI842128|Kup|Zfp-50|Zfp50	zinc finger and BTB domain containing 25	protein-coding
mm_103214.1	chr11	70654625	70654641	-	1	NA	promoter-TSS (NM_011072)	promoter-TSS (NM_011072)	17	NM_011072	18643	Mm.2647	NM_011072	ENSMUSG00000018293	Pfn1	Pfn	profilin 1	protein-coding
mm_116005.1	chr13	24603893	24603904	-	1	NA	intron (NR_024599, intron 1 of 1)	intron (NR_024599, intron 1 of 1)	869	NR_024599	76024	Mm.440710	NR_024599		Gm11346	5830431A10Rik|AI447617|Gm11347|OTTMUSG00000000601|OTTMUSG00000000602	X-linked lymphocyte-regulated 5 pseudogene	pseudo
mm_10220.1	chr2	5951569	5951589	+	1	NA	intron (NM_001081132, intron 1 of 21)	CpG	110	NM_001081132	326622	Mm.31102	NM_001081132	ENSMUSG00000043241	Upf2	-	UPF2 regulator of nonsense transcripts homolog (yeast)	protein-coding
mm_109740.1	chr12	117250884	117250887	+	1	NA	promoter-TSS (NR_029563)	promoter-TSS (NR_029563)	68	NR_029563	387171		NR_029563	ENSMUSG00000065538	Mir153	Mirn153|mir-153|mmu-mir-153	microRNA 153	ncRNA
mm_59941.1	chr7	30425219	30425225	+	1	NA	exon (NM_172142, exon 4 of 11)	exon (NM_172142, exon 4 of 11)	1918	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_164525.1	chr17	4196915	4196933	-	1	NA	Intergenic	Intergenic	-74822	NR_045462	78043	Mm.398313	NR_045462		4930548J01Rik	1700113K09Rik	RIKEN cDNA 4930548J01 gene	ncRNA
mm_110047.1	chr12	17544587	17544605	-	1	NA	promoter-TSS (NM_013614)	promoter-TSS (NM_013614)	-277	NM_013614	18263	Mm.34102	NM_013614	ENSMUSG00000011179	Odc1	ODC	ornithine decarboxylase, structural 1	protein-coding
mm_129048.1	chr15	75315246	75315272	-	1	NA	Intergenic	Intergenic	46838	NM_008530	17071	Mm.377095	NM_008530	ENSMUSG00000022583	Ly6f	-	lymphocyte antigen 6 complex, locus F	protein-coding
mm_128772.1	chr15	66561071	66561081	-	1	NA	promoter-TSS (NM_172514)	promoter-TSS (NM_172514)	-30	NM_172514	213068	Mm.132299	NM_172514	ENSMUSG00000036944	Tmem71	AI661017|E430024D12	transmembrane protein 71	protein-coding
mm_105758.1	chr11	109473736	109473746	-	1	NA	promoter-TSS (NM_001029842)	promoter-TSS (NM_001029842)	-145	NM_001029842	104681	Mm.265874	NM_134038	ENSMUSG00000041920	Slc16a6	AW743111|ESTM12|MCT 6|MCT 7|MCT6	solute carrier family 16 (monocarboxylic acid transporters), member 6	protein-coding
mm_131104.1	chr16	5007535	5007550	+	1	NA	intron (NR_045596, intron 1 of 2)	intron (NR_045596, intron 1 of 2)	226	NR_045596	432995	Mm.271618	NM_001253796	ENSMUSG00000096215	Smim22	EG432995|Gm5480	small integral membrane protein 22	protein-coding
mm_130092.1	chr15	89416660	89416663	-	1	NA	non-coding (NR_004843, exon 27 of 27)	non-coding (NR_004843, exon 27 of 27)	-6158	NM_001162880	75459	Mm.45462	NM_001162880	ENSMUSG00000078938	Syce3	1700007E06Rik|TSEG-2|TSEG2	synaptonemal complex central element protein 3	protein-coding
mm_4262.1	chr1	171437595	171437605	+	1	NA	promoter-TSS (NM_172647)	promoter-TSS (NM_172647)	39	NM_172647	16456	Mm.294882	NM_172647	ENSMUSG00000038235	F11r	9130004G24|AA638916|ESTM33|JAM|JAM-1|JAM-A|Jcam|Jcam1|Ly106	F11 receptor	protein-coding
mm_56625.1	chr6	112737390	112737390	-	1	NA	intron (NM_080448, intron 17 of 21)	PB1D10|SINE|Alu	-40720	NM_001167730	58186	Mm.103812	NM_021385	ENSMUSG00000030254	Rad18	2810024C04Rik|Rad18sc	RAD18 E3 ubiquitin protein ligase	protein-coding
mm_56977.1	chr6	120294889	120294904	-	1	NA	promoter-TSS (NM_198884)	promoter-TSS (NM_198884)	-337	NM_198884	330406	Mm.321840	NM_198884	ENSMUSG00000041372	B4galnt3	AB114826|B4GalNAcT3|C330047A21	beta-1,4-N-acetyl-galactosaminyl transferase 3	protein-coding
mm_11090.1	chr2	27886445	27886461	+	1	NA	promoter-TSS (NM_015734)	promoter-TSS (NM_015734)	28	NM_015734	12831	Mm.7281	NM_015734	ENSMUSG00000026837	Col5a1	AI413331	collagen, type V, alpha 1	protein-coding
mm_47681.1	chr5	128953048	128953066	-	1	NA	5' UTR (NM_001081388, exon 1 of 22)	5' UTR (NM_001081388, exon 1 of 22)	429	NM_001081388	231760	Mm.233996	NM_001081388	ENSMUSG00000029420	Rimbp2	A930033C01Rik|mKIAA0318	RIMS binding protein 2	protein-coding
mm_170596.1	chr19	5802238	5802241	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	433	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_171822.1	chr5	142401465	142401481	+	1	NA	promoter-TSS (NM_199068)	promoter-TSS (NM_199068)	-24	NM_199068	17425	Mm.24214	NM_010812	ENSMUSG00000056493	Foxk1	A630048H08Rik|AI463295|ENSMUSG00000075577|Gm10868|Mnf	forkhead box K1	protein-coding
mm_45574.1	chr5	73630304	73630343	-	1	NA	intron (NM_153568, intron 1 of 4)	intron (NM_153568, intron 1 of 4)	2098	NM_153568	231296	Mm.168948	NM_153568	ENSMUSG00000067206	Lrrc66	-	leucine rich repeat containing 66	protein-coding
mm_92622.1	chr10	80260904	80260945	-	1	NA	promoter-TSS (NM_001347119)	promoter-TSS (NM_001347119)	88	NM_001347119	14431	Mm.7329	NM_010255	ENSMUSG00000020150	Gamt	AA571402|Spintz1	guanidinoacetate methyltransferase	protein-coding
mm_132394.1	chr16	35000721	35000731	+	1	NA	3' UTR (NM_139300, exon 32 of 32)	3' UTR (NM_139300, exon 32 of 32)	-21695	NM_023587	70757	Mm.27286	NM_023587	ENSMUSG00000035376	Hacd2	6330408J20Rik|AI255777|AI481689|Hcad2|Ptplb	3-hydroxyacyl-CoA dehydratase 2	protein-coding
mm_124832.1	chr15	9186263	9186273	+	1	NA	intron (NM_177178, intron 15 of 17)	intron (NM_177178, intron 15 of 17)	-30843	NM_001285980	27401	Mm.35584	NM_013787	ENSMUSG00000054115	Skp2	4930500A04Rik|FBXL1|FWD1|p45	S-phase kinase-associated protein 2 (p45)	protein-coding
mm_105508.1	chr11	106199732	106199766	-	1	NA	3' UTR (NM_026009, exon 13 of 13)	3' UTR (NM_026009, exon 13 of 13)	-6146	NM_001252449	72149	Mm.403722	NM_028126	ENSMUSG00000069631	Strada	2610019A05Rik|6030402H20Rik|AI480680|E130112C09Rik	STE20-related kinase adaptor alpha	protein-coding
mm_25523.1	chr3	114094559	114094580	+	1	NA	exon (NM_007729, exon 6 of 67)	exon (NM_007729, exon 6 of 67)	64029	NM_007729	12814	Mm.209715	NM_007729	ENSMUSG00000027966	Col11a1	C530001D20Rik|cho	collagen, type XI, alpha 1	protein-coding
mm_23427.1	chr3	59005466	59005480	+	1	NA	Intergenic	CpG	-1505	NM_177855	329650	Mm.240059	NM_177855	ENSMUSG00000056476	Med12l	A130035F20|A630079M02|AU044581|TRALPUSH	mediator complex subunit 12-like	protein-coding
mm_83266.1	chr9	42472199	42472263	-	1	NA	promoter-TSS (NM_173038)	promoter-TSS (NM_173038)	-5	NM_173038	272589	Mm.34483	NM_173038	ENSMUSG00000037287	Tbcel	D330014K23|E130107N23Rik|Lrrc35	tubulin folding cofactor E-like	protein-coding
mm_78956.1	chr9	45138900	45138918	+	1	NA	promoter-TSS (NM_001013390)	promoter-TSS (NM_001013390)	-133	NM_001013390	399548	Mm.335112	NM_001013390	ENSMUSG00000046480	Scn4b	Gm1471	sodium channel, type IV, beta	protein-coding
mm_34103.1	chr4	139130336	139130357	+	1	NA	intron (NM_001163006, intron 1 of 3)	CpG	691	NR_033745	433771	Mm.305990	NM_001163006	ENSMUSG00000050608	Minos1	2310028O11Rik	mitochondrial inner membrane organizing system 1	protein-coding
mm_53972.1	chr6	6217024	6217125	-	1	NA	promoter-TSS (NM_001177572)	promoter-TSS (NM_001177572)	99	NM_015829	50799	Mm.24513	NM_015829	ENSMUSG00000015112	Slc25a13	AI785475|Ctrn	solute carrier family 25 (mitochondrial carrier, adenine nucleotide translocator), member 13	protein-coding
mm_25017.1	chr3	98013504	98013547	+	1	NA	promoter-TSS (NM_010928)	promoter-TSS (NM_010928)	-13	NM_010928	18129	Mm.485843	NM_010928	ENSMUSG00000027878	Notch2	AI853703|N2	notch 2	protein-coding
mm_146870.1	chr18	25168887	25168921	-	1	NA	promoter-TSS (NM_001142698)	promoter-TSS (NM_001142698)	-27	NM_001004361	66648	Mm.263189	NM_001004361	ENSMUSG00000024269	Tpgs2	5730437P09Rik|5730494M16Rik|AI666318|Pgs2	tubulin polyglutamylase complex subunit 2	protein-coding
mm_53128.1	chr6	125145211	125145234	+	1	NA	promoter-TSS (NM_001039669)	promoter-TSS (NM_001039669)	-2	NR_126495	320678	Mm.129415	NM_178787	ENSMUSG00000038271	Iffo1	4733401N06Rik|A930037G23Rik|HOM-TES-103|Iffo	intermediate filament family orphan 1	protein-coding
mm_92373.1	chr10	76237823	76237867	-	1	NA	promoter-TSS (NM_133182)	promoter-TSS (NM_133182)	20	NR_126571	15468	Mm.32020	NM_133182	ENSMUSG00000020230	Prmt2	AI504737|Hrmt1l1	protein arginine N-methyltransferase 2	protein-coding
mm_151657.1	chr19	4125821	4125831	-	1	NA	promoter-TSS (NM_016666)	promoter-TSS (NM_016666)	32	NM_016666	11632	Mm.10433	NM_016666	ENSMUSG00000024847	Aip	AA408703|AW476050|Ara9|D19Bwg1412e|Fkbp16|Xap2	aryl-hydrocarbon receptor-interacting protein	protein-coding
mm_171539.1	chr4	146971955	146971959	+	1	NA	Intergenic	Intergenic	-49893	NM_001177767	100043034	Mm.422606	NM_001177767	ENSMUSG00000067919	Rex2	Gm13138|OTTMUSG00000010655	reduced expression 2	protein-coding
mm_65918.1	chr7	30198852	30198879	-	1	NA	Intergenic	Intergenic	-3817	NM_009795	12336	Mm.439782	NM_009795	ENSMUSG00000001794	Capns1	Capa-4|Capa4|Capn4|D7Ertd146e	calpain, small subunit 1	protein-coding
mm_16353.1	chr2	174415816	174415871	+	1	NA	promoter-TSS (NM_020580)	promoter-TSS (NM_020580)	39	NM_020580	57314	Mm.271709	NM_020580	ENSMUSG00000016253	Nelfcd	2410003I03Rik|C77797|Th1|Th1l	negative elongation factor complex member C/D, Th1l	protein-coding
mm_126642.1	chr15	83780000	83780033	+	1	NA	promoter-TSS (NM_172610)	promoter-TSS (NM_172610)	-7	NM_172610	223726	Mm.36395	NM_172610	ENSMUSG00000041708	Mpped1	6230403M19|AW456965|D15Bwg0669e	metallophosphoesterase domain containing 1	protein-coding
mm_111626.1	chr12	102435851	102435854	-	1	NA	intron (NM_011175, intron 1 of 13)	B1_Mur2|SINE|Alu	3961	NM_011175	19141	Mm.17185	NM_011175	ENSMUSG00000021190	Lgmn	AEP|AI746452|AU022324|Prsc1	legumain	protein-coding
mm_69691.1	chr7	139992502	139992520	-	1	NA	promoter-TSS (NM_001291066)	promoter-TSS (NM_001291066)	51	NM_007403	11501	Mm.15969	NM_007403	ENSMUSG00000025473	Adam8	ADAM 8|CD156|CD156a|E430039A18Rik|MS2	a disintegrin and metallopeptidase domain 8	protein-coding
mm_77767.1	chr9	3004795	3004817	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	33937	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_133188.1	chr16	72663545	72663622	+	1	NA	5' UTR (NM_019413, exon 1 of 29)	5' UTR (NM_019413, exon 1 of 29)	434	NM_019413	19876	Mm.310772	NM_019413	ENSMUSG00000022883	Robo1	AW494633|AW742721|DUTT1|Gm310	roundabout guidance receptor 1	protein-coding
mm_163864.1	chr14	19418907	19418946	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	183661	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_132865.1	chr16	48598884	48598886	+	1	NA	intron (NM_010816, intron 20 of 26)	intron (NM_010816, intron 20 of 26)	167648	NM_010816	17450	Mm.250060	NM_010816	ENSMUSG00000022652	Morc1	Morc	microrchidia 1	protein-coding
mm_142988.1	chr17	56287958	56288001	-	1	NA	intron (NM_025836, intron 1 of 7)	intron (NM_025836, intron 1 of 7)	2532	NM_025836	66905	Mm.311696	NM_025836	ENSMUSG00000024197	Plin3	1300012C15Rik|M6prbp1|Tip47	perilipin 3	protein-coding
mm_4112.1	chr1	167688621	167688633	+	1	NA	promoter-TSS (NM_033652)	promoter-TSS (NM_033652)	-931	NM_033652	110648	Mm.330081	NM_033652	ENSMUSG00000026686	Lmx1a	Lmx1.1|dr|dreher|sst	LIM homeobox transcription factor 1 alpha	protein-coding
mm_26196.1	chr3	138526419	138526436	+	1	NA	promoter-TSS (NR_035481)	promoter-TSS (NR_035481)	6	NR_035481	100316706		NR_035481	ENSMUSG00000088373	Mir1956	mir-1956|mmu-mir-1956	microRNA 1956	ncRNA
mm_65995.1	chr7	30554666	30554688	-	1	NA	TTS (NM_001290569)	TTS (NM_001290569)	1375	NM_001012401	243912	Mm.34885	NM_001012401	ENSMUSG00000036854	Hspb6	AA387366|Gm479|Hsp20	heat shock protein, alpha-crystallin-related, B6	protein-coding
mm_13295.1	chr2	102039596	102039597	+	1	NA	intron (NM_001290784, intron 4 of 5)	intron (NM_001290784, intron 4 of 5)	146864	NM_178886	241576	Mm.489740	NM_178886	ENSMUSG00000048058	Ldlrad3	6430500P08|AI194318|Lrad3	low density lipoprotein receptor class A domain containing 3	protein-coding
mm_79228.1	chr9	50479126	50479127	+	1	NA	Intergenic	Intergenic	-15399	NM_029639	76509	Mm.29959	NM_029639	ENSMUSG00000032068	Plet1	0610037B23Rik|1600029D21Rik|AA407923|AU043048	placenta expressed transcript 1	protein-coding
mm_73723.1	chr8	112569828	112569856	+	1	NA	promoter-TSS (NM_130457)	promoter-TSS (NM_130457)	-201	NM_130457	170571	Mm.209232	NM_130457	ENSMUSG00000031772	Cntnap4	Caspr4|E130114F09Rik	contactin associated protein-like 4	protein-coding
mm_123187.1	chr14	57849091	57849094	-	1	NA	intron (NM_029492, intron 7 of 12)	B2_Mm2|SINE|B2	22853	NM_026401	67840	Mm.319530	NM_026401	ENSMUSG00000021967	Mrpl57	2610025P17Rik|AV005697|Mrp63	mitochondrial ribosomal protein L57	protein-coding
mm_117391.1	chr13	73603894	73603943	-	1	NA	promoter-TSS (NM_146047)	promoter-TSS (NM_146047)	-84	NM_146047	218335	Mm.30099	NM_146047	ENSMUSG00000021610	Clptm1l	C130052I12Rik|Crr9	CLPTM1-like	protein-coding
mm_94315.1	chr11	4233000	4233012	+	1	NA	Intergenic	Intergenic	-3779	NM_001013365	18413	Mm.131422	NM_001013365	ENSMUSG00000058755	Osm	OncoM	oncostatin M	protein-coding
mm_19620.1	chr2	102812616	102812629	-	1	NA	3' UTR (NM_009851, exon 19 of 19)	3' UTR (NM_009851, exon 19 of 19)	89043	NM_001177785	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_5890.1	chr1	54250592	54250603	-	1	NA	promoter-TSS (NM_030025)	promoter-TSS (NM_030025)	-86	NM_030025	78016	Mm.67455	NM_030025	ENSMUSG00000025983	Ccdc150	4930511H11Rik	coiled-coil domain containing 150	protein-coding
mm_155684.1	chrX	93675405	93675433	+	1	NA	exon (NM_211138, exon 1 of 8)	exon (NM_211138, exon 1 of 8)	307	NM_211138	236899	Mm.166467	NM_177546	ENSMUSG00000035246	Pcyt1b	AW045697|CTTbeta	phosphate cytidylyltransferase 1, choline, beta isoform	protein-coding
mm_76101.1	chr8	80395058	80395062	-	1	NA	Intergenic	Intergenic	-98985	NM_010369	14934	Mm.13123	NM_010369	ENSMUSG00000051839	Gypa	AI853584|CD235a|GPA	glycophorin A	protein-coding
mm_4909.1	chr1	190170323	190170331	+	1	NA	5' UTR (NM_008937, exon 1 of 5)	5' UTR (NM_008937, exon 1 of 5)	353	NM_008937	19130	Mm.132579	NM_008937	ENSMUSG00000010175	Prox1	A230003G05Rik	prospero homeobox 1	protein-coding
mm_50145.1	chr6	41543573	41543577	+	1	NA	Intergenic	Intergenic	21799	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_33215.1	chr4	126609935	126609941	+	1	NA	promoter-TSS (NM_001145950)	promoter-TSS (NM_001145950)	84	NM_001145950	230757	Mm.296838	NM_001013755	ENSMUSG00000073755	5730409E04Rik	7530403E16Rik|AI849033	RIKEN cDNA 5730409E04Rik gene	protein-coding
mm_54435.1	chr6	34177049	34177071	-	1	NA	promoter-TSS (NM_021435)	promoter-TSS (NM_021435)	-6	NM_021435	58246	Mm.245527	NM_021435	ENSMUSG00000018999	Slc35b4	4930474D06Rik|AB041549|AW494345	solute carrier family 35, member B4	protein-coding
mm_101019.1	chr11	8575590	8575592	-	1	NA	intron (NM_001083587, intron 4 of 30)	intron (NM_001083587, intron 4 of 30)	88944	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_37202.1	chr4	117871325	117871335	-	1	NA	intron (NM_001034876, intron 3 of 7)	MIR|SINE|MIR	1140	NM_001034876	381546	Mm.440118	NM_001034876	ENSMUSG00000078588	Ccdc24	Gm1028	coiled-coil domain containing 24	protein-coding
mm_128446.1	chr15	50763401	50763411	-	1	NA	intron (NM_001310481, intron 4 of 5)	intron (NM_001310481, intron 4 of 5)	125643	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_120067.1	chr14	56929159	56929173	+	1	NA	intron (NM_029498, intron 10 of 23)	intron (NM_029498, intron 10 of 23)	41371	NM_029498	76007	Mm.31417	NM_029498	ENSMUSG00000021945	Zmym2	5830413P05Rik|FIM|MYM|RAMP|SCLL|Zfp198|Znf198	zinc finger, MYM-type 2	protein-coding
mm_170877.1	chr2	20900051	20900051	+	1	NA	intron (NM_001128084, intron 3 of 24)	LSU-rRNA_Hsa|rRNA|rRNA	67670	NM_001081364	71435	Mm.28507	NM_001081364	ENSMUSG00000036591	Arhgap21	5530401C11Rik|AA416458|ARHGAP10	Rho GTPase activating protein 21	protein-coding
mm_93984.1	chr10	127370536	127370542	-	1	NA	promoter-TSS (NM_010565)	promoter-TSS (NM_010565)	9	NM_010565	16325	Mm.2594	NM_010565	ENSMUSG00000025405	Inhbc	-	inhibin beta-C	protein-coding
mm_65651.1	chr7	28129321	28129328	-	1	NA	promoter-TSS (NM_001164655)	promoter-TSS (NM_001164655)	-142	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_75102.1	chr8	34146148	34146161	-	1	NA	intron (NM_026609, intron 1 of 3)	intron (NM_026609, intron 1 of 3)	585	NM_026609	68192	Mm.34212	NM_026609	ENSMUSG00000031513	Leprotl1	1110067H13Rik|1520402O14Rik|AI854296	leptin receptor overlapping transcript-like 1	protein-coding
mm_124196.1	chr14	98169209	98169263	-	1	NA	exon (NM_001038610, exon 1 of 11)	exon (NM_001038610, exon 1 of 11)	529	NM_001038610	13134	Mm.320593	NM_007826	ENSMUSG00000055639	Dach1	Dac|Dach	dachshund 1 (Drosophila)	protein-coding
mm_94887.1	chr11	27572983	27572983	+	1	NA	Intergenic	Lx3C|LINE|L1	787875	NR_002890	654472	Mm.347777	NR_002890		Gm12070	OTTMUSG00000005300	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_90578.1	chr10	128254186	128254196	+	1	NA	promoter-TSS (NM_133996)	promoter-TSS (NM_133996)	60	NM_133996	28194	Mm.439846	NM_133996	ENSMUSG00000051716	Apon	AI195275|D10Ucla2	apolipoprotein N	protein-coding
mm_103865.1	chr11	83462982	83463038	-	1	NA	promoter-TSS (NM_080453)	promoter-TSS (NM_080453)	30	NM_172797	118453	Mm.264648	NM_080453	ENSMUSG00000020682	Mmp28	D130023P12	matrix metallopeptidase 28 (epilysin)	protein-coding
mm_99528.1	chr11	103170993	103171009	+	1	NA	promoter-TSS (NM_001077698)	promoter-TSS (NM_001077698)	-137	NM_001077698	57778	Mm.138913	NM_019679	ENSMUSG00000055805	Fmnl1	8030453N10Rik|AI553564|Fmnl|Fnrl|Frls	formin-like 1	protein-coding
mm_127840.1	chr15	6874292	6874293	-	1	NA	promoter-TSS (NM_011019)	promoter-TSS (NM_011019)	21	NM_011019	18414	Mm.10760	NM_011019	ENSMUSG00000022146	Osmr	OSMRB	oncostatin M receptor	protein-coding
mm_40076.1	chr5	34336965	34337016	+	1	NA	promoter-TSS (NM_001304270)	promoter-TSS (NM_001304270)	58	NM_001304270	19822	Mm.21281	NM_011278	ENSMUSG00000029110	Rnf4	AU018689|Gtrgeo8|SNURF	ring finger protein 4	protein-coding
mm_159977.1	chr6	113127789	113127789	+	1	NA	intron (NM_173005, intron 14 of 20)	intron (NM_173005, intron 14 of 20)	22854	NM_173005	72895	Mm.367159	NM_028385	ENSMUSG00000034269	Setd5	2900045N06Rik|C330007C20|C85544|mKIAA1757	SET domain containing 5	protein-coding
mm_89198.1	chr10	86348130	86348169	+	1	NA	3' UTR (NM_011595, exon 5 of 5)	3' UTR (NM_011595, exon 5 of 5)	47737	NM_011595	21859	Mm.4871	NM_011595	ENSMUSG00000020044	Timp3	Timp-3	tissue inhibitor of metalloproteinase 3	protein-coding
mm_86943.1	chr10	24596440	24596456	+	1	NA	exon (NM_010217, exon 3 of 5)	exon (NM_010217, exon 3 of 5)	1006	NM_010217	14219	Mm.390287	NM_010217	ENSMUSG00000019997	Ctgf	Ccn2|Fisp12|Hcs24|fisp-12	connective tissue growth factor	protein-coding
mm_169712.1	chr15	76199730	76199735	-	1	NA	promoter-TSS (NM_201392)	promoter-TSS (NM_201392)	103	NM_201391	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
mm_77964.1	chr9	7764180	7764190	+	1	NA	5' UTR (NM_133739, exon 1 of 5)	5' UTR (NM_133739, exon 1 of 5)	108	NM_133739	71929	Mm.283293	NM_133739	ENSMUSG00000050912	Tmem123	2310075C12Rik	transmembrane protein 123	protein-coding
mm_7976.1	chr1	134079115	134079119	-	1	NA	promoter-TSS (NM_007570)	promoter-TSS (NM_007570)	38	NM_007570	12227	Mm.392646	NM_007570	ENSMUSG00000020423	Btg2	AA959598|APRO1|Pc3|TIS21	B cell translocation gene 2, anti-proliferative	protein-coding
mm_75356.1	chr8	45262003	45262009	-	1	NA	promoter-TSS (NM_028066)	promoter-TSS (NM_028066)	25	NM_028066	109821	Mm.33326	NM_028066	ENSMUSG00000031645	F11	1600027G01Rik|AI503996|Cf11|FXI|PTA	coagulation factor XI	protein-coding
mm_121302.1	chr14	105681974	105681992	+	1	NA	Intergenic	Intergenic	-58213	NR_105814	102465207		NR_105814	ENSMUSG00000098780	Mir6390	Gm27562|mmu-mir-6390	microRNA 6390	ncRNA
mm_163548.1	chr13	21780446	21780456	-	1	NA	exon (NM_020034, exon 1 of 1)	exon (NM_020034, exon 1 of 1)	174	NM_020034	56702	Mm.221314	NM_020034	ENSMUSG00000058773	Hist1h1b	H1.5|H1B|H1f5|H1s-3	histone cluster 1, H1b	protein-coding
mm_125318.1	chr15	38237900	38237901	+	1	NA	Intergenic	Intergenic	18697	NM_008757	18285	Mm.252830	NM_008757	ENSMUSG00000061923	Odf1	-	outer dense fiber of sperm tails 1	protein-coding
mm_19713.1	chr2	104006741	104006754	-	1	NA	Intergenic	Intergenic	-21052	NM_020593	57443	Mm.143768	NM_020593	ENSMUSG00000027180	Fbxo3	1200002G09Rik|1700026K02Rik|AI046358|Fba	F-box protein 3	protein-coding
mm_136226.1	chr16	90259531	90259547	-	1	NA	intron (NM_178923, intron 4 of 19)	intron (NM_178923, intron 4 of 19)	24964	NM_178923	224432	Mm.439811	NM_178923	ENSMUSG00000022983	Scaf4	AA517739|Sfrs15|Sra4|Srsf15	SR-related CTD-associated factor 4	protein-coding
mm_102932.1	chr11	69600954	69600965	-	1	NA	3' UTR (NM_013415, exon 7 of 7)	3' UTR (NM_013415, exon 7 of 7)	5001	NM_013415	11932	Mm.235204	NM_013415	ENSMUSG00000041329	Atp1b2	Amog|Atpb-2	ATPase, Na+/K+ transporting, beta 2 polypeptide	protein-coding
mm_2145.1	chr1	88095579	88095592	+	1	NA	exon (NM_201642, exon 1 of 5)	exon (NM_201642, exon 1 of 5)	584	NM_201642	394432	Mm.300095	NM_201642	ENSMUSG00000090124	Ugt1a7c	A10'|A13|Ugt1a10	UDP glucuronosyltransferase 1 family, polypeptide A7C	protein-coding
mm_72188.1	chr8	72491820	72491839	+	1	NA	intron (NM_177766, intron 2 of 5)	intron (NM_177766, intron 2 of 5)	785	NM_177766	270066	Mm.291461	NM_177766	ENSMUSG00000019731	Slc35e1	6030458H05|AA408278	solute carrier family 35, member E1	protein-coding
mm_5851.1	chr1	53187597	53187635	-	1	NA	promoter-TSS (NM_027070)	promoter-TSS (NM_027070)	1	NM_027070	69397	Mm.307084	NM_027070	ENSMUSG00000060715	1700019A02Rik	-	RIKEN cDNA 1700019A02 gene	protein-coding
mm_81252.1	chr9	107982970	107982989	+	1	NA	intron (NM_023738, intron 21 of 23)	intron (NM_023738, intron 21 of 23)	2937	NM_026597	68176	Mm.76166	NM_026597	ENSMUSG00000042106	Fam212a	6230427J02Rik|Inka1	family with sequence similarity 212, member A	protein-coding
mm_67377.1	chr7	79842077	79842101	-	1	NA	exon (NM_008486, exon 1 of 20)	exon (NM_008486, exon 1 of 20)	263	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_20737.1	chr2	137116443	137116451	-	1	NA	promoter-TSS (NM_013822)	promoter-TSS (NM_013822)	73	NM_013822	16449	Mm.22398	NM_013822	ENSMUSG00000027276	Jag1	ABE2|Gsfabe2|Htu|Ozz|Ser-1	jagged 1	protein-coding
mm_56362.1	chr6	93912504	93912514	-	1	NA	intron (NM_001029850, intron 2 of 23)	intron (NM_001029850, intron 2 of 23)	454	NR_104594	14924	Mm.217216	NM_010367	ENSMUSG00000045095	Magi1	AIP3|BAP1|Baiap1|Gukmi1|MAGI1c|Magi-1|TNRC19|WWP3|mKIAA4129	membrane associated guanylate kinase, WW and PDZ domain containing 1	protein-coding
mm_32470.1	chr4	107707077	107707079	+	1	NA	Intergenic	Intergenic	-22916	NM_019872	56296	Mm.141324	NM_019872	ENSMUSG00000028610	Dmrtb1	Dmrt6|Prp13	DMRT-like family B with proline-rich C-terminal, 1	protein-coding
mm_16092.1	chr2	168962146	168962162	+	1	NA	Intergenic	RMER10B|LTR|ERVL	-6567	NM_009564	22722	Mm.2095	NM_009564	ENSMUSG00000027551	Zfp64	-	zinc finger protein 64	protein-coding
mm_85400.1	chr9	103364940	103364964	-	1	NA	promoter-TSS (NM_001134427)	promoter-TSS (NM_001134427)	27	NM_001134427	321022	Mm.261025	NM_175565	ENSMUSG00000032803	Cdv3	2510010F10Rik|C230084J24Rik|C79446|TPP36	carnitine deficiency-associated gene expressed in ventricle 3	protein-coding
mm_48486.1	chr5	142509654	142509664	-	1	NA	intron (NM_001289588, intron 2 of 14)	intron (NM_001289588, intron 2 of 14)	20417	NM_019943	56522	Mm.441372	NM_019943	ENSMUSG00000074817	Papolb	PAP|Paplob|Papola-ps|Papt|Plap-ps|Tpap	poly (A) polymerase beta (testis specific)	protein-coding
mm_104988.1	chr11	100265974	100265991	-	1	NA	intron (NM_212483, intron 3 of 7)	intron (NM_212483, intron 3 of 7)	3889	NM_212483	68239	Mm.158190	NM_212483	ENSMUSG00000053654	Krt42	2410039E07Rik|K17n|Ka22|ecat6	keratin 42	protein-coding
mm_156134.1	chrX	123103547	123103572	+	1	NA	promoter-TSS (NM_028426)	promoter-TSS (NM_028426)	36	NM_028426	73061	Mm.292979	NM_028426	ENSMUSG00000079450	Cldn34c1	3110007F17Rik	claudin 34C1	protein-coding
mm_152085.1	chr19	6906880	6906892	-	1	NA	TTS (NM_012021)	TTS (NM_012021)	2759	NM_012021	54683	Mm.279782	NM_012021	ENSMUSG00000024953	Prdx5	AOEB166|AOPP|Pmp20|Prdx6|PrxV	peroxiredoxin 5	protein-coding
mm_148258.1	chr18	80860937	80860952	-	1	NA	intron (NM_001201569, intron 7 of 29)	intron (NM_001201569, intron 7 of 29)	73114	NM_001201569	50771	Mm.247138	NM_015805	ENSMUSG00000024566	Atp9b	AA934181|Atpc2b|IIb|MMR	ATPase, class II, type 9B	protein-coding
mm_129336.1	chr15	77836162	77836174	-	1	NA	intron (NM_022410, intron 1 of 40)	intron (NM_022410, intron 1 of 40)	6007	NM_022410	17886	Mm.29677	NM_022410	ENSMUSG00000022443	Myh9	Fltn|Myhn-1|Myhn1|NMHCIIA|NMMHC-A|NMMHC-IIA|TU72.6	myosin, heavy polypeptide 9, non-muscle	protein-coding
mm_43231.1	chr5	129918549	129918569	+	1	NA	Intergenic	B1_Mm|SINE|Alu	10019	NM_026916	69034	Mm.211372	NM_026916	ENSMUSG00000095789	Nupr1l	1810010E01Rik|4930579G22Rik|Nupr2	nuclear protein transcriptional regulator 1 like	protein-coding
mm_139018.1	chr17	46030641	46030643	+	1	NA	intron (NM_001317041, intron 1 of 6)	CpG	1735	NM_001287058	22339	Mm.282184	NM_009505	ENSMUSG00000023951	Vegfa	Vegf|Vpf	vascular endothelial growth factor A	protein-coding
mm_3763.1	chr1	156067832	156067834	+	1	NA	3' UTR (NM_172843, exon 7 of 7)	3' UTR (NM_172843, exon 7 of 7)	26972	NM_022329	240832	Mm.253335	NM_022329	ENSMUSG00000050565	Tor1aip2	1110020D10Rik|15kDa|A130072J07|AA103493|AW060462|AW610675|C77739|Ifrg15|Lull1	torsin A interacting protein 2	protein-coding
mm_16830.1	chr2	11492612	11492648	-	1	NA	exon (NM_001177754, exon 3 of 16)	exon (NM_001177754, exon 3 of 16)	9460	NM_001177754	170768	Mm.19669	NM_133232	ENSMUSG00000026773	Pfkfb3	E330010H22Rik|iPFK-2|uPFK-2	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	protein-coding
mm_6535.1	chr1	74900977	74900979	-	1	NA	promoter-TSS (NR_029876)	promoter-TSS (NR_029876)	-257	NR_029876	723900		NR_029876	ENSMUSG00000065616	Mir375	Mirn375|mir-375|mmu-mir-375	microRNA 375	ncRNA
mm_55326.1	chr6	55679615	55679634	-	1	NA	exon (NM_009717, exon 2 of 2)	exon (NM_009717, exon 2 of 2)	1639	NM_009717	11922	Mm.5106	NM_009717	ENSMUSG00000037984	Neurod6	Atoh2|Math-2|Math2|Nex|Nex1m|bHLHa2	neurogenic differentiation 6	protein-coding
mm_24868.1	chr3	95937904	95937920	+	1	NA	exon (NM_001253757, exon 5 of 7)	exon (NM_001253757, exon 5 of 7)	8655	NM_023210	66471	Mm.218657	NM_023210	ENSMUSG00000015749	Anp32e	2810018A15Rik|AI047746|AI326868|CPD1|LANP-L|LANPL|mLANP-L	acidic (leucine-rich) nuclear phosphoprotein 32 family, member E	protein-coding
mm_124243.1	chr14	101573030	101573034	-	1	NA	intron (NM_001081278, intron 1 of 18)	intron (NM_001081278, intron 1 of 18)	36159	NM_001081278	210789	Mm.320639	NM_173380	ENSMUSG00000033083	Tbc1d4	5930406J04Rik|A930035N22|AV295684|As160	TBC1 domain family, member 4	protein-coding
mm_69735.1	chr7	140882253	140882272	-	1	NA	promoter-TSS (NM_001127351)	promoter-TSS (NM_001127351)	47	NM_022433	64384	Mm.29760	NM_022433	ENSMUSG00000025486	Sirt3	2310003L23Rik|AI848213|Sir2l3	sirtuin 3	protein-coding
mm_2639.1	chr1	124305151	124305151	+	1	NA	Intergenic	Intergenic	-259592	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_66036.1	chr7	30649997	30650011	-	1	NA	exon (NM_133693, exon 1 of 10)	exon (NM_133693, exon 1 of 10)	224	NM_133693	68035	Mm.401747	NM_133693	ENSMUSG00000036733	Rbm42	1700003D06Rik|3100004P22Rik	RNA binding motif protein 42	protein-coding
mm_903.1	chr1	53823713	53823723	+	1	NA	intron (NM_001001883, intron 28 of 28)	intron (NM_001001883, intron 28 of 28)	-25706	NR_106149	102465783		NR_106149	ENSMUSG00000098443	Mir7681	Gm27806|mmu-mir-7681	microRNA 7681	ncRNA
mm_54000.1	chr6	7692856	7692864	-	1	NA	intron (NM_012055, intron 1 of 11)	intron (NM_012055, intron 1 of 11)	322	NM_012055	27053	Mm.2942	NM_012055	ENSMUSG00000029752	Asns	-	asparagine synthetase	protein-coding
mm_3843.1	chr1	160044654	160044701	+	1	NA	non-coding (NR_028111, exon 1 of 3)	non-coding (NR_028111, exon 1 of 3)	297	NM_001162896	67647	Mm.171518	NM_001024470	ENSMUSG00000090394	4930523C07Rik	-	RIKEN cDNA 4930523C07 gene	protein-coding
mm_13458.1	chr2	105674407	105674422	+	1	NA	intron (NM_001244201, intron 1 of 11)	intron (NM_001244201, intron 1 of 11)	-1330	NM_001244200	18508	Mm.3608	NM_013627	ENSMUSG00000027168	Pax6	1500038E17Rik|AEY11|Dey|Gsfaey11|Pax-6|Sey	paired box 6	protein-coding
mm_9922.1	chr1	189679579	189679588	-	1	NA	intron (NM_001081363, intron 6 of 17)	intron (NM_001081363, intron 6 of 17)	8503	NM_001081363	108000	Mm.129746	NM_001081363	ENSMUSG00000026605	Cenpf	6530404A22Rik|AI325968|CENF|Lek1|PRO1779|mitosin	centromere protein F	protein-coding
mm_123007.1	chr14	54993768	54993797	-	1	NA	intron (NM_080728, intron 1 of 40)	MIRb|SINE|MIR	767	NM_080728	140781	Mm.457983	NM_080728	ENSMUSG00000053093	Myh7	B-MHC|MyHC-I|Myhc-b|Myhcb|beta-MHC	myosin, heavy polypeptide 7, cardiac muscle, beta	protein-coding
mm_168211.1	chr10	75860200	75860200	-	1	NA	promoter-TSS (NM_010798)	promoter-TSS (NM_010798)	50	NM_010798	17319	Mm.2326	NM_010798	ENSMUSG00000033307	Mif	GIF|Glif	macrophage migration inhibitory factor	protein-coding
mm_7036.1	chr1	87100563	87100571	-	1	NA	exon (NM_001081082, exon 5 of 11)	exon (NM_001081082, exon 5 of 11)	1039	NM_001081082	76768	Mm.58068	NM_001081082	ENSMUSG00000079440	Alpi	2010001C14Rik|Akp6|gIAP	alkaline phosphatase, intestinal	protein-coding
mm_162293.1	chr1	31142437	31142459	+	1	NA	intron (NR_033445, intron 2 of 2)	intron (NR_033445, intron 2 of 2)	-33987	NM_153601	266744	Mm.389093	NM_153601	ENSMUSG00000050217	Lgsn	Gluld1|Lgs|lengsin	lengsin, lens protein with glutamine synthetase domain	protein-coding
mm_103742.1	chr11	80139943	80139969	-	1	NA	exon (NM_183275, exon 2 of 4)	exon (NM_183275, exon 2 of 4)	2197	NM_183275	68550	Mm.18466	NM_183275	ENSMUSG00000046909	Tefm	1110002N22Rik	transcription elongation factor, mitochondrial	protein-coding
mm_121035.1	chr14	79891093	79891103	+	1	NA	Intergenic	Intergenic	-21922	NR_033535	100038734	Mm.387484	NR_033535		Gm10845	ENSMUSG00000075496	predicted gene 10845	ncRNA
mm_148509.1	chr19	4214417	4214432	+	1	NA	promoter-TSS (NM_001310039)	promoter-TSS (NM_001310039)	35	NM_001310039	56708	Mm.347919	NM_019952	ENSMUSG00000040663	Clcf1	BSF-3|Bsf3|CLC|NNT-1	cardiotrophin-like cytokine factor 1	protein-coding
mm_173112.1	chrX	158870610	158870612	+	1	NA	Intergenic	L1Md_T|LINE|L1	-385171	NM_148945	110651	Mm.328476	NM_148945	ENSMUSG00000031309	Rps6ka3	MAPKAPK-1b|MPK-9|Rsk2|S6K-alpha3|p90RSK3|pp90RSK2	ribosomal protein S6 kinase polypeptide 3	protein-coding
mm_52662.1	chr6	117900404	117900417	+	1	NA	promoter-TSS (NM_001166432)	promoter-TSS (NM_001166432)	70	NM_001166432	98758	Mm.422979	NM_133834	ENSMUSG00000042079	Hnrnpf	4833420I20Rik|AA407306|Hnrpf	heterogeneous nuclear ribonucleoprotein F	protein-coding
mm_83805.1	chr9	53404526	53404548	-	1	NA	promoter-TSS (NM_029247)	promoter-TSS (NM_029247)	-749	NM_029247	75311	Mm.26078	NM_029247	ENSMUSG00000005131	4930550C14Rik	AU017961	RIKEN cDNA 4930550C14 gene	protein-coding
mm_64734.1	chr7	4724461	4724473	-	1	NA	exon (NM_177887, exon 2 of 5)	exon (NM_177887, exon 2 of 5)	615	NM_001142792	330460	Mm.361851	NM_177887	ENSMUSG00000046456	Tmem150b	A630041N19|Tmem224	transmembrane protein 150B	protein-coding
mm_140763.1	chr17	17624459	17624496	-	1	NA	promoter-TSS (NM_172827)	promoter-TSS (NM_172827)	12	NM_172827	240028	Mm.328807	NM_172827	ENSMUSG00000023845	Lnpep	2010309L07Rik|4732490P18Rik|CAP|IRAP|PLAP|gp160|vp165	leucyl/cystinyl aminopeptidase	protein-coding
mm_80204.1	chr9	72438520	72438533	+	1	NA	promoter-TSS (NM_008613)	promoter-TSS (NM_008613)	-3	NM_008613	17427	Mm.387671	NM_008613	ENSMUSG00000032221	Mns1	AW546487	meiosis-specific nuclear structural protein 1	protein-coding
mm_168284.1	chr11	100493455	100493457	-	1	NA	intron (NM_001199296, intron 19 of 28)	intron (NM_001199296, intron 19 of 28)	-14976	NR_130343	102465671		NR_130343	ENSMUSG00000104854	Mir7116	mmu-mir-7116	microRNA 7116	ncRNA
mm_172405.1	chr7	145340951	145340952	-	1	NA	Intergenic	(TTAGGG)n|Simple_repeat|Simple_repeat	26116	NM_203490	211578	Mm.370299	NM_203490	ENSMUSG00000051207	Mrgprd	Gm499|Mgrd|MrgD|TGR7	MAS-related GPR, member D	protein-coding
mm_41281.1	chr5	90367572	90367589	+	1	NA	non-coding (NR_045618, exon 1 of 1)	non-coding (NR_045618, exon 1 of 1)	583	NR_045618	791294	Mm.30508	NR_045618	ENSMUSG00000054945	Gm9958	ENSMUSG00000054945	predicted gene 9958	ncRNA
mm_105713.1	chr11	108343880	108343897	-	1	NA	promoter-TSS (NM_011101)	promoter-TSS (NM_011101)	0	NM_011101	18750	Mm.222178	NM_011101	ENSMUSG00000050965	Prkca	AI875142|Pkca	protein kinase C, alpha	protein-coding
mm_69607.1	chr7	137194694	137194706	-	1	NA	3' UTR (NM_001113414, exon 16 of 16)	3' UTR (NM_001113414, exon 16 of 16)	-39983	NR_045885	100038555	Mm.444788	NR_045885	ENSMUSG00000109722	Gm10578	ENSMUSG00000073800	predicted gene 10578	ncRNA
mm_133825.1	chr16	95831843	95831852	+	1	NA	non-coding (NR_040485, exon 4 of 4)	non-coding (NR_040485, exon 4 of 4)	66866	NR_040485	69776	Mm.120470	NR_040484	ENSMUSG00000086899	1600002D24Rik	-	RIKEN cDNA 1600002D24 gene	ncRNA
mm_72251.1	chr8	75094171	75094189	+	1	NA	intron (NM_010442, intron 1 of 4)	intron (NM_010442, intron 1 of 4)	562	NM_010442	15368	Mm.276389	NM_010442	ENSMUSG00000005413	Hmox1	D8Wsu38e|HO-1|HO1|Hemox|Hmox|Hsp32	heme oxygenase 1	protein-coding
mm_11111.1	chr2	28193129	28193183	+	1	NA	promoter-TSS (NM_001038613)	promoter-TSS (NM_001038613)	63	NM_001038614	56177	Mm.43278	NM_019498	ENSMUSG00000026833	Olfm1	AMY|AW742568|Noe1|OlfA|Pancortin|Pancortin3	olfactomedin 1	protein-coding
mm_165430.1	chr2	153413803	153413815	+	1	NA	intron (NM_001001986, intron 7 of 7)	intron (NM_001001986, intron 7 of 7)	30670	NM_001001986	329540	Mm.50600	NM_001001986	ENSMUSG00000061411	Nol4l	4931410H15|8430427H17Rik|AI429157|Gm1636	nucleolar protein 4-like	protein-coding
mm_133445.1	chr16	87732653	87732658	+	1	NA	3' UTR (NM_007520, exon 5 of 5)	3' UTR (NM_007520, exon 5 of 5)	33701	NM_007520	12013	Mm.26147	NM_007520	ENSMUSG00000025612	Bach1	6230421P05Rik|AI323795	BTB and CNC homology 1, basic leucine zipper transcription factor 1	protein-coding
mm_121593.1	chr14	7967713	7967727	-	1	NA	3' UTR (NM_007870, exon 8 of 8)	3' UTR (NM_007870, exon 8 of 8)	26462	NM_007870	13421	Mm.272258	NM_007870	ENSMUSG00000025279	Dnase1l3	DNasegamma|Dhp2|Lsd	deoxyribonuclease 1-like 3	protein-coding
mm_75494.1	chr8	50916111	50916121	-	1	NA	Intergenic	CpG	548004	NR_046067	100039954	Mm.400419	NR_046067	ENSMUSG00000110281	Gm2516	-	predicted gene 2516	ncRNA
mm_61039.1	chr7	49687663	49687666	+	1	NA	Intergenic	Intergenic	-50829	NM_001005232	13172	Mm.307176	NM_001005232	ENSMUSG00000030507	Dbx1	AI426026|Dbx	developing brain homeobox 1	protein-coding
mm_70327.1	chr8	4354145	4354155	+	1	NA	exon (NM_009138, exon 4 of 6)	exon (NM_009138, exon 4 of 6)	4562	NM_009138	20300	Mm.7275	NM_009138	ENSMUSG00000023235	Ccl25	A130072A22Rik|AI852536|CKb15|Scya25|TECK	chemokine (C-C motif) ligand 25	protein-coding
mm_44552.1	chr5	24598934	24598955	-	1	NA	intron (NM_025891, intron 1 of 12)	CpG-10886	3058	NM_025891	66993	Mm.436539	NM_025891	ENSMUSG00000028949	Smarcd3	1500001J14Rik|2210409C08Rik|BAF60C	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3	protein-coding
mm_108358.1	chr12	80721697	80721719	+	1	NA	intron (NM_001177503, intron 11 of 12)	intron (NM_001177503, intron 11 of 12)	29107	NM_001177503	217682	Mm.154541	NM_001177503	ENSMUSG00000066438	Plekhd1	3830431G21Rik	pleckstrin homology domain containing, family D (with coiled-coil domains) member 1	protein-coding
mm_168436.1	chr1	135729189	135729190	+	1	NA	promoter-TSS (NM_007791)	promoter-TSS (NM_007791)	-8	NM_007791	13007	Mm.196484	NM_007791	ENSMUSG00000026421	Csrp1	AA408841|AA959891|AW545626|CRP1|Csrp	cysteine and glycine-rich protein 1	protein-coding
mm_115562.1	chr13	9764432	9764475	-	1	NA	promoter-TSS (NM_001347480)	promoter-TSS (NM_001347480)	17	NM_001347470	66505	Mm.397307	NM_144516	ENSMUSG00000021156	Zmynd11	2210402G22Rik|BS69	zinc finger, MYND domain containing 11	protein-coding
mm_115990.1	chr13	24375943	24375959	-	1	NA	intron (NM_001284519, intron 2 of 17)	intron (NM_001284519, intron 2 of 17)	-39171	NM_007717	12763	Mm.8396	NM_007717	ENSMUSG00000016756	Cmah	-	cytidine monophospho-N-acetylneuraminic acid hydroxylase	protein-coding
mm_63255.1	chr7	126649351	126649367	+	1	NA	promoter-TSS (NM_029339)	promoter-TSS (NM_029339)	50	NM_029339	75565	Mm.45686	NM_029339	ENSMUSG00000030714	Sgf29	1700023O11Rik|9530025I05Rik|Ccdc101	SAGA complex associated factor 29	protein-coding
mm_112778.1	chr13	20090501	20090518	+	1	NA	promoter-TSS (NM_080288)	promoter-TSS (NM_080288)	2	NM_080288	140580	Mm.342392	NM_080288	ENSMUSG00000041112	Elmo1	6330578D22Rik|C230095H21Rik|CED-12	engulfment and cell motility 1	protein-coding
mm_59673.1	chr7	28381284	28381295	+	1	NA	Intergenic	Intergenic	-2061	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_51905.1	chr6	91156773	91156827	+	1	NA	promoter-TSS (NM_144919)	promoter-TSS (NM_144919)	-15	NM_144919	232232	Mm.206218	NM_144919	ENSMUSG00000034245	Hdac11	-	histone deacetylase 11	protein-coding
mm_11956.1	chr2	53015497	53015500	+	1	NA	intron (NM_172409, intron 2 of 26)	intron (NM_172409, intron 2 of 26)	157630	NM_172409	71409	Mm.394427	NM_172409	ENSMUSG00000036053	Fmnl2	5430425K04Rik|Man	formin-like 2	protein-coding
mm_31836.1	chr4	72201259	72201365	+	1	NA	promoter-TSS (NM_001285532)	promoter-TSS (NM_001285532)	68	NR_027923	68285	Mm.37541	NR_027923		C630043F03Rik	AI851307	RIKEN cDNA C630043F03 gene	ncRNA
mm_92706.1	chr10	80754667	80754671	-	1	NA	promoter-TSS (NM_199322)	promoter-TSS (NM_199322)	-537	NM_199322	208266	Mm.152371	NM_199322	ENSMUSG00000061589	Dot1l	A630076O07|AW907654|Dot1|KMT4|mDot1	DOT1-like, histone H3 methyltransferase (S. cerevisiae)	protein-coding
mm_58702.1	chr7	12928269	12928300	+	1	NA	exon (NM_029809, exon 2 of 2)	exon (NM_029809, exon 2 of 2)	868	NM_029809	381845	Mm.439896	NM_029809	ENSMUSG00000033967	Rnf225	2310014L17Rik|AV237412|C77118	ring finger protein 225	protein-coding
mm_151883.1	chr19	5798558	5798566	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	-2581	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_148703.1	chr19	5801123	5801222	+	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	1500	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_159651.1	chr4	146252045	146252045	+	1	NA	Intergenic	Intergenic	-18340	NM_001083918	666532	Mm.392861	NM_001083918	ENSMUSG00000067916	Zfp991	Gm13139|OTTMUSG00000010657	zinc finger protein 991	protein-coding
mm_24436.1	chr3	90587256	90587271	+	1	NA	Intergenic	Intergenic	-2984	NM_001195760	628324	Mm.33816	NM_001195760	ENSMUSG00000094018	S100a2	CaN19|EG628324|S100L	S100 calcium binding protein A2	protein-coding
mm_59680.1	chr7	28436125	28436133	+	1	NA	promoter-TSS (NM_175021)	promoter-TSS (NM_175021)	62	NM_175021	233033	Mm.54120	NM_175021	ENSMUSG00000109336	Samd4b	BC042901	sterile alpha motif domain containing 4B	protein-coding
mm_94521.1	chr11	9010676	9010709	+	1	NA	5' UTR (NM_001303610, exon 1 of 7)	5' UTR (NM_001303610, exon 1 of 7)	499	NM_001303610	15574	Mm.42201	NM_008316	ENSMUSG00000020413	Hus1	-	HUS1 checkpoint clamp component	protein-coding
mm_53886.1	chr6	3373572	3373593	-	1	NA	exon (NM_010156, exon 2 of 2)	exon (NM_010156, exon 2 of 2)	25989	NM_010156	209086	Mm.196013	NM_010156	ENSMUSG00000047735	Samd9l	AA175286|ESTM25|mKIAA2005	sterile alpha motif domain containing 9-like	protein-coding
mm_55598.1	chr6	71632988	71632991	-	1	NA	promoter-TSS (NM_173001)	promoter-TSS (NM_173001)	-72	NM_001038695	104263	Mm.260479	NM_173001	ENSMUSG00000053470	Kdm3a	1700105C21Rik|C230043E16Rik|JHDM2a|Jmjd1|Jmjd1a|KDM2A|TGSA|Tsga	lysine (K)-specific demethylase 3A	protein-coding
mm_66720.1	chr7	46100705	46100721	-	1	NA	promoter-TSS (NM_001204411)	promoter-TSS (NM_001204411)	51	NM_001204411	16514	Mm.333863	NM_010602	ENSMUSG00000096146	Kcnj11	Kir6.2|mBIR	potassium inwardly rectifying channel, subfamily J, member 11	protein-coding
mm_37834.1	chr4	132048989	132049012	-	1	NA	promoter-TSS (NM_001128606)	promoter-TSS (NM_001128606)	78	NM_001128606	269587	Mm.30038	NM_183428	ENSMUSG00000028906	Epb41	4.1R|AI415518|D4Ertd442e|Elp-1|Elp1|Epb4.1|mKIAA4056	erythrocyte membrane protein band 4.1	protein-coding
mm_145203.1	chr18	49982778	49982783	+	1	NA	intron (NM_001177759, intron 1 of 1)	intron (NM_001177759, intron 1 of 1)	3353	NM_001177759	106869	Mm.27740	NM_134131	ENSMUSG00000062210	Tnfaip8	AA987150|E130304C20Rik|ENSMUSG00000073567|Gg2-1|Gm10539|Nded|Ssc-2|Tipe	tumor necrosis factor, alpha-induced protein 8	protein-coding
mm_134892.1	chr16	29788197	29788200	-	1	NA	Intergenic	Intergenic	190926	NR_037689	328657	Mm.425982	NM_001033403		Gm1968	-	predicted gene 1968	ncRNA
mm_80226.1	chr9	72662421	72662468	+	1	NA	promoter-TSS (NM_010890)	promoter-TSS (NM_010890)	97	NM_010890	17999	Mm.279923	NM_010890	ENSMUSG00000032216	Nedd4	AA959633|AL023035|AU019897|E430025J12Rik|Nedd4-1|Nedd4a|mKIAA0093	neural precursor cell expressed, developmentally down-regulated 4	protein-coding
mm_79268.1	chr9	50753312	50753325	+	1	NA	promoter-TSS (NM_024441)	promoter-TSS (NM_024441)	347	NM_009964	12955	Mm.178	NM_009964	ENSMUSG00000032060	Cryab	Crya-2|Crya2|HspB5|P23	crystallin, alpha B	protein-coding
mm_156466.1	chrX	143518540	143518556	+	1	NA	promoter-TSS (NM_001195048)	promoter-TSS (NM_001195048)	-43	NM_001195048	18481	Mm.40035	NM_008778	ENSMUSG00000031284	Pak3	PAK-3|Pak65alpha|Pak65beta|Stk4	p21 protein (Cdc42/Rac)-activated kinase 3	protein-coding
mm_152654.1	chr19	12792161	12792163	-	1	NA	intron (NR_024093, intron 1 of 12)	intron (NR_024093, intron 1 of 12)	3961	NR_024093	664779	Mm.290924	NM_001039718	ENSMUSG00000024695	Gm44505	Zfp91-Cntf|Zfp91Cntf	predicted readthrough transcript (NMD candidate), 44505	ncRNA
mm_22373.1	chr2	181155420	181155443	-	1	NA	5' UTR (NM_007906, exon 2 of 8)	5' UTR (NM_007906, exon 2 of 8)	1584	NM_007906	13628	Mm.2645	NM_007906	ENSMUSG00000016349	Eef1a2	Eef1a|S1|wasted|wst	eukaryotic translation elongation factor 1 alpha 2	protein-coding
mm_23069.1	chr3	36075913	36075915	+	1	NA	intron (NM_172678, intron 5 of 17)	intron (NM_172678, intron 5 of 17)	9914	NM_172678	229211	Mm.260997	NM_172678	ENSMUSG00000027710	Acad9	2600017P15Rik|4732402K02|C630012L17Rik|NPD002	acyl-Coenzyme A dehydrogenase family, member 9	protein-coding
mm_99473.1	chr11	102436476	102436484	+	1	NA	TTS (NM_199200)	TTS (NM_199200)	6158	NM_008175	14824	Mm.1568	NM_008175	ENSMUSG00000034708	Grn	Pgrn|epithelin	granulin	protein-coding
mm_91945.1	chr10	60831604	60831617	-	1	NA	promoter-TSS (NM_029770)	promoter-TSS (NM_029770)	-29	NM_029770	107449	Mm.290433	NM_029770	ENSMUSG00000020099	Unc5b	6330415E02Rik|A630020F16|D10Bwg0792e|Unc5h2	unc-5 netrin receptor B	protein-coding
mm_118101.1	chr13	103920341	103920367	-	1	NA	5' UTR (NM_001289475, exon 1 of 26)	5' UTR (NM_001289475, exon 1 of 26)	232	NM_001289473	59079	Mm.277354	NM_021563	ENSMUSG00000021709	Erbin	1700028E05Rik|Erbb2ip|mKIAA1225	Erbb2 interacting protein	protein-coding
mm_168870.1	chr12	36157144	36157155	+	1	NA	promoter-TSS (NM_025840)	promoter-TSS (NM_025840)	25	NM_146033	217473	Mm.130422	NM_146033	ENSMUSG00000036188	Ankmy2	AI035571|ZMYND20	ankyrin repeat and MYND domain containing 2	protein-coding
mm_149332.1	chr19	10845737	10845761	+	1	NA	intron (NM_023044, intron 1 of 7)	intron (NM_023044, intron 1 of 7)	3205	NM_023044	65221	Mm.27387	NM_023044	ENSMUSG00000024737	Slc15a3	Ci1|cI-1	solute carrier family 15, member 3	protein-coding
mm_56055.1	chr6	86765426	86765427	-	1	NA	intron (NM_013471, intron 2 of 12)	intron (NM_013471, intron 2 of 12)	9688	NM_001331120	11746	Mm.259702	NM_013471	ENSMUSG00000029994	Anxa4	AI265406|AIV|AW106930|Anx4|Xanx-4	annexin A4	protein-coding
mm_167753.1	chr9	110421290	110421296	-	1	NA	intron (NM_008694, intron 2 of 3)	intron (NM_008694, intron 2 of 3)	1485	NM_008694	18054	Mm.236225	NM_008694	ENSMUSG00000032484	Ngp	bectenecin	neutrophilic granule protein	protein-coding
mm_77063.1	chr8	109737715	109737786	-	1	NA	promoter-TSS (NM_001080930)	promoter-TSS (NM_001080930)	-11	NM_001080930	52335	Mm.276770	NM_001080930	ENSMUSG00000069895	Atxn1l	AW558552|Boat|C330011L24Rik|D6Mgi37|D8Ertd587e|ENSMUSG00000069895	ataxin 1-like	protein-coding
mm_140325.1	chr17	86753810	86753820	+	1	NA	promoter-TSS (NM_010137)	promoter-TSS (NM_010137)	-49	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_135872.1	chr16	62811984	62811994	-	1	NA	exon (NM_026577, exon 5 of 10)	exon (NM_026577, exon 5 of 10)	-2687	NM_026588	68159	Mm.386793	NM_026588	ENSMUSG00000047854	Stx19	A030009B12Rik	syntaxin 19	protein-coding
mm_156598.1	chrX	152432681	152432702	+	1	NA	Intergenic	Intergenic	63663	NR_045452	75693	Mm.287381	NR_045451	ENSMUSG00000084885	3010001F23Rik	-	RIKEN cDNA 3010001F23 gene	ncRNA
mm_67203.1	chr7	74302591	74302601	-	1	NA	intron (NM_001038643, intron 8 of 10)	B4|SINE|B4	252184	NM_023908	108116	Mm.425467	NM_023908	ENSMUSG00000025790	Slco3a1	5830414C08Rik|Anr1|MJAM|OATP-D|R75096|Slc21a11	solute carrier organic anion transporter family, member 3a1	protein-coding
mm_74114.1	chr8	123042664	123042672	+	1	NA	promoter-TSS (NR_045268)	promoter-TSS (NR_045268)	93	NR_045268	100503178	Mm.294938	NR_045268	ENSMUSG00000099881	2810013P06Rik	-	RIKEN cDNA 2810013P06 gene	ncRNA
mm_68478.1	chr7	110862964	110862970	-	1	NA	promoter-TSS (NM_053247)	promoter-TSS (NM_053247)	-14	NM_053247	114332	Mm.396078	NM_053247	ENSMUSG00000030787	Lyve1	1200012G08Rik|Crsbp-1|Lyve-1|Xlkd1	lymphatic vessel endothelial hyaluronan receptor 1	protein-coding
mm_154924.1	chrX	23705957	23705982	+	1	NA	intron (NM_001305675, intron 2 of 20)	intron (NM_001305675, intron 2 of 20)	12918	NM_001305675	72404	Mm.423	NM_175180	ENSMUSG00000036769	Wdr44	2610034K17Rik|RAB11BP|RPH11	WD repeat domain 44	protein-coding
mm_31076.1	chr4	41388026	41388041	+	1	NA	intron (NM_023305, intron 5 of 6)	intron (NM_023305, intron 5 of 6)	39037	NM_023305	67123	Mm.289795	NM_023305	ENSMUSG00000028437	Ubap1	2700092A01Rik|NAG20|UBAP-1|Ubap	ubiquitin-associated protein 1	protein-coding
mm_148374.1	chr19	3134205	3134205	+	1	NA	Intergenic	Intergenic	63498	NR_045304	70011	Mm.393871	NR_045304	ENSMUSG00000100969	1700030N03Rik	1700087C08Rik	RIKEN cDNA 1700030N03 gene	ncRNA
mm_111535.1	chr12	100837415	100837433	-	1	NA	intron (NM_145448, intron 3 of 12)	ORR1F|LTR|ERVL-MaLR	58301	NM_145448	217830	Mm.218590	NM_145448	ENSMUSG00000021185	9030617O03Rik	-	RIKEN cDNA 9030617O03 gene	protein-coding
mm_28696.1	chr3	95538813	95538848	-	1	NA	exon (NM_021281, exon 3 of 8)	exon (NM_021281, exon 3 of 8)	12044	NM_001267695	13040	Mm.3619	NM_021281	ENSMUSG00000038642	Ctss	Cats	cathepsin S	protein-coding
mm_112969.1	chr13	21286898	21286912	+	1	NA	3' UTR (NM_010343, exon 5 of 5)	3' UTR (NM_010343, exon 5 of 5)	5781	NM_010343	14780	Mm.1332	NM_010343	ENSMUSG00000004344	Gpx5	AV379049|Arep	glutathione peroxidase 5	protein-coding
mm_64110.1	chr7	141061304	141061311	+	1	NA	promoter-TSS (NM_177897)	promoter-TSS (NM_177897)	33	NM_177897	330671	Mm.133741	NM_177897	ENSMUSG00000055629	B4galnt4	BC038881|Gm1095|beta4GalNAcT4	beta-1,4-N-acetyl-galactosaminyl transferase 4	protein-coding
mm_20884.1	chr2	148850960	148850985	-	1	NA	promoter-TSS (NM_029960)	promoter-TSS (NM_029960)	-38	NM_029960	77705	Mm.159975	NM_029960	ENSMUSG00000027446	9230104L09Rik	mCST E2	RIKEN cDNA 9230104L09 gene	protein-coding
mm_107621.1	chr12	51377561	51377587	+	1	NA	promoter-TSS (NM_001306178)	promoter-TSS (NM_001306178)	61	NM_029825	76983	Mm.216511	NM_029825	ENSMUSG00000020952	Scfd1	3110021P21Rik|RA410|STXBP1L2	Sec1 family domain containing 1	protein-coding
mm_45532.1	chr5	72752733	72752762	-	1	NA	promoter-TSS (NM_001289495)	promoter-TSS (NM_001289495)	30	NM_001289494	22165	Mm.3264	NM_013698	ENSMUSG00000054892	Txk	A130089B16Rik|Btkl|PTK-RL-18|PTK4|Rlk	TXK tyrosine kinase	protein-coding
mm_64013.1	chr7	140218322	140218340	+	1	NA	promoter-TSS (NM_172909)	promoter-TSS (NM_172909)	64	NM_172909	244233	Mm.19283	NM_172909	ENSMUSG00000025461	Cd163l1	B430307C05|E430002D04Rik|Scart1	CD163 molecule-like 1	protein-coding
mm_2157.1	chr1	88205843	88205853	+	1	NA	promoter-TSS (NM_008299)	promoter-TSS (NM_008299)	-100	NM_008299	15504	Mm.439983	NM_008299	ENSMUSG00000081984	Dnajb3	Hsj3|MSJ-1|Msj1	DnaJ heat shock protein family (Hsp40) member B3	protein-coding
mm_158505.1	chrX	142390604	142390614	-	1	NA	promoter-TSS (NM_207625)	promoter-TSS (NM_207625)	-74	NM_019477	50790	Mm.391337	NM_019477	ENSMUSG00000031278	Acsl4	9430020A05Rik|ACS4|AU018108|Facl4|Lacs4	acyl-CoA synthetase long-chain family member 4	protein-coding
mm_64241.1	chr7	141701426	141701436	+	1	NA	exon (NM_023566, exon 24 of 46)	exon (NM_023566, exon 24 of 46)	11091	NM_023566	17831	Mm.2041	NM_023566		Muc2	2010015E03Rik|MCM|wnn	mucin 2	protein-coding
mm_56073.1	chr6	86796569	86796585	-	1	NA	Intergenic	HAL1|LINE|L1	-2993	NM_013471	11746	Mm.259702	NM_013471	ENSMUSG00000029994	Anxa4	AI265406|AIV|AW106930|Anx4|Xanx-4	annexin A4	protein-coding
mm_114705.1	chr13	83524813	83524838	+	1	NA	promoter-TSS (NM_001347567)	promoter-TSS (NM_001347567)	82	NM_001347580	17260	Mm.24001	NM_025282	ENSMUSG00000005583	Mef2c	5430401D19Rik|9930028G15Rik|AV011172|Mef2	myocyte enhancer factor 2C	protein-coding
mm_5142.1	chr1	9746494	9746513	-	1	NA	exon (NM_173443, exon 1 of 3)	exon (NM_173443, exon 1 of 3)	-1145	NR_040462	73331	Mm.460470	NR_040462		1700034P13Rik	-	RIKEN cDNA 1700034P13 gene	ncRNA
mm_4630.1	chr1	179668188	179668198	+	1	NA	promoter-TSS (NM_178653)	promoter-TSS (NM_178653)	-38	NM_178653	109232	Mm.136458	NM_178653	ENSMUSG00000038936	Sccpdh	AW214504|C330023F11Rik	saccharopine dehydrogenase (putative)	protein-coding
mm_131798.1	chr16	22899164	22899173	+	1	NA	non-coding (NR_075099, exon 6 of 6)	non-coding (NR_075099, exon 6 of 6)	-4782	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_147747.1	chr18	61176995	61177057	-	1	NA	promoter-TSS (NM_178277)	promoter-TSS (NM_178277)	23	NM_178277	106894	Mm.22574	NM_134134	ENSMUSG00000024622	Hmgxb3	2510002C16Rik|A630042L21Rik|AI413166|mKIAA0194	HMG box domain containing 3	protein-coding
mm_104224.1	chr11	88541636	88541646	-	1	NA	intron (NM_054043, intron 6 of 13)	intron (NM_054043, intron 6 of 13)	-77610	NR_131025	68397	Mm.426889	NR_131025		0610039H22Rik	-	RIKEN cDNA 0610039H22 gene	ncRNA
mm_142471.1	chr17	45613026	45613073	-	1	NA	Intergenic	ORR1D2|LTR|ERVL-MaLR	-10947	NM_001177469	653016	Mm.45676	NM_001177468	ENSMUSG00000079471	Gm7325	EG653016|Esgp	predicted gene 7325	protein-coding
mm_90040.1	chr10	115817357	115817369	+	1	NA	promoter-TSS (NM_001168680)	promoter-TSS (NM_001168680)	79	NM_001168679	216350	Mm.22270	NM_146010	ENSMUSG00000034127	Tspan8	C76990|E330007O21Rik|Tm4sf3	tetraspanin 8	protein-coding
mm_56176.1	chr6	88045162	88045175	-	1	NA	promoter-TSS (NM_001293653)	promoter-TSS (NM_001293653)	102	NM_001293652	19349	Mm.333233	NM_009005	ENSMUSG00000079477	Rab7	Rab7a	RAB7, member RAS oncogene family	protein-coding
mm_132846.1	chr16	46010554	46010580	+	1	NA	promoter-TSS (NM_001134480)	promoter-TSS (NM_001134480)	-154	NM_001134480	433022	Mm.380993	NM_001134480	ENSMUSG00000087141	Plcxd2	AW494639|EG433022	phosphatidylinositol-specific phospholipase C, X domain containing 2	protein-coding
mm_95238.1	chr11	44617376	44617397	+	1	NA	promoter-TSS (NM_001290711)	promoter-TSS (NM_001290711)	-714	NM_001290711	13591	Mm.439662	NM_007897	ENSMUSG00000057098	Ebf1	Ebf|O/E-1|OE-1|Olf-1|Olf1	early B cell factor 1	protein-coding
mm_168417.1	chr1	132291786	132291787	-	1	NA	Intergenic	Intergenic	-6840	NM_144810	213417	Mm.39723	NM_144810	ENSMUSG00000042115	Klhdc8a	A630065K24Rik	kelch domain containing 8A	protein-coding
mm_74312.1	chr8	126594828	126594853	+	1	NA	Intergenic	CpG-14677	-1404	NM_001164598	270110	Mm.334918	NM_001164598	ENSMUSG00000051495	Irf2bp2	E130305N23Rik|IRF-2BP2	interferon regulatory factor 2 binding protein 2	protein-coding
mm_113982.1	chr13	52582565	52582596	+	1	NA	promoter-TSS (NM_001198977)	promoter-TSS (NM_001198977)	-857	NM_001198977	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_44956.1	chr5	36696575	36696603	-	1	NA	promoter-TSS (NM_001081232)	promoter-TSS (NM_001081232)	-568	NM_001081232	320661	Mm.26480	NM_177221	ENSMUSG00000029190	D5Ertd579e	9030221A05Rik|A930018H20Rik|Kiaa0232	DNA segment, Chr 5, ERATO Doi 579, expressed	protein-coding
mm_140140.1	chr17	79955511	79955527	+	1	NA	Intergenic	B4A|SINE|B4	-59396	NM_001286647	56298	Mm.175403	NM_019717	ENSMUSG00000059811	Atl2	2010110I21Rik|AA407293|AV334690|Aip-2|Arl6ip2	atlastin GTPase 2	protein-coding
mm_153300.1	chr19	37957402	37957425	-	1	NA	intron (NM_001302140, intron 21 of 53)	L1MC4|LINE|L1	86164	NM_001099634	226101	Mm.34674	NM_177035	ENSMUSG00000048612	Myof	2310004N10Rik|2310051D19Rik|E030042N20Rik|Fer1l3	myoferlin	protein-coding
mm_33233.1	chr4	127021286	127021292	+	1	NA	promoter-TSS (NM_023603)	promoter-TSS (NM_023603)	-12	NR_045010	71514	Mm.257276	NM_023603	ENSMUSG00000028820	Sfpq	1110004P21Rik|2810416M14Rik|5730453G22Rik|9030402K04Rik|AU021830|D4Ertd314e|Gm12940|OTTMUSG00000009329|PSF|REP1	splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)	protein-coding
mm_139774.1	chr17	64755568	64755576	+	1	NA	TTS (NM_008549)	TTS (NM_008549)	-11539	NR_105051	101202683	Mm.393309	NR_105051		Dreh	-	down-regulated in hepatocellular carcinoma	ncRNA
mm_34710.1	chr4	152116313	152116337	+	1	NA	promoter-TSS (NM_033042)	promoter-TSS (NM_033042)	-18	NM_033042	85030	Mm.101198	NM_033042	ENSMUSG00000024793	Tnfrsf25	APO-3|DDR3|DR3|LARD|TR3|TRAMP|Tnfrsf12|WSL-1|WSL-LR|Wsl	tumor necrosis factor receptor superfamily, member 25	protein-coding
mm_111739.1	chr12	103865759	103865772	-	1	NA	Intergenic	Intergenic	-2146	NM_009243	20700	Mm.439692	NM_009243	ENSMUSG00000066366	Serpina1a	Aat-2|Aat2|Dom1|PI1|Spi1-1|Spi1-3	serine (or cysteine) peptidase inhibitor, clade A, member 1A	protein-coding
mm_105701.1	chr11	108261245	108261252	-	1	NA	intron (NM_011101, intron 2 of 16)	intron (NM_011101, intron 2 of 16)	82640	NM_011101	18750	Mm.222178	NM_011101	ENSMUSG00000050965	Prkca	AI875142|Pkca	protein kinase C, alpha	protein-coding
mm_14701.1	chr2	142570466	142570467	+	1	NA	Intergenic	Intergenic	330998	NM_001081133	16558	Mm.251934	NM_001081133	ENSMUSG00000038844	Kif16b	8430434E15Rik|AA623607|AI789011|C80253|C80902|mKIAA1590	kinesin family member 16B	protein-coding
mm_163533.1	chr13	10581558	10581559	+	1	NA	Intergenic	L2a|LINE|L2	-220755	NM_033269	12671	Mm.342315	NM_033269	ENSMUSG00000046159	Chrm3	Chrm-3|M3|M3R	cholinergic receptor, muscarinic 3, cardiac	protein-coding
mm_73203.1	chr8	95678231	95678259	+	1	NA	Intergenic	CpG	-24792	NM_001195006	234593	Mm.29846	NM_145602	ENSMUSG00000036564	Ndrg4	D8Bwg1337e|Ndr1-rs|Ndr4|R74996|SMAP-8	N-myc downstream regulated gene 4	protein-coding
mm_21878.1	chr2	166132679	166132705	-	1	NA	exon (NM_028072, exon 2 of 21)	exon (NM_028072, exon 2 of 21)	22593	NM_001252578	72043	Mm.1011	NM_028072	ENSMUSG00000006800	Sulf2	2010004N24Rik|AU020235|MSulf-2|mKIAA1247	sulfatase 2	protein-coding
mm_36433.1	chr4	82294712	82294726	-	1	NA	3' UTR (NM_001113209, exon 12 of 12)	3' UTR (NM_001113209, exon 12 of 12)	211060	NM_001286127	18028	Mm.317947	NM_008687	ENSMUSG00000008575	Nfib	6720429L07Rik|CTF|E030026I10Rik|NF-I/B|NF1-B|NFI-B	nuclear factor I/B	protein-coding
mm_82324.1	chr9	8042786	8042882	-	1	NA	promoter-TSS (NM_199017)	promoter-TSS (NM_199017)	-11	NM_199017	234912	Mm.172430	NM_199017	ENSMUSG00000053070	9230110C19Rik	-	RIKEN cDNA 9230110C19 gene	protein-coding
mm_48221.1	chr5	137625060	137625067	-	1	NA	promoter-TSS (NM_027708)	promoter-TSS (NM_027708)	15	NM_027708	71176	Mm.474695	NM_027708	ENSMUSG00000089984	Fbxo24	4933422D21Rik|Fbx24	F-box protein 24	protein-coding
mm_130139.1	chr15	90898464	90898472	-	1	NA	promoter-TSS (NR_033583)	promoter-TSS (NR_033583)	8	NR_033583	20738	Mm.431547	NR_033583		Spn-ps	Cd43-ps	sialophorin, pseudogene	pseudo
mm_109642.1	chr12	112809272	112809285	+	1	NA	5' UTR (NM_145450, exon 1 of 5)	5' UTR (NM_145450, exon 1 of 5)	303	NM_145450	217887	Mm.186678	NM_145450	ENSMUSG00000037594	BC022687	AW050009|C130001I08Rik|Flj20080	cDNA sequence BC022687	protein-coding
mm_98090.1	chr11	86593286	86593301	+	1	NA	intron (NM_029478, intron 10 of 11)	intron (NM_029478, intron 10 of 11)	-9135	NR_029738	387140		NR_029738	ENSMUSG00000065455	Mir21a	Mir21|Mirn21|mmu-mir-21|mmu-mir-21a	microRNA 21a	ncRNA
mm_142450.1	chr17	45592828	45592856	-	1	NA	promoter-TSS (NM_022880)	promoter-TSS (NM_022880)	-449	NM_022880	63959	Mm.29744	NM_022880	ENSMUSG00000023942	Slc29a1	1200014D21Rik|AA407560|ENT1	solute carrier family 29 (nucleoside transporters), member 1	protein-coding
mm_57377.1	chr6	124813066	124813092	-	1	NA	intron (NM_009415, intron 1 of 6)	intron (NM_009415, intron 1 of 6)	1217	NM_009415	21991	Mm.4222	NM_009415	ENSMUSG00000023456	Tpi1	AI255506|Tpi|Tpi-1	triosephosphate isomerase 1	protein-coding
mm_59989.1	chr7	30554848	30554860	+	1	NA	TTS (NM_001290569)	TTS (NM_001290569)	1552	NM_001012401	243912	Mm.34885	NM_001012401	ENSMUSG00000036854	Hspb6	AA387366|Gm479|Hsp20	heat shock protein, alpha-crystallin-related, B6	protein-coding
mm_165675.1	chr3	90231076	90231081	+	1	NA	promoter-TSS (NM_206924)	promoter-TSS (NM_206924)	-519	NM_206924	23922	Mm.13912	NM_206924	ENSMUSG00000027937	Jtb	Gm622	jumping translocation breakpoint	protein-coding
mm_161351.1	chr14	55094785	55094785	+	1	NA	promoter-TSS (NM_153083)	promoter-TSS (NM_153083)	1	NM_153083	105663	Mm.319204	NM_153083	ENSMUSG00000045691	Thtpa	AW122966	thiamine triphosphatase	protein-coding
mm_108688.1	chr12	86891608	86891624	+	1	NA	Intergenic	Intergenic	-6802	NM_145836	238330	Mm.248358	NM_145836	ENSMUSG00000034168	Irf2bpl	6430527G18Rik|Eap1	interferon regulatory factor 2 binding protein-like	protein-coding
mm_136427.1	chr16	94290243	94290296	-	1	NA	Intergenic	GC_rich|Low_complexity|Low_complexity	-2413	NM_139145	110948	Mm.30921	NM_139145	ENSMUSG00000040820	Hlcs	410I21.SP6|D16Jhu34	holocarboxylase synthetase (biotin- [propriony-Coenzyme A-carboxylase (ATP-hydrolysing)] ligase)	protein-coding
mm_144253.1	chr18	10921042	10921061	+	1	NA	Intergenic	Intergenic	-131459	NM_010258	14465	Mm.329287	NM_010258	ENSMUSG00000005836	Gata6	AA410133|GATA-6	GATA binding protein 6	protein-coding
mm_74274.1	chr8	125013098	125013108	+	1	NA	5' UTR (NM_016909, exon 1 of 6)	5' UTR (NM_016909, exon 1 of 6)	106	NM_016909	53424	Mm.5248	NM_016909	ENSMUSG00000056820	Tsnax	R74833|Trax	translin-associated factor X	protein-coding
mm_93865.1	chr10	123076368	123076391	-	1	NA	5' UTR (NM_001163024, exon 1 of 35)	5' UTR (NM_001163024, exon 1 of 35)	126	NM_001163024	67074	Mm.169924	NM_153395	ENSMUSG00000034602	Mon2	2610528O22Rik|AW495628|Sf21|mKIAA1040	MON2 homolog, regulator of endosome to Golgi trafficking	protein-coding
mm_141278.1	chr17	27826038	27826044	-	1	NA	Intergenic	Intergenic	-5499	NM_001271511	224647	Mm.196577	NM_001033279	ENSMUSG00000056692	D17Wsu92e	AU020189|C030010A15|C80239	DNA segment, Chr 17, Wayne State University 92, expressed	protein-coding
mm_73199.1	chr8	95633501	95633586	+	1	NA	promoter-TSS (NM_030198)	promoter-TSS (NM_030198)	-16	NM_030198	78833	Mm.35546	NM_030198	ENSMUSG00000031669	Gins3	2700085M18Rik|AI616142	GINS complex subunit 3 (Psf3 homolog)	protein-coding
mm_61809.1	chr7	87246789	87246807	+	1	NA	5' UTR (NM_001285835, exon 1 of 18)	5' UTR (NM_001285835, exon 1 of 18)	149	NM_001285833	50490	Mm.31748	NM_015760	ENSMUSG00000030562	Nox4	AI648021	NADPH oxidase 4	protein-coding
mm_17870.1	chr2	34940146	34940159	-	1	NA	Intergenic	Intergenic	21620	NM_009421	22029	Mm.239514	NM_009421	ENSMUSG00000026875	Traf1	4732496E14Rik	TNF receptor-associated factor 1	protein-coding
mm_171840.1	chr5	150491777	150491790	-	1	NA	intron (NM_172887, intron 59 of 60)	RLTR17|LTR|ERVK	10436	NR_024513	194292	Mm.300184	NR_024513		Gm5	Gm1812	predicted gene 5	ncRNA
mm_31245.1	chr4	44884940	44884943	+	1	NA	intron (NM_138590, intron 2 of 8)	intron (NM_138590, intron 2 of 8)	-96453	NM_080289	76238	Mm.196574	NM_080289	ENSMUSG00000035637	Grhpr	1110059D05Rik|6430629L09Rik|Glxr	glyoxylate reductase/hydroxypyruvate reductase	protein-coding
mm_170701.1	chr2	135659663	135659668	+	1	NA	Intergenic	CpG	-76445	NR_015544	320684	Mm.421433	NR_015544	ENSMUSG00000085631	9630028H03Rik	-	RIKEN cDNA 9630028H03 gene	ncRNA
mm_33340.1	chr4	129287647	129287666	+	1	NA	promoter-TSS (NM_023485)	promoter-TSS (NM_023485)	35	NM_023485	68828	Mm.132243	NM_023485	ENSMUSG00000001333	Sync	1110057H03Rik|SNIP4	syncoilin	protein-coding
mm_108627.1	chr12	85608293	85608304	+	1	NA	exon (NM_001205053, exon 2 of 4)	exon (NM_001205053, exon 2 of 4)	8280	NM_001205053	81703	Mm.103560	NM_030887	ENSMUSG00000034271	Jdp2	Jundm2|Jundp2|TIF	Jun dimerization protein 2	protein-coding
mm_69154.1	chr7	127144530	127144538	-	1	NA	Intergenic	MTE2b|LTR|ERVL-MaLR	-6711	NM_001037810	20737	Mm.283714	NM_009259	ENSMUSG00000051457	Spn	A630014B01Rik|Cd43|Galgp|Ly-48|Ly48	sialophorin	protein-coding
mm_31840.1	chr4	74242469	74242481	+	1	NA	promoter-TSS (NM_001172095)	promoter-TSS (NM_001172095)	-22	NM_001172095	76804	Mm.209059	NM_144787	ENSMUSG00000028397	Kdm4c	2410141F18Rik|AA517467|Gasc1|Jmjd2c	lysine (K)-specific demethylase 4C	protein-coding
mm_3713.1	chr1	153909177	153909189	+	1	NA	3' UTR (NM_008131, exon 7 of 7)	3' UTR (NM_008131, exon 7 of 7)	9254	NM_008131	14645	Mm.210745	NM_008131	ENSMUSG00000026473	Glul	GS|Glns	glutamate-ammonia ligase (glutamine synthetase)	protein-coding
mm_133358.1	chr16	84702047	84702052	+	1	NA	Intergenic	Intergenic	-10974	NR_132106	100653389	Mm.261808	NR_132106	ENSMUSG00000097418	Mir155hg	Bic|Gm26667	Mir155 host gene (non-protein coding)	ncRNA
mm_62479.1	chr7	101871591	101871612	+	1	NA	promoter-TSS (NM_008034)	promoter-TSS (NM_008034)	-813	NM_001252552	14275	Mm.2135	NM_008034	ENSMUSG00000001827	Folr1	FBP1|Folbp-1|Folbp1	folate receptor 1 (adult)	protein-coding
mm_38017.1	chr4	133754261	133754297	-	1	NA	promoter-TSS (NM_001080819)	promoter-TSS (NM_001080819)	-668	NM_001080819	93760	Mm.22478	NM_001080819	ENSMUSG00000007880	Arid1a	1110030E03Rik|BAF250a|Osa1|Smarcf1	AT rich interactive domain 1A (SWI-like)	protein-coding
mm_155536.1	chrX	74304026	74304036	+	1	NA	promoter-TSS (NM_010273)	promoter-TSS (NM_010273)	-981	NM_010273	14567	Mm.205830	NM_010273	ENSMUSG00000015291	Gdi1	GDIA|GDIalpha	guanosine diphosphate (GDP) dissociation inhibitor 1	protein-coding
mm_168815.1	chr12	21899192	21899211	-	1	NA	Intergenic	CpG	257445	NR_136920	100043416		NM_001004167	ENSMUSG00000093846	Gm4425	EG432637|Gm5433	KRAB-domain protein pseudogene	pseudo
mm_5534.1	chr1	38060587	38060590	-	1	NA	intron (NM_019570, intron 13 of 22)	L1_Rod|LINE|L1	62578	NM_198303	226982	Mm.260943	NM_198303	ENSMUSG00000026083	Eif5b	A030003E17Rik|BC018347|IF2	eukaryotic translation initiation factor 5B	protein-coding
mm_154685.1	chrX	7922321	7922351	+	1	NA	exon (NM_013892, exon 2 of 3)	exon (NM_013892, exon 2 of 3)	2514	NM_013892	30052	Mm.4881	NM_013892	ENSMUSG00000039278	Pcsk1n	AI848336|KEP|PEN|PEN19|PEN20|Pan3|SAAS|SAASCT|bLEN|lLEN|proSAAS	proprotein convertase subtilisin/kexin type 1 inhibitor	protein-coding
mm_57055.1	chr6	122486125	122486180	-	1	NA	5' UTR (NM_027664, exon 1 of 6)	5' UTR (NM_027664, exon 1 of 6)	153	NM_027664	108653	Mm.277939	NM_027664	ENSMUSG00000040649	Rimklb	4931417E21Rik|4933426K21Rik|AA097693|AI325948|AU015629|Naags	ribosomal modification protein rimK-like family member B	protein-coding
mm_129042.1	chr15	75111968	75111972	-	1	NA	promoter-TSS (NM_001099217)	promoter-TSS (NM_001099217)	-21	NM_001099217	100041546	Mm.482110	NM_001099217	ENSMUSG00000022584	Ly6c2	Ly-6C.2|Ly-6C2	lymphocyte antigen 6 complex, locus C2	protein-coding
mm_76560.1	chr8	88388758	88388767	-	1	NA	Intergenic	Intergenic	-26571	NM_012047	26992	Mm.5400	NM_012047	ENSMUSG00000031660	Brd7	BP75|CELTIX1|Ptpn13ip	bromodomain containing 7	protein-coding
mm_77418.1	chr8	120668125	120668133	-	1	NA	promoter-TSS (NM_009941)	promoter-TSS (NM_009941)	13	NM_001308449	105734727	Mm.473736	NM_001308449	ENSMUSG00000097919	Emc8-1190005i06rik	-	Emc8-1190005I06Rik readthrough	protein-coding
mm_10147.1	chr2	4300605	4300617	+	1	NA	intron (NM_172475, intron 1 of 22)	intron (NM_172475, intron 1 of 22)	-100365	NM_001177843	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding
mm_49307.1	chr6	18109160	18109179	+	1	NA	promoter-TSS (NM_023729)	promoter-TSS (NM_023729)	-108	NM_023729	74068	Mm.73091	NM_023729	ENSMUSG00000010796	Asz1	4933400N19Rik|Gasz|ORF3	ankyrin repeat, SAM and basic leucine zipper domain containing 1	protein-coding
mm_13659.1	chr2	114055271	114055287	+	1	NA	non-coding (NR_028422, exon 1 of 3)	non-coding (NR_028422, exon 1 of 3)	883	NR_028422	100303644	Mm.330469	NR_028422	ENSMUSG00000092397	C130080G10Rik	-	RIKEN cDNA C130080G10 gene	ncRNA
mm_113570.1	chr13	38345151	38345159	+	1	NA	promoter-TSS (NM_007556)	promoter-TSS (NM_007556)	-561	NM_007556	12161	Mm.385759	NM_007556	ENSMUSG00000039004	Bmp6	D13Wsu115e|Vgr1	bone morphogenetic protein 6	protein-coding
mm_163702.1	chr13	104229008	104229012	+	1	NA	promoter-TSS (NM_021790)	promoter-TSS (NM_021790)	-166	NM_172807	238831	Mm.98910	NM_172807	ENSMUSG00000021713	Ppwd1	4632422M10Rik|A330090G21Rik	peptidylprolyl isomerase domain and WD repeat containing 1	protein-coding
mm_97863.1	chr11	83116953	83116968	+	1	NA	5' UTR (NM_011407, exon 1 of 2)	5' UTR (NM_011407, exon 1 of 2)	115	NM_011407	20555	Mm.10948	NM_011407	ENSMUSG00000078763	Slfn1	AV316259	schlafen 1	protein-coding
mm_106072.1	chr11	116173086	116173103	-	1	NA	3' UTR (NM_015729, exon 14 of 14)	3' UTR (NM_015729, exon 14 of 14)	-4916	NM_172571	217335	Mm.35241	NM_172571	ENSMUSG00000020776	Fbf1	1110033G01Rik|5930413D20|mKIAA1863	Fas (TNFRSF6) binding factor 1	protein-coding
mm_109902.1	chr12	7950124	7950146	-	1	NA	Intergenic	Intergenic	-27542	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_91415.1	chr10	31609819	31609870	-	1	NA	promoter-TSS (NM_001146349)	promoter-TSS (NM_001146349)	-119	NM_001146349	268291	Mm.295212	NM_001146349	ENSMUSG00000063760	Rnf217	AU016819|Ibrdc1	ring finger protein 217	protein-coding
mm_137170.1	chr17	23813420	23813466	+	1	NA	intron (NM_175229, intron 9 of 13)	intron (NM_175229, intron 9 of 13)	10256	NM_175229	75956	Mm.5222	NM_175229	ENSMUSG00000039218	Srrm2	5033413A03Rik|AA410130|SRm300|mKIAA0324	serine/arginine repetitive matrix 2	protein-coding
mm_122162.1	chr14	31398102	31398112	-	1	NA	intron (NM_011894, intron 3 of 8)	intron (NM_011894, intron 3 of 8)	19570	NM_001347585	24056	Mm.383198	NM_011894	ENSMUSG00000021892	Sh3bp5	AI606498|SH3BP-5|Sab	SH3-domain binding protein 5 (BTK-associated)	protein-coding
mm_109474.1	chr12	111421492	111421504	+	1	NA	intron (NM_001289487, intron 2 of 13)	intron (NM_001289487, intron 2 of 13)	4053	NM_001289488	74190	Mm.248640	NM_028807	ENSMUSG00000021280	Exoc3l4	1200009I06Rik|1600013K19Rik	exocyst complex component 3-like 4	protein-coding
mm_56794.1	chr6	116647834	116647850	-	1	NA	intron (NM_178045, intron 3 of 10)	intron (NM_178045, intron 3 of 10)	-1795	NR_106010	102466793		NR_106010	ENSMUSG00000098334	Mir7043	Gm27776|mmu-mir-7043	microRNA 7043	ncRNA
mm_33294.1	chr4	128962597	128962601	+	1	NA	promoter-TSS (NM_172875)	promoter-TSS (NM_172875)	-144	NM_001301841	242669	Mm.215814	NM_172875	ENSMUSG00000028789	Azin2	4933429I20Rik|Adc|Azi2|B930082O19|ODC-p|Odcp	antizyme inhibitor 2	protein-coding
mm_78282.1	chr9	22108101	22108113	+	1	NA	exon (NM_009922, exon 7 of 7)	exon (NM_009922, exon 7 of 7)	5906	NR_106052	102466221		NR_106052	ENSMUSG00000098646	Mir7084	Gm27978|mmu-mir-7084	microRNA 7084	ncRNA
mm_102252.1	chr11	55151680	55151691	-	1	NA	promoter-TSS (NM_172258)	promoter-TSS (NM_172258)	21	NM_172258	215332	Mm.87054	NM_172258	ENSMUSG00000049491	Slc36a3	PAT3|TRAMD2|tramdorin2	solute carrier family 36 (proton/amino acid symporter), member 3	protein-coding
mm_104554.1	chr11	96800807	96800868	-	1	NA	exon (NM_007622, exon 2 of 6)	exon (NM_007622, exon 2 of 6)	-2681	NR_033523	629750	Mm.390396	NR_033523		Gm11517	OTTMUSG00000001634	ubiquitin A-52 residue ribosomal protein fusion product 1 pseudogene	pseudo
mm_94938.1	chr11	29707398	29707416	+	1	NA	exon (NM_194051, exon 3 of 9)	exon (NM_194051, exon 3 of 9)	-11156	NM_024226	68585	Mm.192580	NM_024226	ENSMUSG00000020458	Rtn4	1110020G17Rik|AA407876|AA409940|AA960376|ASY|C130026I10Rik|NOGO|NSP-CL|NgA|Nogo-A|Nogo-B|Nogo-C|mKIAA0886|mKIAA4153	reticulon 4	protein-coding
mm_117212.1	chr13	64089223	64089236	-	1	NA	promoter-TSS (NM_008291)	promoter-TSS (NM_008291)	-28	NM_008291	15487	Mm.5109	NM_008291	ENSMUSG00000033122	Hsd17b3	-	hydroxysteroid (17-beta) dehydrogenase 3	protein-coding
mm_36929.1	chr4	108301115	108301125	-	1	NA	promoter-TSS (NM_001033634)	promoter-TSS (NM_001033634)	-30	NM_001033634	414872	Mm.426241	NM_001033634	ENSMUSG00000034636	Zyg11b	1110046I03Rik|2810482G21Rik|D4Mgi23|Gm431|mKIAA1730	zyg-ll family member B, cell cycle regulator	protein-coding
mm_157049.1	chrX	8018450	8018490	-	1	NA	promoter-TSS (NM_027227)	promoter-TSS (NM_027227)	22	NM_027227	69824	Mm.279756	NM_027227	ENSMUSG00000031163	Glod5	2010001H14Rik|AV061890	glyoxalase domain containing 5	protein-coding
mm_172602.1	chr8	15519930	15519939	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	462281	NM_008664	17930	Mm.272115	NM_008664	ENSMUSG00000031461	Myom2	AW146149	myomesin 2	protein-coding
mm_60547.1	chr7	44480718	44480761	+	1	NA	Intergenic	Intergenic	-3778	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_153608.1	chr19	43940204	43940232	-	1	NA	promoter-TSS (NM_028029)	promoter-TSS (NM_028029)	-20	NM_028029	71972	Mm.159024	NM_028029	ENSMUSG00000025195	Dnmbp	2410003L07Rik|2410003M15Rik|TUBA	dynamin binding protein	protein-coding
mm_6710.1	chr1	82287374	82287387	-	1	NA	exon (NM_010570, exon 1 of 2)	exon (NM_010570, exon 1 of 2)	4059	NM_010570	16367	Mm.4952	NM_010570	ENSMUSG00000055980	Irs1	G972R|IRS-1	insulin receptor substrate 1	protein-coding
mm_153414.1	chr19	40588454	40588464	-	1	NA	promoter-TSS (NM_153554)	promoter-TSS (NM_153554)	4	NM_019698	56454	Mm.233117	NM_019698	ENSMUSG00000025007	Aldh18a1	2810433K04Rik|AI429789|Pycs	aldehyde dehydrogenase 18 family, member A1	protein-coding
mm_160865.1	chr11	61140851	61140851	+	1	NA	promoter-TSS (NM_021349)	promoter-TSS (NM_021349)	16	NM_021349	57916	Mm.265915	NM_021349	ENSMUSG00000010142	Tnfrsf13b	1200009E08Rik|Taci	tumor necrosis factor receptor superfamily, member 13b	protein-coding
mm_31627.1	chr4	59260037	59260053	+	1	NA	promoter-TSS (NR_105031)	promoter-TSS (NR_105031)	-6	NR_105031	101055769	Mm.421401	NR_105031		Gm12596	OTTMUSG00000007649	predicted gene 12596	ncRNA
mm_97713.1	chr11	80179323	80179335	+	1	NA	TTS (NM_172133)	TTS (NM_172133)	-4543	NM_028019	71956	Mm.22985	NM_028019	ENSMUSG00000020707	Rnf135	0610037N03Rik|2410006N06Rik	ring finger protein 135	protein-coding
mm_19405.1	chr2	91649752	91649784	-	1	NA	promoter-TSS (NM_001145902)	promoter-TSS (NM_001145902)	10	NM_001347175	381410	Mm.330401	NM_001033451	ENSMUSG00000075040	Zfp408	Gm1011	zinc finger protein 408	protein-coding
mm_100496.1	chr11	120467801	120467827	+	1	NA	promoter-TSS (NM_197995)	promoter-TSS (NM_197995)	179	NM_001159328	15239	Mm.7919	NM_008244	ENSMUSG00000025793	Hgs	Hgr|Hrs|ZFYVE8|tn	HGF-regulated tyrosine kinase substrate	protein-coding
mm_133846.1	chr16	96205814	96205833	+	1	NA	intron (NM_015825, intron 1 of 7)	intron (NM_015825, intron 1 of 7)	5353	NM_015825	50795	Mm.28638	NM_015825	ENSMUSG00000040666	Sh3bgr	5430437A18Rik	SH3-binding domain glutamic acid-rich protein	protein-coding
mm_17351.1	chr2	26608153	26608163	-	1	NA	Intergenic	Intergenic	-3741	NM_026212	67512	Mm.24244	NM_026212	ENSMUSG00000026922	Agpat2	2510002J07Rik|AV000834|BSCL|BSCL1|LPAAB|LPAAT-beta	1-acylglycerol-3-phosphate O-acyltransferase 2 (lysophosphatidic acid acyltransferase, beta)	protein-coding
mm_135243.1	chr16	37112569	37112583	-	1	NA	3' UTR (NM_172440, exon 28 of 28)	3' UTR (NM_172440, exon 28 of 28)	100790	NM_001159369	77782	Mm.259114	NM_029977	ENSMUSG00000034206	Polq	A430110D14Rik	polymerase (DNA directed), theta	protein-coding
mm_29008.1	chr3	101604540	101604552	-	1	NA	5' UTR (NM_144900, exon 1 of 23)	5' UTR (NM_144900, exon 1 of 23)	161	NM_144900	11928	Mm.193670	NM_144900	ENSMUSG00000033161	Atp1a1	Atpa-1|BC010319	ATPase, Na+/K+ transporting, alpha 1 polypeptide	protein-coding
mm_55422.1	chr6	65130938	65130951	-	1	NA	intron (NM_019455, intron 4 of 5)	ID_B1|SINE|B4	13786	NM_019455	54486	Mm.410688	NM_019455	ENSMUSG00000029919	Hpgds	H-PGDS|Ptgds2	hematopoietic prostaglandin D synthase	protein-coding
mm_48399.1	chr5	140174802	140174813	-	1	NA	intron (NM_010752, intron 11 of 17)	intron (NM_010752, intron 11 of 17)	146745	NM_010752	17120	Mm.27250	NM_010752	ENSMUSG00000029554	Mad1l1	AI173502|AW550425|Mad1	MAD1 mitotic arrest deficient 1-like 1	protein-coding
mm_40529.1	chr5	57920225	57920237	+	1	NA	intron (NM_001122758, intron 2 of 2)	B1_Mur2|SINE|Alu	202150	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_55826.1	chr6	83115413	83115476	-	1	NA	promoter-TSS (NM_020619)	promoter-TSS (NM_020619)	-62	NM_020619	57377	Mm.28188	NM_020619	ENSMUSG00000030036	Mogs	1810017N02Rik|AI181835|Gcs1	mannosyl-oligosaccharide glucosidase	protein-coding
mm_23042.1	chr3	34764189	34764198	+	1	NA	Intergenic	B1_Mur3|SINE|Alu	-7882	NR_110488	102638436	Mm.261793	NR_110488	ENSMUSG00000106519	Gm38509	Peril	predicted gene, 38509	ncRNA
mm_140637.1	chr17	12652671	12652679	-	1	NA	intron (NM_009202, intron 8 of 10)	intron (NM_009202, intron 8 of 10)	23163	NM_009202	20517	Mm.594	NM_009202	ENSMUSG00000023829	Slc22a1	Lx1|Oct1|Orct|Orct1	solute carrier family 22 (organic cation transporter), member 1	protein-coding
mm_114572.1	chr13	75089676	75089682	+	1	NA	promoter-TSS (NM_013628)	promoter-TSS (NM_013628)	-308	NM_013628	18548	Mm.1333	NM_013628	ENSMUSG00000021587	Pcsk1	Nec-1|Nec1|PC1|PC3|Phpp-1|SPC3	proprotein convertase subtilisin/kexin type 1	protein-coding
mm_61824.1	chr7	87828483	87828485	+	1	NA	intron (NM_001143834, intron 4 of 10)	intron (NM_001143834, intron 4 of 10)	244316	NM_001143834	108071	Mm.235018	NM_001033224	ENSMUSG00000049583	Grm5	6430542K11Rik|AI850523|Glu5R|Gprc1e|mGluR5|mGluR5b	glutamate receptor, metabotropic 5	protein-coding
mm_43200.1	chr5	129020692	129020711	+	1	NA	exon (NM_009391, exon 3 of 7)	exon (NM_009391, exon 3 of 7)	545	NM_009391	19384	Mm.297440	NM_009391	ENSMUSG00000029430	Ran	-	RAN, member RAS oncogene family	protein-coding
mm_159156.1	chr2	89609919	89609919	-	1	NA	exon (NM_146966, exon 1 of 1)	exon (NM_146966, exon 1 of 1)	234	NM_146966	258968	Mm.330384	NM_146966	ENSMUSG00000075081	Olfr1247	MOR231-6	olfactory receptor 1247	protein-coding
mm_136953.1	chr17	14945146	14945164	+	1	NA	exon (NM_024250, exon 12 of 12)	exon (NM_024250, exon 12 of 12)	1971	NM_026451	67912	Mm.390949	NM_026451	ENSMUSG00000050088	1600012H06Rik	-	RIKEN cDNA 1600012H06 gene	protein-coding
mm_138771.1	chr17	37175710	37175719	+	1	NA	Intergenic	Intergenic	-18178	NM_023137	24108	Mm.140210	NM_023137	ENSMUSG00000035186	Ubd	FAT10	ubiquitin D	protein-coding
mm_115928.1	chr13	23571152	23571170	-	1	NA	promoter-TSS (NM_178196)	promoter-TSS (NM_178196)	59	NM_178187	319166	Mm.261665	NM_178187	ENSMUSG00000069272	Hist1h2ae	1190022L06	histone cluster 1, H2ae	protein-coding
mm_137806.1	chr17	30004357	30004393	+	1	NA	promoter-TSS (NM_148926)	promoter-TSS (NM_148926)	-712	NM_148926	21769	Mm.220972	NM_148926	ENSMUSG00000044477	Zfand3	AW539211|TEG-27|Tex27	zinc finger, AN1-type domain 3	protein-coding
mm_111816.1	chr12	105685157	105685173	-	1	NA	promoter-TSS (NM_178613)	promoter-TSS (NM_178613)	76	NM_029654	76559	Mm.114362	NM_029654	ENSMUSG00000041341	Atg2b	2410024A21Rik|AI047755|AI503411|AW558123|C030004M05Rik|C630028L02Rik|mKIAA4067	autophagy related 2B	protein-coding
mm_142331.1	chr17	43504279	43504304	-	1	NA	Intergenic	Intergenic	-1518	NM_008585	17287	Mm.5346	NM_008585	ENSMUSG00000023914	Mep1a	AI098089|AW107200|Mep-1|Mep-1a|Mep1	meprin 1 alpha	protein-coding
mm_65406.1	chr7	25237720	25237730	-	1	NA	5' UTR (NM_001031667, exon 1 of 11)	5' UTR (NM_001031667, exon 1 of 11)	126	NM_001031667	606496	Mm.491101	NM_001031667	ENSMUSG00000057177	Gsk3a	2700086H06Rik	glycogen synthase kinase 3 alpha	protein-coding
mm_124764.1	chr15	6665060	6665073	+	1	NA	3' UTR (NM_001278269, exon 17 of 17)	3' UTR (NM_001278269, exon 17 of 17)	-43315	NM_030168	78757	Mm.275811	NM_030168	ENSMUSG00000050310	Rictor	4921505C17Rik|6030405M08Rik|AVO3|AW492497|D530039E11Rik	RPTOR independent companion of MTOR, complex 2	protein-coding
mm_27404.1	chr3	51334285	51334293	-	1	NA	intron (NM_023502, intron 1 of 9)	intron (NM_023502, intron 1 of 9)	6355	NM_001291059	69257	Mm.131038	NM_023502	ENSMUSG00000037174	Elf2	2610036A20Rik|A230104O07Rik|AW111824|BB183398|EU32|NERF|NERF-1A|NERF-1B|NERF-2	E74-like factor 2	protein-coding
mm_92660.1	chr10	80417481	80417485	-	1	NA	intron (NM_001164148, intron 9 of 18)	intron (NM_001164148, intron 9 of 18)	-10662	NM_025650	66594	Mm.379119	NM_025650	ENSMUSG00000020163	Uqcr11	0710008D09Rik|AL022707|Uqcr	ubiquinol-cytochrome c reductase, complex III subunit XI	protein-coding
mm_134860.1	chr16	28446524	28446541	-	1	NA	promoter-TSS (NM_183064)	promoter-TSS (NM_183064)	-457	NM_001276420	14167	Mm.7996	NM_010199	ENSMUSG00000022523	Fgf12	AV114868|B230343J05Rik|FGF-12|FHF-1|Fhf1	fibroblast growth factor 12	protein-coding
mm_40939.1	chr5	76677275	76677279	+	1	NA	Intergenic	Intergenic	85563	NM_199032	381644	Mm.332452	NM_199032	ENSMUSG00000036403	Cep135	BC062951|Cep4|Gm1044	centrosomal protein 135	protein-coding
mm_105877.1	chr11	114924286	114924300	-	1	NA	3' UTR (NM_199221, exon 4 of 4)	3' UTR (NM_199221, exon 4 of 4)	10093	NM_001347651	217304	Mm.185355	NM_199221	ENSMUSG00000063193	Cd300lb	CLM-7|Clm7|Gm253|LMIR5	CD300 molecule like family member B	protein-coding
mm_50795.1	chr6	54264802	54264837	+	1	NA	promoter-TSS (NM_001311133)	promoter-TSS (NM_001311133)	-39	NM_001311133	69993	Mm.321147	NM_023543	ENSMUSG00000004633	Chn2	1700026N20Rik|4930557O16Rik|ARHGAP3|Bch	chimerin 2	protein-coding
mm_156897.1	chrX	167207216	167207270	+	1	NA	3' UTR (NM_021278, exon 3 of 3)	3' UTR (NM_021278, exon 3 of 3)	1975	NM_021278	19241	Mm.142729	NM_021278	ENSMUSG00000049775	Tmsb4x	Ptmb4|Tb4	thymosin, beta 4, X chromosome	protein-coding
mm_167639.1	chr9	64173399	64173399	+	1	NA	promoter-TSS (NM_026507)	promoter-TSS (NM_026507)	12	NM_024212	67891	Mm.280083	NM_024212	ENSMUSG00000032399	Rpl4	2010004J23Rik	ribosomal protein L4	protein-coding
mm_84265.1	chr9	62666029	62666043	-	1	NA	Intergenic	Intergenic	-11819	NM_176922	319480	Mm.34883	NM_176922	ENSMUSG00000032243	Itga11	4732459H24Rik	integrin alpha 11	protein-coding
mm_41625.1	chr5	96918356	96918360	+	1	NA	Intergenic	Intergenic	-2914	NR_131152	666266	Mm.32442	NR_131152	ENSMUSG00000106357	Gm8013	EG666266	predicted gene 8013	ncRNA
mm_9481.1	chr1	173437213	173437236	-	1	NA	intron (NM_001013779, intron 2 of 8)	LTR16A|LTR|ERVL	16620	NM_001013779	383619	Mm.131453	NM_001013779	ENSMUSG00000037860	Aim2	Gm1313|Ifi210	absent in melanoma 2	protein-coding
mm_4214.1	chr1	171288042	171288050	+	1	NA	promoter-TSS (NM_013919)	promoter-TSS (NM_013919)	-85	NM_013919	30941	Mm.27510	NM_013919	ENSMUSG00000053483	Usp21	ESTM28|Usp16|Usp23|W53272	ubiquitin specific peptidase 21	protein-coding
mm_57128.1	chr6	122600821	122600850	-	1	NA	intron (NM_001134391, intron 1 of 7)	intron (NM_001134391, intron 1 of 7)	1609	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_159062.1	chr2	14739708	14739708	+	1	NA	intron (NM_023116, intron 2 of 13)	intron (NM_023116, intron 2 of 13)	19066	NR_028497	625342	Mm.484784	NR_028497		Gm13315	OTTMUSG00000011384	lactate dehydrogenase A pseudogene	pseudo
mm_69007.1	chr7	126702497	126702517	-	1	NA	intron (NM_001301374, intron 2 of 10)	intron (NM_001301374, intron 2 of 10)	1713	NM_001301374	12721	Mm.290482	NM_009898	ENSMUSG00000030707	Coro1a	Clabp|Lmb3|TACO|p57	coronin, actin binding protein 1A	protein-coding
mm_24985.1	chr3	96833266	96833276	+	1	NA	intron (NM_001146001, intron 1 of 8)	B3A|SINE|B2	597	NM_001146001	59020	Mm.489677	NM_021517	ENSMUSG00000038298	Pdzk1	1700023D20Rik|2610507N21Rik|4921513F16Rik|AI267131|AI314638|AL022680|D3Ertd537e|Pdzd1|mPDZK1	PDZ domain containing 1	protein-coding
mm_106717.1	chr12	3834875	3834877	+	1	NA	intron (NM_001271753, intron 1 of 22)	intron (NM_001271753, intron 1 of 22)	27368	NR_045884	100038522	Mm.417270	NR_045884	ENSMUSG00000073242	Dnmt3aos	ENSMUSG00000073242|Gm10485	DNA methyltransferase 3A, opposite strand	ncRNA
mm_46955.1	chr5	114971057	114971079	-	1	NA	promoter-TSS (NM_009327)	promoter-TSS (NM_009327)	-6	NM_009327	21405	Mm.332607	NM_009327	ENSMUSG00000029556	Hnf1a	AI323641|HNF1|HNF1-alpha|HNF1[a]|Hnf-1|Hnf1alpha|LFB1|Tcf-1|Tcf1	HNF1 homeobox A	protein-coding
mm_80308.1	chr9	74110373	74110411	+	1	NA	promoter-TSS (NM_001033500)	promoter-TSS (NM_001033500)	58	NM_001033500	546144	Mm.335289	NM_177908	ENSMUSG00000044976	Wdr72	AW558070|D230040E23	WD repeat domain 72	protein-coding
mm_88915.1	chr10	81180243	81180276	+	1	NA	exon (NM_007907, exon 9 of 14)	exon (NM_007907, exon 9 of 14)	1298	NR_028549	100217454		NR_028549	ENSMUSG00000064441	Snord37	MBII-376	small nucleolar RNA, C/D box 37	snoRNA
mm_101842.1	chr11	48805584	48805619	-	1	NA	TTS (NM_145377)	TTS (NM_145377)	2462	NR_028564	100216540		NR_028564	ENSMUSG00000064780	Snord95	-	small nucleolar RNA, C/D box 95	snoRNA
mm_148684.1	chr19	5692853	5692874	+	1	NA	intron (NM_022012, intron 3 of 11)	intron (NM_022012, intron 3 of 11)	3732	NM_022012	26403	Mm.185026	NM_022012	ENSMUSG00000004054	Map3k11	2610017K16Rik|Mlk3|PTK1|SPRK	mitogen-activated protein kinase kinase kinase 11	protein-coding
mm_101000.1	chr11	8468556	8468560	-	1	NA	intron (NM_001083587, intron 20 of 30)	intron (NM_001083587, intron 20 of 30)	195977	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_18592.1	chr2	66682701	66682705	-	1	NA	intron (NM_009135, intron 22 of 24)	intron (NM_009135, intron 22 of 24)	-47741	NM_001290675	20274	Mm.440889	NM_018852	ENSMUSG00000075316	Scn9a	Nav1.7|PN1|mKIAA4197	sodium channel, voltage-gated, type IX, alpha	protein-coding
mm_94076.1	chr10	128409767	128409862	-	1	NA	promoter-TSS (NM_027257)	promoter-TSS (NM_027257)	-18	NM_027257	69917	Mm.46614	NM_027257	ENSMUSG00000025374	Nabp2	2610036N15Rik|Obfc2b|SSB1	nucleic acid binding protein 2	protein-coding
mm_102838.1	chr11	69332092	69332100	-	1	NA	exon (NM_010599, exon 14 of 14)	exon (NM_010599, exon 14 of 14)	5838	NM_010599	16499	Mm.232472	NM_010599	ENSMUSG00000018470	Kcnab3	C330022D06Rik|Kcnab4|mKv(beta)4	potassium voltage-gated channel, shaker-related subfamily, beta member 3	protein-coding
mm_108317.1	chr12	79645813	79645833	+	1	NA	intron (NM_009014, intron 7 of 10)	intron (NM_009014, intron 7 of 10)	278910	NR_131075	77290	Mm.395042	NR_131073		9430078K24Rik	-	RIKEN cDNA 9430078K24 gene	ncRNA
mm_153823.1	chr19	46305292	46305303	-	1	NA	promoter-TSS (NM_001177370)	promoter-TSS (NM_001177370)	-398	NM_019408	18034	Mm.102365	NM_019408	ENSMUSG00000025225	Nfkb2	NF-kappaB2|lyt|p49|p49/p100|p50B|p52	nuclear factor of kappa light polypeptide gene enhancer in B cells 2, p49/p100	protein-coding
mm_29679.1	chr3	122984273	122984296	-	1	NA	5' UTR (NM_133857, exon 1 of 16)	5' UTR (NM_133857, exon 1 of 16)	163	NM_133857	99526	Mm.491248	NM_133857	ENSMUSG00000039701	Usp53	AA939927|Phxr3|Sp6|mKIAA1350|mbo	ubiquitin specific peptidase 53	protein-coding
mm_168902.1	chr12	55080571	55080573	+	1	NA	promoter-TSS (NM_011899)	promoter-TSS (NM_011899)	76	NM_011899	24067	Mm.471968	NM_011899	ENSMUSG00000073079	Srp54a	54kDa|Srp54	signal recognition particle 54A	protein-coding
mm_5592.1	chr1	39555998	39556022	-	1	NA	intron (NM_001033135, intron 5 of 6)	intron (NM_001033135, intron 5 of 6)	-7170	NR_028555	100217461		NR_028555	ENSMUSG00000077704	Snord89	MBII-289	small nucleolar RNA, C/D box 89	snoRNA
mm_131307.1	chr16	11461831	11461842	+	1	NA	intron (NM_001290148, intron 6 of 13)	intron (NM_001290148, intron 6 of 13)	56188	NM_001290148	74478	Mm.325831	NM_028964	ENSMUSG00000071669	Snx29	4933437K13Rik|ENSMUSG00000079738|Gm11170|Gm1737|Gm930|Rundc2a	sorting nexin 29	protein-coding
mm_151244.1	chr19	53893808	53893826	+	1	NA	intron (NM_011050, intron 1 of 11)	intron (NM_011050, intron 1 of 11)	1586	NM_011050	18569	Mm.1605	NM_011050	ENSMUSG00000024975	Pdcd4	D19Ucla1|Ma3|Tis	programmed cell death 4	protein-coding
mm_39808.1	chr5	30628057	30628063	+	1	NA	Intergenic	Intergenic	-19876	NR_049199	100885838		NR_049199	ENSMUSG00000093710	Mir5625	Gm23930|mmu-mir-5625	microRNA 5625	ncRNA
mm_141370.1	chr17	29007834	29007856	-	1	NA	promoter-TSS (NM_134115)	promoter-TSS (NM_134115)	92	NM_134115	106504	Mm.439986	NM_134115	ENSMUSG00000024006	Stk38	5830476G13Rik|9530097A09Rik|AA617404|Ndr1	serine/threonine kinase 38	protein-coding
mm_13042.1	chr2	91089803	91089831	+	1	NA	Intergenic	Intergenic	-6861	NM_011355	20375	Mm.1302	NM_011355	ENSMUSG00000002111	Spi1	Dis-1|Dis1|PU.1|Sfpi-1|Sfpi1|Spi-1|Tcfpu1|Tfpu.1	spleen focus forming virus (SFFV) proviral integration oncogene	protein-coding
mm_101319.1	chr11	22858768	22858769	-	1	NA	intron (NM_001169114, intron 1 of 1)	intron (NM_001169114, intron 1 of 1)	967	NM_016888	53625	Mm.395495	NM_016888	ENSMUSG00000051650	B3gnt2	AA408337|AA409404|AW260308|B3Galt6|B3gnt1|BGnT-1|BGnT-2|BGnT1|BGnT2|Beta3gnt	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 2	protein-coding
mm_121842.1	chr14	20610280	20610305	-	1	NA	intron (NM_030180, intron 1 of 20)	intron (NM_030180, intron 1 of 20)	8062	NM_030180	78787	Mm.301173	NM_030180	ENSMUSG00000034235	Usp54	4930429G18Rik|AI115571|C030002J06Rik	ubiquitin specific peptidase 54	protein-coding
mm_82211.1	chr9	124142303	124142330	+	1	NA	Intergenic	RMER17D|LTR|ERVK	20773	NM_009917	12774	Mm.14302	NM_009917	ENSMUSG00000079227	Ccr5	AM4-7|CD195|Cmkbr5	chemokine (C-C motif) receptor 5	protein-coding
mm_68669.1	chr7	118856362	118856373	-	1	NA	promoter-TSS (NM_001168218)	promoter-TSS (NM_001168218)	-369	NM_023197	66356	Mm.482278	NM_023197	ENSMUSG00000030980	Knop1	2310008H09Rik|Tsg118	lysine rich nucleolar protein 1	protein-coding
mm_63935.1	chr7	139553022	139553034	+	1	NA	intron (NM_183144, intron 9 of 15)	intron (NM_183144, intron 9 of 15)	29769	NM_183248	14912	Mm.28308	NM_183248	ENSMUSG00000041309	Nkx6-2	Gtx|Nkx6.2	NK6 homeobox 2	protein-coding
mm_92003.1	chr10	62327603	62327655	-	1	NA	intron (NM_010438, intron 4 of 21)	intron (NM_010438, intron 4 of 21)	12792	NM_001146100	15275	Mm.196605	NM_010438	ENSMUSG00000037012	Hk1	BB404130|Hk-1|Hk1-s|dea|mHk1-s	hexokinase 1	protein-coding
mm_82290.1	chr9	7763749	7763761	-	1	NA	promoter-TSS (NM_133739)	promoter-TSS (NM_133739)	-322	NM_133739	71929	Mm.283293	NM_133739	ENSMUSG00000050912	Tmem123	2310075C12Rik	transmembrane protein 123	protein-coding
mm_104933.1	chr11	100085444	100085448	-	1	NA	intron (NM_001159374, intron 3 of 6)	intron (NM_001159374, intron 3 of 6)	2780	NM_001159374	16670	Mm.4161	NM_010665	ENSMUSG00000046095	Krt32	Ha3|Hka2|K32|Krt1-2|Krtha2	keratin 32	protein-coding
mm_49258.1	chr6	17463750	17463809	+	1	NA	promoter-TSS (NM_008591)	promoter-TSS (NM_008591)	-178	NM_008591	17295	Mm.86844	NM_008591	ENSMUSG00000009376	Met	AI838057|HGF|HGFR|Par4|c-Met	met proto-oncogene	protein-coding
mm_153231.1	chr19	34879453	34879465	-	1	NA	promoter-TSS (NM_001114339)	promoter-TSS (NM_001114339)	-4	NM_001114339	75735	Mm.24742	NM_023792	ENSMUSG00000033610	Pank1	Pank|Pank1b	pantothenate kinase 1	protein-coding
mm_46210.1	chr5	98035071	98035090	-	1	NA	Intergenic	Intergenic	-4118	NM_133738	71914	Mm.24842	NM_133738	ENSMUSG00000029338	Antxr2	2310046B19Rik|AW561899|CMG-2|CMG2|cI-35	anthrax toxin receptor 2	protein-coding
mm_68692.1	chr7	119523463	119523474	-	1	NA	promoter-TSS (NM_027943)	promoter-TSS (NM_027943)	14	NM_027943	71830	Mm.84631	NM_027943	ENSMUSG00000030968	Pdilt	1700007B13Rik	protein disulfide isomerase-like, testis expressed	protein-coding
mm_95325.1	chr11	46562005	46562006	+	1	NA	intron (NR_105955, intron 2 of 4)	intron (NR_105955, intron 2 of 4)	-9508	NM_001025435	407814	Mm.271088	NM_001025435	ENSMUSG00000046974	BC053393	-	cDNA sequence BC053393	protein-coding
mm_158367.1	chrX	134973137	134973147	-	1	NA	exon (NM_175446, exon 7 of 7)	exon (NM_175446, exon 7 of 7)	-8388	NM_031259	83454	Mm.103155	NM_031259	ENSMUSG00000009941	Nxf2	4930455N06Rik|Nxf-b	nuclear RNA export factor 2	protein-coding
mm_157742.1	chrX	73039689	73039701	-	1	NA	Intergenic	Intergenic	-2592	NM_001100461	385377	Mm.327861	NM_001100461	ENSMUSG00000050424	Pnma5	mKIAA1934	paraneoplastic antigen family 5	protein-coding
mm_114341.1	chr13	60762468	60762482	+	1	NA	3' UTR (NM_134062, exon 27 of 27)	3' UTR (NM_134062, exon 27 of 27)	23889	NM_199148	218275	Mm.222427	NM_199148	ENSMUSG00000042243	BC051665	-	cDNA sequence BC051665	protein-coding
mm_103431.1	chr11	75764668	75764727	-	1	NA	3' UTR (NM_009536, exon 6 of 6)	3' UTR (NM_009536, exon 6 of 6)	-31112	NR_136933	102641247	Mm.411386	NR_136932		Gm12339	OTTMUSG00000006218	predicted gene 12339	ncRNA
mm_10528.1	chr2	16401726	16401779	+	1	NA	intron (NM_026162, intron 1 of 13)	RSINE1|SINE|B4	45448	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding
mm_85215.1	chr9	96892667	96892688	-	1	NA	Intergenic	Intergenic	-3203	NM_001289645	235534	Mm.233031	NM_153420	ENSMUSG00000043587	Pxylp1	9430094M07Rik|Acpl2|BB177120|C130099A20Rik	2-phosphoxylose phosphatase 1	protein-coding
mm_42960.1	chr5	123076412	123076426	+	1	NA	5' UTR (NM_001039723, exon 1 of 12)	5' UTR (NM_001039723, exon 1 of 12)	144	NM_001039723	330189	Mm.391872	NM_001039723	ENSMUSG00000054434	Tmem120b	-	transmembrane protein 120B	protein-coding
mm_11440.1	chr2	32034410	32034419	+	1	NA	exon (NM_172268, exon 29 of 36)	exon (NM_172268, exon 29 of 36)	-16532	NR_106135	102466844		NR_106135	ENSMUSG00000099075	Mir7674	Gm27563|mmu-mir-7674	microRNA 7674	ncRNA
mm_391.1	chr1	34097266	34097294	+	1	NA	intron (NM_001276764, intron 5 of 102)	intron (NM_001276764, intron 5 of 102)	-20079	NR_105861	102466987		NR_105861	ENSMUSG00000105982	Mir6896	mmu-mir-6896	microRNA 6896	ncRNA
mm_61346.1	chr7	68286183	68286206	+	1	NA	intron (NM_001013811, intron 1 of 8)	intron (NM_001013811, intron 1 of 8)	-9600	NR_040340	100504026	Mm.426764	NR_040340	ENSMUSG00000086628	Gm16157	OTTMUSG00000031023	predicted gene 16157	ncRNA
mm_163624.1	chr13	56128313	56128326	+	1	NA	exon (NM_001159515, exon 2 of 9)	exon (NM_001159515, exon 2 of 9)	7231	NM_012015	26914	Mm.283802	NM_012015	ENSMUSG00000015937	H2afy	H2AF12M|mH2a1|macroH2A1	H2A histone family, member Y	protein-coding
mm_119545.1	chr14	48227127	48227130	+	1	NA	intron (NR_003630, intron 2 of 2)	intron (NR_003630, intron 2 of 2)	28412	NR_003630	624367	Mm.445185	NM_001037921	ENSMUSG00000063885	Gm6498	EG624367	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_87669.1	chr10	58812360	58812409	+	1	NA	promoter-TSS (NM_172788)	promoter-TSS (NM_172788)	-975	NM_172788	237353	Mm.333078	NM_172788	ENSMUSG00000037990	Sh3rf3	4831416G18Rik|Igfbp5-ip|Sh3md4|Sh3rf31	SH3 domain containing ring finger 3	protein-coding
mm_81176.1	chr9	107313522	107313534	+	1	NA	Intergenic	Intergenic	16869	NM_009895	12700	Mm.4592	NM_009895	ENSMUSG00000032578	Cish	CIS-1|CIS1|Cis|F17|F23|SOCS	cytokine inducible SH2-containing protein	protein-coding
mm_111872.1	chr12	108003519	108003571	-	1	NA	promoter-TSS (NM_021399)	promoter-TSS (NM_021399)	-131	NM_021399	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_32237.1	chr4	102255142	102255159	+	1	NA	5' UTR (NM_001177983, exon 1 of 6)	5' UTR (NM_001177983, exon 1 of 6)	211	NM_019840	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_13376.1	chr2	103761414	103761426	+	1	NA	promoter-TSS (NM_153126)	promoter-TSS (NM_153126)	-170	NM_153126	98956	Mm.288005	NM_153126	ENSMUSG00000027185	Nat10	AI429152	N-acetyltransferase 10	protein-coding
mm_100089.1	chr11	115536472	115536516	+	1	NA	promoter-TSS (NM_133354)	promoter-TSS (NM_133354)	-264	NM_133354	170930	Mm.29923	NM_133354	ENSMUSG00000020738	Sumo2	SUMO-2|Smt3A|Smt3b|Smt3h2	small ubiquitin-like modifier 2	protein-coding
mm_59855.1	chr7	29944558	29944596	+	1	NA	intron (NM_178384, intron 1 of 4)	RLTR31B2|LTR|ERVK	7316	NM_178384	72723	Mm.371648	NM_178384	ENSMUSG00000059975	Zfp74	2810054M15Rik|KRAB8|Zfp66|Znf569|mszf21|mszf77	zinc finger protein 74	protein-coding
mm_14186.1	chr2	127080253	127080262	+	1	NA	intron (NM_026678, intron 1 of 7)	intron (NM_026678, intron 1 of 7)	9600	NM_026678	109778	Mm.22028	NM_026678	ENSMUSG00000001999	Blvra	0610006A11Rik|2500001N03Rik|Blvr	biliverdin reductase A	protein-coding
mm_14021.1	chr2	122150974	122150980	+	1	NA	exon (NM_009735, exon 2 of 4)	exon (NM_009735, exon 2 of 4)	3290	NM_009735	12010	Mm.163	NM_009735	ENSMUSG00000060802	B2m	Ly-m11|beta2-m|beta2m	beta-2 microglobulin	protein-coding
mm_61231.1	chr7	64502191	64502205	+	1	NA	promoter-TSS (NM_001291167)	promoter-TSS (NM_001291167)	60	NM_001291167	11784	Mm.4657	NM_007461	ENSMUSG00000030519	Apba2	X11-like|X11L|XllL|mXllL	amyloid beta (A4) precursor protein-binding, family A, member 2	protein-coding
mm_97746.1	chr11	80472660	80472676	+	1	NA	TTS (NM_178616)	TTS (NM_178616)	-4378	NM_009871	12569	Mm.142275	NM_009871	ENSMUSG00000048895	Cdk5r1	Cdk5r|D11Bwg0379e|p25|p35	cyclin-dependent kinase 5, regulatory subunit 1 (p35)	protein-coding
mm_108259.1	chr12	78356778	78356784	+	1	NA	intron (NM_145965, intron 2 of 22)	RLTR33|LTR|ERVK	130126	NM_145965	268566	Mm.341742	NM_145965	ENSMUSG00000047454	Gphn	5730552E08Rik|AI662856|BC027112|C230040D23|GPH|GPHRYN|geph	gephyrin	protein-coding
mm_24604.1	chr3	93445545	93445556	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	3220	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_169910.1	chr16	54868222	54868222	-	1	NA	Intergenic	L1Md_T|LINE|L1	415015	NM_178720	239852	Mm.245045	NM_178720	ENSMUSG00000064310	Zpld1	9430016A21Rik	zona pellucida like domain containing 1	protein-coding
mm_84566.1	chr9	68771459	68771462	-	1	NA	non-coding (NR_033299, exon 1 of 1)	non-coding (NR_033299, exon 1 of 1)	6114	NR_033299	320440	Mm.483129	NM_177159		9530091C08Rik	-	RIKEN cDNA 9530091C08 gene	ncRNA
mm_41926.1	chr5	105684347	105684361	+	1	NA	Intergenic	PB1D9|SINE|Alu	-15615	NM_001122768	231549	Mm.23837	NM_178701	ENSMUSG00000046079	Lrrc8d	2810473G09Rik|4930525N13Rik|A930019F03|Lrrc5	leucine rich repeat containing 8D	protein-coding
mm_164873.1	chr18	57615570	57615571	+	1	NA	intron (NM_001311063, intron 5 of 5)	Tigger7|DNA|TcMar-Tigger	23015	NR_045360	70157	Mm.490532	NR_045360		2210409D07Rik	-	RIKEN cDNA 2210409D07 gene	ncRNA
mm_94874.1	chr11	24098560	24098573	+	1	NA	intron (NM_016707, intron 2 of 4)	intron (NM_016707, intron 2 of 4)	17871	NM_001159290	14025	Mm.53687	NM_016707	ENSMUSG00000000861	Bcl11a	2810047E18Rik|BCL-11A|Ctip1|D930021L15Rik|Evi9|Evi9a|Evi9b|Evi9c|mKIAA1809	B cell CLL/lymphoma 11A (zinc finger protein)	protein-coding
mm_121953.1	chr14	24369802	24369808	-	1	NA	Intergenic	Intergenic	76441	NM_001033214	105418	Mm.2077	NM_001033214	ENSMUSG00000038925	E330034G19Rik	AA415275|Zpac	RIKEN cDNA E330034G19 gene	protein-coding
mm_42899.1	chr5	122422497	122422520	+	1	NA	promoter-TSS (NM_019805)	promoter-TSS (NM_019805)	64	NM_019805	56317	Mm.37341	NM_019805	ENSMUSG00000029466	Anapc7	APC7|AW545589	anaphase promoting complex subunit 7	protein-coding
mm_147565.1	chr18	54990333	54990355	-	1	NA	promoter-TSS (NM_175751)	promoter-TSS (NM_175751)	-164	NM_175751	269023	Mm.192984	NM_175751	ENSMUSG00000052713	Zfp608	4932417D18Rik|D430007A19Rik|Znf608	zinc finger protein 608	protein-coding
mm_153528.1	chr19	41848056	41848066	-	1	NA	promoter-TSS (NM_177603)	promoter-TSS (NM_177603)	71	NM_177603	212398	Mm.222723	NM_177603	ENSMUSG00000047604	Frat2	-	frequently rearranged in advanced T cell lymphomas 2	protein-coding
mm_122041.1	chr14	30009284	30009293	-	1	NA	promoter-TSS (NM_019583)	promoter-TSS (NM_019583)	288	NM_001136240	218865	Mm.259916	NM_172264	ENSMUSG00000015970	Chdh	AU041472|D630034H06Rik	choline dehydrogenase	protein-coding
mm_153045.1	chr19	32068771	32068779	-	1	NA	intron (NM_018830, intron 2 of 23)	intron (NM_018830, intron 2 of 23)	34365	NM_018830	54447	Mm.491229	NM_018830	ENSMUSG00000024887	Asah2	AI585898	N-acylsphingosine amidohydrolase 2	protein-coding
mm_169516.1	chr14	8666290	8666292	-	1	NA	promoter-TSS (NM_028934)	promoter-TSS (NM_028934)	-1	NM_028934	74430	Mm.271901	NM_028934	ENSMUSG00000021747	4930452B06Rik	4933406L09Rik|AI854000	RIKEN cDNA 4930452B06 gene	protein-coding
mm_145113.1	chr18	44270103	44270135	+	1	NA	promoter-TSS (NM_010935)	promoter-TSS (NM_010935)	-8	NM_010935	18169	Mm.57234	NM_010935	ENSMUSG00000038071	Npy6r	-	neuropeptide Y receptor Y6	protein-coding
mm_155244.1	chrX	57223487	57223493	+	1	NA	exon (NM_011616, exon 5 of 5)	exon (NM_011616, exon 5 of 5)	11347	NM_011616	21947	Mm.4861	NM_011616	ENSMUSG00000031132	Cd40lg	CD154|CD40-L|Cd40l|HIGM1|IGM|IMD3|Ly-62|Ly62|T-BAM|TRAP|Tnfsf5|Tnlg8b|gp39	CD40 ligand	protein-coding
mm_120183.1	chr14	61309861	61309871	+	1	NA	5' UTR (NM_177337, exon 1 of 2)	5' UTR (NM_177337, exon 1 of 2)	113	NM_177337	219144	Mm.206566	NM_177337	ENSMUSG00000043157	Arl11	ARLTS1|C730007L20Rik	ADP-ribosylation factor-like 11	protein-coding
mm_17661.1	chr2	32083221	32083271	-	1	NA	5' UTR (NM_175511, exon 1 of 2)	5' UTR (NM_175511, exon 1 of 2)	459	NM_175511	241303	Mm.250441	NM_175511	ENSMUSG00000050592	Fam78a	A130092J06Rik	family with sequence similarity 78, member A	protein-coding
mm_126442.1	chr15	80671687	80671696	+	1	NA	promoter-TSS (NM_145986)	promoter-TSS (NM_145986)	-156	NM_145986	213956	Mm.132439	NM_145986	ENSMUSG00000022408	Fam83f	AW544981	family with sequence similarity 83, member F	protein-coding
mm_169598.1	chr15	34008610	34008616	-	1	NA	Intergenic	RLTR9A|LTR|ERVK	-74106	NM_026002	67154	Mm.130883	NM_026002	ENSMUSG00000022255	Mtdh	2610103J23Rik|3D3|3D3/Lyric|AEG-1|AV353288|D8Bwg1112e|Lyric	metadherin	protein-coding
mm_131325.1	chr16	12811386	12811408	+	1	NA	promoter-TSS (NR_040507)	promoter-TSS (NR_040507)	7	NR_040507	75493	Mm.396146	NR_040507	ENSMUSG00000101565	1700003L19Rik	-	RIKEN cDNA 1700003L19 gene	ncRNA
mm_44570.1	chr5	24752156	24752176	-	1	NA	intron (NM_153076, intron 3 of 3)	(AGGGGG)n|Simple_repeat|Simple_repeat	5677	NM_153076	214301	Mm.63484	NM_153076	ENSMUSG00000038135	Crygn	-	crystallin, gamma N	protein-coding
mm_141666.1	chr17	33824431	33824473	-	1	NA	promoter-TSS (NM_023202)	promoter-TSS (NM_023202)	46	NM_016844	54127	Mm.352374	NM_016844	ENSMUSG00000067288	Rps28	-	ribosomal protein S28	protein-coding
mm_110325.1	chr12	34906881	34906895	-	1	NA	intron (NM_001271386, intron 2 of 27)	CpG	10207	NM_001271386	79221	Mm.310551	NM_024124	ENSMUSG00000004698	Hdac9	AV022454|D030072B18Rik|HD7B|HD9|HDRP|Hdac7b|Mitr|mKIAA0744	histone deacetylase 9	protein-coding
mm_145830.1	chr18	65438819	65438832	+	1	NA	intron (NM_172833, intron 2 of 15)	B3A|SINE|B2	7828	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_10273.1	chr2	9882197	9882208	+	1	NA	TTS (NR_040511)	TTS (NR_040511)	956	NR_024257	381347	Mm.441450	NR_024257		4930412O13Rik	ENSMUSG00000075535|Gm10853	RIKEN cDNA 4930412O13 gene	ncRNA
mm_108908.1	chr12	100206115	100206139	+	1	NA	exon (NM_009790, exon 5 of 6)	exon (NM_009790, exon 5 of 6)	5983	NM_001313934	12313	Mm.285993	NM_009790	ENSMUSG00000001175	Calm1	AI256814|AI327027|AI461935|AL024000|CaM|Calm	calmodulin 1	protein-coding
mm_74223.1	chr8	124047608	124047615	+	1	NA	3' UTR (NM_001029876, exon 9 of 9)	3' UTR (NM_001029876, exon 9 of 9)	24138	NM_001029876	382038	Mm.334891	NM_001029876	ENSMUSG00000031976	Urb2	C77575|mKIAA0133	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	protein-coding
mm_126440.1	chr15	80671637	80671646	+	1	NA	promoter-TSS (NM_145986)	promoter-TSS (NM_145986)	-206	NM_145986	213956	Mm.132439	NM_145986	ENSMUSG00000022408	Fam83f	AW544981	family with sequence similarity 83, member F	protein-coding
mm_115741.1	chr13	17805307	17805368	-	1	NA	promoter-TSS (NM_001081058)	promoter-TSS (NM_001081058)	-240	NM_027118	69562	Mm.193924	NM_027118	ENSMUSG00000041297	Cdk13	2310015O17Rik|Cdc2l5	cyclin-dependent kinase 13	protein-coding
mm_26974.1	chr3	24955145	24955146	-	1	NA	Intergenic	Lx7|LINE|L1	-171139	NM_001326288	635702	Mm.448351	NM_001326288	ENSMUSG00000102758	Naaladl2	2810043G22Rik|EG635702|Gm1021	N-acetylated alpha-linked acidic dipeptidase-like 2	protein-coding
mm_79974.1	chr9	66713710	66713716	+	1	NA	promoter-TSS (NM_178396)	promoter-TSS (NM_178396)	27	NM_001306148	76459	Mm.277921	NM_178396	ENSMUSG00000032373	Car12	2310047E01Rik|AI314958|CA-XII|Ca12	carbonic anhydrase 12	protein-coding
mm_154841.1	chrX	20059582	20059592	+	1	NA	promoter-TSS (NM_021715)	promoter-TSS (NM_021715)	17	NM_021715	60322	Mm.44827	NM_021715	ENSMUSG00000037347	Chst7	2600013M07Rik|C6ST-2|GST5|Gn6st-4|glcNAc6ST-4	carbohydrate (N-acetylglucosamino) sulfotransferase 7	protein-coding
mm_72345.1	chr8	79639427	79639471	+	1	NA	promoter-TSS (NM_001256033)	promoter-TSS (NM_001256033)	-227	NM_001256033	73945	Mm.34348	NM_001081164	ENSMUSG00000036990	Otud4	4930431L18Rik|AI449692|D8Ertd69e|mKIAA1046	OTU domain containing 4	protein-coding
mm_173314.1	chrY	90735261	90735266	+	1	NA	Intergenic	IMPB_01|Satellite|Satellite	19787	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_54078.1	chr6	14757597	14757615	-	1	NA	Intergenic	Intergenic	-2332	NM_080464	140491	Mm.209429	NM_080464	ENSMUSG00000042717	Ppp1r3a	GM|RG1|RGL	protein phosphatase 1, regulatory (inhibitor) subunit 3A	protein-coding
mm_72457.1	chr8	83236075	83236077	+	1	NA	intron (NM_001111304, intron 5 of 20)	intron (NM_001111304, intron 5 of 20)	-54272	NM_009463	22227	Mm.4177	NM_009463	ENSMUSG00000031710	Ucp1	AI385626|Slc25a7|Ucp	uncoupling protein 1 (mitochondrial, proton carrier)	protein-coding
mm_3874.1	chr1	160997635	160997649	+	1	NA	exon (NM_080844, exon 6 of 8)	exon (NM_080844, exon 6 of 8)	19036	NM_080844	11905	Mm.260770	NM_080844	ENSMUSG00000026715	Serpinc1	AI114908|ATIII|At-3|At3	serine (or cysteine) peptidase inhibitor, clade C (antithrombin), member 1	protein-coding
mm_50723.1	chr6	52245002	52245014	+	1	NA	promoter-TSS (NR_015348)	promoter-TSS (NR_015348)	-235	NR_015348	15397	Mm.469918	NR_015348	ENSMUSG00000086427	Hoxa11os	Hoxa11as|Hoxa11s	homeobox A11, opposite strand	ncRNA
mm_139988.1	chr17	72871677	72871691	+	1	NA	Intergenic	Intergenic	34980	NM_027166	383295	Mm.277533	NM_027166	ENSMUSG00000039770	Ypel5	2310076K21Rik|CGI-127	yippee-like 5 (Drosophila)	protein-coding
mm_132930.1	chr16	49854348	49854359	+	1	NA	Intergenic	Intergenic	-1301	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_63881.1	chr7	137370673	137370684	+	1	NA	Intergenic	Intergenic	40078	NM_029886	77252	Mm.29184	NM_029886	ENSMUSG00000040139	9430038I01Rik	-	RIKEN cDNA 9430038I01 gene	protein-coding
mm_171913.1	chr5	54453404	54453407	+	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	103413	NR_038045	330086	Mm.254449	NM_177871	ENSMUSG00000105912	Gm10440	D130065D13|ENSMUSG00000072936	predicted gene 10440	ncRNA
mm_33702.1	chr4	133629541	133629549	+	1	NA	intron (NM_001017968, intron 1 of 7)	ID4_|SINE|ID	3884	NM_001017968	503610	Mm.331948	NM_001017968	ENSMUSG00000037553	Zdhhc18	-	zinc finger, DHHC domain containing 18	protein-coding
mm_6241.1	chr1	67038705	67038745	-	1	NA	5' UTR (NM_001190985, exon 1 of 9)	5' UTR (NM_001190985, exon 1 of 9)	109	NM_001190984	14768	Mm.20522	NM_021295	ENSMUSG00000026000	Lancl1	AW124738|Gpr69|Gpr69a|p40	LanC (bacterial lantibiotic synthetase component C)-like 1	protein-coding
mm_96298.1	chr11	63134455	63134468	+	1	NA	exon (NM_008885, exon 3 of 5)	exon (NM_008885, exon 3 of 5)	1658	NM_001302260	18858	Mm.1237	NM_008885	ENSMUSG00000018217	Pmp22	22kDa|Gas-3|HNPP|Tr|trembler	peripheral myelin protein 22	protein-coding
mm_32055.1	chr4	97777322	97777354	+	1	NA	promoter-TSS (NM_001122953)	promoter-TSS (NM_001122953)	-288	NM_001122953	18027	Mm.31274	NM_010905	ENSMUSG00000028565	Nfia	1110047K16Rik|9430022M17Rik|CTF|NF1-A|NF1A	nuclear factor I/A	protein-coding
mm_20267.1	chr2	126675518	126675532	-	1	NA	promoter-TSS (NM_010249)	promoter-TSS (NM_010249)	67	NM_001271469	14391	Mm.293266	NM_010249	ENSMUSG00000027361	Gabpb1	BABPB2|E4TF1|E4TF1-47|E4TF1-53|E4Tf1B|GABPB|GABPB-1|GABPB-2|GABPB1-1|GABPB1-2|NRF2B1|NRF2B2	GA repeat binding protein, beta 1	protein-coding
mm_151844.1	chr19	5731490	5731503	-	1	NA	exon (NM_020491, exon 2 of 4)	exon (NM_020491, exon 2 of 4)	236	NM_020491	56390	Mm.455818	NM_020491	ENSMUSG00000079478	Sssca1	1500016H19Rik|C184L	Sjogren's syndrome/scleroderma autoantigen 1 homolog (human)	protein-coding
mm_125865.1	chr15	75474487	75474495	+	1	NA	Intergenic	Intergenic	25039	NM_001347049	102637705		NM_001347049	ENSMUSG00000093626	Ly6l	Gm20654	lymphocyte antigen 6 complex, locus L	protein-coding
mm_145861.1	chr18	65456450	65456459	+	1	NA	intron (NM_172833, intron 8 of 15)	ID4_|SINE|ID	25457	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_152924.1	chr19	28011187	28011221	-	1	NA	promoter-TSS (NM_011265)	promoter-TSS (NM_011265)	-38	NM_011265	19726	Mm.313321	NM_011265	ENSMUSG00000040929	Rfx3	C230093O12Rik|MRFX3	regulatory factor X, 3 (influences HLA class II expression)	protein-coding
mm_169616.1	chr1	5380695	5380698	-	1	NA	Intergenic	IAP1-MM_LTR|LTR|ERVK	-207797	NM_011011	18387	Mm.7977	NM_011011	ENSMUSG00000025905	Oprk1	K-OR-1|KOR|KOR-1|MSL-1|Oprk2|R21	opioid receptor, kappa 1	protein-coding
mm_49616.1	chr6	30747809	30747840	+	1	NA	3' UTR (NM_001252293, exon 12 of 12)	3' UTR (NM_001252293, exon 12 of 12)	6525	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_147159.1	chr18	36700543	36700574	-	1	NA	Intergenic	MER21-int|LTR|ERVL	-4633	NM_172831	240216	Mm.252323	NM_172831	ENSMUSG00000044719	E230025N22Rik	EG240216	Riken cDNA E230025N22 gene	protein-coding
mm_61940.1	chr7	90182743	90182756	+	1	NA	intron (NM_001252520, intron 13 of 20)	intron (NM_001252520, intron 13 of 20)	52517	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_154744.1	chrX	10416676	10416682	+	1	NA	Intergenic	Intergenic	-68437	NM_019634	21912	Mm.18590	NM_019634	ENSMUSG00000058254	Tspan7	1200014P11Rik|A15|AI323365|Cd231|Mxs1|PE31|R74651|TALLA|Tm4sf2	tetraspanin 7	protein-coding
mm_102644.1	chr11	62760526	62760568	-	1	NA	Intergenic	L1_Rod|LINE|L1	28870	NM_138949	192651	Mm.168530	NM_138949	ENSMUSG00000047342	Zfp286	BC027023	zinc finger protein 286	protein-coding
mm_42123.1	chr5	110895271	110895304	+	1	NA	intron (NM_001267622, intron 2 of 22)	intron (NM_001267622, intron 2 of 22)	15484	NM_001267622	209683	Mm.295660	NM_024477	ENSMUSG00000033209	Ttc28	2310015L07Rik|6030435N04|AI428795|AI851761|BC002262|TPRBK	tetratricopeptide repeat domain 28	protein-coding
mm_93157.1	chr10	93160521	93160533	-	1	NA	promoter-TSS (NM_146239)	promoter-TSS (NM_146239)	-349	NM_146239	237459	Mm.217404	NM_146239	ENSMUSG00000020015	Cdk17	6430598J10Rik|Pctk2	cyclin-dependent kinase 17	protein-coding
mm_85828.1	chr9	110422547	110422575	-	1	NA	3' UTR (NM_008694, exon 4 of 4)	3' UTR (NM_008694, exon 4 of 4)	2753	NM_008694	18054	Mm.236225	NM_008694	ENSMUSG00000032484	Ngp	bectenecin	neutrophilic granule protein	protein-coding
mm_143279.1	chr17	65748484	65748489	-	1	NA	intron (NM_133685, intron 1 of 6)	B3|SINE|B2	24266	NM_133685	106572	Mm.29274	NM_133685	ENSMUSG00000056515	Rab31	1700093E07Rik|AI415285|Rab22B	RAB31, member RAS oncogene family	protein-coding
mm_163025.1	chr11	49177098	49177103	+	1	NA	intron (NM_172793, intron 4 of 9)	intron (NM_172793, intron 4 of 9)	9989	NM_172793	237754	Mm.130787	NM_172793	ENSMUSG00000040283	Btnl9	B430208I01|Btn3|D330012D11Rik	butyrophilin-like 9	protein-coding
mm_124551.1	chr14	122912916	122912960	-	1	NA	intron (NM_145466, intron 1 of 2)	CpG	227	NM_145466	223267	Mm.379358	NM_145466	ENSMUSG00000041625	Ggact	A2ld1	gamma-glutamylamine cyclotransferase	protein-coding
mm_106115.1	chr11	116335401	116335415	-	1	NA	promoter-TSS (NM_008240)	promoter-TSS (NM_008240)	-54	NM_008240	15223	Mm.378938	NM_008240	ENSMUSG00000034227	Foxj1	FKHL-13|HFH-4|Hfh4	forkhead box J1	protein-coding
mm_4133.1	chr1	170642841	170642851	+	1	NA	Intergenic	Intergenic	-1686	NM_177068	320078	Mm.287131	NM_177068	ENSMUSG00000038463	Olfml2b	1110018N05Rik|4832415H08Rik|AI467542	olfactomedin-like 2B	protein-coding
mm_130789.1	chr15	101676281	101676288	-	1	NA	3' UTR (NM_010669, exon 9 of 9)	3' UTR (NM_010669, exon 9 of 9)	4005	NM_010669	16688	Mm.441891	NM_010669	ENSMUSG00000023041	Krt6b	BB144589|Krt2-6b|mK6[b]	keratin 6B	protein-coding
mm_41512.1	chr5	92376955	92376970	+	1	NA	intron (NM_001310664, intron 2 of 10)	intron (NM_001310664, intron 2 of 10)	-11172	NM_181728	109979	Mm.263514	NM_181728	ENSMUSG00000034842	Art3	4930569O04Rik|ARTC3	ADP-ribosyltransferase 3	protein-coding
mm_100622.1	chr11	121673449	121673464	+	1	NA	promoter-TSS (NM_178664)	promoter-TSS (NM_178664)	-305	NM_178664	210004	Mm.386847	NM_178664	ENSMUSG00000046605	B3gntl1	6030413G23Rik	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase-like 1	protein-coding
mm_48827.1	chr5	149053061	149053071	-	1	NA	promoter-TSS (NM_010439)	promoter-TSS (NM_010439)	-9	NM_010439	15289	Mm.207047	NM_010439	ENSMUSG00000066551	Hmgb1	HMG-1|Hmg1|SBP-1|p30	high mobility group box 1	protein-coding
mm_7002.1	chr1	86442481	86442491	-	1	NA	Intergenic	CpG	16157	NM_027966	71863	Mm.179627	NM_027966	ENSMUSG00000036574	1700019O17Rik	-	RIKEN cDNA 1700019O17 gene	protein-coding
mm_164637.1	chr17	34460308	34460320	+	1	NA	exon (NM_001001177, exon 20 of 20)	exon (NM_001001177, exon 20 of 20)	15623	NM_030746	632126	Mm.484958	NM_030746	ENSMUSG00000058435	Btnl4	Btn3a3|EG632126|NG11	butyrophilin-like 4	protein-coding
mm_69390.1	chr7	131362740	131362750	-	1	NA	promoter-TSS (NM_026655)	promoter-TSS (NM_026655)	-47	NM_026655	68277	Mm.121122	NM_026655	ENSMUSG00000040177	2310057M21Rik	3110040E10Rik|AI429544	RIKEN cDNA 2310057M21 gene	protein-coding
mm_67467.1	chr7	80410210	80410215	-	1	NA	Intergenic	MIRb|SINE|MIR	-4776	NM_001081454	18550	Mm.5241	NM_011046	ENSMUSG00000030530	Furin	9130404I01Rik|Fur|PACE|Pcsk3|SPC1	furin (paired basic amino acid cleaving enzyme)	protein-coding
mm_20827.1	chr2	146511947	146511979	-	1	NA	promoter-TSS (NM_001033348)	promoter-TSS (NM_001033348)	41	NM_001033348	241694	Mm.222310	NM_001033348	ENSMUSG00000037110	Ralgapa2	A230067G21Rik|AS250|BC053994|RGC2|pp250	Ral GTPase activating protein, alpha subunit 2 (catalytic)	protein-coding
mm_28710.1	chr3	95652011	95652014	-	1	NA	Intergenic	PB1D11|SINE|Alu	-6709	NM_008562	17210	Mm.1639	NM_008562	ENSMUSG00000038612	Mcl1	AW556805|Mcl-1	myeloid cell leukemia sequence 1	protein-coding
mm_48482.1	chr5	141268481	141268481	-	1	NA	intron (NM_177879, intron 1 of 44)	intron (NM_177879, intron 1 of 44)	26947	NM_177879	330222	Mm.151931	NM_177879	ENSMUSG00000039683	Sdk1	5330440E10|6720466O15Rik	sidekick cell adhesion molecule 1	protein-coding
mm_29989.1	chr3	135438603	135438638	-	1	NA	promoter-TSS (NM_025356)	promoter-TSS (NM_025356)	45	NR_030689	319587	Mm.358971	NR_030689	ENSMUSG00000097032	4930539J05Rik	8030475D13Rik	RIKEN cDNA 4930539J05 gene	ncRNA
mm_95023.1	chr11	32001843	32001853	+	1	NA	exon (NM_008741, exon 2 of 5)	exon (NM_008741, exon 2 of 5)	571	NM_001290681	18197	Mm.3304	NM_008741	ENSMUSG00000020297	Nsg2	-	neuron specific gene family member 2	protein-coding
mm_62198.1	chr7	97788490	97788582	+	1	NA	Intergenic	CpG	-50289	NM_175105	66333	Mm.29756	NM_175105	ENSMUSG00000042797	Aqp11	1700015P13Rik|AI648923|sjds	aquaporin 11	protein-coding
mm_66030.1	chr7	30626080	30626122	-	1	NA	promoter-TSS (NM_025628)	promoter-TSS (NM_025628)	50	NM_025628	110323	Mm.400	NM_025628	ENSMUSG00000036751	Cox6b1	2010000G05Rik|Cox6b	cytochrome c oxidase, subunit VIb polypeptide 1	protein-coding
mm_109232.1	chr12	108838546	108838605	+	1	NA	Intergenic	Intergenic	1602	NR_029773	723946		NR_029773	ENSMUSG00000065429	Mir345	Mirn345|mir-345|mmu-mir-345	microRNA 345	ncRNA
mm_98542.1	chr11	95010177	95010185	+	1	NA	5' UTR (NM_146025, exon 1 of 10)	5' UTR (NM_146025, exon 1 of 10)	302	NM_146025	217125	Mm.297199	NM_146025	ENSMUSG00000047181	Samd14	AI839049|AI854782|BC034054	sterile alpha motif domain containing 14	protein-coding
mm_6284.1	chr1	69685938	69685966	-	1	NA	promoter-TSS (NM_011770)	promoter-TSS (NM_011770)	8	NM_011770	22779	Mm.106343	NM_011770	ENSMUSG00000025997	Ikzf2	A730095J18Rik|Helios|Zfpn1a2|Znfn1a2	IKAROS family zinc finger 2	protein-coding
mm_34293.1	chr4	141614314	141614315	+	1	NA	promoter-TSS (NR_033566)	promoter-TSS (NR_033566)	-56	NR_033566	100165	Mm.439819	NR_033566	ENSMUSG00000073731	AI507597	-	expressed sequence AI507597	ncRNA
mm_145658.1	chr18	61130645	61130697	+	1	NA	TTS (NM_178277)	TTS (NM_178277)	13203	NR_105949	102466212		NR_105949	ENSMUSG00000098389	Mir6983	Gm27496|mmu-mir-6983	microRNA 6983	ncRNA
mm_102793.1	chr11	68825072	68825074	-	1	NA	intron (NM_023668, intron 8 of 8)	intron (NM_023668, intron 8 of 8)	28058	NM_023668	83431	Mm.31979	NM_023668	ENSMUSG00000018736	Ndel1	2600006O07Rik|MITAP1|NUDEL|mNudel	nudE neurodevelopment protein 1 like 1	protein-coding
mm_89836.1	chr10	106638390	106638417	+	1	NA	intron (NM_001205341, intron 3 of 31)	L1_Mur3|LINE|L1	-35923	NR_131026	75833	Mm.159596	NR_131026		4930532I03Rik	-	RIKEN cDNA 4930532I03 gene	ncRNA
mm_100815.1	chr11	5110118	5110122	-	1	NA	intron (NM_080595, intron 14 of 14)	intron (NM_080595, intron 14 of 14)	9955	NM_001290493	279766	Mm.260866	NM_177370	ENSMUSG00000034175	Rhbdd3	Ptag	rhomboid domain containing 3	protein-coding
mm_16120.1	chr2	169970808	169970819	+	1	NA	Intergenic	MTE2b|LTR|ERVL-MaLR	-7626	NR_131974	446211	Mm.266854	NR_131974	ENSMUSG00000103935	AY702102	STDP1	cDNA sequence AY702102	ncRNA
mm_15365.1	chr2	156421053	156421065	+	1	NA	5' UTR (NM_001291121, exon 1 of 22)	5' UTR (NM_001291121, exon 1 of 22)	150	NM_001291123	13821	Mm.20852	NM_013510	ENSMUSG00000027624	Epb41l1	4.1N|Epb4.1l1|NBL1|mKIAA0338	erythrocyte membrane protein band 4.1 like 1	protein-coding
mm_78580.1	chr9	37208177	37208195	+	1	NA	promoter-TSS (NM_025464)	promoter-TSS (NM_025464)	-37	NM_025464	66279	Mm.41451	NM_025464	ENSMUSG00000032121	Tmem218	1810021J13Rik|AV004931	transmembrane protein 218	protein-coding
mm_47904.1	chr5	134932672	134932688	-	1	NA	5' UTR (NM_024479, exon 2 of 6)	5' UTR (NM_024479, exon 2 of 6)	307	NM_001347490	79565	Mm.34235	NM_024479	ENSMUSG00000040557	Wbscr27	AW492986|BC002286	Williams Beuren syndrome chromosome region 27 (human)	protein-coding
mm_38936.1	chr4	150196110	150196117	-	1	NA	exon (NM_009802, exon 4 of 8)	exon (NM_009802, exon 4 of 8)	5022	NM_009802	12353	Mm.232523	NM_009802	ENSMUSG00000028972	Car6	Ca6|DOC1	carbonic anhydrase 6	protein-coding
mm_83909.1	chr9	56266418	56266423	-	1	NA	intron (NM_172924, intron 3 of 6)	intron (NM_172924, intron 3 of 6)	-105350	NM_019793	56434	Mm.28484	NM_019793	ENSMUSG00000032324	Tspan3	1700055K04Rik|TM4-A|Tm4sf8	tetraspanin 3	protein-coding
mm_148771.1	chr19	6095799	6095843	+	1	NA	Intergenic	Intergenic	-9977	NM_001009546	381204	Mm.359041	NM_001009546	ENSMUSG00000054999	Naaladl1	Gm964|Naaladasel	N-acetylated alpha-linked acidic dipeptidase-like 1	protein-coding
mm_15092.1	chr2	153278721	153278725	+	1	NA	Intergenic	Intergenic	-12693	NM_008444	16569	Mm.315560	NM_008444	ENSMUSG00000027475	Kif3b	AI854312|AW549267|mKIAA0359	kinesin family member 3B	protein-coding
mm_25482.1	chr3	109123001	109123059	+	1	NA	promoter-TSS (NM_172685)	promoter-TSS (NM_172685)	-119	NM_172685	229731	Mm.33574	NM_172685	ENSMUSG00000040322	Slc25a24	2610016M12Rik	solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 24	protein-coding
mm_89069.1	chr10	82958212	82958213	+	1	NA	Intergenic	ORR1B1-int|LTR|ERVL-MaLR	-27285	NM_021439	58250	Mm.360747	NM_021439	ENSMUSG00000034612	Chst11	1110020P09Rik|C4ST|C4ST-1|C4ST1|C4s	carbohydrate sulfotransferase 11	protein-coding
mm_162634.1	chr1	190116785	190116787	+	1	NA	Intergenic	Intergenic	53894	NM_008937	19130	Mm.132579	NM_008937	ENSMUSG00000010175	Prox1	A230003G05Rik	prospero homeobox 1	protein-coding
mm_34269.1	chr4	141423997	141424009	+	1	NA	exon (NM_013868, exon 3 of 3)	exon (NM_013868, exon 3 of 3)	3224	NM_013868	29818	Mm.46181	NM_013868	ENSMUSG00000006221	Hspb7	27kDa|Hsp25-2|cvHsp	heat shock protein family, member 7 (cardiovascular)	protein-coding
mm_145460.1	chr18	60242895	60242900	+	1	NA	intron (NM_001033767, intron 2 of 2)	intron (NM_001033767, intron 2 of 2)	30370	NM_001034859	225594	Mm.329460	NM_001034859	ENSMUSG00000068606	Gm4841	EG225594|Ifgga3	predicted gene 4841	protein-coding
mm_72102.1	chr8	71597673	71597675	+	1	NA	promoter-TSS (NM_001166213)	promoter-TSS (NM_001166213)	28	NM_001166213	100037278	Mm.482159	NM_001166213	ENSMUSG00000043243	Fam129c	Bcnp1	family with sequence similarity 129, member C	protein-coding
mm_90128.1	chr10	117710154	117710192	+	1	NA	intron (NM_001288586, intron 1 of 10)	CpG-1528	585	NM_010786	17246	Mm.22670	NM_010786	ENSMUSG00000020184	Mdm2	1700007J15Rik|AA415488|Mdm-2	transformed mouse 3T3 cell double minute 2	protein-coding
mm_172049.1	chr6	128653418	128653418	-	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	-8967	NM_053165	94071	Mm.197689	NM_053165	ENSMUSG00000030364	Clec2h	Clrf|clr-f	C-type lectin domain family 2, member h	protein-coding
mm_122920.1	chr14	54960479	54960487	-	1	NA	exon (NM_010856, exon 13 of 39)	exon (NM_010856, exon 13 of 39)	6124	NM_001164171	17888	Mm.290003	NM_010856	ENSMUSG00000040752	Myh6	A830009F23Rik|AA517445|Myhc-a|Myhca|alpha-MHC	myosin, heavy polypeptide 6, cardiac muscle, alpha	protein-coding
mm_127361.1	chr15	100684579	100684604	+	1	NA	exon (NM_033612, exon 4 of 8)	exon (NM_033612, exon 4 of 8)	3329	NM_033612	109901	Mm.2131	NM_033612	ENSMUSG00000023031	Cela1	1810009A17Rik|1810062B19Rik|Ela-1|Ela1|PC-TsF	chymotrypsin-like elastase family, member 1	protein-coding
mm_97048.1	chr11	72435566	72435578	+	1	NA	promoter-TSS (NM_027819)	promoter-TSS (NM_027819)	46	NM_027819	71522	Mm.23336	NM_027819	ENSMUSG00000040471	Ggt6	9030405D14Rik|AI427679|AW490214	gamma-glutamyltransferase 6	protein-coding
mm_100520.1	chr11	120534740	120534740	+	1	NA	5' UTR (NM_008101, exon 2 of 14)	5' UTR (NM_008101, exon 2 of 14)	4013	NM_008101	14527	Mm.22329	NM_008101	ENSMUSG00000025127	Gcgr	GR	glucagon receptor	protein-coding
mm_116966.1	chr13	56176365	56176386	-	1	NA	exon (NM_001168615, exon 3 of 3)	exon (NM_001168615, exon 3 of 3)	2510	NM_145976	212937	Mm.116697	NM_145976	ENSMUSG00000049625	Tifab	-	TRAF-interacting protein with forkhead-associated domain, family member B	protein-coding
mm_101624.1	chr11	35980443	35980456	-	1	NA	promoter-TSS (NM_170779)	promoter-TSS (NM_170779)	-360	NM_170779	211652	Mm.31267	NM_170779	ENSMUSG00000018849	Wwc1	AA408228|AU017197|BC037006|Kibra|mKIAA0869	WW, C2 and coiled-coil domain containing 1	protein-coding
mm_25030.1	chr3	98149804	98149805	+	1	NA	3' UTR (NM_010928, exon 34 of 34)	3' UTR (NM_010928, exon 34 of 34)	-10830	NM_027665	71078	Mm.50711	NM_027665	ENSMUSG00000043468	Adam30	4933424D07Rik|svph4	a disintegrin and metallopeptidase domain 30	protein-coding
mm_139294.1	chr17	48316157	48316168	+	1	NA	promoter-TSS (NM_177083)	promoter-TSS (NM_177083)	0	NM_177083	320148	Mm.123455	NM_177083	ENSMUSG00000043740	B430306N03Rik	Treml6	RIKEN cDNA B430306N03 gene	protein-coding
mm_113112.1	chr13	24416976	24416982	+	1	NA	5' UTR (NM_001111110, exon 3 of 17)	5' UTR (NM_001111110, exon 3 of 17)	1857	NM_001284520	12763	Mm.8396	NM_007717	ENSMUSG00000016756	Cmah	-	cytidine monophospho-N-acetylneuraminic acid hydroxylase	protein-coding
mm_100093.1	chr11	115603976	115603994	+	1	NA	promoter-TSS (NM_173048)	promoter-TSS (NM_173048)	-69	NM_173048	260302	Mm.119479	NM_173048	ENSMUSG00000020740	Gga3	C230037M19Rik|mKIAA0154	golgi associated, gamma adaptin ear containing, ARF binding protein 3	protein-coding
mm_126277.1	chr15	79209207	79209239	+	1	NA	intron (NR_029470, intron 2 of 4)	intron (NR_029470, intron 2 of 4)	-19950	NM_008837	18693	Mm.259464	NM_008837	ENSMUSG00000068206	Pick1	Prkcabp	protein interacting with C kinase 1	protein-coding
mm_150537.1	chr19	39307609	39307624	+	1	NA	exon (NM_007815, exon 4 of 9)	exon (NM_007815, exon 4 of 9)	20531	NM_007815	13095	Mm.20764	NM_007815	ENSMUSG00000003053	Cyp2c29	AHOH|AHOHase|AI159681|AI196010|Ah-2|Ahh-1|Cyp2c|P450-2C	cytochrome P450, family 2, subfamily c, polypeptide 29	protein-coding
mm_5667.1	chr1	42695192	42695204	-	1	NA	promoter-TSS (NR_027826)	promoter-TSS (NR_027826)	-373	NR_027826	66297	Mm.45203	NM_183252	ENSMUSG00000060424	Pantr1	2610017I09Rik|Pou3f3os|linc-Brn1a	POU domain, class 3, transcription factor 3 adjacent noncoding transcript 1	ncRNA
mm_95295.1	chr11	46056089	46056097	+	1	NA	5' UTR (NM_009616, exon 1 of 23)	5' UTR (NM_009616, exon 1 of 23)	109	NM_001291891	11492	Mm.89940	NM_009616	ENSMUSG00000011256	Adam19	AL024287|MADDAM|MTLNB|Mltnb	a disintegrin and metallopeptidase domain 19 (meltrin beta)	protein-coding
mm_116243.1	chr13	33928395	33928398	-	1	NA	intron (NM_001243192, intron 4 of 7)	ID_B1|SINE|B4	-7636	NR_040707	68808	Mm.443347	NR_040707	ENSMUSG00000085457	1110046J04Rik	-	RIKEN cDNA 1110046J04 gene	ncRNA
mm_128939.1	chr15	74716675	74716699	-	1	NA	3' UTR (NM_028216, exon 3 of 3)	3' UTR (NM_028216, exon 3 of 3)	1848	NM_028216	72373	Mm.46395	NM_028216	ENSMUSG00000022598	Psca	2210408B04Rik	prostate stem cell antigen	protein-coding
mm_170801.1	chr2	175606171	175606187	-	1	NA	Intergenic	Intergenic	-34212	NM_001177543	100039060	Mm.289463	NM_001177543	ENSMUSG00000078886	0610010B08Rik	Gm2026	RIKEN cDNA 0610010B08 gene	protein-coding
mm_73556.1	chr8	108959564	108959587	+	1	NA	3' UTR (NM_007496, exon 10 of 10)	3' UTR (NM_007496, exon 10 of 10)	22715	NR_037295	100526511		NR_037295	ENSMUSG00000093241	Mir3108	mir-3108|mmu-mir-3108	microRNA 3108	ncRNA
mm_58571.1	chr7	4793161	4793170	+	1	NA	intron (NM_009081, intron 1 of 4)	CpG	200	NM_009081	19943	Mm.379002	NM_009081	ENSMUSG00000030432	Rpl28	D7Wsu21e	ribosomal protein L28	protein-coding
mm_5763.1	chr1	46925757	46925772	-	1	NA	Intergenic	Intergenic	-72255	NM_172653	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|mKIAA1265	solute carrier family 39 (zinc transporter), member 10	protein-coding
mm_147475.1	chr18	46959037	46959045	-	1	NA	intron (NM_178377, intron 1 of 6)	CpG	165	NM_178377	69456	Mm.210734	NM_178377	ENSMUSG00000042705	Commd10	2310003A05Rik|AU019438|DRWMS2	COMM domain containing 10	protein-coding
mm_155599.1	chrX	82814746	82814758	+	1	NA	Intergenic	Intergenic	-134118	NM_007868	13405	Mm.275608	NM_007868	ENSMUSG00000045103	Dmd	DXSmh7|DXSmh9|Dp427|Dp71|dys|mdx|pke	dystrophin, muscular dystrophy	protein-coding
mm_43820.1	chr5	142960478	142960493	+	1	NA	exon (NM_007984, exon 1 of 5)	exon (NM_007984, exon 1 of 5)	130	NM_007984	14086	Mm.289707	NM_007984	ENSMUSG00000029581	Fscn1	AI663989|Fan1|fascin-1	fascin actin-bundling protein 1	protein-coding
mm_159150.1	chr2	87950478	87950478	-	1	NA	promoter-TSS (NM_146817)	promoter-TSS (NM_146817)	-213	NM_146817	258814	Mm.377703	NM_146817	ENSMUSG00000075144	Olfr1156	MOR174-3	olfactory receptor 1156	protein-coding
mm_21719.1	chr2	164638750	164638758	-	1	NA	promoter-TSS (NM_001012723)	promoter-TSS (NM_001012723)	48	NM_001012723	277345	Mm.247244	NM_001012723	ENSMUSG00000070530	Wfdc16	BC043944|WAP16	WAP four-disulfide core domain 16	protein-coding
mm_61747.1	chr7	82649381	82649391	+	1	NA	promoter-TSS (NM_177894)	promoter-TSS (NM_177894)	772	NM_175317	101592	Mm.238020	NM_175317	ENSMUSG00000038563	Efl1	4932434J20Rik|6030468D11Rik|AI451340|AU019507|AU022896|D7Ertd791e|Eftud1	elongation factor like GPTase 1	protein-coding
mm_13269.1	chr2	98666982	98667007	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	1199337	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_19269.1	chr2	85035492	85035506	-	1	NA	5' UTR (NM_145526, exon 1 of 12)	5' UTR (NM_145526, exon 1 of 12)	335	NM_145526	228139	Mm.440375	NM_145526	ENSMUSG00000027071	P2rx3	4930513E20Rik|P2X3	purinergic receptor P2X, ligand-gated ion channel, 3	protein-coding
mm_123086.1	chr14	55754455	55754482	-	1	NA	exon (NM_009894, exon 5 of 5)	exon (NM_009894, exon 5 of 5)	3956	NM_009894	12684	Mm.466766	NM_009894	ENSMUSG00000022219	Cideb	1110030C18Rik|AI790179|CIDE-B	cell death-inducing DNA fragmentation factor, alpha subunit-like effector B	protein-coding
mm_15222.1	chr2	154449494	154449496	+	1	NA	intron (NM_009823, intron 1 of 10)	B2_Mm2|SINE|B2	13011	NM_009823	12396	Mm.29914	NM_009823	ENSMUSG00000038533	Cbfa2t2	A430091M07|C330013D05Rik|Cbfa2t2h|MTGR1	core-binding factor, runt domain, alpha subunit 2, translocated to, 2 (human)	protein-coding
mm_96916.1	chr11	70463889	70463929	+	1	NA	intron (NM_001029929, intron 6 of 13)	intron (NM_001029929, intron 6 of 13)	-3925	NM_023158	66102	Mm.425692	NM_023158	ENSMUSG00000018920	Cxcl16	0910001K24Rik|AV290116|BB024863|CXCL16v1|CXCL16v2|SR-PSOX|Zmynd15|b2b498Clo	chemokine (C-X-C motif) ligand 16	protein-coding
mm_135049.1	chr16	33251325	33251376	-	1	NA	promoter-TSS (NM_080557)	promoter-TSS (NM_080557)	-106	NM_080557	69150	Mm.28196	NM_080557	ENSMUSG00000022808	Snx4	1810036H14Rik|AI037066	sorting nexin 4	protein-coding
mm_3172.1	chr1	135711373	135711395	+	1	NA	Intergenic	Intergenic	-17813	NM_007791	13007	Mm.196484	NM_007791	ENSMUSG00000026421	Csrp1	AA408841|AA959891|AW545626|CRP1|Csrp	cysteine and glycine-rich protein 1	protein-coding
mm_47495.1	chr5	124010791	124010803	-	1	NA	exon (NM_177876, exon 2 of 4)	exon (NM_177876, exon 2 of 4)	13945	NR_105999	102465625		NR_105999	ENSMUSG00000098454	Mir7032	Gm27309|mmu-mir-7032	microRNA 7032	ncRNA
mm_87565.1	chr10	56377324	56377338	+	1	NA	promoter-TSS (NM_010288)	promoter-TSS (NM_010288)	31	NM_010288	14609	Mm.378921	NM_010288	ENSMUSG00000050953	Gja1	AU042049|AW546267|Cnx43|Cx43|Cx43alpha1|Gja-1|Npm1|connexin43	gap junction protein, alpha 1	protein-coding
mm_36479.1	chr4	82859797	82859817	-	1	NA	promoter-TSS (NM_026647)	promoter-TSS (NM_026647)	-146	NM_026647	68268	Mm.32047	NM_026647	ENSMUSG00000028403	Zdhhc21	9130404H11Rik|AL024349|D130004H04Rik|dep	zinc finger, DHHC domain containing 21	protein-coding
mm_84614.1	chr9	70455670	70455673	-	1	NA	intron (NM_033604, intron 6 of 14)	AT_rich|Low_complexity|Low_complexity	-34117	NM_007630	12442	Mm.22592	NM_007630	ENSMUSG00000032218	Ccnb2	CycB2	cyclin B2	protein-coding
mm_161440.1	chr15	66286127	66286127	-	1	NA	promoter-TSS (NM_152923)	promoter-TSS (NM_152923)	97	NM_152923	110862	Mm.255585	NM_152923	ENSMUSG00000056258	Kcnq3	-	potassium voltage-gated channel, subfamily Q, member 3	protein-coding
mm_54023.1	chr6	8778214	8778230	-	1	NA	5' UTR (NM_010492, exon 1 of 14)	5' UTR (NM_010492, exon 1 of 14)	262	NM_010492	15893	Mm.275683	NM_010492	ENSMUSG00000062995	Ica1	69kDa|ICA69	islet cell autoantigen 1	protein-coding
mm_109339.1	chr12	109590524	109590526	+	1	NA	promoter-TSS (NR_029951)	promoter-TSS (NR_029951)	78	NR_029951	723866		NR_029951	ENSMUSG00000070080	Mir431	Mirn431|mir-431|mmu-mir-431	microRNA 431	ncRNA
mm_156216.1	chrX	134687091	134687106	+	1	NA	promoter-TSS (NR_045454)	promoter-TSS (NR_045454)	579	NM_001202500	100503043	Mm.31961	NM_001202500	ENSMUSG00000049804	Armcx4	AI448196|Gm195	armadillo repeat containing, X-linked 4	protein-coding
mm_100334.1	chr11	118319096	118319127	+	1	NA	intron (NM_011594, intron 2 of 4)	intron (NM_011594, intron 2 of 4)	23423	NM_021440	58251	Mm.439815	NM_021440	ENSMUSG00000076433	BC100451	Cep295nl|Ddc8|FS39|Kiaa1731nl	cDNA sequence BC100451	protein-coding
mm_82839.1	chr9	31164662	31164680	-	1	NA	exon (NM_009691, exon 7 of 16)	exon (NM_009691, exon 7 of 16)	-32872	NM_011176	19143	Mm.243926	NM_011176	ENSMUSG00000031995	St14	Epithin|MT-SP1|Prss14|Tmprss14|mCAP3|matriptase	suppression of tumorigenicity 14 (colon carcinoma)	protein-coding
mm_56917.1	chr6	119388753	119388772	-	1	NA	intron (NM_197985, intron 1 of 7)	CpG	28721	NM_197985	68465	Mm.291826	NM_197985	ENSMUSG00000030168	Adipor2	1110001I14Rik|ADCR2|AI115388|AW554121|D6Ucla1e|Paqr2	adiponectin receptor 2	protein-coding
mm_61592.1	chr7	80025814	80025829	+	1	NA	promoter-TSS (NM_175433)	promoter-TSS (NM_175433)	-407	NM_175433	209225	Mm.290925	NM_175433	ENSMUSG00000048897	Zfp710	5430400N05Rik|9830165K13|AI324798|Znf710	zinc finger protein 710	protein-coding
mm_32864.1	chr4	118428079	118428194	+	1	NA	promoter-TSS (NM_001039175)	promoter-TSS (NM_001039175)	43	NM_019422	54325	Mm.282096	NM_019422	ENSMUSG00000006390	Elovl1	AA407424|BB151133|Ssc1	elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 1	protein-coding
mm_123236.1	chr14	60121758	60121764	-	1	NA	Intergenic	Intergenic	-34927	NM_015803	50769	Mm.319599	NM_015803	ENSMUSG00000021983	Atp8a2	AI415030|Atpc1b|agil|wl	ATPase, aminophospholipid transporter-like, class I, type 8A, member 2	protein-coding
mm_118975.1	chr14	28029319	28029322	+	1	NA	intron (NM_177814, intron 10 of 15)	intron (NM_177814, intron 10 of 15)	406913	NM_177814	238988	Mm.318004	NM_177814	ENSMUSG00000040640	Erc2	6430531D06|CAST|CAST1/ERC2|D14Ertd171e|ELKS2alpha	ELKS/RAB6-interacting/CAST family member 2	protein-coding
mm_57912.1	chr6	133381052	133381058	-	1	NA	Intergenic	Intergenic	88839	NM_027784	232426	Mm.158689	NM_027784	ENSMUSG00000055594	5530400C23Rik	GRP	RIKEN cDNA 5530400C23 gene	protein-coding
mm_142097.1	chr17	35834896	35834998	-	1	NA	3' UTR (NM_011655, exon 4 of 4)	3' UTR (NM_011655, exon 4 of 4)	3354	NM_011655	22154	Mm.273538	NM_011655	ENSMUSG00000001525	Tubb5	AA408537|AI596182|B130022C14Rik|M(beta)5	tubulin, beta 5 class I	protein-coding
mm_86757.1	chr10	19610014	19610015	+	1	NA	3' UTR (NM_010511, exon 7 of 7)	3' UTR (NM_010511, exon 7 of 7)	-12014	NM_178258	237310	Mm.331979	NM_178258	ENSMUSG00000039760	Il22ra2	CRF2-10|CRF2-s1|CRF2X|Il-22bp	interleukin 22 receptor, alpha 2	protein-coding
mm_43988.1	chr5	146472659	146472675	+	1	NA	Intergenic	Intergenic	-9276	NM_001243104	623198	Mm.489582	NM_001243104	ENSMUSG00000096344	Gm6408	-	predicted gene 6408	protein-coding
mm_113826.1	chr13	47043528	47043591	+	1	NA	promoter-TSS (NM_016785)	promoter-TSS (NM_016785)	60	NM_172262	218214	Mm.31259	NM_172262	ENSMUSG00000038080	Kdm1b	4632428N09Rik|AI482520|Aof1	lysine (K)-specific demethylase 1B	protein-coding
mm_155347.1	chrX	68678677	68678691	+	1	NA	promoter-TSS (NR_033481)	promoter-TSS (NR_033481)	143	NM_001290424	14265	Mm.3451	NM_008031	ENSMUSG00000000838	Fmr1	FMRP|Fmr-1	fragile X mental retardation syndrome 1	protein-coding
mm_29858.1	chr3	130052226	130052239	-	1	NA	intron (NM_207209, intron 1 of 23)	intron (NM_207209, intron 1 of 23)	8675	NM_207209	99683	Mm.192303	NM_207209	ENSMUSG00000001052	Sec24b	AI605202|SEC24	Sec24 related gene family, member B (S. cerevisiae)	protein-coding
mm_7506.1	chr1	122357225	122357246	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-789255	NM_025860	66942	Mm.44219	NM_025860	ENSMUSG00000001674	Ddx18	2310005B10Rik	DEAD (Asp-Glu-Ala-Asp) box polypeptide 18	protein-coding
mm_69578.1	chr7	135701929	135701940	-	1	NA	exon (NM_001081117, exon 11 of 14)	exon (NM_001081117, exon 11 of 14)	14445	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_161174.1	chr13	38528827	38528827	-	1	NA	promoter-TSS (NM_145367)	promoter-TSS (NM_145367)	-3	NM_001289598	105245	Mm.28622	NM_145367	ENSMUSG00000038991	Txndc5	AL022641|ERp46|PC-TRP	thioredoxin domain containing 5	protein-coding
mm_86763.1	chr10	19933616	19933625	+	1	NA	promoter-TSS (NM_008580)	promoter-TSS (NM_008580)	-906	NM_008580	26408	Mm.6595	NM_008580	ENSMUSG00000071369	Map3k5	7420452D20Rik|ASK|ASK1|MAPKKK5|Mekk5	mitogen-activated protein kinase kinase kinase 5	protein-coding
mm_65113.1	chr7	19320011	19320028	-	1	NA	Intergenic	CpG	-9974	NM_001347586	14282	Mm.248335	NM_008036	ENSMUSG00000003545	Fosb	-	FBJ osteosarcoma oncogene B	protein-coding
mm_133059.1	chr16	58458324	58458364	+	1	NA	intron (NM_028523, intron 12 of 15)	intron (NM_028523, intron 12 of 15)	49809	NM_028523	73379	Mm.373589	NM_028523	ENSMUSG00000035107	Dcbld2	1700055P21Rik|AW146002|CLCP1|Esdn	discoidin, CUB and LCCL domain containing 2	protein-coding
mm_102925.1	chr11	69600655	69600655	-	1	NA	3' UTR (NM_013415, exon 7 of 7)	3' UTR (NM_013415, exon 7 of 7)	5305	NM_013415	11932	Mm.235204	NM_013415	ENSMUSG00000041329	Atp1b2	Amog|Atpb-2	ATPase, Na+/K+ transporting, beta 2 polypeptide	protein-coding
mm_100883.1	chr11	6003203	6003218	-	1	NA	intron (NM_007595, intron 3 of 20)	intron (NM_007595, intron 3 of 20)	47452	NM_019661	56418	Mm.294821	NM_019661	ENSMUSG00000002741	Ykt6	0610042I15Rik|1810013M05Rik|AW105923	YKT6 v-SNARE homolog (S. cerevisiae)	protein-coding
mm_56704.1	chr6	114969987	114970006	-	1	NA	Intergenic	CpG	-48244	NM_177683	232334	Mm.268357	NM_177683	ENSMUSG00000030315	Vgll4	BC048841|VGL-4	vestigial like family member 4	protein-coding
mm_16984.1	chr2	18047874	18047895	-	1	NA	exon (NM_028317, exon 1 of 1)	exon (NM_028317, exon 1 of 1)	565	NM_028317	72668	Mm.102183	NM_028317	ENSMUSG00000054074	Skida1	2810030E01Rik|5730507N06Rik|BB088113	SKI/DACH domain containing 1	protein-coding
mm_103654.1	chr11	78973135	78973144	-	1	NA	exon (NM_010708, exon 3 of 11)	exon (NM_010708, exon 3 of 11)	11785	NM_001159301	16859	Mm.341434	NM_010708	ENSMUSG00000001123	Lgals9	AA407335|AI194909|AI265545|LGALS35|Lgals5|gal-9|galectin-9	lectin, galactose binding, soluble 9	protein-coding
mm_81170.1	chr9	107300001	107300019	+	1	NA	exon (NM_009895, exon 2 of 3)	exon (NM_009895, exon 2 of 3)	3351	NM_009895	12700	Mm.4592	NM_009895	ENSMUSG00000032578	Cish	CIS-1|CIS1|Cis|F17|F23|SOCS	cytokine inducible SH2-containing protein	protein-coding
mm_106296.1	chr11	118219034	118219047	-	1	NA	intron (NM_001112699, intron 1 of 12)	intron (NM_001112699, intron 1 of 12)	-6298	NM_001112700	19157	Mm.86413	NM_011180	ENSMUSG00000017132	Cyth1	CLM1|CTH-1|CYTIP|Pscd1	cytohesin 1	protein-coding
mm_155579.1	chrX	78125467	78125470	+	1	NA	promoter-TSS (NM_001085534)	promoter-TSS (NM_001085534)	1	NM_001085534	546335	Mm.476683	NM_001085534	ENSMUSG00000079521	Gm5938	EG546335|OBP6	predicted gene 5938	protein-coding
mm_151646.1	chr19	4059038	4059061	-	1	NA	intron (NM_144869, intron 1 of 5)	intron (NM_144869, intron 1 of 5)	245	NM_144869	225884	Mm.440201	NM_144869	ENSMUSG00000058216	Gstp3	-	glutathione S-transferase pi 3	protein-coding
mm_157292.1	chrX	20862174	20862185	-	1	NA	TTS (NR_049190)	TTS (NR_049190)	1003	NR_049190	100885829		NR_049190	ENSMUSG00000093408	Mir5617	Gm25192|mir-5617|mmu-mir-5617	microRNA 5617	ncRNA
mm_154417.1	chrM	16008	16061	+	1	NA	NA	Intergenic	NA	NA								
mm_29688.1	chr3	123041052	123041053	-	1	NA	Intergenic	Intergenic	-6065	NM_021503	59006	Mm.141157	NM_021503	ENSMUSG00000028116	Myoz2	1110012I24Rik|Fatz-2|Myozl2	myozenin 2	protein-coding
mm_80642.1	chr9	89335375	89335380	+	1	NA	Intergenic	Intergenic	124187	NM_026829	107885	Mm.486274	NM_026829	ENSMUSG00000066442	Mthfs	1110034I12Rik|2310020H23Rik|AI119695	5, 10-methenyltetrahydrofolate synthetase	protein-coding
mm_77456.1	chr8	121907631	121907636	-	1	NA	promoter-TSS (NM_011404)	promoter-TSS (NM_011404)	53	NM_011404	20539	Mm.22374	NM_011404	ENSMUSG00000040010	Slc7a5	4F2LC|D0H16S474E|LAT1|TA1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 5	protein-coding
mm_149394.1	chr19	11387631	11387644	+	1	NA	intron (NM_001310331, intron 4 of 6)	intron (NM_001310331, intron 4 of 6)	12149	NM_001310331	666907		NM_001310331	ENSMUSG00000101389	Ms4a4a	EG666907	membrane-spanning 4-domains, subfamily A, member 4A	protein-coding
mm_135909.1	chr16	67545839	67545850	-	1	NA	intron (NM_178721, intron 1 of 9)	Lx2|LINE|L1	75064	NM_001347247	239857	Mm.394300	NM_178721	ENSMUSG00000064115	Cadm2	2900078E11Rik|9330131D06|A830029E02Rik|Igdf4d|Igsf4d|NECL3|SynCAM 2|SynCAM2	cell adhesion molecule 2	protein-coding
mm_167380.1	chr8	94340521	94340531	+	1	NA	exon (NM_001205311, exon 10 of 25)	exon (NM_001205311, exon 10 of 25)	11318	NM_001205311	20497	Mm.25804	NM_019415	ENSMUSG00000031766	Slc12a3	AI035291|NCC|NCCT|TSC	solute carrier family 12, member 3	protein-coding
mm_137658.1	chr17	28691329	28691333	+	1	NA	promoter-TSS (NM_011951)	promoter-TSS (NM_011951)	-11	NM_001168508	26416	Mm.311337	NM_011951	ENSMUSG00000053436	Mapk14	CSBP2|Crk1|Csbp1|Mxi2|PRKM14|PRKM15|p38|p38-alpha|p38MAPK|p38a|p38alpha	mitogen-activated protein kinase 14	protein-coding
mm_165896.1	chr4	45972145	45972174	+	1	NA	promoter-TSS (NM_146142)	promoter-TSS (NM_146142)	-138	NM_146142	100121	Mm.275413	NM_146142	ENSMUSG00000035517	Tdrd7	5730495N10Rik|AI447470|PCTAIRE2BP	tudor domain containing 7	protein-coding
mm_116051.1	chr13	27435418	27435423	-	1	NA	exon (NM_011167, exon 4 of 6)	exon (NM_011167, exon 4 of 6)	3268	NM_001271379	19112	Mm.142728	NM_011167	ENSMUSG00000021345	Prl8a6	Ghd13|PLP-C1|PLP-Ca|PLP-calpha|Prlpc|Prlpc1	prolactin family 8, subfamily a, member 6	protein-coding
mm_42939.1	chr5	122989349	122989366	+	1	NA	promoter-TSS (NM_001003953)	promoter-TSS (NM_001003953)	3	NR_045820	109202	Mm.30769	NM_175405	ENSMUSG00000056735	A930024E05Rik	-	RIKEN cDNA A930024E05 gene	ncRNA
mm_151597.1	chr19	3441287	3441304	-	1	NA	Intergenic	Intergenic	-26751	NM_010253	14419	Mm.4655	NM_010253	ENSMUSG00000024907	Gal	Galn	galanin	protein-coding
mm_128591.1	chr15	58119329	58119335	-	1	NA	intron (NM_027435, intron 8 of 27)	intron (NM_027435, intron 8 of 27)	15750	NM_027435	70472	Mm.221758	NM_027435	ENSMUSG00000022360	Atad2	2610509G12Rik	ATPase family, AAA domain containing 2	protein-coding
mm_153412.1	chr19	40588375	40588426	-	1	NA	promoter-TSS (NM_153554)	promoter-TSS (NM_153554)	63	NM_019698	56454	Mm.233117	NM_019698	ENSMUSG00000025007	Aldh18a1	2810433K04Rik|AI429789|Pycs	aldehyde dehydrogenase 18 family, member A1	protein-coding
mm_30435.1	chr3	153474644	153474655	-	1	NA	intron (NM_011372, intron 2 of 4)	intron (NM_011372, intron 2 of 4)	-176000	NR_126464	75489	Mm.443252	NR_126464	ENSMUSG00000105023	1700012D16Rik	-	RIKEN cDNA 1700012D16 gene	ncRNA
mm_86590.1	chr10	13124952	13124965	+	1	NA	5' UTR (NM_009538, exon 5 of 6)	5' UTR (NM_009538, exon 5 of 6)	34113	NR_131912	338438		NR_131912		Hymai	-	hydatidiform mole associated and imprinted transcript	ncRNA
mm_14599.1	chr2	136059776	136059804	+	1	NA	exon (NM_029530, exon 4 of 6)	exon (NM_029530, exon 4 of 6)	1863	NM_029530	76161	Mm.41638	NM_029530	ENSMUSG00000027270	Lamp5	3110035N03Rik|6330527O06Rik|BAD-LAMP|LAMP-5	lysosomal-associated membrane protein family, member 5	protein-coding
mm_139283.1	chr17	48299488	48299501	+	1	NA	promoter-TSS (NM_001033405)	promoter-TSS (NM_001033405)	-544	NM_001033405	328833	Mm.329104	NM_001033405	ENSMUSG00000071068	Treml2	AW049306|Gm750|Tlt2	triggering receptor expressed on myeloid cells-like 2	protein-coding
mm_93460.1	chr10	110456215	110456244	-	1	NA	Intergenic	Intergenic	-144421	NR_028438	109335	Mm.367727	NR_028438		9230102K24Rik	-	RIKEN cDNA 9230102K24 gene	ncRNA
mm_60079.1	chr7	34022811	34022817	+	1	NA	TTS (NM_009596)	TTS (NM_009596)	1247	NM_009596	11354	Mm.8025	NM_009596	ENSMUSG00000066583	Scgb1b27	Abp|Abpa|Abpa27|Sal-1|Tcp	secretoglobin, family 1B, member 27	protein-coding
mm_149711.1	chr19	21653277	21653301	+	1	NA	promoter-TSS (NM_025423)	promoter-TSS (NM_025423)	-20	NM_146096	226016	Mm.28796	NM_146096	ENSMUSG00000047368	Abhd17b	5730446C15Rik|Cgi67|Fam108b|Fam108b1	abhydrolase domain containing 17B	protein-coding
mm_107740.1	chr12	58212271	58212286	+	1	NA	5' UTR (NM_009216, exon 2 of 2)	5' UTR (NM_009216, exon 2 of 2)	474	NM_009216	20605	Mm.278336	NM_009216	ENSMUSG00000035431	Sstr1	SRIF-2|SS-1-R|SS1-R|SS1R|Smstr-1|Smstr1|sst1	somatostatin receptor 1	protein-coding
mm_21256.1	chr2	156312471	156312575	-	1	NA	promoter-TSS (NM_027585)	promoter-TSS (NM_027585)	50	NM_001316755	70873	Mm.475234	NM_027585	ENSMUSG00000038085	Cnbd2	4921517L17Rik|5430421B09Rik|Cris	cyclic nucleotide binding domain containing 2	protein-coding
mm_109920.1	chr12	8498667	8498682	-	1	NA	3' UTR (NM_007483, exon 1 of 1)	3' UTR (NM_007483, exon 1 of 1)	1311	NM_007483	11852	Mm.687	NM_007483	ENSMUSG00000054364	Rhob	AA017882|Arh6|Arhb	ras homolog family member B	protein-coding
mm_64273.1	chr7	141808508	141808521	+	1	NA	intron (NM_010844, intron 31 of 49)	intron (NM_010844, intron 31 of 49)	19503	NM_010844	17833	Mm.334332	NM_010844	ENSMUSG00000037974	Muc5ac	2210005L13Rik|MGM	mucin 5, subtypes A and C, tracheobronchial/gastric	protein-coding
mm_155313.1	chrX	61709598	61709620	+	1	NA	promoter-TSS (NM_001018087)	promoter-TSS (NM_001018087)	-7	NM_001018087	434784	Mm.23468	NM_001018087	ENSMUSG00000057615	Ldoc1	Gm366|Mar7|Mart7|Sirh7	leucine zipper, down-regulated in cancer 1	protein-coding
mm_74978.1	chr8	27141533	27141558	-	1	NA	3' UTR (NM_001080813, exon 6 of 6)	3' UTR (NM_001080813, exon 6 of 6)	-1365	NR_045840	71082	Mm.395259	NR_045840		4933416M07Rik	-	RIKEN cDNA 4933416M07 gene	ncRNA
mm_101835.1	chr11	47989387	47989409	-	1	NA	intron (NR_105801, intron 3 of 3)	intron (NR_105801, intron 3 of 3)	85185	NR_105801	102466638		NR_105801	ENSMUSG00000099011	Mir6380	Gm27356|mmu-mir-6380	microRNA 6380	ncRNA
mm_111018.1	chr12	79007348	79007358	-	1	NA	promoter-TSS (NM_178745)	promoter-TSS (NM_178745)	-76	NM_178745	268567	Mm.341747	NM_178745	ENSMUSG00000046157	Tmem229b	6330442E10Rik|9830138K24|AU019070	transmembrane protein 229B	protein-coding
mm_10870.1	chr2	25218742	25218750	+	1	NA	promoter-TSS (NM_026624)	promoter-TSS (NM_026624)	1	NM_026624	68222	Mm.227260	NM_026624	ENSMUSG00000026969	Fam166a	4931415M17	family with sequence similarity 166, member A	protein-coding
mm_156681.1	chrX	159364288	159364314	+	1	NA	3' UTR (NM_148945, exon 22 of 22)	3' UTR (NM_148945, exon 22 of 22)	-7894	NM_025437	66235	Mm.294623	NM_025437	ENSMUSG00000067194	Eif1ax	1500010B24Rik|AI426898|Eif1ay	eukaryotic translation initiation factor 1A, X-linked	protein-coding
mm_152004.1	chr19	5918428	5918467	-	1	NA	exon (NM_026772, exon 2 of 2)	exon (NM_026772, exon 2 of 2)	-5576	NM_001291078	19708	Mm.2651	NM_011262	ENSMUSG00000024826	Dpf2	2210010M07Rik|BAF45D|Req|ubi-d4	D4, zinc and double PHD fingers family 2	protein-coding
mm_141828.1	chr17	34627366	34627451	-	1	NA	promoter-TSS (NM_019441)	promoter-TSS (NM_019441)	27	NM_001302396	54397	Mm.373627	NM_019441	ENSMUSG00000015474	Ppt2	0610007M19Rik|AA672937	palmitoyl-protein thioesterase 2	protein-coding
mm_113035.1	chr13	23535412	23535427	+	1	NA	promoter-TSS (NM_145073)	promoter-TSS (NM_145073)	1	NM_145073	97908	Mm.261657	NM_145073	ENSMUSG00000099517	Hist1h3g	H3.1-221|M32460	histone cluster 1, H3g	protein-coding
mm_21339.1	chr2	157107508	157107518	-	1	NA	exon (NM_001139520, exon 12 of 17)	exon (NM_001139520, exon 12 of 17)	20458	NM_001177439	383766	Mm.480305	NM_001177439	ENSMUSG00000074628	Tldc2	Gm1332	TBC/LysM associated domain containing 2	protein-coding
mm_103193.1	chr11	70646865	70646888	-	1	NA	promoter-TSS (NM_001316728)	promoter-TSS (NM_001316728)	163	NM_024211	67863	Mm.296082	NM_024211	ENSMUSG00000014606	Slc25a11	2310022P18Rik|2oxoc	solute carrier family 25 (mitochondrial carrier oxoglutarate carrier), member 11	protein-coding
mm_160428.1	chr8	88288985	88288985	+	1	NA	promoter-TSS (NM_001037723)	promoter-TSS (NM_001037723)	-81	NM_001037723	11513	Mm.288206	NM_007406	ENSMUSG00000031659	Adcy7	AA407758	adenylate cyclase 7	protein-coding
mm_134373.1	chr16	17132326	17132367	-	1	NA	promoter-TSS (NM_022324)	promoter-TSS (NM_022324)	37	NM_022324	64136	Mm.30222	NM_022324	ENSMUSG00000022769	Sdf2l1	-	stromal cell-derived factor 2-like 1	protein-coding
mm_119542.1	chr14	48120874	48120956	+	1	NA	promoter-TSS (NM_033602)	promoter-TSS (NM_033602)	46	NM_033602	93834	Mm.296457	NM_033602	ENSMUSG00000021846	Peli2	AW047589|BB129927	pellino 2	protein-coding
mm_112889.1	chr13	20884098	20884103	+	1	NA	intron (NM_012054, intron 4 of 20)	intron (NM_012054, intron 4 of 20)	89987	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_49450.1	chr6	29348176	29348184	+	1	NA	promoter-TSS (NM_184053)	promoter-TSS (NM_184053)	74	NM_184053	12321	Mm.392075	NM_007594	ENSMUSG00000029767	Calu	9530075H20Rik	calumenin	protein-coding
mm_7087.1	chr1	88559346	88559348	-	1	NA	intron (NR_037971, intron 4 of 5)	intron (NR_037971, intron 4 of 5)	7830	NR_037971	100503197	Mm.99352	NR_037971	ENSMUSG00000100798	Gm19589	-	predicted gene, 19589	ncRNA
mm_112891.1	chr13	20885109	20885136	+	1	NA	intron (NM_012054, intron 4 of 20)	B4|SINE|B4	91009	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_35635.1	chr4	43515303	43515321	-	1	NA	3' UTR (NM_009416, exon 9 of 9)	3' UTR (NM_009416, exon 9 of 9)	8242	NM_009416	22004	Mm.646	NM_009416	ENSMUSG00000028464	Tpm2	Tpm-2|Trop-2	tropomyosin 2, beta	protein-coding
mm_10919.1	chr2	25403129	25403200	+	1	NA	5' UTR (NM_008721, exon 1 of 9)	5' UTR (NM_008721, exon 1 of 9)	114	NM_008721	18146	Mm.1131	NM_008721	ENSMUSG00000015094	Npdc1	AI314472|NPDC-1	neural proliferation, differentiation and control 1	protein-coding
mm_161157.1	chr13	24831993	24831993	+	1	NA	promoter-TSS (NM_025790)	promoter-TSS (NM_025790)	334	NM_019551	56196	Mm.427162	NM_019551	ENSMUSG00000035958	Tdp2	D13Ertd656e|Ttrap	tyrosyl-DNA phosphodiesterase 2	protein-coding
mm_127209.1	chr15	99228533	99228541	+	1	NA	exon (NM_010601, exon 5 of 15)	exon (NM_010601, exon 5 of 15)	3561	NM_010601	16512	Mm.374793	NM_010601	ENSMUSG00000037579	Kcnh3	AU019351|C030044P22Rik|Elk2|Kv12.2|Melk2	potassium voltage-gated channel, subfamily H (eag-related), member 3	protein-coding
mm_22293.1	chr2	180257120	180257162	-	1	NA	promoter-TSS (NM_025587)	promoter-TSS (NM_025587)	-238	NM_025587	66481	Mm.289669	NM_025587	ENSMUSG00000039001	Rps21	1810049N11Rik|2410030A14Rik	ribosomal protein S21	protein-coding
mm_71170.1	chr8	40546680	40546705	+	1	NA	3' UTR (NM_033560, exon 12 of 12)	3' UTR (NM_033560, exon 12 of 12)	-30845	NM_001271542	18983	Mm.272551	NM_011135	ENSMUSG00000031601	Cnot7	AU022737|CAF-1|Caf1|Pop2	CCR4-NOT transcription complex, subunit 7	protein-coding
mm_63682.1	chr7	130552993	130553009	+	1	NA	Intergenic	Intergenic	-5620	NM_001162855	67872	Mm.21714	NM_001162855	ENSMUSG00000040331	Nsmce4a	2410003A14Rik	NSE4 homolog A, SMC5-SMC6 complex component	protein-coding
mm_68175.1	chr7	103827923	103827931	-	1	NA	promoter-TSS (NM_001278161)	promoter-TSS (NM_001278161)	1	NM_001201391	100503605	Mm.288567	NM_001201391	ENSMUSG00000052305	Hbb-bs	Beta-s|Hbbt1|Hbbt2	hemoglobin, beta adult s chain	protein-coding
mm_27511.1	chr3	56045810	56045813	-	1	NA	intron (NM_030595, intron 10 of 57)	intron (NM_030595, intron 10 of 57)	137890	NM_030595	26422	Mm.384353	NM_030595	ENSMUSG00000027799	Nbea	Lyst2|mKIAA1544	neurobeachin	protein-coding
mm_158386.1	chrX	136085387	136085403	-	1	NA	promoter-TSS (NM_001024141)	promoter-TSS (NM_001024141)	-140	NM_001024141	245610	Mm.336244	NM_001024141	ENSMUSG00000057000	Nxf3	Gm384	nuclear RNA export factor 3	protein-coding
mm_54087.1	chr6	15845991	15846001	-	1	NA	Intergenic	LTR33A_|LTR|ERVL	125335	NM_175088	16543	Mm.1314	NM_175088	ENSMUSG00000041390	Mdfic	Kdt1|Mdfid	MyoD family inhibitor domain containing	protein-coding
mm_25636.1	chr3	120595503	120595528	+	1	NA	intron (NR_130170, intron 12 of 18)	SSU-rRNA_Hsa|rRNA|rRNA	291217	NR_130170	320739	Mm.388474	NR_130170		6530403H02Rik	-	RIKEN cDNA 6530403H02 gene	ncRNA
mm_146086.1	chr18	73551698	73551704	+	1	NA	Intergenic	Tigger16b|DNA|TcMar-Tigger	-21004	NM_001039214	240396	Mm.24131	NM_001039214	ENSMUSG00000037253	Mex3c	A130001D14Rik|BC035207|BM-013|Rkhd2	mex3 RNA binding family member C	protein-coding
mm_19071.1	chr2	77816594	77816628	-	1	NA	5' UTR (NM_178723, exon 1 of 10)	5' UTR (NM_178723, exon 1 of 10)	205	NM_178723	241494	Mm.490320	NM_178723	ENSMUSG00000027016	Zfp385b	B830010L13Rik|C130013B13Rik|Zfp533|Znf385b	zinc finger protein 385B	protein-coding
mm_137096.1	chr17	21535635	21535661	+	1	NA	5' UTR (NM_144515, exon 1 of 5)	5' UTR (NM_144515, exon 1 of 5)	109	NM_144515	22710	Mm.296100	NM_144515	ENSMUSG00000051341	Zfp52	KRAB11|Zfp-52|Zfp76|mszf23-2|mszf24|mszf34|mszf75|zfec29	zinc finger protein 52	protein-coding
mm_168827.1	chr12	22623345	22623346	-	1	NA	Intergenic	CpG	386898	NR_015504	69732	Mm.391403	NM_028362	ENSMUSG00000073164	2410018L13Rik	2810480C08Rik	RIKEN cDNA 2410018L13 gene	ncRNA
mm_105599.1	chr11	106752209	106752223	-	1	NA	intron (NM_001033435, intron 2 of 6)	intron (NM_001033435, intron 2 of 6)	990	NM_001033435	380732	Mm.343952	NM_001033435	ENSMUSG00000040528	Milr1	Allergin-1|Gm885|Mca32	mast cell immunoglobulin like receptor 1	protein-coding
mm_48424.1	chr5	140418727	140418756	-	1	NA	promoter-TSS (NM_133916)	promoter-TSS (NM_133916)	-564	NM_133916	27979	Mm.21671	NM_133916	ENSMUSG00000056076	Eif3b	AL033316|AL033334|AL033369|AW208965|D5Wsu45e|EIF3-ETA|EIF3-P110|EIF3-P116|Eif3s9|PRT1	eukaryotic translation initiation factor 3, subunit B	protein-coding
mm_157342.1	chrX	36902878	36902904	-	1	NA	promoter-TSS (NM_029891)	promoter-TSS (NM_029891)	8	NM_029891	77286	Mm.21649	NM_029891	ENSMUSG00000044149	Nkrf	9430034D17Rik|AW124770|C80287	NF-kappaB repressing factor	protein-coding
mm_31216.1	chr4	43983474	43983491	+	1	NA	promoter-TSS (NM_001002787)	promoter-TSS (NM_001002787)	-22	NM_001002787	442829	Mm.348215	NM_001002787	ENSMUSG00000070999	Ccin	4933417A14Rik	calicin	protein-coding
mm_323.1	chr1	24678684	24678694	+	1	NA	promoter-TSS (NM_001310483)	promoter-TSS (NM_001310483)	145	NM_026719	68421	Mm.336563	NM_026719	ENSMUSG00000073725	Lmbrd1	0910001K20Rik|AV347960	LMBR1 domain containing 1	protein-coding
mm_47784.1	chr5	131997435	131997445	-	1	NA	intron (NM_177047, intron 4 of 18)	intron (NM_177047, intron 4 of 18)	117171	NR_040704	75369	Mm.389696	NR_040704	ENSMUSG00000105773	4930563F08Rik	-	RIKEN cDNA 4930563F08 gene	ncRNA
mm_172868.1	chr9	41905622	41905635	-	1	NA	Intergenic	RLTR4_Mm|LTR|ERV1	218661	NM_011436	20660	Mm.121920	NM_011436	ENSMUSG00000049313	Sorl1	2900010L19Rik|AI596264|AW261561|LR11|SorLA|gp250|mSorLA	sortilin-related receptor, LDLR class A repeats-containing	protein-coding
mm_3803.1	chr1	157526157	157526186	+	1	NA	promoter-TSS (NM_001159986)	promoter-TSS (NM_001159986)	1	NM_001159986	89867	Mm.87114	NM_033354	ENSMUSG00000026589	Sec16b	Lztr2|Rgpr|Rgpr-p117	SEC16 homolog B (S. cerevisiae)	protein-coding
mm_143550.1	chr17	74021460	74021482	-	1	NA	exon (NM_053188, exon 4 of 5)	exon (NM_053188, exon 4 of 5)	26445	NM_053188	94224	Mm.38933	NM_053188	ENSMUSG00000038541	Srd5a2	5ART2|S5AR 2	steroid 5 alpha-reductase 2	protein-coding
mm_79301.1	chr9	51914422	51914434	+	1	NA	promoter-TSS (NR_040731)	promoter-TSS (NR_040731)	-1	NR_040731	74072	Mm.84915	NR_040731	ENSMUSG00000111836	4933407I05Rik	-	RIKEN cDNA 4933407I05 gene	ncRNA
mm_80602.1	chr9	86545257	86545269	+	1	NA	exon (NM_177208, exon 34 of 39)	exon (NM_177208, exon 34 of 39)	26579	NM_001163746	109785	Mm.390201	NM_028352	ENSMUSG00000056131	Pgm3	2810473H05Rik|Agm1|BB187688|C77933|PAGM|Pgm-3	phosphoglucomutase 3	protein-coding
mm_120121.1	chr14	59625303	59625318	+	1	NA	promoter-TSS (NM_145463)	promoter-TSS (NM_145463)	29	NM_145463	219134	Mm.275409	NM_145463	ENSMUSG00000044461	Shisa2	9430059P22Rik|MAd2|Tmem46|mShisa|shisa	shisa family member 2	protein-coding
mm_64120.1	chr7	141079849	141079859	+	1	NA	promoter-TSS (NM_019762)	promoter-TSS (NM_019762)	85	NM_019762	56460	Mm.350037	NM_019762	ENSMUSG00000054065	Pkp3	2310056L12Rik	plakophilin 3	protein-coding
mm_26628.1	chr3	152884347	152884366	+	1	NA	intron (NM_012028, intron 2 of 4)	intron (NM_012028, intron 2 of 4)	97851	NM_012028	26938	Mm.40915	NM_012028	ENSMUSG00000039037	St6galnac5	AI851940|Siat7e	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 5	protein-coding
mm_81861.1	chr9	118835522	118835558	+	1	NA	intron (NM_001113514, intron 6 of 13)	B3A|SINE|B2	-90996	NM_133710	69274	Mm.439928	NM_133710	ENSMUSG00000047409	Ctdspl	2810418J22Rik|AI426263|HYA22|SCP3	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase-like	protein-coding
mm_78084.1	chr9	17047230	17047254	+	1	NA	Intergenic	B1F2|SINE|Alu	-669011	NM_001080814	270120	Mm.195010	NM_001080814	ENSMUSG00000074505	Fat3	9430076A06Rik|D430038H04Rik|Gm1132|Gm510|MFAT3F	FAT atypical cadherin 3	protein-coding
mm_60291.1	chr7	43998911	43998919	+	1	NA	exon (NM_010640, exon 3 of 5)	exon (NM_010640, exon 3 of 5)	3038	NM_010640	16613	Mm.443378	NM_010640	ENSMUSG00000044485	Klk1b11	Klk11|mGK-11	kallikrein 1-related peptidase b11	protein-coding
mm_135241.1	chr16	36990450	36990467	-	1	NA	Intergenic	Intergenic	-11322	NM_001037321	207215	Mm.211899	NM_001037321	ENSMUSG00000047746	Fbxo40	9830003A13Rik|mKIAA1195	F-box protein 40	protein-coding
mm_9601.1	chr1	175607984	175607993	-	1	NA	exon (NM_010209, exon 7 of 10)	exon (NM_010209, exon 7 of 10)	17647	NM_010209	14194	Mm.41502	NM_010209	ENSMUSG00000026526	Fh1	Fh|Fh-1	fumarate hydratase 1	protein-coding
mm_33694.1	chr4	133518982	133519010	+	1	NA	promoter-TSS (NM_001083916)	promoter-TSS (NM_001083916)	33	NM_133707	69073	Mm.299081	NM_133707	ENSMUSG00000037600	Kdf1	1810019J16Rik	keratinocyte differentiation factor 1	protein-coding
mm_67191.1	chr7	73941587	73941591	-	1	NA	3' UTR (NM_009181, exon 6 of 6)	3' UTR (NM_009181, exon 6 of 6)	72093	NM_009181	20450	Mm.4954	NM_009181	ENSMUSG00000025789	St8sia2	AI323367|ST8SiaII|STX|Siat8b	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 2	protein-coding
mm_20551.1	chr2	131071149	131071159	-	1	NA	exon (NM_011426, exon 18 of 21)	exon (NM_011426, exon 18 of 21)	-7340	NM_001163529	110751	Mm.108550	NM_033615	ENSMUSG00000027318	Adam33	Adaml	a disintegrin and metallopeptidase domain 33	protein-coding
mm_61080.1	chr7	51622063	51622124	+	1	NA	5' UTR (NM_080853, exon 1 of 12)	5' UTR (NM_080853, exon 1 of 12)	263	NM_080853	140919	Mm.256618	NM_080853	ENSMUSG00000030500	Slc17a6	2900073D12Rik|DNPI|VGLUT2	solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 6	protein-coding
mm_92472.1	chr10	78043608	78043611	-	1	NA	promoter-TSS (NM_001271556)	promoter-TSS (NM_001271556)	1	NM_001271552	11634	Mm.35300	NM_009646	ENSMUSG00000000731	Aire	-	autoimmune regulator (autoimmune polyendocrinopathy candidiasis ectodermal dystrophy)	protein-coding
mm_41212.1	chr5	88565315	88565337	+	1	NA	exon (NM_001289775, exon 1 of 13)	exon (NM_001289775, exon 1 of 13)	286	NM_001289775	52822	Mm.270469	NM_027530	ENSMUSG00000029291	Rufy3	2810428M05Rik|6330416M07Rik|AW455998|AW538594|D5Bwg0860e|Ripx|Rpipx	RUN and FYVE domain containing 3	protein-coding
mm_102246.1	chr11	55109418	55109445	-	1	NA	exon (NM_010299, exon 4 of 4)	exon (NM_010299, exon 4 of 4)	11446	NM_010299	14667	Mm.287807	NM_010299	ENSMUSG00000000594	Gm2a	AA408702|AW215435|GM2-AP|SAP-3	GM2 ganglioside activator protein	protein-coding
mm_38319.1	chr4	137325545	137325566	-	1	NA	intron (NM_001243769, intron 5 of 5)	U6|snRNA|snRNA	32204	NM_009861	12540	Mm.1022	NM_009861	ENSMUSG00000006699	Cdc42	AI747189|AU018915	cell division cycle 42	protein-coding
mm_172723.1	chr8	72445324	72445327	+	1	NA	exon (NM_028170, exon 2 of 8)	exon (NM_028170, exon 2 of 8)	1445	NM_028170	72254	Mm.30136	NM_028170	ENSMUSG00000052794	1700030K09Rik	-	RIKEN cDNA 1700030K09 gene	protein-coding
mm_55155.1	chr6	51471030	51471069	-	1	NA	intron (NM_007624, intron 1 of 5)	CpG-12058	433	NM_007624	12417	Mm.280968	NM_007624	ENSMUSG00000029836	Cbx3	HP1g|M32	chromobox 3	protein-coding
mm_77404.1	chr8	120537643	120537658	-	1	NA	intron (NM_001145896, intron 1 of 15)	CpG-14578	241	NM_001145896	382034	Mm.334856	NM_198671	ENSMUSG00000031822	Gse1	2210013I18Rik|mKIAA0182	genetic suppressor element 1, coiled-coil protein	protein-coding
mm_81554.1	chr9	110344072	110344077	+	1	NA	intron (NM_001001144, intron 1 of 22)	intron (NM_001001144, intron 1 of 22)	10718	NM_001001144	235623	Mm.288741	NM_001001144	ENSMUSG00000032485	Scap	9530044G19|mKIAA0199	SREBF chaperone	protein-coding
mm_46481.1	chr5	105131916	105131938	-	1	NA	intron (NM_008620, intron 3 of 10)	L1MA6|LINE|L1	7625	NM_008620	17472	Mm.440525	NM_008620	ENSMUSG00000079363	Gbp4	AW228052|Mag-2|Mpa-2|Mpa2	guanylate binding protein 4	protein-coding
mm_134323.1	chr16	16292035	16292038	-	1	NA	Intergenic	RLTR46B|LTR|ERVK	-10929	NR_038046	70120	Mm.37486	NM_198246	ENSMUSG00000022792	Yars2	2210023C10Rik|tyrRS	tyrosyl-tRNA synthetase 2 (mitochondrial)	protein-coding
mm_58632.1	chr7	5093847	5093878	+	1	NA	intron (NM_010147, intron 6 of 11)	intron (NM_010147, intron 6 of 11)	13627	NM_001252454	13854	Mm.3091	NM_010147	ENSMUSG00000035203	Epn1	AA269831|Ibp1	epsin 1	protein-coding
mm_75284.1	chr8	41020542	41020545	-	1	NA	intron (NR_015457, intron 2 of 2)	intron (NR_015457, intron 2 of 2)	3075	NR_015457	78849	Mm.440930	NR_015457	ENSMUSG00000084960	B430010I23Rik	-	RIKEN cDNA B430010I23 gene	ncRNA
mm_104702.1	chr11	97996053	97996075	-	1	NA	5' UTR (NM_207231, exon 1 of 6)	5' UTR (NM_207231, exon 1 of 6)	109	NM_207231	217151	Mm.277896	NM_207231	ENSMUSG00000038352	Arl5c	Arl12|BC065791	ADP-ribosylation factor-like 5C	protein-coding
mm_166459.1	chr5	139372244	139372256	-	1	NA	intron (NM_028469, intron 2 of 4)	CpG	-2505	NR_029768	723898		NR_029768	ENSMUSG00000065593	Mir339	Mirn339|mir-339|mmu-mir-339	microRNA 339	ncRNA
mm_71145.1	chr8	39159356	39159358	+	1	NA	Intergenic	Intergenic	-138623	NR_044988	621335	Mm.208080	NR_044988	ENSMUSG00000109827	Gm6213	EG621335	predicted gene 6213	ncRNA
mm_98196.1	chr11	87795214	87795227	+	1	NA	exon (NM_010824, exon 4 of 14)	exon (NM_010824, exon 4 of 14)	1436	NM_010824	17523	Mm.4668	NM_010824	ENSMUSG00000009350	Mpo	mKIAA4033	myeloperoxidase	protein-coding
mm_91651.1	chr10	42502828	42502846	-	1	NA	intron (NM_017472, intron 1 of 3)	intron (NM_017472, intron 1 of 3)	783	NM_017472	54198	Mm.277870	NM_017472	ENSMUSG00000019804	Snx3	SDP3	sorting nexin 3	protein-coding
mm_171789.1	chr5	114356836	114356853	+	1	NA	intron (NM_001164573, intron 21 of 30)	intron (NM_001164573, intron 21 of 30)	23661	NM_001159941	330171	Mm.238285	NM_026145	ENSMUSG00000001098	Kctd10	AW536343|C87062|mBACURD3	potassium channel tetramerisation domain containing 10	protein-coding
mm_14484.1	chr2	131561639	131561651	+	1	NA	exon (NM_013460, exon 1 of 2)	exon (NM_013460, exon 1 of 2)	640	NM_013460	11550	Mm.389380	NM_013460	ENSMUSG00000027335	Adra1d	Adra-1|Adra1|Adra1a|Gpcr8|Spr8|[a]1d|alpha1D-AR	adrenergic receptor, alpha 1d	protein-coding
mm_45270.1	chr5	64610692	64610709	-	1	NA	promoter-TSS (NR_045078)	promoter-TSS (NR_045078)	-1	NR_045078	100042198	Mm.25191	NR_045078	ENSMUSG00000105402	Gm3716	Gm1683	predicted gene 3716	ncRNA
mm_136186.1	chr16	88962936	88962960	-	1	NA	promoter-TSS (NM_183296)	promoter-TSS (NM_183296)	-75	NM_183296	71369	Mm.251757	NM_130872	ENSMUSG00000096534	Krtap16-3	5430404J20Rik|Krtap16-10	keratin associated protein 16-3	protein-coding
mm_118167.1	chr13	105294820	105294829	-	1	NA	Intergenic	Intergenic	-1810	NM_027934	71816	Mm.317015	NM_027934	ENSMUSG00000021720	Rnf180	3110001E11Rik|Rines	ring finger protein 180	protein-coding
mm_125268.1	chr15	35591848	35591857	+	1	NA	intron (NM_177151, intron 21 of 61)	intron (NM_177151, intron 21 of 61)	69066	NR_035527	100316736		NR_035527	ENSMUSG00000076333	Mir599	mmu-mir-599	microRNA 599	ncRNA
mm_106876.1	chr12	8010809	8010829	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	33142	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_147788.1	chr18	61639875	61639885	-	1	NA	intron (NR_045420, intron 1 of 2)	intron (NR_045420, intron 1 of 2)	227	NR_045420	545261	Mm.426593	NR_045420	ENSMUSG00000098098	Bvht	Braveheart|Gm20748	braveheart long non-coding RNA	ncRNA
mm_5640.1	chr1	40444710	40444748	-	1	NA	intron (NM_001025602, intron 6 of 10)	intron (NM_001025602, intron 6 of 10)	5100	NM_010743	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_169622.1	chr15	39403413	39403415	-	1	NA	intron (NM_001256382, intron 3 of 26)	BGLII|LTR|ERVK	205128	NM_053271	116838	Mm.309296	NM_053271	ENSMUSG00000037386	Rims2	2810036I15Rik|AW048769|RIM2|Rab3ip2|Rim2(+40A)|Rim2(+44A)|Rim2(+4A)|Serg2|Syt3-rs|mKIAA0751	regulating synaptic membrane exocytosis 2	protein-coding
mm_97970.1	chr11	83852136	83852169	+	1	NA	promoter-TSS (NM_001291269)	promoter-TSS (NM_001291269)	-808	NM_001291269	21410	Mm.7226	NM_009330	ENSMUSG00000020679	Hnf1b	HNF-1-beta|HNF-1B|HNF-1Beta|Hnf1beta|LFB3|Tcf-2|Tcf2|vHNF1	HNF1 homeobox B	protein-coding
mm_146071.1	chr18	70474971	70474972	+	1	NA	intron (NM_029019, intron 3 of 8)	intron (NM_029019, intron 3 of 8)	2305	NM_001289650	170461	Mm.83623	NM_029019	ENSMUSG00000079608	Stard6	1700011K09Rik|4833424I06Rik|4933429L05Rik|AI644424	StAR-related lipid transfer (START) domain containing 6	protein-coding
mm_69627.1	chr7	137314834	137314842	-	1	NA	promoter-TSS (NM_001113414)	promoter-TSS (NM_001113414)	-393	NM_010096	13593	Mm.258708	NM_010096	ENSMUSG00000010476	Ebf3	3110018A08Rik|O/E-2|mKIAA4201	early B cell factor 3	protein-coding
mm_119208.1	chr14	32878376	32878386	+	1	NA	intron (NM_178791, intron 2 of 7)	intron (NM_178791, intron 2 of 7)	21625	NM_178791	320736	Mm.187910	NM_178791	ENSMUSG00000050666	Vstm4	E130203B14Rik	V-set and transmembrane domain containing 4	protein-coding
mm_21481.1	chr2	162932428	162932462	-	1	NA	intron (NM_026499, intron 2 of 5)	intron (NM_026499, intron 2 of 5)	937	NM_026499	67996	Mm.24042	NM_026499	ENSMUSG00000016921	Srsf6	1210001E11Rik|AI314910|AW146126|Sfrs6	serine/arginine-rich splicing factor 6	protein-coding
mm_133378.1	chr16	84711850	84711860	+	1	NA	Intergenic	Intergenic	-1168	NR_132106	100653389	Mm.261808	NR_132106	ENSMUSG00000097418	Mir155hg	Bic|Gm26667	Mir155 host gene (non-protein coding)	ncRNA
mm_107215.1	chr12	26445205	26445218	+	1	NA	3' UTR (NM_021384, exon 6 of 6)	3' UTR (NM_021384, exon 6 of 6)	11241	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_60641.1	chr7	44849095	44849114	+	1	NA	promoter-TSS (NM_001290695)	promoter-TSS (NM_001290695)	-25	NM_001042655	233204	Mm.27567	NM_144924	ENSMUSG00000038520	Tbc1d17	BC017607	TBC1 domain family, member 17	protein-coding
mm_129494.1	chr15	78804365	78804378	-	1	NA	Intergenic	MIR3|SINE|MIR	-1329	NM_130859	105844	Mm.17629	NM_130859	ENSMUSG00000033170	Card10	AI449026|Bimp1|Carma3	caspase recruitment domain family, member 10	protein-coding
mm_64394.1	chr7	142489402	142489415	+	1	NA	intron (NM_001271508, intron 7 of 10)	intron (NM_001271508, intron 7 of 10)	-9428	NM_001347549	21957	Mm.389992	NM_011620	ENSMUSG00000061723	Tnnt3	fTnT	troponin T3, skeletal, fast	protein-coding
mm_68352.1	chr7	106510055	106510073	-	1	NA	Intergenic	Intergenic	-68991	NR_003967	209380	Mm.461779	NM_001001318		Gm4759	EG209380	GTPase, very large interferon inducible 1 pseudogene	pseudo
mm_134181.1	chr16	10960912	10960914	-	1	NA	3' UTR (NM_019980, exon 4 of 4)	3' UTR (NM_019980, exon 4 of 4)	32208	NM_019980	56722	Mm.294753	NM_019980	ENSMUSG00000022500	Litaf	3222402J11Rik|C85531|N4WBP3|TBX1	LPS-induced TN factor	protein-coding
mm_64722.1	chr7	4658966	4658977	-	1	NA	promoter-TSS (NM_172894)	promoter-TSS (NM_172894)	-21	NM_172894	243819	Mm.258670	NM_172894	ENSMUSG00000052296	Ppp6r1	2010309P17Rik|AI836219|B430201G11Rik|D030074N20Rik|Pp6r1|Saps1|mKIAA1115	protein phosphatase 6, regulatory subunit 1	protein-coding
mm_123522.1	chr14	66561562	66561565	-	1	NA	Intergenic	Intergenic	-73688	NM_001271759	11549	Mm.57064	NM_013461	ENSMUSG00000045875	Adra1a	Adra1c	adrenergic receptor, alpha 1a	protein-coding
mm_48271.1	chr5	137962976	137962984	-	1	NA	promoter-TSS (NM_080450)	promoter-TSS (NM_080450)	-21	NM_080450	118446	Mm.332771	NM_080450	ENSMUSG00000056966	Gjc3	Cx29|Gje1	gap junction protein, gamma 3	protein-coding
mm_134226.1	chr16	11254433	11254448	-	1	NA	promoter-TSS (NM_001130008)	promoter-TSS (NM_001130008)	5	NR_035466	100316833		NR_035466	ENSMUSG00000088544	Mir1945	mir-1945|mmu-mir-1945	microRNA 1945	ncRNA
mm_35112.1	chr4	9669069	9669113	-	1	NA	promoter-TSS (NM_001177850)	promoter-TSS (NM_001177850)	71	NM_023066	65973	Mm.222206	NM_023066	ENSMUSG00000028207	Asph	2310005F16Rik|3110001L23Rik|AI848629|AW261690|AW561901|BAH|C79816|cI-37	aspartate-beta-hydroxylase	protein-coding
mm_135851.1	chr16	59557374	59557380	-	1	NA	Intergenic	Intergenic	-1625	NM_174848	224273	Mm.246424	NM_174848	ENSMUSG00000022723	Crybg3	5031404N19|AU022790|Gm9581	beta-gamma crystallin domain containing 3	protein-coding
mm_49261.1	chr6	17463902	17463906	+	1	NA	promoter-TSS (NM_008591)	promoter-TSS (NM_008591)	-53	NM_008591	17295	Mm.86844	NM_008591	ENSMUSG00000009376	Met	AI838057|HGF|HGFR|Par4|c-Met	met proto-oncogene	protein-coding
mm_139614.1	chr17	57361044	57361056	+	1	NA	intron (NM_010130, intron 1 of 21)	B3|SINE|B2	2364	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_20015.1	chr2	119271203	119271235	-	1	NA	promoter-TSS (NM_145530)	promoter-TSS (NM_145530)	7	NM_145530	228543	Mm.120274	NM_145530	ENSMUSG00000034226	Rhov	A030005A06Rik|Arhv	ras homolog family member V	protein-coding
mm_145244.1	chr18	51117676	51117750	+	1	NA	promoter-TSS (NM_001081224)	promoter-TSS (NM_001081224)	-185	NM_001081224	71373	Mm.63546	NM_001081224	ENSMUSG00000073565	Prr16	5430406M13Rik|AI607429	proline rich 16	protein-coding
mm_78595.1	chr9	37401994	37402057	+	1	NA	5' UTR (NM_028783, exon 1 of 18)	5' UTR (NM_028783, exon 1 of 18)	128	NM_001309390	74144	Mm.485070	NM_028783	ENSMUSG00000032125	Robo4	1200012D01Rik|AI593217	roundabout guidance receptor 4	protein-coding
mm_39503.1	chr5	21194474	21194484	+	1	NA	intron (NM_175437, intron 2 of 30)	intron (NM_175437, intron 2 of 30)	8212	NM_175437	212167	Mm.121705	NM_175437	ENSMUSG00000039934	Gsap	A530088I07Rik|Pion	gamma-secretase activating protein	protein-coding
mm_90398.1	chr10	127324774	127324797	+	1	NA	intron (NM_146011, intron 1 of 14)	(CCCCG)n|Simple_repeat|Simple_repeat	1058	NM_146011	216445	Mm.227198	NM_146011	ENSMUSG00000040345	Arhgap9	AU043488	Rho GTPase activating protein 9	protein-coding
mm_32363.1	chr4	105193117	105193120	+	1	NA	intron (NM_080555, intron 1 of 5)	intron (NM_080555, intron 1 of 5)	35771	NM_080555	67916	Mm.348326	NM_080555	ENSMUSG00000028517	Plpp3	1110003O22Rik|2610002D05Rik|AV025606|D4Bwg0538e|D4Bwg1535e|Lpp3|Ppab2b|Ppap2b	phospholipid phosphatase 3	protein-coding
mm_166137.1	chr4	156192552	156192575	-	1	NA	intron (NM_021604, intron 2 of 35)	intron (NM_021604, intron 2 of 35)	4925	NM_021604	11603	Mm.273098	NM_021604	ENSMUSG00000041936	Agrn	Agrin|nmf380	agrin	protein-coding
mm_62506.1	chr7	102072522	102072535	+	1	NA	intron (NM_001286689, intron 3 of 10)	intron (NM_001286689, intron 3 of 10)	1309	NM_011644	102443351	Mm.292904	NM_011644	ENSMUSG00000070425	Xntrpc	Xndr-trpc2	Xndc1-transient receptor potential cation channel, subfamily C, member 2 readthrough	protein-coding
mm_100158.1	chr11	116274165	116274183	+	1	NA	promoter-TSS (NM_146032)	promoter-TSS (NM_146032)	43	NM_146032	217337	Mm.29655	NM_146032	ENSMUSG00000020780	Srp68	2610024I03Rik	signal recognition particle 68	protein-coding
mm_602.1	chr1	39901030	39901074	+	1	NA	5' UTR (NM_001252202, exon 1 of 30)	5' UTR (NM_001252202, exon 1 of 30)	139	NM_008696	26921	Mm.491139	NM_008696	ENSMUSG00000026074	Map4k4	9430080K19Rik|AU043147|AU045934|AW046177|HGK|Nik	mitogen-activated protein kinase kinase kinase kinase 4	protein-coding
mm_63193.1	chr7	125603588	125603600	+	1	NA	5' UTR (NM_021887, exon 1 of 9)	5' UTR (NM_021887, exon 1 of 9)	165	NM_021887	60504	Mm.155643	NM_021887	ENSMUSG00000030745	Il21r	NILR	interleukin 21 receptor	protein-coding
mm_26989.1	chr3	25705066	25705073	-	1	NA	intron (NM_001163387, intron 3 of 5)	Lx7|LINE|L1	448238	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_41079.1	chr5	87675002	87675030	+	1	NA	exon (NM_007784, exon 13 of 34)	exon (NM_007784, exon 13 of 34)	8808	NM_001286016	12990	Mm.427467	NM_007784	ENSMUSG00000070702	Csn1s1	AA959832|AW212882|Csna	casein alpha s1	protein-coding
mm_92408.1	chr10	76719146	76719167	-	1	NA	exon (NM_009933, exon 10 of 35)	exon (NM_009933, exon 10 of 35)	6888	NM_009933	12833	Mm.2509	NM_009933	ENSMUSG00000001119	Col6a1	AI747156|Col6a-1	collagen, type VI, alpha 1	protein-coding
mm_79751.1	chr9	62373190	62373197	+	1	NA	intron (NM_009672, intron 3 of 6)	intron (NM_009672, intron 3 of 6)	31850	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	protein-coding
mm_82431.1	chr9	15045107	15045135	-	1	NA	5' UTR (NM_019482, exon 1 of 5)	5' UTR (NM_019482, exon 1 of 5)	357	NM_019482	55991	Mm.142253	NM_019482	ENSMUSG00000031934	Panx1	AI847747	pannexin 1	protein-coding
mm_79567.1	chr9	58134205	58134228	+	1	NA	promoter-TSS (NM_001162479)	promoter-TSS (NM_001162479)	141	NM_001162476	20897	Mm.10801	NM_009291	ENSMUSG00000032327	Stra6	AI891933	stimulated by retinoic acid gene 6	protein-coding
mm_53807.1	chr6	146888594	146888605	+	1	NA	5' UTR (NM_001170433, exon 1 of 28)	5' UTR (NM_001170433, exon 1 of 28)	105	NM_026221	67533	Mm.103382	NM_026221	ENSMUSG00000016487	Ppfibp1	4632409B19Rik|AW214454|AW261454	PTPRF interacting protein, binding protein 1 (liprin beta 1)	protein-coding
mm_29069.1	chr3	103792606	103792616	-	1	NA	Intergenic	Intergenic	-1048	NM_001301304	15257	Mm.20827	NM_010432	ENSMUSG00000008730	Hipk1	1110062K04Rik|Myak	homeodomain interacting protein kinase 1	protein-coding
mm_87373.1	chr10	44268449	44268528	+	1	NA	5' UTR (NM_053069, exon 1 of 8)	5' UTR (NM_053069, exon 1 of 8)	149	NM_053069	11793	Mm.22264	NM_053069	ENSMUSG00000038160	Atg5	2010107M05Rik|3110067M24Rik|AW319544|Apg5l|Atg5l|C88337|Paddy	autophagy related 5	protein-coding
mm_14066.1	chr2	122738496	122738600	+	1	NA	promoter-TSS (NM_019788)	promoter-TSS (NM_019788)	43	NM_019788	18457	Mm.268921	NM_019788	ENSMUSG00000005804	Bloc1s6	BLOC-1|Pldn|Stx13bp1|pa	biogenesis of lysosomal organelles complex-1, subunit 6, pallidin	protein-coding
mm_76384.1	chr8	84842534	84842542	-	1	NA	3' UTR (NM_007591, exon 9 of 9)	3' UTR (NM_007591, exon 9 of 9)	-1873	NM_009010	19358	Mm.255539	NM_009010	ENSMUSG00000003813	Rad23a	2310040P19Rik|AL024030|HR23A|mHR23A	RAD23 homolog A, nucleotide excision repair protein	protein-coding
mm_159634.1	chr4	138777894	138777894	+	1	NA	5' UTR (NM_001347230, exon 2 of 5)	5' UTR (NM_001347230, exon 2 of 5)	2159	NM_011109	18782	Mm.71913	NM_011109	ENSMUSG00000041202	Pla2g2d	Splash|mGIID	phospholipase A2, group IID	protein-coding
mm_137502.1	chr17	26998042	26998050	+	1	NA	Intergenic	RLTR17|LTR|ERVK	-19989	NM_001251881	70772	Mm.440437	NM_027544	ENSMUSG00000048731	Ggnbp1	0610031G08Rik|mdf	gametogenetin binding protein 1	protein-coding
mm_25407.1	chr3	107279029	107279058	+	1	NA	exon (NM_026774, exon 1 of 4)	exon (NM_026774, exon 1 of 4)	185	NM_026774	68576	Mm.290035	NM_026774	ENSMUSG00000087260	Lamtor5	1110003H18Rik|Hbxip|XIP	late endosomal/lysosomal adaptor, MAPK and MTOR activator 5	protein-coding
mm_12030.1	chr2	58194744	58194750	+	1	NA	Intergenic	Intergenic	30773	NR_045895	100042926	Mm.446515	NR_045895	ENSMUSG00000086862	Gm13546	OTTMUSG00000012675	predicted gene 13546	ncRNA
mm_159783.1	chr5	106695975	106695975	-	1	NA	intron (NM_026856, intron 1 of 6)	CpG	855	NM_026856	52397	Mm.249474	NM_026856	ENSMUSG00000049606	Zfp644	1110068L01Rik|AA408882|BM-005|D5Ertd689e|Zep-2	zinc finger protein 644	protein-coding
mm_109960.1	chr12	12492763	12492772	-	1	NA	Intergenic	MLT1F-int|LTR|ERVL-MaLR	-100292	NR_045829	70858	Mm.410838	NR_045829		4921511I17Rik	-	RIKEN cDNA 4921511I17 gene	ncRNA
mm_137838.1	chr17	30938555	30938557	+	1	NA	Intergenic	Intergenic	-16127	NM_177465	52020	Mm.25923	NM_177465	ENSMUSG00000054134	Umodl1	D17Ertd488e	uromodulin-like 1	protein-coding
mm_40914.1	chr5	75632636	75632640	+	1	NA	intron (NM_021099, intron 7 of 20)	intron (NM_021099, intron 7 of 20)	57647	NM_021099	16590	Mm.247073	NM_021099	ENSMUSG00000005672	Kit	Bs|CD117|Fdc|Gsfsco1|Gsfsco5|Gsfsow3|SCO1|SCO5|SOW3|Ssm|Tr-kit|W|c-KIT	KIT proto-oncogene receptor tyrosine kinase	protein-coding
mm_162621.1	chr1	183418490	183418494	+	1	NA	promoter-TSS (NM_030175)	promoter-TSS (NM_030175)	22	NM_030175	78772	Mm.29003	NM_030175	ENSMUSG00000053461	Hhipl2	4930507C10Rik|AW208802|Hhip3	hedgehog interacting protein-like 2	protein-coding
mm_159308.1	chr2	180499926	180499926	+	1	NA	promoter-TSS (NM_018766)	promoter-TSS (NM_018766)	-50	NM_018766	18216	Mm.301712	NM_018766	ENSMUSG00000027568	Ntsr1	NT-1R|NTR-1|NTR1	neurotensin receptor 1	protein-coding
mm_167362.1	chr8	84946049	84946083	-	1	NA	promoter-TSS (NM_144929)	promoter-TSS (NM_144929)	-925	NM_144929	234542	Mm.461701	NM_144929	ENSMUSG00000048617	Rtbdn	A330096I21Rik|BC022744|Rtbnd	retbindin	protein-coding
mm_22543.1	chr3	8923551	8923569	+	1	NA	intron (NM_025434, intron 1 of 2)	CpG	297	NM_025434	66230	Mm.38460	NM_025434	ENSMUSG00000040269	Mrps28	1500012D08Rik|AW061224	mitochondrial ribosomal protein S28	protein-coding
mm_87.1	chr1	7088999	7089077	+	1	NA	5' UTR (NM_183028, exon 1 of 6)	5' UTR (NM_183028, exon 1 of 6)	118	NM_183028	319263	Mm.21539	NM_183028	ENSMUSG00000051285	Pcmtd1	8430411F12Rik|A030012M09Rik	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding
mm_47236.1	chr5	121451304	121451315	-	1	NA	intron (NM_026129, intron 1 of 2)	intron (NM_026129, intron 1 of 2)	1165	NM_026129	67397	Mm.154570	NM_026129	ENSMUSG00000029616	Erp29	1200015M03Rik|2810446M09Rik|AW209030|Erp28|Erp31|PDI-Db	endoplasmic reticulum protein 29	protein-coding
mm_31066.1	chr4	41316856	41316861	+	1	NA	Intergenic	Intergenic	-1957	NM_026893	68970	Mm.28891	NM_026893	ENSMUSG00000028436	Dcaf12	1500001L20Rik|5830424K06Rik|AA420338|AI851081|Wdr40a	DDB1 and CUL4 associated factor 12	protein-coding
mm_126578.1	chr15	82275051	82275069	+	1	NA	intron (NM_011889, intron 1 of 9)	CpG	125	NM_011889	24050	Mm.309707	NM_011889	ENSMUSG00000022456	Sept3	3110018K01Rik|AV154067|B530002E20Rik|Sep3	septin 3	protein-coding
mm_154888.1	chrX	20798392	20798414	+	1	NA	Intergenic	Intergenic	-50140	NM_009703	11836	Mm.220946	NM_009703	ENSMUSG00000001127	Araf	1200013E08Rik|A-Raf|AW495444|Araf1	Araf proto-oncogene, serine/threonine kinase	protein-coding
mm_110441.1	chr12	50411425	50411429	-	1	NA	intron (NM_008858, intron 5 of 18)	Lx7|LINE|L1	237796	NM_008858	18760	Mm.133719	NM_008858	ENSMUSG00000002688	Prkd1	PKD|PKD1|Pkcm|Prkcm	protein kinase D1	protein-coding
mm_46563.1	chr5	107090019	107090035	-	1	NA	Intergenic	Intergenic	125466	NM_001271566	12545	Mm.20842	NM_009863	ENSMUSG00000029283	Cdc7	AI597260|Cdc7l1|muCdc7	cell division cycle 7 (S. cerevisiae)	protein-coding
mm_104079.1	chr11	86587028	86587036	-	1	NA	intron (NM_029478, intron 10 of 11)	intron (NM_029478, intron 10 of 11)	-2874	NR_029738	387140		NR_029738	ENSMUSG00000065455	Mir21a	Mir21|Mirn21|mmu-mir-21|mmu-mir-21a	microRNA 21a	ncRNA
mm_89549.1	chr10	94688648	94688682	+	1	NA	promoter-TSS (NM_029852)	promoter-TSS (NM_029852)	-52	NR_015524	67723	Mm.116284	NR_015524	ENSMUSG00000097164	Cep83os	4932415G12Rik|Ccdc41os1	centrosomal protein 83, opposite strand	ncRNA
mm_167397.1	chr8	95311583	95311587	+	1	NA	promoter-TSS (NM_028532)	promoter-TSS (NM_028532)	-13	NM_028532	73407	Mm.472783	NM_028532	ENSMUSG00000090206	Tepp	1700055M20Rik	testis, prostate and placenta expressed	protein-coding
mm_114762.1	chr13	86160130	86160130	+	1	NA	Intergenic	MERV1_I-int|LTR|ERV1	-113335	NM_007749	12867	Mm.378898	NM_007749	ENSMUSG00000017778	Cox7c	COXVIIc|Cox7c1	cytochrome c oxidase subunit VIIc	protein-coding
mm_113575.1	chr13	40553322	40553326	+	1	NA	Intergenic	Intergenic	-174484	NR_125899	102633805		NR_125899	ENSMUSG00000097752	Gm26688	Tfap2a-as1	predicted gene, 26688	ncRNA
mm_82382.1	chr9	14643556	14643571	-	1	NA	Intergenic	Intergenic	-28563	NM_001081395	75723	Mm.159552	NM_001081395	ENSMUSG00000013076	Amotl1	2310010G08Rik|2310067L22Rik|4932416D09Rik|JEAP|mFLJ00155	angiomotin-like 1	protein-coding
mm_151953.1	chr19	5801323	5801327	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	1347	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_111191.1	chr12	84177372	84177402	-	1	NA	intron (NM_001163501, intron 1 of 12)	intron (NM_001163501, intron 1 of 12)	16628	NM_001163502	238317	Mm.31256	NM_001163501	ENSMUSG00000042507	Elmsan1	9430029N19Rik|C130039O16Rik|Gm260	ELM2 and Myb/SANT-like domain containing 1	protein-coding
mm_3703.1	chr1	153874336	153874354	+	1	NA	promoter-TSS (NM_001008426)	promoter-TSS (NM_001008426)	0	NM_001008426	433365	Mm.229362	NM_001008426	ENSMUSG00000043282	Teddm1b	EG433365|Gm5531	transmembrane epididymal protein 1B	protein-coding
mm_17090.1	chr2	23026087	23026093	-	1	NA	intron (NM_001331043, intron 1 of 10)	AT_rich|Low_complexity|Low_complexity	14151	NM_001077192	11308	Mm.205647	NM_007380	ENSMUSG00000058835	Abi1	E3B1|NAP1|Ssh3bp1|abi-1	abl-interactor 1	protein-coding
mm_113070.1	chr13	23756985	23756995	+	1	NA	promoter-TSS (NM_178193)	promoter-TSS (NM_178193)	53	NM_178193	326620	Mm.261642	NM_178193	ENSMUSG00000069266	Hist1h4b	-	histone cluster 1, H4b	protein-coding
mm_84802.1	chr9	77251872	77251880	-	1	NA	intron (NM_027150, intron 1 of 7)	intron (NM_027150, intron 1 of 7)	95994	NM_027150	69642	Mm.35008	NM_027150	ENSMUSG00000032355	Mlip	2310046A06Rik|AI931782|CIP	muscular LMNA-interacting protein	protein-coding
mm_36360.1	chr4	76142076	76142086	-	1	NA	intron (NM_011211, intron 13 of 39)	intron (NM_011211, intron 13 of 39)	-863795	NM_025849	66928	Mm.24332	NM_025849	ENSMUSG00000028398	Tmem261	1700027K24Rik|3110001D03Rik	transmembrane protein 261	protein-coding
mm_123152.1	chr14	57103289	57103307	-	1	NA	intron (NM_008125, intron 1 of 1)	intron (NM_008125, intron 1 of 1)	1404	NM_008125	14619	Mm.390683	NM_008125	ENSMUSG00000046352	Gjb2	AI325222|Cnx26|Cx26|Gjb-2	gap junction protein, beta 2	protein-coding
mm_45587.1	chr5	74262685	74262707	-	1	NA	intron (NM_001286437, intron 5 of 7)	intron (NM_001286437, intron 5 of 7)	67370	NM_026878	68939	Mm.293316	NM_026878	ENSMUSG00000049907	Rasl11b	1190017B18Rik	RAS-like, family 11, member B	protein-coding
mm_52914.1	chr6	122826697	122826704	+	1	NA	intron (NM_021899, intron 1 of 10)	intron (NM_021899, intron 1 of 10)	-4677	NR_106090	102465710		NR_106090	ENSMUSG00000106580	Mir7231	mmu-mir-7231	microRNA 7231	ncRNA
mm_138762.1	chr17	37050974	37050981	+	1	NA	intron (NM_019439, intron 5 of 22)	CpG	5011	NM_019439	54393	Mm.32191	NM_019439	ENSMUSG00000024462	Gabbr1	GABAB1|GABAbR1|bM573K1.1	gamma-aminobutyric acid (GABA) B receptor, 1	protein-coding
mm_117107.1	chr13	60177065	60177083	-	1	NA	5' UTR (NM_008086, exon 1 of 1)	5' UTR (NM_008086, exon 1 of 1)	461	NM_008086	14451	Mm.22701	NM_008086	ENSMUSG00000052957	Gas1	AW554192|Gas-1	growth arrest specific 1	protein-coding
mm_123590.1	chr14	67308182	67308216	-	1	NA	intron (NM_001037931, intron 3 of 3)	intron (NM_001037931, intron 3 of 3)	6512	NM_001037931	628416	Mm.390723	NM_001037931		Gm6878	EG628416	predicted gene 6878	protein-coding
mm_5217.1	chr1	13669789	13669792	-	1	NA	intron (NM_001011873, intron 1 of 3)	MLT1B|LTR|ERVL-MaLR	1019	NM_001011873	381246	Mm.311142	NM_001011873	ENSMUSG00000067813	Xkr9	Gm1620|XRG9	X-linked Kx blood group related 9	protein-coding
mm_49024.1	chr6	4759555	4759563	+	1	NA	3' UTR (NM_130877, exon 2 of 2)	3' UTR (NM_130877, exon 2 of 2)	12253	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_95689.1	chr11	54304181	54304236	+	1	NA	promoter-TSS (NM_144823)	promoter-TSS (NM_144823)	4	NM_001033597	216739	Mm.267478	NM_144823	ENSMUSG00000020333	Acsl6	A330035H04Rik|AW050338|Facl6|LACS|Lacsl|mKIAA0837	acyl-CoA synthetase long-chain family member 6	protein-coding
mm_18438.1	chr2	60881298	60881316	-	1	NA	5' UTR (NM_001141932, exon 1 of 15)	5' UTR (NM_001141932, exon 1 of 15)	131	NM_001141932	56878	Mm.259667	NM_020296	ENSMUSG00000026970	Rbms1	2600014B10Rik|AI255215|MSSP-1|MSSP-2|MSSP-3|YC1	RNA binding motif, single stranded interacting protein 1	protein-coding
mm_6271.1	chr1	69649445	69649449	-	1	NA	intron (NM_011770, intron 3 of 7)	intron (NM_011770, intron 3 of 7)	36513	NM_011770	22779	Mm.106343	NM_011770	ENSMUSG00000025997	Ikzf2	A730095J18Rik|Helios|Zfpn1a2|Znfn1a2	IKAROS family zinc finger 2	protein-coding
mm_26964.1	chr3	22076139	22076207	-	1	NA	promoter-TSS (NM_030732)	promoter-TSS (NM_030732)	-479	NM_030732	81004	Mm.202966	NM_030732	ENSMUSG00000027630	Tbl1xr1	8030499H02Rik|A630076E03Rik|AW539987|C21|C230089I12Rik|DC42|Ira1|TBLR1	transducin (beta)-like 1X-linked receptor 1	protein-coding
mm_136101.1	chr16	85120573	85120602	-	1	NA	exon (NM_001198823, exon 2 of 18)	exon (NM_001198823, exon 2 of 18)	53120	NM_001198825	11820	Mm.277585	NM_007471	ENSMUSG00000022892	App	Abeta|Abpp|Adap|Ag|Cvap|E030013M08Rik|betaApp	amyloid beta (A4) precursor protein	protein-coding
mm_129583.1	chr15	79742466	79742476	-	1	NA	promoter-TSS (NM_194342)	promoter-TSS (NM_194342)	65	NM_194342	223697	Mm.202715	NM_194342	ENSMUSG00000042524	Sun2	B230369L08Rik|C030011B15|Unc84b	Sad1 and UNC84 domain containing 2	protein-coding
mm_104732.1	chr11	98328173	98328199	-	1	NA	exon (NM_010895, exon 2 of 2)	exon (NM_010895, exon 2 of 2)	1459	NM_010895	18013	Mm.4814	NM_010895	ENSMUSG00000038255	Neurod2	Ndrf|bHLHa1	neurogenic differentiation 2	protein-coding
mm_29203.1	chr3	106767363	106767417	-	1	NA	exon (NM_007651, exon 5 of 8)	exon (NM_007651, exon 5 of 8)	22759	NM_007651	12508	Mm.316861	NM_007651	ENSMUSG00000040747	Cd53	AI323659|Ox-44|Tspan25	CD53 antigen	protein-coding
mm_144928.1	chr18	37707097	37707111	+	1	NA	promoter-TSS (NM_033589)	promoter-TSS (NM_033589)	-125	NM_033589	93714	Mm.247203	NM_033589	ENSMUSG00000103793	Pcdhga6	-	protocadherin gamma subfamily A, 6	protein-coding
mm_118384.1	chr13	117033733	117033789	-	1	NA	Intergenic	Intergenic	-8245	NM_001081009	52552	Mm.274466	NM_027272	ENSMUSG00000021725	Parp8	2810430O08Rik|ARTD16|D13Ertd275e	poly (ADP-ribose) polymerase family, member 8	protein-coding
mm_124377.1	chr14	106486489	106486513	-	1	NA	promoter-TSS (NR_045938)	promoter-TSS (NR_045938)	19	NR_045938	73631	Mm.48862	NR_045938	ENSMUSG00000099794	1700128A07Rik	-	RIKEN cDNA 1700128A07 gene	ncRNA
mm_65925.1	chr7	30243500	30243535	-	1	NA	exon (NM_146186, exon 25 of 33)	exon (NM_146186, exon 25 of 33)	-6752	NM_001289817	381867	Mm.483986	NM_001289817	ENSMUSG00000100512	Ovol3	Gm1903|movo3	ovo like zinc finger 3	protein-coding
mm_45863.1	chr5	87929964	87929974	-	1	NA	exon (NM_007786, exon 4 of 5)	exon (NM_007786, exon 4 of 5)	4336	NM_007786	12994	Mm.296303	NM_007786	ENSMUSG00000001622	Csn3	AW208918|CSN10|Csnk	casein kappa	protein-coding
mm_122294.1	chr14	34578630	34578641	-	1	NA	exon (NM_001039071, exon 4 of 13)	exon (NM_001039071, exon 4 of 13)	9972	NM_001039074	24131	Mm.29733	NM_011918	ENSMUSG00000021798	Ldb3	AW742271|PDLIM6|ZASP	LIM domain binding 3	protein-coding
mm_126320.1	chr15	79693951	79693971	+	1	NA	intron (NM_013818, intron 1 of 11)	intron (NM_013818, intron 1 of 11)	3065	NM_013818	14904	Mm.19080	NM_013818	ENSMUSG00000042535	Gtpbp1	AL022987|AW045683|C85212|GP-1|Gtpbp	GTP binding protein 1	protein-coding
mm_48185.1	chr5	137477072	137477102	-	1	NA	promoter-TSS (NM_011741)	promoter-TSS (NM_011741)	-23	NM_011741	22635	Mm.7984	NM_011741	ENSMUSG00000079173	Zan	Zan-test	zonadhesin	protein-coding
mm_44505.1	chr5	23922915	23922929	-	1	NA	intron (NM_001310471, intron 10 of 10)	intron (NM_001310471, intron 10 of 10)	70689	NR_028536	100217436		NR_028536		Snord93	Gm22397|MBII-336	small nucleolar RNA, C/D box 93	snoRNA
mm_40844.1	chr5	73293317	73293319	+	1	NA	intron (NM_023429, intron 1 of 8)	intron (NM_023429, intron 1 of 8)	524	NM_001159888	68095	Mm.247039	NM_023429	ENSMUSG00000029152	Ociad1	6030432N09Rik|AI481327|AW557942|Asrij|B230209J16Rik|BB021357|Emi2|Imi2|OCIA|TPA018	OCIA domain containing 1	protein-coding
mm_31150.1	chr4	43401233	43401293	+	1	NA	intron (NM_001037709, intron 1 of 11)	intron (NM_001037709, intron 1 of 11)	-5239	NM_199057	100213	Mm.235730	NM_199057	ENSMUSG00000035969	Rusc2	AI840675|mKIAA0375	RUN and SH3 domain containing 2	protein-coding
mm_127966.1	chr15	11996945	11996962	-	1	NA	promoter-TSS (NM_011294)	promoter-TSS (NM_011294)	-946	NM_011294	20024	Mm.41746	NM_011294	ENSMUSG00000022205	Sub1	AI842364|P15|P9|Pc4|Rpo2tc1	SUB1 homolog (S. cerevisiae)	protein-coding
mm_79895.1	chr9	65332573	65332579	+	1	NA	Intergenic	Intergenic	-13492	NM_016688	50996	Mm.29193	NM_016688	ENSMUSG00000041837	Pdcd7	C80112|ES18	programmed cell death 7	protein-coding
mm_127542.1	chr15	102106151	102106163	+	1	NA	intron (NM_153533, intron 3 of 28)	intron (NM_153533, intron 3 of 28)	3169	NM_153533	209039	Mm.29389	NM_153533	ENSMUSG00000037003	Tns2	C1-ten|Tenc1|nep|nph	tensin 2	protein-coding
mm_145591.1	chr18	60986003	60986019	+	1	NA	3' UTR (NM_001286809, exon 6 of 6)	3' UTR (NM_001286809, exon 6 of 6)	22457	NM_001286809	12322	Mm.131530	NM_009792	ENSMUSG00000024617	Camk2a	CaMKII|R74975|mKIAA0968	calcium/calmodulin-dependent protein kinase II alpha	protein-coding
mm_20352.1	chr2	127811889	127811905	-	1	NA	intron (NM_009772, intron 15 of 24)	L1MD3|LINE|L1	-19409	NR_015476	67885	Mm.27359	NM_175125	ENSMUSG00000051319	1500011K16Rik	-	RIKEN cDNA 1500011K16 gene	ncRNA
mm_30175.1	chr3	144204887	144204929	-	1	NA	5' UTR (NM_010723, exon 1 of 5)	5' UTR (NM_010723, exon 1 of 5)	347	NM_010723	16911	Mm.29187	NM_010723	ENSMUSG00000028266	Lmo4	A730077C12Rik|Crp3|Etohi4	LIM domain only 4	protein-coding
mm_105669.1	chr11	107454769	107454783	-	1	NA	intron (NM_145823, intron 1 of 9)	intron (NM_145823, intron 1 of 9)	15944	NM_145823	71795	Mm.397413	NM_145823	ENSMUSG00000040430	Pitpnc1	1110020B03Rik|5830436L09Rik|AI662802|AI851387|C330017I21Rik|Dnr411|RDGBB|RDGBB1|rdgB-beta	phosphatidylinositol transfer protein, cytoplasmic 1	protein-coding
mm_124174.1	chr14	93812369	93812382	-	1	NA	intron (NM_001346722, intron 2 of 4)	B1_Mur2|SINE|Alu	76513	NM_001271800	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding
mm_119636.1	chr14	51885744	51885752	+	1	NA	intron (NM_001029990, intron 3 of 13)	intron (NM_001029990, intron 3 of 13)	906	NM_001029990	52535	Mm.5750	NM_001029990	ENSMUSG00000004561	Mettl17	2310032K15Rik|D14Ertd209e|Mett11d1	methyltransferase like 17	protein-coding
mm_130406.1	chr15	97976743	97976760	-	1	NA	exon (NM_001113515, exon 52 of 53)	exon (NM_001113515, exon 52 of 53)	12522	NM_001252153	380967	Mm.196630	NM_201359	ENSMUSG00000052369	Tmem106c	AI046681|BC046621|D15Ertd405e	transmembrane protein 106C	protein-coding
mm_172442.1	chr7	29965621	29965621	-	1	NA	Intergenic	Intergenic	-13728	NM_178384	72723	Mm.371648	NM_178384	ENSMUSG00000059975	Zfp74	2810054M15Rik|KRAB8|Zfp66|Znf569|mszf21|mszf77	zinc finger protein 74	protein-coding
mm_71752.1	chr8	65639863	65639866	+	1	NA	intron (NM_175188, intron 1 of 7)	intron (NM_175188, intron 1 of 7)	21339	NM_175188	72925	Mm.380457	NM_175188	ENSMUSG00000036469	March1	2900024D24Rik|BB085186	membrane-associated ring finger (C3HC4) 1	protein-coding
mm_148508.1	chr19	4214384	4214397	+	1	NA	promoter-TSS (NM_001310039)	promoter-TSS (NM_001310039)	1	NM_001310039	56708	Mm.347919	NM_019952	ENSMUSG00000040663	Clcf1	BSF-3|Bsf3|CLC|NNT-1	cardiotrophin-like cytokine factor 1	protein-coding
mm_44133.1	chr5	149847756	149847765	+	1	NA	promoter-TSS (NR_045758)	promoter-TSS (NR_045758)	13	NR_045758	70969	Mm.78499	NR_045758	ENSMUSG00000107214	4930500F04Rik	4931407C17Rik	RIKEN cDNA 4930500F04 gene	ncRNA
mm_114148.1	chr13	55369737	55369766	+	1	NA	promoter-TSS (NM_016758)	promoter-TSS (NM_016758)	19	NM_016758	51791	Mm.1426	NM_016758	ENSMUSG00000052087	Rgs14	RPIP1	regulator of G-protein signaling 14	protein-coding
mm_167131.1	chr7	126800150	126800165	-	1	NA	promoter-TSS (NM_001177307)	promoter-TSS (NM_001177307)	290	NM_001177308	11674	Mm.275831	NM_007438	ENSMUSG00000030695	Aldoa	Aldo-1|Aldo1	aldolase A, fructose-bisphosphate	protein-coding
mm_43944.1	chr5	145128005	145128007	+	1	NA	TTS (NM_001033313)	TTS (NM_001033313)	12083	NM_001033313	231887	Mm.188851	NM_001033313	ENSMUSG00000029623	Pdap1	HASPP28|PAP|PAP1	PDGFA associated protein 1	protein-coding
mm_53749.1	chr6	145240466	145240471	+	1	NA	intron (NM_021284, intron 2 of 4)	intron (NM_021284, intron 2 of 4)	9763	NM_021284	16653	Mm.383182	NM_021284	ENSMUSG00000030265	Kras	AI929937|K-Ras|K-Ras 2|K-ras|Ki-ras|Kras-2|Kras2|c-K-ras|c-Ki-ras|p21B|ras	Kirsten rat sarcoma viral oncogene homolog	protein-coding
mm_134541.1	chr16	19708477	19708497	-	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-2122	NM_177356	239739	Mm.258059	NM_177356	ENSMUSG00000041247	Lamp3	1200002D17Rik|Cd208|DC-LAMP|DCLAMP|LAMP|TSC403	lysosomal-associated membrane protein 3	protein-coding
mm_122415.1	chr14	41069194	41069212	-	1	NA	promoter-TSS (NM_027717)	promoter-TSS (NM_027717)	-129	NM_027717	71200	Mm.443973	NM_027717	ENSMUSG00000021791	Dydc2	4933428D01Rik	DPY30 domain containing 2	protein-coding
mm_23940.1	chr3	84479516	84479547	+	1	NA	promoter-TSS (NM_001205355)	promoter-TSS (NM_001205355)	-40	NM_001205355	229474	Mm.331107	NM_001033301	ENSMUSG00000041842	Fhdc1	6330505N24Rik|Gm126	FH2 domain containing 1	protein-coding
mm_128702.1	chr15	63479662	63479670	-	1	NA	promoter-TSS (NR_045279)	promoter-TSS (NR_045279)	-58	NR_045279	432958	Mm.255105	NR_045279		Gm20740	-	predicted gene, 20740	ncRNA
mm_108657.1	chr12	86421604	86421625	+	1	NA	promoter-TSS (NM_011934)	promoter-TSS (NM_011934)	-30	NM_011934	26380	Mm.235550	NM_011934	ENSMUSG00000021255	Esrrb	Err2|Errb|Estrrb|Nr3b2	estrogen related receptor, beta	protein-coding
mm_64634.1	chr7	3706767	3706795	-	1	NA	exon (NM_029767, exon 5 of 5)	exon (NM_029767, exon 5 of 5)	2740	NM_029767	76846	Mm.13944	NM_029767	ENSMUSG00000006333	Rps9	3010033P07Rik|AL022771|AL022885	ribosomal protein S9	protein-coding
mm_50967.1	chr6	60177655	60177678	+	1	NA	Intergenic	Intergenic	226041	NR_015565	208079	Mm.131226	NM_177329	ENSMUSG00000046764	A530053G22Rik	-	RIKEN cDNA A530053G22 gene	ncRNA
mm_150869.1	chr19	45047782	45047838	+	1	NA	5' UTR (NM_053197, exon 1 of 11)	5' UTR (NM_053197, exon 1 of 11)	234	NM_001178013	94280	Mm.36169	NM_053197	ENSMUSG00000025212	Sfxn3	-	sideroflexin 3	protein-coding
mm_112209.1	chr12	113427333	113427396	-	1	NA	Intergenic	Intergenic	-62201	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_104571.1	chr11	96943801	96943850	-	1	NA	promoter-TSS (NR_003293)	promoter-TSS (NR_003293)	194	NM_134021	103711	Mm.254704	NM_134021	ENSMUSG00000018659	Pnpo	AI415282	pyridoxine 5'-phosphate oxidase	protein-coding
mm_86509.1	chr10	7654464	7654465	+	1	NA	intron (NM_001347228, intron 1 of 7)	MTE-int|LTR|ERVL-MaLR	-8907	NR_030698	320642	Mm.398806	NR_030698		A630066F11Rik	-	RIKEN cDNA A630066F11 gene	ncRNA
mm_46233.1	chr5	99217799	99217800	-	1	NA	3' UTR (NM_181318, exon 14 of 14)	3' UTR (NM_181318, exon 14 of 14)	35128	NM_181318	320292	Mm.259074	NM_145839	ENSMUSG00000089809	Rasgef1b	4732452O09Rik|GPIgamma4|Gpig4	RasGEF domain family, member 1B	protein-coding
mm_33432.1	chr4	130056767	130056776	+	1	NA	intron (NM_028266, intron 11 of 69)	intron (NM_028266, intron 11 of 69)	8931	NM_028266	107581	Mm.41860	NM_028266	ENSMUSG00000040690	Col16a1	2700007F12Rik|A530052M23Rik|AI838662|CA1F	collagen, type XVI, alpha 1	protein-coding
mm_128306.1	chr15	37780325	37780345	-	1	NA	intron (NM_134094, intron 1 of 6)	intron (NM_134094, intron 1 of 6)	11665	NM_001170866	52589	Mm.283370	NM_134094	ENSMUSG00000051359	Ncald	AI848120|D030020D09Rik|D15Ertd412e	neurocalcin delta	protein-coding
mm_164040.1	chr14	87416379	87416409	+	1	NA	promoter-TSS (NM_001253755)	promoter-TSS (NM_001253755)	-189	NM_172605	219249	Mm.35168	NM_172605	ENSMUSG00000022019	Tdrd3	4732418C03Rik|6720468N18	tudor domain containing 3	protein-coding
mm_5119.1	chr1	7136614	7136616	-	1	NA	intron (NM_183028, intron 2 of 5)	intron (NM_183028, intron 2 of 5)	47695	NM_183028	319263	Mm.21539	NM_183028	ENSMUSG00000051285	Pcmtd1	8430411F12Rik|A030012M09Rik	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding
mm_40333.1	chr5	43910911	43910976	+	1	NA	3' UTR (NM_007646, exon 8 of 8)	3' UTR (NM_007646, exon 8 of 8)	42134	NM_007646	12494	Mm.249873	NM_007646	ENSMUSG00000029084	Cd38	ADPRC 1|Cd38-rs1|I-19	CD38 antigen	protein-coding
mm_136244.1	chr16	90934803	90934857	-	1	NA	promoter-TSS (NM_026502)	promoter-TSS (NM_026502)	19	NM_026502	68001	Mm.45374	NM_026502	ENSMUSG00000022972	1110004E09Rik	-	RIKEN cDNA 1110004E09 gene	protein-coding
mm_155693.1	chrX	94234983	94234997	+	1	NA	promoter-TSS (NM_153165)	promoter-TSS (NM_153165)	60	NM_001039061	236904	Mm.115533	NM_153165	ENSMUSG00000043929	Klhl15	6330500C13Rik	kelch-like 15	protein-coding
mm_2687.1	chr1	127320128	127320166	+	1	NA	intron (NM_145128, intron 3 of 17)	B4A|SINE|B4	115161	NM_145128	107895	Mm.214682	NM_145128	ENSMUSG00000036155	Mgat5	4930471A21Rik|5330407H02Rik|AI480971|GlcNAc-TV	mannoside acetylglucosaminyltransferase 5	protein-coding
mm_84107.1	chr9	58313156	58313166	-	1	NA	promoter-TSS (NM_010729)	promoter-TSS (NM_010729)	51	NM_010729	16949	Mm.250492	NM_010729	ENSMUSG00000032334	Loxl1	Loxl	lysyl oxidase-like 1	protein-coding
mm_75317.1	chr8	41374603	41374677	-	1	NA	promoter-TSS (NM_019734)	promoter-TSS (NM_019734)	57	NM_019734	11886	Mm.22547	NM_019734	ENSMUSG00000031591	Asah1	2310081N20Rik|AC|Asah	N-acylsphingosine amidohydrolase 1	protein-coding
mm_42019.1	chr5	108269291	108269302	+	1	NA	5' UTR (NM_026106, exon 1 of 3)	5' UTR (NM_026106, exon 1 of 3)	399	NM_026106	13486	Mm.303534	NM_026106	ENSMUSG00000029265	Dr1	1700121L09Rik|Dr1l|NC2|NC2beta	down-regulator of transcription 1	protein-coding
mm_163595.1	chr13	41569022	41569040	-	1	NA	Intergenic	Intergenic	-37185	NM_001163572	621976	Mm.259830	NM_001163572	ENSMUSG00000087370	Tmem170b	EG621976	transmembrane protein 170B	protein-coding
mm_72240.1	chr8	75016230	75016246	+	1	NA	promoter-TSS (NM_001316754)	promoter-TSS (NM_001316754)	16	NM_001316754	70823	Mm.261739	NM_178017	ENSMUSG00000034518	Hmgxb4	4733401K04Rik|AI316803|Hmgb2l1	HMG box domain containing 4	protein-coding
mm_6861.1	chr1	84278296	84278320	-	1	NA	intron (NM_001003948, intron 1 of 2)	intron (NM_001003948, intron 1 of 2)	6337	NM_001003948	98496	Mm.187470	NM_001003948	ENSMUSG00000045658	Pid1	5033414K04Rik|NYGGF4	phosphotyrosine interaction domain containing 1	protein-coding
mm_101524.1	chr11	33039774	33039782	-	1	NA	Intergenic	Intergenic	107622	NM_008005	14172	Mm.339812	NM_008005	ENSMUSG00000057967	Fgf18	D130055P09Rik|FGF-18	fibroblast growth factor 18	protein-coding
mm_132822.1	chr16	45224172	45224192	+	1	NA	promoter-TSS (NM_001037719)	promoter-TSS (NM_001037719)	-155	NM_001037719	208154	Mm.38199	NM_177584	ENSMUSG00000052013	Btla	A630002H24	B and T lymphocyte associated	protein-coding
mm_168844.1	chr12	23698085	23698086	+	1	NA	Intergenic	ERVB4_2-LTR_MM|LTR|ERVK	399184	NM_001256489	66808	Mm.379124	NM_001256489	ENSMUSG00000073158	9030624G23Rik	-	RIKEN cDNA 9030624G23 gene	protein-coding
mm_116873.1	chr13	55020127	55020135	-	1	NA	intron (NM_001033245, intron 1 of 18)	intron (NM_001033245, intron 1 of 18)	688	NM_001206390	212032	Mm.267479	NM_001033245	ENSMUSG00000025877	Hk3	HK III|HK-III	hexokinase 3	protein-coding
mm_67096.1	chr7	69908050	69908052	-	1	NA	Intergenic	Intergenic	411957	NR_045940	73796	Mm.410832	NR_045940	ENSMUSG00000108885	4930402F11Rik	-	RIKEN cDNA 4930402F11 gene	ncRNA
mm_72434.1	chr8	83084300	83084343	+	1	NA	3' UTR (NM_177378, exon 7 of 7)	3' UTR (NM_177378, exon 7 of 7)	-81031	NM_001111304	71310	Mm.24031	NM_027758	ENSMUSG00000031709	Tbc1d9	4933431N12Rik|AI847101|AW490653|C76116	TBC1 domain family, member 9	protein-coding
mm_84126.1	chr9	58741544	58741580	-	1	NA	promoter-TSS (NM_028598)	promoter-TSS (NM_028598)	-3	NM_028598	73673	Mm.205196	NM_028598	ENSMUSG00000074269	Rec114	2410076I21Rik|4930527A11Rik	REC114 meiotic recombination protein	protein-coding
mm_91218.1	chr10	21994515	21994552	-	1	NA	promoter-TSS (NM_011361)	promoter-TSS (NM_011361)	-133	NM_011361	20393	Mm.28405	NM_011361	ENSMUSG00000019970	Sgk1	Sgk	serum/glucocorticoid regulated kinase 1	protein-coding
mm_83922.1	chr9	56620619	56620633	-	1	NA	exon (NM_181074, exon 4 of 4)	exon (NM_181074, exon 4 of 4)	15022	NM_001311076	235402	Mm.246605	NM_181074	ENSMUSG00000049556	Lingo1	4930471K13Rik|AV148400|LERN1|LINGO-1|Lrrn6a|UNQ201	leucine rich repeat and Ig domain containing 1	protein-coding
mm_19489.1	chr2	93203440	93203456	-	1	NA	3' UTR (NM_183180, exon 10 of 10)	3' UTR (NM_183180, exon 10 of 10)	15864	NM_001025246	277414	Mm.41033	NM_001025246	ENSMUSG00000068735	Trp53i11	Tp53i11	transformation related protein 53 inducible protein 11	protein-coding
mm_130334.1	chr15	97730710	97730729	-	1	NA	intron (NM_001168693, intron 1 of 9)	intron (NM_001168693, intron 1 of 9)	686	NM_001168693	19011	Mm.1001	NM_008902	ENSMUSG00000022468	Endou	Pp11r|Tcl-30	endonuclease, polyU-specific	protein-coding
mm_164911.1	chr18	73301549	73301551	+	1	NA	Intergenic	Intergenic	-271155	NM_001039214	240396	Mm.24131	NM_001039214	ENSMUSG00000037253	Mex3c	A130001D14Rik|BC035207|BM-013|Rkhd2	mex3 RNA binding family member C	protein-coding
mm_83453.1	chr9	45204068	45204077	-	1	NA	promoter-TSS (NM_145403)	promoter-TSS (NM_145403)	3	NM_145403	214523	Mm.436756	NM_145403	ENSMUSG00000032091	Tmprss4	mCAP2	transmembrane protease, serine 4	protein-coding
mm_21205.1	chr2	155640642	155640669	-	1	NA	intron (NM_019828, intron 12 of 18)	intron (NM_019828, intron 12 of 18)	17775	NR_030757	735275		NR_030757	ENSMUSG00000076312	Mir499	Mirn499|mir-499|mmu-mir-499	microRNA 499	ncRNA
mm_78575.1	chr9	36726676	36726722	+	1	NA	promoter-TSS (NM_007691)	promoter-TSS (NM_007691)	-41	NM_007691	12649	Mm.16753	NM_007691	ENSMUSG00000032113	Chek1	C85740|Chk1|rad27	checkpoint kinase 1	protein-coding
mm_152076.1	chr19	6851102	6851108	-	1	NA	intron (NM_001081291, intron 14 of 26)	intron (NM_001081291, intron 14 of 26)	7106	NM_001081291	78317	Mm.329596	NM_198008	ENSMUSG00000047810	Ccdc88b	2610041P08Rik|Ccdc88	coiled-coil domain containing 88B	protein-coding
mm_142500.1	chr17	46031868	46031886	-	1	NA	exon (NM_001025250, exon 1 of 8)	exon (NM_001025250, exon 1 of 8)	500	NM_001287058	22339	Mm.282184	NM_009505	ENSMUSG00000023951	Vegfa	Vegf|Vpf	vascular endothelial growth factor A	protein-coding
mm_115113.1	chr13	104109738	104109746	+	1	NA	promoter-TSS (NM_029447)	promoter-TSS (NM_029447)	-48	NM_144838	218544	Mm.44416	NM_144838	ENSMUSG00000042743	Sgtb	C630001O05Rik	small glutamine-rich tetratricopeptide repeat (TPR)-containing, beta	protein-coding
mm_95450.1	chr11	50325875	50325897	+	1	NA	promoter-TSS (NM_001110500)	promoter-TSS (NM_001110500)	-213	NM_001110500	12330	Mm.248827	NM_007597	ENSMUSG00000020368	Canx	1110069N15Rik|AI988026|Cnx|D11Ertd153e	calnexin	protein-coding
mm_91418.1	chr10	32478763	32478765	-	1	NA	intron (NM_001013411, intron 1 of 6)	intron (NM_001013411, intron 1 of 6)	411151	NM_001013411	432450	Mm.49665	NM_001013411	ENSMUSG00000069670	Nkain2	6330571D19Rik|AW455467|Tcba1	Na+/K+ transporting ATPase interacting 2	protein-coding
mm_44233.1	chr5	5265670	5265683	-	1	NA	5' UTR (NM_001310448, exon 1 of 14)	5' UTR (NM_001310448, exon 1 of 14)	392	NM_001310448	18647	Mm.389061	NM_011074	ENSMUSG00000028926	Cdk14	Pftk1|mKIAA0834	cyclin-dependent kinase 14	protein-coding
mm_110963.1	chr12	76822421	76822431	-	1	NA	promoter-TSS (NM_134050)	promoter-TSS (NM_134050)	98	NM_134050	104886	Mm.172847	NM_134050	ENSMUSG00000021062	Rab15	2310012G06Rik|AI840042	RAB15, member RAS oncogene family	protein-coding
mm_74997.1	chr8	27223815	27223833	-	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	5764	NM_013462	11556	Mm.278475	NM_013462	ENSMUSG00000031489	Adrb3	Adrb-3	adrenergic receptor, beta 3	protein-coding
mm_152481.1	chr19	11048032	11048042	-	1	NA	non-coding (NR_102366, exon 3 of 3)	non-coding (NR_102366, exon 3 of 3)	2529	NR_102366	107350	Mm.6381	NM_001177351	ENSMUSG00000075010	AW112010	-	expressed sequence AW112010	ncRNA
mm_128444.1	chr15	50763196	50763217	-	1	NA	intron (NM_001310481, intron 4 of 5)	intron (NM_001310481, intron 4 of 5)	125843	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_77949.1	chr9	7464140	7464145	+	1	NA	promoter-TSS (NM_032006)	promoter-TSS (NM_032006)	1	NM_032006	83995	Mm.156952	NM_032006	ENSMUSG00000043089	Mmp1a	MMP-1a|Mcol-A|Mcola	matrix metallopeptidase 1a (interstitial collagenase)	protein-coding
mm_165149.1	chr2	19389045	19389058	+	1	NA	intron (NM_029619, intron 3 of 4)	MIRc|SINE|MIR	17415	NM_029619	76467	Mm.27166	NM_029619	ENSMUSG00000023094	Msrb2	2310050L06Rik|Mrsb|Msrb|Pilb	methionine sulfoxide reductase B2	protein-coding
mm_85145.1	chr9	95845216	95845285	-	1	NA	promoter-TSS (NM_001033210)	promoter-TSS (NM_001033210)	29	NM_001033210	102502	Mm.11869	NM_001033210	ENSMUSG00000049493	Pls1	AI427122	plastin 1 (I-isoform)	protein-coding
mm_160479.1	chr8	121651817	121651817	-	1	NA	exon (NM_080855, exon 1 of 13)	exon (NM_080855, exon 1 of 13)	116	NM_080855	142682	Mm.103202	NM_080855	ENSMUSG00000061410	Zcchc14	AA792890|BDG29	zinc finger, CCHC domain containing 14	protein-coding
mm_10100.1	chr2	3453701	3453716	+	1	NA	exon (NM_146114, exon 14 of 14)	exon (NM_146114, exon 14 of 14)	21278	NM_022724	64707	Mm.23483	NM_022724	ENSMUSG00000026646	Suv39h2	4930507K23Rik|AA536750|D030054H19Rik|D2Ertd544e|KMT1B	suppressor of variegation 3-9 homolog 2 (Drosophila)	protein-coding
mm_143843.1	chr17	84127108	84127123	-	1	NA	Intergenic	Intergenic	48455	NR_045458	74473	Mm.399575	NR_045458		4933433H22Rik	-	RIKEN cDNA 4933433H22 gene	ncRNA
mm_92666.1	chr10	80433603	80433613	-	1	NA	promoter-TSS (NM_011548)	promoter-TSS (NM_011548)	45	NM_001164150	21423	Mm.3406	NM_011548	ENSMUSG00000020167	Tcf3	A1|AA408400|ALF2|AW209082|E12|E12/E47|E2A|E47|KA1|ME2|Pan1|Pan2|TCF-3|Tcfe2a|VDIR|bHLHb21	transcription factor 3	protein-coding
mm_159307.1	chr2	180289871	180289871	-	1	NA	promoter-TSS (NM_173031)	promoter-TSS (NM_173031)	8	NM_173031	271887	Mm.246640	NM_173031	ENSMUSG00000038980	Rbbp8nl	4732416F18	RBBP8 N-terminal like	protein-coding
mm_30497.1	chr3	157888922	157888928	-	1	NA	Intergenic	Intergenic	36138	NM_145953	107869	Mm.28301	NM_145953	ENSMUSG00000028179	Cth	0610010I13Rik|AI314617|BC019483|CSE|Cys3	cystathionase (cystathionine gamma-lyase)	protein-coding
mm_14699.1	chr2	142219648	142219648	+	1	NA	intron (NM_001013802, intron 11 of 18)	intron (NM_001013802, intron 11 of 18)	681816	NM_001081133	16558	Mm.251934	NM_001081133	ENSMUSG00000038844	Kif16b	8430434E15Rik|AA623607|AI789011|C80253|C80902|mKIAA1590	kinesin family member 16B	protein-coding
mm_97624.1	chr11	78957576	78957583	+	1	NA	exon (NM_010927, exon 26 of 27)	exon (NM_010927, exon 26 of 27)	27345	NM_001159301	16859	Mm.341434	NM_010708	ENSMUSG00000001123	Lgals9	AA407335|AI194909|AI265545|LGALS35|Lgals5|gal-9|galectin-9	lectin, galactose binding, soluble 9	protein-coding
mm_47160.1	chr5	120694591	120694603	-	1	NA	exon (NM_008052, exon 3 of 10)	exon (NM_008052, exon 3 of 10)	17072	NM_008052	14357	Mm.1645	NM_008052	ENSMUSG00000029603	Dtx1	Fxit1|mKIAA4160	deltex 1, E3 ubiquitin ligase	protein-coding
mm_85707.1	chr9	108139366	108139377	-	1	NA	TTS (NR_126078)	TTS (NR_126078)	2516	NR_126077	76873	Mm.436935	NR_126077	ENSMUSG00000102224	4930447F24Rik	-	RIKEN cDNA 4930447F24 gene	ncRNA
mm_21764.1	chr2	164840522	164840557	-	1	NA	3' UTR (NM_008906, exon 15 of 15)	3' UTR (NM_008906, exon 15 of 15)	6766	NM_008906	19025	Mm.359633	NM_008906	ENSMUSG00000017760	Ctsa	AU019505|PPCA|Ppgb	cathepsin A	protein-coding
mm_125325.1	chr15	38518509	38518513	+	1	NA	intron (NR_125913, intron 1 of 11)	CpG	755	NM_001301688	54375	Mm.250214	NM_018745	ENSMUSG00000037458	Azin1	1700085L02Rik|AZI|Oazi|Oazin	antizyme inhibitor 1	protein-coding
mm_10055.1	chr1	193242347	193242368	-	1	NA	promoter-TSS (NM_001044751)	promoter-TSS (NM_001044751)	3	NM_001044751	15483	Mm.28328	NM_008288	ENSMUSG00000016194	Hsd11b1	-	hydroxysteroid 11-beta dehydrogenase 1	protein-coding
mm_58994.1	chr7	19137529	19137532	+	1	NA	3' UTR (NM_175530, exon 2 of 2)	3' UTR (NM_175530, exon 2 of 2)	11666	NM_026111	67369	Mm.234876	NM_026111	ENSMUSG00000030407	Qpctl	1810019P04Rik|BB101812|gQC	glutaminyl-peptide cyclotransferase-like	protein-coding
mm_57218.1	chr6	122952402	122952416	-	1	NA	promoter-TSS (NM_153197)	promoter-TSS (NM_153197)	-106	NM_001204241	73149	Mm.25684	NM_153197	ENSMUSG00000043832	Clec4a3	3110037K17Rik|Dcir3	C-type lectin domain family 4, member a3	protein-coding
mm_95920.1	chr11	58221099	58221115	+	1	NA	3' UTR (NM_019440, exon 2 of 2)	3' UTR (NM_019440, exon 2 of 2)	6130	NM_019440	54396	Mm.458517	NM_019440	ENSMUSG00000069874	Irgm2	AI481100|GTPI|Ifggd2|Iigp2	immunity-related GTPase family M member 2	protein-coding
mm_76423.1	chr8	84977875	84977888	-	1	NA	exon (NM_008416, exon 1 of 1)	exon (NM_008416, exon 1 of 1)	867	NM_008416	16477	Mm.1167	NM_008416	ENSMUSG00000052837	Junb	-	jun B proto-oncogene	protein-coding
mm_167185.1	chr7	141997537	141997541	+	1	NA	intron (NM_001009930, intron 16 of 19)	intron (NM_001009930, intron 16 of 19)	5360	NR_037291	100526509		NR_037291	ENSMUSG00000092652	Mir3104	mir-3104|mmu-mir-3104	microRNA 3104	ncRNA
mm_65688.1	chr7	28372511	28372519	-	1	NA	5' UTR (NM_001083912, exon 1 of 19)	5' UTR (NM_001083912, exon 1 of 19)	147	NM_138752	101497	Mm.235700	NM_138752	ENSMUSG00000037552	Plekhg2	AI194308|Clg|Cslg	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	protein-coding
mm_64902.1	chr7	15967471	15967484	-	1	NA	promoter-TSS (NM_153068)	promoter-TSS (NM_153068)	58	NM_153068	259300	Mm.138215	NM_153068	ENSMUSG00000074364	Ehd2	BC027084|C130052H20Rik	EH-domain containing 2	protein-coding
mm_13317.1	chr2	102675515	102675525	+	1	NA	intron (NM_001077514, intron 1 of 10)	intron (NM_001077514, intron 1 of 10)	16837	NM_001077514	20511	Mm.267547	NM_011393	ENSMUSG00000005089	Slc1a2	1700091C19Rik|2900019G14Rik|AI159670|Eaat2|GLT-1|GLT1|MGLT1	solute carrier family 1 (glial high affinity glutamate transporter), member 2	protein-coding
mm_109217.1	chr12	108761524	108761536	+	1	NA	Intergenic	Intergenic	-31781	NM_009537	22632	Mm.3868	NM_009537	ENSMUSG00000021264	Yy1	AW488674|NF-E1	YY1 transcription factor	protein-coding
mm_120949.1	chr14	76735377	76735381	+	1	NA	Intergenic	RMER17A2|LTR|ERVK	57811	NR_015485	73272	Mm.116804	NR_015485	ENSMUSG00000101009	1700108F19Rik	1700020I02Rik|BB065030	RIKEN cDNA 1700108F19 gene	ncRNA
mm_136095.1	chr16	85079862	85079876	-	1	NA	exon (NM_001198823, exon 5 of 18)	exon (NM_001198823, exon 5 of 18)	93838	NM_001198825	11820	Mm.277585	NM_007471	ENSMUSG00000022892	App	Abeta|Abpp|Adap|Ag|Cvap|E030013M08Rik|betaApp	amyloid beta (A4) precursor protein	protein-coding
mm_86713.1	chr10	18917273	18917290	+	1	NA	Intergenic	Intergenic	72210	NM_022032	64058	Mm.28209	NM_022032	ENSMUSG00000019851	Perp	1110017A08Rik|KCP1|KRTCAP1|PIGPC1|THW	PERP, TP53 apoptosis effector	protein-coding
mm_38157.1	chr4	135211816	135211820	-	1	NA	Intergenic	Intergenic	60942	NM_013885	29876	Mm.257765	NM_013885	ENSMUSG00000037242	Clic4	D0Jmb3|TU-74|mc3s5|mtCLIC	chloride intracellular channel 4 (mitochondrial)	protein-coding
mm_10494.1	chr2	14873699	14873708	+	1	NA	promoter-TSS (NM_001309519)	promoter-TSS (NM_001309519)	47	NM_001309519	12296	Mm.313930	NM_023116	ENSMUSG00000057914	Cacnb2	AW060387|CAB2|Cavbeta2|Cchb2	calcium channel, voltage-dependent, beta 2 subunit	protein-coding
mm_9314.1	chr1	171645951	171645973	-	1	NA	intron (NM_001347184, intron 1 of 5)	RSINE1|SINE|B4	3037	NM_001347184	75345	Mm.164642	NM_144539	ENSMUSG00000038179	Slamf7	19A|19A24|4930560D03Rik|CRACC|CS1	SLAM family member 7	protein-coding
mm_66342.1	chr7	43473518	43473538	-	1	NA	3' UTR (NM_001164518, exon 8 of 8)	3' UTR (NM_001164518, exon 8 of 8)	10295	NM_001290316	75690	Mm.30200	NM_001290316	ENSMUSG00000070604	Vsig10l	-	V-set and immunoglobulin domain containing 10 like	protein-coding
mm_90334.1	chr10	127079116	127079127	+	1	NA	5' UTR (NM_001301014, exon 1 of 18)	5' UTR (NM_001301014, exon 1 of 18)	214	NM_001033263	216439	Mm.336761	NM_001033263	ENSMUSG00000025422	Agap2	AGAP-2|Centg1|PIKE|cnt-g1|mKIAA0167	ArfGAP with GTPase domain, ankyrin repeat and PH domain 2	protein-coding
mm_136043.1	chr16	78375020	78375029	-	1	NA	intron (NM_001297747, intron 1 of 4)	intron (NM_001297747, intron 1 of 4)	1733	NR_002700	654432	Mm.458574	NR_002700	ENSMUSG00000044645	Gm7334	EG654432	B-cell translocation gene 3 pseudogene	pseudo
mm_137311.1	chr17	24878792	24878799	+	1	NA	promoter-TSS (NM_008340)	promoter-TSS (NM_008340)	25	NM_008340	16005	Mm.3135	NM_008340	ENSMUSG00000046070	Igfals	ALS|Albs|mKIAA4111	insulin-like growth factor binding protein, acid labile subunit	protein-coding
mm_30433.1	chr3	153298647	153298683	-	1	NA	promoter-TSS (NR_126464)	promoter-TSS (NR_126464)	-16	NR_126464	75489	Mm.443252	NR_126464	ENSMUSG00000105023	1700012D16Rik	-	RIKEN cDNA 1700012D16 gene	ncRNA
mm_161050.1	chr12	52028104	52028104	-	1	NA	promoter-TSS (NM_008159)	promoter-TSS (NM_008159)	-41	NM_008159	14762	Mm.12890	NM_008159	ENSMUSG00000035148	Gpr33	-	G protein-coupled receptor 33	protein-coding
mm_133375.1	chr16	84710468	84710478	+	1	NA	Intergenic	Intergenic	-2550	NR_132106	100653389	Mm.261808	NR_132106	ENSMUSG00000097418	Mir155hg	Bic|Gm26667	Mir155 host gene (non-protein coding)	ncRNA
mm_91629.1	chr10	42018364	42018401	-	1	NA	promoter-TSS (NM_001034858)	promoter-TSS (NM_001034858)	0	NM_001034858	213402	Mm.211320	NM_001034858	ENSMUSG00000071324	Armc2	2610018I05Rik	armadillo repeat containing 2	protein-coding
mm_98902.1	chr11	98022793	98022802	+	1	NA	promoter-TSS (NM_031173)	promoter-TSS (NM_031173)	-170	NM_001282978	12295	Mm.41252	NM_031173	ENSMUSG00000020882	Cacnb1	CAB1|Cchb1|Cchlb1	calcium channel, voltage-dependent, beta 1 subunit	protein-coding
mm_90813.1	chr10	7833277	7833289	-	1	NA	intron (NM_172785, intron 1 of 5)	L1MB3|LINE|L1	813	NM_172785	237256	Mm.140055	NM_172785	ENSMUSG00000039981	Zc3h12d	D730019B10Rik|TFL	zinc finger CCCH type containing 12D	protein-coding
mm_50694.1	chr6	51597626	51597638	+	1	NA	Intergenic	B1_Mur4|SINE|Alu	53109	NM_001127348	71982	Mm.294166	NM_028035	ENSMUSG00000038301	Snx10	2410004M09Rik	sorting nexin 10	protein-coding
mm_58076.1	chr6	136939567	136939622	-	1	NA	promoter-TSS (NM_001301303)	promoter-TSS (NM_001301303)	-67	NM_001301303	11857	Mm.2241	NM_007486	ENSMUSG00000030220	Arhgdib	D4|Gdid4|Ly-GDI	Rho, GDP dissociation inhibitor (GDI) beta	protein-coding
mm_52172.1	chr6	99172391	99172422	+	1	NA	intron (NM_001347345, intron 4 of 19)	intron (NM_001347345, intron 4 of 19)	94109	NM_001197321	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_52762.1	chr6	120836269	120836283	+	1	NA	promoter-TSS (NM_153516)	promoter-TSS (NM_153516)	46	NM_153516	94044	Mm.27990	NM_153516	ENSMUSG00000009112	Bcl2l13	BCL-RAMBO|E430016C20Rik|Mil-1|Mil1	BCL2-like 13 (apoptosis facilitator)	protein-coding
mm_165875.1	chr4	40766456	40766462	-	1	NA	Intergenic	Intergenic	-8574	NM_021535	74255	Mm.289929	NM_021535	ENSMUSG00000028409	Smu1	2600001O03Rik|2610203K23Rik|AB044414|AI845086|AW556129|Bwd	smu-1 suppressor of mec-8 and unc-52 homolog (C. elegans)	protein-coding
mm_163005.1	chr11	35834458	35834476	-	1	NA	promoter-TSS (NM_025936)	promoter-TSS (NM_025936)	61	NM_025936	104458	Mm.284906	NM_025936	ENSMUSG00000018848	Rars	2610011N19Rik|2610037E21Rik|AL033339|AW985894	arginyl-tRNA synthetase	protein-coding
mm_116252.1	chr13	33967962	33967965	-	1	NA	intron (NM_001163242, intron 1 of 6)	intron (NM_001163242, intron 1 of 6)	810	NM_001163242	18105	Mm.264036	NM_020282	ENSMUSG00000046949	Nqo2	NMO2|Nmor2|Ox2	NAD(P)H dehydrogenase, quinone 2	protein-coding
mm_167349.1	chr8	83608215	83608225	+	1	NA	promoter-TSS (NM_018808)	promoter-TSS (NM_018808)	45	NM_018808	81489	Mm.282092	NM_018808	ENSMUSG00000005483	Dnajb1	0610007I11Rik|DjB1|HSPF1|Hdj1|Hsp40	DnaJ heat shock protein family (Hsp40) member B1	protein-coding
mm_128222.1	chr15	36374342	36374354	-	1	NA	Intergenic	Intergenic	-91201	NM_013923	30945	Mm.5181	NM_013923	ENSMUSG00000022280	Rnf19a	AA032313|Dorfin|Rnf19|UIP117|Ubce7ip2|XYbp	ring finger protein 19A	protein-coding
mm_121686.1	chr14	13906483	13906525	-	1	NA	Intergenic	Intergenic	54809	NM_001285780	66231	Mm.295875	NM_025435	ENSMUSG00000053453	Thoc7	Nif3l1bp1	THO complex 7	protein-coding
mm_50309.1	chr6	47835750	47835777	+	1	NA	5' UTR (NM_027477, exon 1 of 6)	5' UTR (NM_027477, exon 1 of 6)	102	NM_027477	272347	Mm.169059	NM_027477	ENSMUSG00000062519	Zfp398	5730513I23Rik	zinc finger protein 398	protein-coding
mm_14482.1	chr2	131538504	131538511	+	1	NA	intron (NR_037281, intron 1 of 2)	intron (NR_037281, intron 1 of 2)	23778	NM_013460	11550	Mm.389380	NM_013460	ENSMUSG00000027335	Adra1d	Adra-1|Adra1|Adra1a|Gpcr8|Spr8|[a]1d|alpha1D-AR	adrenergic receptor, alpha 1d	protein-coding
mm_36358.1	chr4	76102845	76102849	-	1	NA	intron (NM_011211, intron 22 of 39)	A-rich|Low_complexity|Low_complexity	-824561	NM_025849	66928	Mm.24332	NM_025849	ENSMUSG00000028398	Tmem261	1700027K24Rik|3110001D03Rik	transmembrane protein 261	protein-coding
mm_124239.1	chr14	101477441	101477452	-	1	NA	intron (NM_001081278, intron 9 of 18)	intron (NM_001081278, intron 9 of 18)	131745	NM_001081278	210789	Mm.320639	NM_173380	ENSMUSG00000033083	Tbc1d4	5930406J04Rik|A930035N22|AV295684|As160	TBC1 domain family, member 4	protein-coding
mm_160030.1	chr6	131316398	131316398	-	1	NA	Intergenic	Intergenic	-2571	NM_172891	243659	Mm.20114	NM_172891	ENSMUSG00000032899	Styk1	9130025L13|AI326477|Nok	serine/threonine/tyrosine kinase 1	protein-coding
mm_132507.1	chr16	36962013	36962024	+	1	NA	exon (NM_008225, exon 12 of 14)	exon (NM_008225, exon 12 of 14)	17118	NM_001037321	207215	Mm.211899	NM_001037321	ENSMUSG00000047746	Fbxo40	9830003A13Rik|mKIAA1195	F-box protein 40	protein-coding
mm_122229.1	chr14	33162955	33162967	-	1	NA	intron (NM_001146022, intron 1 of 58)	intron (NM_001146022, intron 1 of 58)	22105	NM_001146022	545030	Mm.318345	NM_001146022	ENSMUSG00000051506	Wdfy4	Gm18810	WD repeat and FYVE domain containing 4	protein-coding
mm_160354.1	chr8	21456499	21456499	-	1	NA	promoter-TSS (NM_001177526)	promoter-TSS (NM_001177526)	18	NM_001177518	665927	Mm.422762	NM_001177518	ENSMUSG00000079114	Gm7849	EG665927	predicted gene 7849	protein-coding
mm_80790.1	chr9	95991001	95991011	+	1	NA	exon (NM_001311130, exon 17 of 42)	exon (NM_001311130, exon 17 of 42)	36246	NM_001311130	24127	Mm.291179	NM_011916	ENSMUSG00000032410	Xrn1	Dhm2|exo|mXrn1	5'-3' exoribonuclease 1	protein-coding
mm_33327.1	chr4	129106791	129106803	+	1	NA	intron (NM_025452, intron 1 of 5)	intron (NM_025452, intron 1 of 5)	1249	NM_001290706	66260	Mm.25295	NM_025452	ENSMUSG00000028786	Tmem54	1810017F10Rik|AI507302	transmembrane protein 54	protein-coding
mm_155544.1	chrX	74309953	74309972	+	1	NA	intron (NM_010273, intron 7 of 10)	intron (NM_010273, intron 7 of 10)	-3071	NM_138607	108160	Mm.4370	NM_138607	ENSMUSG00000001962	Fam50a	D0HXS9928E|XAP-5	family with sequence similarity 50, member A	protein-coding
mm_93280.1	chr10	96077887	96077897	-	1	NA	Intergenic	Intergenic	137229	NM_001001932	216238	Mm.210035	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding
mm_33761.1	chr4	134343883	134343909	+	1	NA	intron (NM_001346578, intron 1 of 7)	intron (NM_001346578, intron 1 of 7)	430	NM_001346578	230810	Mm.358876	NM_001039677	ENSMUSG00000028836	Slc30a2	ZnT-2|Znt2	solute carrier family 30 (zinc transporter), member 2	protein-coding
mm_113872.1	chr13	48662960	48662966	+	1	NA	promoter-TSS (NM_007526)	promoter-TSS (NM_007526)	-73	NM_007526	12022	Mm.42241	NM_007526	ENSMUSG00000021381	Barx1	-	BarH-like homeobox 1	protein-coding
mm_107567.1	chr12	44269242	44269248	+	1	NA	promoter-TSS (NM_026164)	promoter-TSS (NM_026164)	91	NM_026164	67452	Mm.54126	NM_026164	ENSMUSG00000036257	Pnpla8	1200006O19Rik|AI467579|Ipla2(gamma)	patatin-like phospholipase domain containing 8	protein-coding
mm_101340.1	chr11	23520112	23520126	-	1	NA	promoter-TSS (NM_026105)	promoter-TSS (NM_026105)	-177	NM_001110133	67358	Mm.87328	NM_026105	ENSMUSG00000020286	1700093K21Rik	-	RIKEN cDNA 1700093K21 gene	protein-coding
mm_45179.1	chr5	51567718	51567732	-	1	NA	promoter-TSS (NR_132764)	promoter-TSS (NR_132764)	0	NR_132764	19017	Mm.259072	NM_008904	ENSMUSG00000029167	Ppargc1a	A830037N07Rik|ENSMUSG00000079510|Gm11133|PGC-1|PPARGC-1-alpha|Pgc-1alpha|Pgc1|Pgco1|Ppargc1	peroxisome proliferative activated receptor, gamma, coactivator 1 alpha	protein-coding
mm_31036.1	chr4	40964853	40964869	+	1	NA	3' UTR (NM_029814, exon 8 of 8)	3' UTR (NM_029814, exon 8 of 8)	-6045	NM_001290449	74164	Mm.247456	NM_023739	ENSMUSG00000028423	Nfx1	1300017N15Rik|3000003M19Rik|NFX.1|TEG-42|Tex42	nuclear transcription factor, X-box binding 1	protein-coding
mm_143986.1	chr17	87628244	87628256	-	1	NA	Intergenic	Intergenic	-7729	NM_008532	17075	Mm.4259	NM_008532	ENSMUSG00000045394	Epcam	CD326|EGP|EGP-2|Egp314|Ep-CAM|EpCAM1|GA733-2|Ly74|TROP1|Tacsd1|Tacstd1|gp40	epithelial cell adhesion molecule	protein-coding
mm_173308.1	chrY	88061732	88061732	+	1	NA	Intergenic	Intergenic	-2532213	NM_001160131	100040911	Mm.457993	NM_001160131	ENSMUSG00000095650	Gm20854	-	predicted gene, 20854	protein-coding
mm_167956.1	chrX	141437847	141437848	+	1	NA	intron (NM_053185, intron 2 of 44)	intron (NM_053185, intron 2 of 44)	36229	NM_053185	94216	Mm.155586	NM_053185	ENSMUSG00000031273	Col4a6	BB116301	collagen, type IV, alpha 6	protein-coding
mm_61648.1	chr7	80401282	80401298	+	1	NA	intron (NM_001081454, intron 1 of 15)	intron (NM_001081454, intron 1 of 15)	1522	NM_011046	18550	Mm.5241	NM_011046	ENSMUSG00000030530	Furin	9130404I01Rik|Fur|PACE|Pcsk3|SPC1	furin (paired basic amino acid cleaving enzyme)	protein-coding
mm_21507.1	chr2	163624546	163624565	-	1	NA	3' UTR (NM_012032, exon 10 of 10)	3' UTR (NM_012032, exon 10 of 10)	17343	NM_001305803	76080	Mm.89828	NM_029512	ENSMUSG00000017679	Ttpal	3110080A02Rik|5830472M02Rik	tocopherol (alpha) transfer protein-like	protein-coding
mm_160912.1	chr11	82954641	82954641	+	1	NA	intron (NM_183201, intron 1 of 5)	MER89|LTR|ERV1	2539	NM_183201	327978	Mm.42147	NM_183201	ENSMUSG00000054404	Slfn5	AI956840	schlafen 5	protein-coding
mm_83761.1	chr9	51963471	51963525	-	1	NA	5' UTR (NM_007996, exon 1 of 4)	5' UTR (NM_007996, exon 1 of 4)	104	NM_007996	14148	Mm.1061	NM_007996	ENSMUSG00000032051	Fdx1	-	ferredoxin 1	protein-coding
mm_36716.1	chr4	98699102	98699111	-	1	NA	intron (NM_172696, intron 42 of 43)	intron (NM_172696, intron 42 of 43)	-27648	NM_001081202	381591	Mm.34340	NM_001081202	ENSMUSG00000087166	L1td1	AA546746|AB211064|D76865|ECAT11	LINE-1 type transposase domain containing 1	protein-coding
mm_125209.1	chr15	34050420	34050443	+	1	NA	Intergenic	Lx7|LINE|L1	-32288	NM_026002	67154	Mm.130883	NM_026002	ENSMUSG00000022255	Mtdh	2610103J23Rik|3D3|3D3/Lyric|AEG-1|AV353288|D8Bwg1112e|Lyric	metadherin	protein-coding
mm_168954.1	chr12	78350936	78350942	+	1	NA	intron (NM_145965, intron 2 of 22)	LSU-rRNA_Hsa|rRNA|rRNA	124284	NM_145965	268566	Mm.341742	NM_145965	ENSMUSG00000047454	Gphn	5730552E08Rik|AI662856|BC027112|C230040D23|GPH|GPHRYN|geph	gephyrin	protein-coding
mm_46392.1	chr5	104022115	104022129	-	1	NA	promoter-TSS (NM_053262)	promoter-TSS (NM_053262)	-326	NM_053262	114664	Mm.46019	NM_053262	ENSMUSG00000029311	Hsd17b11	Dhrs8|Pan1b|SDR2|retSDR2	hydroxysteroid (17-beta) dehydrogenase 11	protein-coding
mm_104545.1	chr11	96773346	96773352	-	1	NA	intron (NM_001163389, intron 3 of 7)	B1F2|SINE|Alu	4206	NM_028965	74479	Mm.270781	NM_028965	ENSMUSG00000020876	Snx11	4933439F10Rik|A930041K09Rik|AI117694	sorting nexin 11	protein-coding
mm_58730.1	chr7	13029773	13029789	+	1	NA	exon (NM_011588, exon 13 of 17)	exon (NM_011588, exon 13 of 17)	4996	NM_026885	68953	Mm.295670	NM_026885	ENSMUSG00000033916	Chmp2a	1500016L11Rik	charged multivesicular body protein 2A	protein-coding
mm_29233.1	chr3	107213525	107213529	-	1	NA	intron (NM_001111143, intron 6 of 8)	intron (NM_001111143, intron 6 of 8)	8205	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_134220.1	chr16	11254162	11254246	-	1	NA	TTS (NR_035466)	TTS (NR_035466)	121	NM_001130008	14852	Mm.325827	NM_146066	ENSMUSG00000062203	Gspt1	AI314175|AI326449|AV307676|C79774|G1st|Gst-1	G1 to S phase transition 1	protein-coding
mm_84125.1	chr9	58657888	58657898	-	1	NA	intron (NM_028598, intron 4 of 5)	intron (NM_028598, intron 4 of 5)	75653	NM_009145	20320	Mm.15125	NM_009145	ENSMUSG00000032336	Nptn	AW554172|SDR-1|Sdfr1	neuroplastin	protein-coding
mm_51148.1	chr6	70663250	70663256	+	1	NA	Intergenic	Intergenic	128922	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_47566.1	chr5	124476438	124476446	-	1	NA	intron (NM_030259, intron 1 of 3)	intron (NM_030259, intron 1 of 3)	1793	NM_030259	80291	Mm.425280	NM_030259	ENSMUSG00000029401	Rilpl2	-	Rab interacting lysosomal protein-like 2	protein-coding
mm_107537.1	chr12	40560391	40560401	+	1	NA	intron (NM_172803, intron 1 of 52)	B1F|SINE|Alu	114343	NM_172803	238130	Mm.341423	NM_172803	ENSMUSG00000035954	Dock4	5330406C03|6330411N01Rik|AF263288|C030023J22|mKIAA0716	dedicator of cytokinesis 4	protein-coding
mm_144003.1	chr17	88065853	88065873	-	1	NA	promoter-TSS (NM_001081034)	promoter-TSS (NM_001081034)	-578	NM_001081034	225055	Mm.386857	NM_001081034	ENSMUSG00000005371	Fbxo11	C80048|Jf	F-box protein 11	protein-coding
mm_126465.1	chr15	81044690	81044700	+	1	NA	intron (NM_001082536, intron 3 of 13)	intron (NM_001082536, intron 3 of 13)	60352	NM_153049	223701	Mm.439814	NM_153049	ENSMUSG00000042292	Mkl1	AMKL|Bsac|Mal|Mrtf-A	MKL (megakaryoblastic leukemia)/myocardin-like 1	protein-coding
mm_47859.1	chr5	134565547	134565561	-	1	NA	Intergenic	Intergenic	-5383	NM_001013751	214292	Mm.425290	NM_001013751	ENSMUSG00000085957	Syna	Gm453|Gm52|syncytin-A	syncytin a	protein-coding
mm_139621.1	chr17	57362678	57362689	+	1	NA	intron (NM_010130, intron 2 of 21)	RLTR22_Mur|LTR|ERVK	3997	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_107833.1	chr12	69258172	69258182	+	1	NA	intron (NM_178253, intron 7 of 12)	intron (NM_178253, intron 7 of 12)	16345	NM_178253	271005	Mm.180969	NM_178253	ENSMUSG00000051890	Klhdc1	-	kelch domain containing 1	protein-coding
mm_164702.1	chr17	51642052	51642054	+	1	NA	Intergenic	Intergenic	170001	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_133598.1	chr16	91465080	91465111	+	1	NA	promoter-TSS (NR_077219)	promoter-TSS (NR_077219)	-9	NR_077219	100503120	Mm.387130	NR_077219	ENSMUSG00000084866	A930006K02Rik	-	RIKEN cDNA A930006K02 gene	ncRNA
mm_50256.1	chr6	42800650	42800651	+	1	NA	Intergenic	Intergenic	10609	NM_001011869	258207	Mm.377378	NM_001011869	ENSMUSG00000094192	Olfr452	MOR257-5P	olfactory receptor 452	protein-coding
mm_50775.1	chr6	53680936	53680958	+	1	NA	exon (NM_172728, exon 4 of 7)	exon (NM_172728, exon 4 of 7)	107573	NM_172728	231991	Mm.227444	NM_172728	ENSMUSG00000053007	Creb5	9430076C15Rik|CRE-BPa|Crebpa|D430026C09Rik	cAMP responsive element binding protein 5	protein-coding
mm_4921.1	chr1	190928502	190928550	+	1	NA	promoter-TSS (NM_021421)	promoter-TSS (NM_021421)	21	NR_037579	52477	Mm.289914	NM_021421	ENSMUSG00000026634	Angel2	2610307I21Rik|5730410O10Rik|AI845692|D1Ertd396e|D1Ertd654e	angel homolog 2	protein-coding
mm_22909.1	chr3	31038951	31038966	+	1	NA	promoter-TSS (NR_105975)	promoter-TSS (NR_105975)	-8	NR_105975	102465610		NR_105975	ENSMUSG00000098890	Mir7008	Gm27752|mmu-mir-7008	microRNA 7008	ncRNA
mm_101688.1	chr11	40694990	40695041	-	1	NA	5' UTR (NM_001199274, exon 1 of 7)	5' UTR (NM_001199274, exon 1 of 7)	188	NM_001199274	108645	Mm.293771	NM_134017	ENSMUSG00000042032	Mat2b	1110064C04Rik|2410018D16Rik|AI182287|AU022853|MAT-II|MATIIbeta|TGR	methionine adenosyltransferase II, beta	protein-coding
mm_164732.1	chr17	66211529	66211534	+	1	NA	Intergenic	Intergenic	88011	NM_001003919	320209	Mm.259605	NM_001003919	ENSMUSG00000035842	Ddx11	4732462I11Rik|CHL1|CHLR1|KRG2|essa15a	DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11	protein-coding
mm_152180.1	chr19	7418307	7418309	-	1	NA	intron (NM_175381, intron 1 of 4)	CpG	683	NM_175381	108899	Mm.386838	NM_175381	ENSMUSG00000053080	2700081O15Rik	AI255177|AI848741|AW742297	RIKEN cDNA 2700081O15 gene	protein-coding
mm_63091.1	chr7	122366077	122366087	+	1	NA	intron (NM_001316672, intron 2 of 16)	intron (NM_001316672, intron 2 of 16)	76957	NM_008855	18751	Mm.207496	NM_008855	ENSMUSG00000052889	Prkcb	PKC-B|PKC-Beta|Pkcb|Prkcb1|Prkcb2	protein kinase C, beta	protein-coding
mm_68224.1	chr7	104428535	104428545	-	1	NA	intron (NM_009099, intron 4 of 7)	intron (NM_009099, intron 4 of 7)	36653	NM_009099	20128	Mm.295578	NM_009099	ENSMUSG00000030921	Trim30a	Rpt-1|Rpt1|Trim30	tripartite motif-containing 30A	protein-coding
mm_134338.1	chr16	16527365	16527419	-	1	NA	promoter-TSS (NM_001301818)	promoter-TSS (NM_001301818)	19	NM_001301818	224014	Mm.256131	NM_139232	ENSMUSG00000022788	Fgd4	9030023J02Rik|9330209B17Rik|Frabp|ZFYVE6	FYVE, RhoGEF and PH domain containing 4	protein-coding
mm_165066.1	chr19	44396360	44396364	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	11347	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_123289.1	chr14	61556633	61556641	-	1	NA	5' UTR (NM_001310603, exon 1 of 4)	5' UTR (NM_001310603, exon 1 of 4)	249	NM_025697	66674	Mm.282706	NM_025697	ENSMUSG00000021930	Spryd7	6330409N04Rik|Clld6	SPRY domain containing 7	protein-coding
mm_55934.1	chr6	84588696	84588706	-	1	NA	intron (NM_175475, intron 1 of 6)	G-rich|Low_complexity|Low_complexity	5109	NM_175475	232174	Mm.255246	NM_175475	ENSMUSG00000063415	Cyp26b1	CP26|P450RAI-2	cytochrome P450, family 26, subfamily b, polypeptide 1	protein-coding
mm_98067.1	chr11	85886061	85886073	+	1	NA	Intergenic	Intergenic	-3996	NM_011536	21387	Mm.275336	NM_011536	ENSMUSG00000000094	Tbx4	3930401C23	T-box 4	protein-coding
mm_100720.1	chr11	3913718	3913728	-	1	NA	5' UTR (NM_153142, exon 1 of 2)	5' UTR (NM_153142, exon 1 of 2)	941	NM_153142	103710	Mm.171514	NM_153142	ENSMUSG00000048807	Slc35e4	A330108F03Rik|AI414849|AI536442	solute carrier family 35, member E4	protein-coding
mm_17353.1	chr2	26608255	26608261	-	1	NA	Intergenic	Intergenic	-3841	NM_026212	67512	Mm.24244	NM_026212	ENSMUSG00000026922	Agpat2	2510002J07Rik|AV000834|BSCL|BSCL1|LPAAB|LPAAT-beta	1-acylglycerol-3-phosphate O-acyltransferase 2 (lysophosphatidic acid acyltransferase, beta)	protein-coding
mm_116825.1	chr13	54607098	54607114	-	1	NA	intron (NM_001347512, intron 1 of 5)	intron (NM_001347512, intron 1 of 5)	4267	NM_028870	74325	Mm.290026	NM_028870	ENSMUSG00000047547	Cltb	2310046E19Rik|lcb	clathrin, light polypeptide (Lcb)	protein-coding
mm_83679.1	chr9	50430355	50430371	-	1	NA	Intergenic	Intergenic	-64162	NM_029639	76509	Mm.29959	NM_029639	ENSMUSG00000032068	Plet1	0610037B23Rik|1600029D21Rik|AA407923|AU043048	placenta expressed transcript 1	protein-coding
mm_53939.1	chr6	4903918	4903924	-	1	NA	intron (NM_181595, intron 1 of 15)	intron (NM_181595, intron 1 of 15)	601	NM_181595	243725	Mm.332901	NM_181595	ENSMUSG00000032827	Ppp1r9a	2810430P21Rik|4930518N04Rik|5330407E15|A230094E16Rik|BB181831|NRB|mKIAA1222|neurabin-I	protein phosphatase 1, regulatory (inhibitor) subunit 9A	protein-coding
mm_102187.1	chr11	54248555	54248561	-	1	NA	exon (NM_009969, exon 3 of 4)	exon (NM_009969, exon 3 of 4)	1341	NM_009969	12981	Mm.4922	NM_009969	ENSMUSG00000018916	Csf2	Csfgm|GMCSF|Gm-CSf|MGI-IGM	colony stimulating factor 2 (granulocyte-macrophage)	protein-coding
mm_142474.1	chr17	45686081	45686087	-	1	NA	promoter-TSS (NM_026732)	promoter-TSS (NM_026732)	134	NM_198167	224807	Mm.157904	NM_198167	ENSMUSG00000036026	Tmem63b	BC026370	transmembrane protein 63b	protein-coding
mm_130054.1	chr15	89173932	89173977	-	1	NA	promoter-TSS (NM_001159521)	promoter-TSS (NM_001159521)	-3	NM_001159521	140570	Mm.267514	NM_138749	ENSMUSG00000036606	Plxnb2	Debt|plexin-B2	plexin B2	protein-coding
mm_69564.1	chr7	135700547	135700558	-	1	NA	exon (NM_001081117, exon 12 of 14)	exon (NM_001081117, exon 12 of 14)	15827	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_82733.1	chr9	25211063	25211075	-	1	NA	Intergenic	Intergenic	-41370	NM_009859	235072	Mm.270259	NM_009859	ENSMUSG00000001833	Sept7	Cdc10|E430034N22	septin 7	protein-coding
mm_48346.1	chr5	139325444	139325488	-	1	NA	promoter-TSS (NM_172723)	promoter-TSS (NM_172723)	-2	NM_172723	231821	Mm.297819	NM_172723	ENSMUSG00000056413	Adap1	4930431P11Rik|Centa1|GC1L|p42IP4	ArfGAP with dual PH domains 1	protein-coding
mm_60831.1	chr7	45708196	45708219	+	1	NA	intron (NM_016974, intron 2 of 3)	intron (NM_016974, intron 2 of 3)	2960	NM_016974	13170	Mm.24222	NM_016974	ENSMUSG00000059824	Dbp	-	D site albumin promoter binding protein	protein-coding
mm_147819.1	chr18	61786637	61786691	-	1	NA	promoter-TSS (NM_178928)	promoter-TSS (NM_178928)	-2	NM_178928	106877	Mm.26632	NM_178928	ENSMUSG00000033032	Afap1l1	AI173486	actin filament associated protein 1-like 1	protein-coding
mm_10920.1	chr2	25423235	25423250	+	1	NA	promoter-TSS (NM_001177367)	promoter-TSS (NM_001177367)	0	NM_001289453	14347	Mm.1203	NM_013524	ENSMUSG00000036587	Fut7	AI853193|FTVII|Fuc-TVII|FucT-VII	fucosyltransferase 7	protein-coding
mm_23536.1	chr3	60877003	60877017	+	1	NA	Intergenic	Intergenic	-125775	NM_008772	18441	Mm.281452	NM_008772	ENSMUSG00000027765	P2ry1	P2Y1	purinergic receptor P2Y, G-protein coupled 1	protein-coding
mm_14239.1	chr2	127695899	127695903	+	1	NA	Intergenic	Intergenic	33996	NM_145532	228576	Mm.133036	NM_145532	ENSMUSG00000027377	Mall	BC012256|BENE	mal, T cell differentiation protein-like	protein-coding
mm_146270.1	chr18	77879497	77879524	+	1	NA	intron (NM_013831, intron 14 of 14)	intron (NM_013831, intron 14 of 14)	-58957	NM_001195633	100502841	Mm.297782	NM_001195633	ENSMUSG00000039840	Epg5	4732475F16|5430411K18Rik|AI661957|AW456499|mKIAA1632	ectopic P-granules autophagy protein 5 homolog (C. elegans)	protein-coding
mm_159713.1	chr5	32239066	32239066	+	1	NA	promoter-TSS (NM_001081407)	promoter-TSS (NM_001081407)	-18	NM_001081407	665270	Mm.160067	NM_030072	ENSMUSG00000029134	Plb1	4632413E21Rik|4930433E17Rik|4930539A06Rik|BC033606	phospholipase B1	protein-coding
mm_79660.1	chr9	59657105	59657122	+	1	NA	intron (NM_001253883, intron 1 of 10)	CpG	745	NM_001253883	18746	Mm.326167	NM_011099	ENSMUSG00000032294	Pkm	AA414905|AL024370|AL024424|Pk-2|Pk-3|Pk3|Pkm2	pyruvate kinase, muscle	protein-coding
mm_10326.1	chr2	11339462	11339501	+	1	NA	promoter-TSS (NR_040369)	promoter-TSS (NR_040369)	-8	NR_040369	100503147	Mm.91961	NR_040369	ENSMUSG00000086006	Gm13293	OTTMUSG00000011311	predicted gene 13293	ncRNA
mm_115372.1	chr13	113037611	113037614	+	1	NA	promoter-TSS (NR_029961)	promoter-TSS (NR_029961)	78	NR_029961	723868		NR_029961	ENSMUSG00000065575	Mir449a	Mirn449|Mirn449a|mir-449a|mmu-mir-449	microRNA 449a	ncRNA
mm_45198.1	chr5	52550893	52550897	-	1	NA	intron (NM_144945, intron 5 of 6)	intron (NM_144945, intron 5 of 6)	15411	NM_001310604	246316	Mm.44721	NM_144945	ENSMUSG00000039252	Lgi2	mKIAA1916	leucine-rich repeat LGI family, member 2	protein-coding
mm_75373.1	chr8	45333101	45333111	-	1	NA	promoter-TSS (NM_133969)	promoter-TSS (NM_133969)	90	NM_133969	102294	Mm.245297	NM_133969	ENSMUSG00000079057	Cyp4v3	AU043077|AW111961|Cyp4v2	cytochrome P450, family 4, subfamily v, polypeptide 3	protein-coding
mm_14058.1	chr2	122631196	122631226	+	1	NA	exon (NM_001033256, exon 1 of 2)	exon (NM_001033256, exon 1 of 2)	586	NM_001033256	214616	Mm.271306	NM_001033256		Spata5l1	AV141009|C130039A10Rik	spermatogenesis associated 5-like 1	protein-coding
mm_87167.1	chr10	37136016	37136049	+	1	NA	3' UTR (NM_008538, exon 2 of 2)	3' UTR (NM_008538, exon 2 of 2)	2894	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_6966.1	chr1	86154599	86154607	-	1	NA	promoter-TSS (NM_027456)	promoter-TSS (NM_027456)	-177	NM_030184	78795	Mm.379264	NM_027456	ENSMUSG00000062590	Armc9	3830422A13Rik|4831423D23Rik|4930438O05Rik|5730415N24Rik	armadillo repeat containing 9	protein-coding
mm_109941.1	chr12	11326262	11326314	-	1	NA	3' UTR (NM_012038, exon 4 of 4)	3' UTR (NM_012038, exon 4 of 4)	26401	NR_106136	102465775		NR_106136	ENSMUSG00000098879	Mir7675	Gm27965|mmu-mir-7675	microRNA 7675	ncRNA
mm_119399.1	chr14	41172321	41172328	+	1	NA	3' UTR (NM_009160, exon 8 of 8)	3' UTR (NM_009160, exon 8 of 8)	12874	NM_009160	20390	Mm.1321	NM_009160	ENSMUSG00000021795	Sftpd	AI573415|SP-D|Sfpd|Sftp4	surfactant associated protein D	protein-coding
mm_129258.1	chr15	76722162	76722199	-	1	NA	promoter-TSS (NM_198119)	promoter-TSS (NM_198119)	-7	NM_198119	378937	Mm.289666	NM_198119	ENSMUSG00000033707	Lrrc24	6430402H13Rik	leucine rich repeat containing 24	protein-coding
mm_91295.1	chr10	24915650	24915656	-	1	NA	exon (NM_007482, exon 8 of 8)	exon (NM_007482, exon 8 of 8)	4989	NR_105870	102465545		NR_105870	ENSMUSG00000099181	Mir6905	Gm27879|mmu-mir-6905	microRNA 6905	ncRNA
mm_157697.1	chrX	60446693	60446698	-	1	NA	intron (NM_001039240, intron 2 of 3)	intron (NM_001039240, intron 2 of 3)	9500	NM_001039240	631784	Mm.424878	NM_001039240	ENSMUSG00000079583	Gm7073	-	predicted gene 7073	protein-coding
mm_156991.1	chrX	7421088	7421121	-	1	NA	promoter-TSS (NR_027925)	promoter-TSS (NR_027925)	-57	NR_027925	68355	Mm.45111	NR_027924		2010204K13Rik	0610010M13Rik|Cip7	RIKEN cDNA 2010204K13 gene	ncRNA
mm_132416.1	chr16	35068584	35068602	+	1	NA	intron (NM_023587, intron 3 of 6)	intron (NM_023587, intron 3 of 6)	46172	NM_023587	70757	Mm.27286	NM_023587	ENSMUSG00000035376	Hacd2	6330408J20Rik|AI255777|AI481689|Hcad2|Ptplb	3-hydroxyacyl-CoA dehydratase 2	protein-coding
mm_50087.1	chr6	41523943	41523958	+	1	NA	exon (NM_009430, exon 3 of 5)	exon (NM_009430, exon 3 of 5)	2174	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_117782.1	chr13	97022396	97022408	-	1	NA	non-coding (NR_104276, exon 3 of 3)	non-coding (NR_104276, exon 3 of 3)	11960	NM_025585	66479	Mm.390629	NM_025585	ENSMUSG00000052075	1700029F12Rik	-	RIKEN cDNA 1700029F12 gene	protein-coding
mm_106806.1	chr12	5808194	5808200	+	1	NA	Intergenic	Intergenic	431695	NR_015579	72669	Mm.10434	NM_028318		2810032G03Rik	AI461720	RIKEN cDNA 2810032G03 gene	ncRNA
mm_135526.1	chr16	49255749	49255778	-	1	NA	Intergenic	Intergenic	198277	NM_001166210	667772	Mm.301387	NM_001166210	ENSMUSG00000092009	Myh15	EG667772	myosin, heavy chain 15	protein-coding
mm_15312.1	chr2	155567324	155567326	+	1	NA	intron (NM_008180, intron 10 of 12)	ORR1A4|LTR|ERVL-MaLR	-10395	NR_040613	74945	Mm.401956	NR_040613	ENSMUSG00000086529	Acss2os	4930471I20Rik	acyl-CoA synthetase short-chain family member 2, opposite strand	ncRNA
mm_35459.1	chr4	40703205	40703213	-	1	NA	promoter-TSS (NM_025545)	promoter-TSS (NM_025545)	-15	NM_001025445	66408	Mm.430710	NM_025545	ENSMUSG00000028411	Aptx	2410016G21Rik|AA388047|FHA-HIT	aprataxin	protein-coding
mm_438.1	chr1	34697546	34697551	+	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	-61338	NR_033627	241051	Mm.282827	NR_033627		AA619741	-	PHD finger protein 19 pseudogene	pseudo
mm_33306.1	chr4	129035659	129035664	+	1	NA	Intergenic	RMER17C|LTR|ERVK	-22610	NM_029219	75234	Mm.259672	NM_029219	ENSMUSG00000028793	Rnf19b	4930534K13Rik|4930555L03Rik|Ibrdc3	ring finger protein 19B	protein-coding
mm_151573.1	chr19	60890364	60890392	+	1	NA	5' UTR (NM_018869, exon 1 of 16)	5' UTR (NM_018869, exon 1 of 16)	629	NM_018869	14773	Mm.279400	NM_018869	ENSMUSG00000003228	Grk5	Gprk5	G protein-coupled receptor kinase 5	protein-coding
mm_8938.1	chr1	164437740	164437760	-	1	NA	TTS (NM_001293313)	TTS (NM_001293313)	20605	NM_009721	11931	Mm.4550	NM_009721	ENSMUSG00000026576	Atp1b1	Atp4b|Atpb|Atpb-1|NKbeta1	ATPase, Na+/K+ transporting, beta 1 polypeptide	protein-coding
mm_145443.1	chr18	59175409	59175463	+	1	NA	promoter-TSS (NM_001081328)	promoter-TSS (NM_001081328)	96	NM_001081328	78923	Mm.84007	NM_001081328	ENSMUSG00000058152	Chsy3	4833446K15Rik|AI662215	chondroitin sulfate synthase 3	protein-coding
mm_172580.1	chr8	120719997	120719997	-	1	NA	Intergenic	Intergenic	-16361	NM_008320	15900	Mm.334861	NM_008320	ENSMUSG00000041515	Irf8	AI893568|ICSBP|IRF-8|Icsbp1|Myls	interferon regulatory factor 8	protein-coding
mm_125890.1	chr15	75863762	75863763	+	1	NA	intron (NM_026960, intron 2 of 10)	AT_rich|Low_complexity|Low_complexity	1423	NM_026960	69146	Mm.27385	NM_026960	ENSMUSG00000022575	Gsdmd	1810036L03Rik|AW558049|DF5L|Dfna5l|Gsdmdc1|M2-4	gasdermin D	protein-coding
mm_63406.1	chr7	127332355	127332362	+	1	NA	intron (NM_001253874, intron 30 of 30)	PB1D10|SINE|Alu	12956	NM_146202	233890	Mm.23031	NM_146202	ENSMUSG00000047371	Zfp768	BC026432|Znf768	zinc finger protein 768	protein-coding
mm_123607.1	chr14	68087391	68087403	-	1	NA	exon (NM_010910, exon 4 of 4)	exon (NM_010910, exon 4 of 4)	3513	NM_010910	18039	Mm.1956	NM_010910	ENSMUSG00000022055	Nefl	AI847934|CMT2E|NF-L|NF68|Nfl	neurofilament, light polypeptide	protein-coding
mm_29653.1	chr3	122391843	122391862	-	1	NA	Intergenic	Intergenic	-27928	NM_013867	29815	Mm.45815	NM_013867	ENSMUSG00000028121	Bcar3	AI131758|AND-34	breast cancer anti-estrogen resistance 3	protein-coding
mm_112989.1	chr13	21495358	21495381	+	1	NA	Intergenic	Intergenic	11155	NR_026798	100038371	Mm.133328	NR_026798		Zfp389	ENSMUSG00000075041|OTTMUSG00000018077	zinc finger protein 389	pseudo
mm_100796.1	chr11	4941395	4941405	-	1	NA	exon (NM_010904, exon 4 of 4)	exon (NM_010904, exon 4 of 4)	-6121	NM_001243043	11764	Mm.274816	NM_007454	ENSMUSG00000009090	Ap1b1	Adtb1|b2b1660Clo	adaptor protein complex AP-1, beta 1 subunit	protein-coding
mm_121345.1	chr14	116394996	116394996	+	1	NA	intron (NM_175500, intron 7 of 7)	intron (NM_175500, intron 7 of 7)	-530301	NM_001079844	23888	Mm.440025	NM_011821	ENSMUSG00000058571	Gpc6	-	glypican 6	protein-coding
mm_157777.1	chrX	73786594	73786626	-	1	NA	promoter-TSS (NM_001166480)	promoter-TSS (NM_001166480)	287	NM_008323	15929	Mm.14825	NM_008323	ENSMUSG00000002010	Idh3g	-	isocitrate dehydrogenase 3 (NAD+), gamma	protein-coding
mm_51095.1	chr6	67266988	67267021	+	1	NA	promoter-TSS (NM_025814)	promoter-TSS (NM_025814)	25	NM_025814	66870	Mm.240490	NM_025814	ENSMUSG00000036371	Serbp1	1200009K13Rik|9330147J08Rik|AL022786|Pairbp1	serpine1 mRNA binding protein 1	protein-coding
mm_54512.1	chr6	35511595	35511618	-	1	NA	3' UTR (NM_008098, exon 4 of 4)	3' UTR (NM_008098, exon 4 of 4)	28282	NM_008098	14489	Mm.182746	NM_008098	ENSMUSG00000029840	Mtpn	5033418D15Rik|Gcdp|V1	myotrophin	protein-coding
mm_103980.1	chr11	84825594	84825604	-	1	NA	intron (NM_177564, intron 1 of 6)	intron (NM_177564, intron 1 of 6)	3404	NM_177564	192970	Mm.192213	NM_177564	ENSMUSG00000034449	Dhrs11	-	dehydrogenase/reductase (SDR family) member 11	protein-coding
mm_6822.1	chr1	84194459	84194471	-	1	NA	intron (NM_001003948, intron 1 of 2)	intron (NM_001003948, intron 1 of 2)	24496	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_162444.1	chr1	118590968	118590968	-	1	NA	intron (NM_001293300, intron 38 of 40)	intron (NM_001293300, intron 38 of 40)	-36977	NM_023755	81879	Mm.24621	NM_023755	ENSMUSG00000026380	Tfcp2l1	1810030F05Rik|4932442M07Rik|AA575098|Cp2l1|Crtr-1|D930018N21Rik|LBP-9|Tcfcp2l1	transcription factor CP2-like 1	protein-coding
mm_141311.1	chr17	28357452	28357452	-	1	NA	intron (NM_021478, intron 11 of 14)	intron (NM_021478, intron 11 of 14)	-6647	NM_011566	21678	Mm.6655	NM_011566	ENSMUSG00000002249	Tead3	DTEF-1|ETFR-1|TEAD-3|TEF-5|Tcf13r2	TEA domain family member 3	protein-coding
mm_162839.1	chr10	84599528	84599530	+	1	NA	intron (NM_146008, intron 6 of 9)	intron (NM_146008, intron 6 of 9)	22582	NM_146008	216198	Mm.296142	NM_146008	ENSMUSG00000020034	Tcp11l2	E430026E19Rik	t-complex 11 (mouse) like 2	protein-coding
mm_159462.1	chr3	158026696	158026696	-	1	NA	intron (NM_001093752, intron 3 of 12)	intron (NM_001093752, intron 3 of 12)	5058	NM_001093753	69207	Mm.223946	NM_026989	ENSMUSG00000055436	Srsf11	0610009J05Rik|2610019N13Rik|BF642805|Sfrs11	serine/arginine-rich splicing factor 11	protein-coding
mm_96430.1	chr11	67292426	67292430	+	1	NA	exon (NM_177369, exon 19 of 40)	exon (NM_177369, exon 19 of 40)	15304	NM_177369	17885	Mm.340163	NM_177369	ENSMUSG00000055775	Myh8	4832426G23Rik|AI327267|MHCp|MyHC-pn|Myhs-p|Myhsp	myosin, heavy polypeptide 8, skeletal muscle, perinatal	protein-coding
mm_98562.1	chr11	95340007	95340011	+	1	NA	intron (NM_172543, intron 1 of 7)	AT_rich|Low_complexity|Low_complexity	2991	NM_172543	215512	Mm.262113	NM_172543	ENSMUSG00000038893	Fam117a	5730593F17Rik|AW548096	family with sequence similarity 117, member A	protein-coding
mm_50553.1	chr6	49047400	49047413	+	1	NA	exon (NM_053110, exon 5 of 11)	exon (NM_053110, exon 5 of 11)	10888	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_30906.1	chr4	32415579	32415582	+	1	NA	Intergenic	Intergenic	-1855	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_144838.1	chr18	36531033	36531048	+	1	NA	intron (NM_172830, intron 7 of 20)	intron (NM_172830, intron 7 of 20)	2888	NM_001271544	240215	Mm.135463	NM_172830	ENSMUSG00000024485	Slc4a9	AE4|D630003B07|D630024F24Rik	solute carrier family 4, sodium bicarbonate cotransporter, member 9	protein-coding
mm_140278.1	chr17	84962987	84962990	+	1	NA	intron (NM_001159496, intron 1 of 5)	ID4_|SINE|ID	4987	NM_001159496	19043	Mm.249695	NM_011151	ENSMUSG00000061130	Ppm1b	PP2CB	protein phosphatase 1B, magnesium dependent, beta isoform	protein-coding
mm_131051.1	chr16	4037121	4037129	+	1	NA	promoter-TSS (NM_010061)	promoter-TSS (NM_010061)	-20	NM_010061	13419	Mm.291048	NM_010061	ENSMUSG00000005980	Dnase1	AI788650|DNaseI|Dnl1	deoxyribonuclease I	protein-coding
mm_111201.1	chr12	84219102	84219120	-	1	NA	promoter-TSS (NM_001163501)	promoter-TSS (NM_001163501)	-230	NM_001163501	238317	Mm.31256	NM_001163501	ENSMUSG00000042507	Elmsan1	9430029N19Rik|C130039O16Rik|Gm260	ELM2 and Myb/SANT-like domain containing 1	protein-coding
mm_33428.1	chr4	130055024	130055047	+	1	NA	intron (NM_028266, intron 8 of 69)	intron (NM_028266, intron 8 of 69)	7195	NM_028266	107581	Mm.41860	NM_028266	ENSMUSG00000040690	Col16a1	2700007F12Rik|A530052M23Rik|AI838662|CA1F	collagen, type XVI, alpha 1	protein-coding
mm_119937.1	chr14	54976672	54976676	+	1	NA	promoter-TSS (NR_030607)	promoter-TSS (NR_030607)	-898	NR_030607	100124433		NR_030607	ENSMUSG00000077928	Mir208b	Mirn208b|mir-208b	microRNA 208b	ncRNA
mm_103897.1	chr11	83575328	83575338	-	1	NA	3' UTR (NM_011338, exon 4 of 4)	3' UTR (NM_011338, exon 4 of 4)	3303	NM_011338	20308	Mm.416125	NM_011338	ENSMUSG00000019122	Ccl9	CCF18|MRP-2|Scya10|Scya9	chemokine (C-C motif) ligand 9	protein-coding
mm_129591.1	chr15	79790945	79790951	-	1	NA	intron (NM_030689, intron 3 of 4)	intron (NM_030689, intron 3 of 4)	13761	NM_030689	73340	Mm.38438	NM_030689	ENSMUSG00000022421	Nptxr	1200009K17Rik|1700036C17Rik|5730406O18Rik|AI452369|AI785356|D15Bwg0580e|NPR|Npcd	neuronal pentraxin receptor	protein-coding
mm_12010.1	chr2	57359759	57359763	+	1	NA	intron (NM_001145820, intron 13 of 16)	intron (NM_001145820, intron 13 of 16)	121379	NM_010274	14571	Mm.3711	NM_010274	ENSMUSG00000026827	Gpd2	AA408484|AI448216|AU021455|AW494132|GPDH|Gdm1|Gpd-m|Gpdh-m|TISP38	glycerol phosphate dehydrogenase 2, mitochondrial	protein-coding
mm_163747.1	chr13	119755845	119755909	-	1	NA	promoter-TSS (NM_175538)	promoter-TSS (NM_175538)	5	NM_175538	245269	Mm.403943	NM_175538	ENSMUSG00000095930	Nim1k	E130304F04Rik|Nim1	NIM1 serine/threonine protein kinase	protein-coding
mm_138431.1	chr17	35089230	35089307	+	1	NA	promoter-TSS (NM_178592)	promoter-TSS (NM_178592)	-23	NM_178592	193742	Mm.43745	NM_178592	ENSMUSG00000007036	Abhd16a	AI326074|Bat-5|Bat5|D17H6S82E|NG26	abhydrolase domain containing 16A	protein-coding
mm_119292.1	chr14	34673997	34674014	+	1	NA	promoter-TSS (NM_001301330)	promoter-TSS (NM_001301330)	77	NM_001301330	218914	Mm.27957	NM_001004436	ENSMUSG00000041408	Wapl	A530089A20Rik|BC037674|DIF-2|FOE|Wapal	WAPL cohesin release factor	protein-coding
mm_22868.1	chr3	28892618	28892619	+	1	NA	promoter-TSS (NM_001033479)	promoter-TSS (NM_001033479)	1	NM_001033479	385263	Mm.60893	NM_001033479	ENSMUSG00000074655	Gm1527	Gm1136	predicted gene 1527	protein-coding
mm_42849.1	chr5	122209815	122209843	+	1	NA	promoter-TSS (NM_001042489)	promoter-TSS (NM_001042489)	100	NM_001042489	74096	Mm.28804	NM_028752	ENSMUSG00000064267	Hvcn1	0610039P13Rik|AI450555|BTS|HV1|Vsop.|mVSOP	hydrogen voltage-gated channel 1	protein-coding
mm_171206.1	chr3	56016630	56016632	-	1	NA	intron (NM_030595, intron 18 of 57)	B1_Mus1|SINE|Alu	167070	NM_030595	26422	Mm.384353	NM_030595	ENSMUSG00000027799	Nbea	Lyst2|mKIAA1544	neurobeachin	protein-coding
mm_129780.1	chr15	82794202	82794223	-	1	NA	promoter-TSS (NM_029562)	promoter-TSS (NM_029562)	33	NM_029562	76279	Mm.439931	NM_029562	ENSMUSG00000022445	Cyp2d26	1300006E06Rik	cytochrome P450, family 2, subfamily d, polypeptide 26	protein-coding
mm_9151.1	chr1	170925657	170925659	-	1	NA	intron (NM_001160215, intron 1 of 4)	intron (NM_001160215, intron 1 of 4)	1925	NM_001160215	98752	Mm.1850	NM_145141	ENSMUSG00000038421	Fcrla	BB219290|FCRL|FCRL1|FREB|Fcrlm1|Fcrx|Freb1|mFREB|mFcrX	Fc receptor-like A	protein-coding
mm_115138.1	chr13	104672440	104672440	+	1	NA	intron (NM_026072, intron 11 of 13)	intron (NM_026072, intron 11 of 13)	144513	NM_026072	67285	Mm.235398	NM_026072	ENSMUSG00000021715	Cwc27	3110009E13Rik|NY-CO-10|Sdccag10	CWC27 spliceosome-associated protein	protein-coding
mm_101023.1	chr11	8579180	8579184	-	1	NA	intron (NM_001083587, intron 3 of 30)	intron (NM_001083587, intron 3 of 30)	85353	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_61174.1	chr7	60003690	60003698	+	1	NA	intron (NM_001082962, intron 2 of 10)	intron (NM_001082962, intron 2 of 10)	1462	NM_013670	20646	Mm.274995	NM_013670	ENSMUSG00000102252	Snrpn	2410045I01Rik|HCERN3|Peg4|Pwcr1|SMN	small nuclear ribonucleoprotein N	protein-coding
mm_144547.1	chr18	29442186	29442204	+	1	NA	promoter-TSS (NR_045395)	promoter-TSS (NR_045395)	-5	NR_045395	78199	Mm.243850	NR_045395		4930527G23Rik	-	RIKEN cDNA 4930527G23 gene	ncRNA
mm_25144.1	chr3	102734497	102734530	+	1	NA	promoter-TSS (NM_001243132)	promoter-TSS (NM_001243132)	-257	NM_027533	70747	Mm.27469	NM_027533	ENSMUSG00000027858	Tspan2	6330415F13Rik|B230119D02Rik|tspan-2	tetraspanin 2	protein-coding
mm_58242.1	chr6	145048586	145048592	-	1	NA	exon (NM_001024468, exon 1 of 11)	exon (NM_001024468, exon 1 of 11)	223	NM_001024468	12035	Mm.4606	NM_007532	ENSMUSG00000030268	Bcat1	BCATc|Eca39	branched chain aminotransferase 1, cytosolic	protein-coding
mm_138758.1	chr17	37050634	37050649	+	1	NA	intron (NM_019439, intron 5 of 22)	CpG	4675	NM_019439	54393	Mm.32191	NM_019439	ENSMUSG00000024462	Gabbr1	GABAB1|GABAbR1|bM573K1.1	gamma-aminobutyric acid (GABA) B receptor, 1	protein-coding
mm_15494.1	chr2	157793507	157793523	+	1	NA	intron (NM_025680, intron 4 of 15)	intron (NM_025680, intron 4 of 15)	56114	NM_025680	66642	Mm.45193	NM_025680	ENSMUSG00000027649	Ctnnbl1	5730471K09Rik|NAP|NYD-SP19|P14L	catenin, beta like 1	protein-coding
mm_120465.1	chr14	65971165	65971182	+	1	NA	intron (NM_013492, intron 1 of 8)	intron (NM_013492, intron 1 of 8)	2690	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_96816.1	chr11	69994456	69994466	+	1	NA	exon (NM_019749, exon 4 of 4)	exon (NM_019749, exon 4 of 4)	-1305	NM_001291125	78246	Mm.20805	NM_030064	ENSMUSG00000018572	Phf23	JUNE-1	PHD finger protein 23	protein-coding
mm_103952.1	chr11	84068767	84068777	-	1	NA	promoter-TSS (NM_019819)	promoter-TSS (NM_019819)	-415	NM_019819	56405	Mm.240885	NM_019819	ENSMUSG00000018648	Dusp14	1110014C10Rik|2310042C07Rik|D11Ertd395e|MKP-L|Mkp6	dual specificity phosphatase 14	protein-coding
mm_141223.1	chr17	27323183	27323193	-	1	NA	Intergenic	RMER4A|LTR|ERVK	-5197	NR_106075	102466818		NR_106075	ENSMUSG00000099237	Mir7216	Gm27555|mmu-mir-7216	microRNA 7216	ncRNA
mm_68340.1	chr7	106506268	106506303	-	1	NA	Intergenic	Intergenic	-65212	NR_003967	209380	Mm.461779	NM_001001318		Gm4759	EG209380	GTPase, very large interferon inducible 1 pseudogene	pseudo
mm_36755.1	chr4	101265237	101265254	-	1	NA	promoter-TSS (NM_146145)	promoter-TSS (NM_146145)	37	NM_146145	16451	Mm.289657	NM_146145	ENSMUSG00000028530	Jak1	AA960307|BAP004|C130039L05Rik	Janus kinase 1	protein-coding
mm_159446.1	chr3	133092024	133092024	-	1	NA	promoter-TSS (NM_026231)	promoter-TSS (NM_026231)	169	NM_027927	71793	Mm.246726	NM_027927	ENSMUSG00000028016	Ints12	1110020M19Rik|2810027J24Rik|4930529N21Rik|A230056J18Rik|AI666778|Phf22|int12	integrator complex subunit 12	protein-coding
mm_43935.1	chr5	145104587	145104648	+	1	NA	intron (NM_019767, intron 7 of 9)	intron (NM_019767, intron 7 of 9)	-9639	NM_023142	11867	Mm.30010	NM_023142	ENSMUSG00000029622	Arpc1b	41kDa|AA408064|AA408534|AA571392|AF007010|AW208418|L72|SOP2Hs|p41-ARC	actin related protein 2/3 complex, subunit 1B	protein-coding
mm_137263.1	chr17	24665983	24665996	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-3763	NM_183149	213753	Mm.219581	NM_183149	ENSMUSG00000041130	Zfp598	BC023040|Ntrap|Znf598	zinc finger protein 598	protein-coding
mm_153738.1	chr19	44555399	44555437	-	1	NA	promoter-TSS (NM_026061)	promoter-TSS (NM_026061)	-3	NM_026061	67264	Mm.2060	NM_026061	ENSMUSG00000025204	Ndufb8	2900010I05Rik|AI987932	NADH dehydrogenase (ubiquinone) 1 beta subcomplex 8	protein-coding
mm_117253.1	chr13	64366601	64366652	-	1	NA	exon (NM_009984, exon 6 of 8)	exon (NM_009984, exon 6 of 8)	3894	NM_009984	13039	Mm.930	NM_009984	ENSMUSG00000021477	Ctsl	1190035F06Rik|CatL|Ctsl1|MEP|fs|nkt	cathepsin L	protein-coding
mm_25591.1	chr3	116890867	116890908	+	1	NA	intron (NM_009146, intron 7 of 16)	intron (NM_009146, intron 7 of 16)	29207	NM_009146	20321	Mm.66293	NM_009146	ENSMUSG00000033386	Frrs1	AI131732|Sdfr2	ferric-chelate reductase 1	protein-coding
mm_122573.1	chr14	50807741	50807756	-	1	NA	promoter-TSS (NR_002142)	promoter-TSS (NR_002142)	23	NR_002142	85029		NR_002142	ENSMUSG00000092837	Rpph1	Gm24821|H1RNA|Rmrp5|Rpr	ribonuclease P RNA component H1	ncRNA
mm_126481.1	chr15	81586207	81586250	+	1	NA	promoter-TSS (NM_177821)	promoter-TSS (NM_177821)	14	NM_177821	328572	Mm.258397	NM_177821	ENSMUSG00000055024	Ep300	A430090G16|A730011L11|KAT3B|p300|p300 HAT	E1A binding protein p300	protein-coding
mm_74331.1	chr8	127063642	127063697	+	1	NA	promoter-TSS (NM_033620)	promoter-TSS (NM_033620)	-387	NM_033620	93742	Mm.299254	NM_033620	ENSMUSG00000025812	Pard3	AA960621|AI256638|Asip|D8Ertd580e|Par-3|Par3|Pard-3|Pard3a|Phip	par-3 family cell polarity regulator	protein-coding
mm_161259.1	chr13	119374665	119374665	-	1	NA	exon (NM_008710, exon 8 of 17)	exon (NM_008710, exon 8 of 17)	34346	NM_008710	18115	Mm.132584	NM_008710	ENSMUSG00000025453	Nnt	4930423F13Rik|AI323702|BB168308	nicotinamide nucleotide transhydrogenase	protein-coding
mm_77058.1	chr8	109608416	109608422	-	1	NA	5' UTR (NM_020046, exon 1 of 9)	5' UTR (NM_020046, exon 1 of 9)	254	NM_020046	56749	Mm.23894	NM_020046	ENSMUSG00000031730	Dhodh	2810417D19Rik|AI834883	dihydroorotate dehydrogenase	protein-coding
mm_47648.1	chr5	125389916	125390055	-	1	NA	promoter-TSS (NM_019639)	promoter-TSS (NM_019639)	32	NM_019639	22190	Mm.331	NM_019639	ENSMUSG00000008348	Ubc	2700054O04Rik|AI194771|Rps27a|TI-225|Uba52|Ubb	ubiquitin C	protein-coding
mm_79950.1	chr9	66060196	66060273	+	1	NA	promoter-TSS (NM_011149)	promoter-TSS (NM_011149)	65	NM_011149	19035	Mm.335249	NM_011149	ENSMUSG00000032383	Ppib	AA408962|AA553318|AI844835|Cphn-2|Cphn2|CyP-20b	peptidylprolyl isomerase B	protein-coding
mm_75684.1	chr8	68121321	68121369	-	1	NA	Intergenic	Intergenic	-146771	NM_177698	234353	Mm.32525	NM_027626	ENSMUSG00000030465	Psd3	4931420C21Rik|AI661273|BC003498|D430018P08|EFA6D	pleckstrin and Sec7 domain containing 3	protein-coding
mm_18695.1	chr2	71546345	71546367	-	1	NA	exon (NM_010054, exon 1 of 3)	exon (NM_010054, exon 1 of 3)	398	NM_010054	13392	Mm.3896	NM_010054	ENSMUSG00000023391	Dlx2	AW121999|Dlx-2|Tes-1	distal-less homeobox 2	protein-coding
mm_145056.1	chr18	40306069	40306080	+	1	NA	intron (NM_026135, intron 1 of 1)	B4|SINE|B4	47713	NM_026135	383348	Mm.76366	NM_026135	ENSMUSG00000051401	Kctd16	4930434H12Rik|Gm1267	potassium channel tetramerisation domain containing 16	protein-coding
mm_101916.1	chr11	50139727	50139744	-	1	NA	intron (NM_001290760, intron 2 of 21)	intron (NM_001290760, intron 2 of 21)	8375	NM_029745	76795	Mm.290975	NM_029745	ENSMUSG00000036644	Tbc1d9b	-	TBC1 domain family, member 9B	protein-coding
mm_152386.1	chr19	10457566	10457584	-	1	NA	promoter-TSS (NM_001111140)	promoter-TSS (NM_001111140)	-128	NM_001111140	278795	Mm.490638	NM_001111140	ENSMUSG00000090291	Lrrc10b	Gm705|SerdinR	leucine rich repeat containing 10B	protein-coding
mm_95914.1	chr11	58220180	58220190	+	1	NA	exon (NM_019440, exon 2 of 2)	exon (NM_019440, exon 2 of 2)	5208	NM_019440	54396	Mm.458517	NM_019440	ENSMUSG00000069874	Irgm2	AI481100|GTPI|Ifggd2|Iigp2	immunity-related GTPase family M member 2	protein-coding
mm_7782.1	chr1	131278757	131278768	-	1	NA	5' UTR (NM_019777, exon 2 of 22)	5' UTR (NM_019777, exon 2 of 22)	801	NM_019777	56489	Mm.386783	NM_019777	ENSMUSG00000042349	Ikbke	AW558201|IKK-i|IKKepsilon|Ikki	inhibitor of kappaB kinase epsilon	protein-coding
mm_114539.1	chr13	73733052	73733103	+	1	NA	Intergenic	Intergenic	-30620	NM_011390	20499	Mm.275800	NM_011390	ENSMUSG00000017756	Slc12a7	AA408796|D13Ertd261e|Kcc4	solute carrier family 12, member 7	protein-coding
mm_91209.1	chr10	21161592	21161659	-	1	NA	promoter-TSS (NM_001198914)	promoter-TSS (NM_001198914)	-641	NM_010848	17863	Mm.52109	NM_010848	ENSMUSG00000019982	Myb	AI550390|M16449|c-myb	myeloblastosis oncogene	protein-coding
mm_94093.1	chr10	128525862	128525880	-	1	NA	promoter-TSS (NM_011843)	promoter-TSS (NM_011843)	-12	NM_011843	23943	Mm.66056	NM_011843	ENSMUSG00000025366	Esyt1	Fam62a|Mbc2|vp115	extended synaptotagmin-like protein 1	protein-coding
mm_13558.1	chr2	112265559	112265647	+	1	NA	promoter-TSS (NM_133649)	promoter-TSS (NM_133649)	-711	NM_133649	107723	Mm.491155	NM_133648	ENSMUSG00000027130	Slc12a6	9530023I19Rik|KCC3|gaxp	solute carrier family 12, member 6	protein-coding
mm_148479.1	chr19	4113390	4113408	+	1	NA	TTS (NM_016666)	TTS (NM_016666)	8176	NM_001276284	11632	Mm.10433	NM_016666	ENSMUSG00000024847	Aip	AA408703|AW476050|Ara9|D19Bwg1412e|Fkbp16|Xap2	aryl-hydrocarbon receptor-interacting protein	protein-coding
mm_147031.1	chr18	34720270	34720311	-	1	NA	promoter-TSS (NM_010280)	promoter-TSS (NM_010280)	97	NM_010280	14587	Mm.16520	NM_010280	ENSMUSG00000024366	Gfra3	GFRalpha3|Y15110	glial cell line derived neurotrophic factor family receptor alpha 3	protein-coding
mm_65400.1	chr7	25205445	25205455	-	1	NA	intron (NM_207677, intron 4 of 4)	intron (NM_207677, intron 4 of 4)	12275	NR_106015	102466794		NR_106015	ENSMUSG00000098325	Mir7048	Gm27274|mmu-mir-7048	microRNA 7048	ncRNA
mm_64061.1	chr7	140856444	140856464	+	1	NA	promoter-TSS (NM_053194)	promoter-TSS (NM_053194)	-71	NM_018742	54399	Mm.155696	NM_018742	ENSMUSG00000025484	Bet1l	2610021K23Rik|Gs15	Bet1 golgi vesicular membrane trafficking protein like	protein-coding
mm_69941.1	chr7	142120792	142120795	-	1	NA	5' UTR (NM_001347558, exon 1 of 1)	5' UTR (NM_001347558, exon 1 of 1)	107	NM_001347558	108167466	Mm.365101	NM_001347558	ENSMUSG00000109859	Gm45618	-	predicted gene 45618	protein-coding
mm_118306.1	chr13	113101149	113101159	-	1	NA	promoter-TSS (NM_010370)	promoter-TSS (NM_010370)	-173	NM_010370	14938	Mm.15510	NM_010370	ENSMUSG00000023132	Gzma	AW494114|Ctla-3|Ctla3|Hf|Hf1|SE1|TSP-1|TSP1	granzyme A	protein-coding
mm_59927.1	chr7	30423363	30423371	+	1	NA	promoter-TSS (NM_172142)	promoter-TSS (NM_172142)	63	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_154707.1	chrX	8276579	8276604	+	1	NA	exon (NM_172479, exon 9 of 16)	exon (NM_172479, exon 9 of 16)	5210	NM_172479	209837	Mm.6055	NM_172479	ENSMUSG00000031170	Slc38a5	C81234|E330031E14|JM24|SN2	solute carrier family 38, member 5	protein-coding
mm_118992.1	chr14	28505607	28505617	+	1	NA	5' UTR (NM_009524, exon 1 of 5)	5' UTR (NM_009524, exon 1 of 5)	139	NM_009524	22418	Mm.287544	NM_009524	ENSMUSG00000021994	Wnt5a	8030457G12Rik|Wnt-5a	wingless-type MMTV integration site family, member 5A	protein-coding
mm_101289.1	chr11	22001606	22001631	-	1	NA	promoter-TSS (NM_011023)	promoter-TSS (NM_011023)	33	NM_011023	18423	Mm.129663	NM_011023	ENSMUSG00000005917	Otx1	A730044F23Rik|jv	orthodenticle homeobox 1	protein-coding
mm_78478.1	chr9	32695716	32695719	+	1	NA	promoter-TSS (NM_001038642)	promoter-TSS (NM_001038642)	-325	NM_011808	23871	Mm.292415	NM_011808	ENSMUSG00000032035	Ets1	AI196000|AI448617|D230050P06|Ets-1|Tpl1|vs	E26 avian leukemia oncogene 1, 5' domain	protein-coding
mm_15440.1	chr2	157318001	157318014	+	1	NA	exon (NM_019642, exon 14 of 17)	exon (NM_019642, exon 14 of 17)	19419	NM_001329683	14601	Mm.389327	NM_010285	ENSMUSG00000027643	Ghrh	GRF|Ghrf	growth hormone releasing hormone	protein-coding
mm_117921.1	chr13	99433533	99433539	-	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-20710	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_160134.1	chr7	30649631	30649631	-	1	NA	exon (NM_133693, exon 2 of 10)	exon (NM_133693, exon 2 of 10)	597	NM_133693	68035	Mm.401747	NM_133693	ENSMUSG00000036733	Rbm42	1700003D06Rik|3100004P22Rik	RNA binding motif protein 42	protein-coding
mm_135645.1	chr16	52372698	52372702	-	1	NA	intron (NM_009655, intron 1 of 15)	L1Md_T|LINE|L1	80381	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_143579.1	chr17	74316387	74316434	-	1	NA	promoter-TSS (NM_001146223)	promoter-TSS (NM_001146223)	-16	NM_001146222	66310	Mm.28536	NM_024428	ENSMUSG00000024067	Dpy30	2810410M20Rik|C87842	dpy-30, histone methyltransferase complex regulatory subunit	protein-coding
mm_9695.1	chr1	178337674	178337694	-	1	NA	promoter-TSS (NM_016805)	promoter-TSS (NM_016805)	100	NM_016805	51810	Mm.86589	NM_016805	ENSMUSG00000039630	Hnrnpu	AA408410|AI256620|AL024194|AL024437|AW557595|C86794|Hnrpu|SAFA|Sp120|hnRNP U	heterogeneous nuclear ribonucleoprotein U	protein-coding
mm_68096.1	chr7	101933908	101933918	-	1	NA	promoter-TSS (NM_027053)	promoter-TSS (NM_027053)	-56	NM_001162973	69358	Mm.214841	NM_027053	ENSMUSG00000064307	Lrrc51	1700008D07Rik|Lrtomt	leucine rich repeat containing 51	protein-coding
mm_21570.1	chr2	164236990	164237021	-	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	1336	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_10389.1	chr2	12938680	12938683	+	1	NA	intron (NM_001305436, intron 1 of 4)	AT_rich|Low_complexity|Low_complexity	14640	NM_001305437	19212	Mm.229322	NM_008961	ENSMUSG00000026730	Pter	AI790318|Mpr56-1	phosphotriesterase related	protein-coding
mm_57954.1	chr6	135168109	135168121	-	1	NA	promoter-TSS (NM_013546)	promoter-TSS (NM_013546)	100	NM_013546	15199	Mm.378937	NM_013546	ENSMUSG00000042770	Hebp1	Hebp|p22HBP	heme binding protein 1	protein-coding
mm_130849.1	chr15	101940256	101940268	-	1	NA	promoter-TSS (NM_146063)	promoter-TSS (NM_146063)	62	NM_146063	223917	Mm.162744	NM_146063	ENSMUSG00000061397	Krt79	BC031593	keratin 79	protein-coding
mm_16641.1	chr2	6081159	6081161	-	1	NA	Intergenic	AmnSINE1|SINE|Deu	49025	NM_144883	227545	Mm.133542	NM_144883	ENSMUSG00000045319	Proser2	5430407P10Rik|AU067770	proline and serine rich 2	protein-coding
mm_37577.1	chr4	126301082	126301095	-	1	NA	intron (NM_199473, intron 2 of 3)	CpG	14294	NM_199473	329941	Mm.296327	NM_199473	ENSMUSG00000056174	Col8a2	AI429819	collagen, type VIII, alpha 2	protein-coding
mm_12211.1	chr2	67173900	67173910	+	1	NA	promoter-TSS (NM_001033477)	promoter-TSS (NM_001033477)	71	NM_001033477	383709	Mm.244520	NM_001033477		Gm1322	-	predicted gene 1322	protein-coding
mm_100943.1	chr11	6528497	6528521	-	1	NA	intron (NR_045893, intron 1 of 3)	intron (NR_045893, intron 1 of 3)	251	NR_045893	100041286	Mm.459507	NR_045893	ENSMUSG00000085156	Snhg15	Gm11974|OTTMUSG00000005115	small nucleolar RNA host gene 15	ncRNA
mm_12375.1	chr2	69822715	69822776	+	1	NA	intron (NM_177784, intron 1 of 3)	CpG	375	NM_177784	277396	Mm.138073	NM_177784	ENSMUSG00000042155	Klhl23	C130068N17Rik	kelch-like 23	protein-coding
mm_64136.1	chr7	141194149	141194191	+	1	NA	promoter-TSS (NM_153777)	promoter-TSS (NM_153777)	40	NM_001172064	70552	Mm.45104	NM_153777	ENSMUSG00000038637	Lrrc56	5730427C23Rik|BB110509|mFLJ00101	leucine rich repeat containing 56	protein-coding
mm_170198.1	chr17	6663009	6663025	+	1	NA	Intergenic	Lx4A|LINE|L1	-7078	NM_001166627	100040531	Mm.457987	NM_001166627	ENSMUSG00000095677	Dynlt1f	100040631|Dynlt1e	dynein light chain Tctex-type 1F	protein-coding
mm_59968.1	chr7	30428473	30428483	+	1	NA	3' UTR (NM_172142, exon 11 of 11)	3' UTR (NM_172142, exon 11 of 11)	5174	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_21736.1	chr2	164777808	164777819	-	1	NA	exon (NM_009394, exon 4 of 6)	exon (NM_009394, exon 4 of 6)	1921	NM_009394	21925	Mm.1716	NM_009394	ENSMUSG00000017300	Tnnc2	Tncs	troponin C2, fast	protein-coding
mm_171439.1	chr4	141207855	141207857	-	1	NA	Intergenic	IAPLTR2_Mm|LTR|ERVK	-6100	NM_001081174	76166	Mm.271064	NM_001081174	ENSMUSG00000073733	Rsg1	6330545A04Rik|Gm723	REM2 and RAB-like small GTPase 1	protein-coding
mm_40335.1	chr5	43911167	43911177	+	1	NA	3' UTR (NM_007646, exon 8 of 8)	3' UTR (NM_007646, exon 8 of 8)	42363	NM_007646	12494	Mm.249873	NM_007646	ENSMUSG00000029084	Cd38	ADPRC 1|Cd38-rs1|I-19	CD38 antigen	protein-coding
mm_35766.1	chr4	46184313	46184318	-	1	NA	exon (NM_011728, exon 4 of 6)	exon (NM_011728, exon 4 of 6)	11996	NM_011728	22590	Mm.247036	NM_011728	ENSMUSG00000028329	Xpa	AI573865|Xpac	xeroderma pigmentosum, complementation group A	protein-coding
mm_35415.1	chr4	34952457	34952464	-	1	NA	3' UTR (NM_178061, exon 4 of 4)	3' UTR (NM_178061, exon 4 of 4)	-40979	NR_040652	73696	Mm.1361	NR_040652	ENSMUSG00000085824	Platr9	2410114N07Rik	pluripotency associated transcript 9	ncRNA
mm_106956.1	chr12	8807804	8807808	+	1	NA	Intergenic	Intergenic	36410	NM_011519	20969	Mm.2580	NM_011519	ENSMUSG00000020592	Sdc1	AA408134|AA409076|CD138|Sstn|Synd|Synd1|syn-1	syndecan 1	protein-coding
mm_8808.1	chr1	161876748	161876759	-	1	NA	promoter-TSS (NM_172645)	promoter-TSS (NM_172645)	-92	NM_172645	226551	Mm.170002	NM_172645	ENSMUSG00000040297	Suco	4732491B11|AI848100|AU016931|Opt	SUN domain containing ossification factor	protein-coding
mm_907.1	chr1	54250674	54250699	+	1	NA	promoter-TSS (NM_030025)	promoter-TSS (NM_030025)	3	NM_030025	78016	Mm.67455	NM_030025	ENSMUSG00000025983	Ccdc150	4930511H11Rik	coiled-coil domain containing 150	protein-coding
mm_99939.1	chr11	111027246	111027256	+	1	NA	3' UTR (NM_001252208, exon 2 of 2)	3' UTR (NM_001252208, exon 2 of 2)	3391	NM_001252208	16517	Mm.30176	NM_010604	ENSMUSG00000051497	Kcnj16	6430410F18Rik|AI132396|Kir5.1	potassium inwardly-rectifying channel, subfamily J, member 16	protein-coding
mm_15184.1	chr2	154200309	154200320	+	1	NA	promoter-TSS (NM_153418)	promoter-TSS (NM_153418)	-66	NM_153418	228801	Mm.3783	NM_153418	ENSMUSG00000027485	Bpifb1	Lplunc1	BPI fold containing family B, member 1	protein-coding
mm_151672.1	chr19	4190986	4191029	-	1	NA	promoter-TSS (NM_178650)	promoter-TSS (NM_178650)	40	NM_178650	108995	Mm.288312	NM_178650	ENSMUSG00000040247	Tbc1d10c	1810062O14Rik|AI428527	TBC1 domain family, member 10c	protein-coding
mm_17046.1	chr2	20943414	20943424	-	1	NA	intron (NM_001128084, intron 1 of 24)	intron (NM_001128084, intron 1 of 24)	24302	NM_001081364	71435	Mm.28507	NM_001081364	ENSMUSG00000036591	Arhgap21	5530401C11Rik|AA416458|ARHGAP10	Rho GTPase activating protein 21	protein-coding
mm_42880.1	chr5	122354357	122354359	+	1	NA	promoter-TSS (NM_019780)	promoter-TSS (NM_019780)	-11	NM_001347453	56433	Mm.216528	NM_019780	ENSMUSG00000029462	Vps29	2010015D08Rik|AW049835|PEP11	VPS29 retromer complex component	protein-coding
mm_83850.1	chr9	54501829	54501849	-	1	NA	promoter-TSS (NM_172771)	promoter-TSS (NM_172771)	-213	NM_172771	235380	Mm.93636	NM_172771	ENSMUSG00000041268	Dmxl2	6330586A12|6430411K14Rik|E130119P06Rik|mKIAA0856	Dmx-like 2	protein-coding
mm_101838.1	chr11	48753210	48753222	-	1	NA	Intergenic	Intergenic	-47144	NM_008143	14694	Mm.5305	NM_008143	ENSMUSG00000020372	Rack1	AL033335|GB-like|Gnb2-rs1|Gnb2l1|p205	receptor for activated C kinase 1	protein-coding
mm_152106.1	chr19	6933271	6933281	-	1	NA	intron (NM_008431, intron 1 of 6)	intron (NM_008431, intron 1 of 6)	1239	NM_008431	16528	Mm.12894	NM_008431	ENSMUSG00000024957	Kcnk4	MLZ-622|TRAAK|TRAAKt|Tex40	potassium channel, subfamily K, member 4	protein-coding
mm_30484.1	chr3	155030318	155030353	-	1	NA	exon (NM_177066, exon 5 of 25)	exon (NM_177066, exon 5 of 25)	25072	NM_177066	435766	Mm.210428	NM_177066	ENSMUSG00000040086	Tnni3k	Cark|D830019J24Rik	TNNI3 interacting kinase	protein-coding
mm_7308.1	chr1	98047717	98047727	-	1	NA	promoter-TSS (NR_037993)	promoter-TSS (NR_037993)	71	NR_037993	78603	Mm.442597	NR_037993	ENSMUSG00000089706	B230216N24Rik	-	RIKEN cDNA B230216N24 gene	ncRNA
mm_102433.1	chr11	59506295	59506299	-	1	NA	non-coding (NR_135273, exon 1 of 4)	non-coding (NR_135273, exon 1 of 4)	343	NM_001291014	268417	Mm.239793	NM_172941	ENSMUSG00000020472	Zkscan17	Nizp1|Zfp496|Znf496	zinc finger with KRAB and SCAN domains 17	protein-coding
mm_99261.1	chr11	101246048	101246058	+	1	NA	promoter-TSS (NM_019444)	promoter-TSS (NM_019444)	-281	NM_019444	54409	Mm.260698	NM_019444	ENSMUSG00000001240	Ramp2	-	receptor (calcitonin) activity modifying protein 2	protein-coding
mm_89120.1	chr10	84838104	84838134	+	1	NA	promoter-TSS (NM_027689)	promoter-TSS (NM_027689)	-29	NM_027689	71137	Mm.79070	NM_027689	ENSMUSG00000020037	Rfx4	4933412G19Rik|NYD-sp10	regulatory factor X, 4 (influences HLA class II expression)	protein-coding
mm_154651.1	chrX	7841354	7841383	+	1	NA	promoter-TSS (NM_001290536)	promoter-TSS (NM_001290536)	-463	NM_001290536	54644	Mm.142827	NM_138604	ENSMUSG00000031154	Otud5	AA407879|AI553596|BB114028|DUBA|DXImx46e|Sfc7	OTU domain containing 5	protein-coding
mm_156561.1	chrX	151803400	151803404	+	1	NA	5' UTR (NM_021523, exon 1 of 83)	5' UTR (NM_021523, exon 1 of 83)	120	NM_021523	59026	Mm.27372	NM_021523	ENSMUSG00000025261	Huwe1	5430439H10Rik|AU041296|Arf-bp1|C430014N20Rik|C80292|Gm1718|Ib772|LASU1|Mule|Ureb1	HECT, UBA and WWE domain containing 1	protein-coding
mm_127502.1	chr15	101427690	101427708	+	1	NA	3' UTR (NM_033073, exon 9 of 9)	3' UTR (NM_033073, exon 9 of 9)	11105	NM_001003668	406219	Mm.347934	NM_001003668	ENSMUSG00000047641	Krt87	K83|K87|Krt2-25|Krt83	keratin 87	protein-coding
mm_149542.1	chr19	12564525	12564541	+	1	NA	Intergenic	Intergenic	-8977	NM_001346545	107373	Mm.1643	NM_026640	ENSMUSG00000024691	Fam111a	4632417K18Rik|AW413625	family with sequence similarity 111, member A	protein-coding
mm_18391.1	chr2	60209698	60209708	-	1	NA	promoter-TSS (NM_020575)	promoter-TSS (NM_020575)	-233	NM_020575	57438	Mm.260635	NM_020575	ENSMUSG00000026977	March7	Axo|Axot|Gtrgeo17	membrane-associated ring finger (C3HC4) 7	protein-coding
mm_39962.1	chr5	32136718	32136781	+	1	NA	exon (NM_008037, exon 1 of 4)	exon (NM_008037, exon 1 of 4)	277	NM_008037	14284	Mm.24684	NM_008037	ENSMUSG00000029135	Fosl2	Fra-2	fos-like antigen 2	protein-coding
mm_99460.1	chr11	102435239	102435257	+	1	NA	exon (NM_008175, exon 10 of 13)	exon (NM_008175, exon 10 of 13)	4926	NM_008175	14824	Mm.1568	NM_008175	ENSMUSG00000034708	Grn	Pgrn|epithelin	granulin	protein-coding
mm_56317.1	chr6	92242892	92242905	-	1	NA	exon (NM_009426, exon 3 of 3)	exon (NM_009426, exon 3 of 3)	1752	NM_009426	22044	Mm.1363	NM_009426	ENSMUSG00000005892	Trh	Pro-TRH|Trf	thyrotropin releasing hormone	protein-coding
mm_18669.1	chr2	70825675	70825725	-	1	NA	promoter-TSS (NM_172664)	promoter-TSS (NM_172664)	-220	NM_172664	228012	Mm.136511	NM_172664	ENSMUSG00000041997	Tlk1	4930545J15Rik	tousled-like kinase 1	protein-coding
mm_107519.1	chr12	40451026	40451061	+	1	NA	intron (NM_172803, intron 1 of 52)	intron (NM_172803, intron 1 of 52)	4990	NM_172803	238130	Mm.341423	NM_172803	ENSMUSG00000035954	Dock4	5330406C03|6330411N01Rik|AF263288|C030023J22|mKIAA0716	dedicator of cytokinesis 4	protein-coding
mm_37198.1	chr4	117765551	117765570	-	1	NA	5' UTR (NM_029416, exon 1 of 3)	5' UTR (NM_029416, exon 1 of 3)	106	NM_029416	75753	Mm.3848	NM_029416	ENSMUSG00000048626	Klf17	7420700M05Rik|AA420409|AU043468|C85123|D4Ertd561e|Gzf|Zfp393	Kruppel-like factor 17	protein-coding
mm_127982.1	chr15	12493490	12493533	-	1	NA	intron (NM_001081064, intron 1 of 23)	intron (NM_001081064, intron 1 of 23)	99045	NM_001081064	68070	Mm.423205	NM_001081064	ENSMUSG00000022197	Pdzd2	4930537L06Rik|A930022H17Rik|Gm21706|Gm82|Pdzk3|mKIAA0300	PDZ domain containing 2	protein-coding
mm_8747.1	chr1	160307305	160307322	-	1	NA	intron (NM_001038621, intron 2 of 8)	intron (NM_001038621, intron 2 of 8)	-11341	NR_035448	100316784		NR_035448	ENSMUSG00000089204	Mir1927	mmu-mir-1927	microRNA 1927	ncRNA
mm_168780.1	chr12	17956695	17956699	+	1	NA	Intergenic	Intergenic	265883	NM_016677	53602	Mm.313619	NM_016677	ENSMUSG00000071379	Hpcal1	NVP-3|Nvp3|VILIP3|Vnsl3|Vsnl3	hippocalcin-like 1	protein-coding
mm_161608.1	chr16	44820808	44820808	+	1	NA	promoter-TSS (NM_207244)	promoter-TSS (NM_207244)	80	NM_207244	239849	Mm.445045	NM_207244	ENSMUSG00000062082	Cd200r4	F630107N04Rik|MCD200RLa	CD200 receptor 4	protein-coding
mm_173121.1	chrX	162909221	162909224	-	1	NA	intron (NR_033143, intron 2 of 18)	intron (NR_033143, intron 2 of 18)	7051	NR_033143	55936	Mm.2065	NM_018737	ENSMUSG00000031360	Ctps2	A830031M15Rik|AI326475|Ctpsh	cytidine 5'-triphosphate synthase 2	protein-coding
mm_27497.1	chr3	55054984	55055022	-	1	NA	promoter-TSS (NM_007628)	promoter-TSS (NM_007628)	52	NM_007628	12427	Mm.4815	NM_007628	ENSMUSG00000027793	Ccna1	-	cyclin A1	protein-coding
mm_168621.1	chr1	178336975	178336981	-	1	NA	exon (NM_016805, exon 1 of 14)	exon (NM_016805, exon 1 of 14)	806	NM_016805	51810	Mm.86589	NM_016805	ENSMUSG00000039630	Hnrnpu	AA408410|AI256620|AL024194|AL024437|AW557595|C86794|Hnrpu|SAFA|Sp120|hnRNP U	heterogeneous nuclear ribonucleoprotein U	protein-coding
mm_106861.1	chr12	8009302	8009315	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	31631	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_119726.1	chr14	54059280	54059290	+	1	NA	Intergenic	Intergenic	194644	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_168243.1	chr10	81863951	81863953	+	1	NA	promoter-TSS (NM_001243067).2	promoter-TSS (NM_001243067).2	18	NM_001243067	73610	Mm.490466	NM_001243067	ENSMUSG00000096795	Zfp433	1700123A16Rik	zinc finger protein 433	protein-coding
mm_78578.1	chr9	36832701	36832855	+	1	NA	Intergenic	Intergenic	-10881	NM_183171	235180	Mm.5264	NM_183171	ENSMUSG00000032118	Fez1	UNC-76|UNC76	fasciculation and elongation protein zeta 1 (zygin I)	protein-coding
mm_38587.1	chr4	141821721	141821730	-	1	NA	exon (NM_007919, exon 4 of 8)	exon (NM_007919, exon 4 of 8)	4280	NM_007919	13706	Mm.45316	NM_007919	ENSMUSG00000058579	Cela2a	Ela-2|Ela2|Ela2a	chymotrypsin-like elastase family, member 2A	protein-coding
mm_137307.1	chr17	24877835	24877875	+	1	NA	promoter-TSS (NM_008340)	promoter-TSS (NM_008340)	-915	NM_008340	16005	Mm.3135	NM_008340	ENSMUSG00000046070	Igfals	ALS|Albs|mKIAA4111	insulin-like growth factor binding protein, acid labile subunit	protein-coding
mm_64857.1	chr7	13036625	13036662	-	1	NA	exon (NM_145578, exon 2 of 6)	exon (NM_145578, exon 2 of 6)	984	NM_001243968	22192	Mm.196580	NM_145578	ENSMUSG00000005575	Ube2m	2510040H03Rik|UBC12|Ubc-rs2	ubiquitin-conjugating enzyme E2M	protein-coding
mm_21035.1	chr2	152490186	152490190	-	1	NA	promoter-TSS (NM_001002791)	promoter-TSS (NM_001002791)	-50	NM_001002791	442835	Mm.99065	NM_001002791	ENSMUSG00000027468	Defb22	9230002F21Rik	defensin beta 22	protein-coding
mm_54612.1	chr6	38354232	38354240	-	1	NA	5' UTR (NM_028421, exon 1 of 12)	5' UTR (NM_028421, exon 1 of 12)	367	NM_028864	78781	Mm.25243	NM_028421	ENSMUSG00000029826	Zc3hav1	1200014N16Rik|2900058M19Rik|9130009D18Rik|9830115L13Rik|ARTD13|D6Bwg1452e|ZAP	zinc finger CCCH type, antiviral 1	protein-coding
mm_58190.1	chr6	143057912	143057912	-	1	NA	intron (NM_001109688, intron 10 of 24)	intron (NM_001109688, intron 10 of 24)	42240	NM_001286578	74741	Mm.130260	NM_029081	ENSMUSG00000030279	C2cd5	5730419I09Rik|C030008B15Rik|CDP138	C2 calcium-dependent domain containing 5	protein-coding
mm_125515.1	chr15	57694102	57694117	+	1	NA	promoter-TSS (NM_199449)	promoter-TSS (NM_199449)	-558	NM_199449	387609	Mm.36557	NM_199449	ENSMUSG00000071757	Zhx2	Afr-1|Afr1|Raf|mKIAA0854	zinc fingers and homeoboxes 2	protein-coding
mm_84755.1	chr9	75567322	75567354	-	1	NA	3' UTR (NM_001038710, exon 10 of 10)	3' UTR (NM_001038710, exon 10 of 10)	-7681	NM_016963	50875	Mm.38445	NM_016963	ENSMUSG00000058587	Tmod3	U-Tmod|UTMOD	tropomodulin 3	protein-coding
mm_116794.1	chr13	53472801	53472810	-	1	NA	promoter-TSS (NM_013601)	promoter-TSS (NM_013601)	-25	NM_013601	17702	Mm.1763	NM_013601	ENSMUSG00000021469	Msx2	BB122635|Hox-8|Hox8|Hox8.1	msh homeobox 2	protein-coding
mm_154381.1	chrM	11324	11336	+	1	NA	NA	Intergenic	NA	NA								
mm_53391.1	chr6	129578209	129578217	+	1	NA	promoter-TSS (NM_153590)	promoter-TSS (NM_153590)	-73	NM_153590	243655	Mm.30968	NM_153590	ENSMUSG00000050241	Klre1	Klre-1|NKG2I	killer cell lectin-like receptor family E member 1	protein-coding
mm_26191.1	chr3	138451456	138451468	+	1	NA	exon (NM_001288578, exon 6 of 9)	exon (NM_001288578, exon 6 of 9)	8369	NM_007410	11532	Mm.3874	NM_007410	ENSMUSG00000028138	Adh5	Adh-5|Adh3|GSNOR	alcohol dehydrogenase 5 (class III), chi polypeptide	protein-coding
mm_107088.1	chr12	17372923	17372956	+	1	NA	intron (NM_001008421, intron 11 of 20)	intron (NM_001008421, intron 11 of 20)	17547	NR_037226	100526470		NR_037226	ENSMUSG00000093037	Mir3066	mir-3066|mmu-mir-3066	microRNA 3066	ncRNA
mm_45944.1	chr5	90260155	90260183	-	1	NA	exon (NM_030886, exon 23 of 34)	exon (NM_030886, exon 23 of 34)	-36173	NM_001163456	231430	Mm.319697	NM_001033310	ENSMUSG00000035505	Cox18	BC038311	cytochrome c oxidase assembly protein 18	protein-coding
mm_88033.1	chr10	67285538	67285551	+	1	NA	promoter-TSS (NM_001036293)	promoter-TSS (NM_001036293)	-263	NM_001036293	641340	Mm.136223	NM_001036293	ENSMUSG00000075000	Nrbf2	NRBF-2	nuclear receptor binding factor 2	protein-coding
mm_149829.1	chr19	24521434	24521440	+	1	NA	intron (NM_008846, intron 1 of 14)	intron (NM_008846, intron 1 of 14)	34390	NM_008846	18719	Mm.217214	NM_008846	ENSMUSG00000024867	Pip5k1b	PI4P5K-I[b]|PIP5K1-beta|PIP5KIbeta|Pipk5b|STM7	phosphatidylinositol-4-phosphate 5-kinase, type 1 beta	protein-coding
mm_91654.1	chr10	42583605	42583616	-	1	NA	promoter-TSS (NM_152229)	promoter-TSS (NM_152229)	-22	NM_152229	21907	Mm.287100	NM_152229	ENSMUSG00000019803	Nr2e1	Mtl1|Mtll|TLL|Tlx|XTLL|fierce|frc|tailless	nuclear receptor subfamily 2, group E, member 1	protein-coding
mm_14832.1	chr2	147364956	147364962	+	1	NA	promoter-TSS (NM_008780)	promoter-TSS (NM_008780)	-35	NM_008780	18503	Mm.315502	NM_008780	ENSMUSG00000037034	Pax1	Pax-1|hbs|hunchback|un|undulated|wt	paired box 1	protein-coding
mm_140691.1	chr17	13760355	13760402	-	1	NA	promoter-TSS (NM_010806)	promoter-TSS (NM_010806)	-163	NM_010806	17356	Mm.59167	NM_010806	ENSMUSG00000068036	Afdn	5033403D15Rik|AF6|Af-6|Afadin|Gm314|I-afadin|Mllt4|S-afadin	afadin, adherens junction formation factor	protein-coding
mm_92432.1	chr10	77154332	77154335	-	1	NA	intron (NM_009929, intron 2 of 41)	B1_Mur3|SINE|Alu	12197	NM_009929	12822	Mm.4352	NM_009929	ENSMUSG00000001435	Col18a1	-	collagen, type XVIII, alpha 1	protein-coding
mm_139601.1	chr17	57279171	57279181	+	1	NA	promoter-TSS (NM_001163815)	promoter-TSS (NM_001163815)	76	NM_001163815	22324	Mm.248172	NM_011691	ENSMUSG00000034116	Vav1	Vav|vav-T	vav 1 oncogene	protein-coding
mm_6755.1	chr1	84037465	84037485	-	1	NA	3' UTR (NM_001003948, exon 3 of 3)	3' UTR (NM_001003948, exon 3 of 3)	181486	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_2091.1	chr1	87701151	87701168	+	1	NA	intron (NM_010566, intron 15 of 26)	intron (NM_010566, intron 15 of 26)	-54852	NM_029846	77040	Mm.272972	NM_029846	ENSMUSG00000026289	Atg16l1	1500009K01Rik|Apg16l|Atg16l|WDR30	autophagy related 16-like 1 (S. cerevisiae)	protein-coding
mm_165055.1	chr19	41339502	41339516	+	1	NA	intron (NM_031376, intron 2 of 16)	intron (NM_031376, intron 2 of 16)	45561	NM_031376	83490	Mm.222266	NM_031376	ENSMUSG00000025017	Pik3ap1	1810044J04Rik|BCAP	phosphoinositide-3-kinase adaptor protein 1	protein-coding
mm_51399.1	chr6	78371849	78371866	+	1	NA	exon (NM_011036, exon 3 of 6)	exon (NM_011036, exon 3 of 6)	972	NM_011036	18489	Mm.2553	NM_011036	ENSMUSG00000071356	Reg3b	HIP|PAP1|Pap|REG-III	regenerating islet-derived 3 beta	protein-coding
mm_89008.1	chr10	81628571	81628601	+	1	NA	promoter-TSS (NM_027480)	promoter-TSS (NM_027480)	46	NM_027480	70615	Mm.304382	NM_027480	ENSMUSG00000054708	Ankrd24	4631433D01Rik|5730519E19Rik|D10Bur2e	ankyrin repeat domain 24	protein-coding
mm_157613.1	chrX	53776393	53776401	-	1	NA	promoter-TSS (NM_001009549)	promoter-TSS (NM_001009549)	-3	NM_001009549	333473	Mm.327378	NM_001009549	ENSMUSG00000059334	Zfp36l3	AY661338	zinc finger protein 36, C3H type-like 3	protein-coding
mm_26254.1	chr3	142496792	142496804	+	1	NA	promoter-TSS (NM_153564)	promoter-TSS (NM_153564)	-136	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_66067.1	chr7	30823767	30823774	-	1	NA	promoter-TSS (NM_146187)	promoter-TSS (NM_146187)	5	NM_146187	233079	Mm.97338	NM_146187	ENSMUSG00000051314	Ffar2	GPCR43|Gpr43	free fatty acid receptor 2	protein-coding
mm_28126.1	chr3	86999265	86999275	-	1	NA	promoter-TSS (NM_007639)	promoter-TSS (NM_007639)	70	NM_007639	12479	Mm.1894	NM_007639	ENSMUSG00000028076	Cd1d1	AI747460|CD1.1|Cd1a|Cd1d|Ly-38	CD1d1 antigen	protein-coding
mm_134060.1	chr16	7951667	7951676	-	1	NA	Intergenic	RLTR17|LTR|ERVK	473465	NM_029070	74720	Mm.159318	NM_029070	ENSMUSG00000022715	Tmem114	4930511J11Rik|Cldn26	transmembrane protein 114	protein-coding
mm_99994.1	chr11	114765445	114765456	+	1	NA	promoter-TSS (NM_001102615)	promoter-TSS (NM_001102615)	61	NM_001102615	286942	Mm.308713	NM_001102615	ENSMUSG00000010021	Kif19a	Kif19	kinesin family member 19A	protein-coding
mm_160796.1	chr11	4441086	4441086	-	1	NA	promoter-TSS (NM_029458)	promoter-TSS (NM_029458)	-4	NM_029458	75828	Mm.159592	NM_029458	ENSMUSG00000020419	Hormad2	4930529M09Rik	HORMA domain containing 2	protein-coding
mm_165647.1	chr3	82903954	82903960	-	1	NA	promoter-TSS (NR_040381)	promoter-TSS (NR_040381)	17	NM_023624	79235	Mm.33921	NM_023624	ENSMUSG00000028003	Lrat	1300010A18Rik|AI449251	lecithin-retinol acyltransferase (phosphatidylcholine-retinol-O-acyltransferase)	protein-coding
mm_161323.1	chr14	47663748	47663748	+	1	NA	promoter-TSS (NM_008477)	promoter-TSS (NM_008477)	-8	NM_008477	16709	Mm.3110	NM_008477	ENSMUSG00000021843	Ktn1	-	kinectin 1	protein-coding
mm_71796.1	chr8	67685510	67685526	+	1	NA	Intergenic	RMER17A|LTR|ERVK	132777	NM_027626	234353	Mm.32525	NM_027626	ENSMUSG00000030465	Psd3	4931420C21Rik|AI661273|BC003498|D430018P08|EFA6D	pleckstrin and Sec7 domain containing 3	protein-coding
mm_161524.1	chr15	100586955	100586955	-	1	NA	promoter-TSS (NM_010127)	promoter-TSS (NM_010127)	-590	NM_010127	19009	Mm.28825	NM_010127	ENSMUSG00000009739	Pou6f1	2310038G18Rik|C79593|Emb|cns-1	POU domain, class 6, transcription factor 1	protein-coding
mm_24112.1	chr3	88143350	88143448	+	1	NA	intron (NM_133665, intron 1 of 10)	intron (NM_133665, intron 1 of 10)	1027	NM_001310593	17261	Mm.28184	NM_133665	ENSMUSG00000001419	Mef2d	C80750	myocyte enhancer factor 2D	protein-coding
mm_168667.1	chr11	9118797	9118805	+	1	NA	intron (NM_001159402, intron 1 of 8)	intron (NM_001159402, intron 1 of 8)	294	NM_001159402	22271	Mm.4610	NM_009477	ENSMUSG00000020407	Upp1	AI325217|UPase|UdRPase|Up|Upp	uridine phosphorylase 1	protein-coding
mm_80807.1	chr9	96363925	96363938	+	1	NA	intron (NM_007502, intron 1 of 6)	CpG	368	NM_007502	11933	Mm.424	NM_007502	ENSMUSG00000032412	Atp1b3	AA409958|AI664000|AW212096	ATPase, Na+/K+ transporting, beta 3 polypeptide	protein-coding
mm_14640.1	chr2	136809345	136809350	+	1	NA	Intergenic	Intergenic	-81871	NM_028201	74243	Mm.330612	NM_028201	ENSMUSG00000027281	Slx4ip	2210009G21Rik|2410004I22Rik|C85661|Slxip	SLX4 interacting protein	protein-coding
mm_122003.1	chr14	26917104	26917140	-	1	NA	Intergenic	ID_B1|SINE|B4	22518	NM_080856	142687	Mm.138259	NM_080856	ENSMUSG00000021898	Asb14	Asb-14	ankyrin repeat and SOCS box-containing 14	protein-coding
mm_66031.1	chr7	30626125	30626126	-	1	NA	promoter-TSS (NM_025628)	promoter-TSS (NM_025628)	26	NM_025628	110323	Mm.400	NM_025628	ENSMUSG00000036751	Cox6b1	2010000G05Rik|Cox6b	cytochrome c oxidase, subunit VIb polypeptide 1	protein-coding
mm_4765.1	chr1	182458646	182458656	+	1	NA	intron (NM_173378, intron 16 of 17)	intron (NM_173378, intron 16 of 17)	49484	NM_173378	209456	Mm.287450	NM_173378	ENSMUSG00000026510	Trp53bp2	53BP2|AI746547|ASPP2|PPP1R13A|Tp53bp2|X98550	transformation related protein 53 binding protein 2	protein-coding
mm_154966.1	chrX	37126764	37126774	+	1	NA	promoter-TSS (NM_025937)	promoter-TSS (NM_025937)	6	NM_025937	67050	Mm.55422	NM_025937	ENSMUSG00000016409	Nkap	2610020O08Rik|AA987160|AI849147|AL024236	NFKB activating protein	protein-coding
mm_6986.1	chr1	86357184	86357221	-	1	NA	promoter-TSS (NR_002851)	promoter-TSS (NR_002851)	-875	NR_002851	80828		NR_002851	ENSMUSG00000064823	Snord82	Rnu82|U82|Z25	small nucleolar RNA, C/D box 82	snoRNA
mm_167532.1	chr9	21291357	21291363	-	1	NA	promoter-TSS (NM_009878)	promoter-TSS (NM_009878)	-151	NM_009878	12581	Mm.29020	NM_009878	ENSMUSG00000096472	Cdkn2d	INK4d|p19|p19INK4d	cyclin-dependent kinase inhibitor 2D (p19, inhibits CDK4)	protein-coding
mm_97839.1	chr11	83065175	83065185	+	1	NA	promoter-TSS (NM_011408)	promoter-TSS (NM_011408)	68	NM_011408	20556	Mm.278689	NM_011408	ENSMUSG00000072620	Slfn2	Shlf2	schlafen 2	protein-coding
mm_9077.1	chr1	168431548	168431558	-	1	NA	5' UTR (NM_001291509, exon 1 of 7)	5' UTR (NM_001291509, exon 1 of 7)	616	NM_001291508	18514	Mm.43358	NM_008783	ENSMUSG00000052534	Pbx1	2310056B04Rik|D230003C07Rik|Pbx-1	pre B cell leukemia homeobox 1	protein-coding
mm_80763.1	chr9	95559350	95559367	+	1	NA	promoter-TSS (NM_198414)	promoter-TSS (NM_198414)	-459	NM_198414	75552	Mm.151485	NM_198414	ENSMUSG00000064225	Paqr9	1700020G04Rik	progestin and adipoQ receptor family member IX	protein-coding
mm_140393.1	chr17	87447226	87447238	+	1	NA	promoter-TSS (NM_007589)	promoter-TSS (NM_007589)	-297	NM_007589	12314	Mm.329243	NM_007589	ENSMUSG00000036438	Calm2	1500001E21Rik|AL024017	calmodulin 2	protein-coding
mm_170169.1	chr17	55878936	55878947	-	1	NA	promoter-TSS (NM_144546)	promoter-TSS (NM_144546)	12	NM_144546	104349	Mm.460659	NM_144546	ENSMUSG00000057835	Zfp119a	AL024077|Mzf13|Zfp119	zinc finger protein 119a	protein-coding
mm_77993.1	chr9	8544501	8544532	+	1	NA	exon (NM_001282087, exon 1 of 3)	exon (NM_001282087, exon 1 of 3)	374	NM_001282087	22068	Mm.325086	NM_013838	ENSMUSG00000031997	Trpc6	AV025995|LLHWJM002|LLHWJM003|LLHWJM004|TRP-6|Trrp6|mtrp6	transient receptor potential cation channel, subfamily C, member 6	protein-coding
mm_142356.1	chr17	43649688	43649695	-	1	NA	exon (NM_028711, exon 6 of 9)	exon (NM_028711, exon 6 of 9)	17324	NM_028711	74011	Mm.288697	NM_028711	ENSMUSG00000023912	Slc25a27	3632410G24Rik|9430092A03Rik|D530043E16Rik|Ucp4	solute carrier family 25, member 27	protein-coding
mm_80559.1	chr9	83548310	83548334	+	1	NA	promoter-TSS (NM_172507)	promoter-TSS (NM_172507)	-16	NM_172507	212531	Mm.491246	NM_172507	ENSMUSG00000032261	Sh3bgrl2	A930014C21Rik|AA408038|B930089I21	SH3 domain binding glutamic acid-rich protein like 2	protein-coding
mm_67740.1	chr7	90265403	90265444	-	1	NA	promoter-TSS (NM_183293)	promoter-TSS (NM_183293)	9	NM_029256	75338	Mm.487222	NM_029256	ENSMUSG00000030617	Ccdc83	4930549K11Rik|4930554C01Rik|4932423M01Rik	coiled-coil domain containing 83	protein-coding
mm_122304.1	chr14	34675086	34675097	-	1	NA	intron (NM_001004436, intron 1 of 18)	intron (NM_001004436, intron 1 of 18)	1163	NM_001301330	218914	Mm.27957	NM_001004436	ENSMUSG00000041408	Wapl	A530089A20Rik|BC037674|DIF-2|FOE|Wapal	WAPL cohesin release factor	protein-coding
mm_81294.1	chr9	108337452	108337481	+	1	NA	3' UTR (NM_016802, exon 6 of 6)	3' UTR (NM_016802, exon 6 of 6)	-1614	NM_008160	14775	Mm.1090	NM_008160	ENSMUSG00000063856	Gpx1	AI195024|AL033363|CGPx|GPx-1|GSHPx-1|Gpx	glutathione peroxidase 1	protein-coding
mm_37548.1	chr4	125127818	125127843	-	1	NA	promoter-TSS (NM_153159)	promoter-TSS (NM_153159)	51	NM_153159	230738	Mm.402	NM_153159	ENSMUSG00000042677	Zc3h12a	BC036563|MCPIP|MCPIP-1|Mcpip1|Reg1	zinc finger CCCH type containing 12A	protein-coding
mm_35577.1	chr4	41740841	41740864	-	1	NA	exon (NM_001286551, exon 2 of 4)	exon (NM_001286551, exon 2 of 4)	507	NM_001286540	18391	Mm.425181	NM_011014	ENSMUSG00000036078	Sigmar1	Oprs1|Sig1R|sigma1R	sigma non-opioid intracellular receptor 1	protein-coding
mm_43052.1	chr5	124116086	124116124	+	1	NA	promoter-TSS (NM_144509)	promoter-TSS (NM_144509)	-3	NM_144509	65105	Mm.29430	NM_144509	ENSMUSG00000029404	Arl6ip4	AA408210|AA408365|Aip-4|Srp25	ADP-ribosylation factor-like 6 interacting protein 4	protein-coding
mm_6751.1	chr1	83408268	83408290	-	1	NA	promoter-TSS (NM_172430)	promoter-TSS (NM_172430)	-79	NM_172430	77629	Mm.154303	NM_172430	ENSMUSG00000026163	Sphkap	4930544G21Rik|A930009L15Rik|AI852220|SKIP|mKIAA1678	SPHK1 interactor, AKAP domain containing	protein-coding
mm_157970.1	chrX	93632114	93632186	-	1	NA	promoter-TSS (NM_008892)	promoter-TSS (NM_008892)	5	NM_008892	18968	Mm.1923	NM_008892	ENSMUSG00000006678	Pola1	AW321876|Pola	polymerase (DNA directed), alpha 1	protein-coding
mm_101752.1	chr11	43383453	43383466	-	1	NA	Intergenic	Intergenic	-8998	NR_029558	387164		NR_029558	ENSMUSG00000065601	Mir146	Mirn146|miR-146a|mmu-mir-146	microRNA 146	ncRNA
mm_80985.1	chr9	103223010	103223038	+	1	NA	exon (NM_133977, exon 7 of 17)	exon (NM_133977, exon 7 of 17)	7262	NM_133977	22041	Mm.37214	NM_133977	ENSMUSG00000032554	Trf	AI266983|Cd176|HP|Tf|Tfn|hpx	transferrin	protein-coding
mm_90074.1	chr10	116387470	116387475	+	1	NA	3' UTR (NM_029928, exon 32 of 32)	3' UTR (NM_029928, exon 32 of 32)	-30649	NR_028107	67342	Mm.245800	NM_026098	ENSMUSG00000020164	Kcnmb4os1	1700058G18Rik	potassium large conductance calcium-activated channel, subfamily M, beta member 4, opposite strand 1	ncRNA
mm_63461.1	chr7	127573346	127573368	+	1	NA	promoter-TSS (NM_026888)	promoter-TSS (NM_026888)	9	NM_026888	68961	Mm.274473	NM_026888	ENSMUSG00000030815	Phkg2	1500017I02Rik	phosphorylase kinase, gamma 2 (testis)	protein-coding
mm_78874.1	chr9	44482784	44482815	+	1	NA	Intergenic	CpG	-16337	NM_030256	80288	Mm.370270	NM_030256	ENSMUSG00000063382	Bcl9l	B9L|BC003321|BCL9-2|DLNB11	B cell CLL/lymphoma 9-like	protein-coding
mm_147507.1	chr18	50224701	50224702	-	1	NA	Intergenic	B1F2|SINE|Alu	-53668	NM_001004061	225497	Mm.329435	NM_001004061	ENSMUSG00000035420	Fam170a	Gm93|Znfd	family with sequence similarity 170, member A	protein-coding
mm_119343.1	chr14	41096952	41096956	+	1	NA	Intergenic	L1_Mus3|LINE|L1	-8079	NM_133653	11720	Mm.14064	NM_133653	ENSMUSG00000037798	Mat1a	AI046368|AdoMet|Ams|MAT|MATA1|SAMS|SAMS1	methionine adenosyltransferase I, alpha	protein-coding
mm_6438.1	chr1	73998389	73998399	-	1	NA	intron (NM_027884, intron 6 of 34)	intron (NM_027884, intron 6 of 34)	126053	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_18504.1	chr2	62611768	62611778	-	1	NA	exon (NM_027835, exon 6 of 16)	exon (NM_027835, exon 6 of 16)	34482	NM_027835	71586	Mm.136224	NM_027835	ENSMUSG00000026896	Ifih1	9130009C22Rik|Helicard|Hlcd|MDA5|RLR-2	interferon induced with helicase C domain 1	protein-coding
mm_75667.1	chr8	67515555	67515594	-	1	NA	Intergenic	Intergenic	-8280	NM_008674	17962	Mm.57193	NM_008674	ENSMUSG00000056426	Nat3	-	N-acetyltransferase 3	protein-coding
mm_136136.1	chr16	87049256	87049264	-	1	NA	Intergenic	Intergenic	-304925	NM_001159331	67768	Mm.296532	NM_026366	ENSMUSG00000044442	N6amt1	5830445C04Rik|Hemk2|Pred28	N-6 adenine-specific DNA methyltransferase 1 (putative)	protein-coding
mm_30972.1	chr4	34550588	34550662	+	1	NA	promoter-TSS (NM_001007589)	promoter-TSS (NM_001007589)	10	NM_001007589	433693	Mm.389532	NM_026019	ENSMUSG00000028291	Akirin2	2700059D21Rik|AA114675|AA522011|AU019887|Akirin-2	akirin 2	protein-coding
mm_151101.1	chr19	47857850	47857893	+	1	NA	exon (NM_010362, exon 3 of 6)	exon (NM_010362, exon 3 of 6)	2898	NM_010362	14873	Mm.378931	NM_010362	ENSMUSG00000025068	Gsto1	AA407097|AI194287|AU018802|Gsto-1|Gstx|Spg-r|p28	glutathione S-transferase omega 1	protein-coding
mm_27551.1	chr3	58153289	58153294	-	1	NA	intron (NR_040538, intron 3 of 5)	intron (NR_040538, intron 3 of 5)	10516	NR_040538	67850	Mm.416968	NR_040538	ENSMUSG00000100666	1700007F19Rik	-	RIKEN cDNA 1700007F19 gene	ncRNA
mm_68703.1	chr7	119642455	119642466	-	1	NA	intron (NM_054094, intron 6 of 13)	RLTR19-int|LTR|ERVK	24632	NM_054094	117147	Mm.427560	NM_054094	ENSMUSG00000033533	Acsm1	Acas3|Bucs1|Macs	acyl-CoA synthetase medium-chain family member 1	protein-coding
mm_61471.1	chr7	75612229	75612314	+	1	NA	intron (NM_029332, intron 7 of 36)	intron (NM_029332, intron 7 of 36)	156737	NM_029332	75547	Mm.216107	NM_029332	ENSMUSG00000066406	Akap13	1700026G02Rik|5730522G15Rik|5830460E08Rik|AKAP-13|AKAP-Lbc|BRX|Ht31|LBC|PROTO-LB|PROTO-LBC	A kinase (PRKA) anchor protein 13	protein-coding
mm_51686.1	chr6	86525328	86525352	+	1	NA	exon (NM_011865, exon 1 of 1)	exon (NM_011865, exon 1 of 1)	825	NM_011865	23983	Mm.274146	NM_011865	ENSMUSG00000051695	Pcbp1	WBP17|[a]CP-1|alphaCP-1|hnRNP E1	poly(rC) binding protein 1	protein-coding
mm_156467.1	chrX	143518563	143518574	+	1	NA	promoter-TSS (NM_001195048)	promoter-TSS (NM_001195048)	-23	NM_001195048	18481	Mm.40035	NM_008778	ENSMUSG00000031284	Pak3	PAK-3|Pak65alpha|Pak65beta|Stk4	p21 protein (Cdc42/Rac)-activated kinase 3	protein-coding
mm_148410.1	chr19	3913042	3913059	+	1	NA	promoter-TSS (NM_001271444)	promoter-TSS (NM_001271444)	-276	NM_001271444	225887	Mm.44227	NM_144870	ENSMUSG00000059734	Ndufs8	BC021616|CI-23kD|TYKY	NADH dehydrogenase (ubiquinone) Fe-S protein 8	protein-coding
mm_142778.1	chr17	50101175	50101193	-	1	NA	intron (NM_181397, intron 3 of 9)	intron (NM_181397, intron 3 of 9)	89313	NM_181397	76438	Mm.41854	NM_181397	ENSMUSG00000039316	Rftn1	2310015N21Rik|AI853526	raftlin lipid raft linker 1	protein-coding
mm_11303.1	chr2	30237666	30237672	+	1	NA	promoter-TSS (NM_177725)	promoter-TSS (NM_177725)	-38	NR_028299	67350	Mm.402683	NR_028299		1700084E18Rik	-	RIKEN cDNA 1700084E18 gene	ncRNA
mm_146201.1	chr18	76268218	76268222	+	1	NA	intron (NM_001311070, intron 1 of 8)	B2_Mm2|SINE|B2	5775	NM_001311070	17126	Mm.152699	NM_010754	ENSMUSG00000024563	Smad2	7120426M23Rik|Madh2|Madr2|Smad-2|mMad2	SMAD family member 2	protein-coding
mm_133984.1	chr16	4559722	4559747	-	1	NA	promoter-TSS (NM_031182)	promoter-TSS (NM_031182)	-14	NM_031182	83383	Mm.273210	NM_031182	ENSMUSG00000005718	Tfap4	AI642933|AP-4|D930048N17Rik|Tcfap4|bHLHc41	transcription factor AP4	protein-coding
mm_6173.1	chr1	65082285	65082299	-	1	NA	promoter-TSS (NM_144761)	promoter-TSS (NM_144761)	-2	NM_144761	12965	Mm.440053	NM_144761	ENSMUSG00000073658	Crygb	Cryg-3|DGcry-3|Nop	crystallin, gamma B	protein-coding
mm_121029.1	chr14	79704303	79704312	+	1	NA	intron (NR_045060, intron 1 of 3)	intron (NR_045060, intron 1 of 3)	1387	NR_045060	73989	Mm.107775	NR_045060		4930452G13Rik	-	RIKEN cDNA 4930452G13 gene	ncRNA
mm_137205.1	chr17	23953292	23953300	+	1	NA	exon (NM_001077421, exon 4 of 4)	exon (NM_001077421, exon 4 of 4)	1977	NM_001077421	638345	Mm.46428	NM_001077421	ENSMUSG00000024125	Sbpl	2310068J22Rik	spermine binding protein-like	protein-coding
mm_136210.1	chr16	89837875	89837883	-	1	NA	intron (NM_009384, intron 13 of 27)	intron (NM_009384, intron 13 of 27)	-19527	NM_001145887	21844	Mm.310902	NM_009384	ENSMUSG00000002489	Tiam1	AI847750|D16Ium10|D16Ium10e	T cell lymphoma invasion and metastasis 1	protein-coding
mm_128813.1	chr15	67104955	67104964	-	1	NA	3' UTR (NM_009177, exon 9 of 9)	3' UTR (NM_009177, exon 9 of 9)	71923	NM_009177	20442	Mm.248334	NM_009177	ENSMUSG00000013846	St3gal1	5330418N22Rik|AI467004|ST3GalI|Siat4|Siat4a|St3gal-1	ST3 beta-galactoside alpha-2,3-sialyltransferase 1	protein-coding
mm_148726.1	chr19	5848496	5848522	+	1	NA	Intergenic	Intergenic	-3029	NR_003513	66961	Mm.281895	NR_003513	ENSMUSG00000092274	Neat1	2310043N10Rik|VINC	nuclear paraspeckle assembly transcript 1 (non-protein coding)	ncRNA
mm_171176.1	chr3	34183230	34183239	+	1	NA	Intergenic	Intergenic	-101880	NM_026332	67713	Mm.274266	NM_026332	ENSMUSG00000027679	Dnajc19	1810055D05Rik|AA959924|Tim14	DnaJ heat shock protein family (Hsp40) member C19	protein-coding
mm_170561.1	chr19	45649970	45649985	+	1	NA	intron (NM_013907, intron 1 of 8)	intron (NM_013907, intron 1 of 8)	10216	NM_013907	30838	Mm.254739	NM_013907	ENSMUSG00000040913	Fbxw4	Dac|Fbw4|SHFM3|SHSF3|dactylin|dactylyn	F-box and WD-40 domain protein 4	protein-coding
mm_90238.1	chr10	121395252	121395273	+	1	NA	3' UTR (NM_029364, exon 14 of 14)	3' UTR (NM_029364, exon 14 of 14)	30172	NM_029364	75612	Mm.207683	NM_029364	ENSMUSG00000034707	Gns	2610016K11Rik|AU042285|C87209|G6S|N28088	glucosamine (N-acetyl)-6-sulfatase	protein-coding
mm_4421.1	chr1	172501203	172501239	+	1	NA	intron (NM_178598, intron 1 of 4)	intron (NM_178598, intron 1 of 4)	975	NM_178598	21346	Mm.271711	NM_178598	ENSMUSG00000026547	Tagln2	2700094C18Rik|SM22beta|Sm22B|Sm22a	transgelin 2	protein-coding
mm_76601.1	chr8	90325927	90325938	-	1	NA	intron (NM_172913, intron 1 of 6)	intron (NM_172913, intron 1 of 6)	22320	NM_172913	244579	Mm.302755	NM_172913	ENSMUSG00000043668	Tox3	500-9|BC052044|C230068E13|CAGF9|Tnrc9	TOX high mobility group box family member 3	protein-coding
mm_16967.1	chr2	17690177	17690186	-	1	NA	intron (NM_028757, intron 2 of 6)	L1MB7|LINE|L1	40887	NM_028757	74103	Mm.120298	NM_028757	ENSMUSG00000053702	Nebl	1200007O21Rik|A630080F05Rik|BB140644|D830029A09Rik|Lnebl	nebulette	protein-coding
mm_89390.1	chr10	89872978	89872998	+	1	NA	promoter-TSS (NM_001128086)	promoter-TSS (NM_001128086)	-521	NM_001128086	77531	Mm.440605	NM_181398	ENSMUSG00000058589	Anks1b	AIDA-1b|C030032C09Rik|E530015N03Rik|ENSMUSG00000078431|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding
mm_19495.1	chr2	93452681	93452687	-	1	NA	promoter-TSS (NM_001271462)	promoter-TSS (NM_001271462)	-12	NM_001271462	12521	Mm.4261	NM_007656	ENSMUSG00000027215	Cd82	AA682076|AL023070|C33|IA4|Kai1|Tspan27	CD82 antigen	protein-coding
mm_41263.1	chr5	89028036	89028096	+	1	NA	intron (NM_001197147, intron 3 of 25)	intron (NM_001197147, intron 3 of 25)	140806	NM_018760	54403	Mm.41044	NM_018760	ENSMUSG00000060961	Slc4a4	AI835705|NBC|NBC1	solute carrier family 4 (anion exchanger), member 4	protein-coding
mm_9477.1	chr1	173367484	173367486	-	1	NA	exon (NM_053199, exon 1 of 9)	exon (NM_053199, exon 1 of 9)	210	NM_053199	94332	Mm.330524	NM_053199	ENSMUSG00000005338	Cadm3	BIgR|Igsf4b|Necl-1|Necl1|SynCAM3|Tsll1	cell adhesion molecule 3	protein-coding
mm_37790.1	chr4	130359916	130359966	-	1	NA	promoter-TSS (NM_025645)	promoter-TSS (NM_025645)	2	NM_153160	619605	Mm.297196	NM_153160	ENSMUSG00000028772	Zcchc17	2810055E05Rik|HSPC251|LDC4|pNO40|pS1D	zinc finger, CCHC domain containing 17	protein-coding
mm_158178.1	chrX	103980151	103980199	-	1	NA	intron (NM_011276, intron 1 of 4)	intron (NM_011276, intron 1 of 4)	1109	NM_011276	19820	Mm.427762	NM_011276	ENSMUSG00000056537	Rlim	AL022832|AW743871|Ha1r|Rlim1|Rnf12	ring finger protein, LIM domain interacting	protein-coding
mm_44573.1	chr5	24830049	24830055	-	1	NA	intron (NM_053075, intron 1 of 7)	intron (NM_053075, intron 1 of 7)	12309	NM_053075	19744	Mm.319175	NM_053075	ENSMUSG00000028945	Rheb	Rheb1	Ras homolog enriched in brain	protein-coding
mm_102251.1	chr11	55147189	55147210	-	1	NA	intron (NM_172258, intron 3 of 10)	intron (NM_172258, intron 3 of 10)	4507	NM_172258	215332	Mm.87054	NM_172258	ENSMUSG00000049491	Slc36a3	PAT3|TRAMD2|tramdorin2	solute carrier family 36 (proton/amino acid symporter), member 3	protein-coding
mm_144740.1	chr18	35571481	35571486	+	1	NA	intron (NM_010771, intron 1 of 14)	AT_rich|Low_complexity|Low_complexity	9325	NM_010771	17184	Mm.215034	NM_010771	ENSMUSG00000037236	Matr3	1110061A14Rik|2810017I02Rik|AI841759|AW555618|D030046F20Rik|mKIAA0723	matrin 3	protein-coding
mm_89493.1	chr10	93833783	93833817	+	1	NA	intron (NM_001206851, intron 1 of 6)	CpG	2245	NM_001206851	327799	Mm.491598	NM_183199	ENSMUSG00000020020	Usp44	E430004F17Rik	ubiquitin specific peptidase 44	protein-coding
mm_78590.1	chr9	37379845	37379873	+	1	NA	intron (NM_175189, intron 1 of 6)	intron (NM_175189, intron 1 of 6)	12253	NM_175189	72927	Mm.266133	NM_175189	ENSMUSG00000046240	Hepacam	2900042E01Rik|Glialcam|Hepn1	hepatocyte cell adhesion molecule	protein-coding
mm_29720.1	chr3	124581077	124581097	-	1	NA	promoter-TSS (NR_015460)	promoter-TSS (NR_015460)	4	NR_015460	384775	Mm.489851	NR_015460	ENSMUSG00000039174	1700003H04Rik	4930538K10Rik|4933400D22Rik	RIKEN cDNA 1700003H04 gene	ncRNA
mm_61230.1	chr7	64502158	64502176	+	1	NA	promoter-TSS (NM_001291167)	promoter-TSS (NM_001291167)	29	NM_001291167	11784	Mm.4657	NM_007461	ENSMUSG00000030519	Apba2	X11-like|X11L|XllL|mXllL	amyloid beta (A4) precursor protein-binding, family A, member 2	protein-coding
mm_72015.1	chr8	70715754	70715759	+	1	NA	Intergenic	Intergenic	-2787	NM_001195253	100502950	Mm.52981	NM_001195253	ENSMUSG00000095026	Gm3336	100041434|2410018E23Rik	predicted gene 3336	protein-coding
mm_131185.1	chr16	7217685	7217712	+	1	NA	intron (NM_183188, intron 1 of 12)	intron (NM_183188, intron 1 of 12)	147863	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_118151.1	chr13	105242798	105242810	-	1	NA	intron (NM_027934, intron 5 of 7)	Lx9|LINE|L1	50210	NM_027934	71816	Mm.317015	NM_027934	ENSMUSG00000021720	Rnf180	3110001E11Rik|Rines	ring finger protein 180	protein-coding
mm_75165.1	chr8	36613859	36613889	-	1	NA	promoter-TSS (NM_015802)	promoter-TSS (NM_015802)	69	NM_015802	50768	Mm.125155	NM_015802	ENSMUSG00000031523	Dlc1	A730069N07Rik|Arhgap7|HP|STARD12|dlc-1	deleted in liver cancer 1	protein-coding
mm_105759.1	chr11	109473762	109473785	-	1	NA	promoter-TSS (NM_001029842)	promoter-TSS (NM_001029842)	-177	NM_001029842	104681	Mm.265874	NM_134038	ENSMUSG00000041920	Slc16a6	AW743111|ESTM12|MCT 6|MCT 7|MCT6	solute carrier family 16 (monocarboxylic acid transporters), member 6	protein-coding
mm_28186.1	chr3	88058447	88058535	-	1	NA	promoter-TSS (NM_144897)	promoter-TSS (NM_144897)	4	NM_144897	246703	Mm.205996	NM_144897	ENSMUSG00000028070	Apoa1bp	AA087124|AI-BP|AIBP|Apoa1ip|ESTM37|Naxe	apolipoprotein A-I binding protein	protein-coding
mm_4814.1	chr1	185363077	185363150	+	1	NA	promoter-TSS (NM_029735)	promoter-TSS (NM_029735)	18	NM_029735	107508	Mm.154511	NM_029735	ENSMUSG00000026615	Eprs	2410081F06Rik|3010002K18Rik|C79379|Qprs	glutamyl-prolyl-tRNA synthetase	protein-coding
mm_83636.1	chr9	49486210	49486230	-	1	NA	promoter-TSS (NM_172770)	promoter-TSS (NM_172770)	5	NM_172770	235330	Mm.177413	NM_172770	ENSMUSG00000040219	Ttc12	E330017O07Rik	tetratricopeptide repeat domain 12	protein-coding
mm_125553.1	chr15	58823773	58823783	+	1	NA	promoter-TSS (NM_175212)	promoter-TSS (NM_175212)	-351	NM_175212	74868	Mm.293754	NM_175212	ENSMUSG00000062373	Tmem65	2610029O13Rik|4930438D12Rik	transmembrane protein 65	protein-coding
mm_110782.1	chr12	71015571	71015605	-	1	NA	promoter-TSS (NM_001081195)	promoter-TSS (NM_001081195)	235	NR_045056	73204	Mm.363770	NR_045055	ENSMUSG00000085622	3110056K07Rik	4921536K06Rik	RIKEN cDNA 3110056K07 gene	ncRNA
mm_18004.1	chr2	38228212	38228221	-	1	NA	intron (NM_146122, intron 2 of 21)	AT_rich|Low_complexity|Low_complexity	59168	NM_146122	227801	Mm.314245	NM_146122	ENSMUSG00000035392	Dennd1a	6030446I19Rik|connecdenn	DENN/MADD domain containing 1A	protein-coding
mm_154738.1	chrX	10252362	10252383	+	1	NA	promoter-TSS (NM_008769)	promoter-TSS (NM_008769)	67	NM_008769	18416	Mm.2611	NM_008769	ENSMUSG00000031173	Otc	AI265390|Sf|spf	ornithine transcarbamylase	protein-coding
mm_146143.1	chr18	74779179	74779189	+	1	NA	promoter-TSS (NR_028560)	promoter-TSS (NR_028560)	-28	NM_177470	52538	Mm.245724	NM_177470	ENSMUSG00000036880	Acaa2	0610011L04Rik|AI255831|AI265397|D18Ertd240e	acetyl-Coenzyme A acyltransferase 2 (mitochondrial 3-oxoacyl-Coenzyme A thiolase)	protein-coding
mm_74481.1	chr8	4324971	4324985	-	1	NA	promoter-TSS (NR_033527)	promoter-TSS (NR_033527)	122	NM_010485	15568	Mm.119162	NM_010485	ENSMUSG00000040028	Elavl1	2410055N02Rik|HUR|Hua|W91709	ELAV (embryonic lethal, abnormal vision)-like 1 (Hu antigen R)	protein-coding
mm_121651.1	chr14	10278006	10278010	-	1	NA	intron (NM_001308286, intron 2 of 6)	intron (NM_001308286, intron 2 of 6)	175450	NM_001308286	14198	Mm.397619	NM_010210	ENSMUSG00000060579	Fhit	AW045638|Fra14A2	fragile histidine triad gene	protein-coding
mm_34338.1	chr4	143394411	143394416	+	1	NA	promoter-TSS (NM_031377)	promoter-TSS (NM_031377)	-28	NM_031377	83491	Mm.190607	NM_031377	ENSMUSG00000041805	Pramel1	-	preferentially expressed antigen in melanoma-like 1	protein-coding
mm_122508.1	chr14	46901609	46901609	-	1	NA	intron (NM_001037221, intron 2 of 12)	intron (NM_001037221, intron 2 of 12)	18644	NM_001037221	74480	Mm.214454	NM_028966	ENSMUSG00000021838	Samd4	1700024G08Rik|1700111L17Rik|4933436G17Rik|Samd4a|Smaug|Smaug1|sunk	sterile alpha motif domain containing 4	protein-coding
mm_51733.1	chr6	87069547	87069557	+	1	NA	intron (NM_013528, intron 11 of 18)	intron (NM_013528, intron 11 of 18)	26706	NM_013528	14583	Mm.19893	NM_013528	ENSMUSG00000029992	Gfpt1	2810423A18Rik|AI324119|AI449986|GFA|GFAT|GFAT1|GFAT1m|Gfpt	glutamine fructose-6-phosphate transaminase 1	protein-coding
mm_2363.1	chr1	93006350	93006393	+	1	NA	promoter-TSS (NM_177587)	promoter-TSS (NM_177587)	37	NM_001159658	208760	Mm.235537	NM_177587	ENSMUSG00000045091	Aqp12	AB084104|mAQP12	aquaporin 12	protein-coding
mm_50314.1	chr6	47877572	47877594	+	1	NA	promoter-TSS (NM_146175)	promoter-TSS (NM_146175)	28	NM_146175	101095	Mm.440186	NM_146175	ENSMUSG00000025821	Zfp282	AI449432|C81429|E430019K09Rik|HUB1	zinc finger protein 282	protein-coding
mm_93927.1	chr10	127165517	127165530	-	1	NA	promoter-TSS (NM_027739)	promoter-TSS (NM_027739)	-308	NM_027739	14421	Mm.386762	NM_008080	ENSMUSG00000006731	B4galnt1	4933429D13Rik|Gal-NAc-T|GalNAc-T|GalNAcT|Galgt1|Ggm-2|Ggm2	beta-1,4-N-acetyl-galactosaminyl transferase 1	protein-coding
mm_86889.1	chr10	22299601	22299606	+	1	NA	intron (NM_009018, intron 5 of 5)	intron (NM_009018, intron 5 of 5)	-7117	NR_015465	606736	Mm.387042	NR_015465	ENSMUSG00000097352	C920009B18Rik	-	RIKEN cDNA C920009B18 gene	ncRNA
mm_28886.1	chr3	97868192	97868204	-	1	NA	intron (NM_001039376, intron 1 of 46)	CpG	20509	NM_001289702	83679	Mm.129840	NM_031401	ENSMUSG00000038170	Pde4dip	4732458A06Rik|9430063L05Rik|C87016|D130016K21Rik|D3Bwg1078e|Usmg4|mKIAA0454	phosphodiesterase 4D interacting protein (myomegalin)	protein-coding
mm_166628.1	chr6	78373431	78373437	+	1	NA	TTS (NM_011036)	TTS (NM_011036)	2549	NM_011036	18489	Mm.2553	NM_011036	ENSMUSG00000071356	Reg3b	HIP|PAP1|Pap|REG-III	regenerating islet-derived 3 beta	protein-coding
mm_50784.1	chr6	53978697	53978715	+	1	NA	promoter-TSS (NM_027749)	promoter-TSS (NM_027749)	15	NR_110484	320178	Mm.320413	NR_110484	ENSMUSG00000108060	4921529L05Rik	-	RIKEN cDNA 4921529L05 gene	ncRNA
mm_106250.1	chr11	117819104	117819143	-	1	NA	intron (NM_009387, intron 4 of 6)	intron (NM_009387, intron 4 of 6)	-6796	NM_027827	71562	Mm.273958	NM_027827	ENSMUSG00000017718	Afmid	9030621K19Rik|Ammd|FKF|KFA|Kf|formylase	arylformamidase	protein-coding
mm_7037.1	chr1	87100580	87100592	-	1	NA	exon (NM_001081082, exon 5 of 11)	exon (NM_001081082, exon 5 of 11)	1020	NM_001081082	76768	Mm.58068	NM_001081082	ENSMUSG00000079440	Alpi	2010001C14Rik|Akp6|gIAP	alkaline phosphatase, intestinal	protein-coding
mm_24613.1	chr3	93447828	93447833	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	5500	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_87402.1	chr10	45633835	45633837	+	1	NA	intron (NM_172473, intron 6 of 23)	intron (NM_172473, intron 6 of 23)	56007	NM_172473	209462	Mm.458633	NM_172473	ENSMUSG00000038822	Hace1	1700042J16Rik|A730034A22Rik|BC025474	HECT domain and ankyrin repeat containing, E3 ubiquitin protein ligase 1	protein-coding
mm_113088.1	chr13	23892808	23892818	+	1	NA	intron (NR_121611, intron 12 of 12)	intron (NR_121611, intron 12 of 12)	22194	NM_177016	319848	Mm.97959	NM_177016	ENSMUSG00000021336	Slc17a4	9130214H05Rik	solute carrier family 17 (sodium phosphate), member 4	protein-coding
mm_26300.1	chr3	142508234	142508247	+	1	NA	intron (NM_153564, intron 10 of 10)	MIR|SINE|MIR	11306	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_55984.1	chr6	85945963	85945976	-	1	NA	3' UTR (NM_028099, exon 9 of 9)	3' UTR (NM_028099, exon 9 of 9)	15698	NM_028099	72102	Mm.24007	NM_028099	ENSMUSG00000030002	Dusp11	2010300F21Rik|AI481497	dual specificity phosphatase 11 (RNA/RNP complex 1-interacting)	protein-coding
mm_152333.1	chr19	9974863	9974868	-	1	NA	Intergenic	MIRc|SINE|MIR	-5735	NR_073181	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
mm_161112.1	chr12	104387167	104387167	+	1	NA	promoter-TSS (NM_009253)	promoter-TSS (NM_009253)	3	NM_009253	20717	Mm.395085	NM_009253	ENSMUSG00000079012	Serpina3m	3e46|AI195004|MMCM7|MMSPi2.4|Spi-2l|Spi-2rs1|Spi2-rs1|Spi2.4|spi2	serine (or cysteine) peptidase inhibitor, clade A, member 3M	protein-coding
mm_23264.1	chr3	51483946	51483961	+	1	NA	promoter-TSS (NM_016858)	promoter-TSS (NM_016858)	-13	NM_016858	19338	Mm.1664	NM_016858	ENSMUSG00000027739	Rab33b	-	RAB33B, member RAS oncogene family	protein-coding
mm_143023.1	chr17	56571235	56571264	-	1	NA	exon (NM_001029979, exon 11 of 21)	exon (NM_001029979, exon 11 of 21)	13334	NM_001029979	224902	Mm.214973	NM_001029979	ENSMUSG00000042625	Safb2	AA389433|AI255170|mKIAA0138	scaffold attachment factor B2	protein-coding
mm_105174.1	chr11	101784667	101784675	-	1	NA	intron (NM_008815, intron 1 of 12)	CpG-2651	639	NM_008815	18612	Mm.5025	NM_008815	ENSMUSG00000017724	Etv4	AW414408|Pea-3|Pea3	ets variant 4	protein-coding
mm_47958.1	chr5	135586120	135586130	-	1	NA	Intergenic	Intergenic	-13082	NM_019577	56221	Mm.31505	NM_019577	ENSMUSG00000004814	Ccl24	CKb-6|MPIF-2|Scya24	chemokine (C-C motif) ligand 24	protein-coding
mm_112837.1	chr13	20826485	20826501	+	1	NA	intron (NM_012054, intron 2 of 20)	RMER10B|LTR|ERVL	32380	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_76494.1	chr8	86580648	86580660	-	1	NA	Intergenic	Intergenic	-14064	NM_172912	244562	Mm.67485	NM_172912	ENSMUSG00000036872	Abcc12	4930467B22Rik|MRP9	ATP-binding cassette, sub-family C (CFTR/MRP), member 12	protein-coding
mm_128638.1	chr15	59270225	59270234	-	1	NA	Intergenic	Intergenic	-36719	NR_045613	100416830	Mm.490788	NR_045613	ENSMUSG00000098528	Zfp572	4930472F24Rik	zinc finger protein 572	pseudo
mm_91586.1	chr10	40246992	40247045	-	1	NA	promoter-TSS (NM_023323)	promoter-TSS (NM_023323)	21	NM_023323	67239	Mm.11480	NM_023323	ENSMUSG00000038510	Rpf2	2810470K21Rik|AU040229|AU043242|Bxdc1	ribosome production factor 2 homolog	protein-coding
mm_31479.1	chr4	52240861	52240872	+	1	NA	Intergenic	Intergenic	-189756	NR_040668	329844	Mm.128934	NR_040668	ENSMUSG00000085515	C630028M04Rik	-	RIKEN cDNA C630028M04 gene	ncRNA
mm_154722.1	chrX	9272809	9272854	+	1	NA	promoter-TSS (NM_023500)	promoter-TSS (NM_023500)	47	NM_023500	22439	Mm.56468	NM_023500	ENSMUSG00000015342	Xk	1810038K19Rik|XRG1|Xkh	X-linked Kx blood group	protein-coding
mm_2985.1	chr1	133131409	133131437	+	1	NA	5' UTR (NM_133819, exon 1 of 2)	5' UTR (NM_133819, exon 1 of 2)	257	NM_133819	108954	Mm.293628	NM_133819	ENSMUSG00000046062	Ppp1r15b	1810033K10Rik|AI606441|C530022L24Rik|CReP	protein phosphatase 1, regulatory (inhibitor) subunit 15b	protein-coding
mm_162791.1	chr10	75643995	75643995	-	1	NA	promoter-TSS (NM_001162913)	promoter-TSS (NM_001162913)	13	NM_001162913	71733	Mm.247956	NM_027890	ENSMUSG00000006342	Susd2	1200011D11Rik	sushi domain containing 2	protein-coding
mm_36515.1	chr4	84383929	84383932	-	1	NA	intron (NM_172870, intron 4 of 5)	B1_Mus1|SINE|Alu	291156	NM_172870	242509	Mm.190774	NM_172870	ENSMUSG00000028487	Bnc2	5031434M05Rik|8430420F16Rik	basonuclin 2	protein-coding
mm_33210.1	chr4	126556972	126556992	+	1	NA	promoter-TSS (NM_175554)	promoter-TSS (NM_175554)	2	NM_175554	269582	Mm.243962	NM_175554	ENSMUSG00000042489	Clspn	B130025E01|C85083|E130314M08Rik	claspin	protein-coding
mm_141038.1	chr17	25273800	25273855	-	1	NA	promoter-TSS (NR_027452)	promoter-TSS (NR_027452)	87	NM_001177609	22196	Mm.240044	NM_011665	ENSMUSG00000015120	Ube2i	5830467E05Rik|F830028O17Rik|UBC9|Ubce2i|Ubce9	ubiquitin-conjugating enzyme E2I	protein-coding
mm_1108.1	chr1	59764265	59764286	+	1	NA	promoter-TSS (NM_007561)	promoter-TSS (NM_007561)	-4	NM_007561	12168	Mm.7106	NM_007561	ENSMUSG00000067336	Bmpr2	2610024H22Rik|AL117858|AW546137|BB189135|BMP-2|BMPR-2|BMPR-II|BMPRII|BRK-3|Gm20272	bone morphogenetic protein receptor, type II (serine/threonine kinase)	protein-coding
mm_173063.1	chrX	13280776	13280785	+	1	NA	promoter-TSS (NM_010028)	promoter-TSS (NM_010028)	-242	NM_010028	13205	Mm.289662	NM_010028	ENSMUSG00000000787	Ddx3x	D1Pas1-rs2|Ddx3|Fin14	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 3, X-linked	protein-coding
mm_64082.1	chr7	140943070	140943080	+	1	NA	exon (NM_145387, exon 3 of 14)	exon (NM_145387, exon 3 of 14)	1494	NM_145387	212974	Mm.260139	NM_145387	ENSMUSG00000062031	Pgghg	5730511L01Rik|Athl1|BC023151	protein glucosylgalactosylhydroxylysine glucosidase	protein-coding
mm_60604.1	chr7	44572349	44572360	+	1	NA	promoter-TSS (NM_008437)	promoter-TSS (NM_008437)	-91	NM_008437	16541	Mm.383181	NM_008437	ENSMUSG00000002204	Napsa	KAP|Kdap|NAP1|SNAPA|pronapsin	napsin A aspartic peptidase	protein-coding
mm_169358.1	chr14	27428696	27428697	-	1	NA	promoter-TSS (NM_001114879)	promoter-TSS (NM_001114879)	-151	NM_028945	218850	Mm.247767	NM_028945	ENSMUSG00000040651	Fam208a	4732418E12|4933409E02Rik|D14Abb1e|MommeD6	family with sequence similarity 208, member A	protein-coding
mm_34959.1	chr4	155996340	155996356	+	1	NA	exon (NM_011341, exon 2 of 7)	exon (NM_011341, exon 2 of 7)	3011	NM_001302468	20318	Mm.293517	NM_011341	ENSMUSG00000029076	Sdf4	Cab45	stromal cell derived factor 4	protein-coding
mm_39233.1	chr4	156254544	156254562	-	1	NA	intron (NM_001110516, intron 1 of 10)	intron (NM_001110516, intron 1 of 10)	785	NM_001110516	231004	Mm.406833	NM_173736	ENSMUSG00000096351	Samd11	BC026991|mr-s	sterile alpha motif domain containing 11	protein-coding
mm_73599.1	chr8	109998890	109998894	+	1	NA	3' UTR (NM_146214, exon 12 of 12)	3' UTR (NM_146214, exon 12 of 12)	8456	NM_146214	234724	Mm.28110	NM_146214	ENSMUSG00000001670	Tat	-	tyrosine aminotransferase	protein-coding
mm_59785.1	chr7	28895178	28895190	+	1	NA	intron (NM_021895, intron 19 of 20)	intron (NM_021895, intron 19 of 20)	13528	NM_001110807	60594	Mm.476990	NM_021894	ENSMUSG00000054083	Capn12	CANP 12	calpain 12	protein-coding
mm_36939.1	chr4	108579331	108579352	-	1	NA	promoter-TSS (NM_172697)	promoter-TSS (NM_172697)	-5	NM_172697	230596	Mm.157534	NM_172697	ENSMUSG00000063800	Prpf38a	2410002M20Rik	PRP38 pre-mRNA processing factor 38 (yeast) domain containing A	protein-coding
mm_170512.1	chr19	29003855	29003872	-	1	NA	intron (NM_001302382, intron 3 of 6)	intron (NM_001302382, intron 3 of 6)	13511	NM_025950	67072	Mm.78875	NM_025950	ENSMUSG00000024780	Cdc37l1	2700033A15Rik|BB159850|Cdc37l|Harc	cell division cycle 37-like 1	protein-coding
mm_112489.1	chr13	6548155	6548174	+	1	NA	promoter-TSS (NM_145131)	promoter-TSS (NM_145131)	7	NM_145131	69617	Mm.41933	NM_145131	ENSMUSG00000021193	Pitrm1	2310012C15Rik|AA410010|MP-1|MP1|Ntup1|PreP|mKIAA1104	pitrilysin metallepetidase 1	protein-coding
mm_12163.1	chr2	62325938	62325939	+	1	NA	3' UTR (NM_001242379, exon 25 of 25)	3' UTR (NM_001242379, exon 25 of 25)	86293	NM_010074	13482	Mm.1151	NM_010074	ENSMUSG00000035000	Dpp4	Cd26|Dpp-4|THAM	dipeptidylpeptidase 4	protein-coding
mm_170142.1	chr17	41367226	41367237	-	1	NA	Intergenic	RLTR9D|LTR|ERVK	432546	NM_008650	17850	Mm.259884	NM_008650	ENSMUSG00000023921	Mut	D230010K02Rik|Mcm	methylmalonyl-Coenzyme A mutase	protein-coding
mm_132469.1	chr16	36694025	36694037	+	1	NA	promoter-TSS (NM_134109)	promoter-TSS (NM_134109)	53	NM_001285791	106347	Mm.17807	NM_134109	ENSMUSG00000022900	Ildr1	AU041483|AU044638	immunoglobulin-like domain containing receptor 1	protein-coding
mm_1560.1	chr1	74153982	74154003	+	1	NA	promoter-TSS (NM_009909)	promoter-TSS (NM_009909)	-2	NM_009909	12765	Mm.234466	NM_009909	ENSMUSG00000026180	Cxcr2	CD128|CDw128|Cmkar2|Gpcr16|IL-8Rh|IL-8rb|IL8RA|Il8rb|mIL-8RH	chemokine (C-X-C motif) receptor 2	protein-coding
mm_97426.1	chr11	78071914	78071916	+	1	NA	Intergenic	Intergenic	-1090	NR_029556	387162		NR_029556	ENSMUSG00000065401	Mir144	Mirn144|mir-144|mmu-mir-144	microRNA 144	ncRNA
mm_146369.1	chr18	82584608	82584616	+	1	NA	3' UTR (NM_010777, exon 7 of 7)	3' UTR (NM_010777, exon 7 of 7)	30104	NM_001025254	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_144467.1	chr18	23753736	23753759	+	1	NA	promoter-TSS (NM_001162941)	promoter-TSS (NM_001162941)	22	NM_001162941	212307	Mm.132237	NM_153058	ENSMUSG00000024277	Mapre2	AI314113|C820009F03Rik|D18Abb1e|EB1|EB2|RP1	microtubule-associated protein, RP/EB family, member 2	protein-coding
mm_151995.1	chr19	5875269	5875279	-	1	NA	promoter-TSS (NM_026169)	promoter-TSS (NM_026169)	-66	NM_026169	67457	Mm.202092	NM_026169	ENSMUSG00000024816	Frmd8	1200004M23Rik|2310035N23Rik|4931429L16Rik|AU018809	FERM domain containing 8	protein-coding
mm_33977.1	chr4	137681590	137681618	+	1	NA	promoter-TSS (NM_001081155)	promoter-TSS (NM_001081155)	-23	NM_001081155	110351	Mm.180763	NM_029563	ENSMUSG00000041351	Rap1gap	1300019I11Rik|2310004O14Rik|AI427470|ARPP-90|Gap|Rap1GAP1|Rap1ga1	Rap1 GTPase-activating protein	protein-coding
mm_148511.1	chr19	4231911	4231928	+	1	NA	promoter-TSS (NM_027196)	promoter-TSS (NM_027196)	26	NM_027196	69745	Mm.32518	NM_027196	ENSMUSG00000024854	Pold4	2410012M21Rik|AI463381|AW060307|Polds|p12	polymerase (DNA-directed), delta 4	protein-coding
mm_108117.1	chr12	75669814	75669830	+	1	NA	promoter-TSS (NM_028203)	promoter-TSS (NM_028203)	-285	NM_028203	72338	Mm.341719	NM_028203	ENSMUSG00000045690	Wdr89	2600001A11Rik	WD repeat domain 89	protein-coding
mm_150037.1	chr19	29377330	29377361	+	1	NA	intron (NM_021893, intron 3 of 6)	MIR|SINE|MIR	9907	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_64222.1	chr7	141613826	141613834	+	1	NA	promoter-TSS (NR_040337)	promoter-TSS (NR_040337)	-83	NR_040337	100036523	Mm.398994	NR_040337	ENSMUSG00000097170	Gm16982	-	predicted gene, 16982	ncRNA
mm_22904.1	chr3	30856015	30856026	+	1	NA	promoter-TSS (NM_027965)	promoter-TSS (NM_027965)	70	NM_001286994	71862	Mm.272019	NM_027965	ENSMUSG00000037661	Gpr160	1700025D19Rik|GPCR150	G protein-coupled receptor 160	protein-coding
mm_67807.1	chr7	98117773	98117810	-	1	NA	intron (NM_001256081, intron 1 of 48)	intron (NM_001256081, intron 1 of 48)	1702	NM_001256081	17921	Mm.1403	NM_008663	ENSMUSG00000030761	Myo7a	Hdb|Myo7|USH1B|nmf371|polka|sh-1|sh1	myosin VIIA	protein-coding
mm_69959.1	chr7	142376345	142376355	-	1	NA	3' UTR (NM_009983, exon 9 of 9)	3' UTR (NM_009983, exon 9 of 9)	-2604	NM_001347541	320802	Mm.154486	NM_177265	ENSMUSG00000045777	Ifitm10	6330512M04Rik|AI848576|DSPA3	interferon induced transmembrane protein 10	protein-coding
mm_168793.1	chr12	19387828	19387829	+	1	NA	Intergenic	CpG	873318	NM_001201330	236366	Mm.352227	NM_001033157	ENSMUSG00000073197	5730507C01Rik	-	RIKEN cDNA 5730507C01 gene	protein-coding
mm_18752.1	chr2	73394288	73394299	-	1	NA	Intergenic	Intergenic	-7813	NM_001276444	68526	Mm.451014	NM_001080707	ENSMUSG00000041762	Gpr155	1110017O10Rik|DEPDC3|F730029F15Rik|PGR22	G protein-coupled receptor 155	protein-coding
mm_29715.1	chr3	123690851	123690883	-	1	NA	promoter-TSS (NR_121616)	promoter-TSS (NR_121616)	-15	NR_121616	83398	Mm.443908	NM_031186	ENSMUSG00000027977	Ndst3	4921531K01Rik|4930511P15Rik|N-HSST 3|NDST-3	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 3	protein-coding
mm_119940.1	chr14	54983334	54983362	+	1	NA	exon (NM_080728, exon 25 of 41)	exon (NM_080728, exon 25 of 41)	-7572	NR_030607	100124433		NR_030607	ENSMUSG00000077928	Mir208b	Mirn208b|mir-208b	microRNA 208b	ncRNA
mm_133498.1	chr16	90430512	90430534	+	1	NA	intron (NM_015755, intron 1 of 10)	intron (NM_015755, intron 1 of 10)	44126	NM_015755	26559	Mm.125874	NM_015755	ENSMUSG00000053414	Hunk	Bstk1|Mak-v	hormonally upregulated Neu-associated kinase	protein-coding
mm_91657.1	chr10	42699080	42699090	-	1	NA	intron (NM_172416, intron 5 of 5)	intron (NM_172416, intron 5 of 5)	20169	NM_172416	14628	Mm.46636	NM_172416	ENSMUSG00000038280	Ostm1	1200002H13Rik|HSPC019|gl	osteopetrosis associated transmembrane protein 1	protein-coding
mm_98338.1	chr11	93014435	93014480	+	1	NA	Intergenic	Intergenic	-84833	NM_028296	72605	Mm.342160	NM_028296	ENSMUSG00000056158	Car10	2700029L05Rik|BB085816|Ca10	carbonic anhydrase 10	protein-coding
mm_1740.1	chr1	75442373	75442389	+	1	NA	intron (NM_133708, intron 11 of 12)	intron (NM_133708, intron 11 of 12)	6438	NM_133708	69080	Mm.23951	NM_133708	ENSMUSG00000033021	Gmppa	1810012N01Rik	GDP-mannose pyrophosphorylase A	protein-coding
mm_61472.1	chr7	75612320	75612324	+	1	NA	intron (NM_029332, intron 7 of 36)	intron (NM_029332, intron 7 of 36)	156788	NM_029332	75547	Mm.216107	NM_029332	ENSMUSG00000066406	Akap13	1700026G02Rik|5730522G15Rik|5830460E08Rik|AKAP-13|AKAP-Lbc|BRX|Ht31|LBC|PROTO-LB|PROTO-LBC	A kinase (PRKA) anchor protein 13	protein-coding
mm_116697.1	chr13	49652890	49652914	-	1	NA	promoter-TSS (NM_001271397)	promoter-TSS (NM_001271397)	-171	NM_025495	66336	Mm.440323	NM_025495	ENSMUSG00000021391	Cenpp	1700022C02Rik|4921518G09Rik	centromere protein P	protein-coding
mm_106226.1	chr11	117165718	117165742	-	1	NA	Intergenic	Intergenic	-33931	NM_001113486	53860	Mm.38450	NM_017380	ENSMUSG00000059248	Sept9	MSF1|Msf|PNUTL4|Sint1	septin 9	protein-coding
mm_108194.1	chr12	76775130	76775141	+	1	NA	intron (NM_206534, intron 2 of 3)	intron (NM_206534, intron 2 of 3)	9562	NM_206534	211151	Mm.80970	NM_206534	ENSMUSG00000090258	Churc1	1700030P15Rik|My015|chch	churchill domain containing 1	protein-coding
mm_145442.1	chr18	59175334	59175406	+	1	NA	promoter-TSS (NM_001081328)	promoter-TSS (NM_001081328)	30	NM_001081328	78923	Mm.84007	NM_001081328	ENSMUSG00000058152	Chsy3	4833446K15Rik|AI662215	chondroitin sulfate synthase 3	protein-coding
mm_12343.1	chr2	69741504	69741523	+	1	NA	exon (NM_001081086, exon 10 of 14)	exon (NM_001081086, exon 10 of 14)	18425	NM_001081086	228005	Mm.11815	NM_001081086	ENSMUSG00000042133	Ppig	AU019516|AU022200|B230312B02Rik|CYP|SRCyp	peptidyl-prolyl isomerase G (cyclophilin G)	protein-coding
mm_55199.1	chr6	52204316	52204338	-	1	NA	exon (NM_010453, exon 1 of 2)	exon (NM_010453, exon 1 of 2)	260	NM_010453	15402	Mm.173	NM_010453	ENSMUSG00000038253	Hoxa5	Hox-1.3	homeobox A5	protein-coding
mm_9202.1	chr1	171229602	171229613	-	1	NA	TTS (NM_010185)	TTS (NM_010185)	4553	NM_013474	11807	Mm.389209	NM_013474	ENSMUSG00000005681	Apoa2	Alp-2|Apo-AII|ApoA-II|ApoAII|Apoa-2|Hdl-1	apolipoprotein A-II	protein-coding
mm_150145.1	chr19	31873531	31873543	+	1	NA	intron (NM_001081074, intron 1 of 11)	RSINE1|SINE|B4	4776	NM_001081074	69865	Mm.87538	NM_001081074	ENSMUSG00000052595	A1cf	1810073H04Rik|ACF64|ACF65|ASP|Acf|MCM|MerCreMer|Tg(Myh6-cre/Esr1*)1Jmk|mer	APOBEC1 complementation factor	protein-coding
mm_168848.1	chr12	23969103	23969104	-	1	NA	Intergenic	CpG	128166	NM_001256489	66808	Mm.379124	NM_001256489	ENSMUSG00000073158	9030624G23Rik	-	RIKEN cDNA 9030624G23 gene	protein-coding
mm_91779.1	chr10	52195313	52195332	-	1	NA	promoter-TSS (NM_011282)	promoter-TSS (NM_011282)	-78	NM_011282	19886	Mm.236163	NM_011282	ENSMUSG00000019893	Ros1	Ros-1|c-ros	Ros1 proto-oncogene	protein-coding
mm_131269.1	chr16	10837981	10838002	+	1	NA	intron (NM_001162932, intron 1 of 1)	intron (NM_001162932, intron 1 of 1)	2932	NM_001162932	223970	Mm.325777	NM_001033278	ENSMUSG00000037991	Rmi2	A630055G03Rik|Gm537|Gm929	RecQ mediated genome instability 2	protein-coding
mm_93434.1	chr10	109010861	109010918	-	1	NA	promoter-TSS (NM_001252342)	promoter-TSS (NM_001252342)	86	NM_009306	20979	Mm.289702	NM_009306	ENSMUSG00000035864	Syt1	AW124717|G630098F17Rik|SytI	synaptotagmin I	protein-coding
mm_21293.1	chr2	157006847	157006892	-	1	NA	intron (NM_025853, intron 1 of 10)	CpG	206	NM_025853	66934	Mm.25410	NM_025853	ENSMUSG00000027635	Dsn1	1700022L09Rik|AW552447	DSN1 homolog, MIS12 kinetochore complex component	protein-coding
mm_159926.1	chr6	57844285	57844285	-	1	NA	exon (NM_134183, exon 1 of 1)	exon (NM_134183, exon 1 of 1)	172	NM_134183	171201	Mm.377179	NM_134183	ENSMUSG00000058588	Vmn1r21	V1rc28	vomeronasal 1 receptor 21	protein-coding
mm_48235.1	chr5	137720760	137720789	-	1	NA	Intergenic	Intergenic	19224	NM_175521	243300	Mm.74750	NM_175521	ENSMUSG00000045348	Nyap1	6430598A04Rik	neuronal tyrosine-phosphorylated phosphoinositide 3-kinase adaptor 1	protein-coding
mm_160573.1	chr9	57834154	57834154	-	1	NA	promoter-TSS (NM_019689)	promoter-TSS (NM_019689)	80	NM_019689	56380	Mm.425588	NM_019689	ENSMUSG00000004661	Arid3b	Bdp|Dri2	AT rich interactive domain 3B (BRIGHT-like)	protein-coding
mm_153708.1	chr19	44397889	44397895	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	9817	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_108554.1	chr12	84417307	84417321	+	1	NA	5' UTR (NM_025525, exon 1 of 1)	5' UTR (NM_025525, exon 1 of 1)	114	NM_025525	66381	Mm.24846	NM_025525	ENSMUSG00000098134	Rnf113a2	2310020H19Rik|AI426758|Rnf113a	ring finger protein 113A2	protein-coding
mm_78567.1	chr9	35909593	35909599	+	1	NA	Intergenic	Intergenic	-59716	NR_030730	100041605	Mm.99350	NR_030730	ENSMUSG00000098705	Gm3428	-	predicted gene 3428	ncRNA
mm_129933.1	chr15	84855071	84855084	-	1	NA	intron (NR_030731, intron 1 of 11)	CpG-5189	1052	NM_001081166	271305	Mm.101022	NM_001081166	ENSMUSG00000016624	Phf21b	A730032D07Rik	PHD finger protein 21B	protein-coding
mm_6805.1	chr1	84155955	84155962	-	1	NA	intron (NM_001003948, intron 2 of 2)	intron (NM_001003948, intron 2 of 2)	63003	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_117377.1	chr13	72628564	72628586	-	1	NA	promoter-TSS (NR_030701)	promoter-TSS (NR_030701)	-11	NR_030701	328287	Mm.235072	NR_030701		Gm20554	D430050G20	predicted gene, 20554	ncRNA
mm_60557.1	chr7	44481185	44481203	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-3323	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_60636.1	chr7	44816387	44816406	+	1	NA	promoter-TSS (NM_030693)	promoter-TSS (NM_030693)	26	NM_001171024	100328588	Mm.2565	NM_001171024	ENSMUSG00000074141	Gm21948	Nup62-il4i1	predicted gene, 21948	protein-coding
mm_72159.1	chr8	72189614	72189664	+	1	NA	promoter-TSS (NM_197944)	promoter-TSS (NM_197944)	-29	NM_197944	209488	Mm.157431	NM_197944	ENSMUSG00000062007	Hsh2d	ALX|Hsh2	hematopoietic SH2 domain containing	protein-coding
mm_144470.1	chr18	23803963	23804054	+	1	NA	promoter-TSS (NM_153058)	promoter-TSS (NM_153058)	38	NM_153058	212307	Mm.132237	NM_153058	ENSMUSG00000024277	Mapre2	AI314113|C820009F03Rik|D18Abb1e|EB1|EB2|RP1	microtubule-associated protein, RP/EB family, member 2	protein-coding
mm_59708.1	chr7	28716847	28716861	+	1	NA	promoter-TSS (NM_015796)	promoter-TSS (NM_015796)	64	NM_015796	50760	Mm.358659	NM_015796	ENSMUSG00000030598	Fbxo17	Fbg4|Fbx17|Fbxo26	F-box protein 17	protein-coding
mm_64592.1	chr7	3169146	3169150	-	1	NA	promoter-TSS (NM_001004153)	promoter-TSS (NM_001004153)	55	NM_001004153	245128	Mm.268551	NM_001004153	ENSMUSG00000054753	AU018091	-	expressed sequence AU018091	protein-coding
mm_20165.1	chr2	122153063	122153086	-	1	NA	TTS (NM_009735)	TTS (NM_009735)	5387	NM_009735	12010	Mm.163	NM_009735	ENSMUSG00000060802	B2m	Ly-m11|beta2-m|beta2m	beta-2 microglobulin	protein-coding
mm_136862.1	chr17	12822086	12822088	+	1	NA	intron (NR_027773, intron 1 of 2)	Lx3B|LINE|L1	46056	NM_008552	17171	Mm.425994	NM_008552	ENSMUSG00000068037	Mas1	Mas-1|Mgra	MAS1 oncogene	protein-coding
mm_25678.1	chr3	122077149	122077159	+	1	NA	intron (NM_007378, intron 6 of 49)	intron (NM_007378, intron 6 of 49)	32694	NM_007378	11304	Mm.3918	NM_007378	ENSMUSG00000028125	Abca4	AW050280|Abc10|Abcr|D430003I15Rik|RmP	ATP-binding cassette, sub-family A (ABC1), member 4	protein-coding
mm_89755.1	chr10	99299090	99299093	+	1	NA	Intergenic	Intergenic	35860	NM_026268	67603	Mm.1791	NM_026268	ENSMUSG00000019960	Dusp6	1300019I03Rik|MKP-3|MKP3|PYST1	dual specificity phosphatase 6	protein-coding
mm_79288.1	chr9	51213538	51213562	+	1	NA	promoter-TSS (NM_011136)	promoter-TSS (NM_011136)	-140	NM_011136	18985	Mm.897	NM_011136	ENSMUSG00000032053	Pou2af1	BOB.1|Bob-1|Bob1|OBF-1|OBF.1|OCA-B|OCAB	POU domain, class 2, associating factor 1	protein-coding
mm_107429.1	chr12	35579543	35579553	+	1	NA	Intergenic	Intergenic	-44559	NM_001314027	11622	Mm.341377	NM_013464	ENSMUSG00000019256	Ahr	Ah|Ahh|Ahre|In|bHLHe76	aryl-hydrocarbon receptor	protein-coding
mm_12740.1	chr2	78972729	78972737	+	1	NA	Intergenic	Intergenic	103686	NM_009454	22193	Mm.1485	NM_009454	ENSMUSG00000027011	Ube2e3	Ubce4|ubcM2	ubiquitin-conjugating enzyme E2E 3	protein-coding
mm_86261.1	chr9	121597210	121597215	-	1	NA	intron (NR_040740, intron 1 of 3)	RMER19B|LTR|ERVK	10192	NR_040740	75384	Mm.445955	NR_040740	ENSMUSG00000084995	Lyzl4os	4930589B17Rik|4930596M17Rik	lysozyme-like 4, opposite strand	ncRNA
mm_43621.1	chr5	138161132	138161144	+	1	NA	promoter-TSS (NM_012002)	promoter-TSS (NM_012002)	36	NM_012002	26893	Mm.3981	NM_012002	ENSMUSG00000019494	Cops6	Sgn3|VIP/MOV34	COP9 signalosome subunit 6	protein-coding
mm_55402.1	chr6	60828833	60828883	-	1	NA	5' UTR (NM_001042451, exon 1 of 6)	5' UTR (NM_001042451, exon 1 of 6)	146	NM_001042451	20617	Mm.17484	NM_009221	ENSMUSG00000025889	Snca	NACP|alphaSYN	synuclein, alpha	protein-coding
mm_112939.1	chr13	20986295	20986306	+	1	NA	intron (NM_012054, intron 13 of 20)	MT2B|LTR|ERVL	86999	NM_146535	258528	Mm.377554	NM_146535	ENSMUSG00000042869	Olfr1370	MOR256-14	olfactory receptor 1370	protein-coding
mm_125715.1	chr15	68928463	68928483	+	1	NA	promoter-TSS (NM_010158)	promoter-TSS (NM_010158)	53	NM_010158	13992	Mm.17964	NM_010158	ENSMUSG00000022332	Khdrbs3	Etle|SLM-2|Salp|Slm2|T-STAR	KH domain containing, RNA binding, signal transduction associated 3	protein-coding
mm_3566.1	chr1	150433764	150433774	+	1	NA	exon (NM_133780, exon 37 of 52)	exon (NM_133780, exon 37 of 52)	32396	NM_021400	96875	Mm.174256	NM_021400	ENSMUSG00000006014	Prg4	CACP|DOL54|JCAP|MSF|SZP|lubricin	proteoglycan 4 (megakaryocyte stimulating factor, articular superficial zone protein)	protein-coding
mm_49786.1	chr6	35177896	35177936	+	1	NA	intron (NM_027513, intron 1 of 42)	CpG	300	NM_027513	70699	Mm.261208	NM_027513	ENSMUSG00000038759	Nup205	3830404O05Rik|AV248391|mKIAA0225	nucleoporin 205	protein-coding
mm_124566.1	chr14	124095091	124095095	-	1	NA	intron (NM_010201, intron 3 of 4)	ORR1B2-int|LTR|ERVL-MaLR	97453	NM_010201	14169	Mm.206362	NM_010201	ENSMUSG00000025551	Fgf14	FHF-4|Fhf4|mFHF-4(1B)	fibroblast growth factor 14	protein-coding
mm_78631.1	chr9	39074024	39074031	+	1	NA	Intergenic	Intergenic	4716	NM_146438	258430	Mm.271358	NM_146438	ENSMUSG00000048501	Olfr938	MOR171-25	olfactory receptor 938	protein-coding
mm_75795.1	chr8	70108507	70108530	-	1	NA	exon (NM_007789, exon 8 of 15)	exon (NM_007789, exon 8 of 15)	-5932	NR_106033	102465646		NR_106033	ENSMUSG00000099042	Mir7066	Gm27290|mmu-mir-7066	microRNA 7066	ncRNA
mm_124798.1	chr15	8444734	8444749	+	1	NA	promoter-TSS (NM_027707)	promoter-TSS (NM_027707)	-278	NM_201232	71175	Mm.240329	NM_027707	ENSMUSG00000022141	Nipbl	Idn3	Nipped-B homolog (Drosophila)	protein-coding
mm_108620.1	chr12	85598288	85598308	+	1	NA	promoter-TSS (NM_001205052)	promoter-TSS (NM_001205052)	-807	NM_001205052	81703	Mm.103560	NM_030887	ENSMUSG00000034271	Jdp2	Jundm2|Jundp2|TIF	Jun dimerization protein 2	protein-coding
mm_94355.1	chr11	4947357	4947391	+	1	NA	promoter-TSS (NM_001243043)	promoter-TSS (NM_001243043)	-147	NM_001243043	11764	Mm.274816	NM_007454	ENSMUSG00000009090	Ap1b1	Adtb1|b2b1660Clo	adaptor protein complex AP-1, beta 1 subunit	protein-coding
mm_119593.1	chr14	50952253	50952256	+	1	NA	3' UTR (NM_013632, exon 6 of 6)	3' UTR (NM_013632, exon 6 of 6)	-3887	NM_001123371	667034	Mm.482171	NM_001123371	ENSMUSG00000068417	Pnp2	-	purine-nucleoside phosphorylase 2	protein-coding
mm_117356.1	chr13	69933246	69933255	-	1	NA	Intergenic	Intergenic	-26583	NR_138559	67550	Mm.158159	NR_138559		4933416O17Rik	-	RIKEN cDNA 4933416O17 gene	ncRNA
mm_49400.1	chr6	28426295	28426320	+	1	NA	3' UTR (NM_007480, exon 6 of 6)	3' UTR (NM_007480, exon 6 of 6)	-1594	NM_019569	56223	Mm.31708	NM_019569	ENSMUSG00000029707	Fscn3	-	fascin actin-bundling protein 3	protein-coding
mm_101628.1	chr11	36007862	36007873	-	1	NA	3' UTR (NM_001290702, exon 28 of 28)	3' UTR (NM_001290702, exon 28 of 28)	-27778	NM_170779	211652	Mm.31267	NM_170779	ENSMUSG00000018849	Wwc1	AA408228|AU017197|BC037006|Kibra|mKIAA0869	WW, C2 and coiled-coil domain containing 1	protein-coding
mm_59520.1	chr7	27605802	27605841	+	1	NA	promoter-TSS (NM_007434)	promoter-TSS (NM_007434)	24	NM_007434	11652	Mm.177194	NM_007434	ENSMUSG00000004056	Akt2	2410016A19Rik|AW554154|PKB|PKBbeta	thymoma viral proto-oncogene 2	protein-coding
mm_63946.1	chr7	139834321	139834352	+	1	NA	5' UTR (NM_177469, exon 1 of 8)	5' UTR (NM_177469, exon 1 of 8)	162	NM_177469	52389	Mm.39863	NM_177469	ENSMUSG00000025475	Adgra1	2900059M17Rik|D7Ertd680e|Gpr123	adhesion G protein-coupled receptor A1	protein-coding
mm_87727.1	chr10	60106453	60106466	+	1	NA	5' UTR (NM_052994, exon 1 of 11)	5' UTR (NM_052994, exon 1 of 11)	202	NM_052994	94214	Mm.153429	NM_052994	ENSMUSG00000058297	Spock2	AA407235|Gcap26|mKIAA0275	sparc/osteonectin, cwcv and kazal-like domains proteoglycan 2	protein-coding
mm_2484.1	chr1	105988347	105988378	+	1	NA	Intergenic	Intergenic	-2044	NM_001122676	227449	Mm.210188	NM_001122675	ENSMUSG00000038866	Zcchc2	9930114B20Rik|AW212015	zinc finger, CCHC domain containing 2	protein-coding
mm_12963.1	chr2	90599518	90599518	+	1	NA	Intergenic	Intergenic	-18871	NM_008982	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_98803.1	chr11	97041570	97041602	+	1	NA	promoter-TSS (NM_027026)	promoter-TSS (NM_027026)	0	NM_026154	107732	Mm.208946	NM_026154	ENSMUSG00000001445	Mrpl10	0610040E02Rik|C78440|MRP-L8|Rpml8	mitochondrial ribosomal protein L10	protein-coding
mm_150132.1	chr19	30042760	30042787	+	1	NA	intron (NM_144873, intron 2 of 15)	L1MC3|LINE|L1	12260	NM_144873	109113	Mm.313364	NM_144873	ENSMUSG00000024817	Uhrf2	2310065A22Rik|AI426270|AW214556|D130071B19Rik|Nirf	ubiquitin-like, containing PHD and RING finger domains 2	protein-coding
mm_7616.1	chr1	126738168	126738230	-	1	NA	intron (NM_001081756, intron 1 of 16)	intron (NM_001081756, intron 1 of 16)	92433	NM_001081756	210356	Mm.377234	NM_172484	ENSMUSG00000049690	Nckap5	8430408F21|D130011D22Rik|E030049G20Rik|Erih1|Erih2|Gm1548|Nap5	NCK-associated protein 5	protein-coding
mm_142485.1	chr17	45746803	45746819	-	1	NA	Intergenic	Intergenic	-12967	NM_028164	72240	Mm.482897	NM_028164	ENSMUSG00000094690	1600014C23Rik	-	RIKEN cDNA 1600014C23 gene	protein-coding
mm_89848.1	chr10	107271329	107271364	+	1	NA	promoter-TSS (NM_001039354)	promoter-TSS (NM_001039354)	-485	NM_001039354	108030	Mm.268025	NM_001033223	ENSMUSG00000019906	Lin7a	AI848705|LIN-7A|MALS-1|TIP-33|Veli|Veli1	lin-7 homolog A (C. elegans)	protein-coding
mm_89358.1	chr10	88357185	88357204	+	1	NA	promoter-TSS (NM_027878)	promoter-TSS (NM_027878)	-119	NM_027878	71712	Mm.35450	NM_027878	ENSMUSG00000020057	Dram1	1200002N14Rik|Dram	DNA-damage regulated autophagy modulator 1	protein-coding
mm_167959.1	chrX	142297503	142297504	+	1	NA	promoter-TSS (NR_002883).2	promoter-TSS (NR_002883).2	-2	NR_002883	434858	Mm.391346	NR_002883		Gm5643	EG434858	heterogeneous nuclear ribonucleoprotein A1 pseudogene	pseudo
mm_19505.1	chr2	93822524	93822534	-	1	NA	promoter-TSS (NM_010163)	promoter-TSS (NM_010163)	39	NM_010163	14043	Mm.4336	NM_010163	ENSMUSG00000027198	Ext2	AI893565	exostoses (multiple) 2	protein-coding
mm_120973.1	chr14	78434998	78435010	+	1	NA	Intergenic	Intergenic	87698	NM_001346784	219181	Mm.89413	NM_001164503	ENSMUSG00000022016	Akap11	6330501D17Rik|AKAP220|Gm80|PRKA11|mKIAA0629	A kinase (PRKA) anchor protein 11	protein-coding
mm_5845.1	chr1	52963251	52963266	-	1	NA	Intergenic	Intergenic	-10418	NM_144953	67080	Mm.236287	NM_144953	ENSMUSG00000043629	1700019D03Rik	2410136C24Rik|AA410151|smAKAP	RIKEN cDNA 1700019D03 gene	protein-coding
mm_94833.1	chr11	23497746	23497789	+	1	NA	intron (NM_001290655, intron 1 of 8)	CpG	272	NM_001290655	268390	Mm.13148	NM_172391	ENSMUSG00000020288	Ahsa2	-	AHA1, activator of heat shock protein ATPase 2	protein-coding
mm_101218.1	chr11	20140304	20140316	-	1	NA	Intergenic	Intergenic	-27359	NM_146243	66713	Mm.259045	NM_146243	ENSMUSG00000020152	Actr2	4921510D23Rik|AA409782|Arp2|D6Ertd746e	ARP2 actin-related protein 2	protein-coding
mm_47570.1	chr5	124478302	124478328	-	1	NA	promoter-TSS (NM_030259)	promoter-TSS (NM_030259)	-80	NM_030259	80291	Mm.425280	NM_030259	ENSMUSG00000029401	Rilpl2	-	Rab interacting lysosomal protein-like 2	protein-coding
mm_102221.1	chr11	54909876	54909884	-	1	NA	TTS (NM_021327)	TTS (NM_021327)	7026	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_93152.1	chr10	93081505	93081524	-	1	NA	promoter-TSS (NM_001347060)	promoter-TSS (NM_001347060)	82	NM_001347060	380654	Mm.34980	NM_001347060	ENSMUSG00000020014	Cfap54	4930485B16Rik|Gm872	cilia and flagella associated protein 54	protein-coding
mm_117085.1	chr13	59731735	59731758	-	1	NA	promoter-TSS (NM_177711)	promoter-TSS (NM_177711)	6	NM_177711	238663	Mm.444776	NM_177711	ENSMUSG00000043986	Spata31d1d	4932411G14Rik|Fam75d1d	spermatogenesis associated 31 subfamily D, member 1D	protein-coding
mm_166373.1	chr5	128444338	128444346	+	1	NA	Intergenic	Intergenic	-11265	NM_172885	243274	Mm.447698	NM_172885	ENSMUSG00000034310	Tmem132d	C630028F04Rik	transmembrane protein 132D	protein-coding
mm_140825.1	chr17	23641724	23641766	-	1	NA	intron (NM_001320258, intron 2 of 9)	intron (NM_001320258, intron 2 of 9)	3524	NM_001033339	240047	Mm.235343	NM_001033339	ENSMUSG00000023903	Mmp25	F730048C11Rik|Leukolysin|MMP20|MT6-MMP	matrix metallopeptidase 25	protein-coding
mm_112180.1	chr12	113422068	113422118	-	1	NA	Intergenic	Intergenic	-67472	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_33208.1	chr4	126556957	126556957	+	1	NA	promoter-TSS (NM_175554)	promoter-TSS (NM_175554)	-23	NM_175554	269582	Mm.243962	NM_175554	ENSMUSG00000042489	Clspn	B130025E01|C85083|E130314M08Rik	claspin	protein-coding
mm_59988.1	chr7	30554773	30554794	+	1	NA	TTS (NM_001290569)	TTS (NM_001290569)	1481	NM_001012401	243912	Mm.34885	NM_001012401	ENSMUSG00000036854	Hspb6	AA387366|Gm479|Hsp20	heat shock protein, alpha-crystallin-related, B6	protein-coding
mm_171163.1	chr3	25212715	25212734	-	1	NA	Intergenic	Intergenic	-428718	NM_001326288	635702	Mm.448351	NM_001326288	ENSMUSG00000102758	Naaladl2	2810043G22Rik|EG635702|Gm1021	N-acetylated alpha-linked acidic dipeptidase-like 2	protein-coding
mm_110351.1	chr12	37474990	37475004	-	1	NA	intron (NM_178767, intron 12 of 12)	RMER1C|Other|Other	233358	NM_178767	319660	Mm.485540	NM_178767	ENSMUSG00000050103	Agmo	A530016O06Rik|AI790538|Tmem195	alkylglycerol monooxygenase	protein-coding
mm_168121.1	chr10	19288930	19288935	-	1	NA	Intergenic	RLTR20B3|LTR|ERVK	-67607	NM_053008	94222	Mm.156946	NM_053008	ENSMUSG00000045591	Olig3	Bhlhb7|bHLHe20|oligo3	oligodendrocyte transcription factor 3	protein-coding
mm_29261.1	chr3	107310367	107310370	-	1	NA	intron (NM_146136, intron 8 of 8)	intron (NM_146136, intron 8 of 8)	19076	NM_146136	229699	Mm.38384	NM_146136	ENSMUSG00000027896	Slc16a4	AW146050|MCT 5	solute carrier family 16 (monocarboxylic acid transporters), member 4	protein-coding
mm_108083.1	chr12	73964545	73964563	+	1	NA	promoter-TSS (NM_178392)	promoter-TSS (NM_178392)	24	NM_178392	75627	Mm.25937	NM_178392	ENSMUSG00000021113	Snapc1	2700033G17Rik|AU015787	small nuclear RNA activating complex, polypeptide 1	protein-coding
mm_60057.1	chr7	31151514	31151536	+	1	NA	promoter-TSS (NM_027898)	promoter-TSS (NM_027898)	-475	NM_027898	52857	Mm.27366	NM_027898	ENSMUSG00000001248	Gramd1a	1300003M23Rik|AI415002|AW547240|D7Bwg0611e	GRAM domain containing 1A	protein-coding
mm_61934.1	chr7	90168302	90168310	+	1	NA	intron (NM_001252520, intron 4 of 20)	AT_rich|Low_complexity|Low_complexity	38074	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_75085.1	chr8	33917303	33917322	-	1	NA	intron (NM_001042674, intron 1 of 7)	intron (NM_001042674, intron 1 of 7)	12551	NM_019733	19663	Mm.323997	NM_019733	ENSMUSG00000031586	Rbpms	2010300K22Rik|2700019M19Rik|AU017537|RBP-MS|hermes	RNA binding protein gene with multiple splicing	protein-coding
mm_16923.1	chr2	13581641	13581699	-	1	NA	exon (NM_011701, exon 8 of 9)	exon (NM_011701, exon 8 of 9)	7359	NM_011701	22352	Mm.268000	NM_011701	ENSMUSG00000026728	Vim	-	vimentin	protein-coding
mm_17194.1	chr2	25467909	25467927	-	1	NA	exon (NM_008963, exon 5 of 7)	exon (NM_008963, exon 5 of 7)	1831	NM_008963	19215	Mm.1008	NM_008963	ENSMUSG00000015090	Ptgds	21kDa|L-PGDS|PGD2|PGDS|PGDS2|Ptgs3	prostaglandin D2 synthase (brain)	protein-coding
mm_3209.1	chr1	135827273	135827303	+	1	NA	exon (NM_133664, exon 3 of 10)	exon (NM_133664, exon 3 of 10)	8690	NM_133664	16763	Mm.36726	NM_133664	ENSMUSG00000041782	Lad1	-	ladinin	protein-coding
mm_11567.1	chr2	32887390	32887414	+	1	NA	intron (NM_146119, intron 1 of 13)	B1_Mur2|SINE|Alu	11268	NM_146119	227737	Mm.301646	NM_146119	ENSMUSG00000026796	Fam129b	9130404D14Rik	family with sequence similarity 129, member B	protein-coding
mm_143.1	chr1	10998700	10998707	+	1	NA	intron (NM_029525, intron 1 of 39)	(T)n|Simple_repeat|Simple_repeat	5238	NM_029525	109294	Mm.123247	NM_029525	ENSMUSG00000048960	Prex2	6230420N16Rik|AI316880|AI553603|C030045D06Rik|D430013K02|Depdc2|P-Rex2	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	protein-coding
mm_40930.1	chr5	76529304	76529386	+	1	NA	promoter-TSS (NM_027270)	promoter-TSS (NM_027270)	34	NM_001289770	69940	Mm.403233	NM_027270	ENSMUSG00000036435	Exoc1	2810407P21Rik|A730011E05Rik|SEC3|Sec3l1|Sec3p	exocyst complex component 1	protein-coding
mm_102294.1	chr11	55419844	55419855	-	1	NA	5' UTR (NM_009242, exon 1 of 10)	5' UTR (NM_009242, exon 1 of 10)	231	NM_009242	20692	Mm.291442	NM_009242	ENSMUSG00000018593	Sparc	BM-40|ON	secreted acidic cysteine rich glycoprotein	protein-coding
mm_63697.1	chr7	130627835	130627837	+	1	NA	intron (NM_001004468, intron 3 of 21)	intron (NM_001004468, intron 3 of 21)	50352	NM_206856	57752	Mm.86322	NM_021314	ENSMUSG00000030852	Tacc2	mKIAA4180	transforming, acidic coiled-coil containing protein 2	protein-coding
mm_169310.1	chr14	104715948	104715948	-	1	NA	intron (NR_015593, intron 1 of 5)	LSU-rRNA_Hsa|rRNA|rRNA	76801	NR_015593	320249	Mm.320725	NR_015593		D130009I18Rik	-	RIKEN cDNA D130009I18 gene	ncRNA
mm_71671.1	chr8	60674547	60674557	+	1	NA	3' UTR (NM_001177882, exon 3 of 3)	3' UTR (NM_001177882, exon 3 of 3)	18995	NM_001177882	71306	Mm.23242	NM_027756	ENSMUSG00000031647	Mfap3l	4933428A15Rik|5430405D20Rik|AI461995|AW125052|NYD-sp9|mKIAA0626	microfibrillar-associated protein 3-like	protein-coding
mm_73174.1	chr8	95055095	95055126	+	1	NA	promoter-TSS (NM_001042715)	promoter-TSS (NM_001042715)	7	NM_001042715	330830	Mm.277112	NM_001042715	ENSMUSG00000031786	Drc7	Ccdc135|Gm770|SRG-L|SRG-S	dynein regulatory complex subunit 7	protein-coding
mm_87087.1	chr10	31313432	31313442	+	1	NA	promoter-TSS (NM_027168)	promoter-TSS (NM_027168)	32	NM_027168	69692	Mm.245537	NM_027168	ENSMUSG00000000295	Hddc2	2310057G13Rik	HD domain containing 2	protein-coding
mm_132198.1	chr16	32520789	32520816	+	1	NA	Intergenic	Intergenic	24521	NM_199309	245308	Mm.76859	NM_199309	ENSMUSG00000052363	Zdhhc19	Gm1744|Gm616	zinc finger, DHHC domain containing 19	protein-coding
mm_33670.1	chr4	133189137	133189160	+	1	NA	exon (NM_153423, exon 5 of 9)	exon (NM_153423, exon 5 of 9)	-6507	NR_105984	102466215		NR_105984	ENSMUSG00000099202	Mir7017	Gm27945|mmu-mir-7017	microRNA 7017	ncRNA
mm_15873.1	chr2	164835228	164835280	+	1	NA	exon (NM_008906, exon 6 of 15)	exon (NM_008906, exon 6 of 15)	1481	NM_008906	19025	Mm.359633	NM_008906	ENSMUSG00000017760	Ctsa	AU019505|PPCA|Ppgb	cathepsin A	protein-coding
mm_12823.1	chr2	80317355	80317363	+	1	NA	5' UTR (NM_024181, exon 2 of 23)	5' UTR (NM_024181, exon 2 of 23)	1893	NM_024181	66861	Mm.21762	NM_024181	ENSMUSG00000027006	Dnajc10	1200006L06Rik|D2Ertd706e|ERdj5|JPDI	DnaJ heat shock protein family (Hsp40) member C10	protein-coding
mm_16914.1	chr2	13493696	13493705	-	1	NA	Intergenic	Intergenic	-1824	NM_001081084	65969	Mm.313915	NM_001081084	ENSMUSG00000026726	Cubn	AA408369|AL022750|D2Wsu88e	cubilin (intrinsic factor-cobalamin receptor)	protein-coding
mm_161369.1	chr14	64086278	64086278	+	1	NA	promoter-TSS (NM_001081063)	promoter-TSS (NM_001081063)	-2	NM_001347631	100504162	Mm.72752	NM_001193631	ENSMUSG00000052099	Prss51	1700007N14Rik	protease, serine 51	protein-coding
mm_50518.1	chr6	49040870	49040882	+	1	NA	intron (NM_053110, intron 1 of 10)	B3|SINE|B2	4358	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_32583.1	chr4	110817847	110817850	+	1	NA	intron (NM_001048189, intron 3 of 12)	intron (NM_001048189, intron 3 of 12)	420150	NM_030231	78933	Mm.435620	NM_030231	ENSMUSG00000061298	Agbl4	4930578N11Rik|4931433A01Rik	ATP/GTP binding protein-like 4	protein-coding
mm_14116.1	chr2	125866320	125866330	+	1	NA	5' UTR (NM_001291002, exon 1 of 10)	5' UTR (NM_001291002, exon 1 of 10)	102	NM_001291002	69976	Mm.20216	NM_175154	ENSMUSG00000027207	Galk2	2810017M24Rik|AI327030|Gk2	galactokinase 2	protein-coding
mm_28247.1	chr3	88503332	88503350	-	1	NA	promoter-TSS (NM_001111102)	promoter-TSS (NM_001111102)	11	NM_001111102	16905	Mm.243014	NM_019390	ENSMUSG00000028063	Lmna	Dhe	lamin A	protein-coding
mm_2285.1	chr1	91338677	91338687	+	1	NA	intron (NM_001033292, intron 5 of 8)	intron (NM_001033292, intron 5 of 8)	-12391	NM_027551	70788	Mm.68617	NM_027551	ENSMUSG00000026308	Klhl30	4631423F02Rik	kelch-like 30	protein-coding
mm_151061.1	chr19	47229021	47229047	+	1	NA	5' UTR (NM_001163480, exon 1 of 6)	5' UTR (NM_001163480, exon 1 of 6)	191	NM_001163480	18011	Mm.313651	NM_021360	ENSMUSG00000006435	Neurl1a	2410129E16Rik|AI450910|AI481072|Neu1|Neur1|Neurl|Neurl1|Nlz|Rnf67	neuralized E3 ubiquitin protein ligase 1A	protein-coding
mm_75312.1	chr8	41215147	41215168	-	1	NA	promoter-TSS (NM_145594)	promoter-TSS (NM_145594)	-1	NM_145594	234199	Mm.277955	NM_145594	ENSMUSG00000031594	Fgl1	Mfire1	fibrinogen-like protein 1	protein-coding
mm_125036.1	chr15	25758780	25758793	+	1	NA	intron (NM_019472, intron 19 of 40)	intron (NM_019472, intron 19 of 40)	-84512	NM_001034851	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_52813.1	chr6	121343815	121343827	+	1	NA	intron (NM_001347433, intron 1 of 14)	intron (NM_001347433, intron 1 of 14)	745	NM_001347433	14411	Mm.274506	NM_133661	ENSMUSG00000030109	Slc6a12	BGT1|GAT-2|GAT2|Gabt2	solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12	protein-coding
mm_41504.1	chr5	92346641	92346647	+	1	NA	TTS (NM_021274)	TTS (NM_021274)	2245	NM_021274	15945	Mm.877	NM_021274	ENSMUSG00000034855	Cxcl10	C7|CRG-2|INP10|IP-10|IP10|Ifi10|Scyb10|gIP-10|mob-1	chemokine (C-X-C motif) ligand 10	protein-coding
mm_104595.1	chr11	97114534	97114536	-	1	NA	intron (NM_019507, intron 1 of 5)	intron (NM_019507, intron 1 of 5)	796	NM_019507	57765	Mm.94519	NM_019507	ENSMUSG00000001444	Tbx21	TBT1|Tbet|Tblym	T-box 21	protein-coding
mm_13267.1	chr2	98666838	98666870	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	1199197	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_124231.1	chr14	101200315	101200323	-	1	NA	promoter-TSS (NM_029680)	promoter-TSS (NM_029680)	-250	NM_029680	76627	Mm.31415	NM_029680	ENSMUSG00000042888	Prr30	1700110M21Rik	proline rich 30	protein-coding
mm_104906.1	chr11	99644087	99644090	-	1	NA	promoter-TSS (NM_029613)	promoter-TSS (NM_029613)	1	NM_029613	76444	Mm.348022	NM_029613	ENSMUSG00000045109	Krtap4-7	2310037K05Rik|KAP4.7|KRTAP4.7	keratin associated protein 4-7	protein-coding
mm_29479.1	chr3	115712540	115712554	-	1	NA	exon (NM_007901, exon 2 of 2)	exon (NM_007901, exon 2 of 2)	2508	NM_007901	13609	Mm.982	NM_007901	ENSMUSG00000045092	S1pr1	AI849002|Edg1|Lpb1|S1p|S1p1	sphingosine-1-phosphate receptor 1	protein-coding
mm_143156.1	chr17	57223856	57223893	-	1	NA	exon (NM_009778, exon 11 of 41)	exon (NM_009778, exon 11 of 41)	4262	NM_009778	12266	Mm.19131	NM_009778	ENSMUSG00000024164	C3	AI255234|ASP|HSE-MSF|Plp	complement component 3	protein-coding
mm_108517.1	chr12	84042516	84042527	+	1	NA	intron (NM_134247, intron 2 of 2)	intron (NM_134247, intron 2 of 2)	4142	NM_134247	171282	Mm.482217	NM_134247	ENSMUSG00000052392	Acot4	B430212I04Rik|PTE-Ib|Pte1b|Pte2b	acyl-CoA thioesterase 4	protein-coding
mm_25434.1	chr3	107897284	107897313	+	1	NA	exon (NM_010360, exon 4 of 8)	exon (NM_010360, exon 4 of 8)	-1085	NR_015459	329735	Mm.270500	NM_177858	ENSMUSG00000086968	4933431E20Rik	-	RIKEN cDNA 4933431E20 gene	ncRNA
mm_122360.1	chr14	39240186	39240195	-	1	NA	intron (NM_001190187, intron 1 of 9)	intron (NM_001190187, intron 1 of 9)	-232239	NR_131973	432842	Mm.352566	NR_131973		LOC432842	-	uncharacterized LOC432842	ncRNA
mm_99355.1	chr11	101587916	101587964	+	1	NA	intron (NM_144830, intron 5 of 8)	RMER19B|LTR|ERVK	5698	NM_144830	217203	Mm.280559	NM_144830	ENSMUSG00000034947	Tmem106a	0610008L10Rik|AI043106|BC022145	transmembrane protein 106A	protein-coding
mm_96606.1	chr11	69091489	69091498	+	1	NA	3' UTR (NM_009497, exon 5 of 5)	3' UTR (NM_009497, exon 5 of 5)	2965	NM_009497	22318	Mm.28643	NM_009497	ENSMUSG00000020894	Vamp2	Syb-2|Syb2|sybII	vesicle-associated membrane protein 2	protein-coding
mm_78552.1	chr9	35423583	35423589	+	1	NA	Intergenic	Intergenic	-28490	NM_021339	57810	Mm.80509	NM_021339	ENSMUSG00000038119	Cdon	CDO|Cd0|Orcam	cell adhesion molecule-related/down-regulated by oncogenes	protein-coding
mm_73817.1	chr8	117401552	117401585	+	1	NA	intron (NM_028941, intron 3 of 20)	(CA)n|Simple_repeat|Simple_repeat	-51455	NR_106045	102466801		NR_106045	ENSMUSG00000099062	Mir7077	Gm27774|mmu-mir-7077	microRNA 7077	ncRNA
mm_157272.1	chrX	20171439	20171439	-	1	NA	intron (NM_177353, intron 5 of 16)	MLT1J2|LTR|ERVL-MaLR	111869	NM_021715	60322	Mm.44827	NM_021715	ENSMUSG00000037347	Chst7	2600013M07Rik|C6ST-2|GST5|Gn6st-4|glcNAc6ST-4	carbohydrate (N-acetylglucosamino) sulfotransferase 7	protein-coding
mm_12352.1	chr2	69749480	69749494	+	1	NA	exon (NM_001081086, exon 14 of 14)	exon (NM_001081086, exon 14 of 14)	26399	NM_001081086	228005	Mm.11815	NM_001081086	ENSMUSG00000042133	Ppig	AU019516|AU022200|B230312B02Rik|CYP|SRCyp	peptidyl-prolyl isomerase G (cyclophilin G)	protein-coding
mm_147623.1	chr18	58072845	58072852	-	1	NA	intron (NM_010181, intron 25 of 64)	intron (NM_010181, intron 25 of 64)	137078	NM_010181	14119	Mm.20271	NM_010181	ENSMUSG00000024598	Fbn2	BC063774|Fib-2|mKIAA4226|sne|sy	fibrillin 2	protein-coding
mm_114565.1	chr13	74609226	74609237	+	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	-30641	NM_030711	80898	Mm.83526	NM_030711	ENSMUSG00000021583	Erap1	Arts1|ERAAP|PILSA|PILSAP	endoplasmic reticulum aminopeptidase 1	protein-coding
mm_111488.1	chr12	98901312	98901322	-	1	NA	5' UTR (NM_001081191, exon 1 of 44)	5' UTR (NM_001081191, exon 1 of 44)	167	NM_001081191	319670	Mm.390484	NM_001081191	ENSMUSG00000051166	Eml5	BC027154|C130068M19Rik	echinoderm microtubule associated protein like 5	protein-coding
mm_144784.1	chr18	35854718	35854732	+	1	NA	intron (NM_133687, intron 1 of 2)	intron (NM_133687, intron 1 of 2)	24907	NM_133687	67393	Mm.94560	NM_133687	ENSMUSG00000046668	Cxxc5	4930415K17Rik	CXXC finger 5	protein-coding
mm_4660.1	chr1	180364650	180364657	+	1	NA	intron (NM_001081175, intron 2 of 7)	intron (NM_001081175, intron 2 of 7)	-34104	NR_003623	277333	Mm.389223	NM_199472		Gm5069	EG277333	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_126609.1	chr15	82899040	82899058	+	1	NA	promoter-TSS (NR_027799)	promoter-TSS (NR_027799)	-31	NR_045068	100504637	Mm.440928	NR_045068	ENSMUSG00000100199	Gm20324	-	predicted gene, 20324	ncRNA
mm_63308.1	chr7	126861948	126861986	+	1	NA	promoter-TSS (NM_153580)	promoter-TSS (NM_153580)	-5	NM_172746	233876	Mm.363427	NM_172746	ENSMUSG00000042606	Hirip3	B130036O03|C86302	HIRA interacting protein 3	protein-coding
mm_95103.1	chr11	34047647	34047657	+	1	NA	intron (NM_010696, intron 1 of 20)	intron (NM_010696, intron 1 of 20)	451	NM_010696	16822	Mm.265350	NM_010696	ENSMUSG00000002699	Lcp2	AI323664|BB161688|SLP-76|SLP76|m1Khoe|twm	lymphocyte cytosolic protein 2	protein-coding
mm_157532.1	chrX	51018718	51018746	-	1	NA	promoter-TSS (NM_172413)	promoter-TSS (NM_172413)	-714	NM_172413	72065	Mm.43152	NM_172413	ENSMUSG00000050029	Rap2c	2010200P20Rik|AI194294|AL022976	RAP2C, member of RAS oncogene family	protein-coding
mm_8453.1	chr1	153127133	153127156	-	1	NA	exon (NM_008485, exon 22 of 24)	exon (NM_008485, exon 22 of 24)	59303	NM_008485	16782	Mm.329272	NM_008485	ENSMUSG00000026479	Lamc2	AA589349	laminin, gamma 2	protein-coding
mm_74483.1	chr8	4325097	4325110	-	1	NA	promoter-TSS (NM_010485)	promoter-TSS (NM_010485)	-3	NM_010485	15568	Mm.119162	NM_010485	ENSMUSG00000040028	Elavl1	2410055N02Rik|HUR|Hua|W91709	ELAV (embryonic lethal, abnormal vision)-like 1 (Hu antigen R)	protein-coding
mm_152154.1	chr19	7241148	7241160	-	1	NA	promoter-TSS (NM_027643)	promoter-TSS (NM_027643)	68	NM_027643	70999	Mm.329605	NM_027643	ENSMUSG00000024764	Naa40	4931433E08Rik|AU023197|Nat11	N(alpha)-acetyltransferase 40, NatD catalytic subunit	protein-coding
mm_16440.1	chr2	180397342	180397355	+	1	NA	intron (NR_045331, intron 3 of 3)	RLTR20C1_MM|LTR|ERVK	-1031	NR_029901	723954		NR_029901	ENSMUSG00000065460	Mir133a-2	Mirn133a-2|mir-133a-2	microRNA 133a-2	ncRNA
mm_5362.1	chr1	25829780	25829812	-	1	NA	promoter-TSS (NM_175642)	promoter-TSS (NM_175642)	-89	NM_175642	210933	Mm.336569	NM_175642	ENSMUSG00000033569	Adgrb3	A830096D10Rik|Bai3	adhesion G protein-coupled receptor B3	protein-coding
mm_71851.1	chr8	68906077	68906087	+	1	NA	3' UTR (NM_008509, exon 10 of 10)	3' UTR (NM_008509, exon 10 of 10)	25527	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_137025.1	chr17	17873740	17873745	+	1	NA	Intergenic	Lx8b|LINE|L1	10197	NM_013521	14293	Mm.56951	NM_013521	ENSMUSG00000045551	Fpr1	FPR|LXA4R|fMLF-R	formyl peptide receptor 1	protein-coding
mm_49784.1	chr6	35177815	35177826	+	1	NA	intron (NM_027513, intron 1 of 42)	CpG	204	NM_027513	70699	Mm.261208	NM_027513	ENSMUSG00000038759	Nup205	3830404O05Rik|AV248391|mKIAA0225	nucleoporin 205	protein-coding
mm_143861.1	chr17	84186272	84186341	-	1	NA	exon (NM_001001806, exon 2 of 2)	exon (NM_001001806, exon 2 of 2)	1641	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_82173.1	chr9	123851039	123851073	+	1	NA	intron (NM_148925, intron 1 of 18)	intron (NM_148925, intron 1 of 18)	605	NM_148925	17281	Mm.252941	NM_148925	ENSMUSG00000025241	Fyco1	2810409M01Rik|Mem2|RUFY3|ZFYVE7	FYVE and coiled-coil domain containing 1	protein-coding
mm_77501.1	chr8	122678131	122678182	-	1	NA	promoter-TSS (NM_001109873)	promoter-TSS (NM_001109873)	19	NM_001109873	12398	Mm.194339	NM_009824	ENSMUSG00000006362	Cbfa2t3	A630044F12Rik|AI465270|AW229127|Cbfa2t3h|ETO-2|Eto2|MTGR2	core-binding factor, runt domain, alpha subunit 2, translocated to, 3 (human)	protein-coding
mm_150465.1	chr19	38395801	38395817	+	1	NA	promoter-TSS (NM_175507)	promoter-TSS (NM_175507)	-171	NM_175507	240660	Mm.262085	NM_175507	ENSMUSG00000044026	Slc35g1	AA590464|D330039I19Rik|Tmem20	solute carrier family 35, member G1	protein-coding
mm_6383.1	chr1	72806082	72806086	-	1	NA	Intergenic	Intergenic	-18396	NM_008342	16008	Mm.141936	NM_008342	ENSMUSG00000039323	Igfbp2	AI255832|IBP-2|Igfbp-2|mIGFBP-2	insulin-like growth factor binding protein 2	protein-coding
mm_81029.1	chr9	104569634	104569665	+	1	NA	promoter-TSS (NM_028719)	promoter-TSS (NM_028719)	-139	NM_028719	74020	Mm.326240	NM_028719	ENSMUSG00000032564	Cpne4	3632411M23Rik|4933406O10Rik	copine IV	protein-coding
mm_19326.1	chr2	90572204	90572215	-	1	NA	intron (NM_008982, intron 1 of 23)	intron (NM_008982, intron 1 of 23)	8438	NM_008982	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_122060.1	chr14	30353575	30353603	-	1	NA	promoter-TSS (NM_001083616)	promoter-TSS (NM_001083616)	-103	NM_001083616	12289	Mm.9772	NM_028981	ENSMUSG00000015968	Cacna1d	8430418G19Rik|C79217|Cach3|Cacn4|Cacnl1a2|Cav1.3|Cchl1a|Cchl1a2|D-LTCC	calcium channel, voltage-dependent, L type, alpha 1D subunit	protein-coding
mm_37440.1	chr4	123139930	123139960	-	1	NA	promoter-TSS (NM_019489)	promoter-TSS (NM_019489)	-4	NM_019489	56031	Mm.126873	NM_019489	ENSMUSG00000028651	Ppie	2010010D16Rik|Cyp33	peptidylprolyl isomerase E (cyclophilin E)	protein-coding
mm_16444.1	chr2	180443044	180443064	+	1	NA	Intergenic	Intergenic	-17924	NM_148933	108115	Mm.133687	NM_148933	ENSMUSG00000038963	Slco4a1	OATP-E|Slc21a12	solute carrier organic anion transporter family, member 4a1	protein-coding
mm_141792.1	chr17	34342951	34342977	-	1	NA	exon (NM_010381, exon 3 of 4)	exon (NM_010381, exon 3 of 4)	1681	NM_010381	100504404	Mm.15680	NM_010381		H2-Ea-ps	AI323765|E-alpha-f|H-2Ea|H2-Ea|I-Ealpha|Ia-3|Ia3|MHC-H2-Ea	histocompatibility 2, class II antigen E alpha, pseudogene	protein-coding
mm_93600.1	chr10	117215844	117215852	-	1	NA	intron (NM_026570, intron 6 of 6)	intron (NM_026570, intron 6 of 6)	8659	NM_026570	64050	Mm.233529	NM_026570	ENSMUSG00000020171	Yeats4	4930573H17Rik|B230215M10Rik|GAS41|NuBI-1	YEATS domain containing 4	protein-coding
mm_90712.1	chr10	4387437	4387479	-	1	NA	intron (NM_001033466, intron 1 of 2)	CpG	650	NM_001033466	381990	Mm.262466	NM_001033466	ENSMUSG00000075327	Zbtb2	Gm1103	zinc finger and BTB domain containing 2	protein-coding
mm_25690.1	chr3	122245911	122245921	+	1	NA	5' UTR (NM_008129, exon 1 of 7)	5' UTR (NM_008129, exon 1 of 7)	359	NM_008129	14630	Mm.292676	NM_008129	ENSMUSG00000028124	Gclm	AI649393|Gcmc|Glclr	glutamate-cysteine ligase, modifier subunit	protein-coding
mm_105770.1	chr11	109676131	109676147	-	1	NA	intron (NM_153782, intron 7 of 10)	intron (NM_153782, intron 7 of 10)	25218	NM_001313976	19084	Mm.30039	NM_021880	ENSMUSG00000020612	Prkar1a	1300018C22Rik|RIalpha|Tse-1|Tse1	protein kinase, cAMP dependent regulatory, type I, alpha	protein-coding
mm_153090.1	chr19	32389903	32389909	-	1	NA	non-coding (NR_033198, exon 2 of 2)	non-coding (NR_033198, exon 2 of 2)	690	NR_033198	67188	Mm.391160	NR_033198	ENSMUSG00000097787	2700046G09Rik	-	RIKEN cDNA 2700046G09 gene	ncRNA
mm_41407.1	chr5	90786667	90786680	+	1	NA	intron (NM_203320, intron 3 of 3)	intron (NM_203320, intron 3 of 3)	572	NM_203320	330122	Mm.244289	NM_203320	ENSMUSG00000029379	Cxcl3	Dcip1|Gm1960	chemokine (C-X-C motif) ligand 3	protein-coding
mm_12291.1	chr2	69035889	69035907	+	1	NA	intron (NM_172856, intron 4 of 9)	intron (NM_172856, intron 4 of 9)	-99902	NM_181547	329416	Mm.90047	NM_181547	ENSMUSG00000034738	Nostrin	Daip2|mDaIP2	nitric oxide synthase trafficker	protein-coding
mm_124071.1	chr14	78583943	78583983	-	1	NA	intron (NM_001081336, intron 25 of 28)	MTD|LTR|ERVL-MaLR	45327	NM_001253766	380921	Mm.89591	NM_001081336	ENSMUSG00000034731	Dgkh	5930402B05Rik|D130015C16|DGK	diacylglycerol kinase, eta	protein-coding
mm_15391.1	chr2	156721086	156721094	+	1	NA	promoter-TSS (NM_001042487)	promoter-TSS (NM_001042487)	125	NM_001042488	228836	Mm.22094	NM_146128	ENSMUSG00000061689	Dlgap4	AI225853|BC024558|DAP-4|DAP4|SAPAP-4|Sapap4|WBP16	discs, large homolog-associated protein 4 (Drosophila)	protein-coding
mm_171876.1	chr5	31206154	31206159	-	1	NA	exon (NM_008014, exon 5 of 10)	exon (NM_008014, exon 5 of 10)	-3853	NM_175311	101023	Mm.45033	NM_175311	ENSMUSG00000043059	Zfp513	AW990386|D430028M17Rik|Znf513	zinc finger protein 513	protein-coding
mm_120280.1	chr14	63130929	63130945	+	1	NA	intron (NM_007798, intron 1 of 9)	intron (NM_007798, intron 1 of 9)	8475	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_112563.1	chr13	13490109	13490125	+	1	NA	exon (NM_010917, exon 12 of 20)	exon (NM_010917, exon 12 of 20)	52515	NM_010917	18073	Mm.4691	NM_010917	ENSMUSG00000005397	Nid1	A630025O17|Nid|entactin|entactin-1|nidogen-1	nidogen 1	protein-coding
mm_63024.1	chr7	121034783	121034793	+	1	NA	5' UTR (NM_021554, exon 1 of 5)	5' UTR (NM_021554, exon 1 of 5)	343	NM_021554	59052	Mm.29122	NM_021554	ENSMUSG00000030876	Mettl9	0610012D09Rik|AA517660|Drev|MNCb-5680	methyltransferase like 9	protein-coding
mm_142304.1	chr17	42742053	42742085	-	1	NA	5' UTR (NM_001033493, exon 1 of 6)	5' UTR (NM_001033493, exon 1 of 6)	110	NM_001033493	435529	Mm.136350	NM_001033493	ENSMUSG00000057899	Adgrf2	Gpr111|PGR20	adhesion G protein-coupled receptor F2	protein-coding
mm_65115.1	chr7	19327237	19327263	-	1	NA	Intergenic	Intergenic	-17205	NM_001347586	14282	Mm.248335	NM_008036	ENSMUSG00000003545	Fosb	-	FBJ osteosarcoma oncogene B	protein-coding
mm_37770.1	chr4	129810909	129810919	-	1	NA	Intergenic	CpG	-9565	NM_008974	19244	Mm.193688	NM_008974	ENSMUSG00000028788	Ptp4a2	Prl-2	protein tyrosine phosphatase 4a2	protein-coding
mm_124561.1	chr14	123626842	123626888	-	1	NA	5' UTR (NM_177393, exon 1 of 44)	5' UTR (NM_177393, exon 1 of 44)	279	NM_177393	338370	Mm.255348	NM_177393	ENSMUSG00000000197	Nalcn	A530023G15Rik|AI849508|Vgcnl1	sodium leak channel, non-selective	protein-coding
mm_138067.1	chr17	33936615	33936618	+	1	NA	intron (NM_009059, intron 16 of 17)	intron (NM_009059, intron 16 of 17)	3714	NM_001185182	14976	Mm.2948	NM_010385	ENSMUSG00000024309	Pfdn6	H-2Ke2|H2-Ke2|Ke-2	prefoldin subunit 6	protein-coding
mm_154055.1	chr19	55103342	55103349	-	1	NA	Intergenic	Intergenic	-3898	NM_008149	14732	Mm.210196	NM_008149	ENSMUSG00000024978	Gpam	GPAT|GPAT1	glycerol-3-phosphate acyltransferase, mitochondrial	protein-coding
mm_142300.1	chr17	42692212	42692238	-	1	NA	promoter-TSS (NM_001289499)	promoter-TSS (NM_001289499)	59	NM_001289501	78249	Mm.66217	NM_030067	ENSMUSG00000023918	Adgrf4	4632435A09Rik|AV239010|Gpr115	adhesion G protein-coupled receptor F4	protein-coding
mm_85039.1	chr9	88731719	88731759	-	1	NA	5' UTR (NM_007536, exon 1 of 2)	5' UTR (NM_007536, exon 1 of 2)	111	NM_007536	12047	Mm.378888	NM_007536	ENSMUSG00000099974	Bcl2a1d	A1-d	B cell leukemia/lymphoma 2 related protein A1d	protein-coding
mm_75981.1	chr8	72284937	72284945	-	1	NA	Intergenic	B4A|SINE|B4	-34121	NM_008452	16598	Mm.26938	NM_008452	ENSMUSG00000055148	Klf2	Lklf	Kruppel-like factor 2 (lung)	protein-coding
mm_137222.1	chr17	24172047	24172076	+	1	NA	Intergenic	Intergenic	-2632	NM_009729	11984	Mm.30155	NM_009729	ENSMUSG00000024121	Atp6v0c	Atp6c|Atp6c2|Atp6l|Atpl|Atpl-rs1|PL16|VATL|Vma3	ATPase, H+ transporting, lysosomal V0 subunit C	protein-coding
mm_90051.1	chr10	116143911	116143922	+	1	NA	promoter-TSS (NM_001161837)	promoter-TSS (NM_001161837)	18	NM_001161837	19279	Mm.336316	NM_011217	ENSMUSG00000020151	Ptprr	Gmcp1|PTP-SL|PTPBR7|RPTPRR|mPTP213	protein tyrosine phosphatase, receptor type, R	protein-coding
mm_75606.1	chr8	61877561	61877591	-	1	NA	exon (NM_001293772, exon 2 of 22)	exon (NM_001293772, exon 2 of 22)	25114	NM_001081390	72333	Mm.29933	NM_001081390	ENSMUSG00000058056	Palld	2410003B16Rik|6030492A02	palladin, cytoskeletal associated protein	protein-coding
mm_31534.1	chr4	55356500	55356534	+	1	NA	intron (NM_009011, intron 1 of 9)	ORR1D2|LTR|ERVL-MaLR	6475	NM_009011	19359	Mm.196846	NM_009011	ENSMUSG00000028426	Rad23b	0610007D13Rik|AV001138|HR23B|mHR23B|p58	RAD23 homolog B, nucleotide excision repair protein	protein-coding
mm_3806.1	chr1	158362262	158362296	+	1	NA	promoter-TSS (NM_001205204)	promoter-TSS (NM_001205204)	-25	NM_007495	11899	Mm.329586	NM_007495	ENSMUSG00000026587	Astn1	Astn|GC14|mKIAA0289	astrotactin 1	protein-coding
mm_37159.1	chr4	117131495	117131498	-	1	NA	exon (NM_013807, exon 8 of 15)	exon (NM_013807, exon 8 of 15)	2467	NM_013807	12795	Mm.259022	NM_013807	ENSMUSG00000028680	Plk3	Cnk|Fnk|PLK-3|PRK	polo-like kinase 3	protein-coding
mm_158549.1	chrX	145505166	145505172	-	1	NA	Intergenic	Intergenic	-17530	NM_153319	27494	Mm.100068	NM_153319	ENSMUSG00000041688	Amot	CAG-2|D0Kist1|Sii6	angiomotin	protein-coding
mm_75363.1	chr8	45294781	45294795	-	1	NA	promoter-TSS (NM_008455)	promoter-TSS (NM_008455)	47	NM_008455	16621	Mm.482691	NM_008455	ENSMUSG00000109764	Klkb1	APS|Kal-3|Kal3|Klk3|PSA	kallikrein B, plasma 1	protein-coding
mm_147190.1	chr18	37642180	37642182	-	1	NA	3' UTR (NM_175770, exon 2 of 2)	3' UTR (NM_175770, exon 2 of 2)	2023	NM_175770	24074	Mm.236009	NM_175770	ENSMUSG00000051316	Taf7	55kDa|AI607308|BB007175|TAFII55|Taf2f	TATA-box binding protein associated factor 7	protein-coding
mm_30647.1	chr4	8838990	8839003	+	1	NA	intron (NM_001277149, intron 16 of 37)	B1_Mur4|SINE|Alu	148590	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_151385.1	chr19	56362822	56362824	+	1	NA	intron (NM_001286552, intron 16 of 39)	intron (NM_001286552, intron 16 of 39)	27215	NM_198059	18175	Mm.386769	NM_008733	ENSMUSG00000049134	Nrap	-	nebulin-related anchoring protein	protein-coding
mm_134528.1	chr16	19236899	19236907	-	1	NA	Intergenic	RMER17B|LTR|ERVK	49838	NM_146451	258443	Mm.377506	NM_146451	ENSMUSG00000050742	Olfr164	MOR279-2	olfactory receptor 164	protein-coding
mm_37737.1	chr4	129575389	129575401	-	1	NA	Intergenic	Intergenic	-1754	NM_001162433	16818	Mm.293753	NM_010693	ENSMUSG00000000409	Lck	Hck-3|Lsk|Lskt|p56<lck>|p56Lck	lymphocyte protein tyrosine kinase	protein-coding
mm_157979.1	chrX	94123088	94123159	-	1	NA	5' UTR (NM_011768, exon 1 of 8)	5' UTR (NM_011768, exon 1 of 8)	284	NM_011768	22764	Mm.919	NM_011768	ENSMUSG00000079509	Zfx	Zfx5|Zfx5,6|Zfx6	zinc finger protein X-linked	protein-coding
mm_15988.1	chr2	166937375	166937389	+	1	NA	exon (NM_023565, exon 17 of 25)	exon (NM_023565, exon 17 of 25)	27335	NR_111895	20853	Mm.73276	NM_011490	ENSMUSG00000039536	Stau1	5830401L18Rik|AW549911|C85792|Stau	staufen (RNA binding protein) homolog 1 (Drosophila)	protein-coding
mm_63806.1	chr7	133637550	133637559	+	1	NA	promoter-TSS (NM_178115)	promoter-TSS (NM_178115)	-121	NM_178115	214764	Mm.174044	NM_145995	ENSMUSG00000039990	Edrf1	2700050L05Rik|AU022667|AW558805	erythroid differentiation regulatory factor 1	protein-coding
mm_100036.1	chr11	114983028	114983042	+	1	NA	3' UTR (NM_145437, exon 4 of 4)	3' UTR (NM_145437, exon 4 of 4)	6851	NM_145437	217305	Mm.275986	NM_145437	ENSMUSG00000034641	Cd300ld	4732429D16Rik|CLM5|Cd300ld1|LMIR4|MAIR-IV|clm-5	CD300 molecule like family member d	protein-coding
mm_157340.1	chrX	36902827	36902833	-	1	NA	promoter-TSS (NM_029891)	promoter-TSS (NM_029891)	69	NM_029891	77286	Mm.21649	NM_029891	ENSMUSG00000044149	Nkrf	9430034D17Rik|AW124770|C80287	NF-kappaB repressing factor	protein-coding
mm_26643.1	chr3	153844236	153844270	+	1	NA	promoter-TSS (NM_025758)	promoter-TSS (NM_025758)	6	NM_025758	66772	Mm.116960	NM_025758	ENSMUSG00000038997	Asb17	4933436O18Rik	ankyrin repeat and SOCS box-containing 17	protein-coding
mm_149417.1	chr19	11426427	11426440	+	1	NA	3' UTR (NM_029499, exon 7 of 7)	3' UTR (NM_029499, exon 7 of 7)	-17125	NM_021718	60361	Mm.33957	NM_021718	ENSMUSG00000056290	Ms4a4b	AI463180|Chandra|Ly116	membrane-spanning 4-domains, subfamily A, member 4B	protein-coding
mm_118768.1	chr14	22547354	22547359	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	-4558	NR_046307	74896	Mm.444661	NR_046307		4930405A10Rik	4930456G20Rik	RIKEN cDNA 4930405A10 gene	ncRNA
mm_39104.1	chr4	154921678	154921693	-	1	NA	TTS (NM_178931)	TTS (NM_178931)	6392	NM_178931	230979	Mm.215147	NM_178931	ENSMUSG00000042333	Tnfrsf14	Atar|HveA|Hvem|Tnfrs14	tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)	protein-coding
mm_154254.1	chr19	60766835	60766847	-	1	NA	exon (NM_010123, exon 19 of 22)	exon (NM_010123, exon 19 of 22)	7544	NR_034047	100217439		NR_034047		Snora19	MBI-51	small nucleolar RNA, H/ACA box 19	snoRNA
mm_37146.1	chr4	116994355	116994372	-	1	NA	promoter-TSS (NM_009478)	promoter-TSS (NM_009478)	50	NM_009478	22275	Mm.46484	NM_009478	ENSMUSG00000028684	Urod	AI323803|UPD|Uro-d	uroporphyrinogen decarboxylase	protein-coding
mm_133705.1	chr16	93144329	93144340	+	1	NA	Intergenic	L1MD3|LINE|L1	208855	NR_040486	69857	Mm.81192	NR_040486	ENSMUSG00000100277	1810053B23Rik	1810008L18Rik|1810056K14Rik	RIKEN cDNA 1810053B23 gene	ncRNA
mm_105245.1	chr11	102349405	102349414	-	1	NA	3' UTR (NM_011403, exon 20 of 20)	3' UTR (NM_011403, exon 20 of 20)	15872	NM_011403	20533	Mm.7248	NM_011403	ENSMUSG00000006574	Slc4a1	Ae1|CD233|Empb3|l11Jus51	solute carrier family 4 (anion exchanger), member 1	protein-coding
mm_66931.1	chr7	61530180	61530188	-	1	NA	non-coding (NR_045727, exon 5 of 5)	non-coding (NR_045727, exon 5 of 5)	85143	NR_045727	319752	Mm.294476	NR_045727		B230209E15Rik	-	RIKEN cDNA B230209E15 gene	ncRNA
mm_136668.1	chr17	6106809	6106819	+	1	NA	promoter-TSS (NM_001103181)	promoter-TSS (NM_001103181)	-16	NM_001103181	68842	Mm.449307	NM_054040	ENSMUSG00000034377	Tulp4	1110057P05Rik|2210038L17Rik|Tusp	tubby like protein 4	protein-coding
mm_2235.1	chr1	91044487	91044498	+	1	NA	intron (NM_001111312, intron 1 of 12)	intron (NM_001111312, intron 1 of 12)	-8952	NM_001310732	16978	Mm.45039	NM_008515	ENSMUSG00000026305	Lrrfip1	AU024550|Fliiap1	leucine rich repeat (in FLII) interacting protein 1	protein-coding
mm_70231.1	chr7	145289016	145289026	-	1	NA	Intergenic	Intergenic	-5010	NR_132642	233979	Mm.102235	NM_146206	ENSMUSG00000048677	Tpcn2	D830047E22Rik|Gm35086	two pore segment channel 2	protein-coding
mm_82207.1	chr9	124103611	124103624	+	1	NA	intron (NM_009915, intron 1 of 2)	intron (NM_009915, intron 1 of 2)	1434	NM_009915	12772	Mm.6272	NM_009915	ENSMUSG00000049103	Ccr2	Cc-ckr-2|Ccr2a|Ccr2b|Ckr2|Ckr2a|Ckr2b|Cmkbr2|mJe-r	chemokine (C-C motif) receptor 2	protein-coding
mm_63443.1	chr7	127483109	127483138	+	1	NA	Intergenic	Intergenic	-2098	NM_010183	14123	Mm.323505	NM_010183	ENSMUSG00000042423	Fbrs	Fbs|Fbs1	fibrosin	protein-coding
mm_115185.1	chr13	108449915	108449965	+	1	NA	Intergenic	Intergenic	133603	NM_178683	218581	Mm.32318	NM_178683	ENSMUSG00000021697	Depdc1b	9830132O03|AW260467|XTP1	DEP domain containing 1B	protein-coding
mm_59746.1	chr7	28818751	28818763	+	1	NA	exon (NM_177301, exon 8 of 13)	exon (NM_177301, exon 8 of 13)	-6581	NM_016772	51798	Mm.291776	NM_016772	ENSMUSG00000053898	Ech1	AA617331	enoyl coenzyme A hydratase 1, peroxisomal	protein-coding
mm_42445.1	chr5	115431360	115431382	+	1	NA	intron (NM_008629, intron 4 of 14)	intron (NM_008629, intron 4 of 14)	1686	NM_008629	17690	Mm.5077	NM_008629	ENSMUSG00000054256	Msi1	Msi1h|Musahi1|m-Msi-1	musashi RNA-binding protein 1	protein-coding
mm_140420.1	chr17	87825918	87825925	+	1	NA	Intergenic	RMER17B|LTR|ERVK	-27927	NM_199251	210741	Mm.312046	NM_199251	ENSMUSG00000050138	Kcnk12	mntk1	potassium channel, subfamily K, member 12	protein-coding
mm_169750.1	chr15	89355635	89355641	-	1	NA	promoter-TSS (NM_001271601)	promoter-TSS (NM_001271601)	21	NM_178919	105847	Mm.34511	NM_178919	ENSMUSG00000022614	Lmf2	AI451006|Tmem112b|Tmem153	lipase maturation factor 2	protein-coding
mm_107602.1	chr12	49384126	49384157	+	1	NA	5' UTR (NM_001160112, exon 1 of 1)	5' UTR (NM_001160112, exon 1 of 1)	1134	NM_008241	15228	Mm.4704	NM_008241	ENSMUSG00000020950	Foxg1	2900064B05Rik|BF-1|Bf1|Hfh9|Hfhbf1	forkhead box G1	protein-coding
mm_103858.1	chr11	83286744	83286752	-	1	NA	promoter-TSS (NM_001166028)	promoter-TSS (NM_001166028)	-22	NM_001166028	237890	Mm.297670	NM_001166028	ENSMUSG00000082101	Slfn14	Gm20|Slfn14-ps	schlafen 14	protein-coding
mm_15478.1	chr2	157560813	157560828	+	1	NA	intron (NM_001291128, intron 2 of 2)	intron (NM_001291128, intron 2 of 2)	742	NM_180960	18111	Mm.34330	NM_010923	ENSMUSG00000067786	Nnat	5730414I02Rik|AW107673|Peg5	neuronatin	protein-coding
mm_145624.1	chr18	61109636	61109642	+	1	NA	exon (NM_001037859, exon 3 of 22)	exon (NM_001037859, exon 3 of 22)	4067	NM_001037859	12978	Mm.22574	NM_007779	ENSMUSG00000024621	Csf1r	AI323359|CD115|CSF-1R|Csfmr|Fim-2|Fim2|Fms|M-CSF-R|M-CSFR	colony stimulating factor 1 receptor	protein-coding
mm_13420.1	chr2	104493769	104493784	+	1	NA	intron (NM_010434, intron 1 of 15)	CpG	713	NM_010434	15259	Mm.257925	NM_010434	ENSMUSG00000027177	Hipk3	DYRK6|FIST3|PKY|mir-1902	homeodomain interacting protein kinase 3	protein-coding
mm_1138.1	chr1	60703914	60703920	+	1	NA	Intergenic	Intergenic	-42471	NM_007642	12487	Mm.255003	NM_007642	ENSMUSG00000026012	Cd28	-	CD28 antigen	protein-coding
mm_88835.1	chr10	80826368	80826381	+	1	NA	promoter-TSS (NR_027656)	promoter-TSS (NR_027656)	-282	NM_001301034	18245	Mm.398119	NM_008753	ENSMUSG00000035242	Oaz1	AZ-1|AZ1|Antizyme|ODC-Az|Oaz	ornithine decarboxylase antizyme 1	protein-coding
mm_145530.1	chr18	60774627	60774663	+	1	NA	promoter-TSS (NM_020600)	promoter-TSS (NM_020600)	49	NM_020600	20044	Mm.43778	NM_020600	ENSMUSG00000024608	Rps14	2600014J02Rik|AL023078	ribosomal protein S14	protein-coding
mm_113334.1	chr13	31625729	31625744	+	1	NA	promoter-TSS (NM_010225)	promoter-TSS (NM_010225)	-80	NM_010225	14238	Mm.125548	NM_010225	ENSMUSG00000038402	Foxf2	FREAC2|Fkh20|LUN	forkhead box F2	protein-coding
mm_31446.1	chr4	48585277	48585328	+	1	NA	5' UTR (NM_021436, exon 1 of 10)	5' UTR (NM_021436, exon 1 of 10)	109	NM_021436	230157	Mm.422686	NM_021436	ENSMUSG00000028347	Tmeff1	A830033E11|M7365|Tr1	transmembrane protein with EGF-like and two follistatin-like domains 1	protein-coding
mm_154006.1	chr19	53038657	53038666	-	1	NA	promoter-TSS (NM_133216)	promoter-TSS (NM_133216)	-7	NM_133216	170750	Mm.99776	NM_133216	ENSMUSG00000025027	Xpnpep1	D230045I08Rik|sAMP	X-prolyl aminopeptidase (aminopeptidase P) 1, soluble	protein-coding
mm_169900.1	chr16	52083731	52083737	+	1	NA	intron (NM_001033238, intron 3 of 17)	intron (NM_001033238, intron 3 of 17)	52185	NM_001033238	208650	Mm.328206	NM_001033238	ENSMUSG00000022637	Cblb	AI429560|AI851073|Cbl-b	Casitas B-lineage lymphoma b	protein-coding
mm_128720.1	chr15	64022990	64022993	-	1	NA	intron (NM_144846, intron 1 of 11)	B1_Mur2|SINE|Alu	37457	NM_144846	223601	Mm.246108	NM_144846	ENSMUSG00000022378	Fam49b	0910001A06Rik|AW122079	family with sequence similarity 49, member B	protein-coding
mm_47520.1	chr5	124111786	124111795	-	1	NA	promoter-TSS (NM_001347478)	promoter-TSS (NM_001347478)	-510	NM_001347478	66627	Mm.7050	NM_025671	ENSMUSG00000023707	Ogfod2	1300006G11Rik|5730405M13Rik|AU041636|AW552395	2-oxoglutarate and iron-dependent oxygenase domain containing 2	protein-coding
mm_54739.1	chr6	40999480	40999498	-	1	NA	promoter-TSS (NM_001102660)	promoter-TSS (NM_001102660)	-10	NM_001102660	100040208	Mm.333011	NM_001102660	ENSMUSG00000096525	Gm2663	-	predicted gene 2663	protein-coding
mm_46101.1	chr5	92347513	92347520	-	1	NA	intron (NM_021274, intron 3 of 3)	intron (NM_021274, intron 3 of 3)	1373	NM_021274	15945	Mm.877	NM_021274	ENSMUSG00000034855	Cxcl10	C7|CRG-2|INP10|IP-10|IP10|Ifi10|Scyb10|gIP-10|mob-1	chemokine (C-X-C motif) ligand 10	protein-coding
mm_49445.1	chr6	29323289	29323333	+	1	NA	intron (NM_207258, intron 2 of 6)	intron (NM_207258, intron 2 of 6)	4171	NM_001289664	330277	Mm.87624	NM_207258	ENSMUSG00000039742	Fam71f1	GARI-L1|Gm764|NYD-SP18	family with sequence similarity 71, member F1	protein-coding
mm_159757.1	chr5	88887197	88887197	+	1	NA	promoter-TSS (NM_001136260)	promoter-TSS (NM_001136260)	-63	NM_001197147	54403	Mm.41044	NM_018760	ENSMUSG00000060961	Slc4a4	AI835705|NBC|NBC1	solute carrier family 4 (anion exchanger), member 4	protein-coding
mm_166254.1	chr5	86926509	86926520	-	1	NA	promoter-TSS (NM_152811)	promoter-TSS (NM_152811)	-11	NM_152811	71773	Mm.26741	NM_152811	ENSMUSG00000035836	Ugt2b1	1300012D20Rik	UDP glucuronosyltransferase 2 family, polypeptide B1	protein-coding
mm_26682.1	chr3	156561793	156561869	+	1	NA	promoter-TSS (NM_001039094)	promoter-TSS (NM_001039094)	37	NM_001039094	320840	Mm.317293	NM_177274	ENSMUSG00000040037	Negr1	5330422G01Rik|KILON|Ntra	neuronal growth regulator 1	protein-coding
mm_85495.1	chr9	106136366	106136373	-	1	NA	Intergenic	Intergenic	-17755	NR_029549	387153		NR_029549	ENSMUSG00000065407	Mir135a-1	Mir135a01|Mirn135|Mirn135a-1|mir-135a-1	microRNA 135a-1	ncRNA
mm_126008.1	chr15	76539039	76539057	+	1	NA	promoter-TSS (NM_013909)	promoter-TSS (NM_013909)	105	NM_029643	52710	Mm.28597	NM_029643	ENSMUSG00000022560	Slc52a2	2010003P03Rik|D15Ertd747e|GPCR42|Gpr172b|PAR2|mRFT1	solute carrier protein 52, member 2	protein-coding
mm_116275.1	chr13	34874397	34874450	-	1	NA	Intergenic	CpG	-1071	NM_013830	19134	Mm.10027	NM_013830	ENSMUSG00000021413	Prpf4b	2610037H07|Prp4|Prp4k|Prpk|cbp143	pre-mRNA processing factor 4B	protein-coding
mm_110405.1	chr12	45074316	45074347	-	1	NA	5' UTR (NM_144552, exon 1 of 6)	5' UTR (NM_144552, exon 1 of 6)	152	NM_144552	217517	Mm.285400	NM_144552	ENSMUSG00000046314	Stxbp6	BC024598|C85317	syntaxin binding protein 6 (amisyn)	protein-coding
mm_15000.1	chr2	152459395	152459433	+	1	NA	exon (NM_001037933, exon 2 of 2)	exon (NM_001037933, exon 2 of 2)	5206	NM_001037933	629114	Mm.389372	NM_001037933	ENSMUSG00000074681	Defb23	EG629114	defensin beta 23	protein-coding
mm_137628.1	chr17	28328605	28328615	+	1	NA	5' UTR (NM_011287, exon 1 of 6)	5' UTR (NM_011287, exon 1 of 6)	139	NM_011287	19896	Mm.336955	NM_011287	ENSMUSG00000037805	Rpl10a	CsA-19|Nedd6	ribosomal protein L10A	protein-coding
mm_87040.1	chr10	28736131	28736144	+	1	NA	intron (NM_001305663, intron 3 of 5)	intron (NM_001305663, intron 3 of 5)	67777	NM_178666	210757	Mm.123021	NM_178666	ENSMUSG00000049109	Themis	E430004N04Rik|Gasp|Spot|Tsepa|thylex	thymocyte selection associated	protein-coding
mm_168026.1	chrY	90738303	90738320	+	1	NA	Intergenic	IMPB_01|Satellite|Satellite	16739	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_19099.1	chr2	79453917	79453960	-	1	NA	3' UTR (NM_010894, exon 2 of 2)	3' UTR (NM_010894, exon 2 of 2)	2698	NM_010894	18012	Mm.4636	NM_010894	ENSMUSG00000034701	Neurod1	BETA2|BHF-1|Nd1|Neurod|bHLHa3	neurogenic differentiation 1	protein-coding
mm_68049.1	chr7	101538325	101538370	-	1	NA	Intergenic	Intergenic	17455	NM_007490	11871	Mm.439746	NM_007490	ENSMUSG00000092517	Art2a-ps	ARTC2|Art2a|Ly92a|Rt-6|Rt6|Rt6-1	ADP-ribosyltransferase 2a, pseudogene	protein-coding
mm_129369.1	chr15	77995070	77995085	-	1	NA	3' UTR (NM_007583, exon 4 of 4)	3' UTR (NM_007583, exon 4 of 4)	-24253	NM_018749	55944	Mm.3955	NM_018749	ENSMUSG00000016554	Eif3d	66/67kDa|AA407891|Eif3s7|eIF3p66	eukaryotic translation initiation factor 3, subunit D	protein-coding
mm_166953.1	chr7	44474001	44474007	+	1	NA	Intergenic	Intergenic	3657	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_4019.1	chr1	165689757	165689767	+	1	NA	intron (NM_178593, intron 1 of 6)	intron (NM_178593, intron 1 of 6)	18332	NM_178593	226594	Mm.265552	NM_178593	ENSMUSG00000040723	Rcsd1	A430105K13Rik|BC025872|CapZIP	RCSD domain containing 1	protein-coding
mm_3509.1	chr1	150107318	150107333	+	1	NA	3' UTR (NM_011198, exon 10 of 10)	3' UTR (NM_011198, exon 10 of 10)	7294	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_173098.1	chrX	152524450	152524467	+	1	NA	Intergenic	L1Md_T|LINE|L1	-38876	NM_001199311	635396	Mm.485766	NM_001199311	ENSMUSG00000091863	Cldn34a	Gm7157	claudin 34A	protein-coding
mm_34425.1	chr4	145410281	145410317	+	1	NA	Intergenic	Intergenic	-53911	NR_002888	545700	Mm.389595	NR_002888	ENSMUSG00000052912	Smarca5-ps	9230115A19Rik|OTTMUSG00000011029	SWI/SNF related, matrix associated, actin depenent ragulator of chromatin, subfamily a, member 5, pseudogene	pseudo
mm_146650.1	chr18	11051410	11051437	-	1	NA	intron (NR_105022, intron 1 of 3)	intron (NR_105022, intron 1 of 3)	-1087	NM_010258	14465	Mm.329287	NM_010258	ENSMUSG00000005836	Gata6	AA410133|GATA-6	GATA binding protein 6	protein-coding
mm_137143.1	chr17	23642198	23642213	+	1	NA	intron (NM_001320258, intron 2 of 9)	intron (NM_001320258, intron 2 of 9)	3064	NM_001033339	240047	Mm.235343	NM_001033339	ENSMUSG00000023903	Mmp25	F730048C11Rik|Leukolysin|MMP20|MT6-MMP	matrix metallopeptidase 25	protein-coding
mm_105584.1	chr11	106715077	106715099	-	1	NA	5' UTR (NM_008816, exon 1 of 15)	5' UTR (NM_008816, exon 1 of 15)	193	NM_001305158	18613	Mm.343951	NM_008816	ENSMUSG00000020717	Pecam1	C85791|Cd31|PECAM-1|Pecam	platelet/endothelial cell adhesion molecule 1	protein-coding
mm_99408.1	chr11	102262241	102262252	+	1	NA	exon (NM_153544, exon 9 of 10)	exon (NM_153544, exon 9 of 10)	-6577	NM_148953	217217	Mm.216432	NM_148953	ENSMUSG00000034768	Asb16	-	ankyrin repeat and SOCS box-containing 16	protein-coding
mm_97774.1	chr11	82101819	82101829	+	1	NA	promoter-TSS (NM_011331)	promoter-TSS (NM_011331)	-21	NM_011331	20293	Mm.867	NM_011331	ENSMUSG00000035352	Ccl12	MCP-5|Scya12	chemokine (C-C motif) ligand 12	protein-coding
mm_19842.1	chr2	113217027	113217039	-	1	NA	promoter-TSS (NM_001319156)	promoter-TSS (NM_001319156)	50	NM_001319156	20192	Mm.436657	NM_177652	ENSMUSG00000057378	Ryr3	AI851294|C230090H21|RYR-3	ryanodine receptor 3	protein-coding
mm_162879.1	chr10	99467277	99467298	-	1	NA	Intergenic	Intergenic	-141884	NR_038019	100504202	Mm.403801	NR_038019		Gm20110	-	predicted gene, 20110	ncRNA
mm_47593.1	chr5	124862240	124862250	-	1	NA	promoter-TSS (NM_001081750)	promoter-TSS (NM_001081750)	-24	NM_144819	215707	Mm.389693	NM_144819	ENSMUSG00000037979	Ccdc92	AW050178|D5Bwg0834e	coiled-coil domain containing 92	protein-coding
mm_18806.1	chr2	73911286	73911308	-	1	NA	promoter-TSS (NM_175015)	promoter-TSS (NM_175015)	29	NM_175015	228033	Mm.2966	NM_175015	ENSMUSG00000018770	Atp5g3	6030447M23	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit C3 (subunit 9)	protein-coding
mm_49375.1	chr6	24543352	24543366	+	1	NA	intron (NM_080847, intron 1 of 9)	intron (NM_080847, intron 1 of 9)	15215	NM_080847	78910	Mm.160150	NM_080847	ENSMUSG00000029685	Asb15	4930400E23Rik|Asb-15	ankyrin repeat and SOCS box-containing 15	protein-coding
mm_106750.1	chr12	4082597	4082638	+	1	NA	promoter-TSS (NM_153082)	promoter-TSS (NM_153082)	43	NM_153082	217378	Mm.271656	NM_153082	ENSMUSG00000020657	Dnajc27	AI639580|C330021A05Rik|Rabj|Rbj	DnaJ heat shock protein family (Hsp40) member C27	protein-coding
mm_74373.1	chr8	128504111	128504126	+	1	NA	3' UTR (NM_008737, exon 17 of 17)	3' UTR (NM_008737, exon 17 of 17)	144877	NR_035436	100316680		NR_035436	ENSMUSG00000084523	Mir1903	Mirn1903|mmu-mir-1903	microRNA 1903	ncRNA
mm_115228.1	chr13	109902638	109902700	+	1	NA	intron (NM_011056, intron 7 of 16)	CpG	-1140	NR_035442	100316683		NR_035442	ENSMUSG00000084651	Mir1904	Mirn1904|mmu-mir-1904	microRNA 1904	ncRNA
mm_66402.1	chr7	44375007	44375035	-	1	NA	promoter-TSS (NM_027049)	promoter-TSS (NM_027049)	9	NM_027049	69349	Mm.358922	NM_027049	ENSMUSG00000008028	1700008O03Rik	-	RIKEN cDNA 1700008O03 gene	protein-coding
mm_56300.1	chr6	91755232	91755237	-	1	NA	3' UTR (NM_009320, exon 15 of 15)	3' UTR (NM_009320, exon 15 of 15)	52159	NM_001159507	243547	Mm.333264	NM_001033353	ENSMUSG00000030098	Grip2	-	glutamate receptor interacting protein 2	protein-coding
mm_13001.1	chr2	90889996	90890011	+	1	NA	exon (NM_026161, exon 2 of 2)	exon (NM_026161, exon 2 of 2)	4217	NM_026161	67445	Mm.258993	NM_026161	ENSMUSG00000040794	C1qtnf4	0710001E10Rik|9430004J15Rik|CTRP4	C1q and tumor necrosis factor related protein 4	protein-coding
mm_90469.1	chr10	127849890	127849901	+	1	NA	promoter-TSS (NM_147222)	promoter-TSS (NM_147222)	-33	NM_147222	216453	Mm.222953	NM_147222	ENSMUSG00000054052	Rdh19	RDH-S|RDH-S2|Rdhs	retinol dehydrogenase 19	protein-coding
mm_73355.1	chr8	105503199	105503202	+	1	NA	Intergenic	Intergenic	-6330	NM_175160	70796	Mm.100917	NM_175160	ENSMUSG00000039199	Zdhhc1	4432412D04Rik	zinc finger, DHHC domain containing 1	protein-coding
mm_79447.1	chr9	56101533	56101543	+	1	NA	intron (NM_011193, intron 1 of 14)	L1M4|LINE|L1	11562	NM_011193	19200	Mm.2534	NM_011193	ENSMUSG00000032322	Pstpip1	CD2BP1|def-2	proline-serine-threonine phosphatase-interacting protein 1	protein-coding
mm_42894.1	chr5	122401630	122401650	+	1	NA	intron (NM_019824, intron 2 of 6)	intron (NM_019824, intron 2 of 6)	9762	NM_019824	56378	Mm.275942	NM_019824	ENSMUSG00000029465	Arpc3	1110006A04Rik|p21-ARC|p21-Ar|p21Arc	actin related protein 2/3 complex, subunit 3	protein-coding
mm_57548.1	chr6	126740290	126740323	-	1	NA	5' UTR (NM_013568, exon 1 of 2)	5' UTR (NM_013568, exon 1 of 2)	368	NM_013568	16494	Mm.62535	NM_013568	ENSMUSG00000038077	Kcna6	Kv1.6|MK1.6	potassium voltage-gated channel, shaker-related, subfamily, member 6	protein-coding
mm_91380.1	chr10	30618418	30618428	-	1	NA	promoter-TSS (NM_025798)	promoter-TSS (NM_025798)	-57	NM_025798	66847	Mm.46218	NM_025798	ENSMUSG00000019791	Hint3	0610010I17Rik|AV009015|HINT-3|HINT-4|HINT4	histidine triad nucleotide binding protein 3	protein-coding
mm_157507.1	chrX	48877712	48877715	-	1	NA	promoter-TSS (NM_001085499)	promoter-TSS (NM_001085499)	0	NM_001085499	209005	Mm.336054	NM_001085499	ENSMUSG00000079606	Gm595	-	predicted gene 595	protein-coding
mm_145270.1	chr18	52768218	52768299	+	1	NA	5' UTR (NM_001199154, exon 1 of 11)	5' UTR (NM_001199154, exon 1 of 11)	114	NM_001199154	67847	Mm.292168	NM_026408	ENSMUSG00000024534	Sncaip	2810407O15Rik|4933427B05Rik|BB104594|SYPH1	synuclein, alpha interacting protein (synphilin)	protein-coding
mm_170018.1	chr17	18607585	18607598	-	1	NA	Intergenic	L1Md_T|LINE|L1	25864	NM_001104547	433070	Mm.215962	NM_001104547	ENSMUSG00000091679	Vmn2r96	EG433070	vomeronasal 2, receptor 96	protein-coding
mm_58133.1	chr6	140720191	140720200	-	1	NA	Intergenic	MTEb|LTR|ERVL-MaLR	93310	NM_001309436	11569	Mm.86453	NM_009637	ENSMUSG00000030232	Aebp2	AU023766|B230313N05Rik	AE binding protein 2	protein-coding
mm_157335.1	chrX	36492621	36492637	-	1	NA	Intergenic	Intergenic	89152	NR_044989	621901	Mm.491051	NR_044989		Gm6268	EG621901	predicted gene 6268	ncRNA
mm_24146.1	chr3	88326163	88326180	+	1	NA	exon (NM_020003, exon 3 of 6)	exon (NM_020003, exon 3 of 6)	1148	NM_020003	56700	Mm.439922	NM_020003	ENSMUSG00000001418	Glmp	0610031J06Rik|AB027141|NCU-G1	glycosylated lysosomal membrane protein	protein-coding
mm_153494.1	chr19	41331627	41331643	-	1	NA	intron (NM_031376, intron 3 of 16)	intron (NM_031376, intron 3 of 16)	53435	NM_031376	83490	Mm.222266	NM_031376	ENSMUSG00000025017	Pik3ap1	1810044J04Rik|BCAP	phosphoinositide-3-kinase adaptor protein 1	protein-coding
mm_19538.1	chr2	94438163	94438171	-	1	NA	promoter-TSS (NM_001305258)	promoter-TSS (NM_001305258)	19	NM_007466	11800	Mm.181824	NM_007466	ENSMUSG00000027193	Api5	AAC-11|AI196452|API-5	apoptosis inhibitor 5	protein-coding
mm_118280.1	chr13	112673250	112673264	-	1	NA	intron (NM_178746, intron 2 of 14)	intron (NM_178746, intron 2 of 14)	12491	NM_178746	268706	Mm.40834	NM_175376	ENSMUSG00000047789	Slc38a9	4833412L08Rik|6720411P22Rik|9130023D20Rik|9430067K09Rik|A730092C09	solute carrier family 38, member 9	protein-coding
mm_34626.1	chr4	150569485	150569496	+	1	NA	intron (NM_001085492, intron 11 of 22)	CpG	82684	NM_173774	242773	Mm.29280	NM_173774	ENSMUSG00000039838	Slc45a1	C230078B22|Dnb5	solute carrier family 45, member 1	protein-coding
mm_155266.1	chrX	58031004	58031018	+	1	NA	5' UTR (NM_009575, exon 1 of 3)	5' UTR (NM_009575, exon 1 of 3)	383	NM_009575	22773	Mm.255890	NM_009575	ENSMUSG00000067860	Zic3	Bn|Ka	zinc finger protein of the cerebellum 3	protein-coding
mm_143411.1	chr17	70834492	70834502	-	1	NA	Intergenic	Intergenic	12280	NM_001164077	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_119272.1	chr14	34092531	34092532	+	1	NA	exon (NM_001281845, exon 5 of 12)	exon (NM_001281845, exon 5 of 12)	6552	NM_013473	11752	Mm.3267	NM_013473	ENSMUSG00000021950	Anxa8	AI466995|Anx8	annexin A8	protein-coding
mm_112399.1	chr13	3298865	3298875	+	1	NA	Intergenic	Intergenic	149395	NR_001581	73266	Mm.335891	NR_001581		Speer6-ps1	1700039A02Rik|SPEER-6	spermatogenesis associated glutamate (E)-rich protein 6, pseudogene 1	pseudo
mm_99186.1	chr11	100860648	100860654	+	1	NA	intron (NM_001164062, intron 1 of 17)	intron (NM_001164062, intron 1 of 17)	167	NM_001164062	20850	Mm.277403	NM_011488	ENSMUSG00000004043	Stat5a	AA959963|STAT5	signal transducer and activator of transcription 5A	protein-coding
mm_22457.1	chr3	3188101	3188105	+	1	NA	Intergenic	Intergenic	-319927	NM_013920	30942	Mm.330897	NM_013920	ENSMUSG00000017688	Hnf4g	NR2A2	hepatocyte nuclear factor 4, gamma	protein-coding
mm_155424.1	chrX	73492064	73492074	+	1	NA	exon (NM_007542, exon 4 of 8)	exon (NM_007542, exon 4 of 8)	8468	NM_007542	12111	Mm.2608	NM_007542	ENSMUSG00000031375	Bgn	BG|DSPG1|PG-S1|PGI|SLRR1A	biglycan	protein-coding
mm_120721.1	chr14	73111767	73111784	+	1	NA	Intergenic	URR1A|DNA|hAT-Charlie	-30735	NM_001170694	105670	Mm.280068	NM_134083	ENSMUSG00000022106	Rcbtb2	2610028E02Rik|2810420M18Rik|AI448345|AW240694|Chc1l|RC/BTB2	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 2	protein-coding
mm_44243.1	chr5	5328145	5328181	-	1	NA	intron (NM_011074, intron 2 of 14)	B3|SINE|B2	52088	NM_011074	18647	Mm.389061	NM_011074	ENSMUSG00000028926	Cdk14	Pftk1|mKIAA0834	cyclin-dependent kinase 14	protein-coding
mm_84653.1	chr9	71592381	71592387	-	1	NA	promoter-TSS (NM_001033208)	promoter-TSS (NM_001033208)	-24	NM_001033208	102371	Mm.27585	NM_001033208	ENSMUSG00000041361	Myzap	AA407270|AV006038|Gcom1|Gm640|Grinl1a7|Myozap	myocardial zonula adherens protein	protein-coding
mm_108184.1	chr12	76533632	76533646	+	1	NA	promoter-TSS (NR_039597)	promoter-TSS (NR_039597)	79	NM_153804	263406	Mm.291854	NM_153804	ENSMUSG00000052609	Plekhg3	BC030417	pleckstrin homology domain containing, family G (with RhoGef domain) member 3	protein-coding
mm_14809.1	chr2	145934777	145934797	+	1	NA	promoter-TSS (NM_025820)	promoter-TSS (NM_025820)	3	NM_175280	78774	Mm.136347	NM_175280	ENSMUSG00000037143	Cfap61	4930529M08Rik|BB178539|BC024760	cilia and flagella associated protein 61	protein-coding
mm_105878.1	chr11	114924814	114924833	-	1	NA	3' UTR (NM_199221, exon 4 of 4)	3' UTR (NM_199221, exon 4 of 4)	9563	NM_001347651	217304	Mm.185355	NM_199221	ENSMUSG00000063193	Cd300lb	CLM-7|Clm7|Gm253|LMIR5	CD300 molecule like family member B	protein-coding
mm_75559.1	chr8	58257816	58257826	-	1	NA	intron (NM_175032, intron 4 of 11)	Lx8b|LINE|L1	442975	NM_001177534	100271928	Mm.484123	NM_001177534		Gm15881	OTTMUSG00000027193	predicted gene 15881	protein-coding
mm_33755.1	chr4	134343199	134343211	+	1	NA	promoter-TSS (NM_001346578)	promoter-TSS (NM_001346578)	159	NM_001039677	230810	Mm.358876	NM_001039677	ENSMUSG00000028836	Slc30a2	ZnT-2|Znt2	solute carrier family 30 (zinc transporter), member 2	protein-coding
mm_398.1	chr1	34121470	34121484	+	1	NA	intron (NM_001276764, intron 8 of 102)	intron (NM_001276764, intron 8 of 102)	4118	NR_105861	102466987		NR_105861	ENSMUSG00000105982	Mir6896	mmu-mir-6896	microRNA 6896	ncRNA
mm_130467.1	chr15	98610071	98610110	-	1	NA	Intergenic	CpG	-2457	NM_007405	11512	Mm.157091	NM_007405	ENSMUSG00000022994	Adcy6	AC6|mKIAA0422	adenylate cyclase 6	protein-coding
mm_172471.1	chr7	44205096	44205114	+	1	NA	Intergenic	RLTR27|LTR|ERVK	-2328	NM_010915	18048	Mm.440886	NM_010915	ENSMUSG00000066513	Klk1b4	Ngfa|alpha-NGF|mGk-4	kallikrein 1-related pepidase b4	protein-coding
mm_123025.1	chr14	55116641	55116649	-	1	NA	5' UTR (NM_177049, exon 1 of 6)	5' UTR (NM_177049, exon 1 of 6)	290	NM_177049	319984	Mm.19047	NM_177049	ENSMUSG00000022208	Jph4	9330157P13Rik|JP-4|JPHL1	junctophilin 4	protein-coding
mm_154436.1	chrM	848	854	-	1	NA	NA	Intergenic	NA	NA								
mm_58920.1	chr7	17812677	17812688	+	1	NA	promoter-TSS (NM_025957)	promoter-TSS (NM_025957)	0	NM_025957	67084	Mm.33709	NM_025957	ENSMUSG00000023185	Ceacam14	1600021E03Rik|1600025E09Rik|AV033953	carcinoembryonic antigen-related cell adhesion molecule 14	protein-coding
mm_114208.1	chr13	56150380	56150383	+	1	NA	Intergenic	Intergenic	-14831	NM_001159513	26914	Mm.283802	NM_012015	ENSMUSG00000015937	H2afy	H2AF12M|mH2a1|macroH2A1	H2A histone family, member Y	protein-coding
mm_26463.1	chr3	144135898	144135925	+	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	66421	NM_001161770	16911	Mm.29187	NM_010723	ENSMUSG00000028266	Lmo4	A730077C12Rik|Crp3|Etohi4	LIM domain only 4	protein-coding
mm_121547.1	chr14	122475135	122475149	+	1	NA	promoter-TSS (NR_045046)	promoter-TSS (NR_045046)	57	NR_045046	69248	Mm.235369	NR_045046	ENSMUSG00000085555	2610035F20Rik	-	RIKEN cDNA 2610035F20 gene	ncRNA
mm_83751.1	chr9	51216020	51216026	-	1	NA	intron (NM_011136, intron 1 of 4)	RMER2|LTR|ERV1	2333	NM_011136	18985	Mm.897	NM_011136	ENSMUSG00000032053	Pou2af1	BOB.1|Bob-1|Bob1|OBF-1|OBF.1|OCA-B|OCAB	POU domain, class 2, associating factor 1	protein-coding
mm_54534.1	chr6	36715593	36715664	-	1	NA	TTS (NM_008973)	TTS (NM_008973)	95733	NM_008973	19242	Mm.279690	NM_008973	ENSMUSG00000029838	Ptn	HARP|HB-GAM|HBBN|HBGF-8|HBNF|OSF|Osf-1|Osf1	pleiotrophin	protein-coding
mm_162743.1	chr10	56389232	56389263	+	1	NA	3' UTR (NM_010288, exon 2 of 2)	3' UTR (NM_010288, exon 2 of 2)	11947	NM_010288	14609	Mm.378921	NM_010288	ENSMUSG00000050953	Gja1	AU042049|AW546267|Cnx43|Cx43|Cx43alpha1|Gja-1|Npm1|connexin43	gap junction protein, alpha 1	protein-coding
mm_51252.1	chr6	71831442	71831452	+	1	NA	5' UTR (NM_029673, exon 1 of 15)	5' UTR (NM_029673, exon 1 of 15)	127	NM_001253688	76614	Mm.235123	NM_029673	ENSMUSG00000052337	Immt	1700082C19Rik|D830041H16Rik|HMP|P87|P87/89|P89	inner membrane protein, mitochondrial	protein-coding
mm_49781.1	chr6	35177387	35177426	+	1	NA	promoter-TSS (NM_027513)	promoter-TSS (NM_027513)	-210	NM_027513	70699	Mm.261208	NM_027513	ENSMUSG00000038759	Nup205	3830404O05Rik|AV248391|mKIAA0225	nucleoporin 205	protein-coding
mm_77549.1	chr8	123254087	123254123	-	1	NA	promoter-TSS (NM_020497)	promoter-TSS (NM_020497)	-90	NM_020497	57247	Mm.379084	NM_020497	ENSMUSG00000001065	Zfp276	AW048709|D8Ertd370e|D8Ertd377e|Znf276	zinc finger protein (C2H2 type) 276	protein-coding
mm_170331.1	chr18	44724576	44724578	-	1	NA	exon (NM_001085373, exon 3 of 19)	exon (NM_001085373, exon 3 of 19)	-62311	NM_001085374	328949	Mm.312511	NM_001033406	ENSMUSG00000071856	Mcc	D18Ertd451e|E330037C19	mutated in colorectal cancers	protein-coding
mm_24358.1	chr3	90068161	90068167	+	1	NA	3' UTR (NM_028567, exon 4 of 4)	3' UTR (NM_028567, exon 4 of 4)	-1856	NR_030543	100124481		NR_030543	ENSMUSG00000077996	Mir190b	Mirn190b|mir-190b	microRNA 190b	ncRNA
mm_97101.1	chr11	73329728	73329748	+	1	NA	promoter-TSS (NM_001045531)	promoter-TSS (NM_001045531)	-3	NM_001045531	380709	Mm.340910	NM_001045531	ENSMUSG00000069825	Spata22	Gm882	spermatogenesis associated 22	protein-coding
mm_77987.1	chr9	7873197	7873213	+	1	NA	promoter-TSS (NM_007464)	promoter-TSS (NM_007464)	-35	NM_007464	11796	Mm.2026	NM_007464	ENSMUSG00000032000	Birc3	AW107670|Api1|Api2|Birc2|C-IAP2|HIAP2|IAP1|IAP2|MIAP1|MIAP2|MIHB|MIHC|RNF49|cIAP-1|cIAP-2|cIAP1|cIAP2	baculoviral IAP repeat-containing 3	protein-coding
mm_22662.1	chr3	14871768	14871772	+	1	NA	3' UTR (NM_007606, exon 7 of 7)	3' UTR (NM_007606, exon 7 of 7)	8232	NM_007606	12350	Mm.300	NM_007606	ENSMUSG00000027559	Car3	BB219044|Ca3|Car-3	carbonic anhydrase 3	protein-coding
mm_131283.1	chr16	11144043	11144081	+	1	NA	intron (NR_027502, intron 19 of 22)	LSU-rRNA_Hsa|rRNA|rRNA	-9530	NM_029582	106200	Mm.291015	NM_029582	ENSMUSG00000022498	Txndc11	2810408E11Rik|AI427833|EFP1|Txdc11	thioredoxin domain containing 11	protein-coding
mm_87834.1	chr10	60372489	60372491	+	1	NA	3' UTR (NM_001159572, exon 7 of 7)	3' UTR (NM_001159572, exon 7 of 7)	25639	NM_028732	74048	Mm.273584	NM_028732	ENSMUSG00000020101	Vsir	4632428N05Rik|Dies1|PD-1H|VISTA	V-set immunoregulatory receptor	protein-coding
mm_41327.1	chr5	90475265	90475312	+	1	NA	exon (NM_009654, exon 14 of 15)	exon (NM_009654, exon 14 of 15)	14418	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_49752.1	chr6	34746462	34746473	+	1	NA	intron (NM_001347100, intron 5 of 13)	GA-rich|Low_complexity|Low_complexity	-33965	NM_001289657	76223	Mm.150047	NM_178630	ENSMUSG00000038836	Agbl3	2900053G10Rik|4930431N21Rik|6530406M24Rik|CCP3	ATP/GTP binding protein-like 3	protein-coding
mm_29691.1	chr3	123112891	123112904	-	1	NA	exon (NM_080451, exon 4 of 5)	exon (NM_080451, exon 4 of 5)	-77910	NM_021503	59006	Mm.141157	NM_021503	ENSMUSG00000028116	Myoz2	1110012I24Rik|Fatz-2|Myozl2	myozenin 2	protein-coding
mm_90859.1	chr10	8861443	8861446	-	1	NA	intron (NM_175155, intron 1 of 19)	intron (NM_175155, intron 1 of 19)	24626	NM_175155	70097	Mm.338275	NM_175155	ENSMUSG00000015305	Sash1	1100001C18Rik|2500002E12Rik|A330076K04Rik|mKIAA0790	SAM and SH3 domain containing 1	protein-coding
mm_73300.1	chr8	105104844	105104846	+	1	NA	Intergenic	Intergenic	21090	NM_001159415	13909	Mm.482444	NM_144511	ENSMUSG00000062181	Ces3b	Ces31L|Ces3L|EG13909|ES31L|Es31|Gm4738	carboxylesterase 3B	protein-coding
mm_67554.1	chr7	81688478	81688482	-	1	NA	intron (NM_011983, intron 1 of 8)	intron (NM_011983, intron 1 of 8)	4485	NM_001164087	26557	Mm.228	NM_011983	ENSMUSG00000025813	Homer2	9330120H11Rik|AW539445|CPD|Vesl-2	homer scaffolding protein 2	protein-coding
mm_34797.1	chr4	154637142	154637148	+	1	NA	promoter-TSS (NM_027504)	promoter-TSS (NM_027504)	-272	NM_027504	70673	Mm.257785	NM_027504	ENSMUSG00000039410	Prdm16	5730557K01Rik|csp1|mel1	PR domain containing 16	protein-coding
mm_20914.1	chr2	150608491	150608501	-	1	NA	promoter-TSS (NM_027977)	promoter-TSS (NM_027977)	27	NM_027977	71881	Mm.26599	NM_027977	ENSMUSG00000033096	Apmap	2310001A20Rik|AI314817	adipocyte plasma membrane associated protein	protein-coding
mm_11525.1	chr2	32621782	32621798	+	1	NA	promoter-TSS (NM_001198790)	promoter-TSS (NM_001198790)	32	NM_001198790	11636	Mm.29189	NM_021515	ENSMUSG00000026817	Ak1	Ak-1|B430205N08Rik	adenylate kinase 1	protein-coding
mm_50310.1	chr6	47835787	47835797	+	1	NA	5' UTR (NM_027477, exon 1 of 6)	5' UTR (NM_027477, exon 1 of 6)	131	NM_027477	272347	Mm.169059	NM_027477	ENSMUSG00000062519	Zfp398	5730513I23Rik	zinc finger protein 398	protein-coding
mm_152209.1	chr19	7802647	7802666	-	1	NA	promoter-TSS (NM_146232)	promoter-TSS (NM_146232)	11	NM_146232	236149	Mm.207060	NM_146232	ENSMUSG00000053303	Slc22a26	-	solute carrier family 22 (organic cation transporter), member 26	protein-coding
mm_75351.1	chr8	43703414	43703424	-	1	NA	Intergenic	Intergenic	-3928	NM_001079931	384814	Mm.491652	NM_001079931		Gm5347	EG384814	predicted gene 5347	protein-coding
mm_172460.1	chr7	42107256	42107259	-	1	NA	Intergenic	Intergenic	-9214	NM_001105057	637898	Mm.469900	NM_001105057	ENSMUSG00000090619	Vmn2r60	Casr-rs3|EG637898|Gprc2a-rs3	vomeronasal 2, receptor 60	protein-coding
mm_140028.1	chr17	74016698	74016721	+	1	NA	TTS (NM_053188)	TTS (NM_053188)	31207	NM_053188	94224	Mm.38933	NM_053188	ENSMUSG00000038541	Srd5a2	5ART2|S5AR 2	steroid 5 alpha-reductase 2	protein-coding
mm_135386.1	chr16	44262853	44262862	-	1	NA	intron (NM_198034, intron 15 of 24)	intron (NM_198034, intron 15 of 24)	69981	NM_198034	320007	Mm.242144	NM_198034	ENSMUSG00000022696	Sidt1	AW045928|B830021E24Rik	SID1 transmembrane family, member 1	protein-coding
mm_4991.1	chr1	191779678	191779681	+	1	NA	3' UTR (NM_001134829, exon 8 of 8)	3' UTR (NM_001134829, exon 8 of 8)	-41794	NM_010892	18005	Mm.33773	NM_010892	ENSMUSG00000026622	Nek2	AA617254|C77054	NIMA (never in mitosis gene a)-related expressed kinase 2	protein-coding
mm_85332.1	chr9	102354686	102354699	-	1	NA	promoter-TSS (NM_173447)	promoter-TSS (NM_173447)	1	NM_001168296	270190	Mm.22897	NM_173447	ENSMUSG00000032537	Ephb1	9330129L11|AW488255|C130099E04Rik|Cek6|ENSMUSG00000074119|Elk|Elkh|Hek6|Net	Eph receptor B1	protein-coding
mm_138983.1	chr17	45487388	45487398	+	1	NA	Intergenic	Intergenic	-12455	NM_027649	71020	Mm.44257	NM_027649	ENSMUSG00000023935	Spats1	1700011H05Rik|4933400B06Rik|Daip2|Ddip|Srsp1	spermatogenesis associated, serine-rich 1	protein-coding
mm_150267.1	chr19	34217589	34217603	+	1	NA	intron (NM_029682, intron 1 of 10)	intron (NM_029682, intron 1 of 10)	25326	NM_029682	76630	Mm.130952	NM_029682	ENSMUSG00000024776	Stambpl1	1700095N21Rik|8230401J17Rik|ALMalpha|AMSH-FP	STAM binding protein like 1	protein-coding
mm_156428.1	chrX	140979824	140979860	+	1	NA	Intergenic	Intergenic	-23131	NM_001164177	53380	Mm.17640	NM_016883	ENSMUSG00000031429	Psmd10	AW554874	proteasome (prosome, macropain) 26S subunit, non-ATPase, 10	protein-coding
mm_139238.1	chr17	47732979	47733058	+	1	NA	exon (NM_025973, exon 7 of 9)	exon (NM_025973, exon 7 of 9)	-4019	NM_001161722	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_23686.1	chr3	68691368	68691370	+	1	NA	promoter-TSS (NM_008351)	promoter-TSS (NM_008351)	-55	NM_008351	16159	Mm.103783	NM_008351	ENSMUSG00000027776	Il12a	IL-12p35|Il-12a|Ll12a|p35	interleukin 12a	protein-coding
mm_34971.1	chr4	156009148	156009231	+	1	NA	exon (NM_011341, exon 6 of 7)	exon (NM_011341, exon 6 of 7)	-4506	NM_011659	22163	Mm.13885	NM_011659	ENSMUSG00000029075	Tnfrsf4	ACT35|CD134|Ly-70|Ox40|TXGP1L|Txgp1	tumor necrosis factor receptor superfamily, member 4	protein-coding
mm_146161.1	chr18	75047294	75047314	+	1	NA	intron (NM_027727, intron 2 of 16)	intron (NM_027727, intron 2 of 16)	28532	NM_027727	69190	Mm.173826	NM_027727	ENSMUSG00000035765	Dym	1810041M12Rik|4933427L07Rik|C030019K18Rik	dymeclin	protein-coding
mm_102801.1	chr11	68860006	68860017	-	1	NA	Intergenic	Intergenic	-6880	NM_023668	83431	Mm.31979	NM_023668	ENSMUSG00000018736	Ndel1	2600006O07Rik|MITAP1|NUDEL|mNudel	nudE neurodevelopment protein 1 like 1	protein-coding
mm_24719.1	chr3	95232327	95232349	+	1	NA	intron (NM_001038708, intron 2 of 4)	intron (NM_001038708, intron 2 of 4)	3395	NM_001038708	57912	Mm.28189	NM_172395	ENSMUSG00000046722	Cdc42se1	1300002M12Rik|AW558204|Cdcse1|SCIP1|Spec1	CDC42 small effector 1	protein-coding
mm_145751.1	chr18	64554667	64554670	+	1	NA	intron (NM_001001488, intron 17 of 27)	intron (NM_001001488, intron 17 of 27)	-38111	NM_001142950	70223	Mm.29192	NM_027350	ENSMUSG00000024587	Nars	3010001M15Rik|AA960128|ASNRS|C78150	asparaginyl-tRNA synthetase	protein-coding
mm_105218.1	chr11	102185240	102185316	-	1	NA	promoter-TSS (NM_172947)	promoter-TSS (NM_172947)	-22	NM_172947	268490	Mm.259079	NM_172947	ENSMUSG00000020922	Lsm12	1110032E16Rik|1110059P07|2600001B17Rik	LSM12 homolog	protein-coding
mm_19282.1	chr2	89921964	89921967	-	1	NA	Intergenic	RMER19B|LTR|ERVK	-7846	NM_146978	258980	Mm.223370	NM_146978	ENSMUSG00000049149	Olfr1258	MOR232-3	olfactory receptor 1258	protein-coding
mm_53905.1	chr6	3570571	3570583	-	1	NA	intron (NM_001167750, intron 19 of 27)	L1_Rod|LINE|L1	72184	NM_001167750	73288	Mm.45539	NM_024260	ENSMUSG00000001376	Vps50	1700034M03Rik|8430415E05Rik|BLM|C87205|Ccdc132|mKIAA1861	VPS50 EARP/GARPII complex subunit	protein-coding
mm_60032.1	chr7	30981863	30981873	+	1	NA	promoter-TSS (NM_001242647)	promoter-TSS (NM_001242647)	-53	NM_001242647	76415	Mm.259739	NM_175240	ENSMUSG00000046826	Fam187b	1700020B09Rik|Tmem162	family with sequence similarity 187, member B	protein-coding
mm_23591.1	chr3	64949230	64949243	+	1	NA	Intergenic	Intergenic	-104493	NR_003962	319210	Mm.246646	NM_175670	ENSMUSG00000097538	Vmn2r-ps11	4930518C23Rik	vomeronasal 2, receptor, pseudogene 11	pseudo
mm_18687.1	chr2	71389078	71389121	-	1	NA	promoter-TSS (NM_026115)	promoter-TSS (NM_026115)	-161	NM_026115	107435	Mm.272472	NM_026115	ENSMUSG00000027018	Hat1	2410071B14Rik|AA536933|Hat-1|KAT1	histone aminotransferase 1	protein-coding
mm_153919.1	chr19	47272478	47272481	-	1	NA	intron (NM_001164717, intron 11 of 13)	AT_rich|Low_complexity|Low_complexity	1110	NR_105961	102466782		NR_105961	ENSMUSG00000098786	Mir6995	Gm27576|mmu-mir-6995	microRNA 6995	ncRNA
mm_136931.1	chr17	13874902	13874912	+	1	NA	intron (NM_010806, intron 22 of 32)	intron (NM_010806, intron 22 of 32)	-73466	NM_001122977	635895	Mm.388844	NM_001122977	ENSMUSG00000067941	Gm7168	EG635895	predicted gene 7168	protein-coding
mm_99180.1	chr11	100860271	100860273	+	1	NA	promoter-TSS (NM_001164062)	promoter-TSS (NM_001164062)	-212	NM_001164062	20850	Mm.277403	NM_011488	ENSMUSG00000004043	Stat5a	AA959963|STAT5	signal transducer and activator of transcription 5A	protein-coding
mm_135804.1	chr16	57265523	57265542	-	1	NA	TTS (NM_027651)	TTS (NM_027651)	27319	NM_027651	71027	Mm.158563	NM_027651	ENSMUSG00000022753	Tmem30c	4933401B01Rik|4933409A18Rik|Cdc50c	transmembrane protein 30C	protein-coding
mm_75131.1	chr8	34965590	34965601	-	1	NA	promoter-TSS (NM_175091)	promoter-TSS (NM_175091)	95	NM_175091	21951	Mm.88364	NM_175091	ENSMUSG00000031529	Tnks	4930554K12Rik|AI662855|ARTD5|C86528|D130072O21Rik|TANK1|mTNKS1	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase	protein-coding
mm_59836.1	chr7	29309430	29309462	+	1	NA	exon (NM_013874, exon 2 of 12)	exon (NM_013874, exon 2 of 12)	5441	NM_013874	29861	Mm.101885	NM_013874	ENSMUSG00000030584	Dpf1	Neud4	D4, zinc and double PHD fingers family 1	protein-coding
mm_33823.1	chr4	135495953	135495959	+	1	NA	promoter-TSS (NM_030189)	promoter-TSS (NM_030189)	-31	NM_030189	78806	Mm.374844	NM_030189	ENSMUSG00000028801	Stpg1	4930403G18Rik|4930555I21Rik|Mapo2	sperm tail PG rich repeat containing 1	protein-coding
mm_29099.1	chr3	104805466	104805472	-	1	NA	intron (NM_001163441, intron 2 of 20)	intron (NM_001163441, intron 2 of 20)	12836	NM_008619	17454	Mm.1597	NM_008619	ENSMUSG00000002227	Mov10	C77703|Mov-10	Moloney leukemia virus 10	protein-coding
mm_40600.1	chr5	64264317	64264370	+	1	NA	exon (NM_019636, exon 6 of 20)	exon (NM_019636, exon 6 of 20)	33986	NM_001289514	57915	Mm.286353	NM_019636	ENSMUSG00000029174	Tbc1d1	1110062G02Rik|AI385682|AW555803|Nob1|Nobq1|Tbc1|mKIAA1108	TBC1 domain family, member 1	protein-coding
mm_95286.1	chr11	45904211	45904222	+	1	NA	intron (NM_001346760, intron 9 of 11)	(T)n|Simple_repeat|Simple_repeat	40719	NM_028185	72290	Mm.249827	NM_028185	ENSMUSG00000044847	Lsm11	2210404M20Rik|AV079530	U7 snRNP-specific Sm-like protein LSM11	protein-coding
mm_28702.1	chr3	95545441	95545502	-	1	NA	exon (NM_021281, exon 5 of 8)	exon (NM_021281, exon 5 of 8)	-14206	NM_026489	67981	Mm.179050	NM_026489	ENSMUSG00000028109	Hormad1	4921522K05Rik|Nohma	HORMA domain containing 1	protein-coding
mm_111707.1	chr12	103694714	103694718	-	1	NA	promoter-TSS (NM_001164742)	promoter-TSS (NM_001164742)	-27	NM_001164742	68348	Mm.20149	NM_026687	ENSMUSG00000021081	Serpina1f	0610012A11Rik|AI327419|Serpina2|epserin	serine (or cysteine) peptidase inhibitor, clade A, member 1F	protein-coding
mm_163206.1	chr11	98927815	98927824	+	1	NA	Intergenic	Intergenic	-9877	NM_009024	19401	Mm.439744	NM_009024	ENSMUSG00000037992	Rara	Nr1b1|RAR|RARalpha1	retinoic acid receptor, alpha	protein-coding
mm_104047.1	chr11	86357571	86357614	-	1	NA	promoter-TSS (NM_001080931)	promoter-TSS (NM_001080931)	-67	NM_001080931	327987	Mm.341886	NM_001080931	ENSMUSG00000034297	Med13	1110067M05Rik|D030023K18|Thrap1|Trap240	mediator complex subunit 13	protein-coding
mm_2159.1	chr1	88212549	88212569	+	1	NA	exon (NM_201645, exon 1 of 5)	exon (NM_201645, exon 1 of 5)	600	NM_201645	394436	Mm.300095	NM_201645	ENSMUSG00000089960	Ugt1a1	Gnt1|UDPGT 1-1|UGT1A01|Udpgt-1a|UgtBr1	UDP glucuronosyltransferase 1 family, polypeptide A1	protein-coding
mm_140946.1	chr17	24527815	24527829	-	1	NA	promoter-TSS (NR_045289)	promoter-TSS (NR_045289)	116	NM_153792	224619	Mm.275150	NM_153792	ENSMUSG00000052752	Traf7	RFWD1	TNF receptor-associated factor 7	protein-coding
mm_83309.1	chr9	44046728	44046766	-	1	NA	exon (NM_009382, exon 3 of 4)	exon (NM_009382, exon 3 of 4)	3363	NM_009382	21838	Mm.3951	NM_009382	ENSMUSG00000032011	Thy1	CD90|T25|Thy-1|Thy-1.2|Thy1.1|Thy1.2	thymus cell antigen 1, theta	protein-coding
mm_66156.1	chr7	31151146	31151171	-	1	NA	promoter-TSS (NM_027898)	promoter-TSS (NM_027898)	-108	NM_027898	52857	Mm.27366	NM_027898	ENSMUSG00000001248	Gramd1a	1300003M23Rik|AI415002|AW547240|D7Bwg0611e	GRAM domain containing 1A	protein-coding
mm_45080.1	chr5	43981758	43981773	-	1	NA	promoter-TSS (NM_008009)	promoter-TSS (NM_008009)	34	NM_008009	14181	Mm.46053	NM_008009	ENSMUSG00000048373	Fgfbp1	FGF-BP|FGF-BP1|FGFBP-1	fibroblast growth factor binding protein 1	protein-coding
mm_30073.1	chr3	137981506	137981522	-	1	NA	promoter-TSS (NM_001310753)	promoter-TSS (NM_001310753)	35	NM_011932	26377	Mm.254835	NM_011932	ENSMUSG00000028159	Dapp1	Bam32	dual adaptor for phosphotyrosine and 3-phosphoinositides 1	protein-coding
mm_21118.1	chr2	153529942	153529985	-	1	NA	promoter-TSS (NM_001134300)	promoter-TSS (NM_001134300)	8	NM_001134300	329540	Mm.50600	NM_001001986	ENSMUSG00000061411	Nol4l	4931410H15|8430427H17Rik|AI429157|Gm1636	nucleolar protein 4-like	protein-coding
mm_13578.1	chr2	112368084	112368110	+	1	NA	promoter-TSS (NM_026519)	promoter-TSS (NM_026519)	-70	NM_026519	68032	Mm.220942	NM_026519	ENSMUSG00000027131	Emc4	2610318K02Rik|Tmem85	ER membrane protein complex subunit 4	protein-coding
mm_157399.1	chrX	38420991	38421003	-	1	NA	3' UTR (NM_010685, exon 9 of 9)	3' UTR (NM_010685, exon 9 of 9)	35463	NM_010685	16784	Mm.486	NM_010685	ENSMUSG00000016534	Lamp2	CD107b|LGP-B|Lamp II|Lamp-2|Lamp-2a|Lamp-2b|Lamp-2c|Mac3	lysosomal-associated membrane protein 2	protein-coding
mm_153875.1	chr19	46863641	46863653	-	1	NA	intron (NM_033569, intron 4 of 7)	intron (NM_033569, intron 4 of 7)	98704	NM_029810	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_112006.1	chr12	110889088	110889118	-	1	NA	promoter-TSS (NM_026048)	promoter-TSS (NM_026048)	42	NM_027223	67236	Mm.287157	NM_026048	ENSMUSG00000021276	Cinp	1810047K05Rik|2810452K22Rik	cyclin-dependent kinase 2 interacting protein	protein-coding
mm_75059.1	chr8	33660646	33660654	-	1	NA	intron (NM_010344, intron 1 of 12)	intron (NM_010344, intron 1 of 12)	7412	NM_010344	14782	Mm.283573	NM_010344	ENSMUSG00000031584	Gsr	AI325518|D8Ertd238e|Gr-1|Gr1	glutathione reductase	protein-coding
mm_156190.1	chrX	133908668	133908709	+	1	NA	5' UTR (NM_026838, exon 1 of 12)	5' UTR (NM_026838, exon 1 of 12)	263	NM_001083895	68792	Mm.263553	NM_026838	ENSMUSG00000031253	Srpx2	1110039C07Rik|SRP|SRPUL	sushi-repeat-containing protein, X-linked 2	protein-coding
mm_43075.1	chr5	124446865	124446879	+	1	NA	5' UTR (NM_001310727, exon 1 of 7)	5' UTR (NM_001310727, exon 1 of 7)	168	NM_001310727	67956	Mm.137966	NM_030241	ENSMUSG00000049327	Kmt5a	2410195B05Rik|AA617402|AW536475|PR-SET7|PR/SET07|Setd8	lysine methyltransferase 5A	protein-coding
mm_45301.1	chr5	65391386	65391405	-	1	NA	promoter-TSS (NM_024471)	promoter-TSS (NM_024471)	36	NM_011292	20005	Mm.300271	NM_011292	ENSMUSG00000047215	Rpl9	-	ribosomal protein L9	protein-coding
mm_120116.1	chr14	59501887	59501903	+	1	NA	intron (NM_026908, intron 5 of 10)	intron (NM_026908, intron 5 of 10)	60914	NM_026908	69008	Mm.179091	NM_026908	ENSMUSG00000021981	Cab39l	1500031K13Rik|2810425O13Rik|4930520C08Rik|AA589432|MO2L	calcium binding protein 39-like	protein-coding
mm_126913.1	chr15	90986233	90986233	+	1	NA	intron (NM_001109040, intron 7 of 36)	intron (NM_001109040, intron 7 of 36)	63718	NM_001109041	16564	Mm.41379	NM_016705	ENSMUSG00000022629	Kif21a	-	kinesin family member 21A	protein-coding
mm_57831.1	chr6	129464620	129464647	-	1	NA	intron (NR_132130, intron 5 of 5)	L1M5|LINE|L1	8146	NM_001309637	56644	Mm.239516	NM_020008	ENSMUSG00000079293	Clec7a	BGR|Clecsf12|beta-GR	C-type lectin domain family 7, member a	protein-coding
mm_136868.1	chr17	12916386	12916403	+	1	NA	promoter-TSS (NM_013686)	promoter-TSS (NM_013686)	65	NM_013686	21454	Mm.229342	NM_013686	ENSMUSG00000068039	Tcp1	AI528772|CCT|Cct1|Ccta|TRic|Tcp-1|Tp63|c-cpn|p63	t-complex protein 1	protein-coding
mm_75446.1	chr8	47673473	47673483	-	1	NA	intron (NM_023503, intron 1 of 1)	intron (NM_023503, intron 1 of 1)	1681	NM_023503	69260	Mm.430733	NM_023503	ENSMUSG00000063049	Ing2	2810011M06Rik|Ing1l|Ing2b|P33ING2	inhibitor of growth family, member 2	protein-coding
mm_15472.1	chr2	157471277	157471291	+	1	NA	3' UTR (NM_001025395, exon 14 of 14)	3' UTR (NM_001025395, exon 14 of 14)	46991	NM_001025395	20779	Mm.22845	NM_009271	ENSMUSG00000027646	Src	AW259666|pp60c-src	Rous sarcoma oncogene	protein-coding
mm_47420.1	chr5	123141080	123141094	-	1	NA	Intergenic	Intergenic	-1106	NM_001040398	208043	Mm.250391	NM_177581	ENSMUSG00000038384	Setd1b	AA516740|BC035291|KMT2G|mKIAA1076	SET domain containing 1B	protein-coding
mm_63642.1	chr7	128611364	128611416	+	1	NA	promoter-TSS (NM_178641)	promoter-TSS (NM_178641)	25	NM_178641	101490	Mm.490344	NM_178641	ENSMUSG00000042105	Inpp5f	5830435P03Rik|AI115354|AW561896|SAC2|cI-27|hSAC2|mKIAA0966	inositol polyphosphate-5-phosphatase F	protein-coding
mm_77691.1	chr8	126588648	126588655	-	1	NA	3' UTR (NM_001164598, exon 2 of 2)	3' UTR (NM_001164598, exon 2 of 2)	4785	NM_001164598	270110	Mm.334918	NM_001164598	ENSMUSG00000051495	Irf2bp2	E130305N23Rik|IRF-2BP2	interferon regulatory factor 2 binding protein 2	protein-coding
mm_72380.1	chr8	81498665	81498667	+	1	NA	intron (NM_001297591, intron 2 of 24)	intron (NM_001297591, intron 2 of 24)	156104	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_96182.1	chr11	61656330	61656333	+	1	NA	intron (NM_027817, intron 1 of 4)	intron (NM_027817, intron 1 of 4)	3010	NM_027817	71520	Mm.202760	NM_027817	ENSMUSG00000004837	Grap	8430435N19Rik|BB233594	GRB2-related adaptor protein	protein-coding
mm_160927.1	chr11	87422867	87422867	+	1	NA	intron (NM_031386, intron 1 of 30)	U1|snRNA|snRNA	-4724	NM_001199293	83560	Mm.440758	NM_031386	ENSMUSG00000010342	Tex14	C85585	testis expressed gene 14	protein-coding
mm_80027.1	chr9	68653716	68653731	+	1	NA	promoter-TSS (NM_001289917)	promoter-TSS (NM_001289917)	-63	NM_001289917	19883	Mm.378450	NM_013646	ENSMUSG00000032238	Rora	9530021D13Rik|Nr1f1|ROR1|ROR2|ROR3|nmf267|sg|staggerer|tmgc26	RAR-related orphan receptor alpha	protein-coding
mm_172766.1	chr8	93603426	93603442	-	1	NA	Intergenic	RLTR45|LTR|ERVK	-67727	NM_001003951	67935	Mm.65457	NM_001003951	ENSMUSG00000058019	Ces5a	1700081L16Rik|1700122C07Rik|BB081581|Ces7|Gm503|cauxin	carboxylesterase 5A	protein-coding
mm_95520.1	chr11	52121903	52121957	+	1	NA	exon (NM_019411, exon 7 of 7)	exon (NM_019411, exon 7 of 7)	-4816	NR_037221	100526467		NR_037221	ENSMUSG00000092870	Mir3061	mir-3061|mmu-mir-3061	microRNA 3061	ncRNA
mm_21469.1	chr2	160982699	160982709	-	1	NA	exon (NM_173368, exon 24 of 37)	exon (NM_173368, exon 24 of 37)	-70365	NM_182840	280635	Mm.330747	NM_182840	ENSMUSG00000050700	Emilin3	1110013O17Rik|EMILIN-3|EMILIN-5|EMILIN-T|Emilin5	elastin microfibril interfacer 3	protein-coding
mm_171363.1	chr4	117210844	117210845	+	1	NA	Intergenic	U5|snRNA|snRNA	-28220	NM_134471	73804	Mm.247651	NM_134471	ENSMUSG00000028678	Kif2c	4930402F02Rik|ESTM5|Knsl6|MCAK|X83316	kinesin family member 2C	protein-coding
mm_77292.1	chr8	116944325	116944330	-	1	NA	intron (NM_177700, intron 1 of 3)	intron (NM_177700, intron 1 of 3)	934	NM_177700	234776	Mm.259736	NM_177700	ENSMUSG00000047388	Atmin	Asciz|gpg6|mKIAA0431	ATM interactor	protein-coding
mm_162340.1	chr1	46893080	46893084	-	1	NA	Intergenic	Intergenic	-39573	NM_172653	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|mKIAA1265	solute carrier family 39 (zinc transporter), member 10	protein-coding
mm_67577.1	chr7	82359662	82359666	-	1	NA	intron (NM_001190374, intron 2 of 29)	intron (NM_001190374, intron 2 of 29)	23970	NM_001190374	269959	Mm.65306	NM_001190374	ENSMUSG00000070469	Adamtsl3	9230119C12Rik|C130057K09|mKIAA1233	ADAMTS-like 3	protein-coding
mm_20937.1	chr2	150904621	150904748	-	1	NA	promoter-TSS (NM_024465)	promoter-TSS (NM_024465)	47	NM_024465	76192	Mm.112632	NM_024465	ENSMUSG00000032046	Abhd12	1500011G07Rik|6330583M11Rik|AI431047|AW547313	abhydrolase domain containing 12	protein-coding
mm_145309.1	chr18	53862230	53862319	+	1	NA	5' UTR (NM_152809, exon 1 of 13)	5' UTR (NM_152809, exon 1 of 13)	161	NM_152809	70425	Mm.368668	NM_152809	ENSMUSG00000073563	Csnk1g3	3300002K07Rik|C330049O21Rik	casein kinase 1, gamma 3	protein-coding
mm_65854.1	chr7	29281980	29281990	-	1	NA	promoter-TSS (NM_001082548)	promoter-TSS (NM_001082548)	-8	NM_011464	20733	Mm.295230	NM_011464	ENSMUSG00000074227	Spint2	AL024025|C76321|HAI-2	serine protease inhibitor, Kunitz type 2	protein-coding
mm_63601.1	chr7	128146077	128146081	+	1	NA	intron (NM_021334, intron 23 of 29)	URR1A|DNA|hAT-Charlie	16511	NM_021334	16411	Mm.22378	NM_021334	ENSMUSG00000030789	Itgax	AI449405|Cd11c|Cr4|N418	integrin alpha X	protein-coding
mm_156191.1	chrX	134059109	134059112	+	1	NA	promoter-TSS (NM_133196)	promoter-TSS (NM_133196)	-66	NM_001290398	108062	Mm.67938	NM_133196	ENSMUSG00000031256	Cstf2	C630034J23Rik|Cstf64|mir-3112	cleavage stimulation factor, 3' pre-RNA subunit 2	protein-coding
mm_118729.1	chr14	22240978	22240988	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	221271	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_89573.1	chr10	95515171	95515180	+	1	NA	promoter-TSS (NM_080560)	promoter-TSS (NM_080560)	13	NM_080560	93765	Mm.371667	NM_080560	ENSMUSG00000074781	Ube2n	1500026J17Rik|AL022654|BB101821|UBC13	ubiquitin-conjugating enzyme E2N	protein-coding
mm_1851.1	chr1	83314452	83314471	+	1	NA	intron (NM_172430, intron 3 of 10)	intron (NM_172430, intron 3 of 10)	93739	NM_172430	77629	Mm.154303	NM_172430	ENSMUSG00000026163	Sphkap	4930544G21Rik|A930009L15Rik|AI852220|SKIP|mKIAA1678	SPHK1 interactor, AKAP domain containing	protein-coding
mm_158542.1	chrX	145348895	145348928	-	1	NA	promoter-TSS (NM_178358)	promoter-TSS (NM_178358)	-17	NM_178358	237091	Mm.135547	NM_178358	ENSMUSG00000041700	Lhfpl1	Lhfp	lipoma HMGIC fusion partner-like 1	protein-coding
mm_70158.1	chr7	143548029	143548032	-	1	NA	intron (NM_001285489, intron 1 of 14)	intron (NM_001285489, intron 1 of 14)	798	NM_001285490	17955	Mm.294625	NM_008672	ENSMUSG00000059119	Nap1l4	2810410H14Rik|AI316776|D7Wsu30e|Nap2	nucleosome assembly protein 1-like 4	protein-coding
mm_58537.1	chr7	4480686	4480718	+	1	NA	TTS (NM_001290416)	TTS (NM_001290416)	-9818	NR_028416	320749	Mm.396688	NR_028416		D630041G03Rik	-	RIKEN cDNA D630041G03 gene	ncRNA
mm_161891.1	chr18	42298891	42298891	+	1	NA	intron (NM_172626, intron 4 of 19)	intron (NM_172626, intron 4 of 19)	23538	NM_172626	225432	Mm.329400	NM_172626	ENSMUSG00000024491	Rbm27	A730010I06|AI043120|Psc1|mKIAA1311	RNA binding motif protein 27	protein-coding
mm_156465.1	chrX	143518514	143518528	+	1	NA	promoter-TSS (NM_001195048)	promoter-TSS (NM_001195048)	-70	NM_001195048	18481	Mm.40035	NM_008778	ENSMUSG00000031284	Pak3	PAK-3|Pak65alpha|Pak65beta|Stk4	p21 protein (Cdc42/Rac)-activated kinase 3	protein-coding
mm_111790.1	chr12	104856630	104856636	-	1	NA	intron (NM_001040682, intron 1 of 12)	intron (NM_001040682, intron 1 of 12)	8443	NR_104436	94040	Mm.244078	NM_053155	ENSMUSG00000021097	Clmn	9330188N17Rik|AI428889|AI788815|mKIAA1188	calmin	protein-coding
mm_152007.1	chr19	5924798	5924823	-	1	NA	promoter-TSS (NM_026772)	promoter-TSS (NM_026772)	6	NM_026772	104252	Mm.491103	NM_026772	ENSMUSG00000045664	Cdc42ep2	1110008C05Rik|Borg1|Cep2|D19Bwg1013e	CDC42 effector protein (Rho GTPase binding) 2	protein-coding
mm_27667.1	chr3	65381041	65381057	-	1	NA	3' UTR (NM_026155, exon 5 of 5)	3' UTR (NM_026155, exon 5 of 5)	11504	NM_026155	67437	Mm.232728	NM_026155	ENSMUSG00000027828	Ssr3	0610038P07Rik|AL022999|AU022074|AW553833|TRAPG	signal sequence receptor, gamma	protein-coding
mm_15258.1	chr2	154893012	154893034	+	1	NA	promoter-TSS (NM_026030)	promoter-TSS (NM_026030)	-117	NM_026030	67204	Mm.377134	NM_026030	ENSMUSG00000074656	Eif2s2	2810026E11Rik|38kDa|AA408636|AA571381|AA986487|AW822225|D2Ertd303e|EIF2|EIF2B	eukaryotic translation initiation factor 2, subunit 2 (beta)	protein-coding
mm_33863.1	chr4	135929755	135929777	+	1	NA	intron (NM_024243, intron 3 of 7)	ID4|SINE|ID	9040	NM_024243	71665	Mm.439940	NM_024243	ENSMUSG00000028673	Fuca1	0610006A03Rik|9530055J05Rik|Afuc|Fuca	fucosidase, alpha-L- 1, tissue	protein-coding
mm_104215.1	chr11	88343415	88343418	-	1	NA	3' UTR (NM_054043, exon 14 of 14)	3' UTR (NM_054043, exon 14 of 14)	-9357	NR_039545	100628571		NR_039545	ENSMUSG00000092985	Mir378b	mir-378b|mmu-mir-378b	microRNA 378b	ncRNA
mm_68121.1	chr7	102116764	102116774	-	1	NA	promoter-TSS (NM_001081424)	promoter-TSS (NM_001081424)	-56	NM_001081424	504186	Mm.334074	NM_001081424	ENSMUSG00000066279	Chrna10	-	cholinergic receptor, nicotinic, alpha polypeptide 10	protein-coding
mm_81156.1	chr9	107295900	107295910	+	1	NA	promoter-TSS (NM_009895)	promoter-TSS (NM_009895)	-754	NM_001317354	12700	Mm.4592	NM_009895	ENSMUSG00000032578	Cish	CIS-1|CIS1|Cis|F17|F23|SOCS	cytokine inducible SH2-containing protein	protein-coding
mm_104088.1	chr11	86624393	86624435	-	1	NA	intron (NM_029478, intron 7 of 11)	intron (NM_029478, intron 7 of 11)	-31657	NR_106195	102465902		NR_106195	ENSMUSG00000099324	Mir8115	Gm28012|mmu-mir-8115	microRNA 8115	ncRNA
mm_168554.1	chr11	65158513	65158517	-	1	NA	intron (NM_175003, intron 1 of 20)	intron (NM_175003, intron 1 of 20)	4446	NM_001099288	216831	Mm.134338	NM_175003	ENSMUSG00000033389	Arhgap44	6330543G20|AI840762|AU040829|AW493732|Rich2	Rho GTPase activating protein 44	protein-coding
mm_75792.1	chr8	70095804	70095814	-	1	NA	3' UTR (NM_007789, exon 15 of 15)	3' UTR (NM_007789, exon 15 of 15)	6777	NR_106033	102465646		NR_106033	ENSMUSG00000099042	Mir7066	Gm27290|mmu-mir-7066	microRNA 7066	ncRNA
mm_86146.1	chr9	117252112	117252125	-	1	NA	5' UTR (NM_001172126, exon 1 of 13)	5' UTR (NM_001172126, exon 1 of 13)	365	NM_001172123	207181	Mm.326411	NM_178660	ENSMUSG00000039607	Rbms3	6720477E09Rik|8430436O14Rik	RNA binding motif, single stranded interacting protein	protein-coding
mm_43506.1	chr5	136987473	136987482	+	1	NA	promoter-TSS (NM_001310748)	promoter-TSS (NM_001310748)	458	NM_011962	26433	Mm.251003	NM_011962	ENSMUSG00000004846	Plod3	AI414586|LH3	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3	protein-coding
mm_63169.1	chr7	124186734	124186739	+	1	NA	intron (NM_001252072, intron 1 of 1)	intron (NM_001252072, intron 1 of 1)	203555	NM_001252072	628779	Mm.40210	NM_001252072	ENSMUSG00000078591	Hs3st4	EG628779|Gm6915	heparan sulfate (glucosamine) 3-O-sulfotransferase 4	protein-coding
mm_72295.1	chr8	75219284	75219298	+	1	NA	intron (NM_029182, intron 2 of 2)	B4|SINE|B4	5347	NM_029182	75141	Mm.179267	NM_029182	ENSMUSG00000034472	Rasd2	4930526B11Rik|AU045414|Rhes|TEM-2|TEM2	RASD family, member 2	protein-coding
mm_11396.1	chr2	31470241	31470247	+	1	NA	promoter-TSS (NM_007494)	promoter-TSS (NM_007494)	-26	NM_007494	11898	Mm.3217	NM_007494	ENSMUSG00000076441	Ass1	AA408052|ASS|Ass-1|fold	argininosuccinate synthetase 1	protein-coding
mm_10316.1	chr2	11175864	11175873	+	1	NA	intron (NM_008859, intron 1 of 17)	B4A|SINE|B4	3486	NM_008859	18761	Mm.329993	NM_008859	ENSMUSG00000026778	Prkcq	A130035A12Rik|AW494342|PKC-0|PKC-theta|PKCtheta|Pkcq	protein kinase C, theta	protein-coding
mm_42537.1	chr5	115908515	115908522	+	1	NA	intron (NM_007708, intron 8 of 46)	intron (NM_007708, intron 8 of 46)	62862	NM_007708	12704	Mm.8321	NM_007708	ENSMUSG00000029516	Cit	C030025P15Rik|CRIK|CRIK-SK|Cit-k	citron	protein-coding
mm_123355.1	chr14	63142624	63142651	-	1	NA	3' UTR (NM_007798, exon 10 of 10)	3' UTR (NM_007798, exon 10 of 10)	20175	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_169003.1	chr13	102421804	102421811	+	1	NA	Intergenic	L1Md_T|LINE|L1	-271751	NM_008533	17079	Mm.373974	NM_008533	ENSMUSG00000021624	Cd180	F630107B15|Ly78|RP105	CD180 antigen	protein-coding
mm_168140.1	chr10	31672595	31672599	-	1	NA	Intergenic	L1Md_T|LINE|L1	-62872	NM_001146349	268291	Mm.295212	NM_001146349	ENSMUSG00000063760	Rnf217	AU016819|Ibrdc1	ring finger protein 217	protein-coding
mm_18473.1	chr2	62411992	62412023	-	1	NA	5' UTR (NM_010074, exon 1 of 26)	5' UTR (NM_010074, exon 1 of 26)	224	NM_010074	13482	Mm.1151	NM_010074	ENSMUSG00000035000	Dpp4	Cd26|Dpp-4|THAM	dipeptidylpeptidase 4	protein-coding
mm_28003.1	chr3	83010123	83010138	-	1	NA	exon (NM_133862, exon 5 of 10)	exon (NM_133862, exon 5 of 10)	2406	NM_001317105	99571	Mm.16422	NM_133862	ENSMUSG00000033860	Fgg	3010002H13Rik|AI256424	fibrinogen gamma chain	protein-coding
mm_155066.1	chrX	42502597	42502652	+	1	NA	promoter-TSS (NM_011364)	promoter-TSS (NM_011364)	59	NM_001313689	20400	Mm.441197	NM_011364	ENSMUSG00000005696	Sh2d1a	Gm686|SAP	SH2 domain containing 1A	protein-coding
mm_70824.1	chr8	23139158	23139168	+	1	NA	5' UTR (NM_001310437, exon 1 of 5)	5' UTR (NM_001310437, exon 1 of 5)	133	NM_001310437	11733	Mm.334444	NM_031158	ENSMUSG00000031543	Ank1	Ank-1|nb|pale	ankyrin 1, erythroid	protein-coding
mm_30093.1	chr3	138239628	138239645	-	1	NA	promoter-TSS (NR_045760)	promoter-TSS (NR_045760)	27	NR_045760	68369	Mm.441136	NR_045760	ENSMUSG00000099146	0610031O16Rik	-	RIKEN cDNA 0610031O16 gene	ncRNA
mm_126110.1	chr15	78253222	78253233	+	1	NA	intron (NM_008677, intron 3 of 9)	intron (NM_008677, intron 3 of 9)	8416	NM_008677	17972	Mm.2068	NM_008677	ENSMUSG00000071715	Ncf4	AI451400|p40phox	neutrophil cytosolic factor 4	protein-coding
mm_116695.1	chr13	49652715	49652754	-	1	NA	promoter-TSS (NM_001271397)	promoter-TSS (NM_001271397)	-3	NM_025495	66336	Mm.440323	NM_025495	ENSMUSG00000021391	Cenpp	1700022C02Rik|4921518G09Rik	centromere protein P	protein-coding
mm_19045.1	chr2	77170535	77170576	-	1	NA	promoter-TSS (NM_001025576)	promoter-TSS (NM_001025576)	80	NM_001025576	545428	Mm.26579	NM_001025576	ENSMUSG00000044033	Ccdc141	2610301F02Rik|CAMDI|ENSMUSG00000075261	coiled-coil domain containing 141	protein-coding
mm_2543.1	chr1	107511490	107511502	+	1	NA	promoter-TSS (NM_001174170)	promoter-TSS (NM_001174170)	-14	NM_011111	18788	Mm.271870	NM_011111	ENSMUSG00000062345	Serpinb2	PAI-2|Planh2|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 2	protein-coding
mm_120119.1	chr14	59598043	59598053	+	1	NA	promoter-TSS (NM_027986)	promoter-TSS (NM_027986)	-89	NM_001168536	71891	Mm.439850	NM_027986	ENSMUSG00000021982	Cdadc1	2310010M10Rik|AI449174|AI463398|BB130816|NYD-SP15	cytidine and dCMP deaminase domain containing 1	protein-coding
mm_119255.1	chr14	33934867	33934879	+	1	NA	3' UTR (NM_145741, exon 3 of 3)	3' UTR (NM_145741, exon 3 of 3)	-6166	NM_019506	12165	Mm.422844	NM_019506	ENSMUSG00000072625	Gdf2	Bmp9	growth differentiation factor 2	protein-coding
mm_135450.1	chr16	45708172	45708219	-	1	NA	Intergenic	Intergenic	-14537	NM_172455	208171	Mm.186306	NM_172455	ENSMUSG00000033177	Tmprss7	B230219I23Rik|Gm1748	transmembrane serine protease 7	protein-coding
mm_126251.1	chr15	79029303	79029334	+	1	NA	3' UTR (NM_008197, exon 1 of 1)	3' UTR (NM_008197, exon 1 of 1)	1106	NM_008197	14958	Mm.24350	NM_008197	ENSMUSG00000096210	H1f0	D130017D06Rik|H1(0)|H1fv	H1 histone family, member 0	protein-coding
mm_53833.1	chr6	148109485	148109496	+	1	NA	intron (NM_001347516, intron 1 of 11)	intron (NM_001347516, intron 1 of 11)	62074	NM_178797	330450	Mm.447274	NM_178797	ENSMUSG00000030303	Far2	A230046P18|AW048109|BC055759|Mlstd1	fatty acyl CoA reductase 2	protein-coding
mm_49803.1	chr6	36365005	36365005	+	1	NA	intron (NR_015589, intron 3 of 5)	intron (NR_015589, intron 3 of 5)	-23079	NM_203491	243764	Mm.448632	NM_203491	ENSMUSG00000045613	Chrm2	AChR-M2|Chrm-2|M2	cholinergic receptor, muscarinic 2, cardiac	protein-coding
mm_152055.1	chr19	6296659	6296665	-	1	NA	intron (NM_010119, intron 3 of 4)	intron (NM_010119, intron 3 of 4)	-9795	NM_001033342	240505	Mm.329622	NM_001033342	ENSMUSG00000024769	Cdc42bpg	BC046418|MRCKgamma	CDC42 binding protein kinase gamma (DMPK-like)	protein-coding
mm_80691.1	chr9	91378637	91378646	+	1	NA	intron (NM_009576, intron 2 of 4)	CpG	9669	NM_009576	22774	Mm.8062	NM_009576	ENSMUSG00000036972	Zic4	-	zinc finger protein of the cerebellum 4	protein-coding
mm_163253.1	chr11	109230968	109230971	-	1	NA	3' UTR (NM_001165934, exon 17 of 17)	3' UTR (NM_001165934, exon 17 of 17)	67212	NM_001165934	19739	Mm.38548	NM_011268	ENSMUSG00000020599	Rgs9	RGS9-1|Rgs9-2	regulator of G-protein signaling 9	protein-coding
mm_168809.1	chr12	20990489	20990508	+	1	NA	Intergenic	CpG	-121258	NM_001004364	211914	Mm.358946	NM_001004364	ENSMUSG00000052632	Asap2	6530401G17Rik|Ddef2|Gm1523|Gm592|PAG3|PAP	ArfGAP with SH3 domain, ankyrin repeat and PH domain 2	protein-coding
mm_37203.1	chr4	117872027	117872038	-	1	NA	TTS (NM_001253381)	TTS (NM_001253381)	438	NM_001034876	381546	Mm.440118	NM_001034876	ENSMUSG00000078588	Ccdc24	Gm1028	coiled-coil domain containing 24	protein-coding
mm_147757.1	chr18	61224343	61224357	-	1	NA	intron (NM_146086, intron 1 of 21)	intron (NM_146086, intron 1 of 21)	3851	NM_146086	225600	Mm.391106	NM_146086	ENSMUSG00000024575	Pde6a	Pdea|nmf282	phosphodiesterase 6A, cGMP-specific, rod, alpha	protein-coding
mm_90269.1	chr10	122679242	122679244	+	1	NA	promoter-TSS (NR_106182)	promoter-TSS (NR_106182)	-72	NR_106182	102466884		NR_106182	ENSMUSG00000099225	Mir8104	Gm27380|mmu-mir-8104	microRNA 8104	ncRNA
mm_134485.1	chr16	18626672	18626681	-	1	NA	intron (NM_213614, intron 2 of 11)	CpG	3262	NM_213614	18951	Mm.20365	NM_213614	ENSMUSG00000072214	Sept5	Cdcrel-1|Cdcrel1|Pnutl1	septin 5	protein-coding
mm_43477.1	chr5	136695241	136695246	+	1	NA	intron (NM_001085387, intron 1 of 4)	intron (NM_001085387, intron 1 of 4)	1066	NM_001085387	59310	Mm.5178	NM_021611	ENSMUSG00000005474	Myl10	1700027I08Rik|Mylc2pl|PLRLC	myosin, light chain 10, regulatory	protein-coding
mm_118082.1	chr13	103335943	103335954	-	1	NA	Intergenic	Intergenic	-1456	NM_175171	328329	Mm.202606	NM_175171	ENSMUSG00000034751	Mast4	4930420O11Rik|AI642422|mKIAA0303	microtubule associated serine/threonine kinase family member 4	protein-coding
mm_100288.1	chr11	117813448	117813464	+	1	NA	exon (NM_009304, exon 4 of 4)	exon (NM_009304, exon 4 of 4)	3789	NM_009304	20973	Mm.468228	NM_009304	ENSMUSG00000048277	Syngr2	Clast2|cellugyrin	synaptogyrin 2	protein-coding
mm_72758.1	chr8	85492640	85492650	+	1	NA	promoter-TSS (NM_173866)	promoter-TSS (NM_173866)	28	NM_173866	108682	Mm.200423	NM_173866	ENSMUSG00000031700	Gpt2	4631422C05Rik|ALT2|AU014768|AU041193|C87201	glutamic pyruvate transaminase (alanine aminotransferase) 2	protein-coding
mm_163795.1	chr14	15130584	15130587	-	1	NA	Intergenic	Intergenic	308402	NM_146052	218763	Mm.138039	NM_146052	ENSMUSG00000045201	Lrrc3b	BC019794|LRP15	leucine rich repeat containing 3B	protein-coding
mm_80299.1	chr9	73125388	73125396	+	1	NA	Intergenic	Intergenic	11923	NM_198609	225215	Mm.379366	NM_198609	ENSMUSG00000032215	Rsl24d1	2410159K22Rik	ribosomal L24 domain containing 1	protein-coding
mm_47363.1	chr5	122900268	122900377	-	1	NA	promoter-TSS (NM_013910)	promoter-TSS (NM_013910)	28	NM_013910	30841	Mm.86406	NM_013910	ENSMUSG00000029475	Kdm2b	Cxxc2|Fbl10|Fbxl10|Jhdm1b|PCCX2	lysine (K)-specific demethylase 2B	protein-coding
mm_35048.1	chr4	4793276	4793382	-	1	NA	promoter-TSS (NM_177730)	promoter-TSS (NM_177730)	-23	NM_177730	242291	Mm.218889	NM_177730	ENSMUSG00000066324	Impad1	1110001C20Rik|AA408880|AI451589|AL022796|B230207P20|Jaws|gPAPP	inositol monophosphatase domain containing 1	protein-coding
mm_100970.1	chr11	6717139	6717183	-	1	NA	intron (NR_046025, intron 3 of 4)	intron (NR_046025, intron 3 of 4)	2876	NR_046025	626419	Mm.390334	NR_046025	ENSMUSG00000086808	Gm11981	OTTMUSG00000005129	predicted gene 11981	ncRNA
mm_102023.1	chr11	51650755	51650764	-	1	NA	promoter-TSS (NR_027958)	promoter-TSS (NR_027958)	-195	NR_027958	97775	Mm.220299	NM_175289	ENSMUSG00000052563	D930048N14Rik	AI315703|R75254	RIKEN cDNA D930048N14 gene	ncRNA
mm_39440.1	chr5	16870225	16870238	+	1	NA	Intergenic	Intergenic	316330	NM_001289461	15234	Mm.267078	NM_010427	ENSMUSG00000028864	Hgf	C230052L06Rik|HGF/SF|NK1|NK2|SF|SF/HGF	hepatocyte growth factor	protein-coding
mm_110948.1	chr12	76643820	76643835	-	1	NA	intron (NM_013675, intron 2 of 35)	intron (NM_013675, intron 2 of 35)	66720	NM_013675	20741	Mm.32881	NM_013675	ENSMUSG00000021061	Sptb	AI842465|D330027P03Rik|Gm1301|Spnb-1|Spnb1|ja|jaundiced|mKIAA4219	spectrin beta, erythrocytic	protein-coding
mm_79149.1	chr9	47722016	47722030	+	1	NA	intron (NM_001025600, intron 1 of 8)	intron (NM_001025600, intron 1 of 8)	96185	NR_046048	100038460	Mm.447649	NR_046048		Gm10677	ENSMUSG00000074363	predicted gene 10677	ncRNA
mm_101308.1	chr11	22610405	22610416	-	1	NA	Intergenic	Intergenic	98127	NM_153596	103765	Mm.221274	NM_153596	ENSMUSG00000049904	Tmem17	AI503894|AW049890	transmembrane protein 17	protein-coding
mm_20477.1	chr2	129593942	129593948	-	1	NA	intron (NM_001291022, intron 1 of 4)	intron (NM_001291022, intron 1 of 4)	776	NM_001291022	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_150013.1	chr19	29367129	29367176	+	1	NA	promoter-TSS (NM_021893)	promoter-TSS (NM_021893)	-286	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_146811.1	chr18	20746403	20746422	-	1	NA	promoter-TSS (NM_019737)	promoter-TSS (NM_019737)	-8	NM_019737	56386	Mm.393827	NM_019737	ENSMUSG00000056124	B4galt6	AA536803|AU022389	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 6	protein-coding
mm_47775.1	chr5	131616742	131616767	-	1	NA	intron (NM_177047, intron 5 of 18)	intron (NM_177047, intron 5 of 18)	-263515	NR_040704	75369	Mm.389696	NR_040704	ENSMUSG00000105773	4930563F08Rik	-	RIKEN cDNA 4930563F08 gene	ncRNA
mm_122848.1	chr14	54752165	54752212	-	1	NA	intron (NM_016972, intron 3 of 10)	BC1_Mm|scRNA|scRNA	29698	NM_016972	50934	Mm.276831	NM_016972	ENSMUSG00000022180	Slc7a8	AA408822|LAT2	solute carrier family 7 (cationic amino acid transporter, y+ system), member 8	protein-coding
mm_106459.1	chr11	120041751	120041767	-	1	NA	promoter-TSS (NM_001198787)	promoter-TSS (NM_001198787)	22	NM_001198787	11302	Mm.6826	NM_007377	ENSMUSG00000025375	Aatk	AATYK|aatyk1|mKIAA0641	apoptosis-associated tyrosine kinase	protein-coding
mm_93106.1	chr10	91082557	91082577	-	1	NA	promoter-TSS (NM_026166)	promoter-TSS (NM_026166)	176	NM_001042558	11783	Mm.220289	NM_009684	ENSMUSG00000019979	Apaf1	6230400I06Rik|Apaf-1|Apaf1l|fog|mKIAA0413	apoptotic peptidase activating factor 1	protein-coding
mm_49787.1	chr6	35178105	35178114	+	1	NA	intron (NM_027513, intron 1 of 42)	CpG	493	NM_027513	70699	Mm.261208	NM_027513	ENSMUSG00000038759	Nup205	3830404O05Rik|AV248391|mKIAA0225	nucleoporin 205	protein-coding
mm_45658.1	chr5	77114911	77114922	-	1	NA	5' UTR (NM_175606, exon 1 of 3)	5' UTR (NM_175606, exon 1 of 3)	207	NM_175606	74318	Mm.181852	NM_175606	ENSMUSG00000059325	Hopx	1110018K11Rik|1200015P04Rik|2300002F06Rik|AI848177|AW490897|Cameo|Hdop|Hod|Hop|Ob1|Obl|Toto	HOP homeobox	protein-coding
mm_12998.1	chr2	90889894	90889904	+	1	NA	exon (NM_026161, exon 2 of 2)	exon (NM_026161, exon 2 of 2)	4113	NM_026161	67445	Mm.258993	NM_026161	ENSMUSG00000040794	C1qtnf4	0710001E10Rik|9430004J15Rik|CTRP4	C1q and tumor necrosis factor related protein 4	protein-coding
mm_61845.1	chr7	88290956	88290964	+	1	NA	3' UTR (NM_001311790, exon 4 of 4)	3' UTR (NM_001311790, exon 4 of 4)	12875	NM_001311790	13032	Mm.89295	NM_009982	ENSMUSG00000030560	Ctsc	AI047818|CatC|DPP1|DPPI	cathepsin C	protein-coding
mm_35528.1	chr4	41275349	41275359	-	1	NA	promoter-TSS (NM_026872)	promoter-TSS (NM_026872)	-219	NM_026872	68926	Mm.41864	NM_026872	ENSMUSG00000028433	Ubap2	1190005K07Rik|AA408600|AU045235|UBAP-2|mKIAA1491	ubiquitin-associated protein 2	protein-coding
mm_112261.1	chr12	113964866	113964874	-	1	NA	Intergenic	Intergenic	420962	NM_174885	238406	Mm.188683	NM_174885	ENSMUSG00000043945	Adam6a	Adam6|tMDCIV	a disintegrin and metallopeptidase domain 6A	protein-coding
mm_6020.1	chr1	59094915	59094920	-	1	NA	promoter-TSS (NM_175200)	promoter-TSS (NM_175200)	-17	NM_175200	73463	Mm.252811	NM_175200	ENSMUSG00000072295	Als2cr11	1700052H20Rik|4930408G06Rik	amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 11 (human)	protein-coding
mm_33218.1	chr4	126665227	126665227	+	1	NA	Intergenic	Intergenic	-12416	NM_011970	26445	Mm.22233	NM_011970	ENSMUSG00000028837	Psmb2	AU045357|AW108089|C7-I|D4Wsu33e|HC7-I	proteasome (prosome, macropain) subunit, beta type 2	protein-coding
mm_70806.1	chr8	22974924	22974932	+	1	NA	promoter-TSS (NM_001110783)	promoter-TSS (NM_001110783)	92	NM_001277280	11733	Mm.334444	NM_031158	ENSMUSG00000031543	Ank1	Ank-1|nb|pale	ankyrin 1, erythroid	protein-coding
mm_33713.1	chr4	133816475	133816490	+	1	NA	Intergenic	Intergenic	58249	NM_001285506	20111	Mm.301827	NM_009097	ENSMUSG00000003644	Rps6ka1	Mapkapk-1a|Rsk|Rsk-1|Rsk1|S6K-alpha-1|p90-Rsk1|p90Rsk1|p90S6K|p90rsk	ribosomal protein S6 kinase polypeptide 1	protein-coding
mm_131305.1	chr16	11447286	11447296	+	1	NA	intron (NM_001290148, intron 5 of 13)	intron (NM_001290148, intron 5 of 13)	41643	NM_001290148	74478	Mm.325831	NM_028964	ENSMUSG00000071669	Snx29	4933437K13Rik|ENSMUSG00000079738|Gm11170|Gm1737|Gm930|Rundc2a	sorting nexin 29	protein-coding
mm_81601.1	chr9	110547127	110547137	+	1	NA	intron (NM_001081340, intron 2 of 20)	intron (NM_001081340, intron 2 of 20)	14535	NM_001081340	235626	Mm.288949	NM_001081340	ENSMUSG00000044791	Setd2	4921524K10Rik|BC031601|KMT3A	SET domain containing 2	protein-coding
mm_44947.1	chr5	36581793	36581809	-	1	NA	intron (NM_001113362, intron 2 of 14)	CpG	596	NM_133910	100855	Mm.486203	NM_133910	ENSMUSG00000029192	Tbc1d14	2810413P16Rik|AU043625|C86258|D5Ertd110e|mKIAA1322	TBC1 domain family, member 14	protein-coding
mm_100466.1	chr11	119916304	119916337	+	1	NA	intron (NM_001085498, intron 4 of 7)	intron (NM_001085498, intron 4 of 7)	2510	NM_001085498	208092	Mm.306673	NM_001085498	ENSMUSG00000025371	Chmp6	2400004G01Rik	charged multivesicular body protein 6	protein-coding
mm_94619.1	chr11	16759587	16759610	+	1	NA	intron (NM_207655, intron 1 of 27)	intron (NM_207655, intron 1 of 27)	7395	NM_007912	13649	Mm.8534	NM_007912	ENSMUSG00000020122	Egfr	9030024J15Rik|AI552599|Erbb|Errb1|Errp|Wa5|wa-2|wa2	epidermal growth factor receptor	protein-coding
mm_99017.1	chr11	98903202	98903214	+	1	NA	3' UTR (NM_197940, exon 8 of 8)	3' UTR (NM_197940, exon 8 of 8)	-4681	NM_001025779	23834	Mm.20912	NM_011799	ENSMUSG00000017499	Cdc6	CDC18L	cell division cycle 6	protein-coding
mm_156611.1	chrX	153498167	153498172	+	1	NA	promoter-TSS (NM_018798)	promoter-TSS (NM_018798)	-63	NM_018798	54609	Mm.430772	NM_018798	ENSMUSG00000050148	Ubqln2	Chap1|Dsk2|HRIHFB2157|Plic-2|Plic2	ubiquilin 2	protein-coding
mm_172311.1	chr7	105374401	105374401	-	1	NA	promoter-TSS (NM_001195727)	promoter-TSS (NM_001195727)	-637	NM_001195727	100503879	Mm.380109	NM_001195727	ENSMUSG00000078611	Gm5901	EG545989	predicted gene 5901	protein-coding
mm_30871.1	chr4	32165151	32165161	+	1	NA	Intergenic	Intergenic	201049	NM_172688	26409	Mm.258589	NM_009316	ENSMUSG00000028284	Map3k7	B430101B05|C87327|Tak1	mitogen-activated protein kinase kinase kinase 7	protein-coding
mm_29523.1	chr3	116594849	116594898	-	1	NA	promoter-TSS (NM_001289571)	promoter-TSS (NM_001289571)	-85	NM_001289568	72776	Mm.440836	NM_028349	ENSMUSG00000027959	Sass6	2810453L12Rik	SAS-6 centriolar assembly protein	protein-coding
mm_96268.1	chr11	62760602	62760628	+	1	NA	Intergenic	L1_Rod|LINE|L1	28802	NM_138949	192651	Mm.168530	NM_138949	ENSMUSG00000047342	Zfp286	BC027023	zinc finger protein 286	protein-coding
mm_156933.1	chrX	169685255	169685279	+	1	NA	promoter-TSS (NM_010797)	promoter-TSS (NM_010797)	68	NM_001290512	17318	Mm.34441	NM_010797	ENSMUSG00000035299	Mid1	61B3-R|DXHXS1141|Fxy|Trim18	midline 1	protein-coding
mm_115679.1	chr13	13359657	13359660	-	1	NA	intron (NM_031999, intron 6 of 6)	intron (NM_031999, intron 6 of 6)	33966	NM_031999	83924	Mm.379269	NM_031999	ENSMUSG00000021306	Gpr137b	AI788917|AU016435|AW546472|C730041E01|C80550|C80741|D13Abb1e|Tm7sf1	G protein-coupled receptor 137B	protein-coding
mm_143714.1	chr17	80728131	80728171	-	1	NA	promoter-TSS (NM_001290345)	promoter-TSS (NM_001290345)	-126	NM_001290345	225028	Mm.311948	NM_001081357	ENSMUSG00000024242	Map4k3	4833416M01Rik|4833416M07Rik|9530052P13Rik|Glk|MAPKKKK3|MEKKK 3|MEKKK3|RAB8IPL1	mitogen-activated protein kinase kinase kinase kinase 3	protein-coding
mm_16548.1	chr2	181763316	181763335	+	1	NA	promoter-TSS (NM_001171615)	promoter-TSS (NM_001171615)	-7	NM_001171615	17932	Mm.458718	NM_008665	ENSMUSG00000010505	Myt1	Nzf2|Nzf2a|Nzf2b|Nztf2	myelin transcription factor 1	protein-coding
mm_65514.1	chr7	25754953	25754963	-	1	NA	promoter-TSS (NM_178089)	promoter-TSS (NM_178089)	-238	NM_144922	232989	Mm.254223	NM_144922	ENSMUSG00000040725	Hnrnpul1	E130317O14Rik|E1B-AP5|E1BAP5|Hnrnpul|Hnrpul1	heterogeneous nuclear ribonucleoprotein U-like 1	protein-coding
mm_171323.1	chr3	96374018	96374024	+	1	NA	Intergenic	U1|snRNA|snRNA	40812	NR_001579	21748		NR_001579	ENSMUSG00000064796	Terc	mTER|mTR	telomerase RNA component	ncRNA
mm_9106.1	chr1	170110492	170110532	-	1	NA	Intergenic	Intergenic	-21568	NM_022563	18214	Mm.229249	NM_022563	ENSMUSG00000026674	Ddr2	AW495251|Ntrkr3|tyro10	discoidin domain receptor family, member 2	protein-coding
mm_2281.1	chr1	91320219	91320232	+	1	NA	exon (NM_016717, exon 12 of 12)	exon (NM_016717, exon 12 of 12)	-1850	NM_001033292	227357	Mm.318167	NM_001033292	ENSMUSG00000049515	Espnl	Gm556	espin-like	protein-coding
mm_51511.1	chr6	83137369	83137400	+	1	NA	5' UTR (NM_133641, exon 1 of 12)	5' UTR (NM_133641, exon 1 of 12)	300	NM_009106	20166	Mm.4139	NM_009106	ENSMUSG00000034930	Rtkn	-	rhotekin	protein-coding
mm_125861.1	chr15	75216677	75216692	+	1	NA	Intergenic	Intergenic	-51737	NM_008530	17071	Mm.377095	NM_008530	ENSMUSG00000022583	Ly6f	-	lymphocyte antigen 6 complex, locus F	protein-coding
mm_132482.1	chr16	36875228	36875242	+	1	NA	promoter-TSS (NM_134111)	promoter-TSS (NM_134111)	-409	NM_134111	106389	Mm.432078	NM_134111	ENSMUSG00000022838	Eaf2	AW048865|FESTA-L|FESTA-S|Festa|Traits|U19	ELL associated factor 2	protein-coding
mm_12421.1	chr2	70562148	70562208	+	1	NA	promoter-TSS (NM_008077)	promoter-TSS (NM_008077)	49	NM_008077	14415	Mm.272120	NM_008077	ENSMUSG00000070880	Gad1	EP10|Gad-1	glutamate decarboxylase 1	protein-coding
mm_88876.1	chr10	81102684	81102688	+	1	NA	Intergenic	RSINE1|SINE|B4	-1930	NR_049187	100885826		NR_049187	ENSMUSG00000093498	Mir5615-2	Gm23367|mir-5615-2|mmu-mir-5615-2	microRNA 5615-2	ncRNA
mm_141325.1	chr17	28441719	28441732	-	1	NA	intron (NM_010220, intron 1 of 10)	intron (NM_010220, intron 1 of 10)	44424	NM_010220	14229	Mm.276405	NM_010220	ENSMUSG00000024222	Fkbp5	D17Ertd592e|Dit1|FKBP-5|FKBP51	FK506 binding protein 5	protein-coding
mm_168504.1	chr1	153486735	153486750	-	1	NA	intron (NM_007842, intron 1 of 27)	PB1D9|SINE|Alu	918	NM_007842	13211	Mm.20000	NM_007842	ENSMUSG00000042699	Dhx9	AI326842|Ddx9|HEL-5|NDHII|RHA|mHEL-5	DEAH (Asp-Glu-Ala-His) box polypeptide 9	protein-coding
mm_120866.1	chr14	75229846	75229877	+	1	NA	3' UTR (NM_001247984, exon 16 of 16)	3' UTR (NM_001247984, exon 16 of 16)	-12426	NM_019775	56373	Mm.24242	NM_019775	ENSMUSG00000021999	Cpb2	1110032P04Rik|4930405E17Rik|AI255929|CPR|Cpu|TAFI	carboxypeptidase B2 (plasma)	protein-coding
mm_141145.1	chr17	26505956	26505967	-	1	NA	3' UTR (NM_013642, exon 4 of 4)	3' UTR (NM_013642, exon 4 of 4)	2511	NM_013642	19252	Mm.239041	NM_013642	ENSMUSG00000024190	Dusp1	3CH134|MKP1|Ptpn16|U19515|erp|mkp-1	dual specificity phosphatase 1	protein-coding
mm_6605.1	chr1	75366812	75366847	-	1	NA	exon (NM_010043, exon 8 of 9)	exon (NM_010043, exon 8 of 9)	6537	NM_010043	13346	Mm.6712	NM_010043	ENSMUSG00000026208	Des	-	desmin	protein-coding
mm_171561.1	chr4	147230297	147230316	+	1	NA	intron (NM_001039209, intron 1 of 2)	intron (NM_001039209, intron 1 of 2)	54440	NM_001039209	195531	Mm.270762	NM_001039209	ENSMUSG00000078496	Zfp982	Gm13152|OTTMUSG00000010671	zinc finger protein 982	protein-coding
mm_34080.1	chr4	138706869	138706908	+	1	NA	Intergenic	RMER15|LTR|ERVL	17968	NM_001285930	212190	Mm.292226	NM_178671	ENSMUSG00000043621	Ubxn10	5730509E04Rik|A830047D02|Ubxd3	UBX domain protein 10	protein-coding
mm_111508.1	chr12	99563904	99563917	-	1	NA	promoter-TSS (NR_136760)	promoter-TSS (NR_136760)	69	NR_136760	102639404	Mm.396324	NR_136760	ENSMUSG00000097917	Gm26839	-	predicted gene, 26839	ncRNA
mm_64657.1	chr7	4151865	4151876	-	1	NA	intron (NM_021454, intron 2 of 2)	intron (NM_021454, intron 2 of 2)	-1998	NM_175529	243813	Mm.347643	NM_175529	ENSMUSG00000043432	Leng9	9530024C23Rik|F630035L11Rik	leukocyte receptor cluster (LRC) member 9	protein-coding
mm_131498.1	chr16	17336470	17336484	+	1	NA	exon (NM_001331047, exon 2 of 5)	exon (NM_001331047, exon 2 of 5)	5106	NM_001331047	15160	Mm.6609	NM_008223	ENSMUSG00000022766	Serpind1	AA985900|AI303446|HC-II|HCII|Hcf2	serine (or cysteine) peptidase inhibitor, clade D, member 1	protein-coding
mm_146209.1	chr18	76860500	76860516	+	1	NA	exon (NM_001109743, exon 2 of 9)	exon (NM_001109743, exon 2 of 9)	4103	NM_001109743	664805	Mm.329543	NM_001109743	ENSMUSG00000091519	Skor2	Corl2|EG664805|Fussel18|Gm7348	SKI family transcriptional corepressor 2	protein-coding
mm_83524.1	chr9	46230071	46230079	-	1	NA	exon (NM_009692, exon 4 of 4)	exon (NM_009692, exon 4 of 4)	1445	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2|apo-AI|apoA-I	apolipoprotein A-I	protein-coding
mm_101841.1	chr11	48799959	48800005	-	1	NA	promoter-TSS (NM_008143)	promoter-TSS (NM_008143)	-378	NM_008143	14694	Mm.5305	NM_008143	ENSMUSG00000020372	Rack1	AL033335|GB-like|Gnb2-rs1|Gnb2l1|p205	receptor for activated C kinase 1	protein-coding
mm_8862.1	chr1	162740492	162740533	-	1	NA	promoter-TSS (NM_001081290)	promoter-TSS (NM_001081290)	44	NM_001081290	226562	Mm.245446	NM_001081290	ENSMUSG00000040225	Prrc2c	1810043M20Rik|9630039I18Rik|A630006J20|Bat2d|Bat2d1|Bat2l2|E130112L15Rik|Prrc3|mKIAA1096	proline-rich coiled-coil 2C	protein-coding
mm_75295.1	chr8	41054834	41054842	-	1	NA	promoter-TSS (NM_001005864)	promoter-TSS (NM_001005864)	-42	NM_001005864	102103	Mm.149438	NM_001005863	ENSMUSG00000045636	Mtus1	AI481402|ATBP135|Atip1|B430010I23Rik|B430305I03Rik|C85752|Cctsg1-440|MD44|MTSG1|mKIAA1288	mitochondrial tumor suppressor 1	protein-coding
mm_168623.1	chr1	179925444	179925451	-	1	NA	Intergenic	Intergenic	-35313	NM_001346804	226751	Mm.259655	NM_001033285	ENSMUSG00000026490	Cdc42bpa	A930014J19Rik|DMPK-like	CDC42 binding protein kinase alpha	protein-coding
mm_128623.1	chr15	59016224	59016228	-	1	NA	intron (NM_001146180, intron 3 of 13)	intron (NM_001146180, intron 3 of 13)	65800	NM_001146180	211401	Mm.215481	NM_144800	ENSMUSG00000022353	Mtss1	2310003N14Rik|BC024131|D130001D01Rik|Mim|mKIAA0429	metastasis suppressor 1	protein-coding
mm_124804.1	chr15	8569965	8569979	+	1	NA	Intergenic	ID_B1|SINE|B4	-125509	NM_201232	71175	Mm.240329	NM_027707	ENSMUSG00000022141	Nipbl	Idn3	Nipped-B homolog (Drosophila)	protein-coding
mm_103869.1	chr11	83525822	83525829	-	1	NA	TTS (NM_013653)	TTS (NM_013653)	-3726	NM_001045543	629303	Mm.390417	NM_001045543	ENSMUSG00000018925	Heatr9	Gm11435|OTTMUSG00000000990	HEAT repeat containing 9	protein-coding
mm_30003.1	chr3	135608222	135608290	-	1	NA	exon (NM_008689, exon 13 of 25)	exon (NM_008689, exon 13 of 25)	83291	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_40214.1	chr5	37050870	37050892	+	1	NA	promoter-TSS (NM_178394)	promoter-TSS (NM_178394)	24	NM_178394	76071	Mm.85280	NM_178394	ENSMUSG00000063646	Jakmip1	5830437M04Rik|C330021K24Rik|Gababrbp|Marlin-1	janus kinase and microtubule interacting protein 1	protein-coding
mm_48838.1	chr5	149244780	149244790	-	1	NA	Intergenic	Intergenic	-20219	NM_001308462	11690	Mm.19844	NM_009663	ENSMUSG00000060063	Alox5ap	Flap	arachidonate 5-lipoxygenase activating protein	protein-coding
mm_10732.1	chr2	22928558	22928562	+	1	NA	intron (NM_019501, intron 7 of 10)	intron (NM_019501, intron 7 of 10)	33038	NM_019501	56075	Mm.249752	NM_019501	ENSMUSG00000026784	Pdss1	2610203G20Rik|2700031G06Rik|TPT|TPT 1|Tprt|mDLP1|mSPS1	prenyl (solanesyl) diphosphate synthase, subunit 1	protein-coding
mm_24277.1	chr3	89215171	89215181	+	1	NA	promoter-TSS (NM_013604)	promoter-TSS (NM_013604)	-11	NM_013691	21827	Mm.2114	NM_013691	ENSMUSG00000028047	Thbs3	TSP3|Thbs-3	thrombospondin 3	protein-coding
mm_28786.1	chr3	95995699	95995722	-	1	NA	intron (NM_023320, intron 1 of 5)	CpG-9390	129	NM_023320	67220	Mm.458147	NM_023320	ENSMUSG00000015745	Plekho1	2810052M02Rik|CKIP-1|Ckip1|JZA-20|Jza2	pleckstrin homology domain containing, family O member 1	protein-coding
mm_117858.1	chr13	98815264	98815275	-	1	NA	5' UTR (NM_172591, exon 1 of 26)	5' UTR (NM_172591, exon 1 of 26)	180	NM_172591	218503	Mm.23928	NM_172591	ENSMUSG00000041685	Fcho2	5832424M12Rik|AA387320	FCH domain only 2	protein-coding
mm_137632.1	chr17	28329318	28329366	+	1	NA	intron (NM_011287, intron 3 of 5)	intron (NM_011287, intron 3 of 5)	871	NM_011287	19896	Mm.336955	NM_011287	ENSMUSG00000037805	Rpl10a	CsA-19|Nedd6	ribosomal protein L10A	protein-coding
mm_69206.1	chr7	127421788	127421797	-	1	NA	intron (NM_026999, intron 1 of 2)	CpG	242	NM_026999	69234	Mm.20301	NM_026999	ENSMUSG00000045251	Zfp688	2810407K09Rik|AI326029	zinc finger protein 688	protein-coding
mm_3938.1	chr1	163779576	163779592	+	1	NA	promoter-TSS (NM_010629)	promoter-TSS (NM_010629)	1	NM_010629	16579	Mm.4651	NM_010629	ENSMUSG00000026585	Kifap3	KAP-3|KAP3|SMAP	kinesin-associated protein 3	protein-coding
mm_40604.1	chr5	64379218	64379233	+	1	NA	Intergenic	Intergenic	88717	NR_040681	69999	Mm.261413	NR_040681	ENSMUSG00000100911	1700027F09Rik	-	RIKEN cDNA 1700027F09 gene	ncRNA
mm_86562.1	chr10	11281554	11281560	+	1	NA	promoter-TSS (NM_001168297)	promoter-TSS (NM_001168297)	-30	NM_001168297	71865	Mm.276229	NM_027968	ENSMUSG00000047648	Fbxo30	1700026A16Rik|MUSA1	F-box protein 30	protein-coding
mm_2699.1	chr1	127797523	127797527	+	1	NA	intron (NM_028399, intron 5 of 8)	intron (NM_028399, intron 5 of 8)	23361	NM_028399	72949	Mm.268672	NM_028399	ENSMUSG00000026349	Ccnt2	2900041I18Rik|C81304|CycT2|CycT2a|CycT2b	cyclin T2	protein-coding
mm_108024.1	chr12	73636694	73636695	+	1	NA	intron (NM_001313977, intron 2 of 14)	intron (NM_001313977, intron 2 of 14)	51898	NM_008856	18755	Mm.341677	NM_008856	ENSMUSG00000021108	Prkch	Pkch	protein kinase C, eta	protein-coding
mm_38113.1	chr4	134535269	134535314	-	1	NA	promoter-TSS (NM_001256112)	promoter-TSS (NM_001256112)	-23	NM_001256112	76824	Mm.30153	NM_029759	ENSMUSG00000046671	Mtfr1l	2410166I05Rik|AI480750|Fam54b	mitochondrial fission regulator 1-like	protein-coding
mm_136478.1	chr16	95990891	95990928	-	1	NA	promoter-TSS (NM_019537)	promoter-TSS (NM_019537)	-6	NM_019537	56088	Mm.396248	NM_019537	ENSMUSG00000022913	Psmg1	AW552102|Dscr2	proteasome (prosome, macropain) assembly chaperone 1	protein-coding
mm_8782.1	chr1	161243613	161243641	-	1	NA	exon (NM_007453, exon 4 of 5)	exon (NM_007453, exon 4 of 5)	7583	NR_130150	11758	Mm.186185	NM_007453	ENSMUSG00000026701	Prdx6	1-Cys Prx|1-cysPrx|9430088D19Rik|AA690119|Aop2|Brp-12|CP-3|GPx|Ltw-4|Ltw4|Lvtw-4|NSGPx|ORF06|Prdx5|aiPLA2	peroxiredoxin 6	protein-coding
mm_56472.1	chr6	99028435	99028456	-	1	NA	promoter-TSS (NM_001197322)	promoter-TSS (NM_001197322)	-147	NM_001197322	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_14917.1	chr2	150909566	150909642	+	1	NA	promoter-TSS (NM_001163476)	promoter-TSS (NM_001163476)	10	NM_001163476	69270	Mm.271603	NM_027014	ENSMUSG00000027454	Gins1	2810418N01Rik|Gins4|PSF1|mKIAA0186	GINS complex subunit 1 (Psf1 homolog)	protein-coding
mm_76331.1	chr8	84706312	84706328	-	1	NA	3' UTR (NM_010906, exon 9 of 9)	3' UTR (NM_010906, exon 9 of 9)	4863	NM_008535	17095	Mm.4925	NM_008535	ENSMUSG00000034041	Lyl1	Lyl-1|bHLHa18	lymphoblastomic leukemia 1	protein-coding
mm_72204.1	chr8	72573682	72573694	+	1	NA	intron (NM_144534, intron 1 of 5)	intron (NM_144534, intron 1 of 5)	1585	NM_144534	74166	Mm.212927	NM_144534	ENSMUSG00000031791	Tmem38a	1110001E17Rik|AI413399|TRIC-A|mg33a	transmembrane protein 38A	protein-coding
mm_23145.1	chr3	39011790	39011793	+	1	NA	3' UTR (NM_183221, exon 17 of 17)	3' UTR (NM_183221, exon 17 of 17)	124851	NM_183221	329628	Mm.316210	NM_183221	ENSMUSG00000046743	Fat4	6030410K14Rik|9430004M15	FAT atypical cadherin 4	protein-coding
mm_118905.1	chr14	26656002	26656040	+	1	NA	3' UTR (NM_007479, exon 6 of 6)	3' UTR (NM_007479, exon 6 of 6)	13587	NR_106132	102465773		NR_106132	ENSMUSG00000098751	Mir7672	Gm27314|mmu-mir-7672	microRNA 7672	ncRNA
mm_146192.1	chr18	76165119	76165128	+	1	NA	Intergenic	Intergenic	-5429	NR_105776	102465184		NR_105776	ENSMUSG00000098276	Mir6358	Gm27830|mmu-mir-6358	microRNA 6358	ncRNA
mm_114553.1	chr13	74062409	74062410	+	1	NA	promoter-TSS (NM_028959)	promoter-TSS (NM_028959)	-124	NM_028959	74470	Mm.73234	NM_028959	ENSMUSG00000021572	Cep72	2610029E11Rik|4933440J22Rik	centrosomal protein 72	protein-coding
mm_110880.1	chr12	74889979	74889996	-	1	NA	Intergenic	Intergenic	287345	NM_172805	238271	Mm.44465	NM_172805	ENSMUSG00000034402	Kcnh5	Eag2	potassium voltage-gated channel, subfamily H (eag-related), member 5	protein-coding
mm_77702.1	chr8	126590745	126590769	-	1	NA	3' UTR (NM_001164598, exon 2 of 2)	3' UTR (NM_001164598, exon 2 of 2)	2679	NM_001164598	270110	Mm.334918	NM_001164598	ENSMUSG00000051495	Irf2bp2	E130305N23Rik|IRF-2BP2	interferon regulatory factor 2 binding protein 2	protein-coding
mm_135350.1	chr16	43664361	43664408	-	1	NA	promoter-TSS (NM_001146325)	promoter-TSS (NM_001146325)	-200	NM_001146325	100043314	Mm.390896	NM_001146325	ENSMUSG00000071552	Tigit	ENSMUSG00000071552|Vstm3	T cell immunoreceptor with Ig and ITIM domains	protein-coding
mm_66263.1	chr7	35754356	35754366	-	1	NA	promoter-TSS (NM_178704)	promoter-TSS (NM_178704)	93	NM_178704	233115	Mm.257808	NM_178704	ENSMUSG00000043671	Dpy19l3	6030410G08|9330164H19Rik	dpy-19-like 3 (C. elegans)	protein-coding
mm_139356.1	chr17	50518081	50518086	+	1	NA	intron (NM_013880, intron 1 of 5)	intron (NM_013880, intron 1 of 5)	8536	NM_013880	224860	Mm.217362	NM_013880	ENSMUSG00000038910	Plcl2	PLC-L2|PRIP-2|Plce2|mKIAA1092	phospholipase C-like 2	protein-coding
mm_85096.1	chr9	93005727	93005761	-	1	NA	promoter-TSS (NR_040756)	promoter-TSS (NR_040756)	-11	NR_040756	78349	Mm.52612	NR_040756	ENSMUSG00000100294	1700034K08Rik	-	RIKEN cDNA 1700034K08 gene	ncRNA
mm_139910.1	chr17	70900992	70901007	+	1	NA	Intergenic	Intergenic	-47467	NM_001164074	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_69014.1	chr7	126704776	126704806	-	1	NA	promoter-TSS (NM_009898)	promoter-TSS (NM_009898)	25	NM_009898	12721	Mm.290482	NM_009898	ENSMUSG00000030707	Coro1a	Clabp|Lmb3|TACO|p57	coronin, actin binding protein 1A	protein-coding
mm_112964.1	chr13	21181160	21181168	+	1	NA	intron (NM_009054, intron 1 of 7)	intron (NM_009054, intron 1 of 7)	1233	NM_009054	19720	Mm.314056	NM_009054	ENSMUSG00000021326	Trim27	AW538890|Gm19403|Rfp	tripartite motif-containing 27	protein-coding
mm_107156.1	chr12	24572401	24572429	+	1	NA	5' UTR (NM_001161406, exon 1 of 16)	5' UTR (NM_001161406, exon 1 of 16)	128	NM_001161406	195733	Mm.263068	NM_145890	ENSMUSG00000020656	Grhl1	LBP-32|MGR|Tcfcp2l2	grainyhead-like 1 (Drosophila)	protein-coding
mm_159020.1	chr1	171411629	171411629	+	1	NA	promoter-TSS (NM_009480)	promoter-TSS (NM_009480)	-52	NM_009480	22278	Mm.8	NM_009480	ENSMUSG00000026641	Usf1	bHLHb11	upstream transcription factor 1	protein-coding
mm_31095.1	chr4	41755533	41755565	+	1	NA	promoter-TSS (NM_001302511)	promoter-TSS (NM_001302511)	321	NM_016658	14430	Mm.439669	NM_016658	ENSMUSG00000036073	Galt	AW553376	galactose-1-phosphate uridyl transferase	protein-coding
mm_33449.1	chr4	130663803	130663805	+	1	NA	intron (NM_001159606, intron 1 of 17)	CpG	445	NM_001159605	80912	Mm.440206	NM_030722	ENSMUSG00000028580	Pum1	AA517475|Pumm|mKIAA0099	pumilio RNA-binding family member 1	protein-coding
mm_103372.1	chr11	75318894	75318918	-	1	NA	intron (NM_001164223, intron 6 of 17)	intron (NM_001164223, intron 6 of 17)	29477	NM_001164223	68275	Mm.102574	NM_026653	ENSMUSG00000000751	Rpa1	5031405K23Rik|70kDa|AA589576|AW557552|RF-A|RP-A|Rpa	replication protein A1	protein-coding
mm_134509.1	chr16	19067105	19067109	-	1	NA	Intergenic	Intergenic	190357	NM_010435	15260	Mm.15694	NM_010435	ENSMUSG00000022702	Hira	AA138857|D16Ertd95e|Gm15797|N28177|OTTMUSG00000026264|Tuple1	histone cell cycle regulator	protein-coding
mm_143580.1	chr17	74323871	74323872	-	1	NA	promoter-TSS (NM_024428)	promoter-TSS (NM_024428)	73	NM_024428	66310	Mm.28536	NM_024428	ENSMUSG00000024067	Dpy30	2810410M20Rik|C87842	dpy-30, histone methyltransferase complex regulatory subunit	protein-coding
mm_97982.1	chr11	83885676	83885706	+	1	NA	intron (NM_001291269, intron 5 of 8)	B4A|SINE|B4	32731	NM_001291269	21410	Mm.7226	NM_009330	ENSMUSG00000020679	Hnf1b	HNF-1-beta|HNF-1B|HNF-1Beta|Hnf1beta|LFB3|Tcf-2|Tcf2|vHNF1	HNF1 homeobox B	protein-coding
mm_19007.1	chr2	76890155	76890175	-	1	NA	exon (NM_011652, exon 72 of 313)	exon (NM_011652, exon 72 of 313)	92382	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_97824.1	chr11	82964589	82964598	+	1	NA	3' UTR (NM_183201, exon 6 of 6)	3' UTR (NM_183201, exon 6 of 6)	-3912	NR_045932	76392	Mm.295205	NR_045932	ENSMUSG00000086327	Slfn5os	1700003F17Rik	schlafen 5, opposite strand	ncRNA
mm_165406.1	chr2	143080014	143080021	-	1	NA	exon (NM_020595, exon 3 of 4)	exon (NM_020595, exon 3 of 4)	1525	NM_020595	57329	Mm.157751	NM_020595	ENSMUSG00000027416	Otor	CDRAP|Fdp|MIA|MIAL	otoraplin	protein-coding
mm_108108.1	chr12	75308417	75308434	+	1	NA	5' UTR (NM_023275, exon 1 of 5)	5' UTR (NM_023275, exon 1 of 5)	112	NM_023275	80837	Mm.27467	NM_023275	ENSMUSG00000046768	Rhoj	1110005O19Rik|AW210585|Arhj|TC10L|TCL	ras homolog family member J	protein-coding
mm_18373.1	chr2	59948222	59948250	-	1	NA	exon (NM_001001182, exon 13 of 36)	exon (NM_001001182, exon 13 of 36)	-65630	NM_028118	72137	Mm.288734	NM_028118	ENSMUSG00000026988	Wdsub1	1700048E19Rik|2610014F08Rik	WD repeat, SAM and U-box domain containing 1	protein-coding
mm_4576.1	chr1	177840372	177840391	+	1	NA	Intergenic	Intergenic	-43872	NM_007422	11566	Mm.338021	NM_007422	ENSMUSG00000015961	Adss	AI314886|AS|Adss2	adenylosuccinate synthetase, non muscle	protein-coding
mm_114663.1	chr13	78199014	78199036	+	1	NA	promoter-TSS (NM_010151)	promoter-TSS (NM_010151)	-152	NM_010151	13865	Mm.439653	NM_010151	ENSMUSG00000069171	Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR-3|EAR3|Erbal3|SVP44|Tcfcoup1	nuclear receptor subfamily 2, group F, member 1	protein-coding
mm_131696.1	chr16	20695018	20695029	+	1	NA	promoter-TSS (NM_133778)	promoter-TSS (NM_133778)	-34	NM_133778	78408	Mm.196512	NM_133778	ENSMUSG00000050821	Fam131a	2900046G09Rik	family with sequence similarity 131, member A	protein-coding
mm_122880.1	chr14	54926745	54926770	-	1	NA	promoter-TSS (NM_010112)	promoter-TSS (NM_010112)	31	NM_010112	13644	Mm.236438	NM_010112	ENSMUSG00000022203	Efs	-	embryonal Fyn-associated substrate	protein-coding
mm_160317.1	chr7	142303540	142303540	+	1	NA	promoter-TSS (NM_015809)	promoter-TSS (NM_015809)	38	NM_015809	50775	Mm.389990	NM_015809	ENSMUSG00000045236	Krtap5-4	-	keratin associated protein 5-4	protein-coding
mm_18168.1	chr2	45103549	45103549	-	1	NA	intron (NM_001289521, intron 1 of 8)	intron (NM_001289521, intron 1 of 8)	6728	NM_001289521	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_116940.1	chr13	56088666	56088668	-	1	NA	intron (NM_001159514, intron 5 of 8)	intron (NM_001159514, intron 5 of 8)	46883	NM_012015	26914	Mm.283802	NM_012015	ENSMUSG00000015937	H2afy	H2AF12M|mH2a1|macroH2A1	H2A histone family, member Y	protein-coding
mm_164382.1	chr16	31297553	31297584	-	1	NA	exon (NM_007470, exon 6 of 6)	exon (NM_007470, exon 6 of 6)	17240	NM_001301353	11815	Mm.2082	NM_007470	ENSMUSG00000022548	Apod	-	apolipoprotein D	protein-coding
mm_138956.1	chr17	44188626	44188632	+	1	NA	promoter-TSS (NM_172621)	promoter-TSS (NM_172621)	57	NM_172621	224796	Mm.37666	NM_172621	ENSMUSG00000023959	Clic5	5730531E12Rik|B330005L24|Gm322|jbg	chloride intracellular channel 5	protein-coding
mm_23968.1	chr3	84977947	84977961	+	1	NA	3' UTR (NM_080428, exon 11 of 11)	3' UTR (NM_080428, exon 11 of 11)	25743	NM_080428	50754	Mm.196475	NM_080428	ENSMUSG00000028086	Fbxw7	1110001A17Rik|AGO|Cdc4|Fbw7|Fbwd6|Fbx30|Fbxo30|Fbxw6|SEL-10	F-box and WD-40 domain protein 7	protein-coding
mm_151779.1	chr19	5364860	5364878	-	1	NA	non-coding (NR_104482, exon 2 of 2)	non-coding (NR_104482, exon 2 of 2)	1494	NM_001038231	23825	Mm.358649	NM_011793	ENSMUSG00000024844	Banf1	Baf|Bcrp1|L2bp1/Baf	barrier to autointegration factor 1	protein-coding
mm_42040.1	chr5	108404974	108404978	+	1	NA	intron (NM_008806, intron 3 of 21)	intron (NM_008806, intron 3 of 21)	16603	NM_008806	18587	Mm.1372	NM_008806	ENSMUSG00000029491	Pde6b	Pdeb|r|rd|rd-1|rd1|rd10	phosphodiesterase 6B, cGMP, rod receptor, beta polypeptide	protein-coding
mm_122823.1	chr14	54654220	54654222	-	1	NA	promoter-TSS (NM_001242606)	promoter-TSS (NM_001242606)	-520	NM_001085472	56215	Mm.297078	NM_019567	ENSMUSG00000022185	Acin1	2610036I19Rik|2610510L13Rik|Acinus|Acn|C79325|acinusL|acinusS|mKIAA0670	apoptotic chromatin condensation inducer 1	protein-coding
mm_88842.1	chr10	80874242	80874247	+	1	NA	Intergenic	Intergenic	-5572	NM_001081688	432478	Mm.235302	NM_001081688	ENSMUSG00000059406	Tmprss9	Serase-1B	transmembrane protease, serine 9	protein-coding
mm_75164.1	chr8	36612789	36612792	-	1	NA	intron (NM_001194940, intron 5 of 17)	intron (NM_001194940, intron 5 of 17)	1153	NM_015802	50768	Mm.125155	NM_015802	ENSMUSG00000031523	Dlc1	A730069N07Rik|Arhgap7|HP|STARD12|dlc-1	deleted in liver cancer 1	protein-coding
mm_81957.1	chr9	120658009	120658024	+	1	NA	Intergenic	Intergenic	80685	NR_073359	76100	Mm.48212	NR_073359	ENSMUSG00000052658	5830454E08Rik	-	RIKEN cDNA 5830454E08 gene	ncRNA
mm_86972.1	chr10	25398594	25398604	+	1	NA	intron (NM_001199265, intron 1 of 19)	intron (NM_001199265, intron 1 of 19)	-9769	NM_013511	13822	Mm.306026	NM_013511	ENSMUSG00000019978	Epb41l2	4.1G|AW555191|D10Ertd398e|Epb4.1l2|NBL2	erythrocyte membrane protein band 4.1 like 2	protein-coding
mm_49658.1	chr6	31124198	31124213	+	1	NA	intron (NR_110471, intron 3 of 3)	intron (NR_110471, intron 3 of 3)	-61112	NR_029532	387223		NR_029532	ENSMUSG00000065604	Mir29b-1	Mirn29b|Mirn29b-1|mir-29b-1	microRNA 29b-1	ncRNA
mm_85660.1	chr9	107669000	107669020	-	1	NA	promoter-TSS (NM_001199218)	promoter-TSS (NM_001199218)	-42	NM_001199218	76257	Mm.296560	NM_023805	ENSMUSG00000010064	Slc38a3	0610012J02Rik|D9Ucla2|Nat1|Slc38-3|Sn1|Snat3|mNAT	solute carrier family 38, member 3	protein-coding
mm_64220.1	chr7	141562194	141562276	+	1	NA	promoter-TSS (NM_007459)	promoter-TSS (NM_007459)	55	NM_007459	11772	Mm.253090	NM_007459	ENSMUSG00000002957	Ap2a2	2410074K14Rik|AF006990|AW146353|Adtab|C78001|L25	adaptor-related protein complex 2, alpha 2 subunit	protein-coding
mm_50574.1	chr6	49051869	49051913	+	1	NA	exon (NM_053110, exon 9 of 11)	exon (NM_053110, exon 9 of 11)	15373	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_165268.1	chr2	74887029	74887029	-	1	NA	Intergenic	Intergenic	61217	NM_016804	53375	Mm.292613	NM_016804	ENSMUSG00000027099	Mtx2	1500012G02Rik	metaxin 2	protein-coding
mm_120501.1	chr14	66209907	66209923	+	1	NA	intron (NM_001162366, intron 1 of 29)	intron (NM_001162366, intron 1 of 29)	3637	NM_001162366	19229	Mm.21613	NM_172498	ENSMUSG00000059456	Ptk2b	CADTK|CAKB|CAKbeta|E430023O05Rik|FADK2|FAK2|PYK2|Raftk	PTK2 protein tyrosine kinase 2 beta	protein-coding
mm_149734.1	chr19	21992574	21992596	+	1	NA	Intergenic	Intergenic	-146532	NM_001035239	226025	Mm.131943	NM_177341	ENSMUSG00000052387	Trpm3	6330504P12Rik|9330180E14|AU018608|B930001P07Rik|LTRPC3|MLSN2	transient receptor potential cation channel, subfamily M, member 3	protein-coding
mm_133520.1	chr16	90830406	90830425	+	1	NA	promoter-TSS (NM_001316761)	promoter-TSS (NM_001316761)	-444	NR_133572	70967	Mm.253077	NM_027627	ENSMUSG00000039903	Eva1c	1700092M14Rik|4931408A02Rik|Fam176c	eva-1 homolog C (C. elegans)	protein-coding
mm_12344.1	chr2	69746020	69746039	+	1	NA	exon (NM_001081086, exon 12 of 14)	exon (NM_001081086, exon 12 of 14)	22941	NM_001081086	228005	Mm.11815	NM_001081086	ENSMUSG00000042133	Ppig	AU019516|AU022200|B230312B02Rik|CYP|SRCyp	peptidyl-prolyl isomerase G (cyclophilin G)	protein-coding
mm_12766.1	chr2	79279097	79279113	+	1	NA	exon (NM_010576, exon 6 of 28)	exon (NM_010576, exon 6 of 28)	23679	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D|Itga4B	integrin alpha 4	protein-coding
mm_142362.1	chr17	43816440	43816460	-	1	NA	intron (NM_001286653, intron 1 of 4)	intron (NM_001286653, intron 1 of 4)	12447	NM_001286653	53901	Mm.251242	NM_030598	ENSMUSG00000039601	Rcan2	Csp2|Dscr1l1|MCIP2|ZAKI-4	regulator of calcineurin 2	protein-coding
mm_9466.1	chr1	173333411	173333422	-	1	NA	promoter-TSS (NM_010045)	promoter-TSS (NM_010045)	87	NM_010045	13349	Mm.6393	NM_010045	ENSMUSG00000037872	Ackr1	AA162249|CCBP1|CD234|Darc|Dfy|ESTM35|FY|GPD	atypical chemokine receptor 1 (Duffy blood group)	protein-coding
mm_30414.1	chr3	152265738	152265744	-	1	NA	intron (NM_199465, intron 1 of 12)	CpG	579	NM_199465	68810	Mm.200188	NM_199465	ENSMUSG00000039103	Nexn	1110046H09Rik|AA553326|NELIN	nexilin	protein-coding
mm_105852.1	chr11	113710109	113710113	-	1	NA	promoter-TSS (NM_001164532)	promoter-TSS (NM_001164532)	-94	NM_029794	52670	Mm.229207	NM_026682	ENSMUSG00000018727	Cpsf4l	0610010C04Rik|1500000C01Rik|D11Ertd636e	cleavage and polyadenylation specific factor 4-like	protein-coding
mm_44916.1	chr5	35722608	35722615	-	1	NA	intron (NM_194344, intron 2 of 17)	RSINE1|SINE|B4	6665	NM_194344	231147	Mm.290429	NM_194344	ENSMUSG00000036553	Sh3tc1	4631428G15|BC024909	SH3 domain and tetratricopeptide repeats 1	protein-coding
mm_32546.1	chr4	109372333	109372337	+	1	NA	intron (NM_001159964, intron 8 of 12)	intron (NM_001159964, intron 8 of 12)	29279	NM_001159964	13858	Mm.318250	NM_007943	ENSMUSG00000028552	Eps15	2410112D09Rik	epidermal growth factor receptor pathway substrate 15	protein-coding
mm_4525.1	chr1	175632105	175632111	+	1	NA	promoter-TSS (NM_133809)	promoter-TSS (NM_133809)	-85	NM_133809	98256	Mm.27217	NM_133809	ENSMUSG00000039783	Kmo	AI046660	kynurenine 3-monooxygenase (kynurenine 3-hydroxylase)	protein-coding
mm_74672.1	chr8	13889985	13890000	-	1	NA	intron (NM_025556, intron 1 of 3)	CpG	279	NM_025556	66423	Mm.29063	NM_025556	ENSMUSG00000031458	Coprs	1700029I03Rik|2410022L05Rik|AA409325|AI256813|C85432|Copr5	coordinator of PRMT5, differentiation stimulator	protein-coding
mm_101546.1	chr11	33544283	33544325	-	1	NA	Intergenic	Intergenic	-30558	NM_023146	66011	Mm.383775	NM_023146	ENSMUSG00000040594	Ranbp17	-	RAN binding protein 17	protein-coding
mm_99316.1	chr11	101442368	101442378	+	1	NA	5' UTR (NM_011289, exon 1 of 5)	5' UTR (NM_011289, exon 1 of 5)	128	NM_011289	19942	Mm.340658	NM_011289	ENSMUSG00000063316	Rpl27	-	ribosomal protein L27	protein-coding
mm_39610.1	chr5	24159846	24159848	+	1	NA	3' UTR (NM_026448, exon 11 of 11)	3' UTR (NM_026448, exon 11 of 11)	-5116	NM_153092	231042	Mm.45513	NM_153092	ENSMUSG00000048439	Nupl2	AV116043|CG1|NLP-1|Nlp1	nucleoporin like 2	protein-coding
mm_76711.1	chr8	94601721	94601739	-	1	NA	promoter-TSS (NM_028221)	promoter-TSS (NM_028221)	-4	NM_028221	102122	Mm.250425	NM_028221	ENSMUSG00000031774	Fam192a	1700001O11Rik|2310065K24Rik|AI596259|Nip30	family with sequence similarity 192, member A	protein-coding
mm_26545.1	chr3	146182982	146183004	+	1	NA	intron (NM_001005846, intron 9 of 13)	intron (NM_001005846, intron 9 of 13)	32819	NM_001005846	68279	Mm.116862	NM_026656	ENSMUSG00000011008	Mcoln2	3300002C04Rik|AI549968|C86638|TRPML2	mucolipin 2	protein-coding
mm_106800.1	chr12	4917377	4917438	+	1	NA	promoter-TSS (NM_001099628)	promoter-TSS (NM_001099628)	54	NM_001099628	320817	Mm.210966	NM_001099628	ENSMUSG00000052812	Atad2b	1110014E10Rik|BC032887|C79189|D530031C13Rik	ATPase family, AAA domain containing 2B	protein-coding
mm_5033.1	chr1	193302036	193302047	+	1	NA	promoter-TSS (NM_001277928)	promoter-TSS (NM_001277928)	47	NM_008484	16780	Mm.435441	NM_008484	ENSMUSG00000026639	Lamb3	-	laminin, beta 3	protein-coding
mm_65151.1	chr7	19604445	19604492	-	1	NA	promoter-TSS (NR_125836)	promoter-TSS (NR_125836)	18	NR_125832	53609	Mm.20913	NM_016680	ENSMUSG00000061028	Clasrp	Clasp|Sfrs16|Srsf16|Swap2	CLK4-associating serine/arginine rich protein	protein-coding
mm_111794.1	chr12	104865083	104865138	-	1	NA	promoter-TSS (NR_104437)	promoter-TSS (NR_104437)	-34	NR_104435	94040	Mm.244078	NM_053155	ENSMUSG00000021097	Clmn	9330188N17Rik|AI428889|AI788815|mKIAA1188	calmin	protein-coding
mm_29863.1	chr3	130060851	130060865	-	1	NA	promoter-TSS (NM_207209)	promoter-TSS (NM_207209)	49	NM_207209	99683	Mm.192303	NM_207209	ENSMUSG00000001052	Sec24b	AI605202|SEC24	Sec24 related gene family, member B (S. cerevisiae)	protein-coding
mm_125929.1	chr15	76247013	76247023	+	1	NA	intron (NM_023168, intron 1 of 6)	CpG	211	NM_023168	66168	Mm.41665	NM_023168	ENSMUSG00000022564	Grina	1110025J15Rik|Lag|Tmbim3	glutamate receptor, ionotropic, N-methyl D-aspartate-associated protein 1 (glutamate binding)	protein-coding
mm_62851.1	chr7	114415273	114415297	+	1	NA	promoter-TSS (NM_011055)	promoter-TSS (NM_011055)	31	NM_011055	18576	Mm.430730	NM_011055	ENSMUSG00000030671	Pde3b	9830102A01Rik|AI847709	phosphodiesterase 3B, cGMP-inhibited	protein-coding
mm_81868.1	chr9	119037662	119037663	+	1	NA	intron (NM_133710, intron 7 of 7)	MIRb|SINE|MIR	5866	NR_029742	387218		NR_029742	ENSMUSG00000065513	Mir26a-1	Mirn26a|Mirn26a-1|miR-26a|mir-26a-1	microRNA 26a-1	ncRNA
mm_51239.1	chr6	71543901	71543957	+	1	NA	promoter-TSS (NM_025783)	promoter-TSS (NM_025783)	75	NM_025783	66700	Mm.181278	NM_025783	ENSMUSG00000053119	Chmp3	25.1|4921505F14Rik|9130011K15Rik|CGI-49|D6Ertd286e|NEDF|Vps24	charged multivesicular body protein 3	protein-coding
mm_69643.1	chr7	138909423	138909431	-	1	NA	promoter-TSS (NM_009760)	promoter-TSS (NM_009760)	79	NM_009760	12176	Mm.378890	NM_009760	ENSMUSG00000078566	Bnip3	Nip3	BCL2/adenovirus E1B interacting protein 3	protein-coding
mm_23904.1	chr3	83031998	83032032	+	1	NA	3' UTR (NM_010196, exon 5 of 5)	3' UTR (NM_010196, exon 5 of 5)	5862	NM_001111048	14161	Mm.88793	NM_010196	ENSMUSG00000028001	Fga	ENSMUSG00000059807|Fib	fibrinogen alpha chain	protein-coding
mm_94122.1	chr10	128645966	128645988	-	1	NA	promoter-TSS (NM_011772)	promoter-TSS (NM_011772)	16	NM_011772	22781	Mm.358648	NM_011772	ENSMUSG00000002578	Ikzf4	A630026H08Rik|Eos|Zfpn1a4|Znfn1a4	IKAROS family zinc finger 4	protein-coding
mm_36775.1	chr4	102859353	102859392	-	1	NA	intron (NM_001285852, intron 2 of 25)	ORR1D2|LTR|ERVL-MaLR	99237	NM_001285859	73094	Mm.54201	NM_144906	ENSMUSG00000028524	Sgip1	3110007P09Rik|SGIP1alpha|gag	SH3-domain GRB2-like (endophilin) interacting protein 1	protein-coding
mm_129417.1	chr15	78390266	78390274	-	1	NA	intron (NM_001163612, intron 1 of 5)	intron (NM_001163612, intron 1 of 5)	-1501	NM_001163613	73376	Mm.73222	NM_028522	ENSMUSG00000062154	Tex33	1700061J05Rik|Ean57	testis expressed 33	protein-coding
mm_170309.1	chr18	34954270	34954270	-	1	NA	promoter-TSS (NM_010481)	promoter-TSS (NM_010481)	81	NM_010481	15526	Mm.209419	NM_010481	ENSMUSG00000024359	Hspa9	74kDa|Csa|Grp75|Hsc74|Hsp74|Hsp74a|Hspa9a|Mortalin|Mot-2|Mot2|Mthsp70|Pbp74	heat shock protein 9	protein-coding
mm_99750.1	chr11	106688659	106688665	+	1	NA	intron (NM_001305157, intron 7 of 15)	intron (NM_001305157, intron 7 of 15)	26619	NM_001305158	18613	Mm.343951	NM_008816	ENSMUSG00000020717	Pecam1	C85791|Cd31|PECAM-1|Pecam	platelet/endothelial cell adhesion molecule 1	protein-coding
mm_141195.1	chr17	27020831	27020871	-	1	NA	3' UTR (NM_007523, exon 6 of 6)	3' UTR (NM_007523, exon 6 of 6)	2816	NM_001251881	70772	Mm.440437	NM_027544	ENSMUSG00000048731	Ggnbp1	0610031G08Rik|mdf	gametogenetin binding protein 1	protein-coding
mm_125080.1	chr15	26308862	26308875	+	1	NA	promoter-TSS (NM_001310774)	promoter-TSS (NM_001310774)	-180	NM_177597	211147	Mm.54257	NM_177597	ENSMUSG00000022269	March11	9630025C22	membrane-associated ring finger (C3HC4) 11	protein-coding
mm_100354.1	chr11	118428518	118428548	+	1	NA	promoter-TSS (NM_001204129)	promoter-TSS (NM_001204129)	76	NM_001204129	56745	Mm.23845	NM_019959	ENSMUSG00000017446	C1qtnf1	1600017K21Rik|CTRP1|Zsig37	C1q and tumor necrosis factor related protein 1	protein-coding
mm_95754.1	chr11	54902900	54902905	+	1	NA	promoter-TSS (NM_008161)	promoter-TSS (NM_008161)	48	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_113340.1	chr13	31785134	31785145	+	1	NA	Intergenic	Intergenic	-21507	NM_008592	17300	Mm.12949	NM_008592	ENSMUSG00000050295	Foxc1	FREAC3|Fkh1|Mf1|Mf4|ch|fkh-1|frkhda	forkhead box C1	protein-coding
mm_56839.1	chr6	117214106	117214114	-	1	NA	Intergenic	Intergenic	45575	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_115655.1	chr13	12340724	12340739	-	1	NA	promoter-TSS (NM_033268)	promoter-TSS (NM_033268)	1	NM_033268	11472	Mm.37638	NM_033268	ENSMUSG00000052374	Actn2	1110008F24Rik	actinin alpha 2	protein-coding
mm_42535.1	chr5	115907449	115907508	+	1	NA	intron (NM_007708, intron 8 of 46)	intron (NM_007708, intron 8 of 46)	61822	NM_007708	12704	Mm.8321	NM_007708	ENSMUSG00000029516	Cit	C030025P15Rik|CRIK|CRIK-SK|Cit-k	citron	protein-coding
mm_20045.1	chr2	120154513	120154590	-	1	NA	promoter-TSS (NM_133838)	promoter-TSS (NM_133838)	24	NM_133838	98878	Mm.132226	NM_133838	ENSMUSG00000027293	Ehd4	2210022F10Rik|AI197390|AI846352|AV006278|Past2	EH-domain containing 4	protein-coding
mm_124302.1	chr14	103059022	103059036	-	1	NA	Intergenic	Intergenic	-11187	NM_001033242	211286	Mm.295289	NM_001033242	ENSMUSG00000022125	Cln5	A730075N08Rik	ceroid-lipofuscinosis, neuronal 5	protein-coding
mm_73782.1	chr8	117051035	117051050	+	1	NA	exon (NM_029686, exon 16 of 43)	exon (NM_029686, exon 16 of 43)	31407	NM_029686	76645	Mm.159753	NM_029686	ENSMUSG00000034416	Pkd1l2	1700126L06Rik	polycystic kidney disease 1 like 2	protein-coding
mm_171734.1	chr4	94705556	94705558	-	1	NA	Intergenic	Intergenic	-33732	NM_001290549	21687	Mm.14313	NM_013690	ENSMUSG00000006386	Tek	AA517024|Cd202b|Hyk|STK1|Tie-2|Tie2	endothelial-specific receptor tyrosine kinase	protein-coding
mm_131060.1	chr16	4381732	4381749	+	1	NA	intron (NM_001291910, intron 3 of 11)	intron (NM_001291910, intron 3 of 11)	38758	NM_001291910	11515	Mm.439750	NM_009624	ENSMUSG00000005580	Adcy9	AC9|ACtp10|AW125421|D16Wsu65e|mKIAA0520	adenylate cyclase 9	protein-coding
mm_13264.1	chr2	98666620	98666664	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	1198985	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_103189.1	chr11	70615658	70615670	-	1	NA	promoter-TSS (NM_001145537)	promoter-TSS (NM_001145537)	-230	NM_001145537	668433	Mm.425687	NM_001145537	ENSMUSG00000087279	4930544D05Rik	-	RIKEN cDNA 4930544D05 gene	protein-coding
mm_69613.1	chr7	137231552	137231556	-	1	NA	intron (NM_001113415, intron 7 of 15)	intron (NM_001113415, intron 7 of 15)	-3129	NR_045885	100038555	Mm.444788	NR_045885	ENSMUSG00000109722	Gm10578	ENSMUSG00000073800	predicted gene 10578	ncRNA
mm_40505.1	chr5	57731617	57731637	+	1	NA	intron (NM_001310608, intron 1 of 3)	intron (NM_001310608, intron 1 of 3)	13546	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_52571.1	chr6	116338000	116338010	+	1	NA	promoter-TSS (NM_027920)	promoter-TSS (NM_027920)	-17	NM_001302385	71779	Mm.27064	NM_027920	ENSMUSG00000025702	March8	1300017E09Rik|MARCH-VIII|Mir	membrane-associated ring finger (C3HC4) 8	protein-coding
mm_157826.1	chrX	74229188	74229191	-	1	NA	exon (NM_001290421, exon 35 of 47)	exon (NM_001290421, exon 35 of 47)	17345	NM_010227	192176	Mm.295533	NM_010227	ENSMUSG00000031328	Flna	ABP-280|Dilp2|F730004A14Rik|Fln1|GENA 379|filamin-1	filamin, alpha	protein-coding
mm_51376.1	chr6	72993589	72993623	+	1	NA	Intergenic	Intergenic	-34858	NM_001190327	19240	Mm.3532	NM_025284	ENSMUSG00000079523	Tmsb10	Ptmb10|Tb10	thymosin, beta 10	protein-coding
mm_148492.1	chr19	4154621	4154629	+	1	NA	promoter-TSS (NM_016933)	promoter-TSS (NM_016933)	-21	NM_016933	19265	Mm.271937	NM_016933	ENSMUSG00000045826	Ptprcap	AI605264|CD-45-AP|LPAP|LSM-1	protein tyrosine phosphatase, receptor type, C polypeptide-associated protein	protein-coding
mm_114392.1	chr13	63272988	63273005	+	1	NA	intron (NR_110520, intron 2 of 5)	intron (NR_110520, intron 2 of 5)	24151	NR_045794	100504114	Mm.437070	NR_045794	ENSMUSG00000097242	Gm16907	-	predicted gene, 16907	ncRNA
mm_87412.1	chr10	46065299	46065301	+	1	NA	Intergenic	Intergenic	-179448	NR_028274	100302593		NR_028274	ENSMUSG00000095118	Snord14d	Gm23710	small nucleolar RNA, C/D box 14D	snoRNA
mm_73652.1	chr8	110940952	110940975	+	1	NA	intron (NM_009179, intron 1 of 6)	intron (NM_009179, intron 1 of 6)	21098	NM_009179	20444	Mm.200388	NM_009179	ENSMUSG00000031749	St3gal2	AI429591|AW822065|ST3GalII|Siat5	ST3 beta-galactoside alpha-2,3-sialyltransferase 2	protein-coding
mm_37042.1	chr4	115781046	115781064	-	1	NA	promoter-TSS (NM_029196)	promoter-TSS (NM_029196)	-21	NM_029196	75173	Mm.331798	NM_029196	ENSMUSG00000044556	Tex38	4930544O15Rik|Theg4	testis expressed 38	protein-coding
mm_122097.1	chr14	30912689	30912694	-	1	NA	exon (NM_008407, exon 17 of 21)	exon (NM_008407, exon 17 of 21)	10896	NM_008407	16426	Mm.4517	NM_008407	ENSMUSG00000006522	Itih3	AW108094|ITI-HC3|Intin3|Itih-3	inter-alpha trypsin inhibitor, heavy chain 3	protein-coding
mm_118157.1	chr13	105250491	105250499	-	1	NA	exon (NM_027934, exon 4 of 8)	exon (NM_027934, exon 4 of 8)	42519	NM_027934	71816	Mm.317015	NM_027934	ENSMUSG00000021720	Rnf180	3110001E11Rik|Rines	ring finger protein 180	protein-coding
mm_91292.1	chr10	24915539	24915555	-	1	NA	3' UTR (NM_007482, exon 8 of 8)	3' UTR (NM_007482, exon 8 of 8)	4883	NR_105870	102465545		NR_105870	ENSMUSG00000099181	Mir6905	Gm27879|mmu-mir-6905	microRNA 6905	ncRNA
mm_56759.1	chr6	116107505	116107551	-	1	NA	intron (NM_177412, intron 3 of 5)	intron (NM_177412, intron 3 of 5)	85846	NM_177412	330401	Mm.425352	NM_177412	ENSMUSG00000030126	Tmcc1	3632431M01Rik|mKIAA0779	transmembrane and coiled coil domains 1	protein-coding
mm_82498.1	chr9	19928321	19928324	-	1	NA	Intergenic	Intergenic	11093	NM_146339	258336	Mm.261577	NM_146339	ENSMUSG00000051118	Olfr77	18A|MOR143-1	olfactory receptor 77	protein-coding
mm_33081.1	chr4	123917421	123917510	+	1	NA	promoter-TSS (NM_017475)	promoter-TSS (NM_017475)	32	NM_017475	54170	Mm.220922	NM_017475	ENSMUSG00000028646	Rragc	AU041672|Gtr2|RAGC|TIB929|YGR163W	Ras-related GTP binding C	protein-coding
mm_163924.1	chr14	46884031	46884050	+	1	NA	intron (NM_001037221, intron 1 of 12)	CpG	1075	NM_001037221	74480	Mm.214454	NM_028966	ENSMUSG00000021838	Samd4	1700024G08Rik|1700111L17Rik|4933436G17Rik|Samd4a|Smaug|Smaug1|sunk	sterile alpha motif domain containing 4	protein-coding
mm_24612.1	chr3	93447633	93447643	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	5308	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_71243.1	chr8	40911011	40911065	+	1	NA	exon (NM_001044740, exon 8 of 12)	exon (NM_001044740, exon 8 of 12)	-15195	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_16081.1	chr2	168549049	168549059	+	1	NA	intron (NR_111898, intron 2 of 5)	intron (NR_111898, intron 2 of 5)	41311	NM_001291178	18019	Mm.116802	NM_010899	ENSMUSG00000027544	Nfatc2	AI607462|NF-ATc2|NF-ATp|NFAT1|NFAT1-D|Nfatp	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 2	protein-coding
mm_46069.1	chr5	92310004	92310016	-	1	NA	promoter-TSS (NM_172713)	promoter-TSS (NM_172713)	14	NM_172713	231452	Mm.86564	NM_172713	ENSMUSG00000029415	Sdad1	4931421J16|AA591032|AW538460	SDA1 domain containing 1	protein-coding
mm_34969.1	chr4	156008829	156008850	+	1	NA	exon (NM_011341, exon 5 of 7)	exon (NM_011341, exon 5 of 7)	-4856	NM_011659	22163	Mm.13885	NM_011659	ENSMUSG00000029075	Tnfrsf4	ACT35|CD134|Ly-70|Ox40|TXGP1L|Txgp1	tumor necrosis factor receptor superfamily, member 4	protein-coding
mm_67819.1	chr7	98178255	98178267	-	1	NA	promoter-TSS (NM_007602)	promoter-TSS (NM_007602)	13	NM_007602	12337	Mm.326847	NM_007602	ENSMUSG00000035547	Capn5	nCL-3	calpain 5	protein-coding
mm_159483.1	chr4	41569466	41569466	-	1	NA	promoter-TSS (NM_027993)	promoter-TSS (NM_027993)	61	NM_001159583	71901	Mm.39215	NM_027993	ENSMUSG00000028439	Fam219a	2310028H24Rik	family with sequence similarity 219, member A	protein-coding
mm_21181.1	chr2	155050787	155050801	-	1	NA	exon (NM_015770, exon 4 of 4)	exon (NM_015770, exon 4 of 4)	23703	NM_016661	269378	Mm.330692	NM_016661	ENSMUSG00000027597	Ahcy	AA987153|AL024110|CuBP|SAHH	S-adenosylhomocysteine hydrolase	protein-coding
mm_111126.1	chr12	81421911	81421921	-	1	NA	5' UTR (NM_009620, exon 1 of 1)	5' UTR (NM_009620, exon 1 of 1)	123	NM_009620	11498	Mm.408462	NM_009620	ENSMUSG00000072972	Adam4	AV274654|tMDCV	a disintegrin and metallopeptidase domain 4	protein-coding
mm_46203.1	chr5	98031336	98031347	-	1	NA	promoter-TSS (NM_133738)	promoter-TSS (NM_133738)	-379	NM_133738	71914	Mm.24842	NM_133738	ENSMUSG00000029338	Antxr2	2310046B19Rik|AW561899|CMG-2|CMG2|cI-35	anthrax toxin receptor 2	protein-coding
mm_83124.1	chr9	40414486	40414533	-	1	NA	intron (NM_172768, intron 1 of 19)	RLTR16C_MM|LTR|ERVK	41255	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_38001.1	chr4	133674068	133674115	-	1	NA	Intergenic	Intergenic	-1444	NM_001145956	230801	Mm.217004	NM_178698	ENSMUSG00000043257	Pigv	B330013B03|D430024F16Rik	phosphatidylinositol glycan anchor biosynthesis, class V	protein-coding
mm_16850.1	chr2	11605036	11605038	-	1	NA	Intergenic	B3|SINE|B2	-1838	NM_152824	76938	Mm.182769	NM_152824	ENSMUSG00000037197	Rbm17	2700027J02Rik	RNA binding motif protein 17	protein-coding
mm_70319.1	chr8	4249458	4249459	+	1	NA	exon (NM_001195258, exon 3 of 7)	exon (NM_001195258, exon 3 of 7)	1244	NM_001195258	100044509	Mm.439193	NM_001195258	ENSMUSG00000089736	Tgfbr3l	Gm14378|OTTMUSG00000016477	transforming growth factor, beta receptor III-like	protein-coding
mm_36439.1	chr4	82296641	82296644	-	1	NA	3' UTR (NM_001113209, exon 12 of 12)	3' UTR (NM_001113209, exon 12 of 12)	209137	NM_001286127	18028	Mm.317947	NM_008687	ENSMUSG00000008575	Nfib	6720429L07Rik|CTF|E030026I10Rik|NF-I/B|NF1-B|NFI-B	nuclear factor I/B	protein-coding
mm_31856.1	chr4	78212015	78212049	+	1	NA	promoter-TSS (NM_011211)	promoter-TSS (NM_011211)	-137	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding
mm_6637.1	chr1	78968085	78968100	-	1	NA	Intergenic	Intergenic	151143	NM_021342	57814	Mm.24386	NM_021342	ENSMUSG00000047330	Kcne4	AW487937|MiRP3	potassium voltage-gated channel, Isk-related subfamily, gene 4	protein-coding
mm_23881.1	chr3	83031021	83031025	+	1	NA	exon (NM_010196, exon 5 of 5)	exon (NM_010196, exon 5 of 5)	4870	NM_001111048	14161	Mm.88793	NM_010196	ENSMUSG00000028001	Fga	ENSMUSG00000059807|Fib	fibrinogen alpha chain	protein-coding
mm_39498.1	chr5	21186238	21186248	+	1	NA	promoter-TSS (NM_175437)	promoter-TSS (NM_175437)	-24	NM_175437	212167	Mm.121705	NM_175437	ENSMUSG00000039934	Gsap	A530088I07Rik|Pion	gamma-secretase activating protein	protein-coding
mm_69445.1	chr7	132991657	132991678	-	1	NA	exon (NM_001170744, exon 5 of 9)	exon (NM_001170744, exon 5 of 9)	23580	NM_001170744	13017	Mm.246240	NM_009980	ENSMUSG00000030970	Ctbp2	AA407280|D7Ertd45e|Gtrgeo6|Ribeye	C-terminal binding protein 2	protein-coding
mm_19823.1	chr2	110950160	110950169	-	1	NA	promoter-TSS (NM_001128103)	promoter-TSS (NM_001128103)	80	NM_001128103	228432	Mm.483325	NM_001081556	ENSMUSG00000074968	Ano3	AI838058|B230324K02Rik|Tmem16c	anoctamin 3	protein-coding
mm_74070.1	chr8	122433020	122433032	+	1	NA	promoter-TSS (NM_007806)	promoter-TSS (NM_007806)	-86	NM_007806	13057	Mm.271671	NM_007806	ENSMUSG00000006519	Cyba	b558|nmf333|p22-phox|p22phox	cytochrome b-245, alpha polypeptide	protein-coding
mm_2236.1	chr1	91049527	91049536	+	1	NA	intron (NM_001111312, intron 1 of 12)	intron (NM_001111312, intron 1 of 12)	-3913	NM_001310732	16978	Mm.45039	NM_008515	ENSMUSG00000026305	Lrrfip1	AU024550|Fliiap1	leucine rich repeat (in FLII) interacting protein 1	protein-coding
mm_11477.1	chr2	32384723	32384731	+	1	NA	TTS (NM_008491)	TTS (NM_008491)	-2812	NM_198001	73737	Mm.27608	NM_198001	ENSMUSG00000039195	1110008P14Rik	C79326	RIKEN cDNA 1110008P14 gene	protein-coding
mm_138797.1	chr17	37532687	37532696	+	1	NA	Intergenic	Intergenic	2734	NM_001005485	545205	Mm.383371	NM_001005485	ENSMUSG00000090675	Olfr111	-	olfactory receptor 111	protein-coding
mm_140680.1	chr17	12992586	12992598	-	1	NA	promoter-TSS (NM_175394)	promoter-TSS (NM_175394)	-53	NM_175394	60532	Mm.275521	NM_175394	ENSMUSG00000060475	Wtap	2810408K05Rik|9430038B09Rik	Wilms tumour 1-associating protein	protein-coding
mm_172033.1	chr6	125008968	125008985	+	1	NA	promoter-TSS (NM_175557)	promoter-TSS (NM_175557)	-262	NM_001252083	269800	Mm.108677	NM_175557	ENSMUSG00000038346	Zfp384	BB163993|C130073D16Rik|Ciz|NP|Nmp4	zinc finger protein 384	protein-coding
mm_162002.1	chr19	40089681	40089681	+	1	NA	promoter-TSS (NM_001167877)	promoter-TSS (NM_001167877)	2	NM_001167875	107141	Mm.474575	NM_134144	ENSMUSG00000054827	Cyp2c50	AI266900	cytochrome P450, family 2, subfamily c, polypeptide 50	protein-coding
mm_122505.1	chr14	46822233	46822266	-	1	NA	promoter-TSS (NM_022023)	promoter-TSS (NM_022023)	-7	NM_022023	63985	Mm.87312	NM_022023	ENSMUSG00000062014	Gmfb	3110001H22Rik|3110001O16Rik|AI851627|C79176|D14Ertd630e	glia maturation factor, beta	protein-coding
mm_167611.1	chr9	55242495	55242510	-	1	NA	intron (NM_032002, intron 3 of 7)	PB1|SINE|Alu	33567	NM_028049	71999	Mm.276429	NM_028049	ENSMUSG00000032309	Fbxo22	0610033L19Rik|1600016C16Rik	F-box protein 22	protein-coding
mm_32913.1	chr4	119133428	119133490	+	1	NA	exon (NM_011400, exon 6 of 10)	exon (NM_011400, exon 6 of 10)	24714	NM_011400	20525	Mm.21002	NM_011400	ENSMUSG00000028645	Slc2a1	Glut-1|Glut1	solute carrier family 2 (facilitated glucose transporter), member 1	protein-coding
mm_157920.1	chrX	78583815	78583821	-	1	NA	promoter-TSS (NM_001289683)	promoter-TSS (NM_001289683)	-13	NM_001164275	546336	Mm.211712	NM_027322	ENSMUSG00000047996	Prrg1	2010007L08Rik	proline rich Gla (G-carboxyglutamic acid) 1	protein-coding
mm_20113.1	chr2	121159736	121159749	-	1	NA	3' UTR (NM_001290819, exon 5 of 5)	3' UTR (NM_001290819, exon 5 of 5)	11383	NM_001290819	99334	Mm.188422	NM_178889	ENSMUSG00000050619	Zscan29	AW125441|Zfp690	zinc finger SCAN domains 29	protein-coding
mm_144077.1	chr17	91092824	91092858	-	1	NA	promoter-TSS (NM_020252)	promoter-TSS (NM_020252)	-39	NM_020252	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_86642.1	chr10	14134358	14134362	+	1	NA	intron (NM_010437, intron 5 of 8)	intron (NM_010437, intron 5 of 8)	167981	NM_010437	15273	Mm.42157	NM_010437	ENSMUSG00000015501	Hivep2	Gm20114|MIBP1|Schnurri-2|Shn-2	human immunodeficiency virus type I enhancer binding protein 2	protein-coding
mm_22626.1	chr3	14766459	14766467	+	1	NA	3' UTR (NM_001083957, exon 7 of 7)	3' UTR (NM_001083957, exon 7 of 7)	11997	NM_001083957	12346	Mm.273195	NM_009799	ENSMUSG00000027556	Car1	AW555628|Ca1|Car-1	carbonic anhydrase 1	protein-coding
mm_149716.1	chr19	21653523	21653536	+	1	NA	promoter-TSS (NM_025423)	promoter-TSS (NM_025423)	220	NM_146096	226016	Mm.28796	NM_146096	ENSMUSG00000047368	Abhd17b	5730446C15Rik|Cgi67|Fam108b|Fam108b1	abhydrolase domain containing 17B	protein-coding
mm_112627.1	chr13	15851027	15851035	+	1	NA	Intergenic	Intergenic	43788	NR_046131	328190	Mm.446957	NR_046131		A530046M15Rik	A530046M15	RIKEN cDNA A530046M15 gene	ncRNA
mm_59743.1	chr7	28818541	28818551	+	1	NA	intron (NM_177301, intron 7 of 12)	intron (NM_177301, intron 7 of 12)	-6792	NM_016772	51798	Mm.291776	NM_016772	ENSMUSG00000053898	Ech1	AA617331	enoyl coenzyme A hydratase 1, peroxisomal	protein-coding
mm_87965.1	chr10	63386645	63386662	+	1	NA	promoter-TSS (NM_013888)	promoter-TSS (NM_013888)	90	NM_013888	30045	Mm.32550	NM_013888	ENSMUSG00000036764	Dnajc12	Jdp1|mJDP1	DnaJ heat shock protein family (Hsp40) member C12	protein-coding
mm_150724.1	chr19	43647481	43647485	+	1	NA	Intergenic	Intergenic	27398	NM_145156	246696	Mm.23827	NM_145156	ENSMUSG00000040414	Slc25a28	2210403D18Rik|Mfrn2|Mrs3/4	solute carrier family 25, member 28	protein-coding
mm_98940.1	chr11	98377980	98377990	+	1	NA	intron (NM_021547, intron 9 of 14)	intron (NM_021547, intron 9 of 14)	-5826	NM_011540	21393	Mm.10762	NM_011540	ENSMUSG00000007877	Tcap	AI503981|AJ223855	titin-cap	protein-coding
mm_66556.1	chr7	45235463	45235478	-	1	NA	exon (NM_007645, exon 6 of 8)	exon (NM_007645, exon 6 of 8)	3369	NM_007645	12493	Mm.3689	NM_007645	ENSMUSG00000030798	Cd37	Tspan26	CD37 antigen	protein-coding
mm_63653.1	chr7	128748925	128748947	+	1	NA	intron (NM_001029982, intron 1 of 18)	intron (NM_001029982, intron 1 of 18)	4066	NM_001029982	207352	Mm.297105	NM_001029982	ENSMUSG00000055319	Sec23ip	D7Ertd373e|p125	Sec23 interacting protein	protein-coding
mm_158776.1	chrX	167091951	167091978	-	1	NA	Intergenic	Intergenic	-21594	NM_001101606	667794	Mm.302232	NM_001101606		Gm8817	EG667794	predicted gene 8817	protein-coding
mm_171086.1	chr3	124385501	124385513	+	1	NA	Intergenic	Intergenic	40521	NM_027939	71824	Mm.331353	NM_027939	ENSMUSG00000027973	1700006A11Rik	-	RIKEN cDNA 1700006A11 gene	protein-coding
mm_143914.1	chr17	85615001	85615010	-	1	NA	intron (NR_038084, intron 2 of 3)	CpG	3391	NR_038084	100043902	Mm.150838	NR_015385	ENSMUSG00000093460	Six3os1	D17Mgi26|E130112H22Rik|Rncr1|Six3os	SIX homeobox 3, opposite strand 1	ncRNA
mm_99217.1	chr11	101031387	101031390	+	1	NA	TTS (NR_105893)	TTS (NR_105893)	1048	NR_105893	102466767		NR_105893	ENSMUSG00000098415	Mir6928	Gm27728|mmu-mir-6928	microRNA 6928	ncRNA
mm_184.1	chr1	15201848	15201850	+	1	NA	Intergenic	RMER21B|LTR|ERV1	-110603	NM_001098528	98741	Mm.156081	NM_001033195	ENSMUSG00000092083	Kcnb2	9630047L19Rik|BB130875|Kv2.2	potassium voltage gated channel, Shab-related subfamily, member 2	protein-coding
mm_96716.1	chr11	69664326	69664353	+	1	NA	non-coding (NR_110993, exon 5 of 5)	non-coding (NR_110993, exon 5 of 5)	1296	NR_035455	100316840		NR_035455	ENSMUSG00000088752	Mir1934	mir-1934|mmu-mir-1934	microRNA 1934	ncRNA
mm_25165.1	chr3	103065044	103065057	+	1	NA	3' UTR (NM_010937, exon 7 of 7)	3' UTR (NM_010937, exon 7 of 7)	6765	NM_010937	18176	Mm.400954	NM_010937	ENSMUSG00000027852	Nras	AV095280|N-ras	neuroblastoma ras oncogene	protein-coding
mm_108499.1	chr12	83763657	83763671	+	1	NA	promoter-TSS (NM_130887)	promoter-TSS (NM_130887)	30	NM_130887	170721	Mm.133443	NM_130887	ENSMUSG00000021223	Papln	E030033C16Rik	papilin, proteoglycan-like sulfated glycoprotein	protein-coding
mm_109157.1	chr12	108179137	108179169	+	1	NA	promoter-TSS (NM_009832)	promoter-TSS (NM_009832)	131	NM_028262	52690	Mm.159185	NM_028262	ENSMUSG00000056770	Setd3	2610102I01Rik|2610305M23Rik|6030490B17Rik|D12Ertd771e	SET domain containing 3	protein-coding
mm_54133.1	chr6	21784048	21784051	-	1	NA	intron (NM_173007, intron 8 of 8)	(A)n|Simple_repeat|Simple_repeat	68466	NM_173007	269831	Mm.21950	NM_173007	ENSMUSG00000029669	Tspan12	9030619E17|AI426782|AI663988|AW111457|Tm4sf12	tetraspanin 12	protein-coding
mm_152100.1	chr19	6910135	6910142	-	1	NA	promoter-TSS (NM_012021)	promoter-TSS (NM_012021)	440	NM_026306	67674	Mm.318804	NM_026306	ENSMUSG00000038812	Trmt112	0610038D11Rik|Trm112p	tRNA methyltransferase 11-2	protein-coding
mm_37657.1	chr4	128961881	128961884	-	1	NA	intron (NM_172875, intron 2 of 10)	intron (NM_172875, intron 2 of 10)	573	NM_172875	242669	Mm.215814	NM_172875	ENSMUSG00000028789	Azin2	4933429I20Rik|Adc|Azi2|B930082O19|ODC-p|Odcp	antizyme inhibitor 2	protein-coding
mm_97798.1	chr11	82951407	82951448	+	1	NA	promoter-TSS (NM_183201)	promoter-TSS (NM_183201)	-675	NM_183201	327978	Mm.42147	NM_183201	ENSMUSG00000054404	Slfn5	AI956840	schlafen 5	protein-coding
mm_148608.1	chr19	5328050	5328061	+	1	NA	Intergenic	Intergenic	-7686	NM_139301	225865	Mm.87321	NM_139301	ENSMUSG00000038498	Catsper1	Catsper|KSper	cation channel, sperm associated 1	protein-coding
mm_89374.1	chr10	88740147	88740153	+	1	NA	intron (NM_025859, intron 4 of 5)	ORR1D2|LTR|ERVL-MaLR	8736	NM_025859	104303	Mm.291247	NM_025859	ENSMUSG00000060904	Arl1	2310008D22Rik|AU019749	ADP-ribosylation factor-like 1	protein-coding
mm_85218.1	chr9	96984189	96984199	-	1	NA	intron (NM_145134, intron 2 of 2)	intron (NM_145134, intron 2 of 2)	34161	NM_145134	211949	Mm.491271	NM_145134	ENSMUSG00000046997	Spsb4	D030068E18Rik|SSB-4|Ssb4	splA/ryanodine receptor domain and SOCS box containing 4	protein-coding
mm_100363.1	chr11	118515785	118515787	+	1	NA	intron (NM_001285436, intron 3 of 13)	intron (NM_001285436, intron 3 of 13)	38826	NM_172573	217364	Mm.473963	NM_172573	ENSMUSG00000033857	Engase	C130099A03|D230014K01Rik	endo-beta-N-acetylglucosaminidase	protein-coding
mm_43091.1	chr5	124450832	124450848	+	1	NA	exon (NM_001310723, exon 3 of 7)	exon (NM_001310723, exon 3 of 7)	4136	NM_001310727	67956	Mm.137966	NM_030241	ENSMUSG00000049327	Kmt5a	2410195B05Rik|AA617402|AW536475|PR-SET7|PR/SET07|Setd8	lysine methyltransferase 5A	protein-coding
mm_44223.1	chr5	4803634	4803638	-	1	NA	3' UTR (NM_001310448, exon 14 of 14)	3' UTR (NM_001310448, exon 14 of 14)	-45420	NM_021457	14362	Mm.246003	NM_021457	ENSMUSG00000044674	Fzd1	AW227548|FZ-1|Fz1	frizzled class receptor 1	protein-coding
mm_149579.1	chr19	14834712	14834718	+	1	NA	Intergenic	L1ME4c|LINE|L1	-236532	NM_001302947	21888	Mm.103638	NM_011600	ENSMUSG00000024642	Tle4	5730411M05Rik|AA792082|Bce-1|Bce1|ESTM13|ESTM14|Grg4|X83332|X83333|grg-4	transducin-like enhancer of split 4	protein-coding
mm_149410.1	chr19	11407704	11407716	+	1	NA	promoter-TSS (NM_029499)	promoter-TSS (NM_029499)	49	NM_029499	64380	Mm.440715	NM_029499	ENSMUSG00000024675	Ms4a4c	5830413L19Rik|AI449185|Ms4a9	membrane-spanning 4-domains, subfamily A, member 4C	protein-coding
mm_36678.1	chr4	96507329	96507348	-	1	NA	promoter-TSS (NM_001104927)	promoter-TSS (NM_001104927)	48	NM_001104927	665095	Mm.331717	NM_001104927	ENSMUSG00000082932	Cyp2j8	Cyp2j8-ps|OTTMUSG00000007938	cytochrome P450, family 2, subfamily j, polypeptide 8	protein-coding
mm_39282.1	chr5	3928268	3928300	+	1	NA	promoter-TSS (NM_194462)	promoter-TSS (NM_194462)	98	NM_194462	100986	Mm.46044	NM_194462	ENSMUSG00000040407	Akap9	5730481H23Rik|AKAP-9|AKAP450|AW545847|C79026|G1-448-15|PRKA9|mKIAA0803|mei2-5|repro12	A kinase (PRKA) anchor protein (yotiao) 9	protein-coding
mm_103400.1	chr11	75438436	75438438	-	1	NA	exon (NM_008878, exon 2 of 10)	exon (NM_008878, exon 2 of 10)	1064	NM_008878	18816	Mm.279733	NM_008878	ENSMUSG00000038224	Serpinf2	AI747498|Pli|Serpimf2	serine (or cysteine) peptidase inhibitor, clade F, member 2	protein-coding
mm_109734.1	chr12	117153822	117153830	+	1	NA	intron (NM_011215, intron 12 of 22)	GC_rich|Low_complexity|Low_complexity	-2557	NR_033538	100038689	Mm.445351	NR_033538	ENSMUSG00000099907	Gm10421	ENSMUSG00000072792	predicted gene 10421	ncRNA
mm_107857.1	chr12	69597761	69597767	+	1	NA	intron (NM_001135559, intron 17 of 22)	intron (NM_001135559, intron 17 of 22)	-14736	NM_001033236	207965	Mm.102487	NM_001033236	ENSMUSG00000049882	Vcpkmt	Gm71|Mettl21d|Mettl221d|VCP-KMT	valosin containing protein lysine (K) methyltransferase	protein-coding
mm_4143.1	chr1	170978807	170978817	+	1	NA	Intergenic	RMER1A|Other|Other	-2741	NM_010187	14130	Mm.425062	NM_010187	ENSMUSG00000026656	Fcgr2b	AI528646|CD32|F630109E10Rik|Fc[g]RII|FcgRII|Fcgr2|Fcgr2a|Fcr-2|Fcr-3|Ly-17|Ly-m20|LyM-1|Lym-1|fcRII	Fc receptor, IgG, low affinity IIb	protein-coding
mm_123006.1	chr14	54993738	54993746	-	1	NA	intron (NM_080728, intron 1 of 40)	MIRb|SINE|MIR	807	NM_080728	140781	Mm.457983	NM_080728	ENSMUSG00000053093	Myh7	B-MHC|MyHC-I|Myhc-b|Myhcb|beta-MHC	myosin, heavy polypeptide 7, cardiac muscle, beta	protein-coding
mm_64357.1	chr7	142390263	142390274	+	1	NA	Intergenic	Intergenic	-2398	NM_009983	13033	Mm.231395	NM_009983	ENSMUSG00000007891	Ctsd	CD|CatD	cathepsin D	protein-coding
mm_153362.1	chr19	40187278	40187294	-	1	NA	promoter-TSS (NM_145499)	promoter-TSS (NM_145499)	0	NM_145499	226105	Mm.29119	NM_145499	ENSMUSG00000060613	Cyp2c70	-	cytochrome P450, family 2, subfamily c, polypeptide 70	protein-coding
mm_3849.1	chr1	160246239	160246246	+	1	NA	intron (NM_001038621, intron 4 of 8)	MTD|LTR|ERVL-MaLR	-33350	NM_009786	12301	Mm.10702	NM_009786	ENSMUSG00000014226	Cacybp	SIP	calcyclin binding protein	protein-coding
mm_158692.1	chrX	160976502	160976509	-	1	NA	intron (NM_001024624, intron 1 of 18)	intron (NM_001024624, intron 1 of 18)	18176	NM_001024624	382253	Mm.443717	NM_001024624	ENSMUSG00000031292	Cdkl5	BC038161|Stk9	cyclin-dependent kinase-like 5	protein-coding
mm_60075.1	chr7	33943210	33943222	+	1	NA	exon (NM_178308, exon 3 of 3)	exon (NM_178308, exon 3 of 3)	1769	NM_178308	110187	Mm.155750	NM_178308	ENSMUSG00000066586	Scgb2b26	Abpbg26|Abpbg4|Abpg|C2d|Scgb2b4	secretoglobin, family 2B, member 26	protein-coding
mm_117530.1	chr13	82950549	82950554	-	1	NA	Intergenic	Intergenic	-252218	NR_039537	100628621		NR_039537	ENSMUSG00000106655	Mir3961	mmu-mir-3961	microRNA 3961	ncRNA
mm_110228.1	chr12	28808692	28808712	-	1	NA	intron (NM_201357, intron 3 of 8)	intron (NM_201357, intron 3 of 8)	56874	NM_201357	380752	Mm.273724	NM_201357	ENSMUSG00000036613	Tssc1	D12Ertd604e|Eipr1	tumor suppressing subtransferable candidate 1	protein-coding
mm_100556.1	chr11	120729487	120729497	+	1	NA	TTS (NM_007621)	TTS (NM_007621)	-2208	NM_001347608	67880	Mm.231091	NM_026428	ENSMUSG00000039450	Dcxr	0610038K04Rik|1810027P18Rik|XR	dicarbonyl L-xylulose reductase	protein-coding
mm_130417.1	chr15	98004700	98004708	-	1	NA	promoter-TSS (NM_001113515)	promoter-TSS (NM_001113515)	20	NM_031163	12824	Mm.2423	NM_031163	ENSMUSG00000022483	Col2a1	Col2|Col2a|Col2a-1|Del1|Dmm|Lpk|Rgsc856	collagen, type II, alpha 1	protein-coding
mm_98807.1	chr11	97050858	97050877	+	1	NA	promoter-TSS (NM_001081434)	promoter-TSS (NM_001081434)	47	NM_001081434	71240	Mm.190450	NM_001081434	ENSMUSG00000038534	Osbpl7	4933437E18Rik	oxysterol binding protein-like 7	protein-coding
mm_69456.1	chr7	133123195	133123224	-	1	NA	5' UTR (NM_009980, exon 1 of 11)	5' UTR (NM_009980, exon 1 of 11)	274	NM_009980	13017	Mm.246240	NM_009980	ENSMUSG00000030970	Ctbp2	AA407280|D7Ertd45e|Gtrgeo6|Ribeye	C-terminal binding protein 2	protein-coding
mm_124413.1	chr14	118012824	118012837	-	1	NA	TTS (NM_010024)	TTS (NM_010024)	39416	NM_010024	13190	Mm.19987	NM_010024	ENSMUSG00000022129	Dct	DT|TRP-2|TRP2|Tyrp-2|Tyrp2|slaty|slt	dopachrome tautomerase	protein-coding
mm_66168.1	chr7	33854836	33854839	-	1	NA	Intergenic	Intergenic	90148	NM_178308	110187	Mm.155750	NM_178308	ENSMUSG00000066586	Scgb2b26	Abpbg26|Abpbg4|Abpg|C2d|Scgb2b4	secretoglobin, family 2B, member 26	protein-coding
mm_165691.1	chr3	93279560	93279567	+	1	NA	Intergenic	Intergenic	-40186	NM_133698	68723	Mm.208047	NM_133698	ENSMUSG00000041991	Hrnr	1110033K19Rik|A530063N20Rik|S100a18	hornerin	protein-coding
mm_12429.1	chr2	70563678	70563709	+	1	NA	promoter-TSS (NR_040496)	promoter-TSS (NR_040496)	-336	NR_040496	68986	Mm.437697	NR_040496	ENSMUSG00000087264	Gad1os	1500002O10Rik	glutamate decarboxylase 1, opposite strand	ncRNA
mm_121509.1	chr14	121951544	121951553	+	1	NA	TTS (NM_183031)	TTS (NM_183031)	13645	NM_183031	321019	Mm.265618	NM_183031	ENSMUSG00000051212	Gpr183	Ebi2	G protein-coupled receptor 183	protein-coding
mm_36261.1	chr4	63467458	63467469	-	1	NA	intron (NM_001008791, intron 2 of 12)	intron (NM_001008791, intron 2 of 12)	28528	NM_001008793	73750	Mm.300397	NM_028640	ENSMUSG00000039137	Whrn	1110035G07Rik|AW122018|AW742671|C430046P22Rik|Dfnb31|Ush2d|wi	whirlin	protein-coding
mm_31691.1	chr4	62361583	62361587	+	1	NA	intron (NM_175090, intron 1 of 4)	intron (NM_175090, intron 1 of 4)	884	NM_175090	20529	Mm.248637	NM_175090	ENSMUSG00000066150	Slc31a1	4930445G01Rik|AI787263|AU016967|Ctr1	solute carrier family 31, member 1	protein-coding
mm_22119.1	chr2	170155102	170155107	-	1	NA	Intergenic	Intergenic	-12429	NM_001159683	228913	Mm.22858	NM_001033299	ENSMUSG00000052056	Zfp217	4933431C08Rik|AW987152|Gm562|ZABC1|Znf217	zinc finger protein 217	protein-coding
mm_11196.1	chr2	29124973	29125048	+	1	NA	promoter-TSS (NM_198033)	promoter-TSS (NM_198033)	18	NM_198033	269254	Mm.41867	NM_198033	ENSMUSG00000043535	Setx	A130090N03|A930037J23Rik|AOA2|AW060766|Als4|SCAR1|Sen1|mKIAA0625	senataxin	protein-coding
mm_106628.1	chr11	120866606	120866617	-	1	NA	exon (NM_027745, exon 16 of 19)	exon (NM_027745, exon 16 of 19)	-42064	NM_007988	14104	Mm.236443	NM_007988	ENSMUSG00000025153	Fasn	A630082H08Rik|FAS	fatty acid synthase	protein-coding
mm_77408.1	chr8	120589020	120589050	-	1	NA	promoter-TSS (NM_178856)	promoter-TSS (NM_178856)	40	NM_178856	272551	Mm.275910	NM_178856	ENSMUSG00000031821	Gins2	2210013I18Rik|4833427B12Rik|AI323585|Pfs2	GINS complex subunit 2 (Psf2 homolog)	protein-coding
mm_28609.1	chr3	94757412	94757416	-	1	NA	Intergenic	Intergenic	29101	NM_001293727	70737	Mm.87634	NM_001037711	ENSMUSG00000068876	Cgn	6330408J11Rik	cingulin	protein-coding
mm_133043.1	chr16	57498172	57498175	+	1	NA	intron (NM_001040397, intron 1 of 4)	intron (NM_001040397, intron 1 of 4)	-51069	NM_001177871	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding
mm_75004.1	chr8	27230806	27230847	-	1	NA	Intergenic	Intergenic	-1238	NM_013462	11556	Mm.278475	NM_013462	ENSMUSG00000031489	Adrb3	Adrb-3	adrenergic receptor, beta 3	protein-coding
mm_139659.1	chr17	57404441	57404446	+	1	NA	intron (NM_010130, intron 5 of 21)	L1_Mur2|LINE|L1	45757	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_166454.1	chr5	137981490	137981499	+	1	NA	promoter-TSS (NM_013478)	promoter-TSS (NM_013478)	-27	NM_013478	12007	Mm.30061	NM_013478	ENSMUSG00000037053	Azgp1	Zag	alpha-2-glycoprotein 1, zinc	protein-coding
mm_15688.1	chr2	163658371	163658510	+	1	NA	promoter-TSS (NM_001039391)	promoter-TSS (NM_001039391)	-18	NM_001164053	18769	Mm.10091	NM_011106	ENSMUSG00000035268	Pkig	PKIgamma	protein kinase inhibitor, gamma	protein-coding
mm_39472.1	chr5	19907775	19907811	+	1	NA	5' UTR (NM_001170745, exon 1 of 21)	5' UTR (NM_001170745, exon 1 of 21)	275	NM_015823	50791	Mm.332231	NM_015823	ENSMUSG00000040003	Magi2	AIP-1|Acvri1|Acvrinp1|Acvrip1|Magi-2|S-SCAM|mKIAA0705	membrane associated guanylate kinase, WW and PDZ domain containing 2	protein-coding
mm_127604.1	chr15	102406968	102406977	+	1	NA	intron (NM_013672, intron 1 of 5)	intron (NM_013672, intron 1 of 5)	656	NM_013672	20683	Mm.4618	NM_013672	ENSMUSG00000001280	Sp1	1110003E12Rik|AA450830|AI845540|Sp1-1	trans-acting transcription factor 1	protein-coding
mm_136749.1	chr17	8525246	8525254	+	1	NA	Intergenic	Intergenic	-1551	NM_001290707	23984	Mm.87161	NM_011866	ENSMUSG00000023868	Pde10a	-	phosphodiesterase 10A	protein-coding
mm_130578.1	chr15	99527662	99527673	-	1	NA	5' UTR (NM_028224, exon 1 of 12)	5' UTR (NM_028224, exon 1 of 12)	498	NM_028224	72393	Mm.39760	NM_028224	ENSMUSG00000023011	Faim2	2900002L20Rik|Lfg|Lfg2|NMP25|Nmp35|Tmbim2	Fas apoptotic inhibitory molecule 2	protein-coding
mm_56417.1	chr6	97252679	97252698	-	1	NA	promoter-TSS (NM_001081157)	promoter-TSS (NM_001081157)	92	NM_001081157	320502	Mm.68163	NM_001081157	ENSMUSG00000044086	Lmod3	5430424A14Rik	leiomodin 3 (fetal)	protein-coding
mm_164995.1	chr19	17145556	17145559	+	1	NA	intron (NM_181348, intron 9 of 19)	Lx6|LINE|L1	189439	NM_181348	353211	Mm.257354	NM_181348	ENSMUSG00000039126	Prune2	6330414G02Rik|A230083H22Rik|A330102H22Rik|Bmcc1|mKIAA0367	prune homolog 2	protein-coding
mm_49943.1	chr6	39871552	39871560	+	1	NA	Intergenic	CpG	-60620	NM_001010930	14548	Mm.377071	NM_010270	ENSMUSG00000029918	Mrps33	AI841153|CGI-139|Gdap3|MRP-S33|PTD003	mitochondrial ribosomal protein S33	protein-coding
mm_150945.1	chr19	46308225	46308231	+	1	NA	exon (NM_001177370, exon 9 of 22)	exon (NM_001177370, exon 9 of 22)	2298	NM_001177370	18034	Mm.102365	NM_019408	ENSMUSG00000025225	Nfkb2	NF-kappaB2|lyt|p49|p49/p100|p50B|p52	nuclear factor of kappa light polypeptide gene enhancer in B cells 2, p49/p100	protein-coding
mm_65164.1	chr7	19676750	19676767	-	1	NA	5' UTR (NM_001277944, exon 2 of 5)	5' UTR (NM_001277944, exon 2 of 5)	1183	NM_001277944	11813	Mm.28394	NM_001277944	ENSMUSG00000002992	Apoc2	apo-CII|apoC-II	apolipoprotein C-II	protein-coding
mm_112105.1	chr12	112785584	112785599	-	1	NA	Intergenic	Intergenic	-23384	NM_145450	217887	Mm.186678	NM_145450	ENSMUSG00000037594	BC022687	AW050009|C130001I08Rik|Flj20080	cDNA sequence BC022687	protein-coding
mm_88076.1	chr10	67979650	67979660	+	1	NA	promoter-TSS (NM_001081346)	promoter-TSS (NM_001081346)	57	NM_001081346	170799	Mm.209844	NM_133244	ENSMUSG00000037846	Rtkn2	B130039D23Rik|Mbf|Plekhk1	rhotekin 2	protein-coding
mm_100469.1	chr11	119943083	119943099	+	1	NA	promoter-TSS (NM_001037755)	promoter-TSS (NM_001037755)	-1	NM_001037754	108100	Mm.197534	NM_130862	ENSMUSG00000025372	Baiap2	IRSp53|R75030	brain-specific angiogenesis inhibitor 1-associated protein 2	protein-coding
mm_52910.1	chr6	122820779	122820802	+	1	NA	5' UTR (NM_021899, exon 1 of 11)	5' UTR (NM_021899, exon 1 of 11)	606	NM_021899	60611	Mm.87142	NM_021899	ENSMUSG00000003154	Foxj2	Fhx	forkhead box J2	protein-coding
mm_9969.1	chr1	191183245	191183260	-	1	NA	promoter-TSS (NM_007498)	promoter-TSS (NM_007498)	81	NM_007498	11910	Mm.2706	NM_007498	ENSMUSG00000026628	Atf3	LRG-21	activating transcription factor 3	protein-coding
mm_56662.1	chr6	113501951	113501963	-	1	NA	promoter-TSS (NM_172487)	promoter-TSS (NM_172487)	-26	NM_001289700	210673	Mm.133060	NM_172487	ENSMUSG00000045009	Prrt3	6330505P20|B230206N24Rik	proline-rich transmembrane protein 3	protein-coding
mm_39358.1	chr5	9101320	9101345	+	1	NA	exon (NM_001081029, exon 2 of 5)	exon (NM_001081029, exon 2 of 5)	595	NM_001081029	652925	Mm.439954	NM_001081029	ENSMUSG00000079659	Tmem243	4930420K17Rik|E030031F02Rik	transmembrane protein 243, mitochondrial	protein-coding
mm_152466.1	chr19	10948551	10948567	-	1	NA	exon (NM_023731, exon 1 of 4)	exon (NM_023731, exon 1 of 4)	707	NM_023731	108673	Mm.294908	NM_023731	ENSMUSG00000024732	Ccdc86	4933411H20Rik|6720480F16Rik|D19Ertd678e	coiled-coil domain containing 86	protein-coding
mm_127875.1	chr15	8465277	8465305	-	1	NA	Intergenic	Intergenic	-20828	NM_201232	71175	Mm.240329	NM_027707	ENSMUSG00000022141	Nipbl	Idn3	Nipped-B homolog (Drosophila)	protein-coding
mm_123383.1	chr14	63271855	63271881	-	1	NA	Intergenic	Intergenic	-26597	NM_001310610	14463	Mm.247669	NM_008092	ENSMUSG00000021944	Gata4	Gata-4	GATA binding protein 4	protein-coding
mm_12968.1	chr2	90738432	90738441	+	1	NA	Intergenic	B4|SINE|B4	-6934	NM_018828	55935	Mm.489638	NM_018828	ENSMUSG00000008200	Fnbp4	FBP30|Fnbp30|mKIAA1014	formin binding protein 4	protein-coding
mm_137659.1	chr17	28691389	28691399	+	1	NA	promoter-TSS (NM_011951)	promoter-TSS (NM_011951)	52	NM_001168514	26416	Mm.311337	NM_011951	ENSMUSG00000053436	Mapk14	CSBP2|Crk1|Csbp1|Mxi2|PRKM14|PRKM15|p38|p38-alpha|p38MAPK|p38a|p38alpha	mitogen-activated protein kinase 14	protein-coding
mm_8304.1	chr1	144003828	144003869	-	1	NA	intron (NM_009061, intron 1 of 4)	intron (NM_009061, intron 1 of 4)	301	NM_009061	19735	Mm.28262	NM_009061	ENSMUSG00000026360	Rgs2	GOS8	regulator of G-protein signaling 2	protein-coding
mm_14495.1	chr2	131950856	131950867	+	1	NA	promoter-TSS (NM_001278257)	promoter-TSS (NM_001278257)	0	NM_001278257	26434	Mm.180750	NM_023043	ENSMUSG00000027338	Prnd	AI450264|Dpl|PrPLP|doppel	prion protein dublet	protein-coding
mm_13281.1	chr2	101624697	101624730	+	1	NA	promoter-TSS (NM_009020)	promoter-TSS (NM_009020)	-35	NM_009020	19374	Mm.4988	NM_009020	ENSMUSG00000032864	Rag2	Rag-2	recombination activating gene 2	protein-coding
mm_61511.1	chr7	78882620	78882634	+	1	NA	Intergenic	CpG	-5650	NR_029826	723884		NR_029826	ENSMUSG00000065609	Mir7-2	Mir7a2|Mirn7-2|mir-7a-2|mir-7a2|mmu-mir-7-2|mmu-mir-7a2	microRNA 7-2	ncRNA
mm_127137.1	chr15	98168274	98168290	+	1	NA	5' UTR (NM_177716, exon 1 of 1)	5' UTR (NM_177716, exon 1 of 1)	476	NM_177716	239650	Mm.54140	NM_177716	ENSMUSG00000029875	Ccdc184	5630400A08|AI836003	coiled-coil domain containing 184	protein-coding
mm_49036.1	chr6	4759904	4759934	+	1	NA	3' UTR (NM_130877, exon 2 of 2)	3' UTR (NM_130877, exon 2 of 2)	12613	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_139201.1	chr17	47668760	47668792	+	1	NA	intron (NM_198421, intron 2 of 6)	B1F|SINE|Alu	-18834	NR_045945	100415787	Mm.392206	NR_045945	ENSMUSG00000084880	Tomm6os	Gm14872|OTTMUSG00000018355|Prickle4os	translocase of outer mitochondrial membrane 6, opposite strand	ncRNA
mm_123023.1	chr14	55116587	55116609	-	1	NA	5' UTR (NM_177049, exon 1 of 6)	5' UTR (NM_177049, exon 1 of 6)	337	NM_177049	319984	Mm.19047	NM_177049	ENSMUSG00000022208	Jph4	9330157P13Rik|JP-4|JPHL1	junctophilin 4	protein-coding
mm_64361.1	chr7	142399489	142399499	+	1	NA	Intergenic	Intergenic	-11624	NM_009983	13033	Mm.231395	NM_009983	ENSMUSG00000007891	Ctsd	CD|CatD	cathepsin D	protein-coding
mm_10018.1	chr1	192074014	192074036	-	1	NA	intron (NM_011633, intron 1 of 9)	intron (NM_011633, intron 1 of 9)	18574	NM_011633	22033	Mm.380491	NM_011633		Traf5	-	TNF receptor-associated factor 5	protein-coding
mm_8121.1	chr1	136133046	136133068	-	1	NA	intron (NM_001039472, intron 1 of 34)	intron (NM_001039472, intron 1 of 34)	1656	NM_001039472	16565	Mm.276135	NM_019962	ENSMUSG00000041642	Kif21b	2610511N21Rik|mKIAA0449	kinesin family member 21B	protein-coding
mm_89173.1	chr10	86331627	86331629	+	1	NA	intron (NM_011595, intron 1 of 4)	intron (NM_011595, intron 1 of 4)	31216	NM_011595	21859	Mm.4871	NM_011595	ENSMUSG00000020044	Timp3	Timp-3	tissue inhibitor of metalloproteinase 3	protein-coding
mm_86797.1	chr10	20267245	20267266	+	1	NA	exon (NM_008635, exon 10 of 18)	exon (NM_008635, exon 10 of 18)	30433	NR_105840	102466647		NR_105840	ENSMUSG00000098887	Mir6413	Gm27432|mmu-mir-6413	microRNA 6413	ncRNA
mm_59608.1	chr7	28142286	28142302	+	1	NA	exon (NM_001164655, exon 6 of 20)	exon (NM_001164655, exon 6 of 20)	12828	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_107819.1	chr12	67059182	67059193	+	1	NA	intron (NM_001193266, intron 1 of 16)	GSAT_MM|Satellite|Satellite	163362	NM_001193266	320772	Mm.227680	NM_207010	ENSMUSG00000034912	Mdga2	6720489L24Rik|9330209L04Rik|Adp|Mamdc1	MAM domain containing glycosylphosphatidylinositol anchor 2	protein-coding
mm_82880.1	chr9	32486331	32486354	-	1	NA	intron (NM_008026, intron 1 of 8)	B1_Mur3|SINE|Alu	55110	NM_008026	14247	Mm.258908	NM_008026	ENSMUSG00000016087	Fli1	EWSR2|Fli-1|SIC-1|Sic1	Friend leukemia integration 1	protein-coding
mm_86095.1	chr9	115243713	115243728	-	1	NA	3' UTR (NM_024222, exon 16 of 16)	3' UTR (NM_024222, exon 16 of 16)	38350	NR_029430	111186	Mm.484753	NR_029430		Stmn1-rs1	Lag-rs1|Lap18-rs1	stathmin 1, related sequence 1	pseudo
mm_43455.1	chr5	136217552	136217578	+	1	NA	TTS (NM_018825)	TTS (NM_018825)	-18611	NM_025774	66801	Mm.425295	NM_025774	ENSMUSG00000039737	Prkrip1	8430424D23Rik|C114	Prkr interacting protein 1 (IL11 inducible)	protein-coding
mm_165946.1	chr4	82591221	82591223	+	1	NA	Intergenic	Intergenic	83233	NR_137202	102635783	Mm.41666	NR_137202		Gm11266	OTTMUSG00000000396	predicted gene 11266	ncRNA
mm_142423.1	chr17	45569034	45569072	-	1	NA	exon (NM_008302, exon 9 of 11)	exon (NM_008302, exon 9 of 11)	4208	NM_008302	15516	Mm.2180	NM_008302	ENSMUSG00000023944	Hsp90ab1	90kDa|AL022974|C81438|Hsp84|Hsp84-1|Hsp90|Hspcb	heat shock protein 90 alpha (cytosolic), class B member 1	protein-coding
mm_47090.1	chr5	117389030	117389051	-	1	NA	promoter-TSS (NM_028128)	promoter-TSS (NM_028128)	-17	NM_028128	72151	Mm.27997	NM_028128	ENSMUSG00000029363	Rfc5	2610020K06Rik|2610209F07Rik|36.5kDa|36kDa|Recc5	replication factor C (activator 1) 5	protein-coding
mm_107466.1	chr12	37241926	37241939	+	1	NA	5' UTR (NM_178767, exon 1 of 13)	5' UTR (NM_178767, exon 1 of 13)	293	NM_178767	319660	Mm.485540	NM_178767	ENSMUSG00000050103	Agmo	A530016O06Rik|AI790538|Tmem195	alkylglycerol monooxygenase	protein-coding
mm_63776.1	chr7	131560364	131560398	+	1	NA	promoter-TSS (NM_009774)	promoter-TSS (NM_009774)	11	NM_009774	12237	Mm.927	NM_009774	ENSMUSG00000066979	Bub3	AU019800|AU021329|AU043350|AW146323|C78067	BUB3 mitotic checkpoint protein	protein-coding
mm_42914.1	chr5	122655592	122655595	+	1	NA	TTS (NM_001038887)	TTS (NM_001038887)	5169	NM_001284402	18439	Mm.42026	NM_011027	ENSMUSG00000029468	P2rx7	AI467586|P2X(7)|P2X7R	purinergic receptor P2X, ligand-gated ion channel, 7	protein-coding
mm_109743.1	chr12	117533858	117533910	+	1	NA	intron (NM_175930, intron 3 of 27)	CpG	17405	NM_175930	217944	Mm.227642	NM_175930	ENSMUSG00000041992	Rapgef5	4932413M22|C86120|D030051B22Rik|GFR|Mrgef|mKIAA0277|mmr-gef	Rap guanine nucleotide exchange factor (GEF) 5	protein-coding
mm_171873.1	chr5	29356467	29356492	-	1	NA	intron (NM_020295, intron 3 of 16)	L1Md_T|LINE|L1	21911	NM_020295	56873	Mm.41572	NM_020295	ENSMUSG00000010721	Lmbr1	1110048D14Rik|AU017641	limb region 1	protein-coding
mm_13952.1	chr2	121303395	121303406	+	1	NA	exon (NM_001173506, exon 4 of 6)	exon (NM_001173506, exon 4 of 6)	7946	NM_001173506	17754	Mm.36501	NM_032393	ENSMUSG00000027254	Map1a	6330416M19Rik|AI853608|Mtap-1|Mtap1|Mtap1a|moth1	microtubule-associated protein 1 A	protein-coding
mm_61138.1	chr7	56239744	56239781	+	1	NA	promoter-TSS (NM_021879)	promoter-TSS (NM_021879)	-9	NM_021879	18431	Mm.137052	NM_021879	ENSMUSG00000030450	Oca2	D7H15S12|D7Icr28RN|D7Nic1|p|p<cas>	oculocutaneous albinism II	protein-coding
mm_127088.1	chr15	97782188	97782194	+	1	NA	Intergenic	Intergenic	-2174	NM_026353	67739	Mm.28955	NM_026353	ENSMUSG00000081534	Slc48a1	4930570C03Rik	solute carrier family 48 (heme transporter), member 1	protein-coding
mm_116325.1	chr13	37994076	37994091	-	1	NA	exon (NM_025965, exon 1 of 8)	exon (NM_025965, exon 1 of 8)	107	NM_025965	107513	Mm.426670	NM_025965	ENSMUSG00000021427	Ssr1	2510001K09Rik|6330400D04|AI159733|AI452176|SSR|TRAPA	signal sequence receptor, alpha	protein-coding
mm_168457.1	chr1	143683172	143683188	+	1	NA	intron (NM_145991, intron 6 of 16)	intron (NM_145991, intron 6 of 16)	19713	NM_145991	214498	Mm.156727	NM_145991	ENSMUSG00000026361	Cdc73	8430414L16Rik|C130030P16Rik|C81219|Hrpt2	cell division cycle 73, Paf1/RNA polymerase II complex component	protein-coding
mm_142913.1	chr17	53539412	53539459	-	1	NA	promoter-TSS (NM_173449)	promoter-TSS (NM_173449)	16	NM_173449	110332	Mm.444633	NM_173449	ENSMUSG00000044957	Pp2d1	4921523A10Rik	protein phosphatase 2C-like domain containing 1	protein-coding
mm_140589.1	chr17	10216776	10216779	-	1	NA	intron (NM_021881, intron 5 of 6)	intron (NM_021881, intron 5 of 6)	102584	NM_021881	19317	Mm.130694	NM_021881	ENSMUSG00000062078	Qk	1110003F05Rik|1500005P18|QkI|l(17)-1Wis|l17Wis1	quaking	protein-coding
mm_78789.1	chr9	44043268	44043280	+	1	NA	promoter-TSS (NM_009382)	promoter-TSS (NM_009382)	-110	NM_009382	21838	Mm.3951	NM_009382	ENSMUSG00000032011	Thy1	CD90|T25|Thy-1|Thy-1.2|Thy1.1|Thy1.2	thymus cell antigen 1, theta	protein-coding
mm_46200.1	chr5	98030995	98031038	-	1	NA	promoter-TSS (NM_133738)	promoter-TSS (NM_133738)	-54	NM_133738	71914	Mm.24842	NM_133738	ENSMUSG00000029338	Antxr2	2310046B19Rik|AW561899|CMG-2|CMG2|cI-35	anthrax toxin receptor 2	protein-coding
mm_154456.1	chrM	2420	2428	-	1	NA	NA	Intergenic	NA	NA								
mm_74117.1	chr8	123102345	123102351	+	1	NA	promoter-TSS (NM_016738)	promoter-TSS (NM_016738)	-2	NM_016738	270106	Mm.319719	NM_016738	ENSMUSG00000000740	Rpl13	A52|L13	ribosomal protein L13	protein-coding
mm_62124.1	chr7	96825528	96825532	+	1	NA	intron (NM_001310760, intron 18 of 32)	B4A|SINE|B4	-23981	NR_045874	791381	Mm.402112	NR_045874	ENSMUSG00000053049	Gm15413	ENSMUSG00000053049|OTTMUSG00000021246	predicted gene 15413	ncRNA
mm_19362.1	chr2	91098833	91098837	-	1	NA	intron (NM_011355, intron 1 of 4)	intron (NM_011355, intron 1 of 4)	2157	NM_011355	20375	Mm.1302	NM_011355	ENSMUSG00000002111	Spi1	Dis-1|Dis1|PU.1|Sfpi-1|Sfpi1|Spi-1|Tcfpu1|Tfpu.1	spleen focus forming virus (SFFV) proviral integration oncogene	protein-coding
mm_25765.1	chr3	125404326	125404340	+	1	NA	5' UTR (NM_022565, exon 1 of 14)	5' UTR (NM_022565, exon 1 of 14)	242	NM_022565	64580	Mm.444289	NM_022565	ENSMUSG00000027971	Ndst4	4930439H17Rik	N-deacetylase/N-sulfotransferase (heparin glucosaminyl) 4	protein-coding
mm_18789.1	chr2	73775060	73775140	-	1	NA	5' UTR (NM_001113246, exon 1 of 13)	5' UTR (NM_001113246, exon 1 of 13)	246	NM_001166603	108699	Mm.257073	NM_029716	ENSMUSG00000056486	Chn1	0610007I19Rik|0710001E19Rik|1700112L09Rik|2900046J01Rik|AI413815|ARHGAP2	chimerin 1	protein-coding
mm_26044.1	chr3	135584656	135584659	+	1	NA	TTS (NM_008689)	TTS (NM_008689)	99046	NM_027288	110173	Mm.280536	NM_027288	ENSMUSG00000028164	Manba	2410030O07Rik|B930014J03Rik|Bmn	mannosidase, beta A, lysosomal	protein-coding
mm_147290.1	chr18	39490412	39490424	-	1	NA	Intergenic	CpG	-3173	NM_008173	14815	Mm.129481	NM_008173	ENSMUSG00000024431	Nr3c1	GR|Grl-1|Grl1	nuclear receptor subfamily 3, group C, member 1	protein-coding
mm_113505.1	chr13	37581117	37581144	+	1	NA	Intergenic	Intergenic	235785	NM_010745	17084	Mm.2639	NM_010745	ENSMUSG00000021423	Ly86	MD-1|MD1|ly86_tv2	lymphocyte antigen 86	protein-coding
mm_105422.1	chr11	103697724	103697734	-	1	NA	promoter-TSS (NM_019650)	promoter-TSS (NM_019650)	5	NR_102396	399609	Mm.351922	NR_102388		C130046K22Rik	-	RIKEN cDNA C130046K22 gene	ncRNA
mm_29247.1	chr3	107218201	107218208	-	1	NA	exon (NM_001111143, exon 4 of 9)	exon (NM_001111143, exon 4 of 9)	3528	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_149054.1	chr19	8839276	8839286	+	1	NA	promoter-TSS (NM_008144)	promoter-TSS (NM_008144)	-35	NM_010316	14704	Mm.329700	NM_010316	ENSMUSG00000071658	Gng3	-	guanine nucleotide binding protein (G protein), gamma 3	protein-coding
mm_100369.1	chr11	119086820	119086825	+	1	NA	promoter-TSS (NM_007625)	promoter-TSS (NM_007625)	-585	NM_007625	12418	Mm.268070	NM_007625	ENSMUSG00000039989	Cbx4	MPc2|PC2	chromobox 4	protein-coding
mm_95142.1	chr11	35121398	35121512	+	1	NA	promoter-TSS (NM_011412)	promoter-TSS (NM_011412)	-1	NM_011412	20564	Mm.478604	NM_011412	ENSMUSG00000056427	Slit3	Slil2|Slit1|b2b2362.1Clo	slit homolog 3 (Drosophila)	protein-coding
mm_74832.1	chr8	23193527	23193531	-	1	NA	intron (NM_018743, intron 1 of 12)	intron (NM_018743, intron 1 of 12)	14924	NM_018743	102247	Mm.200898	NM_018743	ENSMUSG00000031545	Gpat4	AU041707|AW545732|Agpat6|Tsarg7	glycerol-3-phosphate acyltransferase 4	protein-coding
mm_5857.1	chr1	53706776	53706841	-	1	NA	promoter-TSS (NM_001252070)	promoter-TSS (NM_001252070)	-24	NM_001252070	627872	Mm.184692	NM_001252070	ENSMUSG00000096141	Dnah7a	Dnahc7|Dnahc7a|Gm992	dynein, axonemal, heavy chain 7A	protein-coding
mm_75196.1	chr8	39006216	39006224	-	1	NA	intron (NM_030254, intron 1 of 7)	CpG	353	NM_030254	80286	Mm.272722	NM_030254	ENSMUSG00000039530	Tusc3	AU022242|BC003311|N33	tumor suppressor candidate 3	protein-coding
mm_149019.1	chr19	8741816	8741865	+	1	NA	promoter-TSS (NM_019829)	promoter-TSS (NM_019829)	37	NM_019829	56389	Mm.153061	NM_019829	ENSMUSG00000010110	Stx5a	0610031F24Rik|D19Ertd627e|Stx5	syntaxin 5A	protein-coding
mm_40424.1	chr5	53471309	53471352	+	1	NA	Intergenic	Intergenic	-84449	NM_001080928	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_54257.1	chr6	28262670	28262678	-	1	NA	Intergenic	Intergenic	-1073	NM_001081678	627049	Mm.84441	NM_001081678	ENSMUSG00000039841	Zfp800	AA407452|Znf800	zinc finger protein 800	protein-coding
mm_60791.1	chr7	45570321	45570334	+	1	NA	promoter-TSS (NM_001243052)	promoter-TSS (NM_001243052)	174	NM_009737	12036	Mm.24210	NM_009737	ENSMUSG00000030826	Bcat2	Bcat-2|Eca40	branched chain aminotransferase 2, mitochondrial	protein-coding
mm_114880.1	chr13	94192072	94192083	+	1	NA	exon (NM_172589, exon 4 of 4)	exon (NM_172589, exon 4 of 4)	93204	NM_029153	107767	Mm.201455	NM_029153	ENSMUSG00000021687	Scamp1	4930505M11Rik|AI415563|AW122395	secretory carrier membrane protein 1	protein-coding
mm_39553.1	chr5	21790607	21790607	+	1	NA	intron (NM_011188, intron 2 of 12)	intron (NM_011188, intron 2 of 12)	5324	NM_011188	19181	Mm.2462	NM_011188	ENSMUSG00000028932	Psmc2	-	proteasome (prosome, macropain) 26S subunit, ATPase 2	protein-coding
mm_147699.1	chr18	60808056	60808065	-	1	NA	exon (NM_010545, exon 2 of 8)	exon (NM_010545, exon 2 of 8)	-4016	NR_039567	100628611		NR_039567	ENSMUSG00000093327	Mir5107	mir-5107|mmu-mir-5107|mu-mir-5107	microRNA 5107	ncRNA
mm_101036.1	chr11	8600783	8600803	-	1	NA	intron (NM_001083587, intron 2 of 30)	intron (NM_001083587, intron 2 of 30)	63742	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_78870.1	chr9	44407630	44407683	+	1	NA	promoter-TSS (NM_021789)	promoter-TSS (NM_021789)	-58	NM_024266	75617	Mm.292027	NM_024266	ENSMUSG00000009927	Rps25	2810009D21Rik	ribosomal protein S25	protein-coding
mm_51753.1	chr6	87657778	87657784	+	1	NA	intron (NM_024251, intron 5 of 9)	intron (NM_024251, intron 5 of 9)	14387	NM_024251	72103	Mm.31770	NM_024251	ENSMUSG00000030051	Aplf	2010301N04Rik|AI452191	aprataxin and PNKP like factor	protein-coding
mm_121814.1	chr14	20393604	20393643	-	1	NA	promoter-TSS (NM_025440)	promoter-TSS (NM_025440)	-68	NM_025440	66242	Mm.23747	NM_025440	ENSMUSG00000049960	Mrps16	1500011E11Rik|Mprs16	mitochondrial ribosomal protein S16	protein-coding
mm_2662.1	chr1	125780028	125780031	+	1	NA	intron (NM_027677, intron 1 of 1)	MIRb|SINE|MIR	103033	NM_027677	71111	Mm.32727	NM_027677	ENSMUSG00000026343	Gpr39	4933415E13Rik	G protein-coupled receptor 39	protein-coding
mm_37288.1	chr4	119173850	119173901	-	1	NA	promoter-TSS (NM_001145935)	promoter-TSS (NM_001145935)	-19	NM_183140	195522	Mm.169620	NM_183140	ENSMUSG00000045268	Zfp691	6430544H17Rik|Znf691	zinc finger protein 691	protein-coding
mm_134562.1	chr16	20302359	20302401	-	1	NA	promoter-TSS (NM_001005767)	promoter-TSS (NM_001005767)	-18	NM_001005767	381038	Mm.371737	NM_001005767	ENSMUSG00000033918	Parl	D16Ertd607e|PRO2207|PSARL1|PSENIP2|Psarl	presenilin associated, rhomboid-like	protein-coding
mm_141703.1	chr17	33999467	33999487	-	1	NA	exon (NM_001001892, exon 3 of 8)	exon (NM_001001892, exon 3 of 8)	856	NM_001001892	14972	Mm.422886	NM_001001892	ENSMUSG00000061232	H2-K1	H-2K|H-2K(d)|H2-K|K-f	histocompatibility 2, K1, K region	protein-coding
mm_135720.1	chr16	55818514	55818537	-	1	NA	exon (NM_030612, exon 7 of 14)	exon (NM_030612, exon 7 of 14)	3613	NM_001159394	80859	Mm.247272	NM_030612	ENSMUSG00000035356	Nfkbiz	AA408868|INAP|Mail	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, zeta	protein-coding
mm_78521.1	chr9	33728401	33728419	+	1	NA	Intergenic	CpG	-313961	NR_040744	77119	Mm.367930	NR_040744	ENSMUSG00000098758	7630403G23Rik	-	RIKEN cDNA 7630403G23 gene	ncRNA
mm_81595.1	chr9	110529188	110529204	+	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-3401	NM_001081340	235626	Mm.288949	NM_001081340	ENSMUSG00000044791	Setd2	4921524K10Rik|BC031601|KMT3A	SET domain containing 2	protein-coding
mm_123827.1	chr14	70626866	70626899	-	1	NA	5' UTR (NM_001252663, exon 1 of 14)	5' UTR (NM_001252663, exon 1 of 14)	183	NM_001252662	13829	Mm.210863	NM_013514	ENSMUSG00000022099	Dmtn	AI325486|Epb4.9|Epb49|dematin	dematin actin binding protein	protein-coding
mm_167601.1	chr9	50659933	50659973	-	1	NA	promoter-TSS (NM_145614)	promoter-TSS (NM_145614)	-173	NM_145614	235339	Mm.285076	NM_145614	ENSMUSG00000000168	Dlat	6332404G05Rik|DLTA|PDC-E2	dihydrolipoamide S-acetyltransferase (E2 component of pyruvate dehydrogenase complex)	protein-coding
mm_159786.1	chr5	107403562	107403562	+	1	NA	promoter-TSS (NM_001001804)	promoter-TSS (NM_001001804)	49	NM_001001804	384214	Mm.489863	NM_001001804	ENSMUSG00000033805	Ephx4	Abhd7|Ephxrp|Gm1382	epoxide hydrolase 4	protein-coding
mm_106428.1	chr11	119347905	119347917	-	1	NA	intron (NM_018822, intron 6 of 7)	intron (NM_018822, intron 6 of 7)	7599	NM_018822	27029	Mm.103788	NM_018822	ENSMUSG00000005043	Sgsh	4632406A19Rik	N-sulfoglucosamine sulfohydrolase (sulfamidase)	protein-coding
mm_19571.1	chr2	101640227	101640236	-	1	NA	3' UTR (NM_009019, exon 2 of 2)	3' UTR (NM_009019, exon 2 of 2)	9301	NM_009019	19373	Mm.828	NM_009019	ENSMUSG00000061311	Rag1	Rag-1	recombination activating gene 1	protein-coding
mm_170611.1	chr19	5845605	5845606	-	1	NA	promoter-TSS (NR_003513)	promoter-TSS (NR_003513)	-125	NR_003513	66961	Mm.281895	NR_003513	ENSMUSG00000092274	Neat1	2310043N10Rik|VINC	nuclear paraspeckle assembly transcript 1 (non-protein coding)	ncRNA
mm_33572.1	chr4	132274445	132274455	+	1	NA	promoter-TSS (NM_025579)	promoter-TSS (NM_025579)	75	NM_025579	66464	Mm.331926	NM_025579	ENSMUSG00000028899	Taf12	20kDa|2810422D08Rik|AW557038|Taf2J	TATA-box binding protein associated factor 12	protein-coding
mm_130519.1	chr15	98872159	98872184	-	1	NA	promoter-TSS (NM_001033276)	promoter-TSS (NM_001033276)	-966	NM_001033276	381022	Mm.264889	NM_001033276	ENSMUSG00000048154	Kmt2d	ALR|BC032281|BC058659|C430014K11Rik|KMT2B|Mll2|Mll4	lysine (K)-specific methyltransferase 2D	protein-coding
mm_150994.1	chr19	46612486	46612494	+	1	NA	intron (NM_001177812, intron 2 of 4)	ID2|SINE|ID	-10911	NM_001177813	226178	Mm.329895	NM_146099	ENSMUSG00000047731	Wbp1l	D19Wsu162e|Opal1	WW domain binding protein 1 like	protein-coding
mm_166935.1	chr7	35466133	35466145	+	1	NA	TTS (NM_001199016)	TTS (NM_001199016)	16960	NM_021291	30962	Mm.45874	NM_021291	ENSMUSG00000030492	Slc7a9	CSNU3	solute carrier family 7 (cationic amino acid transporter, y+ system), member 9	protein-coding
mm_143832.1	chr17	84083583	84083614	-	1	NA	intron (NR_045458, intron 2 of 5)	intron (NR_045458, intron 2 of 5)	4938	NR_045458	74473	Mm.399575	NR_045458		4933433H22Rik	-	RIKEN cDNA 4933433H22 gene	ncRNA
mm_116443.1	chr13	43154750	43154766	-	1	NA	exon (NM_025935, exon 6 of 8)	exon (NM_025935, exon 6 of 8)	16743	NM_001252639	67046	Mm.269213	NM_025935	ENSMUSG00000021368	Tbc1d7	2610009C09Rik	TBC1 domain family, member 7	protein-coding
mm_22001.1	chr2	167744159	167744169	-	1	NA	Intergenic	Intergenic	52987	NR_015500	329562	Mm.123101	NM_177851	ENSMUSG00000006462	A530013C23Rik	-	RIKEN cDNA A530013C23 gene	ncRNA
mm_13255.1	chr2	98664880	98664902	+	1	NA	Intergenic	SYNREP_MM|Satellite|Satellite	1197234	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_76356.1	chr8	84772165	84772187	-	1	NA	exon (NM_010906, exon 2 of 9)	exon (NM_010906, exon 2 of 9)	2193	NM_001081981	18032	Mm.9394	NM_010906	ENSMUSG00000001911	Nfix	CTF|NF-I/X|NF1-X|NFI-X	nuclear factor I/X	protein-coding
mm_156196.1	chrX	134187506	134187513	+	1	NA	promoter-TSS (NM_028947)	promoter-TSS (NM_028947)	8	NM_028947	74448	Mm.159203	NM_028947	ENSMUSG00000052549	Arl13a	4933422M21Rik|Arl13	ADP-ribosylation factor-like 13A	protein-coding
mm_148306.1	chr18	83325864	83325886	-	1	NA	promoter-TSS (NR_045361)	promoter-TSS (NR_045361)	9	NR_045361	70960	Mm.410834	NR_045361		4921531P14Rik	1700108N05Rik	RIKEN cDNA 4921531P14 gene	ncRNA
mm_162692.1	chr10	19851420	19851442	-	1	NA	promoter-TSS (NM_029529)	promoter-TSS (NM_029529)	28	NM_029529	76157	Mm.74324	NM_029529	ENSMUSG00000050473	Slc35d3	6230421J19Rik|Frcl1	solute carrier family 35, member D3	protein-coding
mm_141143.1	chr17	26503093	26503101	-	1	NA	Intergenic	Intergenic	5375	NM_013642	19252	Mm.239041	NM_013642	ENSMUSG00000024190	Dusp1	3CH134|MKP1|Ptpn16|U19515|erp|mkp-1	dual specificity phosphatase 1	protein-coding
mm_108403.1	chr12	81631047	81631121	+	1	NA	promoter-TSS (NM_001033149)	promoter-TSS (NM_001033149)	-165	NM_001033149	69480	Mm.130002	NM_001033149	ENSMUSG00000042734	Ttc9	-	tetratricopeptide repeat domain 9	protein-coding
mm_161069.1	chr12	76370198	76370198	+	1	NA	promoter-TSS (NM_001172104)	promoter-TSS (NM_001172104)	-68	NM_178744	268564	Mm.77065	NM_178744	ENSMUSG00000033454	Zbtb1	9430077A12|AI256369|Bsg2|C430003J21Rik	zinc finger and BTB domain containing 1	protein-coding
mm_168739.1	chr12	115158885	115158890	-	1	NA	Intergenic	Intergenic	536907	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
mm_5262.1	chr1	16996938	16996940	-	1	NA	3' UTR (NM_020604, exon 5 of 5)	3' UTR (NM_020604, exon 5 of 5)	100950	NM_020604	57339	Mm.143761	NM_020604	ENSMUSG00000042686	Jph1	ENSMUSG00000054314|JP-1|Jp1	junctophilin 1	protein-coding
mm_144532.1	chr18	25168994	25169029	+	1	NA	promoter-TSS (NM_001142698)	promoter-TSS (NM_001142698)	-9	NM_001033532	225289	Mm.391081	NM_001033532	ENSMUSG00000033632	AW554918	4921538P22|AI461742|Kiaa1328|mKIAA1328	expressed sequence AW554918	protein-coding
mm_90643.1	chr10	128706252	128706264	+	1	NA	promoter-TSS (NM_021882)	promoter-TSS (NM_021882)	0	NM_021882	20431	Mm.16756	NM_021882	ENSMUSG00000025359	Pmel	D10H12S53E|D12S53Eh|Pmel17|Si|Silv|gp100|gp87	premelanosome protein	protein-coding
mm_76125.1	chr8	80879781	80879801	-	1	NA	5' UTR (NM_001301298, exon 1 of 11)	5' UTR (NM_001301298, exon 1 of 11)	688	NM_021356	14388	Mm.277409	NM_021356	ENSMUSG00000031714	Gab1	AA408973|AW107238	growth factor receptor bound protein 2-associated protein 1	protein-coding
mm_78719.1	chr9	41579689	41579717	+	1	NA	intron (NR_131930, intron 3 of 3)	intron (NR_131930, intron 3 of 3)	-1550	NR_015483	73144	Mm.38166	NM_001033153	ENSMUSG00000074415	3110039I08Rik	2610203C20Rik|AI848448|D230004N17Rik|D3Mgi9|Mir100hg	RIKEN cDNA 3110039I08 gene	ncRNA
mm_151770.1	chr19	5273266	5273290	-	1	NA	promoter-TSS (NM_153129)	promoter-TSS (NM_153129)	-159	NM_153129	107975	Mm.234923	NM_153129	ENSMUSG00000024855	Pacs1	AI325977	phosphofurin acidic cluster sorting protein 1	protein-coding
mm_136883.1	chr17	13008286	13008297	+	1	NA	exon (NM_013671, exon 2 of 5)	exon (NM_013671, exon 2 of 5)	452	NM_013671	20656	Mm.290876	NM_013671	ENSMUSG00000006818	Sod2	MnSOD|Sod-2	superoxide dismutase 2, mitochondrial	protein-coding
mm_70034.1	chr7	142576888	142576888	-	1	NA	TTS (NR_030416)	TTS (NR_030416)	259	NR_030416	735280		NR_030416	ENSMUSG00000076275	Mir675	Mirn675|mir-675|mmu-mir-675	microRNA 675	ncRNA
mm_120435.1	chr14	65806045	65806065	+	1	NA	5' UTR (NM_023209, exon 1 of 8)	5' UTR (NM_023209, exon 1 of 8)	144	NM_023209	52033	Mm.24337	NM_023209	ENSMUSG00000022033	Pbk	2810434B10Rik|AW538537|D14Ertd732e|TOPK	PDZ binding kinase	protein-coding
mm_112863.1	chr13	20847264	20847272	+	1	NA	intron (NM_012054, intron 3 of 20)	L1M2|LINE|L1	53155	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_125936.1	chr15	76247845	76247856	+	1	NA	promoter-TSS (NR_105918)	promoter-TSS (NR_105918)	-341	NR_105918	102465575		NR_105918	ENSMUSG00000098625	Mir6953	Gm27738|mmu-mir-6953	microRNA 6953	ncRNA
mm_131825.1	chr16	22939385	22939395	+	1	NA	exon (NM_021564, exon 8 of 8)	exon (NM_021564, exon 8 of 8)	-11682	NM_053176	94175	Mm.358794	NM_053176	ENSMUSG00000022877	Hrg	AI265597|AW413091|D16jh2|D18020|Hprg|Hrgp	histidine-rich glycoprotein	protein-coding
mm_123968.1	chr14	75130609	75130622	-	1	NA	promoter-TSS (NM_001247984)	promoter-TSS (NM_001247984)	268	NM_027581	70859	Mm.320289	NM_027581	ENSMUSG00000021997	Lrrc63	4921509B22Rik	leucine rich repeat containing 63	protein-coding
mm_113737.1	chr13	44467497	44467499	+	1	NA	Intergenic	Intergenic	27771	NR_045489	69491	Mm.392410	NR_045489	ENSMUSG00000098144	1700029N11Rik	-	RIKEN cDNA 1700029N11 gene	ncRNA
mm_91816.1	chr10	54075731	54075751	-	1	NA	promoter-TSS (NM_008548)	promoter-TSS (NM_008548)	55	NM_008548	17155	Mm.117294	NM_008548	ENSMUSG00000003746	Man1a	Man1a1|PCR1	mannosidase 1, alpha	protein-coding
mm_5683.1	chr1	43163892	43163962	-	1	NA	promoter-TSS (NM_010212)	promoter-TSS (NM_010212)	34	NM_010212	14200	Mm.6799	NM_010212	ENSMUSG00000008136	Fhl2	FHL-2|SLIM-3|SLIM3	four and a half LIM domains 2	protein-coding
mm_128278.1	chr15	36866250	36866265	-	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-69328	NM_001253806	22631	Mm.3360	NM_011740	ENSMUSG00000022285	Ywhaz	1110013I11Rik|14-3-3zeta|AI596267|AL022924|AU020854	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide	protein-coding
mm_82247.1	chr9	4795562	4795644	-	1	NA	intron (NM_019691, intron 1 of 16)	intron (NM_019691, intron 1 of 16)	631	NM_001113180	14802	Mm.209263	NM_019691	ENSMUSG00000025892	Gria4	GluA4|GluR-D|Glur-4|Glur4|Gluralpha4|spkw1	glutamate receptor, ionotropic, AMPA4 (alpha 4)	protein-coding
mm_144111.1	chr18	4353538	4353554	+	1	NA	promoter-TSS (NM_007746)	promoter-TSS (NM_007746)	-1	NR_040328	73915	Mm.482777	NR_040328		4833419F23Rik	-	RIKEN cDNA 4833419F23 gene	ncRNA
mm_137187.1	chr17	23820943	23821025	+	1	NA	exon (NM_175229, exon 10 of 14)	exon (NM_175229, exon 10 of 14)	8125	NM_026305	67673	Mm.153758	NM_026305	ENSMUSG00000055839	Elob	0610040H15Rik|Tceb2	elongin B	protein-coding
mm_53992.1	chr6	6881118	6881132	-	1	NA	intron (NM_010056, intron 1 of 2)	intron (NM_010056, intron 1 of 2)	943	NM_198854	13395	Mm.4873	NM_010056	ENSMUSG00000029755	Dlx5	AI385752	distal-less homeobox 5	protein-coding
mm_167173.1	chr7	139339259	139339260	+	1	NA	Intergenic	Intergenic	-49850	NM_183144	212111	Mm.28308	NM_183144	ENSMUSG00000025477	Inpp5a	-	inositol polyphosphate-5-phosphatase A	protein-coding
mm_92000.1	chr10	62231209	62231232	-	1	NA	promoter-TSS (NM_197996)	promoter-TSS (NM_197996)	-2	NM_197996	70423	Mm.416781	NM_197996	ENSMUSG00000037031	Tspan15	1110036D12Rik|2700063A19Rik|AW048364|Tm4sf15	tetraspanin 15	protein-coding
mm_61331.1	chr7	68274518	68274522	+	1	NA	intron (NM_001013811, intron 1 of 8)	RMER10B|LTR|ERVL	578	NR_040341	100504026	Mm.426764	NR_040340	ENSMUSG00000086628	Gm16157	OTTMUSG00000031023	predicted gene 16157	ncRNA
mm_53722.1	chr6	144672844	144672851	+	1	NA	promoter-TSS (NR_040519)	promoter-TSS (NR_040519)	-21	NR_040519	66760	Mm.233631	NR_040519	ENSMUSG00000085785	Sox5os3	4933425H06Rik	SRY (sex determining region Y)-box 5, opposite strand 3	ncRNA
mm_150063.1	chr19	29386074	29386084	+	1	NA	3' UTR (NM_021893, exon 7 of 7)	3' UTR (NM_021893, exon 7 of 7)	18641	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_1571.1	chr1	74260017	74260020	+	1	NA	intron (NM_029711, intron 6 of 9)	intron (NM_029711, intron 6 of 9)	-18582	NM_174985	227289	Mm.246587	NM_174985	ENSMUSG00000064272	Gpbar1	BG37|GPCR|GPR131|M-BAR|TGR5	G protein-coupled bile acid receptor 1	protein-coding
mm_37552.1	chr4	125346987	125346996	-	1	NA	Intergenic	Intergenic	-143840	NM_001081097	14807	Mm.40896	NM_001081097	ENSMUSG00000001985	Grik3	9630027E11|GluK3|GluR7-3|Glur-7|Glur7	glutamate receptor, ionotropic, kainate 3	protein-coding
mm_159440.1	chr3	125956677	125956677	-	1	NA	Intergenic	ORR1A1|LTR|ERVL-MaLR	-18127	NM_011674	22239	Mm.306021	NM_011674	ENSMUSG00000032854	Ugt8a	AI850488|AW455908|Cgt|Ugt8|mCerGT	UDP galactosyltransferase 8A	protein-coding
mm_102933.1	chr11	69600976	69600986	-	1	NA	3' UTR (NM_013415, exon 7 of 7)	3' UTR (NM_013415, exon 7 of 7)	4979	NM_013415	11932	Mm.235204	NM_013415	ENSMUSG00000041329	Atp1b2	Amog|Atpb-2	ATPase, Na+/K+ transporting, beta 2 polypeptide	protein-coding
mm_33692.1	chr4	133518722	133518732	+	1	NA	promoter-TSS (NM_001083916)	promoter-TSS (NM_001083916)	-236	NM_001083916	69073	Mm.299081	NM_133707	ENSMUSG00000037600	Kdf1	1810019J16Rik	keratinocyte differentiation factor 1	protein-coding
mm_74441.1	chr8	3878550	3878568	-	1	NA	promoter-TSS (NM_130904)	promoter-TSS (NM_130904)	-60	NM_130904	170779	Mm.111026	NM_130904	ENSMUSG00000031495	Cd209d	SIGN-R3|SIGNR3|mSIGNR3	CD209d antigen	protein-coding
mm_48579.1	chr5	143506199	143506209	-	1	NA	3' UTR (NM_009007, exon 6 of 6)	3' UTR (NM_009007, exon 6 of 6)	21789	NM_009007	19353	Mm.292510	NM_009007	ENSMUSG00000001847	Rac1	AL023026|D5Ertd559e	RAS-related C3 botulinum substrate 1	protein-coding
mm_24898.1	chr3	96172535	96172564	+	1	NA	promoter-TSS (NM_153053)	promoter-TSS (NM_153053)	43	NM_153053	107701	Mm.219671	NM_153053	ENSMUSG00000068856	Sf3b4	SF3b49|SF3b50|Sap49	splicing factor 3b, subunit 4	protein-coding
mm_111637.1	chr12	102631887	102631914	-	1	NA	intron (NM_172584, intron 2 of 9)	intron (NM_172584, intron 2 of 9)	53120	NR_035457	100316812		NR_035457	ENSMUSG00000089324	Mir1936	mir-1936|mmu-mir-1936	microRNA 1936	ncRNA
mm_106031.1	chr11	116077518	116077534	-	1	NA	exon (NM_001009573, exon 2 of 33)	exon (NM_001009573, exon 2 of 33)	435	NM_001009573	70450	Mm.259460	NM_001009573	ENSMUSG00000057948	Unc13d	2610108D09Rik|Jinx|Munc13-4|mFLJ00067	unc-13 homolog D (C. elegans)	protein-coding
mm_90647.1	chr10	128744938	128745023	+	1	NA	promoter-TSS (NM_016811)	promoter-TSS (NM_016811)	-924	NM_016811	13139	Mm.291235	NM_016811	ENSMUSG00000025357	Dgka	80kDa|AW146112|Dagk1	diacylglycerol kinase, alpha	protein-coding
mm_42139.1	chr5	111416610	111416619	+	1	NA	Intergenic	CpG	-1552	NM_001081235	433938	Mm.332576	NM_001081235	ENSMUSG00000070576	Mn1	AA003644|AA009236	meningioma 1	protein-coding
mm_152667.1	chr19	14597698	14597722	-	1	NA	promoter-TSS (NM_001302951)	promoter-TSS (NM_001302951)	473	NM_001302950	21888	Mm.103638	NM_011600	ENSMUSG00000024642	Tle4	5730411M05Rik|AA792082|Bce-1|Bce1|ESTM13|ESTM14|Grg4|X83332|X83333|grg-4	transducin-like enhancer of split 4	protein-coding
mm_118990.1	chr14	28505496	28505509	+	1	NA	promoter-TSS (NM_009524)	promoter-TSS (NM_009524)	29	NM_009524	22418	Mm.287544	NM_009524	ENSMUSG00000021994	Wnt5a	8030457G12Rik|Wnt-5a	wingless-type MMTV integration site family, member 5A	protein-coding
mm_166929.1	chr7	33741839	33741843	+	1	NA	Intergenic	Intergenic	-1958	NM_001099329	100043860	Mm.389875	NM_001099329	ENSMUSG00000078753	Scgb1b24	Abpa24|Gm12769|OTTMUSG00000008385	secretoglobin, family 1B, member 24	protein-coding
mm_18886.1	chr2	76709140	76709156	-	1	NA	exon (NM_011652, exon 307 of 313)	exon (NM_011652, exon 307 of 313)	33833	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_30722.1	chr4	13743425	13743478	+	1	NA	5' UTR (NM_001111026, exon 1 of 11)	5' UTR (NM_001111026, exon 1 of 11)	149	NM_001111026	12395	Mm.4909	NM_009822	ENSMUSG00000006586	Runx1t1	Cbfa2t1h|ETO|MTG8	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	protein-coding
mm_16256.1	chr2	173265051	173265057	+	1	NA	intron (NM_022995, intron 1 of 3)	intron (NM_022995, intron 1 of 3)	11479	NM_022995	65112	Mm.73682	NM_022995	ENSMUSG00000038400	Pmepa1	2210418I02Rik|AW455466|Erg1.2|N4wbp4|Stag1|Tmepai	prostate transmembrane protein, androgen induced 1	protein-coding
mm_160492.1	chr8	127405534	127405534	+	1	NA	exon (NM_033620, exon 16 of 25)	exon (NM_033620, exon 16 of 25)	105882	NM_001013580	93742	Mm.299254	NM_033620	ENSMUSG00000025812	Pard3	AA960621|AI256638|Asip|D8Ertd580e|Par-3|Par3|Pard-3|Pard3a|Phip	par-3 family cell polarity regulator	protein-coding
mm_57413.1	chr6	124888166	124888181	-	1	NA	promoter-TSS (NM_013488)	promoter-TSS (NM_013488)	36	NM_013488	12504	Mm.2209	NM_013488	ENSMUSG00000023274	Cd4	L3T4|Ly-4	CD4 antigen	protein-coding
mm_131757.1	chr16	22871699	22871736	+	1	NA	exon (NM_001190805, exon 10 of 11)	exon (NM_001190805, exon 10 of 11)	13872	NM_001190804	67838	Mm.37516	NM_026400	ENSMUSG00000004460	Dnajb11	1810031F23Rik|ABBP-2|AL024055|Dj9|ERdj3|ERj3p	DnaJ heat shock protein family (Hsp40) member B11	protein-coding
mm_146303.1	chr18	80255228	80255278	+	1	NA	promoter-TSS (NM_001164424)	promoter-TSS (NM_001164424)	8	NM_001164420	66943	Mm.29247	NM_025861	ENSMUSG00000034006	Pqlc1	2310009N05Rik|4933425L21Rik|5730564E11Rik|C78974	PQ loop repeat containing 1	protein-coding
mm_90462.1	chr10	127759755	127759766	+	1	NA	promoter-TSS (NM_080436)	promoter-TSS (NM_080436)	-3	NM_080436	107605	Mm.484271	NM_080436	ENSMUSG00000089789	Rdh1	-	retinol dehydrogenase 1 (all trans)	protein-coding
mm_34305.1	chr4	141793706	141793735	+	1	NA	5' UTR (NM_015733, exon 1 of 9)	5' UTR (NM_015733, exon 1 of 9)	108	NM_001277932	12371	Mm.88829	NM_015733	ENSMUSG00000028914	Casp9	AI115399|APAF-3|AW493809|CASP-9|Caspase-9|ICE-LAP6|Mch6	caspase 9	protein-coding
mm_105811.1	chr11	110951910	110951914	-	1	NA	Intergenic	U2|snRNA|snRNA	-16121	NM_010604	16517	Mm.30176	NM_010604	ENSMUSG00000051497	Kcnj16	6430410F18Rik|AI132396|Kir5.1	potassium inwardly-rectifying channel, subfamily J, member 16	protein-coding
mm_136955.1	chr17	14945519	14945550	+	1	NA	3' UTR (NM_001083881, exon 2 of 2)	3' UTR (NM_001083881, exon 2 of 2)	2350	NM_026451	67912	Mm.390949	NM_026451	ENSMUSG00000050088	1600012H06Rik	-	RIKEN cDNA 1600012H06 gene	protein-coding
mm_136845.1	chr17	12765350	12765375	+	1	NA	intron (NM_010515, intron 1 of 47)	intron (NM_010515, intron 1 of 47)	4344	NM_010515	16004	Mm.26553	NM_010515	ENSMUSG00000023830	Igf2r	AI661837|CD222|CI-MPR|M6P/IGF2R|Mpr300	insulin-like growth factor 2 receptor	protein-coding
mm_19540.1	chr2	94730733	94730737	-	1	NA	Intergenic	Intergenic	-292549	NM_001305258	11800	Mm.181824	NM_007466	ENSMUSG00000027193	Api5	AAC-11|AI196452|API-5	apoptosis inhibitor 5	protein-coding
mm_108258.1	chr12	78356732	78356748	+	1	NA	intron (NM_145965, intron 2 of 22)	RLTR33|LTR|ERVK	130085	NM_145965	268566	Mm.341742	NM_145965	ENSMUSG00000047454	Gphn	5730552E08Rik|AI662856|BC027112|C230040D23|GPH|GPHRYN|geph	gephyrin	protein-coding
mm_172113.1	chr6	3200991	3200993	+	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	-87527	NR_036696	667335	Mm.380219	NR_036696	ENSMUSG00000106779	Gm8579	EG667335	spermatogenesis associated glutamate (E)-rich protein 4a pseudogene	pseudo
mm_108158.1	chr12	76329275	76329283	+	1	NA	exon (NM_001101471, exon 2 of 2)	exon (NM_001101471, exon 2 of 2)	4388	NM_001101471	238276	Mm.311452	NM_001101471	ENSMUSG00000021057	Akap5	3526401B18Rik|AKAP 150|AKAP-5|AKAP150|BB098886|Gm258|P150	A kinase (PRKA) anchor protein 5	protein-coding
mm_52616.1	chr6	117173941	117173947	+	1	NA	3' UTR (NM_021704, exon 3 of 3)	3' UTR (NM_021704, exon 3 of 3)	5409	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_149187.1	chr19	9914552	9914562	+	1	NA	Intergenic	Lx8|LINE|L1	-15024	NM_016692	16319	Mm.29755	NM_016692	ENSMUSG00000024660	Incenp	2700067E22Rik|AU019509|C130081E20|C77457	inner centromere protein	protein-coding
mm_131252.1	chr16	10690228	10690268	+	1	NA	intron (NM_001204229, intron 19 of 22)	intron (NM_001204229, intron 19 of 22)	95288	NM_009896	12703	Mm.130	NM_009896	ENSMUSG00000038037	Socs1	Cish1|Cish7|JAB|SOCS-1|SSI-1	suppressor of cytokine signaling 1	protein-coding
mm_151940.1	chr19	5800852	5800857	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	1818	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_111541.1	chr12	100888027	100888037	-	1	NA	5' UTR (NM_175493, exon 2 of 3)	5' UTR (NM_175493, exon 2 of 3)	11492	NM_001177674	238377	Mm.32160	NM_175493	ENSMUSG00000047415	Gpr68	BB131428|Ogr1	G protein-coupled receptor 68	protein-coding
mm_100040.1	chr11	114998361	114998384	+	1	NA	intron (NM_134158, intron 2 of 3)	intron (NM_134158, intron 2 of 3)	3508	NM_134158	140497	Mm.2699	NM_134158	ENSMUSG00000044811	Cd300c2	CLM4|Cd300c|Cd300d|DIgR1|Igsf7|Lmir2|MAIR-II	CD300C molecule 2	protein-coding
mm_1483.1	chr1	71615493	71615527	+	1	NA	exon (NM_001276413, exon 24 of 44)	exon (NM_001276413, exon 24 of 44)	37724	NM_010233	14268	Mm.193099	NM_010233	ENSMUSG00000026193	Fn1	E330027I09|Fn|Fn-1	fibronectin 1	protein-coding
mm_155851.1	chrX	101274199	101274252	+	1	NA	5' UTR (NM_021521, exon 1 of 45)	5' UTR (NM_021521, exon 1 of 45)	134	NM_021521	59024	Mm.20873	NM_021521	ENSMUSG00000079487	Med12	230kDa|Mopa|OPA-1|Tnrc11|Trap230	mediator complex subunit 12	protein-coding
mm_11354.1	chr2	30913366	30913374	+	1	NA	Intergenic	Intergenic	-10073	NM_022415	64292	Mm.28768	NM_022415	ENSMUSG00000050737	Ptges	2410099E23Rik|D2Ertd369e|Pges|mPGES|mPGES-1	prostaglandin E synthase	protein-coding
mm_140953.1	chr17	24608984	24609010	-	1	NA	exon (NM_001286716, exon 22 of 40)	exon (NM_001286716, exon 22 of 40)	23630	NM_011647	22084	Mm.30435	NM_011647	ENSMUSG00000002496	Tsc2	Nafld|Tcs2	tuberous sclerosis 2	protein-coding
mm_135251.1	chr16	37621910	37621936	-	1	NA	non-coding (NR_027778, exon 10 of 13)	non-coding (NR_027778, exon 10 of 13)	32445	NM_026610	68194	Mm.379154	NM_026610	ENSMUSG00000022820	Ndufb4	0610006N12Rik|1300010H20Rik	NADH dehydrogenase (ubiquinone) 1 beta subcomplex 4	protein-coding
mm_168728.1	chr12	112795773	112795773	-	1	NA	Intergenic	Intergenic	-13202	NM_145450	217887	Mm.186678	NM_145450	ENSMUSG00000037594	BC022687	AW050009|C130001I08Rik|Flj20080	cDNA sequence BC022687	protein-coding
mm_141013.1	chr17	25015742	25015753	-	1	NA	promoter-TSS (NM_020608)	promoter-TSS (NM_020608)	-339	NM_134126	106633	Mm.32802	NM_134126	ENSMUSG00000024169	Ift140	AI661311|Tce5|Wdtc2|mKIAA0590	intraflagellar transport 140	protein-coding
mm_103443.1	chr11	76027727	76027802	-	1	NA	promoter-TSS (NM_029658)	promoter-TSS (NM_029658)	18	NM_029658	76566	Mm.34131	NM_029658	ENSMUSG00000020846	Rflnb	1500005K14Rik|Fam101b|RefilinB|cfm	refilin B	protein-coding
mm_84577.1	chr9	69300395	69300411	-	1	NA	intron (NM_001289916, intron 1 of 9)	intron (NM_001289916, intron 1 of 9)	10562	NM_001289916	19883	Mm.378450	NM_013646	ENSMUSG00000032238	Rora	9530021D13Rik|Nr1f1|ROR1|ROR2|ROR3|nmf267|sg|staggerer|tmgc26	RAR-related orphan receptor alpha	protein-coding
mm_41937.1	chr5	105702152	105702189	+	1	NA	intron (NM_178701, intron 1 of 2)	intron (NM_178701, intron 1 of 2)	1360	NM_178701	231549	Mm.23837	NM_178701	ENSMUSG00000046079	Lrrc8d	2810473G09Rik|4930525N13Rik|A930019F03|Lrrc5	leucine rich repeat containing 8D	protein-coding
mm_71101.1	chr8	35376646	35376668	+	1	NA	intron (NM_177741, intron 1 of 1)	CpG	916	NM_177741	244416	Mm.247126	NM_177741	ENSMUSG00000046794	Ppp1r3b	6430576E21|AW821953|GL|PTG	protein phosphatase 1, regulatory (inhibitor) subunit 3B	protein-coding
mm_88266.1	chr10	74096159	74096162	+	1	NA	intron (NM_001142740, intron 3 of 31)	Lx7|LINE|L1	274293	NM_001142735	11994	Mm.338933	NM_023115	ENSMUSG00000052613	Pcdh15	BB078305|ENSMUSG00000046980|Gm9815|Ush1f|av|nmf19|roda	protocadherin 15	protein-coding
mm_126512.1	chr15	81811449	81811491	+	1	NA	promoter-TSS (NM_017376)	promoter-TSS (NM_017376)	56	NM_017376	21685	Mm.270278	NM_017376	ENSMUSG00000022389	Tef	2310028D20Rik	thyrotroph embryonic factor	protein-coding
mm_30591.1	chr4	6357672	6357683	+	1	NA	Intergenic	Intergenic	-8003	NM_016807	53378	Mm.247473	NM_016807	ENSMUSG00000028249	Sdcbp	MDA-9|Sycl|syntenin-1	syndecan binding protein	protein-coding
mm_156555.1	chrX	151801014	151801083	+	1	NA	Intergenic	Intergenic	-2234	NM_021523	59026	Mm.27372	NM_021523	ENSMUSG00000025261	Huwe1	5430439H10Rik|AU041296|Arf-bp1|C430014N20Rik|C80292|Gm1718|Ib772|LASU1|Mule|Ureb1	HECT, UBA and WWE domain containing 1	protein-coding
mm_96141.1	chr11	60945237	60945241	+	1	NA	intron (NM_008928, intron 6 of 11)	intron (NM_008928, intron 6 of 11)	13182	NM_008928	26397	Mm.18494	NM_008928	ENSMUSG00000018932	Map2k3	AW212142|MEK3|MKK3|Prkmk3|mMKK3b	mitogen-activated protein kinase kinase 3	protein-coding
mm_111213.1	chr12	84400930	84400946	-	1	NA	promoter-TSS (NM_001286049)	promoter-TSS (NM_001286049)	-4	NM_001286049	12499	Mm.10211	NM_007647	ENSMUSG00000021236	Entpd5	AI196558|AI987697|Cd39l4|ER-UDPase|NTPDase-5|NTPDase5|Pcph|mNTPase	ectonucleoside triphosphate diphosphohydrolase 5	protein-coding
mm_171157.1	chr3	22297889	22297891	-	1	NA	Intergenic	RLTR9E|LTR|ERVK	46520	NR_004439	19784		NR_004439		Rprl2	RPRH3|Rmrp3	ribonuclease P RNA-like 2	ncRNA
mm_150958.1	chr19	46395375	46395393	+	1	NA	intron (NM_016860, intron 1 of 10)	CpG	351	NM_016860	54130	Mm.3118	NM_016860	ENSMUSG00000025228	Actr1a	Arp1|alpha-Arp1	ARP1 actin-related protein 1A, centractin alpha	protein-coding
mm_91074.1	chr10	19009479	19009484	-	1	NA	intron (NM_001166402, intron 1 of 7)	intron (NM_001166402, intron 1 of 7)	2482	NM_001166402	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_46188.1	chr5	97925675	97925683	-	1	NA	intron (NM_133738, intron 16 of 16)	intron (NM_133738, intron 16 of 16)	105283	NM_133738	71914	Mm.24842	NM_133738	ENSMUSG00000029338	Antxr2	2310046B19Rik|AW561899|CMG-2|CMG2|cI-35	anthrax toxin receptor 2	protein-coding
mm_26155.1	chr3	138143923	138143937	+	1	NA	promoter-TSS (NM_001163457)	promoter-TSS (NM_001163457)	392	NM_175389	108943	Mm.471692	NM_175389	ENSMUSG00000004127	Trmt10a	3110023L08Rik|AA794508|Rg9mtd2|Rnmtd2	tRNA methyltransferase 10A	protein-coding
mm_141272.1	chr17	27797573	27797574	-	1	NA	intron (NM_001033279, intron 1 of 4)	intron (NM_001033279, intron 1 of 4)	22969	NM_001033279	224647	Mm.196577	NM_001033279	ENSMUSG00000056692	D17Wsu92e	AU020189|C030010A15|C80239	DNA segment, Chr 17, Wayne State University 92, expressed	protein-coding
mm_163730.1	chr13	119623797	119623811	+	1	NA	promoter-TSS (NM_020279)	promoter-TSS (NM_020279)	-15	NM_020279	56838	Mm.143745	NM_020279	ENSMUSG00000074715	Ccl28	CCK1|MEC|Scya28	chemokine (C-C motif) ligand 28	protein-coding
mm_119455.1	chr14	47001380	47001393	+	1	NA	promoter-TSS (NM_001163433)	promoter-TSS (NM_001163433)	46	NM_001163433	74480	Mm.214454	NM_028966	ENSMUSG00000021838	Samd4	1700024G08Rik|1700111L17Rik|4933436G17Rik|Samd4a|Smaug|Smaug1|sunk	sterile alpha motif domain containing 4	protein-coding
mm_164883.1	chr18	60386191	60386201	+	1	NA	intron (NM_001146275, intron 2 of 2)	intron (NM_001146275, intron 2 of 2)	10167	NM_001146275	60440	Mm.261140	NM_021792	ENSMUSG00000054072	Iigp1	2900074L10Rik|AI046432|AW111922|Ifgga1|Iigp|Irga6	interferon inducible GTPase 1	protein-coding
mm_85967.1	chr9	112156007	112156022	-	1	NA	intron (NM_001177619, intron 10 of 10)	intron (NM_001177619, intron 10 of 10)	29935	NM_001177618	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_167408.1	chr8	104795237	104795238	+	1	NA	Intergenic	Intergenic	-36407	NM_198171	234669	Mm.443387	NM_198171	ENSMUSG00000050097	Ces2b	-	carboxyesterase 2B	protein-coding
mm_103235.1	chr11	70683650	70683673	-	1	NA	intron (NM_178116, intron 5 of 22)	intron (NM_178116, intron 5 of 22)	4444	NM_001190376	216874	Mm.473726	NM_178116	ENSMUSG00000040712	Camta2	Kiaa0909-hp|mKIAA0909	calmodulin binding transcription activator 2	protein-coding
mm_69241.1	chr7	127806627	127806637	-	1	NA	TTS (NM_024414)	TTS (NM_024414)	6023	NM_001040684	101502	Mm.157103	NM_133943	ENSMUSG00000042289	Hsd3b7	AI195443|BB098564	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 7	protein-coding
mm_129888.1	chr15	83489672	83489689	-	1	NA	intron (NM_178869, intron 10 of 11)	CpG	21227	NM_178869	319953	Mm.235007	NM_178869	ENSMUSG00000022442	Ttll1	6330444E16Rik|AV014541	tubulin tyrosine ligase-like 1	protein-coding
mm_121497.1	chr14	121878770	121878780	+	1	NA	promoter-TSS (NR_131002)	promoter-TSS (NR_131002)	169	NM_026861	68889	Mm.441151	NM_026861	ENSMUSG00000041765	Ubac2	1190008A14Rik|AW554959|Phgdhl1	ubiquitin associated domain containing 2	protein-coding
mm_172371.1	chr7	125418554	125418558	-	1	NA	Intergenic	Intergenic	-26064	NM_029842	77035	Mm.307239	NM_029842	ENSMUSG00000030752	Kdm8	3110005O21Rik|Jmjd5	lysine (K)-specific demethylase 8	protein-coding
mm_87384.1	chr10	44852590	44852590	+	1	NA	Intergenic	Intergenic	-214624	NM_011156	19072	Mm.10281	NM_011156	ENSMUSG00000019849	Prep	AI047692|AI450383|D10Wsu136e|PEP|Pop	prolyl endopeptidase	protein-coding
mm_105038.1	chr11	100584695	100584706	-	1	NA	intron (NM_019795, intron 10 of 13)	intron (NM_019795, intron 10 of 13)	8809	NM_001146318	12799	Mm.15711	NM_009923	ENSMUSG00000006782	Cnp	CNPase|Cnp-1|Cnp1	2',3'-cyclic nucleotide 3' phosphodiesterase	protein-coding
mm_22784.1	chr3	22076726	22076797	+	1	NA	5' UTR (NM_030732, exon 1 of 16)	5' UTR (NM_030732, exon 1 of 16)	109	NM_030732	81004	Mm.202966	NM_030732	ENSMUSG00000027630	Tbl1xr1	8030499H02Rik|A630076E03Rik|AW539987|C21|C230089I12Rik|DC42|Ira1|TBLR1	transducin (beta)-like 1X-linked receptor 1	protein-coding
mm_158872.1	chrY	1286430	1286437	-	1	NA	intron (NM_012008, intron 1 of 16)	intron (NM_012008, intron 1 of 16)	180	NM_012008	26900	Mm.302938	NM_012008	ENSMUSG00000069045	Ddx3y	8030469F12Rik|D1Pas1-rs1|Dby	DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, Y-linked	protein-coding
mm_35728.1	chr4	44710964	44710977	-	1	NA	promoter-TSS (NM_008782)	promoter-TSS (NM_008782)	-530	NM_008782	18507	Mm.439659	NM_008782	ENSMUSG00000014030	Pax5	BSAP|EBB-1|KLP|Pax-5	paired box 5	protein-coding
mm_1219.1	chr1	62730329	62730343	+	1	NA	intron (NM_001077405, intron 2 of 15)	intron (NM_001077405, intron 2 of 15)	27019	NM_001077405	18187	Mm.266341	NM_010939	ENSMUSG00000025969	Nrp2	1110048P06Rik|Np-2|Np2|Npn-2|Npn2	neuropilin 2	protein-coding
mm_169997.1	chr17	16394879	16394885	-	1	NA	Intergenic	L1Md_T|LINE|L1	-568296	NM_178615	68799	Mm.293466	NM_178615	ENSMUSG00000048027	Rgmb	1110059F19Rik|DRAGON	repulsive guidance molecule family member B	protein-coding
mm_95258.1	chr11	44658910	44658924	+	1	NA	intron (NM_007897, intron 6 of 15)	intron (NM_007897, intron 6 of 15)	40817	NM_001290710	13591	Mm.439662	NM_007897	ENSMUSG00000057098	Ebf1	Ebf|O/E-1|OE-1|Olf-1|Olf1	early B cell factor 1	protein-coding
mm_7160.1	chr1	91650700	91650738	-	1	NA	Intergenic	B1_Mus1|SINE|Alu	109639	NM_023046	65247	Mm.234152	NM_023046	ENSMUSG00000026311	Asb1	1700029O08Rik|1700054C17Rik|AI426616|AI851378|mKIAA1146	ankyrin repeat and SOCS box-containing 1	protein-coding
mm_15047.1	chr2	152847994	152848076	+	1	NA	promoter-TSS (NM_001141978)	promoter-TSS (NM_001141978)	71	NM_028109	72119	Mm.407737	NM_028109	ENSMUSG00000027469	Tpx2	2610005B21Rik|DIL2|REPP86|p100	TPX2, microtubule-associated	protein-coding
mm_91155.1	chr10	20505593	20505628	-	1	NA	intron (NM_013875, intron 2 of 12)	intron (NM_013875, intron 2 of 12)	42718	NM_001347366	29863	Mm.425617	NM_013875	ENSMUSG00000019990	Pde7b	-	phosphodiesterase 7B	protein-coding
mm_82603.1	chr9	21367394	21367402	-	1	NA	promoter-TSS (NM_001042707)	promoter-TSS (NM_001042707)	-473	NM_001042708	16201	Mm.440026	NM_010561	ENSMUSG00000032178	Ilf3	MBII-26|MPHOSPH4|NF90|NFAR	interleukin enhancer binding factor 3	protein-coding
mm_98716.1	chr11	96318732	96318745	+	1	NA	5' UTR (NM_010459, exon 1 of 2)	5' UTR (NM_010459, exon 1 of 2)	471	NM_010459	15412	Mm.3546	NM_010459	ENSMUSG00000038692	Hoxb4	Hox-2.6	homeobox B4	protein-coding
mm_126725.1	chr15	85462741	85462741	+	1	NA	intron (NM_016843, intron 11 of 11)	intron (NM_016843, intron 11 of 11)	40486	NM_001256072	328577	Mm.212960	NM_001256072	ENSMUSG00000096607	7530416G11Rik	-	RIKEN cDNA 7530416G11 gene	protein-coding
mm_72037.1	chr8	70808379	70808400	+	1	NA	promoter-TSS (NM_008353)	promoter-TSS (NM_008353)	-60	NM_008353	16161	Mm.731	NM_008353	ENSMUSG00000000791	Il12rb1	CD212|IL-12R[b]	interleukin 12 receptor, beta 1	protein-coding
mm_125132.1	chr15	30333832	30333848	+	1	NA	intron (NM_008729, intron 2 of 22)	intron (NM_008729, intron 2 of 22)	161247	NM_008729	18163	Mm.321648	NM_008729	ENSMUSG00000022240	Ctnnd2	Catnd2|Nprap|neurojugin	catenin (cadherin associated protein), delta 2	protein-coding
mm_69806.1	chr7	141215641	141215661	-	1	NA	promoter-TSS (NM_025886)	promoter-TSS (NM_025886)	-209	NM_025886	66985	Mm.21202	NM_025886	ENSMUSG00000038618	Rassf7	2400009B11Rik|AW210608	Ras association (RalGDS/AF-6) domain family (N-terminal) member 7	protein-coding
mm_109465.1	chr12	111274656	111274683	+	1	NA	intron (NM_033603, intron 5 of 11)	CpG-3529	3573	NM_033603	93835	Mm.197639	NM_033603	ENSMUSG00000021278	Amn	-	amnionless	protein-coding
mm_66841.1	chr7	48882352	48882354	-	1	NA	Intergenic	MIR3|SINE|MIR	-1312	NM_001013368	108961	Mm.240566	NM_001013368	ENSMUSG00000046179	E2f8	4432406C08Rik|AA410048	E2F transcription factor 8	protein-coding
mm_27231.1	chr3	36453540	36453593	-	1	NA	intron (NM_009673, intron 8 of 12)	intron (NM_009673, intron 8 of 12)	21958	NR_105976	102466786		NR_105976	ENSMUSG00000098808	Mir7009	Gm27472|mmu-mir-7009	microRNA 7009	ncRNA
mm_17294.1	chr2	26237349	26237367	-	1	NA	promoter-TSS (NM_153559)	promoter-TSS (NM_153559)	41	NM_153559	227638	Mm.116769	NM_153559	ENSMUSG00000036327	Qsox2	BC030934|Qscn6l1|Soxn	quiescin Q6 sulfhydryl oxidase 2	protein-coding
mm_167887.1	chrX	58884473	58884473	-	1	NA	Intergenic	Lx7|LINE|L1	-26988	NM_023774	75352	Mm.60906	NM_023774	ENSMUSG00000046180	4930550L24Rik	mage-k1	RIKEN cDNA 4930550L24 gene	protein-coding
mm_97955.1	chr11	83709102	83709116	+	1	NA	5' UTR (NM_007969, exon 1 of 3)	5' UTR (NM_007969, exon 1 of 3)	105	NM_007969	14038	Mm.1650	NM_007969	ENSMUSG00000000983	Wfdc18	Expi|Kal1|WDNM1	WAP four-disulfide core domain 18	protein-coding
mm_92194.1	chr10	68127485	68127488	-	1	NA	intron (NM_023598, intron 6 of 9)	intron (NM_023598, intron 6 of 9)	147888	NM_001081346	170799	Mm.209844	NM_133244	ENSMUSG00000037846	Rtkn2	B130039D23Rik|Mbf|Plekhk1	rhotekin 2	protein-coding
mm_121158.1	chr14	102981436	102981470	+	1	NA	3' UTR (NM_177715, exon 1 of 1)	3' UTR (NM_177715, exon 1 of 1)	1179	NR_039592	100628599		NR_039592	ENSMUSG00000092901	Mir5130	mir-5130|mmu-mir-5130|mu-mir-5130	microRNA 5130	ncRNA
mm_108729.1	chr12	87388633	87388676	+	1	NA	promoter-TSS (NM_011479)	promoter-TSS (NM_011479)	-299	NM_011479	20773	Mm.565	NM_011479	ENSMUSG00000021036	Sptlc2	LCB2|LCB2a|Spt2	serine palmitoyltransferase, long chain base subunit 2	protein-coding
mm_93070.1	chr10	89257807	89257831	-	1	NA	promoter-TSS (NM_001277188)	promoter-TSS (NM_001277188)	-29	NR_102339	320091	Mm.236464	NM_178773	ENSMUSG00000035189	Ano4	A330096O15Rik|Gm65|Tmem16d	anoctamin 4	protein-coding
mm_45544.1	chr5	72868432	72868451	-	1	NA	promoter-TSS (NM_001113460)	promoter-TSS (NM_001113460)	7	NM_001113461	21682	Mm.319581	NM_013689	ENSMUSG00000029217	Tec	-	tec protein tyrosine kinase	protein-coding
mm_128634.1	chr15	59082093	59082101	-	1	NA	promoter-TSS (NM_144800)	promoter-TSS (NM_144800)	-71	NM_144800	211401	Mm.215481	NM_144800	ENSMUSG00000022353	Mtss1	2310003N14Rik|BC024131|D130001D01Rik|Mim|mKIAA0429	metastasis suppressor 1	protein-coding
mm_69398.1	chr7	132307147	132307150	-	1	NA	intron (NM_029935, intron 1 of 7)	ORR1E-int|LTR|ERVL-MaLR	-8516	NR_028578	100043682	Mm.482794	NR_028578	ENSMUSG00000109270	Gm10584	ENSMUSG00000073814	predicted gene 10584	ncRNA
mm_165072.1	chr19	44918433	44918467	+	1	NA	Intergenic	Intergenic	-12669	NM_001081225	226151	Mm.212609	NM_172638	ENSMUSG00000036097	Fam178a	3632432H19|6030443O07Rik|AU014917|Slf2	family with sequence similarity 178, member A	protein-coding
mm_70452.1	chr8	11782454	11782481	+	1	NA	intron (NM_001113517, intron 3 of 18)	intron (NM_001113517, intron 3 of 18)	24137	NM_001113518	54126	Mm.244068	NM_017402	ENSMUSG00000031511	Arhgef7	Cool|PIX|Pak3bp|betaPix|betaPix-b|betaPix-c|cool-1|mKIAA0142|p85Cool1|p85SPR	Rho guanine nucleotide exchange factor (GEF7)	protein-coding
mm_110241.1	chr12	31075312	31075349	-	1	NA	intron (NM_027828, intron 1 of 1)	intron (NM_027828, intron 1 of 1)	1362	NM_027828	104943	Mm.248938	NM_027828	ENSMUSG00000036136	Fam110c	9030611O19Rik|AU019489	family with sequence similarity 110, member C	protein-coding
mm_40860.1	chr5	73558325	73558356	+	1	NA	3' UTR (NM_001190734, exon 12 of 12)	3' UTR (NM_001190734, exon 12 of 12)	67314	NM_178896	100737	Mm.220312	NM_178896	ENSMUSG00000051674	Dcun1d4	AI836376	DCN1, defective in cullin neddylation 1, domain containing 4 (S. cerevisiae)	protein-coding
mm_43047.1	chr5	124076087	124076100	+	1	NA	exon (NM_019875, exon 9 of 12)	exon (NM_019875, exon 9 of 12)	19705	NM_019875	56325	Mm.254839	NM_019875	ENSMUSG00000029408	Abcb9	TAPL|mKIAA1520	ATP-binding cassette, sub-family B (MDR/TAP), member 9	protein-coding
mm_150305.1	chr19	34570370	34570375	+	1	NA	intron (NM_008332, intron 2 of 2)	intron (NM_008332, intron 2 of 2)	-13157	NM_010501	15959	Mm.426079	NM_010501	ENSMUSG00000074896	Ifit3	Ifi49|P49	interferon-induced protein with tetratricopeptide repeats 3	protein-coding
mm_2221.1	chr1	90203996	90204012	+	1	NA	promoter-TSS (NM_007722)	promoter-TSS (NM_007722)	24	NM_007722	12778	Mm.6522	NM_007722	ENSMUSG00000044337	Ackr3	AW541270|CXC-R7|CXCR-7|Cmkor1|Cxcr7|RDC-1|Rdc1	atypical chemokine receptor 3	protein-coding
mm_86994.1	chr10	26229744	26229763	+	1	NA	promoter-TSS (NM_001013766)	promoter-TSS (NM_001013766)	46	NM_001115154	268288	Mm.213322	NM_001013766	ENSMUSG00000051354	Samd3	Gm623	sterile alpha motif domain containing 3	protein-coding
mm_62123.1	chr7	96797294	96797341	+	1	NA	intron (NR_045874, intron 2 of 3)	intron (NR_045874, intron 2 of 3)	4232	NR_045874	791381	Mm.402112	NR_045874	ENSMUSG00000053049	Gm15413	ENSMUSG00000053049|OTTMUSG00000021246	predicted gene 15413	ncRNA
mm_41561.1	chr5	93105987	93105989	+	1	NA	intron (NM_001347377, intron 1 of 10)	intron (NM_001347377, intron 1 of 10)	12572	NM_001347377	52398	Mm.394184	NM_001009818	ENSMUSG00000058013	Sept11	6230410I01Rik|AW548875|D5Ertd606e	septin 11	protein-coding
mm_68855.1	chr7	126369501	126369526	-	1	NA	promoter-TSS (NM_010689)	promoter-TSS (NM_010689)	55	NM_010689	16797	Mm.10280	NM_010689	ENSMUSG00000030742	Lat	p36-38|pp36	linker for activation of T cells	protein-coding
mm_139898.1	chr17	70852796	70852806	+	1	NA	intron (NM_001164074, intron 1 of 2)	CpG	731	NM_001164074	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_150615.1	chr19	40945482	40945491	+	1	NA	intron (NM_008528, intron 9 of 16)	intron (NM_008528, intron 9 of 16)	49049	NM_008528	17060	Mm.9749	NM_008528	ENSMUSG00000061132	Blnk	BASH|Bca|Ly-57|Ly57|Lyw-57|SLP-65	B cell linker	protein-coding
mm_37854.1	chr4	132212256	132212262	-	1	NA	promoter-TSS (NM_145393)	promoter-TSS (NM_145393)	-3	NM_145393	213541	Mm.23998	NM_145393	ENSMUSG00000040025	Ythdf2	9430020E02Rik|HGRG8|NY-REN-2	YTH domain family 2	protein-coding
mm_148606.1	chr19	5308368	5308371	+	1	NA	3' UTR (NM_001024717, exon 3 of 3)	3' UTR (NM_001024717, exon 3 of 3)	10038	NM_001024717	545276	Mm.447174	NM_001024717	ENSMUSG00000047658	Gal3st3	-	galactose-3-O-sulfotransferase 3	protein-coding
mm_133002.1	chr16	55966380	55966404	+	1	NA	5' UTR (NM_024218, exon 1 of 6)	5' UTR (NM_024218, exon 1 of 6)	117	NM_024218	68193	Mm.29221	NM_024218	ENSMUSG00000098274	Rpl24	0610008L05Rik|Bst	ribosomal protein L24	protein-coding
mm_113257.1	chr13	28142482	28142485	+	1	NA	promoter-TSS (NM_023746)	promoter-TSS (NM_023746)	-1	NM_023746	28078	Mm.155058	NM_023746	ENSMUSG00000017064	Prl5a1	1600013P04Rik|D13Wsu14e|Ghd24|PLP-L|Prlpl	prolactin family 5, subfamily a, member 1	protein-coding
mm_52722.1	chr6	119922192	119922202	+	1	NA	TTS (NM_001166383)	TTS (NM_001166383)	19499	NM_001166381	19365	Mm.149	NM_011236	ENSMUSG00000030166	Rad52	Rad52yh	RAD52 homolog, DNA repair protein	protein-coding
mm_112459.1	chr13	5866411	5866427	+	1	NA	intron (NM_011803, intron 2 of 3)	intron (NM_011803, intron 2 of 3)	4930	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_165831.1	chr3	152147378	152147386	+	1	NA	intron (NM_016867, intron 1 of 5)	intron (NM_016867, intron 1 of 5)	18518	NM_016867	54120	Mm.97	NM_016867	ENSMUSG00000039131	Gipc2	2200002N01Rik|AU021850|Semcap2	GIPC PDZ domain containing family, member 2	protein-coding
mm_66106.1	chr7	31041540	31041564	-	1	NA	TTS (NM_022007)	TTS (NM_022007)	287	NM_001111073	18301	Mm.1870	NM_008761	ENSMUSG00000009687	Fxyd5	EF-8|Oit2|RIC	FXYD domain-containing ion transport regulator 5	protein-coding
mm_87881.1	chr10	61689628	61689664	+	1	NA	intron (NM_009120, intron 5 of 6)	intron (NM_009120, intron 5 of 6)	-5868	NM_001272090	71767	Mm.71514	NM_027912	ENSMUSG00000020087	Tysnd1	1300019N10Rik	trypsin domain containing 1	protein-coding
mm_67627.1	chr7	84151989	84151999	-	1	NA	promoter-TSS (NM_133722)	promoter-TSS (NM_133722)	-101	NM_133722	70178	Mm.23914	NM_133722	ENSMUSG00000038459	Abhd17c	2210412D01Rik|AL023007|Fam108c|Fam108c1	abhydrolase domain containing 17C	protein-coding
mm_58974.1	chr7	19024365	19024385	+	1	NA	promoter-TSS (NM_026605)	promoter-TSS (NM_026605)	-2	NM_026605	68188	Mm.130902	NM_026605	ENSMUSG00000023118	Sympk	1500016F02Rik|4632415H16Rik|AA125406|AI449890|SPK|SYM	symplekin	protein-coding
mm_23924.1	chr3	83766174	83766187	+	1	NA	promoter-TSS (NM_009144)	promoter-TSS (NM_009144)	-141	NM_009144	20319	Mm.19155	NM_009144	ENSMUSG00000027996	Sfrp2	AI851596|Sdf5	secreted frizzled-related protein 2	protein-coding
mm_93765.1	chr10	120201197	120201233	-	1	NA	intron (NM_028679, intron 1 of 11)	intron (NM_028679, intron 1 of 11)	322	NM_028679	73914	Mm.146194	NM_028679	ENSMUSG00000020227	Irak3	4833428C18Rik|AI563835|IRAK-M	interleukin-1 receptor-associated kinase 3	protein-coding
mm_8302.1	chr1	144002271	144002287	-	1	NA	exon (NM_009061, exon 4 of 5)	exon (NM_009061, exon 4 of 5)	1870	NM_009061	19735	Mm.28262	NM_009061	ENSMUSG00000026360	Rgs2	GOS8	regulator of G-protein signaling 2	protein-coding
mm_103010.1	chr11	69696059	69696102	-	1	NA	promoter-TSS (NM_001159503)	promoter-TSS (NM_001159503)	18	NM_011614	21944	Mm.8983	NM_011614	ENSMUSG00000097328	Tnfsf12	Apo3l|Dr3l|Dr3lg|Tweak	tumor necrosis factor (ligand) superfamily, member 12	protein-coding
mm_55016.1	chr6	48840760	48840770	-	1	NA	promoter-TSS (NM_025326)	promoter-TSS (NM_025326)	223	NM_023056	65963	Mm.28385	NM_023056	ENSMUSG00000029810	Tmem176b	1810009M01Rik|Clast1|Lr8	transmembrane protein 176B	protein-coding
mm_45666.1	chr5	77211165	77211170	-	1	NA	promoter-TSS (NM_001289764)	promoter-TSS (NM_001289764)	38	NM_001289767	69982	Mm.46106	NM_183284	ENSMUSG00000053030	Spink2	1700007F22Rik|AV038945|HUSI-II	serine peptidase inhibitor, Kazal type 2	protein-coding
mm_70809.1	chr8	23035117	23035185	+	1	NA	promoter-TSS (NM_001277281)	promoter-TSS (NM_001277281)	52	NM_001277284	11733	Mm.334444	NM_031158	ENSMUSG00000031543	Ank1	Ank-1|nb|pale	ankyrin 1, erythroid	protein-coding
mm_41162.1	chr5	87932394	87932398	+	1	NA	TTS (NM_007786)	TTS (NM_007786)	6763	NM_007786	12994	Mm.296303	NM_007786	ENSMUSG00000001622	Csn3	AW208918|CSN10|Csnk	casein kappa	protein-coding
mm_63415.1	chr7	127470355	127470370	+	1	NA	Intergenic	Intergenic	-1252	NM_145589	233895	Mm.44183	NM_145589	ENSMUSG00000030822	Prr14	BC006909	proline rich 14	protein-coding
mm_137531.1	chr17	27555559	27555603	+	1	NA	promoter-TSS (NM_001166545)	promoter-TSS (NM_001166545)	-993	NM_001166536	15361	Mm.4438	NM_016660	ENSMUSG00000046711	Hmga1	AL023995|Hmga1a|Hmga1b|Hmgi|Hmgiy|Hmgy	high mobility group AT-hook 1	protein-coding
mm_6469.1	chr1	74037121	74037139	-	1	NA	intron (NM_027884, intron 3 of 34)	CpG	87317	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_154106.1	chr19	57118857	57118868	-	1	NA	5' UTR (NM_001103178, exon 1 of 20)	5' UTR (NM_001103178, exon 1 of 20)	162	NM_001347459	226251	Mm.217161	NM_178688	ENSMUSG00000025085	Ablim1	2210411C18Rik|2610209L21Rik|4833406P10Rik|9330196J19Rik|AV079770|AW060987|AW215784|Limab1|mKIAA0059	actin-binding LIM protein 1	protein-coding
mm_42824.1	chr5	122093852	122093864	+	1	NA	Intergenic	Intergenic	-7122	NM_010861	17906	Mm.1529	NM_010861	ENSMUSG00000013936	Myl2	MLC-2|MLC-2s/v|MLC-2v|Mlc2v|Mylpc	myosin, light polypeptide 2, regulatory, cardiac, slow	protein-coding
mm_30580.1	chr4	5472441	5472445	+	1	NA	Intergenic	Intergenic	-159885	NR_038183	73872	Mm.427301	NR_038183	ENSMUSG00000086066	4930423M02Rik	-	RIKEN cDNA 4930423M02 gene	ncRNA
mm_65955.1	chr7	30428558	30428566	-	1	NA	3' UTR (NM_172142, exon 11 of 11)	3' UTR (NM_172142, exon 11 of 11)	5258	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_39899.1	chr5	31220749	31220795	+	1	NA	promoter-TSS (NM_008014)	promoter-TSS (NM_008014)	-227	NM_008014	14208	Mm.14501	NM_008014	ENSMUSG00000029147	Ppm1g	AI385652|Fin13	protein phosphatase 1G (formerly 2C), magnesium-dependent, gamma isoform	protein-coding
mm_153792.1	chr19	45998223	45998229	-	1	NA	intron (NM_198296, intron 1 of 25)	CpG	262	NM_198296	71617	Mm.210949	NM_198296	ENSMUSG00000039901	9130011E15Rik	AI431055|AW050122	RIKEN cDNA 9130011E15 gene	protein-coding
mm_147128.1	chr18	36067631	36067635	-	1	NA	intron (NM_001167891, intron 1 of 9)	(A)n|Simple_repeat|Simple_repeat	-38570	NR_015571	74966	Mm.379238	NM_030089		4930471G03Rik	1700007N01Rik	RIKEN cDNA 4930471G03 gene	ncRNA
mm_9003.1	chr1	165836482	165836505	-	1	NA	intron (NM_001113391, intron 1 of 7)	intron (NM_001113391, intron 1 of 7)	47812	NM_001113392	12503	Mm.217308	NM_031162	ENSMUSG00000005763	Cd247	4930549J05Rik|A430104F18Rik|AW552088|Cd3|Cd3-eta|Cd3-zeta|Cd3h|Cd3z|Cd3zeta|T3z|Tcrk|Tcrz	CD247 antigen	protein-coding
mm_99268.1	chr11	101246925	101246935	+	1	NA	intron (NM_019444, intron 1 of 3)	intron (NM_019444, intron 1 of 3)	596	NM_019444	54409	Mm.260698	NM_019444	ENSMUSG00000001240	Ramp2	-	receptor (calcitonin) activity modifying protein 2	protein-coding
mm_26651.1	chr3	154193015	154193043	+	1	NA	intron (NM_001081263, intron 2 of 21)	intron (NM_001081263, intron 2 of 21)	137531	NM_010713	16875	Mm.15530	NM_010713	ENSMUSG00000096225	Lhx8	L3|Lhx7	LIM homeobox protein 8	protein-coding
mm_42201.1	chr5	112325441	112325452	+	1	NA	promoter-TSS (NM_018783)	promoter-TSS (NM_018783)	-923	NM_018783	54723	Mm.172947	NM_018783	ENSMUSG00000029345	Tfip11	2810002G02Rik|AF097181|AW046167|Srr1|TIP33|Tip39	tuftelin interacting protein 11	protein-coding
mm_18367.1	chr2	59882498	59882513	-	1	NA	5' UTR (NM_028118, exon 1 of 11)	5' UTR (NM_028118, exon 1 of 11)	101	NM_001159636	72137	Mm.288734	NM_028118	ENSMUSG00000026988	Wdsub1	1700048E19Rik|2610014F08Rik	WD repeat, SAM and U-box domain containing 1	protein-coding
mm_50469.1	chr6	48986897	48986912	+	1	NA	promoter-TSS (NM_172888)	promoter-TSS (NM_172888)	43	NM_172888	243377	Mm.446302	NM_172888	ENSMUSG00000039215	Svs1	9530003A11	seminal vesicle secretory protein 1	protein-coding
mm_11085.1	chr2	27744702	27744719	+	1	NA	intron (NM_001290482, intron 4 of 9)	intron (NM_001290482, intron 4 of 9)	34127	NM_001290482	20181	Mm.24624	NM_011305	ENSMUSG00000015846	Rxra	9530071D11Rik|Nr2b1|RXRalpha1	retinoid X receptor alpha	protein-coding
mm_117450.1	chr13	74808528	74808540	-	1	NA	promoter-TSS (NM_009817)	promoter-TSS (NM_009817)	226	NM_001301153	12380	Mm.29163	NM_009817	ENSMUSG00000021585	Cast	-	calpastatin	protein-coding
mm_96215.1	chr11	62457470	62457484	+	1	NA	promoter-TSS (NM_177229)	promoter-TSS (NM_177229)	-145	NM_177229	20185	Mm.271814	NM_011308	ENSMUSG00000018501	Ncor1	5730405M06Rik|A230020K14Rik|N-CoR|RIP13|Rxrip13|mKIAA1047	nuclear receptor co-repressor 1	protein-coding
mm_93459.1	chr10	110456198	110456213	-	1	NA	Intergenic	Intergenic	-144445	NR_028438	109335	Mm.367727	NR_028438		9230102K24Rik	-	RIKEN cDNA 9230102K24 gene	ncRNA
mm_91652.1	chr10	42578303	42578313	-	1	NA	exon (NM_152229, exon 2 of 9)	exon (NM_152229, exon 2 of 9)	5280	NM_152229	21907	Mm.287100	NM_152229	ENSMUSG00000019803	Nr2e1	Mtl1|Mtll|TLL|Tlx|XTLL|fierce|frc|tailless	nuclear receptor subfamily 2, group E, member 1	protein-coding
mm_95005.1	chr11	31900791	31900794	+	1	NA	intron (NM_001290678, intron 2 of 7)	intron (NM_001290678, intron 2 of 7)	29852	NM_026252	67579	Mm.339792	NM_026252	ENSMUSG00000020300	Cpeb4	Cpe-bp4|Cpeb-4|mCPEB-4	cytoplasmic polyadenylation element binding protein 4	protein-coding
mm_63366.1	chr7	127090758	127090782	+	1	NA	promoter-TSS (NM_178901)	promoter-TSS (NM_178901)	-666	NM_178901	101602	Mm.490357	NM_178901	ENSMUSG00000045165	AI467606	-	expressed sequence AI467606	protein-coding
mm_34662.1	chr4	150867048	150867072	+	1	NA	exon (NM_133753, exon 4 of 4)	exon (NM_133753, exon 4 of 4)	11969	NM_133753	74155	Mm.318841	NM_133753	ENSMUSG00000028967	Errfi1	1300002F13Rik|AI788755|Mig-6|Mig6|RALT	ERBB receptor feedback inhibitor 1	protein-coding
mm_151982.1	chr19	5834924	5834937	-	1	NA	non-coding (NR_131212, exon 1 of 1)	non-coding (NR_131212, exon 1 of 1)	10548	NR_131212	66961	Mm.281895	NR_003513	ENSMUSG00000092274	Neat1	2310043N10Rik|VINC	nuclear paraspeckle assembly transcript 1 (non-protein coding)	ncRNA
mm_124171.1	chr14	93797953	93797958	-	1	NA	intron (NM_001346722, intron 2 of 4)	intron (NM_001346722, intron 2 of 4)	90933	NM_001271800	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding
mm_102546.1	chr11	61331713	61331716	-	1	NA	intron (NM_001033542, intron 5 of 16)	intron (NM_001033542, intron 5 of 16)	11146	NM_001033542	380701	Mm.340166	NM_001033542	ENSMUSG00000069855	Slc47a2	4933429E10Rik	solute carrier family 47, member 2	protein-coding
mm_35041.1	chr4	4138818	4138828	-	1	NA	promoter-TSS (NM_001002927)	promoter-TSS (NM_001002927)	-378	NM_001002927	18619	Mm.475097	NM_001002927	ENSMUSG00000045573	Penk	AI326464|ENK|PPA|Penk1	preproenkephalin	protein-coding
mm_173143.1	chrX	21853516	21853518	-	1	NA	Intergenic	L1Md_F2|LINE|L1	138617	NM_020049	56774	Mm.253984	NM_020049	ENSMUSG00000031089	Slc6a14	1110007A17Rik|9030613J17Rik|ATB0plus|CATB0plus	solute carrier family 6 (neurotransmitter transporter), member 14	protein-coding
mm_50951.1	chr6	58644213	58644217	+	1	NA	intron (NM_011920, intron 1 of 15)	B1F2|SINE|Alu	47543	NM_011920	26357	Mm.333096	NM_011920	ENSMUSG00000029802	Abcg2	ABC15|ABCP|AI428558|BCRP|Bcrp1|MXR|MXR1	ATP-binding cassette, sub-family G (WHITE), member 2	protein-coding
mm_101108.1	chr11	11932888	11932903	-	1	NA	3' UTR (NM_010345, exon 17 of 17)	3' UTR (NM_010345, exon 17 of 17)	-34751	NM_001190448	13195	Mm.12906	NM_016672	ENSMUSG00000020182	Ddc	Aadc	dopa decarboxylase	protein-coding
mm_75861.1	chr8	70723540	70723573	-	1	NA	promoter-TSS (NM_201607)	promoter-TSS (NM_201607)	-508	NM_001310465	110385	Mm.255180	NM_201607	ENSMUSG00000031842	Pde4c	Dpde1|E130301F19Rik|dunce	phosphodiesterase 4C, cAMP specific	protein-coding
mm_61651.1	chr7	80406563	80406573	+	1	NA	Intergenic	L1MA10|LINE|L1	-1132	NM_001081454	18550	Mm.5241	NM_011046	ENSMUSG00000030530	Furin	9130404I01Rik|Fur|PACE|Pcsk3|SPC1	furin (paired basic amino acid cleaving enzyme)	protein-coding
mm_33567.1	chr4	132075605	132075609	+	1	NA	promoter-TSS (NM_001128607)	promoter-TSS (NM_001128607)	-294	NM_001128607	269587	Mm.30038	NM_183428	ENSMUSG00000028906	Epb41	4.1R|AI415518|D4Ertd442e|Elp-1|Elp1|Epb4.1|mKIAA4056	erythrocyte membrane protein band 4.1	protein-coding
mm_29947.1	chr3	132950190	132950198	-	1	NA	promoter-TSS (NM_001287103)	promoter-TSS (NM_001287103)	97	NM_001287102	114249	Mm.279310	NM_033525	ENSMUSG00000040998	Npnt	1110009H02Rik|AA682063|AI314031|Nctn|POEM	nephronectin	protein-coding
mm_8077.1	chr1	135585368	135585380	-	1	NA	promoter-TSS (NM_173437)	promoter-TSS (NM_173437)	-19	NM_173437	215690	Mm.34977	NM_173437	ENSMUSG00000009418	Nav1	9530089B19|9930003A20Rik|C230080M11Rik|Pomfil3|Unc53h1|mKIAA1151|steerin-1	neuron navigator 1	protein-coding
mm_30424.1	chr3	152668136	152668147	-	1	NA	promoter-TSS (NM_001081277)	promoter-TSS (NM_001081277)	-1	NM_001081277	229949	Mm.207057	NM_001081277	ENSMUSG00000039058	Ak5	-	adenylate kinase 5	protein-coding
mm_86091.1	chr9	114982740	114982742	-	1	NA	Intergenic	Intergenic	-48754	NM_175380	333433	Mm.38198	NM_175380	ENSMUSG00000050627	Gpd1l	2210409H23Rik|D9Ertd660e	glycerol-3-phosphate dehydrogenase 1-like	protein-coding
mm_43451.1	chr5	136136224	136136256	+	1	NA	promoter-TSS (NM_027891)	promoter-TSS (NM_027891)	95	NM_001347492	72041	Mm.486605	NM_028070	ENSMUSG00000039754	Alkbh4	2010004B12Rik|Abj4	alkB homolog 4, lysine demethylase	protein-coding
mm_109905.1	chr12	7979372	7979378	-	1	NA	intron (NM_009693, intron 3 of 28)	intron (NM_009693, intron 3 of 28)	1698	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_90016.1	chr10	115358762	115358795	+	1	NA	intron (NM_133683, intron 3 of 6)	Arthur1|DNA|hAT-Tip100	3484	NM_133683	67226	Mm.29647	NM_133683	ENSMUSG00000069520	Tmem19	2810428F02Rik|AW125171	transmembrane protein 19	protein-coding
mm_36838.1	chr4	106617215	106617226	-	1	NA	promoter-TSS (NM_183182)	promoter-TSS (NM_183182)	18	NM_183182	242602	Mm.235591	NM_183182	ENSMUSG00000054362	Lexm	-	lymphocyte expansion molecule	protein-coding
mm_167267.1	chr8	30920062	30920062	+	1	NA	Intergenic	Intergenic	-169600	NM_025869	66959	Mm.23916	NM_025869	ENSMUSG00000039661	Dusp26	2310043K02Rik|Skrp3	dual specificity phosphatase 26 (putative)	protein-coding
mm_153774.1	chr19	45742883	45742899	-	1	NA	promoter-TSS (NM_010205)	promoter-TSS (NM_010205)	-7	NM_001166362	14179	Mm.4012	NM_010205	ENSMUSG00000025219	Fgf8	Aigf|Fgf-8	fibroblast growth factor 8	protein-coding
mm_150144.1	chr19	31868806	31868820	+	1	NA	promoter-TSS (NM_001081074)	promoter-TSS (NM_001081074)	52	NM_001081074	69865	Mm.87538	NM_001081074	ENSMUSG00000052595	A1cf	1810073H04Rik|ACF64|ACF65|ASP|Acf|MCM|MerCreMer|Tg(Myh6-cre/Esr1*)1Jmk|mer	APOBEC1 complementation factor	protein-coding
mm_37914.1	chr4	132783439	132783454	-	1	NA	exon (NM_001033308, exon 5 of 6)	exon (NM_001033308, exon 5 of 6)	12918	NM_001033308	230787	Mm.290912	NM_001033308	ENSMUSG00000037731	Themis2	ICB-1	thymocyte selection associated family member 2	protein-coding
mm_51233.1	chr6	71377302	71377317	+	1	NA	3' UTR (NM_009857, exon 4 of 4)	3' UTR (NM_009857, exon 4 of 4)	3882	NM_001081110	12525	Mm.1858	NM_009857	ENSMUSG00000053977	Cd8a	BB154331|Ly-2|Ly-35|Ly-B|Lyt-2	CD8 antigen, alpha chain	protein-coding
mm_129680.1	chr15	81399781	81399791	-	1	NA	promoter-TSS (NM_133726)	promoter-TSS (NM_133726)	-92	NM_133726	70356	Mm.180337	NM_133726	ENSMUSG00000022403	St13	1110007I03Rik|3110002K08Rik|AW555194|HIP|HOP|HSPABP|HSPABP1|PRO0786|SNC6|p48	suppression of tumorigenicity 13	protein-coding
mm_67220.1	chr7	74501100	74501126	-	1	NA	intron (NM_001038643, intron 2 of 10)	intron (NM_001038643, intron 2 of 10)	53667	NM_023908	108116	Mm.425467	NM_023908	ENSMUSG00000025790	Slco3a1	5830414C08Rik|Anr1|MJAM|OATP-D|R75096|Slc21a11	solute carrier organic anion transporter family, member 3a1	protein-coding
mm_165868.1	chr4	34950666	34950669	-	1	NA	3' UTR (NM_178061, exon 4 of 4)	3' UTR (NM_178061, exon 4 of 4)	-39186	NR_040652	73696	Mm.1361	NR_040652	ENSMUSG00000085824	Platr9	2410114N07Rik	pluripotency associated transcript 9	ncRNA
mm_82251.1	chr9	4796023	4796033	-	1	NA	5' UTR (NM_001113181, exon 1 of 11)	5' UTR (NM_001113181, exon 1 of 11)	206	NM_001113180	14802	Mm.209263	NM_019691	ENSMUSG00000025892	Gria4	GluA4|GluR-D|Glur-4|Glur4|Gluralpha4|spkw1	glutamate receptor, ionotropic, AMPA4 (alpha 4)	protein-coding
mm_141040.1	chr17	25274276	25274296	-	1	NA	promoter-TSS (NM_011665)	promoter-TSS (NM_011665)	24	NM_011665	22196	Mm.240044	NM_011665	ENSMUSG00000015120	Ube2i	5830467E05Rik|F830028O17Rik|UBC9|Ubce2i|Ubce9	ubiquitin-conjugating enzyme E2I	protein-coding
mm_145875.1	chr18	65473033	65473047	+	1	NA	exon (NM_172833, exon 14 of 16)	exon (NM_172833, exon 14 of 16)	42043	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_5328.1	chr1	23397560	23397562	-	1	NA	Intergenic	Intergenic	-14386	NM_001081079	70155	Mm.28013	NM_001081079	ENSMUSG00000026158	Ogfrl1	2210417C17Rik	opioid growth factor receptor-like 1	protein-coding
mm_159887.1	chr6	28261531	28261531	-	1	NA	promoter-TSS (NM_001081678)	promoter-TSS (NM_001081678)	70	NM_001081678	627049	Mm.84441	NM_001081678	ENSMUSG00000039841	Zfp800	AA407452|Znf800	zinc finger protein 800	protein-coding
mm_83242.1	chr9	42399770	42399793	-	1	NA	5' UTR (NM_001324548, exon 1 of 24)	5' UTR (NM_001324548, exon 1 of 24)	148	NM_009347	21683	Mm.42209	NM_009347	ENSMUSG00000037705	Tecta	Tctna	tectorin alpha	protein-coding
mm_147431.1	chr18	46357133	46357144	-	1	NA	Intergenic	Intergenic	-45210	NM_001160399	240261	Mm.329416	NM_001160399	ENSMUSG00000071855	Ccdc112	8430438M01Rik|AW108467	coiled-coil domain containing 112	protein-coding
mm_128229.1	chr15	36595296	36595299	-	1	NA	TTS (NM_008774)	TTS (NM_008774)	13676	NM_008774	18458	Mm.371570	NM_008774	ENSMUSG00000022283	Pabpc1	PABP|Pabp1|PabpI|Pabpl1|ePAB	poly(A) binding protein, cytoplasmic 1	protein-coding
mm_39659.1	chr5	24996034	24996050	+	1	NA	promoter-TSS (NM_001310480)	promoter-TSS (NM_001310480)	-289	NM_001310480	108099	Mm.33649	NM_145401	ENSMUSG00000028944	Prkag2	2410051C13Rik|AAKG|AAKG2|AI854673|H91620p|WPWS	protein kinase, AMP-activated, gamma 2 non-catalytic subunit	protein-coding
mm_16670.1	chr2	6722188	6722236	-	1	NA	promoter-TSS (NM_001310447)	promoter-TSS (NM_001310447)	-550	NM_001310447	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_59813.1	chr7	29170852	29170860	+	1	NA	intron (NM_182696, intron 1 of 2)	intron (NM_182696, intron 1 of 2)	466	NM_182696	243897	Mm.389886	NM_182694	ENSMUSG00000031493	Ggn	AI593290	gametogenetin	protein-coding
mm_103891.1	chr11	83575103	83575109	-	1	NA	3' UTR (NM_011338, exon 4 of 4)	3' UTR (NM_011338, exon 4 of 4)	3530	NM_011338	20308	Mm.416125	NM_011338	ENSMUSG00000019122	Ccl9	CCF18|MRP-2|Scya10|Scya9	chemokine (C-C motif) ligand 9	protein-coding
mm_103859.1	chr11	83298846	83298870	-	1	NA	5' UTR (NM_134025, exon 1 of 4)	5' UTR (NM_134025, exon 1 of 4)	119	NM_134025	103737	Mm.102205	NM_134025	ENSMUSG00000018733	Pex12	AI451906	peroxisomal biogenesis factor 12	protein-coding
mm_113678.1	chr13	42785174	42785188	+	1	NA	intron (NM_001005740, intron 1 of 12)	intron (NM_001005740, intron 1 of 12)	75600	NM_001005740	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding
mm_15448.1	chr2	157392723	157392751	+	1	NA	intron (NM_026968, intron 2 of 2)	intron (NM_026968, intron 2 of 2)	25143	NM_026968	69161	Mm.228619	NM_026968	ENSMUSG00000063019	Manbal	1810024K12Rik|AI836500	mannosidase, beta A, lysosomal-like	protein-coding
mm_39769.1	chr5	30013835	30013846	+	1	NA	intron (NM_001314054, intron 2 of 4)	intron (NM_001314054, intron 2 of 4)	726	NM_031168	16193	Mm.1019	NM_031168	ENSMUSG00000025746	Il6	Il-6	interleukin 6	protein-coding
mm_133629.1	chr16	91647843	91647858	+	1	NA	promoter-TSS (NM_019973)	promoter-TSS (NM_019973)	26	NM_178880	20658	Mm.46401	NM_019973	ENSMUSG00000022961	Son	2900011L12Rik|AA409051|AU067731|C81487|mKIAA1019|nrebp	Son DNA binding protein	protein-coding
mm_46485.1	chr5	105132063	105132077	-	1	NA	intron (NM_008620, intron 3 of 10)	intron (NM_008620, intron 3 of 10)	7482	NM_008620	17472	Mm.440525	NM_008620	ENSMUSG00000079363	Gbp4	AW228052|Mag-2|Mpa-2|Mpa2	guanylate binding protein 4	protein-coding
mm_169276.1	chr13	92354626	92354634	-	1	NA	promoter-TSS (NM_010049)	promoter-TSS (NM_010049)	-153	NM_010049	13361	Mm.23695	NM_010049	ENSMUSG00000021707	Dhfr	8430436I03Rik|AA607882|AI662710|AW555094	dihydrofolate reductase	protein-coding
mm_83064.1	chr9	37552665	37552711	-	1	NA	promoter-TSS (NM_022029)	promoter-TSS (NM_022029)	57	NM_022029	64011	Mm.335065	NM_022029	ENSMUSG00000053310	Nrgn	0710001B06Rik|AI838505|NG|NG/RC3|Pss1|R75334|RC3	neurogranin	protein-coding
mm_128779.1	chr15	66801543	66801567	-	1	NA	intron (NM_001029841, intron 1 of 7)	intron (NM_001029841, intron 1 of 7)	30274	NM_001029841	20491	Mm.7601	NM_009192	ENSMUSG00000022372	Sla	Slap|Slap-1	src-like adaptor	protein-coding
mm_47255.1	chr5	121660379	121660397	-	1	NA	promoter-TSS (NM_001289543)	promoter-TSS (NM_001289543)	122	NM_028037	71985	Mm.45423	NM_028037	ENSMUSG00000029456	Acad10	2410021P16Rik	acyl-Coenzyme A dehydrogenase family, member 10	protein-coding
mm_165725.1	chr3	103914243	103914244	+	1	NA	5' UTR (NM_172684, exon 1 of 7)	5' UTR (NM_172684, exon 1 of 7)	123	NM_172684	229675	Mm.29366	NM_172684	ENSMUSG00000044098	Rsbn1	C230004D03Rik|E330004N01|Rosbin|Rsbn|Rsbp|mKIAA3002	rosbin, round spermatid basic protein 1	protein-coding
mm_104134.1	chr11	86860080	86860107	-	1	NA	intron (NR_106195, intron 4 of 8)	intron (NR_106195, intron 4 of 8)	-52433	NM_026191	67487	Mm.260627	NM_026191	ENSMUSG00000018425	Dhx40	2410016C14Rik|ARG147|DDX40|PAD	DEAH (Asp-Glu-Ala-His) box polypeptide 40	protein-coding
mm_36105.1	chr4	58803750	58803764	-	1	NA	exon (NM_172381, exon 47 of 49)	exon (NM_172381, exon 47 of 49)	-18037	NM_146920	258922	Mm.223327	NM_146920	ENSMUSG00000043385	Olfr267	MOR262-1	olfactory receptor 267	protein-coding
mm_158992.1	chr1	134846384	134846384	-	1	NA	intron (NM_001081307, intron 13 of 23)	intron (NM_001081307, intron 13 of 23)	-42663	NR_015606	329251	Mm.188709	NM_001081307	ENSMUSG00000073557	Ppp1r12b	1810037O03Rik|9530009M10Rik|AI132431|Mypt2	protein phosphatase 1, regulatory (inhibitor) subunit 12B	protein-coding
mm_105391.1	chr11	103374085	103374100	-	1	NA	intron (NM_183034, intron 7 of 11)	intron (NM_183034, intron 7 of 11)	-10400	NM_001205236	544817	Mm.259113	NM_133715	ENSMUSG00000034255	Arhgap27	2310069I04Rik|5730442P18Rik|Gm21552|Sh3d20	Rho GTPase activating protein 27	protein-coding
mm_149717.1	chr19	21653556	21653566	+	1	NA	promoter-TSS (NM_025423)	promoter-TSS (NM_025423)	252	NM_146096	226016	Mm.28796	NM_146096	ENSMUSG00000047368	Abhd17b	5730446C15Rik|Cgi67|Fam108b|Fam108b1	abhydrolase domain containing 17B	protein-coding
mm_109111.1	chr12	105454010	105454027	+	1	NA	5' UTR (NM_001252508, exon 1 of 2)	5' UTR (NM_001252508, exon 1 of 2)	162	NM_001252508	268595	Mm.2388	NM_001252508	ENSMUSG00000094910	D430019H16Rik	AI852661	RIKEN cDNA D430019H16 gene	protein-coding
mm_167165.1	chr7	135806809	135806814	-	1	NA	Intergenic	Intergenic	-90432	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_79515.1	chr9	57521334	57521342	+	1	NA	exon (NM_007747, exon 1 of 5)	exon (NM_007747, exon 1 of 5)	106	NM_007747	12858	Mm.273403	NM_007747	ENSMUSG00000000088	Cox5a	AA959768|CcOX	cytochrome c oxidase subunit Va	protein-coding
mm_76087.1	chr8	79399477	79399481	-	1	NA	promoter-TSS (NM_008539)	promoter-TSS (NM_008539)	-11	NM_008539	17125	Mm.223717	NM_008539	ENSMUSG00000031681	Smad1	AI528653|Madh1|Madr1|Mlp1|MusMLP	SMAD family member 1	protein-coding
mm_169201.1	chr13	66312228	66312231	+	1	NA	Intergenic	Intergenic	128889	NM_183119	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
mm_113681.1	chr13	42838734	42838740	+	1	NA	intron (NM_001005740, intron 1 of 12)	intron (NM_001005740, intron 1 of 12)	-27510	NM_001302636	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding
mm_87116.1	chr10	33256542	33256564	+	1	NA	promoter-TSS (NR_040657)	promoter-TSS (NR_040657)	-196	NR_040657	442820	Mm.490725	NR_040657		D830005E20Rik	-	RIKEN cDNA D830005E20 gene	ncRNA
mm_74518.1	chr8	8969776	8969788	-	1	NA	Intergenic	Intergenic	162506	NR_045854	71249	Mm.158635	NR_045854	ENSMUSG00000108848	4933430N04Rik	-	RIKEN cDNA 4933430N04 gene	ncRNA
mm_49252.1	chr6	17339479	17339493	+	1	NA	3' UTR (NM_001243064, exon 2 of 2)	3' UTR (NM_001243064, exon 2 of 2)	31846	NM_001243064	12389	Mm.28278	NM_007616	ENSMUSG00000007655	Cav1	Cav|Cav-1	caveolin 1, caveolae protein	protein-coding
mm_134942.1	chr16	31201151	31201243	-	1	NA	promoter-TSS (NM_030138)	promoter-TSS (NM_030138)	41	NM_030138	78618	Mm.274646	NM_030138	ENSMUSG00000049076	Acap2	4832442G16|9530039J15Rik|CNT-B2|Centb2|mKIAA0041	ArfGAP with coiled-coil, ankyrin repeat and PH domains 2	protein-coding
mm_169331.1	chr14	118182136	118182136	-	1	NA	Intergenic	Intergenic	45009	NM_021434	58245	Mm.275411	NM_021434	ENSMUSG00000022131	Gpr180	AB041545|E130016I23Rik|Itr	G protein-coupled receptor 180	protein-coding
mm_167793.1	chr9	123924673	123924687	-	1	NA	Intergenic	(CAGA)n|Simple_repeat|Simple_repeat	44012	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_10211.1	chr2	5683716	5683718	+	1	NA	intron (NM_001290374, intron 1 of 9)	intron (NM_001290374, intron 1 of 9)	-7671	NM_001290376	227541	Mm.191949	NM_177343	ENSMUSG00000039145	Camk1d	A630059D12Rik|CKLiK|CaMKIdelta|E030025C11Rik|mCKLiK	calcium/calmodulin-dependent protein kinase ID	protein-coding
mm_1145.1	chr1	60746430	60746477	+	1	NA	promoter-TSS (NM_007642)	promoter-TSS (NM_007642)	65	NM_007642	12487	Mm.255003	NM_007642	ENSMUSG00000026012	Cd28	-	CD28 antigen	protein-coding
mm_21984.1	chr2	167543629	167543634	-	1	NA	TTS (NM_011427)	TTS (NM_011427)	5436	NM_011427	20613	Mm.2093	NM_011427	ENSMUSG00000042821	Snai1	Sna|Sna1|Snail|Snail1	snail family zinc finger 1	protein-coding
mm_20252.1	chr2	126500632	126500675	-	1	NA	Intergenic	Intergenic	-9100	NM_001080944	241633	Mm.222235	NM_001080944	ENSMUSG00000060131	Atp8b4	A530043E15|Im	ATPase, class I, type 8B, member 4	protein-coding
mm_66657.1	chr7	45714681	45714696	-	1	NA	5' UTR (NM_020011, exon 1 of 6)	5' UTR (NM_020011, exon 1 of 6)	519	NM_020011	56632	Mm.24222	NM_020011	ENSMUSG00000057342	Sphk2	C76851	sphingosine kinase 2	protein-coding
mm_70214.1	chr7	144931945	144931961	-	1	NA	TTS (NR_039539)	TTS (NR_039539)	182	NR_039539	100628615		NR_039539	ENSMUSG00000092633	Mir3962	mmu-mir-3962|mu-mir-3962	microRNA 3962	ncRNA
mm_17466.1	chr2	28558075	28558082	-	1	NA	exon (NM_009885, exon 8 of 11)	exon (NM_009885, exon 8 of 11)	5325	NM_009885	12613	Mm.236017	NM_009885	ENSMUSG00000026818	Cel	1810036E18Rik|BAL	carboxyl ester lipase	protein-coding
mm_50928.1	chr6	57654424	57654466	+	1	NA	exon (NM_025992, exon 17 of 23)	exon (NM_025992, exon 17 of 23)	37633	NM_025574	66459	Mm.44201	NM_025574	ENSMUSG00000043162	Pyurf	2610022G08Rik|AI847956|Prey	Pigy upstream reading frame	protein-coding
mm_106557.1	chr11	120628080	120628103	-	1	NA	TTS (NM_010756)	TTS (NM_010756)	-3089	NM_153056	209011	Mm.292957	NM_153056	ENSMUSG00000025138	Sirt7	-	sirtuin 7	protein-coding
mm_5730.1	chr1	45312971	45312987	-	1	NA	intron (NM_009930, intron 1 of 50)	intron (NM_009930, intron 1 of 50)	1441	NM_009930	12825	Mm.249555	NM_009930	ENSMUSG00000026043	Col3a1	AW550625|Col3a-1|Tsk-2|Tsk2	collagen, type III, alpha 1	protein-coding
mm_151599.1	chr19	3521799	3521819	-	1	NA	exon (NM_028999, exon 4 of 24)	exon (NM_028999, exon 4 of 24)	53940	NM_001164159	52036	Mm.284686	NM_028999	ENSMUSG00000024908	Ppp6r3	4930528G08Rik|9130026N02Rik|D19Bwg1430e|D19Ertd703e|Pp6r3|Ppcs3|Pptcs3|Sapl|Saps3|mKIAA1558	protein phosphatase 6, regulatory subunit 3	protein-coding
mm_10640.1	chr2	20547459	20547470	+	1	NA	intron (NM_029895, intron 3 of 18)	intron (NM_029895, intron 3 of 18)	27951	NM_001177631	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding
mm_97905.1	chr11	83437679	83437708	+	1	NA	promoter-TSS (NM_025492)	promoter-TSS (NM_025492)	-1	NM_025492	66330	Mm.44800	NM_025492	ENSMUSG00000035085	1700020L24Rik	-	RIKEN cDNA 1700020L24 gene	protein-coding
mm_153379.1	chr19	40376682	40376703	-	1	NA	exon (NM_178362, exon 7 of 29)	exon (NM_178362, exon 7 of 29)	25618	NM_001034964	20411	Mm.210815	NM_009166	ENSMUSG00000025006	Sorbs1	2310065E01Rik|9530001P15Rik|CAP|SH3P12|Sh3d5|mKIAA1296	sorbin and SH3 domain containing 1	protein-coding
mm_57770.1	chr6	129237047	129237064	-	1	NA	intron (NR_040265, intron 1 of 2)	MTE2a|LTR|ERVL-MaLR	990	NR_040265	76432	Mm.261738	NR_040265	ENSMUSG00000097354	2310001H17Rik	AI646108	RIKEN cDNA 2310001H17 gene	ncRNA
mm_30641.1	chr4	8821784	8821802	+	1	NA	intron (NM_001277149, intron 7 of 37)	intron (NM_001277149, intron 7 of 37)	131387	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_152325.1	chr19	9945865	9945875	-	1	NA	Intergenic	MTEa|LTR|ERVL-MaLR	-34730	NR_073181	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
mm_94145.1	chr10	128740100	128740109	-	1	NA	intron (NM_016811, intron 1 of 23)	B2_Mm2|SINE|B2	3952	NM_016811	13139	Mm.291235	NM_016811	ENSMUSG00000025357	Dgka	80kDa|AW146112|Dagk1	diacylglycerol kinase, alpha	protein-coding
mm_7747.1	chr1	131066299	131066330	-	1	NA	intron (NM_008551, intron 1 of 9)	intron (NM_008551, intron 1 of 9)	31529	NM_008551	17164	Mm.221235	NM_008551	ENSMUSG00000016528	Mapkapk2	AA960234|MAPKAP-K2|MK-2|MK2|Rps6kc1	MAP kinase-activated protein kinase 2	protein-coding
mm_18467.1	chr2	62411295	62411336	-	1	NA	intron (NM_001159543, intron 1 of 24)	intron (NM_001159543, intron 1 of 24)	916	NM_010074	13482	Mm.1151	NM_010074	ENSMUSG00000035000	Dpp4	Cd26|Dpp-4|THAM	dipeptidylpeptidase 4	protein-coding
mm_85392.1	chr9	103259495	103259518	-	1	NA	exon (NM_027918, exon 13 of 17)	exon (NM_027918, exon 13 of 17)	28791	NM_027918	71775	Mm.18802	NM_027918	ENSMUSG00000033688	1300017J02Rik	Ica|mICA	RIKEN cDNA 1300017J02 gene	protein-coding
mm_53236.1	chr6	127453609	127453662	+	1	NA	promoter-TSS (NM_181402)	promoter-TSS (NM_181402)	8	NM_001346512	101187	Mm.110818	NM_181402	ENSMUSG00000037997	Parp11	5330431N24Rik|AI851877|ARTD11|HIN1L|PARP-11	poly (ADP-ribose) polymerase family, member 11	protein-coding
mm_91216.1	chr10	21844855	21844868	-	1	NA	Intergenic	Intergenic	-37323	NM_001161845	20393	Mm.28405	NM_011361	ENSMUSG00000019970	Sgk1	Sgk	serum/glucocorticoid regulated kinase 1	protein-coding
mm_80755.1	chr9	95554416	95554422	+	1	NA	Intergenic	Intergenic	-5398	NM_198414	75552	Mm.151485	NM_198414	ENSMUSG00000064225	Paqr9	1700020G04Rik	progestin and adipoQ receptor family member IX	protein-coding
mm_146827.1	chr18	21652000	21652015	-	1	NA	exon (NM_001081403, exon 1 of 8)	exon (NM_001081403, exon 1 of 8)	361	NM_001081403	225266	Mm.436836	NM_001081403	ENSMUSG00000042514	Klhl14	6330403N15Rik|AI785250|printor	kelch-like 14	protein-coding
mm_56232.1	chr6	90662054	90662064	-	1	NA	3' UTR (NM_001134384, exon 14 of 14)	3' UTR (NM_001134384, exon 14 of 14)	42813	NM_001037493	71699	Mm.272633	NM_027868	ENSMUSG00000030089	Slc41a3	1010001P06Rik|AI480742|SLC41A1-L2	solute carrier family 41, member 3	protein-coding
mm_170645.1	chr19	9515759	9515761	-	1	NA	Intergenic	RLTR9F|LTR|ERVK	43488	NR_073559	619371	Mm.316894	NM_001030317		Stxbp3-ps	Munc18c(L)|Stxbp3-1|Stxbp3b	syntaxin-binding protein 3, pseudogene	pseudo
mm_7319.1	chr1	99791822	99791843	-	1	NA	intron (NM_172851, intron 1 of 23)	intron (NM_172851, intron 1 of 23)	19067	NM_172851	241175	Mm.251301	NM_172851	ENSMUSG00000067028	Cntnap5b	C230078M14Rik|Caspr5-2	contactin associated protein-like 5B	protein-coding
mm_22485.1	chr3	5401048	5401051	+	1	NA	exon (NM_030708, exon 10 of 11)	exon (NM_030708, exon 10 of 11)	175199	NM_001163301	19302	Mm.132336	NM_008994	ENSMUSG00000040374	Pex2	D3Ertd138e|PAF-1|PMP35|Pxmp3	peroxisomal biogenesis factor 2	protein-coding
mm_40156.1	chr5	35583019	35583110	+	1	NA	promoter-TSS (NM_030721)	promoter-TSS (NM_030721)	4	NM_030721	80911	Mm.291503	NM_030721	ENSMUSG00000029098	Acox3	BI685180|EST-s59|PCOX	acyl-Coenzyme A oxidase 3, pristanoyl	protein-coding
mm_62122.1	chr7	96754803	96754806	+	1	NA	intron (NM_001310760, intron 11 of 32)	intron (NM_001310760, intron 11 of 32)	46745	NR_045874	791381	Mm.402112	NR_045874	ENSMUSG00000053049	Gm15413	ENSMUSG00000053049|OTTMUSG00000021246	predicted gene 15413	ncRNA
mm_40784.1	chr5	67360368	67360377	+	1	NA	Intergenic	Intergenic	53417	NM_001310629	109108	Mm.234455	NM_178651	ENSMUSG00000029221	Slc30a9	2310024J23Rik|AL024256|GAC63|HUEL|znT-9	solute carrier family 30 (zinc transporter), member 9	protein-coding
mm_43071.1	chr5	124446690	124446717	+	1	NA	promoter-TSS (NM_001310727)	promoter-TSS (NM_001310727)	-1	NM_001310727	67956	Mm.137966	NM_030241	ENSMUSG00000049327	Kmt5a	2410195B05Rik|AA617402|AW536475|PR-SET7|PR/SET07|Setd8	lysine methyltransferase 5A	protein-coding
mm_130382.1	chr15	97856626	97856665	-	1	NA	3' UTR (NM_009504, exon 10 of 10)	3' UTR (NM_009504, exon 10 of 10)	-12143	NM_001204278	56233	Mm.384027	NM_019572	ENSMUSG00000022475	Hdac7	5830434K02Rik|HD7|HD7a|Hdac7a|mFLJ00062	histone deacetylase 7	protein-coding
mm_63117.1	chr7	122671402	122671417	+	1	NA	promoter-TSS (NM_019430)	promoter-TSS (NM_019430)	-335	NM_019430	54376	Mm.444212	NM_019430	ENSMUSG00000066189	Cacng3	-	calcium channel, voltage-dependent, gamma subunit 3	protein-coding
mm_30098.1	chr3	138460250	138460254	-	1	NA	3' UTR (NM_175224, exon 11 of 11)	3' UTR (NM_175224, exon 11 of 11)	17159	NM_007410	11532	Mm.3874	NM_007410	ENSMUSG00000028138	Adh5	Adh-5|Adh3|GSNOR	alcohol dehydrogenase 5 (class III), chi polypeptide	protein-coding
mm_46238.1	chr5	99218540	99218553	-	1	NA	3' UTR (NM_181318, exon 14 of 14)	3' UTR (NM_181318, exon 14 of 14)	34381	NM_181318	320292	Mm.259074	NM_145839	ENSMUSG00000089809	Rasgef1b	4732452O09Rik|GPIgamma4|Gpig4	RasGEF domain family, member 1B	protein-coding
mm_106196.1	chr11	116842832	116842846	-	1	NA	promoter-TSS (NM_028865)	promoter-TSS (NM_028865)	610	NM_033398	107817	Mm.481684	NM_033398	ENSMUSG00000056962	Jmjd6	5730436I23Rik|D11Ertd195e|PSR|PtdSerR|Ptdsr|mKIAA0585	jumonji domain containing 6	protein-coding
mm_114740.1	chr13	83739050	83739065	+	1	NA	TTS (NR_029545)	TTS (NR_029545)	243	NR_029545	723967		NR_029545	ENSMUSG00000065424	Mir9-2	Mirn9-2|mir-9-2|mmu-mir-9-2	microRNA 9-2	ncRNA
mm_73917.1	chr8	119666499	119666511	+	1	NA	5' UTR (NM_023395, exon 1 of 7)	5' UTR (NM_023395, exon 1 of 7)	140	NM_023395	67866	Mm.87599	NM_023395	ENSMUSG00000023336	Wfdc1	2310058A03Rik|ps20	WAP four-disulfide core domain 1	protein-coding
mm_30222.1	chr3	145032958	145032969	-	1	NA	promoter-TSS (NM_017474)	promoter-TSS (NM_017474)	-187	NM_017474	23844	Mm.33483	NM_017474	ENSMUSG00000028255	Clca1	Clca2|Clca3|gob-5|gob5	chloride channel accessory 1	protein-coding
mm_82843.1	chr9	31168811	31168842	-	1	NA	exon (NM_009691, exon 6 of 16)	exon (NM_009691, exon 6 of 16)	-37027	NM_011176	19143	Mm.243926	NM_011176	ENSMUSG00000031995	St14	Epithin|MT-SP1|Prss14|Tmprss14|mCAP3|matriptase	suppression of tumorigenicity 14 (colon carcinoma)	protein-coding
mm_3743.1	chr1	155558113	155558232	+	1	NA	promoter-TSS (NM_026683)	promoter-TSS (NM_026683)	52	NM_026683	72482	Mm.288249	NM_026683	ENSMUSG00000033701	Acbd6	0610010G04Rik|2610100E10Rik	acyl-Coenzyme A binding domain containing 6	protein-coding
mm_109776.1	chr12	119030792	119030803	+	1	NA	Intergenic	RLTR31C_MM|LTR|ERVK	-64376	NM_029961	77706	Mm.261496	NM_029961	ENSMUSG00000072791	Abcb5	9230106F14Rik	ATP-binding cassette, sub-family B (MDR/TAP), member 5	protein-coding
mm_7617.1	chr1	126830372	126830389	-	1	NA	5' UTR (NM_176957, exon 1 of 13)	5' UTR (NM_176957, exon 1 of 13)	252	NM_001081756	210356	Mm.377234	NM_172484	ENSMUSG00000049690	Nckap5	8430408F21|D130011D22Rik|E030049G20Rik|Erih1|Erih2|Gm1548|Nap5	NCK-associated protein 5	protein-coding
mm_163980.1	chr14	55951348	55951348	-	1	NA	intron (NR_028284, intron 1 of 3)	intron (NR_028284, intron 1 of 3)	1023	NR_028284	17223	Mm.437339	NR_028284		Mcpt-ps1	MMCP-(Y)1|Mmcpy1	mast cell protease, pseudogene 1	pseudo
mm_122445.1	chr14	45287846	45287863	-	1	NA	exon (NM_015774, exon 15 of 16)	exon (NM_015774, exon 15 of 16)	30718	NM_015774	50527	Mm.387108	NM_015774	ENSMUSG00000021831	Ero1l	ERO1-L|Ero1a	ERO1-like (S. cerevisiae)	protein-coding
mm_24111.1	chr3	88142803	88142822	+	1	NA	intron (NM_133665, intron 1 of 10)	CpG	440	NM_001310593	17261	Mm.28184	NM_133665	ENSMUSG00000001419	Mef2d	C80750	myocyte enhancer factor 2D	protein-coding
mm_71268.1	chr8	40919033	40919043	+	1	NA	3' UTR (NM_001044740, exon 12 of 12)	3' UTR (NM_001044740, exon 12 of 12)	-7195	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_170025.1	chr17	21650635	21650637	+	1	NA	promoter-TSS (NM_001166497)	promoter-TSS (NM_001166497)	25	NM_001166497	73229	Mm.296733	NM_001166497	ENSMUSG00000035868	Zfp983	3110052M02Rik|mszf57|mszf71	zinc finger protein 983	protein-coding
mm_128831.1	chr15	67903089	67903116	-	1	NA	Intergenic	Intergenic	355754	NM_001145888	380993	Mm.309526	NM_198644	ENSMUSG00000022335	Zfat	Gm922|Zfat1|Zfp406	zinc finger and AT hook domain containing	protein-coding
mm_121060.1	chr14	87416763	87416778	+	1	NA	5' UTR (NM_001253755, exon 1 of 12)	5' UTR (NM_001253755, exon 1 of 12)	187	NM_001253755	219249	Mm.35168	NM_172605	ENSMUSG00000022019	Tdrd3	4732418C03Rik|6720468N18	tudor domain containing 3	protein-coding
mm_144678.1	chr18	34758854	34758879	+	1	NA	promoter-TSS (NM_175104)	promoter-TSS (NM_175104)	-40	NM_175104	66306	Mm.29424	NM_175104	ENSMUSG00000034300	Fam53c	2810012G03Rik|Gm21179	family with sequence similarity 53, member C	protein-coding
mm_40176.1	chr5	36000355	36000359	+	1	NA	3' UTR (NM_027373, exon 17 of 17)	3' UTR (NM_027373, exon 17 of 17)	107038	NM_027373	70292	Mm.125167	NM_027373	ENSMUSG00000029094	Afap1	2600003E23Rik|9630044L16Rik|AI848729|Afap|mKIAA3018	actin filament associated protein 1	protein-coding
mm_117667.1	chr13	93598396	93598403	-	1	NA	Intergenic	Intergenic	39359	NM_016668	12116	Mm.329582	NM_016668	ENSMUSG00000074768	Bhmt	-	betaine-homocysteine methyltransferase	protein-coding
mm_64328.1	chr7	142211793	142211796	+	1	NA	promoter-TSS (NM_001347555)	promoter-TSS (NM_001347555)	-23	NM_001347555	105243090	Mm.440541	NM_001347555	ENSMUSG00000073786	LOC105243090	-	keratin-associated protein 5-5-like	protein-coding
mm_63456.1	chr7	127530218	127530237	+	1	NA	exon (NM_001304266, exon 11 of 34)	exon (NM_001304266, exon 11 of 34)	2330	NR_034045	100217442	Mm.451113	NR_034045	ENSMUSG00000065259	Snora30	MBI-26	small nucleolar RNA, H/ACA box 30	snoRNA
mm_66505.1	chr7	45092131	45092181	-	1	NA	promoter-TSS (NM_026555)	promoter-TSS (NM_026555)	57	NM_026555	52377	Mm.29997	NM_026555	ENSMUSG00000019539	Rcn3	6030455P07Rik|D530026G20Rik|D7Ertd671e|RLP49	reticulocalbin 3, EF-hand calcium binding domain	protein-coding
mm_49858.1	chr6	38513938	38513947	+	1	NA	Intergenic	B1_Mus2|SINE|Alu	6617	NR_106130	102466843		NR_106130	ENSMUSG00000098285	Mir7670	Gm27707|mmu-mir-7670	microRNA 7670	ncRNA
mm_138190.1	chr17	34269142	34269201	+	1	NA	3' UTR (NM_207105, exon 6 of 6)	3' UTR (NM_207105, exon 6 of 6)	5944	NM_207105	14961	Mm.254067	NM_207105	ENSMUSG00000073421	H2-Ab1	AI845868|Abeta|H-2Ab|H2-Ab|I-Abeta|IAb|Ia-2|Ia2|Rmcs1	histocompatibility 2, class II antigen A, beta 1	protein-coding
mm_81926.1	chr9	120175027	120175044	+	1	NA	3' UTR (NM_001039364, exon 3 of 3)	3' UTR (NM_001039364, exon 3 of 3)	25293	NM_001039364	17433	Mm.486167	NM_008614	ENSMUSG00000032517	Mobp	AI835053|AI839848|MOBP155|MOBP170|MOBP69|MOBP73|MOBP81|R74645	myelin-associated oligodendrocytic basic protein	protein-coding
mm_11541.1	chr2	32646587	32646602	+	1	NA	promoter-TSS (NM_001146350)	promoter-TSS (NM_001146350)	-1	NM_007932	13805	Mm.225297	NM_007932	ENSMUSG00000026814	Eng	AI528660|AI662476|CD105|Endo|S-endoglin	endoglin	protein-coding
mm_167689.1	chr9	86743661	86743669	+	1	NA	promoter-TSS (NM_178738)	promoter-TSS (NM_178738)	32	NM_178738	244954	Mm.257629	NM_178738	ENSMUSG00000033491	Prss35	6030424L22Rik|P3D9	protease, serine 35	protein-coding
mm_166584.1	chr6	53469539	53469540	+	1	NA	intron (NM_001327821, intron 5 of 10)	intron (NM_001327821, intron 5 of 10)	-103835	NM_172728	231991	Mm.227444	NM_172728	ENSMUSG00000053007	Creb5	9430076C15Rik|CRE-BPa|Crebpa|D430026C09Rik	cAMP responsive element binding protein 5	protein-coding
mm_73015.1	chr8	93967034	93967054	+	1	NA	exon (NM_010308, exon 8 of 9)	exon (NM_010308, exon 8 of 9)	45596	NM_011787	23802	Mm.34641	NM_011787	ENSMUSG00000031751	Amfr	gp78	autocrine motility factor receptor	protein-coding
mm_43083.1	chr5	124447186	124447196	+	1	NA	intron (NM_001310727, intron 1 of 6)	intron (NM_001310727, intron 1 of 6)	487	NM_001310727	67956	Mm.137966	NM_030241	ENSMUSG00000049327	Kmt5a	2410195B05Rik|AA617402|AW536475|PR-SET7|PR/SET07|Setd8	lysine methyltransferase 5A	protein-coding
mm_86221.1	chr9	120110741	120110772	-	1	NA	intron (NM_144793, intron 1 of 6)	CpG	357	NM_144793	208638	Mm.236656	NM_144793	ENSMUSG00000032519	Slc25a38	AV019094|BC010801|appoptosin	solute carrier family 25, member 38	protein-coding
mm_170853.1	chr2	178170565	178170572	-	1	NA	intron (NM_028806, intron 1 of 12)	B4A|SINE|B4	-4781	NM_001177791	74189	Mm.44413	NM_028806	ENSMUSG00000027525	Phactr3	1500003N10Rik|4930415A02Rik|H17739|Scapin1|Scapinin|mKIAA4224	phosphatase and actin regulator 3	protein-coding
mm_57803.1	chr6	129385476	129385486	-	1	NA	promoter-TSS (NM_027709)	promoter-TSS (NM_027709)	22	NM_027709	71183	Mm.79402	NM_027709	ENSMUSG00000030158	Clec12b	4933425B16Rik	C-type lectin domain family 12, member B	protein-coding
mm_66278.1	chr7	37769666	37769677	-	1	NA	promoter-TSS (NM_172385)	promoter-TSS (NM_172385)	81	NM_172385	243937	Mm.322505	NM_172385	ENSMUSG00000043456	Zfp536	9630010P11Rik|Znf536|mKIAA0390	zinc finger protein 536	protein-coding
mm_117047.1	chr13	58365194	58365195	-	1	NA	Intergenic	RLTR26_Mus|LTR|ERVK	-10332	NM_175214	75050	Mm.446094	NM_175214	ENSMUSG00000060176	Kif27	4930517I18Rik	kinesin family member 27	protein-coding
mm_27257.1	chr3	37312419	37312465	-	1	NA	promoter-TSS (NM_001255992)	promoter-TSS (NM_001255992)	4	NM_145825	207175	Mm.344708	NM_145825	ENSMUSG00000045031	Cetn4	-	centrin 4	protein-coding
mm_52624.1	chr6	117174147	117174152	+	1	NA	3' UTR (NM_021704, exon 3 of 3)	3' UTR (NM_021704, exon 3 of 3)	5614	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_6427.1	chr1	73937319	73937338	-	1	NA	intron (NM_027884, intron 21 of 34)	intron (NM_027884, intron 21 of 34)	-72862	NR_045311	109198	Mm.359721	NR_045311	ENSMUSG00000100301	6030407O03Rik	-	RIKEN cDNA 6030407O03 gene	ncRNA
mm_61514.1	chr7	78895904	78895990	+	1	NA	promoter-TSS (NM_001162939)	promoter-TSS (NM_001162939)	20	NM_001162939	68048	Mm.34109	NM_026531	ENSMUSG00000030609	Aen	2700083B06Rik|Isg20l1	apoptosis enhancing nuclease	protein-coding
mm_19783.1	chr2	106974384	106974422	-	1	NA	promoter-TSS (NM_001025102)	promoter-TSS (NM_001025102)	-6	NM_001025102	212772	Mm.381231	NM_173750	ENSMUSG00000027122	Arl14ep	2700007P21Rik|4930448O08Rik|ARF7EP	ADP-ribosylation factor-like 14 effector protein	protein-coding
mm_115823.1	chr13	20228437	20228440	-	1	NA	intron (NM_080288, intron 4 of 21)	intron (NM_080288, intron 4 of 21)	137931	NM_080288	140580	Mm.342392	NM_080288	ENSMUSG00000041112	Elmo1	6330578D22Rik|C230095H21Rik|CED-12	engulfment and cell motility 1	protein-coding
mm_17414.1	chr2	27247261	27247303	-	1	NA	promoter-TSS (NM_138665)	promoter-TSS (NM_138665)	21	NM_138665	192166	Mm.278467	NM_138665	ENSMUSG00000009614	Sardh	-	sarcosine dehydrogenase	protein-coding
mm_106817.1	chr12	7980583	7980599	+	1	NA	exon (NM_009693, exon 4 of 29)	exon (NM_009693, exon 4 of 29)	2914	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_31.1	chr1	6214858	6214866	+	1	NA	5' UTR (NM_009826, exon 1 of 24)	5' UTR (NM_009826, exon 1 of 24)	200	NM_009826	12421	Mm.293811	NM_009826	ENSMUSG00000025907	Rb1cc1	2900055E04Rik|5930404L04Rik|Cc1|FIP200|LaXp180	RB1-inducible coiled-coil 1	protein-coding
mm_113049.1	chr13	23621852	23621872	+	1	NA	promoter-TSS (NM_178194)	promoter-TSS (NM_178194)	696	NM_015787	50709	Mm.170587	NM_015787	ENSMUSG00000051627	Hist1h1e	H1-4|H1.4|H1e|H1f4|H1s-4|H1var2	histone cluster 1, H1e	protein-coding
mm_1443.1	chr1	67220559	67220572	+	1	NA	exon (NM_001080809, exon 34 of 38)	exon (NM_001080809, exon 34 of 38)	97538	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_108315.1	chr12	79575049	79575053	+	1	NA	intron (NM_009014, intron 7 of 10)	intron (NM_009014, intron 7 of 10)	277700	NM_001252562	19363	Mm.341756	NM_009014	ENSMUSG00000059060	Rad51b	AI553500|R51H2|Rad51l1|mREC2	RAD51 paralog B	protein-coding
mm_36163.1	chr4	60582153	60582153	-	1	NA	promoter-TSS (NM_001122647)	promoter-TSS (NM_001122647)	2	NM_001122647	100039008	Mm.335875	NM_001122647	ENSMUSG00000078680	Mup10	2610016E04Rik|Mup8	major urinary protein 10	protein-coding
mm_12323.1	chr2	69392987	69392995	+	1	NA	exon (NM_175512, exon 2 of 5)	exon (NM_175512, exon 2 of 5)	12529	NM_175512	241452	Mm.211655	NM_175512	ENSMUSG00000027068	Dhrs9	C730025I08Rik|Rdh15	dehydrogenase/reductase (SDR family) member 9	protein-coding
mm_37580.1	chr4	126323705	126323737	-	1	NA	exon (NM_011902, exon 5 of 10)	exon (NM_011902, exon 5 of 10)	1478	NM_011902	24084	Mm.23895	NM_011902	ENSMUSG00000028845	Tekt2	AU014974|tektin-t	tektin 2	protein-coding
mm_152430.1	chr19	10678002	10678020	-	1	NA	promoter-TSS (NM_021453)	promoter-TSS (NM_021453)	60	NM_021453	58803	Mm.34037	NM_021453	ENSMUSG00000024738	Pga5	1110035E17Rik|Pepf	pepsinogen 5, group I	protein-coding
mm_156781.1	chrX	161717056	161717073	+	1	NA	promoter-TSS (NM_198409)	promoter-TSS (NM_198409)	28	NM_001103367	24004	Mm.328503	NM_198409	ENSMUSG00000043518	Rai2	3f8	retinoic acid induced 2	protein-coding
mm_78930.1	chr9	45086631	45086649	+	1	NA	intron (NM_001005421, intron 3 of 10)	intron (NM_001005421, intron 3 of 10)	7457	NM_001005421	270152	Mm.190461	NM_001005421	ENSMUSG00000048534	Amica1	AMICA|Crea7|Gm638|Jaml	adhesion molecule, interacts with CXADR antigen 1	protein-coding
mm_118710.1	chr14	22181696	22181697	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	161984	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_66043.1	chr7	30671542	30671544	-	1	NA	promoter-TSS (NR_027849)	promoter-TSS (NR_027849)	62	NR_027849	74927	Mm.87326	NM_183108	ENSMUSG00000049761	Pmis2	1700071L20Rik|4930479M11Rik	Pmis2, sperm specific protein	ncRNA
mm_52101.1	chr6	97869377	97869387	+	1	NA	intron (NM_001113198, intron 1 of 9)	intron (NM_001113198, intron 1 of 9)	-60435	NM_001178049	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_172214.1	chr6	60504591	60504595	+	1	NA	Intergenic	(CAGAGA)n|Simple_repeat|Simple_repeat	-100886	NR_015565	208079	Mm.131226	NM_177329	ENSMUSG00000046764	A530053G22Rik	-	RIKEN cDNA A530053G22 gene	ncRNA
mm_121874.1	chr14	21047946	21047957	-	1	NA	intron (NM_018829, intron 1 of 8)	intron (NM_018829, intron 1 of 8)	4491	NM_018829	55946	Mm.376269	NM_018829	ENSMUSG00000021824	Ap3m1	1200013D09Rik|C78982|R75378	adaptor-related protein complex 3, mu 1 subunit	protein-coding
mm_147656.1	chr18	60526087	60526103	-	1	NA	promoter-TSS (NM_026302)	promoter-TSS (NM_026302)	-126	NM_026302	67665	Mm.272801	NM_026302	ENSMUSG00000024603	Dctn4	1110001K06Rik|4930547K17Rik|C130039E17Rik|p62	dynactin 4	protein-coding
mm_133941.1	chr16	3907737	3907746	-	1	NA	intron (NM_028484, intron 1 of 2)	intron (NM_028484, intron 1 of 2)	948	NM_028484	73261	Mm.486226	NM_028484	ENSMUSG00000005983	1700037C18Rik	2810022L20Rik	RIKEN cDNA 1700037C18 gene	protein-coding
mm_167850.1	chrX	7923169	7923195	+	1	NA	3' UTR (NM_013892, exon 3 of 3)	3' UTR (NM_013892, exon 3 of 3)	3360	NM_013892	30052	Mm.4881	NM_013892	ENSMUSG00000039278	Pcsk1n	AI848336|KEP|PEN|PEN19|PEN20|Pan3|SAAS|SAASCT|bLEN|lLEN|proSAAS	proprotein convertase subtilisin/kexin type 1 inhibitor	protein-coding
mm_139692.1	chr17	57425120	57425148	+	1	NA	intron (NM_010130, intron 12 of 21)	L1Md_F2|LINE|L1	66448	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_111389.1	chr12	88021273	88021281	-	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	66797	NM_001270792	100039087	Mm.458830	NM_001270792	ENSMUSG00000096276	Gm2042	-	predicted gene 2042	protein-coding
mm_83991.1	chr9	57443093	57443108	-	1	NA	3' UTR (NM_020270, exon 7 of 7)	3' UTR (NM_020270, exon 7 of 7)	-2986	NM_176831	66812	Mm.250508	NM_176831	ENSMUSG00000063849	Ppcdc	1810057I13Rik|8430432M10Rik	phosphopantothenoylcysteine decarboxylase	protein-coding
mm_120274.1	chr14	63125485	63125489	+	1	NA	intron (NM_007798, intron 1 of 9)	intron (NM_007798, intron 1 of 9)	3025	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_113980.1	chr13	52096726	52096747	+	1	NA	promoter-TSS (NR_045061)	promoter-TSS (NR_045061)	-5	NR_045061	74050	Mm.84860	NR_045061		4921525O09Rik	-	RIKEN cDNA 4921525O09 gene	ncRNA
mm_82132.1	chr9	123529778	123529837	+	1	NA	promoter-TSS (NM_030692)	promoter-TSS (NM_030692)	-75	NM_030692	83493	Mm.273671	NM_030692	ENSMUSG00000025240	Sacm1l	SAC1|Sac1p|mKIAA0851	SAC1 suppressor of actin mutations 1-like (yeast)	protein-coding
mm_153906.1	chr19	47132055	47132071	-	1	NA	TTS (NM_011053)	TTS (NM_011053)	6231	NM_133746	72691	Mm.31663	NM_133746	ENSMUSG00000033033	Calhm2	2810048G17Rik|Fam26b	calcium homeostasis modulator 2	protein-coding
mm_126801.1	chr15	87544287	87544304	+	1	NA	promoter-TSS (NM_001252310)	promoter-TSS (NM_001252310)	-4	NM_001252310	106014	Mm.244319	NM_134096	ENSMUSG00000054863	Fam19a5	TAFA5|Tafa-5|Tara-5	family with sequence similarity 19, member A5	protein-coding
mm_68335.1	chr7	106504946	106504955	-	1	NA	Intergenic	Intergenic	-63877	NR_003967	209380	Mm.461779	NM_001001318		Gm4759	EG209380	GTPase, very large interferon inducible 1 pseudogene	pseudo
mm_134480.1	chr16	18621640	18621669	-	1	NA	TTS (NM_213614)	TTS (NM_213614)	749	NM_001001999	14724	Mm.475622	NM_010327	ENSMUSG00000050761	Gp1bb	-	glycoprotein Ib, beta polypeptide	protein-coding
mm_129818.1	chr15	83031108	83031111	-	1	NA	intron (NM_001271411, intron 1 of 5)	intron (NM_001271411, intron 1 of 5)	-1159	NM_001271413	74039	Mm.32584	NM_028728	ENSMUSG00000058099	Nfam1	4921501M20Rik|Cnaip	Nfat activating molecule with ITAM motif 1	protein-coding
mm_125615.1	chr15	61987360	61987388	+	1	NA	intron (NM_001177353, intron 1 of 2)	CpG	2033	NM_001177352	17869	Mm.2444	NM_010849	ENSMUSG00000022346	Myc	AU016757|Myc2|Niard|Nird|bHLHe39	myelocytomatosis oncogene	protein-coding
mm_15794.1	chr2	164426116	164426160	+	1	NA	exon (NM_011521, exon 5 of 5)	exon (NM_011521, exon 5 of 5)	17050	NM_011521	20971	Mm.3815	NM_011521	ENSMUSG00000017009	Sdc4	AA959608|AW108331|S4|Synd4|ryudocan|syndecan-4	syndecan 4	protein-coding
mm_141236.1	chr17	27436943	27436960	-	1	NA	intron (NM_001013385, intron 7 of 8)	intron (NM_001013385, intron 7 of 8)	66582	NM_001013385	268934	Mm.358940	NM_001013385	ENSMUSG00000063239	Grm4	Gprc1d|mGluR4	glutamate receptor, metabotropic 4	protein-coding
mm_131766.1	chr16	22892779	22892820	+	1	NA	intron (NR_075099, intron 1 of 5)	intron (NR_075099, intron 1 of 5)	784	NM_001276449	11625	Mm.197554	NM_013465	ENSMUSG00000022868	Ahsg	-	alpha-2-HS-glycoprotein	protein-coding
mm_62096.1	chr7	96210108	96210183	+	1	NA	promoter-TSS (NM_011858)	promoter-TSS (NM_011858)	-492	NM_011858	23966	Mm.254610	NM_011858	ENSMUSG00000048078	Tenm4	Doc4|ELM2|Odz4|R75022|Ten-m4|l(7)-3Rn|l7Rn3|mKIAA1302	teneurin transmembrane protein 4	protein-coding
mm_63403.1	chr7	127297609	127297619	+	1	NA	intron (NM_001253874, intron 1 of 30)	intron (NM_001253874, intron 1 of 30)	1354	NM_001253874	16408	Mm.1618	NM_008400	ENSMUSG00000030830	Itgal	(p180)|Cd11a|LFA-1|LFA-1A|Ly-15|Ly-21	integrin alpha L	protein-coding
mm_27891.1	chr3	79287171	79287236	-	1	NA	Intergenic	CpG	-58173	NM_001142953	100233207	Mm.373801	NM_001142953	ENSMUSG00000091685	Gm17359	-	predicted gene, 17359	protein-coding
mm_105735.1	chr11	109298073	109298079	-	1	NA	5' UTR (NM_011268, exon 1 of 19)	5' UTR (NM_011268, exon 1 of 19)	105	NM_001165934	19739	Mm.38548	NM_011268	ENSMUSG00000020599	Rgs9	RGS9-1|Rgs9-2	regulator of G-protein signaling 9	protein-coding
mm_1324.1	chr1	65100654	65100696	+	1	NA	exon (NM_007774, exon 3 of 3)	exon (NM_007774, exon 3 of 3)	2688	NM_007774	12964	Mm.26904	NM_007774	ENSMUSG00000044429	Cryga	Cryg-4|DGcry-4	crystallin, gamma A	protein-coding
mm_155644.1	chrX	85269564	85269580	+	1	NA	5' UTR (NM_028046, exon 2 of 2)	5' UTR (NM_028046, exon 2 of 2)	19895	NM_028046	71996	Mm.20201	NM_028046	ENSMUSG00000035491	Fthl17a	1600014K23Rik|AI324104	ferritin, heavy polypeptide-like 17, member A	protein-coding
mm_4482.1	chr1	173444564	173444599	+	1	NA	intron (NM_001013779, intron 2 of 8)	intron (NM_001013779, intron 2 of 8)	23977	NM_001013779	383619	Mm.131453	NM_001013779	ENSMUSG00000037860	Aim2	Gm1313|Ifi210	absent in melanoma 2	protein-coding
mm_29255.1	chr3	107219749	107219760	-	1	NA	exon (NM_001111143, exon 2 of 9)	exon (NM_001111143, exon 2 of 9)	1978	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_99272.1	chr11	101255719	101255724	+	1	NA	intron (NM_001284411, intron 3 of 5)	intron (NM_001284411, intron 3 of 5)	2014	NM_026776	28084	Mm.301020	NM_026776	ENSMUSG00000078656	Vps25	1110020N13Rik|AW107467|D11Wsu68e	vacuolar protein sorting 25	protein-coding
mm_118219.1	chr13	110280992	110281037	-	1	NA	promoter-TSS (NM_023852)	promoter-TSS (NM_023852)	-808	NM_023852	67295	Mm.151600	NM_023852	ENSMUSG00000021700	Rab3c	2700062I01Rik|3110015B08Rik|3110037E15Rik|AI850886	RAB3C, member RAS oncogene family	protein-coding
mm_129487.1	chr15	78773425	78773435	-	1	NA	promoter-TSS (NM_008595)	promoter-TSS (NM_008595)	15	NM_008595	17305	Mm.149235	NM_008595	ENSMUSG00000018169	Mfng	AW546563	MFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	protein-coding
mm_86262.1	chr9	121675103	121675112	-	1	NA	Intergenic	ORR1D2|LTR|ERVL-MaLR	29922	NM_001164562	215474	Mm.31421	NM_178677	ENSMUSG00000061536	Sec22c	4932412K21|5930407I15Rik|C530046H07|Sec22l3	SEC22 homolog C, vesicle trafficking protein	protein-coding
mm_43622.1	chr5	138161699	138161712	+	1	NA	exon (NM_012002, exon 3 of 10)	exon (NM_012002, exon 3 of 10)	603	NM_012002	26893	Mm.3981	NM_012002	ENSMUSG00000019494	Cops6	Sgn3|VIP/MOV34	COP9 signalosome subunit 6	protein-coding
mm_35069.1	chr4	6763901	6763903	-	1	NA	intron (NM_145711, intron 3 of 8)	intron (NM_145711, intron 3 of 8)	226821	NM_145711	252838	Mm.435828	NM_145711	ENSMUSG00000041272	Tox	1700007F02Rik	thymocyte selection-associated high mobility group box	protein-coding
mm_108774.1	chr12	89812623	89812633	+	1	NA	5' UTR (NM_001252074, exon 1 of 7)	5' UTR (NM_001252074, exon 1 of 7)	145	NM_001252074	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding
mm_47370.1	chr5	122951825	122951860	-	1	NA	intron (NM_001003953, intron 6 of 22)	CpG	37257	NM_001003953	30841	Mm.86406	NM_013910	ENSMUSG00000029475	Kdm2b	Cxxc2|Fbl10|Fbxl10|Jhdm1b|PCCX2	lysine (K)-specific demethylase 2B	protein-coding
mm_145251.1	chr18	52486152	52486167	+	1	NA	intron (NM_026040, intron 4 of 7)	intron (NM_026040, intron 4 of 7)	20466	NM_026040	67222	Mm.100617	NM_026040	ENSMUSG00000024528	Srfbp1	2810036K01Rik|p49/STRAP	serum response factor binding protein 1	protein-coding
mm_75400.1	chr8	46208439	46208469	-	1	NA	exon (NM_007450, exon 3 of 4)	exon (NM_007450, exon 3 of 4)	2555	NM_007450	11739	Mm.16228	NM_007450	ENSMUSG00000031633	Slc25a4	AU019225|Ant1	solute carrier family 25 (mitochondrial carrier, adenine nucleotide translocator), member 4	protein-coding
mm_50245.1	chr6	42353528	42353532	+	1	NA	intron (NM_001289619, intron 4 of 8)	intron (NM_001289619, intron 4 of 8)	3702	NM_001289619	22793	Mm.282303	NM_011777	ENSMUSG00000029860	Zyx	9530098H06Rik|R75157	zyxin	protein-coding
mm_171032.1	chr2	90804293	90804310	+	1	NA	intron (NM_178755, intron 10 of 17)	intron (NM_178755, intron 10 of 17)	21557	NM_178755	271813	Mm.61146	NM_178755	ENSMUSG00000040812	Agbl2	4930524K04|A430081C19Rik|CCP2	ATP/GTP binding protein-like 2	protein-coding
mm_49620.1	chr6	30803210	30803228	+	1	NA	intron (NM_017478, intron 20 of 23)	intron (NM_017478, intron 20 of 23)	61920	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_55572.1	chr6	71395010	71395023	-	1	NA	intron (NM_024288, intron 7 of 8)	intron (NM_024288, intron 7 of 8)	21589	NM_001081110	12525	Mm.1858	NM_009857	ENSMUSG00000053977	Cd8a	BB154331|Ly-2|Ly-35|Ly-B|Lyt-2	CD8 antigen, alpha chain	protein-coding
mm_20564.1	chr2	131080594	131080603	-	1	NA	exon (NM_011426, exon 7 of 21)	exon (NM_011426, exon 7 of 21)	6167	NM_011426	20612	Mm.1374	NM_011426	ENSMUSG00000027322	Siglec1	Cd169|Siglec-1|Sn	sialic acid binding Ig-like lectin 1, sialoadhesin	protein-coding
mm_163860.1	chr14	19418674	19418698	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	183901	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_85337.1	chr9	102626201	102626239	-	1	NA	promoter-TSS (NM_181394)	promoter-TSS (NM_181394)	-76	NM_181394	69010	Mm.2000	NM_181394	ENSMUSG00000035048	Anapc13	1810004D07Rik|APC13|SWM1	anaphase promoting complex subunit 13	protein-coding
mm_33058.1	chr4	123201226	123201270	+	1	NA	promoter-TSS (NM_001085502)	promoter-TSS (NM_001085502)	-305	NM_001085502	230718	Mm.354635	NM_001085502	ENSMUSG00000054958	Nt5c1a	Cn1a|Gm49	5'-nucleotidase, cytosolic IA	protein-coding
mm_165033.1	chr19	34252583	34252591	-	1	NA	intron (NM_007392, intron 1 of 8)	intron (NM_007392, intron 1 of 8)	2786	NM_007392	11475	Mm.213025	NM_007392	ENSMUSG00000035783	Acta2	0610041G09Rik|Actvs|SMalphaA|a-SMA|alphaSMA	actin, alpha 2, smooth muscle, aorta	protein-coding
mm_79321.1	chr9	52584779	52584784	+	1	NA	Intergenic	MTEa|LTR|ERVL-MaLR	94656	NM_178906	330941	Mm.335160	NM_177907	ENSMUSG00000078307	AI593442	E130102D23	expressed sequence AI593442	protein-coding
mm_67167.1	chr7	73552067	73552086	-	1	NA	intron (NR_037569, intron 3 of 4)	(A)n|Simple_repeat|Simple_repeat	6319	NR_037569	69170	Mm.34539	NR_037569	ENSMUSG00000101970	1810026B05Rik	-	RIKEN cDNA 1810026B05 gene	ncRNA
mm_20527.1	chr2	130906320	130906333	-	1	NA	promoter-TSS (NR_015523)	promoter-TSS (NR_015523)	70	NR_015523	613258	Mm.271990	NR_015523		A730017L22Rik	-	RIKEN cDNA A730017L22 gene	ncRNA
mm_128890.1	chr15	73184864	73184971	-	1	NA	promoter-TSS (NM_153178)	promoter-TSS (NM_153178)	30	NM_153178	239528	Mm.23095	NM_153178	ENSMUSG00000036698	Ago2	1110029L17Rik|2310051F07Rik|AI225898|AL022874|AW546247|ENSMUSG00000072493|Eif2c2|Gerp95|Gm10365|mKIAA4215	argonaute RISC catalytic subunit 2	protein-coding
mm_165216.1	chr2	38351497	38351515	+	1	NA	5' UTR (NM_010710, exon 1 of 5)	5' UTR (NM_010710, exon 1 of 5)	198	NM_010710	16870	Mm.142856	NM_010710	ENSMUSG00000000247	Lhx2	LH2A|Lh-2|Lim2|ap|apterous	LIM homeobox protein 2	protein-coding
mm_62383.1	chr7	100831364	100831399	+	1	NA	exon (NM_178764, exon 6 of 9)	exon (NM_178764, exon 6 of 9)	32032	NM_177073	320100	Mm.40336	NM_177073	ENSMUSG00000008318	Relt	E430021K24Rik|Tnfrsf19l	RELT tumor necrosis factor receptor	protein-coding
mm_33836.1	chr4	135686283	135686301	+	1	NA	promoter-TSS (NM_174851)	promoter-TSS (NM_174851)	-165	NM_174851	242700	Mm.259623	NM_174851	ENSMUSG00000062157	Ifnlr1	CRF2-12|Il28ra	interferon lambda receptor 1	protein-coding
mm_19368.1	chr2	91182942	91182952	-	1	NA	promoter-TSS (NM_145527)	promoter-TSS (NM_145527)	100	NM_001177719	228355	Mm.36410	NM_145527	ENSMUSG00000040687	Madd	9630059K23Rik|IG20	MAP-kinase activating death domain	protein-coding
mm_126129.1	chr15	78335231	78335283	+	1	NA	exon (NM_007780, exon 2 of 14)	exon (NM_007780, exon 2 of 14)	9267	NM_007780	12983	Mm.235324	NM_007780	ENSMUSG00000071713	Csf2rb	AI848964|AIC2B|Bc|CDw131|Csf2rb1|Csfgmrb|Il3r|Il3rb|Il3rb1|Il5rb	colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage)	protein-coding
mm_45674.1	chr5	77216256	77216270	-	1	NA	Intergenic	Lx8|LINE|L1	-4792	NM_001289768	69982	Mm.46106	NM_183284	ENSMUSG00000053030	Spink2	1700007F22Rik|AV038945|HUSI-II	serine peptidase inhibitor, Kazal type 2	protein-coding
mm_106286.1	chr11	118202705	118202750	-	1	NA	intron (NM_001112699, intron 1 of 12)	intron (NM_001112699, intron 1 of 12)	10015	NM_001112700	19157	Mm.86413	NM_011180	ENSMUSG00000017132	Cyth1	CLM1|CTH-1|CYTIP|Pscd1	cytohesin 1	protein-coding
mm_85259.1	chr9	99408216	99408220	-	1	NA	intron (NM_008624, intron 2 of 5)	B2_Mm2|SINE|B2	28494	NM_008624	17532	Mm.2045	NM_008624	ENSMUSG00000032470	Mras	2900078C09Rik|AI326250	muscle and microspikes RAS	protein-coding
mm_136507.1	chr16	96980132	96980135	-	1	NA	intron (NM_031174, intron 3 of 32)	intron (NM_031174, intron 3 of 32)	190602	NM_031174	13508	Mm.102437	NM_031174	ENSMUSG00000050272	Dscam	4932410A21Rik	Down syndrome cell adhesion molecule	protein-coding
mm_30664.1	chr4	10874539	10874607	+	1	NA	promoter-TSS (NM_026005)	promoter-TSS (NM_026005)	75	NM_026005	67157	Mm.440552	NM_026005	ENSMUSG00000059482	2610301B20Rik	AI428449	RIKEN cDNA 2610301B20 gene	protein-coding
mm_124845.1	chr15	9436109	9436125	+	1	NA	promoter-TSS (NM_029341)	promoter-TSS (NM_029341)	89	NM_029341	75568	Mm.82143	NM_029341	ENSMUSG00000039676	Capsl	1700028N11Rik|AW125205	calcyphosine-like	protein-coding
mm_17630.1	chr2	31036784	31036794	-	1	NA	intron (NM_001038700, intron 11 of 14)	intron (NM_001038700, intron 11 of 14)	54510	NM_028846	74270	Mm.346654	NM_028846	ENSMUSG00000026854	Usp20	1700055M05Rik|AI467231|Vdu2	ubiquitin specific peptidase 20	protein-coding
mm_164459.1	chr16	57397713	57397739	+	1	NA	intron (NM_001040397, intron 1 of 4)	intron (NM_001040397, intron 1 of 4)	44449	NM_001040397	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding
mm_87954.1	chr10	63099783	63099792	+	1	NA	promoter-TSS (NM_016864)	promoter-TSS (NM_016864)	-369	NM_016864	53404	Mm.228661	NM_016864	ENSMUSG00000036816	Atoh7	Math5|bHLHa13	atonal bHLH transcription factor 7	protein-coding
mm_77721.1	chr8	126817096	126817099	-	1	NA	Intergenic	RLTR14|LTR|ERV1	128824	NM_024214	67952	Mm.6932	NM_024214	ENSMUSG00000093904	Tomm20	1810060K07Rik|BB284719|Gm19268|MAS20|MOM19|TOM20|mKIAA0016	translocase of outer mitochondrial membrane 20 homolog (yeast)	protein-coding
mm_60211.1	chr7	43444105	43444142	+	1	NA	promoter-TSS (NM_026695)	promoter-TSS (NM_026695)	51	NR_075104	110826	Mm.30200	NM_026695	ENSMUSG00000004610	Etfb	0610009I16Rik|2810441H06Rik	electron transferring flavoprotein, beta polypeptide	protein-coding
mm_124615.1	chr15	3279570	3279584	+	1	NA	exon (NM_009155, exon 5 of 5)	exon (NM_009155, exon 5 of 5)	8600	NM_009155	20363	Mm.392203	NM_009155	ENSMUSG00000064373	Selenop	AU018766|D15Ucla1|Se-P|Sepp1|selp	selenoprotein P	protein-coding
mm_55980.1	chr6	85902247	85902276	-	1	NA	5' UTR (NM_001145895, exon 1 of 4)	5' UTR (NM_001145895, exon 1 of 4)	272	NM_001145895	75541	Mm.24454	NM_029331	ENSMUSG00000068299	Nat8f4	1700019G17Rik	N-acetyltransferase 8 (GCN5-related) family member 4	protein-coding
mm_8620.1	chr1	156037434	156037454	-	1	NA	promoter-TSS (NM_144791)	promoter-TSS (NM_144791)	-964	NM_001160018	208263	Mm.211654	NM_144791	ENSMUSG00000026466	Tor1aip1	LAP1|Lap1B	torsin A interacting protein 1	protein-coding
mm_134933.1	chr16	31140539	31140541	-	1	NA	intron (NM_030138, intron 5 of 22)	PB1D7|SINE|Alu	-59108	NM_198626	268880	Mm.286693	NM_198626	ENSMUSG00000047434	Xxylt1	AI480653	xyloside xylosyltransferase 1	protein-coding
mm_112434.1	chr13	4614127	4614127	+	1	NA	Intergenic	Intergenic	-4963	NM_018859	56043	Mm.251908	NM_018859	ENSMUSG00000045410	Akr1e1	1810061I10Rik|Akr1e2	aldo-keto reductase family 1, member E1	protein-coding
mm_131809.1	chr16	22918301	22918311	+	1	NA	promoter-TSS (NM_001083905)	promoter-TSS (NM_001083905)	-76	NM_001083905	59083	Mm.28461	NM_021564	ENSMUSG00000022871	Fetub	2310011O17Rik|AI255764|D17980|Gugu	fetuin beta	protein-coding
mm_97006.1	chr11	70884768	70884785	+	1	NA	exon (NM_019400, exon 3 of 18)	exon (NM_019400, exon 3 of 18)	40015	NM_001291142	54189	Mm.7087	NM_019400	ENSMUSG00000020817	Rabep1	Rab5ep|rabaptin-5|rabaptin-5alpha	rabaptin, RAB GTPase binding effector protein 1	protein-coding
mm_27596.1	chr3	59131123	59131141	-	1	NA	promoter-TSS (NM_001287124)	promoter-TSS (NM_001287124)	-14	NM_001287122	140795	Mm.439021	NM_133200	ENSMUSG00000036381	P2ry14	A330108O13Rik|Gpr105|P2Y14	purinergic receptor P2Y, G-protein coupled, 14	protein-coding
mm_21776.1	chr2	164846860	164846875	-	1	NA	exon (NM_011125, exon 9 of 16)	exon (NM_011125, exon 9 of 16)	10841	NM_011125	18830	Mm.6105	NM_011125	ENSMUSG00000017754	Pltp	Bpife|OD107	phospholipid transfer protein	protein-coding
mm_67317.1	chr7	79596685	79596698	-	1	NA	intron (NM_019799, intron 9 of 10)	intron (NM_019799, intron 9 of 10)	20966	NM_019799	56315	Mm.10909	NM_019799	ENSMUSG00000030549	Rhcg	BB065800	Rhesus blood group-associated C glycoprotein	protein-coding
mm_94125.1	chr10	128670754	128670754	-	1	NA	exon (NM_173733, exon 4 of 4)	exon (NM_173733, exon 4 of 4)	3164	NM_173733	211389	Mm.23352	NM_173733	ENSMUSG00000049858	Suox	SO	sulfite oxidase	protein-coding
mm_8109.1	chr1	135871888	135871889	-	1	NA	3' UTR (NM_019645, exon 14 of 14)	3' UTR (NM_019645, exon 14 of 14)	31027	NM_001130176	21956	Mm.247470	NM_011619	ENSMUSG00000026414	Tnnt2	Tnt|cTnT	troponin T2, cardiac	protein-coding
mm_47937.1	chr5	135349998	135350040	-	1	NA	promoter-TSS (NM_001277893)	promoter-TSS (NM_001277893)	25	NM_001277893	94244	Mm.26037	NM_033571	ENSMUSG00000040013	Fkbp6	1700008G22Rik|36kDa|AU017274|D5Ertd724e|FKBP-36|FKBP-6	FK506 binding protein 6	protein-coding
mm_162661.1	chr10	5310007	5310009	+	1	NA	intron (NM_001347732, intron 45 of 145)	intron (NM_001347732, intron 45 of 145)	-115301	NM_001079686	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_140239.1	chr17	84125109	84125116	+	1	NA	Intergenic	Intergenic	46452	NR_045458	74473	Mm.399575	NR_045458		4933433H22Rik	-	RIKEN cDNA 4933433H22 gene	ncRNA
mm_6938.1	chr1	85727001	85727021	-	1	NA	intron (NM_177055, intron 1 of 5)	intron (NM_177055, intron 1 of 5)	9595	NM_177055	319997	Mm.116691	NM_177055	ENSMUSG00000052760	A630001G21Rik	-	RIKEN cDNA A630001G21 gene	protein-coding
mm_78184.1	chr9	21225397	21225431	+	1	NA	intron (NR_106127, intron 1 of 3)	intron (NR_106127, intron 1 of 3)	867	NR_106127	102465769		NR_106127	ENSMUSG00000098764	Mir7667	Gm27756|mmu-mir-7667	microRNA 7667	ncRNA
mm_133863.1	chr16	96361655	96361665	+	1	NA	promoter-TSS (NM_028078)	promoter-TSS (NM_028078)	-97	NM_001177887	72058	Mm.119714	NM_028078	ENSMUSG00000000159	Igsf5	2010003D20Rik|JCAM|Jam4	immunoglobulin superfamily, member 5	protein-coding
mm_96681.1	chr11	69573820	69573833	+	1	NA	intron (NM_144824, intron 3 of 9)	intron (NM_144824, intron 3 of 9)	5498	NM_144824	216853	Mm.31586	NM_144824	ENSMUSG00000041346	Wrap53	BC021790|Wdr79	WD repeat containing, antisense to Trp53	protein-coding
mm_117181.1	chr13	63431588	63431617	-	1	NA	5' UTR (NM_007985, exon 1 of 15)	5' UTR (NM_007985, exon 1 of 15)	143	NM_001347515	14088	Mm.126106	NM_007985	ENSMUSG00000021461	Fancc	Facc	Fanconi anemia, complementation group C	protein-coding
mm_32408.1	chr4	106949422	106949430	+	1	NA	intron (NM_023672, intron 4 of 17)	intron (NM_023672, intron 4 of 17)	37956	NM_023672	72475	Mm.195635	NM_023672	ENSMUSG00000061887	Ssbp3	2610021L12Rik|2610200M23Rik|5730488C10Rik|AI854733|AW551939|LAST|SSDP1	single-stranded DNA binding protein 3	protein-coding
mm_153111.1	chr19	32980240	32980250	-	1	NA	Intergenic	Intergenic	222668	NM_008960	19211	Mm.245395	NM_008960	ENSMUSG00000013663	Pten	2310035O07Rik|A130070J02Rik|AI463227|B430203M17Rik|MMAC1|TEP1	phosphatase and tensin homolog	protein-coding
mm_61260.1	chr7	66079644	66079703	+	1	NA	promoter-TSS (NM_024439)	promoter-TSS (NM_024439)	24	NM_024439	109815	Mm.482127	NM_024439	ENSMUSG00000075701	Selenos	1500011E07Rik|C78786|H-4|H-47|H4|H47|Sels|Vimp	selenoprotein S	protein-coding
mm_150510.1	chr19	39024064	39024071	+	1	NA	intron (NM_028089, intron 4 of 8)	Lx9|LINE|L1	17048	NM_028089	72082	Mm.142581	NM_028089	ENSMUSG00000025002	Cyp2c55	2010318C06Rik	cytochrome P450, family 2, subfamily c, polypeptide 55	protein-coding
mm_46408.1	chr5	104093223	104093243	-	1	NA	exon (NM_010097, exon 4 of 11)	exon (NM_010097, exon 4 of 11)	-15625	NM_001163772	100271704	Mm.366664	NM_001163772	ENSMUSG00000091034	Gm17660	Scpppq1	predicted gene, 17660	protein-coding
mm_6054.1	chr1	60098168	60098187	-	1	NA	promoter-TSS (NM_139150)	promoter-TSS (NM_139150)	-43	NM_001199061	57750	Mm.281079	NM_021312	ENSMUSG00000026019	Wdr12	4933402C23Rik|Ytm1|Ytm1p	WD repeat domain 12	protein-coding
mm_49139.1	chr6	9096390	9096395	+	1	NA	intron (NM_008751, intron 1 of 1)	intron (NM_008751, intron 1 of 1)	146373	NM_008751	18231	Mm.46954	NM_008751	ENSMUSG00000046178	Nxph1	C130005L03Rik	neurexophilin 1	protein-coding
mm_151249.1	chr19	53906525	53906545	+	1	NA	intron (NM_001168491, intron 1 of 11)	B3A|SINE|B2	3184	NM_001168491	18569	Mm.1605	NM_011050	ENSMUSG00000024975	Pdcd4	D19Ucla1|Ma3|Tis	programmed cell death 4	protein-coding
mm_12321.1	chr2	69382051	69382057	+	1	NA	intron (NM_175512, intron 1 of 4)	intron (NM_175512, intron 1 of 4)	1592	NM_175512	241452	Mm.211655	NM_175512	ENSMUSG00000027068	Dhrs9	C730025I08Rik|Rdh15	dehydrogenase/reductase (SDR family) member 9	protein-coding
mm_120660.1	chr14	70545220	70545236	+	1	NA	promoter-TSS (NM_180588)	promoter-TSS (NM_180588)	-23	NM_180588	72549	Mm.46742	NM_180588	ENSMUSG00000033589	Reep4	2700029E10Rik	receptor accessory protein 4	protein-coding
mm_163422.1	chr12	80816650	80816654	+	1	NA	intron (NM_001242419, intron 1 of 6)	intron (NM_001242419, intron 1 of 6)	26120	NM_001242419	217684	Mm.341776	NM_178682	ENSMUSG00000021133	Susd6	4933426M11Rik|mKIAA0247	sushi domain containing 6	protein-coding
mm_51979.1	chr6	91904277	91904281	+	1	NA	promoter-TSS (NM_198668)	promoter-TSS (NM_198668)	46	NM_198668	381798	Mm.444785	NM_198668	ENSMUSG00000034063	4930590J08Rik	Gm1071	RIKEN cDNA 4930590J08 gene	protein-coding
mm_104719.1	chr11	98101508	98101520	-	1	NA	intron (NM_028149, intron 7 of 14)	B2_Mm2|SINE|B2	-48052	NM_146028	217154	Mm.181008	NM_146028	ENSMUSG00000017400	Stac2	24b2|24b2/STAC2|AW240854	SH3 and cysteine rich domain 2	protein-coding
mm_152392.1	chr19	10525105	10525150	-	1	NA	promoter-TSS (NM_025333)	promoter-TSS (NM_025333)	82	NM_025333	66072	Mm.180063	NM_025333	ENSMUSG00000024668	Sdhaf2	0610038F07Rik|AA407634|AW049997	succinate dehydrogenase complex assembly factor 2	protein-coding
mm_91131.1	chr10	19594719	19594735	-	1	NA	intron (NM_010511, intron 1 of 6)	intron (NM_010511, intron 1 of 6)	2778	NM_010511	15979	Mm.549	NM_010511	ENSMUSG00000020009	Ifngr1	CD119|IFN-gammaR|Ifgr|Ifngr|Nktar	interferon gamma receptor 1	protein-coding
mm_166065.1	chr4	134472809	134472821	+	1	NA	exon (NM_019641, exon 4 of 5)	exon (NM_019641, exon 4 of 5)	4495	NM_019641	16765	Mm.378957	NM_019641	ENSMUSG00000028832	Stmn1	19k|Lag|Lap18|Op18|P18|P19|Pig|Pp17|Pp18|Pp19|Pr22|Smn	stathmin 1	protein-coding
mm_4092.1	chr1	167308650	167308670	+	1	NA	promoter-TSS (NM_001039483)	promoter-TSS (NM_001039483)	-10	NM_001039483	68944	Mm.330045	NM_026881	ENSMUSG00000052428	Tmco1	1190006A08Rik|4930403O06Rik|AA109065|AU022572|ESTM39	transmembrane and coiled-coil domains 1	protein-coding
mm_163771.1	chr13	120018159	120018171	+	1	NA	Intergenic	Intergenic	34039	NM_001302966	100861753	Mm.165042	NM_001302966	ENSMUSG00000095609	Gm21188	-	predicted gene, 21188	protein-coding
mm_98268.1	chr11	88999386	88999434	+	1	NA	promoter-TSS (NM_009546)	promoter-TSS (NM_009546)	7	NM_009546	217069	Mm.248445	NM_009546	ENSMUSG00000000275	Trim25	AA960166|AL022677|EFP|Zfp147	tripartite motif-containing 25	protein-coding
mm_26093.1	chr3	136805301	136805318	+	1	NA	intron (NM_008913, intron 2 of 13)	intron (NM_008913, intron 2 of 13)	135243	NM_001293622	19055	Mm.331389	NM_008913	ENSMUSG00000028161	Ppp3ca	2900074D19Rik|CN|Caln|Calna|CnA	protein phosphatase 3, catalytic subunit, alpha isoform	protein-coding
mm_53374.1	chr6	129462866	129462883	+	1	NA	non-coding (NR_132130, exon 6 of 6)	non-coding (NR_132130, exon 6 of 6)	9905	NM_001309637	56644	Mm.239516	NM_020008	ENSMUSG00000079293	Clec7a	BGR|Clecsf12|beta-GR	C-type lectin domain family 7, member a	protein-coding
mm_143623.1	chr17	78858708	78858713	-	1	NA	intron (NM_011163, intron 12 of 15)	B1_Mur4|SINE|Alu	-6166	NR_003363	625054	Mm.311918	NR_003363		Gm6548	EG625054	eukaryotic translation elongation factor 1 alpha 1 pseudogene	pseudo
mm_21910.1	chr2	166579618	166579632	-	1	NA	intron (NM_177782, intron 29 of 39)	intron (NM_177782, intron 29 of 39)	-93093	NR_105783	102465188		NR_105783	ENSMUSG00000098675	Mir6364	Gm27327|mmu-mir-6364	microRNA 6364	ncRNA
mm_23659.1	chr3	68064399	68064407	+	1	NA	promoter-TSS (NM_001113421)	promoter-TSS (NM_001113421)	-399	NM_001113421	30953	Mm.331064	NM_013928	ENSMUSG00000027777	Schip1	Nf2ip|Schip-1	schwannomin interacting protein 1	protein-coding
mm_82663.1	chr9	22117071	22117079	-	1	NA	intron (NR_030448, intron 3 of 4)	CpG	-2906	NM_170777	66126	Mm.29801	NM_170777	ENSMUSG00000013822	Elof1	1110011K10Rik	ELF1 homolog, elongation factor 1	protein-coding
mm_28828.1	chr3	96401996	96402005	-	1	NA	Intergenic	CpG	12833	NR_001579	21748		NR_001579	ENSMUSG00000064796	Terc	mTER|mTR	telomerase RNA component	ncRNA
mm_145140.1	chr18	45559535	45559548	+	1	NA	promoter-TSS (NM_080465)	promoter-TSS (NM_080465)	-613	NM_080465	140492	Mm.411614	NM_080465	ENSMUSG00000054477	Kcnn2	KCa2.2|SK2|SKCA2|bc|fri	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2	protein-coding
mm_91138.1	chr10	19718783	19718794	-	1	NA	intron (NM_172786, intron 1 of 6)	intron (NM_172786, intron 1 of 6)	6201	NM_172786	237313	Mm.234667	NM_172786	ENSMUSG00000020007	Il20ra	E230031K19	interleukin 20 receptor, alpha	protein-coding
mm_110238.1	chr12	30373359	30373380	-	1	NA	promoter-TSS (NM_172951)	promoter-TSS (NM_172951)	6	NM_172951	268534	Mm.279765	NM_172951	ENSMUSG00000020672	Sntg2	2210008K22Rik|9530013L23|BB121248|G2syn|Syn5	syntrophin, gamma 2	protein-coding
mm_87205.1	chr10	39641156	39641168	+	1	NA	intron (NM_134000, intron 4 of 8)	intron (NM_134000, intron 4 of 8)	28228	NM_134000	103213	Mm.436686	NM_134000	ENSMUSG00000019842	Traf3ip2	AI429613|Act1|CIKS	TRAF3 interacting protein 2	protein-coding
mm_162893.1	chr10	111473267	111473267	+	1	NA	promoter-TSS (NM_015781)	promoter-TSS (NM_015781)	75	NM_015781	53605	Mm.290407	NM_015781	ENSMUSG00000058799	Nap1l1	AA407126|AI256722|D10Ertd68e|NAP-1	nucleosome assembly protein 1-like 1	protein-coding
mm_48868.1	chr5	150522541	150522566	-	1	NA	promoter-TSS (NM_009765)	promoter-TSS (NM_009765)	-68	NM_009765	12190	Mm.236256	NM_009765	ENSMUSG00000041147	Brca2	Fancd1|RAB163	breast cancer 2, early onset	protein-coding
mm_92970.1	chr10	86186549	86186572	-	1	NA	intron (NM_013722, intron 6 of 13)	MER45B|DNA|hAT-Tip100	90706	NR_038024	78170	Mm.444790	NR_038024		4930486F22Rik	-	RIKEN cDNA 4930486F22 gene	ncRNA
mm_167541.1	chr9	24896854	24896854	+	1	NA	Intergenic	Intergenic	-122551	NM_001205085	57246	Mm.31452	NM_020496	ENSMUSG00000031965	Tbx20	9430010M06Rik|AL022859|Tbx12	T-box 20	protein-coding
mm_64963.1	chr7	16614793	16614805	-	1	NA	5' UTR (NM_172739, exon 1 of 7)	5' UTR (NM_172739, exon 1 of 7)	194	NM_172739	232906	Mm.28646	NM_172739	ENSMUSG00000058230	Arhgap35	6430596G11Rik|AI841135|Grlf1|mKIAA1722|p190A|p190RhoGAP	Rho GTPase activating protein 35	protein-coding
mm_18484.1	chr2	62596458	62596472	-	1	NA	3' UTR (NM_027835, exon 16 of 16)	3' UTR (NM_027835, exon 16 of 16)	-22444	NM_007986	14089	Mm.41816	NM_007986	ENSMUSG00000000392	Fap	SIMP	fibroblast activation protein	protein-coding
mm_75154.1	chr8	36218666	36218697	-	1	NA	intron (NM_001081150, intron 11 of 11)	intron (NM_001081150, intron 11 of 11)	30835	NM_001081150	244421	Mm.324032	NM_001081150	ENSMUSG00000039633	Lonrf1	-	LON peptidase N-terminal domain and ring finger 1	protein-coding
mm_13396.1	chr2	103970179	103970192	+	1	NA	promoter-TSS (NM_008505)	promoter-TSS (NM_008505)	-102	NM_008505	16909	Mm.29266	NM_008505	ENSMUSG00000032698	Lmo2	Rbtn-2|Rbtn2|Rhom-2|Ttg2	LIM domain only 2	protein-coding
mm_137856.1	chr17	31111007	31111025	+	1	NA	exon (NM_009593, exon 12 of 15)	exon (NM_009593, exon 12 of 15)	18595	NM_011575	21786	Mm.4641	NM_011575	ENSMUSG00000024029	Tff3	ITF|mITF	trefoil factor 3, intestinal	protein-coding
mm_47271.1	chr5	121860104	121860106	-	1	NA	TTS (NM_007804)	TTS (NM_007804)	11077	NM_175474	231717	Mm.12654	NM_175474	ENSMUSG00000044134	Fam109a	A230106M15Rik|AU017694|IPIP27A|Ses1	family with sequence similarity 109, member A	protein-coding
mm_27910.1	chr3	79525950	79525971	-	1	NA	intron (NM_001162999, intron 1 of 16)	intron (NM_001162999, intron 1 of 16)	41719	NM_001162999	329679	Mm.244005	NM_001162999	ENSMUSG00000061175	Fnip2	D630023B12Rik|mKIAA1450	folliculin interacting protein 2	protein-coding
mm_79063.1	chr9	46230386	46230396	+	1	NA	TTS (NM_009692)	TTS (NM_009692)	1761	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2|apo-AI|apoA-I	apolipoprotein A-I	protein-coding
mm_58532.1	chr7	4337711	4337736	+	1	NA	promoter-TSS (NM_010746)	promoter-TSS (NM_010746)	-1	NM_010746	17086	Mm.240231	NM_010746	ENSMUSG00000062524	Ncr1	Ly94|NKp46	natural cytotoxicity triggering receptor 1	protein-coding
mm_35739.1	chr4	45320463	45320473	-	1	NA	exon (NM_025513, exon 1 of 4)	exon (NM_025513, exon 1 of 4)	135	NM_025513	66362	Mm.275788	NM_025513	ENSMUSG00000028322	Exosc3	2310005D06Rik|AI593501|Rrp40	exosome component 3	protein-coding
mm_141822.1	chr17	34616001	34616010	-	1	NA	promoter-TSS (NM_152922)	promoter-TSS (NM_152922)	-34	NM_152922	81701	Mm.231343	NM_152922	ENSMUSG00000015467	Egfl8	Ng3	EGF-like domain 8	protein-coding
mm_120671.1	chr14	70554394	70554402	+	1	NA	intron (NM_021877, intron 1 of 19)	CpG	342	NM_021877	15460	Mm.7598	NM_021877	ENSMUSG00000022096	Hr	ALUNC|AU|N|ba|bldy|hr|rh|rh-bmh|rhino	hairless	protein-coding
mm_67213.1	chr7	74408505	74408509	-	1	NA	intron (NM_001038643, intron 2 of 10)	intron (NM_001038643, intron 2 of 10)	146273	NM_023908	108116	Mm.425467	NM_023908	ENSMUSG00000025790	Slco3a1	5830414C08Rik|Anr1|MJAM|OATP-D|R75096|Slc21a11	solute carrier organic anion transporter family, member 3a1	protein-coding
mm_123301.1	chr14	61648763	61648807	-	1	NA	intron (NR_028264, intron 1 of 6)	CpG	-16675	NR_029733	387174		NR_029733	ENSMUSG00000093007	Mir15a	Mirn15a|mir-15a|mmu-mir-15a	microRNA 15a	ncRNA
mm_51418.1	chr6	78382181	78382196	+	1	NA	intron (NM_011259, intron 3 of 5)	intron (NM_011259, intron 3 of 5)	1479	NM_011259	19694	Mm.2552	NM_011259	ENSMUSG00000079516	Reg3a	AV063448	regenerating islet-derived 3 alpha	protein-coding
mm_127747.1	chr15	103464574	103464587	+	1	NA	exon (NM_153505, exon 9 of 31)	exon (NM_153505, exon 9 of 31)	10755	NM_153505	105855	Mm.30805	NM_153505	ENSMUSG00000022488	Nckap1l	4930568P13Rik|AI463083|Hem1|Hemp1	NCK associated protein 1 like	protein-coding
mm_99789.1	chr11	107428243	107428257	+	1	NA	intron (NM_145823, intron 1 of 9)	intron (NM_145823, intron 1 of 9)	42470	NM_145823	71795	Mm.397413	NM_145823	ENSMUSG00000040430	Pitpnc1	1110020B03Rik|5830436L09Rik|AI662802|AI851387|C330017I21Rik|Dnr411|RDGBB|RDGBB1|rdgB-beta	phosphatidylinositol transfer protein, cytoplasmic 1	protein-coding
mm_85949.1	chr9	112113865	112113871	-	1	NA	intron (NM_001177618, intron 17 of 18)	intron (NM_001177618, intron 17 of 18)	4843	NR_029823	723815		NR_029823	ENSMUSG00000065441	Mir128-2	Mirn128-2|Mirn128b|mir-128-2|mir-128b	microRNA 128-2	ncRNA
mm_112244.1	chr12	113482584	113482593	-	1	NA	Intergenic	Intergenic	-6977	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_48516.1	chr5	142895162	142895229	-	1	NA	promoter-TSS (NM_001033312)	promoter-TSS (NM_001033312)	43	NM_001033312	231863	Mm.89753	NM_001033312	ENSMUSG00000066640	Fbxl18	AI427077|B130019G13Rik|C330021B20Rik	F-box and leucine-rich repeat protein 18	protein-coding
mm_105128.1	chr11	101302230	101302291	-	1	NA	promoter-TSS (NM_019584)	promoter-TSS (NM_019584)	7	NM_019584	56208	Mm.178947	NM_019584	ENSMUSG00000035086	Becn1	4921513J16Rik|5430417M23Rik|Atg6	beclin 1, autophagy related	protein-coding
mm_84352.1	chr9	64341020	64341038	-	1	NA	promoter-TSS (NM_001177784)	promoter-TSS (NM_001177784)	228	NM_001001295	213550	Mm.268341	NM_172519	ENSMUSG00000032396	Dis3l	AV340375	DIS3 like exosome 3'-5' exoribonuclease	protein-coding
mm_41712.1	chr5	101888188	101888198	+	1	NA	exon (NM_172882, exon 39 of 67)	exon (NM_172882, exon 39 of 67)	123063	NM_173370	74596	Mm.46764	NM_173370	ENSMUSG00000029330	Cds1	4833409J18Rik|AI314024|AW125888	CDP-diacylglycerol synthase 1	protein-coding
mm_51016.1	chr6	65023400	65023413	+	1	NA	Intergenic	RLTR19A2|LTR|ERVK	-19261	NM_007958	13990	Mm.99113	NM_007958	ENSMUSG00000029920	Smarcad1	AV081750|AW226546|D6Pas1|Etl1|mKIAA1122	SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1	protein-coding
mm_33854.1	chr4	135870403	135870403	+	1	NA	TTS (NM_001284196)	TTS (NM_001284196)	3443	NM_026383	52830	Mm.29159	NM_026383	ENSMUSG00000028675	Pnrc2	0610011E17Rik|D4Bwg0593e	proline-rich nuclear receptor coactivator 2	protein-coding
mm_130542.1	chr15	98953542	98953560	-	1	NA	promoter-TSS (NM_011653)	promoter-TSS (NM_011653)	-50	NM_011653	22142	Mm.405359	NM_011653	ENSMUSG00000072235	Tuba1a	Tuba-1|Tuba1	tubulin, alpha 1A	protein-coding
mm_156176.1	chrX	130337508	130337521	+	1	NA	intron (NM_172493, intron 26 of 26)	intron (NM_172493, intron 26 of 26)	587772	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diaph2	Dia3|Diap2|Drf2|E430022I22Rik	diaphanous related formin 2	protein-coding
mm_102590.1	chr11	61915173	61915173	-	1	NA	exon (NM_019921, exon 4 of 15)	exon (NM_019921, exon 4 of 15)	15084	NM_019921	56697	Mm.274404	NM_019921	ENSMUSG00000047804	Akap10	1500031L16Rik|B130049N18Rik|D-AKAP-2|D-AKAP2|PRKA10	A kinase (PRKA) anchor protein 10	protein-coding
mm_44131.1	chr5	149831724	149831734	+	1	NA	Intergenic	Intergenic	-16018	NR_045758	70969	Mm.78499	NR_045758	ENSMUSG00000107214	4930500F04Rik	4931407C17Rik	RIKEN cDNA 4930500F04 gene	ncRNA
mm_96462.1	chr11	67596522	67596573	+	1	NA	promoter-TSS (NM_001277080)	promoter-TSS (NM_001277080)	-8	NM_001277080	14457	Mm.40338	NM_008088	ENSMUSG00000033066	Gas7	AW124766|B230343A10Rik|Gas7-cb	growth arrest specific 7	protein-coding
mm_161382.1	chr14	70682619	70682619	-	1	NA	intron (NM_023045, intron 17 of 27)	intron (NM_023045, intron 17 of 27)	-29535	NM_181345	328440	Mm.347749	NM_181345	ENSMUSG00000047911	Npm2	-	nucleophosmin/nucleoplasmin 2	protein-coding
mm_6833.1	chr1	84225088	84225098	-	1	NA	intron (NM_001003948, intron 1 of 2)	B3|SINE|B2	-6132	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_60007.1	chr7	30722605	30722612	+	1	NA	exon (NM_018731, exon 17 of 22)	exon (NM_018731, exon 17 of 22)	6926	NM_027215	69804	Mm.27499	NM_027215	ENSMUSG00000006315	Tmem147	2010004E11Rik|5033425B17Rik|Nifie14	transmembrane protein 147	protein-coding
mm_80871.1	chr9	98864744	98864803	+	1	NA	promoter-TSS (NM_028033)	promoter-TSS (NM_028033)	6	NM_028033	71979	Mm.140843	NM_028033	ENSMUSG00000090470	Prr23a3	2410012M07Rik	proline rich 23A, member 3	protein-coding
mm_109897.1	chr12	7876429	7876435	-	1	NA	Intergenic	RMER19B|LTR|ERVK	-101245	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_158660.1	chrX	157415094	157415104	-	1	NA	5' UTR (NM_011077, exon 1 of 22)	5' UTR (NM_011077, exon 1 of 22)	187	NM_011077	18675	Mm.2529	NM_011077	ENSMUSG00000057457	Phex	Gy|HPDR|HPDR1|Hyp|PEX	phosphate regulating endopeptidase homolog, X-linked	protein-coding
mm_120080.1	chr14	57702778	57702778	+	1	NA	intron (NM_015771, intron 3 of 7)	intron (NM_015771, intron 3 of 7)	31640	NM_153382	50523	Mm.347899	NM_015771	ENSMUSG00000021959	Lats2	4932411G09Rik|AV277261|AW228608	large tumor suppressor 2	protein-coding
mm_126157.1	chr15	78410280	78410284	+	1	NA	exon (NM_138670, exon 2 of 3)	exon (NM_138670, exon 2 of 3)	3178	NM_138670	246221	Mm.294215	NM_138670	ENSMUSG00000071711	Mpst	Mst	mercaptopyruvate sulfurtransferase	protein-coding
mm_118526.1	chr14	14804134	14804144	+	1	NA	Intergenic	Intergenic	-16676	NM_001195229	674895	Mm.317563	NM_001034865	ENSMUSG00000042567	Nek10	Gm282	NIMA (never in mitosis gene a)- related kinase 10	protein-coding
mm_65250.1	chr7	19861296	19861299	-	1	NA	promoter-TSS (NM_001033419)	promoter-TSS (NM_001033419)	2	NM_001033419	330483	Mm.260192	NM_001033419	ENSMUSG00000014686	Ceacam16	Gm769	carcinoembryonic antigen-related cell adhesion molecule 16	protein-coding
mm_112850.1	chr13	20836122	20836132	+	1	NA	intron (NM_012054, intron 2 of 20)	intron (NM_012054, intron 2 of 20)	42014	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_124417.1	chr14	118052025	118052027	-	1	NA	5' UTR (NM_010024, exon 1 of 8)	5' UTR (NM_010024, exon 1 of 8)	220	NM_010024	13190	Mm.19987	NM_010024	ENSMUSG00000022129	Dct	DT|TRP-2|TRP2|Tyrp-2|Tyrp2|slaty|slt	dopachrome tautomerase	protein-coding
mm_49592.1	chr6	30645248	30645276	+	1	NA	TTS (NM_025350)	TTS (NM_025350)	6044	NM_025350	109697	Mm.25377	NM_025350	ENSMUSG00000054446	Cpa1	0910001L12Rik|Cpa	carboxypeptidase A1, pancreatic	protein-coding
mm_74667.1	chr8	13677537	13677553	-	1	NA	promoter-TSS (NM_009025)	promoter-TSS (NM_009025)	42	NM_009025	19414	Mm.18517	NM_009025	ENSMUSG00000031453	Rasa3	AI326412|C86362|E130011G04|GAPIII|hlb381|scat	RAS p21 protein activator 3	protein-coding
mm_62684.1	chr7	110018297	110018300	+	1	NA	promoter-TSS (NM_181517)	promoter-TSS (NM_181517)	-127	NM_181517	233726	Mm.222328	NM_181517	ENSMUSG00000066232	Ipo7	A330055O14Rik|C330016G14|Imp7|Ranbp7	importin 7	protein-coding
mm_145154.1	chr18	46474939	46474959	+	1	NA	Intergenic	MTEa-int|LTR|ERVL-MaLR	-9133	NR_045438	72076	Mm.82766	NM_028086		Mospd4	2010013H21Rik	motile sperm domain containing 4	pseudo
mm_90692.1	chr10	128971217	128971229	+	1	NA	Intergenic	L1M4|LINE|L1	-10235	NM_027853	71664	Mm.337232	NM_027853	ENSMUSG00000025347	Mettl7b	0610006F02Rik|AI266817	methyltransferase like 7B	protein-coding
mm_158962.1	chr1	92596504	92596504	+	1	NA	promoter-TSS (NM_146490)	promoter-TSS (NM_146490)	-17	NM_146490	258483	Mm.271573	NM_146490	ENSMUSG00000062497	Olfr1411	MOR208-3	olfactory receptor 1411	protein-coding
mm_67777.1	chr7	97211161	97211176	-	1	NA	intron (NM_001162477, intron 1 of 9)	intron (NM_001162477, intron 1 of 9)	114796	NM_001177412	244144	Mm.297541	NM_001177412	ENSMUSG00000035713	Usp35	Gm1088|Gm493	ubiquitin specific peptidase 35	protein-coding
mm_46944.1	chr5	114859416	114859436	-	1	NA	intron (NM_026263, intron 2 of 11)	intron (NM_026263, intron 2 of 11)	5712	NM_026263	67593	Mm.251409	NM_026263	ENSMUSG00000029564	4930519G04Rik	1700014B12Rik	RIKEN cDNA 4930519G04 gene	protein-coding
mm_38066.1	chr4	134093801	134093811	-	1	NA	exon (NM_013706, exon 2 of 2)	exon (NM_013706, exon 2 of 2)	1267	NM_013706	23833	Mm.24130	NM_013706	ENSMUSG00000000682	Cd52	AI463198|B7|B7-Ag|CAMPATH-1|CLS1|MB7	CD52 antigen	protein-coding
mm_171356.1	chr4	115453985	115453990	-	1	NA	intron (NM_001100185, intron 1 of 11)	intron (NM_001100185, intron 1 of 11)	1383	NM_001100185	435802	Mm.466611	NM_001100185	ENSMUSG00000084346	Cyp4a30b	Cyp4a30b-ps|OTTMUSG00000008626	cytochrome P450, family 4, subfamily a, polypeptide 30b	protein-coding
mm_24424.1	chr3	90537243	90537270	+	1	NA	Intergenic	Intergenic	-3967	NM_026416	67860	Mm.331185	NM_026416	ENSMUSG00000074457	S100a16	2300002L21Rik|AI325039|AI663996|DT1P1A7|S100F	S100 calcium binding protein A16	protein-coding
mm_12177.1	chr2	62968178	62968182	+	1	NA	intron (NM_133207, intron 2 of 15)	intron (NM_133207, intron 2 of 15)	216107	NM_133207	170738	Mm.242532	NM_133207	ENSMUSG00000059742	Kcnh7	9330137I11Rik|Kv11.3|erg3	potassium voltage-gated channel, subfamily H (eag-related), member 7	protein-coding
mm_6950.1	chr1	85864602	85864615	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-29902	NM_022417	64294	Mm.29870	NM_022417	ENSMUSG00000026223	Itm2c	3110038L02Rik|BRI3|Bricd2c|E25|E25C|ITM3	integral membrane protein 2C	protein-coding
mm_75982.1	chr8	72284949	72284957	-	1	NA	Intergenic	B4A|SINE|B4	-34109	NM_008452	16598	Mm.26938	NM_008452	ENSMUSG00000055148	Klf2	Lklf	Kruppel-like factor 2 (lung)	protein-coding
mm_171638.1	chr4	23288592	23288593	+	1	NA	Intergenic	Intergenic	798044	NR_131335	105500046		NR_131335	ENSMUSG00000107859	Gm30731	Pnky|lnc-pou3f2	predicted gene, 30731	ncRNA
mm_129121.1	chr15	76119149	76119162	-	1	NA	TTS (NM_001142968)	TTS (NM_001142968)	1040	NM_144848	223650	Mm.259929	NM_144848		Eppk1	6230424I18Rik|EPIPL|EPIPL1|EPPK	epiplakin 1	protein-coding
mm_147765.1	chr18	61375239	61375254	-	1	NA	intron (NM_133249, intron 1 of 11)	(TG)n|Simple_repeat|Simple_repeat	25185	NM_133249	170826	Mm.415302	NM_133249	ENSMUSG00000033871	Ppargc1b	4631412G21Rik|Perc	peroxisome proliferative activated receptor, gamma, coactivator 1 beta	protein-coding
mm_13608.1	chr2	113364546	113364570	+	1	NA	exon (NM_010230, exon 2 of 20)	exon (NM_010230, exon 2 of 20)	36822	NM_010230	14260	Mm.4938	NM_010230	ENSMUSG00000044042	Fmn1	Fmn|formin-1|ld	formin 1	protein-coding
mm_127556.1	chr15	102151047	102151059	+	1	NA	intron (NM_146064, intron 1 of 14)	intron (NM_146064, intron 1 of 14)	478	NM_146064	223920	Mm.358862	NM_146064	ENSMUSG00000023045	Soat2	ACAT2|D15Wsu97e	sterol O-acyltransferase 2	protein-coding
mm_104852.1	chr11	99322944	99322957	-	1	NA	promoter-TSS (NM_133730)	promoter-TSS (NM_133730)	-9	NM_133730	70810	Mm.268173	NM_133730	ENSMUSG00000035831	Krt25	4631426H08Rik|Ka38|Krt25a|mIRSa1	keratin 25	protein-coding
mm_85084.1	chr9	91365757	91365774	-	1	NA	promoter-TSS (NM_009573)	promoter-TSS (NM_009573)	34	NM_009573	22771	Mm.335350	NM_009573	ENSMUSG00000032368	Zic1	ZIC|ZNF201	zinc finger protein of the cerebellum 1	protein-coding
mm_27832.1	chr3	79126528	79126540	-	1	NA	intron (NM_001099624, intron 1 of 23)	(CCCA)n|Simple_repeat|Simple_repeat	18353	NM_001310536	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_89309.1	chr10	87916428	87916438	+	1	NA	intron (NM_001111274, intron 4 of 4)	intron (NM_001111274, intron 4 of 4)	-50238	NR_000040	22172	Mm.391420	NR_000040		Tyms-ps	-	thymidylate synthase, pseudogene	pseudo
mm_84666.1	chr9	71996305	71996307	-	1	NA	intron (NM_001253862, intron 5 of 19)	intron (NM_001253862, intron 5 of 19)	32865	NR_029879	723889		NR_029879	ENSMUSG00000105200	Mir378a	Mir378|Mirn378|mmu-mir-378|mmu-mir-378a	microRNA 378a	ncRNA
mm_51758.1	chr6	87778085	87778112	+	1	NA	promoter-TSS (NM_018762)	promoter-TSS (NM_018762)	-38	NM_018762	54368	Mm.12897	NM_018762	ENSMUSG00000030054	Gp9	Cd42|GPIX	glycoprotein 9 (platelet)	protein-coding
mm_98698.1	chr11	96303592	96303605	+	1	NA	promoter-TSS (NM_008268)	promoter-TSS (NM_008268)	86	NM_008268	15413	Mm.207	NM_008268	ENSMUSG00000038700	Hoxb5	AI385717|Hox-2.1	homeobox B5	protein-coding
mm_5385.1	chr1	31016829	31016836	-	1	NA	Intergenic	Intergenic	-67077	NM_011200	19243	Mm.491181	NM_011200	ENSMUSG00000026064	Ptp4a1	AA415290|AU019864|C130021B01|Prl-1	protein tyrosine phosphatase 4a1	protein-coding
mm_38374.1	chr4	138457137	138457149	-	1	NA	3' UTR (NM_025451, exon 2 of 2)	3' UTR (NM_025451, exon 2 of 2)	1995	NM_025451	66259	Mm.41603	NM_025451	ENSMUSG00000046447	Camk2n1	1810006K23Rik|AI848599|AI891706	calcium/calmodulin-dependent protein kinase II inhibitor 1	protein-coding
mm_160741.1	chr10	80547938	80547938	-	1	NA	exon (NM_025852, exon 4 of 15)	exon (NM_025852, exon 4 of 15)	-8814	NM_026094	67331	Mm.52511	NM_026094	ENSMUSG00000003341	Atp8b3	1700042F02Rik|1700056N23Rik|ATPIK|SAPLT	ATPase, class I, type 8B, member 3	protein-coding
mm_57441.1	chr6	124965232	124965243	-	1	NA	intron (NM_001164089, intron 1 of 7)	CpG	160	NM_012003	26894	Mm.244536	NM_012003	ENSMUSG00000030127	Cops7a	D6Ertd35e	COP9 signalosome subunit 7A	protein-coding
mm_60948.1	chr7	47021195	47021237	+	1	NA	Intergenic	Intergenic	-12802	NM_175318	101685	Mm.155687	NM_175318	ENSMUSG00000049516	Spty2d1	5830435K17Rik|AI852426|P16H6	SPT2, Suppressor of Ty, domain containing 1 (S. cerevisiae)	protein-coding
mm_14052.1	chr2	122382938	122382952	+	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	-14027	NM_001013829	435684	Mm.458215	NM_001013829	ENSMUSG00000033256	Shf	-	Src homology 2 domain containing F	protein-coding
mm_97539.1	chr11	78830400	78830403	+	1	NA	intron (NM_001076681, intron 1 of 3)	intron (NM_001076681, intron 1 of 3)	3806	NM_001076681	66274	Mm.258932	NM_001076681	ENSMUSG00000072640	Lyrm9	1810012P15Rik	LYR motif containing 9	protein-coding
mm_103291.1	chr11	72411696	72411718	-	1	NA	promoter-TSS (NM_177776)	promoter-TSS (NM_177776)	6	NM_177776	276829	Mm.46732	NM_177776	ENSMUSG00000045667	Smtnl2	D130058I21Rik	smoothelin-like 2	protein-coding
mm_132363.1	chr16	34745202	34745216	+	1	NA	Intergenic	CpG	-39741	NM_139300	107589	Mm.33360	NM_139300	ENSMUSG00000022836	Mylk	9530072E15Rik|A930019C19Rik|AW489456|KRP|MLCK108|MLCK210|Mlck|nmMlck|smMLCK	myosin, light polypeptide kinase	protein-coding
mm_116597.1	chr13	48546471	48546492	-	1	NA	Intergenic	CpG	-8209	NR_029725	387244		NR_029725	ENSMUSG00000065421	Mirlet7a-1	Let-7a|Mirnlet7a|Mirnlet7a-1|let-7a-1	microRNA let7a-1	ncRNA
mm_113274.1	chr13	29664204	29664212	+	1	NA	intron (NR_131896, intron 8 of 16)	L1ME1|LINE|L1	191465	NR_131896	68916	Mm.212227	NM_144536	ENSMUSG00000006191	Cdkal1	1190005B03Rik|6620401C13Rik	CDK5 regulatory subunit associated protein 1-like 1	protein-coding
mm_143073.1	chr17	57024273	57024300	-	1	NA	exon (NM_010613, exon 12 of 18)	exon (NM_010613, exon 12 of 18)	7221	NM_010613	16549	Mm.34296	NM_010613	ENSMUSG00000007670	Khsrp	6330409F21Rik|Fbp2|Fubp2|Ksrp	KH-type splicing regulatory protein	protein-coding
mm_82215.1	chr9	3002992	3003011	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	35742	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_70237.1	chr8	3353339	3353352	+	1	NA	promoter-TSS (NM_001033378)	promoter-TSS (NM_001033378)	-70	NM_001033378	319493	Mm.234565	NM_001033378	ENSMUSG00000074497	A430078G23Rik	-	RIKEN cDNA A430078G23 gene	protein-coding
mm_1720.1	chr1	75360322	75360338	+	1	NA	promoter-TSS (NM_010043)	promoter-TSS (NM_010043)	38	NM_010043	13346	Mm.6712	NM_010043	ENSMUSG00000026208	Des	-	desmin	protein-coding
mm_3151.1	chr1	135152801	135152836	+	1	NA	exon (NM_026823, exon 3 of 7)	exon (NM_026823, exon 3 of 7)	5984	NM_026823	68724	Mm.174998	NM_026823	ENSMUSG00000026426	Arl8a	1110033P22Rik|Arl10b|gie2	ADP-ribosylation factor-like 8A	protein-coding
mm_88113.1	chr10	69192095	69192096	+	1	NA	Intergenic	Intergenic	-16457	NM_001252636	69288	Mm.26659	NM_001081347	ENSMUSG00000019944	Rhobtb1	1700008H16Rik|3110048G13Rik|AI173445|AI573858|AV350930	Rho-related BTB domain containing 1	protein-coding
mm_116499.1	chr13	44982794	44982802	-	1	NA	exon (NM_025772, exon 5 of 10)	exon (NM_025772, exon 5 of 10)	19298	NM_025772	94245	Mm.352311	NM_025772	ENSMUSG00000057531	Dtnbp1	5430437B18Rik|AW048963|Bloc1s8|dysbindin|sdy	dystrobrevin binding protein 1	protein-coding
mm_141415.1	chr17	29430214	29430217	-	1	NA	Intergenic	Intergenic	-60830	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_86020.1	chr9	112235831	112235842	-	1	NA	promoter-TSS (NM_001177619)	promoter-TSS (NM_001177619)	-995	NM_001177619	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_9865.1	chr1	184845861	184845871	-	1	NA	promoter-TSS (NM_133684)	promoter-TSS (NM_133684)	-19	NM_133684	67247	Mm.177724	NM_133684	ENSMUSG00000073481	Marc2	2810484M10Rik|Mosc2|mARC1	mitochondrial amidoxime reducing component 2	protein-coding
mm_159000.1	chr1	153425393	153425393	+	1	NA	exon (NM_001033162, exon 1 of 10)	exon (NM_001033162, exon 1 of 10)	184	NM_001033162	71836	Mm.49460	NM_001033162	ENSMUSG00000042708	Shcbp1l	1700012A16Rik	Shc SH2-domain binding protein 1-like	protein-coding
mm_5143.1	chr1	9748228	9748243	-	1	NA	non-coding (NR_040462, exon 1 of 4)	non-coding (NR_040462, exon 1 of 4)	147	NM_173443	70675	Mm.274493	NM_173443	ENSMUSG00000045210	Vcpip1	4932442A08|5730421J18Rik|5730538E15Rik|VCIP135|mKIAA1850	valosin containing protein (p97)/p47 complex interacting protein 1	protein-coding
mm_62891.1	chr7	115995267	115995286	+	1	NA	promoter-TSS (NM_011445)	promoter-TSS (NM_011445)	-190	NM_011445	20679	Mm.323365	NM_011445	ENSMUSG00000051910	Sox6	AI987981|SOX-LZ	SRY (sex determining region Y)-box 6	protein-coding
mm_127426.1	chr15	101267985	101267991	+	1	NA	intron (NM_010444, intron 1 of 6)	intron (NM_010444, intron 1 of 6)	1142	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_1105.1	chr1	59763717	59763730	+	1	NA	promoter-TSS (NM_007561)	promoter-TSS (NM_007561)	-556	NM_007561	12168	Mm.7106	NM_007561	ENSMUSG00000067336	Bmpr2	2610024H22Rik|AL117858|AW546137|BB189135|BMP-2|BMPR-2|BMPR-II|BMPRII|BRK-3|Gm20272	bone morphogenetic protein receptor, type II (serine/threonine kinase)	protein-coding
mm_172263.1	chr6	75296940	75296947	-	1	NA	Intergenic	Intergenic	-1825922	NR_108032	73408	Mm.233629	NR_108032	ENSMUSG00000107408	1700065L07Rik	-	RIKEN cDNA 1700065L07 gene	ncRNA
mm_111792.1	chr12	104865008	104865029	-	1	NA	promoter-TSS (NR_104437)	promoter-TSS (NR_104437)	58	NR_104436	94040	Mm.244078	NM_053155	ENSMUSG00000021097	Clmn	9330188N17Rik|AI428889|AI788815|mKIAA1188	calmin	protein-coding
mm_37104.1	chr4	116627973	116627988	-	1	NA	promoter-TSS (NM_016777)	promoter-TSS (NM_016777)	-29	NM_016777	50927	Mm.257181	NM_016777	ENSMUSG00000028693	Nasp	5033430J04Rik|AI131596|AI317140|D4Ertd767e|Epcs32|Nasp-T	nuclear autoantigenic sperm protein (histone-binding)	protein-coding
mm_91057.1	chr10	18831917	18831941	-	1	NA	promoter-TSS (NR_102728)	promoter-TSS (NR_102728)	1	NR_038035	73968	Mm.55591	NR_038034		4930444F02Rik	1700010L24Rik|mpiR	RIKEN cDNA 4930444F02 gene	ncRNA
mm_18633.1	chr2	69342605	69342624	-	1	NA	promoter-TSS (NM_021022)	promoter-TSS (NM_021022)	2	NM_021022	27413	Mm.439855	NM_021022	ENSMUSG00000027048	Abcb11	ABC16|Bsep|Lith1|PFIC2|PGY4|SPGP	ATP-binding cassette, sub-family B (MDR/TAP), member 11	protein-coding
mm_101487.1	chr11	31370099	31370110	-	1	NA	promoter-TSS (NM_011491)	promoter-TSS (NM_011491)	-43	NM_011491	20856	Mm.32506	NM_011491	ENSMUSG00000020303	Stc2	AW125853|Stc2l|mustc2	stanniocalcin 2	protein-coding
mm_8175.1	chr1	138064054	138064101	-	1	NA	3' UTR (NM_001268286, exon 29 of 29)	3' UTR (NM_001268286, exon 29 of 29)	97438	NR_029820	723890		NR_029820	ENSMUSG00000065458	Mir181b-1	Mirn181b-1|mir-181b-1	microRNA 181b-1	ncRNA
mm_90749.1	chr10	5488201	5488237	-	1	NA	promoter-TSS (NM_001347711)	promoter-TSS (NM_001347711)	95	NM_001347711	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_11366.1	chr2	30981980	30981994	+	1	NA	promoter-TSS (NM_028846)	promoter-TSS (NM_028846)	-46	NM_144885	227707	Mm.235238	NM_144885	ENSMUSG00000026851	BC005624	-	cDNA sequence BC005624	protein-coding
mm_161279.1	chr14	19602595	19602595	-	1	NA	promoter-TSS (NM_001024706)	promoter-TSS (NM_001024706)	-8	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_147140.1	chr18	36454488	36454516	-	1	NA	promoter-TSS (NM_026027)	promoter-TSS (NM_026027)	-7	NM_026027	67199	Mm.30184	NM_026027	ENSMUSG00000024346	Pfdn1	2700086I23Rik|AA408327|AU044714	prefoldin 1	protein-coding
mm_142247.1	chr17	37483177	37483198	-	1	NA	exon (NM_008204, exon 2 of 4)	exon (NM_008204, exon 2 of 4)	342	NM_008204	14990	Mm.329041	NM_008204	ENSMUSG00000016283	H2-M2	H-2M2|Thy19.4	histocompatibility 2, M region locus 2	protein-coding
mm_111906.1	chr12	108765865	108765904	-	1	NA	Intergenic	Intergenic	-27427	NM_009537	22632	Mm.3868	NM_009537	ENSMUSG00000021264	Yy1	AW488674|NF-E1	YY1 transcription factor	protein-coding
mm_88283.1	chr10	75173791	75173798	+	1	NA	intron (NM_001081412, intron 16 of 22)	intron (NM_001081412, intron 16 of 22)	-38279	NM_153406	74392	Mm.27716	NM_153406	ENSMUSG00000033444	Specc1l	4930470P14Rik|4932439K10Rik|9530057A13Rik|AI317249|Cytsa|mKIAA0376	sperm antigen with calponin homology and coiled-coil domains 1-like	protein-coding
mm_11444.1	chr2	32052051	32052064	+	1	NA	intron (NM_172268, intron 35 of 35)	intron (NM_172268, intron 35 of 35)	1111	NR_106135	102466844		NR_106135	ENSMUSG00000099075	Mir7674	Gm27563|mmu-mir-7674	microRNA 7674	ncRNA
mm_150619.1	chr19	41044874	41044882	+	1	NA	intron (NM_009345, intron 6 of 11)	intron (NM_009345, intron 6 of 11)	15603	NM_009345	21673	Mm.25620	NM_009345	ENSMUSG00000025014	Dntt	Tdt	deoxynucleotidyltransferase, terminal	protein-coding
mm_120640.1	chr14	70521041	70521051	+	1	NA	promoter-TSS (NM_009755)	promoter-TSS (NM_009755)	-786	NR_033241	12153	Mm.27757	NM_009755	ENSMUSG00000022098	Bmp1	Pcp|Tld	bone morphogenetic protein 1	protein-coding
mm_109838.1	chr12	4233959	4233981	-	1	NA	promoter-TSS (NM_001204912)	promoter-TSS (NM_001204912)	-57	NM_001204912	69709	Mm.250552	NM_001204912	ENSMUSG00000096199	Ptrhd1	2410017P09Rik	peptidyl-tRNA hydrolase domain containing 1	protein-coding
mm_103465.1	chr11	76437199	76437228	-	1	NA	intron (NM_001346670, intron 15 of 21)	CpG	30070	NM_019818	56322	Mm.18803	NM_019818	ENSMUSG00000020843	Timm22	Tim22	translocase of inner mitochondrial membrane 22	protein-coding
mm_44375.1	chr5	17814285	17814300	-	1	NA	exon (NM_001159558, exon 7 of 16)	exon (NM_001159558, exon 7 of 16)	21604	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_70006.1	chr7	142398064	142398072	-	1	NA	Intergenic	Intergenic	-10198	NM_009983	13033	Mm.231395	NM_009983	ENSMUSG00000007891	Ctsd	CD|CatD	cathepsin D	protein-coding
mm_150012.1	chr19	29366557	29366568	+	1	NA	promoter-TSS (NM_021893)	promoter-TSS (NM_021893)	-876	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_121397.1	chr14	119137829	119137841	+	1	NA	promoter-TSS (NM_015820)	promoter-TSS (NM_015820)	-430	NM_015820	50787	Mm.445777	NM_015820	ENSMUSG00000053465	Hs6st3	6OST3|HS6ST-3	heparan sulfate 6-O-sulfotransferase 3	protein-coding
mm_30071.1	chr3	137969637	137969640	-	1	NA	intron (NM_011932, intron 1 of 8)	intron (NM_011932, intron 1 of 8)	11911	NM_011932	26377	Mm.254835	NM_011932	ENSMUSG00000028159	Dapp1	Bam32	dual adaptor for phosphotyrosine and 3-phosphoinositides 1	protein-coding
mm_74009.1	chr8	121116867	121116872	+	1	NA	exon (NM_013519, exon 1 of 1)	exon (NM_013519, exon 1 of 1)	698	NM_013519	14234	Mm.14092	NM_013519	ENSMUSG00000046714	Foxc2	Fkh14|Hfhbf3|MFH-1|Mfh1	forkhead box C2	protein-coding
mm_121909.1	chr14	21987995	21988009	-	1	NA	5' UTR (NM_145459, exon 2 of 3)	5' UTR (NM_145459, exon 2 of 3)	1599	NM_145459	218820	Mm.292401	NM_145459	ENSMUSG00000039081	Zfp503	AI181838|B830002A16Rik|Nolz-1|Nolz1|Znf503	zinc finger protein 503	protein-coding
mm_88107.1	chr10	69151236	69151281	+	1	NA	Intergenic	Intergenic	-57294	NM_001252636	69288	Mm.26659	NM_001081347	ENSMUSG00000019944	Rhobtb1	1700008H16Rik|3110048G13Rik|AI173445|AI573858|AV350930	Rho-related BTB domain containing 1	protein-coding
mm_119465.1	chr14	47276991	47277009	+	1	NA	promoter-TSS (NM_080843)	promoter-TSS (NM_080843)	-143	NM_172598	218973	Mm.265615	NM_172598	ENSMUSG00000037572	Wdhd1	A630092E18|AND-1|D630024B06Rik	WD repeat and HMG-box DNA binding protein 1	protein-coding
mm_89895.1	chr10	110920171	110920188	+	1	NA	promoter-TSS (NM_007792)	promoter-TSS (NM_007792)	3	NM_007792	13008	Mm.2020	NM_007792	ENSMUSG00000020186	Csrp2	AW551867|Crp2|SmLim	cysteine and glycine-rich protein 2	protein-coding
mm_24469.1	chr3	90654254	90654279	+	1	NA	promoter-TSS (NM_199422)	promoter-TSS (NM_199422)	-36	NM_199422	381493	Mm.291525	NM_199422	ENSMUSG00000063767	S100a7a	AY465109|Gm1020|S100A7L1|S100A7f|S100a15|S100a15a|S100a17l1	S100 calcium binding protein A7A	protein-coding
mm_69146.1	chr7	127091176	127091201	-	1	NA	promoter-TSS (NM_178901)	promoter-TSS (NM_178901)	-248	NM_178901	101602	Mm.490357	NM_178901	ENSMUSG00000045165	AI467606	-	expressed sequence AI467606	protein-coding
mm_25908.1	chr3	131112555	131112579	+	1	NA	promoter-TSS (NM_001276403)	promoter-TSS (NM_001276403)	-224	NM_001276403	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_86688.1	chr10	18431206	18431238	+	1	NA	intron (NM_173390, intron 1 of 6)	intron (NM_173390, intron 1 of 6)	23547	NM_173390	215819	Mm.297971	NM_173390	ENSMUSG00000039835	Nhsl1	5730409E15Rik|A630035H13Rik|A730096F01|BC013565|D10Bwg0940e|mKIAA1357	NHS-like 1	protein-coding
mm_34593.1	chr4	150197311	150197322	+	1	NA	intron (NM_009802, intron 3 of 7)	intron (NM_009802, intron 3 of 7)	3819	NM_009802	12353	Mm.232523	NM_009802	ENSMUSG00000028972	Car6	Ca6|DOC1	carbonic anhydrase 6	protein-coding
mm_107810.1	chr12	65061732	65061734	+	1	NA	TTS (NM_013902)	TTS (NM_013902)	12205	NM_013902	30795	Mm.28480	NM_013902	ENSMUSG00000020949	Fkbp3	25kDa|FKBP-3|FKBP25	FK506 binding protein 3	protein-coding
mm_38540.1	chr4	141586804	141586806	-	1	NA	intron (NM_001163256, intron 5 of 8)	RMER4B|LTR|ERVK	13119	NM_001163256	74202	Mm.490327	NM_133754	ENSMUSG00000006219	Fblim1	2410043F08Rik|Cal|Fblp1|Gt10|migfilin|migfilin(s)	filamin binding LIM protein 1	protein-coding
mm_172716.1	chr8	70685783	70685784	+	1	NA	Intergenic	B1_Mus1|SINE|Alu	-11956	NM_010592	16478	Mm.419851	NM_010592	ENSMUSG00000071076	Jund	Jund1	jun D proto-oncogene	protein-coding
mm_165744.1	chr3	107291303	107291304	+	1	NA	promoter-TSS (NM_146136)	promoter-TSS (NM_146136)	11	NM_146136	229699	Mm.38384	NM_146136	ENSMUSG00000027896	Slc16a4	AW146050|MCT 5	solute carrier family 16 (monocarboxylic acid transporters), member 4	protein-coding
mm_121924.1	chr14	23554813	23554823	-	1	NA	intron (NM_001253366, intron 5 of 29)	intron (NM_001253366, intron 5 of 29)	449387	NM_001253375	16531	Mm.343607	NM_010610	ENSMUSG00000063142	Kcnma1	5730414M22Rik|BKCa|MaxiK|Slo|Slo1|mSlo|mSlo1	potassium large conductance calcium-activated channel, subfamily M, alpha member 1	protein-coding
mm_152463.1	chr19	10920630	10920635	-	1	NA	promoter-TSS (NM_009580)	promoter-TSS (NM_009580)	-31	NM_009580	22786	Mm.24767	NM_009580	ENSMUSG00000024734	Zp1	-	zona pellucida glycoprotein 1	protein-coding
mm_129793.1	chr15	82852685	82852719	-	1	NA	exon (NM_013836, exon 2 of 5)	exon (NM_013836, exon 2 of 5)	45759	NR_027799	21378	Mm.417272	NR_027799		Tbrg3	TB-11	transforming growth factor beta regulated gene 3	ncRNA
mm_38324.1	chr4	137345254	137345261	-	1	NA	intron (NM_009861, intron 1 of 5)	intron (NM_009861, intron 1 of 5)	12502	NM_009861	12540	Mm.1022	NM_009861	ENSMUSG00000006699	Cdc42	AI747189|AU018915	cell division cycle 42	protein-coding
mm_94601.1	chr11	12053935	12053938	+	1	NA	Intergenic	Intergenic	-16516	NM_010345	14783	Mm.273117	NM_010345	ENSMUSG00000020176	Grb10	5730571D09Rik|AI325020|Meg1|mKIAA0207	growth factor receptor bound protein 10	protein-coding
mm_52847.1	chr6	121846718	121846742	+	1	NA	intron (NM_008645, intron 4 of 35)	B1_Mur1|SINE|Alu	8189	NM_008645	17836	Mm.1311	NM_008645	ENSMUSG00000059908	Mug1	-	murinoglobulin 1	protein-coding
mm_149871.1	chr19	25155792	25155807	+	1	NA	intron (NM_028785, intron 27 of 47)	intron (NM_028785, intron 27 of 47)	-81403	NM_181404	107351	Mm.260722	NM_181404	ENSMUSG00000032702	Kank1	A930031B09Rik|AU015049|AW121052|Ankrd15|D330024H06Rik|mKIAA0172	KN motif and ankyrin repeat domains 1	protein-coding
mm_8899.1	chr1	162984520	162984533	-	1	NA	promoter-TSS (NM_008030)	promoter-TSS (NM_008030)	2	NM_008030	14262	Mm.2900	NM_008030	ENSMUSG00000026691	Fmo3	AW111792	flavin containing monooxygenase 3	protein-coding
mm_13856.1	chr2	119695051	119695062	+	1	NA	intron (NM_030112, intron 2 of 17)	RSINE1|SINE|B4	19988	NM_030112	76246	Mm.33437	NM_030112	ENSMUSG00000027304	Rtf1	2900005O08Rik|6530416A09Rik|AI853581|AU043144|AW553985|Gtl7|cbp82	RTF1, Paf1/RNA polymerase II complex component	protein-coding
mm_168430.1	chr11	33754896	33754899	-	1	NA	intron (NM_001190885, intron 1 of 8)	LSU-rRNA_Hsa|rRNA|rRNA	88688	NM_027398	70357	Mm.252514	NM_027398	ENSMUSG00000053519	Kcnip1	KCHIP1|Kchip1.2	Kv channel-interacting protein 1	protein-coding
mm_2343.1	chr1	92859836	92859839	+	1	NA	3' UTR (NM_016696, exon 9 of 9)	3' UTR (NM_016696, exon 9 of 9)	9459	NR_029559	387167		NR_029559	ENSMUSG00000065470	Mir149	Mirn149|mir-149|mmu-mir-149	microRNA 149	ncRNA
mm_16159.1	chr2	172440566	172440630	+	1	NA	promoter-TSS (NM_025542)	promoter-TSS (NM_025542)	20	NM_025542	66404	Mm.25157	NM_025542	ENSMUSG00000027502	Rtfdc1	1700067C04Rik|2410001C21Rik|5730427M17Rik|AA589417	replication termination factor 2 domain containing 1	protein-coding
mm_96596.1	chr11	69090904	69090929	+	1	NA	3' UTR (NM_009497, exon 5 of 5)	3' UTR (NM_009497, exon 5 of 5)	2388	NM_009497	22318	Mm.28643	NM_009497	ENSMUSG00000020894	Vamp2	Syb-2|Syb2|sybII	vesicle-associated membrane protein 2	protein-coding
mm_120907.1	chr14	76084382	76084420	+	1	NA	Intergenic	Intergenic	26414	NM_026177	67467	Mm.260767	NM_026177	ENSMUSG00000022008	Gpalpp1	1200011I18Rik|Kiaa1704	GPALPP motifs containing 1	protein-coding
mm_42651.1	chr5	118765071	118765099	+	1	NA	3' UTR (NM_172424, exon 31 of 31)	3' UTR (NM_172424, exon 31 of 31)	-187254	NR_040694	74627	Mm.410828	NR_040694	ENSMUSG00000107144	4930413E15Rik	-	RIKEN cDNA 4930413E15 gene	ncRNA
mm_58033.1	chr6	136714113	136714114	-	1	NA	intron (NM_145067, intron 19 of 25)	intron (NM_145067, intron 19 of 25)	-52220	NM_025806	66857	Mm.3311	NM_025806	ENSMUSG00000030214	Plbd1	1100001H23Rik	phospholipase B domain containing 1	protein-coding
mm_143230.1	chr17	63451791	63451822	-	1	NA	intron (NM_015794, intron 4 of 8)	intron (NM_015794, intron 4 of 8)	48774	NM_015794	50758	Mm.136366	NM_015794	ENSMUSG00000023965	Fbxl17	6330576B01Rik|AI452053|BB073797|C130023C01Rik|Fbx13|Fbxo13	F-box and leucine-rich repeat protein 17	protein-coding
mm_122802.1	chr14	54554360	54554370	-	1	NA	promoter-TSS (NM_145462)	promoter-TSS (NM_145462)	-4	NM_145462	219072	Mm.202152	NM_145462	ENSMUSG00000022177	Haus4	9430093H08Rik|AU016300|D14Ertd500e	HAUS augmin-like complex, subunit 4	protein-coding
mm_108950.1	chr12	102354746	102354754	+	1	NA	intron (NM_177620, intron 4 of 9)	intron (NM_177620, intron 4 of 9)	71109	NM_001161365	217835	Mm.24145	NM_177620	ENSMUSG00000044456	Rin3	6430500K07|C86933	Ras and Rab interactor 3	protein-coding
mm_113902.1	chr13	49215661	49215676	+	1	NA	intron (NM_026738, intron 1 of 5)	CpG	358	NM_026738	68480	Mm.3336	NM_026738	ENSMUSG00000037960	Card19	1110007C09Rik|AI851695|Bincard	caspase recruitment domain family, member 19	protein-coding
mm_31574.1	chr4	57637817	57637846	+	1	NA	intron (NM_001304544, intron 1 of 8)	intron (NM_001304544, intron 1 of 8)	69583	NM_172868	242481	Mm.331630	NM_172868	ENSMUSG00000090053	Palm2	53-H12|B130066I24|R75368|pEN70	paralemmin 2	protein-coding
mm_97911.1	chr11	83490609	83490612	+	1	NA	intron (NM_027427, intron 7 of 15)	B2_Mm2|SINE|B2	17502	NM_027427	70439	Mm.181050	NM_027427	ENSMUSG00000020680	Taf15	2610111C21Rik|68kDa|TAFII68|Taf2n	TATA-box binding protein associated factor 15	protein-coding
mm_43766.1	chr5	140735532	140735548	+	1	NA	intron (NM_173405, intron 2 of 7)	CpG	11413	NM_173405	231842	Mm.491298	NM_173405	ENSMUSG00000050022	Amz1	5330426I05|6530401C20Rik	archaelysin family metallopeptidase 1	protein-coding
mm_89329.1	chr10	87932777	87932788	+	1	NA	3' UTR (NM_010512, exon 5 of 5)	3' UTR (NM_010512, exon 5 of 5)	-33889	NR_000040	22172	Mm.391420	NR_000040		Tyms-ps	-	thymidylate synthase, pseudogene	pseudo
mm_112663.1	chr13	16027084	16027095	+	1	NA	exon (NM_008380, exon 5 of 5)	exon (NM_008380, exon 5 of 5)	15238	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_8261.1	chr1	139255675	139255683	-	1	NA	intron (NM_133239, intron 5 of 11)	intron (NM_133239, intron 5 of 11)	121397	NM_133239	170788	Mm.95700	NM_133239	ENSMUSG00000063681	Crb1	7530426H14Rik|A930008G09Rik	crumbs family member 1, photoreceptor morphogenesis associated	protein-coding
mm_166131.1	chr4	155563265	155563274	+	1	NA	promoter-TSS (NM_001159637)	promoter-TSS (NM_001159637)	-546	NM_001159637	192185	Mm.28347	NM_138671	ENSMUSG00000029063	Nadk	4432404C02Rik|BC004012	NAD kinase	protein-coding
mm_90777.1	chr10	6916327	6916327	-	1	NA	intron (NM_001033391, intron 7 of 7)	intron (NM_001033391, intron 7 of 7)	63954	NM_001347225	320495	Mm.331674	NM_001033391	ENSMUSG00000064065	Ipcef1	A130090K04Rik	interaction protein for cytohesin exchange factors 1	protein-coding
mm_159349.1	chr3	68869824	68869824	+	1	NA	exon (NM_001167996, exon 1 of 1)	exon (NM_001167996, exon 1 of 1)	238	NM_001167996	68725	Mm.45741	NM_001167996	ENSMUSG00000046999	1110032F04Rik	AI115547	RIKEN cDNA 1110032F04 gene	protein-coding
mm_101344.1	chr11	23633593	23633601	-	1	NA	promoter-TSS (NM_001347242)	promoter-TSS (NM_001347242)	34	NM_001347242	71675	Mm.48031	NM_027860	ENSMUSG00000042208	0610010F05Rik	Kiaa1841|mKIAA1841	RIKEN cDNA 0610010F05 gene	protein-coding
mm_147097.1	chr18	35649570	35649589	-	1	NA	promoter-TSS (NM_027222)	promoter-TSS (NM_027222)	-212	NM_027222	69816	Mm.27252	NM_027222	ENSMUSG00000024353	Mzb1	2010001M09Rik|AV064572|PACAP|pERp1	marginal zone B and B1 cell-specific protein 1	protein-coding
mm_73412.1	chr8	106053010	106053028	+	1	NA	exon (NM_025518, exon 15 of 16)	exon (NM_025518, exon 15 of 16)	-6584	NM_010901	18021	Mm.383185	NM_010901	ENSMUSG00000031902	Nfatc3	C80703|D8Ertd281e|NFAT4|NFATx	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 3	protein-coding
mm_98651.1	chr11	96251675	96251696	+	1	NA	promoter-TSS (NR_037977)	promoter-TSS (NR_037977)	25	NR_037977	193022	Mm.169508	NR_037977		Gm53	-	predicted gene 53	ncRNA
mm_63741.1	chr7	130911409	130911413	+	1	NA	3' UTR (NM_133942, exon 10 of 10)	3' UTR (NM_133942, exon 10 of 10)	3143	NR_106028	102466219		NR_106028	ENSMUSG00000104914	Mir7061	mmu-mir-7061	microRNA 7061	ncRNA
mm_67018.1	chr7	65635982	65635993	-	1	NA	Intergenic	Intergenic	-8911	NM_172310	272396	Mm.35127	NM_172310	ENSMUSG00000030515	Tarsl2	A530046H20Rik	threonyl-tRNA synthetase-like 2	protein-coding
mm_85227.1	chr9	97111118	97111159	-	1	NA	promoter-TSS (NM_138756)	promoter-TSS (NM_138756)	-97	NM_138756	192287	Mm.228067	NM_138756	ENSMUSG00000032449	Slc25a36	C330005L02Rik	solute carrier family 25, member 36	protein-coding
mm_136891.1	chr17	13011208	13011211	+	1	NA	intron (NM_013671, intron 3 of 4)	intron (NM_013671, intron 3 of 4)	3370	NM_013671	20656	Mm.290876	NM_013671	ENSMUSG00000006818	Sod2	MnSOD|Sod-2	superoxide dismutase 2, mitochondrial	protein-coding
mm_87571.1	chr10	56387521	56387524	+	1	NA	intron (NM_010288, intron 1 of 1)	intron (NM_010288, intron 1 of 1)	10222	NM_010288	14609	Mm.378921	NM_010288	ENSMUSG00000050953	Gja1	AU042049|AW546267|Cnx43|Cx43|Cx43alpha1|Gja-1|Npm1|connexin43	gap junction protein, alpha 1	protein-coding
mm_139563.1	chr17	56990261	56990267	+	1	NA	promoter-TSS (NM_017393)	promoter-TSS (NM_017393)	0	NM_017393	53895	Mm.287892	NM_017393	ENSMUSG00000002660	Clpp	AU019820|D17Wsu160e	caseinolytic mitochondrial matrix peptidase proteolytic subunit	protein-coding
mm_139795.1	chr17	66005627	66005648	+	1	NA	intron (NM_001025572, intron 8 of 12)	intron (NM_001025572, intron 8 of 12)	-54450	NM_023053	65960	Mm.10153	NM_023053	ENSMUSG00000024098	Twsg1	1810013J15Rik|9030422N06Rik|AW552143|D17Ertd403e|Tsg|Twg	twisted gastrulation BMP signaling modulator 1	protein-coding
mm_57172.1	chr6	122847752	122847786	-	1	NA	3' UTR (NM_009779, exon 2 of 2)	3' UTR (NM_009779, exon 2 of 2)	8388	NM_009779	12267	Mm.2408	NM_009779	ENSMUSG00000040552	C3ar1	AZ3B|C3AR|HNFAG09	complement component 3a receptor 1	protein-coding
mm_45241.1	chr5	53999492	53999502	-	1	NA	intron (NM_001081103, intron 1 of 11)	intron (NM_001081103, intron 1 of 11)	974	NM_001081103	116873	Mm.265985	NM_054083	ENSMUSG00000039156	Stim2	-	stromal interaction molecule 2	protein-coding
mm_43132.1	chr5	125389269	125389273	+	1	NA	intron (NM_019639, intron 1 of 1)	CpG	746	NM_019639	22190	Mm.331	NM_019639	ENSMUSG00000008348	Ubc	2700054O04Rik|AI194771|Rps27a|TI-225|Uba52|Ubb	ubiquitin C	protein-coding
mm_151974.1	chr19	5826768	5826788	-	1	NA	non-coding (NR_131212, exon 1 of 1)	non-coding (NR_131212, exon 1 of 1)	18700	NR_131212	66961	Mm.281895	NR_003513	ENSMUSG00000092274	Neat1	2310043N10Rik|VINC	nuclear paraspeckle assembly transcript 1 (non-protein coding)	ncRNA
mm_143761.1	chr17	81625151	81625153	-	1	NA	intron (NR_104580, intron 2 of 8)	intron (NR_104580, intron 2 of 8)	113235	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_120994.1	chr14	79426411	79426453	+	1	NA	promoter-TSS (NM_001024135)	promoter-TSS (NM_001024135)	-79	NM_001024135	211255	Mm.284526	NM_001024135	ENSMUSG00000043881	Kbtbd7	1110008P08Rik|AU045792|Gm295	kelch repeat and BTB (POZ) domain containing 7	protein-coding
mm_130746.1	chr15	101258417	101258426	-	1	NA	Intergenic	Intergenic	-8425	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_142249.1	chr17	37483544	37483559	-	1	NA	promoter-TSS (NM_008204)	promoter-TSS (NM_008204)	3	NM_001347387	14990	Mm.329041	NM_008204	ENSMUSG00000016283	H2-M2	H-2M2|Thy19.4	histocompatibility 2, M region locus 2	protein-coding
mm_100028.1	chr11	114912048	114912083	+	1	NA	Intergenic	Intergenic	22024	NM_170758	217303	Mm.294439	NM_170758	ENSMUSG00000034652	Cd300a	B230315M08Rik|Clm8|LMIR1|MAIR-I|MAIR-Ia|MMAC8|Pigr4|mcpir1	CD300A molecule	protein-coding
mm_41690.1	chr5	100570233	100570249	+	1	NA	intron (NM_139198, intron 1 of 4)	intron (NM_139198, intron 1 of 4)	1964	NM_139198	231507	Mm.34609	NM_139198	ENSMUSG00000029322	Plac8	C15|D5Wsu111e	placenta-specific 8	protein-coding
mm_36207.1	chr4	62434634	62434644	-	1	NA	promoter-TSS (NM_153504)	promoter-TSS (NM_153504)	87	NM_153504	76072	Mm.169565	NM_153504	ENSMUSG00000063851	Rnf183	5830442J12Rik	ring finger protein 183	protein-coding
mm_96734.1	chr11	69758857	69758869	+	1	NA	promoter-TSS (NM_001291068)	promoter-TSS (NM_001291068)	-230	NM_001291068	20020	Mm.16533	NM_009089	ENSMUSG00000005198	Polr2a	220kDa|Rpb1|Rpo2-1	polymerase (RNA) II (DNA directed) polypeptide A	protein-coding
mm_170300.1	chr18	33394897	33394897	+	1	NA	Intergenic	Intergenic	68737	NM_001267717	27528	Mm.407415	NM_053078	ENSMUSG00000042834	Nrep	AI325076|D0H4S114|Harp|P311|PTZ17|SEZ17	neuronal regeneration related protein	protein-coding
mm_160818.1	chr11	29547907	29547907	+	1	NA	promoter-TSS (NM_028504)	promoter-TSS (NM_028504)	-43	NM_028504	73324	Mm.69388	NM_028504	ENSMUSG00000020461	Clhc1	1700034F02Rik	clathrin heavy chain linker domain containing 1	protein-coding
mm_132578.1	chr16	38244997	38245011	+	1	NA	3' UTR (NM_019827, exon 11 of 11)	3' UTR (NM_019827, exon 11 of 11)	49820	NM_010936	18171	Mm.8509	NM_010936	ENSMUSG00000022809	Nr1i2	PXR|PXR.1|PXR.2|PXR1|SXR|mPXR	nuclear receptor subfamily 1, group I, member 2	protein-coding
mm_90582.1	chr10	128268657	128268722	+	1	NA	5' UTR (NM_133997, exon 1 of 2)	5' UTR (NM_133997, exon 1 of 2)	692	NM_133997	103161	Mm.26513	NM_133997	ENSMUSG00000047631	Apof	AI255964	apolipoprotein F	protein-coding
mm_160022.1	chr6	130129899	130129899	-	1	NA	promoter-TSS (NM_053151)	promoter-TSS (NM_053151)	-1	NM_001101620	16639	Mm.439698	NM_010650	ENSMUSG00000089727	Klra8	Cmv-1|Cmv1|Ly49h|Ly49u<129>	killer cell lectin-like receptor, subfamily A, member 8	protein-coding
mm_130427.1	chr15	98145626	98145667	-	1	NA	promoter-TSS (NM_030121)	promoter-TSS (NM_030121)	56	NM_030121	78541	Mm.200766	NM_030121	ENSMUSG00000048175	Asb8	4930539L19Rik|AI788835|C430011H06Rik	ankyrin repeat and SOCS box-containing 8	protein-coding
mm_29489.1	chr3	115715032	115715062	-	1	NA	promoter-TSS (NM_007901)	promoter-TSS (NM_007901)	8	NM_007901	13609	Mm.982	NM_007901	ENSMUSG00000045092	S1pr1	AI849002|Edg1|Lpb1|S1p|S1p1	sphingosine-1-phosphate receptor 1	protein-coding
mm_148993.1	chr19	8618161	8618184	+	1	NA	5' UTR (NM_008766, exon 1 of 10)	5' UTR (NM_008766, exon 1 of 10)	176	NM_008766	18399	Mm.30090	NM_008766	ENSMUSG00000024650	Slc22a6	NKT|Oat1|Orctl1|mOat1	solute carrier family 22 (organic anion transporter), member 6	protein-coding
mm_115335.1	chr13	112481464	112481476	+	1	NA	exon (NM_010560, exon 5 of 17)	exon (NM_010560, exon 5 of 17)	17400	NM_010560	16195	Mm.4364	NM_010560	ENSMUSG00000021756	Il6st	5133400A03Rik|AA389424|BB405851|CD130|D13Ertd699e|gp130	interleukin 6 signal transducer	protein-coding
mm_114097.1	chr13	54717609	54717617	+	1	NA	exon (NM_001033364, exon 8 of 32)	exon (NM_001033364, exon 8 of 32)	16150	NM_001033364	268663	Mm.315382	NM_001033364	ENSMUSG00000034918	Cdhr2	Gm624|PC-LKC|Pcdh24	cadherin-related family member 2	protein-coding
mm_48383.1	chr5	139774429	139774439	-	1	NA	exon (NM_026748, exon 2 of 47)	exon (NM_026748, exon 2 of 47)	1244	NM_026748	68510	Mm.292942	NM_026748	ENSMUSG00000029547	Ints1	1110015K06Rik	integrator complex subunit 1	protein-coding
mm_150819.1	chr19	44406684	44406731	+	1	NA	exon (NM_009127, exon 2 of 6)	exon (NM_009127, exon 2 of 6)	1002	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_151476.1	chr19	58673805	58673825	+	1	NA	exon (NM_026925, exon 5 of 13)	exon (NM_026925, exon 5 of 13)	3450	NM_026925	69060	Mm.20407	NM_026925	ENSMUSG00000046008	Pnlip	1810007A24Rik|PL|PTL	pancreatic lipase	protein-coding
mm_112763.1	chr13	19352349	19352366	+	1	NA	Intergenic	Intergenic	43456	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_159222.1	chr2	127854623	127854623	+	1	NA	promoter-TSS (NM_028765)	promoter-TSS (NM_028765)	-5	NM_028765	74121	Mm.244835	NM_028765	ENSMUSG00000027380	Acoxl	1200014P05Rik|AV025673	acyl-Coenzyme A oxidase-like	protein-coding
mm_30055.1	chr3	136669893	136669937	-	1	NA	promoter-TSS (NM_001293622)	promoter-TSS (NM_001293622)	-151	NM_008913	19055	Mm.331389	NM_008913	ENSMUSG00000028161	Ppp3ca	2900074D19Rik|CN|Caln|Calna|CnA	protein phosphatase 3, catalytic subunit, alpha isoform	protein-coding
mm_138717.1	chr17	36837124	36837211	+	1	NA	promoter-TSS (NM_001286727)	promoter-TSS (NM_001286727)	21	NM_001286726	22670	Mm.34587	NM_030698	ENSMUSG00000024457	Trim26	AI462198|Zfp173|Zfp1736	tripartite motif-containing 26	protein-coding
mm_123570.1	chr14	66911063	66911073	-	1	NA	promoter-TSS (NM_175498)	promoter-TSS (NM_175498)	-140	NM_175498	239157	Mm.44358	NM_175498	ENSMUSG00000046204	Pnma2	A830049P17Rik|mKIAA0883	paraneoplastic antigen MA2	protein-coding
mm_80734.1	chr9	94669620	94669641	+	1	NA	promoter-TSS (NM_177909)	promoter-TSS (NM_177909)	-262	NM_177909	331004	Mm.326125	NM_177909	ENSMUSG00000031129	Slc9a9	5730527A11Rik|9930105B05|AI854429|Nhe9	solute carrier family 9 (sodium/hydrogen exchanger), member 9	protein-coding
mm_12263.1	chr2	68959840	68959850	+	1	NA	intron (NM_172856, intron 3 of 9)	intron (NM_172856, intron 3 of 9)	98404	NM_001347161	241447	Mm.222222	NM_172856	ENSMUSG00000027035	Cers6	4732462C07Rik|AW544719|Lass6|T1L	ceramide synthase 6	protein-coding
mm_108796.1	chr12	91588479	91588493	+	1	NA	intron (NM_175335, intron 1 of 8)	CpG	1163	NM_031391	83602	Mm.275728	NM_031391	ENSMUSG00000020962	Gtf2a1	6330549H03Rik|AA536742|AA959775|AW060250|TfIIAa/b|Tfiia1	general transcription factor II A, 1	protein-coding
mm_24536.1	chr3	93279547	93279557	+	1	NA	Intergenic	Intergenic	-40197	NM_133698	68723	Mm.208047	NM_133698	ENSMUSG00000041991	Hrnr	1110033K19Rik|A530063N20Rik|S100a18	hornerin	protein-coding
mm_84930.1	chr9	82900802	82900844	-	1	NA	exon (NM_001081216, exon 23 of 40)	exon (NM_001081216, exon 23 of 40)	71017	NM_022986	65099	Mm.41415	NM_022986	ENSMUSG00000032251	Irak1bp1	4921528N06Rik|AI851240|Aabp3|Aip70|Simpl	interleukin-1 receptor-associated kinase 1 binding protein 1	protein-coding
mm_36986.1	chr4	109666729	109666765	-	1	NA	promoter-TSS (NM_001301368)	promoter-TSS (NM_001301368)	9	NM_001301368	12580	Mm.1912	NM_007671	ENSMUSG00000028551	Cdkn2c	C77269|INK4c|p18|p18-INK4c|p18-INK6|p18INK4c	cyclin-dependent kinase inhibitor 2C (p18, inhibits CDK4)	protein-coding
mm_168877.1	chr12	40884508	40884512	-	1	NA	Intergenic	Intergenic	-139580	NM_053122	93757	Mm.363813	NM_053122	ENSMUSG00000056899	Immp2l	AI853880|IMP2	IMP2 inner mitochondrial membrane peptidase-like (S. cerevisiae)	protein-coding
mm_8895.1	chr1	162898486	162898498	-	1	NA	intron (NM_018881, intron 1 of 8)	intron (NM_018881, intron 1 of 8)	220	NM_018881	55990	Mm.10929	NM_018881	ENSMUSG00000040170	Fmo2	2310008D08Rik|2310042I22Rik|AW107733	flavin containing monooxygenase 2	protein-coding
mm_28022.1	chr3	83046106	83046143	-	1	NA	exon (NM_181849, exon 3 of 8)	exon (NM_181849, exon 3 of 8)	3739	NM_181849	110135	Mm.30063	NM_181849	ENSMUSG00000033831	Fgb	2510049G14Rik	fibrinogen beta chain	protein-coding
mm_51407.1	chr6	78373416	78373422	+	1	NA	TTS (NM_011036)	TTS (NM_011036)	2534	NM_011036	18489	Mm.2553	NM_011036	ENSMUSG00000071356	Reg3b	HIP|PAP1|Pap|REG-III	regenerating islet-derived 3 beta	protein-coding
mm_64674.1	chr7	4500838	4500854	-	1	NA	intron (NM_029834, intron 1 of 21)	intron (NM_029834, intron 1 of 21)	834	NM_029834	232807	Mm.360391	NM_029834	ENSMUSG00000019254	Ppp1r12c	2410197A17Rik|AI839747|B430101M08|Mbs85	protein phosphatase 1, regulatory (inhibitor) subunit 12C	protein-coding
mm_3740.1	chr1	155161539	155161544	+	1	NA	intron (NM_021433, intron 1 of 7)	B1_Mur4|SINE|Alu	2838	NM_021433	58244	Mm.66264	NM_021433	ENSMUSG00000026470	Stx6	2310039E05Rik|2410005I16Rik|AA437559|AI415714|AI845861	syntaxin 6	protein-coding
mm_159395.1	chr3	94658838	94658838	-	1	NA	promoter-TSS (NM_011656)	promoter-TSS (NM_011656)	34	NM_001293728	22156	Mm.10214	NM_011656	ENSMUSG00000005968	Tuft1	-	tuftelin 1	protein-coding
mm_32834.1	chr4	117787252	117787262	+	1	NA	Intergenic	Intergenic	-21591	NM_029416	75753	Mm.3848	NM_029416	ENSMUSG00000048626	Klf17	7420700M05Rik|AA420409|AU043468|C85123|D4Ertd561e|Gzf|Zfp393	Kruppel-like factor 17	protein-coding
mm_151801.1	chr19	5424769	5424811	-	1	NA	promoter-TSS (NM_001256515)	promoter-TSS (NM_001256515)	189	NM_024176	66556	Mm.275446	NM_024176	ENSMUSG00000024914	Drap1	2310074H19Rik|NC2-alpha	Dr1 associated protein 1 (negative cofactor 2 alpha)	protein-coding
mm_144648.1	chr18	33889473	33889509	+	1	NA	intron (NM_013512, intron 4 of 23)	intron (NM_013512, intron 4 of 23)	94599	NR_038151	69749	Mm.248787	NR_038151	ENSMUSG00000087590	Epb41l4aos	2410004N09Rik|Epb4.1l4aos	erythrocyte membrane protein band 4.1 like 4a, opposite strand	ncRNA
mm_60863.1	chr7	45897401	45897434	+	1	NA	promoter-TSS (NM_001291064)	promoter-TSS (NM_001291064)	348	NM_144801	70209	Mm.163766	NM_144801	ENSMUSG00000002781	Tmem143	2310076O21Rik|AI481604	transmembrane protein 143	protein-coding
mm_86810.1	chr10	20341227	20341230	+	1	NA	3' UTR (NM_001025393, exon 12 of 12)	3' UTR (NM_001025393, exon 12 of 12)	-6591	NM_027930	71804	Mm.262151	NM_027930	ENSMUSG00000019992	Mtfr2	2610016C23Rik|4933412C16Rik|Dufd1|Fam54a	mitochondrial fission regulator 2	protein-coding
mm_51708.1	chr6	86668930	86668935	+	1	NA	intron (NM_010751, intron 1 of 5)	CpG	227	NM_010751	17119	Mm.279580	NM_010751	ENSMUSG00000001156	Mxd1	AW122478|Mad|Mad1	MAX dimerization protein 1	protein-coding
mm_53719.1	chr6	143642820	143642825	+	1	NA	intron (NR_045732, intron 1 of 4)	intron (NR_045732, intron 1 of 4)	8466	NR_045732	73425	Mm.417844	NR_045732	ENSMUSG00000086887	1700060C16Rik	-	RIKEN cDNA 1700060C16 gene	ncRNA
mm_17764.1	chr2	32788421	32788443	-	1	NA	3' UTR (NM_001113569, exon 20 of 20)	3' UTR (NM_001113569, exon 20 of 20)	-4027	NM_025619	227736	Mm.441499	NM_025619	ENSMUSG00000038987	Cfap157	1700019L03Rik	cilia and flagella associated protein 157	protein-coding
mm_60074.1	chr7	33743782	33743788	+	1	NA	promoter-TSS (NM_001099329)	promoter-TSS (NM_001099329)	-14	NM_001099329	100043860	Mm.389875	NM_001099329	ENSMUSG00000078753	Scgb1b24	Abpa24|Gm12769|OTTMUSG00000008385	secretoglobin, family 1B, member 24	protein-coding
mm_115730.1	chr13	17744053	17744055	-	1	NA	intron (NM_027118, intron 7 of 13)	PB1D10|SINE|Alu	-3419	NR_035412	100316665		NR_035412	ENSMUSG00000080574	Mir466i	Mirn466i|mmu-mir-466i	microRNA 466i	ncRNA
mm_41440.1	chr5	90904439	90904445	+	1	NA	intron (NM_009140, intron 3 of 3)	intron (NM_009140, intron 3 of 3)	543	NM_009140	20310	Mm.4979	NM_009140	ENSMUSG00000058427	Cxcl2	CINC-2a|GROb|Gro2|MIP-2|MIP-2a|Mgsa-b|Mip2|Scyb|Scyb2	chemokine (C-X-C motif) ligand 2	protein-coding
mm_148001.1	chr18	67724287	67724307	-	1	NA	intron (NM_008977, intron 1 of 9)	CpG	324	NM_001127177	19255	Mm.260433	NM_008977	ENSMUSG00000024539	Ptpn2	AI325124|Ptpt|TC-PTP	protein tyrosine phosphatase, non-receptor type 2	protein-coding
mm_157523.1	chrX	50942763	50942773	-	1	NA	promoter-TSS (NM_001190332)	promoter-TSS (NM_001190332)	-58	NM_001190332	385354	Mm.393050	NM_001190332	ENSMUSG00000036131	Frmd7	EG665849|Gm1533	FERM domain containing 7	protein-coding
mm_148664.1	chr19	5601855	5601916	+	1	NA	promoter-TSS (NM_026616)	promoter-TSS (NM_026616)	12	NM_026616	68209	Mm.246200	NM_026616	ENSMUSG00000024925	Rnaseh2c	1500026D16Rik|AYP1	ribonuclease H2, subunit C	protein-coding
mm_130276.1	chr15	96699679	96699684	-	1	NA	promoter-TSS (NM_175121)	promoter-TSS (NM_175121)	17	NM_175121	67760	Mm.46754	NM_175121	ENSMUSG00000022462	Slc38a2	5033402L14Rik|AI316867|ATA2|SAT2|mKIAA1382	solute carrier family 38, member 2	protein-coding
mm_36911.1	chr4	108051878	108051918	-	1	NA	intron (NM_011327, intron 14 of 15)	ORR1F|LTR|ERVL-MaLR	-19808	NM_172874	242608	Mm.74710	NM_172874	ENSMUSG00000028600	Podn	9430070G18|Pcan|SLRR5A	podocan	protein-coding
mm_129892.1	chr15	83555682	83555743	-	1	NA	promoter-TSS (NM_001030014)	promoter-TSS (NM_001030014)	-1	NM_001030014	223722	Mm.37560	NM_001030014	ENSMUSG00000048755	Mcat	AI225907|BC025519	malonyl CoA:ACP acyltransferase (mitochondrial)	protein-coding
mm_52162.1	chr6	98020401	98020431	+	1	NA	3' UTR (NM_001178049, exon 10 of 10)	3' UTR (NM_001178049, exon 10 of 10)	28633	NM_008601	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_38913.1	chr4	149996398	149996415	-	1	NA	intron (NM_173371, intron 1 of 4)	intron (NM_173371, intron 1 of 4)	6830	NM_001291004	100198	Mm.22183	NM_173371	ENSMUSG00000028980	H6pd	AI785303|G6pd1|Gpd-1|Gpd1	hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase)	protein-coding
mm_37506.1	chr4	123841968	123841980	-	1	NA	Intergenic	Intergenic	54099	NM_183163	230726	Mm.37334	NM_183163	ENSMUSG00000043333	Rhbdl2	9130416B15|RRP2	rhomboid, veinlet-like 2 (Drosophila)	protein-coding
mm_144024.1	chr17	90036685	90036713	-	1	NA	3' UTR (NM_001347419, exon 3 of 3)	3' UTR (NM_001347419, exon 3 of 3)	51669	NM_001346962	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_30998.1	chr4	40143461	40143502	+	1	NA	5' UTR (NM_007386, exon 1 of 21)	5' UTR (NM_007386, exon 1 of 21)	216	NM_007386	11428	Mm.331547	NM_007386	ENSMUSG00000028405	Aco1	Aco-1|Irebp|Irp1	aconitase 1	protein-coding
mm_14398.1	chr2	130038451	130038476	+	1	NA	exon (NM_009374, exon 9 of 13)	exon (NM_009374, exon 9 of 13)	-22055	NR_105757	102466628		NR_105757	ENSMUSG00000098347	Mir6339	Gm27848|mmu-mir-6339	microRNA 6339	ncRNA
mm_161939.1	chr19	3992809	3992809	+	1	NA	promoter-TSS (NM_011533)	promoter-TSS (NM_011533)	57	NM_011533	109575	Mm.246555	NM_011533	ENSMUSG00000037477	Tbx10	Dc|Tbx13|Tbx7	T-box 10	protein-coding
mm_108226.1	chr12	77238094	77238122	+	1	NA	promoter-TSS (NM_016893)	promoter-TSS (NM_016893)	4	NM_016893	53618	Mm.35628	NM_016893	ENSMUSG00000021065	Fut8	-	fucosyltransferase 8	protein-coding
mm_151931.1	chr19	5800286	5800288	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	2385	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_37535.1	chr4	124936853	124936924	-	1	NA	promoter-TSS (NM_177573)	promoter-TSS (NM_177573)	29	NM_026560	52276	Mm.28038	NM_026560	ENSMUSG00000028873	Cdca8	4831429J16Rik|AU044747|BOR|Borealin|D4Ertd421e|DasraB|MESRGP	cell division cycle associated 8	protein-coding
mm_117609.1	chr13	91223956	91223994	-	1	NA	promoter-TSS (NM_025770)	promoter-TSS (NM_025770)	12	NM_025770	66795	Mm.235385	NM_025770	ENSMUSG00000021619	Atg10	5330424L23Rik|5430428K15Rik|AI852123|APG10|Agp10|Apg10l|Apg10p|Atg10l	autophagy related 10	protein-coding
mm_157136.1	chrX	9456990	9457054	-	1	NA	exon (NM_007807, exon 4 of 13)	exon (NM_007807, exon 4 of 13)	12302	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_111901.1	chr12	108761331	108761342	-	1	NA	Intergenic	Intergenic	-31975	NM_009537	22632	Mm.3868	NM_009537	ENSMUSG00000021264	Yy1	AW488674|NF-E1	YY1 transcription factor	protein-coding
mm_48532.1	chr5	142904177	142904207	-	1	NA	exon (NM_007393, exon 5 of 6)	exon (NM_007393, exon 5 of 6)	2562	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_73354.1	chr8	105455277	105455287	+	1	NA	exon (NM_001170788, exon 10 of 14)	exon (NM_001170788, exon 10 of 14)	16140	NM_026481	67971	Mm.29358	NM_026481	ENSMUSG00000014846	Tppp3	2700055K07Rik|CGI-38|Ceacam9|mmCGM8	tubulin polymerization-promoting protein family member 3	protein-coding
mm_109562.1	chr12	111944604	111944615	+	1	NA	promoter-TSS (NR_029464)	promoter-TSS (NR_029464)	-127	NR_029464	77675	Mm.98331	NR_029464		5033406O09Rik	9130204G15Rik	RIKEN cDNA 5033406O09 gene	ncRNA
mm_33829.1	chr4	135626691	135626701	+	1	NA	promoter-TSS (NR_027909)	promoter-TSS (NR_027909)	41	NR_027909	73937	Mm.292326	NM_028688	ENSMUSG00000086788	1700029M20Rik	4930406E24Rik	RIKEN cDNA 1700029M20 gene	ncRNA
mm_37458.1	chr4	123444887	123444899	-	1	NA	exon (NM_001199137, exon 46 of 93)	exon (NM_001199137, exon 46 of 93)	-32982	NM_001167918	442834	Mm.483803	NM_001167918		D830031N03Rik	Kiaa0754|mKIAA0754	RIKEN cDNA D830031N03 gene	protein-coding
mm_156089.1	chrX	110815683	110815692	+	1	NA	3' UTR (NM_008901, exon 1 of 1)	3' UTR (NM_008901, exon 1 of 1)	1308	NM_008901	18994	Mm.56946	NM_008901	ENSMUSG00000056854	Pou3f4	Brn-4|Brn4|OTF-9|Otf9|Slf|oct-9	POU domain, class 3, transcription factor 4	protein-coding
mm_118483.1	chr14	12189949	12189953	+	1	NA	promoter-TSS (NM_001347593)	promoter-TSS (NM_001347593)	8	NM_001347593	19270	Mm.431266	NM_008981	ENSMUSG00000021745	Ptprg	5430405N12Rik|AW046354|AW549872|RPTPgamma	protein tyrosine phosphatase, receptor type, G	protein-coding
mm_159024.1	chr1	173215519	173215519	+	1	NA	promoter-TSS (NM_146881)	promoter-TSS (NM_146881)	-88	NM_146881	258881	Mm.377733	NM_146881	ENSMUSG00000049456	Olfr1404	MOR267-2	olfactory receptor 1404	protein-coding
mm_40197.1	chr5	36868585	36868685	+	1	NA	promoter-TSS (NM_172994)	promoter-TSS (NM_172994)	65	NM_172994	269643	Mm.41694	NM_172994	ENSMUSG00000029120	Ppp2r2c	6330548O06Rik|IMYPNO|IMYPNO1|PR52	protein phosphatase 2, regulatory subunit B, gamma	protein-coding
mm_161043.1	chr12	34528431	34528431	-	1	NA	intron (NM_001271386, intron 3 of 27)	intron (NM_001271386, intron 3 of 27)	458	NM_024124	79221	Mm.310551	NM_024124	ENSMUSG00000004698	Hdac9	AV022454|D030072B18Rik|HD7B|HD9|HDRP|Hdac7b|Mitr|mKIAA0744	histone deacetylase 9	protein-coding
mm_171127.1	chr3	144947821	144947827	+	1	NA	Intergenic	RLTR9F|LTR|ERVK	-15295	NM_001033199	99709	Mm.440040	NM_001033199	ENSMUSG00000074195	Clca4b	AI747448|Clca7	chloride channel accessory 4B	protein-coding
mm_76013.1	chr8	73171729	73171733	-	1	NA	intron (NM_001317391, intron 3 of 15)	intron (NM_001317391, intron 3 of 15)	155219	NR_039551	100628574		NR_039551	ENSMUSG00000093140	Mir28b	mmu-mir-28b	microRNA 28b	ncRNA
mm_114353.1	chr13	60939978	60939997	+	1	NA	exon (NM_009411, exon 4 of 5)	exon (NM_009411, exon 4 of 5)	1948	NM_009411	21984	Mm.2372	NM_009411	ENSMUSG00000033834	Tpbpa	AV033951|Tb-1|Tb1|Tpbp|b2b1247Clo	trophoblast specific protein alpha	protein-coding
mm_23547.1	chr3	61366096	61366106	+	1	NA	3' UTR (NM_028712, exon 1 of 1)	3' UTR (NM_028712, exon 1 of 1)	1594	NM_028712	74012	Mm.422674	NM_028712	ENSMUSG00000036894	Rap2b	4021402C18Rik|AA408554	RAP2B, member of RAS oncogene family	protein-coding
mm_165154.1	chr2	21986195	21986195	+	1	NA	Intergenic	ERVB4_1B-LTR_MM|LTR|ERVK	-241308	NM_148413	667663	Mm.330033	NM_148413	ENSMUSG00000025716	Myo3a	9030416P08Rik	myosin IIIA	protein-coding
mm_165113.1	chr19	58673122	58673127	+	1	NA	exon (NM_026925, exon 4 of 13)	exon (NM_026925, exon 4 of 13)	2759	NM_026925	69060	Mm.20407	NM_026925	ENSMUSG00000046008	Pnlip	1810007A24Rik|PL|PTL	pancreatic lipase	protein-coding
mm_45560.1	chr5	73191849	73191922	-	1	NA	intron (NM_028194, intron 3 of 62)	intron (NM_028194, intron 3 of 62)	64733	NM_028194	72313	Mm.260594	NM_028194	ENSMUSG00000070733	Fryl	2010313D22Rik|2310004H21Rik|2510002A14Rik|9030227G01Rik|mKIAA0826	FRY like transcription coactivator	protein-coding
mm_89752.1	chr10	99266125	99266150	+	1	NA	exon (NM_026268, exon 3 of 3)	exon (NM_026268, exon 3 of 3)	2906	NM_026268	67603	Mm.1791	NM_026268	ENSMUSG00000019960	Dusp6	1300019I03Rik|MKP-3|MKP3|PYST1	dual specificity phosphatase 6	protein-coding
mm_78068.1	chr9	15306253	15306268	+	1	NA	promoter-TSS (NM_001199485)	promoter-TSS (NM_001199485)	46	NM_027261	75316	Mm.354115	NM_026541	ENSMUSG00000031939	Taf1d	2810003M17Rik|4930553M18Rik|5930426I11Rik|Josd3|TAF(I)41|TAFI41	TATA-box binding protein associated factor, RNA polymerase I, D	protein-coding
mm_153604.1	chr19	43890593	43890610	-	1	NA	intron (NM_028029, intron 4 of 15)	intron (NM_028029, intron 4 of 15)	-10833	NM_001306088	71972	Mm.159024	NM_028029	ENSMUSG00000025195	Dnmbp	2410003L07Rik|2410003M15Rik|TUBA	dynamin binding protein	protein-coding
mm_148223.1	chr18	80340982	80340984	-	1	NA	intron (NM_001190373, intron 1 of 3)	intron (NM_001190373, intron 1 of 3)	23271	NM_001190373	240444	Mm.279568	NM_001190373	ENSMUSG00000059852	Kcng2	AA591524	potassium voltage-gated channel, subfamily G, member 2	protein-coding
mm_120955.1	chr14	77156831	77156843	+	1	NA	promoter-TSS (NM_172813)	promoter-TSS (NM_172813)	74	NM_172813	239188	Mm.441158	NM_172813	ENSMUSG00000022012	Enox1	B230207J08|D230005D02Rik	ecto-NOX disulfide-thiol exchanger 1	protein-coding
mm_172537.1	chr7	95187991	95187991	+	1	NA	Intergenic	L1Md_T|LINE|L1	-983253	NM_001310762	23966	Mm.254610	NM_011858	ENSMUSG00000048078	Tenm4	Doc4|ELM2|Odz4|R75022|Ten-m4|l(7)-3Rn|l7Rn3|mKIAA1302	teneurin transmembrane protein 4	protein-coding
mm_88424.1	chr10	77225720	77225729	+	1	NA	Intergenic	Intergenic	33499	NR_026944	100169878	Mm.420901	NR_026944	ENSMUSG00000078444	Gm10941	ENSMUSG00000078444	predicted gene 10941	ncRNA
mm_111839.1	chr12	107915025	107915033	-	1	NA	3' UTR (NM_021399, exon 3 of 3)	3' UTR (NM_021399, exon 3 of 3)	88385	NM_001079883	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_31480.1	chr4	52439225	52439232	+	1	NA	promoter-TSS (NR_045175)	promoter-TSS (NR_045175)	7	NM_001301412	14211	Mm.2999	NM_008017	ENSMUSG00000028312	Smc2	5730502P04Rik|AI255214|AW545314|CAP-E|CAPE|Fin16|SMC-2|Smc2l1	structural maintenance of chromosomes 2	protein-coding
mm_72585.1	chr8	84237313	84237331	+	1	NA	promoter-TSS (NM_172503)	promoter-TSS (NM_172503)	-280	NM_172503	212168	Mm.117094	NM_172503	ENSMUSG00000035671	Zswim4	D330002I24|E130119J17Rik	zinc finger SWIM-type containing 4	protein-coding
mm_89687.1	chr10	97565553	97565564	+	1	NA	promoter-TSS (NM_008524)	promoter-TSS (NM_008524)	57	NM_008524	17022	Mm.18888	NM_008524	ENSMUSG00000036446	Lum	Ldc|SLRR2D	lumican	protein-coding
mm_162034.1	chr19	55240987	55240987	-	1	NA	exon (NM_001081076, exon 1 of 21)	exon (NM_001081076, exon 1 of 21)	249	NM_001081076	73707	Mm.489987	NM_001081076	ENSMUSG00000055523	Gucy2g	2410077I05Rik|GC-G	guanylate cyclase 2g	protein-coding
mm_162213.1	chrX	136741755	136741755	-	1	NA	promoter-TSS (NM_019768)	promoter-TSS (NM_019768)	-146	NM_019768	56397	Mm.27218	NM_019768	ENSMUSG00000031422	Morf4l2	2410017O14Rik|Mrgx|Sid393p|mKIAA0026	mortality factor 4 like 2	protein-coding
mm_33256.1	chr4	127168759	127168779	+	1	NA	promoter-TSS (NM_198618)	promoter-TSS (NM_198618)	-435	NM_198618	242667	Mm.331885	NM_198618	ENSMUSG00000042388	Dlgap3	BC058433|DAP-3|DAP3|Prpl8|Sapap3	discs, large (Drosophila) homolog-associated protein 3	protein-coding
mm_11985.1	chr2	55435891	55435916	+	1	NA	promoter-TSS (NM_001304810)	promoter-TSS (NM_001304810)	-67	NM_001304810	16519	Mm.5127	NM_008426	ENSMUSG00000026824	Kcnj3	GIRK-1|GIRK1|Kcnf3|Kir3.1	potassium inwardly-rectifying channel, subfamily J, member 3	protein-coding
mm_103456.1	chr11	76287362	76287385	-	1	NA	intron (NM_008750, intron 1 of 7)	MIR|SINE|MIR	43637	NM_183263	67390	Mm.24886	NM_183263	ENSMUSG00000038046	Rnmtl1	4833420N02Rik|AI255153|HC90|Mrm3	RNA methyltransferase like 1	protein-coding
mm_131877.1	chr16	23223695	23223718	+	1	NA	Intergenic	Intergenic	-1034	NM_145933	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_112454.1	chr13	5864487	5864497	+	1	NA	intron (NM_011803, intron 1 of 3)	intron (NM_011803, intron 1 of 3)	3003	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_30903.1	chr4	32363935	32363942	+	1	NA	Intergenic	Intergenic	-53497	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_10251.1	chr2	9189568	9189574	+	1	NA	promoter-TSS (NR_038180)	promoter-TSS (NR_038180)	56	NR_038180	73438	Mm.23558	NR_038180	ENSMUSG00000085580	1700061F12Rik	-	RIKEN cDNA 1700061F12 gene	ncRNA
mm_3525.1	chr1	150165131	150165147	+	1	NA	promoter-TSS (NR_110420)	promoter-TSS (NR_110420)	-191	NR_110420	102639566	Mm.417208	NR_110420	ENSMUSG00000097754	Ptgs2os2	Gm26687|Linc-cox2|Lincrna-cox2	prostaglandin-endoperoxide synthase 2, opposite strand 2	ncRNA
mm_137883.1	chr17	31591720	31591759	+	1	NA	intron (NR_027493, intron 5 of 11)	L1MD|LINE|L1	26966	NM_016670	18771	Mm.259295	NM_016670	ENSMUSG00000006705	Pknox1	D17Wsu76e|PREP1	Pbx/knotted 1 homeobox	protein-coding
mm_20474.1	chr2	129515084	129515134	-	1	NA	intron (NM_177653, intron 1 of 6)	intron (NM_177653, intron 1 of 6)	21493	NM_177653	228592	Mm.452175	NM_177653	ENSMUSG00000043727	F830045P16Rik	Sirpb3	RIKEN cDNA F830045P16 gene	protein-coding
mm_126718.1	chr15	85336402	85336417	+	1	NA	promoter-TSS (NM_016843)	promoter-TSS (NM_016843)	28	NM_016843	54138	Mm.248906	NM_016843	ENSMUSG00000016541	Atxn10	AI325283|C77170|E46|Sca10|TEG-169|Tex169	ataxin 10	protein-coding
mm_129032.1	chr15	74959309	74959333	-	1	NA	3' UTR (NM_001164036, exon 4 of 4)	3' UTR (NM_001164036, exon 4 of 4)	4215	NM_001164040	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_81134.1	chr9	106514607	106514611	+	1	NA	promoter-TSS (NM_029300)	promoter-TSS (NM_029300)	36	NM_029300	75470	Mm.63799	NM_029300	ENSMUSG00000066382	Iqcf5	1700007L12Rik	IQ motif containing F5	protein-coding
mm_78163.1	chr9	21028216	21028228	+	1	NA	3' UTR (NM_010493, exon 7 of 7)	3' UTR (NM_010493, exon 7 of 7)	-1151	NM_023892	78369	Mm.30220	NM_023892	ENSMUSG00000001014	Icam4	1810015M19Rik|Cd242|ICAM-4	intercellular adhesion molecule 4, Landsteiner-Wiener blood group	protein-coding
mm_136765.1	chr17	8849924	8849933	+	1	NA	promoter-TSS (NM_001347321)	promoter-TSS (NM_001347321)	-57	NM_001347321	23984	Mm.87161	NM_011866	ENSMUSG00000023868	Pde10a	-	phosphodiesterase 10A	protein-coding
mm_119042.1	chr14	30593436	30593446	+	1	NA	Intergenic	MIR|SINE|MIR	16869	NM_001310682	18753	Mm.2314	NM_011103	ENSMUSG00000021948	Prkcd	AI385711|D14Ertd420e|PKC[d]|PKCdelta|Pkcd	protein kinase C, delta	protein-coding
mm_110081.1	chr12	24680891	24680943	-	1	NA	5' UTR (NM_001161807, exon 1 of 5)	5' UTR (NM_001161807, exon 1 of 5)	878	NM_138686	12879	Mm.52265	NM_138686	ENSMUSG00000062563	Cys1	2900006B19Rik|AV218859|Ccap|ck|cpk	cystin 1	protein-coding
mm_16423.1	chr2	180257406	180257428	+	1	NA	promoter-TSS (NM_025587)	promoter-TSS (NM_025587)	38	NM_025587	66481	Mm.289669	NM_025587	ENSMUSG00000039001	Rps21	1810049N11Rik|2410030A14Rik	ribosomal protein S21	protein-coding
mm_98863.1	chr11	97766629	97766687	+	1	NA	promoter-TSS (NM_026186)	promoter-TSS (NM_026186)	-45	NM_026186	67480	Mm.33206	NM_026186	ENSMUSG00000018541	Cwc25	1300013D05Rik|AA473636|Ccdc49|R75228	CWC25 spliceosome-associated protein	protein-coding
mm_166072.1	chr4	135873752	135873758	-	1	NA	promoter-TSS (NM_026383)	promoter-TSS (NM_026383)	91	NM_026383	52830	Mm.29159	NM_026383	ENSMUSG00000028675	Pnrc2	0610011E17Rik|D4Bwg0593e	proline-rich nuclear receptor coactivator 2	protein-coding
mm_27735.1	chr3	69069620	69069667	-	1	NA	Intergenic	Intergenic	-24901	NM_025863	66949	Mm.176695	NM_025863	ENSMUSG00000034317	Trim59	2310035M22Rik|2700022F13Rik|Mrf1|TSBF1	tripartite motif-containing 59	protein-coding
mm_66846.1	chr7	49634719	49634723	-	1	NA	intron (NM_001005232, intron 2 of 3)	intron (NM_001005232, intron 2 of 3)	2114	NM_001005232	13172	Mm.307176	NM_001005232	ENSMUSG00000030507	Dbx1	AI426026|Dbx	developing brain homeobox 1	protein-coding
mm_162218.1	chrX	139217141	139217141	+	1	NA	promoter-TSS (NM_001164633)	promoter-TSS (NM_001164633)	-25	NM_001164631	245631	Mm.131001	NM_175541	ENSMUSG00000042515	Mum1l1	9430086K21Rik	melanoma associated antigen (mutated) 1-like 1	protein-coding
mm_28915.1	chr3	98853277	98853290	-	1	NA	exon (NM_001304800, exon 4 of 4)	exon (NM_001304800, exon 4 of 4)	6511	NM_001304800	15492	Mm.140811	NM_008293	ENSMUSG00000027871	Hsd3b1	3-beta-HSD I|D3Ertd383e	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1	protein-coding
mm_7652.1	chr1	128324498	128324502	-	1	NA	intron (NM_001081078, intron 1 of 16)	PB1D11|SINE|Alu	3818	NM_001081078	226413	Mm.26930	NM_001081078	ENSMUSG00000026354	Lct	Gm100|LAC|LPH|Lphl	lactase	protein-coding
mm_83326.1	chr9	44233335	44233336	-	1	NA	intron (NM_007619, intron 1 of 15)	intron (NM_007619, intron 1 of 15)	711	NM_007619	12402	Mm.266871	NM_007619	ENSMUSG00000034342	Cbl	4732447J05Rik|Cbl-2|c-Cbl|cbl	Casitas B-lineage lymphoma	protein-coding
mm_161133.1	chr12	113543952	113543952	+	1	NA	promoter-TSS (NM_174885)	promoter-TSS (NM_174885)	44	NM_174885	238406	Mm.188683	NM_174885	ENSMUSG00000043945	Adam6a	Adam6|tMDCIV	a disintegrin and metallopeptidase domain 6A	protein-coding
mm_111341.1	chr12	86884717	86884750	-	1	NA	promoter-TSS (NM_145836)	promoter-TSS (NM_145836)	81	NM_145836	238330	Mm.248358	NM_145836	ENSMUSG00000034168	Irf2bpl	6430527G18Rik|Eap1	interferon regulatory factor 2 binding protein-like	protein-coding
mm_157671.1	chrX	59134394	59134420	-	1	NA	promoter-TSS (NM_010200)	promoter-TSS (NM_010200)	29	NM_010200	14168	Mm.7995	NM_010200	ENSMUSG00000031137	Fgf13	Fhf2	fibroblast growth factor 13	protein-coding
mm_85596.1	chr9	107490760	107490760	-	1	NA	intron (NM_001174047, intron 3 of 38)	intron (NM_001174047, intron 3 of 38)	-43185	NM_019704	56395	Mm.260153	NM_019704	ENSMUSG00000010045	Tmem115	C78915|Pl6|Pp6	transmembrane protein 115	protein-coding
mm_57042.1	chr6	122340500	122340510	-	1	NA	promoter-TSS (NM_001271579)	promoter-TSS (NM_001271579)	-278	NM_001271579	13619	Mm.6822	NM_007905	ENSMUSG00000040669	Phc1	AW557034|Edr|Edr1|Mph1|Rae-28|rae28	polyhomeotic-like 1 (Drosophila)	protein-coding
mm_64157.1	chr7	141342058	141342074	+	1	NA	exon (NM_133191, exon 3 of 21)	exon (NM_133191, exon 3 of 21)	3064	NM_133191	98845	Mm.27451	NM_133191	ENSMUSG00000025504	Eps8l2	AI042819|AW545405|Eps8r2	EPS8-like 2	protein-coding
mm_2900.1	chr1	131935290	131935313	+	1	NA	3' UTR (NM_001145804, exon 7 of 7)	3' UTR (NM_001145804, exon 7 of 7)	24843	NM_001145804	98415	Mm.246869	NM_175294	ENSMUSG00000026434	Nucks1	2700010L10Rik|8430423A01Rik|AI647518|C78391|Nucks	nuclear casein kinase and cyclin-dependent kinase substrate 1	protein-coding
mm_169221.1	chr13	66752888	66752893	-	1	NA	Intergenic	Intergenic	152460	NM_026219	67530	Mm.379136	NM_026219	ENSMUSG00000021520	Uqcrb	2210415M14Rik|QP-C|QPC|UQBC|UQBP|UQPC	ubiquinol-cytochrome c reductase binding protein	protein-coding
mm_65101.1	chr7	19303376	19303386	-	1	NA	3' UTR (NM_008036, exon 4 of 4)	3' UTR (NM_008036, exon 4 of 4)	6664	NM_008036	14282	Mm.248335	NM_008036	ENSMUSG00000003545	Fosb	-	FBJ osteosarcoma oncogene B	protein-coding
mm_50724.1	chr6	52245025	52245039	+	1	NA	promoter-TSS (NR_015348)	promoter-TSS (NR_015348)	-211	NR_015348	15397	Mm.469918	NR_015348	ENSMUSG00000086427	Hoxa11os	Hoxa11as|Hoxa11s	homeobox A11, opposite strand	ncRNA
mm_47900.1	chr5	134906727	134906744	-	1	NA	promoter-TSS (NM_194065)	promoter-TSS (NM_194065)	-2	NM_194065	76629	Mm.159750	NM_029681	ENSMUSG00000040576	Wbscr28	1700111I05Rik	Williams-Beuren syndrome chromosome region 28 (human)	protein-coding
mm_9412.1	chr1	172291324	172291354	-	1	NA	exon (NM_178405, exon 4 of 23)	exon (NM_178405, exon 4 of 23)	6725	NM_178405	98660	Mm.207432	NM_178405	ENSMUSG00000007097	Atp1a2	AW060654|Atpa-3|mKIAA0778	ATPase, Na+/K+ transporting, alpha 2 polypeptide	protein-coding
mm_155913.1	chrX	101961692	101961733	+	1	NA	intron (NM_001163610, intron 1 of 7)	intron (NM_001163610, intron 1 of 7)	109595	NM_001278534	331474	Mm.23297	NM_183318	ENSMUSG00000049191	Rgag4	6430402L03Rik|Mar5|Mart5|mKIAA2001	retrotransposon gag domain containing 4	protein-coding
mm_97904.1	chr11	83437656	83437671	+	1	NA	promoter-TSS (NM_025492)	promoter-TSS (NM_025492)	-31	NM_025492	66330	Mm.44800	NM_025492	ENSMUSG00000035085	1700020L24Rik	-	RIKEN cDNA 1700020L24 gene	protein-coding
mm_100476.1	chr11	120150529	120150567	+	1	NA	intron (NM_024249, intron 1 of 16)	intron (NM_024249, intron 1 of 16)	803	NM_001164799	72055	Mm.253403	NM_024249	ENSMUSG00000061306	Slc38a10	1810073N04Rik	solute carrier family 38, member 10	protein-coding
mm_159577.1	chr4	117582590	117582590	+	1	NA	intron (NM_001285901, intron 2 of 7)	intron (NM_001285901, intron 2 of 7)	32225	NM_080469	140546	Mm.235891	NM_080469	ENSMUSG00000033423	Eri3	PINT1|Prnpip1	exoribonuclease 3	protein-coding
mm_40328.1	chr5	43910569	43910575	+	1	NA	3' UTR (NM_007646, exon 8 of 8)	3' UTR (NM_007646, exon 8 of 8)	41763	NM_007646	12494	Mm.249873	NM_007646	ENSMUSG00000029084	Cd38	ADPRC 1|Cd38-rs1|I-19	CD38 antigen	protein-coding
mm_156101.1	chrX	112600825	112600835	+	1	NA	5' UTR (NM_177747, exon 1 of 9)	5' UTR (NM_177747, exon 1 of 9)	304	NM_177747	245595	Mm.259846	NM_177747	ENSMUSG00000025529	Zfp711	2810409C01Rik|A230078I01Rik|Znf711	zinc finger protein 711	protein-coding
mm_138776.1	chr17	37195708	37195730	+	1	NA	3' UTR (NM_023137, exon 2 of 2)	3' UTR (NM_023137, exon 2 of 2)	1827	NM_023137	24108	Mm.140210	NM_023137	ENSMUSG00000035186	Ubd	FAT10	ubiquitin D	protein-coding
mm_138556.1	chr17	35267005	35267042	+	1	NA	TTS (NM_001267808)	TTS (NM_001267808)	3900	NM_001267808	14980	Mm.439675	NM_001267808		H2-L	H-2L	histocompatibility 2, D region locus L	protein-coding
mm_48001.1	chr5	136161246	136161281	-	1	NA	intron (NM_178751, intron 2 of 2)	RSINE1|SINE|B4	9393	NM_178751	269717	Mm.308396	NM_178751	ENSMUSG00000039747	Orai2	A730041O15Rik|Tmem142b	ORAI calcium release-activated calcium modulator 2	protein-coding
mm_11327.1	chr2	30439508	30439534	+	1	NA	intron (NM_138748, intron 7 of 9)	intron (NM_138748, intron 7 of 9)	23471	NM_138748	110854	Mm.275393	NM_138748	ENSMUSG00000039515	Ptpa	2610042B21Rik|C77440|N28142|PR53|Ppp2r4	protein phosphatase 2 protein activator	protein-coding
mm_90503.1	chr10	128035638	128035655	+	1	NA	5' UTR (NM_013608, exon 1 of 8)	5' UTR (NM_013608, exon 1 of 8)	300	NM_001113199	17938	Mm.3746	NM_013608	ENSMUSG00000061315	Naca	AL022831|AL024382|Gm1878|mKIAA0363|skNAC	nascent polypeptide-associated complex alpha polypeptide	protein-coding
mm_127568.1	chr15	102270541	102270580	+	1	NA	Intergenic	Intergenic	-8896	NM_134100	106073	Mm.287740	NM_134100	ENSMUSG00000045665	Mfsd5	AA409375|AW556797|D15Mgi27	major facilitator superfamily domain containing 5	protein-coding
mm_73228.1	chr8	104101629	104101650	+	1	NA	promoter-TSS (NM_009868)	promoter-TSS (NM_009868)	14	NM_009868	12562	Mm.21767	NM_009868	ENSMUSG00000031871	Cdh5	7B4|AA408225|Cd144|VE-Cad|VECD|VEcad|Vec	cadherin 5	protein-coding
mm_75217.1	chr8	39605726	39605732	-	1	NA	3' UTR (NM_031195, exon 9 of 9)	3' UTR (NM_031195, exon 9 of 9)	36949	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_48962.1	chr6	4600335	4600355	+	1	NA	promoter-TSS (NM_145398)	promoter-TSS (NM_145398)	-721	NM_145398	213819	Mm.270703	NM_145398	ENSMUSG00000015189	Casd1	Cas1|Cast1	CAS1 domain containing 1	protein-coding
mm_67909.1	chr7	99701049	99701065	-	1	NA	intron (NM_175316, intron 1 of 13)	intron (NM_175316, intron 1 of 13)	-5248	NM_001252531	101488	Mm.11249	NM_175316	ENSMUSG00000030737	Slco2b1	AI060904|AI852653|OATP-B|Slc21a9	solute carrier organic anion transporter family, member 2b1	protein-coding
mm_28139.1	chr3	87254341	87254345	-	1	NA	intron (NM_030707, intron 6 of 7)	B1_Mur1|SINE|Alu	9181	NM_030707	80891	Mm.45173	NM_030707	ENSMUSG00000015852	Fcrls	2810439C17Rik|9330158F12|FcRH2sc|Fcrh2|IFGP2|IgSR|MMAN-g|Msr2|moFcRH2sc	Fc receptor-like S, scavenger receptor	protein-coding
mm_72009.1	chr8	70703424	70703433	+	1	NA	Intergenic	Intergenic	5689	NM_001286944	16478	Mm.419851	NM_010592	ENSMUSG00000071076	Jund	Jund1	jun D proto-oncogene	protein-coding
mm_61361.1	chr7	68748194	68748220	+	1	NA	intron (NM_025549, intron 1 of 4)	intron (NM_025549, intron 1 of 4)	1031	NM_001042592	66412	Mm.251199	NM_025549	ENSMUSG00000042659	Arrdc4	2410003C09Rik|AV216361	arrestin domain containing 4	protein-coding
mm_24074.1	chr3	87921896	87921921	+	1	NA	TTS (NM_153562)	TTS (NM_153562)	2364	NM_026591	67707	Mm.393802	NM_026591	ENSMUSG00000019710	Mrpl24	2010005E08Rik|2810470K06Rik|6720473G22Rik|AA407670	mitochondrial ribosomal protein L24	protein-coding
mm_139014.1	chr17	45695423	45695433	+	1	NA	intron (NM_026732, intron 1 of 2)	intron (NM_026732, intron 1 of 2)	9056	NM_026732	68463	Mm.379158	NM_026732	ENSMUSG00000023939	Mrpl14	1110006I11Rik|AI846816|MRP-L32|Rpml32	mitochondrial ribosomal protein L14	protein-coding
mm_161659.1	chr17	8101225	8101225	-	1	NA	promoter-TSS (NM_001033442).2	promoter-TSS (NM_001033442).2	3	NM_001033442	381059	Mm.490353	NM_001033442	ENSMUSG00000095720	Gm1604b	ENSMUSG00000073470|Gm1604	predicted gene 1604b	protein-coding
mm_129239.1	chr15	76639796	76639798	-	1	NA	intron (NM_183091, intron 1 of 25)	CpG	132	NM_183091	72749	Mm.358749	NM_183091	ENSMUSG00000059323	Tonsl	2810439M11Rik|Nfkbil2	tonsoku-like, DNA repair protein	protein-coding
mm_96282.1	chr11	62951198	62951231	+	1	NA	promoter-TSS (NM_025496)	promoter-TSS (NM_025496)	21	NM_025496	66338	Mm.46166	NM_025496	ENSMUSG00000042200	Cdrt4	1700019I23Rik	CMT1A duplicated region transcript 4	protein-coding
mm_135852.1	chr16	59557389	59557398	-	1	NA	Intergenic	Intergenic	-1641	NM_174848	224273	Mm.246424	NM_174848	ENSMUSG00000022723	Crybg3	5031404N19|AU022790|Gm9581	beta-gamma crystallin domain containing 3	protein-coding
mm_77053.1	chr8	109577536	109577572	-	1	NA	exon (NM_017370, exon 2 of 5)	exon (NM_017370, exon 2 of 5)	1618	NM_017370	15439	Mm.26730	NM_017370	ENSMUSG00000031722	Hp	HP-1|preHP2	haptoglobin	protein-coding
mm_118672.1	chr14	22019834	22019856	+	1	NA	5' UTR (NM_028275, exon 1 of 7)	5' UTR (NM_028275, exon 1 of 7)	133	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_36810.1	chr4	103214846	103214856	-	1	NA	promoter-TSS (NM_177732)	promoter-TSS (NM_177732)	33	NM_177732	242585	Mm.281800	NM_177732	ENSMUSG00000028521	Slc35d1	AI834976|C330011J09|UGTREL7|mKIAA0260	solute carrier family 35 (UDP-glucuronic acid/UDP-N-acetylgalactosamine dual transporter), member D1	protein-coding
mm_156736.1	chrX	159942906	159942919	+	1	NA	5' UTR (NM_001290664, exon 1 of 6)	5' UTR (NM_001290664, exon 1 of 6)	219	NM_001290664	58194	Mm.286495	NM_021389	ENSMUSG00000040990	Sh3kbp1	1200007H22Rik|1700125L08Rik|5830464D22Rik|AI447724|Cin85|IN85|Ruk|Seta	SH3-domain kinase binding protein 1	protein-coding
mm_39299.1	chr5	5754766	5754768	+	1	NA	Intergenic	Intergenic	-5450	NM_027399	70358	Mm.85429	NM_027399	ENSMUSG00000015652	Steap1	2410007B19Rik|Prss24|Steap	six transmembrane epithelial antigen of the prostate 1	protein-coding
mm_59858.1	chr7	29983949	29983964	+	1	NA	promoter-TSS (NM_001167873)	promoter-TSS (NM_001167873)	1	NM_001167872	243905	Mm.322432	NM_001033355	ENSMUSG00000074221	Zfp568	C80731|Gm1691|Znf568|chato	zinc finger protein 568	protein-coding
mm_13771.1	chr2	118663236	118663309	+	1	NA	promoter-TSS (NM_001033254)	promoter-TSS (NM_001033254)	-305	NM_001033254	214230	Mm.241857	NM_001033254	ENSMUSG00000074923	Pak6	4732456M09	p21 protein (Cdc42/Rac)-activated kinase 6	protein-coding
mm_85724.1	chr9	108326713	108326721	-	1	NA	intron (NM_001313962, intron 2 of 5)	B1F|SINE|Alu	-12363	NM_008160	14775	Mm.1090	NM_008160	ENSMUSG00000063856	Gpx1	AI195024|AL033363|CGPx|GPx-1|GSHPx-1|Gpx	glutathione peroxidase 1	protein-coding
mm_169781.1	chr16	11144186	11144189	+	1	NA	intron (NR_027502, intron 19 of 22)	LSU-rRNA_Hsa|rRNA|rRNA	-9655	NM_029582	106200	Mm.291015	NM_029582	ENSMUSG00000022498	Txndc11	2810408E11Rik|AI427833|EFP1|Txdc11	thioredoxin domain containing 11	protein-coding
mm_132922.1	chr16	49782031	49782045	+	1	NA	Intergenic	Intergenic	-73616	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_128126.1	chr15	31336743	31336751	-	1	NA	intron (NM_027496, intron 1 of 3)	intron (NM_027496, intron 1 of 3)	31012	NM_001164441	67434	Mm.102470	NM_026153	ENSMUSG00000022237	Ankrd33b	0610012A05Rik|3021401C12Rik|5730557B15Rik	ankyrin repeat domain 33B	protein-coding
mm_1621.1	chr1	74391848	74391870	+	1	NA	5' UTR (NM_153088, exon 1 of 7)	5' UTR (NM_153088, exon 1 of 7)	250	NM_153088	227292	Mm.165042	NM_153088	ENSMUSG00000026176	Ctdsp1	GIP|NLIIF|Nif3|SCP1	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 1	protein-coding
mm_91875.1	chr10	59583047	59583058	-	1	NA	intron (NM_001033259, intron 1 of 7)	intron (NM_001033259, intron 1 of 7)	33640	NM_001033259	215999	Mm.296470	NM_001033259	ENSMUSG00000009647	Mcu	2010012O16Rik|AV064928|C10orf42|Ccdc109a|D130073L02Rik|Gm64	mitochondrial calcium uniporter	protein-coding
mm_65600.1	chr7	27355981	27356014	-	1	NA	promoter-TSS (NM_138676)	promoter-TSS (NM_138676)	11	NM_138676	192192	Mm.21297	NM_138676	ENSMUSG00000089832	Shkbp1	B930062H15Rik|Sb1	Sh3kbp1 binding protein 1	protein-coding
mm_28219.1	chr3	88410378	88410388	-	1	NA	promoter-TSS (NM_025928)	promoter-TSS (NM_025928)	14	NM_001310605	67037	Mm.36715	NM_025928	ENSMUSG00000028066	Pmf1	2600009M07Rik|AL033286|AW060657	polyamine-modulated factor 1	protein-coding
mm_153706.1	chr19	44397838	44397848	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	9866	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_142329.1	chr17	43504014	43504021	-	1	NA	Intergenic	ID_B1|SINE|B4	-1244	NM_008585	17287	Mm.5346	NM_008585	ENSMUSG00000023914	Mep1a	AI098089|AW107200|Mep-1|Mep-1a|Mep1	meprin 1 alpha	protein-coding
mm_27059.1	chr3	27691546	27691556	-	1	NA	intron (NM_173182, intron 1 of 25)	L2b|LINE|L2	18888	NM_173182	72007	Mm.38832	NM_173182	ENSMUSG00000039286	Fndc3b	1600019O04Rik|AW550168|Fad104|mKIAA4164	fibronectin type III domain containing 3B	protein-coding
mm_108422.1	chr12	82170147	82170173	+	1	NA	intron (NM_001167983, intron 1 of 23)	CpG	144	NM_001167983	217692	Mm.261333	NM_172579	ENSMUSG00000042700	Sipa1l1	4931426N11Rik|AW213287|Spar|mKIAA0440	signal-induced proliferation-associated 1 like 1	protein-coding
mm_60442.1	chr7	44477059	44477069	+	1	NA	Intergenic	L1MEd|LINE|L1	6717	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_105806.1	chr11	110251712	110251734	-	1	NA	promoter-TSS (NM_147218)	promoter-TSS (NM_147218)	53	NM_147218	76184	Mm.159704	NM_147218	ENSMUSG00000044749	Abca6	6330565N06Rik	ATP-binding cassette, sub-family A (ABC1), member 6	protein-coding
mm_17755.1	chr2	32771960	32771974	-	1	NA	exon (NM_001290563, exon 7 of 15)	exon (NM_001290563, exon 7 of 15)	3372	NM_001290564	338348	Mm.475130	NM_177384	ENSMUSG00000039021	Ttc16	1200002K10Rik	tetratricopeptide repeat domain 16	protein-coding
mm_53101.1	chr6	125067674	125067686	+	1	NA	promoter-TSS (NM_001163269)	promoter-TSS (NM_001163269)	-240	NM_001163269	381810	Mm.333386	NM_001163268	ENSMUSG00000067714	Lpar5	GPR93|Gm1072|Gpr92|LPA5	lysophosphatidic acid receptor 5	protein-coding
mm_163697.1	chr13	101845590	101845594	+	1	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	-77375	NM_001077495	18708	Mm.259333	NM_001024955	ENSMUSG00000041417	Pik3r1	PI3K|p50alpha|p55alpha|p85alpha	phosphatidylinositol 3-kinase, regulatory subunit, polypeptide 1 (p85 alpha)	protein-coding
mm_99871.1	chr11	109399342	109399369	+	1	NA	3' UTR (NM_010303, exon 4 of 4)	3' UTR (NM_010303, exon 4 of 4)	-26591	NM_025275	13929	Mm.211850	NM_025275	ENSMUSG00000020610	Amz2	AA408420|ESTM12|X83328	archaelysin family metallopeptidase 2	protein-coding
mm_59081.1	chr7	19673223	19673254	+	1	NA	exon (NM_001309795, exon 3 of 4)	exon (NM_001309795, exon 3 of 4)	682	NM_001309795	11813	Mm.28394	NM_001277944	ENSMUSG00000002992	Apoc2	apo-CII|apoC-II	apolipoprotein C-II	protein-coding
mm_118606.1	chr14	20838756	20838780	+	1	NA	intron (NM_008873, intron 5 of 10)	B3|SINE|B2	2106	NM_008873	18792	Mm.4183	NM_008873	ENSMUSG00000021822	Plau	u-PA|uPA	plasminogen activator, urokinase	protein-coding
mm_16473.1	chr2	180725331	180725383	+	1	NA	promoter-TSS (NM_183161)	promoter-TSS (NM_183161)	18	NM_183161	228993	Mm.87189	NM_183161	ENSMUSG00000023393	Slc17a9	1700019H03Rik|BC019537|Vnut	solute carrier family 17, member 9	protein-coding
mm_87139.1	chr10	34389975	34389990	+	1	NA	promoter-TSS (NM_009925)	promoter-TSS (NM_009925)	1	NM_009925	12813	Mm.443177	NM_009925	ENSMUSG00000039462	Col10a1	Col10|Col10a-1	collagen, type X, alpha 1	protein-coding
mm_111571.1	chr12	101818802	101818812	-	1	NA	5' UTR (NM_011812, exon 1 of 11)	5' UTR (NM_011812, exon 1 of 11)	312	NM_011812	23876	Mm.288381	NM_011812	ENSMUSG00000021186	Fbln5	A55|DANCE|EVEC	fibulin 5	protein-coding
mm_2045.1	chr1	87327009	87327042	+	1	NA	promoter-TSS (NM_001110212)	promoter-TSS (NM_001110212)	27	NM_001110212	227331	Mm.23065	NM_146112	ENSMUSG00000048000	Gigyf2	2610016F01Rik|A830080H02Rik|AI852361|AW259676|BC006835|Tnrc15|mKIAA0642	GRB10 interacting GYF protein 2	protein-coding
mm_35231.1	chr4	19708923	19709004	-	1	NA	promoter-TSS (NM_177327)	promoter-TSS (NM_177327)	41	NM_177327	107568	Mm.78312	NM_177327	ENSMUSG00000041058	Wwp1	8030445B08Rik|AIP5|SDRP1|Tiul1	WW domain containing E3 ubiquitin protein ligase 1	protein-coding
mm_105087.1	chr11	100850488	100850596	-	1	NA	promoter-TSS (NM_001113563)	promoter-TSS (NM_001113563)	43	NM_001113563	20851	Mm.34064	NM_011489	ENSMUSG00000020919	Stat5b	-	signal transducer and activator of transcription 5B	protein-coding
mm_74696.1	chr8	15046837	15046841	-	1	NA	promoter-TSS (NR_037972)	promoter-TSS (NR_037972)	-761	NR_037972	434285	Mm.334425	NM_001007591	ENSMUSG00000049008	BB014433	-	expressed sequence BB014433	ncRNA
mm_133311.1	chr16	77626360	77626377	+	1	NA	Intergenic	Intergenic	-19905	NR_029540	723952		NR_029540	ENSMUSG00000065472	Mir125b-2	Mirn125b-2|mir-125b-2	microRNA 125b-2	ncRNA
mm_157648.1	chrX	57305151	57305172	-	1	NA	intron (NM_152801, intron 2 of 21)	intron (NM_152801, intron 2 of 21)	33568	NM_152801	73341	Mm.261443	NM_152801	ENSMUSG00000031133	Arhgef6	1600028C08Rik|1700038J06Rik|4930592P22Rik|alpha-PIX	Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_111922.1	chr12	108875644	108875654	-	1	NA	intron (NM_011710, intron 5 of 10)	intron (NM_011710, intron 5 of 10)	17549	NM_001164488	22375	Mm.38433	NM_011710	ENSMUSG00000021266	Wars	TrpRS|WRS	tryptophanyl-tRNA synthetase	protein-coding
mm_94629.1	chr11	16815404	16815407	+	1	NA	intron (NM_207655, intron 1 of 27)	intron (NM_207655, intron 1 of 27)	63202	NM_007912	13649	Mm.8534	NM_007912	ENSMUSG00000020122	Egfr	9030024J15Rik|AI552599|Erbb|Errb1|Errp|Wa5|wa-2|wa2	epidermal growth factor receptor	protein-coding
mm_162111.1	chrX	51680392	51680392	-	1	NA	promoter-TSS (NM_015819)	promoter-TSS (NM_015819)	85	NM_001290468	50786	Mm.252561	NM_015819	ENSMUSG00000062184	Hs6st2	6OST2	heparan sulfate 6-O-sulfotransferase 2	protein-coding
mm_98676.1	chr11	96284224	96284242	+	1	NA	exon (NM_010461, exon 2 of 2)	exon (NM_010461, exon 2 of 2)	2328	NM_010461	15416	Mm.4822	NM_010461	ENSMUSG00000056648	Hoxb8	Hox-2.4	homeobox B8	protein-coding
mm_85373.1	chr9	103222200	103222210	-	1	NA	exon (NM_133977, exon 8 of 17)	exon (NM_133977, exon 8 of 17)	8081	NM_133977	22041	Mm.37214	NM_133977	ENSMUSG00000032554	Trf	AI266983|Cd176|HP|Tf|Tfn|hpx	transferrin	protein-coding
mm_76756.1	chr8	95488775	95488852	-	1	NA	promoter-TSS (NM_009974)	promoter-TSS (NM_009974)	7	NM_009974	13000	Mm.51136	NM_009974	ENSMUSG00000046707	Csnk2a2	1110035J23Rik|C77789|CK2	casein kinase 2, alpha prime polypeptide	protein-coding
mm_25329.1	chr3	106569423	106569438	+	1	NA	intron (NM_001025582, intron 5 of 6)	Lx7|LINE|L1	-21628	NM_133869	99712	Mm.429443	NM_133869	ENSMUSG00000040774	Cept1	9930118K05Rik|mCEPT1	choline/ethanolaminephosphotransferase 1	protein-coding
mm_8880.1	chr1	162866426	162866432	-	1	NA	5' UTR (NM_010231, exon 1 of 9)	5' UTR (NM_010231, exon 1 of 9)	181	NM_010231	14261	Mm.976	NM_010231	ENSMUSG00000040181	Fmo1	-	flavin containing monooxygenase 1	protein-coding
mm_33719.1	chr4	134060740	134060748	+	1	NA	Intergenic	Intergenic	-7708	NM_001162970	230806	Mm.240080	NM_001162970	ENSMUSG00000012123	Aim1l	-	absent in melanoma 1-like	protein-coding
mm_76899.1	chr8	105817569	105817589	-	1	NA	intron (NM_145824, intron 2 of 13)	MTC|LTR|ERVL-MaLR	9771	NM_145824	74334	Mm.4206	NM_145824	ENSMUSG00000037415	Ranbp10	4432417N03Rik	RAN binding protein 10	protein-coding
mm_159764.1	chr5	93268664	93268664	+	1	NA	exon (NM_007635, exon 2 of 8)	exon (NM_007635, exon 2 of 8)	1091	NM_007635	12452	Mm.3527	NM_007635	ENSMUSG00000029385	Ccng2	-	cyclin G2	protein-coding
mm_163459.1	chr12	98771004	98771010	+	1	NA	promoter-TSS (NM_001160108)	promoter-TSS (NM_001160108)	-15	NM_001160108	75553	Mm.25549	NM_029334	ENSMUSG00000021012	Zc3h14	1010001P15Rik|1700016A15Rik|2700069A02Rik|AU014748	zinc finger CCCH type containing 14	protein-coding
mm_51797.1	chr6	88465484	88465495	+	1	NA	promoter-TSS (NM_019685)	promoter-TSS (NM_019685)	80	NM_019685	56505	Mm.42195	NM_019685	ENSMUSG00000030079	Ruvbl1	2510009G06Rik|Pontin52|Tip49a	RuvB-like protein 1	protein-coding
mm_101929.1	chr11	50202960	50203007	-	1	NA	exon (NM_011018, exon 6 of 8)	exon (NM_011018, exon 6 of 8)	7837	NM_001290769	18412	Mm.40828	NM_011018	ENSMUSG00000015837	Sqstm1	A170|OSF-6|Osi|STAP|STONE14|p62	sequestosome 1	protein-coding
mm_101228.1	chr11	20290475	20290475	-	1	NA	Intergenic	MERV1_I-int|LTR|ERV1	-41051	NM_172260	216543	Mm.260314	NM_172260	ENSMUSG00000044066	Cep68	6030463E10Rik|AI481761|BC027174|Kiaa0582	centrosomal protein 68	protein-coding
mm_34265.1	chr4	141421809	141421822	+	1	NA	exon (NM_013868, exon 1 of 3)	exon (NM_013868, exon 1 of 3)	1036	NM_013868	29818	Mm.46181	NM_013868	ENSMUSG00000006221	Hspb7	27kDa|Hsp25-2|cvHsp	heat shock protein family, member 7 (cardiovascular)	protein-coding
mm_72647.1	chr8	84721683	84721748	+	1	NA	exon (NM_010906, exon 7 of 9)	exon (NM_010906, exon 7 of 9)	20258	NM_008535	17095	Mm.4925	NM_008535	ENSMUSG00000034041	Lyl1	Lyl-1|bHLHa18	lymphoblastomic leukemia 1	protein-coding
mm_170695.1	chr2	133233778	133233780	-	1	NA	Intergenic	(CAG)n|Simple_repeat|Simple_repeat	-287743	NM_198029	241639	Mm.209784	NM_198029	ENSMUSG00000027356	Fermt1	5830467P10Rik|Kindlin-1	fermitin family member 1	protein-coding
mm_11658.1	chr2	35066833	35066843	+	1	NA	Intergenic	Intergenic	-5397	NM_010406	15139	Mm.2168	NM_010406	ENSMUSG00000026874	Hc	C5|C5a|He	hemolytic complement	protein-coding
mm_101129.1	chr11	12354028	12354032	-	1	NA	intron (NM_001282993, intron 5 of 13)	intron (NM_001282993, intron 5 of 13)	58110	NM_001282994	12808	Mm.22847	NM_172496	ENSMUSG00000020173	Cobl	-	cordon-bleu WH2 repeat	protein-coding
mm_17370.1	chr2	26915691	26915698	-	1	NA	promoter-TSS (NM_013678)	promoter-TSS (NM_013678)	-727	NM_013678	20931	Mm.389260	NM_013678	ENSMUSG00000014873	Surf2	Surf-2	surfeit gene 2	protein-coding
mm_110886.1	chr12	75483369	75483372	-	1	NA	intron (NM_012024, intron 5 of 13)	intron (NM_012024, intron 5 of 13)	-66589	NM_175644	217674	Mm.252250	NM_175644	ENSMUSG00000048982	Gphb5	OGH|Zlut1	glycoprotein hormone beta 5	protein-coding
mm_146548.1	chr18	6214605	6214617	-	1	NA	exon (NM_008448, exon 16 of 26)	exon (NM_008448, exon 16 of 26)	26913	NM_008448	16573	Mm.223744	NM_008448	ENSMUSG00000006740	Kif5b	AL022807|Khc|Khcs|Kns1|Ukhc	kinesin family member 5B	protein-coding
mm_108059.1	chr12	73928198	73928211	+	1	NA	intron (NM_001313920, intron 3 of 14)	intron (NM_001313920, intron 3 of 14)	20337	NM_001313919	15251	Mm.3879	NM_010431	ENSMUSG00000021109	Hif1a	AA959795|HIF-1-alpha|HIF1-alpha|HIF1alpha|MOP1|bHLHe78	hypoxia inducible factor 1, alpha subunit	protein-coding
mm_162438.1	chr1	106439507	106439518	+	1	NA	Intergenic	L1_Mur3|LINE|L1	107119	NR_106164	102466254		NR_106164	ENSMUSG00000098344	Mir3473f	Gm27846|mmu-mir-3473f	microRNA 3473f	ncRNA
mm_26426.1	chr3	142618316	142618328	+	1	NA	3' UTR (NM_010259, exon 11 of 11)	3' UTR (NM_010259, exon 11 of 11)	-2341	NM_010260	14469	Mm.24038	NM_010260	ENSMUSG00000028270	Gbp2	-	guanylate binding protein 2	protein-coding
mm_3510.1	chr1	150107342	150107353	+	1	NA	3' UTR (NM_011198, exon 10 of 10)	3' UTR (NM_011198, exon 10 of 10)	7316	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_94807.1	chr11	23008543	23008553	+	1	NA	Intergenic	CpG	-4839	NM_028672	73873	Mm.252406	NM_028672	ENSMUSG00000049811	Fam161a	4930430E16Rik	family with sequence similarity 161, member A	protein-coding
mm_66808.1	chr7	47252875	47252883	-	1	NA	promoter-TSS (NM_001288801)	promoter-TSS (NM_001288801)	-31	NM_001288801	668725	Mm.436563	NM_001177566	ENSMUSG00000074111	Mrgpra9	EG668725|MrgA9	MAS-related GPR, member A9	protein-coding
mm_141711.1	chr17	34000329	34000338	-	1	NA	promoter-TSS (NM_001001892)	promoter-TSS (NM_001001892)	0	NM_001001892	14972	Mm.422886	NM_001001892	ENSMUSG00000061232	H2-K1	H-2K|H-2K(d)|H2-K|K-f	histocompatibility 2, K1, K region	protein-coding
mm_90973.1	chr10	13474362	13474441	-	1	NA	promoter-TSS (NM_001195065)	promoter-TSS (NM_001195065)	-5	NM_001195065	215789	Mm.283359	NM_001033257	ENSMUSG00000062866	Phactr2	AV158170|BC012871	phosphatase and actin regulator 2	protein-coding
mm_147358.1	chr18	43373293	43373293	-	1	NA	promoter-TSS (NM_001136086)	promoter-TSS (NM_001136086)	-21	NM_001136086	22240	Mm.8180	NM_009468	ENSMUSG00000024501	Dpysl3	CRMP-4|DRP-3|TUC4|ULIP-1|Ulip|Ulip1	dihydropyrimidinase-like 3	protein-coding
mm_150191.1	chr19	32665793	32665821	+	1	NA	3' UTR (NM_011864, exon 13 of 13)	3' UTR (NM_011864, exon 13 of 13)	45802	NM_011864	23972	Mm.203916	NM_011864	ENSMUSG00000024899	Papss2	1810018P12Rik|AI159688|AtpsU2|Atpsk2|Sk2|bm	3'-phosphoadenosine 5'-phosphosulfate synthase 2	protein-coding
mm_135486.1	chr16	46038577	46038581	-	1	NA	intron (NM_032465, intron 13 of 14)	intron (NM_032465, intron 13 of 14)	-28166	NM_001134480	433022	Mm.380993	NM_001134480	ENSMUSG00000087141	Plcxd2	AW494639|EG433022	phosphatidylinositol-specific phospholipase C, X domain containing 2	protein-coding
mm_18092.1	chr2	44986478	44986488	-	1	NA	3' UTR (NM_015753, exon 10 of 10)	3' UTR (NM_015753, exon 10 of 10)	36694	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_162532.1	chr1	165838924	165838928	+	1	NA	intron (NM_001113391, intron 1 of 7)	intron (NM_001113391, intron 1 of 7)	50245	NM_001113392	12503	Mm.217308	NM_031162	ENSMUSG00000005763	Cd247	4930549J05Rik|A430104F18Rik|AW552088|Cd3|Cd3-eta|Cd3-zeta|Cd3h|Cd3z|Cd3zeta|T3z|Tcrk|Tcrz	CD247 antigen	protein-coding
mm_42562.1	chr5	117141989	117142002	+	1	NA	intron (NM_001081308, intron 1 of 19)	intron (NM_001081308, intron 1 of 19)	8407	NM_183306	330177	Mm.24343	NM_183306	ENSMUSG00000061288	Taok3	2900006A08Rik|A130052D22|A430105I05Rik	TAO kinase 3	protein-coding
mm_101553.1	chr11	33843406	33843416	-	1	NA	5' UTR (NM_001290690, exon 1 of 8)	5' UTR (NM_001290690, exon 1 of 8)	174	NM_027398	70357	Mm.252514	NM_027398	ENSMUSG00000053519	Kcnip1	KCHIP1|Kchip1.2	Kv channel-interacting protein 1	protein-coding
mm_150303.1	chr19	34570280	34570296	+	1	NA	5' UTR (NM_008332, exon 2 of 3)	5' UTR (NM_008332, exon 2 of 3)	-13241	NM_010501	15959	Mm.426079	NM_010501	ENSMUSG00000074896	Ifit3	Ifi49|P49	interferon-induced protein with tetratricopeptide repeats 3	protein-coding
mm_68368.1	chr7	107757898	107757935	-	1	NA	intron (NM_177216, intron 1 of 8)	intron (NM_177216, intron 1 of 8)	116	NM_001205227	320635	Mm.132828	NM_177216	ENSMUSG00000048065	Cyb5r2	D630003K02Rik|b5R.2	cytochrome b5 reductase 2	protein-coding
mm_59963.1	chr7	30428185	30428188	+	1	NA	exon (NM_172142, exon 11 of 11)	exon (NM_172142, exon 11 of 11)	4882	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_47126.1	chr5	119831981	119831992	-	1	NA	Intergenic	Intergenic	-2677	NM_011537	21388	Mm.103636	NM_011537	ENSMUSG00000018263	Tbx5	-	T-box 5	protein-coding
mm_111370.1	chr12	87237006	87237019	-	1	NA	intron (NM_027744, intron 2 of 7)	intron (NM_027744, intron 2 of 7)	1589	NM_027744	71275	Mm.79198	NM_027744	ENSMUSG00000072919	Noxred1	4933437F05Rik	NADP+ dependent oxidoreductase domain containing 1	protein-coding
mm_144684.1	chr18	34776204	34776207	+	1	NA	promoter-TSS (NM_001081256)	promoter-TSS (NM_001081256)	-803	NM_001081256	277250	Mm.277906	NM_029518	ENSMUSG00000038773	Kdm3b	5830462I21Rik|JHDM2B|Jmjd1b|mKIAA1082	KDM3B lysine (K)-specific demethylase 3B	protein-coding
mm_132549.1	chr16	37883451	37883492	+	1	NA	3' UTR (NM_177093, exon 4 of 4)	3' UTR (NM_177093, exon 4 of 4)	15071	NM_177093	320184	Mm.390882	NM_177093	ENSMUSG00000034158	Lrrc58	1810012N18Rik|C330018J07Rik	leucine rich repeat containing 58	protein-coding
mm_113635.1	chr13	42051997	42052007	+	1	NA	promoter-TSS (NM_007772)	promoter-TSS (NM_007772)	-19	NM_007772	110521	Mm.4808	NM_007772	ENSMUSG00000021366	Hivep1	Cryabp1	human immunodeficiency virus type I enhancer binding protein 1	protein-coding
mm_85359.1	chr9	103215938	103215945	-	1	NA	exon (NM_133977, exon 13 of 17)	exon (NM_133977, exon 13 of 17)	-13876	NM_009275	20818	Mm.273053	NM_009275	ENSMUSG00000032553	Srprb	AA409543	signal recognition particle receptor, B subunit	protein-coding
mm_29498.1	chr3	115989311	115989339	-	1	NA	intron (NM_023214, intron 5 of 10)	B1F2|SINE|Alu	9423	NR_130332	100316705		NR_130332	ENSMUSG00000089261	Mir669n	mmu-mir-669n	microRNA 669n	ncRNA
mm_164944.1	chr19	4038049	4038068	-	1	NA	promoter-TSS (NM_013541)	promoter-TSS (NM_013541)	-146	NM_013541	14870	Mm.299292	NM_013541	ENSMUSG00000060803	Gstp1	GstpiB	glutathione S-transferase, pi 1	protein-coding
mm_145137.1	chr18	45559408	45559418	+	1	NA	promoter-TSS (NM_080465)	promoter-TSS (NM_080465)	-741	NM_080465	140492	Mm.411614	NM_080465	ENSMUSG00000054477	Kcnn2	KCa2.2|SK2|SKCA2|bc|fri	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2	protein-coding
mm_158070.1	chrX	101264019	101264027	-	1	NA	promoter-TSS (NM_001317221)	promoter-TSS (NM_001317221)	-31	NM_001317221	245536	Mm.212463	NM_001033362	ENSMUSG00000090141	Gm614	-	predicted gene 614	protein-coding
mm_164670.1	chr17	45545754	45545759	+	1	NA	exon (NM_001013749, exon 3 of 3)	exon (NM_001013749, exon 3 of 3)	3921	NM_001013749	210573	Mm.329064	NM_001013749	ENSMUSG00000096847	Tmem151b	Gm323	transmembrane protein 151B	protein-coding
mm_127881.1	chr15	8639190	8639190	-	1	NA	exon (NM_148938, exon 9 of 10)	exon (NM_148938, exon 9 of 10)	71617	NM_148938	20512	Mm.204834	NM_148938	ENSMUSG00000005360	Slc1a3	AI504299|B430115D02Rik|Eaat1|GLAST|GLAST-1|GLU-T|GluT-1|Gmt1|MGluT1	solute carrier family 1 (glial high affinity glutamate transporter), member 3	protein-coding
mm_3058.1	chr1	134077847	134077849	+	1	NA	intron (NM_007570, intron 1 of 1)	intron (NM_007570, intron 1 of 1)	1307	NM_007570	12227	Mm.392646	NM_007570	ENSMUSG00000020423	Btg2	AA959598|APRO1|Pc3|TIS21	B cell translocation gene 2, anti-proliferative	protein-coding
mm_76901.1	chr8	105827191	105827214	-	1	NA	promoter-TSS (NM_024445)	promoter-TSS (NM_024445)	148	NM_145824	74334	Mm.4206	NM_145824	ENSMUSG00000037415	Ranbp10	4432417N03Rik	RAN binding protein 10	protein-coding
mm_132118.1	chr16	31695505	31695524	+	1	NA	intron (NR_045516, intron 4 of 24)	intron (NR_045516, intron 4 of 24)	31579	NM_001252434	13383	Mm.382	NM_007862	ENSMUSG00000022770	Dlg1	B130052P05Rik|Dlgh1|E-dlg/SAP97|SAP-97|SAP97|mKIAA4187	discs, large homolog 1 (Drosophila)	protein-coding
mm_40885.1	chr5	74581569	74581572	+	1	NA	intron (NM_001159574, intron 11 of 15)	intron (NM_001159574, intron 11 of 15)	46088	NM_001159574	66899	Mm.272468	NM_024183	ENSMUSG00000029227	Fip1l1	1300019H17Rik|Rje	FIP1 like 1 (S. cerevisiae)	protein-coding
mm_118573.1	chr14	19278149	19278179	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	324423	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_76921.1	chr8	105933716	105933720	-	1	NA	intron (NM_023182, intron 1 of 6)	intron (NM_023182, intron 1 of 6)	144	NM_023182	109660	Mm.2745	NM_023182	ENSMUSG00000031896	Ctrl	0910001G08Rik|1810004D15Rik|AV005227|Ctra-1|Ctra1|chymopasin|mFLJ00366	chymotrypsin-like	protein-coding
mm_26596.1	chr3	151439389	151439429	+	1	NA	intron (NM_133222, intron 2 of 15)	intron (NM_133222, intron 2 of 15)	1527	NM_133222	170757	Mm.317261	NM_133222	ENSMUSG00000039167	Adgrl4	1110033N21Rik|ETL1|Eltd1|Etl	adhesion G protein-coupled receptor L4	protein-coding
mm_126527.1	chr15	81980510	81980546	+	1	NA	promoter-TSS (NM_025503)	promoter-TSS (NM_025503)	-12	NM_025503	66346	Mm.54292	NM_025503	ENSMUSG00000061633	1700029P11Rik	-	RIKEN cDNA 1700029P11 gene	protein-coding
mm_64737.1	chr7	4725232	4725295	-	1	NA	promoter-TSS (NM_177887)	promoter-TSS (NM_177887)	-12	NM_177887	330460	Mm.361851	NM_177887	ENSMUSG00000046456	Tmem150b	A630041N19|Tmem224	transmembrane protein 150B	protein-coding
mm_48585.1	chr5	143732274	143732316	-	1	NA	promoter-TSS (NM_029749)	promoter-TSS (NM_029749)	-15	NM_029749	76800	Mm.259620	NM_029749	ENSMUSG00000051306	Usp42	2410140K03Rik|3110031A07Rik|A630018G05Rik|D5Ertd591e	ubiquitin specific peptidase 42	protein-coding
mm_63681.1	chr7	130552972	130552985	+	1	NA	Intergenic	Intergenic	-5597	NM_001162855	67872	Mm.21714	NM_001162855	ENSMUSG00000040331	Nsmce4a	2410003A14Rik	NSE4 homolog A, SMC5-SMC6 complex component	protein-coding
mm_7439.1	chr1	120073737	120073803	-	1	NA	promoter-TSS (NM_019432)	promoter-TSS (NM_019432)	10	NM_019432	170706	Mm.24750	NM_019432	ENSMUSG00000050777	Tmem37	AI173373|AW540203|Pr|Pr1	transmembrane protein 37	protein-coding
mm_146822.1	chr18	21300081	21300091	-	1	NA	promoter-TSS (NM_001033445)	promoter-TSS (NM_001033445)	53	NM_001033445	381126	Mm.312276	NM_001033445	ENSMUSG00000042680	Garem1	C86169|Fam59a|Garem|Gm944|mKIAA4238	GRB2 associated regulator of MAPK1 subtype 1	protein-coding
mm_100127.1	chr11	115912316	115912335	+	1	NA	5' UTR (NM_001162998, exon 1 of 2)	5' UTR (NM_001162998, exon 1 of 2)	308	NM_001162998	68528	Mm.441893	NM_001162998	ENSMUSG00000075420	Smim6	1110017F19Rik	small integral membrane protein 6	protein-coding
mm_95499.1	chr11	51884008	51884014	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-26530	NM_199299	76901	Mm.259996	NM_199299	ENSMUSG00000020387	Jade2	1200017K05Rik|AI480685|Phf15|mKIAA0239	jade family PHD finger 2	protein-coding
mm_168912.1	chr12	55230479	55230481	+	1	NA	promoter-TSS (NM_001100110)	promoter-TSS (NM_001100110)	2	NM_001100110	100101806	Mm.471968	NM_001100110	ENSMUSG00000079108	Srp54c	E330029E12Rik	signal recognition particle 54C	protein-coding
mm_36291.1	chr4	64046926	64046944	-	1	NA	promoter-TSS (NM_011607)	promoter-TSS (NM_011607)	80	NM_011607	21923	Mm.980	NM_011607	ENSMUSG00000028364	Tnc	AI528729|C130033P17Rik|Hxb|TN|TN-C|Ten|cytotactin|tenascin-C	tenascin C	protein-coding
mm_35604.1	chr4	43045687	43045747	-	1	NA	intron (NR_045567, intron 1 of 7)	intron (NR_045567, intron 1 of 7)	503	NR_045567	230088	Mm.260162	NM_172691	ENSMUSG00000036002	Fam214b	B230312A22Rik	family with sequence similarity 214, member B	protein-coding
mm_120590.1	chr14	69840479	69840481	+	1	NA	promoter-TSS (NM_028526)	promoter-TSS (NM_028526)	73	NM_028526	73523	Mm.23509	NM_028526	ENSMUSG00000022085	Pebp4	PEBP-4	phosphatidylethanolamine binding protein 4	protein-coding
mm_41443.1	chr5	90905258	90905262	+	1	NA	3' UTR (NM_009140, exon 4 of 4)	3' UTR (NM_009140, exon 4 of 4)	1361	NM_009140	20310	Mm.4979	NM_009140	ENSMUSG00000058427	Cxcl2	CINC-2a|GROb|Gro2|MIP-2|MIP-2a|Mgsa-b|Mip2|Scyb|Scyb2	chemokine (C-X-C motif) ligand 2	protein-coding
mm_113545.1	chr13	37930215	37930241	+	1	NA	exon (NM_001039188, exon 10 of 10)	exon (NM_001039188, exon 10 of 10)	41357	NM_001177869	68750	Mm.491109	NM_026830	ENSMUSG00000039087	Rreb1	1110037N09Rik|AA414966|B930013M22Rik	ras responsive element binding protein 1	protein-coding
mm_94841.1	chr11	23666379	23666430	+	1	NA	promoter-TSS (NM_023651)	promoter-TSS (NM_023651)	428	NM_028304	74467	Mm.29536	NM_028304	ENSMUSG00000020280	Pus10	2810013G11Rik|4933435A13Rik|AU014648|C77560|Ccdc139	pseudouridylate synthase 10	protein-coding
mm_90684.1	chr10	128911570	128911598	+	1	NA	exon (NM_007653, exon 3 of 8)	exon (NM_007653, exon 3 of 8)	1718	NM_007653	12512	Mm.371552	NM_007653	ENSMUSG00000025351	Cd63	C75951|ME491|Tspan30	CD63 antigen	protein-coding
mm_126820.1	chr15	88752654	88752658	+	1	NA	intron (NM_181412, intron 1 of 2)	intron (NM_181412, intron 1 of 2)	945	NM_181412	223773	Mm.396622	NM_181412	ENSMUSG00000034333	Zbed4	1700009F06Rik	zinc finger, BED type containing 4	protein-coding
mm_58607.1	chr7	5056883	5056906	+	1	NA	5' UTR (NM_146178, exon 1 of 5)	5' UTR (NM_146178, exon 1 of 5)	168	NM_146178	232821	Mm.482157	NM_146178	ENSMUSG00000035228	Ccdc106	BC018462	coiled-coil domain containing 106	protein-coding
mm_153696.1	chr19	44397432	44397438	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	10274	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_38275.1	chr4	136886163	136886175	-	1	NA	promoter-TSS (NM_009777)	promoter-TSS (NM_009777)	8	NM_009777	12260	Mm.2570	NM_009777	ENSMUSG00000036905	C1qb	-	complement component 1, q subcomponent, beta polypeptide	protein-coding
mm_5494.1	chr1	36939667	36939667	-	1	NA	promoter-TSS (NM_018872)	promoter-TSS (NM_018872)	-140	NM_018872	56030	Mm.186943	NM_018872	ENSMUSG00000026116	Tmem131	2610524E03Rik|CC28|D1Bwg0491e|Neg|RW1|YR-23|mKIAA0257	transmembrane protein 131	protein-coding
mm_98821.1	chr11	97362206	97362254	+	1	NA	promoter-TSS (NM_138657)	promoter-TSS (NM_138657)	-321	NM_138657	192157	Mm.34339	NM_138657	ENSMUSG00000038485	Socs7	2310063P06Rik|C85125|Nap4	suppressor of cytokine signaling 7	protein-coding
mm_63326.1	chr7	126942140	126942159	+	1	NA	exon (NM_172747, exon 5 of 6)	exon (NM_172747, exon 5 of 6)	7432	NM_001347657	233879	Mm.444143	NM_001039645	ENSMUSG00000046378	Asphd1	A830007L07Rik|Gm168	aspartate beta-hydroxylase domain containing 1	protein-coding
mm_34826.1	chr4	155086579	155086610	+	1	NA	promoter-TSS (NM_001081100)	promoter-TSS (NM_001081100)	17	NM_001081100	76866	Mm.200590	NM_001081100	ENSMUSG00000029049	Morn1	2900057D20Rik|4930417P05Rik|AU042805	MORN repeat containing 1	protein-coding
mm_110958.1	chr12	76795426	76795464	-	1	NA	5' UTR (NM_030677, exon 1 of 2)	5' UTR (NM_030677, exon 1 of 2)	109	NM_030677	14776	Mm.441856	NM_030677	ENSMUSG00000042808	Gpx2	GI-GPx|GPx-GI|GSHPx-2|GSHPx-GI	glutathione peroxidase 2	protein-coding
mm_91276.1	chr10	24692379	24692391	-	1	NA	intron (NM_001308327, intron 1 of 24)	intron (NM_001308327, intron 1 of 24)	19774	NM_001308327	18605	Mm.27254	NM_008813	ENSMUSG00000037370	Enpp1	4833416E15Rik|AI428932|C76301|CD203c|E-NPP 1|E-NPP1|Ly-41|M6S1|NPP1|Npps|PC-1|Pca|Pca-1|Pdnp1|ttw|twy	ectonucleotide pyrophosphatase/phosphodiesterase 1	protein-coding
mm_173306.1	chrY	83039359	83039359	+	1	NA	Intergenic	Intergenic	814144	NM_001037748	380994	Mm.391354	NM_001037748	ENSMUSG00000093993	Gm20736	-	predicted gene, 20736	protein-coding
mm_21117.1	chr2	153505316	153505320	-	1	NA	intron (NM_001134300, intron 1 of 10)	intron (NM_001134300, intron 1 of 10)	24653	NM_001134300	329540	Mm.50600	NM_001001986	ENSMUSG00000061411	Nol4l	4931410H15|8430427H17Rik|AI429157|Gm1636	nucleolar protein 4-like	protein-coding
mm_169823.1	chr16	22431100	22431115	-	1	NA	intron (NM_023794, intron 5 of 12)	intron (NM_023794, intron 5 of 12)	8463	NM_023794	104156	Mm.155708	NM_023794	ENSMUSG00000013089	Etv5	1110005E01Rik|8430401F14Rik|ERM	ets variant 5	protein-coding
mm_4284.1	chr1	171681992	171681992	+	1	NA	promoter-TSS (NM_007649)	promoter-TSS (NM_007649)	-63	NM_007649	12506	Mm.1738	NM_007649	ENSMUSG00000015355	Cd48	AI449234|AW610730|BCM1|BLAST|BLAST-1|BLAST1|Bcm-1|MEM-102|SLAMF2|Sgp-60	CD48 antigen	protein-coding
mm_121212.1	chr14	103054532	103054551	+	1	NA	exon (NM_008392, exon 5 of 5)	exon (NM_008392, exon 5 of 5)	7529	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_69415.1	chr7	132576373	132576392	-	1	NA	promoter-TSS (NM_016978)	promoter-TSS (NM_016978)	16	NM_016978	18242	Mm.13694	NM_016978	ENSMUSG00000030934	Oat	AI194874|rhg	ornithine aminotransferase	protein-coding
mm_64803.1	chr7	6691214	6691225	-	1	NA	intron (NM_011769, intron 2 of 7)	B4A|SINE|B4	5213	NM_011769	22776	Mm.89976	NM_011769	ENSMUSG00000002266	Zim1	-	zinc finger, imprinted 1	protein-coding
mm_46259.1	chr5	99617914	99617917	-	1	NA	intron (NR_030692, intron 1 of 3)	intron (NR_030692, intron 1 of 3)	111145	NR_030692	319818	Mm.295233	NR_030692	ENSMUSG00000089809	A930011G23Rik	-	RIKEN cDNA A930011G23 gene	ncRNA
mm_89378.1	chr10	88885996	88886010	+	1	NA	promoter-TSS (NM_145423)	promoter-TSS (NM_145423)	11	NM_145423	216225	Mm.77381	NM_145423	ENSMUSG00000020062	Slc5a8	Ait|SMCT	solute carrier family 5 (iodide transporter), member 8	protein-coding
mm_40881.1	chr5	74535536	74535558	+	1	NA	promoter-TSS (NM_001159573)	promoter-TSS (NM_001159573)	65	NM_001159574	66899	Mm.272468	NM_024183	ENSMUSG00000029227	Fip1l1	1300019H17Rik|Rje	FIP1 like 1 (S. cerevisiae)	protein-coding
mm_86245.1	chr9	121313701	121313706	-	1	NA	Intergenic	RMER17C|LTR|ERVK	-36531	NM_177589	209012	Mm.371804	NM_177589	ENSMUSG00000040936	Ulk4	4932415A06Rik|A730098P15	unc-51-like kinase 4	protein-coding
mm_43605.1	chr5	137887963	137887963	+	1	NA	Intergenic	Intergenic	-16205	NM_001024932	545812	Mm.332769	NM_001024932	ENSMUSG00000066682	Pilrb2	EG545812	paired immunoglobin-like type 2 receptor beta 2	protein-coding
mm_67340.1	chr7	79801540	79801553	-	1	NA	Intergenic	Intergenic	-7956	NM_008588	17292	Mm.1404	NM_008588	ENSMUSG00000030544	Mesp1	bHLHc5	mesoderm posterior 1	protein-coding
mm_20700.1	chr2	132945594	132945639	-	1	NA	5' UTR (NM_198029, exon 1 of 15)	5' UTR (NM_198029, exon 1 of 15)	420	NM_198029	241639	Mm.209784	NM_198029	ENSMUSG00000027356	Fermt1	5830467P10Rik|Kindlin-1	fermitin family member 1	protein-coding
mm_65553.1	chr7	27133320	27133341	-	1	NA	exon (NM_007817, exon 10 of 10)	exon (NM_007817, exon 10 of 10)	13375	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_118388.1	chr13	117273074	117273104	-	1	NA	3' UTR (NM_010330, exon 9 of 9)	3' UTR (NM_010330, exon 9 of 9)	52516	NM_010330	13723	Mm.274926	NM_010330	ENSMUSG00000021728	Emb	AL022799|Gp70	embigin	protein-coding
mm_98514.1	chr11	94952457	94952474	+	1	NA	3' UTR (NM_007742, exon 51 of 51)	3' UTR (NM_007742, exon 51 of 51)	-15128	NM_018792	54388	Mm.30482	NM_018792	ENSMUSG00000038994	Hils1	H1.9|TISP64	histone H1-like protein in spermatids 1	protein-coding
mm_136491.1	chr16	96124959	96124967	-	1	NA	intron (NM_008251, intron 4 of 5)	intron (NM_008251, intron 4 of 5)	2762	NM_008251	15312	Mm.2756	NM_008251	ENSMUSG00000040681	Hmgn1	HMG-14|Hmg14	high mobility group nucleosomal binding domain 1	protein-coding
mm_170316.1	chr18	37618919	37618925	+	1	NA	intron (NM_001301259, intron 1 of 3)	RLTR31M|LTR|ERVK	19801	NM_001159275	83885	Mm.193029	NM_001159275	ENSMUSG00000050304	Slc25a2	Ornt2	solute carrier family 25 (mitochondrial carrier, ornithine transporter) member 2	protein-coding
mm_166612.1	chr6	70726851	70726851	+	1	NA	Intergenic	Intergenic	65324	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_130769.1	chr15	101412287	101412312	-	1	NA	promoter-TSS (NM_033073)	promoter-TSS (NM_033073)	-104	NM_033073	110310	Mm.486285	NM_033073	ENSMUSG00000023039	Krt7	D15Wsu77e|K7|Krt2-7	keratin 7	protein-coding
mm_152715.1	chr19	17394519	17394531	-	1	NA	intron (NM_019437, intron 1 of 3)	intron (NM_019437, intron 1 of 3)	482	NM_019437	54391	Mm.7013	NM_019437	ENSMUSG00000024712	Rfk	0610038L10Rik|AF031381|KOI-4	riboflavin kinase	protein-coding
mm_51077.1	chr6	66918512	66918523	+	1	NA	intron (NM_001177556, intron 2 of 3)	intron (NM_001177556, intron 2 of 3)	21626	NM_001177558	14701	Mm.234342	NM_025278	ENSMUSG00000036402	Gng12	2010305F15Rik|AA536815|AI115529|AI314170|AI842738	guanine nucleotide binding protein (G protein), gamma 12	protein-coding
mm_72678.1	chr8	84913424	84913438	+	1	NA	promoter-TSS (NR_103491)	promoter-TSS (NR_103491)	96	NR_103491	100503676	Mm.437155	NR_103491	ENSMUSG00000003812	Gm38426	-	predicted gene, 38426	ncRNA
mm_30398.1	chr3	152250160	152250173	-	1	NA	intron (NM_199465, intron 4 of 12)	B1_Mur3|SINE|Alu	16154	NM_199465	68810	Mm.200188	NM_199465	ENSMUSG00000039103	Nexn	1110046H09Rik|AA553326|NELIN	nexilin	protein-coding
mm_146894.1	chr18	29496514	29496519	-	1	NA	promoter-TSS (NR_045391)	promoter-TSS (NR_045391)	-100	NR_045391	78058	Mm.416952	NR_045391		4930578E11Rik	-	RIKEN cDNA 4930578E11 gene	ncRNA
mm_110368.1	chr12	40134176	40134190	-	1	NA	promoter-TSS (NM_001146196)	promoter-TSS (NM_001146196)	45	NM_009132	20259	Mm.2416	NM_009132	ENSMUSG00000002565	Scin	AW545522|adseverin	scinderin	protein-coding
mm_91360.1	chr10	28985380	28985385	-	1	NA	intron (NM_026336, intron 1 of 5)	intron (NM_026336, intron 1 of 5)	924	NM_026336	67719	Mm.440480	NM_026336	ENSMUSG00000015519	2310057J18Rik	2210414P04Rik|Leg1	RIKEN cDNA 2310057J18 gene	protein-coding
mm_57974.1	chr6	135713442	135713472	-	1	NA	Intergenic	Intergenic	54544	NR_126088	75024	Mm.399147	NR_126088	ENSMUSG00000107396	4930425L21Rik	4930473P14Rik	RIKEN cDNA 4930425L21 gene	ncRNA
mm_69426.1	chr7	132808432	132808459	-	1	NA	intron (NM_212473, intron 1 of 4)	(TAAAAA)n|Simple_repeat|Simple_repeat	4751	NM_212473	77938	Mm.225649	NM_175268	ENSMUSG00000030956	Fam53b	A930008G19Rik|mKIAA0140	family with sequence similarity 53, member B	protein-coding
mm_41256.1	chr5	88886810	88886825	+	1	NA	promoter-TSS (NM_001136260)	promoter-TSS (NM_001136260)	-443	NM_001197147	54403	Mm.41044	NM_018760	ENSMUSG00000060961	Slc4a4	AI835705|NBC|NBC1	solute carrier family 4 (anion exchanger), member 4	protein-coding
mm_110801.1	chr12	72212207	72212257	-	1	NA	non-coding (NR_104446, exon 7 of 7)	non-coding (NR_104446, exon 7 of 7)	23514	NR_104446	104001	Mm.221275	NM_153457	ENSMUSG00000021087	Rtn1	Nsp	reticulon 1	protein-coding
mm_53766.1	chr6	145816502	145816521	+	1	NA	exon (NM_027760, exon 3 of 4)	exon (NM_027760, exon 3 of 4)	8128	NM_027760	71323	Mm.158669	NM_027760	ENSMUSG00000030259	Rassf8	5133400D11Rik|AA815821|AW123240|Hoj1|mHoj-1	Ras association (RalGDS/AF-6) domain family (N-terminal) member 8	protein-coding
mm_18737.1	chr2	72997149	72997160	-	1	NA	Intergenic	Intergenic	-16708	NM_001018042	20687	Mm.124328	NM_011450	ENSMUSG00000027109	Sp3	D130027J01Rik	trans-acting transcription factor 3	protein-coding
mm_60447.1	chr7	44477243	44477253	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	6901	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_101133.1	chr11	12464747	12464759	-	1	NA	5' UTR (NM_001282993, exon 1 of 14)	5' UTR (NM_001282993, exon 1 of 14)	207	NM_172496	12808	Mm.22847	NM_172496	ENSMUSG00000020173	Cobl	-	cordon-bleu WH2 repeat	protein-coding
mm_69137.1	chr7	127042422	127042444	-	1	NA	promoter-TSS (NM_145588)	promoter-TSS (NM_145588)	-13	NM_145588	110033	Mm.286488	NM_145588	ENSMUSG00000030677	Kif22	AU021460|C81217|Kid|Kif22a	kinesin family member 22	protein-coding
mm_41205.1	chr5	88521247	88521264	+	1	NA	3' UTR (NM_152839, exon 4 of 4)	3' UTR (NM_152839, exon 4 of 4)	6642	NM_152839	16069	Mm.1192	NM_152839	ENSMUSG00000067149	Jchain	9530090F24Rik|AI323815|Igj|Jch	immunoglobulin joining chain	protein-coding
mm_166419.1	chr5	137151685	137151693	-	1	NA	Intergenic	Intergenic	-35482	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_90231.1	chr10	121374402	121374439	+	1	NA	exon (NM_029364, exon 3 of 14)	exon (NM_029364, exon 3 of 14)	9330	NM_029364	75612	Mm.207683	NM_029364	ENSMUSG00000034707	Gns	2610016K11Rik|AU042285|C87209|G6S|N28088	glucosamine (N-acetyl)-6-sulfatase	protein-coding
mm_5841.1	chr1	52953117	52953156	-	1	NA	promoter-TSS (NM_144953)	promoter-TSS (NM_144953)	-296	NM_144953	67080	Mm.236287	NM_144953	ENSMUSG00000043629	1700019D03Rik	2410136C24Rik|AA410151|smAKAP	RIKEN cDNA 1700019D03 gene	protein-coding
mm_169736.1	chr15	83432860	83432873	-	1	NA	promoter-TSS (NM_001159510)	promoter-TSS (NM_001159510)	-16	NM_001159510	23970	Mm.23978	NM_011862	ENSMUSG00000016664	Pacsin2	AI197433	protein kinase C and casein kinase substrate in neurons 2	protein-coding
mm_122914.1	chr14	54958612	54958628	-	1	NA	exon (NM_010856, exon 15 of 39)	exon (NM_010856, exon 15 of 39)	7987	NM_001164171	17888	Mm.290003	NM_010856	ENSMUSG00000040752	Myh6	A830009F23Rik|AA517445|Myhc-a|Myhca|alpha-MHC	myosin, heavy polypeptide 6, cardiac muscle, alpha	protein-coding
mm_170978.1	chr2	69766296	69766298	+	1	NA	intron (NM_001077684, intron 7 of 8)	intron (NM_001077684, intron 7 of 8)	23189	NM_001077684	75051	Mm.195726	NM_001077684	ENSMUSG00000070883	Ccdc173	4930525K21Rik|4930578N16Rik	coiled-coil domain containing 173	protein-coding
mm_67625.1	chr7	84151774	84151787	-	1	NA	exon (NM_133722, exon 1 of 3)	exon (NM_133722, exon 1 of 3)	113	NM_133722	70178	Mm.23914	NM_133722	ENSMUSG00000038459	Abhd17c	2210412D01Rik|AL023007|Fam108c|Fam108c1	abhydrolase domain containing 17C	protein-coding
mm_86827.1	chr10	21159201	21159207	+	1	NA	intron (NM_010848, intron 1 of 14)	CpG	1780	NM_001198914	17863	Mm.52109	NM_010848	ENSMUSG00000019982	Myb	AI550390|M16449|c-myb	myeloblastosis oncogene	protein-coding
mm_39793.1	chr5	30588175	30588185	+	1	NA	promoter-TSS (NM_010608)	promoter-TSS (NM_010608)	10	NM_010608	16527	Mm.439936	NM_010608	ENSMUSG00000049265	Kcnk3	TASK|Task-1|cTBAK-1	potassium channel, subfamily K, member 3	protein-coding
mm_102896.1	chr11	69423885	69423892	-	1	NA	exon (NM_001081330, exon 78 of 86)	exon (NM_001081330, exon 78 of 86)	-10213	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_51498.1	chr6	83101566	83101609	+	1	NA	promoter-TSS (NM_001081266)	promoter-TSS (NM_001081266)	71	NM_001081266	243510	Mm.436553	NM_001081266	ENSMUSG00000079511	Ccdc142	A230058J24Rik	coiled-coil domain containing 142	protein-coding
mm_2988.1	chr1	133132223	133132235	+	1	NA	exon (NM_133819, exon 1 of 2)	exon (NM_133819, exon 1 of 2)	1063	NM_133819	108954	Mm.293628	NM_133819	ENSMUSG00000046062	Ppp1r15b	1810033K10Rik|AI606441|C530022L24Rik|CReP	protein phosphatase 1, regulatory (inhibitor) subunit 15b	protein-coding
mm_155161.1	chrX	52988120	52988148	+	1	NA	promoter-TSS (NM_013556)	promoter-TSS (NM_013556)	56	NM_013556	15452	Mm.299381	NM_013556	ENSMUSG00000025630	Hprt	C81579|HPGRT|Hprt1	hypoxanthine guanine phosphoribosyl transferase	protein-coding
mm_21382.1	chr2	157450984	157450989	-	1	NA	intron (NM_009271, intron 2 of 14)	intron (NM_009271, intron 2 of 14)	26693	NM_001025395	20779	Mm.22845	NM_009271	ENSMUSG00000027646	Src	AW259666|pp60c-src	Rous sarcoma oncogene	protein-coding
mm_158362.1	chrX	134751371	134751424	-	1	NA	promoter-TSS (NM_001007578)	promoter-TSS (NM_001007578)	22	NM_001007578	278097	Mm.113272	NM_001007578	ENSMUSG00000050394	Armcx6	AW060994	armadillo repeat containing, X-linked 6	protein-coding
mm_84206.1	chr9	60687960	60687974	-	1	NA	promoter-TSS (NM_001146047)	promoter-TSS (NM_001146047)	167	NM_145616	102747	Mm.269413	NM_145616	ENSMUSG00000047766	Lrrc49	AI430817|AW050057|D430025H09Rik|PGs4|p79	leucine rich repeat containing 49	protein-coding
mm_164207.1	chr15	82197415	82197417	+	1	NA	promoter-TSS (NR_029804)	promoter-TSS (NR_029804)	-706	NR_029804	723897		NR_029804	ENSMUSG00000065465	Mir33	Mirn33|mir-33|mmu-mir-33	microRNA 33	ncRNA
mm_16760.1	chr2	9877444	9877459	-	1	NA	exon (NM_008091, exon 2 of 6)	exon (NM_008091, exon 2 of 6)	1149	NM_008091	14462	Mm.313866	NM_008091	ENSMUSG00000015619	Gata3	Gata-3|jal	GATA binding protein 3	protein-coding
mm_41536.1	chr5	92843672	92843675	+	1	NA	intron (NM_001077595, intron 1 of 9)	intron (NM_001077595, intron 1 of 9)	34291	NM_001077595	27428	Mm.46014	NM_015756	ENSMUSG00000029381	Shroom3	AL022960|D5Ertd287e|Shrm|Shrm3	shroom family member 3	protein-coding
mm_128252.1	chr15	36770964	36770974	-	1	NA	3' UTR (NM_001253807, exon 5 of 5)	3' UTR (NM_001253807, exon 5 of 5)	19963	NM_001253807	22631	Mm.3360	NM_011740	ENSMUSG00000022285	Ywhaz	1110013I11Rik|14-3-3zeta|AI596267|AL022924|AU020854	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide	protein-coding
mm_72532.1	chr8	83995414	83995430	+	1	NA	3' UTR (NM_008854, exon 10 of 10)	3' UTR (NM_008854, exon 10 of 10)	-2250	NM_001081415	666704	Mm.298091	NM_001081415	ENSMUSG00000079003	Samd1	AA589507	sterile alpha motif domain containing 1	protein-coding
mm_67444.1	chr7	80388720	80388730	-	1	NA	promoter-TSS (NM_010194)	promoter-TSS (NM_010194)	-779	NM_010194	14159	Mm.48757	NM_010194	ENSMUSG00000053158	Fes	AI586313|BB137047|FPS|c-fes	feline sarcoma oncogene	protein-coding
mm_20804.1	chr2	144270837	144270847	-	1	NA	promoter-TSS (NM_024225)	promoter-TSS (NM_024225)	60	NM_001199188	69178	Mm.273379	NM_024225	ENSMUSG00000027423	Snx5	0910001N05Rik|1810032P22Rik|AU019504|D2Ertd52e	sorting nexin 5	protein-coding
mm_150106.1	chr19	29522264	29522341	+	1	NA	promoter-TSS (NM_001081319)	promoter-TSS (NM_001081319)	20	NM_001081319	226089	Mm.353838	NM_177641	ENSMUSG00000038658	Ric1	C030046E11Rik|C130057E09Rik|Kiaa1432	RAB6A GEF complex partner 1	protein-coding
mm_9341.1	chr1	172028965	172028975	-	1	NA	Intergenic	Intergenic	-1675	NM_033509	93840	Mm.36148	NM_033509	ENSMUSG00000026556	Vangl2	C530001F03Rik|Lootl|Lp|Lpp1|Ltap|Vang1l2|loop-tail|ska17|ska<m17Jus>|stbm|strabismus	vang-like 2 (van gogh, Drosophila)	protein-coding
mm_32211.1	chr4	101550341	101550374	+	1	NA	promoter-TSS (NM_001164583)	promoter-TSS (NM_001164583)	-237	NM_001164583	72685	Mm.76494	NM_198412	ENSMUSG00000028528	Dnajc6	2810027M23Rik|mKIAA0473	DnaJ heat shock protein family (Hsp40) member C6	protein-coding
mm_11514.1	chr2	32587160	32587176	+	1	NA	promoter-TSS (NM_011373)	promoter-TSS (NM_011373)	90	NM_011373	20448	Mm.27446	NM_011373	ENSMUSG00000079442	St6galnac4	SIAT7-D|ST6GalNAcIV|Siat7d	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 4	protein-coding
mm_75686.1	chr8	68158490	68158516	-	1	NA	Intergenic	Intergenic	-118025	NM_028182	72281	Mm.40974	NM_028182	ENSMUSG00000053886	Sh2d4a	2210402M20Rik|SH2A	SH2 domain containing 4A	protein-coding
mm_59492.1	chr7	27523234	27523242	+	1	NA	promoter-TSS (NM_001033315)	promoter-TSS (NM_001033315)	-23	NM_001033315	233020	Mm.429716	NM_001033315	ENSMUSG00000040424	Hipk4	Gm162	homeodomain interacting protein kinase 4	protein-coding
mm_121462.1	chr14	120798711	120798720	+	1	NA	Intergenic	RMER17A2|LTR|ERVK	-112479	NM_023579	70572	Mm.221452	NM_023579	ENSMUSG00000030662	Ipo5	1110011C18Rik|5730478E03Rik|AA409333|C76941|IMB3|Kpnb3|Ranbp5	importin 5	protein-coding
mm_103618.1	chr11	78652683	78652685	-	1	NA	intron (NM_008702, intron 1 of 10)	intron (NM_008702, intron 1 of 10)	44741	NM_008702	18099	Mm.9001	NM_008702	ENSMUSG00000017376	Nlk	AI194375	nemo like kinase	protein-coding
mm_60893.1	chr7	46397328	46397339	+	1	NA	5' UTR (NM_001112739, exon 1 of 4)	5' UTR (NM_001112739, exon 1 of 4)	865	NM_001112739	16502	Mm.249386	NM_008421	ENSMUSG00000058975	Kcnc1	C230009H10Rik|KShIIIB|KV4|Kcr2-1|Kv3.1|NGK2|Shaw	potassium voltage gated channel, Shaw-related subfamily, member 1	protein-coding
mm_65648.1	chr7	28115282	28115293	-	1	NA	intron (NM_001122603, intron 17 of 19)	intron (NM_001122603, intron 17 of 19)	-14179	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_43216.1	chr5	129725082	129725143	+	1	NA	promoter-TSS (NM_008095)	promoter-TSS (NM_008095)	37	NM_008095	14467	Mm.12468	NM_008095	ENSMUSG00000029432	Gbas	AV006093|Nipsnap2	glioblastoma amplified sequence	protein-coding
mm_95861.1	chr11	58009080	58009090	+	1	NA	promoter-TSS (NM_028451)	promoter-TSS (NM_028451)	21	NM_028451	73158	Mm.248843	NM_028451	ENSMUSG00000037331	Larp1	1810024J12Rik|3110040D16Rik|Larp|mKIAA0731	La ribonucleoprotein domain family, member 1	protein-coding
mm_31368.1	chr4	47312196	47312226	+	1	NA	exon (NM_009928, exon 40 of 40)	exon (NM_009928, exon 40 of 40)	-41011	NM_001312868	21812	Mm.197552	NM_009370	ENSMUSG00000007613	Tgfbr1	ALK5|AU017191|Alk-5|ESK2|TGFR-1|TbetaR-I|TbetaRI	transforming growth factor, beta receptor I	protein-coding
mm_61600.1	chr7	80026633	80026658	+	1	NA	intron (NM_175433, intron 1 of 4)	intron (NM_175433, intron 1 of 4)	417	NM_175433	209225	Mm.290925	NM_175433	ENSMUSG00000048897	Zfp710	5430400N05Rik|9830165K13|AI324798|Znf710	zinc finger protein 710	protein-coding
mm_63244.1	chr7	126585911	126585924	+	1	NA	promoter-TSS (NM_001146311)	promoter-TSS (NM_001146311)	-100	NM_001146311	12752	Mm.268930	NM_009907	ENSMUSG00000030720	Cln3	AI323623	ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease)	protein-coding
mm_101606.1	chr11	34833632	34833663	-	1	NA	promoter-TSS (NM_027411)	promoter-TSS (NM_027411)	-6	NM_027411	70385	Mm.194368	NM_027411	ENSMUSG00000069910	Spdl1	1700018I02Rik|2600001J17Rik|2810049B11Rik|AA409762|Ccdc99	spindle apparatus coiled-coil protein 1	protein-coding
mm_66123.1	chr7	31053445	31053463	-	1	NA	exon (NM_019503, exon 4 of 8)	exon (NM_019503, exon 4 of 8)	1399	NM_052991	56188	Mm.1491	NM_019503	ENSMUSG00000036570	Fxyd1	0610012C17Rik|1110006M24Rik|Plm|Pml	FXYD domain-containing ion transport regulator 1	protein-coding
mm_33110.1	chr4	124737649	124737659	+	1	NA	Intergenic	Intergenic	-4196	NM_008385	16330	Mm.296202	NM_008385	ENSMUSG00000028894	Inpp5b	5PTase|AW260155|INPP5P	inositol polyphosphate-5-phosphatase B	protein-coding
mm_97985.1	chr11	83942085	83942105	+	1	NA	promoter-TSS (NM_030096)	promoter-TSS (NM_030096)	5	NM_030096	78394	Mm.280544	NM_030096	ENSMUSG00000020677	Ddx52	2700029C06Rik|ROK1	DEAD (Asp-Glu-Ala-Asp) box polypeptide 52	protein-coding
mm_6811.1	chr1	84157336	84157349	-	1	NA	intron (NM_001003948, intron 2 of 2)	intron (NM_001003948, intron 2 of 2)	61619	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_155018.1	chrX	42059604	42059664	+	1	NA	Intergenic	PB1D7|SINE|Alu	-8202	NM_009688	11798	Mm.259879	NM_009688	ENSMUSG00000025860	Xiap	1110015C02Rik|Aipa|Api3|Birc4|IAP3|ILP-1|MIHA	X-linked inhibitor of apoptosis	protein-coding
mm_82967.1	chr9	35687387	35687391	-	1	NA	promoter-TSS (NM_001199953)	promoter-TSS (NM_001199953)	-18	NM_001199953	100312987	Mm.445254	NM_001167677	ENSMUSG00000091215	Pate1	Gm17252|Pate	prostate and testis expressed 1	protein-coding
mm_13510.1	chr2	109896308	109896318	+	1	NA	exon (NM_011699, exon 4 of 5)	exon (NM_011699, exon 4 of 5)	5435	NM_011699	22343	Mm.235300	NM_011699	ENSMUSG00000027162	Lin7c	9130007B12Rik|AI303698|AU019331|AW125731|D2Ertd520e|LIN-7-C|LIN-7C|MALS-3|Veli3	lin-7 homolog C (C. elegans)	protein-coding
mm_138780.1	chr17	37270256	37270260	+	1	NA	promoter-TSS (NM_013819)	promoter-TSS (NM_013819)	24	NM_013819	14991	Mm.14437	NM_013819	ENSMUSG00000016206	H2-M3	H-2M3|Hmt|M3a|MuprM3|MuprM301|MuprM302|R4B2	histocompatibility 2, M region locus 3	protein-coding
mm_96790.1	chr11	69965863	69965900	+	1	NA	5' UTR (NM_016887, exon 1 of 4)	5' UTR (NM_016887, exon 1 of 4)	460	NM_016887	53624	Mm.281896	NM_016887	ENSMUSG00000018569	Cldn7	-	claudin 7	protein-coding
mm_28821.1	chr3	96285979	96285992	-	1	NA	exon (NM_010186, exon 5 of 6)	exon (NM_010186, exon 5 of 6)	7984	NM_010186	14129	Mm.150	NM_010186	ENSMUSG00000015947	Fcgr1	AI323638|AV092959|CD64|FcgammaRI|IGGHAFC	Fc receptor, IgG, high affinity I	protein-coding
mm_77712.1	chr8	126592086	126592107	-	1	NA	intron (NM_001164598, intron 1 of 1)	intron (NM_001164598, intron 1 of 1)	1340	NM_001164598	270110	Mm.334918	NM_001164598	ENSMUSG00000051495	Irf2bp2	E130305N23Rik|IRF-2BP2	interferon regulatory factor 2 binding protein 2	protein-coding
mm_87346.1	chr10	43524135	43524158	+	1	NA	TTS (NM_026411)	TTS (NM_026411)	16848	NM_026411	67851	Mm.209953	NM_026411	ENSMUSG00000019797	1700021F05Rik	-	RIKEN cDNA 1700021F05 gene	protein-coding
mm_35304.1	chr4	24430839	24430855	-	1	NA	Intergenic	Intergenic	-65615	NM_199467	212377	Mm.120919	NM_199467	ENSMUSG00000045751	Mms22l	F730047E07Rik|Gm134	MMS22-like, DNA repair protein	protein-coding
mm_169426.1	chr14	53461069	53461083	+	1	NA	Intergenic	Intergenic	792853	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_25623.1	chr3	118712960	118712986	+	1	NA	intron (NM_170778, intron 3 of 22)	intron (NM_170778, intron 3 of 22)	150795	NM_170778	99586	Mm.27907	NM_170778	ENSMUSG00000033308	Dpyd	AI315208|DPD|E330028L06Rik	dihydropyrimidine dehydrogenase	protein-coding
mm_7641.1	chr1	128016154	128016189	-	1	NA	intron (NM_027678, intron 7 of 20)	intron (NM_027678, intron 7 of 20)	86300	NM_027678	226409	Mm.425048	NM_027678	ENSMUSG00000036086	Zranb3	4933425L19Rik|AH2|AI316834|C730006D09	zinc finger, RAN-binding domain containing 3	protein-coding
mm_3301.1	chr1	136699651	136699659	+	1	NA	intron (NR_037986, intron 1 of 4)	(T)n|Simple_repeat|Simple_repeat	3444	NR_037986	100503474	Mm.428276	NR_037986		Platr22	Gm16880	pluripotency associated transcript 22	ncRNA
mm_125472.1	chr15	54410736	54410748	+	1	NA	promoter-TSS (NM_173422)	promoter-TSS (NM_173422)	-32	NM_173422	239447	Mm.82400	NM_173422	ENSMUSG00000038591	Colec10	CL-L1	collectin sub-family member 10	protein-coding
mm_6622.1	chr1	77457265	77457272	-	1	NA	intron (NM_007936, intron 3 of 17)	(A)n|Simple_repeat|Simple_repeat	39500	NR_105770	102465180		NR_105770	ENSMUSG00000099141	Mir6352	Gm27481|mmu-mir-6352	microRNA 6352	ncRNA
mm_38631.1	chr4	142239357	142239418	-	1	NA	promoter-TSS (NM_001109685)	promoter-TSS (NM_001109685)	14	NM_001109685	71529	Mm.255986	NM_144531	ENSMUSG00000040606	Kazn	2310007B04Rik|9030409G11Rik|AI256607|AI666764|AW061099|Kaz|Kazrin	kazrin, periplakin interacting protein	protein-coding
mm_115535.1	chr13	6604380	6604395	-	1	NA	intron (NM_019703, intron 10 of 21)	intron (NM_019703, intron 10 of 21)	44384	NM_019703	56421	Mm.273874	NM_019703	ENSMUSG00000021196	Pfkp	1200015H23Rik|9330125N24Rik|ATP-PFK|PFK-C|PFK-P	phosphofructokinase, platelet	protein-coding
mm_76877.1	chr8	105567633	105567648	-	1	NA	5' UTR (NM_001271806, exon 2 of 5)	5' UTR (NM_001271806, exon 2 of 5)	661	NM_007427	11604	Mm.441696	NM_007427	ENSMUSG00000005705	Agrp	Agrt|Art	agouti related neuropeptide	protein-coding
mm_96961.1	chr11	70647259	70647294	+	1	NA	promoter-TSS (NM_024211)	promoter-TSS (NM_024211)	-11	NM_001316728	70510	Mm.261818	NM_027445	ENSMUSG00000040746	Rnf167	0610010G05Rik|5730408C10Rik|AU019305|AV328608	ring finger protein 167	protein-coding
mm_33550.1	chr4	130934895	130934907	+	1	NA	3' UTR (NM_010686, exon 8 of 8)	3' UTR (NM_010686, exon 8 of 8)	-9484	NM_010769	17180	Mm.271796	NM_010769	ENSMUSG00000040533	Matn1	CMP|Crtm|Mat1|matrilin-1	matrilin 1, cartilage matrix protein	protein-coding
mm_6332.1	chr1	71626231	71626251	-	1	NA	exon (NM_001276413, exon 19 of 44)	exon (NM_001276413, exon 19 of 44)	26993	NM_010233	14268	Mm.193099	NM_010233	ENSMUSG00000026193	Fn1	E330027I09|Fn|Fn-1	fibronectin 1	protein-coding
mm_18075.1	chr2	42653030	42653050	-	1	NA	5' UTR (NM_053011, exon 1 of 91)	5' UTR (NM_053011, exon 1 of 91)	558	NM_053011	94217	Mm.441398	NM_053011	ENSMUSG00000049252	Lrp1b	9630004P12Rik|LRP-DIT	low density lipoprotein-related protein 1B (deleted in tumors)	protein-coding
mm_91347.1	chr10	26772369	26772402	-	1	NA	promoter-TSS (NM_176837)	promoter-TSS (NM_176837)	-127	NM_176837	73910	Mm.356496	NM_176837	ENSMUSG00000039031	Arhgap18	4833419J07Rik|AI314906|AI843501	Rho GTPase activating protein 18	protein-coding
mm_82011.1	chr9	121719125	121719137	+	1	NA	promoter-TSS (NM_010918)	promoter-TSS (NM_010918)	-50	NM_010918	18087	Mm.32842	NM_010918	ENSMUSG00000032525	Nktr	5330401F18Rik|D9Wsu172e	natural killer tumor recognition sequence	protein-coding
mm_54744.1	chr6	41031685	41031744	-	1	NA	exon (NM_023333, exon 5 of 5)	exon (NM_023333, exon 5 of 5)	3795	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_89467.1	chr10	93453473	93453483	+	1	NA	promoter-TSS (NM_008517)	promoter-TSS (NM_008517)	82	NM_008517	16993	Mm.271071	NM_008517	ENSMUSG00000015889	Lta4h	-	leukotriene A4 hydrolase	protein-coding
mm_73463.1	chr8	106660921	106660931	+	1	NA	exon (NM_009864, exon 10 of 16)	exon (NM_009864, exon 10 of 16)	-22142	NM_173037	272538	Mm.87151	NM_173037	ENSMUSG00000041949	Tango6	AW413431|E330010G16|Tmco7	transport and golgi organization 6	protein-coding
mm_522.1	chr1	37603594	37603595	+	1	NA	Intergenic	B3A|SINE|B2	-62578	NM_173870	269181	Mm.25861	NM_173870	ENSMUSG00000026110	Mgat4a	9530018I07Rik|GnT-IVa|glcNAc-T-IVa	mannoside acetylglucosaminyltransferase 4, isoenzyme A	protein-coding
mm_129396.1	chr15	78246274	78246299	-	1	NA	intron (NM_008677, intron 1 of 9)	intron (NM_008677, intron 1 of 9)	1475	NM_008677	17972	Mm.2068	NM_008677	ENSMUSG00000071715	Ncf4	AI451400|p40phox	neutrophil cytosolic factor 4	protein-coding
mm_142136.1	chr17	35916341	35916411	-	1	NA	promoter-TSS (NM_025878)	promoter-TSS (NM_025878)	-7	NM_025878	66973	Mm.29484	NM_025878	ENSMUSG00000024436	Mrps18b	2400002C15Rik	mitochondrial ribosomal protein S18B	protein-coding
mm_91261.1	chr10	23349893	23349919	-	1	NA	promoter-TSS (NM_001347372)	promoter-TSS (NM_001347372)	-16	NM_001347372	14051	Mm.332128	NM_010167	ENSMUSG00000010461	Eya4	B130023L16Rik	EYA transcriptional coactivator and phosphatase 4	protein-coding
mm_156823.1	chrX	164157921	164157934	+	1	NA	exon (NM_027286, exon 4 of 18)	exon (NM_027286, exon 4 of 18)	17447	NM_027286	70008	Mm.13451	NM_027286	ENSMUSG00000015405	Ace2	2010305L05Rik	angiotensin I converting enzyme (peptidyl-dipeptidase A) 2	protein-coding
mm_73552.1	chr8	108957864	108957867	+	1	NA	3' UTR (NM_007496, exon 10 of 10)	3' UTR (NM_007496, exon 10 of 10)	21005	NR_037295	100526511		NR_037295	ENSMUSG00000093241	Mir3108	mir-3108|mmu-mir-3108	microRNA 3108	ncRNA
mm_137689.1	chr17	28872619	28872627	+	1	NA	intron (NM_001034885, intron 1 of 9)	MTE2b|LTR|ERVL-MaLR	14212	NM_001034885	433091	Mm.328925	NM_001034885	ENSMUSG00000043286	Pnpla1	-	patatin-like phospholipase domain containing 1	protein-coding
mm_14871.1	chr2	148799657	148799674	+	1	NA	intron (NM_009978, intron 1 of 3)	intron (NM_009978, intron 1 of 3)	826	NM_009978	13012	Mm.20435	NM_009978	ENSMUSG00000027442	Cst8	Cres|Cst-rs1	cystatin 8 (cystatin-related epididymal spermatogenic)	protein-coding
mm_164217.1	chr15	84923107	84923154	-	1	NA	promoter-TSS (NM_016714)	promoter-TSS (NM_016714)	-298	NM_016714	18141	Mm.28379	NM_016714	ENSMUSG00000016619	Nup50	1700030K07Rik|AI413123|Npap60	nucleoporin 50	protein-coding
mm_122036.1	chr14	30008781	30008796	-	1	NA	promoter-TSS (NM_001136240)	promoter-TSS (NM_001136240)	108	NM_019583	50905	Mm.269363	NM_019583	ENSMUSG00000015966	Il17rb	Evi27|IL-17ER|IL-17Rh1|IL17RH1|Il17br	interleukin 17 receptor B	protein-coding
mm_103719.1	chr11	79530408	79530418	-	1	NA	5' UTR (NM_010161, exon 1 of 2)	5' UTR (NM_010161, exon 1 of 2)	196	NM_146023	101488212	Mm.439665	NM_146023	ENSMUSG00000070354	Gm21975	Evi2a-evi2b	predicted gene 21975	protein-coding
mm_98747.1	chr11	96532882	96532883	+	1	NA	intron (NM_001033186, intron 3 of 12)	intron (NM_001033186, intron 3 of 12)	68291	NM_001177898	78473	Mm.395840	NM_001033186	ENSMUSG00000057058	Skap1	1700091G21Rik|Scap1|Skap-55	src family associated phosphoprotein 1	protein-coding
mm_50761.1	chr6	53573365	53573394	+	1	NA	promoter-TSS (NM_172728)	promoter-TSS (NM_172728)	5	NM_172728	231991	Mm.227444	NM_172728	ENSMUSG00000053007	Creb5	9430076C15Rik|CRE-BPa|Crebpa|D430026C09Rik	cAMP responsive element binding protein 5	protein-coding
mm_50644.1	chr6	51463425	51463461	+	1	NA	exon (NM_182650, exon 9 of 10)	exon (NM_182650, exon 9 of 10)	6451	NM_182650	53379	Mm.155896	NM_016806	ENSMUSG00000004980	Hnrnpa2b1	9130414A06Rik|Hnrpa2|Hnrpa2b1|hnrnp-A	heterogeneous nuclear ribonucleoprotein A2/B1	protein-coding
mm_145087.1	chr18	42516219	42516223	+	1	NA	intron (NR_110344, intron 1 of 22)	PB1D11|SINE|Alu	4734	NR_110344	56070	Mm.270511	NM_001039474	ENSMUSG00000024498	Tcerg1	2410022J09Rik|2900090C16Rik|AI428505|CA150b|FBP23|FBP28|Taf2s|ca150|p144	transcription elongation regulator 1 (CA150)	protein-coding
mm_7099.1	chr1	88702122	88702180	-	1	NA	promoter-TSS (NM_177305)	promoter-TSS (NM_177305)	40	NM_177305	320982	Mm.27968	NM_177305	ENSMUSG00000049866	Arl4c	A630084M22Rik|Arl7|LAK	ADP-ribosylation factor-like 4C	protein-coding
mm_86931.1	chr10	24188786	24188802	+	1	NA	3' UTR (NM_016797, exon 10 of 10)	3' UTR (NM_016797, exon 10 of 10)	-34723	NM_021509	59012	Mm.285934	NM_021509	ENSMUSG00000020000	Moxd1	3230402N08Rik|MNCb-5203	monooxygenase, DBH-like 1	protein-coding
mm_60383.1	chr7	44473744	44473873	+	1	NA	Intergenic	IMPB_01|Satellite|Satellite	3461	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_15495.1	chr2	157793546	157793555	+	1	NA	intron (NM_025680, intron 4 of 15)	intron (NM_025680, intron 4 of 15)	56149	NM_025680	66642	Mm.45193	NM_025680	ENSMUSG00000027649	Ctnnbl1	5730471K09Rik|NAP|NYD-SP19|P14L	catenin, beta like 1	protein-coding
mm_628.1	chr1	40240971	40240971	+	1	NA	intron (NM_008362, intron 1 of 10)	intron (NM_008362, intron 1 of 10)	15891	NM_008362	16177	Mm.896	NM_008362	ENSMUSG00000026072	Il1r1	CD121a|CD121b|IL-1R1|IL-iR|Il1r-1	interleukin 1 receptor, type I	protein-coding
mm_161039.1	chr12	30911558	30911558	-	1	NA	promoter-TSS (NM_013709)	promoter-TSS (NM_013709)	54	NM_021330	11431	Mm.359831	NM_021330	ENSMUSG00000044573	Acp1	4632432E04Rik|AI427468|Acp-1|LMW-PTP|Lmptp	acid phosphatase 1, soluble	protein-coding
mm_88184.1	chr10	69993103	69993117	+	1	NA	intron (NM_146005, intron 36 of 42)	intron (NM_146005, intron 36 of 42)	67578	NM_009670	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_128592.1	chr15	58119350	58119354	-	1	NA	intron (NM_027435, intron 8 of 27)	intron (NM_027435, intron 8 of 27)	15730	NM_027435	70472	Mm.221758	NM_027435	ENSMUSG00000022360	Atad2	2610509G12Rik	ATPase family, AAA domain containing 2	protein-coding
mm_73454.1	chr8	106415401	106415412	+	1	NA	promoter-TSS (NM_011764)	promoter-TSS (NM_011764)	67	NM_011764	22751	Mm.295582	NM_011764	ENSMUSG00000031907	Zfp90	6430515L01Rik|KRAB17|NK10|Zfp64|Zfp83|mKIAA1954	zinc finger protein 90	protein-coding
mm_104613.1	chr11	97279614	97279634	-	1	NA	intron (NM_008942, intron 1 of 22)	intron (NM_008942, intron 1 of 22)	952	NM_008942	19155	Mm.29824	NM_008942	ENSMUSG00000001441	Npepps	AAP-S|MP100|Psa|R74825|goku	aminopeptidase puromycin sensitive	protein-coding
mm_65876.1	chr7	29518567	29518620	-	1	NA	Intergenic	CpG	-13133	NM_001081028	74206	Mm.447042	NM_001081028	ENSMUSG00000030583	Sipa1l3	2610511M17Rik	signal-induced proliferation-associated 1 like 3	protein-coding
mm_22306.1	chr2	180381231	180381244	-	1	NA	intron (NR_040745, intron 4 of 6)	intron (NR_040745, intron 4 of 6)	-4367	NR_045331	622283	Mm.447602	NR_045331		Mir1a-1hg	EG622283|Gm6307	Mir1a-1 and Mir133a-2 host gene	ncRNA
mm_20149.1	chr2	121551265	121551275	-	1	NA	intron (NM_172673, intron 13 of 14)	intron (NM_172673, intron 13 of 14)	44547	NM_001290986	241627	Mm.293284	NM_030234	ENSMUSG00000027242	Wdr76	5830411K18Rik|6030457D09|AA517836	WD repeat domain 76	protein-coding
mm_38341.1	chr4	137766461	137766466	-	1	NA	promoter-TSS (NM_001287172)	promoter-TSS (NM_001287172)	12	NM_001287172	11647	Mm.288186	NM_007431	ENSMUSG00000028766	Alpl	ALP|APTNAP|Akp-2|Akp2|TNAP|TNSALP	alkaline phosphatase, liver/bone/kidney	protein-coding
mm_85581.1	chr9	107295757	107295763	-	1	NA	promoter-TSS (NM_009895)	promoter-TSS (NM_009895)	-899	NM_001317354	12700	Mm.4592	NM_009895	ENSMUSG00000032578	Cish	CIS-1|CIS1|Cis|F17|F23|SOCS	cytokine inducible SH2-containing protein	protein-coding
mm_98672.1	chr11	96283263	96283289	+	1	NA	exon (NM_010461, exon 1 of 2)	exon (NM_010461, exon 1 of 2)	1371	NM_010461	15416	Mm.4822	NM_010461	ENSMUSG00000056648	Hoxb8	Hox-2.4	homeobox B8	protein-coding
mm_103611.1	chr11	78536217	78536227	-	1	NA	promoter-TSS (NM_018854)	promoter-TSS (NM_018854)	38	NM_001159392	21927	Mm.386774	NM_009395	ENSMUSG00000017615	Tnfaip1	Bacurd2|Edp-1|Edp1|Tnfip1	tumor necrosis factor, alpha-induced protein 1 (endothelial)	protein-coding
mm_72441.1	chr8	83165349	83165360	+	1	NA	promoter-TSS (NM_001111304)	promoter-TSS (NM_001111304)	2	NM_027758	71310	Mm.24031	NM_027758	ENSMUSG00000031709	Tbc1d9	4933431N12Rik|AI847101|AW490653|C76116	TBC1 domain family, member 9	protein-coding
mm_155054.1	chrX	42241071	42241092	+	1	NA	intron (NM_001077712, intron 16 of 32)	L1M5|LINE|L1	39226	NM_001290713	20843	Mm.290422	NM_021465	ENSMUSG00000025862	Stag2	9230105L23Rik|B230112I07Rik|SA-2|SAP2	stromal antigen 2	protein-coding
mm_60933.1	chr7	46861229	46861245	+	1	NA	promoter-TSS (NM_013580)	promoter-TSS (NM_013580)	-26	NM_013580	16833	Mm.16563	NM_013580	ENSMUSG00000030851	Ldhc	LDH-C4|Ldh-3|Ldh-x|Ldh3|Ldhc4	lactate dehydrogenase C	protein-coding
mm_151574.1	chr19	60896210	60896212	+	1	NA	intron (NM_018869, intron 1 of 15)	B1F|SINE|Alu	6462	NM_018869	14773	Mm.279400	NM_018869	ENSMUSG00000003228	Grk5	Gprk5	G protein-coupled receptor kinase 5	protein-coding
mm_11262.1	chr2	29966059	29966070	+	1	NA	intron (NM_001309460, intron 1 of 57)	CpG	504	NM_001309460	20740	Mm.204969	NM_001076554	ENSMUSG00000057738	Sptan1	2610027H02Rik|Spna-2|Spna2	spectrin alpha, non-erythrocytic 1	protein-coding
mm_169652.1	chr15	54920169	54920170	-	1	NA	promoter-TSS (NM_001285995)	promoter-TSS (NM_001285995)	-23	NM_001285994	18606	Mm.250256	NM_015744	ENSMUSG00000022425	Enpp2	ATX|E-NPP 2|Npps2|PD-Ialpha|Pdnp2|lysoPLD	ectonucleotide pyrophosphatase/phosphodiesterase 2	protein-coding
mm_157663.1	chrX	58038615	58038624	-	1	NA	Intergenic	CpG	7991	NM_009575	22773	Mm.255890	NM_009575	ENSMUSG00000067860	Zic3	Bn|Ka	zinc finger protein of the cerebellum 3	protein-coding
mm_144066.1	chr17	90958895	90958905	-	1	NA	intron (NM_001346957, intron 3 of 18)	intron (NM_001346957, intron 3 of 18)	97731	NR_045463	78800	Mm.410772	NR_045463	ENSMUSG00000090160	4930480K15Rik	-	RIKEN cDNA 4930480K15 gene	ncRNA
mm_50266.1	chr6	45060037	45060067	+	1	NA	promoter-TSS (NM_001004357)	promoter-TSS (NM_001004357)	-9	NM_001004357	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding
mm_66239.1	chr7	35537678	35537719	-	1	NA	promoter-TSS (NM_028034)	promoter-TSS (NM_028034)	46	NM_028034	71981	Mm.47904	NM_028034	ENSMUSG00000030491	Tdrd12	2410004F06Rik|2410070K17Rik|ECAT8|EG434165|G1-476-14|repro23	tudor domain containing 12	protein-coding
mm_98700.1	chr11	96303651	96303718	+	1	NA	exon (NM_008268, exon 1 of 2)	exon (NM_008268, exon 1 of 2)	172	NM_008268	15413	Mm.207	NM_008268	ENSMUSG00000038700	Hoxb5	AI385717|Hox-2.1	homeobox B5	protein-coding
mm_146364.1	chr18	82584470	82584492	+	1	NA	3' UTR (NM_010777, exon 7 of 7)	3' UTR (NM_010777, exon 7 of 7)	29973	NM_001025254	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_92647.1	chr10	80395358	80395405	-	1	NA	intron (NM_001306143, intron 2 of 6)	CpG	4150	NM_013595	17192	Mm.7142	NM_013595	ENSMUSG00000035478	Mbd3	AI181826|AU019209	methyl-CpG binding domain protein 3	protein-coding
mm_112926.1	chr13	20945047	20945050	+	1	NA	intron (NM_012054, intron 12 of 20)	RLTR24|LTR|ERV1	128251	NM_146535	258528	Mm.377554	NM_146535	ENSMUSG00000042869	Olfr1370	MOR256-14	olfactory receptor 1370	protein-coding
mm_49846.1	chr6	38354754	38354767	+	1	NA	promoter-TSS (NM_028421)	promoter-TSS (NM_028421)	-157	NM_028421	78781	Mm.25243	NM_028421	ENSMUSG00000029826	Zc3hav1	1200014N16Rik|2900058M19Rik|9130009D18Rik|9830115L13Rik|ARTD13|D6Bwg1452e|ZAP	zinc finger CCCH type, antiviral 1	protein-coding
mm_34314.1	chr4	141819025	141819044	+	1	NA	exon (NM_007919, exon 6 of 8)	exon (NM_007919, exon 6 of 8)	6971	NM_007919	13706	Mm.45316	NM_007919	ENSMUSG00000058579	Cela2a	Ela-2|Ela2|Ela2a	chymotrypsin-like elastase family, member 2A	protein-coding
mm_50060.1	chr6	41178983	41178996	+	1	NA	Intergenic	Intergenic	-123283	NM_011646	22074	Mm.383263	NM_011646	ENSMUSG00000054106	Try4	0910001B19Rik|Td	trypsin 4	protein-coding
mm_153442.1	chr19	40994255	40994272	-	1	NA	5' UTR (NM_008528, exon 1 of 17)	5' UTR (NM_008528, exon 1 of 17)	272	NM_008528	17060	Mm.9749	NM_008528	ENSMUSG00000061132	Blnk	BASH|Bca|Ly-57|Ly57|Lyw-57|SLP-65	B cell linker	protein-coding
mm_150000.1	chr19	29282526	29282565	+	1	NA	exon (NM_008413, exon 7 of 25)	exon (NM_008413, exon 7 of 25)	30742	NM_008413	16452	Mm.275839	NM_008413	ENSMUSG00000024789	Jak2	Fd17	Janus kinase 2	protein-coding
mm_110366.1	chr12	40114128	40114164	-	1	NA	intron (NM_009132, intron 3 of 13)	intron (NM_009132, intron 3 of 13)	20082	NM_009132	20259	Mm.2416	NM_009132	ENSMUSG00000002565	Scin	AW545522|adseverin	scinderin	protein-coding
mm_96921.1	chr11	70505256	70505312	+	1	NA	promoter-TSS (NM_029360)	promoter-TSS (NM_029360)	10	NM_029360	75604	Mm.24400	NM_029360	ENSMUSG00000018919	Tm4sf5	2010003F10Rik|AI323987	transmembrane 4 superfamily member 5	protein-coding
mm_95859.1	chr11	58008938	58008959	+	1	NA	promoter-TSS (NM_028451)	promoter-TSS (NM_028451)	-116	NM_028451	73158	Mm.248843	NM_028451	ENSMUSG00000037331	Larp1	1810024J12Rik|3110040D16Rik|Larp|mKIAA0731	La ribonucleoprotein domain family, member 1	protein-coding
mm_65205.1	chr7	19697062	19697111	-	1	NA	exon (NM_009696, exon 4 of 4)	exon (NM_009696, exon 4 of 4)	1312	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_134133.1	chr16	10668576	10668594	-	1	NA	intron (NM_001204229, intron 18 of 22)	intron (NM_001204229, intron 18 of 22)	116951	NM_009896	12703	Mm.130	NM_009896	ENSMUSG00000038037	Socs1	Cish1|Cish7|JAB|SOCS-1|SSI-1	suppressor of cytokine signaling 1	protein-coding
mm_31708.1	chr4	62619649	62619669	+	1	NA	promoter-TSS (NM_001081650)	promoter-TSS (NM_001081650)	-13	NM_001081650	50780	Mm.286753	NM_019492	ENSMUSG00000059810	Rgs3	4930506N09Rik|C2PA-RGS3|C2pa|PDZ-RGS3|RGS3S	regulator of G-protein signaling 3	protein-coding
mm_55605.1	chr6	71830859	71830866	-	1	NA	promoter-TSS (NM_029673)	promoter-TSS (NM_029673)	-458	NM_001253681	76614	Mm.235123	NM_029673	ENSMUSG00000052337	Immt	1700082C19Rik|D830041H16Rik|HMP|P87|P87/89|P89	inner membrane protein, mitochondrial	protein-coding
mm_161698.1	chr17	23844120	23844120	-	1	NA	promoter-TSS (NM_027644)	promoter-TSS (NM_027644)	36	NM_027644	71003	Mm.328839	NM_027644	ENSMUSG00000024114	Prss41	4931440B09Rik|Tessp-1|Tessp1	protease, serine 41	protein-coding
mm_95265.1	chr11	44962930	44962935	+	1	NA	intron (NM_007897, intron 10 of 15)	intron (NM_007897, intron 10 of 15)	153996	NR_045100	100504255	Mm.123608	NR_045100	ENSMUSG00000084773	Gm12159	OTTMUSG00000005475	predicted gene 12159	ncRNA
mm_140193.1	chr17	83351030	83351040	+	1	NA	5' UTR (NM_001114361, exon 1 of 24)	5' UTR (NM_001114361, exon 1 of 24)	104	NM_001114362	78798	Mm.295565	NM_199466	ENSMUSG00000032624	Eml4	4930443C24Rik|AI644019	echinoderm microtubule associated protein like 4	protein-coding
mm_113136.1	chr13	24634678	24634684	+	1	NA	intron (NM_178658, intron 1 of 13)	intron (NM_178658, intron 1 of 13)	-3967	NM_001080381	193385	Mm.217319	NM_029679	ENSMUSG00000036006	Fam65b	-	family with sequence similarity 65, member B	protein-coding
mm_88052.1	chr10	67540048	67540089	+	1	NA	exon (NM_010118, exon 2 of 2)	exon (NM_010118, exon 2 of 2)	2138	NM_001347458	13654	Mm.290421	NM_010118	ENSMUSG00000037868	Egr2	Egr-2|Krox-20|Krox20|NGF1-B|Zfp-25|Zfp-6	early growth response 2	protein-coding
mm_54567.1	chr6	37871328	37871344	-	1	NA	exon (NM_145076, exon 1 of 19)	exon (NM_145076, exon 1 of 19)	525	NM_145076	21848	Mm.41063	NM_145076	ENSMUSG00000029833	Trim24	A130082H20Rik|AI447469|D430004I05Rik|TIF1|TIF1-alpha|TIF1alpha|Tif1a	tripartite motif-containing 24	protein-coding
mm_38241.1	chr4	136249941	136249943	-	1	NA	intron (NM_011542, intron 1 of 10)	intron (NM_011542, intron 1 of 10)	1985	NM_011542	21401	Mm.112	NM_011542	ENSMUSG00000001604	Tcea3	S-II|SII-K1	transcription elongation factor A (SII), 3	protein-coding
mm_168807.1	chr12	20615086	20615090	+	1	NA	Intergenic	CpG	200691	NR_015521	69513	Mm.273972	NR_015521	ENSMUSG00000099759	1700030C10Rik	-	RIKEN cDNA 1700030C10 gene	ncRNA
mm_115204.1	chr13	109116326	109116334	+	1	NA	intron (NM_011056, intron 3 of 16)	intron (NM_011056, intron 3 of 16)	-208414	NR_030644	100124489		NR_030644	ENSMUSG00000076946	Mir582	Mirn582|mir-582|mmu-mir-582	microRNA 582	ncRNA
mm_67901.1	chr7	99626937	99626953	-	1	NA	5' UTR (NM_001195529, exon 1 of 1)	5' UTR (NM_001195529, exon 1 of 1)	158	NM_001195529	100503386	Mm.180719	NM_001195529	ENSMUSG00000096606	Tpbgl	EG245190|Gm4980	trophoblast glycoprotein-like	protein-coding
mm_10850.1	chr2	24983677	24983685	+	1	NA	intron (NM_146251, intron 7 of 34)	intron (NM_146251, intron 7 of 34)	7648	NM_146251	241274	Mm.389243	NM_146251	ENSMUSG00000036833	Pnpla7	BC027342|E430013P11Rik|Nre	patatin-like phospholipase domain containing 7	protein-coding
mm_84432.1	chr9	65908801	65908833	-	1	NA	promoter-TSS (NM_019797)	promoter-TSS (NM_019797)	-23	NM_019797	56404	Mm.208379	NM_019797	ENSMUSG00000032386	Trip4	4930558E03Rik|ASC-1|Asc1|BB191711	thyroid hormone receptor interactor 4	protein-coding
mm_135283.1	chr16	38447603	38447630	-	1	NA	intron (NM_007414, intron 2 of 3)	intron (NM_007414, intron 2 of 3)	5073	NM_007414	11544	Mm.20047	NM_007414	ENSMUSG00000002844	Adprh	Arh1	ADP-ribosylarginine hydrolase	protein-coding
mm_44646.1	chr5	28209905	28209914	-	1	NA	5' UTR (NM_001310511, exon 1 of 3)	5' UTR (NM_001310511, exon 1 of 3)	259	NM_001310511	269637	Mm.68286	NM_175651	ENSMUSG00000044681	Cnpy1	1500012D20Rik|9630008K15Rik|AI853839	canopy FGF signaling regulator 1	protein-coding
mm_100205.1	chr11	116843708	116843730	+	1	NA	promoter-TSS (NM_033398)	promoter-TSS (NM_033398)	204	NM_028865	74319	Mm.429312	NM_028865	ENSMUSG00000090266	Mettl23	1110005A03Rik|1500035B17Rik|4933424L15Rik	methyltransferase like 23	protein-coding
mm_124717.1	chr15	6579842	6579882	+	1	NA	promoter-TSS (NM_001278269)	promoter-TSS (NM_001278269)	15	NM_011815	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_64773.1	chr7	4996096	4996116	-	1	NA	promoter-TSS (NM_026741)	promoter-TSS (NM_026741)	-5	NM_026741	68490	Mm.76400	NM_026741	ENSMUSG00000051550	Zfp579	1110003A17Rik|Znf579	zinc finger protein 579	protein-coding
mm_149078.1	chr19	8888881	8888925	+	1	NA	promoter-TSS (NM_025463)	promoter-TSS (NM_025463)	20	NR_104416	66276	Mm.27503	NM_025463	ENSMUSG00000071653	1810009A15Rik	-	RIKEN cDNA 1810009A15 gene	protein-coding
mm_90151.1	chr10	118141918	118141928	+	1	NA	5' UTR (NM_010785, exon 1 of 13)	5' UTR (NM_010785, exon 1 of 13)	136	NM_010785	17245	Mm.101191	NM_010785	ENSMUSG00000020212	Mdm1	Arrd2|Mdm-1	transformed mouse 3T3 cell double minute 1	protein-coding
mm_76408.1	chr8	84893159	84893169	-	1	NA	exon (NM_001044744, exon 4 of 12)	exon (NM_001044744, exon 4 of 12)	757	NM_001044744	270076	Mm.2475	NM_008097	ENSMUSG00000003809	Gcdh	9030411L18|AI266902|D17825|GCD	glutaryl-Coenzyme A dehydrogenase	protein-coding
mm_159806.1	chr5	115186172	115186172	-	1	NA	promoter-TSS (NM_013879)	promoter-TSS (NM_013879)	-51	NM_001310715	29867	Mm.38551	NM_013879	ENSMUSG00000029544	Cabp1	caldendrin	calcium binding protein 1	protein-coding
mm_105090.1	chr11	100888575	100888584	-	1	NA	3' UTR (NM_011486, exon 24 of 24)	3' UTR (NM_011486, exon 24 of 24)	28095	NM_001164062	20850	Mm.277403	NM_011488	ENSMUSG00000004043	Stat5a	AA959963|STAT5	signal transducer and activator of transcription 5A	protein-coding
mm_67511.1	chr7	80802954	80802994	-	1	NA	intron (NM_016721, intron 1 of 37)	CpG	357	NM_016721	29875	Mm.207619	NM_016721	ENSMUSG00000030536	Iqgap1	AA682088|D7Ertd237e|D7Ertd257e|mKIAA0051	IQ motif containing GTPase activating protein 1	protein-coding
mm_12021.1	chr2	58157165	58157172	+	1	NA	intron (NM_139200, intron 1 of 7)	intron (NM_139200, intron 1 of 7)	2954	NM_139200	227929	Mm.273905	NM_139200	ENSMUSG00000026832	Cytip	A130053M09Rik|AI462064|C80816|Cbp|Cybr|Pscdbp	cytohesin 1 interacting protein	protein-coding
mm_144301.1	chr18	12333954	12334003	+	1	NA	promoter-TSS (NM_010680)	promoter-TSS (NM_010680)	-46	NM_010680	16774	Mm.42012	NM_010680	ENSMUSG00000024421	Lama3	Lama3B|[a]3B	laminin, alpha 3	protein-coding
mm_161260.1	chr13	119488178	119488178	+	1	NA	promoter-TSS (NM_001177666)	promoter-TSS (NM_001177666)	139	NM_001039244	633640	Mm.46679	NM_001039244	ENSMUSG00000074634	Tmem267	EG633640|Gm7120	transmembrane protein 267	protein-coding
mm_57788.1	chr6	129270051	129270060	-	1	NA	exon (NM_001033122, exon 3 of 5)	exon (NM_001033122, exon 3 of 5)	5314	NM_001033122	12515	Mm.74745	NM_001033122	ENSMUSG00000030156	Cd69	5830438K24Rik|AI452015|AIM|VEA	CD69 antigen	protein-coding
mm_154221.1	chr19	59458275	59458320	-	1	NA	promoter-TSS (NM_010132)	promoter-TSS (NM_010132)	338	NR_002863	329078	Mm.80382	NR_002863	ENSMUSG00000087095	Emx2os	-	Emx2 opposite strand/antisense transcript (non-protein coding)	ncRNA
mm_116733.1	chr13	51734684	51734693	-	1	NA	intron (NM_001281880, intron 2 of 16)	intron (NM_001281880, intron 2 of 16)	59059	NM_001281880	20354	Mm.33903	NM_013660	ENSMUSG00000021451	Sema4d	CD100|Semacl2|Semaj|Semcl2|coll-4	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D	protein-coding
mm_103772.1	chr11	82179809	82179815	-	1	NA	promoter-TSS (NM_011329)	promoter-TSS (NM_011329)	0	NM_011329	20290	Mm.1283	NM_011329	ENSMUSG00000020702	Ccl1	BF534335|I-309|Scya1|Tca-3	chemokine (C-C motif) ligand 1	protein-coding
mm_95609.1	chr11	53457185	53457201	+	1	NA	promoter-TSS (NM_027917)	promoter-TSS (NM_027917)	-12	NM_001290789	71774	Mm.274370	NM_027917	ENSMUSG00000018387	Shroom1	Apx|Shrm1	shroom family member 1	protein-coding
mm_1508.1	chr1	72307515	72307539	+	1	NA	5' UTR (NM_009533, exon 1 of 21)	5' UTR (NM_009533, exon 1 of 21)	106	NM_009533	22596	Mm.246952	NM_009533	ENSMUSG00000026187	Xrcc5	AI314015|Ku80|Ku86	X-ray repair complementing defective repair in Chinese hamster cells 5	protein-coding
mm_143790.1	chr17	81738356	81738366	-	1	NA	promoter-TSS (NM_001112798)	promoter-TSS (NM_001112798)	26	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_151089.1	chr19	47705942	47705946	+	1	NA	Intergenic	Intergenic	-13902	NM_001290825	12821	Mm.1225	NM_007732	ENSMUSG00000025064	Col17a1	BP180|Bpag|Bpag2	collagen, type XVII, alpha 1	protein-coding
mm_19061.1	chr2	77317049	77317063	-	1	NA	Intergenic	Intergenic	-36464	NM_175465	228071	Mm.27120	NM_175465	ENSMUSG00000042272	Sestd1	1500031J16Rik|A930010O20|Solo/Trio8	SEC14 and spectrin domains 1	protein-coding
mm_508.1	chr1	37219192	37219201	+	1	NA	promoter-TSS (NM_009918)	promoter-TSS (NM_009918)	-9	NM_009918	12790	Mm.214224	NM_009918	ENSMUSG00000026114	Cnga3	CNG3	cyclic nucleotide gated channel alpha 3	protein-coding
mm_60196.1	chr7	43408520	43408539	+	1	NA	5' UTR (NM_172900, exon 2 of 12)	5' UTR (NM_172900, exon 2 of 12)	249	NM_172900	243958	Mm.24444	NM_172900	ENSMUSG00000030468	Siglecg	9830164H23|A630096C01Rik|Siglec-G|Siglec10|mSiglec-G	sialic acid binding Ig-like lectin G	protein-coding
mm_104312.1	chr11	93884263	93884265	-	1	NA	intron (NM_001013375, intron 1 of 13)	intron (NM_001013375, intron 1 of 13)	1502	NM_001013375	217109	Mm.379350	NM_001013375	ENSMUSG00000054079	Utp18	6230425C22Rik|6430513M13|Wdr50	UTP18 small subunit processome component	protein-coding
mm_142420.1	chr17	45568536	45568549	-	1	NA	TTS (NM_028662)	TTS (NM_028662)	4390	NM_028662	73836	Mm.289716	NM_028662	ENSMUSG00000037089	Slc35b2	1110003M08Rik|AA407792|AI842275|PAPST1|Slc35b1	solute carrier family 35, member B2	protein-coding
mm_120914.1	chr14	76414733	76414793	+	1	NA	promoter-TSS (NM_001310646)	promoter-TSS (NM_001310646)	-198	NM_001310646	21807	Mm.153272	NM_009366	ENSMUSG00000022010	Tsc22d1	AA589566|AW105905|Egr5|TSC-22|Tgfb1i4|Tsc|Tsc22	TSC22 domain family, member 1	protein-coding
mm_20209.1	chr2	125506024	125506047	-	1	NA	intron (NM_007993, intron 1 of 65)	CpG	403	NM_007993	14118	Mm.271644	NM_007993	ENSMUSG00000027204	Fbn1	AI536462|B430209H23|Fib-1|Tsk	fibrillin 1	protein-coding
mm_14513.1	chr2	132289399	132289410	+	1	NA	intron (NM_001291039, intron 1 of 12)	RLTR17|LTR|ERVK	3465	NM_001291039	110911	Mm.284503	NM_138651	ENSMUSG00000058793	Cds2	5730450N06Rik|5730460C18Rik|AI854580|D2Wsu127e	CDP-diacylglycerol synthase (phosphatidate cytidylyltransferase) 2	protein-coding
mm_145204.1	chr18	50001244	50001276	+	1	NA	intron (NM_001177759, intron 1 of 1)	intron (NM_001177759, intron 1 of 1)	21833	NM_001177759	106869	Mm.27740	NM_134131	ENSMUSG00000062210	Tnfaip8	AA987150|E130304C20Rik|ENSMUSG00000073567|Gg2-1|Gm10539|Nded|Ssc-2|Tipe	tumor necrosis factor, alpha-induced protein 8	protein-coding
mm_65320.1	chr7	24954409	24954443	-	1	NA	Intergenic	Intergenic	15649	NR_106013	102465633		NR_106013	ENSMUSG00000098802	Mir7046	Gm27469|mmu-mir-7046	microRNA 7046	ncRNA
mm_98167.1	chr11	87749879	87749901	+	1	NA	Intergenic	Intergenic	-6974	NR_029555	387160		NR_029555	ENSMUSG00000105196	Mir142	Mirn142|miR-142|mir-142a|mmu-mir-142|mmu-mir-142a	microRNA 142	ncRNA
mm_42682.1	chr5	119796660	119796682	+	1	NA	Intergenic	CpG	-37992	NM_011537	21388	Mm.103636	NM_011537	ENSMUSG00000018263	Tbx5	-	T-box 5	protein-coding
mm_23059.1	chr3	35822582	35822585	+	1	NA	intron (NM_029570, intron 19 of 29)	Lx3C|LINE|L1	68445	NM_029570	76295	Mm.239416	NM_029570	ENSMUSG00000037400	Atp11b	1110019I14Rik|ATPIF|ATPIR|mKIAA0956	ATPase, class VI, type 11B	protein-coding
mm_115742.1	chr13	17888574	17888586	-	1	NA	exon (NM_019491, exon 4 of 5)	exon (NM_019491, exon 4 of 5)	55637	NM_019491	56044	Mm.27348	NM_019491	ENSMUSG00000008859	Rala	3010001O15Rik|AW322615|Ral|Rasl1	v-ral simian leukemia viral oncogene A (ras related)	protein-coding
mm_71289.1	chr8	40926269	40926353	+	1	NA	promoter-TSS (NM_026840)	promoter-TSS (NM_026840)	78	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_54220.1	chr6	26766819	26766824	-	1	NA	Intergenic	Intergenic	835395	NR_040771	626904	Mm.126787	NR_040771	ENSMUSG00000106799	Gm20756	-	predicted gene, 20756	ncRNA
mm_159946.1	chr6	85187904	85187904	+	1	NA	promoter-TSS (NM_010131)	promoter-TSS (NM_010131)	-27	NM_010131	13796	Mm.391473	NM_010131	ENSMUSG00000033726	Emx1	-	empty spiracles homeobox 1	protein-coding
mm_149740.1	chr19	22448008	22448040	+	1	NA	promoter-TSS (NM_177341)	promoter-TSS (NM_177341)	-184	NM_177341	226025	Mm.131943	NM_177341	ENSMUSG00000052387	Trpm3	6330504P12Rik|9330180E14|AU018608|B930001P07Rik|LTRPC3|MLSN2	transient receptor potential cation channel, subfamily M, member 3	protein-coding
mm_54059.1	chr6	13871074	13871129	-	1	NA	promoter-TSS (NR_045995)	promoter-TSS (NR_045995)	382	NR_024619	66520	Mm.29615	NM_183258		2610001J05Rik	C79299	RIKEN cDNA 2610001J05 gene	ncRNA
mm_116771.1	chr13	52929619	52929629	-	1	NA	promoter-TSS (NM_016709)	promoter-TSS (NM_016709)	53	NM_016709	11992	Mm.252034	NM_016709	ENSMUSG00000021460	Auh	C77140|W91705	AU RNA binding protein/enoyl-coenzyme A hydratase	protein-coding
mm_49154.1	chr6	12128562	12128563	+	1	NA	Intergenic	Intergenic	-18982	NR_003631	625347	Mm.389084	NM_001039041	ENSMUSG00000057223	Gm6578	EG625347	mitochondrial ribosomal protein L32 pseudogene	pseudo
mm_59741.1	chr7	28815143	28815157	+	1	NA	exon (NM_177301, exon 5 of 13)	exon (NM_177301, exon 5 of 13)	4260	NM_177301	15388	Mm.9043	NM_177301	ENSMUSG00000015165	Hnrnpl	C79783|D830027H13Rik|Hnrpl	heterogeneous nuclear ribonucleoprotein L	protein-coding
mm_102142.1	chr11	53617334	53617366	-	1	NA	promoter-TSS (NR_027491)	promoter-TSS (NR_027491)	-12	NR_027491	16189	Mm.276360	NM_021283	ENSMUSG00000000869	Il4	BSF-1|Il-4	interleukin 4	protein-coding
mm_136661.1	chr17	6079822	6079892	+	1	NA	promoter-TSS (NM_001111017)	promoter-TSS (NM_001111017)	29	NM_181392	66467	Mm.303441	NM_181392	ENSMUSG00000034345	Gtf2h5	2700017P07Rik|2810432H05Rik|D17Wsu155e	general transcription factor IIH, polypeptide 5	protein-coding
mm_136270.1	chr16	91044676	91044686	-	1	NA	promoter-TSS (NM_026110)	promoter-TSS (NM_026110)	-302	NM_026110	67367	Mm.347	NM_026110	ENSMUSG00000022974	Paxbp1	1810007M14Rik|C21orf66|Gcfc|Gcfc1|Pax3/7bp	PAX3 and PAX7 binding protein 1	protein-coding
mm_76822.1	chr8	104609365	104609375	-	1	NA	intron (NM_001252628, intron 17 of 17)	intron (NM_001252628, intron 17 of 17)	15026	NM_007663	12556	Mm.19423	NM_007663	ENSMUSG00000031881	Cdh16	-	cadherin 16	protein-coding
mm_31646.1	chr4	59581722	59581732	+	1	NA	5' UTR (NM_024255, exon 1 of 11)	5' UTR (NM_024255, exon 1 of 11)	164	NM_024255	72479	Mm.272905	NM_024255	ENSMUSG00000028383	Hsdl2	2610207I16Rik	hydroxysteroid dehydrogenase like 2	protein-coding
mm_7.1	chr1	4807643	4807672	+	1	NA	promoter-TSS (NM_008866)	promoter-TSS (NM_008866)	-236	NM_008866	18777	Mm.299955	NM_008866	ENSMUSG00000025903	Lypla1	Pla1a	lysophospholipase 1	protein-coding
mm_63137.1	chr7	123123871	123123901	+	1	NA	promoter-TSS (NM_144925)	promoter-TSS (NM_144925)	1	NM_144925	233833	Mm.102305	NM_144925	ENSMUSG00000052707	Tnrc6a	2010321I05Rik|3110054G10Rik|AW557223|CAGH26|D130023A07Rik|GW182|Tnrc6	trinucleotide repeat containing 6a	protein-coding
mm_108031.1	chr12	73734803	73734807	+	1	NA	intron (NM_001313977, intron 11 of 14)	intron (NM_001313977, intron 11 of 14)	150009	NM_008856	18755	Mm.341677	NM_008856	ENSMUSG00000021108	Prkch	Pkch	protein kinase C, eta	protein-coding
mm_166966.1	chr7	44481034	44481035	+	1	NA	Intergenic	Intergenic	-3483	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_118491.1	chr14	12822865	12822872	+	1	NA	5' UTR (NM_001042617, exon 1 of 31)	5' UTR (NM_001042617, exon 1 of 31)	211	NM_001042617	27062	Mm.260881	NM_012061	ENSMUSG00000054423	Cadps	AU067781|CAPS|CAPS1|mKIAA1121	Ca2+-dependent secretion activator	protein-coding
mm_115865.1	chr13	21453715	21453761	-	1	NA	promoter-TSS (NM_001347491)	promoter-TSS (NM_001347491)	-11	NM_001347491	432731	Mm.390557	NM_001013786	ENSMUSG00000022228	Zscan26	BC068174|Zfp187|Znf187	zinc finger and SCAN domain containing 26	protein-coding
mm_157836.1	chrX	74281613	74281655	-	1	NA	5' UTR (NM_027109, exon 1 of 8)	5' UTR (NM_027109, exon 1 of 8)	102	NM_027109	69537	Mm.20169	NM_027109	ENSMUSG00000019088	Dnase1l1	2310005K03Rik|AI324885|Dnase1ll|Dnasex|Dnl1ll|G4.8	deoxyribonuclease 1-like 1	protein-coding
mm_111647.1	chr12	102727333	102727354	-	1	NA	Intergenic	MTE2a|LTR|ERVL-MaLR	16318	NM_001142937	64113	Mm.291222	NM_022323	ENSMUSG00000096458	Moap1	AA987038|Map-1|Pnma4	modulator of apoptosis 1	protein-coding
mm_77385.1	chr8	120113897	120113906	-	1	NA	promoter-TSS (NM_001163762)	promoter-TSS (NM_001163762)	-251	NM_001163762	234797	Mm.101958	NM_172286	ENSMUSG00000031824	6430548M08Rik	AW049007|Kiaa0513|mKIAA0513	RIKEN cDNA 6430548M08 gene	protein-coding
mm_111194.1	chr12	84193829	84193862	-	1	NA	5' UTR (NM_001163502, exon 1 of 13)	5' UTR (NM_001163502, exon 1 of 13)	170	NM_001163502	238317	Mm.31256	NM_001163501	ENSMUSG00000042507	Elmsan1	9430029N19Rik|C130039O16Rik|Gm260	ELM2 and Myb/SANT-like domain containing 1	protein-coding
mm_93585.1	chr10	116950446	116950456	-	1	NA	promoter-TSS (NR_038026)	promoter-TSS (NR_038026)	-71	NM_001003950	216363	Mm.336394	NM_001003950	ENSMUSG00000064181	Rab3ip	B230311A06|Gtpat12|Rabin3	RAB3A interacting protein	protein-coding
mm_60527.1	chr7	44480136	44480152	+	1	NA	Intergenic	Intergenic	-4373	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_96627.1	chr11	69157033	69157051	+	1	NA	promoter-TSS (NM_009659)	promoter-TSS (NM_009659)	-30	NM_009659	11686	Mm.340329	NM_009659	ENSMUSG00000032807	Alox12b	12R-LOX|Aloxe2|e-LOX2	arachidonate 12-lipoxygenase, 12R type	protein-coding
mm_71682.1	chr8	60993554	60993568	+	1	NA	5' UTR (NM_001293639, exon 1 of 32)	5' UTR (NM_001293639, exon 1 of 32)	368	NM_175089	18004	Mm.486881	NM_175089	ENSMUSG00000031644	Nek1	D8Ertd790e|kat	NIMA (never in mitosis gene a)-related expressed kinase 1	protein-coding
mm_70836.1	chr8	23237020	23237020	+	1	NA	exon (NM_024240, exon 2 of 8)	exon (NM_024240, exon 2 of 8)	648	NM_024240	109145	Mm.27945	NM_024240	ENSMUSG00000031546	Gins4	2810037C03Rik|4933405K01Rik|Sld5	GINS complex subunit 4 (Sld5 homolog)	protein-coding
mm_78679.1	chr9	40784938	40784956	+	1	NA	TTS (NM_133733)	TTS (NM_133733)	-16326	NM_031165	15481	Mm.290774	NM_031165	ENSMUSG00000015656	Hspa8	2410008N15Rik|Hsc70|Hsc71|Hsc73|Hsp73|Hspa10	heat shock protein 8	protein-coding
mm_17275.1	chr2	26091993	26092003	-	1	NA	5' UTR (NM_001037098, exon 1 of 6)	5' UTR (NM_001037098, exon 1 of 6)	398	NM_001037098	67991	Mm.131074	NM_026495	ENSMUSG00000026932	Nacc2	0610020I02Rik|AI448087|Btbd14a|C030048H19Rik	nucleus accumbens associated 2, BEN and BTB (POZ) domain containing	protein-coding
mm_42294.1	chr5	114444267	114444306	+	1	NA	promoter-TSS (NM_029956)	promoter-TSS (NM_029956)	17	NM_023556	17855	Mm.28088	NM_023556	ENSMUSG00000041939	Mvk	2310010A05Rik|AI256848|AI414037|MK	mevalonate kinase	protein-coding
mm_26737.1	chr3	5950467	5950480	-	1	NA	Intergenic	Intergenic	-374225	NM_001163305	19302	Mm.132336	NM_008994	ENSMUSG00000040374	Pex2	D3Ertd138e|PAF-1|PMP35|Pxmp3	peroxisomal biogenesis factor 2	protein-coding
mm_36213.1	chr4	62470925	62470932	-	1	NA	promoter-TSS (NM_023597)	promoter-TSS (NM_023597)	-33	NM_001290521	71354	Mm.155573	NM_023597	ENSMUSG00000028391	Wdr31	5430402I10Rik|spWD	WD repeat domain 31	protein-coding
mm_13091.1	chr2	91237173	91237184	+	1	NA	promoter-TSS (NM_028119)	promoter-TSS (NM_028119)	32	NR_015464	606735	Mm.246808	NR_015464	ENSMUSG00000097868	A330069E16Rik	-	RIKEN cDNA A330069E16 gene	ncRNA
mm_145100.1	chr18	43963235	43963252	+	1	NA	promoter-TSS (NM_001081180)	promoter-TSS (NM_001081180)	2	NM_001081180	72432	Mm.35369	NM_001081180	ENSMUSG00000055561	Spink5	2310065D10Rik|AV238912|LEKT1|LETK1|VAKT1	serine peptidase inhibitor, Kazal type 5	protein-coding
mm_161906.1	chr18	60630104	60630104	-	1	NA	Intergenic	Intergenic	-5799	NM_177340	104027	Mm.252321	NM_177340	ENSMUSG00000043079	Synpo	9030217H17Rik|9130229N11|9330140I15Rik|AW046661	synaptopodin	protein-coding
mm_106408.1	chr11	119040884	119040903	-	1	NA	promoter-TSS (NM_013926)	promoter-TSS (NM_013926)	20	NM_013926	30951	Mm.99953	NM_013926	ENSMUSG00000025578	Cbx8	Pc3	chromobox 8	protein-coding
mm_40117.1	chr5	34974815	34974825	+	1	NA	intron (NM_173402, intron 2 of 16)	intron (NM_173402, intron 2 of 16)	-24258	NM_001163512	71729	Mm.196208	NM_173402	ENSMUSG00000029101	Rgs12	1200016K18Rik|4632412M04Rik|AI481290|E130309H11	regulator of G-protein signaling 12	protein-coding
mm_15906.1	chr2	164995984	164995987	+	1	NA	intron (NM_020333, intron 21 of 25)	intron (NM_020333, intron 21 of 25)	27997	NM_020333	57138	Mm.252987	NM_020333	ENSMUSG00000017740	Slc12a5	KCC2|mKIAA1176	solute carrier family 12, member 5	protein-coding
mm_141125.1	chr17	26113552	26113591	-	1	NA	intron (NM_021793, intron 1 of 12)	CpG	255	NM_021793	60455	Mm.304656	NM_021793	ENSMUSG00000024180	Tmem8	AW490096|M83|Tmem8a	transmembrane protein 8 (five membrane-spanning domains)	protein-coding
mm_91498.1	chr10	37136056	37136060	-	1	NA	3' UTR (NM_008538, exon 2 of 2)	3' UTR (NM_008538, exon 2 of 2)	2868	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_149176.1	chr19	9170729	9170729	+	1	NA	Intergenic	MurERV4-int|LTR|ERVK	-35163	NM_025610	66514	Mm.272847	NM_025610	ENSMUSG00000024654	Asrgl1	2410004D18Rik|ALP|ALP1|AU040643|AW060375	asparaginase like 1	protein-coding
mm_141060.1	chr17	25754344	25754382	-	1	NA	promoter-TSS (NM_018857)	promoter-TSS (NM_018857)	-36	NM_018857	56047	Mm.17510	NM_018857	ENSMUSG00000063011	Msln	MPF	mesothelin	protein-coding
mm_63828.1	chr7	135108751	135108763	+	1	NA	exon (NM_001033420, exon 35 of 52)	exon (NM_001033420, exon 35 of 52)	87245	NR_046050	74314	Mm.415339	NR_046050	ENSMUSG00000100717	1700120G07Rik	-	RIKEN cDNA 1700120G07 gene	ncRNA
mm_171830.1	chr5	145280574	145280580	+	1	NA	Intergenic	(CGGGG)n|Simple_repeat|Simple_repeat	-2766	NM_001081431	666311	Mm.260773	NM_001081431	ENSMUSG00000070420	Zscan25	EG666311|Zfp498	zinc finger and SCAN domain containing 25	protein-coding
mm_39671.1	chr5	25249984	25250001	+	1	NA	intron (NM_144908, intron 3 of 11)	intron (NM_144908, intron 3 of 11)	27099	NM_144908	231050	Mm.21814	NM_144908	ENSMUSG00000038072	Galnt11	A430075I06Rik|AI648252|E430002F06Rik	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 11	protein-coding
mm_33411.1	chr4	129899043	129899048	+	1	NA	Intergenic	Intergenic	-7181	NR_045190	319894	Mm.59196	NR_045190	ENSMUSG00000086369	E330017L17Rik	-	RIKEN cDNA E330017L17 gene	ncRNA
mm_109118.1	chr12	105684124	105684149	+	1	NA	intron (NM_029654, intron 1 of 41)	intron (NM_029654, intron 1 of 41)	1105	NM_029654	76559	Mm.114362	NM_029654	ENSMUSG00000041341	Atg2b	2410024A21Rik|AI047755|AI503411|AW558123|C030004M05Rik|C630028L02Rik|mKIAA4067	autophagy related 2B	protein-coding
mm_125716.1	chr15	68928704	68928729	+	1	NA	5' UTR (NM_010158, exon 1 of 9)	5' UTR (NM_010158, exon 1 of 9)	296	NM_010158	13992	Mm.17964	NM_010158	ENSMUSG00000022332	Khdrbs3	Etle|SLM-2|Salp|Slm2|T-STAR	KH domain containing, RNA binding, signal transduction associated 3	protein-coding
mm_112494.1	chr13	6563470	6563478	+	1	NA	exon (NM_145131, exon 14 of 27)	exon (NM_145131, exon 14 of 27)	15317	NM_145131	69617	Mm.41933	NM_145131	ENSMUSG00000021193	Pitrm1	2310012C15Rik|AA410010|MP-1|MP1|Ntup1|PreP|mKIAA1104	pitrilysin metallepetidase 1	protein-coding
mm_52410.1	chr6	113389193	113389220	+	1	NA	promoter-TSS (NM_001142732)	promoter-TSS (NM_001142732)	-54	NM_001142732	101100	Mm.388573	NM_133923	ENSMUSG00000030276	Ttll3	4833441J24Rik|AI450050	tubulin tyrosine ligase-like family, member 3	protein-coding
mm_136161.1	chr16	88506972	88506994	-	1	NA	promoter-TSS (NM_181490)	promoter-TSS (NM_181490)	-5	NM_181490	239931	Mm.126860	NM_181490	ENSMUSG00000055811	Cldn17	-	claudin 17	protein-coding
mm_18542.1	chr2	64975634	64975638	-	1	NA	intron (NM_016719, intron 2 of 13)	intron (NM_016719, intron 2 of 13)	47130	NM_016719	50915	Mm.214554	NM_016719	ENSMUSG00000026888	Grb14	AI505286	growth factor receptor bound protein 14	protein-coding
mm_142186.1	chr17	36867203	36867253	-	1	NA	promoter-TSS (NM_001024134)	promoter-TSS (NM_001024134)	-18	NM_001177872	69097	Mm.307027	NM_001024134	ENSMUSG00000050747	Trim15	1810012B10Rik	tripartite motif-containing 15	protein-coding
mm_98441.1	chr11	94939901	94939928	+	1	NA	exon (NM_007742, exon 8 of 51)	exon (NM_007742, exon 8 of 51)	3690	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_70294.1	chr8	3676458	3676501	+	1	NA	promoter-TSS (NM_025701)	promoter-TSS (NM_025701)	2	NM_025701	66682	Mm.29090	NM_025701	ENSMUSG00000040236	Trappc5	4021401A16Rik|TRS31	trafficking protein particle complex 5	protein-coding
mm_172469.1	chr7	43253722	43253731	+	1	NA	Intergenic	Intergenic	39687	NM_001177525	100170401		NM_001177525		EU599041	TU7	expressed sequence EU599041	protein-coding
mm_81963.1	chr9	120933839	120933862	+	1	NA	intron (NM_007614, intron 1 of 14)	CpG	272	NM_001165902	12387	Mm.291928	NM_007614	ENSMUSG00000006932	Ctnnb1	Bfc|Catnb|Mesc	catenin (cadherin associated protein), beta 1	protein-coding
mm_16569.1	chr2	3419067	3419073	-	1	NA	intron (NM_008579, intron 1 of 2)	CpG	3578	NM_008579	104362	Mm.2688	NM_008579	ENSMUSG00000026650	Meig1	MLZ-278|Meg1	meiosis expressed gene 1	protein-coding
mm_138582.1	chr17	35470975	35471019	+	1	NA	exon (NM_010391, exon 3 of 7)	exon (NM_010391, exon 3 of 7)	908	NM_010391	15007	Mm.88795	NM_010391	ENSMUSG00000067235	H2-Q10	H-2Q10|Q10|Qa10	histocompatibility 2, Q region locus 10	protein-coding
mm_106219.1	chr11	117040227	117040235	-	1	NA	Intergenic	LTR53|LTR|ERVL	-36552	NR_027059	76972	Mm.309167	NR_027059	ENSMUSG00000086859	Snhg20	2810008D09Rik	small nucleolar RNA host gene 20	ncRNA
mm_91645.1	chr10	42277636	42277640	-	1	NA	promoter-TSS (NM_019740)	promoter-TSS (NM_019740)	-896	NM_019740	56484	Mm.338613	NM_019740	ENSMUSG00000048756	Foxo3	1110048B16Rik|2010203A17Rik|C76856|FKHRL1|Fkhr2|Foxo3a	forkhead box O3	protein-coding
mm_52955.1	chr6	123050027	123050064	+	1	NA	promoter-TSS (NM_027218)	promoter-TSS (NM_027218)	83	NM_001190310	69810	Mm.333374	NM_027218	ENSMUSG00000030147	Clec4b1	1810046I24Rik|Aplra2|Clec4b|DCAR|DCARbeta|Dcar2	C-type lectin domain family 4, member b1	protein-coding
mm_78834.1	chr9	44240669	44240693	+	1	NA	promoter-TSS (NM_001081369)	promoter-TSS (NM_001081369)	4	NM_001081369	270150	Mm.347681	NM_001081369	ENSMUSG00000070306	Ccdc153	-	coiled-coil domain containing 153	protein-coding
mm_99773.1	chr11	107026051	107026073	+	1	NA	Intergenic	Intergenic	-2161	NM_001163473	69066	Mm.40679	NM_001163473	ENSMUSG00000078607	1810010H24Rik	OTTMUSG00000003581	RIKEN cDNA 1810010H24 gene	protein-coding
mm_46917.1	chr5	114444037	114444053	-	1	NA	promoter-TSS (NM_029956)	promoter-TSS (NM_029956)	-18	NM_001347398	77697	Mm.105182	NM_029956	ENSMUSG00000029575	Mmab	9130222L19Rik|ATR	methylmalonic aciduria (cobalamin deficiency) cblB type homolog (human)	protein-coding
mm_42768.1	chr5	121220422	121220424	+	1	NA	5' UTR (NM_181421, exon 1 of 76)	5' UTR (NM_181421, exon 1 of 76)	204	NM_181421	269700	Mm.184589	NM_181421	ENSMUSG00000042744	Gm15800	A130010L24|AU042671|BC019639|EG545802|OTTMUSG00000026283|mKIAA0614	predicted gene 15800	protein-coding
mm_170764.1	chr2	160880755	160880773	+	1	NA	promoter-TSS (NM_022883)	promoter-TSS (NM_022883)	94	NM_022883	64899	Mm.292111	NM_022883	ENSMUSG00000027412	Lpin3	9130206L11Rik|AA438110|AV236139|mKIAA4023	lipin 3	protein-coding
mm_110954.1	chr12	76710078	76710088	-	1	NA	5' UTR (NM_013675, exon 1 of 36)	5' UTR (NM_013675, exon 1 of 36)	464	NM_013675	20741	Mm.32881	NM_013675	ENSMUSG00000021061	Sptb	AI842465|D330027P03Rik|Gm1301|Spnb-1|Spnb1|ja|jaundiced|mKIAA4219	spectrin beta, erythrocytic	protein-coding
mm_4608.1	chr1	178528594	178528631	+	1	NA	promoter-TSS (NM_001161665)	promoter-TSS (NM_001161665)	-513	NM_001161665	269152	Mm.129727	NM_177724	ENSMUSG00000026494	Kif26b	4832420M10|BC056349|D230039L06Rik	kinesin family member 26B	protein-coding
mm_141171.1	chr17	26570714	26570750	-	1	NA	intron (NM_026170, intron 1 of 9)	intron (NM_026170, intron 1 of 9)	9220	NM_026170	67458	Mm.30496	NM_026170	ENSMUSG00000001576	Ergic1	1200007D18Rik|maa-136	endoplasmic reticulum-golgi intermediate compartment (ERGIC) 1	protein-coding
mm_51578.1	chr6	83758924	83758935	+	1	NA	TTS (NM_134157)	TTS (NM_134157)	3579	NR_105027	67934	Mm.126190	NR_105027	ENSMUSG00000099354	1700124L16Rik	-	RIKEN cDNA 1700124L16 gene	ncRNA
mm_139274.1	chr17	48232756	48232777	+	1	NA	promoter-TSS (NM_021406)	promoter-TSS (NM_021406)	27	NM_021406	58217	Mm.248352	NM_021406	ENSMUSG00000042265	Trem1	-	triggering receptor expressed on myeloid cells 1	protein-coding
mm_164416.1	chr16	38403965	38403978	+	1	NA	intron (NM_134102, intron 8 of 10)	intron (NM_134102, intron 8 of 10)	29174	NM_134102	85031	Mm.279805	NM_134102	ENSMUSG00000002847	Pla1a	AA986889|Ps-pla1|Pspla1	phospholipase A1 member A	protein-coding
mm_79336.1	chr9	53341342	53341352	+	1	NA	intron (NM_176846, intron 3 of 5)	intron (NM_176846, intron 3 of 5)	39677	NM_176846	320051	Mm.277540	NM_176846	ENSMUSG00000034584	Exph5	AC079869.22gm5|B130009M24Rik|E030050P12|Kiaa0624|Slac2b|slac2-b	exophilin 5	protein-coding
mm_157396.1	chrX	38407535	38407604	-	1	NA	intron (NM_001017959, intron 8 of 8)	intron (NM_001017959, intron 8 of 8)	48891	NM_010685	16784	Mm.486	NM_010685	ENSMUSG00000016534	Lamp2	CD107b|LGP-B|Lamp II|Lamp-2|Lamp-2a|Lamp-2b|Lamp-2c|Mac3	lysosomal-associated membrane protein 2	protein-coding
mm_41296.1	chr5	90464128	90464156	+	1	NA	exon (NM_009654, exon 4 of 15)	exon (NM_009654, exon 4 of 15)	3272	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_149278.1	chr19	10605920	10605948	+	1	NA	intron (NM_015735, intron 1 of 26)	CpG	309	NM_015735	13194	Mm.289915	NM_015735	ENSMUSG00000024740	Ddb1	127kDa|AA408517|p127-Ddb1	damage specific DNA binding protein 1	protein-coding
mm_43006.1	chr5	123630015	123630032	+	1	NA	intron (NM_001291229, intron 9 of 23)	intron (NM_001291229, intron 9 of 23)	54338	NM_019765	56430	Mm.241109	NM_019765	ENSMUSG00000049550	Clip1	1110007I12Rik|4631429H07Rik|AV017631|C81039|CLIP-170|CLIP170|CYLN1|Clip50|Rsn|mKIAA4046|restin	CAP-GLY domain containing linker protein 1	protein-coding
mm_15062.1	chr2	152967936	152967952	+	1	NA	intron (NM_001083618, intron 1 of 14)	ORR1A2|LTR|ERVL-MaLR	5459	NM_001083618	74711	Mm.44746	NM_029064	ENSMUSG00000074673	Ttll9	1700016F23Rik|4930509O20Rik|AW046572	tubulin tyrosine ligase-like family, member 9	protein-coding
mm_75893.1	chr8	70895714	70895719	-	1	NA	promoter-TSS (NR_106034)	promoter-TSS (NR_106034)	140	NR_002901	104370		NR_002901		Snora68	MBI-30|Rnu68	small nucleolar RNA, H/ACA box 68	snoRNA
mm_65494.1	chr7	25712134	25712147	-	1	NA	3' UTR (NM_028771, exon 5 of 5)	3' UTR (NM_028771, exon 5 of 5)	6913	NM_028771	52132	Mm.278798	NM_028771	ENSMUSG00000002608	Ccdc97	1200014H14Rik|2810446P04Rik|AA545218|D7Ertd462e	coiled-coil domain containing 97	protein-coding
mm_19573.1	chr2	101641564	101641577	-	1	NA	3' UTR (NM_009019, exon 2 of 2)	3' UTR (NM_009019, exon 2 of 2)	7962	NM_009019	19373	Mm.828	NM_009019	ENSMUSG00000061311	Rag1	Rag-1	recombination activating gene 1	protein-coding
mm_76224.1	chr8	83572917	83572954	-	1	NA	exon (NM_027179, exon 6 of 12)	exon (NM_027179, exon 6 of 12)	6177	NM_025843	66916	Mm.29683	NM_025843	ENSMUSG00000033938	Ndufb7	1110002H15Rik	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 7	protein-coding
mm_142378.1	chr17	44736287	44736296	-	1	NA	promoter-TSS (NM_001271631)	promoter-TSS (NM_001271631)	-115	NM_001271631	12393	Mm.391013	NM_009820	ENSMUSG00000039153	Runx2	AML3|Cbf|Cbfa-1|Cbfa1|LS3|Osf2|PEBP2aA|Pebp2a1|Pebpa2a	runt related transcription factor 2	protein-coding
mm_107185.1	chr12	25095718	25095739	+	1	NA	exon (NM_010496, exon 1 of 3)	exon (NM_010496, exon 1 of 3)	364	NM_010496	15902	Mm.34871	NM_010496	ENSMUSG00000020644	Id2	AI255428|C78922|Idb2|bHLHb26	inhibitor of DNA binding 2	protein-coding
mm_47515.1	chr5	124080077	124080102	-	1	NA	exon (NM_019875, exon 6 of 12)	exon (NM_019875, exon 6 of 12)	15709	NM_019875	56325	Mm.254839	NM_019875	ENSMUSG00000029408	Abcb9	TAPL|mKIAA1520	ATP-binding cassette, sub-family B (MDR/TAP), member 9	protein-coding
mm_50303.1	chr6	47781619	47781628	+	1	NA	Intergenic	Intergenic	22029	NR_030485	735289		NR_030485	ENSMUSG00000076060	Mir704	Mirn704|mir-704|mmu-mir-704	microRNA 704	ncRNA
mm_110190.1	chr12	27340200	27340204	-	1	NA	3' UTR (NM_009234, exon 1 of 1)	3' UTR (NM_009234, exon 1 of 1)	2516	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding
mm_67413.1	chr7	80115295	80115355	-	1	NA	promoter-TSS (NM_173011)	promoter-TSS (NM_173011)	25	NM_173011	269951	Mm.246432	NM_173011	ENSMUSG00000030541	Idh2	E430004F23|IDPm|Idh-2	isocitrate dehydrogenase 2 (NADP+), mitochondrial	protein-coding
mm_153777.1	chr19	45777452	45777482	-	1	NA	intron (NM_023799, intron 3 of 15)	B1F|SINE|Alu	5824	NM_023799	76055	Mm.122725	NM_023799	ENSMUSG00000025220	Mgea5	2810009A20Rik|4833427O07Rik|5830447M11Rik|AA408215|Hy5|Ncoat|OGA|mKIAA0679	meningioma expressed antigen 5 (hyaluronidase)	protein-coding
mm_87658.1	chr10	58484043	58484051	+	1	NA	intron (NM_011240, intron 22 of 28)	B1_Mur3|SINE|Alu	-13890	NM_001162956	76138	Mm.211744	NM_001162956	ENSMUSG00000038010	Ccdc138	6230424H07Rik|BC042726	coiled-coil domain containing 138	protein-coding
mm_137845.1	chr17	31057720	31057734	+	1	NA	promoter-TSS (NM_009593)	promoter-TSS (NM_009593)	33	NM_009593	11307	Mm.15691	NM_009593	ENSMUSG00000024030	Abcg1	AW413978|Abc8|White	ATP-binding cassette, sub-family G (WHITE), member 1	protein-coding
mm_137825.1	chr17	30603195	30603204	+	1	NA	intron (NM_025374, intron 2 of 5)	intron (NM_025374, intron 2 of 5)	9460	NM_025374	109801	Mm.261984	NM_025374	ENSMUSG00000024026	Glo1	0610009E22Rik|1110008E19Rik|2510049H23Rik|AW550643|GLY1|Glo-1|Glo-1r|Glo-1s|Glo1-r|Glo1-s|Qglo	glyoxalase 1	protein-coding
mm_32689.1	chr4	115878297	115878331	+	1	NA	3' UTR (NM_001285488, exon 14 of 14)	3' UTR (NM_001285488, exon 14 of 14)	-6086	NM_001039124	654462	Mm.388913	NM_001039124	ENSMUSG00000073774	Kncn	Kino|L5	kinocilin	protein-coding
mm_145759.1	chr18	64888857	64888869	+	1	NA	intron (NM_001114386, intron 1 of 30)	intron (NM_001114386, intron 1 of 30)	1107	NM_001114386	83814	Mm.98668	NM_031881	ENSMUSG00000024589	Nedd4l	1300012C07Rik|Nedd4-2|Nedd4b	neural precursor cell expressed, developmentally down-regulated gene 4-like	protein-coding
mm_120800.1	chr14	74745546	74745557	+	1	NA	exon (NM_016903, exon 8 of 9)	exon (NM_016903, exon 8 of 9)	13254	NM_016903	13885	Mm.38055	NM_016903	ENSMUSG00000021996	Esd	Es-10|Es10|FGH|sid478	esterase D/formylglutathione hydrolase	protein-coding
mm_74609.1	chr8	12466959	12466966	-	1	NA	Intergenic	Intergenic	71443	NM_009233	20664	Mm.39088	NM_009233	ENSMUSG00000096014	Sox1	BB176347|Sox-1	SRY (sex determining region Y)-box 1	protein-coding
mm_25310.1	chr3	106113362	106113378	+	1	NA	promoter-TSS (NM_023186)	promoter-TSS (NM_023186)	-12	NM_023186	81600	Mm.46418	NM_023186	ENSMUSG00000062778	Chia1	2200003E03Rik|AMCase|Chia|YNL	chitinase, acidic 1	protein-coding
mm_17904.1	chr2	35303267	35303272	-	1	NA	exon (NM_001206369, exon 13 of 17)	exon (NM_001206369, exon 13 of 17)	20889	NM_146120	227753	Mm.443	NM_146120	ENSMUSG00000026879	Gsn	ADF	gelsolin	protein-coding
mm_37831.1	chr4	132016145	132016146	-	1	NA	intron (NM_183428, intron 1 of 20)	intron (NM_183428, intron 1 of 20)	32933	NM_001128606	269587	Mm.30038	NM_183428	ENSMUSG00000028906	Epb41	4.1R|AI415518|D4Ertd442e|Elp-1|Elp1|Epb4.1|mKIAA4056	erythrocyte membrane protein band 4.1	protein-coding
mm_141856.1	chr17	34803486	34803496	-	1	NA	intron (NM_009995, intron 3 of 9)	intron (NM_009995, intron 3 of 9)	935	NM_009995	13079	Mm.440407	NM_009995	ENSMUSG00000024365	Cyp21a1	21-OH|21OH|21OHA|21OHB|CYP21OH-A|Cyp21|Cyp21-ps1|Cyp21B|Cyp21a2-ps|Cyp21a2ps|Oh21-1|Oh21-2	cytochrome P450, family 21, subfamily a, polypeptide 1	protein-coding
mm_141549.1	chr17	32165004	32165015	-	1	NA	intron (NM_008716, intron 1 of 32)	intron (NM_008716, intron 1 of 32)	1843	NM_008716	18131	Mm.439741	NM_008716	ENSMUSG00000038146	Notch3	AW229011|N3|hpbk	notch 3	protein-coding
mm_156440.1	chrX	142228183	142228250	+	1	NA	promoter-TSS (NM_001290533)	promoter-TSS (NM_001290533)	39	NM_172782	237082	Mm.41899	NM_172782	ENSMUSG00000042271	Nxt2	6330587F24Rik|AI787442|P15-2	nuclear transport factor 2-like export factor 2	protein-coding
mm_157466.1	chrX	46456342	46456347	-	1	NA	Intergenic	Intergenic	127337	NM_028514	73360	Mm.60929	NM_028514	ENSMUSG00000046615	Actrt1	1700061J02Rik|Arp-T1	actin-related protein T1	protein-coding
mm_31718.1	chr4	62652482	62652497	+	1	NA	intron (NM_134257, intron 9 of 15)	intron (NM_134257, intron 9 of 15)	-21485	NM_001310706	50780	Mm.286753	NM_019492	ENSMUSG00000059810	Rgs3	4930506N09Rik|C2PA-RGS3|C2pa|PDZ-RGS3|RGS3S	regulator of G-protein signaling 3	protein-coding
mm_110148.1	chr12	26450538	26450549	-	1	NA	intron (NM_021384, intron 3 of 5)	intron (NM_021384, intron 3 of 5)	5909	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_18827.1	chr2	74661244	74661252	-	1	NA	Intergenic	Intergenic	-1691	NM_007967	14029	Mm.25365	NM_007967	ENSMUSG00000001815	Evx2	Evx-2	even-skipped homeobox 2	protein-coding
mm_136459.1	chr16	95259699	95259710	-	1	NA	intron (NM_001271687, intron 3 of 4)	intron (NM_001271687, intron 3 of 4)	2146	NM_001271690	16516	Mm.272239	NM_019664	ENSMUSG00000062609	Kcnj15	4930414N08Rik|AI182284|AI267127|IRKK|Kir4.2	potassium inwardly-rectifying channel, subfamily J, member 15	protein-coding
mm_84527.1	chr9	67046109	67046121	-	1	NA	intron (NM_001164249, intron 2 of 8)	intron (NM_001164249, intron 2 of 8)	-2244	NM_001164253	22003	Mm.121878	NM_024427	ENSMUSG00000032366	Tpm1	AA986836|AI854628|TM2|Tm3|Tmpa|Tpm-1|alpha-TM	tropomyosin 1, alpha	protein-coding
mm_170795.1	chr2	175372425	175372441	+	1	NA	promoter-TSS (NM_001177405).2	promoter-TSS (NM_001177405).2	-29	NM_001177405	667962	Mm.422667	NM_001177405	ENSMUSG00000089756	Zfp966	Gm8898|OTTMUSG00000016203	zinc finger protein 966	protein-coding
mm_68565.1	chr7	115550576	115550601	-	1	NA	intron (NM_001277327, intron 8 of 14)	intron (NM_001277327, intron 8 of 14)	251021	NM_001277328	20679	Mm.323365	NM_011445	ENSMUSG00000051910	Sox6	AI987981|SOX-LZ	SRY (sex determining region Y)-box 6	protein-coding
mm_103606.1	chr11	78497526	78497539	-	1	NA	5' UTR (NM_001168521, exon 1 of 9)	5' UTR (NM_001168521, exon 1 of 9)	222	NM_001168521	237868	Mm.210332	NM_172795	ENSMUSG00000050132	Sarm1	A830091I15Rik|C78606|MyD885|Sarm	sterile alpha and HEAT/Armadillo motif containing 1	protein-coding
mm_78659.1	chr9	40458425	40458429	+	1	NA	Intergenic	Intergenic	-2663	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_75660.1	chr8	66481337	66481341	-	1	NA	intron (NM_025465, intron 4 of 6)	intron (NM_025465, intron 4 of 6)	5168	NM_025465	66282	Mm.294985	NM_025465	ENSMUSG00000025591	Tma16	1810029B16Rik	translation machinery associated 16	protein-coding
mm_150265.1	chr19	34217258	34217268	+	1	NA	intron (NM_029682, intron 1 of 10)	MLT1N2|LTR|ERVL-MaLR	24993	NM_029682	76630	Mm.130952	NM_029682	ENSMUSG00000024776	Stambpl1	1700095N21Rik|8230401J17Rik|ALMalpha|AMSH-FP	STAM binding protein like 1	protein-coding
mm_146066.1	chr18	70472407	70472455	+	1	NA	promoter-TSS (NM_001289649)	promoter-TSS (NM_001289649)	-23	NM_029019	170461	Mm.83623	NM_029019	ENSMUSG00000079608	Stard6	1700011K09Rik|4833424I06Rik|4933429L05Rik|AI644424	StAR-related lipid transfer (START) domain containing 6	protein-coding
mm_75926.1	chr8	71507629	71507640	-	1	NA	exon (NM_032398, exon 3 of 6)	exon (NM_032398, exon 3 of 6)	4135	NM_032398	84094	Mm.260768	NM_032398	ENSMUSG00000034845	Plvap	MECA32|Pv1	plasmalemma vesicle associated protein	protein-coding
mm_36364.1	chr4	76344228	76344250	-	1	NA	intron (NM_011211, intron 10 of 39)	intron (NM_011211, intron 10 of 39)	-1065953	NM_025849	66928	Mm.24332	NM_025849	ENSMUSG00000028398	Tmem261	1700027K24Rik|3110001D03Rik	transmembrane protein 261	protein-coding
mm_110519.1	chr12	54862673	54862691	-	1	NA	intron (NM_007688, intron 1 of 3)	CpG	195	NM_007688	12632	Mm.276826	NM_007688	ENSMUSG00000062929	Cfl2	-	cofilin 2, muscle	protein-coding
mm_101736.1	chr11	43311136	43311145	-	1	NA	Intergenic	MER5A|DNA|hAT-Charlie	63321	NR_029558	387164		NR_029558	ENSMUSG00000065601	Mir146	Mirn146|miR-146a|mmu-mir-146	microRNA 146	ncRNA
mm_79646.1	chr9	59564860	59564879	+	1	NA	exon (NM_010421, exon 14 of 14)	exon (NM_010421, exon 14 of 14)	-13468	NM_175235	76183	Mm.265415	NM_175235	ENSMUSG00000032297	Celf6	6330569O16Rik|Brunol6	CUGBP, Elav-like family member 6	protein-coding
mm_19286.1	chr2	90439659	90439688	-	1	NA	intron (NM_001135657, intron 23 of 25)	intron (NM_001135657, intron 23 of 25)	39033	NM_146263	258330	Mm.330392	NM_146263	ENSMUSG00000082980	Olfr1274-ps	GA_x5J8B7W2BV0-3116-4045|MOR228-4|MOR228-5|Olfr1274	olfactory receptor 1274, pseudogene	protein-coding
mm_152762.1	chr19	20382887	20382986	-	1	NA	exon (NM_010730, exon 5 of 13)	exon (NM_010730, exon 5 of 13)	7735	NM_010730	16952	Mm.248360	NM_010730	ENSMUSG00000024659	Anxa1	Anx-1|Anx-A1|C430014K04Rik|Lpc-1|Lpc1	annexin A1	protein-coding
mm_46556.1	chr5	106696531	106696586	-	1	NA	5' UTR (NM_026856, exon 1 of 7)	5' UTR (NM_026856, exon 1 of 7)	272	NM_026856	52397	Mm.249474	NM_026856	ENSMUSG00000049606	Zfp644	1110068L01Rik|AA408882|BM-005|D5Ertd689e|Zep-2	zinc finger protein 644	protein-coding
mm_137214.1	chr17	24168768	24168770	+	1	NA	intron (NR_037854, intron 1 of 2)	intron (NR_037854, intron 1 of 2)	626	NR_037854	100039636	Mm.30155	NR_037854		Atp6v0c-ps2	Atp6l-ps2|Gm15487	ATPase, H+ transporting, lysosomal V0 subunit C, pseudogene 2	pseudo
mm_84313.1	chr9	63714744	63714769	-	1	NA	intron (NM_016769, intron 1 of 8)	L1MB7|LINE|L1	43238	NM_016769	17127	Mm.7320	NM_016769	ENSMUSG00000032402	Smad3	AU022421|Madh3	SMAD family member 3	protein-coding
mm_138642.1	chr17	35866607	35866675	+	1	NA	promoter-TSS (NM_175242)	promoter-TSS (NM_175242)	26	NM_175242	76448	Mm.359982	NM_175242	ENSMUSG00000034595	Ppp1r18	2310014H01Rik|AA407849|AI450394	protein phosphatase 1, regulatory subunit 18	protein-coding
mm_139385.1	chr17	52149306	52149339	+	1	NA	Intergenic	Intergenic	266595	NR_045095	100504169	Mm.417731	NR_045095		Gm20098	-	predicted gene, 20098	ncRNA
mm_98643.1	chr11	96203442	96203458	+	1	NA	promoter-TSS (NR_108029)	promoter-TSS (NR_108029)	-4	NR_108029	432593	Mm.342467	NR_108029		Gm11538	OTTMUSG00000001983	predicted gene 11538	ncRNA
mm_8956.1	chr1	164460855	164460871	-	1	NA	Intergenic	MIRb|SINE|MIR	-2508	NM_009721	11931	Mm.4550	NM_009721	ENSMUSG00000026576	Atp1b1	Atp4b|Atpb|Atpb-1|NKbeta1	ATPase, Na+/K+ transporting, beta 1 polypeptide	protein-coding
mm_32262.1	chr4	102589688	102589716	+	1	NA	promoter-TSS (NM_001177981)	promoter-TSS (NM_001177981)	-141	NM_001177981	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_125591.1	chr15	59648357	59648369	+	1	NA	promoter-TSS (NM_144549)	promoter-TSS (NM_144549)	-291	NM_144549	211770	Mm.40298	NM_144549	ENSMUSG00000032501	Trib1	A530090O15Rik|TRB-1|Trb1	tribbles pseudokinase 1	protein-coding
mm_89206.1	chr10	86693953	86694004	+	1	NA	exon (NM_011631, exon 13 of 18)	exon (NM_011631, exon 13 of 18)	8451	NR_015572	66263	Mm.392261	NR_015572		1810014B01Rik	-	RIKEN cDNA 1810014B01 gene	pseudo
mm_63996.1	chr7	140115840	140115850	+	1	NA	intron (NM_053119, intron 1 of 7)	intron (NM_053119, intron 1 of 7)	578	NM_053119	93747	Mm.24452	NM_053119	ENSMUSG00000025465	Echs1	C80529	enoyl Coenzyme A hydratase, short chain, 1, mitochondrial	protein-coding
mm_26512.1	chr3	145891602	145891615	+	1	NA	3' UTR (NM_026993, exon 6 of 6)	3' UTR (NM_026993, exon 6 of 6)	-32654	NM_009740	12042	Mm.239141	NM_009740	ENSMUSG00000028191	Bcl10	AI132454|BCL-10|C81403|CARMEN|CIPER|CLAP|ME10|cE10	B cell leukemia/lymphoma 10	protein-coding
mm_77495.1	chr8	122576900	122576927	-	1	NA	promoter-TSS (NM_009698)	promoter-TSS (NM_009698)	-6	NM_009698	11821	Mm.1786	NM_009698	ENSMUSG00000006589	Aprt	C85684	adenine phosphoribosyl transferase	protein-coding
mm_42341.1	chr5	114904836	114904846	+	1	NA	exon (NM_011854, exon 4 of 6)	exon (NM_011854, exon 4 of 6)	7907	NM_011854	23962	Mm.228363	NM_011854	ENSMUSG00000029561	Oasl2	M1204|Mmu-OASL|Oasl	2'-5' oligoadenylate synthetase-like 2	protein-coding
mm_109722.1	chr12	116140984	116140993	+	1	NA	intron (NM_009511, intron 10 of 12)	MTC|LTR|ERVL-MaLR	63262	NM_009511	22355	Mm.395245	NM_009511	ENSMUSG00000011171	Vipr2	VPAC2|VPAC2R|Vip2	vasoactive intestinal peptide receptor 2	protein-coding
mm_112685.1	chr13	16030579	16030597	+	1	NA	3' UTR (NM_008380, exon 5 of 5)	3' UTR (NM_008380, exon 5 of 5)	18737	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_104998.1	chr11	100356117	100356127	-	1	NA	promoter-TSS (NM_177981)	promoter-TSS (NM_177981)	19	NM_177981	15114	Mm.281700	NM_010404	ENSMUSG00000006930	Hap1	HAP-1	huntingtin-associated protein 1	protein-coding
mm_98998.1	chr11	98795496	98795574	+	1	NA	promoter-TSS (NM_028722)	promoter-TSS (NM_028722)	-234	NM_028722	74026	Mm.258352	NM_028722	ENSMUSG00000052915	Msl1	2810017F12Rik|4121402D02Rik|4930463F05Rik|AA682082|Msl-1	male-specific lethal 1 homolog (Drosophila)	protein-coding
mm_77891.1	chr9	7347465	7347473	+	1	NA	promoter-TSS (NM_008605)	promoter-TSS (NM_008605)	95	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_70945.1	chr8	26266858	26266894	+	1	NA	Intergenic	Intergenic	108707	NM_199042	73754	Mm.383241	NM_199042	ENSMUSG00000037214	Thap1	4833431A01Rik|AW490810	THAP domain containing, apoptosis associated protein 1	protein-coding
mm_58685.1	chr7	12834744	12834811	+	1	NA	promoter-TSS (NM_022981)	promoter-TSS (NM_022981)	-33	NM_022981	65020	Mm.292297	NM_022981	ENSMUSG00000058638	Zfp110	2900024E01Rik|N28112|NRIF|Nrif1	zinc finger protein 110	protein-coding
mm_124647.1	chr15	5116635	5116678	+	1	NA	promoter-TSS (NM_026069)	promoter-TSS (NM_026069)	43	NM_026069	67281	Mm.10474	NM_026069	ENSMUSG00000041841	Rpl37	3110005M08Rik	ribosomal protein L37	protein-coding
mm_76528.1	chr8	87501219	87501243	-	1	NA	intron (NR_125722, intron 1 of 3)	MIR3|SINE|MIR	28115	NR_125722	100040294	Mm.213632	NR_033430	ENSMUSG00000097248	Gm2694	C230036H16Rik|linc1582	predicted gene 2694	ncRNA
mm_63349.1	chr7	126976339	126976400	+	1	NA	5' UTR (NM_026638, exon 1 of 6)	5' UTR (NM_026638, exon 1 of 6)	455	NM_001347656	52858	Mm.28219	NM_026638	ENSMUSG00000030682	Cdipt	9530042F15Rik|D7Bwg0575e|Pis|Pis1	CDP-diacylglycerol--inositol 3-phosphatidyltransferase (phosphatidylinositol synthase)	protein-coding
mm_131154.1	chr16	6842386	6842387	+	1	NA	intron (NM_021477, intron 5 of 16)	intron (NM_021477, intron 5 of 16)	-227449	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_114951.1	chr13	96748319	96748347	+	1	NA	Intergenic	CpG	-77397	NM_008255	15357	Mm.316652	NM_008255	ENSMUSG00000021670	Hmgcr	HMG-CoAR|Red	3-hydroxy-3-methylglutaryl-Coenzyme A reductase	protein-coding
mm_76041.1	chr8	77477213	77477221	-	1	NA	intron (NM_030113, intron 1 of 22)	intron (NM_030113, intron 1 of 22)	-39839	NR_028125	70345	Mm.411813	NR_028125	ENSMUSG00000097882	0610038B21Rik	-	RIKEN cDNA 0610038B21 gene	ncRNA
mm_164247.1	chr15	96457233	96457246	+	1	NA	intron (NM_028148, intron 1 of 14)	RSINE1|SINE|B4	3604	NM_028148	72193	Mm.324474	NM_028148	ENSMUSG00000033228	Scaf11	1110061H03Rik|2610510E10Rik|AI462454|CASP11|SIP1|SRRP129|Sfrs2ip|Srsf2ip|mKIAA3013	SR-related CTD-associated factor 11	protein-coding
mm_73061.1	chr8	94386468	94386468	+	1	NA	promoter-TSS (NM_022331)	promoter-TSS (NM_022331)	-32	NM_022331	64209	Mm.29151	NM_022331	ENSMUSG00000031770	Herpud1	Herp|Mifl|SUP	homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1	protein-coding
mm_143534.1	chr17	73950138	73950152	-	1	NA	promoter-TSS (NM_011723)	promoter-TSS (NM_011723)	51	NM_011723	22436	Mm.11223	NM_011723	ENSMUSG00000024066	Xdh	XO|Xor|Xox-1|Xox1	xanthine dehydrogenase	protein-coding
mm_127376.1	chr15	100810588	100810601	+	1	NA	exon (NM_021530, exon 21 of 25)	exon (NM_021530, exon 21 of 25)	29340	NM_001347102	59033	Mm.209856	NM_021530	ENSMUSG00000023032	Slc4a8	AW493845|C230026C11|NDCBE|kNBC-3	solute carrier family 4 (anion exchanger), member 8	protein-coding
mm_112631.1	chr13	15931680	15931683	+	1	NA	Intergenic	Intergenic	-80170	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_43384.1	chr5	135728657	135728667	+	1	NA	exon (NM_008898, exon 3 of 16)	exon (NM_008898, exon 3 of 16)	7227	NR_106001	102466791		NR_106001	ENSMUSG00000099197	Mir7034	Gm27372|mmu-mir-7034	microRNA 7034	ncRNA
mm_149939.1	chr19	27217407	27217424	+	1	NA	5' UTR (NM_013703, exon 1 of 19)	5' UTR (NM_013703, exon 1 of 19)	395	NM_001161420	22359	Mm.4141	NM_013703	ENSMUSG00000024924	Vldlr	AA408956|AI451093|AW047288	very low density lipoprotein receptor	protein-coding
mm_167455.1	chr8	123193576	123193579	+	1	NA	intron (NM_007876, intron 1 of 10)	B1_Mus1|SINE|Alu	7342	NM_007876	13479	Mm.20388	NM_007876	ENSMUSG00000019278	Dpep1	AI327012|MBD	dipeptidase 1 (renal)	protein-coding
mm_17221.1	chr2	25500280	25500290	-	1	NA	promoter-TSS (NM_013908)	promoter-TSS (NM_013908)	221	NM_027062	69379	Mm.24596	NM_027062	ENSMUSG00000015083	C8g	-	complement component 8, gamma polypeptide	protein-coding
mm_7825.1	chr1	132067925	132067948	-	1	NA	5' UTR (NM_001114662, exon 1 of 10)	5' UTR (NM_001114662, exon 1 of 10)	126	NM_172510	213006	Mm.208445	NM_172510	ENSMUSG00000059149	Mfsd4a	A230072B04|A930031D07Rik|AI850289|Mfsd4	major facilitator superfamily domain containing 4A	protein-coding
mm_7492.1	chr1	121332572	121332587	-	1	NA	promoter-TSS (NM_178082)	promoter-TSS (NM_178082)	10	NM_178082	72999	Mm.27136	NM_133748	ENSMUSG00000003721	Insig2	2900053I11Rik|C730043J18Rik|Insig-2	insulin induced gene 2	protein-coding
mm_27142.1	chr3	32616876	32616892	-	1	NA	promoter-TSS (NM_013531)	promoter-TSS (NM_013531)	-349	NM_013531	14696	Mm.139192	NM_013531	ENSMUSG00000027669	Gnb4	6720453A21Rik|G(beta)4	guanine nucleotide binding protein (G protein), beta 4	protein-coding
mm_143901.1	chr17	84790812	84790829	-	1	NA	promoter-TSS (NM_028233)	promoter-TSS (NM_028233)	-34	NM_028233	72416	Mm.217027	NM_028233	ENSMUSG00000024120	Lrpprc	3110001K13Rik|C76645|Gp130|Lrp130|Lsfc	leucine-rich PPR-motif containing	protein-coding
mm_21394.1	chr2	157566320	157566350	-	1	NA	promoter-TSS (NM_016916)	promoter-TSS (NM_016916)	26	NM_016916	53619	Mm.480461	NM_016916	ENSMUSG00000067787	Blcap	AI462828|Bc10	bladder cancer associated protein	protein-coding
mm_95432.1	chr11	50207459	50207479	+	1	NA	exon (NM_011018, exon 3 of 8)	exon (NM_011018, exon 3 of 8)	3351	NM_001290769	18412	Mm.40828	NM_011018	ENSMUSG00000015837	Sqstm1	A170|OSF-6|Osi|STAP|STONE14|p62	sequestosome 1	protein-coding
mm_22033.1	chr2	168184106	168184128	-	1	NA	exon (NM_009628, exon 4 of 4)	exon (NM_009628, exon 4 of 4)	22995	NM_009628	11538	Mm.201322	NM_009628	ENSMUSG00000051149	Adnp	AA589558|mKIAA0784	activity-dependent neuroprotective protein	protein-coding
mm_125974.1	chr15	76294826	76294856	+	1	NA	exon (NM_001195537, exon 1 of 7)	exon (NM_001195537, exon 1 of 7)	407	NM_001195537	100503915	Mm.393455	NM_001195537	ENSMUSG00000071724	Smpd5	ENSMUSG00000071724|Gm10345|MA-nSMase	sphingomyelin phosphodiesterase 5	protein-coding
mm_28674.1	chr3	95307133	95307181	-	1	NA	promoter-TSS (NM_023628)	promoter-TSS (NM_023628)	19	NM_023628	71790	Mm.218844	NM_023628	ENSMUSG00000015702	Anxa9	1110003P15Rik|2310069F17Rik	annexin A9	protein-coding
mm_164168.1	chr15	74617468	74617468	+	1	NA	intron (NM_001177437, intron 12 of 26)	intron (NM_001177437, intron 12 of 26)	18850	NM_001177437	69439	Mm.263708	NM_001177437	ENSMUSG00000022603	Mroh4	1700016M24Rik	maestro heat-like repeat family member 4	protein-coding
mm_163539.1	chr13	13845589	13845589	+	1	NA	Intergenic	MT2B2|LTR|ERVL	61282	NM_010317	14706	Mm.215394	NM_010317	ENSMUSG00000021303	Gng4	-	guanine nucleotide binding protein (G protein), gamma 4	protein-coding
mm_83912.1	chr9	56382124	56382126	-	1	NA	intron (NM_172924, intron 1 of 6)	MTC|LTR|ERVL-MaLR	35925	NM_172924	244895	Mm.490331	NM_172924	ENSMUSG00000074305	Peak1	1110049L02Rik|9530046P14|AA690169|BE132841|C230081A13Rik|SGK269|mKIAA2002	pseudopodium-enriched atypical kinase 1	protein-coding
mm_133017.1	chr16	56282153	56282161	+	1	NA	Intergenic	L1M3|LINE|L1	77844	NM_174876	224224	Mm.151998	NM_174876	ENSMUSG00000035270	Impg2	IPM200|PG10.2|Rsbp|Spacrcan	interphotoreceptor matrix proteoglycan 2	protein-coding
mm_50170.1	chr6	41554855	41554865	+	1	NA	Intergenic	Intergenic	33084	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_150256.1	chr19	34192364	34192377	+	1	NA	promoter-TSS (NM_029682)	promoter-TSS (NM_029682)	100	NM_029682	76630	Mm.130952	NM_029682	ENSMUSG00000024776	Stambpl1	1700095N21Rik|8230401J17Rik|ALMalpha|AMSH-FP	STAM binding protein like 1	protein-coding
mm_3181.1	chr1	135766208	135766208	+	1	NA	5' UTR (NM_013750, exon 1 of 2)	5' UTR (NM_013750, exon 1 of 2)	123	NM_013750	27280	Mm.34346	NM_013750	ENSMUSG00000041801	Phlda3	Tih1	pleckstrin homology like domain, family A, member 3	protein-coding
mm_172194.1	chr6	51466186	51466192	-	1	NA	exon (NM_182650, exon 6 of 10)	exon (NM_182650, exon 6 of 10)	3705	NM_182650	53379	Mm.155896	NM_016806	ENSMUSG00000004980	Hnrnpa2b1	9130414A06Rik|Hnrpa2|Hnrpa2b1|hnrnp-A	heterogeneous nuclear ribonucleoprotein A2/B1	protein-coding
mm_141374.1	chr17	29032397	29032412	-	1	NA	promoter-TSS (NM_013663)	promoter-TSS (NM_013663)	-256	NM_013663	20383	Mm.6787	NM_013663	ENSMUSG00000071172	Srsf3	AL024116|Sfrs3|X16	serine/arginine-rich splicing factor 3	protein-coding
mm_163648.1	chr13	64066066	64066081	-	1	NA	intron (NM_008291, intron 6 of 10)	B4A|SINE|B4	23128	NM_008291	15487	Mm.5109	NM_008291	ENSMUSG00000033122	Hsd17b3	-	hydroxysteroid (17-beta) dehydrogenase 3	protein-coding
mm_116677.1	chr13	49242863	49242878	-	1	NA	intron (NM_028340, intron 1 of 4)	intron (NM_028340, intron 1 of 4)	5293	NM_025491	66329	Mm.34308	NM_025491	ENSMUSG00000021384	Susd3	1700017I11Rik|2810440J20Rik	sushi domain containing 3	protein-coding
mm_30747.1	chr4	14864201	14864334	+	1	NA	promoter-TSS (NM_028264)	promoter-TSS (NM_028264)	48	NM_028264	72519	Mm.279158	NM_028264	ENSMUSG00000028221	Tmem55a	2610319K07Rik|AI315591|AV001360	transmembrane protein 55A	protein-coding
mm_152839.1	chr19	23448250	23448279	-	1	NA	promoter-TSS (NM_174857)	promoter-TSS (NM_174857)	58	NM_174857	71738	Mm.50841	NM_174857	ENSMUSG00000033207	Mamdc2	1200015L10Rik|AI591564|mamcan	MAM domain containing 2	protein-coding
mm_2295.1	chr1	91483018	91483030	+	1	NA	Intergenic	Intergenic	-11644	NM_028718	74019	Mm.318430	NM_028718	ENSMUSG00000034292	Traf3ip1	3930402D05Rik|AU041749|MIP-T3	TRAF3 interacting protein 1	protein-coding
mm_36304.1	chr4	68954352	68954397	-	1	NA	promoter-TSS (NM_019967)	promoter-TSS (NM_019967)	23	NM_019967	56710	Mm.248788	NM_019967	ENSMUSG00000028351	Brinp1	BRINP|Dbc1|Dbccr1|Fam5a	bone morphogenic protein/retinoic acid inducible neural specific 1	protein-coding
mm_93812.1	chr10	121311035	121311051	-	1	NA	5' UTR (NM_029057, exon 1 of 12)	5' UTR (NM_029057, exon 1 of 12)	146	NM_029057	74694	Mm.233833	NM_029057	ENSMUSG00000052302	Tbc1d30	4930505D03Rik	TBC1 domain family, member 30	protein-coding
mm_95182.1	chr11	42419938	42419955	+	1	NA	5' UTR (NM_008070, exon 1 of 10)	5' UTR (NM_008070, exon 1 of 10)	189	NM_008070	14401	Mm.338723	NM_008070	ENSMUSG00000007653	Gabrb2	AI834970|C030002O17Rik|C030021G16Rik|Gabrab2|Gabrb-2	gamma-aminobutyric acid (GABA) A receptor, subunit beta 2	protein-coding
mm_121149.1	chr14	101910761	101910803	+	1	NA	exon (NM_201529, exon 16 of 31)	exon (NM_201529, exon 16 of 31)	70159	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_143220.1	chr17	63216949	63216952	-	1	NA	intron (NM_015794, intron 7 of 8)	intron (NM_015794, intron 7 of 8)	96023	NR_130176	414079	Mm.444282	NR_130176	ENSMUSG00000090565	4930405O22Rik	-	RIKEN cDNA 4930405O22 gene	ncRNA
mm_32819.1	chr4	117445824	117445835	+	1	NA	intron (NM_025739, intron 2 of 14)	intron (NM_025739, intron 2 of 14)	51223	NM_025739	66743	Mm.318331	NM_025739	ENSMUSG00000028677	Rnf220	4732477A13|4931406I20Rik|5730503K05Rik|AV302541	ring finger protein 220	protein-coding
mm_26873.1	chr3	17403173	17403175	-	1	NA	Intergenic	Lx7|LINE|L1	-386747	NR_033490	70441	Mm.458192	NR_033490	ENSMUSG00000100252	Mir124-2hg	100040120|2610100L16Rik|6430547I21Rik|A930005K07Rik|AW125202|Gm2612	Mir124-2 host gene (non-protein coding)	ncRNA
mm_33471.1	chr4	130818592	130818606	+	1	NA	exon (NM_011520, exon 3 of 5)	exon (NM_011520, exon 3 of 5)	26062	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_170778.1	chr2	169823092	169823103	-	1	NA	intron (NM_080455, intron 1 of 1)	(CA)n|Simple_repeat|Simple_repeat	140090	NR_131974	446211	Mm.266854	NR_131974	ENSMUSG00000103935	AY702102	STDP1	cDNA sequence AY702102	ncRNA
mm_4492.1	chr1	173641290	173641313	+	1	NA	intron (NM_175026, intron 4 of 6)	intron (NM_175026, intron 4 of 6)	10442	NM_175026	236312	Mm.447	NM_175026	ENSMUSG00000043263	Ifi209	4930422C14|AI447904|Ifix|Pyhin-1|Pyhin1	interferon activated gene 209	protein-coding
mm_28657.1	chr3	95241021	95241025	-	1	NA	promoter-TSS (NM_001024841)	promoter-TSS (NM_001024841)	86	NM_001024841	229588	Mm.387177	NM_001024841	ENSMUSG00000068860	Gm128	Ment|pmis1	predicted gene 128	protein-coding
mm_14591.1	chr2	136057956	136057981	+	1	NA	promoter-TSS (NM_029530)	promoter-TSS (NM_029530)	41	NM_029530	76161	Mm.41638	NM_029530	ENSMUSG00000027270	Lamp5	3110035N03Rik|6330527O06Rik|BAD-LAMP|LAMP-5	lysosomal-associated membrane protein family, member 5	protein-coding
mm_171042.1	chr2	97949730	97949737	-	1	NA	Intergenic	Intergenic	482076	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_11682.1	chr2	35562759	35562771	+	1	NA	intron (NM_001114125, intron 1 of 16)	intron (NM_001114125, intron 1 of 16)	-4063	NR_045894	100042194	Mm.330165	NR_045894	ENSMUSG00000086555	Gm13446	OTTMUSG00000012261	predicted gene 13446	ncRNA
mm_83469.1	chr9	45410076	45410099	-	1	NA	non-coding (NR_028499, exon 6 of 6)	non-coding (NR_028499, exon 6 of 6)	4010	NM_007503	11936	Mm.22742	NM_007503	ENSMUSG00000059412	Fxyd2	Atp1g1	FXYD domain-containing ion transport regulator 2	protein-coding
mm_37484.1	chr4	123572973	123572988	-	1	NA	intron (NM_001199136, intron 1 of 97)	intron (NM_001199136, intron 1 of 97)	-43440	NR_105824	102465214		NR_105824	ENSMUSG00000099005	Mir6398	Gm27657|mmu-mir-6398	microRNA 6398	ncRNA
mm_139498.1	chr17	56256803	56256836	+	1	NA	promoter-TSS (NM_010192)	promoter-TSS (NM_010192)	26	NM_010192	14154	Mm.290813	NM_010192	ENSMUSG00000043683	Fem1a	AW611390|Fem1aa	feminization 1 homolog a (C. elegans)	protein-coding
mm_69997.1	chr7	142385908	142385924	-	1	NA	intron (NM_009983, intron 1 of 8)	intron (NM_009983, intron 1 of 8)	1954	NM_009983	13033	Mm.231395	NM_009983	ENSMUSG00000007891	Ctsd	CD|CatD	cathepsin D	protein-coding
mm_118958.1	chr14	27403341	27403343	+	1	NA	3' UTR (NM_027871, exon 11 of 11)	3' UTR (NM_027871, exon 11 of 11)	-25505	NM_028945	218850	Mm.247767	NM_028945	ENSMUSG00000040651	Fam208a	4732418E12|4933409E02Rik|D14Abb1e|MommeD6	family with sequence similarity 208, member A	protein-coding
mm_140242.1	chr17	84146101	84146116	+	1	NA	Intergenic	Intergenic	41839	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_116807.1	chr13	54190173	54190187	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-1949	NM_001010973	15466	Mm.57243	NM_008286	ENSMUSG00000034987	Hrh2	-	histamine receptor H2	protein-coding
mm_161394.1	chr14	99176572	99176572	+	1	NA	intron (NM_029320, intron 10 of 17)	intron (NM_029320, intron 10 of 17)	-76802	NM_028315	72662	Mm.163339	NM_028315	ENSMUSG00000033166	Dis3	2810028N01Rik	DIS3 homolog, exosome endoribonuclease and 3'-5' exoribonuclease	protein-coding
mm_97358.1	chr11	77503801	77503835	+	1	NA	intron (NM_001004144, intron 10 of 19)	intron (NM_001004144, intron 10 of 19)	9455	NM_001024920	216964	Mm.341211	NM_001024920	ENSMUSG00000044328	Trp53i13	2410019G02Rik|Tp53i13	transformation related protein 53 inducible protein 13	protein-coding
mm_65175.1	chr7	19692018	19692039	-	1	NA	exon (NM_001110009, exon 3 of 4)	exon (NM_001110009, exon 3 of 4)	631	NM_001110009	11812	Mm.182440	NM_007469	ENSMUSG00000040564	Apoc1	Apo-CIB|ApoC-IB|apo-CI|apoC-I	apolipoprotein C-I	protein-coding
mm_96086.1	chr11	60175858	60175887	+	1	NA	intron (NM_001037764, intron 1 of 4)	CpG	24745	NR_105886	102465555		NR_105886	ENSMUSG00000098547	Mir6921	Gm27352|mmu-mir-6921	microRNA 6921	ncRNA
mm_113764.1	chr13	44800784	44800788	+	1	NA	intron (NM_001205044, intron 2 of 18)	intron (NM_001205044, intron 2 of 18)	69515	NM_001205043	16468	Mm.25059	NM_021878	ENSMUSG00000038518	Jarid2	Jmj|jumonji	jumonji, AT rich interactive domain 2	protein-coding
mm_110434.1	chr12	46819500	46819517	-	1	NA	promoter-TSS (NM_021361)	promoter-TSS (NM_021361)	-733	NM_021361	664883	Mm.247195	NM_021361	ENSMUSG00000021047	Nova1	9430099M15Rik|G630039L02|Nova-1	neuro-oncological ventral antigen 1	protein-coding
mm_90125.1	chr10	117629494	117629506	+	1	NA	promoter-TSS (NM_027468)	promoter-TSS (NM_027468)	0	NM_027468	70574	Mm.339332	NM_027468	ENSMUSG00000020183	Cpm	1110060I01Rik|5730456K23Rik|AA589379|E030045M14Rik	carboxypeptidase M	protein-coding
mm_9139.1	chr1	170867762	170867784	-	1	NA	promoter-TSS (NM_001081304)	promoter-TSS (NM_001081304)	-2	NM_001081304	226641	Mm.377046	NM_001081304	ENSMUSG00000026663	Atf6	9130025P16Rik|9630036G24|AA789574|Atf6alpha|ESTM49	activating transcription factor 6	protein-coding
mm_76506.1	chr8	86884961	86885049	-	1	NA	exon (NM_030563, exon 1 of 7)	exon (NM_030563, exon 1 of 7)	253	NM_030563	80750	Mm.25117	NM_030563	ENSMUSG00000031652	N4bp1	AI481586|C81621	NEDD4 binding protein 1	protein-coding
mm_168315.1	chr11	109012097	109012099	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	91749	NM_015732	12006	Mm.71710	NM_015732	ENSMUSG00000000142	Axin2	Axi1|Axil|Conductin	axin 2	protein-coding
mm_139415.1	chr17	53421921	53421930	+	1	NA	exon (NM_172497, exon 9 of 13)	exon (NM_172497, exon 9 of 13)	41396	NM_172497	211482	Mm.60887	NM_172497	ENSMUSG00000023931	Efhb	4921525D22Rik	EF hand domain family, member B	protein-coding
mm_94301.1	chr11	4135234	4135246	+	1	NA	promoter-TSS (NM_027859)	promoter-TSS (NM_027859)	80	NM_027859	71673	Mm.240586	NM_027859	ENSMUSG00000003581	Rnf215	0610009J22Rik|AW557025|C77903	ring finger protein 215	protein-coding
mm_148437.1	chr19	3947037	3947055	+	1	NA	exon (NM_019449, exon 10 of 11)	exon (NM_019449, exon 10 of 11)	-11762	NM_028545	73458	Mm.482922	NM_028545	ENSMUSG00000037263	Aldh3b3	1700055N04Rik	aldehyde dehydrogenase 3 family, member B3	protein-coding
mm_140580.1	chr17	10212021	10212055	-	1	NA	3' UTR (NM_001159516, exon 7 of 7)	3' UTR (NM_001159516, exon 7 of 7)	107323	NM_021881	19317	Mm.130694	NM_021881	ENSMUSG00000062078	Qk	1110003F05Rik|1500005P18|QkI|l(17)-1Wis|l17Wis1	quaking	protein-coding
mm_133124.1	chr16	65815818	65815841	+	1	NA	intron (NM_028572, intron 1 of 3)	CpG	196	NM_028572	73569	Mm.25670	NM_028572	ENSMUSG00000091243	Vgll3	1700110N18Rik|4832416J22|C80713|Vgl-3|Vito-2	vestigial like family member 3	protein-coding
mm_58153.1	chr6	142338991	142338996	-	1	NA	Intergenic	MRLTR33|LTR|ERVK	-6704	NM_183165	232491	Mm.490474	NM_183165	ENSMUSG00000041671	Pyroxd1	-	pyridine nucleotide-disulphide oxidoreductase domain 1	protein-coding
mm_160284.1	chr7	123179896	123179896	+	1	NA	intron (NM_144925, intron 12 of 23)	intron (NM_144925, intron 12 of 23)	-34970	NM_146198	233836	Mm.211838	NM_146198	ENSMUSG00000030769	Slc5a11	2010013B02Rik|Kst1|RKST2|SMIT2|Slc5a10	solute carrier family 5 (sodium/glucose cotransporter), member 11	protein-coding
mm_154944.1	chrX	36195969	36195993	+	1	NA	promoter-TSS (NM_028325)	promoter-TSS (NM_028325)	77	NM_028325	72693	Mm.297698	NM_028325	ENSMUSG00000036699	Zcchc12	2810028A01Rik|AV136720|Sizn1	zinc finger, CCHC domain containing 12	protein-coding
mm_84059.1	chr9	58199122	58199132	-	1	NA	exon (NM_177193, exon 3 of 3)	exon (NM_177193, exon 3 of 3)	2588	NM_001161535	320563	Mm.186499	NM_177193	ENSMUSG00000051243	Islr2	B930052A04Rik|Linx|Mbu-3|mKIAA1465	immunoglobulin superfamily containing leucine-rich repeat 2	protein-coding
mm_125833.1	chr15	74957798	74957822	+	1	NA	exon (NM_001164036, exon 2 of 4)	exon (NM_001164036, exon 2 of 4)	2704	NM_001164040	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_121901.1	chr14	21848925	21848938	-	1	NA	promoter-TSS (NM_026965)	promoter-TSS (NM_026965)	-21	NM_026965	69156	Mm.11827	NM_026965	ENSMUSG00000021773	Comtd1	1810030M08Rik|MT773	catechol-O-methyltransferase domain containing 1	protein-coding
mm_117514.1	chr13	80885549	80885559	-	1	NA	intron (NM_001042591, intron 1 of 7)	CpG	2132	NM_001042591	105171	Mm.423137	NM_001042591	ENSMUSG00000074794	Arrdc3	AI450344|mKIAA1376	arrestin domain containing 3	protein-coding
mm_65786.1	chr7	28810202	28810238	-	1	NA	promoter-TSS (NM_177301)	promoter-TSS (NM_177301)	-670	NM_177301	15388	Mm.9043	NM_177301	ENSMUSG00000015165	Hnrnpl	C79783|D830027H13Rik|Hnrpl	heterogeneous nuclear ribonucleoprotein L	protein-coding
mm_16939.1	chr2	14739929	14739956	-	1	NA	intron (NM_023116, intron 2 of 13)	intron (NM_023116, intron 2 of 13)	19300	NR_028497	625342	Mm.484784	NR_028497		Gm13315	OTTMUSG00000011384	lactate dehydrogenase A pseudogene	pseudo
mm_7032.1	chr1	87099550	87099561	-	1	NA	exon (NM_001081082, exon 9 of 11)	exon (NM_001081082, exon 9 of 11)	2051	NM_001081082	76768	Mm.58068	NM_001081082	ENSMUSG00000079440	Alpi	2010001C14Rik|Akp6|gIAP	alkaline phosphatase, intestinal	protein-coding
mm_165686.1	chr3	90695994	90696000	+	1	NA	promoter-TSS (NM_001281852)	promoter-TSS (NM_001281852)	-276	NM_009114	20202	Mm.2128	NM_009114	ENSMUSG00000056071	S100a9	60B8Ag|AW546964|BEE22|Cagb|GAGB|L1Ag|MRP14|p14	S100 calcium binding protein A9 (calgranulin B)	protein-coding
mm_12877.1	chr2	84670227	84670244	+	1	NA	intron (NM_001037279, intron 2 of 3)	CpG	473	NM_001033166	72657	Mm.259293	NM_001033166	ENSMUSG00000076437	Selenoh	2700094K13Rik|Selh	selenoprotein H	protein-coding
mm_161362.1	chr14	57798217	57798217	+	1	NA	promoter-TSS (NM_001142441)	promoter-TSS (NM_001142441)	-1	NM_001142441	100041953	Mm.290178	NM_001142441	ENSMUSG00000061104	Sap18b	ENSMUSG00000061104|Gm10094	Sin3-associated polypeptide 18B	protein-coding
mm_3093.1	chr1	134415415	134415504	+	1	NA	promoter-TSS (NM_001306069)	promoter-TSS (NM_001306069)	81	NM_028320	72674	Mm.259976	NM_028320	ENSMUSG00000026457	Adipor1	2810031L11Rik|ACDCR1|CGI-45|Paqr1	adiponectin receptor 1	protein-coding
mm_70559.1	chr8	13074162	13074164	+	1	NA	3' UTR (NM_025834, exon 8 of 8)	3' UTR (NM_025834, exon 8 of 8)	13255	NM_025834	66901	Mm.441140	NM_025834	ENSMUSG00000031445	Proz	1300015B06Rik	protein Z, vitamin K-dependent plasma glycoprotein	protein-coding
mm_109728.1	chr12	116405342	116405363	+	1	NA	promoter-TSS (NR_028421)	promoter-TSS (NR_028421)	-50	NM_133762	76044	Mm.491196	NM_133762	ENSMUSG00000042029	Ncapg2	5830426I05Rik|Luzp5|Mtb|mCAP-G2	non-SMC condensin II complex, subunit G2	protein-coding
mm_129167.1	chr15	76248015	76248048	-	1	NA	promoter-TSS (NR_105918)	promoter-TSS (NR_105918)	-160	NR_105918	102465575		NR_105918	ENSMUSG00000098625	Mir6953	Gm27738|mmu-mir-6953	microRNA 6953	ncRNA
mm_44448.1	chr5	21665288	21665303	-	1	NA	exon (NM_178728, exon 5 of 5)	exon (NM_178728, exon 5 of 5)	19311	NM_026034	67211	Mm.260782	NM_026034	ENSMUSG00000038525	Armc10	2810037C14Rik|Svh	armadillo repeat containing 10	protein-coding
mm_53041.1	chr6	124663094	124663174	+	1	NA	promoter-TSS (NM_145130)	promoter-TSS (NM_145130)	30	NM_145130	14792	Mm.273915	NM_145130	ENSMUSG00000004270	Lpcat3	C3f|Grcc3f|Lpcat|Lpeat|Lplat5|Lpsat|Mboat5|Moact5|Oact5|PTG	lysophosphatidylcholine acyltransferase 3	protein-coding
mm_23072.1	chr3	36208123	36208167	+	1	NA	intron (NM_198192, intron 1 of 5)	intron (NM_198192, intron 1 of 5)	14130	NM_198192	229214	Mm.330975	NM_198192	ENSMUSG00000058400	Qrfpr	AQ27|Gpr103|SP9155	pyroglutamylated RFamide peptide receptor	protein-coding
mm_151938.1	chr19	5800798	5800802	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	1872	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_27252.1	chr3	37125872	37125882	-	1	NA	promoter-TSS (NM_008366)	promoter-TSS (NM_008366)	77	NM_008366	16183	Mm.14190	NM_008366	ENSMUSG00000027720	Il2	Il-2	interleukin 2	protein-coding
mm_42635.1	chr5	118556441	118556463	+	1	NA	Intergenic	Intergenic	-4267	NM_001347445	76199	Mm.206238	NM_172424	ENSMUSG00000018076	Med13l	2210413I17Rik|6330591G05Rik|9030618F05Rik|Thrap2|Trap240L|mKIAA1025	mediator complex subunit 13-like	protein-coding
mm_21463.1	chr2	160888036	160888043	-	1	NA	promoter-TSS (NM_001199118)	promoter-TSS (NM_001199118)	-129	NM_001199118	64899	Mm.292111	NM_022883	ENSMUSG00000027412	Lpin3	9130206L11Rik|AA438110|AV236139|mKIAA4023	lipin 3	protein-coding
mm_163490.1	chr12	109453650	109453657	+	1	NA	non-coding (NR_033813, exon 2 of 6)	non-coding (NR_033813, exon 2 of 6)	198	NM_010052	13386	Mm.157069	NM_010052	ENSMUSG00000040856	Dlk1	AW742678|DLK-1|DlkI|FA1|Ly107|Peg9|SCP1|ZOG|pG2|pref-1	delta-like 1 homolog (Drosophila)	protein-coding
mm_99552.1	chr11	103638920	103638931	+	1	NA	promoter-TSS (NM_027083)	promoter-TSS (NM_027083)	-11	NR_131109	78629	Mm.398236	NR_131109		1700072I22Rik	-	RIKEN cDNA 1700072I22 gene	ncRNA
mm_47244.1	chr5	121545714	121545748	-	1	NA	5' UTR (NM_010765, exon 1 of 14)	5' UTR (NM_010765, exon 1 of 14)	161	NM_010765	17165	Mm.272206	NM_010765	ENSMUSG00000029454	Mapkapk5	MK5|PRAK	MAP kinase-activated protein kinase 5	protein-coding
mm_100827.1	chr11	5390915	5390920	-	1	NA	intron (NM_001080924, intron 1 of 8)	intron (NM_001080924, intron 1 of 8)	-9177	NM_001290501	407821	Mm.216313	NM_001080924	ENSMUSG00000041961	Znrf3	Gm1167	zinc and ring finger 3	protein-coding
mm_113690.1	chr13	42916793	42916811	+	1	NA	intron (NM_001302636, intron 1 of 12)	CpG	50555	NM_001302636	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding
mm_47595.1	chr5	124862297	124862301	-	1	NA	promoter-TSS (NM_001081750)	promoter-TSS (NM_001081750)	-78	NM_144819	215707	Mm.389693	NM_144819	ENSMUSG00000037979	Ccdc92	AW050178|D5Bwg0834e	coiled-coil domain containing 92	protein-coding
mm_159.1	chr1	12692570	12692585	+	1	NA	5' UTR (NM_001198566, exon 1 of 21)	5' UTR (NM_001198566, exon 1 of 21)	147	NM_001198566	240725	Mm.45563	NM_172294	ENSMUSG00000016918	Sulf1	AI467640|AW121680|mKIAA1077	sulfatase 1	protein-coding
mm_111027.1	chr12	79132194	79132215	-	1	NA	intron (NM_009705, intron 2 of 7)	intron (NM_009705, intron 2 of 7)	1416	NM_009705	11847	Mm.3506	NM_009705	ENSMUSG00000021125	Arg2	AII|AU022422	arginase type II	protein-coding
mm_124564.1	chr14	123627060	123627154	-	1	NA	promoter-TSS (NM_177393)	promoter-TSS (NM_177393)	37	NM_177393	338370	Mm.255348	NM_177393	ENSMUSG00000000197	Nalcn	A530023G15Rik|AI849508|Vgcnl1	sodium leak channel, non-selective	protein-coding
mm_12659.1	chr2	75633974	75634005	+	1	NA	Intergenic	RMER20B|LTR|ERVK	-25270	NM_146130	229279	Mm.316306	NM_053263	ENSMUSG00000059005	Hnrnpa3	2410013L13Rik|2610209F03Rik|2610510D13Rik|Hnrpa3	heterogeneous nuclear ribonucleoprotein A3	protein-coding
mm_127383.1	chr15	100870998	100871008	+	1	NA	intron (NM_001077499, intron 1 of 26)	CpG	358	NM_001077499	20273	Mm.385012	NM_011323	ENSMUSG00000023033	Scn8a	AI853486|C630029C19Rik|NaCh6|Nav1.6|dmu|med|mnd-2|mnd2|nmf2|nmf335|nmf58|nur14|seal	sodium channel, voltage-gated, type VIII, alpha	protein-coding
mm_63053.1	chr7	121905621	121905632	+	1	NA	intron (NR_073548, intron 4 of 12)	B4A|SINE|B4	40588	NR_073548	20277	Mm.7709	NM_011325	ENSMUSG00000030873	Scnn1b	-	sodium channel, nonvoltage-gated 1 beta	protein-coding
mm_157098.1	chrX	9437432	9437438	-	1	NA	3' UTR (NM_007807, exon 13 of 13)	3' UTR (NM_007807, exon 13 of 13)	31889	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_35462.1	chr4	40757819	40757821	-	1	NA	promoter-TSS (NM_021535)	promoter-TSS (NM_021535)	65	NM_021535	74255	Mm.289929	NM_021535	ENSMUSG00000028409	Smu1	2600001O03Rik|2610203K23Rik|AB044414|AI845086|AW556129|Bwd	smu-1 suppressor of mec-8 and unc-52 homolog (C. elegans)	protein-coding
mm_27289.1	chr3	41708756	41708766	-	1	NA	intron (NM_001081411, intron 8 of 20)	intron (NM_001081411, intron 8 of 20)	33753	NM_001081411	67161	Mm.331001	NM_026008	ENSMUSG00000059834	Sclt1	2610207F23Rik|4931421F20Rik	sodium channel and clathrin linker 1	protein-coding
mm_1801.1	chr1	80445915	80445922	+	1	NA	promoter-TSS (NR_040460)	promoter-TSS (NR_040460)	-14	NR_040460	72208	Mm.396181	NR_040460	ENSMUSG00000101483	1700016L21Rik	Jr3	RIKEN cDNA 1700016L21 gene	ncRNA
mm_97647.1	chr11	79390340	79390362	+	1	NA	exon (NM_010897, exon 4 of 58)	exon (NM_010897, exon 4 of 58)	50459	NM_010897	18015	Mm.255596	NM_010897	ENSMUSG00000020716	Nf1	AW494271|Dsk9|E030030H24Rik|Mhdadsk9|Nf-1	neurofibromin 1	protein-coding
mm_36953.1	chr4	109109755	109109772	-	1	NA	intron (NM_001346502, intron 4 of 23)	intron (NM_001346502, intron 4 of 23)	8273	NM_173350	100273	Mm.366315	NM_133885	ENSMUSG00000028559	Osbpl9	2600011I06Rik|AU015843|Orp-9	oxysterol binding protein-like 9	protein-coding
mm_118736.1	chr14	22308268	22308270	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	234529	NR_046307	74896	Mm.444661	NR_046307		4930405A10Rik	4930456G20Rik	RIKEN cDNA 4930405A10 gene	ncRNA
mm_36743.1	chr4	99929316	99929324	-	1	NA	promoter-TSS (NM_028132)	promoter-TSS (NM_028132)	-131	NM_028132	72157	Mm.217764	NM_028132	ENSMUSG00000025791	Pgm2	2610020G18Rik|AA407108|AI098105|Pgm-2|Pgm1	phosphoglucomutase 2	protein-coding
mm_14488.1	chr2	131909932	131909948	+	1	NA	promoter-TSS (NM_001278256)	promoter-TSS (NM_001278256)	12	NM_001278256	19122	Mm.648	NM_011170	ENSMUSG00000079037	Prnp	AA960666|AI325101|CD230|PrP|PrP<C>|PrPC|PrPSc|Prn-i|Prn-p|Sinc|prP27-30|prP33-35C	prion protein	protein-coding
mm_79.1	chr1	6734828	6734874	+	1	NA	intron (NM_173868, intron 1 of 21)	intron (NM_173868, intron 1 of 21)	4800	NR_045188	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding
mm_74502.1	chr8	8226464	8226473	-	1	NA	Intergenic	RSINE1|SINE|B4	434305	NM_010111	13642	Mm.209813	NM_010111	ENSMUSG00000001300	Efnb2	ELF-2|Epl5|Eplg5|Htk-L|LERK-5|Lerk5|NLERK-1	ephrin B2	protein-coding
mm_20772.1	chr2	143081230	143081246	-	1	NA	3' UTR (NM_020595, exon 4 of 4)	3' UTR (NM_020595, exon 4 of 4)	2746	NM_020595	57329	Mm.157751	NM_020595	ENSMUSG00000027416	Otor	CDRAP|Fdp|MIA|MIAL	otoraplin	protein-coding
mm_18365.1	chr2	59160645	59160663	-	1	NA	promoter-TSS (NM_026361)	promoter-TSS (NM_026361)	-196	NM_026361	227937	Mm.260938	NM_026361	ENSMUSG00000026991	Pkp4	5031422I09Rik|9430019K17Rik|Armrp|p0071	plakophilin 4	protein-coding
mm_115143.1	chr13	104817228	104817247	+	1	NA	promoter-TSS (NM_026072)	promoter-TSS (NM_026072)	67	NR_135272	67288	Mm.125465	NM_026075	ENSMUSG00000021716	Srek1ip1	3110031B13Rik|AI462702|AV348305|AW121048|Sfrs12ip1|Srsf12ip1	splicing regulatory glutamine/lysine-rich protein 1interacting protein 1	protein-coding
mm_150093.1	chr19	29454434	29454472	+	1	NA	intron (NM_021396, intron 4 of 5)	intron (NM_021396, intron 4 of 5)	43534	NM_021396	58205	Mm.116737	NM_021396	ENSMUSG00000016498	Pdcd1lg2	B7-DC|Btdc|F730015O22Rik|PD-L2	programmed cell death 1 ligand 2	protein-coding
mm_163308.1	chr12	4459629	4459654	+	1	NA	intron (NM_010881, intron 1 of 22)	intron (NM_010881, intron 1 of 22)	17541	NM_010881	17977	Mm.301039	NM_010881	ENSMUSG00000020647	Ncoa1	KAT13A|NCoA-1|NRC-1|SRC-1|SRC-a|SRC1|bHLHe74|mNRC-1	nuclear receptor coactivator 1	protein-coding
mm_63521.1	chr7	127904056	127904066	+	1	NA	promoter-TSS (NM_009739)	promoter-TSS (NM_009739)	-12	NM_009739	12041	Mm.425495	NM_009739	ENSMUSG00000030802	Bckdk	AI327402	branched chain ketoacid dehydrogenase kinase	protein-coding
mm_162762.1	chr10	62055383	62055387	+	1	NA	Intergenic	Intergenic	55628	NM_027251	69894	Mm.294126	NM_027251	ENSMUSG00000020083	2010107G23Rik	AA545165	RIKEN cDNA 2010107G23 gene	protein-coding
mm_136577.1	chr17	3482468	3482489	+	1	NA	intron (NM_001286758, intron 1 of 12)	intron (NM_001286758, intron 1 of 12)	163	NM_001286758	24001	Mm.137134	NM_011878	ENSMUSG00000023800	Tiam2	3000002F19Rik|STEF|mKIAA2016	T cell lymphoma invasion and metastasis 2	protein-coding
mm_164062.1	chr14	117331096	117331101	+	1	NA	intron (NM_001079844, intron 2 of 9)	intron (NM_001079844, intron 2 of 9)	405801	NM_011821	23888	Mm.440025	NM_011821	ENSMUSG00000058571	Gpc6	-	glypican 6	protein-coding
mm_92453.1	chr10	77795124	77795128	-	1	NA	intron (NM_001287074, intron 1 of 11)	intron (NM_001287074, intron 1 of 11)	4007	NM_001205034	100503388	Mm.482880	NM_001205034	ENSMUSG00000096380	Gm19668	-	predicted gene, 19668	protein-coding
mm_159433.1	chr3	115081002	115081002	+	1	NA	promoter-TSS (NM_153157)	promoter-TSS (NM_153157)	37	NM_153157	229759	Mm.54183	NM_153157	ENSMUSG00000027965	Olfm3	B230206G02Rik	olfactomedin 3	protein-coding
mm_68554.1	chr7	114416484	114416532	-	1	NA	intron (NM_011055, intron 1 of 15)	CpG	1254	NM_011055	18576	Mm.430730	NM_011055	ENSMUSG00000030671	Pde3b	9830102A01Rik|AI847709	phosphodiesterase 3B, cGMP-inhibited	protein-coding
mm_135893.1	chr16	65105672	65105679	-	1	NA	5' UTR (NM_008310, exon 1 of 3)	5' UTR (NM_008310, exon 1 of 3)	109	NM_008310	15557	Mm.5040	NM_008310	ENSMUSG00000050783	Htr1f	Htr1eb	5-hydroxytryptamine (serotonin) receptor 1F	protein-coding
mm_144549.1	chr18	30283833	30283844	+	1	NA	intron (NM_181414, intron 4 of 24)	intron (NM_181414, intron 4 of 24)	10942	NM_181414	225326	Mm.194127	NM_181414	ENSMUSG00000033628	Pik3c3	5330434F23Rik|Vps34	phosphoinositide-3-kinase, class 3	protein-coding
mm_80020.1	chr9	67935298	67935329	+	1	NA	intron (NM_177184, intron 49 of 84)	intron (NM_177184, intron 49 of 84)	90401	NR_045745	434412	Mm.490707	NR_045745	ENSMUSG00000111841	Gm20745	-	predicted gene, 20745	ncRNA
mm_134154.1	chr16	10787978	10788009	-	1	NA	TTS (NM_013694)	TTS (NM_013694)	662	NM_013694	21959	Mm.206798	NM_013694	ENSMUSG00000043050	Tnp2	TP2|Tp-2	transition protein 2	protein-coding
mm_92581.1	chr10	80018842	80018861	-	1	NA	promoter-TSS (NM_027521)	promoter-TSS (NM_027521)	-824	NM_027521	70719	Mm.243954	NM_027521	ENSMUSG00000035697	Hmha1	6330406L22Rik|AW539505|Ha-1	histocompatibility (minor) HA-1	protein-coding
mm_148908.1	chr19	6950722	6950736	+	1	NA	exon (NM_007522, exon 3 of 4)	exon (NM_007522, exon 3 of 4)	8167	NM_001285453	12015	Mm.4387	NM_007522	ENSMUSG00000024959	Bad	AI325008|Bbc2	BCL2-associated agonist of cell death	protein-coding
mm_162480.1	chr1	134040302	134040308	+	1	NA	exon (NM_021355, exon 2 of 3)	exon (NM_021355, exon 2 of 3)	2790	NM_021355	14264	Mm.287146	NM_021355	ENSMUSG00000041559	Fmod	AI131919|AU041740|SLRR2E	fibromodulin	protein-coding
mm_136073.1	chr16	84783491	84783492	-	1	NA	intron (NM_023844, intron 1 of 9)	intron (NM_023844, intron 1 of 9)	9368	NM_023844	67374	Mm.41758	NM_023844	ENSMUSG00000053062	Jam2	1110002N23Rik|2410030G21Rik|2410167M24Rik|JAM-2|JAM-B|Jcam2|VE-JAM	junction adhesion molecule 2	protein-coding
mm_89111.1	chr10	84639746	84639769	+	1	NA	exon (NM_027423, exon 9 of 28)	exon (NM_027423, exon 9 of 28)	17320	NM_027423	70428	Mm.335007	NM_027423	ENSMUSG00000034453	Polr3b	2700078H01Rik|A330032P03Rik|C85372|RPC2	polymerase (RNA) III (DNA directed) polypeptide B	protein-coding
mm_87228.1	chr10	40570333	40570352	+	1	NA	promoter-TSS (NM_027572)	promoter-TSS (NM_027572)	-20	NM_027572	70840	Mm.332570	NM_027572	ENSMUSG00000019834	Slc22a16	4921504E14Rik|CT2|FLIPT2|OCT6|OKB1	solute carrier family 22 (organic cation transporter), member 16	protein-coding
mm_126758.1	chr15	85811349	85811353	+	1	NA	intron (NM_197998, intron 1 of 4)	CpG	346	NM_001164626	72355	Mm.33706	NM_197998	ENSMUSG00000064284	Cdpf1	2210021J22Rik	cysteine rich, DPF motif domain containing 1	protein-coding
mm_30490.1	chr3	155352826	155352827	-	1	NA	Intergenic	Intergenic	259392	NM_028938	74435	Mm.195711	NM_028938	ENSMUSG00000028182	Lrriq3	4930438B07Rik|4930511J15Rik|4933403H06Rik|BB020367|Lrrc44	leucine-rich repeats and IQ motif containing 3	protein-coding
mm_54658.1	chr6	39118165	39118177	-	1	NA	promoter-TSS (NR_045813)	promoter-TSS (NR_045813)	178	NM_172893	243771	Mm.268462	NM_172893	ENSMUSG00000038507	Parp12	9930021O16|AA409132|AA536654|ARTD12|PARP-12|Zc3hdc1	poly (ADP-ribose) polymerase family, member 12	protein-coding
mm_125158.1	chr15	31224372	31224400	+	1	NA	promoter-TSS (NM_146057)	promoter-TSS (NM_146057)	1	NM_146057	223453	Mm.222867	NM_146057	ENSMUSG00000039168	Dap	4921531N22Rik|AI789753|AU040360	death-associated protein	protein-coding
mm_40001.1	chr5	32746522	32746549	+	1	NA	promoter-TSS (NM_001347332)	promoter-TSS (NM_001347332)	-193	NM_001347332	320951	Mm.273765	NM_177298	ENSMUSG00000023452	Pisd	9030221M09Rik	phosphatidylserine decarboxylase	protein-coding
mm_49220.1	chr6	15782079	15782104	+	1	NA	intron (NM_175088, intron 4 of 4)	(TG)n|Simple_repeat|Simple_repeat	61430	NM_175088	16543	Mm.1314	NM_175088	ENSMUSG00000041390	Mdfic	Kdt1|Mdfid	MyoD family inhibitor domain containing	protein-coding
mm_156056.1	chrX	109150015	109150074	+	1	NA	exon (NM_019989, exon 2 of 4)	exon (NM_019989, exon 2 of 4)	-46712	NM_001037917	622976	Mm.482747	NM_001037917	ENSMUSG00000048621	Gm6377	EG622976	predicted gene 6377	protein-coding
mm_40858.1	chr5	73557305	73557326	+	1	NA	exon (NM_001190734, exon 11 of 12)	exon (NM_001190734, exon 11 of 12)	66289	NM_178896	100737	Mm.220312	NM_178896	ENSMUSG00000051674	Dcun1d4	AI836376	DCN1, defective in cullin neddylation 1, domain containing 4 (S. cerevisiae)	protein-coding
mm_143523.1	chr17	73710417	73710440	-	1	NA	promoter-TSS (NM_027864)	promoter-TSS (NM_027864)	23	NM_027864	71685	Mm.271953	NM_027864	ENSMUSG00000024064	Galnt14	0610033M06Rik	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 14	protein-coding
mm_141508.1	chr17	31644800	31644809	-	1	NA	Intergenic	Intergenic	-7599	NM_178224	12411	Mm.206417	NM_144855	ENSMUSG00000024039	Cbs	AI047524|AI303044|HIP4	cystathionine beta-synthase	protein-coding
mm_93429.1	chr10	109009056	109009105	-	1	NA	intron (NM_001252341, intron 1 of 11)	intron (NM_001252341, intron 1 of 11)	1895	NM_009306	20979	Mm.289702	NM_009306	ENSMUSG00000035864	Syt1	AW124717|G630098F17Rik|SytI	synaptotagmin I	protein-coding
mm_81111.1	chr9	106453415	106453435	+	1	NA	promoter-TSS (NM_021567)	promoter-TSS (NM_021567)	-413	NM_021567	59092	Mm.286394	NM_021567	ENSMUSG00000023495	Pcbp4	1200003L19Rik|AlphaCP-4	poly(rC) binding protein 4	protein-coding
mm_48781.1	chr5	148552436	148552517	-	1	NA	5' UTR (NM_011908, exon 1 of 5)	5' UTR (NM_011908, exon 1 of 5)	312	NM_011908	24109	Mm.21846	NM_011908	ENSMUSG00000001687	Ubl3	AW108023|HCG	ubiquitin-like 3	protein-coding
mm_85902.1	chr9	111056267	111056287	-	1	NA	exon (NM_017466, exon 2 of 2)	exon (NM_017466, exon 2 of 2)	967	NM_001302377	54199	Mm.7336	NM_017466	ENSMUSG00000043953	Ccrl2	1810047I05Rik|Ackr5|CCR11|Cmkbr1l2|E01|L-CCR	chemokine (C-C motif) receptor-like 2	protein-coding
mm_142209.1	chr17	36989529	36989536	-	1	NA	promoter-TSS (NM_001115075)	promoter-TSS (NM_001115075)	-28	NM_001115075	240095	Mm.246609	NM_001115075	ENSMUSG00000024459	H2-M5	CRW2|D130003B22Rik|H-2M5	histocompatibility 2, M region locus 5	protein-coding
mm_152531.1	chr19	11326796	11326816	-	1	NA	intron (NM_027836, intron 3 of 6)	intron (NM_027836, intron 3 of 6)	7889	NM_001276398	109225	Mm.491251	NM_027836	ENSMUSG00000024672	Ms4a7	9130422I10Rik|A430103C15Rik|CD20l4|CFFMA	membrane-spanning 4-domains, subfamily A, member 7	protein-coding
mm_81413.1	chr9	109054840	109054871	+	1	NA	promoter-TSS (NM_026381)	promoter-TSS (NM_026381)	-11	NM_026381	66940	Mm.196533	NM_025858	ENSMUSG00000025647	Shisa5	2310008D10Rik|6430628I05Rik|Scotin|mShisa5	shisa family member 5	protein-coding
mm_107487.1	chr12	38780255	38780261	+	1	NA	5' UTR (NM_007960, exon 1 of 13)	5' UTR (NM_007960, exon 1 of 13)	176	NM_007960	14009	Mm.4866	NM_007960	ENSMUSG00000004151	Etv1	ER81|Etsrp81	ets variant 1	protein-coding
mm_161088.1	chr12	87602844	87602844	+	1	NA	intron (NM_001270792, intron 1 of 3)	intron (NM_001270792, intron 1 of 3)	179	NM_001270793	100039087	Mm.458830	NM_001270792	ENSMUSG00000096276	Gm2042	-	predicted gene 2042	protein-coding
mm_129570.1	chr15	79658890	79658933	-	1	NA	promoter-TSS (NM_028634)	promoter-TSS (NM_028634)	45	NM_029407	75729	Mm.78946	NM_029407	ENSMUSG00000042564	Fam227a	4933432B09Rik	family with sequence similarity 227, member A	protein-coding
mm_107433.1	chr12	35925680	35925708	+	1	NA	promoter-TSS (NM_207531)	promoter-TSS (NM_207531)	73	NM_207531	403205	Mm.190508	NM_207531	ENSMUSG00000036231	Agr3	BCMP11|E030025L21Rik|Gm888	anterior gradient 3	protein-coding
mm_78201.1	chr9	21378107	21378115	+	1	NA	intron (NM_001277322, intron 2 of 21)	intron (NM_001277322, intron 2 of 21)	9579	NM_001277322	16201	Mm.440026	NM_010561	ENSMUSG00000032178	Ilf3	MBII-26|MPHOSPH4|NF90|NFAR	interleukin enhancer binding factor 3	protein-coding
mm_82465.1	chr9	15710252	15710270	-	1	NA	intron (NM_172289, intron 1 of 10)	intron (NM_172289, intron 1 of 10)	492	NM_172289	234967	Mm.138815	NM_172289	ENSMUSG00000043885	Slc36a4	6330573I15Rik|PAT4	solute carrier family 36 (proton/amino acid symporter), member 4	protein-coding
mm_76297.1	chr8	84204110	84204128	-	1	NA	Intergenic	Intergenic	-4399	NR_029740	387216		NR_029740	ENSMUSG00000065611	Mir23a	Mirn23a|mir-23a|mmu-mir-23a	microRNA 23a	ncRNA
mm_151662.1	chr19	4139606	4139613	-	1	NA	promoter-TSS (NM_206973)	promoter-TSS (NM_206973)	0	NM_144532	73660	Mm.379226	NM_144532	ENSMUSG00000024842	Cabp4	2410038D05Rik	calcium binding protein 4	protein-coding
mm_139180.1	chr17	47593553	47593573	+	1	NA	promoter-TSS (NM_007632)	promoter-TSS (NM_007632)	96	NM_007632	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_54226.1	chr6	28134356	28134385	-	1	NA	promoter-TSS (NM_008174)	promoter-TSS (NM_008174)	-1	NM_008174	14823	Mm.320732	NM_008174	ENSMUSG00000024211	Grm8	A230002O04|Gprc1h|mGluR8	glutamate receptor, metabotropic 8	protein-coding
mm_34366.1	chr4	144893013	144893042	+	1	NA	promoter-TSS (NM_011303)	promoter-TSS (NM_011303)	-110	NM_011303	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding
mm_133303.1	chr16	77594785	77594797	+	1	NA	Intergenic	Intergenic	-4145	NR_029535	387229		NR_029535	ENSMUSG00000065530	Mir99a	Mirn99a|mir-99a|mmu-mir-99a	microRNA 99a	ncRNA
mm_107511.1	chr12	40124754	40124795	+	1	NA	intron (NM_009132, intron 2 of 13)	intron (NM_009132, intron 2 of 13)	9454	NM_009132	20259	Mm.2416	NM_009132	ENSMUSG00000002565	Scin	AW545522|adseverin	scinderin	protein-coding
mm_156137.1	chrX	128261261	128261300	+	1	NA	Intergenic	Intergenic	-524726	NM_001281537	73934	Mm.159093	NM_001281537	ENSMUSG00000043569	Cldn34c4	4930412D23Rik	claudin 34C4	protein-coding
mm_14888.1	chr2	148875149	148875171	+	1	NA	exon (NM_009976, exon 1 of 3)	exon (NM_009976, exon 1 of 3)	352	NM_009976	13010	Mm.4263	NM_009976	ENSMUSG00000027447	Cst3	CysC	cystatin C	protein-coding
mm_77753.1	chr8	128488500	128488515	-	1	NA	intron (NM_008737, intron 12 of 16)	intron (NM_008737, intron 12 of 16)	129266	NR_035436	100316680		NR_035436	ENSMUSG00000084523	Mir1903	Mirn1903|mmu-mir-1903	microRNA 1903	ncRNA
mm_130001.1	chr15	86186920	86186926	-	1	NA	promoter-TSS (NM_145475)	promoter-TSS (NM_145475)	-782	NM_145475	223753	Mm.222685	NM_145475	ENSMUSG00000035891	Cerk	AI848610|D330016D08Rik|mKIAA1646	ceramide kinase	protein-coding
mm_117961.1	chr13	99470328	99470376	-	1	NA	intron (NM_008634, intron 2 of 6)	intron (NM_008634, intron 2 of 6)	46250	NM_008634	17755	Mm.4173	NM_008634	ENSMUSG00000052727	Map1b	A230055D22|AI843217|LC1|MAP5|Mtap-5|Mtap1b|Mtap5	microtubule-associated protein 1B	protein-coding
mm_114709.1	chr13	83572366	83572390	+	1	NA	intron (NM_001347566, intron 1 of 10)	intron (NM_001347566, intron 1 of 10)	-1229	NM_001347577	17260	Mm.24001	NM_025282	ENSMUSG00000005583	Mef2c	5430401D19Rik|9930028G15Rik|AV011172|Mef2	myocyte enhancer factor 2C	protein-coding
mm_85829.1	chr9	110423009	110423010	-	1	NA	TTS (NM_008694)	TTS (NM_008694)	3201	NM_008694	18054	Mm.236225	NM_008694	ENSMUSG00000032484	Ngp	bectenecin	neutrophilic granule protein	protein-coding
mm_64590.1	chr7	3169086	3169092	-	1	NA	exon (NM_001004153, exon 1 of 12)	exon (NM_001004153, exon 1 of 12)	114	NM_001004153	245128	Mm.268551	NM_001004153	ENSMUSG00000054753	AU018091	-	expressed sequence AU018091	protein-coding
mm_88267.1	chr10	74303106	74303155	+	1	NA	exon (NM_001142743, exon 10 of 35)	exon (NM_001142743, exon 10 of 35)	481263	NM_001142735	11994	Mm.338933	NM_023115	ENSMUSG00000052613	Pcdh15	BB078305|ENSMUSG00000046980|Gm9815|Ush1f|av|nmf19|roda	protocadherin 15	protein-coding
mm_84072.1	chr9	58201686	58201697	-	1	NA	promoter-TSS (NM_001161537)	promoter-TSS (NM_001161537)	24	NM_001161535	320563	Mm.186499	NM_177193	ENSMUSG00000051243	Islr2	B930052A04Rik|Linx|Mbu-3|mKIAA1465	immunoglobulin superfamily containing leucine-rich repeat 2	protein-coding
mm_68723.1	chr7	120201474	120201500	-	1	NA	intron (NM_016669, intron 1 of 7)	intron (NM_016669, intron 1 of 7)	501	NM_016669	12971	Mm.9114	NM_016669	ENSMUSG00000030905	Crym	-	crystallin, mu	protein-coding
mm_53679.1	chr6	142298420	142298435	+	1	NA	promoter-TSS (NM_010491)	promoter-TSS (NM_010491)	2	NM_010491	15874	Mm.415	NM_010491	ENSMUSG00000041681	Iapp	DAP	islet amyloid polypeptide	protein-coding
mm_148149.1	chr18	77531163	77531194	-	1	NA	intron (NM_001164504, intron 1 of 7)	intron (NM_001164504, intron 1 of 7)	33958	NM_001164504	225743	Mm.23293	NM_001164504	ENSMUSG00000025427	Rnf165	2900024M11Rik|AI427432|Akd2|Ark2c|G630064H08Rik|Gm96	ring finger protein 165	protein-coding
mm_42160.1	chr5	112255814	112255827	+	1	NA	promoter-TSS (NM_001312894)	promoter-TSS (NM_001312894)	0	NM_001312895	12960	Mm.29488	NM_023695	ENSMUSG00000029343	Crybb1	3110006K12Rik|BB1CRY	crystallin, beta B1	protein-coding
mm_92782.1	chr10	81285764	81285798	-	1	NA	promoter-TSS (NM_001282096)	promoter-TSS (NM_001282096)	0	NM_001282096	27375	Mm.27984	NM_013769	ENSMUSG00000034917	Tjp3	-	tight junction protein 3	protein-coding
mm_72107.1	chr8	71611204	71611212	+	1	NA	exon (NM_146211, exon 1 of 12)	exon (NM_146211, exon 1 of 12)	184	NM_146211	234407	Mm.240885	NM_146211	ENSMUSG00000034807	Colgalt1	2810024B22Rik|Glt25d1	collagen beta(1-O)galactosyltransferase 1	protein-coding
mm_120506.1	chr14	66297017	66297027	+	1	NA	promoter-TSS (NM_029979)	promoter-TSS (NM_029979)	-3	NM_029979	66854	Mm.43871	NM_029979	ENSMUSG00000022043	Trim35	0710005M05Rik|A430106H13Rik|AW046487|HLS5|Mair|NC8|mKIAA1098	tripartite motif-containing 35	protein-coding
mm_36216.1	chr4	62502234	62502260	-	1	NA	promoter-TSS (NM_024257)	promoter-TSS (NM_024257)	-47	NM_024257	72748	Mm.41506	NM_024257	ENSMUSG00000038422	Hdhd3	2810435D12Rik	haloacid dehalogenase-like hydrolase domain containing 3	protein-coding
mm_16196.1	chr2	173000115	173000125	+	1	NA	promoter-TSS (NM_175112)	promoter-TSS (NM_175112)	3	NM_175112	66679	Mm.4113	NM_175112	ENSMUSG00000027509	Rae1	3230401I12Rik|D2Ertd342e|MNRP|MNRP41	ribonucleic acid export 1	protein-coding
mm_169561.1	chr15	12574812	12574814	+	1	NA	intron (NM_001081064, intron 1 of 23)	intron (NM_001081064, intron 1 of 23)	17743	NM_001081064	68070	Mm.423205	NM_001081064	ENSMUSG00000022197	Pdzd2	4930537L06Rik|A930022H17Rik|Gm21706|Gm82|Pdzk3|mKIAA0300	PDZ domain containing 2	protein-coding
mm_100516.1	chr11	120530689	120530705	+	1	NA	promoter-TSS (NM_008101)	promoter-TSS (NM_008101)	-30	NM_008101	14527	Mm.22329	NM_008101	ENSMUSG00000025127	Gcgr	GR	glucagon receptor	protein-coding
mm_48743.1	chr5	147726327	147726357	-	1	NA	promoter-TSS (NM_010228)	promoter-TSS (NM_010228)	-354	NM_010228	14254	Mm.389712	NM_010228	ENSMUSG00000029648	Flt1	AI323757|Flt-1|VEGFR-1|VEGFR1|sFlt1	FMS-like tyrosine kinase 1	protein-coding
mm_129305.1	chr15	77399212	77399235	-	1	NA	promoter-TSS (NM_029419)	promoter-TSS (NM_029419)	-113	NM_001164640	75761	Mm.232636	NM_029419	ENSMUSG00000010601	Apol7a	9130022K13Rik|Apol3	apolipoprotein L 7a	protein-coding
mm_18327.1	chr2	57124133	57124147	-	1	NA	promoter-TSS (NM_001139509)	promoter-TSS (NM_001139509)	-137	NM_001139509	18227	Mm.3507	NM_013613	ENSMUSG00000026826	Nr4a2	HZF-3|NOT|Nurr1|RNR-1|TINOR|TINUR	nuclear receptor subfamily 4, group A, member 2	protein-coding
mm_5862.1	chr1	53774074	53774085	-	1	NA	intron (NM_133810, intron 2 of 7)	intron (NM_133810, intron 2 of 7)	11136	NM_133810	98267	Mm.25559	NM_133810	ENSMUSG00000026094	Stk17b	3110009A03Rik|AI120141|Drak2	serine/threonine kinase 17b (apoptosis-inducing)	protein-coding
mm_97346.1	chr11	77462606	77462652	+	1	NA	Intergenic	CpG	-1284	NM_139129	216961	Mm.33477	NM_139128	ENSMUSG00000020836	Coro6	-	coronin 6	protein-coding
mm_82409.1	chr9	14780347	14780358	-	1	NA	3' UTR (NM_019683, exon 2 of 2)	3' UTR (NM_019683, exon 2 of 2)	2612	NM_019683	56503	Mm.395005	NM_019683	ENSMUSG00000031931	Ankrd49	AW060934|C86108|Gbif	ankyrin repeat domain 49	protein-coding
mm_123878.1	chr14	72673039	72673054	-	1	NA	intron (NM_207636, intron 2 of 25)	intron (NM_207636, intron 2 of 25)	36957	NM_207636	319448	Mm.205421	NM_207636	ENSMUSG00000033487	Fndc3a	1700094E19Rik|D14Ertd453e|F730017H24Rik|Fndc3|sys	fibronectin type III domain containing 3A	protein-coding
mm_54721.1	chr6	40436079	40436088	-	1	NA	promoter-TSS (NM_175528)	promoter-TSS (NM_175528)	50	NM_175528	243780	Mm.333006	NM_175528	ENSMUSG00000037172	E330009J07Rik	AI841796|Lchn|mKIAA1147	RIKEN cDNA E330009J07 gene	protein-coding
mm_124791.1	chr15	8109378	8109386	+	1	NA	promoter-TSS (NM_133227)	promoter-TSS (NM_133227)	69	NM_133227	170762	Mm.295168	NM_133227	ENSMUSG00000022142	Nup155	D930027M19Rik|mKIAA0791	nucleoporin 155	protein-coding
mm_171033.1	chr2	90804664	90804673	-	1	NA	intron (NM_178755, intron 10 of 17)	RLTR1B|LTR|ERV1	21924	NM_178755	271813	Mm.61146	NM_178755	ENSMUSG00000040812	Agbl2	4930524K04|A430081C19Rik|CCP2	ATP/GTP binding protein-like 2	protein-coding
mm_1717.1	chr1	75236974	75236991	+	1	NA	intron (NM_020266, intron 2 of 8)	intron (NM_020266, intron 2 of 8)	280	NM_001159885	56812	Mm.489660	NM_020266	ENSMUSG00000026203	Dnajb2	2700059H22Rik|Dnajb10|Hsj1|mDj8	DnaJ heat shock protein family (Hsp40) member B2	protein-coding
mm_36663.1	chr4	95051175	95051210	-	1	NA	exon (NM_010591, exon 1 of 1)	exon (NM_010591, exon 1 of 1)	1030	NM_010591	16476	Mm.275071	NM_010591	ENSMUSG00000052684	Jun	AP-1|Junc|c-jun	jun proto-oncogene	protein-coding
mm_12593.1	chr2	74272511	74272515	+	1	NA	Intergenic	Intergenic	35204	NR_040501	73962	Mm.50289	NR_040501	ENSMUSG00000085405	4930441J16Rik	Astx1a|Astx1b|Astx1c	RIKEN cDNA 4930441J16 gene	ncRNA
mm_169657.1	chr15	57314767	57314777	+	1	NA	intron (NM_172378, intron 2 of 11)	RLTR9E|LTR|ERVK	162853	NM_172378	210463	Mm.26555	NM_172378	ENSMUSG00000022366	Slc22a22	oat-pg	solute carrier family 22 (organic cation transporter), member 22	protein-coding
mm_50360.1	chr6	48647323	48647327	+	1	NA	promoter-TSS (NM_001286629)	promoter-TSS (NM_001286629)	-36	NM_001286629	243374	Mm.86514	NM_212486	ENSMUSG00000064262	Gimap8	Gm457|IAN9|IMAP8	GTPase, IMAP family member 8	protein-coding
mm_42567.1	chr5	117155273	117155310	+	1	NA	intron (NM_001081308, intron 1 of 19)	PB1D11|SINE|Alu	21703	NM_183306	330177	Mm.24343	NM_183306	ENSMUSG00000061288	Taok3	2900006A08Rik|A130052D22|A430105I05Rik	TAO kinase 3	protein-coding
mm_116768.1	chr13	52820244	52820255	-	1	NA	Intergenic	Intergenic	-63044	NR_027893	105404	Mm.184173	NR_027893		BB123696	-	expressed sequence BB123696	ncRNA
mm_113409.1	chr13	33964936	33964967	+	1	NA	intron (NM_001163239, intron 1 of 5)	intron (NM_001163239, intron 1 of 5)	292	NM_001163241	18105	Mm.264036	NM_020282	ENSMUSG00000046949	Nqo2	NMO2|Nmor2|Ox2	NAD(P)H dehydrogenase, quinone 2	protein-coding
mm_172087.1	chr6	149434579	149434597	-	1	NA	intron (NM_009753, intron 1 of 8)	intron (NM_009753, intron 1 of 8)	25604	NM_009753	12121	Mm.177181	NM_009753	ENSMUSG00000003452	Bicd1	B830009D06Rik|bic-D 1	bicaudal D homolog 1 (Drosophila)	protein-coding
mm_27745.1	chr3	69127068	69127085	-	1	NA	promoter-TSS (NM_008467)	promoter-TSS (NM_008467)	16	NM_008467	16649	Mm.30601	NM_008467	ENSMUSG00000027782	Kpna4	1110058D08Rik|IPOA3	karyopherin (importin) alpha 4	protein-coding
mm_105953.1	chr11	115297619	115297631	-	1	NA	promoter-TSS (NM_178035)	promoter-TSS (NM_178035)	-79	NM_178035	328035	Mm.21995	NM_178035	ENSMUSG00000044788	Fads6	BC044804|OTTMUSG00000021749	fatty acid desaturase domain family, member 6	protein-coding
mm_84678.1	chr9	72090395	72090398	-	1	NA	intron (NM_001253862, intron 3 of 19)	intron (NM_001253862, intron 3 of 19)	20805	NM_001253862	21406	Mm.171615	NM_011544	ENSMUSG00000032228	Tcf12	A130037E08Rik|ALF1|HEB|HEBAlt|HTF-4|HTF4|ME1|REB|bHLHb20	transcription factor 12	protein-coding
mm_41501.1	chr5	92331794	92331817	+	1	NA	promoter-TSS (NM_001310664)	promoter-TSS (NM_001310664)	-22	NM_001310664	109979	Mm.263514	NM_181728	ENSMUSG00000034842	Art3	4930569O04Rik|ARTC3	ADP-ribosyltransferase 3	protein-coding
mm_16744.1	chr2	9594062	9594086	-	1	NA	Intergenic	Intergenic	284526	NM_008091	14462	Mm.313866	NM_008091	ENSMUSG00000015619	Gata3	Gata-3|jal	GATA binding protein 3	protein-coding
mm_122959.1	chr14	54968342	54968360	-	1	NA	promoter-TSS (NR_033497)	promoter-TSS (NR_033497)	-436	NR_033497	791403	Mm.319176	NR_033497	ENSMUSG00000097652	Mhrt	D830015G02Rik|ENSMUSG00000053118|Myheart	myosin heavy chain associated RNA transcript	ncRNA
mm_115736.1	chr13	17790616	17790627	-	1	NA	intron (NM_027118, intron 1 of 13)	B1_Mus1|SINE|Alu	14476	NM_001081058	69562	Mm.193924	NM_027118	ENSMUSG00000041297	Cdk13	2310015O17Rik|Cdc2l5	cyclin-dependent kinase 13	protein-coding
mm_1320.1	chr1	65100519	65100530	+	1	NA	exon (NM_007774, exon 3 of 3)	exon (NM_007774, exon 3 of 3)	2839	NM_007774	12964	Mm.26904	NM_007774	ENSMUSG00000044429	Cryga	Cryg-4|DGcry-4	crystallin, gamma A	protein-coding
mm_46971.1	chr5	115158366	115158390	-	1	NA	promoter-TSS (NM_175403)	promoter-TSS (NM_175403)	-202	NM_175403	109154	Mm.153963	NM_175403	ENSMUSG00000048578	Mlec	2410014A08Rik|AI850530|ESTM19|X83352|mKIAA0152	malectin	protein-coding
mm_106869.1	chr12	8010287	8010302	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	32617	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_170270.1	chr18	23521625	23521632	-	1	NA	intron (NM_001285817, intron 1 of 19)	intron (NM_001285817, intron 1 of 19)	24146	NM_001285810	13527	Mm.94371	NM_010087	ENSMUSG00000024302	Dtna	2210407P21Rik|DTN-A|Dtn|Gm19389|a-DB-1|adbn	dystrobrevin alpha	protein-coding
mm_91529.1	chr10	37141306	37141328	-	1	NA	Intergenic	Intergenic	-2391	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_46425.1	chr5	104310077	104310098	-	1	NA	exon (NM_008318, exon 7 of 7)	exon (NM_008318, exon 7 of 7)	10800	NM_008318	15891	Mm.4987	NM_008318	ENSMUSG00000029306	Ibsp	BSP|BSP II|BSPII|Bsp2	integrin binding sialoprotein	protein-coding
mm_123705.1	chr14	69805219	69805292	-	1	NA	5' UTR (NM_153514, exon 1 of 10)	5' UTR (NM_153514, exon 1 of 10)	290	NM_153514	246710	Mm.102367	NM_153514	ENSMUSG00000022075	Rhobtb2	Dbc2|E130206H14Rik|mKIAA0717	Rho-related BTB domain containing 2	protein-coding
mm_161065.1	chr12	72916887	72916887	-	1	NA	intron (NM_029444, intron 1 of 17)	intron (NM_029444, intron 1 of 17)	878	NM_029444	75801	Mm.242892	NM_029444	ENSMUSG00000021098	4930447C04Rik	4921504I02Rik|A930035O15Rik|Six6OS|Six6as|Six6os1	RIKEN cDNA 4930447C04 gene	protein-coding
mm_91914.1	chr10	60295068	60295092	-	1	NA	exon (NM_011179, exon 6 of 15)	exon (NM_011179, exon 6 of 15)	10619	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_103440.1	chr11	75937727	75937752	-	1	NA	Intergenic	Intergenic	-11848	NM_001291159	380714	Mm.425697	NM_029548	ENSMUSG00000020847	Rph3al	Gm1753|Noc2	rabphilin 3A-like (without C2 domains)	protein-coding
mm_82285.1	chr9	7604110	7604118	-	1	NA	Intergenic	Intergenic	-24117	NM_013903	30800	Mm.390121	NM_013903	ENSMUSG00000018620	Mmp20	-	matrix metallopeptidase 20 (enamelysin)	protein-coding
mm_122205.1	chr14	31781997	31782023	-	1	NA	intron (NM_001024604, intron 1 of 27)	intron (NM_001024604, intron 1 of 27)	48405	NM_001024604	105522	Mm.37660	NM_001024604	ENSMUSG00000014496	Ankrd28	AI465466|AI604979|E430019N21Rik|mKIAA0379	ankyrin repeat domain 28	protein-coding
mm_121802.1	chr14	20181774	20181790	-	1	NA	promoter-TSS (NM_021542)	promoter-TSS (NM_021542)	0	NM_021542	16529	Mm.68998	NM_021542	ENSMUSG00000023243	Kcnk5	KCNK5b|TASK-2	potassium channel, subfamily K, member 5	protein-coding
mm_54771.1	chr6	41523963	41523982	-	1	NA	exon (NM_009430, exon 3 of 5)	exon (NM_009430, exon 3 of 5)	2196	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_116425.1	chr13	41829080	41829107	-	1	NA	intron (NM_001145875, intron 1 of 6)	intron (NM_001145875, intron 1 of 6)	18395	NM_175417	109254	Mm.25195	NM_175417	ENSMUSG00000058022	Adtrp	9530008L14Rik	androgen dependent TFPI regulating protein	protein-coding
mm_129507.1	chr15	79025865	79025867	-	1	NA	Intergenic	Intergenic	-2346	NM_008197	14958	Mm.24350	NM_008197	ENSMUSG00000096210	H1f0	D130017D06Rik|H1(0)|H1fv	H1 histone family, member 0	protein-coding
mm_55514.1	chr6	70074603	70074621	-	1	NA	Intergenic	Intergenic	717563	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_123176.1	chr14	57598617	57598617	-	1	NA	intron (NM_020506, intron 13 of 22)	intron (NM_020506, intron 13 of 22)	-27048	NM_026526	68043	Mm.45225	NM_026526	ENSMUSG00000021951	Eef1akmt1	2510005D08Rik|AW045965|Ayu21-96|Gt(pU21)96Imeg|GtAyu21-96|N6amt2	eukaryotic translation elongation factor 1 alpha lysine methyltransferase 1	protein-coding
mm_86915.1	chr10	23796947	23797051	+	1	NA	promoter-TSS (NM_183116)	promoter-TSS (NM_183116)	13	NM_183116	76306	Mm.294271	NM_183116	ENSMUSG00000037455	Slc18b1	1110021L09Rik	solute carrier family 18, subfamily B, member 1	protein-coding
mm_57501.1	chr6	125380461	125380502	-	1	NA	promoter-TSS (NM_198604)	promoter-TSS (NM_198604)	23	NM_198604	213522	Mm.333396	NM_198604	ENSMUSG00000038167	Plekhg6	BC026778|Gm155	pleckstrin homology domain containing, family G (with RhoGef domain) member 6	protein-coding
mm_135463.1	chr16	45795385	45795389	-	1	NA	intron (NM_001252442, intron 5 of 18)	intron (NM_001252442, intron 5 of 18)	48991	NM_153412	208177	Mm.211477	NM_153412	ENSMUSG00000033149	Phldb2	AV253284|C820004H04Rik|LL5b|LL5beta	pleckstrin homology like domain, family B, member 2	protein-coding
mm_153770.1	chr19	45660461	45660493	-	1	NA	promoter-TSS (NM_013907)	promoter-TSS (NM_013907)	-284	NM_013907	30838	Mm.254739	NM_013907	ENSMUSG00000040913	Fbxw4	Dac|Fbw4|SHFM3|SHSF3|dactylin|dactylyn	F-box and WD-40 domain protein 4	protein-coding
mm_123732.1	chr14	70175307	70175329	-	1	NA	intron (NM_145978, intron 1 of 9)	intron (NM_145978, intron 1 of 9)	1497	NM_001253736	213019	Mm.283968	NM_145978	ENSMUSG00000022090	Pdlim2	4732462F18Rik|Slim	PDZ and LIM domain 2	protein-coding
mm_151038.1	chr19	47023501	47023513	+	1	NA	exon (NM_146100, exon 3 of 3)	exon (NM_146100, exon 3 of 3)	-8318	NM_001164363	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_156908.1	chrX	169048949	169048965	+	1	NA	intron (NR_109847, intron 1 of 14)	intron (NR_109847, intron 1 of 14)	12346	NR_109847	11856	Mm.441810	NM_009707	ENSMUSG00000031355	Arhgap6	AI504284|RhoGAPX-1	Rho GTPase activating protein 6	protein-coding
mm_117703.1	chr13	95038325	95038332	-	1	NA	intron (NM_001346782, intron 17 of 21)	L1MA4|LINE|L1	61984	NM_172590	218460	Mm.33856	NM_172590	ENSMUSG00000042015	Wdr41	B830029I03Rik|MSTP048	WD repeat domain 41	protein-coding
mm_81744.1	chr9	113919358	113919361	+	1	NA	3' UTR (NM_001114347, exon 40 of 40)	3' UTR (NM_001114347, exon 40 of 40)	-11575	NM_001083319	22221	Mm.28052	NM_013699	ENSMUSG00000009741	Ubp1	Cp2b|LBP-1a|LBP-1b|NF2d9	upstream binding protein 1	protein-coding
mm_17112.1	chr2	24385185	24385226	-	1	NA	promoter-TSS (NM_177611)	promoter-TSS (NM_177611)	-192	NM_177611	215632	Mm.490434	NM_177611	ENSMUSG00000026979	Psd4	BC046518|EFA6B	pleckstrin and Sec7 domain containing 4	protein-coding
mm_138401.1	chr17	35059146	35059156	+	1	NA	TTS (NM_033444)	TTS (NM_033444)	116	NM_016765	51793	Mm.1457	NM_016765	ENSMUSG00000007039	Ddah2	1110003M04Rik|AU019324|AW413173|DDAH-2|DDAHII|Ddah|G6a|NG30	dimethylarginine dimethylaminohydrolase 2	protein-coding
mm_144338.1	chr18	14706146	14706232	+	1	NA	promoter-TSS (NM_001163609)	promoter-TSS (NM_001163609)	38	NM_001163609	73677	Mm.87277	NM_001163609	ENSMUSG00000036743	Psma8	2410072D24Rik	proteasome (prosome, macropain) subunit, alpha type, 8	protein-coding
mm_29433.1	chr3	109361973	109361985	-	1	NA	intron (NM_020505, intron 1 of 26)	intron (NM_020505, intron 1 of 26)	21296	NM_020505	57257	Mm.282257	NM_020505	ENSMUSG00000033721	Vav3	A530094I06Rik|AA986410|Idd18.1	vav 3 oncogene	protein-coding
mm_105004.1	chr11	100376862	100376878	-	1	NA	exon (NM_010593, exon 9 of 14)	exon (NM_010593, exon 9 of 14)	-20729	NM_010404	15114	Mm.281700	NM_010404	ENSMUSG00000006930	Hap1	HAP-1	huntingtin-associated protein 1	protein-coding
mm_135729.1	chr16	55831137	55831166	-	1	NA	intron (NM_030612, intron 2 of 13)	B4|SINE|B4	7490	NM_030612	80859	Mm.247272	NM_030612	ENSMUSG00000035356	Nfkbiz	AA408868|INAP|Mail	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, zeta	protein-coding
mm_93905.1	chr10	126905965	126905980	-	1	NA	Intergenic	CpG	-4601	NM_001159559	68876	Mm.276769	NM_026858	ENSMUSG00000025436	Xrcc6bp1	1110068E08Rik|2410012H02Rik|Atp23	XRCC6 binding protein 1	protein-coding
mm_106.1	chr1	9601136	9601144	+	1	NA	promoter-TSS (NM_178399)	promoter-TSS (NM_178399)	-127	NM_178399	76982	Mm.491098	NM_178399	ENSMUSG00000067879	3110035E14Rik	AI415019|AV164974|R75066	RIKEN cDNA 3110035E14 gene	protein-coding
mm_172588.1	chr8	124211642	124211661	-	1	NA	Intergenic	Intergenic	-19743	NM_139272	108148	Mm.33808	NM_139272	ENSMUSG00000089704	Galnt2	AI480629	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2	protein-coding
mm_100778.1	chr11	4808323	4808329	-	1	NA	intron (NM_001252251, intron 4 of 16)	intron (NM_001252251, intron 4 of 16)	24809	NM_001252253	18016	Mm.297109	NM_010898	ENSMUSG00000009073	Nf2	merlin	neurofibromin 2	protein-coding
mm_50806.1	chr6	54293065	54293075	+	1	NA	exon (NM_001311133, exon 5 of 8)	exon (NM_001311133, exon 5 of 8)	20248	NM_023543	69993	Mm.321147	NM_023543	ENSMUSG00000004633	Chn2	1700026N20Rik|4930557O16Rik|ARHGAP3|Bch	chimerin 2	protein-coding
mm_151345.1	chr19	55895558	55895566	+	1	NA	5' UTR (NM_001142924, exon 1 of 12)	5' UTR (NM_001142924, exon 1 of 12)	241	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_74798.1	chr8	22411289	22411313	-	1	NA	promoter-TSS (NM_020560)	promoter-TSS (NM_020560)	-39	NM_020560	57312	Mm.289402	NM_020560	ENSMUSG00000031533	Mrps31	1500002D03Rik|AA960481|Imogen38|Imogen44	mitochondrial ribosomal protein S31	protein-coding
mm_116600.1	chr13	48554713	48554723	-	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-16446	NR_029725	387244		NR_029725	ENSMUSG00000065421	Mirlet7a-1	Let-7a|Mirnlet7a|Mirnlet7a-1|let-7a-1	microRNA let7a-1	ncRNA
mm_165679.1	chr3	90669954	90669966	-	1	NA	TTS (NM_013650)	TTS (NM_013650)	889	NM_013650	20201	Mm.21567	NM_013650	ENSMUSG00000056054	S100a8	60B8Ag|AI323541|B8Ag|CFAg|CP-10|Caga|MRP8|p8	S100 calcium binding protein A8 (calgranulin A)	protein-coding
mm_161355.1	chr14	55761910	55761910	+	1	NA	5' UTR (NM_020490, exon 2 of 2)	5' UTR (NM_020490, exon 2 of 2)	482	NM_020490	57260	Mm.159670	NM_020490	ENSMUSG00000040432	Ltb4r2	5830462O07Rik|BLT2|LTB4-R 2|LTB4-R-2|LTB4-R2	leukotriene B4 receptor 2	protein-coding
mm_108156.1	chr12	76328930	76328945	+	1	NA	exon (NM_001101471, exon 2 of 2)	exon (NM_001101471, exon 2 of 2)	4046	NM_001101471	238276	Mm.311452	NM_001101471	ENSMUSG00000021057	Akap5	3526401B18Rik|AKAP 150|AKAP-5|AKAP150|BB098886|Gm258|P150	A kinase (PRKA) anchor protein 5	protein-coding
mm_65671.1	chr7	28294575	28294602	-	1	NA	exon (NM_007866, exon 7 of 9)	exon (NM_007866, exon 7 of 9)	-3454	NM_175033	280621	Mm.212777	NM_175033	ENSMUSG00000046750	Selenov	Selv	selenoprotein V	protein-coding
mm_155640.1	chrX	85249675	85249684	+	1	NA	promoter-TSS (NM_028046)	promoter-TSS (NM_028046)	2	NM_028046	71996	Mm.20201	NM_028046	ENSMUSG00000035491	Fthl17a	1600014K23Rik|AI324104	ferritin, heavy polypeptide-like 17, member A	protein-coding
mm_170728.1	chr2	151160753	151160771	+	1	NA	Intergenic	L1Md_A|LINE|L1	62517	NM_001097977	433486	Mm.422661	NM_001097977	ENSMUSG00000079006	Gm14151	OTTMUSG00000015806	predicted gene 14151	protein-coding
mm_157194.1	chrX	12080546	12080561	-	1	NA	promoter-TSS (NM_029510)	promoter-TSS (NM_029510)	0	NM_175045	71458	Mm.196328	NM_029510	ENSMUSG00000040363	Bcor	2900008C10Rik|5830466J11Rik|8430401K06Rik|BcorR|D930024N20Rik|mKIAA1575	BCL6 interacting corepressor	protein-coding
mm_165770.1	chr3	122211145	122211193	-	1	NA	Intergenic	Intergenic	-34388	NM_008129	14630	Mm.292676	NM_008129	ENSMUSG00000028124	Gclm	AI649393|Gcmc|Glclr	glutamate-cysteine ligase, modifier subunit	protein-coding
mm_53809.1	chr6	146932900	146932909	+	1	NA	intron (NM_026221, intron 1 of 26)	intron (NM_026221, intron 1 of 26)	21517	NM_001164236	73344	Mm.391543	NM_028509	ENSMUSG00000040163	1700034J05Rik	-	RIKEN cDNA 1700034J05 gene	protein-coding
mm_145789.1	chr18	65178334	65178336	+	1	NA	intron (NM_001114386, intron 16 of 30)	intron (NM_001114386, intron 16 of 30)	-70526	NR_029600	387231		NR_029600	ENSMUSG00000065402	Mir122	Mir122a|Mirn122a|mir-122|mmu-mir-122	microRNA 122	ncRNA
mm_103396.1	chr11	75436802	75436817	-	1	NA	exon (NM_008878, exon 6 of 10)	exon (NM_008878, exon 6 of 10)	2692	NM_008878	18816	Mm.279733	NM_008878	ENSMUSG00000038224	Serpinf2	AI747498|Pli|Serpimf2	serine (or cysteine) peptidase inhibitor, clade F, member 2	protein-coding
mm_7225.1	chr1	93342735	93342803	-	1	NA	promoter-TSS (NM_080850)	promoter-TSS (NM_080850)	19	NM_080850	269224	Mm.379454	NM_080850	ENSMUSG00000026274	Pask	mKIAA0135	PAS domain containing serine/threonine kinase	protein-coding
mm_67229.1	chr7	74555158	74555180	-	1	NA	promoter-TSS (NM_023908)	promoter-TSS (NM_023908)	-389	NM_001038643	108116	Mm.425467	NM_023908	ENSMUSG00000025790	Slco3a1	5830414C08Rik|Anr1|MJAM|OATP-D|R75096|Slc21a11	solute carrier organic anion transporter family, member 3a1	protein-coding
mm_41593.1	chr5	93270862	93270902	+	1	NA	exon (NM_007635, exon 4 of 8)	exon (NM_007635, exon 4 of 8)	3309	NM_007635	12452	Mm.3527	NM_007635	ENSMUSG00000029385	Ccng2	-	cyclin G2	protein-coding
mm_49349.1	chr6	21986182	21986210	+	1	NA	5' UTR (NM_001081351, exon 1 of 22)	5' UTR (NM_001081351, exon 1 of 22)	286	NM_001081351	214642	Mm.221404	NM_001081351	ENSMUSG00000062980	Cped1	6720481P07|A430107O13Rik|AI552584	cadherin-like and PC-esterase domain containing 1	protein-coding
mm_56138.1	chr6	87731499	87731533	-	1	NA	exon (NM_001159697, exon 1 of 8)	exon (NM_001159697, exon 1 of 8)	647	NM_001159697	58229	Mm.333229	NM_021418	ENSMUSG00000068263	Efcc1	Ccdc48	EF hand and coiled-coil domain containing 1	protein-coding
mm_28802.1	chr3	96219938	96219946	-	1	NA	promoter-TSS (NM_178213)	promoter-TSS (NM_178213)	26	NM_178213	621893		NM_178213	ENSMUSG00000063689	Hist2h2ab	EG621893|H2a-613a	histone cluster 2, H2ab	protein-coding
mm_117906.1	chr13	99430329	99430373	-	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-17525	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_31023.1	chr4	40731277	40731302	+	1	NA	intron (NM_008298, intron 6 of 8)	intron (NM_008298, intron 6 of 8)	8359	NM_001164672	15502	Mm.27897	NM_008298	ENSMUSG00000028410	Dnaja1	HSJ-2|Hsj2|Nedd7	DnaJ heat shock protein family (Hsp40) member A1	protein-coding
mm_96641.1	chr11	69326697	69326716	+	1	NA	TTS (NM_001024206)	TTS (NM_001024206)	448	NM_010599	16499	Mm.232472	NM_010599	ENSMUSG00000018470	Kcnab3	C330022D06Rik|Kcnab4|mKv(beta)4	potassium voltage-gated channel, shaker-related subfamily, beta member 3	protein-coding
mm_100395.1	chr11	119390639	119390663	+	1	NA	TTS (NR_035453)	TTS (NR_035453)	179	NR_035453	100316690		NR_035453	ENSMUSG00000088015	Mir1932	mir-1932|mmu-mir-1932	microRNA 1932	ncRNA
mm_101511.1	chr11	32277764	32277774	-	1	NA	exon (NM_010405, exon 2 of 3)	exon (NM_010405, exon 2 of 3)	1169	NM_010405	15126	Mm.141758	NM_010405	ENSMUSG00000055609	Hba-x	AI450015|Hbz	hemoglobin X, alpha-like embryonic chain in Hba complex	protein-coding
mm_32977.1	chr4	120134409	120134427	+	1	NA	3' UTR (NM_010657, exon 9 of 9)	3' UTR (NM_010657, exon 9 of 9)	-26788	NM_007902	13615	Mm.284855	NM_007902	ENSMUSG00000028635	Edn2	ET-2|PPET2|VIC	endothelin 2	protein-coding
mm_116939.1	chr13	56088565	56088569	-	1	NA	intron (NM_001159514, intron 5 of 8)	intron (NM_001159514, intron 5 of 8)	46983	NM_012015	26914	Mm.283802	NM_012015	ENSMUSG00000015937	H2afy	H2AF12M|mH2a1|macroH2A1	H2A histone family, member Y	protein-coding
mm_107090.1	chr12	17544707	17544722	+	1	NA	promoter-TSS (NM_013614)	promoter-TSS (NM_013614)	-159	NM_013614	18263	Mm.34102	NM_013614	ENSMUSG00000011179	Odc1	ODC	ornithine decarboxylase, structural 1	protein-coding
mm_101862.1	chr11	48871345	48871407	-	1	NA	promoter-TSS (NM_008326)	promoter-TSS (NM_008326)	-30	NM_008326	15944	Mm.29938	NM_008326	ENSMUSG00000046879	Irgm1	Ifggd3|Ifi1|Iigp3|Iipg3|Irgm|LRG-47	immunity-related GTPase family M member 1	protein-coding
mm_159367.1	chr3	88378699	88378699	-	1	NA	promoter-TSS (NM_001032298)	promoter-TSS (NM_001032298)	2	NM_001032298	12097	Mm.425160	NM_001032298	ENSMUSG00000074486	Bglap2	BGP2|Bglap1|Bgp|Og2|mOC-B	bone gamma-carboxyglutamate protein 2	protein-coding
mm_129835.1	chr15	83154262	83154324	-	1	NA	3' UTR (NM_029787, exon 9 of 9)	3' UTR (NM_029787, exon 9 of 9)	4648	NR_004432	104307	Mm.471434	NR_004432	ENSMUSG00000065176	Rnu12	-	RNA U12, small nuclear	snRNA
mm_168547.1	chr11	62820225	62820236	+	1	NA	promoter-TSS (NM_053169)	promoter-TSS (NM_053169)	-23	NM_053169	94092	Mm.117087	NM_053169	ENSMUSG00000047821	Trim16	9130006M08Rik|AI482483|EBBP	tripartite motif-containing 16	protein-coding
mm_101427.1	chr11	29825650	29825680	-	1	NA	promoter-TSS (NM_176829)	promoter-TSS (NM_176829)	3	NM_176829	216622	Mm.443260	NM_176829	ENSMUSG00000078157	4931440F15Rik	Fem1ab	RIKEN cDNA 4931440F15 gene	protein-coding
mm_12979.1	chr2	90783196	90783204	+	1	NA	intron (NM_178755, intron 1 of 17)	CpG	456	NM_178755	271813	Mm.61146	NM_178755	ENSMUSG00000040812	Agbl2	4930524K04|A430081C19Rik|CCP2	ATP/GTP binding protein-like 2	protein-coding
mm_13429.1	chr2	104820800	104820823	+	1	NA	Intergenic	Intergenic	-4115	NM_001123327	99003	Mm.274314	NM_001123327	ENSMUSG00000074994	Qser1	4732486I23Rik|AI502974	glutamine and serine rich 1	protein-coding
mm_44446.1	chr5	21665062	21665084	-	1	NA	3' UTR (NM_178728, exon 5 of 5)	3' UTR (NM_178728, exon 5 of 5)	19089	NM_026034	67211	Mm.260782	NM_026034	ENSMUSG00000038525	Armc10	2810037C14Rik|Svh	armadillo repeat containing 10	protein-coding
mm_26182.1	chr3	138341948	138341961	+	1	NA	Intergenic	RMER15|LTR|ERVL	28668	NM_026945	69117	Mm.46265	NM_026945	ENSMUSG00000053054	Adh6a	1810009C16Rik|Adh5a	alcohol dehydrogenase 6A (class V)	protein-coding
mm_152761.1	chr19	20379674	20379714	-	1	NA	exon (NM_010730, exon 8 of 13)	exon (NM_010730, exon 8 of 13)	10977	NM_010730	16952	Mm.248360	NM_010730	ENSMUSG00000024659	Anxa1	Anx-1|Anx-A1|C430014K04Rik|Lpc-1|Lpc1	annexin A1	protein-coding
mm_101783.1	chr11	45944911	45944960	-	1	NA	promoter-TSS (NM_028185)	promoter-TSS (NM_028185)	0	NM_028185	72290	Mm.249827	NM_028185	ENSMUSG00000044847	Lsm11	2210404M20Rik|AV079530	U7 snRNP-specific Sm-like protein LSM11	protein-coding
mm_6124.1	chr1	64303051	64303065	-	1	NA	Intergenic	Intergenic	-181669	NM_033563	93691	Mm.29466	NM_033563	ENSMUSG00000025959	Klf7	9830124P08Rik	Kruppel-like factor 7 (ubiquitous)	protein-coding
mm_162498.1	chr1	138283547	138283556	+	1	NA	intron (NM_177397, intron 1 of 2)	B1_Mur1|SINE|Alu	9813	NM_177397	338375	Mm.114424	NM_177397	ENSMUSG00000026394	Atp6v1g3	-	ATPase, H+ transporting, lysosomal V1 subunit G3	protein-coding
mm_74554.1	chr8	10892048	10892071	-	1	NA	Intergenic	Intergenic	-7863	NR_102285	71624	Mm.139075	NR_102285	ENSMUSG00000109089	4833411C07Rik	-	RIKEN cDNA 4833411C07 gene	ncRNA
mm_82347.1	chr9	13826912	13826945	-	1	NA	promoter-TSS (NM_176836)	promoter-TSS (NM_176836)	125	NR_037622	74360	Mm.157212	NM_026665	ENSMUSG00000031922	Cep57	3110002L15Rik|4921510P06Rik|4931428M20Rik|AI467480|Tsp57|mKIAA0092	centrosomal protein 57	protein-coding
mm_61492.1	chr7	75730519	75730530	+	1	NA	exon (NM_029332, exon 26 of 37)	exon (NM_029332, exon 26 of 37)	-117814	NM_001122780	207952	Mm.206223	NM_029652	ENSMUSG00000055652	Klhl25	2810402K13Rik|BC027373|Enc-1	kelch-like 25	protein-coding
mm_41164.1	chr5	87956253	87956272	+	1	NA	intron (NR_045924, intron 1 of 4)	intron (NR_045924, intron 1 of 4)	23089	NR_045924	73471	Mm.396240	NR_045924	ENSMUSG00000099605	1700066N21Rik	-	RIKEN cDNA 1700066N21 gene	ncRNA
mm_148154.1	chr18	77565243	77565270	-	1	NA	promoter-TSS (NM_001164504)	promoter-TSS (NM_001164504)	-120	NM_001164504	225743	Mm.23293	NM_001164504	ENSMUSG00000025427	Rnf165	2900024M11Rik|AI427432|Akd2|Ark2c|G630064H08Rik|Gm96	ring finger protein 165	protein-coding
mm_129863.1	chr15	83366972	83366991	-	1	NA	intron (NR_027980, intron 1 of 3)	CpG	316	NR_027980	69291	Mm.66794	NM_001033147		1700001L05Rik	-	RIKEN cDNA 1700001L05 gene	ncRNA
mm_41564.1	chr5	93133594	93133608	+	1	NA	intron (NM_001347377, intron 1 of 10)	intron (NM_001347377, intron 1 of 10)	40185	NM_001347377	52398	Mm.394184	NM_001009818	ENSMUSG00000058013	Sept11	6230410I01Rik|AW548875|D5Ertd606e	septin 11	protein-coding
mm_158168.1	chrX	103616784	103616818	-	1	NA	intron (NR_028380, intron 1 of 10)	intron (NR_028380, intron 1 of 10)	6953	NR_028381	78878	Mm.259724	NR_028380	ENSMUSG00000086370	Ftx	B230206F22Rik|BB219131|NCRNA00182|Thcytx	Ftx transcript, Xist regulator (non-protein coding)	ncRNA
mm_5441.1	chr1	34843058	34843065	-	1	NA	promoter-TSS (NM_001160236)	promoter-TSS (NM_001160236)	-11	NM_174997	214469	Mm.120151	NM_174997	ENSMUSG00000037503	Fam168b	mKIAA4042	family with sequence similarity 168, member B	protein-coding
mm_98976.1	chr11	98700166	98700206	+	1	NA	Intergenic	Intergenic	-1127	NM_009971	12985	Mm.1238	NM_009971	ENSMUSG00000038067	Csf3	Csfg|G-CSF|MGI-IG	colony stimulating factor 3 (granulocyte)	protein-coding
mm_86841.1	chr10	21400461	21400468	+	1	NA	Intergenic	Intergenic	23164	NM_178713	237320	Mm.90181	NM_178713	ENSMUSG00000037542	Aldh8a1	Raldh4	aldehyde dehydrogenase 8 family, member A1	protein-coding
mm_130245.1	chr15	96640121	96640124	-	1	NA	intron (NM_001166458, intron 1 of 15)	intron (NM_001166458, intron 1 of 15)	1840	NM_134086	105727	Mm.103568	NM_134086	ENSMUSG00000023169	Slc38a1	AA408026|AA409865|AL022800|AU015942|NAT2	solute carrier family 38, member 1	protein-coding
mm_9143.1	chr1	170885143	170885198	-	1	NA	exon (NM_023173, exon 1 of 6)	exon (NM_023173, exon 1 of 6)	370	NM_023173	80915	Mm.34365	NM_023173	ENSMUSG00000026659	Dusp12	1190004O14Rik|AA027408|AW049275|ENSMUSG00000045460|ESTM36|LMW-DSP4|T-DSP4|VH1|mVH1	dual specificity phosphatase 12	protein-coding
mm_51049.1	chr6	65627159	65627172	+	1	NA	intron (NM_001001495, intron 7 of 7)	intron (NM_001001495, intron 7 of 7)	36767	NM_001001495	414084	Mm.117558	NM_001001495	ENSMUSG00000044162	Tnip3	9030611K07Rik|ABIN-3|LIND	TNFAIP3 interacting protein 3	protein-coding
mm_104263.1	chr11	88955367	88955447	-	1	NA	promoter-TSS (NM_029023)	promoter-TSS (NM_029023)	35	NM_029023	74617	Mm.34126	NM_029023	ENSMUSG00000000278	Scpep1	2410018F01Rik|4833411K15Rik|AI957256|Risc	serine carboxypeptidase 1	protein-coding
mm_55685.1	chr6	72627008	72627024	-	1	NA	3' UTR (NM_009332, exon 12 of 12)	3' UTR (NM_009332, exon 12 of 12)	-2272	NR_040422	100038714	Mm.321330	NR_040421		Gm15401	ENSMUSG00000072999|OTTMUSG00000021199	predicted gene 15401	ncRNA
mm_141899.1	chr17	34895984	34895996	-	1	NA	exon (NM_198886, exon 2 of 2)	exon (NM_198886, exon 2 of 2)	1431	NM_198886	193736	Mm.161119	NM_198886	ENSMUSG00000049823	Zbtb12	BC020447|Bat-9|Bat9|G10|NG35	zinc finger and BTB domain containing 12	protein-coding
mm_144774.1	chr18	35829731	35829756	+	1	NA	promoter-TSS (NM_133687)	promoter-TSS (NM_133687)	-75	NM_133687	67393	Mm.94560	NM_133687	ENSMUSG00000046668	Cxxc5	4930415K17Rik	CXXC finger 5	protein-coding
mm_77815.1	chr9	3199931	3199939	+	1	NA	promoter-TSS (NR_027988)	promoter-TSS (NR_027988)	-122	NR_027988	114673	Mm.422774	NM_053265	ENSMUSG00000042360	4930433N12Rik	-	RIKEN cDNA 4930433N12 gene	ncRNA
mm_19624.1	chr2	102813450	102813469	-	1	NA	3' UTR (NM_009851, exon 19 of 19)	3' UTR (NM_009851, exon 19 of 19)	88206	NM_001177785	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_103903.1	chr11	83577138	83577147	-	1	NA	intron (NM_011338, intron 1 of 3)	intron (NM_011338, intron 1 of 3)	1494	NM_011338	20308	Mm.416125	NM_011338	ENSMUSG00000019122	Ccl9	CCF18|MRP-2|Scya10|Scya9	chemokine (C-C motif) ligand 9	protein-coding
mm_86910.1	chr10	22814968	22814987	+	1	NA	Intergenic	Intergenic	5151	NM_011545	21412	Mm.16497	NM_011545	ENSMUSG00000045680	Tcf21	Pod-1|Pod1|bHLHa23|capsulin|epc|epicardin	transcription factor 21	protein-coding
mm_150298.1	chr19	34550881	34550947	+	1	NA	5' UTR (NM_008332, exon 1 of 3)	5' UTR (NM_008332, exon 1 of 3)	220	NM_008332	15958	Mm.2036	NM_008332	ENSMUSG00000045932	Ifit2	AV302338|Ifi54|P54	interferon-induced protein with tetratricopeptide repeats 2	protein-coding
mm_100097.1	chr11	115613486	115613500	+	1	NA	promoter-TSS (NM_027162)	promoter-TSS (NM_027162)	-524	NM_001243587	69674	Mm.390387	NM_027162	ENSMUSG00000020743	Mif4gd	1110014L05Rik|2310075G12Rik	MIF4G domain containing	protein-coding
mm_56550.1	chr6	100286324	100286327	-	1	NA	intron (NM_019743, intron 2 of 4)	intron (NM_019743, intron 2 of 4)	1033	NM_019743	56353	Mm.321633	NM_019743	ENSMUSG00000072872	Rybp	2410018J24Rik|DEDAF|YEAF1	RING1 and YY1 binding protein	protein-coding
mm_163584.1	chr13	35961389	35961393	+	1	NA	Intergenic	RLTR22_Mur|LTR|ERVK	-6515	NM_029628	76487	Mm.44745	NM_029628	ENSMUSG00000050423	Ppp1r3g	1600032L17Rik	protein phosphatase 1, regulatory (inhibitor) subunit 3G	protein-coding
mm_162182.1	chrX	102866191	102866191	-	1	NA	intron (NM_028496, intron 1 of 6)	intron (NM_028496, intron 1 of 6)	162	NM_028496	73300	Mm.158984	NM_028496	ENSMUSG00000032894	1700031F05Rik	-	RIKEN cDNA 1700031F05 gene	protein-coding
mm_42785.1	chr5	121463151	121463189	+	1	NA	promoter-TSS (NM_001161627)	promoter-TSS (NM_001161627)	-11	NM_001161626	77462	Mm.358781	NM_029912	ENSMUSG00000029452	Tmem116	4930406A18Rik|4930513P12Rik|C030022K24Rik	transmembrane protein 116	protein-coding
mm_39728.1	chr5	28354849	28354853	+	1	NA	intron (NM_028234, intron 7 of 18)	(T)n|Simple_repeat|Simple_repeat	37662	NM_028234	381626	Mm.304075	NM_028234	ENSMUSG00000048271	Rbm33	3200001K10Rik|6430512A10Rik|AA386890|Prr8	RNA binding motif protein 33	protein-coding
mm_158209.1	chrX	105867908	105867925	-	1	NA	exon (NM_009530, exon 10 of 35)	exon (NM_009530, exon 10 of 35)	61456	NM_009530	22589	Mm.10141	NM_009530	ENSMUSG00000031229	Atrx	4833408C14Rik|AI447451|ATR2|DXHXS6677E|HP1-BP38|Hp1bp2|Hp1bp38|MRXS3|RAD54L|Rad54|XH2|Xnp|ZNF-HX	alpha thalassemia/mental retardation syndrome X-linked	protein-coding
mm_47975.1	chr5	135910682	135910692	-	1	NA	3' UTR (NM_018871, exon 2 of 2)	3' UTR (NM_018871, exon 2 of 2)	22768	NM_013560	15507	Mm.13849	NM_013560	ENSMUSG00000004951	Hspb1	27kDa|Hsp25	heat shock protein 1	protein-coding
mm_22500.1	chr3	7366674	7366694	+	1	NA	promoter-TSS (NM_008862)	promoter-TSS (NM_008862)	80	NM_008862	18767	Mm.3193	NM_008862	ENSMUSG00000027499	Pkia	AI415001|PKIalpha	protein kinase inhibitor, alpha	protein-coding
mm_130521.1	chr15	98881221	98881240	-	1	NA	5' UTR (NM_026967, exon 1 of 8)	5' UTR (NM_026967, exon 1 of 8)	184	NM_026967	69159	Mm.259708	NM_026967	ENSMUSG00000023755	Rhebl1	1810036J22Rik|Rheb2	Ras homolog enriched in brain like 1	protein-coding
mm_98015.1	chr11	84879881	84879922	+	1	NA	promoter-TSS (NM_025414)	promoter-TSS (NM_025414)	294	NM_027388	70325	Mm.390414	NM_027388	ENSMUSG00000045140	Pigw	2610044A17Rik|Gwt1	phosphatidylinositol glycan anchor biosynthesis, class W	protein-coding
mm_26808.1	chr3	10197217	10197228	-	1	NA	promoter-TSS (NM_011598)	promoter-TSS (NM_011598)	61	NM_011598	21884	Mm.26654	NM_011598	ENSMUSG00000027528	Fabp9	1700007P10Rik|Perf|Perf15|Tlbp	fatty acid binding protein 9, testis	protein-coding
mm_32541.1	chr4	109280317	109280326	+	1	NA	promoter-TSS (NM_007943)	promoter-TSS (NM_007943)	46	NM_007943	13858	Mm.318250	NM_007943	ENSMUSG00000028552	Eps15	2410112D09Rik	epidermal growth factor receptor pathway substrate 15	protein-coding
mm_1827.1	chr1	82604074	82604093	+	1	NA	intron (NM_007734, intron 1 of 51)	intron (NM_007734, intron 1 of 51)	17162	NM_007734	12828	Mm.389135	NM_007734	ENSMUSG00000079465	Col4a3	[a]3(IV)|alpha3(IV)	collagen, type IV, alpha 3	protein-coding
mm_78435.1	chr9	32032379	32032426	+	1	NA	Intergenic	CpG	-83734	NM_001195632	330914	Mm.46683	NM_177379	ENSMUSG00000041444	Arhgap32	3426406O18Rik|Gc-gap|Grit|Px-rics|Rics|mKIAA0712|p200Rhogap|p250Gap	Rho GTPase activating protein 32	protein-coding
mm_149794.1	chr19	23141677	23141701	+	1	NA	5' UTR (NM_010638, exon 1 of 2)	5' UTR (NM_010638, exon 1 of 2)	463	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_161437.1	chr15	63847316	63847316	+	1	NA	promoter-TSS (NR_108051)	promoter-TSS (NR_108051)	7	NR_108051	74236	Mm.443274	NM_001167581	ENSMUSG00000062543	Gsdmcl1	1700022L20Rik|Gsdmdc2	gasdermin C-like 1	pseudo
mm_23755.1	chr3	69963153	69963160	+	1	NA	Intergenic	L1_Mus2|LINE|L1	-44457	NM_001018031	229389	Mm.331071	NM_001018031	ENSMUSG00000027788	Otol1	Gm414	otolin 1	protein-coding
mm_48321.1	chr5	138993094	138993113	-	1	NA	intron (NM_008808, intron 2 of 5)	CpG	1850	NM_008808	18590	Mm.2675	NM_008808	ENSMUSG00000025856	Pdgfa	-	platelet derived growth factor, alpha	protein-coding
mm_22174.1	chr2	173211795	173211809	-	1	NA	intron (NM_021394, intron 4 of 7)	intron (NM_021394, intron 4 of 7)	7120	NM_021394	58203	Mm.116687	NM_021394	ENSMUSG00000027514	Zbp1	2010010H03Rik|Dai|Dlm1|mZaDLM	Z-DNA binding protein 1	protein-coding
mm_57064.1	chr6	122570750	122570757	-	1	NA	Intergenic	Intergenic	16944	NM_009645	11628	Mm.391503	NM_009645	ENSMUSG00000040627	Aicda	Aid|Arp2	activation-induced cytidine deaminase	protein-coding
mm_10077.1	chr1	195131445	195131453	-	1	NA	5' UTR (NM_013499, exon 1 of 10)	5' UTR (NM_013499, exon 1 of 10)	121	NM_013499	12946	Mm.301652	NM_013499	ENSMUSG00000016481	Cr1l	Crry|Mcp|mCRY	complement component (3b/4b) receptor 1-like	protein-coding
mm_52111.1	chr6	97894037	97894064	+	1	NA	intron (NM_001113198, intron 1 of 9)	RLTR20A4|LTR|ERVK	-35767	NM_001178049	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_38786.1	chr4	148088037	148088056	-	1	NA	promoter-TSS (NM_001301281)	promoter-TSS (NM_001301281)	18	NM_009642	11610	Mm.46247	NM_009642	ENSMUSG00000029007	Agtrap	3300002E14Rik|AT1R|Atrap|D4Wsu124e	angiotensin II, type I receptor-associated protein	protein-coding
mm_15634.1	chr2	162991588	162991598	+	1	NA	5' UTR (NM_001291152, exon 1 of 13)	5' UTR (NM_001291152, exon 1 of 13)	178	NM_001291152	27219	Mm.26462	NM_013731	ENSMUSG00000017868	Sgk2	AI098171|AW146006|Sgkl	serum/glucocorticoid regulated kinase 2	protein-coding
mm_111495.1	chr12	99194717	99194720	-	1	NA	TTS (NM_183186)	TTS (NM_183186)	-31910	NR_038130	67639	Mm.87374	NR_038130		4930474N09Rik	-	RIKEN cDNA 4930474N09 gene	ncRNA
mm_53043.1	chr6	124701514	124701527	+	1	NA	exon (NM_145130, exon 7 of 13)	exon (NM_145130, exon 7 of 13)	10658	NM_013536	14791	Mm.6390	NM_013536	ENSMUSG00000004268	Emg1	C2f|Grcc2f	EMG1 N1-specific pseudouridine methyltransferase	protein-coding
mm_103060.1	chr11	69837162	69837210	-	1	NA	Intergenic	CpG	-1339	NM_026982	69186	Mm.248772	NM_026982	ENSMUSG00000070394	Tmem256	1810027O10Rik|3110009M16Rik	transmembrane protein 256	protein-coding
mm_83233.1	chr9	42398702	42398710	-	1	NA	intron (NM_009347, intron 1 of 23)	intron (NM_009347, intron 1 of 23)	1223	NM_009347	21683	Mm.42209	NM_009347	ENSMUSG00000037705	Tecta	Tctna	tectorin alpha	protein-coding
mm_57782.1	chr6	129268018	129268033	-	1	NA	3' UTR (NM_001033122, exon 5 of 5)	3' UTR (NM_001033122, exon 5 of 5)	7344	NM_001033122	12515	Mm.74745	NM_001033122	ENSMUSG00000030156	Cd69	5830438K24Rik|AI452015|AIM|VEA	CD69 antigen	protein-coding
mm_27420.1	chr3	51517854	51517864	-	1	NA	3' UTR (NM_080793, exon 8 of 8)	3' UTR (NM_080793, exon 8 of 8)	33893	NM_016858	19338	Mm.1664	NM_016858	ENSMUSG00000027739	Rab33b	-	RAB33B, member RAS oncogene family	protein-coding
mm_132242.1	chr16	32750946	32751029	+	1	NA	exon (NM_080457, exon 2 of 27)	exon (NM_080457, exon 2 of 27)	15101	NM_080457	140474	Mm.214599	NM_080457	ENSMUSG00000079620	Muc4	4933405I11Rik|Asgp	mucin 4	protein-coding
mm_46306.1	chr5	100562837	100562858	-	1	NA	intron (NM_139198, intron 1 of 4)	intron (NM_139198, intron 1 of 4)	9358	NM_139198	231507	Mm.34609	NM_139198	ENSMUSG00000029322	Plac8	C15|D5Wsu111e	placenta-specific 8	protein-coding
mm_169715.1	chr15	77436536	77436543	-	1	NA	intron (NM_001024848, intron 1 of 4)	MT2_Mm|LTR|ERVL	10921	NM_001024848	278679	Mm.440965	NM_001024848	ENSMUSG00000068252	Apol7b	-	apolipoprotein L 7b	protein-coding
mm_77223.1	chr8	115703108	115703133	-	1	NA	TTS (NM_001025577)	TTS (NM_001025577)	3774	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_160042.1	chr6	138582038	138582038	-	1	NA	promoter-TSS (NM_207222)	promoter-TSS (NM_207222)	-70	NM_207222	109593	Mm.490545	NM_207222	ENSMUSG00000030226	Lmo3	AI854781|BB106490|Rbtn-3|Rbtn3	LIM domain only 3	protein-coding
mm_170201.1	chr17	6941928	6941928	+	1	NA	intron (NM_001083945, intron 1 of 7)	LSU-rRNA_Hsa|rRNA|rRNA	6428	NM_001083945	100037282	Mm.29830	NM_001083945	ENSMUSG00000023806	Rsph3b	Rshl2b	radial spoke 3B homolog (Chlamydomonas)	protein-coding
mm_113813.1	chr13	46669446	46669501	+	1	NA	promoter-TSS (NM_001033192)	promoter-TSS (NM_001033192)	-49	NM_001033192	97863	Mm.275934	NM_001033192	ENSMUSG00000069237	Fam8a1	C78339	family with sequence similarity 8, member A1	protein-coding
mm_51127.1	chr6	68282320	68282328	+	1	NA	Intergenic	L1_Mur2|LINE|L1	-716625	NR_003100	75070	Mm.463364	NR_003100		4930515G16Rik	-	myc induced nuclear antigen pseudogene	pseudo
mm_86553.1	chr10	10748966	10748974	+	1	NA	intron (NM_016976, intron 4 of 8)	intron (NM_016976, intron 4 of 8)	-2076	NR_046010	78056	Mm.271285	NR_046010		4930567K20Rik	1700038H22Rik	RIKEN cDNA 4930567K20 gene	ncRNA
mm_156990.1	chrX	7421040	7421085	-	1	NA	promoter-TSS (NR_027925)	promoter-TSS (NR_027925)	-15	NR_027925	68355	Mm.45111	NR_027924		2010204K13Rik	0610010M13Rik|Cip7	RIKEN cDNA 2010204K13 gene	ncRNA
mm_123367.1	chr14	63164968	63164980	-	1	NA	intron (NM_010191, intron 3 of 9)	intron (NM_010191, intron 3 of 9)	14604	NM_010191	14137	Mm.474432	NM_010191	ENSMUSG00000021273	Fdft1	SQS|SS	farnesyl diphosphate farnesyl transferase 1	protein-coding
mm_132618.1	chr16	38742281	38742307	+	1	NA	promoter-TSS (NM_019804)	promoter-TSS (NM_019804)	35	NM_001285793	56375	Mm.182377	NM_019804	ENSMUSG00000022793	B4galt4	9130402O08Rik|B4galt-IV|b4Gal-T4|beta4Gal-T4|beta4GalT-IV	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 4	protein-coding
mm_104965.1	chr11	100145967	100145978	-	1	NA	promoter-TSS (NM_008471)	promoter-TSS (NM_008471)	-46	NM_008471	16669	Mm.439699	NM_008471	ENSMUSG00000020911	Krt19	AI663979|CK-19|EndoC|K19|Krt-1.19|Krt1-19	keratin 19	protein-coding
mm_69929.1	chr7	142025953	142025967	-	1	NA	intron (NM_028308, intron 1 of 4)	intron (NM_028308, intron 1 of 4)	33781	NR_037291	100526509		NR_037291	ENSMUSG00000092652	Mir3104	mir-3104|mmu-mir-3104	microRNA 3104	ncRNA
mm_136580.1	chr17	3557848	3557877	+	1	NA	promoter-TSS (NR_045303)	promoter-TSS (NR_045303)	38	NR_045302	68230	Mm.431352	NR_045302		1700102H20Rik	-	RIKEN cDNA 1700102H20 gene	ncRNA
mm_121227.1	chr14	103055618	103055626	+	1	NA	3' UTR (NM_008392, exon 5 of 5)	3' UTR (NM_008392, exon 5 of 5)	8610	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_129212.1	chr15	76522370	76522379	-	1	NA	promoter-TSS (NM_130893)	promoter-TSS (NM_130893)	-245	NM_130893	170729	Mm.218747	NM_130893	ENSMUSG00000048385	Scrt1	-	scratch family zinc finger 1	protein-coding
mm_37365.1	chr4	120815704	120815761	-	1	NA	intron (NM_001048168, intron 1 of 9)	intron (NM_001048168, intron 1 of 9)	10009	NM_001277095	18046	Mm.435590	NM_008692	ENSMUSG00000032897	Nfyc	-	nuclear transcription factor-Y gamma	protein-coding
mm_111343.1	chr12	86884809	86884842	-	1	NA	promoter-TSS (NM_145836)	promoter-TSS (NM_145836)	-11	NM_145836	238330	Mm.248358	NM_145836	ENSMUSG00000034168	Irf2bpl	6430527G18Rik|Eap1	interferon regulatory factor 2 binding protein-like	protein-coding
mm_165202.1	chr2	32966983	32966994	+	1	NA	Intergenic	CpG	3687	NR_002898	104367	Mm.250030	NR_002898	ENSMUSG00000065124	Snora65	MBII-351|Rnu65	small nucleolar RNA, H/ACA box 65	snoRNA
mm_144990.1	chr18	38296641	38296719	+	1	NA	promoter-TSS (NM_020012)	promoter-TSS (NM_020012)	45	NM_001164622	56736	Mm.228903	NM_020012	ENSMUSG00000060450	Rnf14	2310075C09Rik|2610005D23Rik|AA986456|AU041447|D18Ertd188e|D7Bwg0165e|Triad2	ring finger protein 14	protein-coding
mm_93971.1	chr10	127302808	127302812	-	1	NA	intron (NM_001003913, intron 11 of 20)	intron (NM_001003913, intron 11 of 20)	8976	NM_001003913	216443	Mm.28173	NM_001003913	ENSMUSG00000040354	Mars	Metrs|Mtrns	methionine-tRNA synthetase	protein-coding
mm_159140.1	chr2	85721261	85721261	+	1	NA	promoter-TSS (NM_146572)	promoter-TSS (NM_146572)	-146	NM_146572	258565	Mm.377570	NM_146572	ENSMUSG00000043226	Olfr1009	MOR175-3	olfactory receptor 1009	protein-coding
mm_95875.1	chr11	58059322	58059337	+	1	NA	3' UTR (NM_028451, exon 19 of 19)	3' UTR (NM_028451, exon 19 of 19)	-44824	NM_026949	69125	Mm.28910	NM_026949	ENSMUSG00000020515	Cnot8	1500015I04Rik|1810022F04Rik|AA536816|AU015770|AU043059	CCR4-NOT transcription complex, subunit 8	protein-coding
mm_142499.1	chr17	46031814	46031863	-	1	NA	exon (NM_001025250, exon 1 of 8)	exon (NM_001025250, exon 1 of 8)	539	NM_001287058	22339	Mm.282184	NM_009505	ENSMUSG00000023951	Vegfa	Vegf|Vpf	vascular endothelial growth factor A	protein-coding
mm_125948.1	chr15	76248800	76248812	+	1	NA	TTS (NR_105918)	TTS (NR_105918)	615	NR_105918	102465575		NR_105918	ENSMUSG00000098625	Mir6953	Gm27738|mmu-mir-6953	microRNA 6953	ncRNA
mm_6490.1	chr1	74124516	74124572	-	1	NA	promoter-TSS (NM_001289895)	promoter-TSS (NM_001289895)	-95	NM_001289895	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_167497.1	chr9	13296622	13296670	+	1	NA	Intergenic	Intergenic	49690	NM_025534	66396	Mm.290620	NM_025534	ENSMUSG00000079084	Ccdc82	2310043N13Rik	coiled-coil domain containing 82	protein-coding
mm_69156.1	chr7	127144585	127144591	-	1	NA	Intergenic	Intergenic	-6765	NM_001037810	20737	Mm.283714	NM_009259	ENSMUSG00000051457	Spn	A630014B01Rik|Cd43|Galgp|Ly-48|Ly48	sialophorin	protein-coding
mm_368.1	chr1	33974652	33974671	+	1	NA	intron (NM_001276764, intron 3 of 102)	MER57C2|LTR|ERV1	-37164	NM_133833	13518	Mm.336625	NM_010081	ENSMUSG00000026131	Dst	2310001O04Rik|A830042E19Rik|AW554249|BP230|BPAG1-n|Bpag|Bpag1|Macf2|ah|athetoid|dt|mKIAA0728|nmf203|nmf339	dystonin	protein-coding
mm_82972.1	chr9	35844066	35844088	-	1	NA	promoter-TSS (NM_029863)	promoter-TSS (NM_029863)	73	NM_029863	77080	Mm.159846	NM_029863	ENSMUSG00000047980	9230110F15Rik	Pate-A|Pate5|mANLP3	RIKEN cDNA 9230110F15 gene	protein-coding
mm_30160.1	chr3	143936642	143936642	-	1	NA	Intergenic	Intergenic	-224499	NR_040405	621809	Mm.360134	NR_040405	ENSMUSG00000105279	Gm6260	EG621809	predicted gene 6260	ncRNA
mm_114407.1	chr13	64183862	64183870	+	1	NA	intron (NM_019986, intron 6 of 7)	intron (NM_019986, intron 6 of 7)	22000	NM_019986	56541	Mm.40989	NM_019986	ENSMUSG00000021476	Habp4	4933413D03Rik|4933428J01Rik	hyaluronic acid binding protein 4	protein-coding
mm_154554.1	chrM	15369	15379	-	1	NA	NA	Intergenic	NA	NA								
mm_104436.1	chr11	94951685	94951707	-	1	NA	3' UTR (NM_007742, exon 51 of 51)	3' UTR (NM_007742, exon 51 of 51)	15472	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_23760.1	chr3	72868620	72868626	+	1	NA	Intergenic	RLTR13D6|LTR|ERVK	98243	NM_001081137	69983	Mm.261054	NM_001081137	ENSMUSG00000027790	Sis	2010204N08Rik|SI|Si-s	sucrase isomaltase (alpha-glucosidase)	protein-coding
mm_163032.1	chr11	52224621	52224641	+	1	NA	Intergenic	RLTR26C_MM|LTR|ERVK	-7364	NM_011543	21402	Mm.42944	NM_011543	ENSMUSG00000036309	Skp1a	15kDa|2610043E24Rik|2610206H23Rik|EMC19|OCP-II|OCP2|SKP1|Tceb1l|p19A|p19Skp1	S-phase kinase-associated protein 1A	protein-coding
mm_162956.1	chr11	4236878	4236882	+	1	NA	promoter-TSS (NM_001013365)	promoter-TSS (NM_001013365)	95	NM_001013365	18413	Mm.131422	NM_001013365	ENSMUSG00000058755	Osm	OncoM	oncostatin M	protein-coding
mm_34371.1	chr4	144893306	144893320	+	1	NA	5' UTR (NM_011303, exon 1 of 6)	5' UTR (NM_011303, exon 1 of 6)	176	NM_011303	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding
mm_66611.1	chr7	45466513	45466542	-	1	NA	intron (NM_007527, intron 1 of 5)	intron (NM_007527, intron 1 of 5)	371	NM_007527	12028	Mm.19904	NM_007527	ENSMUSG00000003873	Bax	-	BCL2-associated X protein	protein-coding
mm_18807.1	chr2	73911312	73911316	-	1	NA	promoter-TSS (NM_175015)	promoter-TSS (NM_175015)	12	NM_175015	228033	Mm.2966	NM_175015	ENSMUSG00000018770	Atp5g3	6030447M23	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit C3 (subunit 9)	protein-coding
mm_112566.1	chr13	13529544	13529551	+	1	NA	Intergenic	Intergenic	-60862	NM_010748	17101	Mm.342337	NM_010748	ENSMUSG00000019726	Lyst	D13Sfk13|beige|bg	lysosomal trafficking regulator	protein-coding
mm_22467.1	chr3	3657182	3657184	+	1	NA	3' UTR (NM_013920, exon 10 of 10)	3' UTR (NM_013920, exon 10 of 10)	149153	NM_013920	30942	Mm.330897	NM_013920	ENSMUSG00000017688	Hnf4g	NR2A2	hepatocyte nuclear factor 4, gamma	protein-coding
mm_13551.1	chr2	112239816	112239860	+	1	NA	promoter-TSS (NM_207206)	promoter-TSS (NM_207206)	-3	NM_207206	99010	Mm.33438	NM_207206	ENSMUSG00000027134	Lpcat4	AI505034|Agpat7|Aytl3|LPEAT2	lysophosphatidylcholine acyltransferase 4	protein-coding
mm_118288.1	chr13	112927464	112927470	-	1	NA	promoter-TSS (NM_172594)	promoter-TSS (NM_172594)	-87	NM_028151	72198	Mm.291029	NM_028151	ENSMUSG00000016018	Skiv2l2	2610528A15Rik|mKIAA0052	superkiller viralicidic activity 2-like 2 (S. cerevisiae)	protein-coding
mm_31855.1	chr4	76995708	76995709	+	1	NA	intron (NM_011211, intron 7 of 39)	intron (NM_011211, intron 7 of 39)	1216187	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding
mm_45559.1	chr5	73191837	73191847	-	1	NA	intron (NM_028194, intron 3 of 62)	intron (NM_028194, intron 3 of 62)	64776	NM_028194	72313	Mm.260594	NM_028194	ENSMUSG00000070733	Fryl	2010313D22Rik|2310004H21Rik|2510002A14Rik|9030227G01Rik|mKIAA0826	FRY like transcription coactivator	protein-coding
mm_126432.1	chr15	80578368	80578391	+	1	NA	intron (NM_001289442, intron 1 of 7)	B4A|SINE|B4	5782	NM_001289442	17444	Mm.12947	NM_010815	ENSMUSG00000042351	Grap2	GRAP-2|GRB2L|GRBLG|GRID|Gads|GrbX|Grf40|GrpL|Mona|P38	GRB2-related adaptor protein 2	protein-coding
mm_156476.1	chrX	143685078	143685085	+	1	NA	intron (NM_001195049, intron 4 of 17)	intron (NM_001195049, intron 4 of 17)	-8206	NM_001195047	18481	Mm.40035	NM_008778	ENSMUSG00000031284	Pak3	PAK-3|Pak65alpha|Pak65beta|Stk4	p21 protein (Cdc42/Rac)-activated kinase 3	protein-coding
mm_35968.1	chr4	53144254	53144264	-	1	NA	intron (NM_013454, intron 1 of 49)	intron (NM_013454, intron 1 of 49)	15636	NM_013454	11303	Mm.277376	NM_013454	ENSMUSG00000015243	Abca1	ABC-1|Abc1	ATP-binding cassette, sub-family A (ABC1), member 1	protein-coding
mm_106417.1	chr11	119170971	119171013	-	1	NA	intron (NM_001347625, intron 3 of 11)	B4A|SINE|B4	-16855	NR_105899	102465563		NR_105899	ENSMUSG00000098704	Mir6934	Gm27523|mmu-mir-6934	microRNA 6934	ncRNA
mm_91964.1	chr10	61273410	61273453	-	1	NA	promoter-TSS (NM_001081127)	promoter-TSS (NM_001081127)	7	NM_001081127	237360	Mm.333252	NM_001081127	ENSMUSG00000059901	Adamts14	Adamts-14|TS14	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 14	protein-coding
mm_29428.1	chr3	109022075	109022088	-	1	NA	intron (NM_001163567, intron 1 of 10)	intron (NM_001163567, intron 1 of 10)	5526	NM_001163567	329739	Mm.69013	NM_001163567	ENSMUSG00000040339	Fam102b	1600010D10Rik|B430201A12Rik	family with sequence similarity 102, member B	protein-coding
mm_118555.1	chr14	17784649	17784674	+	1	NA	intron (NM_001113417, intron 1 of 9)	intron (NM_001113417, intron 1 of 9)	123701	NM_001113417	21834	Mm.32563	NM_009380	ENSMUSG00000021779	Thrb	Nr1a2|T3R[b]|T3Rbeta|Thrb1|Thrb2|c-erbAbeta	thyroid hormone receptor beta	protein-coding
mm_31576.1	chr4	57674606	57674616	+	1	NA	intron (NM_001304544, intron 3 of 8)	intron (NM_001304544, intron 3 of 8)	106363	NM_172868	242481	Mm.331630	NM_172868	ENSMUSG00000090053	Palm2	53-H12|B130066I24|R75368|pEN70	paralemmin 2	protein-coding
mm_12640.1	chr2	74711912	74711939	+	1	NA	promoter-TSS (NM_010468)	promoter-TSS (NM_010468)	-68	NM_010468	15434	Mm.430708	NM_010468	ENSMUSG00000079277	Hoxd3	Hox-4.1|Hox-5.5	homeobox D3	protein-coding
mm_50526.1	chr6	49045349	49045357	+	1	NA	exon (NM_053110, exon 4 of 11)	exon (NM_053110, exon 4 of 11)	8835	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_138531.1	chr17	35243094	35243150	+	1	NA	promoter-TSS (NR_105941)	promoter-TSS (NR_105941)	305	NM_001252457	53817	Mm.439827	NM_019693	ENSMUSG00000019432	Ddx39b	0610030D10Rik|AI428441|Bat-1|Bat1|Bat1a|D17H6S81E|D17H6S81E-1|D6S81Eh	DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B	protein-coding
mm_68699.1	chr7	119627766	119627774	-	1	NA	intron (NM_054094, intron 2 of 13)	Lx|LINE|L1	9942	NM_054094	117147	Mm.427560	NM_054094	ENSMUSG00000033533	Acsm1	Acas3|Bucs1|Macs	acyl-CoA synthetase medium-chain family member 1	protein-coding
mm_50444.1	chr6	48874795	48874809	+	1	NA	Intergenic	Intergenic	-20453	NM_029638	76507	Mm.213898	NM_029638	ENSMUSG00000029811	Aoc1	1600012D06Rik|Abp1|DAO	amine oxidase, copper-containing 1	protein-coding
mm_101660.1	chr11	36677868	36677894	-	1	NA	intron (NM_011856, intron 2 of 28)	intron (NM_011856, intron 2 of 28)	266360	NM_001290702	23964	Mm.439889	NM_011856	ENSMUSG00000049336	Tenm2	Odz2|Odz3|Ten-2|Ten-m2	teneurin transmembrane protein 2	protein-coding
mm_23262.1	chr3	51418392	51418394	+	1	NA	intron (NM_053089, intron 1 of 19)	intron (NM_053089, intron 1 of 19)	2377	NM_053089	74838	Mm.275281	NM_053089	ENSMUSG00000063273	Naa15	5730450D16Rik|6330400I15|ASTBDN|Narg1|Tbdn-1|mNAT1	N(alpha)-acetyltransferase 15, NatA auxiliary subunit	protein-coding
mm_5384.1	chr1	30950142	30950154	-	1	NA	promoter-TSS (NR_002688)	promoter-TSS (NR_002688)	-393	NM_011200	19243	Mm.491181	NM_011200	ENSMUSG00000026064	Ptp4a1	AA415290|AU019864|C130021B01|Prl-1	protein tyrosine phosphatase 4a1	protein-coding
mm_125356.1	chr15	39391901	39391907	+	1	NA	intron (NM_001256382, intron 3 of 26)	intron (NM_001256382, intron 3 of 26)	193618	NM_053271	116838	Mm.309296	NM_053271	ENSMUSG00000037386	Rims2	2810036I15Rik|AW048769|RIM2|Rab3ip2|Rim2(+40A)|Rim2(+44A)|Rim2(+4A)|Serg2|Syt3-rs|mKIAA0751	regulating synaptic membrane exocytosis 2	protein-coding
mm_126675.1	chr15	84663189	84663234	+	1	NA	promoter-TSS (NM_001346662)	promoter-TSS (NM_001346662)	5	NM_001346662	109270	Mm.291372	NM_146061	ENSMUSG00000036106	Prr5	AU043908|Arhgap8|C030017C09Rik|C78947|Protor-1|Protor1	proline rich 5 (renal)	protein-coding
mm_89730.1	chr10	98986936	98986962	+	1	NA	exon (NM_026482, exon 4 of 21)	exon (NM_026482, exon 4 of 21)	71797	NM_026482	67972	Mm.166944	NM_026482	ENSMUSG00000019943	Atp2b1	2810442I22Rik|E130111D10Rik|Pmca1	ATPase, Ca++ transporting, plasma membrane 1	protein-coding
mm_22672.1	chr3	14886684	14886700	+	1	NA	5' UTR (NM_009801, exon 1 of 7)	5' UTR (NM_009801, exon 1 of 7)	266	NM_009801	12349	Mm.1186	NM_009801	ENSMUSG00000027562	Car2	AI131712|CAII|Ca2|Car-2|Ltw-5|Lvtw-5	carbonic anhydrase 2	protein-coding
mm_144958.1	chr18	37815391	37815437	+	1	NA	5' UTR (NM_033582, exon 1 of 4)	5' UTR (NM_033582, exon 1 of 4)	335	NM_033582	93707	Mm.247203	NM_033582	ENSMUSG00000023036	Pcdhgc4	-	protocadherin gamma subfamily C, 4	protein-coding
mm_134518.1	chr16	19218450	19218456	-	1	NA	Intergenic	L1_Rod|LINE|L1	68288	NM_146451	258443	Mm.377506	NM_146451	ENSMUSG00000050742	Olfr164	MOR279-2	olfactory receptor 164	protein-coding
mm_63734.1	chr7	130891238	130891248	+	1	NA	intron (NM_001346515, intron 4 of 12)	intron (NM_001346515, intron 4 of 12)	-17025	NR_106028	102466219		NR_106028	ENSMUSG00000104914	Mir7061	mmu-mir-7061	microRNA 7061	ncRNA
mm_113683.1	chr13	42856845	42856880	+	1	NA	intron (NM_001005740, intron 1 of 12)	(CA)n|Simple_repeat|Simple_repeat	-9385	NM_001302636	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding
mm_63258.1	chr7	126656025	126656044	+	1	NA	intron (NM_029339, intron 1 of 9)	ORR1B1|LTR|ERVL-MaLR	6725	NM_029339	75565	Mm.45686	NM_029339	ENSMUSG00000030714	Sgf29	1700023O11Rik|9530025I05Rik|Ccdc101	SAGA complex associated factor 29	protein-coding
mm_81764.1	chr9	114401093	114401133	+	1	NA	promoter-TSS (NM_009752)	promoter-TSS (NM_009752)	18	NM_001200002	100504715	Mm.290516	NM_001200002	ENSMUSG00000079260	Tmppe	-	transmembrane protein with metallophosphoesterase domain	protein-coding
mm_111902.1	chr12	108761385	108761400	-	1	NA	Intergenic	Intergenic	-31919	NM_009537	22632	Mm.3868	NM_009537	ENSMUSG00000021264	Yy1	AW488674|NF-E1	YY1 transcription factor	protein-coding
mm_40535.1	chr5	57948002	57948013	+	1	NA	intron (NM_001310608, intron 3 of 3)	intron (NM_001310608, intron 3 of 3)	229926	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_53213.1	chr6	126761790	126761802	+	1	NA	Intergenic	Intergenic	-21122	NM_013568	16494	Mm.62535	NM_013568	ENSMUSG00000038077	Kcna6	Kv1.6|MK1.6	potassium voltage-gated channel, shaker-related, subfamily, member 6	protein-coding
mm_47428.1	chr5	123172281	123172289	-	1	NA	exon (NM_008277, exon 13 of 14)	exon (NM_008277, exon 13 of 14)	10401	NM_008277	15445	Mm.439709	NM_008277	ENSMUSG00000029445	Hpd	Fla|Flp|Hppd|Laf	4-hydroxyphenylpyruvic acid dioxygenase	protein-coding
mm_27911.1	chr3	79531660	79531670	-	1	NA	intron (NM_001162999, intron 1 of 16)	intron (NM_001162999, intron 1 of 16)	36014	NM_001162999	329679	Mm.244005	NM_001162999	ENSMUSG00000061175	Fnip2	D630023B12Rik|mKIAA1450	folliculin interacting protein 2	protein-coding
mm_113874.1	chr13	48663063	48663074	+	1	NA	promoter-TSS (NM_007526)	promoter-TSS (NM_007526)	32	NM_007526	12022	Mm.42241	NM_007526	ENSMUSG00000021381	Barx1	-	BarH-like homeobox 1	protein-coding
mm_31956.1	chr4	86844801	86844815	+	1	NA	intron (NM_184088, intron 29 of 31)	intron (NM_184088, intron 29 of 31)	12559	NM_009096	20104	Mm.379007	NM_009096	ENSMUSG00000028495	Rps6	S6R	ribosomal protein S6	protein-coding
mm_27952.1	chr3	79825563	79825572	-	1	NA	intron (NM_027495, intron 7 of 11)	intron (NM_027495, intron 7 of 11)	17095	NM_027495	70652	Mm.46635	NM_027495	ENSMUSG00000027956	Tmem144	1110057I03Rik|5730537D05Rik	transmembrane protein 144	protein-coding
mm_138651.1	chr17	35867180	35867233	+	1	NA	5' UTR (NM_175242, exon 1 of 3)	5' UTR (NM_175242, exon 1 of 3)	591	NM_175242	76448	Mm.359982	NM_175242	ENSMUSG00000034595	Ppp1r18	2310014H01Rik|AA407849|AI450394	protein phosphatase 1, regulatory subunit 18	protein-coding
mm_133620.1	chr16	91561317	91561331	+	1	NA	intron (NM_008338, intron 5 of 6)	intron (NM_008338, intron 5 of 6)	14230	NM_008338	15980	Mm.249364	NM_008338	ENSMUSG00000022965	Ifngr2	Ifgr2|Ifgt	interferon gamma receptor 2	protein-coding
mm_38908.1	chr4	149976494	149976498	-	1	NA	Intergenic	RMER17C2|LTR|ERVK	-21490	NM_029035	74646	Mm.30	NM_029035	ENSMUSG00000039911	Spsb1	1110014L01Rik|4930422J18Rik|AI596360|AI854583|SSB-1|SSB1	splA/ryanodine receptor domain and SOCS box containing 1	protein-coding
mm_153510.1	chr19	41370208	41370232	-	1	NA	intron (NM_031376, intron 2 of 16)	MER5A|DNA|hAT-Charlie	14850	NM_031376	83490	Mm.222266	NM_031376	ENSMUSG00000025017	Pik3ap1	1810044J04Rik|BCAP	phosphoinositide-3-kinase adaptor protein 1	protein-coding
mm_162616.1	chr1	183345542	183345554	+	1	NA	intron (NM_177389, intron 6 of 26)	intron (NM_177389, intron 6 of 26)	24017	NM_177389	338366	Mm.41152	NM_177389		Mia3	9130229H14Rik|A930039G15Rik|AU022327|B230399H06Rik|C80126|Gm1525|TANGO1|Tango	melanoma inhibitory activity 3	protein-coding
mm_139172.1	chr17	47587586	47587589	+	1	NA	intron (NM_001081635, intron 2 of 6)	intron (NM_001081635, intron 2 of 6)	-5880	NM_007632	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_66684.1	chr7	45824706	45824712	-	1	NA	promoter-TSS (NM_145963)	promoter-TSS (NM_145963)	38	NM_145963	211480	Mm.68170	NM_145963	ENSMUSG00000058743	Kcnj14	A930026G01Rik|IRK4|Kir2.4	potassium inwardly-rectifying channel, subfamily J, member 14	protein-coding
mm_1407.1	chr1	67152740	67152757	+	1	NA	intron (NM_001080809, intron 7 of 37)	intron (NM_001080809, intron 7 of 37)	29721	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_19359.1	chr2	91084333	91084347	-	1	NA	Intergenic	Intergenic	-12338	NM_011355	20375	Mm.1302	NM_011355	ENSMUSG00000002111	Spi1	Dis-1|Dis1|PU.1|Sfpi-1|Sfpi1|Spi-1|Tcfpu1|Tfpu.1	spleen focus forming virus (SFFV) proviral integration oncogene	protein-coding
mm_115268.1	chr13	111255011	111255018	+	1	NA	promoter-TSS (NM_175497)	promoter-TSS (NM_175497)	1	NM_175497	238880	Mm.107293	NM_175497	ENSMUSG00000055194	Actbl2	4732495G21Rik	actin, beta-like 2	protein-coding
mm_74172.1	chr8	123442970	123443026	+	1	NA	promoter-TSS (NM_054046)	promoter-TSS (NM_054046)	42	NM_054046	23854	Mm.275127	NM_054046	ENSMUSG00000001482	Def8	AI449518|D8Ertd713e|DEF-8	differentially expressed in FDCP 8	protein-coding
mm_51318.1	chr6	72314598	72314608	+	1	NA	TTS (NM_001282071)	TTS (NM_001282071)	9993	NM_147779	20388	Mm.46033	NM_147779	ENSMUSG00000056370	Sftpb	AI562151|SF-B|SP-B|Sftp-3|Sftp3	surfactant associated protein B	protein-coding
mm_22936.1	chr3	31220058	31220070	+	1	NA	intron (NM_172861, intron 7 of 7)	intron (NM_172861, intron 7 of 7)	70144	NM_008770	18417	Mm.4425	NM_008770	ENSMUSG00000037625	Cldn11	Claudin-11|Claudin11|Osp|Otm	claudin 11	protein-coding
mm_48145.1	chr5	137150607	137150616	-	1	NA	Intergenic	Intergenic	-34404	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_48982.1	chr6	4755443	4755462	+	1	NA	exon (NM_130877, exon 2 of 2)	exon (NM_130877, exon 2 of 2)	8146	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_145373.1	chr18	56734018	56734028	+	1	NA	intron (NM_010721, intron 5 of 10)	intron (NM_010721, intron 5 of 10)	26210	NM_010721	16906	Mm.4105	NM_010721	ENSMUSG00000024590	Lmnb1	-	lamin B1	protein-coding
mm_56393.1	chr6	95718771	95718794	-	1	NA	promoter-TSS (NM_011507)	promoter-TSS (NM_011507)	64	NM_011507	20917	Mm.371585	NM_011507	ENSMUSG00000061838	Suclg2	AF171077|AW556404|D6Wsu120e|G-SCS|GTPSCS|SCS-betaG	succinate-Coenzyme A ligase, GDP-forming, beta subunit	protein-coding
mm_67995.1	chr7	100894746	100894766	-	1	NA	intron (NM_001081116, intron 1 of 20)	CpG	-12347	NR_037289	100526508		NR_037289	ENSMUSG00000093296	Mir3102	mmu-mir-3102	microRNA 3102	ncRNA
mm_128136.1	chr15	31467908	31467921	-	1	NA	intron (NM_172606, intron 22 of 25)	Lx8b|LINE|L1	-14225	NM_145852	252967	Mm.436668	NM_145852	ENSMUSG00000022236	Ropn1l	ASP|AV047578|Akapasp	ropporin 1-like	protein-coding
mm_56633.1	chr6	113046164	113046177	-	1	NA	promoter-TSS (NM_008188)	promoter-TSS (NM_008188)	-157	NM_008188	14911	Mm.781	NM_008188	ENSMUSG00000030264	Thumpd3	AW556087|Gt(ROSA)26asSor|Gtrosa26as	THUMP domain containing 3	protein-coding
mm_99061.1	chr11	99155220	99155230	+	1	NA	promoter-TSS (NM_007719)	promoter-TSS (NM_007719)	-148	NM_007719	12775	Mm.2932	NM_007719	ENSMUSG00000037944	Ccr7	CC-CKR-7|CCR-7|CD197|Cdw197|Cmkbr7|EBI1|Ebi1h	chemokine (C-C motif) receptor 7	protein-coding
mm_43005.1	chr5	123508477	123508491	+	1	NA	TTS (NM_001289821)	TTS (NM_001289821)	-1976	NM_198611	231727	Mm.484068	NM_198611	ENSMUSG00000029431	B3gnt4	1010001G17Rik|BGnT-4	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 4	protein-coding
mm_21858.1	chr2	165884544	165884585	-	1	NA	intron (NM_027230, intron 1 of 23)	intron (NM_027230, intron 1 of 23)	274	NM_001252584	228880	Mm.227598	NM_027230	ENSMUSG00000039671	Zmynd8	1110013E22Rik|2010005I16Rik|3632413B07Rik|AI316811|AL024039|Prkcbp1|RACK7	zinc finger, MYND-type containing 8	protein-coding
mm_39097.1	chr4	154918971	154919013	-	1	NA	Intergenic	Intergenic	9085	NM_178931	230979	Mm.215147	NM_178931	ENSMUSG00000042333	Tnfrsf14	Atar|HveA|Hvem|Tnfrs14	tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)	protein-coding
mm_112381.1	chr12	119238021	119238061	-	1	NA	5' UTR (NM_177290, exon 1 of 14)	5' UTR (NM_177290, exon 1 of 14)	235	NM_177290	320910	Mm.217000	NM_177290	ENSMUSG00000025321	Itgb8	4832412O06Rik	integrin beta 8	protein-coding
mm_19850.1	chr2	113749099	113749104	-	1	NA	3' UTR (NM_011824, exon 2 of 2)	3' UTR (NM_011824, exon 2 of 2)	9547	NM_011824	23892	Mm.166318	NM_011824	ENSMUSG00000074934	Grem1	Cktsf1b1|Drm|Grem|ld	gremlin 1, DAN family BMP antagonist	protein-coding
mm_35497.1	chr4	41047956	41047974	-	1	NA	5' UTR (NM_007473, exon 1 of 8)	5' UTR (NM_007473, exon 1 of 8)	171	NM_007473	11832	Mm.8728	NM_007473	ENSMUSG00000028427	Aqp7	AQP7L|AQPap	aquaporin 7	protein-coding
mm_26944.1	chr3	20266451	20266489	-	1	NA	exon (NM_029706, exon 4 of 11)	exon (NM_029706, exon 4 of 11)	9263	NM_029706	76703	Mm.34692	NM_029706	ENSMUSG00000011463	Cpb1	0910001A18Rik|1810063F02Rik|2210008M23Rik|AI504870	carboxypeptidase B1 (tissue)	protein-coding
mm_18134.1	chr2	45017932	45017942	-	1	NA	intron (NM_001289521, intron 2 of 8)	intron (NM_001289521, intron 2 of 8)	5240	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_144129.1	chr18	4920691	4920706	+	1	NA	Intergenic	CpG	108212	NR_045881	100038439	Mm.387569	NR_045881	ENSMUSG00000097043	Gm10556	ENSMUSG00000073646	predicted gene 10556	ncRNA
mm_117932.1	chr13	99434411	99434433	-	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-21596	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_130348.1	chr15	97749744	97749765	-	1	NA	intron (NM_144850, intron 21 of 27)	intron (NM_144850, intron 21 of 27)	17912	NM_001177810	223864	Mm.24028	NM_144850	ENSMUSG00000022469	Rapgef3	2310016P22Rik|9330170P05Rik|Epac|Epac1	Rap guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_166768.1	chr6	134935144	134935162	+	1	NA	intron (NR_037956, intron 1 of 1)	B3A|SINE|B2	6061	NR_037955	381822	Mm.5935	NR_037955	ENSMUSG00000098318	Lockd	1190002F15Rik|AI120476|Droc	lncRNA downstream of Cdkn1b	ncRNA
mm_38086.1	chr4	134156904	134156917	-	1	NA	intron (NM_144527, intron 3 of 13)	intron (NM_144527, intron 3 of 13)	-28157	NM_080559	73723	Mm.22240	NM_080559	ENSMUSG00000028843	Sh3bgrl3	1110004L05Rik|AU022188	SH3 domain binding glutamic acid-rich protein-like 3	protein-coding
mm_63987.1	chr7	140093405	140093415	+	1	NA	promoter-TSS (NM_009475)	promoter-TSS (NM_009475)	14	NM_009475	22264	Mm.439707	NM_009475	ENSMUSG00000025467	Prap1	Upa	proline-rich acidic protein 1	protein-coding
mm_2731.1	chr1	128244235	128244249	+	1	NA	promoter-TSS (NM_026390)	promoter-TSS (NM_026390)	61	NM_026390	67812	Mm.293321	NM_026390	ENSMUSG00000026353	Ubxn4	1300013G12Rik|Ubxd2|mKIAA0242	UBX domain protein 4	protein-coding
mm_23041.1	chr3	34764156	34764186	+	1	NA	Intergenic	B1_Mur3|SINE|Alu	-7904	NR_110488	102638436	Mm.261793	NR_110488	ENSMUSG00000106519	Gm38509	Peril	predicted gene, 38509	ncRNA
mm_140082.1	chr17	75182653	75182669	+	1	NA	intron (NM_206958, intron 1 of 29)	ID4_|SINE|ID	3880	NM_001331235	268977	Mm.269747	NM_019919	ENSMUSG00000001870	Ltbp1	9430031G15Rik|9830146M04|Ltbp-1|Ltbp1L|TGF-beta1-BP-1|Tgfb|b2b1000Clo	latent transforming growth factor beta binding protein 1	protein-coding
mm_166740.1	chr6	124722120	124722135	-	1	NA	intron (NM_001077705, intron 11 of 15)	intron (NM_001077705, intron 11 of 15)	-3737	NR_029792	723944		NR_029792	ENSMUSG00000065462	Mir200c	Mirn200c|mir-200c	microRNA 200c	ncRNA
mm_136558.1	chr17	3115211	3115268	+	1	NA	5' UTR (NM_134123, exon 1 of 20)	5' UTR (NM_134123, exon 1 of 20)	267	NM_134123	106583	Mm.124373	NM_134123	ENSMUSG00000046201	Scaf8	A630086M08Rik|A930036P18Rik|AA408306|AI447644|AI448652|AU015035|Rbm16|mKIAA1116	SR-related CTD-associated factor 8	protein-coding
mm_96917.1	chr11	70465348	70465375	+	1	NA	exon (NM_001029929, exon 13 of 14)	exon (NM_001029929, exon 13 of 14)	-5377	NM_023158	66102	Mm.425692	NM_023158	ENSMUSG00000018920	Cxcl16	0910001K24Rik|AV290116|BB024863|CXCL16v1|CXCL16v2|SR-PSOX|Zmynd15|b2b498Clo	chemokine (C-X-C motif) ligand 16	protein-coding
mm_78092.1	chr9	18312856	18312873	+	1	NA	exon (NM_025844, exon 11 of 11)	exon (NM_025844, exon 11 of 11)	20597	NM_025844	66917	Mm.103534	NM_025844	ENSMUSG00000001774	Chordc1	1110001O09Rik|AA409036|Chp-1|morgana	cysteine and histidine-rich domain (CHORD)-containing, zinc-binding protein 1	protein-coding
mm_97712.1	chr11	80179159	80179174	+	1	NA	TTS (NM_172133)	TTS (NM_172133)	-4706	NM_028019	71956	Mm.22985	NM_028019	ENSMUSG00000020707	Rnf135	0610037N03Rik|2410006N06Rik	ring finger protein 135	protein-coding
mm_111178.1	chr12	83864308	83864309	-	1	NA	intron (NR_073563, intron 2 of 10)	intron (NR_073563, intron 2 of 10)	12504	NM_001272056	18222	Mm.4390	NM_010949	ENSMUSG00000021224	Numb	Nb	numb homolog (Drosophila)	protein-coding
mm_123653.1	chr14	69242433	69242444	-	1	NA	3' UTR (NM_026331, exon 4 of 4)	3' UTR (NM_026331, exon 4 of 4)	42665	NM_026331	67712	Mm.293635	NM_026331	ENSMUSG00000034248	Slc25a37	1700020E22Rik|4930513O14Rik|4930526G11Rik|AI848481|C330015G08Rik|Mfrn|Mfrn1|Mscp|frascati|mitoferrin	solute carrier family 25, member 37	protein-coding
mm_146812.1	chr18	20771598	20771611	-	1	NA	Intergenic	MT2B1|LTR|ERVL	-25200	NM_019737	56386	Mm.393827	NM_019737	ENSMUSG00000056124	B4galt6	AA536803|AU022389	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 6	protein-coding
mm_158055.1	chrX	100626598	100626611	-	1	NA	promoter-TSS (NM_028303)	promoter-TSS (NM_028303)	539	NM_008446	16571	Mm.383091	NM_008446	ENSMUSG00000034311	Kif4	AI323435|D330050K22Rik|Kns4	kinesin family member 4	protein-coding
mm_18978.1	chr2	76848951	76848962	-	1	NA	exon (NM_011652, exon 137 of 313)	exon (NM_011652, exon 137 of 313)	133591	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_77527.1	chr8	123013201	123013214	-	1	NA	intron (NM_001081379, intron 1 of 12)	intron (NM_001081379, intron 1 of 12)	29077	NR_037865	77087	Mm.31567	NM_001081379	ENSMUSG00000035569	Ankrd11	2410104C19Rik|3010027A04Rik|6330578C09Rik|9530048I21Rik|AA930108|Gm176|Yod	ankyrin repeat domain 11	protein-coding
mm_54942.1	chr6	48554718	48554731	-	1	NA	promoter-TSS (NM_177736)	promoter-TSS (NM_177736)	-75	NM_001110160	243371	Mm.290764	NM_177736	ENSMUSG00000073096	Lrrc61	BC027309	leucine rich repeat containing 61	protein-coding
mm_170204.1	chr17	69542025	69542042	-	1	NA	Intergenic	IAPLTR1_Mm|LTR|ERVK	102707	NM_001145192	320722	Mm.400254	NM_001145192	ENSMUSG00000091636	Akain1	A330050F15Rik	A kinase (PRKA) anchor inhibitor 1	protein-coding
mm_166620.1	chr6	72356173	72356200	+	1	NA	5' UTR (NM_144916, exon 2 of 8)	5' UTR (NM_144916, exon 2 of 8)	703	NM_144916	232086	Mm.491165	NM_144916	ENSMUSG00000055912	Tmem150a	BC014685|Tmem150	transmembrane protein 150A	protein-coding
mm_73503.1	chr8	107294406	107294410	+	1	NA	intron (NM_001286260, intron 1 of 12)	CpG	938	NM_133957	54446	Mm.390057	NM_018823	ENSMUSG00000003847	Nfat5	AI225870|B130038B15Rik|CAG-8|CAG80|NFATL1|OREBP|TonEBP|mKIAA0827|nfatz	nuclear factor of activated T cells 5	protein-coding
mm_143926.1	chr17	85688242	85688248	-	1	NA	promoter-TSS (NM_011380)	promoter-TSS (NM_011380)	9	NM_011380	20472	Mm.5039	NM_011380	ENSMUSG00000024134	Six2	-	sine oculis-related homeobox 2	protein-coding
mm_160630.1	chr9	106475117	106475117	-	1	NA	exon (NM_145619, exon 3 of 11)	exon (NM_145619, exon 3 of 11)	1832	NM_001311150	235587	Mm.273659	NM_145619	ENSMUSG00000023249	Parp3	A930002C11Rik|AW990611|Adprt3|Adprtl3|PARP-3|pADPRT-3	poly (ADP-ribose) polymerase family, member 3	protein-coding
mm_48180.1	chr5	137333472	137333482	-	1	NA	5' UTR (NM_031406, exon 1 of 14)	5' UTR (NM_031406, exon 1 of 14)	105	NM_031406	83704	Mm.235625	NM_031406	ENSMUSG00000037344	Slc12a9	CIP1	solute carrier family 12 (potassium/chloride transporters), member 9	protein-coding
mm_17649.1	chr2	31635907	31635907	-	1	NA	Intergenic	CpG	-4130	NM_001123362	381359	Mm.379512	NM_001123362	ENSMUSG00000079466	Prdm12	Gm998	PR domain containing 12	protein-coding
mm_144104.1	chr18	3508003	3508014	+	1	NA	promoter-TSS (NM_026505)	promoter-TSS (NM_026505)	51	NM_026505	68010	Mm.284863	NM_026505	ENSMUSG00000024232	Bambi	2610003H06Rik	BMP and activin membrane-bound inhibitor	protein-coding
mm_89616.1	chr10	96094370	96094382	+	1	NA	Intergenic	Intergenic	-131831	NR_110448	74881	Mm.410819	NR_110448		4930459C07Rik	-	RIKEN cDNA 4930459C07 gene	ncRNA
mm_145871.1	chr18	65466638	65466654	+	1	NA	intron (NM_172833, intron 12 of 15)	B1_Mur3|SINE|Alu	35649	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_25576.1	chr3	116859575	116859591	+	1	NA	promoter-TSS (NM_001113478)	promoter-TSS (NM_001113478)	16	NM_001113478	20321	Mm.66293	NM_009146	ENSMUSG00000033386	Frrs1	AI131732|Sdfr2	ferric-chelate reductase 1	protein-coding
mm_78158.1	chr9	21027922	21027938	+	1	NA	exon (NM_010493, exon 7 of 7)	exon (NM_010493, exon 7 of 7)	-1443	NM_023892	78369	Mm.30220	NM_023892	ENSMUSG00000001014	Icam4	1810015M19Rik|Cd242|ICAM-4	intercellular adhesion molecule 4, Landsteiner-Wiener blood group	protein-coding
mm_115638.1	chr13	12258094	12258134	-	1	NA	promoter-TSS (NM_001081128)	promoter-TSS (NM_001081128)	-1	NM_001081128	238505	Mm.40335	NM_001081128	ENSMUSG00000021311	Mtr	AI894170|D830038K18Rik|MS	5-methyltetrahydrofolate-homocysteine methyltransferase	protein-coding
mm_881.1	chr1	52500649	52500651	+	1	NA	promoter-TSS (NM_008667)	promoter-TSS (NM_008667)	-202	NM_008667	17936	Mm.25903	NM_008667	ENSMUSG00000002881	Nab1	-	Ngfi-A binding protein 1	protein-coding
mm_152536.1	chr19	11327154	11327165	-	1	NA	intron (NM_027836, intron 3 of 6)	intron (NM_027836, intron 3 of 6)	7536	NM_001276398	109225	Mm.491251	NM_027836	ENSMUSG00000024672	Ms4a7	9130422I10Rik|A430103C15Rik|CD20l4|CFFMA	membrane-spanning 4-domains, subfamily A, member 7	protein-coding
mm_36333.1	chr4	72169581	72169585	-	1	NA	intron (NM_001285530, intron 5 of 17)	intron (NM_001285530, intron 5 of 17)	31310	NM_011599	21885	Mm.278444	NM_011599	ENSMUSG00000008305	Tle1	C230057C06Rik|Estm14|Grg-1|Grg1|Tle4l	transducin-like enhancer of split 1	protein-coding
mm_78532.1	chr9	35116931	35116946	+	1	NA	promoter-TSS (NM_009178)	promoter-TSS (NM_009178)	-128	NM_009178	20443	Mm.275973	NM_009178	ENSMUSG00000032038	St3gal4	Siat4c	ST3 beta-galactoside alpha-2,3-sialyltransferase 4	protein-coding
mm_134079.1	chr16	8721667	8721690	-	1	NA	intron (NM_001003918, intron 1 of 30)	intron (NM_001003918, intron 1 of 30)	16664	NM_001003918	252870	Mm.295330	NM_001003918	ENSMUSG00000022710	Usp7	2210010O09Rik|AA409944|AA617399|AU019296|AW548146|C80752|Hausp	ubiquitin specific peptidase 7	protein-coding
mm_109956.1	chr12	12177312	12177331	-	1	NA	Intergenic	RMER10A|LTR|ERVL	-84818	NM_029758	76820	Mm.440802	NM_029758	ENSMUSG00000020589	Fam49a	2410157M17Rik|9630047E15|D12Ertd553e	family with sequence similarity 49, member A	protein-coding
mm_66102.1	chr7	31037925	31037949	-	1	NA	intron (NM_001287217, intron 4 of 8)	intron (NM_001287217, intron 4 of 8)	2380	NR_106017	102465635		NR_106017	ENSMUSG00000098783	Mir7050	Gm27578|mmu-mir-7050	microRNA 7050	ncRNA
mm_112849.1	chr13	20836109	20836113	+	1	NA	intron (NM_012054, intron 2 of 20)	intron (NM_012054, intron 2 of 20)	41998	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_75414.1	chr8	46534492	46534511	-	1	NA	3' UTR (NM_007981, exon 21 of 21)	3' UTR (NM_007981, exon 21 of 21)	-17568	NM_027973	71876	Mm.22108	NM_027973	ENSMUSG00000031629	Cenpu	1700029A22Rik|Mlf1ip	centromere protein U	protein-coding
mm_4418.1	chr1	172500242	172500248	+	1	NA	promoter-TSS (NM_178598)	promoter-TSS (NM_178598)	-1	NM_178598	21346	Mm.271711	NM_178598	ENSMUSG00000026547	Tagln2	2700094C18Rik|SM22beta|Sm22B|Sm22a	transgelin 2	protein-coding
mm_65214.1	chr7	19698189	19698199	-	1	NA	exon (NM_009696, exon 2 of 4)	exon (NM_009696, exon 2 of 4)	204	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_168486.1	chr1	149506403	149506403	-	1	NA	Intergenic	IAPLTR1_Mm|LTR|ERVK	416036	NM_001305632	18783	Mm.4186	NM_008869	ENSMUSG00000056220	Pla2g4a	Pla2g4|cPLA2|cPLA2-alpha|cPLA2alpha	phospholipase A2, group IVA (cytosolic, calcium-dependent)	protein-coding
mm_43150.1	chr5	125496053	125496056	+	1	NA	intron (NM_030210, intron 5 of 17)	intron (NM_030210, intron 5 of 17)	20181	NM_030210	78894	Mm.431573	NM_030210	ENSMUSG00000029482	Aacs	2210408B16Rik|SUR5	acetoacetyl-CoA synthetase	protein-coding
mm_125046.1	chr15	25828773	25828787	+	1	NA	Intergenic	Intergenic	-14518	NM_001034851	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_115033.1	chr13	99247899	99247909	+	1	NA	TTS (NM_001004149)	TTS (NM_001004149)	63081	NM_001004149	238803	Mm.343207	NM_001004149	ENSMUSG00000050919	Zfp366	DC-SCRIPT|Znf366	zinc finger protein 366	protein-coding
mm_31560.1	chr4	57434491	57434497	+	1	NA	Intergenic	CpG	-70202	NR_038178	73349	Mm.393774	NR_038178		1700042G15Rik	-	RIKEN cDNA 1700042G15 gene	ncRNA
mm_28350.1	chr3	89655141	89655170	-	1	NA	intron (NM_080466, intron 5 of 7)	intron (NM_080466, intron 5 of 7)	-59867	NM_001038587	56417	Mm.316628	NM_019655	ENSMUSG00000027951	Adar	AV242451|Adar1|Adar1p110|Adar1p150|mZaADAR	adenosine deaminase, RNA-specific	protein-coding
mm_135518.1	chr16	48786406	48786414	-	1	NA	Intergenic	Intergenic	-14454	NM_198297	77647	Mm.167298	NM_198297	ENSMUSG00000030775	Trat1	C030046M14Rik|Tcrim|Trim	T cell receptor associated transmembrane adaptor 1	protein-coding
mm_62607.1	chr7	106503605	106503638	+	1	NA	Intergenic	Intergenic	-62548	NR_003967	209380	Mm.461779	NM_001001318		Gm4759	EG209380	GTPase, very large interferon inducible 1 pseudogene	pseudo
mm_8287.1	chr1	142367371	142367371	-	1	NA	Intergenic	Intergenic	-1273326	NM_020025	26878	Mm.285580	NM_020025	ENSMUSG00000033849	B3galt2	-	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 2	protein-coding
mm_25120.1	chr3	102012350	102012367	+	1	NA	intron (NM_178777, intron 2 of 2)	CpG	2213	NM_178777	18072	Mm.137286	NM_178777	ENSMUSG00000048540	Nhlh2	6230401I09Rik|Hen2|NSCL2|Nscl-2|bHLHa34	nescient helix loop helix 2	protein-coding
mm_105133.1	chr11	101425331	101425388	-	1	NA	promoter-TSS (NM_026865)	promoter-TSS (NM_026865)	-26	NM_026865	73635	Mm.472804	NM_026865	ENSMUSG00000097487	Ptges3l	1110069E20Rik|1700113I22Rik	prostaglandin E synthase 3 (cytosolic)-like	protein-coding
mm_114227.1	chr13	56522450	56522495	+	1	NA	promoter-TSS (NM_178674)	promoter-TSS (NM_178674)	0	NM_001346732	213311	Mm.233904	NM_178674	ENSMUSG00000035509	Fbxl21	D630045D17Rik|FBL3B|FBXL3B|Psttm	F-box and leucine-rich repeat protein 21	protein-coding
mm_24271.1	chr3	89202964	89202976	+	1	NA	promoter-TSS (NM_001077411)	promoter-TSS (NM_001077411)	45	NR_122037	14466	Mm.5031	NM_008094	ENSMUSG00000028048	Gba	GBA1|GC|GCase|GLUC|betaGC	glucosidase, beta, acid	protein-coding
mm_141525.1	chr17	31808045	31808065	-	1	NA	Intergenic	Intergenic	47737	NM_010831	17691	Mm.290941	NM_010831	ENSMUSG00000024042	Sik1	Msk|Sik|Snf1lk	salt inducible kinase 1	protein-coding
mm_165079.1	chr19	46356947	46356949	+	1	NA	promoter-TSS (NM_029186)	promoter-TSS (NM_029186)	68	NM_029186	75146	Mm.159290	NM_029186	ENSMUSG00000025227	Mfsd13a	4930449A08Rik|4930538D17Rik|Tmem180	major facilitator superfamily domain containing 13a	protein-coding
mm_117322.1	chr13	67755133	67755169	-	1	NA	promoter-TSS (NM_001001130)	promoter-TSS (NM_001001130)	-17	NM_001001130	22746	Mm.288396	NM_001001130	ENSMUSG00000058331	Zfp85	KRAB19|Rslcan2|Zfp71|Zfp85-rs1	zinc finger protein 85	protein-coding
mm_95778.1	chr11	54909794	54909804	+	1	NA	TTS (NM_021327)	TTS (NM_021327)	6945	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_119939.1	chr14	54982171	54982176	+	1	NA	exon (NM_080728, exon 26 of 41)	exon (NM_080728, exon 26 of 41)	-6397	NR_030607	100124433		NR_030607	ENSMUSG00000077928	Mir208b	Mirn208b|mir-208b	microRNA 208b	ncRNA
mm_33379.1	chr4	129556637	129556659	+	1	NA	exon (NM_010693, exon 5 of 12)	exon (NM_010693, exon 5 of 12)	1163	NR_106199	102465997		NR_106199	ENSMUSG00000099070	Mir8119	Gm27567|mmu-mir-8119	microRNA 8119	ncRNA
mm_108485.1	chr12	83664195	83664232	+	1	NA	exon (NM_027349, exon 10 of 19)	exon (NM_027349, exon 10 of 19)	-24350	NM_008943	19164	Mm.998	NM_008943	ENSMUSG00000019969	Psen1	Ad3h|PS-1|PS1|S182	presenilin 1	protein-coding
mm_153754.1	chr19	45159303	45159312	-	1	NA	Intergenic	CpG	8592	NM_021901	21908	Mm.391203	NM_021901	ENSMUSG00000025215	Tlx1	Hox-11|Hox11|Tlx-1	T cell leukemia, homeobox 1	protein-coding
mm_78283.1	chr9	22136266	22136273	+	1	NA	promoter-TSS (NM_001102405)	promoter-TSS (NM_001102405)	-523	NM_001102405	11433	Mm.46354	NM_007388	ENSMUSG00000001348	Acp5	TRACP|TRAP	acid phosphatase 5, tartrate resistant	protein-coding
mm_119823.1	chr14	54232994	54233006	+	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	20929	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_158318.1	chrX	131850467	131850500	-	1	NA	Intergenic	Intergenic	1838510	NM_001105245	279653	Mm.39738	NM_001105245	ENSMUSG00000051323	Pcdh19	B530002L05Rik|Gm717|mKIAA1313	protocadherin 19	protein-coding
mm_22154.1	chr2	172550936	172550940	-	1	NA	promoter-TSS (NM_001159696)	promoter-TSS (NM_001159696)	-53	NM_001159696	21420	Mm.3629	NM_009335	ENSMUSG00000028640	Tfap2c	AA409384|AP2gamma|Ap-2.2|Stra2|Tcfap2c	transcription factor AP-2, gamma	protein-coding
mm_83252.1	chr9	42401583	42401593	-	1	NA	Intergenic	Intergenic	-1659	NM_001324548	21683	Mm.42209	NM_009347	ENSMUSG00000037705	Tecta	Tctna	tectorin alpha	protein-coding
mm_113935.1	chr13	49653099	49653136	+	1	NA	promoter-TSS (NM_001271397)	promoter-TSS (NM_001271397)	39	NR_073167	70930	Mm.258915	NM_001081350	ENSMUSG00000021392	Nol8	4921532D18Rik|5730412B09Rik	nucleolar protein 8	protein-coding
mm_63592.1	chr7	128138391	128138414	+	1	NA	intron (NM_021334, intron 14 of 29)	RLTR12A|LTR|ERVK	8834	NM_021334	16411	Mm.22378	NM_021334	ENSMUSG00000030789	Itgax	AI449405|Cd11c|Cr4|N418	integrin alpha X	protein-coding
mm_171435.1	chr4	141053728	141053728	-	1	NA	promoter-TSS (NM_172122)	promoter-TSS (NM_172122)	-67	NM_172122	230872	Mm.80685	NM_172122	ENSMUSG00000040860	Crocc	-	ciliary rootlet coiled-coil, rootletin	protein-coding
mm_33307.1	chr4	129058076	129058091	+	1	NA	promoter-TSS (NM_029219)	promoter-TSS (NM_029219)	-188	NM_029219	75234	Mm.259672	NM_029219	ENSMUSG00000028793	Rnf19b	4930534K13Rik|4930555L03Rik|Ibrdc3	ring finger protein 19B	protein-coding
mm_138183.1	chr17	34267920	34267930	+	1	NA	exon (NM_207105, exon 4 of 6)	exon (NM_207105, exon 4 of 6)	4698	NM_207105	14961	Mm.254067	NM_207105	ENSMUSG00000073421	H2-Ab1	AI845868|Abeta|H-2Ab|H2-Ab|I-Abeta|IAb|Ia-2|Ia2|Rmcs1	histocompatibility 2, class II antigen A, beta 1	protein-coding
mm_124303.1	chr14	103070127	103070143	-	1	NA	promoter-TSS (NM_001033242)	promoter-TSS (NM_001033242)	-81	NM_001033242	211286	Mm.295289	NM_001033242	ENSMUSG00000022125	Cln5	A730075N08Rik	ceroid-lipofuscinosis, neuronal 5	protein-coding
mm_126582.1	chr15	82292815	82292829	+	1	NA	3' UTR (NM_011889, exon 10 of 10)	3' UTR (NM_011889, exon 10 of 10)	-6162	NM_029066	74716	Mm.159315	NM_029066	ENSMUSG00000022455	Wbp2nl	4930521I23Rik|PAWP	WBP2 N-terminal like	protein-coding
mm_6077.1	chr1	62703243	62703247	-	1	NA	promoter-TSS (NM_001077407)	promoter-TSS (NM_001077407)	-72	NM_001077406	18187	Mm.266341	NM_010939	ENSMUSG00000025969	Nrp2	1110048P06Rik|Np-2|Np2|Npn-2|Npn2	neuropilin 2	protein-coding
mm_53829.1	chr6	148047363	148047378	+	1	NA	promoter-TSS (NM_178797)	promoter-TSS (NM_178797)	-46	NM_001347516	330450	Mm.447274	NM_178797	ENSMUSG00000030303	Far2	A230046P18|AW048109|BC055759|Mlstd1	fatty acyl CoA reductase 2	protein-coding
mm_135928.1	chr16	72264402	72264405	-	1	NA	Intergenic	U4|snRNA|snRNA	-30076	NR_131115	319533	Mm.373754	NR_131115		8030451O07Rik	-	RIKEN cDNA 8030451O07 gene	ncRNA
mm_89934.1	chr10	111247857	111247892	+	1	NA	intron (NM_175489, intron 4 of 23)	intron (NM_175489, intron 4 of 23)	-50805	NM_027914	71769	Mm.45256	NM_027914	ENSMUSG00000035759	Bbs10	1300007O09Rik|AI452285	Bardet-Biedl syndrome 10 (human)	protein-coding
mm_4090.1	chr1	167242410	167242423	+	1	NA	intron (NM_030724, intron 1 of 6)	MIR|SINE|MIR	42711	NM_030724	80914	Mm.280895	NM_030724	ENSMUSG00000026558	Uck2	AA407809|AI481316|AU018180|AU020720|TSA903|UK|UMK|Umpk	uridine-cytidine kinase 2	protein-coding
mm_92599.1	chr10	80102654	80102728	-	1	NA	promoter-TSS (NM_183426)	promoter-TSS (NM_183426)	11	NM_183426	216161	Mm.262102	NM_183426	ENSMUSG00000035673	Sbno2	BC019206|F730040C21|Sno|Stno	strawberry notch homolog 2 (Drosophila)	protein-coding
mm_72742.1	chr8	85086883	85086922	+	1	NA	exon (NM_010764, exon 5 of 24)	exon (NM_010764, exon 5 of 24)	3633	NM_010764	17159	Mm.4219	NM_010764	ENSMUSG00000005142	Man2b1	AW107687|LAMAN	mannosidase 2, alpha B1	protein-coding
mm_50497.1	chr6	49033038	49033052	+	1	NA	Intergenic	Intergenic	-3473	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_51474.1	chr6	83005847	83005873	+	1	NA	intron (NM_033079, intron 6 of 9)	intron (NM_033079, intron 6 of 9)	27611	NM_010070	13448	Mm.156	NM_010070	ENSMUSG00000068335	Dok1	AW557123|p62DOK	docking protein 1	protein-coding
mm_90979.1	chr10	13553064	13553085	-	1	NA	promoter-TSS (NM_019961)	promoter-TSS (NM_019961)	68	NM_019961	56535	Mm.282711	NM_019961	ENSMUSG00000019809	Pex3	1700014F15Rik|2810027F19Rik|2900010N04Rik	peroxisomal biogenesis factor 3	protein-coding
mm_154815.1	chrX	13669068	13669102	+	1	NA	intron (NM_009806, intron 5 of 24)	LSU-rRNA_Hsa|rRNA|rRNA	7722	NM_175669	319200	Mm.383294	NM_175669	ENSMUSG00000047678	Gpr82	-	G protein-coupled receptor 82	protein-coding
mm_55987.1	chr6	85961604	85961627	-	1	NA	promoter-TSS (NM_028099)	promoter-TSS (NM_028099)	52	NM_028099	72102	Mm.24007	NM_028099	ENSMUSG00000030002	Dusp11	2010300F21Rik|AI481497	dual specificity phosphatase 11 (RNA/RNP complex 1-interacting)	protein-coding
mm_158938.1	chr1	74885224	74885224	-	1	NA	5' UTR (NM_153111, exon 1 of 3)	5' UTR (NM_153111, exon 1 of 3)	184	NM_153111	260298	Mm.150496	NM_153111	ENSMUSG00000055197	Fev	Pet-1|Pet1|mPet-1	FEV (ETS oncogene family)	protein-coding
mm_65849.1	chr7	29256492	29256594	-	1	NA	3' UTR (NM_001082548, exon 6 of 6)	3' UTR (NM_001082548, exon 6 of 6)	-8076	NM_028179	72275	Mm.441142	NM_028179	ENSMUSG00000030587	2200002D01Rik	2010005J02Rik|H2RSP|IMUP|IMUP-1|IMUP-2	RIKEN cDNA 2200002D01 gene	protein-coding
mm_111652.1	chr12	102757770	102757809	-	1	NA	promoter-TSS (NM_001142939)	promoter-TSS (NM_001142939)	21	NM_001142939	100859931	Mm.291222	NM_001142939	ENSMUSG00000041716	Gm20604	AK010878-Moap1	predicted gene 20604	protein-coding
mm_121594.1	chr14	7994006	7994020	-	1	NA	5' UTR (NM_007870, exon 1 of 8)	5' UTR (NM_007870, exon 1 of 8)	169	NM_007870	13421	Mm.272258	NM_007870	ENSMUSG00000025279	Dnase1l3	DNasegamma|Dhp2|Lsd	deoxyribonuclease 1-like 3	protein-coding
mm_82995.1	chr9	36638596	36638609	-	1	NA	promoter-TSS (NM_001033325)	promoter-TSS (NM_001033325)	0	NM_001033325	235973	Mm.118804	NM_001033325	ENSMUSG00000070313	A630095E13Rik	Gm191|Pate14|Sslp-1|Sslp1	RIKEN cDNA A630095E13 gene	protein-coding
mm_67389.1	chr7	79842616	79842626	-	1	NA	promoter-TSS (NM_008486)	promoter-TSS (NM_008486)	-269	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_20749.1	chr2	140066662	140066796	-	1	NA	promoter-TSS (NM_175225)	promoter-TSS (NM_175225)	76	NM_001159640	75812	Mm.293449	NM_175225	ENSMUSG00000039033	Tasp1	4930485D02Rik|AW986064	taspase, threonine aspartase 1	protein-coding
mm_146582.1	chr18	7626778	7626792	-	1	NA	promoter-TSS (NM_001161620)	promoter-TSS (NM_001161620)	78	NM_001081287	75739	Mm.133293	NM_001081287	ENSMUSG00000057440	Mpp7	1110068J02Rik|2810038M04Rik|5430426E14Rik|AI415104|Gm955	membrane protein, palmitoylated 7 (MAGUK p55 subfamily member 7)	protein-coding
mm_25988.1	chr3	133646648	133646656	+	1	NA	Intergenic	Intergenic	-102262	NM_001040400	214133	Mm.347816	NM_145989	ENSMUSG00000040943	Tet2	Ayu17-449|E130014J05Rik|mKIAA1546	tet methylcytosine dioxygenase 2	protein-coding
mm_65914.1	chr7	30195047	30195090	-	1	NA	promoter-TSS (NM_009795)	promoter-TSS (NM_009795)	-20	NM_009795	12336	Mm.439782	NM_009795	ENSMUSG00000001794	Capns1	Capa-4|Capa4|Capn4|D7Ertd146e	calpain, small subunit 1	protein-coding
mm_53166.1	chr6	125322907	125322913	+	1	NA	intron (NM_011324, intron 1 of 11)	intron (NM_011324, intron 1 of 11)	1570	NM_011324	20276	Mm.144114	NM_011324	ENSMUSG00000030340	Scnn1a	ENaC|SCNEA|Scnn1|mENaC	sodium channel, nonvoltage-gated 1 alpha	protein-coding
mm_91745.1	chr10	49364426	49364450	-	1	NA	intron (NM_001111268, intron 10 of 16)	L1_Mur3|LINE|L1	-268595	NR_046212	100418235	Mm.185993	NR_046212		C130030K03Rik	-	proteasome (prosome, macropain) subunit, alpha type 6 pseudogene	pseudo
mm_58796.1	chr7	16175343	16175356	+	1	NA	promoter-TSS (NM_008627)	promoter-TSS (NM_008627)	-46	NM_001277988	17537	Mm.360516	NM_008627	ENSMUSG00000041420	Meis3	AI573393|Mrg2	Meis homeobox 3	protein-coding
mm_19752.1	chr2	104849942	104849950	-	1	NA	promoter-TSS (NM_178695)	promoter-TSS (NM_178695)	-96	NM_178695	228413	Mm.259609	NM_178695	ENSMUSG00000027171	Prrg4	9930111I18Rik|TMG4	proline rich Gla (G-carboxyglutamic acid) 4 (transmembrane)	protein-coding
mm_19110.1	chr2	79456302	79456304	-	1	NA	intron (NM_010894, intron 1 of 1)	intron (NM_010894, intron 1 of 1)	333	NM_010894	18012	Mm.4636	NM_010894	ENSMUSG00000034701	Neurod1	BETA2|BHF-1|Nd1|Neurod|bHLHa3	neurogenic differentiation 1	protein-coding
mm_143348.1	chr17	67047976	67048018	-	1	NA	intron (NM_008984, intron 5 of 30)	LTR79|LTR|ERVL	-21762	NR_049205	100885844		NR_049205	ENSMUSG00000093508	Mir5709	Gm22041|mir-5709|mmu-mir-5709	microRNA 5709	ncRNA
mm_23184.1	chr3	40949916	40949940	+	1	NA	promoter-TSS (NM_001040399)	promoter-TSS (NM_001040399)	-703	NM_001040399	214048	Mm.46782	NM_027663	ENSMUSG00000025762	Larp1b	1700108L22Rik|4933421B21Rik|AA690246|Larp2	La ribonucleoprotein domain family, member 1B	protein-coding
mm_94446.1	chr11	6366237	6366244	+	1	NA	Intergenic	Intergenic	-28885	NM_001005867	52915	Mm.1144	NM_028601	ENSMUSG00000041164	Zmiz2	Zimp7	zinc finger, MIZ-type containing 2	protein-coding
mm_142295.1	chr17	40880345	40880358	-	1	NA	exon (NM_027834, exon 1 of 2)	exon (NM_027834, exon 1 of 2)	207	NM_027834	71583	Mm.158733	NM_027834	ENSMUSG00000054951	9130008F23Rik	-	RIKEN cDNA 9130008F23 gene	protein-coding
mm_58598.1	chr7	5038309	5038323	+	1	NA	intron (NM_001039532, intron 1 of 1)	CpG	130	NM_001039532	654801	Mm.333548	NM_001039532	ENSMUSG00000043290	Zfp784	C730049F21Rik|Znf784	zinc finger protein 784	protein-coding
mm_153881.1	chr19	46932299	46932302	-	1	NA	intron (NM_001164365, intron 2 of 17)	intron (NM_001164365, intron 2 of 17)	30051	NM_029810	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_136826.1	chr17	12596345	12596360	+	1	NA	intron (NM_013667, intron 2 of 10)	intron (NM_013667, intron 2 of 10)	12163	NM_013667	20518	Mm.17322	NM_013667	ENSMUSG00000040966	Slc22a2	Oct2|Orct2	solute carrier family 22 (organic cation transporter), member 2	protein-coding
mm_55832.1	chr6	83125073	83125135	-	1	NA	promoter-TSS (NM_023547)	promoter-TSS (NM_023547)	-75	NM_023547	70020	Mm.27814	NM_023547	ENSMUSG00000030034	Ino80b	2510009I23Rik|HMG1YL4|Hmga1l4|Papa1|Znhit4	INO80 complex subunit B	protein-coding
mm_165431.1	chr2	153424694	153424704	-	1	NA	intron (NM_001001986, intron 2 of 7)	intron (NM_001001986, intron 2 of 7)	19780	NM_001001986	329540	Mm.50600	NM_001001986	ENSMUSG00000061411	Nol4l	4931410H15|8430427H17Rik|AI429157|Gm1636	nucleolar protein 4-like	protein-coding
mm_7219.1	chr1	93305851	93305885	-	1	NA	promoter-TSS (NM_001310756)	promoter-TSS (NM_001310756)	11	NM_178051	69821	Mm.52809	NM_178051	ENSMUSG00000026273	Mterf4	1810059A23Rik|4933412H03Rik|Mterfd2	mitochondrial transcription termination factor 4	protein-coding
mm_59009.1	chr7	19212554	19212605	+	1	NA	promoter-TSS (NM_175668)	promoter-TSS (NM_175668)	41	NM_175668	319197	Mm.135984	NM_175668	ENSMUSG00000044317	Gpr4	-	G protein-coupled receptor 4	protein-coding
mm_100974.1	chr11	6895100	6895133	-	1	NA	Intergenic	Intergenic	-168373	NM_009622	432530	Mm.259733	NM_009622	ENSMUSG00000020431	Adcy1	AC1|D11Bwg1392e|I-AC|brl|mKIAA4070	adenylate cyclase 1	protein-coding
mm_75429.1	chr8	47288131	47288160	-	1	NA	5' UTR (NM_001286376, exon 1 of 5)	5' UTR (NM_001286376, exon 1 of 5)	1257	NM_001286376	71069	Mm.23973	NM_175162	ENSMUSG00000038143	Stox2	4933409N07Rik|AI449080|AI835114|mKIAA1392	storkhead box 2	protein-coding
mm_107293.1	chr12	30479064	30479072	+	1	NA	Intergenic	Intergenic	-11710	NR_045491	69566	Mm.396405	NR_045491	ENSMUSG00000102098	2310016D03Rik	-	RIKEN cDNA 2310016D03 gene	ncRNA
mm_70736.1	chr8	19062952	19062955	+	1	NA	intron (NM_183038, intron 1 of 1)	intron (NM_183038, intron 1 of 1)	1857	NM_183038	360214	Mm.271559	NM_183038	ENSMUSG00000061847	Defb39	BD-39	defensin beta 39	protein-coding
mm_32684.1	chr4	115828116	115828130	+	1	NA	promoter-TSS (NM_175308)	promoter-TSS (NM_175308)	31	NM_175308	100465	Mm.35571	NM_175308	ENSMUSG00000028709	Mob3c	AW822253|D130076I06Rik|Mobkl2c	MOB kinase activator 3C	protein-coding
mm_1211.1	chr1	62726726	62726783	+	1	NA	intron (NM_001077405, intron 2 of 15)	intron (NM_001077405, intron 2 of 15)	23437	NM_001077405	18187	Mm.266341	NM_010939	ENSMUSG00000025969	Nrp2	1110048P06Rik|Np-2|Np2|Npn-2|Npn2	neuropilin 2	protein-coding
mm_82493.1	chr9	18674576	18674624	-	1	NA	Intergenic	Intergenic	81033	NM_146606	18322	Mm.246530	NM_146606	ENSMUSG00000054141	Olfr24	MOR132-1|MTPCR51	olfactory receptor 24	protein-coding
mm_17788.1	chr2	33086230	33086241	-	1	NA	intron (NM_178888, intron 1 of 28)	intron (NM_178888, intron 1 of 28)	969	NM_178888	99326	Mm.41290	NM_178888	ENSMUSG00000038860	Garnl3	AW120551	GTPase activating RANGAP domain-like 3	protein-coding
mm_118002.1	chr13	100552667	100552677	-	1	NA	promoter-TSS (NM_008756)	promoter-TSS (NM_008756)	-174	NM_008756	18260	Mm.4807	NM_008756	ENSMUSG00000021638	Ocln	AI503564|Ocl	occludin	protein-coding
mm_11119.1	chr2	28208076	28208087	+	1	NA	exon (NM_001038613, exon 2 of 6)	exon (NM_001038613, exon 2 of 6)	2392	NM_019498	56177	Mm.43278	NM_019498	ENSMUSG00000026833	Olfm1	AMY|AW742568|Noe1|OlfA|Pancortin|Pancortin3	olfactomedin 1	protein-coding
mm_42811.1	chr5	121835227	121835232	+	1	NA	intron (NM_001306127, intron 1 of 8)	intron (NM_001306127, intron 1 of 8)	875	NM_001306126	16923	Mm.65493	NM_008507	ENSMUSG00000042594	Sh2b3	AI429800|Lnk	SH2B adaptor protein 3	protein-coding
mm_143098.1	chr17	57080957	57080969	-	1	NA	exon (NM_009451, exon 4 of 4)	exon (NM_009451, exon 4 of 4)	-2453	NM_153551	70785	Mm.284447	NM_153551	ENSMUSG00000002668	Dennd1c	4432409M07Rik	DENN/MADD domain containing 1C	protein-coding
mm_146456.1	chr18	86395547	86395563	+	1	NA	5' UTR (NM_144946, exon 1 of 11)	5' UTR (NM_144946, exon 1 of 11)	603	NM_144946	246317	Mm.329578	NM_144946	ENSMUSG00000050321	Neto1	AI851453|Btcl1|C130005O10Rik	neuropilin (NRP) and tolloid (TLL)-like 1	protein-coding
mm_92301.1	chr10	75032539	75032588	-	1	NA	promoter-TSS (NM_027730)	promoter-TSS (NM_027730)	-10	NM_001163534	71236	Mm.414817	NM_027730	ENSMUSG00000009070	Rsph14	4933431K05Rik|Rtdr1	radial spoke head homolog 14 (Chlamydomonas)	protein-coding
mm_1359.1	chr1	66322109	66322119	+	1	NA	5' UTR (NM_001310634, exon 1 of 15)	5' UTR (NM_001310634, exon 1 of 15)	390	NM_001310634	17756	Mm.256966	NM_008632	ENSMUSG00000015222	Map2	G1-397-34|MAP-2|Mtap-2|Mtap2|repro4	microtubule-associated protein 2	protein-coding
mm_39691.1	chr5	26904825	26904875	+	1	NA	promoter-TSS (NM_001198886)	promoter-TSS (NM_001198886)	72	NM_001198886	13483	Mm.42078	NM_010075	ENSMUSG00000061576	Dpp6	B930011P16Rik|D5Buc3|D5Buc4|D5Buc5|DPP VI|Dpp-6|Gm1377|In(5)6H-p|Peplb|Rw	dipeptidylpeptidase 6	protein-coding
mm_151543.1	chr19	59260890	59260901	+	1	NA	promoter-TSS (NM_172523)	promoter-TSS (NM_172523)	17	NM_172523	214084	Mm.268797	NM_172523	ENSMUSG00000025094	Slc18a2	1110037L13Rik|9330105E13|Vmat2	solute carrier family 18 (vesicular monoamine), member 2	protein-coding
mm_127363.1	chr15	100684626	100684637	+	1	NA	exon (NM_033612, exon 4 of 8)	exon (NM_033612, exon 4 of 8)	3289	NM_033612	109901	Mm.2131	NM_033612	ENSMUSG00000023031	Cela1	1810009A17Rik|1810062B19Rik|Ela-1|Ela1|PC-TsF	chymotrypsin-like elastase family, member 1	protein-coding
mm_92520.1	chr10	78578240	78578262	-	1	NA	intron (NM_173751, intron 6 of 15)	intron (NM_173751, intron 6 of 15)	3751	NM_173751	216136	Mm.2644	NM_173751	ENSMUSG00000032763	Ilvbl	5830463I21|AI415009	ilvB (bacterial acetolactate synthase)-like	protein-coding
mm_150768.1	chr19	44280965	44280970	+	1	NA	Intergenic	Intergenic	-12709	NM_009128	20250	Mm.487021	NM_009128	ENSMUSG00000025203	Scd2	Mir5114|Scd-2|mir-5114|swty	stearoyl-Coenzyme A desaturase 2	protein-coding
mm_44845.1	chr5	34187645	34187669	-	1	NA	promoter-TSS (NM_010753)	promoter-TSS (NM_010753)	53	NM_010753	17122	Mm.259260	NM_010753	ENSMUSG00000037235	Mxd4	2810410A03Rik|Mad4|bHLHc12	Max dimerization protein 4	protein-coding
mm_87671.1	chr10	58812567	58812600	+	1	NA	promoter-TSS (NM_172788)	promoter-TSS (NM_172788)	-776	NM_172788	237353	Mm.333078	NM_172788	ENSMUSG00000037990	Sh3rf3	4831416G18Rik|Igfbp5-ip|Sh3md4|Sh3rf31	SH3 domain containing ring finger 3	protein-coding
mm_69064.1	chr7	126898250	126898288	-	1	NA	promoter-TSS (NM_028389)	promoter-TSS (NM_028389)	9	NM_026827	68742	Mm.248646	NM_026827	ENSMUSG00000060538	Tmem219	1110032O16Rik|2900045G02Rik|IGFBP-3R	transmembrane protein 219	protein-coding
mm_142802.1	chr17	50420136	50420144	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-89407	NM_013880	224860	Mm.217362	NM_013880	ENSMUSG00000038910	Plcl2	PLC-L2|PRIP-2|Plce2|mKIAA1092	phospholipase C-like 2	protein-coding
mm_81411.1	chr9	109052868	109052880	+	1	NA	intron (NM_025858, intron 3 of 5)	intron (NM_025858, intron 3 of 5)	-1992	NM_026381	66940	Mm.196533	NM_025858	ENSMUSG00000025647	Shisa5	2310008D10Rik|6430628I05Rik|Scotin|mShisa5	shisa family member 5	protein-coding
mm_73608.1	chr8	110079711	110079756	+	1	NA	promoter-TSS (NM_175480)	promoter-TSS (NM_175480)	-1	NM_175480	234725	Mm.87487	NM_175480	ENSMUSG00000044676	Zfp612	B230354B21Rik	zinc finger protein 612	protein-coding
mm_146073.1	chr18	70568269	70568398	+	1	NA	promoter-TSS (NM_010773)	promoter-TSS (NM_010773)	41	NM_010773	17191	Mm.322	NM_010773	ENSMUSG00000024513	Mbd2	MBD2a	methyl-CpG binding domain protein 2	protein-coding
mm_32875.1	chr4	118527268	118527303	+	1	NA	promoter-TSS (NM_025572)	promoter-TSS (NM_025572)	10	NM_025572	66451	Mm.34431	NM_025572	ENSMUSG00000028536	2610528J11Rik	TEMP	RIKEN cDNA 2610528J11 gene	protein-coding
mm_163377.1	chr12	44525673	44525675	+	1	NA	intron (NM_001146031, intron 3 of 27)	intron (NM_001146031, intron 3 of 27)	196789	NM_001146031	319504	Mm.208439	NM_176930	ENSMUSG00000020598	Nrcam	Bravo|C030017F07Rik|C130076O07Rik|mKIAA0343	neuronal cell adhesion molecule	protein-coding
mm_53826.1	chr6	147531368	147531383	+	1	NA	intron (NM_025911, intron 3 of 12)	intron (NM_025911, intron 3 of 12)	55504	NM_025911	67015	Mm.209774	NM_025911	ENSMUSG00000030301	Ccdc91	1700086G08Rik|1810060J02Rik|AU045683|AW555238|p56	coiled-coil domain containing 91	protein-coding
mm_95921.1	chr11	58274807	58274856	+	1	NA	Intergenic	Intergenic	-32238	NM_182996	103836	Mm.41440	NM_182996	ENSMUSG00000037243	Zfp692	AI746306|AI839920|Zfp692-ps|Znf692	zinc finger protein 692	protein-coding
mm_141463.1	chr17	30576402	30576423	-	1	NA	promoter-TSS (NM_027060)	promoter-TSS (NM_027060)	-125	NM_027060	224671	Mm.41220	NM_027060	ENSMUSG00000062202	Btbd9	1700023F20Rik|4930402L05|AI464421	BTB (POZ) domain containing 9	protein-coding
mm_58627.1	chr7	5080327	5080384	+	1	NA	TTS (NM_001205231)	TTS (NM_001205231)	120	NM_001252454	13854	Mm.3091	NM_010147	ENSMUSG00000035203	Epn1	AA269831|Ibp1	epsin 1	protein-coding
mm_142852.1	chr17	51810867	51810873	-	1	NA	intron (NM_001163632, intron 1 of 10)	intron (NM_001163632, intron 1 of 10)	1184	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_78716.1	chr9	41531493	41531499	+	1	NA	promoter-TSS (NR_029790)	promoter-TSS (NR_029790)	71	NR_029790	723892		NR_029790	ENSMUSG00000093011	Mir100	Mirn100|mir-100|mmu-mir-100	microRNA 100	ncRNA
mm_86377.1	chr9	123844574	123844584	-	1	NA	intron (NM_001110253, intron 1 of 17)	intron (NM_001110253, intron 1 of 17)	7082	NM_148925	17281	Mm.252941	NM_148925	ENSMUSG00000025241	Fyco1	2810409M01Rik|Mem2|RUFY3|ZFYVE7	FYVE and coiled-coil domain containing 1	protein-coding
mm_43737.1	chr5	139820092	139820102	+	1	NA	Intergenic	Intergenic	-5814	NM_001161548	231832	Mm.482655	NM_144914	ENSMUSG00000036687	Tmem184a	Sdmg1	transmembrane protein 184a	protein-coding
mm_48289.1	chr5	138187178	138187237	-	1	NA	promoter-TSS (NM_178612)	promoter-TSS (NM_178612)	-21	NM_009315	21343	Mm.248517	NM_009315	ENSMUSG00000036980	Taf6	80kDa|AW549759|TAF(II)80|TAFII70|Taf2e|p80	TATA-box binding protein associated factor 6	protein-coding
mm_35882.1	chr4	49538742	49538900	-	1	NA	exon (NM_144903, exon 7 of 9)	exon (NM_144903, exon 7 of 9)	10725	NM_144903	230163	Mm.482116	NM_144903	ENSMUSG00000028307	Aldob	Aldo-2|Aldo2|BC016435	aldolase B, fructose-bisphosphate	protein-coding
mm_42224.1	chr5	113489105	113489125	+	1	NA	Intergenic	MTEa|LTR|ERVL-MaLR	-61305	NM_177292	320916	Mm.102783	NM_177292	ENSMUSG00000063430	Wscd2	4933413A10Rik|C530024P05Rik|Gm450	WSC domain containing 2	protein-coding
mm_12046.1	chr2	59160839	59160881	+	1	NA	promoter-TSS (NM_026361)	promoter-TSS (NM_026361)	10	NM_175464	227937	Mm.260938	NM_026361	ENSMUSG00000026991	Pkp4	5031422I09Rik|9430019K17Rik|Armrp|p0071	plakophilin 4	protein-coding
mm_105547.1	chr11	106365524	106365528	-	1	NA	Intergenic	Intergenic	-9300	NM_029345	75573	Mm.159539	NM_029345	ENSMUSG00000009210	Prr29	2310007L24Rik	proline rich 29	protein-coding
mm_152743.1	chr19	19067589	19067629	-	1	NA	intron (NM_001043354, intron 1 of 9)	intron (NM_001043354, intron 1 of 9)	43587	NM_001043354	225998	Mm.234641	NM_146095	ENSMUSG00000036192	Rorb	Nr1f2|RZR-beta|RZRB|Rorbeta|hstp	RAR-related orphan receptor beta	protein-coding
mm_155004.1	chrX	41400688	41400700	+	1	NA	promoter-TSS (NM_001290451)	promoter-TSS (NM_001290451)	-607	NM_016886	53623	Mm.327681	NM_016886	ENSMUSG00000001986	Gria3	2900064I19Rik|GluA3|GluR-C|GluR-K3|Glur-3|Glur3|Gluralpha3	glutamate receptor, ionotropic, AMPA3 (alpha 3)	protein-coding
mm_114193.1	chr13	55784616	55784620	+	1	NA	promoter-TSS (NM_001252487)	promoter-TSS (NM_001252487)	39	NM_001252487	76856	Mm.159795	NM_029772	ENSMUSG00000021499	Catsper3	4921522D01Rik|CACRC	cation channel, sperm associated 3	protein-coding
mm_113392.1	chr13	33040362	33040371	+	1	NA	3' UTR (NM_011452, exon 7 of 7)	3' UTR (NM_011452, exon 7 of 7)	12952	NM_011452	20706	Mm.45371	NM_011452	ENSMUSG00000021403	Serpinb9b	1600019A21Rik|R86|SPI-CI|Spi10|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 9b	protein-coding
mm_54847.1	chr6	42589789	42589798	-	1	NA	exon (NM_203396, exon 6 of 7)	exon (NM_203396, exon 6 of 7)	7579	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_94534.1	chr11	9119224	9119230	+	1	NA	intron (NM_001159402, intron 1 of 8)	intron (NM_001159402, intron 1 of 8)	720	NM_001159402	22271	Mm.4610	NM_009477	ENSMUSG00000020407	Upp1	AI325217|UPase|UdRPase|Up|Upp	uridine phosphorylase 1	protein-coding
mm_165286.1	chr2	84937251	84937273	+	1	NA	intron (NM_021398, intron 1 of 12)	intron (NM_021398, intron 1 of 12)	616	NM_021398	58207	Mm.290729	NM_021398	ENSMUSG00000027074	Slc43a3	Eeg1|SEEEG-1	solute carrier family 43, member 3	protein-coding
mm_158607.1	chrX	152342420	152342430	-	1	NA	promoter-TSS (NM_029836)	promoter-TSS (NM_029836)	59	NM_029836	52808	Mm.9997	NM_029836	ENSMUSG00000041096	Tspyl2	CDA1|CINAP|DENTT|DXBwg1396e|DXHXS1008E|E130307F10Rik	TSPY-like 2	protein-coding
mm_171627.1	chr4	17218052	17218056	+	1	NA	Intergenic	L1Md_T|LINE|L1	-634839	NR_135158	17389	Mm.187315	NM_019724	ENSMUSG00000028226	Mmp16	MT-MMP 3|MT3-MMP|Mt3mmp	matrix metallopeptidase 16	protein-coding
mm_10717.1	chr2	22804644	22804656	+	1	NA	intron (NM_019456, intron 1 of 13)	intron (NM_019456, intron 1 of 13)	30323	NM_019456	54519	Mm.14255	NM_019456	ENSMUSG00000026786	Apbb1ip	9930118P07Rik|Prp48	amyloid beta (A4) precursor protein-binding, family B, member 1 interacting protein	protein-coding
mm_151769.1	chr19	5273081	5273129	-	1	NA	promoter-TSS (NM_153129)	promoter-TSS (NM_153129)	14	NM_153129	107975	Mm.234923	NM_153129	ENSMUSG00000024855	Pacs1	AI325977	phosphofurin acidic cluster sorting protein 1	protein-coding
mm_115407.1	chr13	114335073	114335076	+	1	NA	intron (NM_010887, intron 2 of 4)	intron (NM_010887, intron 2 of 4)	53020	NM_010887	17993	Mm.253142	NM_010887	ENSMUSG00000021764	Ndufs4	6720411N02Rik|C1-18k	NADH dehydrogenase (ubiquinone) Fe-S protein 4	protein-coding
mm_88506.1	chr10	77893057	77893089	+	1	NA	promoter-TSS (NR_015547)	promoter-TSS (NR_015547)	-347	NR_015547	75188	Mm.348012	NM_029200	ENSMUSG00000096573	1700009J07Rik	4930535B06Rik	RIKEN cDNA 1700009J07 gene	ncRNA
mm_4064.1	chr1	166126990	166127000	+	1	NA	intron (NM_001033344, intron 2 of 5)	intron (NM_001033344, intron 2 of 5)	903	NM_001033344	240892	Mm.35315	NM_001033344	ENSMUSG00000026564	Dusp27	C130085G02Rik|Gm209	dual specificity phosphatase 27 (putative)	protein-coding
mm_147933.1	chr18	66002613	66002637	-	1	NA	promoter-TSS (NM_027400)	promoter-TSS (NM_027400)	10	NM_027400	70361	Mm.290857	NM_027400	ENSMUSG00000041891	Lman1	2610020P13Rik|AI326273|AU043785|C730041J05|ERGIC53|F5F8D|MCFD1|MR60|P58|gp58	lectin, mannose-binding, 1	protein-coding
mm_37075.1	chr4	116164408	116164415	-	1	NA	exon (NM_133681, exon 3 of 8)	exon (NM_133681, exon 3 of 8)	3187	NM_133681	66805	Mm.45994	NM_133681	ENSMUSG00000028699	Tspan1	9030418M05Rik	tetraspanin 1	protein-coding
mm_131218.1	chr16	8837763	8837766	+	1	NA	intron (NM_001081400, intron 2 of 3)	B1_Mur1|SINE|Alu	7664	NM_001081400	69053	Mm.390868	NM_001081400	ENSMUSG00000022507	1810013L24Rik	1110017P05Rik|3010002C02Rik|AA792997|AW124177|Gm19906|R74903	RIKEN cDNA 1810013L24 gene	protein-coding
mm_123877.1	chr14	72669398	72669405	-	1	NA	intron (NM_207636, intron 2 of 25)	intron (NM_207636, intron 2 of 25)	40602	NM_207636	319448	Mm.205421	NM_207636	ENSMUSG00000033487	Fndc3a	1700094E19Rik|D14Ertd453e|F730017H24Rik|Fndc3|sys	fibronectin type III domain containing 3A	protein-coding
mm_89771.1	chr10	100099826	100099841	+	1	NA	3' UTR (NM_013598, exon 10 of 10)	3' UTR (NM_013598, exon 10 of 10)	84012	NM_013598	17311	Mm.45124	NM_013598	ENSMUSG00000019966	Kitl	Clo|Con|Gb|Kitlg|Mgf|SCF|SF|SLF|Sl|blz|contrasted	kit ligand	protein-coding
mm_6972.1	chr1	86308395	86308403	-	1	NA	Intergenic	Intergenic	5178	NM_145222	227327	Mm.86467	NM_145222	ENSMUSG00000079445	B3gnt7	C330001H22Rik|beta-3GnT7	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 7	protein-coding
mm_130691.1	chr15	100682061	100682071	-	1	NA	intron (NM_033612, intron 5 of 7)	B3A|SINE|B2	5854	NM_033612	109901	Mm.2131	NM_033612	ENSMUSG00000023031	Cela1	1810009A17Rik|1810062B19Rik|Ela-1|Ela1|PC-TsF	chymotrypsin-like elastase family, member 1	protein-coding
mm_76610.1	chr8	91124025	91124028	-	1	NA	TTS (NM_001282001)	TTS (NM_001282001)	10001	NM_001302337	14339	Mm.324588	NM_010241	ENSMUSG00000031667	Aktip	AL023020|Fif|Ft|Ft1|Fts	thymoma viral proto-oncogene 1 interacting protein	protein-coding
mm_42707.1	chr5	120172817	120172831	+	1	NA	intron (NM_028762, intron 21 of 23)	intron (NM_028762, intron 21 of 23)	-33561	NR_045793	100503427	Mm.446834	NR_045793	ENSMUSG00000097368	Gm10390	ENSMUSG00000072671	predicted gene 10390	ncRNA
mm_18740.1	chr2	73012911	73012926	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-32472	NM_001018042	20687	Mm.124328	NM_011450	ENSMUSG00000027109	Sp3	D130027J01Rik	trans-acting transcription factor 3	protein-coding
mm_147716.1	chr18	60812597	60812605	-	1	NA	TTS (NM_010545)	TTS (NM_010545)	525	NR_039567	100628611		NR_039567	ENSMUSG00000093327	Mir5107	mir-5107|mmu-mir-5107|mu-mir-5107	microRNA 5107	ncRNA
mm_85176.1	chr9	96525407	96525415	-	1	NA	Intergenic	Intergenic	-46736	NM_001311135	19823	Mm.28235	NM_011279	ENSMUSG00000051234	Rnf7	Rbx2|SAG	ring finger protein 7	protein-coding
mm_106995.1	chr12	11266485	11266523	+	1	NA	promoter-TSS (NM_177331)	promoter-TSS (NM_177331)	618	NM_025695	67241	Mm.173953	NM_025695	ENSMUSG00000020608	Smc6	2810489L22Rik|3830418C19Rik|AA990493|AU018782|AW742439|SMC-6|Smc6l1|mKIAA4103	structural maintenance of chromosomes 6	protein-coding
mm_55161.1	chr6	51864351	51864392	-	1	NA	intron (NM_018773, intron 11 of 12)	intron (NM_018773, intron 11 of 12)	148178	NM_018773	54353	Mm.221479	NM_018773	ENSMUSG00000059182	Skap2	2610021A10Rik|AA960083|BB137539|RA70|SKAP-HOM|Saps|Scap2|mSKAP55R	src family associated phosphoprotein 2	protein-coding
mm_38823.1	chr4	148751820	148751836	-	1	NA	Intergenic	Intergenic	-52564	NM_001159344	69743	Mm.233879	NM_027195	ENSMUSG00000028977	Casz1	2410019P08Rik|AV096627|BC040081|Cst|D4Ertd432e	castor zinc finger 1	protein-coding
mm_125814.1	chr15	74932257	74932278	+	1	NA	Intergenic	RLTR6-int|LTR|ERV1	-22784	NM_001164039	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_121895.1	chr14	21751376	21751384	-	1	NA	intron (NM_026283, intron 1 of 5)	intron (NM_026283, intron 1 of 5)	849	NM_026283	67630	Mm.102765	NM_026283	ENSMUSG00000021770	Samd8	1110053F04Rik|1700010P07Rik|SMSr	sterile alpha motif domain containing 8	protein-coding
mm_85110.1	chr9	95407109	95407119	-	1	NA	5' UTR (NM_018763, exon 1 of 2)	5' UTR (NM_018763, exon 1 of 2)	156	NM_018763	54371	Mm.212446	NM_018763	ENSMUSG00000033350	Chst2	AI428561|AW121776|C130041E03Rik|Chts2|GST-2|GlcNAc6ST|Gn6st	carbohydrate sulfotransferase 2	protein-coding
mm_37425.1	chr4	122886008	122886018	-	1	NA	promoter-TSS (NM_007598)	promoter-TSS (NM_007598)	44	NM_007598	12331	Mm.8687	NM_007598	ENSMUSG00000028656	Cap1	-	CAP, adenylate cyclase-associated protein 1 (yeast)	protein-coding
mm_28880.1	chr3	97779263	97779266	-	1	NA	intron (NM_001039376, intron 8 of 46)	intron (NM_001039376, intron 8 of 46)	-11250	NM_178080	83679	Mm.129840	NM_031401	ENSMUSG00000038170	Pde4dip	4732458A06Rik|9430063L05Rik|C87016|D130016K21Rik|D3Bwg1078e|Usmg4|mKIAA0454	phosphodiesterase 4D interacting protein (myomegalin)	protein-coding
mm_121294.1	chr14	105339877	105339887	+	1	NA	Intergenic	Intergenic	81209	NM_001190989	76273	Mm.290669	NM_029561	ENSMUSG00000053253	Ndfip2	0710001O20Rik|2810436B12Rik|9130207N19Rik|N4wbp5a|mKIAA1165	Nedd4 family interacting protein 2	protein-coding
mm_19097.1	chr2	79451924	79451962	-	1	NA	TTS (NM_010894)	TTS (NM_010894)	4693	NM_010894	18012	Mm.4636	NM_010894	ENSMUSG00000034701	Neurod1	BETA2|BHF-1|Nd1|Neurod|bHLHa3	neurogenic differentiation 1	protein-coding
mm_153611.1	chr19	43968670	43968698	-	1	NA	intron (NM_030703, intron 4 of 8)	intron (NM_030703, intron 4 of 8)	17836	NM_030703	93721	Mm.206774	NM_030703	ENSMUSG00000025196	Cpn1	0610011F20Rik|CPN	carboxypeptidase N, polypeptide 1	protein-coding
mm_159085.1	chr2	30002346	30002346	+	1	NA	exon (NM_001177668, exon 23 of 56)	exon (NM_001177668, exon 23 of 56)	6396	NR_105963	102465603		NR_105963	ENSMUSG00000098453	Mir6997	Gm27310|mmu-mir-6997	microRNA 6997	ncRNA
mm_126802.1	chr15	87624259	87624291	+	1	NA	promoter-TSS (NM_134096)	promoter-TSS (NM_134096)	-955	NM_134096	106014	Mm.244319	NM_134096	ENSMUSG00000054863	Fam19a5	TAFA5|Tafa-5|Tara-5	family with sequence similarity 19, member A5	protein-coding
mm_126728.1	chr15	85634843	85634857	+	1	NA	Intergenic	CpG	-53029	NM_009528	22422	Mm.306946	NM_009528	ENSMUSG00000022382	Wnt7b	Wnt-7b	wingless-type MMTV integration site family, member 7B	protein-coding
mm_171573.1	chr4	147361510	147361510	+	1	NA	intron (NM_001039209, intron 1 of 2)	intron (NM_001039209, intron 1 of 2)	185644	NM_001039209	195531	Mm.270762	NM_001039209	ENSMUSG00000078496	Zfp982	Gm13152|OTTMUSG00000010671	zinc finger protein 982	protein-coding
mm_17832.1	chr2	34262888	34262890	-	1	NA	intron (NM_016768, intron 2 of 8)	intron (NM_016768, intron 2 of 8)	109156	NM_001290576	18516	Mm.239941	NM_016768	ENSMUSG00000038718	Pbx3	-	pre B cell leukemia homeobox 3	protein-coding
mm_136813.1	chr17	12393165	12393174	+	1	NA	exon (NM_008877, exon 7 of 19)	exon (NM_008877, exon 7 of 19)	14560	NM_008877	18815	Mm.971	NM_008877	ENSMUSG00000059481	Plg	AI649309|Pg	plasminogen	protein-coding
mm_7871.1	chr1	132707340	132707351	-	1	NA	promoter-TSS (NM_001160318)	promoter-TSS (NM_001160318)	-19	NM_001160318	269116	Mm.326702	NM_182716	ENSMUSG00000026442	Nfasc	AA387016|D430023G06Rik|NF|mKIAA0756	neurofascin	protein-coding
mm_55521.1	chr6	70407019	70407023	-	1	NA	Intergenic	Intergenic	385154	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_122905.1	chr14	54953515	54953539	-	1	NA	exon (NM_010856, exon 22 of 39)	exon (NM_010856, exon 22 of 39)	-4385	NR_029724	387204		NR_029724	ENSMUSG00000065432	Mir208a	Mirn208|Mirn208a|mir-208|mir-208a|mmu-mir-208	microRNA 208a	ncRNA
mm_131379.1	chr16	13986597	13986665	+	1	NA	promoter-TSS (NM_144518)	promoter-TSS (NM_144518)	-6	NM_144518	67254	Mm.216217	NM_144518	ENSMUSG00000044117	2900011O08Rik	MINP	RIKEN cDNA 2900011O08 gene	protein-coding
mm_58503.1	chr7	3712658	3712666	+	1	NA	exon (NM_011095, exon 15 of 15)	exon (NM_011095, exon 15 of 15)	7720	NM_011095	18733	Mm.326531	NM_011095	ENSMUSG00000058818	Pirb	Gp91|LIR-3|Lilrb3|PIR-B	paired Ig-like receptor B	protein-coding
mm_128276.1	chr15	36794499	36794544	-	1	NA	promoter-TSS (NM_011740)	promoter-TSS (NM_011740)	17	NM_011740	22631	Mm.3360	NM_011740	ENSMUSG00000022285	Ywhaz	1110013I11Rik|14-3-3zeta|AI596267|AL022924|AU020854	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide	protein-coding
mm_8455.1	chr1	153140999	153141003	-	1	NA	intron (NM_008485, intron 12 of 23)	intron (NM_008485, intron 12 of 23)	45446	NM_008485	16782	Mm.329272	NM_008485	ENSMUSG00000026479	Lamc2	AA589349	laminin, gamma 2	protein-coding
mm_4191.1	chr1	171221775	171221785	+	1	NA	5' UTR (NM_001305585, exon 1 of 4)	5' UTR (NM_001305585, exon 1 of 4)	216	NM_001305585	11807	Mm.389209	NM_013474	ENSMUSG00000005681	Apoa2	Alp-2|Apo-AII|ApoA-II|ApoAII|Apoa-2|Hdl-1	apolipoprotein A-II	protein-coding
mm_84127.1	chr9	58869434	58869456	-	1	NA	Intergenic	L1M4|LINE|L1	45933	NM_001081192	330953	Mm.151967	NM_001081192	ENSMUSG00000032338	Hcn4	Bcng3|Hcn3	hyperpolarization-activated, cyclic nucleotide-gated K+ 4	protein-coding
mm_97504.1	chr11	78465668	78465689	+	1	NA	promoter-TSS (NM_026740)	promoter-TSS (NM_026740)	-23	NM_026740	52466	Mm.131618	NM_026740	ENSMUSG00000020829	Slc46a1	1110002C08Rik|D11Ertd18e|HCP1|Pcft	solute carrier family 46, member 1	protein-coding
mm_164940.1	chr19	3377632	3377641	+	1	NA	intron (NM_013495, intron 14 of 18)	intron (NM_013495, intron 14 of 18)	-11221	NM_001039658	17771	Mm.209941	NM_010841	ENSMUSG00000024905	Mtl5	tesmin	metallothionein-like 5, testis-specific (tesmin)	protein-coding
mm_79643.1	chr9	59559370	59559383	+	1	NA	exon (NM_010421, exon 7 of 14)	exon (NM_010421, exon 7 of 14)	-18961	NM_175235	76183	Mm.265415	NM_175235	ENSMUSG00000032297	Celf6	6330569O16Rik|Brunol6	CUGBP, Elav-like family member 6	protein-coding
mm_114641.1	chr13	76579590	76579622	+	1	NA	intron (NM_030174, intron 1 of 20)	intron (NM_030174, intron 1 of 20)	194645	NM_030174	78771	Mm.316249	NM_030174	ENSMUSG00000021596	Mctp1	2810465F10Rik	multiple C2 domains, transmembrane 1	protein-coding
mm_143375.1	chr17	67632731	67632748	-	1	NA	promoter-TSS (NM_001033340)	promoter-TSS (NM_001033340)	-16	NM_001033340	240131	Mm.295736	NM_001033340	ENSMUSG00000073375	Lrrc30	Gm326	leucine rich repeat containing 30	protein-coding
mm_109859.1	chr12	4841538	4841580	-	1	NA	promoter-TSS (NM_016863)	promoter-TSS (NM_016863)	36	NM_016863	14226	Mm.20453	NM_016863	ENSMUSG00000020635	Fkbp1b	12.6kDa|AW494148|FKBP12.6|calstabin2	FK506 binding protein 1b	protein-coding
mm_110212.1	chr12	28582539	28582559	-	1	NA	promoter-TSS (NM_053156)	promoter-TSS (NM_053156)	-66	NM_053156	94041	Mm.84927	NM_053156	ENSMUSG00000020636	Allc	1700012B22Rik|Alc	allantoicase	protein-coding
mm_26696.1	chr3	157534352	157534411	+	1	NA	promoter-TSS (NM_017381)	promoter-TSS (NM_017381)	-16	NM_017381	53861	Mm.259036	NM_017381	ENSMUSG00000028180	Zranb2	AI227013|Zfp265|Zis|Znf265	zinc finger, RAN-binding domain containing 2	protein-coding
mm_59579.1	chr7	28129143	28129182	+	1	NA	promoter-TSS (NM_001164655)	promoter-TSS (NM_001164655)	-304	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_65517.1	chr7	25755257	25755276	-	1	NA	promoter-TSS (NM_178089)	promoter-TSS (NM_178089)	-546	NM_144922	232989	Mm.254223	NM_144922	ENSMUSG00000040725	Hnrnpul1	E130317O14Rik|E1B-AP5|E1BAP5|Hnrnpul|Hnrpul1	heterogeneous nuclear ribonucleoprotein U-like 1	protein-coding
mm_86214.1	chr9	120012861	120012879	-	1	NA	TTS (NM_011724)	TTS (NM_011724)	10728	NM_011724	22437	Mm.10117	NM_011724	ENSMUSG00000079243	Xirp1	AI415219|Cmya1	xin actin-binding repeat containing 1	protein-coding
mm_39148.1	chr4	155397982	155397997	-	1	NA	promoter-TSS (NM_008072)	promoter-TSS (NM_008072)	80	NM_008072	14403	Mm.388925	NM_008072	ENSMUSG00000029054	Gabrd	AI853201	gamma-aminobutyric acid (GABA) A receptor, subunit delta	protein-coding
mm_148687.1	chr19	5724813	5724829	+	1	NA	intron (NM_001114595, intron 1 of 17)	intron (NM_001114595, intron 1 of 17)	1496	NM_001114595	114601	Mm.210447	NM_053252	ENSMUSG00000024937	Ehbp1l1	G430002G23Rik	EH domain binding protein 1-like 1	protein-coding
mm_133143.1	chr16	70225011	70225025	+	1	NA	Intergenic	RMER17A|LTR|ERVK	-88931	NM_028803	74185	Mm.396102	NM_028803	ENSMUSG00000022707	Gbe1	2310045H19Rik|2810426P10Rik|D16Ertd536e	glucan (1,4-alpha-), branching enzyme 1	protein-coding
mm_170035.1	chr17	22739880	22739880	-	1	NA	Intergenic	Intergenic	77867	NR_030709	100042679	Mm.484007	NR_030709		Gm16386	EG545191|ENSMUSG00000073442|Gm21017	zinc finger protein 946 pseudogene	pseudo
mm_9611.1	chr1	176213770	176213779	-	1	NA	5' UTR (NM_001195816, exon 1 of 10)	5' UTR (NM_001195816, exon 1 of 10)	168	NM_001195816	319455	Mm.338001	NM_176916	ENSMUSG00000055214	Pld5	B230365F16Rik	phospholipase D family, member 5	protein-coding
mm_148523.1	chr19	4396485	4396497	+	1	NA	5' UTR (NM_001001984, exon 1 of 21)	5' UTR (NM_001001984, exon 1 of 21)	586	NM_001001984	225876	Mm.31941	NM_001001984	ENSMUSG00000054611	Kdm2a	100043628|5530401A10Rik|AA589516|AW536790|Cxxc8|Fbl11|Fbl7|Fbxl11|Gm4560|Jhdm1|Jhdm1a|lalina	lysine (K)-specific demethylase 2A	protein-coding
mm_32.1	chr1	6222704	6222707	+	1	NA	intron (NM_009826, intron 1 of 23)	intron (NM_009826, intron 1 of 23)	8043	NM_009826	12421	Mm.293811	NM_009826	ENSMUSG00000025907	Rb1cc1	2900055E04Rik|5930404L04Rik|Cc1|FIP200|LaXp180	RB1-inducible coiled-coil 1	protein-coding
mm_115137.1	chr13	104623458	104623460	+	1	NA	Intergenic	Intergenic	193494	NM_026072	67285	Mm.235398	NM_026072	ENSMUSG00000021715	Cwc27	3110009E13Rik|NY-CO-10|Sdccag10	CWC27 spliceosome-associated protein	protein-coding
mm_158576.1	chrX	150654868	150654912	-	1	NA	exon (NM_019548, exon 3 of 14)	exon (NM_019548, exon 3 of 14)	2546	NM_019548	56191	Mm.3597	NM_019548	ENSMUSG00000025272	Tro	AA409408|Maged3|Maged3l|Tnn|Trol|magphinin	trophinin	protein-coding
mm_157791.1	chrX	73854469	73854487	-	1	NA	3' UTR (NM_008478, exon 29 of 29)	3' UTR (NM_008478, exon 29 of 29)	26356	NM_008478	16728	Mm.260568	NM_008478	ENSMUSG00000031391	L1cam	CD171|L1|N-CAM-L1|NCAM-L1	L1 cell adhesion molecule	protein-coding
mm_145086.1	chr18	42511497	42511521	+	1	NA	promoter-TSS (NM_001289526)	promoter-TSS (NM_001289526)	22	NR_110344	56070	Mm.270511	NM_001039474	ENSMUSG00000024498	Tcerg1	2410022J09Rik|2900090C16Rik|AI428505|CA150b|FBP23|FBP28|Taf2s|ca150|p144	transcription elongation regulator 1 (CA150)	protein-coding
mm_23082.1	chr3	36861996	36862011	+	1	NA	Intergenic	Intergenic	-1103	NM_172679	229227	Mm.207907	NM_172679	ENSMUSG00000037270	4932438A13Rik	4732443H21|B830039D19Rik|D630029K19Rik|FSA|Kiaa1109|Tweek	RIKEN cDNA 4932438A13 gene	protein-coding
mm_47329.1	chr5	122491753	122491767	-	1	NA	exon (NM_009722, exon 4 of 21)	exon (NM_009722, exon 4 of 21)	10465	NM_001110140	11938	Mm.227583	NM_009722	ENSMUSG00000029467	Atp2a2	9530097L16Rik|D5Wsu150e|SERCA2|SERCA2B|Serca2a|mKIAA4195	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	protein-coding
mm_71409.1	chr8	46471720	46471785	+	1	NA	intron (NM_007981, intron 1 of 20)	intron (NM_007981, intron 1 of 20)	715	NM_007981	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_165884.1	chr4	42875001	42875002	-	1	NA	promoter-TSS (NM_177785)	promoter-TSS (NM_177785)	-798	NM_177785	277773	Mm.212727	NM_177785	ENSMUSG00000050141	Fam205c	4931430D02|FAM205CP	family with sequence similarity 205, member C	protein-coding
mm_35629.1	chr4	43483697	43483730	-	1	NA	promoter-TSS (NM_019436)	promoter-TSS (NM_019436)	-4	NM_019436	54390	Mm.31775	NM_019436	ENSMUSG00000028460	Sit1	Sit	suppression inducing transmembrane adaptor 1	protein-coding
mm_13296.1	chr2	102039617	102039636	+	1	NA	intron (NM_001290784, intron 4 of 5)	intron (NM_001290784, intron 4 of 5)	146834	NM_178886	241576	Mm.489740	NM_178886	ENSMUSG00000048058	Ldlrad3	6430500P08|AI194318|Lrad3	low density lipoprotein receptor class A domain containing 3	protein-coding
mm_51121.1	chr6	68036789	68036813	+	1	NA	Intergenic	Intergenic	-471102	NR_003100	75070	Mm.463364	NR_003100		4930515G16Rik	-	myc induced nuclear antigen pseudogene	pseudo
mm_39042.1	chr4	152418751	152418761	-	1	NA	intron (NM_001252654, intron 2 of 14)	intron (NM_001252654, intron 2 of 14)	30099	NM_001252655	16498	Mm.388924	NM_010598	ENSMUSG00000028931	Kcnab2	F5|I2rf5|Kcnb3|kv-beta-2	potassium voltage-gated channel, shaker-related subfamily, beta member 2	protein-coding
mm_61771.1	chr7	83408932	83408936	+	1	NA	Intergenic	MT2B1|LTR|ERVL	-175997	NM_177695	233424	Mm.486619	NM_177695	ENSMUSG00000038540	Tmc3	9030203A06	transmembrane channel-like gene family 3	protein-coding
mm_12492.1	chr2	71787015	71787045	+	1	NA	promoter-TSS (NM_008397)	promoter-TSS (NM_008397)	91	NM_001277970	16403	Mm.225096	NM_008397	ENSMUSG00000027111	Itga6	5033401O05Rik|AI115430|Cd49f|VLA-6	integrin alpha 6	protein-coding
mm_95322.1	chr11	46454958	46454984	+	1	NA	promoter-TSS (NM_134250)	promoter-TSS (NM_134250)	40	NM_134250	171285	Mm.72168	NM_134250	ENSMUSG00000020399	Havcr2	TIM-3|Tim3|Timd3	hepatitis A virus cellular receptor 2	protein-coding
mm_60045.1	chr7	31059643	31059657	+	1	NA	promoter-TSS (NM_144556)	promoter-TSS (NM_144556)	-285	NM_144556	243914	Mm.389870	NM_144556	ENSMUSG00000036560	Lgi4	Lgil3|clp	leucine-rich repeat LGI family, member 4	protein-coding
mm_46699.1	chr5	110108278	110108287	-	1	NA	promoter-TSS (NM_145147)	promoter-TSS (NM_145147)	-85	NM_145147	107999	Mm.86267	NM_145147	ENSMUSG00000033434	Gtpbp6	AV119224|Pgbpll|pgpl	GTP binding protein 6 (putative)	protein-coding
mm_48304.1	chr5	138279961	138280016	-	1	NA	promoter-TSS (NM_016964)	promoter-TSS (NM_016964)	-51	NM_172412	71951	Mm.77066	NM_172412	ENSMUSG00000029510	Gpc2	2410016G05Rik	glypican 2 (cerebroglycan)	protein-coding
mm_127699.1	chr15	102990916	102990925	+	1	NA	exon (NM_010466, exon 1 of 2)	exon (NM_010466, exon 1 of 2)	381	NM_010466	15426	Mm.6167	NM_010466	ENSMUSG00000001657	Hoxc8	D130011F21Rik|Hox-3.1	homeobox C8	protein-coding
mm_64332.1	chr7	142283255	142283265	+	1	NA	Intergenic	ERVB4_1C-LTR_Mm|LTR|ERVK	-8897	NM_001199309	100043627	Mm.388589	NM_001199309	ENSMUSG00000056885	Gm4559	-	predicted gene 4559	protein-coding
mm_167197.1	chr7	142661081	142661084	-	1	NA	5' UTR (NM_001122736, exon 1 of 4)	intron (NR_002855, intron 1 of 3)	189	NM_001122736	16002	Mm.3862	NM_010514	ENSMUSG00000048583	Igf2	AL033362|Igf-2|Igf-II|M6pr|Mpr|Peg2	insulin-like growth factor 2	protein-coding
mm_49785.1	chr6	35177842	35177860	+	1	NA	intron (NM_027513, intron 1 of 42)	CpG	235	NM_027513	70699	Mm.261208	NM_027513	ENSMUSG00000038759	Nup205	3830404O05Rik|AV248391|mKIAA0225	nucleoporin 205	protein-coding
mm_78330.1	chr9	25252590	25252591	+	1	NA	5' UTR (NM_001205367, exon 1 of 13)	5' UTR (NM_001205367, exon 1 of 13)	151	NM_001205367	235072	Mm.270259	NM_009859	ENSMUSG00000001833	Sept7	Cdc10|E430034N22	septin 7	protein-coding
mm_86984.1	chr10	25441796	25441810	+	1	NA	exon (NM_013511, exon 2 of 20)	exon (NM_013511, exon 2 of 20)	33435	NM_013511	13822	Mm.306026	NM_013511	ENSMUSG00000019978	Epb41l2	4.1G|AW555191|D10Ertd398e|Epb4.1l2|NBL2	erythrocyte membrane protein band 4.1 like 2	protein-coding
mm_73244.1	chr8	104250926	104250940	+	1	NA	promoter-TSS (NR_104433)	promoter-TSS (NR_104433)	72	NM_001286383	75458	Mm.269219	NM_029295	ENSMUSG00000054400	Cklf	1700001C14Rik|1810018M11Rik|A730028G07Rik|C32|CKLF1|CKLF3|CKLF4|CKLF5|Cklf2|Cklf6|HSPC224|UCK-1	chemokine-like factor	protein-coding
mm_945.1	chr1	56972556	56972589	+	1	NA	non-coding (NR_024325, exon 1 of 1)	non-coding (NR_024325, exon 1 of 1)	1103	NR_024325	329160	Mm.419039	NR_024325	ENSMUSG00000087022	9130024F11Rik	B530002L08|EG329160	RIKEN cDNA 9130024F11 gene	ncRNA
mm_86520.1	chr10	7726682	7726694	+	1	NA	intron (NM_011835, intron 1 of 10)	intron (NM_011835, intron 1 of 10)	688	NM_011835	23924	Mm.28127	NM_011835	ENSMUSG00000019794	Katna1	-	katanin p60 (ATPase-containing) subunit A1	protein-coding
mm_97470.1	chr11	78301580	78301606	+	1	NA	promoter-TSS (NM_017407)	promoter-TSS (NM_017407)	2	NM_017407	54141	Mm.24250	NM_017407	ENSMUSG00000002055	Spag5	AI874642|D11Bhm180e|Deepest|MAP126|Mastrin|S17	sperm associated antigen 5	protein-coding
mm_93223.1	chr10	95232707	95232709	-	1	NA	intron (NM_009950, intron 2 of 2)	intron (NM_009950, intron 2 of 2)	-86883	NR_131146	628062		NR_131146		Gm29684	-	predicted gene, 29684	ncRNA
mm_158585.1	chrX	150813638	150813712	-	1	NA	promoter-TSS (NM_001199246)	promoter-TSS (NM_001199246)	28	NM_001199246	80884	Mm.22575	NM_030700	ENSMUSG00000025268	Maged2	4833439A22Rik|Mage-d2|ORF1	melanoma antigen, family D, 2	protein-coding
mm_132408.1	chr16	35022451	35022479	+	1	NA	promoter-TSS (NM_023587)	promoter-TSS (NM_023587)	44	NM_023587	70757	Mm.27286	NM_023587	ENSMUSG00000035376	Hacd2	6330408J20Rik|AI255777|AI481689|Hcad2|Ptplb	3-hydroxyacyl-CoA dehydratase 2	protein-coding
mm_93141.1	chr10	92165132	92165156	-	1	NA	promoter-TSS (NR_028262)	promoter-TSS (NR_028262)	34	NR_028262	110333	Mm.429764	NR_028262		Rmst	100041799|AI853140|C230053E11Rik|D930049J19Rik|Dmt2|Gm3515|M2|Ncrms	rhabdomyosarcoma 2 associated transcript (non-coding RNA)	ncRNA
mm_80158.1	chr9	70956689	70956696	+	1	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	-4471	NM_001324472	15450	Mm.390187	NM_008280	ENSMUSG00000032207	Lipc	AI256194|HL|Hpl	lipase, hepatic	protein-coding
mm_154457.1	chrM	2467	2504	-	1	NA	NA	Intergenic	NA	NA								
mm_88815.1	chr10	80798631	80798642	+	1	NA	promoter-TSS (NM_013651)	promoter-TSS (NM_013651)	-10	NM_023900	78670	Mm.41479	NM_023900	ENSMUSG00000035278	Plekhj1	9530063M10Rik	pleckstrin homology domain containing, family J member 1	protein-coding
mm_64840.1	chr7	12998173	12998210	-	1	NA	promoter-TSS (NM_009512)	promoter-TSS (NM_009512)	1	NM_009512	26459	Mm.10984	NM_009512	ENSMUSG00000030382	Slc27a5	FACVL3|FATP5|VLCS-H2|VLCSH2|Vlacsr	solute carrier family 27 (fatty acid transporter), member 5	protein-coding
mm_23977.1	chr3	85971222	85971236	+	1	NA	Intergenic	CpG	31262	NM_001001650	368202	Mm.253822	NM_001001650	ENSMUSG00000049013	Prss48	Esspl|Gm1019	protease, serine 48	protein-coding
mm_59161.1	chr7	24381649	24381688	+	1	NA	exon (NM_001163510, exon 5 of 9)	exon (NM_001163510, exon 5 of 9)	11405	NM_008433	16534	Mm.9911	NM_008433	ENSMUSG00000054342	Kcnn4	IK1|IKCA1|KCA4|KCa3.1|SK4|SKCas|mIKCa1	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4	protein-coding
mm_57588.1	chr6	127768776	127768790	-	1	NA	5' UTR (NM_201371, exon 1 of 10)	5' UTR (NM_201371, exon 1 of 10)	376	NM_201371	381813	Mm.39750	NM_201371	ENSMUSG00000030350	Prmt8	Hrmt1l3|Hrmt1l4	protein arginine N-methyltransferase 8	protein-coding
mm_14634.1	chr2	136781590	136781607	+	1	NA	3' UTR (NM_001291056, exon 8 of 8)	3' UTR (NM_001291056, exon 8 of 8)	68148	NM_001291056	20614	Mm.45953	NM_011428	ENSMUSG00000027273	Snap25	Bdr|GENA70|SNAP-25|SUP|sp	synaptosomal-associated protein 25	protein-coding
mm_165769.1	chr3	121589379	121589390	-	1	NA	Intergenic	Intergenic	54101	NR_036456	100503044	Mm.65320	NM_176992	ENSMUSG00000044522	A730020M07Rik	-	RIKEN cDNA A730020M07 gene	ncRNA
mm_161205.1	chr13	58610876	58610876	-	1	NA	promoter-TSS (NM_022317)	promoter-TSS (NM_022317)	1	NM_022317	114304	Mm.18188	NM_022317	ENSMUSG00000021553	Slc28a3	Cnt3	solute carrier family 28 (sodium-coupled nucleoside transporter), member 3	protein-coding
mm_112505.1	chr13	8885606	8885626	+	1	NA	promoter-TSS (NM_145360)	promoter-TSS (NM_145360)	10	NM_145360	319554	Mm.29847	NM_145360	ENSMUSG00000058258	Idi1	4832416K17Rik	isopentenyl-diphosphate delta isomerase	protein-coding
mm_166723.1	chr6	120471931	120471971	+	1	NA	intron (NM_008359, intron 1 of 12)	intron (NM_008359, intron 1 of 12)	8754	NM_008359	16172	Mm.4481	NM_008359	ENSMUSG00000002897	Il17ra	AW538159|Cdw217|Il17r|VDw217	interleukin 17 receptor A	protein-coding
mm_148839.1	chr19	6363947	6363960	+	1	NA	non-coding (NR_122118, exon 1 of 12)	non-coding (NR_122118, exon 1 of 12)	263	NR_122118	22668	Mm.256422	NM_011750	ENSMUSG00000024949	Sf1	BBP|MZFM|WBP4|Zfp162	splicing factor 1	protein-coding
mm_168320.1	chr11	114668565	114668567	+	1	NA	promoter-TSS (NM_001048058)	promoter-TSS (NM_001048058)	23	NM_001048057	67671	Mm.238817	NM_023372	ENSMUSG00000057322	Rpl38	0610025G13Rik|Rbt|Ts|Tss	ribosomal protein L38	protein-coding
mm_100072.1	chr11	115440516	115440524	+	1	NA	promoter-TSS (NM_001033775)	promoter-TSS (NM_001033775)	-25	NM_001033775	432613	Mm.308822	NM_001033775	ENSMUSG00000070332	Trim80	4933422H20Rik|Trim47l	tripartite motif-containing 80	protein-coding
mm_115238.1	chr13	109926888	109926913	+	1	NA	intron (NM_011056, intron 8 of 16)	intron (NM_011056, intron 8 of 16)	23091	NR_035442	100316683		NR_035442	ENSMUSG00000084651	Mir1904	Mirn1904|mmu-mir-1904	microRNA 1904	ncRNA
mm_116915.1	chr13	55512340	55512352	-	1	NA	exon (NM_001114088, exon 2 of 13)	exon (NM_001114088, exon 2 of 13)	1100	NM_026131	67399	Mm.275648	NM_026131	ENSMUSG00000021493	Pdlim7	LMP	PDZ and LIM domain 7	protein-coding
mm_172541.1	chr7	96817475	96817485	-	1	NA	intron (NM_001310760, intron 17 of 32)	intron (NM_001310760, intron 17 of 32)	-15931	NR_045874	791381	Mm.402112	NR_045874	ENSMUSG00000053049	Gm15413	ENSMUSG00000053049|OTTMUSG00000021246	predicted gene 15413	ncRNA
mm_100834.1	chr11	5541769	5541774	-	1	NA	intron (NM_134033, intron 1 of 4)	CpG	446	NM_134033	104479	Mm.210403	NM_134033	ENSMUSG00000020482	Ccdc117	1110004K02Rik|1700026O03Rik|AU018638|AU042822|AV173073|BC018601	coiled-coil domain containing 117	protein-coding
mm_1473.1	chr1	70217303	70217305	+	1	NA	intron (NM_029160, intron 11 of 16)	intron (NM_029160, intron 11 of 16)	265689	NM_025728	66722	Mm.440554	NM_025728	ENSMUSG00000053153	Spag16	4921511D23Rik|4930524F24Rik|4930585K05Rik|AV261009|Pf20|Wdr29	sperm associated antigen 16	protein-coding
mm_124698.1	chr15	6439331	6439348	+	1	NA	3' UTR (NM_001102400, exon 13 of 13)	3' UTR (NM_001102400, exon 13 of 13)	-5994	NM_013485	12279	Mm.29095	NM_013485	ENSMUSG00000022149	C9	-	complement component 9	protein-coding
mm_84925.1	chr9	81633443	81633447	-	1	NA	promoter-TSS (NM_010482)	promoter-TSS (NM_010482)	-893	NM_010482	15551	Mm.445308	NM_010482	ENSMUSG00000049511	Htr1b	-	5-hydroxytryptamine (serotonin) receptor 1B	protein-coding
mm_14415.1	chr2	130406505	130406532	+	1	NA	promoter-TSS (NM_025753)	promoter-TSS (NM_025753)	-4	NM_025753	66766	Mm.174834	NM_025753	ENSMUSG00000049692	Tmem239	4933425O20Rik	transmembrane 239	protein-coding
mm_113627.1	chr13	41677201	41677211	+	1	NA	Intergenic	Intergenic	26444	NM_001145878	328231	Mm.227476	NM_177808	ENSMUSG00000054258	Gm5082	A030008J09|EG328231	predicted gene 5082	protein-coding
mm_63229.1	chr7	126447906	126447914	+	1	NA	exon (NM_007504, exon 17 of 23)	exon (NM_007504, exon 17 of 23)	15163	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_45715.1	chr5	84417299	84417309	-	1	NA	promoter-TSS (NM_007937)	promoter-TSS (NM_007937)	78	NM_007937	13839	Mm.137991	NM_007937	ENSMUSG00000029245	Epha5	AI854630|AW125296|Cek7|Ehk1|Els1|Hek7|Rek7|bsk	Eph receptor A5	protein-coding
mm_149634.1	chr19	17354978	17354988	+	1	NA	intron (NM_010265, intron 1 of 2)	intron (NM_010265, intron 1 of 2)	1684	NM_173442	14537	Mm.244825	NM_010265	ENSMUSG00000038843	Gcnt1	5630400D21Rik|B130048E03|C2 GlcNAcT|C2GNT|IGnT	glucosaminyl (N-acetyl) transferase 1, core 2	protein-coding
mm_5367.1	chr1	28780251	28780252	-	1	NA	promoter-TSS (NM_001013750)	promoter-TSS (NM_001013750)	1	NM_001013750	210962	Mm.214178	NM_001013750	ENSMUSG00000048411	Gm597	-	predicted gene 597	protein-coding
mm_55151.1	chr6	51467820	51467821	-	1	NA	intron (NR_104468, intron 1 of 10)	intron (NR_104468, intron 1 of 10)	2074	NM_182650	53379	Mm.155896	NM_016806	ENSMUSG00000004980	Hnrnpa2b1	9130414A06Rik|Hnrpa2|Hnrpa2b1|hnrnp-A	heterogeneous nuclear ribonucleoprotein A2/B1	protein-coding
mm_141656.1	chr17	33713373	33713390	-	1	NA	intron (NR_045522, intron 1 of 6)	intron (NR_045522, intron 1 of 6)	5296	NM_145486	224703	Mm.311439	NM_145486	ENSMUSG00000079557	March2	9530046H09Rik|MARCH-II	membrane-associated ring finger (C3HC4) 2	protein-coding
mm_72304.1	chr8	76902278	76902376	+	1	NA	promoter-TSS (NM_001083906)	promoter-TSS (NM_001083906)	-181	NM_001083906	110784	Mm.324393	NM_001083906	ENSMUSG00000031618	Nr3c2	MR|Mlr	nuclear receptor subfamily 3, group C, member 2	protein-coding
mm_111770.1	chr12	104035811	104035820	-	1	NA	exon (NM_026535, exon 3 of 5)	exon (NM_026535, exon 3 of 5)	8628	NM_026535	68054	Mm.20286	NM_026535	ENSMUSG00000041567	Serpina12	4632419J12Rik	serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 12	protein-coding
mm_43498.1	chr5	136967910	136967924	+	1	NA	promoter-TSS (NM_021719)	promoter-TSS (NM_021719)	48	NM_021719	60363	Mm.87202	NM_021719	ENSMUSG00000001739	Cldn15	2210009B08Rik|BB107105	claudin 15	protein-coding
mm_19595.1	chr2	102385579	102385581	-	1	NA	intron (NM_020267, intron 1 of 4)	Lx8|LINE|L1	15320	NM_020267	80985	Mm.315002	NM_020267	ENSMUSG00000027189	Trim44	Dipb|Mc7	tripartite motif-containing 44	protein-coding
mm_44939.1	chr5	36398091	36398149	-	1	NA	promoter-TSS (NM_030889)	promoter-TSS (NM_030889)	19	NM_030889	81840	Mm.34113	NM_030889	ENSMUSG00000029093	Sorcs2	N28137|mKIAA1329	sortilin-related VPS10 domain containing receptor 2	protein-coding
mm_116006.1	chr13	24604215	24604231	-	1	NA	intron (NR_024599, intron 1 of 1)	RMER17C|LTR|ERVK	544	NR_024599	76024	Mm.440710	NR_024599		Gm11346	5830431A10Rik|AI447617|Gm11347|OTTMUSG00000000601|OTTMUSG00000000602	X-linked lymphocyte-regulated 5 pseudogene	pseudo
mm_94147.1	chr10	128743834	128743845	-	1	NA	5' UTR (NM_016811, exon 1 of 24)	5' UTR (NM_016811, exon 1 of 24)	217	NM_016811	13139	Mm.291235	NM_016811	ENSMUSG00000025357	Dgka	80kDa|AW146112|Dagk1	diacylglycerol kinase, alpha	protein-coding
mm_131464.1	chr16	17026411	17026434	+	1	NA	exon (NM_001038663, exon 6 of 8)	exon (NM_001038663, exon 6 of 8)	43040	NM_001038663	26413	Mm.196581	NM_011949	ENSMUSG00000063358	Mapk1	9030612K14Rik|AA407128|AU018647|C78273|ERK|Erk2|MAPK2|PRKM2|Prkm1|p41mapk|p42mapk	mitogen-activated protein kinase 1	protein-coding
mm_14463.1	chr2	131232752	131232769	+	1	NA	intron (NR_037281, intron 2 of 2)	ORR1B2|LTR|ERVL-MaLR	-1303	NM_001206383	228607	Mm.287226	NM_144888	ENSMUSG00000037523	Mavs	D430028G21Rik|IPS-1|Visa|cardif	mitochondrial antiviral signaling protein	protein-coding
mm_38014.1	chr4	133753916	133753926	-	1	NA	promoter-TSS (NM_001080819)	promoter-TSS (NM_001080819)	-310	NM_001080819	93760	Mm.22478	NM_001080819	ENSMUSG00000007880	Arid1a	1110030E03Rik|BAF250a|Osa1|Smarcf1	AT rich interactive domain 1A (SWI-like)	protein-coding
mm_88851.1	chr10	80930640	80930649	+	1	NA	intron (NM_008655, intron 2 of 3)	CpG-1325	553	NM_008655	17873	Mm.1360	NM_008655	ENSMUSG00000015312	Gadd45b	AI323528|Myd118	growth arrest and DNA-damage-inducible 45 beta	protein-coding
mm_130670.1	chr15	100674658	100674659	-	1	NA	3' UTR (NM_033612, exon 8 of 8)	3' UTR (NM_033612, exon 8 of 8)	-5158	NM_001270537	668218	Mm.451225	NM_001270537	ENSMUSG00000098112	Bin2	-	bridging integrator 2	protein-coding
mm_25171.1	chr3	103090231	103090241	+	1	NA	intron (NM_001033303, intron 7 of 15)	intron (NM_001033303, intron 7 of 15)	16222	NM_001033303	229665	Mm.331272	NM_001033303	ENSMUSG00000070385	Ampd1	AI553520|Ampd-1	adenosine monophosphate deaminase 1	protein-coding
mm_42173.1	chr5	112261725	112261735	+	1	NA	intron (NM_023695, intron 3 of 5)	intron (NM_023695, intron 3 of 5)	5910	NM_001312893	12960	Mm.29488	NM_023695	ENSMUSG00000029343	Crybb1	3110006K12Rik|BB1CRY	crystallin, beta B1	protein-coding
mm_1640.1	chr1	74542862	74542877	+	1	NA	promoter-TSS (NM_001081456)	promoter-TSS (NM_001081456)	-20	NM_001081456	18802	Mm.290731	NM_148937	ENSMUSG00000026173	Plcd4	4921507K24Rik	phospholipase C, delta 4	protein-coding
mm_18608.1	chr2	68366488	68366506	-	1	NA	intron (NM_016866, intron 7 of 17)	intron (NM_016866, intron 7 of 17)	105484	NM_016866	53416	Mm.198414	NM_016866	ENSMUSG00000027030	Stk39	AW227544|AW556857|DCHT|RF005|Rnl5|SPAK	serine/threonine kinase 39	protein-coding
mm_139876.1	chr17	70748001	70748019	+	1	NA	intron (NM_001347411, intron 9 of 14)	intron (NM_001347411, intron 9 of 14)	98767	NM_001164077	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_48081.1	chr5	136883204	136883214	-	1	NA	promoter-TSS (NM_024474)	promoter-TSS (NM_024474)	6	NM_001346699	140709	Mm.295020	NM_024474	ENSMUSG00000004415	Col26a1	9430032K24Rik|BC002218|Col26a|Emid2|Emu2	collagen, type XXVI, alpha 1	protein-coding
mm_141531.1	chr17	31848833	31848847	-	1	NA	exon (NM_010831, exon 11 of 14)	exon (NM_010831, exon 11 of 14)	6952	NM_010831	17691	Mm.290941	NM_010831	ENSMUSG00000024042	Sik1	Msk|Sik|Snf1lk	salt inducible kinase 1	protein-coding
mm_14627.1	chr2	136781072	136781081	+	1	NA	exon (NM_001291056, exon 8 of 8)	exon (NM_001291056, exon 8 of 8)	67626	NM_001291056	20614	Mm.45953	NM_011428	ENSMUSG00000027273	Snap25	Bdr|GENA70|SNAP-25|SUP|sp	synaptosomal-associated protein 25	protein-coding
mm_108960.1	chr12	102383880	102383939	+	1	NA	intron (NM_177620, intron 8 of 9)	(TCCA)n|Simple_repeat|Simple_repeat	55904	NM_011175	19141	Mm.17185	NM_011175	ENSMUSG00000021190	Lgmn	AEP|AI746452|AU022324|Prsc1	legumain	protein-coding
mm_125703.1	chr15	67873782	67873786	+	1	NA	Intergenic	Intergenic	385072	NM_001145888	380993	Mm.309526	NM_198644	ENSMUSG00000022335	Zfat	Gm922|Zfat1|Zfp406	zinc finger and AT hook domain containing	protein-coding
mm_58921.1	chr7	17812704	17812706	+	1	NA	promoter-TSS (NM_025957)	promoter-TSS (NM_025957)	23	NM_025957	67084	Mm.33709	NM_025957	ENSMUSG00000023185	Ceacam14	1600021E03Rik|1600025E09Rik|AV033953	carcinoembryonic antigen-related cell adhesion molecule 14	protein-coding
mm_19542.1	chr2	98662474	98662499	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	1194829	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_77817.1	chr9	3258830	3258856	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-59030	NR_027988	114673	Mm.422774	NM_053265	ENSMUSG00000042360	4930433N12Rik	-	RIKEN cDNA 4930433N12 gene	ncRNA
mm_109427.1	chr12	110601460	110601477	+	1	NA	promoter-TSS (NM_030238)	promoter-TSS (NM_030238)	73	NM_030238	13424	Mm.181430	NM_030238	ENSMUSG00000018707	Dync1h1	9930018I23Rik|AI894280|DHC1|DHC1a|DNCL|Dnchc1|Dnec1|Dnecl|Loa|MAP1C|P22|Swl|mKIAA0325	dynein cytoplasmic 1 heavy chain 1	protein-coding
mm_103910.1	chr11	83578621	83578641	-	1	NA	promoter-TSS (NM_011338)	promoter-TSS (NM_011338)	5	NM_011338	20308	Mm.416125	NM_011338	ENSMUSG00000019122	Ccl9	CCF18|MRP-2|Scya10|Scya9	chemokine (C-C motif) ligand 9	protein-coding
mm_170737.1	chr2	154285534	154285548	-	1	NA	Intergenic	Intergenic	-21703	NM_001025574	433492	Mm.330682	NM_001025574	ENSMUSG00000067996	Bpifb9b	5430413K10Rik|AI413838|OTTMUSG00000015915	BPI fold containing family B, member 9B	protein-coding
mm_11166.1	chr2	28557921	28557932	+	1	NA	intron (NM_009885, intron 8 of 10)	intron (NM_009885, intron 8 of 10)	5477	NM_009885	12613	Mm.236017	NM_009885	ENSMUSG00000026818	Cel	1810036E18Rik|BAL	carboxyl ester lipase	protein-coding
mm_1967.1	chr1	86503580	86503589	+	1	NA	Intergenic	Intergenic	-23152	NM_008972	19231	Mm.19187	NM_008972	ENSMUSG00000026238	Ptma	Thym	prothymosin alpha	protein-coding
mm_20458.1	chr2	129365952	129365963	-	1	NA	intron (NM_008361, intron 6 of 6)	intron (NM_008361, intron 6 of 6)	-3945	NR_015474	329514	Mm.207315	NM_177848	ENSMUSG00000074805	Il1bos	9430083I22|Gm14047|OTTMUSG00000015529	interleukin 1 beta, opposite strand	ncRNA
mm_49391.1	chr6	24890501	24890516	+	1	NA	intron (NM_028957, intron 3 of 3)	intron (NM_028957, intron 3 of 3)	32511	NM_028957	74468	Mm.251601	NM_028957	ENSMUSG00000029678	Hyal5	4933439A12Rik	hyaluronoglucosaminidase 5	protein-coding
mm_16033.1	chr2	167656787	167656795	+	1	NA	intron (NM_145538, intron 1 of 5)	intron (NM_145538, intron 1 of 5)	4753	NM_145538	407243	Mm.4863	NM_145538	ENSMUSG00000090213	Tmem189	AI840826|Kua	transmembrane protein 189	protein-coding
mm_125972.1	chr15	76294392	76294409	+	1	NA	promoter-TSS (NM_001195537)	promoter-TSS (NM_001195537)	-34	NM_001195537	100503915	Mm.393455	NM_001195537	ENSMUSG00000071724	Smpd5	ENSMUSG00000071724|Gm10345|MA-nSMase	sphingomyelin phosphodiesterase 5	protein-coding
mm_119775.1	chr14	54176254	54176256	+	1	NA	Intergenic	Intergenic	77674	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_164266.1	chr15	101115824	101115831	+	1	NA	promoter-TSS (NM_144790)	promoter-TSS (NM_144790)	72	NM_144790	208258	Mm.152952	NM_144790	ENSMUSG00000047034	Ankrd33	A930021G21Rik|Panky|Panky-a	ankyrin repeat domain 33	protein-coding
mm_123337.1	chr14	63130739	63130750	-	1	NA	intron (NM_007798, intron 1 of 9)	intron (NM_007798, intron 1 of 9)	8282	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_123962.1	chr14	74939763	74939766	-	1	NA	intron (NM_001252132, intron 1 of 18)	AT_rich|Low_complexity|Low_complexity	8113	NM_001252132	380916	Mm.288868	NM_001033439	ENSMUSG00000068015	Lrch1	4832412D13Rik|AI552548|AW215503|Chdc1|mKIAA1016	leucine-rich repeats and calponin homology (CH) domain containing 1	protein-coding
mm_158722.1	chrX	162888427	162888473	-	1	NA	promoter-TSS (NM_025932)	promoter-TSS (NM_025932)	12	NM_025932	67043	Mm.44207	NM_025932	ENSMUSG00000031357	Syap1	2010110O17Rik|AW011796	synapse associated protein 1	protein-coding
mm_135577.1	chr16	50430350	50430363	-	1	NA	intron (NM_001347240, intron 1 of 16)	CpG	2033	NM_027444	70508	Mm.28940	NM_027444	ENSMUSG00000022641	Bbx	5530401J07Rik|5730403O13Rik	bobby sox HMG box containing	protein-coding
mm_9571.1	chr1	173979886	173979896	-	1	NA	intron (NM_008327, intron 1 of 6)	Lx9|LINE|L1	2953	NM_008327	26388	Mm.218770	NM_008327	ENSMUSG00000026535	Ifi202b	Ifbip-1|Ifi202|Ifi202a|p202	interferon activated gene 202B	protein-coding
mm_57369.1	chr6	124779687	124779742	-	1	NA	promoter-TSS (NM_001302555)	promoter-TSS (NM_001302555)	13	NM_001302555	16977	Mm.3207	NM_013588	ENSMUSG00000030125	Lrrc23	4921537K05Rik|B7|Lrpb7	leucine rich repeat containing 23	protein-coding
mm_128946.1	chr15	74746789	74746797	-	1	NA	promoter-TSS (NM_001081961)	promoter-TSS (NM_001081961)	-106	NM_001081961	69462	Mm.64338	NM_001081961	ENSMUSG00000075605	Slurp2	2300005B03Rik|SLURP-2	secreted Ly6/Plaur domain containing 2	protein-coding
mm_142726.1	chr17	48232617	48232649	-	1	NA	promoter-TSS (NM_021406)	promoter-TSS (NM_021406)	-106	NM_001347399	58217	Mm.248352	NM_021406	ENSMUSG00000042265	Trem1	-	triggering receptor expressed on myeloid cells 1	protein-coding
mm_53970.1	chr6	6169776	6169778	-	1	NA	intron (NM_015829, intron 3 of 17)	intron (NM_015829, intron 3 of 17)	47396	NM_015829	50799	Mm.24513	NM_015829	ENSMUSG00000015112	Slc25a13	AI785475|Ctrn	solute carrier family 25 (mitochondrial carrier, adenine nucleotide translocator), member 13	protein-coding
mm_63109.1	chr7	122671124	122671130	+	1	NA	promoter-TSS (NM_019430)	promoter-TSS (NM_019430)	-617	NM_019430	54376	Mm.444212	NM_019430	ENSMUSG00000066189	Cacng3	-	calcium channel, voltage-dependent, gamma subunit 3	protein-coding
mm_119433.1	chr14	46221140	46221152	+	1	NA	Intergenic	MLT1A1|LTR|ERVL-MaLR	137119	NR_002875	218963	Mm.282093	NR_002875		Gm1821	-	ubiquitin pseudogene	pseudo
mm_131488.1	chr16	17233561	17233590	+	1	NA	promoter-TSS (NM_178922)	promoter-TSS (NM_178922)	-12	NM_178922	58180	Mm.261602	NM_178922	ENSMUSG00000050240	Hic2	AA409108|HRG22|mKIAA1020	hypermethylated in cancer 2	protein-coding
mm_63787.1	chr7	132406002	132406008	+	1	NA	Intergenic	Intergenic	-88850	NM_029935	77590	Mm.213582	NM_029935	ENSMUSG00000030930	Chst15	4631426J05Rik|BRAG|GalNAcS-6ST|MAd5|mKIAA0598	carbohydrate (N-acetylgalactosamine 4-sulfate 6-O) sulfotransferase 15	protein-coding
mm_14792.1	chr2	145860761	145860763	+	1	NA	exon (NM_028724, exon 9 of 13)	exon (NM_028724, exon 9 of 13)	-42479	NM_026425	67877	Mm.151168	NM_026425	ENSMUSG00000002728	Naa20	1500004D14Rik|2900026I01Rik|AU041458|D2Ertd186e|Nat5	N(alpha)-acetyltransferase 20, NatB catalytic subunit	protein-coding
mm_160458.1	chr8	108714745	108714745	+	1	NA	5' UTR (NM_007496, exon 1 of 10)	5' UTR (NM_007496, exon 1 of 10)	101	NM_007496	11906	Mm.416972	NM_007496	ENSMUSG00000038872	Zfhx3	A230102L03Rik|Atbf1|Sci|WBP9|mKIAA4228	zinc finger homeobox 3	protein-coding
mm_147076.1	chr18	35498857	35498925	-	1	NA	promoter-TSS (NM_030749)	promoter-TSS (NM_030749)	34	NM_030749	81500	Mm.291482	NM_030749	ENSMUSG00000024357	Sil1	1810057E01Rik|AI042831|wz	endoplasmic reticulum chaperone SIL1 homolog (S. cerevisiae)	protein-coding
mm_62482.1	chr7	101879887	101879922	+	1	NA	Intergenic	B2_Mm1a|SINE|B2	-1421	NM_001291353	75430	Mm.284491	NM_027532	ENSMUSG00000030649	Anapc15	3200002M19Rik|6330414C15Rik|APC15	anaphase prompoting complex C subunit 15	protein-coding
mm_58030.1	chr6	136662160	136662200	-	1	NA	promoter-TSS (NM_025806)	promoter-TSS (NM_025806)	-287	NM_025806	66857	Mm.3311	NM_025806	ENSMUSG00000030214	Plbd1	1100001H23Rik	phospholipase B domain containing 1	protein-coding
mm_25850.1	chr3	129532637	129532644	+	1	NA	intron (NM_130450, intron 1 of 4)	intron (NM_130450, intron 1 of 4)	254	NM_130450	170439	Mm.314113	NM_130450	ENSMUSG00000041220	Elovl6	C77826|FAE|LCE	ELOVL family member 6, elongation of long chain fatty acids (yeast)	protein-coding
mm_62861.1	chr7	114717294	114717305	+	1	NA	Intergenic	Intergenic	-1344	NM_054084	116903	Mm.273838	NM_054084	ENSMUSG00000030666	Calcb	CGRP2|Calc2	calcitonin-related polypeptide, beta	protein-coding
mm_127174.1	chr15	98917652	98917698	+	1	NA	intron (NM_029098, intron 1 of 16)	CpG	423	NM_029098	74775	Mm.385020	NM_029098	ENSMUSG00000022999	Lmbr1l	1110013E13Rik|AA415653|D15Ertd735e|Limr	limb region 1 like	protein-coding
mm_155351.1	chrX	68761840	68761873	+	1	NA	promoter-TSS (NM_001166620)	promoter-TSS (NM_001166620)	17	NM_001166619	207854	Mm.284945	NM_174993	ENSMUSG00000062170	Fmr1nb	3830422N12Rik|NY-SAR-35|NYSAR35	fragile X mental retardation 1 neighbor	protein-coding
mm_67655.1	chr7	84689949	84689964	-	1	NA	intron (NR_038175, intron 1 of 4)	CpG	316	NR_038175	72495	Mm.382914	NR_038175	ENSMUSG00000085236	2610206C17Rik	-	RIKEN cDNA 2610206C17 gene	ncRNA
mm_16779.1	chr2	9887776	9887795	-	1	NA	intron (NR_040511, intron 1 of 3)	intron (NR_040511, intron 1 of 3)	1755	NR_040511	77682	Mm.488621	NR_040511	ENSMUSG00000079602	9230102O04Rik	-	RIKEN cDNA 9230102O04 gene	ncRNA
mm_129826.1	chr15	83127463	83127490	-	1	NA	3' UTR (NM_178627, exon 9 of 9)	3' UTR (NM_178627, exon 9 of 9)	-4675	NM_029101	74778	Mm.30056	NM_029101	ENSMUSG00000018040	Rrp7a	1110014J01Rik|AA408146|Kheg1	ribosomal RNA processing 7 homolog A (S. cerevisiae)	protein-coding
mm_129020.1	chr15	74954059	74954066	-	1	NA	promoter-TSS (NM_001164039)	promoter-TSS (NM_001164039)	-989	NM_001164039	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_130378.1	chr15	97844235	97844245	-	1	NA	5' UTR (NM_001204278, exon 1 of 24)	5' UTR (NM_001204278, exon 1 of 24)	262	NM_001204279	56233	Mm.384027	NM_019572	ENSMUSG00000022475	Hdac7	5830434K02Rik|HD7|HD7a|Hdac7a|mFLJ00062	histone deacetylase 7	protein-coding
mm_125821.1	chr15	74957119	74957144	+	1	NA	intron (NM_001164039, intron 2 of 4)	intron (NM_001164039, intron 2 of 4)	2025	NM_001164040	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_130974.1	chr15	103334272	103334347	-	1	NA	intron (NM_013866, intron 1 of 7)	intron (NM_013866, intron 1 of 7)	5777	NM_013866	29813	Mm.14099	NM_013866	ENSMUSG00000000552	Zfp385a	Hzf|Zfp385|Znf385a	zinc finger protein 385A	protein-coding
mm_66253.1	chr7	35646455	35646457	-	1	NA	intron (NM_019746, intron 1 of 5)	intron (NM_019746, intron 1 of 5)	1026	NM_019746	56330	Mm.371609	NM_019746	ENSMUSG00000030417	Pdcd5	2200003D22Rik|AA408513|Tfar19	programmed cell death 5	protein-coding
mm_166308.1	chr5	106351567	106351573	+	1	NA	Intergenic	Intergenic	30230	NR_136913	102635633	Mm.383511	NR_136913	ENSMUSG00000105508	Gm32921	-	predicted gene, 32921	ncRNA
mm_21153.1	chr2	154421309	154421320	-	1	NA	Intergenic	Intergenic	-13230	NM_009228	20648	Mm.1541	NM_009228	ENSMUSG00000027488	Snta1	AW228934|Snt1	syntrophin, acidic 1	protein-coding
mm_29370.1	chr3	108711439	108711445	-	1	NA	5' UTR (NM_029522, exon 2 of 15)	5' UTR (NM_029522, exon 2 of 15)	10857	NM_029522	76123	Mm.226941	NM_029522	ENSMUSG00000027883	Gpsm2	6230410J09Rik|LGN|Pins	G-protein signalling modulator 2 (AGS3-like, C. elegans)	protein-coding
mm_164916.1	chr18	75367421	75367424	+	1	NA	promoter-TSS (NM_001042660)	promoter-TSS (NM_001042660)	57	NM_001042660	17131	Mm.34407	NM_008543	ENSMUSG00000025880	Smad7	Madh7	SMAD family member 7	protein-coding
mm_138700.1	chr17	35998015	35998022	+	1	NA	intron (NR_015618, intron 1 of 1)	MTEb|LTR|ERVL-MaLR	3514	NR_015618	77810	Mm.483143	NR_015618		A930015D03Rik	-	RIKEN cDNA A930015D03 gene	ncRNA
mm_40101.1	chr5	34584981	34584984	+	1	NA	intron (NM_013457, intron 1 of 15)	intron (NM_013457, intron 1 of 15)	10831	NR_106111	102466999		NR_106111	ENSMUSG00000099082	Mir7036b	Gm27625|mmu-mir-7036b	microRNA 7036b	ncRNA
mm_34279.1	chr4	141424610	141424618	+	1	NA	3' UTR (NM_013868, exon 3 of 3)	3' UTR (NM_013868, exon 3 of 3)	3835	NM_013868	29818	Mm.46181	NM_013868	ENSMUSG00000006221	Hspb7	27kDa|Hsp25-2|cvHsp	heat shock protein family, member 7 (cardiovascular)	protein-coding
mm_92940.1	chr10	84576145	84576155	-	1	NA	promoter-TSS (NM_146008)	promoter-TSS (NM_146008)	-797	NM_146008	216198	Mm.296142	NM_146008	ENSMUSG00000020034	Tcp11l2	E430026E19Rik	t-complex 11 (mouse) like 2	protein-coding
mm_5251.1	chr1	16619246	16619302	-	1	NA	promoter-TSS (NM_001271017)	promoter-TSS (NM_001271017)	64	NM_025773	66799	Mm.122430	NM_025773	ENSMUSG00000025939	Ube2w	6130401J04Rik	ubiquitin-conjugating enzyme E2W (putative)	protein-coding
mm_4924.1	chr1	190942411	190942413	+	1	NA	intron (NR_037578, intron 6 of 8)	intron (NR_037578, intron 6 of 8)	13907	NR_037579	52477	Mm.289914	NM_021421	ENSMUSG00000026634	Angel2	2610307I21Rik|5730410O10Rik|AI845692|D1Ertd396e|D1Ertd654e	angel homolog 2	protein-coding
mm_46700.1	chr5	110118946	110118947	-	1	NA	intron (NM_001163996, intron 2 of 4)	intron (NM_001163996, intron 2 of 4)	8854	NM_001163996	675812	Mm.442122	NM_001163996	ENSMUSG00000023284	Zfp605	A830023I12Rik	zinc finger protein 605	protein-coding
mm_91480.1	chr10	34388811	34388814	-	1	NA	intron (NM_001347463, intron 5 of 10)	intron (NM_001347463, intron 5 of 10)	-1169	NM_009925	12813	Mm.443177	NM_009925	ENSMUSG00000039462	Col10a1	Col10|Col10a-1	collagen, type X, alpha 1	protein-coding
mm_130940.1	chr15	103239813	103239888	-	1	NA	promoter-TSS (NM_010447)	promoter-TSS (NM_010447)	-34	NM_001076789	12419	Mm.262059	NM_007626	ENSMUSG00000009575	Cbx5	2610029O15Rik|C75991|HP1|Hp1a|Hp1alpha	chromobox 5	protein-coding
mm_81064.1	chr9	106171313	106171331	+	1	NA	exon (NM_029896, exon 1 of 9)	exon (NM_029896, exon 1 of 9)	393	NM_029896	77305	Mm.265125	NM_029896	ENSMUSG00000020257	Wdr82	9430077D24Rik|CDW5/WDR82	WD repeat domain containing 82	protein-coding
mm_75039.1	chr8	32649645	32649647	-	1	NA	Intergenic	L1M2|LINE|L1	300380	NM_001177589	100042715	Mm.291093	NM_001177589		Gm3985	-	predicted gene 3985	protein-coding
mm_88531.1	chr10	78352563	78352568	+	1	NA	promoter-TSS (NM_053014)	promoter-TSS (NM_053014)	-865	NM_053014	28169	Mm.141230	NM_053014	ENSMUSG00000001211	Agpat3	AW061257|AW493985|D10Jhu12e|lpaat3	1-acylglycerol-3-phosphate O-acyltransferase 3	protein-coding
mm_149897.1	chr19	25505737	25505771	+	1	NA	promoter-TSS (NM_015826)	promoter-TSS (NM_015826)	48	NM_015826	50796	Mm.391208	NM_015826	ENSMUSG00000024837	Dmrt1	-	doublesex and mab-3 related transcription factor 1	protein-coding
mm_24099.1	chr3	88055485	88055492	+	1	NA	exon (NM_001110809, exon 8 of 8)	exon (NM_001110809, exon 8 of 8)	3007	NM_144897	246703	Mm.205996	NM_144897	ENSMUSG00000028070	Apoa1bp	AA087124|AI-BP|AIBP|Apoa1ip|ESTM37|Naxe	apolipoprotein A-I binding protein	protein-coding
mm_133051.1	chr16	57572167	57572179	+	1	NA	exon (NM_001040397, exon 5 of 5)	exon (NM_001040397, exon 5 of 5)	22931	NM_001177871	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding
mm_86089.1	chr9	114933812	114933890	-	1	NA	5' UTR (NM_175380, exon 1 of 8)	5' UTR (NM_175380, exon 1 of 8)	136	NM_175380	333433	Mm.38198	NM_175380	ENSMUSG00000050627	Gpd1l	2210409H23Rik|D9Ertd660e	glycerol-3-phosphate dehydrogenase 1-like	protein-coding
mm_43449.1	chr5	136136138	136136174	+	1	NA	promoter-TSS (NM_027891)	promoter-TSS (NM_027891)	11	NM_001347492	72041	Mm.486605	NM_028070	ENSMUSG00000039754	Alkbh4	2010004B12Rik|Abj4	alkB homolog 4, lysine demethylase	protein-coding
mm_104849.1	chr11	99285261	99285264	-	1	NA	promoter-TSS (NM_029393)	promoter-TSS (NM_029393)	-24	NM_029393	75706	Mm.46378	NM_029393	ENSMUSG00000020913	Krt24	2310058N18Rik|2310075C18Rik	keratin 24	protein-coding
mm_80628.1	chr9	89067048	89067051	+	1	NA	Intergenic	Intergenic	25786	NM_001170884	666747	Mm.425592	NM_001170884	ENSMUSG00000079162	Trim43b	EG666747|Gm8269	tripartite motif-containing 43B	protein-coding
mm_61808.1	chr7	87246709	87246719	+	1	NA	promoter-TSS (NM_001285835)	promoter-TSS (NM_001285835)	65	NM_001285833	50490	Mm.31748	NM_015760	ENSMUSG00000030562	Nox4	AI648021	NADPH oxidase 4	protein-coding
mm_162725.1	chr10	40421892	40421936	+	1	NA	intron (NM_198164, intron 2 of 11)	B1_Mur4|SINE|Alu	72606	NM_001291816	78334	Mm.200924	NM_198164	ENSMUSG00000038481	Cdk19	2700084L06Rik|AI845279|AW228747|CDK11|Cdc2l6|mKIAA1028	cyclin-dependent kinase 19	protein-coding
mm_81702.1	chr9	111271833	111271914	+	1	NA	promoter-TSS (NM_026810)	promoter-TSS (NM_026810)	28	NM_175266	77781	Mm.209005	NM_175266	ENSMUSG00000046785	Epm2aip1	A930003G21Rik|mKIAA0766	EPM2A (laforin) interacting protein 1	protein-coding
mm_46364.1	chr5	103377313	103377329	-	1	NA	Intergenic	Intergenic	-47871	NM_011204	19249	Mm.3414	NM_011204	ENSMUSG00000034573	Ptpn13	AI324989|PTP-BL|PTPL1|Ptpri|RIP	protein tyrosine phosphatase, non-receptor type 13	protein-coding
mm_58222.1	chr6	144209472	144209487	-	1	NA	promoter-TSS (NM_011444)	promoter-TSS (NM_011444)	89	NM_001113559	20678	Mm.1752	NM_011444	ENSMUSG00000041540	Sox5	A730017D01Rik|AI528773	SRY (sex determining region Y)-box 5	protein-coding
mm_70103.1	chr7	142661274	142661287	-	1	NA	promoter-TSS (NM_001122736)	promoter-TSS (NM_001122736)	-9	NM_001122736	16002	Mm.3862	NM_010514	ENSMUSG00000048583	Igf2	AL033362|Igf-2|Igf-II|M6pr|Mpr|Peg2	insulin-like growth factor 2	protein-coding
mm_46096.1	chr5	92347290	92347298	-	1	NA	3' UTR (NM_021274, exon 4 of 4)	3' UTR (NM_021274, exon 4 of 4)	1595	NM_021274	15945	Mm.877	NM_021274	ENSMUSG00000034855	Cxcl10	C7|CRG-2|INP10|IP-10|IP10|Ifi10|Scyb10|gIP-10|mob-1	chemokine (C-X-C motif) ligand 10	protein-coding
mm_29588.1	chr3	117868906	117868921	-	1	NA	promoter-TSS (NM_029655)	promoter-TSS (NM_029655)	23	NM_001190156	76561	Mm.33824	NM_029655	ENSMUSG00000028007	Snx7	2510028H01Rik	sorting nexin 7	protein-coding
mm_23320.1	chr3	53463667	53463681	+	1	NA	promoter-TSS (NM_172501)	promoter-TSS (NM_172501)	-143	NM_173382	212127	Mm.491292	NM_173382	ENSMUSG00000049504	Proser1	2810046L04Rik|9330161F11	proline and serine rich 1	protein-coding
mm_138694.1	chr17	35980081	35980091	+	1	NA	promoter-TSS (NM_001282025)	promoter-TSS (NM_001282025)	131	NM_008136	14670	Mm.335754	NM_008136	ENSMUSG00000024429	Gnl1	Gna-rs1|Gnal1	guanine nucleotide binding protein-like 1	protein-coding
mm_97984.1	chr11	83886093	83886102	+	1	NA	intron (NM_001291269, intron 5 of 8)	(CA)n|Simple_repeat|Simple_repeat	33137	NM_001291269	21410	Mm.7226	NM_009330	ENSMUSG00000020679	Hnf1b	HNF-1-beta|HNF-1B|HNF-1Beta|Hnf1beta|LFB3|Tcf-2|Tcf2|vHNF1	HNF1 homeobox B	protein-coding
mm_101299.1	chr11	22286822	22286865	-	1	NA	promoter-TSS (NM_153078)	promoter-TSS (NM_153078)	-48	NM_001252515	216565	Mm.491265	NM_153078	ENSMUSG00000042302	Ehbp1	AF424697|Flj21950|NACSIN	EH domain binding protein 1	protein-coding
mm_145339.1	chr18	56469209	56469214	+	1	NA	intron (NM_026240, intron 1 of 13)	intron (NM_026240, intron 1 of 13)	37079	NM_026240	107022	Mm.24356	NM_026240	ENSMUSG00000001700	Gramd3	9030613F08Rik|9130427A09Rik|AW061306|NS3TP2	GRAM domain containing 3	protein-coding
mm_114055.1	chr13	54371341	54371352	+	1	NA	promoter-TSS (NM_009946)	promoter-TSS (NM_009946)	-3	NM_009946	12890	Mm.268902	NM_009946	ENSMUSG00000025867	Cplx2	921-L|AI413745|AW492120	complexin 2	protein-coding
mm_168699.1	chr11	97781715	97781718	-	1	NA	promoter-TSS (NR_028078)	promoter-TSS (NR_028078)	50	NR_028078	100302498	Mm.453536	NR_028078	ENSMUSG00000064901	Snora21	MBI-3	small nucleolar RNA, H/ACA box 21	snoRNA
mm_83484.1	chr9	45930459	45930471	-	1	NA	TTS (NM_008794)	TTS (NM_008794)	5593	NM_011526	21345	Mm.283283	NM_011526	ENSMUSG00000032085	Tagln	Sm22|Sm22a|Ws310	transgelin	protein-coding
mm_172009.1	chr6	109505312	109505312	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	676671	NM_138677	192193	Mm.21596	NM_138677	ENSMUSG00000030104	Edem1	A130059K23Rik|EDEM|mKIAA0212	ER degradation enhancer, mannosidase alpha-like 1	protein-coding
mm_3348.1	chr1	138145414	138145423	+	1	NA	intron (NM_001111316, intron 1 of 31)	intron (NM_001111316, intron 1 of 31)	29708	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_154931.1	chrX	35888686	35888709	+	1	NA	promoter-TSS (NM_001009947)	promoter-TSS (NM_001009947)	-135	NM_001009947	75974	Mm.32873	NM_177745	ENSMUSG00000031093	Dock11	5033414A21Rik|8030476J24|Zizimin2|sph238	dedicator of cytokinesis 11	protein-coding
mm_2103.1	chr1	87803916	87803929	+	1	NA	5' UTR (NM_009118, exon 1 of 16)	5' UTR (NM_009118, exon 1 of 16)	242	NM_009118	20215	Mm.1276	NM_009118	ENSMUSG00000056055	Sag	A930001K18Rik|Arr1|Irbp|arrestin	S-antigen, retina and pineal gland (arrestin)	protein-coding
mm_88995.1	chr10	81575236	81575254	+	1	NA	promoter-TSS (NM_019725)	promoter-TSS (NM_019725)	-42	NM_019725	21886	Mm.38608	NM_019725	ENSMUSG00000034771	Tle2	Grg2|mKIAA4188	transducin-like enhancer of split 2	protein-coding
mm_87695.1	chr10	59636936	59636946	+	1	NA	Intergenic	Intergenic	-20249	NM_001033259	215999	Mm.296470	NM_001033259	ENSMUSG00000009647	Mcu	2010012O16Rik|AV064928|C10orf42|Ccdc109a|D130073L02Rik|Gm64	mitochondrial calcium uniporter	protein-coding
mm_80121.1	chr9	70576719	70576731	+	1	NA	exon (NM_025690, exon 9 of 21)	exon (NM_025690, exon 9 of 21)	33855	NM_025690	66660	Mm.22379	NM_025690	ENSMUSG00000032212	Sltm	5730455C01Rik|5730555F13Rik|9130215G10Rik|Met	SAFB-like, transcription modulator	protein-coding
mm_111891.1	chr12	108275353	108275408	-	1	NA	promoter-TSS (NM_001159910)	promoter-TSS (NM_001159910)	37	NM_001159910	668158	Mm.482792	NM_001159910	ENSMUSG00000084883	Ccdc85c	EG668158|Gm265|Gm9010	coiled-coil domain containing 85C	protein-coding
mm_1466.1	chr1	69769385	69769387	+	1	NA	Intergenic	Intergenic	-57584	NM_029160	66722	Mm.440554	NM_025728	ENSMUSG00000053153	Spag16	4921511D23Rik|4930524F24Rik|4930585K05Rik|AV261009|Pf20|Wdr29	sperm associated antigen 16	protein-coding
mm_167761.1	chr9	110422703	110422717	-	1	NA	3' UTR (NM_008694, exon 4 of 4)	3' UTR (NM_008694, exon 4 of 4)	2902	NM_008694	18054	Mm.236225	NM_008694	ENSMUSG00000032484	Ngp	bectenecin	neutrophilic granule protein	protein-coding
mm_132001.1	chr16	25423494	25423513	+	1	NA	Intergenic	Intergenic	136686	NM_175165	71338	Mm.126851	NM_175165	ENSMUSG00000048399	Tprg	5430420C16Rik|Tprg1	transformation related protein 63 regulated	protein-coding
mm_35478.1	chr4	40853639	40853661	-	1	NA	exon (NM_022305, exon 1 of 6)	exon (NM_022305, exon 1 of 6)	887	NM_022305	14595	Mm.15622	NM_022305	ENSMUSG00000028413	B4galt1	B-1,4-GalT|B-1,4-GalT1|GalT|Ggtb|Ggtb2|b4Gal-T1|beta-1,4-GalT|beta-1,4-GalT1|beta4Gal-T1	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1	protein-coding
mm_136179.1	chr16	88874309	88874313	-	1	NA	promoter-TSS (NM_130870)	promoter-TSS (NM_130870)	-42	NM_130870	170651	Mm.196827	NM_130870	ENSMUSG00000057650	Krtap19-2	Krtap16-1	keratin associated protein 19-2	protein-coding
mm_6781.1	chr1	84137989	84138005	-	1	NA	intron (NM_001003948, intron 2 of 2)	Lx7|LINE|L1	80964	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_110947.1	chr12	76643764	76643775	-	1	NA	intron (NM_013675, intron 2 of 35)	intron (NM_013675, intron 2 of 35)	66778	NM_013675	20741	Mm.32881	NM_013675	ENSMUSG00000021061	Sptb	AI842465|D330027P03Rik|Gm1301|Spnb-1|Spnb1|ja|jaundiced|mKIAA4219	spectrin beta, erythrocytic	protein-coding
mm_148613.1	chr19	5366949	5366962	+	1	NA	promoter-TSS (NM_011793)	promoter-TSS (NM_011793)	-79	NM_011793	23825	Mm.358649	NM_011793	ENSMUSG00000024844	Banf1	Baf|Bcrp1|L2bp1/Baf	barrier to autointegration factor 1	protein-coding
mm_165050.1	chr19	40678781	40678816	+	1	NA	intron (NM_009848, intron 1 of 9)	intron (NM_009848, intron 1 of 9)	19028	NM_009848	12495	Mm.2824	NM_009848	ENSMUSG00000048120	Entpd1	2610206B08Rik|AA408691|Cd39|NTPDase-1	ectonucleoside triphosphate diphosphohydrolase 1	protein-coding
mm_142566.1	chr17	46674285	46674289	-	1	NA	promoter-TSS (NM_144857)	promoter-TSS (NM_144857)	-32	NM_144857	224823	Mm.45101	NM_144857	ENSMUSG00000023971	Rrp36	-	ribosomal RNA processing 36 homolog (S. cerevisiae)	protein-coding
mm_24047.1	chr3	87858004	87858014	+	1	NA	TTS (NM_033573)	TTS (NM_033573)	11254	NM_021309	27371	Mm.86361	NM_021309	ENSMUSG00000028071	Sh2d2a	Lad|Ribp|Tsad	SH2 domain containing 2A	protein-coding
mm_81089.1	chr9	106329440	106329441	+	1	NA	intron (NM_027354, intron 9 of 10)	intron (NM_027354, intron 9 of 10)	-39192	NM_153459	235584	Mm.275584	NM_153459	ENSMUSG00000053716	Dusp7	AU015694|Mkpx|Pyst2	dual specificity phosphatase 7	protein-coding
mm_25856.1	chr3	129634699	129634711	+	1	NA	3' UTR (NM_130450, exon 5 of 5)	3' UTR (NM_130450, exon 5 of 5)	90381	NM_001310737	13645	Mm.252481	NM_010113	ENSMUSG00000028017	Egf	AI790464	epidermal growth factor	protein-coding
mm_98953.1	chr11	98458298	98458307	+	1	NA	Intergenic	Intergenic	11468	NM_010346	14786	Mm.276702	NM_010346	ENSMUSG00000019312	Grb7	mKIAA4028	growth factor receptor bound protein 7	protein-coding
mm_92175.1	chr10	67647479	67647485	-	1	NA	Intergenic	Intergenic	-98527	NM_001005419	211488	Mm.297250	NM_001005419	ENSMUSG00000057134	Ado	Gm237	2-aminoethanethiol (cysteamine) dioxygenase	protein-coding
mm_27196.1	chr3	34861250	34861262	-	1	NA	Intergenic	Intergenic	61395	NR_105799	102466155		NR_105799	ENSMUSG00000098862	Mir6378	Gm27706|mmu-mir-6378	microRNA 6378	ncRNA
mm_64649.1	chr7	4063156	4063188	-	1	NA	promoter-TSS (NM_178611)	promoter-TSS (NM_178611)	32	NM_001302677	52855	Mm.290880	NM_178611	ENSMUSG00000055541	Lair1	5133400O11Rik|BB115266|D7Bwg0421e|Lair-1	leukocyte-associated Ig-like receptor 1	protein-coding
mm_76945.1	chr8	105966127	105966137	-	1	NA	promoter-TSS (NM_001253804)	promoter-TSS (NM_001253804)	-17	NR_045594	20498	Mm.292447	NM_009195	ENSMUSG00000017765	Slc12a4	AW546649|KCC1|RBCKCC1	solute carrier family 12, member 4	protein-coding
mm_35161.1	chr4	13483228	13483237	-	1	NA	Intergenic	Intergenic	-260070	NM_001111026	12395	Mm.4909	NM_009822	ENSMUSG00000006586	Runx1t1	Cbfa2t1h|ETO|MTG8	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	protein-coding
mm_32455.1	chr4	107368062	107368072	+	1	NA	5' UTR (NM_028355, exon 1 of 18)	5' UTR (NM_028355, exon 1 of 18)	283	NM_028355	72787	Mm.28478	NM_028355	ENSMUSG00000028614	Ndc1	2810475A17Rik|AI450313|Tmem48|sks	NDC1 transmembrane nucleoporin	protein-coding
mm_10720.1	chr2	22823430	22823441	+	1	NA	exon (NM_019456, exon 4 of 14)	exon (NM_019456, exon 4 of 14)	49108	NM_019456	54519	Mm.14255	NM_019456	ENSMUSG00000026786	Apbb1ip	9930118P07Rik|Prp48	amyloid beta (A4) precursor protein-binding, family B, member 1 interacting protein	protein-coding
mm_1029.1	chr1	58755082	58755092	+	1	NA	3' UTR (NM_207653, exon 10 of 10)	3' UTR (NM_207653, exon 10 of 10)	24535	NM_001293805	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_156385.1	chrX	139684981	139685082	+	1	NA	promoter-TSS (NM_001081499)	promoter-TSS (NM_001081499)	35	NM_001081499	245638	Mm.275869	NM_001081499	ENSMUSG00000042473	Tbc1d8b	4921505D17Rik|9030605E16Rik	TBC1 domain family, member 8B	protein-coding
mm_83626.1	chr9	48910921	48910946	-	1	NA	exon (NM_013561, exon 1 of 9)	exon (NM_013561, exon 1 of 9)	166	NM_013561	15561	Mm.4831	NM_013561	ENSMUSG00000032269	Htr3a	5-HT3	5-hydroxytryptamine (serotonin) receptor 3A	protein-coding
mm_100346.1	chr11	118428116	118428141	+	1	NA	promoter-TSS (NM_001204129)	promoter-TSS (NM_001204129)	-329	NM_001204129	56745	Mm.23845	NM_019959	ENSMUSG00000017446	C1qtnf1	1600017K21Rik|CTRP1|Zsig37	C1q and tumor necrosis factor related protein 1	protein-coding
mm_138852.1	chr17	40816707	40816708	+	1	NA	intron (NM_011269, intron 1 of 9)	intron (NM_011269, intron 1 of 9)	5558	NM_011269	19743	Mm.12961	NM_011269	ENSMUSG00000023926	Rhag	CD241|Rh50|Rh50A	Rhesus blood group-associated A glycoprotein	protein-coding
mm_167857.1	chrX	12156497	12156537	+	1	NA	intron (NR_045434, intron 1 of 3)	intron (NR_045434, intron 1 of 3)	3829	NR_045434	71458	Mm.196328	NM_029510	ENSMUSG00000040363	Bcor	2900008C10Rik|5830466J11Rik|8430401K06Rik|BcorR|D930024N20Rik|mKIAA1575	BCL6 interacting corepressor	protein-coding
mm_26070.1	chr3	136670189	136670207	+	1	NA	5' UTR (NM_001293622, exon 1 of 13)	5' UTR (NM_001293622, exon 1 of 13)	132	NM_001293622	19055	Mm.331389	NM_008913	ENSMUSG00000028161	Ppp3ca	2900074D19Rik|CN|Caln|Calna|CnA	protein phosphatase 3, catalytic subunit, alpha isoform	protein-coding
mm_47445.1	chr5	123397957	123397991	-	1	NA	intron (NM_133917, intron 1 of 16)	intron (NM_133917, intron 1 of 16)	3176	NM_177582	208104	Mm.83277	NM_133917	ENSMUSG00000038342	Mlxip	AW228700|Mir|bHLHe36	MLX interacting protein	protein-coding
mm_36812.1	chr4	103215148	103215201	-	1	NA	promoter-TSS (NM_177732)	promoter-TSS (NM_177732)	-290	NM_177732	242585	Mm.281800	NM_177732	ENSMUSG00000028521	Slc35d1	AI834976|C330011J09|UGTREL7|mKIAA0260	solute carrier family 35 (UDP-glucuronic acid/UDP-N-acetylgalactosamine dual transporter), member D1	protein-coding
mm_154200.1	chr19	58988060	58988068	-	1	NA	intron (NM_175172, intron 14 of 14)	intron (NM_175172, intron 14 of 14)	-44392	NM_001327998	73442	Mm.39739	NM_175199	ENSMUSG00000025092	Hspa12a	1700063D12Rik|AI118035|AI840429|AW048913|AW556406|D5Mgi40|Gm19925|mKIAA0417	heat shock protein 12A	protein-coding
mm_154642.1	chrX	7767525	7767557	+	1	NA	exon (NM_001271491, exon 4 of 9)	exon (NM_001271491, exon 4 of 9)	3500	NM_001271491	209446	Mm.249142	NM_172472	ENSMUSG00000000134	Tfe3	F830016E06Rik|Tcfe3|Tfe-3|bHLHe33	transcription factor E3	protein-coding
mm_107765.1	chr12	59129735	59129755	+	1	NA	promoter-TSS (NM_001165254)	promoter-TSS (NM_001165254)	-1	NM_146034	338320	Mm.213215	NM_146034	ENSMUSG00000021000	Mia2	Ctage5|D12Bwg0579e|Mea6|Mgea|Mgea6	melanoma inhibitory activity 2	protein-coding
mm_5690.1	chr1	43186082	43186089	-	1	NA	intron (NM_001289533, intron 1 of 5)	B4|SINE|B4	10676	NM_001289533	14200	Mm.6799	NM_010212	ENSMUSG00000008136	Fhl2	FHL-2|SLIM-3|SLIM3	four and a half LIM domains 2	protein-coding
mm_130177.1	chr15	93387843	93387861	-	1	NA	exon (NM_026025, exon 6 of 8)	exon (NM_026025, exon 6 of 8)	10438	NM_026025	67197	Mm.293181	NM_026025	ENSMUSG00000022635	Zcrb1	2700088M22Rik|Madp-1	zinc finger CCHC-type and RNA binding motif 1	protein-coding
mm_28065.1	chr3	84259837	84259847	-	1	NA	promoter-TSS (NM_001271727)	promoter-TSS (NM_001271727)	-63	NM_001271727	80890	Mm.44876	NM_030706	ENSMUSG00000027993	Trim2	mKIAA0517|narf	tripartite motif-containing 2	protein-coding
mm_64806.1	chr7	6706309	6706324	-	1	NA	promoter-TSS (NR_023846)	promoter-TSS (NR_023846)	-444	NR_023846	100169889	Mm.491213	NR_023846		Peg3os	Apeg3|Peg3as	Peg3 opposite strand	ncRNA
mm_142512.1	chr17	46202488	46202515	-	1	NA	promoter-TSS (NM_028198)	promoter-TSS (NM_028198)	124	NM_030715	80905	Mm.311585	NM_030715	ENSMUSG00000023953	Polh	RAD30A|XPV	polymerase (DNA directed), eta (RAD 30 related)	protein-coding
mm_18713.1	chr2	72398319	72398320	-	1	NA	exon (NM_001164791, exon 11 of 12)	exon (NM_001164791, exon 11 of 12)	-77900	NM_025866	66953	Mm.270676	NM_025866	ENSMUSG00000055612	Cdca7	2310021G01Rik|AU044109|JPO1	cell division cycle associated 7	protein-coding
mm_140598.1	chr17	10319236	10319251	-	1	NA	promoter-TSS (NR_037588)	promoter-TSS (NR_037588)	118	NM_021881	19317	Mm.130694	NM_021881	ENSMUSG00000062078	Qk	1110003F05Rik|1500005P18|QkI|l(17)-1Wis|l17Wis1	quaking	protein-coding
mm_19201.1	chr2	84476726	84476788	-	1	NA	promoter-TSS (NM_001177319)	promoter-TSS (NM_001177319)	2	NM_001177319	21788	Mm.124316	NM_011576	ENSMUSG00000027082	Tfpi	A630013F22Rik|AW552122|EPI|LACI	tissue factor pathway inhibitor	protein-coding
mm_139194.1	chr17	47611624	47611636	+	1	NA	promoter-TSS (NM_020048)	promoter-TSS (NM_020048)	34	NM_020048	56771	Mm.59393	NM_020048	ENSMUSG00000092558	Med20	1110011O05Rik|2410115I17Rik|AU018348|Trfp	mediator complex subunit 20	protein-coding
mm_89539.1	chr10	94550946	94550962	+	1	NA	intron (NM_172051, intron 1 of 3)	intron (NM_172051, intron 1 of 3)	-24303	NM_001168684	319880	Mm.23047	NM_172051	ENSMUSG00000020023	Tmcc3	AW488095|C630016B22Rik|C88213|Tmcc1	transmembrane and coiled coil domains 3	protein-coding
mm_147148.1	chr18	36606092	36606127	-	1	NA	intron (NM_175375, intron 10 of 33)	Lx8|LINE|L1	45506	NM_175375	108857	Mm.482287	NM_175375	ENSMUSG00000024483	Ankhd1	1110004O12Rik|4933432B13Rik|9130019P20Rik|A530027J04Rik|A630021B20Rik|AA571404|Mask|mFLJ00246|mKIAA1085	ankyrin repeat and KH domain containing 1	protein-coding
mm_18572.1	chr2	65567293	65567309	-	1	NA	5' UTR (NM_018732, exon 1 of 27)	5' UTR (NM_018732, exon 1 of 27)	191	NM_018732	20269	Mm.330256	NM_018732	ENSMUSG00000057182	Scn3a	Gm1000|Nav1.3	sodium channel, voltage-gated, type III, alpha	protein-coding
mm_45589.1	chr5	74395645	74395647	-	1	NA	intron (NM_001286437, intron 5 of 7)	intron (NM_001286437, intron 5 of 7)	136096	NM_178672	212986	Mm.134147	NM_178672	ENSMUSG00000062110	Scfd2	E430013M20Rik|STXBP1L1	Sec1 family domain containing 2	protein-coding
mm_162380.1	chr1	72284306	72284313	-	1	NA	promoter-TSS (NM_175564)	promoter-TSS (NM_175564)	5	NM_023523	111175	Mm.281738	NM_023523	ENSMUSG00000026189	Pecr	2400003B18Rik|TERP	peroxisomal trans-2-enoyl-CoA reductase	protein-coding
mm_64921.1	chr7	16248506	16248516	-	1	NA	exon (NM_001173550, exon 2 of 2)	exon (NM_001173550, exon 2 of 2)	-4357	NM_176912	319430	Mm.239570	NM_176912	ENSMUSG00000074361	C5ar2	C5L2|E030029A11Rik|Gpr77	complement component 5a receptor 2	protein-coding
mm_6865.1	chr1	84278474	84278486	-	1	NA	intron (NM_001003948, intron 1 of 2)	intron (NM_001003948, intron 1 of 2)	6165	NM_001003948	98496	Mm.187470	NM_001003948	ENSMUSG00000045658	Pid1	5033414K04Rik|NYGGF4	phosphotyrosine interaction domain containing 1	protein-coding
mm_62745.1	chr7	111083175	111083205	+	1	NA	promoter-TSS (NM_013507)	promoter-TSS (NM_013507)	-160	NM_013507	13690	Mm.185453	NM_013507	ENSMUSG00000005610	Eif4g2	DAP-5|E130105L11Rik|Nat1|Natm1|p97	eukaryotic translation initiation factor 4, gamma 2	protein-coding
mm_130002.1	chr15	86202697	86202722	-	1	NA	Intergenic	Intergenic	-11750	NM_145476	223754	Mm.28904	NM_145476	ENSMUSG00000051864	Tbc1d22a	BC023106|D15Ertd781e	TBC1 domain family, member 22a	protein-coding
mm_86258.1	chr9	121586949	121586966	-	1	NA	promoter-TSS (NR_040740)	promoter-TSS (NR_040740)	-63	NR_040740	75384	Mm.445955	NR_040740	ENSMUSG00000084995	Lyzl4os	4930589B17Rik|4930596M17Rik	lysozyme-like 4, opposite strand	ncRNA
mm_43618.1	chr5	138103736	138103739	+	1	NA	3' UTR (NM_029869, exon 4 of 4)	3' UTR (NM_029869, exon 4 of 4)	-13168	NM_001044703	22697	Mm.2760	NM_011757	ENSMUSG00000037017	Zscan21	AI326272|CTfin51|RU49|Zfp-38|Zfp38|Zipro1	zinc finger and SCAN domain containing 21	protein-coding
mm_125718.1	chr15	69041008	69041010	+	1	NA	intron (NM_010158, intron 6 of 8)	intron (NM_010158, intron 6 of 8)	112589	NM_010158	13992	Mm.17964	NM_010158	ENSMUSG00000022332	Khdrbs3	Etle|SLM-2|Salp|Slm2|T-STAR	KH domain containing, RNA binding, signal transduction associated 3	protein-coding
mm_66441.1	chr7	44848527	44848568	-	1	NA	promoter-TSS (NM_001290695)	promoter-TSS (NM_001290695)	532	NM_001042655	233204	Mm.27567	NM_144924	ENSMUSG00000038520	Tbc1d17	BC017607	TBC1 domain family, member 17	protein-coding
mm_74613.1	chr8	12573312	12573336	-	1	NA	intron (NM_024279, intron 1 of 6)	intron (NM_024279, intron 1 of 6)	275	NM_024279	78634	Mm.116871	NM_024279	ENSMUSG00000010435	Spaca7	1700094C09Rik	sperm acrosome associated 7	protein-coding
mm_140410.1	chr17	87646302	87646313	+	1	NA	exon (NM_008532, exon 8 of 10)	exon (NM_008532, exon 8 of 10)	10328	NM_008532	17075	Mm.4259	NM_008532	ENSMUSG00000045394	Epcam	CD326|EGP|EGP-2|Egp314|Ep-CAM|EpCAM1|GA733-2|Ly74|TROP1|Tacsd1|Tacstd1|gp40	epithelial cell adhesion molecule	protein-coding
mm_64132.1	chr7	141172667	141172677	+	1	NA	intron (NM_001172100, intron 1 of 9)	CpG	179	NM_001172100	107702	Mm.197493	NM_145135	ENSMUSG00000038650	Rnh1	AW546468|C80305|RNH	ribonuclease/angiogenin inhibitor 1	protein-coding
mm_18224.1	chr2	51139944	51139948	-	1	NA	intron (NM_028810, intron 2 of 4)	intron (NM_028810, intron 2 of 4)	9165	NM_028810	74194	Mm.46497	NM_028810	ENSMUSG00000017144	Rnd3	2610017M01Rik|AI661404|Arhe|Rhoe	Rho family GTPase 3	protein-coding
mm_94733.1	chr11	21048158	21048171	+	1	NA	Intergenic	Intergenic	-43160	NM_023324	67245	Mm.28957	NM_023324	ENSMUSG00000020134	Peli1	2810468L03Rik|A930031K15Rik|AA409794|AI586297|D11Ertd676e	pellino 1	protein-coding
mm_37449.1	chr4	123399021	123399024	-	1	NA	intron (NM_001199136, intron 60 of 97)	intron (NM_001199136, intron 60 of 97)	12889	NM_001167918	442834	Mm.483803	NM_001167918		D830031N03Rik	Kiaa0754|mKIAA0754	RIKEN cDNA D830031N03 gene	protein-coding
mm_3512.1	chr1	150107372	150107374	+	1	NA	3' UTR (NM_011198, exon 10 of 10)	3' UTR (NM_011198, exon 10 of 10)	7342	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_126623.1	chr15	83172311	83172406	+	1	NA	promoter-TSS (NM_029787)	promoter-TSS (NM_029787)	-150	NM_029787	109754	Mm.22560	NM_029787	ENSMUSG00000018042	Cyb5r3	0610016L08Rik|2500002N19Rik|C85115|Dia-1|Dia1|WU:AL591952.1-001|WU:AL591952.1-002|WU:AL591952.1-003|WU:Cyb5r3	cytochrome b5 reductase 3	protein-coding
mm_145671.1	chr18	61555226	61555239	+	1	NA	promoter-TSS (NM_146087)	promoter-TSS (NM_146087)	-350	NM_146087	93687	Mm.26908	NM_146087	ENSMUSG00000024576	Csnk1a1	2610208K14Rik|4632404G05Rik|5430427P18Rik|CK1a|Csnk1a	casein kinase 1, alpha 1	protein-coding
mm_63925.1	chr7	139389326	139389334	+	1	NA	5' UTR (NM_001127363, exon 1 of 16)	5' UTR (NM_001127363, exon 1 of 16)	221	NM_001127363	212111	Mm.28308	NM_183144	ENSMUSG00000025477	Inpp5a	-	inositol polyphosphate-5-phosphatase A	protein-coding
mm_101460.1	chr11	30268138	30268162	-	1	NA	Intergenic	CpG	-48378	NM_175836	20742	Mm.123110	NM_009260	ENSMUSG00000020315	Sptbn1	9930031C03Rik|AL033301|SPTB2|Spnb-2|Spnb2|elf1|elf3|mKIAA4049	spectrin beta, non-erythrocytic 1	protein-coding
mm_56352.1	chr6	93678927	93678942	-	1	NA	exon (NM_001083320, exon 23 of 23)	exon (NM_001083320, exon 23 of 23)	234029	NR_104594	14924	Mm.217216	NM_010367	ENSMUSG00000045095	Magi1	AIP3|BAP1|Baiap1|Gukmi1|MAGI1c|Magi-1|TNRC19|WWP3|mKIAA4129	membrane associated guanylate kinase, WW and PDZ domain containing 1	protein-coding
mm_154217.1	chr19	59345539	59345558	-	1	NA	exon (NM_001033222, exon 1 of 5)	exon (NM_001033222, exon 1 of 5)	232	NM_001033222	107368	Mm.27250	NM_001033222	ENSMUSG00000074746	Pdzd8	A630041P07Rik|AV329468|AW228944|Pdzk8	PDZ domain containing 8	protein-coding
mm_91404.1	chr10	30842812	30842831	-	1	NA	promoter-TSS (NM_013904)	promoter-TSS (NM_013904)	-38	NM_013904	15214	Mm.103573	NM_013904	ENSMUSG00000019789	Hey2	CHF1|Herp1|Hrt2|bHLHb32|hesr2	hairy/enhancer-of-split related with YRPW motif 2	protein-coding
mm_165037.1	chr19	37561574	37561579	-	1	NA	intron (NM_175353, intron 1 of 21)	intron (NM_175353, intron 1 of 21)	11158	NM_175353	107371	Mm.24865	NM_175353	ENSMUSG00000053799	Exoc6	4833405E05Rik|AW413330|C430002C19|Sec15|Sec15l1|hbd|msec15	exocyst complex component 6	protein-coding
mm_3666.1	chr1	153487777	153487823	+	1	NA	promoter-TSS (NM_007842)	promoter-TSS (NM_007842)	-140	NM_007842	13211	Mm.20000	NM_007842	ENSMUSG00000042699	Dhx9	AI326842|Ddx9|HEL-5|NDHII|RHA|mHEL-5	DEAH (Asp-Glu-Ala-His) box polypeptide 9	protein-coding
mm_167652.1	chr9	66060180	66060186	+	1	NA	promoter-TSS (NM_011149)	promoter-TSS (NM_011149)	14	NM_011149	19035	Mm.335249	NM_011149	ENSMUSG00000032383	Ppib	AA408962|AA553318|AI844835|Cphn-2|Cphn2|CyP-20b	peptidylprolyl isomerase B	protein-coding
mm_29357.1	chr3	108536467	108536522	-	1	NA	promoter-TSS (NM_001033304)	promoter-TSS (NM_001033304)	28	NM_001033304	229722	Mm.316890	NM_001033304	ENSMUSG00000040412	5330417C22Rik	BB183350	RIKEN cDNA 5330417C22 gene	protein-coding
mm_154689.1	chrX	7966341	7966366	+	1	NA	intron (NM_008089, intron 1 of 5)	intron (NM_008089, intron 1 of 5)	1557	NM_008089	14460	Mm.335973	NM_008089	ENSMUSG00000031162	Gata1	Gata-1|Gf-1|eryf1	GATA binding protein 1	protein-coding
mm_171621.1	chr4	153153125	153153137	+	1	NA	Intergenic	(TTAGGG)n|Simple_repeat|Simple_repeat	329699	NM_001099299	230959	Mm.318874	NM_001099299	ENSMUSG00000039546	Ajap1	Gm573	adherens junction associated protein 1	protein-coding
mm_113603.1	chr13	41236336	41236347	+	1	NA	Intergenic	Intergenic	-13503	NM_001135577	108934	Mm.38578	NM_001135577	ENSMUSG00000091264	Smim13	2900036K02Rik	small integral membrane protein 13	protein-coding
mm_153056.1	chr19	32151288	32151292	-	1	NA	intron (NM_001168526, intron 2 of 5)	intron (NM_001168526, intron 2 of 5)	-48150	NM_018830	54447	Mm.491229	NM_018830	ENSMUSG00000024887	Asah2	AI585898	N-acylsphingosine amidohydrolase 2	protein-coding
mm_158511.1	chrX	142966746	142966762	-	1	NA	promoter-TSS (NM_019496)	promoter-TSS (NM_019496)	-26	NM_019496	56068	Mm.143724	NM_019496	ENSMUSG00000042225	Ammecr1	6230420G18Rik	Alport syndrome, mental retardation, midface hypoplasia and elliptocytosis chromosomal region gene 1	protein-coding
mm_79572.1	chr9	58134322	58134343	+	1	NA	promoter-TSS (NM_001162479)	promoter-TSS (NM_001162479)	257	NM_001162476	20897	Mm.10801	NM_009291	ENSMUSG00000032327	Stra6	AI891933	stimulated by retinoic acid gene 6	protein-coding
mm_88291.1	chr10	75223535	75223569	+	1	NA	intron (NM_001145826, intron 2 of 18)	intron (NM_001145826, intron 2 of 18)	11162	NM_001145826	74392	Mm.27716	NM_153406	ENSMUSG00000033444	Specc1l	4930470P14Rik|4932439K10Rik|9530057A13Rik|AI317249|Cytsa|mKIAA0376	sperm antigen with calponin homology and coiled-coil domains 1-like	protein-coding
mm_164844.1	chr18	43687673	43687683	-	1	NA	promoter-TSS (NM_001163637)	promoter-TSS (NM_001163637)	95	NM_001163637	76217	Mm.134602	NM_001163637	ENSMUSG00000024502	Jakmip2	6430702L21Rik|AI850334|D930046L20Rik	janus kinase and microtubule interacting protein 2	protein-coding
mm_57251.1	chr6	123283514	123283526	-	1	NA	3' UTR (NM_019948, exon 6 of 6)	3' UTR (NM_019948, exon 6 of 6)	6351	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_82312.1	chr9	7872952	7872958	-	1	NA	5' UTR (NM_007464, exon 1 of 9)	5' UTR (NM_007464, exon 1 of 9)	215	NM_007464	11796	Mm.2026	NM_007464	ENSMUSG00000032000	Birc3	AW107670|Api1|Api2|Birc2|C-IAP2|HIAP2|IAP1|IAP2|MIAP1|MIAP2|MIHB|MIHC|RNF49|cIAP-1|cIAP-2|cIAP1|cIAP2	baculoviral IAP repeat-containing 3	protein-coding
mm_53588.1	chr6	137745570	137745581	+	1	NA	exon (NM_011499, exon 7 of 10)	exon (NM_011499, exon 7 of 10)	-9002	NM_172733	232449	Mm.29181	NM_172733	ENSMUSG00000030225	Dera	2010002D22Rik|2500002K03Rik|DEOC	deoxyribose-phosphate aldolase (putative)	protein-coding
mm_164591.1	chr17	26535399	26535408	-	1	NA	Intergenic	Intergenic	-26109	NM_026170	67458	Mm.30496	NM_026170	ENSMUSG00000001576	Ergic1	1200007D18Rik|maa-136	endoplasmic reticulum-golgi intermediate compartment (ERGIC) 1	protein-coding
mm_4031.1	chr1	165770643	165770717	+	1	NA	exon (NM_011804, exon 3 of 4)	exon (NM_011804, exon 3 of 4)	6900	NM_011804	433375	Mm.294885	NM_011804	ENSMUSG00000040713	Creg1	AA755314|Creg	cellular repressor of E1A-stimulated genes 1	protein-coding
mm_97803.1	chr11	82956895	82956905	+	1	NA	exon (NM_183201, exon 3 of 6)	exon (NM_183201, exon 3 of 6)	3781	NR_045932	76392	Mm.295205	NR_045932	ENSMUSG00000086327	Slfn5os	1700003F17Rik	schlafen 5, opposite strand	ncRNA
mm_130321.1	chr15	97469707	97469733	-	1	NA	Intergenic	PB1D10|SINE|Alu	-222433	NM_001164602	105827	Mm.24005	NM_178114	ENSMUSG00000048218	Amigo2	AI415330|AMIGO-2|AW208913|Ali1	adhesion molecule with Ig like domain 2	protein-coding
mm_98059.1	chr11	85831227	85831266	+	1	NA	intron (NR_077059, intron 1 of 4)	intron (NR_077059, intron 1 of 4)	1142	NR_077059	69909	Mm.440214	NR_077059	ENSMUSG00000087013	2610027K06Rik	-	RIKEN cDNA 2610027K06 gene	ncRNA
mm_53112.1	chr6	125096133	125096141	+	1	NA	promoter-TSS (NR_106012)	promoter-TSS (NR_106012)	-26	NM_145979	107932	Mm.333388	NM_145979	ENSMUSG00000063870	Chd4	9530019N15Rik|AA617397|BC005710|D6Ertd380e|Mi-2beta|mKIAA4075	chromodomain helicase DNA binding protein 4	protein-coding
mm_87096.1	chr10	33083245	33083264	+	1	NA	promoter-TSS (NM_029726)	promoter-TSS (NM_029726)	-229	NM_029726	76757	Mm.338508	NM_029726	ENSMUSG00000019787	Trdn	2310045H21Rik|EG432451|TDN	triadin	protein-coding
mm_150874.1	chr19	45055704	45055735	+	1	NA	3' UTR (NM_053197, exon 11 of 11)	3' UTR (NM_053197, exon 11 of 11)	8143	NM_001178013	94280	Mm.36169	NM_053197	ENSMUSG00000025212	Sfxn3	-	sideroflexin 3	protein-coding
mm_37942.1	chr4	133095326	133095353	-	1	NA	Intergenic	Intergenic	-35294	NM_153423	242687	Mm.23566	NM_153423	ENSMUSG00000028868	Wasf2	AW742646|D4Ertd13e|WAVE2	WAS protein family, member 2	protein-coding
mm_78892.1	chr9	44606943	44606947	+	1	NA	intron (NM_001110826, intron 1 of 13)	intron (NM_001110826, intron 1 of 13)	2053	NM_181324	13209	Mm.267061	NM_007841	ENSMUSG00000032097	Ddx6	1110001P04Rik|E230023J21Rik|HLR2|mRCK/P54|p54|rck	DEAD (Asp-Glu-Ala-Asp) box polypeptide 6	protein-coding
mm_19425.1	chr2	91931775	91931793	-	1	NA	promoter-TSS (NM_001291481)	promoter-TSS (NM_001291481)	75	NM_001012336	17242	Mm.906	NM_010784	ENSMUSG00000027239	Mdk	MK|Mek	midkine	protein-coding
mm_167978.1	chrX	159508846	159508863	-	1	NA	Intergenic	RMER13B|LTR|ERVK	-23814	NM_001033472	382252	Mm.296254	NM_001033472	ENSMUSG00000044150	A830080D01Rik	2310067E24Rik|Gm1146	RIKEN cDNA A830080D01 gene	protein-coding
mm_9347.1	chr1	172066769	172066783	-	1	NA	exon (NM_021607, exon 17 of 17)	exon (NM_021607, exon 17 of 17)	-9180	NM_010916	18071	Mm.2474	NM_010916	ENSMUSG00000051251	Nhlh1	Hen1|Nscl|Tal2|bHLHa35	nescient helix loop helix 1	protein-coding
mm_56862.1	chr6	118197795	118197808	-	1	NA	promoter-TSS (NM_009050)	promoter-TSS (NM_009050)	-57	NM_001080780	19713	Mm.57199	NM_009050	ENSMUSG00000030110	Ret	PTC|RET51|RET9|c-Ret	ret proto-oncogene	protein-coding
mm_84867.1	chr9	78630381	78630396	-	1	NA	intron (NM_153098, intron 2 of 32)	intron (NM_153098, intron 2 of 32)	14842	NM_153098	235505	Mm.32955	NM_153098	ENSMUSG00000046186	Cd109	9930012E15Rik|AI480638|GARP	CD109 antigen	protein-coding
mm_40582.1	chr5	64156516	64156533	+	1	NA	Intergenic	Intergenic	-3736	NM_019636	57915	Mm.286353	NM_019636	ENSMUSG00000029174	Tbc1d1	1110062G02Rik|AI385682|AW555803|Nob1|Nobq1|Tbc1|mKIAA1108	TBC1 domain family, member 1	protein-coding
mm_37620.1	chr4	127141484	127141511	-	1	NA	Intergenic	Intergenic	15454	NM_001099319	100039968	Mm.392655	NM_001099319	ENSMUSG00000070737	Tmem35b	Gm12942|OTTMUSG00000009332|Zmym6nb	transmembrane protein 35B	protein-coding
mm_131891.1	chr16	23227853	23227856	+	1	NA	intron (NM_001252505, intron 1 of 7)	MIR3|SINE|MIR	1833	NM_001252505	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_135323.1	chr16	38783861	38783866	-	1	NA	intron (NM_178924, intron 5 of 7)	intron (NM_178924, intron 5 of 7)	16340	NM_178924	22268	Mm.130793	NM_178924	ENSMUSG00000049436	Upk1b	AI413235|Tspan20|UPIb|Upk1	uroplakin 1B	protein-coding
mm_152492.1	chr19	11055819	11055829	-	1	NA	Intergenic	Lx|LINE|L1	-5258	NR_102366	107350	Mm.6381	NM_001177351	ENSMUSG00000075010	AW112010	-	expressed sequence AW112010	ncRNA
mm_146998.1	chr18	34372046	34372056	-	1	NA	intron (NM_007874, intron 2 of 4)	intron (NM_007874, intron 2 of 4)	1364	NM_007874	13476	Mm.280075	NM_007874	ENSMUSG00000005873	Reep5	AI324241|AU022809|AW495741|DP1/TB2|Dp1|R74856|TB2/DP1	receptor accessory protein 5	protein-coding
mm_70257.1	chr8	3515403	3515418	+	1	NA	promoter-TSS (NM_015801)	promoter-TSS (NM_015801)	26	NM_015801	50767	Mm.23085	NM_015801	ENSMUSG00000004565	Pnpla6	AI661849|MSws|Nte	patatin-like phospholipase domain containing 6	protein-coding
mm_35121.1	chr4	11007636	11007655	-	1	NA	promoter-TSS (NM_175175)	promoter-TSS (NM_175175)	-26	NM_175175	71801	Mm.34351	NM_175175	ENSMUSG00000049969	Plekhf2	1110070J07Rik|AA673237|ZFYVE18	pleckstrin homology domain containing, family F (with FYVE domain) member 2	protein-coding
mm_20081.1	chr2	120609501	120609524	-	1	NA	promoter-TSS (NM_025657)	promoter-TSS (NM_025657)	-4	NM_001159609	66606	Mm.428639	NM_025657	ENSMUSG00000027286	Lrrc57	2810002D13Rik|AA407405	leucine rich repeat containing 57	protein-coding
mm_20999.1	chr2	152332640	152332678	-	1	NA	promoter-TSS (NM_019705)	promoter-TSS (NM_019705)	-20	NM_019705	24105	Mm.182145	NM_019705	ENSMUSG00000027466	Rbck1	AL033326|HOIL-1|HOIL-1L|UIP28|Ubce7ip3	RanBP-type and C3HC4-type zinc finger containing 1	protein-coding
mm_57210.1	chr6	122855853	122855856	-	1	NA	intron (NM_009779, intron 1 of 1)	B1_Mur1|SINE|Alu	303	NM_009779	12267	Mm.2408	NM_009779	ENSMUSG00000040552	C3ar1	AZ3B|C3AR|HNFAG09	complement component 3a receptor 1	protein-coding
mm_125007.1	chr15	25364822	25364891	+	1	NA	exon (NM_027395, exon 2 of 2)	exon (NM_027395, exon 2 of 2)	48908	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	brain abundant, membrane attached signal protein 1	protein-coding
mm_115136.1	chr13	104622702	104622718	+	1	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	194243	NM_026072	67285	Mm.235398	NM_026072	ENSMUSG00000021715	Cwc27	3110009E13Rik|NY-CO-10|Sdccag10	CWC27 spliceosome-associated protein	protein-coding
mm_14536.1	chr2	132781702	132781716	+	1	NA	5' UTR (NM_007694, exon 1 of 5)	5' UTR (NM_007694, exon 1 of 5)	431	NM_007694	12653	Mm.255241	NM_007694	ENSMUSG00000027350	Chgb	Scg-1	chromogranin B	protein-coding
mm_28501.1	chr3	92484698	92484713	-	1	NA	5' UTR (NM_009264, exon 2 of 2)	5' UTR (NM_009264, exon 2 of 2)	1176	NM_009264	20753	Mm.331191	NM_009264	ENSMUSG00000050359	Sprr1a	AI528815|SPR1a|mSPRR1A	small proline-rich protein 1A	protein-coding
mm_46150.1	chr5	93306439	93306447	-	1	NA	Intergenic	Intergenic	38870	NM_007635	12452	Mm.3527	NM_007635	ENSMUSG00000029385	Ccng2	-	cyclin G2	protein-coding
mm_136259.1	chr16	91011094	91011104	-	1	NA	promoter-TSS (NM_001045515)	promoter-TSS (NM_001045515)	-4	NM_001045515	104015	Mm.187079	NM_001045515	ENSMUSG00000022973	Synj1	A930006D20Rik|AA675315|mKIAA0910	synaptojanin 1	protein-coding
mm_93062.1	chr10	88826710	88826718	-	1	NA	promoter-TSS (NM_175158)	promoter-TSS (NM_175158)	100	NM_175158	70683	Mm.29631	NM_175158	ENSMUSG00000004356	Utp20	3830408P06Rik|AA617408|Drim|mDRIM|mDRIN	UTP20 small subunit processome component	protein-coding
mm_26229.1	chr3	139205645	139205655	+	1	NA	promoter-TSS (NM_198659)	promoter-TSS (NM_198659)	-243	NM_198659	381476	Mm.188334	NM_198659	ENSMUSG00000047940	Stpg2	B930007M17Rik|Gm1017	sperm tail PG rich repeat containing 2	protein-coding
mm_102588.1	chr11	61878659	61878664	-	1	NA	intron (NM_019921, intron 12 of 14)	intron (NM_019921, intron 12 of 14)	-23569	NM_013881	29869	Mm.162025	NM_013881	ENSMUSG00000004798	Ulk2	A830085I22Rik|AU015340|Unc51.2|mKIAA0623	unc-51 like kinase 2	protein-coding
mm_59040.1	chr7	19344543	19344555	+	1	NA	promoter-TSS (NM_007948)	promoter-TSS (NM_007948)	-522	NM_001127324	13870	Mm.280913	NM_007948	ENSMUSG00000003549	Ercc1	Ercc-1	excision repair cross-complementing rodent repair deficiency, complementation group 1	protein-coding
mm_149592.1	chr19	16146087	16146100	+	1	NA	intron (NM_008139, intron 1 of 6)	T-rich|Low_complexity|Low_complexity	13262	NM_008139	14682	Mm.439701	NM_008139	ENSMUSG00000024639	Gnaq	1110005L02Rik|6230401I02Rik|AA408290|AW060788|Dsk1|Dsk10|Galphaq|Gq|GqI	guanine nucleotide binding protein, alpha q polypeptide	protein-coding
mm_49551.1	chr6	30512323	30512333	+	1	NA	promoter-TSS (NM_029373)	promoter-TSS (NM_029373)	42	NM_029373	75647	Mm.46117	NM_027073	ENSMUSG00000029784	Ssmem1	1700016K02Rik|1700025E21Rik	serine-rich single-pass membrane protein 1	protein-coding
mm_16403.1	chr2	180024952	180025007	+	1	NA	promoter-TSS (NM_177727)	promoter-TSS (NM_177727)	-8	NM_177727	241846	Mm.21577	NM_177727	ENSMUSG00000039108	Lsm14b	9430078B04|BC040823	LSM family member 14B	protein-coding
mm_148673.1	chr19	5637778	5637778	+	1	NA	5' UTR (NM_009045, exon 1 of 11)	5' UTR (NM_009045, exon 1 of 11)	288	NM_009045	19697	Mm.249966	NM_009045	ENSMUSG00000024927	Rela	p65	v-rel reticuloendotheliosis viral oncogene homolog A (avian)	protein-coding
mm_108655.1	chr12	86361459	86361469	+	1	NA	5' UTR (NM_001159500, exon 1 of 7)	5' UTR (NM_001159500, exon 1 of 7)	347	NM_001159500	26380	Mm.235550	NM_011934	ENSMUSG00000021255	Esrrb	Err2|Errb|Estrrb|Nr3b2	estrogen related receptor, beta	protein-coding
mm_147423.1	chr18	46212570	46212590	-	1	NA	promoter-TSS (NM_178872)	promoter-TSS (NM_178872)	27	NM_178872	28105	Mm.277382	NM_178872	ENSMUSG00000033949	Trim36	D18Wsu100e|haprin	tripartite motif-containing 36	protein-coding
mm_107758.1	chr12	59071554	59071570	+	1	NA	exon (NM_008891, exon 9 of 9)	exon (NM_008891, exon 9 of 9)	4643	NM_008891	18949	Mm.22347	NM_008891	ENSMUSG00000020994	Pnn	AU045199|D12Ertd512e	pinin	protein-coding
mm_80732.1	chr9	94668867	94668882	+	1	NA	Intergenic	Intergenic	-1018	NM_177909	331004	Mm.326125	NM_177909	ENSMUSG00000031129	Slc9a9	5730527A11Rik|9930105B05|AI854429|Nhe9	solute carrier family 9 (sodium/hydrogen exchanger), member 9	protein-coding
mm_118031.1	chr13	101659134	101659142	-	1	NA	Intergenic	Intergenic	33492	NM_001024955	18708	Mm.259333	NM_001024955	ENSMUSG00000041417	Pik3r1	PI3K|p50alpha|p55alpha|p85alpha	phosphatidylinositol 3-kinase, regulatory subunit, polypeptide 1 (p85 alpha)	protein-coding
mm_107548.1	chr12	40794285	40794298	+	1	NA	intron (NM_172803, intron 32 of 52)	intron (NM_172803, intron 32 of 52)	-229799	NM_053122	93757	Mm.363813	NM_053122	ENSMUSG00000056899	Immp2l	AI853880|IMP2	IMP2 inner mitochondrial membrane peptidase-like (S. cerevisiae)	protein-coding
mm_65043.1	chr7	18567375	18567395	-	1	NA	promoter-TSS (NM_001037168)	promoter-TSS (NM_001037168)	-80	NM_001037168	545925	Mm.440302	NM_001037168	ENSMUSG00000070797	Psg27	EG545925|cea15	pregnancy-specific glycoprotein 27	protein-coding
mm_164953.1	chr19	5447725	5447729	+	1	NA	promoter-TSS (NM_010235)	promoter-TSS (NM_010235)	29	NM_010235	14283	Mm.6215	NM_010235	ENSMUSG00000024912	Fosl1	AW538199|Fra1|fra-1	fos-like antigen 1	protein-coding
mm_69367.1	chr7	130573131	130573137	-	1	NA	Intergenic	Intergenic	-4350	NM_001004468	57752	Mm.86322	NM_021314	ENSMUSG00000030852	Tacc2	mKIAA4180	transforming, acidic coiled-coil containing protein 2	protein-coding
mm_29058.1	chr3	103778157	103778177	-	1	NA	non-coding (NR_125731, exon 2 of 16)	non-coding (NR_125731, exon 2 of 16)	13108	NM_001301306	15257	Mm.20827	NM_010432	ENSMUSG00000008730	Hipk1	1110062K04Rik|Myak	homeodomain interacting protein kinase 1	protein-coding
mm_140867.1	chr17	23771608	23771636	-	1	NA	promoter-TSS (NM_153791)	promoter-TSS (NM_153791)	-31	NM_153791	224613	Mm.328835	NM_153791	ENSMUSG00000040097	Flywch1	E030034P13Rik|mKIAA1552	FLYWCH-type zinc finger 1	protein-coding
mm_46410.1	chr5	104093284	104093293	-	1	NA	exon (NM_010097, exon 4 of 11)	exon (NM_010097, exon 4 of 11)	-15680	NM_001163772	100271704	Mm.366664	NM_001163772	ENSMUSG00000091034	Gm17660	Scpppq1	predicted gene, 17660	protein-coding
mm_16948.1	chr2	16712120	16712159	-	1	NA	exon (NM_026162, exon 11 of 14)	exon (NM_026162, exon 11 of 14)	301587	NR_040632	75069	Mm.50378	NR_040632		4930515L03Rik	-	RIKEN cDNA 4930515L03 gene	ncRNA
mm_46421.1	chr5	104113691	104113738	-	1	NA	5' UTR (NM_010097, exon 1 of 11)	5' UTR (NM_010097, exon 1 of 11)	374	NM_010097	13602	Mm.29027	NM_010097	ENSMUSG00000029309	Sparcl1	Ecm2|Sc1|hevin|mast9	SPARC-like 1	protein-coding
mm_7913.1	chr1	133690101	133690115	-	1	NA	promoter-TSS (NM_001159649)	promoter-TSS (NM_001159649)	0	NM_001159649	240754	Mm.36534	NM_172842	ENSMUSG00000051998	Lax1	A530029E09|E430019B13Rik	lymphocyte transmembrane adaptor 1	protein-coding
mm_79778.1	chr9	62851419	62851443	+	1	NA	3' UTR (NM_001033175, exon 7 of 7)	3' UTR (NM_001033175, exon 7 of 7)	-6673	NM_001102468	75600	Mm.440576	NM_138304	ENSMUSG00000032246	Calml4	2010002G05Rik	calmodulin-like 4	protein-coding
mm_38191.1	chr4	135353127	135353157	-	1	NA	promoter-TSS (NM_001130477)	promoter-TSS (NM_001130477)	72	NM_016799	51796	Mm.1963	NM_016799	ENSMUSG00000028809	Srrm1	AA407769|POP101|Srm160	serine/arginine repetitive matrix 1	protein-coding
mm_4004.1	chr1	164796724	164796734	+	1	NA	promoter-TSS (NM_019759)	promoter-TSS (NM_019759)	-3	NM_019759	56429	Mm.28935	NM_019759	ENSMUSG00000026574	Dpt	1810032B19Rik|5033416F05Rik|EQ-1|Eq1	dermatopontin	protein-coding
mm_166610.1	chr6	69869222	69869225	-	1	NA	Intergenic	Intergenic	-542049	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_8642.1	chr1	156430033	156430036	-	1	NA	3' UTR (NM_009230, exon 16 of 16)	3' UTR (NM_009230, exon 16 of 16)	-9119	NM_001346967	77352	Mm.428709	NM_001033180	ENSMUSG00000026601	Axdnd1	9430070O13Rik|Gm979	axonemal dynein light chain domain containing 1	protein-coding
mm_28433.1	chr3	90465833	90465846	-	1	NA	promoter-TSS (NM_008727)	promoter-TSS (NM_008727)	27	NM_008727	18160	Mm.4627	NM_008727	ENSMUSG00000027931	Npr1	AI893888|GC-A|NPR-A|NPRA|Pndr	natriuretic peptide receptor 1	protein-coding
mm_157259.1	chrX	19154206	19154227	-	1	NA	Intergenic	Intergenic	-7245	NR_029807	723828		NR_029807	ENSMUSG00000065471	Mir222	Mirn222|mir-222|mmu-mir-222	microRNA 222	ncRNA
mm_115900.1	chr13	23313401	23313414	-	1	NA	promoter-TSS (NR_126443)	promoter-TSS (NR_126443)	0	NR_126443	75322	Mm.108666	NR_126443	ENSMUSG00000085488	4930557F10Rik	-	RIKEN cDNA 4930557F10 gene	ncRNA
mm_150677.1	chr19	42052744	42052760	+	1	NA	exon (NM_025752, exon 1 of 1)	exon (NM_025752, exon 1 of 1)	524	NM_025752	66765	Mm.440412	NM_025752	ENSMUSG00000090369	4933411K16Rik	-	RIKEN cDNA 4933411K16 gene	protein-coding
mm_50653.1	chr6	51470422	51470430	+	1	NA	promoter-TSS (NM_007624)	promoter-TSS (NM_007624)	-190	NM_007624	12417	Mm.280968	NM_007624	ENSMUSG00000029836	Cbx3	HP1g|M32	chromobox 3	protein-coding
mm_163468.1	chr12	102423726	102423740	-	1	NA	5' UTR (NM_011175, exon 2 of 14)	5' UTR (NM_011175, exon 2 of 14)	16080	NM_011175	19141	Mm.17185	NM_011175	ENSMUSG00000021190	Lgmn	AEP|AI746452|AU022324|Prsc1	legumain	protein-coding
mm_102137.1	chr11	53480160	53480176	-	1	NA	promoter-TSS (NM_183173)	promoter-TSS (NM_183173)	27	NM_183173	237761	Mm.145208	NM_183173	ENSMUSG00000044352	Sowaha	A830006N08Rik|Ankrd43	sosondowah ankyrin repeat domain family member A	protein-coding
mm_45144.1	chr5	49159373	49159376	-	1	NA	intron (NM_001199244, intron 1 of 7)	intron (NM_001199244, intron 1 of 7)	126285	NM_001199244	80334	Mm.160172	NM_030265	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding
mm_121540.1	chr14	122464957	122464958	+	1	NA	exon (NM_022987, exon 1 of 2)	exon (NM_022987, exon 1 of 2)	701	NM_022987	65100	Mm.390761	NM_022987	ENSMUSG00000041703	Zic5	1700049L20Rik|Opr	zinc finger protein of the cerebellum 5	protein-coding
mm_62561.1	chr7	103826650	103826668	+	1	NA	3' UTR (NM_001278161, exon 3 of 3)	3' UTR (NM_001278161, exon 3 of 3)	1269	NM_001201391	100503605	Mm.288567	NM_001201391	ENSMUSG00000052305	Hbb-bs	Beta-s|Hbbt1|Hbbt2	hemoglobin, beta adult s chain	protein-coding
mm_139544.1	chr17	56764723	56764733	+	1	NA	promoter-TSS (NM_144858)	promoter-TSS (NM_144858)	-23	NM_144858	224907	Mm.293973	NM_144858	ENSMUSG00000007603	Dus3l	AI662135|AW557805	dihydrouridine synthase 3-like (S. cerevisiae)	protein-coding
mm_59782.1	chr7	28866225	28866255	+	1	NA	TTS (NM_008496)	TTS (NM_008496)	1854	NM_008496	16858	Mm.20973	NM_008496	ENSMUSG00000053522	Lgals7	Galectin-7|Pig1	lectin, galactose binding, soluble 7	protein-coding
mm_46627.1	chr5	108447100	108447110	-	1	NA	intron (NM_172883, intron 1 of 9)	intron (NM_172883, intron 1 of 9)	1786	NM_172883	243197	Mm.106818	NM_172883	ENSMUSG00000029490	Mfsd7a	4732482E20Rik|Mfsd7	major facilitator superfamily domain containing 7A	protein-coding
mm_62236.1	chr7	98656175	98656201	+	1	NA	intron (NM_172280, intron 1 of 19)	CpG	381	NM_172280	233545	Mm.387819	NM_172280	ENSMUSG00000035401	Emsy	2210018M11Rik|2310016L09Rik|AU019521|AU019557	EMSY, BRCA2-interacting transcriptional repressor	protein-coding
mm_100225.1	chr11	117115196	117115257	+	1	NA	promoter-TSS (NM_001166506)	promoter-TSS (NM_001166506)	54	NM_001166506	74136	Mm.272312	NM_028777	ENSMUSG00000020823	Sec14l1	1200017E04Rik|2810012L19Rik|Naa-35	SEC14-like lipid binding 1	protein-coding
mm_76957.1	chr8	106052570	106052581	-	1	NA	intron (NM_001301176, intron 13 of 14)	intron (NM_001301176, intron 13 of 14)	-7028	NM_010901	18021	Mm.383185	NM_010901	ENSMUSG00000031902	Nfatc3	C80703|D8Ertd281e|NFAT4|NFATx	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 3	protein-coding
mm_72508.1	chr8	83900097	83900110	+	1	NA	promoter-TSS (NM_181039)	promoter-TSS (NM_181039)	5	NM_181039	330814	Mm.260733	NM_181039	ENSMUSG00000013033	Adgrl1	2900070I05Rik|AI182398|CLIBA|Lec2|Lphn1|mKIAA0821	adhesion G protein-coupled receptor L1	protein-coding
mm_60271.1	chr7	43842266	43842305	+	1	NA	promoter-TSS (NM_026806)	promoter-TSS (NM_026806)	16	NM_026806	68668	Mm.458122	NM_026806	ENSMUSG00000074155	Klk5	1110030O19Rik	kallikrein related-peptidase 5	protein-coding
mm_2631.1	chr1	121431129	121431152	+	1	NA	promoter-TSS (NM_029955)	promoter-TSS (NM_029955)	73	NM_001025156	70829	Mm.25788	NM_027567	ENSMUSG00000026339	Ccdc93	4633402D15Rik|9230102M16Rik	coiled-coil domain containing 93	protein-coding
mm_112392.1	chr12	119238589	119238602	-	1	NA	promoter-TSS (NM_177290)	promoter-TSS (NM_177290)	-319	NM_177290	320910	Mm.217000	NM_177290	ENSMUSG00000025321	Itgb8	4832412O06Rik	integrin beta 8	protein-coding
mm_75961.1	chr8	71721816	71721819	-	1	NA	intron (NR_131256, intron 2 of 25)	intron (NR_131256, intron 2 of 25)	3864	NR_131256	74015	Mm.22025	NM_028715	ENSMUSG00000070000	Fcho1	3322402E17Rik|N28152	FCH domain only 1	protein-coding
mm_62435.1	chr7	101363044	101363090	+	1	NA	intron (NM_001040111, intron 1 of 33)	intron (NM_001040111, intron 1 of 33)	14998	NM_001040111	69710	Mm.277687	NM_027180	ENSMUSG00000032812	Arap1	2410002L19Rik|Centd2|mKIAA0782	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	protein-coding
mm_54733.1	chr6	40929732	40929745	-	1	NA	intron (NM_028550, intron 2 of 6)	intron (NM_028550, intron 2 of 6)	10819	NM_028550	73481	Mm.333010	NM_028550	ENSMUSG00000029883	1700074P13Rik	AV047902|Tryx5	RIKEN cDNA 1700074P13 gene	protein-coding
mm_150555.1	chr19	39329152	39329186	+	1	NA	exon (NM_007815, exon 8 of 9)	exon (NM_007815, exon 8 of 9)	42084	NM_007815	13095	Mm.20764	NM_007815	ENSMUSG00000003053	Cyp2c29	AHOH|AHOHase|AI159681|AI196010|Ah-2|Ahh-1|Cyp2c|P450-2C	cytochrome P450, family 2, subfamily c, polypeptide 29	protein-coding
mm_154118.1	chr19	57182319	57182354	-	1	NA	intron (NM_001290813, intron 1 of 20)	intron (NM_001290813, intron 1 of 20)	15295	NM_001103177	226251	Mm.217161	NM_178688	ENSMUSG00000025085	Ablim1	2210411C18Rik|2610209L21Rik|4833406P10Rik|9330196J19Rik|AV079770|AW060987|AW215784|Limab1|mKIAA0059	actin-binding LIM protein 1	protein-coding
mm_63939.1	chr7	139834092	139834102	+	1	NA	promoter-TSS (NM_177469)	promoter-TSS (NM_177469)	-77	NM_177469	52389	Mm.39863	NM_177469	ENSMUSG00000025475	Adgra1	2900059M17Rik|D7Ertd680e|Gpr123	adhesion G protein-coupled receptor A1	protein-coding
mm_1334.1	chr1	65926520	65926523	+	1	NA	promoter-TSS (NM_027010)	promoter-TSS (NM_027010)	-1	NM_027010	12969	Mm.275362	NM_027010	ENSMUSG00000025945	Crygf	3110001K11Rik|Cryg-2|DGcry-2|Len-2	crystallin, gamma F	protein-coding
mm_17099.1	chr2	23496397	23496400	-	1	NA	Intergenic	L1_Rod|LINE|L1	75706	NM_029773	76857	Mm.276415	NM_029773	ENSMUSG00000026771	Spopl	4921517N04Rik|AU014935|BB233739|E430033K04Rik	speckle-type POZ protein-like	protein-coding
mm_111755.1	chr12	103956570	103956592	-	1	NA	intron (NM_009247, intron 1 of 4)	intron (NM_009247, intron 1 of 4)	316	NM_009247	20704	Mm.312593	NM_009247	ENSMUSG00000072849	Serpina1e	Dom5|PI5|Spi1-5	serine (or cysteine) peptidase inhibitor, clade A, member 1E	protein-coding
mm_503.1	chr1	37100610	37100616	+	1	NA	Intergenic	Intergenic	-117665	NM_001282010	12790	Mm.214224	NM_009918	ENSMUSG00000026114	Cnga3	CNG3	cyclic nucleotide gated channel alpha 3	protein-coding
mm_92986.1	chr10	86701763	86701783	-	1	NA	exon (NM_011631, exon 5 of 18)	exon (NM_011631, exon 5 of 18)	3671	NM_011631	22027	Mm.87773	NM_011631	ENSMUSG00000020048	Hsp90b1	ERp99|GRP94|TA-3|Targ2|Tra-1|Tra1|endoplasmin|gp96	heat shock protein 90, beta (Grp94), member 1	protein-coding
mm_170961.1	chr2	57020337	57020337	+	1	NA	Intergenic	L1Md_A|LINE|L1	94701	NM_013613	18227	Mm.3507	NM_013613	ENSMUSG00000026826	Nr4a2	HZF-3|NOT|Nurr1|RNR-1|TINOR|TINUR	nuclear receptor subfamily 4, group A, member 2	protein-coding
mm_85138.1	chr9	95795883	95795886	-	1	NA	intron (NM_001033210, intron 1 of 15)	intron (NM_001033210, intron 1 of 15)	-45526	NM_011643	22063	Mm.149633	NM_011643	ENSMUSG00000032839	Trpc1	Mtrp1|Trp1|Trrp1	transient receptor potential cation channel, subfamily C, member 1	protein-coding
mm_130258.1	chr15	96642620	96642672	-	1	NA	promoter-TSS (NM_001166456)	promoter-TSS (NM_001166456)	267	NM_001166458	105727	Mm.103568	NM_134086	ENSMUSG00000023169	Slc38a1	AA408026|AA409865|AL022800|AU015942|NAT2	solute carrier family 38, member 1	protein-coding
mm_130031.1	chr15	88954561	88954570	-	1	NA	promoter-TSS (NM_172818)	promoter-TSS (NM_172818)	-147	NM_172818	239591	Mm.86807	NM_172818	ENSMUSG00000022388	Ttll8	1700019P01Rik|4933401B17	tubulin tyrosine ligase-like family, member 8	protein-coding
mm_90268.1	chr10	122679042	122679052	+	1	NA	promoter-TSS (NR_106182)	promoter-TSS (NR_106182)	-268	NR_106182	102466884		NR_106182	ENSMUSG00000099225	Mir8104	Gm27380|mmu-mir-8104	microRNA 8104	ncRNA
mm_65138.1	chr7	19562413	19562437	-	1	NA	promoter-TSS (NM_199149)	promoter-TSS (NM_199149)	-27	NM_199149	232947	Mm.219662	NM_199149	ENSMUSG00000051403	Ppp1r37	Gm158|Lrrc68	protein phosphatase 1, regulatory subunit 37	protein-coding
mm_24689.1	chr3	94974969	94974990	+	1	NA	5' UTR (NM_001293716, exon 1 of 10)	5' UTR (NM_001293716, exon 1 of 10)	248	NM_001293716	107650	Mm.217222	NM_175356	ENSMUSG00000038861	Pi4kb	ESTM41|PI4K-beta|PI4Kbeta|Pik4cb	phosphatidylinositol 4-kinase, catalytic, beta polypeptide	protein-coding
mm_37694.1	chr4	129261395	129261406	-	1	NA	promoter-TSS (NM_001285867)	promoter-TSS (NM_001285867)	4	NM_001285867	97130	Mm.331907	NM_001033189	ENSMUSG00000050390	C77080	Kiaa1522|mKIAA1522	expressed sequence C77080	protein-coding
mm_166431.1	chr5	137166165	137166181	-	1	NA	Intergenic	Intergenic	-49966	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_49520.1	chr6	29894788	29894799	+	1	NA	intron (NM_001347084, intron 11 of 17)	intron (NM_001347084, intron 11 of 17)	-22220	NM_001037740	320609	Mm.56097	NM_177204	ENSMUSG00000039629	Strip2	D330017J20Rik|Fam40b	striatin interacting protein 2	protein-coding
mm_142383.1	chr17	44738022	44738060	-	1	NA	intron (NM_001271627, intron 1 of 7)	intron (NM_001271627, intron 1 of 7)	-1393	NM_001145920	12393	Mm.391013	NM_009820	ENSMUSG00000039153	Runx2	AML3|Cbf|Cbfa-1|Cbfa1|LS3|Osf2|PEBP2aA|Pebp2a1|Pebpa2a	runt related transcription factor 2	protein-coding
mm_12443.1	chr2	71055732	71055816	+	1	NA	promoter-TSS (NM_001165981)	promoter-TSS (NM_001165981)	30	NM_001165980	75763	Mm.281668	NM_198005	ENSMUSG00000041966	Dcaf17	2810055O12Rik|4833418A01Rik|A030004A10Rik|A930009G19Rik|AI448937	DDB1 and CUL4 associated factor 17	protein-coding
mm_127866.1	chr15	8387079	8387081	-	1	NA	intron (NM_201232, intron 1 of 45)	intron (NM_201232, intron 1 of 45)	57383	NM_027707	71175	Mm.240329	NM_027707	ENSMUSG00000022141	Nipbl	Idn3	Nipped-B homolog (Drosophila)	protein-coding
mm_121386.1	chr14	118953486	118953505	+	1	NA	intron (NM_008929, intron 2 of 11)	B3A|SINE|B2	15563	NM_008929	100037258	Mm.12616	NM_008929	ENSMUSG00000022136	Dnajc3	AA408985|AU067833|Dnajc3a|Dnajc3b|Prkri|mp58|p58|p58IPK	DnaJ heat shock protein family (Hsp40) member C3	protein-coding
mm_167155.1	chr7	131334578	131334580	+	1	NA	promoter-TSS (NM_183272)	promoter-TSS (NM_183272)	-43	NM_183272	68223	Mm.233827	NM_183272	ENSMUSG00000030859	Fam24a	1700063I17Rik	family with sequence similarity 24, member A	protein-coding
mm_68463.1	chr7	110372654	110372696	-	1	NA	intron (NM_177324, intron 19 of 40)	intron (NM_177324, intron 19 of 40)	150972	NM_009302	20947	Mm.334144	NM_009302	ENSMUSG00000031015	Swap70	70kDa|AV235546	SWA-70 protein	protein-coding
mm_56607.1	chr6	112475755	112475759	-	1	NA	3' UTR (NM_001081147, exon 2 of 2)	3' UTR (NM_001081147, exon 2 of 2)	14051	NM_001081147	18430	Mm.333310	NM_001081147	ENSMUSG00000049112	Oxtr	OTR	oxytocin receptor	protein-coding
mm_157184.1	chrX	10216686	10216765	-	1	NA	promoter-TSS (NM_001177954)	promoter-TSS (NM_001177954)	70	NM_001177954	19893	Mm.247556	NM_011285	ENSMUSG00000031174	Rpgr	Rp3h	retinitis pigmentosa GTPase regulator	protein-coding
mm_34001.1	chr4	137920766	137920778	+	1	NA	intron (NM_199307, intron 3 of 19)	intron (NM_199307, intron 3 of 19)	58535	NM_199307	230857	Mm.401062	NM_199307	ENSMUSG00000057530	Ece1	AW322500|ECE-1|ECE-1a|ECE-1b|ECE-1d	endothelin converting enzyme 1	protein-coding
mm_29934.1	chr3	131613727	131613739	-	1	NA	intron (NM_001289477, intron 10 of 12)	intron (NM_001289477, intron 10 of 12)	47701	NM_001289477	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_97085.1	chr11	73126755	73126777	+	1	NA	intron (NM_172944, intron 19 of 25)	intron (NM_172944, intron 19 of 25)	11528	NM_010353	14841	Mm.42045	NM_010353	ENSMUSG00000050107	Gsg2	Haspin	germ cell associated 2, haspin	protein-coding
mm_74968.1	chr8	27042982	27043004	-	1	NA	intron (NM_001039077, intron 1 of 4)	CpG	438	NM_054057	114863	Mm.277501	NM_054057	ENSMUSG00000031485	Prosc	1700024N20Rik|2200002F22Rik	proline synthetase co-transcribed	protein-coding
mm_28608.1	chr3	94680859	94680873	-	1	NA	Intergenic	MMERGLN-int|LTR|ERV1	-12707	NM_019414	20342	Mm.225405	NM_019414	ENSMUSG00000068877	Selenbp2	AP56|Lpsb2	selenium binding protein 2	protein-coding
mm_110038.1	chr12	17011513	17011561	-	1	NA	5' UTR (NM_001201332, exon 1 of 5)	5' UTR (NM_001201332, exon 1 of 5)	190	NM_001201332	73667	Mm.159048	NM_001201332	ENSMUSG00000071398	2410004P03Rik	-	RIKEN cDNA 2410004P03 gene	protein-coding
mm_49419.1	chr6	29060218	29060223	+	1	NA	promoter-TSS (NM_008493)	promoter-TSS (NM_008493)	-1	NM_008493	16846	Mm.277072	NM_008493	ENSMUSG00000059201	Lep	ob|obese	leptin	protein-coding
mm_41521.1	chr5	92505031	92505039	+	1	NA	intron (NM_007644, intron 1 of 11)	intron (NM_007644, intron 1 of 11)	622	NM_007644	12492	Mm.297964	NM_007644	ENSMUSG00000029426	Scarb2	9330185J12Rik|Cd36l2|LGP85|LIMP II|LIMP-2|MLGP85	scavenger receptor class B, member 2	protein-coding
mm_111473.1	chr12	98578107	98578121	-	1	NA	promoter-TSS (NM_029911)	promoter-TSS (NM_029911)	99	NM_029911	72258	Mm.196158	NM_029911	ENSMUSG00000033854	Kcnk10	1700024D23Rik|3010005K24Rik|Trek2	potassium channel, subfamily K, member 10	protein-coding
mm_20574.1	chr2	131085766	131085779	-	1	NA	exon (NM_011426, exon 2 of 21)	exon (NM_011426, exon 2 of 21)	993	NM_011426	20612	Mm.1374	NM_011426	ENSMUSG00000027322	Siglec1	Cd169|Siglec-1|Sn	sialic acid binding Ig-like lectin 1, sialoadhesin	protein-coding
mm_20187.1	chr2	122606904	122606915	-	1	NA	intron (NM_025961, intron 2 of 8)	PB1D10|SINE|Alu	4368	NM_025961	67092	Mm.29975	NM_025961	ENSMUSG00000027199	Gatm	1810003P21Rik|AI314789|AT	glycine amidinotransferase (L-arginine:glycine amidinotransferase)	protein-coding
mm_31926.1	chr4	85514284	85514292	+	1	NA	Intergenic	CpG	308832	NM_019535	20404	Mm.143603	NM_019535	ENSMUSG00000028488	Sh3gl2	9530001L19Rik|AI120490|AW555077|B930049H17Rik|EEN-B1|SH3PA|Sh3d2a	SH3-domain GRB2-like 2	protein-coding
mm_383.1	chr1	34065763	34065767	+	1	NA	intron (NM_133833, intron 1 of 92)	intron (NM_133833, intron 1 of 92)	-51594	NR_105861	102466987		NR_105861	ENSMUSG00000105982	Mir6896	mmu-mir-6896	microRNA 6896	ncRNA
mm_155527.1	chrX	74281894	74281924	+	1	NA	promoter-TSS (NM_001242616)	promoter-TSS (NM_001242616)	-173	NM_027109	69537	Mm.20169	NM_027109	ENSMUSG00000019088	Dnase1l1	2310005K03Rik|AI324885|Dnase1ll|Dnasex|Dnl1ll|G4.8	deoxyribonuclease 1-like 1	protein-coding
mm_16184.1	chr2	172977554	172977558	+	1	NA	Intergenic	Intergenic	-2286	NM_012046	26972	Mm.23495	NM_012046	ENSMUSG00000005883	Spo11	AI449549|Spo11a|Spo11b	SPO11 meiotic protein covalently bound to DSB	protein-coding
mm_56158.1	chr6	87851075	87851085	-	1	NA	promoter-TSS (NM_013493)	promoter-TSS (NM_013493)	26	NM_001109746	12785	Mm.290251	NM_013493	ENSMUSG00000030057	Cnbp	AA408710|Cnbp1|Znf9	cellular nucleic acid binding protein	protein-coding
mm_4937.1	chr1	191171611	191171648	+	1	NA	exon (NM_007498, exon 4 of 4)	exon (NM_007498, exon 4 of 4)	-6812	NM_001109759	619288	Mm.61148	NM_001109759	ENSMUSG00000091017	Fam71a	4933417M04Rik|GARI-L4	family with sequence similarity 71, member A	protein-coding
mm_168033.1	chrY	90739393	90739398	-	1	NA	Intergenic	Intergenic	15655	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_131929.1	chr16	23609963	23609999	+	1	NA	promoter-TSS (NM_023386)	promoter-TSS (NM_023386)	62	NM_023386	67775	Mm.475107	NM_023386	ENSMUSG00000033355	Rtp4	5830458K16Rik|Ifrg28	receptor transporter protein 4	protein-coding
mm_30057.1	chr3	136935775	136935782	-	1	NA	3' UTR (NM_001293622, exon 13 of 13)	3' UTR (NM_001293622, exon 13 of 13)	265712	NM_001293622	19055	Mm.331389	NM_008913	ENSMUSG00000028161	Ppp3ca	2900074D19Rik|CN|Caln|Calna|CnA	protein phosphatase 3, catalytic subunit, alpha isoform	protein-coding
mm_117730.1	chr13	95604904	95604913	-	1	NA	exon (NM_010169, exon 2 of 2)	exon (NM_010169, exon 2 of 2)	13525	NM_010169	14062	Mm.24816	NM_010169	ENSMUSG00000048376	F2r	AI482343|Cf2r|Par1|ThrR	coagulation factor II (thrombin) receptor	protein-coding
mm_17846.1	chr2	34372641	34372651	-	1	NA	promoter-TSS (NM_001290576)	promoter-TSS (NM_001290576)	-601	NM_016768	18516	Mm.239941	NM_016768	ENSMUSG00000038718	Pbx3	-	pre B cell leukemia homeobox 3	protein-coding
mm_83820.1	chr9	53706212	53706251	-	1	NA	promoter-TSS (NM_175562)	promoter-TSS (NM_175562)	1	NM_175562	270160	Mm.290285	NM_175562	ENSMUSG00000055069	Rab39	C230094F14Rik|Rab39a	RAB39, member RAS oncogene family	protein-coding
mm_1783.1	chr1	78537939	78537941	+	1	NA	intron (NM_026713, intron 6 of 6)	intron (NM_026713, intron 6 of 6)	26880	NM_026713	68393	Mm.41325	NM_026713	ENSMUSG00000012187	Mogat1	0610030A14Rik|1110064N14Rik|Dgat2l|Dgat2l1|MGAT1|WI1-2612I11.1|mDC2	monoacylglycerol O-acyltransferase 1	protein-coding
mm_170896.1	chr2	29066086	29066086	+	1	NA	intron (NM_009442, intron 2 of 11)	intron (NM_009442, intron 2 of 11)	5823	NM_009442	22130	Mm.252195	NM_009442	ENSMUSG00000026803	Ttf1	AV245725|TTF-1|TTF-I	transcription termination factor, RNA polymerase I	protein-coding
mm_111870.1	chr12	108002115	108002123	-	1	NA	intron (NM_001079883, intron 1 of 3)	intron (NM_001079883, intron 1 of 3)	1295	NM_001079883	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_134125.1	chr16	10384064	10384092	-	1	NA	intron (NM_001291001, intron 3 of 6)	intron (NM_001291001, intron 3 of 6)	11370	NM_001099275	70426	Mm.142181	NM_001099275	ENSMUSG00000039179	Tekt5	3300001K11Rik	tektin 5	protein-coding
mm_99047.1	chr11	99041263	99041267	+	1	NA	promoter-TSS (NM_010517)	promoter-TSS (NM_010517)	5	NM_010517	16010	Mm.233799	NM_010517	ENSMUSG00000017493	Igfbp4	AI875747|Deb2|IGFBP-4	insulin-like growth factor binding protein 4	protein-coding
mm_123587.1	chr14	67072418	67072461	-	1	NA	promoter-TSS (NM_028032)	promoter-TSS (NM_028032)	32	NM_028032	71978	Mm.273997	NM_028032	ENSMUSG00000022052	Ppp2r2a	2410004D02Rik|mKIAA1541	protein phosphatase 2, regulatory subunit B, alpha	protein-coding
mm_9521.1	chr1	173760168	173760207	-	1	NA	exon (NM_008329, exon 3 of 9)	exon (NM_008329, exon 3 of 9)	6732	NM_008329	15951	Mm.261270	NM_008329	ENSMUSG00000073489	Ifi204	Ifi16|p204	interferon activated gene 204	protein-coding
mm_131937.1	chr16	23613352	23613365	+	1	NA	exon (NM_023386, exon 2 of 2)	exon (NM_023386, exon 2 of 2)	3439	NM_023386	67775	Mm.475107	NM_023386	ENSMUSG00000033355	Rtp4	5830458K16Rik|Ifrg28	receptor transporter protein 4	protein-coding
mm_169676.1	chr15	66453877	66453877	-	1	NA	intron (NM_019457, intron 5 of 11)	intron (NM_019457, intron 5 of 11)	47033	NM_019457	54562	Mm.244890	NM_019457	ENSMUSG00000022375	Lrrc6	LRTP	leucine rich repeat containing 6 (testis)	protein-coding
mm_168742.1	chr12	115335561	115335570	-	1	NA	Intergenic	Intergenic	360229	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
mm_2585.1	chr1	118653752	118653755	+	1	NA	exon (NM_023755, exon 5 of 15)	exon (NM_023755, exon 5 of 15)	25808	NM_023755	81879	Mm.24621	NM_023755	ENSMUSG00000026380	Tfcp2l1	1810030F05Rik|4932442M07Rik|AA575098|Cp2l1|Crtr-1|D930018N21Rik|LBP-9|Tcfcp2l1	transcription factor CP2-like 1	protein-coding
mm_158127.1	chrX	102644187	102644204	-	1	NA	promoter-TSS (NM_008832)	promoter-TSS (NM_008832)	51	NM_008832	18679	Mm.212889	NM_008832	ENSMUSG00000034055	Phka1	5330411D17|9830108K24Rik|Phka	phosphorylase kinase alpha 1	protein-coding
mm_76351.1	chr8	84746307	84746335	-	1	NA	intron (NM_001297601, intron 2 of 8)	intron (NM_001297601, intron 2 of 8)	28048	NM_001081981	18032	Mm.9394	NM_010906	ENSMUSG00000001911	Nfix	CTF|NF-I/X|NF1-X|NFI-X	nuclear factor I/X	protein-coding
mm_149748.1	chr19	22641498	22641503	+	1	NA	intron (NM_177341, intron 1 of 26)	L1M2|LINE|L1	-51119	NM_001035245	226025	Mm.131943	NM_177341	ENSMUSG00000052387	Trpm3	6330504P12Rik|9330180E14|AU018608|B930001P07Rik|LTRPC3|MLSN2	transient receptor potential cation channel, subfamily M, member 3	protein-coding
mm_169920.1	chr16	57391260	57391260	-	1	NA	intron (NM_001040397, intron 1 of 4)	LSU-rRNA_Hsa|rRNA|rRNA	37983	NM_001040397	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding
mm_146536.1	chr18	5404576	5404589	-	1	NA	Intergenic	Intergenic	-70143	NM_178722	240186	Mm.118257	NM_178722	ENSMUSG00000050945	Zfp438	9430031G09|9430091M14Rik|B830013J05Rik	zinc finger protein 438	protein-coding
mm_89196.1	chr10	86347814	86347825	+	1	NA	3' UTR (NM_011595, exon 5 of 5)	3' UTR (NM_011595, exon 5 of 5)	47407	NM_011595	21859	Mm.4871	NM_011595	ENSMUSG00000020044	Timp3	Timp-3	tissue inhibitor of metalloproteinase 3	protein-coding
mm_70504.1	chr8	12873903	12873929	+	1	NA	Intergenic	Intergenic	-41977	NM_178076	17207	Mm.334413	NM_178076	ENSMUSG00000031442	Mcf2l	C130040G20Rik|Dbs|Ost|mKIAA0362	mcf.2 transforming sequence-like	protein-coding
mm_62398.1	chr7	101108601	101108642	+	1	NA	promoter-TSS (NM_001146010)	promoter-TSS (NM_001146010)	-154	NM_001146010	207278	Mm.263041	NM_199012	ENSMUSG00000030691	Fchsd2	BC034086|R74866|Sh3md3|mKIAA0769	FCH and double SH3 domains 2	protein-coding
mm_4910.1	chr1	190170342	190170358	+	1	NA	5' UTR (NM_008937, exon 1 of 5)	5' UTR (NM_008937, exon 1 of 5)	330	NM_008937	19130	Mm.132579	NM_008937	ENSMUSG00000010175	Prox1	A230003G05Rik	prospero homeobox 1	protein-coding
mm_80661.1	chr9	90055281	90055311	+	1	NA	intron (NM_001312649, intron 1 of 10)	intron (NM_001312649, intron 1 of 10)	1029	NM_001312649	13036	Mm.2277	NM_007801	ENSMUSG00000032359	Ctsh	AL022844	cathepsin H	protein-coding
mm_48627.1	chr5	145135133	145135152	-	1	NA	exon (NM_001033313, exon 3 of 6)	exon (NM_001033313, exon 3 of 6)	4947	NM_001033313	231887	Mm.188851	NM_001033313	ENSMUSG00000029623	Pdap1	HASPP28|PAP|PAP1	PDGFA associated protein 1	protein-coding
mm_86822.1	chr10	20959596	20959643	+	1	NA	5' UTR (NM_026203, exon 2 of 24)	5' UTR (NM_026203, exon 2 of 24)	7072	NM_026203	52906	Mm.253280	NM_026203	ENSMUSG00000019986	Ahi1	1700015F03Rik|Ahi-1|D10Bwg0629e	Abelson helper integration site 1	protein-coding
mm_150507.1	chr19	39023914	39023927	+	1	NA	intron (NM_028089, intron 4 of 8)	Lx9|LINE|L1	16901	NM_028089	72082	Mm.142581	NM_028089	ENSMUSG00000025002	Cyp2c55	2010318C06Rik	cytochrome P450, family 2, subfamily c, polypeptide 55	protein-coding
mm_654.1	chr1	40431044	40431057	+	1	NA	intron (NM_001294171, intron 1 of 7)	intron (NM_001294171, intron 1 of 7)	1480	NM_001294171	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_29683.1	chr3	123026140	123026150	-	1	NA	exon (NM_021503, exon 3 of 6)	exon (NM_021503, exon 3 of 6)	8842	NM_021503	59006	Mm.141157	NM_021503	ENSMUSG00000028116	Myoz2	1110012I24Rik|Fatz-2|Myozl2	myozenin 2	protein-coding
mm_135625.1	chr16	52278341	52278342	-	1	NA	intron (NM_009655, intron 8 of 15)	Lx9|LINE|L1	174740	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_110691.1	chr12	69184421	69184438	-	1	NA	promoter-TSS (NM_025589)	promoter-TSS (NM_025589)	271	NM_146035	217664	Mm.206642	NM_146035	ENSMUSG00000043998	Mgat2	AA407964|CDGS2|GLCNACTII|GNT-II|GNT2	mannoside acetylglucosaminyltransferase 2	protein-coding
mm_146820.1	chr18	21148920	21148921	-	1	NA	intron (NM_001033445, intron 3 of 5)	intron (NM_001033445, intron 3 of 5)	76576	NM_008586	17288	Mm.2682	NM_008586	ENSMUSG00000024313	Mep1b	Mep-1b	meprin 1 beta	protein-coding
mm_1378.1	chr1	66700877	66700898	+	1	NA	promoter-TSS (NM_001310644)	promoter-TSS (NM_001310644)	56	NM_001310644	66646	Mm.240912	NM_025683	ENSMUSG00000026005	Rpe	2810429B02Rik|5730518J08Rik	ribulose-5-phosphate-3-epimerase	protein-coding
mm_74065.1	chr8	122424771	122424787	+	1	NA	TTS (NM_007806)	TTS (NM_007806)	2694	NM_145834	234836	Mm.222808	NM_145834	ENSMUSG00000046108	Il17c	IL-17C	interleukin 17C	protein-coding
mm_43176.1	chr5	127632239	127632271	+	1	NA	promoter-TSS (NM_177005)	promoter-TSS (NM_177005)	-7	NM_177005	319804	Mm.237888	NM_177005	ENSMUSG00000049971	Glt1d1	5730455A04Rik	glycosyltransferase 1 domain containing 1	protein-coding
mm_143318.1	chr17	66206675	66206714	-	1	NA	Intergenic	Intergenic	83174	NM_001003919	320209	Mm.259605	NM_001003919	ENSMUSG00000035842	Ddx11	4732462I11Rik|CHL1|CHLR1|KRG2|essa15a	DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11	protein-coding
mm_102359.1	chr11	58323296	58323357	-	1	NA	promoter-TSS (NM_001256517)	promoter-TSS (NM_001256517)	39	NM_001256517	319475	Mm.72124	NM_178761	ENSMUSG00000049755	Zfp672	4930488P06Rik|4930511N19Rik|Znf672	zinc finger protein 672	protein-coding
mm_155416.1	chrX	73490821	73490829	+	1	NA	exon (NM_007542, exon 2 of 8)	exon (NM_007542, exon 2 of 8)	7224	NM_007542	12111	Mm.2608	NM_007542	ENSMUSG00000031375	Bgn	BG|DSPG1|PG-S1|PGI|SLRR1A	biglycan	protein-coding
mm_129088.1	chr15	75909320	75909330	-	1	NA	promoter-TSS (NM_001285430)	promoter-TSS (NM_001285430)	19	NM_001285433	66656	Mm.258927	NM_023240	ENSMUSG00000055762	Eef1d	EF-1-delta	eukaryotic translation elongation factor 1 delta (guanine nucleotide exchange protein)	protein-coding
mm_98004.1	chr11	84179612	84179657	+	1	NA	Intergenic	CpG	-12158	NM_001037932	628813	Mm.390389	NM_001037932	ENSMUSG00000051452	Gm11437	AI463690|OTTMUSG00000000997	predicted gene 11437	protein-coding
mm_114968.1	chr13	97190537	97190575	+	1	NA	intron (NM_010422, intron 3 of 13)	LSU-rRNA_Hsa|rRNA|rRNA	7801	NM_010422	15212	Mm.27816	NM_010422	ENSMUSG00000021665	Hexb	-	hexosaminidase B	protein-coding
mm_105544.1	chr11	106324935	106324962	-	1	NA	intron (NM_133199, intron 18 of 23)	intron (NM_133199, intron 18 of 23)	-10386	NM_001313939	15985	Mm.2987	NM_008339	ENSMUSG00000040592	Cd79b	B29|Ig-beta|Igb|Igbeta	CD79B antigen	protein-coding
mm_117824.1	chr13	98016264	98016283	-	1	NA	intron (NM_012026, intron 9 of 35)	intron (NM_012026, intron 9 of 35)	189892	NM_012026	110596	Mm.252718	NM_012026	ENSMUSG00000021662	Arhgef28	9230110L08Rik|AI323540|D13Bwg1089e|RIP2|Rgnef|RhoGEF|Rhoip2|p190RhoGEF	Rho guanine nucleotide exchange factor (GEF) 28	protein-coding
mm_30451.1	chr3	153852484	153852485	-	1	NA	promoter-TSS (NR_040373)	promoter-TSS (NR_040373)	-60	NR_040373	72317	Mm.440147	NR_040373	ENSMUSG00000086438	Asb17os	2510003D18Rik	ankyrin repeat and SOCS box-containing 17, opposite strand	ncRNA
mm_76094.1	chr8	79712744	79712746	-	1	NA	intron (NM_026904, intron 1 of 4)	RMER10B|LTR|ERVL	925	NM_026904	68999	Mm.257445	NM_026904	ENSMUSG00000036977	Anapc10	1500026N15Rik|A830003M23Rik|APC10	anaphase promoting complex subunit 10	protein-coding
mm_97756.1	chr11	80509798	80509798	+	1	NA	promoter-TSS (NR_126552)	promoter-TSS (NR_126552)	-692	NR_126552	77417	Mm.437510	NR_126552	ENSMUSG00000085078	C030013C21Rik	-	RIKEN cDNA C030013C21 gene	ncRNA
mm_28374.1	chr3	89959119	89959130	-	1	NA	intron (NM_001081182, intron 2 of 27)	intron (NM_001081182, intron 2 of 27)	4208	NM_001081182	54667	Mm.30455	NM_001081182	ENSMUSG00000060671	Atp8b2	Id	ATPase, class I, type 8B, member 2	protein-coding
mm_76477.1	chr8	85536913	85536919	-	1	NA	TTS (NM_019794)	TTS (NM_019794)	18355	NM_019794	56445	Mm.475573	NM_019794	ENSMUSG00000031701	Dnaja2	1500017M13Rik|2010206B19Rik|DNAJ|DNJ3|Dnaj3|HIRIP4|PRO3015|mDj3	DnaJ heat shock protein family (Hsp40) member A2	protein-coding
mm_10255.1	chr2	9352469	9352480	+	1	NA	Intergenic	Intergenic	162959	NR_038180	73438	Mm.23558	NR_038180	ENSMUSG00000085580	1700061F12Rik	-	RIKEN cDNA 1700061F12 gene	ncRNA
mm_100049.1	chr11	115163418	115163419	+	1	NA	promoter-TSS (NM_012030)	promoter-TSS (NM_012030)	77	NM_012030	26941	Mm.27842	NM_012030	ENSMUSG00000020733	Slc9a3r1	EBP-50|NHE-RF|NHERF-1|NHERF1	solute carrier family 9 (sodium/hydrogen exchanger), member 3 regulator 1	protein-coding
mm_55123.1	chr6	50505722	50505752	-	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-49383	NM_001347213	71720	Mm.44153	NM_027881	ENSMUSG00000029822	Osbpl3	1200014M06Rik|6720421I08Rik|A530055M08|ORP-3|ORP3|OSBP3	oxysterol binding protein-like 3	protein-coding
mm_87495.1	chr10	51496086	51496090	+	1	NA	intron (NM_001291894, intron 8 of 8)	intron (NM_001291894, intron 8 of 8)	5190	NM_013532	14728	Mm.34408	NM_013532	ENSMUSG00000062593	Lilrb4a	CD85K|Gp49b|HM18|ILT3|LIR-5|Lilrb4|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4A	protein-coding
mm_13133.1	chr2	91880540	91880543	+	1	NA	intron (NM_172669, intron 12 of 17)	intron (NM_172669, intron 12 of 17)	-41648	NM_007699	12672	Mm.330405	NM_007699	ENSMUSG00000040495	Chrm4	Chrm-4|M4	cholinergic receptor, muscarinic 4	protein-coding
mm_119501.1	chr14	47380276	47380306	+	1	NA	exon (NM_010705, exon 3 of 6)	exon (NM_010705, exon 3 of 6)	6431	NM_001145953	16854	Mm.248615	NM_010705	ENSMUSG00000050335	Lgals3	GBP|L-34|Mac-2|gal3	lectin, galactose binding, soluble 3	protein-coding
mm_116968.1	chr13	56178602	56178637	-	1	NA	5' UTR (NM_001168615, exon 1 of 3)	5' UTR (NM_001168615, exon 1 of 3)	266	NM_145976	212937	Mm.116697	NM_145976	ENSMUSG00000049625	Tifab	-	TRAF-interacting protein with forkhead-associated domain, family member B	protein-coding
mm_103387.1	chr11	75416255	75416260	-	1	NA	exon (NM_011340, exon 3 of 8)	exon (NM_011340, exon 3 of 8)	6366	NM_011340	20317	Mm.2044	NM_011340	ENSMUSG00000000753	Serpinf1	AI195227|EPC-1|Pedf|Pedfl|Sdf3	serine (or cysteine) peptidase inhibitor, clade F, member 1	protein-coding
mm_123602.1	chr14	67933513	67933585	-	1	NA	promoter-TSS (NM_177780)	promoter-TSS (NM_177780)	23	NM_177780	68813	Mm.258155	NM_177780	ENSMUSG00000044447	Dock5	1110060D06Rik|AI666732|AI956923|BC016533|E130320D18|lr2|rlc	dedicator of cytokinesis 5	protein-coding
mm_100980.1	chr11	7209507	7209512	-	1	NA	exon (NM_008343, exon 3 of 5)	exon (NM_008343, exon 3 of 5)	4414	NM_008343	16009	Mm.29254	NM_008343	ENSMUSG00000020427	Igfbp3	AI649005|IGFBP-3|IGgfbp3	insulin-like growth factor binding protein 3	protein-coding
mm_12470.1	chr2	71437101	71437146	+	1	NA	intron (NM_026115, intron 9 of 10)	L2b|LINE|L2	-16215	NM_025633	66559	Mm.152796	NM_025633	ENSMUSG00000041921	Metap1d	2310066F24Rik|3110033D18Rik|AV117938|MAP 1D|Map1d|MetAP 1D|Metapl1	methionyl aminopeptidase type 1D (mitochondrial)	protein-coding
mm_17936.1	chr2	35979810	35979825	-	1	NA	promoter-TSS (NM_029774)	promoter-TSS (NM_029774)	-193	NM_029774	74410	Mm.21591	NM_028921	ENSMUSG00000026885	Ttll11	4932702F08Rik|4933424A20Rik|AU043211|D2Ertd624e	tubulin tyrosine ligase-like family, member 11	protein-coding
mm_152171.1	chr19	7334207	7334229	-	1	NA	intron (NM_007928, intron 1 of 17)	intron (NM_007928, intron 1 of 17)	7642	NM_001080389	13728	Mm.258986	NM_007928	ENSMUSG00000024969	Mark2	EMK-1|Emk|Par-1|Par-1b	MAP/microtubule affinity regulating kinase 2	protein-coding
mm_61724.1	chr7	81859041	81859053	+	1	NA	promoter-TSS (NM_145375)	promoter-TSS (NM_145375)	46	NM_145375	107769	Mm.221412	NM_145375	ENSMUSG00000038623	Tm6sf1	AI428514|BC023123|C630016D09Rik	transmembrane 6 superfamily member 1	protein-coding
mm_27941.1	chr3	79628661	79628745	-	1	NA	promoter-TSS (NM_025794)	promoter-TSS (NM_025794)	64	NM_025794	66841	Mm.28336	NM_025794	ENSMUSG00000027809	Etfdh	0610010I20Rik|AV001013	electron transferring flavoprotein, dehydrogenase	protein-coding
mm_30958.1	chr4	33923846	33923856	+	1	NA	promoter-TSS (NM_007726)	promoter-TSS (NM_007726)	-781	NM_007726	12801	Mm.7992	NM_007726	ENSMUSG00000044288	Cnr1	CB-R|CB1|CB1R	cannabinoid receptor 1 (brain)	protein-coding
mm_158975.1	chr1	118389098	118389098	+	1	NA	promoter-TSS (NM_029709)	promoter-TSS (NM_029709)	40	NM_001293301	76707	Mm.138740	NM_029709	ENSMUSG00000064302	Clasp1	1700030C23Rik|5730583A19Rik|B130045P17Rik|CLASP1alpha	CLIP associating protein 1	protein-coding
mm_18530.1	chr2	63184535	63184549	-	1	NA	promoter-TSS (NM_133207)	promoter-TSS (NM_133207)	-255	NM_133207	170738	Mm.242532	NM_133207	ENSMUSG00000059742	Kcnh7	9330137I11Rik|Kv11.3|erg3	potassium voltage-gated channel, subfamily H (eag-related), member 7	protein-coding
mm_115530.1	chr13	6109069	6109078	-	1	NA	Intergenic	Intergenic	247584	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_6341.1	chr1	71637280	71637290	-	1	NA	exon (NM_001276413, exon 12 of 44)	exon (NM_001276413, exon 12 of 44)	15949	NM_010233	14268	Mm.193099	NM_010233	ENSMUSG00000026193	Fn1	E330027I09|Fn|Fn-1	fibronectin 1	protein-coding
mm_165991.1	chr4	109665282	109665296	-	1	NA	promoter-TSS (NM_007671)	promoter-TSS (NM_007671)	83	NM_007671	12580	Mm.1912	NM_007671	ENSMUSG00000028551	Cdkn2c	C77269|INK4c|p18|p18-INK4c|p18-INK6|p18INK4c	cyclin-dependent kinase inhibitor 2C (p18, inhibits CDK4)	protein-coding
mm_132026.1	chr16	27388756	27388758	+	1	NA	promoter-TSS (NM_001289436)	promoter-TSS (NM_001289436)	-199	NM_001025615	67501	Mm.258985	NM_026202	ENSMUSG00000038127	Ccdc50	C3orf6	coiled-coil domain containing 50	protein-coding
mm_63334.1	chr7	126950688	126950698	+	1	NA	5' UTR (NM_001252566, exon 1 of 17)	5' UTR (NM_001252566, exon 1 of 17)	158	NM_001252566	233878	Mm.283926	NM_144926	ENSMUSG00000030683	Sez6l2	AI835913|AW121566|BSRP-A|Psk1	seizure related 6 homolog like 2	protein-coding
mm_79293.1	chr9	51273801	51273816	+	1	NA	intron (NM_001195681, intron 3 of 4)	intron (NM_001195681, intron 3 of 4)	4746	NM_001195681	100502940	Mm.235705	NM_001195681	ENSMUSG00000079559	Gm684	-	predicted gene 684	protein-coding
mm_168332.1	chr11	118304335	118304337	+	1	NA	intron (NM_011594, intron 4 of 4)	RLTR9D|LTR|ERVK	-14092	NM_001033528	72344	Mm.232293	NM_001033528	ENSMUSG00000033909	Usp36	2700002L06Rik|mKIAA1453	ubiquitin specific peptidase 36	protein-coding
mm_16468.1	chr2	180710203	180710216	+	1	NA	promoter-TSS (NM_001291432)	promoter-TSS (NM_001291432)	-17	NM_001289652	76425	Mm.41464	NM_029607	ENSMUSG00000027573	Gid8	2310003C23Rik|4833420G11Rik|AI451474|Twa1	GID complex subunit 8	protein-coding
mm_102689.1	chr11	65648396	65648427	-	1	NA	Intergenic	Intergenic	86421	NR_030417	791070		NR_030417	ENSMUSG00000076460	Mir744	Mirn744|mir-744|mmu-mir-744	microRNA 744	ncRNA
mm_11.1	chr1	4845594	4845604	+	1	NA	3' UTR (NM_008866, exon 9 of 9)	3' UTR (NM_008866, exon 9 of 9)	-12095	NM_001159750	21399	Mm.207263	NM_011541	ENSMUSG00000033813	Tcea1	S-II	transcription elongation factor A (SII) 1	protein-coding
mm_50810.1	chr6	54326853	54326888	+	1	NA	promoter-TSS (NM_030024)	promoter-TSS (NM_030024)	-142	NM_030024	78004	Mm.41984	NM_030024	ENSMUSG00000045725	Prr15	E130201N16Rik|G90	proline rich 15	protein-coding
mm_50680.1	chr6	51569947	51569995	+	1	NA	intron (NM_028035, intron 2 of 6)	intron (NM_028035, intron 2 of 6)	25448	NM_001127348	71982	Mm.294166	NM_028035	ENSMUSG00000038301	Snx10	2410004M09Rik	sorting nexin 10	protein-coding
mm_17136.1	chr2	24975832	24975839	-	1	NA	promoter-TSS (NM_001031808)	promoter-TSS (NM_001031808)	-198	NM_146251	241274	Mm.389243	NM_146251	ENSMUSG00000036833	Pnpla7	BC027342|E430013P11Rik|Nre	patatin-like phospholipase domain containing 7	protein-coding
mm_112447.1	chr13	5861627	5861637	+	1	NA	5' UTR (NM_011803, exon 1 of 4)	5' UTR (NM_011803, exon 1 of 4)	143	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_38134.1	chr4	134703786	134703813	-	1	NA	5' UTR (NM_207237, exon 1 of 12)	5' UTR (NM_207237, exon 1 of 12)	491	NM_207237	230815	Mm.18905	NM_207237	ENSMUSG00000037306	Man1c1	AI593348	mannosidase, alpha, class 1C, member 1	protein-coding
mm_7583.1	chr1	125414724	125414736	-	1	NA	intron (NM_001205385, intron 4 of 12)	intron (NM_001205385, intron 4 of 12)	20997	NM_023735	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding
mm_37725.1	chr4	129558750	129558760	-	1	NA	promoter-TSS (NM_010693)	promoter-TSS (NM_010693)	-383	NM_010693	16818	Mm.293753	NM_010693	ENSMUSG00000000409	Lck	Hck-3|Lsk|Lskt|p56<lck>|p56Lck	lymphocyte protein tyrosine kinase	protein-coding
mm_118657.1	chr14	21797795	21797806	+	1	NA	3' UTR (NM_026283, exon 6 of 6)	3' UTR (NM_026283, exon 6 of 6)	-33761	NM_011695	22334	Mm.262327	NM_011695	ENSMUSG00000021771	Vdac2	Vdac6|mVDAC2|mVDAC6	voltage-dependent anion channel 2	protein-coding
mm_153807.1	chr19	46045225	46045244	-	1	NA	promoter-TSS (NM_001113408)	promoter-TSS (NM_001113408)	-23	NM_001113408	16825	Mm.327442	NM_010697	ENSMUSG00000025223	Ldb1	CLIM2|NLI	LIM domain binding 1	protein-coding
mm_127722.1	chr15	103135831	103135845	+	1	NA	intron (NR_045743, intron 3 of 6)	intron (NR_045743, intron 3 of 6)	10990	NR_045743	432989	Mm.383979	NR_045743	ENSMUSG00000097003	D930007P13Rik	-	Riken cDNA D930007P13 gene	ncRNA
mm_26756.1	chr3	8665783	8665799	-	1	NA	intron (NM_010423, intron 4 of 4)	intron (NM_010423, intron 4 of 4)	1247	NM_010423	15213	Mm.29581	NM_010423	ENSMUSG00000040289	Hey1	AI316788|AI414254|CHF2|HRT1|Herp2|Hesr1|bHLHb31|hesr-1	hairy/enhancer-of-split related with YRPW motif 1	protein-coding
mm_130755.1	chr15	101270542	101270548	-	1	NA	exon (NM_010444, exon 2 of 7)	exon (NM_010444, exon 2 of 7)	3699	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_88496.1	chr10	77837567	77837571	+	1	NA	TTS (NM_001024709)	TTS (NM_001024709)	1622	NM_001024709	544710	Mm.441890	NM_001024709		Krtap10-10	EG544710	keratin associated protein 10-10	protein-coding
mm_154949.1	chrX	36350960	36350961	+	1	NA	intron (NM_028894, intron 5 of 10)	intron (NM_028894, intron 5 of 10)	22551	NM_028894	74365	Mm.327654	NM_028894	ENSMUSG00000016239	Lonrf3	4932412G04Rik|5730439E01Rik|A830039N02Rik|AU023707|Rnf127	LON peptidase N-terminal domain and ring finger 3	protein-coding
mm_148894.1	chr19	6907980	6907990	+	1	NA	exon (NM_012021, exon 2 of 6)	exon (NM_012021, exon 2 of 6)	1660	NM_012021	54683	Mm.279782	NM_012021	ENSMUSG00000024953	Prdx5	AOEB166|AOPP|Pmp20|Prdx6|PrxV	peroxiredoxin 5	protein-coding
mm_70679.1	chr8	14992993	14993010	+	1	NA	intron (NM_172751, intron 27 of 28)	intron (NM_172751, intron 27 of 28)	-18024	NM_029116	74901	Mm.46675	NM_029116	ENSMUSG00000055675	Kbtbd11	2900016B01Rik|4930465M17Rik|mKIAA0711	kelch repeat and BTB (POZ) domain containing 11	protein-coding
mm_137518.1	chr17	27122275	27122278	+	1	NA	TTS (NM_080553)	TTS (NM_080553)	11615	NM_026063	67267	Mm.272389	NM_026063	ENSMUSG00000024208	Uqcc2	2900010M23Rik|Cbp6|M19|Mnf1	ubiquinol-cytochrome c reductase complex assembly factor 2	protein-coding
mm_139945.1	chr17	71198650	71198653	+	1	NA	intron (NM_022882, intron 1 of 19)	intron (NM_022882, intron 1 of 19)	-6003	NM_001164885	64898	Mm.227924	NM_022882	ENSMUSG00000024052	Lpin2	2610511G02Rik|AI481352|AW742896	lipin 2	protein-coding
mm_21882.1	chr2	166155105	166155133	-	1	NA	5' UTR (NM_001252578, exon 1 of 21)	5' UTR (NM_001252578, exon 1 of 21)	166	NM_001252578	72043	Mm.1011	NM_028072	ENSMUSG00000006800	Sulf2	2010004N24Rik|AU020235|MSulf-2|mKIAA1247	sulfatase 2	protein-coding
mm_103260.1	chr11	71019271	71019290	-	1	NA	promoter-TSS (NM_001291148)	promoter-TSS (NM_001291148)	23	NM_001291147	116891	Mm.28131	NM_033562	ENSMUSG00000018442	Derl2	CGI-101|Derlin-2|F-lana|Flana	Der1-like domain family, member 2	protein-coding
mm_107719.1	chr12	56289167	56289174	+	1	NA	Intergenic	Intergenic	35927	NR_045048	100503961	Mm.136732	NR_045048		Gm19990	-	predicted gene, 19990	ncRNA
mm_62878.1	chr7	114753781	114753793	+	1	NA	intron (NM_173767, intron 1 of 12)	intron (NM_173767, intron 1 of 12)	8021	NM_173767	233752	Mm.83037	NM_173767	ENSMUSG00000048782	Insc	3830422K02Rik|C730020D23	inscuteable homolog (Drosophila)	protein-coding
mm_54601.1	chr6	38306750	38306768	-	1	NA	3' UTR (NM_001347122, exon 13 of 13)	3' UTR (NM_001347122, exon 13 of 13)	-7500	NM_172467	209032	Mm.101389	NM_172467	ENSMUSG00000047749	Zc3hav1l	B130055L09Rik|E430016P22Rik	zinc finger CCCH-type, antiviral 1-like	protein-coding
mm_43800.1	chr5	142821785	142821818	+	1	NA	Intergenic	Intergenic	-4414	NM_001122730	231861	Mm.354649	NM_178242	ENSMUSG00000039477	Tnrc18	BC025631|EG381742|Zfp469	trinucleotide repeat containing 18	protein-coding
mm_170047.1	chr17	25273387	25273388	-	1	NA	promoter-TSS (NR_027452)	promoter-TSS (NR_027452)	44	NM_001177610	22196	Mm.240044	NM_011665	ENSMUSG00000015120	Ube2i	5830467E05Rik|F830028O17Rik|UBC9|Ubce2i|Ubce9	ubiquitin-conjugating enzyme E2I	protein-coding
mm_167221.1	chr8	11758251	11758262	-	1	NA	promoter-TSS (NM_001113518)	promoter-TSS (NM_001113518)	-74	NM_017402	54126	Mm.244068	NM_017402	ENSMUSG00000031511	Arhgef7	Cool|PIX|Pak3bp|betaPix|betaPix-b|betaPix-c|cool-1|mKIAA0142|p85Cool1|p85SPR	Rho guanine nucleotide exchange factor (GEF7)	protein-coding
mm_172235.1	chr6	68121037	68121052	+	1	NA	Intergenic	Intergenic	-555345	NR_003100	75070	Mm.463364	NR_003100		4930515G16Rik	-	myc induced nuclear antigen pseudogene	pseudo
mm_22027.1	chr2	168050353	168050364	-	1	NA	Intergenic	CpG	-30646	NM_021409	58220	Mm.292834	NM_021409	ENSMUSG00000044641	Pard6b	AV025615|Par6b	par-6 family cell polarity regulator beta	protein-coding
mm_162103.1	chrX	38085144	38085144	-	1	NA	promoter-TSS (NM_198598)	promoter-TSS (NM_198598)	-5	NM_198598	194738	Mm.233621	NM_198598	ENSMUSG00000051038	Rhox11	BC049711|Gm39	reproductive homeobox 11	protein-coding
mm_163565.1	chr13	27241812	27241837	+	1	NA	promoter-TSS (NM_008865)	promoter-TSS (NM_008865)	-606	NM_008865	18776	Mm.37203	NM_008865	ENSMUSG00000038891	Prl3b1	Csh2|Ghd8|PL|Pl-2|Pl2|mPL-II|mplII	prolactin family 3, subfamily b, member 1	protein-coding
mm_155052.1	chrX	42237753	42237755	+	1	NA	intron (NM_001077712, intron 16 of 32)	intron (NM_001077712, intron 16 of 32)	35899	NM_001290713	20843	Mm.290422	NM_021465	ENSMUSG00000025862	Stag2	9230105L23Rik|B230112I07Rik|SA-2|SAP2	stromal antigen 2	protein-coding
mm_68764.1	chr7	121707464	121707472	-	1	NA	promoter-TSS (NM_001033173)	promoter-TSS (NM_001033173)	-215	NM_001033173	76179	Mm.122538	NM_001033173	ENSMUSG00000063317	Usp31	6330567E21Rik|mKIAA1203	ubiquitin specific peptidase 31	protein-coding
mm_12136.1	chr2	61711705	61711786	+	1	NA	promoter-TSS (NM_021526)	promoter-TSS (NM_021526)	51	NM_021526	59029	Mm.218198	NM_021526	ENSMUSG00000026914	Psmd14	2610312C03Rik|3200001M20Rik|AA986732|Pad1|Poh1|rpm11	proteasome (prosome, macropain) 26S subunit, non-ATPase, 14	protein-coding
mm_59531.1	chr7	27689530	27689572	+	1	NA	intron (NM_001112731, intron 1 of 5)	intron (NM_001112731, intron 1 of 5)	211	NM_001112731	112415	Mm.145362	NM_198417	ENSMUSG00000057093	Zfp607b	C030039L03Rik	zinc finger protein 607B	protein-coding
mm_46472.1	chr5	105126868	105126878	-	1	NA	intron (NM_008620, intron 3 of 10)	intron (NM_008620, intron 3 of 10)	12679	NM_008620	17472	Mm.440525	NM_008620	ENSMUSG00000079363	Gbp4	AW228052|Mag-2|Mpa-2|Mpa2	guanylate binding protein 4	protein-coding
mm_105397.1	chr11	103403885	103403918	-	1	NA	5' UTR (NM_183034, exon 2 of 12)	5' UTR (NM_183034, exon 2 of 12)	8763	NM_183034	353047	Mm.18556	NM_183034	ENSMUSG00000034247	Plekhm1	AP162|B2|BC038943|D330036J23Rik	pleckstrin homology domain containing, family M (with RUN domain) member 1	protein-coding
mm_52198.1	chr6	100604657	100604663	+	1	NA	intron (NM_181590, intron 10 of 10)	intron (NM_181590, intron 10 of 10)	66497	NM_181590	72171	Mm.256022	NM_181590	ENSMUSG00000035378	Shq1	2810403P18Rik|Grim-1	SHQ1 homolog (S. cerevisiae)	protein-coding
mm_119496.1	chr14	47380062	47380071	+	1	NA	exon (NM_010705, exon 3 of 6)	exon (NM_010705, exon 3 of 6)	6206	NM_001145953	16854	Mm.248615	NM_010705	ENSMUSG00000050335	Lgals3	GBP|L-34|Mac-2|gal3	lectin, galactose binding, soluble 3	protein-coding
mm_151164.1	chr19	53194527	53194544	+	1	NA	intron (NM_013758, intron 1 of 15)	intron (NM_013758, intron 1 of 15)	50538	NM_013758	27360	Mm.426080	NM_013758	ENSMUSG00000025026	Add3	AI463285|R75380	adducin 3 (gamma)	protein-coding
mm_172185.1	chr6	50554236	50554238	-	1	NA	Intergenic	ORR1A1|LTR|ERVL-MaLR	12237	NM_007808	13063	Mm.35389	NM_007808	ENSMUSG00000063694	Cycs	-	cytochrome c, somatic	protein-coding
mm_166998.1	chr7	46839045	46839061	+	1	NA	Intergenic	Intergenic	-6751	NM_010699	16828	Mm.29324	NM_010699	ENSMUSG00000063229	Ldha	Ldh1|Ldhm|l7R2	lactate dehydrogenase A	protein-coding
mm_59270.1	chr7	24899312	24899325	+	1	NA	exon (NM_007655, exon 2 of 5)	exon (NM_007655, exon 2 of 5)	1807	NM_007655	12518	Mm.1355	NM_007655	ENSMUSG00000003379	Cd79a	Ig-alpha|Iga|Igalpha|Ly-54|Ly54|mb-1	CD79A antigen (immunoglobulin-associated alpha)	protein-coding
mm_147578.1	chr18	56431920	56431934	-	1	NA	promoter-TSS (NM_026240)	promoter-TSS (NM_026240)	-205	NM_026240	107022	Mm.24356	NM_026240	ENSMUSG00000001700	Gramd3	9030613F08Rik|9130427A09Rik|AW061306|NS3TP2	GRAM domain containing 3	protein-coding
mm_107437.1	chr12	36157168	36157238	+	1	NA	promoter-TSS (NM_025840)	promoter-TSS (NM_025840)	79	NM_146033	217473	Mm.130422	NM_146033	ENSMUSG00000036188	Ankmy2	AI035571|ZMYND20	ankyrin repeat and MYND domain containing 2	protein-coding
mm_140688.1	chr17	13683486	13683523	-	1	NA	Intergenic	Intergenic	-77037	NM_010806	17356	Mm.59167	NM_010806	ENSMUSG00000068036	Afdn	5033403D15Rik|AF6|Af-6|Afadin|Gm314|I-afadin|Mllt4|S-afadin	afadin, adherens junction formation factor	protein-coding
mm_81474.1	chr9	109931810	109931835	+	1	NA	promoter-TSS (NM_008633)	promoter-TSS (NM_008633)	48	NM_008633	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_170798.1	chr2	175469974	175469990	+	1	NA	promoter-TSS (NM_001242944)	promoter-TSS (NM_001242944)	-3	NM_001242943	545490	Mm.484023	NM_001242943	ENSMUSG00000078879	Zfp973	6230416C02Rik|Gm14306|Gm14436|OTTMUSG00000016614	zinc finger protein 973	protein-coding
mm_86694.1	chr10	18469878	18469878	+	1	NA	promoter-TSS (NM_001163592)	promoter-TSS (NM_001163592)	-103	NM_001163592	215819	Mm.297971	NM_173390	ENSMUSG00000039835	Nhsl1	5730409E15Rik|A630035H13Rik|A730096F01|BC013565|D10Bwg0940e|mKIAA1357	NHS-like 1	protein-coding
mm_75352.1	chr8	44316813	44316817	-	1	NA	Intergenic	Intergenic	-617324	NM_001079931	384814	Mm.491652	NM_001079931		Gm5347	EG384814	predicted gene 5347	protein-coding
mm_2968.1	chr1	133046165	133046187	+	1	NA	5' UTR (NM_001099276, exon 1 of 33)	5' UTR (NM_001099276, exon 1 of 33)	164	NM_001099276	240752	Mm.387308	NM_001099276	ENSMUSG00000026447	Pik3c2b	C330011J12Rik|Gm199|PI3K-C2beta|PI3KC2beta	phosphoinositide-3-kinase, class 2, beta polypeptide	protein-coding
mm_19708.1	chr2	103797593	103797612	-	1	NA	promoter-TSS (NM_016739)	promoter-TSS (NM_016739)	38	NM_001111291	53872	Mm.427589	NM_016739	ENSMUSG00000027184	Caprin1	AL022980|Caprin-1|Gpiap|Gpiap1|Mmgpip137|P137|rng105	cell cycle associated protein 1	protein-coding
mm_148303.1	chr18	82920535	82920551	-	1	NA	promoter-TSS (NR_033307)	promoter-TSS (NR_033307)	17	NR_033307	75853	Mm.420737	NR_033307		4930592I03Rik	-	RIKEN cDNA 4930592I03 gene	ncRNA
mm_105751.1	chr11	109472973	109472991	-	1	NA	promoter-TSS (NM_028710)	promoter-TSS (NM_028710)	247	NM_134038	104681	Mm.265874	NM_134038	ENSMUSG00000041920	Slc16a6	AW743111|ESTM12|MCT 6|MCT 7|MCT6	solute carrier family 16 (monocarboxylic acid transporters), member 6	protein-coding
mm_26692.1	chr3	156734746	156734747	+	1	NA	intron (NM_177274, intron 1 of 6)	intron (NM_177274, intron 1 of 6)	172952	NM_001039094	320840	Mm.317293	NM_177274	ENSMUSG00000040037	Negr1	5330422G01Rik|KILON|Ntra	neuronal growth regulator 1	protein-coding
mm_21809.1	chr2	165065366	165065384	-	1	NA	intron (NM_170703, intron 5 of 7)	(CA)n|Simple_repeat|Simple_repeat	9739	NM_011611	21939	Mm.271833	NM_011611	ENSMUSG00000017652	Cd40	AI326936|Bp50|GP39|HIGM1|IGM|IMD3|T-BAM|TRAP|Tnfrsf5|p50	CD40 antigen	protein-coding
mm_153073.1	chr19	32257205	32257239	-	1	NA	intron (NM_144792, intron 3 of 9)	ORR1C2|LTR|ERVL-MaLR	-46209	NM_001168526	208449	Mm.329810	NM_144792	ENSMUSG00000040451	Sgms1	9530058O11Rik|AI841905|C80702|Mob|Sms1|Sor1|Tmem23	sphingomyelin synthase 1	protein-coding
mm_135958.1	chr16	74731380	74731381	-	1	NA	Intergenic	L1MA6|LINE|L1	-320468	NM_175549	268902	Mm.171736	NM_175549	ENSMUSG00000052516	Robo2	2600013A04Rik|9430089E08Rik|BB097918|D230004I22Rik|mKIAA1568	roundabout guidance receptor 2	protein-coding
mm_56734.1	chr6	115731099	115731115	-	1	NA	intron (NM_144805, intron 9 of 11)	intron (NM_144805, intron 9 of 11)	27892	NM_144805	94346	Mm.29739	NM_144805	ENSMUSG00000059900	Tmem40	9030407H20Rik|AV091463|W64236	transmembrane protein 40	protein-coding
mm_166301.1	chr5	104440228	104440258	+	1	NA	exon (NM_001204203, exon 7 of 7)	exon (NM_001204203, exon 7 of 7)	4051	NM_001204233	20750	Mm.288474	NM_009263	ENSMUSG00000029304	Spp1	2AR|Apl-1|BNSP|BSPI|Bsp|ETA-1|Eta|OP|Opn|Opnl|Ric|Spp-1	secreted phosphoprotein 1	protein-coding
mm_171600.1	chr4	147775818	147775837	-	1	NA	intron (NM_001127189, intron 3 of 5)	intron (NM_001127189, intron 3 of 5)	33961	NM_001127189	100041677	Mm.327194	NM_001127189	ENSMUSG00000078495	Zfp984	Gm13157|OTTMUSG00000010679	zinc finger protein 984	protein-coding
mm_22665.1	chr3	14872046	14872068	+	1	NA	3' UTR (NM_007606, exon 7 of 7)	3' UTR (NM_007606, exon 7 of 7)	8519	NM_007606	12350	Mm.300	NM_007606	ENSMUSG00000027559	Car3	BB219044|Ca3|Car-3	carbonic anhydrase 3	protein-coding
mm_43397.1	chr5	135778701	135778712	+	1	NA	promoter-TSS (NM_029659)	promoter-TSS (NM_029659)	57	NM_008617	17448	Mm.297096	NM_008617	ENSMUSG00000019179	Mdh2	MDH|Mdh-2|Mor-1|Mor1	malate dehydrogenase 2, NAD (mitochondrial)	protein-coding
mm_139573.1	chr17	57062318	57062337	+	1	NA	promoter-TSS (NM_177638)	promoter-TSS (NM_177638)	50	NM_177638	224912	Mm.284447	NM_177638	ENSMUSG00000044279	Crb3	5730439B18|AU015179|AU041752	crumbs family member 3	protein-coding
mm_87243.1	chr10	40936172	40936206	+	1	NA	exon (NM_031877, exon 8 of 9)	exon (NM_031877, exon 8 of 9)	52655	NM_031877	83767	Mm.41353	NM_031877	ENSMUSG00000019831	Wasf1	AI195380|AI838537|Scar|WAVE|WAVE-1	WAS protein family, member 1	protein-coding
mm_167529.1	chr9	21290477	21290481	-	1	NA	intron (NM_009878, intron 1 of 1)	intron (NM_009878, intron 1 of 1)	730	NM_009878	12581	Mm.29020	NM_009878	ENSMUSG00000096472	Cdkn2d	INK4d|p19|p19INK4d	cyclin-dependent kinase inhibitor 2D (p19, inhibits CDK4)	protein-coding
mm_65188.1	chr7	19696534	19696558	-	1	NA	exon (NM_009696, exon 4 of 4)	exon (NM_009696, exon 4 of 4)	1852	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_89160.1	chr10	86095837	86095860	+	1	NA	promoter-TSS (NR_038024)	promoter-TSS (NR_038024)	-6	NR_038024	78170	Mm.444790	NR_038024		4930486F22Rik	-	RIKEN cDNA 4930486F22 gene	ncRNA
mm_62705.1	chr7	110614332	110614351	+	1	NA	intron (NM_177324, intron 1 of 40)	CpG	579	NM_177324	319934	Mm.102970	NM_177324	ENSMUSG00000038371	Sbf2	4833411B01Rik|AA414977|AI317167|B430219L04Rik|Mtmr13|mMTMH1	SET binding factor 2	protein-coding
mm_138816.1	chr17	39847178	39847215	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	4199	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_152906.1	chr19	26046462	26046469	-	1	NA	Intergenic	MLT1G1|LTR|ERVL-MaLR	374054	NM_145831	226049	Mm.275572	NM_145831	ENSMUSG00000048138	Dmrt2	Terra	doublesex and mab-3 related transcription factor 2	protein-coding
mm_148034.1	chr18	70244374	70244378	-	1	NA	exon (NM_029346, exon 1 of 3)	exon (NM_029346, exon 1 of 3)	208	NM_029346	75577	Mm.58214	NM_029346	ENSMUSG00000024512	Dynap	2310002L13Rik	dynactin associated protein	protein-coding
mm_147069.1	chr18	35214981	35214992	-	1	NA	promoter-TSS (NM_178005)	promoter-TSS (NM_178005)	38	NM_178005	107065	Mm.39900	NM_178005	ENSMUSG00000071862	Lrrtm2	AI851755|BB129880|C630011A14Rik|mKIAA0416	leucine rich repeat transmembrane neuronal 2	protein-coding
mm_121239.1	chr14	103056244	103056254	+	1	NA	3' UTR (NM_008392, exon 5 of 5)	3' UTR (NM_008392, exon 5 of 5)	9237	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_93687.1	chr10	117815688	117815698	-	1	NA	3' UTR (NM_024457, exon 8 of 8)	3' UTR (NM_024457, exon 8 of 8)	-22988	NM_134010	103468	Mm.12568	NM_134010	ENSMUSG00000052798	Nup107	AW541137|C76801	nucleoporin 107	protein-coding
mm_71683.1	chr8	61224163	61224174	+	1	NA	promoter-TSS (NM_021506)	promoter-TSS (NM_021506)	-3	NM_021506	59009	Mm.27949	NM_021506	ENSMUSG00000031642	Sh3rf1	2200003J05Rik|Posh|R75531|Sh3md2	SH3 domain containing ring finger 1	protein-coding
mm_77835.1	chr9	4376534	4376600	+	1	NA	Intergenic	Intergenic	-6970	NM_145609	78100	Mm.206549	NM_145609	ENSMUSG00000041124	Msantd4	8430410K20Rik|Mysantd4	Myb/SANT-like DNA-binding domain containing 4 with coiled-coils	protein-coding
mm_96648.1	chr11	69340764	69340838	+	1	NA	promoter-TSS (NR_027827)	promoter-TSS (NR_027827)	32	NR_027827	80515	Mm.5324	NM_020591	ENSMUSG00000043419	Chd3os	2310043C11Rik|A030009H04Rik|AA589459|AB041807|MNCb-2875|RNF21	chromodomain helicase DNA binding protein 3, opposite strand	ncRNA
mm_158808.1	chrX	167304772	167304780	-	1	NA	TTS (NM_001290758)	TTS (NM_001290758)	25795	NM_001290757	170743	Mm.23979	NM_133211	ENSMUSG00000044583	Tlr7	-	toll-like receptor 7	protein-coding
mm_84649.1	chr9	71589203	71589204	-	1	NA	intron (NM_001033208, intron 1 of 12)	intron (NM_001033208, intron 1 of 12)	3157	NM_001033208	102371	Mm.27585	NM_001033208	ENSMUSG00000041361	Myzap	AA407270|AV006038|Gcom1|Gm640|Grinl1a7|Myozap	myocardial zonula adherens protein	protein-coding
mm_133082.1	chr16	59636942	59636949	+	1	NA	promoter-TSS (NR_040564)	promoter-TSS (NR_040564)	0	NR_040564	75145	Mm.399348	NR_040564		4930547E14Rik	-	RIKEN cDNA 4930547E14 gene	ncRNA
mm_92130.1	chr10	64090266	64090297	-	1	NA	promoter-TSS (NM_178678)	promoter-TSS (NM_178678)	-26	NM_178678	216028	Mm.431318	NM_178678	ENSMUSG00000042846	Lrrtm3	9630044H04Rik	leucine rich repeat transmembrane neuronal 3	protein-coding
mm_89187.1	chr10	86346229	86346244	+	1	NA	3' UTR (NM_011595, exon 5 of 5)	3' UTR (NM_011595, exon 5 of 5)	45824	NM_011595	21859	Mm.4871	NM_011595	ENSMUSG00000020044	Timp3	Timp-3	tissue inhibitor of metalloproteinase 3	protein-coding
mm_94102.1	chr10	128566005	128566019	-	1	NA	promoter-TSS (NM_011119)	promoter-TSS (NM_011119)	-78	NM_011119	18813	Mm.4742	NM_011119	ENSMUSG00000025364	Pa2g4	38kDa|AA672939|Ebp1|Plfap	proliferation-associated 2G4	protein-coding
mm_74682.1	chr8	14095642	14095655	-	1	NA	promoter-TSS (NM_001145965)	promoter-TSS (NM_001145965)	-227	NM_001145965	244310	Mm.404697	NM_172910	ENSMUSG00000047495	Dlgap2	6430596N04Rik|Dap-2|Dap2|Sapap2	discs, large (Drosophila) homolog-associated protein 2	protein-coding
mm_114311.1	chr13	59769929	59769996	+	1	NA	promoter-TSS (NR_015349)	promoter-TSS (NR_015349)	-4	NR_015349	13996	Mm.490435	NR_015349	ENSMUSG00000089875	Etohd2	AW491659	ethanol decreased 2	ncRNA
mm_51667.1	chr6	86365674	86365723	+	1	NA	promoter-TSS (NM_025591)	promoter-TSS (NM_025591)	15	NM_025591	66488	Mm.422972	NM_025591	ENSMUSG00000057497	Fam136a	2010309E21Rik|AW124904|Hyccin	family with sequence similarity 136, member A	protein-coding
mm_81532.1	chr9	110064409	110064418	+	1	NA	exon (NM_008633, exon 10 of 19)	exon (NM_008633, exon 10 of 19)	12392	NM_001311164	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_111147.1	chr12	82122801	82122804	-	1	NA	Intergenic	Intergenic	-47214	NM_001167983	217692	Mm.261333	NM_172579	ENSMUSG00000042700	Sipa1l1	4931426N11Rik|AW213287|Spar|mKIAA0440	signal-induced proliferation-associated 1 like 1	protein-coding
mm_104255.1	chr11	88924338	88924348	-	1	NA	3' UTR (NM_029023, exon 13 of 13)	3' UTR (NM_029023, exon 13 of 13)	18415	NR_045955	73921	Mm.439148	NR_045955	ENSMUSG00000087338	Scpep1os	4930405P13Rik	serine carboxypeptidase 1, opposite strand	ncRNA
mm_126402.1	chr15	80235574	80235594	+	1	NA	intron (NM_178719, intron 1 of 5)	intron (NM_178719, intron 1 of 5)	1504	NM_178719	239555	Mm.307163	NM_178719	ENSMUSG00000022412	Mief1	A230016E22|AI452372|Smcr7l	mitochondrial elongation factor 1	protein-coding
mm_9068.1	chr1	168215484	168215489	-	1	NA	intron (NM_008783, intron 2 of 7)	intron (NM_008783, intron 2 of 7)	216683	NM_001291508	18514	Mm.43358	NM_008783	ENSMUSG00000052534	Pbx1	2310056B04Rik|D230003C07Rik|Pbx-1	pre B cell leukemia homeobox 1	protein-coding
mm_108020.1	chr12	73603887	73603913	+	1	NA	intron (NM_001313977, intron 2 of 14)	intron (NM_001313977, intron 2 of 14)	19104	NM_008856	18755	Mm.341677	NM_008856	ENSMUSG00000021108	Prkch	Pkch	protein kinase C, eta	protein-coding
mm_29718.1	chr3	124426004	124426012	-	1	NA	promoter-TSS (NM_027939)	promoter-TSS (NM_027939)	20	NM_027939	71824	Mm.331353	NM_027939	ENSMUSG00000027973	1700006A11Rik	-	RIKEN cDNA 1700006A11 gene	protein-coding
mm_49249.1	chr6	17307900	17307921	+	1	NA	exon (NM_007616, exon 2 of 3)	exon (NM_007616, exon 2 of 3)	270	NM_001243064	12389	Mm.28278	NM_007616	ENSMUSG00000007655	Cav1	Cav|Cav-1	caveolin 1, caveolae protein	protein-coding
mm_14725.1	chr2	144033112	144033123	+	1	NA	promoter-TSS (NM_207275)	promoter-TSS (NM_207275)	15	NM_207275	403171	Mm.389362	NM_207275	ENSMUSG00000037307	Banf2	4930517K23Rik|Baf-L|Baf-like|Gm115	barrier to autointegration factor 2	protein-coding
mm_25179.1	chr3	103279782	103279799	+	1	NA	5' UTR (NM_053170, exon 1 of 20)	5' UTR (NM_053170, exon 1 of 20)	497	NM_001079830	94093	Mm.195036	NM_053170	ENSMUSG00000033014	Trim33	8030451N04Rik|AI413936|Ecto|Tif1g	tripartite motif-containing 33	protein-coding
mm_136475.1	chr16	95808720	95808722	-	1	NA	Intergenic	Intergenic	89992	NR_040485	69776	Mm.120470	NR_040484	ENSMUSG00000086899	1600002D24Rik	-	RIKEN cDNA 1600002D24 gene	ncRNA
mm_132285.1	chr16	33062513	33062549	+	1	NA	promoter-TSS (NM_172823)	promoter-TSS (NM_172823)	10	NM_172823	239833	Mm.131951	NM_172823	ENSMUSG00000022802	Lmln	5330415H22Rik|AI465495	leishmanolysin-like (metallopeptidase M8 family)	protein-coding
mm_97111.1	chr11	74653144	74653179	+	1	NA	intron (NM_001081158, intron 1 of 25)	intron (NM_001081158, intron 1 of 25)	3666	NM_001081158	74148	Mm.214574	NM_001081158	ENSMUSG00000020741	Cluh	1300001I01Rik|Kiaa0664|mKIAA0664	clustered mitochondria (cluA/CLU1) homolog	protein-coding
mm_55767.1	chr6	78467505	78467515	-	1	NA	exon (NM_011260, exon 4 of 6)	exon (NM_011260, exon 4 of 6)	1364	NM_011260	19695	Mm.252385	NM_011260	ENSMUSG00000030017	Reg3g	AI449515|REG-3-gamma|reg III-gamma	regenerating islet-derived 3 gamma	protein-coding
mm_116830.1	chr13	54683158	54683185	-	1	NA	exon (NM_001146025, exon 5 of 11)	exon (NM_001146025, exon 5 of 11)	4637	NM_001146025	105239	Mm.25366	NM_134064	ENSMUSG00000034928	Rnf44	AI854545|mKIAA1100	ring finger protein 44	protein-coding
mm_130068.1	chr15	89309971	89310002	-	1	NA	intron (NM_001081030, intron 1 of 39)	intron (NM_001081030, intron 1 of 39)	-4254	NR_105924	102465981		NR_105924	ENSMUSG00000098442	Mir6959	Gm27807|mmu-mir-6959	microRNA 6959	ncRNA
mm_72964.1	chr8	92840163	92840175	+	1	NA	intron (NM_008610, intron 8 of 12)	intron (NM_008610, intron 8 of 12)	12872	NM_008610	17390	Mm.29564	NM_008610	ENSMUSG00000031740	Mmp2	Clg4a|GelA|MMP-2	matrix metallopeptidase 2	protein-coding
mm_118897.1	chr14	26638158	26638224	+	1	NA	promoter-TSS (NM_007479)	promoter-TSS (NM_007479)	-6	NM_007479	11843	Mm.297768	NM_007479	ENSMUSG00000021877	Arf4	AA407803	ADP-ribosylation factor 4	protein-coding
mm_146447.1	chr18	85697928	85697935	+	1	NA	Intergenic	RLTR27|LTR|ERVK	-697021	NM_144946	246317	Mm.329578	NM_144946	ENSMUSG00000050321	Neto1	AI851453|Btcl1|C130005O10Rik	neuropilin (NRP) and tolloid (TLL)-like 1	protein-coding
mm_47450.1	chr5	123525393	123525424	-	1	NA	Intergenic	Intergenic	-1244	NM_023232	66593	Mm.46716	NM_023232	ENSMUSG00000029433	Diablo	0610041G12Rik|1700006L01Rik|AU040403|Smac	diablo, IAP-binding mitochondrial protein	protein-coding
mm_135083.1	chr16	34514064	34514079	-	1	NA	promoter-TSS (NM_177357)	promoter-TSS (NM_177357)	-44	NM_177357	545156	Mm.82274	NM_177357	ENSMUSG00000061751	Kalrn	2210407G14Rik|AV235988|DUET|E530005C20Rik|Gm539|Hapip|TRAD	kalirin, RhoGEF kinase	protein-coding
mm_129313.1	chr15	77760787	77760802	-	1	NA	3' UTR (NM_022410, exon 41 of 41)	3' UTR (NM_022410, exon 41 of 41)	-5565	NM_001081970	239552	Mm.125650	NM_001081970	ENSMUSG00000056656	Apol8	9830006J20Rik|APOL-II|Apol2	apolipoprotein L 8	protein-coding
mm_15259.1	chr2	155013431	155013465	+	1	NA	promoter-TSS (NM_015770)	promoter-TSS (NM_015770)	-122	NM_015770	50518	Mm.315593	NM_015770	ENSMUSG00000027596	a	A<y>|ASIP|ASP|As	nonagouti	protein-coding
mm_11061.1	chr2	27515163	27515217	+	1	NA	promoter-TSS (NM_080848)	promoter-TSS (NM_080848)	43	NM_080848	140858	Mm.28265	NM_080848	ENSMUSG00000026917	Wdr5	2410008O07Rik|AA408785|AA960360|Big|Big-3	WD repeat domain 5	protein-coding
mm_28646.1	chr3	95228276	95228286	-	1	NA	promoter-TSS (NM_172395)	promoter-TSS (NM_172395)	-143	NM_172395	57912	Mm.28189	NM_172395	ENSMUSG00000046722	Cdc42se1	1300002M12Rik|AW558204|Cdcse1|SCIP1|Spec1	CDC42 small effector 1	protein-coding
mm_168361.1	chr1	115448059	115448078	+	1	NA	Intergenic	L1Md_T|LINE|L1	-237069	NM_001077425	636808	Mm.101576	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding
mm_125423.1	chr15	41859933	41859944	+	1	NA	3' UTR (NM_001130164, exon 6 of 6)	3' UTR (NM_001130164, exon 6 of 6)	9782	NM_175456	223513	Mm.148913	NM_175456	ENSMUSG00000042895	Abra	C130068O12Rik|STARS	actin-binding Rho activating protein	protein-coding
mm_79997.1	chr9	67041146	67041157	+	1	NA	intron (NM_001164249, intron 2 of 8)	intron (NM_001164249, intron 2 of 8)	2720	NM_001164252	22003	Mm.121878	NM_024427	ENSMUSG00000032366	Tpm1	AA986836|AI854628|TM2|Tm3|Tmpa|Tpm-1|alpha-TM	tropomyosin 1, alpha	protein-coding
mm_110301.1	chr12	32770981	32770994	-	1	NA	Intergenic	Intergenic	-49348	NM_021524	59027	Mm.202727	NM_021524	ENSMUSG00000020572	Nampt	1110035O14Rik|AI314458|AI480535|NAmPRTase|Pbef|Pbef1|Visfatin	nicotinamide phosphoribosyltransferase	protein-coding
mm_59375.1	chr7	25722886	25722897	+	1	NA	exon (NM_144922, exon 14 of 15)	exon (NM_144922, exon 14 of 15)	-3838	NM_028771	52132	Mm.278798	NM_028771	ENSMUSG00000002608	Ccdc97	1200014H14Rik|2810446P04Rik|AA545218|D7Ertd462e	coiled-coil domain containing 97	protein-coding
mm_166575.1	chr6	51465178	51465201	+	1	NA	exon (NM_182650, exon 7 of 10)	exon (NM_182650, exon 7 of 10)	4705	NM_182650	53379	Mm.155896	NM_016806	ENSMUSG00000004980	Hnrnpa2b1	9130414A06Rik|Hnrpa2|Hnrpa2b1|hnrnp-A	heterogeneous nuclear ribonucleoprotein A2/B1	protein-coding
mm_34569.1	chr4	150048192	150048244	+	1	NA	Intergenic	Intergenic	-20236	NR_029751	723848		NR_029751	ENSMUSG00000065493	Mir34a	Mirn34a|mir-34a|mmu-mir-34a	microRNA 34a	ncRNA
mm_135863.1	chr16	60605272	60605291	-	1	NA	5' UTR (NM_007938, exon 1 of 18)	5' UTR (NM_007938, exon 1 of 18)	250	NM_007938	13840	Mm.455790	NM_007938	ENSMUSG00000055540	Epha6	Ehk2|Hek12|m-ehk2	Eph receptor A6	protein-coding
mm_120172.1	chr14	61038040	61038050	+	1	NA	promoter-TSS (NM_001164155)	promoter-TSS (NM_001164155)	-58	NM_001164155	29820	Mm.281356	NM_013869	ENSMUSG00000060548	Tnfrsf19	AL023044|AW123854|TAJ|TAJ-ALPHA|TRADE|Troy	tumor necrosis factor receptor superfamily, member 19	protein-coding
mm_89783.1	chr10	101681859	101681873	+	1	NA	5' UTR (NM_001205098, exon 1 of 8)	5' UTR (NM_001205098, exon 1 of 8)	379	NM_001205098	67569	Mm.25252	NM_026243	ENSMUSG00000019888	Mgat4c	9130411I17Rik|GntIVh	MGAT4 family, member C	protein-coding
mm_80505.1	chr9	78615758	78615786	+	1	NA	5' UTR (NM_153098, exon 1 of 33)	5' UTR (NM_153098, exon 1 of 33)	226	NM_153098	235505	Mm.32955	NM_153098	ENSMUSG00000046186	Cd109	9930012E15Rik|AI480638|GARP	CD109 antigen	protein-coding
mm_170329.1	chr18	43477815	43477829	-	1	NA	Intergenic	CpG	-39536	NM_001291455	22240	Mm.8180	NM_009468	ENSMUSG00000024501	Dpysl3	CRMP-4|DRP-3|TUC4|ULIP-1|Ulip|Ulip1	dihydropyrimidinase-like 3	protein-coding
mm_101163.1	chr11	16973256	16973302	-	1	NA	3' UTR (NM_019549, exon 10 of 10)	3' UTR (NM_019549, exon 10 of 10)	21869	NM_176982	319701	Mm.120672	NM_176982	ENSMUSG00000044966	Fbxo48	A630050E13Rik	F-box protein 48	protein-coding
mm_25289.1	chr3	105803921	105803941	+	1	NA	Intergenic	Intergenic	-2550	NM_145541	109905	Mm.101922	NM_145541	ENSMUSG00000068798	Rap1a	AI848598|G-22K|Krev-1|Rap1	RAS-related protein-1a	protein-coding
mm_63332.1	chr7	126950519	126950583	+	1	NA	promoter-TSS (NM_001039645)	promoter-TSS (NM_001039645)	16	NM_001252566	233878	Mm.283926	NM_144926	ENSMUSG00000030683	Sez6l2	AI835913|AW121566|BSRP-A|Psk1	seizure related 6 homolog like 2	protein-coding
mm_111387.1	chr12	87477198	87477210	-	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-4905	NM_025507	66354	Mm.271174	NM_025507	ENSMUSG00000021039	Snw1	2310008B08Rik|AW048543|NCoA-62|SKIP|Skiip	SNW domain containing 1	protein-coding
mm_15921.1	chr2	165066706	165066718	+	1	NA	intron (NM_170702, intron 6 of 7)	MIRc|SINE|MIR	11076	NM_011611	21939	Mm.271833	NM_011611	ENSMUSG00000017652	Cd40	AI326936|Bp50|GP39|HIGM1|IGM|IMD3|T-BAM|TRAP|Tnfrsf5|p50	CD40 antigen	protein-coding
mm_161664.1	chr17	8801589	8801589	+	1	NA	promoter-TSS (NM_011866)	promoter-TSS (NM_011866)	-156	NM_011866	23984	Mm.87161	NM_011866	ENSMUSG00000023868	Pde10a	-	phosphodiesterase 10A	protein-coding
mm_139109.1	chr17	47368883	47368910	+	1	NA	promoter-TSS (NM_001146212)	promoter-TSS (NM_001146212)	9	NM_001146211	64657	Mm.216250	NM_183086	ENSMUSG00000034729	Mrps10	1110038B19Rik|AW743084|Rpms10	mitochondrial ribosomal protein S10	protein-coding
mm_109075.1	chr12	104387664	104387666	+	1	NA	intron (NM_009253, intron 1 of 4)	intron (NM_009253, intron 1 of 4)	501	NM_009253	20717	Mm.395085	NM_009253	ENSMUSG00000079012	Serpina3m	3e46|AI195004|MMCM7|MMSPi2.4|Spi-2l|Spi-2rs1|Spi2-rs1|Spi2.4|spi2	serine (or cysteine) peptidase inhibitor, clade A, member 3M	protein-coding
mm_79735.1	chr9	62344784	62344799	+	1	NA	intron (NM_009672, intron 1 of 6)	intron (NM_009672, intron 1 of 6)	3448	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	protein-coding
mm_87793.1	chr10	60299530	60299535	+	1	NA	exon (NM_011179, exon 10 of 15)	exon (NM_011179, exon 10 of 15)	15071	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_118470.1	chr14	11553703	11553773	+	1	NA	5' UTR (NM_008981, exon 1 of 30)	5' UTR (NM_008981, exon 1 of 30)	185	NM_008981	19270	Mm.431266	NM_008981	ENSMUSG00000021745	Ptprg	5430405N12Rik|AW046354|AW549872|RPTPgamma	protein tyrosine phosphatase, receptor type, G	protein-coding
mm_89333.1	chr10	87933333	87933371	+	1	NA	3' UTR (NM_010512, exon 5 of 5)	3' UTR (NM_010512, exon 5 of 5)	-33319	NR_000040	22172	Mm.391420	NR_000040		Tyms-ps	-	thymidylate synthase, pseudogene	pseudo
mm_99197.1	chr11	101012075	101012081	+	1	NA	intron (NM_001243050, intron 2 of 20)	(T)n|Simple_repeat|Simple_repeat	2626	NM_001243051	11975	Mm.340818	NM_016920	ENSMUSG00000019302	Atp6v0a1	AA959968|ATP6a1|Atp6n1|Atp6n1a|Atpv0a1|Vpp-1|Vpp1	ATPase, H+ transporting, lysosomal V0 subunit A1	protein-coding
mm_96228.1	chr11	62550524	62550545	+	1	NA	promoter-TSS (NR_002875).2	promoter-TSS (NR_002875).2	-637	NM_011664	22187	Mm.371592	NM_011664	ENSMUSG00000019505	Ubb	AL033289|Rps27a|Uba52|Ubb2|Ubc	ubiquitin B	protein-coding
mm_138767.1	chr17	37062671	37062707	+	1	NA	exon (NM_019439, exon 12 of 23)	exon (NM_019439, exon 12 of 23)	16723	NM_019439	54393	Mm.32191	NM_019439	ENSMUSG00000024462	Gabbr1	GABAB1|GABAbR1|bM573K1.1	gamma-aminobutyric acid (GABA) B receptor, 1	protein-coding
mm_36222.1	chr4	62520022	62520035	-	1	NA	promoter-TSS (NM_001276446)	promoter-TSS (NM_001276446)	35	NM_008525	17025	Mm.6988	NM_008525	ENSMUSG00000028393	Alad	ALADH|Lv	aminolevulinate, delta-, dehydratase	protein-coding
mm_83947.1	chr9	56883008	56883017	-	1	NA	intron (NM_139001, intron 1 of 9)	intron (NM_139001, intron 1 of 9)	17908	NM_139001	121021	Mm.41329	NM_139001	ENSMUSG00000032911	Cspg4	4732461B14Rik|AN2|NG2	chondroitin sulfate proteoglycan 4	protein-coding
mm_169814.1	chr16	20177114	20177128	-	1	NA	promoter-TSS (NR_030454).5	promoter-TSS (NR_030454).5	-887	NR_030454	735274		NR_030454	ENSMUSG00000106252	Mir684-1	Mirn684-1	microRNA 684-1	ncRNA
mm_6403.1	chr1	72862314	72862325	-	1	NA	3' UTR (NM_010518, exon 4 of 4)	3' UTR (NM_010518, exon 4 of 4)	12546	NM_010518	16011	Mm.405761	NM_010518	ENSMUSG00000026185	Igfbp5	AI256729|AW208790|IGFBP-5|IGFBP-5P	insulin-like growth factor binding protein 5	protein-coding
mm_163672.1	chr13	81805492	81805494	+	1	NA	Intergenic	HAL1|LINE|L1	22201	NM_007684	12626	Mm.12481	NM_007684	ENSMUSG00000021537	Cetn3	MmCEN3	centrin 3	protein-coding
mm_158806.1	chrX	167264281	167264291	-	1	NA	promoter-TSS (NM_001313760)	promoter-TSS (NM_001313760)	43	NM_001313761	170744	Mm.196676	NM_133212	ENSMUSG00000040522	Tlr8	-	toll-like receptor 8	protein-coding
mm_62810.1	chr7	113207501	113207595	+	1	NA	promoter-TSS (NM_007489)	promoter-TSS (NM_007489)	83	NM_007489	11865	Mm.33970	NM_007489	ENSMUSG00000055116	Arntl	Arnt3|BMAL1b|Bmal1|MOP3|bHLHe5|bmal1b'	aryl hydrocarbon receptor nuclear translocator-like	protein-coding
mm_62696.1	chr7	110122508	110122579	+	1	NA	exon (NM_009516, exon 1 of 11)	exon (NM_009516, exon 1 of 11)	484	NM_009516	22390	Mm.287173	NM_009516	ENSMUSG00000031016	Wee1	Wee1A	WEE 1 homolog 1 (S. pombe)	protein-coding
mm_52521.1	chr6	115544673	115544712	+	1	NA	promoter-TSS (NM_199033)	promoter-TSS (NM_199033)	-12	NM_199033	381802	Mm.291208	NM_199033	ENSMUSG00000042389	Tsen2	AU067695	tRNA splicing endonuclease subunit 2	protein-coding
mm_169389.1	chr14	42737585	42737589	+	1	NA	Intergenic	RLTR13A1|LTR|ERVK	60348	NM_001244671	100042055	Mm.429109	NM_001244671	ENSMUSG00000095226	Gm10377	ENSMUSG00000072606	predicted gene 10377	protein-coding
mm_82652.1	chr9	22024735	22024766	-	1	NA	intron (NM_010487, intron 5 of 6)	intron (NM_010487, intron 5 of 6)	21762	NM_008925	19089	Mm.214593	NM_008925	ENSMUSG00000003402	Prkcsh	80K-H|PKCSH	protein kinase C substrate 80K-H	protein-coding
mm_146437.1	chr18	84934595	84934617	+	1	NA	promoter-TSS (NM_015798)	promoter-TSS (NM_015798)	-419	NM_015798	50764	Mm.28369	NM_015798	ENSMUSG00000034391	Fbxo15	AU019763|Fbx15|ecat3	F-box protein 15	protein-coding
mm_163323.1	chr12	7995673	7995675	+	1	NA	intron (NM_009693, intron 18 of 28)	intron (NM_009693, intron 18 of 28)	17997	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_59604.1	chr7	28140184	28140189	+	1	NA	exon (NM_001164655, exon 5 of 20)	exon (NM_001164655, exon 5 of 20)	10720	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_59565.1	chr7	28089813	28089827	+	1	NA	exon (NM_001122603, exon 6 of 20)	exon (NM_001122603, exon 6 of 20)	18584	NM_001122603	215384	Mm.292276	NM_175444	ENSMUSG00000047730	Fcgbp	A430096B05Rik	Fc fragment of IgG binding protein	protein-coding
mm_137126.1	chr17	22876349	22876367	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-9224	NM_001110254	240041	Mm.328828	NM_177358	ENSMUSG00000059142	Zfp945	A630033E08Rik|C730040L01Rik	zinc finger protein 945	protein-coding
mm_17780.1	chr2	32929789	32929796	-	1	NA	intron (NM_199302, intron 21 of 24)	intron (NM_199302, intron 21 of 24)	31463	NM_199302	227738	Mm.248037	NM_199302	ENSMUSG00000026792	Lrsam1	-	leucine rich repeat and sterile alpha motif containing 1	protein-coding
mm_49855.1	chr6	38434337	38434382	+	1	NA	exon (NM_177185, exon 1 of 17)	exon (NM_177185, exon 1 of 17)	434	NM_177185	320538	Mm.302831	NM_177185	ENSMUSG00000038538	Ubn2	2900060J04Rik|6030408G03Rik|BC060116|D130059P03Rik|mKIAA2030	ubinuclein 2	protein-coding
mm_57386.1	chr6	124828314	124828343	-	1	NA	intron (NM_013700, intron 1 of 19)	intron (NM_013700, intron 1 of 19)	1156	NM_001326594	22225	Mm.3571	NM_013700	ENSMUSG00000038429	Usp5	AA407472|ISOT|ISOT-1|Ucht	ubiquitin specific peptidase 5 (isopeptidase T)	protein-coding
mm_56294.1	chr6	91515797	91515859	-	1	NA	promoter-TSS (NM_009531)	promoter-TSS (NM_009531)	60	NM_009531	22591	Mm.2806	NM_009531	ENSMUSG00000030094	Xpc	-	xeroderma pigmentosum, complementation group C	protein-coding
mm_9399.1	chr1	172220465	172220471	-	1	NA	promoter-TSS (NM_009813)	promoter-TSS (NM_009813)	-573	NM_009813	12372	Mm.12829	NM_009813	ENSMUSG00000007122	Casq1	CSQ|CSQ-1|CSQ1|sCSQ	calsequestrin 1	protein-coding
mm_14490.1	chr2	131936699	131936714	+	1	NA	exon (NM_001278256, exon 4 of 4)	exon (NM_001278256, exon 4 of 4)	-14155	NM_001278257	26434	Mm.180750	NM_023043	ENSMUSG00000027338	Prnd	AI450264|Dpl|PrPLP|doppel	prion protein dublet	protein-coding
mm_74551.1	chr8	10865316	10865329	-	1	NA	Intergenic	B3A|SINE|B2	17132	NR_040705	320014	Mm.403203	NR_040705	ENSMUSG00000109473	B930025P03Rik	-	RIKEN cDNA B930025P03 gene	ncRNA
mm_134056.1	chr16	6106680	6106682	-	1	NA	intron (NM_021477, intron 1 of 16)	intron (NM_021477, intron 1 of 16)	131094	NR_045799	68238	Mm.434605	NR_045799	ENSMUSG00000101481	1700123O21Rik	-	RIKEN cDNA 1700123O21 gene	ncRNA
mm_61269.1	chr7	66176509	66176540	+	1	NA	Intergenic	Intergenic	67009	NM_001081163	269941	Mm.333916	NM_001081163	ENSMUSG00000032640	Chsy1	mKIAA0990	chondroitin sulfate synthase 1	protein-coding
mm_143811.1	chr17	83690446	83690474	-	1	NA	Intergenic	MTE2b|LTR|ERVL-MaLR	-15703	NM_001171054	116871	Mm.277668	NM_054082	ENSMUSG00000055817	Mta3	1110002J22Rik|mKIAA1266	metastasis associated 3	protein-coding
mm_34417.1	chr4	145274121	145274140	+	1	NA	intron (NM_009401, intron 12 of 12)	intron (NM_009401, intron 12 of 12)	-27260	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_123169.1	chr14	57379368	57379419	-	1	NA	intron (NM_030004, intron 2 of 7)	B3A|SINE|B2	19090	NM_030004	68631	Mm.25539	NM_030004	ENSMUSG00000021947	Cryl1	1110025H08Rik|A230106J09Rik|C85932|gul3dh	crystallin, lambda 1	protein-coding
mm_86779.1	chr10	20170762	20170796	+	1	NA	intron (NM_001198635, intron 1 of 17)	intron (NM_001198635, intron 1 of 17)	21859	NM_001198635	17761	Mm.20928	NM_008635	ENSMUSG00000019996	Map7	E-MAP-115|MAP-7|Mtap7|R75000|mshi|mste|ste	microtubule-associated protein 7	protein-coding
mm_129706.1	chr15	81729852	81729854	-	1	NA	promoter-TSS (NM_011241)	promoter-TSS (NM_011241)	66	NM_011241	19387	Mm.270975	NM_011241	ENSMUSG00000022391	Rangap1	C79654|Fug1|mKIAA1835	RAN GTPase activating protein 1	protein-coding
mm_104257.1	chr11	88924581	88924597	-	1	NA	3' UTR (NM_029023, exon 13 of 13)	3' UTR (NM_029023, exon 13 of 13)	18661	NR_045955	73921	Mm.439148	NR_045955	ENSMUSG00000087338	Scpep1os	4930405P13Rik	serine carboxypeptidase 1, opposite strand	ncRNA
mm_76390.1	chr8	84843018	84843040	-	1	NA	exon (NM_007591, exon 8 of 9)	exon (NM_007591, exon 8 of 9)	-2364	NM_009010	19358	Mm.255539	NM_009010	ENSMUSG00000003813	Rad23a	2310040P19Rik|AL024030|HR23A|mHR23A	RAD23 homolog A, nucleotide excision repair protein	protein-coding
mm_89373.1	chr10	88739800	88739803	+	1	NA	intron (NM_025859, intron 4 of 5)	intron (NM_025859, intron 4 of 5)	8387	NM_025859	104303	Mm.291247	NM_025859	ENSMUSG00000060904	Arl1	2310008D22Rik|AU019749	ADP-ribosylation factor-like 1	protein-coding
mm_149435.1	chr19	11477652	11477666	+	1	NA	intron (NM_028595, intron 4 of 6)	intron (NM_028595, intron 4 of 6)	8291	NM_028595	73656	Mm.440719	NM_028595	ENSMUSG00000079419	Ms4a6c	2200009H22Rik|2210417N07Rik	membrane-spanning 4-domains, subfamily A, member 6C	protein-coding
mm_110136.1	chr12	26447479	26447495	-	1	NA	intron (NM_021384, intron 4 of 5)	intron (NM_021384, intron 4 of 5)	8965	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_36274.1	chr4	63729557	63729567	-	1	NA	3' UTR (NM_177371, exon 4 of 4)	3' UTR (NM_177371, exon 4 of 4)	15551	NM_177371	326623	Mm.208152	NM_177371	ENSMUSG00000050395	Tnfsf15	Tl1|Tl1a|Tnlg1b|Vegi	tumor necrosis factor (ligand) superfamily, member 15	protein-coding
mm_110902.1	chr12	75722715	75722729	-	1	NA	exon (NM_030750, exon 2 of 3)	exon (NM_030750, exon 2 of 3)	13007	NM_030750	81535	Mm.280199	NM_030750	ENSMUSG00000021054	Sgpp1	AI463453|SPP|SPP1|Spph1	sphingosine-1-phosphate phosphatase 1	protein-coding
mm_106782.1	chr12	4712337	4712343	+	1	NA	intron (NM_011365, intron 37 of 38)	intron (NM_011365, intron 37 of 38)	26043	NM_029107	74855	Mm.269534	NM_029107	ENSMUSG00000079177	Fam228a	4930417G10Rik	family with sequence similarity 228, member A	protein-coding
mm_97146.1	chr11	75459438	75459462	+	1	NA	Intergenic	Intergenic	-2089	NR_030711	100042498	Mm.482242	NR_030711	ENSMUSG00000085148	Mir22hg	2210403K04Rik|mir-22	Mir22 host gene (non-protein coding)	ncRNA
mm_124285.1	chr14	103048740	103048755	-	1	NA	intron (NM_008392, intron 1 of 4)	intron (NM_008392, intron 1 of 4)	1735	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_124048.1	chr14	77856295	77856298	-	1	NA	intron (NM_025384, intron 2 of 5)	intron (NM_025384, intron 2 of 5)	18621	NM_025384	66148	Mm.248046	NM_025384	ENSMUSG00000022013	Dnajc15	1110003P16Rik|Dnajd1	DnaJ heat shock protein family (Hsp40) member C15	protein-coding
mm_162257.1	chrX	169113033	169113033	+	1	NA	5' UTR (NM_001287530, exon 1 of 13)	5' UTR (NM_001287530, exon 1 of 13)	155	NM_001287530	11856	Mm.441810	NM_009707	ENSMUSG00000031355	Arhgap6	AI504284|RhoGAPX-1	Rho GTPase activating protein 6	protein-coding
mm_148151.1	chr18	77565112	77565162	-	1	NA	promoter-TSS (NM_001164504)	promoter-TSS (NM_001164504)	-1	NM_001164504	225743	Mm.23293	NM_001164504	ENSMUSG00000025427	Rnf165	2900024M11Rik|AI427432|Akd2|Ark2c|G630064H08Rik|Gm96	ring finger protein 165	protein-coding
mm_119548.1	chr14	48464183	48464184	+	1	NA	intron (NM_001310584, intron 4 of 16)	intron (NM_001310584, intron 4 of 16)	17831	NR_132324	218989	Mm.85211	NM_172600	ENSMUSG00000036339	Tmem260	5930435P15|6720456H20Rik	transmembrane protein 260	protein-coding
mm_51421.1	chr6	78426041	78426049	+	1	NA	promoter-TSS (NM_009042)	promoter-TSS (NM_009042)	62	NM_009042	19692	Mm.142731	NM_009042	ENSMUSG00000059654	Reg1	-	regenerating islet-derived 1	protein-coding
mm_136038.1	chr16	77421888	77421911	-	1	NA	intron (NR_015543, intron 2 of 4)	intron (NR_015543, intron 2 of 4)	92571	NR_015543	77994	Mm.394688	NR_015543	ENSMUSG00000090386	Mir99ahg	2810055G20Rik|D730043B02Rik	Mir99a and Mirlet7c-1 host gene (non-protein coding)	ncRNA
mm_72663.1	chr8	84872188	84872241	+	1	NA	promoter-TSS (NM_001168244)	promoter-TSS (NM_001168244)	-44	NM_001168244	71846	Mm.229128	NM_027954	ENSMUSG00000003824	Syce2	1700013H19Rik|AA407907|Cesc1	synaptonemal complex central element protein 2	protein-coding
mm_50576.1	chr6	49052901	49052917	+	1	NA	intron (NM_053110, intron 9 of 10)	B4|SINE|B4	16391	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_99323.1	chr11	101442678	101442684	+	1	NA	intron (NM_011289, intron 1 of 4)	CpG	436	NM_011289	19942	Mm.340658	NM_011289	ENSMUSG00000063316	Rpl27	-	ribosomal protein L27	protein-coding
mm_136717.1	chr17	7945982	7945990	+	1	NA	exon (NM_025789, exon 1 of 8)	exon (NM_025789, exon 1 of 8)	372	NM_025789	66832	Mm.29830	NM_025789	ENSMUSG00000073471	Rsph3a	1700012G05Rik|4930524H12Rik|R74860|Rshl2|Rshl2a	radial spoke 3A homolog (Chlamydomonas)	protein-coding
mm_105876.1	chr11	114923970	114923980	-	1	NA	3' UTR (NM_199221, exon 4 of 4)	3' UTR (NM_199221, exon 4 of 4)	10411	NM_001347651	217304	Mm.185355	NM_199221	ENSMUSG00000063193	Cd300lb	CLM-7|Clm7|Gm253|LMIR5	CD300 molecule like family member B	protein-coding
mm_47526.1	chr5	124171644	124171649	-	1	NA	intron (NM_011256, intron 2 of 24)	intron (NM_011256, intron 2 of 24)	15536	NM_001289472	19679	Mm.44261	NM_011256	ENSMUSG00000029406	Pitpnm2	NIR3|RDGBA2|Rdgb2|mKIAA1457	phosphatidylinositol transfer protein, membrane-associated 2	protein-coding
mm_75331.1	chr8	43180283	43180301	-	1	NA	Intergenic	Intergenic	-2830	NM_001160412	622117	Mm.390031	NM_001160412	ENSMUSG00000091490	Triml2	EG622117|Tu4	tripartite motif family-like 2	protein-coding
mm_61077.1	chr7	51621881	51621891	+	1	NA	promoter-TSS (NM_080853)	promoter-TSS (NM_080853)	56	NM_080853	140919	Mm.256618	NM_080853	ENSMUSG00000030500	Slc17a6	2900073D12Rik|DNPI|VGLUT2	solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 6	protein-coding
mm_16624.1	chr2	5676956	5676969	-	1	NA	promoter-TSS (NM_001290376)	promoter-TSS (NM_001290376)	-916	NM_001290376	227541	Mm.191949	NM_177343	ENSMUSG00000039145	Camk1d	A630059D12Rik|CKLiK|CaMKIdelta|E030025C11Rik|mCKLiK	calcium/calmodulin-dependent protein kinase ID	protein-coding
mm_82740.1	chr9	26791892	26791920	-	1	NA	intron (NM_001310768, intron 4 of 18)	intron (NM_001310768, intron 4 of 18)	14511	NM_153803	244757	Mm.293696	NM_153803	ENSMUSG00000036395	Glb1l2	-	galactosidase, beta 1-like 2	protein-coding
mm_37668.1	chr4	129118710	129118716	-	1	NA	exon (NM_010471, exon 2 of 4)	exon (NM_010471, exon 2 of 4)	1459	NM_001286083	15444	Mm.384452	NM_010471	ENSMUSG00000028785	Hpca	-	hippocalcin	protein-coding
mm_25997.1	chr3	134239287	134239307	+	1	NA	intron (NM_001004367, intron 2 of 3)	intron (NM_001004367, intron 2 of 3)	1286	NR_035435	100316832		NR_035435	ENSMUSG00000084564	Mir1895	Mirn1895|mmu-mir-1895	microRNA 1895	ncRNA
mm_148765.1	chr19	6061531	6061562	+	1	NA	exon (NM_013859, exon 1 of 1)	exon (NM_013859, exon 1 of 1)	339	NM_013859	29805	Mm.2310	NM_013859	ENSMUSG00000075227	Znhit2	C11orf5|Fon|ORF6|Znhit2-ps	zinc finger, HIT domain containing 2	protein-coding
mm_64263.1	chr7	141746737	141746748	+	1	NA	exon (NM_023566, exon 31 of 46)	exon (NM_023566, exon 31 of 46)	-42269	NM_010844	17833	Mm.334332	NM_010844	ENSMUSG00000037974	Muc5ac	2210005L13Rik|MGM	mucin 5, subtypes A and C, tracheobronchial/gastric	protein-coding
mm_22279.1	chr2	179976647	179976665	-	1	NA	promoter-TSS (NM_001081092)	promoter-TSS (NM_001081092)	-10	NM_001081092	228980	Mm.235542	NM_001081092	ENSMUSG00000039117	Taf4	135kDa|AI450312|TAFII130|TAFII135|Taf2c1|Taf4a	TATA-box binding protein associated factor 4	protein-coding
mm_31939.1	chr4	86575797	86575807	+	1	NA	5' UTR (NM_178376, exon 1 of 1)	5' UTR (NM_178376, exon 1 of 1)	129	NM_178376	68441	Mm.31178	NM_178376	ENSMUSG00000070934	Rraga	1300010C19Rik|AI255374|FIP-1|RAGA	Ras-related GTP binding A	protein-coding
mm_695.1	chr1	40580364	40580374	+	1	NA	5' UTR (NM_177084, exon 1 of 12)	5' UTR (NM_177084, exon 1 of 12)	142	NM_177084	110895	Mm.108602	NM_177084	ENSMUSG00000026065	Slc9a4	AW990558|D730009J23Rik|NHE4	solute carrier family 9 (sodium/hydrogen exchanger), member 4	protein-coding
mm_70510.1	chr8	12926300	12926317	+	1	NA	intron (NM_178076, intron 1 of 30)	intron (NM_178076, intron 1 of 30)	10415	NM_178076	17207	Mm.334413	NM_178076	ENSMUSG00000031442	Mcf2l	C130040G20Rik|Dbs|Ost|mKIAA0362	mcf.2 transforming sequence-like	protein-coding
mm_14293.1	chr2	128862948	128862958	+	1	NA	promoter-TSS (NM_024237)	promoter-TSS (NM_024237)	-979	NM_024237	70370	Mm.5107	NM_024237	ENSMUSG00000027386	Fbln7	1600015H20Rik|AI464334|TM14	fibulin 7	protein-coding
mm_160164.1	chr7	44665264	44665264	-	1	NA	exon (NM_001271540, exon 2 of 42)	exon (NM_001271540, exon 2 of 42)	239	NM_001271538	71960	Mm.158289	NM_028021	ENSMUSG00000030739	Myh14	2400004E04Rik|II-C|NHMCII|NMHC II-C	myosin, heavy polypeptide 14	protein-coding
mm_165587.1	chr3	32547876	32547876	-	1	NA	intron (NM_024200, intron 7 of 17)	B1_Mm|SINE|Alu	18394	NM_024200	67414	Mm.290414	NM_024200	ENSMUSG00000027668	Mfn1	2310002F04Rik|6330416C07Rik|D3Ertd265e|HR2|mKIAA4032	mitofusin 1	protein-coding
mm_134837.1	chr16	26359110	26359140	-	1	NA	exon (NM_016674, exon 4 of 4)	exon (NM_016674, exon 4 of 4)	12714	NM_016674	12737	Mm.289441	NM_016674	ENSMUSG00000022512	Cldn1	AI596271	claudin 1	protein-coding
mm_127500.1	chr15	101420506	101420518	+	1	NA	exon (NM_033073, exon 6 of 9)	exon (NM_033073, exon 6 of 9)	8109	NM_033073	110310	Mm.486285	NM_033073	ENSMUSG00000023039	Krt7	D15Wsu77e|K7|Krt2-7	keratin 7	protein-coding
mm_104277.1	chr11	89696851	89696873	-	1	NA	promoter-TSS (NM_001327810)	promoter-TSS (NM_001327810)	74	NM_001327810	382543	Mm.60997	NM_172534	ENSMUSG00000047773	Ankfn1	4932411E22Rik|Gm1175|nmf9	ankyrin-repeat and fibronectin type III domain containing 1	protein-coding
mm_156526.1	chrX	150826926	150826929	+	1	NA	promoter-TSS (NM_001289875)	promoter-TSS (NM_001289875)	10	NM_001289875	634882		NM_001289875		Itih5l-ps	Gm386|Itih5l	inter-alpha (globulin) inhibitor H5-like, pseudogene	protein-coding
mm_28992.1	chr3	101296556	101296566	-	1	NA	Intergenic	Intergenic	-8622	NM_013486	12481	Mm.22842	NM_013486	ENSMUSG00000027863	Cd2	LFA-2|Ly-37|Ly37	CD2 antigen	protein-coding
mm_158600.1	chrX	151762691	151762696	-	1	NA	Intergenic	MERVL_2A-int|LTR|ERVL	-40589	NM_021523	59026	Mm.27372	NM_021523	ENSMUSG00000025261	Huwe1	5430439H10Rik|AU041296|Arf-bp1|C430014N20Rik|C80292|Gm1718|Ib772|LASU1|Mule|Ureb1	HECT, UBA and WWE domain containing 1	protein-coding
mm_61619.1	chr7	80186298	80186326	+	1	NA	promoter-TSS (NM_013659)	promoter-TSS (NM_013659)	-529	NM_013659	20352	Mm.275909	NM_013659	ENSMUSG00000030539	Sema4b	SemC|Semac|mKIAA1745	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B	protein-coding
mm_106407.1	chr11	118910091	118910102	-	1	NA	promoter-TSS (NM_001039167)	promoter-TSS (NM_001039167)	-524	NM_001039167	52897	Mm.341103	NM_001024931	ENSMUSG00000025576	Rbfox3	Fox-3|Hrnbp3|NeuN|Neuna60	RNA binding protein, fox-1 homolog (C. elegans) 3	protein-coding
mm_8408.1	chr1	151945284	151945288	-	1	NA	intron (NM_197990, intron 3 of 5)	intron (NM_197990, intron 3 of 5)	145034	NM_197990	69399	Mm.278031	NM_197990	ENSMUSG00000032666	1700025G04Rik	2610510E02Rik|2900042O04Rik|ENSMUSG00000073540	RIKEN cDNA 1700025G04 gene	protein-coding
mm_67669.1	chr7	87493372	87493438	-	1	NA	5' UTR (NM_011661, exon 1 of 5)	5' UTR (NM_011661, exon 1 of 5)	107	NM_011661	22173	Mm.238127	NM_011661	ENSMUSG00000004651	Tyr	Oca1|albino|c|skc35	tyrosinase	protein-coding
mm_20135.1	chr2	121380960	121380975	-	1	NA	promoter-TSS (NM_080459)	promoter-TSS (NM_080459)	-27	NM_080459	140476	Mm.467475	NM_080459	ENSMUSG00000033498	Strc	DFNB16	stereocilin	protein-coding
mm_123372.1	chr14	63193489	63193508	-	1	NA	promoter-TSS (NM_201610)	promoter-TSS (NM_201610)	27	NM_201610	382913	Mm.239490	NM_201610	ENSMUSG00000035121	Neil2	Gm1212|NEH2	nei like 2 (E. coli)	protein-coding
mm_143101.1	chr17	57081647	57081658	-	1	NA	exon (NM_009451, exon 4 of 4)	exon (NM_009451, exon 4 of 4)	-3142	NM_153551	70785	Mm.284447	NM_153551	ENSMUSG00000002668	Dennd1c	4432409M07Rik	DENN/MADD domain containing 1C	protein-coding
mm_76832.1	chr8	105171442	105171454	-	1	NA	intron (NM_001161456, intron 2 of 4)	CpG-14413	774	NM_001161458	12400	Mm.2018	NM_022309	ENSMUSG00000031885	Cbfb	AI893578|PEA2|PEBP2b|Pebp2|Pebpb2	core binding factor beta	protein-coding
mm_45466.1	chr5	67847446	67847458	-	1	NA	promoter-TSS (NM_009727)	promoter-TSS (NM_009727)	-21	NM_001038999	11980	Mm.153230	NM_009727	ENSMUSG00000037685	Atp8a1	AI481521|AI853962|APLT|AW743152|AW822227|Atp3a2|B230107D19Rik|ClassI	ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1	protein-coding
mm_13595.1	chr2	112507187	112507198	+	1	NA	intron (NM_028844, intron 1 of 5)	intron (NM_028844, intron 1 of 5)	14228	NM_028844	74268	Mm.315125	NM_028844	ENSMUSG00000003604	Aven	1700013A01Rik|1700056A21Rik|mAven-L|mAven-S	apoptosis, caspase activation inhibitor	protein-coding
mm_67988.1	chr7	100856290	100856308	-	1	NA	intron (NM_177073, intron 1 of 10)	L2b|LINE|L2	7114	NM_177073	320100	Mm.40336	NM_177073	ENSMUSG00000008318	Relt	E430021K24Rik|Tnfrsf19l	RELT tumor necrosis factor receptor	protein-coding
mm_33510.1	chr4	130914350	130914353	+	1	NA	intron (NM_010686, intron 1 of 7)	MIRb|SINE|MIR	1017	NM_010686	16792	Mm.271868	NM_010686	ENSMUSG00000028581	Laptm5	E3	lysosomal-associated protein transmembrane 5	protein-coding
mm_18219.1	chr2	50297152	50297158	-	1	NA	promoter-TSS (NM_133839)	promoter-TSS (NM_133839)	345	NR_040362	100502624	Mm.382825	NR_040361	ENSMUSG00000085862	Gm13483	OTTMUSG00000012382	predicted gene 13483	ncRNA
mm_116834.1	chr13	54687624	54687643	-	1	NA	5' UTR (NM_001146025, exon 1 of 11)	5' UTR (NM_001146025, exon 1 of 11)	175	NM_001146025	105239	Mm.25366	NM_134064	ENSMUSG00000034928	Rnf44	AI854545|mKIAA1100	ring finger protein 44	protein-coding
mm_48524.1	chr5	142903485	142903507	-	1	NA	3' UTR (NM_007393, exon 6 of 6)	3' UTR (NM_007393, exon 6 of 6)	3258	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_28817.1	chr3	96262330	96262349	-	1	NA	TTS (NM_033596)	TTS (NM_033596)	978	NM_033596	97122	Mm.227295	NM_033596	ENSMUSG00000091405	Hist2h4	H4|X04652	histone cluster 2, H4	protein-coding
mm_77558.1	chr8	123374315	123374327	-	1	NA	intron (NM_001286362, intron 1 of 16)	CpG	610	NM_001286363	66855	Mm.178818	NM_025804	ENSMUSG00000001472	Tcf25	1100001J13Rik|1810041K11Rik|D8Ertd325e|Nulp1|mKIAA1049	transcription factor 25 (basic helix-loop-helix)	protein-coding
mm_135097.1	chr16	35000587	35000595	-	1	NA	3' UTR (NM_139300, exon 32 of 32)	3' UTR (NM_139300, exon 32 of 32)	-21830	NM_023587	70757	Mm.27286	NM_023587	ENSMUSG00000035376	Hacd2	6330408J20Rik|AI255777|AI481689|Hcad2|Ptplb	3-hydroxyacyl-CoA dehydratase 2	protein-coding
mm_11526.1	chr2	32625432	32625442	+	1	NA	promoter-TSS (NM_001198791)	promoter-TSS (NM_001198791)	0	NM_001198791	11636	Mm.29189	NM_021515	ENSMUSG00000026817	Ak1	Ak-1|B430205N08Rik	adenylate kinase 1	protein-coding
mm_127829.1	chr15	6565276	6565302	-	1	NA	Intergenic	Intergenic	-14558	NM_001278269	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_118362.1	chr13	115101796	115101802	-	1	NA	5' UTR (NM_001033228, exon 1 of 29)	5' UTR (NM_001033228, exon 1 of 29)	165	NM_001033228	109700	Mm.317280	NM_001033228	ENSMUSG00000042284	Itga1	CD49A|E130012M19Rik|Vla1	integrin alpha 1	protein-coding
mm_125963.1	chr15	76270935	76270945	+	1	NA	intron (NM_028852, intron 1 of 4)	B1F|SINE|Alu	-1101	NR_045747	100038659	Mm.448549	NR_045747		Mirt2	ENSMUSG00000075583|Gm10872|Gm24562	myocardial infraction associated transcript 2	ncRNA
mm_19656.1	chr2	102923728	102923740	-	1	NA	Intergenic	Intergenic	-22069	NM_001039150	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_55113.1	chr6	50392922	50392930	-	1	NA	intron (NM_001347213, intron 2 of 23)	ORR1C2|LTR|ERVL-MaLR	-10089	NM_027881	71720	Mm.44153	NM_027881	ENSMUSG00000029822	Osbpl3	1200014M06Rik|6720421I08Rik|A530055M08|ORP-3|ORP3|OSBP3	oxysterol binding protein-like 3	protein-coding
mm_23752.1	chr3	69721997	69722071	+	1	NA	promoter-TSS (NM_133787)	promoter-TSS (NM_133787)	-21	NM_133787	97112	Mm.21062	NM_133787	ENSMUSG00000027787	Nmd3	C87860	NMD3 ribosome export adaptor	protein-coding
mm_120748.1	chr14	73238154	73238165	+	1	NA	5' UTR (NM_175116, exon 1 of 1)	5' UTR (NM_175116, exon 1 of 1)	268	NM_175116	67168	Mm.390681	NM_175116	ENSMUSG00000033446	Lpar6	2610302I02Rik|P2ry5|P2y5	lysophosphatidic acid receptor 6	protein-coding
mm_74329.1	chr8	126971179	126971223	+	1	NA	promoter-TSS (NM_172762)	promoter-TSS (NM_172762)	-122	NM_172762	52202	Mm.28199	NM_172762	ENSMUSG00000033931	Rbm34	4930547K05Rik|6330444B11|D8Ertd233e	RNA binding motif protein 34	protein-coding
mm_19789.1	chr2	108685833	108685840	-	1	NA	Intergenic	Intergenic	592454	NM_029790	76894	Mm.330451	NM_029790	ENSMUSG00000057234	Mettl15	0610027B03Rik|AI303697|AW049952|Mett5d1	methyltransferase like 15	protein-coding
mm_7537.1	chr1	124445673	124445698	-	1	NA	Intergenic	Intergenic	-400126	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_72106.1	chr8	71611161	71611200	+	1	NA	5' UTR (NM_146211, exon 1 of 12)	5' UTR (NM_146211, exon 1 of 12)	156	NM_146211	234407	Mm.240885	NM_146211	ENSMUSG00000034807	Colgalt1	2810024B22Rik|Glt25d1	collagen beta(1-O)galactosyltransferase 1	protein-coding
mm_95460.1	chr11	50378373	50378388	+	1	NA	exon (NM_021510, exon 2 of 14)	exon (NM_021510, exon 2 of 14)	661	NM_001347487	59013	Mm.21740	NM_021510	ENSMUSG00000007850	Hnrnph1	AI642080|E430005G16Rik|Hnrnph|Hnrph1	heterogeneous nuclear ribonucleoprotein H1	protein-coding
mm_91669.1	chr10	43174522	43174569	-	1	NA	promoter-TSS (NR_102361)	promoter-TSS (NR_102361)	-15	NM_175407	109205	Mm.153750	NM_175407	ENSMUSG00000038248	Sobp	2900009C16Rik|5330439J01Rik|JXC1|jc	sine oculis-binding protein homolog (Drosophila)	protein-coding
mm_89411.1	chr10	90829539	90829556	+	1	NA	promoter-TSS (NM_001347054)	promoter-TSS (NM_001347054)	-107	NM_001347054	77531	Mm.440605	NM_181398	ENSMUSG00000058589	Anks1b	AIDA-1b|C030032C09Rik|E530015N03Rik|ENSMUSG00000078431|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding
mm_114387.1	chr13	63251725	63251750	+	1	NA	intron (NR_110520, intron 2 of 5)	(CTG)n|Simple_repeat|Simple_repeat	11708	NR_110521	72061	Mm.188105	NM_028079	ENSMUSG00000021458	2010111I01Rik	2300006M17Rik|AP-O|AW742919|Aopep|ApO|mir-23b|mir-24-1|mir-27b	RIKEN cDNA 2010111I01 gene	protein-coding
mm_34070.1	chr4	138456875	138456885	+	1	NA	3' UTR (NM_025451, exon 2 of 2)	3' UTR (NM_025451, exon 2 of 2)	1732	NM_025451	66259	Mm.41603	NM_025451	ENSMUSG00000046447	Camk2n1	1810006K23Rik|AI848599|AI891706	calcium/calmodulin-dependent protein kinase II inhibitor 1	protein-coding
mm_141873.1	chr17	34839342	34839356	-	1	NA	TTS (NM_001163770)	TTS (NM_001163770)	2330	NM_001163770	112403	Mm.275309	NM_033613	ENSMUSG00000040482	Dxo	Dom3z|NG6	decapping exoribonuclease	protein-coding
mm_54708.1	chr6	39705724	39705771	-	1	NA	intron (NM_139294, intron 1 of 21)	ORR1B1|LTR|ERVL-MaLR	19716	NM_139294	109880	Mm.245513	NM_139294	ENSMUSG00000002413	Braf	9930012E13Rik|AA120551|AA387315|AA473386|B-raf|Braf-2|Braf2|C230098H17|C87398|D6Ertd631e	Braf transforming gene	protein-coding
mm_149393.1	chr19	11387496	11387515	+	1	NA	intron (NM_001310331, intron 4 of 6)	RSINE1|SINE|B4	12017	NM_001310331	666907		NM_001310331	ENSMUSG00000101389	Ms4a4a	EG666907	membrane-spanning 4-domains, subfamily A, member 4A	protein-coding
mm_20874.1	chr2	148701173	148701183	-	1	NA	intron (NM_019632, intron 7 of 10)	intron (NM_019632, intron 7 of 10)	20058	NM_028986	74533	Mm.136913	NM_028986	ENSMUSG00000027439	Gzf1	8430437G08Rik|Zfp336|mGZF1	GDNF-inducible zinc finger protein 1	protein-coding
mm_37874.1	chr4	132353727	132353732	-	1	NA	promoter-TSS (NR_003270)	promoter-TSS (NR_003270)	-43	NR_003270	399101	Mm.486919	NR_002904	ENSMUSG00000085241	Snhg3	Rnu17d|U17HG	small nucleolar RNA host gene 3	ncRNA
mm_48971.1	chr6	4752803	4752812	+	1	NA	intron (NM_001040611, intron 1 of 1)	intron (NM_001040611, intron 1 of 1)	5501	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_22338.1	chr2	180710031	180710081	-	1	NA	promoter-TSS (NM_001291432)	promoter-TSS (NM_001291432)	-57	NM_001291432	23856	Mm.253836	NM_011805	ENSMUSG00000038914	Dido1	6720461J16Rik|D130048F08Rik|DATF-1|DIO-1|Datf1|dido	death inducer-obliterator 1	protein-coding
mm_29593.1	chr3	119742696	119742712	-	1	NA	intron (NM_001310711, intron 7 of 13)	intron (NM_001310711, intron 7 of 13)	40684	NM_001310711	56195	Mm.29966	NM_019550	ENSMUSG00000028134	Ptbp2	Ptb2|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding
mm_125947.1	chr15	76248602	76248624	+	1	NA	TTS (NR_105918)	TTS (NR_105918)	422	NR_105918	102465575		NR_105918	ENSMUSG00000098625	Mir6953	Gm27738|mmu-mir-6953	microRNA 6953	ncRNA
mm_159456.1	chr3	153879749	153879749	-	1	NA	intron (NM_031870, intron 8 of 19)	intron (NM_031870, intron 8 of 19)	25142	NM_001282054	55993	Mm.272226	NM_031870	ENSMUSG00000005493	Msh4	4930485C04Rik|AV144863|mMsh4	mutS homolog 4	protein-coding
mm_88197.1	chr10	70097213	70097235	+	1	NA	5' UTR (NM_001111121, exon 1 of 9)	5' UTR (NM_001111121, exon 1 of 9)	103	NM_001111121	76551	Mm.281741	NM_001111121	ENSMUSG00000048701	Ccdc6	2810012H18Rik|AA536681|AA960498|AW061011	coiled-coil domain containing 6	protein-coding
mm_42660.1	chr5	119670659	119670676	+	1	NA	promoter-TSS (NM_011535)	promoter-TSS (NM_011535)	-195	NM_198052	21386	Mm.219139	NM_011535	ENSMUSG00000018604	Tbx3	D5Ertd189e	T-box 3	protein-coding
mm_38811.1	chr4	148444456	148444499	-	1	NA	5' UTR (NM_027873, exon 1 of 2)	5' UTR (NM_027873, exon 1 of 2)	274	NM_027873	71707	Mm.292503	NM_027873	ENSMUSG00000047719	Ubiad1	1200002M06Rik|AI426463|AW320947|Tere1	UbiA prenyltransferase domain containing 1	protein-coding
mm_114903.1	chr13	94788874	94788951	+	1	NA	promoter-TSS (NM_009321)	promoter-TSS (NM_009321)	-31	NM_009321	21371	Mm.379025	NM_009321	ENSMUSG00000042043	Tbca	Tbca13	tubulin cofactor A	protein-coding
mm_92604.1	chr10	80105669	80105704	-	1	NA	intron (NR_038088, intron 1 of 4)	intron (NR_038088, intron 1 of 4)	-2984	NM_183426	216161	Mm.262102	NM_183426	ENSMUSG00000035673	Sbno2	BC019206|F730040C21|Sno|Stno	strawberry notch homolog 2 (Drosophila)	protein-coding
mm_149127.1	chr19	8993349	8993368	+	1	NA	intron (NR_104460, intron 1 of 6)	intron (NR_104460, intron 1 of 6)	4074	NM_001286518	66395	Mm.203866	NM_009643	ENSMUSG00000069833	Ahnak	DY6	AHNAK nucleoprotein (desmoyokin)	protein-coding
mm_15816.1	chr2	164508249	164508258	+	1	NA	TTS (NM_133779)	TTS (NM_133779)	10728	NM_133779	78928	Mm.28228	NM_133779	ENSMUSG00000017721	Pigt	2510012P17Rik|4930534E15Rik|CGI-06|NDAP|Ndap7	phosphatidylinositol glycan anchor biosynthesis, class T	protein-coding
mm_4612.1	chr1	178555871	178555881	+	1	NA	intron (NM_001161665, intron 2 of 14)	intron (NM_001161665, intron 2 of 14)	26751	NM_001161665	269152	Mm.129727	NM_177724	ENSMUSG00000026494	Kif26b	4832420M10|BC056349|D230039L06Rik	kinesin family member 26B	protein-coding
mm_166797.1	chr7	3330884	3330897	+	1	NA	3' UTR (NM_011102, exon 18 of 18)	3' UTR (NM_011102, exon 18 of 18)	-5695	NM_133189	81904	Mm.214994	NM_133189	ENSMUSG00000069806	Cacng7	-	calcium channel, voltage-dependent, gamma subunit 7	protein-coding
mm_83101.1	chr9	40333261	40333301	-	1	NA	promoter-TSS (NR_040728)	promoter-TSS (NR_040728)	-191	NR_040728	73558	Mm.398307	NR_040728		1700110K17Rik	-	RIKEN cDNA 1700110K17 gene	ncRNA
mm_91631.1	chr10	42182229	42182252	-	1	NA	Intergenic	Intergenic	94502	NM_019740	56484	Mm.338613	NM_019740	ENSMUSG00000048756	Foxo3	1110048B16Rik|2010203A17Rik|C76856|FKHRL1|Fkhr2|Foxo3a	forkhead box O3	protein-coding
mm_157389.1	chrX	38252530	38252541	-	1	NA	promoter-TSS (NM_001289728)	promoter-TSS (NM_001289728)	-54	NM_001289728	245386	Mm.72979	NM_172930	ENSMUSG00000036502	Tmem255a	4933417N17|6430550H21Rik|Fam70a	transmembrane protein 255A	protein-coding
mm_165633.1	chr3	69004413	69004413	-	1	NA	promoter-TSS (NM_133786)	promoter-TSS (NM_133786)	157	NM_026641	68259	Mm.389451	NM_026641	ENSMUSG00000027778	Ift80	4921524P20Rik|Wdr56|mKIAA1374	intraflagellar transport 80	protein-coding
mm_147779.1	chr18	61536787	61536805	-	1	NA	promoter-TSS (NM_177828)	promoter-TSS (NM_177828)	-260	NM_177828	328967	Mm.488098	NM_177828	ENSMUSG00000045094	Arhgef37	4933429F08Rik	Rho guanine nucleotide exchange factor (GEF) 37	protein-coding
mm_119684.1	chr14	53418353	53418393	+	1	NA	Intergenic	Intergenic	835556	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_48882.1	chr5	151176446	151176449	-	1	NA	intron (NM_146258, intron 1 of 13)	Lx8b|LINE|L1	13746	NM_001163493	243362	Mm.209272	NM_146258	ENSMUSG00000016128	Stard13	DLC2|GT650	StAR-related lipid transfer (START) domain containing 13	protein-coding
mm_83537.1	chr9	46233250	46233278	-	1	NA	exon (NM_001289755, exon 4 of 4)	exon (NM_001289755, exon 4 of 4)	2035	NM_001289833	11814	Mm.390161	NM_023114	ENSMUSG00000032081	Apoc3	apo-CIII|apoC-III	apolipoprotein C-III	protein-coding
mm_152048.1	chr19	6232303	6232306	-	1	NA	exon (NM_198168, exon 6 of 14)	exon (NM_198168, exon 6 of 14)	3536	NM_198168	225849	Mm.118076	NM_198168	ENSMUSG00000024777	Ppp2r5b	B'beta|BC026670	protein phosphatase 2, regulatory subunit B', beta	protein-coding
mm_88139.1	chr10	69399004	69399011	+	1	NA	Intergenic	CpG	-46095	NM_007659	12534	Mm.281367	NM_007659	ENSMUSG00000019942	Cdk1	Cdc2|Cdc2a|p34<CDC2>	cyclin-dependent kinase 1	protein-coding
mm_32193.1	chr4	101292326	101292335	+	1	NA	Intergenic	CpG	-27048	NM_146145	16451	Mm.289657	NM_146145	ENSMUSG00000028530	Jak1	AA960307|BAP004|C130039L05Rik	Janus kinase 1	protein-coding
mm_141090.1	chr17	25979888	25979898	-	1	NA	intron (NM_001347334, intron 1 of 11)	intron (NM_001347334, intron 1 of 11)	5981	NM_001347334	50817	Mm.216072	NM_015830	ENSMUSG00000037326	Capn15	Solh	calpain 15	protein-coding
mm_3952.1	chr1	164062113	164062124	+	1	NA	promoter-TSS (NM_001164059)	promoter-TSS (NM_001164059)	42	NM_001164059	20343	Mm.1461	NM_011346	ENSMUSG00000026581	Sell	AI528707|CD62L|L-selectin|LECAM-1|Lnhr|Ly-22|Ly-m22|Lyam-1|Lyam1	selectin, lymphocyte	protein-coding
mm_64973.1	chr7	16719926	16719940	-	1	NA	Intergenic	Intergenic	-1996	NM_011927	26368	Mm.27096	NM_011927	ENSMUSG00000007209	Ceacam9	AA410097|AW545709|Cea-5|Cea5|mmCGM8	carcinoembryonic antigen-related cell adhesion molecule 9	protein-coding
mm_22344.1	chr2	180892932	180892939	-	1	NA	Intergenic	CpG	-1105	NR_029538	723951		NR_029538	ENSMUSG00000065454	Mir124a-3	Mirn124a-3|mir-124-3|mir-124a-3	microRNA 124a-3	ncRNA
mm_89442.1	chr10	92203012	92203017	+	1	NA	intron (NR_046027, intron 7 of 8)	intron (NR_046027, intron 7 of 8)	-37836	NR_028262	110333	Mm.429764	NR_028262		Rmst	100041799|AI853140|C230053E11Rik|D930049J19Rik|Dmt2|Gm3515|M2|Ncrms	rhabdomyosarcoma 2 associated transcript (non-coding RNA)	ncRNA
mm_9318.1	chr1	171648504	171648512	-	1	NA	intron (NM_001347184, intron 1 of 5)	intron (NM_001347184, intron 1 of 5)	491	NM_001347184	75345	Mm.164642	NM_144539	ENSMUSG00000038179	Slamf7	19A|19A24|4930560D03Rik|CRACC|CS1	SLAM family member 7	protein-coding
mm_17662.1	chr2	32083305	32083330	-	1	NA	5' UTR (NM_175511, exon 1 of 2)	5' UTR (NM_175511, exon 1 of 2)	388	NM_175511	241303	Mm.250441	NM_175511	ENSMUSG00000050592	Fam78a	A130092J06Rik	family with sequence similarity 78, member A	protein-coding
mm_42406.1	chr5	115011323	115011335	+	1	NA	promoter-TSS (NM_029012)	promoter-TSS (NM_029012)	-195	NM_029012	74585	Mm.355894	NM_029012	ENSMUSG00000029550	Sppl3	4833416I09Rik|Psl4|Usmg3	signal peptide peptidase 3	protein-coding
mm_155035.1	chrX	42069465	42069469	+	1	NA	intron (NR_125870, intron 1 of 5)	intron (NR_125870, intron 1 of 5)	1069	NR_125870	11798	Mm.259879	NM_009688	ENSMUSG00000025860	Xiap	1110015C02Rik|Aipa|Api3|Birc4|IAP3|ILP-1|MIHA	X-linked inhibitor of apoptosis	protein-coding
mm_131598.1	chr16	18893776	18893777	+	1	NA	intron (NM_010435, intron 1 of 24)	RMER15|LTR|ERVL	17026	NM_010435	15260	Mm.15694	NM_010435	ENSMUSG00000022702	Hira	AA138857|D16Ertd95e|Gm15797|N28177|OTTMUSG00000026264|Tuple1	histone cell cycle regulator	protein-coding
mm_148450.1	chr19	3979985	3980016	+	1	NA	intron (NM_001177438, intron 7 of 9)	intron (NM_001177438, intron 7 of 9)	-6570	NM_001302479	71670	Mm.29735	NM_027857	ENSMUSG00000024866	Acy3	0610006H10Rik|AA3|AAIII|AW107362|Acy-3|HCBP1	aspartoacylase (aminoacylase) 3	protein-coding
mm_117440.1	chr13	74734210	74734239	-	1	NA	promoter-TSS (NM_001301181)	promoter-TSS (NM_001301181)	37	NM_001301158	12380	Mm.29163	NM_009817	ENSMUSG00000021585	Cast	-	calpastatin	protein-coding
mm_76841.1	chr8	105289085	105289114	-	1	NA	TTS (NM_177788)	TTS (NM_177788)	429	NM_001166394	74356	Mm.204876	NM_028888	ENSMUSG00000014837	4931428F04Rik	AI426165|Kiaa0895l	RIKEN cDNA 4931428F04 gene	protein-coding
mm_165829.1	chr3	152114910	152114932	-	1	NA	intron (NM_016867, intron 3 of 5)	intron (NM_016867, intron 3 of 5)	50979	NM_016867	54120	Mm.97	NM_016867	ENSMUSG00000039131	Gipc2	2200002N01Rik|AU021850|Semcap2	GIPC PDZ domain containing family, member 2	protein-coding
mm_69621.1	chr7	137314224	137314230	-	1	NA	5' UTR (NM_001113414, exon 1 of 16)	5' UTR (NM_001113414, exon 1 of 16)	218	NM_001113415	13593	Mm.258708	NM_010096	ENSMUSG00000010476	Ebf3	3110018A08Rik|O/E-2|mKIAA4201	early B cell factor 3	protein-coding
mm_60569.1	chr7	44481492	44481517	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-3013	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_81402.1	chr9	109040860	109040907	+	1	NA	exon (NM_001284332, exon 2 of 6)	exon (NM_001284332, exon 2 of 6)	2316	NM_001284332	66940	Mm.196533	NM_025858	ENSMUSG00000025647	Shisa5	2310008D10Rik|6430628I05Rik|Scotin|mShisa5	shisa family member 5	protein-coding
mm_5199.1	chr1	13374073	13374075	-	1	NA	promoter-TSS (NM_008678)	promoter-TSS (NM_008678)	9	NM_008678	17978	Mm.2537	NM_008678	ENSMUSG00000005886	Ncoa2	D1Ertd433e|GRIP-1|Grip1|KAT13C|NCoA-2|SRC-2|TIF2|bHLHe75	nuclear receptor coactivator 2	protein-coding
mm_39348.1	chr5	8893944	8893954	+	1	NA	intron (NM_008830, intron 1 of 27)	CpG	228	NM_008830	18670	Mm.297825	NM_008830	ENSMUSG00000042476	Abcb4	Mdr2|Pgy-2|Pgy2|mdr-2	ATP-binding cassette, sub-family B (MDR/TAP), member 4	protein-coding
mm_4227.1	chr1	171345685	171345708	+	1	NA	promoter-TSS (NM_012049)	promoter-TSS (NM_012049)	-3	NM_011070	18637	Mm.10756	NM_011070	ENSMUSG00000006412	Pfdn2	ESTM27|W48336	prefoldin 2	protein-coding
mm_93159.1	chr10	93165940	93165974	-	1	NA	intron (NM_146239, intron 1 of 16)	MIRb|SINE|MIR	3172	NR_035452	100316689		NR_035452	ENSMUSG00000089214	Mir1931	mir-1931|mmu-mir-1931	microRNA 1931	ncRNA
mm_87557.1	chr10	54579289	54579311	+	1	NA	Intergenic	RLTR44-int|LTR|ERVK	503378	NR_038016	100502920	Mm.403982	NR_038016	ENSMUSG00000097069	Gm16998	-	predicted gene, 16998	ncRNA
mm_105342.1	chr11	102997406	102997444	-	1	NA	exon (NM_026551, exon 4 of 5)	exon (NM_026551, exon 4 of 5)	2496	NR_105896	102466988		NR_105896	ENSMUSG00000098613	Mir6931	Gm27303|mmu-mir-6931	microRNA 6931	ncRNA
mm_10823.1	chr2	24367566	24367620	+	1	NA	Intergenic	CpG	-17804	NM_177611	215632	Mm.490434	NM_177611	ENSMUSG00000026979	Psd4	BC046518|EFA6B	pleckstrin and Sec7 domain containing 4	protein-coding
mm_11840.1	chr2	45112270	45112280	+	1	NA	promoter-TSS (NR_110571)	promoter-TSS (NR_110571)	15	NR_110571	433424	Mm.441408	NR_110571	ENSMUSG00000052248	Zeb2os	Gm13476|OTTMUSG00000012358|Zeb2nat	zinc finger E-box binding homeobox 2, opposite strand	ncRNA
mm_149962.1	chr19	28990454	28990466	+	1	NA	5' UTR (NM_025950, exon 1 of 7)	5' UTR (NM_025950, exon 1 of 7)	108	NM_025950	67072	Mm.78875	NM_025950	ENSMUSG00000024780	Cdc37l1	2700033A15Rik|BB159850|Cdc37l|Harc	cell division cycle 37-like 1	protein-coding
mm_158493.1	chrX	142338984	142338999	-	1	NA	exon (NM_207625, exon 11 of 16)	exon (NM_207625, exon 11 of 16)	-32793	NM_021487	66240	Mm.58507	NM_021487	ENSMUSG00000090122	Kcne1l	1500015C14Rik|Kcne5|Mink	potassium voltage-gated channel, Isk-related family, member 1-like, pseudogene	protein-coding
mm_172335.1	chr7	10953563	10953563	+	1	NA	Intergenic	IAPLTR4|LTR|ERVK	-48513	NM_001185173	665780	Mm.482067	NM_001185173	ENSMUSG00000095339	Zscan4b	EG665780	zinc finger and SCAN domain containing 4B	protein-coding
mm_37851.1	chr4	132212042	132212059	-	1	NA	5' UTR (NM_145393, exon 1 of 5)	5' UTR (NM_145393, exon 1 of 5)	206	NM_145393	213541	Mm.23998	NM_145393	ENSMUSG00000040025	Ythdf2	9430020E02Rik|HGRG8|NY-REN-2	YTH domain family 2	protein-coding
mm_106259.1	chr11	117875764	117875782	-	1	NA	Intergenic	Intergenic	-2247	NM_027919	71776	Mm.3200	NM_027919	ENSMUSG00000017713	Tha1	1300017K07Rik|GLY1	threonine aldolase 1	protein-coding
mm_1678.1	chr1	74817066	74817076	+	1	NA	Intergenic	CpG	25052	NM_009518	22409	Mm.5130	NM_009518	ENSMUSG00000026167	Wnt10a	-	wingless-type MMTV integration site family, member 10A	protein-coding
mm_169195.1	chr13	66113419	66113422	+	1	NA	promoter-TSS (NM_001177832)	promoter-TSS (NM_001177832)	-33	NM_001177832	628709	Mm.390595	NM_001177832	ENSMUSG00000095909	Gm10324	ENSMUSG00000071302	predicted gene 10324	protein-coding
mm_140965.1	chr17	24658507	24658516	-	1	NA	promoter-TSS (NM_001099664)	promoter-TSS (NM_001099664)	-86	NM_001099664	381073	Mm.291772	NM_001099664	ENSMUSG00000071230	Npw	Gm935	neuropeptide W	protein-coding
mm_56700.1	chr6	114921779	114921837	-	1	NA	promoter-TSS (NM_177683)	promoter-TSS (NM_177683)	-56	NM_177683	232334	Mm.268357	NM_177683	ENSMUSG00000030315	Vgll4	BC048841|VGL-4	vestigial like family member 4	protein-coding
mm_31206.1	chr4	43875525	43875558	+	1	NA	promoter-TSS (NM_016678)	promoter-TSS (NM_016678)	11	NM_016678	53614	Mm.331573	NM_016678	ENSMUSG00000028476	Reck	St15|mRECK	reversion-inducing-cysteine-rich protein with kazal motifs	protein-coding
mm_159227.1	chr2	131043095	131043095	-	1	NA	promoter-TSS (NM_020014)	promoter-TSS (NM_020014)	-7	NM_001136063	14588	Mm.198399	NM_020014	ENSMUSG00000027316	Gfra4	AW060733|G630015H18Rik	glial cell line derived neurotrophic factor family receptor alpha 4	protein-coding
mm_81771.1	chr9	114422129	114422131	+	1	NA	intron (NR_108101, intron 3 of 14)	intron (NR_108101, intron 3 of 14)	21035	NM_001200002	100504715	Mm.290516	NM_001200002	ENSMUSG00000079260	Tmppe	-	transmembrane protein with metallophosphoesterase domain	protein-coding
mm_162751.1	chr10	59450867	59450867	-	1	NA	intron (NM_001033259, intron 7 of 7)	ID_B1|SINE|B4	-9088	NM_010959	18302	Mm.123013	NM_010959	ENSMUSG00000009654	Oit3	EF-9|LZP	oncoprotein induced transcript 3	protein-coding
mm_160504.1	chr9	18816320	18816320	-	1	NA	promoter-TSS (NM_146605)	promoter-TSS (NM_146605)	-28	NM_146605	258598	Mm.271453	NM_146605	ENSMUSG00000078116	Olfr828	MOR149-1	olfactory receptor 828	protein-coding
mm_60398.1	chr7	44475529	44475539	+	1	NA	Intergenic	Intergenic	5187	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_30314.1	chr3	151731394	151731406	-	1	NA	3' UTR (NM_133871, exon 8 of 8)	3' UTR (NM_133871, exon 8 of 8)	18559	NM_133871	99899	Mm.30756	NM_133871	ENSMUSG00000028037	Ifi44	A430056A10Rik|AW261460|MTAP44|p44	interferon-induced protein 44	protein-coding
mm_29840.1	chr3	129822518	129822530	-	1	NA	promoter-TSS (NM_009102)	promoter-TSS (NM_009102)	-19	NM_009102	20132	Mm.278758	NM_009102	ENSMUSG00000028012	Rrh	-	retinal pigment epithelium derived rhodopsin homolog	protein-coding
mm_154146.1	chr19	58454316	58454321	-	1	NA	exon (NM_010279, exon 2 of 11)	exon (NM_010279, exon 2 of 11)	1080	NM_001285457	14585	Mm.88367	NM_010279	ENSMUSG00000025089	Gfra1	AU042498	glial cell line derived neurotrophic factor family receptor alpha 1	protein-coding
mm_30502.1	chr3	157925057	157925070	-	1	NA	promoter-TSS (NM_145953)	promoter-TSS (NM_145953)	0	NM_145953	107869	Mm.28301	NM_145953	ENSMUSG00000028179	Cth	0610010I13Rik|AI314617|BC019483|CSE|Cys3	cystathionase (cystathionine gamma-lyase)	protein-coding
mm_46938.1	chr5	114813903	114813937	-	1	NA	promoter-TSS (NR_027818)	promoter-TSS (NR_027818)	56	NR_027818	66236	Mm.268546	NR_027817	ENSMUSG00000072694	1500011B03Rik	AI415201|AV141149|AW556386	RIKEN cDNA 1500011B03 gene	ncRNA
mm_33587.1	chr4	132563454	132563481	+	1	NA	promoter-TSS (NM_001081211)	promoter-TSS (NM_001081211)	-600	NM_001081211	19204	Mm.89389	NM_001081211	ENSMUSG00000056529	Ptafr	PAFR	platelet-activating factor receptor	protein-coding
mm_25377.1	chr3	107211438	107211440	+	1	NA	exon (NM_001111143, exon 9 of 9)	exon (NM_001111143, exon 9 of 9)	10293	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_145848.1	chr18	65449942	65449950	+	1	NA	intron (NM_172833, intron 6 of 15)	intron (NM_172833, intron 6 of 15)	18949	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_14371.1	chr2	129630093	129630100	+	1	NA	exon (NM_001291022, exon 5 of 5)	exon (NM_001291022, exon 5 of 5)	36927	NM_001291022	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_21518.1	chr2	163630976	163631103	-	1	NA	exon (NM_012032, exon 6 of 10)	exon (NM_012032, exon 6 of 10)	-13811	NR_028113	68386	Mm.410649	NR_028113	ENSMUSG00000058812	0610039K10Rik	-	RIKEN cDNA 0610039K10 gene	ncRNA
mm_79079.1	chr9	46242286	46242378	+	1	NA	exon (NM_007468, exon 3 of 3)	exon (NM_007468, exon 3 of 3)	1488	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_89175.1	chr10	86338408	86338424	+	1	NA	exon (NM_011595, exon 2 of 5)	exon (NM_011595, exon 2 of 5)	38004	NM_011595	21859	Mm.4871	NM_011595	ENSMUSG00000020044	Timp3	Timp-3	tissue inhibitor of metalloproteinase 3	protein-coding
mm_121247.1	chr14	103057277	103057281	+	1	NA	TTS (NM_008392)	TTS (NM_008392)	10267	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_151800.1	chr19	5424469	5424565	-	1	NA	promoter-TSS (NM_001256515)	promoter-TSS (NM_001256515)	462	NM_024176	66556	Mm.275446	NM_024176	ENSMUSG00000024914	Drap1	2310074H19Rik|NC2-alpha	Dr1 associated protein 1 (negative cofactor 2 alpha)	protein-coding
mm_34188.1	chr4	140701523	140701548	+	1	NA	promoter-TSS (NM_173867)	promoter-TSS (NM_173867)	62	NM_173867	108911	Mm.253	NM_173867	ENSMUSG00000040945	Rcc2	2610510H01Rik|2610529N02Rik|AA536646|AA675016|Td60|mKIAA1470	regulator of chromosome condensation 2	protein-coding
mm_15598.1	chr2	160646039	160646057	+	1	NA	5' UTR (NM_009408, exon 1 of 21)	5' UTR (NM_009408, exon 1 of 21)	151	NM_009408	21969	Mm.217233	NM_009408	ENSMUSG00000070544	Top1	AI467334|D130064I21Rik|Top-1	topoisomerase (DNA) I	protein-coding
mm_24088.1	chr3	87975948	87975962	+	1	NA	exon (NM_016701, exon 4 of 4)	exon (NM_016701, exon 4 of 4)	4862	NM_016701	18008	Mm.331129	NM_016701	ENSMUSG00000004891	Nes	AA166324|C78523|ESTM46	nestin	protein-coding
mm_33190.1	chr4	126227623	126227650	+	1	NA	Intergenic	Intergenic	-24926	NM_146153	230753	Mm.29813	NM_146153	ENSMUSG00000043962	Thrap3	9330151F09Rik|B230333E16Rik|Trap150	thyroid hormone receptor associated protein 3	protein-coding
mm_136634.1	chr17	5700167	5700204	+	1	NA	intron (NM_146073, intron 3 of 8)	intron (NM_146073, intron 3 of 8)	-98472	NR_045081	78512	Mm.23696	NR_045079	ENSMUSG00000096965	3300005D01Rik	-	RIKEN cDNA 3300005D01 gene	ncRNA
mm_62754.1	chr7	112023448	112023462	+	1	NA	promoter-TSS (NM_177249)	promoter-TSS (NM_177249)	-51	NM_133758	74996	Mm.16974	NM_133758	ENSMUSG00000059263	Usp47	4930502N04Rik|A630020C16Rik	ubiquitin specific peptidase 47	protein-coding
mm_54293.1	chr6	29280987	29280995	-	1	NA	promoter-TSS (NM_001101486)	promoter-TSS (NM_001101486)	-150	NM_001101486	245884	Mm.33683	NM_001101486	ENSMUSG00000079652	Fam71f2	AI507611|GARI	family with sequence similarity 71, member F2	protein-coding
mm_127554.1	chr15	102150503	102150577	+	1	NA	promoter-TSS (NM_146064)	promoter-TSS (NM_146064)	-35	NM_146064	223920	Mm.358862	NM_146064	ENSMUSG00000023045	Soat2	ACAT2|D15Wsu97e	sterol O-acyltransferase 2	protein-coding
mm_67058.1	chr7	67373097	67373126	-	1	NA	promoter-TSS (NM_001291196)	promoter-TSS (NM_001291196)	-253	NM_001291195	17258	Mm.132788	NM_001033713	ENSMUSG00000030557	Mef2a	A430079H05Rik	myocyte enhancer factor 2A	protein-coding
mm_159189.1	chr2	117121423	117121423	+	1	NA	5' UTR (NM_001277256, exon 1 of 5)	5' UTR (NM_001277256, exon 1 of 5)	352	NM_033524	114715	Mm.245890	NM_033524	ENSMUSG00000027351	Spred1	5730461F13Rik|AL024345|AW047647	sprouty protein with EVH-1 domain 1, related sequence	protein-coding
mm_72387.1	chr8	81756897	81756912	+	1	NA	intron (NM_001297593, intron 4 of 23)	intron (NM_001297593, intron 4 of 23)	414342	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_77447.1	chr8	121792336	121792349	-	1	NA	Intergenic	Intergenic	37227	NM_145605	234825	Mm.209329	NM_145605	ENSMUSG00000040263	Klhdc4	AA408426|AV352552|BC012312|G430025P05Rik	kelch domain containing 4	protein-coding
mm_84284.1	chr9	62886610	62886613	-	1	NA	intron (NM_019663, intron 12 of 13)	PB1D9|SINE|Alu	-24587	NR_003965	677044	Mm.422004	NR_003965	ENSMUSG00000074250	Gm10653	ENSMUSG00000074250	ribsomal protein S2 pseudogene	pseudo
mm_41644.1	chr5	98033301	98033311	+	1	NA	Intergenic	Intergenic	-2344	NM_133738	71914	Mm.24842	NM_133738	ENSMUSG00000029338	Antxr2	2310046B19Rik|AW561899|CMG-2|CMG2|cI-35	anthrax toxin receptor 2	protein-coding
mm_153327.1	chr19	38124365	38124383	-	1	NA	exon (NM_011255, exon 3 of 6)	exon (NM_011255, exon 3 of 6)	437	NM_011255	19662	Mm.2605	NM_011255	ENSMUSG00000024990	Rbp4	Rbp-4	retinol binding protein 4, plasma	protein-coding
mm_141368.1	chr17	28981302	28981345	-	1	NA	intron (NM_134115, intron 7 of 13)	RLTR20B5_MM|LTR|ERVK	26614	NM_134115	106504	Mm.439986	NM_134115	ENSMUSG00000024006	Stk38	5830476G13Rik|9530097A09Rik|AA617404|Ndr1	serine/threonine kinase 38	protein-coding
mm_38150.1	chr4	134914976	134915009	-	1	NA	promoter-TSS (NM_027935)	promoter-TSS (NM_027935)	-76	NM_027935	71817	Mm.88349	NM_027935	ENSMUSG00000028822	Tmem50a	3200001F09Rik|CAM|Smp1	transmembrane protein 50A	protein-coding
mm_171013.1	chr2	83947518	83947522	-	1	NA	Intergenic	MT2_Mm|LTR|ERVL	-6294	NM_027964	71861	Mm.116957	NM_027964	ENSMUSG00000034552	Zswim2	1700025P14Rik|4933437F18Rik|MEX	zinc finger SWIM-type containing 2	protein-coding
mm_124562.1	chr14	123626946	123626988	-	1	NA	5' UTR (NM_177393, exon 1 of 44)	5' UTR (NM_177393, exon 1 of 44)	177	NM_177393	338370	Mm.255348	NM_177393	ENSMUSG00000000197	Nalcn	A530023G15Rik|AI849508|Vgcnl1	sodium leak channel, non-selective	protein-coding
mm_89625.1	chr10	96266632	96266640	+	1	NA	Intergenic	Intergenic	40429	NR_110448	74881	Mm.410819	NR_110448		4930459C07Rik	-	RIKEN cDNA 4930459C07 gene	ncRNA
mm_25918.1	chr3	131156356	131156366	+	1	NA	intron (NM_001276403, intron 3 of 11)	intron (NM_001276403, intron 3 of 11)	43570	NM_001276403	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_163832.1	chr14	19417658	19417673	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	184922	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_151408.1	chr19	56548580	56548623	+	1	NA	promoter-TSS (NM_018831)	promoter-TSS (NM_018831)	340	NM_025811	66866	Mm.46346	NM_025811	ENSMUSG00000025078	Nhlrc2	1200003G01Rik|AI835049|AV002846|AW496455	NHL repeat containing 2	protein-coding
mm_152338.1	chr19	9982442	9982449	-	1	NA	promoter-TSS (NM_010239)	promoter-TSS (NM_010239)	-201	NM_010239	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
mm_96386.1	chr11	67245770	67245783	+	1	NA	exon (NM_010855, exon 14 of 40)	exon (NM_010855, exon 14 of 40)	7964	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_60309.1	chr7	44137251	44137257	+	1	NA	promoter-TSS (NM_008454)	promoter-TSS (NM_008454)	-36	NM_008454	16615	Mm.440887	NM_008454	ENSMUSG00000038968	Klk1b16	Klk16|mGk-16	kallikrein 1-related peptidase b16	protein-coding
mm_59325.1	chr7	25316758	25316903	+	1	NA	promoter-TSS (NM_001160400)	promoter-TSS (NM_001160400)	-334	NM_001160400	269878	Mm.38527	NM_001160400	ENSMUSG00000045039	Megf8	AW049492|Egfl4|b2b1702.2Clo|b2b1702Clo|b2b288Clo|m687Ddg|mKIAA0817	multiple EGF-like-domains 8	protein-coding
mm_134636.1	chr16	21761872	21761876	-	1	NA	3' UTR (NM_023737, exon 7 of 7)	3' UTR (NM_023737, exon 7 of 7)	25960	NM_023737	74147	Mm.28100	NM_023737	ENSMUSG00000022853	Ehhadh	1300002P22Rik|HD|L-PBE|LBFP|LBP|MFP|MFP1|PBFE	enoyl-Coenzyme A, hydratase/3-hydroxyacyl Coenzyme A dehydrogenase	protein-coding
mm_109238.1	chr12	108893939	108893944	+	1	NA	promoter-TSS (NM_177602)	promoter-TSS (NM_177602)	233	NM_001164314	22375	Mm.38433	NM_011710	ENSMUSG00000021266	Wars	TrpRS|WRS	tryptophanyl-tRNA synthetase	protein-coding
mm_117875.1	chr13	98926313	98926357	-	1	NA	promoter-TSS (NM_178716)	promoter-TSS (NM_178716)	49	NM_178716	238799	Mm.173286	NM_178716	ENSMUSG00000009470	Tnpo1	AU021749|D13Ertd688e|IPO2|Kpnb2|MIP|MIP1|TRN	transportin 1	protein-coding
mm_55208.1	chr6	52217461	52217493	-	1	NA	5' UTR (NM_010455, exon 1 of 2)	5' UTR (NM_010455, exon 1 of 2)	1096	NM_010455	15404	Mm.294826	NM_010455	ENSMUSG00000038236	Hoxa7	AV118143|Hox-1.1|M6	homeobox A7	protein-coding
mm_62900.1	chr7	116504438	116504452	+	1	NA	promoter-TSS (NM_001130479)	promoter-TSS (NM_001130479)	76	NM_001130479	53322	Mm.9901	NM_016773	ENSMUSG00000030659	Nucb2	AI607786|Calnuc|Nefa|Nesfatin-1	nucleobindin 2	protein-coding
mm_118210.1	chr13	110060933	110060955	-	1	NA	3' UTR (NM_023852, exon 5 of 5)	3' UTR (NM_023852, exon 5 of 5)	157135	NR_035442	100316683		NR_035442	ENSMUSG00000084651	Mir1904	Mirn1904|mmu-mir-1904	microRNA 1904	ncRNA
mm_4325.1	chr1	171852031	171852041	+	1	NA	exon (NM_013489, exon 3 of 9)	exon (NM_013489, exon 3 of 9)	12339	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_31310.1	chr4	46082177	46082188	+	1	NA	intron (NM_021883, intron 3 of 9)	intron (NM_021883, intron 3 of 9)	42960	NM_021883	21916	Mm.249594	NM_021883	ENSMUSG00000028328	Tmod1	E-Tmod|Tmod	tropomodulin 1	protein-coding
mm_117302.1	chr13	67332499	67332510	-	1	NA	promoter-TSS (NM_177622)	promoter-TSS (NM_177622)	56	NM_177622	218314	Mm.289695	NM_177622	ENSMUSG00000057842	Zfp595	A230042K10Rik|Rslcan23	zinc finger protein 595	protein-coding
mm_61318.1	chr7	68148565	68148582	+	1	NA	intron (NM_010513, intron 2 of 20)	intron (NM_010513, intron 2 of 20)	115660	NM_030101	78444	Mm.425468	NM_030101	ENSMUSG00000030553	Pgpep1l	C330024D12Rik	pyroglutamyl-peptidase I-like	protein-coding
mm_158654.1	chrX	155624081	155624104	-	1	NA	promoter-TSS (NM_001093750)	promoter-TSS (NM_001093750)	-765	NM_001093750	211612	Mm.218811	NM_001093750	ENSMUSG00000041552	Ptchd1	9630036J22Rik|AI848149|Gm387	patched domain containing 1	protein-coding
mm_23520.1	chr3	60603754	60603766	+	1	NA	exon (NM_001253711, exon 3 of 8)	exon (NM_001253711, exon 3 of 8)	102581	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_94283.1	chr11	3983705	3983737	+	1	NA	promoter-TSS (NM_001177703)	promoter-TSS (NM_001177703)	85	NM_016922	53897	Mm.103414	NM_016922	ENSMUSG00000049721	Gal3st1	Cst|Gcst	galactose-3-O-sulfotransferase 1	protein-coding
mm_112987.1	chr13	21416021	21416024	+	1	NA	Intergenic	Intergenic	-13267	NM_023685	72739	Mm.296071	NM_023685	ENSMUSG00000021327	Zkscan3	2810435N07Rik|AA408594|AI132359|Skz1|Zf47|Zfp-47|Zfp306|Zfp307|mszf35	zinc finger with KRAB and SCAN domains 3	protein-coding
mm_65506.1	chr7	25745231	25745242	-	1	NA	intron (NM_144922, intron 4 of 14)	intron (NM_144922, intron 4 of 14)	9465	NM_178089	232989	Mm.254223	NM_144922	ENSMUSG00000040725	Hnrnpul1	E130317O14Rik|E1B-AP5|E1BAP5|Hnrnpul|Hnrpul1	heterogeneous nuclear ribonucleoprotein U-like 1	protein-coding
mm_33024.1	chr4	121134655	121134659	+	1	NA	Intergenic	7SK|RNA|RNA	-25431	NM_001081312	69469	Mm.481120	NM_001081312	ENSMUSG00000078577	Tmco2	1700028F16Rik	transmembrane and coiled-coil domains 2	protein-coding
mm_132635.1	chr16	39119489	39119491	+	1	NA	Intergenic	Intergenic	217145	NM_170599	207683	Mm.245564	NM_170599	ENSMUSG00000022790	Igsf11	1700025L02Rik|BT-IgSF|Igsf13	immunoglobulin superfamily, member 11	protein-coding
mm_60548.1	chr7	44480780	44480790	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-3732	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_147189.1	chr18	37638720	37638737	-	1	NA	promoter-TSS (NM_001159275)	promoter-TSS (NM_001159275)	-5	NM_001159275	83885	Mm.193029	NM_001159275	ENSMUSG00000050304	Slc25a2	Ornt2	solute carrier family 25 (mitochondrial carrier, ornithine transporter) member 2	protein-coding
mm_128640.1	chr15	59275192	59275194	-	1	NA	Intergenic	Intergenic	-31755	NR_045613	100416830	Mm.490788	NR_045613	ENSMUSG00000098528	Zfp572	4930472F24Rik	zinc finger protein 572	pseudo
mm_73704.1	chr8	111686700	111686711	+	1	NA	exon (NM_025583, exon 7 of 7)	exon (NM_025583, exon 7 of 7)	2969	NR_106044	102466993		NR_106044	ENSMUSG00000099129	Mir7076	Gm27318|mmu-mir-7076	microRNA 7076	ncRNA
mm_92569.1	chr10	79881127	79881163	-	1	NA	exon (NM_011178, exon 3 of 5)	exon (NM_011178, exon 3 of 5)	1478	NM_011178	19152	Mm.2364	NM_011178	ENSMUSG00000057729	Prtn3	PR3|mPR3	proteinase 3	protein-coding
mm_127654.1	chr15	102498510	102498525	+	1	NA	exon (NM_001174073, exon 13 of 13)	exon (NM_001174073, exon 13 of 13)	18487	NM_001163643	26404	Mm.172897	NM_009582	ENSMUSG00000023050	Map3k12	DLK|MUK|Zpk	mitogen-activated protein kinase kinase kinase 12	protein-coding
mm_168278.1	chr1	105764566	105764567	-	1	NA	Intergenic	Intergenic	-16157	NM_009399	21934	Mm.6251	NM_009399	ENSMUSG00000026321	Tnfrsf11a	Ly109|ODFR|OFE|Rank|TRANCE-R|mRANK	tumor necrosis factor receptor superfamily, member 11a, NFKB activator	protein-coding
mm_133695.1	chr16	92818804	92818814	+	1	NA	intron (NM_001111022, intron 2 of 6)	intron (NM_001111022, intron 2 of 6)	7265	NM_001111021	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_108498.1	chr12	83763629	83763648	+	1	NA	promoter-TSS (NM_130887)	promoter-TSS (NM_130887)	4	NM_130887	170721	Mm.133443	NM_130887	ENSMUSG00000021223	Papln	E030033C16Rik	papilin, proteoglycan-like sulfated glycoprotein	protein-coding
mm_137254.1	chr17	24549122	24549141	+	1	NA	promoter-TSS (NM_013630)	promoter-TSS (NM_013630)	-819	NM_013630	18763	Mm.30435	NM_013630	ENSMUSG00000032855	Pkd1	PC1|mFLJ00285	polycystic kidney disease 1 homolog	protein-coding
mm_159429.1	chr3	108881871	108881871	-	1	NA	intron (NM_001165965, intron 3 of 11)	intron (NM_001165965, intron 3 of 11)	8137	NM_177091	320181	Mm.244233	NM_177091	ENSMUSG00000045326	Fndc7	E230011A21Rik	fibronectin type III domain containing 7	protein-coding
mm_173248.1	chrX	91845537	91845539	+	1	NA	Intergenic	IAPLTR1_Mm|LTR|ERVK	-62562	NM_028847	74271	Mm.141337	NM_028847	ENSMUSG00000061392	Mageb5	1700056A17Rik|mMage-b5	melanoma antigen, family B, 5	protein-coding
mm_10941.1	chr2	25500790	25500864	+	1	NA	promoter-TSS (NM_027062)	promoter-TSS (NM_027062)	49	NM_013908	30839	Mm.29170	NM_013908	ENSMUSG00000015095	Fbxw5	AI159739|Fbw5	F-box and WD-40 domain protein 5	protein-coding
mm_53774.1	chr6	146115792	146115802	+	1	NA	intron (NM_010586, intron 54 of 55)	intron (NM_010586, intron 54 of 55)	181650	NM_010656	16651	Mm.49689	NM_010656	ENSMUSG00000030255	Sspn	Krag	sarcospan	protein-coding
mm_93873.1	chr10	123196973	123196975	-	1	NA	promoter-TSS (NM_027604)	promoter-TSS (NM_027604)	45	NM_027604	14479	Mm.244209	NM_027604	ENSMUSG00000020124	Usp15	4921514G19Rik|AI327321|E430033I05Rik|Gcap18	ubiquitin specific peptidase 15	protein-coding
mm_133189.1	chr16	72663744	72663754	+	1	NA	5' UTR (NM_019413, exon 1 of 29)	5' UTR (NM_019413, exon 1 of 29)	600	NM_019413	19876	Mm.310772	NM_019413	ENSMUSG00000022883	Robo1	AW494633|AW742721|DUTT1|Gm310	roundabout guidance receptor 1	protein-coding
mm_10267.1	chr2	9876115	9876137	+	1	NA	intron (NM_008091, intron 2 of 5)	intron (NM_008091, intron 2 of 5)	2474	NM_008091	14462	Mm.313866	NM_008091	ENSMUSG00000015619	Gata3	Gata-3|jal	GATA binding protein 3	protein-coding
mm_103713.1	chr11	79523717	79523753	-	1	NA	promoter-TSS (NM_001077496)	promoter-TSS (NM_001077496)	27	NM_001077496	216984	Mm.439665	NM_001077496	ENSMUSG00000093938	Evi2b	Evi-2|Evi2	ecotropic viral integration site 2b	protein-coding
mm_78366.1	chr9	26999700	26999733	+	1	NA	promoter-TSS (NM_144543)	promoter-TSS (NM_144543)	39	NM_001326361	77862	Mm.16925	NM_144543	ENSMUSG00000035443	Thyn1	D730042P09Rik|HSPC144|MDS012|MY105|Thy28	thymocyte nuclear protein 1	protein-coding
mm_17474.1	chr2	28560522	28560575	-	1	NA	exon (NM_009885, exon 4 of 11)	exon (NM_009885, exon 4 of 11)	2855	NM_009885	12613	Mm.236017	NM_009885	ENSMUSG00000026818	Cel	1810036E18Rik|BAL	carboxyl ester lipase	protein-coding
mm_123111.1	chr14	55884368	55884376	-	1	NA	promoter-TSS (NM_019820)	promoter-TSS (NM_019820)	-116	NM_019820	56410	Mm.97163	NM_019820	ENSMUSG00000040380	Cbln3	-	cerebellin 3 precursor protein	protein-coding
mm_23394.1	chr3	57736057	57736128	+	1	NA	promoter-TSS (NM_011883)	promoter-TSS (NM_011883)	30	NR_130743	24017	Mm.274360	NM_011883	ENSMUSG00000036503	Rnf13	2010001H16Rik|Rzf	ring finger protein 13	protein-coding
mm_117501.1	chr13	78200122	78200159	-	1	NA	intron (NR_045195, intron 1 of 2)	LTR78B|LTR|ERV1	-1267	NM_010151	13865	Mm.439653	NM_010151	ENSMUSG00000069171	Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR-3|EAR3|Erbal3|SVP44|Tcfcoup1	nuclear receptor subfamily 2, group F, member 1	protein-coding
mm_94130.1	chr10	128695992	128696003	-	1	NA	intron (NM_177411, intron 1 of 5)	CpG	271	NM_177411	19344	Mm.12815	NM_011229	ENSMUSG00000000711	Rab5b	C030027M18Rik	RAB5B, member RAS oncogene family	protein-coding
mm_49976.1	chr6	40891222	40891242	+	1	NA	intron (NR_035473, intron 2 of 3)	intron (NR_035473, intron 2 of 3)	-3738	NM_139296	194357	Mm.207087	NM_139296	ENSMUSG00000029885	Moxd2	Dbhl1	monooxygenase, DBH-like 2	protein-coding
mm_128015.1	chr15	20666765	20666780	-	1	NA	promoter-TSS (NM_022816)	promoter-TSS (NM_022816)	-22	NM_022816	64833	Mm.352763	NM_022816	ENSMUSG00000047565	Acot10	Acate3|MT-ACT48|p48	acyl-CoA thioesterase 10	protein-coding
mm_122771.1	chr14	54398635	54398648	-	1	NA	intron (NM_001253679, intron 3 of 10)	PB1D10|SINE|Alu	10831	NM_001253680	20540	Mm.142455	NM_011405	ENSMUSG00000000958	Slc7a7	AI790233|my+lat1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 7	protein-coding
mm_169609.1	chr15	37007256	37007257	-	1	NA	5' UTR (NM_026521, exon 1 of 4)	5' UTR (NM_026521, exon 1 of 4)	146	NM_026521	68036	Mm.371631	NM_026521	ENSMUSG00000062397	Zfp706	3110006P09Rik|AA793007|AW536850|C77232|Znf706	zinc finger protein 706	protein-coding
mm_162745.1	chr10	56389393	56389418	+	1	NA	3' UTR (NM_010288, exon 2 of 2)	3' UTR (NM_010288, exon 2 of 2)	12105	NM_010288	14609	Mm.378921	NM_010288	ENSMUSG00000050953	Gja1	AU042049|AW546267|Cnx43|Cx43|Cx43alpha1|Gja-1|Npm1|connexin43	gap junction protein, alpha 1	protein-coding
mm_31955.1	chr4	86844780	86844790	+	1	NA	intron (NM_184088, intron 29 of 31)	intron (NM_184088, intron 29 of 31)	12582	NM_009096	20104	Mm.379007	NM_009096	ENSMUSG00000028495	Rps6	S6R	ribosomal protein S6	protein-coding
mm_68428.1	chr7	109807980	109807998	-	1	NA	intron (NM_020052, intron 18 of 21)	intron (NM_020052, intron 18 of 21)	-26444	NM_020610	78593	Mm.275374	NM_020610	ENSMUSG00000034825	Nrip3	A330103B05Rik|D7H11orf14|ICRFP703B1614Q5.2	nuclear receptor interacting protein 3	protein-coding
mm_153488.1	chr19	41310328	41310332	-	1	NA	intron (NM_031376, intron 8 of 16)	intron (NM_031376, intron 8 of 16)	-46326	NM_133352	107358	Mm.246440	NM_133352	ENSMUSG00000025016	Tm9sf3	1810073M23Rik|2810031D16Rik|AI115521|AI413748|AW146116|AW549777|Smbp|mKIAA4036	transmembrane 9 superfamily member 3	protein-coding
mm_147365.1	chr18	43393347	43393381	-	1	NA	promoter-TSS (NM_009468)	promoter-TSS (NM_009468)	13	NM_009468	22240	Mm.8180	NM_009468	ENSMUSG00000024501	Dpysl3	CRMP-4|DRP-3|TUC4|ULIP-1|Ulip|Ulip1	dihydropyrimidinase-like 3	protein-coding
mm_26933.1	chr3	20262600	20262619	-	1	NA	exon (NM_029706, exon 9 of 11)	exon (NM_029706, exon 9 of 11)	13124	NM_029706	76703	Mm.34692	NM_029706	ENSMUSG00000011463	Cpb1	0910001A18Rik|1810063F02Rik|2210008M23Rik|AI504870	carboxypeptidase B1 (tissue)	protein-coding
mm_31780.1	chr4	63560654	63560660	+	1	NA	intron (NM_144905, intron 1 of 9)	intron (NM_144905, intron 1 of 9)	297	NM_144905	230279	Mm.41523	NM_144905	ENSMUSG00000045917	Tmem268	6330416G13Rik|AW492431|bM230C2.2	transmembrane protein 268	protein-coding
mm_90132.1	chr10	117719222	117719237	+	1	NA	Intergenic	MLTR14|LTR|ERV1	-8471	NM_001288586	17246	Mm.22670	NM_010786	ENSMUSG00000020184	Mdm2	1700007J15Rik|AA415488|Mdm-2	transformed mouse 3T3 cell double minute 2	protein-coding
mm_157454.1	chrX	43428846	43428862	-	1	NA	Intergenic	Intergenic	-154070	NM_011855	23963	Mm.327698	NM_011855	ENSMUSG00000016150	Tenm1	Odz1|Odz2|TCAP-1|Ten-m1|ten-1	teneurin transmembrane protein 1	protein-coding
mm_35771.1	chr4	46389392	46389456	-	1	NA	promoter-TSS (NM_029086)	promoter-TSS (NM_029086)	-1	NM_029086	74753	Mm.45973	NM_029086	ENSMUSG00000028331	Trmo	5830415F09Rik|AV014846|Nap1	tRNA methyltransferase O	protein-coding
mm_126522.1	chr15	81936847	81936874	+	1	NA	5' UTR (NM_145473, exon 1 of 4)	5' UTR (NM_145473, exon 1 of 4)	101	NM_145473	105859	Mm.22524	NM_145473	ENSMUSG00000042109	Csdc2	AI415250|AI481750|Pippin	cold shock domain containing C2, RNA binding	protein-coding
mm_134664.1	chr16	22251821	22251831	-	1	NA	intron (NM_009186, intron 4 of 8)	intron (NM_009186, intron 4 of 8)	14179	NM_001330554	20462	Mm.210352	NM_009186	ENSMUSG00000022858	Tra2b	5730405G21Rik|D16Ertd266e|SIG-41|Sfrs10|Silg41|TRA2beta	transformer 2 beta homolog (Drosophila)	protein-coding
mm_50320.1	chr6	47953459	47953468	+	1	NA	promoter-TSS (NM_178898)	promoter-TSS (NM_178898)	73	NM_178898	101197	Mm.241063	NM_178898	ENSMUSG00000045466	Zfp956	AI894139	zinc finger protein 956	protein-coding
mm_46075.1	chr5	92323794	92323796	-	1	NA	3' UTR (NM_008599, exon 4 of 4)	3' UTR (NM_008599, exon 4 of 4)	4284	NM_008599	17329	Mm.766	NM_008599	ENSMUSG00000029417	Cxcl9	BB139920|CMK|Mig|MuMIG|Scyb9|crg-10	chemokine (C-X-C motif) ligand 9	protein-coding
mm_143505.1	chr17	71680701	71680704	-	1	NA	intron (NM_177087, intron 1 of 19)	intron (NM_177087, intron 1 of 19)	7441	NM_177087	320159	Mm.187372	NM_177087	ENSMUSG00000045761	Fam179a	4632412N22Rik	family with sequence similarity 179, member A	protein-coding
mm_111183.1	chr12	83984822	83984843	-	1	NA	Intergenic	Intergenic	-3029	NM_134188	171210	Mm.371675	NM_134188	ENSMUSG00000021226	Acot2	AA571646|MTE-I|Mte1	acyl-CoA thioesterase 2	protein-coding
mm_87775.1	chr10	60294635	60294711	+	1	NA	exon (NM_011179, exon 5 of 15)	exon (NM_011179, exon 5 of 15)	10212	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_38389.1	chr4	138819162	138819168	-	1	NA	promoter-TSS (NM_011110)	promoter-TSS (NM_011110)	92	NM_011110	18784	Mm.486532	NM_011110	ENSMUSG00000041193	Pla2g5	PLA2|sPLA2	phospholipase A2, group V	protein-coding
mm_165507.1	chr2	167925000	167925015	-	1	NA	Intergenic	Intergenic	-7320	NM_011201	19246	Mm.277916	NM_011201	ENSMUSG00000027540	Ptpn1	PTP-1B|PTP-HA2|PTP1B	protein tyrosine phosphatase, non-receptor type 1	protein-coding
mm_164162.1	chr15	73148553	73148565	-	1	NA	intron (NM_153178, intron 1 of 18)	intron (NM_153178, intron 1 of 18)	36388	NM_153178	239528	Mm.23095	NM_153178	ENSMUSG00000036698	Ago2	1110029L17Rik|2310051F07Rik|AI225898|AL022874|AW546247|ENSMUSG00000072493|Eif2c2|Gerp95|Gm10365|mKIAA4215	argonaute RISC catalytic subunit 2	protein-coding
mm_86040.1	chr9	114417600	114417642	-	1	NA	intron (NM_009752, intron 2 of 15)	intron (NM_009752, intron 2 of 15)	16526	NM_001200002	100504715	Mm.290516	NM_001200002	ENSMUSG00000079260	Tmppe	-	transmembrane protein with metallophosphoesterase domain	protein-coding
mm_43400.1	chr5	135789203	135789225	+	1	NA	exon (NM_008617, exon 7 of 9)	exon (NM_008617, exon 7 of 9)	10565	NM_008617	17448	Mm.297096	NM_008617	ENSMUSG00000019179	Mdh2	MDH|Mdh-2|Mor-1|Mor1	malate dehydrogenase 2, NAD (mitochondrial)	protein-coding
mm_101619.1	chr11	35842244	35842264	-	1	NA	intron (NM_170779, intron 20 of 22)	intron (NM_170779, intron 20 of 22)	-7726	NM_025936	104458	Mm.284906	NM_025936	ENSMUSG00000018848	Rars	2610011N19Rik|2610037E21Rik|AL033339|AW985894	arginyl-tRNA synthetase	protein-coding
mm_45893.1	chr5	88565555	88565561	-	1	NA	intron (NM_001289774, intron 1 of 17)	CpG	518	NM_001289775	52822	Mm.270469	NM_027530	ENSMUSG00000029291	Rufy3	2810428M05Rik|6330416M07Rik|AW455998|AW538594|D5Bwg0860e|Ripx|Rpipx	RUN and FYVE domain containing 3	protein-coding
mm_91408.1	chr10	31445803	31445848	-	1	NA	promoter-TSS (NM_009413)	promoter-TSS (NM_009413)	96	NM_009413	21987	Mm.439966	NM_009413	ENSMUSG00000000296	Tpd52l1	D53	tumor protein D52-like 1	protein-coding
mm_20407.1	chr2	129299915	129299987	-	1	NA	3' UTR (NM_010554, exon 7 of 7)	3' UTR (NM_010554, exon 7 of 7)	2581	NR_040371	100503468	Mm.446943	NR_040371	ENSMUSG00000085498	Gm14023	OTTMUSG00000015408	predicted gene 14023	ncRNA
mm_133564.1	chr16	91399014	91399022	+	1	NA	intron (NM_001347258, intron 7 of 7)	intron (NM_001347258, intron 7 of 7)	-7217	NM_008349	16155	Mm.4154	NM_008349	ENSMUSG00000022969	Il10rb	6620401D04Rik|AI528744|CRF2-4|Crfb4|D16H21S58|D21S58h|IL-10R2|Il10r2	interleukin 10 receptor, beta	protein-coding
mm_57819.1	chr6	129462762	129462777	-	1	NA	non-coding (NR_132130, exon 6 of 6)	non-coding (NR_132130, exon 6 of 6)	10010	NM_001309637	56644	Mm.239516	NM_020008	ENSMUSG00000079293	Clec7a	BGR|Clecsf12|beta-GR	C-type lectin domain family 7, member a	protein-coding
mm_29085.1	chr3	104476705	104476707	-	1	NA	intron (NM_001310698, intron 11 of 17)	PB1D9|SINE|Alu	35212	NM_001310698	269473	Mm.34855	NM_001025067	ENSMUSG00000032913	Lrig2	4632419I10Rik|BB096938|LIG-2	leucine-rich repeats and immunoglobulin-like domains 2	protein-coding
mm_80141.1	chr9	70768804	70768817	+	1	NA	exon (NM_007399, exon 14 of 16)	exon (NM_007399, exon 14 of 16)	89828	NM_007399	11487	Mm.3037	NM_007399	ENSMUSG00000054693	Adam10	1700031C13Rik|MADM|kuz|kuzbanian	a disintegrin and metallopeptidase domain 10	protein-coding
mm_60886.1	chr7	46396541	46396557	+	1	NA	promoter-TSS (NM_001112739)	promoter-TSS (NM_001112739)	81	NM_001112739	16502	Mm.249386	NM_008421	ENSMUSG00000058975	Kcnc1	C230009H10Rik|KShIIIB|KV4|Kcr2-1|Kv3.1|NGK2|Shaw	potassium voltage gated channel, Shaw-related subfamily, member 1	protein-coding
mm_152330.1	chr19	9954505	9954526	-	1	NA	Intergenic	Intergenic	-26085	NR_073181	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
mm_120276.1	chr14	63129321	63129342	+	1	NA	intron (NM_007798, intron 1 of 9)	intron (NM_007798, intron 1 of 9)	6869	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_170995.1	chr2	75659289	75659289	+	1	NA	promoter-TSS (NM_198090)	promoter-TSS (NM_198090)	-1	NR_033513	627828	Mm.459502	NR_033513	ENSMUSG00000092086	Gm6793	EG627828	heterogeneous nuclear ribonucleoprotein A3 pseudogene	pseudo
mm_122519.1	chr14	47275350	47275354	-	1	NA	intron (NM_172598, intron 1 of 24)	intron (NM_172598, intron 1 of 24)	1505	NM_172598	218973	Mm.265615	NM_172598	ENSMUSG00000037572	Wdhd1	A630092E18|AND-1|D630024B06Rik	WD repeat and HMG-box DNA binding protein 1	protein-coding
mm_83614.1	chr9	48656509	48656522	-	1	NA	3' UTR (NM_001033324, exon 7 of 7)	3' UTR (NM_001033324, exon 7 of 7)	-51392	NM_010924	18113	Mm.8362	NM_010924	ENSMUSG00000032271	Nnmt	-	nicotinamide N-methyltransferase	protein-coding
mm_124703.1	chr15	6540293	6540312	+	1	NA	Intergenic	Intergenic	-39545	NM_001278269	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_128397.1	chr15	43783982	43783984	-	1	NA	Intergenic	Intergenic	86046	NM_175502	239408	Mm.41219	NM_175502	ENSMUSG00000054409	Tmem74	AA549547|B230382K22Rik	transmembrane protein 74	protein-coding
mm_156403.1	chrX	140062875	140062889	+	1	NA	promoter-TSS (NM_001081668)	promoter-TSS (NM_001081668)	3	NM_177921	331537	Mm.328336	NM_177921	ENSMUSG00000042433	Pih1h3b	E230019M04Rik	PIH1 domain containing 3B	protein-coding
mm_8968.1	chr1	165219095	165219105	-	1	NA	intron (NM_145513, intron 5 of 6)	B1_Mur2|SINE|Alu	17858	NM_145513	226591	Mm.21520	NM_145513	ENSMUSG00000040843	Tiprl	1810011K17Rik	TIP41, TOR signalling pathway regulator-like (S. cerevisiae)	protein-coding
mm_63373.1	chr7	127208845	127208887	+	1	NA	promoter-TSS (NM_144522)	promoter-TSS (NM_144522)	-33	NM_001347655	17907	Mm.14526	NM_016754	ENSMUSG00000030672	Mylpf	2410014J02Rik|MLC-2|Mlc2	myosin light chain, phosphorylatable, fast skeletal muscle	protein-coding
mm_130195.1	chr15	94579209	94579230	-	1	NA	3' UTR (NM_008971, exon 9 of 9)	3' UTR (NM_008971, exon 9 of 9)	10605	NM_008971	19230	Mm.490250	NM_008971	ENSMUSG00000022451	Twf1	A6|Ptk9|twinfilin	twinfilin actin binding protein 1	protein-coding
mm_54667.1	chr6	39206783	39206831	-	1	NA	promoter-TSS (NM_001033430)	promoter-TSS (NM_001033430)	-34	NM_001033430	338523	Mm.293175	NM_001033430	ENSMUSG00000042599	Kdm7a	A630082K20Rik|BB041802|ENSMUSG00000073143|Jhdm1d|mKIAA1718	lysine (K)-specific demethylase 7A	protein-coding
mm_29338.1	chr3	108210439	108210502	-	1	NA	promoter-TSS (NM_001289545)	promoter-TSS (NM_001289545)	57	NM_001289545	72522	Mm.187326	NM_175183	ENSMUSG00000048997	Atxn7l2	2610528J18Rik	ataxin 7-like 2	protein-coding
mm_31593.1	chr4	57872810	57872817	+	1	NA	intron (NM_009649, intron 2 of 2)	intron (NM_009649, intron 2 of 2)	18251	NM_001035533	11641	Mm.467752	NM_009649	ENSMUSG00000038729	Akap2	AA959716|AI649048|Akap-2|Akap-kl|B230340M18Rik|Prka2	A kinase (PRKA) anchor protein 2	protein-coding
mm_145697.1	chr18	62548919	62548950	+	1	NA	promoter-TSS (NM_177829)	promoter-TSS (NM_177829)	23	NM_177829	328971	Mm.312675	NM_177829	ENSMUSG00000044176	Spink10	A230091H23Rik	serine peptidase inhibitor, Kazal type 10	protein-coding
mm_2784.1	chr1	130844692	130844701	+	1	NA	exon (NM_011082, exon 4 of 11)	exon (NM_011082, exon 4 of 11)	18012	NM_011082	18703	Mm.276414	NM_011082	ENSMUSG00000026417	Pigr	-	polymeric immunoglobulin receptor	protein-coding
mm_22668.1	chr3	14872241	14872247	+	1	NA	3' UTR (NM_007606, exon 7 of 7)	3' UTR (NM_007606, exon 7 of 7)	8706	NM_007606	12350	Mm.300	NM_007606	ENSMUSG00000027559	Car3	BB219044|Ca3|Car-3	carbonic anhydrase 3	protein-coding
mm_84297.1	chr9	63377836	63377914	-	1	NA	promoter-TSS (NM_011840)	promoter-TSS (NM_011840)	-23	NM_011840	23938	Mm.325746	NM_011840	ENSMUSG00000058444	Map2k5	AI324775|AI428457|MEK5|Mapkk5|Prkmk5	mitogen-activated protein kinase kinase 5	protein-coding
mm_41657.1	chr5	98854474	98854487	+	1	NA	promoter-TSS (NM_001310677)	promoter-TSS (NM_001310677)	65	NM_001310677	110075	Mm.136461	NM_173404	ENSMUSG00000029335	Bmp3	9530029I04Rik	bone morphogenetic protein 3	protein-coding
mm_74699.1	chr8	16297095	16297095	-	1	NA	intron (NM_053171, intron 10 of 69)	intron (NM_053171, intron 10 of 69)	-128257	NR_037214	100526464		NR_037214	ENSMUSG00000093142	Mir3106	mir-3106|mmu-mir-3106	microRNA 3106	ncRNA
mm_37598.1	chr4	126744231	126744244	-	1	NA	3' UTR (NM_011986, exon 7 of 7)	3' UTR (NM_011986, exon 7 of 7)	-7968	NM_198960	332937	Mm.331881	NM_198960	ENSMUSG00000042477	Tfap2e	AI505200|AP-2e|Tcfap2e	transcription factor AP-2, epsilon	protein-coding
mm_57048.1	chr6	122345109	122345116	-	1	NA	Intergenic	PB1D9|SINE|Alu	-4885	NM_001271579	13619	Mm.6822	NM_007905	ENSMUSG00000040669	Phc1	AW557034|Edr|Edr1|Mph1|Rae-28|rae28	polyhomeotic-like 1 (Drosophila)	protein-coding
mm_170335.1	chr18	45071311	45071312	-	1	NA	Intergenic	Intergenic	-197549	NM_001312905	140492	Mm.411614	NM_080465	ENSMUSG00000054477	Kcnn2	KCa2.2|SK2|SKCA2|bc|fri	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2	protein-coding
mm_138128.1	chr17	34187546	34187571	+	1	NA	promoter-TSS (NM_001161730)	promoter-TSS (NM_001161730)	2	NM_013683	21354	Mm.482076	NM_013683	ENSMUSG00000037321	Tap1	ABC17|APT1|Abcb2|Ham-1|Ham1|MTP1|PSF1|RING4|TAP|Tap-1|Y3	transporter 1, ATP-binding cassette, sub-family B (MDR/TAP)	protein-coding
mm_95382.1	chr11	49203286	49203298	+	1	NA	promoter-TSS (NM_001024846)	promoter-TSS (NM_001024846)	-208	NM_001024846	22720	Mm.16650	NM_009562	ENSMUSG00000046311	Zfp62	-	zinc finger protein 62	protein-coding
mm_173195.1	chrX	62617039	62617040	+	1	NA	Intergenic	Intergenic	-90028	NR_045442	75545	Mm.391270	NR_045442	ENSMUSG00000085757	1700019B21Rik	-	RIKEN cDNA 1700019B21 gene	ncRNA
mm_153039.1	chr19	32061354	32061362	-	1	NA	5' UTR (NM_018830, exon 3 of 24)	5' UTR (NM_018830, exon 3 of 24)	41782	NM_018830	54447	Mm.491229	NM_018830	ENSMUSG00000024887	Asah2	AI585898	N-acylsphingosine amidohydrolase 2	protein-coding
mm_28768.1	chr3	95904632	95904646	-	1	NA	promoter-TSS (NM_011797)	promoter-TSS (NM_011797)	0	NM_011797	23831	Mm.489647	NM_011797	ENSMUSG00000038526	Car14	AW536446|Ca14	carbonic anhydrase 14	protein-coding
mm_84786.1	chr9	76581662	76581674	-	1	NA	Intergenic	MT2C_Mm|LTR|ERVL	-35864	NM_001045518	208994	Mm.256929	NM_001045518	ENSMUSG00000032358	Fam83b	C530008M07Rik|Gm516	family with sequence similarity 83, member B	protein-coding
mm_27150.1	chr3	33082005	33082030	-	1	NA	exon (NM_021483, exon 2 of 15)	exon (NM_021483, exon 2 of 15)	1043	NM_021483	58869	Mm.151332	NM_021483	ENSMUSG00000027674	Pex5l	1700016J08Rik|PXR2|Pex2|TRIP8b|pex5Rp	peroxisomal biogenesis factor 5-like	protein-coding
mm_137402.1	chr17	25875493	25875536	+	1	NA	promoter-TSS (NM_026686)	promoter-TSS (NM_026686)	14	NM_026686	68347	Mm.35098	NM_026686	ENSMUSG00000025731	Mettl26	0610011F06Rik	methyltransferase like 26	protein-coding
mm_125899.1	chr15	75941025	75941091	+	1	NA	5' UTR (NM_030199, exon 1 of 2)	5' UTR (NM_030199, exon 1 of 2)	106	NM_030199	78834	Mm.273264	NM_030199	ENSMUSG00000050846	Zfp623	2610029D06Rik|AI847036	zinc finger protein 623	protein-coding
mm_122834.1	chr14	54723367	54723391	-	1	NA	3' UTR (NM_016972, exon 11 of 11)	3' UTR (NM_016972, exon 11 of 11)	-11205	NM_207131	110794	Mm.236223	NM_207131	ENSMUSG00000052435	Cebpe	C/EBPe|CRP1|Gm294	CCAAT/enhancer binding protein (C/EBP), epsilon	protein-coding
mm_125911.1	chr15	76016687	76016687	+	1	NA	Intergenic	Intergenic	-2351	NM_134087	105732	Mm.267178	NM_134087	ENSMUSG00000046761	Fam83h	AA409316	family with sequence similarity 83, member H	protein-coding
mm_18704.1	chr2	71810184	71810189	-	1	NA	intron (NM_001277970, intron 1 of 24)	RMER19C|LTR|ERVK	23247	NM_001277970	16403	Mm.225096	NM_008397	ENSMUSG00000027111	Itga6	5033401O05Rik|AI115430|Cd49f|VLA-6	integrin alpha 6	protein-coding
mm_116714.1	chr13	51569077	51569116	-	1	NA	Intergenic	Intergenic	-2012	NM_009167	20418	Mm.131870	NM_009167	ENSMUSG00000021448	Shc3	N-Shc|Rai|ShcC	src homology 2 domain-containing transforming protein C3	protein-coding
mm_80700.1	chr9	92249657	92249667	+	1	NA	promoter-TSS (NM_011636)	promoter-TSS (NM_011636)	-532	NM_011636	22038	Mm.421956	NM_011636	ENSMUSG00000032369	Plscr1	MmTRA1a|MmTRA1b|Nor1|Tra1|Tra1a|Tra1b|Tras1|Tras2	phospholipid scramblase 1	protein-coding
mm_171569.1	chr4	147310629	147310633	+	1	NA	intron (NM_001039209, intron 1 of 2)	intron (NM_001039209, intron 1 of 2)	134765	NM_001039209	195531	Mm.270762	NM_001039209	ENSMUSG00000078496	Zfp982	Gm13152|OTTMUSG00000010671	zinc finger protein 982	protein-coding
mm_107457.1	chr12	37108662	37108673	+	1	NA	5' UTR (NM_008584, exon 1 of 3)	5' UTR (NM_008584, exon 1 of 3)	121	NM_008584	17286	Mm.341398	NM_008584	ENSMUSG00000036144	Meox2	AI528662|Gax|Mox-2|Mox2	mesenchyme homeobox 2	protein-coding
mm_100341.1	chr11	118393520	118393543	+	1	NA	exon (NM_011150, exon 6 of 6)	exon (NM_011150, exon 6 of 6)	8400	NM_011150	19039	Mm.3152	NM_011150	ENSMUSG00000033880	Lgals3bp	90K|CyCAP|MAC-2BP|Ppicap|Tango10b	lectin, galactoside-binding, soluble, 3 binding protein	protein-coding
mm_37201.1	chr4	117871301	117871317	-	1	NA	intron (NM_001034876, intron 3 of 7)	MIR|SINE|MIR	1161	NM_001034876	381546	Mm.440118	NM_001034876	ENSMUSG00000078588	Ccdc24	Gm1028	coiled-coil domain containing 24	protein-coding
mm_129231.1	chr15	76615913	76615960	-	1	NA	exon (NM_028064, exon 2 of 12)	exon (NM_028064, exon 2 of 12)	916	NM_028064	72027	Mm.276829	NM_028064	ENSMUSG00000063354	Slc39a4	1600025H15Rik|AU041686|AWMS2|ZIP4	solute carrier family 39 (zinc transporter), member 4	protein-coding
mm_166465.1	chr5	142733913	142733930	-	1	NA	intron (NM_001122730, intron 22 of 27)	intron (NM_001122730, intron 22 of 27)	31820	NM_146257	243328	Mm.125942	NM_146257	ENSMUSG00000050822	Slc29a4	ENT4|mPMAT	solute carrier family 29 (nucleoside transporters), member 4	protein-coding
mm_140812.1	chr17	22739893	22739937	-	1	NA	Intergenic	Intergenic	77832	NR_030709	100042679	Mm.484007	NR_030709		Gm16386	EG545191|ENSMUSG00000073442|Gm21017	zinc finger protein 946 pseudogene	pseudo
mm_77865.1	chr9	5327279	5327295	+	1	NA	exon (NM_007609, exon 6 of 9)	exon (NM_007609, exon 6 of 9)	-18189	NM_009808	12364	Mm.42163	NM_009808	ENSMUSG00000025887	Casp12	-	caspase 12	protein-coding
mm_54743.1	chr6	41031587	41031681	-	1	NA	3' UTR (NM_023333, exon 5 of 5)	3' UTR (NM_023333, exon 5 of 5)	3875	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_24444.1	chr3	90605735	90605784	+	1	NA	exon (NM_011311, exon 3 of 3)	exon (NM_011311, exon 3 of 3)	1989	NM_011311	20198	Mm.3925	NM_011311	ENSMUSG00000001020	S100a4	18A2|42a|Capl|FSp1|Mts1|PeL98|metastasin|pk9a	S100 calcium binding protein A4	protein-coding
mm_47986.1	chr5	135934558	135934568	-	1	NA	promoter-TSS (NM_018871)	promoter-TSS (NM_018871)	78	NM_018871	22628	Mm.233813	NM_018871	ENSMUSG00000051391	Ywhag	14-3-3gamma|D7Bwg1348e	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, gamma polypeptide	protein-coding
mm_141616.1	chr17	32830196	32830252	-	1	NA	promoter-TSS (NM_001293229)	promoter-TSS (NM_001293229)	37	NM_001293229	240064	Mm.476307	NM_177359	ENSMUSG00000095253	Zfp799	6030490I01Rik	zinc finger protein 799	protein-coding
mm_5671.1	chr1	42713687	42713698	-	1	NA	promoter-TSS (NR_110495)	promoter-TSS (NR_110495)	-238	NR_110495	66620	Mm.383631	NR_110495	ENSMUSG00000097063	Pantr2	2610207O16Rik|Pou3f3os2|linc-Brn1b	POU domain, class 3, transcription factor 3 adjacent noncoding transcript 2	ncRNA
mm_49796.1	chr6	35261363	35261413	+	1	NA	non-coding (NR_015608, exon 3 of 3)	non-coding (NR_015608, exon 3 of 3)	8656	NR_027875	67705	Mm.228046	NR_015608	ENSMUSG00000073155	1810058I24Rik	AI414869|AI848234	RIKEN cDNA 1810058I24 gene	ncRNA
mm_170199.1	chr17	67827818	67827829	-	1	NA	Intergenic	IAP1-MM_LTR|LTR|ERVK	123117	NM_001347410	268970	Mm.9935	NM_172964	ENSMUSG00000024043	Arhgap28	AU044757|AW550892|E130310N06	Rho GTPase activating protein 28	protein-coding
mm_116221.1	chr13	32932416	32932439	-	1	NA	Intergenic	Lx3C|LINE|L1	-33086	NM_011454	20708	Mm.36526	NM_011454	ENSMUSG00000042842	Serpinb6b	NK13|Spi12|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 6b	protein-coding
mm_50842.1	chr6	54817061	54817080	+	1	NA	exon (NM_199143, exon 1 of 5)	exon (NM_199143, exon 1 of 5)	154	NM_199143	387524	Mm.286149	NM_199143	ENSMUSG00000058446	Znrf2	1190002C14Rik|AU044205|D6Ertd365e	zinc and ring finger 2	protein-coding
mm_108524.1	chr12	84100798	84100815	+	1	NA	5' UTR (NM_172580, exon 1 of 3)	5' UTR (NM_172580, exon 1 of 3)	152	NM_172580	217700	Mm.49245	NM_172580	ENSMUSG00000043487	Acot6	4632408A20Rik|A330054B07|BE688602	acyl-CoA thioesterase 6	protein-coding
mm_71061.1	chr8	33914369	33914378	+	1	NA	intron (NM_001042674, intron 1 of 7)	RMER10B|LTR|ERVL	15490	NM_019733	19663	Mm.323997	NM_019733	ENSMUSG00000031586	Rbpms	2010300K22Rik|2700019M19Rik|AU017537|RBP-MS|hermes	RNA binding protein gene with multiple splicing	protein-coding
mm_157048.1	chrX	8015812	8015839	-	1	NA	intron (NM_027227, intron 1 of 3)	B3|SINE|B2	2667	NM_027227	69824	Mm.279756	NM_027227	ENSMUSG00000031163	Glod5	2010001H14Rik|AV061890	glyoxalase domain containing 5	protein-coding
mm_29335.1	chr3	108154872	108154908	-	1	NA	promoter-TSS (NM_001305461)	promoter-TSS (NM_001305461)	42	NM_001305461	229714	Mm.73666	NM_175470	ENSMUSG00000046793	Gpr61	-	G protein-coupled receptor 61	protein-coding
mm_145348.1	chr18	56471102	56471112	+	1	NA	intron (NM_026240, intron 2 of 13)	intron (NM_026240, intron 2 of 13)	38975	NM_026240	107022	Mm.24356	NM_026240	ENSMUSG00000001700	Gramd3	9030613F08Rik|9130427A09Rik|AW061306|NS3TP2	GRAM domain containing 3	protein-coding
mm_68981.1	chr7	126589402	126589406	-	1	NA	TTS (NM_138310)	TTS (NM_138310)	-3587	NM_001146311	12752	Mm.268930	NM_009907	ENSMUSG00000030720	Cln3	AI323623	ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease)	protein-coding
mm_150621.1	chr19	41263344	41263378	+	1	NA	intron (NM_133352, intron 1 of 14)	CpG	643	NM_133352	107358	Mm.246440	NM_133352	ENSMUSG00000025016	Tm9sf3	1810073M23Rik|2810031D16Rik|AI115521|AI413748|AW146116|AW549777|Smbp|mKIAA4036	transmembrane 9 superfamily member 3	protein-coding
mm_109056.1	chr12	104340528	104340565	+	1	NA	exon (NM_011458, exon 2 of 5)	exon (NM_011458, exon 2 of 5)	2060	NM_011458	20714	Mm.291569	NM_011458	ENSMUSG00000058207	Serpina3k	1300001I07Rik|D12Rp54|MMCM2|MMSpi2|RP54|Spi-2|Spi2|contrapsin	serine (or cysteine) peptidase inhibitor, clade A, member 3K	protein-coding
mm_97410.1	chr11	77953509	77953523	+	1	NA	exon (NM_021286, exon 2 of 17)	exon (NM_021286, exon 2 of 17)	22677	NM_021286	20370	Mm.229330	NM_021286	ENSMUSG00000000632	Sez6	BSRP-C|D11Bhm177e|sez-6	seizure related gene 6	protein-coding
mm_101697.1	chr11	40751339	40751351	-	1	NA	exon (NM_009831, exon 5 of 6)	exon (NM_009831, exon 5 of 6)	3941	NM_009831	12450	Mm.2103	NM_009831	ENSMUSG00000020326	Ccng1	AI314029	cyclin G1	protein-coding
mm_87281.1	chr10	42018175	42018203	+	1	NA	intron (NM_001034858, intron 1 of 17)	CpG	193	NM_001034858	213402	Mm.211320	NM_001034858	ENSMUSG00000071324	Armc2	2610018I05Rik	armadillo repeat containing 2	protein-coding
mm_42923.1	chr5	122721629	122721644	+	1	NA	intron (NM_001310720, intron 5 of 10)	B1_Mur3|SINE|Alu	14092	NM_001310718	18438	Mm.290884	NM_011026	ENSMUSG00000029470	P2rx4	AI504491|AW555605|D5Ertd444e|P2X4	purinergic receptor P2X, ligand-gated ion channel 4	protein-coding
mm_130327.1	chr15	97705788	97705842	-	1	NA	promoter-TSS (NM_028003)	promoter-TSS (NM_028003)	7	NM_028003	71919	Mm.12255	NM_028003	ENSMUSG00000022466	Rpap3	2310042P20Rik|D15Ertd682e	RNA polymerase II associated protein 3	protein-coding
mm_118261.1	chr13	112463868	112463878	-	1	NA	promoter-TSS (NM_010560)	promoter-TSS (NM_010560)	-197	NM_010560	16195	Mm.4364	NM_010560	ENSMUSG00000021756	Il6st	5133400A03Rik|AA389424|BB405851|CD130|D13Ertd699e|gp130	interleukin 6 signal transducer	protein-coding
mm_76147.1	chr8	82340728	82340738	-	1	NA	intron (NM_008357, intron 5 of 7)	L1MDb|LINE|L1	61853	NM_001254747	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_65560.1	chr7	27166713	27166724	-	1	NA	promoter-TSS (NM_053208)	promoter-TSS (NM_053208)	84	NM_053208	112406	Mm.29978	NM_053208	ENSMUSG00000058709	Egln2	0610011A13Rik|C85656|Hif-p4h-1|Ier4|Phd1|SM-20	egl-9 family hypoxia-inducible factor 2	protein-coding
mm_109725.1	chr12	116281269	116281280	+	1	NA	promoter-TSS (NM_028731)	promoter-TSS (NM_028731)	52	NM_028731	52635	Mm.273755	NM_028731	ENSMUSG00000021171	Esyt2	2410017M09Rik|4921504I16Rik|CHR2SYT|D12Ertd551e|Fam62b	extended synaptotagmin-like protein 2	protein-coding
mm_69029.1	chr7	126797432	126797435	-	1	NA	exon (NM_001177307, exon 4 of 10)	exon (NM_001177307, exon 4 of 10)	1745	NM_001177307	11674	Mm.275831	NM_007438	ENSMUSG00000030695	Aldoa	Aldo-1|Aldo1	aldolase A, fructose-bisphosphate	protein-coding
mm_95742.1	chr11	54694622	54694641	+	1	NA	intron (NM_175258, intron 27 of 27)	intron (NM_175258, intron 27 of 27)	93072	NM_178626	72729	Mm.29476	NM_178626	ENSMUSG00000052298	Cdc42se2	2810404F18Rik|AA408783|AA536669|SPEC2	CDC42 small effector 2	protein-coding
mm_18579.1	chr2	66124846	66124852	-	1	NA	promoter-TSS (NM_015736)	promoter-TSS (NM_015736)	-56	NM_015736	14425	Mm.439760	NM_015736	ENSMUSG00000026994	Galnt3	-	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 3	protein-coding
mm_106639.1	chr11	120991104	120991106	-	1	NA	5' UTR (NM_139059, exon 1 of 9)	5' UTR (NM_139059, exon 1 of 9)	228	NM_139059	104318	Mm.216227	NM_027874	ENSMUSG00000025162	Csnk1d	1200006A05Rik|AA409348|D930010H05Rik	casein kinase 1, delta	protein-coding
mm_136733.1	chr17	8311083	8311093	+	1	NA	promoter-TSS (NM_134114)	promoter-TSS (NM_134114)	-15	NM_134114	106489	Mm.311080	NM_134114	ENSMUSG00000073468	Sft2d1	5630401J11Rik|AA409698	SFT2 domain containing 1	protein-coding
mm_126523.1	chr15	81936881	81936900	+	1	NA	5' UTR (NM_145473, exon 1 of 4)	5' UTR (NM_145473, exon 1 of 4)	131	NM_145473	105859	Mm.22524	NM_145473	ENSMUSG00000042109	Csdc2	AI415250|AI481750|Pippin	cold shock domain containing C2, RNA binding	protein-coding
mm_52147.1	chr6	97978803	97978815	+	1	NA	intron (NM_001113198, intron 2 of 9)	intron (NM_001113198, intron 2 of 9)	-12974	NM_008601	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_29892.1	chr3	131272806	131272855	-	1	NA	promoter-TSS (NM_008212)	promoter-TSS (NM_008212)	-729	NM_008212	15107	Mm.260164	NM_008212	ENSMUSG00000027984	Hadh	AA409008|AU019341|AW742602|HCDH|Hadhsc|Schad	hydroxyacyl-Coenzyme A dehydrogenase	protein-coding
mm_51595.1	chr6	83978289	83978293	+	1	NA	intron (NM_008717, intron 23 of 26)	intron (NM_008717, intron 23 of 26)	-30307	NM_001077694	26903	Mm.220982	NM_021469	ENSMUSG00000033788	Dysf	2310004N10Rik|AI604795|D6Pas3	dysferlin	protein-coding
mm_168206.1	chr10	70841417	70841429	+	1	NA	Intergenic	MMERVK9C_I-int|LTR|ERVK	-185460	NR_045292	319646	Mm.483039	NR_045291	ENSMUSG00000037747	D630013N20Rik	-	RIKEN cDNA D630013N20 gene	ncRNA
mm_125076.1	chr15	25984398	25984451	+	1	NA	promoter-TSS (NM_144523)	promoter-TSS (NM_144523)	58	NM_144523	52521	Mm.29145	NM_144523	ENSMUSG00000052253	Zfp622	1110033B05Rik|D15Ertd806e|ZPR9|Znf622	zinc finger protein 622	protein-coding
mm_84049.1	chr9	58102314	58102316	-	1	NA	promoter-TSS (NM_029212)	promoter-TSS (NM_029212)	-18	NM_001311085	382077	Mm.335193	NM_029212	ENSMUSG00000037716	Ccdc33	4930535E21Rik|Gm1117|Tzip1	coiled-coil domain containing 33	protein-coding
mm_132499.1	chr16	36949381	36949385	+	1	NA	intron (NM_008225, intron 5 of 13)	G-rich|Low_complexity|Low_complexity	14400	NM_008225	15163	Mm.4091	NM_008225	ENSMUSG00000022831	Hcls1	AW213261|HS1	hematopoietic cell specific Lyn substrate 1	protein-coding
mm_49617.1	chr6	30751695	30751705	+	1	NA	intron (NM_017478, intron 20 of 23)	intron (NM_017478, intron 20 of 23)	10401	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_66832.1	chr7	48848024	48848041	-	1	NA	promoter-TSS (NM_001198841)	promoter-TSS (NM_001198841)	19	NM_001198841	13009	Mm.17235	NM_013808	ENSMUSG00000030470	Csrp3	CRP3|MLP|MMLP	cysteine and glycine-rich protein 3	protein-coding
mm_158321.1	chrX	133689047	133689055	-	1	NA	promoter-TSS (NM_001105246)	promoter-TSS (NM_001105246)	-58	NM_001105246	279653	Mm.39738	NM_001105245	ENSMUSG00000051323	Pcdh19	B530002L05Rik|Gm717|mKIAA1313	protocadherin 19	protein-coding
mm_27173.1	chr3	34005491	34005514	-	1	NA	Intergenic	Intergenic	-14577	NM_001113189	14359	Mm.259021	NM_008053	ENSMUSG00000027680	Fxr1	1110050J02Rik|9530073J07Rik|AI851072|Fxr1h|Fxr1p	fragile X mental retardation gene 1, autosomal homolog	protein-coding
mm_105376.1	chr11	103265291	103265297	-	1	NA	intron (NM_016896, intron 1 of 15)	intron (NM_016896, intron 1 of 15)	2107	NM_016896	53859	Mm.158981	NM_016896	ENSMUSG00000020941	Map3k14	Nik|aly	mitogen-activated protein kinase kinase kinase 14	protein-coding
mm_166807.1	chr7	6343725	6343767	+	1	NA	Intergenic	Intergenic	-13312	NM_001033249	213011	Mm.333558	NM_001033249	ENSMUSG00000030443	Zfp583	BC056221|Znf583	zinc finger protein 583	protein-coding
mm_170317.1	chr18	37655938	37655950	+	1	NA	intron (NM_001301259, intron 1 of 3)	intron (NM_001301259, intron 1 of 3)	-6001	NM_033584	93709	Mm.247203	NM_033584	ENSMUSG00000103144	Pcdhga1	-	protocadherin gamma subfamily A, 1	protein-coding
mm_162550.1	chr1	171219133	171219137	+	1	NA	TTS (NM_001243062)	TTS (NM_001243062)	-2429	NM_001305585	11807	Mm.389209	NM_013474	ENSMUSG00000005681	Apoa2	Alp-2|Apo-AII|ApoA-II|ApoAII|Apoa-2|Hdl-1	apolipoprotein A-II	protein-coding
mm_88135.1	chr10	69398901	69398921	+	1	NA	Intergenic	CpG	-45999	NM_007659	12534	Mm.281367	NM_007659	ENSMUSG00000019942	Cdk1	Cdc2|Cdc2a|p34<CDC2>	cyclin-dependent kinase 1	protein-coding
mm_21086.1	chr2	153015332	153015398	-	1	NA	promoter-TSS (NM_178939)	promoter-TSS (NM_178939)	18	NM_178939	68559	Mm.12746	NM_178939	ENSMUSG00000027472	Pdrg1	1110004D19Rik|AU020945|AV006589|Pdrg	p53 and DNA damage regulated 1	protein-coding
mm_150434.1	chr19	37536996	37536998	+	1	NA	Intergenic	PB1D7|SINE|Alu	-13421	NM_175353	107371	Mm.24865	NM_175353	ENSMUSG00000053799	Exoc6	4833405E05Rik|AW413330|C430002C19|Sec15|Sec15l1|hbd|msec15	exocyst complex component 6	protein-coding
mm_95555.1	chr11	52310990	52310998	+	1	NA	Intergenic	Intergenic	-27980	NM_001313981	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_25629.1	chr3	119085036	119085049	+	1	NA	intron (NM_170778, intron 14 of 22)	MYSERV6-int|LTR|ERVK	522864	NM_170778	99586	Mm.27907	NM_170778	ENSMUSG00000033308	Dpyd	AI315208|DPD|E330028L06Rik	dihydropyrimidine dehydrogenase	protein-coding
mm_136155.1	chr16	87902276	87902280	-	1	NA	intron (NM_146072, intron 15 of 16)	intron (NM_146072, intron 15 of 16)	203324	NM_007520	12013	Mm.26147	NM_007520	ENSMUSG00000025612	Bach1	6230421P05Rik|AI323795	BTB and CNC homology 1, basic leucine zipper transcription factor 1	protein-coding
mm_43098.1	chr5	124475490	124475568	+	1	NA	intron (NM_030259, intron 1 of 3)	intron (NM_030259, intron 1 of 3)	2706	NM_030259	80291	Mm.425280	NM_030259	ENSMUSG00000029401	Rilpl2	-	Rab interacting lysosomal protein-like 2	protein-coding
mm_149188.1	chr19	9914575	9914591	+	1	NA	Intergenic	Lx8|LINE|L1	-15050	NM_016692	16319	Mm.29755	NM_016692	ENSMUSG00000024660	Incenp	2700067E22Rik|AU019509|C130081E20|C77457	inner centromere protein	protein-coding
mm_96453.1	chr11	67571216	67571267	+	1	NA	intron (NM_008088, intron 1 of 13)	intron (NM_008088, intron 1 of 13)	-15259	NM_001109657	14457	Mm.40338	NM_008088	ENSMUSG00000033066	Gas7	AW124766|B230343A10Rik|Gas7-cb	growth arrest specific 7	protein-coding
mm_4708.1	chr1	180935038	180935041	+	1	NA	promoter-TSS (NM_010094)	promoter-TSS (NM_010094)	17	NM_010094	13590	Mm.378911	NM_010094	ENSMUSG00000038793	Lefty1	AI450052|Ebaf|Leftb|Stra3|Tgfb4|lefty|lefty-1	left right determination factor 1	protein-coding
mm_40150.1	chr5	35388964	35388974	+	1	NA	promoter-TSS (NM_010445)	promoter-TSS (NM_010445)	-148	NM_010445	15371	Mm.358606	NM_010445	ENSMUSG00000067438	Hmx1	Nkx5-3	H6 homeobox 1	protein-coding
mm_159359.1	chr3	85746220	85746220	-	1	NA	promoter-TSS (NM_172682)	promoter-TSS (NM_172682)	-11	NM_172682	229488	Mm.119926	NM_172682	ENSMUSG00000051000	Fam160a1	9930021J17Rik	family with sequence similarity 160, member A1	protein-coding
mm_82516.1	chr9	20636371	20636380	-	1	NA	Intergenic	Intergenic	6431	NM_013911	30843	Mm.24608	NM_013911	ENSMUSG00000066892	Fbxl12	3110048D16Rik|Fbl12	F-box and leucine-rich repeat protein 12	protein-coding
mm_37471.1	chr4	123564648	123564663	-	1	NA	intron (NM_001199136, intron 1 of 97)	intron (NM_001199136, intron 1 of 97)	-51765	NR_105824	102465214		NR_105824	ENSMUSG00000099005	Mir6398	Gm27657|mmu-mir-6398	microRNA 6398	ncRNA
mm_167565.1	chr9	41876198	41876205	-	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	248088	NM_011436	20660	Mm.121920	NM_011436	ENSMUSG00000049313	Sorl1	2900010L19Rik|AI596264|AW261561|LR11|SorLA|gp250|mSorLA	sortilin-related receptor, LDLR class A repeats-containing	protein-coding
mm_99140.1	chr11	100376310	100376324	+	1	NA	intron (NM_010593, intron 9 of 13)	intron (NM_010593, intron 9 of 13)	-20176	NM_010404	15114	Mm.281700	NM_010404	ENSMUSG00000006930	Hap1	HAP-1	huntingtin-associated protein 1	protein-coding
mm_96128.1	chr11	60786139	60786145	+	1	NA	3' UTR (NM_001085440, exon 2 of 2)	3' UTR (NM_001085440, exon 2 of 2)	8617	NM_175491	237782	Mm.57726	NM_175491	ENSMUSG00000049323	Smcr8	2310076G09Rik|AI642055|D030073L15Rik	Smith-Magenis syndrome chromosome region, candidate 8 homolog (human)	protein-coding
mm_27816.1	chr3	78647184	78647199	-	1	NA	Intergenic	Intergenic	497696	NM_001310536	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_134279.1	chr16	14195133	14195151	-	1	NA	exon (NM_001161775, exon 41 of 41)	exon (NM_001161775, exon 41 of 41)	31867	NM_001114085	67203	Mm.24105	NM_023317	ENSMUSG00000022678	Nde1	2810027M15Rik|AU042936|AW822251|Nude|mNudE	nudE neurodevelopment protein 1	protein-coding
mm_106591.1	chr11	120730452	120730465	-	1	NA	exon (NM_007621, exon 5 of 8)	exon (NM_007621, exon 5 of 8)	1563	NM_007621	12409	Mm.21454	NM_007621	ENSMUSG00000025150	Cbr2	MLCR	carbonyl reductase 2	protein-coding
mm_84000.1	chr9	57552282	57552289	-	1	NA	intron (NM_025837, intron 1 of 7)	intron (NM_025837, intron 1 of 7)	467	NM_025837	110119	Mm.247218	NM_025837	ENSMUSG00000032306	Mpi	1110002E17Rik|AI315153|Mpi-1|Mpi1	mannose phosphate isomerase	protein-coding
mm_158305.1	chrX	122397309	122397328	-	1	NA	promoter-TSS (NM_138742)	promoter-TSS (NM_138742)	67	NM_138742	54561	Mm.490573	NM_138742	ENSMUSG00000055733	Nap1l3	MB20	nucleosome assembly protein 1-like 3	protein-coding
mm_136170.1	chr16	88612274	88612279	-	1	NA	promoter-TSS (NM_001163141)	promoter-TSS (NM_001163141)	3	NM_001163141	239932	Mm.120273	NM_001163141	ENSMUSG00000050239	Krtap24-1	Gm312	keratin associated protein 24-1	protein-coding
mm_79898.1	chr9	65361024	65361047	+	1	NA	promoter-TSS (NM_001111145)	promoter-TSS (NM_001111145)	-25	NM_001111145	208080	Mm.291862	NM_001111145	ENSMUSG00000086228	Ubap1l	Gm514	ubiquitin-associated protein 1-like	protein-coding
mm_88656.1	chr10	79996456	79996475	+	1	NA	intron (NR_038088, intron 1 of 4)	intron (NR_038088, intron 1 of 4)	-1143	NM_001347081	27403	Mm.103351	NM_013850	ENSMUSG00000035722	Abca7	ABCX|Abc51	ATP-binding cassette, sub-family A (ABC1), member 7	protein-coding
mm_94758.1	chr11	21149060	21149083	+	1	NA	3' UTR (NM_023324, exon 7 of 7)	3' UTR (NM_023324, exon 7 of 7)	57747	NM_023324	67245	Mm.28957	NM_023324	ENSMUSG00000020134	Peli1	2810468L03Rik|A930031K15Rik|AA409794|AI586297|D11Ertd676e	pellino 1	protein-coding
mm_166412.1	chr5	137151448	137151464	+	1	NA	Intergenic	Intergenic	-35249	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_130891.1	chr15	102366272	102366282	-	1	NA	promoter-TSS (NM_130458)	promoter-TSS (NM_130458)	-6	NM_130458	170574	Mm.263284	NM_130458	ENSMUSG00000060284	Sp7	6430578P22Rik|C22|Osx	Sp7 transcription factor 7	protein-coding
mm_59075.1	chr7	19517717	19517730	+	1	NA	Intergenic	MIRc|SINE|MIR	-1008	NM_027116	69547	Mm.77325	NM_027116	ENSMUSG00000060621	Nkpd1	2310015G09Rik	NTPase, KAP family P-loop domain containing 1	protein-coding
mm_25894.1	chr3	131110669	131110686	+	1	NA	5' UTR (NM_001276402, exon 1 of 10)	5' UTR (NM_001276402, exon 1 of 10)	380	NM_001276402	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_55081.1	chr6	49214699	49214721	-	1	NA	5' UTR (NM_023670, exon 1 of 15)	5' UTR (NM_023670, exon 1 of 15)	244	NM_023670	140488	Mm.281018	NM_023670	ENSMUSG00000029814	Igf2bp3	2610101N11Rik|AA522010|AL022933|AU045931|IMP-3|IMP3|Koc13|Neilsen|mimp3	insulin-like growth factor 2 mRNA binding protein 3	protein-coding
mm_26116.1	chr3	137833916	137833929	+	1	NA	Intergenic	Intergenic	-30565	NM_001316995	51788	Mm.117541	NM_016750	ENSMUSG00000037894	H2afz	H2A.Z|H2a.z-1	H2A histone family, member Z	protein-coding
mm_44523.1	chr5	24392013	24392031	-	1	NA	5' UTR (NM_001002897, exon 1 of 14)	5' UTR (NM_001002897, exon 1 of 14)	121	NM_001002897	213948	Mm.332252	NM_001002897	ENSMUSG00000038295	Atg9b	Apg912|Apg9l2|Apgdc2|Gm574|Nos3as|eONE|sONE	autophagy related 9B	protein-coding
mm_170377.1	chr1	85598752	85598756	-	1	NA	promoter-TSS (NM_030194)	promoter-TSS (NM_030194)	56	NM_030194	109032	Mm.335802	NM_030194	ENSMUSG00000070034	Sp110	5031415C07Rik|52kDa|5830484A20Rik|ENSMUSG00000075603|Ifi75|Ipr1	Sp110 nuclear body protein	protein-coding
mm_25731.1	chr3	122834561	122834584	+	1	NA	intron (NM_153422, intron 14 of 20)	intron (NM_153422, intron 14 of 20)	-32592	NR_045168	71647	Mm.449992	NR_045168	ENSMUSG00000106583	4930447N08Rik	-	RIKEN cDNA 4930447N08 gene	ncRNA
mm_71634.1	chr8	57488054	57488065	+	1	NA	promoter-TSS (NM_021788)	promoter-TSS (NM_021788)	96	NR_126555	78353	Mm.426240	NR_126553	ENSMUSG00000096917	2500002B13Rik	-	RIKEN cDNA 2500002B13 gene	ncRNA
mm_96600.1	chr11	69091056	69091066	+	1	NA	3' UTR (NM_009497, exon 5 of 5)	3' UTR (NM_009497, exon 5 of 5)	2533	NM_009497	22318	Mm.28643	NM_009497	ENSMUSG00000020894	Vamp2	Syb-2|Syb2|sybII	vesicle-associated membrane protein 2	protein-coding
mm_142379.1	chr17	44736310	44736332	-	1	NA	promoter-TSS (NM_001271631)	promoter-TSS (NM_001271631)	-145	NM_001271631	12393	Mm.391013	NM_009820	ENSMUSG00000039153	Runx2	AML3|Cbf|Cbfa-1|Cbfa1|LS3|Osf2|PEBP2aA|Pebp2a1|Pebpa2a	runt related transcription factor 2	protein-coding
mm_5086.1	chr1	4496425	4496446	-	1	NA	5' UTR (NM_001289467, exon 1 of 3)	5' UTR (NM_001289467, exon 1 of 3)	919	NM_001289464	20671	Mm.279103	NM_011441	ENSMUSG00000025902	Sox17	-	SRY (sex determining region Y)-box 17	protein-coding
mm_56050.1	chr6	86743175	86743206	-	1	NA	intron (NM_013471, intron 10 of 12)	intron (NM_013471, intron 10 of 12)	-9812	NM_011818	23885	Mm.321452	NM_011818	ENSMUSG00000001157	Gmcl1	2810049L19Rik|Btbd13|DIP|Gcl|Gcl-1|glc-1|mglc-1	germ cell-less, spermatogenesis associated 1	protein-coding
mm_41459.1	chr5	90930740	90930792	+	1	NA	promoter-TSS (NM_026788)	promoter-TSS (NM_026788)	-430	NM_026788	665563	Mm.153030	NM_026788	ENSMUSG00000029376	Mthfd2l	1110019K23Rik|C630010D07Rik	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2-like	protein-coding
mm_168799.1	chr12	20071620	20071639	+	1	NA	Intergenic	CpG	744150	NR_015521	69513	Mm.273972	NR_015521	ENSMUSG00000099759	1700030C10Rik	-	RIKEN cDNA 1700030C10 gene	ncRNA
mm_71679.1	chr8	60890411	60890483	+	1	NA	promoter-TSS (NM_028299)	promoter-TSS (NM_028299)	-4	NM_028299	72612	Mm.25263	NM_028299	ENSMUSG00000038005	Hpf1	2700029M09Rik|C230006B22Rik|C4orf27	histone PARylation factor 1	protein-coding
mm_85948.1	chr9	112113768	112113804	-	1	NA	intron (NM_001177618, intron 17 of 18)	intron (NM_001177618, intron 17 of 18)	4925	NR_029823	723815		NR_029823	ENSMUSG00000065441	Mir128-2	Mirn128-2|Mirn128b|mir-128-2|mir-128b	microRNA 128-2	ncRNA
mm_56375.1	chr6	94229106	94229118	-	1	NA	intron (NR_130996, intron 1 of 1)	AT_rich|Low_complexity|Low_complexity	8330	NR_130996	78178	Mm.452749	NR_130996	ENSMUSG00000045095	4930511A08Rik	-	RIKEN cDNA 4930511A08 gene	ncRNA
mm_59175.1	chr7	24450777	24450804	+	1	NA	Intergenic	Intergenic	-5108	NM_199013	210145	Mm.33811	NM_199013	ENSMUSG00000062028	Irgc1	F630044M05Rik|Gm1102|Gm474|Ifgge|Iigp5|Irgc	immunity-related GTPase family, cinema 1	protein-coding
mm_142580.1	chr17	46681914	46681924	-	1	NA	promoter-TSS (NM_027910)	promoter-TSS (NM_027910)	739	NM_001277312	17256	Mm.329083	NM_010787	ENSMUSG00000002768	Mea1	Mea-1	male enhanced antigen 1	protein-coding
mm_94985.1	chr11	31832709	31832716	+	1	NA	Intergenic	MIRb|SINE|MIR	-8165	NR_102312	414116	Mm.150222	NR_102310	ENSMUSG00000085772	D630024D03Rik	-	RIKEN cDNA D630024D03 gene	ncRNA
mm_6668.1	chr1	80340344	80340354	-	1	NA	5' UTR (NM_016716, exon 1 of 16)	5' UTR (NM_016716, exon 1 of 16)	341	NM_001313728	26554	Mm.12665	NM_016716	ENSMUSG00000004364	Cul3	KIAA0617	cullin 3	protein-coding
mm_40194.1	chr5	36796492	36796522	+	1	NA	exon (NM_026242, exon 1 of 2)	exon (NM_026242, exon 1 of 2)	247	NM_026242	67568	Mm.332336	NM_026242	ENSMUSG00000055302	Mrfap1	9130413I22Rik|AL022827|Pam14	Morf4 family associated protein 1	protein-coding
mm_18655.1	chr2	69789569	69789583	-	1	NA	promoter-TSS (NM_028521)	promoter-TSS (NM_028521)	-90	NM_001077684	75051	Mm.195726	NM_001077684	ENSMUSG00000070883	Ccdc173	4930525K21Rik|4930578N16Rik	coiled-coil domain containing 173	protein-coding
mm_89226.1	chr10	87518932	87518936	+	1	NA	Intergenic	Intergenic	-2861	NM_008777	18478	Mm.263539	NM_008777	ENSMUSG00000020051	Pah	AW106920	phenylalanine hydroxylase	protein-coding
mm_74050.1	chr8	122230234	122230289	+	1	NA	Intergenic	CpG	-51880	NM_009569	22761	Mm.3105	NM_009569	ENSMUSG00000049577	Zfpm1	FOG|Fog1	zinc finger protein, multitype 1	protein-coding
mm_92466.1	chr10	77990222	77990238	-	1	NA	exon (NM_008826, exon 17 of 22)	exon (NM_008826, exon 17 of 22)	11580	NM_026431	67884	Mm.297512	NM_026431	ENSMUSG00000020284	1810043G02Rik	AV026620|D10Jhu13e	RIKEN cDNA 1810043G02 gene	protein-coding
mm_14557.1	chr2	134786155	134786170	+	1	NA	promoter-TSS (NM_001145830)	promoter-TSS (NM_001145830)	-2	NM_019677	18795	Mm.330607	NM_019677	ENSMUSG00000051177	Plcb1	3110043I21Rik|AI132408|Plcb|mKIAA0581	phospholipase C, beta 1	protein-coding
mm_117225.1	chr13	64153130	64153145	-	1	NA	promoter-TSS (NM_175494)	promoter-TSS (NM_175494)	62	NM_175494	238673	Mm.300065	NM_175494	ENSMUSG00000044934	Zfp367	8030486J21Rik|ZFF29a|ZFF29b|Znf367	zinc finger protein 367	protein-coding
mm_99556.1	chr11	103649531	103649557	+	1	NA	promoter-TSS (NM_001033212)	promoter-TSS (NM_001033212)	35	NM_001033212	104582	Mm.44618	NM_001033212	ENSMUSG00000046215	Rprml	AW049332	reprimo-like	protein-coding
mm_47914.1	chr5	134966505	134966514	-	1	NA	Intergenic	Intergenic	-19575	NM_009903	12740	Mm.7339	NM_009903	ENSMUSG00000047501	Cldn4	Cep-r|Cpetr|Cpetr1	claudin 4	protein-coding
mm_169429.1	chr14	53709887	53709903	+	1	NA	Intergenic	Intergenic	544034	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_1004.1	chr1	58717451	58717469	+	1	NA	intron (NM_009805, intron 1 of 4)	intron (NM_009805, intron 1 of 4)	4174	NM_207653	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_60166.1	chr7	40898748	40898778	+	1	NA	promoter-TSS (NM_021387)	promoter-TSS (NM_021387)	-439	NR_040329	320210	Mm.126237	NR_040329	ENSMUSG00000100600	A230077H06Rik	-	RIKEN cDNA A230077H06 gene	ncRNA
mm_59602.1	chr7	28140165	28140165	+	1	NA	exon (NM_001164655, exon 5 of 20)	exon (NM_001164655, exon 5 of 20)	10699	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_151496.1	chr19	58707627	58707633	+	1	NA	Intergenic	L1MA6|LINE|L1	8713	NR_038140	69166	Mm.491059	NR_038140	ENSMUSG00000101088	1810018F18Rik	1810031L05Rik|1810047O18Rik	RIKEN cDNA 1810018F18 gene	ncRNA
mm_113725.1	chr13	43797600	43797618	+	1	NA	exon (NM_009856, exon 3 of 5)	exon (NM_009856, exon 3 of 5)	12497	NM_001289915	12522	Mm.57175	NM_009856	ENSMUSG00000015396	Cd83	-	CD83 antigen	protein-coding
mm_44100.1	chr5	149289321	149289341	+	1	NA	Intergenic	Intergenic	24327	NM_009663	11690	Mm.19844	NM_009663	ENSMUSG00000060063	Alox5ap	Flap	arachidonate 5-lipoxygenase activating protein	protein-coding
mm_110995.1	chr12	78256505	78256520	-	1	NA	intron (NM_145965, intron 1 of 22)	intron (NM_145965, intron 1 of 22)	29857	NM_145965	268566	Mm.341742	NM_145965	ENSMUSG00000047454	Gphn	5730552E08Rik|AI662856|BC027112|C230040D23|GPH|GPHRYN|geph	gephyrin	protein-coding
mm_156814.1	chrX	164118326	164118342	+	1	NA	exon (NM_020626, exon 6 of 6)	exon (NM_020626, exon 6 of 6)	-21008	NM_001130513	70008	Mm.13451	NM_027286	ENSMUSG00000015405	Ace2	2010305L05Rik	angiotensin I converting enzyme (peptidyl-dipeptidase A) 2	protein-coding
mm_146969.1	chr18	33463616	33463630	-	1	NA	promoter-TSS (NM_001267717)	promoter-TSS (NM_001267717)	11	NM_001267717	27528	Mm.407415	NM_053078	ENSMUSG00000042834	Nrep	AI325076|D0H4S114|Harp|P311|PTZ17|SEZ17	neuronal regeneration related protein	protein-coding
mm_147318.1	chr18	42196700	42196739	-	1	NA	promoter-TSS (NM_027072)	promoter-TSS (NM_027072)	-10	NM_027072	69401	Mm.34841	NM_027072	ENSMUSG00000059455	Plac8l1	1700009N18Rik|1700015M15Rik	PLAC8-like 1	protein-coding
mm_76178.1	chr8	82401640	82401650	-	1	NA	intron (NM_001254747, intron 1 of 7)	intron (NM_001254747, intron 1 of 7)	941	NM_001254747	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_161772.1	chr17	37093940	37093940	-	1	NA	promoter-TSS (NM_182714)	promoter-TSS (NM_182714)	-68	NM_182714	258470	Mm.377519	NM_182714	ENSMUSG00000095377	Olfr91	MOR256-20|bM573K1.3	olfactory receptor 91	protein-coding
mm_90730.1	chr10	5289378	5289391	-	1	NA	exon (NM_001347711, exon 55 of 146)	exon (NM_001347711, exon 55 of 146)	-94677	NM_001079686	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_147152.1	chr18	36679142	36679168	-	1	NA	promoter-TSS (NM_026404)	promoter-TSS (NM_026404)	-60	NM_001083317	67843	Mm.273350	NM_026404	ENSMUSG00000033272	Slc35a4	2610030J16Rik	solute carrier family 35, member A4	protein-coding
mm_161015.1	chr11	120274540	120274540	+	1	NA	exon (NM_198423, exon 9 of 28)	exon (NM_198423, exon 9 of 28)	41593	NM_198423	268515	Mm.309498	NM_198423	ENSMUSG00000039741	Bahcc1	B930044J06|BC060615	BAH domain and coiled-coil containing 1	protein-coding
mm_10394.1	chr2	13574007	13574028	+	1	NA	promoter-TSS (NM_011701)	promoter-TSS (NM_011701)	-294	NM_011701	22352	Mm.268000	NM_011701	ENSMUSG00000026728	Vim	-	vimentin	protein-coding
mm_142863.1	chr17	51813906	51813916	-	1	NA	intron (NM_001163632, intron 1 of 10)	intron (NM_001163632, intron 1 of 10)	-1857	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_28901.1	chr3	98319034	98319036	-	1	NA	intron (NM_016966, intron 8 of 11)	intron (NM_016966, intron 8 of 11)	20934	NM_016966	236539	Mm.16898	NM_016966	ENSMUSG00000053398	Phgdh	3-PGDH|3PGDH|4930479N23|A10|PGAD|PGD|PGDH|SERA	3-phosphoglycerate dehydrogenase	protein-coding
mm_46893.1	chr5	113993741	113993806	-	1	NA	promoter-TSS (NM_198109)	promoter-TSS (NM_198109)	-16	NM_198109	231637	Mm.389682	NM_198109	ENSMUSG00000042121	Ssh1	AW551225|Gm1394|Gm1395|SSH-1|SSH-1L	slingshot homolog 1 (Drosophila)	protein-coding
mm_38327.1	chr4	137357712	137357722	-	1	NA	promoter-TSS (NM_001243769)	promoter-TSS (NM_001243769)	42	NM_009861	12540	Mm.1022	NM_009861	ENSMUSG00000006699	Cdc42	AI747189|AU018915	cell division cycle 42	protein-coding
mm_27782.1	chr3	73708400	73708423	-	1	NA	promoter-TSS (NM_009738)	promoter-TSS (NM_009738)	4	NM_009738	12038	Mm.250719	NM_009738	ENSMUSG00000027792	Bche	C730038G20Rik	butyrylcholinesterase	protein-coding
mm_24461.1	chr3	90654083	90654093	+	1	NA	promoter-TSS (NM_199422)	promoter-TSS (NM_199422)	-214	NM_199422	381493	Mm.291525	NM_199422	ENSMUSG00000063767	S100a7a	AY465109|Gm1020|S100A7L1|S100A7f|S100a15|S100a15a|S100a17l1	S100 calcium binding protein A7A	protein-coding
mm_121638.1	chr14	8378754	8378804	-	1	NA	promoter-TSS (NM_146050)	promoter-TSS (NM_146050)	-16	NM_146050	18300	Mm.25351	NM_146050	ENSMUSG00000021749	Oit1	2310076N21Rik|AV067083|EF-7|Fam3d	oncoprotein induced transcript 1	protein-coding
mm_96888.1	chr11	70436176	70436193	+	1	NA	exon (NM_001271358, exon 3 of 15)	exon (NM_001271358, exon 3 of 15)	-2071	NR_106064	102465670		NR_106064	ENSMUSG00000099109	Mir7115	Gm27902|mmu-mir-7115	microRNA 7115	ncRNA
mm_87774.1	chr10	60294614	60294614	+	1	NA	exon (NM_011179, exon 5 of 15)	exon (NM_011179, exon 5 of 15)	10153	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_14196.1	chr2	127135082	127135086	+	1	NA	Intergenic	Intergenic	-1130	NM_144818	215387	Mm.29786	NM_144818	ENSMUSG00000034906	Ncaph	A730011O11Rik|Brrn1|HCAP-H|mKIAA0074	non-SMC condensin I complex, subunit H	protein-coding
mm_100462.1	chr11	119856278	119856301	+	1	NA	exon (NM_001306081, exon 17 of 33)	exon (NM_001306081, exon 17 of 33)	-21924	NR_045312	319454	Mm.442144	NR_045312	ENSMUSG00000085081	Rptoros	A430071A18Rik	regulatory associated protein of MTOR, complex 1, opposite strand	ncRNA
mm_44328.1	chr5	12355772	12355780	-	1	NA	Intergenic	MT2B1|LTR|ERVL	-27390	NM_028882	108151	Mm.89313	NM_028882	ENSMUSG00000040254	Sema3d	4631426B19Rik	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D	protein-coding
mm_26722.1	chr3	159599178	159599191	+	1	NA	promoter-TSS (NM_029987)	promoter-TSS (NM_029987)	3	NM_029987	19892	Mm.131708	NM_029987	ENSMUSG00000028174	Rpe65	65kDa|A930029L06Rik|LCA2|Mord1|RP20|rd12	retinal pigment epithelium 65	protein-coding
mm_16054.1	chr2	167773181	167773192	+	1	NA	Intergenic	Intergenic	82009	NR_015500	329562	Mm.123101	NM_177851	ENSMUSG00000006462	A530013C23Rik	-	RIKEN cDNA A530013C23 gene	ncRNA
mm_28097.1	chr3	86002516	86002535	-	1	NA	promoter-TSS (NM_001001650)	promoter-TSS (NM_001001650)	-34	NM_001001650	368202	Mm.253822	NM_001001650	ENSMUSG00000049013	Prss48	Esspl|Gm1019	protease, serine 48	protein-coding
mm_5444.1	chr1	36017257	36017271	-	1	NA	Intergenic	Intergenic	-51136	NM_015818	50785	Mm.213566	NM_015818	ENSMUSG00000045216	Hs6st1	6Ost1	heparan sulfate 6-O-sulfotransferase 1	protein-coding
mm_89875.1	chr10	108285228	108285238	+	1	NA	Intergenic	Intergenic	-46956	NM_054056	114774	Mm.391419	NM_054056	ENSMUSG00000035873	Pawr	2310001G03Rik|PAR4|Par-4	PRKC, apoptosis, WT1, regulator	protein-coding
mm_78172.1	chr9	21131490	21131531	+	1	NA	promoter-TSS (NM_018793)	promoter-TSS (NM_018793)	-235	NM_001205312	54721	Mm.20249	NM_018793	ENSMUSG00000032175	Tyk2	JTK1	tyrosine kinase 2	protein-coding
mm_50380.1	chr6	48685503	48685513	+	1	NA	intron (NM_174990, intron 1 of 2)	intron (NM_174990, intron 1 of 2)	930	NM_174990	107526	Mm.333048	NM_174990	ENSMUSG00000054435	Gimap4	AU019574|E430007K16Rik|Ian-1|Ian1|Imap4	GTPase, IMAP family member 4	protein-coding
mm_106651.1	chr11	121081130	121081144	-	1	NA	promoter-TSS (NM_145373)	promoter-TSS (NM_145373)	2	NM_145373	209588	Mm.69553	NM_145373	ENSMUSG00000025165	Sectm1a	BC010462	secreted and transmembrane 1A	protein-coding
mm_164080.1	chr15	3279258	3279260	+	1	NA	exon (NM_009155, exon 5 of 5)	exon (NM_009155, exon 5 of 5)	8282	NM_009155	20363	Mm.392203	NM_009155	ENSMUSG00000064373	Selenop	AU018766|D15Ucla1|Se-P|Sepp1|selp	selenoprotein P	protein-coding
mm_85544.1	chr9	106682361	106682364	-	1	NA	intron (NM_001286498, intron 2 of 5)	intron (NM_001286498, intron 2 of 5)	3454	NM_011573	21767	Mm.22266	NM_011573	ENSMUSG00000040813	Tex264	TEG-264	testis expressed gene 264	protein-coding
mm_85326.1	chr9	101862498	101862508	-	1	NA	Intergenic	Intergenic	442472	NR_106163	102466241		NR_106163	ENSMUSG00000098521	Mir7243	Gm27363|mmu-mir-7243	microRNA 7243	ncRNA
mm_87552.1	chr10	54074538	54074572	+	1	NA	exon (NM_008548, exon 2 of 13)	exon (NM_008548, exon 2 of 13)	1241	NM_008548	17155	Mm.117294	NM_008548	ENSMUSG00000003746	Man1a	Man1a1|PCR1	mannosidase 1, alpha	protein-coding
mm_47561.1	chr5	124425576	124425601	-	1	NA	intron (NM_001081203, intron 1 of 31)	CpG	326	NM_001081203	243272	Mm.23879	NM_001081203	ENSMUSG00000038095	Sbno1	9330180L10Rik|AI849128|AW557836|BC021875|Sbno|mSno1|sno	strawberry notch homolog 1 (Drosophila)	protein-coding
mm_172928.1	chr9	72293361	72293370	-	1	NA	intron (NM_001311105, intron 1 of 20)	RSINE1|SINE|B4	18477	NM_001311105	235469	Mm.242791	NM_146224	ENSMUSG00000038535	Zfp280d	A930005F02Rik|BC027163|Suhw4|ZNF634|Znf280d	zinc finger protein 280D	protein-coding
mm_25240.1	chr3	103914372	103914405	+	1	NA	5' UTR (NM_172684, exon 1 of 7)	5' UTR (NM_172684, exon 1 of 7)	268	NM_172684	229675	Mm.29366	NM_172684	ENSMUSG00000044098	Rsbn1	C230004D03Rik|E330004N01|Rosbin|Rsbn|Rsbp|mKIAA3002	rosbin, round spermatid basic protein 1	protein-coding
mm_52483.1	chr6	114316646	114316664	+	1	NA	3' UTR (NM_178703, exon 16 of 16)	3' UTR (NM_178703, exon 16 of 16)	34020	NM_178703	232333	Mm.5260	NM_178703	ENSMUSG00000030310	Slc6a1	A730043E01|GABATHG|GABATR|GAT-1|Gabt|Gabt1|Gat1|XT-1|Xtrp1	solute carrier family 6 (neurotransmitter transporter, GABA), member 1	protein-coding
mm_66412.1	chr7	44491990	44492013	-	1	NA	exon (NM_197991, exon 6 of 7)	exon (NM_197991, exon 6 of 7)	4512	NM_197991	69683	Mm.294759	NM_197991	ENSMUSG00000008140	Emc10	2310044H10Rik|5430410O10Rik|Inm02|Mirta22	ER membrane protein complex subunit 10	protein-coding
mm_141634.1	chr17	32965707	32965717	-	1	NA	promoter-TSS (NM_153063)	promoter-TSS (NM_153063)	4	NR_033585	77875	Mm.245027	NR_033585		Cyp4f41-ps	6030422M01Rik	cytochrome P450, family 4, subfamily f, polypeptide 41 pseudogene	pseudo
mm_70423.1	chr8	11477005	11477016	+	1	NA	promoter-TSS (NR_126558)	promoter-TSS (NR_126558)	-919	NR_126558	102132	Mm.37632	NR_126558	ENSMUSG00000096957	E230013L22Rik	AI645545	RIKEN cDNA E230013L22 gene	ncRNA
mm_50324.1	chr6	48395605	48395646	+	1	NA	promoter-TSS (NM_133922)	promoter-TSS (NM_133922)	39	NM_001347153	77827	Mm.107646	NM_133922	ENSMUSG00000042810	Krba1	A930040G15Rik|AI448780	KRAB-A domain containing 1	protein-coding
mm_27763.1	chr3	69858871	69858874	-	1	NA	intron (NM_001286959, intron 1 of 3)	MTA_Mm|LTR|ERVL-MaLR	1022	NM_001164210	66183	Mm.45481	NM_133675	ENSMUSG00000043461	Sptssb	1110032A04Rik|ADMP|Sssptb	serine palmitoyltransferase, small subunit B	protein-coding
mm_15870.1	chr2	164834108	164834138	+	1	NA	promoter-TSS (NM_001082974)	promoter-TSS (NM_001082974)	350	NM_008906	19025	Mm.359633	NM_008906	ENSMUSG00000017760	Ctsa	AU019505|PPCA|Ppgb	cathepsin A	protein-coding
mm_135672.1	chr16	52411761	52411778	-	1	NA	intron (NM_009655, intron 1 of 15)	L1MA7|LINE|L1	41312	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_132801.1	chr16	45094624	45094668	+	1	NA	intron (NM_026439, intron 1 of 7)	intron (NM_026439, intron 1 of 7)	593	NM_026439	67896	Mm.181074	NM_026439	ENSMUSG00000022665	Ccdc80	2610001E17Rik|DRO1|Ssg1|Urb	coiled-coil domain containing 80	protein-coding
mm_32775.1	chr4	116699388	116699455	+	1	NA	3' UTR (NM_011034, exon 6 of 6)	3' UTR (NM_011034, exon 6 of 6)	8964	NM_025962	67096	Mm.252785	NM_025962	ENSMUSG00000028690	Mmachc	1810037K07Rik|CblC	methylmalonic aciduria cblC type, with homocystinuria	protein-coding
mm_95877.1	chr11	58061000	58061011	+	1	NA	3' UTR (NM_028451, exon 19 of 19)	3' UTR (NM_028451, exon 19 of 19)	-43148	NM_026949	69125	Mm.28910	NM_026949	ENSMUSG00000020515	Cnot8	1500015I04Rik|1810022F04Rik|AA536816|AU015770|AU043059	CCR4-NOT transcription complex, subunit 8	protein-coding
mm_110558.1	chr12	55491739	55491777	-	1	NA	TTS (NR_035430)	TTS (NR_035430)	889	NM_010907	18035	Mm.170515	NM_010907	ENSMUSG00000021025	Nfkbia	AI462015|Nfkbi	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, alpha	protein-coding
mm_46535.1	chr5	105700666	105700698	-	1	NA	promoter-TSS (NM_178701)	promoter-TSS (NM_178701)	-128	NM_178701	231549	Mm.23837	NM_178701	ENSMUSG00000046079	Lrrc8d	2810473G09Rik|4930525N13Rik|A930019F03|Lrrc5	leucine rich repeat containing 8D	protein-coding
mm_110036.1	chr12	17000109	17000122	-	1	NA	promoter-TSS (NM_001161111)	promoter-TSS (NM_001161111)	3	NM_172574	217430	Mm.379451	NM_172574	ENSMUSG00000045679	Pqlc3	C78076|E030024M05Rik	PQ loop repeat containing	protein-coding
mm_45572.1	chr5	73338974	73339005	-	1	NA	promoter-TSS (NM_001310636)	promoter-TSS (NM_001310636)	-42	NM_001310636	433904	Mm.274892	NM_026950	ENSMUSG00000029153	Ociad2	1810027I20Rik	OCIA domain containing 2	protein-coding
mm_134593.1	chr16	20454367	20454375	-	1	NA	Intergenic	RLTR17|LTR|ERVK	-27977	NM_176839	27416	Mm.20845	NM_013790	ENSMUSG00000022822	Abcc5	2900011L11Rik|AI132311|Abcc5a|Abcc5b|Mrp5	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	protein-coding
mm_128945.1	chr15	74746685	74746708	-	1	NA	promoter-TSS (NM_001081961)	promoter-TSS (NM_001081961)	-9	NM_001081961	69462	Mm.64338	NM_001081961	ENSMUSG00000075605	Slurp2	2300005B03Rik|SLURP-2	secreted Ly6/Plaur domain containing 2	protein-coding
mm_74924.1	chr8	25597460	25597517	-	1	NA	promoter-TSS (NM_173012)	promoter-TSS (NM_173012)	-1	NM_173012	270035	Mm.268349	NM_173012	ENSMUSG00000037363	Letm2	6030453H13|D030041N04Rik	leucine zipper-EF-hand containing transmembrane protein 2	protein-coding
mm_15436.1	chr2	157279066	157279130	+	1	NA	promoter-TSS (NM_019642)	promoter-TSS (NM_019642)	0	NM_019642	20014	Mm.22130	NM_019642	ENSMUSG00000027642	Rpn2	1300012C06Rik|AV261018|Rpn-2	ribophorin II	protein-coding
mm_750.1	chr1	43730594	43730633	+	1	NA	promoter-TSS (NM_024283)	promoter-TSS (NM_024283)	11	NM_024283	78896	Mm.50109	NM_024283	ENSMUSG00000026051	1500015O10Rik	Ecrg4	RIKEN cDNA 1500015O10 gene	protein-coding
mm_13962.1	chr2	121413966	121413970	+	1	NA	promoter-TSS (NM_007952)	promoter-TSS (NM_007952)	66	NM_007952	14827	Mm.263177	NM_007952	ENSMUSG00000027248	Pdia3	58kDa|ERp57|ERp60|ERp61|Erp|Grp58|PDI|PDI-Q2|PI-PLC|PLC[a]|Plca	protein disulfide isomerase associated 3	protein-coding
mm_38361.1	chr4	137994713	137994759	-	1	NA	intron (NM_172703, intron 2 of 34)	intron (NM_172703, intron 2 of 34)	1280	NM_172703	230861	Mm.268903	NM_172703	ENSMUSG00000028760	Eif4g3	1500002J22Rik|4930523M17Rik|G1-419-52|eIF4GII|repro8	eukaryotic translation initiation factor 4 gamma, 3	protein-coding
mm_112977.1	chr13	21295509	21295533	+	1	NA	Intergenic	RMER1B|Other|Other	-2835	NM_010343	14780	Mm.1332	NM_010343	ENSMUSG00000004344	Gpx5	AV379049|Arep	glutathione peroxidase 5	protein-coding
mm_22364.1	chr2	181043541	181043554	-	1	NA	Intergenic	Intergenic	-4370	NM_015730	11438	Mm.252369	NM_015730	ENSMUSG00000027577	Chrna4	Acra-4|Acra4|EBN1|ENFL1	cholinergic receptor, nicotinic, alpha polypeptide 4	protein-coding
mm_141826.1	chr17	34627112	34627124	-	1	NA	promoter-TSS (NM_019441)	promoter-TSS (NM_019441)	30	NM_019441	54397	Mm.373627	NM_019441	ENSMUSG00000015474	Ppt2	0610007M19Rik|AA672937	palmitoyl-protein thioesterase 2	protein-coding
mm_30063.1	chr3	137878124	137878134	-	1	NA	intron (NM_001033155, intron 1 of 7)	HAL1M8|LINE|L1	10454	NM_001033155	70604	Mm.256488	NM_001033155	ENSMUSG00000074212	Dnajb14	5730496F10Rik	DnaJ heat shock protein family (Hsp40) member B14	protein-coding
mm_86007.1	chr9	112233275	112233286	-	1	NA	promoter-TSS (NM_001177616)	promoter-TSS (NM_001177616)	-779	NM_001177616	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_40395.1	chr5	52810216	52810220	+	1	NA	intron (NM_001308144, intron 8 of 12)	intron (NM_001308144, intron 8 of 12)	-23917	NM_024213	52206	Mm.272568	NM_024213	ENSMUSG00000029176	Anapc4	2610306D21Rik|APC4|D5Ertd249e	anaphase promoting complex subunit 4	protein-coding
mm_16689.1	chr2	6884902	6884906	-	1	NA	promoter-TSS (NM_001110228)	promoter-TSS (NM_001110228)	92	NM_010160	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_461.1	chr1	36307775	36307779	+	1	NA	promoter-TSS (NM_001290727)	promoter-TSS (NM_001290727)	44	NM_001172205	214855	Mm.34316	NM_145996	ENSMUSG00000037447	Arid5a	D430024K22Rik|Mrf1	AT rich interactive domain 5A (MRF1-like)	protein-coding
mm_130507.1	chr15	98845730	98845743	-	1	NA	exon (NM_001033276, exon 40 of 55)	exon (NM_001033276, exon 40 of 55)	-14228	NM_016781	19082	Mm.6670	NM_016781	ENSMUSG00000067713	Prkag1	AA571379|BB036179|Prkaac	protein kinase, AMP-activated, gamma 1 non-catalytic subunit	protein-coding
mm_103059.1	chr11	69837081	69837121	-	1	NA	Intergenic	CpG	-1424	NM_026982	69186	Mm.248772	NM_026982	ENSMUSG00000070394	Tmem256	1810027O10Rik|3110009M16Rik	transmembrane protein 256	protein-coding
mm_113337.1	chr13	31625803	31625813	+	1	NA	promoter-TSS (NM_010225)	promoter-TSS (NM_010225)	-8	NM_010225	14238	Mm.125548	NM_010225	ENSMUSG00000038402	Foxf2	FREAC2|Fkh20|LUN	forkhead box F2	protein-coding
mm_144659.1	chr18	34313161	34313173	+	1	NA	exon (NM_007462, exon 16 of 16)	exon (NM_007462, exon 16 of 16)	-17978	NM_025527	66384	Mm.29452	NM_025527	ENSMUSG00000014504	Srp19	2310020D23Rik	signal recognition particle 19	protein-coding
mm_141645.1	chr17	33607753	33607759	-	1	NA	TTS (NM_053214)	TTS (NM_053214)	-21336	NR_034153	328801	Mm.181488	NM_026712	ENSMUSG00000073423	Zfp414	0610030H11Rik|Znf414	zinc finger protein 414	protein-coding
mm_71582.1	chr8	54600816	54600826	+	1	NA	promoter-TSS (NM_133711)	promoter-TSS (NM_133711)	40	NM_133711	69281	Mm.45833	NM_133711	ENSMUSG00000031518	Spata4	1700001N01Rik|Srg2|TSARG2	spermatogenesis associated 4	protein-coding
mm_26572.1	chr3	146602638	146602672	+	1	NA	intron (NM_009474, intron 1 of 7)	(CA)n|Simple_repeat|Simple_repeat	5506	NM_009474	22262	Mm.10865	NM_009474	ENSMUSG00000028186	Uox	AI663847	urate oxidase	protein-coding
mm_34191.1	chr4	140701896	140701922	+	1	NA	intron (NM_173867, intron 1 of 12)	CpG	436	NM_173867	108911	Mm.253	NM_173867	ENSMUSG00000040945	Rcc2	2610510H01Rik|2610529N02Rik|AA536646|AA675016|Td60|mKIAA1470	regulator of chromosome condensation 2	protein-coding
mm_47576.1	chr5	124531292	124531307	-	1	NA	promoter-TSS (NM_021430)	promoter-TSS (NM_021430)	92	NM_021430	75695	Mm.41180	NM_021430	ENSMUSG00000029392	Rilpl1	2900002H16Rik|6330559I19Rik|GOSPEL	Rab interacting lysosomal protein-like 1	protein-coding
mm_153075.1	chr19	32276928	32276938	-	1	NA	intron (NM_001168525, intron 2 of 9)	intron (NM_001168525, intron 2 of 9)	-65920	NM_001168526	208449	Mm.329810	NM_144792	ENSMUSG00000040451	Sgms1	9530058O11Rik|AI841905|C80702|Mob|Sms1|Sor1|Tmem23	sphingomyelin synthase 1	protein-coding
mm_72314.1	chr8	78013985	78014018	+	1	NA	Intergenic	RLTR9A|LTR|ERVK	-199341	NM_183096	73301	Mm.61243	NM_183096	ENSMUSG00000037101	Ttc29	1700031F13Rik	tetratricopeptide repeat domain 29	protein-coding
mm_100161.1	chr11	116434068	116434078	+	1	NA	promoter-TSS (NR_003376)	promoter-TSS (NR_003376)	-21	NM_176902	319370	Mm.258466	NM_176902	ENSMUSG00000050628	Ubald2	1110014K08Rik|D030012E24Rik|Fam100b	UBA-like domain containing 2	protein-coding
mm_133390.1	chr16	84774176	84774197	+	1	NA	promoter-TSS (NM_023844)	promoter-TSS (NM_023844)	63	NM_023844	67374	Mm.41758	NM_023844	ENSMUSG00000053062	Jam2	1110002N23Rik|2410030G21Rik|2410167M24Rik|JAM-2|JAM-B|Jcam2|VE-JAM	junction adhesion molecule 2	protein-coding
mm_15471.1	chr2	157471222	157471253	+	1	NA	3' UTR (NM_001025395, exon 14 of 14)	3' UTR (NM_001025395, exon 14 of 14)	46944	NM_001025395	20779	Mm.22845	NM_009271	ENSMUSG00000027646	Src	AW259666|pp60c-src	Rous sarcoma oncogene	protein-coding
mm_152618.1	chr19	12436047	12436059	-	1	NA	Intergenic	B4A|SINE|B4	8148	NM_019540	56093	Mm.285849	NM_019540	ENSMUSG00000040065	Pfpl	Epcs5|Epcs50	pore forming protein-like	protein-coding
mm_89706.1	chr10	97649819	97649825	+	1	NA	exon (NM_007884, exon 3 of 8)	exon (NM_007884, exon 3 of 8)	5754	NM_007884	13516	Mm.148886	NM_007884	ENSMUSG00000019936	Epyc	Dspg3|PG-Lb|SLRR3B	epiphycan	protein-coding
mm_65743.1	chr7	28543983	28544001	-	1	NA	3' UTR (NM_001081115, exon 6 of 6)	3' UTR (NM_001081115, exon 6 of 6)	3107	NM_026716	68416	Mm.25210	NM_026716	ENSMUSG00000084174	Sycn	0910001K16Rik|1810038B08Rik|SYL	syncollin	protein-coding
mm_15065.1	chr2	153031986	153032014	+	1	NA	5' UTR (NM_001011732, exon 1 of 3)	5' UTR (NM_001011732, exon 1 of 3)	148	NM_001011732	228787	Mm.376111	NM_001011732	ENSMUSG00000042631	Xkr7	AY534253	X-linked Kx blood group related 7	protein-coding
mm_139625.1	chr17	57363296	57363326	+	1	NA	intron (NM_010130, intron 2 of 21)	RLTR17D_Mm|LTR|ERVK	4625	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_125053.1	chr15	25843355	25843361	+	1	NA	promoter-TSS (NM_001034851)	promoter-TSS (NM_001034851)	60	NM_001034851	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_169084.1	chr13	35853520	35853522	+	1	NA	intron (NM_001123386, intron 2 of 6)	RLTR12E|LTR|ERVK	52826	NM_145938	208366	Mm.35545	NM_145938	ENSMUSG00000021418	Rpp40	D8Bwg1265e|Rnasep1	ribonuclease P 40 subunit	protein-coding
mm_160613.1	chr9	87015558	87015558	+	1	NA	promoter-TSS (NM_001037907)	promoter-TSS (NM_001037907)	21	NM_001037907	382089	Mm.92244	NM_001037907	ENSMUSG00000047897	Ripply2	C030002E08Rik|Gm1122	ripply transcriptional repressor 2	protein-coding
mm_152255.1	chr19	8756899	8756913	-	1	NA	promoter-TSS (NM_001276704)	promoter-TSS (NM_001276704)	63	NR_132423	102640359	Mm.440831	NR_132423		LOC102640359	-	uncharacterized LOC102640359	ncRNA
mm_73947.1	chr8	120120145	120120150	+	1	NA	intron (NM_172286, intron 1 of 12)	L1MB8|LINE|L1	5995	NM_001163761	234797	Mm.101958	NM_172286	ENSMUSG00000031824	6430548M08Rik	AW049007|Kiaa0513|mKIAA0513	RIKEN cDNA 6430548M08 gene	protein-coding
mm_68779.1	chr7	122186152	122186213	-	1	NA	promoter-TSS (NM_001316689)	promoter-TSS (NM_001316689)	49	NM_012016	26918	Mm.20452	NM_012016	ENSMUSG00000030866	Ern2	Ern1|Ire1|Ire1b|ire1-beta|mIre1	endoplasmic reticulum (ER) to nucleus signalling 2	protein-coding
mm_65318.1	chr7	24902828	24902844	-	1	NA	promoter-TSS (NM_008488)	promoter-TSS (NM_008488)	-150	NM_001130150	16801	Mm.3181	NM_008488	ENSMUSG00000040940	Arhgef1	Lbcl2|Lsc	Rho guanine nucleotide exchange factor (GEF) 1	protein-coding
mm_48215.1	chr5	137610627	137610651	-	1	NA	intron (NM_008788, intron 1 of 8)	intron (NM_008788, intron 1 of 8)	765	NM_008788	18542	Mm.262345	NM_008788	ENSMUSG00000029718	Pcolce	Astt-2|Astt2|P14|PCPE-1	procollagen C-endopeptidase enhancer protein	protein-coding
mm_89565.1	chr10	95416984	95416993	+	1	NA	promoter-TSS (NM_007706)	promoter-TSS (NM_007706)	-131	NM_007706	216233	Mm.474283	NM_007706	ENSMUSG00000020027	Socs2	8030460M17|AI527257|AW108012|CIS2|Cish2|D130043N08Rik|JAB|SOCS-2|SSI-2|hg	suppressor of cytokine signaling 2	protein-coding
mm_138664.1	chr17	35873869	35873914	+	1	NA	exon (NM_001146711, exon 3 of 4)	exon (NM_001146711, exon 3 of 4)	-5887	NM_026987	69192	Mm.390986	NM_026987	ENSMUSG00000024422	Dhx16	2410006N22Rik|DBP2|Ddx16|mKIAA0577	DEAH (Asp-Glu-Ala-His) box polypeptide 16	protein-coding
mm_129539.1	chr15	79357712	79357724	-	1	NA	exon (NM_001304830, exon 3 of 3)	exon (NM_001304830, exon 3 of 3)	9316	NM_001304832	17133	Mm.86646	NM_010755	ENSMUSG00000042622	Maff	-	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein F (avian)	protein-coding
mm_31499.1	chr4	53246217	53246227	+	1	NA	promoter-TSS (NR_040665)	promoter-TSS (NR_040665)	26	NR_040665	78180	Mm.243847	NR_040665	ENSMUSG00000086947	4930522O17Rik	-	RIKEN cDNA 4930522O17 gene	ncRNA
mm_128361.1	chr15	41329673	41329677	-	1	NA	Intergenic	RMER19C|LTR|ERVK	-117807	NM_001130166	170719	Mm.254267	NM_130885	ENSMUSG00000022307	Oxr1	2210416C20Rik|C7|C7B	oxidation resistance 1	protein-coding
mm_171431.1	chr4	136050314	136050322	-	1	NA	exon (NM_025919, exon 5 of 6)	exon (NM_025919, exon 5 of 6)	3053	NM_025919	67025	Mm.276856	NM_025919	ENSMUSG00000059291	Rpl11	2010203J19Rik	ribosomal protein L11	protein-coding
mm_159896.1	chr6	30958840	30958840	-	1	NA	5' UTR (NM_001135093, exon 1 of 1)	5' UTR (NM_001135093, exon 1 of 1)	150	NM_001135093	619665	Mm.204671	NM_001135093	ENSMUSG00000073209	Klf14	5330411L03Rik|AL022736|BTEB5	Kruppel-like factor 14	protein-coding
mm_17676.1	chr2	32260058	32260114	-	1	NA	promoter-TSS (NM_011675)	promoter-TSS (NM_011675)	19	NM_011675	22245	Mm.425076	NM_011675	ENSMUSG00000002550	Uck1	URK1|Umpk	uridine-cytidine kinase 1	protein-coding
mm_50401.1	chr6	48720475	48720481	+	1	NA	intron (NM_146167, intron 1 of 1)	intron (NM_146167, intron 1 of 1)	1857	NM_146167	231932	Mm.30479	NM_146167	ENSMUSG00000043931	Gimap7	IAN7|Ian3	GTPase, IMAP family member 7	protein-coding
mm_80825.1	chr9	96786316	96786326	+	1	NA	Intergenic	Intergenic	20759	NR_102296	319707	Mm.392191	NR_102293	ENSMUSG00000101581	C430002N11Rik	-	RIKEN cDNA C430002N11 gene	ncRNA
mm_126114.1	chr15	78260903	78260927	+	1	NA	intron (NM_008677, intron 8 of 9)	intron (NM_008677, intron 8 of 9)	16104	NM_008677	17972	Mm.2068	NM_008677	ENSMUSG00000071715	Ncf4	AI451400|p40phox	neutrophil cytosolic factor 4	protein-coding
mm_27858.1	chr3	79157614	79157623	-	1	NA	Intergenic	L1_Mur3|LINE|L1	-11743	NM_001099624	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_66863.1	chr7	56019560	56019605	-	1	NA	promoter-TSS (NM_153578)	promoter-TSS (NM_153578)	-9	NM_153578	233280	Mm.389901	NM_153578	ENSMUSG00000047037	Nipa1	1110027G09Rik|A830014A18Rik|FSP3|Spg6	non imprinted in Prader-Willi/Angelman syndrome 1 homolog (human)	protein-coding
mm_55328.1	chr6	55681258	55681271	-	1	NA	promoter-TSS (NM_009717)	promoter-TSS (NM_009717)	-1	NM_009717	11922	Mm.5106	NM_009717	ENSMUSG00000037984	Neurod6	Atoh2|Math-2|Math2|Nex|Nex1m|bHLHa2	neurogenic differentiation 6	protein-coding
mm_94015.1	chr10	127661416	127661424	-	1	NA	TTS (NM_009284)	TTS (NM_009284)	5283	NM_001122895	17937	Mm.336898	NM_008668	ENSMUSG00000025402	Nab2	AI451907	Ngfi-A binding protein 2	protein-coding
mm_118015.1	chr13	100775804	100775843	-	1	NA	promoter-TSS (NM_021886)	promoter-TSS (NM_021886)	76	NM_021886	26886	Mm.273502	NM_021886	ENSMUSG00000045273	Cenph	1700021I11Rik|2410018A12Rik|2610042E16Rik|2810046K12Rik|AU044255|CENP-H|ENP	centromere protein H	protein-coding
mm_146179.1	chr18	75370573	75370581	+	1	NA	intron (NM_001042660, intron 1 of 3)	intron (NM_001042660, intron 1 of 3)	3212	NM_001042660	17131	Mm.34407	NM_008543	ENSMUSG00000025880	Smad7	Madh7	SMAD family member 7	protein-coding
mm_74802.1	chr8	22586096	22586099	-	1	NA	intron (NM_011696, intron 3 of 8)	ID4|SINE|ID	7716	NM_001198998	22335	Mm.227704	NM_011696	ENSMUSG00000008892	Vdac3	-	voltage-dependent anion channel 3	protein-coding
mm_139682.1	chr17	57416616	57416617	+	1	NA	intron (NM_010130, intron 10 of 21)	L1_Mus3|LINE|L1	57930	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_111683.1	chr12	103416224	103416243	-	1	NA	exon (NM_001159502, exon 6 of 9)	exon (NM_001159502, exon 6 of 9)	9547	NM_001159502	27225	Mm.3935	NM_020494	ENSMUSG00000041645	Ddx24	1700055J08Rik|2510027P10Rik|AI649272	DEAD (Asp-Glu-Ala-Asp) box polypeptide 24	protein-coding
mm_45931.1	chr5	89457764	89457784	-	1	NA	5' UTR (NM_008096, exon 1 of 13)	5' UTR (NM_008096, exon 1 of 13)	124	NM_008096	14473	Mm.196595	NM_008096	ENSMUSG00000035540	Gc	DBP|VDB	group specific component	protein-coding
mm_75806.1	chr8	70212269	70212300	-	1	NA	promoter-TSS (NM_001007570)	promoter-TSS (NM_001007570)	-3	NM_001007570	73095	Mm.185413	NM_001007570	ENSMUSG00000002346	Slc25a42	2900084M01Rik	solute carrier family 25, member 42	protein-coding
mm_30468.1	chr3	154330332	154330334	-	1	NA	promoter-TSS (NR_040387)	promoter-TSS (NR_040387)	227	NM_010713	16875	Mm.15530	NM_010713	ENSMUSG00000096225	Lhx8	L3|Lhx7	LIM homeobox protein 8	protein-coding
mm_132410.1	chr16	35025609	35025643	+	1	NA	intron (NM_023587, intron 1 of 6)	ORR1F|LTR|ERVL-MaLR	3205	NM_023587	70757	Mm.27286	NM_023587	ENSMUSG00000035376	Hacd2	6330408J20Rik|AI255777|AI481689|Hcad2|Ptplb	3-hydroxyacyl-CoA dehydratase 2	protein-coding
mm_60999.1	chr7	49304081	49304119	+	1	NA	intron (NM_175272, intron 1 of 37)	intron (NM_175272, intron 1 of 37)	57911	NM_175272	78286	Mm.333881	NM_175272	ENSMUSG00000052512	Nav2	5330421F07Rik|AU067780|BQ960892|HELAD1|POMFIL2|RAINB1|RAINB2|Unc53H2|mKIAA3015	neuron navigator 2	protein-coding
mm_58370.1	chr6	148944751	148944778	-	1	NA	promoter-TSS (NR_144294)	promoter-TSS (NR_144294)	-93	NR_144294	109163	Mm.440359	NM_175404		3010003L21Rik	-	RIKEN cDNA 3010003L21 gene	ncRNA
mm_148190.1	chr18	79009625	79009655	-	1	NA	intron (NM_053099, intron 2 of 5)	intron (NM_053099, intron 2 of 5)	99751	NM_053099	240427	Mm.312871	NM_053099	ENSMUSG00000024548	Setbp1	C130092E12|Seb|mKIAA0437	SET binding protein 1	protein-coding
mm_122326.1	chr14	37048958	37048970	-	1	NA	promoter-TSS (NM_021340)	promoter-TSS (NM_021340)	50	NM_001301694	57811	Mm.20460	NM_021340	ENSMUSG00000021804	Rgr	-	retinal G protein coupled receptor	protein-coding
mm_74043.1	chr8	122006872	122006887	+	1	NA	intron (NM_001285983, intron 8 of 12)	intron (NM_001285983, intron 8 of 12)	28855	NR_106096	102466915		NR_106096	ENSMUSG00000099140	Mir7237	Gm27482|mmu-mir-7237	microRNA 7237	ncRNA
mm_172686.1	chr8	57397220	57397223	-	1	NA	Intergenic	Intergenic	-58702	NM_009136	20284	Mm.12886	NM_009136	ENSMUSG00000031610	Scrg1	AW124307	scrapie responsive gene 1	protein-coding
mm_50562.1	chr6	49047946	49047956	+	1	NA	exon (NM_053110, exon 6 of 11)	exon (NM_053110, exon 6 of 11)	11433	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_62044.1	chr7	92258824	92258832	+	1	NA	intron (NM_001243047, intron 1 of 10)	intron (NM_001243047, intron 1 of 10)	23858	NM_001243047	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_67211.1	chr7	74382291	74382305	-	1	NA	intron (NM_001038643, intron 2 of 10)	intron (NM_001038643, intron 2 of 10)	172482	NM_023908	108116	Mm.425467	NM_023908	ENSMUSG00000025790	Slco3a1	5830414C08Rik|Anr1|MJAM|OATP-D|R75096|Slc21a11	solute carrier organic anion transporter family, member 3a1	protein-coding
mm_111674.1	chr12	103338504	103338547	-	1	NA	intron (NM_023049, intron 2 of 9)	intron (NM_023049, intron 2 of 9)	17476	NM_023049	65256	Mm.27159	NM_023049	ENSMUSG00000021200	Asb2	1110008E15Rik	ankyrin repeat and SOCS box-containing 2	protein-coding
mm_29352.1	chr3	108445148	108445178	-	1	NA	promoter-TSS (NM_011319)	promoter-TSS (NM_011319)	96	NM_011319	20226	Mm.28688	NM_011319	ENSMUSG00000068739	Sars	Sars1|Strs|serRS	seryl-aminoacyl-tRNA synthetase	protein-coding
mm_75968.1	chr8	72002532	72002547	-	1	NA	intron (NM_024444, intron 2 of 12)	intron (NM_024444, intron 2 of 12)	7087	NM_024444	72054	Mm.160020	NM_024444	ENSMUSG00000003484	Cyp4f18	1810054N16Rik|Cyp4f3|Cypf18	cytochrome P450, family 4, subfamily f, polypeptide 18	protein-coding
mm_155441.1	chrX	73494881	73494916	+	1	NA	3' UTR (NM_007542, exon 8 of 8)	3' UTR (NM_007542, exon 8 of 8)	-8188	NM_001310537	320707	Mm.210095	NM_177236	ENSMUSG00000031376	Atp2b3	6430519O13Rik|Pmca3	ATPase, Ca++ transporting, plasma membrane 3	protein-coding
mm_47094.1	chr5	117900384	117900385	-	1	NA	intron (NM_008712, intron 6 of 27)	intron (NM_008712, intron 6 of 27)	33545	NM_008712	18125	Mm.44249	NM_008712	ENSMUSG00000029361	Nos1	2310005C01Rik|N-NOS|NC-NOS|NO|NOS|NOS-I|Nos-1|bNOS|nNOS	nitric oxide synthase 1, neuronal	protein-coding
mm_12993.1	chr2	90885789	90885849	+	1	NA	promoter-TSS (NM_026161)	promoter-TSS (NM_026161)	33	NM_026161	67445	Mm.258993	NM_026161	ENSMUSG00000040794	C1qtnf4	0710001E10Rik|9430004J15Rik|CTRP4	C1q and tumor necrosis factor related protein 4	protein-coding
mm_83486.1	chr9	45936050	45936106	-	1	NA	promoter-TSS (NM_011526)	promoter-TSS (NM_011526)	-20	NM_011526	21345	Mm.283283	NM_011526	ENSMUSG00000032085	Tagln	Sm22|Sm22a|Ws310	transgelin	protein-coding
mm_58064.1	chr6	136872772	136872791	-	1	NA	exon (NM_008597, exon 4 of 4)	exon (NM_008597, exon 4 of 4)	3042	NM_008597	17313	Mm.243085	NM_008597	ENSMUSG00000030218	Mgp	Mglap	matrix Gla protein	protein-coding
mm_17624.1	chr2	31031657	31031660	-	1	NA	intron (NM_001038700, intron 14 of 14)	PB1D10|SINE|Alu	49379	NM_028846	74270	Mm.346654	NM_028846	ENSMUSG00000026854	Usp20	1700055M05Rik|AI467231|Vdu2	ubiquitin specific peptidase 20	protein-coding
mm_141081.1	chr17	25868728	25868769	-	1	NA	promoter-TSS (NM_026633)	promoter-TSS (NM_026633)	-10	NM_026633	68241	Mm.328870	NM_026633	ENSMUSG00000025732	Fam195a	9530058B02Rik|Mcrip2	family with sequence similarity 195, member A	protein-coding
mm_76161.1	chr8	82372172	82372182	-	1	NA	intron (NM_008357, intron 2 of 7)	intron (NM_008357, intron 2 of 7)	30409	NM_001254747	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_167495.1	chr9	13246946	13247002	+	1	NA	promoter-TSS (NM_025534)	promoter-TSS (NM_025534)	18	NM_025534	66396	Mm.290620	NM_025534	ENSMUSG00000079084	Ccdc82	2310043N13Rik	coiled-coil domain containing 82	protein-coding
mm_159048.1	chr1	185247708	185247708	+	1	NA	intron (NM_001163754, intron 10 of 34)	intron (NM_001163754, intron 10 of 34)	4733	NR_035529	100316737		NR_035529	ENSMUSG00000105770	Mir664	mir-664|mmu-mir-664	microRNA 664	ncRNA
mm_22008.1	chr2	167775181	167775187	-	1	NA	Intergenic	Intergenic	84007	NR_015500	329562	Mm.123101	NM_177851	ENSMUSG00000006462	A530013C23Rik	-	RIKEN cDNA A530013C23 gene	ncRNA
mm_101931.1	chr11	50206050	50206055	-	1	NA	exon (NM_011018, exon 5 of 8)	exon (NM_011018, exon 5 of 8)	4768	NM_001290769	18412	Mm.40828	NM_011018	ENSMUSG00000015837	Sqstm1	A170|OSF-6|Osi|STAP|STONE14|p62	sequestosome 1	protein-coding
mm_74886.1	chr8	25102108	25102169	-	1	NA	promoter-TSS (NM_031257)	promoter-TSS (NM_031257)	-327	NM_031257	83436	Mm.261122	NM_031257	ENSMUSG00000031557	Plekha2	6430512N22Rik|AI851530|AU041791|TAPP2|W91773	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 2	protein-coding
mm_52282.1	chr6	108660773	108660787	+	1	NA	5' UTR (NM_011498, exon 1 of 5)	5' UTR (NM_011498, exon 1 of 5)	151	NM_011498	20893	Mm.2436	NM_011498	ENSMUSG00000030103	Bhlhe40	Bhlhb2|C130042M06Rik|CR8|Clast5|Dec1|Sharp2|Stra13|Stra14	basic helix-loop-helix family, member e40	protein-coding
mm_27655.1	chr3	63964775	63964785	-	1	NA	promoter-TSS (NM_001272035)	promoter-TSS (NM_001272035)	-47	NM_015728	11416	Mm.135619	NM_015728	ENSMUSG00000027822	Slc33a1	AI315656|AI788741|Acatn|D630022N01Rik	solute carrier family 33 (acetyl-CoA transporter), member 1	protein-coding
mm_157738.1	chrX	72656136	72656199	-	1	NA	promoter-TSS (NM_008067)	promoter-TSS (NM_008067)	79	NM_008067	14396	Mm.102286	NM_008067	ENSMUSG00000031343	Gabra3	Gabra-3	gamma-aminobutyric acid (GABA) A receptor, subunit alpha 3	protein-coding
mm_162627.1	chr1	185283126	185283152	+	1	NA	intron (NM_001163754, intron 33 of 34)	intron (NM_001163754, intron 33 of 34)	-30180	NR_029580	387189		NR_029580	ENSMUSG00000065581	Mir194-1	Mirn194|Mirn194-1|miR-194|mir-194-1	microRNA 194-1	ncRNA
mm_108680.1	chr12	86734343	86734349	+	1	NA	promoter-TSS (NM_001195767)	promoter-TSS (NM_001195767)	-23	NM_001195767	627607	Mm.341880	NM_001195767	ENSMUSG00000059114	Lrrc74a	EG627607|Gm6772|Lrrc74	leucine rich repeat containing 74A	protein-coding
mm_50070.1	chr6	41271378	41271411	+	1	NA	Intergenic	Intergenic	-30878	NM_011646	22074	Mm.383263	NM_011646	ENSMUSG00000054106	Try4	0910001B19Rik|Td	trypsin 4	protein-coding
mm_66523.1	chr7	45126219	45126256	-	1	NA	TTS (NR_039581)	TTS (NR_039581)	198	NR_000003	27211		NR_000003	ENSMUSG00000065818	Snord35a	Rnu35a|U35|U35A	small nucleolar RNA, C/D box 35A	snoRNA
mm_47331.1	chr5	122500365	122500375	-	1	NA	intron (NM_001110140, intron 3 of 19)	intron (NM_001110140, intron 3 of 19)	1855	NM_001110140	11938	Mm.227583	NM_009722	ENSMUSG00000029467	Atp2a2	9530097L16Rik|D5Wsu150e|SERCA2|SERCA2B|Serca2a|mKIAA4195	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	protein-coding
mm_165954.1	chr4	86796566	86796568	+	1	NA	intron (NM_184088, intron 10 of 31)	MIR|SINE|MIR	48012	NM_184088	329877	Mm.273718	NM_184088	ENSMUSG00000038024	Dennd4c	1700065A05Rik|AA420392	DENN/MADD domain containing 4C	protein-coding
mm_135126.1	chr16	35843834	35843845	-	1	NA	intron (NM_001039530, intron 12 of 16)	RLTR17B_Mm|LTR|ERVK	27543	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_142815.1	chr17	51739924	51739938	-	1	NA	exon (NM_001163632, exon 11 of 11)	exon (NM_001163632, exon 11 of 11)	72123	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_169230.1	chr13	67239292	67239311	+	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	29767	NM_001001152	238690	Mm.306358	NM_001001152	ENSMUSG00000055480	Zfp458	BC062958|Rslcan-7|Znf728|mszf59-2	zinc finger protein 458	protein-coding
mm_164604.1	chr17	29886818	29886828	+	1	NA	intron (NM_001081160, intron 1 of 15)	intron (NM_001081160, intron 1 of 15)	1059	NM_001081160	74762	Mm.40901	NM_001081160	ENSMUSG00000043557	Mdga1	1200011I03Rik|GPIM|Mamdc3	MAM domain containing glycosylphosphatidylinositol anchor 1	protein-coding
mm_112962.1	chr13	21180550	21180604	+	1	NA	exon (NM_009054, exon 1 of 8)	exon (NM_009054, exon 1 of 8)	646	NM_009054	19720	Mm.314056	NM_009054	ENSMUSG00000021326	Trim27	AW538890|Gm19403|Rfp	tripartite motif-containing 27	protein-coding
mm_47397.1	chr5	123046967	123046988	-	1	NA	promoter-TSS (NM_029112)	promoter-TSS (NM_029112)	39	NM_001347456	74890	Mm.141383	NM_029112	ENSMUSG00000029477	Morn3	4930438O03Rik	MORN repeat containing 3	protein-coding
mm_100825.1	chr11	5277562	5277567	-	1	NA	3' UTR (NM_001290501, exon 9 of 9)	3' UTR (NM_001290501, exon 9 of 9)	-15954	NM_032396	84035	Mm.209989	NM_032396	ENSMUSG00000020393	Kremen1	AV002070|Kremen|Krm1	kringle containing transmembrane protein 1	protein-coding
mm_69008.1	chr7	126703144	126703166	-	1	NA	exon (NM_009898, exon 2 of 11)	exon (NM_009898, exon 2 of 11)	1065	NM_001301374	12721	Mm.290482	NM_009898	ENSMUSG00000030707	Coro1a	Clabp|Lmb3|TACO|p57	coronin, actin binding protein 1A	protein-coding
mm_115370.1	chr13	113033040	113033054	+	1	NA	Intergenic	(CCA)n|Simple_repeat|Simple_repeat	-2332	NM_001281487	238896		NM_001281487	ENSMUSG00000078926	Cdc20b	EG238896|EG622422	cell division cycle 20B	protein-coding
mm_164284.1	chr15	102954474	102954496	+	1	NA	promoter-TSS (NM_001024842)	promoter-TSS (NM_001024842)	-41	NM_001024842	109663	Mm.37692	NM_001024842	ENSMUSG00000001656	Hoxc11	Hox-3.7	homeobox C11	protein-coding
mm_36727.1	chr4	99120837	99120853	-	1	NA	promoter-TSS (NM_026082)	promoter-TSS (NM_026082)	70	NM_001290636	67299	Mm.260623	NM_026082	ENSMUSG00000028556	Dock7	3110056M06Rik|Gm430	dedicator of cytokinesis 7	protein-coding
mm_156699.1	chrX	159489310	159489327	+	1	NA	exon (NM_001081124, exon 11 of 17)	exon (NM_001081124, exon 11 of 17)	30193	NM_001313753	78283	Mm.160079	NM_001081124	ENSMUSG00000041020	Map7d2	1600028E09Rik|2900002G04Rik|5330432J06Rik|C030036K04Rik|Mtap7d2	MAP7 domain containing 2	protein-coding
mm_82743.1	chr9	26802564	26802590	-	1	NA	intron (NM_153803, intron 1 of 19)	intron (NM_153803, intron 1 of 19)	3840	NM_153803	244757	Mm.293696	NM_153803	ENSMUSG00000036395	Glb1l2	-	galactosidase, beta 1-like 2	protein-coding
mm_136108.1	chr16	85455124	85455127	-	1	NA	Intergenic	Tigger1|DNA|TcMar-Tigger	95248	NM_144853	224405	Mm.213203	NM_144853	ENSMUSG00000041134	Cyyr1	-	cysteine and tyrosine-rich protein 1	protein-coding
mm_37602.1	chr4	126752591	126752602	-	1	NA	promoter-TSS (NM_001035525)	promoter-TSS (NM_001035525)	833	NM_011986	26562	Mm.206206	NM_011986	ENSMUSG00000028833	Ncdn	AU042419|MMS10-AE|Ms10ae|mKIAA0607|norbin	neurochondrin	protein-coding
mm_31902.1	chr4	83773639	83773642	+	1	NA	intron (NM_001081012, intron 23 of 25)	intron (NM_001081012, intron 23 of 25)	248095	NM_001081012	320226	Mm.180032	NM_029117	ENSMUSG00000052407	Ccdc171	4930418J05Rik|4930473A06Rik|A330015D16Rik	coiled-coil domain containing 171	protein-coding
mm_20180.1	chr2	122595125	122595142	-	1	NA	3' UTR (NM_025961, exon 9 of 9)	3' UTR (NM_025961, exon 9 of 9)	16144	NM_025961	67092	Mm.29975	NM_025961	ENSMUSG00000027199	Gatm	1810003P21Rik|AI314789|AT	glycine amidinotransferase (L-arginine:glycine amidinotransferase)	protein-coding
mm_82186.1	chr9	123936947	123936954	+	1	NA	Intergenic	Intergenic	31742	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_34222.1	chr4	140992366	140992378	+	1	NA	exon (NM_029097, exon 3 of 29)	exon (NM_029097, exon 3 of 29)	5499	NM_001164366	74772	Mm.205625	NM_029097	ENSMUSG00000036622	Atp13a2	1110012E06Rik|AA589443	ATPase type 13A2	protein-coding
mm_107650.1	chr12	52575408	52575408	+	1	NA	Intergenic	MER74A|LTR|ERVL	26914	NR_045910	73278	Mm.396209	NR_045910	ENSMUSG00000100315	1700031P21Rik	-	RIKEN cDNA 1700031P21 gene	ncRNA
mm_92117.1	chr10	63244136	63244170	-	1	NA	5' UTR (NM_026101, exon 1 of 25)	5' UTR (NM_026101, exon 1 of 25)	356	NM_026101	67345	Mm.234437	NM_026101	ENSMUSG00000020064	Herc4	1700056O17Rik|4921531D01Rik|9530080M15Rik|mKIAA1593	hect domain and RLD 4	protein-coding
mm_86665.1	chr10	17919316	17919318	+	1	NA	intron (NM_001033432, intron 1 of 3)	intron (NM_001033432, intron 1 of 3)	28750	NM_001033432	380629	Mm.276430	NM_001033432	ENSMUSG00000039879	Heca	Gm869|HDC|HDCL	hdc homolog, cell cycle regulator	protein-coding
mm_42057.1	chr5	108694223	108694255	+	1	NA	promoter-TSS (NM_001164259)	promoter-TSS (NM_001164259)	10	NM_054071	116701	Mm.35691	NM_054071	ENSMUSG00000008090	Fgfrl1	FGFR5|FGFR5beta|FGFR5gamma	fibroblast growth factor receptor-like 1	protein-coding
mm_6317.1	chr1	71601243	71601294	-	1	NA	exon (NM_001276413, exon 33 of 44)	exon (NM_001276413, exon 33 of 44)	44112	NM_026195	108147	Mm.38010	NM_026195	ENSMUSG00000026192	Atic	2610509C24Rik|AA536954|AW212393	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	protein-coding
mm_91317.1	chr10	24953998	24954008	-	1	NA	Intergenic	Intergenic	-26533	NM_007482	11846	Mm.154144	NM_007482	ENSMUSG00000019987	Arg1	AI|AI256583|Arg-1|PGIF	arginase, liver	protein-coding
mm_82400.1	chr9	14751988	14752016	-	1	NA	5' UTR (NM_010242, exon 1 of 1)	5' UTR (NM_010242, exon 1 of 1)	120	NM_010242	14345	Mm.63450	NM_010242	ENSMUSG00000049307	Fut4	AI451562|CD15|FAL|FucT-IV|LeX|SSEA-1|Ssea1	fucosyltransferase 4	protein-coding
mm_79961.1	chr9	66350417	66350435	+	1	NA	promoter-TSS (NM_145617)	promoter-TSS (NM_145617)	-24	NM_145617	235439	Mm.244179	NM_145617	ENSMUSG00000038664	Herc1	2810449H11Rik|B230218H07|D130015N03Rik|tbl	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	protein-coding
mm_136301.1	chr16	91548288	91548310	-	1	NA	intron (NM_008338, intron 1 of 6)	intron (NM_008338, intron 1 of 6)	1205	NM_008338	15980	Mm.249364	NM_008338	ENSMUSG00000022965	Ifngr2	Ifgr2|Ifgt	interferon gamma receptor 2	protein-coding
mm_63298.1	chr7	126814001	126814015	+	1	NA	Intergenic	Intergenic	-2877	NM_026884	68952	Mm.440393	NM_026884	ENSMUSG00000058966	Fam57b	1500016O10Rik|A330104J06Rik|AI413816|AW060769	family with sequence similarity 57, member B	protein-coding
mm_53657.1	chr6	141275084	141275117	+	1	NA	intron (NM_018779, intron 1 of 15)	intron (NM_018779, intron 1 of 15)	25831	NM_018779	54611	Mm.103728	NM_018779	ENSMUSG00000041741	Pde3a	A930022O17Rik|C87899	phosphodiesterase 3A, cGMP inhibited	protein-coding
mm_170104.1	chr17	39844661	39844664	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	1665	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_71660.1	chr8	60632807	60632815	+	1	NA	promoter-TSS (NM_027756)	promoter-TSS (NM_027756)	-14	NM_027756	71306	Mm.23242	NM_027756	ENSMUSG00000031647	Mfap3l	4933428A15Rik|5430405D20Rik|AI461995|AW125052|NYD-sp9|mKIAA0626	microfibrillar-associated protein 3-like	protein-coding
mm_160885.1	chr11	69801510	69801510	-	1	NA	exon (NM_010198, exon 1 of 6)	exon (NM_010198, exon 1 of 6)	206	NM_001291104	14166	Mm.269011	NM_010198	ENSMUSG00000042826	Fgf11	Fgf-11|Fhf-3|Fhf3	fibroblast growth factor 11	protein-coding
mm_112821.1	chr13	20801166	20801177	+	1	NA	intron (NM_012054, intron 1 of 20)	RMER5|LTR|ERV1	7058	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_131483.1	chr16	17208632	17208663	+	1	NA	5' UTR (NM_001033338, exon 1 of 1)	5' UTR (NM_001033338, exon 1 of 1)	512	NM_001033338	239731	Mm.86671	NM_001033338	ENSMUSG00000071636	Rimbp3	Gm1759|Gm603|RIM-BP3|mKIAA1666	RIMS binding protein 3	protein-coding
mm_164828.1	chr18	37477847	37477856	+	1	NA	promoter-TSS (NM_053141)	promoter-TSS (NM_053141)	83	NM_053141	93887	Mm.197441	NM_053141	ENSMUSG00000047910	Pcdhb16	Pcdhb8|PcdhbP	protocadherin beta 16	protein-coding
mm_29134.1	chr3	105771006	105771011	-	1	NA	intron (NM_145541, intron 1 of 7)	intron (NM_145541, intron 1 of 7)	30373	NM_145541	109905	Mm.101922	NM_145541	ENSMUSG00000068798	Rap1a	AI848598|G-22K|Krev-1|Rap1	RAS-related protein-1a	protein-coding
mm_117810.1	chr13	97711224	97711228	-	1	NA	Intergenic	MER5A|DNA|hAT-Charlie	151226	NR_046157	328314	Mm.138047	NR_046157	ENSMUSG00000110235	Gm5086	B230311A21|EG328314	predicted gene 5086	ncRNA
mm_161256.1	chr13	108653981	108653981	+	1	NA	promoter-TSS (NM_011056)	promoter-TSS (NM_011056)	-196	NM_011056	238871	Mm.434429	NM_011056	ENSMUSG00000021699	Pde4d	9630011N22Rik|Dpde3	phosphodiesterase 4D, cAMP specific	protein-coding
mm_89576.1	chr10	95563867	95563871	+	1	NA	5' UTR (NM_027722, exon 1 of 5)	5' UTR (NM_027722, exon 1 of 5)	298	NM_027722	71207	Mm.24397	NM_027722	ENSMUSG00000020029	Nudt4	4933436C10Rik|DIPP2|DIPP2alpha|DIPP2beta|HDCMB47P	nudix (nucleoside diphosphate linked moiety X)-type motif 4	protein-coding
mm_97898.1	chr11	83409217	83409289	+	1	NA	promoter-TSS (NM_001013386)	promoter-TSS (NM_001013386)	-819	NM_001013386	276952	Mm.66275	NM_001013386	ENSMUSG00000020684	Rasl10b	B230331P10Rik|Gm729|VTS58635	RAS-like, family 10, member B	protein-coding
mm_30911.1	chr4	32445529	32445533	+	1	NA	intron (NM_001109661, intron 1 of 4)	AT_rich|Low_complexity|Low_complexity	28096	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_119336.1	chr14	40448388	40448389	+	1	NA	Intergenic	Intergenic	444577	NM_177816	328381	Mm.235694	NM_177816	ENSMUSG00000037833	Sh2d4b	A430109M18Rik|D030001E08	SH2 domain containing 4B	protein-coding
mm_70255.1	chr8	3509161	3509173	+	1	NA	exon (NM_053177, exon 7 of 14)	exon (NM_053177, exon 7 of 14)	-6217	NM_001122818	50767	Mm.23085	NM_015801	ENSMUSG00000004565	Pnpla6	AI661849|MSws|Nte	patatin-like phospholipase domain containing 6	protein-coding
mm_69492.1	chr7	134224952	134224985	-	1	NA	5' UTR (NM_007400, exon 1 of 23)	5' UTR (NM_007400, exon 1 of 23)	129	NM_007400	11489	Mm.439714	NM_007400	ENSMUSG00000054555	Adam12	Mltna	a disintegrin and metallopeptidase domain 12 (meltrin alpha)	protein-coding
mm_172003.1	chr6	107966696	107966706	+	1	NA	Intergenic	BGLII|LTR|ERVK	-98344	NM_001276356	74729	Mm.56539	NM_178391	ENSMUSG00000034639	Setmar	5830404F24Rik|Etet2	SET domain without mariner transposase fusion	protein-coding
mm_97422.1	chr11	78037911	78037922	+	1	NA	promoter-TSS (NM_001284227)	promoter-TSS (NM_001284227)	-25	NM_001040403	14252	Mm.130227	NM_008028	ENSMUSG00000061981	Flot2	AI573412|Esa|reggie-2	flotillin 2	protein-coding
mm_82684.1	chr9	22213851	22213866	-	1	NA	promoter-TSS (NR_027981)	promoter-TSS (NR_027981)	2	NR_027981	69862	Mm.488068	NM_001033151	ENSMUSG00000090925	1810064F22Rik	-	RIKEN cDNA 1810064F22 gene	ncRNA
mm_162565.1	chr1	172484271	172484274	+	1	NA	intron (NM_033608, intron 1 of 20)	intron (NM_033608, intron 1 of 20)	1955	NM_033608	93842	Mm.214530	NM_033608	ENSMUSG00000037995	Igsf9	644ETD8|Dasm1|Kiaa1355-hp|NRT1|Ncaml|mKIAA1355	immunoglobulin superfamily, member 9	protein-coding
mm_37058.1	chr4	116053385	116053404	-	1	NA	intron (NM_028142, intron 1 of 5)	G-rich|Low_complexity|Low_complexity	482	NM_028142	72181	Mm.282560	NM_028142	ENSMUSG00000028706	Nsun4	2310010O12Rik|2810405F18Rik|AI507900|Shtap	NOL1/NOP2/Sun domain family, member 4	protein-coding
mm_13011.1	chr2	90917758	90917768	+	1	NA	exon (NM_025576, exon 1 of 5)	exon (NM_025576, exon 1 of 5)	287	NM_025576	66461	Mm.23926	NM_025576		Ptpmt1	1110001D10Rik|2810004N20Rik|PLIP	protein tyrosine phosphatase, mitochondrial 1	protein-coding
mm_117383.1	chr13	73346290	73346296	-	1	NA	intron (NR_045293, intron 2 of 2)	RMER20B|LTR|ERVK	1091	NR_045293	432777	Mm.415319	NR_045293		D630045M09Rik	AU019512	RIKEN cDNA D630045M09 gene	ncRNA
mm_59636.1	chr7	28157630	28157640	+	1	NA	exon (NM_001164655, exon 16 of 20)	exon (NM_001164655, exon 16 of 20)	-12113	NM_007991	14113	Mm.4595	NM_007991	ENSMUSG00000046865	Fbl	AL022665|FIB|FLRN|RNU3IP1	fibrillarin	protein-coding
mm_34939.1	chr4	155841413	155841476	+	1	NA	intron (NM_024263, intron 3 of 9)	CpG	1764	NM_024263	74761	Mm.159028	NM_024263	ENSMUSG00000029070	Mxra8	1200013A08Rik|1700095D18Rik|AI131686|Asp3|Dicam	matrix-remodelling associated 8	protein-coding
mm_132503.1	chr16	36954682	36954704	+	1	NA	intron (NM_008225, intron 6 of 13)	intron (NM_008225, intron 6 of 13)	19710	NM_008225	15163	Mm.4091	NM_008225	ENSMUSG00000022831	Hcls1	AW213261|HS1	hematopoietic cell specific Lyn substrate 1	protein-coding
mm_40608.1	chr5	64505511	64505518	+	1	NA	Intergenic	Intergenic	28506	NR_045413	77382	Mm.366742	NR_045411	ENSMUSG00000105352	C030018K13Rik	-	RIKEN cDNA C030018K13 gene	ncRNA
mm_115538.1	chr13	6640663	6640679	-	1	NA	intron (NM_019703, intron 1 of 21)	intron (NM_019703, intron 1 of 21)	8100	NM_019703	56421	Mm.273874	NM_019703	ENSMUSG00000021196	Pfkp	1200015H23Rik|9330125N24Rik|ATP-PFK|PFK-C|PFK-P	phosphofructokinase, platelet	protein-coding
mm_11645.1	chr2	34958856	34958869	+	1	NA	intron (NM_009421, intron 3 of 10)	intron (NM_009421, intron 3 of 10)	2910	NM_009421	22029	Mm.239514	NM_009421	ENSMUSG00000026875	Traf1	4732496E14Rik	TNF receptor-associated factor 1	protein-coding
mm_98204.1	chr11	87796361	87796408	+	1	NA	exon (NM_010824, exon 7 of 14)	exon (NM_010824, exon 7 of 14)	2600	NM_010824	17523	Mm.4668	NM_010824	ENSMUSG00000009350	Mpo	mKIAA4033	myeloperoxidase	protein-coding
mm_159229.1	chr2	133553316	133553316	+	1	NA	5' UTR (NM_007553, exon 1 of 3)	5' UTR (NM_007553, exon 1 of 3)	1157	NM_007553	12156	Mm.103205	NM_007553	ENSMUSG00000027358	Bmp2	AI467020|Bmp2a	bone morphogenetic protein 2	protein-coding
mm_168360.1	chr1	115152055	115152064	+	1	NA	Intergenic	IAPLTR2b|LTR|ERVK	-533078	NM_001077425	636808	Mm.101576	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding
mm_1939.1	chr1	86191033	86191053	+	1	NA	exon (NM_027456, exon 12 of 21)	exon (NM_027456, exon 12 of 21)	36263	NM_001310702	78795	Mm.379264	NM_027456	ENSMUSG00000062590	Armc9	3830422A13Rik|4831423D23Rik|4930438O05Rik|5730415N24Rik	armadillo repeat containing 9	protein-coding
mm_129861.1	chr15	83350152	83350262	-	1	NA	promoter-TSS (NM_025445)	promoter-TSS (NM_025445)	40	NM_025445	66251	Mm.258910	NM_025445	ENSMUSG00000054277	Arfgap3	0610009H19Rik|1810004P07Rik|1810035F16Rik|9130416J18Rik|Arfgap1	ADP-ribosylation factor GTPase activating protein 3	protein-coding
mm_21036.1	chr2	152490197	152490199	-	1	NA	promoter-TSS (NM_001002791)	promoter-TSS (NM_001002791)	-60	NM_001002791	442835	Mm.99065	NM_001002791	ENSMUSG00000027468	Defb22	9230002F21Rik	defensin beta 22	protein-coding
mm_115643.1	chr13	12274137	12274156	-	1	NA	intron (NM_033268, intron 18 of 20)	B1F2|SINE|Alu	-16033	NM_001081128	238505	Mm.40335	NM_001081128	ENSMUSG00000021311	Mtr	AI894170|D830038K18Rik|MS	5-methyltetrahydrofolate-homocysteine methyltransferase	protein-coding
mm_101124.1	chr11	12037350	12037360	-	1	NA	promoter-TSS (NM_010345)	promoter-TSS (NM_010345)	65	NM_010345	14783	Mm.273117	NM_010345	ENSMUSG00000020176	Grb10	5730571D09Rik|AI325020|Meg1|mKIAA0207	growth factor receptor bound protein 10	protein-coding
mm_42620.1	chr5	118037975	118037988	+	1	NA	intron (NM_021344, intron 1 of 7)	intron (NM_021344, intron 1 of 7)	10157	NM_021344	57816	Mm.273285	NM_021344	ENSMUSG00000029359	Tesc	1010001A17Rik|2410011K10Rik|TE-1	tescalcin	protein-coding
mm_126788.1	chr15	86277637	86277682	+	1	NA	intron (NM_145476, intron 4 of 12)	intron (NM_145476, intron 4 of 12)	63200	NM_145476	223754	Mm.28904	NM_145476	ENSMUSG00000051864	Tbc1d22a	BC023106|D15Ertd781e	TBC1 domain family, member 22a	protein-coding
mm_7004.1	chr1	86467422	86467439	-	1	NA	Intergenic	Intergenic	41101	NM_027966	71863	Mm.179627	NM_027966	ENSMUSG00000036574	1700019O17Rik	-	RIKEN cDNA 1700019O17 gene	protein-coding
mm_154863.1	chrX	20662899	20662909	+	1	NA	promoter-TSS (NM_001136085)	promoter-TSS (NM_001136085)	8	NM_001136085	22201	Mm.1104	NM_009457	ENSMUSG00000001924	Uba1	A1S9|Sbx|Ube-1|Ube1x	ubiquitin-like modifier activating enzyme 1	protein-coding
mm_138577.1	chr17	35439193	35439195	+	1	NA	promoter-TSS (NM_001201460)	promoter-TSS (NM_001201460)	27	NM_001201460	110558	Mm.431282	NM_001201460		H2-Q9	H-2Q9|Ped|Qa-2|Qa-9|Qa9	histocompatibility 2, Q region locus 9	protein-coding
mm_116067.1	chr13	27637624	27637645	-	1	NA	exon (NM_001164058, exon 5 of 7)	exon (NM_001164058, exon 5 of 7)	4859	NM_001164058	19113	Mm.196424	NM_008930	ENSMUSG00000006488	Prl7a1	AA407021|AA409971|AA410116|PLP-E|PLP-G|Prlpe|Prlpg	prolactin family 7, subfamily a, member 1	protein-coding
mm_3102.1	chr1	134455510	134455523	+	1	NA	promoter-TSS (NM_153128)	promoter-TSS (NM_153128)	-15	NM_153128	240756	Mm.87398	NM_153128	ENSMUSG00000026455	Klhl12	C3ip1	kelch-like 12	protein-coding
mm_12035.1	chr2	58755678	58755687	+	1	NA	intron (NM_029692, intron 1 of 6)	RSINE1|SINE|B4	498	NM_029692	76654	Mm.200370	NM_029692	ENSMUSG00000026839	Upp2	1700124F02Rik|AI266885|UDRPASE2|UP2|UPASE2	uridine phosphorylase 2	protein-coding
mm_101796.1	chr11	46221401	46221409	-	1	NA	exon (NM_001252459, exon 26 of 31)	exon (NM_001252459, exon 26 of 31)	-10730	NR_105955	102465598		NR_105955	ENSMUSG00000099230	Mir6989	Gm27885|mmu-mir-6989	microRNA 6989	ncRNA
mm_44122.1	chr5	149527452	149527458	+	1	NA	intron (NR_045423, intron 1 of 4)	RMER17C|LTR|ERVK	-1224	NM_029440	381693	Mm.136919	NM_029440	ENSMUSG00000029658	Wdr95	4930434E21Rik	WD40 repeat domain 95	protein-coding
mm_147367.1	chr18	43438237	43438239	-	1	NA	promoter-TSS (NM_001291455)	promoter-TSS (NM_001291455)	48	NM_001291455	22240	Mm.8180	NM_009468	ENSMUSG00000024501	Dpysl3	CRMP-4|DRP-3|TUC4|ULIP-1|Ulip|Ulip1	dihydropyrimidinase-like 3	protein-coding
mm_93430.1	chr10	109010609	109010619	-	1	NA	5' UTR (NM_001252342, exon 1 of 11)	5' UTR (NM_001252342, exon 1 of 11)	361	NM_009306	20979	Mm.289702	NM_009306	ENSMUSG00000035864	Syt1	AW124717|G630098F17Rik|SytI	synaptotagmin I	protein-coding
mm_96002.1	chr11	59450041	59450095	+	1	NA	promoter-TSS (NM_178659)	promoter-TSS (NM_178659)	23	NM_001205068	194952	Mm.295954	NM_178659	ENSMUSG00000036819	Jmjd4	6430559I23	jumonji domain containing 4	protein-coding
mm_45566.1	chr5	73212639	73212646	-	1	NA	intron (NM_028194, intron 2 of 62)	intron (NM_028194, intron 2 of 62)	43976	NM_028194	72313	Mm.260594	NM_028194	ENSMUSG00000070733	Fryl	2010313D22Rik|2310004H21Rik|2510002A14Rik|9030227G01Rik|mKIAA0826	FRY like transcription coactivator	protein-coding
mm_8383.1	chr1	151252810	151252852	-	1	NA	Intergenic	Lx7|LINE|L1	-91667	NM_001039512	117198	Mm.33764	NM_028582	ENSMUSG00000023150	Ivns1abp	1190004M08Rik|1700126I16Rik|AA960440|HSPC068|ND1|NS-1|NS1-BP|Nd1-L|Nd1-S|mKIAA0850	influenza virus NS1A binding protein	protein-coding
mm_42292.1	chr5	114412546	114412555	+	1	NA	intron (NM_001331219, intron 22 of 26)	intron (NM_001331219, intron 22 of 26)	8082	NR_105994	102465621		NR_105994	ENSMUSG00000098731	Mir7027	Gm27831|mmu-mir-7027	microRNA 7027	ncRNA
mm_28715.1	chr3	95658607	95658625	-	1	NA	promoter-TSS (NM_008562)	promoter-TSS (NM_008562)	-105	NM_008562	17210	Mm.1639	NM_008562	ENSMUSG00000038612	Mcl1	AW556805|Mcl-1	myeloid cell leukemia sequence 1	protein-coding
mm_3016.1	chr1	133363782	133363813	+	1	NA	exon (NM_175443, exon 1 of 8)	exon (NM_175443, exon 1 of 8)	225	NM_175443	214253	Mm.52111	NM_175443	ENSMUSG00000070644	Etnk2	4933417N20Rik|AI197444|EKI 2|Eki2|Tuc1	ethanolamine kinase 2	protein-coding
mm_95261.1	chr11	44682440	44682442	+	1	NA	intron (NM_007897, intron 6 of 15)	intron (NM_007897, intron 6 of 15)	64341	NM_001290710	13591	Mm.439662	NM_007897	ENSMUSG00000057098	Ebf1	Ebf|O/E-1|OE-1|Olf-1|Olf1	early B cell factor 1	protein-coding
mm_153233.1	chr19	35748804	35748808	-	1	NA	Intergenic	MLT1D|LTR|ERVL-MaLR	308554	NM_001347442	15566	Mm.254266	NM_008315	ENSMUSG00000024798	Htr7	5-HT7	5-hydroxytryptamine (serotonin) receptor 7	protein-coding
mm_17692.1	chr2	32337802	32337819	-	1	NA	non-coding (NR_125959, exon 6 of 22)	non-coding (NR_125959, exon 6 of 22)	15519	NM_001301737	13429	Mm.44736	NM_010065	ENSMUSG00000026825	Dnm1	AI838169|Dnm|Ftfl|mKIAA4093	dynamin 1	protein-coding
mm_72729.1	chr8	85080850	85080854	+	1	NA	promoter-TSS (NM_026399)	promoter-TSS (NM_026399)	-106	NM_026399	67836	Mm.334680	NM_026399	ENSMUSG00000005150	Wdr83	1500041N16Rik|Morg1	WD repeat domain containing 83	protein-coding
mm_62672.1	chr7	109439127	109439137	+	1	NA	promoter-TSS (NM_054103)	promoter-TSS (NM_054103)	-79	NM_054103	117229	Mm.389950	NM_054103	ENSMUSG00000031027	Stk33	4921505G21Rik|AW061264	serine/threonine kinase 33	protein-coding
mm_165100.1	chr19	55251835	55251843	+	1	NA	Intergenic	Intergenic	-1530	NM_027976	433256	Mm.292056	NM_027976	ENSMUSG00000024981	Acsl5	1700030F05Rik|ACS2|ACS5|Facl5	acyl-CoA synthetase long-chain family member 5	protein-coding
mm_106681.1	chr12	3110064	3110073	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	-125723	NR_015551	74173	Mm.309774	NM_028796	ENSMUSG00000079179	Rab10os	1700012B15Rik|1810036A22Rik	RAB10, member RAS oncogene family, opposite strand	ncRNA
mm_123136.1	chr14	56571831	56571860	-	1	NA	promoter-TSS (NM_001014996)	promoter-TSS (NM_001014996)	1	NM_001014996	219103	Mm.212525	NM_001014996	ENSMUSG00000064128	Cenpj	4932437H03Rik|CPAP|Gm81|LAP|LIP1|Sas4	centromere protein J	protein-coding
mm_142959.1	chr17	56120614	56120620	-	1	NA	exon (NM_029796, exon 2 of 2)	exon (NM_029796, exon 2 of 2)	1329	NM_029796	76905	Mm.348025	NM_029796	ENSMUSG00000037095	Lrg1	1300008B03Rik|2310031E04Rik|Lrg|Lrhg	leucine-rich alpha-2-glycoprotein 1	protein-coding
mm_91405.1	chr10	30843134	30843163	-	1	NA	promoter-TSS (NM_013904)	promoter-TSS (NM_013904)	-365	NM_013904	15214	Mm.103573	NM_013904	ENSMUSG00000019789	Hey2	CHF1|Herp1|Hrt2|bHLHb32|hesr2	hairy/enhancer-of-split related with YRPW motif 2	protein-coding
mm_110620.1	chr12	57117632	57117634	-	1	NA	intron (NM_172577, intron 1 of 9)	intron (NM_172577, intron 1 of 9)	43010	NM_001167976	217593	Mm.32835	NM_172577	ENSMUSG00000035472	Slc25a21	9930033G19Rik|A630030I10|BB158148	solute carrier family 25 (mitochondrial oxodicarboxylate carrier), member 21	protein-coding
mm_89492.1	chr10	93831442	93831452	+	1	NA	promoter-TSS (NM_183199)	promoter-TSS (NM_183199)	-108	NM_183199	327799	Mm.491598	NM_183199	ENSMUSG00000020020	Usp44	E430004F17Rik	ubiquitin specific peptidase 44	protein-coding
mm_122992.1	chr14	54989368	54989376	-	1	NA	exon (NM_080728, exon 13 of 41)	exon (NM_080728, exon 13 of 41)	5177	NM_080728	140781	Mm.457983	NM_080728	ENSMUSG00000053093	Myh7	B-MHC|MyHC-I|Myhc-b|Myhcb|beta-MHC	myosin, heavy polypeptide 7, cardiac muscle, beta	protein-coding
mm_160964.1	chr11	99603327	99603327	-	1	NA	promoter-TSS (NM_001127354)	promoter-TSS (NM_001127354)	-19	NM_001127354	100041412	Mm.351891	NM_001127354	ENSMUSG00000057674	Gm11938	-	predicted gene 11938	protein-coding
mm_100693.1	chr11	3529881	3529889	-	1	NA	exon (NM_001284429, exon 11 of 22)	exon (NM_001284429, exon 11 of 22)	9407	NM_013870	29856	Mm.188516	NM_013870	ENSMUSG00000020439	Smtn	smsmo	smoothelin	protein-coding
mm_69433.1	chr7	132813800	132813905	-	1	NA	promoter-TSS (NM_212473)	promoter-TSS (NM_212473)	-656	NM_212473	77938	Mm.225649	NM_175268	ENSMUSG00000030956	Fam53b	A930008G19Rik|mKIAA0140	family with sequence similarity 53, member B	protein-coding
mm_154633.1	chrX	7762813	7762837	+	1	NA	5' UTR (NM_001271489, exon 1 of 10)	5' UTR (NM_001271489, exon 1 of 10)	164	NM_172472	209446	Mm.249142	NM_172472	ENSMUSG00000000134	Tfe3	F830016E06Rik|Tcfe3|Tfe-3|bHLHe33	transcription factor E3	protein-coding
mm_133715.1	chr16	93607905	93607919	+	1	NA	promoter-TSS (NM_007620)	promoter-TSS (NM_007620)	75	NM_007620	12408	Mm.26940	NM_007620	ENSMUSG00000051483	Cbr1	AW261796|CR|Cbr	carbonyl reductase 1	protein-coding
mm_25024.1	chr3	98114359	98114377	+	1	NA	intron (NM_010928, intron 14 of 33)	intron (NM_010928, intron 14 of 33)	-46266	NM_027665	71078	Mm.50711	NM_027665	ENSMUSG00000043468	Adam30	4933424D07Rik|svph4	a disintegrin and metallopeptidase domain 30	protein-coding
mm_14602.1	chr2	136501952	136501959	+	1	NA	Intergenic	Intergenic	-30366	NM_175667	319196	Mm.477841	NM_175667	ENSMUSG00000074771	Ankef1	AV276460|Ankrd5	ankyrin repeat and EF-hand domain containing 1	protein-coding
mm_127878.1	chr15	8634862	8634884	-	1	NA	3' UTR (NM_148938, exon 10 of 10)	3' UTR (NM_148938, exon 10 of 10)	75934	NM_148938	20512	Mm.204834	NM_148938	ENSMUSG00000005360	Slc1a3	AI504299|B430115D02Rik|Eaat1|GLAST|GLAST-1|GLU-T|GluT-1|Gmt1|MGluT1	solute carrier family 1 (glial high affinity glutamate transporter), member 3	protein-coding
mm_127793.1	chr15	3583147	3583187	-	1	NA	5' UTR (NM_010284, exon 1 of 11)	5' UTR (NM_010284, exon 1 of 11)	185	NM_001048178	14600	Mm.3986	NM_010284	ENSMUSG00000055737	Ghr	GHBP|GHR/BP	growth hormone receptor	protein-coding
mm_106442.1	chr11	119834409	119834421	-	1	NA	promoter-TSS (NR_045313)	promoter-TSS (NR_045313)	-50	NR_045312	319454	Mm.442144	NR_045312	ENSMUSG00000085081	Rptoros	A430071A18Rik	regulatory associated protein of MTOR, complex 1, opposite strand	ncRNA
mm_70755.1	chr8	19784624	19784658	+	1	NA	intron (NM_001270553, intron 6 of 9)	CpG	55065	NM_001039553	626415	Mm.425517	NM_001039553	ENSMUSG00000096265	4930467E23Rik	ENSMUSG00000074453|OTTMUSG00000018948|TSAP	RIKEN cDNA 4930467E23 gene	protein-coding
mm_24123.1	chr3	88200286	88200318	+	1	NA	Intergenic	Intergenic	-14869	NR_037276	100526540		NR_037276	ENSMUSG00000092988	Mir3093	mir-3093|mmu-mir-3093	microRNA 3093	ncRNA
mm_111032.1	chr12	79175881	79175898	-	1	NA	3' UTR (NM_021557, exon 7 of 7)	3' UTR (NM_021557, exon 7 of 7)	-3431	NM_016800	53612	Mm.265929	NM_016800	ENSMUSG00000021124	Vti1b	AU015348|GES30|MVti1b|SNARE|Vti1-rp1	vesicle transport through interaction with t-SNAREs 1B	protein-coding
mm_139453.1	chr17	55952629	55952699	+	1	NA	promoter-TSS (NM_015766)	promoter-TSS (NM_015766)	41	NM_015766	50498	Mm.256798	NM_015766	ENSMUSG00000003206	Ebi3	EBI-3|IL-27	Epstein-Barr virus induced gene 3	protein-coding
mm_67396.1	chr7	79878305	79878318	-	1	NA	3' UTR (NM_009682, exon 6 of 6)	3' UTR (NM_009682, exon 6 of 6)	-35959	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_25645.1	chr3	121369648	121369659	+	1	NA	Intergenic	ORR1D2|LTR|ERVL-MaLR	-56888	NM_028044	71994	Mm.275555	NM_028044	ENSMUSG00000053931	Cnn3	1600014M03Rik|C85854|Calpo3	calponin 3, acidic	protein-coding
mm_20756.1	chr2	140671407	140671427	-	1	NA	promoter-TSS (NM_178382)	promoter-TSS (NM_178382)	59	NM_001172160	71436	Mm.426781	NM_178382	ENSMUSG00000051379	Flrt3	5530600M07Rik|C430047I10Rik|mKIAA1469	fibronectin leucine rich transmembrane protein 3	protein-coding
mm_61345.1	chr7	68286167	68286178	+	1	NA	intron (NM_001013811, intron 1 of 8)	intron (NM_001013811, intron 1 of 8)	-9578	NR_040340	100504026	Mm.426764	NR_040340	ENSMUSG00000086628	Gm16157	OTTMUSG00000031023	predicted gene 16157	ncRNA
mm_140108.1	chr17	78573898	78573920	+	1	NA	intron (NM_028813, intron 4 of 13)	intron (NM_028813, intron 4 of 13)	65846	NM_028813	74199	Mm.292983	NM_028813	ENSMUSG00000024076	Vit	1700052E02Rik|1700110E08Rik|2810429K11Rik	vitrin	protein-coding
mm_88631.1	chr10	79887626	79887644	+	1	NA	exon (NM_015779, exon 4 of 5)	exon (NM_015779, exon 4 of 5)	1323	NM_015779	50701	Mm.262194	NM_015779	ENSMUSG00000020125	Elane	Ela2|F430011M15Rik|NE	elastase, neutrophil expressed	protein-coding
mm_156595.1	chrX	152235955	152235957	+	1	NA	intron (NM_013668, intron 1 of 25)	intron (NM_013668, intron 1 of 25)	2729	NM_013668	20591	Mm.142655	NM_013668	ENSMUSG00000025332	Kdm5c	D930009K15Rik|Jarid1c|Smcx|mKIAA0234	lysine (K)-specific demethylase 5C	protein-coding
mm_61486.1	chr7	75701966	75702014	+	1	NA	intron (NM_029332, intron 16 of 36)	intron (NM_029332, intron 16 of 36)	-146348	NM_001122780	207952	Mm.206223	NM_029652	ENSMUSG00000055652	Klhl25	2810402K13Rik|BC027373|Enc-1	kelch-like 25	protein-coding
mm_36824.1	chr4	105109830	105109913	-	1	NA	promoter-TSS (NM_178143)	promoter-TSS (NM_178143)	27	NM_178143	108079	Mm.48638	NM_178143	ENSMUSG00000028518	Prkaa2	2310008I11Rik|A830082D05|AMPKalpha2	protein kinase, AMP-activated, alpha 2 catalytic subunit	protein-coding
mm_30250.1	chr3	146596519	146596533	-	1	NA	promoter-TSS (NM_009474)	promoter-TSS (NM_009474)	-623	NM_009474	22262	Mm.10865	NM_009474	ENSMUSG00000028186	Uox	AI663847	urate oxidase	protein-coding
mm_94636.1	chr11	16871801	16871816	+	1	NA	exon (NM_007912, exon 10 of 16)	exon (NM_007912, exon 10 of 16)	79474	NR_110421	72735	Mm.268598	NR_015469		Eldr	2810442I21Rik|4930500E12Rik|Fabl	Egfr long non-coding downstream RNA	ncRNA
mm_170523.1	chr19	33187531	33187531	+	1	NA	intron (NM_001167818, intron 5 of 6)	(CAG)n|Simple_repeat|Simple_repeat	204764	NM_001167818	67795	Mm.204591	NM_001146342	ENSMUSG00000071573	Rnls	6530404N21Rik|AI452315|AW060440|C10orf59	renalase, FAD-dependent amine oxidase	protein-coding
mm_114282.1	chr13	58364600	58364618	+	1	NA	Intergenic	Intergenic	-9747	NM_175214	75050	Mm.446094	NM_175214	ENSMUSG00000060176	Kif27	4930517I18Rik	kinesin family member 27	protein-coding
mm_92316.1	chr10	75517274	75517309	-	1	NA	promoter-TSS (NM_026095)	promoter-TSS (NM_026095)	90	NM_175133	68778	Mm.29382	NM_175133	ENSMUSG00000033416	Gucd1	1110038D17Rik	guanylyl cyclase domain containing 1	protein-coding
mm_49974.1	chr6	40812576	40812607	+	1	NA	intron (NR_035473, intron 2 of 3)	L1_Mus3|LINE|L1	74903	NM_139296	194357	Mm.207087	NM_139296	ENSMUSG00000029885	Moxd2	Dbhl1	monooxygenase, DBH-like 2	protein-coding
mm_79464.1	chr9	56419486	56419489	+	1	NA	intron (NM_025812, intron 1 of 9)	intron (NM_025812, intron 1 of 9)	641	NM_025812	66867	Mm.150856	NM_025812	ENSMUSG00000032329	Hmg20a	1200004E06Rik|5730490E10Rik|Hmgxb1|Ibraf	high mobility group 20A	protein-coding
mm_50095.1	chr6	41533009	41533015	+	1	NA	Intergenic	Intergenic	11236	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_114760.1	chr13	85196247	85196292	+	1	NA	exon (NM_001347588, exon 3 of 9)	exon (NM_001347588, exon 3 of 9)	6884	NM_023243	66671	Mm.18474	NM_023243	ENSMUSG00000021548	Ccnh	6330408H09Rik|AI661354|AV102684|AW538719	cyclin H	protein-coding
mm_129153.1	chr15	76232062	76232076	-	1	NA	promoter-TSS (NM_001163542)	promoter-TSS (NM_001163542)	-691	NM_011117	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
mm_18908.1	chr2	76730167	76730185	-	1	NA	exon (NM_011652, exon 284 of 313)	exon (NM_011652, exon 284 of 313)	54861	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_88404.1	chr10	76717253	76717288	+	1	NA	exon (NM_009933, exon 17 of 35)	exon (NM_009933, exon 17 of 35)	8774	NM_009933	12833	Mm.2509	NM_009933	ENSMUSG00000001119	Col6a1	AI747156|Col6a-1	collagen, type VI, alpha 1	protein-coding
mm_121754.1	chr14	19626999	19627009	-	1	NA	Intergenic	Intergenic	-24417	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_113227.1	chr13	27094189	27094191	+	1	NA	promoter-TSS (NM_001205322)	promoter-TSS (NM_001205322)	1	NM_008864	18775	Mm.233151	NM_008864	ENSMUSG00000057170	Prl3d1	AI325057|Csh1|Ghd4|PL-I|PL-I-alpha|PL-Ia|Pl-1|Pl1|mPL-I	prolactin family 3, subfamily d, member 1	protein-coding
mm_42391.1	chr5	114937127	114937144	+	1	NA	exon (NM_145209, exon 7 of 7)	exon (NM_145209, exon 7 of 7)	-5067	NM_028211	72357	Mm.292672	NM_028211	ENSMUSG00000029559	2210016L21Rik	-	RIKEN cDNA 2210016L21 gene	protein-coding
mm_35181.1	chr4	15945360	15945388	-	1	NA	5' UTR (NM_026172, exon 1 of 10)	5' UTR (NM_026172, exon 1 of 10)	133	NM_026172	67460	Mm.393293	NM_026172	ENSMUSG00000028223	Decr1	1200012F07Rik|Decr|Nadph	2,4-dienoyl CoA reductase 1, mitochondrial	protein-coding
mm_63837.1	chr7	135605632	135605645	+	1	NA	promoter-TSS (NM_001316679)	promoter-TSS (NM_001316679)	-190	NM_001316679	19267	Mm.945	NM_011212	ENSMUSG00000041836	Ptpre	PTPe|PTPepsilon|RPTPepsilon	protein tyrosine phosphatase, receptor type, E	protein-coding
mm_121395.1	chr14	119137705	119137725	+	1	NA	promoter-TSS (NM_015820)	promoter-TSS (NM_015820)	-550	NM_015820	50787	Mm.445777	NM_015820	ENSMUSG00000053465	Hs6st3	6OST3|HS6ST-3	heparan sulfate 6-O-sulfotransferase 3	protein-coding
mm_30788.1	chr4	19575564	19575590	+	1	NA	intron (NM_025476, intron 1 of 9)	intron (NM_025476, intron 1 of 9)	511	NM_025476	66302	Mm.440686	NM_025476	ENSMUSG00000028229	Rmdn1	Fam82b|RMD-1	regulator of microtubule dynamics 1	protein-coding
mm_41548.1	chr5	92919623	92919666	+	1	NA	intron (NM_001077596, intron 1 of 9)	intron (NM_001077596, intron 1 of 9)	21651	NM_001077596	27428	Mm.46014	NM_015756	ENSMUSG00000029381	Shroom3	AL022960|D5Ertd287e|Shrm|Shrm3	shroom family member 3	protein-coding
mm_124234.1	chr14	101463180	101463189	-	1	NA	intron (NM_001081278, intron 11 of 18)	intron (NM_001081278, intron 11 of 18)	146007	NM_001081278	210789	Mm.320639	NM_173380	ENSMUSG00000033083	Tbc1d4	5930406J04Rik|A930035N22|AV295684|As160	TBC1 domain family, member 4	protein-coding
mm_152164.1	chr19	7295078	7295110	-	1	NA	5' UTR (NM_001080390, exon 1 of 18)	5' UTR (NM_001080390, exon 1 of 18)	353	NM_001080390	13728	Mm.258986	NM_007928	ENSMUSG00000024969	Mark2	EMK-1|Emk|Par-1|Par-1b	MAP/microtubule affinity regulating kinase 2	protein-coding
mm_83021.1	chr9	36923620	36923628	-	1	NA	exon (NM_001029838, exon 7 of 13)	exon (NM_001029838, exon 7 of 13)	79965	NM_183171	235180	Mm.5264	NM_183171	ENSMUSG00000032118	Fez1	UNC-76|UNC76	fasciculation and elongation protein zeta 1 (zygin I)	protein-coding
mm_35909.1	chr4	49844886	49844887	-	1	NA	exon (NM_001276355, exon 1 of 9)	exon (NM_001276355, exon 1 of 9)	883	NM_001033351	242443	Mm.440095	NM_001033351	ENSMUSG00000039579	Grin3a	6430537F04|A830097C19Rik|NMDAR-L|NR3A|mKIAA1973	glutamate receptor ionotropic, NMDA3A	protein-coding
mm_26942.1	chr3	20266285	20266295	-	1	NA	exon (NM_029706, exon 5 of 11)	exon (NM_029706, exon 5 of 11)	9443	NM_029706	76703	Mm.34692	NM_029706	ENSMUSG00000011463	Cpb1	0910001A18Rik|1810063F02Rik|2210008M23Rik|AI504870	carboxypeptidase B1 (tissue)	protein-coding
mm_123131.1	chr14	56262218	56262228	-	1	NA	5' UTR (NM_013542, exon 1 of 5)	5' UTR (NM_013542, exon 1 of 5)	111	NM_013542	14939	Mm.14874	NM_013542	ENSMUSG00000015437	Gzmb	AI553453|CCP-1/C11|CCP1|Ctla-1|Ctla1|GZB	granzyme B	protein-coding
mm_164078.1	chr14	122451194	122451200	-	1	NA	promoter-TSS (NR_033325)	promoter-TSS (NR_033325)	-51	NR_033326	328479	Mm.86095	NR_033325	ENSMUSG00000064052	Gm5089	6530402A20|C030005G22Rik|EG328479	predicted gene 5089	ncRNA
mm_106006.1	chr11	115808069	115808106	-	1	NA	intron (NM_080643, intron 2 of 19)	intron (NM_080643, intron 2 of 19)	5505	NM_080643	140721	Mm.383737	NM_080643	ENSMUSG00000034471	Caskin2	1600028L06Rik|mKIAA1139	CASK-interacting protein 2	protein-coding
mm_48797.1	chr5	148928821	148928825	-	1	NA	promoter-TSS (NM_153572)	promoter-TSS (NM_153572)	-176	NM_153572	231912	Mm.397405	NM_153572	ENSMUSG00000041298	Katnal1	-	katanin p60 subunit A-like 1	protein-coding
mm_11337.1	chr2	30658690	30658732	+	1	NA	non-coding (NR_136917, exon 4 of 4)	non-coding (NR_136917, exon 4 of 4)	19300	NR_136917	665635	Mm.450149	NR_136917		Gm14486	OTTMUSG00000016802	predicted gene 14486	ncRNA
mm_24095.1	chr3	88030873	88030885	+	1	NA	Intergenic	Intergenic	-3368	NM_022031	73940	Mm.294467	NM_022031	ENSMUSG00000004894	Hapln2	4930401E20Rik|Bral1	hyaluronan and proteoglycan link protein 2	protein-coding
mm_86696.1	chr10	18469939	18469949	+	1	NA	promoter-TSS (NM_001163592)	promoter-TSS (NM_001163592)	-37	NM_001163592	215819	Mm.297971	NM_173390	ENSMUSG00000039835	Nhsl1	5730409E15Rik|A630035H13Rik|A730096F01|BC013565|D10Bwg0940e|mKIAA1357	NHS-like 1	protein-coding
mm_8189.1	chr1	138099644	138099682	-	1	NA	exon (NM_001268286, exon 10 of 29)	exon (NM_001268286, exon 10 of 29)	75463	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_122283.1	chr14	34503225	34503231	-	1	NA	promoter-TSS (NM_009758)	promoter-TSS (NM_009758)	-682	NM_009758	12166	Mm.237825	NM_009758	ENSMUSG00000021796	Bmpr1a	1110037I22Rik|ALK3|AU045487|BMPR-IA|Bmpr	bone morphogenetic protein receptor, type 1A	protein-coding
mm_43888.1	chr5	143909974	143910047	+	1	NA	promoter-TSS (NM_146165)	promoter-TSS (NM_146165)	9	NM_008886	18861	Mm.2950	NM_008886	ENSMUSG00000075569	Pms2	AW555130|Pmsl2	postmeiotic segregation increased 2 (S. cerevisiae)	protein-coding
mm_93365.1	chr10	103369063	103369069	-	1	NA	intron (NM_001252330, intron 1 of 11)	intron (NM_001252330, intron 1 of 11)	1258	NM_175328	103098	Mm.458408	NM_175328	ENSMUSG00000019894	Slc6a15	AA536730|AI326450|AI326451|v7-3	solute carrier family 6 (neurotransmitter transporter), member 15	protein-coding
mm_147184.1	chr18	36783114	36783141	-	1	NA	promoter-TSS (NM_080636)	promoter-TSS (NM_080636)	78	NM_008214	15115	Mm.10528	NM_008214	ENSMUSG00000001380	Hars	MMHRS	histidyl-tRNA synthetase	protein-coding
mm_9866.1	chr1	184858412	184858417	-	1	NA	Intergenic	7SK|RNA|RNA	-12567	NM_133684	67247	Mm.177724	NM_133684	ENSMUSG00000073481	Marc2	2810484M10Rik|Mosc2|mARC1	mitochondrial amidoxime reducing component 2	protein-coding
mm_14363.1	chr2	129616508	129616520	+	1	NA	exon (NM_007547, exon 4 of 8)	exon (NM_007547, exon 4 of 8)	23345	NM_001291022	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_76204.1	chr8	83332368	83332370	-	1	NA	5' UTR (NM_178736, exon 1 of 9)	5' UTR (NM_178736, exon 1 of 9)	117	NM_001170691	244548	Mm.38762	NM_178736	ENSMUSG00000035151	Elmod2	9830169G11Rik	ELMO/CED-12 domain containing 2	protein-coding
mm_59634.1	chr7	28157572	28157581	+	1	NA	exon (NM_001164655, exon 16 of 20)	exon (NM_001164655, exon 16 of 20)	-12172	NM_007991	14113	Mm.4595	NM_007991	ENSMUSG00000046865	Fbl	AL022665|FIB|FLRN|RNU3IP1	fibrillarin	protein-coding
mm_148024.1	chr18	68590878	68590889	-	1	NA	Intergenic	Intergenic	-148517	NR_105774	102465183		NR_105774	ENSMUSG00000099300	Mir6356	Gm27461|mmu-mir-6356	microRNA 6356	ncRNA
mm_17195.1	chr2	25468090	25468110	-	1	NA	exon (NM_008963, exon 4 of 7)	exon (NM_008963, exon 4 of 7)	1649	NM_008963	19215	Mm.1008	NM_008963	ENSMUSG00000015090	Ptgds	21kDa|L-PGDS|PGD2|PGDS|PGDS2|Ptgs3	prostaglandin D2 synthase (brain)	protein-coding
mm_55692.1	chr6	72789241	72789262	-	1	NA	promoter-TSS (NM_009332)	promoter-TSS (NM_009332)	-206	NM_009332	21415	Mm.440067	NM_009332	ENSMUSG00000055799	Tcf7l1	Tcf-3|Tcf3|bHLHb21	transcription factor 7 like 1 (T cell specific, HMG box)	protein-coding
mm_35971.1	chr4	53157723	53157726	-	1	NA	intron (NM_013454, intron 1 of 49)	intron (NM_013454, intron 1 of 49)	2171	NM_013454	11303	Mm.277376	NM_013454	ENSMUSG00000015243	Abca1	ABC-1|Abc1	ATP-binding cassette, sub-family A (ABC1), member 1	protein-coding
mm_131438.1	chr16	16072743	16072751	+	1	NA	intron (NM_146068, intron 5 of 19)	intron (NM_146068, intron 5 of 19)	74104	NM_146068	224008	Mm.244703	NM_146068	ENSMUSG00000041974	Spidr	2310008H04Rik|Kiaa0146	scaffolding protein involved in DNA repair	protein-coding
mm_67173.1	chr7	73558388	73558405	-	1	NA	promoter-TSS (NR_037569)	promoter-TSS (NR_037569)	-1	NR_037569	69170	Mm.34539	NR_037569	ENSMUSG00000101970	1810026B05Rik	-	RIKEN cDNA 1810026B05 gene	ncRNA
mm_20533.1	chr2	131041318	131041356	-	1	NA	promoter-TSS (NR_105969)	promoter-TSS (NR_105969)	-939	NR_105969	102465606		NR_105969	ENSMUSG00000098686	Mir6973b	Gm27815|mmu-mir-6973b	microRNA 6973b	ncRNA
mm_135545.1	chr16	49792781	49792784	-	1	NA	Intergenic	Intergenic	-62872	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_45755.1	chr5	86795224	86795229	-	1	NA	Intergenic	MERV1_LTR|LTR|ERV1	-9040	NM_001347375	231386	Mm.196325	NM_177680	ENSMUSG00000035851	Ythdc1	A730098D12Rik|C80342|mKIAA1966	YTH domain containing 1	protein-coding
mm_85841.1	chr9	110532919	110532939	-	1	NA	intron (NM_001081340, intron 1 of 20)	CpG	332	NM_001081340	235626	Mm.288949	NM_001081340	ENSMUSG00000044791	Setd2	4921524K10Rik|BC031601|KMT3A	SET domain containing 2	protein-coding
mm_32008.1	chr4	94735212	94735224	+	1	NA	Intergenic	PB1D10|SINE|Alu	-4071	NM_001290549	21687	Mm.14313	NM_013690	ENSMUSG00000006386	Tek	AA517024|Cd202b|Hyk|STK1|Tie-2|Tie2	endothelial-specific receptor tyrosine kinase	protein-coding
mm_114319.1	chr13	60601696	60601704	+	1	NA	promoter-TSS (NM_134062)	promoter-TSS (NM_134062)	-247	NM_001285917	69635	Mm.24103	NM_029653	ENSMUSG00000021559	Dapk1	D13Ucla1|DAP-Kinase	death associated protein kinase 1	protein-coding
mm_168632.1	chr1	182393610	182393611	-	1	NA	Intergenic	Lx9|LINE|L1	-15557	NM_173378	209456	Mm.287450	NM_173378	ENSMUSG00000026510	Trp53bp2	53BP2|AI746547|ASPP2|PPP1R13A|Tp53bp2|X98550	transformation related protein 53 binding protein 2	protein-coding
mm_33715.1	chr4	133968150	133968153	+	1	NA	promoter-TSS (NM_016957)	promoter-TSS (NM_016957)	-160	NM_016957	15331	Mm.319660	NM_016957	ENSMUSG00000003038	Hmgn2	HMG-17|Hmg17	high mobility group nucleosomal binding domain 2	protein-coding
mm_27226.1	chr3	36222303	36222318	-	1	NA	promoter-TSS (NM_198192)	promoter-TSS (NM_198192)	-35	NM_198192	229214	Mm.330975	NM_198192	ENSMUSG00000058400	Qrfpr	AQ27|Gpr103|SP9155	pyroglutamylated RFamide peptide receptor	protein-coding
mm_86962.1	chr10	25128583	25128597	+	1	NA	Intergenic	RMER15|LTR|ERVL	71580	NM_001347460	432442	Mm.485937	NM_018747	ENSMUSG00000039166	Akap7	6430401D08|AI662165|AKAP15|Akap18|BB170514	A kinase (PRKA) anchor protein 7	protein-coding
mm_74488.1	chr8	4779462	4779471	-	1	NA	promoter-TSS (NM_011369)	promoter-TSS (NM_011369)	68	NM_011369	20419	Mm.37801	NM_011369	ENSMUSG00000022322	Shcbp1	mPAL	Shc SH2-domain binding protein 1	protein-coding
mm_159141.1	chr2	85823214	85823214	+	1	NA	exon (NM_146586, exon 1 of 1)	exon (NM_146586, exon 1 of 1)	241	NM_146586	258579	Mm.223106	NM_146586	ENSMUSG00000043892	Olfr1018	MOR260-5	olfactory receptor 1018	protein-coding
mm_79194.1	chr9	48495050	48495057	+	1	NA	promoter-TSS (NM_001004191)	promoter-TSS (NM_001004191)	277	NM_001326355	67010	Mm.76911	NM_144948	ENSMUSG00000042396	Rbm7	1200007M24Rik|1500011D06Rik|AU041934|AW554393	RNA binding motif protein 7	protein-coding
mm_126249.1	chr15	79028472	79028482	+	1	NA	5' UTR (NM_008197, exon 1 of 1)	5' UTR (NM_008197, exon 1 of 1)	265	NM_008197	14958	Mm.24350	NM_008197	ENSMUSG00000096210	H1f0	D130017D06Rik|H1(0)|H1fv	H1 histone family, member 0	protein-coding
mm_114908.1	chr13	94875654	94875661	+	1	NA	promoter-TSS (NM_011021)	promoter-TSS (NM_011021)	30	NM_011021	18420	Mm.42051	NM_011021	ENSMUSG00000021685	Otp	-	orthopedia homeobox	protein-coding
mm_54689.1	chr6	39420648	39420665	-	1	NA	promoter-TSS (NM_018810)	promoter-TSS (NM_018810)	-287	NM_018810	54484	Mm.270484	NM_018810	ENSMUSG00000029922	Mkrn1	RFP	makorin, ring finger protein, 1	protein-coding
mm_121997.1	chr14	26591623	26591634	-	1	NA	intron (NM_001134465, intron 1 of 19)	intron (NM_001134465, intron 1 of 19)	12078	NM_145969	211922	Mm.260512	NM_145969	ENSMUSG00000040818	Dennd6a	Fam116a	DENN/MADD domain containing 6A	protein-coding
mm_119046.1	chr14	30626335	30626359	+	1	NA	promoter-TSS (NM_011103)	promoter-TSS (NM_011103)	-139	NM_011103	18753	Mm.2314	NM_011103	ENSMUSG00000021948	Prkcd	AI385711|D14Ertd420e|PKC[d]|PKCdelta|Pkcd	protein kinase C, delta	protein-coding
mm_159922.1	chr6	54603113	54603113	+	1	NA	promoter-TSS (NM_001001335)	promoter-TSS (NM_001001335)	-34	NM_001001335	231999	Mm.35416	NM_001001335	ENSMUSG00000005225	Plekha8	6330400G01|AA517676|BC052360|Fapp-2|Fapp2	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 8	protein-coding
mm_26563.1	chr3	146500190	146500211	+	1	NA	promoter-TSS (NM_001316756)	promoter-TSS (NM_001316756)	364	NM_010318	14707	Mm.140804	NM_010318	ENSMUSG00000068523	Gng5	G(y)5	guanine nucleotide binding protein (G protein), gamma 5	protein-coding
mm_148818.1	chr19	6298701	6298738	+	1	NA	3' UTR (NM_010119, exon 5 of 5)	3' UTR (NM_010119, exon 5 of 5)	-7738	NM_001033342	240505	Mm.329622	NM_001033342	ENSMUSG00000024769	Cdc42bpg	BC046418|MRCKgamma	CDC42 binding protein kinase gamma (DMPK-like)	protein-coding
mm_91102.1	chr10	19065368	19065372	-	1	NA	Intergenic	Intergenic	-49960	NM_009397	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_1066.1	chr1	59150915	59150921	+	1	NA	intron (NM_001164682, intron 5 of 22)	intron (NM_001164682, intron 5 of 22)	10718	NM_145143	227157	Mm.474049	NM_145143	ENSMUSG00000079550	Mpp4	Dlg6	membrane protein, palmitoylated 4 (MAGUK p55 subfamily member 4)	protein-coding
mm_109837.1	chr12	4233928	4233951	-	1	NA	promoter-TSS (NM_001204912)	promoter-TSS (NM_001204912)	-88	NM_001204912	69709	Mm.250552	NM_001204912	ENSMUSG00000096199	Ptrhd1	2410017P09Rik	peptidyl-tRNA hydrolase domain containing 1	protein-coding
mm_152047.1	chr19	6141403	6141424	-	1	NA	promoter-TSS (NM_019722)	promoter-TSS (NM_019722)	-276	NM_019722	56327	Mm.21071	NM_019722	ENSMUSG00000024944	Arl2	2610009M23Rik|AI115441|AW553335	ADP-ribosylation factor-like 2	protein-coding
mm_97694.1	chr11	80154597	80154616	+	1	NA	intron (NM_172133, intron 1 of 10)	CpG	444	NM_172133	216991	Mm.341520	NM_172133	ENSMUSG00000020709	Adap2	Centa2	ArfGAP with dual PH domains 2	protein-coding
mm_113884.1	chr13	49187486	49187539	+	1	NA	promoter-TSS (NM_013610)	promoter-TSS (NM_013610)	-35	NM_013610	18081	Mm.18503	NM_013610	ENSMUSG00000037966	Ninj1	AU024536	ninjurin 1	protein-coding
mm_43945.1	chr5	145128018	145128034	+	1	NA	TTS (NM_001033313)	TTS (NM_001033313)	12063	NM_001033313	231887	Mm.188851	NM_001033313	ENSMUSG00000029623	Pdap1	HASPP28|PAP|PAP1	PDGFA associated protein 1	protein-coding
mm_6506.1	chr1	74304192	74304202	-	1	NA	5' UTR (NM_027154, exon 1 of 12)	5' UTR (NM_027154, exon 1 of 12)	139	NM_027154	69660	Mm.261182	NM_027154	ENSMUSG00000006301	Tmbim1	2310061B02Rik|AA960455|AU024746|C78899|RECS1|Tmbib1|mKIAA4161	transmembrane BAX inhibitor motif containing 1	protein-coding
mm_99436.1	chr11	102432823	102432845	+	1	NA	intron (NM_008175, intron 1 of 12)	intron (NM_008175, intron 1 of 12)	2512	NM_008175	14824	Mm.1568	NM_008175	ENSMUSG00000034708	Grn	Pgrn|epithelin	granulin	protein-coding
mm_65961.1	chr7	30435197	30435215	-	1	NA	3' UTR (NM_007467, exon 17 of 17)	3' UTR (NM_007467, exon 17 of 17)	10376	NM_007467	11803	Mm.2381	NM_007467	ENSMUSG00000006651	Aplp1	-	amyloid beta (A4) precursor-like protein 1	protein-coding
mm_165467.1	chr2	164212575	164212580	+	1	NA	Intergenic	MTD-int|LTR|ERVL-MaLR	9086	NM_138685	192201	Mm.330764	NM_138685	ENSMUSG00000018211	Wfdc15b	9230106L14Rik|SWAM1|Wfdc15	WAP four-disulfide core domain 15B	protein-coding
mm_113272.1	chr13	29172554	29172555	+	1	NA	Intergenic	ID_B1|SINE|B4	156299	NR_045075	77920	Mm.197051	NR_045073	ENSMUSG00000086363	A330102I10Rik	-	RIKEN cDNA A330102I10 gene	ncRNA
mm_21611.1	chr2	164254748	164254755	-	1	NA	3' UTR (NM_173377, exon 3 of 3)	3' UTR (NM_173377, exon 3 of 3)	1892	NM_173377	329557	Mm.118769	NM_173377	ENSMUSG00000050383	Svs3b	9530004A22Rik	seminal vesicle secretory protein 3B	protein-coding
mm_5658.1	chr1	42654493	42654497	-	1	NA	intron (NR_027826, intron 3 of 3)	Lx8|LINE|L1	40330	NR_027826	66297	Mm.45203	NM_183252	ENSMUSG00000060424	Pantr1	2610017I09Rik|Pou3f3os|linc-Brn1a	POU domain, class 3, transcription factor 3 adjacent noncoding transcript 1	ncRNA
mm_153908.1	chr19	47138180	47138190	-	1	NA	5' UTR (NM_133746, exon 1 of 3)	5' UTR (NM_133746, exon 1 of 3)	109	NM_133746	72691	Mm.31663	NM_133746	ENSMUSG00000033033	Calhm2	2810048G17Rik|Fam26b	calcium homeostasis modulator 2	protein-coding
mm_144901.1	chr18	37307446	37307462	+	1	NA	promoter-TSS (NM_053129)	promoter-TSS (NM_053129)	-1	NM_053129	93875	Mm.196711	NM_053129	ENSMUSG00000045689	Pcdhb4	Pcdhb5A|PcdhbD	protocadherin beta 4	protein-coding
mm_5693.1	chr1	43186279	43186298	-	1	NA	intron (NM_001289533, intron 1 of 5)	B4|SINE|B4	10473	NM_001289533	14200	Mm.6799	NM_010212	ENSMUSG00000008136	Fhl2	FHL-2|SLIM-3|SLIM3	four and a half LIM domains 2	protein-coding
mm_62663.1	chr7	108934518	108934528	+	1	NA	exon (NM_025344, exon 1 of 8)	exon (NM_025344, exon 1 of 8)	108	NM_025344	66085	Mm.182962	NM_025344	ENSMUSG00000031029	Eif3f	0610037M02Rik|AA409853|Eif3s5	eukaryotic translation initiation factor 3, subunit F	protein-coding
mm_66676.1	chr7	45759498	45759511	-	1	NA	promoter-TSS (NM_017465)	promoter-TSS (NM_017465)	51	NM_017465	54200	Mm.271634	NM_017465	ENSMUSG00000003271	Sult2b1	AI326997|BB173635|ST2B1|SULT2B	sulfotransferase family, cytosolic, 2B, member 1	protein-coding
mm_76754.1	chr8	95452761	95452764	-	1	NA	intron (NM_009974, intron 11 of 11)	intron (NM_009974, intron 11 of 11)	-17893	NM_008187	14894	Mm.2080	NM_008187	ENSMUSG00000031796	Cfap20	2600014O15Rik|AL024127|Gtl3|T10-2A2	cilia and flagella associated protein 20	protein-coding
mm_56386.1	chr6	94665326	94665347	-	1	NA	intron (NM_008377, intron 1 of 18)	intron (NM_008377, intron 1 of 18)	34809	NM_008377	16206	Mm.245210	NM_008377	ENSMUSG00000030029	Lrig1	D6Bwg0781e|Img|LIG-1	leucine-rich repeats and immunoglobulin-like domains 1	protein-coding
mm_23282.1	chr3	51675151	51675153	+	1	NA	intron (NM_001310482, intron 2 of 3)	intron (NM_001310482, intron 2 of 3)	13973	NM_001310482	211666	Mm.24679	NM_174995	ENSMUSG00000074604	Mgst2	GST2|MGST-II	microsomal glutathione S-transferase 2	protein-coding
mm_39000.1	chr4	151861668	151861679	-	1	NA	promoter-TSS (NM_001195565)	promoter-TSS (NM_001195565)	95	NM_001081557	100072	Mm.318846	NM_001081557	ENSMUSG00000014592	Camta1	1810059M14Rik|2310058O09Rik|AI316882|AW987475|mKIAA0833	calmodulin binding transcription activator 1	protein-coding
mm_18694.1	chr2	71546137	71546148	-	1	NA	exon (NM_010054, exon 1 of 3)	exon (NM_010054, exon 1 of 3)	612	NM_010054	13392	Mm.3896	NM_010054	ENSMUSG00000023391	Dlx2	AW121999|Dlx-2|Tes-1	distal-less homeobox 2	protein-coding
mm_90573.1	chr10	128232311	128232355	+	1	NA	TTS (NM_008600)	TTS (NM_008600)	270	NM_001136082	21853	Mm.6458	NM_011589	ENSMUSG00000039994	Timeless	C77407|Debt69|tim	timeless circadian clock 1	protein-coding
mm_92995.1	chr10	86705388	86705398	-	1	NA	promoter-TSS (NM_011631)	promoter-TSS (NM_011631)	51	NM_011631	22027	Mm.87773	NM_011631	ENSMUSG00000020048	Hsp90b1	ERp99|GRP94|TA-3|Targ2|Tra-1|Tra1|endoplasmin|gp96	heat shock protein 90, beta (Grp94), member 1	protein-coding
mm_78908.1	chr9	44773192	44773207	+	1	NA	intron (NM_023831, intron 1 of 11)	intron (NM_023831, intron 1 of 11)	190	NM_023831	76568	Mm.278597	NM_023831	ENSMUSG00000002031	Ift46	1500035H01Rik|AA408110|AI663846|R75047|c11orf2	intraflagellar transport 46	protein-coding
mm_82787.1	chr9	28996280	28996288	-	1	NA	3' UTR (NM_172290, exon 8 of 8)	3' UTR (NM_172290, exon 8 of 8)	966845	NM_172290	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding
mm_60718.1	chr7	45325237	45325258	+	1	NA	non-coding (NR_110499, exon 1 of 1)	non-coding (NR_110499, exon 1 of 1)	289	NR_110499	100040970	Mm.289810	NR_110499	ENSMUSG00000046721	Rpl14-ps1	ENSMUSG00000046721|Gm9811	ribosomal protein L14, pseudogene 1	pseudo
mm_385.1	chr1	34077191	34077219	+	1	NA	intron (NM_133833, intron 1 of 92)	intron (NM_133833, intron 1 of 92)	-40154	NR_105861	102466987		NR_105861	ENSMUSG00000105982	Mir6896	mmu-mir-6896	microRNA 6896	ncRNA
mm_32347.1	chr4	104856440	104856466	+	1	NA	exon (NM_146148, exon 5 of 11)	exon (NM_146148, exon 5 of 11)	19945	NM_001290645	230558	Mm.197638	NM_146148	ENSMUSG00000035031	C8a	-	complement component 8, alpha polypeptide	protein-coding
mm_715.1	chr1	42694894	42694942	+	1	NA	promoter-TSS (NR_027826)	promoter-TSS (NR_027826)	-93	NR_027826	66297	Mm.45203	NM_183252	ENSMUSG00000060424	Pantr1	2610017I09Rik|Pou3f3os|linc-Brn1a	POU domain, class 3, transcription factor 3 adjacent noncoding transcript 1	ncRNA
mm_71302.1	chr8	41280349	41280356	+	1	NA	intron (NM_023662, intron 14 of 37)	intron (NM_023662, intron 14 of 37)	40593	NM_023662	18536	Mm.117896	NM_023662	ENSMUSG00000031592	Pcm1	2600002H09Rik|9430077F19Rik|C030044G17Rik	pericentriolar material 1	protein-coding
mm_102285.1	chr11	55399311	55399336	-	1	NA	exon (NM_009242, exon 7 of 10)	exon (NM_009242, exon 7 of 10)	20757	NM_009242	20692	Mm.291442	NM_009242	ENSMUSG00000018593	Sparc	BM-40|ON	secreted acidic cysteine rich glycoprotein	protein-coding
mm_91045.1	chr10	18604978	18604983	-	1	NA	intron (NM_001033258, intron 26 of 33)	RMER17D|LTR|ERVK	-58904	NM_019487	56016	Mm.35551	NM_019487	ENSMUSG00000019853	Hebp2	SOUL	heme binding protein 2	protein-coding
mm_31537.1	chr4	55370195	55370337	+	1	NA	exon (NM_009011, exon 4 of 10)	exon (NM_009011, exon 4 of 10)	20224	NM_009011	19359	Mm.196846	NM_009011	ENSMUSG00000028426	Rad23b	0610007D13Rik|AV001138|HR23B|mHR23B|p58	RAD23 homolog B, nucleotide excision repair protein	protein-coding
mm_148175.1	chr18	78123381	78123390	-	1	NA	promoter-TSS (NM_028122)	promoter-TSS (NM_028122)	41	NM_001171010	108052	Mm.33832	NM_028122	ENSMUSG00000059336	Slc14a1	2610507K20Rik|3021401A05Rik|UT-B|Utb1	solute carrier family 14 (urea transporter), member 1	protein-coding
mm_168885.1	chr12	4553793	4553814	-	1	NA	Intergenic	ORR1A1|LTR|ERVL-MaLR	29690	NR_136891	102634330	Mm.402324	NR_136891		Gm31938	-	predicted gene, 31938	ncRNA
mm_7503.1	chr1	121567658	121567726	-	1	NA	intron (NM_025860, intron 1 of 12)	CpG	288	NM_025860	66942	Mm.44219	NM_025860	ENSMUSG00000001674	Ddx18	2310005B10Rik	DEAD (Asp-Glu-Ala-Asp) box polypeptide 18	protein-coding
mm_157255.1	chrX	19153479	19153507	-	1	NA	Intergenic	Intergenic	-6522	NR_029807	723828		NR_029807	ENSMUSG00000065471	Mir222	Mirn222|mir-222|mmu-mir-222	microRNA 222	ncRNA
mm_113784.1	chr13	45507565	45507576	+	1	NA	5' UTR (NM_025508, exon 1 of 9)	5' UTR (NM_025508, exon 1 of 9)	126	NM_025508	66355	Mm.290802	NM_025508	ENSMUSG00000000253	Gmpr	2310004P21Rik|AV028449|GMPR 1	guanosine monophosphate reductase	protein-coding
mm_85670.1	chr9	107676433	107676448	-	1	NA	intron (NM_008140, intron 6 of 8)	CpG-15374	3152	NM_008140	14685	Mm.284853	NM_008140	ENSMUSG00000034837	Gnat1	Gnat-1|Ird1|Ird2|Tralpha|irdc|irdr|transducin	guanine nucleotide binding protein, alpha transducing 1	protein-coding
mm_168593.1	chr1	17389768	17389781	-	1	NA	Intergenic	L1Md_T|LINE|L1	-212127	NM_053191	94227	Mm.442452	NM_053191	ENSMUSG00000067780	Pi15	P24TI|P25TI|PI-15|SugarCrisp	peptidase inhibitor 15	protein-coding
mm_142404.1	chr17	45458944	45458953	-	1	NA	intron (NM_027649, intron 3 of 7)	intron (NM_027649, intron 3 of 7)	15990	NM_027649	71020	Mm.44257	NM_027649	ENSMUSG00000023935	Spats1	1700011H05Rik|4933400B06Rik|Daip2|Ddip|Srsp1	spermatogenesis associated, serine-rich 1	protein-coding
mm_96656.1	chr11	69395748	69395754	+	1	NA	promoter-TSS (NM_030083)	promoter-TSS (NM_030083)	-40	NM_030083	78304	Mm.45683	NM_030083	ENSMUSG00000059278	Naa38	1500034E06Rik|Lsmd1	N(alpha)-acetyltransferase 38, NatC auxiliary subunit	protein-coding
mm_40321.1	chr5	43900374	43900421	+	1	NA	exon (NM_007646, exon 2 of 8)	exon (NM_007646, exon 2 of 8)	31588	NM_007646	12494	Mm.249873	NM_007646	ENSMUSG00000029084	Cd38	ADPRC 1|Cd38-rs1|I-19	CD38 antigen	protein-coding
mm_159627.1	chr4	137336142	137336142	-	1	NA	intron (NM_009861, intron 1 of 5)	intron (NM_009861, intron 1 of 5)	21617	NM_009861	12540	Mm.1022	NM_009861	ENSMUSG00000006699	Cdc42	AI747189|AU018915	cell division cycle 42	protein-coding
mm_101330.1	chr11	22982253	22982291	-	1	NA	promoter-TSS (NM_144514)	promoter-TSS (NM_144514)	12	NM_144514	17846	Mm.259903	NM_144514	ENSMUSG00000051355	Commd1	AI256843|Murr1|U2/Mu	COMM domain containing 1	protein-coding
mm_71023.1	chr8	33517307	33517325	+	1	NA	Intergenic	CpG	33005	NR_033589	628431	Mm.376526	NR_033589		Hmgb1-rs17	Hmg1-rs17	high mobility group box 1, related sequence 17	pseudo
mm_19677.1	chr2	103454516	103454534	-	1	NA	3' UTR (NM_009804, exon 13 of 13)	3' UTR (NM_009804, exon 13 of 13)	30457	NM_010125	13711	Mm.20888	NM_010125	ENSMUSG00000027186	Elf5	ESE-2|ESE-5|ESE-5.	E74-like factor 5	protein-coding
mm_38954.1	chr4	150570115	150570125	-	1	NA	intron (NM_001085492, intron 11 of 22)	intron (NM_001085492, intron 11 of 22)	82054	NM_173774	242773	Mm.29280	NM_173774	ENSMUSG00000039838	Slc45a1	C230078B22|Dnb5	solute carrier family 45, member 1	protein-coding
mm_153389.1	chr19	40382799	40382815	-	1	NA	intron (NM_001034963, intron 4 of 22)	intron (NM_001034963, intron 4 of 22)	19503	NM_001034964	20411	Mm.210815	NM_009166	ENSMUSG00000025006	Sorbs1	2310065E01Rik|9530001P15Rik|CAP|SH3P12|Sh3d5|mKIAA1296	sorbin and SH3 domain containing 1	protein-coding
mm_170509.1	chr19	27858023	27858034	+	1	NA	intron (NM_011265, intron 3 of 16)	intron (NM_011265, intron 3 of 16)	124920	NM_001166414	19726	Mm.313321	NM_011265	ENSMUSG00000040929	Rfx3	C230093O12Rik|MRFX3	regulatory factor X, 3 (influences HLA class II expression)	protein-coding
mm_19756.1	chr2	105126389	105126429	-	1	NA	promoter-TSS (NM_144783)	promoter-TSS (NM_144783)	101	NR_015462	329480	Mm.246679	NR_015462	ENSMUSG00000074987	Wt1os	6030498F17|AI314831|Wt1-as	Wilms tumor 1 homolog, opposite strand	ncRNA
mm_46995.1	chr5	115334517	115334531	-	1	NA	3' UTR (NM_029645, exon 3 of 3)	3' UTR (NM_029645, exon 3 of 3)	6637	NM_029645	384281	Mm.229308	NM_029645	ENSMUSG00000029536	Gatc	2010003O18Rik	glutamyl-tRNA(Gln) amidotransferase, subunit C	protein-coding
mm_143930.1	chr17	85928564	85928582	-	1	NA	Intergenic	Intergenic	216602	NM_030133	78586	Mm.146236	NM_030133	ENSMUSG00000024135	Srbd1	AI461933|C85414|D530025C17Rik	S1 RNA binding domain 1	protein-coding
mm_100600.1	chr11	121204755	121204781	+	1	NA	promoter-TSS (NM_025402)	promoter-TSS (NM_025402)	-120	NM_025402	66179	Mm.390403	NM_025402	ENSMUSG00000025169	Ogfod3	1110031I02Rik	2-oxoglutarate and iron-dependent oxygenase domain containing 3	protein-coding
mm_48672.1	chr5	146009097	146009112	-	1	NA	intron (NR_030782, intron 1 of 11)	MTD|LTR|ERVL-MaLR	513	NM_019792	56388	Mm.301900	NM_019792	ENSMUSG00000029630	Cyp3a25	AI327008	cytochrome P450, family 3, subfamily a, polypeptide 25	protein-coding
mm_88523.1	chr10	78057278	78057288	+	1	NA	exon (NM_019448, exon 11 of 13)	exon (NM_019448, exon 11 of 13)	1948	NM_001284200	54427	Mm.13433	NM_019448	ENSMUSG00000000730	Dnmt3l	D6Ertd14e|ecat7	DNA (cytosine-5-)-methyltransferase 3-like	protein-coding
mm_49482.1	chr6	29534010	29534025	+	1	NA	exon (NM_001252382, exon 3 of 9)	exon (NM_001252382, exon 3 of 9)	4735	NM_001252382	27056	Mm.6479	NM_012057	ENSMUSG00000029771	Irf5	AW491843|mirf5	interferon regulatory factor 5	protein-coding
mm_147523.1	chr18	52529657	52529673	-	1	NA	promoter-TSS (NM_001286181)	promoter-TSS (NM_001286181)	56	NM_001286181	16948	Mm.172	NM_010728	ENSMUSG00000024529	Lox	AI893619|TSC-160|rrg	lysyl oxidase	protein-coding
mm_107656.1	chr12	52783255	52783271	+	1	NA	intron (NM_198111, intron 1 of 13)	intron (NM_198111, intron 1 of 13)	83880	NM_198111	238161	Mm.310822	NM_198111	ENSMUSG00000061603	Akap6	AI482140|Akapalpha|Akapbeta|PRKA	A kinase (PRKA) anchor protein 6	protein-coding
mm_7943.1	chr1	133914877	133914886	-	1	NA	exon (NM_054077, exon 2 of 3)	exon (NM_054077, exon 2 of 3)	6520	NM_054077	116847	Mm.214514	NM_054077	ENSMUSG00000041577	Prelp	7330409J17Rik|SLRR2A	proline arginine-rich end leucine-rich repeat	protein-coding
mm_36998.1	chr4	110290918	110290932	-	1	NA	intron (NM_001163397, intron 1 of 5)	intron (NM_001163397, intron 1 of 5)	-3398	NM_001347178	15572	Mm.3970	NM_010488	ENSMUSG00000028546	Elavl4	Elav|Hud|PNEM	ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4 (Hu antigen D)	protein-coding
mm_80134.1	chr9	70678951	70679010	+	1	NA	promoter-TSS (NM_007399)	promoter-TSS (NM_007399)	-2	NM_007399	11487	Mm.3037	NM_007399	ENSMUSG00000054693	Adam10	1700031C13Rik|MADM|kuz|kuzbanian	a disintegrin and metallopeptidase domain 10	protein-coding
mm_157017.1	chrX	7681231	7681256	-	1	NA	promoter-TSS (NR_037581)	promoter-TSS (NR_037581)	8	NR_037581	54634	Mm.67912	NM_018832	ENSMUSG00000031147	Magix	Pdzx|Sfc18	MAGI family member, X-linked	protein-coding
mm_128949.1	chr15	74752964	74753029	-	1	NA	promoter-TSS (NM_011838)	promoter-TSS (NM_011838)	-17	NM_011838	23936	Mm.257067	NM_011838	ENSMUSG00000022594	Lynx1	AI838844|SLURP-2	Ly6/neurotoxin 1	protein-coding
mm_87574.1	chr10	56388266	56388294	+	1	NA	exon (NM_010288, exon 2 of 2)	exon (NM_010288, exon 2 of 2)	10980	NM_010288	14609	Mm.378921	NM_010288	ENSMUSG00000050953	Gja1	AU042049|AW546267|Cnx43|Cx43|Cx43alpha1|Gja-1|Npm1|connexin43	gap junction protein, alpha 1	protein-coding
mm_33260.1	chr4	127173221	127173233	+	1	NA	5' UTR (NM_001302081, exon 1 of 12)	5' UTR (NM_001302081, exon 1 of 12)	347	NM_001302081	242667	Mm.331885	NM_198618	ENSMUSG00000042388	Dlgap3	BC058433|DAP-3|DAP3|Prpl8|Sapap3	discs, large (Drosophila) homolog-associated protein 3	protein-coding
mm_131986.1	chr16	25042182	25042237	+	1	NA	Intergenic	Intergenic	-17430	NR_040374	319487	Mm.137341	NR_040374	ENSMUSG00000096960	A230028O05Rik	-	RIKEN cDNA A230028O05 gene	ncRNA
mm_92161.1	chr10	67547494	67547499	-	1	NA	3' UTR (NM_001005419, exon 1 of 1)	3' UTR (NM_001005419, exon 1 of 1)	1459	NM_001005419	211488	Mm.297250	NM_001005419	ENSMUSG00000057134	Ado	Gm237	2-aminoethanethiol (cysteamine) dioxygenase	protein-coding
mm_148704.1	chr19	5801771	5801779	+	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	897	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_169488.1	chr14	73797329	73797331	-	1	NA	Intergenic	Intergenic	244544	NM_011506	20916	Mm.38951	NM_011506	ENSMUSG00000022110	Sucla2	4930547K18Rik|A-SCS	succinate-Coenzyme A ligase, ADP-forming, beta subunit	protein-coding
mm_43940.1	chr5	145126877	145126905	+	1	NA	exon (NM_023142, exon 8 of 10)	exon (NM_023142, exon 8 of 10)	12635	NM_023142	11867	Mm.30010	NM_023142	ENSMUSG00000029622	Arpc1b	41kDa|AA408064|AA408534|AA571392|AF007010|AW208418|L72|SOP2Hs|p41-ARC	actin related protein 2/3 complex, subunit 1B	protein-coding
mm_39101.1	chr4	154921469	154921482	-	1	NA	TTS (NM_178931)	TTS (NM_178931)	6602	NM_178931	230979	Mm.215147	NM_178931	ENSMUSG00000042333	Tnfrsf14	Atar|HveA|Hvem|Tnfrs14	tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)	protein-coding
mm_115758.1	chr13	19192847	19192849	-	1	NA	Intergenic	MIR3|SINE|MIR	202965	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_29841.1	chr3	129822535	129822545	-	1	NA	promoter-TSS (NM_009102)	promoter-TSS (NM_009102)	-35	NM_009102	20132	Mm.278758	NM_009102	ENSMUSG00000028012	Rrh	-	retinal pigment epithelium derived rhodopsin homolog	protein-coding
mm_24881.1	chr3	95996107	95996126	+	1	NA	promoter-TSS (NM_023320)	promoter-TSS (NM_023320)	-277	NM_023320	67220	Mm.458147	NM_023320	ENSMUSG00000015745	Plekho1	2810052M02Rik|CKIP-1|Ckip1|JZA-20|Jza2	pleckstrin homology domain containing, family O member 1	protein-coding
mm_49357.1	chr6	22288222	22288238	+	1	NA	promoter-TSS (NM_053116)	promoter-TSS (NM_053116)	3	NM_053116	93735	Mm.137403	NM_053116	ENSMUSG00000029671	Wnt16	E130309I19Rik	wingless-type MMTV integration site family, member 16	protein-coding
mm_103752.1	chr11	80779919	80779929	-	1	NA	5' UTR (NM_177390, exon 1 of 22)	5' UTR (NM_177390, exon 1 of 22)	101	NM_177390	338367	Mm.151948	NM_177390	ENSMUSG00000035441	Myo1d	9930104H07Rik|AW544947|D11Ertd9e|myosin-1d	myosin ID	protein-coding
mm_50696.1	chr6	51597760	51597771	+	1	NA	Intergenic	Intergenic	53242	NM_001127348	71982	Mm.294166	NM_028035	ENSMUSG00000038301	Snx10	2410004M09Rik	sorting nexin 10	protein-coding
mm_147827.1	chr18	62156671	62156675	-	1	NA	Intergenic	Intergenic	23308	NM_007420	11555	Mm.5598	NM_007420	ENSMUSG00000045730	Adrb2	Adrb-2|Badm|Gpcr7	adrenergic receptor, beta 2	protein-coding
mm_4917.1	chr1	190760958	190760966	+	1	NA	Intergenic	MLT1A|LTR|ERVL-MaLR	150808	NM_178775	320119	Mm.220912	NM_178775	ENSMUSG00000089872	Rps6kc1	AA682037|B130003F20Rik|C80612|Rpk118	ribosomal protein S6 kinase polypeptide 1	protein-coding
mm_44677.1	chr5	30008837	30008845	-	1	NA	Intergenic	Intergenic	-4273	NM_001314054	16193	Mm.1019	NM_031168	ENSMUSG00000025746	Il6	Il-6	interleukin 6	protein-coding
mm_95180.1	chr11	42419702	42419719	+	1	NA	promoter-TSS (NM_008070)	promoter-TSS (NM_008070)	-47	NM_008070	14401	Mm.338723	NM_008070	ENSMUSG00000007653	Gabrb2	AI834970|C030002O17Rik|C030021G16Rik|Gabrab2|Gabrb-2	gamma-aminobutyric acid (GABA) A receptor, subunit beta 2	protein-coding
mm_144655.1	chr18	34247649	34247653	+	1	NA	intron (NM_007462, intron 1 of 15)	intron (NM_007462, intron 1 of 15)	-25879	NR_040534	633395	Mm.414290	NR_040534	ENSMUSG00000073607	Gm10548	ENSMUSG00000073607	ribosomal protein L29 pseudogene	pseudo
mm_35066.1	chr4	6454234	6454244	-	1	NA	promoter-TSS (NM_010945)	promoter-TSS (NM_010945)	32	NM_010945	18201	Mm.3059	NM_010945	ENSMUSG00000028245	Nsmaf	AA959567|C630007J05|Fan	neutral sphingomyelinase (N-SMase) activation associated factor	protein-coding
mm_104991.1	chr11	100274737	100274742	-	1	NA	Intergenic	Intergenic	-4868	NM_212483	68239	Mm.158190	NM_212483	ENSMUSG00000053654	Krt42	2410039E07Rik|K17n|Ka22|ecat6	keratin 42	protein-coding
mm_12893.1	chr2	84798553	84798588	+	1	NA	promoter-TSS (NM_019949)	promoter-TSS (NM_019949)	-258	NM_019949	56791	Mm.38261	NM_019949	ENSMUSG00000027078	Ube2l6	2810489I21Rik|RIG-B|UBCH8|Ubce8|Ubcm8	ubiquitin-conjugating enzyme E2L 6	protein-coding
mm_123577.1	chr14	67000489	67000502	-	1	NA	intron (NM_009761, intron 1 of 5)	intron (NM_009761, intron 1 of 5)	8382	NM_009761	12177	Mm.29820	NM_009761	ENSMUSG00000022051	Bnip3l	C86132|D14Ertd719e|Nip3L|Nix	BCL2/adenovirus E1B interacting protein 3-like	protein-coding
mm_123568.1	chr14	66911035	66911047	-	1	NA	promoter-TSS (NM_175498)	promoter-TSS (NM_175498)	-167	NM_175498	239157	Mm.44358	NM_175498	ENSMUSG00000046204	Pnma2	A830049P17Rik|mKIAA0883	paraneoplastic antigen MA2	protein-coding
mm_52503.1	chr6	115360855	115360881	+	1	NA	promoter-TSS (NM_001127330)	promoter-TSS (NM_001127330)	-83	NM_001127330	19016	Mm.3020	NM_011146	ENSMUSG00000000440	Pparg	Nr1c3|PPAR-gamma|PPAR-gamma2|PPARgamma|PPARgamma2	peroxisome proliferator activated receptor gamma	protein-coding
mm_11616.1	chr2	34608482	34608491	+	1	NA	intron (NM_001290626, intron 9 of 10)	MLT1F2|LTR|ERVL-MaLR	146746	NM_025709	66691	Mm.156452	NM_025709	ENSMUSG00000026867	Gapvd1	2010005B09Rik|4432404J10Rik|AW108497|Gapex-5|RAP6|RME-6|mKIAA1521	GTPase activating protein and VPS9 domains 1	protein-coding
mm_105897.1	chr11	114982619	114982636	-	1	NA	3' UTR (NM_145437, exon 4 of 4)	3' UTR (NM_145437, exon 4 of 4)	7259	NM_145437	217305	Mm.275986	NM_145437	ENSMUSG00000034641	Cd300ld	4732429D16Rik|CLM5|Cd300ld1|LMIR4|MAIR-IV|clm-5	CD300 molecule like family member d	protein-coding
mm_170170.1	chr17	55892098	55892109	+	1	NA	promoter-TSS (NM_145490)	promoter-TSS (NM_145490)	10	NM_145490	224893	Mm.294853	NM_145490	ENSMUSG00000003198	Zfp959	-	zinc finger protein 959	protein-coding
mm_63419.1	chr7	127471089	127471098	+	1	NA	promoter-TSS (NM_145589)	promoter-TSS (NM_145589)	-521	NM_145589	233895	Mm.44183	NM_145589	ENSMUSG00000030822	Prr14	BC006909	proline rich 14	protein-coding
mm_55226.1	chr6	52234818	52234825	-	1	NA	exon (NM_008263, exon 1 of 2)	exon (NM_008263, exon 1 of 2)	118	NM_008263	15395	Mm.5	NM_008263	ENSMUSG00000000938	Hoxa10	Hox-1.8|Hoxa-10	homeobox A10	protein-coding
mm_132987.1	chr16	52426163	52426180	+	1	NA	intron (NM_009655, intron 1 of 15)	intron (NM_009655, intron 1 of 15)	26910	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_114926.1	chr13	95696852	95696869	+	1	NA	promoter-TSS (NM_010170)	promoter-TSS (NM_010170)	-60	NM_010170	14064	Mm.440952	NM_010170	ENSMUSG00000021675	F2rl2	F730031A08|PAR3	coagulation factor II (thrombin) receptor-like 2	protein-coding
mm_13705.1	chr2	117157481	117157490	+	1	NA	intron (NM_033524, intron 2 of 6)	intron (NM_033524, intron 2 of 6)	-27642	NR_030440	732489		NR_030440	ENSMUSG00000076376	Mir674	Mirn674|mir-674|mmu-mir-674	microRNA 674	ncRNA
mm_1919.1	chr1	86026388	86026407	+	1	NA	intron (NM_027300, intron 2 of 3)	intron (NM_027300, intron 2 of 3)	4455	NM_027029	70060	Mm.196313	NM_027029	ENSMUSG00000026226	Spata3	1700011N12Rik|1700029H01Rik|4930424D10Rik|Mtsarg1|Tsarg1	spermatogenesis associated 3	protein-coding
mm_64585.1	chr7	145308343	145308344	+	1	NA	exon (NM_145379, exon 3 of 3)	exon (NM_145379, exon 3 of 3)	-6492	NM_203490	211578	Mm.370299	NM_203490	ENSMUSG00000051207	Mrgprd	Gm499|Mgrd|MrgD|TGR7	MAS-related GPR, member D	protein-coding
mm_10083.1	chr1	195176773	195176783	-	1	NA	promoter-TSS (NM_007758)	promoter-TSS (NM_007758)	-63	NM_007758	12902	Mm.235387	NM_007758	ENSMUSG00000026616	Cr2	C3DR|CD21|CD35|Cr-1|Cr-2|Cr1	complement receptor 2	protein-coding
mm_142977.1	chr17	56183888	56183938	-	1	NA	promoter-TSS (NM_080837)	promoter-TSS (NM_080837)	7	NM_080837	28106	Mm.294870	NM_080837	ENSMUSG00000019579	Mydgf	D17Wsu104e|Il25|Ly6elg	myeloid derived growth factor	protein-coding
mm_87590.1	chr10	57486529	57486535	+	1	NA	promoter-TSS (NR_045353)	promoter-TSS (NR_045353)	147	NM_008297	15500	Mm.261395	NM_008297	ENSMUSG00000019878	Hsf2	AI661205	heat shock factor 2	protein-coding
mm_16347.1	chr2	174346318	174346333	+	1	NA	non-coding (NR_003258, exon 13 of 13)	non-coding (NR_003258, exon 13 of 13)	16236	NM_001077510	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_49236.1	chr6	17281278	17281286	+	1	NA	promoter-TSS (NM_001277756)	promoter-TSS (NM_001277756)	97	NM_016900	12390	Mm.396075	NM_016900	ENSMUSG00000000058	Cav2	AI447843	caveolin 2	protein-coding
mm_77977.1	chr9	7870722	7870735	+	1	NA	intron (NM_007464, intron 1 of 8)	ORR1C2|LTR|ERVL-MaLR	2442	NM_007464	11796	Mm.2026	NM_007464	ENSMUSG00000032000	Birc3	AW107670|Api1|Api2|Birc2|C-IAP2|HIAP2|IAP1|IAP2|MIAP1|MIAP2|MIHB|MIHC|RNF49|cIAP-1|cIAP-2|cIAP1|cIAP2	baculoviral IAP repeat-containing 3	protein-coding
mm_44902.1	chr5	35575047	35575083	-	1	NA	promoter-TSS (NM_030208)	promoter-TSS (NM_030208)	5	NM_030208	78890	Mm.98522	NM_030208	ENSMUSG00000029097	Trmt44	2310079F23Rik|Mettl19	tRNA methyltransferase 44	protein-coding
mm_84545.1	chr9	67327648	67327666	-	1	NA	intron (NM_001081242, intron 27 of 57)	intron (NM_001081242, intron 27 of 57)	-90931	NR_029576	387185		NR_029576	ENSMUSG00000076379	Mir190a	Mir190|Mirn190|mir-190|mir-190a|mmu-mir-190|mmu-mir-190a	microRNA 190a	ncRNA
mm_79884.1	chr9	65265674	65265693	+	1	NA	intron (NM_173385, intron 1 of 9)	intron (NM_173385, intron 1 of 9)	503	NM_173385	214425	Mm.138455	NM_173385	ENSMUSG00000042254	Cilp	9830114D16|C130036G17Rik	cartilage intermediate layer protein, nucleotide pyrophosphohydrolase	protein-coding
mm_41905.1	chr5	105579526	105579533	+	1	NA	exon (NM_133897, exon 3 of 4)	exon (NM_133897, exon 3 of 4)	60058	NM_133897	100604	Mm.319847	NM_133897	ENSMUSG00000054720	Lrrc8c	AD158|AI326115|E430036I04Rik|fad158	leucine rich repeat containing 8 family, member C	protein-coding
mm_69301.1	chr7	128346072	128346092	-	1	NA	Intergenic	RSINE1|SINE|B4	-47951	NM_145590	233913	Mm.220880	NM_145590	ENSMUSG00000030780	BC017158	-	cDNA sequence BC017158	protein-coding
mm_44403.1	chr5	17842228	17842250	-	1	NA	intron (NM_001159558, intron 1 of 15)	intron (NM_001159558, intron 1 of 15)	-6343	NM_007643	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_28203.1	chr3	88296591	88296610	-	1	NA	promoter-TSS (NM_009836)	promoter-TSS (NM_009836)	238	NM_029801	76927	Mm.273330	NM_029801	ENSMUSG00000010538	Tsacc	1700021C14Rik|SIP	TSSK6 activating co-chaperone	protein-coding
mm_167632.1	chr9	62344904	62344908	-	1	NA	intron (NM_009672, intron 1 of 6)	intron (NM_009672, intron 1 of 6)	3563	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	protein-coding
mm_32676.1	chr4	115775996	115776000	+	1	NA	3' UTR (NM_172698, exon 12 of 12)	3' UTR (NM_172698, exon 12 of 12)	5036	NM_029196	75173	Mm.331798	NM_029196	ENSMUSG00000044556	Tex38	4930544O15Rik|Theg4	testis expressed 38	protein-coding
mm_87792.1	chr10	60299453	60299526	+	1	NA	exon (NM_011179, exon 10 of 15)	exon (NM_011179, exon 10 of 15)	15028	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_63728.1	chr7	130865836	130865942	+	1	NA	promoter-TSS (NM_133942)	promoter-TSS (NM_133942)	-21	NM_133942	101476	Mm.323554	NM_133942	ENSMUSG00000040268	Plekha1	AA960558|C920009D07Rik|TAPP1	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 1	protein-coding
mm_96039.1	chr11	59556473	59556482	+	1	NA	intron (NM_145827, intron 6 of 9)	ID_B1|SINE|B4	13791	NM_145827	216799	Mm.54174	NM_145827	ENSMUSG00000032691	Nlrp3	AGTAVPRL|AII/AVP|Cias1|FCAS|FCU|MWS|Mmig1|NALP3|Pypaf1	NLR family, pyrin domain containing 3	protein-coding
mm_96753.1	chr11	69901849	69901894	+	1	NA	promoter-TSS (NM_001291119)	promoter-TSS (NM_001291119)	55	NM_001013414	216860	Mm.268347	NM_001013414	ENSMUSG00000047284	Neurl4	-	neuralized E3 ubiquitin protein ligase 4	protein-coding
mm_63242.1	chr7	126585604	126585621	+	1	NA	exon (NM_138310, exon 2 of 4)	exon (NM_138310, exon 2 of 4)	205	NM_001146311	12752	Mm.268930	NM_009907	ENSMUSG00000030720	Cln3	AI323623	ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease)	protein-coding
mm_125851.1	chr15	74959224	74959233	+	1	NA	3' UTR (NM_001164036, exon 4 of 4)	3' UTR (NM_001164036, exon 4 of 4)	4122	NM_001164040	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_45110.1	chr5	45450144	45450201	-	1	NA	promoter-TSS (NM_024236)	promoter-TSS (NM_024236)	57	NM_024236	110391	Mm.30204	NM_024236	ENSMUSG00000015806	Qdpr	2610008L04Rik|D5Ertd371e|Dhpr|PKU2	quinoid dihydropteridine reductase	protein-coding
mm_23673.1	chr3	68572536	68572540	+	1	NA	5' UTR (NM_013928, exon 1 of 7)	5' UTR (NM_013928, exon 1 of 7)	170	NM_013928	30953	Mm.331064	NM_013928	ENSMUSG00000027777	Schip1	Nf2ip|Schip-1	schwannomin interacting protein 1	protein-coding
mm_59427.1	chr7	27129183	27129296	+	1	NA	exon (NM_007817, exon 5 of 10)	exon (NM_007817, exon 5 of 10)	9284	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_150285.1	chr19	34309986	34309987	+	1	NA	TTS (NM_001146708)	TTS (NM_001146708)	19327	NM_001146708	14102	Mm.1626	NM_007987	ENSMUSG00000024778	Fas	AI196731|APO1|APT1|CD95|TNFR6|Tnfrsf6|lpr	Fas (TNF receptor superfamily member 6)	protein-coding
mm_104573.1	chr11	96943946	96944023	-	1	NA	promoter-TSS (NR_003293)	promoter-TSS (NR_003293)	35	NM_134021	103711	Mm.254704	NM_134021	ENSMUSG00000018659	Pnpo	AI415282	pyridoxine 5'-phosphate oxidase	protein-coding
mm_97570.1	chr11	78938184	78938191	+	1	NA	intron (NM_001313921, intron 8 of 25)	intron (NM_001313921, intron 8 of 25)	12896	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_42459.1	chr5	115436623	115436633	+	1	NA	intron (NM_008629, intron 6 of 14)	CpG	6943	NM_008629	17690	Mm.5077	NM_008629	ENSMUSG00000054256	Msi1	Msi1h|Musahi1|m-Msi-1	musashi RNA-binding protein 1	protein-coding
mm_134174.1	chr16	10836507	10836517	-	1	NA	intron (NM_001162932, intron 1 of 1)	intron (NM_001162932, intron 1 of 1)	1453	NM_001162932	223970	Mm.325777	NM_001033278	ENSMUSG00000037991	Rmi2	A630055G03Rik|Gm537|Gm929	RecQ mediated genome instability 2	protein-coding
mm_80601.1	chr9	86545231	86545242	+	1	NA	intron (NM_177208, intron 33 of 38)	intron (NM_177208, intron 33 of 38)	26606	NM_001163746	109785	Mm.390201	NM_028352	ENSMUSG00000056131	Pgm3	2810473H05Rik|Agm1|BB187688|C77933|PAGM|Pgm-3	phosphoglucomutase 3	protein-coding
mm_39628.1	chr5	24428249	24428268	+	1	NA	intron (NM_009207, intron 2 of 22)	intron (NM_009207, intron 2 of 22)	737	NM_001253892	20535	Mm.4580	NM_009207	ENSMUSG00000028962	Slc4a2	Ae2|B3RP	solute carrier family 4 (anion exchanger), member 2	protein-coding
mm_68707.1	chr7	119793959	119793992	-	1	NA	promoter-TSS (NM_028129)	promoter-TSS (NM_028129)	83	NM_027698	71151	Mm.274160	NM_027698	ENSMUSG00000030929	Eri2	4933424N09Rik|Exod1|mKIAA1504	exoribonuclease 2	protein-coding
mm_54861.1	chr6	42597391	42597397	-	1	NA	promoter-TSS (NM_203396)	promoter-TSS (NM_203396)	-22	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_130144.1	chr15	90940681	90940706	-	1	NA	intron (NM_001109040, intron 32 of 36)	intron (NM_001109040, intron 32 of 36)	-42217	NR_033583	20738	Mm.431547	NR_033583		Spn-ps	Cd43-ps	sialophorin, pseudogene	pseudo
mm_123113.1	chr14	55885998	55886009	-	1	NA	intron (NR_138134, intron 2 of 7)	intron (NR_138134, intron 2 of 7)	1061	NR_138134	219094	Mm.37592	NM_027143	ENSMUSG00000047153	Khnyn	6330555F21|9130227C08Rik|AI605259|Kiaa0323|mKIAA0323	KH and NYN domain containing	protein-coding
mm_42988.1	chr5	123302498	123302508	+	1	NA	Intergenic	Intergenic	-41945	NM_029850	77045	Mm.151960	NM_029850	ENSMUSG00000029438	Bcl7a	4432415N06Rik|AI448316	B cell CLL/lymphoma 7A	protein-coding
mm_150921.1	chr19	46108932	46108944	+	1	NA	Intergenic	L2b|LINE|L2	-22961	NM_007703	12686	Mm.21806	NM_007703	ENSMUSG00000038754	Elovl3	CIN-2|Cig30	elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 3	protein-coding
mm_106740.1	chr12	3906809	3906821	+	1	NA	exon (NM_153743, exon 17 of 18)	exon (NM_153743, exon 17 of 18)	15071	NM_153743	13435	Mm.5001	NM_007872	ENSMUSG00000020661	Dnmt3a	MmuIIIA	DNA methyltransferase 3A	protein-coding
mm_64190.1	chr7	141461106	141461137	+	1	NA	promoter-TSS (NM_001025103)	promoter-TSS (NM_001025103)	27	NM_001025103	213573	Mm.386851	NM_001025103	ENSMUSG00000048200	Cracr2b	6330520A15Rik|BC026645|Cracr2a|Efcab4|Efcab4a	calcium release activated channel regulator 2B	protein-coding
mm_87297.1	chr10	42534643	42534669	+	1	NA	exon (NM_017472, exon 4 of 4)	exon (NM_017472, exon 4 of 4)	32602	NM_017472	54198	Mm.277870	NM_017472	ENSMUSG00000019804	Snx3	SDP3	sorting nexin 3	protein-coding
mm_69188.1	chr7	127273131	127273160	-	1	NA	exon (NM_009266, exon 1 of 1)	exon (NM_009266, exon 1 of 1)	914	NM_009266	20768	Mm.20294	NM_009266	ENSMUSG00000049091	Sephs2	Sps2|Ysg3	selenophosphate synthetase 2	protein-coding
mm_42244.1	chr5	113842145	113842153	+	1	NA	TTS (NM_011779)	TTS (NM_011779)	-11648	NM_009151	20345	Mm.332590	NM_009151	ENSMUSG00000048163	Selplg	CD162|Psgl-1|Psgl1|Selp1|Selpl	selectin, platelet (p-selectin) ligand	protein-coding
mm_21254.1	chr2	156312348	156312356	-	1	NA	promoter-TSS (NM_027585)	promoter-TSS (NM_027585)	-121	NM_027585	70873	Mm.475234	NM_027585	ENSMUSG00000038085	Cnbd2	4921517L17Rik|5430421B09Rik|Cris	cyclic nucleotide binding domain containing 2	protein-coding
mm_120431.1	chr14	65805848	65805897	+	1	NA	promoter-TSS (NM_023209)	promoter-TSS (NM_023209)	-39	NM_023209	52033	Mm.24337	NM_023209	ENSMUSG00000022033	Pbk	2810434B10Rik|AW538537|D14Ertd732e|TOPK	PDZ binding kinase	protein-coding
mm_113199.1	chr13	24943579	24943593	+	1	NA	5' UTR (NM_008156, exon 2 of 26)	5' UTR (NM_008156, exon 2 of 26)	434	NM_008156	14756	Mm.291831	NM_008156	ENSMUSG00000021340	Gpld1	6330541J12Rik|AW546131	glycosylphosphatidylinositol specific phospholipase D1	protein-coding
mm_110215.1	chr12	28623336	28623346	-	1	NA	promoter-TSS (NM_027866)	promoter-TSS (NM_027866)	-11	NM_027866	71693	Mm.30724	NM_027866	ENSMUSG00000036655	Colec11	CL-K1	collectin sub-family member 11	protein-coding
mm_100502.1	chr11	120485033	120485049	+	1	NA	intron (NM_027204, intron 1 of 4)	intron (NM_027204, intron 1 of 4)	372	NM_027204	56282	Mm.133851	NM_027204	ENSMUSG00000039640	Mrpl12	0610034O11Rik|1500031N16Rik|MRP-L12|Rpml12	mitochondrial ribosomal protein L12	protein-coding
mm_42750.1	chr5	120754108	120754123	+	1	NA	3' UTR (NM_145226, exon 16 of 16)	3' UTR (NM_145226, exon 16 of 16)	-4267	NM_001347448	246728	Mm.260926	NM_145227	ENSMUSG00000032690	Oas2	Oasl11	2'-5' oligoadenylate synthetase 2	protein-coding
mm_127748.1	chr15	103470703	103470713	+	1	NA	intron (NM_153505, intron 9 of 30)	intron (NM_153505, intron 9 of 30)	16883	NM_153505	105855	Mm.30805	NM_153505	ENSMUSG00000022488	Nckap1l	4930568P13Rik|AI463083|Hem1|Hemp1	NCK associated protein 1 like	protein-coding
mm_78893.1	chr9	44607493	44607498	+	1	NA	exon (NM_001110826, exon 2 of 14)	exon (NM_001110826, exon 2 of 14)	2603	NM_181324	13209	Mm.267061	NM_007841	ENSMUSG00000032097	Ddx6	1110001P04Rik|E230023J21Rik|HLR2|mRCK/P54|p54|rck	DEAD (Asp-Glu-Ala-Asp) box polypeptide 6	protein-coding
mm_52206.1	chr6	100835282	100835287	+	1	NA	intron (NM_182939, intron 2 of 8)	intron (NM_182939, intron 2 of 8)	1646	NM_182939	232314	Mm.27223	NM_182939	ENSMUSG00000052144	Ppp4r2	BE691708|C230060M08Rik	protein phosphatase 4, regulatory subunit 2	protein-coding
mm_41169.1	chr5	87979433	87979458	+	1	NA	promoter-TSS (NM_027631)	promoter-TSS (NM_027631)	-6	NM_027631	70977	Mm.272787	NM_027631	ENSMUSG00000007907	Cabs1	4931407G18Rik|AI428159|Clph	calcium binding protein, spermatid specific 1	protein-coding
mm_141896.1	chr17	34862474	34862535	-	1	NA	promoter-TSS (NM_008198)	promoter-TSS (NM_008198)	10	NM_001142706	14962	Mm.653	NM_008198	ENSMUSG00000090231	Cfb	AI195813|AI255840|B|Bf|C2|Fb|H2-Bf	complement factor B	protein-coding
mm_144207.1	chr18	9505679	9505686	+	1	NA	Intergenic	(CAGGA)n|Simple_repeat|Simple_repeat	-55532	NM_026484	67974	Mm.86523	NM_026484	ENSMUSG00000024286	Ccny	1700025H17Rik|3110050L10Rik|4631402G10Rik|5730405I09Rik	cyclin Y	protein-coding
mm_3560.1	chr1	150424687	150424732	+	1	NA	exon (NM_133780, exon 28 of 52)	exon (NM_133780, exon 28 of 52)	-31654	NM_145511	226499	Mm.222093	NM_145511	ENSMUSG00000006010	BC003331	1810053E15Rik|Odr4|odr-4	cDNA sequence BC003331	protein-coding
mm_91530.1	chr10	37160497	37160503	-	1	NA	Intergenic	Intergenic	-21574	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_8966.1	chr1	165194290	165194304	-	1	NA	exon (NM_145512, exon 1 of 8)	exon (NM_145512, exon 1 of 8)	136	NM_145512	108735	Mm.288369	NM_145512	ENSMUSG00000040848	Sft2d2	2010005O13Rik|AI506168|AW561909|cI-45	SFT2 domain containing 2	protein-coding
mm_77722.1	chr8	126837299	126837304	-	1	NA	Intergenic	Intergenic	108620	NM_024214	67952	Mm.6932	NM_024214	ENSMUSG00000093904	Tomm20	1810060K07Rik|BB284719|Gm19268|MAS20|MOM19|TOM20|mKIAA0016	translocase of outer mitochondrial membrane 20 homolog (yeast)	protein-coding
mm_3539.1	chr1	150393600	150393610	+	1	NA	promoter-TSS (NM_145511)	promoter-TSS (NM_145511)	-550	NM_145511	226499	Mm.222093	NM_145511	ENSMUSG00000006010	BC003331	1810053E15Rik|Odr4|odr-4	cDNA sequence BC003331	protein-coding
mm_155388.1	chrX	71915578	71915616	+	1	NA	Intergenic	Intergenic	-16841	NR_027801	382221	Mm.295937	NM_001033470	ENSMUSG00000073130	Gm1141	Pasd1	predicted gene 1141	ncRNA
mm_29006.1	chr3	101592574	101592584	-	1	NA	exon (NM_144900, exon 4 of 23)	exon (NM_144900, exon 4 of 23)	12128	NM_144900	11928	Mm.193670	NM_144900	ENSMUSG00000033161	Atp1a1	Atpa-1|BC010319	ATPase, Na+/K+ transporting, alpha 1 polypeptide	protein-coding
mm_127821.1	chr15	5116352	5116365	-	1	NA	promoter-TSS (NM_026069)	promoter-TSS (NM_026069)	-255	NM_026069	67281	Mm.10474	NM_026069	ENSMUSG00000041841	Rpl37	3110005M08Rik	ribosomal protein L37	protein-coding
mm_147976.1	chr18	67439446	67439455	-	1	NA	intron (NM_027130, intron 5 of 16)	intron (NM_027130, intron 5 of 16)	9686	NM_027130	69597	Mm.426052	NM_027130	ENSMUSG00000024527	Afg3l2	2310036I02Rik|AW260507|Emv66|par	AFG3-like AAA ATPase 2	protein-coding
mm_86534.1	chr10	7839688	7839712	+	1	NA	intron (NM_172785, intron 1 of 5)	intron (NM_172785, intron 1 of 5)	3319	NR_039563	100628581		NR_039563	ENSMUSG00000093060	Mir5104	mir-5104|mmu-mir-5104|mu-mir-5104	microRNA 5104	ncRNA
mm_135968.1	chr16	74879450	74879452	-	1	NA	Intergenic	RMER1A|Other|Other	-468539	NM_175549	268902	Mm.171736	NM_175549	ENSMUSG00000052516	Robo2	2600013A04Rik|9430089E08Rik|BB097918|D230004I22Rik|mKIAA1568	roundabout guidance receptor 2	protein-coding
mm_32039.1	chr4	95947147	95947155	+	1	NA	Intergenic	Intergenic	19884	NR_045777	319247	Mm.473527	NM_175680	ENSMUSG00000044125	9530080O11Rik	-	RIKEN cDNA 9530080O11 gene	ncRNA
mm_101906.1	chr11	49243879	49243894	-	1	NA	promoter-TSS (NM_010794)	promoter-TSS (NM_010794)	-305	NM_010794	17308	Mm.196933	NM_010794	ENSMUSG00000020346	Mgat1	Mgat-1	mannoside acetylglucosaminyltransferase 1	protein-coding
mm_90191.1	chr10	120201587	120201660	+	1	NA	promoter-TSS (NM_028679)	promoter-TSS (NM_028679)	-86	NM_028679	73914	Mm.146194	NM_028679	ENSMUSG00000020227	Irak3	4833428C18Rik|AI563835|IRAK-M	interleukin-1 receptor-associated kinase 3	protein-coding
mm_46731.1	chr5	110779938	110779943	-	1	NA	intron (NM_001347390, intron 1 of 4)	intron (NM_001347390, intron 1 of 4)	656	NM_019700	56361	Mm.23528	NM_019700	ENSMUSG00000029507	Pus1	A730013B20Rik|MPUS1|mPus1p	pseudouridine synthase 1	protein-coding
mm_141083.1	chr17	25930519	25930521	-	1	NA	intron (NM_001291025, intron 10 of 11)	intron (NM_001291025, intron 10 of 11)	-10806	NM_139154	224624	Mm.328872	NM_139154	ENSMUSG00000025730	Rab40c	RAR3	Rab40C, member RAS oncogene family	protein-coding
mm_75510.1	chr8	54525710	54525717	-	1	NA	intron (NM_029701, intron 3 of 4)	ORR1B1|LTR|ERVL-MaLR	4285	NM_029701	76687	Mm.86437	NM_029701	ENSMUSG00000054408	Spcs3	1810011E08Rik|SPC22/23	signal peptidase complex subunit 3 homolog (S. cerevisiae)	protein-coding
mm_85729.1	chr9	108340320	108340341	-	1	NA	TTS (NM_008160)	TTS (NM_008160)	1250	NM_001329528	14775	Mm.1090	NM_008160	ENSMUSG00000063856	Gpx1	AI195024|AL033363|CGPx|GPx-1|GSHPx-1|Gpx	glutathione peroxidase 1	protein-coding
mm_107525.1	chr12	40465728	40465769	+	1	NA	intron (NM_172803, intron 1 of 52)	intron (NM_172803, intron 1 of 52)	19695	NM_172803	238130	Mm.341423	NM_172803	ENSMUSG00000035954	Dock4	5330406C03|6330411N01Rik|AF263288|C030023J22|mKIAA0716	dedicator of cytokinesis 4	protein-coding
mm_105967.1	chr11	115491159	115491198	-	1	NA	promoter-TSS (NR_136931)	promoter-TSS (NR_136931)	-351	NR_136931	102634812	Mm.390379	NR_136931		LOC102634812	-	ribosomal protein L39 pseudogene	pseudo
mm_65722.1	chr7	28380282	28380285	-	1	NA	Intergenic	PB1D11|SINE|Alu	-1055	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_127436.1	chr15	101270267	101270284	+	1	NA	exon (NM_010444, exon 2 of 7)	exon (NM_010444, exon 2 of 7)	3429	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_149175.1	chr19	9135155	9135160	+	1	NA	intron (NM_025610, intron 1 of 6)	intron (NM_025610, intron 1 of 6)	409	NM_025610	66514	Mm.272847	NM_025610	ENSMUSG00000024654	Asrgl1	2410004D18Rik|ALP|ALP1|AU040643|AW060375	asparaginase like 1	protein-coding
mm_10462.1	chr2	14310900	14310905	+	1	NA	intron (NM_008625, intron 21 of 29)	intron (NM_008625, intron 21 of 29)	49899	NR_030609	100124488		NR_030609	ENSMUSG00000077897	Mir511	Mirn511|mir-511|mmu-mir-511	microRNA 511	ncRNA
mm_102173.1	chr11	53980272	53980283	-	1	NA	promoter-TSS (NM_019723)	promoter-TSS (NM_019723)	-250	NM_019723	56517	Mm.154284	NM_019723	ENSMUSG00000063652	Slc22a21	Octn3|Slc22a9	solute carrier family 22 (organic cation transporter), member 21	protein-coding
mm_48954.1	chr6	4540675	4540679	+	1	NA	3' UTR (NM_007743, exon 52 of 52)	3' UTR (NM_007743, exon 52 of 52)	35059	NM_007743	12843	Mm.277792	NM_007743	ENSMUSG00000029661	Col1a2	AA960264|AI325291|Col1a-2|Cola-2|Cola2|oim	collagen, type I, alpha 2	protein-coding
mm_157628.1	chrX	56598032	56598045	-	1	NA	promoter-TSS (NM_146234)	promoter-TSS (NM_146234)	-119	NM_146234	236792	Mm.291824	NM_146234	ENSMUSG00000061273	Mmgt1	9630048L06Rik|BC032271|Emc5|Mir5116|Tmem32|mir-5116	membrane magnesium transporter 1	protein-coding
mm_41137.1	chr5	87825676	87825754	+	1	NA	promoter-TSS (NM_001163551)	promoter-TSS (NM_001163551)	18	NM_001163551	73779	Mm.263642	NM_028648	ENSMUSG00000002240	Prr27	4930432K09Rik	proline rich 27	protein-coding
mm_19697.1	chr2	103761079	103761090	-	1	NA	5' UTR (NM_153126, exon 1 of 29)	5' UTR (NM_153126, exon 1 of 29)	166	NM_153126	98956	Mm.288005	NM_153126	ENSMUSG00000027185	Nat10	AI429152	N-acetyltransferase 10	protein-coding
mm_147345.1	chr18	43322463	43322471	-	1	NA	3' UTR (NM_001291455, exon 14 of 14)	3' UTR (NM_001291455, exon 14 of 14)	50805	NM_001136086	22240	Mm.8180	NM_009468	ENSMUSG00000024501	Dpysl3	CRMP-4|DRP-3|TUC4|ULIP-1|Ulip|Ulip1	dihydropyrimidinase-like 3	protein-coding
mm_56669.1	chr6	113639364	113639377	-	1	NA	intron (NM_001113553, intron 1 of 11)	B1_Mur3|SINE|Alu	903	NM_001113553	108960	Mm.152142	NM_172161	ENSMUSG00000060477	Irak2	6330415L08Rik|AI649099|IRAK-2	interleukin-1 receptor-associated kinase 2	protein-coding
mm_87910.1	chr10	62300550	62300570	+	1	NA	intron (NM_001146100, intron 3 of 17)	intron (NM_001146100, intron 3 of 17)	39861	NM_001146100	15275	Mm.196605	NM_010438	ENSMUSG00000037012	Hk1	BB404130|Hk-1|Hk1-s|dea|mHk1-s	hexokinase 1	protein-coding
mm_96452.1	chr11	67564477	67564487	+	1	NA	intron (NM_008088, intron 1 of 13)	intron (NM_008088, intron 1 of 13)	-22018	NM_001109657	14457	Mm.40338	NM_008088	ENSMUSG00000033066	Gas7	AW124766|B230343A10Rik|Gas7-cb	growth arrest specific 7	protein-coding
mm_88900.1	chr10	81173304	81173327	+	1	NA	Intergenic	Intergenic	-3316	NM_007907	13629	Mm.2903	NM_007907	ENSMUSG00000034994	Eef2	Ef-2	eukaryotic translation elongation factor 2	protein-coding
mm_16072.1	chr2	168125711	168125716	+	1	NA	Intergenic	B1_Mur2|SINE|Alu	28800	NR_040327	77017	Mm.407822	NR_040327	ENSMUSG00000087648	E130018N17Rik	-	RIKEN cDNA E130018N17 gene	ncRNA
mm_126959.1	chr15	92321883	92321895	+	1	NA	intron (NM_007727, intron 23 of 23)	intron (NM_007727, intron 23 of 23)	-74921	NM_001164593	239618	Mm.309826	NM_001164593	ENSMUSG00000036218	Pdzrn4	1110017D07Rik|LNX4|SAMCAP3L|mKIAA3027	PDZ domain containing RING finger 4	protein-coding
mm_100274.1	chr11	117762499	117762513	+	1	NA	3' UTR (NM_198022, exon 22 of 22)	3' UTR (NM_198022, exon 22 of 22)	18115	NM_181321	217353	Mm.286963	NM_145439	ENSMUSG00000025572	Tmc6	D11Ertd204e|EVER1	transmembrane channel-like gene family 6	protein-coding
mm_55673.1	chr6	72552220	72552231	-	1	NA	intron (NM_001271395, intron 1 of 9)	MER31A|LTR|ERV1	2578	NM_001271395	12332	Mm.18626	NM_007599	ENSMUSG00000056737	Capg	gCap39|mbh1	capping protein (actin filament), gelsolin-like	protein-coding
mm_44716.1	chr5	30945672	30945676	-	1	NA	promoter-TSS (NM_026770)	promoter-TSS (NM_026770)	-194	NM_026770	68567	Mm.45127	NM_026770	ENSMUSG00000029161	Cgref1	1110004G24Rik|AW045201|Cgr11	cell growth regulator with EF hand domain 1	protein-coding
mm_55725.1	chr6	74025746	74025746	-	1	NA	Intergenic	Intergenic	-554725	NR_108032	73408	Mm.233629	NR_108032	ENSMUSG00000107408	1700065L07Rik	-	RIKEN cDNA 1700065L07 gene	ncRNA
mm_127131.1	chr15	98165738	98165746	+	1	NA	promoter-TSS (NM_001170711)	promoter-TSS (NM_001170711)	-164	NM_001170711	78541	Mm.200766	NM_030121	ENSMUSG00000048175	Asb8	4930539L19Rik|AI788835|C430011H06Rik	ankyrin repeat and SOCS box-containing 8	protein-coding
mm_128329.1	chr15	38294980	38294983	-	1	NA	3' UTR (NM_013692, exon 4 of 4)	3' UTR (NM_013692, exon 4 of 4)	5730	NM_013692	21847	Mm.4292	NM_013692	ENSMUSG00000037465	Klf10	AI115143|EGR[a]|Egral|Gdnfif|TIEG-1|Tieg|Tieg1|mGIF	Kruppel-like factor 10	protein-coding
mm_156596.1	chrX	152251277	152251280	+	1	NA	intron (NM_013668, intron 10 of 25)	intron (NM_013668, intron 10 of 25)	18051	NM_013668	20591	Mm.142655	NM_013668	ENSMUSG00000025332	Kdm5c	D930009K15Rik|Jarid1c|Smcx|mKIAA0234	lysine (K)-specific demethylase 5C	protein-coding
mm_76912.1	chr8	105932402	105932411	-	1	NA	TTS (NM_173432)	TTS (NM_173432)	1456	NM_023182	109660	Mm.2745	NM_023182	ENSMUSG00000031896	Ctrl	0910001G08Rik|1810004D15Rik|AV005227|Ctra-1|Ctra1|chymopasin|mFLJ00366	chymotrypsin-like	protein-coding
mm_94029.1	chr10	127751740	127751751	-	1	NA	promoter-TSS (NM_007412)	promoter-TSS (NM_007412)	53	NM_007412	11536	Mm.2857	NM_007412	ENSMUSG00000058396	Gpr182	AM-R|Admr|G10-D|Gpcr17|Gpcr22|MB10|NOW	G protein-coupled receptor 182	protein-coding
mm_77098.1	chr8	110997765	110997839	-	1	NA	promoter-TSS (NM_007916)	promoter-TSS (NM_007916)	21	NM_007916	13680	Mm.287901	NM_007916	ENSMUSG00000015023	Ddx19a	DBP5|Ddx19|Eif4a-rs1	DEAD (Asp-Glu-Ala-Asp) box polypeptide 19a	protein-coding
mm_109212.1	chr12	108677754	108677760	+	1	NA	intron (NM_001163394, intron 7 of 13)	RLTR21|LTR|ERVK	19137	NR_029771	723909		NR_029771	ENSMUSG00000065436	Mir342	Mirn342|mmu-mir-342	microRNA 342	ncRNA
mm_60916.1	chr7	46831009	46831026	+	1	NA	Intergenic	Intergenic	-14787	NM_010699	16828	Mm.29324	NM_010699	ENSMUSG00000063229	Ldha	Ldh1|Ldhm|l7R2	lactate dehydrogenase A	protein-coding
mm_47618.1	chr5	125179156	125179229	-	1	NA	promoter-TSS (NM_001253904)	promoter-TSS (NM_001253904)	22	NM_001253905	20602	Mm.278646	NM_011424	ENSMUSG00000029478	Ncor2	N-CoR|SMRT|SMRTe	nuclear receptor co-repressor 2	protein-coding
mm_81119.1	chr9	106460691	106460698	+	1	NA	exon (NM_021567, exon 5 of 13)	exon (NM_021567, exon 5 of 13)	5246	NM_001159652	436090	Mm.482905	NM_001159652	ENSMUSG00000091735	Gpr62	4933402E03Rik	G protein-coupled receptor 62	protein-coding
mm_61498.1	chr7	75753517	75753526	+	1	NA	3' UTR (NM_029332, exon 37 of 37)	3' UTR (NM_029332, exon 37 of 37)	-94817	NM_001122780	207952	Mm.206223	NM_029652	ENSMUSG00000055652	Klhl25	2810402K13Rik|BC027373|Enc-1	kelch-like 25	protein-coding
mm_21622.1	chr2	164277078	164277082	-	1	NA	exon (NM_009300, exon 2 of 3)	exon (NM_009300, exon 2 of 3)	1227	NM_009300	20941	Mm.1286	NM_009300	ENSMUSG00000016998	Svs4	SVS-IV|Svp-2|Svp-4|Svp2|Svp4	seminal vesicle secretory protein 4	protein-coding
mm_63836.1	chr7	135537845	135537859	+	1	NA	promoter-TSS (NM_011212)	promoter-TSS (NM_011212)	28	NM_001316678	19267	Mm.945	NM_011212	ENSMUSG00000041836	Ptpre	PTPe|PTPepsilon|RPTPepsilon	protein tyrosine phosphatase, receptor type, E	protein-coding
mm_129664.1	chr15	81190721	81190768	-	1	NA	promoter-TSS (NM_001082536)	promoter-TSS (NM_001082536)	13	NM_001082536	223701	Mm.439814	NM_153049	ENSMUSG00000042292	Mkl1	AMKL|Bsac|Mal|Mrtf-A	MKL (megakaryoblastic leukemia)/myocardin-like 1	protein-coding
mm_161580.1	chr16	31429435	31429435	+	1	NA	intron (NM_001122683, intron 1 of 6)	CpG	682	NM_001122683	71911	Mm.293470	NM_175177	ENSMUSG00000046598	Bdh1	2310032J20Rik|AI327223|Bdh	3-hydroxybutyrate dehydrogenase, type 1	protein-coding
mm_170657.1	chr2	105948995	105948998	-	1	NA	intron (NM_028260, intron 5 of 6)	intron (NM_028260, intron 5 of 6)	44358	NM_028260	66541	Mm.272253	NM_028260	ENSMUSG00000042670	Immp1l	1500034J20Rik|2610528O17Rik|AU042386	IMP1 inner mitochondrial membrane peptidase-like (S. cerevisiae)	protein-coding
mm_18154.1	chr2	45090840	45090844	-	1	NA	intron (NM_001289521, intron 1 of 8)	ID_B1|SINE|B4	19435	NM_001289521	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_100473.1	chr11	120041069	120041070	+	1	NA	intron (NM_001198785, intron 1 of 13)	intron (NM_001198785, intron 1 of 13)	712	NM_001198787	11302	Mm.6826	NM_007377	ENSMUSG00000025375	Aatk	AATYK|aatyk1|mKIAA0641	apoptosis-associated tyrosine kinase	protein-coding
mm_52780.1	chr6	121249370	121249385	+	1	NA	intron (NM_011909, intron 1 of 10)	intron (NM_011909, intron 1 of 10)	3471	NM_011909	24110	Mm.326911	NM_011909	ENSMUSG00000030107	Usp18	1110058H21Rik|AW047653|UBP43|Ubp15	ubiquitin specific peptidase 18	protein-coding
mm_58433.1	chr7	3297599	3297606	+	1	NA	exon (NM_016969, exon 3 of 3)	exon (NM_016969, exon 3 of 3)	4574	NM_001093766	50918	Mm.29874	NM_016969	ENSMUSG00000068566	Myadm	D7Wsu62e	myeloid-associated differentiation marker	protein-coding
mm_170506.1	chr19	24875648	24875648	+	1	NA	Intergenic	Intergenic	-13806	NM_175013	226041	Mm.105222	NM_175013	ENSMUSG00000041731	Pgm5	4833423B07|9530034F03Rik|D830025G17|aciculin	phosphoglucomutase 5	protein-coding
mm_35966.1	chr4	53144092	53144111	-	1	NA	intron (NM_013454, intron 1 of 49)	intron (NM_013454, intron 1 of 49)	15794	NM_013454	11303	Mm.277376	NM_013454	ENSMUSG00000015243	Abca1	ABC-1|Abc1	ATP-binding cassette, sub-family A (ABC1), member 1	protein-coding
mm_11521.1	chr2	32609048	32609084	+	1	NA	intron (NM_001289549, intron 2 of 6)	intron (NM_001289549, intron 2 of 6)	2081	NR_110347	50935	Mm.88831	NM_016973	ENSMUSG00000026811	St6galnac6	ST6GalNAcVI|Siat7f	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 6	protein-coding
mm_85404.1	chr9	103365600	103365613	-	1	NA	promoter-TSS (NM_001134427)	promoter-TSS (NM_001134427)	174	NM_175833	321022	Mm.261025	NM_175565	ENSMUSG00000032803	Cdv3	2510010F10Rik|C230084J24Rik|C79446|TPP36	carnitine deficiency-associated gene expressed in ventricle 3	protein-coding
mm_56430.1	chr6	97312276	97312289	-	1	NA	intron (NM_001346639, intron 11 of 22)	intron (NM_001346639, intron 11 of 22)	-59502	NM_001081157	320502	Mm.68163	NM_001081157	ENSMUSG00000044086	Lmod3	5430424A14Rik	leiomodin 3 (fetal)	protein-coding
mm_142124.1	chr17	35897300	35897324	-	1	NA	promoter-TSS (NM_001033630)	promoter-TSS (NM_001033630)	66	NM_001033630	69662	Mm.260159	NM_001033630	ENSMUSG00000050705	2310061I04Rik	-	RIKEN cDNA 2310061I04 gene	protein-coding
mm_75031.1	chr8	32009471	32009480	-	1	NA	Intergenic	CpG	-91272	NM_178591	211323	Mm.153432	NM_178591	ENSMUSG00000062991	Nrg1	6030402G23Rik|ARIA|D230005F13Rik|GGF|GGFII|HRG|HRGalpha|Hgl|NDF|SMDF	neuregulin 1	protein-coding
mm_3150.1	chr1	135147630	135147668	+	1	NA	intron (NM_026823, intron 1 of 6)	intron (NM_026823, intron 1 of 6)	815	NM_026823	68724	Mm.174998	NM_026823	ENSMUSG00000026426	Arl8a	1110033P22Rik|Arl10b|gie2	ADP-ribosylation factor-like 8A	protein-coding
mm_141627.1	chr17	32917049	32917118	-	1	NA	promoter-TSS (NM_022434)	promoter-TSS (NM_022434)	4	NM_022434	64385	Mm.486449	NM_022434	ENSMUSG00000024292	Cyp4f14	1300014O15Rik|cyp4f-14	cytochrome P450, family 4, subfamily f, polypeptide 14	protein-coding
mm_103264.1	chr11	71144801	71144813	-	1	NA	promoter-TSS (NM_001004142)	promoter-TSS (NM_001004142)	-103	NM_001004142	195046	Mm.240227	NM_001004142	ENSMUSG00000069830	Nlrp1a	CARD7|DEFCAP|Gm14|Gm15|NAC|Nalp1|Nalp1a|Nlrp1|PP1044	NLR family, pyrin domain containing 1A	protein-coding
mm_39283.1	chr5	3936519	3936522	+	1	NA	intron (NM_194462, intron 1 of 47)	intron (NM_194462, intron 1 of 47)	8334	NM_194462	100986	Mm.46044	NM_194462	ENSMUSG00000040407	Akap9	5730481H23Rik|AKAP-9|AKAP450|AW545847|C79026|G1-448-15|PRKA9|mKIAA0803|mei2-5|repro12	A kinase (PRKA) anchor protein (yotiao) 9	protein-coding
mm_28238.1	chr3	88458853	88458899	-	1	NA	promoter-TSS (NM_001163491)	promoter-TSS (NM_001163491)	8	NM_001163491	20351	Mm.439752	NM_013658	ENSMUSG00000028064	Sema4a	AI132332|SemB|Semab	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A	protein-coding
mm_124376.1	chr14	106267753	106267757	-	1	NA	Intergenic	Intergenic	161557	NR_073203	212085	Mm.78128	NM_198601	ENSMUSG00000022113	Trim52	4921513B05Rik	tripartite motif-containing 52	protein-coding
mm_66887.1	chr7	59244268	59244273	-	1	NA	intron (NM_011668, intron 3 of 12)	intron (NM_011668, intron 3 of 12)	15518	NM_011668	22215	Mm.9002	NM_011668	ENSMUSG00000025326	Ube3a	4732496B02|5830462N02Rik|A130086L21Rik|Hpve6a|mKIAA4216	ubiquitin protein ligase E3A	protein-coding
mm_113827.1	chr13	47043882	47043905	+	1	NA	promoter-TSS (NM_016785)	promoter-TSS (NM_016785)	394	NM_172262	218214	Mm.31259	NM_172262	ENSMUSG00000038080	Kdm1b	4632428N09Rik|AI482520|Aof1	lysine (K)-specific demethylase 1B	protein-coding
mm_159362.1	chr3	87687907	87687907	+	1	NA	exon (NM_001003912, exon 6 of 40)	exon (NM_001003912, exon 6 of 40)	60716	NM_028971	74485	Mm.474494	NM_028971	ENSMUSG00000023084	Lrrc71	4933430H15Rik	leucine rich repeat containing 71	protein-coding
mm_14429.1	chr2	130541296	130541323	+	1	NA	exon (NM_008980, exon 14 of 22)	exon (NM_008980, exon 14 of 22)	22440	NR_040348	321014	Mm.442588	NR_040348	ENSMUSG00000060029	4930473A02Rik	-	RIKEN cDNA 4930473A02 gene	ncRNA
mm_61691.1	chr7	81057590	81057603	+	1	NA	promoter-TSS (NM_054085)	promoter-TSS (NM_054085)	-4	NM_054085	116904	Mm.475768	NM_054085	ENSMUSG00000038763	Alpk3	AW319487|D330016D04|MAK|Midori|mKIAA1330	alpha-kinase 3	protein-coding
mm_27687.1	chr3	65974691	65974697	-	1	NA	Intergenic	CpG	-16469	NM_019937	56706	Mm.175612	NM_019937	ENSMUSG00000027829	Ccnl1	2610030E23Rik|AU018493|Ccnl|ania-6a	cyclin L1	protein-coding
mm_169100.1	chr1	34163649	34163651	+	1	NA	exon (NM_134448, exon 15 of 98)	exon (NM_134448, exon 15 of 98)	3320	NM_010081	13518	Mm.336625	NM_010081	ENSMUSG00000026131	Dst	2310001O04Rik|A830042E19Rik|AW554249|BP230|BPAG1-n|Bpag|Bpag1|Macf2|ah|athetoid|dt|mKIAA0728|nmf203|nmf339	dystonin	protein-coding
mm_36111.1	chr4	58878855	58878859	-	1	NA	intron (NM_172381, intron 3 of 48)	intron (NM_172381, intron 3 of 48)	33868	NM_172381	230249	Mm.234801	NM_172381	ENSMUSG00000050812	AI314180	AW558785|BB181316|mKIAA0368	expressed sequence AI314180	protein-coding
mm_142618.1	chr17	46880528	46880532	-	1	NA	Intergenic	Intergenic	-10091	NM_178385	72726	Mm.33780	NM_178385	ENSMUSG00000036430	Tbcc	2810055C19Rik	tubulin-specific chaperone C	protein-coding
mm_3309.1	chr1	137898710	137898731	+	1	NA	Intergenic	Intergenic	-67735	NR_029795	735252		NR_029795	ENSMUSG00000065565	Mir181a-1	Mirn181a-1|Mirn213|miR-213|mir-181a-1|mmu-mir-213	microRNA 181a-1	ncRNA
mm_58676.1	chr7	11899933	11899937	+	1	NA	Intergenic	Intergenic	19592	NM_134207	171241	Mm.377197	NM_134207	ENSMUSG00000043308	Vmn1r75	V1rg6	vomeronasal 1 receptor 75	protein-coding
mm_15612.1	chr2	160757157	160757166	+	1	NA	intron (NM_021280, intron 23 of 33)	intron (NM_021280, intron 23 of 33)	25851	NM_021280	18803	Mm.44463	NM_021280	ENSMUSG00000016933	Plcg1	AI894140|Cded|Plc-1|Plc-gamma1|Plcg-1	phospholipase C, gamma 1	protein-coding
mm_146972.1	chr18	33463822	33463856	-	1	NA	promoter-TSS (NM_001267717)	promoter-TSS (NM_001267717)	-140	NM_001109989	27528	Mm.407415	NM_053078	ENSMUSG00000042834	Nrep	AI325076|D0H4S114|Harp|P311|PTZ17|SEZ17	neuronal regeneration related protein	protein-coding
mm_15562.1	chr2	158512806	158512812	+	1	NA	promoter-TSS (NM_001145015)	promoter-TSS (NM_001145015)	13	NM_001145015	545481	Mm.125371	NM_001145015	ENSMUSG00000074625	Arhgap40	C20orf95|Gm14203|OTTMUSG00000015933	Rho GTPase activating protein 40	protein-coding
mm_84690.1	chr9	72271325	72271327	-	1	NA	Intergenic	MTB|LTR|ERVL-MaLR	-3562	NM_146224	235469	Mm.242791	NM_146224	ENSMUSG00000038535	Zfp280d	A930005F02Rik|BC027163|Suhw4|ZNF634|Znf280d	zinc finger protein 280D	protein-coding
mm_148390.1	chr19	3388923	3388931	+	1	NA	promoter-TSS (NM_001286558)	promoter-TSS (NM_001286558)	70	NM_001039657	17771	Mm.209941	NM_010841	ENSMUSG00000024905	Mtl5	tesmin	metallothionein-like 5, testis-specific (tesmin)	protein-coding
mm_142241.1	chr17	37482467	37482479	-	1	NA	intron (NM_001347387, intron 3 of 4)	intron (NM_001347387, intron 3 of 4)	1056	NM_008204	14990	Mm.329041	NM_008204	ENSMUSG00000016283	H2-M2	H-2M2|Thy19.4	histocompatibility 2, M region locus 2	protein-coding
mm_65200.1	chr7	19696910	19696910	-	1	NA	exon (NM_009696, exon 4 of 4)	exon (NM_009696, exon 4 of 4)	1488	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_44714.1	chr5	30945597	30945622	-	1	NA	promoter-TSS (NM_026770)	promoter-TSS (NM_026770)	-129	NM_026770	68567	Mm.45127	NM_026770	ENSMUSG00000029161	Cgref1	1110004G24Rik|AW045201|Cgr11	cell growth regulator with EF hand domain 1	protein-coding
mm_974.1	chr1	58393120	58393147	+	1	NA	promoter-TSS (NM_025824)	promoter-TSS (NM_025824)	-3	NM_025824	66882	Mm.21848	NM_025824	ENSMUSG00000051223	Bzw1	1200015E15Rik|mKIAA0005	basic leucine zipper and W2 domains 1	protein-coding
mm_110294.1	chr12	32208528	32208542	-	1	NA	promoter-TSS (NM_001146201)	promoter-TSS (NM_001146201)	-65	NM_020272	30955	Mm.101369	NM_020272	ENSMUSG00000020573	Pik3cg	5830428L06Rik|PI3Kgamma|p110gamma	phosphoinositide-3-kinase, catalytic, gamma polypeptide	protein-coding
mm_147575.1	chr18	56419109	56419117	-	1	NA	Intergenic	Intergenic	-13019	NM_026240	107022	Mm.24356	NM_026240	ENSMUSG00000001700	Gramd3	9030613F08Rik|9130427A09Rik|AW061306|NS3TP2	GRAM domain containing 3	protein-coding
mm_162143.1	chrX	74393290	74393290	+	1	NA	promoter-TSS (NM_001161424)	promoter-TSS (NM_001161424)	-1	NM_001161424	16151	Mm.12967	NM_010547	ENSMUSG00000004221	Ikbkg	1110037D23Rik|AI848108|AI851264|AW124339|IKK[g]|NEMO	inhibitor of kappaB kinase gamma	protein-coding
mm_100537.1	chr11	120633184	120633194	+	1	NA	intron (NM_010756, intron 1 of 2)	CpG	358	NM_010756	17134	Mm.268010	NM_010756	ENSMUSG00000051510	Mafg	AA545192|C630022N07Rik	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein G (avian)	protein-coding
mm_42187.1	chr5	112269458	112269464	+	1	NA	exon (NM_001312894, exon 6 of 6)	exon (NM_001312894, exon 6 of 6)	-7230	NM_001326590	22022	Mm.250631	NM_009419	ENSMUSG00000029344	Tpst2	AI448750|D5Ucla3|Tango13b|grm|grt	protein-tyrosine sulfotransferase 2	protein-coding
mm_171660.1	chr4	44065861	44065863	-	1	NA	intron (NM_015828, intron 2 of 11)	intron (NM_015828, intron 2 of 11)	6811	NM_001190414	50798	Mm.256718	NM_015828	ENSMUSG00000028479	Gne	2310066H07Rik|DMRV|GLCNE|IBM2|NM|Uae1	glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase	protein-coding
mm_111244.1	chr12	84801789	84801832	-	1	NA	intron (NM_013589, intron 16 of 34)	intron (NM_013589, intron 16 of 34)	28540	NM_028863	74316	Mm.25719	NM_028863	ENSMUSG00000021241	Isca2	0710001C05Rik|5730594E03Rik|Hbld1	iron-sulfur cluster assembly 2	protein-coding
mm_106147.1	chr11	116579628	116579631	-	1	NA	intron (NM_173755, intron 1 of 17)	B1_Mur2|SINE|Alu	1818	NM_173755	217342	Mm.243950	NM_173755	ENSMUSG00000020802	Ube2o	9630022H21|B230113M03Rik|E2-230K|mKIAA1734	ubiquitin-conjugating enzyme E2O	protein-coding
mm_57288.1	chr6	124433434	124433438	-	1	NA	intron (NM_001346656, intron 16 of 17)	intron (NM_001346656, intron 16 of 17)	-18369	NM_001277805	19305	Mm.22418	NM_008995	ENSMUSG00000005069	Pex5	AW212715|ESTM1|PTS1R|Pxr1|X83306	peroxisomal biogenesis factor 5	protein-coding
mm_129021.1	chr15	74955497	74955507	-	1	NA	5' UTR (NM_001164036, exon 1 of 4)	5' UTR (NM_001164036, exon 1 of 4)	396	NM_001164040	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_68301.1	chr7	105745766	105745781	-	1	NA	3' UTR (NM_009906, exon 13 of 13)	3' UTR (NM_009906, exon 13 of 13)	-1435	NM_020024	24075	Mm.274846	NM_020024	ENSMUSG00000043866	Taf10	30kDa|AU041226|TAFII30|Taf2h	TATA-box binding protein associated factor 10	protein-coding
mm_102848.1	chr11	69369683	69369706	-	1	NA	promoter-TSS (NM_146019)	promoter-TSS (NM_146019)	-268	NM_146019	216848	Mm.178246	NM_146019	ENSMUSG00000018474	Chd3	2600010P09Rik|AF020312|Chd7|Prp7|Prp9-1	chromodomain helicase DNA binding protein 3	protein-coding
mm_19907.1	chr2	114175300	114175317	-	1	NA	promoter-TSS (NM_009702)	promoter-TSS (NM_009702)	31	NM_009702	11834	Mm.2545	NM_009702	ENSMUSG00000040383	Aqr	AW495846|mKIAA0560	aquarius	protein-coding
mm_28362.1	chr3	89870218	89870226	-	1	NA	3' UTR (NM_010559, exon 10 of 10)	3' UTR (NM_010559, exon 10 of 10)	38852	NM_172530	214547	Mm.225	NM_172530	ENSMUSG00000046280	She	9430022A14	src homology 2 domain-containing transforming protein E	protein-coding
mm_55614.1	chr6	72042570	72042572	-	1	NA	promoter-TSS (NR_046180)	promoter-TSS (NR_046180)	-43	NR_046180	330350	Mm.246787	NR_046180	ENSMUSG00000108356	9130221F21Rik	9130221F21	RIKEN cDNA 9130221F21 gene	ncRNA
mm_13664.1	chr2	114061185	114061195	+	1	NA	non-coding (NR_028422, exon 3 of 3)	non-coding (NR_028422, exon 3 of 3)	6794	NR_028422	100303644	Mm.330469	NR_028422	ENSMUSG00000092397	C130080G10Rik	-	RIKEN cDNA C130080G10 gene	ncRNA
mm_21146.1	chr2	154364037	154364049	-	1	NA	intron (NM_025876, intron 5 of 13)	RSINE1|SINE|B4	8676	NM_025876	66971	Mm.289427	NM_025876	ENSMUSG00000027487	Cdk5rap1	2310066P17Rik	CDK5 regulatory subunit associated protein 1	protein-coding
mm_52977.1	chr6	123260527	123260536	+	1	NA	Intergenic	Intergenic	-1576	NM_001163161	17474	Mm.441101	NM_010819	ENSMUSG00000030144	Clec4d	Clecsf8|Mpcl|mcl	C-type lectin domain family 4, member d	protein-coding
mm_91132.1	chr10	19598169	19598183	-	1	NA	intron (NM_010511, intron 2 of 6)	MRLTR33|LTR|ERVK	6227	NM_010511	15979	Mm.549	NM_010511	ENSMUSG00000020009	Ifngr1	CD119|IFN-gammaR|Ifgr|Ifngr|Nktar	interferon gamma receptor 1	protein-coding
mm_41991.1	chr5	107726142	107726167	+	1	NA	promoter-TSS (NM_001267621)	promoter-TSS (NM_001267621)	-349	NM_001267621	14581	Mm.2078	NM_010278	ENSMUSG00000029275	Gfi1	AW495828|Gfi-1|Pal-1|Pal1	growth factor independent 1	protein-coding
mm_77655.1	chr8	124569697	124569714	-	1	NA	promoter-TSS (NM_007428)	promoter-TSS (NM_007428)	2	NM_007428	11606	Mm.301626	NM_007428	ENSMUSG00000031980	Agt	AI265500|AngI|AngII|Aogen|Serpina8	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	protein-coding
mm_133902.1	chr16	97548623	97548641	+	1	NA	intron (NM_013606, intron 7 of 13)	L1_Mur3|LINE|L1	12549	NM_013606	17858	Mm.14157	NM_013606	ENSMUSG00000023341	Mx2	AI528743|Mx-2	MX dynamin-like GTPase 2	protein-coding
mm_79830.1	chr9	64790957	64790967	+	1	NA	Intergenic	Intergenic	-20049	NM_001162917	102442	Mm.222473	NM_176935	ENSMUSG00000053641	Dennd4a	AI115600|AI851943|F730015K02Rik	DENN/MADD domain containing 4A	protein-coding
mm_81769.1	chr9	114411012	114411015	+	1	NA	3' UTR (NM_001200002, exon 2 of 2)	3' UTR (NM_001200002, exon 2 of 2)	9918	NM_001200002	100504715	Mm.290516	NM_001200002	ENSMUSG00000079260	Tmppe	-	transmembrane protein with metallophosphoesterase domain	protein-coding
mm_88893.1	chr10	81139506	81139512	+	1	NA	intron (NM_010731, intron 1 of 2)	intron (NM_010731, intron 1 of 2)	3238	NM_010731	16969	Mm.20920	NM_010731	ENSMUSG00000035011	Zbtb7a	9030619K07Rik|9130006G12Rik|AI452336|FBI-1|Lrf|Pokemon|Zbtb7	zinc finger and BTB domain containing 7a	protein-coding
mm_3991.1	chr1	164443227	164443260	+	1	NA	exon (NM_009721, exon 3 of 6)	exon (NM_009721, exon 3 of 6)	15112	NM_009721	11931	Mm.4550	NM_009721	ENSMUSG00000026576	Atp1b1	Atp4b|Atpb|Atpb-1|NKbeta1	ATPase, Na+/K+ transporting, beta 1 polypeptide	protein-coding
mm_84987.1	chr9	86464945	86464958	-	1	NA	promoter-TSS (NM_027394)	promoter-TSS (NM_027394)	-35	NM_027394	70348	Mm.53469	NM_027394	ENSMUSG00000032415	Ube2cbp	2610018I03Rik|Ube3d	ubiquitin-conjugating enzyme E2C binding protein	protein-coding
mm_133587.1	chr16	91421774	91421796	+	1	NA	exon (NM_008349, exon 6 of 7)	exon (NM_008349, exon 6 of 7)	15550	NM_008349	16155	Mm.4154	NM_008349	ENSMUSG00000022969	Il10rb	6620401D04Rik|AI528744|CRF2-4|Crfb4|D16H21S58|D21S58h|IL-10R2|Il10r2	interleukin 10 receptor, beta	protein-coding
mm_116934.1	chr13	55831379	55831395	-	1	NA	promoter-TSS (NM_011097)	promoter-TSS (NM_011097)	38	NM_011097	18740	Mm.135195	NM_011097	ENSMUSG00000021506	Pitx1	Bft|P-OTX|Potx|Ptx1	paired-like homeodomain transcription factor 1	protein-coding
mm_93411.1	chr10	108443049	108443051	-	1	NA	Intergenic	MT2B2|LTR|ERVL	110861	NM_054056	114774	Mm.391419	NM_054056	ENSMUSG00000035873	Pawr	2310001G03Rik|PAR4|Par-4	PRKC, apoptosis, WT1, regulator	protein-coding
mm_96786.1	chr11	69965494	69965510	+	1	NA	promoter-TSS (NM_016887)	promoter-TSS (NM_016887)	81	NM_016887	53624	Mm.281896	NM_016887	ENSMUSG00000018569	Cldn7	-	claudin 7	protein-coding
mm_21116.1	chr2	153492556	153492566	-	1	NA	intron (NM_001134300, intron 1 of 10)	CpG	37410	NM_001134300	329540	Mm.50600	NM_001001986	ENSMUSG00000061411	Nol4l	4931410H15|8430427H17Rik|AI429157|Gm1636	nucleolar protein 4-like	protein-coding
mm_18413.1	chr2	60673645	60673653	-	1	NA	promoter-TSS (NM_021359)	promoter-TSS (NM_021359)	44	NM_021359	16420	Mm.98193	NM_021359	ENSMUSG00000026971	Itgb6	2210409C20Rik|4831415H04Rik	integrin beta 6	protein-coding
mm_76439.1	chr8	84990912	84990927	-	1	NA	intron (NM_133255, intron 1 of 21)	intron (NM_133255, intron 1 of 21)	324	NM_001167991	170833	Mm.247775	NM_133255	ENSMUSG00000052566	Hook2	A630054I03Rik	hook microtubule tethering protein 2	protein-coding
mm_58282.1	chr6	145862635	145862680	-	1	NA	3' UTR (NM_001271768, exon 5 of 5)	3' UTR (NM_001271768, exon 5 of 5)	2763	NM_001271768	79362	Mm.154529	NM_024469	ENSMUSG00000030256	Bhlhe41	6430520M22Rik|Bhlhb2l|Bhlhb3|DEC2|Sharp1	basic helix-loop-helix family, member e41	protein-coding
mm_135891.1	chr16	64873930	64873942	-	1	NA	Intergenic	Intergenic	21851	NM_178647	106143	Mm.10160	NM_178647	ENSMUSG00000054604	Cggbp1	AA960172|AL023996|AW045841	CGG triplet repeat binding protein 1	protein-coding
mm_71719.1	chr8	61951821	61951823	+	1	NA	intron (NM_001293783, intron 8 of 37)	Lx3C|LINE|L1	23735	NM_001293783	234311	Mm.275233	NM_144928	ENSMUSG00000037921	Ddx60	9830118M07	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	protein-coding
mm_62948.1	chr7	119580931	119580934	+	1	NA	intron (NM_001177978, intron 8 of 13)	intron (NM_001177978, intron 8 of 13)	19224	NM_001177978	233799	Mm.268448	NM_146197	ENSMUSG00000030945	Acsm2	AI315615|BC031140	acyl-CoA synthetase medium-chain family member 2	protein-coding
mm_1469.1	chr1	69826987	69827003	+	1	NA	promoter-TSS (NM_029160)	promoter-TSS (NM_029160)	25	NM_001271533	66722	Mm.440554	NM_025728	ENSMUSG00000053153	Spag16	4921511D23Rik|4930524F24Rik|4930585K05Rik|AV261009|Pf20|Wdr29	sperm associated antigen 16	protein-coding
mm_150108.1	chr19	29522413	29522423	+	1	NA	promoter-TSS (NR_015567)	promoter-TSS (NR_015567)	136	NM_001081319	226089	Mm.353838	NM_177641	ENSMUSG00000038658	Ric1	C030046E11Rik|C130057E09Rik|Kiaa1432	RAB6A GEF complex partner 1	protein-coding
mm_76977.1	chr8	106573462	106573462	-	1	NA	Intergenic	Intergenic	-13681	NR_045470	68692	Mm.416843	NR_045470	ENSMUSG00000099139	1110028F18Rik	-	RIKEN cDNA 1110028F18 gene	ncRNA
mm_122937.1	chr14	54963936	54963950	-	1	NA	exon (NM_010856, exon 4 of 39)	exon (NM_010856, exon 4 of 39)	2664	NM_001164171	17888	Mm.290003	NM_010856	ENSMUSG00000040752	Myh6	A830009F23Rik|AA517445|Myhc-a|Myhca|alpha-MHC	myosin, heavy polypeptide 6, cardiac muscle, alpha	protein-coding
mm_5711.1	chr1	43827724	43827742	-	1	NA	promoter-TSS (NM_026430)	promoter-TSS (NM_026430)	-25	NM_026430	67883	Mm.387202	NM_026430	ENSMUSG00000057363	Uxs1	1600025I13Rik|AI451869|AI649125|AW550562	UDP-glucuronate decarboxylase 1	protein-coding
mm_48093.1	chr5	137046027	137046085	-	1	NA	promoter-TSS (NM_007457)	promoter-TSS (NM_007457)	4	NM_007457	11769	Mm.833	NM_007457	ENSMUSG00000004849	Ap1s1	AP19	adaptor protein complex AP-1, sigma 1	protein-coding
mm_126500.1	chr15	81745173	81745188	+	1	NA	5' UTR (NM_001081016, exon 1 of 23)	5' UTR (NM_001081016, exon 1 of 23)	332	NM_001081016	20286	Mm.432075	NM_001081016	ENSMUSG00000022390	Zc3h7b	Gm627|Scrg3|Zc2h7b|mKIAA1031	zinc finger CCCH type containing 7B	protein-coding
mm_17648.1	chr2	31492343	31492365	-	1	NA	exon (NM_007494, exon 8 of 16)	exon (NM_007494, exon 8 of 16)	22046	NR_002687	432466	Mm.333323	NR_002687	ENSMUSG00000046687	Gm5424	EG432466	argininosuccinate synthase pseudogene	pseudo
mm_44205.1	chr5	3803082	3803119	-	1	NA	promoter-TSS (NM_001003909)	promoter-TSS (NM_001003909)	24	NM_001289528	70797	Mm.130148	NM_001003909	ENSMUSG00000040351	Ankib1	2310061P20Rik|4631416I11Rik|AW494740|C80642|mKIAA1386	ankyrin repeat and IBR domain containing 1	protein-coding
mm_173114.1	chrX	159510803	159510817	-	1	NA	Intergenic	MERV1_I-int|LTR|ERV1	-21858	NM_001033472	382252	Mm.296254	NM_001033472	ENSMUSG00000044150	A830080D01Rik	2310067E24Rik|Gm1146	RIKEN cDNA A830080D01 gene	protein-coding
mm_130535.1	chr15	98934603	98934612	-	1	NA	promoter-TSS (NM_011654)	promoter-TSS (NM_011654)	-217	NM_011654	22143	Mm.392113	NM_011654	ENSMUSG00000023004	Tuba1b	Tuba2	tubulin, alpha 1B	protein-coding
mm_67750.1	chr7	92618975	92618978	-	1	NA	intron (NM_028665, intron 5 of 11)	B3A|SINE|B2	18166	NM_028665	73845	Mm.73248	NM_028665	ENSMUSG00000041343	Ankrd42	4931426M20|4933417L02Rik|Ikbn	ankyrin repeat domain 42	protein-coding
mm_51716.1	chr6	86849444	86849454	+	1	NA	promoter-TSS (NM_177762)	promoter-TSS (NM_177762)	-9	NR_028298	67170	Mm.119489	NR_028298	ENSMUSG00000100164	2610306M01Rik	-	RIKEN cDNA 2610306M01 gene	ncRNA
mm_157859.1	chrX	75111992	75112011	-	1	NA	exon (NM_008621, exon 11 of 12)	exon (NM_008621, exon 11 of 12)	16147	NM_001030307	245474	Mm.291062	NM_001030307	ENSMUSG00000031403	Dkc1	BC068171	dyskeratosis congenita 1, dyskerin	protein-coding
mm_115375.1	chr13	113086233	113086252	+	1	NA	intron (NM_001281487, intron 11 of 11)	Lx8|LINE|L1	14739	NM_010370	14938	Mm.15510	NM_010370	ENSMUSG00000023132	Gzma	AW494114|Ctla-3|Ctla3|Hf|Hf1|SE1|TSP-1|TSP1	granzyme A	protein-coding
mm_58298.1	chr6	145865484	145865536	-	1	NA	promoter-TSS (NM_001271768)	promoter-TSS (NM_001271768)	-90	NM_024469	79362	Mm.154529	NM_024469	ENSMUSG00000030256	Bhlhe41	6430520M22Rik|Bhlhb2l|Bhlhb3|DEC2|Sharp1	basic helix-loop-helix family, member e41	protein-coding
mm_42471.1	chr5	115454486	115454506	+	1	NA	TTS (NM_008629)	TTS (NM_008629)	-11770	NM_011107	18778	Mm.20190	NM_011107	ENSMUSG00000029522	Pla2g1b	Pla2a|sPLA2IB	phospholipase A2, group IB, pancreas	protein-coding
mm_37738.1	chr4	129578513	129578517	-	1	NA	promoter-TSS (NM_182783)	promoter-TSS (NM_182783)	65	NM_182783	230766	Mm.20377	NM_182783	ENSMUSG00000050493	Fam167b	SEC	family with sequence similarity 167, member B	protein-coding
mm_25846.1	chr3	129461948	129461948	+	1	NA	Intergenic	Intergenic	28275	NR_033594	435755	Mm.430561	NR_033594	ENSMUSG00000105712	Pou5f1-rs4	EG435755|Gm5712|Oct4P1|Otf3-rs4|Otf3d	POU domain, class 5, transcription factor 1, related sequence 4	pseudo
mm_13958.1	chr2	121359274	121359278	+	1	NA	intron (NM_009897, intron 1 of 8)	intron (NM_009897, intron 1 of 8)	635	NM_009897	12716	Mm.252145	NM_009897	ENSMUSG00000000308	Ckmt1	Mt-CK|ScCKmit|UbCKmit|mi-CK	creatine kinase, mitochondrial 1, ubiquitous	protein-coding
mm_78813.1	chr9	44069463	44069478	+	1	NA	promoter-TSS (NM_016808)	promoter-TSS (NM_016808)	41	NM_016808	53376	Mm.272770	NM_016808	ENSMUSG00000032010	Usp2	B930035K21Rik|Ubp41	ubiquitin specific peptidase 2	protein-coding
mm_121340.1	chr14	115201587	115201593	+	1	NA	intron (NM_175500, intron 2 of 7)	(T)n|Simple_repeat|Simple_repeat	109375	NM_175500	103978	Mm.320791	NM_175500	ENSMUSG00000022112	Gpc5	A230034F01Rik	glypican 5	protein-coding
mm_90450.1	chr10	127703466	127703517	+	1	NA	Intergenic	Intergenic	-1765	NM_001081219	432516	Mm.90450	NM_001081219	ENSMUSG00000025401	Myo1a	BBM-I|Myhl	myosin IA	protein-coding
mm_105774.1	chr11	109721705	109721716	-	1	NA	exon (NM_153782, exon 1 of 11)	exon (NM_153782, exon 1 of 11)	546	NM_153782	208659	Mm.208662	NM_153782	ENSMUSG00000020614	Fam20a	AI606893	family with sequence similarity 20, member A	protein-coding
mm_167343.1	chr8	77955856	77955864	+	1	NA	Intergenic	Intergenic	-231408	NM_010332	13617	Mm.283168	NM_010332	ENSMUSG00000031616	Ednra	ET-AR|ETa|Gpcr10	endothelin receptor type A	protein-coding
mm_48957.1	chr6	4540865	4540875	+	1	NA	3' UTR (NM_007743, exon 52 of 52)	3' UTR (NM_007743, exon 52 of 52)	35252	NM_007743	12843	Mm.277792	NM_007743	ENSMUSG00000029661	Col1a2	AA960264|AI325291|Col1a-2|Cola-2|Cola2|oim	collagen, type I, alpha 2	protein-coding
mm_113783.1	chr13	45507528	45507549	+	1	NA	promoter-TSS (NM_025508)	promoter-TSS (NM_025508)	94	NM_025508	66355	Mm.290802	NM_025508	ENSMUSG00000000253	Gmpr	2310004P21Rik|AV028449|GMPR 1	guanosine monophosphate reductase	protein-coding
mm_6150.1	chr1	64937825	64937836	-	1	NA	exon (NM_001039493, exon 2 of 8)	exon (NM_001039493, exon 2 of 8)	18994	NM_001039493	241075	Mm.239534	NM_175509	ENSMUSG00000051344	Plekhm3	9430067K14Rik|A230102O09Rik|AI449570|DAPR|Plekhm1l	pleckstrin homology domain containing, family M, member 3	protein-coding
mm_155710.1	chrX	96096035	96096056	+	1	NA	promoter-TSS (NM_010833)	promoter-TSS (NM_010833)	0	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_138549.1	chr17	35264047	35264058	+	1	NA	exon (NM_001267808, exon 7 of 11)	exon (NM_001267808, exon 7 of 11)	929	NM_001267808	14980	Mm.439675	NM_001267808		H2-L	H-2L	histocompatibility 2, D region locus L	protein-coding
mm_72376.1	chr8	81342608	81342617	+	1	NA	promoter-TSS (NM_001297596)	promoter-TSS (NM_001297596)	50	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_90382.1	chr10	127288081	127288085	+	1	NA	intron (NM_033072, intron 1 of 12)	intron (NM_033072, intron 1 of 12)	935	NM_001347171	110962	Mm.372826	NM_033072	ENSMUSG00000025409	Mbd6	D10Wsu93e	methyl-CpG binding domain protein 6	protein-coding
mm_41094.1	chr5	87694657	87694700	+	1	NA	exon (NM_001286023, exon 5 of 7)	exon (NM_001286023, exon 5 of 7)	4747	NM_001286020	12991	Mm.268737	NM_009972	ENSMUSG00000063157	Csn2	Csnb	casein beta	protein-coding
mm_33560.1	chr4	131873685	131873698	+	1	NA	promoter-TSS (NM_020587)	promoter-TSS (NM_020587)	52	NM_020587	57317	Mm.2478	NM_020587	ENSMUSG00000028911	Srsf4	5730499P16Rik|AW550192|MNCb-2616|SRp75|Sfrs4	serine/arginine-rich splicing factor 4	protein-coding
mm_147013.1	chr18	34523029	34523050	-	1	NA	Intergenic	Intergenic	-16216	NM_146084	225358	Mm.226899	NM_146084	ENSMUSG00000036501	Fam13b	2610024E20Rik|AW060714|AW546153	family with sequence similarity 13, member B	protein-coding
mm_137267.1	chr17	24696661	24696664	+	1	NA	promoter-TSS (NM_023040)	promoter-TSS (NM_023040)	428	NM_027988	71893	Mm.390971	NM_027988	ENSMUSG00000019320	Noxo1	2310034C04Rik|P41NOX|P41NOXA|P41NOXB|P41NOXC|Snx28|hslt	NADPH oxidase organizer 1	protein-coding
mm_160095.1	chr7	18176626	18176626	+	1	NA	intron (NM_001003393, intron 1 of 3)	(TCTA)n|Simple_repeat|Simple_repeat	132	NM_001003393	232925	Mm.37237	NM_001003393	ENSMUSG00000066756	Igfl3	Gm580|Igfl|Rprc483	IGF-like family member 3	protein-coding
mm_13087.1	chr2	91210820	91210844	+	1	NA	TTS (NM_028119)	TTS (NM_028119)	7920	NM_007387	11432	Mm.45570	NM_007387	ENSMUSG00000002103	Acp2	Acp-2|LAP	acid phosphatase 2, lysosomal	protein-coding
mm_156358.1	chrX	139335908	139335931	+	1	NA	intron (NM_011635, intron 1 of 2)	C-rich|Low_complexity|Low_complexity	2236	NM_011635	22037	Mm.1297	NM_011635	ENSMUSG00000051257	Trap1a	Tra-P1A	tumor rejection antigen P1A	protein-coding
mm_61066.1	chr7	50599205	50599218	+	1	NA	promoter-TSS (NM_172901)	promoter-TSS (NM_172901)	21	NM_172901	243996	Mm.443270	NM_172901	ENSMUSG00000084234	4933405O20Rik	-	RIKEN cDNA 4933405O20 gene	protein-coding
mm_75760.1	chr8	69924796	69924798	-	1	NA	intron (NM_145596, intron 3 of 12)	PB1D9|SINE|Alu	-22239	NM_023312	67184	Mm.21162	NM_023312	ENSMUSG00000036199	Ndufa13	2700054G14Rik|AU022060|CDA016|CGI-39|GRIM-19|Grim19	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 13	protein-coding
mm_159585.1	chr4	121423101	121423101	-	1	NA	promoter-TSS (NM_001144948)	promoter-TSS (NM_001144948)	-2	NM_001144948	666921	Mm.477980	NM_001144948	ENSMUSG00000078576	Gm12886	OTTMUSG00000008908	predicted gene 12886	protein-coding
mm_5852.1	chr1	53296959	53296997	-	1	NA	promoter-TSS (NM_145517)	promoter-TSS (NM_145517)	50	NM_153556	227099	Mm.60499	NM_153556	ENSMUSG00000026098	Pms1	-	postmeiotic segregation increased 1 (S. cerevisiae)	protein-coding
mm_24033.1	chr3	87620918	87620922	+	1	NA	intron (NM_001003912, intron 1 of 39)	intron (NM_001003912, intron 1 of 39)	2169	NM_001003912	213498	Mm.287267	NM_001003912	ENSMUSG00000041977	Arhgef11	B930073M02|E130307F09|PDZ-RhoGEF|Prg|RhoGEF|mKIAA0380	Rho guanine nucleotide exchange factor (GEF) 11	protein-coding
mm_51204.1	chr6	71325500	71325519	+	1	NA	intron (NM_009858, intron 1 of 5)	RSINE1|SINE|B4	2697	NM_009858	12526	Mm.333148	NM_009858	ENSMUSG00000053044	Cd8b1	Cd8b|Ly-3|Ly-C|Lyt-3	CD8 antigen, beta chain 1	protein-coding
mm_133945.1	chr16	3929210	3929235	-	1	NA	intron (NM_029738, intron 8 of 11)	intron (NM_029738, intron 8 of 11)	20213	NM_029738	76779	Mm.458921	NM_029738	ENSMUSG00000014232	Cluap1	2310030D15Rik|2610111M03Rik	clusterin associated protein 1	protein-coding
mm_27797.1	chr3	75655731	75655746	-	1	NA	promoter-TSS (NR_040539)	promoter-TSS (NR_040539)	-7	NR_040539	69193	Mm.374088	NR_040539	ENSMUSG00000099370	Platr10	2410007B07Rik	pluripotency associated transcript 10	ncRNA
mm_24464.1	chr3	90654137	90654139	+	1	NA	promoter-TSS (NM_199422)	promoter-TSS (NM_199422)	-164	NM_199422	381493	Mm.291525	NM_199422	ENSMUSG00000063767	S100a7a	AY465109|Gm1020|S100A7L1|S100A7f|S100a15|S100a15a|S100a17l1	S100 calcium binding protein A7A	protein-coding
mm_77315.1	chr8	117714220	117714227	-	1	NA	intron (NM_008290, intron 1 of 4)	ORR1D2|LTR|ERVL-MaLR	12277	NM_008290	15486	Mm.276466	NM_008290	ENSMUSG00000031844	Hsd17b2	AI194836|AI194967|AI255511	hydroxysteroid (17-beta) dehydrogenase 2	protein-coding
mm_116404.1	chr13	41425044	41425096	-	1	NA	intron (NM_001111324, intron 2 of 7)	(TG)n|Simple_repeat|Simple_repeat	62290	NM_001111324	18003	Mm.288980	NM_017464	ENSMUSG00000021365	Nedd9	Cas-L|CasL|HEF1|MEF1|Nedd-9|p105	neural precursor cell expressed, developmentally down-regulated gene 9	protein-coding
mm_63397.1	chr7	127296292	127296320	+	1	NA	promoter-TSS (NM_001253873)	promoter-TSS (NM_001253873)	46	NM_001253874	16408	Mm.1618	NM_008400	ENSMUSG00000030830	Itgal	(p180)|Cd11a|LFA-1|LFA-1A|Ly-15|Ly-21	integrin alpha L	protein-coding
mm_151524.1	chr19	58741078	58741125	+	1	NA	exon (NM_018874, exon 12 of 13)	exon (NM_018874, exon 12 of 13)	12214	NM_018874	18946	Mm.10753	NM_018874	ENSMUSG00000042179	Pnliprp1	Plrp1	pancreatic lipase related protein 1	protein-coding
mm_114634.1	chr13	76384197	76384209	+	1	NA	promoter-TSS (NM_030174)	promoter-TSS (NM_030174)	-758	NM_030174	78771	Mm.316249	NM_030174	ENSMUSG00000021596	Mctp1	2810465F10Rik	multiple C2 domains, transmembrane 1	protein-coding
mm_166838.1	chr7	19271784	19271792	-	1	NA	promoter-TSS (NM_001282022)	promoter-TSS (NM_001282022)	66	NM_001282021	22323	Mm.9684	NM_009499	ENSMUSG00000030403	Vasp	-	vasodilator-stimulated phosphoprotein	protein-coding
mm_126191.1	chr15	78670671	78670680	+	1	NA	3' UTR (NM_183141, exon 2 of 2)	3' UTR (NM_183141, exon 2 of 2)	47438	NM_183141	207393	Mm.323188	NM_183141	ENSMUSG00000043460	Elfn2	6330514E13|AW048948|BC094219|Lrrc62|Ppp1r29	leucine rich repeat and fibronectin type III, extracellular 2	protein-coding
mm_47298.1	chr5	122264379	122264455	-	1	NA	promoter-TSS (NM_001039153)	promoter-TSS (NM_001039153)	43	NR_104441	654470	Mm.28804	NM_001039153	ENSMUSG00000038593	Tctn1	G730031O11Rik|Tect1	tectonic family member 1	protein-coding
mm_8819.1	chr1	162134705	162134733	-	1	NA	intron (NM_001038619, intron 14 of 20)	intron (NM_001038619, intron 14 of 20)	-82904	NR_002870	474332	Mm.479755	NR_002870	ENSMUSG00000078190	Dnm3os	6030416H16Rik|Hag2|Npn1|P/L01	dynamin 3, opposite strand	ncRNA
mm_17665.1	chr2	32083784	32083796	-	1	NA	promoter-TSS (NM_175511)	promoter-TSS (NM_175511)	-85	NM_175511	241303	Mm.250441	NM_175511	ENSMUSG00000050592	Fam78a	A130092J06Rik	family with sequence similarity 78, member A	protein-coding
mm_61209.1	chr7	64185496	64185506	+	1	NA	promoter-TSS (NM_018752)	promoter-TSS (NM_018752)	42	NM_018752	17364	Mm.38875	NM_018752	ENSMUSG00000030523	Trpm1	4732499L03Rik|AI606771|Ltrpc1|Mlsn1	transient receptor potential cation channel, subfamily M, member 1	protein-coding
mm_148409.1	chr19	3907449	3907459	+	1	NA	promoter-TSS (NM_001136091)	promoter-TSS (NM_001136091)	-321	NM_001136091	27060	Mm.271689	NM_016921	ENSMUSG00000001750	Tcirg1	ATP6N1C|ATP6a3|Atp6i|OC-116|OPTB1|Stv1|TIRC7|Vph1|oc	T cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 protein A3	protein-coding
mm_56057.1	chr6	86765867	86765921	-	1	NA	intron (NM_013471, intron 1 of 12)	intron (NM_013471, intron 1 of 12)	9220	NM_001331120	11746	Mm.259702	NM_013471	ENSMUSG00000029994	Anxa4	AI265406|AIV|AW106930|Anx4|Xanx-4	annexin A4	protein-coding
mm_157263.1	chrX	19168263	19168278	-	1	NA	Intergenic	Intergenic	-21299	NR_029807	723828		NR_029807	ENSMUSG00000065471	Mir222	Mirn222|mir-222|mmu-mir-222	microRNA 222	ncRNA
mm_165437.1	chr2	153982918	153982941	+	1	NA	exon (NM_001080811, exon 2 of 11)	exon (NM_001080811, exon 2 of 11)	7984	NM_001080811	545477	Mm.379973	NM_001080811	ENSMUSG00000078998	Bpifa6	EG545477|Gm5840|Splunc6	BPI fold containing family A, member 6	protein-coding
mm_58478.1	chr7	3423601	3423611	+	1	NA	promoter-TSS (NR_126426)	promoter-TSS (NR_126426)	-161	NR_126426	70230	Mm.458356	NR_126426	ENSMUSG00000107585	3300002P13Rik	-	RIKEN cDNA 3300002P13 gene	ncRNA
mm_87481.1	chr10	51493812	51493851	+	1	NA	intron (NM_001291894, intron 5 of 8)	intron (NM_001291894, intron 5 of 8)	2933	NM_013532	14728	Mm.34408	NM_013532	ENSMUSG00000062593	Lilrb4a	CD85K|Gp49b|HM18|ILT3|LIR-5|Lilrb4|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4A	protein-coding
mm_81803.1	chr9	116197965	116197973	+	1	NA	Intergenic	Intergenic	-22606	NM_009371	21813	Mm.172346	NM_009371	ENSMUSG00000032440	Tgfbr2	1110020H15Rik|AU042018|DNIIR|RIIDN|TBR-II|TbetaR-II|TbetaRII	transforming growth factor, beta receptor II	protein-coding
mm_150936.1	chr19	46305944	46305961	+	1	NA	promoter-TSS (NM_001177370)	promoter-TSS (NM_001177370)	22	NM_001177370	18034	Mm.102365	NM_019408	ENSMUSG00000025225	Nfkb2	NF-kappaB2|lyt|p49|p49/p100|p50B|p52	nuclear factor of kappa light polypeptide gene enhancer in B cells 2, p49/p100	protein-coding
mm_111152.1	chr12	83122114	83122123	-	1	NA	intron (NM_001310478, intron 15 of 17)	intron (NM_001310478, intron 15 of 17)	-182963	NR_046045	74283	Mm.398247	NR_046045	ENSMUSG00000100890	1700085C21Rik	-	RIKEN cDNA 1700085C21 gene	ncRNA
mm_25412.1	chr3	107342891	107342895	+	1	NA	Intergenic	Intergenic	-9604	NM_001045807	229700	Mm.27966	NM_001045807	ENSMUSG00000048109	Rbm15	C230088J01Rik|mKIAA1438	RNA binding motif protein 15	protein-coding
mm_24972.1	chr3	96751057	96751102	+	1	NA	intron (NM_026406, intron 1 of 8)	intron (NM_026406, intron 1 of 8)	23468	NM_026406	67845	Mm.386792	NM_026406	ENSMUSG00000028098	Rnf115	2610028E05Rik|AU042696|Zfp364	ring finger protein 115	protein-coding
mm_235.1	chr1	19104689	19104693	+	1	NA	exon (NM_153154, exon 2 of 8)	exon (NM_153154, exon 2 of 8)	1669	NM_153154	226896	Mm.244858	NM_153154	ENSMUSG00000042596	Tfap2d	Tcfap2d	transcription factor AP-2, delta	protein-coding
mm_140432.1	chr17	88130677	88130679	+	1	NA	intron (NM_001190356, intron 1 of 1)	intron (NM_001190356, intron 1 of 1)	5166	NM_001190356	225058	Mm.312053	NM_001190356		Gm4832	EG225058	predicted gene 4832	protein-coding
mm_20229.1	chr2	125789470	125789491	-	1	NA	Intergenic	Intergenic	-6610	NM_177608	70354	Mm.138091	NM_133725	ENSMUSG00000035093	Secisbp2l	3110001I20Rik|AI504340|C630011I23	SECIS binding protein 2-like	protein-coding
mm_146032.1	chr18	69521760	69521770	+	1	NA	intron (NM_013685, intron 6 of 19)	intron (NM_013685, intron 6 of 19)	176044	NM_001083967	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding
mm_146281.1	chr18	77882601	77882616	+	1	NA	3' UTR (NM_013831, exon 15 of 15)	3' UTR (NM_013831, exon 15 of 15)	-55859	NM_001195633	100502841	Mm.297782	NM_001195633	ENSMUSG00000039840	Epg5	4732475F16|5430411K18Rik|AI661957|AW456499|mKIAA1632	ectopic P-granules autophagy protein 5 homolog (C. elegans)	protein-coding
mm_162327.1	chr1	40266540	40266557	+	1	NA	promoter-TSS (NM_001123382)	promoter-TSS (NM_001123382)	-38	NM_001123382	16177	Mm.896	NM_008362	ENSMUSG00000026072	Il1r1	CD121a|CD121b|IL-1R1|IL-iR|Il1r-1	interleukin 1 receptor, type I	protein-coding
mm_103301.1	chr11	72550231	72550244	-	1	NA	promoter-TSS (NM_029932)	promoter-TSS (NM_029932)	9	NM_029932	77577	Mm.46185	NM_029932	ENSMUSG00000020798	Spns3	9830002I17Rik	spinster homolog 3	protein-coding
mm_168638.1	chr1	184165857	184165861	+	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	131398	NM_022019	63953	Mm.404024	NM_022019	ENSMUSG00000039384	Dusp10	2610306G15Rik|AI158871|MKP-5|MKP5	dual specificity phosphatase 10	protein-coding
mm_67323.1	chr7	79721241	79721253	-	1	NA	TTS (NM_175640)	TTS (NM_175640)	-7061	NM_001291222	16576	Mm.101633	NM_010626	ENSMUSG00000050382	Kif7	-	kinesin family member 7	protein-coding
mm_65682.1	chr7	28338723	28338784	-	1	NA	promoter-TSS (NM_013676)	promoter-TSS (NM_013676)	-34	NM_013676	20924	Mm.285906	NM_013676	ENSMUSG00000003435	Supt5	AL033283|AL033321|AU019549|Spt5|Supt5h	suppressor of Ty 5	protein-coding
mm_43017.1	chr5	123907377	123907387	+	1	NA	intron (NM_026603, intron 1 of 7)	CpG	107	NM_026603	68184	Mm.28549	NM_026603	ENSMUSG00000023106	Denr	1500003K04Rik	density-regulated protein	protein-coding
mm_19441.1	chr2	91965566	91965596	-	1	NA	Intergenic	CpG	-2018	NM_138306	104418	Mm.314923	NM_138306	ENSMUSG00000040479	Dgkz	E130307B02Rik|ENSMUSG00000075035|F730209L11Rik|mDGK[z]	diacylglycerol kinase zeta	protein-coding
mm_103915.1	chr11	83588781	83588824	-	1	NA	3' UTR (NM_009139, exon 4 of 4)	3' UTR (NM_009139, exon 4 of 4)	4285	NM_009139	20305	Mm.137	NM_009139	ENSMUSG00000018927	Ccl6	MRP-1|Scya6|c10	chemokine (C-C motif) ligand 6	protein-coding
mm_35694.1	chr4	44129122	44129126	-	1	NA	3' UTR (NM_175201, exon 11 of 11)	3' UTR (NM_175201, exon 11 of 11)	7231	NR_040414	623796	Mm.490409	NR_040414	ENSMUSG00000084274	Gm12504	OTTMUSG00000007209	prothymosin alpha pseudogene	pseudo
mm_4037.1	chr1	165774360	165774380	+	1	NA	3' UTR (NM_011804, exon 4 of 4)	3' UTR (NM_011804, exon 4 of 4)	10590	NM_011804	433375	Mm.294885	NM_011804	ENSMUSG00000040713	Creg1	AA755314|Creg	cellular repressor of E1A-stimulated genes 1	protein-coding
mm_47052.1	chr5	116288945	116288977	-	1	NA	promoter-TSS (NM_177759)	promoter-TSS (NM_177759)	24	NM_177759	269693	Mm.10946	NM_177759	ENSMUSG00000043913	Ccdc60	AU018954|C130098D09	coiled-coil domain containing 60	protein-coding
mm_56674.1	chr6	113696701	113696706	-	1	NA	promoter-TSS (NM_001347356)	promoter-TSS (NM_001347356)	-347	NM_001347356	381801	Mm.333322	NM_001033463	ENSMUSG00000056952	Tatdn2	AI646012|mKIAA0218	TatD DNase domain containing 2	protein-coding
mm_157703.1	chrX	60893438	60893440	-	1	NA	promoter-TSS (NM_009237)	promoter-TSS (NM_009237)	-9	NM_009237	20675	Mm.35784	NM_009237	ENSMUSG00000045179	Sox3	Sox-3	SRY (sex determining region Y)-box 3	protein-coding
mm_53612.1	chr6	139841653	139841658	+	1	NA	5' UTR (NM_011084, exon 1 of 16)	5' UTR (NM_011084, exon 1 of 16)	210	NM_011084	18705	Mm.333471	NM_011084	ENSMUSG00000030228	Pik3c2g	C80387|PI3K-C2-gamma	phosphatidylinositol 3-kinase, C2 domain containing, gamma polypeptide	protein-coding
mm_17655.1	chr2	32065065	32065083	-	1	NA	Intergenic	Intergenic	14128	NR_106135	102466844		NR_106135	ENSMUSG00000099075	Mir7674	Gm27563|mmu-mir-7674	microRNA 7674	ncRNA
mm_48384.1	chr5	139775632	139775681	-	1	NA	promoter-TSS (NM_026748)	promoter-TSS (NM_026748)	22	NM_026748	68510	Mm.292942	NM_026748	ENSMUSG00000029547	Ints1	1110015K06Rik	integrator complex subunit 1	protein-coding
mm_88797.1	chr10	80692696	80692721	+	1	NA	intron (NM_172457, intron 1 of 3)	intron (NM_172457, intron 1 of 3)	9112	NM_172457	208228	Mm.49309	NM_172457	ENSMUSG00000003348	Mob3a	5330417K06Rik|A630029F06|AV218468|Mobkl2a	MOB kinase activator 3A	protein-coding
mm_15609.1	chr2	160740992	160740998	+	1	NA	intron (NM_021280, intron 2 of 33)	intron (NM_021280, intron 2 of 33)	9685	NM_021280	18803	Mm.44463	NM_021280	ENSMUSG00000016933	Plcg1	AI894140|Cded|Plc-1|Plc-gamma1|Plcg-1	phospholipase C, gamma 1	protein-coding
mm_34558.1	chr4	149635241	149635252	+	1	NA	exon (NM_023051, exon 9 of 19)	exon (NM_023051, exon 9 of 19)	20321	NR_105990	102465983		NR_105990	ENSMUSG00000098580	Mir7023	Gm27912|mmu-mir-7023	microRNA 7023	ncRNA
mm_131267.1	chr16	10835491	10835504	+	1	NA	intron (NM_001162932, intron 1 of 1)	intron (NM_001162932, intron 1 of 1)	438	NM_001162932	223970	Mm.325777	NM_001033278	ENSMUSG00000037991	Rmi2	A630055G03Rik|Gm537|Gm929	RecQ mediated genome instability 2	protein-coding
mm_32304.1	chr4	103134843	103134850	+	1	NA	intron (NM_001039081, intron 3 of 12)	intron (NM_001039081, intron 3 of 12)	15456	NM_001039081	71148	Mm.288721	NM_027696	ENSMUSG00000028522	Mier1	4933425I22Rik|5830411K19Rik|er1	MEIR1 treanscription regulator	protein-coding
mm_75905.1	chr8	71273137	71273159	-	1	NA	promoter-TSS (NM_001163042)	promoter-TSS (NM_001163042)	434	NM_001142323	17925	Mm.33779	NM_015742	ENSMUSG00000004677	Myo9b	-	myosin IXb	protein-coding
mm_114278.1	chr13	58274253	58274280	+	1	NA	promoter-TSS (NM_019832)	promoter-TSS (NM_019832)	-78	NM_019832	56278	Mm.296625	NM_019832	ENSMUSG00000021552	Gkap1	42kDa|4933400B15Rik|D13Ertd340e|Gkap42	G kinase anchoring protein 1	protein-coding
mm_172015.1	chr6	111462693	111462695	+	1	NA	intron (NM_001346640, intron 8 of 10)	intron (NM_001346640, intron 8 of 10)	-748014	NR_027865	67336	Mm.378014	NR_027865	ENSMUSG00000100219	1700054K19Rik	-	RIKEN cDNA 1700054K19 gene	ncRNA
mm_145943.1	chr18	67363775	67363776	+	1	NA	intron (NM_007702, intron 3 of 4)	intron (NM_007702, intron 3 of 4)	-19672	NR_033214	338360	Mm.441590	NR_033214	ENSMUSG00000046415	B430212C06Rik	-	RIKEN cDNA B430212C06 gene	ncRNA
mm_24960.1	chr3	96696401	96696477	+	1	NA	promoter-TSS (NM_001165949)	promoter-TSS (NM_001165949)	64	NM_146135	229615	Mm.1635	NM_018812	ENSMUSG00000028101	Pias3	Pias3l	protein inhibitor of activated STAT 3	protein-coding
mm_88100.1	chr10	68751248	68751274	+	1	NA	exon (NM_177794, exon 4 of 6)	exon (NM_177794, exon 4 of 6)	27515	NM_177794	327766	Mm.2479	NM_177794	ENSMUSG00000060044	Tmem26	3230401A06|AI195372	transmembrane protein 26	protein-coding
mm_147844.1	chr18	63386512	63386526	-	1	NA	5' UTR (NM_001039485, exon 1 of 54)	5' UTR (NM_001039485, exon 1 of 54)	664	NM_001039485	667742	Mm.158720	NM_172629	ENSMUSG00000041482	Piezo2	5930434P17|9030411M15Rik|9430028L06Rik|Fam38b|Fam38b2	piezo-type mechanosensitive ion channel component 2	protein-coding
mm_163735.1	chr13	119690385	119690400	+	1	NA	promoter-TSS (NM_001291439)	promoter-TSS (NM_001291439)	41	NM_001291439	208715	Mm.61526	NM_145942	ENSMUSG00000093930	Hmgcs1	B130032C06Rik	3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1	protein-coding
mm_63914.1	chr7	139235846	139235856	+	1	NA	intron (NM_027164, intron 8 of 10)	intron (NM_027164, intron 8 of 10)	-12631	NM_001033206	101631	Mm.334300	NM_001033206	ENSMUSG00000060260	Pwwp2b	AI594893|D7Ertd517e|D930023J19Rik|Pwwp2	PWWP domain containing 2B	protein-coding
mm_46225.1	chr5	99021596	99021598	-	1	NA	intron (NM_008926, intron 2 of 18)	intron (NM_008926, intron 2 of 18)	15482	NM_008926	19092	Mm.263002	NM_008926	ENSMUSG00000029334	Prkg2	AW212535|CGKII|Prkgr2|cGK-II	protein kinase, cGMP-dependent, type II	protein-coding
mm_9800.1	chr1	181853184	181853193	-	1	NA	Intergenic	Intergenic	-10787	NM_133815	98386	Mm.4538	NM_133815	ENSMUSG00000004880	Lbr	AI505894|ic	lamin B receptor	protein-coding
mm_124284.1	chr14	103048715	103048734	-	1	NA	intron (NM_008392, intron 1 of 4)	intron (NM_008392, intron 1 of 4)	1712	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_163255.1	chr11	109650347	109650349	+	1	NA	promoter-TSS (NM_021880)	promoter-TSS (NM_021880)	-573	NM_021880	19084	Mm.30039	NM_021880	ENSMUSG00000020612	Prkar1a	1300018C22Rik|RIalpha|Tse-1|Tse1	protein kinase, cAMP dependent regulatory, type I, alpha	protein-coding
mm_55138.1	chr6	51320930	51320936	-	1	NA	Intergenic	Intergenic	-51023	NR_029719	387166		NR_029719	ENSMUSG00000065505	Mir148a	Mirn148|Mirn148a|mir-148a	microRNA 148a	ncRNA
mm_161427.1	chr15	44428260	44428260	-	1	NA	promoter-TSS (NM_026149)	promoter-TSS (NM_026149)	47	NM_001113554	67429	Mm.490404	NM_026149	ENSMUSG00000038736	Nudcd1	4921532K09Rik|AA407246|AW260430|AW556235|CML66-L|Cml66	NudC domain containing 1	protein-coding
mm_77134.1	chr8	111366476	111366503	-	1	NA	intron (NM_178086, intron 1 of 6)	intron (NM_178086, intron 1 of 6)	27332	NM_178086	338521	Mm.41083	NM_178086	ENSMUSG00000033579	Fa2h	FAAH|Faxdc1|G630055L08Rik	fatty acid 2-hydroxylase	protein-coding
mm_160313.1	chr7	141406515	141406515	+	1	NA	Intergenic	Intergenic	7610	NM_172116	213350	Mm.290953	NM_172116	ENSMUSG00000051007	Pddc1	BC023835|D230016J19Rik	Parkinson disease 7 domain containing 1	protein-coding
mm_144004.1	chr17	88065983	88065993	-	1	NA	promoter-TSS (NM_001081034)	promoter-TSS (NM_001081034)	-703	NM_001081034	225055	Mm.386857	NM_001081034	ENSMUSG00000005371	Fbxo11	C80048|Jf	F-box protein 11	protein-coding
mm_55625.1	chr6	72235560	72235618	-	1	NA	promoter-TSS (NM_153778)	promoter-TSS (NM_153778)	-12	NM_153778	71093	Mm.87449	NM_153778	ENSMUSG00000037621	Atoh8	4933425C05Rik|Hath6|Math6|bHLHa21|okadin	atonal bHLH transcription factor 8	protein-coding
mm_100001.1	chr11	114851508	114851553	+	1	NA	promoter-TSS (NM_147217)	promoter-TSS (NM_147217)	-2	NM_001110337	70355	Mm.242413	NM_147217	ENSMUSG00000051043	Gprc5c	1110028I06Rik|3200002M13Rik|Raig3	G protein-coupled receptor, family C, group 5, member C	protein-coding
mm_93725.1	chr10	119240007	119240092	-	1	NA	promoter-TSS (NM_027994)	promoter-TSS (NM_027994)	6	NM_027994	71902	Mm.203965	NM_027994	ENSMUSG00000020114	Cand1	2310038O07Rik|6330512O03Rik|AI195005|AI846556|D10Ertd516e|Tp120a|mKIAA0829	cullin associated and neddylation disassociated 1	protein-coding
mm_14976.1	chr2	152106257	152106262	+	1	NA	intron (NM_029688, intron 1 of 1)	(T)n|Simple_repeat|Simple_repeat	735	NM_029688	76650	Mm.218639	NM_029688	ENSMUSG00000032802	Srxn1	1700127B04Rik|AI854065|AW488194|Npn3|Srx|Srx1|TX01	sulfiredoxin 1 homolog (S. cerevisiae)	protein-coding
mm_51606.1	chr6	84088957	84088957	+	1	NA	intron (NM_001077694, intron 17 of 54)	ID4|SINE|ID	69571	NM_021469	26903	Mm.220982	NM_021469	ENSMUSG00000033788	Dysf	2310004N10Rik|AI604795|D6Pas3	dysferlin	protein-coding
mm_63656.1	chr7	129257028	129257056	+	1	NA	promoter-TSS (NM_001080963)	promoter-TSS (NM_001080963)	-52	NM_001080963	381925	Mm.39184	NM_001080963	ENSMUSG00000070366	Plpp4	C030048B12Rik|Gm1090|Ppapdc1a	phospholipid phosphatase 4	protein-coding
mm_142751.1	chr17	48451511	48451530	-	1	NA	promoter-TSS (NM_027292)	promoter-TSS (NM_027292)	-19	NM_027292	70026	Mm.22613	NM_027292	ENSMUSG00000023995	Tspo2	2510027D20Rik|Bzrpl1	translocator protein 2	protein-coding
mm_87345.1	chr10	43524081	43524093	+	1	NA	Intergenic	Intergenic	16907	NM_026411	67851	Mm.209953	NM_026411	ENSMUSG00000019797	1700021F05Rik	-	RIKEN cDNA 1700021F05 gene	protein-coding
mm_83254.1	chr9	42401637	42401670	-	1	NA	Intergenic	Intergenic	-1724	NM_001324548	21683	Mm.42209	NM_009347	ENSMUSG00000037705	Tecta	Tctna	tectorin alpha	protein-coding
mm_166199.1	chr5	37469648	37469648	+	1	NA	intron (NM_022416, intron 6 of 11)	MLT1C|LTR|ERVL-MaLR	131170	NM_145920	68525	Mm.25506	NM_145920	ENSMUSG00000050248	Evc2	1110017L09Rik|Lbn|limbin	Ellis van Creveld syndrome 2	protein-coding
mm_134540.1	chr16	19706371	19706399	-	1	NA	promoter-TSS (NM_177356)	promoter-TSS (NM_177356)	-20	NM_177356	239739	Mm.258059	NM_177356	ENSMUSG00000041247	Lamp3	1200002D17Rik|Cd208|DC-LAMP|DCLAMP|LAMP|TSC403	lysosomal-associated membrane protein 3	protein-coding
mm_46436.1	chr5	104982657	104982714	-	1	NA	promoter-TSS (NM_030239)	promoter-TSS (NM_030239)	32	NM_030239	27405	Mm.389663	NM_030239	ENSMUSG00000029299	Abcg3	Abcp2|Mxr2	ATP-binding cassette, sub-family G (WHITE), member 3	protein-coding
mm_81775.1	chr9	114688745	114688778	+	1	NA	promoter-TSS (NM_146229)	promoter-TSS (NM_146229)	-70	NM_146229	235661	Mm.128627	NM_146229	ENSMUSG00000032435	Dync1li1	1110053F02Rik|Dnclic1|LIC-1	dynein cytoplasmic 1 light intermediate chain 1	protein-coding
mm_65392.1	chr7	25092607	25092613	-	1	NA	3' UTR (NM_001163556, exon 14 of 14)	3' UTR (NM_001163556, exon 14 of 14)	4565	NR_105855	102465968		NR_105855	ENSMUSG00000098441	Mir6537	Gm27808|mmu-mir-6537	microRNA 6537	ncRNA
mm_166029.1	chr4	126058631	126058635	+	1	NA	promoter-TSS (NM_172701)	promoter-TSS (NM_172701)	68	NM_172701	230751	Mm.38907	NM_172701	ENSMUSG00000042616	Oscp1	1810007P19Rik|5730415O04|6030436A01Rik	organic solute carrier partner 1	protein-coding
mm_138644.1	chr17	35866701	35866719	+	1	NA	promoter-TSS (NM_175242)	promoter-TSS (NM_175242)	95	NM_175242	76448	Mm.359982	NM_175242	ENSMUSG00000034595	Ppp1r18	2310014H01Rik|AA407849|AI450394	protein phosphatase 1, regulatory subunit 18	protein-coding
mm_32301.1	chr4	103120271	103120295	+	1	NA	intron (NM_001039081, intron 1 of 12)	intron (NM_001039081, intron 1 of 12)	893	NM_001039081	71148	Mm.288721	NM_027696	ENSMUSG00000028522	Mier1	4933425I22Rik|5830411K19Rik|er1	MEIR1 treanscription regulator	protein-coding
mm_172433.1	chr7	29628327	29628340	+	1	NA	Intergenic	RLTR9E|LTR|ERVK	98682	NM_029714	76718	Mm.69030	NM_029714	ENSMUSG00000049123	Catsperg2	1700067C01Rik|CATSPERG	catsper channel auxiliary subunit gamma 2	protein-coding
mm_143251.1	chr17	65510025	65510043	-	1	NA	intron (NM_001008973, intron 2 of 14)	RMER19B2|LTR|ERVK	30748	NM_001008973	381107	Mm.141275	NM_001008973	ENSMUSG00000045036	Tmem232	E130009J12Rik|Gm940|Tes13-L|Tes13-S	transmembrane protein 232	protein-coding
mm_84267.1	chr9	62666064	62666069	-	1	NA	Intergenic	Intergenic	-11789	NM_176922	319480	Mm.34883	NM_176922	ENSMUSG00000032243	Itga11	4732459H24Rik	integrin alpha 11	protein-coding
mm_41627.1	chr5	96968822	96968837	+	1	NA	Intergenic	Intergenic	-28860	NM_080708	140780	Mm.281490	NM_080708	ENSMUSG00000034663	Bmp2k	4933417M22Rik|AA673486|AV128808|BIKE	BMP2 inducible kinase	protein-coding
mm_103366.1	chr11	75169138	75169151	-	1	NA	promoter-TSS (NM_001098203)	promoter-TSS (NM_001098203)	-992	NM_001098203	15248	Mm.57250	NM_010430	ENSMUSG00000043099	Hic1	AA408311|HIC-1	hypermethylated in cancer 1	protein-coding
mm_89691.1	chr10	97565757	97565774	+	1	NA	5' UTR (NM_008524, exon 1 of 3)	5' UTR (NM_008524, exon 1 of 3)	264	NM_008524	17022	Mm.18888	NM_008524	ENSMUSG00000036446	Lum	Ldc|SLRR2D	lumican	protein-coding
mm_157729.1	chrX	70385814	70385838	-	1	NA	promoter-TSS (NM_026787)	promoter-TSS (NM_026787)	-87	NM_026787	68618	Mm.293255	NM_026787	ENSMUSG00000045237	1110012L19Rik	-	RIKEN cDNA 1110012L19 gene	protein-coding
mm_50587.1	chr6	49059255	49059270	+	1	NA	Intergenic	Intergenic	-14533	NM_029353	75593	Mm.439947	NM_029353	ENSMUSG00000029815	Malsu1	2410003K15Rik|Matsu1	mitochondrial assembly of ribosomal large subunit 1	protein-coding
mm_139165.1	chr17	47557718	47557726	+	1	NA	intron (NM_001081635, intron 1 of 6)	intron (NM_001081635, intron 1 of 6)	-35745	NM_007632	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_108154.1	chr12	76324861	76324898	+	1	NA	promoter-TSS (NM_001101471)	promoter-TSS (NM_001101471)	-12	NM_001101471	238276	Mm.311452	NM_001101471	ENSMUSG00000021057	Akap5	3526401B18Rik|AKAP 150|AKAP-5|AKAP150|BB098886|Gm258|P150	A kinase (PRKA) anchor protein 5	protein-coding
mm_13483.1	chr2	106226450	106226458	+	1	NA	Intergenic	Intergenic	-222905	NR_033993	99349	Mm.25661	NM_026992	ENSMUSG00000027166	Dnajc24	1700030A21Rik|2610027M02Rik|AV066965|AW240712|Dph4|MmDjC7|Zcsl3	DnaJ heat shock protein family (Hsp40) member C24	protein-coding
mm_89961.1	chr10	111296433	111296450	+	1	NA	3' UTR (NM_001003717, exon 23 of 23)	3' UTR (NM_001003717, exon 23 of 23)	-2238	NM_027914	71769	Mm.45256	NM_027914	ENSMUSG00000035759	Bbs10	1300007O09Rik|AI452285	Bardet-Biedl syndrome 10 (human)	protein-coding
mm_29692.1	chr3	123113568	123113578	-	1	NA	exon (NM_080451, exon 4 of 5)	exon (NM_080451, exon 4 of 5)	-78586	NM_021503	59006	Mm.141157	NM_021503	ENSMUSG00000028116	Myoz2	1110012I24Rik|Fatz-2|Myozl2	myozenin 2	protein-coding
mm_67952.1	chr7	100498822	100498862	-	1	NA	exon (NM_011671, exon 7 of 8)	exon (NM_011671, exon 7 of 8)	5484	NM_011671	22228	Mm.171378	NM_011671	ENSMUSG00000033685	Ucp2	Slc25a8	uncoupling protein 2 (mitochondrial, proton carrier)	protein-coding
mm_113510.1	chr13	37778385	37778403	+	1	NA	Intergenic	CpG	-47644	NM_026830	68750	Mm.491109	NM_026830	ENSMUSG00000039087	Rreb1	1110037N09Rik|AA414966|B930013M22Rik	ras responsive element binding protein 1	protein-coding
mm_87865.1	chr10	61297750	61297788	+	1	NA	promoter-TSS (NM_011073)	promoter-TSS (NM_011073)	-67	NM_011073	18646	Mm.240313	NM_011073	ENSMUSG00000037202	Prf1	Pfn|Pfp|Prf-1	perforin 1 (pore forming protein)	protein-coding
mm_31056.1	chr4	41191063	41191110	+	1	NA	3' UTR (NM_026275, exon 5 of 5)	3' UTR (NM_026275, exon 5 of 5)	55065	NM_026275	67615	Mm.389540	NM_026275	ENSMUSG00000036241	Ube2r2	1200003M11Rik|Cdc34b|Ubc3b	ubiquitin-conjugating enzyme E2R 2	protein-coding
mm_143682.1	chr17	80062176	80062189	-	1	NA	promoter-TSS (NM_144802)	promoter-TSS (NM_144802)	86	NM_144802	72692	Mm.64579	NM_144802	ENSMUSG00000024095	Hnrnpll	2510028H02Rik|2810036L13Rik|AI256697|AI852082|Hnrpll	heterogeneous nuclear ribonucleoprotein L-like	protein-coding
mm_107097.1	chr12	17690828	17690858	+	1	NA	promoter-TSS (NM_016677)	promoter-TSS (NM_016677)	29	NM_016677	53602	Mm.313619	NM_016677	ENSMUSG00000071379	Hpcal1	NVP-3|Nvp3|VILIP3|Vnsl3|Vsnl3	hippocalcin-like 1	protein-coding
mm_22290.1	chr2	180234984	180234998	-	1	NA	Intergenic	Intergenic	-9132	NM_001081171	16776	Mm.4339	NM_001081171	ENSMUSG00000015647	Lama5	AA408760|AA408762|AI853660|[a]5|laminin-511|mKIAA0533	laminin, alpha 5	protein-coding
mm_16713.1	chr2	7125578	7125583	-	1	NA	intron (NM_001110231, intron 3 of 15)	intron (NM_001110231, intron 3 of 15)	-44278	NM_001160292	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_171631.1	chr4	19298890	19298891	+	1	NA	intron (NM_013927, intron 2 of 17)	intron (NM_013927, intron 2 of 17)	18040	NM_013927	30952	Mm.445778	NM_013927	ENSMUSG00000056494	Cngb3	CCNC2|CNG6|Cngbeta2	cyclic nucleotide gated channel beta 3	protein-coding
mm_54644.1	chr6	38875905	38875920	-	1	NA	5' UTR (NM_010433, exon 1 of 15)	5' UTR (NM_010433, exon 1 of 15)	278	NM_010433	15258	Mm.23790	NM_010433	ENSMUSG00000061436	Hipk2	1110014O20Rik|B230339E18Rik|Stank	homeodomain interacting protein kinase 2	protein-coding
mm_30054.1	chr3	136449482	136449485	-	1	NA	promoter-TSS (NR_040592)	promoter-TSS (NR_040592)	-134	NR_040592	70055	Mm.261063	NR_040592	ENSMUSG00000099508	1700030L20Rik	-	RIKEN cDNA 1700030L20 gene	ncRNA
mm_3418.1	chr1	145183820	145183829	+	1	NA	Intergenic	Intergenic	-408403	NM_022881	64214	Mm.253927	NM_022881	ENSMUSG00000026357	Rgs18	-	regulator of G-protein signaling 18	protein-coding
mm_7158.1	chr1	91459255	91459336	-	1	NA	promoter-TSS (NM_011066)	promoter-TSS (NM_011066)	33	NM_011066	18627	Mm.482463	NM_011066	ENSMUSG00000055866	Per2	mKIAA0347|mPer2	period circadian clock 2	protein-coding
mm_3745.1	chr1	155558412	155558421	+	1	NA	5' UTR (NM_026683, exon 1 of 4)	5' UTR (NM_026683, exon 1 of 4)	296	NM_026683	72482	Mm.288249	NM_026683	ENSMUSG00000033701	Acbd6	0610010G04Rik|2610100E10Rik	acyl-Coenzyme A binding domain containing 6	protein-coding
mm_53654.1	chr6	141274955	141274972	+	1	NA	intron (NM_018779, intron 1 of 15)	intron (NM_018779, intron 1 of 15)	25694	NM_018779	54611	Mm.103728	NM_018779	ENSMUSG00000041741	Pde3a	A930022O17Rik|C87899	phosphodiesterase 3A, cGMP inhibited	protein-coding
mm_4215.1	chr1	171288071	171288081	+	1	NA	promoter-TSS (NM_013919)	promoter-TSS (NM_013919)	-115	NM_013919	30941	Mm.27510	NM_013919	ENSMUSG00000053483	Usp21	ESTM28|Usp16|Usp23|W53272	ubiquitin specific peptidase 21	protein-coding
mm_62178.1	chr7	97451268	97451270	+	1	NA	promoter-TSS (NM_001136235)	promoter-TSS (NM_001136235)	-65	NM_001136235	233529	Mm.334033	NM_001010826	ENSMUSG00000051727	Kctd14	AI449310|D7Ertd760e	potassium channel tetramerisation domain containing 14	protein-coding
mm_171985.1	chr5	93093468	93093470	+	1	NA	promoter-TSS (NM_001310669)	promoter-TSS (NM_001310669)	53	NM_001347377	52398	Mm.394184	NM_001009818	ENSMUSG00000058013	Sept11	6230410I01Rik|AW548875|D5Ertd606e	septin 11	protein-coding
mm_140594.1	chr17	10280611	10280614	-	1	NA	intron (NM_021881, intron 2 of 6)	AT_rich|Low_complexity|Low_complexity	38749	NM_021881	19317	Mm.130694	NM_021881	ENSMUSG00000062078	Qk	1110003F05Rik|1500005P18|QkI|l(17)-1Wis|l17Wis1	quaking	protein-coding
mm_30099.1	chr3	138472252	138472277	-	1	NA	exon (NM_175224, exon 7 of 11)	exon (NM_175224, exon 7 of 11)	17118	NM_175224	75624	Mm.26833	NM_175224	ENSMUSG00000005813	Metap1	1700029C17Rik|AW047992|mKIAA0094	methionyl aminopeptidase 1	protein-coding
mm_7385.1	chr1	110959811	110959816	-	1	NA	intron (NM_001081386, intron 1 of 11)	MLT1D|LTR|ERVL-MaLR	17559	NM_001081386	227485	Mm.322070	NM_001081386	ENSMUSG00000047216	Cdh19	-	cadherin 19, type 2	protein-coding
mm_17635.1	chr2	31116290	31116320	-	1	NA	intron (NM_001038700, intron 1 of 14)	intron (NM_001038700, intron 1 of 14)	-19805	NM_001177650	14269	Mm.52297	NM_019406	ENSMUSG00000075415	Fnbp1	1110057E06Rik|2210010H06Rik|FBP1|Fbp17	formin binding protein 1	protein-coding
mm_64859.1	chr7	13037685	13037692	-	1	NA	promoter-TSS (NM_001243968)	promoter-TSS (NM_001243968)	-61	NM_001243968	22192	Mm.196580	NM_145578	ENSMUSG00000005575	Ube2m	2510040H03Rik|UBC12|Ubc-rs2	ubiquitin-conjugating enzyme E2M	protein-coding
mm_71371.1	chr8	45763939	45763951	+	1	NA	intron (NM_172752, intron 8 of 22)	intron (NM_172752, intron 8 of 22)	55352	NR_045739	319940	Mm.441720	NR_045739	ENSMUSG00000085440	Sorbs2os	D330022K07Rik	sorbin and SH3 domain containing 2, opposite strand	ncRNA
mm_109355.1	chr12	109617936	109617939	+	1	NA	promoter-TSS (NR_029918)	promoter-TSS (NR_029918)	-321	NR_029918	723854		NR_029918	ENSMUSG00000065433	Mir370	Mirn370|mir-370|mmu-mir-370	microRNA 370	ncRNA
mm_153489.1	chr19	41319655	41319668	-	1	NA	intron (NM_031376, intron 8 of 16)	B1_Mus1|SINE|Alu	-55657	NM_133352	107358	Mm.246440	NM_133352	ENSMUSG00000025016	Tm9sf3	1810073M23Rik|2810031D16Rik|AI115521|AI413748|AW146116|AW549777|Smbp|mKIAA4036	transmembrane 9 superfamily member 3	protein-coding
mm_127537.1	chr15	102104377	102104388	+	1	NA	intron (NM_153533, intron 1 of 28)	intron (NM_153533, intron 1 of 28)	1394	NM_153533	209039	Mm.29389	NM_153533	ENSMUSG00000037003	Tns2	C1-ten|Tenc1|nep|nph	tensin 2	protein-coding
mm_55615.1	chr6	72123188	72123220	-	1	NA	promoter-TSS (NR_045165)	promoter-TSS (NR_045165)	-7	NR_045165	71265	Mm.442035	NR_045163	ENSMUSG00000108709	4933431G14Rik	4930565C19Rik	RIKEN cDNA 4933431G14 gene	ncRNA
mm_46265.1	chr5	99963772	99963794	-	1	NA	exon (NM_001077266, exon 6 of 8)	exon (NM_001077266, exon 6 of 8)	15155	NM_001077266	11991	Mm.150231	NM_007516	ENSMUSG00000000568	Hnrnpd	Auf1|Hnrpd	heterogeneous nuclear ribonucleoprotein D	protein-coding
mm_142174.1	chr17	36257837	36257855	-	1	NA	promoter-TSS (NM_026308)	promoter-TSS (NM_026308)	0	NM_026308	67676	Mm.27131	NM_026308	ENSMUSG00000024446	Rpp21	0610037N01Rik	ribonuclease P 21 subunit	protein-coding
mm_101918.1	chr11	50200621	50200637	-	1	NA	TTS (NM_026543)	TTS (NM_026543)	10191	NM_001290769	18412	Mm.40828	NM_011018	ENSMUSG00000015837	Sqstm1	A170|OSF-6|Osi|STAP|STONE14|p62	sequestosome 1	protein-coding
mm_140161.1	chr17	80224496	80224510	+	1	NA	promoter-TSS (NM_026053)	promoter-TSS (NM_026053)	14	NM_026053	67242	Mm.279985	NM_026053	ENSMUSG00000055760	Gemin6	2610019B15Rik|2810470M17Rik	gem (nuclear organelle) associated protein 6	protein-coding
mm_47085.1	chr5	117116086	117116097	-	1	NA	promoter-TSS (NM_178622)	promoter-TSS (NM_178622)	-98	NM_178622	71954	Mm.34456	NM_178622	ENSMUSG00000066900	Suds3	2400003N08Rik|2410008L21Rik|AU067672|mSds3	suppressor of defective silencing 3 homolog (S. cerevisiae)	protein-coding
mm_69298.1	chr7	128289087	128289091	-	1	NA	promoter-TSS (NR_037290)	promoter-TSS (NR_037290)	-654	NR_037290	100526559		NR_037290	ENSMUSG00000093215	Mir3103	mir-3103|mmu-mir-3103	microRNA 3103	ncRNA
mm_116655.1	chr13	49188014	49188029	-	1	NA	intron (NM_013610, intron 1 of 3)	CpG	474	NM_013610	18081	Mm.18503	NM_013610	ENSMUSG00000037966	Ninj1	AU024536	ninjurin 1	protein-coding
mm_145602.1	chr18	61045423	61045442	+	1	NA	5' UTR (NM_001146268, exon 1 of 23)	5' UTR (NM_001146268, exon 1 of 23)	282	NM_008809	18596	Mm.4146	NM_008809	ENSMUSG00000024620	Pdgfrb	AI528809|CD140b|PDGFR-1|Pdgfr	platelet derived growth factor receptor, beta polypeptide	protein-coding
mm_74300.1	chr8	126298527	126298594	+	1	NA	promoter-TSS (NM_175434)	promoter-TSS (NM_175434)	-19	NM_175434	210027	Mm.405238	NM_175434	ENSMUSG00000057060	Slc35f3	B230375D17Rik	solute carrier family 35, member F3	protein-coding
mm_170939.1	chr2	4919919	4919922	+	1	NA	intron (NM_010726, intron 1 of 8)	B1_Mus1|SINE|Alu	924	NM_010726	16922	Mm.391704	NM_010726	ENSMUSG00000026664	Phyh	AI256161|AI265699|Lnap1|PAHX	phytanoyl-CoA hydroxylase	protein-coding
mm_170166.1	chr17	53867029	53867046	-	1	NA	Intergenic	Intergenic	-21079	NM_026935	69083	Mm.19320	NM_026935	ENSMUSG00000023122	Sult1c2	1810008N17Rik|ST1C1|ST1C2|Sult1c1	sulfotransferase family, cytosolic, 1C, member 2	protein-coding
mm_127926.1	chr15	10358683	10358705	-	1	NA	intron (NM_001310736, intron 1 of 13)	intron (NM_001310736, intron 1 of 13)	115	NM_001031851	268782	Mm.482244	NM_001031851	ENSMUSG00000089678	Agxt2	AI303810|AI663818	alanine-glyoxylate aminotransferase 2	protein-coding
mm_48530.1	chr5	142903802	142903850	-	1	NA	exon (NM_007393, exon 6 of 6)	exon (NM_007393, exon 6 of 6)	2928	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_52439.1	chr6	113623989	113624037	+	1	NA	promoter-TSS (NM_009507)	promoter-TSS (NM_009507)	-8	NM_009507	22346	Mm.29407	NM_009507	ENSMUSG00000033933	Vhl	Vhlh	von Hippel-Lindau tumor suppressor	protein-coding
mm_110447.1	chr12	51134991	51134991	-	1	NA	Intergenic	Intergenic	129835	NR_126468	75494	Mm.416848	NR_126468		1700008C04Rik	-	RIKEN cDNA 1700008C04 gene	ncRNA
mm_61931.1	chr7	90166098	90166108	+	1	NA	intron (NM_001252520, intron 4 of 20)	PB1D9|SINE|Alu	35871	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_166040.1	chr4	130047547	130047599	+	1	NA	promoter-TSS (NM_028266)	promoter-TSS (NM_028266)	-267	NM_028266	107581	Mm.41860	NM_028266	ENSMUSG00000040690	Col16a1	2700007F12Rik|A530052M23Rik|AI838662|CA1F	collagen, type XVI, alpha 1	protein-coding
mm_373.1	chr1	34005873	34005908	+	1	NA	intron (NM_001276764, intron 3 of 102)	intron (NM_001276764, intron 3 of 102)	-5935	NM_133833	13518	Mm.336625	NM_010081	ENSMUSG00000026131	Dst	2310001O04Rik|A830042E19Rik|AW554249|BP230|BPAG1-n|Bpag|Bpag1|Macf2|ah|athetoid|dt|mKIAA0728|nmf203|nmf339	dystonin	protein-coding
mm_87482.1	chr10	51493884	51493905	+	1	NA	intron (NM_001291894, intron 5 of 8)	MIR3|SINE|MIR	2996	NM_013532	14728	Mm.34408	NM_013532	ENSMUSG00000062593	Lilrb4a	CD85K|Gp49b|HM18|ILT3|LIR-5|Lilrb4|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4A	protein-coding
mm_172495.1	chr7	63023821	63023821	+	1	NA	Intergenic	Lx7|LINE|L1	188705	NM_007390	11441	Mm.113464	NM_007390	ENSMUSG00000030525	Chrna7	Acra7|alpha7|nAchR	cholinergic receptor, nicotinic, alpha polypeptide 7	protein-coding
mm_18424.1	chr2	60751889	60751903	-	1	NA	TTS (NM_001141932)	TTS (NM_001141932)	-29293	NM_001159564	16420	Mm.98193	NM_021359	ENSMUSG00000026971	Itgb6	2210409C20Rik|4831415H04Rik	integrin beta 6	protein-coding
mm_148599.1	chr19	5286804	5286822	+	1	NA	exon (NM_030109, exon 10 of 21)	exon (NM_030109, exon 10 of 21)	8642	NM_030109	319322	Mm.196532	NM_030109	ENSMUSG00000024853	Sf3b2	145kDa|2610311M13Rik|2810441F20Rik|B230398H18Rik|SAP145|SF3b1|SF3b145|SF3b150	splicing factor 3b, subunit 2	protein-coding
mm_14958.1	chr2	152080915	152080939	+	1	NA	promoter-TSS (NM_001160410)	promoter-TSS (NM_001160410)	-602	NM_001160410	545474	Mm.214317	NM_001160410	ENSMUSG00000060257	Scrt2	AW060659	scratch family zinc finger 2	protein-coding
mm_14645.1	chr2	136892281	136892294	+	1	NA	promoter-TSS (NM_001286983)	promoter-TSS (NM_001286983)	24	NM_028834	74243	Mm.330612	NM_028201	ENSMUSG00000027281	Slx4ip	2210009G21Rik|2410004I22Rik|C85661|Slxip	SLX4 interacting protein	protein-coding
mm_25666.1	chr3	121823929	121823931	+	1	NA	Intergenic	Intergenic	-8715	NM_008991	19299	Mm.399042	NM_008991	ENSMUSG00000028127	Abcd3	AI313901|AU018866|AW146054|PMP68|PMP70|Pxmp1	ATP-binding cassette, sub-family D (ALD), member 3	protein-coding
mm_169564.1	chr15	15914701	15914719	+	1	NA	Intergenic	L1Md_T|LINE|L1	-863391	NM_009869	12565	Mm.439758	NM_009869	ENSMUSG00000025370	Cdh9	-	cadherin 9	protein-coding
mm_106450.1	chr11	119942663	119942676	-	1	NA	promoter-TSS (NM_001037755)	promoter-TSS (NM_001037755)	-423	NM_001037754	108100	Mm.197534	NM_130862	ENSMUSG00000025372	Baiap2	IRSp53|R75030	brain-specific angiogenesis inhibitor 1-associated protein 2	protein-coding
mm_39620.1	chr5	24413407	24413420	+	1	NA	promoter-TSS (NM_183000)	promoter-TSS (NM_183000)	-38	NM_183000	171209	Mm.299636	NM_183000	ENSMUSG00000038276	Asic3	AW742291|Accn3|DRASIC|SLNAC1|TNAC1	acid-sensing (proton-gated) ion channel 3	protein-coding
mm_95085.1	chr11	33513032	33513055	+	1	NA	intron (NM_023146, intron 1 of 27)	CpG	703	NR_110973	66011	Mm.383775	NM_023146	ENSMUSG00000040594	Ranbp17	-	RAN binding protein 17	protein-coding
mm_93161.1	chr10	93247273	93247295	-	1	NA	TTS (NM_001322268)	TTS (NM_001322268)	63875	NM_001322268	13713	Mm.4454	NM_013508	ENSMUSG00000008398	Elk3	D430049E23Rik|Erp|Etrp|Net|Sap-2	ELK3, member of ETS oncogene family	protein-coding
mm_170203.1	chr17	69537147	69537164	-	1	NA	Intergenic	IAPLTR1_Mm|LTR|ERVK	97829	NM_001145192	320722	Mm.400254	NM_001145192	ENSMUSG00000091636	Akain1	A330050F15Rik	A kinase (PRKA) anchor inhibitor 1	protein-coding
mm_138971.1	chr17	45283191	45283220	+	1	NA	Intergenic	Intergenic	150502	NM_152810	71702	Mm.28270	NM_152810	ENSMUSG00000023932	Cdc5l	1200002I02Rik|AA408004|PCDC5RP	cell division cycle 5-like (S. pombe)	protein-coding
mm_66089.1	chr7	30973178	30973205	-	1	NA	promoter-TSS (NR_038860)	promoter-TSS (NR_038860)	278	NM_001164185	54135	Mm.4067	NM_017405	ENSMUSG00000001247	Lsr	ILDR3|Lisch7	lipolysis stimulated lipoprotein receptor	protein-coding
mm_10917.1	chr2	25400546	25400557	+	1	NA	intron (NM_009849, intron 7 of 8)	intron (NM_009849, intron 7 of 8)	-2499	NM_008721	18146	Mm.1131	NM_008721	ENSMUSG00000015094	Npdc1	AI314472|NPDC-1	neural proliferation, differentiation and control 1	protein-coding
mm_139934.1	chr17	71086163	71086199	+	1	NA	intron (NM_010867, intron 19 of 37)	intron (NM_010867, intron 19 of 37)	66624	NM_001083934	17929	Mm.4103	NM_010867	ENSMUSG00000024049	Myom1	D430047A17Rik	myomesin 1	protein-coding
mm_4853.1	chr1	187607276	187607308	+	1	NA	Intergenic	Intergenic	-1714	NM_001243792	26381	Mm.89989	NM_011935	ENSMUSG00000026610	Esrrg	ERR3|Errg|NR3B3|mKIAA0832	estrogen-related receptor gamma	protein-coding
mm_63671.1	chr7	130252423	130252427	+	1	NA	intron (NM_010207, intron 2 of 17)	intron (NM_010207, intron 2 of 17)	14383	NM_010207	14183	Mm.16340	NM_010207	ENSMUSG00000030849	Fgfr2	AU043015|AW556123|Bek|Fgfr-2|Fgfr-7|Fgfr7|KGFR|KGFRTr|svs	fibroblast growth factor receptor 2	protein-coding
mm_124637.1	chr15	4375463	4375511	+	1	NA	promoter-TSS (NM_177355)	promoter-TSS (NM_177355)	-4	NM_177355	239318	Mm.308996	NM_177355	ENSMUSG00000049148	Plcxd3	B130016O10Rik	phosphatidylinositol-specific phospholipase C, X domain containing 3	protein-coding
mm_113891.1	chr13	49190954	49190959	+	1	NA	intron (NM_013610, intron 1 of 3)	intron (NM_013610, intron 1 of 3)	3409	NM_013610	18081	Mm.18503	NM_013610	ENSMUSG00000037966	Ninj1	AU024536	ninjurin 1	protein-coding
mm_59501.1	chr7	27545306	27545329	+	1	NA	intron (NM_011116, intron 1 of 13)	B3|SINE|B2	7901	NM_011116	18807	Mm.6483	NM_011116	ENSMUSG00000003363	Pld3	Sam-9	phospholipase D family, member 3	protein-coding
mm_66490.1	chr7	45053056	45053064	-	1	NA	promoter-TSS (NM_175022)	promoter-TSS (NM_175022)	-179	NM_175022	233210	Mm.219137	NM_175022	ENSMUSG00000046574	Prr12	6720469B10|BC058674	proline rich 12	protein-coding
mm_165049.1	chr19	40665962	40665966	-	1	NA	intron (NM_009848, intron 1 of 9)	intron (NM_009848, intron 1 of 9)	6194	NM_009848	12495	Mm.2824	NM_009848	ENSMUSG00000048120	Entpd1	2610206B08Rik|AA408691|Cd39|NTPDase-1	ectonucleoside triphosphate diphosphohydrolase 1	protein-coding
mm_44643.1	chr5	28209748	28209764	-	1	NA	5' UTR (NM_001310511, exon 1 of 3)	5' UTR (NM_001310511, exon 1 of 3)	412	NM_001310511	269637	Mm.68286	NM_175651	ENSMUSG00000044681	Cnpy1	1500012D20Rik|9630008K15Rik|AI853839	canopy FGF signaling regulator 1	protein-coding
mm_5416.1	chr1	33907682	33907691	-	1	NA	promoter-TSS (NM_001310484)	promoter-TSS (NM_001310484)	-65	NM_177235	320705	Mm.336619	NM_177235	ENSMUSG00000042182	Bend6	B230209C24Rik	BEN domain containing 6	protein-coding
mm_30465.1	chr3	154094132	154094142	-	1	NA	intron (NM_001081263, intron 1 of 21)	intron (NM_001081263, intron 1 of 21)	120701	NM_001081263	242259	Mm.239962	NM_001081263	ENSMUSG00000028360	Slc44a5	AA117069|Gm422	solute carrier family 44, member 5	protein-coding
mm_25834.1	chr3	129199961	129199975	+	1	NA	promoter-TSS (NM_001042504)	promoter-TSS (NM_001042504)	90	NM_001042504	18741	Mm.246804	NM_011098	ENSMUSG00000028023	Pitx2	9430085M16Rik|Brx1|Brx1b|Munc30|Otlx2|Ptx2|Rieg	paired-like homeodomain transcription factor 2	protein-coding
mm_93148.1	chr10	92722357	92722409	-	1	NA	promoter-TSS (NM_008682)	promoter-TSS (NM_008682)	35	NM_008682	17997	Mm.2998	NM_008682	ENSMUSG00000019988	Nedd1	-	neural precursor cell expressed, developmentally down-regulated gene 1	protein-coding
mm_14601.1	chr2	136501905	136501917	+	1	NA	Intergenic	Intergenic	-30410	NM_175667	319196	Mm.477841	NM_175667	ENSMUSG00000074771	Ankef1	AV276460|Ankrd5	ankyrin repeat and EF-hand domain containing 1	protein-coding
mm_81491.1	chr9	110009559	110009565	+	1	NA	intron (NM_001205330, intron 3 of 18)	B1_Mus1|SINE|Alu	-42459	NM_001311163	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_91064.1	chr10	19004961	19004976	-	1	NA	exon (NM_009397, exon 7 of 9)	exon (NM_009397, exon 7 of 9)	6995	NM_001166402	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_75903.1	chr8	71272449	71272478	-	1	NA	promoter-TSS (NM_001142322)	promoter-TSS (NM_001142322)	127	NM_001163042	76478	Mm.27355	NM_029621	ENSMUSG00000035439	Haus8	2410004L22Rik|Hice1	4HAUS augmin-like complex, subunit 8	protein-coding
mm_68555.1	chr7	114416604	114416620	-	1	NA	intron (NM_011055, intron 1 of 15)	intron (NM_011055, intron 1 of 15)	1358	NM_011055	18576	Mm.430730	NM_011055	ENSMUSG00000030671	Pde3b	9830102A01Rik|AI847709	phosphodiesterase 3B, cGMP-inhibited	protein-coding
mm_55118.1	chr6	50394256	50394277	-	1	NA	intron (NM_001347213, intron 2 of 23)	intron (NM_001347213, intron 2 of 23)	-11429	NM_027881	71720	Mm.44153	NM_027881	ENSMUSG00000029822	Osbpl3	1200014M06Rik|6720421I08Rik|A530055M08|ORP-3|ORP3|OSBP3	oxysterol binding protein-like 3	protein-coding
mm_143720.1	chr17	81375453	81375464	-	1	NA	non-coding (NR_104580, exon 9 of 9)	non-coding (NR_104580, exon 9 of 9)	-310373	NM_028138	72167	Mm.273257	NM_028138	ENSMUSG00000024246	Thumpd2	2810025A12Rik	THUMP domain containing 2	protein-coding
mm_110174.1	chr12	27336843	27336851	-	1	NA	3' UTR (NM_009234, exon 1 of 1)	3' UTR (NM_009234, exon 1 of 1)	5871	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding
mm_92085.1	chr10	62791989	62792023	-	1	NA	intron (NM_026201, intron 1 of 24)	CpG	362	NM_026201	67500	Mm.196371	NM_026201	ENSMUSG00000020074	Ccar1	2610511G16Rik|9430036H15Rik|Carp1	cell division cycle and apoptosis regulator 1	protein-coding
mm_1442.1	chr1	67220542	67220550	+	1	NA	exon (NM_001080809, exon 34 of 38)	exon (NM_001080809, exon 34 of 38)	97519	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_102808.1	chr11	68927062	68927101	-	1	NA	promoter-TSS (NM_145746)	promoter-TSS (NM_145746)	0	NM_145746	252868	Mm.76826	NM_145746	ENSMUSG00000032921	Odf4	Oppo1	outer dense fiber of sperm tails 4	protein-coding
mm_54394.1	chr6	31318118	31318151	-	1	NA	intron (NR_040261, intron 3 of 4)	intron (NR_040261, intron 3 of 4)	80639	NR_040300	100503869	Mm.370532	NR_040300	ENSMUSG00000086212	Mkln1os	Gm13845|OTTMUSG00000014733	muskelin 1, intracellular mediator containing kelch motifs, opposite strand	ncRNA
mm_60729.1	chr7	45418329	45418360	+	1	NA	Intergenic	Intergenic	-2602	NM_008497	16866	Mm.57061	NM_008497	ENSMUSG00000100916	Lhb	Gm29035|LH|LH-B|LSH-B|LSH-beta	luteinizing hormone beta	protein-coding
mm_70916.1	chr8	25720460	25720474	+	1	NA	TTS (NM_001081269)	TTS (NM_001081269)	419	NR_121643	71910	Mm.385055	NM_028000	ENSMUSG00000031570	Plpp5	1810019D05Rik|2310022A04Rik|AW045471|Ppapdc1|Ppapdc1b	phospholipid phosphatase 5	protein-coding
mm_9541.1	chr1	173907441	173907468	-	1	NA	intron (NM_001033450, intron 2 of 6)	intron (NM_001033450, intron 2 of 6)	5592	NM_001301745	381308	Mm.490248	NM_001033450	ENSMUSG00000026536	Ifi211	A730048F03|Ifi205b|Mnda|ifi-205-B	interferon activated gene 211	protein-coding
mm_148117.1	chr18	74981539	74981554	-	1	NA	promoter-TSS (NR_110446)	promoter-TSS (NR_110446)	1	NR_110446	71545	Mm.488094	NR_110446		9030625G05Rik	-	RIKEN cDNA 9030625G05 gene	ncRNA
mm_78247.1	chr9	21660611	21660620	+	1	NA	intron (NM_001174079, intron 15 of 33)	intron (NM_001174079, intron 15 of 33)	44446	NM_001174078	20586	Mm.286593	NM_011417	ENSMUSG00000032187	Smarca4	Brg1|HP1-BP72|SNF2beta|SW1/SNF|b2b508.1Clo|b2b692Clo	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	protein-coding
mm_27220.1	chr3	36000651	36000660	-	1	NA	promoter-TSS (NM_023644)	promoter-TSS (NM_023644)	23	NM_023644	72039	Mm.249016	NM_023644	ENSMUSG00000027709	Mccc1	1810045E08Rik|2310058B18Rik|MCCalpha|Mcca|R75106	methylcrotonoyl-Coenzyme A carboxylase 1 (alpha)	protein-coding
mm_65019.1	chr7	17710974	17710982	-	1	NA	Intergenic	RMER17A2|LTR|ERVK	-2274	NM_028480	73250	Mm.244138	NM_028480	ENSMUSG00000008789	Ceacam5	1600029H12Rik|Psg30	carcinoembryonic antigen-related cell adhesion molecule 5	protein-coding
mm_141225.1	chr17	27325024	27325034	-	1	NA	Intergenic	Intergenic	-3356	NR_106075	102466818		NR_106075	ENSMUSG00000099237	Mir7216	Gm27555|mmu-mir-7216	microRNA 7216	ncRNA
mm_136617.1	chr17	5492559	5492646	+	1	NA	promoter-TSS (NM_146073)	promoter-TSS (NM_146073)	2	NM_146073	224454	Mm.487663	NM_146073	ENSMUSG00000034265	Zdhhc14	B530001K09Rik|New1cp	zinc finger, DHHC domain containing 14	protein-coding
mm_61788.1	chr7	83883648	83883668	+	1	NA	5' UTR (NM_030705, exon 1 of 1)	5' UTR (NM_030705, exon 1 of 1)	683	NM_030705	80889	Mm.272998	NM_030705	ENSMUSG00000070462	Mesdc1	AW061151	mesoderm development candidate 1	protein-coding
mm_157000.1	chrX	7570839	7570853	-	1	NA	intron (NM_138605, intron 1 of 3)	intron (NM_138605, intron 1 of 3)	-2754	NR_029473	78185	Mm.160055	NR_029473	ENSMUSG00000039545	Ppp1r3fos	4930524L23Rik	protein phosphatase 1, regulatory subunit 3F, opposite strand	ncRNA
mm_9519.1	chr1	173748933	173748951	-	1	NA	intron (NM_008329, intron 8 of 8)	intron (NM_008329, intron 8 of 8)	-7133	NM_001204910	226691	Mm.440876	NM_001204910	ENSMUSG00000073490	Ifi207	AI607873|Pyhin-A	interferon activated gene 207	protein-coding
mm_108536.1	chr12	84235844	84235853	+	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-16967	NM_001163501	238317	Mm.31256	NM_001163501	ENSMUSG00000042507	Elmsan1	9430029N19Rik|C130039O16Rik|Gm260	ELM2 and Myb/SANT-like domain containing 1	protein-coding
mm_68587.1	chr7	116033864	116033895	-	1	NA	intron (NM_001025559, intron 1 of 15)	CpG	-2832	NM_001025560	20679	Mm.323365	NM_011445	ENSMUSG00000051910	Sox6	AI987981|SOX-LZ	SRY (sex determining region Y)-box 6	protein-coding
mm_62028.1	chr7	91672456	91672483	+	1	NA	intron (NM_011807, intron 2 of 22)	intron (NM_011807, intron 2 of 22)	-389925	NM_001243046	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_24235.1	chr3	88950789	88950852	+	1	NA	promoter-TSS (NM_022994)	promoter-TSS (NM_022994)	-538	NM_001164533	65111	Mm.29028	NM_022994	ENSMUSG00000068921	Dap3	4921514D13Rik|DAP-3|MRP-S29|S29mt	death associated protein 3	protein-coding
mm_62522.1	chr7	102230822	102230824	+	1	NA	intron (NR_111937, intron 2 of 5)	intron (NR_111937, intron 2 of 5)	7795	NR_111937	233575	Mm.302013	NM_145583	ENSMUSG00000030990	Pgap2	1810006G21Rik|C76649|Frag1	post-GPI attachment to proteins 2	protein-coding
mm_39670.1	chr5	25248479	25248481	+	1	NA	intron (NM_144908, intron 2 of 11)	B1_Mur1|SINE|Alu	25587	NM_144908	231050	Mm.21814	NM_144908	ENSMUSG00000038072	Galnt11	A430075I06Rik|AI648252|E430002F06Rik	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 11	protein-coding
mm_109428.1	chr12	110601488	110601498	+	1	NA	promoter-TSS (NM_030238)	promoter-TSS (NM_030238)	98	NM_030238	13424	Mm.181430	NM_030238	ENSMUSG00000018707	Dync1h1	9930018I23Rik|AI894280|DHC1|DHC1a|DNCL|Dnchc1|Dnec1|Dnecl|Loa|MAP1C|P22|Swl|mKIAA0325	dynein cytoplasmic 1 heavy chain 1	protein-coding
mm_67160.1	chr7	73541739	73541758	-	1	NA	promoter-TSS (NM_001081345)	promoter-TSS (NM_001081345)	-2	NM_001081345	244059	Mm.34539	NM_001081345	ENSMUSG00000078671	Chd2	2810013C04Rik|2810040A01Rik|5630401D06Rik|AI851092|BC029703|CHD-2	chromodomain helicase DNA binding protein 2	protein-coding
mm_159260.1	chr2	154892831	154892831	-	1	NA	promoter-TSS (NM_026030)	promoter-TSS (NM_026030)	75	NM_026030	67204	Mm.377134	NM_026030	ENSMUSG00000074656	Eif2s2	2810026E11Rik|38kDa|AA408636|AA571381|AA986487|AW822225|D2Ertd303e|EIF2|EIF2B	eukaryotic translation initiation factor 2, subunit 2 (beta)	protein-coding
mm_20520.1	chr2	130772066	130772069	-	1	NA	intron (NM_029432, intron 16 of 36)	B1_Mur2|SINE|Alu	32034	NR_024097	100043766	Mm.447040	NR_024097		Gm14057	OTTMUSG00000015563	Ppp1r14c pseudogene	pseudo
mm_57568.1	chr6	127129173	127129183	-	1	NA	3' UTR (NM_009829, exon 5 of 5)	3' UTR (NM_009829, exon 5 of 5)	-19626	NM_177003	319801	Mm.101836	NM_177003	ENSMUSG00000038028	Tigar	9630033F20Rik|AA793651|AI595337|C79710|C85509	Trp53 induced glycolysis repulatory phosphatase	protein-coding
mm_95744.1	chr11	54848360	54848364	+	1	NA	intron (NM_029327, intron 4 of 4)	RLTR1B|LTR|ERV1	12229	NM_029327	75530	Mm.83578	NM_029327	ENSMUSG00000020268	Lyrm7	1700024C24Rik|9330147L21Rik	LYR motif containing 7	protein-coding
mm_6995.1	chr1	86359019	86359046	-	1	NA	promoter-TSS (NR_015507)	promoter-TSS (NR_015507)	423	NM_010880	17975	Mm.154378	NM_010880	ENSMUSG00000026234	Ncl	B530004O11Rik|C23|D0Nds28|D1Nds28|Nucl	nucleolin	protein-coding
mm_3758.1	chr1	156051387	156051393	+	1	NA	5' UTR (NM_001160182, exon 3 of 3)	5' UTR (NM_001160182, exon 3 of 3)	10529	NM_022329	240832	Mm.253335	NM_022329	ENSMUSG00000050565	Tor1aip2	1110020D10Rik|15kDa|A130072J07|AA103493|AW060462|AW610675|C77739|Ifrg15|Lull1	torsin A interacting protein 2	protein-coding
mm_107115.1	chr12	18217170	18217218	+	1	NA	Intergenic	Intergenic	-297316	NM_001033157	236366	Mm.352227	NM_001033157	ENSMUSG00000073197	5730507C01Rik	-	RIKEN cDNA 5730507C01 gene	protein-coding
mm_22205.1	chr2	173578301	173578334	-	1	NA	promoter-TSS (NM_001199955)	promoter-TSS (NM_001199955)	24	NM_001199955	70065	Mm.425115	NM_027303	ENSMUSG00000027517	Ankrd60	1700019A24Rik|1700030G11Rik	ankyrin repeat domain 60	protein-coding
mm_144093.1	chr18	3337847	3337870	+	1	NA	promoter-TSS (NM_001110852)	promoter-TSS (NM_001110852)	-269	NM_001110852	12916	Mm.5244	NM_013498	ENSMUSG00000063889	Crem	ICER|ICERI	cAMP responsive element modulator	protein-coding
mm_83380.1	chr9	44567715	44567721	-	1	NA	Intergenic	B4A|SINE|B4	-37174	NM_001110826	13209	Mm.267061	NM_007841	ENSMUSG00000032097	Ddx6	1110001P04Rik|E230023J21Rik|HLR2|mRCK/P54|p54|rck	DEAD (Asp-Glu-Ala-Asp) box polypeptide 6	protein-coding
mm_101595.1	chr11	34696220	34696233	-	1	NA	intron (NM_033374, intron 15 of 51)	intron (NM_033374, intron 15 of 51)	87679	NM_033374	94176	Mm.380679	NM_033374	ENSMUSG00000020143	Dock2	AI662014|AW122239|CED-5|Hch|MBC	dedicator of cyto-kinesis 2	protein-coding
mm_26258.1	chr3	142500548	142500554	+	1	NA	intron (NM_153564, intron 1 of 10)	intron (NM_153564, intron 1 of 10)	3617	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_160751.1	chr10	81532139	81532139	-	1	NA	intron (NM_010301, intron 4 of 6)	intron (NM_010301, intron 4 of 6)	-7914	NM_010304	14676	Mm.1546	NM_010304	ENSMUSG00000034792	Gna15	G[a]15|Galpha15	guanine nucleotide binding protein, alpha 15	protein-coding
mm_146965.1	chr18	33438742	33438760	-	1	NA	exon (NM_001267717, exon 5 of 5)	exon (NM_001267717, exon 5 of 5)	24883	NM_001267717	27528	Mm.407415	NM_053078	ENSMUSG00000042834	Nrep	AI325076|D0H4S114|Harp|P311|PTZ17|SEZ17	neuronal regeneration related protein	protein-coding
mm_113459.1	chr13	35963571	35963575	+	1	NA	Intergenic	Intergenic	-4333	NM_029628	76487	Mm.44745	NM_029628	ENSMUSG00000050423	Ppp1r3g	1600032L17Rik	protein phosphatase 1, regulatory (inhibitor) subunit 3G	protein-coding
mm_72241.1	chr8	75016259	75016271	+	1	NA	promoter-TSS (NM_001316754)	promoter-TSS (NM_001316754)	43	NM_001316754	70823	Mm.261739	NM_178017	ENSMUSG00000034518	Hmgxb4	4733401K04Rik|AI316803|Hmgb2l1	HMG box domain containing 4	protein-coding
mm_110584.1	chr12	56529397	56529397	-	1	NA	promoter-TSS (NR_045082)	promoter-TSS (NR_045082)	23	NR_045082	104798	Mm.310950	NR_045082		E030019B13Rik	AI413669	RIKEN cDNA E030019B13 gene	ncRNA
mm_142701.1	chr17	47868415	47868442	-	1	NA	3' UTR (NM_028767, exon 17 of 17)	3' UTR (NM_028767, exon 17 of 17)	-33737	NM_001109973	17240	Mm.329100	NM_010783	ENSMUSG00000032717	Mdfi	I-mf|I-mfa	MyoD family inhibitor	protein-coding
mm_54596.1	chr6	38254275	38254327	-	1	NA	promoter-TSS (NM_194061)	promoter-TSS (NM_194061)	-292	NM_194061	330286	Mm.277163	NM_194061	ENSMUSG00000063455	D630045J12Rik	Kiaa1549|mKIAA1549	RIKEN cDNA D630045J12 gene	protein-coding
mm_118722.1	chr14	22214291	22214313	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	194590	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_67252.1	chr7	75508599	75508605	-	1	NA	intron (NM_029332, intron 1 of 36)	intron (NM_029332, intron 1 of 36)	53068	NM_029332	75547	Mm.216107	NM_029332	ENSMUSG00000066406	Akap13	1700026G02Rik|5730522G15Rik|5830460E08Rik|AKAP-13|AKAP-Lbc|BRX|Ht31|LBC|PROTO-LB|PROTO-LBC	A kinase (PRKA) anchor protein 13	protein-coding
mm_39750.1	chr5	29659000	29659002	+	1	NA	intron (NM_133907, intron 19 of 22)	intron (NM_133907, intron 19 of 22)	-76897	NM_001037940	23950	Mm.290110	NM_011847	ENSMUSG00000029131	Dnajb6	Mrj|mDj4	DnaJ heat shock protein family (Hsp40) member B6	protein-coding
mm_20612.1	chr2	131854457	131854467	-	1	NA	3' UTR (NM_001166206, exon 2 of 2)	3' UTR (NM_001166206, exon 2 of 2)	5285	NM_001166206	71995	Mm.22	NM_028045	ENSMUSG00000037482	Erv3	1600014E20Rik|AA389086|AI426069|AI448024|D19349	endogenous retroviral sequence 3	protein-coding
mm_10207.1	chr2	5137851	5137868	+	1	NA	promoter-TSS (NM_028804)	promoter-TSS (NM_028804)	83	NM_028804	74186	Mm.274715	NM_028804	ENSMUSG00000026676	Ccdc3	2310045O21Rik	coiled-coil domain containing 3	protein-coding
mm_149593.1	chr19	16149077	16149112	+	1	NA	intron (NM_008139, intron 1 of 6)	B1F|SINE|Alu	-15004	NR_033228	595139	Mm.405662	NR_033228		E030024N20Rik	9030417F11Rik|Ppia-ps8	peptidylprolyl isomerase A pseudogene 8	pseudo
mm_77759.1	chr9	3000036	3000062	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	38694	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_131539.1	chr16	17759688	17759699	+	1	NA	promoter-TSS (NM_145479)	promoter-TSS (NM_145479)	72	NM_145479	224023	Mm.282807	NM_145479	ENSMUSG00000022750	Klhl22	2610318I18Rik|Kelchl	kelch-like 22	protein-coding
mm_125001.1	chr15	23489868	23489869	+	1	NA	Intergenic	Intergenic	453405	NM_001081299	320865	Mm.241965	NM_001081299	ENSMUSG00000040420	Cdh18	B230220E17Rik|Cdh14l	cadherin 18	protein-coding
mm_108073.1	chr12	73942256	73942266	+	1	NA	exon (NM_010431, exon 12 of 15)	exon (NM_010431, exon 12 of 15)	-22269	NM_178392	75627	Mm.25937	NM_178392	ENSMUSG00000021113	Snapc1	2700033G17Rik|AU015787	small nuclear RNA activating complex, polypeptide 1	protein-coding
mm_63742.1	chr7	130936161	130936171	+	1	NA	promoter-TSS (NM_019564)	promoter-TSS (NM_019564)	-37	NM_019564	56213	Mm.30156	NM_019564	ENSMUSG00000006205	Htra1	AI429470|HTRA|L56|Prss11|RSPP11	HtrA serine peptidase 1	protein-coding
mm_105066.1	chr11	100721315	100721320	-	1	NA	intron (NM_024456, intron 1 of 5)	intron (NM_024456, intron 1 of 5)	7467	NM_029307	75482	Mm.46175	NM_029307	ENSMUSG00000017832	Hspb9	1700007H20Rik	heat shock protein, alpha-crystallin-related, B9	protein-coding
mm_41899.1	chr5	105519510	105519512	+	1	NA	promoter-TSS (NM_133897)	promoter-TSS (NM_133897)	40	NM_133897	100604	Mm.319847	NM_133897	ENSMUSG00000054720	Lrrc8c	AD158|AI326115|E430036I04Rik|fad158	leucine rich repeat containing 8 family, member C	protein-coding
mm_168832.1	chr12	22906453	22906464	-	1	NA	Intergenic	CpG	103785	NR_015504	69732	Mm.391403	NM_028362	ENSMUSG00000073164	2410018L13Rik	2810480C08Rik	RIKEN cDNA 2410018L13 gene	ncRNA
mm_117663.1	chr13	93499668	93499674	-	1	NA	5' UTR (NM_021310, exon 1 of 11)	5' UTR (NM_021310, exon 1 of 11)	137	NM_021310	57748	Mm.100273	NM_021310	ENSMUSG00000021690	Jmy	-	junction-mediating and regulatory protein	protein-coding
mm_13477.1	chr2	105904630	105904685	+	1	NA	promoter-TSS (NM_023876)	promoter-TSS (NM_023876)	19	NM_028260	66541	Mm.272253	NM_028260	ENSMUSG00000042670	Immp1l	1500034J20Rik|2610528O17Rik|AU042386	IMP1 inner mitochondrial membrane peptidase-like (S. cerevisiae)	protein-coding
mm_43864.1	chr5	143472936	143472944	+	1	NA	intron (NM_144915, intron 2 of 14)	intron (NM_144915, intron 2 of 14)	8447	NM_144915	231871	Mm.469963	NM_144915	ENSMUSG00000039206	Daglb	E330036I19Rik	diacylglycerol lipase, beta	protein-coding
mm_135180.1	chr16	35981354	35981372	-	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-2000	NM_008465	16646	Mm.3991	NM_008465	ENSMUSG00000022905	Kpna1	AW494490|IPOA5|NPI1|Rch2|mSRP1	karyopherin (importin) alpha 1	protein-coding
mm_105413.1	chr11	103638853	103638861	-	1	NA	promoter-TSS (NM_027083)	promoter-TSS (NM_027083)	17	NM_027083	69444	Mm.275677	NM_027083	ENSMUSG00000020945	Lyzl6	1700023H08Rik|Lyc1|Lyzb	lysozyme-like 6	protein-coding
mm_73505.1	chr8	107334901	107334908	+	1	NA	intron (NM_001286260, intron 2 of 12)	B2_Mm1t|SINE|B2	41434	NM_133957	54446	Mm.390057	NM_018823	ENSMUSG00000003847	Nfat5	AI225870|B130038B15Rik|CAG-8|CAG80|NFATL1|OREBP|TonEBP|mKIAA0827|nfatz	nuclear factor of activated T cells 5	protein-coding
mm_121559.1	chr14	122484379	122484387	+	1	NA	Intergenic	Intergenic	8999	NM_009574	22772	Mm.308936	NM_009574	ENSMUSG00000061524	Zic2	HPE5|Ku	zinc finger protein of the cerebellum 2	protein-coding
mm_109846.1	chr12	4593738	4593753	-	1	NA	intron (NM_011365, intron 1 of 38)	intron (NM_011365, intron 1 of 38)	737	NM_001198968	20403	Mm.341204	NM_011365	ENSMUSG00000020640	Itsn2	AI327390|Ese2|Sh3d1B|Sh3p18|mKIAA1256	intersectin 2	protein-coding
mm_139056.1	chr17	46383726	46383792	+	1	NA	promoter-TSS (NM_021346)	promoter-TSS (NM_021346)	-7	NM_207671	57908	Mm.439916	NM_021346	ENSMUSG00000015597	Zfp318	2610034E08Rik|D530032D06Rik|TZF|Znf318	zinc finger protein 318	protein-coding
mm_120339.1	chr14	63493689	63493702	+	1	NA	intron (NM_021480, intron 8 of 8)	CpG	15397	NM_021480	58865	Mm.354229	NM_021480	ENSMUSG00000021953	Tdh	-	L-threonine dehydrogenase	protein-coding
mm_213.1	chr1	16688033	16688073	+	1	NA	promoter-TSS (NM_001159711)	promoter-TSS (NM_001159711)	-403	NM_001159711	17087	Mm.116844	NM_016923	ENSMUSG00000025779	Ly96	ESOP-1|MD-2|MD2	lymphocyte antigen 96	protein-coding
mm_52632.1	chr6	117174375	117174381	+	1	NA	3' UTR (NM_021704, exon 3 of 3)	3' UTR (NM_021704, exon 3 of 3)	5843	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_21179.1	chr2	154892905	154892915	-	1	NA	promoter-TSS (NM_026030)	promoter-TSS (NM_026030)	-4	NM_026030	67204	Mm.377134	NM_026030	ENSMUSG00000074656	Eif2s2	2810026E11Rik|38kDa|AA408636|AA571381|AA986487|AW822225|D2Ertd303e|EIF2|EIF2B	eukaryotic translation initiation factor 2, subunit 2 (beta)	protein-coding
mm_109277.1	chr12	109547059	109547086	+	1	NA	intron (NR_027651, intron 5 of 8)	intron (NR_027651, intron 5 of 8)	1674	NR_003633	17263	Mm.289645	NM_144513	ENSMUSG00000021268	Meg3	2900016C05Rik|3110050O07Rik|6330408G06Rik|AI425946|AW108224|D12Bwg1266e|Gtl2|R74756|R75394	maternally expressed 3	ncRNA
mm_50994.1	chr6	63257808	63257809	+	1	NA	intron (NM_008167, intron 1 of 15)	intron (NM_008167, intron 1 of 15)	951	NM_008167	14804	Mm.439651	NM_008167	ENSMUSG00000071424	Grid2	B230104L07Rik|GluD2|GluRdelta2|Lc|Lc<J>|MMS10-AC|Ms10ac|cpr|ho|nmf408|tpr	glutamate receptor, ionotropic, delta 2	protein-coding
mm_28133.1	chr3	87174459	87174485	-	1	NA	5' UTR (NM_130867, exon 1 of 16)	5' UTR (NM_130867, exon 1 of 16)	275	NM_001170985	170643	Mm.89552	NM_130867	ENSMUSG00000041734	Kirrel	6720469N11Rik|Kirrel1|Neph1	kin of IRRE like (Drosophila)	protein-coding
mm_54155.1	chr6	22444430	22444437	-	1	NA	Intergenic	Intergenic	-88352	NM_138587	27999	Mm.490307	NM_138587	ENSMUSG00000029672	Fam3c	D6Wsu176e|Ilei	family with sequence similarity 3, member C	protein-coding
mm_3683.1	chr1	153740345	153740360	+	1	NA	promoter-TSS (NM_011267)	promoter-TSS (NM_011267)	-1	NM_011267	19734	Mm.181709	NM_011267	ENSMUSG00000026475	Rgs16	Rgs14|Rgsr	regulator of G-protein signaling 16	protein-coding
mm_85458.1	chr9	105420447	105420457	-	1	NA	intron (NM_001253834, intron 23 of 27)	B4A|SINE|B4	19664	NM_001164828	66595	Mm.84941	NM_025651	ENSMUSG00000032567	Aste1	1100001A21Rik|AV006403	asteroid homolog 1 (Drosophila)	protein-coding
mm_127264.1	chr15	99712805	99712821	+	1	NA	3' UTR (NM_031842, exon 13 of 13)	3' UTR (NM_031842, exon 13 of 13)	-4780	NM_010271	14555	Mm.252391	NM_010271	ENSMUSG00000023019	Gpd1	AI747587|Gdc-1|Gdc1|mKIAA4010	glycerol-3-phosphate dehydrogenase 1 (soluble)	protein-coding
mm_70987.1	chr8	27261424	27261433	+	1	NA	intron (NM_007918, intron 1 of 2)	intron (NM_007918, intron 1 of 2)	1101	NM_007918	13685	Mm.6700	NM_007918	ENSMUSG00000031490	Eif4ebp1	4e-bp1|AA959816|PHAS-I	eukaryotic translation initiation factor 4E binding protein 1	protein-coding
mm_136872.1	chr17	12917273	12917276	+	1	NA	intron (NM_001290712, intron 1 of 10)	intron (NM_001290712, intron 1 of 10)	945	NM_013686	21454	Mm.229342	NM_013686	ENSMUSG00000068039	Tcp1	AI528772|CCT|Cct1|Ccta|TRic|Tcp-1|Tp63|c-cpn|p63	t-complex protein 1	protein-coding
mm_137315.1	chr17	24886021	24886035	+	1	NA	promoter-TSS (NM_001163750)	promoter-TSS (NM_001163750)	322	NM_011956	26426	Mm.36718	NM_011956	ENSMUSG00000039183	Nubp2	D17Wsu11e	nucleotide binding protein 2	protein-coding
mm_94767.1	chr11	21238876	21238966	+	1	NA	promoter-TSS (NM_001290628)	promoter-TSS (NM_001290628)	-111	NM_139061	245944	Mm.170103	NM_139061	ENSMUSG00000020128	Vps54	Hcc8|Vps54l|mSLP8|wr	VPS54 GARP complex subunit	protein-coding
mm_78940.1	chr9	45138297	45138305	+	1	NA	promoter-TSS (NM_001013390)	promoter-TSS (NM_001013390)	-741	NM_001013390	399548	Mm.335112	NM_001013390	ENSMUSG00000046480	Scn4b	Gm1471	sodium channel, type IV, beta	protein-coding
mm_1580.1	chr1	74281226	74281228	+	1	NA	intron (NM_001190444, intron 8 of 10)	intron (NM_001190444, intron 8 of 10)	2627	NM_174985	227289	Mm.246587	NM_174985	ENSMUSG00000064272	Gpbar1	BG37|GPCR|GPR131|M-BAR|TGR5	G protein-coupled bile acid receptor 1	protein-coding
mm_121879.1	chr14	21052421	21052448	-	1	NA	promoter-TSS (NM_134079)	promoter-TSS (NM_134079)	8	NM_018829	55946	Mm.376269	NM_018829	ENSMUSG00000021824	Ap3m1	1200013D09Rik|C78982|R75378	adaptor-related protein complex 3, mu 1 subunit	protein-coding
mm_45632.1	chr5	76331103	76331142	-	1	NA	promoter-TSS (NM_023508)	promoter-TSS (NM_023508)	34	NM_001310637	79455	Mm.143764	NM_023508	ENSMUSG00000029235	Pdcl2	1700010B22Rik|1700016K07Rik|Mgcphlp|Tphlp	phosducin-like 2	protein-coding
mm_57098.1	chr6	122590507	122590544	-	1	NA	intron (NM_001134391, intron 4 of 7)	B3A|SINE|B2	11919	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_54384.1	chr6	31217665	31217668	-	1	NA	intron (NR_110469, intron 1 of 3)	intron (NR_110469, intron 1 of 3)	808	NR_110470	232685	Mm.443019	NM_144555	ENSMUSG00000044471	Lncpint	Lincpint|MNCb-1768|Pint|linc-Pint	long non-protein coding RNA, Trp53 induced transcript	ncRNA
mm_14750.1	chr2	144556307	144556323	+	1	NA	promoter-TSS (NM_001252545)	promoter-TSS (NM_001252545)	86	NM_001252545	27054	Mm.248492	NM_019787	ENSMUSG00000027429	Sec23b	-	SEC23 homolog B, COPII coat complex component	protein-coding
mm_140851.1	chr17	23680431	23680442	-	1	NA	intron (NM_018777, intron 2 of 2)	intron (NM_018777, intron 2 of 2)	1071	NM_018777	54419	Mm.86421	NM_018777	ENSMUSG00000023906	Cldn6	AL024037	claudin 6	protein-coding
mm_52601.1	chr6	117173493	117173505	+	1	NA	exon (NM_021704, exon 3 of 3)	exon (NM_021704, exon 3 of 3)	4964	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_3859.1	chr1	160978626	160978656	+	1	NA	promoter-TSS (NM_080844)	promoter-TSS (NM_080844)	35	NM_080844	11905	Mm.260770	NM_080844	ENSMUSG00000026715	Serpinc1	AI114908|ATIII|At-3|At3	serine (or cysteine) peptidase inhibitor, clade C (antithrombin), member 1	protein-coding
mm_17989.1	chr2	37919987	37920008	-	1	NA	intron (NM_146122, intron 13 of 21)	intron (NM_146122, intron 13 of 21)	143748	NM_001163566	241324	Mm.392369	NM_001163566	ENSMUSG00000035403	Crb2	5930402A21|BC043114	crumbs family member 2	protein-coding
mm_69755.1	chr7	140997960	140997982	-	1	NA	Intergenic	Intergenic	12773	NM_025378	66141	Mm.141021	NM_025378	ENSMUSG00000025492	Ifitm3	1110004C05Rik|Cd225|Cdw217|DSPA2b|Fgls|IP15|mil-1	interferon induced transmembrane protein 3	protein-coding
mm_155832.1	chrX	100740906	100740907	+	1	NA	Intergenic	Intergenic	10720	NM_001305941	71584	Mm.283495	NM_023608	ENSMUSG00000019359	Gdpd2	9130017L10Rik|Gde3|Obdpf	glycerophosphodiester phosphodiesterase domain containing 2	protein-coding
mm_53894.1	chr6	3382001	3382014	-	1	NA	intron (NM_010156, intron 1 of 1)	RMER6C|LTR|ERVK	17564	NM_010156	209086	Mm.196013	NM_010156	ENSMUSG00000047735	Samd9l	AA175286|ESTM25|mKIAA2005	sterile alpha motif domain containing 9-like	protein-coding
mm_117481.1	chr13	77131313	77131329	-	1	NA	intron (NM_134071, intron 1 of 20)	intron (NM_134071, intron 1 of 20)	4147	NM_134071	105377	Mm.209730	NM_134071	ENSMUSG00000021597	Slf1	2700017A04Rik|AW545819|Ankrd32|Brctd1|Brctx|C730024G01Rik	SMC5-SMC6 complex localization factor 1	protein-coding
mm_112564.1	chr13	13512152	13512158	+	1	NA	3' UTR (NM_010917, exon 20 of 20)	3' UTR (NM_010917, exon 20 of 20)	74553	NM_010917	18073	Mm.4691	NM_010917	ENSMUSG00000005397	Nid1	A630025O17|Nid|entactin|entactin-1|nidogen-1	nidogen 1	protein-coding
mm_116515.1	chr13	45709020	45709025	-	1	NA	intron (NM_001199305, intron 5 of 7)	intron (NM_001199305, intron 5 of 7)	201578	NM_025508	66355	Mm.290802	NM_025508	ENSMUSG00000000253	Gmpr	2310004P21Rik|AV028449|GMPR 1	guanosine monophosphate reductase	protein-coding
mm_75889.1	chr8	70873232	70873238	-	1	NA	intron (NM_026964, intron 1 of 4)	intron (NM_026964, intron 1 of 4)	255	NM_026964	234388	Mm.295791	NM_026964	ENSMUSG00000007721	Ccdc124	1810023B24Rik	coiled-coil domain containing 124	protein-coding
mm_5974.1	chr1	57519424	57519441	-	1	NA	Intergenic	Intergenic	-112758	NM_001302963	68736	Mm.288490	NM_001037742	ENSMUSG00000048495	Tyw5	1110034B05Rik	tRNA-yW synthesizing protein 5	protein-coding
mm_46791.1	chr5	112767319	112767329	-	1	NA	intron (NM_028901, intron 34 of 43)	intron (NM_028901, intron 34 of 43)	-25968	NR_040675	67360	Mm.59218	NR_040675	ENSMUSG00000098230	1700095B10Rik	-	RIKEN cDNA 1700095B10 gene	ncRNA
mm_157055.1	chrX	8090443	8090494	-	1	NA	promoter-TSS (NM_009515)	promoter-TSS (NM_009515)	23	NM_009515	22376	Mm.4735	NM_009515	ENSMUSG00000031165	Was	U42471|Wasp	Wiskott-Aldrich syndrome	protein-coding
mm_29730.1	chr3	126669005	126669044	-	1	NA	intron (NM_001346636, intron 2 of 20)	intron (NM_001346636, intron 2 of 20)	72073	NM_023813	108058	Mm.255822	NM_023813	ENSMUSG00000053819	Camk2d	2810011D23Rik|8030469K03Rik|CaMK II|[d]-CaMKII	calcium/calmodulin-dependent protein kinase II, delta	protein-coding
mm_145307.1	chr18	53464183	53464185	+	1	NA	promoter-TSS (NM_001033281)	promoter-TSS (NM_001033281)	-362	NM_001033281	225518	Mm.297645	NM_001033281	ENSMUSG00000069378	Prdm6	Gm92|PRISM	PR domain containing 6	protein-coding
mm_123370.1	chr14	63177907	63177961	-	1	NA	5' UTR (NM_010191, exon 3 of 10)	5' UTR (NM_010191, exon 3 of 10)	1644	NM_010191	14137	Mm.474432	NM_010191	ENSMUSG00000021273	Fdft1	SQS|SS	farnesyl diphosphate farnesyl transferase 1	protein-coding
mm_114864.1	chr13	93771657	93771702	+	1	NA	promoter-TSS (NM_009712)	promoter-TSS (NM_009712)	0	NM_009712	11881	Mm.300178	NM_009712	ENSMUSG00000042082	Arsb	1110007C02Rik|AI480648|As-1|As-1r|As-1s|As-1t|As1|As1-r|As1-s|As1-t|Asr-1|Ast-1	arylsulfatase B	protein-coding
mm_171670.1	chr4	48658038	48658047	+	1	NA	intron (NM_021436, intron 8 of 9)	B1_Mm|SINE|Alu	-5472	NM_026509	68016	Mm.133444	NM_026509	ENSMUSG00000028348	Murc	2310039E09Rik	muscle-related coiled-coil protein	protein-coding
mm_61463.1	chr7	75609898	75609908	+	1	NA	exon (NM_029332, exon 7 of 37)	exon (NM_029332, exon 7 of 37)	154369	NM_029332	75547	Mm.216107	NM_029332	ENSMUSG00000066406	Akap13	1700026G02Rik|5730522G15Rik|5830460E08Rik|AKAP-13|AKAP-Lbc|BRX|Ht31|LBC|PROTO-LB|PROTO-LBC	A kinase (PRKA) anchor protein 13	protein-coding
mm_144988.1	chr18	38251081	38251092	+	1	NA	promoter-TSS (NR_015475)	promoter-TSS (NR_015475)	-521	NR_027904	73516	Mm.48776	NR_015475	ENSMUSG00000097080	1700086O06Rik	-	RIKEN cDNA 1700086O06 gene	ncRNA
mm_105451.1	chr11	104469433	104469467	-	1	NA	Intergenic	CpG	-27159	NM_001081045	76719	Mm.136418	NM_001081045	ENSMUSG00000018412	Kansl1	1700081L11Rik|9430041J06Rik|mKIAA1267	KAT8 regulatory NSL complex subunit 1	protein-coding
mm_102306.1	chr11	55608282	55608295	-	1	NA	promoter-TSS (NM_020492)	promoter-TSS (NM_020492)	-90	NM_020492	14654	Mm.89320	NM_020492	ENSMUSG00000000263	Glra1	nmf11|oscillator|ot|spasmodic|spd	glycine receptor, alpha 1 subunit	protein-coding
mm_74401.1	chr8	3279491	3279603	-	1	NA	promoter-TSS (NM_001330056)	promoter-TSS (NM_001330056)	70	NM_010568	16337	Mm.268003	NM_010568	ENSMUSG00000005534	Insr	4932439J01Rik|CD220|D630014A15Rik|IR|IR-A|IR-B	insulin receptor	protein-coding
mm_42199.1	chr5	112292304	112292308	+	1	NA	intron (NM_001326590, intron 1 of 5)	intron (NM_001326590, intron 1 of 5)	15615	NM_009419	22022	Mm.250631	NM_009419	ENSMUSG00000029344	Tpst2	AI448750|D5Ucla3|Tango13b|grm|grt	protein-tyrosine sulfotransferase 2	protein-coding
mm_68165.1	chr7	103812625	103812633	-	1	NA	3' UTR (NM_016956, exon 3 of 3)	3' UTR (NM_016956, exon 3 of 3)	1294	NM_016956	15130	Mm.288567	NM_016956		Hbb-b2	AI036344|Hbb2|Hbbt2|beta2	hemoglobin, beta adult minor chain	protein-coding
mm_166002.1	chr4	115884349	115884356	+	1	NA	promoter-TSS (NM_001039124)	promoter-TSS (NM_001039124)	-48	NM_001039124	654462	Mm.388913	NM_001039124	ENSMUSG00000073774	Kncn	Kino|L5	kinocilin	protein-coding
mm_75513.1	chr8	54529936	54529946	-	1	NA	promoter-TSS (NM_029701)	promoter-TSS (NM_029701)	57	NM_029701	76687	Mm.86437	NM_029701	ENSMUSG00000054408	Spcs3	1810011E08Rik|SPC22/23	signal peptidase complex subunit 3 homolog (S. cerevisiae)	protein-coding
mm_94574.1	chr11	11690115	11690135	+	1	NA	promoter-TSS (NM_001301865)	promoter-TSS (NM_001301865)	-52	NM_001301865	22778	Mm.103545	NM_009578	ENSMUSG00000018654	Ikzf1	5832432G11Rik|Ikaros|LyF-1|Zfpn1a1|Znfn1a1|hlk-1|mKIAA4227	IKAROS family zinc finger 1	protein-coding
mm_83997.1	chr9	57449327	57449340	-	1	NA	intron (NM_001301634, intron 3 of 6)	intron (NM_001301634, intron 3 of 6)	-9219	NM_176831	66812	Mm.250508	NM_176831	ENSMUSG00000063849	Ppcdc	1810057I13Rik|8430432M10Rik	phosphopantothenoylcysteine decarboxylase	protein-coding
mm_71090.1	chr8	34815387	34815399	+	1	NA	intron (NM_176933, intron 1 of 3)	intron (NM_176933, intron 1 of 3)	7783	NM_176933	319520	Mm.170276	NM_176933	ENSMUSG00000031530	Dusp4	2700078F24Rik|AI844617|BB104621|E130306H24Rik|MKP2	dual specificity phosphatase 4	protein-coding
mm_97382.1	chr11	77718797	77718812	+	1	NA	TTS (NM_001024205)	TTS (NM_001024205)	6489	NM_001313933	12957	Mm.22830	NM_009965	ENSMUSG00000000724	Cryba1	BA3/A1|Cryb	crystallin, beta A1	protein-coding
mm_126590.1	chr15	82346043	82346088	+	1	NA	promoter-TSS (NM_026914)	promoter-TSS (NM_026914)	19	NM_026914	69029	Mm.260042	NM_026914	ENSMUSG00000022452	Smdt1	1500032L24Rik|Emre	single-pass membrane protein with aspartate rich tail 1	protein-coding
mm_56526.1	chr6	99521230	99521260	-	1	NA	promoter-TSS (NM_001347345)	promoter-TSS (NM_001347345)	-252	NM_001347345	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_39199.1	chr4	156022276	156022286	-	1	NA	non-coding (NR_040563, exon 3 of 3)	non-coding (NR_040563, exon 3 of 3)	1543	NR_040563	100038526	Mm.191866	NR_040563		Gm10560	ENSMUSG00000073673	predicted gene 10560	ncRNA
mm_120363.1	chr14	64440667	64440720	+	1	NA	intron (NM_001253712, intron 1 of 5)	CpG	333	NM_001253715	110265	Mm.26713	NM_026322	ENSMUSG00000054733	Msra	2310045J23Rik|6530413P12Rik|MSR-A	methionine sulfoxide reductase A	protein-coding
mm_51650.1	chr6	86028835	86028839	+	1	NA	5' UTR (NM_001271860, exon 1 of 13)	5' UTR (NM_001271860, exon 1 of 13)	156	NM_001271860	11519	Mm.104155	NM_013458	ENSMUSG00000030000	Add2	2900072M03Rik|add97	adducin 2 (beta)	protein-coding
mm_121361.1	chr14	117242109	117242111	+	1	NA	intron (NM_001079844, intron 2 of 9)	intron (NM_001079844, intron 2 of 9)	316813	NM_011821	23888	Mm.440025	NM_011821	ENSMUSG00000058571	Gpc6	-	glypican 6	protein-coding
mm_31134.1	chr4	43249575	43249600	+	1	NA	intron (NM_001310758, intron 24 of 38)	intron (NM_001310758, intron 24 of 38)	-17572	NM_177195	320571	Mm.74465	NM_177195	ENSMUSG00000028457	Atp8b5	4930417M19Rik|Feta	ATPase, class I, type 8B, member 5	protein-coding
mm_4920.1	chr1	190916736	190916739	+	1	NA	Intergenic	RSINE1|SINE|B4	-4967	NM_178775	320119	Mm.220912	NM_178775	ENSMUSG00000089872	Rps6kc1	AA682037|B130003F20Rik|C80612|Rpk118	ribosomal protein S6 kinase polypeptide 1	protein-coding
mm_145043.1	chr18	39773506	39773576	+	1	NA	promoter-TSS (NM_011033)	promoter-TSS (NM_011033)	44	NM_011033	18459	Mm.9493	NM_011033	ENSMUSG00000051732	Pabpc2	Pabp|Pabp+|Pabp2	poly(A) binding protein, cytoplasmic 2	protein-coding
mm_115442.1	chr13	117709015	117709017	+	1	NA	intron (NR_045508, intron 4 of 4)	intron (NR_045508, intron 4 of 4)	10995	NR_045508	71100	Mm.414841	NR_045508	ENSMUSG00000079048	4933413L06Rik	-	RIKEN cDNA 4933413L06 gene	ncRNA
mm_77882.1	chr9	7280246	7280256	+	1	NA	exon (NM_008607, exon 8 of 10)	exon (NM_008607, exon 8 of 10)	7737	NM_008607	17386	Mm.5022	NM_008607	ENSMUSG00000050578	Mmp13	Clg|MMP-13|Mmp1	matrix metallopeptidase 13	protein-coding
mm_51969.1	chr6	91758464	91758484	+	1	NA	3' UTR (NM_009320, exon 15 of 15)	3' UTR (NM_009320, exon 15 of 15)	48919	NM_001159507	243547	Mm.333264	NM_001033353	ENSMUSG00000030098	Grip2	-	glutamate receptor interacting protein 2	protein-coding
mm_108018.1	chr12	73598477	73598488	+	1	NA	intron (NM_001313977, intron 2 of 14)	intron (NM_001313977, intron 2 of 14)	13686	NM_008856	18755	Mm.341677	NM_008856	ENSMUSG00000021108	Prkch	Pkch	protein kinase C, eta	protein-coding
mm_94361.1	chr11	5009495	5009506	+	1	NA	intron (NM_007454, intron 1 of 20)	intron (NM_007454, intron 1 of 20)	22676	NM_007454	11764	Mm.274816	NM_007454	ENSMUSG00000009090	Ap1b1	Adtb1|b2b1660Clo	adaptor protein complex AP-1, beta 1 subunit	protein-coding
mm_70522.1	chr8	12949495	12949510	+	1	NA	promoter-TSS (NM_001159485)	promoter-TSS (NM_001159485)	84	NM_001159485	17207	Mm.334413	NM_178076	ENSMUSG00000031442	Mcf2l	C130040G20Rik|Dbs|Ost|mKIAA0362	mcf.2 transforming sequence-like	protein-coding
mm_119085.1	chr14	30889895	30889904	+	1	NA	exon (NM_001289633, exon 4 of 22)	exon (NM_001289633, exon 4 of 22)	3423	NM_001289632	16427	Mm.34819	NM_018746	ENSMUSG00000021922	Itih4	ITI-HC4|Itih-4|PK-120	inter alpha-trypsin inhibitor, heavy chain 4	protein-coding
mm_75652.1	chr8	65129446	65129463	-	1	NA	promoter-TSS (NR_033217)	promoter-TSS (NR_033217)	83	NR_033217	407795	Mm.387876	NR_033217	ENSMUSG00000074300	BC030870	-	cDNA sequence BC030870	ncRNA
mm_57603.1	chr6	127796349	127796364	-	1	NA	Intergenic	Intergenic	-8213	NR_106092	102466996		NR_106092	ENSMUSG00000104804	Mir7233	mmu-mir-7233	microRNA 7233	ncRNA
mm_84671.1	chr9	72017212	72017215	-	1	NA	intron (NM_001253862, intron 3 of 19)	Tigger7|DNA|TcMar-Tigger	53772	NR_029879	723889		NR_029879	ENSMUSG00000105200	Mir378a	Mir378|Mirn378|mmu-mir-378|mmu-mir-378a	microRNA 378a	ncRNA
mm_46792.1	chr5	112767336	112767347	-	1	NA	intron (NM_028901, intron 34 of 43)	intron (NM_028901, intron 34 of 43)	-25951	NR_040675	67360	Mm.59218	NR_040675	ENSMUSG00000098230	1700095B10Rik	-	RIKEN cDNA 1700095B10 gene	ncRNA
mm_38777.1	chr4	148038829	148038847	-	1	NA	promoter-TSS (NM_010840)	promoter-TSS (NM_010840)	-25	NM_011929	26372	Mm.89987	NM_011929	ENSMUSG00000029016	Clcn6	AI850629|Clc6	chloride channel, voltage-sensitive 6	protein-coding
mm_150179.1	chr19	32619998	32620031	+	1	NA	promoter-TSS (NM_011864)	promoter-TSS (NM_011864)	9	NM_011864	23972	Mm.203916	NM_011864	ENSMUSG00000024899	Papss2	1810018P12Rik|AI159688|AtpsU2|Atpsk2|Sk2|bm	3'-phosphoadenosine 5'-phosphosulfate synthase 2	protein-coding
mm_86427.1	chr10	3834912	3834928	+	1	NA	intron (NM_001159942, intron 2 of 16)	intron (NM_001159942, intron 2 of 16)	-37747	NM_001033253	213783	Mm.150831	NM_001033253	ENSMUSG00000040624	Plekhg1	D10Ertd733e|Gm521|mKIAA1209	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	protein-coding
mm_27771.1	chr3	72942204	72942206	-	1	NA	intron (NM_001081137, intron 15 of 46)	intron (NM_001081137, intron 15 of 46)	24661	NM_001081137	69983	Mm.261054	NM_001081137	ENSMUSG00000027790	Sis	2010204N08Rik|SI|Si-s	sucrase isomaltase (alpha-glucosidase)	protein-coding
mm_128585.1	chr15	58076193	58076243	-	1	NA	5' UTR (NM_001042438, exon 1 of 5)	5' UTR (NM_001042438, exon 1 of 5)	290	NM_001042438	22770	Mm.244931	NM_009572	ENSMUSG00000022361	Zhx1	-	zinc fingers and homeoboxes 1	protein-coding
mm_167159.1	chr7	134419949	134419950	-	1	NA	Intergenic	Intergenic	-43121	NM_001081331	71007	Mm.334285	NM_001081331	ENSMUSG00000030994	D7Ertd443e	4933400E14Rik|FATS|Gm497	DNA segment, Chr 7, ERATO Doi 443, expressed	protein-coding
mm_48170.1	chr5	137153168	137153177	-	1	NA	Intergenic	Intergenic	-36965	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_58314.1	chr6	146401339	146401360	-	1	NA	intron (NM_010586, intron 9 of 55)	(TG)n|Simple_repeat|Simple_repeat	100874	NM_010586	16439	Mm.7800	NM_010586	ENSMUSG00000030287	Itpr2	AI649341|InsP3R-2|InsP3R-5|Ip3r2|Itpr5|insP3R2	inositol 1,4,5-triphosphate receptor 2	protein-coding
mm_57932.1	chr6	134566917	134566995	-	1	NA	promoter-TSS (NM_008514)	promoter-TSS (NM_008514)	-43	NM_008514	16974	Mm.321990	NM_008514	ENSMUSG00000030201	Lrp6	C030016K15Rik|Cd|Gw|ska26|ska<m26Jus>|skax26	low density lipoprotein receptor-related protein 6	protein-coding
mm_17802.1	chr2	33353588	33353608	-	1	NA	intron (NM_001290572, intron 1 of 17)	intron (NM_001290572, intron 1 of 17)	17896	NM_001290570	241308	Mm.274249	NM_175211	ENSMUSG00000038831	Ralgps1	5830418G11Rik|AI853783|AI854138|RALGEF2|RALGPS1A|RalGEF 2|mKIAA0351	Ral GEF with PH domain and SH3 binding motif 1	protein-coding
mm_168851.1	chr12	24097225	24097226	-	1	NA	promoter-TSS (NM_001256489)	promoter-TSS (NM_001256489)	44	NM_001256489	66808	Mm.379124	NM_001256489	ENSMUSG00000073158	9030624G23Rik	-	RIKEN cDNA 9030624G23 gene	protein-coding
mm_123605.1	chr14	68086795	68086810	-	1	NA	exon (NM_010910, exon 3 of 4)	exon (NM_010910, exon 3 of 4)	2918	NM_010910	18039	Mm.1956	NM_010910	ENSMUSG00000022055	Nefl	AI847934|CMT2E|NF-L|NF68|Nfl	neurofilament, light polypeptide	protein-coding
mm_129771.1	chr15	82782180	82782184	-	1	NA	Intergenic	Intergenic	12063	NM_029562	76279	Mm.439931	NM_029562	ENSMUSG00000022445	Cyp2d26	1300006E06Rik	cytochrome P450, family 2, subfamily d, polypeptide 26	protein-coding
mm_48740.1	chr5	147688037	147688044	-	1	NA	intron (NM_010228, intron 3 of 29)	L1M4|LINE|L1	37948	NM_010228	14254	Mm.389712	NM_010228	ENSMUSG00000029648	Flt1	AI323757|Flt-1|VEGFR-1|VEGFR1|sFlt1	FMS-like tyrosine kinase 1	protein-coding
mm_168027.1	chrY	90738343	90738372	+	1	NA	Intergenic	IMPB_01|Satellite|Satellite	16693	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_34362.1	chr4	144892784	144892803	+	1	NA	promoter-TSS (NM_001172424)	promoter-TSS (NM_001172424)	-34	NM_001172424	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding
mm_14113.1	chr2	125859164	125859225	+	1	NA	promoter-TSS (NM_001285513)	promoter-TSS (NM_001285513)	85	NM_175154	69976	Mm.20216	NM_175154	ENSMUSG00000027207	Galk2	2810017M24Rik|AI327030|Gk2	galactokinase 2	protein-coding
mm_143320.1	chr17	66319532	66319547	-	1	NA	Intergenic	Intergenic	130211	NM_172963	68617	Mm.33421	NM_172963	ENSMUSG00000052105	Mtcl1	1110012J17Rik|Ccdc165|D130071O13|Kiaa0802|Soga2|mKIAA0802|t8219b25	microtubule crosslinking factor 1	protein-coding
mm_44747.1	chr5	31220492	31220627	-	1	NA	promoter-TSS (NM_008014)	promoter-TSS (NM_008014)	-14	NM_008014	14208	Mm.14501	NM_008014	ENSMUSG00000029147	Ppm1g	AI385652|Fin13	protein phosphatase 1G (formerly 2C), magnesium-dependent, gamma isoform	protein-coding
mm_100523.1	chr11	120573923	120573935	+	1	NA	promoter-TSS (NM_011032)	promoter-TSS (NM_011032)	-993	NM_011032	18453	Mm.16660	NM_011032	ENSMUSG00000025130	P4hb	ERp59|PDI|Pdia1|Thbp	prolyl 4-hydroxylase, beta polypeptide	protein-coding
mm_30767.1	chr4	15989044	15989059	+	1	NA	exon (NM_013752, exon 14 of 16)	exon (NM_013752, exon 14 of 16)	24826	NM_145950	209212	Mm.46455	NM_145950	ENSMUSG00000041153	Osgin2	BC010311|C230027H09Rik	oxidative stress induced growth inhibitor family member 2	protein-coding
mm_77035.1	chr8	109565705	109565715	-	1	NA	promoter-TSS (NM_178380)	promoter-TSS (NM_178380)	-109	NM_178380	64340	Mm.23705	NM_178380	ENSMUSG00000037993	Dhx38	5730550P09Rik|AI325984|AW540902|Ddx38|Prp16|mKIAA0224	DEAH (Asp-Glu-Ala-His) box polypeptide 38	protein-coding
mm_75050.1	chr8	32884634	32884661	-	1	NA	Intergenic	CpG	65379	NM_001177589	100042715	Mm.291093	NM_001177589		Gm3985	-	predicted gene 3985	protein-coding
mm_94969.1	chr11	30885401	30885430	+	1	NA	promoter-TSS (NM_175490)	promoter-TSS (NM_175490)	57	NM_175490	237716	Mm.338361	NM_175490	ENSMUSG00000043999	Gpr75	-	G protein-coupled receptor 75	protein-coding
mm_65253.1	chr7	19871361	19871375	-	1	NA	Intergenic	Intergenic	-10069	NM_001033419	330483	Mm.260192	NM_001033419	ENSMUSG00000014686	Ceacam16	Gm769	carcinoembryonic antigen-related cell adhesion molecule 16	protein-coding
mm_58896.1	chr7	17150192	17150198	+	1	NA	promoter-TSS (NM_054059)	promoter-TSS (NM_054059)	-205	NM_054059	384557	Mm.486145	NM_054059	ENSMUSG00000053228	Ceacam3	EG384557|Psg24|cea12	carcinoembryonic antigen-related cell adhesion molecule 3	protein-coding
mm_45005.1	chr5	38480253	38480259	-	1	NA	promoter-TSS (NM_001102415)	promoter-TSS (NM_001102415)	50	NM_001102414	117591	Mm.260137	NM_145559	ENSMUSG00000005107	Slc2a9	Glut9|SLC2A9B|SLC2a9A	solute carrier family 2 (facilitated glucose transporter), member 9	protein-coding
mm_17319.1	chr2	26445881	26445896	-	1	NA	promoter-TSS (NM_153125)	promoter-TSS (NM_153125)	-672	NM_153125	227648	Mm.206371	NM_153125	ENSMUSG00000026924	Sec16a	AU024582|C230052J16Rik	SEC16 homolog A, endoplasmic reticulum export factor	protein-coding
mm_111540.1	chr12	100887952	100887958	-	1	NA	5' UTR (NM_175493, exon 2 of 3)	5' UTR (NM_175493, exon 2 of 3)	11569	NM_001177674	238377	Mm.32160	NM_175493	ENSMUSG00000047415	Gpr68	BB131428|Ogr1	G protein-coupled receptor 68	protein-coding
mm_112094.1	chr12	112721761	112721774	-	1	NA	promoter-TSS (NM_001024602)	promoter-TSS (NM_001024602)	-407	NM_001024602	217882	Mm.23689	NM_001024602	ENSMUSG00000072825	Cep170b	AI466840|AW555464|Kiaa0284|mKIAA0284	centrosomal protein 170B	protein-coding
mm_72418.1	chr8	81872217	81872219	+	1	NA	intron (NM_001024617, intron 8 of 24)	intron (NM_001024617, intron 8 of 24)	529656	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_62776.1	chr7	112375214	112375259	+	1	NA	intron (NM_027587, intron 1 of 9)	intron (NM_027587, intron 1 of 9)	6928	NM_027587	100504195	Mm.291129	NM_027587	ENSMUSG00000030771	Micalcl	4921517J23Rik	MICAL C-terminal like	protein-coding
mm_36634.1	chr4	93335112	93335122	-	1	NA	exon (NM_026954, exon 1 of 1)	exon (NM_026954, exon 1 of 1)	394	NM_026954	69136	Mm.171558	NM_026954	ENSMUSG00000054000	Tusc1	2200001D17Rik|TSG-9	tumor suppressor candidate 1	protein-coding
mm_125392.1	chr15	41347429	41347463	+	1	NA	Intergenic	MLTR31C_MM|LTR|ERVK	-100036	NM_001130166	170719	Mm.254267	NM_130885	ENSMUSG00000022307	Oxr1	2210416C20Rik|C7|C7B	oxidation resistance 1	protein-coding
mm_22274.1	chr2	178627794	178627800	-	1	NA	Intergenic	Intergenic	197282	NM_198656	381409	Mm.330860	NM_198656	ENSMUSG00000039155	Cdh26	Gm1010	cadherin-like 26	protein-coding
mm_42721.1	chr5	120561037	120561081	+	1	NA	intron (NM_145853, intron 2 of 27)	intron (NM_145853, intron 2 of 27)	27554	NM_145853	252972	Mm.114054	NM_145853	ENSMUSG00000032741	Tpcn1	5730403B01Rik|Tpc1|mKIAA1169	two pore channel 1	protein-coding
mm_160288.1	chr7	126847381	126847381	+	1	NA	promoter-TSS (NM_010069)	promoter-TSS (NM_010069)	-172	NM_010069	13446	Mm.266301	NM_010069	ENSMUSG00000052301	Doc2a	-	double C2, alpha	protein-coding
mm_127060.1	chr15	97247392	97247448	+	1	NA	promoter-TSS (NM_001164602)	promoter-TSS (NM_001164602)	-133	NM_001164602	105827	Mm.24005	NM_178114	ENSMUSG00000048218	Amigo2	AI415330|AMIGO-2|AW208913|Ali1	adhesion molecule with Ig like domain 2	protein-coding
mm_149686.1	chr19	20493038	20493059	+	1	NA	intron (NR_015502, intron 1 of 3)	intron (NR_015502, intron 1 of 3)	333	NR_015502	320092	Mm.482524	NR_015502		E030003E18Rik	1700127G21Rik	RIKEN cDNA E030003E18 gene	ncRNA
mm_132851.1	chr16	47212337	47212359	+	1	NA	Intergenic	Intergenic	-715381	NM_021497	58998	Mm.40477	NM_021495	ENSMUSG00000022656	Nectin3	2610301B19Rik|3000002N23Rik|4921513D19Rik|AA407785|AU016832|AW538082|CD113|Pvrl3	nectin cell adhesion molecule 3	protein-coding
mm_30364.1	chr3	152005499	152005508	-	1	NA	Intergenic	Intergenic	160397	NM_016867	54120	Mm.97	NM_016867	ENSMUSG00000039131	Gipc2	2200002N01Rik|AU021850|Semcap2	GIPC PDZ domain containing family, member 2	protein-coding
mm_140790.1	chr17	19487360	19487394	-	1	NA	Intergenic	ERVB7_2-LTR_MM|LTR|ERVK	-17434	NM_001104562	627537	Mm.469858	NM_001104562	ENSMUSG00000091859	Vmn2r100	EG627537	vomeronasal 2, receptor 100	protein-coding
mm_87585.1	chr10	56655926	56655938	+	1	NA	Intergenic	Intergenic	278632	NM_010288	14609	Mm.378921	NM_010288	ENSMUSG00000050953	Gja1	AU042049|AW546267|Cnx43|Cx43|Cx43alpha1|Gja-1|Npm1|connexin43	gap junction protein, alpha 1	protein-coding
mm_109975.1	chr12	12939646	12939658	-	1	NA	exon (NM_008709, exon 2 of 3)	exon (NM_008709, exon 2 of 3)	2184	NM_008709	18109	Mm.16469	NM_008709	ENSMUSG00000037169	Mycn	N-myc|Nmyc|Nmyc-1|Nmyc1|bHLHe37|c-nmyc	v-myc avian myelocytomatosis viral related oncogene, neuroblastoma derived	protein-coding
mm_158358.1	chrX	134600929	134600965	-	1	NA	promoter-TSS (NM_001313716)	promoter-TSS (NM_001313716)	58	NM_013463	11605	Mm.1114	NM_013463	ENSMUSG00000031266	Gla	Ags	galactosidase, alpha	protein-coding
mm_172482.1	chr7	50873498	50873499	+	1	NA	Intergenic	Intergenic	274308	NM_172901	243996	Mm.443270	NM_172901	ENSMUSG00000084234	4933405O20Rik	-	RIKEN cDNA 4933405O20 gene	protein-coding
mm_21047.1	chr2	152580272	152580288	-	1	NA	promoter-TSS (NM_145157)	promoter-TSS (NM_145157)	32	NM_145157	246700	Mm.82820	NM_145157	ENSMUSG00000050645	Defb19	BD-19|Defb24|Tdl|mBD-19	defensin beta 19	protein-coding
mm_161306.1	chr14	34041052	34041052	+	1	NA	promoter-TSS (NM_001034880)	promoter-TSS (NM_001034880)	-26	NM_001034880	432838	Mm.318383	NM_001034880	ENSMUSG00000072624	Gm5460	EG432838	predicted gene 5460	protein-coding
mm_61996.1	chr7	91143677	91143681	+	1	NA	intron (NM_011807, intron 1 of 22)	intron (NM_011807, intron 1 of 22)	52893	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_128863.1	chr15	72809966	72810013	-	1	NA	non-coding (NR_002864, exon 1 of 1)	non-coding (NR_002864, exon 1 of 1)	335	NR_002864	353342	Mm.440245	NR_002864	ENSMUSG00000106847	Peg13	-	paternally expressed 13	ncRNA
mm_102101.1	chr11	52390050	52390082	-	1	NA	TTS (NM_011694)	TTS (NM_011694)	-6362	NM_153117	213673	Mm.291979	NM_153117	ENSMUSG00000036275	9530068E07Rik	C85061|Kct2	RIKEN cDNA 9530068E07 gene	protein-coding
mm_91042.1	chr10	18545881	18545931	-	1	NA	5' UTR (NM_019487, exon 1 of 4)	5' UTR (NM_019487, exon 1 of 4)	170	NM_019487	56016	Mm.35551	NM_019487	ENSMUSG00000019853	Hebp2	SOUL	heme binding protein 2	protein-coding
mm_81133.1	chr9	106514573	106514602	+	1	NA	promoter-TSS (NM_029300)	promoter-TSS (NM_029300)	14	NM_029300	75470	Mm.63799	NM_029300	ENSMUSG00000066382	Iqcf5	1700007L12Rik	IQ motif containing F5	protein-coding
mm_163959.1	chr14	54894171	54894175	+	1	NA	promoter-TSS (NM_019402)	promoter-TSS (NM_019402)	30	NM_019402	54196	Mm.7723	NM_019402	ENSMUSG00000022194	Pabpn1	PAB2|Pabp3|mPABII	poly(A) binding protein, nuclear 1	protein-coding
mm_101679.1	chr11	40570539	40570541	-	1	NA	Intergenic	ORR1A3|LTR|ERVL-MaLR	122142	NM_134017	108645	Mm.293771	NM_134017	ENSMUSG00000042032	Mat2b	1110064C04Rik|2410018D16Rik|AI182287|AU022853|MAT-II|MATIIbeta|TGR	methionine adenosyltransferase II, beta	protein-coding
mm_74663.1	chr8	13584030	13584052	-	1	NA	intron (NM_009025, intron 14 of 23)	(TCTCTG)n|Simple_repeat|Simple_repeat	-21580	NM_001080781	66501	Mm.46136	NM_025601	ENSMUSG00000031452	1700029H14Rik	-	RIKEN cDNA 1700029H14 gene	protein-coding
mm_150412.1	chr19	36928006	36928013	+	1	NA	intron (NM_001080706, intron 1 of 37)	AT_rich|Low_complexity|Low_complexity	1930	NM_001080706	107182	Mm.295062	NM_001080706	ENSMUSG00000040565	Btaf1	AI414500|AI447930|E430027O22Rik|TAF170	B-TFIID TATA-box binding protein associated factor 1	protein-coding
mm_52145.1	chr6	97978634	97978655	+	1	NA	intron (NM_001113198, intron 2 of 9)	MER20|DNA|hAT-Charlie	-13139	NM_008601	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_103889.1	chr11	83575032	83575042	-	1	NA	3' UTR (NM_011338, exon 4 of 4)	3' UTR (NM_011338, exon 4 of 4)	3599	NM_011338	20308	Mm.416125	NM_011338	ENSMUSG00000019122	Ccl9	CCF18|MRP-2|Scya10|Scya9	chemokine (C-C motif) ligand 9	protein-coding
mm_91140.1	chr10	19851209	19851221	-	1	NA	5' UTR (NM_029529, exon 1 of 2)	5' UTR (NM_029529, exon 1 of 2)	244	NM_029529	76157	Mm.74324	NM_029529	ENSMUSG00000050473	Slc35d3	6230421J19Rik|Frcl1	solute carrier family 35, member D3	protein-coding
mm_114631.1	chr13	76340735	76340745	+	1	NA	Intergenic	L1_Mur3|LINE|L1	-44221	NM_030174	78771	Mm.316249	NM_030174	ENSMUSG00000021596	Mctp1	2810465F10Rik	multiple C2 domains, transmembrane 1	protein-coding
mm_18460.1	chr2	62343658	62343668	-	1	NA	intron (NM_001159543, intron 23 of 24)	intron (NM_001159543, intron 23 of 24)	68568	NM_010074	13482	Mm.1151	NM_010074	ENSMUSG00000035000	Dpp4	Cd26|Dpp-4|THAM	dipeptidylpeptidase 4	protein-coding
mm_122844.1	chr14	54726753	54726802	-	1	NA	exon (NM_016972, exon 9 of 11)	exon (NM_016972, exon 9 of 11)	-14603	NM_207131	110794	Mm.236223	NM_207131	ENSMUSG00000052435	Cebpe	C/EBPe|CRP1|Gm294	CCAAT/enhancer binding protein (C/EBP), epsilon	protein-coding
mm_89931.1	chr10	111239407	111239429	+	1	NA	intron (NM_175489, intron 4 of 23)	Lx5|LINE|L1	-59261	NM_027914	71769	Mm.45256	NM_027914	ENSMUSG00000035759	Bbs10	1300007O09Rik|AI452285	Bardet-Biedl syndrome 10 (human)	protein-coding
mm_91973.1	chr10	61435037	61435065	-	1	NA	exon (NM_010124, exon 2 of 3)	exon (NM_010124, exon 2 of 3)	17079	NM_013611	18119	Mm.57195	NM_013611	ENSMUSG00000037171	Nodal	Tg.413d	nodal	protein-coding
mm_71917.1	chr8	70139688	70139734	+	1	NA	promoter-TSS (NM_001309841)	promoter-TSS (NM_001309841)	212	NR_132133	72368	Mm.644	NM_001145552	ENSMUSG00000002345	Borcs8	2310045N01Rik|Mef2bnb	BLOC-1 related complex subunit 8	protein-coding
mm_8118.1	chr1	135984308	135984321	-	1	NA	intron (NM_177642, intron 3 of 26)	intron (NM_177642, intron 3 of 26)	22028	NM_177642	226438	Mm.119675	NM_177642	ENSMUSG00000051985	Igfn1	9830123M21Rik	immunoglobulin-like and fibronectin type III domain containing 1	protein-coding
mm_110723.1	chr12	69682139	69682182	-	1	NA	promoter-TSS (NM_001135559)	promoter-TSS (NM_001135559)	-308	NM_001135559	20663	Mm.3770	NM_001135559	ENSMUSG00000034801	Sos2	SOS-2|mSOS-2	son of sevenless homolog 2 (Drosophila)	protein-coding
mm_34036.1	chr4	138147468	138147468	+	1	NA	intron (NM_172703, intron 13 of 34)	intron (NM_172703, intron 13 of 34)	-8950	NR_126429	73563	Mm.444294	NR_126429	ENSMUSG00000084804	1700095J12Rik	-	RIKEN cDNA 1700095J12 gene	ncRNA
mm_153911.1	chr19	47138281	47138300	-	1	NA	promoter-TSS (NM_133746)	promoter-TSS (NM_133746)	4	NM_133746	72691	Mm.31663	NM_133746	ENSMUSG00000033033	Calhm2	2810048G17Rik|Fam26b	calcium homeostasis modulator 2	protein-coding
mm_22133.1	chr2	170463880	170463896	-	1	NA	Intergenic	Intergenic	-32540	NM_001013369	109054	Mm.28808	NM_001013369	ENSMUSG00000052033	Pfdn4	0610025M10Rik|1810063B06Rik|C-1|C1|Pfd4	prefoldin 4	protein-coding
mm_47377.1	chr5	122989044	122989080	-	1	NA	promoter-TSS (NM_001003953)	promoter-TSS (NM_001003953)	37	NM_001003953	30841	Mm.86406	NM_013910	ENSMUSG00000029475	Kdm2b	Cxxc2|Fbl10|Fbxl10|Jhdm1b|PCCX2	lysine (K)-specific demethylase 2B	protein-coding
mm_54804.1	chr6	41703085	41703098	-	1	NA	intron (NM_032540, intron 3 of 18)	intron (NM_032540, intron 3 of 18)	1234	NM_032540	23925	Mm.19958	NM_032540	ENSMUSG00000029866	Kel	CD238|Ece3	Kell blood group	protein-coding
mm_107572.1	chr12	44328965	44329009	+	1	NA	5' UTR (NM_176930, exon 1 of 31)	5' UTR (NM_176930, exon 1 of 31)	102	NM_001146031	319504	Mm.208439	NM_176930	ENSMUSG00000020598	Nrcam	Bravo|C030017F07Rik|C130076O07Rik|mKIAA0343	neuronal cell adhesion molecule	protein-coding
mm_124185.1	chr14	94687300	94687318	-	1	NA	Intergenic	Intergenic	-796630	NM_001346722	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding
mm_149291.1	chr19	10675085	10675092	+	1	NA	exon (NM_021453, exon 3 of 9)	exon (NM_021453, exon 3 of 9)	2983	NM_021453	58803	Mm.34037	NM_021453	ENSMUSG00000024738	Pga5	1110035E17Rik|Pepf	pepsinogen 5, group I	protein-coding
mm_27481.1	chr3	53657340	53657391	-	1	NA	promoter-TSS (NM_172862)	promoter-TSS (NM_172862)	-10	NM_172862	242022	Mm.38378	NM_172862	ENSMUSG00000037016	Frem2	6030440P17Rik|8430406N05Rik|Gm409|b2b1562Clo|my|ne|nv1	Fras1 related extracellular matrix protein 2	protein-coding
mm_122117.1	chr14	31001589	31001620	-	1	NA	promoter-TSS (NM_026911)	promoter-TSS (NM_026911)	62	NM_026911	69019	Mm.28852	NM_026911	ENSMUSG00000021917	Spcs1	1810004F21Rik	signal peptidase complex subunit 1 homolog (S. cerevisiae)	protein-coding
mm_57906.1	chr6	132439715	132439718	-	1	NA	Intergenic	Intergenic	-75581	NM_053251	114600	Mm.428480	NM_053251		Gm4736	EG114600|Mp4|Mp6	predicted gene 4736	protein-coding
mm_89119.1	chr10	84762213	84762246	+	1	NA	intron (NM_001024918, intron 1 of 17)	intron (NM_001024918, intron 1 of 17)	6181	NM_001024918	71137	Mm.79070	NM_027689	ENSMUSG00000020037	Rfx4	4933412G19Rik|NYD-sp10	regulatory factor X, 4 (influences HLA class II expression)	protein-coding
mm_97962.1	chr11	83740748	83740764	+	1	NA	Intergenic	Intergenic	-6184	NM_183249	66107	Mm.902	NM_183249	ENSMUSG00000051748	Wfdc21	1100001G20Rik|Wdnm1-like	WAP four-disulfide core domain 21	protein-coding
mm_26783.1	chr3	9443913	9443914	-	1	NA	intron (NM_133218, intron 7 of 8)	MTEb|LTR|ERVL-MaLR	40835	NR_015499	320088	Mm.212908	NR_015499	ENSMUSG00000097365	C030034L19Rik	A130044O20Rik	RIKEN cDNA C030034L19 gene	ncRNA
mm_27113.1	chr3	30950924	30950939	-	1	NA	exon (NM_153421, exon 5 of 15)	exon (NM_153421, exon 5 of 15)	18484	NM_001165954	241915	Mm.233173	NM_153421	ENSMUSG00000037652	Phc3	E030046K01Rik|Edr3|Hph3	polyhomeotic-like 3 (Drosophila)	protein-coding
mm_144647.1	chr18	33794916	33794924	+	1	NA	promoter-TSS (NR_038152)	promoter-TSS (NR_038152)	28	NR_038151	69749	Mm.248787	NR_038151	ENSMUSG00000087590	Epb41l4aos	2410004N09Rik|Epb4.1l4aos	erythrocyte membrane protein band 4.1 like 4a, opposite strand	ncRNA
mm_38116.1	chr4	134538618	134538634	-	1	NA	3' UTR (NM_029100, exon 12 of 12)	3' UTR (NM_029100, exon 12 of 12)	-3239	NM_029759	76824	Mm.30153	NM_029759	ENSMUSG00000046671	Mtfr1l	2410166I05Rik|AI480750|Fam54b	mitochondrial fission regulator 1-like	protein-coding
mm_37087.1	chr4	116406846	116406861	-	1	NA	intron (NM_008641, intron 3 of 28)	intron (NM_008641, intron 3 of 28)	57328	NM_001042743	17776	Mm.9287	NM_008641	ENSMUSG00000003810	Mast2	MAST205|Mtssk	microtubule associated serine/threonine kinase 2	protein-coding
mm_143486.1	chr17	71310834	71310844	-	1	NA	exon (NM_145158, exon 1 of 8)	exon (NM_145158, exon 1 of 8)	126	NM_145158	246707	Mm.23462	NM_145158	ENSMUSG00000024053	Emilin2	FOAP-10	elastin microfibril interfacer 2	protein-coding
mm_128711.1	chr15	63963666	63963679	-	1	NA	intron (NM_144846, intron 2 of 11)	intron (NM_144846, intron 2 of 11)	49211	NR_029414	74460	Mm.390801	NR_029414	ENSMUSG00000100127	Gsdmcl-ps	4933426G20Rik	gasdermin C-like, pseudogene	pseudo
mm_97930.1	chr11	83648183	83648209	+	1	NA	3' UTR (NM_011337, exon 3 of 3)	3' UTR (NM_011337, exon 3 of 3)	1182	NM_011337	20302	Mm.1282	NM_011337	ENSMUSG00000000982	Ccl3	AI323804|G0S19-1|LD78alpha|MIP-1alpha|MIP1-(a)|MIP1-alpha|Mip1a|Scya3	chemokine (C-C motif) ligand 3	protein-coding
mm_42376.1	chr5	114929214	114929232	+	1	NA	intron (NM_145209, intron 3 of 6)	B1_Mur4|SINE|Alu	5983	NM_145209	231655	Mm.95479	NM_145209	ENSMUSG00000041827	Oasl1	7530414C13Rik|oasl9	2'-5' oligoadenylate synthetase-like 1	protein-coding
mm_85656.1	chr9	107664334	107664351	-	1	NA	intron (NM_001199218, intron 1 of 15)	B1_Mur2|SINE|Alu	3057	NM_023805	76257	Mm.296560	NM_023805	ENSMUSG00000010064	Slc38a3	0610012J02Rik|D9Ucla2|Nat1|Slc38-3|Sn1|Snat3|mNAT	solute carrier family 38, member 3	protein-coding
mm_58401.1	chr7	3218316	3218324	+	1	NA	promoter-TSS (NR_029640)	promoter-TSS (NR_029640)	-306	NR_029640	100049710		NR_029640	ENSMUSG00000077815	Mir290a	Mir290|Mirn290|mir-290a|mmu-miR-290|mmu-mir-290a	microRNA 290a	ncRNA
mm_96199.1	chr11	62006512	62006552	+	1	NA	intron (NM_001310526, intron 1 of 7)	intron (NM_001310526, intron 1 of 7)	49769	NM_001310526	432572	Mm.438022	NM_001029936	ENSMUSG00000042331	Specc1	2810012G08Rik|B230396K10Rik|Cytsb	sperm antigen with calponin homology and coiled-coil domains 1	protein-coding
mm_11116.1	chr2	28193324	28193338	+	1	NA	5' UTR (NM_001038613, exon 1 of 6)	5' UTR (NM_001038613, exon 1 of 6)	238	NM_001038614	56177	Mm.43278	NM_019498	ENSMUSG00000026833	Olfm1	AMY|AW742568|Noe1|OlfA|Pancortin|Pancortin3	olfactomedin 1	protein-coding
mm_9976.1	chr1	191224912	191224969	-	1	NA	Intergenic	Intergenic	-41607	NM_007498	11910	Mm.2706	NM_007498	ENSMUSG00000026628	Atf3	LRG-21	activating transcription factor 3	protein-coding
mm_53984.1	chr6	6869366	6869368	-	1	NA	non-coding (NR_015388, exon 1 of 2)	non-coding (NR_015388, exon 1 of 2)	166	NR_015388	320038	Mm.94021	NR_015388		Dlx6os1	A230055N17Rik|Dlx6as1|Evf-1|Evf-2|Evf1|Evf1/2|Evf2|Shhrs|mEvf-1	distal-less homeobox 6, opposite strand 1	ncRNA
mm_153675.1	chr19	44396512	44396524	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	11191	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_136775.1	chr17	10304475	10304476	+	1	NA	intron (NM_021881, intron 1 of 6)	intron (NM_021881, intron 1 of 6)	14886	NM_021881	19317	Mm.130694	NM_021881	ENSMUSG00000062078	Qk	1110003F05Rik|1500005P18|QkI|l(17)-1Wis|l17Wis1	quaking	protein-coding
mm_61347.1	chr7	68287122	68287130	+	1	NA	intron (NM_001013811, intron 1 of 8)	intron (NM_001013811, intron 1 of 8)	-10532	NR_040340	100504026	Mm.426764	NR_040340	ENSMUSG00000086628	Gm16157	OTTMUSG00000031023	predicted gene 16157	ncRNA
mm_100657.1	chr11	3193389	3193450	-	1	NA	promoter-TSS (NM_030207)	promoter-TSS (NM_030207)	44	NM_030207	78887	Mm.394071	NM_030207	ENSMUSG00000023764	Sfi1	-	Sfi1 homolog, spindle assembly associated (yeast)	protein-coding
mm_125819.1	chr15	74955907	74955921	+	1	NA	intron (NM_001164039, intron 2 of 4)	intron (NM_001164039, intron 2 of 4)	808	NM_001164040	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_97245.1	chr11	75734571	75734575	+	1	NA	intron (NM_009536, intron 1 of 5)	intron (NM_009536, intron 1 of 5)	1686	NM_009536	22627	Mm.234700	NM_009536	ENSMUSG00000020849	Ywhae	AU019196	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide	protein-coding
mm_1263.1	chr1	63177120	63177145	+	1	NA	promoter-TSS (NM_001160039)	promoter-TSS (NM_001160039)	301	NM_018796	55949	Mm.2718	NM_018796	ENSMUSG00000025967	Eef1b2	2810017J07Rik|Eef1b	eukaryotic translation elongation factor 1 beta 2	protein-coding
mm_132670.1	chr16	42875840	42875861	+	1	NA	promoter-TSS (NR_040522)	promoter-TSS (NR_040522)	-88	NR_040522	75722	Mm.243747	NR_040521	ENSMUSG00000075070	4932412D23Rik	ENSMUSG00000075070|Gm10809	RIKEN cDNA 4932412D23 gene	ncRNA
mm_81403.1	chr9	109050863	109050900	+	1	NA	intron (NM_025858, intron 2 of 5)	CT-rich|Low_complexity|Low_complexity	-3985	NM_026381	66940	Mm.196533	NM_025858	ENSMUSG00000025647	Shisa5	2310008D10Rik|6430628I05Rik|Scotin|mShisa5	shisa family member 5	protein-coding
mm_68896.1	chr7	126449243	126449246	-	1	NA	intron (NM_007504, intron 14 of 22)	B1_Mur4|SINE|Alu	13829	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_170294.1	chr18	3005807	3005809	+	1	NA	Intergenic	RLTR11A|LTR|ERVK	117604	NM_001167539	100312476	Mm.480293	NM_001167539	ENSMUSG00000091539	Vmn1r238	-	vomeronasal 1 receptor, 238	protein-coding
mm_12184.1	chr2	65238734	65238762	+	1	NA	promoter-TSS (NM_177025)	promoter-TSS (NM_177025)	-122	NM_027225	319876	Mm.34159	NM_027225	ENSMUSG00000034903	Cobll1	1810047P18Rik|Coblr1|D430044D16Rik	Cobl-like 1	protein-coding
mm_73488.1	chr8	107048212	107048285	+	1	NA	TTS (NM_139229)	TTS (NM_139229)	366	NM_026513	68023	Mm.482335	NM_026513	ENSMUSG00000078931	Pdf	2610019N19Rik	peptide deformylase (mitochondrial)	protein-coding
mm_144537.1	chr18	25753257	25753273	+	1	NA	intron (NM_001146292, intron 1 of 12)	CpG	718	NM_133195	108013	Mm.266435	NM_133195	ENSMUSG00000024268	Celf4	A230070D14Rik|BRUNOL-4|Brul4|Brunol4|C130060B05Rik	CUGBP, Elav-like family member 4	protein-coding
mm_130831.1	chr15	101846851	101846870	-	1	NA	exon (NM_008473, exon 7 of 9)	exon (NM_008473, exon 7 of 9)	3926	NM_008473	16678	Mm.183137	NM_008473	ENSMUSG00000046834	Krt1	Krt-2.1|Krt2-1|Krt86	keratin 1	protein-coding
mm_32898.1	chr4	118987471	118987471	+	1	NA	Intergenic	Intergenic	25504	NM_133892	100470	Mm.26698	NM_133892	ENSMUSG00000024903	Lao1	AW990848	L-amino acid oxidase 1	protein-coding
mm_121348.1	chr14	116925260	116925280	+	1	NA	promoter-TSS (NM_011821)	promoter-TSS (NM_011821)	-27	NM_001079844	23888	Mm.440025	NM_011821	ENSMUSG00000058571	Gpc6	-	glypican 6	protein-coding
mm_121726.1	chr14	16575539	16575559	-	1	NA	promoter-TSS (NM_001289762)	promoter-TSS (NM_001289762)	-73	NM_001289762	218772	Mm.259318	NM_011243	ENSMUSG00000017491	Rarb	A830025K23|Hap|Nr1b2	retinoic acid receptor, beta	protein-coding
mm_167552.1	chr9	34948830	34948836	-	1	NA	intron (NM_001190913, intron 4 of 13)	intron (NM_001190913, intron 4 of 13)	-167895	NR_029475	78934	Mm.391688	NR_029475	ENSMUSG00000070315	4930581F22Rik	-	RIKEN cDNA 4930581F22 gene	ncRNA
mm_145092.1	chr18	43207526	43207538	+	1	NA	promoter-TSS (NM_178749)	promoter-TSS (NM_178749)	-165	NM_178749	269019	Mm.150401	NM_178749	ENSMUSG00000039954	Stk32a	A930015B13Rik|YANK1	serine/threonine kinase 32A	protein-coding
mm_110293.1	chr12	32208504	32208514	-	1	NA	promoter-TSS (NM_001146201)	promoter-TSS (NM_001146201)	-39	NM_020272	30955	Mm.101369	NM_020272	ENSMUSG00000020573	Pik3cg	5830428L06Rik|PI3Kgamma|p110gamma	phosphoinositide-3-kinase, catalytic, gamma polypeptide	protein-coding
mm_101469.1	chr11	30649376	30649413	-	1	NA	promoter-TSS (NM_029344)	promoter-TSS (NM_029344)	2	NM_029344	75572	Mm.390319	NM_029344	ENSMUSG00000060923	Acyp2	2310004B09Rik	acylphosphatase 2, muscle type	protein-coding
mm_50181.1	chr6	41605149	41605175	+	1	NA	promoter-TSS (NM_001146351)	promoter-TSS (NM_001146351)	-320	NM_001146351	13848	Mm.271976	NM_007680	ENSMUSG00000029869	Ephb6	Cekl|Mep	Eph receptor B6	protein-coding
mm_28134.1	chr3	87174519	87174578	-	1	NA	5' UTR (NM_130867, exon 1 of 16)	5' UTR (NM_130867, exon 1 of 16)	199	NM_001170985	170643	Mm.89552	NM_130867	ENSMUSG00000041734	Kirrel	6720469N11Rik|Kirrel1|Neph1	kin of IRRE like (Drosophila)	protein-coding
mm_138950.1	chr17	44134769	44134793	+	1	NA	Intergenic	Intergenic	-28973	NM_199016	224794	Mm.255971	NM_199016	ENSMUSG00000023961	Enpp4	4933413N07Rik|AA986363|AI195364|E-NPP 4|Gm90|mKIAA0879	ectonucleotide pyrophosphatase/phosphodiesterase 4	protein-coding
mm_88922.1	chr10	81194601	81194607	+	1	NA	promoter-TSS (NR_015477)	promoter-TSS (NR_015477)	-87	NR_015477	69678	Mm.81562	NR_015477		Atcayos	2310050B05Rik	ataxia, cerebellar, Cayman type, opposite strand	ncRNA
mm_140644.1	chr17	12675834	12675844	-	1	NA	promoter-TSS (NM_009202)	promoter-TSS (NM_009202)	-1	NM_009202	20517	Mm.594	NM_009202	ENSMUSG00000023829	Slc22a1	Lx1|Oct1|Orct|Orct1	solute carrier family 22 (organic cation transporter), member 1	protein-coding
mm_133257.1	chr16	77329512	77329525	+	1	NA	non-coding (NR_015543, exon 1 of 5)	non-coding (NR_015543, exon 1 of 5)	190	NR_015543	77994	Mm.394688	NR_015543	ENSMUSG00000090386	Mir99ahg	2810055G20Rik|D730043B02Rik	Mir99a and Mirlet7c-1 host gene (non-protein coding)	ncRNA
mm_128966.1	chr15	74832138	74832145	-	1	NA	Intergenic	B3|SINE|B2	9502	NM_001033229	110115	Mm.322606	NM_001033229	ENSMUSG00000075604	Cyp11b1	AA389061|CPN1|Cyp11b|Cyp11b-1|FHI	cytochrome P450, family 11, subfamily b, polypeptide 1	protein-coding
mm_6659.1	chr1	80213840	80213854	-	1	NA	promoter-TSS (NM_173425)	promoter-TSS (NM_173425)	97	NM_173425	241128	Mm.145511	NM_173425	ENSMUSG00000043230	Fam124b	A830043J08Rik	family with sequence similarity 124, member B	protein-coding
mm_163299.1	chr11	120350272	120350286	+	1	NA	intron (NR_038126, intron 1 of 1)	CpG	1601	NR_038126	66838	Mm.375010	NR_038126	ENSMUSG00000043644	0610009L18Rik	-	RIKEN cDNA 0610009L18 gene	ncRNA
mm_53369.1	chr6	129408897	129408912	+	1	NA	promoter-TSS (NM_001205364)	promoter-TSS (NM_001205364)	42	NM_172732	232414	Mm.391518	NM_172732	ENSMUSG00000046080	Clec9a	9830005G06Rik|DNGR-1	C-type lectin domain family 9, member a	protein-coding
mm_72405.1	chr8	81770723	81770739	+	1	NA	intron (NM_001024617, intron 6 of 24)	intron (NM_001024617, intron 6 of 24)	428169	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_57326.1	chr6	124738654	124738678	-	1	NA	promoter-TSS (NM_001077705)	promoter-TSS (NM_001077705)	43	NM_001077705	15170	Mm.271799	NM_013545	ENSMUSG00000004266	Ptpn6	70Z-SHP|Hcph|PTPTY-42|Ptp1C|SH-PTP1|SHP-1|hcp|me	protein tyrosine phosphatase, non-receptor type 6	protein-coding
mm_128627.1	chr15	59051242	59051253	-	1	NA	intron (NM_001146180, intron 3 of 13)	L1M2|LINE|L1	30779	NM_001146180	211401	Mm.215481	NM_144800	ENSMUSG00000022353	Mtss1	2310003N14Rik|BC024131|D130001D01Rik|Mim|mKIAA0429	metastasis suppressor 1	protein-coding
mm_80696.1	chr9	92193089	92193100	+	1	NA	5' UTR (NM_001195693, exon 1 of 7)	5' UTR (NM_001195693, exon 1 of 7)	158	NM_001195693	100504689	Mm.464262	NM_001195693	ENSMUSG00000095654	Plscr5	331000	phospholipid scramblase family, member 5	protein-coding
mm_114652.1	chr13	77708684	77708740	+	1	NA	promoter-TSS (NR_028109)	promoter-TSS (NR_028109)	22	NM_001163419	68675	Mm.343005	NM_138312	ENSMUSG00000064138	Fam172a	1110033M05Rik|2610318O14Rik|53-E6|9430037D06Rik|AF064782|pEN87	family with sequence similarity 172, member A	protein-coding
mm_163118.1	chr11	75561086	75561110	-	1	NA	intron (NM_173388, intron 6 of 13)	intron (NM_173388, intron 6 of 13)	9669	NR_039553	100628624		NR_039553	ENSMUSG00000093100	Mir3971	mmu-mir-3971|mu-mir-3971	microRNA 3971	ncRNA
mm_96781.1	chr11	69940720	69940735	+	1	NA	exon (NM_016875, exon 7 of 9)	exon (NM_016875, exon 7 of 9)	4399	NM_001347634	53422	Mm.29286	NM_016875	ENSMUSG00000018554	Ybx2	Msy2	Y box protein 2	protein-coding
mm_28499.1	chr3	92484661	92484671	-	1	NA	exon (NM_009264, exon 2 of 2)	exon (NM_009264, exon 2 of 2)	1215	NM_009264	20753	Mm.331191	NM_009264	ENSMUSG00000050359	Sprr1a	AI528815|SPR1a|mSPRR1A	small proline-rich protein 1A	protein-coding
mm_14432.1	chr2	130589412	130589422	+	1	NA	TTS (NM_001255994)	TTS (NM_001255994)	-6829	NM_009732	11998	Mm.6190	NM_009732	ENSMUSG00000037727	Avp	Vp|Vsp	arginine vasopressin	protein-coding
mm_54241.1	chr6	28247136	28247144	-	1	NA	intron (NM_001081678, intron 4 of 5)	intron (NM_001081678, intron 4 of 5)	14461	NM_001081678	627049	Mm.84441	NM_001081678	ENSMUSG00000039841	Zfp800	AA407452|Znf800	zinc finger protein 800	protein-coding
mm_159817.1	chr5	120914848	120914848	+	1	NA	promoter-TSS (NM_133893)	promoter-TSS (NM_133893)	30	NM_133893	100535	Mm.247620	NM_133893	ENSMUSG00000032623	Oas1d	AA536864|C85127|oasl8	2'-5' oligoadenylate synthetase 1D	protein-coding
mm_135003.1	chr16	32179615	32179637	-	1	NA	promoter-TSS (NM_001033539)	promoter-TSS (NM_001033539)	-174	NM_001033539	328660	Mm.441006	NM_001033539	ENSMUSG00000075269	Bex6	B020003O03Rik	brain expressed family member 6	protein-coding
mm_102672.1	chr11	65221797	65221821	-	1	NA	intron (NM_146386, intron 4 of 12)	B1_Mus1|SINE|Alu	48180	NM_145136	214384	Mm.32257	NM_145136	ENSMUSG00000020542	Myocd	BSAC2A|Srfcp	myocardin	protein-coding
mm_17242.1	chr2	25617637	25617658	-	1	NA	promoter-TSS (NM_029859)	promoter-TSS (NM_029859)	31	NM_029859	77058	Mm.478493	NM_029859	ENSMUSG00000026940	Ccdc183	4921530D09Rik|Cccd183|Kiaa1984	coiled-coil domain containing 183	protein-coding
mm_117790.1	chr13	97137878	97137916	-	1	NA	promoter-TSS (NM_001271464)	promoter-TSS (NM_001271464)	29	NM_021552	59050	Mm.390634	NM_021552	ENSMUSG00000060739	Nsa2	5730427N09Rik|LNR42|Nsa2p|Tinp1|Yr29	NSA2 ribosome biogenesis homolog	protein-coding
mm_98388.1	chr11	94211432	94211446	+	1	NA	promoter-TSS (NM_009427)	promoter-TSS (NM_009427)	-15	NM_009427	22057	Mm.259673	NM_009427	ENSMUSG00000037573	Tob1	Tob|Trob	transducer of ErbB-2.1	protein-coding
mm_125439.1	chr15	44619272	44619328	+	1	NA	promoter-TSS (NM_019480)	promoter-TSS (NM_019480)	-341	NM_019480	55960	Mm.287896	NM_019480	ENSMUSG00000022339	Ebag9	AI835379|Rcas1	estrogen receptor-binding fragment-associated gene 9	protein-coding
mm_48707.1	chr5	147077389	147077419	-	1	NA	promoter-TSS (NM_080795)	promoter-TSS (NM_080795)	58	NM_009087	20018	Mm.317557	NM_009087	ENSMUSG00000029642	Polr1d	1110003G10Rik|AC19|RPA16|Rpo1-3	polymerase (RNA) I polypeptide D	protein-coding
mm_81363.1	chr9	108692291	108692312	+	1	NA	5' UTR (NM_008924, exon 1 of 11)	5' UTR (NM_008924, exon 1 of 11)	158	NM_008924	19087	Mm.253102	NM_008924	ENSMUSG00000032601	Prkar2a	1110061A24Rik|AI317181|AI836829|RII(alpha)	protein kinase, cAMP dependent regulatory, type II alpha	protein-coding
mm_95750.1	chr11	54902119	54902126	+	1	NA	promoter-TSS (NM_008161)	promoter-TSS (NM_008161)	-732	NM_001329860	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_116339.1	chr13	38184013	38184067	-	1	NA	exon (NM_023842, exon 15 of 24)	exon (NM_023842, exon 15 of 24)	-20899	NM_026382	67797	Mm.250783	NM_026382	ENSMUSG00000021431	Snrnp48	1110050F08Rik|6530403A03Rik|C6orf151	small nuclear ribonucleoprotein 48 (U11/U12)	protein-coding
mm_68275.1	chr7	105596416	105596425	-	1	NA	intron (NM_017371, intron 4 of 9)	intron (NM_017371, intron 4 of 9)	3696	NM_017371	15458	Mm.3485	NM_017371	ENSMUSG00000030895	Hpx	Hpxn|hx	hemopexin	protein-coding
mm_45700.1	chr5	83354889	83354911	-	1	NA	exon (NM_153801, exon 1 of 12)	exon (NM_153801, exon 1 of 12)	295	NM_153801	243078	Mm.126783	NM_153801	ENSMUSG00000049537	Tecrl	D330017N19Rik|Srd5a2l2	trans-2,3-enoyl-CoA reductase-like	protein-coding
mm_39427.1	chr5	16553456	16553485	+	1	NA	promoter-TSS (NM_010427)	promoter-TSS (NM_010427)	-25	NM_001289460	15234	Mm.267078	NM_010427	ENSMUSG00000028864	Hgf	C230052L06Rik|HGF/SF|NK1|NK2|SF|SF/HGF	hepatocyte growth factor	protein-coding
mm_140037.1	chr17	74339164	74339218	+	1	NA	exon (NM_001162870, exon 1 of 17)	exon (NM_001162870, exon 1 of 17)	204	NM_016962	50850	Mm.19804	NM_016962	ENSMUSG00000024068	Spast	Spg4|mKIAA1083	spastin	protein-coding
mm_53710.1	chr6	143203961	143203976	+	1	NA	3' UTR (NM_029250, exon 8 of 8)	3' UTR (NM_029250, exon 8 of 8)	36738	NM_029250	75320	Mm.272548	NM_029250	ENSMUSG00000030275	Etnk1	1110061E11Rik|4930555L11Rik|AI195356|AI841245|C80956|D6Ertd3e|EKI1	ethanolamine kinase 1	protein-coding
mm_94160.1	chr10	128745446	128745466	-	1	NA	Intergenic	Intergenic	-1400	NM_016811	13139	Mm.291235	NM_016811	ENSMUSG00000025357	Dgka	80kDa|AW146112|Dagk1	diacylglycerol kinase, alpha	protein-coding
mm_48723.1	chr5	147339047	147339080	-	1	NA	intron (NM_010229, intron 20 of 23)	intron (NM_010229, intron 20 of 23)	-16623	NM_001039678	231903	Mm.291286	NM_001039678	ENSMUSG00000075543	Urad	EG231903|Prhoxnb	ureidoimidazoline (2-oxo-4-hydroxy-4-carboxy-5) decarboxylase	protein-coding
mm_63618.1	chr7	128246938	128246948	+	1	NA	5' UTR (NM_001289552, exon 1 of 10)	5' UTR (NM_001289552, exon 1 of 10)	131	NM_001289552	21804	Mm.3248	NM_009365	ENSMUSG00000030782	Tgfb1i1	ARA55|Hic5|TSC-5|hic-5	transforming growth factor beta 1 induced transcript 1	protein-coding
mm_564.1	chr1	38035694	38035705	+	1	NA	intron (NM_198303, intron 9 of 23)	intron (NM_198303, intron 9 of 23)	37689	NM_198303	226982	Mm.260943	NM_198303	ENSMUSG00000026083	Eif5b	A030003E17Rik|BC018347|IF2	eukaryotic translation initiation factor 5B	protein-coding
mm_155310.1	chrX	61288219	61288223	+	1	NA	Intergenic	Intergenic	96928	NR_033502	320247	Mm.447372	NR_033502		C030023E24Rik	-	RIKEN cDNA C030023E24 gene	ncRNA
mm_152234.1	chr19	8709382	8709417	-	1	NA	exon (NM_008577, exon 6 of 9)	exon (NM_008577, exon 6 of 9)	4498	NM_008577	17254	Mm.4114	NM_008577	ENSMUSG00000010095	Slc3a2	4F2|4F2HC|AI314110|Cd98|Ly-10|Ly-m10|Ly10|Mdu1|Mgp-2hc|NACAE	solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2	protein-coding
mm_141675.1	chr17	33910121	33910147	-	1	NA	promoter-TSS (NR_045146)	promoter-TSS (NR_045146)	533	NM_001199733	13163	Mm.271809	NM_007829	ENSMUSG00000002307	Daxx	-	Fas death domain-associated protein	protein-coding
mm_94241.1	chr11	3293229	3293245	+	1	NA	intron (NM_019574, intron 1 of 3)	intron (NM_019574, intron 1 of 3)	2780	NM_019574	56218	Mm.275563	NM_019574	ENSMUSG00000020453	Patz1	8430401L15Rik|AI447519|Mazr|Patz|Zfp278	POZ (BTB) and AT hook containing zinc finger 1	protein-coding
mm_69588.1	chr7	135705670	135705681	-	1	NA	exon (NM_001081117, exon 7 of 14)	exon (NM_001081117, exon 7 of 14)	10704	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_100219.1	chr11	117077173	117077205	+	1	NA	promoter-TSS (NR_105853)	promoter-TSS (NR_105853)	-159	NR_105853	102465258		NR_105853	ENSMUSG00000104740	Mir6516	mmu-mir-6516	microRNA 6516	ncRNA
mm_86157.1	chr9	118150042	118150077	-	1	NA	5' UTR (NM_026442, exon 1 of 4)	5' UTR (NM_026442, exon 1 of 4)	137	NM_026442	67899	Mm.9953	NM_026442	ENSMUSG00000039163	Cmc1	2010110K16Rik|2010312P05Rik|AI596001	COX assembly mitochondrial protein 1	protein-coding
mm_43517.1	chr5	137150153	137150167	+	1	NA	Intergenic	Intergenic	-33953	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_87053.1	chr10	28827117	28827121	+	1	NA	intron (NM_001305663, intron 5 of 5)	intron (NM_001305663, intron 5 of 5)	96388	NR_033601	114676	Mm.390292	NR_033601		4930519F09Rik	-	pyruvate dehydrogenase E1 alpha 1 pseudogene	pseudo
mm_75678.1	chr8	67974568	67974596	-	1	NA	promoter-TSS (NM_177698)	promoter-TSS (NM_177698)	-8	NM_177698	234353	Mm.32525	NM_027626	ENSMUSG00000030465	Psd3	4931420C21Rik|AI661273|BC003498|D430018P08|EFA6D	pleckstrin and Sec7 domain containing 3	protein-coding
mm_73105.1	chr8	94666615	94666650	+	1	NA	promoter-TSS (NM_024269)	promoter-TSS (NM_024269)	32	NM_024191	107566	Mm.393247	NM_024191	ENSMUSG00000031776	Arl2bp	1700010P10Rik|1700027H16Rik|6330544B05Rik|AI482273|AI849834|BART|Bart1	ADP-ribosylation factor-like 2 binding protein	protein-coding
mm_120232.1	chr14	62882031	62882036	+	1	NA	intron (NM_175546, intron 1 of 11)	intron (NM_175546, intron 1 of 11)	16491	NR_105860	102465311		NR_105860	ENSMUSG00000098858	Mir6541	Gm27311|mmu-mir-6541	microRNA 6541	ncRNA
mm_1730.1	chr1	75382120	75382149	+	1	NA	promoter-TSS (NM_001085371)	promoter-TSS (NM_001085371)	20	NM_001085371	11790	Mm.275397	NM_007463	ENSMUSG00000026207	Speg	AW125581|Apeg1|BPEG|D1Bwg1450e|SPEGalpha|SPEGbeta|mKIAA1297	SPEG complex locus	protein-coding
mm_261.1	chr1	20890548	20890560	+	1	NA	promoter-TSS (NR_040492)	promoter-TSS (NR_040492)	-68	NM_028829	74229	Mm.40780	NM_028829	ENSMUSG00000025931	Paqr8	1700019B16Rik|3110001D06Rik	progestin and adipoQ receptor family member VIII	protein-coding
mm_166694.1	chr6	113670162	113670200	+	1	NA	intron (NM_172161, intron 3 of 12)	intron (NM_172161, intron 3 of 12)	-26869	NM_001347356	381801	Mm.333322	NM_001033463	ENSMUSG00000056952	Tatdn2	AI646012|mKIAA0218	TatD DNase domain containing 2	protein-coding
mm_142349.1	chr17	43624409	43624418	-	1	NA	exon (NM_198418, exon 1 of 5)	exon (NM_198418, exon 1 of 5)	5886	NM_001161366	210510	Mm.329058	NM_198418	ENSMUSG00000040140	Tdrd6	AB097085|Tdr2	tudor domain containing 6	protein-coding
mm_117097.1	chr13	59822959	59822970	-	1	NA	intron (NM_153538, intron 1 of 27)	CpG	183	NM_153538	214290	Mm.233082	NM_153538	ENSMUSG00000035248	Zcchc6	6030448M23Rik|AA420405	zinc finger, CCHC domain containing 6	protein-coding
mm_96643.1	chr11	69331366	69331373	+	1	NA	intron (NM_010599, intron 11 of 13)	intron (NM_010599, intron 11 of 13)	5111	NM_010599	16499	Mm.232472	NM_010599	ENSMUSG00000018470	Kcnab3	C330022D06Rik|Kcnab4|mKv(beta)4	potassium voltage-gated channel, shaker-related subfamily, beta member 3	protein-coding
mm_9897.1	chr1	186705981	186705999	-	1	NA	promoter-TSS (NM_009367)	promoter-TSS (NM_009367)	-1	NM_001329107	21808	Mm.18213	NM_009367	ENSMUSG00000039239	Tgfb2	BB105277|Tgf-beta2|Tgfb-2	transforming growth factor, beta 2	protein-coding
mm_136596.1	chr17	5072990	5072992	+	1	NA	intron (NM_001085355, intron 2 of 19)	HAL1|LINE|L1	77917	NM_001085355	239985	Mm.133401	NM_001085355	ENSMUSG00000069729	Arid1b	8030481M12|9330189K18Rik|AI836955|Ardi1b|B230217J03Rik|mKIAA1235	AT rich interactive domain 1B (SWI-like)	protein-coding
mm_11454.1	chr2	32151075	32151262	+	1	NA	promoter-TSS (NM_001159634)	promoter-TSS (NM_001159634)	20	NM_001159634	227723	Mm.25504	NM_172661	ENSMUSG00000039262	Prrc2b	5830434P21Rik|AI173903|Bat2l|Bat2l1|D430039P21|mKIAA0515	proline-rich coiled-coil 2B	protein-coding
mm_155229.1	chrX	57196387	57196411	+	1	NA	Intergenic	Intergenic	-4238	NR_038463	100502842	Mm.164733	NR_038463	ENSMUSG00000085808	Gm14718	OTTMUSG00000017790	predicted gene 14718	ncRNA
mm_63765.1	chr7	131174401	131174403	+	1	NA	promoter-TSS (NM_175166)	promoter-TSS (NM_175166)	0	NM_175166	71395	Mm.118845	NM_175166	ENSMUSG00000006204	5430419D17Rik	-	RIKEN cDNA 5430419D17 gene	protein-coding
mm_46929.1	chr5	114691017	114691027	-	1	NA	promoter-TSS (NM_019821)	promoter-TSS (NM_019821)	-87	NM_019821	56356	Mm.275766	NM_019821	ENSMUSG00000011884	Gltp	1110001F24Rik|C76925|C77564	glycolipid transfer protein	protein-coding
mm_137911.1	chr17	32113747	32113756	+	1	NA	Intergenic	CpG	-22328	NR_027316	435518	Mm.328944	NR_027316	ENSMUSG00000002791	Pdxk-ps	ENSMUSG00000002791|Gm9743	pyridoxal (pyridoxine, vitamin B6) kinase, pseudogene	pseudo
mm_38550.1	chr4	141605977	141606008	-	1	NA	promoter-TSS (NM_133754)	promoter-TSS (NM_133754)	60	NM_133754	74202	Mm.490327	NM_133754	ENSMUSG00000006219	Fblim1	2410043F08Rik|Cal|Fblp1|Gt10|migfilin|migfilin(s)	filamin binding LIM protein 1	protein-coding
mm_20242.1	chr2	126491534	126491558	-	1	NA	promoter-TSS (NM_001080944)	promoter-TSS (NM_001080944)	7	NM_001080944	241633	Mm.222235	NM_001080944	ENSMUSG00000060131	Atp8b4	A530043E15|Im	ATPase, class I, type 8B, member 4	protein-coding
mm_167432.1	chr8	119213902	119213907	+	1	NA	intron (NM_019707, intron 8 of 13)	intron (NM_019707, intron 8 of 13)	-130634	NM_024219	68196	Mm.358714	NM_024219	ENSMUSG00000031839	Hsbp1	0610007A03Rik|AA408769|Hsp25	heat shock factor binding protein 1	protein-coding
mm_20007.1	chr2	119173169	119173175	-	1	NA	TTS (NM_177157)	TTS (NM_177157)	-1337	NM_001039223	623781	Mm.389344	NM_001039223	ENSMUSG00000055926	Gm14137	OTTMUSG00000015762	predicted gene 14137	protein-coding
mm_85639.1	chr9	107655122	107655130	-	1	NA	exon (NM_001199218, exon 14 of 16)	exon (NM_001199218, exon 14 of 16)	12273	NM_023805	76257	Mm.296560	NM_023805	ENSMUSG00000010064	Slc38a3	0610012J02Rik|D9Ucla2|Nat1|Slc38-3|Sn1|Snat3|mNAT	solute carrier family 38, member 3	protein-coding
mm_136674.1	chr17	6128367	6128375	+	1	NA	intron (NM_001103181, intron 1 of 13)	intron (NM_001103181, intron 1 of 13)	-9777	NM_054040	68842	Mm.449307	NM_054040	ENSMUSG00000034377	Tulp4	1110057P05Rik|2210038L17Rik|Tusp	tubby like protein 4	protein-coding
mm_127498.1	chr15	101415108	101415150	+	1	NA	intron (NM_033073, intron 2 of 8)	intron (NM_033073, intron 2 of 8)	2726	NM_033073	110310	Mm.486285	NM_033073	ENSMUSG00000023039	Krt7	D15Wsu77e|K7|Krt2-7	keratin 7	protein-coding
mm_36971.1	chr4	109476454	109476477	-	1	NA	promoter-TSS (NM_013876)	promoter-TSS (NM_013876)	40	NM_013876	29864	Mm.392580	NM_013876	ENSMUSG00000028557	Rnf11	-	ring finger protein 11	protein-coding
mm_33882.1	chr4	136172851	136172860	+	1	NA	exon (NM_177733, exon 1 of 7)	exon (NM_177733, exon 1 of 7)	581	NM_177733	242705	Mm.307932	NM_177733	ENSMUSG00000018983	E2f2	E2F-2	E2F transcription factor 2	protein-coding
mm_86106.1	chr9	115310426	115310447	-	1	NA	promoter-TSS (NM_024222)	promoter-TSS (NM_024222)	-15	NM_024222	68292	Mm.296158	NM_024222	ENSMUSG00000032437	Stt3b	1300006C19Rik|Simp	STT3, subunit of the oligosaccharyltransferase complex, homolog B (S. cerevisiae)	protein-coding
mm_138584.1	chr17	35473483	35473490	+	1	NA	exon (NM_010391, exon 5 of 7)	exon (NM_010391, exon 5 of 7)	3397	NM_010391	15007	Mm.88795	NM_010391	ENSMUSG00000067235	H2-Q10	H-2Q10|Q10|Qa10	histocompatibility 2, Q region locus 10	protein-coding
mm_88041.1	chr10	67538064	67538074	+	1	NA	5' UTR (NM_010118, exon 1 of 2)	5' UTR (NM_010118, exon 1 of 2)	139	NM_001347458	13654	Mm.290421	NM_010118	ENSMUSG00000037868	Egr2	Egr-2|Krox-20|Krox20|NGF1-B|Zfp-25|Zfp-6	early growth response 2	protein-coding
mm_100138.1	chr11	115975065	115975088	+	1	NA	5' UTR (NM_133663, exon 1 of 39)	5' UTR (NM_133663, exon 1 of 39)	351	NM_133663	192897	Mm.213873	NM_133663	ENSMUSG00000020758	Itgb4	AA407042|C230078O20|CD104	integrin beta 4	protein-coding
mm_102289.1	chr11	55405298	55405312	-	1	NA	intron (NM_001290817, intron 4 of 9)	intron (NM_001290817, intron 4 of 9)	14775	NM_009242	20692	Mm.291442	NM_009242	ENSMUSG00000018593	Sparc	BM-40|ON	secreted acidic cysteine rich glycoprotein	protein-coding
mm_126821.1	chr15	88819585	88819684	+	1	NA	promoter-TSS (NM_001142357)	promoter-TSS (NM_001142357)	-12	NM_029720	76737	Mm.292567	NM_029720	ENSMUSG00000023272	Creld2	5730592L21Rik|C85758	cysteine-rich with EGF-like domains 2	protein-coding
mm_96839.1	chr11	70018835	70018847	+	1	NA	5' UTR (NM_007864, exon 1 of 20)	5' UTR (NM_007864, exon 1 of 20)	236	NM_007864	13385	Mm.27256	NM_007864	ENSMUSG00000020886	Dlg4	Dlgh4|PSD-95|PSD95|SAP90|SAP90A	discs, large homolog 4 (Drosophila)	protein-coding
mm_104909.1	chr11	99663188	99663192	-	1	NA	Intergenic	Intergenic	2770	NM_026834	68768	Mm.416844	NM_026834	ENSMUSG00000075566	Krtap4-6	1110054P19Rik	keratin associated protein 4-6	protein-coding
mm_163887.1	chr14	25857372	25857381	-	1	NA	intron (NM_013469, intron 1 of 14)	intron (NM_013469, intron 1 of 14)	15221	NM_013469	11744	Mm.294083	NM_013469	ENSMUSG00000021866	Anxa11	A830099O17Rik|Anx11	annexin A11	protein-coding
mm_99681.1	chr11	106008143	106008162	+	1	NA	promoter-TSS (NM_001037712)	promoter-TSS (NM_001037712)	-51	NM_001037712	192775	Mm.343850	NM_001037712	ENSMUSG00000001901	Kcnh6	m-erg2	potassium voltage-gated channel, subfamily H (eag-related), member 6	protein-coding
mm_35027.1	chr4	4019489	4019499	-	1	NA	5' UTR (NM_181989, exon 1 of 7)	5' UTR (NM_181989, exon 1 of 7)	169	NM_181989	242285	Mm.98096	NM_181989	ENSMUSG00000028236	Sdr16c5	Rdhe2|Scdr9	short chain dehydrogenase/reductase family 16C, member 5	protein-coding
mm_40411.1	chr5	53063846	53063856	+	1	NA	exon (NM_011402, exon 7 of 13)	exon (NM_011402, exon 7 of 13)	14498	NM_011402	20531	Mm.284891	NM_011402	ENSMUSG00000029188	Slc34a2	AA536683|D5Ertd227e|NaPi-2b|Npt2b	solute carrier family 34 (sodium phosphate), member 2	protein-coding
mm_8015.1	chr1	134866621	134866628	-	1	NA	intron (NM_001081307, intron 12 of 23)	intron (NM_001081307, intron 12 of 23)	-62903	NR_015606	329251	Mm.188709	NM_001081307	ENSMUSG00000073557	Ppp1r12b	1810037O03Rik|9530009M10Rik|AI132431|Mypt2	protein phosphatase 1, regulatory (inhibitor) subunit 12B	protein-coding
mm_119745.1	chr14	54123124	54123159	+	1	NA	Intergenic	Intergenic	130788	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_49298.1	chr6	17731221	17731254	+	1	NA	intron (NM_001289624, intron 1 of 15)	intron (NM_001289624, intron 1 of 15)	-12355	NM_001289629	64213	Mm.12051	NM_022332	ENSMUSG00000029534	St7	9430001H04Rik|Fam4a2|HELG|RAY1|SEN4|TSG7	suppression of tumorigenicity 7	protein-coding
mm_105794.1	chr11	109995748	109995762	-	1	NA	promoter-TSS (NM_013851)	promoter-TSS (NM_013851)	61	NM_013851	27404	Mm.341004	NM_013851	ENSMUSG00000020620	Abca8b	Abca8	ATP-binding cassette, sub-family A (ABC1), member 8b	protein-coding
mm_121915.1	chr14	22542844	22542849	-	1	NA	promoter-TSS (NR_046307)	promoter-TSS (NR_046307)	-48	NR_046307	74896	Mm.444661	NR_046307		4930405A10Rik	4930456G20Rik	RIKEN cDNA 4930405A10 gene	ncRNA
mm_144622.1	chr18	32938766	32938772	+	1	NA	promoter-TSS (NM_009793)	promoter-TSS (NM_009793)	-272	NM_009793	12326	Mm.222329	NM_009793	ENSMUSG00000038128	Camk4	A430110E23Rik|AI666733|CaMKIV|CaMKIV/Gr|D18Bwg0362e	calcium/calmodulin-dependent protein kinase IV	protein-coding
mm_119345.1	chr14	41105013	41105021	+	1	NA	promoter-TSS (NM_133653)	promoter-TSS (NM_133653)	-16	NM_133653	11720	Mm.14064	NM_133653	ENSMUSG00000037798	Mat1a	AI046368|AdoMet|Ams|MAT|MATA1|SAMS|SAMS1	methionine adenosyltransferase I, alpha	protein-coding
mm_72196.1	chr8	72548395	72548424	+	1	NA	promoter-TSS (NM_027485)	promoter-TSS (NM_027485)	-99	NM_027485	70625	Mm.235885	NM_027485	ENSMUSG00000045248	Med26	5730493L18Rik|AI414941|AW495270|Crsp7	mediator complex subunit 26	protein-coding
mm_114145.1	chr13	55322745	55322764	+	1	NA	promoter-TSS (NM_009000)	promoter-TSS (NM_009000)	699	NM_025596	66494	Mm.439805	NM_025596	ENSMUSG00000021486	Prelid1	2610524G07Rik|Preli	PRELI domain containing 1	protein-coding
mm_149603.1	chr19	16349547	16349565	+	1	NA	intron (NM_008139, intron 5 of 6)	L1MB3|LINE|L1	-34552	NR_105832	102465218		NR_105832	ENSMUSG00000098718	Mir496b	Gm28028|mmu-mir-496b	microRNA 496b	ncRNA
mm_94511.1	chr11	8545341	8545342	+	1	NA	exon (NM_001083587, exon 8 of 31)	exon (NM_001083587, exon 8 of 31)	119194	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_87267.1	chr10	41529547	41529560	+	1	NA	3' UTR (NM_016898, exon 6 of 6)	3' UTR (NM_016898, exon 6 of 6)	10053	NM_016898	53599	Mm.269815	NM_016898	ENSMUSG00000019818	Cd164	A115|A24|AA589639|AW540279|MGC-24|MSSP	CD164 antigen	protein-coding
mm_52743.1	chr6	120465890	120465944	+	1	NA	intron (NM_008359, intron 1 of 12)	(CA)n|Simple_repeat|Simple_repeat	2720	NM_008359	16172	Mm.4481	NM_008359	ENSMUSG00000002897	Il17ra	AW538159|Cdw217|Il17r|VDw217	interleukin 17 receptor A	protein-coding
mm_117948.1	chr13	99435395	99435412	-	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-22577	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_144070.1	chr17	90995552	90995594	-	1	NA	intron (NM_001346957, intron 1 of 18)	intron (NM_001346957, intron 1 of 18)	94032	NM_001346957	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_81824.1	chr9	118049991	118050004	+	1	NA	intron (NM_001286508, intron 4 of 7)	intron (NM_001286508, intron 4 of 7)	9475	NM_013727	27215	Mm.92705	NM_013727	ENSMUSG00000039285	Azi2	AA410145|AZ2	5-azacytidine induced gene 2	protein-coding
mm_97764.1	chr11	82023010	82023014	+	1	NA	Intergenic	Intergenic	-12565	NM_011333	20296	Mm.290320	NM_011333	ENSMUSG00000035385	Ccl2	AI323594|HC11|JE|MCAF|MCP-1|MCP1|SMC-CF|Scya2|Sigje	chemokine (C-C motif) ligand 2	protein-coding
mm_67884.1	chr7	99349079	99349103	-	1	NA	exon (NM_009825, exon 2 of 5)	exon (NM_009825, exon 2 of 5)	4148	NM_009825	12406	Mm.22708	NM_009825	ENSMUSG00000070436	Serpinh1	BERF-1|Cbp1|Cbp2|Hsp47|J6|Serpinh2|gp46	serine (or cysteine) peptidase inhibitor, clade H, member 1	protein-coding
mm_110762.1	chr12	70136262	70136276	-	1	NA	Intergenic	Intergenic	-17902	NM_001195033	100504285	Mm.291105	NM_001195033	ENSMUSG00000090121	Abhd12b	Gm804	abhydrolase domain containing 12B	protein-coding
mm_84386.1	chr9	65422984	65422994	-	1	NA	promoter-TSS (NM_178933)	promoter-TSS (NM_178933)	-216	NM_178933	330962	Mm.335247	NM_178933	ENSMUSG00000053862	Slc51b	Ostb	solute carrier family 51, beta subunit	protein-coding
mm_41746.1	chr5	102841053	102841057	+	1	NA	intron (NM_001286468, intron 1 of 7)	intron (NM_001286468, intron 1 of 7)	-3952	NM_001346585	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding
mm_166725.1	chr6	121630435	121630437	+	1	NA	Intergenic	URR1A|DNA|hAT-Charlie	-5737	NM_175628	232345	Mm.30151	NM_175628	ENSMUSG00000030111	A2m	A2mp	alpha-2-macroglobulin	protein-coding
mm_7491.1	chr1	121332546	121332568	-	1	NA	promoter-TSS (NM_178082)	promoter-TSS (NM_178082)	32	NM_178082	72999	Mm.27136	NM_133748	ENSMUSG00000003721	Insig2	2900053I11Rik|C730043J18Rik|Insig-2	insulin induced gene 2	protein-coding
mm_25358.1	chr3	107090914	107090930	+	1	NA	Intergenic	L2a|LINE|L2	-10645	NM_008417	16490	Mm.39285	NM_008417	ENSMUSG00000040724	Kcna2	Akr6a4|ENSMUSG00000074335|Gm10672|Kca1-2|Kv1.2|Mk-2	potassium voltage-gated channel, shaker-related subfamily, member 2	protein-coding
mm_9329.1	chr1	171849531	171849537	-	1	NA	intron (NM_001289470, intron 2 of 8)	intron (NM_001289470, intron 2 of 8)	9837	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_46209.1	chr5	98031514	98031523	-	1	NA	promoter-TSS (NM_133738)	promoter-TSS (NM_133738)	-556	NM_133738	71914	Mm.24842	NM_133738	ENSMUSG00000029338	Antxr2	2310046B19Rik|AW561899|CMG-2|CMG2|cI-35	anthrax toxin receptor 2	protein-coding
mm_102328.1	chr11	57801460	57801487	-	1	NA	promoter-TSS (NM_001081168)	promoter-TSS (NM_001081168)	-6	NR_131042	76516	Mm.28485	NR_131042	ENSMUSG00000087165	2010001A14Rik	-	RIKEN cDNA 2010001A14 gene	ncRNA
mm_14483.1	chr2	131561606	131561619	+	1	NA	exon (NM_013460, exon 1 of 2)	exon (NM_013460, exon 1 of 2)	673	NM_013460	11550	Mm.389380	NM_013460	ENSMUSG00000027335	Adra1d	Adra-1|Adra1|Adra1a|Gpcr8|Spr8|[a]1d|alpha1D-AR	adrenergic receptor, alpha 1d	protein-coding
mm_124169.1	chr14	93719233	93719249	-	1	NA	intron (NM_001346722, intron 2 of 4)	intron (NM_001346722, intron 2 of 4)	169647	NM_001271800	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding
mm_88798.1	chr10	80695572	80695589	+	1	NA	intron (NM_172457, intron 1 of 3)	intron (NM_172457, intron 1 of 3)	6240	NM_172457	208228	Mm.49309	NM_172457	ENSMUSG00000003348	Mob3a	5330417K06Rik|A630029F06|AV218468|Mobkl2a	MOB kinase activator 3A	protein-coding
mm_89497.1	chr10	93897157	93897161	+	1	NA	Intergenic	Intergenic	-5957	NM_019648	56307	Mm.289329	NM_019648	ENSMUSG00000036112	Metap2	4930584B20Rik|A930035J23Rik|AI047573|AL024412|AU014659|Amp2|Mnpep|p67|p67eIF2	methionine aminopeptidase 2	protein-coding
mm_89830.1	chr10	106470282	106470367	+	1	NA	promoter-TSS (NM_177373)	promoter-TSS (NM_177373)	14	NM_001205341	327814	Mm.391424	NM_177373	ENSMUSG00000053825	Ppfia2	5330438O12|B230207K17Rik|E130120L08Rik|mKIAA4112	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 2	protein-coding
mm_33409.1	chr4	129848694	129848705	+	1	NA	3' UTR (NM_001164745, exon 6 of 6)	3' UTR (NM_001164745, exon 6 of 6)	27991	NM_001164745	19244	Mm.193688	NM_008974	ENSMUSG00000028788	Ptp4a2	Prl-2	protein tyrosine phosphatase 4a2	protein-coding
mm_104804.1	chr11	98775218	98775245	-	1	NA	5' UTR (NM_145434, exon 1 of 8)	5' UTR (NM_145434, exon 1 of 8)	146	NM_145434	217166	Mm.390397	NM_145434	ENSMUSG00000020889	Nr1d1	A530070C09Rik|R75201	nuclear receptor subfamily 1, group D, member 1	protein-coding
mm_99177.1	chr11	100859870	100859885	+	1	NA	promoter-TSS (NM_001164062)	promoter-TSS (NM_001164062)	526	NM_011488	20850	Mm.277403	NM_011488	ENSMUSG00000004043	Stat5a	AA959963|STAT5	signal transducer and activator of transcription 5A	protein-coding
mm_81977.1	chr9	121300710	121300714	+	1	NA	Intergenic	ID_B1|SINE|B4	-23540	NM_177589	209012	Mm.371804	NM_177589	ENSMUSG00000040936	Ulk4	4932415A06Rik|A730098P15	unc-51-like kinase 4	protein-coding
mm_142435.1	chr17	45570787	45570805	-	1	NA	exon (NM_008302, exon 5 of 11)	exon (NM_008302, exon 5 of 11)	2465	NM_008302	15516	Mm.2180	NM_008302	ENSMUSG00000023944	Hsp90ab1	90kDa|AL022974|C81438|Hsp84|Hsp84-1|Hsp90|Hspcb	heat shock protein 90 alpha (cytosolic), class B member 1	protein-coding
mm_125875.1	chr15	75616733	75616787	+	1	NA	promoter-TSS (NM_011759)	promoter-TSS (NM_011759)	76	NM_011759	22701	Mm.87210	NM_011759	ENSMUSG00000047003	Zfp41	CTfin92|Zfp-41	zinc finger protein 41	protein-coding
mm_145147.1	chr18	45593345	45593345	+	1	NA	intron (NM_001312905, intron 6 of 10)	HAL1|LINE|L1	33191	NM_080465	140492	Mm.411614	NM_080465	ENSMUSG00000054477	Kcnn2	KCa2.2|SK2|SKCA2|bc|fri	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2	protein-coding
mm_68842.1	chr7	126364845	126364850	-	1	NA	intron (NM_010689, intron 8 of 11)	intron (NM_010689, intron 8 of 11)	3198	NR_106025	102466797		NR_106025	ENSMUSG00000099017	Mir7058	Gm27766|mmu-mir-7058	microRNA 7058	ncRNA
mm_60050.1	chr7	31060064	31060081	+	1	NA	exon (NM_144556, exon 1 of 9)	exon (NM_144556, exon 1 of 9)	137	NM_144556	243914	Mm.389870	NM_144556	ENSMUSG00000036560	Lgi4	Lgil3|clp	leucine-rich repeat LGI family, member 4	protein-coding
mm_87224.1	chr10	40426803	40426814	+	1	NA	intron (NM_198164, intron 2 of 11)	intron (NM_198164, intron 2 of 11)	77500	NM_001291816	78334	Mm.200924	NM_198164	ENSMUSG00000038481	Cdk19	2700084L06Rik|AI845279|AW228747|CDK11|Cdc2l6|mKIAA1028	cyclin-dependent kinase 19	protein-coding
mm_114181.1	chr13	55645387	55645406	+	1	NA	exon (NM_001282055, exon 4 of 23)	exon (NM_001282055, exon 4 of 23)	10397	NM_001282055	212880	Mm.202725	NM_145975	ENSMUSG00000021500	Ddx46	2200005K02Rik|8430438J23Rik|AI325430|AI957095|mKIAA0801	DEAD (Asp-Glu-Ala-Asp) box polypeptide 46	protein-coding
mm_108163.1	chr12	76370477	76370508	+	1	NA	promoter-TSS (NM_028356)	promoter-TSS (NM_028356)	226	NM_178744	268564	Mm.77065	NM_178744	ENSMUSG00000033454	Zbtb1	9430077A12|AI256369|Bsg2|C430003J21Rik	zinc finger and BTB domain containing 1	protein-coding
mm_166366.1	chr5	124451297	124451343	+	1	NA	exon (NM_001310723, exon 4 of 7)	exon (NM_001310723, exon 4 of 7)	4616	NM_001310727	67956	Mm.137966	NM_030241	ENSMUSG00000049327	Kmt5a	2410195B05Rik|AA617402|AW536475|PR-SET7|PR/SET07|Setd8	lysine methyltransferase 5A	protein-coding
mm_123788.1	chr14	70429073	70429096	-	1	NA	promoter-TSS (NM_021308)	promoter-TSS (NM_021308)	10	NM_021308	57746	Mm.85253	NM_021308	ENSMUSG00000033644	Piwil2	Piwil1l|mili	piwi-like RNA-mediated gene silencing 2	protein-coding
mm_16802.1	chr2	10119560	10119576	-	1	NA	exon (NM_010582, exon 6 of 21)	exon (NM_010582, exon 6 of 21)	11115	NM_010582	16425	Mm.182043	NM_010582	ENSMUSG00000037254	Itih2	AI747202|Intin2|Itih-2	inter-alpha trypsin inhibitor, heavy chain 2	protein-coding
mm_89801.1	chr10	102512484	102512521	+	1	NA	5' UTR (NM_146240, exon 1 of 2)	5' UTR (NM_146240, exon 1 of 2)	280	NM_146240	237504	Mm.282672	NM_146240	ENSMUSG00000044921	Rassf9	AW322107|Pamci	Ras association (RalGDS/AF-6) domain family (N-terminal) member 9	protein-coding
mm_137371.1	chr17	25570823	25570848	+	1	NA	promoter-TSS (NR_045176)	promoter-TSS (NR_045176)	24	NR_045176	72834	Mm.33042	NR_045176	ENSMUSG00000091475	2810468N07Rik	-	RIKEN cDNA 2810468N07 gene	ncRNA
mm_77390.1	chr8	120228076	120228095	-	1	NA	non-coding (NR_110496, exon 1 of 3)	non-coding (NR_110496, exon 1 of 3)	145	NR_110496	434353	Mm.411793	NR_110496	ENSMUSG00000097960	A330074K22Rik	-	RIKEN cDNA A330074K22 gene	ncRNA
mm_149086.1	chr19	8920462	8920473	+	1	NA	promoter-TSS (NM_024256)	promoter-TSS (NM_024256)	74	NM_024256	72727	Mm.259	NM_024256	ENSMUSG00000071649	B3gat3	2810405M13Rik	beta-1,3-glucuronyltransferase 3 (glucuronosyltransferase I)	protein-coding
mm_142425.1	chr17	45569298	45569318	-	1	NA	exon (NM_008302, exon 8 of 11)	exon (NM_008302, exon 8 of 11)	3953	NM_008302	15516	Mm.2180	NM_008302	ENSMUSG00000023944	Hsp90ab1	90kDa|AL022974|C81438|Hsp84|Hsp84-1|Hsp90|Hspcb	heat shock protein 90 alpha (cytosolic), class B member 1	protein-coding
mm_116013.1	chr13	24703498	24703538	-	1	NA	intron (NM_001286100, intron 14 of 22)	intron (NM_001286100, intron 14 of 22)	58419	NM_020567	57441	Mm.12239	NM_020567	ENSMUSG00000006715	Gmnn	AW546347|Gem	geminin	protein-coding
mm_157889.1	chrX	75875102	75875151	-	1	NA	promoter-TSS (NM_001166453)	promoter-TSS (NM_001166453)	44	NM_001166453	102866	Mm.28777	NM_145629	ENSMUSG00000016382	Pls3	AI115446|AL024105	plastin 3 (T-isoform)	protein-coding
mm_34817.1	chr4	154943004	154943019	+	1	NA	Intergenic	Intergenic	-14934	NM_178931	230979	Mm.215147	NM_178931	ENSMUSG00000042333	Tnfrsf14	Atar|HveA|Hvem|Tnfrs14	tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)	protein-coding
mm_122196.1	chr14	31781402	31781412	-	1	NA	intron (NM_001024604, intron 1 of 27)	intron (NM_001024604, intron 1 of 27)	49008	NM_001024604	105522	Mm.37660	NM_001024604	ENSMUSG00000014496	Ankrd28	AI465466|AI604979|E430019N21Rik|mKIAA0379	ankyrin repeat domain 28	protein-coding
mm_149011.1	chr19	8735793	8735807	+	1	NA	promoter-TSS (NM_134139)	promoter-TSS (NM_134139)	-39	NM_134139	107071	Mm.29627	NM_134139	ENSMUSG00000042729	Wdr74	5730436H21Rik|AA407588	WD repeat domain 74	protein-coding
mm_75315.1	chr8	41346134	41346153	-	1	NA	exon (NM_019734, exon 10 of 14)	exon (NM_019734, exon 10 of 14)	28554	NM_019734	11886	Mm.22547	NM_019734	ENSMUSG00000031591	Asah1	2310081N20Rik|AC|Asah	N-acylsphingosine amidohydrolase 1	protein-coding
mm_100365.1	chr11	119023033	119023104	+	1	NA	promoter-TSS (NM_007623)	promoter-TSS (NM_007623)	47	NM_007623	12416	Mm.14547	NM_007623	ENSMUSG00000025577	Cbx2	M33|MOD2|pc	chromobox 2	protein-coding
mm_148220.1	chr18	80256026	80256041	-	1	NA	promoter-TSS (NM_001164424)	promoter-TSS (NM_001164424)	-193	NM_001164424	66943	Mm.29247	NM_025861	ENSMUSG00000034006	Pqlc1	2310009N05Rik|4933425L21Rik|5730564E11Rik|C78974	PQ loop repeat containing 1	protein-coding
mm_42008.1	chr5	108065668	108065682	+	1	NA	promoter-TSS (NM_013827)	promoter-TSS (NM_013827)	1	NM_013827	17765	Mm.257149	NM_013827	ENSMUSG00000029267	Mtf2	9230112N11Rik|AA537621|C76717|M96|Pcl2	metal response element binding transcription factor 2	protein-coding
mm_51500.1	chr6	83109072	83109114	+	1	NA	promoter-TSS (NM_026744)	promoter-TSS (NM_026744)	-15	NM_026744	68499	Mm.333183	NM_026744	ENSMUSG00000030037	Mrpl53	1110007K17Rik	mitochondrial ribosomal protein L53	protein-coding
mm_161773.1	chr17	37492350	37492350	+	1	NA	promoter-TSS (NM_146328)	promoter-TSS (NM_146328)	-118	NM_146328	258325	Mm.484339	NM_146328	ENSMUSG00000090894	Olfr110	MOR249-2	olfactory receptor 110	protein-coding
mm_42280.1	chr5	114175890	114175938	+	1	NA	intron (NM_133904, intron 1 of 51)	intron (NM_133904, intron 1 of 51)	10396	NM_133904	100705	Mm.81793	NM_133904	ENSMUSG00000042010	Acacb	AI597064|AW743042|Acc2|Accb	acetyl-Coenzyme A carboxylase beta	protein-coding
mm_72032.1	chr8	70766060	70766073	+	1	NA	intron (NM_023065, intron 1 of 7)	intron (NM_023065, intron 1 of 7)	597	NM_023065	65972	Mm.30241	NM_023065	ENSMUSG00000031838	Ifi30	GILT|IP30	interferon gamma inducible protein 30	protein-coding
mm_159267.1	chr2	160327413	160327413	-	1	NA	promoter-TSS (NM_001033411)	promoter-TSS (NM_001033411)	81	NM_001033411	329554	Mm.291144	NM_001033411	ENSMUSG00000074623	Gm826	-	predicted gene 826	protein-coding
mm_9316.1	chr1	171648365	171648377	-	1	NA	intron (NM_001347184, intron 1 of 5)	intron (NM_001347184, intron 1 of 5)	628	NM_001347184	75345	Mm.164642	NM_144539	ENSMUSG00000038179	Slamf7	19A|19A24|4930560D03Rik|CRACC|CS1	SLAM family member 7	protein-coding
mm_54983.1	chr6	48741463	48741473	-	1	NA	intron (NM_175860, intron 2 of 2)	intron (NM_175860, intron 2 of 2)	2421	NM_008376	16205	Mm.252599	NM_008376	ENSMUSG00000090019	Gimap1	IAP38|Imap38|imap	GTPase, IMAP family member 1	protein-coding
mm_143147.1	chr17	57222331	57222346	-	1	NA	exon (NM_009778, exon 14 of 41)	exon (NM_009778, exon 14 of 41)	-5110	NR_105944	102465591		NR_105944	ENSMUSG00000099066	Mir6978	Gm27858|mmu-mir-6978	microRNA 6978	ncRNA
mm_8797.1	chr1	161788501	161788506	-	1	NA	promoter-TSS (NM_001205243)	promoter-TSS (NM_001205243)	-8	NM_010177	14103	Mm.3355	NM_010177	ENSMUSG00000000817	Fasl	APT1LG1|CD178|CD95-L|CD95L|Fas-L|Faslg|Tnfsf6|Tnlg1a|gld	Fas ligand (TNF superfamily, member 6)	protein-coding
mm_52627.1	chr6	117174212	117174231	+	1	NA	3' UTR (NM_021704, exon 3 of 3)	3' UTR (NM_021704, exon 3 of 3)	5686	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_7530.1	chr1	124278872	124278875	-	1	NA	Intergenic	Lx8|LINE|L1	-233314	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_99907.1	chr11	109755030	109755050	+	1	NA	Intergenic	Intergenic	-32784	NM_153782	208659	Mm.208662	NM_153782	ENSMUSG00000020614	Fam20a	AI606893	family with sequence similarity 20, member A	protein-coding
mm_94424.1	chr11	6230330	6230339	+	1	NA	promoter-TSS (NM_207242)	promoter-TSS (NM_207242)	-89	NM_207242	237636	Mm.212492	NM_207242	ENSMUSG00000020447	Npc1l1	9130221N23Rik|Gm243	NPC1-like 1	protein-coding
mm_165771.1	chr3	122245744	122245744	+	1	NA	5' UTR (NM_008129, exon 1 of 7)	5' UTR (NM_008129, exon 1 of 7)	187	NM_008129	14630	Mm.292676	NM_008129	ENSMUSG00000028124	Gclm	AI649393|Gcmc|Glclr	glutamate-cysteine ligase, modifier subunit	protein-coding
mm_168931.1	chr12	65916095	65916110	+	1	NA	Intergenic	L1Md_T|LINE|L1	368299	NM_001162933	238217	Mm.188575	NM_001162933	ENSMUSG00000060499	Rpl10l	EG238217	ribosomal protein L10-like	protein-coding
mm_29526.1	chr3	116645685	116645714	-	1	NA	intron (NM_008246, intron 4 of 11)	intron (NM_008246, intron 4 of 11)	16978	NM_008246	15247	Mm.280077	NM_008246	ENSMUSG00000089911	Mfsd14a	Hiat1	major facilitator superfamily domain containing 14A	protein-coding
mm_155190.1	chrX	56454815	56454825	+	1	NA	promoter-TSS (NM_172779)	promoter-TSS (NM_172779)	-19	NM_172779	236790	Mm.474772	NM_172779	ENSMUSG00000035967	Ints6l	4930535D10Rik|6330505F04Rik|D130066O12|Ddx26b	integrator complex subunit 6 like	protein-coding
mm_158799.1	chrX	167244865	167244882	-	1	NA	exon (NM_001313760, exon 2 of 2)	exon (NM_001313760, exon 2 of 2)	19456	NM_001313761	170744	Mm.196676	NM_133212	ENSMUSG00000040522	Tlr8	-	toll-like receptor 8	protein-coding
mm_11311.1	chr2	30286384	30286394	+	1	NA	promoter-TSS (NM_177648)	promoter-TSS (NM_177648)	-35	NM_177648	227697	Mm.26690	NM_177648	ENSMUSG00000075419	Dolk	BC026973|Tmem15|mKIAA1094	dolichol kinase	protein-coding
mm_155757.1	chrX	96167566	96167611	+	1	NA	3' UTR (NM_010833, exon 13 of 13)	3' UTR (NM_010833, exon 13 of 13)	71543	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_121667.1	chr14	12346095	12346116	-	1	NA	promoter-TSS (NM_080433)	promoter-TSS (NM_080433)	-240	NM_080433	54713	Mm.34644	NM_080433	ENSMUSG00000021743	Fezf2	AI451466|AI852056|Fez|Fezl|Zfp312	Fez family zinc finger 2	protein-coding
mm_105814.1	chr11	111512455	111512473	-	1	NA	Intergenic	Intergenic	446300	NM_008425	16518	Mm.4951	NM_008425	ENSMUSG00000041695	Kcnj2	IRK1|Kcnf1|Kir2.1	potassium inwardly-rectifying channel, subfamily J, member 2	protein-coding
mm_64452.1	chr7	142659104	142659115	+	1	NA	promoter-TSS (NM_010514)	promoter-TSS (NM_010514)	-305	NM_010514	16002	Mm.3862	NM_010514	ENSMUSG00000048583	Igf2	AL033362|Igf-2|Igf-II|M6pr|Mpr|Peg2	insulin-like growth factor 2	protein-coding
mm_70918.1	chr8	25754493	25754514	+	1	NA	promoter-TSS (NM_028102)	promoter-TSS (NM_028102)	-223	NM_028102	72108	Mm.246875	NM_028102	ENSMUSG00000061313	Ddhd2	2010305K11Rik|SAMWD1|mKIAA0725	DDHD domain containing 2	protein-coding
mm_57949.1	chr6	134920288	134920296	-	1	NA	promoter-TSS (NM_009875)	promoter-TSS (NM_009875)	-109	NM_009875	12576	Mm.2958	NM_009875	ENSMUSG00000003031	Cdkn1b	AA408329|AI843786|Kip1|p27|p27Kip1	cyclin-dependent kinase inhibitor 1B	protein-coding
mm_117473.1	chr13	76271316	76271319	-	1	NA	Intergenic	Intergenic	-113644	NM_030174	78771	Mm.316249	NM_030174	ENSMUSG00000021596	Mctp1	2810465F10Rik	multiple C2 domains, transmembrane 1	protein-coding
mm_5686.1	chr1	43183632	43183658	-	1	NA	intron (NM_001289533, intron 1 of 5)	ORR1A4|LTR|ERVL-MaLR	13116	NM_001289533	14200	Mm.6799	NM_010212	ENSMUSG00000008136	Fhl2	FHL-2|SLIM-3|SLIM3	four and a half LIM domains 2	protein-coding
mm_165118.1	chr19	60890290	60890299	+	1	NA	5' UTR (NM_018869, exon 1 of 16)	5' UTR (NM_018869, exon 1 of 16)	545	NM_018869	14773	Mm.279400	NM_018869	ENSMUSG00000003228	Grk5	Gprk5	G protein-coupled receptor kinase 5	protein-coding
mm_163231.1	chr11	103262396	103262420	-	1	NA	intron (NM_016896, intron 1 of 15)	intron (NM_016896, intron 1 of 15)	4993	NM_016896	53859	Mm.158981	NM_016896	ENSMUSG00000020941	Map3k14	Nik|aly	mitogen-activated protein kinase kinase kinase 14	protein-coding
mm_44525.1	chr5	24392680	24392698	-	1	NA	promoter-TSS (NM_001002897)	promoter-TSS (NM_001002897)	-546	NM_001002897	213948	Mm.332252	NM_001002897	ENSMUSG00000038295	Atg9b	Apg912|Apg9l2|Apgdc2|Gm574|Nos3as|eONE|sONE	autophagy related 9B	protein-coding
mm_88857.1	chr10	80930784	80930792	+	1	NA	intron (NM_008655, intron 2 of 3)	intron (NM_008655, intron 2 of 3)	697	NM_008655	17873	Mm.1360	NM_008655	ENSMUSG00000015312	Gadd45b	AI323528|Myd118	growth arrest and DNA-damage-inducible 45 beta	protein-coding
mm_95335.1	chr11	46815532	46815542	+	1	NA	exon (NM_178759, exon 2 of 9)	exon (NM_178759, exon 2 of 9)	4738	NM_178759	276891	Mm.69002	NM_178759	ENSMUSG00000055546	Timd4	B430010N18Rik|TIM-4|Tim4	T cell immunoglobulin and mucin domain containing 4	protein-coding
mm_131232.1	chr16	10479922	10479940	+	1	NA	promoter-TSS (NM_001243760)	promoter-TSS (NM_001243760)	-141	NM_001302619	12265	Mm.249560	NM_007575	ENSMUSG00000022504	Ciita	C2ta|EG669998|Gm9475|Mhc2ta	class II transactivator	protein-coding
mm_144748.1	chr18	35599220	35599269	+	1	NA	intron (NM_026420, intron 1 of 3)	CpG	577	NM_026420	67869	Mm.126534	NM_026420	ENSMUSG00000037058	Paip2	2310050K10Rik|AU045972	polyadenylate-binding protein-interacting protein 2	protein-coding
mm_114214.1	chr13	56173465	56173475	+	1	NA	TTS (NM_001168615)	TTS (NM_001168615)	5415	NM_145976	212937	Mm.116697	NM_145976	ENSMUSG00000049625	Tifab	-	TRAF-interacting protein with forkhead-associated domain, family member B	protein-coding
mm_137635.1	chr17	28329623	28329641	+	1	NA	intron (NM_011287, intron 4 of 5)	intron (NM_011287, intron 4 of 5)	1161	NM_011287	19896	Mm.336955	NM_011287	ENSMUSG00000037805	Rpl10a	CsA-19|Nedd6	ribosomal protein L10A	protein-coding
mm_121678.1	chr14	12822913	12822926	-	1	NA	5' UTR (NM_001042617, exon 1 of 31)	5' UTR (NM_001042617, exon 1 of 31)	160	NM_001042617	27062	Mm.260881	NM_012061	ENSMUSG00000054423	Cadps	AU067781|CAPS|CAPS1|mKIAA1121	Ca2+-dependent secretion activator	protein-coding
mm_73353.1	chr8	105453563	105453566	+	1	NA	intron (NM_001033371, intron 6 of 10)	intron (NM_001033371, intron 6 of 10)	17858	NM_026481	67971	Mm.29358	NM_026481	ENSMUSG00000014846	Tppp3	2700055K07Rik|CGI-38|Ceacam9|mmCGM8	tubulin polymerization-promoting protein family member 3	protein-coding
mm_131668.1	chr16	20654437	20654440	+	1	NA	intron (NM_134101, intron 3 of 20)	intron (NM_134101, intron 3 of 20)	2786	NM_134101	21762	Mm.243234	NM_134101	ENSMUSG00000006998	Psmd2	9430095H01Rik|AA407121|TEG-190|Tex190	proteasome (prosome, macropain) 26S subunit, non-ATPase, 2	protein-coding
mm_104102.1	chr11	86704957	86704978	-	1	NA	exon (NM_001003908, exon 24 of 32)	exon (NM_001003908, exon 24 of 32)	20886	NM_001098810	217057	Mm.24868	NM_175004	ENSMUSG00000072582	Ptrh2	A230072I16Rik|Bit1|CGI-147	peptidyl-tRNA hydrolase 2	protein-coding
mm_56578.1	chr6	106749173	106749206	-	1	NA	promoter-TSS (NM_008370)	promoter-TSS (NM_008370)	-152	NM_008370	16192	Mm.3448	NM_008370	ENSMUSG00000005364	Il5ra	CD125|CDw125|Il5r	interleukin 5 receptor, alpha	protein-coding
mm_161973.1	chr19	11819360	11819360	-	1	NA	promoter-TSS (NM_001286543)	promoter-TSS (NM_001286543)	43	NM_001286543	20908	Mm.272264	NM_011502	ENSMUSG00000041488	Stx3	Syn-3	syntaxin 3	protein-coding
mm_141099.1	chr17	26004891	26004905	-	1	NA	intron (NM_153140, intron 4 of 11)	intron (NM_153140, intron 4 of 11)	16962	NM_153140	215445	Mm.41191	NM_153140	ENSMUSG00000037098	Rab11fip3	Cart1|D030060O14Rik|Rab11-FIP3|mKIAA0665	RAB11 family interacting protein 3 (class II)	protein-coding
mm_161771.1	chr17	37002410	37002410	+	1	NA	promoter-TSS (NM_001013745)	promoter-TSS (NM_001013745)	-72	NM_001168501	22715	Mm.305561	NM_009559	ENSMUSG00000036036	Zfp57	G19|Zfp-57	zinc finger protein 57	protein-coding
mm_56595.1	chr6	108553094	108553097	-	1	NA	Intergenic	Intergenic	63352	NR_106121	102465766		NR_106121	ENSMUSG00000105697	Mir7661	mmu-mir-7661	microRNA 7661	ncRNA
mm_43398.1	chr5	135783337	135783355	+	1	NA	exon (NM_008617, exon 2 of 9)	exon (NM_008617, exon 2 of 9)	4697	NM_008617	17448	Mm.297096	NM_008617	ENSMUSG00000019179	Mdh2	MDH|Mdh-2|Mor-1|Mor1	malate dehydrogenase 2, NAD (mitochondrial)	protein-coding
mm_80843.1	chr9	98287430	98287440	+	1	NA	Intergenic	RLTR10B|LTR|ERVK	-9148	NM_144533	74080	Mm.294082	NM_144533	ENSMUSG00000032456	Nmnat3	4933408N02Rik|PNAT3	nicotinamide nucleotide adenylyltransferase 3	protein-coding
mm_84650.1	chr9	71592284	71592297	-	1	NA	promoter-TSS (NM_001033208)	promoter-TSS (NM_001033208)	70	NM_001033208	102371	Mm.27585	NM_001033208	ENSMUSG00000041361	Myzap	AA407270|AV006038|Gcom1|Gm640|Grinl1a7|Myozap	myocardial zonula adherens protein	protein-coding
mm_68195.1	chr7	104379628	104379640	-	1	NA	Intergenic	Lx2B2|LINE|L1	-20988	NM_175648	244183	Mm.347647	NM_175648	ENSMUSG00000052749	Trim30b	A530023O14Rik|Trim30-1	tripartite motif-containing 30B	protein-coding
mm_142725.1	chr17	48167266	48167286	-	1	NA	promoter-TSS (NM_178796)	promoter-TSS (NM_178796)	-19	NM_178796	328830	Mm.470939	NM_178796	ENSMUSG00000043939	A530064D06Rik	Trem4|pdctrem	RIKEN cDNA A530064D06 gene	protein-coding
mm_108325.1	chr12	79770085	79770092	+	1	NA	intron (NM_009014, intron 9 of 10)	intron (NM_009014, intron 9 of 10)	154645	NR_131075	77290	Mm.395042	NR_131073		9430078K24Rik	-	RIKEN cDNA 9430078K24 gene	ncRNA
mm_13535.1	chr2	110600788	110600798	+	1	NA	intron (NM_001177624, intron 1 of 14)	MLT1H|LTR|ERVL-MaLR	3494	NM_001177624	241612	Mm.277148	NM_001003915	ENSMUSG00000041644	Slc5a12	AI315119|D630015G19|SMCT2	solute carrier family 5 (sodium/glucose cotransporter), member 12	protein-coding
mm_163986.1	chr14	61147504	61147532	+	1	NA	intron (NM_172809, intron 1 of 9)	intron (NM_172809, intron 1 of 9)	9061	NM_172809	50720	Mm.440703	NM_015788	ENSMUSG00000048279	Sacs	A230052M14|DNAJC29|E130115J16Rik|mKIAA0730	sacsin	protein-coding
mm_18961.1	chr2	76798381	76798393	-	1	NA	exon (NM_011652, exon 196 of 313)	exon (NM_011652, exon 196 of 313)	123072	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_42158.1	chr5	112206759	112206781	+	1	NA	promoter-TSS (NR_045378)	promoter-TSS (NR_045378)	7	NR_045378	75569	Mm.243721	NR_045377	ENSMUSG00000101683	1700028D13Rik	-	RIKEN cDNA 1700028D13 gene	ncRNA
mm_121850.1	chr14	20656489	20656508	-	1	NA	promoter-TSS (NM_021508)	promoter-TSS (NM_021508)	42	NM_021508	59011	Mm.439911	NM_021508	ENSMUSG00000068697	Myoz1	2310001N11Rik|AV090278|FATZ|Myoz	myozenin 1	protein-coding
mm_59360.1	chr7	25687278	25687341	+	1	NA	TTS (NM_172148)	TTS (NM_172148)	307	NM_011577	21803	Mm.248380	NM_011577	ENSMUSG00000002603	Tgfb1	TGF-beta1|TGFbeta1|Tgfb|Tgfb-1	transforming growth factor, beta 1	protein-coding
mm_35717.1	chr4	44526425	44526436	-	1	NA	Intergenic	Intergenic	-176370	NR_073462	70602	Mm.491142	NR_073462	ENSMUSG00000103995	5730488B01Rik	-	RIKEN cDNA 5730488B01 gene	ncRNA
mm_16679.1	chr2	6872536	6872579	-	1	NA	promoter-TSS (NM_001347094)	promoter-TSS (NM_001347094)	-522	NM_001347094	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_135765.1	chr16	56717529	56717539	-	1	NA	promoter-TSS (NM_001252443)	promoter-TSS (NM_001252443)	-84	NM_019678	21787	Mm.425970	NM_019678	ENSMUSG00000022757	Tfg	AI173908	Trk-fused gene	protein-coding
mm_110876.1	chr12	73949832	73949852	-	1	NA	Intergenic	CpG	-14688	NM_178392	75627	Mm.25937	NM_178392	ENSMUSG00000021113	Snapc1	2700033G17Rik|AU015787	small nuclear RNA activating complex, polypeptide 1	protein-coding
mm_58947.1	chr7	18646990	18646999	+	1	NA	3' UTR (NM_027403, exon 5 of 5)	3' UTR (NM_027403, exon 5 of 5)	9731	NM_027403	72242	Mm.326858	NM_027403	ENSMUSG00000070796	Psg21	1600019C01Rik|1600025N01Rik|1600026N13Rik|cea8	pregnancy-specific glycoprotein 21	protein-coding
mm_156966.1	chrX	169994572	169994603	+	1	NA	Intergenic	Intergenic	-15670	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_62801.1	chr7	112856599	112856613	+	1	NA	intron (NM_009346, intron 5 of 12)	intron (NM_009346, intron 5 of 12)	97222	NM_001166585	21676	Mm.24685	NM_009346	ENSMUSG00000055320	Tead1	2610024B07Rik|B230114H05Rik|Gtrgeo5|TEAD-1|TEF-1|Tcf13|mTEF-1	TEA domain family member 1	protein-coding
mm_104107.1	chr11	86711376	86711423	-	1	NA	exon (NM_001003908, exon 17 of 32)	exon (NM_001003908, exon 17 of 32)	27318	NM_001098810	217057	Mm.24868	NM_175004	ENSMUSG00000072582	Ptrh2	A230072I16Rik|Bit1|CGI-147	peptidyl-tRNA hydrolase 2	protein-coding
mm_162946.1	chr10	130592910	130592911	-	1	NA	Intergenic	MTC|LTR|ERVL-MaLR	-95531	NM_001103366	625131	Mm.469844	NM_001103366	ENSMUSG00000091511	Vmn2r87	EG625131	vomeronasal 2, receptor 87	protein-coding
mm_111440.1	chr12	95292719	95292725	-	1	NA	Intergenic	RMER19C|LTR|ERVK	-399504	NM_201518	399558	Mm.341948	NM_201518	ENSMUSG00000047414	Flrt2	-	fibronectin leucine rich transmembrane protein 2	protein-coding
mm_165141.1	chr2	15055036	15055049	-	1	NA	promoter-TSS (NM_001165941)	promoter-TSS (NM_001165941)	-170	NM_001165943	74455	Mm.478923	NM_028950	ENSMUSG00000026707	Nsun6	4933403D21Rik|4933414E04Rik|NOPD1	NOL1/NOP2/Sun domain family member 6	protein-coding
mm_168292.1	chr11	102455833	102455850	+	1	NA	intron (NM_010575, intron 28 of 29)	CpG	-8178	NM_199200	217219	Mm.259924	NM_199200	ENSMUSG00000034685	Fam171a2	-	family with sequence similarity 171, member A2	protein-coding
mm_127222.1	chr15	99393601	99393607	+	1	NA	intron (NM_001171035, intron 1 of 9)	intron (NM_001171035, intron 1 of 9)	385	NM_001171035	110213	Mm.16769	NM_026669	ENSMUSG00000023010	Tmbim6	5031406P05Rik|Bi1|Tegt	transmembrane BAX inhibitor motif containing 6	protein-coding
mm_139794.1	chr17	65954123	65954135	+	1	NA	Intergenic	Intergenic	-2942	NM_023053	65960	Mm.10153	NM_023053	ENSMUSG00000024098	Twsg1	1810013J15Rik|9030422N06Rik|AW552143|D17Ertd403e|Tsg|Twg	twisted gastrulation BMP signaling modulator 1	protein-coding
mm_81343.1	chr9	108559754	108559815	+	1	NA	promoter-TSS (NM_011830)	promoter-TSS (NM_011830)	-717	NM_011830	23918	Mm.6065	NM_011830	ENSMUSG00000062867	Impdh2	IMPD	inosine 5'-phosphate dehydrogenase 2	protein-coding
mm_95069.1	chr11	32554967	32554978	+	1	NA	intron (NM_009288, intron 1 of 18)	intron (NM_009288, intron 1 of 18)	21706	NM_009288	20868	Mm.8235	NM_009288	ENSMUSG00000020272	Stk10	Gek1|Lok|mKIAA4026	serine/threonine kinase 10	protein-coding
mm_163557.1	chr13	24327252	24327271	+	1	NA	promoter-TSS (NM_001111110)	promoter-TSS (NM_001111110)	-143	NM_001284519	12763	Mm.8396	NM_007717	ENSMUSG00000016756	Cmah	-	cytidine monophospho-N-acetylneuraminic acid hydroxylase	protein-coding
mm_107222.1	chr12	26470428	26470456	+	1	NA	intron (NM_020557, intron 1 of 4)	intron (NM_020557, intron 1 of 4)	1227	NM_020557	22169	Mm.271839	NM_020557	ENSMUSG00000020638	Cmpk2	1200004E04Rik|TDKI|Tyki	cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial	protein-coding
mm_12425.1	chr2	70563436	70563461	+	1	NA	promoter-TSS (NR_040496)	promoter-TSS (NR_040496)	-91	NR_040496	68986	Mm.437697	NR_040496	ENSMUSG00000087264	Gad1os	1500002O10Rik	glutamate decarboxylase 1, opposite strand	ncRNA
mm_90143.1	chr10	118112515	118112531	+	1	NA	Intergenic	Intergenic	-29264	NM_001162904	17245	Mm.101191	NM_010785	ENSMUSG00000020212	Mdm1	Arrd2|Mdm-1	transformed mouse 3T3 cell double minute 1	protein-coding
mm_77534.1	chr8	123028987	123028990	-	1	NA	intron (NM_001081379, intron 1 of 12)	intron (NM_001081379, intron 1 of 12)	13296	NR_037865	77087	Mm.31567	NM_001081379	ENSMUSG00000035569	Ankrd11	2410104C19Rik|3010027A04Rik|6330578C09Rik|9530048I21Rik|AA930108|Gm176|Yod	ankyrin repeat domain 11	protein-coding
mm_159663.1	chr4	152038372	152038372	-	1	NA	promoter-TSS (NM_028727)	promoter-TSS (NM_028727)	118	NM_031867	110326	Mm.29232	NM_031867	ENSMUSG00000028950	Tas1r1	Gpr70|T1r1|TR1	taste receptor, type 1, member 1	protein-coding
mm_108919.1	chr12	100779075	100779085	+	1	NA	promoter-TSS (NM_145448)	promoter-TSS (NM_145448)	-43	NM_145448	217830	Mm.218590	NM_145448	ENSMUSG00000021185	9030617O03Rik	-	RIKEN cDNA 9030617O03 gene	protein-coding
mm_162295.1	chr1	33738773	33738798	-	1	NA	intron (NM_001159729, intron 7 of 7)	intron (NM_001159729, intron 7 of 7)	18366	NM_001159729	19335	Mm.86744	NM_008999	ENSMUSG00000004768	Rab23	AW545388|opb|opb2	RAB23, member RAS oncogene family	protein-coding
mm_153591.1	chr19	43524757	43524761	-	1	NA	promoter-TSS (NM_010324)	promoter-TSS (NM_010324)	-154	NM_010324	14718	Mm.19039	NM_010324	ENSMUSG00000025190	Got1	AI789014|Got-1|cAspAT|cCAT	glutamic-oxaloacetic transaminase 1, soluble	protein-coding
mm_168967.1	chr12	81439175	81439175	+	1	NA	intron (NM_001309810, intron 3 of 4)	RLTR10C|LTR|ERVK	-17136	NM_009620	11498	Mm.408462	NM_009620	ENSMUSG00000072972	Adam4	AV274654|tMDCV	a disintegrin and metallopeptidase domain 4	protein-coding
mm_91144.1	chr10	19907632	19907640	-	1	NA	promoter-TSS (NM_008822)	promoter-TSS (NM_008822)	38	NM_008822	18634	Mm.338363	NM_008822	ENSMUSG00000020003	Pex7	MmPEX7	peroxisomal biogenesis factor 7	protein-coding
mm_64188.1	chr7	141460985	141461008	+	1	NA	promoter-TSS (NM_001025103)	promoter-TSS (NM_001025103)	-98	NM_001025103	213573	Mm.386851	NM_001025103	ENSMUSG00000048200	Cracr2b	6330520A15Rik|BC026645|Cracr2a|Efcab4|Efcab4a	calcium release activated channel regulator 2B	protein-coding
mm_23469.1	chr3	60479837	60479847	+	1	NA	intron (NM_001253713, intron 2 of 9)	intron (NM_001253713, intron 2 of 9)	7012	NM_001253713	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_28131.1	chr3	87112437	87112445	-	1	NA	intron (NM_001170985, intron 2 of 15)	intron (NM_001170985, intron 2 of 15)	62306	NM_001170985	170643	Mm.89552	NM_130867	ENSMUSG00000041734	Kirrel	6720469N11Rik|Kirrel1|Neph1	kin of IRRE like (Drosophila)	protein-coding
mm_80925.1	chr9	101991751	101991776	+	1	NA	intron (NM_173447, intron 9 of 15)	MT2A|LTR|ERVL	313212	NR_106163	102466241		NR_106163	ENSMUSG00000098521	Mir7243	Gm27363|mmu-mir-7243	microRNA 7243	ncRNA
mm_76465.1	chr8	85380735	85380745	-	1	NA	intron (NM_001297612, intron 1 of 12)	intron (NM_001297612, intron 1 of 12)	301	NM_001297612	213435	Mm.32804	NM_175441	ENSMUSG00000031698	Mylk3	D830007F02Rik|MLCK	myosin light chain kinase 3	protein-coding
mm_35365.1	chr4	32442009	32442010	-	1	NA	intron (NM_001109661, intron 1 of 4)	MLTR11A|LTR|ERVK	24574	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_172673.1	chr8	46229492	46229493	+	1	NA	Intergenic	Intergenic	-18483	NM_007450	11739	Mm.16228	NM_007450	ENSMUSG00000031633	Slc25a4	AU019225|Ant1	solute carrier family 25 (mitochondrial carrier, adenine nucleotide translocator), member 4	protein-coding
mm_35653.1	chr4	43534328	43534353	-	1	NA	intron (NM_011602, intron 50 of 56)	intron (NM_011602, intron 50 of 56)	-10786	NM_001277875	22004	Mm.646	NM_009416	ENSMUSG00000028464	Tpm2	Tpm-2|Trop-2	tropomyosin 2, beta	protein-coding
mm_30077.1	chr3	138002706	138002724	-	1	NA	Intergenic	Intergenic	-21166	NM_001310753	26377	Mm.254835	NM_011932	ENSMUSG00000028159	Dapp1	Bam32	dual adaptor for phosphotyrosine and 3-phosphoinositides 1	protein-coding
mm_23715.1	chr3	69005300	69005313	+	1	NA	promoter-TSS (NM_026641)	promoter-TSS (NM_026641)	334	NM_133786	70099	Mm.206841	NM_133786	ENSMUSG00000034349	Smc4	2500002A22Rik|C79747|SMC-4|Smc4l1	structural maintenance of chromosomes 4	protein-coding
mm_100860.1	chr11	5878208	5878243	-	1	NA	promoter-TSS (NM_008894)	promoter-TSS (NM_008894)	31	NM_008894	18972	Mm.35788	NM_008894	ENSMUSG00000020471	Pold2	50kDa|p50|po1D2	polymerase (DNA directed), delta 2, regulatory subunit	protein-coding
mm_12616.1	chr2	74691966	74691976	+	1	NA	promoter-TSS (NM_013554)	promoter-TSS (NM_013554)	80	NM_013554	15430	Mm.24420	NM_013554	ENSMUSG00000050368	Hoxd10	AI385591|AI874987|Hox-4.5|Hox-5.3	homeobox D10	protein-coding
mm_9790.1	chr1	181816593	181816594	-	1	NA	3' UTR (NM_133815, exon 14 of 14)	3' UTR (NM_133815, exon 14 of 14)	25808	NM_133815	98386	Mm.4538	NM_133815	ENSMUSG00000004880	Lbr	AI505894|ic	lamin B receptor	protein-coding
mm_159005.1	chr1	160351324	160351324	-	1	NA	exon (NM_001038621, exon 1 of 9)	exon (NM_001038621, exon 1 of 9)	247	NM_001038621	29809	Mm.25833	NM_013862	ENSMUSG00000026721	Rabgap1l	5830411O09Rik|8430421H08Rik|9630005B12Rik|AW049894|HHL|Hh1|mKIAA0471	RAB GTPase activating protein 1-like	protein-coding
mm_107665.1	chr12	52854726	52854735	+	1	NA	intron (NM_198111, intron 2 of 13)	intron (NM_198111, intron 2 of 13)	155347	NM_198111	238161	Mm.310822	NM_198111	ENSMUSG00000061603	Akap6	AI482140|Akapalpha|Akapbeta|PRKA	A kinase (PRKA) anchor protein 6	protein-coding
mm_68598.1	chr7	116202357	116202360	-	1	NA	intron (NM_001305185, intron 3 of 26)	intron (NM_001305185, intron 3 of 26)	-3797	NM_001305189	233765	Mm.3741	NM_172743	ENSMUSG00000045659	Plekha7	A430081P20Rik|AI414265	pleckstrin homology domain containing, family A member 7	protein-coding
mm_36377.1	chr4	76800676	76800681	-	1	NA	intron (NM_011211, intron 8 of 39)	intron (NM_011211, intron 8 of 39)	1411217	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding
mm_83889.1	chr9	55590091	55590092	-	1	NA	intron (NM_001081341, intron 28 of 32)	intron (NM_001081341, intron 28 of 32)	48942	NM_027397	104360	Mm.273996	NM_027397	ENSMUSG00000032318	Isl2	3110001N10Rik	insulin related protein 2 (islet 2)	protein-coding
mm_31704.1	chr4	62583502	62583564	+	1	NA	intron (NM_019492, intron 3 of 19)	CpG	23686	NM_019492	50780	Mm.286753	NM_019492	ENSMUSG00000059810	Rgs3	4930506N09Rik|C2PA-RGS3|C2pa|PDZ-RGS3|RGS3S	regulator of G-protein signaling 3	protein-coding
mm_117061.1	chr13	58610880	58610905	-	1	NA	promoter-TSS (NM_022317)	promoter-TSS (NM_022317)	-15	NM_022317	114304	Mm.18188	NM_022317	ENSMUSG00000021553	Slc28a3	Cnt3	solute carrier family 28 (sodium-coupled nucleoside transporter), member 3	protein-coding
mm_58984.1	chr7	19080657	19080666	+	1	NA	exon (NM_010058, exon 3 of 5)	exon (NM_010058, exon 3 of 5)	-3188	NR_126095	13400	Mm.6529	NM_032418	ENSMUSG00000030409	Dmpk	DM|DMK|Dm15|MDPK|MT-PK	dystrophia myotonica-protein kinase	protein-coding
mm_165919.1	chr4	59134599	59134600	-	1	NA	Intergenic	L1MEf|LINE|L1	-54951	NM_011673	22234	Mm.198803	NM_011673	ENSMUSG00000028381	Ugcg	AU043821|C80537|Epcs21|GlcT-1|Ugcgl	UDP-glucose ceramide glucosyltransferase	protein-coding
mm_44333.1	chr5	14723709	14723721	-	1	NA	intron (NM_001110796, intron 9 of 19)	intron (NM_001110796, intron 9 of 19)	191174	NM_198666	381714	Mm.368256	NM_198666	ENSMUSG00000033219	Gm9758	ENSMUSG00000033219	predicted gene 9758	protein-coding
mm_143525.1	chr17	73883949	73883964	-	1	NA	TTS (NM_011723)	TTS (NM_011723)	66240	NM_011723	22436	Mm.11223	NM_011723	ENSMUSG00000024066	Xdh	XO|Xor|Xox-1|Xox1	xanthine dehydrogenase	protein-coding
mm_116868.1	chr13	55018198	55018208	-	1	NA	intron (NM_001206392, intron 1 of 17)	intron (NM_001206392, intron 1 of 17)	2616	NM_001206390	212032	Mm.267479	NM_001033245	ENSMUSG00000025877	Hk3	HK III|HK-III	hexokinase 3	protein-coding
mm_116158.1	chr13	30551384	30551388	-	1	NA	Intergenic	Intergenic	-6070	NM_025710	66694	Mm.181933	NM_025710	ENSMUSG00000038462	Uqcrfs1	4430402G14Rik|AI875505	ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1	protein-coding
mm_81857.1	chr9	118703496	118703512	+	1	NA	intron (NM_133721, intron 15 of 27)	intron (NM_133721, intron 15 of 27)	-8188	NM_001113514	104099	Mm.335520	NM_133721	ENSMUSG00000039115	Itga9	(alpha)9|2610002H11Rik|6720458D17Rik|AI461869|D130073C02|D9Ertd428e	integrin alpha 9	protein-coding
mm_8065.1	chr1	135441355	135441376	-	1	NA	3' UTR (NM_173437, exon 29 of 29)	3' UTR (NM_173437, exon 29 of 29)	-10874	NM_153774	226432	Mm.271642	NM_153774	ENSMUSG00000041879	Ipo9	0710008K06Rik|AI845704|C78347|Imp9|Ranbp9|mKIAA1192	importin 9	protein-coding
mm_71008.1	chr8	31115093	31115103	+	1	NA	intron (NM_175136, intron 1 of 5)	intron (NM_175136, intron 1 of 5)	3252	NM_175136	68867	Mm.29532	NM_175136	ENSMUSG00000039328	Rnf122	1110063C11Rik	ring finger protein 122	protein-coding
mm_110114.1	chr12	26443735	26443745	-	1	NA	3' UTR (NM_021384, exon 6 of 6)	3' UTR (NM_021384, exon 6 of 6)	12712	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_25061.1	chr3	99141064	99141072	+	1	NA	promoter-TSS (NM_027462)	promoter-TSS (NM_027462)	-22	NM_027462	70560	Mm.316754	NM_027462	ENSMUSG00000004233	Wars2	5730427B17Rik|9430020O07Rik|AI413375|TrpRS	tryptophanyl tRNA synthetase 2 (mitochondrial)	protein-coding
mm_66083.1	chr7	30957061	30957089	-	1	NA	promoter-TSS (NM_011680)	promoter-TSS (NM_011680)	-272	NM_011680	22282	Mm.322453	NM_011680	ENSMUSG00000058239	Usf2	Usf-2|bHLHb12	upstream transcription factor 2	protein-coding
mm_169197.1	chr13	66203707	66203712	+	1	NA	Intergenic	Intergenic	90256	NM_001177832	628709	Mm.390595	NM_001177832	ENSMUSG00000095909	Gm10324	ENSMUSG00000071302	predicted gene 10324	protein-coding
mm_102045.1	chr11	52000357	52000388	-	1	NA	promoter-TSS (NM_009458)	promoter-TSS (NM_009458)	94	NM_009458	22210	Mm.384918	NM_009458	ENSMUSG00000020390	Ube2b	2610301N02Rik|E2-14k|HR6B|Rad6b|mHR6B	ubiquitin-conjugating enzyme E2B	protein-coding
mm_121700.1	chr14	14423221	14423231	-	1	NA	Intergenic	LTRIS2|LTR|ERV1	76731	NM_008369	16188	Mm.425857	NM_008369	ENSMUSG00000068758	Il3ra	CD123|CDw123|SUT-1	interleukin 3 receptor, alpha chain	protein-coding
mm_72160.1	chr8	72219021	72219036	+	1	NA	promoter-TSS (NM_026455)	promoter-TSS (NM_026455)	-702	NM_026455	67922	Mm.28327	NM_026455	ENSMUSG00000003039	Fam32a	2510049I19Rik|AW822030|OTAG-12|Otag12	family with sequence similarity 32, member A	protein-coding
mm_91620.1	chr10	41685986	41686002	-	1	NA	Intergenic	Intergenic	-79399	NM_001303469	75973	Mm.228517	NM_029493	ENSMUSG00000075225	Ccdc162	5033413D22Rik|Ccdc162p|Gm29096|Gm61|Gm6976	coiled-coil domain containing 162	protein-coding
mm_37096.1	chr4	116611343	116611371	-	1	NA	exon (NM_016777, exon 7 of 16)	exon (NM_016777, exon 7 of 16)	-13727	NR_029450	654318	Mm.255685	NR_029450	ENSMUSG00000085408	C530005A16Rik	D930044c15rik	RIKEN cDNA C530005A16 gene	ncRNA
mm_124492.1	chr14	121745801	121745804	-	1	NA	intron (NM_134074, intron 1 of 52)	L1MB8|LINE|L1	-6873	NM_001128307	105445	Mm.378591	NM_134074	ENSMUSG00000025558	Dock9	AA959601|AW538057|B230309H04Rik|D14Wsu89e|Zizimin1|mKIAA1058	dedicator of cytokinesis 9	protein-coding
mm_55923.1	chr6	83892847	83892870	-	1	NA	Intergenic	Intergenic	-21495	NM_001166371	18139	Mm.132392	NM_008717	ENSMUSG00000030016	Zfp638	AI323587|Np220|Zfml|Znf638|mNP220	zinc finger protein 638	protein-coding
mm_147790.1	chr18	61646668	61646673	-	1	NA	intron (NR_045402, intron 4 of 4)	B4A|SINE|B4	1224	NR_029557	387163		NR_029557	ENSMUSG00000065592	Mir145a	Mir145|Mirn145|mir-145a|mmu-mir-145|mmu-mir-145a	microRNA 145a	ncRNA
mm_55349.1	chr6	56797638	56797757	-	1	NA	5' UTR (NM_145958, exon 1 of 4)	5' UTR (NM_145958, exon 1 of 4)	116	NM_145958	210973	Mm.57295	NM_145958	ENSMUSG00000059486	Kbtbd2	BC022962|Bklhd1|mKIAA1489	kelch repeat and BTB (POZ) domain containing 2	protein-coding
mm_103581.1	chr11	78176620	78176660	-	1	NA	promoter-TSS (NM_080849)	promoter-TSS (NM_080849)	26	NM_080849	140859	Mm.23788	NM_080849	ENSMUSG00000017405	Nek8	4632401F23Rik|b2b1449Clo|jck	NIMA (never in mitosis gene a)-related expressed kinase 8	protein-coding
mm_88655.1	chr10	79995259	79995302	+	1	NA	3' UTR (NM_007725, exon 7 of 7)	3' UTR (NM_007725, exon 7 of 7)	-2328	NM_001347081	27403	Mm.103351	NM_013850	ENSMUSG00000035722	Abca7	ABCX|Abc51	ATP-binding cassette, sub-family A (ABC1), member 7	protein-coding
mm_164320.1	chr16	3907724	3907731	-	1	NA	intron (NM_028484, intron 1 of 2)	intron (NM_028484, intron 1 of 2)	962	NM_028484	73261	Mm.486226	NM_028484	ENSMUSG00000005983	1700037C18Rik	2810022L20Rik	RIKEN cDNA 1700037C18 gene	protein-coding
mm_110343.1	chr12	36156748	36156776	-	1	NA	promoter-TSS (NM_025840)	promoter-TSS (NM_025840)	63	NM_025840	66912	Mm.288669	NM_025840	ENSMUSG00000020547	Bzw2	1110001I24Rik|Bdm2|HSPC028	basic leucine zipper and W2 domains 2	protein-coding
mm_132494.1	chr16	36936047	36936085	+	1	NA	intron (NM_008225, intron 1 of 13)	intron (NM_008225, intron 1 of 13)	1083	NM_008225	15163	Mm.4091	NM_008225	ENSMUSG00000022831	Hcls1	AW213261|HS1	hematopoietic cell specific Lyn substrate 1	protein-coding
mm_7129.1	chr1	91024072	91024088	-	1	NA	intron (NM_001111312, intron 1 of 12)	intron (NM_001111312, intron 1 of 12)	25353	NM_001111312	16978	Mm.45039	NM_008515	ENSMUSG00000026305	Lrrfip1	AU024550|Fliiap1	leucine rich repeat (in FLII) interacting protein 1	protein-coding
mm_56782.1	chr6	116634943	116634960	-	1	NA	3' UTR (NM_178045, exon 11 of 11)	3' UTR (NM_178045, exon 11 of 11)	-5952	NM_026057	67255	Mm.18810	NM_026057	ENSMUSG00000059878	Zfp422	2900028O21Rik|AU041373|KOX15|Krox-25-2|Krox-26|Krox25|Krox26|Znf22	zinc finger protein 422	protein-coding
mm_135133.1	chr16	35844326	35844338	-	1	NA	exon (NM_001039530, exon 12 of 17)	exon (NM_001039530, exon 12 of 17)	27050	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_116626.1	chr13	48935129	48935138	-	1	NA	intron (NM_001033268, intron 3 of 17)	intron (NM_001033268, intron 3 of 17)	32695	NM_001033268	218236	Mm.426571	NM_001033268	ENSMUSG00000038014	Fam120a	C9orf10|Ossa	family with sequence similarity 120, member A	protein-coding
mm_113225.1	chr13	27064345	27064356	+	1	NA	exon (NM_011164, exon 4 of 5)	exon (NM_011164, exon 4 of 5)	6780	NM_011164	19109	Mm.1270	NM_011164	ENSMUSG00000021342	Prl	AV290867|Gha1|Prl1a1	prolactin	protein-coding
mm_24942.1	chr3	96596594	96596609	+	1	NA	promoter-TSS (NM_001024851)	promoter-TSS (NM_001024851)	-35	NM_001024851	545554	Mm.267664	NM_001024851	ENSMUSG00000049097	Ankrd34a	AW060394|Ankrd34	ankyrin repeat domain 34A	protein-coding
mm_26557.1	chr3	146499706	146499764	+	1	NA	promoter-TSS (NM_001316756)	promoter-TSS (NM_001316756)	18	NM_001316756	70951	Mm.383235	NM_027617	ENSMUSG00000028188	Spata1	4921536I21Rik|AV266943|SP-2	spermatogenesis associated 1	protein-coding
mm_129797.1	chr15	82886704	82886707	-	1	NA	intron (NM_001114140, intron 1 of 5)	intron (NM_001114140, intron 1 of 5)	11756	NR_027799	21378	Mm.417272	NR_027799		Tbrg3	TB-11	transforming growth factor beta regulated gene 3	ncRNA
mm_79566.1	chr9	58134041	58134070	+	1	NA	promoter-TSS (NM_001162479)	promoter-TSS (NM_001162479)	-20	NM_001162476	20897	Mm.10801	NM_009291	ENSMUSG00000032327	Stra6	AI891933	stimulated by retinoic acid gene 6	protein-coding
mm_71179.1	chr8	40823027	40823065	+	1	NA	promoter-TSS (NM_001025380)	promoter-TSS (NM_001025380)	37	NM_001025380	546055	Mm.334503	NM_001025380	ENSMUSG00000054033	Adam39	1700056P18Rik	a disintegrin and metallopeptidase domain 39	protein-coding
mm_2311.1	chr1	91653411	91653414	+	1	NA	Intergenic	Intergenic	112332	NM_023046	65247	Mm.234152	NM_023046	ENSMUSG00000026311	Asb1	1700029O08Rik|1700054C17Rik|AI426616|AI851378|mKIAA1146	ankyrin repeat and SOCS box-containing 1	protein-coding
mm_18104.1	chr2	44988768	44988794	-	1	NA	exon (NM_015753, exon 10 of 10)	exon (NM_015753, exon 10 of 10)	34396	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_164628.1	chr17	31681376	31681391	+	1	NA	3' UTR (NM_001278570, exon 3 of 3)	3' UTR (NM_001278570, exon 3 of 3)	3452	NM_001278570	12954	Mm.1228	NM_013501	ENSMUSG00000024041	Cryaa	Acry-1|Crya-1|Crya1|DAcry-1|lop18	crystallin, alpha A	protein-coding
mm_165347.1	chr2	119174326	119174342	+	1	NA	promoter-TSS (NM_001039223)	promoter-TSS (NM_001039223)	-175	NM_001039223	623781	Mm.389344	NM_001039223	ENSMUSG00000055926	Gm14137	OTTMUSG00000015762	predicted gene 14137	protein-coding
mm_114090.1	chr13	54621802	54621841	+	1	NA	promoter-TSS (NM_178397)	promoter-TSS (NM_178397)	37	NM_178397	76577	Mm.194459	NM_178397	ENSMUSG00000025873	Faf2	2210404D11Rik|AI462440|Ubxd8|mKIAA0887	Fas associated factor family member 2	protein-coding
mm_23089.1	chr3	37044239	37044244	+	1	NA	intron (NM_172679, intron 80 of 85)	intron (NM_172679, intron 80 of 85)	-19415	NM_009350	21744	Mm.8122	NM_009350	ENSMUSG00000027719	Adad1	Tenr	adenosine deaminase domain containing 1 (testis specific)	protein-coding
mm_90169.1	chr10	119481516	119481518	+	1	NA	intron (NM_133442, intron 1 of 21)	intron (NM_133442, intron 1 of 21)	27483	NM_001277293	74053	Mm.196692	NM_028736	ENSMUSG00000034813	Grip1	4931400F03Rik|GRIP|eb	glutamate receptor interacting protein 1	protein-coding
mm_122110.1	chr14	30938069	30938090	-	1	NA	exon (NM_008406, exon 7 of 22)	exon (NM_008406, exon 7 of 22)	5210	NM_008406	16424	Mm.3227	NM_008406	ENSMUSG00000006529	Itih1	ITI-HC1|Intin1|Itih-1	inter-alpha trypsin inhibitor, heavy chain 1	protein-coding
mm_74247.1	chr8	124831139	124831152	+	1	NA	3' UTR (NM_198632, exon 10 of 10)	3' UTR (NM_198632, exon 10 of 10)	31884	NM_025615	66523	Mm.436864	NM_025615	ENSMUSG00000031984	2810004N23Rik	3110004G14Rik|Ayu21-55|Gt(pU21)55Imeg|GtAyu21-55	RIKEN cDNA 2810004N23 gene	protein-coding
mm_150221.1	chr19	33961185	33961187	+	1	NA	promoter-TSS (NM_026334)	promoter-TSS (NM_026334)	-62	NM_026334	67717	Mm.329816	NM_026334	ENSMUSG00000024768	Lipf	2310051B21Rik|AV082900	lipase, gastric	protein-coding
mm_103245.1	chr11	70789439	70789458	-	1	NA	Intergenic	Intergenic	23113	NM_001045526	327957	Mm.164325	NM_001045526	ENSMUSG00000057135	Scimp	A430084P05Rik	SLP adaptor and CSK interacting membrane protein	protein-coding
mm_38384.1	chr4	138770909	138770921	-	1	NA	Intergenic	Intergenic	-4820	NM_001347230	18782	Mm.71913	NM_011109	ENSMUSG00000041202	Pla2g2d	Splash|mGIID	phospholipase A2, group IID	protein-coding
mm_88579.1	chr10	79687589	79687595	+	1	NA	intron (NM_177613, intron 4 of 4)	intron (NM_177613, intron 4 of 4)	-1428	NM_001302485	16904	Mm.378960	NM_008504	ENSMUSG00000054206	Gzmm	Lmet1|MMET-1	granzyme M (lymphocyte met-ase 1)	protein-coding
mm_62929.1	chr7	118633730	118633749	+	1	NA	promoter-TSS (NM_028930)	promoter-TSS (NM_028930)	3	NM_028930	74424	Mm.11068	NM_028930	ENSMUSG00000030650	Tmc5	4932443L08Rik|AU016085	transmembrane channel-like gene family 5	protein-coding
mm_85980.1	chr9	112166622	112166655	-	1	NA	intron (NM_001177623, intron 9 of 9)	intron (NM_001177623, intron 9 of 9)	19311	NM_001177618	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_114211.1	chr13	56159273	56159280	+	1	NA	Intergenic	Intergenic	19609	NM_145976	212937	Mm.116697	NM_145976	ENSMUSG00000049625	Tifab	-	TRAF-interacting protein with forkhead-associated domain, family member B	protein-coding
mm_110983.1	chr12	77065754	77065782	-	1	NA	Intergenic	RLTR14_RN|LTR|ERV1	-103520	NM_001146176	17187	Mm.268548	NM_008558	ENSMUSG00000059436	Max	AA960152|AI875693|bHLHd4|bHLHd5|bHLHd6|bHLHd7|bHLHd8	Max protein	protein-coding
mm_44671.1	chr5	29609906	29609911	-	1	NA	intron (NM_133907, intron 10 of 22)	intron (NM_133907, intron 10 of 22)	40666	NM_133907	100763	Mm.137746	NM_133907	ENSMUSG00000039000	Ube3c	AI853514|mKIAA0010	ubiquitin protein ligase E3C	protein-coding
mm_10911.1	chr2	25372374	25372396	+	1	NA	5' UTR (NM_001290407, exon 1 of 6)	5' UTR (NM_001290407, exon 1 of 6)	350	NM_001081085	72080	Mm.250293	NM_001081085	ENSMUSG00000026955	Sapcd2	2010317E24Rik|6030458L21Rik|AL033337|ang	suppressor APC domain containing 2	protein-coding
mm_119403.1	chr14	44102656	44102665	+	1	NA	promoter-TSS (NM_017388)	promoter-TSS (NM_017388)	6	NM_007895	13587	Mm.327386	NM_007895	ENSMUSG00000072596	Ear2	EAR-13|EAR-2|ECP|ECP 2|Raf3|Rnase2	eosinophil-associated, ribonuclease A family, member 2	protein-coding
mm_60242.1	chr7	43727028	43727041	+	1	NA	TTS (NM_001039042)	TTS (NM_001039042)	14467	NM_001039042	626834	Mm.389891	NM_001039042	ENSMUSG00000054046	Klk13	Egfbp-2|mGk-13	kallikrein related-peptidase 13	protein-coding
mm_18873.1	chr2	76215364	76215405	-	1	NA	exon (NM_001081033, exon 3 of 20)	exon (NM_001081033, exon 3 of 20)	123269	NM_001081033	241489	Mm.246613	NM_001081033	ENSMUSG00000075270	Pde11a	6330414F14Rik|A630086N24Rik|Gm350|PDE11A1	phosphodiesterase 11A	protein-coding
mm_123664.1	chr14	69244563	69244598	-	1	NA	3' UTR (NM_026331, exon 4 of 4)	3' UTR (NM_026331, exon 4 of 4)	40523	NM_026331	67712	Mm.293635	NM_026331	ENSMUSG00000034248	Slc25a37	1700020E22Rik|4930513O14Rik|4930526G11Rik|AI848481|C330015G08Rik|Mfrn|Mfrn1|Mscp|frascati|mitoferrin	solute carrier family 25, member 37	protein-coding
mm_90784.1	chr10	6982943	6982965	-	1	NA	intron (NM_001039652, intron 4 of 5)	intron (NM_001039652, intron 4 of 5)	-2489	NM_001170801	320495	Mm.331674	NM_001033391	ENSMUSG00000064065	Ipcef1	A130090K04Rik	interaction protein for cytohesin exchange factors 1	protein-coding
mm_62119.1	chr7	96672679	96672681	+	1	NA	intron (NM_001310760, intron 6 of 32)	intron (NM_001310760, intron 6 of 32)	128869	NR_045874	791381	Mm.402112	NR_045874	ENSMUSG00000053049	Gm15413	ENSMUSG00000053049|OTTMUSG00000021246	predicted gene 15413	ncRNA
mm_131467.1	chr16	17043962	17043982	+	1	NA	3' UTR (NM_011949, exon 9 of 9)	3' UTR (NM_011949, exon 9 of 9)	-26167	NM_023249	106369	Mm.237941	NM_023249	ENSMUSG00000022773	Ypel1	0610009L05Rik|1700016N17Rik|1700019O22Rik|4921520K19Rik|4930511F14Rik|AV118478|DGL-1|Dgl1|Ppil2|mdgl-1	yippee-like 1 (Drosophila)	protein-coding
mm_114110.1	chr13	54913227	54913227	+	1	NA	Intergenic	Intergenic	-36184	NM_001311128	107448	Mm.23573	NM_153131	ENSMUSG00000025876	Unc5a	Unc5h1|mKIAA1976	unc-5 netrin receptor A	protein-coding
mm_69251.1	chr7	127842466	127842488	-	1	NA	exon (NM_009294, exon 3 of 11)	exon (NM_009294, exon 3 of 11)	669	NM_009294	20909	Mm.24867	NM_009294	ENSMUSG00000030805	Stx4a	Stx4|Syn-4|Syn4	syntaxin 4A (placental)	protein-coding
mm_95195.1	chr11	43155649	43155704	+	1	NA	intron (NM_176999, intron 3 of 22)	intron (NM_176999, intron 3 of 22)	5799	NM_176999	319767	Mm.252339	NM_176999	ENSMUSG00000055415	Atp10b	5930426O13Rik|9030605H24Rik	ATPase, class V, type 10B	protein-coding
mm_170398.1	chr1	86359213	86359226	-	1	NA	promoter-TSS (NR_015507)	promoter-TSS (NR_015507)	236	NM_010880	17975	Mm.154378	NM_010880	ENSMUSG00000026234	Ncl	B530004O11Rik|C23|D0Nds28|D1Nds28|Nucl	nucleolin	protein-coding
mm_163102.1	chr11	69735415	69735432	-	1	NA	exon (NM_001291068, exon 29 of 29)	exon (NM_001291068, exon 29 of 29)	23210	NM_001291068	20020	Mm.16533	NM_009089	ENSMUSG00000005198	Polr2a	220kDa|Rpb1|Rpo2-1	polymerase (RNA) II (DNA directed) polypeptide A	protein-coding
mm_81368.1	chr9	108808341	108808351	+	1	NA	promoter-TSS (NM_030729)	promoter-TSS (NM_030729)	-34	NM_030729	80987	Mm.192416	NM_030729	ENSMUSG00000032598	Nckipsd	AF3P21|DIP1|ORF1|SPIN90|WASLBP|WISH|Wasbp	NCK interacting protein with SH3 domain	protein-coding
mm_45265.1	chr5	64389793	64389794	-	1	NA	Intergenic	Intergenic	78149	NR_040681	69999	Mm.261413	NR_040681	ENSMUSG00000100911	1700027F09Rik	-	RIKEN cDNA 1700027F09 gene	ncRNA
mm_50107.1	chr6	41533672	41533682	+	1	NA	Intergenic	Intergenic	11901	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_61167.1	chr7	59229423	59229442	+	1	NA	intron (NM_173010, intron 1 of 8)	CpG	680	NM_011668	22215	Mm.9002	NM_011668	ENSMUSG00000025326	Ube3a	4732496B02|5830462N02Rik|A130086L21Rik|Hpve6a|mKIAA4216	ubiquitin protein ligase E3A	protein-coding
mm_66785.1	chr7	47008398	47008421	-	1	NA	promoter-TSS (NM_175318)	promoter-TSS (NM_175318)	5	NM_175318	101685	Mm.155687	NM_175318	ENSMUSG00000049516	Spty2d1	5830435K17Rik|AI852426|P16H6	SPT2, Suppressor of Ty, domain containing 1 (S. cerevisiae)	protein-coding
mm_16535.1	chr2	181579538	181579553	+	1	NA	promoter-TSS (NR_027290)	promoter-TSS (NR_027290)	13	NR_027290	100271841	Mm.438007	NR_027289	ENSMUSG00000010492	Uckl1os	Gm16119|OTTMUSG00000030649	uridine-cytidine kinase 1-like 1, opposite strand	ncRNA
mm_45913.1	chr5	89435611	89435648	-	1	NA	exon (NM_008096, exon 9 of 13)	exon (NM_008096, exon 9 of 13)	22269	NM_008096	14473	Mm.196595	NM_008096	ENSMUSG00000035540	Gc	DBP|VDB	group specific component	protein-coding
mm_11081.1	chr2	27714440	27714463	+	1	NA	intron (NM_001290482, intron 1 of 9)	intron (NM_001290482, intron 1 of 9)	3868	NM_001290482	20181	Mm.24624	NM_011305	ENSMUSG00000015846	Rxra	9530071D11Rik|Nr2b1|RXRalpha1	retinoid X receptor alpha	protein-coding
mm_72287.1	chr8	75126237	75126277	+	1	NA	exon (NM_008566, exon 16 of 17)	exon (NM_008566, exon 16 of 17)	16748	NM_008566	17218	Mm.5048	NM_008566	ENSMUSG00000005410	Mcm5	AA617332|AI324988|AL033333|Cdc46|Mcmd5|P1-CDC46	minichromosome maintenance complex component 5	protein-coding
mm_32329.1	chr4	104344076	104344111	+	1	NA	Intergenic	Intergenic	-23445	NR_104385	13131	Mm.289682	NM_010014	ENSMUSG00000028519	Dab1	AI956902|C630028C02Rik|scm|scr|scrambler|yot	disabled 1	protein-coding
mm_36639.1	chr4	93335827	93335860	-	1	NA	promoter-TSS (NM_026954)	promoter-TSS (NM_026954)	-332	NM_026954	69136	Mm.171558	NM_026954	ENSMUSG00000054000	Tusc1	2200001D17Rik|TSG-9	tumor suppressor candidate 1	protein-coding
mm_75829.1	chr8	70506347	70506376	-	1	NA	intron (NM_025577, intron 2 of 4)	intron (NM_025577, intron 2 of 4)	378	NM_025577	66462	Mm.28242	NM_025577	ENSMUSG00000058833	2810428I15Rik	-	RIKEN cDNA 2810428I15 gene	protein-coding
mm_21111.1	chr2	153444418	153444440	-	1	NA	promoter-TSS (NM_001001986)	promoter-TSS (NM_001001986)	50	NM_001001986	329540	Mm.50600	NM_001001986	ENSMUSG00000061411	Nol4l	4931410H15|8430427H17Rik|AI429157|Gm1636	nucleolar protein 4-like	protein-coding
mm_68273.1	chr7	105596363	105596367	-	1	NA	exon (NM_017371, exon 5 of 10)	exon (NM_017371, exon 5 of 10)	3751	NM_017371	15458	Mm.3485	NM_017371	ENSMUSG00000030895	Hpx	Hpxn|hx	hemopexin	protein-coding
mm_51851.1	chr6	90384494	90384533	+	1	NA	3' UTR (NM_030260, exon 6 of 6)	3' UTR (NM_030260, exon 6 of 6)	15019	NM_030260	80292	Mm.100116	NM_030260	ENSMUSG00000034430	Zxdc	A930012H20|B930086F11Rik|BC003332	ZXD family zinc finger C	protein-coding
mm_29438.1	chr3	109812233	109812234	-	1	NA	intron (NM_001163349, intron 5 of 5)	intron (NM_001163349, intron 5 of 5)	238226	NM_146139	57257	Mm.282257	NM_020505	ENSMUSG00000033721	Vav3	A530094I06Rik|AA986410|Idd18.1	vav 3 oncogene	protein-coding
mm_154432.1	chrM	733	741	-	1	NA	NA	Intergenic	NA	NA								
mm_101737.1	chr11	43374394	43374399	-	1	NA	promoter-TSS (NR_029558)	promoter-TSS (NR_029558)	65	NR_029558	387164		NR_029558	ENSMUSG00000065601	Mir146	Mirn146|miR-146a|mmu-mir-146	microRNA 146	ncRNA
mm_158646.1	chrX	155340748	155340759	-	1	NA	Intergenic	Intergenic	-2293	NM_001313711	53381	Mm.247542	NM_016764	ENSMUSG00000025289	Prdx4	AOE372|Prx-iv|Prx4|TRANK	peroxiredoxin 4	protein-coding
mm_127343.1	chr15	100601978	100601981	+	1	NA	Intergenic	RLTR13D3A1|LTR|ERVK	-1995	NM_001304965	19009	Mm.28825	NM_010127	ENSMUSG00000009739	Pou6f1	2310038G18Rik|C79593|Emb|cns-1	POU domain, class 6, transcription factor 1	protein-coding
mm_172035.1	chr6	125163405	125163421	-	1	NA	exon (NM_008084, exon 3 of 7)	exon (NM_008084, exon 3 of 7)	2360	NM_008084	14433	Mm.304088	NM_008084	ENSMUSG00000057666	Gapdh	Gapd	glyceraldehyde-3-phosphate dehydrogenase	protein-coding
mm_44332.1	chr5	14723700	14723704	-	1	NA	intron (NM_001110796, intron 9 of 19)	intron (NM_001110796, intron 9 of 19)	191187	NM_198666	381714	Mm.368256	NM_198666	ENSMUSG00000033219	Gm9758	ENSMUSG00000033219	predicted gene 9758	protein-coding
mm_66686.1	chr7	45824751	45824761	-	1	NA	promoter-TSS (NM_145963)	promoter-TSS (NM_145963)	-9	NM_145963	211480	Mm.68170	NM_145963	ENSMUSG00000058743	Kcnj14	A930026G01Rik|IRK4|Kir2.4	potassium inwardly-rectifying channel, subfamily J, member 14	protein-coding
mm_149556.1	chr19	12633357	12633369	+	1	NA	promoter-TSS (NM_145935)	promoter-TSS (NM_145935)	55	NM_145935	107146	Mm.39974	NM_145935	ENSMUSG00000063683	Glyat	A330009E03Rik|ACGNAT|AI195249|AI315345|CAT|GAT	glycine-N-acyltransferase	protein-coding
mm_120997.1	chr14	79426618	79426653	+	1	NA	5' UTR (NM_001024135, exon 1 of 1)	5' UTR (NM_001024135, exon 1 of 1)	124	NM_001024135	211255	Mm.284526	NM_001024135	ENSMUSG00000043881	Kbtbd7	1110008P08Rik|AU045792|Gm295	kelch repeat and BTB (POZ) domain containing 7	protein-coding
mm_169134.1	chr13	59468599	59468607	-	1	NA	intron (NM_023328, intron 22 of 25)	intron (NM_023328, intron 22 of 25)	75848	NM_001284221	67269	Mm.153008	NM_023328	ENSMUSG00000021557	Agtpbp1	1700020N17Rik|2310001G17Rik|2900054O13Rik|4930445M19Rik|5730402G09Rik|CCP1|Nna1|nmf243|pcd	ATP/GTP binding protein 1	protein-coding
mm_169212.1	chr13	66588924	66588943	-	1	NA	Intergenic	Intergenic	-147815	NM_001290196	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
mm_115237.1	chr13	109926833	109926881	+	1	NA	intron (NM_011056, intron 8 of 16)	intron (NM_011056, intron 8 of 16)	23048	NR_035442	100316683		NR_035442	ENSMUSG00000084651	Mir1904	Mirn1904|mmu-mir-1904	microRNA 1904	ncRNA
mm_120860.1	chr14	75229344	75229354	+	1	NA	3' UTR (NM_001247984, exon 16 of 16)	3' UTR (NM_001247984, exon 16 of 16)	-12938	NM_019775	56373	Mm.24242	NM_019775	ENSMUSG00000021999	Cpb2	1110032P04Rik|4930405E17Rik|AI255929|CPR|Cpu|TAFI	carboxypeptidase B2 (plasma)	protein-coding
mm_5783.1	chr1	51624402	51624410	-	1	NA	Intergenic	Intergenic	-146007	NM_001310549	109019	Mm.196290	NM_028696	ENSMUSG00000026107	Nabp1	4930434H03Rik|4930442A21Rik|4930488J04Rik|4933440J18Rik|5830411E10Rik|AI852561|Nbp1|Obfc2a|Ssb2	nucleic acid binding protein 1	protein-coding
mm_92265.1	chr10	71143627	71143630	-	1	NA	intron (NM_031397, intron 1 of 20)	L1M3|LINE|L1	16062	NM_031397	83675	Mm.286834	NM_031397	ENSMUSG00000014329	Bicc1	Bic-C|bpk|jcpk	BicC family RNA binding protein 1	protein-coding
mm_31063.1	chr4	41316800	41316807	+	1	NA	Intergenic	Intergenic	-1902	NM_026893	68970	Mm.28891	NM_026893	ENSMUSG00000028436	Dcaf12	1500001L20Rik|5830424K06Rik|AA420338|AI851081|Wdr40a	DDB1 and CUL4 associated factor 12	protein-coding
mm_108706.1	chr12	87021367	87021372	+	1	NA	Intergenic	Intergenic	-5195	NM_172583	217733	Mm.110032	NM_172583	ENSMUSG00000034145	Tmem63c	4932420N09|9330187M14Rik	transmembrane protein 63c	protein-coding
mm_141805.1	chr17	34549306	34549318	-	1	NA	Intergenic	Intergenic	-14983	NM_010929	18132	Mm.173813	NM_010929	ENSMUSG00000015468	Notch4	Int-3|Int3|N4	notch 4	protein-coding
mm_102233.1	chr11	54952423	54952428	-	1	NA	intron (NM_001271455, intron 1 of 17)	B1_Mur3|SINE|Alu	10515	NM_021327	57783	Mm.259671	NM_021327	ENSMUSG00000020400	Tnip1	ABIN|ABIN-1|ABIN1|AU018810|Naf1|Nef|VAN	TNFAIP3 interacting protein 1	protein-coding
mm_5660.1	chr1	42667639	42667673	-	1	NA	intron (NR_027826, intron 1 of 3)	intron (NR_027826, intron 1 of 3)	27169	NR_027826	66297	Mm.45203	NM_183252	ENSMUSG00000060424	Pantr1	2610017I09Rik|Pou3f3os|linc-Brn1a	POU domain, class 3, transcription factor 3 adjacent noncoding transcript 1	ncRNA
mm_64842.1	chr7	13009992	13010031	-	1	NA	promoter-TSS (NM_001024699)	promoter-TSS (NM_001024699)	-211	NM_001024699	232879	Mm.279272	NM_001024699	ENSMUSG00000049600	Zbtb45	BB161562|Gm157|Zfp499	zinc finger and BTB domain containing 45	protein-coding
mm_28193.1	chr3	88142175	88142194	-	1	NA	promoter-TSS (NM_001310593)	promoter-TSS (NM_001310593)	-188	NM_001310587	17261	Mm.28184	NM_133665	ENSMUSG00000001419	Mef2d	C80750	myocyte enhancer factor 2D	protein-coding
mm_5152.1	chr1	9942538	9942550	-	1	NA	promoter-TSS (NR_004410)	promoter-TSS (NR_004410)	-1	NR_004410	266793		NR_004410	ENSMUSG00000093178	Snord87	MBII-276|Rnu87|U87	small nucleolar RNA, C/D box 87	snoRNA
mm_46372.1	chr5	103655710	103655743	-	1	NA	promoter-TSS (NM_001163550)	promoter-TSS (NM_001163550)	-2	NM_028824	74218	Mm.159141	NM_028824	ENSMUSG00000029320	1700016H13Rik	-	RIKEN cDNA 1700016H13 gene	protein-coding
mm_149969.1	chr19	29047586	29047594	+	1	NA	non-coding (NR_028360, exon 1 of 1)	non-coding (NR_028360, exon 1 of 1)	107	NR_028360	67329	Mm.394933	NR_028360		1700018L02Rik	-	RIKEN cDNA 1700018L02 gene	ncRNA
mm_171037.1	chr2	91705849	91705860	-	1	NA	intron (NM_145528, intron 1 of 15)	intron (NM_145528, intron 1 of 15)	4738	NM_145528	51897	Mm.28492	NM_145528	ENSMUSG00000027244	Atg13	1110053A20Rik|D2Ertd391e|Harbi1	autophagy related 13	protein-coding
mm_39723.1	chr5	28316845	28316920	+	1	NA	promoter-TSS (NM_028234)	promoter-TSS (NM_028234)	-307	NM_028234	381626	Mm.304075	NM_028234	ENSMUSG00000048271	Rbm33	3200001K10Rik|6430512A10Rik|AA386890|Prr8	RNA binding motif protein 33	protein-coding
mm_16186.1	chr2	172977654	172977676	+	1	NA	Intergenic	Intergenic	-2177	NM_012046	26972	Mm.23495	NM_012046	ENSMUSG00000005883	Spo11	AI449549|Spo11a|Spo11b	SPO11 meiotic protein covalently bound to DSB	protein-coding
mm_89428.1	chr10	91082092	91082103	+	1	NA	promoter-TSS (NM_026166)	promoter-TSS (NM_026166)	646	NM_001042558	11783	Mm.220289	NM_009684	ENSMUSG00000019979	Apaf1	6230400I06Rik|Apaf-1|Apaf1l|fog|mKIAA0413	apoptotic peptidase activating factor 1	protein-coding
mm_140834.1	chr17	23669947	23669967	-	1	NA	intron (NM_001008425, intron 7 of 12)	intron (NM_001008425, intron 7 of 12)	-3651	NM_181821	353502	Mm.359030	NM_181821	ENSMUSG00000023904	Hcfc1r1	HPIP	host cell factor C1 regulator 1 (XPO1-dependent)	protein-coding
mm_111048.1	chr12	79891126	79891142	-	1	NA	Intergenic	Intergenic	33599	NR_131075	77290	Mm.395042	NR_131073		9430078K24Rik	-	RIKEN cDNA 9430078K24 gene	ncRNA
mm_158684.1	chrX	160338633	160338636	-	1	NA	Intergenic	Intergenic	-52056	NM_001079847	237175	Mm.213016	NM_178712	ENSMUSG00000031298	Adgrg2	AW212196|B830041D06Rik|Gpr64|Me6	adhesion G protein-coupled receptor G2	protein-coding
mm_106731.1	chr12	3891754	3891801	+	1	NA	promoter-TSS (NM_153743)	promoter-TSS (NM_153743)	33	NM_153743	13435	Mm.5001	NM_007872	ENSMUSG00000020661	Dnmt3a	MmuIIIA	DNA methyltransferase 3A	protein-coding
mm_170765.1	chr2	161017656	161017673	-	1	NA	intron (NR_126509, intron 13 of 35)	B2_Mm2|SINE|B2	91422	NM_173368	71389	Mm.122738	NM_173368	ENSMUSG00000057133	Chd6	5430439G14Rik|6330406J24Rik|CHD-6	chromodomain helicase DNA binding protein 6	protein-coding
mm_63766.1	chr7	131223304	131223313	+	1	NA	intron (NM_175166, intron 8 of 22)	intron (NM_175166, intron 8 of 22)	48906	NM_175166	71395	Mm.118845	NM_175166	ENSMUSG00000006204	5430419D17Rik	-	RIKEN cDNA 5430419D17 gene	protein-coding
mm_12929.1	chr2	85040923	85040959	+	1	NA	exon (NM_001136081, exon 7 of 17)	exon (NM_001136081, exon 7 of 17)	3490	NM_001136081	20833	Mm.219793	NM_182990	ENSMUSG00000027067	Ssrp1	C81323|Hmg1-rs1|Hmgi-rs3|Hmgox|T160	structure specific recognition protein 1	protein-coding
mm_3769.1	chr1	156366038	156366044	+	1	NA	intron (NM_001198597, intron 10 of 10)	intron (NM_001198597, intron 10 of 10)	33949	NM_001198597	77352	Mm.428709	NM_001033180	ENSMUSG00000026601	Axdnd1	9430070O13Rik|Gm979	axonemal dynein light chain domain containing 1	protein-coding
mm_171254.1	chr3	81616638	81616642	+	1	NA	Intergenic	L1Md_T|LINE|L1	-185385	NR_138586	320566	Mm.208417	NR_138586	ENSMUSG00000103695	A830029E22Rik	-	RIKEN cDNA A830029E22 gene	ncRNA
mm_170895.1	chr2	29065428	29065428	+	1	NA	exon (NM_009442, exon 2 of 12)	exon (NM_009442, exon 2 of 12)	5165	NM_009442	22130	Mm.252195	NM_009442	ENSMUSG00000026803	Ttf1	AV245725|TTF-1|TTF-I	transcription termination factor, RNA polymerase I	protein-coding
mm_163842.1	chr14	19418004	19418022	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	184574	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_118089.1	chr13	103773925	103773926	-	1	NA	Intergenic	CpG	-9343	NM_172592	218543	Mm.458176	NM_172592	ENSMUSG00000032621	Srek1	8430401B01|AI450757|AI462342|SRrp508|SRrp86|Sfrs12|Srsf12	splicing regulatory glutamine/lysine-rich protein 1	protein-coding
mm_40994.1	chr5	77310479	77310545	+	1	NA	promoter-TSS (NM_019836)	promoter-TSS (NM_019836)	28	NM_153798	231329	Mm.273217	NM_153798	ENSMUSG00000029250	Polr2b	Pol2rb|Rpb140|Rpb2	polymerase (RNA) II (DNA directed) polypeptide B	protein-coding
mm_3185.1	chr1	135767810	135767830	+	1	NA	intron (NM_013750, intron 1 of 1)	intron (NM_013750, intron 1 of 1)	1735	NM_013750	27280	Mm.34346	NM_013750	ENSMUSG00000041801	Phlda3	Tih1	pleckstrin homology like domain, family A, member 3	protein-coding
mm_155620.1	chrX	83583004	83583015	+	1	NA	intron (NM_007868, intron 7 of 78)	B3A|SINE|B2	-95085	NM_021898	100502723	Mm.383210	NM_021898	ENSMUSG00000035522	Tsga8	Halap-X|Halapx	testis specific gene A8	protein-coding
mm_93915.1	chr10	127067518	127067538	-	1	NA	TTS (NM_009870)	TTS (NM_009870)	2733	NM_025982	67125	Mm.35650	NM_025982	ENSMUSG00000006736	Tspan31	2700085A14Rik|AW742554|Sas	tetraspanin 31	protein-coding
mm_114821.1	chr13	91741508	91741531	+	1	NA	promoter-TSS (NM_028790)	promoter-TSS (NM_028790)	-2	NM_028790	74156	Mm.275963	NM_028790	ENSMUSG00000021620	Acot12	1300004O04Rik|4930449F15Rik|AV027244|Cach|mCACH-1	acyl-CoA thioesterase 12	protein-coding
mm_51089.1	chr6	67115672	67115708	+	1	NA	Intergenic	Intergenic	-78283	NM_007836	13197	Mm.72235	NM_007836	ENSMUSG00000036390	Gadd45a	AA545191|Ddit1|GADD45	growth arrest and DNA-damage-inducible 45 alpha	protein-coding
mm_88168.1	chr10	69747046	69747053	+	1	NA	intron (NM_170730, intron 1 of 17)	intron (NM_170730, intron 1 of 17)	-178483	NM_170687	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_133928.1	chr16	3718106	3718150	-	1	NA	promoter-TSS (NM_001161791)	promoter-TSS (NM_001161791)	-4	NM_001161791	54483	Mm.143718	NM_019453	ENSMUSG00000022534	Mefv	FMF|TRIM20|pyrin	Mediterranean fever	protein-coding
mm_163914.1	chr14	35097436	35097436	+	1	NA	intron (NM_008166, intron 4 of 15)	MER102c|DNA|hAT-Charlie	202827	NR_029774	723847		NR_029774	ENSMUSG00000065481	Mir346	Mirn346|mir-346|mmu-mir-346	microRNA 346	ncRNA
mm_47368.1	chr5	122949201	122949210	-	1	NA	intron (NM_001003953, intron 6 of 22)	intron (NM_001003953, intron 6 of 22)	39894	NM_001003953	30841	Mm.86406	NM_013910	ENSMUSG00000029475	Kdm2b	Cxxc2|Fbl10|Fbxl10|Jhdm1b|PCCX2	lysine (K)-specific demethylase 2B	protein-coding
mm_12742.1	chr2	79122711	79122721	+	1	NA	Intergenic	Intergenic	-132710	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D|Itga4B	integrin alpha 4	protein-coding
mm_126461.1	chr15	80977609	80977619	+	1	NA	promoter-TSS (NM_134091)	promoter-TSS (NM_134091)	-151	NM_134091	105835	Mm.274943	NM_134091	ENSMUSG00000042303	Sgsm3	1810012I01Rik|AI428557|BB175482|Cip85|R75178|RUSC3|Rutbc3	small G protein signaling modulator 3	protein-coding
mm_3618.1	chr1	152540859	152540905	+	1	NA	intron (NM_001346119, intron 9 of 17)	intron (NM_001346119, intron 9 of 17)	84335	NM_016846	19731	Mm.245270	NM_016846	ENSMUSG00000026482	Rgl1	Rgl|mKIAA0959	ral guanine nucleotide dissociation stimulator,-like 1	protein-coding
mm_168758.1	chr12	117398354	117398387	-	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	-61358	NR_044987	432713	Mm.459210	NR_044987	ENSMUSG00000101930	Gm5441	-	predicted gene 5441	ncRNA
mm_151492.1	chr19	58680806	58680809	+	1	NA	exon (NM_026925, exon 12 of 13)	exon (NM_026925, exon 12 of 13)	10442	NM_026925	69060	Mm.20407	NM_026925	ENSMUSG00000046008	Pnlip	1810007A24Rik|PL|PTL	pancreatic lipase	protein-coding
mm_118641.1	chr14	21499222	21499238	+	1	NA	promoter-TSS (NM_001205241)	promoter-TSS (NM_001205241)	-540	NM_001205241	54169	Mm.248967	NM_017479	ENSMUSG00000021767	Kat6b	AI507552|B130044K16Rik|MYST-4|Morf|Myst4|mKIAA0383|qkf|querkopf	K(lysine) acetyltransferase 6B	protein-coding
mm_118095.1	chr13	103870295	103870301	-	1	NA	intron (NM_001005868, intron 4 of 26)	intron (NM_001005868, intron 4 of 26)	50288	NM_001289473	59079	Mm.277354	NM_021563	ENSMUSG00000021709	Erbin	1700028E05Rik|Erbb2ip|mKIAA1225	Erbb2 interacting protein	protein-coding
mm_156450.1	chrX	142708797	142708835	+	1	NA	intron (NM_001199360, intron 2 of 6)	intron (NM_001199360, intron 2 of 6)	27090	NM_001199360	209497	Mm.249648	NM_177592	ENSMUSG00000047045	Tmem164	AI316850|AI852450|AW547186|F730011B02	transmembrane protein 164	protein-coding
mm_69185.1	chr7	127260621	127260676	-	1	NA	promoter-TSS (NM_023203)	promoter-TSS (NM_023203)	19	NM_023203	66422	Mm.29898	NM_023203	ENSMUSG00000042462	Dctpp1	2410015N17Rik|AI854235|RS21-C6	dCTP pyrophosphatase 1	protein-coding
mm_159576.1	chr4	117252378	117252378	+	1	NA	promoter-TSS (NM_001033774)	promoter-TSS (NM_001033774)	38	NM_029589	68777	Mm.331805	NM_026837	ENSMUSG00000048772	Tmem53	1110038M16Rik|1500001P22Rik|1700012A05Rik	transmembrane protein 53	protein-coding
mm_120246.1	chr14	62992394	62992411	+	1	NA	Intergenic	Intergenic	-5675	NM_001039125	654465	Mm.424929	NM_001039125	ENSMUSG00000075573	Defb47	Defb41|EG654465	defensin beta 47	protein-coding
mm_168125.1	chr10	22859611	22859624	+	1	NA	Intergenic	L1Md_T|LINE|L1	-39489	NM_011545	21412	Mm.16497	NM_011545	ENSMUSG00000045680	Tcf21	Pod-1|Pod1|bHLHa23|capsulin|epc|epicardin	transcription factor 21	protein-coding
mm_163835.1	chr14	19417764	19417824	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	184793	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_141377.1	chr17	29078833	29078841	-	1	NA	intron (NR_036469, intron 1 of 1)	(GAAA)n|Simple_repeat|Simple_repeat	289	NR_036469	100504267	Mm.438550	NR_036469	ENSMUSG00000085912	Trp53cor1	Gm16197|OTTMUSG00000031656|linc-p21|lincRNA-p21	tumor protein p53 pathway corepressor 1	ncRNA
mm_146873.1	chr18	25477920	25477930	-	1	NA	3' UTR (NM_001146294, exon 13 of 13)	3' UTR (NM_001146294, exon 13 of 13)	276058	NM_133195	108013	Mm.266435	NM_133195	ENSMUSG00000024268	Celf4	A230070D14Rik|BRUNOL-4|Brul4|Brunol4|C130060B05Rik	CUGBP, Elav-like family member 4	protein-coding
mm_85732.1	chr9	108431811	108431845	-	1	NA	Intergenic	Intergenic	-3346	NM_001135198	434438	Mm.425598	NM_001135198	ENSMUSG00000047220	Ccdc36	-	coiled-coil domain containing 36	protein-coding
mm_113591.1	chr13	40918682	40918689	+	1	NA	exon (NM_133219, exon 1 of 3)	exon (NM_133219, exon 1 of 3)	1051	NM_133219	14538	Mm.314757	NM_008105	ENSMUSG00000021360	Gcnt2	5330430K10Rik|IGnT|IGnTA|IGnTB|IGnTC	glucosaminyl (N-acetyl) transferase 2, I-branching enzyme	protein-coding
mm_52400.1	chr6	113326991	113327013	+	1	NA	promoter-TSS (NM_010957)	promoter-TSS (NM_010957)	26	NM_010957	18294	Mm.43612	NM_010957	ENSMUSG00000030271	Ogg1	Mmh	8-oxoguanine DNA-glycosylase 1	protein-coding
mm_88471.1	chr10	77606045	77606067	+	1	NA	promoter-TSS (NM_019929)	promoter-TSS (NM_019929)	-41	NM_001301672	20610	Mm.24433	NM_019929	ENSMUSG00000020265	Sumo3	2810014B19Rik|D10Ertd345e|SMT3A|SUMO-3|Smt3h1	small ubiquitin-like modifier 3	protein-coding
mm_67732.1	chr7	90130087	90130108	-	1	NA	promoter-TSS (NM_001252521)	promoter-TSS (NM_001252521)	-135	NM_001252523	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_47601.1	chr5	125042824	125042826	-	1	NA	exon (NM_001253904, exon 22 of 48)	exon (NM_001253904, exon 22 of 48)	39350	NM_028443	73121	Mm.296138	NM_028443	ENSMUSG00000037962	Rflna	3110032G18Rik|Fam101a|cfm|cfm2	refilin A	protein-coding
mm_96285.1	chr11	63061600	63061676	+	1	NA	promoter-TSS (NM_027660)	promoter-TSS (NM_027660)	-21	NM_027660	71062	Mm.23534	NM_027660	ENSMUSG00000042189	Tekt3	4933407G07Rik	tektin 3	protein-coding
mm_22203.1	chr2	173578204	173578211	-	1	NA	exon (NM_001199955, exon 1 of 2)	exon (NM_001199955, exon 1 of 2)	134	NM_001199955	70065	Mm.425115	NM_027303	ENSMUSG00000027517	Ankrd60	1700019A24Rik|1700030G11Rik	ankyrin repeat domain 60	protein-coding
mm_49519.1	chr6	29894752	29894776	+	1	NA	intron (NM_001347084, intron 11 of 17)	intron (NM_001347084, intron 11 of 17)	-22249	NM_001037740	320609	Mm.56097	NM_177204	ENSMUSG00000039629	Strip2	D330017J20Rik|Fam40b	striatin interacting protein 2	protein-coding
mm_20382.1	chr2	128819078	128819097	-	1	NA	intron (NM_028248, intron 1 of 18)	intron (NM_028248, intron 1 of 18)	784	NM_028248	72477	Mm.259688	NM_028248	ENSMUSG00000014353	Tmem87b	2610301K12Rik|2810431I02Rik|AU014804	transmembrane protein 87B	protein-coding
mm_75593.1	chr8	61663756	61663770	-	1	NA	intron (NM_001293772, intron 10 of 21)	ID_B1|SINE|B4	-72594	NM_001293774	72333	Mm.29933	NM_001081390	ENSMUSG00000058056	Palld	2410003B16Rik|6030492A02	palladin, cytoskeletal associated protein	protein-coding
mm_71497.1	chr8	46791930	46791942	+	1	NA	intron (NM_008391, intron 1 of 8)	intron (NM_008391, intron 1 of 8)	52191	NM_008391	16363	Mm.1149	NM_008391	ENSMUSG00000031627	Irf2	9830146E22Rik|AI646973|Irf-2	interferon regulatory factor 2	protein-coding
mm_104228.1	chr11	88611029	88611046	-	1	NA	intron (NM_054043, intron 5 of 13)	intron (NM_054043, intron 5 of 13)	-8214	NR_131025	68397	Mm.426889	NR_131025		0610039H22Rik	-	RIKEN cDNA 0610039H22 gene	ncRNA
mm_141903.1	chr17	34956672	34956686	-	1	NA	3' UTR (NM_010478, exon 1 of 1)	3' UTR (NM_010478, exon 1 of 1)	2559	NM_010478	15511	Mm.372314	NM_010478	ENSMUSG00000090877	Hspa1b	Hsp70|Hsp70-1|Hsp70.1|hsp68	heat shock protein 1B	protein-coding
mm_115168.1	chr13	107996329	107996347	+	1	NA	Intergenic	MLT1E|LTR|ERVL-MaLR	-48136	NM_001048250	75616	Mm.491164	NM_001048250	ENSMUSG00000071180	Smim15	2810008M24Rik	small integral membrane protein 15	protein-coding
mm_151647.1	chr19	4059078	4059099	-	1	NA	intron (NM_144869, intron 1 of 5)	intron (NM_144869, intron 1 of 5)	206	NM_144869	225884	Mm.440201	NM_144869	ENSMUSG00000058216	Gstp3	-	glutathione S-transferase pi 3	protein-coding
mm_135087.1	chr16	34518189	34518200	-	1	NA	Intergenic	Intergenic	-4167	NM_177357	545156	Mm.82274	NM_177357	ENSMUSG00000061751	Kalrn	2210407G14Rik|AV235988|DUET|E530005C20Rik|Gm539|Hapip|TRAD	kalirin, RhoGEF kinase	protein-coding
mm_58838.1	chr7	16830877	16830883	+	1	NA	intron (NM_133789, intron 7 of 17)	intron (NM_133789, intron 7 of 17)	-12022	NM_001252458	101540	Mm.1881	NM_178900	ENSMUSG00000041187	Prkd2	AI325941|PKD2	protein kinase D2	protein-coding
mm_164278.1	chr15	102102981	102102985	+	1	NA	promoter-TSS (NM_153533)	promoter-TSS (NM_153533)	-5	NM_153533	209039	Mm.29389	NM_153533	ENSMUSG00000037003	Tns2	C1-ten|Tenc1|nep|nph	tensin 2	protein-coding
mm_70906.1	chr8	25643940	25643947	+	1	NA	intron (NM_001001735, intron 2 of 9)	AT_rich|Low_complexity|Low_complexity	3366	NM_001081269	234135	Mm.217337	NM_001001735	ENSMUSG00000054823	Whsc1l1	6720429E03|A530023P05|AI528490|NSD3|WHISTLE	Wolf-Hirschhorn syndrome candidate 1-like 1 (human)	protein-coding
mm_79727.1	chr9	62341394	62341416	+	1	NA	promoter-TSS (NM_009672)	promoter-TSS (NM_009672)	62	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	protein-coding
mm_15462.1	chr2	157448753	157448760	+	1	NA	intron (NM_009271, intron 2 of 14)	intron (NM_009271, intron 2 of 14)	24463	NM_001025395	20779	Mm.22845	NM_009271	ENSMUSG00000027646	Src	AW259666|pp60c-src	Rous sarcoma oncogene	protein-coding
mm_74820.1	chr8	23028721	23028741	-	1	NA	intron (NM_001277280, intron 1 of 42)	intron (NM_001277280, intron 1 of 42)	-6368	NM_001277281	11733	Mm.334444	NM_031158	ENSMUSG00000031543	Ank1	Ank-1|nb|pale	ankyrin 1, erythroid	protein-coding
mm_1182.1	chr1	61814099	61814102	+	1	NA	intron (NM_001081050, intron 2 of 22)	intron (NM_001081050, intron 2 of 22)	175276	NM_001081050	72823	Mm.35153	NM_001081050	ENSMUSG00000052062	Pard3b	1810008K04Rik|2010002N16Rik|2810455B10Rik|Als2cr19|PAR3B|PAR3L|PAR3beta	par-3 family cell polarity regulator beta	protein-coding
mm_115786.1	chr13	19337048	19337075	-	1	NA	Intergenic	Intergenic	58752	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_168978.1	chr12	91473885	91473890	-	1	NA	intron (NM_011648, intron 1 of 9)	L1Md_T|LINE|L1	72894	NM_011648	22095	Mm.173847	NM_011648	ENSMUSG00000020963	Tshr	AI481368|hypothroid|hyt|pet	thyroid stimulating hormone receptor	protein-coding
mm_54261.1	chr6	28398000	28398023	-	1	NA	Intergenic	CpG	23713	NM_028900	74375	Mm.332950	NM_028900	ENSMUSG00000029708	Gcc1	4932417P04Rik	golgi coiled coil 1	protein-coding
mm_89631.1	chr10	96398784	96398793	+	1	NA	Intergenic	Intergenic	172581	NR_110448	74881	Mm.410819	NR_110448		4930459C07Rik	-	RIKEN cDNA 4930459C07 gene	ncRNA
mm_133419.1	chr16	86343070	86343073	+	1	NA	Intergenic	RMER19B|LTR|ERVK	-441946	NM_011782	23794	Mm.112933	NM_011782	ENSMUSG00000022894	Adamts5	9530092O11Rik|ADAM-TS5|ADAMTS1|ADAMTS11|ADMP-2|AI481094|ASMP-2	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)	protein-coding
mm_167582.1	chr9	45944868	45944892	-	1	NA	intron (NM_172257, intron 15 of 25)	intron (NM_172257, intron 15 of 25)	-5290	NR_106055	102465659		NR_106055	ENSMUSG00000098327	Mir7087	Gm27273|mmu-mir-7087	microRNA 7087	ncRNA
mm_167215.1	chr8	4477718	4477736	+	1	NA	Intergenic	Intergenic	-15678	NM_026058	67260	Mm.35511	NM_026058	ENSMUSG00000008206	Cers4	2900019C14Rik|Lass4|Trh1	ceramide synthase 4	protein-coding
mm_86090.1	chr9	114933930	114933999	-	1	NA	promoter-TSS (NM_175380)	promoter-TSS (NM_175380)	23	NM_175380	333433	Mm.38198	NM_175380	ENSMUSG00000050627	Gpd1l	2210409H23Rik|D9Ertd660e	glycerol-3-phosphate dehydrogenase 1-like	protein-coding
mm_43450.1	chr5	136136203	136136211	+	1	NA	promoter-TSS (NM_027891)	promoter-TSS (NM_027891)	62	NM_001347492	72041	Mm.486605	NM_028070	ENSMUSG00000039754	Alkbh4	2010004B12Rik|Abj4	alkB homolog 4, lysine demethylase	protein-coding
mm_157469.1	chrX	47892468	47892489	-	1	NA	promoter-TSS (NM_001290708)	promoter-TSS (NM_001290708)	74	NM_053123	93761	Mm.229151	NM_053123	ENSMUSG00000031099	Smarca1	5730494M04Rik|Snf2l	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1	protein-coding
mm_74303.1	chr8	126422521	126422559	+	1	NA	promoter-TSS (NM_174987)	promoter-TSS (NM_174987)	39	NM_174987	67892	Mm.31946	NM_174987	ENSMUSG00000051671	Coa6	1810063B05Rik|AI447995	cytochrome c oxidase assembly factor 6	protein-coding
mm_49250.1	chr6	17307944	17307959	+	1	NA	exon (NM_001243064, exon 1 of 2)	exon (NM_001243064, exon 1 of 2)	311	NM_001243064	12389	Mm.28278	NM_007616	ENSMUSG00000007655	Cav1	Cav|Cav-1	caveolin 1, caveolae protein	protein-coding
mm_101506.1	chr11	32200467	32200472	-	1	NA	promoter-TSS (NM_008374)	promoter-TSS (NM_008374)	-190	NM_008374	16199	Mm.384	NM_008374	ENSMUSG00000020279	Il9r	-	interleukin 9 receptor	protein-coding
mm_127701.1	chr15	102990950	102990952	+	1	NA	exon (NM_010466, exon 1 of 2)	exon (NM_010466, exon 1 of 2)	412	NM_010466	15426	Mm.6167	NM_010466	ENSMUSG00000001657	Hoxc8	D130011F21Rik|Hox-3.1	homeobox C8	protein-coding
mm_63757.1	chr7	131110957	131110972	+	1	NA	exon (NM_007769, exon 43 of 47)	exon (NM_007769, exon 43 of 47)	35319	NM_173409	233918	Mm.78341	NM_173409	ENSMUSG00000013668	4933402N03Rik	4930412O05	RIKEN cDNA 4933402N03 gene	protein-coding
mm_94470.1	chr11	6521039	6521048	+	1	NA	promoter-TSS (NM_178440)	promoter-TSS (NM_178440)	-85	NM_178440	246177	Mm.239554	NM_178440	ENSMUSG00000020437	Myo1g	E430002D17Rik	myosin IG	protein-coding
mm_135912.1	chr16	67588664	67588665	-	1	NA	intron (NM_178721, intron 1 of 9)	intron (NM_178721, intron 1 of 9)	32244	NM_001347247	239857	Mm.394300	NM_178721	ENSMUSG00000064115	Cadm2	2900078E11Rik|9330131D06|A830029E02Rik|Igdf4d|Igsf4d|NECL3|SynCAM 2|SynCAM2	cell adhesion molecule 2	protein-coding
mm_106665.1	chr11	121519281	121519295	-	1	NA	promoter-TSS (NM_178763)	promoter-TSS (NM_178763)	54	NM_178763	319530	Mm.11395	NM_178763	ENSMUSG00000039238	Zfp750	A030007D23Rik|Znf750	zinc finger protein 750	protein-coding
mm_51420.1	chr6	78425974	78425985	+	1	NA	promoter-TSS (NM_009042)	promoter-TSS (NM_009042)	-4	NM_009042	19692	Mm.142731	NM_009042	ENSMUSG00000059654	Reg1	-	regenerating islet-derived 1	protein-coding
mm_91156.1	chr10	20540374	20540384	-	1	NA	intron (NM_013875, intron 2 of 12)	intron (NM_013875, intron 2 of 12)	7949	NM_001347366	29863	Mm.425617	NM_013875	ENSMUSG00000019990	Pde7b	-	phosphodiesterase 7B	protein-coding
mm_112391.1	chr12	119238577	119238585	-	1	NA	promoter-TSS (NM_177290)	promoter-TSS (NM_177290)	-305	NM_177290	320910	Mm.217000	NM_177290	ENSMUSG00000025321	Itgb8	4832412O06Rik	integrin beta 8	protein-coding
mm_72558.1	chr8	84073877	84073899	+	1	NA	exon (NM_009055, exon 2 of 21)	exon (NM_009055, exon 2 of 21)	7052	NM_009055	19724	Mm.7892	NM_009055	ENSMUSG00000031706	Rfx1	AI047719|AI385641	regulatory factor X, 1 (influences HLA class II expression)	protein-coding
mm_48041.1	chr5	136392394	136392397	-	1	NA	intron (NM_001291239, intron 3 of 22)	intron (NM_001291239, intron 3 of 22)	-16592	NR_030500	723975		NR_030500	ENSMUSG00000106479	Mir721	Mirn721|miRY|mir-721|mmu-mir-721	microRNA 721	ncRNA
mm_42954.1	chr5	123036225	123036228	+	1	NA	TTS (NM_029112)	TTS (NM_029112)	10594	NM_029112	74890	Mm.141383	NM_029112	ENSMUSG00000029477	Morn3	4930438O03Rik	MORN repeat containing 3	protein-coding
mm_117492.1	chr13	78197816	78197850	-	1	NA	promoter-TSS (NR_045195)	promoter-TSS (NR_045195)	-184	NR_045195	320174	Mm.393122	NR_045195		A830082K12Rik	-	RIKEN cDNA A830082K12 gene	ncRNA
mm_155920.1	chrX	102118474	102118504	+	1	NA	promoter-TSS (NM_027181)	promoter-TSS (NM_027181)	-976	NM_027181	69713	Mm.371635	NM_027181	ENSMUSG00000079480	Pin4	2410002I22Rik|EPVH|Par14	protein (peptidyl-prolyl cis/trans isomerase) NIMA-interacting, 4 (parvulin)	protein-coding
mm_116258.1	chr13	34128423	34128455	-	1	NA	exon (NM_023716, exon 4 of 4)	exon (NM_023716, exon 4 of 4)	1915	NM_023716	73710	Mm.379227	NM_023716	ENSMUSG00000045136	Tubb2b	2410129E14Rik|brdp	tubulin, beta 2B class IIB	protein-coding
mm_2226.1	chr1	90857988	90858000	+	1	NA	Intergenic	Intergenic	-14023	NM_001243008	12835	Mm.7562	NM_009935	ENSMUSG00000048126	Col6a3	AI507288|Col6a-3	collagen, type VI, alpha 3	protein-coding
mm_148378.1	chr19	3205832	3205862	+	1	NA	Intergenic	Intergenic	-8144	NR_045304	70011	Mm.393871	NR_045304	ENSMUSG00000100969	1700030N03Rik	1700087C08Rik	RIKEN cDNA 1700030N03 gene	ncRNA
mm_4155.1	chr1	171023672	171023673	+	1	NA	intron (NM_144559, intron 3 of 4)	B1F|SINE|Alu	4746	NM_144559	246256	Mm.251254	NM_144559	ENSMUSG00000059089	Fcgr4	4833442P21Rik|CD16-2|FcgRIV|FcgammaRIV|Fcgr3a|Fcrl3	Fc receptor, IgG, low affinity IV	protein-coding
mm_155265.1	chrX	58030899	58030906	+	1	NA	5' UTR (NM_009575, exon 1 of 3)	5' UTR (NM_009575, exon 1 of 3)	274	NM_009575	22773	Mm.255890	NM_009575	ENSMUSG00000067860	Zic3	Bn|Ka	zinc finger protein of the cerebellum 3	protein-coding
mm_154751.1	chrX	10595703	10595787	+	1	NA	3' UTR (NM_019634, exon 8 of 8)	3' UTR (NM_019634, exon 8 of 8)	110629	NM_019634	21912	Mm.18590	NM_019634	ENSMUSG00000058254	Tspan7	1200014P11Rik|A15|AI323365|Cd231|Mxs1|PE31|R74651|TALLA|Tm4sf2	tetraspanin 7	protein-coding
mm_19462.1	chr2	92392498	92392523	-	1	NA	5' UTR (NM_001202446, exon 1 of 12)	5' UTR (NM_001202446, exon 1 of 12)	173	NM_001202446	19099	Mm.2720	NM_011162	ENSMUSG00000027223	Mapk8ip1	IB1|JIP-1|Jip1|Prkm8ip|Skip|mjip-2a	mitogen-activated protein kinase 8 interacting protein 1	protein-coding
mm_170959.1	chr2	55671388	55671391	+	1	NA	Intergenic	Lx9|LINE|L1	235419	NM_008426	16519	Mm.5127	NM_008426	ENSMUSG00000026824	Kcnj3	GIRK-1|GIRK1|Kcnf3|Kir3.1	potassium inwardly-rectifying channel, subfamily J, member 3	protein-coding
mm_136340.1	chr16	92603151	92603165	-	1	NA	3' UTR (NM_001111021, exon 8 of 8)	3' UTR (NM_001111021, exon 8 of 8)	94171	NM_001111023	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_38960.1	chr4	150717919	150717961	-	1	NA	Intergenic	Intergenic	-65766	NM_173774	242773	Mm.29280	NM_173774	ENSMUSG00000039838	Slc45a1	C230078B22|Dnb5	solute carrier family 45, member 1	protein-coding
mm_150008.1	chr19	29292828	29292839	+	1	NA	intron (NM_001048177, intron 12 of 23)	Lx8|LINE|L1	32485	NM_013754	27356	Mm.306511	NM_013754	ENSMUSG00000050957	Insl6	RIF1	insulin-like 6	protein-coding
mm_148224.1	chr18	80345737	80345745	-	1	NA	intron (NM_001190373, intron 1 of 3)	(TG)n|Simple_repeat|Simple_repeat	18513	NM_001190373	240444	Mm.279568	NM_001190373	ENSMUSG00000059852	Kcng2	AA591524	potassium voltage-gated channel, subfamily G, member 2	protein-coding
mm_155060.1	chrX	42432545	42432565	+	1	NA	Intergenic	Intergenic	-70010	NM_011364	20400	Mm.441197	NM_011364	ENSMUSG00000005696	Sh2d1a	Gm686|SAP	SH2 domain containing 1A	protein-coding
mm_31831.1	chr4	70378220	70378228	+	1	NA	intron (NM_145990, intron 4 of 36)	GSAT_MM|Satellite|Satellite	32211	NM_001313762	214444	Mm.370777	NM_145990	ENSMUSG00000039298	Cdk5rap2	2900018K03Rik|an|mKIAA1633	CDK5 regulatory subunit associated protein 2	protein-coding
mm_156352.1	chrX	139333908	139333918	+	1	NA	5' UTR (NM_011635, exon 1 of 3)	5' UTR (NM_011635, exon 1 of 3)	230	NM_011635	22037	Mm.1297	NM_011635	ENSMUSG00000051257	Trap1a	Tra-P1A	tumor rejection antigen P1A	protein-coding
mm_57211.1	chr6	122856023	122856058	-	1	NA	5' UTR (NM_009779, exon 1 of 2)	5' UTR (NM_009779, exon 1 of 2)	117	NM_009779	12267	Mm.2408	NM_009779	ENSMUSG00000040552	C3ar1	AZ3B|C3AR|HNFAG09	complement component 3a receptor 1	protein-coding
mm_48099.1	chr5	137066592	137066596	-	1	NA	intron (NM_008871, intron 5 of 8)	AT_rich|Low_complexity|Low_complexity	5678	NM_008871	18787	Mm.250422	NM_008871	ENSMUSG00000037411	Serpine1	PAI-1|PAI1|Planh1	serine (or cysteine) peptidase inhibitor, clade E, member 1	protein-coding
mm_40319.1	chr5	43879926	43879932	+	1	NA	intron (NM_007646, intron 1 of 7)	L1MC5a|LINE|L1	11120	NM_007646	12494	Mm.249873	NM_007646	ENSMUSG00000029084	Cd38	ADPRC 1|Cd38-rs1|I-19	CD38 antigen	protein-coding
mm_8125.1	chr1	136139984	136140030	-	1	NA	intron (NM_001039472, intron 1 of 34)	intron (NM_001039472, intron 1 of 34)	8606	NM_001039472	16565	Mm.276135	NM_019962	ENSMUSG00000041642	Kif21b	2610511N21Rik|mKIAA0449	kinesin family member 21B	protein-coding
mm_21445.1	chr2	160364734	160364750	-	1	NA	3' UTR (NM_010658, exon 1 of 1)	3' UTR (NM_010658, exon 1 of 1)	2323	NM_010658	16658	Mm.330745	NM_010658	ENSMUSG00000074622	Mafb	Kreisler|Krml|Krml1|kr	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein B (avian)	protein-coding
mm_162382.1	chr1	73998516	73998524	-	1	NA	intron (NM_027884, intron 6 of 34)	intron (NM_027884, intron 6 of 34)	125927	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_78410.1	chr9	30427034	30427108	+	1	NA	promoter-TSS (NM_028874)	promoter-TSS (NM_028874)	-258	NM_028874	102607	Mm.35084	NM_028874	ENSMUSG00000031993	Snx19	3526401K03Rik|AI195321|AI848208|mKIAA0254	sorting nexin 19	protein-coding
mm_166259.1	chr5	87680891	87680897	+	1	NA	exon (NM_007784, exon 32 of 34)	exon (NM_007784, exon 32 of 34)	14686	NM_001286016	12990	Mm.427467	NM_007784	ENSMUSG00000070702	Csn1s1	AA959832|AW212882|Csna	casein alpha s1	protein-coding
mm_58811.1	chr7	16400066	16400078	+	1	NA	Intergenic	CpG	-1124	NM_198631	330474	Mm.333594	NM_198631	ENSMUSG00000059273	Zc3h4	Bwq1|Gm768|Kiaa1064-hp|mKIAA1064	zinc finger CCCH-type containing 4	protein-coding
mm_97313.1	chr11	76846513	76846528	+	1	NA	exon (NM_007754, exon 1 of 21)	exon (NM_007754, exon 1 of 21)	488	NM_007754	12874	Mm.276736	NM_007754	ENSMUSG00000020841	Cpd	AA960140|AW322530|D830034L15Rik	carboxypeptidase D	protein-coding
mm_62736.1	chr7	111025102	111025123	+	1	NA	Intergenic	Intergenic	-3839	NM_009431	22083	Mm.255858	NM_009431	ENSMUSG00000005609	Ctr9	AA409336|Sh2bp1|Tsbp|Tsp|mKIAA0155	CTR9 homolog, Paf1/RNA polymerase II complex component	protein-coding
mm_46692.1	chr5	110086317	110086326	-	1	NA	Intergenic	Intergenic	-13648	NM_207279	403178	Mm.297057	NM_207279	ENSMUSG00000064247	Plcxd1	A330045H12Rik|Gm576	phosphatidylinositol-specific phospholipase C, X domain containing 1	protein-coding
mm_127450.1	chr15	101270707	101270717	+	1	NA	exon (NM_010444, exon 2 of 7)	exon (NM_010444, exon 2 of 7)	3866	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_132927.1	chr16	49840364	49840372	+	1	NA	Intergenic	Intergenic	-15286	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_55272.1	chr6	53820945	53820955	-	1	NA	promoter-TSS (NM_025817)	promoter-TSS (NM_025817)	-125	NM_025817	66873	Mm.422727	NM_025817	ENSMUSG00000043496	Tril	1200009O22Rik|AI316813|mKIAA0644	TLR4 interactor with leucine-rich repeats	protein-coding
mm_141613.1	chr17	32810735	32810775	-	1	NA	promoter-TSS (NM_001267583)	promoter-TSS (NM_001267583)	-824	NM_183177	240063	Mm.30675	NM_183177	ENSMUSG00000055202	Zfp811	BC052046	zinc finger protein 811	protein-coding
mm_113964.1	chr13	51642683	51642690	+	1	NA	Intergenic	Intergenic	-2546	NM_025415	66197	Mm.222228	NM_025415	ENSMUSG00000062248	Cks2	1110038L14Rik|CKSHS2	CDC28 protein kinase regulatory subunit 2	protein-coding
mm_86432.1	chr10	3863819	3863842	+	1	NA	intron (NM_001159942, intron 2 of 16)	intron (NM_001159942, intron 2 of 16)	-8837	NM_001033253	213783	Mm.150831	NM_001033253	ENSMUSG00000040624	Plekhg1	D10Ertd733e|Gm521|mKIAA1209	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	protein-coding
mm_119930.1	chr14	54969308	54969342	+	1	NA	intron (NR_033497, intron 1 of 4)	intron (NR_033497, intron 1 of 4)	538	NR_033497	791403	Mm.319176	NR_033497	ENSMUSG00000097652	Mhrt	D830015G02Rik|ENSMUSG00000053118|Myheart	myosin heavy chain associated RNA transcript	ncRNA
mm_65171.1	chr7	19681381	19681395	-	1	NA	promoter-TSS (NM_007385)	promoter-TSS (NM_007385)	72	NM_007385	11425	Mm.477720	NM_007385	ENSMUSG00000074336	Apoc4	Acl|apo-CIV|apoC-IV	apolipoprotein C-IV	protein-coding
mm_19578.1	chr2	101644858	101644872	-	1	NA	intron (NM_009019, intron 1 of 1)	intron (NM_009019, intron 1 of 1)	4667	NM_009019	19373	Mm.828	NM_009019	ENSMUSG00000061311	Rag1	Rag-1	recombination activating gene 1	protein-coding
mm_170.1	chr1	13360832	13360871	+	1	NA	intron (NM_008678, intron 1 of 22)	RLTR12BD_Mm|LTR|ERVK	11578	NM_001302702	17978	Mm.2537	NM_008678	ENSMUSG00000005886	Ncoa2	D1Ertd433e|GRIP-1|Grip1|KAT13C|NCoA-2|SRC-2|TIF2|bHLHe75	nuclear receptor coactivator 2	protein-coding
mm_92904.1	chr10	83337811	83337833	-	1	NA	promoter-TSS (NM_177388)	promoter-TSS (NM_177388)	-5	NM_177388	338365	Mm.67073	NM_177388	ENSMUSG00000034591	Slc41a2	A230035L05Rik|SLC41A1-L1	solute carrier family 41, member 2	protein-coding
mm_30192.1	chr3	144700932	144700945	-	1	NA	intron (NM_001282037, intron 6 of 10)	B4A|SINE|B4	19397	NM_001282042	54673	Mm.271775	NM_019464	ENSMUSG00000037062	Sh3glb1	AA409932|AI314629|AU015566|Bif-1|mKIAA0491	SH3-domain GRB2-like B1 (endophilin)	protein-coding
mm_166458.1	chr5	138847036	138847060	+	1	NA	Intergenic	Intergenic	26968	NM_001195128	384244	Mm.485002	NM_001195128	ENSMUSG00000094504	Gm5294	EG384244	predicted gene 5294	protein-coding
mm_1294.1	chr1	64532572	64532594	+	1	NA	promoter-TSS (NM_009952)	promoter-TSS (NM_009952)	-221	NM_133828	12912	Mm.422634	NM_009952	ENSMUSG00000025958	Creb1	2310001E10Rik|3526402H21Rik|AV083133|Creb|Creb-1	cAMP responsive element binding protein 1	protein-coding
mm_167546.1	chr9	27666423	27666424	+	1	NA	Intergenic	Intergenic	-124846	NM_177906	330908	Mm.379474	NM_177906	ENSMUSG00000062257	Opcml	2900075O15Rik|3732419F12|AI844366|B930023M13Rik|C230027C17|Gm181|Obcam	opioid binding protein/cell adhesion molecule-like	protein-coding
mm_162938.1	chr10	127850054	127850059	+	1	NA	exon (NM_147222, exon 1 of 4)	exon (NM_147222, exon 1 of 4)	128	NM_147222	216453	Mm.222953	NM_147222	ENSMUSG00000054052	Rdh19	RDH-S|RDH-S2|Rdhs	retinol dehydrogenase 19	protein-coding
mm_172805.1	chr9	120131154	120131161	+	1	NA	TTS (NR_002902)	TTS (NR_002902)	723	NR_002902	104433	Mm.453530	NR_002902	ENSMUSG00000064925	Snora62	E2|MBI-13|MBI-136|Rnu108	small nucleolar RNA, H/ACA box 62	snoRNA
mm_18271.1	chr2	52335264	52335283	-	1	NA	intron (NM_010889, intron 1 of 156)	intron (NM_010889, intron 1 of 156)	3525	NM_010889	17996	Mm.389247	NM_010889	ENSMUSG00000026950	Neb	AI595938	nebulin	protein-coding
mm_101295.1	chr11	22171344	22171368	-	1	NA	intron (NM_001252515, intron 6 of 24)	intron (NM_001252515, intron 6 of 24)	115439	NM_153078	216565	Mm.491265	NM_153078	ENSMUSG00000042302	Ehbp1	AF424697|Flj21950|NACSIN	EH domain binding protein 1	protein-coding
mm_4498.1	chr1	173673652	173673686	+	1	NA	promoter-TSS (NM_001162938)	promoter-TSS (NM_001162938)	-11	NM_001162938	100033459	Mm.303377	NM_001162938	ENSMUSG00000066677	Ifi208	9830148g24rik|E430029J22Rik|Pydc3|Pyr-rv1	interferon activated gene 208	protein-coding
mm_127874.1	chr15	8444610	8444668	-	1	NA	promoter-TSS (NM_027707)	promoter-TSS (NM_027707)	-176	NM_201232	71175	Mm.240329	NM_027707	ENSMUSG00000022141	Nipbl	Idn3	Nipped-B homolog (Drosophila)	protein-coding
mm_22892.1	chr3	30746326	30746341	+	1	NA	promoter-TSS (NM_029489)	promoter-TSS (NM_029489)	40	NR_028060	75953	Mm.308084	NM_029489	ENSMUSG00000051860	Samd7	4930597A01Rik	sterile alpha motif domain containing 7	protein-coding
mm_108131.1	chr12	76072172	76072178	+	1	NA	exon (NM_001005510, exon 97 of 116)	exon (NM_001005510, exon 97 of 116)	105084	NM_010157	13983	Mm.2561	NM_010157	ENSMUSG00000021055	Esr2	ER[b]|ERbeta|Estrb	estrogen receptor 2 (beta)	protein-coding
mm_29559.1	chr3	116808052	116808061	-	1	NA	5' UTR (NM_001081326, exon 1 of 34)	5' UTR (NM_001081326, exon 1 of 34)	110	NM_001081326	77559	Mm.237099	NM_001081326	ENSMUSG00000033400	Agl	1110061O17Rik|9430004C13Rik|9630046L06Rik|AI850929|C77197	amylo-1,6-glucosidase, 4-alpha-glucanotransferase	protein-coding
mm_97749.1	chr11	80477337	80477383	+	1	NA	5' UTR (NM_009871, exon 1 of 1)	5' UTR (NM_009871, exon 1 of 1)	314	NM_009871	12569	Mm.142275	NM_009871	ENSMUSG00000048895	Cdk5r1	Cdk5r|D11Bwg0379e|p25|p35	cyclin-dependent kinase 5, regulatory subunit 1 (p35)	protein-coding
mm_20241.1	chr2	126490030	126490042	-	1	NA	intron (NM_001080944, intron 1 of 27)	intron (NM_001080944, intron 1 of 27)	1517	NM_001080944	241633	Mm.222235	NM_001080944	ENSMUSG00000060131	Atp8b4	A530043E15|Im	ATPase, class I, type 8B, member 4	protein-coding
mm_153975.1	chr19	47864415	47864432	-	1	NA	exon (NM_010362, exon 6 of 6)	exon (NM_010362, exon 6 of 6)	-1122	NM_030051	68214	Mm.63791	NM_026619	ENSMUSG00000025069	Gsto2	1700020F09Rik|4930425C18Rik|GSTO 2-2	glutathione S-transferase omega 2	protein-coding
mm_171979.1	chr5	89690158	89690158	-	1	NA	intron (NM_001081401, intron 18 of 21)	intron (NM_001081401, intron 18 of 21)	73722	NR_037571	631105	Mm.7732	NR_037571		Gm7056	Gm149	predicted gene 7056	ncRNA
mm_71489.1	chr8	46745437	46745465	+	1	NA	intron (NM_008391, intron 1 of 8)	intron (NM_008391, intron 1 of 8)	5706	NM_008391	16363	Mm.1149	NM_008391	ENSMUSG00000031627	Irf2	9830146E22Rik|AI646973|Irf-2	interferon regulatory factor 2	protein-coding
mm_131824.1	chr16	22939347	22939361	+	1	NA	exon (NM_021564, exon 8 of 8)	exon (NM_021564, exon 8 of 8)	-11718	NM_053176	94175	Mm.358794	NM_053176	ENSMUSG00000022877	Hrg	AI265597|AW413091|D16jh2|D18020|Hprg|Hrgp	histidine-rich glycoprotein	protein-coding
mm_86165.1	chr9	118838091	118838100	-	1	NA	intron (NM_001113514, intron 6 of 13)	intron (NM_001113514, intron 6 of 13)	-88441	NM_133710	69274	Mm.439928	NM_133710	ENSMUSG00000047409	Ctdspl	2810418J22Rik|AI426263|HYA22|SCP3	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase-like	protein-coding
mm_43525.1	chr5	137152850	137152865	+	1	NA	Intergenic	Intergenic	-36650	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_169350.1	chr14	20980700	20980715	+	1	NA	intron (NM_009502, intron 2 of 20)	U2|snRNA|snRNA	51274	NM_009502	22330	Mm.279361	NM_009502	ENSMUSG00000021823	Vcl	9430097D22|AA571387|AI462105|AW545629	vinculin	protein-coding
mm_87783.1	chr10	60296773	60296795	+	1	NA	intron (NM_011179, intron 8 of 14)	intron (NM_011179, intron 8 of 14)	12323	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_147672.1	chr18	60648291	60648325	-	1	NA	Intergenic	Intergenic	-15102	NR_045401	328963	Mm.417203	NR_045401		G630071F17Rik	G630071F17	RIKEN cDNA G630071F17 gene	ncRNA
mm_93867.1	chr10	123147307	123147335	-	1	NA	intron (NM_001301628, intron 6 of 20)	intron (NM_001301628, intron 6 of 20)	49698	NM_027604	14479	Mm.244209	NM_027604	ENSMUSG00000020124	Usp15	4921514G19Rik|AI327321|E430033I05Rik|Gcap18	ubiquitin specific peptidase 15	protein-coding
mm_133069.1	chr16	58670368	58670374	+	1	NA	5' UTR (NM_007757, exon 1 of 7)	5' UTR (NM_007757, exon 1 of 7)	163	NM_007757	12892	Mm.291519	NM_007757	ENSMUSG00000022742	Cpox	CPX|Cpo|HCP|cac|nct	coproporphyrinogen oxidase	protein-coding
mm_141984.1	chr17	35165014	35165026	-	1	NA	promoter-TSS (NM_020027)	promoter-TSS (NM_020027)	-143	NM_020027	53761	Mm.272462	NM_020027	ENSMUSG00000024393	Prrc2a	3110039B05Rik|Bat-2|Bat2|D17H6S51E|G2|Wbp12|mKIAA4178	proline-rich coiled-coil 2A	protein-coding
mm_82750.1	chr9	26829489	26829496	-	1	NA	intron (NM_001113323, intron 10 of 19)	intron (NM_001113323, intron 10 of 19)	-23024	NM_001310768	244757	Mm.293696	NM_153803	ENSMUSG00000036395	Glb1l2	-	galactosidase, beta 1-like 2	protein-coding
mm_31989.1	chr4	89295298	89295307	+	1	NA	promoter-TSS (NM_009877)	promoter-TSS (NM_009877)	122	NR_132431	102633081	Mm.409388	NR_132431		Gm12610	Gm12609|OTTMUSG00000007716|OTTMUSG00000007717	predicted gene 12610	ncRNA
mm_50708.1	chr6	52165704	52165715	+	1	NA	promoter-TSS (NM_010451)	promoter-TSS (NM_010451)	35	NR_131182	105242657	Mm.490651	NR_131182	ENSMUSG00000056445	Hoxaas2	2810043O09Rik|5730446D14Rik	Hoxa cluster antisense RNA 2	ncRNA
mm_55104.1	chr6	50245364	50245367	-	1	NA	intron (NM_018769, intron 3 of 9)	intron (NM_018769, intron 3 of 9)	16404	NM_018769	54722	Mm.248361	NM_018769	ENSMUSG00000029821	Dfna5	2310037D07Rik|4932441K13Rik|Dfna5h|EG14210|Fin15	deafness, autosomal dominant 5 (human)	protein-coding
mm_165443.1	chr2	155219693	155219693	+	1	NA	intron (NM_008395, intron 23 of 24)	intron (NM_008395, intron 23 of 24)	-16840	NR_111891	67068	Mm.23693	NM_025947	ENSMUSG00000047459	Dynlrb1	2010012N15Rik|2010320M17Rik|9430076K19Rik|AV124457|DNLC2A|Dncl2a|km23-1	dynein light chain roadblock-type 1	protein-coding
mm_54422.1	chr6	32994453	32994463	-	1	NA	intron (NM_025336, intron 3 of 7)	intron (NM_025336, intron 3 of 7)	65694	NM_025336	66075	Mm.21501	NM_025336	ENSMUSG00000053768	Chchd3	0610041L09Rik|1700039J09Rik|AW558177	coiled-coil-helix-coiled-coil-helix domain containing 3	protein-coding
mm_122972.1	chr14	54974758	54974768	-	1	NA	TTS (NR_030607)	TTS (NR_030607)	1013	NR_030607	100124433		NR_030607	ENSMUSG00000077928	Mir208b	Mirn208b|mir-208b	microRNA 208b	ncRNA
mm_95745.1	chr11	54860791	54860836	+	1	NA	promoter-TSS (NM_029327)	promoter-TSS (NM_029327)	-222	NM_029327	75530	Mm.83578	NM_029327	ENSMUSG00000020268	Lyrm7	1700024C24Rik|9330147L21Rik	LYR motif containing 7	protein-coding
mm_165383.1	chr2	129315834	129315873	-	1	NA	Intergenic	Intergenic	-5881	NM_010554	16175	Mm.15534	NM_010554	ENSMUSG00000027399	Il1a	Il-1a	interleukin 1 alpha	protein-coding
mm_94715.1	chr11	20542926	20542937	+	1	NA	promoter-TSS (NM_021372)	promoter-TSS (NM_021372)	-322	NM_021372	58172	Mm.339676	NM_021372	ENSMUSG00000049800	Sertad2	AB041541|AU021878|Kiaa0127|MNCb-1504|SEI-2|Sei2|TRIP-Br2|mKIAA0127	SERTA domain containing 2	protein-coding
mm_92002.1	chr10	62327583	62327599	-	1	NA	intron (NM_010438, intron 4 of 21)	intron (NM_010438, intron 4 of 21)	12830	NM_001146100	15275	Mm.196605	NM_010438	ENSMUSG00000037012	Hk1	BB404130|Hk-1|Hk1-s|dea|mHk1-s	hexokinase 1	protein-coding
mm_147696.1	chr18	60779450	60779452	-	1	NA	TTS (NM_020600)	TTS (NM_020600)	4855	NM_020600	20044	Mm.43778	NM_020600	ENSMUSG00000024608	Rps14	2600014J02Rik|AL023078	ribosomal protein S14	protein-coding
mm_84034.1	chr9	57765568	57765600	-	1	NA	5' UTR (NM_007713, exon 1 of 13)	5' UTR (NM_007713, exon 1 of 13)	276	NM_007713	102414	Mm.25720	NM_007713	ENSMUSG00000032316	Clk3	AI256811	CDC-like kinase 3	protein-coding
mm_114981.1	chr13	97292175	97292177	+	1	NA	Intergenic	Intergenic	51071	NM_007930	13803	Mm.241073	NM_007930	ENSMUSG00000041773	Enc1	Nrpb|PIG10	ectodermal-neural cortex 1	protein-coding
mm_128354.1	chr15	39944472	39944491	-	1	NA	promoter-TSS (NM_172814)	promoter-TSS (NM_172814)	-487	NM_001347036	239393	Mm.39874	NM_172814	ENSMUSG00000022305	Lrp12	AI848829|C820005L12Rik|LRP-12	low density lipoprotein-related protein 12	protein-coding
mm_28321.1	chr3	89337964	89337979	-	1	NA	promoter-TSS (NM_007910)	promoter-TSS (NM_007910)	57	NM_007910	13639	Mm.16332	NM_007910	ENSMUSG00000028040	Efna4	EFL-4|Epl4|LERK-4	ephrin A4	protein-coding
mm_63300.1	chr7	126823288	126823323	+	1	NA	promoter-TSS (NM_029978)	promoter-TSS (NM_029978)	2	NM_029978	68952	Mm.440393	NM_026884	ENSMUSG00000058966	Fam57b	1500016O10Rik|A330104J06Rik|AI413816|AW060769	family with sequence similarity 57, member B	protein-coding
mm_52531.1	chr6	115774565	115774609	+	1	NA	promoter-TSS (NM_025958)	promoter-TSS (NM_025958)	30	NM_025958	67088	Mm.277683	NM_025958	ENSMUSG00000030319	Cand2	2210404G23Rik|Tp120b|mKIAA0667	cullin-associated and neddylation-dissociated 2 (putative)	protein-coding
mm_39539.1	chr5	21425039	21425063	+	1	NA	promoter-TSS (NM_029195)	promoter-TSS (NM_029195)	148	NM_177869	330050	Mm.40655	NM_177869	ENSMUSG00000047221	Fam185a	4631428I10|AI847670	family with sequence similarity 185, member A	protein-coding
mm_97625.1	chr11	78958069	78958076	+	1	NA	intron (NM_001313921, intron 25 of 25)	intron (NM_001313921, intron 25 of 25)	26852	NM_001159301	16859	Mm.341434	NM_010708	ENSMUSG00000001123	Lgals9	AA407335|AI194909|AI265545|LGALS35|Lgals5|gal-9|galectin-9	lectin, galactose binding, soluble 9	protein-coding
mm_41784.1	chr5	103722932	103722944	+	1	NA	Intergenic	Intergenic	-31224	NM_133919	17355	Mm.6949	NM_133919	ENSMUSG00000029313	Aff1	9630032B01Rik|AW319193|Af4|Mllt2h|Rob	AF4/FMR2 family, member 1	protein-coding
mm_102119.1	chr11	53300531	53300540	-	1	NA	promoter-TSS (NM_008300)	promoter-TSS (NM_008300)	-56	NM_008300	15525	Mm.239865	NM_008300	ENSMUSG00000020361	Hspa4	70kDa|AI317151|APG-2|Hsp110|Hsp70RY|mKIAA4025	heat shock protein 4	protein-coding
mm_15243.1	chr2	154657166	154657180	+	1	NA	5' UTR (NM_029362, exon 1 of 5)	5' UTR (NM_029362, exon 1 of 5)	147	NM_029362	75608	Mm.262480	NM_029362	ENSMUSG00000038467	Chmp4b	2010012F05Rik|C76846|Snf7-2	charged multivesicular body protein 4B	protein-coding
mm_11285.1	chr2	30066696	30066707	+	1	NA	5' UTR (NM_001204875, exon 1 of 8)	5' UTR (NM_001204875, exon 1 of 8)	227	NM_001204875	56086	Mm.326055	NM_023871	ENSMUSG00000054766	Set	2610030F17Rik|5730420M11Rik|AA407739|I-2PP2A|StF-IT-1|TAF-I	SET nuclear oncogene	protein-coding
mm_138091.1	chr17	34032349	34032375	+	1	NA	promoter-TSS (NM_001205216)	promoter-TSS (NM_001205216)	12	NM_001205215	20182	Mm.1243	NM_011306	ENSMUSG00000039656	Rxrb	AL023085|H-2RIIBP|Nr2b2|RCoR-1|Rub	retinoid X receptor beta	protein-coding
mm_171406.1	chr4	126222571	126222575	-	1	NA	Intergenic	B1_Mus1|SINE|Alu	-19863	NM_146153	230753	Mm.29813	NM_146153	ENSMUSG00000043962	Thrap3	9330151F09Rik|B230333E16Rik|Trap150	thyroid hormone receptor associated protein 3	protein-coding
mm_166266.1	chr5	88328243	88328252	-	1	NA	exon (NM_008644, exon 3 of 3)	exon (NM_008644, exon 3 of 3)	10935	NM_008644	17830	Mm.200411	NM_008644	ENSMUSG00000064156	Prol1	Muc10	proline rich, lacrimal 1	protein-coding
mm_171059.1	chr3	107868669	107868681	-	1	NA	Intergenic	Intergenic	-8555	NM_133867	99662	Mm.108491	NM_133867	ENSMUSG00000040600	Eps8l3	AI504489|Eps8r3	EPS8-like 3	protein-coding
mm_22471.1	chr3	5218517	5218544	+	1	NA	promoter-TSS (NM_030708)	promoter-TSS (NM_030708)	-24	NM_030708	80892	Mm.41522	NM_030708	ENSMUSG00000025255	Zfhx4	A930021B15|C130041O22Rik|Zfh-4|Zfh4	zinc finger homeodomain 4	protein-coding
mm_103057.1	chr11	69822145	69822162	-	1	NA	promoter-TSS (NM_028855)	promoter-TSS (NM_028855)	12	NM_028855	74288	Mm.159159	NM_028855	ENSMUSG00000041165	Spem1	1700095G12Rik	sperm maturation 1	protein-coding
mm_8522.1	chr1	154884171	154884179	-	1	NA	Intergenic	G-rich|Low_complexity|Low_complexity	-158255	NM_009782	12290	Mm.267517	NM_009782	ENSMUSG00000004110	Cacna1e	A430040I15|BII|Cach6|Cacnl1a6|Cav2.3|Cchra1|alpha1E	calcium channel, voltage-dependent, R type, alpha 1E subunit	protein-coding
mm_24583.1	chr3	93444837	93444857	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	2517	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_134087.1	chr16	8792303	8792326	-	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	-37786	NM_001081400	69053	Mm.390868	NM_001081400	ENSMUSG00000022507	1810013L24Rik	1110017P05Rik|3010002C02Rik|AA792997|AW124177|Gm19906|R74903	RIKEN cDNA 1810013L24 gene	protein-coding
mm_158175.1	chrX	103888684	103888685	-	1	NA	Intergenic	Intergenic	-66696	NM_009197	20502	Mm.388973	NM_009197	ENSMUSG00000033965	Slc16a2	AW105741|Mct8|Xpct	solute carrier family 16 (monocarboxylic acid transporters), member 2	protein-coding
mm_1314.1	chr1	65061999	65062014	+	1	NA	exon (NM_007776, exon 3 of 3)	exon (NM_007776, exon 3 of 3)	1434	NM_007776	12967	Mm.425031	NM_007776	ENSMUSG00000067299	Crygd	Aey4|Cryg-1|DGcry-1|Lop12	crystallin, gamma D	protein-coding
mm_170605.1	chr19	5844211	5844217	-	1	NA	non-coding (NR_003513, exon 1 of 1)	non-coding (NR_003513, exon 1 of 1)	1264	NR_131212	66961	Mm.281895	NR_003513	ENSMUSG00000092274	Neat1	2310043N10Rik|VINC	nuclear paraspeckle assembly transcript 1 (non-protein coding)	ncRNA
mm_19518.1	chr2	94010817	94010823	-	1	NA	promoter-TSS (NM_026944)	promoter-TSS (NM_026944)	-90	NM_026944	69113	Mm.272498	NM_026944	ENSMUSG00000040174	Alkbh3	1700108H04Rik|1810020C19Rik|Abh3|mABH3	alkB homolog 3, alpha-ketoglutarate-dependent dioxygenase	protein-coding
mm_50945.1	chr6	58596585	58596615	+	1	NA	promoter-TSS (NM_011920)	promoter-TSS (NM_011920)	-72	NM_011920	26357	Mm.333096	NM_011920	ENSMUSG00000029802	Abcg2	ABC15|ABCP|AI428558|BCRP|Bcrp1|MXR|MXR1	ATP-binding cassette, sub-family G (WHITE), member 2	protein-coding
mm_124136.1	chr14	86721902	86721915	-	1	NA	intron (NM_019670, intron 27 of 27)	intron (NM_019670, intron 27 of 27)	419206	NM_019670	56419	Mm.440585	NM_019670	ENSMUSG00000022021	Diaph3	4930417P13Rik|Dia2|Diap3|Drf3|mDia2|mKIAA4117|p134MDia2	diaphanous related formin 3	protein-coding
mm_114784.1	chr13	88920384	88920386	+	1	NA	intron (NM_010103, intron 1 of 9)	Lx3B|LINE|L1	98913	NM_001037987	13612	Mm.125580	NM_010103	ENSMUSG00000034488	Edil3	Del-1|Del1	EGF-like repeats and discoidin I-like domains 3	protein-coding
mm_155780.1	chrX	96455530	96455599	+	1	NA	promoter-TSS (NM_001159627)	promoter-TSS (NM_001159627)	128	NM_010417	15203	Mm.277092	NM_010417	ENSMUSG00000031209	Heph	C130006F04Rik|Cpl|mKIAA0698|sla	hephaestin	protein-coding
mm_6591.1	chr1	75264267	75264275	-	1	NA	promoter-TSS (NM_008985)	promoter-TSS (NM_008985)	-63	NM_008985	19275	Mm.2902	NM_008985	ENSMUSG00000026204	Ptprn	IA-2|mIA-A|mKIAA4064	protein tyrosine phosphatase, receptor type, N	protein-coding
mm_14563.1	chr2	134991568	134991570	+	1	NA	intron (NM_019677, intron 3 of 32)	L1_Mur1|LINE|L1	205405	NM_001145830	18795	Mm.330607	NM_019677	ENSMUSG00000051177	Plcb1	3110043I21Rik|AI132408|Plcb|mKIAA0581	phospholipase C, beta 1	protein-coding
mm_159103.1	chr2	37331752	37331752	+	1	NA	promoter-TSS (NM_146374)	promoter-TSS (NM_146374)	3	NM_146374	258371	Mm.223061	NM_146374	ENSMUSG00000049018	Olfr368	MOR178-1	olfactory receptor 368	protein-coding
mm_139670.1	chr17	57412188	57412222	+	1	NA	intron (NM_010130, intron 9 of 21)	intron (NM_010130, intron 9 of 21)	53519	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_18526.1	chr2	63184237	63184252	-	1	NA	promoter-TSS (NM_133207)	promoter-TSS (NM_133207)	43	NM_133207	170738	Mm.242532	NM_133207	ENSMUSG00000059742	Kcnh7	9330137I11Rik|Kv11.3|erg3	potassium voltage-gated channel, subfamily H (eag-related), member 7	protein-coding
mm_100917.1	chr11	6274831	6274886	-	1	NA	promoter-TSS (NM_134020)	promoter-TSS (NM_134020)	-21	NM_134020	103694	Mm.254495	NM_134020	ENSMUSG00000004394	Tmed4	1110014L17Rik|AI326346	transmembrane p24 trafficking protein 4	protein-coding
mm_162786.1	chr10	71662722	71662724	+	1	NA	Intergenic	B3|SINE|B2	314960	NM_027184	69718	Mm.245867	NM_027184	ENSMUSG00000060733	Ipmk	2410017C19Rik|AA408208|Impk	inositol polyphosphate multikinase	protein-coding
mm_42363.1	chr5	114922243	114922276	+	1	NA	promoter-TSS (NM_145209)	promoter-TSS (NM_145209)	-981	NM_145209	231655	Mm.95479	NM_145209	ENSMUSG00000041827	Oasl1	7530414C13Rik|oasl9	2'-5' oligoadenylate synthetase-like 1	protein-coding
mm_104690.1	chr11	97782378	97782399	-	1	NA	promoter-TSS (NR_028078)	promoter-TSS (NR_028078)	51	NM_022891	65019	Mm.140380	NM_022891	ENSMUSG00000071415	Rpl23	2810009A01Rik	ribosomal protein L23	protein-coding
mm_52741.1	chr6	120465720	120465751	+	1	NA	intron (NM_008359, intron 1 of 12)	intron (NM_008359, intron 1 of 12)	2538	NM_008359	16172	Mm.4481	NM_008359	ENSMUSG00000002897	Il17ra	AW538159|Cdw217|Il17r|VDw217	interleukin 17 receptor A	protein-coding
mm_65366.1	chr7	25072288	25072366	-	1	NA	promoter-TSS (NM_008168)	promoter-TSS (NM_008168)	42	NM_008168	14809	Mm.2879	NM_008168	ENSMUSG00000003378	Grik5	GluK5|GluRgamma2|KA2	glutamate receptor, ionotropic, kainate 5 (gamma 2)	protein-coding
mm_55423.1	chr6	65131447	65131451	-	1	NA	intron (NM_019455, intron 4 of 5)	RSINE1|SINE|B4	13281	NM_019455	54486	Mm.410688	NM_019455	ENSMUSG00000029919	Hpgds	H-PGDS|Ptgds2	hematopoietic prostaglandin D synthase	protein-coding
mm_516.1	chr1	37430156	37430220	+	1	NA	promoter-TSS (NM_026123)	promoter-TSS (NM_026123)	16	NM_026123	67387	Mm.27404	NM_026123	ENSMUSG00000026111	Unc50	1110002A21Rik|GMH1|UNCL|URP	unc-50 homolog (C. elegans)	protein-coding
mm_133404.1	chr16	84835071	84835097	+	1	NA	promoter-TSS (NM_001302216)	promoter-TSS (NM_001302216)	-40	NM_008065	14390	Mm.18974	NM_008065	ENSMUSG00000008976	Gabpa	GABPalpha	GA repeat binding protein, alpha	protein-coding
mm_78635.1	chr9	40148113	40148132	+	1	NA	promoter-TSS (NM_029379)	promoter-TSS (NM_029379)	0	NM_029379	75667	Mm.45821	NM_029379	ENSMUSG00000040541	Tmem225	1700030E15Rik|Tnen225	transmembrane protein 225	protein-coding
mm_74710.1	chr8	17212974	17212975	-	1	NA	intron (NM_053171, intron 2 of 69)	intron (NM_053171, intron 2 of 69)	322411	NM_053171	94109	Mm.436988	NM_053171	ENSMUSG00000060924	Csmd1	B930082H09|mKIAA1890	CUB and Sushi multiple domains 1	protein-coding
mm_70154.1	chr7	143502121	143502148	-	1	NA	exon (NM_009434, exon 1 of 2)	exon (NM_009434, exon 1 of 2)	390	NM_009434	22113	Mm.334344	NM_009434	ENSMUSG00000010760	Phlda2	Ipl|Tssc3	pleckstrin homology like domain, family A, member 2	protein-coding
mm_172090.1	chr6	18587456	18587456	-	1	NA	Intergenic	Intergenic	-72631	NM_080285	30785	Mm.224189	NM_080285	ENSMUSG00000000416	Cttnbp2	3010022N24Rik|4732477G22Rik|6430526E05|9130022E09Rik|AU040881|Cortbp2|ORF4|mKIAA1758	cortactin binding protein 2	protein-coding
mm_37513.1	chr4	123904827	123904844	-	1	NA	promoter-TSS (NM_019660)	promoter-TSS (NM_019660)	-178	NM_019660	56309	Mm.446553	NM_019660	ENSMUSG00000028647	Mycbp	5730488M09Rik|AW552132|AW742590|Amy-1	MYC binding protein	protein-coding
mm_15968.1	chr2	166069046	166069048	+	1	NA	intron (NM_008679, intron 20 of 22)	intron (NM_008679, intron 20 of 22)	76410	NM_008679	17979	Mm.469663	NM_008679	ENSMUSG00000027678	Ncoa3	2010305B15Rik|AW321064|Actr|Aib1|KAT13B|Rac3|Src3|Tram-1|Tram1|bHLHe42|p/Cip|pCip	nuclear receptor coactivator 3	protein-coding
mm_21122.1	chr2	153632776	153632793	-	1	NA	promoter-TSS (NM_133850)	promoter-TSS (NM_133850)	-3	NM_133850	99311	Mm.294478	NM_133850	ENSMUSG00000056941	Commd7	2310010I22Rik|AW060956|mU3	COMM domain containing 7	protein-coding
mm_99224.1	chr11	101039878	101039888	+	1	NA	exon (NM_001243049, exon 13 of 21)	exon (NM_001243049, exon 13 of 21)	9543	NR_105893	102466767		NR_105893	ENSMUSG00000098415	Mir6928	Gm27728|mmu-mir-6928	microRNA 6928	ncRNA
mm_83601.1	chr9	48495275	48495318	-	1	NA	promoter-TSS (NM_001004191)	promoter-TSS (NM_001004191)	34	NM_001326355	67010	Mm.76911	NM_144948	ENSMUSG00000042396	Rbm7	1200007M24Rik|1500011D06Rik|AU041934|AW554393	RNA binding motif protein 7	protein-coding
mm_507.1	chr1	37153875	37153896	+	1	NA	Intergenic	Intergenic	-64393	NM_001282010	12790	Mm.214224	NM_009918	ENSMUSG00000026114	Cnga3	CNG3	cyclic nucleotide gated channel alpha 3	protein-coding
mm_131883.1	chr16	23224938	23224959	+	1	NA	5' UTR (NM_145933, exon 1 of 8)	5' UTR (NM_145933, exon 1 of 8)	208	NM_145933	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_40450.1	chr5	53601770	53601783	+	1	NA	intron (NM_001277116, intron 3 of 12)	B2_Mm2|SINE|B2	11290	NM_001080927	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_155810.1	chrX	99820159	99820171	+	1	NA	promoter-TSS (NM_001081283)	promoter-TSS (NM_001081283)	-904	NM_001081283	620592	Mm.388976	NM_001081283	ENSMUSG00000071719	Tmem28	EG620592|Fam155b|Tnen28	transmembrane protein 28	protein-coding
mm_73936.1	chr8	120042937	120042944	+	1	NA	intron (NM_030209, intron 14 of 14)	intron (NM_030209, intron 14 of 14)	50502	NM_001310635	78892	Mm.264680	NM_030209	ENSMUSG00000031825	Crispld2	1810049K24Rik|Lcrisp2|Lgl1|coffeecrisp	cysteine-rich secretory protein LCCL domain containing 2	protein-coding
mm_8335.1	chr1	150099669	150099685	-	1	NA	promoter-TSS (NM_011198)	promoter-TSS (NM_011198)	197	NR_015466	320019	Mm.353072	NR_015466	ENSMUSG00000097028	Ptgs2os	7530420F21Rik	prostaglandin-endoperoxide synthase 2, opposite strand	ncRNA
mm_9952.1	chr1	190979262	190979272	-	1	NA	promoter-TSS (NM_144879)	promoter-TSS (NM_144879)	29	NR_027352	226841	Mm.22856	NM_144879	ENSMUSG00000037568	Vash2	B130052G07Rik	vasohibin 2	protein-coding
mm_151891.1	chr19	5798761	5798770	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	-2784	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_109963.1	chr12	12493103	12493117	-	1	NA	Intergenic	MLT1F|LTR|ERVL-MaLR	-100635	NR_045829	70858	Mm.410838	NR_045829		4921511I17Rik	-	RIKEN cDNA 4921511I17 gene	ncRNA
mm_17318.1	chr2	26445838	26445852	-	1	NA	promoter-TSS (NM_153125)	promoter-TSS (NM_153125)	-629	NM_153125	227648	Mm.206371	NM_153125	ENSMUSG00000026924	Sec16a	AU024582|C230052J16Rik	SEC16 homolog A, endoplasmic reticulum export factor	protein-coding
mm_15178.1	chr2	154190764	154190768	+	1	NA	promoter-TSS (NM_001012392)	promoter-TSS (NM_001012392)	-52	NM_001012392	228801	Mm.3783	NM_153418	ENSMUSG00000027485	Bpifb1	Lplunc1	BPI fold containing family B, member 1	protein-coding
mm_6599.1	chr1	75317164	75317177	-	1	NA	promoter-TSS (NM_016878)	promoter-TSS (NM_016878)	-153	NM_016878	13437	Mm.24680	NM_016878	ENSMUSG00000026209	Dnpep	AA407814	aspartyl aminopeptidase	protein-coding
mm_34978.1	chr4	156013859	156013872	+	1	NA	TTS (NM_011341)	TTS (NM_011341)	170	NM_011659	22163	Mm.13885	NM_011659	ENSMUSG00000029075	Tnfrsf4	ACT35|CD134|Ly-70|Ox40|TXGP1L|Txgp1	tumor necrosis factor receptor superfamily, member 4	protein-coding
mm_109205.1	chr12	108675500	108675524	+	1	NA	exon (NM_007965, exon 6 of 13)	exon (NM_007965, exon 6 of 13)	16892	NR_029771	723909		NR_029771	ENSMUSG00000065436	Mir342	Mirn342|mmu-mir-342	microRNA 342	ncRNA
mm_136118.1	chr16	85803956	85803961	-	1	NA	promoter-TSS (NM_009621)	promoter-TSS (NM_009621)	-845	NM_009621	11504	Mm.1421	NM_009621	ENSMUSG00000022893	Adamts1	ADAM-TS1|ADAMTS|ADAMTS-1|C3-C5|METH-1|METH1	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 1	protein-coding
mm_170181.1	chr17	60784317	60784322	+	1	NA	Intergenic	L1Md_T|LINE|L1	-1770997	NM_026497	67993	Mm.36507	NM_026497	ENSMUSG00000024228	Nudt12	0610016O18Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 12	protein-coding
mm_166681.1	chr6	98785913	98785916	+	1	NA	Intergenic	Intergenic	242384	NM_001197322	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_154072.1	chr19	56390005	56390007	-	1	NA	promoter-TSS (NM_198059)	promoter-TSS (NM_198059)	32	NM_198059	18175	Mm.386769	NM_008733	ENSMUSG00000049134	Nrap	-	nebulin-related anchoring protein	protein-coding
mm_115774.1	chr13	19308553	19308563	-	1	NA	Intergenic	Intergenic	87255	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_41482.1	chr5	91963348	91963359	+	1	NA	promoter-TSS (NM_001271797)	promoter-TSS (NM_001271797)	-285	NM_001271797	68098	Mm.159453	NM_026557	ENSMUSG00000029397	Rchy1	ARNIP|CHIMP|Pirh2|Zfp363|Znf363	ring finger and CHY zinc finger domain containing 1	protein-coding
mm_17895.1	chr2	35069266	35069281	-	1	NA	Intergenic	Intergenic	-7832	NM_010406	15139	Mm.2168	NM_010406	ENSMUSG00000026874	Hc	C5|C5a|He	hemolytic complement	protein-coding
mm_90865.1	chr10	8886093	8886101	-	1	NA	promoter-TSS (NM_175155)	promoter-TSS (NM_175155)	-27	NM_175155	70097	Mm.338275	NM_175155	ENSMUSG00000015305	Sash1	1100001C18Rik|2500002E12Rik|A330076K04Rik|mKIAA0790	SAM and SH3 domain containing 1	protein-coding
mm_146735.1	chr18	15402696	15402724	-	1	NA	5' UTR (NM_001308647, exon 1 of 5)	5' UTR (NM_001308647, exon 1 of 5)	289	NM_001308647	11829	Mm.250786	NM_009700	ENSMUSG00000024411	Aqp4	WCH4	aquaporin 4	protein-coding
mm_112280.1	chr12	114367008	114367012	-	1	NA	Intergenic	Intergenic	102456	NR_106062	102465663		NR_106062	ENSMUSG00000105438	Mir7094-1	mmu-mir-7094-1	microRNA 7094-1	ncRNA
mm_94473.1	chr11	6546900	6546941	+	1	NA	promoter-TSS (NM_001190343)	promoter-TSS (NM_001190343)	33	NM_001190343	216527	Mm.221271	NM_146014	ENSMUSG00000000378	Ccm2	BC029157	cerebral cavernous malformation 2	protein-coding
mm_22824.1	chr3	27231538	27231554	+	1	NA	intron (NM_178772, intron 3 of 4)	intron (NM_178772, intron 3 of 4)	48542	NM_178772	320024	Mm.24576	NM_178772	ENSMUSG00000027698	Nceh1	Aadacl1|B230106I24Rik|CPO-BP|Nceh	neutral cholesterol ester hydrolase 1	protein-coding
mm_12339.1	chr2	69722861	69722876	+	1	NA	promoter-TSS (NM_001081086)	promoter-TSS (NM_001081086)	-220	NM_001081086	228005	Mm.11815	NM_001081086	ENSMUSG00000042133	Ppig	AU019516|AU022200|B230312B02Rik|CYP|SRCyp	peptidyl-prolyl isomerase G (cyclophilin G)	protein-coding
mm_3492.1	chr1	150105964	150105969	+	1	NA	3' UTR (NM_011198, exon 10 of 10)	3' UTR (NM_011198, exon 10 of 10)	5935	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_60231.1	chr7	43672004	43672040	+	1	NA	promoter-TSS (NM_145582)	promoter-TSS (NM_145582)	-9	NM_145582	233189	Mm.26514	NM_145582	ENSMUSG00000038888	Ctu1	Atpbd3|BC005752	cytosolic thiouridylase subunit 1	protein-coding
mm_172175.1	chr6	47835831	47835831	+	1	NA	5' UTR (NM_027477, exon 1 of 6)	5' UTR (NM_027477, exon 1 of 6)	170	NM_027477	272347	Mm.169059	NM_027477	ENSMUSG00000062519	Zfp398	5730513I23Rik	zinc finger protein 398	protein-coding
mm_28229.1	chr3	88454833	88454853	-	1	NA	5' UTR (NM_001163490, exon 2 of 15)	5' UTR (NM_001163490, exon 2 of 15)	918	NM_013658	20351	Mm.439752	NM_013658	ENSMUSG00000028064	Sema4a	AI132332|SemB|Semab	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A	protein-coding
mm_150790.1	chr19	44303202	44303218	+	1	NA	promoter-TSS (NR_039574)	promoter-TSS (NR_039574)	39	NR_039574	100628619		NR_039574	ENSMUSG00000093315	Mir5114	mmu-mir-5114|mu-mir-5114	microRNA 5114	ncRNA
mm_60722.1	chr7	45336151	45336184	+	1	NA	exon (NM_010473, exon 1 of 6)	exon (NM_010473, exon 1 of 6)	898	NM_010473	15464	Mm.39968	NM_010473	ENSMUSG00000038239	Hrc	-	histidine rich calcium binding protein	protein-coding
mm_129676.1	chr15	81398297	81398299	-	1	NA	intron (NM_133726, intron 1 of 11)	PB1D9|SINE|Alu	1396	NM_133726	70356	Mm.180337	NM_133726	ENSMUSG00000022403	St13	1110007I03Rik|3110002K08Rik|AW555194|HIP|HOP|HSPABP|HSPABP1|PRO0786|SNC6|p48	suppression of tumorigenicity 13	protein-coding
mm_33277.1	chr4	128722182	128722191	+	1	NA	intron (NM_001195130, intron 7 of 14)	B4A|SINE|B4	-5385	NM_001195083	54383	Mm.473738	NM_018774	ENSMUSG00000028796	Phc2	A3galt2|AA415044|D130050K19Rik|D4Ertd810e|Edr2|Mph2|p36	polyhomeotic-like 2 (Drosophila)	protein-coding
mm_36187.1	chr4	62228522	62228535	-	1	NA	Intergenic	Intergenic	-19982	NM_001290350	22696	Mm.5011	NM_009554	ENSMUSG00000028389	Zfp37	Tzn|Zfp-37	zinc finger protein 37	protein-coding
mm_17778.1	chr2	32876031	32876059	-	1	NA	promoter-TSS (NM_146119)	promoter-TSS (NM_146119)	-89	NM_146119	227737	Mm.301646	NM_146119	ENSMUSG00000026796	Fam129b	9130404D14Rik	family with sequence similarity 129, member B	protein-coding
mm_68831.1	chr7	126200398	126200408	-	1	NA	promoter-TSS (NM_028816)	promoter-TSS (NM_028816)	5	NM_028816	74204	Mm.235663	NM_028816	ENSMUSG00000000131	Xpo6	2610005L19Rik|AL022631|C230091E20Rik|R75304|Ranbp20|mKIAA0370	exportin 6	protein-coding
mm_143454.1	chr17	70978509	70978557	-	1	NA	intron (NM_023402, intron 1 of 3)	intron (NM_023402, intron 1 of 3)	11983	NM_023402	67938	Mm.261329	NM_023402	ENSMUSG00000034868	Myl12b	1500001M02Rik|C77744|Mylc2b|RLC-B	myosin, light chain 12B, regulatory	protein-coding
mm_92335.1	chr10	75798518	75798553	-	1	NA	promoter-TSS (NM_008185)	promoter-TSS (NM_008185)	49	NM_008185	14871	Mm.2746	NM_008185	ENSMUSG00000001663	Gstt1	AI255817|Gstt1-1	glutathione S-transferase, theta 1	protein-coding
mm_43954.1	chr5	145231711	145231754	+	1	NA	promoter-TSS (NM_028298)	promoter-TSS (NM_028298)	7	NM_001347533	72611	Mm.206555	NM_028298	ENSMUSG00000007812	Zfp655	2700038I16Rik|9030409O18Rik|mKIAA4222	zinc finger protein 655	protein-coding
mm_133574.1	chr16	91406368	91406378	+	1	NA	TTS (NM_010509)	TTS (NM_010509)	138	NM_008349	16155	Mm.4154	NM_008349	ENSMUSG00000022969	Il10rb	6620401D04Rik|AI528744|CRF2-4|Crfb4|D16H21S58|D21S58h|IL-10R2|Il10r2	interleukin 10 receptor, beta	protein-coding
mm_154352.1	chrM	5894	5902	+	1	NA	NA	Intergenic	NA	NA								
mm_168296.1	chr11	105181963	105181980	+	1	NA	promoter-TSS (NR_027956)	promoter-TSS (NR_027956)	444	NM_001294329	24086	Mm.126976	NM_011903	ENSMUSG00000020694	Tlk2	4933403M19Rik|PKU-alpha|PKUalpha|Tlk	tousled-like kinase 2 (Arabidopsis)	protein-coding
mm_37887.1	chr4	132515429	132515434	-	1	NA	Intergenic	Intergenic	-4975	NM_144907	230784	Mm.23608	NM_144907	ENSMUSG00000028893	Sesn2	HI95|SEST2|Ses2	sestrin 2	protein-coding
mm_139953.1	chr17	71238498	71238501	+	1	NA	intron (NM_001164885, intron 9 of 19)	intron (NM_001164885, intron 9 of 19)	33845	NM_001164885	64898	Mm.227924	NM_022882	ENSMUSG00000024052	Lpin2	2610511G02Rik|AI481352|AW742896	lipin 2	protein-coding
mm_135888.1	chr16	64851654	64851754	-	1	NA	promoter-TSS (NM_178647)	promoter-TSS (NM_178647)	19	NM_001347245	72020	Mm.25960	NM_028059	ENSMUSG00000047141	Zfp654	1600021C16Rik|1810008K20Rik|433036|Gm5488|Znf654	zinc finger protein 654	protein-coding
mm_156731.1	chrX	159940434	159940447	+	1	NA	intron (NM_001135728, intron 7 of 12)	L1MA5|LINE|L1	-2253	NM_001290661	58194	Mm.286495	NM_021389	ENSMUSG00000040990	Sh3kbp1	1200007H22Rik|1700125L08Rik|5830464D22Rik|AI447724|Cin85|IN85|Ruk|Seta	SH3-domain kinase binding protein 1	protein-coding
mm_143847.1	chr17	84137231	84137243	-	1	NA	Intergenic	Intergenic	50710	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_86038.1	chr9	114368222	114368245	-	1	NA	promoter-TSS (NR_040384)	promoter-TSS (NR_040384)	-91	NR_040383	75116	Mm.72675	NR_040383	ENSMUSG00000074039	4930520O04Rik	-	RIKEN cDNA 4930520O04 gene	ncRNA
mm_49773.1	chr6	34873376	34873390	+	1	NA	3' UTR (NM_197986, exon 2 of 2)	3' UTR (NM_197986, exon 2 of 2)	4682	NM_199145	78412	Mm.248440	NM_199145	ENSMUSG00000046806	3110062M04Rik	AL023049|Mri	RIKEN cDNA 3110062M04 gene	protein-coding
mm_44645.1	chr5	28209844	28209862	-	1	NA	5' UTR (NM_001310511, exon 1 of 3)	5' UTR (NM_001310511, exon 1 of 3)	315	NM_001310511	269637	Mm.68286	NM_175651	ENSMUSG00000044681	Cnpy1	1500012D20Rik|9630008K15Rik|AI853839	canopy FGF signaling regulator 1	protein-coding
mm_67579.1	chr7	82648470	82648545	-	1	NA	promoter-TSS (NM_001159672)	promoter-TSS (NM_001159672)	21	NM_177894	330577	Mm.222812	NM_177894	ENSMUSG00000038570	Saxo2	1700129I04Rik|D030069K18|Fam154b	stabilizer of axonemal microtubules 2	protein-coding
mm_20939.1	chr2	151009365	151009390	-	1	NA	promoter-TSS (NM_207204)	promoter-TSS (NM_207204)	21	NM_207204	78177	Mm.120911	NM_207204	ENSMUSG00000068115	Ninl	4930519N13Rik|Gm1004|Gm1634|mKIAA0980	ninein-like	protein-coding
mm_153425.1	chr19	40769536	40769557	-	1	NA	Intergenic	Intergenic	-61733	NM_172839	240665	Mm.309	NM_172839	ENSMUSG00000025010	Ccnj	D430039C20Rik	cyclin J	protein-coding
mm_92526.1	chr10	78753047	78753076	-	1	NA	promoter-TSS (NM_027630)	promoter-TSS (NM_027630)	6	NM_027630	70976	Mm.188505	NM_027630	ENSMUSG00000078442	Ccdc105	4931413A09Rik	coiled-coil domain containing 105	protein-coding
mm_134884.1	chr16	29378571	29378610	-	1	NA	5' UTR (NM_175650, exon 1 of 30)	5' UTR (NM_175650, exon 1 of 30)	142	NM_001284375	268878	Mm.9823	NM_175650	ENSMUSG00000048939	Atp13a5	C630015F21Rik	ATPase type 13A5	protein-coding
mm_162540.1	chr1	169694031	169694055	+	1	NA	3' UTR (NM_009063, exon 5 of 5)	3' UTR (NM_009063, exon 5 of 5)	38542	NM_009063	19737	Mm.20954	NM_009063	ENSMUSG00000026678	Rgs5	1110070A02Rik	regulator of G-protein signaling 5	protein-coding
mm_142382.1	chr17	44736651	44736674	-	1	NA	promoter-TSS (NM_001271631)	promoter-TSS (NM_001271631)	-14	NM_001145920	12393	Mm.391013	NM_009820	ENSMUSG00000039153	Runx2	AML3|Cbf|Cbfa-1|Cbfa1|LS3|Osf2|PEBP2aA|Pebp2a1|Pebpa2a	runt related transcription factor 2	protein-coding
mm_100540.1	chr11	120672999	120673009	+	1	NA	promoter-TSS (NM_026877)	promoter-TSS (NM_026877)	31	NM_026877	68938	Mm.294020	NM_026877	ENSMUSG00000025142	Aspscr1	1190006K01Rik|ASPC|ASPCR1|ASPL|ASPS|RCC17|TUG	alveolar soft part sarcoma chromosome region, candidate 1 (human)	protein-coding
mm_133673.1	chr16	92291110	92291114	+	1	NA	Intergenic	MLT1D|LTR|ERVL-MaLR	-1277	NM_134110	246133	Mm.156736	NM_134110	ENSMUSG00000039672	Kcne2	2200002I16Rik|AW048273|MiRP1	potassium voltage-gated channel, Isk-related subfamily, gene 2	protein-coding
mm_105356.1	chr11	103028329	103028340	-	1	NA	promoter-TSS (NM_008707)	promoter-TSS (NM_008707)	-228	NM_008707	18107	Mm.10265	NM_008707	ENSMUSG00000020936	Nmt1	AW536594	N-myristoyltransferase 1	protein-coding
mm_52279.1	chr6	108660481	108660497	+	1	NA	promoter-TSS (NM_011498)	promoter-TSS (NM_011498)	-140	NM_011498	20893	Mm.2436	NM_011498	ENSMUSG00000030103	Bhlhe40	Bhlhb2|C130042M06Rik|CR8|Clast5|Dec1|Sharp2|Stra13|Stra14	basic helix-loop-helix family, member e40	protein-coding
mm_53173.1	chr6	125345806	125345810	+	1	NA	TTS (NM_011324)	TTS (NM_011324)	-3915	NM_011609	21937	Mm.1258	NM_011609	ENSMUSG00000030341	Tnfrsf1a	CD120a|FPF|TNF-R|TNF-R-I|TNF-R1|TNF-R55|TNF-alphaR1|TNFAR|TNFR60|TNFRI|TNFRp55|TNFalpha-R1|Tnfr-2|Tnfr1|p55|p55-R	tumor necrosis factor receptor superfamily, member 1a	protein-coding
mm_44145.1	chr5	150259853	150259892	+	1	NA	promoter-TSS (NM_172887)	promoter-TSS (NM_172887)	-58	NM_172887	320365	Mm.216590	NM_172887	ENSMUSG00000056602	Fry	13CDNA73|9330186A19Rik|AF346502|AI462658|C87180|D930046M03|cg003|mKIAA4143	FRY microtubule binding protein	protein-coding
mm_159089.1	chr2	31810492	31810492	-	1	NA	promoter-TSS (NM_183424)	promoter-TSS (NM_183424)	88	NM_183424	227717	Mm.185027	NM_183424	ENSMUSG00000043102	Qrfp	P518	pyroglutamylated RFamide peptide	protein-coding
mm_33153.1	chr4	125490469	125490493	+	1	NA	promoter-TSS (NM_001081097)	promoter-TSS (NM_001081097)	-350	NM_001081097	14807	Mm.40896	NM_001081097	ENSMUSG00000001985	Grik3	9630027E11|GluK3|GluR7-3|Glur-7|Glur7	glutamate receptor, ionotropic, kainate 3	protein-coding
mm_25840.1	chr3	129215477	129215495	+	1	NA	intron (NM_001042502, intron 1 of 2)	intron (NM_001042502, intron 1 of 2)	1554	NM_001287048	18741	Mm.246804	NM_011098	ENSMUSG00000028023	Pitx2	9430085M16Rik|Brx1|Brx1b|Munc30|Otlx2|Ptx2|Rieg	paired-like homeodomain transcription factor 2	protein-coding
mm_121545.1	chr14	122474778	122474800	+	1	NA	promoter-TSS (NM_009574)	promoter-TSS (NM_009574)	410	NR_045046	69248	Mm.235369	NR_045046	ENSMUSG00000085555	2610035F20Rik	-	RIKEN cDNA 2610035F20 gene	ncRNA
mm_88917.1	chr10	81183001	81183048	+	1	NA	promoter-TSS (NM_001190474)	promoter-TSS (NM_001190474)	17	NM_001190474	13144	Mm.10294	NM_007828	ENSMUSG00000034974	Dapk3	ZIPK|dlk	death-associated protein kinase 3	protein-coding
mm_105196.1	chr11	102088472	102088530	-	1	NA	promoter-TSS (NM_016695)	promoter-TSS (NM_016695)	14	NM_016695	50997	Mm.36242	NM_016695	ENSMUSG00000017314	Mpp2	D11Bwg0652e|Dlg2|Dlgh2|Pals4	membrane protein, palmitoylated 2 (MAGUK p55 subfamily member 2)	protein-coding
mm_112836.1	chr13	20826127	20826144	+	1	NA	intron (NM_012054, intron 2 of 20)	intron (NM_012054, intron 2 of 20)	32022	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_23872.1	chr3	83029162	83029172	+	1	NA	exon (NM_010196, exon 3 of 5)	exon (NM_010196, exon 3 of 5)	3014	NM_001111048	14161	Mm.88793	NM_010196	ENSMUSG00000028001	Fga	ENSMUSG00000059807|Fib	fibrinogen alpha chain	protein-coding
mm_138909.1	chr17	43594345	43594378	+	1	NA	exon (NM_013737, exon 3 of 12)	exon (NM_013737, exon 3 of 12)	-2852	NR_045444	73504	Mm.9277	NR_045444	ENSMUSG00000090307	1700071M16Rik	-	RIKEN cDNA 1700071M16 gene	ncRNA
mm_75863.1	chr8	70760500	70760511	-	1	NA	exon (NM_183170, exon 2 of 5)	exon (NM_183170, exon 2 of 5)	416	NM_183170	234384	Mm.213010	NM_183170	ENSMUSG00000035559	Mpv17l2	Fksg24	MPV17 mitochondrial membrane protein-like 2	protein-coding
mm_103649.1	chr11	78971380	78971391	-	1	NA	exon (NM_010708, exon 4 of 11)	exon (NM_010708, exon 4 of 11)	13539	NM_001159301	16859	Mm.341434	NM_010708	ENSMUSG00000001123	Lgals9	AA407335|AI194909|AI265545|LGALS35|Lgals5|gal-9|galectin-9	lectin, galactose binding, soluble 9	protein-coding
mm_73371.1	chr8	105617791	105617836	+	1	NA	exon (NM_001081241, exon 13 of 22)	exon (NM_001081241, exon 13 of 22)	2347	NR_035492	100316712		NR_035492	ENSMUSG00000089432	Mir1966	mir-1966|mmu-mir-1966	microRNA 1966	ncRNA
mm_91768.1	chr10	51526221	51526237	-	1	NA	Intergenic	LTRIS4A|LTR|ERV1	35331	NM_013532	14728	Mm.34408	NM_013532	ENSMUSG00000062593	Lilrb4a	CD85K|Gp49b|HM18|ILT3|LIR-5|Lilrb4|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4A	protein-coding
mm_77874.1	chr9	6168602	6168617	+	1	NA	promoter-TSS (NM_027924)	promoter-TSS (NM_027924)	-3	NM_027924	71785	Mm.390122	NM_027924	ENSMUSG00000032006	Pdgfd	1110003I09Rik	platelet-derived growth factor, D polypeptide	protein-coding
mm_149620.1	chr19	16955688	16955701	+	1	NA	promoter-TSS (NM_181348)	promoter-TSS (NM_181348)	-424	NM_181348	353211	Mm.257354	NM_181348	ENSMUSG00000039126	Prune2	6330414G02Rik|A230083H22Rik|A330102H22Rik|Bmcc1|mKIAA0367	prune homolog 2	protein-coding
mm_92856.1	chr10	81530459	81530478	-	1	NA	3' UTR (NM_010301, exon 7 of 7)	3' UTR (NM_010301, exon 7 of 7)	-6243	NM_010304	14676	Mm.1546	NM_010304	ENSMUSG00000034792	Gna15	G[a]15|Galpha15	guanine nucleotide binding protein, alpha 15	protein-coding
mm_58195.1	chr6	143099792	143099830	-	1	NA	intron (NM_001109688, intron 1 of 24)	CpG-12558	341	NM_001286578	74741	Mm.130260	NM_029081	ENSMUSG00000030279	C2cd5	5730419I09Rik|C030008B15Rik|CDP138	C2 calcium-dependent domain containing 5	protein-coding
mm_89409.1	chr10	90828932	90828947	+	1	NA	promoter-TSS (NM_001347054)	promoter-TSS (NM_001347054)	-715	NM_001347054	77531	Mm.440605	NM_181398	ENSMUSG00000058589	Anks1b	AIDA-1b|C030032C09Rik|E530015N03Rik|ENSMUSG00000078431|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding
mm_56606.1	chr6	112388014	112388037	-	1	NA	promoter-TSS (NM_175525)	promoter-TSS (NM_175525)	-2	NM_175525	243612	Mm.122653	NM_175525	ENSMUSG00000034387	Ssu2	D630042P16Rik|Fls485|Ssuh2	ssu-2 homolog (C. elegans)	protein-coding
mm_24340.1	chr3	89735790	89735805	+	1	NA	exon (NM_001146296, exon 2 of 15)	exon (NM_001146296, exon 2 of 15)	5079	NM_019655	56417	Mm.316628	NM_019655	ENSMUSG00000027951	Adar	AV242451|Adar1|Adar1p110|Adar1p150|mZaADAR	adenosine deaminase, RNA-specific	protein-coding
mm_169671.1	chr15	63334484	63334484	-	1	NA	Intergenic	L1Md_T|LINE|L1	145124	NR_045279	432958	Mm.255105	NR_045279		Gm20740	-	predicted gene, 20740	ncRNA
mm_74819.1	chr8	22859259	22859266	-	1	NA	promoter-TSS (NM_001081149)	promoter-TSS (NM_001081149)	-277	NM_001081149	244349	Mm.182776	NM_001081149	ENSMUSG00000031540	Kat6a	1500036M03|9930021N24Rik|MOZ|Myst3|Zfp220	K(lysine) acetyltransferase 6A	protein-coding
mm_10512.1	chr2	16356366	16356387	+	1	NA	promoter-TSS (NM_026162)	promoter-TSS (NM_026162)	72	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding
mm_98278.1	chr11	89019609	89019620	+	1	NA	3' UTR (NM_009546, exon 9 of 9)	3' UTR (NM_009546, exon 9 of 9)	20211	NM_009546	217069	Mm.248445	NM_009546	ENSMUSG00000000275	Trim25	AA960166|AL022677|EFP|Zfp147	tripartite motif-containing 25	protein-coding
mm_6542.1	chr1	75125183	75125210	-	1	NA	TTS (NM_194333)	TTS (NM_194333)	8694	NM_194333	22626	Mm.68157	NM_194333	ENSMUSG00000026205	Slc23a3	SVCT3|Yspl1	solute carrier family 23 (nucleobase transporters), member 3	protein-coding
mm_696.1	chr1	40580472	40580481	+	1	NA	5' UTR (NM_177084, exon 1 of 12)	5' UTR (NM_177084, exon 1 of 12)	249	NM_177084	110895	Mm.108602	NM_177084	ENSMUSG00000026065	Slc9a4	AW990558|D730009J23Rik|NHE4	solute carrier family 9 (sodium/hydrogen exchanger), member 4	protein-coding
mm_931.1	chr1	55450099	55450111	+	1	NA	intron (NM_001114663, intron 1 of 5)	intron (NM_001114663, intron 1 of 5)	44159	NM_001114663	227120	Mm.194183	NM_001114663	ENSMUSG00000038349	Plcl1	C230017K02Rik|PLC-L|PLC-L1|PLCE|PLCL|PLDL1|PRIP|PRIP-1	phospholipase C-like 1	protein-coding
mm_10074.1	chr1	195018241	195018252	-	1	NA	intron (NR_015566, intron 1 of 7)	intron (NR_015566, intron 1 of 7)	847	NR_015566	320977	Mm.99905	NR_015566	ENSMUSG00000096929	A330023F24Rik	C030002C11Rik	RIKEN cDNA A330023F24 gene	ncRNA
mm_36825.1	chr4	105110073	105110085	-	1	NA	promoter-TSS (NM_178143)	promoter-TSS (NM_178143)	-181	NM_178143	108079	Mm.48638	NM_178143	ENSMUSG00000028518	Prkaa2	2310008I11Rik|A830082D05|AMPKalpha2	protein kinase, AMP-activated, alpha 2 catalytic subunit	protein-coding
mm_992.1	chr1	58711489	58711523	+	1	NA	promoter-TSS (NM_001289704)	promoter-TSS (NM_001289704)	15	NM_001293804	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_165337.1	chr2	116989570	116989584	+	1	NA	Intergenic	Intergenic	89425	NR_040335	320975	Mm.132509	NR_040335	ENSMUSG00000085316	D330050G23Rik	-	RIKEN cDNA D330050G23 gene	ncRNA
mm_136515.1	chr16	97450406	97450419	-	1	NA	exon (NM_010846, exon 10 of 11)	exon (NM_010846, exon 10 of 11)	12493	NM_010846	17857	Mm.33996	NM_010846	ENSMUSG00000000386	Mx1	AI893580|Mx|Mx-1	MX dynamin-like GTPase 1	protein-coding
mm_80545.1	chr9	81632363	81632442	+	1	NA	promoter-TSS (NR_040397)	promoter-TSS (NR_040397)	44	NR_040396	319405	Mm.246494	NR_040393	ENSMUSG00000097466	D430036J16Rik	-	RIKEN cDNA D430036J16 gene	ncRNA
mm_23688.1	chr3	68691431	68691438	+	1	NA	promoter-TSS (NM_008351)	promoter-TSS (NM_008351)	10	NM_008351	16159	Mm.103783	NM_008351	ENSMUSG00000027776	Il12a	IL-12p35|Il-12a|Ll12a|p35	interleukin 12a	protein-coding
mm_130602.1	chr15	99788872	99788873	-	1	NA	intron (NM_023063, intron 6 of 7)	intron (NM_023063, intron 6 of 7)	-16357	NM_028015	71949	Mm.390821	NM_028015	ENSMUSG00000023021	Cers5	2310081H14Rik|AU045339|AW544927|Lass5|Trh4	ceramide synthase 5	protein-coding
mm_99656.1	chr11	105655584	105655617	+	1	NA	intron (NM_181071, intron 2 of 25)	intron (NM_181071, intron 2 of 25)	65614	NM_181071	77097	Mm.22501	NM_175492	ENSMUSG00000053580	Tanc2	3526402J09Rik|5730590C14Rik	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2	protein-coding
mm_127022.1	chr15	96286790	96286844	+	1	NA	promoter-TSS (NM_175251)	promoter-TSS (NM_175251)	-705	NM_175251	77044	Mm.17166	NM_175251	ENSMUSG00000033237	Arid2	1700124K17Rik|4432409D24Rik|zipzap/p200	AT rich interactive domain 2 (ARID, RFX-like)	protein-coding
mm_63367.1	chr7	127091340	127091348	+	1	NA	promoter-TSS (NM_178901)	promoter-TSS (NM_178901)	-92	NM_178901	101602	Mm.490357	NM_178901	ENSMUSG00000045165	AI467606	-	expressed sequence AI467606	protein-coding
mm_30840.1	chr4	24027801	24027810	+	1	NA	Intergenic	Intergenic	-468657	NM_199467	212377	Mm.120919	NM_199467	ENSMUSG00000045751	Mms22l	F730047E07Rik|Gm134	MMS22-like, DNA repair protein	protein-coding
mm_139947.1	chr17	71204574	71204591	+	1	NA	promoter-TSS (NM_001164885)	promoter-TSS (NM_001164885)	-72	NM_001164885	64898	Mm.227924	NM_022882	ENSMUSG00000024052	Lpin2	2610511G02Rik|AI481352|AW742896	lipin 2	protein-coding
mm_142649.1	chr17	47509501	47509511	-	1	NA	intron (NM_001081635, intron 1 of 6)	intron (NM_001081635, intron 1 of 6)	4455	NM_001081635	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_94563.1	chr11	11685543	11685553	+	1	NA	promoter-TSS (NM_009578)	promoter-TSS (NM_009578)	-377	NM_009578	22778	Mm.103545	NM_009578	ENSMUSG00000018654	Ikzf1	5832432G11Rik|Ikaros|LyF-1|Zfpn1a1|Znfn1a1|hlk-1|mKIAA4227	IKAROS family zinc finger 1	protein-coding
mm_157763.1	chrX	73660048	73660093	-	1	NA	promoter-TSS (NM_012040)	promoter-TSS (NM_012040)	0	NM_001199352	93843	Mm.89564	NM_012040	ENSMUSG00000002012	Pnck	Bstk3|CaMKIbeta2|CaMKlb2|Camk1b|Punc|caMKlb1	pregnancy upregulated non-ubiquitously expressed CaM kinase	protein-coding
mm_24140.1	chr3	88296982	88296992	+	1	NA	promoter-TSS (NM_009836)	promoter-TSS (NM_009836)	-148	NM_009836	12462	Mm.256034	NM_009836	ENSMUSG00000001416	Cct3	AL024092|Cctg|Tcp1-rs3|TriC-P5	chaperonin containing Tcp1, subunit 3 (gamma)	protein-coding
mm_131561.1	chr16	18127608	18127649	+	1	NA	promoter-TSS (NM_022982)	promoter-TSS (NM_022982)	-78	NM_022982	65079	Mm.40149	NM_022982	ENSMUSG00000043811	Rtn4r	NOGOR|NgR|NgR1	reticulon 4 receptor	protein-coding
mm_125388.1	chr15	40877483	40877485	+	1	NA	intron (NM_011766, intron 4 of 7)	intron (NM_011766, intron 4 of 7)	222442	NM_011766	22762	Mm.39496	NM_011766	ENSMUSG00000022306	Zfpm2	B330005D23Rik|FOG-2|FOG2	zinc finger protein, multitype 2	protein-coding
mm_75128.1	chr8	34918523	34918537	-	1	NA	intron (NM_175091, intron 2 of 26)	intron (NM_175091, intron 2 of 26)	47160	NM_175091	21951	Mm.88364	NM_175091	ENSMUSG00000031529	Tnks	4930554K12Rik|AI662855|ARTD5|C86528|D130072O21Rik|TANK1|mTNKS1	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase	protein-coding
mm_4308.1	chr1	171840976	171840989	+	1	NA	intron (NM_001289470, intron 2 of 8)	intron (NM_001289470, intron 2 of 8)	1285	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_126206.1	chr15	78889742	78889790	+	1	NA	exon (NM_145929, exon 11 of 17)	exon (NM_145929, exon 11 of 17)	-2074	NR_105920	102466210		NR_105920	ENSMUSG00000099267	Mir6955	Gm27769|mmu-mir-6955	microRNA 6955	ncRNA
mm_19498.1	chr2	93458817	93458828	-	1	NA	intron (NR_040532, intron 2 of 4)	intron (NR_040532, intron 2 of 4)	3029	NM_001271461	12521	Mm.4261	NM_007656	ENSMUSG00000027215	Cd82	AA682076|AL023070|C33|IA4|Kai1|Tspan27	CD82 antigen	protein-coding
mm_61436.1	chr7	74411620	74411648	+	1	NA	intron (NM_001038643, intron 2 of 10)	intron (NM_001038643, intron 2 of 10)	143146	NM_023908	108116	Mm.425467	NM_023908	ENSMUSG00000025790	Slco3a1	5830414C08Rik|Anr1|MJAM|OATP-D|R75096|Slc21a11	solute carrier organic anion transporter family, member 3a1	protein-coding
mm_40906.1	chr5	75378948	75378970	+	1	NA	Intergenic	RMER17C|LTR|ERVK	-196028	NM_001122733	16590	Mm.247073	NM_021099	ENSMUSG00000005672	Kit	Bs|CD117|Fdc|Gsfsco1|Gsfsco5|Gsfsow3|SCO1|SCO5|SOW3|Ssm|Tr-kit|W|c-KIT	KIT proto-oncogene receptor tyrosine kinase	protein-coding
mm_27424.1	chr3	51518628	51518730	-	1	NA	3' UTR (NM_080793, exon 8 of 8)	3' UTR (NM_080793, exon 8 of 8)	34713	NM_016858	19338	Mm.1664	NM_016858	ENSMUSG00000027739	Rab33b	-	RAB33B, member RAS oncogene family	protein-coding
mm_131565.1	chr16	18213943	18213949	+	1	NA	promoter-TSS (NR_027843)	promoter-TSS (NR_027843)	-83	NR_015575	66779	Mm.387525	NR_015575		4933432I09Rik	-	RIKEN cDNA 4933432I09 gene	ncRNA
mm_169146.1	chr13	62383214	62383232	-	1	NA	promoter-TSS (NM_001162910)	promoter-TSS (NM_001162910)	-49	NM_001162910	100041979	Mm.445930	NM_001162910	ENSMUSG00000094942	Gm3604	-	predicted gene 3604	protein-coding
mm_101638.1	chr11	36432956	36432987	-	1	NA	intron (NM_011856, intron 2 of 28)	intron (NM_011856, intron 2 of 28)	-452882	NM_170779	211652	Mm.31267	NM_170779	ENSMUSG00000018849	Wwc1	AA408228|AU017197|BC037006|Kibra|mKIAA0869	WW, C2 and coiled-coil domain containing 1	protein-coding
mm_6670.1	chr1	80340502	80340512	-	1	NA	5' UTR (NM_016716, exon 1 of 16)	5' UTR (NM_016716, exon 1 of 16)	183	NM_001313728	26554	Mm.12665	NM_016716	ENSMUSG00000004364	Cul3	KIAA0617	cullin 3	protein-coding
mm_62889.1	chr7	115171989	115172003	+	1	NA	Intergenic	Intergenic	220722	NR_040319	101786	Mm.395157	NR_040317	ENSMUSG00000108379	A730082K24Rik	AU044236	RIKEN cDNA A730082K24 gene	ncRNA
mm_148241.1	chr18	80609712	80609723	-	1	NA	intron (NM_198429, intron 9 of 9)	intron (NM_198429, intron 9 of 9)	-65171	NR_028424	100039348	Mm.254722	NR_028424		Gm2176	A430076E10Rik	glucosamine-6-phosphate deaminase 1 pseudogene	pseudo
mm_59300.1	chr7	25155956	25155981	+	1	NA	intron (NR_045847, intron 2 of 2)	intron (NR_045847, intron 2 of 2)	899	NR_045848	434147	Mm.59171	NM_001033781	ENSMUSG00000074274	D930028M14Rik	EG434147	RIKEN cDNA D930028M14 gene	ncRNA
mm_13935.1	chr2	121140408	121140461	+	1	NA	promoter-TSS (NM_001290812)	promoter-TSS (NM_001290812)	6	NM_001290812	75894	Mm.384805	NM_029475	ENSMUSG00000027259	Adal	4930578F03Rik	adenosine deaminase-like	protein-coding
mm_44120.1	chr5	149441883	149441918	+	1	NA	intron (NM_001310765, intron 1 of 5)	intron (NM_001310765, intron 1 of 5)	2240	NM_001310765	75860	Mm.159605	NM_029464	ENSMUSG00000029660	Tex26	4930588N13Rik	testis expressed 26	protein-coding
mm_44113.1	chr5	149427119	149427160	+	1	NA	intron (NM_027519, intron 3 of 4)	intron (NM_027519, intron 3 of 4)	-12521	NM_029464	75860	Mm.159605	NM_029464	ENSMUSG00000029660	Tex26	4930588N13Rik	testis expressed 26	protein-coding
mm_32664.1	chr4	115242041	115242048	+	1	NA	promoter-TSS (NM_001100183)	promoter-TSS (NM_001100183)	-40	NM_001100183	230639	Mm.466610	NM_001100183	ENSMUSG00000083138	Cyp4a29	Cyp4a29-ps|OTTMUSG00000008612	cytochrome P450, family 4, subfamily a, polypeptide 29	protein-coding
mm_161294.1	chr14	26534468	26534468	-	1	NA	5' UTR (NM_032008, exon 1 of 23)	5' UTR (NM_032008, exon 1 of 23)	156	NM_032008	83997	Mm.36769	NM_032008	ENSMUSG00000021870	Slmap	D330001L02Rik|Miranda|Slap|mKIAA1601	sarcolemma associated protein	protein-coding
mm_6984.1	chr1	86357074	86357149	-	1	NA	promoter-TSS (NR_002851)	promoter-TSS (NR_002851)	-784	NR_002851	80828		NR_002851	ENSMUSG00000064823	Snord82	Rnu82|U82|Z25	small nucleolar RNA, C/D box 82	snoRNA
mm_22064.1	chr2	168670393	168670425	-	1	NA	intron (NM_001289446, intron 13 of 27)	intron (NM_001289446, intron 13 of 27)	-29650	NR_105971	102466784		NR_105971	ENSMUSG00000105496	Mir7004	mmu-mir-7004	microRNA 7004	ncRNA
mm_16348.1	chr2	174346358	174346370	+	1	NA	non-coding (NR_003258, exon 13 of 13)	non-coding (NR_003258, exon 13 of 13)	16275	NM_001077510	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_64593.1	chr7	3201151	3201158	-	1	NA	Intergenic	Intergenic	-17472	NR_029640	100049710		NR_029640	ENSMUSG00000077815	Mir290a	Mir290|Mirn290|mir-290a|mmu-miR-290|mmu-mir-290a	microRNA 290a	ncRNA
mm_101265.1	chr11	21238174	21238176	-	1	NA	promoter-TSS (NM_001290628)	promoter-TSS (NM_001290628)	-857	NM_139061	245944	Mm.170103	NM_139061	ENSMUSG00000020128	Vps54	Hcc8|Vps54l|mSLP8|wr	VPS54 GARP complex subunit	protein-coding
mm_142059.1	chr17	35669874	35669892	-	1	NA	intron (NM_010364, intron 9 of 13)	intron (NM_010364, intron 9 of 13)	-2291	NM_175137	68915	Mm.32002	NM_175137	ENSMUSG00000038838	Vars2	1190004I24Rik|Vars2l|mKIAA1885	valyl-tRNA synthetase 2, mitochondrial	protein-coding
mm_40539.1	chr5	57978031	57978058	+	1	NA	intron (NM_001310608, intron 3 of 3)	intron (NM_001310608, intron 3 of 3)	259963	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_98320.1	chr11	90249566	90249574	+	1	NA	promoter-TSS (NM_026178)	promoter-TSS (NM_026178)	94	NM_026178	67468	Mm.277518	NM_026178	ENSMUSG00000003948	Mmd	1200017E07Rik|1810073C06Rik|AA690185	monocyte to macrophage differentiation-associated	protein-coding
mm_41894.1	chr5	105518963	105519023	+	1	NA	promoter-TSS (NM_133897)	promoter-TSS (NM_133897)	-478	NM_133897	100604	Mm.319847	NM_133897	ENSMUSG00000054720	Lrrc8c	AD158|AI326115|E430036I04Rik|fad158	leucine rich repeat containing 8 family, member C	protein-coding
mm_40110.1	chr5	34821143	34821146	+	1	NA	intron (NM_010414, intron 18 of 66)	intron (NM_010414, intron 18 of 66)	59404	NM_010414	15194	Mm.209071	NM_010414	ENSMUSG00000029104	Htt	AI256365|C430023I11Rik|Hd|Hdh|IT15	huntingtin	protein-coding
mm_125165.1	chr15	31268294	31268323	+	1	NA	intron (NM_146057, intron 2 of 3)	intron (NM_146057, intron 2 of 3)	43923	NM_146057	223453	Mm.222867	NM_146057	ENSMUSG00000039168	Dap	4921531N22Rik|AI789753|AU040360	death-associated protein	protein-coding
mm_81606.1	chr9	110661690	110661694	+	1	NA	intron (NM_028312, intron 1 of 6)	intron (NM_028312, intron 1 of 6)	5189	NM_028312	72654	Mm.249115	NM_028312	ENSMUSG00000019659	Ccdc12	2700094L05Rik|C76605	coiled-coil domain containing 12	protein-coding
mm_158365.1	chrX	134964696	134964726	-	1	NA	promoter-TSS (NM_031259)	promoter-TSS (NM_031259)	43	NM_001289735	83454	Mm.103155	NM_031259	ENSMUSG00000009941	Nxf2	4930455N06Rik|Nxf-b	nuclear RNA export factor 2	protein-coding
mm_128808.1	chr15	66969633	66969647	-	1	NA	promoter-TSS (NM_008681)	promoter-TSS (NM_008681)	1	NM_008681	17988	Mm.30837	NM_008681	ENSMUSG00000005125	Ndrg1	CAP43|CMT4D|DRG1|HMSNL|NMSL|Ndr1|Ndrl|PROXY1|RTP|TDD5	N-myc downstream regulated gene 1	protein-coding
mm_2962.1	chr1	132880507	132880517	+	1	NA	5' UTR (NM_010732, exon 1 of 2)	5' UTR (NM_010732, exon 1 of 2)	157	NM_010732	16980	Mm.39640	NM_010732	ENSMUSG00000026443	Lrrn2	5730406J09Rik|NLRR-2	leucine rich repeat protein 2, neuronal	protein-coding
mm_108821.1	chr12	95695514	95695526	+	1	NA	intron (NM_201518, intron 1 of 1)	CpG	3294	NM_201518	399558	Mm.341948	NM_201518	ENSMUSG00000047414	Flrt2	-	fibronectin leucine rich transmembrane protein 2	protein-coding
mm_144546.1	chr18	29333415	29333426	+	1	NA	Intergenic	Intergenic	-108780	NR_045395	78199	Mm.243850	NR_045395		4930527G23Rik	-	RIKEN cDNA 4930527G23 gene	ncRNA
mm_153074.1	chr19	32259955	32259967	-	1	NA	intron (NM_144792, intron 3 of 9)	ORR1B2|LTR|ERVL-MaLR	-48948	NM_001168526	208449	Mm.329810	NM_144792	ENSMUSG00000040451	Sgms1	9530058O11Rik|AI841905|C80702|Mob|Sms1|Sor1|Tmem23	sphingomyelin synthase 1	protein-coding
mm_104386.1	chr11	94474387	94474404	-	1	NA	promoter-TSS (NM_001177890)	promoter-TSS (NM_001177890)	-197	NM_001112813	12291	Mm.29585	NM_009783	ENSMUSG00000020866	Cacna1g	Cav3.1d|[a]1G|a1G|alpha-1G|mKIAA1123	calcium channel, voltage-dependent, T type, alpha 1G subunit	protein-coding
mm_101334.1	chr11	23497868	23497962	-	1	NA	5' UTR (NM_172391, exon 1 of 9)	5' UTR (NM_172391, exon 1 of 9)	124	NM_001290655	268390	Mm.13148	NM_172391	ENSMUSG00000020288	Ahsa2	-	AHA1, activator of heat shock protein ATPase 2	protein-coding
mm_7867.1	chr1	132634206	132634222	-	1	NA	exon (NM_001160317, exon 6 of 28)	exon (NM_001160317, exon 6 of 28)	8644	NM_001160316	269116	Mm.326702	NM_182716	ENSMUSG00000026442	Nfasc	AA387016|D430023G06Rik|NF|mKIAA0756	neurofascin	protein-coding
mm_115091.1	chr13	102706847	102706849	+	1	NA	TTS (NM_008533)	TTS (NM_008533)	13290	NM_008533	17079	Mm.373974	NM_008533	ENSMUSG00000021624	Cd180	F630107B15|Ly78|RP105	CD180 antigen	protein-coding
mm_14132.1	chr2	126034968	126034980	+	1	NA	intron (NM_008008, intron 1 of 3)	intron (NM_008008, intron 1 of 3)	316	NM_008008	14178	Mm.330557	NM_008008	ENSMUSG00000027208	Fgf7	Kgf	fibroblast growth factor 7	protein-coding
mm_139745.1	chr17	63424696	63424699	+	1	NA	intron (NM_015794, intron 4 of 8)	intron (NM_015794, intron 4 of 8)	75883	NM_015794	50758	Mm.136366	NM_015794	ENSMUSG00000023965	Fbxl17	6330576B01Rik|AI452053|BB073797|C130023C01Rik|Fbx13|Fbxo13	F-box and leucine-rich repeat protein 17	protein-coding
mm_105467.1	chr11	105406715	105406718	-	1	NA	intron (NM_001039242, intron 5 of 5)	intron (NM_001039242, intron 5 of 5)	50019	NM_172568	632687	Mm.121570	NM_172568	ENSMUSG00000078627	March10	4933417C16Rik|AV039223|OTTMUSG00000002847|Rnf190	membrane-associated ring finger (C3HC4) 10	protein-coding
mm_36077.1	chr4	58206349	58206359	-	1	NA	exon (NM_022814, exon 1 of 48)	exon (NM_022814, exon 1 of 48)	242	NM_022814	64817	Mm.261024	NM_022814	ENSMUSG00000028369	Svep1	1110021D17Rik|4833413O10Rik|AA387071|D430029O09Rik|Polydom	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	protein-coding
mm_145608.1	chr18	61096788	61096800	+	1	NA	Intergenic	Intergenic	-8778	NM_001037859	12978	Mm.22574	NM_007779	ENSMUSG00000024621	Csf1r	AI323359|CD115|CSF-1R|Csfmr|Fim-2|Fim2|Fms|M-CSF-R|M-CSFR	colony stimulating factor 1 receptor	protein-coding
mm_125435.1	chr15	44457499	44457517	+	1	NA	promoter-TSS (NM_138674)	promoter-TSS (NM_138674)	-45	NM_138674	192190	Mm.211494	NM_138674	ENSMUSG00000038725	Pkhd1l1	AB055648|PKHDL1	polycystic kidney and hepatic disease 1-like 1	protein-coding
mm_98509.1	chr11	94952292	94952305	+	1	NA	3' UTR (NM_007742, exon 51 of 51)	3' UTR (NM_007742, exon 51 of 51)	-15295	NM_018792	54388	Mm.30482	NM_018792	ENSMUSG00000038994	Hils1	H1.9|TISP64	histone H1-like protein in spermatids 1	protein-coding
mm_10287.1	chr2	10165686	10165689	+	1	NA	intron (NM_172471, intron 2 of 13)	ID_B1|SINE|B4	12144	NM_172471	209378	Mm.313876	NM_172471	ENSMUSG00000025780	Itih5	4631408O11Rik|5430408M01Rik|E130106B02	inter-alpha (globulin) inhibitor H5	protein-coding
mm_159858.1	chr5	139215208	139215208	+	1	NA	promoter-TSS (NM_001256118)	promoter-TSS (NM_001256118)	50	NM_001256116	77053	Mm.210845	NM_024451	ENSMUSG00000036817	Sun1	4632417G13Rik|5730434D03Rik|Unc84a|mKIAA0810	Sad1 and UNC84 domain containing 1	protein-coding
mm_104423.1	chr11	94937978	94937988	-	1	NA	exon (NM_007742, exon 2 of 51)	exon (NM_007742, exon 2 of 51)	1759	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_158923.1	chr1	59256770	59256770	+	1	NA	promoter-TSS (NM_001033373)	promoter-TSS (NM_001033373)	-137	NM_001033373	271697	Mm.297713	NM_001033373	ENSMUSG00000026023	Cdk15	Als2cr7|Pftk2	cyclin-dependent kinase 15	protein-coding
mm_78148.1	chr9	21003284	21003302	+	1	NA	exon (NM_023167, exon 3 of 9)	exon (NM_023167, exon 3 of 9)	556	NM_023167	66163	Mm.427576	NM_023167	ENSMUSG00000003299	Mrpl4	1110017G11Rik	mitochondrial ribosomal protein L4	protein-coding
mm_66870.1	chr7	57387160	57387170	-	1	NA	promoter-TSS (NM_008074)	promoter-TSS (NM_008074)	-107	NR_033504	791383	Mm.403104	NR_033504	ENSMUSG00000055048	Gm9962	ENSMUSG00000055048	predicted gene 9962	ncRNA
mm_4299.1	chr1	171799616	171799627	+	1	NA	exon (NM_013730, exon 7 of 7)	exon (NM_013730, exon 7 of 7)	32489	NM_013730	27218	Mm.103648	NM_013730	ENSMUSG00000015316	Slamf1	4933415F16|AA177906|CD150|CDw150|ESTM51|IPO-3|Slam	signaling lymphocytic activation molecule family member 1	protein-coding
mm_156133.1	chrX	123103490	123103500	+	1	NA	promoter-TSS (NM_028426)	promoter-TSS (NM_028426)	-28	NM_001310652	73061	Mm.292979	NM_028426	ENSMUSG00000079450	Cldn34c1	3110007F17Rik	claudin 34C1	protein-coding
mm_75549.1	chr8	57619793	57619797	-	1	NA	intron (NM_001167981, intron 1 of 11)	intron (NM_001167981, intron 1 of 11)	-31958	NR_040698	100502619	Mm.393851	NR_040698		AW046200	-	expressed sequence AW046200	ncRNA
mm_131302.1	chr16	11420587	11420598	+	1	NA	intron (NM_001290148, intron 3 of 13)	intron (NM_001290148, intron 3 of 13)	14944	NM_001290148	74478	Mm.325831	NM_028964	ENSMUSG00000071669	Snx29	4933437K13Rik|ENSMUSG00000079738|Gm11170|Gm1737|Gm930|Rundc2a	sorting nexin 29	protein-coding
mm_106011.1	chr11	115843982	115843986	-	1	NA	intron (NM_145438, intron 3 of 25)	intron (NM_145438, intron 3 of 25)	19926	NM_001252532	217325	Mm.290450	NM_145438	ENSMUSG00000020782	Llgl2	9130006H11Rik|Llglh2	lethal giant larvae homolog 2 (Drosophila)	protein-coding
mm_79910.1	chr9	65460985	65460993	+	1	NA	promoter-TSS (NM_138584)	promoter-TSS (NM_138584)	52	NM_138584	27965	Mm.272475	NM_138584	ENSMUSG00000032388	Spg21	ACP33|BM-019|C78576|D9Wsu18e|GL010|MAST	spastic paraplegia 21 homolog (human)	protein-coding
mm_127959.1	chr15	11906099	11906115	-	1	NA	promoter-TSS (NM_001039181)	promoter-TSS (NM_001039181)	-418	NR_131059	381002	Mm.441967	NR_131059		Gm5144	-	predicted gene 5144	ncRNA
mm_64793.1	chr7	6662339	6662345	-	1	NA	promoter-TSS (NR_131759)	promoter-TSS (NR_131759)	26	NR_131759	76637	Mm.159751	NR_131759	ENSMUSG00000108113	Zim2	1700116N21Rik	zinc finger, imprinted 2	ncRNA
mm_42795.1	chr5	121660878	121660896	+	1	NA	promoter-TSS (NM_001289544)	promoter-TSS (NM_001289544)	18	NM_001289544	72399	Mm.153372	NM_028227	ENSMUSG00000029458	Brap	3010002G07Rik|BRAP2|IMP	BRCA1 associated protein	protein-coding
mm_117170.1	chr13	62888128	62888149	-	1	NA	5' UTR (NM_019395, exon 1 of 7)	5' UTR (NM_019395, exon 1 of 7)	144	NM_019395	14121	Mm.423078	NM_019395	ENSMUSG00000069805	Fbp1	Fbp-2|Fbp2|Fbp3	fructose bisphosphatase 1	protein-coding
mm_121835.1	chr14	20538178	20538181	-	1	NA	intron (NM_001310427, intron 1 of 12)	intron (NM_001310427, intron 1 of 12)	-8114	NR_033571	75602	Mm.437061	NR_033571	ENSMUSG00000084925	1810062O18Rik	-	RIKEN cDNA 1810062O18 gene	ncRNA
mm_160972.1	chr11	100193030	100193030	-	1	NA	exon (NM_201255, exon 1 of 8)	exon (NM_201255, exon 1 of 8)	216	NM_201255	107656	Mm.445335	NM_201255	ENSMUSG00000051617	Krt9	EPPK|K9|Krt1-9	keratin 9	protein-coding
mm_120606.1	chr14	70130124	70130130	+	1	NA	intron (NM_021328, intron 6 of 8)	intron (NM_021328, intron 6 of 8)	23664	NM_146055	219158	Mm.218284	NM_146055	ENSMUSG00000033712	Ccar2	2610301G19Rik|Dbc1|mKIAA1967	cell cycle activator and apoptosis regulator 2	protein-coding
mm_103483.1	chr11	76497773	76497794	-	1	NA	intron (NM_198895, intron 2 of 22)	intron (NM_198895, intron 2 of 22)	-3288	NM_001346670	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_117907.1	chr13	99430387	99430398	-	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-17566	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_152680.1	chr19	15962523	15962534	-	1	NA	intron (NM_198019, intron 11 of 14)	intron (NM_198019, intron 11 of 14)	22461	NM_198019	208518	Mm.105652	NM_198019	ENSMUSG00000041491	Cep78	5730599I05Rik|D030027P05	centrosomal protein 78	protein-coding
mm_165527.1	chr2	178142205	178142217	+	1	NA	5' UTR (NM_028806, exon 1 of 13)	5' UTR (NM_028806, exon 1 of 13)	278	NM_028806	74189	Mm.44413	NM_028806	ENSMUSG00000027525	Phactr3	1500003N10Rik|4930415A02Rik|H17739|Scapin1|Scapinin|mKIAA4224	phosphatase and actin regulator 3	protein-coding
mm_137382.1	chr17	25773770	25773778	+	1	NA	promoter-TSS (NM_026238)	promoter-TSS (NM_026238)	-2	NM_026238	67563	Mm.24201	NM_026238	ENSMUSG00000002280	Narfl	9030612I22Rik|AI504405|PRN	nuclear prelamin A recognition factor-like	protein-coding
mm_1638.1	chr1	74529249	74529252	+	1	NA	3' UTR (NM_021383, exon 8 of 8)	3' UTR (NM_021383, exon 8 of 8)	-13639	NM_001081456	18802	Mm.290731	NM_148937	ENSMUSG00000026173	Plcd4	4921507K24Rik	phospholipase C, delta 4	protein-coding
mm_49106.1	chr6	8259328	8259342	+	1	NA	promoter-TSS (NM_026632)	promoter-TSS (NM_026632)	47	NM_001302353	100036521	Mm.446106	NM_001302353	ENSMUSG00000089862	Umad1	Gm16039|OTTMUSG00000029336	UMAP1-MVP12 associated (UMA) domain containing 1	protein-coding
mm_45293.1	chr5	65046135	65046143	-	1	NA	Intergenic	Intergenic	-61429	NM_001347355	71778	Mm.10281	NM_175174	ENSMUSG00000054920	Klhl5	1300013C10Rik	kelch-like 5	protein-coding
mm_39593.1	chr5	23500448	23500462	+	1	NA	exon (NM_026984, exon 24 of 26)	exon (NM_026984, exon 24 of 26)	66026	NM_026984	69188	Mm.205190	NM_026984	ENSMUSG00000029004	Kmt2e	1810033J14Rik|9530077A04Rik|D230038D11Rik|Mll5|NKp44L	lysine (K)-specific methyltransferase 2E	protein-coding
mm_39895.1	chr5	31196712	31196718	+	1	NA	intron (NM_153680, intron 8 of 14)	intron (NM_153680, intron 8 of 14)	3411	NM_153680	266781	Mm.6118	NM_153680	ENSMUSG00000029146	Snx17	5830447M19Rik|AI790646|D5Ertd260e|b2b1625.1Clo|mKIAA0064	sorting nexin 17	protein-coding
mm_33224.1	chr4	126753789	126753835	+	1	NA	promoter-TSS (NM_001035526)	promoter-TSS (NM_001035526)	42	NM_001035526	100317	Mm.206206	NM_133886	ENSMUSG00000028830	AU040320	A730047D20Rik|AAVR|Kiaa0319l	expressed sequence AU040320	protein-coding
mm_90263.1	chr10	122678656	122678664	+	1	NA	promoter-TSS (NR_106182)	promoter-TSS (NR_106182)	-102	NM_176919	319468	Mm.489703	NM_176919	ENSMUSG00000034613	Ppm1h	A430075L18Rik|ARHCL1|C030002B11Rik	protein phosphatase 1H (PP2C domain containing)	protein-coding
mm_59052.1	chr7	19411087	19411101	+	1	NA	promoter-TSS (NM_007710)	promoter-TSS (NM_007710)	0	NM_007710	12715	Mm.2375	NM_007710	ENSMUSG00000030399	Ckm	Ckmm|M-CK|MCK	creatine kinase, muscle	protein-coding
mm_46972.1	chr5	115194183	115194200	-	1	NA	exon (NM_001310712, exon 1 of 6)	exon (NM_001310712, exon 1 of 6)	190	NM_001310712	29867	Mm.38551	NM_013879	ENSMUSG00000029544	Cabp1	caldendrin	calcium binding protein 1	protein-coding
mm_99445.1	chr11	102433474	102433514	+	1	NA	exon (NM_008175, exon 4 of 13)	exon (NM_008175, exon 4 of 13)	3172	NM_008175	14824	Mm.1568	NM_008175	ENSMUSG00000034708	Grn	Pgrn|epithelin	granulin	protein-coding
mm_160531.1	chr9	38498451	38498451	+	1	NA	promoter-TSS (NM_146805)	promoter-TSS (NM_146805)	-220	NM_146805	258801	Mm.223228	NM_146805	ENSMUSG00000094810	Olfr907	MOR165-5	olfactory receptor 907	protein-coding
mm_90863.1	chr10	8886016	8886030	-	1	NA	promoter-TSS (NM_175155)	promoter-TSS (NM_175155)	47	NM_175155	70097	Mm.338275	NM_175155	ENSMUSG00000015305	Sash1	1100001C18Rik|2500002E12Rik|A330076K04Rik|mKIAA0790	SAM and SH3 domain containing 1	protein-coding
mm_143253.1	chr17	65510055	65510084	-	1	NA	intron (NM_001008973, intron 2 of 14)	RMER19B2|LTR|ERVK	30713	NM_001008973	381107	Mm.141275	NM_001008973	ENSMUSG00000045036	Tmem232	E130009J12Rik|Gm940|Tes13-L|Tes13-S	transmembrane protein 232	protein-coding
mm_129502.1	chr15	78877086	78877126	-	1	NA	promoter-TSS (NM_145929)	promoter-TSS (NM_145929)	-84	NM_145929	106039	Mm.251331	NM_145929	ENSMUSG00000033128	Gga1	4930406E12Rik|AU016030|AW209092	golgi associated, gamma adaptin ear containing, ARF binding protein 1	protein-coding
mm_107910.1	chr12	70989982	70990004	+	1	NA	intron (NM_001310596, intron 7 of 10)	B3A|SINE|B2	15370	NM_011184	19167	Mm.296338	NM_011184	ENSMUSG00000060073	Psma3	Lmpc8	proteasome (prosome, macropain) subunit, alpha type 3	protein-coding
mm_171854.1	chr5	17608600	17608614	+	1	NA	intron (NM_013657, intron 2 of 17)	L1Md_T|LINE|L1	33791	NM_013657	20348	Mm.5071	NM_013657	ENSMUSG00000028780	Sema3c	1110036B02Rik|SemE|Semae	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	protein-coding
mm_34784.1	chr4	154170732	154170742	+	1	NA	promoter-TSS (NM_001162977)	promoter-TSS (NM_001162977)	24	NM_001162977	230971	Mm.275216	NM_172273	ENSMUSG00000057751	Megf6	2600001P17Rik|Egfl3	multiple EGF-like-domains 6	protein-coding
mm_137323.1	chr17	24896610	24896628	+	1	NA	TTS (NM_001163447)	TTS (NM_001163447)	119	NM_019730	79059	Mm.430765	NM_019730	ENSMUSG00000073435	Nme3	1810009F08Rik|AI413736|DR-nm23|Ndk3|Nm23-DR|Nm23-M3	NME/NM23 nucleoside diphosphate kinase 3	protein-coding
mm_11197.1	chr2	29125144	29125178	+	1	NA	5' UTR (NM_198033, exon 1 of 26)	5' UTR (NM_198033, exon 1 of 26)	169	NM_198033	269254	Mm.41867	NM_198033	ENSMUSG00000043535	Setx	A130090N03|A930037J23Rik|AOA2|AW060766|Als4|SCAR1|Sen1|mKIAA0625	senataxin	protein-coding
mm_50567.1	chr6	49049883	49049906	+	1	NA	intron (NM_053110, intron 6 of 10)	RSINE1|SINE|B4	13376	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_89986.1	chr10	111993834	111993841	+	1	NA	intron (NM_028608, intron 1 of 5)	intron (NM_028608, intron 1 of 5)	3427	NM_028608	73690	Mm.173790	NM_028608	ENSMUSG00000056888	Glipr1	2410114O14Rik|RTVP-1|RTVP1|mRTVP-1	GLI pathogenesis-related 1 (glioma)	protein-coding
mm_58750.1	chr7	13309581	13309605	+	1	NA	intron (NM_001199310, intron 27 of 28)	intron (NM_001199310, intron 27 of 28)	-16074	NM_001168504	232889	Mm.223639	NM_001004762	ENSMUSG00000033847	Pla2g4c	D7Ertd445e	phospholipase A2, group IVC (cytosolic, calcium-independent)	protein-coding
mm_1346.1	chr1	66302097	66302103	+	1	NA	intron (NM_001039934, intron 3 of 14)	intron (NM_001039934, intron 3 of 14)	-19624	NM_001310634	17756	Mm.256966	NM_008632	ENSMUSG00000015222	Map2	G1-397-34|MAP-2|Mtap-2|Mtap2|repro4	microtubule-associated protein 2	protein-coding
mm_137339.1	chr17	25135947	25135951	+	1	NA	promoter-TSS (NM_001317404)	promoter-TSS (NM_001317404)	-682	NM_001317404	26373	Mm.270587	NM_011930	ENSMUSG00000036636	Clcn7	ClC-7|D17Wsu51e	chloride channel, voltage-sensitive 7	protein-coding
mm_48526.1	chr5	142903602	142903613	-	1	NA	3' UTR (NM_007393, exon 6 of 6)	3' UTR (NM_007393, exon 6 of 6)	3147	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_21700.1	chr2	164549340	164549350	-	1	NA	Intergenic	Intergenic	-13371	NM_026323	67701	Mm.27289	NM_026323	ENSMUSG00000017723	Wfdc2	1600023A02Rik|HE4|WAP5	WAP four-disulfide core domain 2	protein-coding
mm_139569.1	chr17	57011760	57011794	+	1	NA	promoter-TSS (NM_133801)	promoter-TSS (NM_133801)	-489	NM_133801	98053	Mm.24632	NM_133801	ENSMUSG00000002658	Gtf2f1	2810405L04Rik|C76800|RAP74	general transcription factor IIF, polypeptide 1	protein-coding
mm_65704.1	chr7	28377924	28377940	-	1	NA	exon (NM_011756, exon 2 of 2)	exon (NM_011756, exon 2 of 2)	1296	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_39162.1	chr4	155624286	155624321	-	1	NA	promoter-TSS (NM_007661)	promoter-TSS (NM_007661)	452	NR_040441	100502734	Mm.306018	NR_040441	ENSMUSG00000086682	Gm16023	OTTMUSG00000029160	predicted gene 16023	ncRNA
mm_90893.1	chr10	10339729	10339730	-	1	NA	exon (NM_001127353, exon 36 of 37)	exon (NM_001127353, exon 36 of 37)	132585	NM_001127353	215772	Mm.246573	NM_172547	ENSMUSG00000050994	Adgb	9130014G24Rik	androglobin	protein-coding
mm_153218.1	chr19	34747454	34747468	-	1	NA	promoter-TSS (NM_172838)	promoter-TSS (NM_172838)	-350	NM_172838	240638	Mm.74636	NM_172838	ENSMUSG00000009378	Slc16a12	3230401A21|AW210596	solute carrier family 16 (monocarboxylic acid transporters), member 12	protein-coding
mm_40471.1	chr5	53998375	53998442	+	1	NA	promoter-TSS (NM_001081103)	promoter-TSS (NM_001081103)	-115	NM_001081103	116873	Mm.265985	NM_054083	ENSMUSG00000039156	Stim2	-	stromal interaction molecule 2	protein-coding
mm_99221.1	chr11	101033912	101033954	+	1	NA	exon (NM_001243049, exon 9 of 21)	exon (NM_001243049, exon 9 of 21)	3593	NR_105893	102466767		NR_105893	ENSMUSG00000098415	Mir6928	Gm27728|mmu-mir-6928	microRNA 6928	ncRNA
mm_104284.1	chr11	90002847	90002876	-	1	NA	promoter-TSS (NM_001316372)	promoter-TSS (NM_001316372)	33	NM_008796	18559	Mm.5062	NM_008796	ENSMUSG00000020553	Pctp	PC-TP|StarD2	phosphatidylcholine transfer protein	protein-coding
mm_89285.1	chr10	87880815	87880825	+	1	NA	intron (NM_001314010, intron 3 of 4)	intron (NM_001314010, intron 3 of 4)	19709	NM_001111276	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_86846.1	chr10	21592136	21592151	+	1	NA	Intergenic	ORR1C1|LTR|ERVL-MaLR	-1002	NR_027968	67692	Mm.54306	NM_183266	ENSMUSG00000050844	1700020N01Rik	-	RIKEN cDNA 1700020N01 gene	ncRNA
mm_30279.1	chr3	148861003	148861007	-	1	NA	intron (NM_001081298, intron 3 of 23)	intron (NM_001081298, intron 3 of 23)	93630	NM_001081298	99633	Mm.9776	NM_001081298	ENSMUSG00000028184	Adgrl2	AI450192|CIRL-2|Gm619|Lec1|Lphh1|Lphn2|mKIAA0786	adhesion G protein-coupled receptor L2	protein-coding
mm_118028.1	chr13	101538246	101538270	-	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	-140678	NR_046187	78136	Mm.399065	NR_046187		4922502H24Rik	-	RIKEN cDNA 4922502H24 gene	ncRNA
mm_39956.1	chr5	32135840	32135857	+	1	NA	promoter-TSS (NM_008037)	promoter-TSS (NM_008037)	-624	NM_008037	14284	Mm.24684	NM_008037	ENSMUSG00000029135	Fosl2	Fra-2	fos-like antigen 2	protein-coding
mm_25684.1	chr3	122245477	122245550	+	1	NA	promoter-TSS (NM_008129)	promoter-TSS (NM_008129)	-44	NM_008129	14630	Mm.292676	NM_008129	ENSMUSG00000028124	Gclm	AI649393|Gcmc|Glclr	glutamate-cysteine ligase, modifier subunit	protein-coding
mm_163427.1	chr12	82251585	82251586	+	1	NA	intron (NM_001167983, intron 2 of 23)	intron (NM_001167983, intron 2 of 23)	-59764	NM_172579	217692	Mm.261333	NM_172579	ENSMUSG00000042700	Sipa1l1	4931426N11Rik|AW213287|Spar|mKIAA0440	signal-induced proliferation-associated 1 like 1	protein-coding
mm_162838.1	chr10	84556208	84556240	-	1	NA	Intergenic	Intergenic	-2886	NR_040658	442847	Mm.128292	NR_040658	ENSMUSG00000097076	Platr7	C330046G13Rik	pluripotency associated transcript 7	ncRNA
mm_132509.1	chr16	36962685	36962712	+	1	NA	exon (NM_008225, exon 14 of 14)	exon (NM_008225, exon 14 of 14)	16438	NM_001037321	207215	Mm.211899	NM_001037321	ENSMUSG00000047746	Fbxo40	9830003A13Rik|mKIAA1195	F-box protein 40	protein-coding
mm_4471.1	chr1	173419294	173419344	+	1	NA	Intergenic	Intergenic	-1285	NM_001013779	383619	Mm.131453	NM_001013779	ENSMUSG00000037860	Aim2	Gm1313|Ifi210	absent in melanoma 2	protein-coding
mm_52366.1	chr6	112963369	112963386	+	1	NA	Intergenic	(CAG)n|Simple_repeat|Simple_repeat	-16111	NM_080448	259302	Mm.236401	NM_080448	ENSMUSG00000030257	Srgap3	AI452337|Arhgap14|D130026O08Rik|Gbi|MEGAP|WRP|mKIAA0411	SLIT-ROBO Rho GTPase activating protein 3	protein-coding
mm_140720.1	chr17	15432210	15432220	-	1	NA	non-coding (NR_033586, exon 11 of 11)	non-coding (NR_033586, exon 11 of 11)	35969	NM_024203	67544	Mm.35039	NM_024203	ENSMUSG00000014763	Fam120b	4932442K08Rik|AW049283|AW413338|CCPG|Pgcc1|mKIAA1838	family with sequence similarity 120, member B	protein-coding
mm_126696.1	chr15	85037164	85037176	+	1	NA	5' UTR (NM_133750, exon 1 of 9)	5' UTR (NM_133750, exon 1 of 9)	108	NM_133750	73225	Mm.247535	NM_133750	ENSMUSG00000022434	Fam118a	-	family with sequence similarity 118, member A	protein-coding
mm_84489.1	chr9	66846278	66846299	-	1	NA	3' UTR (NM_173413, exon 8 of 8)	3' UTR (NM_173413, exon 8 of 8)	-11582	NM_026674	68318	Mm.284229	NM_026674	ENSMUSG00000053040	Aph1c	0610008A10Rik|APH-1b|Aph1b	aph1 homolog C, gamma secretase subunit	protein-coding
mm_41849.1	chr5	104439256	104439293	+	1	NA	exon (NM_001204203, exon 6 of 7)	exon (NM_001204203, exon 6 of 7)	3082	NM_001204233	20750	Mm.288474	NM_009263	ENSMUSG00000029304	Spp1	2AR|Apl-1|BNSP|BSPI|Bsp|ETA-1|Eta|OP|Opn|Opnl|Ric|Spp-1	secreted phosphoprotein 1	protein-coding
mm_151132.1	chr19	48332177	48332184	+	1	NA	intron (NM_025696, intron 1 of 26)	intron (NM_025696, intron 1 of 26)	126155	NM_025696	66673	Mm.70980	NM_025696	ENSMUSG00000063434	Sorcs3	6330404A12Rik|AW045579	sortilin-related VPS10 domain containing receptor 3	protein-coding
mm_151231.1	chr19	53749026	53749028	+	1	NA	intron (NM_001170847, intron 1 of 13)	intron (NM_001170847, intron 1 of 13)	71721	NM_001170847	73713	Mm.313695	NM_001170847	ENSMUSG00000043639	Rbm20	1110018J23Rik|2010003H22Rik|AI646761	RNA binding motif protein 20	protein-coding
mm_28845.1	chr3	96708525	96708553	-	1	NA	promoter-TSS (NM_030094)	promoter-TSS (NM_030094)	21	NM_001162925	78373	Mm.423186	NM_030094	ENSMUSG00000028100	Nudt17	2410015C20Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 17	protein-coding
mm_3718.1	chr1	154078025	154078025	+	1	NA	Intergenic	Intergenic	-123162	NM_001204908	100503355	Mm.484410	NM_001204908	ENSMUSG00000066797	Zfp648	ENSMUSG00000066797|Gm10178|Gm203	zinc finger protein 648	protein-coding
mm_158073.1	chrX	101264766	101264772	-	1	NA	promoter-TSS (NM_001317221)	promoter-TSS (NM_001317221)	-777	NM_001317221	245536	Mm.212463	NM_001033362	ENSMUSG00000090141	Gm614	-	predicted gene 614	protein-coding
mm_33738.1	chr4	134121820	134121835	+	1	NA	intron (NR_045571, intron 8 of 13)	intron (NR_045571, intron 8 of 13)	6926	NM_080559	73723	Mm.22240	NM_080559	ENSMUSG00000028843	Sh3bgrl3	1110004L05Rik|AU022188	SH3 domain binding glutamic acid-rich protein-like 3	protein-coding
mm_46414.1	chr5	104094671	104094687	-	1	NA	exon (NM_010097, exon 3 of 11)	exon (NM_010097, exon 3 of 11)	-17071	NM_001163772	100271704	Mm.366664	NM_001163772	ENSMUSG00000091034	Gm17660	Scpppq1	predicted gene, 17660	protein-coding
mm_92944.1	chr10	85102426	85102434	-	1	NA	promoter-TSS (NM_001013028)	promoter-TSS (NM_001013028)	65	NM_010214	14202	Mm.46163	NM_010214	ENSMUSG00000050035	Fhl4	-	four and a half LIM domains 4	protein-coding
mm_14160.1	chr2	126602502	126602512	+	1	NA	intron (NM_008230, intron 7 of 11)	intron (NM_008230, intron 7 of 11)	16171	NM_008230	15186	Mm.18603	NM_008230	ENSMUSG00000027360	Hdc	AW108189|Hdc-a|Hdc-c|Hdc-e|Hdc-s	histidine decarboxylase	protein-coding
mm_12091.1	chr2	60335443	60335445	+	1	NA	intron (NM_013825, intron 15 of 34)	intron (NM_013825, intron 15 of 34)	47787	NM_013825	17076	Mm.2074	NM_013825	ENSMUSG00000026980	Ly75	CD205|DEC-205|DEC205	lymphocyte antigen 75	protein-coding
mm_97778.1	chr11	82180116	82180152	+	1	NA	promoter-TSS (NM_011329)	promoter-TSS (NM_011329)	-322	NM_011329	20290	Mm.1283	NM_011329	ENSMUSG00000020702	Ccl1	BF534335|I-309|Scya1|Tca-3	chemokine (C-C motif) ligand 1	protein-coding
mm_161821.1	chr17	71311477	71311477	-	1	NA	promoter-TSS (NM_145158)	promoter-TSS (NM_145158)	-512	NM_145158	246707	Mm.23462	NM_145158	ENSMUSG00000024053	Emilin2	FOAP-10	elastin microfibril interfacer 2	protein-coding
mm_77796.1	chr9	3030156	3030176	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	8577	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_111090.1	chr12	80436542	80436566	-	1	NA	promoter-TSS (NM_177267)	promoter-TSS (NM_177267)	47	NM_177267	320808	Mm.220310	NM_177267	ENSMUSG00000049106	Dcaf5	9430020B07Rik|AI325023|AI430035|AI848110|AW124614|BCRG2|BCRP2|Wdr22	DDB1 and CUL4 associated factor 5	protein-coding
mm_22295.1	chr2	180273375	180273414	-	1	NA	promoter-TSS (NM_145851)	promoter-TSS (NM_145851)	71	NM_145851	252966	Mm.386884	NM_145851	ENSMUSG00000038990	Cables2	ik3-2	CDK5 and Abl enzyme substrate 2	protein-coding
mm_99820.1	chr11	108682615	108682639	+	1	NA	promoter-TSS (NM_029586)	promoter-TSS (NM_029586)	9	NM_029586	76380	Mm.344071	NM_029586	ENSMUSG00000020728	Cep112	1700001M19Rik|1700029K01Rik|8430407H02Rik|AV043680|AV207351|Ccdc46|Macoco	centrosomal protein 112	protein-coding
mm_121499.1	chr14	121879914	121879931	+	1	NA	promoter-TSS (NR_130999)	promoter-TSS (NR_130999)	-514	NR_130999	78312	Mm.188743	NR_130999	ENSMUSG00000102112	1810041H14Rik	-	RIKEN cDNA 1810041H14 gene	ncRNA
mm_28484.1	chr3	92457290	92457300	-	1	NA	exon (NM_011478, exon 2 of 2)	exon (NM_011478, exon 2 of 2)	1425	NM_001204427	20766	Mm.57092	NM_011478	ENSMUSG00000045539	Sprr3	SPR3	small proline-rich protein 3	protein-coding
mm_21422.1	chr2	158146358	158146373	-	1	NA	promoter-TSS (NM_009373)	promoter-TSS (NM_009373)	27	NM_009373	21817	Mm.330731	NM_009373	ENSMUSG00000037820	Tgm2	G[a]h|TG2|TGase2|tTG|tTGas	transglutaminase 2, C polypeptide	protein-coding
mm_35319.1	chr4	25800084	25800104	-	1	NA	promoter-TSS (NM_010243)	promoter-TSS (NM_010243)	-91	NM_010243	14348	Mm.39101	NM_010243	ENSMUSG00000055373	Fut9	AI746471|AU067636|mFUT9|mFuc-TIX	fucosyltransferase 9	protein-coding
mm_134328.1	chr16	16359017	16359040	-	1	NA	promoter-TSS (NM_152816)	promoter-TSS (NM_152816)	3	NM_152816	74006	Mm.218820	NM_152816	ENSMUSG00000022789	Dnm1l	6330417M19Rik|AI450666|Dlp1|Dnmlp1|Drp1|python	dynamin 1-like	protein-coding
mm_126630.1	chr15	83474669	83474674	+	1	NA	Intergenic	MTC|LTR|ERVL-MaLR	-10065	NM_001159509	23970	Mm.23978	NM_011862	ENSMUSG00000016664	Pacsin2	AI197433	protein kinase C and casein kinase substrate in neurons 2	protein-coding
mm_44782.1	chr5	32133117	32133136	-	1	NA	Intergenic	CpG	-3346	NM_008037	14284	Mm.24684	NM_008037	ENSMUSG00000029135	Fosl2	Fra-2	fos-like antigen 2	protein-coding
mm_10570.1	chr2	18064357	18064408	+	1	NA	promoter-TSS (NM_001252561)	promoter-TSS (NM_001252561)	-203	NM_001252560	17354	Mm.209175	NM_010804	ENSMUSG00000026743	Mllt10	Af10|B130021D15Rik|D630001B22Rik|mKIAA4140	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 10	protein-coding
mm_169332.1	chr14	118925359	118925367	-	1	NA	5' UTR (NM_025943, exon 1 of 22)	5' UTR (NM_025943, exon 1 of 22)	107	NM_025943	66573	Mm.87456	NM_025943	ENSMUSG00000042156	Dzip1	2510025K24Rik|2810422M04Rik	DAZ interacting protein 1	protein-coding
mm_29271.1	chr3	107517322	107517374	-	1	NA	intron (NM_172271, intron 1 of 11)	CpG	670	NM_001293689	229706	Mm.212867	NM_172271	ENSMUSG00000027894	Slc6a17	D130012J15Rik|Ntt4	solute carrier family 6 (neurotransmitter transporter), member 17	protein-coding
mm_3158.1	chr1	135155467	135155481	+	1	NA	3' UTR (NM_026823, exon 7 of 7)	3' UTR (NM_026823, exon 7 of 7)	8640	NM_026823	68724	Mm.174998	NM_026823	ENSMUSG00000026426	Arl8a	1110033P22Rik|Arl10b|gie2	ADP-ribosylation factor-like 8A	protein-coding
mm_27787.1	chr3	75165061	75165061	-	1	NA	Intergenic	Intergenic	-21289	NM_172515	213234	Mm.80075	NM_172515	ENSMUSG00000034151	Zbbx	4931432L23	zinc finger, B-box domain containing	protein-coding
mm_88845.1	chr10	80929816	80929830	+	1	NA	promoter-TSS (NM_008655)	promoter-TSS (NM_008655)	-268	NM_008655	17873	Mm.1360	NM_008655	ENSMUSG00000015312	Gadd45b	AI323528|Myd118	growth arrest and DNA-damage-inducible 45 beta	protein-coding
mm_132116.1	chr16	31664131	31664178	+	1	NA	non-coding (NR_045516, exon 1 of 25)	non-coding (NR_045516, exon 1 of 25)	219	NM_001252434	13383	Mm.382	NM_007862	ENSMUSG00000022770	Dlg1	B130052P05Rik|Dlgh1|E-dlg/SAP97|SAP-97|SAP97|mKIAA4187	discs, large homolog 1 (Drosophila)	protein-coding
mm_108662.1	chr12	86466589	86466596	+	1	NA	intron (NM_011934, intron 1 of 6)	intron (NM_011934, intron 1 of 6)	44948	NM_011934	26380	Mm.235550	NM_011934	ENSMUSG00000021255	Esrrb	Err2|Errb|Estrrb|Nr3b2	estrogen related receptor, beta	protein-coding
mm_30755.1	chr4	15265768	15265782	+	1	NA	promoter-TSS (NM_181401)	promoter-TSS (NM_181401)	-45	NM_181401	100201	Mm.394111	NM_181401	ENSMUSG00000043252	Tmem64	9630015D15Rik|AI790744|AV300874	transmembrane protein 64	protein-coding
mm_105334.1	chr11	102946742	102946751	-	1	NA	promoter-TSS (NM_011795)	promoter-TSS (NM_011795)	-285	NM_011795	23829	Mm.57154	NM_011795	ENSMUSG00000045532	C1ql1	C1qrf|CRF|CTRP14|gliacolin	complement component 1, q subcomponent-like 1	protein-coding
mm_62484.1	chr7	101882747	101882754	+	1	NA	intron (NM_001291353, intron 1 of 5)	intron (NM_001291353, intron 1 of 5)	1425	NM_001291353	75430	Mm.284491	NM_027532	ENSMUSG00000030649	Anapc15	3200002M19Rik|6330414C15Rik|APC15	anaphase prompoting complex C subunit 15	protein-coding
mm_701.1	chr1	40606320	40606330	+	1	NA	intron (NM_177084, intron 4 of 11)	intron (NM_177084, intron 4 of 11)	26098	NM_177084	110895	Mm.108602	NM_177084	ENSMUSG00000026065	Slc9a4	AW990558|D730009J23Rik|NHE4	solute carrier family 9 (sodium/hydrogen exchanger), member 4	protein-coding
mm_22965.1	chr3	32529580	32529628	+	1	NA	5' UTR (NM_024200, exon 1 of 18)	5' UTR (NM_024200, exon 1 of 18)	122	NM_024200	67414	Mm.290414	NM_024200	ENSMUSG00000027668	Mfn1	2310002F04Rik|6330416C07Rik|D3Ertd265e|HR2|mKIAA4032	mitofusin 1	protein-coding
mm_4154.1	chr1	171019968	171019984	+	1	NA	exon (NM_144559, exon 3 of 5)	exon (NM_144559, exon 3 of 5)	1050	NM_144559	246256	Mm.251254	NM_144559	ENSMUSG00000059089	Fcgr4	4833442P21Rik|CD16-2|FcgRIV|FcgammaRIV|Fcgr3a|Fcrl3	Fc receptor, IgG, low affinity IV	protein-coding
mm_56328.1	chr6	92534856	92534890	-	1	NA	promoter-TSS (NM_001134459)	promoter-TSS (NM_001134459)	-12	NM_001134459	243548	Mm.248820	NM_001081146	ENSMUSG00000030020	Prickle2	6230400G14Rik|6720451F06Rik|mpk2	prickle planar cell polarity protein 2	protein-coding
mm_71246.1	chr8	40914004	40914082	+	1	NA	exon (NM_001044740, exon 10 of 12)	exon (NM_001044740, exon 10 of 12)	-12190	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_76540.1	chr8	87960663	87960694	-	1	NA	Intergenic	CpG-14330	-1083	NM_033327	94187	Mm.23452	NM_033327	ENSMUSG00000045333	Zfp423	Ebfaz|Roaz|Zfp104|Znf423|ataxia1|mKIAA0760|nur12	zinc finger protein 423	protein-coding
mm_15975.1	chr2	166194234	166194279	+	1	NA	Intergenic	MLTR73|LTR|ERV1	-38573	NM_028072	72043	Mm.1011	NM_028072	ENSMUSG00000006800	Sulf2	2010004N24Rik|AU020235|MSulf-2|mKIAA1247	sulfatase 2	protein-coding
mm_90119.1	chr10	117278137	117278168	+	1	NA	exon (NM_017372, exon 4 of 4)	exon (NM_017372, exon 4 of 4)	4120	NM_017372	17105	Mm.45436	NM_017372	ENSMUSG00000069516	Lyz2	AI326280|Lys|Lysm|Lyzf2|Lyzs|Lzm|Lzm-s1|Lzp	lysozyme 2	protein-coding
mm_86313.1	chr9	122859396	122859401	-	1	NA	intron (NM_173364, intron 2 of 6)	intron (NM_173364, intron 2 of 6)	6608	NM_173364	235682	Mm.326477	NM_173364	ENSMUSG00000047036	Zfp445	AW610627|ZNF168|Znf445|mszf29|mszf50	zinc finger protein 445	protein-coding
mm_140552.1	chr17	7397301	7397308	-	1	NA	Intergenic	Intergenic	-11999	NM_001142539	667055	Mm.327371	NM_001142539	ENSMUSG00000056133	Gm9992	ENSMUSG00000056133	predicted gene 9992	protein-coding
mm_164127.1	chr15	39910730	39910731	-	1	NA	intron (NM_172814, intron 1 of 6)	Lx7|LINE|L1	33027	NM_172814	239393	Mm.39874	NM_172814	ENSMUSG00000022305	Lrp12	AI848829|C820005L12Rik|LRP-12	low density lipoprotein-related protein 12	protein-coding
mm_79363.1	chr9	54469637	54469645	+	1	NA	intron (NM_172771, intron 6 of 43)	L1M2|LINE|L1	31985	NM_172771	235380	Mm.93636	NM_172771	ENSMUSG00000041268	Dmxl2	6330586A12|6430411K14Rik|E130119P06Rik|mKIAA0856	Dmx-like 2	protein-coding
mm_66579.1	chr7	45336548	45336562	-	1	NA	exon (NM_010473, exon 1 of 6)	exon (NM_010473, exon 1 of 6)	1286	NM_010473	15464	Mm.39968	NM_010473	ENSMUSG00000038239	Hrc	-	histidine rich calcium binding protein	protein-coding
mm_19309.1	chr2	90528891	90528903	-	1	NA	intron (NM_008982, intron 1 of 23)	intron (NM_008982, intron 1 of 23)	-49723	NM_001135657	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_19345.1	chr2	90904650	90904727	-	1	NA	promoter-TSS (NM_025991)	promoter-TSS (NM_025991)	33	NM_026688	68349	Mm.30113	NM_026688	ENSMUSG00000005510	Ndufs3	0610010M09Rik|CI-30kD	NADH dehydrogenase (ubiquinone) Fe-S protein 3	protein-coding
mm_38299.1	chr4	136896191	136896207	-	1	NA	exon (NM_007572, exon 3 of 3)	exon (NM_007572, exon 3 of 3)	2645	NM_007572	12259	Mm.439957	NM_007572	ENSMUSG00000036887	C1qa	AI255395|C1q	complement component 1, q subcomponent, alpha polypeptide	protein-coding
mm_104306.1	chr11	90673695	90673710	-	1	NA	exon (NM_028011, exon 5 of 16)	exon (NM_028011, exon 5 of 16)	13899	NM_028011	71943	Mm.167868	NM_028011	ENSMUSG00000020541	Tom1l1	2310045L10Rik|C80573|Srcasm	target of myb1-like 1 (chicken)	protein-coding
mm_11820.1	chr2	44310612	44310612	+	1	NA	intron (NM_001301832, intron 13 of 14)	intron (NM_001301832, intron 13 of 14)	-245288	NR_040622	320872	Mm.445023	NR_040622	ENSMUSG00000085089	Arhgap15os	A430092G05Rik	Rho GTPase activating protein 15, opposite strand	ncRNA
mm_100521.1	chr11	120573421	120573470	+	1	NA	promoter-TSS (NM_011032)	promoter-TSS (NM_011032)	-509	NM_011032	18453	Mm.16660	NM_011032	ENSMUSG00000025130	P4hb	ERp59|PDI|Pdia1|Thbp	prolyl 4-hydroxylase, beta polypeptide	protein-coding
mm_92089.1	chr10	62839879	62839908	-	1	NA	exon (NM_001253857, exon 3 of 12)	exon (NM_001253857, exon 3 of 12)	40121	NM_027384	52463	Mm.17774	NM_027384	ENSMUSG00000047146	Tet1	2510010B09Rik|AA517754|BB001228|Cxxc6|D10Ertd17e|LCX|mKIAA1676	tet methylcytosine dioxygenase 1	protein-coding
mm_100926.1	chr11	6472233	6472239	-	1	NA	3' UTR (NM_011221, exon 1 of 1)	3' UTR (NM_011221, exon 1 of 1)	3840	NM_011221	19291	Mm.296150	NM_011221	ENSMUSG00000094483	Purb	2310015K15Rik|AA114818|Cager-2|D11Bwg0414e	purine rich element binding protein B	protein-coding
mm_153814.1	chr19	46045534	46045542	-	1	NA	promoter-TSS (NM_001113408)	promoter-TSS (NM_001113408)	-327	NM_001113408	16825	Mm.327442	NM_010697	ENSMUSG00000025223	Ldb1	CLIM2|NLI	LIM domain binding 1	protein-coding
mm_129283.1	chr15	77153906	77153963	-	1	NA	promoter-TSS (NM_001110830)	promoter-TSS (NM_001110830)	-122	NM_001286418	93686	Mm.202774	NM_053104	ENSMUSG00000033565	Rbfox2	Fbm2|Fxh|Hrnbp2|Rbm9	RNA binding protein, fox-1 homolog (C. elegans) 2	protein-coding
mm_61447.1	chr7	75585699	75585714	+	1	NA	intron (NM_029332, intron 4 of 36)	intron (NM_029332, intron 4 of 36)	130172	NM_029332	75547	Mm.216107	NM_029332	ENSMUSG00000066406	Akap13	1700026G02Rik|5730522G15Rik|5830460E08Rik|AKAP-13|AKAP-Lbc|BRX|Ht31|LBC|PROTO-LB|PROTO-LBC	A kinase (PRKA) anchor protein 13	protein-coding
mm_6128.1	chr1	64532404	64532411	-	1	NA	promoter-TSS (NM_009952)	promoter-TSS (NM_009952)	-397	NM_133828	12912	Mm.422634	NM_009952	ENSMUSG00000025958	Creb1	2310001E10Rik|3526402H21Rik|AV083133|Creb|Creb-1	cAMP responsive element binding protein 1	protein-coding
mm_70000.1	chr7	142386826	142386848	-	1	NA	intron (NM_009983, intron 1 of 8)	intron (NM_009983, intron 1 of 8)	1033	NM_009983	13033	Mm.231395	NM_009983	ENSMUSG00000007891	Ctsd	CD|CatD	cathepsin D	protein-coding
mm_133147.1	chr16	70314012	70314016	+	1	NA	promoter-TSS (NM_028803)	promoter-TSS (NM_028803)	65	NM_028803	74185	Mm.396102	NM_028803	ENSMUSG00000022707	Gbe1	2310045H19Rik|2810426P10Rik|D16Ertd536e	glucan (1,4-alpha-), branching enzyme 1	protein-coding
mm_41231.1	chr5	88721058	88721065	+	1	NA	5' UTR (NM_026735, exon 1 of 6)	5' UTR (NM_026735, exon 1 of 6)	190	NM_026735	68473	Mm.35764	NM_026735	ENSMUSG00000006262	Mob1b	1110003E08Rik|AU015450|B230364F10|Mobkl1a	MOB kinase activator 1B	protein-coding
mm_50195.1	chr6	41852866	41852872	+	1	NA	TTS (NM_008843)	TTS (NM_008843)	5320	NM_008843	18716	Mm.214755	NM_008843	ENSMUSG00000058499	Pip	GCDFP-15|GP17|mSMGP	prolactin induced protein	protein-coding
mm_98311.1	chr11	90034779	90034792	+	1	NA	intron (NM_026433, intron 2 of 2)	intron (NM_026433, intron 2 of 2)	4437	NM_026433	67888	Mm.212428	NM_026433	ENSMUSG00000069763	Tmem100	1810057C19Rik|AV011897	transmembrane protein 100	protein-coding
mm_46006.1	chr5	90700206	90700210	-	1	NA	Intergenic	Intergenic	-59090	NM_009141	20311	Mm.4660	NM_009141	ENSMUSG00000029371	Cxcl5	AMCF-II|Cxcl6|ENA-78|GCP-2|LIX|Scyb5|Scyb6	chemokine (C-X-C motif) ligand 5	protein-coding
mm_81321.1	chr9	108479943	108479951	+	1	NA	promoter-TSS (NM_008483)	promoter-TSS (NM_008483)	85	NM_008483	16779	Mm.27560	NM_008483	ENSMUSG00000052911	Lamb2	AW211941|Lamb-2|Lams|npht	laminin, beta 2	protein-coding
mm_103773.1	chr11	82179897	82179918	-	1	NA	promoter-TSS (NM_011329)	promoter-TSS (NM_011329)	-95	NM_011329	20290	Mm.1283	NM_011329	ENSMUSG00000020702	Ccl1	BF534335|I-309|Scya1|Tca-3	chemokine (C-C motif) ligand 1	protein-coding
mm_172277.1	chr6	86525197	86525211	+	1	NA	exon (NM_011865, exon 1 of 1)	exon (NM_011865, exon 1 of 1)	961	NM_011865	23983	Mm.274146	NM_011865	ENSMUSG00000051695	Pcbp1	WBP17|[a]CP-1|alphaCP-1|hnRNP E1	poly(rC) binding protein 1	protein-coding
mm_128968.1	chr15	74832179	74832183	-	1	NA	Intergenic	B3|SINE|B2	9462	NM_001033229	110115	Mm.322606	NM_001033229	ENSMUSG00000075604	Cyp11b1	AA389061|CPN1|Cyp11b|Cyp11b-1|FHI	cytochrome P450, family 11, subfamily b, polypeptide 1	protein-coding
mm_74269.1	chr8	124949563	124949566	+	1	NA	promoter-TSS (NM_053207)	promoter-TSS (NM_053207)	-310	NM_053207	112405	Mm.140619	NM_053207	ENSMUSG00000031987	Egln1	AI503754|C1orf12|HIF-PH2|HPH-2|Hif-p4h-2|ORF13|Phd2|SM-20	egl-9 family hypoxia-inducible factor 1	protein-coding
mm_5759.1	chr1	46888142	46888153	-	1	NA	Intergenic	Intergenic	-34638	NM_172653	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|mKIAA1265	solute carrier family 39 (zinc transporter), member 10	protein-coding
mm_29825.1	chr3	129678436	129678445	-	1	NA	exon (NM_010113, exon 24 of 24)	exon (NM_010113, exon 24 of 24)	46646	NM_001310737	13645	Mm.252481	NM_010113	ENSMUSG00000028017	Egf	AI790464	epidermal growth factor	protein-coding
mm_59795.1	chr7	29001516	29001532	+	1	NA	intron (NM_008279, intron 27 of 31)	intron (NM_008279, intron 27 of 31)	18670	NM_008279	26411	Mm.148278	NM_008279	ENSMUSG00000037337	Map4k1	Hpk1|mHPK1	mitogen-activated protein kinase kinase kinase kinase 1	protein-coding
mm_97372.1	chr11	77686162	77686179	+	1	NA	promoter-TSS (NM_001024205)	promoter-TSS (NM_001024205)	31	NM_001024205	68564	Mm.428996	NM_001024205	ENSMUSG00000037857	Nufip2	1110001M19Rik|9530056D24Rik|AI256692|AI461731|PIG1|mKIAA1321	nuclear fragile X mental retardation protein interacting protein 2	protein-coding
mm_157733.1	chrX	71215523	71215555	-	1	NA	intron (NM_019926, intron 1 of 14)	intron (NM_019926, intron 1 of 14)	457	NM_019926	17772	Mm.274981	NM_019926	ENSMUSG00000031337	Mtm1	AF073996|Mtm|mKIAA4176	X-linked myotubular myopathy gene 1	protein-coding
mm_142121.1	chr17	35895991	35896001	-	1	NA	exon (NM_001033630, exon 2 of 6)	exon (NM_001033630, exon 2 of 6)	1382	NM_001033630	69662	Mm.260159	NM_001033630	ENSMUSG00000050705	2310061I04Rik	-	RIKEN cDNA 2310061I04 gene	protein-coding
mm_77036.1	chr8	109565736	109565748	-	1	NA	promoter-TSS (NM_178380)	promoter-TSS (NM_178380)	-141	NM_178380	64340	Mm.23705	NM_178380	ENSMUSG00000037993	Dhx38	5730550P09Rik|AI325984|AW540902|Ddx38|Prp16|mKIAA0224	DEAH (Asp-Glu-Ala-His) box polypeptide 38	protein-coding
mm_122605.1	chr14	51055683	51055695	-	1	NA	Intergenic	(GTTTG)n|Simple_repeat|Simple_repeat	1553	NM_001011875	497106	Mm.379740	NM_001011875	ENSMUSG00000068407	Rnase12	Rai1	ribonuclease, RNase A family, 12 (non-active)	protein-coding
mm_144548.1	chr18	30272830	30272931	+	1	NA	promoter-TSS (NM_181414)	promoter-TSS (NM_181414)	-16	NM_181414	225326	Mm.194127	NM_181414	ENSMUSG00000033628	Pik3c3	5330434F23Rik|Vps34	phosphoinositide-3-kinase, class 3	protein-coding
mm_51358.1	chr6	72616856	72616918	+	1	NA	promoter-TSS (NM_009444)	promoter-TSS (NM_009444)	113	NM_009443	22134	Mm.246563	NM_009443	ENSMUSG00000056429	Tgoln1	AU015504|D6Ertd384e|TGN38|TGN38A|Ttgn1	trans-golgi network protein	protein-coding
mm_40790.1	chr5	67450625	67450633	+	1	NA	Intergenic	Intergenic	-13269	NR_110363	320479	Mm.387187	NR_015582	ENSMUSG00000107385	C330024D21Rik	-	RIKEN cDNA C330024D21 gene	ncRNA
mm_63224.1	chr7	126367886	126367925	+	1	NA	TTS (NR_106025)	TTS (NR_106025)	140	NR_106025	102466797		NR_106025	ENSMUSG00000099017	Mir7058	Gm27766|mmu-mir-7058	microRNA 7058	ncRNA
mm_141952.1	chr17	35112057	35112063	-	1	NA	TTS (NM_148947)	TTS (NM_148947)	3340	NM_148939	266614	Mm.104680	NM_148939	ENSMUSG00000043807	Ly6g5b	-	lymphocyte antigen 6 complex, locus G5B	protein-coding
mm_49231.1	chr6	17105330	17105377	+	1	NA	3' UTR (NM_207176, exon 7 of 7)	3' UTR (NM_207176, exon 7 of 7)	40204	NM_207176	21753	Mm.436548	NM_011570	ENSMUSG00000029552	Tes	D6Ertd352e|TESS|Tes1|Tes2|testin2	testis derived transcript	protein-coding
mm_129230.1	chr15	76615042	76615055	-	1	NA	exon (NM_028064, exon 3 of 12)	exon (NM_028064, exon 3 of 12)	1804	NM_028064	72027	Mm.276829	NM_028064	ENSMUSG00000063354	Slc39a4	1600025H15Rik|AU041686|AWMS2|ZIP4	solute carrier family 39 (zinc transporter), member 4	protein-coding
mm_50277.1	chr6	46563304	46563308	+	1	NA	intron (NM_001004357, intron 13 of 23)	intron (NM_001004357, intron 13 of 23)	-681090	NM_025771	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding
mm_123424.1	chr14	64419523	64419536	-	1	NA	intron (NM_001253712, intron 1 of 5)	Lx8|LINE|L1	-2250	NM_001347639	110265	Mm.26713	NM_026322	ENSMUSG00000054733	Msra	2310045J23Rik|6530413P12Rik|MSR-A	methionine sulfoxide reductase A	protein-coding
mm_66215.1	chr7	34389462	34389473	-	1	NA	promoter-TSS (NM_025948)	promoter-TSS (NM_025948)	73	NM_025948	67070	Mm.276503	NM_025948	ENSMUSG00000066568	Lsm14a	2700023B17Rik|AA407828|AU017544|Tral	LSM14A mRNA processing body assembly factor	protein-coding
mm_129619.1	chr15	80014967	80014984	-	1	NA	promoter-TSS (NM_011057)	promoter-TSS (NM_011057)	-167	NM_011057	18591	Mm.144089	NM_011057	ENSMUSG00000000489	Pdgfb	PDGF-B|Sis	platelet derived growth factor, B polypeptide	protein-coding
mm_38754.1	chr4	147809803	147809821	-	1	NA	promoter-TSS (NM_001127189)	promoter-TSS (NM_001127189)	-24	NM_001127189	100041677	Mm.327194	NM_001127189	ENSMUSG00000078495	Zfp984	Gm13157|OTTMUSG00000010679	zinc finger protein 984	protein-coding
mm_101600.1	chr11	34770689	34770722	-	1	NA	intron (NM_033374, intron 1 of 51)	intron (NM_033374, intron 1 of 51)	13200	NM_033374	94176	Mm.380679	NM_033374	ENSMUSG00000020143	Dock2	AI662014|AW122239|CED-5|Hch|MBC	dedicator of cyto-kinesis 2	protein-coding
mm_66891.1	chr7	59284934	59284936	-	1	NA	intron (NM_173010, intron 5 of 8)	intron (NM_173010, intron 5 of 8)	39214	NR_015479	330544	Mm.9002	NR_015479	ENSMUSG00000100826	C230091D08Rik	-	RIKEN cDNA C230091D08 gene	ncRNA
mm_131943.1	chr16	24096356	24096363	+	1	NA	Intergenic	L2c|LINE|L2	-107747	NM_009744	12053	Mm.347398	NM_009744	ENSMUSG00000022508	Bcl6	Bcl5	B cell leukemia/lymphoma 6	protein-coding
mm_157480.1	chrX	48173001	48173044	-	1	NA	3' UTR (NM_172465, exon 10 of 10)	3' UTR (NM_172465, exon 10 of 10)	26586	NM_028773	74131	Mm.276131	NM_028773	ENSMUSG00000031101	Sash3	1200013B08Rik|AW413946|SLY1	SAM and SH3 domain containing 3	protein-coding
mm_27879.1	chr3	79173135	79173151	-	1	NA	Intergenic	Intergenic	-27268	NM_001099624	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_159876.1	chr5	150764800	150764800	+	1	NA	intron (NM_001346503, intron 17 of 34)	intron (NM_001346503, intron 17 of 34)	90973	NM_001346503	100710	Mm.32959	NM_175310	ENSMUSG00000034021	Pds5b	AI646570|AS3|AW212954|Aprin|Tg(Wap-ERBB2)229Wzw|WAP-Her-2|mKIAA0979	PDS5 cohesin associated factor B	protein-coding
mm_38520.1	chr4	141422624	141422639	-	1	NA	exon (NM_013868, exon 2 of 3)	exon (NM_013868, exon 2 of 3)	1852	NM_013868	29818	Mm.46181	NM_013868	ENSMUSG00000006221	Hspb7	27kDa|Hsp25-2|cvHsp	heat shock protein family, member 7 (cardiovascular)	protein-coding
mm_127865.1	chr15	8361752	8361768	-	1	NA	exon (NM_027707, exon 7 of 47)	exon (NM_027707, exon 7 of 47)	82703	NM_027707	71175	Mm.240329	NM_027707	ENSMUSG00000022141	Nipbl	Idn3	Nipped-B homolog (Drosophila)	protein-coding
mm_172857.1	chr9	40488198	40488203	+	1	NA	Intergenic	Intergenic	-32436	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_66839.1	chr7	48881605	48881619	-	1	NA	promoter-TSS (NM_001013368)	promoter-TSS (NM_001013368)	-571	NM_001013368	108961	Mm.240566	NM_001013368	ENSMUSG00000046179	E2f8	4432406C08Rik|AA410048	E2F transcription factor 8	protein-coding
mm_19101.1	chr2	79454308	79454316	-	1	NA	exon (NM_010894, exon 2 of 2)	exon (NM_010894, exon 2 of 2)	2324	NM_010894	18012	Mm.4636	NM_010894	ENSMUSG00000034701	Neurod1	BETA2|BHF-1|Nd1|Neurod|bHLHa3	neurogenic differentiation 1	protein-coding
mm_127909.1	chr15	9529698	9529708	-	1	NA	exon (NM_008372, exon 1 of 8)	exon (NM_008372, exon 1 of 8)	173	NM_008372	16197	Mm.389	NM_008372	ENSMUSG00000003882	Il7r	CD127|IL-7Ralpha	interleukin 7 receptor	protein-coding
mm_69487.1	chr7	133958797	133958808	-	1	NA	intron (NM_007400, intron 11 of 22)	intron (NM_007400, intron 11 of 22)	-176017	NM_001286031	101437	Mm.199223	NM_133941	ENSMUSG00000030986	Dhx32	3110079L04Rik|4732469F02Rik|AA408140|Ddx32	DEAH (Asp-Glu-Ala-His) box polypeptide 32	protein-coding
mm_138491.1	chr17	35200395	35200403	+	1	NA	exon (NM_013693, exon 4 of 4)	exon (NM_013693, exon 4 of 4)	1608	NM_013693	21926	Mm.1293	NM_013693	ENSMUSG00000024401	Tnf	DIF|TNF-a|TNF-alpha|TNFSF2|TNFalpha|Tnfa|Tnfsf1a|Tnlg1f	tumor necrosis factor	protein-coding
mm_93697.1	chr10	117910512	117910516	-	1	NA	Intergenic	Intergenic	-14945	NR_045342	71067	Mm.410793	NR_045342		4933411E08Rik	-	RIKEN cDNA 4933411E08 gene	ncRNA
mm_156928.1	chrX	169320383	169320420	+	1	NA	promoter-TSS (NM_001331050)	promoter-TSS (NM_001331050)	-29	NM_001331049	15159	Mm.284033	NM_008222	ENSMUSG00000031352	Hccs	-	holocytochrome c synthetase	protein-coding
mm_22060.1	chr2	168601621	168601638	-	1	NA	promoter-TSS (NM_001291173)	promoter-TSS (NM_001291173)	28	NM_001291171	18019	Mm.116802	NM_010899	ENSMUSG00000027544	Nfatc2	AI607462|NF-ATc2|NF-ATp|NFAT1|NFAT1-D|Nfatp	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 2	protein-coding
mm_12827.1	chr2	80617186	80617290	+	1	NA	promoter-TSS (NM_024438)	promoter-TSS (NM_024438)	24	NM_024438	68082	Mm.306818	NM_024438	ENSMUSG00000027001	Dusp19	5930436K22Rik|C79103|SKRP1|TS-DSP1	dual specificity phosphatase 19	protein-coding
mm_172969.1	chr9	90114549	90114552	-	1	NA	exon (NM_024431, exon 1 of 12)	exon (NM_024431, exon 1 of 12)	270	NM_001039147	21761	Mm.426209	NM_024431	ENSMUSG00000062270	Morf4l1	MORFRG15|MRG15|TEG-189|Tex189|mKIAA4002	mortality factor 4 like 1	protein-coding
mm_80826.1	chr9	96799787	96799796	+	1	NA	Intergenic	RMER17C|LTR|ERVK	34229	NR_102296	319707	Mm.392191	NR_102293	ENSMUSG00000101581	C430002N11Rik	-	RIKEN cDNA C430002N11 gene	ncRNA
mm_82467.1	chr9	16034053	16034056	-	1	NA	intron (NM_001080814, intron 3 of 24)	intron (NM_001080814, intron 3 of 24)	-159498	NM_145712	244701	Mm.222631	NM_145712	ENSMUSG00000050901	Mtnr1b	Mel-1B-R|Mel1b|Mt2	melatonin receptor 1B	protein-coding
mm_151120.1	chr19	47865517	47865529	+	1	NA	promoter-TSS (NM_026619)	promoter-TSS (NM_026619)	-22	NM_030051	68214	Mm.63791	NM_026619	ENSMUSG00000025069	Gsto2	1700020F09Rik|4930425C18Rik|GSTO 2-2	glutathione S-transferase omega 2	protein-coding
mm_146610.1	chr18	10016883	10016886	-	1	NA	intron (NM_001038589, intron 3 of 14)	intron (NM_001038589, intron 3 of 14)	13265	NM_021522	59025	Mm.329277	NM_021522	ENSMUSG00000047879	Usp14	2610005K12Rik|2610037B11Rik|AW107924|C78769|ax|nmf375	ubiquitin specific peptidase 14	protein-coding
mm_157387.1	chrX	38252399	38252436	-	1	NA	promoter-TSS (NM_001289728)	promoter-TSS (NM_001289728)	64	NM_001289727	245386	Mm.72979	NM_172930	ENSMUSG00000036502	Tmem255a	4933417N17|6430550H21Rik|Fam70a	transmembrane protein 255A	protein-coding
mm_11881.1	chr2	49562499	49562531	+	1	NA	Intergenic	Intergenic	-56799	NM_008449	16574	Mm.256342	NM_008449	ENSMUSG00000026764	Kif5c	KINN|Khc|NKHC|NKHC2	kinesin family member 5C	protein-coding
mm_147181.1	chr18	36772323	36772346	-	1	NA	exon (NM_008214, exon 5 of 13)	exon (NM_008214, exon 5 of 13)	-6120	NM_173383	213236	Mm.234464	NM_173383	ENSMUSG00000044595	Dnd1	BC034897|RBMS4|Ter	DND microRNA-mediated repression inhibitor 1	protein-coding
mm_109699.1	chr12	113156404	113156442	+	1	NA	promoter-TSS (NM_134041)	promoter-TSS (NM_134041)	2	NM_134041	104732	Mm.87616	NM_134041	ENSMUSG00000037466	4930427A07Rik	AA536649|mFLJ00116	RIKEN cDNA 4930427A07 gene	protein-coding
mm_170254.1	chr18	10274702	10274718	-	1	NA	Intergenic	Intergenic	-50469	NM_001083628	381157	Mm.261535	NM_001083628	ENSMUSG00000042942	Greb1l	mKIAA4095	growth regulation by estrogen in breast cancer-like	protein-coding
mm_46761.1	chr5	112251209	112251219	-	1	NA	intron (NM_001312884, intron 1 of 4)	intron (NM_001312884, intron 1 of 4)	1304	NM_001312884	12959	Mm.40324	NM_021351	ENSMUSG00000066975	Cryba4	-	crystallin, beta A4	protein-coding
mm_73272.1	chr8	104591441	104591454	+	1	NA	promoter-TSS (NM_001024606)	promoter-TSS (NM_001024606)	-21	NM_001024606	382051	Mm.290750	NM_001024606	ENSMUSG00000048371	Pdp2	4833426J09Rik|Gm1705|mKIAA1348	pyruvate dehyrogenase phosphatase catalytic subunit 2	protein-coding
mm_166411.1	chr5	137151428	137151437	-	1	NA	Intergenic	Intergenic	-35225	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_151879.1	chr19	5798476	5798504	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	-2509	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_161962.1	chr19	8131948	8131948	-	1	NA	promoter-TSS (NM_001013820)	promoter-TSS (NM_001013820)	34	NM_001013820	434674	Mm.24053	NM_001013820	ENSMUSG00000063590	Slc22a28	EG434674|Gm5631	solute carrier family 22, member 28	protein-coding
mm_109806.1	chr12	3341357	3341364	-	1	NA	Intergenic	Intergenic	-23772	NM_008445	16570	Mm.7688	NM_008445	ENSMUSG00000020668	Kif3c	mKIAA4058	kinesin family member 3C	protein-coding
mm_96315.1	chr11	63966072	63966080	+	1	NA	intron (NR_131111, intron 2 of 3)	intron (NR_131111, intron 2 of 3)	1850	NR_131111	78883	Mm.410764	NR_131111	ENSMUSG00000086359	9630013K17Rik	-	RIKEN cDNA 9630013K17 gene	ncRNA
mm_142779.1	chr17	50101340	50101376	-	1	NA	intron (NM_181397, intron 3 of 9)	intron (NM_181397, intron 3 of 9)	89139	NM_181397	76438	Mm.41854	NM_181397	ENSMUSG00000039316	Rftn1	2310015N21Rik|AI853526	raftlin lipid raft linker 1	protein-coding
mm_71002.1	chr8	31091594	31091635	+	1	NA	intron (NM_025869, intron 2 of 4)	intron (NM_025869, intron 2 of 4)	1952	NM_025869	66959	Mm.23916	NM_025869	ENSMUSG00000039661	Dusp26	2310043K02Rik|Skrp3	dual specificity phosphatase 26 (putative)	protein-coding
mm_87199.1	chr10	39550989	39550994	+	1	NA	intron (NM_001122892, intron 11 of 12)	ORR1C1|LTR|ERVL-MaLR	-61943	NM_134000	103213	Mm.436686	NM_134000	ENSMUSG00000019842	Traf3ip2	AI429613|Act1|CIKS	TRAF3 interacting protein 2	protein-coding
mm_20053.1	chr2	120289064	120289074	-	1	NA	promoter-TSS (NM_001024137)	promoter-TSS (NM_001024137)	0	NM_001024137	78390	Mm.330507	NM_001024137	ENSMUSG00000070719	Pla2g4d	2610311B01Rik|Pla2delta|cPLA2delta	phospholipase A2, group IVD	protein-coding
mm_140735.1	chr17	15704793	15704810	-	1	NA	promoter-TSS (NM_007690)	promoter-TSS (NM_007690)	-166	NM_007690	12648	Mm.8137	NM_007690	ENSMUSG00000023852	Chd1	4930525N21Rik|AI851787|AW555109	chromodomain helicase DNA binding protein 1	protein-coding
mm_100427.1	chr11	119454090	119454097	+	1	NA	Intergenic	B4A|SINE|B4	-37254	NM_001164636	338371	Mm.271946	NM_177394	ENSMUSG00000039850	Endov	A730011L01Rik	endonuclease V	protein-coding
mm_56322.1	chr6	92450048	92450061	-	1	NA	intron (NM_001081146, intron 3 of 8)	intron (NM_001081146, intron 3 of 8)	31338	NM_001134460	243548	Mm.248820	NM_001081146	ENSMUSG00000030020	Prickle2	6230400G14Rik|6720451F06Rik|mpk2	prickle planar cell polarity protein 2	protein-coding
mm_19954.1	chr2	117338528	117338594	-	1	NA	intron (NM_011246, intron 1 of 16)	intron (NM_011246, intron 1 of 16)	4316	NM_011246	19419	Mm.42150	NM_011246	ENSMUSG00000027347	Rasgrp1	Rasgrp	RAS guanyl releasing protein 1	protein-coding
mm_115518.1	chr13	5845771	5845782	-	1	NA	Intergenic	Intergenic	12316	NR_045891	71867	Mm.179181	NR_045891	ENSMUSG00000100625	1700016G22Rik	-	RIKEN cDNA 1700016G22 gene	ncRNA
mm_87065.1	chr10	29030738	29030761	+	1	NA	Intergenic	Intergenic	-44443	NM_026336	67719	Mm.440480	NM_026336	ENSMUSG00000015519	2310057J18Rik	2210414P04Rik|Leg1	RIKEN cDNA 2310057J18 gene	protein-coding
mm_112655.1	chr13	16026533	16026543	+	1	NA	exon (NM_008380, exon 5 of 5)	exon (NM_008380, exon 5 of 5)	14687	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_74340.1	chr8	127171392	127171407	+	1	NA	intron (NM_001309391, intron 2 of 24)	intron (NM_001309391, intron 2 of 24)	107343	NM_001309391	93742	Mm.299254	NM_033620	ENSMUSG00000025812	Pard3	AA960621|AI256638|Asip|D8Ertd580e|Par-3|Par3|Pard-3|Pard3a|Phip	par-3 family cell polarity regulator	protein-coding
mm_2134.1	chr1	88070754	88070760	+	1	NA	promoter-TSS (NM_201644)	promoter-TSS (NM_201644)	-22	NM_201644	394434	Mm.300095	NM_201644	ENSMUSG00000090175	Ugt1a9	UDPGT|UDPGT 1-9|UGT1-09|UGT1.9|UGTP4|Ugt1a12|mUGTBr/P	UDP glucuronosyltransferase 1 family, polypeptide A9	protein-coding
mm_58400.1	chr7	3218170	3218176	+	1	NA	promoter-TSS (NR_029640)	promoter-TSS (NR_029640)	-453	NR_029640	100049710		NR_029640	ENSMUSG00000077815	Mir290a	Mir290|Mirn290|mir-290a|mmu-miR-290|mmu-mir-290a	microRNA 290a	ncRNA
mm_58938.1	chr7	18067240	18067243	+	1	NA	exon (NM_001162524, exon 2 of 3)	exon (NM_001162524, exon 2 of 3)	1312	NM_001162523	67315	Mm.46089	NM_026087	ENSMUSG00000030366	Ceacam12	1600031J20Rik|Ceacam12-C1|Ceacam12-C3|Ceacam12C1|Ceacam12C3	carcinoembryonic antigen-related cell adhesion molecule 12	protein-coding
mm_112520.1	chr13	9149239	9149245	+	1	NA	intron (NM_001311117, intron 8 of 16)	intron (NM_001311117, intron 8 of 16)	55361	NM_172585	217980	Mm.234944	NM_172585	ENSMUSG00000033499	Larp4b	A630096F19|AI256361|D13Wsu64e|Larp5	La ribonucleoprotein domain family, member 4B	protein-coding
mm_74355.1	chr8	128166450	128166454	+	1	NA	Intergenic	Intergenic	111773	NR_105822	102465212		NR_105822	ENSMUSG00000099326	Mir21c	Gm28013|mmu-mir-21c	microRNA 21c	ncRNA
mm_46614.1	chr5	108066211	108066226	-	1	NA	intron (NM_001253880, intron 1 of 12)	intron (NM_001253880, intron 1 of 12)	544	NM_013827	17765	Mm.257149	NM_013827	ENSMUSG00000029267	Mtf2	9230112N11Rik|AA537621|C76717|M96|Pcl2	metal response element binding transcription factor 2	protein-coding
mm_17581.1	chr2	30415461	30415505	-	1	NA	promoter-TSS (NM_138748)	promoter-TSS (NM_138748)	265	NM_007760	12908	Mm.20396	NM_007760	ENSMUSG00000026853	Crat	AW107812|CARAT	carnitine acetyltransferase	protein-coding
mm_117153.1	chr13	61358194	61358198	-	1	NA	promoter-TSS (NM_019539)	promoter-TSS (NM_019539)	-26	NM_019539	56092	Mm.3692	NM_019539	ENSMUSG00000021440	Cts7	AA408230|AA408952|CTS1|Epcs24|Epcs71	cathepsin 7	protein-coding
mm_87419.1	chr10	50662554	50662562	+	1	NA	intron (NM_198007, intron 13 of 41)	ID_B1|SINE|B4	69889	NM_198007	77987	Mm.222497	NM_198007	ENSMUSG00000038774	Ascc3	ASC1p200|B630009I04Rik|BC023451|D430001L07Rik|D630041L21|Helic1|RNAH	activating signal cointegrator 1 complex subunit 3	protein-coding
mm_160228.1	chr7	102194833	102194833	-	1	NA	exon (NM_001287167, exon 4 of 20)	exon (NM_001287167, exon 4 of 20)	15034	NM_001287167	269966	Mm.439800	NM_022979	ENSMUSG00000063550	Nup98	4732457F17|AI849286|Nup96	nucleoporin 98	protein-coding
mm_173179.1	chrX	53723664	53723667	+	1	NA	Intergenic	B1_Mus1|SINE|Alu	-1166	NM_029142	75013	Mm.336332	NM_029142	ENSMUSG00000055555	4930502E18Rik	Ct55	RIKEN cDNA 4930502E18 gene	protein-coding
mm_66860.1	chr7	55962425	55962461	-	1	NA	promoter-TSS (NM_023647)	promoter-TSS (NM_023647)	50	NM_001256133	93790	Mm.37249	NM_023647	ENSMUSG00000030452	Nipa2	2600017P10Rik|3830408P04Rik|AB041581	non imprinted in Prader-Willi/Angelman syndrome 2 homolog (human)	protein-coding
mm_169890.1	chr16	4697839	4697839	-	1	NA	intron (NM_001135112, intron 7 of 10)	B1_Mus2|SINE|Alu	13769	NM_001135112	83945	Mm.248337	NM_023646	ENSMUSG00000004069	Dnaja3	1200003J13Rik|1810053A11Rik|C81173|Tid-1|Tid1l	DnaJ heat shock protein family (Hsp40) member A3	protein-coding
mm_39523.1	chr5	21258196	21258269	+	1	NA	intron (NM_175437, intron 19 of 30)	intron (NM_175437, intron 19 of 30)	71965	NM_175437	212167	Mm.121705	NM_175437	ENSMUSG00000039934	Gsap	A530088I07Rik|Pion	gamma-secretase activating protein	protein-coding
mm_90614.1	chr10	128376468	128376513	+	1	NA	promoter-TSS (NM_172790)	promoter-TSS (NM_172790)	-634	NM_172790	237615	Mm.440177	NM_172790	ENSMUSG00000014498	Ankrd52	6430544C07|G431002C21Rik	ankyrin repeat domain 52	protein-coding
mm_48906.1	chr6	3574275	3574278	+	1	NA	intron (NM_001167750, intron 20 of 27)	intron (NM_001167750, intron 20 of 27)	75883	NM_001167750	73288	Mm.45539	NM_024260	ENSMUSG00000001376	Vps50	1700034M03Rik|8430415E05Rik|BLM|C87205|Ccdc132|mKIAA1861	VPS50 EARP/GARPII complex subunit	protein-coding
mm_74946.1	chr8	25847706	25847716	-	1	NA	promoter-TSS (NM_001080793)	promoter-TSS (NM_001080793)	-17	NM_001080793	23808	Mm.27706	NM_011791	ENSMUSG00000031575	Ash2l	-	ash2 (absent, small, or homeotic)-like (Drosophila)	protein-coding
mm_136407.1	chr16	93721900	93721905	-	1	NA	intron (NM_027293, intron 2 of 36)	intron (NM_027293, intron 2 of 36)	9995	NM_027293	70028	Mm.23230	NM_026700	ENSMUSG00000022946	Dopey2	0610038M01Rik|2610510B01Rik|AI503246|C21orf5|mKIAA0933	dopey family member 2	protein-coding
mm_105848.1	chr11	113709654	113709690	-	1	NA	promoter-TSS (NM_001164532)	promoter-TSS (NM_001164532)	-146	NM_001164532	52670	Mm.229207	NM_026682	ENSMUSG00000018727	Cpsf4l	0610010C04Rik|1500000C01Rik|D11Ertd636e	cleavage and polyadenylation specific factor 4-like	protein-coding
mm_2029.1	chr1	87186662	87186677	+	1	NA	exon (NM_027084, exon 9 of 13)	exon (NM_027084, exon 9 of 13)	3355	NM_027084	69453	Mm.84618	NM_027084	ENSMUSG00000036480	Prss56	1700027L20Rik	protease, serine 56	protein-coding
mm_10433.1	chr2	14074219	14074235	+	1	NA	promoter-TSS (NR_038162)	promoter-TSS (NR_038162)	115	NM_011484	20844	Mm.273174	NM_011484	ENSMUSG00000026718	Stam	STAM1	signal transducing adaptor molecule (SH3 domain and ITAM motif) 1	protein-coding
mm_93990.1	chr10	127522365	127522423	-	1	NA	promoter-TSS (NM_028230)	promoter-TSS (NM_028230)	50	NM_001252316	108037	Mm.29890	NM_028230	ENSMUSG00000025403	Shmt2	2700043D08Rik|AA408223|AA986903	serine hydroxymethyltransferase 2 (mitochondrial)	protein-coding
mm_73610.1	chr8	110089998	110090009	+	1	NA	exon (NM_175480, exon 5 of 5)	exon (NM_175480, exon 5 of 5)	10269	NM_175480	234725	Mm.87487	NM_175480	ENSMUSG00000044676	Zfp612	B230354B21Rik	zinc finger protein 612	protein-coding
mm_20297.1	chr2	126941989	126941993	-	1	NA	Intergenic	RLTR1B|LTR|ERV1	-8756	NM_023220	66552	Mm.269928	NM_023220	ENSMUSG00000027366	Sppl2a	2010106G01Rik|C130089K23Rik	signal peptide peptidase like 2A	protein-coding
mm_94810.1	chr11	23020465	23020486	+	1	NA	exon (NM_028672, exon 3 of 4)	exon (NM_028672, exon 3 of 4)	7088	NM_028672	73873	Mm.252406	NM_028672	ENSMUSG00000049811	Fam161a	4930430E16Rik	family with sequence similarity 161, member A	protein-coding
mm_96157.1	chr11	61486026	61486039	+	1	NA	intron (NM_001347545, intron 2 of 4)	intron (NM_001347545, intron 2 of 4)	588	NM_029568	76293	Mm.272278	NM_029568	ENSMUSG00000042436	Mfap4	1110007F23Rik	microfibrillar-associated protein 4	protein-coding
mm_22757.1	chr3	19989056	19989069	+	1	NA	exon (NM_007752, exon 18 of 19)	exon (NM_007752, exon 18 of 19)	32008	NM_007752	12870	Mm.13787	NM_007752	ENSMUSG00000003617	Cp	D3Ertd555e	ceruloplasmin	protein-coding
mm_28351.1	chr3	89667250	89667260	-	1	NA	exon (NM_080466, exon 8 of 8)	exon (NM_080466, exon 8 of 8)	-47767	NM_001038587	56417	Mm.316628	NM_019655	ENSMUSG00000027951	Adar	AV242451|Adar1|Adar1p110|Adar1p150|mZaADAR	adenosine deaminase, RNA-specific	protein-coding
mm_149860.1	chr19	25097860	25097908	+	1	NA	intron (NM_028785, intron 12 of 47)	RMER12B|LTR|ERVK	98355	NM_028785	76088	Mm.102485	NM_028785	ENSMUSG00000052085	Dock8	1200017A24Rik|5830472H07Rik|A130095G14Rik|AI461977	dedicator of cytokinesis 8	protein-coding
mm_85914.1	chr9	111057490	111057506	-	1	NA	promoter-TSS (NM_017466)	promoter-TSS (NM_017466)	20	NM_001302376	54199	Mm.7336	NM_017466	ENSMUSG00000043953	Ccrl2	1810047I05Rik|Ackr5|CCR11|Cmkbr1l2|E01|L-CCR	chemokine (C-C motif) receptor-like 2	protein-coding
mm_69405.1	chr7	132317306	132317314	-	1	NA	promoter-TSS (NM_029935)	promoter-TSS (NM_029935)	-155	NM_029935	77590	Mm.213582	NM_029935	ENSMUSG00000030930	Chst15	4631426J05Rik|BRAG|GalNAcS-6ST|MAd5|mKIAA0598	carbohydrate (N-acetylgalactosamine 4-sulfate 6-O) sulfotransferase 15	protein-coding
mm_96970.1	chr11	70647933	70647948	+	1	NA	promoter-TSS (NM_024211)	promoter-TSS (NM_024211)	653	NM_027445	70510	Mm.261818	NM_027445	ENSMUSG00000040746	Rnf167	0610010G05Rik|5730408C10Rik|AU019305|AV328608	ring finger protein 167	protein-coding
mm_36722.1	chr4	98733523	98733533	-	1	NA	exon (NM_001081202, exon 3 of 5)	exon (NM_001081202, exon 3 of 5)	6774	NM_001081202	381591	Mm.34340	NM_001081202	ENSMUSG00000087166	L1td1	AA546746|AB211064|D76865|ECAT11	LINE-1 type transposase domain containing 1	protein-coding
mm_6777.1	chr1	84136798	84136809	-	1	NA	intron (NM_001003948, intron 2 of 2)	Lx7|LINE|L1	82158	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_138468.1	chr17	35186935	35186974	+	1	NA	exon (NM_010734, exon 2 of 4)	exon (NM_010734, exon 2 of 4)	1486	NM_010734	16988	Mm.19379	NM_010734	ENSMUSG00000073412	Lst1	B144	leukocyte specific transcript 1	protein-coding
mm_110181.1	chr12	27337576	27337586	-	1	NA	3' UTR (NM_009234, exon 1 of 1)	3' UTR (NM_009234, exon 1 of 1)	5137	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding
mm_23453.1	chr3	60081862	60081876	+	1	NA	promoter-TSS (NM_032400)	promoter-TSS (NM_032400)	0	NM_032400	84112	Mm.125110	NM_032400	ENSMUSG00000027762	Sucnr1	Gpr91	succinate receptor 1	protein-coding
mm_171244.1	chr3	75650573	75650585	-	1	NA	intron (NR_040539, intron 1 of 2)	RLTR9E|LTR|ERVK	5152	NR_040539	69193	Mm.374088	NR_040539	ENSMUSG00000099370	Platr10	2410007B07Rik	pluripotency associated transcript 10	ncRNA
mm_87292.1	chr10	42502126	42502136	+	1	NA	promoter-TSS (NM_017472)	promoter-TSS (NM_017472)	77	NM_017472	54198	Mm.277870	NM_017472	ENSMUSG00000019804	Snx3	SDP3	sorting nexin 3	protein-coding
mm_80397.1	chr9	76312509	76312518	+	1	NA	intron (NM_198962, intron 1 of 7)	(CCTG)n|Simple_repeat|Simple_repeat	11065	NM_198962	387285	Mm.335300	NM_198962	ENSMUSG00000032360	Hcrtr2	OX2R|mOX2aR|mOX2bR|mOXR2	hypocretin (orexin) receptor 2	protein-coding
mm_48421.1	chr5	140389168	140389176	-	1	NA	exon (NM_172277, exon 1 of 11)	exon (NM_172277, exon 1 of 11)	136	NM_172277	231834	Mm.27098	NM_172277	ENSMUSG00000029560	Snx8	B130023O14Rik	sorting nexin 8	protein-coding
mm_153405.1	chr19	40513715	40513792	-	1	NA	promoter-TSS (NM_009166)	promoter-TSS (NM_009166)	-17	NM_178362	20411	Mm.210815	NM_009166	ENSMUSG00000025006	Sorbs1	2310065E01Rik|9530001P15Rik|CAP|SH3P12|Sh3d5|mKIAA1296	sorbin and SH3 domain containing 1	protein-coding
mm_31754.1	chr4	63350369	63350373	+	1	NA	Intergenic	Intergenic	-5791	NM_013623	18407	Mm.381399	NM_013623	ENSMUSG00000028359	Orm3	Agp-3|Orm-3	orosomucoid 3	protein-coding
mm_94540.1	chr11	9139301	9139301	+	1	NA	Intergenic	Intergenic	20794	NM_001159402	22271	Mm.4610	NM_009477	ENSMUSG00000020407	Upp1	AI325217|UPase|UdRPase|Up|Upp	uridine phosphorylase 1	protein-coding
mm_56019.1	chr6	86526531	86526597	-	1	NA	promoter-TSS (NM_011865)	promoter-TSS (NM_011865)	-399	NM_011865	23983	Mm.274146	NM_011865	ENSMUSG00000051695	Pcbp1	WBP17|[a]CP-1|alphaCP-1|hnRNP E1	poly(rC) binding protein 1	protein-coding
mm_12529.1	chr2	72180440	72180457	+	1	NA	intron (NM_001204165, intron 10 of 30)	intron (NM_001204165, intron 10 of 30)	-105189	NM_023057	65964	Mm.304143	NM_023057	ENSMUSG00000004085	Map3k20	AV006891|B230120H23Rik|MLTK|MLTKalpha|MLTKbeta|Zak	mitogen-activated protein kinase kinase kinase 20	protein-coding
mm_88926.1	chr10	81233148	81233191	+	1	NA	promoter-TSS (NM_001034895)	promoter-TSS (NM_001034895)	6	NM_001034895	103406	Mm.158783	NM_001034895	ENSMUSG00000034949	Zfr2	2010013I23Rik|9130206N08Rik|AW045600|mKIAA1086	zinc finger RNA binding protein 2	protein-coding
mm_105108.1	chr11	100970522	100970532	-	1	NA	promoter-TSS (NM_008986)	promoter-TSS (NM_008986)	90	NM_008986	19285	Mm.21864	NM_008986	ENSMUSG00000004044	Ptrf	2310075E07Rik|AW546441|Cav-p60|Cavin	polymerase I and transcript release factor	protein-coding
mm_6041.1	chr1	59684803	59684831	-	1	NA	promoter-TSS (NM_018868)	promoter-TSS (NM_018868)	-189	NM_018868	55989	Mm.220367	NM_018868	ENSMUSG00000026020	Nop58	MSSP|Nol5|SIK|nop5	NOP58 ribonucleoprotein	protein-coding
mm_86545.1	chr10	9732556	9732558	+	1	NA	Intergenic	Intergenic	47835	NR_038036	620417	Mm.378085	NR_038036		Gm6150	-	predicted gene 6150	ncRNA
mm_40521.1	chr5	57913373	57913386	+	1	NA	intron (NM_001122758, intron 2 of 2)	intron (NM_001122758, intron 2 of 2)	195298	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_23300.1	chr3	52396544	52396552	+	1	NA	Intergenic	Intergenic	128211	NM_019739	56458	Mm.29891	NM_019739	ENSMUSG00000044167	Foxo1	AI876417|Afxh|FKHR|Fkhr1|Foxo1a	forkhead box O1	protein-coding
mm_30549.1	chr4	3684894	3684902	+	1	NA	intron (NM_010747, intron 1 of 12)	Lx9|LINE|L1	6777	NM_010747	17096	Mm.317331	NM_010747	ENSMUSG00000042228	Lyn	AA407514|Hck-2|p53Lyn|p56Lyn	LYN proto-oncogene, Src family tyrosine kinase	protein-coding
mm_81587.1	chr9	110476953	110476980	+	1	NA	promoter-TSS (NM_001163569)	promoter-TSS (NM_001163569)	8	NM_010628	16578	Mm.42170	NM_010628	ENSMUSG00000032489	Kif9	-	kinesin family member 9	protein-coding
mm_147691.1	chr18	60744673	60744683	-	1	NA	Intergenic	Intergenic	-29918	NM_020600	20044	Mm.43778	NM_020600	ENSMUSG00000024608	Rps14	2600014J02Rik|AL023078	ribosomal protein S14	protein-coding
mm_26134.1	chr3	137908464	137908479	+	1	NA	3' UTR (NM_001033155, exon 8 of 8)	3' UTR (NM_001033155, exon 8 of 8)	-10084	NM_019920	56692	Mm.331392	NM_019920	ENSMUSG00000091512	Lamtor3	AW556229|Map2k1ip1|Mapbp|Mapksp1|Mp1	late endosomal/lysosomal adaptor, MAPK and MTOR activator 3	protein-coding
mm_19838.1	chr2	112493253	112493280	-	1	NA	intron (NM_028844, intron 1 of 5)	CpG	302	NM_028844	74268	Mm.315125	NM_028844	ENSMUSG00000003604	Aven	1700013A01Rik|1700056A21Rik|mAven-L|mAven-S	apoptosis, caspase activation inhibitor	protein-coding
mm_37368.1	chr4	120825752	120825796	-	1	NA	promoter-TSS (NM_001277095)	promoter-TSS (NM_001277095)	-33	NM_008692	18046	Mm.435590	NM_008692	ENSMUSG00000032897	Nfyc	-	nuclear transcription factor-Y gamma	protein-coding
mm_153165.1	chr19	34493324	34493338	-	1	NA	3' UTR (NM_021460, exon 10 of 10)	3' UTR (NM_021460, exon 10 of 10)	-18196	NM_009890	12642	Mm.30824	NM_009890	ENSMUSG00000050370	Ch25h	AI462618|m25OH	cholesterol 25-hydroxylase	protein-coding
mm_69302.1	chr7	128376110	128376119	-	1	NA	intron (NM_026418, intron 4 of 4)	intron (NM_026418, intron 4 of 4)	42058	NM_026418	67865	Mm.18635	NM_026418	ENSMUSG00000030844	Rgs10	2310010N19Rik	regulator of G-protein signalling 10	protein-coding
mm_56491.1	chr6	99194510	99194513	-	1	NA	intron (NM_001347345, intron 4 of 19)	intron (NM_001347345, intron 4 of 19)	72004	NM_001197321	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_131911.1	chr16	23290465	23290534	+	1	NA	promoter-TSS (NM_001252506)	promoter-TSS (NM_001252506)	29	NM_001252506	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_128389.1	chr15	43166794	43166803	-	1	NA	intron (NM_172815, intron 2 of 5)	intron (NM_172815, intron 2 of 5)	4020	NM_172815	239405	Mm.193274	NM_172815	ENSMUSG00000051920	Rspo2	2610028F08Rik|AA673245|D430027K22|ftls	R-spondin 2	protein-coding
mm_10820.1	chr2	24351046	24351056	+	1	NA	3' UTR (NM_031167, exon 5 of 5)	3' UTR (NM_031167, exon 5 of 5)	5680	NM_001039701	16181	Mm.882	NM_031167	ENSMUSG00000026981	Il1rn	F630041P17Rik|IL-1ra	interleukin 1 receptor antagonist	protein-coding
mm_24242.1	chr3	89136117	89136123	+	1	NA	promoter-TSS (NM_001099779)	promoter-TSS (NM_001099779)	-22	NM_013631	18770	Mm.383180	NM_013631	ENSMUSG00000041237	Pklr	Pk-1|Pk1|R-PK	pyruvate kinase liver and red blood cell	protein-coding
mm_126612.1	chr15	83033407	83033480	+	1	NA	promoter-TSS (NM_001271412)	promoter-TSS (NM_001271412)	-46	NM_001271411	74039	Mm.32584	NM_028728	ENSMUSG00000058099	Nfam1	4921501M20Rik|Cnaip	Nfat activating molecule with ITAM motif 1	protein-coding
mm_35195.1	chr4	16147153	16147167	-	1	NA	intron (NR_138102, intron 4 of 11)	L1_Mus2|LINE|L1	16483	NM_138952	192656	Mm.112765	NM_138952	ENSMUSG00000041135	Ripk2	2210420D18Rik|CARD3|CARDIAK|CCK|D4Bwg0615e|RICK|RIP2	receptor (TNFRSF)-interacting serine-threonine kinase 2	protein-coding
mm_61292.1	chr7	67647571	67647583	+	1	NA	5' UTR (NM_025905, exon 1 of 12)	5' UTR (NM_025905, exon 1 of 12)	167	NM_025905	67009	Mm.249356	NM_025905	ENSMUSG00000030555	Ttc23	1600012K10Rik	tetratricopeptide repeat domain 23	protein-coding
mm_48614.1	chr5	144479739	144479753	-	1	NA	Intergenic	B4A|SINE|B4	-66141	NM_016789	53324	Mm.10099	NM_016789	ENSMUSG00000059991	Nptx2	Narp|np2	neuronal pentraxin 2	protein-coding
mm_157363.1	chrX	37168830	37168854	-	1	NA	promoter-TSS (NM_001033785)	promoter-TSS (NM_001033785)	0	NM_001033785	434756	Mm.471848	NM_001033785	ENSMUSG00000036551	Akap14	-	A kinase (PRKA) anchor protein 14	protein-coding
mm_6480.1	chr1	74091284	74091320	-	1	NA	intron (NM_027884, intron 1 of 34)	intron (NM_027884, intron 1 of 34)	33145	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_105236.1	chr11	102317861	102317877	-	1	NA	promoter-TSS (NM_001044383)	promoter-TSS (NM_001044383)	-582	NM_001044383	21429	Mm.2845	NM_011551	ENSMUSG00000020923	Ubtf	A930005G04Rik|NOR-90|Tcfubf|UBF|UBF-1|UBF1	upstream binding transcription factor, RNA polymerase I	protein-coding
mm_138460.1	chr17	35140816	35140835	+	1	NA	exon (NM_001252469, exon 7 of 24)	exon (NM_001252469, exon 7 of 24)	5111	NM_001252469	224727	Mm.203962	NM_057171	ENSMUSG00000024392	Bag6	2410045D21Rik|AA408914|BAG-6|Bat3|D17H6S52E|G3|Scythe	BCL2-associated athanogene 6	protein-coding
mm_131649.1	chr16	20535461	20535471	+	1	NA	promoter-TSS (NM_009679)	promoter-TSS (NM_009679)	-14	NM_001302970	11773	Mm.18946	NM_009679	ENSMUSG00000022841	Ap2m1	-	adaptor-related protein complex 2, mu 1 subunit	protein-coding
mm_158515.1	chrX	143393879	143393891	-	1	NA	5' UTR (NM_031258, exon 1 of 9)	5' UTR (NM_031258, exon 1 of 9)	377	NM_031258	83453	Mm.157697	NM_031258	ENSMUSG00000031283	Chrdl1	CHL|CHL1|Nrln1|VOPT	chordin-like 1	protein-coding
mm_102972.1	chr11	69668992	69668996	-	1	NA	intron (NM_001159375, intron 5 of 10)	intron (NM_001159375, intron 5 of 10)	-2824	NR_110993	12514	Mm.15819	NM_009853	ENSMUSG00000018774	Cd68	Lamp4|Scard1|gp110	CD68 antigen	protein-coding
mm_93890.1	chr10	125328559	125328573	-	1	NA	promoter-TSS (NM_011391)	promoter-TSS (NM_011391)	-31	NM_011391	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|Mct2	solute carrier family 16 (monocarboxylic acid transporters), member 7	protein-coding
mm_138570.1	chr17	35381544	35381548	+	1	NA	intron (NM_001143689, intron 3 of 5)	intron (NM_001143689, intron 3 of 5)	1929	NM_001143689	15015	Mm.464284	NM_001143689	ENSMUSG00000035929	H2-Q4	H-2Q4|H2-Gs10|Qa-4|Qa4|Qat-4|Qb-1|Qb1	histocompatibility 2, Q region locus 4	protein-coding
mm_43378.1	chr5	135685751	135685754	+	1	NA	Intergenic	ID_B1|SINE|B4	-3393	NM_008898	18984	Mm.3863	NM_008898	ENSMUSG00000005514	Por	4933424M13Rik|CPR|CYPOR|P450R	P450 (cytochrome) oxidoreductase	protein-coding
mm_85289.1	chr9	99876148	99876193	-	1	NA	promoter-TSS (NM_011440)	promoter-TSS (NM_011440)	0	NM_011440	20669	Mm.261595	NM_011440	ENSMUSG00000053747	Sox14	-	SRY (sex determining region Y)-box 14	protein-coding
mm_140099.1	chr17	78308474	78308480	+	1	NA	intron (NM_015800, intron 5 of 16)	intron (NM_015800, intron 5 of 16)	108229	NM_015800	50766	Mm.311912	NM_015800	ENSMUSG00000024074	Crim1	AU015004	cysteine rich transmembrane BMP regulator 1 (chordin like)	protein-coding
mm_124557.1	chr14	122917589	122917598	-	1	NA	Intergenic	Intergenic	-4428	NM_145466	223267	Mm.379358	NM_145466	ENSMUSG00000041625	Ggact	A2ld1	gamma-glutamylamine cyclotransferase	protein-coding
mm_170011.1	chr17	17179275	17179294	+	1	NA	Intergenic	Intergenic	57901	NM_011765	22759	Mm.436633	NM_011765	ENSMUSG00000095990	Zfp97	NGD16-4	zinc finger protein 97	protein-coding
mm_168677.1	chr11	94653773	94653790	+	1	NA	promoter-TSS (NM_177752)	promoter-TSS (NM_177752)	-10	NM_053161	94064	Mm.34951	NM_053161	ENSMUSG00000024414	Mrpl27	A630055F16Rik|D11Moh47|D18Ertd643e	mitochondrial ribosomal protein L27	protein-coding
mm_141274.1	chr17	27820474	27820482	-	1	NA	promoter-TSS (NM_001271511)	promoter-TSS (NM_001271511)	64	NM_001033279	224647	Mm.196577	NM_001033279	ENSMUSG00000056692	D17Wsu92e	AU020189|C030010A15|C80239	DNA segment, Chr 17, Wayne State University 92, expressed	protein-coding
mm_124143.1	chr14	87141207	87141239	-	1	NA	promoter-TSS (NM_019670)	promoter-TSS (NM_019670)	-109	NM_019670	56419	Mm.440585	NM_019670	ENSMUSG00000022021	Diaph3	4930417P13Rik|Dia2|Diap3|Drf3|mDia2|mKIAA4117|p134MDia2	diaphanous related formin 3	protein-coding
mm_74776.1	chr8	21906427	21906437	-	1	NA	promoter-TSS (NM_139221)	promoter-TSS (NM_139221)	0	NM_139221	246081	Mm.221026	NM_139221	ENSMUSG00000045337	Defb11	BD-11|Defb8	defensin beta 11	protein-coding
mm_124017.1	chr14	76515486	76515506	-	1	NA	intron (NR_045660, intron 3 of 3)	intron (NR_045660, intron 3 of 3)	5359	NR_045660	75789	Mm.159571	NR_045660	ENSMUSG00000097172	4930444M15Rik	-	RIKEN cDNA 4930444M15 gene	ncRNA
mm_72416.1	chr8	81861679	81861686	+	1	NA	intron (NM_001024617, intron 8 of 24)	intron (NM_001024617, intron 8 of 24)	519120	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_95895.1	chr11	58183936	58183947	+	1	NA	promoter-TSS (NM_001135115)	promoter-TSS (NM_001135115)	98	NM_001135115	631323	Mm.394103	NM_001135115		Gm12250	Irgb10|OTTMUSG00000005723	predicted gene 12250	protein-coding
mm_85047.1	chr9	89705018	89705068	-	1	NA	promoter-TSS (NM_025360)	promoter-TSS (NM_025360)	0	NM_025360	66111	Mm.27606	NM_025360	ENSMUSG00000032353	Tmed3	1200002G13Rik|AW546672|P24b	transmembrane p24 trafficking protein 3	protein-coding
mm_26527.1	chr3	145988671	145988683	+	1	NA	exon (NM_001166064, exon 1 of 7)	exon (NM_001166064, exon 1 of 7)	807	NM_001166064	214804	Mm.268854	NM_001166064	ENSMUSG00000036863	Syde2	C430017H16Rik	synapse defective 1, Rho GTPase, homolog 2 (C. elegans)	protein-coding
mm_74178.1	chr8	123454299	123454309	+	1	NA	exon (NM_054046, exon 5 of 12)	exon (NM_054046, exon 5 of 12)	11045	NM_001281803	23854	Mm.275127	NM_054046	ENSMUSG00000001482	Def8	AI449518|D8Ertd713e|DEF-8	differentially expressed in FDCP 8	protein-coding
mm_110965.1	chr12	76822511	76822558	-	1	NA	promoter-TSS (NM_134050)	promoter-TSS (NM_134050)	-10	NM_134050	104886	Mm.172847	NM_134050	ENSMUSG00000021062	Rab15	2310012G06Rik|AI840042	RAB15, member RAS oncogene family	protein-coding
mm_34794.1	chr4	154531270	154531270	+	1	NA	intron (NM_001177995, intron 1 of 15)	intron (NM_001177995, intron 1 of 15)	105097	NR_045643	320939	Mm.436738	NR_045643		5930403L14Rik	-	RIKEN cDNA 5930403L14 gene	ncRNA
mm_147298.1	chr18	39519215	39519240	-	1	NA	Intergenic	Intergenic	-31982	NM_008173	14815	Mm.129481	NM_008173	ENSMUSG00000024431	Nr3c1	GR|Grl-1|Grl1	nuclear receptor subfamily 3, group C, member 1	protein-coding
mm_148346.1	chr18	84669876	84669887	-	1	NA	exon (NM_001289531, exon 8 of 11)	exon (NM_001289531, exon 8 of 11)	12178	NM_001289531	66054	Mm.29646	NM_023149	ENSMUSG00000024644	Cndp2	0610010E05Rik|C76600|Cn2|Dip-2|Pep-1|Pep1	CNDP dipeptidase 2 (metallopeptidase M20 family)	protein-coding
mm_117027.1	chr13	58264732	58264736	-	1	NA	intron (NM_019832, intron 1 of 11)	intron (NM_019832, intron 1 of 11)	9454	NM_019832	56278	Mm.296625	NM_019832	ENSMUSG00000021552	Gkap1	42kDa|4933400B15Rik|D13Ertd340e|Gkap42	G kinase anchoring protein 1	protein-coding
mm_93504.1	chr10	112928975	112929014	-	1	NA	promoter-TSS (NM_001033474)	promoter-TSS (NM_001033474)	32	NM_001033474	382423	Mm.431239	NM_001033474	ENSMUSG00000074748	Atxn7l3b	4921506J03Rik|6230409E21Rik|AI315132|ENSMUSG00000074747	ataxin 7-like 3B	protein-coding
mm_123654.1	chr14	69242578	69242598	-	1	NA	3' UTR (NM_026331, exon 4 of 4)	3' UTR (NM_026331, exon 4 of 4)	42515	NM_026331	67712	Mm.293635	NM_026331	ENSMUSG00000034248	Slc25a37	1700020E22Rik|4930513O14Rik|4930526G11Rik|AI848481|C330015G08Rik|Mfrn|Mfrn1|Mscp|frascati|mitoferrin	solute carrier family 25, member 37	protein-coding
mm_66287.1	chr7	37773984	37773990	-	1	NA	Intergenic	Intergenic	-4235	NM_172385	243937	Mm.322505	NM_172385	ENSMUSG00000043456	Zfp536	9630010P11Rik|Znf536|mKIAA0390	zinc finger protein 536	protein-coding
mm_127219.1	chr15	99393233	99393248	+	1	NA	promoter-TSS (NM_001171035)	promoter-TSS (NM_001171035)	21	NM_001171035	110213	Mm.16769	NM_026669	ENSMUSG00000023010	Tmbim6	5031406P05Rik|Bi1|Tegt	transmembrane BAX inhibitor motif containing 6	protein-coding
mm_8301.1	chr1	144002248	144002266	-	1	NA	exon (NM_009061, exon 4 of 5)	exon (NM_009061, exon 4 of 5)	1892	NM_009061	19735	Mm.28262	NM_009061	ENSMUSG00000026360	Rgs2	GOS8	regulator of G-protein signaling 2	protein-coding
mm_108330.1	chr12	79963740	79963743	+	1	NA	Intergenic	Intergenic	-27477	NR_131074	77290	Mm.395042	NR_131073		9430078K24Rik	-	RIKEN cDNA 9430078K24 gene	ncRNA
mm_70685.1	chr8	15011210	15011235	+	1	NA	5' UTR (NM_029116, exon 1 of 2)	5' UTR (NM_029116, exon 1 of 2)	197	NM_029116	74901	Mm.46675	NM_029116	ENSMUSG00000055675	Kbtbd11	2900016B01Rik|4930465M17Rik|mKIAA0711	kelch repeat and BTB (POZ) domain containing 11	protein-coding
mm_15687.1	chr2	163645241	163645254	+	1	NA	promoter-TSS (NM_012032)	promoter-TSS (NM_012032)	-104	NM_012032	26943	Mm.218473	NM_012032	ENSMUSG00000017707	Serinc3	AA959945|AA960047|AIGP1|DIFF33|TMS-1|Tde1	serine incorporator 3	protein-coding
mm_61481.1	chr7	75669707	75669727	+	1	NA	intron (NM_029332, intron 10 of 36)	intron (NM_029332, intron 10 of 36)	-178621	NM_001122780	207952	Mm.206223	NM_029652	ENSMUSG00000055652	Klhl25	2810402K13Rik|BC027373|Enc-1	kelch-like 25	protein-coding
mm_167281.1	chr8	36732870	36732896	-	1	NA	5' UTR (NM_001194941, exon 1 of 14)	5' UTR (NM_001194941, exon 1 of 14)	171	NM_001194941	50768	Mm.125155	NM_015802	ENSMUSG00000031523	Dlc1	A730069N07Rik|Arhgap7|HP|STARD12|dlc-1	deleted in liver cancer 1	protein-coding
mm_30394.1	chr3	152248326	152248343	-	1	NA	exon (NM_199465, exon 6 of 13)	exon (NM_199465, exon 6 of 13)	17986	NM_199465	68810	Mm.200188	NM_199465	ENSMUSG00000039103	Nexn	1110046H09Rik|AA553326|NELIN	nexilin	protein-coding
mm_58027.1	chr6	136661929	136661982	-	1	NA	promoter-TSS (NM_025806)	promoter-TSS (NM_025806)	-62	NM_025806	66857	Mm.3311	NM_025806	ENSMUSG00000030214	Plbd1	1100001H23Rik	phospholipase B domain containing 1	protein-coding
mm_78792.1	chr9	44045945	44045956	+	1	NA	intron (NM_009382, intron 1 of 3)	intron (NM_009382, intron 1 of 3)	2566	NM_009382	21838	Mm.3951	NM_009382	ENSMUSG00000032011	Thy1	CD90|T25|Thy-1|Thy-1.2|Thy1.1|Thy1.2	thymus cell antigen 1, theta	protein-coding
mm_139324.1	chr17	48450932	48450945	+	1	NA	5' UTR (NM_027292, exon 2 of 5)	5' UTR (NM_027292, exon 2 of 5)	563	NM_027292	70026	Mm.22613	NM_027292	ENSMUSG00000023995	Tspo2	2510027D20Rik|Bzrpl1	translocator protein 2	protein-coding
mm_43475.1	chr5	136695205	136695213	+	1	NA	intron (NM_001085387, intron 1 of 4)	intron (NM_001085387, intron 1 of 4)	1032	NM_001085387	59310	Mm.5178	NM_021611	ENSMUSG00000005474	Myl10	1700027I08Rik|Mylc2pl|PLRLC	myosin, light chain 10, regulatory	protein-coding
mm_91700.1	chr10	44004358	44004385	-	1	NA	5' UTR (NM_172393, exon 1 of 20)	5' UTR (NM_172393, exon 1 of 20)	475	NM_172393	11630	Mm.292082	NM_172393	ENSMUSG00000019866	Aim1	AI462491|AI463325	absent in melanoma 1	protein-coding
mm_83673.1	chr9	49798822	49798855	-	1	NA	5' UTR (NM_001311065, exon 1 of 18)	5' UTR (NM_001311065, exon 1 of 18)	231	NM_001081445	17967	Mm.4974	NM_010875	ENSMUSG00000039542	Ncam1	CD56|E-NCAM|NCAM-1|Ncam	neural cell adhesion molecule 1	protein-coding
mm_14302.1	chr2	129100983	129100989	+	1	NA	promoter-TSS (NM_009086)	promoter-TSS (NM_009086)	-10	NM_009086	20017	Mm.259078	NM_009086	ENSMUSG00000027395	Polr1b	128kDa|D630020H17Rik|RPA116|RPA135|RPA2|Rpo1-2	polymerase (RNA) I polypeptide B	protein-coding
mm_43183.1	chr5	128570734	128570753	+	1	NA	Intergenic	Intergenic	29944	NR_015517	319616	Mm.387738	NR_015517	ENSMUSG00000072591	5930412G12Rik	-	RIKEN cDNA 5930412G12 gene	ncRNA
mm_146431.1	chr18	84871564	84871576	+	1	NA	exon (NM_025797, exon 2 of 5)	exon (NM_025797, exon 2 of 5)	20156	NM_025797	109672	Mm.31018	NM_025797	ENSMUSG00000024646	Cyb5a	0610009N12Rik|Cyb5	cytochrome b5 type A (microsomal)	protein-coding
mm_125031.1	chr15	25754785	25754796	+	1	NA	intron (NM_019472, intron 19 of 40)	intron (NM_019472, intron 19 of 40)	-88508	NM_001034851	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_103239.1	chr11	70687215	70687250	-	1	NA	intron (NM_178116, intron 1 of 22)	intron (NM_178116, intron 1 of 22)	873	NM_001190376	216874	Mm.473726	NM_178116	ENSMUSG00000040712	Camta2	Kiaa0909-hp|mKIAA0909	calmodulin binding transcription activator 2	protein-coding
mm_45991.1	chr5	90504358	90504379	-	1	NA	exon (NM_007423, exon 10 of 15)	exon (NM_007423, exon 10 of 15)	13654	NM_007423	11576	Mm.358570	NM_007423	ENSMUSG00000054932	Afp	-	alpha fetoprotein	protein-coding
mm_89171.1	chr10	86311303	86311350	+	1	NA	intron (NM_011595, intron 1 of 4)	(CA)n|Simple_repeat|Simple_repeat	10914	NM_011595	21859	Mm.4871	NM_011595	ENSMUSG00000020044	Timp3	Timp-3	tissue inhibitor of metalloproteinase 3	protein-coding
mm_47634.1	chr5	125303196	125303222	-	1	NA	exon (NM_001205082, exon 3 of 12)	exon (NM_001205082, exon 3 of 12)	37885	NM_016741	20778	Mm.282242	NM_016741	ENSMUSG00000037936	Scarb1	AI120173|CD36|Cd36l1|Chohd1|Cla-1|Cla1|D5Ertd460e|Hdlq1|Hlb398|SR-B1|SR-BI|SRBI|Srb1|mSR-BI	scavenger receptor class B, member 1	protein-coding
mm_164356.1	chr16	20928883	20928896	+	1	NA	Intergenic	Intergenic	-194378	NM_009379	21832	Mm.3943	NM_009379	ENSMUSG00000022847	Thpo	Mgdf|Ml|Mpllg|Tpo	thrombopoietin	protein-coding
mm_21263.1	chr2	156780516	156780523	-	1	NA	exon (NM_172118, exon 3 of 4)	exon (NM_172118, exon 3 of 4)	5055	NM_172118	98932	Mm.271770	NM_172118	ENSMUSG00000067818	Myl9	AI327049|MLC20|Mylc2c|RLC-C	myosin, light polypeptide 9, regulatory	protein-coding
mm_162070.1	chrX	16522919	16522919	+	1	NA	promoter-TSS (NM_001039943)	promoter-TSS (NM_001039943)	38	NM_001039943	664725	Mm.45302	NM_001039943		Cypt7	-	cysteine-rich perinuclear theca 7	protein-coding
mm_33107.1	chr4	124709168	124709192	+	1	NA	TTS (NM_010213)	TTS (NM_010213)	-5681	NM_029157	75062	Mm.25779	NM_029157	ENSMUSG00000028902	Sf3a3	4930512K19Rik|60kDa	splicing factor 3a, subunit 3	protein-coding
mm_5714.1	chr1	44019930	44019940	-	1	NA	promoter-TSS (NM_001013799)	promoter-TSS (NM_001013799)	71	NM_001013799	433294	Mm.123621	NM_001013799	ENSMUSG00000047343	Mettl21c	A530098C11Rik	methyltransferase like 21C	protein-coding
mm_132031.1	chr16	27389035	27389089	+	1	NA	5' UTR (NM_001289436, exon 1 of 12)	5' UTR (NM_001289436, exon 1 of 12)	106	NM_001289436	67501	Mm.258985	NM_026202	ENSMUSG00000038127	Ccdc50	C3orf6	coiled-coil domain containing 50	protein-coding
mm_80510.1	chr9	79688772	79688811	+	1	NA	intron (NM_001290308, intron 13 of 65)	Lx8|LINE|L1	29931	NM_001290308	12816	Mm.3819	NM_007730	ENSMUSG00000032332	Col12a1	-	collagen, type XII, alpha 1	protein-coding
mm_25424.1	chr3	107874795	107874796	+	1	NA	Intergenic	Intergenic	-2435	NM_133867	99662	Mm.108491	NM_133867	ENSMUSG00000040600	Eps8l3	AI504489|Eps8r3	EPS8-like 3	protein-coding
mm_162546.1	chr1	170707728	170707730	+	1	NA	3' UTR (NM_001081304, exon 16 of 16)	3' UTR (NM_001081304, exon 16 of 16)	63197	NM_177068	320078	Mm.287131	NM_177068	ENSMUSG00000038463	Olfml2b	1110018N05Rik|4832415H08Rik|AI467542	olfactomedin-like 2B	protein-coding
mm_81660.1	chr9	110992816	110992820	+	1	NA	Intergenic	Intergenic	-3105	NM_153100	235636	Mm.441138	NM_153100	ENSMUSG00000066319	Rtp3	Tmem7	receptor transporter protein 3	protein-coding
mm_161475.1	chr15	82015452	82015452	+	1	NA	promoter-TSS (NM_010247)	promoter-TSS (NM_010247)	688	NM_134095	28075	Mm.474453	NM_134095	ENSMUSG00000022472	Desi1	AI427858|AI850401|D15Wsu75e|DeSI-1|Fam152b|Pppde2	desumoylating isopeptidase 1	protein-coding
mm_156200.1	chrX	134404809	134404897	+	1	NA	promoter-TSS (NM_010078)	promoter-TSS (NM_010078)	73	NM_010078	13497	Mm.121662	NM_010078	ENSMUSG00000000223	Drp2	AW495265|DRP-2	dystrophin related protein 2	protein-coding
mm_108133.1	chr12	76081646	76081661	+	1	NA	intron (NM_001005510, intron 99 of 115)	intron (NM_001005510, intron 99 of 115)	95606	NM_010157	13983	Mm.2561	NM_010157	ENSMUSG00000021055	Esr2	ER[b]|ERbeta|Estrb	estrogen receptor 2 (beta)	protein-coding
mm_63127.1	chr7	123001590	123001618	+	1	NA	exon (NM_011247, exon 18 of 18)	exon (NM_011247, exon 18 of 18)	31040	NM_175023	19647	Mm.4480	NM_011247	ENSMUSG00000030779	Rbbp6	4933422O15Rik|AI316869|BB233631|C030034J04Rik|C77662|P2P-R|PACT	retinoblastoma binding protein 6	protein-coding
mm_14914.1	chr2	150770283	150770295	+	1	NA	intron (NM_172117, intron 12 of 13)	intron (NM_172117, intron 12 of 13)	-16507	NM_153781	110078	Mm.222584	NM_153781	ENSMUSG00000033059	Pygb	-	brain glycogen phosphorylase	protein-coding
mm_12527.1	chr2	72180053	72180066	+	1	NA	exon (NM_001204166, exon 7 of 28)	exon (NM_001204166, exon 7 of 28)	-105578	NM_023057	65964	Mm.304143	NM_023057	ENSMUSG00000004085	Map3k20	AV006891|B230120H23Rik|MLTK|MLTKalpha|MLTKbeta|Zak	mitogen-activated protein kinase kinase kinase 20	protein-coding
mm_53297.1	chr6	129045822	129045830	+	1	NA	promoter-TSS (NM_153094)	promoter-TSS (NM_153094)	-75	NR_024262	232408	Mm.259262	NM_153094	ENSMUSG00000030154	Klrb1f	A630024B12Rik|Nkr-p1f|Nkrp1-f|Nkrp1f	killer cell lectin-like receptor subfamily B member 1F	protein-coding
mm_92936.1	chr10	84533940	84533950	-	1	NA	promoter-TSS (NM_175451)	promoter-TSS (NM_175451)	-57	NM_175451	216197	Mm.334999	NM_175451	ENSMUSG00000046841	Ckap4	5630400A09Rik|CLIMP-63|P63	cytoskeleton-associated protein 4	protein-coding
mm_47786.1	chr5	132193383	132193385	-	1	NA	intron (NM_177047, intron 2 of 18)	intron (NM_177047, intron 2 of 18)	313115	NR_040704	75369	Mm.389696	NR_040704	ENSMUSG00000105773	4930563F08Rik	-	RIKEN cDNA 4930563F08 gene	ncRNA
mm_150384.1	chr19	36348385	36348395	+	1	NA	Intergenic	(CCG)n|Simple_repeat|Simple_repeat	-30677	NM_029508	76073	Mm.259180	NM_029508	ENSMUSG00000024805	Pcgf5	0610009F02Rik|1110054A01Rik|5830406C17Rik|5830443C21Rik|9530023M17Rik|AI324127	polycomb group ring finger 5	protein-coding
mm_82035.1	chr9	122117259	122117326	+	1	NA	promoter-TSS (NM_133741)	promoter-TSS (NM_133741)	26	NM_133741	20623	Mm.257989	NM_133741	ENSMUSG00000038145	Snrk	2010012F07Rik|AI448042|AW547029|E030034B15|R74830|mKIAA0096	SNF related kinase	protein-coding
mm_101967.1	chr11	50308851	50308863	-	1	NA	exon (NM_001110500, exon 5 of 15)	exon (NM_001110500, exon 5 of 15)	-16521	NM_175334	103806	Mm.51116	NM_175334	ENSMUSG00000050567	Maml1	AI644666|AW743257|D930008C07Rik|Mam-1|Mam1|mKIAA0200	mastermind like 1 (Drosophila)	protein-coding
mm_101149.1	chr11	16636129	16636141	-	1	NA	Intergenic	Intergenic	-116068	NM_207655	13649	Mm.8534	NM_007912	ENSMUSG00000020122	Egfr	9030024J15Rik|AI552599|Erbb|Errb1|Errp|Wa5|wa-2|wa2	epidermal growth factor receptor	protein-coding
mm_8991.1	chr1	165708058	165708078	-	1	NA	promoter-TSS (NM_001038846)	promoter-TSS (NM_001038846)	26	NM_178593	226594	Mm.265552	NM_178593	ENSMUSG00000040723	Rcsd1	A430105K13Rik|BC025872|CapZIP	RCSD domain containing 1	protein-coding
mm_140020.1	chr17	73804946	73804956	+	1	NA	5' UTR (NM_020578, exon 1 of 6)	5' UTR (NM_020578, exon 1 of 6)	110	NM_020578	57440	Mm.18526	NM_020578	ENSMUSG00000024065	Ehd3	Ehd2	EH-domain containing 3	protein-coding
mm_83728.1	chr9	51008967	51009080	-	1	NA	promoter-TSS (NM_178710)	promoter-TSS (NM_178710)	50	NM_178710	235344	Mm.104932	NM_178710	ENSMUSG00000037112	Sik2	G630080D20Rik|Snf1lk2	salt inducible kinase 2	protein-coding
mm_71476.1	chr8	46535730	46535750	+	1	NA	3' UTR (NM_007981, exon 21 of 21)	3' UTR (NM_007981, exon 21 of 21)	-16329	NM_027973	71876	Mm.22108	NM_027973	ENSMUSG00000031629	Cenpu	1700029A22Rik|Mlf1ip	centromere protein U	protein-coding
mm_75307.1	chr8	41133988	41134002	-	1	NA	promoter-TSS (NM_001005863)	promoter-TSS (NM_001005863)	-269	NM_001005863	102103	Mm.149438	NM_001005863	ENSMUSG00000045636	Mtus1	AI481402|ATBP135|Atip1|B430010I23Rik|B430305I03Rik|C85752|Cctsg1-440|MD44|MTSG1|mKIAA1288	mitochondrial tumor suppressor 1	protein-coding
mm_4720.1	chr1	181144227	181144246	+	1	NA	promoter-TSS (NM_026171)	promoter-TSS (NM_026171)	-32	NM_026171	67459	Mm.263464	NM_026171	ENSMUSG00000026516	Nvl	1200009I24Rik	nuclear VCP-like	protein-coding
mm_13258.1	chr2	98665124	98665134	+	1	NA	Intergenic	SYNREP_MM|Satellite|Satellite	1197472	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_71552.1	chr8	48110157	48110194	+	1	NA	non-coding (NR_027759, exon 1 of 6)	non-coding (NR_027759, exon 1 of 6)	162	NM_001161515	320685	Mm.121549	NM_178788	ENSMUSG00000031562	Dctd	6030466N05Rik	dCMP deaminase	protein-coding
mm_17513.1	chr2	29191510	29191551	-	1	NA	Intergenic	Intergenic	56569	NM_001305805	171171	Mm.442448	NM_133500	ENSMUSG00000035513	Ntng2	2610016D08Rik|Lmnt2	netrin G2	protein-coding
mm_36541.1	chr4	86668488	86668560	-	1	NA	exon (NM_007408, exon 3 of 8)	exon (NM_007408, exon 3 of 8)	1535	NM_007408	11520	Mm.381	NM_007408	ENSMUSG00000028494	Plin2	AA407157|ADPH|Adfp|Adrp	perilipin 2	protein-coding
mm_159114.1	chr2	57998246	57998246	+	1	NA	promoter-TSS (NM_172855)	promoter-TSS (NM_172855)	91	NM_172855	241391	Mm.484118	NM_172855	ENSMUSG00000026828	Galnt5	4832424J23	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 5	protein-coding
mm_109887.1	chr12	5375689	5375705	-	1	NA	promoter-TSS (NM_001164493)	promoter-TSS (NM_001164493)	-15	NM_001164493	208439	Mm.388281	NM_001164493	ENSMUSG00000020627	Klhl29	A230106N14Rik|Gm68|Kbtbd9|mKIAA1921	kelch-like 29	protein-coding
mm_172274.1	chr6	85587861	85587870	+	1	NA	exon (NM_145223, exon 1 of 23)	exon (NM_145223, exon 1 of 23)	334	NM_145223	236266	Mm.246967	NM_145223	ENSMUSG00000063810	Alms1	bbb	Alstrom syndrome 1	protein-coding
mm_4402.1	chr1	172431011	172431021	+	1	NA	Intergenic	MYSERV6-int|LTR|ERVK	-44344	NM_029612	98365	Mm.150050	NM_029612	ENSMUSG00000026548	Slamf9	2310026I04Rik|AI462096|CD2F-10|CD84-H1|Cd2f10|SF2001	SLAM family member 9	protein-coding
mm_40059.1	chr5	33996640	33996690	+	1	NA	5' UTR (NM_001001985, exon 1 of 3)	5' UTR (NM_001001985, exon 1 of 3)	681	NM_001001985	269642	Mm.274610	NM_001001985	ENSMUSG00000048142	Nat8l	1110038O08Rik|Shati	N-acetyltransferase 8-like	protein-coding
mm_132828.1	chr16	45227268	45227309	+	1	NA	intron (NM_177584, intron 1 of 5)	intron (NM_177584, intron 1 of 5)	2951	NM_177584	208154	Mm.38199	NM_177584	ENSMUSG00000052013	Btla	A630002H24	B and T lymphocyte associated	protein-coding
mm_172622.1	chr8	20149004	20149008	+	1	NA	Intergenic	B3|SINE|B2	148426	NR_030708	547150	Mm.359054	NR_030708	ENSMUSG00000071796	6820431F20Rik	-	cadherin 11 pseudogene	pseudo
mm_36721.1	chr4	98727966	98727978	-	1	NA	intron (NM_001081202, intron 2 of 4)	intron (NM_001081202, intron 2 of 4)	1218	NM_001081202	381591	Mm.34340	NM_001081202	ENSMUSG00000087166	L1td1	AA546746|AB211064|D76865|ECAT11	LINE-1 type transposase domain containing 1	protein-coding
mm_99202.1	chr11	101022736	101022746	+	1	NA	intron (NM_001243050, intron 5 of 20)	intron (NM_001243050, intron 5 of 20)	-7599	NR_105893	102466767		NR_105893	ENSMUSG00000098415	Mir6928	Gm27728|mmu-mir-6928	microRNA 6928	ncRNA
mm_27801.1	chr3	75956205	75956240	-	1	NA	exon (NM_175193, exon 1 of 15)	exon (NM_175193, exon 1 of 15)	727	NM_175193	73124	Mm.249232	NM_175193	ENSMUSG00000034109	Golim4	3110027H23Rik|GIMPC|GPP130|Golph4|P138	golgi integral membrane protein 4	protein-coding
mm_99222.1	chr11	101036722	101036748	+	1	NA	exon (NM_001243049, exon 10 of 21)	exon (NM_001243049, exon 10 of 21)	6395	NR_105893	102466767		NR_105893	ENSMUSG00000098415	Mir6928	Gm27728|mmu-mir-6928	microRNA 6928	ncRNA
mm_86514.1	chr10	7680919	7681025	+	1	NA	promoter-TSS (NM_010690)	promoter-TSS (NM_010690)	186	NR_033219	407824	Mm.393120	NR_033219		BC020402	-	cDNA sequence BC020402	ncRNA
mm_15788.1	chr2	164425406	164425428	+	1	NA	3' UTR (NM_011521, exon 5 of 5)	3' UTR (NM_011521, exon 5 of 5)	17771	NM_011521	20971	Mm.3815	NM_011521	ENSMUSG00000017009	Sdc4	AA959608|AW108331|S4|Synd4|ryudocan|syndecan-4	syndecan 4	protein-coding
mm_627.1	chr1	40237216	40237225	+	1	NA	intron (NM_008362, intron 1 of 10)	intron (NM_008362, intron 1 of 10)	12140	NM_008362	16177	Mm.896	NM_008362	ENSMUSG00000026072	Il1r1	CD121a|CD121b|IL-1R1|IL-iR|Il1r-1	interleukin 1 receptor, type I	protein-coding
mm_97772.1	chr11	82057886	82057888	+	1	NA	promoter-TSS (NM_011330)	promoter-TSS (NM_011330)	55	NM_011330	20292	Mm.4686	NM_011330	ENSMUSG00000020676	Ccl11	Scya11|eotaxin	chemokine (C-C motif) ligand 11	protein-coding
mm_138961.1	chr17	44229778	44229781	+	1	NA	intron (NM_172621, intron 1 of 5)	B4|SINE|B4	41207	NM_172621	224796	Mm.37666	NM_172621	ENSMUSG00000023959	Clic5	5730531E12Rik|B330005L24|Gm322|jbg	chloride intracellular channel 5	protein-coding
mm_88335.1	chr10	75573510	75573528	+	1	NA	promoter-TSS (NM_008116)	promoter-TSS (NM_008116)	24	NM_008116	14598	Mm.4559	NM_008116	ENSMUSG00000006345	Ggt1	CD224|GGT|GGT 1|GGT-1|Ggtp|dwg	gamma-glutamyltransferase 1	protein-coding
mm_99572.1	chr11	103979603	103979626	+	1	NA	intron (NM_001304574, intron 3 of 4)	intron (NM_001304574, intron 3 of 4)	12743	NM_007477	11841	Mm.5061	NM_007477	ENSMUSG00000062421	Arf2	-	ADP-ribosylation factor 2	protein-coding
mm_76446.1	chr8	85072076	85072086	-	1	NA	intron (NM_001039514, intron 1 of 8)	CpG	324	NM_001039514	330817	Mm.193086	NM_201408	ENSMUSG00000060038	Dhps	Dhs	deoxyhypusine synthase	protein-coding
mm_90258.1	chr10	122448552	122448575	+	1	NA	promoter-TSS (NM_016847)	promoter-TSS (NM_016847)	64	NM_016847	54140	Mm.4351	NM_016847	ENSMUSG00000020123	Avpr1a	AVPR|Avpr1|V1a|V1aR	arginine vasopressin receptor 1A	protein-coding
mm_166878.1	chr7	25412984	25412987	-	1	NA	promoter-TSS (NM_153576)	promoter-TSS (NM_153576)	-99	NM_153576	232983	Mm.10545	NM_153576	ENSMUSG00000060188	Cxcl17	VCC-1|Vcc1	chemokine (C-X-C motif) ligand 17	protein-coding
mm_65271.1	chr7	24134077	24134094	-	1	NA	promoter-TSS (NM_019941)	promoter-TSS (NM_019941)	-78	NM_019941	56525	Mm.295595	NM_019941	ENSMUSG00000047603	Zfp235	0610030O19Rik|AI428448	zinc finger protein 235	protein-coding
mm_112032.1	chr12	111505053	111505069	-	1	NA	Intergenic	Intergenic	-19238	NM_001033248	212539	Mm.81916	NM_001033248	ENSMUSG00000010529	Gm266	-	predicted gene 266	protein-coding
mm_89584.1	chr10	95778902	95778927	+	1	NA	Intergenic	Intergenic	-161749	NM_001001932	216238	Mm.210035	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding
mm_158957.1	chr1	90967594	90967594	-	1	NA	promoter-TSS (NM_001159725)	promoter-TSS (NM_001159725)	73	NM_001159725	19329	Mm.279780	NM_008998	ENSMUSG00000026304	Rab17	AW413472	RAB17, member RAS oncogene family	protein-coding
mm_82588.1	chr9	21238806	21238826	-	1	NA	5' UTR (NM_016679, exon 1 of 5)	5' UTR (NM_016679, exon 1 of 5)	516	NM_016679	50868	Mm.248266	NM_016679	ENSMUSG00000003308	Keap1	INRF2|mKIAA0132	kelch-like ECH-associated protein 1	protein-coding
mm_157775.1	chrX	73780261	73780282	-	1	NA	exon (NM_008323, exon 9 of 13)	exon (NM_008323, exon 9 of 13)	5866	NM_019684	56504	Mm.111904	NM_019684	ENSMUSG00000002007	Srpk3	Mssk1|Stk23	serine/arginine-rich protein specific kinase 3	protein-coding
mm_31923.1	chr4	85388265	85388285	+	1	NA	3' UTR (NM_019535, exon 9 of 9)	3' UTR (NM_019535, exon 9 of 9)	182819	NM_019535	20404	Mm.143603	NM_019535	ENSMUSG00000028488	Sh3gl2	9530001L19Rik|AI120490|AW555077|B930049H17Rik|EEN-B1|SH3PA|Sh3d2a	SH3-domain GRB2-like 2	protein-coding
mm_170820.1	chr2	176521018	176521024	+	1	NA	promoter-TSS (NM_001177404).3	promoter-TSS (NM_001177404).3	17	NM_001177406	100303732	Mm.484983	NM_001177404	ENSMUSG00000095199	Zfp967	Gm14431|OTTMUSG00000016608	zinc finger protein 967	protein-coding
mm_28551.1	chr3	93279703	93279743	-	1	NA	Intergenic	Intergenic	-40026	NM_133698	68723	Mm.208047	NM_133698	ENSMUSG00000041991	Hrnr	1110033K19Rik|A530063N20Rik|S100a18	hornerin	protein-coding
mm_39140.1	chr4	155223234	155223249	-	1	NA	promoter-TSS (NM_011385)	promoter-TSS (NM_011385)	-706	NM_011385	20481	Mm.28520	NM_011385	ENSMUSG00000029050	Ski	2310012I02Rik|2610001A11Rik|AA062172|AA589460|BC004088	ski sarcoma viral oncogene homolog (avian)	protein-coding
mm_33564.1	chr4	131921151	131921160	+	1	NA	promoter-TSS (NM_001201367)	promoter-TSS (NM_001201367)	-616	NM_001201367	623230	Mm.421179	NM_001201367	ENSMUSG00000070720	Tmem200b	EG623230	transmembrane protein 200B	protein-coding
mm_126662.1	chr15	84298143	84298145	+	1	NA	intron (NM_133167, intron 8 of 12)	intron (NM_133167, intron 8 of 12)	-26576	NM_022321	64099	Mm.251356	NM_022321	ENSMUSG00000022439	Parvg	AI413459	parvin, gamma	protein-coding
mm_12815.1	chr2	80315670	80315678	+	1	NA	5' UTR (NM_024181, exon 1 of 23)	5' UTR (NM_024181, exon 1 of 23)	208	NM_024181	66861	Mm.21762	NM_024181	ENSMUSG00000027006	Dnajc10	1200006L06Rik|D2Ertd706e|ERdj5|JPDI	DnaJ heat shock protein family (Hsp40) member C10	protein-coding
mm_52617.1	chr6	117173957	117173978	+	1	NA	3' UTR (NM_021704, exon 3 of 3)	3' UTR (NM_021704, exon 3 of 3)	5432	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_131157.1	chr16	6914261	6914269	+	1	NA	intron (NM_021477, intron 5 of 16)	intron (NM_021477, intron 5 of 16)	-155570	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_44881.1	chr5	34637108	34637200	-	1	NA	promoter-TSS (NM_026660)	promoter-TSS (NM_026660)	-40	NM_026660	68294	Mm.34564	NM_026660	ENSMUSG00000001082	Mfsd10	0610009O03Rik|Tetran	major facilitator superfamily domain containing 10	protein-coding
mm_29928.1	chr3	131491328	131491336	-	1	NA	Intergenic	Intergenic	-73436	NM_001289479	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_4082.1	chr1	166762133	166762142	+	1	NA	Intergenic	Intergenic	-80292	NM_001347135	240894	Mm.246610	NM_172844	ENSMUSG00000026560	Fmo9	4831428F09Rik	flavin containing monooxygenase 9	protein-coding
mm_59533.1	chr7	27731399	27731441	+	1	NA	promoter-TSS (NM_029531)	promoter-TSS (NM_029531)	11	NM_009560	22718	Mm.66913	NM_009560	ENSMUSG00000037640	Zfp60	6330516O17Rik|AI426106|AI449354|Mfg-3|Mfg3	zinc finger protein 60	protein-coding
mm_113412.1	chr13	34002376	34002423	+	1	NA	promoter-TSS (NM_009068)	promoter-TSS (NM_009068)	395	NM_001243192	20719	Mm.252210	NM_009254	ENSMUSG00000060147	Serpinb6a	4930482L21Rik|D330015H01Rik|PI-6|Serpinb6|Spi3|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 6a	protein-coding
mm_79609.1	chr9	58611519	58611525	+	1	NA	intron (NM_001293673, intron 1 of 7)	B1_Mur1|SINE|Alu	29282	NM_009145	20320	Mm.15125	NM_009145	ENSMUSG00000032336	Nptn	AW554172|SDR-1|Sdfr1	neuroplastin	protein-coding
mm_128827.1	chr15	67176719	67176735	-	1	NA	5' UTR (NM_009177, exon 1 of 9)	5' UTR (NM_009177, exon 1 of 9)	155	NM_009177	20442	Mm.248334	NM_009177	ENSMUSG00000013846	St3gal1	5330418N22Rik|AI467004|ST3GalI|Siat4|Siat4a|St3gal-1	ST3 beta-galactoside alpha-2,3-sialyltransferase 1	protein-coding
mm_43977.1	chr5	146261049	146261088	+	1	NA	intron (NM_153599, intron 2 of 12)	LSU-rRNA_Hsa|rRNA|rRNA	29393	NM_153599	264064	Mm.260576	NM_153599	ENSMUSG00000029635	Cdk8	-	cyclin-dependent kinase 8	protein-coding
mm_115952.1	chr13	23746556	23746567	-	1	NA	promoter-TSS (NM_175664)	promoter-TSS (NM_175664)	-173	NM_175664	319178	Mm.390567	NM_175664	ENSMUSG00000075031	Hist1h2bb	H2b-143	histone cluster 1, H2bb	protein-coding
mm_56693.1	chr6	114411459	114411461	-	1	NA	intron (NM_008285, intron 2 of 2)	MIRc|SINE|MIR	7794	NM_001252643	15465	Mm.333327	NM_008285	ENSMUSG00000053004	Hrh1	Bphs|H1R|HH1R|Hir	histamine receptor H1	protein-coding
mm_128396.1	chr15	43282696	43282728	-	1	NA	promoter-TSS (NM_008388)	promoter-TSS (NM_008388)	24	NM_008388	16341	Mm.289992	NM_008388	ENSMUSG00000022336	Eif3e	48kDa|Eif3s6|Int6|eIF3-p46|eIF3-p48	eukaryotic translation initiation factor 3, subunit E	protein-coding
mm_4864.1	chr1	187662475	187662485	+	1	NA	intron (NM_001243792, intron 1 of 7)	intron (NM_001243792, intron 1 of 7)	53474	NM_001243792	26381	Mm.89989	NM_011935	ENSMUSG00000026610	Esrrg	ERR3|Errg|NR3B3|mKIAA0832	estrogen-related receptor gamma	protein-coding
mm_150828.1	chr19	44746660	44746671	+	1	NA	Intergenic	Intergenic	-10729	NM_011037	18504	Mm.192158	NM_011037	ENSMUSG00000004231	Pax2	Opdc|Pax-2	paired box 2	protein-coding
mm_71185.1	chr8	40863110	40863157	+	1	NA	intron (NM_007514, intron 1 of 11)	intron (NM_007514, intron 1 of 11)	766	NM_001044740	11988	Mm.4676	NM_007514	ENSMUSG00000031596	Slc7a2	20.5|AI158848|Atrc2|CAT-2|Cat2|Tea	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	protein-coding
mm_46809.1	chr5	113077231	113077239	-	1	NA	intron (NM_001159650, intron 5 of 5)	B1_Mur3|SINE|Alu	4349	NM_001159650	12962	Mm.378899	NM_021352	ENSMUSG00000029352	Crybb3	AI852419	crystallin, beta B3	protein-coding
mm_86217.1	chr9	120068264	120068291	-	1	NA	promoter-TSS (NM_009987)	promoter-TSS (NM_009987)	19	NM_009987	13051	Mm.44065	NM_009987	ENSMUSG00000052336	Cx3cr1	-	chemokine (C-X3-C motif) receptor 1	protein-coding
mm_145173.1	chr18	46931762	46931794	+	1	NA	intron (NM_001033446, intron 4 of 4)	MLTR18A_MM|LTR|ERVK	9963	NM_001033446	381142	Mm.329423	NM_001033446	ENSMUSG00000073568	Arl14epl	Gm949	ADP-ribosylation factor-like 14 effector protein-like	protein-coding
mm_170811.1	chr2	176153421	176153428	-	1	NA	Intergenic	Intergenic	-73141	NM_001305137	100504263	Mm.379980	NM_001305136	ENSMUSG00000078894	2210418O10Rik	Gm6182	predicted gene 2210418O10Rik	protein-coding
mm_113688.1	chr13	42866848	42866898	+	1	NA	intron (NM_001302636, intron 1 of 12)	intron (NM_001302636, intron 1 of 12)	626	NM_001302636	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding
mm_166671.1	chr6	91757118	91757122	+	1	NA	3' UTR (NM_009320, exon 15 of 15)	3' UTR (NM_009320, exon 15 of 15)	50273	NM_001159507	243547	Mm.333264	NM_001033353	ENSMUSG00000030098	Grip2	-	glutamate receptor interacting protein 2	protein-coding
mm_51111.1	chr6	67555598	67555612	+	1	NA	Intergenic	Intergenic	10094	NR_003100	75070	Mm.463364	NR_003100		4930515G16Rik	-	myc induced nuclear antigen pseudogene	pseudo
mm_37473.1	chr4	123565315	123565328	-	1	NA	intron (NM_001199136, intron 1 of 97)	intron (NM_001199136, intron 1 of 97)	-51099	NR_105824	102465214		NR_105824	ENSMUSG00000099005	Mir6398	Gm27657|mmu-mir-6398	microRNA 6398	ncRNA
mm_9882.1	chr1	186309314	186309314	-	1	NA	Intergenic	Intergenic	-192004	NM_146106	226791	Mm.257116	NM_146106	ENSMUSG00000039246	Lyplal1	BC027340|Q96AVO	lysophospholipase-like 1	protein-coding
mm_87009.1	chr10	26871740	26871754	+	1	NA	intron (NM_176837, intron 6 of 14)	intron (NM_176837, intron 6 of 14)	99235	NM_176837	73910	Mm.356496	NM_176837	ENSMUSG00000039031	Arhgap18	4833419J07Rik|AI314906|AI843501	Rho GTPase activating protein 18	protein-coding
mm_23024.1	chr3	34638345	34638371	+	1	NA	promoter-TSS (NR_035433)	promoter-TSS (NR_035433)	-106	NR_035433	100316679		NR_035433	ENSMUSG00000104797	Mir1897	Mirn1897|mmu-mir-1897	microRNA 1897	ncRNA
mm_49067.1	chr6	5398422	5398432	+	1	NA	exon (NM_023048, exon 3 of 6)	exon (NM_023048, exon 3 of 6)	15041	NM_023048	65255	Mm.51340	NM_023048	ENSMUSG00000042607	Asb4	8430401O13Rik|AV117194|AW060255	ankyrin repeat and SOCS box-containing 4	protein-coding
mm_12430.1	chr2	70601724	70601762	+	1	NA	3' UTR (NM_008077, exon 17 of 17)	3' UTR (NM_008077, exon 17 of 17)	-38386	NR_040496	68986	Mm.437697	NR_040496	ENSMUSG00000087264	Gad1os	1500002O10Rik	glutamate decarboxylase 1, opposite strand	ncRNA
mm_96401.1	chr11	67250828	67250837	+	1	NA	exon (NM_010855, exon 22 of 40)	exon (NM_010855, exon 22 of 40)	13020	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_158388.1	chrX	136172165	136172194	-	1	NA	promoter-TSS (NM_025703)	promoter-TSS (NM_025703)	72	NM_001168578	66684	Mm.182094	NM_025703	ENSMUSG00000051579	Tceal8	3930402F23Rik	transcription elongation factor A (SII)-like 8	protein-coding
mm_122745.1	chr14	54149336	54149343	-	1	NA	Intergenic	Intergenic	104590	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_2108.1	chr1	87828568	87828593	+	1	NA	intron (NM_009118, intron 10 of 15)	intron (NM_009118, intron 10 of 15)	-24707	NM_177646	227333	Mm.277217	NM_177646	ENSMUSG00000070738	Dgkd	AI841987|D330025K09|DGKdelta|dgkd-2	diacylglycerol kinase, delta	protein-coding
mm_64035.1	chr7	140770142	140770201	+	1	NA	exon (NM_021282, exon 5 of 9)	exon (NM_021282, exon 5 of 9)	6339	NM_021282	13106	Mm.21758	NM_021282	ENSMUSG00000025479	Cyp2e1	Cyp2e	cytochrome P450, family 2, subfamily e, polypeptide 1	protein-coding
mm_45513.1	chr5	72504304	72504310	-	1	NA	promoter-TSS (NM_016869)	promoter-TSS (NM_016869)	-99	NM_016869	53419	Mm.332425	NM_016869	ENSMUSG00000005220	Corin	AV273130|Lrp4	corin	protein-coding
mm_159164.1	chr2	91932297	91932297	-	1	NA	promoter-TSS (NM_010784)	promoter-TSS (NM_010784)	0	NM_001291483	17242	Mm.906	NM_010784	ENSMUSG00000027239	Mdk	MK|Mek	midkine	protein-coding
mm_97993.1	chr11	84092784	84092787	+	1	NA	intron (NM_172562, intron 9 of 15)	intron (NM_172562, intron 9 of 15)	-24428	NM_019819	56405	Mm.240885	NM_019819	ENSMUSG00000018648	Dusp14	1110014C10Rik|2310042C07Rik|D11Ertd395e|MKP-L|Mkp6	dual specificity phosphatase 14	protein-coding
mm_97577.1	chr11	78940636	78940645	+	1	NA	intron (NM_001313921, intron 10 of 25)	intron (NM_001313921, intron 10 of 25)	15349	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_56813.1	chr6	116672440	116672467	-	1	NA	intron (NM_178045, intron 1 of 10)	intron (NM_178045, intron 1 of 10)	1383	NM_178045	213391	Mm.257931	NM_178045	ENSMUSG00000042129	Rassf4	3830411C14Rik|AD037|AI586137	Ras association (RalGDS/AF-6) domain family member 4	protein-coding
mm_47977.1	chr5	135910871	135910887	-	1	NA	3' UTR (NM_018871, exon 2 of 2)	3' UTR (NM_018871, exon 2 of 2)	22960	NM_013560	15507	Mm.13849	NM_013560	ENSMUSG00000004951	Hspb1	27kDa|Hsp25	heat shock protein 1	protein-coding
mm_152280.1	chr19	8839182	8839265	-	1	NA	promoter-TSS (NM_008144)	promoter-TSS (NM_008144)	23	NM_010316	14704	Mm.329700	NM_010316	ENSMUSG00000071658	Gng3	-	guanine nucleotide binding protein (G protein), gamma 3	protein-coding
mm_110716.1	chr12	69537842	69537851	-	1	NA	Intergenic	Intergenic	45182	NM_001033236	207965	Mm.102487	NM_001033236	ENSMUSG00000049882	Vcpkmt	Gm71|Mettl21d|Mettl221d|VCP-KMT	valosin containing protein lysine (K) methyltransferase	protein-coding
mm_79667.1	chr9	59665158	59665194	+	1	NA	intron (NM_001253883, intron 1 of 10)	intron (NM_001253883, intron 1 of 10)	8808	NM_001253883	18746	Mm.326167	NM_011099	ENSMUSG00000032294	Pkm	AA414905|AL024370|AL024424|Pk-2|Pk-3|Pk3|Pkm2	pyruvate kinase, muscle	protein-coding
mm_32792.1	chr4	116877428	116877453	+	1	NA	promoter-TSS (NM_001029912)	promoter-TSS (NM_001029912)	38	NM_001029912	74464	Mm.218946	NM_001029912	ENSMUSG00000033948	Zswim5	4933426E21Rik|AI503093|mKIAA1511	zinc finger SWIM-type containing 5	protein-coding
mm_63596.1	chr7	128141208	128141219	+	1	NA	exon (NM_021334, exon 18 of 30)	exon (NM_021334, exon 18 of 30)	11645	NM_021334	16411	Mm.22378	NM_021334	ENSMUSG00000030789	Itgax	AI449405|Cd11c|Cr4|N418	integrin alpha X	protein-coding
mm_126907.1	chr15	89765321	89765323	+	1	NA	Intergenic	RLTR45-int|LTR|ERVK	76538	NM_018803	54526	Mm.261601	NM_018803	ENSMUSG00000063260	Syt10	-	synaptotagmin X	protein-coding
mm_31352.1	chr4	46854271	46854292	+	1	NA	intron (NM_001081141, intron 2 of 18)	intron (NM_001081141, intron 2 of 18)	137433	NM_001081141	242425	Mm.101909	NM_001081141	ENSMUSG00000039809	Gabbr2	GABABR2|Gb2|Gm425|Gpr51	gamma-aminobutyric acid (GABA) B receptor, 2	protein-coding
mm_158016.1	chrX	95956920	95956948	-	1	NA	promoter-TSS (NM_152822)	promoter-TSS (NM_152822)	40	NM_152822	76130	Mm.274318	NM_152822	ENSMUSG00000057421	Las1l	1810030A06Rik|5830482G23Rik	LAS1-like (S. cerevisiae)	protein-coding
mm_164383.1	chr16	31300509	31300511	-	1	NA	intron (NM_001301353, intron 4 of 5)	A-rich|Low_complexity|Low_complexity	14298	NM_001301353	11815	Mm.2082	NM_007470	ENSMUSG00000022548	Apod	-	apolipoprotein D	protein-coding
mm_140520.1	chr17	6106476	6106488	-	1	NA	promoter-TSS (NM_001103181)	promoter-TSS (NM_001103181)	-348	NM_001103181	68842	Mm.449307	NM_054040	ENSMUSG00000034377	Tulp4	1110057P05Rik|2210038L17Rik|Tusp	tubby like protein 4	protein-coding
mm_64675.1	chr7	4501615	4501634	-	1	NA	promoter-TSS (NM_029834)	promoter-TSS (NM_029834)	56	NM_029834	232807	Mm.360391	NM_029834	ENSMUSG00000019254	Ppp1r12c	2410197A17Rik|AI839747|B430101M08|Mbs85	protein phosphatase 1, regulatory (inhibitor) subunit 12C	protein-coding
mm_31961.1	chr4	86914273	86914276	+	1	NA	intron (NM_001290543, intron 5 of 5)	intron (NM_001290543, intron 5 of 5)	39860	NM_139306	230379	Mm.45019	NM_139306	ENSMUSG00000038007	Acer2	2410116I05Rik|Asah3l|CRG-L1|maCER2	alkaline ceramidase 2	protein-coding
mm_13280.1	chr2	101624678	101624695	+	1	NA	promoter-TSS (NM_009020)	promoter-TSS (NM_009020)	-62	NM_009020	19374	Mm.4988	NM_009020	ENSMUSG00000032864	Rag2	Rag-2	recombination activating gene 2	protein-coding
mm_154678.1	chrX	7919817	7919905	+	1	NA	promoter-TSS (NM_013892)	promoter-TSS (NM_013892)	39	NM_013892	30052	Mm.4881	NM_013892	ENSMUSG00000039278	Pcsk1n	AI848336|KEP|PEN|PEN19|PEN20|Pan3|SAAS|SAASCT|bLEN|lLEN|proSAAS	proprotein convertase subtilisin/kexin type 1 inhibitor	protein-coding
mm_65910.1	chr7	30194095	30194140	-	1	NA	intron (NM_009795, intron 1 of 10)	intron (NM_009795, intron 1 of 10)	931	NM_009795	12336	Mm.439782	NM_009795	ENSMUSG00000001794	Capns1	Capa-4|Capa4|Capn4|D7Ertd146e	calpain, small subunit 1	protein-coding
mm_57342.1	chr6	124747193	124747220	-	1	NA	exon (NM_007881, exon 5 of 10)	exon (NM_007881, exon 5 of 10)	-6127	NM_013535	14790	Mm.439877	NM_013535	ENSMUSG00000072772	Grcc10	2310033H05Rik|C10	gene rich cluster, C10 gene	protein-coding
mm_10578.1	chr2	18105706	18105743	+	1	NA	intron (NR_045539, intron 6 of 24)	intron (NR_045539, intron 6 of 24)	41139	NM_001252561	17354	Mm.209175	NM_010804	ENSMUSG00000026743	Mllt10	Af10|B130021D15Rik|D630001B22Rik|mKIAA4140	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 10	protein-coding
mm_74478.1	chr8	4289537	4289541	-	1	NA	3' UTR (NM_010485, exon 6 of 6)	3' UTR (NM_010485, exon 6 of 6)	-13634	NM_011592	21856	Mm.195249	NM_011592	ENSMUSG00000002949	Timm44	0710005E20Rik|D8Ertd118e|Mimt44|Tim44	translocase of inner mitochondrial membrane 44	protein-coding
mm_166100.1	chr4	144895409	144895421	+	1	NA	intron (NM_011303, intron 1 of 5)	intron (NM_011303, intron 1 of 5)	2278	NM_011303	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding
mm_34634.1	chr4	150614186	150614198	+	1	NA	exon (NM_001085492, exon 17 of 23)	exon (NM_001085492, exon 17 of 23)	37982	NM_173774	242773	Mm.29280	NM_173774	ENSMUSG00000039838	Slc45a1	C230078B22|Dnb5	solute carrier family 45, member 1	protein-coding
mm_161177.1	chr13	41606047	41606047	+	1	NA	promoter-TSS (NM_001163572)	promoter-TSS (NM_001163572)	-169	NM_001163572	621976	Mm.259830	NM_001163572	ENSMUSG00000087370	Tmem170b	EG621976	transmembrane protein 170B	protein-coding
mm_150608.1	chr19	40831965	40832018	+	1	NA	5' UTR (NM_172839, exon 2 of 6)	5' UTR (NM_172839, exon 2 of 6)	712	NM_172839	240665	Mm.309	NM_172839	ENSMUSG00000025010	Ccnj	D430039C20Rik	cyclin J	protein-coding
mm_122537.1	chr14	47418153	47418159	-	1	NA	5' UTR (NM_144553, exon 1 of 19)	5' UTR (NM_144553, exon 1 of 19)	251	NM_144553	218977	Mm.240543	NM_144553	ENSMUSG00000037544	Dlgap5	C77459|C86398|Dap-5|Dlg7|Hurp|mKIAA0008	discs, large (Drosophila) homolog-associated protein 5	protein-coding
mm_47310.1	chr5	122457027	122457047	-	1	NA	non-coding (NR_027838, exon 20 of 21)	non-coding (NR_027838, exon 20 of 21)	34593	NM_019805	56317	Mm.37341	NM_019805	ENSMUSG00000029466	Anapc7	APC7|AW545589	anaphase promoting complex subunit 7	protein-coding
mm_53473.1	chr6	134925135	134925138	+	1	NA	3' UTR (NM_009875, exon 3 of 3)	3' UTR (NM_009875, exon 3 of 3)	-3956	NR_037956	381822	Mm.5935	NR_037955	ENSMUSG00000098318	Lockd	1190002F15Rik|AI120476|Droc	lncRNA downstream of Cdkn1b	ncRNA
mm_94569.1	chr11	11687718	11687732	+	1	NA	intron (NM_001025597, intron 1 of 7)	intron (NM_001025597, intron 1 of 7)	1800	NM_001025597	22778	Mm.103545	NM_009578	ENSMUSG00000018654	Ikzf1	5832432G11Rik|Ikaros|LyF-1|Zfpn1a1|Znfn1a1|hlk-1|mKIAA4227	IKAROS family zinc finger 1	protein-coding
mm_82726.1	chr9	25151611	25151626	-	1	NA	5' UTR (NM_020586, exon 1 of 8)	5' UTR (NM_020586, exon 1 of 8)	163	NM_020586	80517	Mm.142843	NM_020586	ENSMUSG00000008429	Herpud2	5031400M07Rik|AB041580	HERPUD family member 2	protein-coding
mm_130949.1	chr15	103255230	103255250	-	1	NA	5' UTR (NM_008685, exon 1 of 3)	5' UTR (NM_008685, exon 1 of 3)	199	NM_008685	18022	Mm.457989	NM_008685	ENSMUSG00000058794	Nfe2	NF-E2|NF-E2/P45|p45|p45NFE2|p45nf-e2	nuclear factor, erythroid derived 2	protein-coding
mm_128071.1	chr15	27630645	27630714	-	1	NA	promoter-TSS (NM_001013792)	promoter-TSS (NM_001013792)	14	NM_001013792	432940	Mm.309164	NM_001013792	ENSMUSG00000046034	Otulin	C79097|Fam105b|m3Sapc|m7-1Sapc	OTU deubiquitinase with linear linkage specificity	protein-coding
mm_116980.1	chr13	56289194	56289211	-	1	NA	3' UTR (NM_019568, exon 4 of 4)	3' UTR (NM_019568, exon 4 of 4)	7349	NM_019568	57266	Mm.30211	NM_019568	ENSMUSG00000021508	Cxcl14	1110031L23Rik|1200006I23Rik|AI414372|BMAC|BRAK|KS1|Kec|MIP-2g|MIP2gamma|NJAC|Scyb14|bolekine	chemokine (C-X-C motif) ligand 14	protein-coding
mm_113421.1	chr13	34037662	34037665	+	1	NA	promoter-TSS (NM_026512)	promoter-TSS (NM_026512)	22	NM_026512	68021	Mm.140243	NM_026512	ENSMUSG00000038286	Bphl	2010012D11Rik|5730533B08Rik|AI115341	biphenyl hydrolase-like (serine hydrolase, breast epithelial mucin-associated antigen)	protein-coding
mm_145199.1	chr18	49979456	49979475	+	1	NA	promoter-TSS (NM_001177760)	promoter-TSS (NM_001177760)	38	NM_001177759	106869	Mm.27740	NM_134131	ENSMUSG00000062210	Tnfaip8	AA987150|E130304C20Rik|ENSMUSG00000073567|Gg2-1|Gm10539|Nded|Ssc-2|Tipe	tumor necrosis factor, alpha-induced protein 8	protein-coding
mm_22502.1	chr3	7390093	7390096	+	1	NA	intron (NM_008862, intron 1 of 2)	Lx7|LINE|L1	23490	NM_008862	18767	Mm.3193	NM_008862	ENSMUSG00000027499	Pkia	AI415001|PKIalpha	protein kinase inhibitor, alpha	protein-coding
mm_10411.1	chr2	13579148	13579160	+	1	NA	intron (NM_011701, intron 4 of 8)	intron (NM_011701, intron 4 of 8)	4843	NM_011701	22352	Mm.268000	NM_011701	ENSMUSG00000026728	Vim	-	vimentin	protein-coding
mm_100384.1	chr11	119316979	119317009	+	1	NA	intron (NM_130886, intron 2 of 21)	intron (NM_130886, intron 2 of 21)	2207	NM_130886	170720	Mm.130832	NM_130886	ENSMUSG00000013483	Card14	Bimp2|CARMA2	caspase recruitment domain family, member 14	protein-coding
mm_100810.1	chr11	5099037	5099050	-	1	NA	promoter-TSS (NM_177370)	promoter-TSS (NM_177370)	45	NM_001283062	14030	Mm.142822	NM_007968	ENSMUSG00000009079	Ewsr1	Ews|Ewsh	Ewing sarcoma breakpoint region 1	protein-coding
mm_30841.1	chr4	24278783	24278783	+	1	NA	Intergenic	Intergenic	-217679	NM_199467	212377	Mm.120919	NM_199467	ENSMUSG00000045751	Mms22l	F730047E07Rik|Gm134	MMS22-like, DNA repair protein	protein-coding
mm_156661.1	chrX	157711544	157711561	+	1	NA	intron (NR_045569, intron 3 of 6)	Lx9|LINE|L1	12579	NR_103722	66106	Mm.140340	NM_025357	ENSMUSG00000041476	Smpx	1010001C09Rik|Csl	small muscle protein, X-linked	protein-coding
mm_158662.1	chrX	157492023	157492059	-	1	NA	promoter-TSS (NM_009214)	promoter-TSS (NM_009214)	5	NM_009214	20603	Mm.18652	NM_009214	ENSMUSG00000071708	Sms	AI427066|Gy|SPMSY|SpmST|gyro	spermine synthase	protein-coding
mm_20275.1	chr2	126876150	126876171	-	1	NA	5' UTR (NM_001164325, exon 1 of 39)	5' UTR (NM_001164325, exon 1 of 39)	101	NM_001164325	58800	Mm.244705	NM_021450	ENSMUSG00000027365	Trpm7	2310022G15Rik|4833414K03Rik|5033407O22Rik|CHAK|CHAK1|LTrpC-7|Ltpr7|Ltrpc7|TRPPLIK	transient receptor potential cation channel, subfamily M, member 7	protein-coding
mm_153024.1	chr19	31511011	31511015	-	1	NA	intron (NM_011160, intron 2 of 17)	intron (NM_011160, intron 2 of 17)	153357	NM_011160	19091	Mm.381170	NM_011160	ENSMUSG00000052920	Prkg1	AW125416|CGKI|Gm19690|Prkg1b|Prkgr1b	protein kinase, cGMP-dependent, type I	protein-coding
mm_112268.1	chr12	114141123	114141133	-	1	NA	Intergenic	Intergenic	328338	NR_106062	102465663		NR_106062	ENSMUSG00000105438	Mir7094-1	mmu-mir-7094-1	microRNA 7094-1	ncRNA
mm_51296.1	chr6	72306835	72306865	+	1	NA	exon (NM_001282071, exon 5 of 11)	exon (NM_001282071, exon 5 of 11)	2240	NM_147779	20388	Mm.46033	NM_147779	ENSMUSG00000056370	Sftpb	AI562151|SF-B|SP-B|Sftp-3|Sftp3	surfactant associated protein B	protein-coding
mm_13406.1	chr2	104027758	104027780	+	1	NA	promoter-TSS (NM_212433)	promoter-TSS (NM_212433)	-30	NM_020593	57443	Mm.143768	NM_020593	ENSMUSG00000027180	Fbxo3	1200002G09Rik|1700026K02Rik|AI046358|Fba	F-box protein 3	protein-coding
mm_137958.1	chr17	33092447	33092497	+	1	NA	intron (NM_001024950, intron 1 of 3)	intron (NM_001024950, intron 1 of 3)	3105	NM_001024950	240068	Mm.121392	NM_001024950	ENSMUSG00000067424	Zfp563	D10628|D130054H01|NTfin7|Zfp413	zinc finger protein 563	protein-coding
mm_150764.1	chr19	44242054	44242070	+	1	NA	3' UTR (NM_024450, exon 6 of 6)	3' UTR (NM_024450, exon 6 of 6)	38774	NM_024450	30049	Mm.480594	NM_024450	ENSMUSG00000025202	Scd3	4930513N16Rik	stearoyl-coenzyme A desaturase 3	protein-coding
mm_21250.1	chr2	156180136	156180201	-	1	NA	promoter-TSS (NM_001291114)	promoter-TSS (NM_001291114)	70	NM_001291114	170791	Mm.392436	NM_133242	ENSMUSG00000027620	Rbm39	1500012C14Rik|2310040E03Rik|B330012G18Rik|C79248|R75070|Rnpc2|caper	RNA binding motif protein 39	protein-coding
mm_76375.1	chr8	84832226	84832272	-	1	NA	promoter-TSS (NM_183358)	promoter-TSS (NM_183358)	16	NR_033145	23863	Mm.304252	NM_201227	ENSMUSG00000053226	Dand5	Cerl-2|Cerr2|Dte|GREM3|coco	DAN domain family member 5, BMP antagonist	protein-coding
mm_60336.1	chr7	44335720	44335752	+	1	NA	intron (NM_001034115, intron 15 of 24)	C-rich|Low_complexity|Low_complexity	25472	NM_001034115	243961	Mm.360368	NM_001034115	ENSMUSG00000038738	Shank1	-	SH3/ankyrin domain gene 1	protein-coding
mm_14375.1	chr2	129630408	129630427	+	1	NA	3' UTR (NM_001291022, exon 5 of 5)	3' UTR (NM_001291022, exon 5 of 5)	37248	NM_001291022	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_71236.1	chr8	40907901	40907911	+	1	NA	intron (NM_007514, intron 6 of 11)	intron (NM_007514, intron 6 of 11)	-18327	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_104944.1	chr11	100119700	100119719	-	1	NA	exon (NM_010662, exon 3 of 8)	exon (NM_010662, exon 3 of 8)	868	NM_001313949	16663	Mm.4646	NM_010662	ENSMUSG00000044041	Krt13	CK13|K13|Krt-1.13|Krt1-13	keratin 13	protein-coding
mm_15907.1	chr2	165055626	165055661	+	1	NA	promoter-TSS (NR_027852)	promoter-TSS (NR_027852)	7	NM_011611	21939	Mm.271833	NM_011611	ENSMUSG00000017652	Cd40	AI326936|Bp50|GP39|HIGM1|IGM|IMD3|T-BAM|TRAP|Tnfrsf5|p50	CD40 antigen	protein-coding
mm_126099.1	chr15	78244760	78244778	+	1	NA	promoter-TSS (NM_008677)	promoter-TSS (NM_008677)	-42	NM_008677	17972	Mm.2068	NM_008677	ENSMUSG00000071715	Ncf4	AI451400|p40phox	neutrophil cytosolic factor 4	protein-coding
mm_48249.1	chr5	137787502	137787523	-	1	NA	promoter-TSS (NM_001005426)	promoter-TSS (NM_001005426)	-290	NM_001005426	381678	Mm.332765	NM_001005426	ENSMUSG00000037108	Zcwpw1	Gm1053	zinc finger, CW type with PWWP domain 1	protein-coding
mm_112823.1	chr13	20801881	20801912	+	1	NA	intron (NM_012054, intron 1 of 20)	L1M4a1|LINE|L1	7783	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_86652.1	chr10	17724181	17724193	+	1	NA	exon (NM_010828, exon 2 of 2)	exon (NM_010828, exon 2 of 2)	959	NM_010828	17684	Mm.272321	NM_010828	ENSMUSG00000039910	Cited2	AI835299|ER154-like|Mrg1|Msg2|p35srj	Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 2	protein-coding
mm_119257.1	chr14	33941022	33941052	+	1	NA	promoter-TSS (NM_019506)	promoter-TSS (NM_019506)	-2	NM_019506	12165	Mm.422844	NM_019506	ENSMUSG00000072625	Gdf2	Bmp9	growth differentiation factor 2	protein-coding
mm_72211.1	chr8	72646575	72646596	+	1	NA	promoter-TSS (NM_176940)	promoter-TSS (NM_176940)	-126	NM_176940	319555	Mm.212927	NM_176940	ENSMUSG00000048148	Nwd1	A230063L24Rik	NACHT and WD repeat domain containing 1	protein-coding
mm_22222.1	chr2	174427879	174427890	-	1	NA	TTS (NM_020580)	TTS (NM_020580)	11155	NM_022325	64138	Mm.156919	NM_022325	ENSMUSG00000016256	Ctsz	AI787083|AU019819|CTSX|D2Wsu143e	cathepsin Z	protein-coding
mm_78309.1	chr9	22655321	22655323	+	1	NA	exon (NM_181316, exon 15 of 22)	exon (NM_181316, exon 15 of 22)	179607	NM_178415	319845	Mm.176725	NM_178415	ENSMUSG00000035919	Bbs9	E130103I17Rik	Bardet-Biedl syndrome 9 (human)	protein-coding
mm_150787.1	chr19	44301278	44301297	+	1	NA	exon (NM_009128, exon 5 of 6)	exon (NM_009128, exon 5 of 6)	-1884	NR_039574	100628619		NR_039574	ENSMUSG00000093315	Mir5114	mmu-mir-5114|mu-mir-5114	microRNA 5114	ncRNA
mm_141902.1	chr17	34952460	34952475	-	1	NA	promoter-TSS (NR_015536)	promoter-TSS (NR_015536)	1	NR_027943	68763	Mm.28895	NR_015536	ENSMUSG00000092203	1110038B12Rik	0610009C20Rik|0910001G04Rik	RIKEN cDNA 1110038B12 gene	ncRNA
mm_110197.1	chr12	27340528	27340542	-	1	NA	3' UTR (NM_009234, exon 1 of 1)	3' UTR (NM_009234, exon 1 of 1)	2183	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding
mm_158036.1	chrX	98757501	98757508	-	1	NA	intron (NM_001313755, intron 4 of 23)	intron (NM_001313755, intron 4 of 23)	133521	NM_052976	94190	Mm.33536	NM_052976	ENSMUSG00000031214	Ophn1	C130037N19Rik|Wtgr	oligophrenin 1	protein-coding
mm_148080.1	chr18	72725034	72725070	-	1	NA	Intergenic	Intergenic	-373983	NM_007831	13176	Mm.167882	NM_007831	ENSMUSG00000060534	Dcc	C030036D22Rik|Igdcc1	deleted in colorectal carcinoma	protein-coding
mm_39413.1	chr5	14684955	14684958	+	1	NA	intron (NM_001110796, intron 6 of 19)	Lx5|LINE|L1	170038	NM_001110796	26875	Mm.146275	NM_011995	ENSMUSG00000061601	Pclo	Acz|Pico	piccolo (presynaptic cytomatrix protein)	protein-coding
mm_77850.1	chr9	5304323	5304336	+	1	NA	intron (NM_009807, intron 7 of 9)	intron (NM_009807, intron 7 of 9)	-4520	NM_007609	12363	Mm.1569	NM_007609	ENSMUSG00000033538	Casp4	CASP-11|CASP-4|Casp11|Caspl|ich-3	caspase 4, apoptosis-related cysteine peptidase	protein-coding
mm_133014.1	chr16	56193605	56193614	+	1	NA	Intergenic	Intergenic	-10704	NM_174876	224224	Mm.151998	NM_174876	ENSMUSG00000035270	Impg2	IPM200|PG10.2|Rsbp|Spacrcan	interphotoreceptor matrix proteoglycan 2	protein-coding
mm_53552.1	chr6	136872732	136872755	+	1	NA	exon (NM_008597, exon 4 of 4)	exon (NM_008597, exon 4 of 4)	3080	NM_008597	17313	Mm.243085	NM_008597	ENSMUSG00000030218	Mgp	Mglap	matrix Gla protein	protein-coding
mm_39989.1	chr5	32491377	32491446	+	1	NA	3' UTR (NM_172707, exon 8 of 8)	3' UTR (NM_172707, exon 8 of 8)	32441	NM_172707	19046	Mm.241931	NM_172707	ENSMUSG00000014956	Ppp1cb	1200010B19	protein phosphatase 1, catalytic subunit, beta isoform	protein-coding
mm_107561.1	chr12	41825805	41825808	+	1	NA	intron (NM_053122, intron 6 of 6)	Lx6|LINE|L1	-339749	NM_010733	16981	Mm.404786	NM_010733	ENSMUSG00000036295	Lrrn3	NLRR-3	leucine rich repeat protein 3, neuronal	protein-coding
mm_56445.1	chr6	97487802	97487879	-	1	NA	promoter-TSS (NM_001346637)	promoter-TSS (NM_001346637)	-20	NM_001346637	232288	Mm.27789	NM_145148	ENSMUSG00000030064	Frmd4b	6030440G05Rik|C87375|GOBLIN|GRSP1|R74720	FERM domain containing 4B	protein-coding
mm_28385.1	chr3	90002266	90002290	-	1	NA	TTS (NR_045749)	TTS (NR_045749)	3518	NR_045749	100503469	Mm.440636	NR_045749	ENSMUSG00000105552	Gm19710	-	predicted gene, 19710	ncRNA
mm_85796.1	chr9	109892458	109892464	-	1	NA	3' UTR (NM_007658, exon 15 of 15)	3' UTR (NM_007658, exon 15 of 15)	2818	NR_106057	102465660		NR_106057	ENSMUSG00000098490	Mir7089	Gm27418|mmu-mir-7089	microRNA 7089	ncRNA
mm_19874.1	chr2	114048217	114048241	-	1	NA	exon (NM_009608, exon 6 of 7)	exon (NM_009608, exon 6 of 7)	4646	NM_009608	11464	Mm.686	NM_009608	ENSMUSG00000068614	Actc1	Actc-1	actin, alpha, cardiac muscle 1	protein-coding
mm_161835.1	chr17	84596225	84596225	+	1	NA	exon (NM_177606, exon 21 of 30)	exon (NM_177606, exon 21 of 30)	-30274	NM_172256	213575	Mm.246119	NM_172256	ENSMUSG00000024253	Dync2li1	4933404O11Rik|CGI-60|D2lic|LIC3|mD2LIC	dynein cytoplasmic 2 light intermediate chain 1	protein-coding
mm_63907.1	chr7	139213494	139213512	+	1	NA	promoter-TSS (NM_001162540)	promoter-TSS (NM_001162540)	-196	NM_001162540	57740	Mm.65336	NM_021302	ENSMUSG00000015981	Stk32c	PKE|Pkek|YANK3	serine/threonine kinase 32C	protein-coding
mm_130322.1	chr15	97595402	97595410	-	1	NA	Intergenic	RMER17C|LTR|ERVK	110416	NM_028003	71919	Mm.12255	NM_028003	ENSMUSG00000022466	Rpap3	2310042P20Rik|D15Ertd682e	RNA polymerase II associated protein 3	protein-coding
mm_17341.1	chr2	26602203	26602213	-	1	NA	intron (NM_026212, intron 1 of 5)	B1_Mus2|SINE|Alu	2209	NM_026212	67512	Mm.24244	NM_026212	ENSMUSG00000026922	Agpat2	2510002J07Rik|AV000834|BSCL|BSCL1|LPAAB|LPAAT-beta	1-acylglycerol-3-phosphate O-acyltransferase 2 (lysophosphatidic acid acyltransferase, beta)	protein-coding
mm_82703.1	chr9	22468284	22468292	-	1	NA	promoter-TSS (NM_018739)	promoter-TSS (NM_018739)	68	NM_018739	55934	Mm.38235	NM_018739	ENSMUSG00000032239	Rp9	PAP-1|Rp9h	retinitis pigmentosa 9 (human)	protein-coding
mm_27275.1	chr3	40846848	40846860	-	1	NA	promoter-TSS (NM_028140)	promoter-TSS (NM_028140)	0	NM_028140	72175	Mm.130610	NM_028140	ENSMUSG00000025759	Mfsd8	2810423E13Rik|AI836898|AV142426|Cln7	major facilitator superfamily domain containing 8	protein-coding
mm_106927.1	chr12	8393285	8393287	+	1	NA	Intergenic	Intergenic	79853	NM_021429	58240	Mm.309954	NM_021429	ENSMUSG00000020605	Hs1bp3	-	HCLS1 binding protein 3	protein-coding
mm_5853.1	chr1	53297002	53297023	-	1	NA	promoter-TSS (NM_145517)	promoter-TSS (NM_145517)	16	NM_153556	227099	Mm.60499	NM_153556	ENSMUSG00000026098	Pms1	-	postmeiotic segregation increased 1 (S. cerevisiae)	protein-coding
mm_156733.1	chrX	159942684	159942705	+	1	NA	promoter-TSS (NM_001290664)	promoter-TSS (NM_001290664)	1	NM_001290664	58194	Mm.286495	NM_021389	ENSMUSG00000040990	Sh3kbp1	1200007H22Rik|1700125L08Rik|5830464D22Rik|AI447724|Cin85|IN85|Ruk|Seta	SH3-domain kinase binding protein 1	protein-coding
mm_30428.1	chr3	152982188	152982216	-	1	NA	promoter-TSS (NM_012028)	promoter-TSS (NM_012028)	5	NM_012028	26938	Mm.40915	NM_012028	ENSMUSG00000039037	St6galnac5	AI851940|Siat7e	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 5	protein-coding
mm_1390.1	chr1	67123016	67123069	+	1	NA	promoter-TSS (NM_001080809)	promoter-TSS (NM_001080809)	15	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_137286.1	chr17	24736661	24736671	+	1	NA	promoter-TSS (NM_001346668)	promoter-TSS (NM_001346668)	73	NM_001346668	27361	Mm.28212	NM_013759	ENSMUSG00000075705	Msrb1	D17Wsu82e|SELX|SelR|Sepr|Sepx1	methionine sulfoxide reductase B1	protein-coding
mm_133950.1	chr16	3976542	3976567	-	1	NA	promoter-TSS (NM_001081280)	promoter-TSS (NM_001081280)	78	NM_175547	268857	Mm.215994	NM_175547	ENSMUSG00000049871	Nlrc3	CLR16.2|D230007K08Rik|mFLJ00348	NLR family, CARD domain containing 3	protein-coding
mm_15148.1	chr2	153988299	153988305	+	1	NA	intron (NM_001080811, intron 5 of 10)	MIRb|SINE|MIR	13357	NM_001080811	545477	Mm.379973	NM_001080811	ENSMUSG00000078998	Bpifa6	EG545477|Gm5840|Splunc6	BPI fold containing family A, member 6	protein-coding
mm_49033.1	chr6	4759839	4759848	+	1	NA	3' UTR (NM_130877, exon 2 of 2)	3' UTR (NM_130877, exon 2 of 2)	12537	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_139462.1	chr17	55953895	55953906	+	1	NA	TTS (NR_108021)	TTS (NR_108021)	1277	NM_015766	50498	Mm.256798	NM_015766	ENSMUSG00000003206	Ebi3	EBI-3|IL-27	Epstein-Barr virus induced gene 3	protein-coding
mm_39052.1	chr4	153483972	153483975	-	1	NA	Intergenic	Intergenic	-1143	NM_001099299	230959	Mm.318874	NM_001099299	ENSMUSG00000039546	Ajap1	Gm573	adherens junction associated protein 1	protein-coding
mm_37015.1	chr4	113261329	113261331	-	1	NA	intron (NM_001103199, intron 2 of 48)	Lx5c|LINE|L1	25643	NM_001103199	230622	Mm.291107	NM_001103199	ENSMUSG00000087194	Skint6	OTTMUSG00000008519	selection and upkeep of intraepithelial T cells 6	protein-coding
mm_81006.1	chr9	103442517	103442544	+	1	NA	intron (NM_001002896, intron 4 of 6)	B4|SINE|B4	18952	NR_040466	100529079	Mm.437003	NR_040466	ENSMUSG00000086236	5830418P13Rik	-	RIKEN cDNA 5830418P13 gene	ncRNA
mm_6528.1	chr1	74601365	74601402	-	1	NA	promoter-TSS (NM_021313)	promoter-TSS (NM_021313)	14	NM_021313	57751	Mm.280920	NM_021313	ENSMUSG00000026171	Rnf25	0610009H16Rik|AO7	ring finger protein 25	protein-coding
mm_96824.1	chr11	69995799	69995812	+	1	NA	promoter-TSS (NM_030064)	promoter-TSS (NM_030064)	39	NM_030064	78246	Mm.20805	NM_030064	ENSMUSG00000018572	Phf23	JUNE-1	PHD finger protein 23	protein-coding
mm_59424.1	chr7	27124847	27124857	+	1	NA	intron (NM_007817, intron 3 of 9)	intron (NM_007817, intron 3 of 9)	4897	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_69095.1	chr7	127018920	127018926	-	1	NA	exon (NM_001102563, exon 3 of 4)	exon (NM_001102563, exon 3 of 4)	-1571	NM_030240	67278	Mm.345385	NM_030240	ENSMUSG00000030680	Pagr1a	2900092E17Rik|C77040|PA1|PAGR1	PAXIP1 associated glutamate rich protein 1A	protein-coding
mm_161268.1	chr14	7027246	7027246	-	1	NA	intron (NM_001164727, intron 1 of 6)	CpG	203	NM_001164727	100038847	Mm.443041	NM_001164727	ENSMUSG00000093985	Gm10406	ENSMUSG00000072735	predicted gene 10406	protein-coding
mm_171119.1	chr3	141609695	141609695	-	1	NA	intron (NM_001293561, intron 1 of 16)	L1Md_T|LINE|L1	144131	NM_001293561	22253	Mm.24430	NM_009472	ENSMUSG00000059921	Unc5c	B130051O18Rik|Unc5h3|rcm	unc-5 netrin receptor C	protein-coding
mm_113269.1	chr13	29014306	29014324	+	1	NA	promoter-TSS (NR_045077)	promoter-TSS (NR_045077)	-99	NR_045077	77920	Mm.197051	NR_045073	ENSMUSG00000086363	A330102I10Rik	-	RIKEN cDNA A330102I10 gene	ncRNA
mm_111538.1	chr12	100887891	100887901	-	1	NA	5' UTR (NM_175493, exon 2 of 3)	5' UTR (NM_175493, exon 2 of 3)	11628	NM_001177674	238377	Mm.32160	NM_175493	ENSMUSG00000047415	Gpr68	BB131428|Ogr1	G protein-coupled receptor 68	protein-coding
mm_14400.1	chr2	130044532	130044540	+	1	NA	exon (NM_009374, exon 11 of 13)	exon (NM_009374, exon 11 of 13)	-28128	NR_105757	102466628		NR_105757	ENSMUSG00000098347	Mir6339	Gm27848|mmu-mir-6339	microRNA 6339	ncRNA
mm_68380.1	chr7	109175131	109175171	-	1	NA	promoter-TSS (NM_001302205)	promoter-TSS (NM_001302205)	56	NM_001302205	109594	Mm.360145	NM_057173	ENSMUSG00000036111	Lmo1	Rbtn-1|Rbtn1|Ttg1	LIM domain only 1	protein-coding
mm_42711.1	chr5	120431950	120431958	+	1	NA	promoter-TSS (NM_008499)	promoter-TSS (NM_008499)	68	NM_008499	16873	Mm.5151	NM_008499	ENSMUSG00000029595	Lhx5	Lim2	LIM homeobox protein 5	protein-coding
mm_115429.1	chr13	117245449	117245451	+	1	NA	intron (NM_010330, intron 2 of 8)	intron (NM_010330, intron 2 of 8)	24877	NM_010330	13723	Mm.274926	NM_010330	ENSMUSG00000021728	Emb	AL022799|Gp70	embigin	protein-coding
mm_143750.1	chr17	81580626	81580627	-	1	NA	intron (NR_104580, intron 2 of 8)	intron (NR_104580, intron 2 of 8)	157761	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_166357.1	chr5	122458557	122458567	-	1	NA	intron (NM_001110140, intron 16 of 19)	intron (NM_001110140, intron 16 of 19)	36118	NM_019805	56317	Mm.37341	NM_019805	ENSMUSG00000029466	Anapc7	APC7|AW545589	anaphase promoting complex subunit 7	protein-coding
mm_23349.1	chr3	54755629	54755648	+	1	NA	promoter-TSS (NM_019483)	promoter-TSS (NM_019483)	56	NM_019483	55994	Mm.244353	NM_019483	ENSMUSG00000027796	Smad9	MADH6|Madh8|Madh9|Smad8	SMAD family member 9	protein-coding
mm_3572.1	chr1	150517819	150517825	+	1	NA	Intergenic	B1F2|SINE|Alu	-51657	NM_001110146	96875	Mm.174256	NM_021400	ENSMUSG00000006014	Prg4	CACP|DOL54|JCAP|MSF|SZP|lubricin	proteoglycan 4 (megakaryocyte stimulating factor, articular superficial zone protein)	protein-coding
mm_46803.1	chr5	113076540	113076543	-	1	NA	intron (NM_001159650, intron 5 of 5)	intron (NM_001159650, intron 5 of 5)	5043	NM_001159650	12962	Mm.378899	NM_021352	ENSMUSG00000029352	Crybb3	AI852419	crystallin, beta B3	protein-coding
mm_138396.1	chr17	35052606	35052634	+	1	NA	intron (NM_033444, intron 2 of 5)	intron (NM_033444, intron 2 of 5)	2377	NM_033444	114584	Mm.29524	NM_033444	ENSMUSG00000007041	Clic1	Clcp|G6	chloride intracellular channel 1	protein-coding
mm_138080.1	chr17	33974995	33975021	+	1	NA	non-coding (NR_004446, exon 6 of 6)	non-coding (NR_004446, exon 6 of 6)	3783	NR_004446	630499	Mm.440940	NM_001081015		H2-K2	EG630499|Gm7035|H-2K1|H-2K1K|H-2K2|H2-K1	histocompatibility 2, K region locus 2	pseudo
mm_23506.1	chr3	60529221	60529257	+	1	NA	5' UTR (NM_001253708, exon 2 of 9)	5' UTR (NM_001253708, exon 2 of 9)	28060	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_53071.1	chr6	124931379	124931425	+	1	NA	promoter-TSS (NM_001170341)	promoter-TSS (NM_001170341)	14	NM_001170341	30853	Mm.29737	NM_145385	ENSMUSG00000030120	Mlf2	AI256856|AU018944|C77284	myeloid leukemia factor 2	protein-coding
mm_6857.1	chr1	84262642	84262663	-	1	NA	intron (NM_001003948, intron 1 of 2)	intron (NM_001003948, intron 1 of 2)	21993	NM_001003948	98496	Mm.187470	NM_001003948	ENSMUSG00000045658	Pid1	5033414K04Rik|NYGGF4	phosphotyrosine interaction domain containing 1	protein-coding
mm_67514.1	chr7	80815772	80815810	-	1	NA	Intergenic	Intergenic	-12460	NM_016721	29875	Mm.207619	NM_016721	ENSMUSG00000030536	Iqgap1	AA682088|D7Ertd237e|D7Ertd257e|mKIAA0051	IQ motif containing GTPase activating protein 1	protein-coding
mm_36630.1	chr4	91399997	91400007	-	1	NA	promoter-TSS (NM_207685)	promoter-TSS (NM_207685)	-18	NM_207685	15569	Mm.318042	NM_010486	ENSMUSG00000008489	Elavl2	Hub|mel-N1	ELAV (embryonic lethal, abnormal vision, Drosophila)-like 2 (Hu antigen B)	protein-coding
mm_123305.1	chr14	61683848	61683891	-	1	NA	Intergenic	Intergenic	-1496	NR_028264	668253	Mm.32886	NR_028264	ENSMUSG00000097589	Dleu2	1810047A16Rik|4932411A06Rik|7730401J12Rik|AI197277|AI788824|Alt1|Gm9069|Leu2	deleted in lymphocytic leukemia, 2	ncRNA
mm_70361.1	chr8	8661795	8661806	+	1	NA	Intergenic	CpG-13817	-1027	NM_010111	13642	Mm.209813	NM_010111	ENSMUSG00000001300	Efnb2	ELF-2|Epl5|Eplg5|Htk-L|LERK-5|Lerk5|NLERK-1	ephrin B2	protein-coding
mm_123019.1	chr14	55116229	55116273	-	1	NA	5' UTR (NM_177049, exon 1 of 6)	5' UTR (NM_177049, exon 1 of 6)	684	NM_177049	319984	Mm.19047	NM_177049	ENSMUSG00000022208	Jph4	9330157P13Rik|JP-4|JPHL1	junctophilin 4	protein-coding
mm_172769.1	chr8	94179081	94179082	+	1	NA	promoter-TSS (NM_013602)	promoter-TSS (NM_013602)	-8	NM_013602	17748	Mm.192991	NM_013602	ENSMUSG00000031765	Mt1	MT-I|Mt-1	metallothionein 1	protein-coding
mm_29356.1	chr3	108530060	108530062	-	1	NA	intron (NM_001346518, intron 1 of 21)	B1_Mus1|SINE|Alu	6461	NM_001033304	229722	Mm.316890	NM_001033304	ENSMUSG00000040412	5330417C22Rik	BB183350	RIKEN cDNA 5330417C22 gene	protein-coding
mm_87572.1	chr10	56387880	56387890	+	1	NA	exon (NM_010288, exon 2 of 2)	exon (NM_010288, exon 2 of 2)	10585	NM_010288	14609	Mm.378921	NM_010288	ENSMUSG00000050953	Gja1	AU042049|AW546267|Cnx43|Cx43|Cx43alpha1|Gja-1|Npm1|connexin43	gap junction protein, alpha 1	protein-coding
mm_143552.1	chr17	74080273	74080295	-	1	NA	Intergenic	Intergenic	-32368	NM_053188	94224	Mm.38933	NM_053188	ENSMUSG00000038541	Srd5a2	5ART2|S5AR 2	steroid 5 alpha-reductase 2	protein-coding
mm_46074.1	chr5	92323748	92323754	-	1	NA	3' UTR (NM_008599, exon 4 of 4)	3' UTR (NM_008599, exon 4 of 4)	4328	NM_008599	17329	Mm.766	NM_008599	ENSMUSG00000029417	Cxcl9	BB139920|CMK|Mig|MuMIG|Scyb9|crg-10	chemokine (C-X-C motif) ligand 9	protein-coding
mm_88707.1	chr10	80150486	80150513	+	1	NA	intron (NM_001347117, intron 2 of 7)	CpG-1261	817	NM_001305799	59090	Mm.143813	NM_021565	ENSMUSG00000035621	Midn	3000003C15Rik	midnolin	protein-coding
mm_99065.1	chr11	99155399	99155410	+	1	NA	promoter-TSS (NM_007719)	promoter-TSS (NM_007719)	-327	NM_007719	12775	Mm.2932	NM_007719	ENSMUSG00000037944	Ccr7	CC-CKR-7|CCR-7|CD197|Cdw197|Cmkbr7|EBI1|Ebi1h	chemokine (C-C motif) receptor 7	protein-coding
mm_158624.1	chrX	152875555	152875560	-	1	NA	Intergenic	MERV1_LTR|LTR|ERV1	93636	NM_010951	18241	Mm.5157	NM_010951	ENSMUSG00000025333	Gpr143	Oa1	G protein-coupled receptor 143	protein-coding
mm_75868.1	chr8	70763002	70763026	-	1	NA	exon (NM_023065, exon 8 of 8)	exon (NM_023065, exon 8 of 8)	-2093	NM_183170	234384	Mm.213010	NM_183170	ENSMUSG00000035559	Mpv17l2	Fksg24	MPV17 mitochondrial membrane protein-like 2	protein-coding
mm_106685.1	chr12	3345390	3345399	+	1	NA	Intergenic	Lx7|LINE|L1	-19738	NM_008445	16570	Mm.7688	NM_008445	ENSMUSG00000020668	Kif3c	mKIAA4058	kinesin family member 3C	protein-coding
mm_119643.1	chr14	51984489	51984513	+	1	NA	promoter-TSS (NM_001145922)	promoter-TSS (NM_001145922)	-332	NM_001145921	268739	Mm.9239	NM_198249	ENSMUSG00000004562	Arhgef40	E130112L23Rik|Gm669|Solo	Rho guanine nucleotide exchange factor (GEF) 40	protein-coding
mm_122421.1	chr14	43121156	43121158	-	1	NA	Intergenic	AT_rich|Low_complexity|Low_complexity	-105581	NM_001244671	100042055	Mm.429109	NM_001244671	ENSMUSG00000095226	Gm10377	ENSMUSG00000072606	predicted gene 10377	protein-coding
mm_113791.1	chr13	45965456	45965476	+	1	NA	promoter-TSS (NM_009124)	promoter-TSS (NM_009124)	-475	NM_009124	20238	Mm.342683	NM_009124	ENSMUSG00000046876	Atxn1	2900016G23Rik|Atx1|C85907|ENSMUSG00000074917|Gm10786|Sca1	ataxin 1	protein-coding
mm_89104.1	chr10	84576884	84576904	+	1	NA	promoter-TSS (NM_146008)	promoter-TSS (NM_146008)	-53	NM_146008	216198	Mm.296142	NM_146008	ENSMUSG00000020034	Tcp11l2	E430026E19Rik	t-complex 11 (mouse) like 2	protein-coding
mm_130243.1	chr15	96638207	96638222	-	1	NA	intron (NM_001166458, intron 1 of 15)	intron (NM_001166458, intron 1 of 15)	3748	NM_134086	105727	Mm.103568	NM_134086	ENSMUSG00000023169	Slc38a1	AA408026|AA409865|AL022800|AU015942|NAT2	solute carrier family 38, member 1	protein-coding
mm_41962.1	chr5	106458680	106458701	+	1	NA	promoter-TSS (NM_001005477)	promoter-TSS (NM_001005477)	-524	NM_001005477	104382	Mm.271593	NM_001005477	ENSMUSG00000034384	Barhl2	E130309B19Rik|MBH1	BarH-like 2 (Drosophila)	protein-coding
mm_29487.1	chr3	115714890	115714919	-	1	NA	5' UTR (NM_007901, exon 1 of 2)	5' UTR (NM_007901, exon 1 of 2)	151	NM_007901	13609	Mm.982	NM_007901	ENSMUSG00000045092	S1pr1	AI849002|Edg1|Lpb1|S1p|S1p1	sphingosine-1-phosphate receptor 1	protein-coding
mm_99057.1	chr11	99052180	99052190	+	1	NA	3' UTR (NM_010517, exon 4 of 4)	3' UTR (NM_010517, exon 4 of 4)	10925	NM_010517	16010	Mm.233799	NM_010517	ENSMUSG00000017493	Igfbp4	AI875747|Deb2|IGFBP-4	insulin-like growth factor binding protein 4	protein-coding
mm_44659.1	chr5	28458843	28458854	-	1	NA	intron (NM_009170, intron 2 of 2)	CpG	-8136	NR_015562	654796	Mm.57202	NR_015562	ENSMUSG00000097726	9530036O11Rik	-	RIKEN cDNA 9530036O11Rik	ncRNA
mm_55654.1	chr6	72380417	72380483	-	1	NA	promoter-TSS (NM_001080742)	promoter-TSS (NM_001080742)	18	NM_016872	53620	Mm.440321	NM_016872	ENSMUSG00000073002	Vamp5	AF119384|Camp	vesicle-associated membrane protein 5	protein-coding
mm_67268.1	chr7	75780545	75780555	-	1	NA	Intergenic	Intergenic	-67788	NM_001122780	207952	Mm.206223	NM_029652	ENSMUSG00000055652	Klhl25	2810402K13Rik|BC027373|Enc-1	kelch-like 25	protein-coding
mm_20628.1	chr2	131993056	131993060	-	1	NA	3' UTR (NM_175445, exon 11 of 11)	3' UTR (NM_175445, exon 11 of 11)	36930	NM_175445	215653	Mm.204737	NM_175445	ENSMUSG00000027339	Rassf2	3830431H01Rik|9030412M04Rik|AI852669|AW495050	Ras association (RalGDS/AF-6) domain family member 2	protein-coding
mm_125247.1	chr15	34496245	34496250	+	1	NA	intron (NM_152894, intron 1 of 16)	RCHARR1|DNA|hAT-Charlie	936	NM_152894	67724	Mm.248779	NM_026340	ENSMUSG00000022325	Pop1	4932434G09Rik	processing of precursor 1, ribonuclease P/MRP family, (S. cerevisiae)	protein-coding
mm_148157.1	chr18	77565353	77565402	-	1	NA	promoter-TSS (NM_001164504)	promoter-TSS (NM_001164504)	-241	NM_001164504	225743	Mm.23293	NM_001164504	ENSMUSG00000025427	Rnf165	2900024M11Rik|AI427432|Akd2|Ark2c|G630064H08Rik|Gm96	ring finger protein 165	protein-coding
mm_15545.1	chr2	158409792	158409800	+	1	NA	promoter-TSS (NM_001291138)	promoter-TSS (NM_001291138)	-57	NM_001291137	228850	Mm.398185	NM_177227	ENSMUSG00000027652	Ralgapb	AI507211|B230339M05Rik|p170	Ral GTPase activating protein, beta subunit (non-catalytic)	protein-coding
mm_146994.1	chr18	34349750	34349789	-	1	NA	exon (NM_007874, exon 4 of 5)	exon (NM_007874, exon 4 of 5)	18624	NM_025527	66384	Mm.29452	NM_025527	ENSMUSG00000014504	Srp19	2310020D23Rik	signal recognition particle 19	protein-coding
mm_35597.1	chr4	43030441	43030445	-	1	NA	exon (NM_023231, exon 3 of 10)	exon (NM_023231, exon 3 of 10)	941	NM_023231	66592	Mm.331565	NM_023231	ENSMUSG00000028455	Stoml2	0610038F01Rik|MSLP2|SLP-2	stomatin (Epb7.2)-like 2	protein-coding
mm_2587.1	chr1	118679425	118679436	+	1	NA	3' UTR (NM_023755, exon 15 of 15)	3' UTR (NM_023755, exon 15 of 15)	51485	NM_023755	81879	Mm.24621	NM_023755	ENSMUSG00000026380	Tfcp2l1	1810030F05Rik|4932442M07Rik|AA575098|Cp2l1|Crtr-1|D930018N21Rik|LBP-9|Tcfcp2l1	transcription factor CP2-like 1	protein-coding
mm_43922.1	chr5	144768537	144768552	+	1	NA	promoter-TSS (NM_001081362)	promoter-TSS (NM_001081362)	-248	NM_001081362	100683	Mm.273570	NM_001081362	ENSMUSG00000045482	Trrap	AI481500	transformation/transcription domain-associated protein	protein-coding
mm_21149.1	chr2	154408036	154408071	-	1	NA	promoter-TSS (NM_009228)	promoter-TSS (NM_009228)	31	NM_009228	20648	Mm.1541	NM_009228	ENSMUSG00000027488	Snta1	AW228934|Snt1	syntrophin, acidic 1	protein-coding
mm_170073.1	chr17	33414332	33414334	+	1	NA	Intergenic	Lx|LINE|L1	-18566	NM_183282	69481	Mm.154333	NM_183282	ENSMUSG00000092519	Actl9	1700029I08Rik|AV259599	actin-like 9	protein-coding
mm_140340.1	chr17	86821156	86821159	+	1	NA	intron (NM_010137, intron 7 of 15)	intron (NM_010137, intron 7 of 15)	67293	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_145859.1	chr18	65456199	65456209	+	1	NA	intron (NM_172833, intron 8 of 15)	intron (NM_172833, intron 8 of 15)	25207	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_81384.1	chr9	108945353	108945414	+	1	NA	exon (NM_025407, exon 6 of 13)	exon (NM_025407, exon 6 of 13)	-8362	NM_007738	12836	Mm.6200	NM_007738	ENSMUSG00000025650	Col7a1	AW209154	collagen, type VII, alpha 1	protein-coding
mm_74262.1	chr8	124897911	124897927	+	1	NA	promoter-TSS (NM_198103)	promoter-TSS (NM_198103)	33	NM_001111141	244666	Mm.482915	NM_001111141	ENSMUSG00000031986	Sprtn	Gm505	SprT-like N-terminal domain	protein-coding
mm_141233.1	chr17	27436718	27436722	-	1	NA	intron (NM_001013385, intron 7 of 8)	intron (NM_001013385, intron 7 of 8)	66813	NM_001013385	268934	Mm.358940	NM_001013385	ENSMUSG00000063239	Grm4	Gprc1d|mGluR4	glutamate receptor, metabotropic 4	protein-coding
mm_159279.1	chr2	165664587	165664587	+	1	NA	intron (NM_010165, intron 1 of 15)	intron (NM_010165, intron 1 of 15)	9289	NM_010165	14049	Mm.282719	NM_010165	ENSMUSG00000017897	Eya2	Eab1	EYA transcriptional coactivator and phosphatase 2	protein-coding
mm_46681.1	chr5	109558946	109558956	-	1	NA	promoter-TSS (NM_001164735)	promoter-TSS (NM_001164735)	42	NM_016715	57914	Mm.35771	NM_016715	ENSMUSG00000033467	Crlf2	CRLM2|Ly114|Tpte2|Tslpr	cytokine receptor-like factor 2	protein-coding
mm_152300.1	chr19	9083804	9083813	-	1	NA	exon (NM_011681, exon 3 of 3)	exon (NM_011681, exon 3 of 3)	4148	NM_011681	22287	Mm.2258	NM_011681	ENSMUSG00000024653	Scgb1a1	CC10|CC16|CCSP|PCB-BP|UG|UGB|Utg	secretoglobin, family 1A, member 1 (uteroglobin)	protein-coding
mm_168944.1	chr12	72917759	72917766	-	1	NA	promoter-TSS (NM_029444)	promoter-TSS (NM_029444)	3	NM_029444	75801	Mm.242892	NM_029444	ENSMUSG00000021098	4930447C04Rik	4921504I02Rik|A930035O15Rik|Six6OS|Six6as|Six6os1	RIKEN cDNA 4930447C04 gene	protein-coding
mm_164111.1	chr15	29506446	29506446	-	1	NA	Intergenic	L1M4|LINE|L1	-666147	NM_008729	18163	Mm.321648	NM_008729	ENSMUSG00000022240	Ctnnd2	Catnd2|Nprap|neurojugin	catenin (cadherin associated protein), delta 2	protein-coding
mm_60816.1	chr7	45700072	45700080	+	1	NA	5' UTR (NM_009800, exon 1 of 9)	5' UTR (NM_009800, exon 1 of 9)	109	NM_009800	12348	Mm.27736	NM_009800	ENSMUSG00000003273	Car11	Ca11	carbonic anhydrase 11	protein-coding
mm_32708.1	chr4	116123793	116123871	+	1	NA	promoter-TSS (NM_001122958)	promoter-TSS (NM_001122958)	-8	NR_131048	76786	Mm.373813	NR_131048	ENSMUSG00000028700	2510003B16Rik	-	RIKEN cDNA 2510003B16 gene	ncRNA
mm_164583.1	chr17	25827863	25827910	+	1	NA	exon (NM_173741, exon 7 of 9)	exon (NM_173741, exon 7 of 9)	-1157	NM_028101	72106	Mm.277599	NM_028101	ENSMUSG00000025736	Jmjd8	2610003J06Rik	jumonji domain containing 8	protein-coding
mm_114096.1	chr13	54701458	54701479	+	1	NA	promoter-TSS (NM_001033364)	promoter-TSS (NM_001033364)	5	NM_001033364	268663	Mm.315382	NM_001033364	ENSMUSG00000034918	Cdhr2	Gm624|PC-LKC|Pcdh24	cadherin-related family member 2	protein-coding
mm_19687.1	chr2	103460341	103460378	-	1	NA	exon (NM_009804, exon 10 of 13)	exon (NM_009804, exon 10 of 13)	24794	NM_009804	12359	Mm.4215	NM_009804	ENSMUSG00000027187	Cat	2210418N07|Cas-1|Cas1|Cs-1	catalase	protein-coding
mm_59701.1	chr7	28692856	28692870	+	1	NA	promoter-TSS (NM_001163702)	promoter-TSS (NM_001163702)	14	NM_207238	233040	Mm.116116	NM_207238	ENSMUSG00000037463	Fbxo27	E130008B10Rik|FBG5|Gm161	F-box protein 27	protein-coding
mm_83399.1	chr9	44734201	44734211	-	1	NA	intron (NM_153537, intron 1 of 21)	CpG	992	NM_153537	102693	Mm.28639	NM_153537	ENSMUSG00000048537	Phldb1	AU041016|D330037A14Rik|Ll5a	pleckstrin homology like domain, family B, member 1	protein-coding
mm_89592.1	chr10	95940705	95940772	+	1	NA	promoter-TSS (NM_001001932)	promoter-TSS (NM_001001932)	75	NM_001001932	216238	Mm.210035	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding
mm_81621.1	chr9	110827007	110827022	+	1	NA	5' UTR (NM_199471, exon 1 of 6)	5' UTR (NM_199471, exon 1 of 6)	324	NM_199471	272643	Mm.458525	NM_199471	ENSMUSG00000058398	Prss43	Gm661|Tessp3	protease, serine 43	protein-coding
mm_122882.1	chr14	54927009	54927028	-	1	NA	promoter-TSS (NM_010112)	promoter-TSS (NM_010112)	-230	NM_010112	13644	Mm.236438	NM_010112	ENSMUSG00000022203	Efs	-	embryonal Fyn-associated substrate	protein-coding
mm_86108.1	chr9	115310512	115310520	-	1	NA	promoter-TSS (NM_024222)	promoter-TSS (NM_024222)	-95	NM_024222	68292	Mm.296158	NM_024222	ENSMUSG00000032437	Stt3b	1300006C19Rik|Simp	STT3, subunit of the oligosaccharyltransferase complex, homolog B (S. cerevisiae)	protein-coding
mm_80923.1	chr9	101251536	101251537	+	1	NA	intron (NM_001161362, intron 1 of 13)	CpG	296	NM_001161362	235542	Mm.335386	NM_172144	ENSMUSG00000043154	Ppp2r3a	3222402P14Rik|A730042E07	protein phosphatase 2, regulatory subunit B'', alpha	protein-coding
mm_56558.1	chr6	101199197	101199200	-	1	NA	intron (NM_018884, intron 3 of 9)	intron (NM_018884, intron 3 of 9)	178699	NM_018884	55983	Mm.321654	NM_018884	ENSMUSG00000035357	Pdzrn3	1110020C07Rik|AI429718|AL023082|LNX3|SEMACAP3|Semcap3	PDZ domain containing RING finger 3	protein-coding
mm_142123.1	chr17	35897080	35897141	-	1	NA	TTS (NM_001142744)	TTS (NM_001142744)	268	NM_001033630	69662	Mm.260159	NM_001033630	ENSMUSG00000050705	2310061I04Rik	-	RIKEN cDNA 2310061I04 gene	protein-coding
mm_133553.1	chr16	91377538	91377548	+	1	NA	intron (NM_001347258, intron 1 of 7)	intron (NM_001347258, intron 1 of 7)	4760	NM_001110498	15976	Mm.6834	NM_010509	ENSMUSG00000022971	Ifnar2	AI747302|Ifnar-2	interferon (alpha and beta) receptor 2	protein-coding
mm_118889.1	chr14	26590543	26590599	+	1	NA	intron (NM_001134465, intron 1 of 19)	intron (NM_001134465, intron 1 of 19)	11021	NM_145969	211922	Mm.260512	NM_145969	ENSMUSG00000040818	Dennd6a	Fam116a	DENN/MADD domain containing 6A	protein-coding
mm_107105.1	chr12	17765390	17765402	+	1	NA	intron (NM_016677, intron 1 of 3)	intron (NM_016677, intron 1 of 3)	74582	NM_016677	53602	Mm.313619	NM_016677	ENSMUSG00000071379	Hpcal1	NVP-3|Nvp3|VILIP3|Vnsl3|Vsnl3	hippocalcin-like 1	protein-coding
mm_163932.1	chr14	47995200	47995200	+	1	NA	Intergenic	Intergenic	96336	NR_045959	73961	Mm.390702	NR_045959		4930447J18Rik	4930425M13Rik	RIKEN cDNA 4930447J18 gene	ncRNA
mm_118660.1	chr14	21831520	21831530	+	1	NA	promoter-TSS (NM_011695)	promoter-TSS (NM_011695)	-36	NM_011695	22334	Mm.262327	NM_011695	ENSMUSG00000021771	Vdac2	Vdac6|mVDAC2|mVDAC6	voltage-dependent anion channel 2	protein-coding
mm_86679.1	chr10	18318598	18318622	+	1	NA	Intergenic	CpG	-83629	NM_144820	215814	Mm.296565	NM_144820	ENSMUSG00000059554	Ccdc28a	1700009P13Rik|AI480677	coiled-coil domain containing 28A	protein-coding
mm_65233.1	chr7	19733172	19733179	-	1	NA	exon (NM_001159724, exon 3 of 6)	exon (NM_001159724, exon 3 of 6)	16398	NM_008990	19294	Mm.4341	NM_008990	ENSMUSG00000062300	Nectin2	AI325026|AI987993|Cd112|MPH|Pvr|Pvrl2|Pvs|nectin-2	nectin cell adhesion molecule 2	protein-coding
mm_118524.1	chr14	14743445	14743506	+	1	NA	intron (NM_001033270, intron 6 of 24)	B3A|SINE|B2	40450	NM_001033270	218756	Mm.258893	NM_001033270	ENSMUSG00000021733	Slc4a7	E430014N10Rik|NBC3|NBCn1|NBCn1-G	solute carrier family 4, sodium bicarbonate cotransporter, member 7	protein-coding
mm_70621.1	chr8	13584168	13584170	+	1	NA	intron (NM_009025, intron 14 of 23)	intron (NM_009025, intron 14 of 23)	-21708	NM_001080781	66501	Mm.46136	NM_025601	ENSMUSG00000031452	1700029H14Rik	-	RIKEN cDNA 1700029H14 gene	protein-coding
mm_149602.1	chr19	16349524	16349537	+	1	NA	intron (NM_008139, intron 5 of 6)	L1MB3|LINE|L1	-34526	NR_105832	102465218		NR_105832	ENSMUSG00000098718	Mir496b	Gm28028|mmu-mir-496b	microRNA 496b	ncRNA
mm_51588.1	chr6	83795247	83795255	+	1	NA	promoter-TSS (NM_001164187)	promoter-TSS (NM_001164187)	93	NM_001164187	56174	Mm.190650	NM_019542	ENSMUSG00000034744	Nagk	Gnk	N-acetylglucosamine kinase	protein-coding
mm_21108.1	chr2	153346386	153346420	-	1	NA	promoter-TSS (NR_040318)	promoter-TSS (NR_040318)	264	NM_001039939	228790	Mm.330677	NM_001039939	ENSMUSG00000042548	Asxl1	mKIAA0978	additional sex combs like 1	protein-coding
mm_111582.1	chr12	101819109	101819113	-	1	NA	promoter-TSS (NM_011812)	promoter-TSS (NM_011812)	8	NM_011812	23876	Mm.288381	NM_011812	ENSMUSG00000021186	Fbln5	A55|DANCE|EVEC	fibulin 5	protein-coding
mm_87996.1	chr10	66698280	66698298	+	1	NA	Intergenic	Intergenic	222095	NR_138560	68488	Mm.338835	NR_138560		1110002J07Rik	-	RIKEN cDNA 1110002J07 gene	ncRNA
mm_49071.1	chr6	5725878	5725888	+	1	NA	5' UTR (NM_010063, exon 1 of 17)	5' UTR (NM_010063, exon 1 of 17)	244	NM_001191026	13426	Mm.20893	NM_010063	ENSMUSG00000029757	Dync1i1	DH IC-1|DHIC-1|DIC|Dncic1|IC74	dynein cytoplasmic 1 intermediate chain 1	protein-coding
mm_167293.1	chr8	46471712	46471717	+	1	NA	intron (NM_007981, intron 1 of 20)	CpG	677	NM_007981	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_49172.1	chr6	14901378	14901396	+	1	NA	promoter-TSS (NM_053242)	promoter-TSS (NM_053242)	38	NM_053242	114142	Mm.332919	NM_053242	ENSMUSG00000029563	Foxp2	2810043D05Rik|AI449000|CAG-16|D0Kist7	forkhead box P2	protein-coding
mm_34030.1	chr4	138096756	138096773	+	1	NA	exon (NM_001256198, exon 7 of 33)	exon (NM_001256198, exon 7 of 33)	41754	NR_126429	73563	Mm.444294	NR_126429	ENSMUSG00000084804	1700095J12Rik	-	RIKEN cDNA 1700095J12 gene	ncRNA
mm_57967.1	chr6	135310375	135310385	-	1	NA	promoter-TSS (NM_029595)	promoter-TSS (NM_029595)	4	NM_029595	76400	Mm.293018	NM_029595	ENSMUSG00000047104	Pbp2	1700023A18Rik|AI326308|Pebp-2|Pebp2	phosphatidylethanolamine binding protein 2	protein-coding
mm_35054.1	chr4	6355394	6355404	-	1	NA	Intergenic	Intergenic	-10281	NM_016807	53378	Mm.247473	NM_016807	ENSMUSG00000028249	Sdcbp	MDA-9|Sycl|syntenin-1	syndecan binding protein	protein-coding
mm_95562.1	chr11	52360825	52360935	+	1	NA	promoter-TSS (NM_011694)	promoter-TSS (NM_011694)	18	NM_011694	22333	Mm.3555	NM_011694	ENSMUSG00000020402	Vdac1	AL033343|Vdac5|mVDAC1|mVDAC5	voltage-dependent anion channel 1	protein-coding
mm_50736.1	chr6	52714413	52714440	+	1	NA	intron (NM_025816, intron 1 of 17)	intron (NM_025816, intron 1 of 17)	697	NM_025816	52440	Mm.389757	NM_025816	ENSMUSG00000004535	Tax1bp1	1200003J11Rik|1700069J21Rik|AA930106|D6Ertd404e|D6Ertd772e|T6bp|TXBP151	Tax1 (human T cell leukemia virus type I) binding protein 1	protein-coding
mm_29111.1	chr3	104864421	104864450	-	1	NA	promoter-TSS (NM_001253703)	promoter-TSS (NM_001253703)	70	NM_009797	12340	Mm.19142	NM_009797	ENSMUSG00000070372	Capza1	CAPZ|CAZ1|Cappa1	capping protein (actin filament) muscle Z-line, alpha 1	protein-coding
mm_65181.1	chr7	19696367	19696387	-	1	NA	3' UTR (NM_009696, exon 4 of 4)	3' UTR (NM_009696, exon 4 of 4)	2021	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_161546.1	chr16	5884921	5884921	+	1	NA	5' UTR (NM_021477, exon 1 of 17)	5' UTR (NM_021477, exon 1 of 17)	128	NM_021477	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_105555.1	chr11	106486892	106486895	-	1	NA	intron (NM_023913, intron 1 of 21)	intron (NM_023913, intron 1 of 21)	903	NM_023913	78943	Mm.340943	NM_023913	ENSMUSG00000020715	Ern1	9030414B18Rik|AI225830|C85377|Ire1a|Ire1alpha|Ire1p	endoplasmic reticulum (ER) to nucleus signalling 1	protein-coding
mm_68415.1	chr7	109671965	109671992	-	1	NA	Intergenic	Intergenic	-31759	NM_020616	57373	Mm.334138	NM_020616	ENSMUSG00000031023	Akip1	BCA3|C11orf17|D7H11orf17|D930014E17Rik|ICRFP703B1614Q5.6|ORF27	A kinase (PRKA) interacting protein 1	protein-coding
mm_172984.1	chr9	98302126	98302131	+	1	NA	intron (NM_144533, intron 1 of 4)	intron (NM_144533, intron 1 of 4)	5545	NM_144533	74080	Mm.294082	NM_144533	ENSMUSG00000032456	Nmnat3	4933408N02Rik|PNAT3	nicotinamide nucleotide adenylyltransferase 3	protein-coding
mm_8473.1	chr1	153407785	153407790	-	1	NA	intron (NR_033736, intron 2 of 3)	RLTR10A|LTR|ERVK	6446	NR_033736	626058	Mm.31556	NM_001177359		E330020D12Rik	EG626058|F430003O07Rik|Gm6648	Riken cDNA E330020D12 gene	ncRNA
mm_40954.1	chr5	76858725	76858738	+	1	NA	exon (NM_001163793, exon 6 of 9)	exon (NM_001163793, exon 6 of 9)	18132	NM_001163793	320827	Mm.101504	NM_001163793	ENSMUSG00000036377	C530008M17Rik	2810489J07Rik|4930529A19Rik|4931405B09Rik|Kiaa1211|mKIAA1211	RIKEN cDNA C530008M17 gene	protein-coding
mm_114719.1	chr13	83663828	83663840	+	1	NA	3' UTR (NM_025282, exon 11 of 11)	3' UTR (NM_025282, exon 11 of 11)	-64272	NR_015561	320203	Mm.245636	NM_177100	ENSMUSG00000050334	C130071C03Rik	2810449C10Rik	RIKEN cDNA C130071C03 gene	ncRNA
mm_165077.1	chr19	46267836	46267838	+	1	NA	intron (NM_178930, intron 18 of 39)	intron (NM_178930, intron 18 of 39)	-36900	NM_001177369	18034	Mm.102365	NM_019408	ENSMUSG00000025225	Nfkb2	NF-kappaB2|lyt|p49|p49/p100|p50B|p52	nuclear factor of kappa light polypeptide gene enhancer in B cells 2, p49/p100	protein-coding
mm_124217.1	chr14	100243051	100243057	-	1	NA	Intergenic	Intergenic	-93258	NM_010636	16597	Mm.396499	NM_010636	ENSMUSG00000072294	Klf12	2700063E05Rik|AI225908|AI315654|AP-2rep|B130052C06Rik|D530033K05Rik	Kruppel-like factor 12	protein-coding
mm_40165.1	chr5	35757952	35757966	+	1	NA	promoter-TSS (NM_177678)	promoter-TSS (NM_177678)	79	NM_001177698	231148	Mm.254446	NM_177678	ENSMUSG00000029095	Ablim2	AI606905|C230091L11	actin-binding LIM protein 2	protein-coding
mm_122702.1	chr14	52175282	52175285	-	1	NA	exon (NM_033618, exon 15 of 26)	exon (NM_033618, exon 15 of 26)	21956	NM_033618	114741	Mm.21662	NM_033618	ENSMUSG00000035726	Supt16	Cdc68|Fact140|Spt16|Supt16h	suppressor of Ty 16	protein-coding
mm_157334.1	chrX	36457127	36457130	-	1	NA	Intergenic	L1MB5|LINE|L1	53651	NR_044989	621901	Mm.491051	NR_044989		Gm6268	EG621901	predicted gene 6268	ncRNA
mm_151941.1	chr19	5800876	5800884	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	1792	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_18859.1	chr2	75690609	75690610	-	1	NA	TTS (NR_132727)	TTS (NR_132727)	14054	NR_132727	18024	Mm.1025	NM_010902	ENSMUSG00000015839	Nfe2l2	Nrf2	nuclear factor, erythroid derived 2, like 2	protein-coding
mm_145229.1	chr18	50128212	50128267	+	1	NA	promoter-TSS (NM_008292)	promoter-TSS (NM_008292)	38	NM_008292	15488	Mm.277857	NM_008292	ENSMUSG00000024507	Hsd17b4	17-beta-HSD|17[b]-HSD|DBP|MFE-2|MFP2|MPF-2|Mfp-2|perMFE-2	hydroxysteroid (17-beta) dehydrogenase 4	protein-coding
mm_51754.1	chr6	87732558	87732594	+	1	NA	intron (NM_001159697, intron 1 of 7)	intron (NM_001159697, intron 1 of 7)	1707	NM_001159697	58229	Mm.333229	NM_021418	ENSMUSG00000068263	Efcc1	Ccdc48	EF hand and coiled-coil domain containing 1	protein-coding
mm_18169.1	chr2	45104233	45104252	-	1	NA	intron (NM_001289521, intron 1 of 8)	intron (NM_001289521, intron 1 of 8)	6035	NM_001289521	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_152418.1	chr19	10671859	10671871	-	1	NA	exon (NM_021453, exon 6 of 9)	exon (NM_021453, exon 6 of 9)	6206	NM_021453	58803	Mm.34037	NM_021453	ENSMUSG00000024738	Pga5	1110035E17Rik|Pepf	pepsinogen 5, group I	protein-coding
mm_21078.1	chr2	152831244	152831326	-	1	NA	promoter-TSS (NM_001289716)	promoter-TSS (NM_001289716)	443	NM_009743	12048	Mm.238213	NM_009743	ENSMUSG00000007659	Bcl2l1	Bcl(X)L|Bcl-XL|Bcl2l|BclX|bcl-x|bcl2-L-1	BCL2-like 1	protein-coding
mm_147414.1	chr18	45934313	45934317	-	1	NA	intron (NR_040342, intron 2 of 3)	intron (NR_040342, intron 2 of 3)	110945	NR_040342	107003	Mm.395148	NR_040342		A330093E20Rik	AU043608	RIKEN cDNA A330093E20 gene	ncRNA
mm_85150.1	chr9	95959362	95959390	-	1	NA	intron (NM_011916, intron 1 of 41)	(TC)n|Simple_repeat|Simple_repeat	4616	NM_001311130	24127	Mm.291179	NM_011916	ENSMUSG00000032410	Xrn1	Dhm2|exo|mXrn1	5'-3' exoribonuclease 1	protein-coding
mm_99979.1	chr11	114251877	114251887	+	1	NA	Intergenic	Intergenic	53624	NR_045930	73536	Mm.54275	NR_045930	ENSMUSG00000078600	1700092K14Rik	-	RIKEN cDNA 1700092K14 gene	ncRNA
mm_101868.1	chr11	48891662	48891687	-	1	NA	intron (NM_001024230, intron 4 of 4)	RMER17C|LTR|ERVK	10478	NM_001024230	432555	Mm.338931	NM_001024230	ENSMUSG00000058163	Gm5431	EG432555|Irgb9b8	predicted gene 5431	protein-coding
mm_11181.1	chr2	28840605	28840653	+	1	NA	promoter-TSS (NM_001166033)	promoter-TSS (NM_001166033)	223	NM_001033294	227674	Mm.44179	NM_001033294	ENSMUSG00000026806	Ddx31	5830444G11Rik|Gm997	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 31	protein-coding
mm_101030.1	chr11	8579851	8579858	-	1	NA	intron (NM_001083587, intron 3 of 30)	intron (NM_001083587, intron 3 of 30)	84681	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_145179.1	chr18	47155037	47155040	+	1	NA	Intergenic	Intergenic	196162	NM_178377	69456	Mm.210734	NM_178377	ENSMUSG00000042705	Commd10	2310003A05Rik|AU019438|DRWMS2	COMM domain containing 10	protein-coding
mm_144294.1	chr18	12168712	12168791	+	1	NA	promoter-TSS (NM_029623)	promoter-TSS (NM_029623)	21	NM_029623	76482	Mm.196596	NM_029623	ENSMUSG00000024410	3110002H16Rik	2400010D15Rik|Mic-1|Mic1	RIKEN cDNA 3110002H16 gene	protein-coding
mm_121840.1	chr14	20571206	20571210	-	1	NA	TTS (NR_033571)	TTS (NR_033571)	-24635	NM_008914	19056	Mm.274432	NM_008914	ENSMUSG00000021816	Ppp3cb	1110063J16Rik|Calnb|CnAbeta|Cnab	protein phosphatase 3, catalytic subunit, beta isoform	protein-coding
mm_118829.1	chr14	25607352	25607365	+	1	NA	intron (NM_001310666, intron 6 of 23)	CpG	3845	NM_001309430	100188919	Mm.473810	NM_001309430		Israa	-	immune system released activating agent	protein-coding
mm_95601.1	chr11	53351032	53351046	+	1	NA	5' UTR (NM_033565, exon 1 of 21)	5' UTR (NM_033565, exon 1 of 21)	272	NM_033565	93736	Mm.395281	NM_033565	ENSMUSG00000049470	Aff4	AF5Q31|Alf4|Laf4l|MCEF	AF4/FMR2 family, member 4	protein-coding
mm_38820.1	chr4	148627010	148627033	-	1	NA	promoter-TSS (NM_145556)	promoter-TSS (NM_145556)	-25	NM_001003899	230908	Mm.22453	NM_145556	ENSMUSG00000041459	Tardbp	1190002A23Rik|C85084|TDP-43|Tdp43	TAR DNA binding protein	protein-coding
mm_2762.1	chr1	130464107	130464113	+	1	NA	Intergenic	Intergenic	-1366	NM_010016	13136	Mm.101591	NM_010016	ENSMUSG00000026399	Cd55	Daf|Daf-GPI|Daf1|GPI-DAF	CD55 molecule, decay accelerating factor for complement	protein-coding
mm_80885.1	chr9	99243684	99243741	+	1	NA	intron (NM_023873, intron 1 of 17)	intron (NM_023873, intron 1 of 17)	244	NM_023873	68121	Mm.288739	NM_023873	ENSMUSG00000056267	Cep70	6720484E09Rik|Bite|C030018L16Rik	centrosomal protein 70	protein-coding
mm_125602.1	chr15	60112149	60112157	+	1	NA	Intergenic	Intergenic	-95535	NM_027668	71088	Mm.425950	NM_027668	ENSMUSG00000071749	4933412E24Rik	-	RIKEN cDNA 4933412E24 gene	protein-coding
mm_18221.1	chr2	50297199	50297228	-	1	NA	promoter-TSS (NM_133839)	promoter-TSS (NM_133839)	403	NR_040362	100502624	Mm.382825	NR_040361	ENSMUSG00000085862	Gm13483	OTTMUSG00000012382	predicted gene 13483	ncRNA
mm_135393.1	chr16	44333136	44333157	-	1	NA	promoter-TSS (NM_001159419)	promoter-TSS (NM_001159419)	-308	NM_001159419	320007	Mm.242144	NM_198034	ENSMUSG00000022696	Sidt1	AW045928|B830021E24Rik	SID1 transmembrane family, member 1	protein-coding
mm_144503.1	chr18	24603953	24603972	+	1	NA	promoter-TSS (NM_021448)	promoter-TSS (NM_021448)	1	NM_021448	58523	Mm.25298	NM_021448	ENSMUSG00000024271	Elp2	AU023723|Epl2|StIP1|Statip1	elongator acetyltransferase complex subunit 2	protein-coding
mm_125842.1	chr15	74958806	74958833	+	1	NA	3' UTR (NM_001164036, exon 4 of 4)	3' UTR (NM_001164036, exon 4 of 4)	3713	NM_001164040	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_166021.1	chr4	122995615	122995626	+	1	NA	promoter-TSS (NM_008506)	promoter-TSS (NM_008506)	-311	NM_001303121	16918	Mm.1055	NM_008506	ENSMUSG00000028654	Mycl	AW536278|L-myc|Lmyc-1|Lmyc1|Mycl1|bHLHe38	v-myc avian myelocytomatosis viral oncogene lung carcinoma derived	protein-coding
mm_165362.1	chr2	124174432	124174433	+	1	NA	intron (NM_001290997, intron 2 of 20)	intron (NM_001290997, intron 2 of 20)	-44476	NR_040611	74702	Mm.410814	NR_040611	ENSMUSG00000085496	4930517E11Rik	-	RIKEN cDNA 4930517E11 gene	ncRNA
mm_90438.1	chr10	127643086	127643104	+	1	NA	5' UTR (NM_009284, exon 1 of 22)	5' UTR (NM_009284, exon 1 of 22)	109	NM_009284	20852	Mm.121721	NM_009284	ENSMUSG00000002147	Stat6	-	signal transducer and activator of transcription 6	protein-coding
mm_167991.1	chrX	170009723	170009737	+	1	NA	Intergenic	CpG	-30813	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_150056.1	chr19	29383304	29383308	+	1	NA	intron (NM_021893, intron 5 of 6)	intron (NM_021893, intron 5 of 6)	15868	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_125944.1	chr15	76248446	76248472	+	1	NA	TTS (NR_105918)	TTS (NR_105918)	268	NR_105918	102465575		NR_105918	ENSMUSG00000098625	Mir6953	Gm27738|mmu-mir-6953	microRNA 6953	ncRNA
mm_143838.1	chr17	84121559	84121570	-	1	NA	Intergenic	Intergenic	42904	NR_045458	74473	Mm.399575	NR_045458		4933433H22Rik	-	RIKEN cDNA 4933433H22 gene	ncRNA
mm_20484.1	chr2	129801441	129801464	-	1	NA	promoter-TSS (NR_029452)	promoter-TSS (NR_029452)	7	NR_029452	654409	Mm.305555	NR_029452		4932416H05Rik	-	RIKEN cDNA 4932416H05 gene	ncRNA
mm_16000.1	chr2	167349675	167349715	+	1	NA	promoter-TSS (NM_019835)	promoter-TSS (NM_019835)	-517	NM_019835	56336	Mm.200886	NM_019835	ENSMUSG00000017929	B4galt5	9430078I07Rik|AW049941|AW539721	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 5	protein-coding
mm_12366.1	chr2	69790969	69790973	+	1	NA	intron (NM_028521, intron 2 of 3)	intron (NM_028521, intron 2 of 3)	1234	NM_028521	73373	Mm.9621	NM_028521	ENSMUSG00000027088	Phospho2	1700048E23Rik|AI661517|AU021728|AV006103|Phos2	phosphatase, orphan 2	protein-coding
mm_56267.1	chr6	90988642	90988680	-	1	NA	Intergenic	CpG	128165	NM_018815	54563	Mm.28162	NM_018815	ENSMUSG00000030091	Nup210	9830001L10|AI836801|Pom210|gp190|gp210	nucleoporin 210	protein-coding
mm_31931.1	chr4	86053888	86053987	+	1	NA	promoter-TSS (NM_029967)	promoter-TSS (NM_029967)	22	NM_029967	77739	Mm.331690	NM_029967	ENSMUSG00000066113	Adamtsl1	5930437A14Rik|6720426B09Rik|ADAMTSL-1	ADAMTS-like 1	protein-coding
mm_2600.1	chr1	120007046	120007059	+	1	NA	promoter-TSS (NM_001012322)	promoter-TSS (NM_001012322)	72	NM_001311077	319229	Mm.189223	NM_001012322	ENSMUSG00000026387	Sctr	6530402O03Rik	secretin receptor	protein-coding
mm_165354.1	chr2	121358882	121358884	+	1	NA	exon (NM_009897, exon 1 of 9)	exon (NM_009897, exon 1 of 9)	242	NM_009897	12716	Mm.252145	NM_009897	ENSMUSG00000000308	Ckmt1	Mt-CK|ScCKmit|UbCKmit|mi-CK	creatine kinase, mitochondrial 1, ubiquitous	protein-coding
mm_45967.1	chr5	90468550	90468583	-	1	NA	exon (NM_009654, exon 8 of 15)	exon (NM_009654, exon 8 of 15)	7696	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_129887.1	chr15	83489631	83489655	-	1	NA	intron (NM_178869, intron 10 of 11)	CpG	21264	NM_178869	319953	Mm.235007	NM_178869	ENSMUSG00000022442	Ttll1	6330444E16Rik|AV014541	tubulin tyrosine ligase-like 1	protein-coding
mm_65290.1	chr7	24445695	24445703	-	1	NA	promoter-TSS (NM_199013)	promoter-TSS (NM_199013)	-17	NM_199013	210145	Mm.33811	NM_199013	ENSMUSG00000062028	Irgc1	F630044M05Rik|Gm1102|Gm474|Ifgge|Iigp5|Irgc	immunity-related GTPase family, cinema 1	protein-coding
mm_16842.1	chr2	11502070	11502080	-	1	NA	promoter-TSS (NM_001177754)	promoter-TSS (NM_001177754)	15	NM_001177754	170768	Mm.19669	NM_133232	ENSMUSG00000026773	Pfkfb3	E330010H22Rik|iPFK-2|uPFK-2	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	protein-coding
mm_152968.1	chr19	29384442	29384448	-	1	NA	intron (NM_021893, intron 6 of 6)	intron (NM_021893, intron 6 of 6)	17007	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_25648.1	chr3	121426569	121426575	+	1	NA	promoter-TSS (NM_028044)	promoter-TSS (NM_028044)	31	NM_028044	71994	Mm.275555	NM_028044	ENSMUSG00000053931	Cnn3	1600014M03Rik|C85854|Calpo3	calponin 3, acidic	protein-coding
mm_162254.1	chrX	167855136	167855136	-	1	NA	promoter-TSS (NM_001290428)	promoter-TSS (NM_001290428)	-59	NM_001290428	333605	Mm.426168	NM_001033330	ENSMUSG00000049176	Frmpd4	Gm196|PKAP1|Pdzd10|Pdzk10|Preso1|preso	FERM and PDZ domain containing 4	protein-coding
mm_62739.1	chr7	111028962	111028972	+	1	NA	promoter-TSS (NM_009431)	promoter-TSS (NM_009431)	16	NM_009431	22083	Mm.255858	NM_009431	ENSMUSG00000005609	Ctr9	AA409336|Sh2bp1|Tsbp|Tsp|mKIAA0155	CTR9 homolog, Paf1/RNA polymerase II complex component	protein-coding
mm_29973.1	chr3	133544651	133544666	-	1	NA	promoter-TSS (NM_001346736)	promoter-TSS (NM_001346736)	-268	NM_001040400	214133	Mm.347816	NM_145989	ENSMUSG00000040943	Tet2	Ayu17-449|E130014J05Rik|mKIAA1546	tet methylcytosine dioxygenase 2	protein-coding
mm_136900.1	chr17	13015165	13015179	+	1	NA	3' UTR (NM_013671, exon 5 of 5)	3' UTR (NM_013671, exon 5 of 5)	7333	NM_013671	20656	Mm.290876	NM_013671	ENSMUSG00000006818	Sod2	MnSOD|Sod-2	superoxide dismutase 2, mitochondrial	protein-coding
mm_86687.1	chr10	18431178	18431186	+	1	NA	intron (NM_173390, intron 1 of 6)	intron (NM_173390, intron 1 of 6)	23507	NM_173390	215819	Mm.297971	NM_173390	ENSMUSG00000039835	Nhsl1	5730409E15Rik|A630035H13Rik|A730096F01|BC013565|D10Bwg0940e|mKIAA1357	NHS-like 1	protein-coding
mm_64395.1	chr7	142494244	142494260	+	1	NA	3' UTR (NM_001271509, exon 11 of 11)	3' UTR (NM_001271509, exon 11 of 11)	-4584	NM_001347549	21957	Mm.389992	NM_011620	ENSMUSG00000061723	Tnnt3	fTnT	troponin T3, skeletal, fast	protein-coding
mm_50914.1	chr6	57582855	57582863	+	1	NA	intron (NM_025992, intron 1 of 22)	IMPB_01|Satellite|Satellite	1867	NM_025992	67138	Mm.297393	NM_025992	ENSMUSG00000029798	Herc6	1700121D12Rik|2510038N07Rik|4930427L17Rik|AI451296|CEB1|Herc5	hect domain and RLD 6	protein-coding
mm_106332.1	chr11	118355318	118355334	-	1	NA	promoter-TSS (NM_011594)	promoter-TSS (NM_011594)	85	NM_011594	21858	Mm.206505	NM_011594	ENSMUSG00000017466	Timp2	D11Bwg1104e|Timp-2	tissue inhibitor of metalloproteinase 2	protein-coding
mm_159538.1	chr4	88522739	88522739	-	1	NA	promoter-TSS (NM_010510)	promoter-TSS (NM_010510)	55	NM_010510	15977	Mm.1245	NM_010510	ENSMUSG00000048806	Ifnb1	IFN-beta|IFNB|Ifb	interferon beta 1, fibroblast	protein-coding
mm_8374.1	chr1	150993423	150993449	-	1	NA	promoter-TSS (NM_001024720)	promoter-TSS (NM_001024720)	-1	NM_001024720	545370	Mm.379425	NM_001024720	ENSMUSG00000066842	Hmcn1	EG545370|FIBL-6|Gm201	hemicentin 1	protein-coding
mm_101180.1	chr11	16999723	16999726	-	1	NA	intron (NM_019549, intron 1 of 9)	intron (NM_019549, intron 1 of 9)	8994	NM_019549	56193	Mm.98232	NM_019549	ENSMUSG00000020120	Plek	2010300B13Rik	pleckstrin	protein-coding
mm_42686.1	chr5	119832703	119832715	+	1	NA	Intergenic	Intergenic	-1954	NM_011537	21388	Mm.103636	NM_011537	ENSMUSG00000018263	Tbx5	-	T-box 5	protein-coding
mm_60215.1	chr7	43463220	43463226	+	1	NA	promoter-TSS (NM_001290316)	promoter-TSS (NM_001290316)	-10	NM_001290316	75690	Mm.30200	NM_001290316	ENSMUSG00000070604	Vsig10l	-	V-set and immunoglobulin domain containing 10 like	protein-coding
mm_81157.1	chr9	107295929	107295935	+	1	NA	promoter-TSS (NM_009895)	promoter-TSS (NM_009895)	-727	NM_001317354	12700	Mm.4592	NM_009895	ENSMUSG00000032578	Cish	CIS-1|CIS1|Cis|F17|F23|SOCS	cytokine inducible SH2-containing protein	protein-coding
mm_53244.1	chr6	127561348	127561369	+	1	NA	Intergenic	CpG	-16617	NM_001033464	381812	Mm.296093	NM_001033464	ENSMUSG00000061414	Cracr2a	Efcab4b|Gm1073|Gm462	calcium release activated channel regulator 2A	protein-coding
mm_142996.1	chr17	56388327	56388343	-	1	NA	intron (NM_172132, intron 9 of 22)	intron (NM_172132, intron 9 of 22)	30574	NR_105943	102465590		NR_105943	ENSMUSG00000098339	Mir6977	Gm27922|mmu-mir-6977	microRNA 6977	ncRNA
mm_113189.1	chr13	24942715	24942764	+	1	NA	promoter-TSS (NM_008156)	promoter-TSS (NM_008156)	-413	NM_008156	14756	Mm.291831	NM_008156	ENSMUSG00000021340	Gpld1	6330541J12Rik|AW546131	glycosylphosphatidylinositol specific phospholipase D1	protein-coding
mm_793.1	chr1	45345842	45345855	+	1	NA	exon (NM_009930, exon 48 of 51)	exon (NM_009930, exon 48 of 51)	34310	NM_009930	12825	Mm.249555	NM_009930	ENSMUSG00000026043	Col3a1	AW550625|Col3a-1|Tsk-2|Tsk2	collagen, type III, alpha 1	protein-coding
mm_47312.1	chr5	122458518	122458536	-	1	NA	exon (NM_009722, exon 17 of 21)	exon (NM_009722, exon 17 of 21)	36083	NM_019805	56317	Mm.37341	NM_019805	ENSMUSG00000029466	Anapc7	APC7|AW545589	anaphase promoting complex subunit 7	protein-coding
mm_163028.1	chr11	50131429	50131446	+	1	NA	promoter-TSS (NM_001290759)	promoter-TSS (NM_001290759)	77	NM_029745	76795	Mm.290975	NM_029745	ENSMUSG00000036644	Tbc1d9b	-	TBC1 domain family, member 9B	protein-coding
mm_129910.1	chr15	84105663	84105674	-	1	NA	promoter-TSS (NM_013873)	promoter-TSS (NM_013873)	86	NM_013873	29859	Mm.248796	NM_013873	ENSMUSG00000018865	Sult4a1	2400007A17Rik|AI853543|BR-STL-1|ST4A1|Sultx3	sulfotransferase family 4A, member 1	protein-coding
mm_147309.1	chr18	40923768	40923778	-	1	NA	Intergenic	Lx9|LINE|L1	665412	NM_026135	383348	Mm.76366	NM_026135	ENSMUSG00000051401	Kctd16	4930434H12Rik|Gm1267	potassium channel tetramerisation domain containing 16	protein-coding
mm_159154.1	chr2	89002148	89002148	-	1	NA	exon (NM_146459, exon 1 of 1)	exon (NM_146459, exon 1 of 1)	142	NM_146459	258451	Mm.271379	NM_146459	ENSMUSG00000100016	Olfr1215	MOR233-13	olfactory receptor 1215	protein-coding
mm_121010.1	chr14	79535536	79535576	+	1	NA	intron (NM_001286411, intron 1 of 8)	intron (NM_001286411, intron 1 of 8)	19882	NM_001286411	13709	Mm.20938	NM_007920	ENSMUSG00000036461	Elf1	Elf-1|Sts1|mElf-1|p70	E74-like factor 1	protein-coding
mm_36874.1	chr4	107177729	107177735	-	1	NA	promoter-TSS (NM_029565)	promoter-TSS (NM_029565)	634	NM_025617	66526	Mm.246956	NM_025617	ENSMUSG00000028619	Tceanc2	2210010B22Rik|2210012G02Rik|6330404A07Rik|AU015593|Tdeanc2	transcription elongation factor A (SII) N-terminal and central domain containing 2	protein-coding
mm_136737.1	chr17	8340409	8340450	+	1	NA	promoter-TSS (NM_178774)	promoter-TSS (NM_178774)	23	NR_028280	320111	Mm.442510	NM_178774	ENSMUSG00000055945	Prr18	9630019K15Rik	proline rich 18	protein-coding
mm_90828.1	chr10	7956224	7956271	-	1	NA	promoter-TSS (NM_138667)	promoter-TSS (NM_138667)	-124	NM_138667	68652	Mm.193041	NM_138667	ENSMUSG00000015755	Tab2	1110030N06Rik|A530078N03Rik|Map3k7ip2|mKIAA0733	TGF-beta activated kinase 1/MAP3K7 binding protein 2	protein-coding
mm_15867.1	chr2	164833842	164833852	+	1	NA	promoter-TSS (NM_001082974)	promoter-TSS (NM_001082974)	74	NM_008906	19025	Mm.359633	NM_008906	ENSMUSG00000017760	Ctsa	AU019505|PPCA|Ppgb	cathepsin A	protein-coding
mm_151895.1	chr19	5798926	5798936	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	-2950	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_139052.1	chr17	46297918	46297938	+	1	NA	promoter-TSS (NM_001286013)	promoter-TSS (NM_001286013)	0	NM_001286013	106565	Mm.23633	NM_134120	ENSMUSG00000047428	Dlk2	AI413481|DLK-2|Egfl9	delta-like 2 homolog (Drosophila)	protein-coding
mm_77542.1	chr8	123158230	123158264	-	1	NA	promoter-TSS (NM_020564)	promoter-TSS (NM_020564)	33	NM_020564	57429	Mm.6562	NM_020564	ENSMUSG00000000739	Sult5a1	Sult-x1|Sultx1	sulfotransferase family 5A, member 1	protein-coding
mm_172995.1	chrM	1428	1428	+	1	NA	NA	Intergenic	NA	NA								
mm_155452.1	chrX	73495585	73495595	+	1	NA	3' UTR (NM_007542, exon 8 of 8)	3' UTR (NM_007542, exon 8 of 8)	-7496	NM_001310537	320707	Mm.210095	NM_177236	ENSMUSG00000031376	Atp2b3	6430519O13Rik|Pmca3	ATPase, Ca++ transporting, plasma membrane 3	protein-coding
mm_78906.1	chr9	44772989	44773015	+	1	NA	promoter-TSS (NM_023831)	promoter-TSS (NM_023831)	-7	NM_023831	76568	Mm.278597	NM_023831	ENSMUSG00000002031	Ift46	1500035H01Rik|AA408110|AI663846|R75047|c11orf2	intraflagellar transport 46	protein-coding
mm_76993.1	chr8	107065663	107065665	-	1	NA	promoter-TSS (NM_025458)	promoter-TSS (NM_025458)	-20	NM_025458	66269	Mm.23032	NM_025458	ENSMUSG00000031919	Tmed6	1810015P03Rik|1810018I24Rik	transmembrane p24 trafficking protein 6	protein-coding
mm_61341.1	chr7	68279218	68279226	+	1	NA	intron (NM_001013811, intron 1 of 8)	intron (NM_001013811, intron 1 of 8)	-2628	NR_040340	100504026	Mm.426764	NR_040340	ENSMUSG00000086628	Gm16157	OTTMUSG00000031023	predicted gene 16157	ncRNA
mm_12051.1	chr2	59162244	59162247	+	1	NA	intron (NM_175464, intron 1 of 20)	intron (NM_175464, intron 1 of 20)	1395	NM_175464	227937	Mm.260938	NM_026361	ENSMUSG00000026991	Pkp4	5031422I09Rik|9430019K17Rik|Armrp|p0071	plakophilin 4	protein-coding
mm_147865.1	chr18	64345807	64345819	-	1	NA	intron (NM_194268, intron 1 of 1)	intron (NM_194268, intron 1 of 1)	5449	NM_194268	225631	Mm.234723	NM_194268	ENSMUSG00000045991	Onecut2	C730009D12|OC-2|Oc2	one cut domain, family member 2	protein-coding
mm_114438.1	chr13	65950569	65950582	+	1	NA	Intergenic	Intergenic	-162878	NM_001177832	628709	Mm.390595	NM_001177832	ENSMUSG00000095909	Gm10324	ENSMUSG00000071302	predicted gene 10324	protein-coding
mm_104318.1	chr11	93955629	93955707	-	1	NA	5' UTR (NM_001077529, exon 1 of 4)	5' UTR (NM_001077529, exon 1 of 4)	115	NM_001077529	18103	Mm.1260	NM_008705	ENSMUSG00000020857	Nme2	NM23-H2|NM23B|nm23-M2	NME/NM23 nucleoside diphosphate kinase 2	protein-coding
mm_139143.1	chr17	47511894	47511906	+	1	NA	intron (NM_001081635, intron 1 of 6)	intron (NM_001081635, intron 1 of 6)	6849	NM_001081635	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_160411.1	chr8	73352716	73352716	-	1	NA	5' UTR (NM_010687, exon 1 of 15)	5' UTR (NM_010687, exon 1 of 15)	824	NM_001317391	16795	Mm.324371	NM_010687	ENSMUSG00000004383	Large1	BPFD#36|Gyltl1a|Large|Mbp-1|Mbp1|enr|fg|froggy|myd	LARGE xylosyl- and glucuronyltransferase 1	protein-coding
mm_136705.1	chr17	7878173	7878177	+	1	NA	Intergenic	Intergenic	-47825	NM_145968	72536	Mm.119680	NM_145968	ENSMUSG00000033450	Tagap	2610315E15Rik	T cell activation Rho GTPase activating protein	protein-coding
mm_23751.1	chr3	69553355	69553372	+	1	NA	3' UTR (NM_178726, exon 4 of 4)	3' UTR (NM_178726, exon 4 of 4)	45597	NM_020026	26879	Mm.153710	NM_020026	ENSMUSG00000043300	B3galnt1	B3galt3|b3GT3	UDP-GalNAc:betaGlcNAc beta 1,3-galactosaminyltransferase, polypeptide 1	protein-coding
mm_69427.1	chr7	132813135	132813162	-	1	NA	promoter-TSS (NM_212473)	promoter-TSS (NM_212473)	48	NM_212473	77938	Mm.225649	NM_175268	ENSMUSG00000030956	Fam53b	A930008G19Rik|mKIAA0140	family with sequence similarity 53, member B	protein-coding
mm_53064.1	chr6	124914106	124914127	+	1	NA	3' UTR (NM_026988, exon 5 of 5)	3' UTR (NM_026988, exon 5 of 5)	-2411	NM_008479	16768	Mm.4528	NM_008479	ENSMUSG00000030124	Lag3	CD223|LAG-3|Ly66	lymphocyte-activation gene 3	protein-coding
mm_60133.1	chr7	37369223	37369224	+	1	NA	Intergenic	Intergenic	400529	NM_172385	243937	Mm.322505	NM_172385	ENSMUSG00000043456	Zfp536	9630010P11Rik|Znf536|mKIAA0390	zinc finger protein 536	protein-coding
mm_41963.1	chr5	106964320	106964383	+	1	NA	promoter-TSS (NM_001271568)	promoter-TSS (NM_001271568)	29	NM_009863	12545	Mm.20842	NM_009863	ENSMUSG00000029283	Cdc7	AI597260|Cdc7l1|muCdc7	cell division cycle 7 (S. cerevisiae)	protein-coding
mm_15403.1	chr2	156730950	156730989	+	1	NA	intron (NM_001042487, intron 1 of 6)	intron (NM_001042487, intron 1 of 6)	9690	NM_001042487	228836	Mm.22094	NM_146128	ENSMUSG00000061689	Dlgap4	AI225853|BC024558|DAP-4|DAP4|SAPAP-4|Sapap4|WBP16	discs, large homolog-associated protein 4 (Drosophila)	protein-coding
mm_64607.1	chr7	3249660	3249672	-	1	NA	promoter-TSS (NM_001033431)	promoter-TSS (NM_001033431)	74	NM_001033431	378425	Mm.277152	NM_001033431	ENSMUSG00000078817	Nlrp12	Nalp12|PYPAF7	NLR family, pyrin domain containing 12	protein-coding
mm_136109.1	chr16	85456776	85456786	-	1	NA	3' UTR (NM_144853, exon 4 of 4)	3' UTR (NM_144853, exon 4 of 4)	93592	NM_144853	224405	Mm.213203	NM_144853	ENSMUSG00000041134	Cyyr1	-	cysteine and tyrosine-rich protein 1	protein-coding
mm_173089.1	chrX	150530079	150530083	+	1	NA	Intergenic	L1Md_T|LINE|L1	-17336	NM_009653	11656	Mm.302724	NM_009653	ENSMUSG00000025270	Alas2	ALAS|ALAS-E|ALASE|Alas-2	aminolevulinic acid synthase 2, erythroid	protein-coding
mm_54439.1	chr6	34415416	34415426	-	1	NA	exon (NM_009731, exon 2 of 10)	exon (NM_009731, exon 2 of 10)	3059	NM_009731	11997	Mm.482073	NM_009731	ENSMUSG00000052131	Akr1b7	AR|Avdp|MVDP	aldo-keto reductase family 1, member B7	protein-coding
mm_101699.1	chr11	40753890	40753921	-	1	NA	exon (NM_009831, exon 2 of 6)	exon (NM_009831, exon 2 of 6)	1381	NM_009831	12450	Mm.2103	NM_009831	ENSMUSG00000020326	Ccng1	AI314029	cyclin G1	protein-coding
mm_53580.1	chr6	137411057	137411071	+	1	NA	exon (NM_011216, exon 13 of 27)	exon (NM_011216, exon 13 of 27)	343	NM_001164403	19277	Mm.186361	NM_011216	ENSMUSG00000030223	Ptpro	D28|GLEPP1|PTPBK|PTPROt|PTPU2|PTPoc|PTPphi|Ptpn15|R-PTP-O	protein tyrosine phosphatase, receptor type, O	protein-coding
mm_126633.1	chr15	83526855	83526874	+	1	NA	promoter-TSS (NM_007546)	promoter-TSS (NM_007546)	2	NM_007546	12124	Mm.267006	NM_007546	ENSMUSG00000016758	Bik	Biklk|Blk|Nbk	BCL2-interacting killer	protein-coding
mm_85328.1	chr9	102304513	102304527	-	1	NA	TTS (NR_106163)	TTS (NR_106163)	455	NR_106163	102466241		NR_106163	ENSMUSG00000098521	Mir7243	Gm27363|mmu-mir-7243	microRNA 7243	ncRNA
mm_116423.1	chr13	41828419	41828444	-	1	NA	intron (NM_001145875, intron 1 of 6)	intron (NM_001145875, intron 1 of 6)	19057	NM_175417	109254	Mm.25195	NM_175417	ENSMUSG00000058022	Adtrp	9530008L14Rik	androgen dependent TFPI regulating protein	protein-coding
mm_169295.1	chr1	40458385	40458390	-	1	NA	intron (NM_001025602, intron 10 of 10)	L1Md_F3|LINE|L1	-7165	NM_001161842	16182	Mm.253664	NM_008365	ENSMUSG00000026070	Il18r1	Il18ralpha|Il1rrp	interleukin 18 receptor 1	protein-coding
mm_161276.1	chr14	14328163	14328163	+	1	NA	promoter-TSS (NM_147027)	promoter-TSS (NM_147027)	50	NM_147027	18330	Mm.484338	NM_147027	ENSMUSG00000072707	Olfr31	MOR274-1|MTPCR53	olfactory receptor 31	protein-coding
mm_128659.1	chr15	60016589	60016623	-	1	NA	promoter-TSS (NM_027668)	promoter-TSS (NM_027668)	12	NM_027668	71088	Mm.425950	NM_027668	ENSMUSG00000071749	4933412E24Rik	-	RIKEN cDNA 4933412E24 gene	protein-coding
mm_15535.1	chr2	158383087	158383095	+	1	NA	3' UTR (NM_175692, exon 5 of 5)	3' UTR (NM_175692, exon 5 of 5)	7453	NM_175692	319317	Mm.294494	NM_175692	ENSMUSG00000044349	Snhg11	A930034L06Rik|AI854265|AL022637|AW319638|E130013N09Rik	small nucleolar RNA host gene 11	protein-coding
mm_18892.1	chr2	76710730	76710742	-	1	NA	exon (NM_011652, exon 307 of 313)	exon (NM_011652, exon 307 of 313)	35421	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_125743.1	chr15	73723125	73723129	+	1	NA	promoter-TSS (NM_001166390)	promoter-TSS (NM_001166390)	-18	NM_001166390	19245	Mm.390807	NM_008975	ENSMUSG00000059895	Ptp4a3	AV088979|Prl-3|pPtp4a3	protein tyrosine phosphatase 4a3	protein-coding
mm_73180.1	chr8	95059022	95059065	+	1	NA	exon (NM_001042715, exon 5 of 18)	exon (NM_001042715, exon 5 of 18)	3940	NM_001042715	330830	Mm.277112	NM_001042715	ENSMUSG00000031786	Drc7	Ccdc135|Gm770|SRG-L|SRG-S	dynein regulatory complex subunit 7	protein-coding
mm_114865.1	chr13	93771717	93771731	+	1	NA	promoter-TSS (NM_009712)	promoter-TSS (NM_009712)	45	NM_009712	11881	Mm.300178	NM_009712	ENSMUSG00000042082	Arsb	1110007C02Rik|AI480648|As-1|As-1r|As-1s|As-1t|As1|As1-r|As1-s|As1-t|Asr-1|Ast-1	arylsulfatase B	protein-coding
mm_49575.1	chr6	30641538	30641561	+	1	NA	exon (NM_025350, exon 5 of 10)	exon (NM_025350, exon 5 of 10)	2331	NM_025350	109697	Mm.25377	NM_025350	ENSMUSG00000054446	Cpa1	0910001L12Rik|Cpa	carboxypeptidase A1, pancreatic	protein-coding
mm_156126.1	chrX	116727592	116727593	+	1	NA	Intergenic	L1_Mur2|LINE|L1	46414	NM_001281530	624153		NM_001281530	ENSMUSG00000082482	H2afb2	EG624153|H2A.Bbd4|H2afb2-ps	H2A histone family, member B2	protein-coding
mm_1634.1	chr1	74506310	74506374	+	1	NA	promoter-TSS (NM_001310662)	promoter-TSS (NM_001310662)	282	NM_021383	58184	Mm.291708	NM_021383	ENSMUSG00000026174	Cnot9	2610007F23Rik|AI593551|Fl10|Rqcd1	CCR4-NOT transcription complex, subunit 9	protein-coding
mm_104922.1	chr11	99858723	99858741	-	1	NA	3' UTR (NM_001205030, exon 1 of 1)	3' UTR (NM_001205030, exon 1 of 1)	815	NM_001205030	432600	Mm.60039	NM_001205030	ENSMUSG00000069717	Gm11568	OTTMUSG00000002207	predicted gene 11568	protein-coding
mm_167566.1	chr9	42120430	42120469	+	1	NA	intron (NM_011436, intron 1 of 47)	B1F1|SINE|Alu	3840	NM_011436	20660	Mm.121920	NM_011436	ENSMUSG00000049313	Sorl1	2900010L19Rik|AI596264|AW261561|LR11|SorLA|gp250|mSorLA	sortilin-related receptor, LDLR class A repeats-containing	protein-coding
mm_147856.1	chr18	63692421	63692431	-	1	NA	promoter-TSS (NM_016792)	promoter-TSS (NM_016792)	-67	NM_016792	53382	Mm.19169	NM_016792	ENSMUSG00000024583	Txnl1	32kDa|TRP32|Txnl	thioredoxin-like 1	protein-coding
mm_84825.1	chr9	78108568	78108576	-	1	NA	promoter-TSS (NM_001163780)	promoter-TSS (NM_001163780)	84	NM_023605	71538	Mm.28584	NM_023605	ENSMUSG00000001366	Fbxo9	9030401P18Rik|AA986398	f-box protein 9	protein-coding
mm_83553.1	chr9	46242541	46242634	-	1	NA	exon (NM_007468, exon 3 of 3)	exon (NM_007468, exon 3 of 3)	1743	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_108896.1	chr12	100184227	100184250	+	1	NA	Intergenic	MLT1A1|LTR|ERVL-MaLR	-3730	NR_045282	100038378	Mm.387075	NR_045282	ENSMUSG00000072884	Gm10433	ENSMUSG00000072884	predicted gene 10433	ncRNA
mm_170334.1	chr18	45071268	45071272	-	1	NA	Intergenic	Intergenic	-197590	NM_001312905	140492	Mm.411614	NM_080465	ENSMUSG00000054477	Kcnn2	KCa2.2|SK2|SKCA2|bc|fri	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2	protein-coding
mm_160706.1	chr10	52545709	52545709	-	1	NA	promoter-TSS (NR_037920)	promoter-TSS (NR_037920)	30	NR_037920	22639	Mm.490597	NM_009540	ENSMUSG00000049576	Zfa-ps	Zfa|Zfx	zinc finger protein, autosomal, pseudogene	pseudo
mm_4338.1	chr1	171856135	171856171	+	1	NA	intron (NM_001289470, intron 3 of 8)	RMER20A|LTR|ERVK	16456	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_51166.1	chr6	70726519	70726521	+	1	NA	Intergenic	Intergenic	65655	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_119833.1	chr14	54367864	54367886	+	1	NA	exon (NM_026936, exon 8 of 10)	exon (NM_026936, exon 8 of 10)	7034	NM_026936	69089	Mm.182340	NM_026936	ENSMUSG00000000959	Oxa1l	1810020M02Rik|AI894287	oxidase assembly 1-like	protein-coding
mm_87072.1	chr10	29147207	29147282	+	1	NA	exon (NM_026138, exon 2 of 7)	exon (NM_026138, exon 2 of 7)	3248	NM_026138	67412	Mm.390264	NM_026138	ENSMUSG00000038916	Soga3	6330407J23Rik	SOGA family member 3	protein-coding
mm_1387.1	chr1	67109167	67109168	+	1	NA	Intergenic	Intergenic	-13860	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_126634.1	chr15	83526897	83526907	+	1	NA	promoter-TSS (NM_007546)	promoter-TSS (NM_007546)	40	NM_007546	12124	Mm.267006	NM_007546	ENSMUSG00000016758	Bik	Biklk|Blk|Nbk	BCL2-interacting killer	protein-coding
mm_59254.1	chr7	24862223	24862236	+	1	NA	Intergenic	Intergenic	7462	NM_182785	232973	Mm.189648	NM_182785	ENSMUSG00000062732	Lypd4	4933400F01Rik	Ly6/Plaur domain containing 4	protein-coding
mm_164997.1	chr19	18670941	18670950	+	1	NA	5' UTR (NM_026120, exon 1 of 8)	5' UTR (NM_026120, exon 1 of 8)	165	NM_026120	67383	Mm.306602	NM_026120	ENSMUSG00000024726	Carnmt1	2410127L17Rik	carnosine N-methyltransferase 1	protein-coding
mm_104358.1	chr11	94303929	94303948	-	1	NA	exon (NM_026313, exon 4 of 11)	exon (NM_026313, exon 4 of 11)	17973	NM_026313	67684	Mm.30927	NM_026313	ENSMUSG00000020863	Luc7l3	3300001P08Rik|Luc7a	LUC7-like 3 (S. cerevisiae)	protein-coding
mm_80060.1	chr9	69397939	69397972	+	1	NA	promoter-TSS (NM_145618)	promoter-TSS (NM_145618)	-43	NM_145618	93697	Mm.35911	NM_145618	ENSMUSG00000032235	Ice2	B230343B06Rik|Narg2	interactor of little elongation complex ELL subunit 2	protein-coding
mm_94932.1	chr11	29693034	29693047	+	1	NA	promoter-TSS (NM_194051)	promoter-TSS (NM_194051)	142	NM_194052	68585	Mm.192580	NM_024226	ENSMUSG00000020458	Rtn4	1110020G17Rik|AA407876|AA409940|AA960376|ASY|C130026I10Rik|NOGO|NSP-CL|NgA|Nogo-A|Nogo-B|Nogo-C|mKIAA0886|mKIAA4153	reticulon 4	protein-coding
mm_133668.1	chr16	92074998	92075007	+	1	NA	intron (NM_080456, intron 1 of 2)	intron (NM_080456, intron 1 of 2)	16666	NM_080456	121022	Mm.217354	NM_080456	ENSMUSG00000039680	Mrps6	AW046321	mitochondrial ribosomal protein S6	protein-coding
mm_26137.1	chr3	137918471	137918509	+	1	NA	promoter-TSS (NM_019920)	promoter-TSS (NM_019920)	-65	NM_019920	56692	Mm.331392	NM_019920	ENSMUSG00000091512	Lamtor3	AW556229|Map2k1ip1|Mapbp|Mapksp1|Mp1	late endosomal/lysosomal adaptor, MAPK and MTOR activator 3	protein-coding
mm_115956.1	chr13	23761210	23761216	-	1	NA	promoter-TSS (NM_178192)	promoter-TSS (NM_178192)	36	NM_178192	326619	Mm.228709	NM_178192	ENSMUSG00000060093	Hist1h4a	-	histone cluster 1, H4a	protein-coding
mm_46884.1	chr5	113952054	113952069	-	1	NA	intron (NM_198109, intron 11 of 14)	intron (NM_198109, intron 11 of 14)	41696	NM_198109	231637	Mm.389682	NM_198109	ENSMUSG00000042121	Ssh1	AW551225|Gm1394|Gm1395|SSH-1|SSH-1L	slingshot homolog 1 (Drosophila)	protein-coding
mm_38561.1	chr4	141664000	141664021	-	1	NA	5' UTR (NM_001033150, exon 1 of 20)	5' UTR (NM_001033150, exon 1 of 20)	105	NM_001347237	69582	Mm.33220	NM_001033150	ENSMUSG00000028917	Plekhm2	2310034J19Rik|AI854247|mKIAA0842	pleckstrin homology domain containing, family M (with RUN domain) member 2	protein-coding
mm_7066.1	chr1	87626435	87626464	-	1	NA	intron (NM_010566, intron 1 of 26)	intron (NM_010566, intron 1 of 26)	6137	NM_001110193	16331	Mm.15105	NM_010566	ENSMUSG00000026288	Inpp5d	SHIP|SHIP-1|SHIP1|SIP-145|p150Ship|s-SHIP	inositol polyphosphate-5-phosphatase D	protein-coding
mm_61015.1	chr7	49372218	49372239	+	1	NA	intron (NM_175272, intron 2 of 37)	intron (NM_175272, intron 2 of 37)	126039	NM_175272	78286	Mm.333881	NM_175272	ENSMUSG00000052512	Nav2	5330421F07Rik|AU067780|BQ960892|HELAD1|POMFIL2|RAINB1|RAINB2|Unc53H2|mKIAA3015	neuron navigator 2	protein-coding
mm_40481.1	chr5	54053932	54053944	+	1	NA	intron (NM_001081103, intron 2 of 11)	intron (NM_001081103, intron 2 of 11)	55415	NM_001081103	116873	Mm.265985	NM_054083	ENSMUSG00000039156	Stim2	-	stromal interaction molecule 2	protein-coding
mm_27846.1	chr3	79156574	79156586	-	1	NA	Intergenic	L1_Mur3|LINE|L1	-10705	NM_001099624	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_50712.1	chr6	52172948	52172951	+	1	NA	intron (NM_010452, intron 3 of 4)	intron (NM_010452, intron 3 of 4)	7275	NR_131182	105242657	Mm.490651	NR_131182	ENSMUSG00000056445	Hoxaas2	2810043O09Rik|5730446D14Rik	Hoxa cluster antisense RNA 2	ncRNA
mm_45813.1	chr5	87674220	87674256	-	1	NA	exon (NM_007784, exon 12 of 34)	exon (NM_007784, exon 12 of 34)	8030	NM_001286016	12990	Mm.427467	NM_007784	ENSMUSG00000070702	Csn1s1	AA959832|AW212882|Csna	casein alpha s1	protein-coding
mm_74874.1	chr8	25038876	25038921	-	1	NA	promoter-TSS (NM_001081187)	promoter-TSS (NM_001081187)	64	NM_001081187	330723	Mm.334452	NM_001081187	ENSMUSG00000037406	Htra4	B430206E18Rik	HtrA serine peptidase 4	protein-coding
mm_56452.1	chr6	97818220	97818239	-	1	NA	intron (NM_001113198, intron 1 of 9)	intron (NM_001113198, intron 1 of 9)	11171	NM_001113198	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_97023.1	chr11	71751057	71751059	+	1	NA	intron (NM_177618, intron 1 of 8)	CpG	355	NM_177618	216881	Mm.48648	NM_177618	ENSMUSG00000020811	Wscd1	mKIAA0523	WSC domain containing 1	protein-coding
mm_18408.1	chr2	60383309	60383314	-	1	NA	promoter-TSS (NM_013825)	promoter-TSS (NM_013825)	-80	NM_013825	17076	Mm.2074	NM_013825	ENSMUSG00000026980	Ly75	CD205|DEC-205|DEC205	lymphocyte antigen 75	protein-coding
mm_140653.1	chr17	12716020	12716031	-	1	NA	exon (NM_010515, exon 16 of 48)	exon (NM_010515, exon 16 of 48)	-25286	NR_002853	104103	Mm.26553	NR_002853	ENSMUSG00000078247	Airn	2810051F02Rik|2810434M15Rik|AI256653|AI597500|AW049873|Air|B930018I07Rik|D17Ertd663e|IGF2RAS	antisense Igf2r RNA	ncRNA
mm_109016.1	chr12	103434215	103434281	+	1	NA	promoter-TSS (NM_194069)	promoter-TSS (NM_194069)	59	NM_194069	52668	Mm.2121	NM_026790	ENSMUSG00000064215	Ifi27	1110013J02Rik|2900026P10Rik|D12Ertd647e|ISG12a|Ifi27l1	interferon, alpha-inducible protein 27	protein-coding
mm_74830.1	chr8	23191571	23191580	-	1	NA	5' UTR (NM_018743, exon 2 of 13)	5' UTR (NM_018743, exon 2 of 13)	16878	NM_018743	102247	Mm.200898	NM_018743	ENSMUSG00000031545	Gpat4	AU041707|AW545732|Agpat6|Tsarg7	glycerol-3-phosphate acyltransferase 4	protein-coding
mm_16377.1	chr2	178193076	178193099	+	1	NA	promoter-TSS (NM_001007154)	promoter-TSS (NM_001007154)	3	NM_001007154	74189	Mm.44413	NM_028806	ENSMUSG00000027525	Phactr3	1500003N10Rik|4930415A02Rik|H17739|Scapin1|Scapinin|mKIAA4224	phosphatase and actin regulator 3	protein-coding
mm_151958.1	chr19	5801390	5801474	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	1240	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_32743.1	chr4	116637801	116637822	+	1	NA	exon (NM_021473, exon 8 of 9)	exon (NM_021473, exon 8 of 9)	-9860	NM_016777	50927	Mm.257181	NM_016777	ENSMUSG00000028693	Nasp	5033430J04Rik|AI131596|AI317140|D4Ertd767e|Epcs32|Nasp-T	nuclear autoantigenic sperm protein (histone-binding)	protein-coding
mm_53960.1	chr6	5495875	5495881	-	1	NA	intron (NM_013743, intron 1 of 10)	intron (NM_013743, intron 1 of 10)	400	NM_013743	27273	Mm.235547	NM_013743	ENSMUSG00000019577	Pdk4	AV005916	pyruvate dehydrogenase kinase, isoenzyme 4	protein-coding
mm_111193.1	chr12	84193771	84193801	-	1	NA	5' UTR (NM_001163502, exon 1 of 13)	5' UTR (NM_001163502, exon 1 of 13)	229	NM_001163502	238317	Mm.31256	NM_001163501	ENSMUSG00000042507	Elmsan1	9430029N19Rik|C130039O16Rik|Gm260	ELM2 and Myb/SANT-like domain containing 1	protein-coding
mm_68130.1	chr7	102210173	102210183	-	1	NA	promoter-TSS (NM_001291358)	promoter-TSS (NM_001291358)	-12	NM_001287164	269966	Mm.439800	NM_022979	ENSMUSG00000063550	Nup98	4732457F17|AI849286|Nup96	nucleoporin 98	protein-coding
mm_127153.1	chr15	98571008	98571026	+	1	NA	promoter-TSS (NM_001201322)	promoter-TSS (NM_001201322)	13	NM_001201322	73863	Mm.66894	NM_001201322	ENSMUSG00000022993	4930415O20Rik	-	RIKEN cDNA 4930415O20 gene	protein-coding
mm_169156.1	chr13	63793691	63793692	+	1	NA	Intergenic	Intergenic	-21629	NM_001013608	76251	Mm.186610	NM_023507	ENSMUSG00000021470	Ercc6l2	0610007P08Rik|1700019D06Rik|9330134C04Rik|Rad26l|Sr278	excision repair cross-complementing rodent repair deficiency, complementation group 6 like 2	protein-coding
mm_21198.1	chr2	155473789	155473835	-	1	NA	Intergenic	Intergenic	-33029	NM_019825	56406	Mm.27592	NM_019825	ENSMUSG00000038369	Ncoa6	AIB3|ASC-2|ASC2|NRC|Ncoa7|PRIP|RAP250|mKIAA0181	nuclear receptor coactivator 6	protein-coding
mm_70631.1	chr8	13771367	13771389	+	1	NA	exon (NM_027276, exon 13 of 18)	exon (NM_027276, exon 13 of 18)	13688	NM_027276	69957	Mm.182412	NM_027276	ENSMUSG00000038416	Cdc16	2700071J12Rik|2810431D22Rik|APC6	CDC16 cell division cycle 16	protein-coding
mm_56059.1	chr6	86775072	86775098	-	1	NA	promoter-TSS (NM_001331120)	promoter-TSS (NM_001331120)	29	NM_001331120	11746	Mm.259702	NM_013471	ENSMUSG00000029994	Anxa4	AI265406|AIV|AW106930|Anx4|Xanx-4	annexin A4	protein-coding
mm_16930.1	chr2	13793912	13793920	-	1	NA	promoter-TSS (NM_145838)	promoter-TSS (NM_145838)	-396	NM_145838	241230	Mm.330004	NM_145838	ENSMUSG00000003418	St8sia6	1700007J08Rik|AI314453|AI875066|ST8SiaVI|Siat8f	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 6	protein-coding
mm_86695.1	chr10	18469904	18469910	+	1	NA	promoter-TSS (NM_001163592)	promoter-TSS (NM_001163592)	-74	NM_001163592	215819	Mm.297971	NM_173390	ENSMUSG00000039835	Nhsl1	5730409E15Rik|A630035H13Rik|A730096F01|BC013565|D10Bwg0940e|mKIAA1357	NHS-like 1	protein-coding
mm_6163.1	chr1	65061891	65061901	-	1	NA	TTS (NM_007776)	TTS (NM_007776)	1544	NM_007776	12967	Mm.425031	NM_007776	ENSMUSG00000067299	Crygd	Aey4|Cryg-1|DGcry-1|Lop12	crystallin, gamma D	protein-coding
mm_60823.1	chr7	45705445	45705453	+	1	NA	TTS (NM_009800)	TTS (NM_009800)	202	NM_016974	13170	Mm.24222	NM_016974	ENSMUSG00000059824	Dbp	-	D site albumin promoter binding protein	protein-coding
mm_54101.1	chr6	16855949	16856002	-	1	NA	intron (NM_031198, intron 2 of 6)	intron (NM_031198, intron 2 of 6)	42466	NM_031198	21426	Mm.36217	NM_031198	ENSMUSG00000029553	Tfec	BB107417|Tcfec|bHLHe34	transcription factor EC	protein-coding
mm_169011.1	chr13	107121969	107121978	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	99403	NR_015471	100040322	Mm.133867	NR_015471		3830408C21Rik	-	RIKEN cDNA 3830408C21 gene	ncRNA
mm_96505.1	chr11	68447559	68447578	+	1	NA	intron (NM_177320, intron 1 of 18)	intron (NM_177320, intron 1 of 18)	15443	NM_177320	320207	Mm.244960	NM_177320	ENSMUSG00000020901	Pik3r5	AV230647|F730038I15Rik	phosphoinositide-3-kinase, regulatory subunit 5, p101	protein-coding
mm_140058.1	chr17	74665769	74665777	+	1	NA	intron (NM_007566, intron 62 of 72)	B1_Mur1|SINE|Alu	-51977	NM_152817	74196	Mm.209503	NM_152817	ENSMUSG00000024078	Ttc27	2610511O17Rik	tetratricopeptide repeat domain 27	protein-coding
mm_94796.1	chr11	22972950	22973016	+	1	NA	5' UTR (NM_011663, exon 1 of 1)	5' UTR (NM_011663, exon 1 of 1)	978	NM_011663	22183	Mm.29542	NM_011663	ENSMUSG00000044068	Zrsr1	D11Ncvs75|Irlgs2|SP2|U2af1-rs1|U2afbp-rs	zinc finger (CCCH type), RNA binding motif and serine/arginine rich 1	protein-coding
mm_145298.1	chr18	53297303	53297318	+	1	NA	intron (NM_029394, intron 1 of 6)	PB1D9|SINE|Alu	51648	NM_029394	69226	Mm.32414	NM_029394	ENSMUSG00000024535	Snx24	2810011K15Rik|5730433I16Rik|AI451341	sorting nexing 24	protein-coding
mm_68347.1	chr7	106507004	106507018	-	1	NA	Intergenic	Intergenic	-65938	NR_003967	209380	Mm.461779	NM_001001318		Gm4759	EG209380	GTPase, very large interferon inducible 1 pseudogene	pseudo
mm_164572.1	chr17	23670010	23670010	-	1	NA	intron (NM_001008425, intron 7 of 12)	intron (NM_001008425, intron 7 of 12)	-3598	NM_181821	353502	Mm.359030	NM_181821	ENSMUSG00000023904	Hcfc1r1	HPIP	host cell factor C1 regulator 1 (XPO1-dependent)	protein-coding
mm_39535.1	chr5	21376489	21376500	+	1	NA	3' UTR (NM_008013, exon 2 of 2)	3' UTR (NM_008013, exon 2 of 2)	3821	NM_008013	14190	Mm.292100	NM_008013	ENSMUSG00000039899	Fgl2	AI385601|musfiblp	fibrinogen-like protein 2	protein-coding
mm_17604.1	chr2	30897503	30897514	-	1	NA	intron (NM_022415, intron 2 of 2)	intron (NM_022415, intron 2 of 2)	5789	NM_022415	64292	Mm.28768	NM_022415	ENSMUSG00000050737	Ptges	2410099E23Rik|D2Ertd369e|Pges|mPGES|mPGES-1	prostaglandin E synthase	protein-coding
mm_33826.1	chr4	135495980	135496016	+	1	NA	promoter-TSS (NM_030189)	promoter-TSS (NM_030189)	11	NM_030189	78806	Mm.374844	NM_030189	ENSMUSG00000028801	Stpg1	4930403G18Rik|4930555I21Rik|Mapo2	sperm tail PG rich repeat containing 1	protein-coding
mm_63045.1	chr7	121734450	121734473	+	1	NA	promoter-TSS (NM_011326)	promoter-TSS (NM_011326)	-18	NM_011326	20278	Mm.35247	NM_011326	ENSMUSG00000000216	Scnn1g	SCNEG	sodium channel, nonvoltage-gated 1 gamma	protein-coding
mm_49030.1	chr6	4759770	4759781	+	1	NA	3' UTR (NM_130877, exon 2 of 2)	3' UTR (NM_130877, exon 2 of 2)	12469	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_127173.1	chr15	98871016	98871046	+	1	NA	5' UTR (NM_001033276, exon 1 of 55)	5' UTR (NM_001033276, exon 1 of 55)	174	NM_001033276	381022	Mm.264889	NM_001033276	ENSMUSG00000048154	Kmt2d	ALR|BC032281|BC058659|C430014K11Rik|KMT2B|Mll2|Mll4	lysine (K)-specific methyltransferase 2D	protein-coding
mm_84212.1	chr9	61372188	61372211	-	1	NA	promoter-TSS (NM_009389)	promoter-TSS (NM_009389)	-167	NM_001083928	21887	Mm.24255	NM_009389	ENSMUSG00000032280	Tle3	2610103N05Rik|ESG|Grg3a|Grg3b|mKIAA1547	transducin-like enhancer of split 3	protein-coding
mm_39491.1	chr5	20950984	20950994	+	1	NA	promoter-TSS (NR_030699)	promoter-TSS (NR_030699)	0	NR_030699	320770	Mm.491217	NR_030699	ENSMUSG00000101013	A630072M18Rik	Aptr	RIKEN cDNA A630072M18 gene	ncRNA
mm_107663.1	chr12	52854647	52854665	+	1	NA	intron (NM_198111, intron 2 of 13)	intron (NM_198111, intron 2 of 13)	155273	NM_198111	238161	Mm.310822	NM_198111	ENSMUSG00000061603	Akap6	AI482140|Akapalpha|Akapbeta|PRKA	A kinase (PRKA) anchor protein 6	protein-coding
mm_7060.1	chr1	87510284	87510294	-	1	NA	promoter-TSS (NM_019867)	promoter-TSS (NM_019867)	73	NM_019867	53972	Mm.435439	NM_019867	ENSMUSG00000026259	Ngef	Tims2|ephexin	neuronal guanine nucleotide exchange factor	protein-coding
mm_89102.1	chr10	84556460	84556464	+	1	NA	Intergenic	Intergenic	-3124	NR_040658	442847	Mm.128292	NR_040658	ENSMUSG00000097076	Platr7	C330046G13Rik	pluripotency associated transcript 7	ncRNA
mm_124828.1	chr15	9092240	9092243	+	1	NA	intron (NM_001040395, intron 5 of 12)	intron (NM_001040395, intron 5 of 12)	20981	NM_001040395	68646	Mm.244226	NM_001040395	ENSMUSG00000022253	Nadk2	MNADK|Nadkd1	NAD kinase 2, mitochondrial	protein-coding
mm_137033.1	chr17	17890349	17890352	+	1	NA	intron (NM_008039, intron 1 of 1)	intron (NM_008039, intron 1 of 1)	2526	NM_008039	14289	Mm.378918	NM_008039	ENSMUSG00000052270	Fpr2	E330010I07Rik|Fpr-rs2	formyl peptide receptor 2	protein-coding
mm_85946.1	chr9	112108043	112108056	-	1	NA	intron (NM_001177618, intron 17 of 18)	intron (NM_001177618, intron 17 of 18)	10662	NR_029823	723815		NR_029823	ENSMUSG00000065441	Mir128-2	Mirn128-2|Mirn128b|mir-128-2|mir-128b	microRNA 128-2	ncRNA
mm_79319.1	chr9	52115144	52115144	+	1	NA	promoter-TSS (NR_105750)	promoter-TSS (NR_105750)	-479	NR_105750	102465150		NR_105750	ENSMUSG00000099311	Mir6244	Gm27368|mmu-mir-6244	microRNA 6244	ncRNA
mm_157962.1	chrX	88760222	88760248	-	1	NA	promoter-TSS (NR_035440)	promoter-TSS (NR_035440)	-682	NR_037313	100499530		NR_037313	ENSMUSG00000084559	Mir1906-2	mmu-mir-1906-2	microRNA 1906-2	ncRNA
mm_17395.1	chr2	27142407	27142425	-	1	NA	promoter-TSS (NM_175427)	promoter-TSS (NM_175427)	61	NM_175427	109349	Mm.314080	NM_175427	ENSMUSG00000009216	Fam163b	C630035N08Rik	family with sequence similarity 163, member B	protein-coding
mm_122503.1	chr14	46822137	46822167	-	1	NA	promoter-TSS (NM_022023)	promoter-TSS (NM_022023)	90	NM_022023	63985	Mm.87312	NM_022023	ENSMUSG00000062014	Gmfb	3110001H22Rik|3110001O16Rik|AI851627|C79176|D14Ertd630e	glia maturation factor, beta	protein-coding
mm_58227.1	chr6	144630525	144630536	-	1	NA	Intergenic	Intergenic	-42338	NR_040519	66760	Mm.233631	NR_040519	ENSMUSG00000085785	Sox5os3	4933425H06Rik	SRY (sex determining region Y)-box 5, opposite strand 3	ncRNA
mm_115815.1	chr13	19732801	19732815	-	1	NA	5' UTR (NM_175688, exon 1 of 2)	5' UTR (NM_175688, exon 1 of 2)	143	NM_175688	319293	Mm.246657	NM_175688	ENSMUSG00000047462	A530099J19Rik	-	RIKEN cDNA A530099J19 gene	protein-coding
mm_72263.1	chr8	75097188	75097214	+	1	NA	exon (NM_010442, exon 3 of 5)	exon (NM_010442, exon 3 of 5)	3583	NM_010442	15368	Mm.276389	NM_010442	ENSMUSG00000005413	Hmox1	D8Wsu38e|HO-1|HO1|Hemox|Hmox|Hsp32	heme oxygenase 1	protein-coding
mm_81150.1	chr9	106892451	106892475	+	1	NA	promoter-TSS (NM_029103)	promoter-TSS (NM_029103)	-525	NM_029103	74840	Mm.29778	NM_029103	ENSMUSG00000032575	Manf	3230402M22Rik|AA407711|AA408789|AA673178|Armet|D17914|D18Mgi17	mesencephalic astrocyte-derived neurotrophic factor	protein-coding
mm_57699.1	chr6	128525282	128525290	-	1	NA	exon (NM_007376, exon 2 of 36)	exon (NM_007376, exon 2 of 36)	1434	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_41128.1	chr5	87786652	87786654	+	1	NA	exon (NM_001304768, exon 11 of 13)	exon (NM_001304768, exon 11 of 13)	12203	NM_007785	12993	Mm.4908	NM_007785	ENSMUSG00000061937	Csn1s2a	Csng|PP22	casein alpha s2-like A	protein-coding
mm_124796.1	chr15	8225261	8225268	+	1	NA	intron (NM_001162906, intron 31 of 52)	intron (NM_001162906, intron 31 of 52)	56158	NM_001162906	73692	Mm.164436	NM_001162906	ENSMUSG00000039801	2410089E03Rik	4732468D17Rik|Hug|Jbts17|b2b012Clo	RIKEN cDNA 2410089E03 gene	protein-coding
mm_106561.1	chr11	120630557	120630588	-	1	NA	intron (NM_010756, intron 1 of 2)	intron (NM_010756, intron 1 of 2)	2975	NM_010756	17134	Mm.268010	NM_010756	ENSMUSG00000051510	Mafg	AA545192|C630022N07Rik	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein G (avian)	protein-coding
mm_73633.1	chr8	110721656	110721724	+	1	NA	5' UTR (NM_198625, exon 1 of 14)	5' UTR (NM_198625, exon 1 of 14)	214	NM_198625	244654	Mm.490385	NM_198625	ENSMUSG00000033763	Mtss1l	ABBA	metastasis suppressor 1-like	protein-coding
mm_64144.1	chr7	141228767	141228813	+	1	NA	promoter-TSS (NM_001081118)	promoter-TSS (NM_001081118)	2	NM_001081118	101471	Mm.248656	NM_207211	ENSMUSG00000038611	Phrf1	AA673488	PHD and ring finger domains 1	protein-coding
mm_132344.1	chr16	33883635	33883681	+	1	NA	intron (NM_010580, intron 4 of 14)	intron (NM_010580, intron 4 of 14)	53993	NM_001145884	16419	Mm.6424	NM_010580	ENSMUSG00000022817	Itgb5	AA475909|AI874634|ESTM23|[b]-5|[b]5|[b]5A|[b]5B|beta-5|beta5	integrin beta 5	protein-coding
mm_60158.1	chr7	39544421	39544452	+	1	NA	Intergenic	CpG	26670	NM_001004139	70227	Mm.333800	NM_001004139	ENSMUSG00000068959	Zfp619	3000002G13Rik	zinc finger protein 619	protein-coding
mm_61218.1	chr7	64392721	64392731	+	1	NA	promoter-TSS (NM_026483)	promoter-TSS (NM_026483)	-45	NM_028626	73724	Mm.10093	NM_028626	ENSMUSG00000033429	Mcee	1110007A04Rik	methylmalonyl CoA epimerase	protein-coding
mm_22363.1	chr2	181039287	181039320	-	1	NA	promoter-TSS (NM_015730)	promoter-TSS (NM_015730)	-126	NM_015730	11438	Mm.252369	NM_015730	ENSMUSG00000027577	Chrna4	Acra-4|Acra4|EBN1|ENFL1	cholinergic receptor, nicotinic, alpha polypeptide 4	protein-coding
mm_18731.1	chr2	72979603	72979668	-	1	NA	promoter-TSS (NM_001098425)	promoter-TSS (NM_001098425)	203	NR_045269	100503849	Mm.389285	NM_183265		Sp3os	1700011J10Rik	trans-acting transcription factor 3, opposite strand	ncRNA
mm_79946.1	chr9	66004655	66004688	+	1	NA	intron (NM_173185, intron 7 of 13)	intron (NM_173185, intron 7 of 13)	-55498	NM_011149	19035	Mm.335249	NM_011149	ENSMUSG00000032383	Ppib	AA408962|AA553318|AI844835|Cphn-2|Cphn2|CyP-20b	peptidylprolyl isomerase B	protein-coding
mm_73619.1	chr8	110217949	110218004	+	1	NA	promoter-TSS (NM_146215)	promoter-TSS (NM_146215)	16	NM_146215	234728	Mm.275341	NM_146215	ENSMUSG00000046441	Cmtr2	AU022703|C730036L12Rik|Ftsjd1|MTr2	cap methyltransferase 2	protein-coding
mm_88031.1	chr10	67285450	67285470	+	1	NA	promoter-TSS (NM_001036293)	promoter-TSS (NM_001036293)	-179	NM_001036293	641340	Mm.136223	NM_001036293	ENSMUSG00000075000	Nrbf2	NRBF-2	nuclear receptor binding factor 2	protein-coding
mm_24003.1	chr3	87290333	87290359	+	1	NA	Intergenic	ORR1E-int|LTR|ERVL-MaLR	-26822	NM_030707	80891	Mm.45173	NM_030707	ENSMUSG00000015852	Fcrls	2810439C17Rik|9330158F12|FcRH2sc|Fcrh2|IFGP2|IgSR|MMAN-g|Msr2|moFcRH2sc	Fc receptor-like S, scavenger receptor	protein-coding
mm_17658.1	chr2	32065414	32065437	-	1	NA	Intergenic	Intergenic	14479	NR_106135	102466844		NR_106135	ENSMUSG00000099075	Mir7674	Gm27563|mmu-mir-7674	microRNA 7674	ncRNA
mm_36244.1	chr4	63381216	63381253	-	1	NA	intron (NM_001305432, intron 8 of 20)	intron (NM_001305432, intron 8 of 20)	17006	NM_001305432	100182	Mm.387725	NM_001045514	ENSMUSG00000039158	Akna	AI597013	AT-hook transcription factor	protein-coding
mm_118886.1	chr14	26565738	26565755	+	1	NA	Intergenic	Intergenic	-8112	NM_001285467	211922	Mm.260512	NM_145969	ENSMUSG00000040818	Dennd6a	Fam116a	DENN/MADD domain containing 6A	protein-coding
mm_100996.1	chr11	8468451	8468459	-	1	NA	intron (NM_001083587, intron 20 of 30)	intron (NM_001083587, intron 20 of 30)	196080	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_50200.1	chr6	42040067	42040084	+	1	NA	intron (NM_009299, intron 1 of 3)	intron (NM_009299, intron 1 of 3)	1681	NM_009299	20939	Mm.4119	NM_009299	ENSMUSG00000023289	Sva	-	seminal vesicle antigen	protein-coding
mm_118625.1	chr14	21182664	21182674	+	1	NA	intron (NM_001243041, intron 4 of 10)	L1_Mur3|LINE|L1	106517	NM_001243041	11534	Mm.188734	NM_134079	ENSMUSG00000039197	Adk	2310026J05Rik|5033405D03Rik|AI255373|AI987814|Ak	adenosine kinase	protein-coding
mm_39221.1	chr4	156199591	156199603	-	1	NA	exon (NM_015783, exon 2 of 2)	exon (NM_015783, exon 2 of 2)	1221	NM_015783	100038882	Mm.4950	NM_015783	ENSMUSG00000035692	Isg15	G1p2|IGI15|IP17|Irfp|UCRP	ISG15 ubiquitin-like modifier	protein-coding
mm_156423.1	chrX	140923194	140923209	+	1	NA	promoter-TSS (NM_026103)	promoter-TSS (NM_026103)	12	NM_026103	78789	Mm.244932	NM_026103	ENSMUSG00000031430	Vsig1	1700062D20Rik|4930405J24Rik	V-set and immunoglobulin domain containing 1	protein-coding
mm_67678.1	chr7	89328725	89328727	-	1	NA	intron (NM_028343, intron 1 of 14)	intron (NM_028343, intron 1 of 14)	10061	NM_028343	72759	Mm.208477	NM_028343	ENSMUSG00000039428	Tmem135	2810439K08Rik|AW319712|PMP52	transmembrane protein 135	protein-coding
mm_163883.1	chr14	22019642	22019644	+	1	NA	promoter-TSS (NM_028275)	promoter-TSS (NM_028275)	-69	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_106653.1	chr11	121086483	121086512	-	1	NA	Intergenic	Intergenic	-5358	NM_145373	209588	Mm.69553	NM_145373	ENSMUSG00000025165	Sectm1a	BC010462	secreted and transmembrane 1A	protein-coding
mm_50065.1	chr6	41188396	41188406	+	1	NA	Intergenic	Intergenic	-113871	NM_011646	22074	Mm.383263	NM_011646	ENSMUSG00000054106	Try4	0910001B19Rik|Td	trypsin 4	protein-coding
mm_111654.1	chr12	102855749	102855785	-	1	NA	intron (NM_172806, intron 1 of 11)	intron (NM_172806, intron 1 of 11)	22639	NM_172806	238386	Mm.63456	NM_172806	ENSMUSG00000041702	Btbd7	5730507E09Rik|8030448M07|E130118E17Rik|FUP1|mKIAA1525	BTB (POZ) domain containing 7	protein-coding
mm_45510.1	chr5	72504203	72504247	-	1	NA	promoter-TSS (NM_016869)	promoter-TSS (NM_016869)	-17	NM_016869	53419	Mm.332425	NM_016869	ENSMUSG00000005220	Corin	AV273130|Lrp4	corin	protein-coding
mm_25277.1	chr3	105452105	105452145	+	1	NA	promoter-TSS (NM_001039347)	promoter-TSS (NM_001039347)	-205	NM_001039347	56543	Mm.44530	NM_019931	ENSMUSG00000040896	Kcnd3	AW045978|Kncd3|Kv4.3	potassium voltage-gated channel, Shal-related family, member 3	protein-coding
mm_110837.1	chr12	72917851	72917865	-	1	NA	promoter-TSS (NM_029444)	promoter-TSS (NM_029444)	-93	NM_029444	75801	Mm.242892	NM_029444	ENSMUSG00000021098	4930447C04Rik	4921504I02Rik|A930035O15Rik|Six6OS|Six6as|Six6os1	RIKEN cDNA 4930447C04 gene	protein-coding
mm_147582.1	chr18	56498853	56498863	-	1	NA	intron (NM_026240, intron 13 of 13)	intron (NM_026240, intron 13 of 13)	-39281	NR_106160	102465790		NR_106160	ENSMUSG00000099196	Mir1258	Gm27371|mmu-mir-1258	microRNA 1258	ncRNA
mm_4323.1	chr1	171851996	171852007	+	1	NA	exon (NM_013489, exon 3 of 9)	exon (NM_013489, exon 3 of 9)	12304	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_63550.1	chr7	128070619	128070631	+	1	NA	intron (NM_001082960, intron 3 of 29)	intron (NM_001082960, intron 3 of 29)	7985	NM_008401	16409	Mm.262106	NM_008401	ENSMUSG00000030786	Itgam	CD11b/CD18|CR3|CR3A|Cd11b|F730045J24Rik|Ly-40|MAC1|Mac-1|Mac-1a	integrin alpha M	protein-coding
mm_40764.1	chr5	66997032	66997068	+	1	NA	intron (NM_001256122, intron 4 of 20)	intron (NM_001256122, intron 4 of 20)	28634	NM_001256122	77569	Mm.374778	NM_001001980	ENSMUSG00000037736	Limch1	3732412D22Rik|mKIAA1102	LIM and calponin homology domains 1	protein-coding
mm_32884.1	chr4	118961726	118961735	+	1	NA	promoter-TSS (NM_133892)	promoter-TSS (NM_133892)	-237	NM_133892	100470	Mm.26698	NM_133892	ENSMUSG00000024903	Lao1	AW990848	L-amino acid oxidase 1	protein-coding
mm_122926.1	chr14	54961260	54961277	-	1	NA	exon (NM_010856, exon 11 of 39)	exon (NM_010856, exon 11 of 39)	5339	NM_001164171	17888	Mm.290003	NM_010856	ENSMUSG00000040752	Myh6	A830009F23Rik|AA517445|Myhc-a|Myhca|alpha-MHC	myosin, heavy polypeptide 6, cardiac muscle, alpha	protein-coding
mm_60885.1	chr7	46396440	46396539	+	1	NA	promoter-TSS (NM_001112739)	promoter-TSS (NM_001112739)	21	NM_001112739	16502	Mm.249386	NM_008421	ENSMUSG00000058975	Kcnc1	C230009H10Rik|KShIIIB|KV4|Kcr2-1|Kv3.1|NGK2|Shaw	potassium voltage gated channel, Shaw-related subfamily, member 1	protein-coding
mm_137931.1	chr17	32658879	32658913	+	1	NA	promoter-TSS (NM_001101588)	promoter-TSS (NM_001101588)	-587	NM_001101588	631304	Mm.328950	NM_001101588	ENSMUSG00000090700	Cyp4f40	EG631304	cytochrome P450, family 4, subfamily f, polypeptide 40	protein-coding
mm_30296.1	chr3	148990570	148990593	-	1	NA	Intergenic	CpG	-35946	NM_001081298	99633	Mm.9776	NM_001081298	ENSMUSG00000028184	Adgrl2	AI450192|CIRL-2|Gm619|Lec1|Lphh1|Lphn2|mKIAA0786	adhesion G protein-coupled receptor L2	protein-coding
mm_152760.1	chr19	20378412	20378471	-	1	NA	exon (NM_010730, exon 9 of 13)	exon (NM_010730, exon 9 of 13)	12230	NM_010730	16952	Mm.248360	NM_010730	ENSMUSG00000024659	Anxa1	Anx-1|Anx-A1|C430014K04Rik|Lpc-1|Lpc1	annexin A1	protein-coding
mm_151274.1	chr19	55251899	55251903	+	1	NA	Intergenic	Intergenic	-1468	NM_027976	433256	Mm.292056	NM_027976	ENSMUSG00000024981	Acsl5	1700030F05Rik|ACS2|ACS5|Facl5	acyl-CoA synthetase long-chain family member 5	protein-coding
mm_92730.1	chr10	80855176	80855186	-	1	NA	promoter-TSS (NM_025349)	promoter-TSS (NM_025349)	28	NM_025349	66094	Mm.379101	NM_025349	ENSMUSG00000035215	Lsm7	0910001B06Rik|1110033F18Rik	LSM7 homolog, U6 small nuclear RNA and mRNA degradation associated	protein-coding
mm_90369.1	chr10	127167772	127167785	+	1	NA	exon (NM_027739, exon 5 of 10)	exon (NM_027739, exon 5 of 10)	1947	NM_001244618	14421	Mm.386762	NM_008080	ENSMUSG00000006731	B4galnt1	4933429D13Rik|Gal-NAc-T|GalNAc-T|GalNAcT|Galgt1|Ggm-2|Ggm2	beta-1,4-N-acetyl-galactosaminyl transferase 1	protein-coding
mm_76283.1	chr8	84197676	84197680	-	1	NA	Intergenic	CpG	-10840	NR_029740	387216		NR_029740	ENSMUSG00000065611	Mir23a	Mirn23a|mir-23a|mmu-mir-23a	microRNA 23a	ncRNA
mm_112851.1	chr13	20836165	20836167	+	1	NA	intron (NM_012054, intron 2 of 20)	intron (NM_012054, intron 2 of 20)	42053	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_56468.1	chr6	98978160	98978169	-	1	NA	exon (NM_053202, exon 10 of 19)	exon (NM_053202, exon 10 of 19)	50134	NM_001197322	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_44176.1	chr5	150973593	150973604	+	1	NA	intron (NM_013823, intron 1 of 4)	B4|SINE|B4	20991	NM_013823	16591	Mm.6500	NM_013823	ENSMUSG00000058488	Kl	alpha-kl	klotho	protein-coding
mm_30415.1	chr3	152265759	152265782	-	1	NA	intron (NM_199465, intron 1 of 12)	CpG	550	NM_199465	68810	Mm.200188	NM_199465	ENSMUSG00000039103	Nexn	1110046H09Rik|AA553326|NELIN	nexilin	protein-coding
mm_160119.1	chr7	27507806	27507806	+	1	NA	intron (NM_198048, intron 4 of 6)	CpG	8482	NM_019412	19153	Mm.10119	NM_019412	ENSMUSG00000053198	Prx	L-Periaxin	periaxin	protein-coding
mm_103739.1	chr11	80080929	80081001	-	1	NA	promoter-TSS (NM_018776)	promoter-TSS (NM_018776)	26	NM_001277106	54394	Mm.272093	NM_018776	ENSMUSG00000017561	Crlf3	BB164954|Creme9|Cytor4	cytokine receptor-like factor 3	protein-coding
mm_173053.1	chrX	12265140	12265147	+	1	NA	Intergenic	MTC|LTR|ERVL-MaLR	89853	NR_045321	100043946	Mm.211985	NR_045321	ENSMUSG00000087591	Gm14635	OTTMUSG00000017536	predicted gene 14635	ncRNA
mm_15224.1	chr2	154502700	154502702	+	1	NA	intron (NM_009823, intron 2 of 10)	intron (NM_009823, intron 2 of 10)	-46203	NM_029305	75480	Mm.440434	NM_029305	ENSMUSG00000038523	1700003F12Rik	-	RIKEN cDNA 1700003F12 gene	protein-coding
mm_130034.1	chr15	88978543	88978564	-	1	NA	promoter-TSS (NM_133241)	promoter-TSS (NM_133241)	0	NM_133241	170790	Mm.32780	NM_133241	ENSMUSG00000035805	Mlc1	AW048630|BB074274|Kiaa0027-hp|LVM|MLC|VL|WKL1|mKIAA0027	megalencephalic leukoencephalopathy with subcortical cysts 1 homolog (human)	protein-coding
mm_80649.1	chr9	89909535	89909606	+	1	NA	promoter-TSS (NM_001039655)	promoter-TSS (NM_001039655)	-205	NM_011245	19417	Mm.44561	NM_011245	ENSMUSG00000032356	Rasgrf1	AI844718|CDC25|CDC25Mm|Gnrp|Grf1|Grfbeta|P190-A|Ras-GRF1|p190|p190RhoGEF	RAS protein-specific guanine nucleotide-releasing factor 1	protein-coding
mm_47169.1	chr5	120743889	120743893	-	1	NA	intron (NM_001347448, intron 3 of 11)	B4A|SINE|B4	5957	NM_145227	246728	Mm.260926	NM_145227	ENSMUSG00000032690	Oas2	Oasl11	2'-5' oligoadenylate synthetase 2	protein-coding
mm_44245.1	chr5	5353795	5353797	-	1	NA	intron (NM_011074, intron 2 of 14)	intron (NM_011074, intron 2 of 14)	26455	NM_011074	18647	Mm.389061	NM_011074	ENSMUSG00000028926	Cdk14	Pftk1|mKIAA0834	cyclin-dependent kinase 14	protein-coding
mm_40861.1	chr5	73632335	73632336	+	1	NA	promoter-TSS (NM_153568)	promoter-TSS (NM_153568)	86	NM_153568	231296	Mm.168948	NM_153568	ENSMUSG00000067206	Lrrc66	-	leucine rich repeat containing 66	protein-coding
mm_57412.1	chr6	124870522	124870529	-	1	NA	exon (NM_013488, exon 6 of 10)	exon (NM_013488, exon 6 of 10)	-6608	NM_013533	14788	Mm.2514	NM_013533	ENSMUSG00000038390	Gpr162	A-2|BC031437|Grca	G protein-coupled receptor 162	protein-coding
mm_28831.1	chr3	96417733	96417759	-	1	NA	Intergenic	Intergenic	-2913	NR_001579	21748		NR_001579	ENSMUSG00000064796	Terc	mTER|mTR	telomerase RNA component	ncRNA
mm_94779.1	chr11	21456794	21456797	+	1	NA	Intergenic	Intergenic	54385	NR_028259	237694	Mm.72926	NM_172792	ENSMUSG00000078962	4932414J04Rik	-	RIKEN cDNA 4932414J04 gene	ncRNA
mm_71388.1	chr8	46151750	46151781	+	1	NA	Intergenic	CpG	-17791	NM_025747	66756	Mm.133623	NM_025747	ENSMUSG00000031631	Cfap97	1110068E21Rik|4933411K20Rik|AW049273|Kiaa1430|mKIAA1430	cilia and flagella associated protein 97	protein-coding
mm_6799.1	chr1	84150870	84150881	-	1	NA	intron (NM_001003948, intron 2 of 2)	intron (NM_001003948, intron 2 of 2)	68086	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_53328.1	chr6	129230537	129230547	+	1	NA	Intergenic	Intergenic	7503	NR_040265	76432	Mm.261738	NR_040265	ENSMUSG00000097354	2310001H17Rik	AI646108	RIKEN cDNA 2310001H17 gene	ncRNA
mm_106416.1	chr11	119151260	119151293	-	1	NA	intron (NM_001347625, intron 9 of 11)	intron (NM_001347625, intron 9 of 11)	2861	NR_105899	102465563		NR_105899	ENSMUSG00000098704	Mir6934	Gm27523|mmu-mir-6934	microRNA 6934	ncRNA
mm_101549.1	chr11	33578934	33578966	-	1	NA	promoter-TSS (NM_146017)	promoter-TSS (NM_146017)	7	NM_146017	216643	Mm.99989	NM_146017	ENSMUSG00000020159	Gabrp	-	gamma-aminobutyric acid (GABA) A receptor, pi	protein-coding
mm_159060.1	chr2	6352636	6352636	+	1	NA	promoter-TSS (NM_181399)	promoter-TSS (NM_181399)	-100	NM_181399	98910	Mm.40673	NM_181399	ENSMUSG00000039046	Usp6nl	AI316785|RNTRE|TRE2NL|mKIAA0019	USP6 N-terminal like	protein-coding
mm_141424.1	chr17	29437097	29437114	-	1	NA	Intergenic	Intergenic	-53940	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_46729.1	chr5	110770859	110770923	-	1	NA	promoter-TSS (NM_029337)	promoter-TSS (NM_029337)	-174	NM_173066	75560	Mm.270487	NM_029337	ENSMUSG00000029505	Ep400	1700020J09Rik|AU023439|mDomino|mKIAA1498|p400	E1A binding protein p400	protein-coding
mm_4858.1	chr1	187609643	187609669	+	1	NA	intron (NM_001243792, intron 1 of 7)	CpG	650	NM_001243792	26381	Mm.89989	NM_011935	ENSMUSG00000026610	Esrrg	ERR3|Errg|NR3B3|mKIAA0832	estrogen-related receptor gamma	protein-coding
mm_148979.1	chr19	7581336	7581347	+	1	NA	intron (NM_139269, intron 4 of 4)	MTEa|LTR|ERVL-MaLR	23882	NM_139269	225845	Mm.274810	NM_139269	ENSMUSG00000060675	Pla2g16	C78643|HRSL3|Hrasls3|Hrev107|MLP-3	phospholipase A2, group XVI	protein-coding
mm_170407.1	chr1	86529169	86529170	+	1	NA	intron (NM_008972, intron 1 of 4)	intron (NM_008972, intron 1 of 4)	2433	NM_008972	19231	Mm.19187	NM_008972	ENSMUSG00000026238	Ptma	Thym	prothymosin alpha	protein-coding
mm_90107.1	chr10	117247939	117247948	+	1	NA	Intergenic	Intergenic	-9262	NM_029906	77397	Mm.118350	NM_029906	ENSMUSG00000020177	9530003J23Rik	Lyzf1	RIKEN cDNA 9530003J23 gene	protein-coding
mm_63647.1	chr7	128688481	128688500	+	1	NA	promoter-TSS (NM_001346517)	promoter-TSS (NM_001346517)	-380	NM_001346517	101490	Mm.490344	NM_178641	ENSMUSG00000042105	Inpp5f	5830435P03Rik|AI115354|AW561896|SAC2|cI-27|hSAC2|mKIAA0966	inositol polyphosphate-5-phosphatase F	protein-coding
mm_39708.1	chr5	27382765	27382768	+	1	NA	exon (NM_001198886, exon 2 of 26)	exon (NM_001198886, exon 2 of 26)	118626	NM_028561	73526	Mm.389608	NM_028561	ENSMUSG00000048703	Speer4b	1700081O22Rik|SPEER-4B	spermatogenesis associated glutamate (E)-rich protein 4B	protein-coding
mm_54154.1	chr6	22392066	22392073	-	1	NA	Intergenic	Intergenic	-35988	NM_138587	27999	Mm.490307	NM_138587	ENSMUSG00000029672	Fam3c	D6Wsu176e|Ilei	family with sequence similarity 3, member C	protein-coding
mm_119993.1	chr14	55591787	55591809	+	1	NA	promoter-TSS (NM_011190)	promoter-TSS (NM_011190)	8	NM_194346	268749	Mm.23748	NM_194346	ENSMUSG00000047098	Rnf31	AL033293|BC031509|Flj10111|HOIP|Paul|mFLJ00217	ring finger protein 31	protein-coding
mm_115897.1	chr13	23310154	23310172	-	1	NA	intron (NR_126444, intron 1 of 1)	intron (NR_126444, intron 1 of 1)	3244	NR_126443	75322	Mm.108666	NR_126443	ENSMUSG00000085488	4930557F10Rik	-	RIKEN cDNA 4930557F10 gene	ncRNA
mm_53050.1	chr6	124743523	124743525	+	1	NA	intron (NM_007881, intron 8 of 9)	intron (NM_007881, intron 8 of 9)	-2445	NM_013535	14790	Mm.439877	NM_013535	ENSMUSG00000072772	Grcc10	2310033H05Rik|C10	gene rich cluster, C10 gene	protein-coding
mm_35199.1	chr4	17636187	17636192	-	1	NA	Intergenic	Intergenic	-216704	NR_135158	17389	Mm.187315	NM_019724	ENSMUSG00000028226	Mmp16	MT-MMP 3|MT3-MMP|Mt3mmp	matrix metallopeptidase 16	protein-coding
mm_42385.1	chr5	114935912	114935926	+	1	NA	intron (NM_145209, intron 5 of 6)	intron (NM_145209, intron 5 of 6)	-6283	NM_028211	72357	Mm.292672	NM_028211	ENSMUSG00000029559	2210016L21Rik	-	RIKEN cDNA 2210016L21 gene	protein-coding
mm_133593.1	chr16	91458718	91458748	+	1	NA	Intergenic	Intergenic	-6371	NR_077219	100503120	Mm.387130	NR_077219	ENSMUSG00000084866	A930006K02Rik	-	RIKEN cDNA A930006K02 gene	ncRNA
mm_12070.1	chr2	59634300	59634303	+	1	NA	intron (NM_198294, intron 1 of 26)	intron (NM_198294, intron 1 of 26)	-12468	NM_001290659	66860	Mm.27917	NM_198294	ENSMUSG00000035168	Tanc1	1200003E16Rik|Tanc|mKIAA1728	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	protein-coding
mm_135459.1	chr16	45724772	45724782	-	1	NA	promoter-TSS (NM_019754)	promoter-TSS (NM_019754)	-246	NM_019754	56370	Mm.24183	NM_019754	ENSMUSG00000022658	Tagln3	2700038H05Rik|2900005O10Rik|AI426007|Np25	transgelin 3	protein-coding
mm_23488.1	chr3	60501378	60501388	+	1	NA	5' UTR (NM_001253711, exon 1 of 8)	5' UTR (NM_001253711, exon 1 of 8)	204	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_27488.1	chr3	54735002	54735078	-	1	NA	promoter-TSS (NM_025442)	promoter-TSS (NM_025442)	324	NM_027148	69639	Mm.29253	NM_027148	ENSMUSG00000027752	Exosc8	2310032N20Rik|CIP3|mKIAA4013	exosome component 8	protein-coding
mm_81338.1	chr9	108517746	108517756	+	1	NA	intron (NM_175143, intron 1 of 9)	CpG	664	NM_175143	69232	Mm.335449	NM_175143	ENSMUSG00000006673	Qrich1	2610028H07Rik	glutamine-rich 1	protein-coding
mm_29844.1	chr3	129831375	129831406	-	1	NA	promoter-TSS (NM_026578)	promoter-TSS (NM_026578)	6	NM_026578	68147	Mm.24873	NM_026578	ENSMUSG00000028010	Gar1	AA409823|AI326794|C430047J18Rik|Nola1	GAR1 ribonucleoprotein	protein-coding
mm_88465.1	chr10	77565389	77565410	+	1	NA	3' UTR (NM_008404, exon 16 of 16)	3' UTR (NM_008404, exon 16 of 16)	-16368	NM_145925	108705	Mm.28853	NM_145925	ENSMUSG00000009291	Pttg1ip	1810010L20Rik|AI314311|AU018448|C79540	pituitary tumor-transforming 1 interacting protein	protein-coding
mm_120743.1	chr14	73178326	73178336	+	1	NA	intron (NR_033185, intron 14 of 15)	intron (NR_033185, intron 14 of 15)	28520	NR_030459	751541		NR_030459	ENSMUSG00000076121	Mir687	Mirn687|mir-687|mmu-mir-687	microRNA 687	ncRNA
mm_164759.1	chr17	84793825	84793827	+	1	NA	Intergenic	Intergenic	-3040	NM_028233	72416	Mm.217027	NM_028233	ENSMUSG00000024120	Lrpprc	3110001K13Rik|C76645|Gp130|Lrp130|Lsfc	leucine-rich PPR-motif containing	protein-coding
mm_161818.1	chr17	70657511	70657511	+	1	NA	exon (NM_177639, exon 4 of 12)	exon (NM_177639, exon 4 of 12)	95764	NM_001128181	224997	Mm.311840	NM_027712	ENSMUSG00000003279	Dlgap1	4933422O14Rik|9630002F18|AI845682|AI848168|BB075781|D17Bwg0511e|GKAP/SAPAP|GKPA/SAPAP|Gkap|Sapap1|mKIAA4162	discs, large (Drosophila) homolog-associated protein 1	protein-coding
mm_49221.1	chr6	15785267	15785278	+	1	NA	intron (NM_175088, intron 4 of 4)	B3A|SINE|B2	64611	NM_175088	16543	Mm.1314	NM_175088	ENSMUSG00000041390	Mdfic	Kdt1|Mdfid	MyoD family inhibitor domain containing	protein-coding
mm_164418.1	chr16	42350387	42350387	+	1	NA	Intergenic	Intergenic	-9736	NM_008083	14432	Mm.1222	NM_008083	ENSMUSG00000047261	Gap43	B-50|Basp2|GAP-43	growth associated protein 43	protein-coding
mm_20274.1	chr2	126863271	126863274	-	1	NA	intron (NM_021450, intron 1 of 38)	PB1D10|SINE|Alu	12989	NM_001164325	58800	Mm.244705	NM_021450	ENSMUSG00000027365	Trpm7	2310022G15Rik|4833414K03Rik|5033407O22Rik|CHAK|CHAK1|LTrpC-7|Ltpr7|Ltrpc7|TRPPLIK	transient receptor potential cation channel, subfamily M, member 7	protein-coding
mm_95968.1	chr11	58917974	58918002	+	1	NA	promoter-TSS (NM_138678)	promoter-TSS (NM_138678)	-69	NM_138678	192194	Mm.22540	NM_138678	ENSMUSG00000020490	Btnl10	BUTR-1|Butr1	butyrophilin-like 10	protein-coding
mm_137784.1	chr17	29494917	29494942	+	1	NA	3' UTR (NM_008842, exon 6 of 6)	3' UTR (NM_008842, exon 6 of 6)	3884	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_84507.1	chr9	67026657	67026669	-	1	NA	intron (NM_001164255, intron 8 of 8)	intron (NM_001164255, intron 8 of 8)	17208	NM_001164252	22003	Mm.121878	NM_024427	ENSMUSG00000032366	Tpm1	AA986836|AI854628|TM2|Tm3|Tmpa|Tpm-1|alpha-TM	tropomyosin 1, alpha	protein-coding
mm_44173.1	chr5	150952943	150952949	+	1	NA	exon (NM_013823, exon 1 of 5)	exon (NM_013823, exon 1 of 5)	339	NM_013823	16591	Mm.6500	NM_013823	ENSMUSG00000058488	Kl	alpha-kl	klotho	protein-coding
mm_37443.1	chr4	123323604	123323639	-	1	NA	promoter-TSS (NM_022033)	promoter-TSS (NM_022033)	58	NM_022033	64059	Mm.270287	NM_022033	ENSMUSG00000076436	Oxct2a	Oxct|Oxct2|Scot|Scot-t1	3-oxoacid CoA transferase 2A	protein-coding
mm_55486.1	chr6	69198146	69198165	-	1	NA	Intergenic	Intergenic	129019	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_81378.1	chr9	108914599	108914611	+	1	NA	promoter-TSS (NM_027066)	promoter-TSS (NM_027066)	-14	NM_027066	69384	Mm.158271	NM_027066	ENSMUSG00000025652	Tmem89	1700024B07Rik	transmembrane protein 89	protein-coding
mm_160109.1	chr7	24908361	24908361	+	1	NA	exon (NM_008488, exon 4 of 29)	exon (NM_008488, exon 4 of 29)	4015	NM_001130152	16801	Mm.3181	NM_008488	ENSMUSG00000040940	Arhgef1	Lbcl2|Lsc	Rho guanine nucleotide exchange factor (GEF) 1	protein-coding
mm_149741.1	chr19	22448053	22448061	+	1	NA	promoter-TSS (NM_177341)	promoter-TSS (NM_177341)	-151	NM_177341	226025	Mm.131943	NM_177341	ENSMUSG00000052387	Trpm3	6330504P12Rik|9330180E14|AU018608|B930001P07Rik|LTRPC3|MLSN2	transient receptor potential cation channel, subfamily M, member 3	protein-coding
mm_167325.1	chr8	69749980	69749990	-	1	NA	promoter-TSS (NM_001200023)	promoter-TSS (NM_001200023)	-23	NM_001200023	620419	Mm.460423	NM_001200023	ENSMUSG00000092260	Zfp963	-	zinc finger protein 963	protein-coding
mm_53751.1	chr6	145340283	145340296	+	1	NA	Intergenic	Intergenic	-47336	NR_003625	381827	Mm.179075	NM_001001987		1700073E17Rik	-	ribosomal protein L7 pseudogene	pseudo
mm_108079.1	chr12	73946284	73946300	+	1	NA	3' UTR (NM_010431, exon 15 of 15)	3' UTR (NM_010431, exon 15 of 15)	-18238	NM_178392	75627	Mm.25937	NM_178392	ENSMUSG00000021113	Snapc1	2700033G17Rik|AU015787	small nuclear RNA activating complex, polypeptide 1	protein-coding
mm_37379.1	chr4	120975443	120975465	-	1	NA	intron (NM_133716, intron 5 of 9)	intron (NM_133716, intron 5 of 9)	-2132	NR_105982	102465614		NR_105982	ENSMUSG00000106436	Mir7015	mmu-mir-7015	microRNA 7015	ncRNA
mm_27181.1	chr3	34648486	34648489	-	1	NA	intron (NR_015580, intron 3 of 4)	AT_rich|Low_complexity|Low_complexity	-1508	NM_011443	20674	Mm.65396	NM_011443	ENSMUSG00000074637	Sox2	Sox-2|lcc|ysb	SRY (sex determining region Y)-box 2	protein-coding
mm_218.1	chr1	16709470	16709481	+	1	NA	exon (NM_001159711, exon 5 of 5)	exon (NM_001159711, exon 5 of 5)	21019	NM_016923	17087	Mm.116844	NM_016923	ENSMUSG00000025779	Ly96	ESOP-1|MD-2|MD2	lymphocyte antigen 96	protein-coding
mm_66281.1	chr7	37770318	37770341	-	1	NA	promoter-TSS (NM_172385)	promoter-TSS (NM_172385)	-577	NM_172385	243937	Mm.322505	NM_172385	ENSMUSG00000043456	Zfp536	9630010P11Rik|Znf536|mKIAA0390	zinc finger protein 536	protein-coding
mm_52180.1	chr6	99334473	99334482	+	1	NA	intron (NM_001347345, intron 2 of 19)	intron (NM_001347345, intron 2 of 19)	-67962	NM_001197321	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_3696.1	chr1	153752989	153752991	+	1	NA	intron (NM_011882, intron 3 of 8)	intron (NM_011882, intron 3 of 8)	3564	NM_011882	24014	Mm.259254	NM_011882	ENSMUSG00000066800	Rnasel	E230029I04Rik	ribonuclease L (2', 5'-oligoisoadenylate synthetase-dependent)	protein-coding
mm_130780.1	chr15	101531131	101531138	-	1	NA	intron (NM_008474, intron 1 of 8)	intron (NM_008474, intron 1 of 8)	1686	NM_008474	16680	Mm.25292	NM_008474	ENSMUSG00000044294	Krt84	AV235125|HRb-1|Krt2-16|Krt2-3	keratin 84	protein-coding
mm_76291.1	chr8	84201962	84201970	-	1	NA	Intergenic	B1F|SINE|Alu	-6552	NR_029740	387216		NR_029740	ENSMUSG00000065611	Mir23a	Mirn23a|mir-23a|mmu-mir-23a	microRNA 23a	ncRNA
mm_169909.1	chr16	54867872	54867872	-	1	NA	Intergenic	L1Md_T|LINE|L1	415365	NM_178720	239852	Mm.245045	NM_178720	ENSMUSG00000064310	Zpld1	9430016A21Rik	zona pellucida like domain containing 1	protein-coding
mm_15783.1	chr2	164334312	164334344	+	1	NA	TTS (NM_009301)	TTS (NM_009301)	1563	NM_009301	20944	Mm.140154	NM_009301	ENSMUSG00000017004	Svs5	BB115186|Semg1|Svp-1|Svp1|Svp5	seminal vesicle secretory protein 5	protein-coding
mm_58024.1	chr6	136661811	136661866	-	1	NA	promoter-TSS (NM_025806)	promoter-TSS (NM_025806)	55	NM_025806	66857	Mm.3311	NM_025806	ENSMUSG00000030214	Plbd1	1100001H23Rik	phospholipase B domain containing 1	protein-coding
mm_119304.1	chr14	34774552	34774584	+	1	NA	Intergenic	ORR1B2|LTR|ERVL-MaLR	-45568	NM_008166	14803	Mm.121569	NM_008166	ENSMUSG00000041078	Grid1	GluD1|GluRdelta1	glutamate receptor, ionotropic, delta 1	protein-coding
mm_3778.1	chr1	156615819	156615862	+	1	NA	intron (NM_001136104, intron 1 of 12)	intron (NM_001136104, intron 1 of 12)	57053	NM_001136104	11352	Mm.329515	NM_009595	ENSMUSG00000026596	Abl2	AA536808|Abll|Arg	v-abl Abelson murine leukemia viral oncogene 2 (arg, Abelson-related gene)	protein-coding
mm_74475.1	chr8	4259208	4259248	-	1	NA	promoter-TSS (NM_183315)	promoter-TSS (NM_183315)	46	NM_183315	330695	Mm.34210	NM_183315	ENSMUSG00000048644	Ctxn1	BC028881|Ctxn	cortexin 1	protein-coding
mm_47953.1	chr5	135543267	135543274	-	1	NA	intron (NM_146001, intron 1 of 30)	intron (NM_146001, intron 1 of 30)	1852	NM_146001	215114	Mm.280805	NM_146001	ENSMUSG00000039959	Hip1	2610109B09Rik|A930014B11Rik|E130315I21Rik|mKIAA4113	huntingtin interacting protein 1	protein-coding
mm_148864.1	chr19	6413072	6413087	+	1	NA	intron (NM_011242, intron 12 of 16)	intron (NM_011242, intron 12 of 16)	-5659	NM_001205235	18190	Mm.329616	NM_020253	ENSMUSG00000033768	Nrxn2	6430591O13Rik|mKIAA0921	neurexin II	protein-coding
mm_51216.1	chr6	71353905	71353916	+	1	NA	Intergenic	Intergenic	-19517	NM_009857	12525	Mm.1858	NM_009857	ENSMUSG00000053977	Cd8a	BB154331|Ly-2|Ly-35|Ly-B|Lyt-2	CD8 antigen, alpha chain	protein-coding
mm_121942.1	chr14	24081962	24081981	-	1	NA	Intergenic	Intergenic	-6906	NR_106069	102465697		NR_106069	ENSMUSG00000105723	Mir7210	mir-7210|mmu-mir-7210	microRNA 7210	ncRNA
mm_38921.1	chr4	150003136	150003149	-	1	NA	promoter-TSS (NM_001291004)	promoter-TSS (NM_001291004)	94	NM_001291004	100198	Mm.22183	NM_173371	ENSMUSG00000028980	H6pd	AI785303|G6pd1|Gpd-1|Gpd1	hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase)	protein-coding
mm_149781.1	chr19	23136728	23136735	+	1	NA	Intergenic	Intergenic	-4495	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_22747.1	chr3	19957241	19957263	+	1	NA	5' UTR (NM_007752, exon 1 of 19)	5' UTR (NM_007752, exon 1 of 19)	198	NM_007752	12870	Mm.13787	NM_007752	ENSMUSG00000003617	Cp	D3Ertd555e	ceruloplasmin	protein-coding
mm_88142.1	chr10	69493603	69493609	+	1	NA	Intergenic	MTEa|LTR|ERVL-MaLR	-40102	NM_170729	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_144213.1	chr18	9745194	9745207	+	1	NA	intron (NM_130449, intron 2 of 9)	L1_Mur2|LINE|L1	37552	NM_130449	140792	Mm.218571	NM_130449	ENSMUSG00000036103	Colec12	CL-P1|SRCL|Scara4	collectin sub-family member 12	protein-coding
mm_131223.1	chr16	9133176	9133191	+	1	NA	Intergenic	RLTR41C|LTR|ERV1	303083	NM_001081400	69053	Mm.390868	NM_001081400	ENSMUSG00000022507	1810013L24Rik	1110017P05Rik|3010002C02Rik|AA792997|AW124177|Gm19906|R74903	RIKEN cDNA 1810013L24 gene	protein-coding
mm_110552.1	chr12	55490539	55490572	-	1	NA	exon (NM_010907, exon 5 of 6)	exon (NM_010907, exon 5 of 6)	2092	NM_010907	18035	Mm.170515	NM_010907	ENSMUSG00000021025	Nfkbia	AI462015|Nfkbi	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, alpha	protein-coding
mm_99113.1	chr11	100140815	100140817	+	1	NA	TTS (NM_008471)	TTS (NM_008471)	2883	NM_001313963	16669	Mm.439699	NM_008471	ENSMUSG00000020911	Krt19	AI663979|CK-19|EndoC|K19|Krt-1.19|Krt1-19	keratin 19	protein-coding
mm_50875.1	chr6	55452290	55452298	+	1	NA	5' UTR (NM_001025372, exon 1 of 16)	5' UTR (NM_001025372, exon 1 of 16)	316	NM_007407	11517	Mm.44245	NM_007407	ENSMUSG00000029778	Adcyap1r1	2900024I10Rik|AI846590|PAC1|PAC1R|PACAP1-R	adenylate cyclase activating polypeptide 1 receptor 1	protein-coding
mm_16320.1	chr2	174304563	174304571	+	1	NA	intron (NM_001310085, intron 2 of 12)	(CA)n|Simple_repeat|Simple_repeat	6708	NM_001310085	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_90297.1	chr10	125549376	125549382	+	1	NA	Intergenic	Intergenic	-220844	NM_011391	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|Mct2	solute carrier family 16 (monocarboxylic acid transporters), member 7	protein-coding
mm_29462.1	chr3	113574705	113574713	-	1	NA	promoter-TSS (NM_007446)	promoter-TSS (NM_007446)	53	NM_007446	11722	Mm.439727	NM_007446	ENSMUSG00000074264	Amy1	Amy-1|Amy1a|C030014B17Rik	amylase 1, salivary	protein-coding
mm_113966.1	chr13	51645285	51645299	+	1	NA	promoter-TSS (NM_025415)	promoter-TSS (NM_025415)	60	NM_025415	66197	Mm.222228	NM_025415	ENSMUSG00000062248	Cks2	1110038L14Rik|CKSHS2	CDC28 protein kinase regulatory subunit 2	protein-coding
mm_59812.1	chr7	29170346	29170414	+	1	NA	promoter-TSS (NM_182696)	promoter-TSS (NM_182696)	-10	NM_182696	243897	Mm.389886	NM_182694	ENSMUSG00000031493	Ggn	AI593290	gametogenetin	protein-coding
mm_3157.1	chr1	135155376	135155430	+	1	NA	3' UTR (NM_026823, exon 7 of 7)	3' UTR (NM_026823, exon 7 of 7)	8569	NM_026823	68724	Mm.174998	NM_026823	ENSMUSG00000026426	Arl8a	1110033P22Rik|Arl10b|gie2	ADP-ribosylation factor-like 8A	protein-coding
mm_44630.1	chr5	27139127	27139161	-	1	NA	intron (NM_207282, intron 1 of 25)	intron (NM_207282, intron 1 of 25)	89945	NM_207282	13483	Mm.42078	NM_010075	ENSMUSG00000061576	Dpp6	B930011P16Rik|D5Buc3|D5Buc4|D5Buc5|DPP VI|Dpp-6|Gm1377|In(5)6H-p|Peplb|Rw	dipeptidylpeptidase 6	protein-coding
mm_108388.1	chr12	80946217	80946226	+	1	NA	promoter-TSS (NR_045057)	promoter-TSS (NR_045057)	722	NM_001347415	20384	Mm.43331	NM_009159	ENSMUSG00000021134	Srsf5	Sfrs5	serine/arginine-rich splicing factor 5	protein-coding
mm_144458.1	chr18	23415401	23415454	+	1	NA	promoter-TSS (NM_207650)	promoter-TSS (NM_207650)	18	NM_001285811	13527	Mm.94371	NM_010087	ENSMUSG00000024302	Dtna	2210407P21Rik|DTN-A|Dtn|Gm19389|a-DB-1|adbn	dystrobrevin alpha	protein-coding
mm_56482.1	chr6	99096246	99096259	-	1	NA	intron (NM_001347345, intron 5 of 19)	intron (NM_001347345, intron 5 of 19)	-67954	NM_001197322	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_164406.1	chr16	36048103	36048106	-	1	NA	intron (NM_027342, intron 3 of 4)	intron (NM_027342, intron 3 of 4)	6914	NM_027113	69544	Mm.37802	NM_027113	ENSMUSG00000034379	Wdr5b	2310009C03Rik|AI606931	WD repeat domain 5B	protein-coding
mm_19852.1	chr2	113791919	113791931	-	1	NA	exon (NM_009162, exon 3 of 6)	exon (NM_009162, exon 3 of 6)	-33277	NM_011824	23892	Mm.166318	NM_011824	ENSMUSG00000074934	Grem1	Cktsf1b1|Drm|Grem|ld	gremlin 1, DAN family BMP antagonist	protein-coding
mm_21058.1	chr2	152654315	152654333	-	1	NA	Intergenic	Intergenic	-15137	NM_010376	14950	Mm.277327	NM_010376	ENSMUSG00000019188	H13	1200006O09Rik|4930443L17Rik|5031424B04Rik|AV020344|H-13|Hm13|PSL3|Spp	histocompatibility 13	protein-coding
mm_138008.1	chr17	33829232	33829242	+	1	NA	intron (NM_023202, intron 2 of 3)	intron (NM_023202, intron 2 of 3)	4592	NR_103514	66416	Mm.29513	NM_023202	ENSMUSG00000041881	Ndufa7	14.5kDa|2400007M02Rik|CI-B14.5a	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 7 (B14.5a)	protein-coding
mm_40595.1	chr5	64230469	64230479	+	1	NA	5' UTR (NM_001289514, exon 1 of 19)	5' UTR (NM_001289514, exon 1 of 19)	117	NM_001289514	57915	Mm.286353	NM_019636	ENSMUSG00000029174	Tbc1d1	1110062G02Rik|AI385682|AW555803|Nob1|Nobq1|Tbc1|mKIAA1108	TBC1 domain family, member 1	protein-coding
mm_168309.1	chr11	108156926	108156942	-	1	NA	intron (NM_011101, intron 3 of 16)	intron (NM_011101, intron 3 of 16)	160086	NR_106082	102465705		NR_106082	ENSMUSG00000098989	Mir7223	Gm28009|mmu-mir-7223	microRNA 7223	ncRNA
mm_68876.1	chr7	126447442	126447474	-	1	NA	exon (NM_007504, exon 19 of 23)	exon (NM_007504, exon 19 of 23)	15615	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_165131.1	chr2	8730221	8730223	+	1	NA	Intergenic	Intergenic	-459293	NR_038180	73438	Mm.23558	NR_038180	ENSMUSG00000085580	1700061F12Rik	-	RIKEN cDNA 1700061F12 gene	ncRNA
mm_131070.1	chr16	4679827	4679834	+	1	NA	promoter-TSS (NM_030205)	promoter-TSS (NM_030205)	-110	NM_030205	78885	Mm.325512	NM_030205	ENSMUSG00000039637	Coro7	0610011B16Rik|AW048373|AW556392	coronin 7	protein-coding
mm_166864.1	chr7	24512422	24512423	-	1	NA	intron (NR_110958, intron 2 of 2)	intron (NR_110958, intron 2 of 2)	5335	NR_110958	232969	Mm.181332	NM_146183	ENSMUSG00000064264	Zfp428	2410005H09Rik|AV271806|AW047854|Znf428	zinc finger protein 428	protein-coding
mm_165511.1	chr2	172399436	172399443	+	1	NA	intron (NM_001080820, intron 1 of 6)	intron (NM_001080820, intron 1 of 6)	5645	NM_001276423	320664	Mm.210195	NM_001033538	ENSMUSG00000074570	Cass4	F730031O20Rik	Cas scaffolding protein family member 4	protein-coding
mm_118062.1	chr13	102843965	102843968	-	1	NA	intron (NM_175171, intron 5 of 28)	intron (NM_175171, intron 5 of 28)	83711	NR_130171	76624	Mm.426384	NR_130171	ENSMUSG00000091906	1700099I09Rik	-	RIKEN cDNA 1700099I09 gene	ncRNA
mm_42862.1	chr5	122226715	122226734	+	1	NA	intron (NM_028752, intron 2 of 6)	ID_B1|SINE|B4	16437	NM_028752	74096	Mm.28804	NM_028752	ENSMUSG00000064267	Hvcn1	0610039P13Rik|AI450555|BTS|HV1|Vsop.|mVSOP	hydrogen voltage-gated channel 1	protein-coding
mm_58870.1	chr7	16959715	16959800	+	1	NA	promoter-TSS (NM_001007569)	promoter-TSS (NM_001007569)	-38	NM_001007569	71691	Mm.275673	NM_001007569	ENSMUSG00000041141	Pnmal1	0710005I19Rik	PNMA-like 1	protein-coding
mm_2056.1	chr1	87470259	87470281	+	1	NA	promoter-TSS (NM_028473)	promoter-TSS (NM_028473)	6	NM_028473	73234	Mm.7310	NM_028473	ENSMUSG00000026258	3110079O15Rik	Snorc	RIKEN cDNA 3110079O15 gene	protein-coding
mm_119565.1	chr14	49066506	49066587	+	1	NA	promoter-TSS (NM_144535)	promoter-TSS (NM_144535)	51	NM_144535	74385	Mm.379235	NM_144535	ENSMUSG00000036291	Ap5m1	4932432K03Rik|Mu5|Mudeng	adaptor-related protein complex 5, mu 1 subunit	protein-coding
mm_112557.1	chr13	12565956	12565962	+	1	NA	promoter-TSS (NM_026184)	promoter-TSS (NM_026184)	76	NM_026184	67475	Mm.358706	NM_026184	ENSMUSG00000057069	Ero1lb	1300013B24Rik|1700065B09Rik|AI447560|Ero1b|ero1-beta	ERO1-like beta (S. cerevisiae)	protein-coding
mm_60434.1	chr7	44476890	44476890	+	1	NA	Intergenic	L1MEd|LINE|L1	6543	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_147525.1	chr18	52529804	52529829	-	1	NA	promoter-TSS (NM_010728)	promoter-TSS (NM_010728)	7	NM_010728	16948	Mm.172	NM_010728	ENSMUSG00000024529	Lox	AI893619|TSC-160|rrg	lysyl oxidase	protein-coding
mm_87235.1	chr10	40683254	40683267	+	1	NA	promoter-TSS (NM_177793)	promoter-TSS (NM_177793)	-22	NM_177793	327747	Mm.80407	NM_177793	ENSMUSG00000045555	Mettl24	9030224M15Rik	methyltransferase like 24	protein-coding
mm_145334.1	chr18	56419169	56419184	+	1	NA	Intergenic	Intergenic	-12956	NM_026240	107022	Mm.24356	NM_026240	ENSMUSG00000001700	Gramd3	9030613F08Rik|9130427A09Rik|AW061306|NS3TP2	GRAM domain containing 3	protein-coding
mm_116963.1	chr13	56173158	56173161	-	1	NA	TTS (NM_001168615)	TTS (NM_001168615)	5726	NM_145976	212937	Mm.116697	NM_145976	ENSMUSG00000049625	Tifab	-	TRAF-interacting protein with forkhead-associated domain, family member B	protein-coding
mm_113190.1	chr13	24942896	24942930	+	1	NA	promoter-TSS (NM_008156)	promoter-TSS (NM_008156)	-239	NM_008156	14756	Mm.291831	NM_008156	ENSMUSG00000021340	Gpld1	6330541J12Rik|AW546131	glycosylphosphatidylinositol specific phospholipase D1	protein-coding
mm_12971.1	chr2	90745501	90745515	+	1	NA	exon (NM_018828, exon 1 of 17)	exon (NM_018828, exon 1 of 17)	138	NM_018828	55935	Mm.489638	NM_018828	ENSMUSG00000008200	Fnbp4	FBP30|Fnbp30|mKIAA1014	formin binding protein 4	protein-coding
mm_154359.1	chrM	6309	6321	+	1	NA	NA	Intergenic	NA	NA								
mm_3605.1	chr1	151677173	151677182	+	1	NA	intron (NM_022018, intron 5 of 13)	intron (NM_022018, intron 5 of 13)	-78197	NM_001311165	66967	Mm.337691	NM_001039644	ENSMUSG00000043019	Edem3	2310050N11Rik	ER degradation enhancer, mannosidase alpha-like 3	protein-coding
mm_158339.1	chrX	134111827	134111836	-	1	NA	promoter-TSS (NM_172203)	promoter-TSS (NM_172203)	23	NM_172203	237038	Mm.67938	NM_172203	ENSMUSG00000031257	Nox1	GP91-2|MOX1|NOH-1|NOH1|NOX1a|NOX1alpha|Nox-1	NADPH oxidase 1	protein-coding
mm_134045.1	chr16	5203948	5203964	-	1	NA	promoter-TSS (NM_013796)	promoter-TSS (NM_013796)	56	NM_013796	27426	Mm.215641	NM_013796	ENSMUSG00000023143	Nagpa	AI596180|UCE	N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase	protein-coding
mm_16598.1	chr2	4993262	4993300	-	1	NA	intron (NM_001305259, intron 17 of 19)	intron (NM_001305259, intron 17 of 19)	17159	NM_026754	68527	Mm.27791	NM_026754	ENSMUSG00000026668	Ucma	1110017I16Rik|AW121955|Grp	upper zone of growth plate and cartilage matrix associated	protein-coding
mm_91525.1	chr10	37140734	37140761	-	1	NA	Intergenic	Intergenic	-1821	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_67184.1	chr7	73939993	73940019	-	1	NA	3' UTR (NM_009181, exon 6 of 6)	3' UTR (NM_009181, exon 6 of 6)	73676	NM_009181	20450	Mm.4954	NM_009181	ENSMUSG00000025789	St8sia2	AI323367|ST8SiaII|STX|Siat8b	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 2	protein-coding
mm_65733.1	chr7	28382113	28382145	-	1	NA	Intergenic	Intergenic	-2901	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_20544.1	chr2	131068456	131068478	-	1	NA	TTS (NM_011426)	TTS (NM_011426)	-4653	NM_001163529	110751	Mm.108550	NM_033615	ENSMUSG00000027318	Adam33	Adaml	a disintegrin and metallopeptidase domain 33	protein-coding
mm_126538.1	chr15	82022827	82022840	+	1	NA	exon (NM_010247, exon 5 of 13)	exon (NM_010247, exon 5 of 13)	6464	NM_010247	14375	Mm.288809	NM_010247	ENSMUSG00000022471	Xrcc6	70kDa|G22p1|Ku70	X-ray repair complementing defective repair in Chinese hamster cells 6	protein-coding
mm_67984.1	chr7	100664304	100664313	-	1	NA	Intergenic	Intergenic	-1914	NM_001163182	27276	Mm.491216	NM_013746	ENSMUSG00000030701	Plekhb1	AI315628|PHR1|Phret1|evt-1	pleckstrin homology domain containing, family B (evectins) member 1	protein-coding
mm_75123.1	chr8	34807101	34807122	-	1	NA	promoter-TSS (NM_176933)	promoter-TSS (NM_176933)	-499	NM_176933	319520	Mm.170276	NM_176933	ENSMUSG00000031530	Dusp4	2700078F24Rik|AI844617|BB104621|E130306H24Rik|MKP2	dual specificity phosphatase 4	protein-coding
mm_75837.1	chr8	70527946	70527982	-	1	NA	5' UTR (NM_001199631, exon 1 of 9)	5' UTR (NM_001199631, exon 1 of 9)	118	NM_001199631	14232	Mm.141864	NM_010223	ENSMUSG00000019428	Fkbp8	38kDa|FKBP-38|FKBP-8|Fkbp38	FK506 binding protein 8	protein-coding
mm_74843.1	chr8	24554321	24554334	-	1	NA	intron (NM_145949, intron 2 of 9)	intron (NM_145949, intron 2 of 9)	22006	NM_145949	209176	Mm.219580	NM_145949	ENSMUSG00000031549	Ido2	AI265623|C230043N17Rik|Ido-2|Indol1	indoleamine 2,3-dioxygenase 2	protein-coding
mm_17810.1	chr2	33641065	33641081	-	1	NA	promoter-TSS (NM_010725)	promoter-TSS (NM_010725)	-120	NR_046275	100504399	Mm.72070	NM_177842		C130021I20Rik	-	Riken cDNA C130021I20 gene	ncRNA
mm_114340.1	chr13	60761928	60761942	+	1	NA	3' UTR (NM_029653, exon 26 of 26)	3' UTR (NM_029653, exon 26 of 26)	24429	NM_199148	218275	Mm.222427	NM_199148	ENSMUSG00000042243	BC051665	-	cDNA sequence BC051665	protein-coding
mm_49948.1	chr6	40221812	40221823	+	1	NA	intron (NM_001004182, intron 2 of 2)	intron (NM_001004182, intron 2 of 2)	-103661	NM_023538	69923	Mm.32840	NM_023538	ENSMUSG00000029916	Agk	2610037M15Rik|6720408I04Rik|AI465370|Mulk	acylglycerol kinase	protein-coding
mm_54153.1	chr6	22391755	22391767	-	1	NA	Intergenic	MLTR14|LTR|ERV1	-35680	NM_138587	27999	Mm.490307	NM_138587	ENSMUSG00000029672	Fam3c	D6Wsu176e|Ilei	family with sequence similarity 3, member C	protein-coding
mm_49794.1	chr6	35252725	35252752	+	1	NA	promoter-TSS (NR_015608)	promoter-TSS (NR_015608)	6	NR_027875	67705	Mm.228046	NR_015608	ENSMUSG00000073155	1810058I24Rik	AI414869|AI848234	RIKEN cDNA 1810058I24 gene	ncRNA
mm_36542.1	chr4	86668703	86668743	-	1	NA	intron (NM_007408, intron 1 of 7)	intron (NM_007408, intron 1 of 7)	1336	NM_007408	11520	Mm.381	NM_007408	ENSMUSG00000028494	Plin2	AA407157|ADPH|Adfp|Adrp	perilipin 2	protein-coding
mm_132044.1	chr16	27849874	27849903	+	1	NA	promoter-TSS (NR_033475)	promoter-TSS (NR_033475)	-42	NR_033475	100038623	Mm.387135	NR_033475		Gm10823	ENSMUSG00000075290	predicted gene 10823	ncRNA
mm_99394.1	chr11	102145531	102145541	+	1	NA	promoter-TSS (NM_145829)	promoter-TSS (NM_145829)	23	NM_145829	217214	Mm.31686	NM_145829	ENSMUSG00000048217	Nags	1700120E20Rik|argA	N-acetylglutamate synthase	protein-coding
mm_153118.1	chr19	33392096	33392119	-	1	NA	5' UTR (NM_001146342, exon 1 of 5)	5' UTR (NM_001146342, exon 1 of 5)	188	NM_001167818	67795	Mm.204591	NM_001146342	ENSMUSG00000071573	Rnls	6530404N21Rik|AI452315|AW060440|C10orf59	renalase, FAD-dependent amine oxidase	protein-coding
mm_75975.1	chr8	72136775	72136789	-	1	NA	intron (NM_001001491, intron 1 of 7)	intron (NM_001001491, intron 1 of 7)	1490	NM_001001491	326618	Mm.295124	NM_001001491	ENSMUSG00000031799	Tpm4	2610528G24Rik|Tpm4.2|Tpm4.2cy	tropomyosin 4	protein-coding
mm_76217.1	chr8	83458436	83458442	-	1	NA	promoter-TSS (NM_001039137)	promoter-TSS (NM_001039137)	-43	NM_001039137	56367	Mm.246911	NM_019708	ENSMUSG00000063253	Scoc	0610011C06Rik|2810002J11Rik|AA415030|SCOCO	short coiled-coil protein	protein-coding
mm_19826.1	chr2	110950343	110950353	-	1	NA	promoter-TSS (NM_001128103)	promoter-TSS (NM_001128103)	-104	NM_001128103	228432	Mm.483325	NM_001081556	ENSMUSG00000074968	Ano3	AI838058|B230324K02Rik|Tmem16c	anoctamin 3	protein-coding
mm_141051.1	chr17	25570679	25570694	-	1	NA	promoter-TSS (NR_045176)	promoter-TSS (NR_045176)	0	NM_011447	20681	Mm.258220	NM_011447	ENSMUSG00000024176	Sox8	-	SRY (sex determining region Y)-box 8	protein-coding
mm_44923.1	chr5	35740026	35740056	-	1	NA	Intergenic	Intergenic	-10765	NM_194344	231147	Mm.290429	NM_194344	ENSMUSG00000036553	Sh3tc1	4631428G15|BC024909	SH3 domain and tetratricopeptide repeats 1	protein-coding
mm_18183.1	chr2	45111260	45111319	-	1	NA	promoter-TSS (NR_110571)	promoter-TSS (NR_110571)	151	NR_110572	433424	Mm.441408	NR_110571	ENSMUSG00000052248	Zeb2os	Gm13476|OTTMUSG00000012358|Zeb2nat	zinc finger E-box binding homeobox 2, opposite strand	ncRNA
mm_38142.1	chr4	134767941	134768010	-	1	NA	promoter-TSS (NM_145554)	promoter-TSS (NM_145554)	29	NM_145554	100017	Mm.27486	NM_145554	ENSMUSG00000037295	Ldlrap1	AA691260|ARH2|Arh|Arh1|FHCB1|FHCB2	low density lipoprotein receptor adaptor protein 1	protein-coding
mm_89951.1	chr10	111291522	111291546	+	1	NA	exon (NM_001003717, exon 22 of 23)	exon (NM_001003717, exon 22 of 23)	-7145	NM_027914	71769	Mm.45256	NM_027914	ENSMUSG00000035759	Bbs10	1300007O09Rik|AI452285	Bardet-Biedl syndrome 10 (human)	protein-coding
mm_84216.1	chr9	61914383	61914409	-	1	NA	exon (NM_018853, exon 1 of 3)	exon (NM_018853, exon 1 of 3)	114	NM_018853	56040	Mm.3158	NM_018853	ENSMUSG00000007892	Rplp1	2410042H16Rik|Arpp1|C430017H15Rik	ribosomal protein, large, P1	protein-coding
mm_90056.1	chr10	116177703	116177763	+	1	NA	exon (NM_001161837, exon 4 of 13)	exon (NM_001161837, exon 4 of 13)	382	NM_001161840	19279	Mm.336316	NM_011217	ENSMUSG00000020151	Ptprr	Gmcp1|PTP-SL|PTPBR7|RPTPRR|mPTP213	protein tyrosine phosphatase, receptor type, R	protein-coding
mm_116105.1	chr13	28949137	28949147	-	1	NA	Intergenic	Intergenic	4540	NM_009238	20677	Mm.240627	NM_009238	ENSMUSG00000076431	Sox4	AA682046|Sox-4	SRY (sex determining region Y)-box 4	protein-coding
mm_165851.1	chr4	10874508	10874526	+	1	NA	promoter-TSS (NM_026005)	promoter-TSS (NM_026005)	19	NM_026005	67157	Mm.440552	NM_026005	ENSMUSG00000059482	2610301B20Rik	AI428449	RIKEN cDNA 2610301B20 gene	protein-coding
mm_38671.1	chr4	144721472	144721497	-	1	NA	promoter-TSS (NM_001085536)	promoter-TSS (NM_001085536)	-80	NM_001085536	546849	Mm.457885	NM_001085536	ENSMUSG00000041735	Gm13178	Gm437|OTTMUSG00000010750	predicted gene 13178	protein-coding
mm_49790.1	chr6	35205432	35205445	+	1	NA	exon (NM_027513, exon 15 of 43)	exon (NM_027513, exon 15 of 43)	27822	NM_027513	70699	Mm.261208	NM_027513	ENSMUSG00000038759	Nup205	3830404O05Rik|AV248391|mKIAA0225	nucleoporin 205	protein-coding
mm_77300.1	chr8	117158494	117158528	-	1	NA	intron (NM_001081151, intron 1 of 10)	CpG	376	NM_001081151	209239	Mm.132992	NM_001081151	ENSMUSG00000052557	Gan	A330045G18|gigaxonin	giant axonal neuropathy	protein-coding
mm_20665.1	chr2	132127423	132127426	-	1	NA	intron (NM_018824, intron 1 of 15)	intron (NM_018824, intron 1 of 15)	17684	NM_018824	54338	Mm.103581	NM_018824	ENSMUSG00000027340	Slc23a2	AI844736|NBTL1|SVCT2|Slc23a1|YSPL2|YSPL3|mKIAA0238	solute carrier family 23 (nucleobase transporters), member 2	protein-coding
mm_111119.1	chr12	80968037	80968053	-	1	NA	promoter-TSS (NM_001177561)	promoter-TSS (NM_001177561)	34	NM_011387	20493	Mm.486361	NM_011387	ENSMUSG00000021135	Slc10a1	Ntcp	solute carrier family 10 (sodium/bile acid cotransporter family), member 1	protein-coding
mm_135558.1	chr16	49856348	49856380	-	1	NA	intron (NM_010581, intron 1 of 9)	intron (NM_010581, intron 1 of 9)	710	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_66593.1	chr7	45434268	45434308	-	1	NA	promoter-TSS (NM_030678)	promoter-TSS (NM_030678)	176	NM_011304	20174	Mm.34410	NM_011304	ENSMUSG00000003868	Ruvbl2	mp47|p47	RuvB-like protein 2	protein-coding
mm_13245.1	chr2	98662891	98662899	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	1195238	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_149509.1	chr19	11965902	11965930	+	1	NA	promoter-TSS (NM_001033174)	promoter-TSS (NM_001033174)	72	NM_001033174	76303	Mm.291279	NM_001033174	ENSMUSG00000024687	Osbp	1110018F06Rik|AW559088|mKIAA4220	oxysterol binding protein	protein-coding
mm_132546.1	chr16	37883095	37883119	+	1	NA	3' UTR (NM_177093, exon 4 of 4)	3' UTR (NM_177093, exon 4 of 4)	14707	NM_177093	320184	Mm.390882	NM_177093	ENSMUSG00000034158	Lrrc58	1810012N18Rik|C330018J07Rik	leucine rich repeat containing 58	protein-coding
mm_3099.1	chr1	134431148	134431211	+	1	NA	exon (NM_001306069, exon 7 of 8)	exon (NM_001306069, exon 7 of 8)	15515	NM_001306069	72674	Mm.259976	NM_028320	ENSMUSG00000026457	Adipor1	2810031L11Rik|ACDCR1|CGI-45|Paqr1	adiponectin receptor 1	protein-coding
mm_136729.1	chr17	8256052	8256056	+	1	NA	exon (NM_001190333, exon 3 of 3)	exon (NM_001190333, exon 3 of 3)	10996	NM_001190338	12458	Mm.8007	NM_009835	ENSMUSG00000040899	Ccr6	CC-CKR-6|CCR-6|Cmkbr6|KY411	chemokine (C-C motif) receptor 6	protein-coding
mm_49479.1	chr6	29529309	29529325	+	1	NA	promoter-TSS (NM_001252382)	promoter-TSS (NM_001252382)	35	NM_001252382	27056	Mm.6479	NM_012057	ENSMUSG00000029771	Irf5	AW491843|mirf5	interferon regulatory factor 5	protein-coding
mm_45682.1	chr5	77351250	77351267	-	1	NA	exon (NM_008048, exon 4 of 5)	exon (NM_008048, exon 4 of 5)	40774	NM_153798	231329	Mm.273217	NM_153798	ENSMUSG00000029250	Polr2b	Pol2rb|Rpb140|Rpb2	polymerase (RNA) II (DNA directed) polypeptide B	protein-coding
mm_5107.1	chr1	5170640	5170674	-	1	NA	Intergenic	Intergenic	87571	NM_001310442	108664	Mm.27082	NM_133826	ENSMUSG00000033793	Atp6v1h	0710001F19Rik|AU022349|CGI-11|SFD|SFDalpha|SFDbeta|VMA13	ATPase, H+ transporting, lysosomal V1 subunit H	protein-coding
mm_97407.1	chr11	77930873	77930934	+	1	NA	promoter-TSS (NM_021286)	promoter-TSS (NM_021286)	64	NM_021286	20370	Mm.229330	NM_021286	ENSMUSG00000000632	Sez6	BSRP-C|D11Bhm177e|sez-6	seizure related gene 6	protein-coding
mm_147202.1	chr18	37890984	37891000	-	1	NA	exon (NM_001305981, exon 17 of 29)	exon (NM_001305981, exon 17 of 29)	-36332	NR_105945	102465592		NR_105945	ENSMUSG00000098706	Mir6979	Gm27524|mmu-mir-6979	microRNA 6979	ncRNA
mm_94394.1	chr11	5542442	5542446	+	1	NA	promoter-TSS (NM_134033)	promoter-TSS (NM_134033)	-227	NM_134033	104479	Mm.210403	NM_134033	ENSMUSG00000020482	Ccdc117	1110004K02Rik|1700026O03Rik|AU018638|AU042822|AV173073|BC018601	coiled-coil domain containing 117	protein-coding
mm_91775.1	chr10	51970262	51970268	-	1	NA	Intergenic	Intergenic	-52237	NM_001300957	215031	Mm.87237	NM_153786	ENSMUSG00000049641	Vgll2	C130057C21Rik|VITO-1|Vito1|vgl-2	vestigial like family member 2	protein-coding
mm_102056.1	chr11	52252655	52252669	-	1	NA	3' UTR (NM_009331, exon 10 of 10)	3' UTR (NM_009331, exon 10 of 10)	20667	NM_011543	21402	Mm.42944	NM_011543	ENSMUSG00000036309	Skp1a	15kDa|2610043E24Rik|2610206H23Rik|EMC19|OCP-II|OCP2|SKP1|Tceb1l|p19A|p19Skp1	S-phase kinase-associated protein 1A	protein-coding
mm_102574.1	chr11	61647236	61647243	-	1	NA	Intergenic	Intergenic	-6082	NM_027817	71520	Mm.202760	NM_027817	ENSMUSG00000004837	Grap	8430435N19Rik|BB233594	GRB2-related adaptor protein	protein-coding
mm_74635.1	chr8	13201414	13201428	-	1	NA	promoter-TSS (NM_025768)	promoter-TSS (NM_025768)	-797	NM_025768	66790	Mm.34901	NM_025768	ENSMUSG00000038515	Grtp1	5430401C05Rik|C81211|Tbc1d6	GH regulated TBC protein 1	protein-coding
mm_34067.1	chr4	138454935	138454948	+	1	NA	promoter-TSS (NM_025451)	promoter-TSS (NM_025451)	-207	NM_025451	66259	Mm.41603	NM_025451	ENSMUSG00000046447	Camk2n1	1810006K23Rik|AI848599|AI891706	calcium/calmodulin-dependent protein kinase II inhibitor 1	protein-coding
mm_34356.1	chr4	144891421	144891433	+	1	NA	Intergenic	MER5A|DNA|hAT-Charlie	-1400	NM_001172424	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding
mm_26780.1	chr3	9004625	9004635	-	1	NA	promoter-TSS (NM_009412)	promoter-TSS (NM_009412)	-115	NM_001025264	21985	Mm.371590	NM_009412	ENSMUSG00000027506	Tpd52	AI043038|mD52	tumor protein D52	protein-coding
mm_115601.1	chr13	11892811	11892821	-	1	NA	intron (NM_023868, intron 4 of 104)	MTD|LTR|ERVL-MaLR	214129	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding
mm_107440.1	chr12	36314161	36314171	+	1	NA	promoter-TSS (NM_025312)	promoter-TSS (NM_025312)	-3	NM_025312	66042	Mm.43375	NM_025312	ENSMUSG00000036169	Sostdc1	0610006G05Rik|Sostl|USAG-1|Wise|ectodin	sclerostin domain containing 1	protein-coding
mm_118109.1	chr13	103921102	103921116	-	1	NA	promoter-TSS (NM_001289475)	promoter-TSS (NM_001289475)	-523	NM_001005868	59079	Mm.277354	NM_021563	ENSMUSG00000021709	Erbin	1700028E05Rik|Erbb2ip|mKIAA1225	Erbb2 interacting protein	protein-coding
mm_136624.1	chr17	5540110	5540124	+	1	NA	intron (NM_146073, intron 1 of 8)	B4|SINE|B4	47517	NM_146073	224454	Mm.487663	NM_146073	ENSMUSG00000034265	Zdhhc14	B530001K09Rik|New1cp	zinc finger, DHHC domain containing 14	protein-coding
mm_165543.1	chr2	181680335	181680341	+	1	NA	promoter-TSS (NM_009326)	promoter-TSS (NM_009326)	28	NM_009326	21400	Mm.24245	NM_009326	ENSMUSG00000059540	Tcea2	AI326274|S-II-T1|SII-T1|Tceat	transcription elongation factor A (SII), 2	protein-coding
mm_79785.1	chr9	63093425	63093449	+	1	NA	Intergenic	B1_Mus1|SINE|Alu	53543	NM_172446	207667	Mm.36349	NM_172446	ENSMUSG00000022245	Skor1	AV273001|C230094B15Rik|Corl1|Lbxcor1	SKI family transcriptional corepressor 1	protein-coding
mm_170770.1	chr2	162919819	162919826	-	1	NA	Intergenic	Intergenic	-11686	NM_026499	67996	Mm.24042	NM_026499	ENSMUSG00000016921	Srsf6	1210001E11Rik|AI314910|AW146126|Sfrs6	serine/arginine-rich splicing factor 6	protein-coding
mm_153503.1	chr19	41339535	41339580	-	1	NA	intron (NM_031376, intron 2 of 16)	intron (NM_031376, intron 2 of 16)	45513	NM_031376	83490	Mm.222266	NM_031376	ENSMUSG00000025017	Pik3ap1	1810044J04Rik|BCAP	phosphoinositide-3-kinase adaptor protein 1	protein-coding
mm_32903.1	chr4	119106058	119106066	+	1	NA	Intergenic	Intergenic	-2683	NM_011400	20525	Mm.21002	NM_011400	ENSMUSG00000028645	Slc2a1	Glut-1|Glut1	solute carrier family 2 (facilitated glucose transporter), member 1	protein-coding
mm_16066.1	chr2	168078749	168078760	+	1	NA	Intergenic	Intergenic	-2250	NM_021409	58220	Mm.292834	NM_021409	ENSMUSG00000044641	Pard6b	AV025615|Par6b	par-6 family cell polarity regulator beta	protein-coding
mm_105859.1	chr11	113752315	113752349	-	1	NA	promoter-TSS (NM_001163346)	promoter-TSS (NM_001163346)	-517	NM_001163346	56699	Mm.293378	NM_020006	ENSMUSG00000041598	Cdc42ep4	1500041M20Rik|Borg4|CEP4	CDC42 effector protein (Rho GTPase binding) 4	protein-coding
mm_166627.1	chr6	78372865	78372872	-	1	NA	exon (NM_011036, exon 5 of 6)	exon (NM_011036, exon 5 of 6)	1983	NM_011036	18489	Mm.2553	NM_011036	ENSMUSG00000071356	Reg3b	HIP|PAP1|Pap|REG-III	regenerating islet-derived 3 beta	protein-coding
mm_13709.1	chr2	117159314	117159329	+	1	NA	intron (NM_033524, intron 2 of 6)	L1MD2|LINE|L1	-25806	NR_030440	732489		NR_030440	ENSMUSG00000076376	Mir674	Mirn674|mir-674|mmu-mir-674	microRNA 674	ncRNA
mm_168897.1	chr12	54363255	54363272	-	1	NA	Intergenic	RLTR1B|LTR|ERV1	28055	NR_033689	665239	Mm.26856	NR_033689		Gm7550	EG665239|Gm666	predicted gene 7550	ncRNA
mm_75742.1	chr8	69774885	69774916	-	1	NA	promoter-TSS (NM_177899)	promoter-TSS (NM_177899)	11	NM_177899	330788	Mm.41364	NM_177899	ENSMUSG00000043090	Zfp866	9830167H18Rik|AI875089|C85843|D330038O06Rik	zinc finger protein 866	protein-coding
mm_101204.1	chr11	19018980	19018990	-	1	NA	promoter-TSS (NM_010789)	promoter-TSS (NM_010789)	-16	NM_010789	17268	Mm.356578	NM_010789	ENSMUSG00000020160	Meis1	C530044H18Rik|Evi8	Meis homeobox 1	protein-coding
mm_7201.1	chr1	93016080	93016091	-	1	NA	3' UTR (NM_008440, exon 48 of 48)	3' UTR (NM_008440, exon 48 of 48)	9751	NM_001159658	208760	Mm.235537	NM_177587	ENSMUSG00000045091	Aqp12	AB084104|mAQP12	aquaporin 12	protein-coding
mm_36588.1	chr4	88428082	88428085	-	1	NA	intron (NM_025760, intron 3 of 6)	intron (NM_025760, intron 3 of 6)	10843	NM_025760	66775	Mm.386788	NM_025760	ENSMUSG00000028497	Hacd4	4933428I03Rik|Hcad4|Ptplad2	3-hydroxyacyl-CoA dehydratase 4	protein-coding
mm_56098.1	chr6	87458247	87458259	-	1	NA	TTS (NM_001286610)	TTS (NM_001286610)	29259	NM_009756	12154	Mm.483321	NM_009756	ENSMUSG00000030046	Bmp10	-	bone morphogenetic protein 10	protein-coding
mm_14631.1	chr2	136781362	136781370	+	1	NA	3' UTR (NM_001291056, exon 8 of 8)	3' UTR (NM_001291056, exon 8 of 8)	67916	NM_001291056	20614	Mm.45953	NM_011428	ENSMUSG00000027273	Snap25	Bdr|GENA70|SNAP-25|SUP|sp	synaptosomal-associated protein 25	protein-coding
mm_97786.1	chr11	82781231	82781255	+	1	NA	promoter-TSS (NR_126068)	promoter-TSS (NR_126068)	134	NM_010716	16882	Mm.277136	NM_010716	ENSMUSG00000020697	Lig3	D11Wsu78e	ligase III, DNA, ATP-dependent	protein-coding
mm_38773.1	chr4	147936762	147936768	-	1	NA	promoter-TSS (NM_011122)	promoter-TSS (NM_011122)	11	NM_011122	18822	Mm.23951	NM_011122	ENSMUSG00000019055	Plod1	2410042F05Rik|AI854890|AV007929|Lh1|Plod	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1	protein-coding
mm_141055.1	chr17	25751523	25751568	-	1	NA	intron (NM_018857, intron 7 of 15)	intron (NM_018857, intron 7 of 15)	2782	NM_018857	56047	Mm.17510	NM_018857	ENSMUSG00000063011	Msln	MPF	mesothelin	protein-coding
mm_75399.1	chr8	46207595	46207626	-	1	NA	exon (NM_007450, exon 4 of 4)	exon (NM_007450, exon 4 of 4)	3399	NM_007450	11739	Mm.16228	NM_007450	ENSMUSG00000031633	Slc25a4	AU019225|Ant1	solute carrier family 25 (mitochondrial carrier, adenine nucleotide translocator), member 4	protein-coding
mm_69021.1	chr7	126792174	126792209	-	1	NA	5' UTR (NM_019674, exon 2 of 9)	5' UTR (NM_019674, exon 2 of 9)	280	NM_019674	56420	Mm.41998	NM_019674	ENSMUSG00000030697	Ppp4c	1110002D08Rik|AU016079|Ppx	protein phosphatase 4, catalytic subunit	protein-coding
mm_40492.1	chr5	57717330	57717356	+	1	NA	promoter-TSS (NM_001310606)	promoter-TSS (NM_001310606)	576	NR_015588	319216	Mm.332387	NR_015588	ENSMUSG00000097216	4932441J04Rik	-	RIKEN cDNA 4932441J04 gene	ncRNA
mm_10902.1	chr2	25289900	25289935	+	1	NA	promoter-TSS (NM_146117)	promoter-TSS (NM_146117)	6	NM_146117	227618	Mm.275228	NM_146117	ENSMUSG00000026961	Lrrc26	-	leucine rich repeat containing 26	protein-coding
mm_66340.1	chr7	43464247	43464252	-	1	NA	intron (NM_001290316, intron 2 of 9)	intron (NM_001290316, intron 2 of 9)	1016	NM_001290316	75690	Mm.30200	NM_001290316	ENSMUSG00000070604	Vsig10l	-	V-set and immunoglobulin domain containing 10 like	protein-coding
mm_172990.1	chrM	1218	1220	+	1	NA	NA	Intergenic	NA	NA								
mm_52588.1	chr6	116666340	116666361	+	1	NA	intron (NM_178045, intron 1 of 10)	L1MA4|LINE|L1	7486	NM_178045	213391	Mm.257931	NM_178045	ENSMUSG00000042129	Rassf4	3830411C14Rik|AD037|AI586137	Ras association (RalGDS/AF-6) domain family member 4	protein-coding
mm_114250.1	chr13	56639667	56639680	+	1	NA	TTS (NM_009369)	TTS (NM_009369)	30070	NM_009369	21810	Mm.14455	NM_009369	ENSMUSG00000035493	Tgfbi	68kDa|AI181842|AI747162|Beta-ig|big-h3	transforming growth factor, beta induced	protein-coding
mm_172585.1	chr8	123373731	123373743	+	1	NA	promoter-TSS (NM_001037877)	promoter-TSS (NM_001037877)	26	NM_001286363	66855	Mm.178818	NM_025804	ENSMUSG00000001472	Tcf25	1100001J13Rik|1810041K11Rik|D8Ertd325e|Nulp1|mKIAA1049	transcription factor 25 (basic helix-loop-helix)	protein-coding
mm_65966.1	chr7	30435780	30435787	-	1	NA	exon (NM_007467, exon 15 of 17)	exon (NM_007467, exon 15 of 17)	9799	NM_007467	11803	Mm.2381	NM_007467	ENSMUSG00000006651	Aplp1	-	amyloid beta (A4) precursor-like protein 1	protein-coding
mm_84204.1	chr9	60687460	60687485	-	1	NA	promoter-TSS (NM_001146047)	promoter-TSS (NM_001146047)	62	NM_001311095	102747	Mm.269413	NM_145616	ENSMUSG00000047766	Lrrc49	AI430817|AW050057|D430025H09Rik|PGs4|p79	leucine rich repeat containing 49	protein-coding
mm_150722.1	chr19	43612300	43612321	+	1	NA	promoter-TSS (NM_008699)	promoter-TSS (NM_008699)	-15	NM_008699	18089	Mm.56994	NM_008699	ENSMUSG00000044220	Nkx2-3	Nkx-2.3|Nkx2.3|tinman	NK2 homeobox 3	protein-coding
mm_93046.1	chr10	88503860	88503899	-	1	NA	promoter-TSS (NM_001146690)	promoter-TSS (NM_001146690)	91	NR_027477	212862	Mm.288897	NM_144807	ENSMUSG00000060002	Chpt1	-	choline phosphotransferase 1	protein-coding
mm_45547.1	chr5	72914129	72914142	-	1	NA	promoter-TSS (NM_001113423)	promoter-TSS (NM_001113423)	-227	NM_001113423	75991	Mm.121285	NM_153567	ENSMUSG00000036087	Slain2	5033405K12Rik|8030444K12Rik|AI596370	SLAIN motif family, member 2	protein-coding
mm_80257.1	chr9	72807223	72807282	+	1	NA	promoter-TSS (NM_175485)	promoter-TSS (NM_175485)	-22	NM_175485	235472	Mm.31696	NM_175485	ENSMUSG00000036030	Prtg	A230098A12Rik|Igdcc5	protogenin	protein-coding
mm_16239.1	chr2	173156377	173156387	+	1	NA	intron (NM_011044, intron 6 of 9)	RSINE1|SINE|B4	3309	NM_011044	18534	Mm.266867	NM_011044	ENSMUSG00000027513	Pck1	AI265463|PEPCK|Pck-1	phosphoenolpyruvate carboxykinase 1, cytosolic	protein-coding
mm_57554.1	chr6	126854250	126854269	-	1	NA	intron (NM_009650, intron 1 of 5)	B1F|SINE|Alu	1161	NM_009650	11642	Mm.87748	NM_009650	ENSMUSG00000030344	Akap3	Prka3	A kinase (PRKA) anchor protein 3	protein-coding
mm_131147.1	chr16	6523578	6523587	+	1	NA	intron (NM_021477, intron 3 of 16)	B4A|SINE|B4	-546253	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_168187.1	chr10	61063081	61063089	-	1	NA	Intergenic	ORR1A0|LTR|ERVL-MaLR	-26246	NM_025273	13180	Mm.39473	NM_025273	ENSMUSG00000020098	Pcbd1	Dcoh|Pcbd|Pcd|Phs	pterin 4 alpha carbinolamine dehydratase/dimerization cofactor of hepatocyte nuclear factor 1 alpha (TCF1) 1	protein-coding
mm_78208.1	chr9	21490364	21490374	+	1	NA	intron (NM_007871, intron 13 of 19)	intron (NM_007871, intron 13 of 19)	6195	NR_029585	387194		NR_029585	ENSMUSG00000065547	Mir199a-1	Mirn199|Mirn199a-1|mir-199a-1	microRNA 199a-1	ncRNA
mm_158486.1	chrX	142318876	142318879	-	1	NA	3' UTR (NM_207625, exon 16 of 16)	3' UTR (NM_207625, exon 16 of 16)	-12679	NM_021487	66240	Mm.58507	NM_021487	ENSMUSG00000090122	Kcne1l	1500015C14Rik|Kcne5|Mink	potassium voltage-gated channel, Isk-related family, member 1-like, pseudogene	protein-coding
mm_127312.1	chr15	100246225	100246239	+	1	NA	intron (NM_007497, intron 3 of 6)	intron (NM_007497, intron 3 of 6)	18373	NM_007497	11908	Mm.676	NM_007497	ENSMUSG00000023027	Atf1	-	activating transcription factor 1	protein-coding
mm_60917.1	chr7	46832397	46832415	+	1	NA	Intergenic	Intergenic	-13398	NM_010699	16828	Mm.29324	NM_010699	ENSMUSG00000063229	Ldha	Ldh1|Ldhm|l7R2	lactate dehydrogenase A	protein-coding
mm_170448.1	chr18	83707651	83707657	+	1	NA	Intergenic	IAPLTR1_Mm|LTR|ERVK	378908	NM_001081300	110796	Mm.102136	NM_001081300	ENSMUSG00000046982	Tshz1	5730407I04Rik|D18Bwg1409e|Mtsh1|NY-CO-33|Sdccag33|Tsh1|mKIAA4206|teashirt1	teashirt zinc finger family member 1	protein-coding
mm_104007.1	chr11	85083479	85083484	-	1	NA	intron (NM_001029934, intron 3 of 33)	intron (NM_001029934, intron 3 of 33)	56474	NM_001029934	237898	Mm.178524	NM_001029934	ENSMUSG00000000804	Usp32	2900074J03Rik|6430526O11Rik|AW045245	ubiquitin specific peptidase 32	protein-coding
mm_129798.1	chr15	82889202	82889203	-	1	NA	intron (NM_001114140, intron 1 of 5)	intron (NM_001114140, intron 1 of 5)	9259	NR_027799	21378	Mm.417272	NR_027799		Tbrg3	TB-11	transforming growth factor beta regulated gene 3	ncRNA
mm_160539.1	chr9	40964072	40964072	-	1	NA	promoter-TSS (NM_001081121)	promoter-TSS (NM_001081121)	40	NM_001081121	70989	Mm.335087	NM_001081121	ENSMUSG00000032023	Jhy	4931429I11Rik|BB239335	juvenile hydrocephalus	protein-coding
mm_98087.1	chr11	86587230	86587254	+	1	NA	intron (NM_029478, intron 10 of 11)	intron (NM_029478, intron 10 of 11)	-3084	NR_029738	387140		NR_029738	ENSMUSG00000065455	Mir21a	Mir21|Mirn21|mmu-mir-21|mmu-mir-21a	microRNA 21a	ncRNA
mm_167896.1	chrX	71962565	71962597	+	1	NA	promoter-TSS (NM_001303028)	promoter-TSS (NM_001303028)	-44	NM_001303028	208748	Mm.25626	NM_001081135	ENSMUSG00000033361	Prrg3	Gm368	proline rich Gla (G-carboxyglutamic acid) 3 (transmembrane)	protein-coding
mm_103906.1	chr11	83578497	83578508	-	1	NA	5' UTR (NM_011338, exon 1 of 4)	5' UTR (NM_011338, exon 1 of 4)	134	NM_011338	20308	Mm.416125	NM_011338	ENSMUSG00000019122	Ccl9	CCF18|MRP-2|Scya10|Scya9	chemokine (C-C motif) ligand 9	protein-coding
mm_169862.1	chr16	3353053	3353061	+	1	NA	Intergenic	B1_Mur4|SINE|Alu	-239341	NM_146860	258859	Mm.377723	NM_146860	ENSMUSG00000051003	Olfr161	MOR131-1|OR912-47M6	olfactory receptor 161	protein-coding
mm_94712.1	chr11	20542871	20542876	+	1	NA	promoter-TSS (NM_021372)	promoter-TSS (NM_021372)	-380	NM_021372	58172	Mm.339676	NM_021372	ENSMUSG00000049800	Sertad2	AB041541|AU021878|Kiaa0127|MNCb-1504|SEI-2|Sei2|TRIP-Br2|mKIAA0127	SERTA domain containing 2	protein-coding
mm_49630.1	chr6	30804835	30804841	+	1	NA	intron (NM_017478, intron 20 of 23)	intron (NM_017478, intron 20 of 23)	63539	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_34947.1	chr4	155892320	155892322	+	1	NA	promoter-TSS (NM_001033490)	promoter-TSS (NM_001033490)	446	NM_207223	140500	Mm.219591	NM_207223	ENSMUSG00000029033	Acap3	Centb5|Kiaa1716-hp|mKIAA1716	ArfGAP with coiled-coil, ankyrin repeat and PH domains 3	protein-coding
mm_161796.1	chr17	49476375	49476375	-	1	NA	intron (NM_001008231, intron 15 of 25)	intron (NM_001008231, intron 15 of 25)	48011	NM_020042	56738	Mm.22256	NM_020042	ENSMUSG00000064120	Mocs1	3110045D15Rik|AI043170|AW536397	molybdenum cofactor synthesis 1	protein-coding
mm_168800.1	chr12	20196614	20196624	+	1	NA	Intergenic	CpG	619160	NR_015521	69513	Mm.273972	NR_015521	ENSMUSG00000099759	1700030C10Rik	-	RIKEN cDNA 1700030C10 gene	ncRNA
mm_82579.1	chr9	21149565	21149568	-	1	NA	intron (NM_016742, intron 1 of 7)	B1F2|SINE|Alu	340	NM_016742	12539	Mm.32331	NM_016742	ENSMUSG00000019471	Cdc37	p50|p50Cdc37	cell division cycle 37	protein-coding
mm_83983.1	chr9	57421321	57421371	-	1	NA	intron (NM_176831, intron 3 of 6)	intron (NM_176831, intron 3 of 6)	18768	NM_176831	66812	Mm.250508	NM_176831	ENSMUSG00000063849	Ppcdc	1810057I13Rik|8430432M10Rik	phosphopantothenoylcysteine decarboxylase	protein-coding
mm_60006.1	chr7	30722487	30722505	+	1	NA	exon (NM_018731, exon 17 of 22)	exon (NM_018731, exon 17 of 22)	7038	NM_027215	69804	Mm.27499	NM_027215	ENSMUSG00000006315	Tmem147	2010004E11Rik|5033425B17Rik|Nifie14	transmembrane protein 147	protein-coding
mm_105639.1	chr11	106999483	106999503	-	1	NA	promoter-TSS (NM_010655)	promoter-TSS (NM_010655)	32	NM_010655	16647	Mm.12508	NM_010655	ENSMUSG00000018362	Kpna2	2410044B12Rik|IPOA1|PTAC58|Rch1	karyopherin (importin) alpha 2	protein-coding
mm_119010.1	chr14	29968351	29968361	+	1	NA	promoter-TSS (NM_019979)	promoter-TSS (NM_019979)	-24	NM_019979	80795	Mm.104491	NM_019979	ENSMUSG00000042682	Selenok	1110001C03Rik|AA673253|HSPC030|Hsp30|Selk	selenoprotein K	protein-coding
mm_2259.1	chr1	91116663	91116687	+	1	NA	3' UTR (NM_001111311, exon 8 of 8)	3' UTR (NM_001111311, exon 8 of 8)	-28428	NM_001033408	329207	Mm.295940	NM_001033408	ENSMUSG00000070732	Rbm44	Gm817	RNA binding motif protein 44	protein-coding
mm_57200.1	chr6	122850566	122850681	-	1	NA	exon (NM_009779, exon 2 of 2)	exon (NM_009779, exon 2 of 2)	5534	NM_009779	12267	Mm.2408	NM_009779	ENSMUSG00000040552	C3ar1	AZ3B|C3AR|HNFAG09	complement component 3a receptor 1	protein-coding
mm_149682.1	chr19	20492679	20492689	+	1	NA	promoter-TSS (NR_015502)	promoter-TSS (NR_015502)	-31	NR_015502	320092	Mm.482524	NR_015502		E030003E18Rik	1700127G21Rik	RIKEN cDNA E030003E18 gene	ncRNA
mm_40100.1	chr5	34573877	34573881	+	1	NA	promoter-TSS (NR_106111)	promoter-TSS (NR_106111)	215	NM_001331086	11518	Mm.289106	NM_013457	ENSMUSG00000029106	Add1	AI256389	adducin 1 (alpha)	protein-coding
mm_74468.1	chr8	4217467	4217503	-	1	NA	promoter-TSS (NM_207203)	promoter-TSS (NM_207203)	-173	NM_207203	73072	Mm.477379	NM_207203	ENSMUSG00000064125	Prr36	-	proline rich 36	protein-coding
mm_113550.1	chr13	38149476	38149481	+	1	NA	Intergenic	Intergenic	-1816	NM_023842	109620	Mm.355327	NM_023842	ENSMUSG00000054889	Dsp	2300002E22Rik|5730453H04Rik|AA407887|AA407888|AW109828|DP|rul	desmoplakin	protein-coding
mm_105053.1	chr11	100701412	100701447	-	1	NA	intron (NM_030150, intron 6 of 12)	intron (NM_030150, intron 6 of 12)	2842	NM_030150	80861	Mm.271830	NM_030150	ENSMUSG00000017830	Dhx58	B430001I08Rik|D11Lgp2e|LPG2|Lgp2|RLR-3	DEXH (Asp-Glu-X-His) box polypeptide 58	protein-coding
mm_121130.1	chr14	101840906	101840906	+	1	NA	exon (NM_201529, exon 4 of 31)	exon (NM_201529, exon 4 of 31)	283	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_79003.1	chr9	45410105	45410125	+	1	NA	non-coding (NR_028499, exon 6 of 6)	non-coding (NR_028499, exon 6 of 6)	4038	NM_007503	11936	Mm.22742	NM_007503	ENSMUSG00000059412	Fxyd2	Atp1g1	FXYD domain-containing ion transport regulator 2	protein-coding
mm_129697.1	chr15	81586369	81586386	-	1	NA	5' UTR (NM_177821, exon 1 of 31)	5' UTR (NM_177821, exon 1 of 31)	163	NM_177821	328572	Mm.258397	NM_177821	ENSMUSG00000055024	Ep300	A430090G16|A730011L11|KAT3B|p300|p300 HAT	E1A binding protein p300	protein-coding
mm_59923.1	chr7	30422434	30422444	+	1	NA	promoter-TSS (NM_172142)	promoter-TSS (NM_172142)	-865	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_15611.1	chr2	160747373	160747387	+	1	NA	intron (NM_021280, intron 2 of 33)	intron (NM_021280, intron 2 of 33)	16070	NM_021280	18803	Mm.44463	NM_021280	ENSMUSG00000016933	Plcg1	AI894140|Cded|Plc-1|Plc-gamma1|Plcg-1	phospholipase C, gamma 1	protein-coding
mm_152118.1	chr19	6987414	6987446	-	1	NA	TTS (NM_020566)	TTS (NM_020566)	221	NM_001185164	22340	Mm.15607	NM_011697	ENSMUSG00000024962	Vegfb	VEGF-B|Vrf	vascular endothelial growth factor B	protein-coding
mm_141366.1	chr17	28942256	28942270	-	1	NA	promoter-TSS (NM_153390)	promoter-TSS (NM_153390)	-1	NM_153390	69307	Mm.107605	NM_153390	ENSMUSG00000045378	Pxt1	1700001G18Rik|Stepp	peroxisomal, testis specific 1	protein-coding
mm_11094.1	chr2	27951284	27951311	+	1	NA	exon (NM_015734, exon 7 of 66)	exon (NM_015734, exon 7 of 66)	64872	NM_015734	12831	Mm.7281	NM_015734	ENSMUSG00000026837	Col5a1	AI413331	collagen, type V, alpha 1	protein-coding
mm_80103.1	chr9	70321608	70321651	+	1	NA	intron (NM_181072, intron 6 of 27)	intron (NM_181072, intron 6 of 27)	84124	NR_049200	100885839		NR_049200	ENSMUSG00000093763	Mir5626	Gm25590|mir-5626|mmu-mir-5626	microRNA 5626	ncRNA
mm_144402.1	chr18	20774339	20774348	+	1	NA	Intergenic	MTC|LTR|ERVL-MaLR	-27939	NM_019737	56386	Mm.393827	NM_019737	ENSMUSG00000056124	B4galt6	AA536803|AU022389	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 6	protein-coding
mm_137524.1	chr17	27325389	27325400	+	1	NA	Intergenic	Intergenic	-2991	NR_106075	102466818		NR_106075	ENSMUSG00000099237	Mir7216	Gm27555|mmu-mir-7216	microRNA 7216	ncRNA
mm_164395.1	chr16	33794125	33794133	+	1	NA	promoter-TSS (NM_010739)	promoter-TSS (NM_010739)	92	NM_010739	17063	Mm.3177	NM_010739	ENSMUSG00000022824	Muc13	114/A10|14/A10|AI159736|Lrrp|Ly64|NJ-1	mucin 13, epithelial transmembrane	protein-coding
mm_23207.1	chr3	41561716	41561724	+	1	NA	intron (NM_001130184, intron 1 of 10)	intron (NM_001130184, intron 1 of 10)	-1663	NM_172303	269424	Mm.286285	NM_172303	ENSMUSG00000025764	Jade1	AU041499|D530048A03Rik|Phf17|mKIAA1807	jade family PHD finger 1	protein-coding
mm_73439.1	chr8	106163097	106163117	+	1	NA	exon (NM_133792, exon 6 of 6)	exon (NM_133792, exon 6 of 6)	-5768	NM_178798	330836	Mm.46749	NM_178798	ENSMUSG00000031904	Slc7a6	AI643885|LAT-2|LAT3	solute carrier family 7 (cationic amino acid transporter, y+ system), member 6	protein-coding
mm_91841.1	chr10	57531869	57531871	-	1	NA	intron (NM_019760, intron 1 of 8)	intron (NM_019760, intron 1 of 8)	659	NM_019760	56442	Mm.29344	NM_019760	ENSMUSG00000019877	Serinc1	1500011D18Rik|AI315070|AIGP-2|TMS-2|Tde1l|Tde2|Tms2|mKIAA1253	serine incorporator 1	protein-coding
mm_142215.1	chr17	37054171	37054190	-	1	NA	exon (NM_019439, exon 7 of 23)	exon (NM_019439, exon 7 of 23)	8214	NM_019439	54393	Mm.32191	NM_019439	ENSMUSG00000024462	Gabbr1	GABAB1|GABAbR1|bM573K1.1	gamma-aminobutyric acid (GABA) B receptor, 1	protein-coding
mm_155952.1	chrX	105082742	105082773	+	1	NA	exon (NM_001281871, exon 5 of 6)	exon (NM_001281871, exon 5 of 6)	3001	NM_026312	67683	Mm.273405	NM_026312	ENSMUSG00000031226	Pbdc1	2610029G23Rik	polysaccharide biosynthesis domain containing 1	protein-coding
mm_133220.1	chr16	76294101	76294108	+	1	NA	exon (NM_173440, exon 4 of 4)	exon (NM_173440, exon 4 of 4)	78945	NM_173440	268903	Mm.74711	NM_173440	ENSMUSG00000048490	Nrip1	6030458L20Rik|8430438I05Rik|9630050P12|AA959574|AW456757|RIP140	nuclear receptor interacting protein 1	protein-coding
mm_8645.1	chr1	156430796	156430820	-	1	NA	3' UTR (NM_009230, exon 16 of 16)	3' UTR (NM_009230, exon 16 of 16)	-9893	NM_001346967	77352	Mm.428709	NM_001033180	ENSMUSG00000026601	Axdnd1	9430070O13Rik|Gm979	axonemal dynein light chain domain containing 1	protein-coding
mm_2694.1	chr1	127756752	127756763	+	1	NA	intron (NR_045298, intron 1 of 1)	intron (NR_045298, intron 1 of 1)	17297	NR_045298	100502745	Mm.440061	NR_045298	ENSMUSG00000102014	2900009J06Rik	-	RIKEN cDNA 2900009J06 gene	ncRNA
mm_148246.1	chr18	80698391	80698402	-	1	NA	exon (NM_016791, exon 2 of 8)	exon (NM_016791, exon 2 of 8)	9777	NM_001164111	18018	Mm.329560	NM_016791	ENSMUSG00000033016	Nfatc1	2210017P03Rik|AI449492|AV076380|NF-ATc|NFAT2|NFATc|Nfatcb	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 1	protein-coding
mm_117249.1	chr13	64365234	64365240	-	1	NA	exon (NM_009984, exon 7 of 8)	exon (NM_009984, exon 7 of 8)	5283	NM_009984	13039	Mm.930	NM_009984	ENSMUSG00000021477	Ctsl	1190035F06Rik|CatL|Ctsl1|MEP|fs|nkt	cathepsin L	protein-coding
mm_107209.1	chr12	26444486	26444518	+	1	NA	3' UTR (NM_021384, exon 6 of 6)	3' UTR (NM_021384, exon 6 of 6)	11950	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_131139.1	chr16	6348702	6348722	+	1	NA	intron (NM_021477, intron 2 of 16)	intron (NM_021477, intron 2 of 16)	373125	NR_045799	68238	Mm.434605	NR_045799	ENSMUSG00000101481	1700123O21Rik	-	RIKEN cDNA 1700123O21 gene	ncRNA
mm_169374.1	chr14	3652046	3652063	+	1	NA	promoter-TSS (NR_033121).2	promoter-TSS (NR_033121).2	24	NR_033121	100041530	Mm.444311	NR_033121	ENSMUSG00000096488	Gm10409	EG666890|ENSMUSG00000072740|Gm8348	predicted pseudogene 8348	pseudo
mm_3802.1	chr1	157526128	157526153	+	1	NA	promoter-TSS (NM_001159986)	promoter-TSS (NM_001159986)	-30	NM_001159986	89867	Mm.87114	NM_033354	ENSMUSG00000026589	Sec16b	Lztr2|Rgpr|Rgpr-p117	SEC16 homolog B (S. cerevisiae)	protein-coding
mm_140195.1	chr17	83421597	83421639	+	1	NA	exon (NM_001114361, exon 3 of 24)	exon (NM_001114361, exon 3 of 24)	70687	NM_001114362	78798	Mm.295565	NM_199466	ENSMUSG00000032624	Eml4	4930443C24Rik|AI644019	echinoderm microtubule associated protein like 4	protein-coding
mm_100894.1	chr11	6065891	6065911	-	1	NA	promoter-TSS (NM_001174054)	promoter-TSS (NM_001174054)	-153	NM_007595	12323	Mm.439733	NM_007595	ENSMUSG00000057897	Camk2b	CaMKII	calcium/calmodulin-dependent protein kinase II, beta	protein-coding
mm_44518.1	chr5	24351658	24351702	-	1	NA	promoter-TSS (NM_013569)	promoter-TSS (NM_013569)	-76	NM_013569	16511	Mm.6539	NM_013569	ENSMUSG00000038319	Kcnh2	AI326795|ERG1|LQT|Lqt2|M-erg|Merg1|merg1a|merg1b	potassium voltage-gated channel, subfamily H (eag-related), member 2	protein-coding
mm_134635.1	chr16	21743062	21743066	-	1	NA	Intergenic	Intergenic	44770	NM_023737	74147	Mm.28100	NM_023737	ENSMUSG00000022853	Ehhadh	1300002P22Rik|HD|L-PBE|LBFP|LBP|MFP|MFP1|PBFE	enoyl-Coenzyme A, hydratase/3-hydroxyacyl Coenzyme A dehydrogenase	protein-coding
mm_30540.1	chr4	3656509	3656518	+	1	NA	promoter-TSS (NR_040643)	promoter-TSS (NR_040643)	7	NR_040643	70143	Mm.417835	NR_040643	ENSMUSG00000085394	2210414B05Rik	-	RIKEN cDNA 2210414B05 gene	ncRNA
mm_95717.1	chr11	54522814	54522824	+	1	NA	promoter-TSS (NM_001252494)	promoter-TSS (NM_001252494)	-26	NM_001252494	192786	Mm.254404	NM_175258	ENSMUSG00000037533	Rapgef6	A530068K01|AI844632|BB085664|C030018K18Rik|PDZ-GEF2|Pdzgef2|RA-GEF-2|Ragef2|mKIAA4052	Rap guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_19103.1	chr2	79454650	79454674	-	1	NA	exon (NM_010894, exon 2 of 2)	exon (NM_010894, exon 2 of 2)	1974	NM_010894	18012	Mm.4636	NM_010894	ENSMUSG00000034701	Neurod1	BETA2|BHF-1|Nd1|Neurod|bHLHa3	neurogenic differentiation 1	protein-coding
mm_131894.1	chr16	23234139	23234141	+	1	NA	intron (NM_001252505, intron 1 of 7)	ID4_|SINE|ID	8119	NM_001252505	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_48936.1	chr6	4538617	4538645	+	1	NA	exon (NM_007743, exon 50 of 52)	exon (NM_007743, exon 50 of 52)	33013	NM_007743	12843	Mm.277792	NM_007743	ENSMUSG00000029661	Col1a2	AA960264|AI325291|Col1a-2|Cola-2|Cola2|oim	collagen, type I, alpha 2	protein-coding
mm_125919.1	chr15	76188209	76188233	+	1	NA	exon (NM_201393, exon 17 of 32)	exon (NM_201393, exon 17 of 32)	7489	NM_201394	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
mm_15007.1	chr2	152477101	152477105	+	1	NA	promoter-TSS (NM_176950)	promoter-TSS (NM_176950)	40	NM_176950	319579	Mm.190454	NM_176950	ENSMUSG00000049560	Defb20	9230107O10Rik|BD-20|mBD-20	defensin beta 20	protein-coding
mm_80412.1	chr9	77754549	77754620	+	1	NA	promoter-TSS (NM_010295)	promoter-TSS (NM_010295)	49	NM_010295	14629	Mm.89888	NM_010295	ENSMUSG00000032350	Gclc	D9Wsu168e|GLCL-H|Ggcs-hs|Glclc	glutamate-cysteine ligase, catalytic subunit	protein-coding
mm_109060.1	chr12	104340998	104341040	+	1	NA	exon (NM_011458, exon 2 of 5)	exon (NM_011458, exon 2 of 5)	2533	NM_011458	20714	Mm.291569	NM_011458	ENSMUSG00000058207	Serpina3k	1300001I07Rik|D12Rp54|MMCM2|MMSpi2|RP54|Spi-2|Spi2|contrapsin	serine (or cysteine) peptidase inhibitor, clade A, member 3K	protein-coding
mm_141966.1	chr17	35121399	35121409	-	1	NA	promoter-TSS (NM_009975)	promoter-TSS (NM_009975)	25	NM_001303445	13001	Mm.378901	NM_009975	ENSMUSG00000024387	Csnk2b	CK II beta	casein kinase 2, beta polypeptide	protein-coding
mm_115502.1	chr13	3918158	3918219	-	1	NA	promoter-TSS (NM_019671)	promoter-TSS (NM_019671)	32	NM_019671	56349	Mm.22261	NM_019671	ENSMUSG00000021215	Net1	Net1a|mNET1	neuroepithelial cell transforming gene 1	protein-coding
mm_13276.1	chr2	101563320	101563333	+	1	NA	intron (NM_026592, intron 6 of 6)	intron (NM_026592, intron 6 of 6)	-61422	NM_009020	19374	Mm.4988	NM_009020	ENSMUSG00000032864	Rag2	Rag-2	recombination activating gene 2	protein-coding
mm_13066.1	chr2	91118137	91118150	+	1	NA	promoter-TSS (NM_008653)	promoter-TSS (NM_008653)	-1	NM_008653	17868	Mm.10728	NM_008653	ENSMUSG00000002100	Mybpc3	-	myosin binding protein C, cardiac	protein-coding
mm_168123.1	chr10	20166936	20166943	-	1	NA	intron (NM_001198635, intron 1 of 17)	intron (NM_001198635, intron 1 of 17)	18019	NM_001198635	17761	Mm.20928	NM_008635	ENSMUSG00000019996	Map7	E-MAP-115|MAP-7|Mtap7|R75000|mshi|mste|ste	microtubule-associated protein 7	protein-coding
mm_172978.1	chr9	96478576	96478594	-	1	NA	promoter-TSS (NM_011279)	promoter-TSS (NM_011279)	90	NM_011279	19823	Mm.28235	NM_011279	ENSMUSG00000051234	Rnf7	Rbx2|SAG	ring finger protein 7	protein-coding
mm_12053.1	chr2	59237842	59237850	+	1	NA	intron (NM_175464, intron 2 of 20)	T-rich|Low_complexity|Low_complexity	76996	NM_175464	227937	Mm.260938	NM_026361	ENSMUSG00000026991	Pkp4	5031422I09Rik|9430019K17Rik|Armrp|p0071	plakophilin 4	protein-coding
mm_138866.1	chr17	43027123	43027123	+	1	NA	intron (NM_178589, intron 1 of 5)	L1MD|LINE|L1	10568	NM_178589	94185	Mm.200792	NM_178589	ENSMUSG00000023915	Tnfrsf21	AA959878|DR6|R74815|TR7	tumor necrosis factor receptor superfamily, member 21	protein-coding
mm_120821.1	chr14	75136527	75136558	+	1	NA	5' UTR (NM_008879, exon 1 of 17)	5' UTR (NM_008879, exon 1 of 17)	117	NM_008879	18826	Mm.153911	NM_008879	ENSMUSG00000021998	Lcp1	AW536232|D14Ertd310e|LCP-1|Pls2|pp65	lymphocyte cytosolic protein 1	protein-coding
mm_102202.1	chr11	54764155	54764174	-	1	NA	intron (NM_178626, intron 1 of 5)	intron (NM_178626, intron 1 of 5)	23539	NM_178626	72729	Mm.29476	NM_178626	ENSMUSG00000052298	Cdc42se2	2810404F18Rik|AA408783|AA536669|SPEC2	CDC42 small effector 2	protein-coding
mm_92277.1	chr10	71238036	71238084	-	1	NA	promoter-TSS (NM_009360)	promoter-TSS (NM_009360)	-16	NM_009360	21780	Mm.229292	NM_009360	ENSMUSG00000003923	Tfam	AI661103|Hmgts|mtTFA|tsHMG	transcription factor A, mitochondrial	protein-coding
mm_160469.1	chr8	111538197	111538197	+	1	NA	promoter-TSS (NM_001168623)	promoter-TSS (NM_001168623)	-146	NM_001168623	170737	Mm.271578	NM_133206	ENSMUSG00000033545	Znrf1	B830022L21Rik|Rnf42|Zrfp1|nin283	zinc and ring finger 1	protein-coding
mm_18657.1	chr2	69885558	69885630	-	1	NA	promoter-TSS (NR_110977)	promoter-TSS (NR_110977)	21	NM_029280	75422	Mm.10508	NM_029280	ENSMUSG00000051730	Mettl5	2810410A08Rik	methyltransferase like 5	protein-coding
mm_46082.1	chr5	92328069	92328086	-	1	NA	promoter-TSS (NM_008599)	promoter-TSS (NM_008599)	2	NM_008599	17329	Mm.766	NM_008599	ENSMUSG00000029417	Cxcl9	BB139920|CMK|Mig|MuMIG|Scyb9|crg-10	chemokine (C-X-C motif) ligand 9	protein-coding
mm_115658.1	chr13	12459269	12459282	-	1	NA	promoter-TSS (NM_001291055)	promoter-TSS (NM_001291055)	41	NM_001291055	56048	Mm.474138	NM_018886	ENSMUSG00000057554	Lgals8	1200015E08Rik|AI326142|D13Ertd524e|Lgals-8	lectin, galactose binding, soluble 8	protein-coding
mm_103362.1	chr11	74925926	74925985	-	1	NA	promoter-TSS (NM_001163311)	promoter-TSS (NM_001163311)	83	NM_001002764	103677	Mm.288460	NM_001002764	ENSMUSG00000038290	Smg6	AI317223|AU041178	Smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans)	protein-coding
mm_77887.1	chr9	7344325	7344335	+	1	NA	promoter-TSS (NM_001320077)	promoter-TSS (NM_001320077)	-67	NM_001320077	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_83023.1	chr9	37147258	37147323	-	1	NA	promoter-TSS (NM_001029838)	promoter-TSS (NM_001029838)	32	NM_148950	208076	Mm.260335	NM_148950	ENSMUSG00000035934	Pknox2	D230005H23Rik|Prep2	Pbx/knotted 1 homeobox 2	protein-coding
mm_43374.1	chr5	135669978	135669984	+	1	NA	Intergenic	Intergenic	-19164	NM_008898	18984	Mm.3863	NM_008898	ENSMUSG00000005514	Por	4933424M13Rik|CPR|CYPOR|P450R	P450 (cytochrome) oxidoreductase	protein-coding
mm_39893.1	chr5	31193264	31193318	+	1	NA	promoter-TSS (NM_001127356)	promoter-TSS (NM_001127356)	-13	NM_153680	266781	Mm.6118	NM_153680	ENSMUSG00000029146	Snx17	5830447M19Rik|AI790646|D5Ertd260e|b2b1625.1Clo|mKIAA0064	sorting nexin 17	protein-coding
mm_57332.1	chr6	124741184	124741193	-	1	NA	promoter-TSS (NM_013535)	promoter-TSS (NM_013535)	-109	NM_013535	14790	Mm.439877	NM_013535	ENSMUSG00000072772	Grcc10	2310033H05Rik|C10	gene rich cluster, C10 gene	protein-coding
mm_128804.1	chr15	66944026	66944063	-	1	NA	exon (NM_008681, exon 7 of 16)	exon (NM_008681, exon 7 of 16)	25597	NM_008681	17988	Mm.30837	NM_008681	ENSMUSG00000005125	Ndrg1	CAP43|CMT4D|DRG1|HMSNL|NMSL|Ndr1|Ndrl|PROXY1|RTP|TDD5	N-myc downstream regulated gene 1	protein-coding
mm_66915.1	chr7	60005153	60005159	-	1	NA	promoter-TSS (NM_013670)	promoter-TSS (NM_013670)	0	NM_013670	20646	Mm.274995	NM_013670	ENSMUSG00000102252	Snrpn	2410045I01Rik|HCERN3|Peg4|Pwcr1|SMN	small nuclear ribonucleoprotein N	protein-coding
mm_121396.1	chr14	119137800	119137815	+	1	NA	promoter-TSS (NM_015820)	promoter-TSS (NM_015820)	-458	NM_015820	50787	Mm.445777	NM_015820	ENSMUSG00000053465	Hs6st3	6OST3|HS6ST-3	heparan sulfate 6-O-sulfotransferase 3	protein-coding
mm_1957.1	chr1	86413929	86413969	+	1	NA	Intergenic	MLT1B|LTR|ERVL-MaLR	-12380	NM_027966	71863	Mm.179627	NM_027966	ENSMUSG00000036574	1700019O17Rik	-	RIKEN cDNA 1700019O17 gene	protein-coding
mm_8220.1	chr1	138164758	138164766	-	1	NA	intron (NM_001111316, intron 1 of 31)	intron (NM_001111316, intron 1 of 31)	10364	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_42869.1	chr5	122233582	122233618	+	1	NA	exon (NM_001042489, exon 4 of 8)	exon (NM_001042489, exon 4 of 8)	23313	NM_028752	74096	Mm.28804	NM_028752	ENSMUSG00000064267	Hvcn1	0610039P13Rik|AI450555|BTS|HV1|Vsop.|mVSOP	hydrogen voltage-gated channel 1	protein-coding
mm_90206.1	chr10	120462013	120462023	+	1	NA	intron (NM_001347170, intron 3 of 5)	intron (NM_001347170, intron 3 of 5)	-13908	NR_030434	791076		NR_030434	ENSMUSG00000076448	Mir763	Mirn763|mir-763|mmu-mir-763	microRNA 763	ncRNA
mm_61425.1	chr7	73620584	73620586	+	1	NA	Intergenic	B1_Mur2|SINE|Alu	-62190	NR_037569	69170	Mm.34539	NR_037569	ENSMUSG00000101970	1810026B05Rik	-	RIKEN cDNA 1810026B05 gene	ncRNA
mm_116219.1	chr13	32851177	32851186	-	1	NA	promoter-TSS (NM_025429)	promoter-TSS (NM_025429)	4	NM_025429	66222	Mm.20144	NM_025429	ENSMUSG00000044734	Serpinb1a	1190005M04Rik|AI325983|EI|EIA|ELANH2|LEI|M/NEI|MNEI|PI2	serine (or cysteine) peptidase inhibitor, clade B, member 1a	protein-coding
mm_24221.1	chr3	88685786	88685796	+	1	NA	promoter-TSS (NM_028814)	promoter-TSS (NM_028814)	-3	NM_028814	74200	Mm.251800	NM_028814	ENSMUSG00000028060	2810403A07Rik	A430106P18Rik|AI256352|AI451678|Blom7|Kiaa0907	RIKEN cDNA 2810403A07 gene	protein-coding
mm_116958.1	chr13	56138599	56138632	-	1	NA	Intergenic	MTEb|LTR|ERVL-MaLR	-3065	NM_001159513	26914	Mm.283802	NM_012015	ENSMUSG00000015937	H2afy	H2AF12M|mH2a1|macroH2A1	H2A histone family, member Y	protein-coding
mm_77502.1	chr8	122678523	122678572	-	1	NA	promoter-TSS (NM_001109873)	promoter-TSS (NM_001109873)	-372	NM_177289	12398	Mm.194339	NM_009824	ENSMUSG00000006362	Cbfa2t3	A630044F12Rik|AI465270|AW229127|Cbfa2t3h|ETO-2|Eto2|MTGR2	core-binding factor, runt domain, alpha subunit 2, translocated to, 3 (human)	protein-coding
mm_4611.1	chr1	178555698	178555716	+	1	NA	intron (NM_001161665, intron 2 of 14)	B4|SINE|B4	26582	NM_001161665	269152	Mm.129727	NM_177724	ENSMUSG00000026494	Kif26b	4832420M10|BC056349|D230039L06Rik	kinesin family member 26B	protein-coding
mm_9958.1	chr1	191062897	191062911	-	1	NA	promoter-TSS (NM_001163422)	promoter-TSS (NM_001163422)	28	NM_001163421	68972	Mm.237188	NM_026895	ENSMUSG00000026632	Tatdn3	1500010M24Rik	TatD DNase domain containing 3	protein-coding
mm_25647.1	chr3	121426496	121426541	+	1	NA	promoter-TSS (NM_028044)	promoter-TSS (NM_028044)	-23	NM_028044	71994	Mm.275555	NM_028044	ENSMUSG00000053931	Cnn3	1600014M03Rik|C85854|Calpo3	calponin 3, acidic	protein-coding
mm_109536.1	chr12	111544998	111545028	+	1	NA	3' UTR (NM_178041, exon 12 of 12)	3' UTR (NM_178041, exon 12 of 12)	4067	NR_033168	100316932	Mm.484709	NR_033168	ENSMUSG00000064493	Snora28	MBI-13	small nucleolar RNA, H/ACA box 28	snoRNA
mm_160799.1	chr11	4947644	4947644	+	1	NA	exon (NM_010904, exon 1 of 4)	exon (NM_010904, exon 1 of 4)	123	NM_001243043	11764	Mm.274816	NM_007454	ENSMUSG00000009090	Ap1b1	Adtb1|b2b1660Clo	adaptor protein complex AP-1, beta 1 subunit	protein-coding
mm_27440.1	chr3	51788704	51788714	-	1	NA	intron (NM_001004176, intron 2 of 4)	intron (NM_001004176, intron 2 of 4)	127530	NM_001310482	211666	Mm.24679	NM_174995	ENSMUSG00000074604	Mgst2	GST2|MGST-II	microsomal glutathione S-transferase 2	protein-coding
mm_112636.1	chr13	16012231	16012267	+	1	NA	5' UTR (NM_008380, exon 2 of 5)	5' UTR (NM_008380, exon 2 of 5)	398	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_91337.1	chr10	25707994	25708034	-	1	NA	Intergenic	Intergenic	129423	NR_045349	73803	Mm.258921	NR_045349		4930401C15Rik	-	RIKEN cDNA 4930401C15 gene	ncRNA
mm_10535.1	chr2	16424518	16424522	+	1	NA	intron (NM_026162, intron 1 of 13)	RLTR34B_MM|LTR|ERVK	68216	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding
mm_78579.1	chr9	36850378	36850392	+	1	NA	exon (NM_183171, exon 2 of 9)	exon (NM_183171, exon 2 of 9)	6726	NM_183171	235180	Mm.5264	NM_183171	ENSMUSG00000032118	Fez1	UNC-76|UNC76	fasciculation and elongation protein zeta 1 (zygin I)	protein-coding
mm_24196.1	chr3	88609745	88609758	+	1	NA	Intergenic	Intergenic	-6456	NM_001198911	16800	Mm.239329	NM_008487	ENSMUSG00000028059	Arhgef2	AA408978|GEF|GEF-H1|GEFH1|LFP40|Lbcl1|Lfc|P40|mKIAA0651	rho/rac guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_157957.1	chrX	87854216	87854228	-	1	NA	intron (NM_001160403, intron 2 of 10)	intron (NM_001160403, intron 2 of 10)	261401	NM_001160403	331461	Mm.121680	NM_001160403	ENSMUSG00000052372	Il1rapl1	6330532G10Rik|C030039N24|IL1R8|IL1RAPL|MRX34|OPHN4|TIGIRR-2	interleukin 1 receptor accessory protein-like 1	protein-coding
mm_29132.1	chr3	105687726	105687740	-	1	NA	promoter-TSS (NM_017397)	promoter-TSS (NM_017397)	-162	NM_017397	53975	Mm.272826	NM_017397	ENSMUSG00000027905	Ddx20	GEMIN3|dp103	DEAD (Asp-Glu-Ala-Asp) box polypeptide 20	protein-coding
mm_49246.1	chr6	17307747	17307750	+	1	NA	5' UTR (NM_001243064, exon 1 of 2)	5' UTR (NM_001243064, exon 1 of 2)	108	NM_001243064	12389	Mm.28278	NM_007616	ENSMUSG00000007655	Cav1	Cav|Cav-1	caveolin 1, caveolae protein	protein-coding
mm_51119.1	chr6	67913551	67913557	+	1	NA	Intergenic	Intergenic	-347855	NR_003100	75070	Mm.463364	NR_003100		4930515G16Rik	-	myc induced nuclear antigen pseudogene	pseudo
mm_49576.1	chr6	30641756	30641792	+	1	NA	exon (NM_025350, exon 6 of 10)	exon (NM_025350, exon 6 of 10)	2556	NM_025350	109697	Mm.25377	NM_025350	ENSMUSG00000054446	Cpa1	0910001L12Rik|Cpa	carboxypeptidase A1, pancreatic	protein-coding
mm_41002.1	chr5	77465463	77465481	+	1	NA	promoter-TSS (NR_131050)	promoter-TSS (NR_131050)	-16	NR_131050	69370	Mm.426881	NR_131050	ENSMUSG00000107232	1700017L05Rik	-	RIKEN cDNA 1700017L05 gene	ncRNA
mm_114473.1	chr13	67863380	67863393	+	1	NA	promoter-TSS (NM_001001185)	promoter-TSS (NM_001001185)	60	NM_001001185	408058	Mm.177840	NM_001001185	ENSMUSG00000064063	BC048507	-	cDNA sequence BC048507	protein-coding
mm_106264.1	chr11	117968622	117968645	-	1	NA	intron (NM_007707, intron 1 of 1)	CpG	733	NM_007707	12702	Mm.3468	NM_007707	ENSMUSG00000053113	Socs3	Cis3|Cish3|EF-10|Ef10|SSI-3|Ssi3	suppressor of cytokine signaling 3	protein-coding
mm_106693.1	chr12	3426879	3426931	+	1	NA	promoter-TSS (NM_172421)	promoter-TSS (NM_172421)	48	NM_172421	75302	Mm.120475	NM_172421	ENSMUSG00000037486	Asxl2	4930556B16Rik|mKIAA1685	additional sex combs like 2 (Drosophila)	protein-coding
mm_84396.1	chr9	65552039	65552063	-	1	NA	TTS (NM_153119)	TTS (NM_153119)	28036	NM_153119	102595	Mm.247303	NM_153119	ENSMUSG00000050721	Plekho2	AI840980|Plekhq1	pleckstrin homology domain containing, family O member 2	protein-coding
mm_41756.1	chr5	102845942	102845978	+	1	NA	5' UTR (NM_001346585, exon 1 of 7)	5' UTR (NM_001346585, exon 1 of 7)	953	NM_001346585	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding
mm_97017.1	chr11	71019896	71019938	+	1	NA	promoter-TSS (NM_001291148)	promoter-TSS (NM_001291148)	-76	NM_001291146	116891	Mm.28131	NM_033562	ENSMUSG00000018442	Derl2	CGI-101|Derlin-2|F-lana|Flana	Der1-like domain family, member 2	protein-coding
mm_97010.1	chr11	70970468	70970517	+	1	NA	promoter-TSS (NM_001276406)	promoter-TSS (NM_001276406)	292	NM_001252415	69723	Mm.275691	NM_027186	ENSMUSG00000018449	Rpain	2400006N03Rik|Rip	RPA interacting protein	protein-coding
mm_130109.1	chr15	89476093	89476138	-	1	NA	promoter-TSS (NR_077233)	promoter-TSS (NR_077233)	-137	NR_077233	100532730	Mm.461541	NR_077233		C230037L18Rik	-	RIKEN cDNA C230037L18 gene	ncRNA
mm_44937.1	chr5	36398069	36398075	-	1	NA	promoter-TSS (NM_030889)	promoter-TSS (NM_030889)	67	NM_030889	81840	Mm.34113	NM_030889	ENSMUSG00000029093	Sorcs2	N28137|mKIAA1329	sortilin-related VPS10 domain containing receptor 2	protein-coding
mm_98144.1	chr11	87582202	87582215	+	1	NA	intron (NM_001284392, intron 1 of 10)	intron (NM_001284392, intron 1 of 10)	1147	NM_001284392	18952	Mm.2214	NM_011129	ENSMUSG00000020486	Sept4	ARTS|Bh5|OTTMUSG00000001265|Pnutl2	septin 4	protein-coding
mm_26934.1	chr3	20263535	20263597	-	1	NA	exon (NM_029706, exon 8 of 11)	exon (NM_029706, exon 8 of 11)	12167	NM_029706	76703	Mm.34692	NM_029706	ENSMUSG00000011463	Cpb1	0910001A18Rik|1810063F02Rik|2210008M23Rik|AI504870	carboxypeptidase B1 (tissue)	protein-coding
mm_75433.1	chr8	47289355	47289384	-	1	NA	promoter-TSS (NM_001286376)	promoter-TSS (NM_001286376)	33	NM_001286376	71069	Mm.23973	NM_175162	ENSMUSG00000038143	Stox2	4933409N07Rik|AI449080|AI835114|mKIAA1392	storkhead box 2	protein-coding
mm_24308.1	chr3	89395710	89395722	+	1	NA	intron (NR_040404, intron 1 of 1)	intron (NR_040404, intron 1 of 1)	1426	NR_040404	545539	Mm.393389	NR_040403	ENSMUSG00000074466	Gm15417	ENSMUSG00000074466|OTTMUSG00000021274	predicted gene 15417	ncRNA
mm_14338.1	chr2	129593004	129593031	+	1	NA	promoter-TSS (NM_001291022)	promoter-TSS (NM_001291022)	-152	NM_001291019	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_154065.1	chr19	55315905	55315907	-	1	NA	promoter-TSS (NM_016862)	promoter-TSS (NM_016862)	126	NM_025883	66980	Mm.386789	NM_025883	ENSMUSG00000024982	Zdhhc6	2400007G07Rik|5930409M18Rik|AI462345|C77369	zinc finger, DHHC domain containing 6	protein-coding
mm_16912.1	chr2	13493661	13493670	-	1	NA	Intergenic	Intergenic	-1789	NM_001081084	65969	Mm.313915	NM_001081084	ENSMUSG00000026726	Cubn	AA408369|AL022750|D2Wsu88e	cubilin (intrinsic factor-cobalamin receptor)	protein-coding
mm_148780.1	chr19	6112887	6112902	+	1	NA	exon (NM_001009546, exon 13 of 18)	exon (NM_001009546, exon 13 of 18)	5692	NM_133678	66406	Mm.303924	NM_133678	ENSMUSG00000024790	Sac3d1	2410004C24Rik|AU015683|shd1	SAC3 domain containing 1	protein-coding
mm_139323.1	chr17	48411788	48411792	+	1	NA	intron (NM_001289490, intron 3 of 5)	intron (NM_001289490, intron 3 of 5)	1790	NM_207219	106821	Mm.203943	NM_207219	ENSMUSG00000040771	Oard1	AI314976|AW558560	O-acyl-ADP-ribose deacylase 1	protein-coding
mm_71020.1	chr8	33484191	33484203	+	1	NA	promoter-TSS (NR_033589)	promoter-TSS (NR_033589)	-114	NR_033589	628431	Mm.376526	NR_033589		Hmgb1-rs17	Hmg1-rs17	high mobility group box 1, related sequence 17	pseudo
mm_134734.1	chr16	22899220	22899239	-	1	NA	non-coding (NR_075099, exon 6 of 6)	non-coding (NR_075099, exon 6 of 6)	-4843	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_12181.1	chr2	65189541	65189548	+	1	NA	intron (NM_027225, intron 1 of 12)	intron (NM_027225, intron 1 of 12)	49082	NM_177025	319876	Mm.34159	NM_027225	ENSMUSG00000034903	Cobll1	1810047P18Rik|Coblr1|D430044D16Rik	Cobl-like 1	protein-coding
mm_23312.1	chr3	53083612	53083615	+	1	NA	intron (NM_175386, intron 2 of 3)	intron (NM_175386, intron 2 of 3)	42066	NM_175386	108927	Mm.118617	NM_175386	ENSMUSG00000048332	Lhfp	2810489O06Rik|AI194968	lipoma HMGIC fusion partner	protein-coding
mm_23204.1	chr3	41555697	41555707	+	1	NA	promoter-TSS (NM_001130184)	promoter-TSS (NM_001130184)	-32	NM_001130184	269424	Mm.286285	NM_172303	ENSMUSG00000025764	Jade1	AU041499|D530048A03Rik|Phf17|mKIAA1807	jade family PHD finger 1	protein-coding
mm_61365.1	chr7	69579656	69579658	+	1	NA	Intergenic	Intergenic	83563	NR_045940	73796	Mm.410832	NR_045940	ENSMUSG00000108885	4930402F11Rik	-	RIKEN cDNA 4930402F11 gene	ncRNA
mm_110915.1	chr12	76229447	76229468	-	1	NA	intron (NM_001159532, intron 3 of 8)	B3|SINE|B2	17289	NM_019784	80384	Mm.78551	NM_019784	ENSMUSG00000021056	Tex21	4931406F04Rik|4931412D23Rik|4931421K24Rik|tsec-2	testis expressed gene 21	protein-coding
mm_50819.1	chr6	54431483	54431489	+	1	NA	Intergenic	Intergenic	-1265	NR_033635	100042056	Mm.448157	NM_198118	ENSMUSG00000073067	9130019P16Rik	6430501H15Rik|OTTMUSG00000023151	RIKEN cDNA 9130019P16 gene	ncRNA
mm_157201.1	chrX	12354980	12355006	-	1	NA	promoter-TSS (NR_045321)	promoter-TSS (NR_045321)	3	NR_045321	100043946	Mm.211985	NR_045321	ENSMUSG00000087591	Gm14635	OTTMUSG00000017536	predicted gene 14635	ncRNA
mm_132634.1	chr16	39026744	39026747	+	1	NA	3' UTR (NM_170599, exon 7 of 7)	3' UTR (NM_170599, exon 7 of 7)	124400	NM_170599	207683	Mm.245564	NM_170599	ENSMUSG00000022790	Igsf11	1700025L02Rik|BT-IgSF|Igsf13	immunoglobulin superfamily, member 11	protein-coding
mm_148100.1	chr18	73971299	73971321	-	1	NA	intron (NM_172632, intron 1 of 5)	intron (NM_172632, intron 1 of 5)	-46597	NR_045390	77855	Mm.410760	NR_045390	ENSMUSG00000090263	D730045A05Rik	-	RIKEN cDNA D730045A05 gene	ncRNA
mm_18876.1	chr2	76338932	76338965	-	1	NA	promoter-TSS (NM_001081033)	promoter-TSS (NM_001081033)	-295	NM_001081033	241489	Mm.246613	NM_001081033	ENSMUSG00000075270	Pde11a	6330414F14Rik|A630086N24Rik|Gm350|PDE11A1	phosphodiesterase 11A	protein-coding
mm_10769.1	chr2	24215331	24215365	+	1	NA	promoter-TSS (NM_019450)	promoter-TSS (NM_019450)	-69	NM_019450	54448	Mm.133095	NM_019450	ENSMUSG00000026984	Il1f6	Fil1|IL-1H1|IL1RP2|Il1f9|Il36a	interleukin 1 family, member 6	protein-coding
mm_43090.1	chr5	124450804	124450829	+	1	NA	exon (NM_001310723, exon 3 of 7)	exon (NM_001310723, exon 3 of 7)	4112	NM_001310727	67956	Mm.137966	NM_030241	ENSMUSG00000049327	Kmt5a	2410195B05Rik|AA617402|AW536475|PR-SET7|PR/SET07|Setd8	lysine methyltransferase 5A	protein-coding
mm_148350.1	chr18	84680588	84680591	-	1	NA	intron (NM_023149, intron 3 of 11)	Lx6|LINE|L1	1470	NM_001289531	66054	Mm.29646	NM_023149	ENSMUSG00000024644	Cndp2	0610010E05Rik|C76600|Cn2|Dip-2|Pep-1|Pep1	CNDP dipeptidase 2 (metallopeptidase M20 family)	protein-coding
mm_121285.1	chr14	105177358	105177405	+	1	NA	promoter-TSS (NM_134077)	promoter-TSS (NM_134077)	-54	NM_134077	74213	Mm.474531	NM_134077	ENSMUSG00000022119	Rbm26	1700009P03Rik|AI447318|C230097K14Rik|C86225|MLZ-393|Pro1777|Se70-2	RNA binding motif protein 26	protein-coding
mm_9261.1	chr1	171616830	171616842	-	1	NA	Intergenic	Intergenic	-9426	NM_008534	17085	Mm.560	NM_008534	ENSMUSG00000004707	Ly9	AI893573|CD229|Lgp100|Ly-9|SLAMF3|T100	lymphocyte antigen 9	protein-coding
mm_122707.1	chr14	52197183	52197207	-	1	NA	promoter-TSS (NM_033618)	promoter-TSS (NM_033618)	44	NM_033618	114741	Mm.21662	NM_033618	ENSMUSG00000035726	Supt16	Cdc68|Fact140|Spt16|Supt16h	suppressor of Ty 16	protein-coding
mm_97446.1	chr11	78188807	78188835	+	1	NA	promoter-TSS (NM_033475)	promoter-TSS (NM_033475)	73	NM_033475	19376	Mm.275864	NM_033475	ENSMUSG00000002059	Rab34	AI326479|Narr|Rah|Rah1	RAB34, member RAS oncogene family	protein-coding
mm_142283.1	chr17	40223922	40223923	-	1	NA	intron (NM_009639, intron 7 of 7)	intron (NM_009639, intron 7 of 7)	-15313	NM_031190	18663	Mm.717	NM_031190	ENSMUSG00000031233	Pgk2	Pgk-2|Tcp-2	phosphoglycerate kinase 2	protein-coding
mm_122885.1	chr14	54946509	54946522	-	1	NA	exon (NM_010856, exon 34 of 39)	exon (NM_010856, exon 34 of 39)	2627	NR_029724	387204		NR_029724	ENSMUSG00000065432	Mir208a	Mirn208|Mirn208a|mir-208|mir-208a|mmu-mir-208	microRNA 208a	ncRNA
mm_13494.1	chr2	106695595	106695608	+	1	NA	promoter-TSS (NM_029837)	promoter-TSS (NM_029837)	0	NM_029837	77015	Mm.45628	NM_029837	ENSMUSG00000016386	Mpped2	239Fb|2700082O15Rik|AV354767|AW060960	metallophosphoesterase domain containing 2	protein-coding
mm_109839.1	chr12	4248360	4248362	-	1	NA	3' UTR (NM_010881, exon 23 of 23)	3' UTR (NM_010881, exon 23 of 23)	-14067	NM_134046	52504	Mm.70546	NM_134046	ENSMUSG00000020652	Cenpo	2810429O05Rik|8430427C03Rik|D12Ertd482e	centromere protein O	protein-coding
mm_91911.1	chr10	60294591	60294651	-	1	NA	exon (NM_011179, exon 5 of 15)	exon (NM_011179, exon 5 of 15)	10160	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_73681.1	chr8	111540228	111540230	+	1	NA	intron (NM_001168623, intron 1 of 4)	intron (NM_001168623, intron 1 of 4)	1886	NM_001168623	170737	Mm.271578	NM_133206	ENSMUSG00000033545	Znrf1	B830022L21Rik|Rnf42|Zrfp1|nin283	zinc and ring finger 1	protein-coding
mm_93558.1	chr10	116473546	116473561	-	1	NA	promoter-TSS (NM_021452)	promoter-TSS (NM_021452)	-30	NM_021452	58802	Mm.440652	NM_021452	ENSMUSG00000054934	Kcnmb4	1700058G18Rik|2900045G12Rik	potassium large conductance calcium-activated channel, subfamily M, beta member 4	protein-coding
mm_65585.1	chr7	27310614	27310640	-	1	NA	TTS (NM_001310678)	TTS (NM_001310678)	23021	NM_001113549	108075	Mm.272251	NM_175641	ENSMUSG00000040488	Ltbp4	2310046A13Rik	latent transforming growth factor beta binding protein 4	protein-coding
mm_21956.1	chr2	167188788	167188815	-	1	NA	promoter-TSS (NM_008420)	promoter-TSS (NM_008420)	17	NM_008420	16500	Mm.205341	NM_008420	ENSMUSG00000050556	Kcnb1	Kcr1-1|Kv2.1|Shab	potassium voltage gated channel, Shab-related subfamily, member 1	protein-coding
mm_105642.1	chr11	107080835	107080859	-	1	NA	exon (NM_176850, exon 7 of 28)	exon (NM_176850, exon 7 of 28)	51075	NM_176850	207165	Mm.343986	NM_176850	ENSMUSG00000040481	Bptf	9430093H17Rik|Falz	bromodomain PHD finger transcription factor	protein-coding
mm_90695.1	chr10	130322846	130322856	+	1	NA	promoter-TSS (NM_183264)	promoter-TSS (NM_183264)	-1	NM_183264	67596	Mm.131264	NM_183264	ENSMUSG00000034833	Tespa1	5830405N20Rik|A430001F24Rik|AI450549	thymocyte expressed, positive selection associated 1	protein-coding
mm_95721.1	chr11	54522929	54522939	+	1	NA	promoter-TSS (NM_001252494)	promoter-TSS (NM_001252494)	89	NM_001252496	192786	Mm.254404	NM_175258	ENSMUSG00000037533	Rapgef6	A530068K01|AI844632|BB085664|C030018K18Rik|PDZ-GEF2|Pdzgef2|RA-GEF-2|Ragef2|mKIAA4052	Rap guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_85972.1	chr9	112160262	112160273	-	1	NA	3' UTR (NM_001177623, exon 10 of 10)	3' UTR (NM_001177623, exon 10 of 10)	25682	NM_001177618	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_43060.1	chr5	124229747	124229757	+	1	NA	promoter-TSS (NR_045369)	promoter-TSS (NR_045369)	27	NR_045369	75927	Mm.410803	NR_045369	ENSMUSG00000090220	Pitpnm2os1	4930568K20Rik	phosphatidylinositol transfer protein, membrane-associated 2, opposite strand 1	ncRNA
mm_136130.1	chr16	86358192	86358197	-	1	NA	Intergenic	Intergenic	-457069	NM_011782	23794	Mm.112933	NM_011782	ENSMUSG00000022894	Adamts5	9530092O11Rik|ADAM-TS5|ADAMTS1|ADAMTS11|ADMP-2|AI481094|ASMP-2	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)	protein-coding
mm_63999.1	chr7	140133015	140133015	+	1	NA	intron (NM_153783, intron 6 of 6)	BC1_Mm|scRNA|scRNA	-4549	NM_199301	212508	Mm.296088	NM_199301	ENSMUSG00000039018	Mtg1	Gm169|Gtpbp7	mitochondrial ribosome-associated GTPase 1	protein-coding
mm_31284.1	chr4	45848959	45849016	+	1	NA	promoter-TSS (NM_028788)	promoter-TSS (NM_028788)	40	NM_028788	74152	Mm.63645	NM_028788	ENSMUSG00000028327	Stra6l	1300002K09Rik|Rbpr2	STRA6-like	protein-coding
mm_6667.1	chr1	80329149	80329149	-	1	NA	intron (NM_001313728, intron 1 of 16)	L1MEg|LINE|L1	11541	NM_001313728	26554	Mm.12665	NM_016716	ENSMUSG00000004364	Cul3	KIAA0617	cullin 3	protein-coding
mm_134501.1	chr16	18876620	18876653	-	1	NA	promoter-TSS (NM_010922)	promoter-TSS (NM_010922)	1	NM_010922	18100	Mm.20918	NM_010922	ENSMUSG00000022706	Mrpl40	Nlvcf	mitochondrial ribosomal protein L40	protein-coding
mm_34639.1	chr4	150615215	150615275	+	1	NA	exon (NM_001085492, exon 18 of 23)	exon (NM_001085492, exon 18 of 23)	36929	NM_173774	242773	Mm.29280	NM_173774	ENSMUSG00000039838	Slc45a1	C230078B22|Dnb5	solute carrier family 45, member 1	protein-coding
mm_10939.1	chr2	25500765	25500769	+	1	NA	promoter-TSS (NM_027062)	promoter-TSS (NM_027062)	-11	NM_013908	30839	Mm.29170	NM_013908	ENSMUSG00000015095	Fbxw5	AI159739|Fbw5	F-box and WD-40 domain protein 5	protein-coding
mm_22411.1	chr2	181314309	181314319	-	1	NA	5' UTR (NM_009133, exon 1 of 5)	5' UTR (NM_009133, exon 1 of 5)	186	NM_009133	20262	Mm.2319	NM_009133	ENSMUSG00000027581	Stmn3	9330161A03Rik|AI604839|R75323|Sclip	stathmin-like 3	protein-coding
mm_70675.1	chr8	14961814	14961822	+	1	NA	intron (NM_172751, intron 16 of 28)	intron (NM_172751, intron 16 of 28)	-49207	NM_029116	74901	Mm.46675	NM_029116	ENSMUSG00000055675	Kbtbd11	2900016B01Rik|4930465M17Rik|mKIAA0711	kelch repeat and BTB (POZ) domain containing 11	protein-coding
mm_162311.1	chr1	37580152	37580153	+	1	NA	Intergenic	Intergenic	-39136	NM_173870	269181	Mm.25861	NM_173870	ENSMUSG00000026110	Mgat4a	9530018I07Rik|GnT-IVa|glcNAc-T-IVa	mannoside acetylglucosaminyltransferase 4, isoenzyme A	protein-coding
mm_23046.1	chr3	34826652	34826658	+	1	NA	Intergenic	Intergenic	54580	NR_110488	102638436	Mm.261793	NR_110488	ENSMUSG00000106519	Gm38509	Peril	predicted gene, 38509	ncRNA
mm_169621.1	chr15	39248799	39248805	+	1	NA	intron (NM_001256382, intron 1 of 26)	RLTR13G|LTR|ERVK	50516	NM_053271	116838	Mm.309296	NM_053271	ENSMUSG00000037386	Rims2	2810036I15Rik|AW048769|RIM2|Rab3ip2|Rim2(+40A)|Rim2(+44A)|Rim2(+4A)|Serg2|Syt3-rs|mKIAA0751	regulating synaptic membrane exocytosis 2	protein-coding
mm_109095.1	chr12	104862067	104862076	+	1	NA	intron (NM_001040682, intron 1 of 12)	intron (NM_001040682, intron 1 of 12)	3005	NR_104436	94040	Mm.244078	NM_053155	ENSMUSG00000021097	Clmn	9330188N17Rik|AI428889|AI788815|mKIAA1188	calmin	protein-coding
mm_36030.1	chr4	57120157	57120174	-	1	NA	intron (NM_019427, intron 1 of 15)	intron (NM_019427, intron 1 of 15)	22991	NM_019427	54357	Mm.28217	NM_019427	ENSMUSG00000028434	Epb41l4b	6430543G08Rik|AA589614|AU021054|BB007528|D4Ertd346e|Ehm2|Epb4.1l4b|Lulu2	erythrocyte membrane protein band 4.1 like 4b	protein-coding
mm_92405.1	chr10	76709643	76709666	-	1	NA	exon (NM_009933, exon 35 of 35)	exon (NM_009933, exon 35 of 35)	16390	NM_009933	12833	Mm.2509	NM_009933	ENSMUSG00000001119	Col6a1	AI747156|Col6a-1	collagen, type VI, alpha 1	protein-coding
mm_34317.1	chr4	141821326	141821350	+	1	NA	exon (NM_007919, exon 5 of 8)	exon (NM_007919, exon 5 of 8)	4667	NM_007919	13706	Mm.45316	NM_007919	ENSMUSG00000058579	Cela2a	Ela-2|Ela2|Ela2a	chymotrypsin-like elastase family, member 2A	protein-coding
mm_28774.1	chr3	95929010	95929057	-	1	NA	promoter-TSS (NM_001253757)	promoter-TSS (NM_001253757)	-224	NM_001253758	66471	Mm.218657	NM_023210	ENSMUSG00000015749	Anp32e	2810018A15Rik|AI047746|AI326868|CPD1|LANP-L|LANPL|mLANP-L	acidic (leucine-rich) nuclear phosphoprotein 32 family, member E	protein-coding
mm_142438.1	chr17	45571127	45571158	-	1	NA	exon (NM_008302, exon 4 of 11)	exon (NM_008302, exon 4 of 11)	2119	NM_008302	15516	Mm.2180	NM_008302	ENSMUSG00000023944	Hsp90ab1	90kDa|AL022974|C81438|Hsp84|Hsp84-1|Hsp90|Hspcb	heat shock protein 90 alpha (cytosolic), class B member 1	protein-coding
mm_105973.1	chr11	115514143	115514152	-	1	NA	intron (NM_008258, intron 1 of 4)	CpG	223	NM_008258	15374	Mm.1775	NM_008258	ENSMUSG00000020737	Hn1	-	hematological and neurological expressed sequence 1	protein-coding
mm_81279.1	chr9	108296710	108296752	+	1	NA	promoter-TSS (NM_001013814)	promoter-TSS (NM_001013814)	-191	NM_001013814	434437	Mm.390225	NM_001013814	ENSMUSG00000032607	Amt	EG434437	aminomethyltransferase	protein-coding
mm_147063.1	chr18	34954668	34954697	-	1	NA	promoter-TSS (NM_010481)	promoter-TSS (NM_010481)	-331	NM_010481	15526	Mm.209419	NM_010481	ENSMUSG00000024359	Hspa9	74kDa|Csa|Grp75|Hsc74|Hsp74|Hsp74a|Hspa9a|Mortalin|Mot-2|Mot2|Mthsp70|Pbp74	heat shock protein 9	protein-coding
mm_132041.1	chr16	27439631	27439644	+	1	NA	intron (NM_001025615, intron 8 of 9)	Lx2B2|LINE|L1	50681	NM_001289436	67501	Mm.258985	NM_026202	ENSMUSG00000038127	Ccdc50	C3orf6	coiled-coil domain containing 50	protein-coding
mm_146568.1	chr18	6510716	6510722	-	1	NA	intron (NM_007935, intron 1 of 13)	intron (NM_007935, intron 1 of 13)	5389	NM_007935	13831	Mm.312133	NM_007935	ENSMUSG00000024240	Epc1	2400007E14Rik|5730566F07Rik|A930032N02Rik|mir-1893	enhancer of polycomb homolog 1 (Drosophila)	protein-coding
mm_148819.1	chr19	6298846	6298863	+	1	NA	3' UTR (NM_010119, exon 5 of 5)	3' UTR (NM_010119, exon 5 of 5)	-7603	NM_001033342	240505	Mm.329622	NM_001033342	ENSMUSG00000024769	Cdc42bpg	BC046418|MRCKgamma	CDC42 binding protein kinase gamma (DMPK-like)	protein-coding
mm_17412.1	chr2	27247196	27247207	-	1	NA	5' UTR (NM_138665, exon 1 of 21)	5' UTR (NM_138665, exon 1 of 21)	102	NM_138665	192166	Mm.278467	NM_138665	ENSMUSG00000009614	Sardh	-	sarcosine dehydrogenase	protein-coding
mm_157623.1	chrX	56549711	56549717	-	1	NA	promoter-TSS (NM_001033372)	promoter-TSS (NM_001033372)	-108	NM_001033372	270599	Mm.424438	NM_001033372	ENSMUSG00000064016	Gm648	-	predicted gene 648	protein-coding
mm_147303.1	chr18	39519382	39519395	-	1	NA	Intergenic	Intergenic	-32143	NM_008173	14815	Mm.129481	NM_008173	ENSMUSG00000024431	Nr3c1	GR|Grl-1|Grl1	nuclear receptor subfamily 3, group C, member 1	protein-coding
mm_5050.1	chr1	194938839	194938845	+	1	NA	promoter-TSS (NM_133654)	promoter-TSS (NM_133654)	21	NM_001111059	12490	Mm.29798	NM_133654	ENSMUSG00000016494	Cd34	AU040960	CD34 antigen	protein-coding
mm_167594.1	chr9	48495873	48495898	-	1	NA	promoter-TSS (NR_037589)	promoter-TSS (NR_037589)	542	NM_001004191	434402	Mm.386950	NM_001004191	ENSMUSG00000042293	Gm5617	EG434402	predicted gene 5617	protein-coding
mm_75641.1	chr8	64850006	64850024	-	1	NA	promoter-TSS (NM_178633)	promoter-TSS (NM_178633)	-91	NM_178633	77113	Mm.350347	NM_178633	ENSMUSG00000031605	Klhl2	6030411N21Rik|ABP-KELCH|AU020744|Mav	kelch-like 2, Mayven	protein-coding
mm_93986.1	chr10	127518923	127518935	-	1	NA	exon (NM_028230, exon 8 of 12)	exon (NM_028230, exon 8 of 12)	3515	NM_001252316	108037	Mm.29890	NM_028230	ENSMUSG00000025403	Shmt2	2700043D08Rik|AA408223|AA986903	serine hydroxymethyltransferase 2 (mitochondrial)	protein-coding
mm_56218.1	chr6	89364496	89364509	-	1	NA	Intergenic	Intergenic	-1889	NM_008881	18844	Mm.3789	NM_008881	ENSMUSG00000030084	Plxna1	2600013D04Rik|NOV|PlexA1|Plxn1|mKIAA4053	plexin A1	protein-coding
mm_96754.1	chr11	69909007	69909017	+	1	NA	exon (NM_001291119, exon 18 of 28)	exon (NM_001291119, exon 18 of 28)	-5180	NM_019726	56310	Mm.477738	NM_019726	ENSMUSG00000023170	Gps2	AI505953	G protein pathway suppressor 2	protein-coding
mm_92545.1	chr10	79711680	79711727	-	1	NA	3' UTR (NM_001077184, exon 7 of 7)	3' UTR (NM_001077184, exon 7 of 7)	-4931	NM_008226	15166	Mm.12956	NM_008226	ENSMUSG00000020331	Hcn2	BCNG2|HAC1|trls	hyperpolarization-activated, cyclic nucleotide-gated K+ 2	protein-coding
mm_147349.1	chr18	43325806	43325817	-	1	NA	exon (NM_001291455, exon 13 of 14)	exon (NM_001291455, exon 13 of 14)	47461	NM_001136086	22240	Mm.8180	NM_009468	ENSMUSG00000024501	Dpysl3	CRMP-4|DRP-3|TUC4|ULIP-1|Ulip|Ulip1	dihydropyrimidinase-like 3	protein-coding
mm_33961.1	chr4	137554431	137554432	+	1	NA	intron (NM_008305, intron 74 of 96)	intron (NM_008305, intron 74 of 96)	16145	NR_105985	102465616		NR_105985	ENSMUSG00000099134	Mir7018	Gm27606|mmu-mir-7018	microRNA 7018	ncRNA
mm_2412.1	chr1	93831167	93831170	+	1	NA	intron (NM_178882, intron 4 of 9)	RMER12|LTR|ERVK	5928	NM_001310767	98314	Mm.383401	NM_178882	ENSMUSG00000073609	D2hgdh	AA408776|AA408778|AI325464	D-2-hydroxyglutarate dehydrogenase	protein-coding
mm_80098.1	chr9	70281349	70281352	+	1	NA	intron (NM_181072, intron 1 of 27)	intron (NM_181072, intron 1 of 27)	74000	NM_181072	71602	Mm.249311	NM_181072	ENSMUSG00000032220	Myo1e	2310020N23Rik|9130023P14Rik|AA407778|myosin-1e|myr 3	myosin IE	protein-coding
mm_159398.1	chr3	95559628	95559628	+	1	NA	promoter-TSS (NM_001289534)	promoter-TSS (NM_001289534)	-49	NM_026489	67981	Mm.179050	NM_026489	ENSMUSG00000028109	Hormad1	4921522K05Rik|Nohma	HORMA domain containing 1	protein-coding
mm_28369.1	chr3	89904417	89904427	-	1	NA	intron (NM_001310676, intron 1 of 9)	B3A|SINE|B2	8774	NM_001310676	16194	Mm.2856	NM_010559	ENSMUSG00000027947	Il6ra	CD126|IL-6R|IL-6R-alpha|IL-6RA|Il6r	interleukin 6 receptor, alpha	protein-coding
mm_21711.1	chr2	164593589	164593603	-	1	NA	promoter-TSS (NM_029325)	promoter-TSS (NM_029325)	-25	NM_029325	75526	Mm.159533	NM_029325	ENSMUSG00000017733	Eppin	1700024E17Rik|Spinlw1	epididymal peptidase inhibitor	protein-coding
mm_4885.1	chr1	188154334	188154342	+	1	NA	intron (NM_011935, intron 5 of 6)	intron (NM_011935, intron 5 of 6)	-108500	NM_021408	22283	Mm.331238	NM_021408	ENSMUSG00000026609	Ush2a	A930011D15Rik|A930037M10Rik|Gm676|Gm983|Mush2a|Usherin|Ushrn	Usher syndrome 2A	protein-coding
mm_5760.1	chr1	46893023	46893031	-	1	NA	Intergenic	Intergenic	-39518	NM_172653	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|mKIAA1265	solute carrier family 39 (zinc transporter), member 10	protein-coding
mm_109425.1	chr12	110601387	110601397	+	1	NA	promoter-TSS (NM_030238)	promoter-TSS (NM_030238)	-3	NM_030238	13424	Mm.181430	NM_030238	ENSMUSG00000018707	Dync1h1	9930018I23Rik|AI894280|DHC1|DHC1a|DNCL|Dnchc1|Dnec1|Dnecl|Loa|MAP1C|P22|Swl|mKIAA0325	dynein cytoplasmic 1 heavy chain 1	protein-coding
mm_168268.1	chr10	93785653	93785660	+	1	NA	Intergenic	RLTR45|LTR|ERVK	-45899	NM_183199	327799	Mm.491598	NM_183199	ENSMUSG00000020020	Usp44	E430004F17Rik	ubiquitin specific peptidase 44	protein-coding
mm_1840.1	chr1	82839652	82839684	+	1	NA	5' UTR (NM_010472, exon 1 of 13)	5' UTR (NM_010472, exon 1 of 13)	208	NM_001347077	15463	Mm.392569	NM_010472	ENSMUSG00000026159	Agfg1	AU045498|C130049H11Rik|C85612|D730048C23Rik|Hrb|RAB|Rip	ArfGAP with FG repeats 1	protein-coding
mm_30886.1	chr4	32249422	32249428	+	1	NA	Intergenic	Intergenic	-168010	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_21829.1	chr2	165388246	165388315	-	1	NA	promoter-TSS (NM_178411)	promoter-TSS (NM_178411)	-21	NM_178411	228876	Mm.26316	NM_178411	ENSMUSG00000017667	Zfp334	D2Ertd535e	zinc finger protein 334	protein-coding
mm_12142.1	chr2	61804502	61804538	+	1	NA	promoter-TSS (NM_009322)	promoter-TSS (NM_009322)	67	NM_009322	21375	Mm.308525	NM_009322	ENSMUSG00000035033	Tbr1	-	T-box brain gene 1	protein-coding
mm_116562.1	chr13	46929725	46929800	-	1	NA	promoter-TSS (NM_010617)	promoter-TSS (NM_010617)	-44	NM_010617	16553	Mm.342703	NM_010617	ENSMUSG00000021375	Kif13a	4930505I07Rik|mKIAA4109	kinesin family member 13A	protein-coding
mm_105229.1	chr11	102306048	102306070	-	1	NA	3' UTR (NM_001302954, exon 20 of 20)	3' UTR (NM_001302954, exon 20 of 20)	-9430	NM_001098837	217218	Mm.390381	NM_001098836	ENSMUSG00000059995	Atxn7l3	E030022H21Rik	ataxin 7-like 3	protein-coding
mm_103683.1	chr11	79339295	79339299	-	1	NA	promoter-TSS (NM_010897)	promoter-TSS (NM_010897)	-595	NM_010897	18015	Mm.255596	NM_010897	ENSMUSG00000020716	Nf1	AW494271|Dsk9|E030030H24Rik|Mhdadsk9|Nf-1	neurofibromin 1	protein-coding
mm_74066.1	chr8	122424941	122424974	+	1	NA	exon (NM_007806, exon 6 of 6)	exon (NM_007806, exon 6 of 6)	2872	NM_145834	234836	Mm.222808	NM_145834	ENSMUSG00000046108	Il17c	IL-17C	interleukin 17C	protein-coding
mm_32038.1	chr4	95850761	95850765	+	1	NA	intron (NM_001113412, intron 14 of 15)	intron (NM_001113412, intron 14 of 15)	116272	NR_045777	319247	Mm.473527	NM_175680	ENSMUSG00000044125	9530080O11Rik	-	RIKEN cDNA 9530080O11 gene	ncRNA
mm_59062.1	chr7	19416735	19416760	+	1	NA	TTS (NR_073015)	TTS (NR_073015)	4670	NR_073014	100503495	Mm.410762	NR_073014	ENSMUSG00000040705	A930016O22Rik	-	RIKEN cDNA A930016O22 gene	ncRNA
mm_7602.1	chr1	126092514	126092517	-	1	NA	intron (NM_001081756, intron 10 of 16)	intron (NM_001081756, intron 10 of 16)	-179587	NM_001311089	72585	Mm.490405	NM_145100	ENSMUSG00000026344	Lypd1	2700050C12Rik|AI853408|C530008O16Rik|Lynx2|Lypdc1	Ly6/Plaur domain containing 1	protein-coding
mm_8037.1	chr1	135180887	135180894	-	1	NA	Intergenic	Intergenic	-13209	NM_134438	171469	Mm.272290	NM_134438	ENSMUSG00000026424	Gpr37l1	AW047233|CAG-18|D0Kist8	G protein-coupled receptor 37-like 1	protein-coding
mm_71563.1	chr8	53511696	53511739	+	1	NA	promoter-TSS (NM_001205054)	promoter-TSS (NM_001205054)	15	NM_001005847	11593	Mm.334535	NM_001005847	ENSMUSG00000031521	Aga	AW060726	aspartylglucosaminidase	protein-coding
mm_98265.1	chr11	88973920	88973924	+	1	NA	promoter-TSS (NM_016706)	promoter-TSS (NM_016706)	-13	NM_016706	12812	Mm.268004	NM_016706	ENSMUSG00000033983	Coil	C79982|Cln80|p80|p80-coilin	coilin	protein-coding
mm_92507.1	chr10	78405112	78405121	-	1	NA	exon (NM_010925, exon 8 of 13)	exon (NM_010925, exon 8 of 13)	3429	NR_105872	102465547		NR_105872	ENSMUSG00000098376	Mir6907	Gm27351|mmu-mir-6907	microRNA 6907	ncRNA
mm_80886.1	chr9	99247070	99247075	+	1	NA	intron (NM_023873, intron 2 of 17)	intron (NM_023873, intron 2 of 17)	3604	NM_023873	68121	Mm.288739	NM_023873	ENSMUSG00000056267	Cep70	6720484E09Rik|Bite|C030018L16Rik	centrosomal protein 70	protein-coding
mm_53675.1	chr6	141866383	141866389	+	1	NA	Intergenic	Intergenic	-10215	NM_030687	28250	Mm.255586	NM_030687	ENSMUSG00000030237	Slco1a4	AI785519|Oatp1a4|Oatp2|Slc21a5	solute carrier organic anion transporter family, member 1a4	protein-coding
mm_103861.1	chr11	83298911	83298983	-	1	NA	promoter-TSS (NM_134025)	promoter-TSS (NM_134025)	30	NM_134025	103737	Mm.102205	NM_134025	ENSMUSG00000018733	Pex12	AI451906	peroxisomal biogenesis factor 12	protein-coding
mm_10740.1	chr2	23069189	23069208	+	1	NA	5' UTR (NM_001102438, exon 1 of 13)	5' UTR (NM_001102438, exon 1 of 13)	126	NM_001102438	74159	Mm.181973	NM_028793	ENSMUSG00000026781	Acbd5	1300014E15Rik	acyl-Coenzyme A binding domain containing 5	protein-coding
mm_73141.1	chr8	94977379	94977392	+	1	NA	5' UTR (NM_001198894, exon 1 of 14)	5' UTR (NM_001198894, exon 1 of 14)	276	NM_001198894	14766	Mm.290834	NM_018882	ENSMUSG00000031785	Adgrg1	Cyt28|Gpr56|TM7LN4|TM7XN1	adhesion G protein-coupled receptor G1	protein-coding
mm_31861.1	chr4	79768770	79768770	+	1	NA	Intergenic	Intergenic	-1065443	NM_031202	22178	Mm.30438	NM_031202	ENSMUSG00000005994	Tyrp1	Oca3|TRP-1|TRP1|Tyrp|b|brown|isa	tyrosinase-related protein 1	protein-coding
mm_114876.1	chr13	94169625	94169646	+	1	NA	intron (NM_172589, intron 2 of 3)	intron (NM_172589, intron 2 of 3)	111839	NM_172589	218454	Mm.316553	NM_172589	ENSMUSG00000045312	Lhfpl2	6030465B15|AI447312|AW050335|mKIAA0206|vgim	lipoma HMGIC fusion partner-like 2	protein-coding
mm_17758.1	chr2	32775406	32775413	-	1	NA	promoter-TSS (NM_001290566)	promoter-TSS (NM_001290566)	-70	NM_001290566	338348	Mm.475130	NM_177384	ENSMUSG00000039021	Ttc16	1200002K10Rik	tetratricopeptide repeat domain 16	protein-coding
mm_142818.1	chr17	51747696	51747723	-	1	NA	intron (NM_009122, intron 9 of 10)	intron (NM_009122, intron 9 of 10)	64345	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_97581.1	chr11	78944784	78944799	+	1	NA	exon (NM_010927, exon 12 of 27)	exon (NM_010927, exon 12 of 27)	19500	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_110264.1	chr12	31944531	31944531	-	1	NA	intron (NM_177993, intron 1 of 8)	intron (NM_177993, intron 1 of 8)	6004	NM_177993	73389	Mm.390461	NM_153198	ENSMUSG00000002996	Hbp1	1700058O05Rik|BE629963|C330012F01Rik|C86454	high mobility group box transcription factor 1	protein-coding
mm_9383.1	chr1	172213119	172213129	-	1	NA	exon (NM_009813, exon 9 of 11)	exon (NM_009813, exon 9 of 11)	-6320	NM_011063	18611	Mm.544	NM_011063	ENSMUSG00000013698	Pea15a	Mat1|PEA-15|Pea15|Pkcs15	phosphoprotein enriched in astrocytes 15A	protein-coding
mm_157113.1	chrX	9438295	9438305	-	1	NA	exon (NM_007807, exon 13 of 13)	exon (NM_007807, exon 13 of 13)	31024	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_163476.1	chr12	104956260	104956262	-	1	NA	intron (NM_001042699, intron 9 of 18)	B1_Mur1|SINE|Alu	42416	NM_001042699	212073	Mm.212688	NM_172500	ENSMUSG00000054150	Syne3	nesprin-3	spectrin repeat containing, nuclear envelope family member 3	protein-coding
mm_63959.1	chr7	139943761	139943769	+	1	NA	promoter-TSS (NM_009482)	promoter-TSS (NM_009482)	-91	NM_009482	22286	Mm.10205	NM_009482	ENSMUSG00000047751	Utf1	AI505934	undifferentiated embryonic cell transcription factor 1	protein-coding
mm_33417.1	chr4	129984784	129984788	+	1	NA	promoter-TSS (NM_173071)	promoter-TSS (NM_173071)	-84	NM_001290714	230775	Mm.262241	NM_173071	ENSMUSG00000028782	Adgrb2	Bai2	adhesion G protein-coupled receptor B2	protein-coding
mm_30866.1	chr4	32015511	32015521	+	1	NA	intron (NM_172688, intron 13 of 15)	intron (NM_172688, intron 13 of 15)	51409	NM_172688	26409	Mm.258589	NM_009316	ENSMUSG00000028284	Map3k7	B430101B05|C87327|Tak1	mitogen-activated protein kinase kinase kinase 7	protein-coding
mm_154577.1	chrX	7571185	7571191	+	1	NA	intron (NM_138605, intron 1 of 3)	intron (NM_138605, intron 1 of 3)	-2412	NR_029473	78185	Mm.160055	NR_029473	ENSMUSG00000039545	Ppp1r3fos	4930524L23Rik	protein phosphatase 1, regulatory subunit 3F, opposite strand	ncRNA
mm_104563.1	chr11	96829960	96829972	-	1	NA	promoter-TSS (NM_008686)	promoter-TSS (NM_008686)	2	NM_008686	18023	Mm.6743	NM_008686	ENSMUSG00000038615	Nfe2l1	AA408798|AW212678|LCR-F1|Lcrf1|NRF1|TCF-11|TCF11	nuclear factor, erythroid derived 2,-like 1	protein-coding
mm_129822.1	chr15	83052875	83052888	-	1	NA	Intergenic	Intergenic	-19484	NM_001271411	74039	Mm.32584	NM_028728	ENSMUSG00000058099	Nfam1	4921501M20Rik|Cnaip	Nfat activating molecule with ITAM motif 1	protein-coding
mm_106435.1	chr11	119491230	119491264	-	1	NA	promoter-TSS (NM_177394)	promoter-TSS (NM_177394)	-100	NM_001164636	338371	Mm.271946	NM_177394	ENSMUSG00000039850	Endov	A730011L01Rik	endonuclease V	protein-coding
mm_106812.1	chr12	7597935	7597935	+	1	NA	Intergenic	Intergenic	-217605	NR_045045	73575	Mm.179463	NR_045045	ENSMUSG00000102096	1700101O22Rik	-	RIKEN cDNA 1700101O22 gene	ncRNA
mm_74286.1	chr8	125734214	125734307	+	1	NA	promoter-TSS (NM_025636)	promoter-TSS (NM_025636)	57	NM_001310688	66566	Mm.25296	NM_025636	ENSMUSG00000031851	Ntpcr	2310079N02Rik|AI449709	nucleoside-triphosphatase, cancer-related	protein-coding
mm_31472.1	chr4	49650093	49650110	+	1	NA	exon (NM_001163263, exon 13 of 20)	exon (NM_001163263, exon 13 of 20)	18041	NM_182999	109331	Mm.24765	NM_182999	ENSMUSG00000028309	Rnf20	4833430L21Rik|AW540162|C79397|mKIAA4116	ring finger protein 20	protein-coding
mm_88610.1	chr10	79824589	79824618	+	1	NA	intron (NM_030218, intron 1 of 4)	intron (NM_030218, intron 1 of 4)	3582	NM_030218	78906	Mm.33087	NM_030218	ENSMUSG00000035852	Misp	9130017N09Rik	mitotic spindle positioning	protein-coding
mm_55957.1	chr6	85374680	85374704	-	1	NA	promoter-TSS (NM_177466)	promoter-TSS (NM_177466)	-58	NM_001003955	52055	Mm.220334	NM_177466	ENSMUSG00000051343	Rab11fip5	9130206P09Rik|C75969|D6Ertd32e|GAF1|RIP11	RAB11 family interacting protein 5 (class I)	protein-coding
mm_66871.1	chr7	57387173	57387222	-	1	NA	promoter-TSS (NM_008074)	promoter-TSS (NM_008074)	-75	NR_033504	791383	Mm.403104	NR_033504	ENSMUSG00000055048	Gm9962	ENSMUSG00000055048	predicted gene 9962	ncRNA
mm_15920.1	chr2	165066660	165066684	+	1	NA	intron (NM_170702, intron 6 of 7)	intron (NM_170702, intron 6 of 7)	11036	NM_011611	21939	Mm.271833	NM_011611	ENSMUSG00000017652	Cd40	AI326936|Bp50|GP39|HIGM1|IGM|IMD3|T-BAM|TRAP|Tnfrsf5|p50	CD40 antigen	protein-coding
mm_156725.1	chrX	159865333	159865352	+	1	NA	exon (NM_021389, exon 6 of 17)	exon (NM_021389, exon 6 of 17)	24874	NM_001135728	58194	Mm.286495	NM_021389	ENSMUSG00000040990	Sh3kbp1	1200007H22Rik|1700125L08Rik|5830464D22Rik|AI447724|Cin85|IN85|Ruk|Seta	SH3-domain kinase binding protein 1	protein-coding
mm_74998.1	chr8	27227535	27227544	-	1	NA	exon (NM_013462, exon 2 of 4)	exon (NM_013462, exon 2 of 4)	2049	NM_013462	11556	Mm.278475	NM_013462	ENSMUSG00000031489	Adrb3	Adrb-3	adrenergic receptor, beta 3	protein-coding
mm_31029.1	chr4	40876196	40876208	+	1	NA	Intergenic	Intergenic	-21665	NM_022305	14595	Mm.15622	NM_022305	ENSMUSG00000028413	B4galt1	B-1,4-GalT|B-1,4-GalT1|GalT|Ggtb|Ggtb2|b4Gal-T1|beta-1,4-GalT|beta-1,4-GalT1|beta4Gal-T1	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1	protein-coding
mm_94337.1	chr11	4704617	4704631	+	1	NA	promoter-TSS (NM_026015)	promoter-TSS (NM_026015)	-54	NM_026015	67178	Mm.271056	NM_026015	ENSMUSG00000009076	Zmat5	2610510L01Rik|D11Bwg0572e|D11Bwg1548e	zinc finger, matrin type 5	protein-coding
mm_127815.1	chr15	5108368	5108374	-	1	NA	5' UTR (NM_001163138, exon 2 of 4)	5' UTR (NM_001163138, exon 2 of 4)	162	NM_001163138	239319	Mm.31252	NM_001163138	ENSMUSG00000041849	Card6	D730008L15	caspase recruitment domain family, member 6	protein-coding
mm_72319.1	chr8	78390957	78390975	+	1	NA	intron (NM_183096, intron 12 of 13)	ORR1E|LTR|ERVL-MaLR	45686	NM_138944	18997	Mm.234261	NM_138944	ENSMUSG00000031688	Pou4f2	Brn-3.2|Brn-3b|Brn3b|Pou4f-rs1|mBrn3-3R	POU domain, class 4, transcription factor 2	protein-coding
mm_60819.1	chr7	45705294	45705307	+	1	NA	promoter-TSS (NM_016974)	promoter-TSS (NM_016974)	53	NM_016974	13170	Mm.24222	NM_016974	ENSMUSG00000059824	Dbp	-	D site albumin promoter binding protein	protein-coding
mm_27537.1	chr3	57575908	57575912	-	1	NA	promoter-TSS (NM_133784)	promoter-TSS (NM_133784)	0	NM_001168281	97064	Mm.405029	NM_133784	ENSMUSG00000027803	Wwtr1	2310058J06Rik|2610021I22Rik|C78399|Taz	WW domain containing transcription regulator 1	protein-coding
mm_134388.1	chr16	17288556	17288575	-	1	NA	intron (NM_001001983, intron 43 of 54)	PB1D7|SINE|Alu	12265	NM_177473	224019	Mm.246388	NM_177473	ENSMUSG00000055692	Tmem191c	4933405M22Rik|D16Bwg1494e|MNCb-4137	transmembrane protein 191C	protein-coding
mm_108875.1	chr12	99645549	99645564	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-17582	NR_045288	73457	Mm.383439	NR_045288	ENSMUSG00000100211	1700064M15Rik	-	RIKEN cDNA 1700064M15 gene	ncRNA
mm_144264.1	chr18	11053243	11053292	+	1	NA	promoter-TSS (NR_105023)	promoter-TSS (NR_105023)	-700	NR_105023	68434	Mm.57626	NR_105022	ENSMUSG00000097222	1010001N08Rik	Gata6as	RIKEN cDNA 1010001N08 gene	ncRNA
mm_104111.1	chr11	86719496	86719606	-	1	NA	exon (NM_001003908, exon 12 of 32)	exon (NM_001003908, exon 12 of 32)	35470	NM_001098810	217057	Mm.24868	NM_175004	ENSMUSG00000072582	Ptrh2	A230072I16Rik|Bit1|CGI-147	peptidyl-tRNA hydrolase 2	protein-coding
mm_142311.1	chr17	42876418	42876431	-	1	NA	promoter-TSS (NM_009847)	promoter-TSS (NM_009847)	0	NM_009847	12488	Mm.218637	NM_009847	ENSMUSG00000061665	Cd2ap	AL024079|C78928|METS-1|Mets1	CD2-associated protein	protein-coding
mm_132100.1	chr16	31422289	31422308	+	1	NA	promoter-TSS (NM_175177)	promoter-TSS (NM_175177)	1	NM_175177	71911	Mm.293470	NM_175177	ENSMUSG00000046598	Bdh1	2310032J20Rik|AI327223|Bdh	3-hydroxybutyrate dehydrogenase, type 1	protein-coding
mm_123033.1	chr14	55524976	55524985	-	1	NA	promoter-TSS (NM_008736)	promoter-TSS (NM_008736)	1	NM_001271916	18185	Mm.20422	NM_008736	ENSMUSG00000040632	Nrl	D14H14S46E	neural retina leucine zipper gene	protein-coding
mm_28000.1	chr3	82903964	82903981	-	1	NA	promoter-TSS (NR_040381)	promoter-TSS (NR_040381)	2	NM_023624	79235	Mm.33921	NM_023624	ENSMUSG00000028003	Lrat	1300010A18Rik|AI449251	lecithin-retinol acyltransferase (phosphatidylcholine-retinol-O-acyltransferase)	protein-coding
mm_117059.1	chr13	58402534	58402534	-	1	NA	promoter-TSS (NM_025279)	promoter-TSS (NM_025279)	-22	NM_001301344	15387	Mm.142872	NM_025279	ENSMUSG00000021546	Hnrnpk	Hnrpk|KBBP|NOVA	heterogeneous nuclear ribonucleoprotein K	protein-coding
mm_76697.1	chr8	94180319	94180326	-	1	NA	TTS (NM_013602)	TTS (NM_013602)	1233	NM_013602	17748	Mm.192991	NM_013602	ENSMUSG00000031765	Mt1	MT-I|Mt-1	metallothionein 1	protein-coding
mm_153070.1	chr19	32239006	32239053	-	1	NA	intron (NM_001168525, intron 4 of 9)	intron (NM_001168525, intron 4 of 9)	-28016	NM_001168526	208449	Mm.329810	NM_144792	ENSMUSG00000040451	Sgms1	9530058O11Rik|AI841905|C80702|Mob|Sms1|Sor1|Tmem23	sphingomyelin synthase 1	protein-coding
mm_100968.1	chr11	6660260	6660270	-	1	NA	promoter-TSS (NR_028586)	promoter-TSS (NR_028586)	-29	NR_028586	100041311	Mm.388018	NR_028586	ENSMUSG00000086373	Gm11978	OTTMUSG00000005125|OTTMUSG00000005127	predicted gene 11978	pseudo
mm_31400.1	chr4	48045971	48045975	+	1	NA	intron (NM_015743, intron 1 of 7)	intron (NM_015743, intron 1 of 7)	668	NM_015743	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_28062.1	chr3	84259659	84259699	-	1	NA	promoter-TSS (NM_001271727)	promoter-TSS (NM_001271727)	100	NM_001271727	80890	Mm.44876	NM_030706	ENSMUSG00000027993	Trim2	mKIAA0517|narf	tripartite motif-containing 2	protein-coding
mm_165492.1	chr2	164777822	164777849	-	1	NA	exon (NM_009394, exon 4 of 6)	exon (NM_009394, exon 4 of 6)	1899	NM_009394	21925	Mm.1716	NM_009394	ENSMUSG00000017300	Tnnc2	Tncs	troponin C2, fast	protein-coding
mm_159321.1	chr3	15575023	15575023	-	1	NA	promoter-TSS (NM_001173460)	promoter-TSS (NM_001173460)	42	NM_001173460	668101	Mm.423523	NM_001173460	ENSMUSG00000095028	Sirpb1b	-	signal-regulatory protein beta 1B	protein-coding
mm_166068.1	chr4	135069600	135069613	-	1	NA	Intergenic	Intergenic	-51039	NM_019732	12399	Mm.378894	NM_019732	ENSMUSG00000070691	Runx3	AML2|Cbfa3|Pebp2a3	runt related transcription factor 3	protein-coding
mm_27509.1	chr3	55788746	55788749	-	1	NA	intron (NM_030595, intron 40 of 57)	intron (NM_030595, intron 40 of 57)	6237	NM_010750	17116	Mm.440209	NM_010750	ENSMUSG00000056947	Mab21l1	AW047968	mab-21-like 1 (C. elegans)	protein-coding
mm_123170.1	chr14	57398487	57398509	-	1	NA	promoter-TSS (NM_030004)	promoter-TSS (NM_030004)	-15	NM_030004	68631	Mm.25539	NM_030004	ENSMUSG00000021947	Cryl1	1110025H08Rik|A230106J09Rik|C85932|gul3dh	crystallin, lambda 1	protein-coding
mm_84998.1	chr9	86798878	86798884	-	1	NA	intron (NR_102729, intron 15 of 30)	intron (NR_102729, intron 15 of 30)	55248	NM_178738	244954	Mm.257629	NM_178738	ENSMUSG00000033491	Prss35	6030424L22Rik|P3D9	protease, serine 35	protein-coding
mm_113275.1	chr13	29745670	29745674	+	1	NA	intron (NR_131896, intron 5 of 16)	intron (NR_131896, intron 5 of 16)	110001	NR_131896	68916	Mm.212227	NM_144536	ENSMUSG00000006191	Cdkal1	1190005B03Rik|6620401C13Rik	CDK5 regulatory subunit associated protein 1-like 1	protein-coding
mm_56399.1	chr6	96166212	96166258	-	1	NA	promoter-TSS (NR_003643)	promoter-TSS (NR_003643)	-30	NR_003643	78482	Mm.391486	NM_030107	ENSMUSG00000072878	1700123L14Rik	-	nucleoporin 50 pseudogene	pseudo
mm_62433.1	chr7	101361998	101362044	+	1	NA	intron (NM_001040111, intron 1 of 33)	intron (NM_001040111, intron 1 of 33)	13952	NM_001040111	69710	Mm.277687	NM_027180	ENSMUSG00000032812	Arap1	2410002L19Rik|Centd2|mKIAA0782	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	protein-coding
mm_60549.1	chr7	44480812	44480816	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-3703	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_143132.1	chr17	57215879	57215896	-	1	NA	exon (NM_009778, exon 24 of 41)	exon (NM_009778, exon 24 of 41)	1341	NR_105944	102465591		NR_105944	ENSMUSG00000099066	Mir6978	Gm27858|mmu-mir-6978	microRNA 6978	ncRNA
mm_96143.1	chr11	61022269	61022312	+	1	NA	promoter-TSS (NM_001267593)	promoter-TSS (NM_001267593)	-274	NM_001267593	16515	Mm.4970	NM_010603	ENSMUSG00000042529	Kcnj12	IRK-2|IRK2|Kir2.2|MB-IRK2	potassium inwardly-rectifying channel, subfamily J, member 12	protein-coding
mm_26003.1	chr3	135242244	135242253	+	1	NA	exon (NM_173762, exon 27 of 46)	exon (NM_173762, exon 27 of 46)	29685	NM_173762	229841	Mm.161470	NM_173762	ENSMUSG00000045328	Cenpe	312kDa|AU019344|BC049989|C530022J18|CENP-E|Kif10	centromere protein E	protein-coding
mm_28194.1	chr3	88143210	88143229	-	1	NA	intron (NM_133665, intron 1 of 10)	intron (NM_133665, intron 1 of 10)	847	NM_001310593	17261	Mm.28184	NM_133665	ENSMUSG00000001419	Mef2d	C80750	myocyte enhancer factor 2D	protein-coding
mm_72126.1	chr8	71692911	71692922	+	1	NA	exon (NM_028189, exon 3 of 3)	exon (NM_028189, exon 3 of 3)	3664	NM_013564	16336	Mm.476857	NM_013564	ENSMUSG00000079019	Insl3	Rlf|Rlnl	insulin-like 3	protein-coding
mm_34358.1	chr4	144892542	144892591	+	1	NA	promoter-TSS (NM_001172424)	promoter-TSS (NM_001172424)	-261	NM_001172424	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding
mm_55912.1	chr6	83775576	83775580	-	1	NA	intron (NM_009357, intron 1 of 5)	CpG	234	NM_009357	21766	Mm.28371	NM_009357	ENSMUSG00000014748	Tex261	3110001O07Rik|AA409339|AI480706|AL033351|TEG-261	testis expressed gene 261	protein-coding
mm_16335.1	chr2	174330049	174330059	+	1	NA	promoter-TSS (NM_001077510)	promoter-TSS (NM_001077510)	-16	NM_201616	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_115239.1	chr13	109951398	109951416	+	1	NA	3' UTR (NM_011056, exon 17 of 17)	3' UTR (NM_011056, exon 17 of 17)	47598	NR_035442	100316683		NR_035442	ENSMUSG00000084651	Mir1904	Mirn1904|mmu-mir-1904	microRNA 1904	ncRNA
mm_155962.1	chrX	106015765	106015766	+	1	NA	promoter-TSS (NM_025379)	promoter-TSS (NM_025379)	65	NM_025379	66142	Mm.197728	NM_025379	ENSMUSG00000031231	Cox7b	1100001F07Rik|1110004F07Rik|C80563	cytochrome c oxidase subunit VIIb	protein-coding
mm_142926.1	chr17	53846346	53846359	-	1	NA	promoter-TSS (NM_026935)	promoter-TSS (NM_026935)	-394	NM_026935	69083	Mm.19320	NM_026935	ENSMUSG00000023122	Sult1c2	1810008N17Rik|ST1C1|ST1C2|Sult1c1	sulfotransferase family, cytosolic, 1C, member 2	protein-coding
mm_63709.1	chr7	130692508	130692526	+	1	NA	promoter-TSS (NM_021314)	promoter-TSS (NM_021314)	-39	NM_001347637	57752	Mm.86322	NM_021314	ENSMUSG00000030852	Tacc2	mKIAA4180	transforming, acidic coiled-coil containing protein 2	protein-coding
mm_54187.1	chr6	24104141	24104156	-	1	NA	intron (NM_019481, intron 8 of 14)	intron (NM_019481, intron 8 of 14)	63944	NM_019481	55961	Mm.19299	NM_019481	ENSMUSG00000029700	Slc13a1	AI314066|AI987826|NaSi-1|Nas1	solute carrier family 13 (sodium/sulfate symporters), member 1	protein-coding
mm_102527.1	chr11	60931859	60931903	-	1	NA	promoter-TSS (NR_027800)	promoter-TSS (NR_027800)	-14	NR_027800	24082	Mm.46270	NM_025293	ENSMUSG00000042549	Map2k3os	F3-1|Gm16516|Gtlf3a	mitogen-activated protein kinase kinase 3, opposite strand	ncRNA
mm_68441.1	chr7	109986182	109986193	-	1	NA	promoter-TSS (NM_153525)	promoter-TSS (NM_153525)	43	NM_153525	233724	Mm.43212	NM_153525	ENSMUSG00000047554	Tmem41b	1500015G02Rik|1500031M19Rik|AU018901|D7Ertd70e|D7Ertd743e	transmembrane protein 41B	protein-coding
mm_69510.1	chr7	134413874	134413880	-	1	NA	Intergenic	Intergenic	-37049	NM_001081331	71007	Mm.334285	NM_001081331	ENSMUSG00000030994	D7Ertd443e	4933400E14Rik|FATS|Gm497	DNA segment, Chr 7, ERATO Doi 443, expressed	protein-coding
mm_108980.1	chr12	102743792	102743802	+	1	NA	promoter-TSS (NM_177140)	promoter-TSS (NM_177140)	37	NM_177140	320351	Mm.86546	NM_177140	ENSMUSG00000046675	Tmem251	D230037D09Rik	transmembrane protein 251	protein-coding
mm_32960.1	chr4	119814308	119814349	+	1	NA	promoter-TSS (NM_010657)	promoter-TSS (NM_010657)	-350	NM_010657	16656	Mm.302758	NM_010657	ENSMUSG00000028634	Hivep3	2900056N03Rik|A130075N07|AI848000|E030045D18Rik|KBP-1|KBP1|Krc|Rc|Schnurri-3|Shn3|Zas3	human immunodeficiency virus type I enhancer binding protein 3	protein-coding
mm_83512.1	chr9	45985366	45985415	-	1	NA	promoter-TSS (NM_008775)	promoter-TSS (NM_008775)	-519	NM_008775	18475	Mm.200859	NM_008775	ENSMUSG00000003131	Pafah1b2	AI747451|AU021353|Pafahb|mus[b]	platelet-activating factor acetylhydrolase, isoform 1b, subunit 2	protein-coding
mm_156520.1	chrX	150590038	150590046	+	1	NA	5' UTR (NM_008824, exon 1 of 14)	5' UTR (NM_008824, exon 1 of 14)	121	NM_008824	18639	Mm.249131	NM_008824	ENSMUSG00000025271	Pfkfb1	PFK/FBPase 1	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1	protein-coding
mm_51444.1	chr6	80174081	80174089	+	1	NA	intron (NM_001347261, intron 2 of 2)	RLTR12A|LTR|ERVK	154442	NM_178731	243499	Mm.483425	NM_178731	ENSMUSG00000052581	Lrrtm4	7530419J18Rik|A230052N11	leucine rich repeat transmembrane neuronal 4	protein-coding
mm_124654.1	chr15	5237480	5237496	+	1	NA	intron (NM_008965, intron 2 of 2)	intron (NM_008965, intron 2 of 2)	6699	NM_001136079	19219	Mm.18509	NM_008965	ENSMUSG00000039942	Ptger4	EP4|Ptgerep4	prostaglandin E receptor 4 (subtype EP4)	protein-coding
mm_45993.1	chr5	90506558	90506589	-	1	NA	exon (NM_007423, exon 12 of 15)	exon (NM_007423, exon 12 of 15)	-12376	NM_145146	280662	Mm.348786	NM_145146	ENSMUSG00000029369	Afm	Alf|alpha-Alb	afamin	protein-coding
mm_163933.1	chr14	48250565	48250586	+	1	NA	exon (NM_033602, exon 4 of 6)	exon (NM_033602, exon 4 of 6)	51859	NR_003630	624367	Mm.445185	NM_001037921	ENSMUSG00000063885	Gm6498	EG624367	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_90121.1	chr10	117280713	117280732	+	1	NA	exon (NM_017372, exon 2 of 4)	exon (NM_017372, exon 2 of 4)	1550	NM_017372	17105	Mm.45436	NM_017372	ENSMUSG00000069516	Lyz2	AI326280|Lys|Lysm|Lyzf2|Lyzs|Lzm|Lzm-s1|Lzp	lysozyme 2	protein-coding
mm_40082.1	chr5	34462185	34462195	+	1	NA	exon (NM_001243123, exon 17 of 21)	exon (NM_001243123, exon 17 of 21)	51789	NM_139064	231130	Mm.28615	NM_139064	ENSMUSG00000059866	Tnip2	1810020H16Rik|ABIN-2|AI428870	TNFAIP3 interacting protein 2	protein-coding
mm_107448.1	chr12	36676751	36676758	+	1	NA	intron (NM_178629, intron 9 of 9)	intron (NM_178629, intron 9 of 9)	-139451	NR_039558	100628578		NR_039558	ENSMUSG00000092998	Mir5099	mmu-mir-5099|mu-mir-5099	microRNA 5099	ncRNA
mm_168086.1	chr10	126141975	126141985	+	1	NA	Intergenic	Intergenic	175761	NM_177152	320398	Mm.275586	NM_177152	ENSMUSG00000020105	Lrig3	9030421L11Rik|9130004I02Rik|9430095K15Rik|mKIAA3016	leucine-rich repeats and immunoglobulin-like domains 3	protein-coding
mm_152721.1	chr19	18568037	18568041	-	1	NA	Intergenic	RMER17B|LTR|ERVK	63774	NM_017375	20409	Mm.172222	NM_017375	ENSMUSG00000024725	Ostf1	C78236|SH3P2|Sh3d3	osteoclast stimulating factor 1	protein-coding
mm_10550.1	chr2	16675232	16675266	+	1	NA	intron (NM_026162, intron 9 of 13)	intron (NM_026162, intron 9 of 13)	318945	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding
mm_60854.1	chr7	45833595	45833619	+	1	NA	exon (NM_008172, exon 12 of 12)	exon (NM_008172, exon 12 of 12)	-2818	NM_153419	101612	Mm.274847	NM_153419	ENSMUSG00000053801	Grwd1	A301|AI504353|Grwd|Wdr28	glutamate-rich WD repeat containing 1	protein-coding
mm_35270.1	chr4	19901180	19901190	-	1	NA	intron (NM_175406, intron 2 of 7)	intron (NM_175406, intron 2 of 7)	21381	NM_175406	242341	Mm.19298	NM_175406	ENSMUSG00000028238	Atp6v0d2	1620401A02Rik|AI324824|V-ATPase	ATPase, H+ transporting, lysosomal V0 subunit D2	protein-coding
mm_95722.1	chr11	54522952	54522976	+	1	NA	5' UTR (NM_001252494, exon 1 of 29)	5' UTR (NM_001252494, exon 1 of 29)	119	NM_001252496	192786	Mm.254404	NM_175258	ENSMUSG00000037533	Rapgef6	A530068K01|AI844632|BB085664|C030018K18Rik|PDZ-GEF2|Pdzgef2|RA-GEF-2|Ragef2|mKIAA4052	Rap guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_19981.1	chr2	118479638	118479687	-	1	NA	promoter-TSS (NM_009273)	promoter-TSS (NM_009273)	34	NM_009273	20813	Mm.363404	NM_009273	ENSMUSG00000009549	Srp14	14kDa|AW536328	signal recognition particle 14	protein-coding
mm_58118.1	chr6	138658450	138658456	-	1	NA	promoter-TSS (NM_015777)	promoter-TSS (NM_015777)	-9	NM_015777	50540	Mm.84043	NM_015777	ENSMUSG00000046717	Igbp1b	alpha4-b	immunoglobulin (CD79A) binding protein 1b	protein-coding
mm_91904.1	chr10	60219265	60219295	-	1	NA	promoter-TSS (NM_016803)	promoter-TSS (NM_016803)	-20	NM_016803	53374	Mm.12866	NM_016803	ENSMUSG00000057337	Chst3	C6ST|C6ST-1|GST-0	carbohydrate (chondroitin 6/keratan) sulfotransferase 3	protein-coding
mm_40878.1	chr5	74386433	74386435	+	1	NA	intron (NM_001286437, intron 5 of 7)	intron (NM_001286437, intron 5 of 7)	145308	NM_178672	212986	Mm.134147	NM_178672	ENSMUSG00000062110	Scfd2	E430013M20Rik|STXBP1L1	Sec1 family domain containing 2	protein-coding
mm_37736.1	chr4	129575346	129575352	-	1	NA	Intergenic	Intergenic	-1708	NM_001162433	16818	Mm.293753	NM_010693	ENSMUSG00000000409	Lck	Hck-3|Lsk|Lskt|p56<lck>|p56Lck	lymphocyte protein tyrosine kinase	protein-coding
mm_118444.1	chr14	8118214	8118220	+	1	NA	intron (NM_178279, intron 1 of 18)	intron (NM_178279, intron 1 of 18)	20004	NM_178279	218699	Mm.29515	NM_145458	ENSMUSG00000033885	Pxk	C230080L11Rik|D14Ertd813e|MONaKA	PX domain containing serine/threonine kinase	protein-coding
mm_104.1	chr1	9548050	9548101	+	1	NA	promoter-TSS (NM_175236)	promoter-TSS (NM_175236)	29	NR_027664	76187	Mm.28514	NM_175236	ENSMUSG00000025911	Adhfe1	6330565B14Rik|AI043035|Adh8	alcohol dehydrogenase, iron containing, 1	protein-coding
mm_91329.1	chr10	25246884	25246886	-	1	NA	intron (NM_018747, intron 5 of 7)	PB1D10|SINE|Alu	-46715	NM_001347460	432442	Mm.485937	NM_018747	ENSMUSG00000039166	Akap7	6430401D08|AI662165|AKAP15|Akap18|BB170514	A kinase (PRKA) anchor protein 7	protein-coding
mm_149209.1	chr19	9982695	9982711	+	1	NA	promoter-TSS (NM_010239)	promoter-TSS (NM_010239)	57	NM_010239	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
mm_101583.1	chr11	34477891	34477902	-	1	NA	intron (NM_033374, intron 25 of 51)	intron (NM_033374, intron 25 of 51)	163074	NM_001025382	574403	Mm.444796	NM_001025382	ENSMUSG00000069911	Fam196b	EG574403|Gm6041	family with sequence similarity 196, member B	protein-coding
mm_1733.1	chr1	75385545	75385601	+	1	NA	promoter-TSS (NM_001085370)	promoter-TSS (NM_001085370)	-37	NM_001085370	11790	Mm.275397	NM_007463	ENSMUSG00000026207	Speg	AW125581|Apeg1|BPEG|D1Bwg1450e|SPEGalpha|SPEGbeta|mKIAA1297	SPEG complex locus	protein-coding
mm_87721.1	chr10	60106271	60106292	+	1	NA	promoter-TSS (NM_052994)	promoter-TSS (NM_052994)	24	NM_052994	94214	Mm.153429	NM_052994	ENSMUSG00000058297	Spock2	AA407235|Gcap26|mKIAA0275	sparc/osteonectin, cwcv and kazal-like domains proteoglycan 2	protein-coding
mm_58509.1	chr7	4119557	4119596	+	1	NA	promoter-TSS (NM_001109765)	promoter-TSS (NM_001109765)	46	NM_001001454	57776	Mm.29729	NM_021324	ENSMUSG00000030428	Ttyh1	4930459B04Rik|6330408P11Rik|TTY1|mTTY1|tty	tweety family member 1	protein-coding
mm_170551.1	chr19	40957498	40957513	+	1	NA	intron (NM_008528, intron 6 of 16)	RLTRETN_Mm|LTR|ERVK	37030	NM_008528	17060	Mm.9749	NM_008528	ENSMUSG00000061132	Blnk	BASH|Bca|Ly-57|Ly57|Lyw-57|SLP-65	B cell linker	protein-coding
mm_2046.1	chr1	87327045	87327053	+	1	NA	promoter-TSS (NM_001110212)	promoter-TSS (NM_001110212)	51	NM_001110212	227331	Mm.23065	NM_146112	ENSMUSG00000048000	Gigyf2	2610016F01Rik|A830080H02Rik|AI852361|AW259676|BC006835|Tnrc15|mKIAA0642	GRB10 interacting GYF protein 2	protein-coding
mm_138554.1	chr17	35265791	35265812	+	1	NA	exon (NM_001267808, exon 8 of 11)	exon (NM_001267808, exon 8 of 11)	2678	NM_001267808	14980	Mm.439675	NM_001267808		H2-L	H-2L	histocompatibility 2, D region locus L	protein-coding
mm_7715.1	chr1	130629615	130629626	-	1	NA	promoter-TSS (NM_009581)	promoter-TSS (NM_009581)	-14	NM_009581	22789	Mm.4644	NM_009581	ENSMUSG00000042554	Zp3r	AV264399|SP56	zona pellucida 3 receptor	protein-coding
mm_144334.1	chr18	13973023	13973028	+	1	NA	promoter-TSS (NM_145492)	promoter-TSS (NM_145492)	-292	NM_145492	225207	Mm.40325	NM_145492	ENSMUSG00000024420	Zfp521	B930086A16Rik|Evi3|Znf521	zinc finger protein 521	protein-coding
mm_128141.1	chr15	31530824	31530833	-	1	NA	5' UTR (NM_172606, exon 1 of 26)	5' UTR (NM_172606, exon 1 of 26)	209	NM_172606	223455	Mm.272185	NM_172606	ENSMUSG00000039100	March6	3830408G03|F830029L24Rik|mKIAA0597	membrane-associated ring finger (C3HC4) 6	protein-coding
mm_126683.1	chr15	84766875	84766882	+	1	NA	intron (NM_001205334, intron 10 of 12)	intron (NM_001205334, intron 10 of 12)	-46612	NR_040347	328576	Mm.400211	NR_040347		Gm20556	A430075N02	predicted gene, 20556	ncRNA
mm_93664.1	chr10	117695418	117695445	-	1	NA	intron (NM_001288586, intron 7 of 10)	AT_rich|Low_complexity|Low_complexity	15327	NM_010786	17246	Mm.22670	NM_010786	ENSMUSG00000020184	Mdm2	1700007J15Rik|AA415488|Mdm-2	transformed mouse 3T3 cell double minute 2	protein-coding
mm_44938.1	chr5	36398079	36398085	-	1	NA	promoter-TSS (NM_030889)	promoter-TSS (NM_030889)	57	NM_030889	81840	Mm.34113	NM_030889	ENSMUSG00000029093	Sorcs2	N28137|mKIAA1329	sortilin-related VPS10 domain containing receptor 2	protein-coding
mm_94942.1	chr11	29715692	29715703	+	1	NA	intron (NM_194054, intron 3 of 8)	intron (NM_194054, intron 3 of 8)	-2866	NM_024226	68585	Mm.192580	NM_024226	ENSMUSG00000020458	Rtn4	1110020G17Rik|AA407876|AA409940|AA960376|ASY|C130026I10Rik|NOGO|NSP-CL|NgA|Nogo-A|Nogo-B|Nogo-C|mKIAA0886|mKIAA4153	reticulon 4	protein-coding
mm_96694.1	chr11	69601164	69601203	+	1	NA	3' UTR (NM_013415, exon 7 of 7)	3' UTR (NM_013415, exon 7 of 7)	4777	NM_013415	11932	Mm.235204	NM_013415	ENSMUSG00000041329	Atp1b2	Amog|Atpb-2	ATPase, Na+/K+ transporting, beta 2 polypeptide	protein-coding
mm_41350.1	chr5	90503670	90503680	+	1	NA	exon (NM_007423, exon 9 of 15)	exon (NM_007423, exon 9 of 15)	12961	NM_007423	11576	Mm.358570	NM_007423	ENSMUSG00000054932	Afp	-	alpha fetoprotein	protein-coding
mm_115964.1	chr13	23914977	23914989	-	1	NA	promoter-TSS (NM_177016)	promoter-TSS (NM_177016)	24	NM_177016	319848	Mm.97959	NM_177016	ENSMUSG00000021336	Slc17a4	9130214H05Rik	solute carrier family 17 (sodium phosphate), member 4	protein-coding
mm_107888.1	chr12	70455392	70455406	+	1	NA	intron (NM_028339, intron 1 of 7)	intron (NM_028339, intron 1 of 7)	2245	NM_028339	72736	Mm.204670	NM_028339	ENSMUSG00000021072	Tmx1	2810425A04Rik|AI465319|Txndc1	thioredoxin-related transmembrane protein 1	protein-coding
mm_161412.1	chr15	12592777	12592777	-	1	NA	promoter-TSS (NM_001081064)	promoter-TSS (NM_001081064)	-221	NM_001081064	68070	Mm.423205	NM_001081064	ENSMUSG00000022197	Pdzd2	4930537L06Rik|A930022H17Rik|Gm21706|Gm82|Pdzk3|mKIAA0300	PDZ domain containing 2	protein-coding
mm_99632.1	chr11	105178721	105178737	+	1	NA	promoter-TSS (NM_001294331)	promoter-TSS (NM_001294331)	-78	NM_001294331	24086	Mm.126976	NM_011903	ENSMUSG00000020694	Tlk2	4933403M19Rik|PKU-alpha|PKUalpha|Tlk	tousled-like kinase 2 (Arabidopsis)	protein-coding
mm_113626.1	chr13	41677185	41677192	+	1	NA	Intergenic	Intergenic	26426	NM_001145878	328231	Mm.227476	NM_177808	ENSMUSG00000054258	Gm5082	A030008J09|EG328231	predicted gene 5082	protein-coding
mm_76253.1	chr8	83699096	83699206	-	1	NA	promoter-TSS (NM_177262)	promoter-TSS (NM_177262)	28	NM_177262	320795	Mm.213000	NM_177262	ENSMUSG00000057672	Pkn1	DBK|F730027O18Rik|PAK1|PRK1|Pkn|Prkcl1|Stk3	protein kinase N1	protein-coding
mm_12433.1	chr2	70661488	70661494	+	1	NA	promoter-TSS (NM_027352)	promoter-TSS (NM_027352)	-18	NR_027343	70231	Mm.271950	NM_027352	ENSMUSG00000014959	Gorasp2	0610011A07Rik|2410043M02Rik|5730520M13Rik|9430094F20Rik|AW552058|ENSMUSG00000075299|GOLPH2|GRASP55|GRS2|p59	golgi reassembly stacking protein 2	protein-coding
mm_155687.1	chrX	93968650	93968675	+	1	NA	promoter-TSS (NR_028320)	promoter-TSS (NR_028320)	6	NR_028320	385493	Mm.328014	NM_001033480	ENSMUSG00000081044	AU015836	-	expressed sequence AU015836	ncRNA
mm_163068.1	chr11	67250364	67250377	+	1	NA	exon (NM_010855, exon 20 of 40)	exon (NM_010855, exon 20 of 40)	12558	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_50236.1	chr6	42351297	42351311	+	1	NA	exon (NM_011777, exon 4 of 10)	exon (NM_011777, exon 4 of 10)	1476	NM_001289619	22793	Mm.282303	NM_011777	ENSMUSG00000029860	Zyx	9530098H06Rik|R75157	zyxin	protein-coding
mm_79528.1	chr9	57697613	57697616	+	1	NA	promoter-TSS (NM_001136059)	promoter-TSS (NM_001136059)	1	NM_001136059	13076	Mm.14089	NM_009992	ENSMUSG00000032315	Cyp1a1	AHH|AHRR|CP11|Cyp1a2|P450-1	cytochrome P450, family 1, subfamily a, polypeptide 1	protein-coding
mm_109965.1	chr12	12546625	12546635	-	1	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	123287	NR_136889	102637952	Mm.421393	NR_136889		Gm34637	-	predicted gene, 34637	ncRNA
mm_9420.1	chr1	172329318	172329326	-	1	NA	promoter-TSS (NM_008429)	promoter-TSS (NM_008429)	-59	NM_008429	16524	Mm.261168	NM_008429	ENSMUSG00000038026	Kcnj9	1700085N21Rik|Girk3|Kir3.3|mbGIRK3	potassium inwardly-rectifying channel, subfamily J, member 9	protein-coding
mm_137623.1	chr17	28300219	28300232	+	1	NA	3' UTR (NM_011145, exon 8 of 8)	3' UTR (NM_011145, exon 8 of 8)	-13305	NR_028297	72775	Mm.201859	NM_028348	ENSMUSG00000007570	Fance	2810451D06Rik|AI415634|AW209126	Fanconi anemia, complementation group E	protein-coding
mm_2084.1	chr1	87676284	87676306	+	1	NA	exon (NM_001110192, exon 6 of 27)	exon (NM_001110192, exon 6 of 27)	55983	NM_001110193	16331	Mm.15105	NM_010566	ENSMUSG00000026288	Inpp5d	SHIP|SHIP-1|SHIP1|SIP-145|p150Ship|s-SHIP	inositol polyphosphate-5-phosphatase D	protein-coding
mm_6748.1	chr1	83408059	83408152	-	1	NA	promoter-TSS (NM_172430)	promoter-TSS (NM_172430)	95	NM_172430	77629	Mm.154303	NM_172430	ENSMUSG00000026163	Sphkap	4930544G21Rik|A930009L15Rik|AI852220|SKIP|mKIAA1678	SPHK1 interactor, AKAP domain containing	protein-coding
mm_117002.1	chr13	57455161	57455164	-	1	NA	intron (NM_001166464, intron 7 of 10)	intron (NM_001166464, intron 7 of 10)	453170	NM_009262	20745	Mm.379020	NM_009262	ENSMUSG00000056222	Spock1	Spock|Ticn1|testican	sparc/osteonectin, cwcv and kazal-like domains proteoglycan 1	protein-coding
mm_133060.1	chr16	58461807	58461820	+	1	NA	intron (NM_028523, intron 13 of 15)	intron (NM_028523, intron 13 of 15)	53278	NM_028523	73379	Mm.373589	NM_028523	ENSMUSG00000035107	Dcbld2	1700055P21Rik|AW146002|CLCP1|Esdn	discoidin, CUB and LCCL domain containing 2	protein-coding
mm_121017.1	chr14	79539882	79539891	+	1	NA	intron (NM_001286411, intron 2 of 8)	B1_Mus2|SINE|Alu	24212	NM_001286411	13709	Mm.20938	NM_007920	ENSMUSG00000036461	Elf1	Elf-1|Sts1|mElf-1|p70	E74-like factor 1	protein-coding
mm_126605.1	chr15	82555088	82555091	+	1	NA	promoter-TSS (NM_201360)	promoter-TSS (NM_201360)	-9	NM_201360	380997	Mm.482248	NM_201360	ENSMUSG00000096852	Cyp2d12	9030605E09Rik	cytochrome P450, family 2, subfamily d, polypeptide 12	protein-coding
mm_35563.1	chr4	41639970	41639983	-	1	NA	5' UTR (NM_027147, exon 1 of 2)	5' UTR (NM_027147, exon 1 of 2)	326	NM_027147	69638	Mm.372459	NM_027147	ENSMUSG00000028445	Enho	1110065P19Rik|2310040A07Rik	energy homeostasis associated	protein-coding
mm_14964.1	chr2	152081603	152081624	+	1	NA	promoter-TSS (NM_001160410)	promoter-TSS (NM_001160410)	84	NM_001160410	545474	Mm.214317	NM_001160410	ENSMUSG00000060257	Scrt2	AW060659	scratch family zinc finger 2	protein-coding
mm_140282.1	chr17	85028348	85028404	+	1	NA	promoter-TSS (NM_009205)	promoter-TSS (NM_009205)	29	NM_009205	20532	Mm.227176	NM_009205	ENSMUSG00000024131	Slc3a1	D2H|NBAT|NTAA|RBAT	solute carrier family 3, member 1	protein-coding
mm_121551.1	chr14	122475497	122475507	+	1	NA	promoter-TSS (NR_045046)	promoter-TSS (NR_045046)	118	NM_009574	22772	Mm.308936	NM_009574	ENSMUSG00000061524	Zic2	HPE5|Ku	zinc finger protein of the cerebellum 2	protein-coding
mm_105354.1	chr11	103028189	103028203	-	1	NA	promoter-TSS (NM_008707)	promoter-TSS (NM_008707)	-366	NM_008707	18107	Mm.10265	NM_008707	ENSMUSG00000020936	Nmt1	AW536594	N-myristoyltransferase 1	protein-coding
mm_44520.1	chr5	24383609	24383621	-	1	NA	TTS (NM_001002897)	TTS (NM_001002897)	8528	NM_001002897	213948	Mm.332252	NM_001002897	ENSMUSG00000038295	Atg9b	Apg912|Apg9l2|Apgdc2|Gm574|Nos3as|eONE|sONE	autophagy related 9B	protein-coding
mm_94344.1	chr11	4848751	4848786	+	1	NA	intron (NM_001252251, intron 1 of 16)	intron (NM_001252251, intron 1 of 16)	776	NM_001252250	18016	Mm.297109	NM_010898	ENSMUSG00000009073	Nf2	merlin	neurofibromin 2	protein-coding
mm_28970.1	chr3	101012131	101012141	-	1	NA	exon (NM_001167906, exon 6 of 9)	exon (NM_001167906, exon 6 of 9)	17359	NM_001167906	630146	Mm.190915	NM_001099332	ENSMUSG00000086564	Cd101	EWI-101|Gm1016|Gm734|Igsf2	CD101 antigen	protein-coding
mm_116978.1	chr13	56252176	56252181	-	1	NA	promoter-TSS (NM_010896)	promoter-TSS (NM_010896)	-15	NM_010896	18014	Mm.266665	NM_010896	ENSMUSG00000048904	Neurog1	AKA|Math4C|Neurod3|bHLHa6|ngn1	neurogenin 1	protein-coding
mm_153182.1	chr19	34498967	34498994	-	1	NA	intron (NM_001111100, intron 8 of 9)	RSINE1|SINE|B4	-23845	NM_009890	12642	Mm.30824	NM_009890	ENSMUSG00000050370	Ch25h	AI462618|m25OH	cholesterol 25-hydroxylase	protein-coding
mm_121519.1	chr14	122105002	122105030	+	1	NA	non-coding (NR_015586, exon 2 of 4)	non-coding (NR_015586, exon 2 of 4)	1958	NR_015586	319727	Mm.215552	NR_015586		A330035P11Rik	-	RIKEN cDNA A330035P11 gene	ncRNA
mm_73792.1	chr8	117256849	117256877	+	1	NA	promoter-TSS (NM_001163262)	promoter-TSS (NM_001163262)	-156	NM_001163262	74440	Mm.233181	NM_028941	ENSMUSG00000034390	Cmip	4933407C03Rik|5830471E12Rik|AI314065|AI464126	c-Maf inducing protein	protein-coding
mm_108592.1	chr12	85374095	85374124	+	1	NA	intron (NM_026775, intron 1 of 4)	intron (NM_026775, intron 1 of 4)	608	NM_026775	68581	Mm.379159	NM_026775	ENSMUSG00000021248	Tmed10	1110014C03Rik|Tmp21|p23|p24delta1	transmembrane p24 trafficking protein 10	protein-coding
mm_25751.1	chr3	123269693	123269705	+	1	NA	exon (NM_027135, exon 2 of 23)	exon (NM_027135, exon 2 of 23)	2203	NM_027135	69608	Mm.29293	NM_027135	ENSMUSG00000039234	Sec24d	2310020L09Rik|Gm1349	Sec24 related gene family, member D (S. cerevisiae)	protein-coding
mm_155950.1	chrX	105080082	105080098	+	1	NA	intron (NM_026312, intron 2 of 5)	intron (NM_026312, intron 2 of 5)	334	NM_026312	67683	Mm.273405	NM_026312	ENSMUSG00000031226	Pbdc1	2610029G23Rik	polysaccharide biosynthesis domain containing 1	protein-coding
mm_8972.1	chr1	165236981	165236991	-	1	NA	promoter-TSS (NM_145513)	promoter-TSS (NM_145513)	-28	NM_145513	226591	Mm.21520	NM_145513	ENSMUSG00000040843	Tiprl	1810011K17Rik	TIP41, TOR signalling pathway regulator-like (S. cerevisiae)	protein-coding
mm_164414.1	chr16	38396516	38396524	+	1	NA	exon (NM_134102, exon 11 of 11)	exon (NM_134102, exon 11 of 11)	34330	NM_022318	64082	Mm.390856	NM_022318	ENSMUSG00000022803	Popdc2	AV006127|Pop2	popeye domain containing 2	protein-coding
mm_61095.1	chr7	51878973	51879000	+	1	NA	promoter-TSS (NM_001330607)	promoter-TSS (NM_001330607)	19	NM_001330607	14453	Mm.207360	NM_008087	ENSMUSG00000030498	Gas2	Gas-2	growth arrest specific 2	protein-coding
mm_173296.1	chrY	43039073	43039086	-	1	NA	Intergenic	RLTR4_Mm|LTR|ERV1	108756	NR_038299	100041346	Mm.426191	NR_038299	ENSMUSG00000101005	Gm20871	-	Sycp3 like Y-linked pseudogene	pseudo
mm_71762.1	chr8	66397237	66397263	+	1	NA	intron (NM_175188, intron 5 of 7)	intron (NM_175188, intron 5 of 7)	10949	NM_001166375	72925	Mm.380457	NM_175188	ENSMUSG00000036469	March1	2900024D24Rik|BB085186	membrane-associated ring finger (C3HC4) 1	protein-coding
mm_52374.1	chr6	113077456	113077466	+	1	NA	promoter-TSS (NR_027008)	promoter-TSS (NR_027008)	-178	NM_028385	72895	Mm.367159	NM_028385	ENSMUSG00000034269	Setd5	2900045N06Rik|C330007C20|C85544|mKIAA1757	SET domain containing 5	protein-coding
mm_104039.1	chr11	86304695	86304700	-	1	NA	TTS (NR_130959)	TTS (NR_130959)	-47129	NM_027421	70422	Mm.171304	NM_027421	ENSMUSG00000018068	Ints2	2810417D08Rik|AA408260|AI987735|mKIAA1287	integrator complex subunit 2	protein-coding
mm_78062.1	chr9	15045582	15045593	+	1	NA	promoter-TSS (NM_019482)	promoter-TSS (NM_019482)	-109	NM_019482	55991	Mm.142253	NM_019482	ENSMUSG00000031934	Panx1	AI847747	pannexin 1	protein-coding
mm_133013.1	chr16	56127404	56127439	+	1	NA	TTS (NM_001003973)	TTS (NM_001003973)	51941	NM_001304503	66315	Mm.255784	NM_025483	ENSMUSG00000052917	Senp7	2410152H17Rik|2810413I22Rik|2900036C23Rik|6030449K19Rik|AI790676	SUMO1/sentrin specific peptidase 7	protein-coding
mm_171450.1	chr4	145432400	145432403	+	1	NA	Intergenic	Intergenic	-31809	NR_002888	545700	Mm.389595	NR_002888	ENSMUSG00000052912	Smarca5-ps	9230115A19Rik|OTTMUSG00000011029	SWI/SNF related, matrix associated, actin depenent ragulator of chromatin, subfamily a, member 5, pseudogene	pseudo
mm_119374.1	chr14	41122893	41122915	+	1	NA	3' UTR (NM_133653, exon 10 of 10)	3' UTR (NM_133653, exon 10 of 10)	-8884	NM_023134	20387	Mm.46062	NM_023134	ENSMUSG00000021789	Sftpa1	SP-A|Sftp-1|Sftp1	surfactant associated protein A1	protein-coding
mm_62557.1	chr7	103460947	103460986	+	1	NA	Intergenic	Intergenic	-9075	NM_146756	258751	Mm.377673	NM_146756	ENSMUSG00000073948	Olfr608	MOR26-3	olfactory receptor 608	protein-coding
mm_19562.1	chr2	99573922	99573923	-	1	NA	Intergenic	MLT1D|LTR|ERVL-MaLR	-2050826	NM_009020	19374	Mm.4988	NM_009020	ENSMUSG00000032864	Rag2	Rag-2	recombination activating gene 2	protein-coding
mm_78460.1	chr9	32376984	32376985	+	1	NA	intron (NM_019659, intron 1 of 1)	intron (NM_019659, intron 1 of 1)	4566	NM_019659	56379	Mm.390168	NM_019659	ENSMUSG00000041248	Kcnj1	Kir1.1|ROMK|Romk2	potassium inwardly-rectifying channel, subfamily J, member 1	protein-coding
mm_137495.1	chr17	26952862	26952878	+	1	NA	intron (NM_001281491, intron 4 of 18)	intron (NM_001281491, intron 4 of 18)	-4751	NR_037244	100526534		NR_037244	ENSMUSG00000093118	Mir3083	mir-3083|mmu-mir-3083	microRNA 3083	ncRNA
mm_131258.1	chr16	10788305	10788350	+	1	NA	exon (NM_013694, exon 1 of 2)	exon (NM_013694, exon 1 of 2)	328	NM_013694	21959	Mm.206798	NM_013694	ENSMUSG00000043050	Tnp2	TP2|Tp-2	transition protein 2	protein-coding
mm_19724.1	chr2	104491333	104491336	-	1	NA	intron (NM_010434, intron 1 of 15)	intron (NM_010434, intron 1 of 15)	3155	NM_010434	15259	Mm.257925	NM_010434	ENSMUSG00000027177	Hipk3	DYRK6|FIST3|PKY|mir-1902	homeodomain interacting protein kinase 3	protein-coding
mm_57786.1	chr6	129269593	129269593	-	1	NA	exon (NM_001033122, exon 4 of 5)	exon (NM_001033122, exon 4 of 5)	5776	NM_001033122	12515	Mm.74745	NM_001033122	ENSMUSG00000030156	Cd69	5830438K24Rik|AI452015|AIM|VEA	CD69 antigen	protein-coding
mm_51188.1	chr6	70965918	70965941	+	1	NA	Intergenic	RMER17C|LTR|ERVK	9323	NM_001101464	232077	Mm.297656	NM_001101464	ENSMUSG00000055874	Foxi3	-	forkhead box I3	protein-coding
mm_58510.1	chr7	4119599	4119609	+	1	NA	promoter-TSS (NM_001109765)	promoter-TSS (NM_001109765)	74	NM_001001454	57776	Mm.29729	NM_021324	ENSMUSG00000030428	Ttyh1	4930459B04Rik|6330408P11Rik|TTY1|mTTY1|tty	tweety family member 1	protein-coding
mm_60559.1	chr7	44481295	44481305	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-3217	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_58354.1	chr6	147675706	147675710	-	1	NA	Intergenic	Intergenic	-14533	NR_033636	100039727	Mm.396220	NR_033636	ENSMUSG00000085077	1700049E15Rik	Gm15761|OTTMUSG00000026044	RIKEN cDNA 1700049E15 gene	ncRNA
mm_52667.1	chr6	117906898	117906922	+	1	NA	promoter-TSS (NM_001166429)	intron (NM_133834, intron 1 of 3)	128	NM_133834	98758	Mm.422979	NM_133834	ENSMUSG00000042079	Hnrnpf	4833420I20Rik|AA407306|Hnrpf	heterogeneous nuclear ribonucleoprotein F	protein-coding
mm_150854.1	chr19	45005657	45005684	+	1	NA	promoter-TSS (NM_153796)	promoter-TSS (NM_153796)	772	NM_053164	94067	Mm.44174	NM_053164	ENSMUSG00000025208	Mrpl43	4930442D21Rik|bMRP36a	mitochondrial ribosomal protein L43	protein-coding
mm_90138.1	chr10	117982903	117982908	+	1	NA	Intergenic	Intergenic	57446	NR_045342	71067	Mm.410793	NR_045342		4933411E08Rik	-	RIKEN cDNA 4933411E08 gene	ncRNA
mm_90432.1	chr10	127596211	127596248	+	1	NA	intron (NM_008512, intron 6 of 88)	intron (NM_008512, intron 6 of 88)	24919	NM_008512	16971	Mm.271854	NM_008512	ENSMUSG00000040249	Lrp1	A2mr|AI316852|CD91|Lrp|b2b1554Clo	low density lipoprotein receptor-related protein 1	protein-coding
mm_44832.1	chr5	33997582	33997589	-	1	NA	intron (NM_001001985, intron 1 of 2)	CpG	1601	NM_001001985	269642	Mm.274610	NM_001001985	ENSMUSG00000048142	Nat8l	1110038O08Rik|Shati	N-acetyltransferase 8-like	protein-coding
mm_112351.1	chr12	118301430	118301458	-	1	NA	promoter-TSS (NM_009239)	promoter-TSS (NM_009239)	-4	NM_001166385	20688	Mm.34699	NM_009239	ENSMUSG00000025323	Sp4	5730497N03Rik|HF-1b|HF1-b	trans-acting transcription factor 4	protein-coding
mm_13002.1	chr2	90890251	90890263	+	1	NA	exon (NM_026161, exon 2 of 2)	exon (NM_026161, exon 2 of 2)	4471	NM_026161	67445	Mm.258993	NM_026161	ENSMUSG00000040794	C1qtnf4	0710001E10Rik|9430004J15Rik|CTRP4	C1q and tumor necrosis factor related protein 4	protein-coding
mm_94975.1	chr11	31545871	31545891	+	1	NA	Intergenic	RLTR10D2|LTR|ERVK	125981	NM_001024919	69556	Mm.34183	NM_001024919	ENSMUSG00000044502	Bod1	2310022M17Rik|BOD2.1|Fam44b	biorientation of chromosomes in cell division 1	protein-coding
mm_53123.1	chr6	125122471	125122504	+	1	NA	exon (NM_145979, exon 34 of 39)	exon (NM_145979, exon 34 of 39)	-9396	NM_138747	110109	Mm.29203	NM_138747	ENSMUSG00000038279	Nop2	120kDa|A530002O17|Nol1	NOP2 nucleolar protein	protein-coding
mm_98414.1	chr11	94507489	94507500	+	1	NA	intron (NM_170671, intron 12 of 18)	intron (NM_170671, intron 12 of 18)	-7520	NM_027984	71889	Mm.248620	NM_027984	ENSMUSG00000010080	Epn3	2310022G12Rik	epsin 3	protein-coding
mm_100792.1	chr11	4939710	4939724	-	1	NA	exon (NM_010904, exon 4 of 4)	exon (NM_010904, exon 4 of 4)	-7804	NM_001243043	11764	Mm.274816	NM_007454	ENSMUSG00000009090	Ap1b1	Adtb1|b2b1660Clo	adaptor protein complex AP-1, beta 1 subunit	protein-coding
mm_10072.1	chr1	194774884	194774914	-	1	NA	intron (NM_008882, intron 12 of 31)	ORR1A3|LTR|ERVL-MaLR	155070	NM_008882	18845	Mm.2251	NM_008882	ENSMUSG00000026640	Plxna2	2810428A13Rik|AA589422|AW457381|OCT|PlexA2|Plxn2|mKIAA0463	plexin A2	protein-coding
mm_31316.1	chr4	46138530	46138558	+	1	NA	promoter-TSS (NM_173033)	promoter-TSS (NM_173033)	33	NM_001033201	433702	Mm.389536	NM_001033201	ENSMUSG00000028330	Ncbp1	AU014645|AW538051|CBP80	nuclear cap binding protein subunit 1	protein-coding
mm_173156.1	chrX	35812812	35812819	+	1	NA	Intergenic	BGLII|LTR|ERVK	-76017	NM_001009947	75974	Mm.32873	NM_177745	ENSMUSG00000031093	Dock11	5033414A21Rik|8030476J24|Zizimin2|sph238	dedicator of cytokinesis 11	protein-coding
mm_112475.1	chr13	5868639	5868656	+	1	NA	3' UTR (NM_011803, exon 4 of 4)	3' UTR (NM_011803, exon 4 of 4)	7158	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_106140.1	chr11	116494582	116494594	-	1	NA	Intergenic	RSINE1|SINE|B4	-4242	NM_026364	67763	Mm.25125	NM_026364	ENSMUSG00000015869	Prpsap1	5730409F23Rik|PAP39	phosphoribosyl pyrophosphate synthetase-associated protein 1	protein-coding
mm_70941.1	chr8	26119362	26119368	+	1	NA	promoter-TSS (NM_029965)	promoter-TSS (NM_029965)	-15	NM_029965	77733	Mm.291906	NM_029965	ENSMUSG00000013878	Rnf170	6720407G21Rik|AI481227	ring finger protein 170	protein-coding
mm_116458.1	chr13	43304132	43304146	-	1	NA	promoter-TSS (NM_001033399)	promoter-TSS (NM_001033399)	33	NM_001033399	328232	Mm.441399	NM_001033399	ENSMUSG00000051335	Gfod1	9630032O13|AI850995	glucose-fructose oxidoreductase domain containing 1	protein-coding
mm_50585.1	chr6	49056724	49056736	+	1	NA	3' UTR (NM_053110, exon 11 of 11)	3' UTR (NM_053110, exon 11 of 11)	-17065	NM_029353	75593	Mm.439947	NM_029353	ENSMUSG00000029815	Malsu1	2410003K15Rik|Matsu1	mitochondrial assembly of ribosomal large subunit 1	protein-coding
mm_18875.1	chr2	76259218	76259229	-	1	NA	intron (NM_001081033, intron 2 of 19)	intron (NM_001081033, intron 2 of 19)	79430	NM_001081033	241489	Mm.246613	NM_001081033	ENSMUSG00000075270	Pde11a	6330414F14Rik|A630086N24Rik|Gm350|PDE11A1	phosphodiesterase 11A	protein-coding
mm_162376.1	chr1	70220748	70220751	+	1	NA	intron (NM_029160, intron 11 of 16)	intron (NM_029160, intron 11 of 16)	269134	NM_025728	66722	Mm.440554	NM_025728	ENSMUSG00000053153	Spag16	4921511D23Rik|4930524F24Rik|4930585K05Rik|AV261009|Pf20|Wdr29	sperm associated antigen 16	protein-coding
mm_158246.1	chrX	107397316	107397326	-	1	NA	3' UTR (NM_008409, exon 6 of 6)	3' UTR (NM_008409, exon 6 of 6)	6039	NM_008409	16431	Mm.193	NM_008409	ENSMUSG00000031239	Itm2a	AW108051|Bricd2a|E25|Itm2	integral membrane protein 2A	protein-coding
mm_172594.1	chr8	129279261	129279262	-	1	NA	intron (NM_001346808, intron 1 of 3)	intron (NM_001346808, intron 1 of 3)	15631	NR_144501	102635552		NM_001346808		Gm32856	-	predicted gene, 32856	protein-coding
mm_132488.1	chr16	36924653	36924668	+	1	NA	exon (NM_030035, exon 15 of 22)	exon (NM_030035, exon 15 of 22)	-10323	NM_008225	15163	Mm.4091	NM_008225	ENSMUSG00000022831	Hcls1	AW213261|HS1	hematopoietic cell specific Lyn substrate 1	protein-coding
mm_126847.1	chr15	89089074	89089111	+	1	NA	promoter-TSS (NM_027905)	promoter-TSS (NM_027905)	-15	NM_027905	223776	Mm.44763	NM_027905	ENSMUSG00000035757	Selenoo	1300018J18Rik|Selo	selenoprotein O	protein-coding
mm_4524.1	chr1	175632097	175632101	+	1	NA	promoter-TSS (NM_133809)	promoter-TSS (NM_133809)	-94	NM_133809	98256	Mm.27217	NM_133809	ENSMUSG00000039783	Kmo	AI046660	kynurenine 3-monooxygenase (kynurenine 3-hydroxylase)	protein-coding
mm_67283.1	chr7	78623324	78623343	-	1	NA	intron (NR_015542, intron 8 of 10)	intron (NR_015542, intron 8 of 10)	-45495	NM_182809	18213	Mm.33496	NM_008746	ENSMUSG00000059146	Ntrk3	AW125844|Ntrk3_tv3|TrkC	neurotrophic tyrosine kinase, receptor, type 3	protein-coding
mm_20643.1	chr2	132029189	132029205	-	1	NA	intron (NM_175445, intron 1 of 10)	CpG	791	NM_175445	215653	Mm.204737	NM_175445	ENSMUSG00000027339	Rassf2	3830431H01Rik|9030412M04Rik|AI852669|AW495050	Ras association (RalGDS/AF-6) domain family member 2	protein-coding
mm_87469.1	chr10	51491506	51491533	+	1	NA	exon (NM_013532, exon 3 of 9)	exon (NM_013532, exon 3 of 9)	621	NM_013532	14728	Mm.34408	NM_013532	ENSMUSG00000062593	Lilrb4a	CD85K|Gp49b|HM18|ILT3|LIR-5|Lilrb4|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4A	protein-coding
mm_23615.1	chr3	65531666	65531695	+	1	NA	exon (NM_178892, exon 2 of 6)	exon (NM_178892, exon 2 of 6)	-2266	NR_027955	71004	Mm.475465	NM_001033527	ENSMUSG00000074580	4931440P22Rik	-	RIKEN cDNA 4931440P22 gene	ncRNA
mm_144463.1	chr18	23497549	23497608	+	1	NA	promoter-TSS (NM_001285810)	promoter-TSS (NM_001285810)	96	NM_001285810	13527	Mm.94371	NM_010087	ENSMUSG00000024302	Dtna	2210407P21Rik|DTN-A|Dtn|Gm19389|a-DB-1|adbn	dystrobrevin alpha	protein-coding
mm_80400.1	chr9	77636470	77636480	+	1	NA	promoter-TSS (NM_172925)	promoter-TSS (NM_172925)	-257	NM_172925	244923	Mm.138238	NM_172925	ENSMUSG00000044938	Klhl31	9830147P19Rik|D930047P17Rik|Kbtbd1	kelch-like 31	protein-coding
mm_56502.1	chr6	99338280	99338290	-	1	NA	intron (NM_001347345, intron 2 of 19)	intron (NM_001347345, intron 2 of 19)	-71770	NM_001197321	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_127087.1	chr15	97741018	97741025	+	1	NA	Intergenic	Intergenic	-9616	NM_001168693	19011	Mm.1001	NM_008902	ENSMUSG00000022468	Endou	Pp11r|Tcl-30	endonuclease, polyU-specific	protein-coding
mm_157270.1	chrX	20146125	20146132	-	1	NA	intron (NM_177353, intron 12 of 16)	Lx|LINE|L1	86558	NM_021715	60322	Mm.44827	NM_021715	ENSMUSG00000037347	Chst7	2600013M07Rik|C6ST-2|GST5|Gn6st-4|glcNAc6ST-4	carbohydrate (N-acetylglucosamino) sulfotransferase 7	protein-coding
mm_160341.1	chr8	18978149	18978149	-	1	NA	promoter-TSS (NM_183039)	promoter-TSS (NM_183039)	-33	NM_183039	360217	Mm.271560	NM_183039	ENSMUSG00000053678	Defb40	BD-40	defensin beta 40	protein-coding
mm_7699.1	chr1	130422720	130422739	-	1	NA	intron (NM_001317361, intron 1 of 7)	intron (NM_001317361, intron 1 of 7)	314	NM_007827	13137	Mm.436759	NM_007827	ENSMUSG00000026401	Cd55b	AI323748|Daf|Daf-TM|Daf2|TM-DAF	CD55 molecule, decay accelerating factor for complement B	protein-coding
mm_148693.1	chr19	5741682	5741701	+	1	NA	5' UTR (NM_008520, exon 2 of 28)	5' UTR (NM_008520, exon 2 of 28)	787	NM_008520	16998	Mm.182396	NM_008520	ENSMUSG00000024940	Ltbp3	Ltbp2|mFLJ00070	latent transforming growth factor beta binding protein 3	protein-coding
mm_133958.1	chr16	4077779	4077831	-	1	NA	promoter-TSS (NM_026508)	promoter-TSS (NM_026508)	5	NM_026508	68015	Mm.123366	NM_026508	ENSMUSG00000005981	Trap1	2410002K23Rik|HSP75	TNF receptor-associated protein 1	protein-coding
mm_130367.1	chr15	97803764	97803776	-	1	NA	intron (NM_001204275, intron 12 of 24)	RLTR20B5_MM|LTR|ERVK	11093	NM_001204281	56233	Mm.384027	NM_019572	ENSMUSG00000022475	Hdac7	5830434K02Rik|HD7|HD7a|Hdac7a|mFLJ00062	histone deacetylase 7	protein-coding
mm_41871.1	chr5	104508339	104508392	+	1	NA	promoter-TSS (NM_001166581)	promoter-TSS (NM_001166581)	13	NM_001166581	100042165	Mm.482189	NM_001166581	ENSMUSG00000079065	BC005561	-	cDNA sequence BC005561	protein-coding
mm_125164.1	chr15	31268273	31268290	+	1	NA	intron (NM_146057, intron 2 of 3)	intron (NM_146057, intron 2 of 3)	43896	NM_146057	223453	Mm.222867	NM_146057	ENSMUSG00000039168	Dap	4921531N22Rik|AI789753|AU040360	death-associated protein	protein-coding
mm_4802.1	chr1	185247957	185247988	+	1	NA	intron (NM_001163754, intron 11 of 34)	intron (NM_001163754, intron 11 of 34)	4997	NR_035529	100316737		NR_035529	ENSMUSG00000105770	Mir664	mir-664|mmu-mir-664	microRNA 664	ncRNA
mm_72317.1	chr8	78213293	78213371	+	1	NA	promoter-TSS (NM_183096)	promoter-TSS (NM_183096)	-10	NM_183096	73301	Mm.61243	NM_183096	ENSMUSG00000037101	Ttc29	1700031F13Rik	tetratricopeptide repeat domain 29	protein-coding
mm_60613.1	chr7	44591194	44591204	+	1	NA	exon (NM_001290682, exon 1 of 5)	exon (NM_001290682, exon 1 of 5)	313	NM_001290682	16504	Mm.40312	NM_008422	ENSMUSG00000062785	Kcnc3	KShIIID|Kcr2-3|Kv3.3	potassium voltage gated channel, Shaw-related subfamily, member 3	protein-coding
mm_138830.1	chr17	39848151	39848190	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	5173	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_99954.1	chr11	112825164	112825190	+	1	NA	promoter-TSS (NR_130164)	promoter-TSS (NR_130164)	-49	NR_130164	76393	Mm.86795	NR_130164		1700012H19Rik	-	RIKEN cDNA 1700012H19 gene	ncRNA
mm_55265.1	chr6	53820510	53820526	-	1	NA	5' UTR (NM_025817, exon 1 of 1)	5' UTR (NM_025817, exon 1 of 1)	307	NM_025817	66873	Mm.422727	NM_025817	ENSMUSG00000043496	Tril	1200009O22Rik|AI316813|mKIAA0644	TLR4 interactor with leucine-rich repeats	protein-coding
mm_131502.1	chr16	17419276	17419295	+	1	NA	exon (NM_023348, exon 2 of 5)	exon (NM_023348, exon 2 of 5)	-12971	NM_001001983	224020	Mm.5718	NM_001001983	ENSMUSG00000041720	Pi4ka	Pik4ca	phosphatidylinositol 4-kinase, catalytic, alpha polypeptide	protein-coding
mm_88104.1	chr10	69096096	69096112	+	1	NA	Intergenic	Intergenic	-112448	NM_001252636	69288	Mm.26659	NM_001081347	ENSMUSG00000019944	Rhobtb1	1700008H16Rik|3110048G13Rik|AI173445|AI573858|AV350930	Rho-related BTB domain containing 1	protein-coding
mm_54985.1	chr6	48746095	48746104	-	1	NA	promoter-TSS (NM_175035)	promoter-TSS (NM_175035)	-98	NM_175035	317757	Mm.455917	NM_175035	ENSMUSG00000043505	Gimap5	D630024P16|E230026N22Rik	GTPase, IMAP family member 5	protein-coding
mm_46206.1	chr5	98031432	98031449	-	1	NA	promoter-TSS (NM_133738)	promoter-TSS (NM_133738)	-478	NM_133738	71914	Mm.24842	NM_133738	ENSMUSG00000029338	Antxr2	2310046B19Rik|AW561899|CMG-2|CMG2|cI-35	anthrax toxin receptor 2	protein-coding
mm_145713.1	chr18	62951212	62951212	+	1	NA	intron (NM_133237, intron 4 of 4)	intron (NM_133237, intron 4 of 4)	-26704	NM_028017	108123	Mm.292687	NM_028017	ENSMUSG00000024581	Napg	2400003O04Rik|SNARE	N-ethylmaleimide sensitive fusion protein attachment protein gamma	protein-coding
mm_17255.1	chr2	25822113	25822116	-	1	NA	Intergenic	Intergenic	-1039	NM_029959	77704	Mm.159974	NM_029959	ENSMUSG00000023210	Lcn9	9230102I19Rik	lipocalin 9	protein-coding
mm_103506.1	chr11	76608544	76608546	-	1	NA	Intergenic	B1_Mur2|SINE|Alu	-30806	NM_198894	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_30453.1	chr3	153905856	153905862	-	1	NA	promoter-TSS (NM_001282054)	promoter-TSS (NM_001282054)	279	NM_031870	55993	Mm.272226	NM_031870	ENSMUSG00000005493	Msh4	4930485C04Rik|AV144863|mMsh4	mutS homolog 4	protein-coding
mm_35285.1	chr4	21685783	21685805	-	1	NA	exon (NM_001080771, exon 1 of 4)	exon (NM_001080771, exon 1 of 4)	169	NM_001080771	230025	Mm.208541	NM_001080771	ENSMUSG00000040478	Prdm13	-	PR domain containing 13	protein-coding
mm_54781.1	chr6	41543546	41543555	-	1	NA	Intergenic	Intergenic	21774	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_70070.1	chr7	142653050	142653068	-	1	NA	3' UTR (NM_010514, exon 4 of 4)	3' UTR (NM_010514, exon 4 of 4)	1937	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_121299.1	chr14	105589568	105589578	+	1	NA	promoter-TSS (NR_102319)	promoter-TSS (NR_102319)	24	NR_102319	380930	Mm.427836	NR_102319		9330188P03Rik	Gm1589|mgt-6	RIKEN cDNA 9330188P03 gene	ncRNA
mm_172158.1	chr6	43609207	43609219	+	1	NA	intron (NM_001311111, intron 3 of 7)	RLTR34C_MM|LTR|ERVK	57065	NM_001311111	29807	Mm.320979	NM_013861	ENSMUSG00000029735	Tpk1	-	thiamine pyrophosphokinase	protein-coding
mm_98387.1	chr11	94210440	94210454	+	1	NA	Intergenic	CpG	-1007	NM_009427	22057	Mm.259673	NM_009427	ENSMUSG00000037573	Tob1	Tob|Trob	transducer of ErbB-2.1	protein-coding
mm_70389.1	chr8	10899916	10899928	+	1	NA	promoter-TSS (NR_102285)	promoter-TSS (NR_102285)	0	NR_102285	71624	Mm.139075	NR_102285	ENSMUSG00000109089	4833411C07Rik	-	RIKEN cDNA 4833411C07 gene	ncRNA
mm_95482.1	chr11	51263122	51263197	+	1	NA	promoter-TSS (NM_177567)	promoter-TSS (NM_177567)	45	NM_007714	12750	Mm.239354	NM_007714	ENSMUSG00000020385	Clk4	AI987988|C85119	CDC like kinase 4	protein-coding
mm_102910.1	chr11	69560225	69560235	-	1	NA	promoter-TSS (NM_007911)	promoter-TSS (NM_007911)	7	NM_007911	13643	Mm.249637	NM_007911	ENSMUSG00000003934	Efnb3	EFL-6|ELF-3|Elk-L3|Epl8|LERK-8|NLERK-2	ephrin B3	protein-coding
mm_41014.1	chr5	81021743	81021780	+	1	NA	5' UTR (NM_198702, exon 1 of 28)	5' UTR (NM_198702, exon 1 of 28)	168	NM_198702	319387	Mm.273631	NM_198702	ENSMUSG00000037605	Adgrl3	5430402I23Rik|CIRL-3|D130075K09Rik|Gm1379|LEC3|Lphn3|mKIAA0768	adhesion G protein-coupled receptor L3	protein-coding
mm_131557.1	chr16	18052900	18052925	+	1	NA	promoter-TSS (NM_010047)	promoter-TSS (NM_010047)	52	NM_010047	13353	Mm.27155	NM_010047	ENSMUSG00000003531	Dgcr6	-	DiGeorge syndrome critical region gene 6	protein-coding
mm_9554.1	chr1	173937845	173937852	-	1	NA	exon (NM_001302650, exon 3 of 9)	exon (NM_001302650, exon 3 of 9)	4644	NM_001302649	15950	Mm.463437	NM_008328	ENSMUSG00000039997	Ifi203	Mndal	interferon activated gene 203	protein-coding
mm_52125.1	chr6	97941972	97941979	+	1	NA	intron (NM_001113198, intron 2 of 9)	intron (NM_001113198, intron 2 of 9)	12158	NM_001178049	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_115011.1	chr13	98354389	98354399	+	1	NA	5' UTR (NM_008242, exon 1 of 1)	5' UTR (NM_008242, exon 1 of 1)	149	NM_008242	15229	Mm.347441	NM_008242	ENSMUSG00000078302	Foxd1	AI385632|BF-2|FREAC4|Hfh10|Hfhbf2	forkhead box D1	protein-coding
mm_83467.1	chr9	45269136	45269156	-	1	NA	promoter-TSS (NM_001324486)	promoter-TSS (NM_001324486)	3	NM_008348	16154	Mm.379327	NM_008348	ENSMUSG00000032089	Il10ra	AW553859|CDw210|CDw210a|IL-10R1|IL-10RA|Il10r|mIL-10R	interleukin 10 receptor, alpha	protein-coding
mm_75993.1	chr8	72421440	72421483	-	1	NA	promoter-TSS (NM_007944)	promoter-TSS (NM_007944)	13	NM_001122832	13859	Mm.288894	NM_007944	ENSMUSG00000006276	Eps15l1	9830147J04Rik|AI593686|Eps15-rs|Eps15R	epidermal growth factor receptor pathway substrate 15-like 1	protein-coding
mm_144027.1	chr17	90036776	90036786	-	1	NA	3' UTR (NM_001347419, exon 3 of 3)	3' UTR (NM_001347419, exon 3 of 3)	51587	NM_001346962	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_68451.1	chr7	110061320	110061341	-	1	NA	promoter-TSS (NM_009281)	promoter-TSS (NM_009281)	-372	NM_009281	20841	Mm.10815	NM_009281	ENSMUSG00000061079	Zfp143	AA959806|AU015869|D7Ertd805e|KRAB14|SBF|Staf|Zfp79|Zfp80-rs1|Znf143|pHZ-1	zinc finger protein 143	protein-coding
mm_53120.1	chr6	125103431	125103438	+	1	NA	intron (NM_001346610, intron 10 of 38)	intron (NM_001346610, intron 10 of 38)	6410	NR_106012	102466272		NR_106012	ENSMUSG00000098762	Mir7045	Gm27758|mmu-mir-7045	microRNA 7045	ncRNA
mm_106856.1	chr12	8009146	8009177	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	31484	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_37280.1	chr4	118954848	118954858	-	1	NA	promoter-TSS (NR_137285)	promoter-TSS (NR_137285)	66	NR_137285	100038571	Mm.426714	NR_137285	ENSMUSG00000073765	Gm12863	OTTMUSG00000008822	predicted gene 12863	ncRNA
mm_93622.1	chr10	117277887	117277930	-	1	NA	3' UTR (NM_017372, exon 4 of 4)	3' UTR (NM_017372, exon 4 of 4)	4364	NM_017372	17105	Mm.45436	NM_017372	ENSMUSG00000069516	Lyz2	AI326280|Lys|Lysm|Lyzf2|Lyzs|Lzm|Lzm-s1|Lzp	lysozyme 2	protein-coding
mm_20440.1	chr2	129309091	129309101	-	1	NA	exon (NM_010554, exon 2 of 7)	exon (NM_010554, exon 2 of 7)	876	NM_010554	16175	Mm.15534	NM_010554	ENSMUSG00000027399	Il1a	Il-1a	interleukin 1 alpha	protein-coding
mm_57742.1	chr6	129049209	129049219	-	1	NA	intron (NR_024262, intron 1 of 5)	intron (NR_024262, intron 1 of 5)	3313	NR_024263	232408	Mm.259262	NM_153094	ENSMUSG00000030154	Klrb1f	A630024B12Rik|Nkr-p1f|Nkrp1-f|Nkrp1f	killer cell lectin-like receptor subfamily B member 1F	protein-coding
mm_154900.1	chrX	20925708	20925733	+	1	NA	exon (NM_008823, exon 9 of 9)	exon (NM_008823, exon 9 of 9)	-4802	NM_013680	20964	Mm.439844	NM_013680	ENSMUSG00000037217	Syn1	Syn-1|Syn1-S	synapsin I	protein-coding
mm_11220.1	chr2	29724028	29724029	+	1	NA	intron (NM_001039087, intron 14 of 25)	intron (NM_001039087, intron 14 of 25)	-37500	NM_001177392	433416	Mm.330112	NM_001034887	ENSMUSG00000075425	Gm13547	OTTMUSG00000012686	predicted gene 13547	protein-coding
mm_101965.1	chr11	50307642	50307671	-	1	NA	exon (NM_001110500, exon 7 of 15)	exon (NM_001110500, exon 7 of 15)	-15320	NM_175334	103806	Mm.51116	NM_175334	ENSMUSG00000050567	Maml1	AI644666|AW743257|D930008C07Rik|Mam-1|Mam1|mKIAA0200	mastermind like 1 (Drosophila)	protein-coding
mm_108289.1	chr12	79141115	79141136	+	1	NA	intron (NM_009705, intron 2 of 7)	intron (NM_009705, intron 2 of 7)	10337	NM_009705	11847	Mm.3506	NM_009705	ENSMUSG00000021125	Arg2	AII|AU022422	arginase type II	protein-coding
mm_155574.1	chrX	77511223	77511229	+	1	NA	promoter-TSS (NM_020601)	promoter-TSS (NM_020601)	-1	NM_020601	21372	Mm.258476	NM_020601	ENSMUSG00000025246	Tbl1x	5330429M20|Tbl1	transducin (beta)-like 1 X-linked	protein-coding
mm_83743.1	chr9	51102127	51102131	-	1	NA	promoter-TSS (NM_177702)	promoter-TSS (NM_177702)	-51	NM_177702	235345	Mm.72828	NM_177702	ENSMUSG00000032057	4833427G06Rik	-	RIKEN cDNA 4833427G06 gene	protein-coding
mm_24153.1	chr3	88364549	88364606	+	1	NA	promoter-TSS (NM_198410)	promoter-TSS (NM_198410)	-12	NM_198410	68957	Mm.441486	NM_198410	ENSMUSG00000041423	Paqr6	1500001B10Rik	progestin and adipoQ receptor family member VI	protein-coding
mm_30704.1	chr4	11810284	11810305	+	1	NA	exon (NM_019753, exon 15 of 18)	exon (NM_019753, exon 15 of 18)	52137	NM_019753	12557	Mm.33402	NM_019753	ENSMUSG00000028217	Cdh17	HPT-1|HPT-1/LI	cadherin 17	protein-coding
mm_118507.1	chr14	13999994	13999996	+	1	NA	Intergenic	Intergenic	-12496	NM_139227	246103	Mm.133625	NM_139227	ENSMUSG00000021738	Atxn7	A430107N12Rik|AI627028|Sca7|ataxin-7	ataxin 7	protein-coding
mm_48370.1	chr5	139478556	139478571	-	1	NA	exon (NM_001159908, exon 4 of 7)	exon (NM_001159908, exon 4 of 7)	5928	NM_133349	100494	Mm.24521	NM_133349	ENSMUSG00000053581	Zfand2a	AA407930|AU016206|Airap	zinc finger, AN1-type domain 2A	protein-coding
mm_32615.1	chr4	114163438	114163448	+	1	NA	promoter-TSS (NM_177669)	promoter-TSS (NM_177669)	59	NM_001166027	230623	Mm.124482	NM_177669	ENSMUSG00000057977	Skint11	A630098G03Rik|Gm569	selection and upkeep of intraepithelial T cells 11	protein-coding
mm_29594.1	chr3	119745809	119745812	-	1	NA	intron (NM_001310711, intron 7 of 13)	intron (NM_001310711, intron 7 of 13)	37578	NM_001310711	56195	Mm.29966	NM_019550	ENSMUSG00000028134	Ptbp2	Ptb2|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding
mm_69065.1	chr7	126922848	126922886	-	1	NA	Intergenic	Intergenic	-6012	NM_172747	233877	Mm.245897	NM_172747	ENSMUSG00000030685	Kctd13	1500003N18Rik|AV259508|PDIP1alpha|Pdip1|Poldip1	potassium channel tetramerisation domain containing 13	protein-coding
mm_12242.1	chr2	68861565	68861575	+	1	NA	5' UTR (NM_001347161, exon 1 of 11)	5' UTR (NM_001347161, exon 1 of 11)	129	NM_001347161	241447	Mm.222222	NM_172856	ENSMUSG00000027035	Cers6	4732462C07Rik|AW544719|Lass6|T1L	ceramide synthase 6	protein-coding
mm_147114.1	chr18	35722331	35722381	-	1	NA	promoter-TSS (NM_001033141)	promoter-TSS (NM_001033141)	-865	NM_001033141	68545	Mm.329362	NM_001033141	ENSMUSG00000073599	Ecscr	1110006O17Rik|ARIA	endothelial cell surface expressed chemotaxis and apoptosis regulator	protein-coding
mm_60600.1	chr7	44531535	44531578	+	1	NA	intron (NM_019866, intron 1 of 5)	intron (NM_019866, intron 1 of 5)	515	NM_019866	272382	Mm.8012	NM_019866	ENSMUSG00000008193	Spib	Spi-B	Spi-B transcription factor (Spi-1/PU.1 related)	protein-coding
mm_22620.1	chr3	14641761	14641797	+	1	NA	promoter-TSS (NM_024495)	promoter-TSS (NM_024495)	52	NM_024495	71934	Mm.158776	NM_024495	ENSMUSG00000027555	Car13	2310075C21Rik|Ca13	carbonic anhydrase 13	protein-coding
mm_17929.1	chr2	35462719	35462721	-	1	NA	Intergenic	Intergenic	-1271	NM_001145821	14594	Mm.281124	NM_010283	ENSMUSG00000035778	Ggta1	AW108479|GALT|Gal|Ggta|Ggta-1|alpha Gal|alpha3GalT	glycoprotein galactosyltransferase alpha 1, 3	protein-coding
mm_146355.1	chr18	82575169	82575187	+	1	NA	exon (NM_010777, exon 6 of 7)	exon (NM_010777, exon 6 of 7)	20670	NM_001025254	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_140152.1	chr17	80127642	80127684	+	1	NA	5' UTR (NM_176963, exon 1 of 7)	5' UTR (NM_176963, exon 1 of 7)	192	NM_176963	319625	Mm.29098	NM_176963	ENSMUSG00000035473	Galm	A530057M15Rik|AU015645|AU020959	galactose mutarotase	protein-coding
mm_80363.1	chr9	75306291	75306339	+	1	NA	promoter-TSS (NM_010313)	promoter-TSS (NM_010313)	27	NM_010313	14697	Mm.17604	NM_010313	ENSMUSG00000032192	Gnb5	GBS|Gbeta5|flr	guanine nucleotide binding protein (G protein), beta 5	protein-coding
mm_106117.1	chr11	116359106	116359126	-	1	NA	intron (NM_027258, intron 6 of 18)	intron (NM_027258, intron 6 of 18)	-23762	NM_008240	15223	Mm.378938	NM_008240	ENSMUSG00000034227	Foxj1	FKHL-13|HFH-4|Hfh4	forkhead box J1	protein-coding
mm_60767.1	chr7	45554916	45554922	+	1	NA	promoter-TSS (NM_025330)	promoter-TSS (NM_025330)	-9	NM_025330	66065	Mm.285710	NM_025330	ENSMUSG00000030825	Hsd17b14	0610039E24Rik|Dhrs10|retSDR3	hydroxysteroid (17-beta) dehydrogenase 14	protein-coding
mm_40592.1	chr5	64230355	64230376	+	1	NA	promoter-TSS (NM_001289514)	promoter-TSS (NM_001289514)	8	NM_001289514	57915	Mm.286353	NM_019636	ENSMUSG00000029174	Tbc1d1	1110062G02Rik|AI385682|AW555803|Nob1|Nobq1|Tbc1|mKIAA1108	TBC1 domain family, member 1	protein-coding
mm_83235.1	chr9	42399315	42399325	-	1	NA	intron (NM_009347, intron 1 of 23)	intron (NM_009347, intron 1 of 23)	609	NM_009347	21683	Mm.42209	NM_009347	ENSMUSG00000037705	Tecta	Tctna	tectorin alpha	protein-coding
mm_8460.1	chr1	153186143	153186155	-	1	NA	intron (NM_008485, intron 1 of 23)	CpG	298	NM_008485	16782	Mm.329272	NM_008485	ENSMUSG00000026479	Lamc2	AA589349	laminin, gamma 2	protein-coding
mm_160333.1	chr8	12573148	12573148	+	1	NA	promoter-TSS (NM_024279)	promoter-TSS (NM_024279)	99	NM_024279	78634	Mm.116871	NM_024279	ENSMUSG00000010435	Spaca7	1700094C09Rik	sperm acrosome associated 7	protein-coding
mm_88562.1	chr10	79637300	79637330	+	1	NA	intron (NM_001024539, intron 1 of 12)	CpG	603	NM_001024539	216148	Mm.39424	NM_001024539	ENSMUSG00000020312	Shc2	6720466E06|SCK|ShcB|Sli	SHC (Src homology 2 domain containing) transforming protein 2	protein-coding
mm_126156.1	chr15	78409955	78410038	+	1	NA	intron (NM_138670, intron 1 of 2)	intron (NM_138670, intron 1 of 2)	2892	NM_138670	246221	Mm.294215	NM_138670	ENSMUSG00000071711	Mpst	Mst	mercaptopyruvate sulfurtransferase	protein-coding
mm_29141.1	chr3	105900831	105900841	-	1	NA	intron (NM_027025, intron 1 of 6)	intron (NM_027025, intron 1 of 6)	-3585	NM_009631	11542	Mm.235024	NM_009631	ENSMUSG00000000562	Adora3	A3AR|A3R|AA3R|ARA3|Gpcr2	adenosine A3 receptor	protein-coding
mm_32707.1	chr4	116095595	116095622	+	1	NA	intron (NM_153521, intron 7 of 9)	intron (NM_153521, intron 7 of 9)	20339	NM_153521	230654	Mm.3655	NM_153521	ENSMUSG00000028703	Lrrc41	AA409966|AW555107|D630045E04Rik|D730026A16Rik|MUF1	leucine rich repeat containing 41	protein-coding
mm_24817.1	chr3	95625485	95625497	+	1	NA	intron (NM_001026212, intron 1 of 2)	intron (NM_001026212, intron 1 of 2)	511	NM_001026212	56205	Mm.241365	NM_019561	ENSMUSG00000038619	Ensa	1700020C18Rik|2610007F17Rik|AI451924	endosulfine alpha	protein-coding
mm_24205.1	chr3	88621145	88621173	+	1	NA	promoter-TSS (NM_001198913)	promoter-TSS (NM_001198913)	53	NM_008487	16800	Mm.239329	NM_008487	ENSMUSG00000028059	Arhgef2	AA408978|GEF|GEF-H1|GEFH1|LFP40|Lbcl1|Lfc|P40|mKIAA0651	rho/rac guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_10680.1	chr2	21650437	21650439	+	1	NA	intron (NM_001004761, intron 5 of 10)	intron (NM_001004761, intron 5 of 10)	282871	NM_001004761	241263	Mm.166647	NM_175706	ENSMUSG00000045967	Gpr158	5330427M13Rik|mKIAA1136	G protein-coupled receptor 158	protein-coding
mm_17786.1	chr2	32982174	32982185	-	1	NA	promoter-TSS (NM_019488)	promoter-TSS (NM_019488)	-123	NM_019488	56017	Mm.305754	NM_019488	ENSMUSG00000026791	Slc2a8	D2Ertd44e|GLUT8|GlutX1	solute carrier family 2, (facilitated glucose transporter), member 8	protein-coding
mm_111831.1	chr12	107157157	107157171	-	1	NA	Intergenic	L1MA6|LINE|L1	-440840	NR_015512	71033	Mm.159404	NR_015512	ENSMUSG00000085820	4933406K04Rik	4930426M03Rik|4930485I22Rik|4933427G14Rik	RIKEN cDNA 4933406K04 gene	ncRNA
mm_132941.1	chr16	49856597	49856619	+	1	NA	intron (NM_010581, intron 1 of 9)	intron (NM_010581, intron 1 of 9)	954	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_66998.1	chr7	64872960	64872987	-	1	NA	promoter-TSS (NM_023239)	promoter-TSS (NM_023239)	67	NM_023239	66647	Mm.19944	NM_023239	ENSMUSG00000070520	Ndnl2	5730494G16Rik|AI642138|BB044375|HCA4|Mageg1|Nsmce3|mage-g1	necdin-like 2	protein-coding
mm_63812.1	chr7	133747565	133747577	+	1	NA	intron (NM_133941, intron 3 of 11)	intron (NM_133941, intron 3 of 11)	12698	NM_001286030	101437	Mm.199223	NM_133941	ENSMUSG00000030986	Dhx32	3110079L04Rik|4732469F02Rik|AA408140|Ddx32	DEAH (Asp-Glu-Ala-His) box polypeptide 32	protein-coding
mm_56339.1	chr6	92816637	92816655	-	1	NA	intron (NM_175314, intron 19 of 29)	intron (NM_175314, intron 19 of 29)	84795	NM_175314	101401	Mm.158235	NM_175314	ENSMUSG00000030022	Adamts9	1810011L16Rik|8430403M15Rik|AW743315|E030027K14Rik	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 9	protein-coding
mm_38810.1	chr4	148358863	148358871	-	1	NA	Intergenic	Intergenic	-70902	NM_001083342	242748	Mm.33873	NM_001083342	ENSMUSG00000041544	Ptchd2	Disp3|G630052C06Rik|RNDEu-2	patched domain containing 2	protein-coding
mm_21917.1	chr2	166786754	166786792	-	1	NA	Intergenic	CpG	-6994	NM_023815	76367	Mm.330796	NM_023815	ENSMUSG00000042854	Trp53rkb	2810408M09Rik|4933401B08Rik|5630401H01Rik|Nori-2|PRPK|Tp53rk|Trp53rk|Trp53tk|mNori-2p	transformation related protein 53 regulating kinase B	protein-coding
mm_60731.1	chr7	45420940	45420946	+	1	NA	promoter-TSS (NM_008497)	promoter-TSS (NM_008497)	-3	NM_008497	16866	Mm.57061	NM_008497	ENSMUSG00000100916	Lhb	Gm29035|LH|LH-B|LSH-B|LSH-beta	luteinizing hormone beta	protein-coding
mm_103753.1	chr11	80779968	80779984	-	1	NA	promoter-TSS (NM_177390)	promoter-TSS (NM_177390)	49	NM_177390	338367	Mm.151948	NM_177390	ENSMUSG00000035441	Myo1d	9930104H07Rik|AW544947|D11Ertd9e|myosin-1d	myosin ID	protein-coding
mm_169861.1	chr16	33517459	33517469	+	1	NA	promoter-TSS (NM_134251)	promoter-TSS (NM_134251)	-865	NM_134251	171286	Mm.35253	NM_134251	ENSMUSG00000035506	Slc12a8	CCC9|E330020C02Rik	solute carrier family 12 (potassium/chloride transporters), member 8	protein-coding
mm_75169.1	chr8	36730812	36730818	-	1	NA	intron (NM_001194940, intron 5 of 17)	intron (NM_001194940, intron 5 of 17)	2239	NM_001194941	50768	Mm.125155	NM_015802	ENSMUSG00000031523	Dlc1	A730069N07Rik|Arhgap7|HP|STARD12|dlc-1	deleted in liver cancer 1	protein-coding
mm_86322.1	chr9	123021416	123021463	-	1	NA	exon (NM_025339, exon 1 of 3)	exon (NM_025339, exon 1 of 3)	113	NM_001164823	66079	Mm.482265	NM_025339	ENSMUSG00000066233	Tmem42	0610027O18Rik|4933429E06Rik|AV003444|D9Ertd662e	transmembrane protein 42	protein-coding
mm_61237.1	chr7	64754421	64754424	+	1	NA	TTS (NM_001291167)	TTS (NM_001291167)	118618	NM_023239	66647	Mm.19944	NM_023239	ENSMUSG00000070520	Ndnl2	5730494G16Rik|AI642138|BB044375|HCA4|Mageg1|Nsmce3|mage-g1	necdin-like 2	protein-coding
mm_18463.1	chr2	62343818	62343831	-	1	NA	intron (NM_001159543, intron 23 of 24)	intron (NM_001159543, intron 23 of 24)	68407	NM_010074	13482	Mm.1151	NM_010074	ENSMUSG00000035000	Dpp4	Cd26|Dpp-4|THAM	dipeptidylpeptidase 4	protein-coding
mm_41228.1	chr5	88720858	88720876	+	1	NA	promoter-TSS (NM_026735)	promoter-TSS (NM_026735)	-4	NM_026735	68473	Mm.35764	NM_026735	ENSMUSG00000006262	Mob1b	1110003E08Rik|AU015450|B230364F10|Mobkl1a	MOB kinase activator 1B	protein-coding
mm_166555.1	chr6	42397364	42397368	+	1	NA	Intergenic	Intergenic	-2872	NM_001001452	387514	Mm.377921	NM_001001452	ENSMUSG00000046652	Tas2r143	Gm1404|Tas2r43|mt2r36	taste receptor, type 2, member 143	protein-coding
mm_153904.1	chr19	47090866	47090878	-	1	NA	promoter-TSS (NM_023211)	promoter-TSS (NM_023211)	106	NM_011053	18572	Mm.41166	NM_011053	ENSMUSG00000025047	Pdcd11	1110021I22Rik|ALG-4|Pdcd7|mKIAA0185	programmed cell death 11	protein-coding
mm_142596.1	chr17	46763648	46763675	-	1	NA	promoter-TSS (NM_011195)	promoter-TSS (NM_011195)	51	NM_011195	19208	Mm.215173	NM_011195	ENSMUSG00000036858	Ptcra	gp33|pT-alpha|pT-alpha-TCR|pT[a]|pTa|pTalpha	pre T cell antigen receptor alpha	protein-coding
mm_88698.1	chr10	80142410	80142423	+	1	NA	5' UTR (NM_025313, exon 1 of 4)	5' UTR (NM_025313, exon 1 of 4)	101	NM_025313	66043	Mm.278560	NM_025313	ENSMUSG00000003072	Atp5d	0610008F14Rik|1500000I11Rik|AA960090|AI876556|AU020773|C85518	ATP synthase, H+ transporting, mitochondrial F1 complex, delta subunit	protein-coding
mm_109974.1	chr12	12938741	12938752	-	1	NA	intron (NM_008709, intron 2 of 2)	intron (NM_008709, intron 2 of 2)	3090	NM_008709	18109	Mm.16469	NM_008709	ENSMUSG00000037169	Mycn	N-myc|Nmyc|Nmyc-1|Nmyc1|bHLHe37|c-nmyc	v-myc avian myelocytomatosis viral related oncogene, neuroblastoma derived	protein-coding
mm_25223.1	chr3	103857595	103857625	+	1	NA	Intergenic	Lx8|LINE|L1	-2185	NR_104070	19260	Mm.395	NM_008979	ENSMUSG00000027843	Ptpn22	70zpep|PEP|Ptpn8	protein tyrosine phosphatase, non-receptor type 22 (lymphoid)	protein-coding
mm_110399.1	chr12	44210115	44210127	-	1	NA	promoter-TSS (NM_013760)	promoter-TSS (NM_013760)	-53	NM_013760	27362	Mm.27432	NM_013760	ENSMUSG00000014905	Dnajb9	AA408011|AA673251|AA673481|AW556981|ERdj4|Mdg1|mDj7	DnaJ heat shock protein family (Hsp40) member B9	protein-coding
mm_102145.1	chr11	53631866	53631885	-	1	NA	3' UTR (NM_008355, exon 4 of 4)	3' UTR (NM_008355, exon 4 of 4)	2827	NM_008355	16163	Mm.1284	NM_008355	ENSMUSG00000020383	Il13	Il-13	interleukin 13	protein-coding
mm_108888.1	chr12	99999156	99999161	+	1	NA	intron (NM_146037, intron 2 of 2)	intron (NM_146037, intron 2 of 2)	34659	NM_001164427	217826	Mm.312335	NM_146037	ENSMUSG00000045404	Kcnk13	BB085247|F730021E22Rik|Gm1570|Gm1685	potassium channel, subfamily K, member 13	protein-coding
mm_57969.1	chr6	135346408	135346430	-	1	NA	Intergenic	MIRb|SINE|MIR	-16512	NM_010128	13730	Mm.182785	NM_010128	ENSMUSG00000030208	Emp1	I-8-09|TMP	epithelial membrane protein 1	protein-coding
mm_103011.1	chr11	69734729	69734729	-	1	NA	exon (NM_001291068, exon 29 of 29)	exon (NM_001291068, exon 29 of 29)	23904	NM_001291068	20020	Mm.16533	NM_009089	ENSMUSG00000005198	Polr2a	220kDa|Rpb1|Rpo2-1	polymerase (RNA) II (DNA directed) polypeptide A	protein-coding
mm_170028.1	chr17	21845728	21845745	-	1	NA	promoter-TSS (NM_029281)	promoter-TSS (NM_029281)	23	NM_029281	75424	Mm.271252	NM_029281	ENSMUSG00000069743	Zfp820	2610036F08Rik	zinc finger protein 820	protein-coding
mm_96795.1	chr11	69980781	69980828	+	1	NA	promoter-TSS (NM_026017)	promoter-TSS (NM_026017)	-364	NM_026017	67181	Mm.41678	NM_026017	ENSMUSG00000018559	Ctdnep1	2610507E10Rik|Dullard	CTD nuclear envelope phosphatase 1	protein-coding
mm_65110.1	chr7	19310006	19310020	-	1	NA	promoter-TSS (NM_008036)	promoter-TSS (NM_008036)	32	NM_008036	14282	Mm.248335	NM_008036	ENSMUSG00000003545	Fosb	-	FBJ osteosarcoma oncogene B	protein-coding
mm_44997.1	chr5	38159566	38159578	-	1	NA	promoter-TSS (NM_010942)	promoter-TSS (NM_010942)	-105	NM_010942	18196	Mm.7414	NM_010942	ENSMUSG00000029126	Nsg1	Neep21|m234|p21	neuron specific gene family member 1	protein-coding
mm_106069.1	chr11	116138863	116138873	-	1	NA	promoter-TSS (NM_024177)	promoter-TSS (NM_024177)	0	NM_024177	60441	Mm.29974	NM_024177	ENSMUSG00000020775	Mrpl38	1110036N21Rik|4733401F03Rik|MRP-L3|R75240|Rpml3	mitochondrial ribosomal protein L38	protein-coding
mm_67004.1	chr7	65213398	65213442	-	1	NA	Intergenic	Intergenic	-56892	NM_183087	70638	Mm.441986	NM_183087	ENSMUSG00000030518	Fam189a1	5730507A09Rik|AW047451	family with sequence similarity 189, member A1	protein-coding
mm_108660.1	chr12	86421676	86421687	+	1	NA	promoter-TSS (NM_011934)	promoter-TSS (NM_011934)	37	NM_011934	26380	Mm.235550	NM_011934	ENSMUSG00000021255	Esrrb	Err2|Errb|Estrrb|Nr3b2	estrogen related receptor, beta	protein-coding
mm_12795.1	chr2	79635600	79635650	+	1	NA	exon (NM_080558, exon 1 of 18)	exon (NM_080558, exon 1 of 18)	200	NM_080558	70599	Mm.272881	NM_080558	ENSMUSG00000027007	Ssfa2	5730488C15Rik|CS-1|CS1|KRAP|SPAG13|mKIAA1927	sperm specific antigen 2	protein-coding
mm_162114.1	chrX	53670381	53670381	-	1	NA	promoter-TSS (NM_001018063)	promoter-TSS (NM_001018063)	27	NM_001018063	553127	Mm.328602	NM_001018063	ENSMUSG00000067924	Cxx1b	Mart8c	CAAX box 1B	protein-coding
mm_149953.1	chr19	28011741	28011750	+	1	NA	promoter-TSS (NM_011265)	promoter-TSS (NM_011265)	-579	NM_011265	19726	Mm.313321	NM_011265	ENSMUSG00000040929	Rfx3	C230093O12Rik|MRFX3	regulatory factor X, 3 (influences HLA class II expression)	protein-coding
mm_114533.1	chr13	73626887	73626937	+	1	NA	promoter-TSS (NM_009354)	promoter-TSS (NM_009354)	-89	NM_009354	21752	Mm.10109	NM_009354	ENSMUSG00000021611	Tert	EST2|TCS1|TP2|TR|TRT	telomerase reverse transcriptase	protein-coding
mm_6610.1	chr1	75479149	75479159	-	1	NA	promoter-TSS (NM_177056)	promoter-TSS (NM_177056)	317	NM_001001565	74241	Mm.260577	NM_001001565	ENSMUSG00000032997	Chpf	1700028N03Rik|AI414328|D1Bwg1363e	chondroitin polymerizing factor	protein-coding
mm_77233.1	chr8	115704406	115704427	-	1	NA	3' UTR (NM_001025577, exon 1 of 1)	3' UTR (NM_001025577, exon 1 of 1)	2478	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_34096.1	chr4	138879321	138879324	+	1	NA	intron (NM_012044, intron 1 of 4)	intron (NM_012044, intron 1 of 4)	1380	NM_012044	26970	Mm.296007	NM_012044	ENSMUSG00000028751	Pla2g2e	-	phospholipase A2, group IIE	protein-coding
mm_63306.1	chr7	126861193	126861208	+	1	NA	promoter-TSS (NM_172746)	promoter-TSS (NM_172746)	263	NM_153580	233875	Mm.486253	NM_153580	ENSMUSG00000030689	Ino80e	AI225782|AI854876|Ccdc85|Ccdc95	INO80 complex subunit E	protein-coding
mm_33163.1	chr4	126018223	126018229	+	1	NA	Intergenic	Intergenic	-6433	NR_045561	12986	Mm.271701	NM_007782	ENSMUSG00000028859	Csf3r	Cd114|Csfgr|G-CSF-R|G-CSFR	colony stimulating factor 3 receptor (granulocyte)	protein-coding
mm_46704.1	chr5	110269817	110269894	-	1	NA	promoter-TSS (NM_001163538)	promoter-TSS (NM_001163538)	44	NM_028273	72542	Mm.61682	NM_028273	ENSMUSG00000029500	Pgam5	2610528A17Rik	phosphoglycerate mutase family member 5	protein-coding
mm_97823.1	chr11	82964561	82964580	+	1	NA	3' UTR (NM_183201, exon 6 of 6)	3' UTR (NM_183201, exon 6 of 6)	-3889	NR_045932	76392	Mm.295205	NR_045932	ENSMUSG00000086327	Slfn5os	1700003F17Rik	schlafen 5, opposite strand	ncRNA
mm_140387.1	chr17	87282625	87282640	+	1	NA	promoter-TSS (NM_028639)	promoter-TSS (NM_028639)	182	NR_015506	74597	Mm.63783	NR_015506	ENSMUSG00000085287	4833418N02Rik	-	RIKEN cDNA 4833418N02 gene	ncRNA
mm_2352.1	chr1	92911017	92911027	+	1	NA	promoter-TSS (NR_138577)	promoter-TSS (NR_138577)	197	NM_181405	108657	Mm.200971	NM_181405	ENSMUSG00000026269	Rnpepl1	1110014H17Rik|AI894167	arginyl aminopeptidase (aminopeptidase B)-like 1	protein-coding
mm_40433.1	chr5	53590340	53590351	+	1	NA	promoter-TSS (NM_001277116)	promoter-TSS (NM_001277116)	-1	NM_009035	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_96169.1	chr11	61488386	61488420	+	1	NA	TTS (NM_001291037)	TTS (NM_001291037)	2959	NM_029568	76293	Mm.272278	NM_029568	ENSMUSG00000042436	Mfap4	1110007F23Rik	microfibrillar-associated protein 4	protein-coding
mm_45717.1	chr5	84417369	84417389	-	1	NA	promoter-TSS (NM_007937)	promoter-TSS (NM_007937)	3	NM_007937	13839	Mm.137991	NM_007937	ENSMUSG00000029245	Epha5	AI854630|AW125296|Cek7|Ehk1|Els1|Hek7|Rek7|bsk	Eph receptor A5	protein-coding
mm_86084.1	chr9	114819078	114819086	-	1	NA	intron (NM_027294, intron 1 of 3)	Charlie29a|DNA|hAT-Charlie	25070	NM_027294	70031	Mm.150064	NM_027294	ENSMUSG00000041012	Cmtm8	2700018N07Rik|AA408515|Cklfsf8	CKLF-like MARVEL transmembrane domain containing 8	protein-coding
mm_43444.1	chr5	136103364	136103374	+	1	NA	exon (NM_133914, exon 15 of 21)	exon (NM_133914, exon 15 of 21)	-2153	NR_106002	102465626		NR_106002	ENSMUSG00000099003	Mir7035	Gm27661|mmu-mir-7035	microRNA 7035	ncRNA
mm_53405.1	chr6	131837165	131837191	+	1	NA	Intergenic	L1VL1|LINE|L1	-147115	NM_207019	387346	Mm.377908	NM_207019	ENSMUSG00000063478	Tas2r114	T2R14|Tas2r14|mGR14|mt2r46	taste receptor, type 2, member 114	protein-coding
mm_117674.1	chr13	93637751	93637761	-	1	NA	promoter-TSS (NM_016668)	promoter-TSS (NM_016668)	2	NM_016668	12116	Mm.329582	NM_016668	ENSMUSG00000074768	Bhmt	-	betaine-homocysteine methyltransferase	protein-coding
mm_146623.1	chr18	10151141	10151143	-	1	NA	intron (NM_009071, intron 1 of 32)	intron (NM_009071, intron 1 of 32)	30650	NM_009071	19877	Mm.6710	NM_009071	ENSMUSG00000024290	Rock1	1110055K06Rik|Rock-I	Rho-associated coiled-coil containing protein kinase 1	protein-coding
mm_36016.1	chr4	56916159	56916184	-	1	NA	intron (NM_175518, intron 7 of 17)	L1M3|LINE|L1	-20873	NR_029789	723837		NR_029789	ENSMUSG00000065544	Mir32	Mirn32|mir-32|mmu-mir-32	microRNA 32	ncRNA
mm_97857.1	chr11	83078355	83078369	+	1	NA	Intergenic	Intergenic	13250	NM_011408	20556	Mm.278689	NM_011408	ENSMUSG00000072620	Slfn2	Shlf2	schlafen 2	protein-coding
mm_155044.1	chrX	42150727	42150751	+	1	NA	promoter-TSS (NM_021465)	promoter-TSS (NM_021465)	38	NM_021465	20843	Mm.290422	NM_021465	ENSMUSG00000025862	Stag2	9230105L23Rik|B230112I07Rik|SA-2|SAP2	stromal antigen 2	protein-coding
mm_47107.1	chr5	118477751	118477778	-	1	NA	Intergenic	Intergenic	-82955	NM_001347445	76199	Mm.206238	NM_172424	ENSMUSG00000018076	Med13l	2210413I17Rik|6330591G05Rik|9030618F05Rik|Thrap2|Trap240L|mKIAA1025	mediator complex subunit 13-like	protein-coding
mm_25771.1	chr3	126520500	126520506	+	1	NA	Intergenic	L1M2|LINE|L1	-76448	NM_001293663	108058	Mm.255822	NM_023813	ENSMUSG00000053819	Camk2d	2810011D23Rik|8030469K03Rik|CaMK II|[d]-CaMKII	calcium/calmodulin-dependent protein kinase II, delta	protein-coding
mm_10067.1	chr1	193510170	193510177	-	1	NA	Intergenic	Intergenic	-2643	NR_029592	387201		NR_029592	ENSMUSG00000065533	Mir205	Mirn205|mir-205|mmu-mir-205	microRNA 205	ncRNA
mm_160456.1	chr8	107483398	107483398	+	1	NA	exon (NM_025830, exon 5 of 24)	exon (NM_025830, exon 5 of 24)	47000	NM_025830	66894	Mm.390058	NM_025830	ENSMUSG00000031930	Wwp2	1300010O06Rik|AA690238|AIP2|AW554328	WW domain containing E3 ubiquitin protein ligase 2	protein-coding
mm_143197.1	chr17	62733717	62733720	-	1	NA	intron (NM_010109, intron 1 of 3)	intron (NM_010109, intron 1 of 3)	147599	NM_207654	13640	Mm.7978	NM_010109	ENSMUSG00000048915	Efna5	AL-1|AV158822|EFL-5|Ephrin-A5|Epl7|LERK-7|RAGS	ephrin A5	protein-coding
mm_6147.1	chr1	64928113	64928115	-	1	NA	intron (NM_001039493, intron 2 of 7)	LTR79|LTR|ERVL	28710	NM_001039493	241075	Mm.239534	NM_175509	ENSMUSG00000051344	Plekhm3	9430067K14Rik|A230102O09Rik|AI449570|DAPR|Plekhm1l	pleckstrin homology domain containing, family M, member 3	protein-coding
mm_9333.1	chr1	172004091	172004104	-	1	NA	3' UTR (NM_033509, exon 8 of 8)	3' UTR (NM_033509, exon 8 of 8)	23198	NM_033509	93840	Mm.36148	NM_033509	ENSMUSG00000026556	Vangl2	C530001F03Rik|Lootl|Lp|Lpp1|Ltap|Vang1l2|loop-tail|ska17|ska<m17Jus>|stbm|strabismus	vang-like 2 (van gogh, Drosophila)	protein-coding
mm_73311.1	chr8	105174257	105174261	+	1	NA	intron (NM_001161456, intron 2 of 4)	Lx9|LINE|L1	3585	NM_001161458	12400	Mm.2018	NM_022309	ENSMUSG00000031885	Cbfb	AI893578|PEA2|PEBP2b|Pebp2|Pebpb2	core binding factor beta	protein-coding
mm_121757.1	chr14	19642899	19642915	-	1	NA	Intergenic	Intergenic	-40320	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_169567.1	chr15	17790852	17790856	+	1	NA	Intergenic	RLTR27|LTR|ERVK	578773	NR_045711	70886	Mm.399021	NR_045711		4921515E04Rik	-	RIKEN cDNA 4921515E04 gene	ncRNA
mm_38446.1	chr4	139967620	139967630	-	1	NA	promoter-TSS (NR_035519)	promoter-TSS (NR_035519)	-5	NR_035519	100316727		NR_035519	ENSMUSG00000089294	Mir2139	mmu-mir-2139	microRNA 2139	ncRNA
mm_108008.1	chr12	73584789	73584810	+	1	NA	promoter-TSS (NM_008856)	promoter-TSS (NM_008856)	3	NM_008856	18755	Mm.341677	NM_008856	ENSMUSG00000021108	Prkch	Pkch	protein kinase C, eta	protein-coding
mm_136776.1	chr17	10318321	10318337	+	1	NA	intron (NM_021881, intron 1 of 6)	CpG	1032	NM_021881	19317	Mm.130694	NM_021881	ENSMUSG00000062078	Qk	1110003F05Rik|1500005P18|QkI|l(17)-1Wis|l17Wis1	quaking	protein-coding
mm_132934.1	chr16	49855350	49855360	+	1	NA	promoter-TSS (NM_010581)	promoter-TSS (NM_010581)	-299	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_95806.1	chr11	55110091	55110097	+	1	NA	3' UTR (NM_010299, exon 4 of 4)	3' UTR (NM_010299, exon 4 of 4)	12109	NM_010299	14667	Mm.287807	NM_010299	ENSMUSG00000000594	Gm2a	AA408702|AW215435|GM2-AP|SAP-3	GM2 ganglioside activator protein	protein-coding
mm_172053.1	chr6	128799075	128799083	+	1	NA	Intergenic	CpG	-10438	NM_001159904	17059	Mm.480764	NM_008527	ENSMUSG00000030325	Klrb1c	AI462337|CD161|Ly-59|Ly55c|Ly59|NK-RP1|NK1.1|NKR-P1.9|NKRP1|NKRP140|Nk-1|Nk-1.2|Nk1|Nk1.2|Nkrp1c|ly-55c	killer cell lectin-like receptor subfamily B member 1C	protein-coding
mm_70952.1	chr8	26977138	26977162	+	1	NA	promoter-TSS (NM_001110508)	promoter-TSS (NM_001110508)	-186	NM_001101502	353310	Mm.212469	NM_001101502	ENSMUSG00000085795	Zfp703	1110032O19Rik|AI430822|AL022941|Csmn1|End2|Zeppo1|Znf703|Zpo1	zinc finger protein 703	protein-coding
mm_68464.1	chr7	110372713	110372724	-	1	NA	intron (NM_177324, intron 19 of 40)	intron (NM_177324, intron 19 of 40)	151015	NM_009302	20947	Mm.334144	NM_009302	ENSMUSG00000031015	Swap70	70kDa|AV235546	SWA-70 protein	protein-coding
mm_66755.1	chr7	46714299	46714308	-	1	NA	intron (NM_011315, intron 2 of 3)	intron (NM_011315, intron 2 of 3)	1373	NM_011315	20210	Mm.14277	NM_011315	ENSMUSG00000040026	Saa3	AV098916|Saa-3|l7R3	serum amyloid A 3	protein-coding
mm_109015.1	chr12	103393879	103393889	+	1	NA	intron (NM_001177841, intron 2 of 6)	MLT1D|LTR|ERVL-MaLR	5202	NM_001177841	68149	Mm.127378	NM_026580	ENSMUSG00000021203	Otub2	2010015L18Rik|4930586I02Rik|AI413508|AW557219|OTB2|OTU2	OTU domain, ubiquitin aldehyde binding 2	protein-coding
mm_14796.1	chr2	145872477	145872501	+	1	NA	intron (NM_028724, intron 9 of 12)	MLTR73|LTR|ERV1	-30752	NM_026425	67877	Mm.151168	NM_026425	ENSMUSG00000002728	Naa20	1500004D14Rik|2900026I01Rik|AU041458|D2Ertd186e|Nat5	N(alpha)-acetyltransferase 20, NatB catalytic subunit	protein-coding
mm_11534.1	chr2	32629518	32629540	+	1	NA	promoter-TSS (NM_021515)	promoter-TSS (NM_021515)	29	NM_021515	11636	Mm.29189	NM_021515	ENSMUSG00000026817	Ak1	Ak-1|B430205N08Rik	adenylate kinase 1	protein-coding
mm_21010.1	chr2	152396069	152396079	-	1	NA	3' UTR (NM_011438, exon 1 of 1)	3' UTR (NM_011438, exon 1 of 1)	1972	NM_011438	20667	Mm.28424	NM_011438	ENSMUSG00000051817	Sox12	2010205A02Rik	SRY (sex determining region Y)-box 12	protein-coding
mm_59772.1	chr7	28834126	28834146	+	1	NA	promoter-TSS (NM_010707)	promoter-TSS (NM_010707)	-34	NM_010707	16857	Mm.210336	NM_010707		Lgals6	galectin-6	lectin, galactose binding, soluble 6	protein-coding
mm_80789.1	chr9	95955631	95955634	+	1	NA	intron (NM_011916, intron 1 of 41)	intron (NM_011916, intron 1 of 41)	872	NM_001311130	24127	Mm.291179	NM_011916	ENSMUSG00000032410	Xrn1	Dhm2|exo|mXrn1	5'-3' exoribonuclease 1	protein-coding
mm_92586.1	chr10	80039675	80039724	-	1	NA	promoter-TSS (NM_025554)	promoter-TSS (NM_025554)	-40	NM_025554	66420	Mm.18579	NM_025554	ENSMUSG00000004667	Polr2e	2410021N14Rik|25kDa|AW208866|RPB5|XAP4	polymerase (RNA) II (DNA directed) polypeptide E	protein-coding
mm_143311.1	chr17	66077034	66077081	-	1	NA	promoter-TSS (NM_001025572)	promoter-TSS (NM_001025572)	-11	NM_001025572	106585	Mm.34706	NM_001025572	ENSMUSG00000034647	Ankrd12	2900001A12Rik|AI447928|ANCO-2|AV347965|GAC-1|mKIAA0874	ankyrin repeat domain 12	protein-coding
mm_51289.1	chr6	72305069	72305088	+	1	NA	exon (NM_001282071, exon 2 of 11)	exon (NM_001282071, exon 2 of 11)	468	NM_147779	20388	Mm.46033	NM_147779	ENSMUSG00000056370	Sftpb	AI562151|SF-B|SP-B|Sftp-3|Sftp3	surfactant associated protein B	protein-coding
mm_148428.1	chr19	3941867	3941877	+	1	NA	intron (NM_001161428, intron 4 of 9)	intron (NM_001161428, intron 4 of 9)	6686	NM_001161428	54445	Mm.262094	NM_019449	ENSMUSG00000036908	Unc93b1	Unc-93B1|Unc93b	unc-93 homolog B1 (C. elegans)	protein-coding
mm_127077.1	chr15	97385451	97385454	+	1	NA	3' UTR (NM_172293, exon 6 of 6)	3' UTR (NM_172293, exon 6 of 6)	-138165	NM_001164602	105827	Mm.24005	NM_178114	ENSMUSG00000048218	Amigo2	AI415330|AMIGO-2|AW208913|Ali1	adhesion molecule with Ig like domain 2	protein-coding
mm_127913.1	chr15	9529869	9529881	-	1	NA	promoter-TSS (NM_008372)	promoter-TSS (NM_008372)	1	NM_008372	16197	Mm.389	NM_008372	ENSMUSG00000003882	Il7r	CD127|IL-7Ralpha	interleukin 7 receptor	protein-coding
mm_88265.1	chr10	74089765	74089766	+	1	NA	intron (NM_001142740, intron 3 of 31)	MTEa|LTR|ERVL-MaLR	267898	NM_001142735	11994	Mm.338933	NM_023115	ENSMUSG00000052613	Pcdh15	BB078305|ENSMUSG00000046980|Gm9815|Ush1f|av|nmf19|roda	protocadherin 15	protein-coding
mm_61853.1	chr7	88302182	88302203	+	1	NA	exon (NM_009982, exon 5 of 7)	exon (NM_009982, exon 5 of 7)	24107	NM_001311790	13032	Mm.89295	NM_009982	ENSMUSG00000030560	Ctsc	AI047818|CatC|DPP1|DPPI	cathepsin C	protein-coding
mm_853.1	chr1	52119563	52119589	+	1	NA	promoter-TSS (NM_001205313)	promoter-TSS (NM_001205313)	-46	NM_001205313	20846	Mm.277406	NM_009283	ENSMUSG00000026104	Stat1	2010005J02Rik|AA408197	signal transducer and activator of transcription 1	protein-coding
mm_156146.1	chrX	129840607	129840611	+	1	NA	intron (NM_172493, intron 4 of 26)	intron (NM_172493, intron 4 of 26)	90867	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diaph2	Dia3|Diap2|Drf2|E430022I22Rik	diaphanous related formin 2	protein-coding
mm_28670.1	chr3	95283376	95283454	-	1	NA	5' UTR (NM_133858, exon 1 of 10)	5' UTR (NM_133858, exon 1 of 10)	480	NM_199475	75007	Mm.279287	NM_133858	ENSMUSG00000038712	Fam63a	1810005H09Rik|4930504E06Rik|AA562754|AA960384|AW561904|cI-40|mKIAA1390|ni	family with sequence similarity 63, member A	protein-coding
mm_29348.1	chr3	108382501	108382541	-	1	NA	non-coding (NR_040560, exon 2 of 3)	non-coding (NR_040560, exon 2 of 3)	1220	NR_040560	100038453	Mm.214328	NR_040560	ENSMUSG00000074281	Gm12522	OTTMUSG00000007300	predicted gene 12522	ncRNA
mm_15412.1	chr2	156780523	156780534	+	1	NA	exon (NM_172118, exon 3 of 4)	exon (NM_172118, exon 3 of 4)	5064	NM_172118	98932	Mm.271770	NM_172118	ENSMUSG00000067818	Myl9	AI327049|MLC20|Mylc2c|RLC-C	myosin, light polypeptide 9, regulatory	protein-coding
mm_117880.1	chr13	98984602	98984605	-	1	NA	promoter-TSS (NM_027064)	promoter-TSS (NM_027064)	-38	NM_027064	69382	Mm.45466	NM_027064	ENSMUSG00000045022	1700024P04Rik	H2bl1|Subh2bv	RIKEN cDNA 1700024P04 gene	protein-coding
mm_20344.1	chr2	127705668	127705681	-	1	NA	3' UTR (NM_145532, exon 4 of 4)	3' UTR (NM_145532, exon 4 of 4)	24223	NM_145532	228576	Mm.133036	NM_145532	ENSMUSG00000027377	Mall	BC012256|BENE	mal, T cell differentiation protein-like	protein-coding
mm_47249.1	chr5	121576009	121576035	-	1	NA	exon (NM_001308450, exon 6 of 11)	exon (NM_001308450, exon 6 of 11)	17802	NM_009656	11669	Mm.284446	NM_009656	ENSMUSG00000029455	Aldh2	AHD-M1|ALDH-E2|ALDHI|Ahd-5|Ahd5	aldehyde dehydrogenase 2, mitochondrial	protein-coding
mm_160388.1	chr8	47219943	47219943	-	1	NA	intron (NM_175162, intron 1 of 4)	intron (NM_175162, intron 1 of 4)	69459	NM_001286376	71069	Mm.23973	NM_175162	ENSMUSG00000038143	Stox2	4933409N07Rik|AI449080|AI835114|mKIAA1392	storkhead box 2	protein-coding
mm_11512.1	chr2	32576400	32576403	+	1	NA	intron (NM_198191, intron 1 of 9)	intron (NM_198191, intron 1 of 9)	683	NM_198191	227733	Mm.78923	NM_198191	ENSMUSG00000046854	Pip5kl1	BC028795	phosphatidylinositol-4-phosphate 5-kinase-like 1	protein-coding
mm_75374.1	chr8	45333125	45333176	-	1	NA	promoter-TSS (NM_133969)	promoter-TSS (NM_133969)	46	NM_133969	102294	Mm.245297	NM_133969	ENSMUSG00000079057	Cyp4v3	AU043077|AW111961|Cyp4v2	cytochrome P450, family 4, subfamily v, polypeptide 3	protein-coding
mm_113502.1	chr13	37543077	37543103	+	1	NA	Intergenic	Intergenic	197745	NM_010745	17084	Mm.2639	NM_010745	ENSMUSG00000021423	Ly86	MD-1|MD1|ly86_tv2	lymphocyte antigen 86	protein-coding
mm_72587.1	chr8	84338615	84338634	+	1	NA	Intergenic	Intergenic	-68222	NM_026350	67736	Mm.30095	NM_026350	ENSMUSG00000004994	Ccdc130	4930527D15Rik|C77430	coiled-coil domain containing 130	protein-coding
mm_122797.1	chr14	54464070	54464083	-	1	NA	promoter-TSS (NM_022993)	promoter-TSS (NM_022993)	-71	NM_022993	65107	Mm.472719	NM_022993	ENSMUSG00000022175	Lrp10	Lrp9	low-density lipoprotein receptor-related protein 10	protein-coding
mm_158689.1	chrX	160806710	160806750	-	1	NA	intron (NM_001024624, intron 18 of 18)	intron (NM_001024624, intron 18 of 18)	38717	NM_011302	20147	Mm.41982	NM_011302	ENSMUSG00000031293	Rs1	Rs1h|Xlrs1|tmgc1	retinoschisis (X-linked, juvenile) 1 (human)	protein-coding
mm_60475.1	chr7	44478214	44478236	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-6292	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_152070.1	chr19	6543065	6543075	-	1	NA	promoter-TSS (NM_009203)	promoter-TSS (NM_009203)	0	NM_009203	20521	Mm.391146	NM_009203	ENSMUSG00000061742	Slc22a12	AI987855|OAT4L|Rst|Slc22al2|URAT1	solute carrier family 22 (organic anion/cation transporter), member 12	protein-coding
mm_87961.1	chr10	63280965	63280976	+	1	NA	intron (NM_030114, intron 8 of 25)	intron (NM_030114, intron 8 of 25)	37173	NM_026101	67345	Mm.234437	NM_026101	ENSMUSG00000020064	Herc4	1700056O17Rik|4921531D01Rik|9530080M15Rik|mKIAA1593	hect domain and RLD 4	protein-coding
mm_101674.1	chr11	39218278	39218278	-	1	NA	Intergenic	Lx6|LINE|L1	171947	NR_126439	75315	Mm.461295	NR_126439		4930553C11Rik	-	RIKEN cDNA 4930553C11 gene	ncRNA
mm_51477.1	chr6	83014694	83014697	+	1	NA	intron (NM_033079, intron 7 of 9)	intron (NM_033079, intron 7 of 9)	18776	NM_010070	13448	Mm.156	NM_010070	ENSMUSG00000068335	Dok1	AW557123|p62DOK	docking protein 1	protein-coding
mm_26262.1	chr3	142500670	142500695	+	1	NA	exon (NM_153564, exon 2 of 11)	exon (NM_153564, exon 2 of 11)	3748	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_1709.1	chr1	75236499	75236521	+	1	NA	promoter-TSS (NM_001159883)	promoter-TSS (NM_001159883)	87	NM_001159883	56812	Mm.489660	NM_020266	ENSMUSG00000026203	Dnajb2	2700059H22Rik|Dnajb10|Hsj1|mDj8	DnaJ heat shock protein family (Hsp40) member B2	protein-coding
mm_67840.1	chr7	98492889	98492895	-	1	NA	Intergenic	Intergenic	-1330	NM_001113379	434215	Mm.323057	NM_001113379	ENSMUSG00000090958	Lrrc32	AI426318|D11S833Eh|D7H11S833E|EG434215|Garp	leucine rich repeat containing 32	protein-coding
mm_39646.1	chr5	24645483	24645483	+	1	NA	promoter-TSS (NR_003953)	promoter-TSS (NR_003953)	30	NR_003953	72252	Mm.87446	NR_003953	ENSMUSG00000038165	1700022A21Rik	-	glycerol-3-phosphate dehydrogenase 1-like pseudogene	pseudo
mm_152756.1	chr19	20372904	20372928	-	1	NA	TTS (NM_010730)	TTS (NM_010730)	17755	NM_010730	16952	Mm.248360	NM_010730	ENSMUSG00000024659	Anxa1	Anx-1|Anx-A1|C430014K04Rik|Lpc-1|Lpc1	annexin A1	protein-coding
mm_148111.1	chr18	74215940	74215946	-	1	NA	promoter-TSS (NM_028868)	promoter-TSS (NM_028868)	-269	NM_028868	74322	Mm.17537	NM_028868	ENSMUSG00000024560	Cxxc1	2410002I16Rik|5830420C16Rik|AI426635|Cfp1|Cgbp|PHF18	CXXC finger 1 (PHD domain)	protein-coding
mm_133347.1	chr16	81285346	81285350	+	1	NA	intron (NM_001113208, intron 1 of 17)	intron (NM_001113208, intron 1 of 17)	84651	NM_010954	17968	Mm.433941	NM_010954	ENSMUSG00000022762	Ncam2	Ncam-2|Ocam|RNCAM	neural cell adhesion molecule 2	protein-coding
mm_70166.1	chr7	143608206	143608231	-	1	NA	3' UTR (NM_175649, exon 8 of 8)	3' UTR (NM_175649, exon 8 of 8)	-8128	NM_013742	27267	Mm.125659	NM_013742	ENSMUSG00000010755	Cars	CA3	cysteinyl-tRNA synthetase	protein-coding
mm_60.1	chr1	6576045	6576089	+	1	NA	intron (NM_001244693, intron 2 of 22)	Lx2B2|LINE|L1	88836	NM_001244692	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding
mm_82164.1	chr9	123805537	123805544	+	1	NA	promoter-TSS (NM_030712)	promoter-TSS (NM_030712)	-937	NM_030712	80901	Mm.124289	NM_030712	ENSMUSG00000048521	Cxcr6	BB217514|BONZO|STRL33	chemokine (C-X-C motif) receptor 6	protein-coding
mm_172708.1	chr8	6940686	6940692	-	1	NA	Intergenic	RLTR17|LTR|ERVK	1720084	NM_010111	13642	Mm.209813	NM_010111	ENSMUSG00000001300	Efnb2	ELF-2|Epl5|Eplg5|Htk-L|LERK-5|Lerk5|NLERK-1	ephrin B2	protein-coding
mm_69357.1	chr7	130480417	130480464	-	1	NA	intron (NM_001029895, intron 8 of 11)	B2_Mm2|SINE|B2	39140	NM_001136054	11907	Mm.216321	NM_013799	ENSMUSG00000030850	Ate1	AI225793|AW547406	arginyltransferase 1	protein-coding
mm_52047.1	chr6	97210482	97210485	+	1	NA	promoter-TSS (NM_022992)	promoter-TSS (NM_022992)	-309	NM_022992	65106	Mm.291014	NM_022992	ENSMUSG00000035199	Arl6ip5	5930404D22Rik|AV001879|Aip-5|Gtrap3-18|addiscin	ADP-ribosylation factor-like 6 interacting protein 5	protein-coding
mm_27131.1	chr3	32365424	32365426	-	1	NA	promoter-TSS (NR_027966)	promoter-TSS (NR_027966)	-64	NR_027966	67576	Mm.435324	NR_027966		4930429B21Rik	-	RIKEN cDNA 4930429B21 gene	ncRNA
mm_100965.1	chr11	6638792	6638797	-	1	NA	promoter-TSS (NM_011709)	promoter-TSS (NM_011709)	-145	NM_011709	22373	Mm.268094	NM_011709	ENSMUSG00000000381	Wap	-	whey acidic protein	protein-coding
mm_22700.1	chr3	18054259	18054267	+	1	NA	promoter-TSS (NM_021560)	promoter-TSS (NM_021560)	-62	NM_021560	59058	Mm.149938	NM_021560	ENSMUSG00000025128	Bhlhe22	Beta3|Beta3a|Bhlhb5	basic helix-loop-helix family, member e22	protein-coding
mm_81009.1	chr9	104002726	104002776	+	1	NA	5' UTR (NM_028721, exon 1 of 27)	5' UTR (NM_028721, exon 1 of 27)	207	NM_028721	74025	Mm.479273	NM_028721	ENSMUSG00000032558	Nphp3	3632410F03Rik|AI550417|C230078J01|D330020E01Rik|pcy	nephronophthisis 3 (adolescent)	protein-coding
mm_103332.1	chr11	74572736	74572750	-	1	NA	intron (NM_001015046, intron 1 of 24)	intron (NM_001015046, intron 1 of 24)	17415	NM_001015046	380711	Mm.425690	NM_001015046	ENSMUSG00000038807	Rap1gap2	AU067654|Garnl4|Gm1561|mKIAA1039	RAP1 GTPase activating protein 2	protein-coding
mm_95498.1	chr11	51876086	51876110	+	1	NA	Intergenic	ORR1B2|LTR|ERVL-MaLR	-18617	NM_199299	76901	Mm.259996	NM_199299	ENSMUSG00000020387	Jade2	1200017K05Rik|AI480685|Phf15|mKIAA0239	jade family PHD finger 2	protein-coding
mm_9291.1	chr1	171634980	171635001	-	1	NA	exon (NM_144539, exon 8 of 8)	exon (NM_144539, exon 8 of 8)	6910	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_76382.1	chr8	84842452	84842467	-	1	NA	3' UTR (NM_007591, exon 9 of 9)	3' UTR (NM_007591, exon 9 of 9)	-1794	NM_009010	19358	Mm.255539	NM_009010	ENSMUSG00000003813	Rad23a	2310040P19Rik|AL024030|HR23A|mHR23A	RAD23 homolog A, nucleotide excision repair protein	protein-coding
mm_146461.1	chr18	86710883	86710894	+	1	NA	promoter-TSS (NM_001302356)	promoter-TSS (NM_001302356)	-222	NM_001302356	12405	Mm.70775	NM_172633	ENSMUSG00000024647	Cbln2	6330593N19Rik|A730004O05	cerebellin 2 precursor protein	protein-coding
mm_86714.1	chr10	18943855	18943865	+	1	NA	Intergenic	RMER16B|LTR|ERVK	68103	NM_001166402	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_47960.1	chr5	135623596	135623644	-	1	NA	Intergenic	MTEa|LTR|ERVL-MaLR	-9034	NM_146002	215160	Mm.295438	NM_031398	ENSMUSG00000039917	Rhbdd2	0610011L13Rik|AI480532|Rhbdl7|Usmg1	rhomboid domain containing 2	protein-coding
mm_135000.1	chr16	32176923	32176954	-	1	NA	Intergenic	Intergenic	-2862	NM_001033539	328660	Mm.441006	NM_001033539	ENSMUSG00000075269	Bex6	B020003O03Rik	brain expressed family member 6	protein-coding
mm_66651.1	chr7	45711445	45711487	-	1	NA	exon (NM_001172561, exon 6 of 6)	exon (NM_001172561, exon 6 of 6)	3741	NM_020011	56632	Mm.24222	NM_020011	ENSMUSG00000057342	Sphk2	C76851	sphingosine kinase 2	protein-coding
mm_73958.1	chr8	120464487	120464490	+	1	NA	Intergenic	L1MEd|LINE|L1	-24378	NM_198671	382034	Mm.334856	NM_198671	ENSMUSG00000031822	Gse1	2210013I18Rik|mKIAA0182	genetic suppressor element 1, coiled-coil protein	protein-coding
mm_33141.1	chr4	125109602	125109631	+	1	NA	exon (NM_027310, exon 6 of 6)	exon (NM_027310, exon 6 of 6)	18265	NM_153159	230738	Mm.402	NM_153159	ENSMUSG00000042677	Zc3h12a	BC036563|MCPIP|MCPIP-1|Mcpip1|Reg1	zinc finger CCCH type containing 12A	protein-coding
mm_122226.1	chr14	32707759	32707780	-	1	NA	Intergenic	Intergenic	-22497	NM_001195097	100504518	Mm.318319	NM_001195097	ENSMUSG00000071540	3425401B19Rik	-	RIKEN cDNA 3425401B19 gene	protein-coding
mm_71084.1	chr8	34805059	34805067	+	1	NA	Intergenic	Intergenic	-2547	NM_176933	319520	Mm.170276	NM_176933	ENSMUSG00000031530	Dusp4	2700078F24Rik|AI844617|BB104621|E130306H24Rik|MKP2	dual specificity phosphatase 4	protein-coding
mm_16611.1	chr2	5297327	5297342	-	1	NA	3' UTR (NM_001290375, exon 11 of 11)	3' UTR (NM_001290375, exon 11 of 11)	-82056	NR_030601	100124465		NR_030601	ENSMUSG00000078031	Mir466d	Mirn466d	microRNA 466d	ncRNA
mm_153603.1	chr19	43890576	43890586	-	1	NA	intron (NM_028029, intron 4 of 15)	intron (NM_028029, intron 4 of 15)	-10813	NM_001306088	71972	Mm.159024	NM_028029	ENSMUSG00000025195	Dnmbp	2410003L07Rik|2410003M15Rik|TUBA	dynamin binding protein	protein-coding
mm_47657.1	chr5	125393051	125393066	-	1	NA	Intergenic	Intergenic	-3041	NM_019639	22190	Mm.331	NM_019639	ENSMUSG00000008348	Ubc	2700054O04Rik|AI194771|Rps27a|TI-225|Uba52|Ubb	ubiquitin C	protein-coding
mm_60846.1	chr7	45787389	45787428	+	1	NA	non-coding (NR_110987, exon 5 of 16)	non-coding (NR_110987, exon 5 of 16)	2028	NM_001290990	381983	Mm.44928	NM_001005511	ENSMUSG00000062044	Lmtk3	BC059845|aatyk3	lemur tyrosine kinase 3	protein-coding
mm_156574.1	chrX	151928254	151928293	+	1	NA	exon (NM_021523, exon 75 of 83)	exon (NM_021523, exon 75 of 83)	15059	NR_029753	723947		NR_029753	ENSMUSG00000065536	Mir98	Mirn98|mir-98|mmu-mir-98	microRNA 98	ncRNA
mm_17118.1	chr2	24475566	24475580	-	1	NA	promoter-TSS (NM_011040)	promoter-TSS (NM_011040)	26	NM_011040	18510	Mm.2533	NM_011040	ENSMUSG00000026976	Pax8	Pax-8	paired box 8	protein-coding
mm_141922.1	chr17	35000849	35000857	-	1	NA	promoter-TSS (NM_011690)	promoter-TSS (NM_011690)	-54	NM_011690	22321	Mm.28420	NM_011690	ENSMUSG00000007029	Vars	Bat6|D17H6S56E|G7a|Vars2	valyl-tRNA synthetase	protein-coding
mm_75427.1	chr8	47254761	47254773	-	1	NA	intron (NM_175162, intron 1 of 4)	intron (NM_175162, intron 1 of 4)	34635	NM_001286376	71069	Mm.23973	NM_175162	ENSMUSG00000038143	Stox2	4933409N07Rik|AI449080|AI835114|mKIAA1392	storkhead box 2	protein-coding
mm_35894.1	chr4	49549245	49549253	-	1	NA	intron (NM_144903, intron 1 of 8)	intron (NM_144903, intron 1 of 8)	297	NM_144903	230163	Mm.482116	NM_144903	ENSMUSG00000028307	Aldob	Aldo-2|Aldo2|BC016435	aldolase B, fructose-bisphosphate	protein-coding
mm_10743.1	chr2	23069442	23069455	+	1	NA	intron (NM_001102437, intron 1 of 12)	intron (NM_001102437, intron 1 of 12)	376	NM_001102438	74159	Mm.181973	NM_028793	ENSMUSG00000026781	Acbd5	1300014E15Rik	acyl-Coenzyme A binding domain containing 5	protein-coding
mm_109729.1	chr12	116405398	116405466	+	1	NA	promoter-TSS (NR_028421)	promoter-TSS (NR_028421)	30	NM_133762	76044	Mm.491196	NM_133762	ENSMUSG00000042029	Ncapg2	5830426I05Rik|Luzp5|Mtb|mCAP-G2	non-SMC condensin II complex, subunit G2	protein-coding
mm_126724.1	chr15	85462126	85462170	+	1	NA	intron (NM_016843, intron 10 of 11)	intron (NM_016843, intron 10 of 11)	41079	NM_001256072	328577	Mm.212960	NM_001256072	ENSMUSG00000096607	7530416G11Rik	-	RIKEN cDNA 7530416G11 gene	protein-coding
mm_1447.1	chr1	67230434	67230496	+	1	NA	3' UTR (NM_001080809, exon 38 of 38)	3' UTR (NM_001080809, exon 38 of 38)	107438	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_79532.1	chr9	57765147	57765199	+	1	NA	exon (NM_007713, exon 1 of 13)	exon (NM_007713, exon 1 of 13)	687	NM_007713	102414	Mm.25720	NM_007713	ENSMUSG00000032316	Clk3	AI256811	CDC-like kinase 3	protein-coding
mm_43383.1	chr5	135725748	135725774	+	1	NA	intron (NM_008898, intron 2 of 15)	intron (NM_008898, intron 2 of 15)	10128	NR_106001	102466791		NR_106001	ENSMUSG00000099197	Mir7034	Gm27372|mmu-mir-7034	microRNA 7034	ncRNA
mm_24901.1	chr3	96181179	96181233	+	1	NA	promoter-TSS (NM_022030)	promoter-TSS (NM_022030)	-21	NM_022030	64051	Mm.491135	NM_022030	ENSMUSG00000038486	Sv2a	AI746429|mKIAA0736	synaptic vesicle glycoprotein 2 a	protein-coding
mm_18420.1	chr2	60722671	60722671	-	1	NA	promoter-TSS (NM_001159564)	promoter-TSS (NM_001159564)	-68	NM_001159564	16420	Mm.98193	NM_021359	ENSMUSG00000026971	Itgb6	2210409C20Rik|4831415H04Rik	integrin beta 6	protein-coding
mm_17787.1	chr2	33086205	33086215	-	1	NA	intron (NM_178888, intron 1 of 28)	intron (NM_178888, intron 1 of 28)	994	NM_178888	99326	Mm.41290	NM_178888	ENSMUSG00000038860	Garnl3	AW120551	GTPase activating RANGAP domain-like 3	protein-coding
mm_117006.1	chr13	57908311	57908321	-	1	NA	promoter-TSS (NM_001166463)	promoter-TSS (NM_001166463)	16	NM_009262	20745	Mm.379020	NM_009262	ENSMUSG00000056222	Spock1	Spock|Ticn1|testican	sparc/osteonectin, cwcv and kazal-like domains proteoglycan 1	protein-coding
mm_134310.1	chr16	15863294	15863339	-	1	NA	promoter-TSS (NM_029354)	promoter-TSS (NM_029354)	6	NM_029354	72083	Mm.22351	NM_029354	ENSMUSG00000022671	Mzt2	2410018G20Rik|2610001E06Rik|Fam128|Fam128b	mitotic spindle organizing protein 2	protein-coding
mm_32785.1	chr4	116709235	116709239	+	1	NA	promoter-TSS (NM_025962)	promoter-TSS (NM_025962)	307	NM_026714	68394	Mm.425201	NM_026714	ENSMUSG00000028689	Ccdc163	0610037D15Rik|4933430J04Rik	coiled-coil domain containing 163	protein-coding
mm_168499.1	chr1	152718069	152718071	+	1	NA	intron (NM_001346117, intron 1 of 18)	intron (NM_001346117, intron 1 of 18)	-32481	NM_001081197	71281	Mm.158650	NM_001081197	ENSMUSG00000055547	Apobec4	4933431M11Rik	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 4 (putative)	protein-coding
mm_99103.1	chr11	100119075	100119084	+	1	NA	exon (NM_010662, exon 5 of 8)	exon (NM_010662, exon 5 of 8)	1498	NM_001313949	16663	Mm.4646	NM_010662	ENSMUSG00000044041	Krt13	CK13|K13|Krt-1.13|Krt1-13	keratin 13	protein-coding
mm_169386.1	chr14	41939516	41939516	+	1	NA	Intergenic	BGLII|LTR|ERVK	155761	NR_073362	73553	Mm.243777	NM_028570	ENSMUSG00000090462	1700091H14Rik	100041930|Gm3578	RIKEN cDNA 1700091H14 gene	ncRNA
mm_110990.1	chr12	77177403	77177413	-	1	NA	Intergenic	Intergenic	-60696	NM_001252614	53618	Mm.35628	NM_016893	ENSMUSG00000021065	Fut8	-	fucosyltransferase 8	protein-coding
mm_12464.1	chr2	71388048	71388066	+	1	NA	Intergenic	RLTR23|LTR|ERV1	-1203	NM_026115	107435	Mm.272472	NM_026115	ENSMUSG00000027018	Hat1	2410071B14Rik|AA536933|Hat-1|KAT1	histone aminotransferase 1	protein-coding
mm_142200.1	chr17	36958438	36958500	-	1	NA	promoter-TSS (NM_029602)	promoter-TSS (NM_029602)	-41	NM_023162	66136	Mm.486229	NM_023162	ENSMUSG00000036315	Znrd1	1110014N07Rik|Rpa12	zinc ribbon domain containing, 1	protein-coding
mm_144850.1	chr18	36638186	36638206	+	1	NA	intron (NM_175375, intron 20 of 33)	intron (NM_175375, intron 20 of 33)	-25864	NM_201256	108112	Mm.24790	NM_201256	ENSMUSG00000090264	Eif4ebp3	4e-bp3	eukaryotic translation initiation factor 4E binding protein 3	protein-coding
mm_84889.1	chr9	79759868	79759880	-	1	NA	promoter-TSS (NM_009945)	promoter-TSS (NM_009945)	-21	NM_009945	12866	Mm.152627	NM_009945	ENSMUSG00000032330	Cox7a2	COX7AL|Cox7a3|CoxVIIa-L	cytochrome c oxidase subunit VIIa 2	protein-coding
mm_62661.1	chr7	108804486	108804489	+	1	NA	Intergenic	RMER13A|LTR|ERVK	21510	NM_146726	258721	Mm.377655	NM_146726	ENSMUSG00000066241	Olfr514	MOR268-1	olfactory receptor 514	protein-coding
mm_572.1	chr1	38907927	38907930	+	1	NA	Intergenic	Intergenic	-9768	NM_145142	98388	Mm.260054	NM_145142	ENSMUSG00000026080	Chst10	AI507003|AU041319|Hnk-1st|ST	carbohydrate sulfotransferase 10	protein-coding
mm_95702.1	chr11	54438160	54438187	+	1	NA	promoter-TSS (NM_173753)	promoter-TSS (NM_173753)	-6	NM_173753	216742	Mm.34087	NM_173753	ENSMUSG00000035992	Fnip1	A730024A03Rik|AI838773|AW557298	folliculin interacting protein 1	protein-coding
mm_29413.1	chr3	108972306	108972366	-	1	NA	3' UTR (NM_001163567, exon 11 of 11)	3' UTR (NM_001163567, exon 11 of 11)	31779	NM_001078646	66715	Mm.158124	NM_025723	ENSMUSG00000045662	Henmt1	4921515J06Rik|Hen1|mHEN1	HEN1 methyltransferase homolog 1 (Arabidopsis)	protein-coding
mm_70927.1	chr8	25813053	25813061	+	1	NA	3' UTR (NM_011485, exon 7 of 7)	3' UTR (NM_011485, exon 7 of 7)	4583	NM_011485	20845	Mm.293314	NM_011485	ENSMUSG00000031574	Star	AV363654|D8Ertd419e|stARD1	steroidogenic acute regulatory protein	protein-coding
mm_150312.1	chr19	34573284	34573306	+	1	NA	exon (NM_008332, exon 3 of 3)	exon (NM_008332, exon 3 of 3)	-10234	NM_010501	15959	Mm.426079	NM_010501	ENSMUSG00000074896	Ifit3	Ifi49|P49	interferon-induced protein with tetratricopeptide repeats 3	protein-coding
mm_69440.1	chr7	132911003	132911008	-	1	NA	Intergenic	Intergenic	-38617	NM_207302	360216	Mm.389984	NM_207302	ENSMUSG00000030967	Zranb1	9330160G10Rik|D7Wsu87e|Gm1956|Trabid	zinc finger, RAN-binding domain containing 1	protein-coding
mm_98279.1	chr11	89024512	89024525	+	1	NA	Intergenic	Intergenic	25115	NM_009546	217069	Mm.248445	NM_009546	ENSMUSG00000000275	Trim25	AA960166|AL022677|EFP|Zfp147	tripartite motif-containing 25	protein-coding
mm_2876.1	chr1	131828003	131828019	+	1	NA	promoter-TSS (NM_173865)	promoter-TSS (NM_173865)	-1	NM_173865	98396	Mm.389181	NM_173865	ENSMUSG00000013275	Slc41a1	AI573938|B230315F01Rik	solute carrier family 41, member 1	protein-coding
mm_119051.1	chr14	30635500	30635549	+	1	NA	Intergenic	Intergenic	-9316	NM_011103	18753	Mm.2314	NM_011103	ENSMUSG00000021948	Prkcd	AI385711|D14Ertd420e|PKC[d]|PKCdelta|Pkcd	protein kinase C, delta	protein-coding
mm_110260.1	chr12	31713838	31713848	-	1	NA	promoter-TSS (NM_175191)	promoter-TSS (NM_175191)	83	NM_175191	73010	Mm.441517	NM_175191	ENSMUSG00000044067	Gpr22	2900068K05Rik|AW061316	G protein-coupled receptor 22	protein-coding
mm_92719.1	chr10	80798477	80798576	-	1	NA	promoter-TSS (NM_013651)	promoter-TSS (NM_013651)	100	NM_023900	78670	Mm.41479	NM_023900	ENSMUSG00000035278	Plekhj1	9530063M10Rik	pleckstrin homology domain containing, family J member 1	protein-coding
mm_27099.1	chr3	30386396	30386408	-	1	NA	intron (NM_021442, intron 1 of 2)	intron (NM_021442, intron 1 of 2)	123085	NM_021442	14013	Mm.56965	NM_007963	ENSMUSG00000027684	Mecom	D630039M04Rik|Evi-1|Evi1|Jbo|Mds|Mds1|Mds1-Evi1|Prdm3|Znfpr1b1	MDS1 and EVI1 complex locus	protein-coding
mm_5614.1	chr1	39651283	39651321	-	1	NA	promoter-TSS (NM_170597)	promoter-TSS (NM_170597)	-120	NM_170597	263764	Mm.122091	NM_170597	ENSMUSG00000050967	Creg2	A830098L22Rik	cellular repressor of E1A-stimulated genes 2	protein-coding
mm_6143.1	chr1	64924944	64924950	-	1	NA	intron (NM_001039493, intron 2 of 7)	PB1D7|SINE|Alu	31877	NM_001039493	241075	Mm.239534	NM_175509	ENSMUSG00000051344	Plekhm3	9430067K14Rik|A230102O09Rik|AI449570|DAPR|Plekhm1l	pleckstrin homology domain containing, family M, member 3	protein-coding
mm_41051.1	chr5	86496132	86496135	+	1	NA	intron (NM_177162, intron 5 of 9)	intron (NM_177162, intron 5 of 9)	22467	NM_177162	320454	Mm.184522	NM_177162	ENSMUSG00000079451	Tmprss11g	9930032O22Rik|Desc4	transmembrane protease, serine 11g	protein-coding
mm_10180.1	chr2	4717826	4717893	+	1	NA	promoter-TSS (NM_001190400)	promoter-TSS (NM_001190400)	28	NM_178663	209645	Mm.149539	NM_178663	ENSMUSG00000048186	Bend7	1110017O21Rik|E130319B15Rik	BEN domain containing 7	protein-coding
mm_112258.1	chr12	113879555	113879558	-	1	NA	Intergenic	Intergenic	335648	NM_174885	238406	Mm.188683	NM_174885	ENSMUSG00000043945	Adam6a	Adam6|tMDCIV	a disintegrin and metallopeptidase domain 6A	protein-coding
mm_113612.1	chr13	41469814	41469814	+	1	NA	intron (NM_001111324, intron 1 of 7)	intron (NM_001111324, intron 1 of 7)	17546	NM_001111324	18003	Mm.288980	NM_017464	ENSMUSG00000021365	Nedd9	Cas-L|CasL|HEF1|MEF1|Nedd-9|p105	neural precursor cell expressed, developmentally down-regulated gene 9	protein-coding
mm_74309.1	chr8	126592438	126592452	+	1	NA	exon (NM_001164598, exon 1 of 2)	exon (NM_001164598, exon 1 of 2)	991	NM_001164598	270110	Mm.334918	NM_001164598	ENSMUSG00000051495	Irf2bp2	E130305N23Rik|IRF-2BP2	interferon regulatory factor 2 binding protein 2	protein-coding
mm_109437.1	chr12	110695919	110695950	+	1	NA	intron (NM_010480, intron 1 of 10)	CpG	461	NM_010480	15519	Mm.1843	NM_010480	ENSMUSG00000021270	Hsp90aa1	86kDa|89kDa|AL024080|AL024147|Hsp86-1|Hsp89|Hsp90|Hspca|hsp4	heat shock protein 90, alpha (cytosolic), class A member 1	protein-coding
mm_30842.1	chr4	24496435	24496499	+	1	NA	promoter-TSS (NM_199467)	promoter-TSS (NM_199467)	5	NM_199467	212377	Mm.120919	NM_199467	ENSMUSG00000045751	Mms22l	F730047E07Rik|Gm134	MMS22-like, DNA repair protein	protein-coding
mm_82429.1	chr9	15007837	15007871	-	1	NA	exon (NM_019482, exon 4 of 5)	exon (NM_019482, exon 4 of 5)	37624	NM_019482	55991	Mm.142253	NM_019482	ENSMUSG00000031934	Panx1	AI847747	pannexin 1	protein-coding
mm_147950.1	chr18	66674500	66674512	-	1	NA	Intergenic	Intergenic	170328	NR_040528	100503565	Mm.98256	NR_040528		Gm9926	ENSMUSG00000053891	predicted gene 9926	ncRNA
mm_132474.1	chr16	36708668	36708676	+	1	NA	intron (NM_001285791, intron 2 of 6)	intron (NM_001285791, intron 2 of 6)	14694	NM_001285791	106347	Mm.17807	NM_134109	ENSMUSG00000022900	Ildr1	AU041483|AU044638	immunoglobulin-like domain containing receptor 1	protein-coding
mm_119714.1	chr14	53875993	53876005	+	1	NA	Intergenic	Intergenic	377930	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_70827.1	chr8	23140153	23140168	+	1	NA	exon (NM_031158, exon 42 of 45)	exon (NM_031158, exon 42 of 45)	1130	NM_001310437	11733	Mm.334444	NM_031158	ENSMUSG00000031543	Ank1	Ank-1|nb|pale	ankyrin 1, erythroid	protein-coding
mm_66675.1	chr7	45742456	45742468	-	1	NA	intron (NM_017465, intron 1 of 6)	intron (NM_017465, intron 1 of 6)	-16646	NM_027055	69363	Mm.45607	NM_027055	ENSMUSG00000070563	Spaca4	1700008E09Rik|AV043694|Samp14	sperm acrosome associated 4	protein-coding
mm_45714.1	chr5	84417144	84417150	-	1	NA	5' UTR (NM_007937, exon 1 of 16)	5' UTR (NM_007937, exon 1 of 16)	235	NM_007937	13839	Mm.137991	NM_007937	ENSMUSG00000029245	Epha5	AI854630|AW125296|Cek7|Ehk1|Els1|Hek7|Rek7|bsk	Eph receptor A5	protein-coding
mm_34284.1	chr4	141426410	141426420	+	1	NA	Intergenic	Intergenic	5636	NM_013868	29818	Mm.46181	NM_013868	ENSMUSG00000006221	Hspb7	27kDa|Hsp25-2|cvHsp	heat shock protein family, member 7 (cardiovascular)	protein-coding
mm_64474.1	chr7	143052753	143052763	+	1	NA	promoter-TSS (NM_133655)	promoter-TSS (NM_133655)	8	NM_133655	12520	Mm.806	NM_133655	ENSMUSG00000037706	Cd81	Tapa-1|Tapa1|Tspan28	CD81 antigen	protein-coding
mm_55761.1	chr6	78466350	78466367	-	1	NA	TTS (NM_011260)	TTS (NM_011260)	2516	NM_011260	19695	Mm.252385	NM_011260	ENSMUSG00000030017	Reg3g	AI449515|REG-3-gamma|reg III-gamma	regenerating islet-derived 3 gamma	protein-coding
mm_125020.1	chr15	25655264	25655272	+	1	NA	intron (NM_019472, intron 1 of 40)	intron (NM_019472, intron 1 of 40)	32718	NM_019472	17909	Mm.60590	NM_019472	ENSMUSG00000022272	Myo10	AW048724|D15Ertd600e|mKIAA0799|myosin-X	myosin X	protein-coding
mm_47069.1	chr5	116441286	116441296	-	1	NA	3' UTR (NM_026886, exon 13 of 13)	3' UTR (NM_026886, exon 13 of 13)	2569	NR_015595	76798	Mm.444322	NR_015595	ENSMUSG00000086219	Srrm4os	2410137F16Rik	serine/arginine repetitive matrix 4, opposite strand	ncRNA
mm_153594.1	chr19	43735942	43735944	-	1	NA	3' UTR (NM_144874, exon 9 of 9)	3' UTR (NM_144874, exon 9 of 9)	17057	NM_144874	226139	Mm.248237	NM_144874	ENSMUSG00000040018	Cox15	2900026G05Rik	cytochrome c oxidase assembly protein 15	protein-coding
mm_68579.1	chr7	115859821	115859846	-	1	NA	intron (NM_001025560, intron 2 of 15)	intron (NM_001025560, intron 2 of 15)	-13693	NM_001277326	20679	Mm.323365	NM_011445	ENSMUSG00000051910	Sox6	AI987981|SOX-LZ	SRY (sex determining region Y)-box 6	protein-coding
mm_48133.1	chr5	137150124	137150133	-	1	NA	Intergenic	Intergenic	-33921	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_124831.1	chr15	9186246	9186250	+	1	NA	intron (NM_177178, intron 15 of 17)	intron (NM_177178, intron 15 of 17)	-30823	NM_001285980	27401	Mm.35584	NM_013787	ENSMUSG00000054115	Skp2	4930500A04Rik|FBXL1|FWD1|p45	S-phase kinase-associated protein 2 (p45)	protein-coding
mm_5748.1	chr1	46076022	46076053	-	1	NA	intron (NM_001160386, intron 2 of 65)	L1Md_F2|LINE|L1	9299	NM_001160386	227058	Mm.296880	NM_001160386	ENSMUSG00000041144	Dnah7b	Dnahc7b|Gm107	dynein, axonemal, heavy chain 7B	protein-coding
mm_14469.1	chr2	131352997	131353022	+	1	NA	promoter-TSS (NM_178607)	promoter-TSS (NM_178607)	-117	NM_178607	51902	Mm.477523	NM_178607	ENSMUSG00000048911	Rnf24	2810473M14Rik|4930505A13Rik|AI317164|C86507|D2Ertd504e	ring finger protein 24	protein-coding
mm_6584.1	chr1	75236326	75236348	-	1	NA	promoter-TSS (NM_001159883)	promoter-TSS (NM_001159883)	-86	NM_020266	56812	Mm.489660	NM_020266	ENSMUSG00000026203	Dnajb2	2700059H22Rik|Dnajb10|Hsj1|mDj8	DnaJ heat shock protein family (Hsp40) member B2	protein-coding
mm_24382.1	chr3	90248886	90248932	+	1	NA	intron (NM_013901, intron 1 of 3)	intron (NM_013901, intron 1 of 3)	717	NM_013901	30791	Mm.294709	NM_013901	ENSMUSG00000052310	Slc39a1	Zip1|Zirtl	solute carrier family 39 (zinc transporter), member 1	protein-coding
mm_124984.1	chr15	21097695	21097695	+	1	NA	Intergenic	Intergenic	-13757	NM_001008420	215654	Mm.300909	NM_001008420	ENSMUSG00000040452	Cdh12	Cdhb	cadherin 12	protein-coding
mm_26361.1	chr3	142549553	142549561	+	1	NA	3' UTR (NM_001083312, exon 11 of 11)	3' UTR (NM_001083312, exon 11 of 11)	-10495	NM_018734	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_154183.1	chr19	58793278	58793298	-	1	NA	intron (NM_026208, intron 1 of 5)	intron (NM_026208, intron 1 of 5)	1126	NM_026208	67507	Mm.27027	NM_026208	ENSMUSG00000026931	1700019N19Rik	-	RIKEN cDNA 1700019N19 gene	protein-coding
mm_39336.1	chr5	8798678	8798684	+	1	NA	intron (NM_011075, intron 1 of 27)	intron (NM_011075, intron 1 of 27)	534	NM_011075	18669	Mm.146649	NM_011075	ENSMUSG00000028970	Abcb1b	Abcb1|Mdr1|Mdr1b|Pgy-1|Pgy1|mdr	ATP-binding cassette, sub-family B (MDR/TAP), member 1B	protein-coding
mm_67425.1	chr7	80349552	80349560	-	1	NA	3' UTR (NM_172903, exon 24 of 24)	3' UTR (NM_172903, exon 24 of 24)	6419	NM_026812	68695	Mm.21171	NM_026812	ENSMUSG00000030532	Hddc3	1110033O09Rik|C86475|MESH1	HD domain containing 3	protein-coding
mm_54342.1	chr6	30669459	30669461	-	1	NA	intron (NR_130781, intron 3 of 11)	intron (NR_130781, intron 3 of 11)	24289	NM_031998	83922	Mm.65389	NM_031998	ENSMUSG00000029790	Cep41	1700017E11Rik|2810431D15Rik|Tsga14	centrosomal protein 41	protein-coding
mm_2411.1	chr1	93825613	93825632	+	1	NA	intron (NM_001310767, intron 1 of 9)	intron (NM_001310767, intron 1 of 9)	382	NM_001310767	98314	Mm.383401	NM_178882	ENSMUSG00000073609	D2hgdh	AA408776|AA408778|AI325464	D-2-hydroxyglutarate dehydrogenase	protein-coding
mm_9692.1	chr1	178337241	178337253	-	1	NA	exon (NM_016805, exon 1 of 14)	exon (NM_016805, exon 1 of 14)	537	NM_016805	51810	Mm.86589	NM_016805	ENSMUSG00000039630	Hnrnpu	AA408410|AI256620|AL024194|AL024437|AW557595|C86794|Hnrpu|SAFA|Sp120|hnRNP U	heterogeneous nuclear ribonucleoprotein U	protein-coding
mm_68960.1	chr7	126579224	126579237	-	1	NA	TTS (NR_106026)	TTS (NR_106026)	302	NR_106026	102465641		NR_106026	ENSMUSG00000098540	Mir7059	Gm27534|mmu-mir-7059	microRNA 7059	ncRNA
mm_124740.1	chr15	6592880	6592889	+	1	NA	intron (NM_011815, intron 1 of 17)	intron (NM_011815, intron 1 of 17)	13037	NM_011815	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_69881.1	chr7	141636869	141636877	-	1	NA	intron (NM_001330001, intron 31 of 33)	intron (NM_001330001, intron 31 of 33)	16172	NR_106030	102466798		NR_106030	ENSMUSG00000098759	Mir7063	Gm27654|mmu-mir-7063	microRNA 7063	ncRNA
mm_123604.1	chr14	67933736	67933763	-	1	NA	promoter-TSS (NM_177780)	promoter-TSS (NM_177780)	-177	NM_177780	68813	Mm.258155	NM_177780	ENSMUSG00000044447	Dock5	1110060D06Rik|AI666732|AI956923|BC016533|E130320D18|lr2|rlc	dedicator of cytokinesis 5	protein-coding
mm_75389.1	chr8	45555738	45555745	-	1	NA	intron (NM_172752, intron 1 of 22)	ORR1B1|LTR|ERVL-MaLR	47953	NM_001205219	234214	Mm.211096	NM_172752	ENSMUSG00000031626	Sorbs2	2010203O03Rik|9430041O17Rik|A530071H08|Argbp2|mKIAA0777|nArgBP2	sorbin and SH3 domain containing 2	protein-coding
mm_152897.1	chr19	24901011	24901048	-	1	NA	5' UTR (NM_008022, exon 1 of 1)	5' UTR (NM_008022, exon 1 of 1)	280	NM_008022	14237	Mm.377080	NM_008022	ENSMUSG00000051490	Foxd4	FREAC5|Fkh2	forkhead box D4	protein-coding
mm_6768.1	chr1	84128403	84128424	-	1	NA	intron (NM_001003948, intron 2 of 2)	intron (NM_001003948, intron 2 of 2)	90548	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_123765.1	chr14	70207641	70207675	-	1	NA	promoter-TSS (NM_011366)	promoter-TSS (NM_011366)	13	NM_011366	20410	Mm.5068	NM_011366	ENSMUSG00000022091	Sorbs3	SCAM-1|SH3P3|Sh3d4|vinexin-g	sorbin and SH3 domain containing 3	protein-coding
mm_25260.1	chr3	104782339	104782352	+	1	NA	intron (NM_027982, intron 1 of 9)	intron (NM_027982, intron 1 of 9)	1289	NM_027982	71887	Mm.379204	NM_027982	ENSMUSG00000002228	Ppm1j	2310008J22Rik|PP2Czeta|Ppp2cz	protein phosphatase 1J	protein-coding
mm_47872.1	chr5	134670368	134670395	-	1	NA	exon (NM_010717, exon 5 of 16)	exon (NM_010717, exon 5 of 16)	7867	NM_001305875	16885	Mm.15409	NM_010717	ENSMUSG00000029674	Limk1	KIZ-1|LIMK-1|Limk	LIM-domain containing, protein kinase	protein-coding
mm_131720.1	chr16	21558591	21558608	+	1	NA	intron (NM_001285893, intron 36 of 46)	MTE2b|LTR|ERVL-MaLR	135481	NM_001285894	209018	Mm.235683	NM_145948	ENSMUSG00000033653	Vps8	AI315068|AU040738|mKIAA0804	VPS8 CORVET complex subunit	protein-coding
mm_25211.1	chr3	103832867	103832877	+	1	NA	exon (NM_001142960, exon 1 of 4)	exon (NM_001142960, exon 1 of 4)	176	NM_001142960	229672	Mm.297245	NM_001142959	ENSMUSG00000044165	Bcl2l15	Bfk|Gm566	BCLl2-like 15	protein-coding
mm_168012.1	chrY	37763298	37763302	-	1	NA	Intergenic	RLTR6_Mm|LTR|ERV1	-194511	NM_001160143	100040031	Mm.463839	NM_001160143	ENSMUSG00000093950	Gm20823	-	predicted gene, 20823	protein-coding
mm_24075.1	chr3	87930205	87930234	+	1	NA	promoter-TSS (NM_177663)	promoter-TSS (NM_177663)	-24	NM_153562	229503	Mm.296008	NM_153562	ENSMUSG00000004896	Rrnad1	-	ribosomal RNA adenine dimethylase domain containing 1	protein-coding
mm_69676.1	chr7	139985377	139985399	-	1	NA	exon (NM_001291066, exon 18 of 24)	exon (NM_001291066, exon 18 of 24)	1486	NR_106029	102465643		NR_106029	ENSMUSG00000099092	Mir7062	Gm27339|mmu-mir-7062	microRNA 7062	ncRNA
mm_102856.1	chr11	69399178	69399192	-	1	NA	promoter-TSS (NM_025915)	promoter-TSS (NM_025915)	-951	NM_025915	67020	Mm.390406	NM_025915	ENSMUSG00000045377	Tmem88	2600017H02Rik	transmembrane protein 88	protein-coding
mm_6445.1	chr1	74001527	74001555	-	1	NA	intron (NM_027884, intron 6 of 34)	intron (NM_027884, intron 6 of 34)	122906	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_9496.1	chr1	173729920	173729940	-	1	NA	exon (NM_001204910, exon 5 of 8)	exon (NM_001204910, exon 5 of 8)	11879	NM_001204910	226691	Mm.440876	NM_001204910	ENSMUSG00000073490	Ifi207	AI607873|Pyhin-A	interferon activated gene 207	protein-coding
mm_92714.1	chr10	80797920	80797950	-	1	NA	promoter-TSS (NM_013651)	promoter-TSS (NM_013651)	691	NM_023900	78670	Mm.41479	NM_023900	ENSMUSG00000035278	Plekhj1	9530063M10Rik	pleckstrin homology domain containing, family J member 1	protein-coding
mm_159001.1	chr1	153851144	153851144	-	1	NA	promoter-TSS (NM_178243)	promoter-TSS (NM_178243)	51	NM_178243	240817	Mm.439405	NM_178243	ENSMUSG00000045968	Teddm2	5830403L16Rik|AJ554213|Me9|e92	transmembrane epididymal family member 2	protein-coding
mm_82710.1	chr9	24503200	24503231	-	1	NA	promoter-TSS (NM_172920)	promoter-TSS (NM_172920)	-75	NM_172920	244745	Mm.38526	NM_172920	ENSMUSG00000043067	Dpy19l1	1100001I19Rik|6030402K12|AI225861|AW558481	dpy-19-like 1 (C. elegans)	protein-coding
mm_31905.1	chr4	84698009	84698026	+	1	NA	Intergenic	Intergenic	-22931	NM_172870	242509	Mm.190774	NM_172870	ENSMUSG00000028487	Bnc2	5031434M05Rik|8430420F16Rik	basonuclin 2	protein-coding
mm_163782.1	chr13	120258492	120258502	+	1	NA	Intergenic	Intergenic	-4598	NM_001310627	236546	Mm.247428	NM_199060	ENSMUSG00000095071	AF067061	-	cDNA sequence AF067061	protein-coding
mm_90473.1	chr10	127850032	127850040	+	1	NA	exon (NM_147222, exon 1 of 4)	exon (NM_147222, exon 1 of 4)	108	NM_147222	216453	Mm.222953	NM_147222	ENSMUSG00000054052	Rdh19	RDH-S|RDH-S2|Rdhs	retinol dehydrogenase 19	protein-coding
mm_171819.1	chr5	138702346	138702350	-	1	NA	Intergenic	IAPLTR4|LTR|ERVK	-52733	NM_030565	80752	Mm.320355	NM_030565	ENSMUSG00000025854	Fam20c	C76981|DMP-4|DMP4|GEF-CK|mKIAA4081	family with sequence similarity 20, member C	protein-coding
mm_54205.1	chr6	24956349	24956371	-	1	NA	promoter-TSS (NM_177013)	promoter-TSS (NM_177013)	-235	NM_177013	319832	Mm.127446	NM_177013	ENSMUSG00000048022	Tmem229a	6332401O19Rik	transmembrane protein 229A	protein-coding
mm_40972.1	chr5	77001548	77001595	+	1	NA	Intergenic	Intergenic	-2484	NM_206935	384185	Mm.451858	NM_206935	ENSMUSG00000063820	Arl9	1700110A09Rik	ADP-ribosylation factor-like 9	protein-coding
mm_19528.1	chr2	94263044	94263048	-	1	NA	Intergenic	Intergenic	-1647	NR_030431	735259		NR_030431	ENSMUSG00000076335	Mir670	Mirn670|mir-670|mmu-mir-670	microRNA 670	ncRNA
mm_34028.1	chr4	138075153	138075164	+	1	NA	intron (NM_001256195, intron 4 of 34)	L1M3|LINE|L1	63360	NR_126429	73563	Mm.444294	NR_126429	ENSMUSG00000084804	1700095J12Rik	-	RIKEN cDNA 1700095J12 gene	ncRNA
mm_103788.1	chr11	82845836	82845856	-	1	NA	exon (NM_001164569, exon 2 of 8)	exon (NM_001164569, exon 2 of 8)	-16803	NM_026097	67338	Mm.341608	NM_026097	ENSMUSG00000020696	Rffl	1700051E09Rik|4930516L10Rik|BG080975|Carp2	ring finger and FYVE like domain containing protein	protein-coding
mm_112203.1	chr12	113426824	113426882	-	1	NA	Intergenic	Intergenic	-62712	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_154339.1	chrM	4405	4426	+	1	NA	NA	Intergenic	NA	NA								
mm_15749.1	chr2	164237605	164237638	+	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	720	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_79142.1	chr9	47658367	47658403	+	1	NA	intron (NM_001025600, intron 1 of 8)	L1MC5|LINE|L1	128033	NM_018770	54725	Mm.234832	NM_018770	ENSMUSG00000032076	Cadm1	2900073G06Rik|3100001I08Rik|AI987920|Bl2|Igsf4|Igsf4a|Necl2|RA175|RA175A|RA175B|RA175C|RA175N|ST17|SgIGSF|SynCam|Tslc1	cell adhesion molecule 1	protein-coding
mm_128563.1	chr15	56172417	56172425	-	1	NA	Intergenic	Intergenic	-265472	NM_016667	20649	Mm.309425	NM_016667	ENSMUSG00000060429	Sntb1	-	syntrophin, basic 1	protein-coding
mm_159864.1	chr5	143651262	143651262	+	1	NA	promoter-TSS (NM_001163548)	promoter-TSS (NM_001163548)	21	NM_001163548	19159	Mm.281003	NM_011182	ENSMUSG00000018001	Cyth3	AI648983|ARNO3|CLM3|Grp1|Pscd3	cytohesin 3	protein-coding
mm_24250.1	chr3	89167080	89167084	+	1	NA	exon (NM_007712, exon 2 of 13)	exon (NM_007712, exon 2 of 13)	2287	NM_001163432	12748	Mm.288098	NM_007712	ENSMUSG00000068917	Clk2	AU041688	CDC-like kinase 2	protein-coding
mm_1716.1	chr1	75236965	75236972	+	1	NA	intron (NM_020266, intron 2 of 8)	intron (NM_020266, intron 2 of 8)	266	NM_001159885	56812	Mm.489660	NM_020266	ENSMUSG00000026203	Dnajb2	2700059H22Rik|Dnajb10|Hsj1|mDj8	DnaJ heat shock protein family (Hsp40) member B2	protein-coding
mm_47103.1	chr5	118413538	118413553	-	1	NA	Intergenic	MLT1J1|LTR|ERVL-MaLR	-147174	NM_001347445	76199	Mm.206238	NM_172424	ENSMUSG00000018076	Med13l	2210413I17Rik|6330591G05Rik|9030618F05Rik|Thrap2|Trap240L|mKIAA1025	mediator complex subunit 13-like	protein-coding
mm_17897.1	chr2	35100678	35100692	-	1	NA	promoter-TSS (NM_178885)	promoter-TSS (NM_178885)	0	NM_001243102	98870	Mm.415380	NM_178885	ENSMUSG00000035875	AI182371	AI046667	expressed sequence AI182371	protein-coding
mm_112331.1	chr12	115912793	115912797	-	1	NA	Intergenic	Intergenic	-134929	NM_001004066	56220	Mm.254997	NM_019565	ENSMUSG00000042063	Zfp386	Kzf1|mKIAA4205	zinc finger protein 386 (Kruppel-like)	protein-coding
mm_116650.1	chr13	49183969	49183975	-	1	NA	Intergenic	Intergenic	-3575	NM_013610	18081	Mm.18503	NM_013610	ENSMUSG00000037966	Ninj1	AU024536	ninjurin 1	protein-coding
mm_7874.1	chr1	133009640	133009643	-	1	NA	intron (NM_001302801, intron 4 of 10)	B1_Mur3|SINE|Alu	15775	NR_126506	17248	Mm.426531	NM_008575	ENSMUSG00000054387	Mdm4	4933417N07Rik|AA414968|AL023055|AU018793|AU021806|C85810|Mdmx	transformed mouse 3T3 cell double minute 4	protein-coding
mm_82872.1	chr9	32424115	32424135	-	1	NA	exon (NM_008026, exon 9 of 9)	exon (NM_008026, exon 9 of 9)	30140	NM_001168354	56379	Mm.390168	NM_019659	ENSMUSG00000041248	Kcnj1	Kir1.1|ROMK|Romk2	potassium inwardly-rectifying channel, subfamily J, member 1	protein-coding
mm_98694.1	chr11	96299224	96299252	+	1	NA	promoter-TSS (NM_008269)	promoter-TSS (NM_008269)	67	NM_008269	15414	Mm.215	NM_008269	ENSMUSG00000000690	Hoxb6	Hox-2.2	homeobox B6	protein-coding
mm_37326.1	chr4	119422356	119422418	-	1	NA	promoter-TSS (NM_001014900)	promoter-TSS (NM_001014900)	33	NM_026494	106564	Mm.27245	NM_026494	ENSMUSG00000028636	Ppcs	6330579B17Rik|AI413471|AI790434	phosphopantothenoylcysteine synthetase	protein-coding
mm_90102.1	chr10	116966364	116966367	+	1	NA	promoter-TSS (NR_027846)	promoter-TSS (NR_027846)	91	NR_027846	103175	Mm.27138	NR_027846	ENSMUSG00000031294	D630029K05Rik	AI314111|AI875589	RIKEN cDNA D630029K05 gene	ncRNA
mm_110608.1	chr12	56536746	56536790	-	1	NA	5' UTR (NM_009385, exon 1 of 3)	5' UTR (NM_009385, exon 1 of 3)	140	NM_009385	21869	Mm.89972	NM_009385	ENSMUSG00000001496	Nkx2-1	AV026640|Nkx2.1|T/EBP|Titf1|Ttf-1	NK2 homeobox 1	protein-coding
mm_20087.1	chr2	120731742	120731748	-	1	NA	promoter-TSS (NM_026891)	promoter-TSS (NM_026891)	-228	NM_026891	68968	Mm.2289	NM_026891	ENSMUSG00000027284	Cdan1	1500015A01Rik|AI448026|AW492297|CDA-I|CDA1|CDAI	congenital dyserythropoietic anemia, type I (human)	protein-coding
mm_120399.1	chr14	64720320	64720323	+	1	NA	intron (NM_001081177, intron 6 of 39)	B4|SINE|B4	67790	NM_001081177	16554	Mm.23611	NM_001081177	ENSMUSG00000060012	Kif13b	5330429L19Rik|6030414C01|AI429803|C130021D12Rik|GAKIN	kinesin family member 13B	protein-coding
mm_102133.1	chr11	53430751	53430761	-	1	NA	promoter-TSS (NM_025352)	promoter-TSS (NM_025352)	75	NM_025352	22272	Mm.251621	NM_025352	ENSMUSG00000044894	Uqcrq	1100001F06Rik|1500040F11Rik|5830407L17Rik|9.5kDa|AA959903|QP-C|Qpc|Uqcrb|c1502	ubiquinol-cytochrome c reductase, complex III subunit VII	protein-coding
mm_146511.1	chr18	3337506	3337538	-	1	NA	promoter-TSS (NM_001110852)	promoter-TSS (NM_001110852)	67	NM_001110851	12916	Mm.5244	NM_013498	ENSMUSG00000063889	Crem	ICER|ICERI	cAMP responsive element modulator	protein-coding
mm_46005.1	chr5	90696118	90696139	-	1	NA	Intergenic	Intergenic	-55601	NM_001310656	73246	Mm.30172	NM_028478	ENSMUSG00000029370	Rassf6	1600016B17Rik	Ras association (RalGDS/AF-6) domain family member 6	protein-coding
mm_28473.1	chr3	92080914	92080931	-	1	NA	exon (NM_008508, exon 2 of 2)	exon (NM_008508, exon 2 of 2)	2220	NM_008508	16939	Mm.1121	NM_008508	ENSMUSG00000043165	Lor	AI036317|S77319	loricrin	protein-coding
mm_115116.1	chr13	104178799	104178872	+	1	NA	promoter-TSS (NR_003546)	promoter-TSS (NR_003546)	-263	NM_030731	81003	Mm.244190	NM_030731	ENSMUSG00000021712	Trim23	6330516O20Rik|AI450195|Arfd1	tripartite motif-containing 23	protein-coding
mm_22307.1	chr2	180381325	180381332	-	1	NA	intron (NR_040745, intron 4 of 6)	intron (NR_040745, intron 4 of 6)	-4276	NR_045331	622283	Mm.447602	NR_045331		Mir1a-1hg	EG622283|Gm6307	Mir1a-1 and Mir133a-2 host gene	ncRNA
mm_573.1	chr1	38987767	38987779	+	1	NA	promoter-TSS (NM_026850)	promoter-TSS (NM_026850)	-41	NM_026850	68833	Mm.28121	NM_026850	ENSMUSG00000026078	Pdcl3	1110061A19Rik|C80025|Viaf1	phosducin-like 3	protein-coding
mm_70698.1	chr8	15028755	15028769	+	1	NA	exon (NM_029116, exon 2 of 2)	exon (NM_029116, exon 2 of 2)	17316	NR_037972	434285	Mm.334425	NM_001007591	ENSMUSG00000049008	BB014433	-	expressed sequence BB014433	ncRNA
mm_29150.1	chr3	105959213	105959237	-	1	NA	promoter-TSS (NM_027432)	promoter-TSS (NM_027432)	-273	NM_027432	70465	Mm.5110	NM_027432	ENSMUSG00000000561	Wdr77	2610003I18Rik|2610312E17Rik|C79984|p44/MEP50	WD repeat domain 77	protein-coding
mm_59405.1	chr7	27029075	27029087	+	1	NA	promoter-TSS (NM_133657)	promoter-TSS (NM_133657)	-9	NM_133657	13085	Mm.20770	NM_133657	ENSMUSG00000060407	Cyp2a12	-	cytochrome P450, family 2, subfamily a, polypeptide 12	protein-coding
mm_66641.1	chr7	45615485	45615490	-	1	NA	promoter-TSS (NM_020013)	promoter-TSS (NM_020013)	3	NM_020013	56636	Mm.143736	NM_020013	ENSMUSG00000030827	Fgf21	-	fibroblast growth factor 21	protein-coding
mm_134548.1	chr16	19884268	19884285	-	1	NA	promoter-TSS (NR_015488)	promoter-TSS (NR_015488)	-2	NR_015488	68162	Mm.35159	NR_015488		A930003A15Rik	AI853191	RIKEN cDNA A930003A15 gene	ncRNA
mm_151218.1	chr19	53677287	53677291	+	1	NA	promoter-TSS (NM_001170847)	promoter-TSS (NM_001170847)	-17	NM_001170847	73713	Mm.313695	NM_001170847	ENSMUSG00000043639	Rbm20	1110018J23Rik|2010003H22Rik|AI646761	RNA binding motif protein 20	protein-coding
mm_146095.1	chr18	73863616	73863648	+	1	NA	intron (NM_001305882, intron 2 of 8)	intron (NM_001305882, intron 2 of 8)	4247	NM_001305882	71263	Mm.126220	NM_027741	ENSMUSG00000064036	Mro	4930507C04Rik|4933435E20Rik	maestro	protein-coding
mm_54496.1	chr6	35510270	35510281	-	1	NA	3' UTR (NM_008098, exon 4 of 4)	3' UTR (NM_008098, exon 4 of 4)	29613	NM_008098	14489	Mm.182746	NM_008098	ENSMUSG00000029840	Mtpn	5033418D15Rik|Gcdp|V1	myotrophin	protein-coding
mm_142928.1	chr17	53990630	53990675	-	1	NA	promoter-TSS (NM_018751)	promoter-TSS (NM_018751)	-21	NM_018751	20888	Mm.10108	NM_018751	ENSMUSG00000023943	Sult1c1	(PST)G|P-SULT|ST1C1|Stp2|Sult1a2|mOLFST	sulfotransferase family, cytosolic, 1C, member 1	protein-coding
mm_110018.1	chr12	16657276	16657279	-	1	NA	intron (NM_008747, intron 2 of 3)	intron (NM_008747, intron 2 of 3)	3807	NM_008747	18217	Mm.281715	NM_008747	ENSMUSG00000020591	Ntsr2	NT2R|NTRL	neurotensin receptor 2	protein-coding
mm_30799.1	chr4	20008394	20008451	+	1	NA	promoter-TSS (NM_015767)	promoter-TSS (NM_015767)	93	NM_015767	50500	Mm.24375	NM_015767	ENSMUSG00000073988	Ttpa	alpha-TTP	tocopherol (alpha) transfer protein	protein-coding
mm_80598.1	chr9	86467174	86467219	+	1	NA	promoter-TSS (NM_177208)	promoter-TSS (NM_177208)	42	NM_177208	320615	Mm.245500	NM_177208	ENSMUSG00000034973	Dopey1	B130005I07Rik|BC035275|C130028L17|D9Ertd809e	dopey family member 1	protein-coding
mm_86414.1	chr10	3391265	3391266	+	1	NA	intron (NM_133485, intron 1 of 3)	intron (NM_133485, intron 1 of 3)	25115	NM_133485	76142	Mm.308126	NM_133485	ENSMUSG00000040653	Ppp1r14c	6330514J04Rik|KEPI	protein phosphatase 1, regulatory (inhibitor) subunit 14c	protein-coding
mm_143214.1	chr17	62882427	62882460	-	1	NA	Intergenic	CpG-6536	-1126	NM_010109	13640	Mm.7978	NM_010109	ENSMUSG00000048915	Efna5	AL-1|AV158822|EFL-5|Ephrin-A5|Epl7|LERK-7|RAGS	ephrin A5	protein-coding
mm_46052.1	chr5	92137638	92137702	-	1	NA	promoter-TSS (NM_019490)	promoter-TSS (NM_019490)	-268	NM_019490	56041	Mm.15868	NM_019490	ENSMUSG00000029407	Uso1	115kDa|TAP|Vdp	USO1 vesicle docking factor	protein-coding
mm_131505.1	chr16	17451957	17451972	+	1	NA	promoter-TSS (NM_007764)	promoter-TSS (NM_007764)	-21	NM_001277231	12929	Mm.21048	NM_007764	ENSMUSG00000006134	Crkl	1110025F07Rik|AA589403|AI325100|Crkol	v-crk avian sarcoma virus CT10 oncogene homolog-like	protein-coding
mm_121534.1	chr14	122375211	122375232	+	1	NA	intron (NM_029556, intron 3 of 7)	intron (NM_029556, intron 3 of 7)	75894	NR_033325	328479	Mm.86095	NR_033325	ENSMUSG00000064052	Gm5089	6530402A20|C030005G22Rik|EG328479	predicted gene 5089	ncRNA
mm_35579.1	chr4	41740937	41740964	-	1	NA	exon (NM_001286551, exon 2 of 4)	exon (NM_001286551, exon 2 of 4)	409	NM_001286540	18391	Mm.425181	NM_011014	ENSMUSG00000036078	Sigmar1	Oprs1|Sig1R|sigma1R	sigma non-opioid intracellular receptor 1	protein-coding
mm_67341.1	chr7	79822151	79822162	-	1	NA	3' UTR (NM_008486, exon 20 of 20)	3' UTR (NM_008486, exon 20 of 20)	11429	NM_008589	17293	Mm.31472	NM_008589	ENSMUSG00000030543	Mesp2	bHLHc6	mesoderm posterior 2	protein-coding
mm_20701.1	chr2	132945678	132945688	-	1	NA	5' UTR (NM_198029, exon 1 of 15)	5' UTR (NM_198029, exon 1 of 15)	353	NM_198029	241639	Mm.209784	NM_198029	ENSMUSG00000027356	Fermt1	5830467P10Rik|Kindlin-1	fermitin family member 1	protein-coding
mm_157892.1	chrX	76301683	76301693	-	1	NA	Intergenic	Intergenic	37382	NM_001013760	238829	Mm.292319	NM_001013760	ENSMUSG00000071738	Cldn34b3	EG238829|Gm4937	claudin 34B3	protein-coding
mm_85202.1	chr9	96752654	96752735	-	1	NA	non-coding (NR_015511, exon 1 of 4)	non-coding (NR_015511, exon 1 of 4)	137	NR_015511	319859	Mm.259909	NM_177020		E030011O05Rik	-	RIKEN cDNA E030011O05 gene	ncRNA
mm_96313.1	chr11	63271401	63271411	+	1	NA	intron (NR_105772, intron 4 of 6)	intron (NR_105772, intron 4 of 6)	114663	NR_105772	102466632		NR_105772	ENSMUSG00000098829	Mir6354	Gm27282|mmu-mir-6354	microRNA 6354	ncRNA
mm_41997.1	chr5	107830263	107830312	+	1	NA	5' UTR (NM_001276397, exon 1 of 1)	5' UTR (NM_001276397, exon 1 of 1)	125	NM_001276397	73318	Mm.441500	NM_028502	ENSMUSG00000063447	Ube2d2b	1700013N18Rik	ubiquitin-conjugating enzyme E2D 2B	protein-coding
mm_117347.1	chr13	69611422	69611446	-	1	NA	promoter-TSS (NM_175283)	promoter-TSS (NM_175283)	29	NM_175283	78925	Mm.451912	NM_175283	ENSMUSG00000021594	Srd5a1	0610031P22Rik|4930435F02Rik|S5AR 1|Srd5a-1	steroid 5 alpha-reductase 1	protein-coding
mm_19279.1	chr2	85536668	85536695	-	1	NA	Intergenic	Intergenic	-17746	NM_001081664	228151	Mm.17636	NM_001081664	ENSMUSG00000075217	4833423E24Rik	Fads2p1|Gm113	RIKEN cDNA 4833423E24 gene	protein-coding
mm_53707.1	chr6	143169926	143169929	+	1	NA	intron (NM_029250, intron 1 of 7)	intron (NM_029250, intron 1 of 7)	2697	NM_029250	75320	Mm.272548	NM_029250	ENSMUSG00000030275	Etnk1	1110061E11Rik|4930555L11Rik|AI195356|AI841245|C80956|D6Ertd3e|EKI1	ethanolamine kinase 1	protein-coding
mm_128522.1	chr15	54278598	54278630	-	1	NA	promoter-TSS (NM_008764)	promoter-TSS (NM_008764)	-130	NM_008764	18383	Mm.15383	NM_008764	ENSMUSG00000063727	Tnfrsf11b	OCIF|Opg|TR1	tumor necrosis factor receptor superfamily, member 11b (osteoprotegerin)	protein-coding
mm_67045.1	chr7	67280596	67280612	-	1	NA	intron (NM_001033713, intron 4 of 11)	intron (NM_001033713, intron 4 of 11)	57988	NM_001191051	75099	Mm.121691	NM_175215	ENSMUSG00000043831	Lysmd4	4930506D23Rik	LysM, putative peptidoglycan-binding, domain containing 4	protein-coding
mm_60928.1	chr7	46847530	46847533	+	1	NA	intron (NM_001136069, intron 1 of 7)	AT_rich|Low_complexity|Low_complexity	449	NM_001136069	16828	Mm.29324	NM_010699	ENSMUSG00000063229	Ldha	Ldh1|Ldhm|l7R2	lactate dehydrogenase A	protein-coding
mm_53317.1	chr6	129187157	129187167	+	1	NA	TTS (NM_053109)	TTS (NM_053109)	6547	NM_053109	93694	Mm.197536	NM_053109	ENSMUSG00000030157	Clec2d	Clr-b|Clrb|Ocil	C-type lectin domain family 2, member d	protein-coding
mm_53119.1	chr6	125100869	125100882	+	1	NA	exon (NM_145979, exon 4 of 39)	exon (NM_145979, exon 4 of 39)	3851	NR_106012	102466272		NR_106012	ENSMUSG00000098762	Mir7045	Gm27758|mmu-mir-7045	microRNA 7045	ncRNA
mm_168918.1	chr12	58770034	58770038	+	1	NA	Intergenic	L1Md_T|LINE|L1	241981	NM_009147	20334	Mm.491137	NM_009147	ENSMUSG00000020986	Sec23a	Msec23|Sec23r	SEC23 homolog A, COPII coat complex component	protein-coding
mm_156857.1	chrX	164401837	164401848	+	1	NA	TTS (NM_001308489)	TTS (NM_001308489)	-17945	NM_011081	18700	Mm.3781	NM_011081	ENSMUSG00000031381	Piga	AI194334|Pig-a	phosphatidylinositol glycan anchor biosynthesis, class A	protein-coding
mm_5352.1	chr1	25228815	25228834	-	1	NA	intron (NM_175642, intron 16 of 30)	intron (NM_175642, intron 16 of 30)	49130	NM_001204913	100504323	Mm.484176	NM_001204913		Gm20172	-	predicted gene, 20172	protein-coding
mm_29140.1	chr3	105894619	105894629	-	1	NA	intron (NM_027025, intron 1 of 6)	intron (NM_027025, intron 1 of 6)	-9797	NM_009631	11542	Mm.235024	NM_009631	ENSMUSG00000000562	Adora3	A3AR|A3R|AA3R|ARA3|Gpcr2	adenosine A3 receptor	protein-coding
mm_141623.1	chr17	32895443	32895454	-	1	NA	Intergenic	MERV1_LTR|LTR|ERV1	-3845	NM_207245	240066	Mm.26636	NM_207245	ENSMUSG00000095325	Zfp870	AI173952	zinc finger protein 870	protein-coding
mm_96066.1	chr11	59706351	59706389	+	1	NA	intron (NM_012027, intron 3 of 23)	intron (NM_012027, intron 3 of 23)	33784	NR_045476	69320	Mm.443242	NR_045476	ENSMUSG00000086330	1700007J10Rik	4930573L17Rik	RIKEN cDNA 1700007J10 gene	ncRNA
mm_55817.1	chr6	83053678	83053693	-	1	NA	promoter-TSS (NR_125891)	promoter-TSS (NR_125891)	-836	NR_125891	11993	Mm.386752	NM_007517	ENSMUSG00000068328	Aup1	AA589454	ancient ubiquitous protein 1	protein-coding
mm_105131.1	chr11	101417416	101417427	-	1	NA	promoter-TSS (NM_144829)	promoter-TSS (NM_144829)	12	NM_144829	69684	Mm.146283	NM_144829	ENSMUSG00000075528	Aarsd1	1110069E20Rik|2310044P18Rik|AA589600|AlaX|AlaXp-II	alanyl-tRNA synthetase domain containing 1	protein-coding
mm_84438.1	chr9	66096180	66096183	-	1	NA	intron (NM_019727, intron 8 of 14)	intron (NM_019727, intron 8 of 14)	-26450	NM_001025612	382083	Mm.477103	NM_001025612	ENSMUSG00000039452	Snx22	Gm1120	sorting nexin 22	protein-coding
mm_166822.1	chr7	18065952	18065960	+	1	NA	promoter-TSS (NM_001162524)	promoter-TSS (NM_001162524)	27	NM_001162523	67315	Mm.46089	NM_026087	ENSMUSG00000030366	Ceacam12	1600031J20Rik|Ceacam12-C1|Ceacam12-C3|Ceacam12C1|Ceacam12C3	carcinoembryonic antigen-related cell adhesion molecule 12	protein-coding
mm_8299.1	chr1	143702833	143702847	-	1	NA	promoter-TSS (NM_145991)	promoter-TSS (NM_145991)	53	NM_145991	214498	Mm.156727	NM_145991	ENSMUSG00000026361	Cdc73	8430414L16Rik|C130030P16Rik|C81219|Hrpt2	cell division cycle 73, Paf1/RNA polymerase II complex component	protein-coding
mm_151580.1	chr19	61224398	61224440	+	1	NA	TTS (NM_009970)	TTS (NM_009970)	3999	NM_009970	12982	Mm.287228	NM_009970	ENSMUSG00000059326	Csf2ra	CD116|Csfgmra|GM-CSF-Ra|GM-CSFR	colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)	protein-coding
mm_84381.1	chr9	65422781	65422791	-	1	NA	promoter-TSS (NM_178933)	promoter-TSS (NM_178933)	-13	NM_178933	330962	Mm.335247	NM_178933	ENSMUSG00000053862	Slc51b	Ostb	solute carrier family 51, beta subunit	protein-coding
mm_41741.1	chr5	102768712	102768722	+	1	NA	promoter-TSS (NM_001286468)	promoter-TSS (NM_001286468)	-93	NM_001286468	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding
mm_107134.1	chr12	21286309	21286329	+	1	NA	promoter-TSS (NM_008403)	promoter-TSS (NM_008403)	22	NM_018813	54451	Mm.356778	NM_018813	ENSMUSG00000054309	Cpsf3	-	cleavage and polyadenylation specificity factor 3	protein-coding
mm_166336.1	chr5	114601042	114601042	-	1	NA	intron (NM_001004180, intron 2 of 2)	intron (NM_001004180, intron 2 of 2)	32791	NM_001004180	433940	Mm.194212	NM_001004180	ENSMUSG00000041930	Fam222a	-	family with sequence similarity 222, member A	protein-coding
mm_44652.1	chr5	28210088	28210100	-	1	NA	promoter-TSS (NM_001310511)	promoter-TSS (NM_001310511)	74	NM_001310511	269637	Mm.68286	NM_175651	ENSMUSG00000044681	Cnpy1	1500012D20Rik|9630008K15Rik|AI853839	canopy FGF signaling regulator 1	protein-coding
mm_37551.1	chr4	125346964	125346975	-	1	NA	Intergenic	Intergenic	-143862	NM_001081097	14807	Mm.40896	NM_001081097	ENSMUSG00000001985	Grik3	9630027E11|GluK3|GluR7-3|Glur-7|Glur7	glutamate receptor, ionotropic, kainate 3	protein-coding
mm_82882.1	chr9	32502523	32502534	-	1	NA	intron (NM_008026, intron 1 of 8)	intron (NM_008026, intron 1 of 8)	38924	NM_008026	14247	Mm.258908	NM_008026	ENSMUSG00000016087	Fli1	EWSR2|Fli-1|SIC-1|Sic1	Friend leukemia integration 1	protein-coding
mm_65894.1	chr7	30090472	30090536	-	1	NA	promoter-TSS (NM_152814)	promoter-TSS (NM_152814)	6	NM_152814	72556	Mm.441512	NM_152814	ENSMUSG00000078768	Zfp566	2700043M03Rik|mszf4	zinc finger protein 566	protein-coding
mm_120029.1	chr14	55824970	55825011	+	1	NA	5' UTR (NM_001168346, exon 1 of 9)	5' UTR (NM_001168346, exon 1 of 9)	195	NM_023699	73181	Mm.27908	NM_023699	ENSMUSG00000023411	Nfatc4	3110041H08Rik|AW107667|AW546455|Nfat3	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 4	protein-coding
mm_164768.1	chr17	86652963	86652964	-	1	NA	intron (NM_011104, intron 14 of 14)	intron (NM_011104, intron 14 of 14)	-100901	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_32013.1	chr4	94739523	94739537	+	1	NA	5' UTR (NM_001290551, exon 1 of 22)	5' UTR (NM_001290551, exon 1 of 22)	241	NM_001290551	21687	Mm.14313	NM_013690	ENSMUSG00000006386	Tek	AA517024|Cd202b|Hyk|STK1|Tie-2|Tie2	endothelial-specific receptor tyrosine kinase	protein-coding
mm_139633.1	chr17	57367627	57367634	+	1	NA	intron (NM_010130, intron 2 of 21)	Lx10|LINE|L1	8944	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_167256.1	chr8	25101607	25101627	+	1	NA	intron (NM_031257, intron 1 of 11)	intron (NM_031257, intron 1 of 11)	194	NM_031257	83436	Mm.261122	NM_031257	ENSMUSG00000031557	Plekha2	6430512N22Rik|AI851530|AU041791|TAPP2|W91773	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 2	protein-coding
mm_171230.1	chr3	66902727	66902727	+	1	NA	Intergenic	L1Md_T|LINE|L1	76084	NM_001302358	20429	Mm.39093	NM_013665	ENSMUSG00000027833	Shox2	6330543G17Rik|OG12|Og12x|Prx3|SHOT	short stature homeobox 2	protein-coding
mm_98038.1	chr11	85341128	85341133	+	1	NA	intron (NM_016910, intron 5 of 5)	intron (NM_016910, intron 5 of 5)	-12034	NM_001166642	192197	Mm.209989	NM_138681	ENSMUSG00000059439	Bcas3	1500019F07Rik|2610028P08Rik|AU021018|BC028339|K20D4|rudhira	breast carcinoma amplified sequence 3	protein-coding
mm_80055.1	chr9	69340783	69340802	+	1	NA	intron (NM_001289916, intron 1 of 9)	intron (NM_001289916, intron 1 of 9)	23455	NR_136934	102642202	Mm.415363	NR_136934	ENSMUSG00000086648	Gm15511	OTTMUSG00000023029	predicted gene 15511	ncRNA
mm_132480.1	chr16	36828365	36828434	+	1	NA	promoter-TSS (NM_177128)	promoter-TSS (NM_177128)	-1	NM_177128	320299	Mm.222934	NM_177128	ENSMUSG00000022837	Iqcb1	6820449I09Rik|AV128382|NPHP5	IQ calmodulin-binding motif containing 1	protein-coding
mm_116151.1	chr13	29984412	29984465	-	1	NA	promoter-TSS (NM_001289920)	promoter-TSS (NM_001289920)	-47	NM_001289920	13557	Mm.268356	NM_010093	ENSMUSG00000016477	E2f3	E2F3b|E2f3a	E2F transcription factor 3	protein-coding
mm_42421.1	chr5	115327126	115327199	+	1	NA	promoter-TSS (NM_025573)	promoter-TSS (NM_025573)	-15	NM_025573	108014	Mm.287826	NM_025573	ENSMUSG00000029538	Srsf9	25kDa|2610029M16Rik|SRp30c|Sfrs9	serine/arginine-rich splicing factor 9	protein-coding
mm_114091.1	chr13	54633298	54633301	+	1	NA	intron (NM_178397, intron 1 of 10)	intron (NM_178397, intron 1 of 10)	11515	NM_178397	76577	Mm.194459	NM_178397	ENSMUSG00000025873	Faf2	2210404D11Rik|AI462440|Ubxd8|mKIAA0887	Fas associated factor family member 2	protein-coding
mm_87020.1	chr10	28074814	28074873	+	1	NA	promoter-TSS (NM_008983)	promoter-TSS (NM_008983)	23	NM_008983	19272	Mm.332303	NM_008983	ENSMUSG00000019889	Ptprk	AI853699|PTPk|RPTPkappa	protein tyrosine phosphatase, receptor type, K	protein-coding
mm_99983.1	chr11	114675475	114675495	+	1	NA	promoter-TSS (NM_053273)	promoter-TSS (NM_053273)	17	NM_053273	117160	Mm.271934	NM_053273	ENSMUSG00000034714	Ttyh2	1110001A03Rik	tweety family member 2	protein-coding
mm_32923.1	chr4	119137051	119137077	+	1	NA	3' UTR (NM_011400, exon 10 of 10)	3' UTR (NM_011400, exon 10 of 10)	28319	NM_011400	20525	Mm.21002	NM_011400	ENSMUSG00000028645	Slc2a1	Glut-1|Glut1	solute carrier family 2 (facilitated glucose transporter), member 1	protein-coding
mm_5832.1	chr1	52817644	52817693	-	1	NA	promoter-TSS (NM_008384)	promoter-TSS (NM_008384)	20	NM_008384	16329	Mm.917	NM_008384	ENSMUSG00000026102	Inpp1	2300002C06Rik|AV137389	inositol polyphosphate-1-phosphatase	protein-coding
mm_160384.1	chr8	45069137	45069137	+	1	NA	promoter-TSS (NM_008639)	promoter-TSS (NM_008639)	-73	NM_008639	17773	Mm.5133	NM_008639	ENSMUSG00000054764	Mtnr1a	MR|MelR	melatonin receptor 1A	protein-coding
mm_105060.1	chr11	100715775	100715801	-	1	NA	3' UTR (NM_001305003, exon 6 of 6)	3' UTR (NM_001305003, exon 6 of 6)	1938	NM_029307	75482	Mm.46175	NM_029307	ENSMUSG00000017832	Hspb9	1700007H20Rik	heat shock protein, alpha-crystallin-related, B9	protein-coding
mm_42963.1	chr5	123131006	123131039	+	1	NA	intron (NM_175092, intron 2 of 4)	intron (NM_175092, intron 2 of 4)	1607	NM_175092	23912	Mm.253876	NM_175092	ENSMUSG00000029449	Rhof	AI845056|AV026554|Arhf|Ifld1|Rif	ras homolog family member F (in filopodia)	protein-coding
mm_121891.1	chr14	21742905	21742908	-	1	NA	promoter-TSS (NM_013849)	promoter-TSS (NM_013849)	-27	NM_013849	27389	Mm.390674	NM_013849	ENSMUSG00000021768	Dusp13	DUSP13A|DUSP13B|Gm1203|LMW-DSP6|MDSP|TMDP|TS-DSP6	dual specificity phosphatase 13	protein-coding
mm_100772.1	chr11	4789774	4789782	-	1	NA	exon (NM_001252253, exon 12 of 15)	exon (NM_001252253, exon 12 of 15)	-43000	NM_138948	192650	Mm.207056	NM_138948	ENSMUSG00000009075	Cabp7	-	calcium binding protein 7	protein-coding
mm_1386.1	chr1	66944923	66944932	+	1	NA	5' UTR (NM_021285, exon 1 of 7)	5' UTR (NM_021285, exon 1 of 7)	129	NM_021285	17901	Mm.1000	NM_021285	ENSMUSG00000061816	Myl1	AI325107|MLC1f|MLC3f|Mylf	myosin, light polypeptide 1	protein-coding
mm_99115.1	chr11	100140924	100140958	+	1	NA	exon (NM_008471, exon 6 of 6)	exon (NM_008471, exon 6 of 6)	2758	NM_001313963	16669	Mm.439699	NM_008471	ENSMUSG00000020911	Krt19	AI663979|CK-19|EndoC|K19|Krt-1.19|Krt1-19	keratin 19	protein-coding
mm_5745.1	chr1	45926502	45926560	-	1	NA	promoter-TSS (NM_016917)	promoter-TSS (NM_016917)	-937	NM_016917	53945	Mm.28756	NM_016917	ENSMUSG00000025993	Slc40a1	Dusg|Fpn1|IREG1|MTP|MTP1|Ol5|Pcm|Slc11a3|Slc39a1	solute carrier family 40 (iron-regulated transporter), member 1	protein-coding
mm_21912.1	chr2	166603694	166603695	-	1	NA	intron (NM_177782, intron 10 of 39)	intron (NM_177782, intron 10 of 39)	-69024	NR_105783	102465188		NR_105783	ENSMUSG00000098675	Mir6364	Gm27327|mmu-mir-6364	microRNA 6364	ncRNA
mm_6945.1	chr1	85731197	85731242	-	1	NA	intron (NM_177055, intron 1 of 5)	RMER15-int|LTR|ERVL	5387	NM_177055	319997	Mm.116691	NM_177055	ENSMUSG00000052760	A630001G21Rik	-	RIKEN cDNA A630001G21 gene	protein-coding
mm_160229.1	chr7	102195903	102195903	-	1	NA	intron (NM_022979, intron 1 of 22)	intron (NM_022979, intron 1 of 22)	13964	NM_001287167	269966	Mm.439800	NM_022979	ENSMUSG00000063550	Nup98	4732457F17|AI849286|Nup96	nucleoporin 98	protein-coding
mm_54361.1	chr6	31114803	31114820	-	1	NA	intron (NR_110471, intron 3 of 3)	intron (NR_110471, intron 3 of 3)	-51718	NR_029532	387223		NR_029532	ENSMUSG00000065604	Mir29b-1	Mirn29b|Mirn29b-1|mir-29b-1	microRNA 29b-1	ncRNA
mm_109872.1	chr12	4916199	4916220	-	1	NA	Intergenic	Intergenic	-1144	NM_001099628	320817	Mm.210966	NM_001099628	ENSMUSG00000052812	Atad2b	1110014E10Rik|BC032887|C79189|D530031C13Rik	ATPase family, AAA domain containing 2B	protein-coding
mm_13361.1	chr2	103424821	103424829	+	1	NA	intron (NM_010125, intron 1 of 6)	intron (NM_010125, intron 1 of 6)	757	NM_010125	13711	Mm.20888	NM_010125	ENSMUSG00000027186	Elf5	ESE-2|ESE-5|ESE-5.	E74-like factor 5	protein-coding
mm_121266.1	chr14	103075917	103075949	+	1	NA	exon (NM_001033242, exon 4 of 4)	exon (NM_001033242, exon 4 of 4)	5717	NM_001033242	211286	Mm.295289	NM_001033242	ENSMUSG00000022125	Cln5	A730075N08Rik	ceroid-lipofuscinosis, neuronal 5	protein-coding
mm_148909.1	chr19	6950747	6950765	+	1	NA	exon (NM_007522, exon 3 of 4)	exon (NM_007522, exon 3 of 4)	8194	NM_001285453	12015	Mm.4387	NM_007522	ENSMUSG00000024959	Bad	AI325008|Bbc2	BCL2-associated agonist of cell death	protein-coding
mm_12440.1	chr2	70690655	70690684	+	1	NA	exon (NM_027352, exon 10 of 10)	exon (NM_027352, exon 10 of 10)	29160	NM_027352	70231	Mm.271950	NM_027352	ENSMUSG00000014959	Gorasp2	0610011A07Rik|2410043M02Rik|5730520M13Rik|9430094F20Rik|AW552058|ENSMUSG00000075299|GOLPH2|GRASP55|GRS2|p59	golgi reassembly stacking protein 2	protein-coding
mm_92033.1	chr10	62486576	62486604	-	1	NA	promoter-TSS (NM_001113355)	promoter-TSS (NM_001113355)	8	NM_001113355	30930	Mm.260703	NM_133672	ENSMUSG00000020078	Vps26a	AA407240|HB58|Vps26	VPS26 retromer complex component A	protein-coding
mm_90424.1	chr10	127493182	127493208	+	1	NA	intron (NM_027900, intron 20 of 23)	intron (NM_027900, intron 20 of 23)	-8522	NM_177707	237611	Mm.32087	NM_177707	ENSMUSG00000040287	Stac3	9830125E18	SH3 and cysteine rich domain 3	protein-coding
mm_26742.1	chr3	6800307	6800313	-	1	NA	Intergenic	IAPEY_LTR|LTR|ERVK	-179867	NM_027048	69347	Mm.45822	NM_027048	ENSMUSG00000069118	1700008P02Rik	-	RIKEN cDNA 1700008P02 gene	protein-coding
mm_160789.1	chr10	129670594	129670594	-	1	NA	promoter-TSS (NM_146285)	promoter-TSS (NM_146285)	-77	NM_146285	258282	Mm.222982	NM_146285	ENSMUSG00000058513	Olfr801	MOR110-10	olfactory receptor 801	protein-coding
mm_159969.1	chr6	97312405	97312405	-	1	NA	intron (NM_001346639, intron 11 of 22)	intron (NM_001346639, intron 11 of 22)	-59625	NM_001081157	320502	Mm.68163	NM_001081157	ENSMUSG00000044086	Lmod3	5430424A14Rik	leiomodin 3 (fetal)	protein-coding
mm_91198.1	chr10	21160363	21160378	-	1	NA	intron (NM_010848, intron 1 of 14)	CpG	614	NM_001198914	17863	Mm.52109	NM_010848	ENSMUSG00000019982	Myb	AI550390|M16449|c-myb	myeloblastosis oncogene	protein-coding
mm_59057.1	chr7	19414886	19414896	+	1	NA	intron (NM_007710, intron 2 of 7)	intron (NM_007710, intron 2 of 7)	3797	NM_007710	12715	Mm.2375	NM_007710	ENSMUSG00000030399	Ckm	Ckmm|M-CK|MCK	creatine kinase, muscle	protein-coding
mm_1300.1	chr1	64532982	64532996	+	1	NA	5' UTR (NM_009952, exon 1 of 9)	5' UTR (NM_009952, exon 1 of 9)	185	NM_001037726	12912	Mm.422634	NM_009952	ENSMUSG00000025958	Creb1	2310001E10Rik|3526402H21Rik|AV083133|Creb|Creb-1	cAMP responsive element binding protein 1	protein-coding
mm_5898.1	chr1	54585452	54585463	-	1	NA	Intergenic	Intergenic	-27773	NM_001163314	241062	Mm.103539	NM_175508	ENSMUSG00000073678	Pgap1	5033403E17Rik|9030223K07Rik|A530084K22|D230012E17Rik|oto	post-GPI attachment to proteins 1	protein-coding
mm_26505.1	chr3	145758910	145758951	+	1	NA	exon (NM_026993, exon 1 of 6)	exon (NM_026993, exon 1 of 6)	238	NM_026993	69219	Mm.234247	NM_026993	ENSMUSG00000028194	Ddah1	2410006N07Rik|2510015N06Rik|AI987801|AW050362	dimethylarginine dimethylaminohydrolase 1	protein-coding
mm_81522.1	chr9	110055141	110055144	+	1	NA	intron (NM_001311163, intron 1 of 10)	intron (NM_001311163, intron 1 of 10)	3121	NM_001311164	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_44689.1	chr5	30155102	30155112	-	1	NA	promoter-TSS (NM_001289798)	promoter-TSS (NM_001289798)	-127	NM_178878	97212	Mm.200497	NM_178878	ENSMUSG00000025745	Hadha	C77020|Mtpa	hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), alpha subunit	protein-coding
mm_47764.1	chr5	131537760	131537791	-	1	NA	intron (NM_177047, intron 5 of 18)	CpG	-230253	NM_145218	212996	Mm.299204	NM_145218	ENSMUSG00000034040	Wbscr17	AA388321|E330012B09Rik	Williams-Beuren syndrome chromosome region 17 homolog (human)	protein-coding
mm_37735.1	chr4	129575287	129575297	-	1	NA	Intergenic	Intergenic	-1651	NM_001162433	16818	Mm.293753	NM_010693	ENSMUSG00000000409	Lck	Hck-3|Lsk|Lskt|p56<lck>|p56Lck	lymphocyte protein tyrosine kinase	protein-coding
mm_85848.1	chr9	110653958	110654005	-	1	NA	5' UTR (NM_183276, exon 1 of 54)	5' UTR (NM_183276, exon 1 of 54)	180	NM_183276	235627	Mm.335481	NM_183276	ENSMUSG00000056724	Nbeal2	1110014F23Rik|BC042396|mKIAA0540	neurobeachin-like 2	protein-coding
mm_120781.1	chr14	74641506	74641516	+	1	NA	5' UTR (NM_172812, exon 1 of 3)	5' UTR (NM_172812, exon 1 of 3)	671	NM_172812	15558	Mm.214351	NM_172812	ENSMUSG00000034997	Htr2a	E030013E04|Htr-2|Htr2	5-hydroxytryptamine (serotonin) receptor 2A	protein-coding
mm_84098.1	chr9	58249703	58249791	-	1	NA	promoter-TSS (NM_008884)	promoter-TSS (NM_008884)	39	NM_178087	18854	Mm.392123	NM_008884	ENSMUSG00000036986	Pml	1200009E24Rik|AI661194|Trim19	promyelocytic leukemia	protein-coding
mm_75320.1	chr8	41416994	41417036	-	1	NA	5' UTR (NM_013522, exon 1 of 9)	5' UTR (NM_013522, exon 1 of 9)	103	NM_013522	14300	Mm.217312	NM_013522	ENSMUSG00000031590	Frg1	-	FSHD region gene 1	protein-coding
mm_53837.1	chr6	148354649	148354662	+	1	NA	promoter-TSS (NR_003634)	promoter-TSS (NR_003634)	-1	NR_003634	66184	Mm.391542	NM_025405	ENSMUSG00000063171	Rps4l	1110033J19Rik|AA407494|Rps4y2	ribosomal protein S4-like	pseudo
mm_93424.1	chr10	108799860	108799864	-	1	NA	intron (NM_001252341, intron 4 of 11)	intron (NM_001252341, intron 4 of 11)	-99702	NM_203660	368203	Mm.452758	NM_203660		Gm5136	C6.1AL|EG368203	predicted gene 5136	protein-coding
mm_87967.1	chr10	63416366	63416366	+	1	NA	Intergenic	Intergenic	-13732	NM_177612	216033	Mm.444692	NM_177612	ENSMUSG00000060843	Ctnna3	4930429L08Rik|4933408A16|Catna3|Vr22	catenin (cadherin associated protein), alpha 3	protein-coding
mm_70434.1	chr8	11556868	11556918	+	1	NA	5' UTR (NM_011919, exon 1 of 2)	5' UTR (NM_011919, exon 1 of 2)	436	NM_011919	26356	Mm.25709	NM_011919	ENSMUSG00000045969	Ing1	2610028J21Rik|AA407184|AI875420|mING1h|p33Ing1|p37Ing1b	inhibitor of growth family, member 1	protein-coding
mm_161366.1	chr14	62744577	62744577	-	1	NA	intron (NM_008715, intron 3 of 18)	intron (NM_008715, intron 3 of 18)	-15924	NR_045503	71000	Mm.399410	NR_045503	ENSMUSG00000097775	4931440J10Rik	-	RIKEN cDNA 4931440J10 gene	ncRNA
mm_167603.1	chr9	51433297	51433301	+	1	NA	Intergenic	MLT1E2|LTR|ERVL-MaLR	-104382	NM_027217	69809	Mm.75315	NM_027217	ENSMUSG00000036027	1810046K07Rik	-	RIKEN cDNA 1810046K07 gene	protein-coding
mm_166094.1	chr4	141546766	141546799	+	1	NA	non-coding (NR_030695, exon 1 of 1)	non-coding (NR_030695, exon 1 of 1)	620	NR_030695	320456	Mm.32859	NM_177163		B330016D10Rik	-	RIKEN cDNA B330016D10 gene	ncRNA
mm_125958.1	chr15	76266521	76266531	+	1	NA	TTS (NR_045747)	TTS (NR_045747)	-1563	NM_028852	74281	Mm.159156	NM_028852	ENSMUSG00000049653	Spatc1	1700084J23Rik|speriolin	spermatogenesis and centriole associated 1	protein-coding
mm_60622.1	chr7	44668208	44668239	+	1	NA	intron (NM_001271540, intron 1 of 41)	intron (NM_001271540, intron 1 of 41)	2620	NM_001271540	71960	Mm.158289	NM_028021	ENSMUSG00000030739	Myh14	2400004E04Rik|II-C|NHMCII|NMHC II-C	myosin, heavy polypeptide 14	protein-coding
mm_59637.1	chr7	28157647	28157654	+	1	NA	exon (NM_001164655, exon 16 of 20)	exon (NM_001164655, exon 16 of 20)	-12098	NM_007991	14113	Mm.4595	NM_007991	ENSMUSG00000046865	Fbl	AL022665|FIB|FLRN|RNU3IP1	fibrillarin	protein-coding
mm_21352.1	chr2	157121904	157121918	-	1	NA	exon (NM_001139520, exon 5 of 17)	exon (NM_001139520, exon 5 of 17)	13311	NM_001139520	56045	Mm.248478	NM_018851	ENSMUSG00000027639	Samhd1	E330031J07Rik|Mg11	SAM domain and HD domain, 1	protein-coding
mm_147448.1	chr18	46526049	46526055	-	1	NA	promoter-TSS (NM_173423)	promoter-TSS (NM_173423)	-81	NM_173423	240263	Mm.38249	NM_173423	ENSMUSG00000033319	Fem1c	2610312A07Rik|3632443A22Rik|AI646567	fem-1 homolog c (C.elegans)	protein-coding
mm_96309.1	chr11	63158643	63158702	+	1	NA	3' UTR (NM_008885, exon 5 of 5)	3' UTR (NM_008885, exon 5 of 5)	25869	NM_001302260	18858	Mm.1237	NM_008885	ENSMUSG00000018217	Pmp22	22kDa|Gas-3|HNPP|Tr|trembler	peripheral myelin protein 22	protein-coding
mm_69641.1	chr7	138850033	138850057	-	1	NA	intron (NM_026391, intron 2 of 8)	intron (NM_026391, intron 2 of 8)	3659	NM_026391	52432	Mm.258739	NM_026391	ENSMUSG00000041769	Ppp2r2d	1300017E19Rik|D7Ertd753e|MDS026	protein phosphatase 2, regulatory subunit B, delta	protein-coding
mm_94516.1	chr11	8655620	8655656	+	1	NA	intron (NM_001083587, intron 1 of 30)	ORR1F|LTR|ERVL-MaLR	8897	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_7396.1	chr1	118299592	118299592	-	1	NA	3' UTR (NM_011650, exon 6 of 6)	3' UTR (NM_011650, exon 6 of 6)	11540	NM_011650	22099	Mm.426637	NM_011650	ENSMUSG00000026374	Tsn	2610034C24Rik|AU040286|C3PO|TB-RBP	translin	protein-coding
mm_20454.1	chr2	129365055	129365071	-	1	NA	exon (NM_008361, exon 7 of 7)	exon (NM_008361, exon 7 of 7)	-4839	NR_015474	329514	Mm.207315	NM_177848	ENSMUSG00000074805	Il1bos	9430083I22|Gm14047|OTTMUSG00000015529	interleukin 1 beta, opposite strand	ncRNA
mm_111868.1	chr12	108001707	108001720	-	1	NA	intron (NM_001079883, intron 1 of 3)	intron (NM_001079883, intron 1 of 3)	1701	NM_001079883	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_148245.1	chr18	80698173	80698190	-	1	NA	exon (NM_016791, exon 2 of 8)	exon (NM_016791, exon 2 of 8)	9992	NM_001164111	18018	Mm.329560	NM_016791	ENSMUSG00000033016	Nfatc1	2210017P03Rik|AI449492|AV076380|NF-ATc|NFAT2|NFATc|Nfatcb	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 1	protein-coding
mm_74569.1	chr8	11016291	11016301	-	1	NA	intron (NR_046017, intron 1 of 4)	intron (NR_046017, intron 1 of 4)	-7866	NM_001081212	384783	Mm.407207	NM_001081212	ENSMUSG00000038894	Irs2	Irs-2	insulin receptor substrate 2	protein-coding
mm_88023.1	chr10	67193549	67193553	+	1	NA	intron (NM_207221, intron 3 of 25)	intron (NM_207221, intron 3 of 25)	7801	NM_001242396	108829	Mm.23846	NM_207221	ENSMUSG00000037876	Jmjd1c	5430433L24Rik|D630035I23Rik|Jmjdic|TRIP8	jumonji domain containing 1C	protein-coding
mm_43391.1	chr5	135734957	135734976	+	1	NA	TTS (NM_172541)	TTS (NM_172541)	923	NR_106001	102466791		NR_106001	ENSMUSG00000099197	Mir7034	Gm27372|mmu-mir-7034	microRNA 7034	ncRNA
mm_15630.1	chr2	162987475	162987486	+	1	NA	promoter-TSS (NM_013731)	promoter-TSS (NM_013731)	-1	NM_001291154	27219	Mm.26462	NM_013731	ENSMUSG00000017868	Sgk2	AI098171|AW146006|Sgkl	serum/glucocorticoid regulated kinase 2	protein-coding
mm_110032.1	chr12	16875842	16875851	-	1	NA	Intergenic	Intergenic	-19132	NM_009072	19878	Mm.276024	NM_009072	ENSMUSG00000020580	Rock2	B230113H15Rik|ROKalpha|Rho-kinase|Rock-II|Rock2m|mKIAA0619	Rho-associated coiled-coil containing protein kinase 2	protein-coding
mm_164999.1	chr19	20520172	20520172	+	1	NA	intron (NR_015502, intron 2 of 3)	Lx6|LINE|L1	27457	NR_015502	320092	Mm.482524	NR_015502		E030003E18Rik	1700127G21Rik	RIKEN cDNA E030003E18 gene	ncRNA
mm_118141.1	chr13	105054370	105054382	-	1	NA	5' UTR (NM_029879, exon 1 of 6)	5' UTR (NM_029879, exon 1 of 6)	554	NM_029879	52882	Mm.100348	NM_029879	ENSMUSG00000021719	Rgs7bp	A930030I01Rik|AI842293|D13Bwg1146e|R7bp	regulator of G-protein signalling 7 binding protein	protein-coding
mm_100896.1	chr11	6066122	6066137	-	1	NA	promoter-TSS (NM_001174054)	promoter-TSS (NM_001174054)	-381	NM_007595	12323	Mm.439733	NM_007595	ENSMUSG00000057897	Camk2b	CaMKII	calcium/calmodulin-dependent protein kinase II, beta	protein-coding
mm_94150.1	chr10	128743985	128743995	-	1	NA	promoter-TSS (NM_016811)	promoter-TSS (NM_016811)	66	NM_016811	13139	Mm.291235	NM_016811	ENSMUSG00000025357	Dgka	80kDa|AW146112|Dagk1	diacylglycerol kinase, alpha	protein-coding
mm_161571.1	chr16	21891984	21891984	+	1	NA	promoter-TSS (NM_172821)	promoter-TSS (NM_172821)	15	NM_172821	71751	Mm.420837	NM_172821	ENSMUSG00000033618	Map3k13	C130026N12Rik|LZK	mitogen-activated protein kinase kinase kinase 13	protein-coding
mm_68208.1	chr7	104400765	104400786	-	1	NA	Intergenic	Intergenic	-42129	NM_175648	244183	Mm.347647	NM_175648	ENSMUSG00000052749	Trim30b	A530023O14Rik|Trim30-1	tripartite motif-containing 30B	protein-coding
mm_26521.1	chr3	145924406	145924412	+	1	NA	5' UTR (NM_009740, exon 1 of 3)	5' UTR (NM_009740, exon 1 of 3)	147	NM_009740	12042	Mm.239141	NM_009740	ENSMUSG00000028191	Bcl10	AI132454|BCL-10|C81403|CARMEN|CIPER|CLAP|ME10|cE10	B cell leukemia/lymphoma 10	protein-coding
mm_32131.1	chr4	99158769	99158781	+	1	NA	Intergenic	MLT1F2|LTR|ERVL-MaLR	-35159	NM_175029	242557	Mm.241663	NM_175029	ENSMUSG00000028550	Atg4c	Apg4-C|Apg4c|Atg4cl|Autl1	autophagy related 4C, cysteine peptidase	protein-coding
mm_96823.1	chr11	69994735	69994743	+	1	NA	3' UTR (NM_019749, exon 4 of 4)	3' UTR (NM_019749, exon 4 of 4)	-1027	NM_001291125	78246	Mm.20805	NM_030064	ENSMUSG00000018572	Phf23	JUNE-1	PHD finger protein 23	protein-coding
mm_76118.1	chr8	80859237	80859252	-	1	NA	intron (NM_021356, intron 1 of 9)	RLTR15|LTR|ERVK	21235	NM_021356	14388	Mm.277409	NM_021356	ENSMUSG00000031714	Gab1	AA408973|AW107238	growth factor receptor bound protein 2-associated protein 1	protein-coding
mm_87689.1	chr10	59403402	59403433	+	1	NA	promoter-TSS (NM_023530)	promoter-TSS (NM_023530)	-268	NM_023530	69836	Mm.30268	NM_023530	ENSMUSG00000009646	Pla2g12b	2010002E04Rik|Fksg71|Pla2g13|hlb218	phospholipase A2, group XIIB	protein-coding
mm_166324.1	chr5	112257481	112257490	+	1	NA	exon (NM_001312894, exon 2 of 6)	exon (NM_001312894, exon 2 of 6)	1665	NM_001312893	12960	Mm.29488	NM_023695	ENSMUSG00000029343	Crybb1	3110006K12Rik|BB1CRY	crystallin, beta B1	protein-coding
mm_116376.1	chr13	40968711	40968721	-	1	NA	Intergenic	Intergenic	-32294	NM_026550	68083	Mm.24789	NM_026550	ENSMUSG00000038683	Pak1ip1	5830431I15Rik|5930415H02Rik|AA419825|AI314040|AW556169|Gdpd1|PIP1	PAK1 interacting protein 1	protein-coding
mm_160261.1	chr7	109617161	109617161	-	1	NA	promoter-TSS (NR_037617)	promoter-TSS (NR_037617)	-14	NM_029811	76954	Mm.252009	NM_029811	ENSMUSG00000031024	St5	2010004M01Rik|2610305K15Rik	suppression of tumorigenicity 5	protein-coding
mm_161497.1	chr15	88982814	88982814	+	1	NA	promoter-TSS (NM_031260)	promoter-TSS (NM_031260)	-180	NM_031260	83456	Mm.358791	NM_031260	ENSMUSG00000015365	Mov10l1	CHAMP|Csm	Moloney leukemia virus 10-like 1	protein-coding
mm_74721.1	chr8	17438966	17438969	-	1	NA	intron (NM_053171, intron 1 of 69)	Lx9|LINE|L1	96418	NM_053171	94109	Mm.436988	NM_053171	ENSMUSG00000060924	Csmd1	B930082H09|mKIAA1890	CUB and Sushi multiple domains 1	protein-coding
mm_114560.1	chr13	74350314	74350369	+	1	NA	promoter-TSS (NM_024201)	promoter-TSS (NM_024201)	24	NM_001168658	67433	Mm.101586	NM_024201	ENSMUSG00000021578	Ccdc127	0610011N22Rik|5430420E17Rik|A430066A18|AI256405|AW050060|C130002N06	coiled-coil domain containing 127	protein-coding
mm_24116.1	chr3	88159725	88159731	+	1	NA	intron (NM_133665, intron 6 of 10)	B1_Mur1|SINE|Alu	17356	NM_001310593	17261	Mm.28184	NM_133665	ENSMUSG00000001419	Mef2d	C80750	myocyte enhancer factor 2D	protein-coding
mm_168483.1	chr1	14918999	14919006	-	1	NA	promoter-TSS (NM_177781)	promoter-TSS (NM_177781)	-140	NM_177781	277328	Mm.186329	NM_177781	ENSMUSG00000032769	Trpa1	Anktm1|TRPA1b	transient receptor potential cation channel, subfamily A, member 1	protein-coding
mm_120013.1	chr14	55745796	55745804	+	1	NA	promoter-TSS (NM_026819)	promoter-TSS (NM_026819)	107	NM_026403	67842	Mm.180338	NM_026403	ENSMUSG00000019297	Nop9	2610027L16Rik	NOP9 nucleolar protein	protein-coding
mm_118213.1	chr13	110280066	110280074	-	1	NA	5' UTR (NM_023852, exon 1 of 5)	5' UTR (NM_023852, exon 1 of 5)	136	NM_023852	67295	Mm.151600	NM_023852	ENSMUSG00000021700	Rab3c	2700062I01Rik|3110015B08Rik|3110037E15Rik|AI850886	RAB3C, member RAS oncogene family	protein-coding
mm_113260.1	chr13	28575745	28575748	+	1	NA	intron (NR_045053, intron 6 of 8)	intron (NR_045053, intron 6 of 8)	135127	NR_105787	102466635		NR_105787	ENSMUSG00000099158	Mir6368	Gm27800|mmu-mir-6368	microRNA 6368	ncRNA
mm_33113.1	chr4	124737799	124737806	+	1	NA	Intergenic	Intergenic	-4048	NM_008385	16330	Mm.296202	NM_008385	ENSMUSG00000028894	Inpp5b	5PTase|AW260155|INPP5P	inositol polyphosphate-5-phosphatase B	protein-coding
mm_131509.1	chr16	17489692	17489703	+	1	NA	promoter-TSS (NM_175178)	promoter-TSS (NM_175178)	20	NM_175178	72168	Mm.40038	NM_175178	ENSMUSG00000022763	Aifm3	2810401C16Rik|AI840249|Aifl	apoptosis-inducing factor, mitochondrion-associated 3	protein-coding
mm_117783.1	chr13	97022454	97022461	-	1	NA	exon (NM_001284205, exon 3 of 3)	exon (NM_001284205, exon 3 of 3)	11905	NM_025585	66479	Mm.390629	NM_025585	ENSMUSG00000052075	1700029F12Rik	-	RIKEN cDNA 1700029F12 gene	protein-coding
mm_160724.1	chr10	70266812	70266812	+	1	NA	intron (NM_025807, intron 2 of 5)	intron (NM_025807, intron 2 of 5)	21536	NM_025807	66859	Mm.19325	NM_025807	ENSMUSG00000037762	Slc16a9	1200003C15Rik|4930425B13Rik|AI552636	solute carrier family 16 (monocarboxylic acid transporters), member 9	protein-coding
mm_53171.1	chr6	125342780	125342819	+	1	NA	exon (NM_011324, exon 9 of 12)	exon (NM_011324, exon 9 of 12)	-6924	NM_011609	21937	Mm.1258	NM_011609	ENSMUSG00000030341	Tnfrsf1a	CD120a|FPF|TNF-R|TNF-R-I|TNF-R1|TNF-R55|TNF-alphaR1|TNFAR|TNFR60|TNFRI|TNFRp55|TNFalpha-R1|Tnfr-2|Tnfr1|p55|p55-R	tumor necrosis factor receptor superfamily, member 1a	protein-coding
mm_86200.1	chr9	119978289	119978300	-	1	NA	intron (NM_153287, intron 1 of 4)	intron (NM_153287, intron 1 of 4)	6364	NM_153287	215418	Mm.491094	NM_153287	ENSMUSG00000032515	Csrnp1	4931429D10Rik|Axud1|CSRNP-1|URAX1|taip-3	cysteine-serine-rich nuclear protein 1	protein-coding
mm_172128.1	chr6	3201611	3201629	+	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	-86899	NR_036696	667335	Mm.380219	NR_036696	ENSMUSG00000106779	Gm8579	EG667335	spermatogenesis associated glutamate (E)-rich protein 4a pseudogene	pseudo
mm_165323.1	chr2	110050491	110050494	-	1	NA	promoter-TSS (NR_040508)	promoter-TSS (NR_040508)	-13	NR_040508	75517	Mm.363927	NR_040508	ENSMUSG00000086186	Ccdc34os	1700024P03Rik	coiled-coil domain containing 34, opposite strand	ncRNA
mm_152744.1	chr19	19079077	19079091	-	1	NA	intron (NM_001043354, intron 1 of 9)	L2c|LINE|L2	32112	NM_001043354	225998	Mm.234641	NM_146095	ENSMUSG00000036192	Rorb	Nr1f2|RZR-beta|RZRB|Rorbeta|hstp	RAR-related orphan receptor beta	protein-coding
mm_102477.1	chr11	60046479	60046532	-	1	NA	promoter-TSS (NM_001290012)	promoter-TSS (NM_001290012)	-16	NM_001290011	18618	Mm.2731	NM_008819	ENSMUSG00000000301	Pemt	PEAMT|PEMT2|PLMT|Pempt|Pempt2	phosphatidylethanolamine N-methyltransferase	protein-coding
mm_128019.1	chr15	24605522	24605526	-	1	NA	Intergenic	Intergenic	808240	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	brain abundant, membrane attached signal protein 1	protein-coding
mm_24037.1	chr3	87796939	87796982	+	1	NA	promoter-TSS (NM_011832)	promoter-TSS (NM_011832)	9	NM_011832	23920	Mm.42041	NM_011832	ENSMUSG00000005640	Insrr	Irr	insulin receptor-related receptor	protein-coding
mm_171014.1	chr2	83953468	83953472	-	1	NA	Intergenic	MT2_Mm|LTR|ERVL	-12244	NM_027964	71861	Mm.116957	NM_027964	ENSMUSG00000034552	Zswim2	1700025P14Rik|4933437F18Rik|MEX	zinc finger SWIM-type containing 2	protein-coding
mm_64951.1	chr7	16387792	16387840	-	1	NA	promoter-TSS (NM_019748)	promoter-TSS (NM_019748)	80	NM_001285892	56459	Mm.258530	NM_019748	ENSMUSG00000052833	Sae1	2400010M20Rik|2610044L12Rik|AL033372|AOS1|AW743391|D7Ertd177e|HSPC140|Sua1|Uble1a	SUMO1 activating enzyme subunit 1	protein-coding
mm_45716.1	chr5	84417325	84417337	-	1	NA	promoter-TSS (NM_007937)	promoter-TSS (NM_007937)	51	NM_007937	13839	Mm.137991	NM_007937	ENSMUSG00000029245	Epha5	AI854630|AW125296|Cek7|Ehk1|Els1|Hek7|Rek7|bsk	Eph receptor A5	protein-coding
mm_39159.1	chr4	155561893	155561898	-	1	NA	promoter-TSS (NM_138671)	promoter-TSS (NM_138671)	-497	NM_138671	192185	Mm.28347	NM_138671	ENSMUSG00000029063	Nadk	4432404C02Rik|BC004012	NAD kinase	protein-coding
mm_32705.1	chr4	116075538	116075551	+	1	NA	promoter-TSS (NM_025641)	promoter-TSS (NM_025641)	275	NM_153521	230654	Mm.3655	NM_153521	ENSMUSG00000028703	Lrrc41	AA409966|AW555107|D630045E04Rik|D730026A16Rik|MUF1	leucine rich repeat containing 41	protein-coding
mm_123903.1	chr14	73217170	73217183	-	1	NA	intron (NM_009029, intron 17 of 26)	(GA)n|Simple_repeat|Simple_repeat	-10325	NR_030459	751541		NR_030459	ENSMUSG00000076121	Mir687	Mirn687|mir-687|mmu-mir-687	microRNA 687	ncRNA
mm_163045.1	chr11	54910116	54910116	+	1	NA	TTS (NM_021327)	TTS (NM_021327)	7262	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_59914.1	chr7	30417335	30417388	+	1	NA	TTS (NM_011827)	TTS (NM_011827)	2493	NM_011827	23900	Mm.379050	NM_011827	ENSMUSG00000064109	Hcst	DAP10|KAP10	hematopoietic cell signal transducer	protein-coding
mm_111273.1	chr12	85339347	85339391	-	1	NA	promoter-TSS (NM_145138)	promoter-TSS (NM_145138)	-7	NM_145138	217718	Mm.29071	NM_145138	ENSMUSG00000034290	Nek9	C130021H08Rik	NIMA (never in mitosis gene a)-related expressed kinase 9	protein-coding
mm_79742.1	chr9	62351460	62351460	+	1	NA	intron (NM_009672, intron 1 of 6)	intron (NM_009672, intron 1 of 6)	10117	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	protein-coding
mm_5195.1	chr1	13372435	13372457	-	1	NA	promoter-TSS (NM_001302702)	promoter-TSS (NM_001302702)	-17	NM_001302702	17978	Mm.2537	NM_008678	ENSMUSG00000005886	Ncoa2	D1Ertd433e|GRIP-1|Grip1|KAT13C|NCoA-2|SRC-2|TIF2|bHLHe75	nuclear receptor coactivator 2	protein-coding
mm_123958.1	chr14	74811432	74811440	-	1	NA	intron (NM_001252132, intron 9 of 18)	intron (NM_001252132, intron 9 of 18)	79139	NM_016903	13885	Mm.38055	NM_016903	ENSMUSG00000021996	Esd	Es-10|Es10|FGH|sid478	esterase D/formylglutathione hydrolase	protein-coding
mm_78273.1	chr9	22017602	22017620	+	1	NA	3' UTR (NM_010487, exon 7 of 7)	3' UTR (NM_010487, exon 7 of 7)	14623	NM_008925	19089	Mm.214593	NM_008925	ENSMUSG00000003402	Prkcsh	80K-H|PKCSH	protein kinase C substrate 80K-H	protein-coding
mm_76330.1	chr8	84706228	84706254	-	1	NA	3' UTR (NM_010906, exon 9 of 9)	3' UTR (NM_010906, exon 9 of 9)	4784	NM_008535	17095	Mm.4925	NM_008535	ENSMUSG00000034041	Lyl1	Lyl-1|bHLHa18	lymphoblastomic leukemia 1	protein-coding
mm_128837.1	chr15	68362091	68362104	-	1	NA	Intergenic	Intergenic	-20808	NR_029718	387228		NR_029718	ENSMUSG00000065437	Mir30d	Mirn30d|mir-30d|mmu-mir-30d	microRNA 30d	ncRNA
mm_19065.1	chr2	77520710	77520713	-	1	NA	intron (NM_178723, intron 3 of 9)	intron (NM_178723, intron 3 of 9)	-1045	NM_001113400	241494	Mm.490320	NM_178723	ENSMUSG00000027016	Zfp385b	B830010L13Rik|C130013B13Rik|Zfp533|Znf385b	zinc finger protein 385B	protein-coding
mm_927.1	chr1	55237192	55237255	+	1	NA	promoter-TSS (NM_175439)	promoter-TSS (NM_175439)	46	NM_175439	212679	Mm.19223	NM_175439	ENSMUSG00000046994	Mars2	C730026E21Rik|MetRS	methionine-tRNA synthetase 2 (mitochondrial)	protein-coding
mm_9260.1	chr1	171607379	171607403	-	1	NA	promoter-TSS (NM_001277968)	promoter-TSS (NM_001277968)	19	NM_001277968	17085	Mm.560	NM_008534	ENSMUSG00000004707	Ly9	AI893573|CD229|Lgp100|Ly-9|SLAMF3|T100	lymphocyte antigen 9	protein-coding
mm_126150.1	chr15	78406696	78406732	+	1	NA	promoter-TSS (NM_138670)	promoter-TSS (NM_138670)	2	NM_001162493	246221	Mm.294215	NM_138670	ENSMUSG00000071711	Mpst	Mst	mercaptopyruvate sulfurtransferase	protein-coding
mm_163655.1	chr13	71106437	71106486	-	1	NA	promoter-TSS (NR_130325)	promoter-TSS (NR_130325)	-628	NR_130325	100316804		NR_130325	ENSMUSG00000080580	Mir466f-4	Mirn466f-4|mmu-mir-466f-4	microRNA 466f-4	ncRNA
mm_22785.1	chr3	22076831	22076895	+	1	NA	5' UTR (NM_030732, exon 1 of 16)	5' UTR (NM_030732, exon 1 of 16)	211	NM_030732	81004	Mm.202966	NM_030732	ENSMUSG00000027630	Tbl1xr1	8030499H02Rik|A630076E03Rik|AW539987|C21|C230089I12Rik|DC42|Ira1|TBLR1	transducin (beta)-like 1X-linked receptor 1	protein-coding
mm_13644.1	chr2	114050369	114050420	+	1	NA	exon (NM_009608, exon 3 of 7)	exon (NM_009608, exon 3 of 7)	2481	NM_009608	11464	Mm.686	NM_009608	ENSMUSG00000068614	Actc1	Actc-1	actin, alpha, cardiac muscle 1	protein-coding
mm_71969.1	chr8	70534910	70534996	+	1	NA	exon (NM_001199631, exon 9 of 9)	exon (NM_001199631, exon 9 of 9)	-4722	NM_007924	13716	Mm.271973	NM_007924	ENSMUSG00000070002	Ell	Ell1|Men	elongation factor RNA polymerase II	protein-coding
mm_123779.1	chr14	70323784	70323798	-	1	NA	intron (NM_001135152, intron 2 of 9)	intron (NM_001135152, intron 2 of 9)	24642	NM_001135152	213053	Mm.270647	NM_144808	ENSMUSG00000022094	Slc39a14	FAD-123|ZIP-14|Zip14|fad123	solute carrier family 39 (zinc transporter), member 14	protein-coding
mm_7256.1	chr1	93754812	93754857	-	1	NA	promoter-TSS (NM_025920)	promoter-TSS (NM_025920)	4	NM_025920	67026	Mm.272356	NM_025920	ENSMUSG00000026279	Thap4	2010320B01Rik	THAP domain containing 4	protein-coding
mm_79902.1	chr9	65398508	65398580	+	1	NA	promoter-TSS (NM_001162923)	promoter-TSS (NM_001162923)	56	NM_001033158	70784	Mm.35827	NM_001033158	ENSMUSG00000041696	Rasl12	4631404I11Rik	RAS-like, family 12	protein-coding
mm_36948.1	chr4	109071280	109071282	-	1	NA	intron (NM_001346502, intron 15 of 23)	intron (NM_001346502, intron 15 of 23)	46755	NM_173350	100273	Mm.366315	NM_133885	ENSMUSG00000028559	Osbpl9	2600011I06Rik|AU015843|Orp-9	oxysterol binding protein-like 9	protein-coding
mm_151430.1	chr19	57117405	57117421	+	1	NA	intron (NM_001290813, intron 6 of 20)	intron (NM_001290813, intron 6 of 20)	1611	NM_001347459	226251	Mm.217161	NM_178688	ENSMUSG00000025085	Ablim1	2210411C18Rik|2610209L21Rik|4833406P10Rik|9330196J19Rik|AV079770|AW060987|AW215784|Limab1|mKIAA0059	actin-binding LIM protein 1	protein-coding
mm_163679.1	chr13	92021719	92021722	-	1	NA	Intergenic	Intergenic	-33678	NM_009027	19418	Mm.248630	NM_009027	ENSMUSG00000021708	Rasgrf2	6330417G04Rik|AW048350|Grf2|Ras-GRF2	RAS protein-specific guanine nucleotide-releasing factor 2	protein-coding
mm_86360.1	chr9	123760219	123760227	-	1	NA	Intergenic	Intergenic	-6988	NM_009913	12769	Mm.440604	NM_009913	ENSMUSG00000029530	Ccr9	A130091K22Rik|Cmkbr10|GPR-9-6	chemokine (C-C motif) receptor 9	protein-coding
mm_43720.1	chr5	139473017	139473059	+	1	NA	3' UTR (NM_001159908, exon 7 of 7)	3' UTR (NM_001159908, exon 7 of 7)	11453	NM_133349	100494	Mm.24521	NM_133349	ENSMUSG00000053581	Zfand2a	AA407930|AU016206|Airap	zinc finger, AN1-type domain 2A	protein-coding
mm_45948.1	chr5	90339725	90339802	-	1	NA	intron (NM_198010, intron 1 of 32)	intron (NM_198010, intron 1 of 32)	26422	NM_030886	81702	Mm.245522	NM_030886	ENSMUSG00000055204	Ankrd17	4933425K22Rik|A130069E23Rik|A930008M01|AA407558|AA516750|AU040470|Foe|Gtar|Mask|mKIAA0697	ankyrin repeat domain 17	protein-coding
mm_156095.1	chrX	112311376	112311407	+	1	NA	promoter-TSS (NM_026565)	promoter-TSS (NM_026565)	39	NM_026565	68117	Mm.161014	NM_026565	ENSMUSG00000025525	Apool	6720473G16Rik|9430083G14Rik|E130106L15Rik	apolipoprotein O-like	protein-coding
mm_62299.1	chr7	100159242	100159315	+	1	NA	promoter-TSS (NM_026010)	promoter-TSS (NM_026010)	1	NM_026010	67164	Mm.46777	NM_026010	ENSMUSG00000030725	Lipt2	2610209A20Rik	lipoyl(octanoyl) transferase 2 (putative)	protein-coding
mm_93373.1	chr10	105459450	105459484	-	1	NA	intron (NM_177368, intron 1 of 11)	intron (NM_177368, intron 1 of 11)	115012	NM_177368	278279	Mm.25225	NM_177368	ENSMUSG00000036019	Tmtc2	8430438D04Rik|D330034A10Rik	transmembrane and tetratricopeptide repeat containing 2	protein-coding
mm_171453.1	chr4	145510756	145510757	+	1	NA	promoter-TSS (NM_001324553)	promoter-TSS (NM_001324553)	-3	NM_001324553	101056073	Mm.276881	NM_001324553	ENSMUSG00000078503	LOC101056073	-	zinc finger protein 501-like	protein-coding
mm_36455.1	chr4	82505245	82505255	-	1	NA	5' UTR (NM_001113209, exon 1 of 12)	5' UTR (NM_001113209, exon 1 of 12)	529	NM_001286127	18028	Mm.317947	NM_008687	ENSMUSG00000008575	Nfib	6720429L07Rik|CTF|E030026I10Rik|NF-I/B|NF1-B|NFI-B	nuclear factor I/B	protein-coding
mm_120162.1	chr14	60733027	60733042	+	1	NA	5' UTR (NM_001310594, exon 1 of 10)	5' UTR (NM_001310594, exon 1 of 10)	130	NM_001310594	219140	Mm.149776	NM_001033272	ENSMUSG00000021990	Spata13	C79050|ESTM11|X83327|mFLJ00298	spermatogenesis associated 13	protein-coding
mm_52140.1	chr6	97971221	97971266	+	1	NA	intron (NM_001113198, intron 2 of 9)	intron (NM_001113198, intron 2 of 9)	-20540	NM_008601	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_172022.1	chr6	115809085	115809095	+	1	NA	promoter-TSS (NR_028546)	promoter-TSS (NR_028546)	-347	NM_172086	19951	Mm.104368	NM_172086	ENSMUSG00000057841	Rpl32	AU020185|rpL32-3A	ribosomal protein L32	protein-coding
mm_141188.1	chr17	26939440	26939463	-	1	NA	promoter-TSS (NM_026307)	promoter-TSS (NM_026307)	7	NR_104458	67675	Mm.439919	NM_026307	ENSMUSG00000024194	Cuta	0610039D01Rik|1810022E02Rik|1810060C03Rik|2700094G22Rik|AI326454	cutA divalent cation tolerance homolog	protein-coding
mm_169342.1	chr14	13938267	13938268	-	1	NA	Intergenic	LTRIS2|LTR|ERV1	23046	NM_001285780	66231	Mm.295875	NM_025435	ENSMUSG00000053453	Thoc7	Nif3l1bp1	THO complex 7	protein-coding
mm_9884.1	chr1	186623747	186623756	-	1	NA	3' UTR (NM_009367, exon 7 of 7)	3' UTR (NM_009367, exon 7 of 7)	-65070	NR_131158	320449	Mm.404477	NR_131124	ENSMUSG00000103690	A730004F24Rik	-	RIKEN cDNA A730004F24 gene	ncRNA
mm_65612.1	chr7	27508092	27508110	-	1	NA	exon (NM_019412, exon 5 of 6)	exon (NM_019412, exon 5 of 6)	8777	NM_019412	19153	Mm.10119	NM_019412	ENSMUSG00000053198	Prx	L-Periaxin	periaxin	protein-coding
mm_77852.1	chr9	5308843	5308873	+	1	NA	promoter-TSS (NM_007609)	promoter-TSS (NM_007609)	9	NM_007609	12363	Mm.1569	NM_007609	ENSMUSG00000033538	Casp4	CASP-11|CASP-4|Casp11|Caspl|ich-3	caspase 4, apoptosis-related cysteine peptidase	protein-coding
mm_70742.1	chr8	19142605	19142612	+	1	NA	3' UTR (NM_001034905, exon 2 of 2)	3' UTR (NM_001034905, exon 2 of 2)	1849	NM_001286493	546038	Mm.99206	NM_001034905	ENSMUSG00000059463	Spag11b	EG546038|Ep2c/h|Spag11c/h	sperm associated antigen 11B	protein-coding
mm_65345.1	chr7	24988306	24988315	-	1	NA	promoter-TSS (NR_106014)	promoter-TSS (NR_106014)	-643	NR_106014	102465634		NR_106014	ENSMUSG00000099258	Mir7047	Gm27270|mmu-mir-7047	microRNA 7047	ncRNA
mm_5455.1	chr1	36274445	36274467	-	1	NA	Intergenic	Intergenic	-1031	NM_153408	214854	Mm.389110	NM_153408	ENSMUSG00000047180	Neurl3	2010300P06Rik|Lincr	neuralized E3 ubiquitin protein ligase 3	protein-coding
mm_44878.1	chr5	34636490	34636540	-	1	NA	intron (NM_026660, intron 2 of 12)	intron (NM_026660, intron 2 of 12)	599	NM_026660	68294	Mm.34564	NM_026660	ENSMUSG00000001082	Mfsd10	0610009O03Rik|Tetran	major facilitator superfamily domain containing 10	protein-coding
mm_2946.1	chr1	132342298	132342304	+	1	NA	Intergenic	Intergenic	25647	NM_001311108	68875	Mm.273785	NM_178874	ENSMUSG00000042066	Tmcc2	1110063G11Rik	transmembrane and coiled-coil domains 2	protein-coding
mm_37403.1	chr4	121324913	121324928	-	1	NA	promoter-TSS (NM_001033791)	promoter-TSS (NM_001033791)	-3	NM_001033791	545677	Mm.372731	NM_001033791	ENSMUSG00000073764	Gm12888	OTTMUSG00000008911	predicted gene 12888	protein-coding
mm_120250.1	chr14	63003388	63003396	+	1	NA	Intergenic	B3A|SINE|B2	5315	NM_001039125	654465	Mm.424929	NM_001039125	ENSMUSG00000075573	Defb47	Defb41|EG654465	defensin beta 47	protein-coding
mm_88406.1	chr10	76721913	76721934	+	1	NA	exon (NM_009933, exon 4 of 35)	exon (NM_009933, exon 4 of 35)	4121	NM_009933	12833	Mm.2509	NM_009933	ENSMUSG00000001119	Col6a1	AI747156|Col6a-1	collagen, type VI, alpha 1	protein-coding
mm_83308.1	chr9	44041373	44041403	-	1	NA	Intergenic	Intergenic	-1996	NM_009382	21838	Mm.3951	NM_009382	ENSMUSG00000032011	Thy1	CD90|T25|Thy-1|Thy-1.2|Thy1.1|Thy1.2	thymus cell antigen 1, theta	protein-coding
mm_94133.1	chr10	128696215	128696256	-	1	NA	promoter-TSS (NM_177411)	promoter-TSS (NM_177411)	33	NM_177411	19344	Mm.12815	NM_011229	ENSMUSG00000000711	Rab5b	C030027M18Rik	RAB5B, member RAS oncogene family	protein-coding
mm_143083.1	chr17	57077043	57077067	-	1	NA	intron (NM_153551, intron 1 of 23)	intron (NM_153551, intron 1 of 23)	1455	NM_153551	70785	Mm.284447	NM_153551	ENSMUSG00000002668	Dennd1c	4432409M07Rik	DENN/MADD domain containing 1C	protein-coding
mm_127663.1	chr15	102520799	102520805	+	1	NA	intron (NM_009319, intron 3 of 8)	intron (NM_009319, intron 3 of 8)	2610	NM_009319	21357	Mm.291485	NM_009319	ENSMUSG00000023051	Tarbp2	Prbp|TRBP	TARBP2, RISC loading complex RNA binding subunit	protein-coding
mm_2983.1	chr1	133131289	133131364	+	1	NA	5' UTR (NM_133819, exon 1 of 2)	5' UTR (NM_133819, exon 1 of 2)	160	NM_133819	108954	Mm.293628	NM_133819	ENSMUSG00000046062	Ppp1r15b	1810033K10Rik|AI606441|C530022L24Rik|CReP	protein phosphatase 1, regulatory (inhibitor) subunit 15b	protein-coding
mm_143075.1	chr17	57031541	57031551	-	1	NA	promoter-TSS (NM_010613)	promoter-TSS (NM_010613)	-39	NM_010613	16549	Mm.34296	NM_010613	ENSMUSG00000007670	Khsrp	6330409F21Rik|Fbp2|Fubp2|Ksrp	KH-type splicing regulatory protein	protein-coding
mm_84583.1	chr9	69760848	69760856	-	1	NA	promoter-TSS (NR_040765)	promoter-TSS (NR_040765)	88	NM_022378	64290	Mm.440890	NM_022378	ENSMUSG00000059246	Foxb1	C43|Fkh5|Foxb1a|Foxb1b|Hfh-e5.1|Mf3|Twh	forkhead box B1	protein-coding
mm_41943.1	chr5	105731756	105731798	+	1	NA	intron (NM_178701, intron 1 of 2)	intron (NM_178701, intron 1 of 2)	30967	NM_178701	231549	Mm.23837	NM_178701	ENSMUSG00000046079	Lrrc8d	2810473G09Rik|4930525N13Rik|A930019F03|Lrrc5	leucine rich repeat containing 8D	protein-coding
mm_113403.1	chr13	33953203	33953215	+	1	NA	intron (NR_040707, intron 1 of 4)	intron (NR_040707, intron 1 of 4)	-11450	NM_001163239	18105	Mm.264036	NM_020282	ENSMUSG00000046949	Nqo2	NMO2|Nmor2|Ox2	NAD(P)H dehydrogenase, quinone 2	protein-coding
mm_84888.1	chr9	79759859	79759861	-	1	NA	promoter-TSS (NM_009945)	promoter-TSS (NM_009945)	-7	NM_009945	12866	Mm.152627	NM_009945	ENSMUSG00000032330	Cox7a2	COX7AL|Cox7a3|CoxVIIa-L	cytochrome c oxidase subunit VIIa 2	protein-coding
mm_82439.1	chr9	15279861	15279877	-	1	NA	promoter-TSS (NM_144933)	promoter-TSS (NM_144933)	-2	NM_144933	234959	Mm.44151	NM_144933	ENSMUSG00000031935	Med17	77kDa|C330002H14Rik|Crsp6|Trap80	mediator complex subunit 17	protein-coding
mm_127941.1	chr15	10713538	10713544	-	1	NA	promoter-TSS (NM_030690)	promoter-TSS (NM_030690)	-1	NM_030690	75646	Mm.212395	NM_030690	ENSMUSG00000022246	Rai14	1700008J19Rik|1700020L11Rik|Ankycorbin|Norpeg|mKIAA1334	retinoic acid induced 14	protein-coding
mm_154732.1	chrX	9747709	9747747	+	1	NA	Intergenic	Intergenic	-84745	NM_025975	67117	Mm.29150	NM_025975	ENSMUSG00000031176	Dynlt3	2310075M16Rik|AU042796|Tcte1l	dynein light chain Tctex-type 3	protein-coding
mm_68055.1	chr7	101836936	101836988	-	1	NA	intron (NM_010567, intron 1 of 28)	CpG-13418	862	NM_001122739	16332	Mm.476000	NM_010567	ENSMUSG00000032737	Inppl1	51C|SHIP2	inositol polyphosphate phosphatase-like 1	protein-coding
mm_55758.1	chr6	78378998	78379008	-	1	NA	promoter-TSS (NM_001161741)	promoter-TSS (NM_001161741)	-138	NM_013893	30053	Mm.33691	NM_013893	ENSMUSG00000068341	Reg3d	INGAP|Ingaprp	regenerating islet-derived 3 delta	protein-coding
mm_100924.1	chr11	6469969	6469991	-	1	NA	3' UTR (NM_011221, exon 1 of 1)	3' UTR (NM_011221, exon 1 of 1)	6096	NM_011221	19291	Mm.296150	NM_011221	ENSMUSG00000094483	Purb	2310015K15Rik|AA114818|Cager-2|D11Bwg0414e	purine rich element binding protein B	protein-coding
mm_88064.1	chr10	67647410	67647422	+	1	NA	Intergenic	Intergenic	-98461	NM_001005419	211488	Mm.297250	NM_001005419	ENSMUSG00000057134	Ado	Gm237	2-aminoethanethiol (cysteamine) dioxygenase	protein-coding
mm_33230.1	chr4	126830662	126830665	+	1	NA	intron (NM_001035525, intron 8 of 23)	intron (NM_001035525, intron 8 of 23)	76893	NM_001035526	100317	Mm.206206	NM_133886	ENSMUSG00000028830	AU040320	A730047D20Rik|AAVR|Kiaa0319l	expressed sequence AU040320	protein-coding
mm_135586.1	chr16	50578530	50578540	-	1	NA	Intergenic	Intergenic	-11968	NR_040566	75211	Mm.399337	NR_040566		4930542D17Rik	-	RIKEN cDNA 4930542D17 gene	ncRNA
mm_125752.1	chr15	73749583	73749596	+	1	NA	intron (NM_008975, intron 1 of 5)	intron (NM_008975, intron 1 of 5)	1563	NM_008975	19245	Mm.390807	NM_008975	ENSMUSG00000059895	Ptp4a3	AV088979|Prl-3|pPtp4a3	protein tyrosine phosphatase 4a3	protein-coding
mm_128228.1	chr15	36555587	36555592	-	1	NA	promoter-TSS (NM_025712)	promoter-TSS (NM_025712)	-17	NM_025712	66696	Mm.253627	NM_025712	ENSMUSG00000013611	Snx31	4631426E05Rik	sorting nexin 31	protein-coding
mm_118191.1	chr13	107782591	107782602	-	1	NA	intron (NM_145456, intron 3 of 14)	intron (NM_145456, intron 3 of 14)	-21509	NR_029759	723929		NR_029759	ENSMUSG00000065425	Mir325	Mirn325|mmu-mir-325	microRNA 325	ncRNA
mm_9495.1	chr1	173729749	173729770	-	1	NA	exon (NM_001204910, exon 5 of 8)	exon (NM_001204910, exon 5 of 8)	12050	NM_001204910	226691	Mm.440876	NM_001204910	ENSMUSG00000073490	Ifi207	AI607873|Pyhin-A	interferon activated gene 207	protein-coding
mm_52265.1	chr6	108371741	108371743	+	1	NA	intron (NM_010585, intron 13 of 61)	Lx8|LINE|L1	-118001	NR_106121	102465766		NR_106121	ENSMUSG00000105697	Mir7661	mmu-mir-7661	microRNA 7661	ncRNA
mm_121715.1	chr14	16249155	16249182	-	1	NA	promoter-TSS (NM_021504)	promoter-TSS (NM_021504)	-146	NM_021504	59007	Mm.258381	NM_021504	ENSMUSG00000021785	Ngly1	1110002C09Rik|PNGase|Png1	N-glycanase 1	protein-coding
mm_99940.1	chr11	111027458	111027501	+	1	NA	3' UTR (NM_001252208, exon 2 of 2)	3' UTR (NM_001252208, exon 2 of 2)	3619	NM_001252208	16517	Mm.30176	NM_010604	ENSMUSG00000051497	Kcnj16	6430410F18Rik|AI132396|Kir5.1	potassium inwardly-rectifying channel, subfamily J, member 16	protein-coding
mm_73279.1	chr8	104733998	104734024	+	1	NA	promoter-TSS (NM_133960)	promoter-TSS (NM_133960)	8	NM_133960	102022	Mm.212983	NM_133960	ENSMUSG00000055730	Ces2a	9130231C15Rik|AI266984|Ces6	carboxylesterase 2A	protein-coding
mm_67225.1	chr7	74549452	74549455	-	1	NA	intron (NM_001038643, intron 1 of 10)	ID2|SINE|ID	5327	NM_023908	108116	Mm.425467	NM_023908	ENSMUSG00000025790	Slco3a1	5830414C08Rik|Anr1|MJAM|OATP-D|R75096|Slc21a11	solute carrier organic anion transporter family, member 3a1	protein-coding
mm_41489.1	chr5	92127351	92127357	+	1	NA	Intergenic	Intergenic	-10584	NM_019490	56041	Mm.15868	NM_019490	ENSMUSG00000029407	Uso1	115kDa|TAP|Vdp	USO1 vesicle docking factor	protein-coding
mm_123244.1	chr14	60251448	60251458	-	1	NA	promoter-TSS (NM_170591)	promoter-TSS (NM_170591)	-75	NM_170591	71844	Mm.258051	NM_170591	ENSMUSG00000063895	Nupl1	1700017F11Rik|Nup58|mKIAA0410	nucleoporin like 1	protein-coding
mm_115179.1	chr13	108326522	108326537	+	1	NA	intron (NM_178683, intron 2 of 10)	intron (NM_178683, intron 2 of 10)	10192	NM_178683	218581	Mm.32318	NM_178683	ENSMUSG00000021697	Depdc1b	9830132O03|AW260467|XTP1	DEP domain containing 1B	protein-coding
mm_150243.1	chr19	34085451	34085464	+	1	NA	TTS (NM_027340)	TTS (NM_027340)	-15486	NM_023903	78753	Mm.195937	NM_023903	ENSMUSG00000056078	Lipm	4632427C23Rik|AW227514|Lipl3	lipase, family member M	protein-coding
mm_159139.1	chr2	85353725	85353725	-	1	NA	exon (NM_001011534, exon 1 of 1)	exon (NM_001011534, exon 1 of 1)	199	NM_001011534	258166	Mm.389313	NM_001011534	ENSMUSG00000075222	Olfr988	MOR203-5P	olfactory receptor 988	protein-coding
mm_65435.1	chr7	25369713	25369730	-	1	NA	promoter-TSS (NM_028219)	promoter-TSS (NM_028219)	3	NM_001081375	72383	Mm.34382	NM_028219	ENSMUSG00000063651	Cnfn	2210418J09Rik	cornifelin	protein-coding
mm_31944.1	chr4	86670194	86670204	+	1	NA	promoter-TSS (NM_007408)	promoter-TSS (NM_007408)	-140	NM_007408	11520	Mm.381	NM_007408	ENSMUSG00000028494	Plin2	AA407157|ADPH|Adfp|Adrp	perilipin 2	protein-coding
mm_133005.1	chr16	55973787	55973800	+	1	NA	promoter-TSS (NM_173026)	promoter-TSS (NM_173026)	-11	NM_173026	271377	Mm.282814	NM_173026	ENSMUSG00000022601	Zbtb11	9230110G02Rik|ZNF-U69274	zinc finger and BTB domain containing 11	protein-coding
mm_140979.1	chr17	24707618	24707661	-	1	NA	promoter-TSS (NM_145396)	promoter-TSS (NM_145396)	14	NM_145396	213773	Mm.100353	NM_145396	ENSMUSG00000040688	Tbl3	9430070M15Rik	transducin (beta)-like 3	protein-coding
mm_156334.1	chrX	139008741	139008760	+	1	NA	3' UTR (NM_013724, exon 28 of 28)	3' UTR (NM_013724, exon 28 of 28)	76486	NM_177920	331535	Mm.211704	NM_177920	ENSMUSG00000031271	Serpina7	C730040N12Rik|Tbg	serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 7	protein-coding
mm_22791.1	chr3	22155575	22155580	+	1	NA	intron (NM_030732, intron 2 of 15)	intron (NM_030732, intron 2 of 15)	78925	NM_030732	81004	Mm.202966	NM_030732	ENSMUSG00000027630	Tbl1xr1	8030499H02Rik|A630076E03Rik|AW539987|C21|C230089I12Rik|DC42|Ira1|TBLR1	transducin (beta)-like 1X-linked receptor 1	protein-coding
mm_55566.1	chr6	71360920	71360931	-	1	NA	Intergenic	Intergenic	-12502	NM_009857	12525	Mm.1858	NM_009857	ENSMUSG00000053977	Cd8a	BB154331|Ly-2|Ly-35|Ly-B|Lyt-2	CD8 antigen, alpha chain	protein-coding
mm_115476.1	chr13	119488662	119488736	+	1	NA	promoter-TSS (NR_027974)	promoter-TSS (NR_027974)	-161	NM_001177666	633640	Mm.46679	NM_001039244	ENSMUSG00000074634	Tmem267	EG633640|Gm7120	transmembrane protein 267	protein-coding
mm_117692.1	chr13	94294968	94294985	-	1	NA	Intergenic	MTC|LTR|ERVL-MaLR	-9145	NM_001346609	107767	Mm.201455	NM_029153	ENSMUSG00000021687	Scamp1	4930505M11Rik|AI415563|AW122395	secretory carrier membrane protein 1	protein-coding
mm_124756.1	chr15	6644755	6644792	+	1	NA	exon (NM_011815, exon 11 of 18)	exon (NM_011815, exon 11 of 18)	-63608	NM_030168	78757	Mm.275811	NM_030168	ENSMUSG00000050310	Rictor	4921505C17Rik|6030405M08Rik|AVO3|AW492497|D530039E11Rik	RPTOR independent companion of MTOR, complex 2	protein-coding
mm_77136.1	chr8	111393811	111393834	-	1	NA	promoter-TSS (NM_178086)	promoter-TSS (NM_178086)	-1	NM_178086	338521	Mm.41083	NM_178086	ENSMUSG00000033579	Fa2h	FAAH|Faxdc1|G630055L08Rik	fatty acid 2-hydroxylase	protein-coding
mm_36277.1	chr4	63744014	63744041	-	1	NA	intron (NM_177371, intron 1 of 3)	intron (NM_177371, intron 1 of 3)	1086	NM_177371	326623	Mm.208152	NM_177371	ENSMUSG00000050395	Tnfsf15	Tl1|Tl1a|Tnlg1b|Vegi	tumor necrosis factor (ligand) superfamily, member 15	protein-coding
mm_119774.1	chr14	54176228	54176236	+	1	NA	Intergenic	Intergenic	77697	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_118126.1	chr13	104228834	104228849	-	1	NA	promoter-TSS (NM_021790)	promoter-TSS (NM_021790)	3	NM_172807	238831	Mm.98910	NM_172807	ENSMUSG00000021713	Ppwd1	4632422M10Rik|A330090G21Rik	peptidylprolyl isomerase domain and WD repeat containing 1	protein-coding
mm_94040.1	chr10	128082969	128082981	-	1	NA	promoter-TSS (NM_016774)	promoter-TSS (NM_016774)	-332	NM_016774	11947	Mm.238973	NM_016774	ENSMUSG00000025393	Atp5b	-	ATP synthase, H+ transporting mitochondrial F1 complex, beta subunit	protein-coding
mm_126353.1	chr15	79928148	79928159	+	1	NA	intron (NM_144811, intron 2 of 6)	intron (NM_144811, intron 2 of 6)	4493	NM_144811	52609	Mm.323442	NM_144811	ENSMUSG00000053411	Cbx7	1600014J01Rik|AI851678|D15Ertd417e	chromobox 7	protein-coding
mm_124781.1	chr15	7442479	7442489	+	1	NA	Intergenic	Intergenic	-44089	NM_001289498	268780	Mm.203208	NM_178748	ENSMUSG00000042961	Egflam	5930412K08|AU040377	EGF-like, fibronectin type III and laminin G domains	protein-coding
mm_52295.1	chr6	108783065	108783116	+	1	NA	promoter-TSS (NM_026011)	promoter-TSS (NM_026011)	31	NM_026011	67166	Mm.271178	NM_026011	ENSMUSG00000030105	Arl8b	2610313E07Rik|3100002J04Rik|Arl10c|gie1	ADP-ribosylation factor-like 8B	protein-coding
mm_40324.1	chr5	43908584	43908632	+	1	NA	intron (NM_007646, intron 7 of 7)	intron (NM_007646, intron 7 of 7)	39799	NM_007646	12494	Mm.249873	NM_007646	ENSMUSG00000029084	Cd38	ADPRC 1|Cd38-rs1|I-19	CD38 antigen	protein-coding
mm_20100.1	chr2	121036751	121036774	-	1	NA	5' UTR (NM_013513, exon 1 of 13)	5' UTR (NM_013513, exon 1 of 13)	115	NM_013513	13828	Mm.240051	NM_013513	ENSMUSG00000023216	Epb42	Epb4.2	erythrocyte membrane protein band 4.2	protein-coding
mm_2802.1	chr1	130851717	130851734	+	1	NA	3' UTR (NM_011082, exon 11 of 11)	3' UTR (NM_011082, exon 11 of 11)	-14052	NM_026976	69169	Mm.46042	NM_026976	ENSMUSG00000042474	Fcmr	1810037B05Rik|Faim3|FcmuR|Toso	Fc fragment of IgM receptor	protein-coding
mm_166906.1	chr7	28838698	28838736	+	1	NA	intron (NM_010707, intron 4 of 8)	ZP3AR|Satellite|Satellite	4547	NM_010707	16857	Mm.210336	NM_010707		Lgals6	galectin-6	lectin, galactose binding, soluble 6	protein-coding
mm_142519.1	chr17	46270852	46270864	-	1	NA	intron (NM_001252475, intron 1 of 8)	intron (NM_001252475, intron 1 of 8)	12168	NM_001252475	74094	Mm.284594	NM_028751	ENSMUSG00000012296	Tjap1	0610041D19Rik|AI415281|AW121008|Pilt|Tjp4	tight junction associated protein 1	protein-coding
mm_142759.1	chr17	49033297	49033344	-	1	NA	intron (NM_027452, intron 1 of 2)	intron (NM_027452, intron 1 of 2)	80213	NR_038141	69311	Mm.46140	NR_038141	ENSMUSG00000101012	1700008K24Rik	-	RIKEN cDNA 1700008K24 gene	ncRNA
mm_106143.1	chr11	116533070	116533123	-	1	NA	promoter-TSS (NM_025367)	promoter-TSS (NM_025367)	-142	NM_025367	20698	Mm.20944	NM_011451	ENSMUSG00000061878	Sphk1	1110006G24Rik|Sk1|Spk1	sphingosine kinase 1	protein-coding
mm_75304.1	chr8	41118722	41118728	-	1	NA	intron (NM_001005863, intron 1 of 13)	intron (NM_001005863, intron 1 of 13)	-4058	NM_001286413	102103	Mm.149438	NM_001005863	ENSMUSG00000045636	Mtus1	AI481402|ATBP135|Atip1|B430010I23Rik|B430305I03Rik|C85752|Cctsg1-440|MD44|MTSG1|mKIAA1288	mitochondrial tumor suppressor 1	protein-coding
mm_66587.1	chr7	45395216	45395229	-	1	NA	intron (NM_009224, intron 1 of 9)	intron (NM_009224, intron 1 of 9)	520	NM_009224	20637	Mm.216386	NM_009224	ENSMUSG00000063511	Snrnp70	2700022N21Rik|3200002N22Rik|AI325098|R74807|Rnu1p70|Rnulp70|Snrp70|Srnp70|U1-70|U1-70K	small nuclear ribonucleoprotein 70 (U1)	protein-coding
mm_135265.1	chr16	38294844	38294854	-	1	NA	promoter-TSS (NM_010936)	promoter-TSS (NM_010936)	-25	NM_001098404	18171	Mm.8509	NM_010936	ENSMUSG00000022809	Nr1i2	PXR|PXR.1|PXR.2|PXR1|SXR|mPXR	nuclear receptor subfamily 1, group I, member 2	protein-coding
mm_14179.1	chr2	126910375	126910376	+	1	NA	intron (NM_023220, intron 12 of 14)	intron (NM_023220, intron 12 of 14)	-7990	NR_106202	102466258		NR_106202	ENSMUSG00000098896	Mir3473g	Gm27751|mmu-mir-3473g	microRNA 3473g	ncRNA
mm_3813.1	chr1	158958333	158958335	+	1	NA	promoter-TSS (NM_001085376)	promoter-TSS (NM_001085376)	-896	NM_001085376	23850	Mm.458621	NM_001085376	ENSMUSG00000073530	Pappa2	PAPP-A2|PLAC3|Pappe	pappalysin 2	protein-coding
mm_107839.1	chr12	69296939	69296943	+	1	NA	5' UTR (NM_027117, exon 1 of 13)	5' UTR (NM_027117, exon 1 of 13)	260	NM_027117	69554	Mm.234368	NM_027117	ENSMUSG00000020978	Klhdc2	2310022K15Rik|D12Ertd522e|HCLP-1|LCP	kelch domain containing 2	protein-coding
mm_101622.1	chr11	35915574	35915582	-	1	NA	intron (NM_170779, intron 1 of 22)	MIR3|SINE|MIR	64511	NM_170779	211652	Mm.31267	NM_170779	ENSMUSG00000018849	Wwc1	AA408228|AU017197|BC037006|Kibra|mKIAA0869	WW, C2 and coiled-coil domain containing 1	protein-coding
mm_2031.1	chr1	87190671	87190683	+	1	NA	promoter-TSS (NM_021600)	promoter-TSS (NM_021600)	80	NM_021600	11447	Mm.2811	NM_021600	ENSMUSG00000026251	Chrnd	Achr-4|Acrd|L10076	cholinergic receptor, nicotinic, delta polypeptide	protein-coding
mm_12182.1	chr2	65189564	65189574	+	1	NA	intron (NM_027225, intron 1 of 12)	intron (NM_027225, intron 1 of 12)	49057	NM_177025	319876	Mm.34159	NM_027225	ENSMUSG00000034903	Cobll1	1810047P18Rik|Coblr1|D430044D16Rik	Cobl-like 1	protein-coding
mm_464.1	chr1	36308268	36308281	+	1	NA	intron (NM_001172206, intron 1 of 6)	intron (NM_001172206, intron 1 of 6)	541	NM_001172205	214855	Mm.34316	NM_145996	ENSMUSG00000037447	Arid5a	D430024K22Rik|Mrf1	AT rich interactive domain 5A (MRF1-like)	protein-coding
mm_68332.1	chr7	106504164	106504193	-	1	NA	Intergenic	Intergenic	-63105	NR_003967	209380	Mm.461779	NM_001001318		Gm4759	EG209380	GTPase, very large interferon inducible 1 pseudogene	pseudo
mm_62996.1	chr7	120739523	120739544	+	1	NA	promoter-TSS (NM_177697)	promoter-TSS (NM_177697)	-24	NM_177697	233813	Mm.389939	NM_177697	ENSMUSG00000030889	Vwa3a	E030013G06Rik	von Willebrand factor A domain containing 3A	protein-coding
mm_118684.1	chr14	22114329	22114330	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	94617	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_55947.1	chr6	85137744	85137781	-	1	NA	promoter-TSS (NM_011467)	promoter-TSS (NM_011467)	2	NM_011467	20751	Mm.28393	NM_011467	ENSMUSG00000033735	Spr	AA409688|ENSMUSG00000071345|Gm10328	sepiapterin reductase	protein-coding
mm_69684.1	chr7	139989271	139989284	-	1	NA	exon (NM_001291066, exon 6 of 24)	exon (NM_001291066, exon 6 of 24)	-2403	NR_106029	102465643		NR_106029	ENSMUSG00000099092	Mir7062	Gm27339|mmu-mir-7062	microRNA 7062	ncRNA
mm_63546.1	chr7	128064782	128064799	+	1	NA	intron (NM_001082960, intron 2 of 29)	intron (NM_001082960, intron 2 of 29)	2150	NM_008401	16409	Mm.262106	NM_008401	ENSMUSG00000030786	Itgam	CD11b/CD18|CR3|CR3A|Cd11b|F730045J24Rik|Ly-40|MAC1|Mac-1|Mac-1a	integrin alpha M	protein-coding
mm_77428.1	chr8	121108362	121108406	-	1	NA	promoter-TSS (NM_001166482)	promoter-TSS (NM_001166482)	-5	NM_001166482	234814	Mm.31690	NM_172761	ENSMUSG00000031816	Mthfsd	AW049977|BC052066|C920004D05	methenyltetrahydrofolate synthetase domain containing	protein-coding
mm_120990.1	chr14	79301155	79301166	+	1	NA	intron (NM_025427, intron 1 of 4)	CpG	475	NM_025427	66214	Mm.29811	NM_025427	ENSMUSG00000022018	Rgcc	1190002H23Rik|Rgc-32|Rgc32	regulator of cell cycle	protein-coding
mm_72218.1	chr8	72688427	72688439	+	1	NA	intron (NM_176940, intron 11 of 18)	B3A|SINE|B2	-34837	NM_001113248	20467	Mm.2137	NM_009188	ENSMUSG00000031622	Sin3b	2810430C10Rik	transcriptional regulator, SIN3B (yeast)	protein-coding
mm_91205.1	chr10	21161405	21161420	-	1	NA	promoter-TSS (NM_001198914)	promoter-TSS (NM_001198914)	-428	NM_010848	17863	Mm.52109	NM_010848	ENSMUSG00000019982	Myb	AI550390|M16449|c-myb	myeloblastosis oncogene	protein-coding
mm_42722.1	chr5	120587716	120587742	+	1	NA	intron (NM_145853, intron 1 of 27)	intron (NM_145853, intron 1 of 27)	884	NM_145853	252972	Mm.114054	NM_145853	ENSMUSG00000032741	Tpcn1	5730403B01Rik|Tpc1|mKIAA1169	two pore channel 1	protein-coding
mm_38125.1	chr4	134563368	134563390	-	1	NA	3' UTR (NM_207237, exon 12 of 12)	3' UTR (NM_207237, exon 12 of 12)	4472	NR_105829	102465216		NR_105829	ENSMUSG00000099289	Mir6403	Gm27992|mmu-mir-6403	microRNA 6403	ncRNA
mm_108.1	chr1	9601264	9601310	+	1	NA	promoter-TSS (NM_178399)	promoter-TSS (NM_178399)	20	NM_178399	76982	Mm.491098	NM_178399	ENSMUSG00000067879	3110035E14Rik	AI415019|AV164974|R75066	RIKEN cDNA 3110035E14 gene	protein-coding
mm_58719.1	chr7	13023379	13023396	+	1	NA	promoter-TSS (NM_011588)	promoter-TSS (NM_011588)	-765	NM_011588	21849	Mm.15701	NM_011588	ENSMUSG00000005566	Trim28	AA408787|KAP-1|KRIP-1|MommeD9|Tif1b|Tif1beta	tripartite motif-containing 28	protein-coding
mm_103496.1	chr11	76571485	76571502	-	1	NA	promoter-TSS (NM_198895)	promoter-TSS (NM_198895)	-109	NM_198895	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_33810.1	chr4	135152995	135153024	+	1	NA	exon (NM_019732, exon 2 of 6)	exon (NM_019732, exon 2 of 6)	32364	NM_019732	12399	Mm.378894	NM_019732	ENSMUSG00000070691	Runx3	AML2|Cbfa3|Pebp2a3	runt related transcription factor 3	protein-coding
mm_58101.1	chr6	137570786	137570808	-	1	NA	5' UTR (NM_001271587, exon 1 of 21)	5' UTR (NM_001271587, exon 1 of 21)	212	NM_001271595	13860	Mm.235346	NM_007945	ENSMUSG00000015766	Eps8	AW261790	epidermal growth factor receptor pathway substrate 8	protein-coding
mm_144331.1	chr18	13006936	13006950	+	1	NA	promoter-TSS (NM_153087)	promoter-TSS (NM_153087)	-47	NM_153087	225192	Mm.207073	NM_153087	ENSMUSG00000037346	Hrh4	AXOR35|BG26|GPCR105|GPRv53|H4|H4R|HH4R	histamine receptor H4	protein-coding
mm_96223.1	chr11	62511744	62511751	+	1	NA	intron (NM_001039536, intron 5 of 6)	MLTR25A|LTR|ERVK	27514	NM_028448	73139	Mm.390409	NM_028448	ENSMUSG00000018509	Cenpv	3110013H01Rik|AA671303|Prr6	centromere protein V	protein-coding
mm_106670.1	chr11	121548063	121548097	-	1	NA	intron (NM_029878, intron 14 of 38)	RSINE1|SINE|B4	-28738	NM_178763	319530	Mm.11395	NM_178763	ENSMUSG00000039238	Zfp750	A030007D23Rik|Znf750	zinc finger protein 750	protein-coding
mm_150563.1	chr19	39510878	39510890	+	1	NA	promoter-TSS (NM_010003)	promoter-TSS (NM_010003)	62	NM_010003	13098	Mm.42101	NM_010003	ENSMUSG00000025003	Cyp2c39	CYPIIC39	cytochrome P450, family 2, subfamily c, polypeptide 39	protein-coding
mm_76695.1	chr8	94180227	94180255	-	1	NA	TTS (NM_013602)	TTS (NM_013602)	1152	NM_013602	17748	Mm.192991	NM_013602	ENSMUSG00000031765	Mt1	MT-I|Mt-1	metallothionein 1	protein-coding
mm_147591.1	chr18	56572867	56572882	-	1	NA	promoter-TSS (NM_001127338)	promoter-TSS (NM_001127338)	3	NM_019996	56698	Mm.214569	NM_019996	ENSMUSG00000008301	Phax	2810055C14Rik|4933427L19Rik|AU018701|AU018854|D18Ertd65e|Rnuxa|p55	phosphorylated adaptor for RNA export	protein-coding
mm_23665.1	chr3	68494284	68494295	+	1	NA	5' UTR (NM_001282044, exon 1 of 8)	5' UTR (NM_001282044, exon 1 of 8)	108	NM_001282044	30953	Mm.331064	NM_013928	ENSMUSG00000027777	Schip1	Nf2ip|Schip-1	schwannomin interacting protein 1	protein-coding
mm_61228.1	chr7	64502077	64502085	+	1	NA	promoter-TSS (NM_001291167)	promoter-TSS (NM_001291167)	-57	NM_001291166	11784	Mm.4657	NM_007461	ENSMUSG00000030519	Apba2	X11-like|X11L|XllL|mXllL	amyloid beta (A4) precursor protein-binding, family A, member 2	protein-coding
mm_113773.1	chr13	44850947	44850952	+	1	NA	intron (NM_001205044, intron 4 of 18)	intron (NM_001205044, intron 4 of 18)	119678	NM_001205043	16468	Mm.25059	NM_021878	ENSMUSG00000038518	Jarid2	Jmj|jumonji	jumonji, AT rich interactive domain 2	protein-coding
mm_108807.1	chr12	92809559	92809607	+	1	NA	Intergenic	Lx6|LINE|L1	635240	NR_126436	75295	Mm.243878	NR_126436		4930559C10Rik	-	RIKEN cDNA 4930559C10 gene	ncRNA
mm_52670.1	chr6	117907072	117907093	+	1	NA	promoter-TSS (NM_001166429)	intron (NM_133834, intron 1 of 3)	300	NM_133834	98758	Mm.422979	NM_133834	ENSMUSG00000042079	Hnrnpf	4833420I20Rik|AA407306|Hnrpf	heterogeneous nuclear ribonucleoprotein F	protein-coding
mm_172953.1	chr9	87255283	87255300	-	1	NA	5' UTR (NM_199316, exon 1 of 27)	5' UTR (NM_199316, exon 1 of 27)	241	NM_199316	382090	Mm.335338	NM_199316	ENSMUSG00000056919	Cep162	4922501C03Rik|mKIAA1009	centrosomal protein 162	protein-coding
mm_92606.1	chr10	80117116	80117126	-	1	NA	intron (NR_126043, intron 1 of 10)	intron (NR_126043, intron 1 of 10)	1318	NM_001301854	20869	Mm.44231	NM_011492	ENSMUSG00000003068	Stk11	AA408040|Lkb1|Par-4|R75140	serine/threonine kinase 11	protein-coding
mm_25590.1	chr3	116890639	116890643	+	1	NA	intron (NM_009146, intron 7 of 16)	PB1D9|SINE|Alu	28961	NM_009146	20321	Mm.66293	NM_009146	ENSMUSG00000033386	Frrs1	AI131732|Sdfr2	ferric-chelate reductase 1	protein-coding
mm_153087.1	chr19	32389657	32389663	-	1	NA	intron (NR_033198, intron 1 of 1)	CpG-7452	444	NR_033198	67188	Mm.391160	NR_033198	ENSMUSG00000097787	2700046G09Rik	-	RIKEN cDNA 2700046G09 gene	ncRNA
mm_83294.1	chr9	43205835	43205885	-	1	NA	promoter-TSS (NM_011139)	promoter-TSS (NM_011139)	-105	NM_011139	18988	Mm.436650	NM_011139	ENSMUSG00000032015	Pou2f3	Epoc-1|Oct-11a|Oct11|Otf-11|Otf11|Skin|Skin-1a|Skn-1a|Skn-li	POU domain, class 2, transcription factor 3	protein-coding
mm_50527.1	chr6	49045366	49045371	+	1	NA	exon (NM_053110, exon 4 of 11)	exon (NM_053110, exon 4 of 11)	8850	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_9970.1	chr1	191185000	191185009	-	1	NA	Intergenic	CpG	-1671	NM_007498	11910	Mm.2706	NM_007498	ENSMUSG00000026628	Atf3	LRG-21	activating transcription factor 3	protein-coding
mm_143077.1	chr17	57044091	57044110	-	1	NA	3' UTR (NM_025877, exon 10 of 10)	3' UTR (NM_025877, exon 10 of 10)	-2446	NM_175333	103775	Mm.33647	NM_175333	ENSMUSG00000011486	Slc25a41	4933406J04Rik|AI507137	solute carrier family 25, member 41	protein-coding
mm_128417.1	chr15	45114442	45114461	-	1	NA	exon (NM_026200, exon 1 of 3)	exon (NM_026200, exon 1 of 3)	483	NM_026200	67498	Mm.300079	NM_026200	ENSMUSG00000022342	Kcnv1	2700023A03Rik|vibe	potassium channel, subfamily V, member 1	protein-coding
mm_36759.1	chr4	101355886	101355929	-	1	NA	intron (NR_040640, intron 1 of 3)	intron (NR_040640, intron 1 of 3)	341	NR_040708	77866	Mm.137053	NR_040708	ENSMUSG00000086782	E130102H24Rik	-	RIKEN cDNA E130102H24 gene	ncRNA
mm_3656.1	chr1	153116036	153116049	+	1	NA	3' UTR (NM_175460, exon 11 of 11)	3' UTR (NM_175460, exon 11 of 11)	70405	NM_008485	16782	Mm.329272	NM_008485	ENSMUSG00000026479	Lamc2	AA589349	laminin, gamma 2	protein-coding
mm_146400.1	chr18	82910914	82910943	+	1	NA	promoter-TSS (NM_183033)	promoter-TSS (NM_183033)	49	NM_183033	329003	Mm.326526	NM_183033	ENSMUSG00000058881	Zfp516	C330029B10Rik|D230016L03|Zfp26l|Znf516|mKIAA0222	zinc finger protein 516	protein-coding
mm_21059.1	chr2	152686806	152686815	-	1	NA	promoter-TSS (NM_025543)	promoter-TSS (NM_025543)	-338	NM_025543	66405	Mm.440291	NM_025543	ENSMUSG00000042814	Mcts2	2400002F11Rik|MCT-2	malignant T cell amplified sequence 2	protein-coding
mm_103192.1	chr11	70619196	70619207	-	1	NA	promoter-TSS (NM_009603)	promoter-TSS (NM_009603)	-7	NM_009603	11448	Mm.4980	NM_009603	ENSMUSG00000014609	Chrne	AChrepsilon|Acre|nAChRE	cholinergic receptor, nicotinic, epsilon polypeptide	protein-coding
mm_158077.1	chrX	101264934	101264944	-	1	NA	promoter-TSS (NM_001317221)	promoter-TSS (NM_001317221)	-947	NM_001317221	245536	Mm.212463	NM_001033362	ENSMUSG00000090141	Gm614	-	predicted gene 614	protein-coding
mm_102861.1	chr11	69401339	69401367	-	1	NA	exon (NM_001017426, exon 18 of 23)	exon (NM_001017426, exon 18 of 23)	-3119	NM_025915	67020	Mm.390406	NM_025915	ENSMUSG00000045377	Tmem88	2600017H02Rik	transmembrane protein 88	protein-coding
mm_83441.1	chr9	45001047	45001079	-	1	NA	exon (NM_007648, exon 6 of 8)	exon (NM_007648, exon 6 of 8)	8527	NM_007648	12501	Mm.210361	NM_007648	ENSMUSG00000032093	Cd3e	AI504783|CD3|CD3epsilon|T3e	CD3 antigen, epsilon polypeptide	protein-coding
mm_147605.1	chr18	56867599	56867603	-	1	NA	intron (NM_177115, intron 1 of 4)	intron (NM_177115, intron 1 of 4)	57947	NM_177115	320253	Mm.312623	NM_177115	ENSMUSG00000032656	March3	6330411I15Rik|A530081L18Rik|AI843639|MARCH-III	membrane-associated ring finger (C3HC4) 3	protein-coding
mm_67259.1	chr7	75774067	75774073	-	1	NA	Intergenic	MTC-int|LTR|ERVL-MaLR	-74268	NM_001122780	207952	Mm.206223	NM_029652	ENSMUSG00000055652	Klhl25	2810402K13Rik|BC027373|Enc-1	kelch-like 25	protein-coding
mm_165988.1	chr4	109114554	109114559	+	1	NA	intron (NM_001346502, intron 4 of 23)	intron (NM_001346502, intron 4 of 23)	3480	NM_173350	100273	Mm.366315	NM_133885	ENSMUSG00000028559	Osbpl9	2600011I06Rik|AU015843|Orp-9	oxysterol binding protein-like 9	protein-coding
mm_20619.1	chr2	131855622	131855630	-	1	NA	3' UTR (NM_001166206, exon 2 of 2)	3' UTR (NM_001166206, exon 2 of 2)	4121	NM_001166206	71995	Mm.22	NM_028045	ENSMUSG00000037482	Erv3	1600014E20Rik|AA389086|AI426069|AI448024|D19349	endogenous retroviral sequence 3	protein-coding
mm_123132.1	chr14	56262234	56262248	-	1	NA	promoter-TSS (NM_013542)	promoter-TSS (NM_013542)	93	NM_013542	14939	Mm.14874	NM_013542	ENSMUSG00000015437	Gzmb	AI553453|CCP-1/C11|CCP1|Ctla-1|Ctla1|GZB	granzyme B	protein-coding
mm_109394.1	chr12	109748126	109748134	+	1	NA	TTS (NR_037233)	TTS (NR_037233)	252	NR_037233	100499517		NR_037233	ENSMUSG00000093351	Mir3072	mir-3072|mmu-mir-3072	microRNA 3072	ncRNA
mm_33493.1	chr4	130823477	130823480	+	1	NA	3' UTR (NM_011520, exon 5 of 5)	3' UTR (NM_011520, exon 5 of 5)	30941	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_28463.1	chr3	90695185	90695243	-	1	NA	exon (NM_001281852, exon 2 of 3)	exon (NM_001281852, exon 2 of 3)	507	NM_001281852	20202	Mm.2128	NM_009114	ENSMUSG00000056071	S100a9	60B8Ag|AW546964|BEE22|Cagb|GAGB|L1Ag|MRP14|p14	S100 calcium binding protein A9 (calgranulin B)	protein-coding
mm_165145.1	chr2	18699042	18699042	+	1	NA	promoter-TSS (NM_001001334)	promoter-TSS (NM_001001334)	20	NM_001001334	381350	Mm.330024	NM_001001334	ENSMUSG00000037708	Spag6	Spag6l	sperm associated antigen 6	protein-coding
mm_173347.1	chrY	90813098	90813099	+	1	NA	intron (NM_133362, intron 2 of 3)	(TTAGGG)n|Simple_repeat|Simple_repeat	26308	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_116951.1	chr13	56135677	56135688	-	1	NA	promoter-TSS (NM_001159515)	promoter-TSS (NM_001159515)	-132	NM_001159513	26914	Mm.283802	NM_012015	ENSMUSG00000015937	H2afy	H2AF12M|mH2a1|macroH2A1	H2A histone family, member Y	protein-coding
mm_151926.1	chr19	5800103	5800114	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	2564	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_126063.1	chr15	77017632	77017657	+	1	NA	exon (NM_013593, exon 3 of 4)	exon (NM_013593, exon 3 of 4)	5083	NM_001164048	17189	Mm.404074	NM_013593	ENSMUSG00000018893	Mb	AI325109	myoglobin	protein-coding
mm_45984.1	chr5	90476528	90476547	-	1	NA	TTS (NM_009654)	TTS (NM_009654)	-14177	NM_007423	11576	Mm.358570	NM_007423	ENSMUSG00000054932	Afp	-	alpha fetoprotein	protein-coding
mm_117839.1	chr13	98692196	98692217	-	1	NA	exon (NM_001025606, exon 2 of 4)	exon (NM_001025606, exon 2 of 4)	2625	NM_001025606	380863	Mm.28264	NM_001025606	ENSMUSG00000052485	Tmem171	Gm905	transmembrane protein 171	protein-coding
mm_33157.1	chr4	125607631	125607633	+	1	NA	intron (NM_001081097, intron 1 of 15)	B4A|SINE|B4	102883	NR_035409	100124641		NR_035409	ENSMUSG00000076033	Mir692-3	Mir692-2b|Mirn692-2b|mmu-mir-692-3	microRNA 692-3	ncRNA
mm_25088.1	chr3	100785725	100785756	+	1	NA	Intergenic	RLTR20A2B_MM|LTR|ERVK	-39719	NM_178594	242122	Mm.137467	NM_178594	ENSMUSG00000051076	Vtcn1	B7h4|B7s1|B7x|BC032925	V-set domain containing T cell activation inhibitor 1	protein-coding
mm_124599.1	chr15	3275670	3275703	+	1	NA	exon (NM_009155, exon 3 of 5)	exon (NM_009155, exon 3 of 5)	4709	NM_009155	20363	Mm.392203	NM_009155	ENSMUSG00000064373	Selenop	AU018766|D15Ucla1|Se-P|Sepp1|selp	selenoprotein P	protein-coding
mm_166498.1	chr6	3504242	3504245	+	1	NA	intron (NM_001167750, intron 1 of 27)	intron (NM_001167750, intron 1 of 27)	5850	NM_001167750	73288	Mm.45539	NM_024260	ENSMUSG00000001376	Vps50	1700034M03Rik|8430415E05Rik|BLM|C87205|Ccdc132|mKIAA1861	VPS50 EARP/GARPII complex subunit	protein-coding
mm_50714.1	chr6	52177153	52177156	+	1	NA	intron (NM_010452, intron 3 of 4)	intron (NM_010452, intron 3 of 4)	11480	NR_131182	105242657	Mm.490651	NR_131182	ENSMUSG00000056445	Hoxaas2	2810043O09Rik|5730446D14Rik	Hoxa cluster antisense RNA 2	ncRNA
mm_157735.1	chrX	71492800	71492860	-	1	NA	promoter-TSS (NM_138309)	promoter-TSS (NM_138309)	19	NM_138309	171486	Mm.283879	NM_138309	ENSMUSG00000035776	Cd99l2	AW548191|Mic2l1|Xap89	CD99 antigen-like 2	protein-coding
mm_158618.1	chrX	152657472	152657487	-	1	NA	exon (NM_172441, exon 5 of 10)	exon (NM_172441, exon 5 of 10)	-12931	NM_001290685	110380	Mm.40796	NM_172441	ENSMUSG00000045180	Shroom2	4832440C16|Apxl|C630003H05Rik|Shrm2	shroom family member 2	protein-coding
mm_85203.1	chr9	96752823	96752869	-	1	NA	promoter-TSS (NR_015511)	promoter-TSS (NR_015511)	-15	NR_015511	319859	Mm.259909	NM_177020		E030011O05Rik	-	RIKEN cDNA E030011O05 gene	ncRNA
mm_39797.1	chr5	30622041	30622055	+	1	NA	exon (NM_010608, exon 2 of 2)	exon (NM_010608, exon 2 of 2)	-25888	NR_049199	100885838		NR_049199	ENSMUSG00000093710	Mir5625	Gm23930|mmu-mir-5625	microRNA 5625	ncRNA
mm_121023.1	chr14	79587727	79587797	+	1	NA	promoter-TSS (NM_026474)	promoter-TSS (NM_026474)	71	NM_026474	67955	Mm.18972	NM_026474	ENSMUSG00000022024	Sugt1	2410174K12Rik|SGT1	SGT1, suppressor of G2 allele of SKP1 (S. cerevisiae)	protein-coding
mm_98481.1	chr11	94950862	94950865	+	1	NA	exon (NM_007742, exon 49 of 51)	exon (NM_007742, exon 49 of 51)	14639	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_11046.1	chr2	27165521	27165531	+	1	NA	promoter-TSS (NM_138942)	promoter-TSS (NM_138942)	19	NM_138942	13166	Mm.167781	NM_138942	ENSMUSG00000000889	Dbh	-	dopamine beta hydroxylase	protein-coding
mm_105432.1	chr11	103954016	103954034	-	1	NA	promoter-TSS (NM_008740)	promoter-TSS (NM_008740)	31	NM_008740	18195	Mm.260117	NM_008740	ENSMUSG00000034187	Nsf	AI316878|AU020090|AU067812|SKD2	N-ethylmaleimide sensitive fusion protein	protein-coding
mm_47627.1	chr5	125289711	125289719	-	1	NA	exon (NM_001205082, exon 8 of 12)	exon (NM_001205082, exon 8 of 12)	51379	NM_016741	20778	Mm.282242	NM_016741	ENSMUSG00000037936	Scarb1	AI120173|CD36|Cd36l1|Chohd1|Cla-1|Cla1|D5Ertd460e|Hdlq1|Hlb398|SR-B1|SR-BI|SRBI|Srb1|mSR-BI	scavenger receptor class B, member 1	protein-coding
mm_1903.1	chr1	85831941	85831944	+	1	NA	intron (NM_133781, intron 2 of 8)	B1_Mur1|SINE|Alu	38495	NM_133781	12283	Mm.26135	NM_133781	ENSMUSG00000036707	Cab39	AA408805|AA960512|C78372|MO25|MO25alpha	calcium binding protein 39	protein-coding
mm_30941.1	chr4	33031749	33031765	+	1	NA	promoter-TSS (NR_036602)	promoter-TSS (NR_036602)	332	NM_019586	56228	Mm.259095	NM_019586	ENSMUSG00000028277	Ube2j1	0710008M05Rik|1110030I22Rik|NCUBE-1|Ncube|Ncube1|Ubc6p	ubiquitin-conjugating enzyme E2J 1	protein-coding
mm_132689.1	chr16	43235857	43235876	+	1	NA	intron (NM_001285805, intron 3 of 10)	intron (NM_001285805, intron 3 of 10)	-11418	NM_181058	56490	Mm.136238	NM_019778	ENSMUSG00000022708	Zbtb20	1300017A20Rik|7330412A13Rik|A930017C21Rik|D16Wsu73e|DPZF|HOF|ODA-8S|Oda8|Zfp288	zinc finger and BTB domain containing 20	protein-coding
mm_20082.1	chr2	120609537	120609547	-	1	NA	promoter-TSS (NM_025657)	promoter-TSS (NM_025657)	-34	NM_001159609	66606	Mm.428639	NM_025657	ENSMUSG00000027286	Lrrc57	2810002D13Rik|AA407405	leucine rich repeat containing 57	protein-coding
mm_35387.1	chr4	33248724	33248752	-	1	NA	promoter-TSS (NM_001033225)	promoter-TSS (NM_001033225)	49	NM_001033225	108767	Mm.27769	NM_001033225	ENSMUSG00000040128	Pnrc1	5730463C12Rik|B4-2|PRR2|Prol2	proline-rich nuclear receptor coactivator 1	protein-coding
mm_65964.1	chr7	30435325	30435351	-	1	NA	exon (NM_007467, exon 17 of 17)	exon (NM_007467, exon 17 of 17)	10244	NM_007467	11803	Mm.2381	NM_007467	ENSMUSG00000006651	Aplp1	-	amyloid beta (A4) precursor-like protein 1	protein-coding
mm_145615.1	chr18	61105641	61105654	+	1	NA	promoter-TSS (NM_001037859)	promoter-TSS (NM_001037859)	75	NM_001037859	12978	Mm.22574	NM_007779	ENSMUSG00000024621	Csf1r	AI323359|CD115|CSF-1R|Csfmr|Fim-2|Fim2|Fms|M-CSF-R|M-CSFR	colony stimulating factor 1 receptor	protein-coding
mm_110699.1	chr12	69198420	69198420	-	1	NA	promoter-TSS (NM_027269)	promoter-TSS (NM_027269)	9	NM_027269	109065	Mm.107180	NM_027269	ENSMUSG00000020973	Dnaaf2	Ktu|TU54|kintoun|mknt	dynein, axonemal assembly factor 2	protein-coding
mm_139033.1	chr17	46163154	46163183	+	1	NA	intron (NM_019581, intron 1 of 11)	intron (NM_019581, intron 1 of 11)	2136	NM_001145979	56055	Mm.22147	NM_019581	ENSMUSG00000023952	Gtpbp2	nmf205	GTP binding protein 2	protein-coding
mm_132751.1	chr16	44160307	44160325	+	1	NA	3' UTR (NM_028108, exon 5 of 5)	3' UTR (NM_028108, exon 5 of 5)	-13081	NM_001029889	207806	Mm.310566	NM_001029889	ENSMUSG00000068284	Usf3	5530400K22Rik|Gm1779|Gm608|mKIAA2018	upstream transcription factor family member 3	protein-coding
mm_102971.1	chr11	69667371	69667386	-	1	NA	3' UTR (NM_144958, exon 11 of 11)	3' UTR (NM_144958, exon 11 of 11)	-1208	NR_110993	12514	Mm.15819	NM_009853	ENSMUSG00000018774	Cd68	Lamp4|Scard1|gp110	CD68 antigen	protein-coding
mm_128984.1	chr15	74833808	74833824	-	1	NA	Intergenic	Intergenic	7827	NM_001033229	110115	Mm.322606	NM_001033229	ENSMUSG00000075604	Cyp11b1	AA389061|CPN1|Cyp11b|Cyp11b-1|FHI	cytochrome P450, family 11, subfamily b, polypeptide 1	protein-coding
mm_150883.1	chr19	45087038	45087049	+	1	NA	Intergenic	Intergenic	10904	NM_178929	107250	Mm.24417	NM_178929	ENSMUSG00000025213	Kazald1	AI842353|Bono1|IGFBP-rP10	Kazal-type serine peptidase inhibitor domain 1	protein-coding
mm_137580.1	chr17	28007347	28007409	+	1	NA	intron (NM_001286040, intron 11 of 24)	intron (NM_001286040, intron 11 of 24)	73206	NM_013687	21463	Mm.29758	NM_013687	ENSMUSG00000062859	Tcp11	D17Ken1|Tcp-11	t-complex protein 11	protein-coding
mm_51344.1	chr6	72549415	72549428	+	1	NA	promoter-TSS (NM_001271395)	promoter-TSS (NM_001271395)	148	NM_001042534	12332	Mm.18626	NM_007599	ENSMUSG00000056737	Capg	gCap39|mbh1	capping protein (actin filament), gelsolin-like	protein-coding
mm_19056.1	chr2	77280590	77280648	-	1	NA	promoter-TSS (NM_175465)	promoter-TSS (NM_175465)	-27	NM_175465	228071	Mm.27120	NM_175465	ENSMUSG00000042272	Sestd1	1500031J16Rik|A930010O20|Solo/Trio8	SEC14 and spectrin domains 1	protein-coding
mm_108997.1	chr12	102954088	102954091	+	1	NA	intron (NM_001081017, intron 1 of 48)	intron (NM_001081017, intron 1 of 48)	5230	NM_001081017	217843	Mm.387073	NM_177621	ENSMUSG00000021198	Unc79	9030205A07Rik|Mlca3	unc-79 homolog (C. elegans)	protein-coding
mm_53386.1	chr6	129533209	129533249	+	1	NA	promoter-TSS (NR_045270)	promoter-TSS (NR_045270)	37	NM_020590	57436	Mm.14638	NM_020590	ENSMUSG00000030161	Gabarapl1	3110025G09Rik|9130422N19Rik|AI196471|Apg8l|Atg8l|GECI|MNCb-0091	gamma-aminobutyric acid (GABA) A receptor-associated protein-like 1	protein-coding
mm_160607.1	chr9	78328113	78328113	+	1	NA	promoter-TSS (NM_205822)	promoter-TSS (NM_205822)	83	NM_205822	382088	Mm.360477	NM_205822	ENSMUSG00000038750	Omt2b	AU018149|C86230|Mosg|OM2b	oocyte maturation, beta	protein-coding
mm_12997.1	chr2	90885925	90885939	+	1	NA	5' UTR (NM_026161, exon 1 of 2)	5' UTR (NM_026161, exon 1 of 2)	146	NM_026161	67445	Mm.258993	NM_026161	ENSMUSG00000040794	C1qtnf4	0710001E10Rik|9430004J15Rik|CTRP4	C1q and tumor necrosis factor related protein 4	protein-coding
mm_12075.1	chr2	59776068	59776086	+	1	NA	intron (NM_198294, intron 7 of 26)	intron (NM_198294, intron 7 of 26)	106529	NM_001159636	72137	Mm.288734	NM_028118	ENSMUSG00000026988	Wdsub1	1700048E19Rik|2610014F08Rik	WD repeat, SAM and U-box domain containing 1	protein-coding
mm_126944.1	chr15	92051237	92051243	+	1	NA	promoter-TSS (NM_001159648)	promoter-TSS (NM_001159648)	75	NM_001159648	12805	Mm.4911	NM_007727	ENSMUSG00000055022	Cntn1	AW495098|CNTN|F3cam|usl	contactin 1	protein-coding
mm_71050.1	chr8	33697163	33697177	+	1	NA	exon (NM_010344, exon 13 of 13)	exon (NM_010344, exon 13 of 13)	-34744	NM_001167921	68153	Mm.286104	NM_026584	ENSMUSG00000031585	Gtf2e2	34kDa|AI462509|C330006J08Rik	general transcription factor II E, polypeptide 2 (beta subunit)	protein-coding
mm_72392.1	chr8	81767674	81767685	+	1	NA	intron (NM_001297593, intron 4 of 23)	intron (NM_001297593, intron 4 of 23)	425117	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_24970.1	chr3	96729671	96729674	+	1	NA	intron (NM_026406, intron 1 of 8)	intron (NM_026406, intron 1 of 8)	2061	NM_026406	67845	Mm.386792	NM_026406	ENSMUSG00000028098	Rnf115	2610028E05Rik|AU042696|Zfp364	ring finger protein 115	protein-coding
mm_131655.1	chr16	20540587	20540597	+	1	NA	intron (NM_009679, intron 4 of 10)	intron (NM_009679, intron 4 of 10)	5112	NM_009679	11773	Mm.18946	NM_009679	ENSMUSG00000022841	Ap2m1	-	adaptor-related protein complex 2, mu 1 subunit	protein-coding
mm_140805.1	chr17	22081316	22081336	-	1	NA	Intergenic	CpG	84651	NM_177596	210853	Mm.441622	NM_177596	ENSMUSG00000063383	Zfp947	6720451E15|EG210853|Gm4769	zinc finger protein 947	protein-coding
mm_121617.1	chr14	8259326	8259378	-	1	NA	promoter-TSS (NM_053115)	promoter-TSS (NM_053115)	-333	NM_053115	93732	Mm.28700	NM_053115	ENSMUSG00000021751	Acox2	THCCox	acyl-Coenzyme A oxidase 2, branched chain	protein-coding
mm_83729.1	chr9	51056444	51056460	-	1	NA	TTS (NM_001033534)	TTS (NM_001033534)	20642	NM_001033534	244864	Mm.335152	NM_001033534	ENSMUSG00000060594	Layn	E030012M19Rik|Gm511	layilin	protein-coding
mm_22642.1	chr3	14864242	14864258	+	1	NA	exon (NM_007606, exon 2 of 7)	exon (NM_007606, exon 2 of 7)	712	NM_007606	12350	Mm.300	NM_007606	ENSMUSG00000027559	Car3	BB219044|Ca3|Car-3	carbonic anhydrase 3	protein-coding
mm_136863.1	chr17	12823404	12823417	+	1	NA	intron (NR_027773, intron 1 of 2)	Lx3B|LINE|L1	44733	NM_008552	17171	Mm.425994	NM_008552	ENSMUSG00000068037	Mas1	Mas-1|Mgra	MAS1 oncogene	protein-coding
mm_168013.1	chrY	57896498	57896522	+	1	NA	Intergenic	(TCTA)n|Simple_repeat|Simple_repeat	-362784	NM_001017393	434935	Mm.426195	NM_001017393	ENSMUSG00000096122	Gm21943	-	predicted gene, 21943	protein-coding
mm_169326.1	chr14	116641227	116641227	-	1	NA	Intergenic	L1Md_T|LINE|L1	-284070	NM_001079844	23888	Mm.440025	NM_011821	ENSMUSG00000058571	Gpc6	-	glypican 6	protein-coding
mm_164578.1	chr17	24736372	24736377	-	1	NA	promoter-TSS (NM_001346668)	promoter-TSS (NM_001346668)	-219	NM_013759	27361	Mm.28212	NM_013759	ENSMUSG00000075705	Msrb1	D17Wsu82e|SELX|SelR|Sepr|Sepx1	methionine sulfoxide reductase B1	protein-coding
mm_107122.1	chr12	19175885	19175926	+	1	NA	Intergenic	CpG	661395	NM_001201330	236366	Mm.352227	NM_001033157	ENSMUSG00000073197	5730507C01Rik	-	RIKEN cDNA 5730507C01 gene	protein-coding
mm_70485.1	chr8	12396206	12396222	+	1	NA	5' UTR (NM_009233, exon 1 of 1)	5' UTR (NM_009233, exon 1 of 1)	695	NM_009233	20664	Mm.39088	NM_009233	ENSMUSG00000096014	Sox1	BB176347|Sox-1	SRY (sex determining region Y)-box 1	protein-coding
mm_127977.1	chr15	12419546	12419591	-	1	NA	exon (NM_001081064, exon 6 of 24)	exon (NM_001081064, exon 6 of 24)	98072	NM_025673	66629	Mm.157655	NM_025673	ENSMUSG00000022200	Golph3	4733401N08Rik|5730410D03Rik|AW413496	golgi phosphoprotein 3	protein-coding
mm_138884.1	chr17	43389527	43389539	+	1	NA	promoter-TSS (NM_001081178)	promoter-TSS (NM_001081178)	67	NM_001081178	224792	Mm.23478	NM_001081178	ENSMUSG00000056492	Adgrf5	8430401C09Rik|9330185D23|AI528491|Gpr116|mKIAA0758	adhesion G protein-coupled receptor F5	protein-coding
mm_123068.1	chr14	55681742	55681756	-	1	NA	promoter-TSS (NM_145705)	promoter-TSS (NM_145705)	68	NM_145705	28113	Mm.29346	NM_145705	ENSMUSG00000007589	Tinf2	AW552114|D14Wsu146e|Tin2	Terf1 (TRF1)-interacting nuclear factor 2	protein-coding
mm_42489.1	chr5	115472023	115472080	+	1	NA	exon (NM_011107, exon 3 of 4)	exon (NM_011107, exon 3 of 4)	5785	NM_011107	18778	Mm.20190	NM_011107	ENSMUSG00000029522	Pla2g1b	Pla2a|sPLA2IB	phospholipase A2, group IB, pancreas	protein-coding
mm_161173.1	chr13	38527971	38527971	-	1	NA	promoter-TSS (NM_001289599)	promoter-TSS (NM_001289599)	-57	NM_001289599	105245	Mm.28622	NM_145367	ENSMUSG00000038991	Txndc5	AL022641|ERp46|PC-TRP	thioredoxin domain containing 5	protein-coding
mm_60633.1	chr7	44816291	44816308	+	1	NA	promoter-TSS (NM_030693)	promoter-TSS (NM_030693)	-71	NM_001171024	100328588	Mm.2565	NM_001171024	ENSMUSG00000074141	Gm21948	Nup62-il4i1	predicted gene, 21948	protein-coding
mm_157127.1	chrX	9446783	9446794	-	1	NA	exon (NM_007807, exon 9 of 13)	exon (NM_007807, exon 9 of 13)	22536	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_84004.1	chr9	57606235	57606260	-	1	NA	promoter-TSS (NM_146223)	promoter-TSS (NM_146223)	34	NM_146223	235415	Mm.35242	NM_146223	ENSMUSG00000039714	Cplx3	BC016632|CpxIII|ERGIC-53L|ERGL|Lamn1l|Lman1l	complexin 3	protein-coding
mm_47736.1	chr5	130222217	130222233	-	1	NA	promoter-TSS (NM_027854)	promoter-TSS (NM_027854)	-110	NM_027854	71667	Mm.258508	NM_027854	ENSMUSG00000053094	Tmem248	0610007L01Rik|A930023A16Rik|AW557951|G430067H08Rik	transmembrane protein 248	protein-coding
mm_139637.1	chr17	57376361	57376372	+	1	NA	intron (NM_010130, intron 2 of 21)	Lx5b|LINE|L1	17680	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_41661.1	chr5	98880002	98880006	+	1	NA	3' UTR (NM_001310677, exon 3 of 3)	3' UTR (NM_001310677, exon 3 of 3)	25589	NM_001310677	110075	Mm.136461	NM_173404	ENSMUSG00000029335	Bmp3	9530029I04Rik	bone morphogenetic protein 3	protein-coding
mm_19661.1	chr2	103172345	103172353	-	1	NA	Intergenic	Intergenic	98674	NM_019735	56369	Mm.24772	NM_019735	ENSMUSG00000010911	Apip	APIP2|CGI-29|Mmrp19	APAF1 interacting protein	protein-coding
mm_26728.1	chr3	4891316	4891326	-	1	NA	Intergenic	Intergenic	92613	NR_045272	100503859	Mm.75172	NR_045272	ENSMUSG00000098659	1110015O18Rik	-	RIKEN cDNA 1110015O18 gene	ncRNA
mm_120876.1	chr14	75284315	75284325	+	1	NA	promoter-TSS (NM_026083)	promoter-TSS (NM_026083)	-53	NM_026083	67302	Mm.74704	NM_026083	ENSMUSG00000022000	Zc3h13	2600010B19Rik|3110050K21Rik|4930570G11Rik|C87618	zinc finger CCCH type containing 13	protein-coding
mm_84714.1	chr9	73113349	73113401	-	1	NA	promoter-TSS (NM_198609)	promoter-TSS (NM_198609)	-94	NM_198609	225215	Mm.379366	NM_198609	ENSMUSG00000032215	Rsl24d1	2410159K22Rik	ribosomal L24 domain containing 1	protein-coding
mm_52878.1	chr6	122491726	122491728	+	1	NA	Intergenic	Intergenic	-5422	NM_027664	108653	Mm.277939	NM_027664	ENSMUSG00000040649	Rimklb	4931417E21Rik|4933426K21Rik|AA097693|AI325948|AU015629|Naags	ribosomal modification protein rimK-like family member B	protein-coding
mm_149995.1	chr19	29262237	29262250	+	1	NA	exon (NM_008413, exon 3 of 25)	exon (NM_008413, exon 3 of 25)	10440	NM_008413	16452	Mm.275839	NM_008413	ENSMUSG00000024789	Jak2	Fd17	Janus kinase 2	protein-coding
mm_26010.1	chr3	135307682	135307706	+	1	NA	promoter-TSS (NM_178877)	promoter-TSS (NM_178877)	-6	NM_178877	97086	Mm.441764	NM_178877	ENSMUSG00000037994	Slc9b2	C80638|NHA2|NHE10|Nhedc2|nha-oc|nhaoc	solute carrier family 9, subfamily B (NHA2, cation proton antiporter 2), member 2	protein-coding
mm_168489.1	chr1	149513224	149513230	-	1	NA	Intergenic	IAPLTR1_Mm|LTR|ERVK	409212	NM_001305632	18783	Mm.4186	NM_008869	ENSMUSG00000056220	Pla2g4a	Pla2g4|cPLA2|cPLA2-alpha|cPLA2alpha	phospholipase A2, group IVA (cytosolic, calcium-dependent)	protein-coding
mm_2853.1	chr1	131674917	131674938	+	1	NA	exon (NM_007799, exon 10 of 10)	exon (NM_007799, exon 10 of 10)	-13768	NM_145509	226421	Mm.44508	NM_145509	ENSMUSG00000052688	Rab7b	5430435G22Rik	RAB7B, member RAS oncogene family	protein-coding
mm_68573.1	chr7	115824700	115824752	-	1	NA	promoter-TSS (NM_001277327)	promoter-TSS (NM_001277327)	-16	NM_001277327	20679	Mm.323365	NM_011445	ENSMUSG00000051910	Sox6	AI987981|SOX-LZ	SRY (sex determining region Y)-box 6	protein-coding
mm_35021.1	chr4	3903328	3903328	-	1	NA	3' UTR (NM_019969, exon 6 of 6)	3' UTR (NM_019969, exon 6 of 6)	-31223	NM_020021	17451	Mm.459300	NM_020021	ENSMUSG00000078365	Mos	c-mos	Moloney sarcoma oncogene	protein-coding
mm_8511.1	chr1	154726457	154726461	-	1	NA	promoter-TSS (NM_009782)	promoter-TSS (NM_009782)	-539	NM_009782	12290	Mm.267517	NM_009782	ENSMUSG00000004110	Cacna1e	A430040I15|BII|Cach6|Cacnl1a6|Cav2.3|Cchra1|alpha1E	calcium channel, voltage-dependent, R type, alpha 1E subunit	protein-coding
mm_98563.1	chr11	95352738	95352741	+	1	NA	intron (NM_172543, intron 1 of 7)	intron (NM_172543, intron 1 of 7)	15721	NM_172543	215512	Mm.262113	NM_172543	ENSMUSG00000038893	Fam117a	5730593F17Rik|AW548096	family with sequence similarity 117, member A	protein-coding
mm_29434.1	chr3	109361987	109361994	-	1	NA	intron (NM_020505, intron 1 of 26)	intron (NM_020505, intron 1 of 26)	21307	NM_020505	57257	Mm.282257	NM_020505	ENSMUSG00000033721	Vav3	A530094I06Rik|AA986410|Idd18.1	vav 3 oncogene	protein-coding
mm_45633.1	chr5	76331151	76331161	-	1	NA	promoter-TSS (NM_023508)	promoter-TSS (NM_023508)	0	NM_001310637	79455	Mm.143764	NM_023508	ENSMUSG00000029235	Pdcl2	1700010B22Rik|1700016K07Rik|Mgcphlp|Tphlp	phosducin-like 2	protein-coding
mm_20415.1	chr2	129300616	129300649	-	1	NA	3' UTR (NM_010554, exon 7 of 7)	3' UTR (NM_010554, exon 7 of 7)	3262	NR_040371	100503468	Mm.446943	NR_040371	ENSMUSG00000085498	Gm14023	OTTMUSG00000015408	predicted gene 14023	ncRNA
mm_17639.1	chr2	31152235	31152284	-	1	NA	promoter-TSS (NM_178760)	promoter-TSS (NM_178760)	32	NR_040334	320973	Mm.384284	NR_040334		D330023K18Rik	-	RIKEN cDNA D330023K18 gene	ncRNA
mm_163399.1	chr12	71111458	71111461	+	1	NA	promoter-TSS (NM_029227)	promoter-TSS (NM_029227)	31	NM_029227	75266	Mm.402075	NM_029227	ENSMUSG00000021078	Tomm20l	4930553D19Rik	translocase of outer mitochondrial membrane 20 homolog (yeast)-like	protein-coding
mm_54410.1	chr6	32543824	32543827	-	1	NA	intron (NM_175750, intron 1 of 31)	intron (NM_175750, intron 1 of 31)	32684	NR_040277	319849	Mm.440860	NR_040277	ENSMUSG00000086763	Plxna4os1	B230378P21Rik	plexin A4, opposite strand 1	ncRNA
mm_85451.1	chr9	104337701	104337733	-	1	NA	promoter-TSS (NM_019807)	promoter-TSS (NM_019807)	5	NM_019807	56318	Mm.19941	NM_019807	ENSMUSG00000032561	Acpp	5'-NT|A030005E02Rik|FRAP|Lap|PAP|Ppal	acid phosphatase, prostate	protein-coding
mm_6049.1	chr1	60043093	60043175	-	1	NA	promoter-TSS (NM_001316695)	promoter-TSS (NM_001316695)	-12	NM_001316695	70375	Mm.17834	NM_027407	ENSMUSG00000026018	Ica1l	1700030B17Rik|Als2cr15	islet cell autoantigen 1-like	protein-coding
mm_31796.1	chr4	63979910	63979916	+	1	NA	intron (NM_011607, intron 15 of 25)	intron (NM_011607, intron 15 of 25)	67102	NM_011607	21923	Mm.980	NM_011607	ENSMUSG00000028364	Tnc	AI528729|C130033P17Rik|Hxb|TN|TN-C|Ten|cytotactin|tenascin-C	tenascin C	protein-coding
mm_112947.1	chr13	21003459	21003462	+	1	NA	intron (NM_012054, intron 18 of 20)	PB1D7|SINE|Alu	69839	NM_146535	258528	Mm.377554	NM_146535	ENSMUSG00000042869	Olfr1370	MOR256-14	olfactory receptor 1370	protein-coding
mm_26770.1	chr3	8936371	8936374	-	1	NA	intron (NM_001025262, intron 4 of 5)	intron (NM_001025262, intron 4 of 5)	-12515	NM_025434	66230	Mm.38460	NM_025434	ENSMUSG00000040269	Mrps28	1500012D08Rik|AW061224	mitochondrial ribosomal protein S28	protein-coding
mm_135119.1	chr16	35841447	35841478	-	1	NA	exon (NM_001039530, exon 13 of 17)	exon (NM_001039530, exon 13 of 17)	29920	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_105244.1	chr11	102349296	102349299	-	1	NA	3' UTR (NM_011403, exon 20 of 20)	3' UTR (NM_011403, exon 20 of 20)	15984	NM_011403	20533	Mm.7248	NM_011403	ENSMUSG00000006574	Slc4a1	Ae1|CD233|Empb3|l11Jus51	solute carrier family 4 (anion exchanger), member 1	protein-coding
mm_64648.1	chr7	4063127	4063139	-	1	NA	promoter-TSS (NM_178611)	promoter-TSS (NM_178611)	71	NM_001302677	52855	Mm.290880	NM_178611	ENSMUSG00000055541	Lair1	5133400O11Rik|BB115266|D7Bwg0421e|Lair-1	leukocyte-associated Ig-like receptor 1	protein-coding
mm_119335.1	chr14	40081795	40081803	+	1	NA	Intergenic	RLTR23|LTR|ERV1	426136	NR_045936	73591	Mm.65499	NR_045936	ENSMUSG00000101261	1700109I08Rik	-	RIKEN cDNA 1700109I08 gene	ncRNA
mm_106087.1	chr11	116186896	116186899	-	1	NA	intron (NM_015729, intron 2 of 13)	B1_Mur1|SINE|Alu	-11958	NM_027107	69535	Mm.390347	NM_027107	ENSMUSG00000020778	Ten1	2310004N24Rik	TEN1 telomerase capping complex subunit	protein-coding
mm_81341.1	chr9	108534193	108534246	+	1	NA	exon (NM_175143, exon 3 of 10)	exon (NM_175143, exon 3 of 10)	17132	NM_175143	69232	Mm.335449	NM_175143	ENSMUSG00000006673	Qrich1	2610028H07Rik	glutamine-rich 1	protein-coding
mm_7026.1	chr1	87098802	87098811	-	1	NA	exon (NM_001081082, exon 11 of 11)	exon (NM_001081082, exon 11 of 11)	2800	NM_001081082	76768	Mm.58068	NM_001081082	ENSMUSG00000079440	Alpi	2010001C14Rik|Akp6|gIAP	alkaline phosphatase, intestinal	protein-coding
mm_162190.1	chrX	107676444	107676444	+	1	NA	promoter-TSS (NM_145224)	promoter-TSS (NM_145224)	-68	NM_145224	245572	Mm.137011	NM_145224	ENSMUSG00000031241	Tbx22	D230020M15Rik	T-box 22	protein-coding
mm_71162.1	chr8	40511770	40511787	+	1	NA	promoter-TSS (NM_001271543)	promoter-TSS (NM_001271543)	-5	NM_033560	52348	Mm.489696	NM_033560	ENSMUSG00000031600	Vps37a	2210018P21Rik|4930592A21Rik|AW261445|D8Ertd531e	vacuolar protein sorting 37A	protein-coding
mm_121453.1	chr14	120478444	120478510	+	1	NA	promoter-TSS (NM_029519)	promoter-TSS (NM_029519)	16	NM_029519	76108	Mm.261448	NM_029519	ENSMUSG00000051615	Rap2a	5830461H18Rik	RAS related protein 2a	protein-coding
mm_4473.1	chr1	173419385	173419398	+	1	NA	Intergenic	Intergenic	-1213	NM_001013779	383619	Mm.131453	NM_001013779	ENSMUSG00000037860	Aim2	Gm1313|Ifi210	absent in melanoma 2	protein-coding
mm_137605.1	chr17	28222214	28222218	+	1	NA	intron (NM_027185, intron 5 of 10)	Lx8b|LINE|L1	-10538	NM_011145	19015	Mm.328914	NM_011145	ENSMUSG00000002250	Ppard	NUC-1|NUC1|Nr1c2|PPAR-beta|PPAR-delta|PPAR[b]|PPARdelta|Pparb|Pparb/d	peroxisome proliferator activator receptor delta	protein-coding
mm_5818.1	chr1	52726825	52726870	-	1	NA	intron (NM_178081, intron 1 of 5)	CpG	471	NM_178081	98682	Mm.491173	NM_133829	ENSMUSG00000041439	Mfsd6	2210010L05Rik|9630025I22Rik|AI836200|AW212394|MMR2	major facilitator superfamily domain containing 6	protein-coding
mm_2458.1	chr1	104768797	104768823	+	1	NA	promoter-TSS (NM_011800)	promoter-TSS (NM_011800)	-9	NM_011800	23836	Mm.103640	NM_011800	ENSMUSG00000050840	Cdh20	Cdh7	cadherin 20	protein-coding
mm_30120.1	chr3	141211821	141211833	-	1	NA	5' UTR (NM_008811, exon 1 of 1)	5' UTR (NM_008811, exon 1 of 1)	528	NM_008811	18598	Mm.4223	NM_008811	ENSMUSG00000047674	Pdha2	Pdhal	pyruvate dehydrogenase E1 alpha 2	protein-coding
mm_115008.1	chr13	98317070	98317089	+	1	NA	promoter-TSS (NR_137279)	promoter-TSS (NR_137279)	-37	NR_137279	105246056		NR_137279	ENSMUSG00000048603	LOC105246056	-	uncharacterized LOC105246056	ncRNA
mm_167174.1	chr7	139800013	139800016	+	1	NA	Intergenic	Intergenic	20996	NR_105827	102465215		NR_105827	ENSMUSG00000098619	Mir6401	Gm27442|mmu-mir-6401	microRNA 6401	ncRNA
mm_8234.1	chr1	138175719	138175740	-	1	NA	promoter-TSS (NM_001268286)	promoter-TSS (NM_001268286)	-424	NM_001268286	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_140175.1	chr17	80762845	80762857	+	1	NA	Intergenic	Intergenic	-34826	NM_001290345	225028	Mm.311948	NM_001081357	ENSMUSG00000024242	Map4k3	4833416M01Rik|4833416M07Rik|9530052P13Rik|Glk|MAPKKKK3|MEKKK 3|MEKKK3|RAB8IPL1	mitogen-activated protein kinase kinase kinase kinase 3	protein-coding
mm_137765.1	chr17	29490638	29490655	+	1	NA	promoter-TSS (NM_008842)	promoter-TSS (NM_008842)	-399	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_26118.1	chr3	137864504	137864525	+	1	NA	promoter-TSS (NM_016750)	promoter-TSS (NM_016750)	27	NM_016750	51788	Mm.117541	NM_016750	ENSMUSG00000037894	H2afz	H2A.Z|H2a.z-1	H2A histone family, member Z	protein-coding
mm_37740.1	chr4	129578536	129578560	-	1	NA	promoter-TSS (NM_182783)	promoter-TSS (NM_182783)	32	NM_182783	230766	Mm.20377	NM_182783	ENSMUSG00000050493	Fam167b	SEC	family with sequence similarity 167, member B	protein-coding
mm_125106.1	chr15	27796216	27796223	+	1	NA	intron (NM_001081302, intron 34 of 56)	intron (NM_001081302, intron 34 of 56)	-114677	NM_001242423	223433	Mm.266485	NM_198301	ENSMUSG00000056069	Fam105a	9830126M18	family with sequence similarity 105, member A	protein-coding
mm_165281.1	chr2	82991666	82991668	+	1	NA	Intergenic	Intergenic	-652911	NM_026934	69082	Mm.27804	NM_026934	ENSMUSG00000027091	Zc3h15	1700006A17Rik|1810012H02Rik|2610312B22Rik|FM22|Ierepo4	zinc finger CCCH-type containing 15	protein-coding
mm_63402.1	chr7	127297415	127297434	+	1	NA	intron (NM_001253874, intron 1 of 30)	intron (NM_001253874, intron 1 of 30)	1164	NM_001253874	16408	Mm.1618	NM_008400	ENSMUSG00000030830	Itgal	(p180)|Cd11a|LFA-1|LFA-1A|Ly-15|Ly-21	integrin alpha L	protein-coding
mm_44830.1	chr5	33976439	33976442	-	1	NA	Intergenic	Intergenic	-6993	NM_001033458	381633	Mm.4923	NM_001033458	ENSMUSG00000070858	Gm1673	-	predicted gene 1673	protein-coding
mm_24069.1	chr3	87919516	87919526	+	1	NA	promoter-TSS (NM_026591)	promoter-TSS (NM_026591)	-23	NM_026591	67707	Mm.393802	NM_026591	ENSMUSG00000019710	Mrpl24	2010005E08Rik|2810470K06Rik|6720473G22Rik|AA407670	mitochondrial ribosomal protein L24	protein-coding
mm_39404.1	chr5	14514953	14514991	+	1	NA	promoter-TSS (NM_011995)	promoter-TSS (NM_011995)	54	NM_001110796	26875	Mm.146275	NM_011995	ENSMUSG00000061601	Pclo	Acz|Pico	piccolo (presynaptic cytomatrix protein)	protein-coding
mm_41883.1	chr5	105415691	105415730	+	1	NA	promoter-TSS (NM_001033550)	promoter-TSS (NM_001033550)	-65	NM_001033550	433926	Mm.439781	NM_001033550	ENSMUSG00000070639	Lrrc8b	R75581|Ta-lrrp|mKIAA0231	leucine rich repeat containing 8 family, member B	protein-coding
mm_56731.1	chr6	115676624	115676642	-	1	NA	promoter-TSS (NM_029780)	promoter-TSS (NM_029780)	2	NM_029780	110157	Mm.184163	NM_029780	ENSMUSG00000000441	Raf1	6430402F14Rik|AA990557|BB129353|Craf1|D830050J10Rik|Raf-1|c-Raf|v-Raf	v-raf-leukemia viral oncogene 1	protein-coding
mm_85165.1	chr9	96391972	96391981	-	1	NA	Intergenic	Intergenic	-27677	NM_007502	11933	Mm.424	NM_007502	ENSMUSG00000032412	Atp1b3	AA409958|AI664000|AW212096	ATPase, Na+/K+ transporting, beta 3 polypeptide	protein-coding
mm_25400.1	chr3	107241916	107241918	+	1	NA	Intergenic	Intergenic	-2210	NM_001044382	246691	Mm.490697	NM_001044382	ENSMUSG00000070368	Prok1	EG-VEGF	prokineticin 1	protein-coding
mm_70643.1	chr8	14095850	14095915	+	1	NA	promoter-TSS (NM_001145965)	promoter-TSS (NM_001145965)	7	NM_172910	244310	Mm.404697	NM_172910	ENSMUSG00000047495	Dlgap2	6430596N04Rik|Dap-2|Dap2|Sapap2	discs, large (Drosophila) homolog-associated protein 2	protein-coding
mm_24769.1	chr3	95526778	95526797	+	1	NA	promoter-TSS (NM_021281)	promoter-TSS (NM_021281)	1	NM_001267695	13040	Mm.3619	NM_021281	ENSMUSG00000038642	Ctss	Cats	cathepsin S	protein-coding
mm_149216.1	chr19	9985094	9985117	+	1	NA	TTS (NM_010239)	TTS (NM_010239)	2459	NM_010239	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
mm_115046.1	chr13	100108008	100108012	+	1	NA	promoter-TSS (NM_011353)	promoter-TSS (NM_011353)	-9	NM_011353	20365	Mm.286177	NM_011353	ENSMUSG00000021643	Serf1	4F5|Msmac1|m4F5	small EDRK-rich factor 1	protein-coding
mm_59781.1	chr7	28864446	28864460	+	1	NA	promoter-TSS (NM_008496)	promoter-TSS (NM_008496)	67	NM_008496	16858	Mm.20973	NM_008496	ENSMUSG00000053522	Lgals7	Galectin-7|Pig1	lectin, galactose binding, soluble 7	protein-coding
mm_19925.1	chr2	116062515	116062562	-	1	NA	intron (NM_001346047, intron 3 of 13)	intron (NM_001346047, intron 3 of 13)	2081	NM_001346044	17536	Mm.247566	NM_010825	ENSMUSG00000027210	Meis2	A430109D20Rik|Mrg1|Stra10	Meis homeobox 2	protein-coding
mm_52930.1	chr6	122932191	122932204	+	1	NA	exon (NM_199311, exon 5 of 6)	exon (NM_199311, exon 5 of 6)	10349	NM_199311	269799	Mm.297275	NM_199311	ENSMUSG00000049037	Clec4a1	BC049354|Dcir4	C-type lectin domain family 4, member a1	protein-coding
mm_95255.1	chr11	44643120	44643132	+	1	NA	intron (NM_007897, intron 5 of 15)	intron (NM_007897, intron 5 of 15)	25026	NM_001290710	13591	Mm.439662	NM_007897	ENSMUSG00000057098	Ebf1	Ebf|O/E-1|OE-1|Olf-1|Olf1	early B cell factor 1	protein-coding
mm_6095.1	chr1	63273097	63273111	-	1	NA	promoter-TSS (NM_028673)	promoter-TSS (NM_028673)	-165	NM_028673	73884	Mm.86986	NM_028673	ENSMUSG00000027520	Zdbf2	4930431J08Rik|9330107J05Rik	zinc finger, DBF-type containing 2	protein-coding
mm_26429.1	chr3	142618445	142618459	+	1	NA	3' UTR (NM_010259, exon 11 of 11)	3' UTR (NM_010259, exon 11 of 11)	-2211	NM_010260	14469	Mm.24038	NM_010260	ENSMUSG00000028270	Gbp2	-	guanylate binding protein 2	protein-coding
mm_95268.1	chr11	45006123	45006131	+	1	NA	3' UTR (NM_001290711, exon 16 of 16)	3' UTR (NM_001290711, exon 16 of 16)	110801	NR_045100	100504255	Mm.123608	NR_045100	ENSMUSG00000084773	Gm12159	OTTMUSG00000005475	predicted gene 12159	ncRNA
mm_165513.1	chr2	173073277	173073283	+	1	NA	Intergenic	Intergenic	46245	NM_001081387	664799	Mm.389396	NM_001081387	ENSMUSG00000070495	Ctcfl	Boris|OTTMUSG00000016680	CCCTC-binding factor (zinc finger protein)-like	protein-coding
mm_104818.1	chr11	98993713	98993715	-	1	NA	intron (NM_011623, intron 35 of 35)	intron (NM_011623, intron 35 of 35)	-10698	NM_178596	353155	Mm.453253	NM_178596	ENSMUSG00000047197	Gjd3	Gja11|Gjc1|cx30.2	gap junction protein, delta 3	protein-coding
mm_28016.1	chr3	83044248	83044313	-	1	NA	exon (NM_181849, exon 5 of 8)	exon (NM_181849, exon 5 of 8)	5583	NM_181849	110135	Mm.30063	NM_181849	ENSMUSG00000033831	Fgb	2510049G14Rik	fibrinogen beta chain	protein-coding
mm_88373.1	chr10	76147504	76147515	+	1	NA	promoter-TSS (NM_133184)	promoter-TSS (NM_133184)	58	NM_133184	64452	Mm.154797	NM_133184	ENSMUSG00000020229	Slc5a4a	SGLT3-a	solute carrier family 5, member 4a	protein-coding
mm_144371.1	chr18	20510292	20510301	+	1	NA	promoter-TSS (NM_030596)	promoter-TSS (NM_030596)	22	NM_030596	13512	Mm.106811	NM_030596	ENSMUSG00000056632	Dsg3	bal	desmoglein 3	protein-coding
mm_143240.1	chr17	63500601	63500622	-	1	NA	promoter-TSS (NM_015794)	promoter-TSS (NM_015794)	-31	NM_015794	50758	Mm.136366	NM_015794	ENSMUSG00000023965	Fbxl17	6330576B01Rik|AI452053|BB073797|C130023C01Rik|Fbx13|Fbxo13	F-box and leucine-rich repeat protein 17	protein-coding
mm_108404.1	chr12	81631229	81631312	+	1	NA	promoter-TSS (NM_001033149)	promoter-TSS (NM_001033149)	21	NM_001033149	69480	Mm.130002	NM_001033149	ENSMUSG00000042734	Ttc9	-	tetratricopeptide repeat domain 9	protein-coding
mm_92529.1	chr10	79533739	79533749	-	1	NA	promoter-TSS (NM_015817)	promoter-TSS (NM_015817)	43	NM_001302442	50784	Mm.28873	NM_015817	ENSMUSG00000052151	Plpp2	Lpp2|PAP2-G|PAP2-gamma|PAP2c|Ppap2c	phospholipid phosphatase 2	protein-coding
mm_151980.1	chr19	5829770	5829783	-	1	NA	non-coding (NR_131212, exon 1 of 1)	non-coding (NR_131212, exon 1 of 1)	15702	NR_131212	66961	Mm.281895	NR_003513	ENSMUSG00000092274	Neat1	2310043N10Rik|VINC	nuclear paraspeckle assembly transcript 1 (non-protein coding)	ncRNA
mm_4287.1	chr1	171695890	171695907	+	1	NA	exon (NM_007649, exon 2 of 4)	exon (NM_007649, exon 2 of 4)	13843	NM_007649	12506	Mm.1738	NM_007649	ENSMUSG00000015355	Cd48	AI449234|AW610730|BCM1|BLAST|BLAST-1|BLAST1|Bcm-1|MEM-102|SLAMF2|Sgp-60	CD48 antigen	protein-coding
mm_68331.1	chr7	106504150	106504157	-	1	NA	Intergenic	Intergenic	-63080	NR_003967	209380	Mm.461779	NM_001001318		Gm4759	EG209380	GTPase, very large interferon inducible 1 pseudogene	pseudo
mm_83622.1	chr9	48835933	48835962	-	1	NA	promoter-TSS (NM_001033324)	promoter-TSS (NM_001033324)	-2	NM_001033324	235320	Mm.457803	NM_001033324	ENSMUSG00000066687	Zbtb16	AI467657|PLZF|Zfp145|lu	zinc finger and BTB domain containing 16	protein-coding
mm_110287.1	chr12	32123682	32123712	-	1	NA	Intergenic	Intergenic	-62418	NM_011158	19088	Mm.25594	NM_011158	ENSMUSG00000002997	Prkar2b	AI451071|AW061005|PKARIIbeta|Pkarb2|RII(beta)	protein kinase, cAMP dependent regulatory, type II beta	protein-coding
mm_129520.1	chr15	79141198	79141268	-	1	NA	promoter-TSS (NM_001310576)	promoter-TSS (NM_001310576)	18	NM_001310581	27660	Mm.390827	NM_138581	ENSMUSG00000033029	1700088E04Rik	ESTJ0827E04	RIKEN cDNA 1700088E04 gene	protein-coding
mm_73790.1	chr8	117256799	117256803	+	1	NA	promoter-TSS (NM_001163262)	promoter-TSS (NM_001163262)	-218	NM_001163262	74440	Mm.233181	NM_028941	ENSMUSG00000034390	Cmip	4933407C03Rik|5830471E12Rik|AI314065|AI464126	c-Maf inducing protein	protein-coding
mm_69444.1	chr7	132989751	132989754	-	1	NA	intron (NM_001347623, intron 8 of 8)	intron (NM_001347623, intron 8 of 8)	25495	NM_001170744	13017	Mm.246240	NM_009980	ENSMUSG00000030970	Ctbp2	AA407280|D7Ertd45e|Gtrgeo6|Ribeye	C-terminal binding protein 2	protein-coding
mm_130703.1	chr15	100687909	100687924	-	1	NA	promoter-TSS (NM_033612)	promoter-TSS (NM_033612)	4	NM_033612	109901	Mm.2131	NM_033612	ENSMUSG00000023031	Cela1	1810009A17Rik|1810062B19Rik|Ela-1|Ela1|PC-TsF	chymotrypsin-like elastase family, member 1	protein-coding
mm_153794.1	chr19	45998480	45998521	-	1	NA	promoter-TSS (NM_198296)	promoter-TSS (NM_198296)	-12	NM_198296	71617	Mm.210949	NM_198296	ENSMUSG00000039901	9130011E15Rik	AI431055|AW050122	RIKEN cDNA 9130011E15 gene	protein-coding
mm_125581.1	chr15	59494698	59494728	+	1	NA	intron (NM_026746, intron 4 of 6)	intron (NM_026746, intron 4 of 6)	120515	NM_001164604	68501	Mm.27762	NM_026746	ENSMUSG00000059586	Nsmce2	1110014D18Rik|AI661537	NSE2/MMS21 homolog, SMC5-SMC6 complex SUMO ligase	protein-coding
mm_75711.1	chr8	68905127	68905154	-	1	NA	3' UTR (NM_008509, exon 10 of 10)	3' UTR (NM_008509, exon 10 of 10)	24585	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_35135.1	chr4	11386527	11386539	-	1	NA	5' UTR (NM_001290383, exon 1 of 16)	5' UTR (NM_001290383, exon 1 of 16)	245	NM_001347052	207920	Mm.387719	NM_194055	ENSMUSG00000040728	Esrp1	2210008M09Rik|A630065D16|BC031468|Rbm35a	epithelial splicing regulatory protein 1	protein-coding
mm_32511.1	chr4	108579446	108579470	+	1	NA	promoter-TSS (NM_172697)	promoter-TSS (NM_172697)	4	NM_011015	18392	Mm.294154	NM_011015	ENSMUSG00000028587	Orc1	AA545195|MmORC1|Orc1l	origin recognition complex, subunit 1	protein-coding
mm_170497.1	chr19	23620215	23620220	+	1	NA	intron (NM_026188, intron 1 of 5)	intron (NM_026188, intron 1 of 5)	32595	NM_026188	67483	Mm.443287	NM_026188	ENSMUSG00000033053	1700028P14Rik	AV209940	RIKEN cDNA 1700028P14 gene	protein-coding
mm_167580.1	chr9	45868891	45868895	+	1	NA	intron (NM_001310839, intron 10 of 13)	intron (NM_001310839, intron 10 of 13)	30348	NM_011792	23821	Mm.24044	NM_011792	ENSMUSG00000032086	Bace1	ASP2|Bace|C76936	beta-site APP cleaving enzyme 1	protein-coding
mm_70276.1	chr8	3598594	3598614	+	1	NA	intron (NM_001347112, intron 2 of 17)	intron (NM_001347112, intron 2 of 17)	11154	NM_001347111	69697	Mm.390010	NM_027171	ENSMUSG00000044433	Camsap3	2310057J16Rik|Kiaa1543|Nezha	calmodulin regulated spectrin-associated protein family, member 3	protein-coding
mm_65199.1	chr7	19696869	19696895	-	1	NA	exon (NM_009696, exon 4 of 4)	exon (NM_009696, exon 4 of 4)	1516	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_67899.1	chr7	99626858	99626868	-	1	NA	5' UTR (NM_001195529, exon 1 of 1)	5' UTR (NM_001195529, exon 1 of 1)	240	NM_001195529	100503386	Mm.180719	NM_001195529	ENSMUSG00000096606	Tpbgl	EG245190|Gm4980	trophoblast glycoprotein-like	protein-coding
mm_63789.1	chr7	132610621	132610662	+	1	NA	promoter-TSS (NM_029609)	promoter-TSS (NM_029609)	-2	NM_029609	76429	Mm.276721	NM_029609	ENSMUSG00000030946	Lhpp	2310007H09Rik	phospholysine phosphohistidine inorganic pyrophosphate phosphatase	protein-coding
mm_112118.1	chr12	112829352	112829426	-	1	NA	promoter-TSS (NM_028023)	promoter-TSS (NM_028023)	0	NM_028023	71963	Mm.313185	NM_028023	ENSMUSG00000047832	Cdca4	2410018C03Rik|HEPP|SEI-3	cell division cycle associated 4	protein-coding
mm_75730.1	chr8	69387131	69387133	-	1	NA	intron (NR_038043, intron 1 of 5)	B1_Mus1|SINE|Alu	8412	NR_038044	378466	Mm.37846	NM_194351	ENSMUSG00000110444	Gm10033	9330175B10Rik|ENSMUSG00000057924|Gm10311	predicted gene 10033	ncRNA
mm_119329.1	chr14	38898301	38898303	+	1	NA	promoter-TSS (NR_045713)	promoter-TSS (NR_045713)	0	NR_045713	75170	Mm.372967	NR_045713	ENSMUSG00000093528	Nrg3os	4930529F24Rik	neuregulin 3, opposite strand	ncRNA
mm_155356.1	chrX	69390428	69390433	+	1	NA	intron (NM_008032, intron 1 of 19)	intron (NM_008032, intron 1 of 19)	30099	NM_008032	14266	Mm.466576	NM_008032	ENSMUSG00000031189	Aff2	FMR2P|Fmr2|Ox19|Oxh	AF4/FMR2 family, member 2	protein-coding
mm_154791.1	chrX	13072055	13072069	+	1	NA	intron (NM_009481, intron 1 of 44)	CpG	564	NM_009481	22284	Mm.242646	NM_009481	ENSMUSG00000031010	Usp9x	5730589N07Rik|AA407302|AA407699|AL022658|AL022749|Dffrx|FAF-X|Fafl	ubiquitin specific peptidase 9, X chromosome	protein-coding
mm_75822.1	chr8	70485718	70485740	-	1	NA	exon (NM_182991, exon 4 of 8)	exon (NM_182991, exon 4 of 8)	1629	NM_182991	67937	Mm.23002	NM_182991	ENSMUSG00000035964	Tmem59l	5330410G16Rik	transmembrane protein 59-like	protein-coding
mm_172896.1	chr9	56223850	56223852	-	1	NA	intron (NM_172924, intron 6 of 6)	LSU-rRNA_Hsa|rRNA|rRNA	-62781	NM_019793	56434	Mm.28484	NM_019793	ENSMUSG00000032324	Tspan3	1700055K04Rik|TM4-A|Tm4sf8	tetraspanin 3	protein-coding
mm_164729.1	chr17	62780080	62780122	-	1	NA	intron (NM_010109, intron 1 of 3)	IMPB_01|Satellite|Satellite	101216	NM_207654	13640	Mm.7978	NM_010109	ENSMUSG00000048915	Efna5	AL-1|AV158822|EFL-5|Ephrin-A5|Epl7|LERK-7|RAGS	ephrin A5	protein-coding
mm_107544.1	chr12	40695502	40695504	+	1	NA	intron (NM_172803, intron 13 of 52)	Lx4A|LINE|L1	249450	NM_172803	238130	Mm.341423	NM_172803	ENSMUSG00000035954	Dock4	5330406C03|6330411N01Rik|AF263288|C030023J22|mKIAA0716	dedicator of cytokinesis 4	protein-coding
mm_167936.1	chrX	111167743	111167744	+	1	NA	Intergenic	L1MA9|LINE|L1	57325	NM_026134	67407	Mm.426142	NM_026134	ENSMUSG00000073001	Cylc1	4930401M13Rik	cylicin, basic protein of sperm head cytoskeleton 1	protein-coding
mm_108036.1	chr12	73779532	73779541	+	1	NA	Intergenic	Intergenic	-121788	NM_001313920	15251	Mm.3879	NM_010431	ENSMUSG00000021109	Hif1a	AA959795|HIF-1-alpha|HIF1-alpha|HIF1alpha|MOP1|bHLHe78	hypoxia inducible factor 1, alpha subunit	protein-coding
mm_14525.1	chr2	132692012	132692020	+	1	NA	exon (NM_028637, exon 2 of 3)	exon (NM_028637, exon 2 of 3)	1733	NM_028637	73747	Mm.284114	NM_028637	ENSMUSG00000044991	1110034G24Rik	-	RIKEN cDNA 1110034G24 gene	protein-coding
mm_73059.1	chr8	94386168	94386174	+	1	NA	promoter-TSS (NM_022331)	promoter-TSS (NM_022331)	-329	NM_022331	64209	Mm.29151	NM_022331	ENSMUSG00000031770	Herpud1	Herp|Mifl|SUP	homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1	protein-coding
mm_52033.1	chr6	96113449	96113452	+	1	NA	5' UTR (NM_182808, exon 1 of 5)	5' UTR (NM_182808, exon 1 of 5)	296	NM_182808	320265	Mm.489890	NM_182808	ENSMUSG00000059187	Fam19a1	C630007B19Rik|FAM19A1 TAFA-1|TAFA1|Tafa-1	family with sequence similarity 19, member A1	protein-coding
mm_72516.1	chr8	83955658	83955664	+	1	NA	promoter-TSS (NM_024184)	promoter-TSS (NM_024184)	-33	NM_024184	66929	Mm.29680	NM_024184	ENSMUSG00000005470	Asf1b	1700003K02Rik|AA409591	anti-silencing function 1B histone chaperone	protein-coding
mm_30633.1	chr4	8806246	8806252	+	1	NA	intron (NM_001277149, intron 5 of 37)	intron (NM_001277149, intron 5 of 37)	115843	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_117360.1	chr13	70637741	70637745	-	1	NA	promoter-TSS (NM_144837)	promoter-TSS (NM_144837)	-109	NM_144837	218333	Mm.139738	NM_144837	ENSMUSG00000034525	Ice1	C77245|mKIAA0947	interactor of little elongation complex ELL subunit 1	protein-coding
mm_51765.1	chr6	87913987	87913999	+	1	NA	promoter-TSS (NM_173737)	promoter-TSS (NM_173737)	17	NM_173737	232210	Mm.246241	NM_173737	ENSMUSG00000030060	Hmces	8430410A17Rik|C85376	5-hydroxymethylcytosine (hmC) binding, ES cell specific	protein-coding
mm_165448.1	chr2	156369236	156369239	+	1	NA	intron (NM_027585, intron 11 of 12)	B3A|SINE|B2	23742	NR_024329	347740	Mm.324242	NR_024329		2900097C17Rik	1810005K14Rik|4930563C06Rik	RIKEN cDNA 2900097C17 gene	ncRNA
mm_1440.1	chr1	67220498	67220507	+	1	NA	intron (NM_001080809, intron 33 of 37)	intron (NM_001080809, intron 33 of 37)	97475	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_159394.1	chr3	94362398	94362398	+	1	NA	promoter-TSS (NM_001136117)	promoter-TSS (NM_001136117)	-46	NM_001136117	271944	Mm.271006	NM_001136117	ENSMUSG00000091648	C2cd4d	Gm659	C2 calcium-dependent domain containing 4D	protein-coding
mm_131956.1	chr16	24486930	24486945	+	1	NA	intron (NM_001145952, intron 2 of 11)	(CA)n|Simple_repeat|Simple_repeat	38846	NM_001145952	210126	Mm.209385	NM_178665	ENSMUSG00000033306	Lpp	9430020K16Rik|AA959454|AU024130|B130055L10Rik|C79715|D630048H16	LIM domain containing preferred translocation partner in lipoma	protein-coding
mm_134770.1	chr16	23520851	23520860	-	1	NA	promoter-TSS (NM_008555)	promoter-TSS (NM_008555)	-265	NM_008555	17174	Mm.1213	NM_008555	ENSMUSG00000022887	Masp1	AW048060|CCPII|Crarf|Masp1/3	mannan-binding lectin serine peptidase 1	protein-coding
mm_111228.1	chr12	84757064	84757077	-	1	NA	3' UTR (NM_023409, exon 4 of 4)	3' UTR (NM_023409, exon 4 of 4)	16042	NM_023409	67963	Mm.282556	NM_023409	ENSMUSG00000021242	Npc2	2700012J19Rik|AA408070|AU045843|HE1	Niemann-Pick type C2	protein-coding
mm_29907.1	chr3	131474423	131474425	-	1	NA	Intergenic	Intergenic	-90344	NM_001289479	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_129577.1	chr15	79739007	79739018	-	1	NA	intron (NM_001205346, intron 2 of 17)	intron (NM_001205346, intron 2 of 17)	3524	NM_194342	223697	Mm.202715	NM_194342	ENSMUSG00000042524	Sun2	B230369L08Rik|C030011B15|Unc84b	Sad1 and UNC84 domain containing 2	protein-coding
mm_112499.1	chr13	8202886	8202918	+	1	NA	promoter-TSS (NM_001289530)	promoter-TSS (NM_001289530)	36	NM_052977	94191	Mm.425794	NM_052977	ENSMUSG00000052551	Adarb2	Adar3|RED2	adenosine deaminase, RNA-specific, B2	protein-coding
mm_146488.1	chr18	90512874	90512877	+	1	NA	intron (NM_198295, intron 2 of 15)	B4|SINE|B4	2721	NM_198295	67988	Mm.268041	NM_198295	ENSMUSG00000024614	Tmx3	6430411B10Rik|A730024F05Rik|AV259382|Txndc10|mKIAA1830	thioredoxin-related transmembrane protein 3	protein-coding
mm_47010.1	chr5	115474642	115474670	-	1	NA	TTS (NM_011107)	TTS (NM_011107)	8390	NM_011107	18778	Mm.20190	NM_011107	ENSMUSG00000029522	Pla2g1b	Pla2a|sPLA2IB	phospholipase A2, group IB, pancreas	protein-coding
mm_12829.1	chr2	80631748	80631755	+	1	NA	TTS (NM_024438)	TTS (NM_024438)	-2961	NR_030454	735274		NR_030454	ENSMUSG00000106252	Mir684-1	Mirn684-1	microRNA 684-1	ncRNA
mm_150614.1	chr19	40940214	40940230	+	1	NA	exon (NM_008528, exon 12 of 17)	exon (NM_008528, exon 12 of 17)	45517	NM_028319	72672	Mm.313523	NM_028319	ENSMUSG00000049164	Zfp518a	2810401C22Rik|6330417C12Rik|AI426493|Zfp518|Znf518|Znf518a|mKIAA0335	zinc finger protein 518A	protein-coding
mm_39319.1	chr5	8068425	8068440	+	1	NA	3' UTR (NM_025618, exon 8 of 8)	3' UTR (NM_025618, exon 8 of 8)	11890	NM_001080974	109552	Mm.96211	NM_025618	ENSMUSG00000003161	Sri	2210417O06Rik|2900070H08Rik|Sor	sorcin	protein-coding
mm_16214.1	chr2	173073222	173073230	+	1	NA	Intergenic	Intergenic	46299	NM_001081387	664799	Mm.389396	NM_001081387	ENSMUSG00000070495	Ctcfl	Boris|OTTMUSG00000016680	CCCTC-binding factor (zinc finger protein)-like	protein-coding
mm_30008.1	chr3	135650761	135650765	-	1	NA	intron (NM_008689, intron 6 of 24)	intron (NM_008689, intron 6 of 24)	40784	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_118529.1	chr14	15148780	15148806	+	1	NA	Intergenic	Intergenic	290194	NM_146052	218763	Mm.138039	NM_146052	ENSMUSG00000045201	Lrrc3b	BC019794|LRP15	leucine rich repeat containing 3B	protein-coding
mm_75897.1	chr8	71085727	71085729	-	1	NA	Intergenic	Intergenic	-54641	NM_001324526	665858	Mm.411658	NM_001324526		Gm7827	EG665858	predicted gene 7827	protein-coding
mm_114788.1	chr13	89540506	89540510	+	1	NA	promoter-TSS (NM_013500)	promoter-TSS (NM_013500)	-128	NM_013500	12950	Mm.266790	NM_013500	ENSMUSG00000021613	Hapln1	BB099155|CLP|Crtl1|Crtl1l|LP|LP-1	hyaluronan and proteoglycan link protein 1	protein-coding
mm_74095.1	chr8	122574636	122574638	+	1	NA	TTS (NM_009698)	TTS (NM_009698)	2270	NM_009698	11821	Mm.1786	NM_009698	ENSMUSG00000006589	Aprt	C85684	adenine phosphoribosyl transferase	protein-coding
mm_50670.1	chr6	51544478	51544480	+	1	NA	promoter-TSS (NM_001127348)	promoter-TSS (NM_001127348)	-44	NM_028035	71982	Mm.294166	NM_028035	ENSMUSG00000038301	Snx10	2410004M09Rik	sorting nexin 10	protein-coding
mm_43272.1	chr5	130448816	130448830	+	1	NA	promoter-TSS (NM_021371)	promoter-TSS (NM_021371)	31	NM_021371	140904	Mm.40875	NM_021371	ENSMUSG00000060371	Caln1	9630012C17Rik|Cabp8|MNCb-0849	calneuron 1	protein-coding
mm_28404.1	chr3	90243062	90243072	-	1	NA	promoter-TSS (NM_001307935)	promoter-TSS (NM_001307935)	76	NM_001307934	78284	Mm.299952	NM_030080	ENSMUSG00000027938	Creb3l4	1700012K17Rik|5330432F22Rik|AIBZIP|AV040530|AV258827|CREB4|JAL|TISP40|acre1	cAMP responsive element binding protein 3-like 4	protein-coding
mm_85600.1	chr9	107550836	107550837	-	1	NA	promoter-TSS (NM_001243748)	promoter-TSS (NM_001243748)	-719	NM_001243748	56289	Mm.12091	NM_019713	ENSMUSG00000010067	Rassf1	123F2|AA536941|AU044980|NORE2A|RDA32|REH3P21|Rassf1A|Rassf1B|Rassf1C	Ras association (RalGDS/AF-6) domain family member 1	protein-coding
mm_118551.1	chr14	17660873	17660950	+	1	NA	promoter-TSS (NM_001113417)	promoter-TSS (NM_001113417)	-49	NM_001113417	21834	Mm.32563	NM_009380	ENSMUSG00000021779	Thrb	Nr1a2|T3R[b]|T3Rbeta|Thrb1|Thrb2|c-erbAbeta	thyroid hormone receptor beta	protein-coding
mm_44894.1	chr5	35102504	35102520	-	1	NA	exon (NM_013587, exon 2 of 8)	exon (NM_013587, exon 2 of 8)	3185	NM_013587	16976	Mm.277661	NM_013587	ENSMUSG00000029103	Lrpap1	AA617339|AI790446|AU042172|C77774|HBP44|RAP	low density lipoprotein receptor-related protein associated protein 1	protein-coding
mm_36282.1	chr4	63860924	63860946	-	1	NA	exon (NM_009403, exon 1 of 4)	exon (NM_009403, exon 1 of 4)	349	NM_009403	21949	Mm.4664	NM_009403	ENSMUSG00000028362	Tnfsf8	CD153|CD30LG|Cd30l|Tnlg3a	tumor necrosis factor (ligand) superfamily, member 8	protein-coding
mm_115310.1	chr13	112318417	112318437	+	1	NA	exon (NM_029898, exon 2 of 11)	exon (NM_029898, exon 2 of 11)	29909	NM_001168404	77318	Mm.159895	NM_029898	ENSMUSG00000049985	Ankrd55	C030011J08Rik	ankyrin repeat domain 55	protein-coding
mm_68479.1	chr7	110863248	110863253	-	1	NA	promoter-TSS (NM_053247)	promoter-TSS (NM_053247)	-297	NM_053247	114332	Mm.396078	NM_053247	ENSMUSG00000030787	Lyve1	1200012G08Rik|Crsbp-1|Lyve-1|Xlkd1	lymphatic vessel endothelial hyaluronan receptor 1	protein-coding
mm_110177.1	chr12	27336988	27337023	-	1	NA	3' UTR (NM_009234, exon 1 of 1)	3' UTR (NM_009234, exon 1 of 1)	5713	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding
mm_72371.1	chr8	81015152	81015189	+	1	NA	promoter-TSS (NM_027554)	promoter-TSS (NM_027554)	-264	NM_027554	74841	Mm.246018	NM_027554	ENSMUSG00000038250	Usp38	4631402N15Rik|4833420O05Rik|AA536967|AU044701|AW544820|mKIAA1891	ubiquitin specific peptidase 38	protein-coding
mm_110193.1	chr12	27340295	27340310	-	1	NA	3' UTR (NM_009234, exon 1 of 1)	3' UTR (NM_009234, exon 1 of 1)	2416	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding
mm_122155.1	chr14	31369844	31369889	-	1	NA	intron (NM_009796, intron 19 of 20)	intron (NM_009796, intron 19 of 20)	33142	NM_009796	12339	Mm.201535	NM_009796	ENSMUSG00000021893	Capn7	AU022319|PalBH	calpain 7	protein-coding
mm_56081.1	chr6	87287205	87287255	-	1	NA	intron (NM_054041, intron 5 of 17)	intron (NM_054041, intron 5 of 17)	48545	NM_054041	69538	Mm.232525	NM_054041	ENSMUSG00000033420	Antxr1	2310008J16Rik|2810405N18Rik|Antrx1|Tem8	anthrax toxin receptor 1	protein-coding
mm_42654.1	chr5	119322010	119322022	+	1	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	-121998	NR_046033	665194	Mm.491047	NR_046033	ENSMUSG00000107334	Gm7538	EG665194	predicted gene 7538	ncRNA
mm_129073.1	chr15	75683682	75683686	-	1	NA	Intergenic	Intergenic	-4894	NM_028404	72960	Mm.182401	NM_028404	ENSMUSG00000000934	Top1mt	2900052H09Rik	DNA topoisomerase 1, mitochondrial	protein-coding
mm_17950.1	chr2	36808420	36808429	-	1	NA	Intergenic	Intergenic	4666	NM_206903	18328	Mm.377104	NM_206903	ENSMUSG00000075384	Olfr3	MOR136-14|Y71	olfactory receptor 3	protein-coding
mm_10405.1	chr2	13578724	13578734	+	1	NA	exon (NM_011701, exon 4 of 9)	exon (NM_011701, exon 4 of 9)	4418	NM_011701	22352	Mm.268000	NM_011701	ENSMUSG00000026728	Vim	-	vimentin	protein-coding
mm_105718.1	chr11	108424982	108424998	-	1	NA	promoter-TSS (NM_029606)	promoter-TSS (NM_029606)	-276	NM_029606	76380	Mm.344071	NM_029586	ENSMUSG00000020728	Cep112	1700001M19Rik|1700029K01Rik|8430407H02Rik|AV043680|AV207351|Ccdc46|Macoco	centrosomal protein 112	protein-coding
mm_141501.1	chr17	31633104	31633152	-	1	NA	5' UTR (NM_144855, exon 2 of 17)	5' UTR (NM_144855, exon 2 of 17)	4077	NM_144855	12411	Mm.206417	NM_144855	ENSMUSG00000024039	Cbs	AI047524|AI303044|HIP4	cystathionine beta-synthase	protein-coding
mm_116209.1	chr13	32776544	32776558	-	1	NA	intron (NM_001166030, intron 1 of 11)	intron (NM_001166030, intron 1 of 11)	5228	NM_001166030	238564	Mm.60041	NM_001166030	ENSMUSG00000044951	Mylk4	EG238564	myosin light chain kinase family, member 4	protein-coding
mm_157506.1	chrX	48868497	48868540	-	1	NA	intron (NM_001085499, intron 8 of 20)	intron (NM_001085499, intron 8 of 20)	9195	NM_001085499	209005	Mm.336054	NM_001085499	ENSMUSG00000079606	Gm595	-	predicted gene 595	protein-coding
mm_102988.1	chr11	69685338	69685348	-	1	NA	TTS (NM_011614)	TTS (NM_011614)	211	NM_001159505	69583	Mm.8983	NM_023517	ENSMUSG00000089669	Tnfsf13	2310026N09Rik|April|Tall2|Tnlg7b|Trdl1	tumor necrosis factor (ligand) superfamily, member 13	protein-coding
mm_90367.1	chr10	127167485	127167506	+	1	NA	intron (NR_045166, intron 4 of 9)	intron (NR_045166, intron 4 of 9)	1664	NM_001244618	14421	Mm.386762	NM_008080	ENSMUSG00000006731	B4galnt1	4933429D13Rik|Gal-NAc-T|GalNAc-T|GalNAcT|Galgt1|Ggm-2|Ggm2	beta-1,4-N-acetyl-galactosaminyl transferase 1	protein-coding
mm_1281.1	chr1	63595816	63595820	+	1	NA	3' UTR (NM_011780, exon 26 of 26)	3' UTR (NM_011780, exon 26 of 26)	91109	NM_001081658	241073	Mm.297680	NM_001081658	ENSMUSG00000069085	Dytn	Gm215	dystrotelin	protein-coding
mm_140750.1	chr17	16819934	16819935	-	1	NA	Intergenic	MMERGLN_LTR|LTR|ERV1	-244169	NM_001005358	449000	Mm.483718	NM_001005358	ENSMUSG00000096696	Zfp960	-	zinc finger protein 960	protein-coding
mm_48837.1	chr5	149244753	149244763	-	1	NA	Intergenic	Intergenic	-20246	NM_001308462	11690	Mm.19844	NM_009663	ENSMUSG00000060063	Alox5ap	Flap	arachidonate 5-lipoxygenase activating protein	protein-coding
mm_143981.1	chr17	87473763	87473794	-	1	NA	Intergenic	Intergenic	-26843	NM_007589	12314	Mm.329243	NM_007589	ENSMUSG00000036438	Calm2	1500001E21Rik|AL024017	calmodulin 2	protein-coding
mm_50766.1	chr6	53610465	53610477	+	1	NA	exon (NM_172728, exon 3 of 7)	exon (NM_172728, exon 3 of 7)	37097	NM_172728	231991	Mm.227444	NM_172728	ENSMUSG00000053007	Creb5	9430076C15Rik|CRE-BPa|Crebpa|D430026C09Rik	cAMP responsive element binding protein 5	protein-coding
mm_152127.1	chr19	7002269	7002270	-	1	NA	exon (NM_153795, exon 12 of 15)	exon (NM_153795, exon 12 of 15)	6138	NR_027351	107328	Mm.391161	NM_153597	ENSMUSG00000047656	Trpt1	AU079016|AW045591|Tpt1|Tpt1h	tRNA phosphotransferase 1	protein-coding
mm_54874.1	chr6	42644921	42644924	-	1	NA	5' UTR (NM_146174, exon 1 of 8)	5' UTR (NM_146174, exon 1 of 8)	119	NM_146174	232748	Mm.279659	NM_146174	ENSMUSG00000029851	Tcaf2	Fam115c	TRPM8 channel-associated factor 2	protein-coding
mm_7993.1	chr1	134304766	134304782	-	1	NA	intron (NM_001144855, intron 23 of 28)	MTEa|LTR|ERVL-MaLR	14770	NM_031189	17928	Mm.16528	NM_031189	ENSMUSG00000026459	Myog	MYF4|bHLHc3|myo	myogenin	protein-coding
mm_4941.1	chr1	191183552	191183596	+	1	NA	promoter-TSS (NM_007498)	promoter-TSS (NM_007498)	-241	NM_007498	11910	Mm.2706	NM_007498	ENSMUSG00000026628	Atf3	LRG-21	activating transcription factor 3	protein-coding
mm_66543.1	chr7	45189672	45189713	-	1	NA	exon (NM_201374, exon 11 of 20)	exon (NM_201374, exon 11 of 20)	8697	NM_053256	114640	Mm.207078	NM_053256	ENSMUSG00000038300	Pth2	Tifp39|Tip39	parathyroid hormone 2	protein-coding
mm_153747.1	chr19	44984526	44984548	-	1	NA	promoter-TSS (NR_040294)	promoter-TSS (NR_040294)	13	NR_040294	73894	Mm.491408	NR_040294		4930414N06Rik	-	RIKEN cDNA 4930414N06 gene	ncRNA
mm_81605.1	chr9	110656495	110656544	+	1	NA	promoter-TSS (NM_028312)	promoter-TSS (NM_028312)	16	NM_028312	72654	Mm.249115	NM_028312	ENSMUSG00000019659	Ccdc12	2700094L05Rik|C76605	coiled-coil domain containing 12	protein-coding
mm_163410.1	chr12	76910382	76910393	-	1	NA	intron (NM_145927, intron 9 of 11)	intron (NM_145927, intron 9 of 11)	51861	NM_008558	17187	Mm.268548	NM_008558	ENSMUSG00000059436	Max	AA960152|AI875693|bHLHd4|bHLHd5|bHLHd6|bHLHd7|bHLHd8	Max protein	protein-coding
mm_110468.1	chr12	51829526	51829553	-	1	NA	promoter-TSS (NM_144788)	promoter-TSS (NM_144788)	-3	NM_144788	207304	Mm.249391	NM_144788	ENSMUSG00000035247	Hectd1	A630086P08Rik|AI844876|b2b327Clo|opm	HECT domain containing 1	protein-coding
mm_100337.1	chr11	118342631	118342642	+	1	NA	promoter-TSS (NM_021440)	promoter-TSS (NM_021440)	-102	NM_021440	58251	Mm.439815	NM_021440	ENSMUSG00000076433	BC100451	Cep295nl|Ddc8|FS39|Kiaa1731nl	cDNA sequence BC100451	protein-coding
mm_22691.1	chr3	17793909	17793926	+	1	NA	intron (NR_033490, intron 1 of 2)	intron (NR_033490, intron 1 of 2)	-1745	NR_029814	723950		NR_029814	ENSMUSG00000093073	Mir124a-2	Mirn124a-2|mir-124-2|mir-124a-2	microRNA 124a-2	ncRNA
mm_45541.1	chr5	72840498	72840502	-	1	NA	intron (NM_001113461, intron 1 of 17)	intron (NM_001113461, intron 1 of 17)	27948	NM_001113461	21682	Mm.319581	NM_013689	ENSMUSG00000029217	Tec	-	tec protein tyrosine kinase	protein-coding
mm_26467.1	chr3	144283757	144283781	+	1	NA	Intergenic	MLT1E2|LTR|ERVL-MaLR	-78514	NM_010723	16911	Mm.29187	NM_010723	ENSMUSG00000028266	Lmo4	A730077C12Rik|Crp3|Etohi4	LIM domain only 4	protein-coding
mm_25827.1	chr3	128610955	128610963	+	1	NA	Intergenic	Intergenic	-379354	NR_045704	402774	Mm.209170	NR_045704	ENSMUSG00000105816	D030025E07Rik	-	RIKEN cDNA D030025E07 gene	ncRNA
mm_44463.1	chr5	22613222	22613235	-	1	NA	Intergenic	Intergenic	62815	NR_102315	320719	Mm.459265	NR_102315	ENSMUSG00000097207	6030443J06Rik	1700030G06Rik	RIKEN cDNA 6030443J06 gene	ncRNA
mm_98574.1	chr11	95666990	95667005	+	1	NA	promoter-TSS (NM_008831)	promoter-TSS (NM_008831)	40	NM_008831	18673	Mm.263862	NM_008831	ENSMUSG00000038845	Phb	Bap32	prohibitin	protein-coding
mm_154848.1	chrX	20425781	20425794	+	1	NA	promoter-TSS (NM_001289684)	promoter-TSS (NM_001289684)	99	NM_001289684	382207	Mm.281517	NM_199317	ENSMUSG00000037315	Jade3	5730598B06|AI851988|AW544806|Phf16|mKIAA0215	jade family PHD finger 3	protein-coding
mm_158634.1	chrX	154890271	154890314	-	1	NA	promoter-TSS (NM_001097980)	promoter-TSS (NM_001097980)	-25	NM_001097980	100040937	Mm.359511	NM_001097980	ENSMUSG00000072100	Cldn34b1	EG546400|Gm16390	claudin 34B1	protein-coding
mm_162825.1	chr10	81182428	81182462	+	1	NA	promoter-TSS (NM_001190474)	promoter-TSS (NM_001190474)	-562	NM_001190474	13144	Mm.10294	NM_007828	ENSMUSG00000034974	Dapk3	ZIPK|dlk	death-associated protein kinase 3	protein-coding
mm_13723.1	chr2	117417781	117417787	+	1	NA	Intergenic	Intergenic	-74907	NM_011246	19419	Mm.42150	NM_011246	ENSMUSG00000027347	Rasgrp1	Rasgrp	RAS guanyl releasing protein 1	protein-coding
mm_134512.1	chr16	19085491	19085506	-	1	NA	Intergenic	Intergenic	201243	NM_146451	258443	Mm.377506	NM_146451	ENSMUSG00000050742	Olfr164	MOR279-2	olfactory receptor 164	protein-coding
mm_98294.1	chr11	89092283	89092293	+	1	NA	intron (NM_001033266, intron 3 of 3)	intron (NM_001033266, intron 3 of 3)	18447	NM_001033266	217071	Mm.342127	NM_001033266	ENSMUSG00000072553	Gm525	-	predicted gene 525	protein-coding
mm_34351.1	chr4	144529516	144529521	+	1	NA	TTS (NM_198662)	TTS (NM_198662)	9696	NM_198662	381572	Mm.184290	NM_198662	ENSMUSG00000028593	9430007A20Rik	Aadacl4|Gm1034	RIKEN cDNA 9430007A20 gene	protein-coding
mm_78634.1	chr9	40050420	40050424	+	1	NA	promoter-TSS (NR_033613)	promoter-TSS (NR_033613)	-136	NR_033613	72224	Mm.235535	NR_033613	ENSMUSG00000101963	1700001J11Rik	-	ring finger protein 19A pseudogene	pseudo
mm_115812.1	chr13	19619821	19619827	-	1	NA	promoter-TSS (NM_134065)	promoter-TSS (NM_134065)	6	NM_134065	105298	Mm.275054	NM_134065	ENSMUSG00000002808	Epdr1	AU040950|AV006210|Epdm2|Epdr2|MERP-1|MERP-2|MERP2|Ucc1	ependymin related protein 1 (zebrafish)	protein-coding
mm_163439.1	chr12	85475791	85475796	+	1	NA	intron (NM_010234, intron 3 of 3)	intron (NM_010234, intron 3 of 3)	1892	NM_010234	14281	Mm.246513	NM_010234	ENSMUSG00000021250	Fos	D12Rfj1|c-fos|cFos	FBJ osteosarcoma oncogene	protein-coding
mm_11921.1	chr2	52072805	52072814	+	1	NA	promoter-TSS (NM_175238)	promoter-TSS (NM_175238)	-28	NM_175238	51869	Mm.254530	NM_175238	ENSMUSG00000036202	Rif1	5730435J01Rik|6530403D07Rik|AU016181|AW549474|D2Ertd145e	replication timing regulatory factor 1	protein-coding
mm_66320.1	chr7	41499393	41499423	-	1	NA	5' UTR (NM_001033530, exon 1 of 4)	5' UTR (NM_001033530, exon 1 of 4)	482	NM_001033530	101835	Mm.370336	NM_001033530	ENSMUSG00000074166	AW146154	AI451288	expressed sequence AW146154	protein-coding
mm_107200.1	chr12	25320813	25320824	+	1	NA	Intergenic	Intergenic	191644	NR_045844	432641	Mm.112955	NR_045844		Gm17746	-	predicted gene, 17746	ncRNA
mm_19940.1	chr2	116067126	116067141	-	1	NA	5' UTR (NM_001346047, exon 1 of 14)	5' UTR (NM_001346047, exon 1 of 14)	311	NM_001346047	17536	Mm.247566	NM_010825	ENSMUSG00000027210	Meis2	A430109D20Rik|Mrg1|Stra10	Meis homeobox 2	protein-coding
mm_82907.1	chr9	32928330	32928354	-	1	NA	intron (NR_131058, intron 1 of 3)	intron (NR_131058, intron 1 of 3)	624	NR_131058	330917	Mm.488283	NR_131058		Gm27162	A430016B06	predicted gene 27162	ncRNA
mm_35349.1	chr4	32251860	32251869	-	1	NA	Intergenic	Intergenic	-165571	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_107603.1	chr12	49384259	49384282	+	1	NA	5' UTR (NM_001160112, exon 1 of 1)	5' UTR (NM_001160112, exon 1 of 1)	1263	NM_008241	15228	Mm.4704	NM_008241	ENSMUSG00000020950	Foxg1	2900064B05Rik|BF-1|Bf1|Hfh9|Hfhbf1	forkhead box G1	protein-coding
mm_17798.1	chr2	33260907	33260926	-	1	NA	intron (NM_001290572, intron 7 of 17)	intron (NM_001290572, intron 7 of 17)	44955	NM_011923	26360	Mm.208919	NM_011923	ENSMUSG00000004105	Angptl2	AI593246|AW260363|Arp2	angiopoietin-like 2	protein-coding
mm_120234.1	chr14	62887218	62887236	+	1	NA	intron (NM_175546, intron 2 of 11)	intron (NM_175546, intron 2 of 11)	21685	NR_105860	102465311		NR_105860	ENSMUSG00000098858	Mir6541	Gm27311|mmu-mir-6541	microRNA 6541	ncRNA
mm_54095.1	chr6	16837040	16837058	-	1	NA	intron (NM_031198, intron 5 of 6)	Lx8|LINE|L1	61392	NM_031198	21426	Mm.36217	NM_031198	ENSMUSG00000029553	Tfec	BB107417|Tcfec|bHLHe34	transcription factor EC	protein-coding
mm_150708.1	chr19	42531307	42531314	+	1	NA	intron (NM_177464, intron 1 of 6)	B1F1|SINE|Alu	12505	NM_177464	52013	Mm.254169	NM_177464	ENSMUSG00000025184	R3hcc1l	1700036B12Rik|AI450607|C10orf28|D19Ertd386e|GIDRP86|Gidrp88	R3H domain and coiled-coil containing 1 like	protein-coding
mm_147825.1	chr18	61930229	61930250	-	1	NA	Intergenic	Intergenic	-18387	NM_001164491	319713	Mm.329478	NM_198649	ENSMUSG00000032735	Ablim3	AW990719|D930036B08Rik	actin binding LIM protein family, member 3	protein-coding
mm_109335.1	chr12	109581714	109581735	+	1	NA	Intergenic	Intergenic	1491	NR_030573	100124466		NR_030573	ENSMUSG00000077025	Mir493	Mirn493|mmu-mir-493	microRNA 493	ncRNA
mm_31932.1	chr4	86053995	86054012	+	1	NA	promoter-TSS (NM_029967)	promoter-TSS (NM_029967)	88	NM_029967	77739	Mm.331690	NM_029967	ENSMUSG00000066113	Adamtsl1	5930437A14Rik|6720426B09Rik|ADAMTSL-1	ADAMTS-like 1	protein-coding
mm_11910.1	chr2	52038006	52038020	+	1	NA	promoter-TSS (NM_009398)	promoter-TSS (NM_009398)	-100	NM_009398	21930	Mm.3509	NM_009398	ENSMUSG00000053475	Tnfaip6	TSG-6|Tnfip6|Tsg6	tumor necrosis factor alpha induced protein 6	protein-coding
mm_120367.1	chr14	64580760	64580770	+	1	NA	Intergenic	RSINE1|SINE|B4	-7350	NR_040709	268755	Mm.194050	NR_040709	ENSMUSG00000097545	Mir124a-1hg	A930011O12Rik|Rncr3|mir-124-1|mir-3078	Mir124-1 host gene (non-protein coding)	ncRNA
mm_89683.1	chr10	97517681	97517691	+	1	NA	3' UTR (NM_007833, exon 8 of 8)	3' UTR (NM_007833, exon 8 of 8)	35355	NM_007833	13179	Mm.56769	NM_007833	ENSMUSG00000019929	Dcn	DC|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding
mm_170887.1	chr2	22410752	22410757	-	1	NA	intron (NM_148413, intron 19 of 19)	intron (NM_148413, intron 19 of 19)	183251	NM_148413	667663	Mm.330033	NM_148413	ENSMUSG00000025716	Myo3a	9030416P08Rik	myosin IIIA	protein-coding
mm_101359.1	chr11	23740912	23740922	-	1	NA	TTS (NM_009044)	TTS (NM_009044)	30053	NM_009044	19696	Mm.4869	NM_009044	ENSMUSG00000020275	Rel	c-Rel	reticuloendotheliosis oncogene	protein-coding
mm_57256.1	chr6	123283623	123283663	-	1	NA	exon (NM_019948, exon 6 of 6)	exon (NM_019948, exon 6 of 6)	6228	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_145634.1	chr18	61112011	61112055	+	1	NA	exon (NM_001037859, exon 5 of 22)	exon (NM_001037859, exon 5 of 22)	-5435	NR_105949	102466212		NR_105949	ENSMUSG00000098389	Mir6983	Gm27496|mmu-mir-6983	microRNA 6983	ncRNA
mm_153012.1	chr19	30574147	30574157	-	1	NA	intron (NM_011160, intron 16 of 17)	intron (NM_011160, intron 16 of 17)	-24656	NM_010051	13380	Mm.214717	NM_010051	ENSMUSG00000024868	Dkk1	mdkk-1	dickkopf WNT signaling pathway inhibitor 1	protein-coding
mm_115216.1	chr13	109632559	109632562	+	1	NA	intron (NM_011056, intron 3 of 16)	intron (NM_011056, intron 3 of 16)	-271249	NR_035442	100316683		NR_035442	ENSMUSG00000084651	Mir1904	Mirn1904|mmu-mir-1904	microRNA 1904	ncRNA
mm_116033.1	chr13	25986211	25986221	-	1	NA	Intergenic	B1F|SINE|Alu	-19900	NR_045062	100503530	Mm.86763	NR_045062	ENSMUSG00000086531	Gm11351	OTTMUSG00000000620	predicted gene 11351	ncRNA
mm_66936.1	chr7	61604643	61604655	-	1	NA	non-coding (NR_045727, exon 2 of 5)	non-coding (NR_045727, exon 2 of 5)	10678	NR_045727	319752	Mm.294476	NR_045727		B230209E15Rik	-	RIKEN cDNA B230209E15 gene	ncRNA
mm_54053.1	chr6	13839319	13839340	-	1	NA	intron (NM_145066, intron 1 of 3)	intron (NM_145066, intron 1 of 3)	613	NM_001330666	64450	Mm.167625	NM_145066	ENSMUSG00000048216	Gpr85	2900026B03Rik	G protein-coupled receptor 85	protein-coding
mm_51051.1	chr6	65631294	65631307	+	1	NA	3' UTR (NM_001001495, exon 8 of 8)	3' UTR (NM_001001495, exon 8 of 8)	-40311	NM_172399	68169	Mm.52392	NM_172399	ENSMUSG00000049001	Ndnf	A930038C07Rik|epidermacan	neuron-derived neurotrophic factor	protein-coding
mm_75762.1	chr8	69958420	69958435	-	1	NA	intron (NM_145596, intron 1 of 12)	intron (NM_145596, intron 1 of 12)	15956	NM_001113346	234366	Mm.270044	NM_145596	ENSMUSG00000036180	Gatad2a	1110066C11Rik|BC031407|C80248	GATA zinc finger domain containing 2A	protein-coding
mm_6018.1	chr1	59084488	59084535	-	1	NA	intron (NM_175200, intron 1 of 12)	intron (NM_175200, intron 1 of 12)	10389	NM_175200	73463	Mm.252811	NM_175200	ENSMUSG00000072295	Als2cr11	1700052H20Rik|4930408G06Rik	amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 11 (human)	protein-coding
mm_173073.1	chrX	136215391	136215396	-	1	NA	5' UTR (NM_009052, exon 1 of 3)	5' UTR (NM_009052, exon 1 of 3)	120	NM_009052	19716	Mm.422943	NM_009052	ENSMUSG00000050071	Bex1	AA407839|AU018692|Bex4|Rex3	brain expressed X-linked 1	protein-coding
mm_86190.1	chr9	119510806	119510809	-	1	NA	intron (NM_021544, intron 20 of 27)	intron (NM_021544, intron 20 of 27)	51871	NM_001253860	20271	Mm.103584	NM_021544	ENSMUSG00000032511	Scn5a	Nav1.5|Nav1.5c|SkM1|SkM2|mH1	sodium channel, voltage-gated, type V, alpha	protein-coding
mm_43550.1	chr5	137570951	137570990	+	1	NA	exon (NM_001289507, exon 1 of 18)	exon (NM_001289507, exon 1 of 18)	165	NM_001289507	50765	Mm.21757	NM_015799	ENSMUSG00000029716	Tfr2	Trfr2	transferrin receptor 2	protein-coding
mm_117859.1	chr13	98815366	98815402	-	1	NA	promoter-TSS (NM_172591)	promoter-TSS (NM_172591)	65	NM_172591	218503	Mm.23928	NM_172591	ENSMUSG00000041685	Fcho2	5832424M12Rik|AA387320	FCH domain only 2	protein-coding
mm_5927.1	chr1	55226769	55226813	-	1	NA	promoter-TSS (NM_028713)	promoter-TSS (NM_028713)	-9	NM_028713	74013	Mm.292050	NM_028713	ENSMUSG00000025978	Rftn2	2700010E02Rik|3222401M22Rik	raftlin family member 2	protein-coding
mm_75309.1	chr8	41209804	41209816	-	1	NA	exon (NM_145594, exon 3 of 8)	exon (NM_145594, exon 3 of 8)	5346	NM_145594	234199	Mm.277955	NM_145594	ENSMUSG00000031594	Fgl1	Mfire1	fibrinogen-like protein 1	protein-coding
mm_123740.1	chr14	70189567	70189569	-	1	NA	intron (NM_001271409, intron 5 of 9)	B1F|SINE|Alu	2678	NM_001271409	20410	Mm.5068	NM_011366	ENSMUSG00000022091	Sorbs3	SCAM-1|SH3P3|Sh3d4|vinexin-g	sorbin and SH3 domain containing 3	protein-coding
mm_77537.1	chr8	123041047	123041053	-	1	NA	intron (NM_001081379, intron 1 of 12)	intron (NM_001081379, intron 1 of 12)	1234	NR_037865	77087	Mm.31567	NM_001081379	ENSMUSG00000035569	Ankrd11	2410104C19Rik|3010027A04Rik|6330578C09Rik|9530048I21Rik|AA930108|Gm176|Yod	ankyrin repeat domain 11	protein-coding
mm_60062.1	chr7	31208327	31208363	+	1	NA	Intergenic	CpG	45987	NR_046062	100038516	Mm.387223	NR_046062	ENSMUSG00000100985	Gm10640	EG668322|ENSMUSG00000074193	predicted gene 10640	ncRNA
mm_112913.1	chr13	20922991	20923012	+	1	NA	intron (NM_012054, intron 11 of 20)	B4A|SINE|B4	128888	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_157993.1	chrX	94540217	94540239	-	1	NA	exon (NM_019791, exon 3 of 13)	exon (NM_019791, exon 3 of 13)	1846	NM_019791	94275	Mm.27578	NM_019791	ENSMUSG00000025151	Maged1	2810433C11Rik|5430405L04Rik|DXBwg1492e|Dlixin|Dlxin-1|Dlxin1|MAGE-D1|NRAGE|mFLJ00163	melanoma antigen, family D, 1	protein-coding
mm_47772.1	chr5	131616459	131616473	-	1	NA	intron (NM_177047, intron 5 of 18)	CpG	-263803	NR_040704	75369	Mm.389696	NR_040704	ENSMUSG00000105773	4930563F08Rik	-	RIKEN cDNA 4930563F08 gene	ncRNA
mm_119392.1	chr14	41137740	41137747	+	1	NA	Intergenic	Intergenic	5955	NM_023134	20387	Mm.46062	NM_023134	ENSMUSG00000021789	Sftpa1	SP-A|Sftp-1|Sftp1	surfactant associated protein A1	protein-coding
mm_154398.1	chrM	13625	13635	+	1	NA	NA	Intergenic	NA	NA								
mm_52214.1	chr6	103510640	103510660	+	1	NA	promoter-TSS (NM_007697)	promoter-TSS (NM_007697)	-226	NM_007697	12661	Mm.251288	NM_007697	ENSMUSG00000030077	Chl1	A530023M13Rik|AI465420|CALL|LICAM2	cell adhesion molecule L1-like	protein-coding
mm_28408.1	chr3	90265509	90265575	-	1	NA	promoter-TSS (NM_201407)	promoter-TSS (NM_201407)	-972	NM_201407	229541	Mm.30571	NM_201407	ENSMUSG00000042404	Dennd4b	-	DENN/MADD domain containing 4B	protein-coding
mm_35300.1	chr4	22488297	22488359	-	1	NA	promoter-TSS (NM_008899)	promoter-TSS (NM_008899)	38	NM_008899	18992	Mm.129387	NM_008899	ENSMUSG00000095139	Pou3f2	9430075J19Rik|A230098E07Rik|Brn-2|Brn2|OTF-7|Otf7|oct-7	POU domain, class 3, transcription factor 2	protein-coding
mm_4559.1	chr1	177447116	177447135	+	1	NA	exon (NM_013915, exon 1 of 1)	exon (NM_013915, exon 1 of 1)	1304	NM_013915	30928	Mm.330700	NM_013915	ENSMUSG00000063659	Zbtb18	RP58|Zfp238|Znf238	zinc finger and BTB domain containing 18	protein-coding
mm_89095.1	chr10	84488291	84488296	+	1	NA	promoter-TSS (NR_108059)	promoter-TSS (NR_108059)	0	NR_108059	75804		NR_108059	ENSMUSG00000020033	4930463O16Rik	-	RIKEN cDNA 4930463O16 gene	ncRNA
mm_150855.1	chr19	45006476	45006524	+	1	NA	promoter-TSS (NM_153796)	promoter-TSS (NM_153796)	-58	NM_053164	94067	Mm.44174	NM_053164	ENSMUSG00000025208	Mrpl43	4930442D21Rik|bMRP36a	mitochondrial ribosomal protein L43	protein-coding
mm_167525.1	chr9	21287922	21287926	-	1	NA	promoter-TSS (NM_145416)	promoter-TSS (NM_145416)	45	NM_145416	215194	Mm.290690	NM_145416	ENSMUSG00000035047	Kri1	-	KRI1 homolog	protein-coding
mm_64741.1	chr7	4753014	4753031	-	1	NA	promoter-TSS (NM_001289848)	promoter-TSS (NM_001289848)	72	NR_110411	333182	Mm.29625	NM_183405	ENSMUSG00000051811	Cox6b2	1700067P11Rik|BC048670|COXVIB2	cytochrome c oxidase subunit VIb polypeptide 2	protein-coding
mm_124519.1	chr14	121965188	121965198	-	1	NA	promoter-TSS (NM_183031)	promoter-TSS (NM_183031)	0	NM_183031	321019	Mm.265618	NM_183031	ENSMUSG00000051212	Gpr183	Ebi2	G protein-coupled receptor 183	protein-coding
mm_46608.1	chr5	107875036	107875073	-	1	NA	promoter-TSS (NM_007964)	promoter-TSS (NM_007964)	53	NM_007964	14020	Mm.35796	NM_007964	ENSMUSG00000011831	Evi5	NB4S	ecotropic viral integration site 5	protein-coding
mm_61797.1	chr7	83970288	83970305	+	1	NA	intron (NM_030728, intron 13 of 28)	intron (NM_030728, intron 13 of 28)	78296	NM_023403	67943	Mm.117365	NM_023403	ENSMUSG00000038503	Mesdc2	2210015O11Rik|AW537813|mKIAA0081|mesd|msd	mesoderm development candidate 2	protein-coding
mm_162693.1	chr10	19933580	19933591	+	1	NA	promoter-TSS (NM_008580)	promoter-TSS (NM_008580)	-941	NM_008580	26408	Mm.6595	NM_008580	ENSMUSG00000071369	Map3k5	7420452D20Rik|ASK|ASK1|MAPKKK5|Mekk5	mitogen-activated protein kinase kinase kinase 5	protein-coding
mm_157788.1	chrX	73824939	73824977	-	1	NA	promoter-TSS (NM_001290540)	promoter-TSS (NM_001290540)	11	NM_001029868	245469	Mm.103782	NM_001029868	ENSMUSG00000002006	Pdzd4	B230341P03|D130075J17Rik|Kiaa1444-hp|LU1|PDZRN4L|Pdzk4|Pdzrnk4l|Xlu	PDZ domain containing 4	protein-coding
mm_142454.1	chr17	45593627	45593656	-	1	NA	promoter-TSS (NM_001199113)	promoter-TSS (NM_001199113)	-1	NM_001199113	63959	Mm.29744	NM_022880	ENSMUSG00000023942	Slc29a1	1200014D21Rik|AA407560|ENT1	solute carrier family 29 (nucleoside transporters), member 1	protein-coding
mm_49655.1	chr6	31123103	31123140	+	1	NA	intron (NR_110471, intron 3 of 3)	ORR1F|LTR|ERVL-MaLR	-60028	NR_029532	387223		NR_029532	ENSMUSG00000065604	Mir29b-1	Mirn29b|Mirn29b-1|mir-29b-1	microRNA 29b-1	ncRNA
mm_139587.1	chr17	57223289	57223309	+	1	NA	exon (NM_009778, exon 12 of 41)	exon (NM_009778, exon 12 of 41)	4837	NM_009778	12266	Mm.19131	NM_009778	ENSMUSG00000024164	C3	AI255234|ASP|HSE-MSF|Plp	complement component 3	protein-coding
mm_87969.1	chr10	63430093	63430105	+	1	NA	promoter-TSS (NM_177612)	promoter-TSS (NM_177612)	1	NM_177612	216033	Mm.444692	NM_177612	ENSMUSG00000060843	Ctnna3	4930429L08Rik|4933408A16|Catna3|Vr22	catenin (cadherin associated protein), alpha 3	protein-coding
mm_155217.1	chrX	56792583	56792607	+	1	NA	3' UTR (NM_010211, exon 7 of 7)	3' UTR (NM_010211, exon 7 of 7)	6068	NM_001287800	14199	Mm.3126	NM_010211	ENSMUSG00000023092	Fhl1	FHL-1|KyoT|RAM14-1|SLIM|SLIM-1	four and a half LIM domains 1	protein-coding
mm_77588.1	chr8	123859959	123859992	-	1	NA	5' UTR (NM_028536, exon 1 of 4)	5' UTR (NM_028536, exon 1 of 4)	234	NM_028536	73420	Mm.157746	NM_028536	ENSMUSG00000031971	Ccsap	1700054N08Rik|AI853424	centriole, cilia and spindle associated protein	protein-coding
mm_172767.1	chr8	94179069	94179070	+	1	NA	promoter-TSS (NM_013602)	promoter-TSS (NM_013602)	-20	NM_013602	17748	Mm.192991	NM_013602	ENSMUSG00000031765	Mt1	MT-I|Mt-1	metallothionein 1	protein-coding
mm_119754.1	chr14	54159029	54159035	+	1	NA	Intergenic	Intergenic	94897	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_90757.1	chr10	5550566	5550598	-	1	NA	5' UTR (NM_153399, exon 1 of 32)	5' UTR (NM_153399, exon 1 of 32)	110	NM_153399	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_51659.1	chr6	86195215	86195241	+	1	NA	promoter-TSS (NM_031199)	promoter-TSS (NM_031199)	1	NM_031199	21802	Mm.137222	NM_031199	ENSMUSG00000029999	Tgfa	wa-1|wa1	transforming growth factor alpha	protein-coding
mm_127345.1	chr15	100616043	100616109	+	1	NA	promoter-TSS (NR_045701)	promoter-TSS (NR_045701)	414	NM_011873	23994	Mm.486175	NM_011873	ENSMUSG00000000346	Dazap2	AI314727|Brbp|Gcap28|Prtb|gt6-12|mKIAA0058	DAZ associated protein 2	protein-coding
mm_153753.1	chr19	45150504	45150537	-	1	NA	promoter-TSS (NM_021901)	promoter-TSS (NM_021901)	-195	NM_021901	21908	Mm.391203	NM_021901	ENSMUSG00000025215	Tlx1	Hox-11|Hox11|Tlx-1	T cell leukemia, homeobox 1	protein-coding
mm_83108.1	chr9	40346206	40346233	-	1	NA	intron (NM_172768, intron 2 of 19)	RLTR51A_Mm|LTR|ERVK?	12747	NR_040728	73558	Mm.398307	NR_040728		1700110K17Rik	-	RIKEN cDNA 1700110K17 gene	ncRNA
mm_69293.1	chr7	128220891	128220914	-	1	NA	Intergenic	Intergenic	-14536	NM_009943	12862	Mm.43824	NM_009943	ENSMUSG00000030785	Cox6a2	CoxVIaH|VIaH	cytochrome c oxidase subunit VIa polypeptide 2	protein-coding
mm_45834.1	chr5	87694740	87694830	-	1	NA	exon (NM_001286023, exon 5 of 7)	exon (NM_001286023, exon 5 of 7)	4640	NM_001286020	12991	Mm.268737	NM_009972	ENSMUSG00000063157	Csn2	Csnb	casein beta	protein-coding
mm_91644.1	chr10	42277601	42277614	-	1	NA	promoter-TSS (NM_019740)	promoter-TSS (NM_019740)	-865	NM_019740	56484	Mm.338613	NM_019740	ENSMUSG00000048756	Foxo3	1110048B16Rik|2010203A17Rik|C76856|FKHRL1|Fkhr2|Foxo3a	forkhead box O3	protein-coding
mm_167001.1	chr7	47752611	47752613	-	1	NA	Intergenic	ERVB4_1B-LTR_MM|LTR|ERVK	-151240	NM_153067	233222	Mm.240142	NM_153067	ENSMUSG00000078698	Mrgpra3	Mrga3	MAS-related GPR, member A3	protein-coding
mm_57467.1	chr6	125231076	125231079	-	1	NA	promoter-TSS (NR_015604)	promoter-TSS (NR_015604)	-199	NR_015604	78668	Mm.10626	NR_015604	ENSMUSG00000030337	E130112N10Rik	5830448L21Rik|9530059J11Rik	RIKEN cDNA E130112N10 gene	ncRNA
mm_32473.1	chr4	107802211	107802272	+	1	NA	promoter-TSS (NM_001080926)	promoter-TSS (NM_001080926)	-18	NR_033496	16975	Mm.442134	NM_053073	ENSMUSG00000028613	Lrp8	4932703M08Rik|AA921429|AI848122|ApoER2|Lr8b	low density lipoprotein receptor-related protein 8, apolipoprotein e receptor	protein-coding
mm_154358.1	chrM	6240	6248	+	1	NA	NA	Intergenic	NA	NA								
mm_16659.1	chr2	6638137	6638140	-	1	NA	intron (NM_001347094, intron 3 of 12)	intron (NM_001347094, intron 3 of 12)	83524	NM_001310447	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_56961.1	chr6	120038061	120038139	-	1	NA	5' UTR (NM_001185020, exon 1 of 26)	5' UTR (NM_001185020, exon 1 of 26)	555	NM_001199083	232341	Mm.333349	NM_198703	ENSMUSG00000045962	Wnk1	6430573H23Rik|EG406236|Hsn2|Prkwnk1|mKIAA0344	WNK lysine deficient protein kinase 1	protein-coding
mm_147378.1	chr18	43687660	43687671	-	1	NA	5' UTR (NM_001163637, exon 1 of 22)	5' UTR (NM_001163637, exon 1 of 22)	108	NM_001163637	76217	Mm.134602	NM_001163637	ENSMUSG00000024502	Jakmip2	6430702L21Rik|AI850334|D930046L20Rik	janus kinase and microtubule interacting protein 2	protein-coding
mm_5849.1	chr1	52972029	52972051	-	1	NA	Intergenic	Intergenic	-19200	NM_144953	67080	Mm.236287	NM_144953	ENSMUSG00000043629	1700019D03Rik	2410136C24Rik|AA410151|smAKAP	RIKEN cDNA 1700019D03 gene	protein-coding
mm_138555.1	chr17	35266180	35266252	+	1	NA	exon (NM_001267808, exon 9 of 11)	exon (NM_001267808, exon 9 of 11)	3093	NM_001267808	14980	Mm.439675	NM_001267808		H2-L	H-2L	histocompatibility 2, D region locus L	protein-coding
mm_92527.1	chr10	79093371	79093371	-	1	NA	intron (NM_001004362, intron 2 of 5)	RLTR15|LTR|ERVK	4229	NM_001004362	72128	Mm.297854	NM_001004362	ENSMUSG00000060301	2610008E11Rik	-	RIKEN cDNA 2610008E11 gene	protein-coding
mm_105180.1	chr11	101785253	101785289	-	1	NA	promoter-TSS (NM_001316366)	promoter-TSS (NM_001316366)	39	NM_008815	18612	Mm.5025	NM_008815	ENSMUSG00000017724	Etv4	AW414408|Pea-3|Pea3	ets variant 4	protein-coding
mm_170766.1	chr2	161109002	161109006	-	1	NA	promoter-TSS (NM_173368)	promoter-TSS (NM_173368)	82	NM_173368	71389	Mm.122738	NM_173368	ENSMUSG00000057133	Chd6	5430439G14Rik|6330406J24Rik|CHD-6	chromodomain helicase DNA binding protein 6	protein-coding
mm_38040.1	chr4	133910691	133910712	-	1	NA	Intergenic	CpG	-22904	NM_009097	20111	Mm.301827	NM_009097	ENSMUSG00000003644	Rps6ka1	Mapkapk-1a|Rsk|Rsk-1|Rsk1|S6K-alpha-1|p90-Rsk1|p90Rsk1|p90S6K|p90rsk	ribosomal protein S6 kinase polypeptide 1	protein-coding
mm_159457.1	chr3	153905937	153905937	-	1	NA	exon (NM_031870, exon 1 of 20)	exon (NM_031870, exon 1 of 20)	201	NM_031870	55993	Mm.272226	NM_031870	ENSMUSG00000005493	Msh4	4930485C04Rik|AV144863|mMsh4	mutS homolog 4	protein-coding
mm_116166.1	chr13	30787674	30787682	-	1	NA	Intergenic	Intergenic	38445	NM_013674	16364	Mm.4677	NM_013674	ENSMUSG00000021356	Irf4	AI385587|IRF-4|LSIRF|NF-EM5|Spip	interferon regulatory factor 4	protein-coding
mm_71040.1	chr8	33660801	33660808	+	1	NA	intron (NM_010344, intron 1 of 12)	intron (NM_010344, intron 1 of 12)	7566	NM_010344	14782	Mm.283573	NM_010344	ENSMUSG00000031584	Gsr	AI325518|D8Ertd238e|Gr-1|Gr1	glutathione reductase	protein-coding
mm_165651.1	chr3	83841547	83841551	-	1	NA	promoter-TSS (NM_011905)	promoter-TSS (NM_011905)	59	NM_011905	24088	Mm.87596	NM_011905	ENSMUSG00000027995	Tlr2	Ly105	toll-like receptor 2	protein-coding
mm_115125.1	chr13	104287358	104287379	+	1	NA	promoter-TSS (NM_001081020)	promoter-TSS (NM_001081020)	-467	NR_136938	108154	Mm.208125	NM_175496	ENSMUSG00000046169	Adamts6	A930019D11Rik|ADAM-TS6|b2b1879.1Clo|b2b2029Clo|b2b2182Clo|b2b2187.1Clo|b2b2228Clo	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 6	protein-coding
mm_123795.1	chr14	70443414	70443436	-	1	NA	promoter-TSS (NM_025945)	promoter-TSS (NM_025945)	46	NM_025945	67065	Mm.20420	NM_025945	ENSMUSG00000000776	Polr3d	2810426M17Rik|44kDa|AI326118|AW489084|BN51T|RPC4|TSBN51	polymerase (RNA) III (DNA directed) polypeptide D	protein-coding
mm_69886.1	chr7	141637118	141637137	-	1	NA	intron (NM_001330001, intron 31 of 33)	intron (NM_001330001, intron 31 of 33)	16426	NR_106030	102466798		NR_106030	ENSMUSG00000098759	Mir7063	Gm27654|mmu-mir-7063	microRNA 7063	ncRNA
mm_142828.1	chr17	51775200	51775209	-	1	NA	intron (NM_009122, intron 8 of 10)	intron (NM_009122, intron 8 of 10)	36850	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_131210.1	chr16	8682872	8682879	+	1	NA	intron (NM_001324517, intron 1 of 3)	intron (NM_001324517, intron 1 of 3)	2105	NM_001324517	436336	Mm.357666	NM_001324517		Gm5767	EG436336	predicted gene 5767	protein-coding
mm_163337.1	chr12	13501225	13501229	+	1	NA	intron (NM_027706, intron 44 of 51)	intron (NM_027706, intron 44 of 51)	126419	NR_136761	102639399	Mm.122052	NR_136761		Gm35725	-	predicted gene, 35725	ncRNA
mm_29547.1	chr3	116807689	116807693	-	1	NA	intron (NM_001081326, intron 1 of 33)	intron (NM_001081326, intron 1 of 33)	475	NM_001081326	77559	Mm.237099	NM_001081326	ENSMUSG00000033400	Agl	1110061O17Rik|9430004C13Rik|9630046L06Rik|AI850929|C77197	amylo-1,6-glucosidase, 4-alpha-glucanotransferase	protein-coding
mm_72920.1	chr8	91074201	91074229	+	1	NA	exon (NM_001282001, exon 2 of 22)	exon (NM_001282001, exon 2 of 22)	4158	NM_001282000	19651	Mm.235580	NM_011250	ENSMUSG00000031666	Rbl2	PRB2|RBR-2|Rb2|p130	retinoblastoma-like 2	protein-coding
mm_39248.1	chr5	3494612	3494651	+	1	NA	intron (NM_009873, intron 5 of 7)	intron (NM_009873, intron 5 of 7)	-49202	NM_001042501	68152	Mm.240265	NM_026583	ENSMUSG00000058503	Fam133b	2900022K02Rik|5830415L20Rik	family with sequence similarity 133, member B	protein-coding
mm_33426.1	chr4	130050711	130050734	+	1	NA	intron (NM_028266, intron 2 of 69)	intron (NM_028266, intron 2 of 69)	2882	NM_028266	107581	Mm.41860	NM_028266	ENSMUSG00000040690	Col16a1	2700007F12Rik|A530052M23Rik|AI838662|CA1F	collagen, type XVI, alpha 1	protein-coding
mm_123165.1	chr14	57252028	57252039	-	1	NA	Intergenic	Intergenic	-118422	NM_001010937	14623	Mm.25652	NM_008128	ENSMUSG00000040055	Gjb6	AA958971|Cx30|D14Bwg0506e	gap junction protein, beta 6	protein-coding
mm_48712.1	chr5	147307039	147307049	-	1	NA	5' UTR (NM_007673, exon 1 of 3)	5' UTR (NM_007673, exon 1 of 3)	205	NM_007673	12591	Mm.20358	NM_007673	ENSMUSG00000029646	Cdx2	Cdx-2	caudal type homeobox 2	protein-coding
mm_57072.1	chr6	122578178	122578182	-	1	NA	3' UTR (NM_031159, exon 8 of 8)	3' UTR (NM_031159, exon 8 of 8)	24264	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_61330.1	chr7	68264846	68264856	+	1	NA	promoter-TSS (NM_030101)	promoter-TSS (NM_030101)	-618	NM_030101	78444	Mm.425468	NM_030101	ENSMUSG00000030553	Pgpep1l	C330024D12Rik	pyroglutamyl-peptidase I-like	protein-coding
mm_16906.1	chr2	13491901	13491940	-	1	NA	promoter-TSS (NM_001081084)	promoter-TSS (NM_001081084)	-44	NM_001081084	65969	Mm.313915	NM_001081084	ENSMUSG00000026726	Cubn	AA408369|AL022750|D2Wsu88e	cubilin (intrinsic factor-cobalamin receptor)	protein-coding
mm_125976.1	chr15	76295305	76295310	+	1	NA	intron (NM_001195537, intron 1 of 6)	intron (NM_001195537, intron 1 of 6)	873	NM_001195537	100503915	Mm.393455	NM_001195537	ENSMUSG00000071724	Smpd5	ENSMUSG00000071724|Gm10345|MA-nSMase	sphingomyelin phosphodiesterase 5	protein-coding
mm_95425.1	chr11	50160251	50160254	+	1	NA	intron (NM_001290760, intron 15 of 21)	intron (NM_001290760, intron 15 of 21)	-14599	NM_026543	68067	Mm.40828	NM_026543	ENSMUSG00000020381	Mrnip	2900016G09Rik|3010026O09Rik|AI851514|AW475975	MRN complex interacting protein	protein-coding
mm_127269.1	chr15	99723426	99723442	+	1	NA	3' UTR (NM_010271, exon 8 of 8)	3' UTR (NM_010271, exon 8 of 8)	-2184	NM_183256	66379	Mm.5265	NM_183256	ENSMUSG00000023020	Cox14	2310016M24Rik|AA959804	cytochrome c oxidase assembly protein 14	protein-coding
mm_8160.1	chr1	136949503	136949526	-	1	NA	intron (NM_030676, intron 2 of 8)	intron (NM_030676, intron 2 of 8)	4116	NM_001159769	26424	Mm.16794	NM_030676	ENSMUSG00000026398	Nr5a2	AU020803|D1Ertd308e|Ftf|LRH-1|UF2-H3B	nuclear receptor subfamily 5, group A, member 2	protein-coding
mm_44639.1	chr5	28123707	28123718	-	1	NA	Intergenic	Intergenic	-41984	NM_010134	13799	Mm.4298	NM_010134	ENSMUSG00000039095	En2	BB131122|En-2	engrailed 2	protein-coding
mm_54302.1	chr6	29507980	29507992	-	1	NA	promoter-TSS (NM_001029985)	promoter-TSS (NM_001029985)	-34	NM_001029985	333088	Mm.332961	NM_001029985	ENSMUSG00000059022	Kcp	AW060220|CRIM-2|Crim2|Gm793|KCP-1	kielin/chordin-like protein	protein-coding
mm_104256.1	chr11	88924540	88924559	-	1	NA	3' UTR (NM_029023, exon 13 of 13)	3' UTR (NM_029023, exon 13 of 13)	18621	NR_045955	73921	Mm.439148	NR_045955	ENSMUSG00000087338	Scpep1os	4930405P13Rik	serine carboxypeptidase 1, opposite strand	ncRNA
mm_8790.1	chr1	161766724	161766733	-	1	NA	Intergenic	Intergenic	21767	NM_001205243	14103	Mm.3355	NM_010177	ENSMUSG00000000817	Fasl	APT1LG1|CD178|CD95-L|CD95L|Fas-L|Faslg|Tnfsf6|Tnlg1a|gld	Fas ligand (TNF superfamily, member 6)	protein-coding
mm_91593.1	chr10	40350003	40350009	-	1	NA	intron (NM_001291816, intron 1 of 11)	CpG	698	NM_001291816	78334	Mm.200924	NM_198164	ENSMUSG00000038481	Cdk19	2700084L06Rik|AI845279|AW228747|CDK11|Cdc2l6|mKIAA1028	cyclin-dependent kinase 19	protein-coding
mm_167273.1	chr8	33658006	33658013	+	1	NA	intron (NM_010344, intron 1 of 12)	intron (NM_010344, intron 1 of 12)	4771	NM_010344	14782	Mm.283573	NM_010344	ENSMUSG00000031584	Gsr	AI325518|D8Ertd238e|Gr-1|Gr1	glutathione reductase	protein-coding
mm_159489.1	chr4	42612121	42612121	+	1	NA	promoter-TSS (NM_001193666).3	promoter-TSS (NM_001193666).3	-2	NM_001270360	100862177	Mm.407493	NM_001270360	ENSMUSG00000094065	Gm21541	-	predicted gene, 21541	protein-coding
mm_10236.1	chr2	6707550	6707563	+	1	NA	intron (NM_001347094, intron 2 of 12)	intron (NM_001347094, intron 2 of 12)	14106	NM_001310447	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_133203.1	chr16	73072390	73072400	+	1	NA	Intergenic	MTC-int|LTR|ERVL-MaLR	409246	NM_019413	19876	Mm.310772	NM_019413	ENSMUSG00000022883	Robo1	AW494633|AW742721|DUTT1|Gm310	roundabout guidance receptor 1	protein-coding
mm_89669.1	chr10	97506535	97506547	+	1	NA	exon (NM_007833, exon 4 of 8)	exon (NM_007833, exon 4 of 8)	24210	NM_007833	13179	Mm.56769	NM_007833	ENSMUSG00000019929	Dcn	DC|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding
mm_34850.1	chr4	155491051	155491069	+	1	NA	promoter-TSS (NM_008142)	promoter-TSS (NM_008142)	-301	NM_001160017	14688	Mm.2344	NM_008142	ENSMUSG00000029064	Gnb1	AA409223|C77571|Gnb-1	guanine nucleotide binding protein (G protein), beta 1	protein-coding
mm_169690.1	chr15	74652782	74652786	-	1	NA	Intergenic	RLTR16B_MM|LTR|ERVK	-16466	NM_001177437	69439	Mm.263708	NM_001177437	ENSMUSG00000022603	Mroh4	1700016M24Rik	maestro heat-like repeat family member 4	protein-coding
mm_20114.1	chr2	121160157	121160171	-	1	NA	3' UTR (NM_001290819, exon 5 of 5)	3' UTR (NM_001290819, exon 5 of 5)	10961	NM_001290819	99334	Mm.188422	NM_178889	ENSMUSG00000050619	Zscan29	AW125441|Zfp690	zinc finger SCAN domains 29	protein-coding
mm_100358.1	chr11	118449874	118449886	+	1	NA	3' UTR (NM_019959, exon 4 of 4)	3' UTR (NM_019959, exon 4 of 4)	5115	NR_045902	100126224	Mm.441989	NR_045902	ENSMUSG00000086514	Gm11747	OTTMUSG00000003972	predicted gene 11747	ncRNA
mm_97431.1	chr11	78094727	78094737	+	1	NA	promoter-TSS (NM_145430)	promoter-TSS (NM_145430)	59	NM_145430	216971	Mm.119387	NM_145430	ENSMUSG00000037750	Fam222b	9630020I17Rik	family with sequence similarity 222, member B	protein-coding
mm_46839.1	chr5	113333322	113333325	-	1	NA	Intergenic	ORR1D1|LTR|ERVL-MaLR	4322	NR_106089	102466821		NR_106089	ENSMUSG00000104840	Mir7230	mmu-mir-7230	microRNA 7230	ncRNA
mm_121011.1	chr14	79535578	79535591	+	1	NA	intron (NM_001286411, intron 1 of 8)	intron (NM_001286411, intron 1 of 8)	19910	NM_001286411	13709	Mm.20938	NM_007920	ENSMUSG00000036461	Elf1	Elf-1|Sts1|mElf-1|p70	E74-like factor 1	protein-coding
mm_118403.1	chr13	119408986	119409003	-	1	NA	promoter-TSS (NM_008710)	promoter-TSS (NM_008710)	17	NM_008710	18115	Mm.132584	NM_008710	ENSMUSG00000025453	Nnt	4930423F13Rik|AI323702|BB168308	nicotinamide nucleotide transhydrogenase	protein-coding
mm_71923.1	chr8	70234188	70234228	+	1	NA	promoter-TSS (NM_001168290)	promoter-TSS (NM_001168290)	-18	NM_001168290	234373	Mm.284505	NM_172755	ENSMUSG00000036054	Sugp2	Sfrs14|Srsf14|mKIAA0365	SURP and G patch domain containing 2	protein-coding
mm_36653.1	chr4	94603240	94603253	-	1	NA	promoter-TSS (NM_172695)	promoter-TSS (NM_172695)	1	NM_172695	18786	Mm.490101	NM_172695	ENSMUSG00000028577	Plaa	2410007N06|AI536418|AU018445|AW208417|D4Ertd618e|PLA2P|PLAP|Ufd3	phospholipase A2, activating protein	protein-coding
mm_82662.1	chr9	22113287	22113303	-	1	NA	TTS (NR_106052)	TTS (NR_106052)	718	NR_106052	102466221		NR_106052	ENSMUSG00000098646	Mir7084	Gm27978|mmu-mir-7084	microRNA 7084	ncRNA
mm_39054.1	chr4	153950491	153950518	-	1	NA	promoter-TSS (NR_040670)	promoter-TSS (NR_040670)	-28	NR_040670	407793	Mm.260950	NR_040670		BC039966	-	cDNA sequence BC039966	ncRNA
mm_109868.1	chr12	4907740	4907754	-	1	NA	promoter-TSS (NM_145441)	promoter-TSS (NM_145441)	-227	NM_145441	217379	Mm.259170	NM_145441	ENSMUSG00000020634	Ubxn2a	6330407P03Rik|Ubxd4	UBX domain protein 2A	protein-coding
mm_21315.1	chr2	157098935	157098947	-	1	NA	3' UTR (NM_001139520, exon 17 of 17)	3' UTR (NM_001139520, exon 17 of 17)	11886	NM_001177439	383766	Mm.480305	NM_001177439	ENSMUSG00000074628	Tldc2	Gm1332	TBC/LysM associated domain containing 2	protein-coding
mm_65344.1	chr7	24988137	24988153	-	1	NA	promoter-TSS (NR_106014)	promoter-TSS (NR_106014)	-478	NR_106014	102465634		NR_106014	ENSMUSG00000099258	Mir7047	Gm27270|mmu-mir-7047	microRNA 7047	ncRNA
mm_111718.1	chr12	103730352	103730370	-	1	NA	exon (NM_009244, exon 3 of 5)	exon (NM_009244, exon 3 of 5)	7828	NM_009244	20701	Mm.439692	NM_009244	ENSMUSG00000071178	Serpina1b	D12Ucla2|Dom2|PI2|Spi1-2	serine (or cysteine) preptidase inhibitor, clade A, member 1B	protein-coding
mm_51458.1	chr6	82041790	82041802	+	1	NA	5' UTR (NM_145570, exon 1 of 3)	5' UTR (NM_145570, exon 1 of 3)	168	NM_145570	232146	Mm.489683	NM_145570	ENSMUSG00000035104	Eva1a	BC014699|Fam176a|Tmem166	eva-1 homolog A (C. elegans)	protein-coding
mm_55577.1	chr6	71396280	71396290	-	1	NA	intron (NM_024288, intron 7 of 8)	intron (NM_024288, intron 7 of 8)	22858	NM_001081110	12525	Mm.1858	NM_009857	ENSMUSG00000053977	Cd8a	BB154331|Ly-2|Ly-35|Ly-B|Lyt-2	CD8 antigen, alpha chain	protein-coding
mm_63825.1	chr7	134776641	134776651	+	1	NA	intron (NM_001033420, intron 18 of 51)	B4A|SINE|B4	105959	NM_001033420	330662	Mm.436572	NM_001033420	ENSMUSG00000058325	Dock1	9130006G06Rik|AI854900|D630004B07Rik	dedicator of cytokinesis 1	protein-coding
mm_23206.1	chr3	41560688	41560691	+	1	NA	intron (NM_001130184, intron 1 of 10)	intron (NM_001130184, intron 1 of 10)	-2694	NM_172303	269424	Mm.286285	NM_172303	ENSMUSG00000025764	Jade1	AU041499|D530048A03Rik|Phf17|mKIAA1807	jade family PHD finger 1	protein-coding
mm_117660.1	chr13	93192426	93192432	-	1	NA	promoter-TSS (NM_133905)	promoter-TSS (NM_133905)	-146	NM_133905	100715	Mm.242865	NM_133905	ENSMUSG00000042167	Papd4	8030446C20Rik|AI649009|GLD-2|Gld2	PAP associated domain containing 4	protein-coding
mm_93750.1	chr10	120170414	120170422	-	1	NA	intron (NM_028679, intron 5 of 11)	intron (NM_028679, intron 5 of 11)	31119	NM_028679	73914	Mm.146194	NM_028679	ENSMUSG00000020227	Irak3	4833428C18Rik|AI563835|IRAK-M	interleukin-1 receptor-associated kinase 3	protein-coding
mm_73417.1	chr8	106059563	106059623	+	1	NA	promoter-TSS (NM_010901)	promoter-TSS (NM_010901)	-10	NM_010901	18021	Mm.383185	NM_010901	ENSMUSG00000031902	Nfatc3	C80703|D8Ertd281e|NFAT4|NFATx	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 3	protein-coding
mm_152311.1	chr19	9895945	9895962	-	1	NA	intron (NM_016692, intron 1 of 17)	intron (NM_016692, intron 1 of 17)	3580	NM_016692	16319	Mm.29755	NM_016692	ENSMUSG00000024660	Incenp	2700067E22Rik|AU019509|C130081E20|C77457	inner centromere protein	protein-coding
mm_122991.1	chr14	54989319	54989323	-	1	NA	exon (NM_080728, exon 13 of 41)	exon (NM_080728, exon 13 of 41)	5228	NM_080728	140781	Mm.457983	NM_080728	ENSMUSG00000053093	Myh7	B-MHC|MyHC-I|Myhc-b|Myhcb|beta-MHC	myosin, heavy polypeptide 7, cardiac muscle, beta	protein-coding
mm_83405.1	chr9	44767840	44767850	-	1	NA	promoter-TSS (NM_145985)	promoter-TSS (NM_145985)	-37	NM_145985	213827	Mm.371682	NM_145985	ENSMUSG00000032096	Arcn1	4632432M07Rik|nur17	archain 1	protein-coding
mm_61360.1	chr7	68618453	68618464	+	1	NA	promoter-TSS (NR_003648)	promoter-TSS (NR_003648)	2	NR_003648	384639	Mm.261760	NM_001013781		Gm5334	EG384639	tetraspanin 7 pseudogene	pseudo
mm_116814.1	chr13	54412368	54412389	-	1	NA	Intergenic	Intergenic	41029	NM_009946	12890	Mm.268902	NM_009946	ENSMUSG00000025867	Cplx2	921-L|AI413745|AW492120	complexin 2	protein-coding
mm_90949.1	chr10	13060426	13060432	-	1	NA	Intergenic	Intergenic	-30359	NM_009538	22634	Mm.287857	NM_009538	ENSMUSG00000019817	Plagl1	Lot1|Zac1	pleiomorphic adenoma gene-like 1	protein-coding
mm_166012.1	chr4	118449694	118449694	-	1	NA	intron (NM_010823, intron 6 of 11)	intron (NM_010823, intron 6 of 11)	7819	NM_001285496	17480	Mm.4864	NM_010823	ENSMUSG00000006389	Mpl	CD110|TPO-R|c-mpl|hlb219	myeloproliferative leukemia virus oncogene	protein-coding
mm_168945.1	chr12	73062556	73062564	-	1	NA	Intergenic	RMER19C|LTR|ERVK	-15848	NM_009189	20471	Mm.4645	NM_009189	ENSMUSG00000051367	Six1	BB138287	sine oculis-related homeobox 1	protein-coding
mm_171464.1	chr4	145730282	145730284	-	1	NA	Intergenic	CpG	-51260	NM_001083918	666532	Mm.392861	NM_001083918	ENSMUSG00000067916	Zfp991	Gm13139|OTTMUSG00000010657	zinc finger protein 991	protein-coding
mm_15571.1	chr2	158624946	158624950	+	1	NA	promoter-TSS (NM_175419)	promoter-TSS (NM_175419)	35	NM_175419	109275	Mm.27747	NM_175419	ENSMUSG00000037761	Actr5	AA545173|B430109J19Rik	ARP5 actin-related protein 5	protein-coding
mm_30328.1	chr3	151732068	151732085	-	1	NA	3' UTR (NM_133871, exon 8 of 8)	3' UTR (NM_133871, exon 8 of 8)	17883	NM_133871	99899	Mm.30756	NM_133871	ENSMUSG00000028037	Ifi44	A430056A10Rik|AW261460|MTAP44|p44	interferon-induced protein 44	protein-coding
mm_24442.1	chr3	90603768	90603771	+	1	NA	promoter-TSS (NM_011311)	promoter-TSS (NM_011311)	-1	NM_011311	20198	Mm.3925	NM_011311	ENSMUSG00000001020	S100a4	18A2|42a|Capl|FSp1|Mts1|PeL98|metastasin|pk9a	S100 calcium binding protein A4	protein-coding
mm_117233.1	chr13	64274951	64274959	-	1	NA	promoter-TSS (NM_172587)	promoter-TSS (NM_172587)	33	NM_172587	218294	Mm.25335	NM_172587	ENSMUSG00000033102	Cdc14b	2810432N10Rik|A530086E13Rik|AA472821|CDC14B3|Cdc14B1	CDC14 cell division cycle 14B	protein-coding
mm_117264.1	chr13	64370299	64370315	-	1	NA	5' UTR (NM_009984, exon 1 of 8)	5' UTR (NM_009984, exon 1 of 8)	213	NM_009984	13039	Mm.930	NM_009984	ENSMUSG00000021477	Ctsl	1190035F06Rik|CatL|Ctsl1|MEP|fs|nkt	cathepsin L	protein-coding
mm_128163.1	chr15	34068206	34068225	-	1	NA	Intergenic	RMER10B|LTR|ERVL	-14504	NM_026002	67154	Mm.130883	NM_026002	ENSMUSG00000022255	Mtdh	2610103J23Rik|3D3|3D3/Lyric|AEG-1|AV353288|D8Bwg1112e|Lyric	metadherin	protein-coding
mm_117228.1	chr13	64153265	64153277	-	1	NA	promoter-TSS (NM_175494)	promoter-TSS (NM_175494)	-72	NM_175494	238673	Mm.300065	NM_175494	ENSMUSG00000044934	Zfp367	8030486J21Rik|ZFF29a|ZFF29b|Znf367	zinc finger protein 367	protein-coding
mm_22220.1	chr2	174345477	174345540	-	1	NA	non-coding (NR_003258, exon 10 of 13)	non-coding (NR_003258, exon 10 of 13)	15419	NM_001077510	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_107367.1	chr12	32850580	32850608	+	1	NA	3' UTR (NM_021524, exon 11 of 11)	3' UTR (NM_021524, exon 11 of 11)	26478	NR_045032	100504486	Mm.440246	NR_045032		Gdap10	Gdap-ps	ganglioside-induced differentiation-associated-protein 10	ncRNA
mm_123734.1	chr14	70175398	70175443	-	1	NA	intron (NM_145978, intron 1 of 9)	intron (NM_145978, intron 1 of 9)	1395	NM_001253736	213019	Mm.283968	NM_145978	ENSMUSG00000022090	Pdlim2	4732462F18Rik|Slim	PDZ and LIM domain 2	protein-coding
mm_59321.1	chr7	25301477	25301524	+	1	NA	intron (NM_001081294, intron 1 of 2)	intron (NM_001081294, intron 1 of 2)	141	NM_001081294	623131	Mm.172160	NM_001081294	ENSMUSG00000058741	Prr19	EG623131	proline rich 19	protein-coding
mm_90285.1	chr10	123264109	123264125	+	1	NA	promoter-TSS (NM_182807)	promoter-TSS (NM_182807)	41	NM_001252387	268354	Mm.51939	NM_182807	ENSMUSG00000044071	Fam19a2	6330575M02|FAM19A2 TAFA-2|TAFA2|Tafa-2	family with sequence similarity 19, member A2	protein-coding
mm_154808.1	chrX	13623558	13623566	+	1	NA	intron (NM_009806, intron 6 of 24)	intron (NM_009806, intron 6 of 24)	-9207	NM_011823	23890	Mm.487326	NM_011823	ENSMUSG00000040229	Gpr34	Lypsr1	G protein-coupled receptor 34	protein-coding
mm_14508.1	chr2	132263137	132263268	+	1	NA	promoter-TSS (NM_001291040)	promoter-TSS (NM_001291040)	54	NM_138651	110911	Mm.284503	NM_138651	ENSMUSG00000058793	Cds2	5730450N06Rik|5730460C18Rik|AI854580|D2Wsu127e	CDP-diacylglycerol synthase (phosphatidate cytidylyltransferase) 2	protein-coding
mm_35153.1	chr4	12087913	12088011	-	1	NA	promoter-TSS (NR_110955)	promoter-TSS (NR_110955)	-5	NM_177861	329795	Mm.475125	NM_177861	ENSMUSG00000049488	Tmem67	5330408M12Rik|B230117O07|b2b1163.1Clo|b2b1291.1Clo	transmembrane protein 67	protein-coding
mm_152086.1	chr19	6906915	6906938	-	1	NA	exon (NM_012021, exon 6 of 6)	exon (NM_012021, exon 6 of 6)	2719	NM_012021	54683	Mm.279782	NM_012021	ENSMUSG00000024953	Prdx5	AOEB166|AOPP|Pmp20|Prdx6|PrxV	peroxiredoxin 5	protein-coding
mm_909.1	chr1	54329997	54330005	+	1	NA	intron (NM_030025, intron 17 of 27)	intron (NM_030025, intron 17 of 27)	79318	NM_030025	78016	Mm.67455	NM_030025	ENSMUSG00000025983	Ccdc150	4930511H11Rik	coiled-coil domain containing 150	protein-coding
mm_150139.1	chr19	31082883	31082902	+	1	NA	promoter-TSS (NM_031249)	promoter-TSS (NM_031249)	51	NM_031249	83410	Mm.22031	NM_031249	ENSMUSG00000053536	Cstf2t	64kDa|C77975|tCstF-64|tauCstF-64	cleavage stimulation factor, 3' pre-RNA subunit 2, tau	protein-coding
mm_54973.1	chr6	48738918	48738932	-	1	NA	promoter-TSS (NM_008376)	promoter-TSS (NM_008376)	-122	NM_175860	16205	Mm.252599	NM_008376	ENSMUSG00000090019	Gimap1	IAP38|Imap38|imap	GTPase, IMAP family member 1	protein-coding
mm_162328.1	chr1	40359164	40359169	+	1	NA	intron (NM_133193, intron 9 of 10)	intron (NM_133193, intron 9 of 10)	34539	NM_133193	107527	Mm.155583	NM_133193	ENSMUSG00000070942	Il1rl2	AI481289|AW551444|IL-1Rrp2	interleukin 1 receptor-like 2	protein-coding
mm_58613.1	chr7	5061754	5061762	+	1	NA	promoter-TSS (NM_001205231)	promoter-TSS (NM_001205231)	-385	NM_133671	22185	Mm.360389	NM_133671	ENSMUSG00000030435	U2af2	65kDa	U2 small nuclear ribonucleoprotein auxiliary factor (U2AF) 2	protein-coding
mm_12026.1	chr2	58160215	58160228	+	1	NA	promoter-TSS (NM_139200)	promoter-TSS (NM_139200)	-99	NM_139200	227929	Mm.273905	NM_139200	ENSMUSG00000026832	Cytip	A130053M09Rik|AI462064|C80816|Cbp|Cybr|Pscdbp	cytohesin 1 interacting protein	protein-coding
mm_80100.1	chr9	70314210	70314258	+	1	NA	intron (NM_181072, intron 4 of 27)	B3A|SINE|B2	91519	NR_049200	100885839		NR_049200	ENSMUSG00000093763	Mir5626	Gm25590|mir-5626|mmu-mir-5626	microRNA 5626	ncRNA
mm_68318.1	chr7	106441081	106441098	-	1	NA	promoter-TSS (NR_003967)	promoter-TSS (NR_003967)	-16	NR_003967	209380	Mm.461779	NM_001001318		Gm4759	EG209380	GTPase, very large interferon inducible 1 pseudogene	pseudo
mm_6953.1	chr1	85959680	85959688	-	1	NA	intron (NM_001033290, intron 1 of 1)	intron (NM_001033290, intron 1 of 1)	1371	NM_001033290	227326	Mm.244158	NM_001033290	ENSMUSG00000049608	Gpr55	CTFL|Gm218|Lpir1	G protein-coupled receptor 55	protein-coding
mm_71244.1	chr8	40912565	40912637	+	1	NA	exon (NM_001044740, exon 9 of 12)	exon (NM_001044740, exon 9 of 12)	-13632	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_132614.1	chr16	38712298	38712314	+	1	NA	intron (NM_020260, intron 1 of 11)	intron (NM_020260, intron 1 of 11)	729	NM_020260	12549	Mm.370848	NM_020260	ENSMUSG00000022799	Arhgap31	5830477L08Rik|AU041750|Cdgap|D330026I07Rik	Rho GTPase activating protein 31	protein-coding
mm_26569.1	chr3	146602299	146602311	+	1	NA	intron (NM_009474, intron 1 of 7)	intron (NM_009474, intron 1 of 7)	5156	NM_009474	22262	Mm.10865	NM_009474	ENSMUSG00000028186	Uox	AI663847	urate oxidase	protein-coding
mm_55494.1	chr6	69607832	69607856	-	1	NA	Intergenic	Intergenic	-280670	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_113715.1	chr13	43615769	43615788	+	1	NA	promoter-TSS (NM_183204)	promoter-TSS (NM_183204)	-19	NM_183204	328234	Mm.40588	NM_183204	ENSMUSG00000044164	Rnf182	C630023L15Rik	ring finger protein 182	protein-coding
mm_50150.1	chr6	41544003	41544029	+	1	NA	Intergenic	Intergenic	22240	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_68026.1	chr7	100987228	100987236	-	1	NA	Intergenic	Intergenic	-22866	NM_183168	233571	Mm.235193	NM_183168	ENSMUSG00000048779	P2ry6	2010204J23Rik|P2Y6	pyrimidinergic receptor P2Y, G-protein coupled, 6	protein-coding
mm_46708.1	chr5	110286160	110286177	-	1	NA	promoter-TSS (NM_011132)	promoter-TSS (NM_011132)	0	NM_008993	19301	Mm.21853	NM_008993	ENSMUSG00000029499	Pxmp2	22kDa|PMP22	peroxisomal membrane protein 2	protein-coding
mm_45555.1	chr5	73173461	73173463	-	1	NA	intron (NM_028194, intron 3 of 62)	intron (NM_028194, intron 3 of 62)	83156	NM_028194	72313	Mm.260594	NM_028194	ENSMUSG00000070733	Fryl	2010313D22Rik|2310004H21Rik|2510002A14Rik|9030227G01Rik|mKIAA0826	FRY like transcription coactivator	protein-coding
mm_139727.1	chr17	57476679	57476708	+	1	NA	intron (NM_010130, intron 19 of 21)	RLTR17B_Mm|LTR|ERVK	68621	NM_001104591	224916	Mm.469889	NM_001104591	ENSMUSG00000090655	Vmn2r120	EG224916	vomeronasal 2, receptor 120	protein-coding
mm_138708.1	chr17	36043027	36043027	+	1	NA	promoter-TSS (NM_001034909)	promoter-TSS (NM_001034909)	66	NM_001034909	547347	Mm.484641	NM_001034909	ENSMUSG00000073407	Gm6034	EG547347|H2-gs14-2	predicted gene 6034	protein-coding
mm_84766.1	chr9	75611217	75611223	-	1	NA	5' UTR (NM_016711, exon 1 of 10)	5' UTR (NM_016711, exon 1 of 10)	105	NM_016711	50876	Mm.291880	NM_016711	ENSMUSG00000032186	Tmod2	N-Tmod|NTMOD	tropomodulin 2	protein-coding
mm_42887.1	chr5	122372609	122372623	+	1	NA	promoter-TSS (NM_026883)	promoter-TSS (NM_026883)	108	NM_024216	68080	Mm.266328	NM_024216	ENSMUSG00000029464	Gpn3	A930018B01Rik|Atpbd1c|D5Ertd708e	GPN-loop GTPase 3	protein-coding
mm_165470.1	chr2	164255751	164255762	+	1	NA	exon (NM_173377, exon 2 of 3)	exon (NM_173377, exon 2 of 3)	887	NM_173377	329557	Mm.118769	NM_173377	ENSMUSG00000050383	Svs3b	9530004A22Rik	seminal vesicle secretory protein 3B	protein-coding
mm_120300.1	chr14	63139066	63139087	+	1	NA	exon (NM_007798, exon 8 of 10)	exon (NM_007798, exon 8 of 10)	16614	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_24622.1	chr3	93520474	93520501	+	1	NA	promoter-TSS (NM_016740)	promoter-TSS (NM_016740)	-9	NM_016740	20195	Mm.280038	NM_016740	ENSMUSG00000027907	S100a11	EMAPI|Emap1|S100a14|S100c|cal	S100 calcium binding protein A11	protein-coding
mm_1242.1	chr1	62797292	62797310	+	1	NA	TTS (NM_001077407)	TTS (NM_001077407)	-2569	NR_040601	74992	Mm.401979	NR_040601		4930487H11Rik	-	RIKEN cDNA 4930487H11 gene	ncRNA
mm_107404.1	chr12	33394816	33394824	+	1	NA	promoter-TSS (NM_029152)	promoter-TSS (NM_029152)	-34	NM_029152	75040	Mm.156068	NM_029152	ENSMUSG00000020562	Efcab10	4930504H06Rik	EF-hand calcium binding domain 10	protein-coding
mm_103195.1	chr11	70646973	70647047	-	1	NA	promoter-TSS (NM_024211)	promoter-TSS (NM_024211)	29	NM_024211	67863	Mm.296082	NM_024211	ENSMUSG00000014606	Slc25a11	2310022P18Rik|2oxoc	solute carrier family 25 (mitochondrial carrier oxoglutarate carrier), member 11	protein-coding
mm_66442.1	chr7	44848882	44848909	-	1	NA	promoter-TSS (NM_001290695)	promoter-TSS (NM_001290695)	184	NM_001042655	233204	Mm.27567	NM_144924	ENSMUSG00000038520	Tbc1d17	BC017607	TBC1 domain family, member 17	protein-coding
mm_25270.1	chr3	104863982	104863986	+	1	NA	promoter-TSS (NM_001253703)	promoter-TSS (NM_001253703)	521	NM_009797	12340	Mm.19142	NM_009797	ENSMUSG00000070372	Capza1	CAPZ|CAZ1|Cappa1	capping protein (actin filament) muscle Z-line, alpha 1	protein-coding
mm_112832.1	chr13	20824146	20824175	+	1	NA	intron (NM_012054, intron 2 of 20)	intron (NM_012054, intron 2 of 20)	30047	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_14690.1	chr2	140598486	140598496	+	1	NA	intron (NM_001013802, intron 3 of 18)	intron (NM_001013802, intron 3 of 18)	72985	NM_001172160	71436	Mm.426781	NM_178382	ENSMUSG00000051379	Flrt3	5530600M07Rik|C430047I10Rik|mKIAA1469	fibronectin leucine rich transmembrane protein 3	protein-coding
mm_17789.1	chr2	33086254	33086264	-	1	NA	intron (NM_178888, intron 1 of 28)	intron (NM_178888, intron 1 of 28)	945	NM_178888	99326	Mm.41290	NM_178888	ENSMUSG00000038860	Garnl3	AW120551	GTPase activating RANGAP domain-like 3	protein-coding
mm_108164.1	chr12	76370514	76370528	+	1	NA	promoter-TSS (NM_028356)	promoter-TSS (NM_028356)	255	NM_178744	268564	Mm.77065	NM_178744	ENSMUSG00000033454	Zbtb1	9430077A12|AI256369|Bsg2|C430003J21Rik	zinc finger and BTB domain containing 1	protein-coding
mm_163290.1	chr11	118212048	118212052	-	1	NA	intron (NM_001112699, intron 1 of 12)	intron (NM_001112699, intron 1 of 12)	692	NM_001112700	19157	Mm.86413	NM_011180	ENSMUSG00000017132	Cyth1	CLM1|CTH-1|CYTIP|Pscd1	cytohesin 1	protein-coding
mm_108225.1	chr12	77237890	77237910	+	1	NA	promoter-TSS (NM_016893)	promoter-TSS (NM_016893)	-204	NM_001252614	53618	Mm.35628	NM_016893	ENSMUSG00000021065	Fut8	-	fucosyltransferase 8	protein-coding
mm_136963.1	chr17	15704964	15704994	+	1	NA	promoter-TSS (NM_007690)	promoter-TSS (NM_007690)	12	NM_007690	12648	Mm.8137	NM_007690	ENSMUSG00000023852	Chd1	4930525N21Rik|AI851787|AW555109	chromodomain helicase DNA binding protein 1	protein-coding
mm_34756.1	chr4	152338718	152338762	+	1	NA	promoter-TSS (NM_001081376)	promoter-TSS (NM_001081376)	89	NM_001081376	269610	Mm.40192	NM_029216	ENSMUSG00000005045	Chd5	4930532L22Rik|AW060752|B230399N07Rik|CHD-5	chromodomain helicase DNA binding protein 5	protein-coding
mm_110743.1	chr12	69892780	69892792	-	1	NA	promoter-TSS (NM_178628)	promoter-TSS (NM_178628)	-319	NM_178628	73991	Mm.474462	NM_178628	ENSMUSG00000021066	Atl1	4930435M24Rik|Adfsp|Fsp1|Spg3|Spg3a	atlastin GTPase 1	protein-coding
mm_22750.1	chr3	19966364	19966383	+	1	NA	exon (NM_007752, exon 3 of 19)	exon (NM_007752, exon 3 of 19)	9319	NM_007752	12870	Mm.13787	NM_007752	ENSMUSG00000003617	Cp	D3Ertd555e	ceruloplasmin	protein-coding
mm_120828.1	chr14	75174995	75175008	+	1	NA	intron (NM_008879, intron 1 of 16)	intron (NM_008879, intron 1 of 16)	38576	NM_008879	18826	Mm.153911	NM_008879	ENSMUSG00000021998	Lcp1	AW536232|D14Ertd310e|LCP-1|Pls2|pp65	lymphocyte cytosolic protein 1	protein-coding
mm_122700.1	chr14	52104016	52104026	-	1	NA	promoter-TSS (NM_001170982)	promoter-TSS (NM_001170982)	7	NM_001170982	15381	Mm.427321	NM_016884	ENSMUSG00000060373	Hnrnpc	AL022939|D14Wsu171e|Hnrpc|Hnrpc1|Hnrpc2|hnRNPC1|hnRNPC2|hnrnp-C	heterogeneous nuclear ribonucleoprotein C	protein-coding
mm_10891.1	chr2	25263360	25263368	+	1	NA	exon (NM_175286, exon 1 of 4)	exon (NM_175286, exon 1 of 4)	766	NM_175286	97031	Mm.308539	NM_175286	ENSMUSG00000048707	Tprn	C430004E15Rik|C87750	taperin	protein-coding
mm_59388.1	chr7	26307192	26307197	+	1	NA	promoter-TSS (NM_009997)	promoter-TSS (NM_009997)	2	NM_009997	13086	Mm.154643	NM_009997	ENSMUSG00000074254	Cyp2a4	AI893559|Cyp15a1|D7Ucla4	cytochrome P450, family 2, subfamily a, polypeptide 4	protein-coding
mm_11993.1	chr2	55597293	55597307	+	1	NA	3' UTR (NM_001304810, exon 3 of 3)	3' UTR (NM_001304810, exon 3 of 3)	161330	NM_008426	16519	Mm.5127	NM_008426	ENSMUSG00000026824	Kcnj3	GIRK-1|GIRK1|Kcnf3|Kir3.1	potassium inwardly-rectifying channel, subfamily J, member 3	protein-coding
mm_145405.1	chr18	57468471	57468477	+	1	NA	promoter-TSS (NM_001134697)	promoter-TSS (NM_001134697)	-12	NM_001134697	629147	Mm.57415	NM_001134697	ENSMUSG00000069372	Ctxn3	ENSMUSG00000069372	cortexin 3	protein-coding
mm_49512.1	chr6	29859687	29859701	+	1	NA	promoter-TSS (NM_001171001)	promoter-TSS (NM_001171001)	98	NM_001171001	74340	Mm.210899	NM_021414	ENSMUSG00000029772	Ahcyl2	4631427C17Rik|AI227036|Adohcyase3|mKIAA0828	S-adenosylhomocysteine hydrolase-like 2	protein-coding
mm_23084.1	chr3	36863103	36863147	+	1	NA	promoter-TSS (NM_172679)	promoter-TSS (NM_172679)	19	NM_172679	229227	Mm.207907	NM_172679	ENSMUSG00000037270	4932438A13Rik	4732443H21|B830039D19Rik|D630029K19Rik|FSA|Kiaa1109|Tweek	RIKEN cDNA 4932438A13 gene	protein-coding
mm_135666.1	chr16	52407735	52407754	-	1	NA	intron (NM_009655, intron 1 of 15)	B4A|SINE|B4	45337	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_126327.1	chr15	79891632	79891662	+	1	NA	promoter-TSS (NM_001160415)	promoter-TSS (NM_001160415)	-761	NM_001160415	80287	Mm.284059	NM_030255	ENSMUSG00000009585	Apobec3	Apobec|Arp3|BC003314|Cem15|Rfv3	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 3	protein-coding
mm_119079.1	chr14	30881086	30881100	+	1	NA	3' UTR (NM_181390, exon 3 of 3)	3' UTR (NM_181390, exon 3 of 3)	1836	NM_181390	66175	Mm.220895	NM_181390	ENSMUSG00000042485	Mustn1	1110028G01Rik|Mustang	musculoskeletal, embryonic nuclear protein 1	protein-coding
mm_29831.1	chr3	129755013	129755026	-	1	NA	non-coding (NR_040589, exon 2 of 5)	non-coding (NR_040589, exon 2 of 5)	303	NM_010113	13645	Mm.252481	NM_010113	ENSMUSG00000028017	Egf	AI790464	epidermal growth factor	protein-coding
mm_97987.1	chr11	83942153	83942179	+	1	NA	promoter-TSS (NM_030096)	promoter-TSS (NM_030096)	76	NM_030096	78394	Mm.280544	NM_030096	ENSMUSG00000020677	Ddx52	2700029C06Rik|ROK1	DEAD (Asp-Glu-Ala-Asp) box polypeptide 52	protein-coding
mm_144312.1	chr18	12643330	12643395	+	1	NA	promoter-TSS (NM_028341)	promoter-TSS (NM_028341)	-171	NM_028341	72747	Mm.52526	NM_028341	ENSMUSG00000024424	Ttc39c	1700008N02Rik|2810439F02Rik	tetratricopeptide repeat domain 39C	protein-coding
mm_122391.1	chr14	40966815	40966848	-	1	NA	promoter-TSS (NM_145928)	promoter-TSS (NM_145928)	65	NM_145928	52588	Mm.28876	NM_145928	ENSMUSG00000037824	Tspan14	AA958793|D14Ertd226e|Tm4sf14|tspan-14	tetraspanin 14	protein-coding
mm_40570.1	chr5	63649414	63649424	+	1	NA	5' UTR (NM_177006, exon 1 of 7)	5' UTR (NM_177006, exon 1 of 7)	316	NM_177006	319807	Mm.319487	NM_028470	ENSMUSG00000090061	Nwd2	3110047P20Rik|B830017A01Rik|Hn1-ps2|mKIAA1239	NACHT and WD repeat domain containing 2	protein-coding
mm_28842.1	chr3	96594129	96594176	-	1	NA	promoter-TSS (NM_027241)	promoter-TSS (NM_027241)	29	NM_001293701	69870	Mm.292739	NM_027241	ENSMUSG00000028104	Polr3gl	2010003I19Rik	polymerase (RNA) III (DNA directed) polypeptide G like	protein-coding
mm_40796.1	chr5	67608531	67608540	+	1	NA	exon (NM_001033415, exon 1 of 2)	exon (NM_001033415, exon 1 of 2)	652	NM_001033415	330096	Mm.442747	NM_001033415	ENSMUSG00000050010	Shisa3	D830007B15Rik	shisa family member 3	protein-coding
mm_23831.1	chr3	81932609	81932634	+	1	NA	promoter-TSS (NM_177662)	promoter-TSS (NM_177662)	20	NM_177662	229445	Mm.254642	NM_177662	ENSMUSG00000028015	Ctso	A330105D01Rik|AI118514	cathepsin O	protein-coding
mm_138896.1	chr17	43568483	43568493	+	1	NA	promoter-TSS (NM_013737)	promoter-TSS (NM_013737)	37	NM_013737	27226	Mm.9277	NM_013737	ENSMUSG00000023913	Pla2g7	PAF-AH|R75400	phospholipase A2, group VII (platelet-activating factor acetylhydrolase, plasma)	protein-coding
mm_4511.1	chr1	174191057	174191062	+	1	NA	intron (NM_011465, intron 12 of 51)	intron (NM_011465, intron 12 of 51)	18283	NM_011465	20739	Mm.200611	NM_011465	ENSMUSG00000026532	Spta1	AF093576|AI451697|Spna-1|Spna1|ha|ihj|nmf4|sph	spectrin alpha, erythrocytic 1	protein-coding
mm_54922.1	chr6	47813339	47813369	-	1	NA	5' UTR (NM_009787, exon 1 of 10)	5' UTR (NM_009787, exon 1 of 10)	158	NM_009787	12304	Mm.2442	NM_009787	ENSMUSG00000025823	Pdia4	AI987846|Cai|ERp-72|Erp72	protein disulfide isomerase associated 4	protein-coding
mm_54700.1	chr6	39558102	39558111	-	1	NA	promoter-TSS (NM_172477)	promoter-TSS (NM_172477)	-272	NM_172477	209773	Mm.440021	NM_172477	ENSMUSG00000038456	Dennd2a	B930096L08Rik|C130031G22|mKIAA1277	DENN/MADD domain containing 2A	protein-coding
mm_92046.1	chr10	62495097	62495110	-	1	NA	exon (NM_011157, exon 3 of 3)	exon (NM_011157, exon 3 of 3)	-8298	NM_133672	30930	Mm.260703	NM_133672	ENSMUSG00000020078	Vps26a	AA407240|HB58|Vps26	VPS26 retromer complex component A	protein-coding
mm_155494.1	chrX	73737790	73737806	+	1	NA	3' UTR (NM_007435, exon 10 of 10)	3' UTR (NM_007435, exon 10 of 10)	-19305	NM_019587	140571	Mm.275600	NM_019587	ENSMUSG00000031385	Plxnb3	AI451018|Plxn6	plexin B3	protein-coding
mm_79968.1	chr9	66445628	66445639	+	1	NA	exon (NM_145617, exon 35 of 78)	exon (NM_145617, exon 35 of 78)	68960	NM_175206	74165	Mm.297998	NM_175206	ENSMUSG00000050503	Fbxl22	1110004B15Rik	F-box and leucine-rich repeat protein 22	protein-coding
mm_109044.1	chr12	104247893	104247897	+	1	NA	promoter-TSS (NR_033450)	promoter-TSS (NR_033450)	-1	NR_033450	546546	Mm.390522	NM_001034870		Serpina3h	6C28|Spi2	serine (or cysteine) peptidase inhibitor, clade A, member 3H	pseudo
mm_107695.1	chr12	55398815	55398894	+	1	NA	promoter-TSS (NM_011968)	promoter-TSS (NM_011968)	29	NM_011968	26443	Mm.30210	NM_011968	ENSMUSG00000021024	Psma6	IOTA	proteasome (prosome, macropain) subunit, alpha type 6	protein-coding
mm_36247.1	chr4	63403246	63403259	-	1	NA	5' UTR (NM_001045514, exon 1 of 22)	5' UTR (NM_001045514, exon 1 of 22)	193	NM_001045514	100182	Mm.387725	NM_001045514	ENSMUSG00000039158	Akna	AI597013	AT-hook transcription factor	protein-coding
mm_103307.1	chr11	72796029	72796074	-	1	NA	promoter-TSS (NM_001045536)	promoter-TSS (NM_001045536)	-175	NM_001045536	195018	Mm.272030	NM_001045536	ENSMUSG00000055670	Zzef1	8430405D05Rik|BC051585|C130099L13Rik|C85424|NSPA|mKIAA0399	zinc finger, ZZ-type with EF hand domain 1	protein-coding
mm_9368.1	chr1	172200542	172200555	-	1	NA	exon (NM_001329871, exon 2 of 4)	exon (NM_001329871, exon 2 of 4)	6256	NM_001329871	18611	Mm.544	NM_011063	ENSMUSG00000013698	Pea15a	Mat1|PEA-15|Pea15|Pkcs15	phosphoprotein enriched in astrocytes 15A	protein-coding
mm_168959.1	chr12	80127181	80127186	-	1	NA	intron (NR_033514, intron 2 of 2)	ORR1A1|LTR|ERVL-MaLR	5661	NR_033514	69548	Mm.269712	NR_033514	ENSMUSG00000097729	2310015A10Rik	5330419I17Rik	RIKEN cDNA 2310015A10 gene	ncRNA
mm_103803.1	chr11	82960649	82960671	-	1	NA	promoter-TSS (NR_045932)	promoter-TSS (NR_045932)	21	NR_045932	76392	Mm.295205	NR_045932	ENSMUSG00000086327	Slfn5os	1700003F17Rik	schlafen 5, opposite strand	ncRNA
mm_80167.1	chr9	71486059	71486075	+	1	NA	promoter-TSS (NM_178602)	promoter-TSS (NM_178602)	-84	NM_178602	28015	Mm.21094	NM_178602	ENSMUSG00000032199	Polr2m	AA407243|AA408799|AI303746|AW553238|D9Wsu138e|Grinl1a|mKIAA4185	polymerase (RNA) II (DNA directed) polypeptide M	protein-coding
mm_149182.1	chr19	9899644	9899652	+	1	NA	promoter-TSS (NM_016692)	promoter-TSS (NM_016692)	-115	NM_016692	16319	Mm.29755	NM_016692	ENSMUSG00000024660	Incenp	2700067E22Rik|AU019509|C130081E20|C77457	inner centromere protein	protein-coding
mm_37715.1	chr4	129500800	129500838	-	1	NA	Intergenic	CpG	9629	NM_001085491	68233	Mm.424983	NM_001085491	ENSMUSG00000078554	Fam229a	1700125D06Rik	family with sequence similarity 229, member A	protein-coding
mm_150703.1	chr19	42268689	42268692	+	1	NA	3' UTR (NM_001141983, exon 7 of 7)	3' UTR (NM_001141983, exon 7 of 7)	11480	NR_037246	100526549		NR_037246	ENSMUSG00000093234	Mir3085	mir-3085|mmu-mir-3085	microRNA 3085	ncRNA
mm_7415.1	chr1	119504233	119504265	-	1	NA	intron (NM_022327, intron 1 of 4)	intron (NM_022327, intron 1 of 4)	533	NM_022327	64143	Mm.27832	NM_022327	ENSMUSG00000004451	Ralb	5730472O18Rik	v-ral simian leukemia viral oncogene B	protein-coding
mm_18361.1	chr2	58567599	58567611	-	1	NA	promoter-TSS (NM_001110205)	promoter-TSS (NM_001110205)	271	NM_001289660	76654	Mm.200370	NM_029692	ENSMUSG00000026839	Upp2	1700124F02Rik|AI266885|UDRPASE2|UP2|UPASE2	uridine phosphorylase 2	protein-coding
mm_98555.1	chr11	95120111	95120125	+	1	NA	promoter-TSS (NM_010055)	promoter-TSS (NM_010055)	1	NM_010055	13393	Mm.5194	NM_010055	ENSMUSG00000001510	Dlx3	AV237891|Dlx-3	distal-less homeobox 3	protein-coding
mm_14713.1	chr2	143855615	143855620	+	1	NA	intron (NM_009751, intron 2 of 7)	intron (NM_009751, intron 2 of 7)	7556	NM_009751	12075	Mm.275937	NM_009751	ENSMUSG00000027420	Bfsp1	CP95	beaded filament structural protein 1, in lens-CP94	protein-coding
mm_124159.1	chr14	93498087	93498091	-	1	NA	intron (NM_001271798, intron 2 of 3)	Lx2A|LINE|L1	390799	NM_001271800	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding
mm_11727.1	chr2	37430925	37430973	+	1	NA	promoter-TSS (NM_146253)	promoter-TSS (NM_146253)	-30	NM_146253	241322	Mm.330182	NM_146253	ENSMUSG00000066798	Zbtb6	A830092L04Rik|ZID|Zfp482	zinc finger and BTB domain containing 6	protein-coding
mm_106498.1	chr11	120348752	120348791	-	1	NA	promoter-TSS (NM_009609)	promoter-TSS (NM_009609)	93	NR_038126	66838	Mm.375010	NR_038126	ENSMUSG00000043644	0610009L18Rik	-	RIKEN cDNA 0610009L18 gene	ncRNA
mm_158970.1	chr1	106870153	106870153	+	1	NA	intron (NM_009257, intron 1 of 6)	intron (NM_009257, intron 1 of 6)	8973	NM_009257	20724	Mm.268618	NM_009257	ENSMUSG00000067006	Serpinb5	1110036M19Rik|AI462524|AI646751|Maspin|PI-5|Spi7|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 5	protein-coding
mm_77207.1	chr8	113854934	113854942	-	1	NA	Intergenic	Intergenic	-6099	NM_172466	208936	Mm.167471	NM_172466	ENSMUSG00000053399	Adamts18	9630038L21|ADAMTS21|E130314N14Rik	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 18	protein-coding
mm_73908.1	chr8	119558974	119558979	+	1	NA	promoter-TSS (NM_001167910)	promoter-TSS (NM_001167910)	-215	NM_019709	56453	Mm.206934	NM_019709	ENSMUSG00000031835	Mbtps1	0610038M03Rik|AV003995|S1P|SKI-1|Ski1|mKIAA0091	membrane-bound transcription factor peptidase, site 1	protein-coding
mm_28660.1	chr3	95241159	95241182	-	1	NA	promoter-TSS (NM_001024841)	promoter-TSS (NM_001024841)	-61	NM_001024841	229588	Mm.387177	NM_001024841	ENSMUSG00000068860	Gm128	Ment|pmis1	predicted gene 128	protein-coding
mm_56066.1	chr6	86785520	86785532	-	1	NA	intron (NM_013471, intron 1 of 12)	intron (NM_013471, intron 1 of 12)	8058	NM_013471	11746	Mm.259702	NM_013471	ENSMUSG00000029994	Anxa4	AI265406|AIV|AW106930|Anx4|Xanx-4	annexin A4	protein-coding
mm_46962.1	chr5	115147842	115147887	-	1	NA	3' UTR (NM_175403, exon 5 of 5)	3' UTR (NM_175403, exon 5 of 5)	10312	NM_175403	109154	Mm.153963	NM_175403	ENSMUSG00000048578	Mlec	2410014A08Rik|AI850530|ESTM19|X83352|mKIAA0152	malectin	protein-coding
mm_150327.1	chr19	34574658	34574707	+	1	NA	3' UTR (NM_008332, exon 3 of 3)	3' UTR (NM_008332, exon 3 of 3)	-8847	NM_010501	15959	Mm.426079	NM_010501	ENSMUSG00000074896	Ifit3	Ifi49|P49	interferon-induced protein with tetratricopeptide repeats 3	protein-coding
mm_118806.1	chr14	25458880	25458890	+	1	NA	promoter-TSS (NM_183208)	promoter-TSS (NM_183208)	-300	NM_001310666	328365	Mm.227484	NM_183208	ENSMUSG00000007817	Zmiz1	BC065120|E330020C23|ENSMUSG00000072684|Gm10397|I920194n01|Rai17|Zimp10	zinc finger, MIZ-type containing 1	protein-coding
mm_165959.1	chr4	88165554	88165559	+	1	NA	intron (NM_001081184, intron 5 of 43)	MTE2a|LTR|ERVL-MaLR	43516	NR_030478	735282		NR_030478	ENSMUSG00000070077	Mir491	Mirn491|mir-491|mmu-mir-491	microRNA 491	ncRNA
mm_129545.1	chr15	79403237	79403245	-	1	NA	promoter-TSS (NM_001253819)	promoter-TSS (NM_001253819)	-2	NM_001253820	223693	Mm.323358	NM_172608	ENSMUSG00000009035	Tmem184b	2610507A11|4732495E13Rik	transmembrane protein 184b	protein-coding
mm_118442.1	chr14	8118161	8118171	+	1	NA	intron (NM_178279, intron 1 of 18)	intron (NM_178279, intron 1 of 18)	19953	NM_178279	218699	Mm.29515	NM_145458	ENSMUSG00000033885	Pxk	C230080L11Rik|D14Ertd813e|MONaKA	PX domain containing serine/threonine kinase	protein-coding
mm_86656.1	chr10	17724644	17724678	+	1	NA	exon (NM_010828, exon 2 of 2)	exon (NM_010828, exon 2 of 2)	1433	NM_010828	17684	Mm.272321	NM_010828	ENSMUSG00000039910	Cited2	AI835299|ER154-like|Mrg1|Msg2|p35srj	Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 2	protein-coding
mm_49491.1	chr6	29694256	29694271	+	1	NA	promoter-TSS (NM_001301407)	promoter-TSS (NM_001301407)	49	NM_146173	232670	Mm.225289	NM_146173	ENSMUSG00000001763	Tspan33	1300010A20Rik|Pen	tetraspanin 33	protein-coding
mm_150775.1	chr19	44294257	44294259	+	1	NA	5' UTR (NM_009128, exon 1 of 6)	5' UTR (NM_009128, exon 1 of 6)	582	NM_009128	20250	Mm.487021	NM_009128	ENSMUSG00000025203	Scd2	Mir5114|Scd-2|mir-5114|swty	stearoyl-Coenzyme A desaturase 2	protein-coding
mm_82510.1	chr9	20497874	20497879	-	1	NA	3' UTR (NM_001135019, exon 9 of 9)	3' UTR (NM_001135019, exon 9 of 9)	-5130	NM_001110309	235028	Mm.297660	NM_146221	ENSMUSG00000059475	Zfp426	2900057C04Rik|KRAB1|Zfo61|Zfp68-rs1|Znf426|mKIAA4237	zinc finger protein 426	protein-coding
mm_74849.1	chr8	24595612	24595617	-	1	NA	promoter-TSS (NM_001293690)	promoter-TSS (NM_001293690)	52	NM_001293690	15930	Mm.392	NM_008324	ENSMUSG00000031551	Ido1	Ido|Indo	indoleamine 2,3-dioxygenase 1	protein-coding
mm_137451.1	chr17	26534126	26534173	+	1	NA	Intergenic	Intergenic	-25677	NM_013642	19252	Mm.239041	NM_013642	ENSMUSG00000024190	Dusp1	3CH134|MKP1|Ptpn16|U19515|erp|mkp-1	dual specificity phosphatase 1	protein-coding
mm_102452.1	chr11	59809775	59809847	-	1	NA	promoter-TSS (NM_001271357)	promoter-TSS (NM_001271357)	-210	NM_001271357	216805	Mm.339640	NM_146018	ENSMUSG00000032633	Flcn	AU014660|B430214A04Rik|Bhd|FLCL	folliculin	protein-coding
mm_17357.1	chr2	26617463	26617473	-	1	NA	Intergenic	RMER1C|Other|Other	-10989	NM_019833	56279	Mm.279863	NM_019833	ENSMUSG00000036186	Fam69b	AB030186|AW209000|B230317C12Rik|PIP49	family with sequence similarity 69, member B	protein-coding
mm_52425.1	chr6	113472277	113472291	+	1	NA	exon (NM_178942, exon 3 of 18)	exon (NM_178942, exon 3 of 18)	829	NM_134159	171095	Mm.213397	NM_134159	ENSMUSG00000030281	Il17rc	1110025H02Rik|Gm19850|IL-17RC|IL17-RC|IL17-RL|Il17rl	interleukin 17 receptor C	protein-coding
mm_46881.1	chr5	113908666	113908674	-	1	NA	promoter-TSS (NM_011779)	promoter-TSS (NM_011779)	36	NM_011779	23790	Mm.260158	NM_011779	ENSMUSG00000004530	Coro1c	AL022675|AW455561|AW548837	coronin, actin binding protein 1C	protein-coding
mm_157501.1	chrX	48513519	48513565	-	1	NA	promoter-TSS (NM_001290364)	promoter-TSS (NM_001290364)	21	NM_001290364	26926	Mm.240434	NM_012019	ENSMUSG00000036932	Aifm1	AIF|AIFsh2|Hq|Pdcd8	apoptosis-inducing factor, mitochondrion-associated 1	protein-coding
mm_51160.1	chr6	70723661	70723679	+	1	NA	Intergenic	Intergenic	68505	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_30719.1	chr4	13742776	13742810	+	1	NA	promoter-TSS (NM_001111026)	promoter-TSS (NM_001111026)	-509	NM_001111026	12395	Mm.4909	NM_009822	ENSMUSG00000006586	Runx1t1	Cbfa2t1h|ETO|MTG8	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	protein-coding
mm_52716.1	chr6	119481939	119481951	+	1	NA	3' UTR (NM_133940, exon 1 of 1)	3' UTR (NM_133940, exon 1 of 1)	2277	NM_133940	101358	Mm.125477	NM_133940	ENSMUSG00000030019	Fbxl14	AW322056|Fbx14l	F-box and leucine-rich repeat protein 14	protein-coding
mm_1913.1	chr1	85957563	85957573	+	1	NA	intron (NM_001033290, intron 1 of 1)	intron (NM_001033290, intron 1 of 1)	3487	NM_001033290	227326	Mm.244158	NM_001033290	ENSMUSG00000049608	Gpr55	CTFL|Gm218|Lpir1	G protein-coupled receptor 55	protein-coding
mm_70542.1	chr8	13042758	13042769	+	1	NA	intron (NM_001242368, intron 3 of 8)	intron (NM_001242368, intron 3 of 8)	5455	NM_001242368	14058	Mm.262589	NM_007972	ENSMUSG00000031444	F10	Cf10|fX	coagulation factor X	protein-coding
mm_32333.1	chr4	104367629	104367633	+	1	NA	promoter-TSS (NM_177259)	promoter-TSS (NM_177259)	93	NM_177259	13131	Mm.289682	NM_010014	ENSMUSG00000028519	Dab1	AI956902|C630028C02Rik|scm|scr|scrambler|yot	disabled 1	protein-coding
mm_145728.1	chr18	64254360	64254387	+	1	NA	promoter-TSS (NM_009182)	promoter-TSS (NM_009182)	14	NM_009182	20451	Mm.252110	NM_009182	ENSMUSG00000056812	St8sia3	AI847333|ST8SiaIII|Siat8c	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3	protein-coding
mm_102871.1	chr11	69408559	69408562	-	1	NA	intron (NM_001017426, intron 2 of 22)	intron (NM_001017426, intron 2 of 22)	5115	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_81637.1	chr9	110880322	110880346	+	1	NA	promoter-TSS (NM_001146060)	promoter-TSS (NM_001146060)	12	NM_001146060	235633	Mm.86338	NM_146228	ENSMUSG00000044037	Als2cl	79H19D|79H19E|BC022645|D930044G19Rik|mRn.49018	ALS2 C-terminal like	protein-coding
mm_152911.1	chr19	27262298	27262306	-	1	NA	Intergenic	Intergenic	45282	NM_001161420	22359	Mm.4141	NM_013703	ENSMUSG00000024924	Vldlr	AA408956|AI451093|AW047288	very low density lipoprotein receptor	protein-coding
mm_101318.1	chr11	22856528	22856529	-	1	NA	intron (NM_001169114, intron 1 of 1)	intron (NM_001169114, intron 1 of 1)	3207	NM_016888	53625	Mm.395495	NM_016888	ENSMUSG00000051650	B3gnt2	AA408337|AA409404|AW260308|B3Galt6|B3gnt1|BGnT-1|BGnT-2|BGnT1|BGnT2|Beta3gnt	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 2	protein-coding
mm_62249.1	chr7	99267429	99267438	+	1	NA	promoter-TSS (NM_001043355)	promoter-TSS (NM_001043355)	-14	NM_010837	17760	Mm.154087	NM_010837	ENSMUSG00000055407	Map6	2810411E12Rik|Map-6|Mtap6|STOP	microtubule-associated protein 6	protein-coding
mm_148750.1	chr19	6051393	6051406	+	1	NA	promoter-TSS (NR_105954)	promoter-TSS (NR_105954)	65	NR_105954	102465597		NR_105954	ENSMUSG00000098928	Mir6988	Gm27593|mmu-mir-6988	microRNA 6988	ncRNA
mm_156796.1	chrX	162901680	162901693	+	1	NA	promoter-TSS (NM_001168569)	promoter-TSS (NM_001168569)	91	NM_018737	55936	Mm.2065	NM_018737	ENSMUSG00000031360	Ctps2	A830031M15Rik|AI326475|Ctpsh	cytidine 5'-triphosphate synthase 2	protein-coding
mm_62253.1	chr7	99268393	99268420	+	1	NA	promoter-TSS (NM_001043355)	promoter-TSS (NM_001043355)	60	NM_001043355	17760	Mm.154087	NM_010837	ENSMUSG00000055407	Map6	2810411E12Rik|Map-6|Mtap6|STOP	microtubule-associated protein 6	protein-coding
mm_130201.1	chr15	94589871	94589881	-	1	NA	promoter-TSS (NM_008971)	promoter-TSS (NM_008971)	-52	NM_008971	19230	Mm.490250	NM_008971	ENSMUSG00000022451	Twf1	A6|Ptk9|twinfilin	twinfilin actin binding protein 1	protein-coding
mm_12473.1	chr2	71528518	71528530	+	1	NA	promoter-TSS (NM_010053)	promoter-TSS (NM_010053)	-921	NM_010053	13390	Mm.475101	NM_010053	ENSMUSG00000041911	Dlx1	Dlx|Dlx-1	distal-less homeobox 1	protein-coding
mm_170769.1	chr2	162390809	162390814	+	1	NA	promoter-TSS (NR_040617)	promoter-TSS (NR_040617)	-2	NR_040617	77645	Mm.447752	NR_040617	ENSMUSG00000084919	Ptprtos	C330008G21Rik	protein tyrosine phosphatase, receptor type T, opposite strand	ncRNA
mm_173152.1	chrX	32487958	32487960	+	1	NA	Intergenic	RLTR1B|LTR|ERV1	-72096	NM_001168334	100040482	Mm.479861	NM_001168334	ENSMUSG00000096194	Btbd35f2	Gm2799	BTB domain containing 35, family member 2	protein-coding
mm_108646.1	chr12	85960281	85960291	+	1	NA	intron (NM_001347395, intron 29 of 32)	intron (NM_001347395, intron 29 of 32)	118755	NM_009368	21809	Mm.3992	NM_009368	ENSMUSG00000021253	Tgfb3	TGF-beta-3|Tgfb-3	transforming growth factor, beta 3	protein-coding
mm_168861.1	chr12	30062892	30062896	-	1	NA	intron (NM_009417, intron 16 of 16)	MT2_Mm|LTR|ERVL	69730	NM_009417	22018	Mm.4991	NM_009417	ENSMUSG00000020673	Tpo	-	thyroid peroxidase	protein-coding
mm_98652.1	chr11	96251760	96251774	+	1	NA	non-coding (NR_037977, exon 1 of 3)	non-coding (NR_037977, exon 1 of 3)	107	NR_037977	193022	Mm.169508	NR_037977		Gm53	-	predicted gene 53	ncRNA
mm_38723.1	chr4	145234864	145234879	-	1	NA	intron (NM_011610, intron 1 of 9)	intron (NM_011610, intron 1 of 9)	11999	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_129959.1	chr15	85332632	85332638	-	1	NA	Intergenic	MTC|LTR|ERVL-MaLR	-3746	NM_016843	54138	Mm.248906	NM_016843	ENSMUSG00000016541	Atxn10	AI325283|C77170|E46|Sca10|TEG-169|Tex169	ataxin 10	protein-coding
mm_28122.1	chr3	86920489	86920535	-	1	NA	5' UTR (NM_001195500, exon 1 of 12)	5' UTR (NM_001195500, exon 1 of 12)	372	NM_001195496	70762	Mm.44490	NM_027539	ENSMUSG00000028078	Dclk2	6330415M09Rik|AU044875|CL2|CLICK2|Click-II|Dcamkl2	doublecortin-like kinase 2	protein-coding
mm_119188.1	chr14	32326696	32326705	+	1	NA	intron (NM_001081130, intron 3 of 23)	intron (NM_001081130, intron 3 of 23)	4681	NM_001081130	239017	Mm.318302	NM_001081130	ENSMUSG00000021913	Ogdhl	-	oxoglutarate dehydrogenase-like	protein-coding
mm_24030.1	chr3	87536197	87536210	+	1	NA	exon (NM_012051, exon 5 of 5)	exon (NM_012051, exon 5 of 5)	10625	NM_012051	27049	Mm.219460	NM_012051	ENSMUSG00000003382	Etv3	AI414410|METS|Pe1	ets variant 3	protein-coding
mm_122935.1	chr14	54963064	54963118	-	1	NA	exon (NM_010856, exon 7 of 39)	exon (NM_010856, exon 7 of 39)	3516	NM_001164171	17888	Mm.290003	NM_010856	ENSMUSG00000040752	Myh6	A830009F23Rik|AA517445|Myhc-a|Myhca|alpha-MHC	myosin, heavy polypeptide 6, cardiac muscle, alpha	protein-coding
mm_145176.1	chr18	47040595	47040598	+	1	NA	intron (NM_178377, intron 5 of 6)	MMERGLN_LTR|LTR|ERV1	81720	NM_178377	69456	Mm.210734	NM_178377	ENSMUSG00000042705	Commd10	2310003A05Rik|AU019438|DRWMS2	COMM domain containing 10	protein-coding
mm_163525.1	chr12	116757192	116757205	-	1	NA	intron (NM_011215, intron 3 of 22)	RMER6C|LTR|ERVK	271478	NM_011215	19276	Mm.206054	NM_011215	ENSMUSG00000056553	Ptprn2	4930425H11Rik|IA2beta|PTP-NP|Phol|mKIAA0387|phogrin	protein tyrosine phosphatase, receptor type, N polypeptide 2	protein-coding
mm_85733.1	chr9	108452380	108452412	-	1	NA	5' UTR (NM_030075, exon 6 of 11)	5' UTR (NM_030075, exon 6 of 11)	-8122	NM_133744	72454	Mm.46488	NM_133744	ENSMUSG00000049305	Ccdc71	2600016J21Rik	coiled-coil domain containing 71	protein-coding
mm_124297.1	chr14	103055133	103055163	-	1	NA	exon (NM_008392, exon 5 of 5)	exon (NM_008392, exon 5 of 5)	8136	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_28107.1	chr3	86548438	86548452	-	1	NA	promoter-TSS (NM_011839)	promoter-TSS (NM_011839)	-162	NM_011839	23937	Mm.389466	NM_011839	ENSMUSG00000057777	Mab21l2	-	mab-21-like 2 (C. elegans)	protein-coding
mm_146278.1	chr18	77882519	77882546	+	1	NA	3' UTR (NM_013831, exon 15 of 15)	3' UTR (NM_013831, exon 15 of 15)	-55935	NM_001195633	100502841	Mm.297782	NM_001195633	ENSMUSG00000039840	Epg5	4732475F16|5430411K18Rik|AI661957|AW456499|mKIAA1632	ectopic P-granules autophagy protein 5 homolog (C. elegans)	protein-coding
mm_100672.1	chr11	3371283	3371293	-	1	NA	5' UTR (NM_173053, exon 1 of 15)	5' UTR (NM_173053, exon 1 of 15)	104	NM_173053	16886	Mm.124176	NM_010718	ENSMUSG00000020451	Limk2	Limk-2|whe	LIM motif-containing protein kinase 2	protein-coding
mm_72296.1	chr8	75448711	75448739	+	1	NA	promoter-TSS (NM_027944)	promoter-TSS (NM_027944)	31	NM_001164235	71831	Mm.443238	NM_027944	ENSMUSG00000031620	1700007B14Rik	-	RIKEN cDNA 1700007B14 gene	protein-coding
mm_124992.1	chr15	22548907	22548927	+	1	NA	Intergenic	Intergenic	166067	NM_001165971	545091	Mm.475598	NM_001165971		Gm5803	EG545091	predicted gene 5803	protein-coding
mm_172126.1	chr6	3201376	3201383	+	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	-87140	NR_036696	667335	Mm.380219	NR_036696	ENSMUSG00000106779	Gm8579	EG667335	spermatogenesis associated glutamate (E)-rich protein 4a pseudogene	pseudo
mm_16093.1	chr2	168970456	168970477	+	1	NA	Intergenic	Intergenic	-7803	NR_040326	75508	Mm.271256	NR_040326	ENSMUSG00000086348	1700017J07Rik	-	RIKEN cDNA 1700017J07 gene	ncRNA
mm_84617.1	chr9	70488118	70488120	-	1	NA	intron (NM_033604, intron 2 of 14)	ID_B1|SINE|B4	15606	NM_033604	93836	Mm.29783	NM_033604	ENSMUSG00000032217	Rnf111	ARK|Arkadia	ring finger 111	protein-coding
mm_84609.1	chr9	70211722	70211744	-	1	NA	intron (NM_181072, intron 1 of 27)	intron (NM_181072, intron 1 of 27)	4383	NM_181072	71602	Mm.249311	NM_181072	ENSMUSG00000032220	Myo1e	2310020N23Rik|9130023P14Rik|AA407778|myosin-1e|myr 3	myosin IE	protein-coding
mm_65139.1	chr7	19573358	19573363	-	1	NA	promoter-TSS (NM_027189)	promoter-TSS (NM_027189)	-17	NM_027189	69731	Mm.24540	NM_027189	ENSMUSG00000044709	Gemin7	2400008I04Rik|AI120175|AI461688	gem (nuclear organelle) associated protein 7	protein-coding
mm_52146.1	chr6	97978753	97978763	+	1	NA	intron (NM_001113198, intron 2 of 9)	MER20|DNA|hAT-Charlie	-13025	NM_008601	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_150640.1	chr19	41830028	41830049	+	1	NA	promoter-TSS (NM_008043)	promoter-TSS (NM_008043)	68	NM_008043	14296	Mm.4573	NM_008043	ENSMUSG00000067199	Frat1	AW060382	frequently rearranged in advanced T cell lymphomas	protein-coding
mm_101120.1	chr11	12026238	12026249	-	1	NA	intron (NM_010345, intron 1 of 16)	CpG	1728	NM_001177629	14783	Mm.273117	NM_010345	ENSMUSG00000020176	Grb10	5730571D09Rik|AI325020|Meg1|mKIAA0207	growth factor receptor bound protein 10	protein-coding
mm_137.1	chr1	10878613	10878615	+	1	NA	Intergenic	Intergenic	-12740	NR_030645	100124448		NR_030645	ENSMUSG00000076948	Mir467e	Mirn467e	microRNA 467e	ncRNA
mm_48644.1	chr5	145720125	145720136	-	1	NA	promoter-TSS (NM_017396).2	promoter-TSS (NM_017396).2	6	NM_017396	53973	Mm.379071	NM_017396	ENSMUSG00000075551	Cyp3a41a	Cyp3a41	cytochrome P450, family 3, subfamily a, polypeptide 41A	protein-coding
mm_76748.1	chr8	95434630	95434640	-	1	NA	5' UTR (NM_008187, exon 1 of 6)	5' UTR (NM_008187, exon 1 of 6)	234	NM_008187	14894	Mm.2080	NM_008187	ENSMUSG00000031796	Cfap20	2600014O15Rik|AL024127|Gtl3|T10-2A2	cilia and flagella associated protein 20	protein-coding
mm_120522.1	chr14	66784540	66784546	+	1	NA	Intergenic	Intergenic	84057	NM_009955	12934	Mm.352648	NM_009955	ENSMUSG00000022048	Dpysl2	AI851130|Crmp2|DRP2|Musunc33|TOAD-64|Ulip2	dihydropyrimidinase-like 2	protein-coding
mm_69512.1	chr7	134501127	134501131	-	1	NA	Intergenic	Intergenic	-124301	NM_001081331	71007	Mm.334285	NM_001081331	ENSMUSG00000030994	D7Ertd443e	4933400E14Rik|FATS|Gm497	DNA segment, Chr 7, ERATO Doi 443, expressed	protein-coding
mm_118135.1	chr13	104817125	104817153	-	1	NA	promoter-TSS (NM_026072)	promoter-TSS (NM_026072)	-31	NM_026075	67288	Mm.125465	NM_026075	ENSMUSG00000021716	Srek1ip1	3110031B13Rik|AI462702|AV348305|AW121048|Sfrs12ip1|Srsf12ip1	splicing regulatory glutamine/lysine-rich protein 1interacting protein 1	protein-coding
mm_111583.1	chr12	101837521	101837537	-	1	NA	3' UTR (NM_028446, exon 21 of 21)	3' UTR (NM_028446, exon 21 of 21)	-18410	NM_011812	23876	Mm.288381	NM_011812	ENSMUSG00000021186	Fbln5	A55|DANCE|EVEC	fibulin 5	protein-coding
mm_157929.1	chrX	79671523	79671546	-	1	NA	promoter-TSS (NM_028025)	promoter-TSS (NM_028025)	-99	NM_028025	71967	Mm.379207	NM_028025	ENSMUSG00000046942	Mageb16	2410003J06Rik	melanoma antigen family B, 16	protein-coding
mm_60144.1	chr7	38183751	38183757	+	1	NA	promoter-TSS (NM_028166)	promoter-TSS (NM_028166)	-33	NM_028166	72244	Mm.187554	NM_028166		1600014C10Rik	AI428873	RIKEN cDNA 1600014C10 gene	protein-coding
mm_31549.1	chr4	55711702	55711706	+	1	NA	Intergenic	MIR|SINE|MIR	-179229	NM_010637	16600	Mm.4325	NM_010637	ENSMUSG00000003032	Klf4	EZF|Gklf|Zie	Kruppel-like factor 4 (gut)	protein-coding
mm_64262.1	chr7	141746704	141746717	+	1	NA	exon (NM_023566, exon 31 of 46)	exon (NM_023566, exon 31 of 46)	-42301	NM_010844	17833	Mm.334332	NM_010844	ENSMUSG00000037974	Muc5ac	2210005L13Rik|MGM	mucin 5, subtypes A and C, tracheobronchial/gastric	protein-coding
mm_61872.1	chr7	89426301	89426323	+	1	NA	promoter-TSS (NR_102276)	promoter-TSS (NR_102276)	6	NR_102276	101521	Mm.26902	NR_102276	ENSMUSG00000109311	AI314278	-	expressed sequence AI314278	ncRNA
mm_149094.1	chr19	8929629	8929694	+	1	NA	promoter-TSS (NM_144872)	promoter-TSS (NM_144872)	-33	NM_144872	225898	Mm.31008	NM_144872	ENSMUSG00000071647	Eml3	BC022146	echinoderm microtubule associated protein like 3	protein-coding
mm_73370.1	chr8	105617728	105617789	+	1	NA	exon (NM_001081241, exon 13 of 22)	exon (NM_001081241, exon 13 of 22)	2292	NR_035492	100316712		NR_035492	ENSMUSG00000089432	Mir1966	mir-1966|mmu-mir-1966	microRNA 1966	ncRNA
mm_35640.1	chr4	43518686	43518704	-	1	NA	exon (NM_009416, exon 6 of 9)	exon (NM_009416, exon 6 of 9)	4859	NM_009416	22004	Mm.646	NM_009416	ENSMUSG00000028464	Tpm2	Tpm-2|Trop-2	tropomyosin 2, beta	protein-coding
mm_75227.1	chr8	39618434	39618445	-	1	NA	intron (NM_001113326, intron 5 of 9)	intron (NM_001113326, intron 5 of 9)	24239	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_18113.1	chr2	44996149	44996159	-	1	NA	exon (NM_015753, exon 8 of 10)	exon (NM_015753, exon 8 of 10)	27023	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_98114.1	chr11	87109561	87109583	+	1	NA	promoter-TSS (NM_175563)	promoter-TSS (NM_175563)	311	NM_025377	66140	Mm.45008	NM_025377	ENSMUSG00000020492	Ska2	1110001A07Rik|C78640|Fam33a	spindle and kinetochore associated complex subunit 2	protein-coding
mm_41518.1	chr5	92392714	92392724	+	1	NA	exon (NM_001310664, exon 4 of 11)	exon (NM_001310664, exon 4 of 11)	4585	NM_001310665	109979	Mm.263514	NM_181728	ENSMUSG00000034842	Art3	4930569O04Rik|ARTC3	ADP-ribosyltransferase 3	protein-coding
mm_3059.1	chr1	134083254	134083277	+	1	NA	Intergenic	Intergenic	-4110	NM_007570	12227	Mm.392646	NM_007570	ENSMUSG00000020423	Btg2	AA959598|APRO1|Pc3|TIS21	B cell translocation gene 2, anti-proliferative	protein-coding
mm_88689.1	chr10	80116268	80116278	+	1	NA	non-coding (NR_126043, exon 1 of 11)	non-coding (NR_126043, exon 1 of 11)	470	NM_001301854	20869	Mm.44231	NM_011492	ENSMUSG00000003068	Stk11	AA408040|Lkb1|Par-4|R75140	serine/threonine kinase 11	protein-coding
mm_108786.1	chr12	90738216	90738226	+	1	NA	exon (NM_010050, exon 1 of 2)	exon (NM_010050, exon 1 of 2)	816	NM_010050	13371	Mm.21389	NM_010050	ENSMUSG00000007682	Dio2	5DII|AI324267|DIOII	deiodinase, iodothyronine, type II	protein-coding
mm_91663.1	chr10	42888475	42888486	-	1	NA	intron (NM_172938, intron 1 of 8)	intron (NM_172938, intron 1 of 8)	27968	NM_172938	268297	Mm.98731	NM_172938	ENSMUSG00000044770	Scml4	9330161D17|mFLJ00197	sex comb on midleg-like 4 (Drosophila)	protein-coding
mm_101035.1	chr11	8600757	8600766	-	1	NA	intron (NM_001083587, intron 2 of 30)	intron (NM_001083587, intron 2 of 30)	63774	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_118036.1	chr13	101692333	101692384	-	1	NA	5' UTR (NM_001024955, exon 1 of 10)	5' UTR (NM_001024955, exon 1 of 10)	272	NM_001024955	18708	Mm.259333	NM_001024955	ENSMUSG00000041417	Pik3r1	PI3K|p50alpha|p55alpha|p85alpha	phosphatidylinositol 3-kinase, regulatory subunit, polypeptide 1 (p85 alpha)	protein-coding
mm_13623.1	chr2	113441069	113441079	+	1	NA	promoter-TSS (NM_001285459)	promoter-TSS (NM_001285459)	10	NM_001285459	14260	Mm.4938	NM_010230	ENSMUSG00000044042	Fmn1	Fmn|formin-1|ld	formin 1	protein-coding
mm_17458.1	chr2	28556828	28556871	-	1	NA	exon (NM_009885, exon 10 of 11)	exon (NM_009885, exon 10 of 11)	6554	NM_009885	12613	Mm.236017	NM_009885	ENSMUSG00000026818	Cel	1810036E18Rik|BAL	carboxyl ester lipase	protein-coding
mm_122740.1	chr14	54125414	54125425	-	1	NA	Intergenic	Intergenic	128510	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_147984.1	chr18	67610734	67610734	-	1	NA	Intergenic	CpG	30602	NM_001081073	225659	Mm.111928	NM_001081073	ENSMUSG00000073542	Cep76	6230425F05Rik|9630013E05	centrosomal protein 76	protein-coding
mm_112091.1	chr12	112693543	112693618	-	1	NA	Intergenic	CpG	14740	NM_001100460	382639	Mm.11350	NM_001100460	ENSMUSG00000037638	Zbtb42	EG382639|Gm5188|simiRP58	zinc finger and BTB domain containing 42	protein-coding
mm_58553.1	chr7	4740179	4740206	+	1	NA	promoter-TSS (NM_001115018)	promoter-TSS (NM_001115018)	65	NM_001115018	232811	Mm.247844	NM_146177	ENSMUSG00000059851	Kmt5c	BC024816|Suv4-20h2|Suv420h2	lysine methyltransferase 5C	protein-coding
mm_3914.1	chr1	162217488	162217508	+	1	NA	promoter-TSS (NR_029810)	promoter-TSS (NR_029810)	-125	NR_002870	474332	Mm.479755	NR_002870	ENSMUSG00000078190	Dnm3os	6030416H16Rik|Hag2|Npn1|P/L01	dynamin 3, opposite strand	ncRNA
mm_153847.1	chr19	46338375	46338403	-	1	NA	5' UTR (NM_024192, exon 2 of 10)	5' UTR (NM_024192, exon 2 of 10)	271	NM_001164294	67116	Mm.218848	NM_024192	ENSMUSG00000036748	Cuedc2	3010002G01Rik	CUE domain containing 2	protein-coding
mm_102866.1	chr11	69405874	69405911	-	1	NA	exon (NM_001017426, exon 11 of 23)	exon (NM_001017426, exon 11 of 23)	-7658	NM_025915	67020	Mm.390406	NM_025915	ENSMUSG00000045377	Tmem88	2600017H02Rik	transmembrane protein 88	protein-coding
mm_137257.1	chr17	24550065	24550098	+	1	NA	5' UTR (NM_013630, exon 1 of 46)	5' UTR (NM_013630, exon 1 of 46)	131	NM_013630	18763	Mm.30435	NM_013630	ENSMUSG00000032855	Pkd1	PC1|mFLJ00285	polycystic kidney disease 1 homolog	protein-coding
mm_157323.1	chrX	23284604	23284618	-	1	NA	intron (NM_026167, intron 3 of 8)	intron (NM_026167, intron 3 of 8)	948	NM_001290476	67455	Mm.224306	NM_026167	ENSMUSG00000036782	Klhl13	1200009K10Rik|AI451128|Bklhd2|D130072F20Rik	kelch-like 13	protein-coding
mm_79703.1	chr9	60885891	60885894	+	1	NA	Intergenic	Intergenic	91344	NM_028283	72565	Mm.68819	NM_028283	ENSMUSG00000034485	Uaca	2700059D02Rik|nucling	uveal autoantigen with coiled-coil domains and ankyrin repeats	protein-coding
mm_51254.1	chr6	71909047	71909076	+	1	NA	promoter-TSS (NM_009088)	promoter-TSS (NM_009088)	8	NM_009088	20019	Mm.135581	NM_009088	ENSMUSG00000049553	Polr1a	194kDa|3010014K16Rik|RPA194|Rpo1-4|mRPA1	polymerase (RNA) I polypeptide A	protein-coding
mm_65456.1	chr7	25463720	25463729	-	1	NA	3' UTR (NM_001039186, exon 8 of 8)	3' UTR (NM_001039186, exon 8 of 8)	13901	NM_001039185	26365	Mm.322502	NM_011926	ENSMUSG00000074272	Ceacam1	Bgp|Bgp1|C-CAM|CD66a|Cc1|Cea-1|Cea-7|Cea1|Cea7|Hv-2|Hv2|MHVR|MHVR1|Mhv-1|bb-1|mCEA1|mmCGM1|mmCGM1a|mmCGM2	carcinoembryonic antigen-related cell adhesion molecule 1	protein-coding
mm_52491.1	chr6	114648928	114648933	+	1	NA	intron (NM_001253718, intron 2 of 19)	intron (NM_001253718, intron 2 of 19)	5833	NM_001253717	74244	Mm.275332	NM_028835	ENSMUSG00000030314	Atg7	1810013K23Rik|Agp7|Apg7l|Atg7l|Gm21553	autophagy related 7	protein-coding
mm_46743.1	chr5	110839758	110839786	-	1	NA	promoter-TSS (NM_016681)	promoter-TSS (NM_016681)	5	NM_153571	100900	Mm.200231	NM_153571	ENSMUSG00000043510	Hscb	AI325508|AW049829|Hsc20	HscB iron-sulfur cluster co-chaperone	protein-coding
mm_56812.1	chr6	116671408	116671430	-	1	NA	intron (NM_178045, intron 1 of 10)	intron (NM_178045, intron 1 of 10)	2417	NM_178045	213391	Mm.257931	NM_178045	ENSMUSG00000042129	Rassf4	3830411C14Rik|AD037|AI586137	Ras association (RalGDS/AF-6) domain family member 4	protein-coding
mm_35086.1	chr4	7898002	7898018	-	1	NA	Intergenic	Intergenic	337322	NR_040645	71510	Mm.410775	NR_040645	ENSMUSG00000086070	8430436N08Rik	-	RIKEN cDNA 8430436N08 gene	ncRNA
mm_146451.1	chr18	86394919	86394929	+	1	NA	promoter-TSS (NM_144946)	promoter-TSS (NM_144946)	-28	NM_144946	246317	Mm.329578	NM_144946	ENSMUSG00000050321	Neto1	AI851453|Btcl1|C130005O10Rik	neuropilin (NRP) and tolloid (TLL)-like 1	protein-coding
mm_115839.1	chr13	21287250	21287251	-	1	NA	3' UTR (NM_010343, exon 5 of 5)	3' UTR (NM_010343, exon 5 of 5)	5436	NM_010343	14780	Mm.1332	NM_010343	ENSMUSG00000004344	Gpx5	AV379049|Arep	glutathione peroxidase 5	protein-coding
mm_18665.1	chr2	70824690	70824694	-	1	NA	intron (NM_172664, intron 1 of 19)	intron (NM_172664, intron 1 of 19)	788	NM_172664	228012	Mm.136511	NM_172664	ENSMUSG00000041997	Tlk1	4930545J15Rik	tousled-like kinase 1	protein-coding
mm_13134.1	chr2	91922179	91922194	+	1	NA	promoter-TSS (NM_007699)	promoter-TSS (NM_007699)	-3	NM_007699	12672	Mm.330405	NM_007699	ENSMUSG00000040495	Chrm4	Chrm-4|M4	cholinergic receptor, muscarinic 4	protein-coding
mm_150902.1	chr19	45575122	45575130	+	1	NA	intron (NM_172639, intron 4 of 5)	intron (NM_172639, intron 4 of 5)	14511	NM_172639	226162	Mm.21978	NM_172639	ENSMUSG00000041035	Dpcd	5330431N19Rik|Ndac	deleted in primary ciliary dyskinesia	protein-coding
mm_33546.1	chr4	130934717	130934721	+	1	NA	3' UTR (NM_010686, exon 8 of 8)	3' UTR (NM_010686, exon 8 of 8)	-9666	NM_010769	17180	Mm.271796	NM_010769	ENSMUSG00000040533	Matn1	CMP|Crtm|Mat1|matrilin-1	matrilin 1, cartilage matrix protein	protein-coding
mm_168905.1	chr12	55155347	55155360	+	1	NA	5' UTR (NM_001100109, exon 1 of 16).2	5' UTR (NM_001100109, exon 1 of 16).2	249	NM_001100109	665155	Mm.12848	NM_001100109	ENSMUSG00000079108	Srp54b	-	signal recognition particle 54B	protein-coding
mm_90380.1	chr10	127266325	127266442	+	1	NA	5' UTR (NM_027151, exon 1 of 14)	5' UTR (NM_027151, exon 1 of 14)	121	NM_001190453	69654	Mm.167537	NM_027151	ENSMUSG00000025410	Dctn2	2310042E05Rik|C130077D06Rik|C87049|DCTN-50|GMP23-48K|RBP50|p50	dynactin 2	protein-coding
mm_88722.1	chr10	80169722	80169725	+	1	NA	intron (NM_007705, intron 1 of 6)	intron (NM_007705, intron 1 of 6)	1882	NM_007705	12696	Mm.17898	NM_007705	ENSMUSG00000045193	Cirbp	Cirp|R74941	cold inducible RNA binding protein	protein-coding
mm_154868.1	chrX	20680046	20680071	+	1	NA	intron (NM_001276316, intron 21 of 26)	intron (NM_001276316, intron 21 of 26)	-7896	NM_001310456	18555	Mm.102574	NM_011049	ENSMUSG00000031065	Cdk16	Crk5|Pctaire1|Pctk1	cyclin-dependent kinase 16	protein-coding
mm_62531.1	chr7	102240205	102240222	+	1	NA	exon (NM_019566, exon 2 of 2)	exon (NM_019566, exon 2 of 2)	9905	NM_019566	56212	Mm.259795	NM_019566	ENSMUSG00000073982	Rhog	2810426G09Rik|Arhg|Sid10750	ras homolog family member G	protein-coding
mm_94038.1	chr10	128058746	128058754	-	1	NA	promoter-TSS (NM_019766)	promoter-TSS (NM_019766)	-232	NM_019766	56351	Mm.305816	NM_019766	ENSMUSG00000071072	Ptges3	5730442A20Rik|Ptges|Tebp|cPGES|p23|sid3177	prostaglandin E synthase 3 (cytosolic)	protein-coding
mm_78288.1	chr9	22196779	22196783	+	1	NA	intron (NM_001033813, intron 1 of 3)	RLTR26_Mus|LTR|ERVK	8615	NM_001033813	619310	Mm.335016	NM_001033813	ENSMUSG00000074472	Zfp872	9530015I07Rik	zinc finger protein 872	protein-coding
mm_147266.1	chr18	38881513	38881519	-	1	NA	intron (NM_010197, intron 1 of 3)	intron (NM_010197, intron 1 of 3)	-10940	NM_001033789	545253	Mm.244585	NM_001033789	ENSMUSG00000036452	Gm5820	EG545253	predicted gene 5820	protein-coding
mm_102465.1	chr11	59948176	59948181	-	1	NA	promoter-TSS (NR_045273)	promoter-TSS (NR_045273)	-31	NR_045273	100504121	Mm.383770	NR_045273	ENSMUSG00000085260	Med9os	1700013G23Rik	mediator complex subunit 9, opposite strand	ncRNA
mm_172779.1	chr8	97429193	97429196	-	1	NA	Intergenic	Intergenic	-883221	NR_039538	100628567		NR_039538	ENSMUSG00000104794	Mir28c	mmu-mir-28c	microRNA 28c	ncRNA
mm_59765.1	chr7	28833968	28833984	+	1	NA	promoter-TSS (NM_010707)	promoter-TSS (NM_010707)	182	NM_010706	16855	Mm.210336	NM_010706	ENSMUSG00000053964	Lgals4	gal-4	lectin, galactose binding, soluble 4	protein-coding
mm_36108.1	chr4	58840744	58840774	-	1	NA	exon (NM_172381, exon 19 of 49)	exon (NM_172381, exon 19 of 49)	-55039	NM_146920	258922	Mm.223327	NM_146920	ENSMUSG00000043385	Olfr267	MOR262-1	olfactory receptor 267	protein-coding
mm_10476.1	chr2	14388435	14388451	+	1	NA	promoter-TSS (NM_001012305)	promoter-TSS (NM_001012305)	45	NM_001012305	277468	Mm.44662	NM_001012305	ENSMUSG00000036949	Slc39a12	AW046938|Gm731	solute carrier family 39 (zinc transporter), member 12	protein-coding
mm_5270.1	chr1	18058789	18058802	-	1	NA	Intergenic	CpG	78256	NM_030033	78081	Mm.319913	NM_030033	ENSMUSG00000025774	Crisp4	9230112K08Rik	cysteine-rich secretory protein 4	protein-coding
mm_86398.1	chr9	123968649	123968680	-	1	NA	promoter-TSS (NM_009912)	promoter-TSS (NM_009912)	28	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_43758.1	chr5	140607335	140607352	+	1	NA	promoter-TSS (NM_008494)	promoter-TSS (NM_008494)	2	NM_008494	16848	Mm.12834	NM_008494	ENSMUSG00000029570	Lfng	AW061165	LFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	protein-coding
mm_151820.1	chr19	5512851	5512876	-	1	NA	Intergenic	Intergenic	-2374	NM_001024560	225861	Mm.20071	NM_001024560	ENSMUSG00000056185	Snx32	B930037P14Rik|Snx6b	sorting nexin 32	protein-coding
mm_146937.1	chr18	32138021	32138027	-	1	NA	intron (NM_001042768, intron 1 of 9)	intron (NM_001042768, intron 1 of 9)	181	NM_008934	19123	Mm.2786	NM_008934	ENSMUSG00000024386	Proc	PC	protein C	protein-coding
mm_123792.1	chr14	70443159	70443177	-	1	NA	promoter-TSS (NR_029802)	promoter-TSS (NR_029802)	59	NM_001164082	67065	Mm.20420	NM_025945	ENSMUSG00000000776	Polr3d	2810426M17Rik|44kDa|AI326118|AW489084|BN51T|RPC4|TSBN51	polymerase (RNA) III (DNA directed) polypeptide D	protein-coding
mm_116304.1	chr13	36734294	36734308	-	1	NA	5' UTR (NM_153529, exon 1 of 3)	5' UTR (NM_153529, exon 1 of 3)	176	NM_153529	68404	Mm.232930	NM_153529	ENSMUSG00000039114	Nrn1	0710008J23Rik|Cpg15|Nrn	neuritin 1	protein-coding
mm_113027.1	chr13	23472986	23472996	+	1	NA	Intergenic	(T)n|Simple_repeat|Simple_repeat	-7090	NM_013483	12231	Mm.1420	NM_013483	ENSMUSG00000000706	Btn1a1	Btn	butyrophilin, subfamily 1, member A1	protein-coding
mm_36040.1	chr4	57241194	57241200	-	1	NA	intron (NM_011207, intron 10 of 25)	intron (NM_011207, intron 10 of 25)	60640	NM_011207	545622	Mm.246552	NM_011207	ENSMUSG00000038764	Ptpn3	9530011I20Rik|PTP-H1|PTPCL	protein tyrosine phosphatase, non-receptor type 3	protein-coding
mm_9302.1	chr1	171639061	171639074	-	1	NA	exon (NM_144539, exon 4 of 8)	exon (NM_144539, exon 4 of 8)	2833	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_73262.1	chr8	104340761	104340771	+	1	NA	exon (NM_024217, exon 1 of 5)	exon (NM_024217, exon 1 of 5)	172	NM_024217	68119	Mm.390108	NM_024217	ENSMUSG00000031875	Cmtm3	9430096L06Rik|AI413895|BNAS2|Cklfsf3	CKLF-like MARVEL transmembrane domain containing 3	protein-coding
mm_78341.1	chr9	25293677	25293767	+	1	NA	exon (NM_001205367, exon 6 of 13)	exon (NM_001205367, exon 6 of 13)	41283	NM_001205367	235072	Mm.270259	NM_009859	ENSMUSG00000001833	Sept7	Cdc10|E430034N22	septin 7	protein-coding
mm_167127.1	chr7	126458607	126458647	-	1	NA	intron (NM_007504, intron 5 of 22)	intron (NM_007504, intron 5 of 22)	4446	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_37734.1	chr4	129575197	129575201	-	1	NA	Intergenic	Intergenic	-1558	NM_001162433	16818	Mm.293753	NM_010693	ENSMUSG00000000409	Lck	Hck-3|Lsk|Lskt|p56<lck>|p56Lck	lymphocyte protein tyrosine kinase	protein-coding
mm_173364.1	chrY	90819836	90819850	+	1	NA	Intergenic	IMPB_01|Satellite|Satellite	19563	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_20690.1	chr2	132792624	132792657	-	1	NA	exon (NM_007694, exon 4 of 5)	exon (NM_007694, exon 4 of 5)	11362	NM_007694	12653	Mm.255241	NM_007694	ENSMUSG00000027350	Chgb	Scg-1	chromogranin B	protein-coding
mm_100141.1	chr11	115982832	115982849	+	1	NA	exon (NM_133663, exon 8 of 39)	exon (NM_133663, exon 8 of 39)	8115	NM_133663	192897	Mm.213873	NM_133663	ENSMUSG00000020758	Itgb4	AA407042|C230078O20|CD104	integrin beta 4	protein-coding
mm_4415.1	chr1	172499917	172499932	+	1	NA	promoter-TSS (NM_178598)	promoter-TSS (NM_178598)	-322	NM_178598	21346	Mm.271711	NM_178598	ENSMUSG00000026547	Tagln2	2700094C18Rik|SM22beta|Sm22B|Sm22a	transgelin 2	protein-coding
mm_28578.1	chr3	93446209	93446218	-	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	3883	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_117098.1	chr13	59822994	59823005	-	1	NA	intron (NM_153538, intron 1 of 27)	CpG	148	NM_153538	214290	Mm.233082	NM_153538	ENSMUSG00000035248	Zcchc6	6030448M23Rik|AA420405	zinc finger, CCHC domain containing 6	protein-coding
mm_103593.1	chr11	78298484	78298488	-	1	NA	Intergenic	Intergenic	-3105	NM_017407	54141	Mm.24250	NM_017407	ENSMUSG00000002055	Spag5	AI874642|D11Bhm180e|Deepest|MAP126|Mastrin|S17	sperm associated antigen 5	protein-coding
mm_39377.1	chr5	12383484	12383543	+	1	NA	5' UTR (NM_028882, exon 1 of 18)	5' UTR (NM_028882, exon 1 of 18)	347	NM_028882	108151	Mm.89313	NM_028882	ENSMUSG00000040254	Sema3d	4631426B19Rik	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D	protein-coding
mm_167865.1	chrX	20708507	20708511	+	1	NA	intron (NM_145628, intron 1 of 20)	intron (NM_145628, intron 1 of 20)	4600	NM_145628	236733	Mm.34489	NM_145628	ENSMUSG00000031066	Usp11	6230415D12Rik|mKIAA4085	ubiquitin specific peptidase 11	protein-coding
mm_151464.1	chr19	58670174	58670207	+	1	NA	promoter-TSS (NM_026925)	promoter-TSS (NM_026925)	-175	NM_026925	69060	Mm.20407	NM_026925	ENSMUSG00000046008	Pnlip	1810007A24Rik|PL|PTL	pancreatic lipase	protein-coding
mm_128822.1	chr15	67128953	67128963	-	1	NA	intron (NM_009177, intron 2 of 8)	intron (NM_009177, intron 2 of 8)	47924	NM_009177	20442	Mm.248334	NM_009177	ENSMUSG00000013846	St3gal1	5330418N22Rik|AI467004|ST3GalI|Siat4|Siat4a|St3gal-1	ST3 beta-galactoside alpha-2,3-sialyltransferase 1	protein-coding
mm_89234.1	chr10	87573849	87573858	+	1	NA	intron (NM_008777, intron 8 of 12)	L2a|LINE|L2	52058	NM_008777	18478	Mm.263539	NM_008777	ENSMUSG00000020051	Pah	AW106920	phenylalanine hydroxylase	protein-coding
mm_83576.1	chr9	48319372	48319376	-	1	NA	3' UTR (NM_030069, exon 6 of 6)	3' UTR (NM_030069, exon 6 of 6)	21524	NM_030069	78252	Mm.31626	NM_030069	ENSMUSG00000032028	Nxpe2	4432416J03Rik|AI323362|Fam55b	neurexophilin and PC-esterase domain family, member 2	protein-coding
mm_143123.1	chr17	57211638	57211656	-	1	NA	exon (NM_009778, exon 29 of 41)	exon (NM_009778, exon 29 of 41)	5581	NR_105944	102465591		NR_105944	ENSMUSG00000099066	Mir6978	Gm27858|mmu-mir-6978	microRNA 6978	ncRNA
mm_53482.1	chr6	134981999	134982002	+	1	NA	promoter-TSS (NM_001109914)	promoter-TSS (NM_001109914)	-1	NM_001109914	381823	Mm.296104	NM_001109914	ENSMUSG00000090698	Apold1	Gm1075	apolipoprotein L domain containing 1	protein-coding
mm_55710.1	chr6	72958451	72958453	-	1	NA	promoter-TSS (NM_025284)	promoter-TSS (NM_025284)	31	NM_025284	19240	Mm.3532	NM_025284	ENSMUSG00000079523	Tmsb10	Ptmb10|Tb10	thymosin, beta 10	protein-coding
mm_47253.1	chr5	121618840	121618862	-	1	NA	promoter-TSS (NM_178799)	promoter-TSS (NM_178799)	87	NM_178799	338350	Mm.482918	NM_178799	ENSMUSG00000042647	Acad12	9330129D05Rik	acyl-Coenzyme A dehydrogenase family, member 12	protein-coding
mm_120343.1	chr14	63607015	63607029	+	1	NA	exon (NM_173393, exon 1 of 3)	exon (NM_173393, exon 1 of 3)	492	NM_173393	219149	Mm.32071	NM_173393	ENSMUSG00000035067	Xkr6	2700008G24Rik|BC024502|Xrg6	X-linked Kx blood group related 6	protein-coding
mm_35593.1	chr4	43010227	43010271	-	1	NA	promoter-TSS (NM_053081)	promoter-TSS (NM_053081)	52	NM_001163233	60534	Mm.23122	NM_053081	ENSMUSG00000028453	Fancg	AU041407|Xrcc9	Fanconi anemia, complementation group G	protein-coding
mm_138691.1	chr17	35979565	35979591	+	1	NA	promoter-TSS (NM_001282024)	promoter-TSS (NM_001282024)	-111	NM_001165892	75210	Mm.40036	NM_145487	ENSMUSG00000038500	Prr3	4930540G07Rik|Cat56	proline-rich polypeptide 3	protein-coding
mm_20133.1	chr2	121380932	121380938	-	1	NA	promoter-TSS (NM_080459)	promoter-TSS (NM_080459)	5	NM_080459	140476	Mm.467475	NM_080459	ENSMUSG00000033498	Strc	DFNB16	stereocilin	protein-coding
mm_156521.1	chrX	150593941	150593945	+	1	NA	intron (NM_008824, intron 1 of 13)	intron (NM_008824, intron 1 of 13)	4022	NM_008824	18639	Mm.249131	NM_008824	ENSMUSG00000025271	Pfkfb1	PFK/FBPase 1	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1	protein-coding
mm_147528.1	chr18	52529921	52529933	-	1	NA	promoter-TSS (NM_010728)	promoter-TSS (NM_010728)	-60	NM_001286182	16948	Mm.172	NM_010728	ENSMUSG00000024529	Lox	AI893619|TSC-160|rrg	lysyl oxidase	protein-coding
mm_92664.1	chr10	80433385	80433418	-	1	NA	5' UTR (NM_011548, exon 1 of 19)	5' UTR (NM_011548, exon 1 of 19)	252	NM_001164150	21423	Mm.3406	NM_011548	ENSMUSG00000020167	Tcf3	A1|AA408400|ALF2|AW209082|E12|E12/E47|E2A|E47|KA1|ME2|Pan1|Pan2|TCF-3|Tcfe2a|VDIR|bHLHb21	transcription factor 3	protein-coding
mm_63641.1	chr7	128542363	128542373	+	1	NA	intron (NM_013863, intron 3 of 3)	intron (NM_013863, intron 3 of 3)	18785	NM_013863	29810	Mm.84073	NM_013863	ENSMUSG00000030847	Bag3	AA407278|Bis|mg638	BCL2-associated athanogene 3	protein-coding
mm_75477.1	chr8	48555271	48555303	-	1	NA	intron (NM_011857, intron 2 of 28)	CpG	119403	NM_001145937	23965	Mm.42191	NM_011857	ENSMUSG00000031561	Tenm3	2610100B16Rik|Odz1|Odz3|Ten-m3|mKIAA1455	teneurin transmembrane protein 3	protein-coding
mm_52917.1	chr6	122850458	122850509	+	1	NA	exon (NM_009779, exon 2 of 2)	exon (NM_009779, exon 2 of 2)	5674	NM_009779	12267	Mm.2408	NM_009779	ENSMUSG00000040552	C3ar1	AZ3B|C3AR|HNFAG09	complement component 3a receptor 1	protein-coding
mm_111802.1	chr12	105010006	105010021	-	1	NA	promoter-TSS (NM_172500)	promoter-TSS (NM_172500)	-204	NM_172500	212073	Mm.212688	NM_172500	ENSMUSG00000054150	Syne3	nesprin-3	spectrin repeat containing, nuclear envelope family member 3	protein-coding
mm_82634.1	chr9	21963544	21963563	-	1	NA	promoter-TSS (NM_010149)	promoter-TSS (NM_010149)	23	NM_010149	13857	Mm.2653	NM_010149	ENSMUSG00000006235	Epor	-	erythropoietin receptor	protein-coding
mm_22582.1	chr3	12855786	12855795	+	1	NA	Intergenic	Intergenic	-615865	NM_178631	76897	Mm.422625	NM_178631	ENSMUSG00000039717	Ralyl	0710005M24Rik	RALY RNA binding protein-like	protein-coding
mm_13520.1	chr2	110011722	110011728	+	1	NA	exon (NM_172671, exon 18 of 18)	exon (NM_172671, exon 18 of 18)	-6092	NM_026613	68201	Mm.181767	NM_026613	ENSMUSG00000027160	Ccdc34	2810027O19Rik|4930522P10Rik|AI596202	coiled-coil domain containing 34	protein-coding
mm_81254.1	chr9	107983040	107983066	+	1	NA	intron (NM_023738, intron 21 of 23)	intron (NM_023738, intron 21 of 23)	2863	NM_026597	68176	Mm.76166	NM_026597	ENSMUSG00000042106	Fam212a	6230427J02Rik|Inka1	family with sequence similarity 212, member A	protein-coding
mm_67143.1	chr7	73422540	73422540	-	1	NA	Intergenic	Intergenic	-46766	NR_040324	319783	Mm.349813	NR_040324	ENSMUSG00000097756	A730056A06Rik	C76391	RIKEN cDNA A730056A06 gene	ncRNA
mm_20503.1	chr2	130424674	130424728	-	1	NA	promoter-TSS (NM_178762)	promoter-TSS (NM_178762)	-60	NM_001114541	319513	Mm.482539	NM_178762	ENSMUSG00000037773	Pced1a	A930025D01Rik|AI480484|Fam113a	PC-esterase domain containing 1A	protein-coding
mm_83697.1	chr9	50617429	50617467	-	1	NA	promoter-TSS (NM_001134902)	promoter-TSS (NM_001134902)	16	NM_001134902	270156	Mm.335149	NM_212449	ENSMUSG00000059820	AU019823	Gm639	expressed sequence AU019823	protein-coding
mm_69285.1	chr7	128203320	128203332	-	1	NA	promoter-TSS (NR_045183)	promoter-TSS (NR_045183)	2	NR_045183	70973	Mm.441564	NR_045183	ENSMUSG00000108354	4931431B13Rik	1700108I23Rik|AA536668	RIKEN cDNA 4931431B13 gene	ncRNA
mm_64651.1	chr7	4120066	4120077	-	1	NA	non-coding (NR_033568, exon 1 of 9)	non-coding (NR_033568, exon 1 of 9)	541	NM_001001454	57776	Mm.29729	NM_021324	ENSMUSG00000030428	Ttyh1	4930459B04Rik|6330408P11Rik|TTY1|mTTY1|tty	tweety family member 1	protein-coding
mm_43899.1	chr5	144220261	144220301	+	1	NA	intron (NM_027410, intron 1 of 24)	PB1D10|SINE|Alu	3297	NM_027410	70381	Mm.239412	NM_027410	ENSMUSG00000066621	Tecpr1	2210010N04Rik|mKIAA1358	tectonin beta-propeller repeat containing 1	protein-coding
mm_24330.1	chr3	89459298	89459321	+	1	NA	promoter-TSS (NM_027348)	promoter-TSS (NM_027348)	191	NM_026784	68603	Mm.34242	NM_026784	ENSMUSG00000027952	Pmvk	1110011E12Rik|2900002L22Rik|AV001327|PMK|PMKA|PMKASE	phosphomevalonate kinase	protein-coding
mm_52539.1	chr6	115931923	115931937	+	1	NA	promoter-TSS (NM_145383)	promoter-TSS (NM_145383)	3	NM_145383	212541	Mm.2965	NM_145383	ENSMUSG00000030324	Rho	Noerg1|Opn2|Ops|RP4	rhodopsin	protein-coding
mm_57811.1	chr6	129451907	129451917	-	1	NA	promoter-TSS (NM_175526)	promoter-TSS (NM_175526)	88	NM_175526	243653	Mm.131289	NM_175526	ENSMUSG00000033082	Clec1a	5930406N14Rik	C-type lectin domain family 1, member a	protein-coding
mm_18650.1	chr2	69713488	69713526	-	1	NA	promoter-TSS (NM_177244)	promoter-TSS (NM_177244)	-901	NM_177244	320720	Mm.289566	NM_177244	ENSMUSG00000027086	Fastkd1	5330408N05Rik|mKIAA1800	FAST kinase domains 1	protein-coding
mm_153067.1	chr19	32211017	32211036	-	1	NA	promoter-TSS (NM_001168526)	promoter-TSS (NM_001168526)	-13	NM_001168526	208449	Mm.329810	NM_144792	ENSMUSG00000040451	Sgms1	9530058O11Rik|AI841905|C80702|Mob|Sms1|Sor1|Tmem23	sphingomyelin synthase 1	protein-coding
mm_61143.1	chr7	57590504	57590523	+	1	NA	promoter-TSS (NM_001038701)	promoter-TSS (NM_001038701)	-5	NM_001038701	14402	Mm.8004	NM_008071	ENSMUSG00000033676	Gabrb3	A230092K12Rik|AW049585|Cp1|Gabrb-3|beta3	gamma-aminobutyric acid (GABA) A receptor, subunit beta 3	protein-coding
mm_78185.1	chr9	21233510	21233520	+	1	NA	exon (NM_016679, exon 2 of 5)	exon (NM_016679, exon 2 of 5)	5817	NM_016679	50868	Mm.248266	NM_016679	ENSMUSG00000003308	Keap1	INRF2|mKIAA0132	kelch-like ECH-associated protein 1	protein-coding
mm_51850.1	chr6	90369487	90369657	+	1	NA	promoter-TSS (NM_173002)	promoter-TSS (NM_173002)	78	NM_030260	80292	Mm.100116	NM_030260	ENSMUSG00000034430	Zxdc	A930012H20|B930086F11Rik|BC003332	ZXD family zinc finger C	protein-coding
mm_27300.1	chr3	48609081	48609111	-	1	NA	promoter-TSS (NR_003617)	promoter-TSS (NR_003617)	4	NR_003617	66332	Mm.46124	NM_025493		1700018B24Rik	-	enhancer of rudimentary homolog pseudogene	pseudo
mm_114411.1	chr13	64275121	64275131	+	1	NA	promoter-TSS (NM_172587)	promoter-TSS (NM_172587)	-138	NM_172587	218294	Mm.25335	NM_172587	ENSMUSG00000033102	Cdc14b	2810432N10Rik|A530086E13Rik|AA472821|CDC14B3|Cdc14B1	CDC14 cell division cycle 14B	protein-coding
mm_57541.1	chr6	126644808	126644827	-	1	NA	5' UTR (NM_010595, exon 1 of 2)	5' UTR (NM_010595, exon 1 of 2)	984	NM_010595	16485	Mm.40424	NM_010595	ENSMUSG00000047976	Kcna1	AI840627|Kca1-1|Kv1.1|MBK1|Mk-1|Shak|mceph	potassium voltage-gated channel, shaker-related subfamily, member 1	protein-coding
mm_77003.1	chr8	107403198	107403213	-	1	NA	promoter-TSS (NM_008706)	promoter-TSS (NM_008706)	0	NM_008706	18104	Mm.252	NM_008706	ENSMUSG00000003849	Nqo1	AV001255|Dia4|Dtd|Nmo-1|Nmo1|Nmor1|Ox-1|Ox1|Qr1	NAD(P)H dehydrogenase, quinone 1	protein-coding
mm_22480.1	chr3	5221049	5221069	+	1	NA	promoter-TSS (NR_045905)	promoter-TSS (NR_045905)	-236	NR_045905	72608	Mm.384359	NR_045905		2700069I18Rik	-	RIKEN cDNA 2700069I18 gene	ncRNA
mm_166594.1	chr6	60486016	60486017	+	1	NA	Intergenic	Intergenic	-82309	NR_015565	208079	Mm.131226	NM_177329	ENSMUSG00000046764	A530053G22Rik	-	RIKEN cDNA A530053G22 gene	ncRNA
mm_136213.1	chr16	89897310	89897335	-	1	NA	intron (NM_009384, intron 4 of 27)	intron (NM_009384, intron 4 of 27)	63505	NM_009384	21844	Mm.310902	NM_009384	ENSMUSG00000002489	Tiam1	AI847750|D16Ium10|D16Ium10e	T cell lymphoma invasion and metastasis 1	protein-coding
mm_160710.1	chr10	59458145	59458145	-	1	NA	intron (NM_001033259, intron 4 of 7)	intron (NM_001033259, intron 4 of 7)	-16366	NM_010959	18302	Mm.123013	NM_010959	ENSMUSG00000009654	Oit3	EF-9|LZP	oncoprotein induced transcript 3	protein-coding
mm_13983.1	chr2	121506749	121506792	+	1	NA	promoter-TSS (NM_030234)	promoter-TSS (NM_030234)	47	NM_001290986	241627	Mm.293284	NM_030234	ENSMUSG00000027242	Wdr76	5830411K18Rik|6030457D09|AA517836	WD repeat domain 76	protein-coding
mm_152962.1	chr19	29361831	29361894	-	1	NA	promoter-TSS (NM_026362)	promoter-TSS (NM_026362)	9	NM_026362	67759	Mm.275511	NM_026362	ENSMUSG00000016495	Plgrkt	1110007H22Rik|5033414D02Rik|AI852040|Plg-R(KT)|Plg-RKT	plasminogen receptor, C-terminal lysine transmembrane protein	protein-coding
mm_58934.1	chr7	18011291	18011308	+	1	NA	exon (NM_027210, exon 2 of 4)	exon (NM_027210, exon 2 of 4)	1410	NM_028171	69785	Mm.46086	NM_027210	ENSMUSG00000057195	Ceacam13	1600012K03Rik|1600025J19Rik	carcinoembryonic antigen-related cell adhesion molecule 13	protein-coding
mm_51780.1	chr6	88193718	88193723	+	1	NA	Intergenic	CpG	-4944	NM_008090	14461	Mm.491156	NM_008090	ENSMUSG00000015053	Gata2	Gata-2	GATA binding protein 2	protein-coding
mm_19633.1	chr2	102814024	102814034	-	1	NA	3' UTR (NM_009851, exon 19 of 19)	3' UTR (NM_009851, exon 19 of 19)	87636	NM_001177785	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_148026.1	chr18	69415649	69415653	-	1	NA	intron (NM_013685, intron 3 of 19)	intron (NM_013685, intron 3 of 19)	69930	NM_001083967	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding
mm_85122.1	chr9	95474465	95474485	-	1	NA	exon (NM_001114977, exon 23 of 28)	exon (NM_001114977, exon 23 of 28)	37521	NM_026476	67958	Mm.292742	NM_026476	ENSMUSG00000032407	U2surp	2610101N10Rik|AU023006|Sr140	U2 snRNP-associated SURP domain containing	protein-coding
mm_27736.1	chr3	69071548	69071551	-	1	NA	TTS (NM_008467)	TTS (NM_008467)	-26807	NM_025863	66949	Mm.176695	NM_025863	ENSMUSG00000034317	Trim59	2310035M22Rik|2700022F13Rik|Mrf1|TSBF1	tripartite motif-containing 59	protein-coding
mm_48147.1	chr5	137150823	137150836	-	1	NA	Intergenic	(TGG)n|Simple_repeat|Simple_repeat	-34622	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_119105.1	chr14	30951488	30951510	+	1	NA	5' UTR (NM_001308328, exon 1 of 14)	5' UTR (NM_001308328, exon 1 of 14)	122	NM_011849	23955	Mm.251494	NM_011849	ENSMUSG00000021918	Nek4	Stk2	NIMA (never in mitosis gene a)-related expressed kinase 4	protein-coding
mm_101995.1	chr11	50953746	50953768	-	1	NA	promoter-TSS (NM_008936)	promoter-TSS (NM_008936)	-125	NM_008936	19127	Mm.1386	NM_008936	ENSMUSG00000044542	Prop1	Prop-1|df	paired like homeodomain factor 1	protein-coding
mm_67010.1	chr7	65370875	65370884	-	1	NA	5' UTR (NM_001163574, exon 1 of 27)	5' UTR (NM_001163574, exon 1 of 27)	365	NM_001163574	21872	Mm.4342	NM_009386	ENSMUSG00000030516	Tjp1	ZO1	tight junction protein 1	protein-coding
mm_121979.1	chr14	25855315	25855333	-	1	NA	intron (NM_013469, intron 1 of 14)	intron (NM_013469, intron 1 of 14)	13169	NM_013469	11744	Mm.294083	NM_013469	ENSMUSG00000021866	Anxa11	A830099O17Rik|Anx11	annexin A11	protein-coding
mm_57364.1	chr6	124768331	124768380	-	1	NA	intron (NM_001302642, intron 1 of 9)	intron (NM_001302642, intron 1 of 9)	1318	NM_001302642	13807	Mm.3913	NM_013509	ENSMUSG00000004267	Eno2	AI837106|D6Ertd375e|Eno-2|NSE	enolase 2, gamma neuronal	protein-coding
mm_41185.1	chr5	88327805	88327820	+	1	NA	exon (NM_008644, exon 3 of 3)	exon (NM_008644, exon 3 of 3)	10500	NM_008644	17830	Mm.200411	NM_008644	ENSMUSG00000064156	Prol1	Muc10	proline rich, lacrimal 1	protein-coding
mm_141093.1	chr17	25985642	25985772	-	1	NA	5' UTR (NM_001347334, exon 1 of 12)	5' UTR (NM_001347334, exon 1 of 12)	167	NM_001347334	50817	Mm.216072	NM_015830	ENSMUSG00000037326	Capn15	Solh	calpain 15	protein-coding
mm_103177.1	chr11	70459926	70459949	-	1	NA	promoter-TSS (NM_023158)	promoter-TSS (NM_023158)	47	NM_023158	66102	Mm.425692	NM_023158	ENSMUSG00000018920	Cxcl16	0910001K24Rik|AV290116|BB024863|CXCL16v1|CXCL16v2|SR-PSOX|Zmynd15|b2b498Clo	chemokine (C-X-C motif) ligand 16	protein-coding
mm_84020.1	chr9	57681799	57681809	-	1	NA	exon (NM_009993, exon 2 of 7)	exon (NM_009993, exon 2 of 7)	1851	NM_009993	13077	Mm.15537	NM_009993	ENSMUSG00000032310	Cyp1a2	CP12|Cyp1a1|P450-3	cytochrome P450, family 1, subfamily a, polypeptide 2	protein-coding
mm_77649.1	chr8	124563931	124563938	-	1	NA	exon (NM_007428, exon 2 of 5)	exon (NM_007428, exon 2 of 5)	5773	NM_007428	11606	Mm.301626	NM_007428	ENSMUSG00000031980	Agt	AI265500|AngI|AngII|Aogen|Serpina8	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	protein-coding
mm_54553.1	chr6	37138928	37138936	-	1	NA	intron (NM_001347104, intron 2 of 32)	intron (NM_001347104, intron 2 of 32)	161044	NM_001081206	320127	Mm.119469	NM_001081206	ENSMUSG00000038665	Dgki	C130010K08Rik	diacylglycerol kinase, iota	protein-coding
mm_79987.1	chr9	67011923	67011925	+	1	NA	Intergenic	Intergenic	31947	NM_001164252	22003	Mm.121878	NM_024427	ENSMUSG00000032366	Tpm1	AA986836|AI854628|TM2|Tm3|Tmpa|Tpm-1|alpha-TM	tropomyosin 1, alpha	protein-coding
mm_172986.1	chrM	1115	1116	+	1	NA	NA	Intergenic	NA	NA								
mm_108629.1	chr12	85614388	85614390	+	1	NA	intron (NM_001205052, intron 2 of 3)	intron (NM_001205052, intron 2 of 3)	14371	NM_001205053	81703	Mm.103560	NM_030887	ENSMUSG00000034271	Jdp2	Jundm2|Jundp2|TIF	Jun dimerization protein 2	protein-coding
mm_48619.1	chr5	144890233	144890244	-	1	NA	intron (NM_001038627, intron 10 of 17)	intron (NM_001038627, intron 10 of 17)	6578	NR_106006	102465629		NR_106006	ENSMUSG00000098822	Mir7039	Gm27824|mmu-mir-7039	microRNA 7039	ncRNA
mm_9776.1	chr1	181101572	181101595	-	1	NA	exon (NM_026171, exon 19 of 23)	exon (NM_026171, exon 19 of 23)	42621	NM_026171	67459	Mm.263464	NM_026171	ENSMUSG00000026516	Nvl	1200009I24Rik	nuclear VCP-like	protein-coding
mm_37685.1	chr4	129227858	129227879	-	1	NA	promoter-TSS (NM_001285866)	promoter-TSS (NM_001285866)	43	NM_001285866	97130	Mm.331907	NM_001033189	ENSMUSG00000050390	C77080	Kiaa1522|mKIAA1522	expressed sequence C77080	protein-coding
mm_34331.1	chr4	142164617	142164656	+	1	NA	intron (NM_144531, intron 1 of 13)	RMER17C|LTR|ERVK	45572	NM_144531	71529	Mm.255986	NM_144531	ENSMUSG00000040606	Kazn	2310007B04Rik|9030409G11Rik|AI256607|AI666764|AW061099|Kaz|Kazrin	kazrin, periplakin interacting protein	protein-coding
mm_5265.1	chr1	17097709	17097713	-	1	NA	5' UTR (NM_020604, exon 1 of 5)	5' UTR (NM_020604, exon 1 of 5)	178	NM_020604	57339	Mm.143761	NM_020604	ENSMUSG00000042686	Jph1	ENSMUSG00000054314|JP-1|Jp1	junctophilin 1	protein-coding
mm_147311.1	chr18	40923844	40923864	-	1	NA	Intergenic	Lx9|LINE|L1	665493	NM_026135	383348	Mm.76366	NM_026135	ENSMUSG00000051401	Kctd16	4930434H12Rik|Gm1267	potassium channel tetramerisation domain containing 16	protein-coding
mm_124120.1	chr14	79526223	79526239	-	1	NA	intron (NM_001286411, intron 1 of 8)	intron (NM_001286411, intron 1 of 8)	10557	NM_001286411	13709	Mm.20938	NM_007920	ENSMUSG00000036461	Elf1	Elf-1|Sts1|mElf-1|p70	E74-like factor 1	protein-coding
mm_146125.1	chr18	74442655	74442664	+	1	NA	promoter-TSS (NM_201600)	promoter-TSS (NM_201600)	40	NM_201600	17919	Mm.260098	NM_008661	ENSMUSG00000025885	Myo5b	AI661750|mKIAA1119	myosin VB	protein-coding
mm_161579.1	chr16	26991640	26991640	-	1	NA	promoter-TSS (NM_001285918)	promoter-TSS (NM_001285918)	12	NM_001013761	239789	Mm.326909	NM_001013761	ENSMUSG00000068428	Gmnc	Gemc1|Gm1778|Gm606	geminin coiled-coil domain containing	protein-coding
mm_155331.1	chrX	65517128	65517133	+	1	NA	Intergenic	Intergenic	469486	NM_027302	70062	Mm.45791	NM_027302	ENSMUSG00000031181	Ctag2	1700030B21Rik	cancer/testis antigen 2	protein-coding
mm_119618.1	chr14	51128906	51128926	+	1	NA	promoter-TSS (NM_030098)	promoter-TSS (NM_030098)	-152	NM_030098	78416	Mm.103835	NM_030098	ENSMUSG00000021880	Rnase6	9530043P15Rik|BB119466	ribonuclease, RNase A family, 6	protein-coding
mm_41365.1	chr5	90508744	90508746	+	1	NA	3' UTR (NM_007423, exon 15 of 15)	3' UTR (NM_007423, exon 15 of 15)	-10204	NM_145146	280662	Mm.348786	NM_145146	ENSMUSG00000029369	Afm	Alf|alpha-Alb	afamin	protein-coding
mm_41506.1	chr5	92347842	92347851	+	1	NA	exon (NM_021274, exon 3 of 4)	exon (NM_021274, exon 3 of 4)	1043	NM_021274	15945	Mm.877	NM_021274	ENSMUSG00000034855	Cxcl10	C7|CRG-2|INP10|IP-10|IP10|Ifi10|Scyb10|gIP-10|mob-1	chemokine (C-X-C motif) ligand 10	protein-coding
mm_161395.1	chr14	103650375	103650375	+	1	NA	exon (NM_198014, exon 1 of 7)	exon (NM_198014, exon 1 of 7)	132	NM_198014	105439	Mm.27548	NM_198014	ENSMUSG00000055717	Slain1	9630044O09Rik|AA675320|AW742596	SLAIN motif family, member 1	protein-coding
mm_38140.1	chr4	134762492	134762505	-	1	NA	intron (NM_145554, intron 1 of 8)	intron (NM_145554, intron 1 of 8)	5506	NM_145554	100017	Mm.27486	NM_145554	ENSMUSG00000037295	Ldlrap1	AA691260|ARH2|Arh|Arh1|FHCB1|FHCB2	low density lipoprotein receptor adaptor protein 1	protein-coding
mm_117881.1	chr13	99087903	99087926	-	1	NA	promoter-TSS (NR_045495)	promoter-TSS (NR_045495)	7	NR_045495	69603	Mm.390632	NR_045495	ENSMUSG00000100410	2310020H05Rik	-	RIKEN cDNA 2310020H05 gene	ncRNA
mm_68527.1	chr7	112535561	112535577	-	1	NA	intron (NM_020606, intron 1 of 12)	intron (NM_020606, intron 1 of 12)	107863	NM_020606	57342	Mm.143763	NM_020606	ENSMUSG00000030770	Parva	2010012A22Rik|5430400F08Rik|AI225929|AU042898|Actp|CH-ILKBP|Parvin	parvin, alpha	protein-coding
mm_97332.1	chr11	77216181	77216279	+	1	NA	promoter-TSS (NM_177710)	promoter-TSS (NM_177710)	-195	NM_177710	237860	Mm.440381	NM_177710	ENSMUSG00000037926	Ssh2	SSH-2|SSH-2L|mSSH-2L	slingshot homolog 2 (Drosophila)	protein-coding
mm_103615.1	chr11	78550759	78550771	-	1	NA	promoter-TSS (NM_133706)	promoter-TSS (NM_133706)	-30	NM_133706	69071	Mm.29431	NM_133706	ENSMUSG00000037278	Tmem97	1810014L12Rik|AI115531|AL022956|D11Bhm182e	transmembrane protein 97	protein-coding
mm_24281.1	chr3	89229047	89229066	+	1	NA	promoter-TSS (NM_013605)	promoter-TSS (NM_013605)	0	NM_013605	17829	Mm.16193	NM_013605	ENSMUSG00000042784	Muc1	CD227|EMA|Muc-1	mucin 1, transmembrane	protein-coding
mm_155570.1	chrX	77510878	77510897	+	1	NA	promoter-TSS (NM_020601)	promoter-TSS (NM_020601)	-340	NM_020601	21372	Mm.258476	NM_020601	ENSMUSG00000025246	Tbl1x	5330429M20|Tbl1	transducin (beta)-like 1 X-linked	protein-coding
mm_99317.1	chr11	101442380	101442395	+	1	NA	5' UTR (NM_011289, exon 1 of 5)	5' UTR (NM_011289, exon 1 of 5)	142	NM_011289	19942	Mm.340658	NM_011289	ENSMUSG00000063316	Rpl27	-	ribosomal protein L27	protein-coding
mm_120517.1	chr14	66728888	66728908	+	1	NA	intron (NM_013461, intron 3 of 3)	intron (NM_013461, intron 3 of 3)	93647	NM_001271760	11549	Mm.57064	NM_013461	ENSMUSG00000045875	Adra1a	Adra1c	adrenergic receptor, alpha 1a	protein-coding
mm_92740.1	chr10	80939805	80939809	-	1	NA	Intergenic	Intergenic	9716	NM_008655	17873	Mm.1360	NM_008655	ENSMUSG00000015312	Gadd45b	AI323528|Myd118	growth arrest and DNA-damage-inducible 45 beta	protein-coding
mm_90745.1	chr10	5368506	5368527	-	1	NA	intron (NM_001347732, intron 13 of 145)	intron (NM_001347732, intron 13 of 145)	119798	NM_001347711	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_105646.1	chr11	107131944	107131954	-	1	NA	promoter-TSS (NM_176850)	promoter-TSS (NM_176850)	-27	NM_176850	207165	Mm.343986	NM_176850	ENSMUSG00000040481	Bptf	9430093H17Rik|Falz	bromodomain PHD finger transcription factor	protein-coding
mm_161156.1	chr13	24801527	24801527	+	1	NA	promoter-TSS (NM_024473)	promoter-TSS (NM_024473)	-130	NM_024473	79555	Mm.266668	NM_024473	ENSMUSG00000019132	BC005537	8030460C05Rik|C78201	cDNA sequence BC005537	protein-coding
mm_38412.1	chr4	139109294	139109294	-	1	NA	intron (NM_001163006, intron 1 of 3)	intron (NM_001163006, intron 1 of 3)	-16324	NM_008675	17965	Mm.9404	NM_008675	ENSMUSG00000041120	Nbl1	D4H1S1733E|DAN|Dana|NO3	neuroblastoma, suppression of tumorigenicity 1	protein-coding
mm_76926.1	chr8	105936893	105936946	-	1	NA	exon (NM_013640, exon 5 of 8)	exon (NM_013640, exon 5 of 8)	1473	NM_013640	19171	Mm.787	NM_013640	ENSMUSG00000031897	Psmb10	Mecl-1|Mecl1	proteasome (prosome, macropain) subunit, beta type 10	protein-coding
mm_145954.1	chr18	67641632	67641642	+	1	NA	promoter-TSS (NM_001081073)	promoter-TSS (NM_001081073)	38	NM_134138	107047	Mm.150701	NM_134138	ENSMUSG00000024537	Psmg2	1700017I17Rik|AW545363|Clast3|Tnfsf5ip1	proteasome (prosome, macropain) assembly chaperone 2	protein-coding
mm_115291.1	chr13	111978000	111978008	+	1	NA	Intergenic	CpG	110068	NR_130345	102636620	Mm.402328	NR_130345	ENSMUSG00000086111	Gm15326	OTTMUSG00000020187	predicted gene 15326	ncRNA
mm_102244.1	chr11	55078076	55078119	-	1	NA	promoter-TSS (NM_177471)	promoter-TSS (NM_177471)	34	NM_177471	52570	Mm.22361	NM_177471	ENSMUSG00000049588	Ccdc69	2210021E03Rik|D11Ertd461e	coiled-coil domain containing 69	protein-coding
mm_142752.1	chr17	48451534	48451536	-	1	NA	promoter-TSS (NM_027292)	promoter-TSS (NM_027292)	-34	NM_027292	70026	Mm.22613	NM_027292	ENSMUSG00000023995	Tspo2	2510027D20Rik|Bzrpl1	translocator protein 2	protein-coding
mm_170401.1	chr18	6387629	6387647	+	1	NA	Intergenic	RLTR9E|LTR|ERVK	103008	NR_035446	100316773		NR_035446	ENSMUSG00000084514	Mir1893	Mirn1893|mmu-mir-1893	microRNA 1893	ncRNA
mm_57154.1	chr6	122730121	122730132	-	1	NA	exon (NM_011401, exon 10 of 10)	exon (NM_011401, exon 10 of 10)	12619	NM_011401	20527	Mm.395108	NM_011401	ENSMUSG00000003153	Slc2a3	AA408729|AL023014|AL024341|AU040424|C78366|Glut-3|Glut3	solute carrier family 2 (facilitated glucose transporter), member 3	protein-coding
mm_103629.1	chr11	78935467	78935477	-	1	NA	exon (NM_010927, exon 6 of 27)	exon (NM_010927, exon 6 of 27)	10181	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_91407.1	chr10	31390454	31390459	-	1	NA	intron (NM_009413, intron 1 of 6)	intron (NM_009413, intron 1 of 6)	23979	NM_011509	100041294	Mm.7821	NM_011509		Supt4b	Gm3258|Supt4h1b|Supt4h2	suppressor of Ty 4B	protein-coding
mm_42799.1	chr5	121712040	121712050	+	1	NA	exon (NM_009125, exon 1 of 25)	exon (NM_009125, exon 1 of 25)	436	NM_009125	20239	Mm.260900	NM_009125	ENSMUSG00000042605	Atxn2	9630045M23Rik|ATX2|AW544490|Sca2	ataxin 2	protein-coding
mm_82064.1	chr9	122747262	122747264	+	1	NA	promoter-TSS (NM_001199736)	promoter-TSS (NM_001199736)	-83	NM_001199736	671232	Mm.296421	NM_001199736	ENSMUSG00000094985	Topaz1	Gm9524	testis and ovary specific PAZ domain containing 1	protein-coding
mm_137815.1	chr17	30060343	30060359	+	1	NA	intron (NM_148926, intron 1 of 4)	intron (NM_148926, intron 1 of 4)	55264	NM_148926	21769	Mm.220972	NM_148926	ENSMUSG00000044477	Zfand3	AW539211|TEG-27|Tex27	zinc finger, AN1-type domain 3	protein-coding
mm_35876.1	chr4	49536817	49536849	-	1	NA	exon (NM_144903, exon 9 of 9)	exon (NM_144903, exon 9 of 9)	12713	NM_144903	230163	Mm.482116	NM_144903	ENSMUSG00000028307	Aldob	Aldo-2|Aldo2|BC016435	aldolase B, fructose-bisphosphate	protein-coding
mm_84689.1	chr9	72174988	72175004	-	1	NA	Intergenic	Intergenic	-63177	NM_001253865	21406	Mm.171615	NM_011544	ENSMUSG00000032228	Tcf12	A130037E08Rik|ALF1|HEB|HEBAlt|HTF-4|HTF4|ME1|REB|bHLHb20	transcription factor 12	protein-coding
mm_108256.1	chr12	78350907	78350929	+	1	NA	intron (NM_145965, intron 2 of 22)	LSU-rRNA_Hsa|rRNA|rRNA	124263	NM_145965	268566	Mm.341742	NM_145965	ENSMUSG00000047454	Gphn	5730552E08Rik|AI662856|BC027112|C230040D23|GPH|GPHRYN|geph	gephyrin	protein-coding
mm_62961.1	chr7	119760944	119760963	+	1	NA	promoter-TSS (NM_016870)	promoter-TSS (NM_016870)	30	NM_212442	20216	Mm.334199	NM_016870	ENSMUSG00000030935	Acsm3	Sa|Sah	acyl-CoA synthetase medium-chain family member 3	protein-coding
mm_109482.1	chr12	111429159	111429172	+	1	NA	intron (NM_001289487, intron 12 of 13)	intron (NM_001289487, intron 12 of 13)	11720	NM_001289488	74190	Mm.248640	NM_028807	ENSMUSG00000021280	Exoc3l4	1200009I06Rik|1600013K19Rik	exocyst complex component 3-like 4	protein-coding
mm_173032.1	chrX	105876892	105876894	-	1	NA	exon (NM_009530, exon 9 of 35)	exon (NM_009530, exon 9 of 35)	52479	NM_009530	22589	Mm.10141	NM_009530	ENSMUSG00000031229	Atrx	4833408C14Rik|AI447451|ATR2|DXHXS6677E|HP1-BP38|Hp1bp2|Hp1bp38|MRXS3|RAD54L|Rad54|XH2|Xnp|ZNF-HX	alpha thalassemia/mental retardation syndrome X-linked	protein-coding
mm_142065.1	chr17	35680728	35680744	-	1	NA	TTS (NM_001198833)	TTS (NM_001198833)	-6993	NM_010364	14885	Mm.10182	NM_010364	ENSMUSG00000001524	Gtf2h4	AW545633|BTF2 p52|p52	general transcription factor II H, polypeptide 4	protein-coding
mm_85677.1	chr9	107770952	107771007	-	1	NA	promoter-TSS (NM_148930)	promoter-TSS (NM_148930)	23	NM_148930	83486	Mm.259197	NM_148930	ENSMUSG00000032580	Rbm5	D030069N10Rik	RNA binding motif protein 5	protein-coding
mm_40776.1	chr5	67260795	67260814	+	1	NA	5' UTR (NM_030108, exon 1 of 9)	5' UTR (NM_030108, exon 1 of 9)	239	NM_030108	67878	Mm.23217	NM_028975	ENSMUSG00000037720	Tmem33	1110006G02Rik|1600019D15Rik|2410089A21Rik|2700052H22Rik|5430406L04Rik|AA388285|AI314185|AI426615|db83	transmembrane protein 33	protein-coding
mm_147706.1	chr18	60811883	60811917	-	1	NA	promoter-TSS (NR_039567)	promoter-TSS (NR_039567)	-176	NR_039567	100628611		NR_039567	ENSMUSG00000093327	Mir5107	mir-5107|mmu-mir-5107|mu-mir-5107	microRNA 5107	ncRNA
mm_70511.1	chr8	12931673	12931711	+	1	NA	intron (NM_178076, intron 1 of 30)	intron (NM_178076, intron 1 of 30)	15799	NM_178076	17207	Mm.334413	NM_178076	ENSMUSG00000031442	Mcf2l	C130040G20Rik|Dbs|Ost|mKIAA0362	mcf.2 transforming sequence-like	protein-coding
mm_73489.1	chr8	107056871	107056913	+	1	NA	promoter-TSS (NM_139229)	promoter-TSS (NM_139229)	15	NR_028367	66164	Mm.334789	NM_025391	ENSMUSG00000031917	Nip7	1110017C15Rik|6330509M23Rik|AA408773|AA410017|PEachy	NIP7, nucleolar pre-rRNA processing protein	protein-coding
mm_45484.1	chr5	70960503	70960546	-	1	NA	TTS (NM_008066)	TTS (NM_008066)	-117907	NM_010252	14405	Mm.255292	NM_010252	ENSMUSG00000001260	Gabrg1	GabaA|GabaA/BZ	gamma-aminobutyric acid (GABA) A receptor, subunit gamma 1	protein-coding
mm_40719.1	chr5	65955674	65955680	+	1	NA	Intergenic	Intergenic	-11447	NM_001081104	231252	Mm.140015	NM_001081104	ENSMUSG00000029205	Chrna9	2410015I05Rik|Acra9|EG666827|Gm8311	cholinergic receptor, nicotinic, alpha polypeptide 9	protein-coding
mm_172520.1	chr7	81151310	81151318	-	1	NA	intron (NM_001004184, intron 10 of 17)	LTRIS_Mus|LTR|ERV1	36515	NM_001004184	434203	Mm.389909	NM_001004184	ENSMUSG00000025726	Slc28a1	Cnt1	solute carrier family 28 (sodium-coupled nucleoside transporter), member 1	protein-coding
mm_66507.1	chr7	45092199	45092209	-	1	NA	promoter-TSS (NM_026555)	promoter-TSS (NM_026555)	9	NM_026555	52377	Mm.29997	NM_026555	ENSMUSG00000019539	Rcn3	6030455P07Rik|D530026G20Rik|D7Ertd671e|RLP49	reticulocalbin 3, EF-hand calcium binding domain	protein-coding
mm_106882.1	chr12	8011777	8011785	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	34104	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_23658.1	chr3	68046839	68046841	+	1	NA	intron (NM_001113419, intron 2 of 10)	intron (NM_001113419, intron 2 of 10)	-17962	NM_001113421	30953	Mm.331064	NM_013928	ENSMUSG00000027777	Schip1	Nf2ip|Schip-1	schwannomin interacting protein 1	protein-coding
mm_161453.1	chr15	75268421	75268421	+	1	NA	promoter-TSS (NM_008530)	promoter-TSS (NM_008530)	0	NM_008530	17071	Mm.377095	NM_008530	ENSMUSG00000022583	Ly6f	-	lymphocyte antigen 6 complex, locus F	protein-coding
mm_111122.1	chr12	81287111	81287111	-	1	NA	intron (NM_080440, intron 2 of 7)	intron (NM_080440, intron 2 of 7)	46069	NM_001167920	110893	Mm.443748	NM_080440	ENSMUSG00000079055	Slc8a3	AW742262|Ncx3	solute carrier family 8 (sodium/calcium exchanger), member 3	protein-coding
mm_160781.1	chr10	127454633	127454633	+	1	NA	exon (NM_001168293, exon 5 of 24)	exon (NM_001168293, exon 5 of 24)	33766	NM_001168293	71750	Mm.29342	NM_027900	ENSMUSG00000025404	R3hdm2	1300003K24Rik|AU041262|mKIAA1002	R3H domain containing 2	protein-coding
mm_35690.1	chr4	44072713	44072731	-	1	NA	promoter-TSS (NM_001190414)	promoter-TSS (NM_001190414)	-49	NM_001190414	50798	Mm.256718	NM_015828	ENSMUSG00000028479	Gne	2310066H07Rik|DMRV|GLCNE|IBM2|NM|Uae1	glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase	protein-coding
mm_151420.1	chr19	56758268	56758279	+	1	NA	Intergenic	B4A|SINE|B4	35901	NM_007419	11554	Mm.46797	NM_007419	ENSMUSG00000035283	Adrb1	Adrb-1|beta-AR	adrenergic receptor, beta 1	protein-coding
mm_146200.1	chr18	76242136	76242160	+	1	NA	intron (NM_010754, intron 1 of 10)	CpG	447	NM_010754	17126	Mm.152699	NM_010754	ENSMUSG00000024563	Smad2	7120426M23Rik|Madh2|Madr2|Smad-2|mMad2	SMAD family member 2	protein-coding
mm_25943.1	chr3	131491560	131491568	+	1	NA	Intergenic	Intergenic	-73204	NM_001289479	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_132831.1	chr16	45411521	45411526	+	1	NA	Intergenic	Intergenic	-2470	NM_010818	17470	Mm.245851	NM_010818	ENSMUSG00000022661	Cd200	Mox2|OX2	CD200 antigen	protein-coding
mm_118899.1	chr14	26645590	26645593	+	1	NA	intron (NM_007479, intron 1 of 5)	B1_Mus1|SINE|Alu	7394	NM_007479	11843	Mm.297768	NM_007479	ENSMUSG00000021877	Arf4	AA407803	ADP-ribosylation factor 4	protein-coding
mm_110935.1	chr12	76371425	76371441	-	1	NA	intron (NM_178744, intron 1 of 1)	intron (NM_178744, intron 1 of 1)	1167	NM_178744	268564	Mm.77065	NM_178744	ENSMUSG00000033454	Zbtb1	9430077A12|AI256369|Bsg2|C430003J21Rik	zinc finger and BTB domain containing 1	protein-coding
mm_107870.1	chr12	69907901	69907910	+	1	NA	5' UTR (NM_178628, exon 2 of 15)	5' UTR (NM_178628, exon 2 of 15)	-14742	NM_201519	399510	Mm.291936	NM_201519	ENSMUSG00000034761	Map4k5	4432415E19Rik|GCKR|KHS|MAPKKKK5	mitogen-activated protein kinase kinase kinase kinase 5	protein-coding
mm_139406.1	chr17	52468774	52468793	+	1	NA	Intergenic	Intergenic	-133926	NM_001031811	211468	Mm.399068	NM_001031811	ENSMUSG00000035580	Kcnh8	C130090D05Rik|ELK|ELK1|ELK3|Kv12.1	potassium voltage-gated channel, subfamily H (eag-related), member 8	protein-coding
mm_124294.1	chr14	103054961	103055021	-	1	NA	exon (NM_008392, exon 5 of 5)	exon (NM_008392, exon 5 of 5)	7979	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_66132.1	chr7	31070631	31070636	-	1	NA	TTS (NM_008557)	TTS (NM_008557)	6064	NM_008557	17178	Mm.263847	NM_008557	ENSMUSG00000057092	Fxyd3	Mat8	FXYD domain-containing ion transport regulator 3	protein-coding
mm_164827.1	chr18	37010706	37010720	+	1	NA	promoter-TSS (NM_009960)	promoter-TSS (NM_009960)	-145	NM_009960	12942	Mm.308500	NM_009960	ENSMUSG00000102206	Pcdha11	A830022B16Rik|Cnr7|Crnr7	protocadherin alpha 11	protein-coding
mm_86558.1	chr10	11149450	11149513	+	1	NA	promoter-TSS (NM_001077707)	promoter-TSS (NM_001077707)	51	NM_001284354	268281	Mm.133101	NM_172937	ENSMUSG00000090112	Shprh	2610103K11Rik|AA450458|AU024614|BC006883|D230017O13Rik|E130018M05	SNF2 histone linker PHD RING helicase	protein-coding
mm_78969.1	chr9	45319022	45319062	+	1	NA	promoter-TSS (NM_001013373)	promoter-TSS (NM_001013373)	-58	NM_001013373	214531	Mm.394987	NM_001013373	ENSMUSG00000037129	Tmprss13	BC010843|Tpmrss13	transmembrane protease, serine 13	protein-coding
mm_164803.1	chr18	24257355	24257380	+	1	NA	intron (NM_001160404, intron 5 of 12)	intron (NM_001160404, intron 5 of 12)	51373	NM_001160404	14423	Mm.30249	NM_013814	ENSMUSG00000000420	Galnt1	-	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 1	protein-coding
mm_1799.1	chr1	80428242	80428252	+	1	NA	Intergenic	Intergenic	-17685	NR_040460	72208	Mm.396181	NR_040460	ENSMUSG00000101483	1700016L21Rik	Jr3	RIKEN cDNA 1700016L21 gene	ncRNA
mm_811.1	chr1	45796024	45796027	+	1	NA	intron (NM_028599, intron 1 of 20)	intron (NM_028599, intron 1 of 20)	524	NM_028599	73674	Mm.270376	NM_028599	ENSMUSG00000025995	Wdr75	1300003A18Rik|2410118I19Rik|C77608	WD repeat domain 75	protein-coding
mm_11436.1	chr2	32004327	32004374	+	1	NA	exon (NM_172268, exon 17 of 36)	exon (NM_172268, exon 17 of 36)	29900	NM_172268	227720	Mm.289686	NM_172268	ENSMUSG00000001855	Nup214	BC039282|CAN|D2H9S46E	nucleoporin 214	protein-coding
mm_47646.1	chr5	125389556	125389583	-	1	NA	intron (NM_019639, intron 1 of 1)	CpG	448	NM_019639	22190	Mm.331	NM_019639	ENSMUSG00000008348	Ubc	2700054O04Rik|AI194771|Rps27a|TI-225|Uba52|Ubb	ubiquitin C	protein-coding
mm_16393.1	chr2	179414928	179414945	+	1	NA	promoter-TSS (NM_026596)	promoter-TSS (NM_026596)	0	NM_026596	68175	Mm.158187	NM_026596		4930591A17Rik	-	RIKEN cDNA 4930591A17 gene	protein-coding
mm_48188.1	chr5	137528497	137528512	-	1	NA	TTS (NM_031408)	TTS (NM_031408)	1090	NR_105846	102465227		NR_105846	ENSMUSG00000098597	Mir6418	Gm27629|mir-6418|mmu-mir-6418	microRNA 6418	ncRNA
mm_43869.1	chr5	143503569	143503588	+	1	NA	3' UTR (NM_144915, exon 15 of 15)	3' UTR (NM_144915, exon 15 of 15)	24415	NM_009007	19353	Mm.292510	NM_009007	ENSMUSG00000001847	Rac1	AL023026|D5Ertd559e	RAS-related C3 botulinum substrate 1	protein-coding
mm_39307.1	chr5	7961086	7961101	+	1	NA	intron (NM_054098, intron 1 of 4)	intron (NM_054098, intron 1 of 4)	621	NM_054098	117167	Mm.31403	NM_054098	ENSMUSG00000012428	Steap4	1110021O17Rik|AI481214|Tiarp|Tnfaip9	STEAP family member 4	protein-coding
mm_48166.1	chr5	137152953	137152981	-	1	NA	Intergenic	Intergenic	-36760	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_72182.1	chr8	72320066	72320101	+	1	NA	exon (NM_008452, exon 2 of 3)	exon (NM_008452, exon 2 of 3)	1021	NM_008452	16598	Mm.26938	NM_008452	ENSMUSG00000055148	Klf2	Lklf	Kruppel-like factor 2 (lung)	protein-coding
mm_120207.1	chr14	61959904	61959912	+	1	NA	Intergenic	Intergenic	-277535	NR_028264	668253	Mm.32886	NR_028264	ENSMUSG00000097589	Dleu2	1810047A16Rik|4932411A06Rik|7730401J12Rik|AI197277|AI788824|Alt1|Gm9069|Leu2	deleted in lymphocytic leukemia, 2	ncRNA
mm_21931.1	chr2	167046931	167046953	-	1	NA	exon (NM_001033196, exon 7 of 14)	exon (NM_001033196, exon 7 of 14)	-3447	NM_001291162	98999	Mm.297074	NM_001033196	ENSMUSG00000039501	Znfx1	AI481105|Astx3	zinc finger, NFX1-type containing 1	protein-coding
mm_44467.1	chr5	23386985	23387016	-	1	NA	Intergenic	Intergenic	47353	NR_040469	269630	Mm.425231	NR_040469	ENSMUSG00000073147	5031425E22Rik	-	RIKEN cDNA 5031425E22 gene	ncRNA
mm_173130.1	chrX	17945983	17945993	+	1	NA	Intergenic	RLTR17|LTR|ERVK	-199882	NM_028568	73547	Mm.159027	NM_028568	ENSMUSG00000025043	Dusp21	1700094E07Rik|DSP21	dual specificity phosphatase 21	protein-coding
mm_142481.1	chr17	45686900	45686923	-	1	NA	promoter-TSS (NM_198167)	promoter-TSS (NM_198167)	539	NM_026732	68463	Mm.379158	NM_026732	ENSMUSG00000023939	Mrpl14	1110006I11Rik|AI846816|MRP-L32|Rpml32	mitochondrial ribosomal protein L14	protein-coding
mm_137877.1	chr17	31520171	31520211	+	1	NA	promoter-TSS (NM_001083891)	promoter-TSS (NM_001083891)	76	NM_001083891	78330	Mm.28349	NM_030087	ENSMUSG00000024038	Ndufv3	1500032D16Rik	NADH dehydrogenase (ubiquinone) flavoprotein 3	protein-coding
mm_144961.1	chr18	37819544	37819570	+	1	NA	promoter-TSS (NM_033583)	promoter-TSS (NM_033583)	11	NM_033583	93708	Mm.247203	NM_033583	ENSMUSG00000102543	Pcdhgc5	-	protocadherin gamma subfamily C, 5	protein-coding
mm_110350.1	chr12	37106751	37106757	-	1	NA	Intergenic	Intergenic	-1792	NM_008584	17286	Mm.341398	NM_008584	ENSMUSG00000036144	Meox2	AI528662|Gax|Mox-2|Mox2	mesenchyme homeobox 2	protein-coding
mm_2472.1	chr1	105678174	105678177	+	1	NA	exon (NM_029349, exon 2 of 28)	exon (NM_029349, exon 2 of 28)	14314	NM_173187	227446	Mm.337339	NM_029349	ENSMUSG00000026319	2310035C23Rik	6430401N10|Kiaa1468|mKIAA1468	RIKEN cDNA 2310035C23 gene	protein-coding
mm_89393.1	chr10	89873483	89873492	+	1	NA	promoter-TSS (NM_001128086)	promoter-TSS (NM_001128086)	-22	NM_001128086	77531	Mm.440605	NM_181398	ENSMUSG00000058589	Anks1b	AIDA-1b|C030032C09Rik|E530015N03Rik|ENSMUSG00000078431|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding
mm_155781.1	chrX	96455613	96455636	+	1	NA	promoter-TSS (NM_001159627)	promoter-TSS (NM_001159627)	188	NM_010417	15203	Mm.277092	NM_010417	ENSMUSG00000031209	Heph	C130006F04Rik|Cpl|mKIAA0698|sla	hephaestin	protein-coding
mm_32032.1	chr4	95579447	95579462	+	1	NA	promoter-TSS (NM_029347)	promoter-TSS (NM_029347)	33	NM_029347	75578	Mm.276098	NM_029347	ENSMUSG00000028573	Fggy	2310009E04Rik	FGGY carbohydrate kinase domain containing	protein-coding
mm_160181.1	chr7	46241056	46241056	+	1	NA	promoter-TSS (NM_013624)	promoter-TSS (NM_013624)	69	NM_013624	18419	Mm.8020	NM_013624	ENSMUSG00000009487	Otog	4932420K09|Otgn|twt	otogelin	protein-coding
mm_163791.1	chr14	11317528	11317534	+	1	NA	Intergenic	Intergenic	35054	NR_105811	102466641		NR_105811	ENSMUSG00000099218	Mir5124b	Gm27681|mmu-mir-5124b	microRNA 5124b	ncRNA
mm_91253.1	chr10	22731960	22731989	-	1	NA	promoter-TSS (NM_011603)	promoter-TSS (NM_011603)	-527	NM_011603	237336	Mm.86670	NM_011603	ENSMUSG00000071359	Tbpl1	4732475G08|AW011832|AW491032|D18347|STD|TLF|TRF2|TRP|Tlp	TATA box binding protein-like 1	protein-coding
mm_62331.1	chr7	100493771	100493814	+	1	NA	intron (NM_011671, intron 1 of 7)	intron (NM_011671, intron 1 of 7)	434	NM_011671	22228	Mm.171378	NM_011671	ENSMUSG00000033685	Ucp2	Slc25a8	uncoupling protein 2 (mitochondrial, proton carrier)	protein-coding
mm_152569.1	chr19	11589286	11589314	-	1	NA	intron (NM_026835, intron 5 of 6)	intron (NM_026835, intron 5 of 6)	15504	NM_026835	68774	Mm.290390	NM_026835	ENSMUSG00000024679	Ms4a6d	1110058E16Rik|AI447446|Ms4a11	membrane-spanning 4-domains, subfamily A, member 6D	protein-coding
mm_169794.1	chr16	15637833	15637833	+	1	NA	promoter-TSS (NM_011159)	promoter-TSS (NM_011159)	-33	NM_011159	19090	Mm.71	NM_011159	ENSMUSG00000022672	Prkdc	AI326420|AU019811|DNA-PKcs|DNAPDcs|DNAPK|DNPK1|DOXNPH|HYRC1|XRCC7|dxnph|p460|scid|slip	protein kinase, DNA activated, catalytic polypeptide	protein-coding
mm_125255.1	chr15	35303590	35303594	+	1	NA	TTS (NM_054049)	TTS (NM_054049)	7480	NM_054049	107587	Mm.46336	NM_054049	ENSMUSG00000022330	Osr2	5430409I15Rik|Osr2A|Osr2B	odd-skipped related 2	protein-coding
mm_58883.1	chr7	17087975	17087977	+	1	NA	intron (NM_001310628, intron 1 of 5)	intron (NM_001310628, intron 1 of 5)	13936	NM_007676	26436	Mm.143686	NM_007676	ENSMUSG00000066760	Psg16	Cea11|PSG|bCEA	pregnancy specific glycoprotein 16	protein-coding
mm_88298.1	chr10	75316896	75316904	+	1	NA	promoter-TSS (NM_009630)	promoter-TSS (NM_009630)	23	NM_009630	11540	Mm.333734	NM_009630	ENSMUSG00000020178	Adora2a	A2AAR|A2aR|AA2AR	adenosine A2a receptor	protein-coding
mm_37083.1	chr4	116371802	116371818	-	1	NA	intron (NM_008641, intron 4 of 28)	intron (NM_008641, intron 4 of 28)	92371	NM_001042743	17776	Mm.9287	NM_008641	ENSMUSG00000003810	Mast2	MAST205|Mtssk	microtubule associated serine/threonine kinase 2	protein-coding
mm_48562.1	chr5	143165737	143165769	-	1	NA	promoter-TSS (NR_040426)	promoter-TSS (NR_040426)	-2	NR_040425	100042605	Mm.332809	NR_040424	ENSMUSG00000104529	Rbakdn	Gm3925	RB-associated KRAB zinc finger downstream neighbor (non-protein coding)	ncRNA
mm_29992.1	chr3	135543243	135543257	-	1	NA	intron (NM_027288, intron 8 of 16)	MTC|LTR|ERVL-MaLR	57639	NM_027288	110173	Mm.280536	NM_027288	ENSMUSG00000028164	Manba	2410030O07Rik|B930014J03Rik|Bmn	mannosidase, beta A, lysosomal	protein-coding
mm_160342.1	chr8	19239889	19239889	+	1	NA	promoter-TSS (NM_001025351)	promoter-TSS (NM_001025351)	-27	NM_001025351	574081	Mm.390013	NM_001025351	ENSMUSG00000071169	Defb46	Defb53|EG574081	defensin beta 46	protein-coding
mm_39684.1	chr5	25848311	25848325	+	1	NA	intron (NM_001310504, intron 8 of 10)	intron (NM_001310504, intron 8 of 10)	88345	NM_001004365	242894	Mm.150319	NM_001004365	ENSMUSG00000056367	Actr3b	9630005C02|ARP11|AW047569|Arp3b|Arp3beta	ARP3 actin-related protein 3B	protein-coding
mm_126062.1	chr15	77016013	77016036	+	1	NA	exon (NM_013593, exon 4 of 4)	exon (NM_013593, exon 4 of 4)	6703	NM_001164048	17189	Mm.404074	NM_013593	ENSMUSG00000018893	Mb	AI325109	myoglobin	protein-coding
mm_109455.1	chr12	111160191	111160201	+	1	NA	non-coding (NR_130987, exon 4 of 4)	non-coding (NR_130987, exon 4 of 4)	-6174	NM_001286122	22031	Mm.27431	NM_011632	ENSMUSG00000021277	Traf3	AI528849|CAP-1|CD40bp|CRAF1|LAP1|T-BAM|amn	TNF receptor-associated factor 3	protein-coding
mm_136586.1	chr17	4994492	4994531	+	1	NA	promoter-TSS (NM_001085355)	promoter-TSS (NM_001085355)	-563	NM_001085355	239985	Mm.133401	NM_001085355	ENSMUSG00000069729	Arid1b	8030481M12|9330189K18Rik|AI836955|Ardi1b|B230217J03Rik|mKIAA1235	AT rich interactive domain 1B (SWI-like)	protein-coding
mm_131538.1	chr16	17759631	17759683	+	1	NA	promoter-TSS (NM_145479)	promoter-TSS (NM_145479)	36	NM_145479	224023	Mm.282807	NM_145479	ENSMUSG00000022750	Klhl22	2610318I18Rik|Kelchl	kelch-like 22	protein-coding
mm_7813.1	chr1	131827816	131827840	-	1	NA	promoter-TSS (NM_173865)	promoter-TSS (NM_173865)	-184	NM_173865	98396	Mm.389181	NM_173865	ENSMUSG00000013275	Slc41a1	AI573938|B230315F01Rik	solute carrier family 41, member 1	protein-coding
mm_129181.1	chr15	76294723	76294754	-	1	NA	exon (NM_001195537, exon 1 of 7)	exon (NM_001195537, exon 1 of 7)	304	NM_001195537	100503915	Mm.393455	NM_001195537	ENSMUSG00000071724	Smpd5	ENSMUSG00000071724|Gm10345|MA-nSMase	sphingomyelin phosphodiesterase 5	protein-coding
mm_153740.1	chr19	44695461	44695481	-	1	NA	Intergenic	Intergenic	-61923	NM_011037	18504	Mm.192158	NM_011037	ENSMUSG00000004231	Pax2	Opdc|Pax-2	paired box 2	protein-coding
mm_33639.1	chr4	132974173	132974196	+	1	NA	promoter-TSS (NM_010208)	promoter-TSS (NM_010208)	89	NM_010208	14191	Mm.271665	NM_010208	ENSMUSG00000028874	Fgr	-	FGR proto-oncogene, Src family tyrosine kinase	protein-coding
mm_149862.1	chr19	25111561	25111563	+	1	NA	intron (NM_028785, intron 14 of 47)	intron (NM_028785, intron 14 of 47)	112033	NM_028785	76088	Mm.102485	NM_028785	ENSMUSG00000052085	Dock8	1200017A24Rik|5830472H07Rik|A130095G14Rik|AI461977	dedicator of cytokinesis 8	protein-coding
mm_163407.1	chr12	76072236	76072245	+	1	NA	exon (NM_001005510, exon 97 of 116)	exon (NM_001005510, exon 97 of 116)	105019	NM_010157	13983	Mm.2561	NM_010157	ENSMUSG00000021055	Esr2	ER[b]|ERbeta|Estrb	estrogen receptor 2 (beta)	protein-coding
mm_125635.1	chr15	62039285	62039292	+	1	NA	promoter-TSS (NR_132746)	promoter-TSS (NR_132746)	31	NR_132746	19296	Mm.4608	NM_011222	ENSMUSG00000097039	Pvt1	Ayu21-84Imeg|Gt(pU21)84Imeg|Mis-1|Mlvi-1|Pvt-1	plasmacytoma variant translocation 1	ncRNA
mm_52519.1	chr6	115422122	115422134	+	1	NA	promoter-TSS (NM_011146)	promoter-TSS (NM_011146)	62	NM_011146	19016	Mm.3020	NM_011146	ENSMUSG00000000440	Pparg	Nr1c3|PPAR-gamma|PPAR-gamma2|PPARgamma|PPARgamma2	peroxisome proliferator activated receptor gamma	protein-coding
mm_59706.1	chr7	28709702	28709730	+	1	NA	Intergenic	Lx9|LINE|L1	-7066	NM_001310687	50760	Mm.358659	NM_015796	ENSMUSG00000030598	Fbxo17	Fbg4|Fbx17|Fbxo26	F-box protein 17	protein-coding
mm_73067.1	chr8	94394815	94394827	+	1	NA	3' UTR (NM_022331, exon 8 of 8)	3' UTR (NM_022331, exon 8 of 8)	8321	NM_022331	64209	Mm.29151	NM_022331	ENSMUSG00000031770	Herpud1	Herp|Mifl|SUP	homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1	protein-coding
mm_151686.1	chr19	4306011	4306044	-	1	NA	5' UTR (NM_130863, exon 1 of 22)	5' UTR (NM_130863, exon 1 of 22)	195	NM_130863	110355	Mm.254144	NM_130863	ENSMUSG00000024858	Grk2	Adrbk-1|Adrbk1|Bark-1|beta ARK|betaARK1	G protein-coupled receptor kinase 2	protein-coding
mm_129273.1	chr15	77022430	77022469	-	1	NA	intron (NM_001164047, intron 1 of 2)	intron (NM_001164047, intron 1 of 2)	278	NM_001164048	17189	Mm.404074	NM_013593	ENSMUSG00000018893	Mb	AI325109	myoglobin	protein-coding
mm_168830.1	chr12	22745670	22745672	-	1	NA	Intergenic	CpG	264572	NR_015504	69732	Mm.391403	NM_028362	ENSMUSG00000073164	2410018L13Rik	2810480C08Rik	RIKEN cDNA 2410018L13 gene	ncRNA
mm_74665.1	chr8	13676367	13676391	-	1	NA	intron (NM_009025, intron 1 of 23)	intron (NM_009025, intron 1 of 23)	1208	NM_009025	19414	Mm.18517	NM_009025	ENSMUSG00000031453	Rasa3	AI326412|C86362|E130011G04|GAPIII|hlb381|scat	RAS p21 protein activator 3	protein-coding
mm_104771.1	chr11	98545829	98545845	-	1	NA	5' UTR (NM_011771, exon 1 of 8)	5' UTR (NM_011771, exon 1 of 8)	194	NM_011771	22780	Mm.133367	NM_011771	ENSMUSG00000018168	Ikzf3	5830411O07Rik|Aiolos|Zfpn1a3|Znfn1a3	IKAROS family zinc finger 3	protein-coding
mm_86895.1	chr10	22302987	22302989	+	1	NA	intron (NM_009018, intron 5 of 5)	intron (NM_009018, intron 5 of 5)	-3732	NR_015465	606736	Mm.387042	NR_015465	ENSMUSG00000097352	C920009B18Rik	-	RIKEN cDNA C920009B18 gene	ncRNA
mm_3930.1	chr1	162983055	162983056	+	1	NA	exon (NM_008030, exon 2 of 9)	exon (NM_008030, exon 2 of 9)	1473	NM_008030	14262	Mm.2900	NM_008030	ENSMUSG00000026691	Fmo3	AW111792	flavin containing monooxygenase 3	protein-coding
mm_172014.1	chr6	111391348	111391348	+	1	NA	intron (NM_001346640, intron 8 of 10)	intron (NM_001346640, intron 8 of 10)	745750	NM_177328	108073	Mm.240881	NM_177328	ENSMUSG00000056755	Grm7	6330570A01Rik|BB176677|C030018L03|E130018M02Rik|Gpr1g|Gprc1g|SMN2|Tg(SMN2)89Ahmb|mGluR7	glutamate receptor, metabotropic 7	protein-coding
mm_16788.1	chr2	10048581	10048621	-	1	NA	promoter-TSS (NM_027748)	promoter-TSS (NM_027748)	8	NM_027748	209361	Mm.86343	NM_027748	ENSMUSG00000025782	Taf3	140kDa|4933439M23Rik|AW539625|TAF140|TAFII-140|TAFII140|mTAFII140	TATA-box binding protein associated factor 3	protein-coding
mm_36102.1	chr4	58553312	58553322	-	1	NA	promoter-TSS (NM_172989)	promoter-TSS (NM_172989)	-24	NM_172989	14745	Mm.4772	NM_010336	ENSMUSG00000038668	Lpar1	AI326300|Edg2|Gpcr26|Kdt2|lpA1|vzg-1	lysophosphatidic acid receptor 1	protein-coding
mm_132104.1	chr16	31428765	31428837	+	1	NA	promoter-TSS (NM_001122683)	promoter-TSS (NM_001122683)	48	NM_001122683	71911	Mm.293470	NM_175177	ENSMUSG00000046598	Bdh1	2310032J20Rik|AI327223|Bdh	3-hydroxybutyrate dehydrogenase, type 1	protein-coding
mm_172435.1	chr7	29799062	29799071	-	1	NA	Intergenic	Intergenic	14276	NM_013705	22693	Mm.292690	NM_013705	ENSMUSG00000047473	Zfp30	2610306P15Rik|Zfp-30	zinc finger protein 30	protein-coding
mm_156558.1	chrX	151803237	151803243	+	1	NA	promoter-TSS (NM_021523)	promoter-TSS (NM_021523)	-42	NM_021523	59026	Mm.27372	NM_021523	ENSMUSG00000025261	Huwe1	5430439H10Rik|AU041296|Arf-bp1|C430014N20Rik|C80292|Gm1718|Ib772|LASU1|Mule|Ureb1	HECT, UBA and WWE domain containing 1	protein-coding
mm_98978.1	chr11	98701343	98701346	+	1	NA	promoter-TSS (NM_009971)	promoter-TSS (NM_009971)	31	NM_009971	12985	Mm.1238	NM_009971	ENSMUSG00000038067	Csf3	Csfg|G-CSF|MGI-IG	colony stimulating factor 3 (granulocyte)	protein-coding
mm_38273.1	chr4	136886072	136886110	-	1	NA	promoter-TSS (NM_009777)	promoter-TSS (NM_009777)	86	NM_009777	12260	Mm.2570	NM_009777	ENSMUSG00000036905	C1qb	-	complement component 1, q subcomponent, beta polypeptide	protein-coding
mm_64411.1	chr7	142512267	142512280	+	1	NA	exon (NM_001163669, exon 14 of 17)	exon (NM_001163669, exon 14 of 17)	-5502	NR_033261	677289	Mm.350054	NR_033261	ENSMUSG00000043795	Prr33	ENSMUSG00000043795|Gm14492|OTTMUSG00000016823	proline rich 33	ncRNA
mm_169663.1	chr15	59672109	59672110	-	1	NA	Intergenic	Intergenic	23455	NM_144549	211770	Mm.40298	NM_144549	ENSMUSG00000032501	Trib1	A530090O15Rik|TRB-1|Trb1	tribbles pseudokinase 1	protein-coding
mm_73794.1	chr8	117257137	117257147	+	1	NA	exon (NM_001163262, exon 1 of 21)	exon (NM_001163262, exon 1 of 21)	123	NM_001163262	74440	Mm.233181	NM_028941	ENSMUSG00000034390	Cmip	4933407C03Rik|5830471E12Rik|AI314065|AI464126	c-Maf inducing protein	protein-coding
mm_18105.1	chr2	44988856	44988869	-	1	NA	exon (NM_015753, exon 10 of 10)	exon (NM_015753, exon 10 of 10)	34315	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_137507.1	chr17	27029419	27029424	+	1	NA	promoter-TSS (NM_007523)	promoter-TSS (NM_007523)	162	NM_027544	70772	Mm.440437	NM_027544	ENSMUSG00000048731	Ggnbp1	0610031G08Rik|mdf	gametogenetin binding protein 1	protein-coding
mm_1357.1	chr1	66322047	66322073	+	1	NA	5' UTR (NM_001310634, exon 1 of 15)	5' UTR (NM_001310634, exon 1 of 15)	336	NM_001310634	17756	Mm.256966	NM_008632	ENSMUSG00000015222	Map2	G1-397-34|MAP-2|Mtap-2|Mtap2|repro4	microtubule-associated protein 2	protein-coding
mm_26032.1	chr3	135462593	135462606	+	1	NA	intron (NM_025356, intron 6 of 7)	intron (NM_025356, intron 6 of 7)	-23012	NM_027288	110173	Mm.280536	NM_027288	ENSMUSG00000028164	Manba	2410030O07Rik|B930014J03Rik|Bmn	mannosidase, beta A, lysosomal	protein-coding
mm_105731.1	chr11	109231166	109231175	-	1	NA	3' UTR (NM_001165934, exon 17 of 17)	3' UTR (NM_001165934, exon 17 of 17)	67011	NM_001165934	19739	Mm.38548	NM_011268	ENSMUSG00000020599	Rgs9	RGS9-1|Rgs9-2	regulator of G-protein signaling 9	protein-coding
mm_166258.1	chr5	87678991	87679026	+	1	NA	intron (NM_001286015, intron 28 of 32)	intron (NM_001286015, intron 28 of 32)	12800	NM_001286016	12990	Mm.427467	NM_007784	ENSMUSG00000070702	Csn1s1	AA959832|AW212882|Csna	casein alpha s1	protein-coding
mm_122915.1	chr14	54958659	54958670	-	1	NA	exon (NM_010856, exon 15 of 39)	exon (NM_010856, exon 15 of 39)	7943	NM_001164171	17888	Mm.290003	NM_010856	ENSMUSG00000040752	Myh6	A830009F23Rik|AA517445|Myhc-a|Myhca|alpha-MHC	myosin, heavy polypeptide 6, cardiac muscle, alpha	protein-coding
mm_84546.1	chr9	67327668	67327688	-	1	NA	intron (NM_001081242, intron 27 of 57)	intron (NM_001081242, intron 27 of 57)	-90952	NR_029576	387185		NR_029576	ENSMUSG00000076379	Mir190a	Mir190|Mirn190|mir-190|mir-190a|mmu-mir-190|mmu-mir-190a	microRNA 190a	ncRNA
mm_41906.1	chr5	105579536	105579561	+	1	NA	exon (NM_133897, exon 3 of 4)	exon (NM_133897, exon 3 of 4)	60077	NM_133897	100604	Mm.319847	NM_133897	ENSMUSG00000054720	Lrrc8c	AD158|AI326115|E430036I04Rik|fad158	leucine rich repeat containing 8 family, member C	protein-coding
mm_125139.1	chr15	30498581	30498583	+	1	NA	intron (NM_008729, intron 3 of 22)	intron (NM_008729, intron 3 of 22)	325989	NM_008729	18163	Mm.321648	NM_008729	ENSMUSG00000022240	Ctnnd2	Catnd2|Nprap|neurojugin	catenin (cadherin associated protein), delta 2	protein-coding
mm_85766.1	chr9	108855296	108855312	-	1	NA	intron (NM_134420, intron 1 of 17)	intron (NM_134420, intron 1 of 17)	1261	NM_134420	171429	Mm.45201	NM_134420	ENSMUSG00000023259	Slc26a6	B930010B04Rik|CFEX|Pat-1|Pat1	solute carrier family 26, member 6	protein-coding
mm_33073.1	chr4	123787858	123787886	+	1	NA	promoter-TSS (NM_183163)	promoter-TSS (NM_183163)	-3	NM_183163	230726	Mm.37334	NM_183163	ENSMUSG00000043333	Rhbdl2	9130416B15|RRP2	rhomboid, veinlet-like 2 (Drosophila)	protein-coding
mm_145383.1	chr18	57133009	57133029	+	1	NA	promoter-TSS (NM_001001979)	promoter-TSS (NM_001001979)	-71	NM_001001979	70417	Mm.297863	NM_001001979	ENSMUSG00000024593	Megf10	3000002B06Rik|Gm331	multiple EGF-like-domains 10	protein-coding
mm_100260.1	chr11	117332336	117332348	+	1	NA	promoter-TSS (NM_001113488)	promoter-TSS (NM_001113488)	29	NM_001113488	53860	Mm.38450	NM_017380	ENSMUSG00000059248	Sept9	MSF1|Msf|PNUTL4|Sint1	septin 9	protein-coding
mm_65717.1	chr7	28378426	28378434	-	1	NA	exon (NM_011756, exon 2 of 2)	exon (NM_011756, exon 2 of 2)	798	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_159338.1	chr3	55055193	55055193	-	1	NA	promoter-TSS (NM_007628)	promoter-TSS (NM_007628)	-49	NR_040593	70970	Mm.251485	NR_040593	ENSMUSG00000106589	4931419H13Rik	-	RIKEN cDNA 4931419H13 gene	ncRNA
mm_97922.1	chr11	83575351	83575366	+	1	NA	3' UTR (NM_011338, exon 4 of 4)	3' UTR (NM_011338, exon 4 of 4)	3278	NM_011338	20308	Mm.416125	NM_011338	ENSMUSG00000019122	Ccl9	CCF18|MRP-2|Scya10|Scya9	chemokine (C-C motif) ligand 9	protein-coding
mm_64362.1	chr7	142399579	142399614	+	1	NA	Intergenic	Intergenic	-11726	NM_009983	13033	Mm.231395	NM_009983	ENSMUSG00000007891	Ctsd	CD|CatD	cathepsin D	protein-coding
mm_132093.1	chr16	31235585	31235593	+	1	NA	intron (NR_035427, intron 1 of 2)	intron (NR_035427, intron 1 of 2)	-34351	NM_030138	78618	Mm.274646	NM_030138	ENSMUSG00000049076	Acap2	4832442G16|9530039J15Rik|CNT-B2|Centb2|mKIAA0041	ArfGAP with coiled-coil, ankyrin repeat and PH domains 2	protein-coding
mm_71279.1	chr8	40919778	40919801	+	1	NA	3' UTR (NM_001044740, exon 12 of 12)	3' UTR (NM_001044740, exon 12 of 12)	-6444	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_54977.1	chr6	48739245	48739255	-	1	NA	intron (NM_175860, intron 1 of 2)	intron (NM_175860, intron 1 of 2)	203	NM_008376	16205	Mm.252599	NM_008376	ENSMUSG00000090019	Gimap1	IAP38|Imap38|imap	GTPase, IMAP family member 1	protein-coding
mm_9406.1	chr1	172274191	172274213	-	1	NA	3' UTR (NM_178405, exon 23 of 23)	3' UTR (NM_178405, exon 23 of 23)	-15778	NM_013734	27222	Mm.482392	NM_013734	ENSMUSG00000007107	Atp1a4	-	ATPase, Na+/K+ transporting, alpha 4 polypeptide	protein-coding
mm_78890.1	chr9	44604845	44604921	+	1	NA	promoter-TSS (NM_001110826)	promoter-TSS (NM_001110826)	-9	NM_001110826	13209	Mm.267061	NM_007841	ENSMUSG00000032097	Ddx6	1110001P04Rik|E230023J21Rik|HLR2|mRCK/P54|p54|rck	DEAD (Asp-Glu-Ala-Asp) box polypeptide 6	protein-coding
mm_131053.1	chr16	4037278	4037292	+	1	NA	5' UTR (NM_010061, exon 1 of 9)	5' UTR (NM_010061, exon 1 of 9)	140	NM_010061	13419	Mm.291048	NM_010061	ENSMUSG00000005980	Dnase1	AI788650|DNaseI|Dnl1	deoxyribonuclease I	protein-coding
mm_147395.1	chr18	44253859	44253867	-	1	NA	Intergenic	Intergenic	-16264	NM_010935	18169	Mm.57234	NM_010935	ENSMUSG00000038071	Npy6r	-	neuropeptide Y receptor Y6	protein-coding
mm_85757.1	chr9	108649350	108649407	-	1	NA	promoter-TSS (NM_011790)	promoter-TSS (NM_011790)	2	NM_011790	23807	Mm.290447	NM_011790	ENSMUSG00000064145	Arih2	AI843547|ARI2|TRIAD1|UIP48	ariadne RBR E3 ubiquitin protein ligase 2	protein-coding
mm_94707.1	chr11	20249607	20249625	+	1	NA	promoter-TSS (NM_172260)	promoter-TSS (NM_172260)	-192	NM_172260	216543	Mm.260314	NM_172260	ENSMUSG00000044066	Cep68	6030463E10Rik|AI481761|BC027174|Kiaa0582	centrosomal protein 68	protein-coding
mm_8990.1	chr1	165708010	165708029	-	1	NA	promoter-TSS (NM_001038846)	promoter-TSS (NM_001038846)	75	NM_178593	226594	Mm.265552	NM_178593	ENSMUSG00000040723	Rcsd1	A430105K13Rik|BC025872|CapZIP	RCSD domain containing 1	protein-coding
mm_56698.1	chr6	114864718	114864744	-	1	NA	intron (NM_177683, intron 2 of 4)	intron (NM_177683, intron 2 of 4)	57021	NM_177683	232334	Mm.268357	NM_177683	ENSMUSG00000030315	Vgll4	BC048841|VGL-4	vestigial like family member 4	protein-coding
mm_111199.1	chr12	84218836	84218890	-	1	NA	promoter-TSS (NM_001163501)	promoter-TSS (NM_001163501)	18	NM_001163501	238317	Mm.31256	NM_001163501	ENSMUSG00000042507	Elmsan1	9430029N19Rik|C130039O16Rik|Gm260	ELM2 and Myb/SANT-like domain containing 1	protein-coding
mm_63338.1	chr7	126953011	126953026	+	1	NA	exon (NM_001252566, exon 3 of 17)	exon (NM_001252566, exon 3 of 17)	2483	NM_001252566	233878	Mm.283926	NM_144926	ENSMUSG00000030683	Sez6l2	AI835913|AW121566|BSRP-A|Psk1	seizure related 6 homolog like 2	protein-coding
mm_163023.1	chr11	47988427	47988437	-	1	NA	intron (NR_105801, intron 3 of 3)	CpG	86151	NR_105801	102466638		NR_105801	ENSMUSG00000099011	Mir6380	Gm27356|mmu-mir-6380	microRNA 6380	ncRNA
mm_69334.1	chr7	128745268	128745280	-	1	NA	intron (NM_001029982, intron 1 of 18)	intron (NM_001029982, intron 1 of 18)	404	NM_001029982	207352	Mm.297105	NM_001029982	ENSMUSG00000055319	Sec23ip	D7Ertd373e|p125	Sec23 interacting protein	protein-coding
mm_118165.1	chr13	105294427	105294471	-	1	NA	Intergenic	CpG	-1435	NM_027934	71816	Mm.317015	NM_027934	ENSMUSG00000021720	Rnf180	3110001E11Rik|Rines	ring finger protein 180	protein-coding
mm_89791.1	chr10	102201833	102201836	+	1	NA	intron (NM_001162369, intron 1 of 5)	intron (NM_001162369, intron 1 of 5)	42755	NM_001162369	67569	Mm.25252	NM_026243	ENSMUSG00000019888	Mgat4c	9130411I17Rik|GntIVh	MGAT4 family, member C	protein-coding
mm_64128.1	chr7	141148952	141148977	+	1	NA	intron (NM_013782, intron 4 of 11)	L1M4|LINE|L1	17678	NM_013782	27388	Mm.293591	NM_013782	ENSMUSG00000025495	Ptdss2	AI481134|AI988017|PSS2	phosphatidylserine synthase 2	protein-coding
mm_148405.1	chr19	3851958	3851962	+	1	NA	non-coding (NR_073190, exon 1 of 13)	non-coding (NR_073190, exon 1 of 13)	187	NR_073190	12660	Mm.225505	NM_013490	ENSMUSG00000024843	Chka	CK|CK/EK-alpha|Chetk-alpha|Chk|ChoK|EK|EtnK-alpha	choline kinase alpha	protein-coding
mm_14222.1	chr2	127363198	127363217	+	1	NA	promoter-TSS (NM_009633)	promoter-TSS (NM_009633)	-79	NM_009633	11552	Mm.347390	NM_009633	ENSMUSG00000058620	Adra2b	Adra-2b|[a]2B|a2b-AR|alpha2-C2|alpha2B	adrenergic receptor, alpha 2b	protein-coding
mm_135284.1	chr16	38447671	38447681	-	1	NA	intron (NM_007414, intron 2 of 3)	intron (NM_007414, intron 2 of 3)	5013	NM_007414	11544	Mm.20047	NM_007414	ENSMUSG00000002844	Adprh	Arh1	ADP-ribosylarginine hydrolase	protein-coding
mm_169660.1	chr15	58135044	58135044	-	1	NA	promoter-TSS (NM_027435)	promoter-TSS (NM_027435)	38	NM_027435	70472	Mm.221758	NM_027435	ENSMUSG00000022360	Atad2	2610509G12Rik	ATPase family, AAA domain containing 2	protein-coding
mm_114374.1	chr13	63117030	63117039	+	1	NA	intron (NM_001289926, intron 5 of 15)	MER45B|DNA|hAT-Tip100	-122995	NR_110520	72061	Mm.188105	NM_028079	ENSMUSG00000021458	2010111I01Rik	2300006M17Rik|AP-O|AW742919|Aopep|ApO|mir-23b|mir-24-1|mir-27b	RIKEN cDNA 2010111I01 gene	protein-coding
mm_167746.1	chr9	109094386	109094404	+	1	NA	Intergenic	Intergenic	-1041	NM_172775	235611	Mm.53862	NM_172775	ENSMUSG00000053646	Plxnb1	2900002G15Rik|AU042020|mKIAA0407	plexin B1	protein-coding
mm_163659.1	chr13	75618551	75618551	+	1	NA	Intergenic	Intergenic	-26495	NR_030451	751556		NR_030451	ENSMUSG00000076236	Mir682	Mirn682|mir-682|mmu-mir-682	microRNA 682	ncRNA
mm_157865.1	chrX	75130997	75131009	-	1	NA	promoter-TSS (NM_008621)	promoter-TSS (NM_008621)	13	NM_008621	17524	Mm.391267	NM_008621	ENSMUSG00000031402	Mpp1	55kDa|C130070C03Rik|p55	membrane protein, palmitoylated	protein-coding
mm_126830.1	chr15	88864104	88864114	+	1	NA	intron (NM_145478, intron 4 of 5)	intron (NM_145478, intron 4 of 5)	1915	NM_145478	223775	Mm.400129	NM_145478	ENSMUSG00000035828	Pim3	BC026639|Kid1	proviral integration site 3	protein-coding
mm_155931.1	chrX	103489432	103489442	+	1	NA	Intergenic	Intergenic	-4121	NR_015508	70252	Mm.380486	NR_015508	ENSMUSG00000097571	Jpx	2010000I03Rik|2510040I06Rik|Enox	Jpx transcript, Xist activator (non-protein coding)	ncRNA
mm_138512.1	chr17	35236696	35236759	+	1	NA	promoter-TSS (NM_010909)	promoter-TSS (NM_010909)	131	NM_023179	66237	Mm.396107	NM_023179	ENSMUSG00000024403	Atp6v1g2	1500002D01Rik|Atp6g2|NG38|VAG2	ATPase, H+ transporting, lysosomal V1 subunit G2	protein-coding
mm_156840.1	chrX	164373600	164373625	+	1	NA	promoter-TSS (NM_010216)	promoter-TSS (NM_010216)	90	NM_010216	14205	Mm.297978	NM_010216	ENSMUSG00000031380	Vegfd	AI325264|Figf|VEGF-D	vascular endothelial growth factor D	protein-coding
mm_10931.1	chr2	25467310	25467317	+	1	NA	3' UTR (NM_008963, exon 6 of 7)	3' UTR (NM_008963, exon 6 of 7)	2436	NM_008963	19215	Mm.1008	NM_008963	ENSMUSG00000015090	Ptgds	21kDa|L-PGDS|PGD2|PGDS|PGDS2|Ptgs3	prostaglandin D2 synthase (brain)	protein-coding
mm_89786.1	chr10	102158895	102158916	+	1	NA	promoter-TSS (NM_001162369)	promoter-TSS (NM_001162369)	47	NM_001162368	67569	Mm.25252	NM_026243	ENSMUSG00000019888	Mgat4c	9130411I17Rik|GntIVh	MGAT4 family, member C	protein-coding
mm_137280.1	chr17	24727849	24727863	+	1	NA	promoter-TSS (NM_001163945)	promoter-TSS (NM_001163945)	27	NM_001163945	66211	Mm.46198	NM_025425	ENSMUSG00000002500	Rpl3l	1110057H16Rik	ribosomal protein L3-like	protein-coding
mm_143991.1	chr17	87691594	87691627	-	1	NA	intron (NM_008628, intron 7 of 15)	(ACTG)n|Simple_repeat|Simple_repeat	19053	NM_008628	17685	Mm.4619	NM_008628	ENSMUSG00000024151	Msh2	AI788990	mutS homolog 2	protein-coding
mm_146165.1	chr18	75183870	75183883	+	1	NA	intron (NM_027727, intron 13 of 16)	intron (NM_027727, intron 13 of 16)	113441	NR_045394	100503117	Mm.250517	NR_045393	ENSMUSG00000102047	2010010A06Rik	5033420E22Rik	RIKEN cDNA 2010010A06 gene	ncRNA
mm_42407.1	chr5	115011348	115011403	+	1	NA	promoter-TSS (NM_029012)	promoter-TSS (NM_029012)	-149	NM_029012	74585	Mm.355894	NM_029012	ENSMUSG00000029550	Sppl3	4833416I09Rik|Psl4|Usmg3	signal peptide peptidase 3	protein-coding
mm_139632.1	chr17	57367553	57367613	+	1	NA	intron (NM_010130, intron 2 of 21)	Lx10|LINE|L1	8897	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_89053.1	chr10	82879263	82879275	+	1	NA	exon (NM_001042523, exon 6 of 15)	exon (NM_001042523, exon 6 of 15)	12643	NM_025499	66341	Mm.443284	NM_025499	ENSMUSG00000109864	Eid3	1700027M21Rik|NS4EB	EP300 interacting inhibitor of differentiation 3	protein-coding
mm_149940.1	chr19	27217510	27217605	+	1	NA	5' UTR (NM_013703, exon 1 of 19)	5' UTR (NM_013703, exon 1 of 19)	537	NM_001161420	22359	Mm.4141	NM_013703	ENSMUSG00000024924	Vldlr	AA408956|AI451093|AW047288	very low density lipoprotein receptor	protein-coding
mm_26024.1	chr3	135439027	135439053	+	1	NA	promoter-TSS (NR_030689)	promoter-TSS (NR_030689)	281	NM_025356	66105	Mm.49884	NM_025356	ENSMUSG00000078578	Ube2d3	1100001F19Rik|9430029A22Rik|AA414951	ubiquitin-conjugating enzyme E2D 3	protein-coding
mm_97252.1	chr11	75756810	75756847	+	1	NA	exon (NM_009536, exon 4 of 6)	exon (NM_009536, exon 4 of 6)	23941	NM_009536	22627	Mm.234700	NM_009536	ENSMUSG00000020849	Ywhae	AU019196	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide	protein-coding
mm_75030.1	chr8	32004841	32004845	-	1	NA	Intergenic	Intergenic	-86640	NM_178591	211323	Mm.153432	NM_178591	ENSMUSG00000062991	Nrg1	6030402G23Rik|ARIA|D230005F13Rik|GGF|GGFII|HRG|HRGalpha|Hgl|NDF|SMDF	neuregulin 1	protein-coding
mm_35272.1	chr4	19908618	19908642	-	1	NA	intron (NM_175406, intron 2 of 7)	CT-rich|Low_complexity|Low_complexity	13936	NM_175406	242341	Mm.19298	NM_175406	ENSMUSG00000028238	Atp6v0d2	1620401A02Rik|AI324824|V-ATPase	ATPase, H+ transporting, lysosomal V0 subunit D2	protein-coding
mm_135957.1	chr16	74730960	74730963	-	1	NA	Intergenic	L1MA6|LINE|L1	-320049	NM_175549	268902	Mm.171736	NM_175549	ENSMUSG00000052516	Robo2	2600013A04Rik|9430089E08Rik|BB097918|D230004I22Rik|mKIAA1568	roundabout guidance receptor 2	protein-coding
mm_61158.1	chr7	58710517	58710517	+	1	NA	intron (NM_009728, intron 1 of 20)	intron (NM_009728, intron 1 of 20)	52315	NM_009728	11982	Mm.135129	NM_009728	ENSMUSG00000025324	Atp10a	Atp10c|pfatp	ATPase, class V, type 10A	protein-coding
mm_53013.1	chr6	123277834	123277838	+	1	NA	Intergenic	B4|SINE|B4	12035	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_140628.1	chr17	12395658	12395682	-	1	NA	exon (NM_008877, exon 8 of 19)	exon (NM_008877, exon 8 of 19)	17061	NM_008877	18815	Mm.971	NM_008877	ENSMUSG00000059481	Plg	AI649309|Pg	plasminogen	protein-coding
mm_144603.1	chr18	32397555	32397561	+	1	NA	intron (NM_001083334, intron 1 of 14)	intron (NM_001083334, intron 1 of 14)	-19274	NR_045403	402767	Mm.385109	NR_045403	ENSMUSG00000097413	A830052D11Rik	-	RIKEN cDNA A830052D11 gene	ncRNA
mm_63105.1	chr7	122630858	122630891	+	1	NA	3' UTR (NM_008855, exon 17 of 17)	3' UTR (NM_008855, exon 17 of 17)	-40870	NM_019430	54376	Mm.444212	NM_019430	ENSMUSG00000066189	Cacng3	-	calcium channel, voltage-dependent, gamma subunit 3	protein-coding
mm_36879.1	chr4	107178341	107178355	-	1	NA	promoter-TSS (NM_029565)	promoter-TSS (NM_029565)	18	NM_025617	66526	Mm.246956	NM_025617	ENSMUSG00000028619	Tceanc2	2210010B22Rik|2210012G02Rik|6330404A07Rik|AU015593|Tdeanc2	transcription elongation factor A (SII) N-terminal and central domain containing 2	protein-coding
mm_71978.1	chr8	70594426	70594440	+	1	NA	promoter-TSS (NM_023627)	promoter-TSS (NM_023627)	-48	NM_023627	71780	Mm.29357	NM_023627	ENSMUSG00000019139	Isyna1	1300017C10Rik|AU018670	myo-inositol 1-phosphate synthase A1	protein-coding
mm_74810.1	chr8	22653395	22653405	-	1	NA	promoter-TSS (NM_011130)	promoter-TSS (NM_011130)	37	NM_011130	18970	Mm.123211	NM_011130	ENSMUSG00000031536	Polb	A430088C08Rik	polymerase (DNA directed), beta	protein-coding
mm_154542.1	chrM	14533	14543	-	1	NA	NA	Intergenic	NA	NA								
mm_61919.1	chr7	90153374	90153380	+	1	NA	intron (NM_001252520, intron 1 of 20)	intron (NM_001252520, intron 1 of 20)	23145	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_150113.1	chr19	29697906	29697927	+	1	NA	promoter-TSS (NM_029993)	promoter-TSS (NM_029993)	-25	NM_029993	77836	Mm.138437	NM_029993	ENSMUSG00000024806	Mlana	A930034P04Rik|Mart1	melan-A	protein-coding
mm_100649.1	chr11	3146352	3146392	-	1	NA	intron (NM_030207, intron 14 of 32)	intron (NM_030207, intron 14 of 32)	22351	NR_003517	236604	Mm.247625	NM_001004146		Pisd-ps1	-	phosphatidylserine decarboxylase, pseudogene 1	pseudo
mm_22644.1	chr3	14865454	14865494	+	1	NA	intron (NM_007606, intron 2 of 6)	intron (NM_007606, intron 2 of 6)	1936	NM_007606	12350	Mm.300	NM_007606	ENSMUSG00000027559	Car3	BB219044|Ca3|Car-3	carbonic anhydrase 3	protein-coding
mm_106281.1	chr11	118145812	118145828	-	1	NA	Intergenic	Intergenic	-16601	NM_001167746	69926	Mm.473893	NM_001167746	ENSMUSG00000033987	Dnah17	2810003K23Rik|Dnahc17|Dnahcl1|Gm1178|mKIAA3028	dynein, axonemal, heavy chain 17	protein-coding
mm_33119.1	chr4	124751609	124751649	+	1	NA	exon (NM_008385, exon 7 of 24)	exon (NM_008385, exon 7 of 24)	7848	NR_030480	735263		NR_030480	ENSMUSG00000076119	Mir698	Mirn698|mir-698|mmu-mir-698	microRNA 698	ncRNA
mm_34412.1	chr4	145245841	145245856	+	1	NA	intron (NM_011610, intron 1 of 9)	intron (NM_011610, intron 1 of 9)	1022	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_125381.1	chr15	40655209	40655225	+	1	NA	5' UTR (NM_011766, exon 1 of 8)	5' UTR (NM_011766, exon 1 of 8)	175	NM_011766	22762	Mm.39496	NM_011766	ENSMUSG00000022306	Zfpm2	B330005D23Rik|FOG-2|FOG2	zinc finger protein, multitype 2	protein-coding
mm_171866.1	chr5	24256763	24256763	+	1	NA	promoter-TSS (NR_030454).4	promoter-TSS (NR_030454).4	-765	NR_030454	735274		NR_030454	ENSMUSG00000106252	Mir684-1	Mirn684-1	microRNA 684-1	ncRNA
mm_152348.1	chr19	9984874	9984893	-	1	NA	TTS (NM_011913)	TTS (NM_011913)	2237	NM_010239	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
mm_62086.1	chr7	93079860	93079870	+	1	NA	promoter-TSS (NM_021427)	promoter-TSS (NM_021427)	-14	NM_021427	58238	Mm.113787	NM_021427	ENSMUSG00000051515	Fam181b	A830059I20Rik|AB041569	family with sequence similarity 181, member B	protein-coding
mm_83493.1	chr9	45945978	45945988	-	1	NA	intron (NM_172257, intron 12 of 25)	intron (NM_172257, intron 12 of 25)	-6393	NR_106055	102465659		NR_106055	ENSMUSG00000098327	Mir7087	Gm27273|mmu-mir-7087	microRNA 7087	ncRNA
mm_135171.1	chr16	35932730	35932740	-	1	NA	exon (NM_001013371, exon 3 of 5)	exon (NM_001013371, exon 3 of 5)	-5735	NM_030253	80285	Mm.49074	NM_030253	ENSMUSG00000022906	Parp9	ARTD9|AW214463|BC003281|Bagl|Bal|PARP-9	poly (ADP-ribose) polymerase family, member 9	protein-coding
mm_65763.1	chr7	28695256	28695272	-	1	NA	intron (NM_207238, intron 4 of 5)	intron (NM_207238, intron 4 of 5)	2120	NM_001163702	233040	Mm.116116	NM_207238	ENSMUSG00000037463	Fbxo27	E130008B10Rik|FBG5|Gm161	F-box protein 27	protein-coding
mm_109757.1	chr12	117843490	117843507	+	1	NA	promoter-TSS (NM_146040)	promoter-TSS (NM_146040)	-363	NM_146040	217946	Mm.281149	NM_146040	ENSMUSG00000021175	Cdca7l	BC006933|JPO2	cell division cycle associated 7 like	protein-coding
mm_118839.1	chr14	25642512	25642553	+	1	NA	intron (NM_001310666, intron 7 of 23)	intron (NM_001310666, intron 7 of 23)	39019	NM_001309430	100188919	Mm.473810	NM_001309430		Israa	-	immune system released activating agent	protein-coding
mm_39012.1	chr4	152120654	152120670	-	1	NA	TTS (NM_033042)	TTS (NM_033042)	4319	NM_033042	85030	Mm.101198	NM_033042	ENSMUSG00000024793	Tnfrsf25	APO-3|DDR3|DR3|LARD|TR3|TRAMP|Tnfrsf12|WSL-1|WSL-LR|Wsl	tumor necrosis factor receptor superfamily, member 25	protein-coding
mm_108633.1	chr12	85705981	85705983	+	1	NA	intron (NM_016767, intron 2 of 2)	intron (NM_016767, intron 2 of 2)	19262	NM_016767	53314	Mm.6672	NM_016767	ENSMUSG00000034266	Batf	B-ATF|SFA-2	basic leucine zipper transcription factor, ATF-like	protein-coding
mm_151704.1	chr19	4498533	4498543	-	1	NA	promoter-TSS (NM_027237)	promoter-TSS (NM_027237)	45	NM_027237	69861	Mm.282978	NM_027237	ENSMUSG00000042041	2010003K11Rik	-	RIKEN cDNA 2010003K11 gene	protein-coding
mm_9757.1	chr1	180829883	180829892	-	1	NA	Intergenic	Intergenic	-16282	NM_008210	15078	Mm.138832	NM_008210	ENSMUSG00000060743	H3f3a	H3.3A	H3 histone, family 3A	protein-coding
mm_86269.1	chr9	121718859	121718892	-	1	NA	promoter-TSS (NM_010918)	promoter-TSS (NM_010918)	-306	NM_010918	18087	Mm.32842	NM_010918	ENSMUSG00000032525	Nktr	5330401F18Rik|D9Wsu172e	natural killer tumor recognition sequence	protein-coding
mm_43629.1	chr5	138187444	138187462	+	1	NA	promoter-TSS (NM_178612)	promoter-TSS (NM_178612)	-82	NM_178612	66455	Mm.24592	NM_178612	ENSMUSG00000036968	Cnpy4	2610019P18Rik	canopy FGF signaling regulator 4	protein-coding
mm_81762.1	chr9	114368469	114368476	+	1	NA	promoter-TSS (NR_040384)	promoter-TSS (NR_040384)	148	NR_040383	75116	Mm.72675	NR_040383	ENSMUSG00000074039	4930520O04Rik	-	RIKEN cDNA 4930520O04 gene	ncRNA
mm_79157.1	chr9	47799470	47799500	+	1	NA	exon (NM_018770, exon 5 of 10)	exon (NM_018770, exon 5 of 10)	18723	NR_046048	100038460	Mm.447649	NR_046048		Gm10677	ENSMUSG00000074363	predicted gene 10677	ncRNA
mm_143834.1	chr17	84103505	84103526	-	1	NA	Intergenic	Intergenic	24855	NR_045458	74473	Mm.399575	NR_045458		4933433H22Rik	-	RIKEN cDNA 4933433H22 gene	ncRNA
mm_112420.1	chr13	4059566	4059586	+	1	NA	promoter-TSS (NM_134072)	promoter-TSS (NM_134072)	-15	NM_134072	105387	Mm.26838	NM_134072	ENSMUSG00000033715	Akr1c14	9030611N15Rik|AW557061	aldo-keto reductase family 1, member C14	protein-coding
mm_19176.1	chr2	84361993	84361996	-	1	NA	intron (NM_018782, intron 9 of 15)	intron (NM_018782, intron 9 of 15)	63272	NM_018782	54598	Mm.75467	NM_018782	ENSMUSG00000059588	Calcrl	AV071593|CRLR	calcitonin receptor-like	protein-coding
mm_80014.1	chr9	67858828	67858845	+	1	NA	exon (NM_177184, exon 4 of 85)	exon (NM_177184, exon 4 of 85)	18440	NM_177184	320528	Mm.241454	NM_177184	ENSMUSG00000035284	Vps13c	AI552542|AV026040|C230055H22Rik|W51662|chorein	vacuolar protein sorting 13C	protein-coding
mm_65022.1	chr7	18345799	18345814	-	1	NA	TTS (NM_011963)	TTS (NM_011963)	9187	NM_001163685	26438	Mm.89991	NM_011963	ENSMUSG00000003505	Psg18	Cea-3|Cea3|mmCGM6	pregnancy specific glycoprotein 18	protein-coding
mm_72978.1	chr8	92901420	92901437	+	1	NA	promoter-TSS (NM_027112)	promoter-TSS (NM_027112)	33	NM_027112	69543	Mm.440514	NM_027112	ENSMUSG00000078144	Capns2	2310005G05Rik|30K-2	calpain, small subunit 2	protein-coding
mm_126891.1	chr15	89498003	89498012	+	1	NA	Intergenic	Intergenic	-1850	NM_021423	58234	Mm.146855	NM_021423	ENSMUSG00000022623	Shank3	AI841104|SHANK3c-3|SHANK3c-4|Shank3b	SH3/ankyrin domain gene 3	protein-coding
mm_100782.1	chr11	4816656	4816664	-	1	NA	intron (NM_001252251, intron 3 of 16)	intron (NM_001252251, intron 3 of 16)	16475	NM_001252253	18016	Mm.297109	NM_010898	ENSMUSG00000009073	Nf2	merlin	neurofibromin 2	protein-coding
mm_124923.1	chr15	12129506	12129511	+	1	NA	intron (NM_011767, intron 2 of 19)	intron (NM_011767, intron 2 of 19)	11657	NM_011767	22763	Mm.273496	NM_011767	ENSMUSG00000022201	Zfr	C920030H05Rik	zinc finger RNA binding protein	protein-coding
mm_75349.1	chr8	43320749	43320760	-	1	NA	Intergenic	Intergenic	-13745	NM_009556	22702	Mm.285848	NM_009556	ENSMUSG00000051176	Zfp42	Rex-1|Rex1|Zfp-42	zinc finger protein 42	protein-coding
mm_87036.1	chr10	28668561	28668637	+	1	NA	non-coding (NR_131208, exon 1 of 4)	non-coding (NR_131208, exon 1 of 4)	239	NM_178666	210757	Mm.123021	NM_178666	ENSMUSG00000049109	Themis	E430004N04Rik|Gasp|Spot|Tsepa|thylex	thymocyte selection associated	protein-coding
mm_112248.1	chr12	113597975	113597983	-	1	NA	Intergenic	Intergenic	54071	NM_174885	238406	Mm.188683	NM_174885	ENSMUSG00000043945	Adam6a	Adam6|tMDCIV	a disintegrin and metallopeptidase domain 6A	protein-coding
mm_127477.1	chr15	101274023	101274033	+	1	NA	exon (NM_010444, exon 7 of 7)	exon (NM_010444, exon 7 of 7)	7182	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_161702.1	chr17	24199957	24199957	-	1	NA	promoter-TSS (NM_001163853)	promoter-TSS (NM_001163853)	0	NM_001163852	224617	Mm.301585	NM_173186	ENSMUSG00000036473	Tbc1d24	9630033P11|C530046L02Rik|mKIAA1171	TBC1 domain family, member 24	protein-coding
mm_67055.1	chr7	67372773	67372845	-	1	NA	promoter-TSS (NM_001291196)	promoter-TSS (NM_001291196)	49	NM_001291192	17258	Mm.132788	NM_001033713	ENSMUSG00000030557	Mef2a	A430079H05Rik	myocyte enhancer factor 2A	protein-coding
mm_149487.1	chr19	11813411	11813422	+	1	NA	intron (NM_001025307, intron 1 of 10)	intron (NM_001025307, intron 1 of 10)	5987	NM_001286543	20908	Mm.272264	NM_011502	ENSMUSG00000041488	Stx3	Syn-3	syntaxin 3	protein-coding
mm_72475.1	chr8	83608177	83608198	+	1	NA	promoter-TSS (NM_018808)	promoter-TSS (NM_018808)	12	NM_018808	81489	Mm.282092	NM_018808	ENSMUSG00000005483	Dnajb1	0610007I11Rik|DjB1|HSPF1|Hdj1|Hsp40	DnaJ heat shock protein family (Hsp40) member B1	protein-coding
mm_151791.1	chr19	5394386	5394402	-	1	NA	Intergenic	Intergenic	-5691	NM_016882	20227	Mm.34562	NM_016882	ENSMUSG00000039148	Sart1	U5-110K	squamous cell carcinoma antigen recognized by T cells 1	protein-coding
mm_162829.1	chr10	81394829	81394839	-	1	NA	exon (NM_001099917, exon 4 of 4)	exon (NM_001099917, exon 4 of 4)	1770	NM_001099917	72273	Mm.253147	NM_001099917	ENSMUSG00000078439	Smim24	2210404O07Rik	small integral membrane protein 24	protein-coding
mm_30951.1	chr4	33209260	33209319	+	1	NA	exon (NM_177774, exon 1 of 3)	exon (NM_177774, exon 1 of 3)	298	NM_177774	272009	Mm.156636	NM_177774	ENSMUSG00000054679	Srsf12	B830039L16|Sfrs13b|Srrp|Srsf13b	serine/arginine-rich splicing factor 12	protein-coding
mm_12162.1	chr2	62147974	62147976	+	1	NA	intron (NM_001242378, intron 1 of 25)	intron (NM_001242378, intron 1 of 25)	101460	NM_033552	94229	Mm.314497	NM_033552	ENSMUSG00000026904	Slc4a10	NCBE|mKIAA4136	solute carrier family 4, sodium bicarbonate cotransporter-like, member 10	protein-coding
mm_114859.1	chr13	93308007	93308029	+	1	NA	promoter-TSS (NM_152134)	promoter-TSS (NM_152134)	-16	NM_152134	26556	Mm.37533	NM_011982	ENSMUSG00000007617	Homer1	PSD-Zip45|SYN47|Ves-1|homer-1|vesl-1	homer scaffolding protein 1	protein-coding
mm_109788.1	chr12	3249037	3249072	-	1	NA	3' UTR (NM_016676, exon 6 of 6)	3' UTR (NM_016676, exon 6 of 6)	13263	NR_015551	74173	Mm.309774	NM_028796	ENSMUSG00000079179	Rab10os	1700012B15Rik|1810036A22Rik	RAB10, member RAS oncogene family, opposite strand	ncRNA
mm_114210.1	chr13	56159244	56159258	+	1	NA	Intergenic	Intergenic	19634	NM_145976	212937	Mm.116697	NM_145976	ENSMUSG00000049625	Tifab	-	TRAF-interacting protein with forkhead-associated domain, family member B	protein-coding
mm_54934.1	chr6	48445514	48445534	-	1	NA	promoter-TSS (NM_001085415)	promoter-TSS (NM_001085415)	301	NM_020589	68910	Mm.2464	NM_020589	ENSMUSG00000068551	Zfp467	1190001I08Rik|AB041616|AI426952|AV017623|EZI|MNCb-3350|Znf467	zinc finger protein 467	protein-coding
mm_49728.1	chr6	34709439	34709446	+	1	NA	promoter-TSS (NM_145575)	promoter-TSS (NM_145575)	-2	NM_145575	109624	Mm.308134	NM_145575	ENSMUSG00000029761	Cald1	4833423D12Rik|AI195384|AV071549|AW536160|C920027I18Rik	caldesmon 1	protein-coding
mm_131354.1	chr16	13702674	13702682	+	1	NA	3' UTR (NM_001177552, exon 6 of 6)	3' UTR (NM_001177552, exon 6 of 6)	-27158	NR_040574	76684	Mm.491043	NR_040574		Pla2g10os	1810007I06Rik	phospholipase A2, group X, opposite strand	ncRNA
mm_172385.1	chr7	13278485	13278499	-	1	NA	promoter-TSS (NM_010715)	promoter-TSS (NM_010715)	229	NM_177312	321008	Mm.458832	NM_177312	ENSMUSG00000070814	6330408A02Rik	-	RIKEN cDNA 6330408A02 gene	protein-coding
mm_14208.1	chr2	127262115	127262120	+	1	NA	Intergenic	Intergenic	-8112	NM_139308	99138	Mm.41271	NM_139308	ENSMUSG00000027367	Stard7	AI852671|AL022671|AW544915	START domain containing 7	protein-coding
mm_66094.1	chr7	30973630	30973647	-	1	NA	promoter-TSS (NM_017405)	promoter-TSS (NM_017405)	-166	NR_038860	76415	Mm.259739	NM_175240	ENSMUSG00000046826	Fam187b	1700020B09Rik|Tmem162	family with sequence similarity 187, member B	protein-coding
mm_101453.1	chr11	30213604	30213607	-	1	NA	intron (NM_175836, intron 1 of 34)	intron (NM_175836, intron 1 of 34)	6167	NM_175836	20742	Mm.123110	NM_009260	ENSMUSG00000020315	Sptbn1	9930031C03Rik|AL033301|SPTB2|Spnb-2|Spnb2|elf1|elf3|mKIAA4049	spectrin beta, non-erythrocytic 1	protein-coding
mm_36913.1	chr4	108071328	108071408	-	1	NA	exon (NM_011327, exon 12 of 16)	exon (NM_011327, exon 12 of 16)	-15989	NR_105823	102465213		NR_105823	ENSMUSG00000098980	Mir6397	Gm28004|mmu-mir-6397	microRNA 6397	ncRNA
mm_49509.1	chr6	29854061	29854073	+	1	NA	5' UTR (NM_001347084, exon 2 of 18)	5' UTR (NM_001347084, exon 2 of 18)	326	NM_001347084	74340	Mm.210899	NM_021414	ENSMUSG00000029772	Ahcyl2	4631427C17Rik|AI227036|Adohcyase3|mKIAA0828	S-adenosylhomocysteine hydrolase-like 2	protein-coding
mm_115858.1	chr13	21293457	21293460	-	1	NA	promoter-TSS (NM_010343)	promoter-TSS (NM_010343)	-772	NM_010343	14780	Mm.1332	NM_010343	ENSMUSG00000004344	Gpx5	AV379049|Arep	glutathione peroxidase 5	protein-coding
mm_35588.1	chr4	42874228	42874239	-	1	NA	promoter-TSS (NM_177785)	promoter-TSS (NM_177785)	-30	NM_177785	277773	Mm.212727	NM_177785	ENSMUSG00000050141	Fam205c	4931430D02|FAM205CP	family with sequence similarity 205, member C	protein-coding
mm_171003.1	chr2	79329352	79329356	-	1	NA	3' UTR (NM_010576, exon 28 of 28)	3' UTR (NM_010576, exon 28 of 28)	73928	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D|Itga4B	integrin alpha 4	protein-coding
mm_41207.1	chr5	88553775	88553780	+	1	NA	promoter-TSS (NM_023054)	promoter-TSS (NM_023054)	-706	NM_023054	65961	Mm.490364	NM_023054	ENSMUSG00000070697	Utp3	2400011K09Rik|AW557551|C87704|Crl1|Crlz1|Sas10	UTP3 small subunit processome component	protein-coding
mm_76444.1	chr8	85036679	85036734	-	1	NA	promoter-TSS (NM_145390)	promoter-TSS (NM_145390)	-209	NM_145390	212999	Mm.220357	NM_145390	ENSMUSG00000031691	Tnpo2	1110034O24Rik|AA414969|AI464345|AI852433|IPO3|Knpb2b|Kpnb2b|TRN2	transportin 2 (importin 3, karyopherin beta 2b)	protein-coding
mm_168073.1	chr10	110688198	110688203	+	1	NA	Intergenic	L1Md_T|LINE|L1	-57265	NM_178609	52679	Mm.11747	NM_178609	ENSMUSG00000020185	E2f7	A630014C11Rik|D10Ertd739e	E2F transcription factor 7	protein-coding
mm_85509.1	chr9	106247718	106247734	-	1	NA	promoter-TSS (NM_001291835)	promoter-TSS (NM_001291835)	4	NM_001291835	11655	Mm.290578	NM_020559	ENSMUSG00000032786	Alas1	ALAS|ALAS-N|Alas-1|Alas-h	aminolevulinic acid synthase 1	protein-coding
mm_36485.1	chr4	83021130	83021135	-	1	NA	promoter-TSS (NM_177863)	promoter-TSS (NM_177863)	-30	NM_177863	329872	Mm.242337	NM_177863	ENSMUSG00000059049	Frem1	BC037594|D430009N09|D630008K06|crf11|eye<m02Jus>|eyes2|heb|qbrick	Fras1 related extracellular matrix protein 1	protein-coding
mm_79677.1	chr9	59750877	59750918	+	1	NA	promoter-TSS (NM_001172071)	promoter-TSS (NM_001172071)	-248	NM_001172070	71599	Mm.279070	NM_027838	ENSMUSG00000051705	Senp8	9130010J17Rik|AU020827|Den1|Nedp1|Prsc2	SUMO/sentrin specific peptidase 8	protein-coding
mm_144701.1	chr18	34862984	34863019	+	1	NA	exon (NM_007913, exon 2 of 2)	exon (NM_007913, exon 2 of 2)	1794	NM_007913	13653	Mm.181959	NM_007913	ENSMUSG00000038418	Egr1	A530045N19Rik|ETR103|Egr-1|Krox-1|Krox-24|Krox24|NGF1-A|NGFI-A|NGFIA|TIS8|Zenk|Zfp-6|Zif268|egr	early growth response 1	protein-coding
mm_94999.1	chr11	31872708	31872723	+	1	NA	exon (NM_026252, exon 1 of 10)	exon (NM_026252, exon 1 of 10)	1775	NM_026252	67579	Mm.339792	NM_026252	ENSMUSG00000020300	Cpeb4	Cpe-bp4|Cpeb-4|mCPEB-4	cytoplasmic polyadenylation element binding protein 4	protein-coding
mm_2758.1	chr1	130163828	130163834	+	1	NA	intron (NM_172485, intron 19 of 27)	intron (NM_172485, intron 19 of 27)	259212	NM_007827	13137	Mm.436759	NM_007827	ENSMUSG00000026401	Cd55b	AI323748|Daf|Daf-TM|Daf2|TM-DAF	CD55 molecule, decay accelerating factor for complement B	protein-coding
mm_8110.1	chr1	135919125	135919135	-	1	NA	promoter-TSS (NM_019645)	promoter-TSS (NM_019645)	77	NM_001313701	18772	Mm.4494	NM_019645	ENSMUSG00000026413	Pkp1	-	plakophilin 1	protein-coding
mm_4690.1	chr1	180726020	180726106	+	1	NA	promoter-TSS (NM_133225)	promoter-TSS (NM_133225)	20	NM_133225	170760	Mm.272981	NM_133225	ENSMUSG00000026499	Acbd3	60kDa|8430407O11Rik|D1Ertd10e|GCP60|GOLPH1|Gocap1|Pap7	acyl-Coenzyme A binding domain containing 3	protein-coding
mm_66508.1	chr7	45093227	45093233	-	1	NA	3' UTR (NM_010189, exon 7 of 7)	3' UTR (NM_010189, exon 7 of 7)	-1017	NM_026555	52377	Mm.29997	NM_026555	ENSMUSG00000019539	Rcn3	6030455P07Rik|D530026G20Rik|D7Ertd671e|RLP49	reticulocalbin 3, EF-hand calcium binding domain	protein-coding
mm_46801.1	chr5	113069753	113069764	-	1	NA	intron (NM_007773, intron 1 of 6)	intron (NM_007773, intron 1 of 6)	359	NM_007773	12961	Mm.1215	NM_007773	ENSMUSG00000042240	Crybb2	Cryb-2	crystallin, beta B2	protein-coding
mm_126040.1	chr15	76904343	76904361	+	1	NA	exon (NM_012053, exon 2 of 6)	exon (NM_012053, exon 2 of 6)	281	NM_012053	26961	Mm.30066	NM_012053	ENSMUSG00000003970	Rpl8	-	ribosomal protein L8	protein-coding
mm_124523.1	chr14	122106917	122106927	-	1	NA	promoter-TSS (NM_080556)	promoter-TSS (NM_080556)	52	NR_015586	319727	Mm.215552	NR_015586		A330035P11Rik	-	RIKEN cDNA A330035P11 gene	ncRNA
mm_111881.1	chr12	108118713	108118729	-	1	NA	intron (NM_028262, intron 7 of 12)	intron (NM_028262, intron 7 of 12)	60563	NM_028262	52690	Mm.159185	NM_028262	ENSMUSG00000056770	Setd3	2610102I01Rik|2610305M23Rik|6030490B17Rik|D12Ertd771e	SET domain containing 3	protein-coding
mm_134808.1	chr16	24727450	24727453	-	1	NA	intron (NM_001145954, intron 2 of 7)	RMER19C|LTR|ERVK	5596	NM_001145954	210126	Mm.209385	NM_178665	ENSMUSG00000033306	Lpp	9430020K16Rik|AA959454|AU024130|B130055L10Rik|C79715|D630048H16	LIM domain containing preferred translocation partner in lipoma	protein-coding
mm_120554.1	chr14	68083854	68083870	+	1	NA	promoter-TSS (NM_010910)	promoter-TSS (NM_010910)	-22	NM_010910	18039	Mm.1956	NM_010910	ENSMUSG00000022055	Nefl	AI847934|CMT2E|NF-L|NF68|Nfl	neurofilament, light polypeptide	protein-coding
mm_37140.1	chr4	116990154	116990197	-	1	NA	3' UTR (NM_009478, exon 10 of 10)	3' UTR (NM_009478, exon 10 of 10)	4238	NM_009478	22275	Mm.46484	NM_009478	ENSMUSG00000028684	Urod	AI323803|UPD|Uro-d	uroporphyrinogen decarboxylase	protein-coding
mm_116149.1	chr13	29984225	29984254	-	1	NA	5' UTR (NM_001289920, exon 1 of 7)	5' UTR (NM_001289920, exon 1 of 7)	152	NM_001289920	13557	Mm.268356	NM_010093	ENSMUSG00000016477	E2f3	E2F3b|E2f3a	E2F transcription factor 3	protein-coding
mm_105396.1	chr11	103403856	103403866	-	1	NA	exon (NM_183034, exon 2 of 12)	exon (NM_183034, exon 2 of 12)	8803	NM_183034	353047	Mm.18556	NM_183034	ENSMUSG00000034247	Plekhm1	AP162|B2|BC038943|D330036J23Rik	pleckstrin homology domain containing, family M (with RUN domain) member 1	protein-coding
mm_145698.1	chr18	62548952	62548968	+	1	NA	promoter-TSS (NM_177829)	promoter-TSS (NM_177829)	49	NM_177829	328971	Mm.312675	NM_177829	ENSMUSG00000044176	Spink10	A230091H23Rik	serine peptidase inhibitor, Kazal type 10	protein-coding
mm_127917.1	chr15	9535351	9535362	-	1	NA	Intergenic	Intergenic	-5480	NM_008372	16197	Mm.389	NM_008372	ENSMUSG00000003882	Il7r	CD127|IL-7Ralpha	interleukin 7 receptor	protein-coding
mm_111077.1	chr12	80168160	80168179	-	1	NA	3' UTR (NM_134156, exon 21 of 21)	3' UTR (NM_134156, exon 21 of 21)	-35325	NR_033514	69548	Mm.269712	NR_033514	ENSMUSG00000097729	2310015A10Rik	5330419I17Rik	RIKEN cDNA 2310015A10 gene	ncRNA
mm_44779.1	chr5	32132951	32132965	-	1	NA	Intergenic	Intergenic	-3514	NM_008037	14284	Mm.24684	NM_008037	ENSMUSG00000029135	Fosl2	Fra-2	fos-like antigen 2	protein-coding
mm_109611.1	chr12	112731120	112731122	+	1	NA	intron (NM_001024602, intron 2 of 18)	intron (NM_001024602, intron 2 of 18)	-2201	NR_105905	102466989		NR_105905	ENSMUSG00000099165	Mir6940	Gm27655|mmu-mir-6940	microRNA 6940	ncRNA
mm_99412.1	chr11	102276658	102276689	+	1	NA	exon (NM_148953, exon 3 of 5)	exon (NM_148953, exon 3 of 5)	7850	NM_148953	217217	Mm.216432	NM_148953	ENSMUSG00000034768	Asb16	-	ankyrin repeat and SOCS box-containing 16	protein-coding
mm_109875.1	chr12	4917007	4917015	-	1	NA	promoter-TSS (NM_001099628)	promoter-TSS (NM_001099628)	-342	NM_001099628	320817	Mm.210966	NM_001099628	ENSMUSG00000052812	Atad2b	1110014E10Rik|BC032887|C79189|D530031C13Rik	ATPase family, AAA domain containing 2B	protein-coding
mm_65282.1	chr7	24431964	24431966	-	1	NA	TTS (NM_199013)	TTS (NM_199013)	13717	NM_199013	210145	Mm.33811	NM_199013	ENSMUSG00000062028	Irgc1	F630044M05Rik|Gm1102|Gm474|Ifgge|Iigp5|Irgc	immunity-related GTPase family, cinema 1	protein-coding
mm_8407.1	chr1	151920971	151920971	-	1	NA	intron (NM_197990, intron 4 of 5)	intron (NM_197990, intron 4 of 5)	165597	NM_001311166	66967	Mm.337691	NM_001039644	ENSMUSG00000043019	Edem3	2310050N11Rik	ER degradation enhancer, mannosidase alpha-like 3	protein-coding
mm_152283.1	chr19	8888770	8888770	-	1	NA	promoter-TSS (NM_025463)	promoter-TSS (NM_025463)	0	NR_027866	67531	Mm.475113	NR_027866		5730408K05Rik	2610018C13Rik	RIKEN cDNA 5730408K05 gene	ncRNA
mm_8094.1	chr1	135843807	135843823	-	1	NA	intron (NM_001130174, intron 3 of 13)	intron (NM_001130174, intron 3 of 13)	2954	NM_001130176	21956	Mm.247470	NM_011619	ENSMUSG00000026414	Tnnt2	Tnt|cTnT	troponin T2, cardiac	protein-coding
mm_101418.1	chr11	29515018	29515040	-	1	NA	promoter-TSS (NM_001163454)	promoter-TSS (NM_001163454)	4	NM_026465	67939	Mm.251087	NM_026465	ENSMUSG00000032673	Prorsd1	2010316F05Rik|Ncrna00117|Prdxdd1	prolyl-tRNA synthetase domain containing 1	protein-coding
mm_2527.1	chr1	106861218	106861228	+	1	NA	promoter-TSS (NM_009257)	promoter-TSS (NM_009257)	43	NM_009257	20724	Mm.268618	NM_009257	ENSMUSG00000067006	Serpinb5	1110036M19Rik|AI462524|AI646751|Maspin|PI-5|Spi7|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 5	protein-coding
mm_107900.1	chr12	70842722	70842725	+	1	NA	intron (NM_028127, intron 1 of 13)	intron (NM_028127, intron 1 of 13)	17209	NM_028127	319710	Mm.2962	NM_028127	ENSMUSG00000048285	Frmd6	2610019M19Rik|4930488L10Rik|AW212977|Willin	FERM domain containing 6	protein-coding
mm_20765.1	chr2	142766260	142766261	-	1	NA	intron (NM_001081133, intron 12 of 25)	intron (NM_001081133, intron 12 of 25)	135204	NM_001081133	16558	Mm.251934	NM_001081133	ENSMUSG00000038844	Kif16b	8430434E15Rik|AA623607|AI789011|C80253|C80902|mKIAA1590	kinesin family member 16B	protein-coding
mm_150291.1	chr19	34492873	34492916	+	1	NA	3' UTR (NM_021460, exon 10 of 10)	3' UTR (NM_021460, exon 10 of 10)	-17759	NM_009890	12642	Mm.30824	NM_009890	ENSMUSG00000050370	Ch25h	AI462618|m25OH	cholesterol 25-hydroxylase	protein-coding
mm_84103.1	chr9	58312317	58312330	-	1	NA	exon (NM_010729, exon 1 of 7)	exon (NM_010729, exon 1 of 7)	889	NM_010729	16949	Mm.250492	NM_010729	ENSMUSG00000032334	Loxl1	Loxl	lysyl oxidase-like 1	protein-coding
mm_51796.1	chr6	88465418	88465482	+	1	NA	promoter-TSS (NM_019685)	promoter-TSS (NM_019685)	41	NM_019685	56505	Mm.42195	NM_019685	ENSMUSG00000030079	Ruvbl1	2510009G06Rik|Pontin52|Tip49a	RuvB-like protein 1	protein-coding
mm_73314.1	chr8	105178497	105178510	+	1	NA	intron (NM_001161456, intron 2 of 4)	intron (NM_001161456, intron 2 of 4)	7829	NM_001161458	12400	Mm.2018	NM_022309	ENSMUSG00000031885	Cbfb	AI893578|PEA2|PEBP2b|Pebp2|Pebpb2	core binding factor beta	protein-coding
mm_49889.1	chr6	38874803	38874813	+	1	NA	intron (NM_001294144, intron 1 of 14)	intron (NM_001294144, intron 1 of 14)	1382	NM_010433	15258	Mm.23790	NM_010433	ENSMUSG00000061436	Hipk2	1110014O20Rik|B230339E18Rik|Stank	homeodomain interacting protein kinase 2	protein-coding
mm_75204.1	chr8	39604961	39605018	-	1	NA	3' UTR (NM_031195, exon 9 of 9)	3' UTR (NM_031195, exon 9 of 9)	37689	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_34061.1	chr4	138454096	138454153	+	1	NA	Intergenic	CpG	-1024	NM_025451	66259	Mm.41603	NM_025451	ENSMUSG00000046447	Camk2n1	1810006K23Rik|AI848599|AI891706	calcium/calmodulin-dependent protein kinase II inhibitor 1	protein-coding
mm_112764.1	chr13	19352407	19352422	+	1	NA	Intergenic	Intergenic	43399	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_106392.1	chr11	118663522	118663522	-	1	NA	intron (NM_001039168, intron 3 of 14)	MLT1C|LTR|ERVL-MaLR	97519	NM_001285438	52897	Mm.341103	NM_001024931	ENSMUSG00000025576	Rbfox3	Fox-3|Hrnbp3|NeuN|Neuna60	RNA binding protein, fox-1 homolog (C. elegans) 3	protein-coding
mm_3562.1	chr1	150429709	150429716	+	1	NA	intron (NM_133780, intron 32 of 51)	B1_Mus2|SINE|Alu	36453	NM_021400	96875	Mm.174256	NM_021400	ENSMUSG00000006014	Prg4	CACP|DOL54|JCAP|MSF|SZP|lubricin	proteoglycan 4 (megakaryocyte stimulating factor, articular superficial zone protein)	protein-coding
mm_160423.1	chr8	85151913	85151913	+	1	NA	promoter-TSS (NM_001037922)	promoter-TSS (NM_001037922)	-11	NM_001037922	624855	Mm.390061	NM_001037922	ENSMUSG00000062687	Cks1brt	EG624855|Gm6531	CDC28 protein kinase 1b, retrogene	protein-coding
mm_31238.1	chr4	44710915	44710918	+	1	NA	promoter-TSS (NM_008782)	promoter-TSS (NM_008782)	-476	NM_008782	18507	Mm.439659	NM_008782	ENSMUSG00000014030	Pax5	BSAP|EBB-1|KLP|Pax-5	paired box 5	protein-coding
mm_29644.1	chr3	121847149	121847176	-	1	NA	Intergenic	Lx5b|LINE|L1	-31947	NM_008991	19299	Mm.399042	NM_008991	ENSMUSG00000028127	Abcd3	AI313901|AU018866|AW146054|PMP68|PMP70|Pxmp1	ATP-binding cassette, sub-family D (ALD), member 3	protein-coding
mm_24084.1	chr3	87953086	87953097	+	1	NA	3' UTR (NM_007759, exon 4 of 4)	3' UTR (NM_007759, exon 4 of 4)	4398	NM_007759	12904	Mm.4757	NM_007759	ENSMUSG00000004885	Crabp2	AI893628|Crabp-2|CrabpII	cellular retinoic acid binding protein II	protein-coding
mm_101830.1	chr11	47379353	47379368	-	1	NA	promoter-TSS (NM_011891)	promoter-TSS (NM_011891)	-58	NM_011891	24052	Mm.338890	NM_011891	ENSMUSG00000020354	Sgcd	35kDa|delta-SG	sarcoglycan, delta (dystrophin-associated glycoprotein)	protein-coding
mm_49791.1	chr6	35236513	35236556	+	1	NA	intron (NM_027513, intron 34 of 42)	intron (NM_027513, intron 34 of 42)	-16165	NR_015608	67705	Mm.228046	NR_015608	ENSMUSG00000073155	1810058I24Rik	AI414869|AI848234	RIKEN cDNA 1810058I24 gene	ncRNA
mm_169728.1	chr15	8099163	8099167	-	1	NA	promoter-TSS (NM_001081402)	promoter-TSS (NM_001081402)	44	NM_001081402	545085	Mm.321312	NM_198413	ENSMUSG00000039828	Wdr70	4833422F06Rik	WD repeat domain 70	protein-coding
mm_73850.1	chr8	117701938	117701956	+	1	NA	promoter-TSS (NM_008290)	promoter-TSS (NM_008290)	1	NM_008290	15486	Mm.276466	NM_008290	ENSMUSG00000031844	Hsd17b2	AI194836|AI194967|AI255511	hydroxysteroid (17-beta) dehydrogenase 2	protein-coding
mm_2613.1	chr1	120484616	120484651	+	1	NA	exon (NM_010766, exon 12 of 17)	exon (NM_010766, exon 12 of 17)	20451	NM_010766	17167	Mm.1856	NM_010766	ENSMUSG00000026390	Marco	AI323439|Ly112|Scara2	macrophage receptor with collagenous structure	protein-coding
mm_114174.1	chr13	55597303	55597311	+	1	NA	3' UTR (NM_026211, exon 5 of 5)	3' UTR (NM_026211, exon 5 of 5)	-2589	NM_146045	218271	Mm.139825	NM_146045	ENSMUSG00000021504	B4galt7	-	xylosylprotein beta1,4-galactosyltransferase, polypeptide 7 (galactosyltransferase I)	protein-coding
mm_40593.1	chr5	64230378	64230388	+	1	NA	promoter-TSS (NM_001289514)	promoter-TSS (NM_001289514)	26	NM_001289514	57915	Mm.286353	NM_019636	ENSMUSG00000029174	Tbc1d1	1110062G02Rik|AI385682|AW555803|Nob1|Nobq1|Tbc1|mKIAA1108	TBC1 domain family, member 1	protein-coding
mm_148384.1	chr19	3325687	3325690	+	1	NA	intron (NM_013495, intron 1 of 18)	intron (NM_013495, intron 1 of 18)	2387	NM_013495	12894	Mm.18522	NM_013495	ENSMUSG00000024900	Cpt1a	C730027G07|CPTI|Cpt1	carnitine palmitoyltransferase 1a, liver	protein-coding
mm_49831.1	chr6	37870787	37870882	+	1	NA	promoter-TSS (NM_145076)	promoter-TSS (NM_145076)	23	NM_145076	21848	Mm.41063	NM_145076	ENSMUSG00000029833	Trim24	A130082H20Rik|AI447469|D430004I05Rik|TIF1|TIF1-alpha|TIF1alpha|Tif1a	tripartite motif-containing 24	protein-coding
mm_122412.1	chr14	41030968	41030970	-	1	NA	Intergenic	L1MC|LINE|L1	-17136	NM_001316737	70564	Mm.27227	NM_027464	ENSMUSG00000021792	Fam213a	5730469M10Rik|AU040822|Adrx|Pamm	family with sequence similarity 213, member A	protein-coding
mm_142603.1	chr17	46782641	46782677	-	1	NA	promoter-TSS (NM_025433)	promoter-TSS (NM_025433)	-3	NM_025433	66229	Mm.218533	NM_025433	ENSMUSG00000063888	Rpl7l1	1500016H10Rik	ribosomal protein L7-like 1	protein-coding
mm_122241.1	chr14	33382138	33382145	-	1	NA	3' UTR (NM_001310453, exon 12 of 12)	3' UTR (NM_001310453, exon 12 of 12)	28883	NM_001310452	26419	Mm.21495	NM_016700	ENSMUSG00000021936	Mapk8	AI849689|JNK|JNK1|Prkm8|SAPK1	mitogen-activated protein kinase 8	protein-coding
mm_156587.1	chrX	152178946	152178957	+	1	NA	promoter-TSS (NM_001005475)	promoter-TSS (NM_001005475)	-58	NM_001005475	245666	Mm.33027	NM_001005475	ENSMUSG00000041115	Iqsec2	Brag1	IQ motif and Sec7 domain 2	protein-coding
mm_16466.1	chr2	180709309	180709320	+	1	NA	promoter-TSS (NM_001289652)	promoter-TSS (NM_001289652)	685	NM_177852	23856	Mm.253836	NM_011805	ENSMUSG00000038914	Dido1	6720461J16Rik|D130048F08Rik|DATF-1|DIO-1|Datf1|dido	death inducer-obliterator 1	protein-coding
mm_148763.1	chr19	6061467	6061479	+	1	NA	exon (NM_013859, exon 1 of 1)	exon (NM_013859, exon 1 of 1)	266	NM_013859	29805	Mm.2310	NM_013859	ENSMUSG00000075227	Znhit2	C11orf5|Fon|ORF6|Znhit2-ps	zinc finger, HIT domain containing 2	protein-coding
mm_94062.1	chr10	128368944	128369013	-	1	NA	5' UTR (NM_001081040, exon 1 of 5)	5' UTR (NM_001081040, exon 1 of 5)	1059	NM_001081040	210582	Mm.296876	NM_001081040	ENSMUSG00000039914	Coq10a	Gm1	coenzyme Q10A	protein-coding
mm_57943.1	chr6	134792520	134792530	-	1	NA	5' UTR (NM_130447, exon 1 of 7)	5' UTR (NM_130447, exon 1 of 7)	103	NM_130447	70686	Mm.491182	NM_130447	ENSMUSG00000030203	Dusp16	3830417M17Rik|AW558566|D6Ertd213e|MKP-7|MKP7|Mkpm	dual specificity phosphatase 16	protein-coding
mm_17767.1	chr2	32789466	32789474	-	1	NA	3' UTR (NM_001113569, exon 20 of 20)	3' UTR (NM_001113569, exon 20 of 20)	-5065	NM_025619	227736	Mm.441499	NM_025619	ENSMUSG00000038987	Cfap157	1700019L03Rik	cilia and flagella associated protein 157	protein-coding
mm_166403.1	chr5	136060027	136060036	+	1	NA	intron (NM_027158, intron 2 of 5)	intron (NM_027158, intron 2 of 5)	2764	NM_027158	69665	Mm.75713	NM_027158	ENSMUSG00000006143	Upk3bl	2310043J07Rik	uroplakin 3B-like	protein-coding
mm_25622.1	chr3	118609155	118609158	+	1	NA	intron (NM_170778, intron 1 of 22)	intron (NM_170778, intron 1 of 22)	46978	NM_170778	99586	Mm.27907	NM_170778	ENSMUSG00000033308	Dpyd	AI315208|DPD|E330028L06Rik	dihydropyrimidine dehydrogenase	protein-coding
mm_123810.1	chr14	70522680	70522703	-	1	NA	exon (NM_011359, exon 2 of 6)	exon (NM_011359, exon 2 of 6)	1390	NM_011359	20389	Mm.24040	NM_011359	ENSMUSG00000022097	Sftpc	Bricd6|SP-C|SP5|SPC|Sftp-2|Sftp2|pro-SpC	surfactant associated protein C	protein-coding
mm_8084.1	chr1	135607549	135607561	-	1	NA	Intergenic	Intergenic	-22200	NM_173437	215690	Mm.34977	NM_173437	ENSMUSG00000009418	Nav1	9530089B19|9930003A20Rik|C230080M11Rik|Pomfil3|Unc53h1|mKIAA1151|steerin-1	neuron navigator 1	protein-coding
mm_121920.1	chr14	23308879	23308883	-	1	NA	3' UTR (NM_001253364, exon 28 of 28)	3' UTR (NM_001253364, exon 28 of 28)	-214310	NR_033550	791307	Mm.364384	NR_033550	ENSMUSG00000068680	Gm10248	ENSMUSG00000068680	predicted gene 10248	ncRNA
mm_92013.1	chr10	62342645	62342660	-	1	NA	intron (NR_038038, intron 1 of 1)	intron (NR_038038, intron 1 of 1)	2045	NR_038038	70162	Mm.441212	NR_038038		Hk1os	2210417K05Rik	hexokinase 1, opposite strand	ncRNA
mm_134903.1	chr16	30186239	30186259	-	1	NA	Intergenic	Intergenic	81283	NM_027904	71756	Mm.290614	NM_027904	ENSMUSG00000023176	Cpn2	1300018K11Rik	carboxypeptidase N, polypeptide 2	protein-coding
mm_48331.1	chr5	139018401	139018411	-	1	NA	3' UTR (NM_001253890, exon 11 of 11)	3' UTR (NM_001253890, exon 11 of 11)	-23453	NM_008808	18590	Mm.2675	NM_008808	ENSMUSG00000025856	Pdgfa	-	platelet derived growth factor, alpha	protein-coding
mm_46337.1	chr5	101851501	101851505	-	1	NA	intron (NM_172882, intron 59 of 66)	intron (NM_172882, intron 59 of 66)	86373	NM_173370	74596	Mm.46764	NM_173370	ENSMUSG00000029330	Cds1	4833409J18Rik|AI314024|AW125888	CDP-diacylglycerol synthase 1	protein-coding
mm_152652.1	chr19	12765448	12765485	-	1	NA	5' UTR (NM_170786, exon 1 of 2)	5' UTR (NM_170786, exon 1 of 2)	166	NM_170786	12803	Mm.290924	NM_053007	ENSMUSG00000079415	Cntf	AI429687	ciliary neurotrophic factor	protein-coding
mm_74228.1	chr8	124197140	124197154	+	1	NA	Intergenic	Intergenic	-34247	NM_139272	108148	Mm.33808	NM_139272	ENSMUSG00000089704	Galnt2	AI480629	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2	protein-coding
mm_92374.1	chr10	76345255	76345371	-	1	NA	promoter-TSS (NM_001081419)	promoter-TSS (NM_001081419)	-22	NM_001081419	64451	Mm.33183	NM_001081419	ENSMUSG00000020231	Dip2a	4931420H10Rik|AI426328|Dip2|Kiaa0184-hp|mKIAA0184	disco interacting protein 2 homolog A	protein-coding
mm_119749.1	chr14	54153191	54153200	+	1	NA	Intergenic	Intergenic	100734	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_105192.1	chr11	102026925	102026962	-	1	NA	promoter-TSS (NM_007863)	promoter-TSS (NM_007863)	12	NM_007863	13384	Mm.20449	NM_007863	ENSMUSG00000052373	Mpp3	6430514B01|Dlgh3	membrane protein, palmitoylated 3 (MAGUK p55 subfamily member 3)	protein-coding
mm_65228.1	chr7	19715383	19715393	-	1	NA	promoter-TSS (NM_001109748)	promoter-TSS (NM_001109748)	41	NM_001109748	53333	Mm.61682	NM_016871	ENSMUSG00000002984	Tomm40	AW539759|Mom35|Tom40	translocase of outer mitochondrial membrane 40 homolog (yeast)	protein-coding
mm_161724.1	chr17	28042441	28042441	+	1	NA	intron (NM_001286040, intron 13 of 24)	intron (NM_001286040, intron 13 of 24)	38143	NM_013687	21463	Mm.29758	NM_013687	ENSMUSG00000062859	Tcp11	D17Ken1|Tcp-11	t-complex protein 11	protein-coding
mm_31053.1	chr4	41190643	41190656	+	1	NA	exon (NM_026275, exon 5 of 5)	exon (NM_026275, exon 5 of 5)	54628	NM_026275	67615	Mm.389540	NM_026275	ENSMUSG00000036241	Ube2r2	1200003M11Rik|Cdc34b|Ubc3b	ubiquitin-conjugating enzyme E2R 2	protein-coding
mm_120639.1	chr14	70520947	70520955	+	1	NA	promoter-TSS (NM_009755)	promoter-TSS (NM_009755)	-691	NR_033241	12153	Mm.27757	NM_009755	ENSMUSG00000022098	Bmp1	Pcp|Tld	bone morphogenetic protein 1	protein-coding
mm_71200.1	chr8	40886616	40886646	+	1	NA	intron (NM_007514, intron 1 of 11)	intron (NM_007514, intron 1 of 11)	24264	NM_001044740	11988	Mm.4676	NM_007514	ENSMUSG00000031596	Slc7a2	20.5|AI158848|Atrc2|CAT-2|Cat2|Tea	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	protein-coding
mm_55436.1	chr6	66896516	66896516	-	1	NA	promoter-TSS (NM_001177558)	promoter-TSS (NM_001177558)	119	NM_001177556	14701	Mm.234342	NM_025278	ENSMUSG00000036402	Gng12	2010305F15Rik|AA536815|AI115529|AI314170|AI842738	guanine nucleotide binding protein (G protein), gamma 12	protein-coding
mm_37538.1	chr4	125066635	125066648	-	1	NA	promoter-TSS (NM_175246)	promoter-TSS (NM_175246)	-52	NM_175246	76793	Mm.22548	NM_175246	ENSMUSG00000050213	Snip1	2410133M08Rik	Smad nuclear interacting protein 1	protein-coding
mm_114469.1	chr13	67810171	67810173	+	1	NA	intron (NR_045194, intron 2 of 2)	intron (NR_045194, intron 2 of 2)	-3644	NM_198322	212569	Mm.358842	NM_198322	ENSMUSG00000030446	Zfp273	6820416H06Rik|Rslcan1	zinc finger protein 273	protein-coding
mm_69688.1	chr7	139991017	139991048	-	1	NA	intron (NM_007403, intron 2 of 23)	intron (NM_007403, intron 2 of 23)	1530	NM_007403	11501	Mm.15969	NM_007403	ENSMUSG00000025473	Adam8	ADAM 8|CD156|CD156a|E430039A18Rik|MS2	a disintegrin and metallopeptidase domain 8	protein-coding
mm_13082.1	chr2	91206534	91206557	+	1	NA	intron (NM_007387, intron 6 of 10)	intron (NM_007387, intron 6 of 10)	3633	NM_007387	11432	Mm.45570	NM_007387	ENSMUSG00000002103	Acp2	Acp-2|LAP	acid phosphatase 2, lysosomal	protein-coding
mm_33759.1	chr4	134343633	134343680	+	1	NA	intron (NM_001346578, intron 1 of 7)	intron (NM_001346578, intron 1 of 7)	190	NM_001346578	230810	Mm.358876	NM_001039677	ENSMUSG00000028836	Slc30a2	ZnT-2|Znt2	solute carrier family 30 (zinc transporter), member 2	protein-coding
mm_94163.1	chr10	128746301	128746312	-	1	NA	Intergenic	Intergenic	-1573	NM_030100	78428	Mm.27358	NM_030100	ENSMUSG00000064030	Pym1	A030010B05Rik|Pym|Wibg	PYM homolog 1, exon junction complex associated factor	protein-coding
mm_126504.1	chr15	81776294	81776322	+	1	NA	exon (NM_001081016, exon 9 of 23)	exon (NM_001081016, exon 9 of 23)	-26365	NM_153484	21685	Mm.270278	NM_017376	ENSMUSG00000022389	Tef	2310028D20Rik	thyrotroph embryonic factor	protein-coding
mm_74787.1	chr8	22166414	22166435	-	1	NA	promoter-TSS (NM_011848)	promoter-TSS (NM_011848)	11	NM_011848	23954	Mm.41413	NM_011848	ENSMUSG00000031478	Nek3	-	NIMA (never in mitosis gene a)-related expressed kinase 3	protein-coding
mm_33032.1	chr4	122689331	122689369	+	1	NA	promoter-TSS (NM_023865)	promoter-TSS (NM_023865)	91	NM_023865	77432	Mm.491436	NM_023865	ENSMUSG00000023263	9530002B09Rik	Aump|Vpp1|Vppl	RIKEN cDNA 9530002B09 gene	protein-coding
mm_173106.1	chrX	155365790	155365806	+	1	NA	Intergenic	MTA_Mm|LTR|ERVL-MaLR	-27338	NM_001313711	53381	Mm.247542	NM_016764	ENSMUSG00000025289	Prdx4	AOE372|Prx-iv|Prx4|TRANK	peroxiredoxin 4	protein-coding
mm_73934.1	chr8	120002700	120002710	+	1	NA	intron (NM_030209, intron 1 of 14)	intron (NM_030209, intron 1 of 14)	10267	NM_001310635	78892	Mm.264680	NM_030209	ENSMUSG00000031825	Crispld2	1810049K24Rik|Lcrisp2|Lgl1|coffeecrisp	cysteine-rich secretory protein LCCL domain containing 2	protein-coding
mm_111260.1	chr12	85138753	85138764	-	1	NA	intron (NM_146244, intron 7 of 10)	intron (NM_146244, intron 7 of 10)	12506	NM_146244	238323	Mm.44829	NM_146244	ENSMUSG00000019235	Rps6kl1	A830084F09Rik|AW046440	ribosomal protein S6 kinase-like 1	protein-coding
mm_40983.1	chr5	77260311	77260330	+	1	NA	Intergenic	Intergenic	-5174	NM_011263	19712	Mm.28840	NM_011263	ENSMUSG00000029249	Rest	2610008J04Rik|AA407358|NRSF|REST4	RE1-silencing transcription factor	protein-coding
mm_71890.1	chr8	69832634	69832712	+	1	NA	promoter-TSS (NM_001024954)	promoter-TSS (NM_001024954)	-31	NM_001024954	80720	Mm.210823	NM_030555	ENSMUSG00000031860	Pbx4	2410015M21Rik|AI429113|AW045266	pre B cell leukemia homeobox 4	protein-coding
mm_171797.1	chr5	121204501	121204503	+	1	NA	promoter-TSS (NM_011290)	promoter-TSS (NM_011290)	1	NM_011290	19988	Mm.262021	NM_011290	ENSMUSG00000029614	Rpl6	Taxreb107	ribosomal protein L6	protein-coding
mm_144215.1	chr18	9745326	9745333	+	1	NA	intron (NM_130449, intron 2 of 9)	L1_Mur2|LINE|L1	37681	NM_130449	140792	Mm.218571	NM_130449	ENSMUSG00000036103	Colec12	CL-P1|SRCL|Scara4	collectin sub-family member 12	protein-coding
mm_124226.1	chr14	100482220	100482260	-	1	NA	Intergenic	Intergenic	-332444	NM_010636	16597	Mm.396499	NM_010636	ENSMUSG00000072294	Klf12	2700063E05Rik|AI225908|AI315654|AP-2rep|B130052C06Rik|D530033K05Rik	Kruppel-like factor 12	protein-coding
mm_71904.1	chr8	70072897	70072961	+	1	NA	promoter-TSS (NM_001293795)	promoter-TSS (NM_001293795)	5	NM_181540	107770	Mm.37974	NM_181540	ENSMUSG00000036151	Tm6sf2	-	transmembrane 6 superfamily member 2	protein-coding
mm_127211.1	chr15	99235266	99235269	+	1	NA	intron (NM_010601, intron 10 of 14)	intron (NM_010601, intron 10 of 14)	10291	NM_010601	16512	Mm.374793	NM_010601	ENSMUSG00000037579	Kcnh3	AU019351|C030044P22Rik|Elk2|Kv12.2|Melk2	potassium voltage-gated channel, subfamily H (eag-related), member 3	protein-coding
mm_169775.1	chr1	60900890	60900892	+	1	NA	Intergenic	Intergenic	-8134	NM_009843	12477	Mm.390	NM_009843	ENSMUSG00000026011	Ctla4	Cd152|Ctla-4|Ly-56	cytotoxic T-lymphocyte-associated protein 4	protein-coding
mm_157644.1	chrX	57304890	57304898	-	1	NA	intron (NM_152801, intron 2 of 21)	intron (NM_152801, intron 2 of 21)	33835	NM_152801	73341	Mm.261443	NM_152801	ENSMUSG00000031133	Arhgef6	1600028C08Rik|1700038J06Rik|4930592P22Rik|alpha-PIX	Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_70968.1	chr8	27042559	27042589	+	1	NA	promoter-TSS (NM_001039078)	promoter-TSS (NM_001039078)	19	NM_054057	114863	Mm.277501	NM_054057	ENSMUSG00000031485	Prosc	1700024N20Rik|2200002F22Rik	proline synthetase co-transcribed	protein-coding
mm_120085.1	chr14	57798621	57798629	+	1	NA	TTS (NR_037238)	TTS (NR_037238)	201	NR_037238	100526476		NR_037238	ENSMUSG00000092784	Mir3077	mir-3077|mmu-mir-3077	microRNA 3077	ncRNA
mm_59371.1	chr7	25704171	25704223	+	1	NA	exon (NM_011577, exon 6 of 7)	exon (NM_011577, exon 6 of 7)	14856	NM_028771	52132	Mm.278798	NM_028771	ENSMUSG00000002608	Ccdc97	1200014H14Rik|2810446P04Rik|AA545218|D7Ertd462e	coiled-coil domain containing 97	protein-coding
mm_90405.1	chr10	127380816	127380878	+	1	NA	Intergenic	GC_rich|Low_complexity|Low_complexity	-9464	NM_001168292	71750	Mm.29342	NM_027900	ENSMUSG00000025404	R3hdm2	1300003K24Rik|AU041262|mKIAA1002	R3H domain containing 2	protein-coding
mm_56306.1	chr6	91807391	91807411	-	1	NA	promoter-TSS (NM_001159507)	promoter-TSS (NM_001159507)	-8	NM_001159507	243547	Mm.333264	NM_001033353	ENSMUSG00000030098	Grip2	-	glutamate receptor interacting protein 2	protein-coding
mm_49893.1	chr6	38918970	38918995	+	1	NA	promoter-TSS (NM_011539)	promoter-TSS (NM_011539)	-4	NM_011539	21391	Mm.4054	NM_011539	ENSMUSG00000029925	Tbxas1	CYP5|CYP5A1|THAS|TS|TXAS|TXS	thromboxane A synthase 1, platelet	protein-coding
mm_99918.1	chr11	110399116	110399155	+	1	NA	promoter-TSS (NM_011943)	promoter-TSS (NM_011943)	13	NM_011943	26399	Mm.14487	NM_011943	ENSMUSG00000020623	Map2k6	MEK6|MKK6|Prkmk6|SAPKK3	mitogen-activated protein kinase kinase 6	protein-coding
mm_128216.1	chr15	36271368	36271373	-	1	NA	intron (NM_013923, intron 1 of 9)	intron (NM_013923, intron 1 of 9)	11777	NM_013923	30945	Mm.5181	NM_013923	ENSMUSG00000022280	Rnf19a	AA032313|Dorfin|Rnf19|UIP117|Ubce7ip2|XYbp	ring finger protein 19A	protein-coding
mm_74983.1	chr8	27141919	27141933	-	1	NA	promoter-TSS (NR_045840)	promoter-TSS (NR_045840)	-984	NR_045840	71082	Mm.395259	NR_045840		4933416M07Rik	-	RIKEN cDNA 4933416M07 gene	ncRNA
mm_136185.1	chr16	88962866	88962877	-	1	NA	promoter-TSS (NM_183296)	promoter-TSS (NM_183296)	2	NM_183296	71369	Mm.251757	NM_130872	ENSMUSG00000096534	Krtap16-3	5430404J20Rik|Krtap16-10	keratin associated protein 16-3	protein-coding
mm_55185.1	chr6	52175956	52175995	-	1	NA	intron (NM_010452, intron 3 of 4)	CpG	10301	NR_131182	105242657	Mm.490651	NR_131182	ENSMUSG00000056445	Hoxaas2	2810043O09Rik|5730446D14Rik	Hoxa cluster antisense RNA 2	ncRNA
mm_104417.1	chr11	94692545	94692576	-	1	NA	Intergenic	RMER4B|LTR|ERVK	11939	NM_001007584	432589	Mm.342314	NM_001007584	ENSMUSG00000056008	Gm11541	OTTMUSG00000002038	predicted gene 11541	protein-coding
mm_37248.1	chr4	118229008	118229016	-	1	NA	intron (NM_011213, intron 13 of 32)	intron (NM_011213, intron 13 of 32)	-18448	NR_106085	102466820		NR_106085	ENSMUSG00000098596	Mir7226	Gm27630|mmu-mir-7226	microRNA 7226	ncRNA
mm_139605.1	chr17	57303873	57303883	+	1	NA	exon (NM_001163815, exon 16 of 28)	exon (NM_001163815, exon 16 of 28)	24778	NM_001163815	22324	Mm.248172	NM_011691	ENSMUSG00000034116	Vav1	Vav|vav-T	vav 1 oncogene	protein-coding
mm_83498.1	chr9	45952860	45952884	-	1	NA	exon (NM_001289668, exon 3 of 27)	exon (NM_001289668, exon 3 of 27)	2377	NM_172257	214597	Mm.379345	NM_172257	ENSMUSG00000034908	Sidt2	B930096O19|BC023957|CGI-40	SID1 transmembrane family, member 2	protein-coding
mm_92534.1	chr10	79587096	79587102	-	1	NA	promoter-TSS (NM_199226)	promoter-TSS (NM_199226)	37	NM_199226	21830	Mm.89197	NM_011583	ENSMUSG00000020317	Theg	-	testicular haploid expressed gene	protein-coding
mm_37662.1	chr4	129084520	129084527	-	1	NA	TTS (NM_029219)	TTS (NM_029219)	-21007	NM_025452	66260	Mm.25295	NM_025452	ENSMUSG00000028786	Tmem54	1810017F10Rik|AI507302	transmembrane protein 54	protein-coding
mm_8398.1	chr1	151497696	151497697	-	1	NA	intron (NM_011277, intron 1 of 6)	intron (NM_011277, intron 1 of 6)	3127	NM_011277	19821	Mm.474038	NM_011277	ENSMUSG00000026484	Rnf2	AI326319|AI450156|AU019207|Ring1B|dinG	ring finger protein 2	protein-coding
mm_68557.1	chr7	114447396	114447422	-	1	NA	intron (NM_011055, intron 1 of 15)	intron (NM_011055, intron 1 of 15)	32155	NM_011055	18576	Mm.430730	NM_011055	ENSMUSG00000030671	Pde3b	9830102A01Rik|AI847709	phosphodiesterase 3B, cGMP-inhibited	protein-coding
mm_25067.1	chr3	99253755	99253807	+	1	NA	promoter-TSS (NM_009323)	promoter-TSS (NM_009323)	21	NM_009323	21384	Mm.88761	NM_009323	ENSMUSG00000027868	Tbx15	Tbx14|Tbx8|de	T-box 15	protein-coding
mm_98291.1	chr11	89066413	89066428	+	1	NA	intron (NR_110336, intron 2 of 3)	intron (NR_110336, intron 2 of 3)	5669	NR_110336	414094	Mm.124287	NM_001001497		Dgkeos	A930013B10Rik	diacylglycerol kinase, epsilon, opposite strand	ncRNA
mm_26455.1	chr3	142712817	142712821	+	1	NA	intron (NM_173763, intron 2 of 13)	RLTR44B|LTR|ERVK	11771	NM_001293560	229905	Mm.289643	NM_173763	ENSMUSG00000040213	Kyat3	Ccbl2|KATIII|Kat3	kynurenine aminotransferase 3	protein-coding
mm_12044.1	chr2	59160348	59160354	+	1	NA	promoter-TSS (NM_026361)	promoter-TSS (NM_026361)	-499	NM_026361	227937	Mm.260938	NM_026361	ENSMUSG00000026991	Pkp4	5031422I09Rik|9430019K17Rik|Armrp|p0071	plakophilin 4	protein-coding
mm_149090.1	chr19	8926924	8926926	+	1	NA	TTS (NM_009073)	TTS (NM_009073)	2431	NM_009073	19881	Mm.426094	NM_009073	ENSMUSG00000071648	Rom1	M101156|Rgsc1156|Rom-1|Rosp1|Tspan23	rod outer segment membrane protein 1	protein-coding
mm_3649.1	chr1	153076423	153076426	+	1	NA	intron (NM_175460, intron 3 of 10)	intron (NM_175460, intron 3 of 10)	110023	NM_008485	16782	Mm.329272	NM_008485	ENSMUSG00000026479	Lamc2	AA589349	laminin, gamma 2	protein-coding
mm_55788.1	chr6	82688453	82688458	-	1	NA	Intergenic	Intergenic	-35590	NM_025882	66979	Mm.195753	NM_025882	ENSMUSG00000030042	Pole4	2400007P05Rik|5830430F06Rik	polymerase (DNA-directed), epsilon 4 (p12 subunit)	protein-coding
mm_21334.1	chr2	157101761	157101796	-	1	NA	exon (NM_001139520, exon 15 of 17)	exon (NM_001139520, exon 15 of 17)	14723	NM_001177439	383766	Mm.480305	NM_001177439	ENSMUSG00000074628	Tldc2	Gm1332	TBC/LysM associated domain containing 2	protein-coding
mm_76112.1	chr8	80739300	80739338	-	1	NA	5' UTR (NM_053124, exon 1 of 24)	5' UTR (NM_053124, exon 1 of 24)	140	NM_053124	93762	Mm.246803	NM_053124	ENSMUSG00000031715	Smarca5	4933427E24Rik|D030040M08Rik|D330027N15Rik|MommeD4|Snf2h	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5	protein-coding
mm_76257.1	chr8	83740428	83740432	-	1	NA	intron (NM_001163031, intron 1 of 17)	intron (NM_001163031, intron 1 of 17)	881	NM_001163029	26364	Mm.334648	NM_011925	ENSMUSG00000002885	Adgre5	AA409984|Cd97|TM7LN1	adhesion G protein-coupled receptor E5	protein-coding
mm_160233.1	chr7	102714381	102714381	-	1	NA	promoter-TSS (NM_147073)	promoter-TSS (NM_147073)	30	NM_147073	18332	Mm.222837	NM_147073	ENSMUSG00000066273	Olfr33	MOR11-2|MTPCR33|ORL181	olfactory receptor 33	protein-coding
mm_15394.1	chr2	156721311	156721335	+	1	NA	promoter-TSS (NM_001042487)	promoter-TSS (NM_001042487)	44	NM_001042487	228836	Mm.22094	NM_146128	ENSMUSG00000061689	Dlgap4	AI225853|BC024558|DAP-4|DAP4|SAPAP-4|Sapap4|WBP16	discs, large homolog-associated protein 4 (Drosophila)	protein-coding
mm_149460.1	chr19	11519819	11519828	+	1	NA	intron (NM_027209, intron 1 of 6)	intron (NM_027209, intron 1 of 6)	1264	NM_027209	69774	Mm.436639	NM_027209	ENSMUSG00000024677	Ms4a6b	1810027D10Rik	membrane-spanning 4-domains, subfamily A, member 6B	protein-coding
mm_5335.1	chr1	23922371	23922391	-	1	NA	promoter-TSS (NM_028534)	promoter-TSS (NM_028534)	0	NM_028534	98366	Mm.329963	NM_028534	ENSMUSG00000026155	Smap1	1700056O10Rik|4921514B13Rik|4921525H11Rik|AI462175	small ArfGAP 1	protein-coding
mm_36202.1	chr4	62360437	62360511	-	1	NA	promoter-TSS (NM_001045528)	promoter-TSS (NM_001045528)	74	NM_001045528	338355	Mm.357792	NM_001045528	ENSMUSG00000066151	Fkbp15	BB131447|C430014M02Rik|FKBO133|FKBP-133|FKBP-15|FKBP133|mKIAA0674	FK506 binding protein 15	protein-coding
mm_17109.1	chr2	24349574	24349621	-	1	NA	exon (NM_031167, exon 5 of 5)	exon (NM_031167, exon 5 of 5)	4226	NM_001039701	16181	Mm.882	NM_031167	ENSMUSG00000026981	Il1rn	F630041P17Rik|IL-1ra	interleukin 1 receptor antagonist	protein-coding
mm_56814.1	chr6	116673772	116673789	-	1	NA	promoter-TSS (NM_178045)	promoter-TSS (NM_178045)	56	NM_178045	213391	Mm.257931	NM_178045	ENSMUSG00000042129	Rassf4	3830411C14Rik|AD037|AI586137	Ras association (RalGDS/AF-6) domain family member 4	protein-coding
mm_95121.1	chr11	34078918	34078955	+	1	NA	intron (NM_010696, intron 13 of 20)	intron (NM_010696, intron 13 of 20)	31735	NM_010696	16822	Mm.265350	NM_010696	ENSMUSG00000002699	Lcp2	AI323664|BB161688|SLP-76|SLP76|m1Khoe|twm	lymphocyte cytosolic protein 2	protein-coding
mm_106454.1	chr11	120017248	120017286	-	1	NA	intron (NM_001198787, intron 3 of 13)	intron (NM_001198787, intron 3 of 13)	-2405	NR_029767	723844		NR_029767	ENSMUSG00000065600	Mir338	Mirn338|mir-338|mmu-mir-338	microRNA 338	ncRNA
mm_13652.1	chr2	114054635	114054645	+	1	NA	non-coding (NR_028422, exon 1 of 3)	non-coding (NR_028422, exon 1 of 3)	244	NR_028422	100303644	Mm.330469	NR_028422	ENSMUSG00000092397	C130080G10Rik	-	RIKEN cDNA C130080G10 gene	ncRNA
mm_47792.1	chr5	132259035	132259052	-	1	NA	exon (NM_177047, exon 2 of 19)	exon (NM_177047, exon 2 of 19)	283300	NM_177047	319974	Mm.409595	NM_177047	ENSMUSG00000029673	Auts2	2700063G02Rik|A730011F23Rik|D830032G16Rik	autism susceptibility candidate 2	protein-coding
mm_150643.1	chr19	41848789	41848803	+	1	NA	promoter-TSS (NM_177603)	promoter-TSS (NM_177603)	-664	NM_177603	212398	Mm.222723	NM_177603	ENSMUSG00000047604	Frat2	-	frequently rearranged in advanced T cell lymphomas 2	protein-coding
mm_129635.1	chr15	80239874	80239885	-	1	NA	intron (NM_178719, intron 2 of 5)	intron (NM_178719, intron 2 of 5)	5799	NM_178719	239555	Mm.307163	NM_178719	ENSMUSG00000022412	Mief1	A230016E22|AI452372|Smcr7l	mitochondrial elongation factor 1	protein-coding
mm_112649.1	chr13	16018101	16018117	+	1	NA	intron (NM_008380, intron 4 of 4)	intron (NM_008380, intron 4 of 4)	6258	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_96566.1	chr11	69027089	69027123	+	1	NA	intron (NM_001143790, intron 7 of 22)	ID_B1|SINE|B4	11195	NM_001013256	68964	Mm.285785	NM_001013256	ENSMUSG00000020898	Ctc1	1500010J02Rik|AAF-132|AAF132	CTS telomere maintenance complex component 1	protein-coding
mm_163850.1	chr14	19418248	19418277	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	184325	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_45875.1	chr5	88328042	88328046	-	1	NA	exon (NM_008644, exon 3 of 3)	exon (NM_008644, exon 3 of 3)	10732	NM_008644	17830	Mm.200411	NM_008644	ENSMUSG00000064156	Prol1	Muc10	proline rich, lacrimal 1	protein-coding
mm_107295.1	chr12	30584474	30584491	+	1	NA	promoter-TSS (NM_172049)	promoter-TSS (NM_172049)	39	NM_172049	211986	Mm.34035	NM_172049	ENSMUSG00000043061	Tmem18	BC024093	transmembrane protein 18	protein-coding
mm_95101.1	chr11	34047291	34047299	+	1	NA	promoter-TSS (NM_010696)	promoter-TSS (NM_010696)	94	NM_010696	16822	Mm.265350	NM_010696	ENSMUSG00000002699	Lcp2	AI323664|BB161688|SLP-76|SLP76|m1Khoe|twm	lymphocyte cytosolic protein 2	protein-coding
mm_101069.1	chr11	11462251	11462272	-	1	NA	exon (NM_015785, exon 1 of 8)	exon (NM_015785, exon 1 of 8)	158	NM_015785	53604	Mm.9500	NM_015785	ENSMUSG00000020193	Zpbp	4930486K01Rik|Iam38|Sp38	zona pellucida binding protein	protein-coding
mm_169009.1	chr13	107121698	107121708	+	1	NA	Intergenic	B4A|SINE|B4	99133	NR_015471	100040322	Mm.133867	NR_015471		3830408C21Rik	-	RIKEN cDNA 3830408C21 gene	ncRNA
mm_159773.1	chr5	101664955	101664955	-	1	NA	promoter-TSS (NM_144955)	promoter-TSS (NM_144955)	-244	NM_144955	18096	Mm.193072	NM_144955	ENSMUSG00000035187	Nkx6-1	NKX6A|Nkx6.1	NK6 homeobox 1	protein-coding
mm_156361.1	chrX	139481830	139481833	+	1	NA	intron (NM_001346522, intron 1 of 13)	intron (NM_001346522, intron 1 of 13)	1464	NM_001346522	102871	Mm.26565	NM_175326	ENSMUSG00000042498	D330045A20Rik	AI132325	RIKEN cDNA D330045A20 gene	protein-coding
mm_67938.1	chr7	100121433	100121442	-	1	NA	promoter-TSS (NM_133692)	promoter-TSS (NM_133692)	63	NM_133692	67967	Mm.37562	NM_133692	ENSMUSG00000030726	Pold3	2410142G14Rik|C85233|P66|P68	polymerase (DNA-directed), delta 3, accessory subunit	protein-coding
mm_46518.1	chr5	105294065	105294102	-	1	NA	promoter-TSS (NM_194336)	promoter-TSS (NM_194336)	-384	NM_194336	100702	Mm.491210	NM_194336	ENSMUSG00000079362	Gbp6	AI595338|Mpa2l	guanylate binding protein 6	protein-coding
mm_76166.1	chr8	82380266	82380283	-	1	NA	intron (NM_001254747, intron 1 of 7)	intron (NM_001254747, intron 1 of 7)	22312	NM_001254747	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_84571.1	chr9	68972339	68972349	-	1	NA	intron (NM_013646, intron 1 of 10)	intron (NM_013646, intron 1 of 10)	206998	NR_033299	320440	Mm.483129	NM_177159		9530091C08Rik	-	RIKEN cDNA 9530091C08 gene	ncRNA
mm_41931.1	chr5	105700741	105700752	+	1	NA	promoter-TSS (NM_178701)	promoter-TSS (NM_178701)	-64	NM_178701	231549	Mm.23837	NM_178701	ENSMUSG00000046079	Lrrc8d	2810473G09Rik|4930525N13Rik|A930019F03|Lrrc5	leucine rich repeat containing 8D	protein-coding
mm_26075.1	chr3	136670431	136670439	+	1	NA	5' UTR (NM_001293622, exon 1 of 13)	5' UTR (NM_001293622, exon 1 of 13)	369	NM_001293622	19055	Mm.331389	NM_008913	ENSMUSG00000028161	Ppp3ca	2900074D19Rik|CN|Caln|Calna|CnA	protein phosphatase 3, catalytic subunit, alpha isoform	protein-coding
mm_125825.1	chr15	74957217	74957227	+	1	NA	intron (NM_001164039, intron 2 of 4)	intron (NM_001164039, intron 2 of 4)	2116	NM_001164040	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_43307.1	chr5	134703555	134703565	+	1	NA	3' UTR (NM_007925, exon 37 of 37)	3' UTR (NM_007925, exon 37 of 37)	-14970	NM_010717	16885	Mm.15409	NM_010717	ENSMUSG00000029674	Limk1	KIZ-1|LIMK-1|Limk	LIM-domain containing, protein kinase	protein-coding
mm_112750.1	chr13	19341944	19341961	+	1	NA	Intergenic	Intergenic	53861	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_32876.1	chr4	118569041	118569045	+	1	NA	intron (NM_026789, intron 20 of 21)	intron (NM_026789, intron 20 of 21)	-25317	NM_172383	230678	Mm.23639	NM_172383	ENSMUSG00000050854	Tmem125	6330530A05Rik|AV223516	transmembrane protein 125	protein-coding
mm_166331.1	chr5	114003712	114003721	+	1	NA	promoter-TSS (NM_001286397)	promoter-TSS (NM_001286397)	-19	NM_010018	13142	Mm.20115	NM_010018	ENSMUSG00000042096	Dao	AI987963|DAAO|DAMOX|Dao-1|Dao1	D-amino acid oxidase	protein-coding
mm_73622.1	chr8	110444471	110444501	+	1	NA	intron (NM_172916, intron 19 of 86)	ORR1F|LTR|ERVL-MaLR	57870	NR_105058	100861869	Mm.84499	NR_105058		Gm21283	-	predicted gene, 21283	ncRNA
mm_27132.1	chr3	32365609	32365622	-	1	NA	promoter-TSS (NM_009517)	promoter-TSS (NM_009517)	50	NM_009517	22401	Mm.35705	NM_009517	ENSMUSG00000027663	Zmat3	Wig1	zinc finger matrin type 3	protein-coding
mm_105728.1	chr11	109102709	109102750	-	1	NA	Intergenic	Intergenic	41640	NR_037978	268498	Mm.227970	NM_001085512	ENSMUSG00000078605	E030025P04Rik	Gm664	RIKEN cDNA E030025P04 gene	ncRNA
mm_128461.1	chr15	50804142	50804145	-	1	NA	intron (NM_001310485, intron 5 of 7)	intron (NM_001310485, intron 5 of 7)	84906	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_87246.1	chr10	41100968	41100968	+	1	NA	Intergenic	Intergenic	-29384	NM_199058	140741	Mm.290693	NM_199058	ENSMUSG00000046922	Gpr6	AI852874|Gm233	G protein-coupled receptor 6	protein-coding
mm_12134.1	chr2	61660970	61660983	+	1	NA	Intergenic	Intergenic	-50718	NM_021526	59029	Mm.218198	NM_021526	ENSMUSG00000026914	Psmd14	2610312C03Rik|3200001M20Rik|AA986732|Pad1|Poh1|rpm11	proteasome (prosome, macropain) 26S subunit, non-ATPase, 14	protein-coding
mm_79917.1	chr9	65546484	65546522	+	1	NA	Intergenic	ID_B1|SINE|B4	33584	NM_153119	102595	Mm.247303	NM_153119	ENSMUSG00000050721	Plekho2	AI840980|Plekhq1	pleckstrin homology domain containing, family O member 2	protein-coding
mm_30988.1	chr4	35226201	35226221	+	1	NA	promoter-TSS (NM_001081343)	promoter-TSS (NM_001081343)	-331	NM_001081343	73205	Mm.331544	NM_001081343	ENSMUSG00000028300	3110043O21Rik	AI840585	RIKEN cDNA 3110043O21 gene	protein-coding
mm_44536.1	chr5	24540379	24540383	-	1	NA	promoter-TSS (NM_080444)	promoter-TSS (NM_080444)	76	NM_080444	117590	Mm.207071	NM_080444	ENSMUSG00000038204	Asb10	Asb-10|BB137407	ankyrin repeat and SOCS box-containing 10	protein-coding
mm_37119.1	chr4	116651567	116651571	-	1	NA	5' UTR (NM_021473, exon 1 of 9)	5' UTR (NM_021473, exon 1 of 9)	105	NM_021473	58810	Mm.30085	NM_021473	ENSMUSG00000028692	Akr1a1	2610201A18Rik|Akr1a4	aldo-keto reductase family 1, member A1 (aldehyde reductase)	protein-coding
mm_11365.1	chr2	30981955	30981965	+	1	NA	promoter-TSS (NM_028846)	promoter-TSS (NM_028846)	-19	NM_144885	227707	Mm.235238	NM_144885	ENSMUSG00000026851	BC005624	-	cDNA sequence BC005624	protein-coding
mm_105191.1	chr11	102026879	102026902	-	1	NA	promoter-TSS (NM_007863)	promoter-TSS (NM_007863)	65	NM_007863	13384	Mm.20449	NM_007863	ENSMUSG00000052373	Mpp3	6430514B01|Dlgh3	membrane protein, palmitoylated 3 (MAGUK p55 subfamily member 3)	protein-coding
mm_49068.1	chr6	5511149	5511176	+	1	NA	Intergenic	Intergenic	-14884	NM_013743	27273	Mm.235547	NM_013743	ENSMUSG00000019577	Pdk4	AV005916	pyruvate dehydrogenase kinase, isoenzyme 4	protein-coding
mm_38476.1	chr4	140699644	140699650	-	1	NA	Intergenic	Intergenic	-1826	NM_173867	108911	Mm.253	NM_173867	ENSMUSG00000040945	Rcc2	2610510H01Rik|2610529N02Rik|AA536646|AA675016|Td60|mKIAA1470	regulator of chromosome condensation 2	protein-coding
mm_38715.1	chr4	145227522	145227588	-	1	NA	exon (NM_011610, exon 3 of 10)	exon (NM_011610, exon 3 of 10)	19315	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_36600.1	chr4	88910570	88910573	-	1	NA	promoter-TSS (NR_029747)	promoter-TSS (NR_029747)	91	NR_029747	723895		NR_029747	ENSMUSG00000065408	Mir31	Mirn31|miR-31|mmu-mir-31	microRNA 31	ncRNA
mm_145419.1	chr18	58556063	58556073	+	1	NA	promoter-TSS (NM_001081072)	promoter-TSS (NM_001081072)	-172	NM_001081072	225579	Mm.258517	NM_001081072	ENSMUSG00000024600	Slc27a6	4732438L20Rik|FACVL2|FATP6|VLCS-H1	solute carrier family 27 (fatty acid transporter), member 6	protein-coding
mm_25956.1	chr3	132120121	132120130	+	1	NA	intron (NM_020265, intron 1 of 3)	B1_Mur1|SINE|Alu	34833	NM_020265	56811	Mm.103593	NM_020265	ENSMUSG00000028031	Dkk2	-	dickkopf WNT signaling pathway inhibitor 2	protein-coding
mm_78495.1	chr9	32726746	32726750	+	1	NA	intron (NM_011808, intron 1 of 7)	Lx8|LINE|L1	30706	NM_001038642	23871	Mm.292415	NM_011808	ENSMUSG00000032035	Ets1	AI196000|AI448617|D230050P06|Ets-1|Tpl1|vs	E26 avian leukemia oncogene 1, 5' domain	protein-coding
mm_52112.1	chr6	97904653	97904668	+	1	NA	intron (NM_001113198, intron 1 of 9)	intron (NM_001113198, intron 1 of 9)	-25157	NM_001178049	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_163000.1	chr11	32103112	32103113	-	1	NA	Intergenic	Intergenic	-1884	NR_130637	104692	Mm.414035	NR_130637	ENSMUSG00000086386	Gm12108	BB052462|OTTMUSG00000005365	predicted gene 12108	ncRNA
mm_130518.1	chr15	98871967	98872003	-	1	NA	promoter-TSS (NM_001033276)	promoter-TSS (NM_001033276)	-780	NM_001033276	381022	Mm.264889	NM_001033276	ENSMUSG00000048154	Kmt2d	ALR|BC032281|BC058659|C430014K11Rik|KMT2B|Mll2|Mll4	lysine (K)-specific methyltransferase 2D	protein-coding
mm_51763.1	chr6	87887889	87888016	+	1	NA	promoter-TSS (NM_201244)	promoter-TSS (NM_201244)	12	NM_017477	54161	Mm.258785	NM_017477	ENSMUSG00000030058	Copg1	AU019265|BC056168|Copg|D6Ertd71e|D6Wsu16e	coatomer protein complex, subunit gamma 1	protein-coding
mm_77032.1	chr8	109340861	109340872	-	1	NA	promoter-TSS (NR_002928)	promoter-TSS (NR_002928)	42	NR_002928	384864	Mm.390083	NR_002928		Gm1943	-	WD repeat domain 70 pseudogene	pseudo
mm_86626.1	chr10	13967010	13967040	+	1	NA	intron (NM_010437, intron 1 of 8)	CpG-904	646	NM_010437	15273	Mm.42157	NM_010437	ENSMUSG00000015501	Hivep2	Gm20114|MIBP1|Schnurri-2|Shn-2	human immunodeficiency virus type I enhancer binding protein 2	protein-coding
mm_15226.1	chr2	154548855	154548863	+	1	NA	promoter-TSS (NM_029305)	promoter-TSS (NM_029305)	-45	NM_029305	75480	Mm.440434	NM_029305	ENSMUSG00000038523	1700003F12Rik	-	RIKEN cDNA 1700003F12 gene	protein-coding
mm_93966.1	chr10	127288852	127288918	-	1	NA	5' UTR (NM_001347171, exon 1 of 13)	5' UTR (NM_001347171, exon 1 of 13)	133	NM_001347171	110962	Mm.372826	NM_033072	ENSMUSG00000025409	Mbd6	D10Wsu93e	methyl-CpG binding domain protein 6	protein-coding
mm_79012.1	chr9	45597572	45597614	+	1	NA	intron (NM_001081270, intron 3 of 32)	RLTR20A4|LTR|ERVK	-166361	NR_040732	74602	Mm.394117	NR_040732	ENSMUSG00000097074	4833428L15Rik	-	RIKEN cDNA 4833428L15 gene	ncRNA
mm_39819.1	chr5	30778100	30778121	+	1	NA	exon (NM_023047, exon 4 of 13)	exon (NM_023047, exon 4 of 13)	-36531	NM_133350	100732	Mm.332295	NM_133350	ENSMUSG00000029166	Mapre3	AI790651|EB2|EB3|EBF3|RP3	microtubule-associated protein, RP/EB family, member 3	protein-coding
mm_173001.1	chrM	174	176	+	1	NA	NA	Intergenic	NA	NA								
mm_146477.1	chr18	89197315	89197344	+	1	NA	promoter-TSS (NM_178687)	promoter-TSS (NM_178687)	-98	NM_178687	225825	Mm.139293	NM_178687	ENSMUSG00000034028	Cd226	BC051526|DNAM-1|DNAM1|Pta1|TLiSA1	CD226 antigen	protein-coding
mm_95419.1	chr11	50131014	50131051	+	1	NA	promoter-TSS (NM_001290759)	promoter-TSS (NM_001290759)	-328	NM_001290759	76795	Mm.290975	NM_029745	ENSMUSG00000036644	Tbc1d9b	-	TBC1 domain family, member 9B	protein-coding
mm_132843.1	chr16	46002035	46002042	+	1	NA	intron (NM_001134480, intron 1 of 3)	intron (NM_001134480, intron 1 of 3)	8375	NM_001134480	433022	Mm.380993	NM_001134480	ENSMUSG00000087141	Plcxd2	AW494639|EG433022	phosphatidylinositol-specific phospholipase C, X domain containing 2	protein-coding
mm_4534.1	chr1	175767065	175767073	+	1	NA	exon (NM_029453, exon 12 of 28)	exon (NM_029453, exon 12 of 28)	68476	NM_029453	75820	Mm.50361	NM_029453	ENSMUSG00000026523	Wdr64	4930415O10Rik|4930511H01Rik	WD repeat domain 64	protein-coding
mm_49524.1	chr6	29985318	29985344	+	1	NA	promoter-TSS (NR_040264)	promoter-TSS (NR_040264)	2	NR_040263	76419	Mm.84522	NR_040263	ENSMUSG00000045709	Smkr-ps	1700023L04Rik	smal lysine rich protein 1, pseudogene	ncRNA
mm_139331.1	chr17	49087120	49087124	+	1	NA	intron (NM_027452, intron 2 of 2)	intron (NM_027452, intron 2 of 2)	26411	NR_038141	69311	Mm.46140	NR_038141	ENSMUSG00000101012	1700008K24Rik	-	RIKEN cDNA 1700008K24 gene	ncRNA
mm_98669.1	chr11	96282737	96282751	+	1	NA	5' UTR (NM_010461, exon 1 of 2)	5' UTR (NM_010461, exon 1 of 2)	839	NM_010461	15416	Mm.4822	NM_010461	ENSMUSG00000056648	Hoxb8	Hox-2.4	homeobox B8	protein-coding
mm_159108.1	chr2	39005125	39005125	-	1	NA	promoter-TSS (NM_025592)	promoter-TSS (NM_025592)	6	NM_025592	66489	Mm.345333	NM_025592	ENSMUSG00000062997	Rpl35	2410039E09Rik	ribosomal protein L35	protein-coding
mm_89560.1	chr10	95319271	95319283	+	1	NA	intron (NM_009950, intron 2 of 2)	intron (NM_009950, intron 2 of 2)	4432	NM_001330138	12905	Mm.473739	NM_009950	ENSMUSG00000045867	Cradd	RAIDD	CASP2 and RIPK1 domain containing adaptor with death domain	protein-coding
mm_2409.1	chr1	93825231	93825251	+	1	NA	promoter-TSS (NM_001310767)	promoter-TSS (NM_001310767)	1	NM_001310767	98314	Mm.383401	NM_178882	ENSMUSG00000073609	D2hgdh	AA408776|AA408778|AI325464	D-2-hydroxyglutarate dehydrogenase	protein-coding
mm_7436.1	chr1	119997162	119997170	-	1	NA	Intergenic	Intergenic	-1956	NM_001115074	226356	Mm.297290	NM_001115074	ENSMUSG00000036962	Cfap221	Gm101|Pcdp1	cilia and flagella associated protein 221	protein-coding
mm_58157.1	chr6	142472814	142472840	-	1	NA	5' UTR (NM_145572, exon 1 of 17)	5' UTR (NM_145572, exon 1 of 17)	282	NM_145572	232493	Mm.275975	NM_145572	ENSMUSG00000030244	Gys2	BC021322|LGS	glycogen synthase 2	protein-coding
mm_171760.1	chr5	105139546	105139559	-	1	NA	promoter-TSS (NM_001256005)	promoter-TSS (NM_001256005)	0	NM_008620	17472	Mm.440525	NM_008620	ENSMUSG00000079363	Gbp4	AW228052|Mag-2|Mpa-2|Mpa2	guanylate binding protein 4	protein-coding
mm_27062.1	chr3	27710374	27710388	-	1	NA	promoter-TSS (NM_173182)	promoter-TSS (NM_173182)	58	NM_173182	72007	Mm.38832	NM_173182	ENSMUSG00000039286	Fndc3b	1600019O04Rik|AW550168|Fad104|mKIAA4164	fibronectin type III domain containing 3B	protein-coding
mm_124877.1	chr15	10223861	10223872	+	1	NA	promoter-TSS (NM_001253781)	promoter-TSS (NM_001253781)	-40	NM_001253781	19116	Mm.10516	NM_011169	ENSMUSG00000005268	Prlr	AI987712|Pr-1|Pr-3|Prlr-rs1	prolactin receptor	protein-coding
mm_142978.1	chr17	56218563	56218637	-	1	NA	intron (NM_172624, intron 1 of 20)	(CGCGG)n|Simple_repeat|Simple_repeat	289	NM_172624	224897	Mm.205535	NM_172624	ENSMUSG00000001229	Dpp9	6430584G11Rik|A330078I11|DPP IX|DPRP2	dipeptidylpeptidase 9	protein-coding
mm_2537.1	chr1	107399644	107399665	+	1	NA	Intergenic	Intergenic	-23035	NM_027548	116872	Mm.66015	NM_027548	ENSMUSG00000067001	Serpinb7	4631416M05Rik|megsin|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 7	protein-coding
mm_62532.1	chr7	102242610	102242624	+	1	NA	intron (NM_019566, intron 1 of 1)	MIRc|SINE|MIR	7501	NM_019566	56212	Mm.259795	NM_019566	ENSMUSG00000073982	Rhog	2810426G09Rik|Arhg|Sid10750	ras homolog family member G	protein-coding
mm_172971.1	chr9	90114623	90114624	-	1	NA	5' UTR (NM_024431, exon 1 of 12)	5' UTR (NM_024431, exon 1 of 12)	197	NM_001039147	21761	Mm.426209	NM_024431	ENSMUSG00000062270	Morf4l1	MORFRG15|MRG15|TEG-189|Tex189|mKIAA4002	mortality factor 4 like 1	protein-coding
mm_34925.1	chr4	155812495	155812529	+	1	NA	promoter-TSS (NM_207678)	promoter-TSS (NM_207678)	23	NM_207678	56036	Mm.23492	NM_018856	ENSMUSG00000029068	Ccnl2	1700010A01Rik|1810019L15Rik|2010319M22Rik|AA409936|AW261738|Ania-6b|HCLA-150|Pcee|SB138	cyclin L2	protein-coding
mm_136849.1	chr17	12789176	12789186	+	1	NA	intron (NR_027784, intron 2 of 2)	intron (NR_027784, intron 2 of 2)	-19475	NM_010515	16004	Mm.26553	NM_010515	ENSMUSG00000023830	Igf2r	AI661837|CD222|CI-MPR|M6P/IGF2R|Mpr300	insulin-like growth factor 2 receptor	protein-coding
mm_56192.1	chr6	88726780	88726801	-	1	NA	intron (NM_011844, intron 2 of 7)	intron (NM_011844, intron 2 of 7)	2086	NM_001166251	23945	Mm.272197	NM_011844	ENSMUSG00000033174	Mgll	AA589436|Magl|Mgl	monoglyceride lipase	protein-coding
mm_98936.1	chr11	98358403	98358457	+	1	NA	promoter-TSS (NR_045477)	promoter-TSS (NR_045477)	62	NM_021547	59045	Mm.265546	NM_021547	ENSMUSG00000018167	Stard3	Mln64|es64	START domain containing 3	protein-coding
mm_39647.1	chr5	24645495	24645500	+	1	NA	promoter-TSS (NR_003953)	promoter-TSS (NR_003953)	44	NR_003953	72252	Mm.87446	NR_003953	ENSMUSG00000038165	1700022A21Rik	-	glycerol-3-phosphate dehydrogenase 1-like pseudogene	pseudo
mm_140174.1	chr17	80479391	80479434	+	1	NA	intron (NM_009231, intron 1 of 21)	intron (NM_009231, intron 1 of 21)	1041	NM_009231	20662	Mm.60975	NM_009231	ENSMUSG00000024241	Sos1	4430401P03Rik|9630010N06|AI449023	son of sevenless homolog 1 (Drosophila)	protein-coding
mm_44749.1	chr5	31254566	31254626	-	1	NA	intron (NM_026298, intron 43 of 47)	intron (NM_026298, intron 43 of 47)	2890	NM_027221	69815	Mm.389609	NM_027221	ENSMUSG00000029149	Krtcap3	2010001C09Rik|AW321088|Kcp3	keratinocyte associated protein 3	protein-coding
mm_22083.1	chr2	168766642	168766660	-	1	NA	intron (NM_201395, intron 1 of 3)	CpG	550	NM_201395	99377	Mm.434054	NM_175303	ENSMUSG00000027547	Sall4	5730441M18Rik|AA407717|AL022809|AW536104|C330011P20Rik|C78083|C78563|Tex20	sal-like 4 (Drosophila)	protein-coding
mm_22455.1	chr3	3188058	3188066	+	1	NA	Intergenic	Intergenic	-319968	NM_013920	30942	Mm.330897	NM_013920	ENSMUSG00000017688	Hnf4g	NR2A2	hepatocyte nuclear factor 4, gamma	protein-coding
mm_66790.1	chr7	47091425	47091433	-	1	NA	exon (NM_001163565, exon 3 of 14)	exon (NM_001163565, exon 3 of 14)	-8205	NR_106023	102465639		NR_106023	ENSMUSG00000098960	Mir7056	Gm27696|mmu-mir-7056	microRNA 7056	ncRNA
mm_47656.1	chr5	125392996	125393015	-	1	NA	Intergenic	Intergenic	-2988	NM_019639	22190	Mm.331	NM_019639	ENSMUSG00000008348	Ubc	2700054O04Rik|AI194771|Rps27a|TI-225|Uba52|Ubb	ubiquitin C	protein-coding
mm_107379.1	chr12	32954301	32954306	+	1	NA	promoter-TSS (NR_044986)	promoter-TSS (NR_044986)	117	NM_198710	19027	Mm.246304	NM_013635	ENSMUSG00000020570	Sypl	AI314763|AI604763|D12Ertd446e|PanI|Pphn|Sypl1	synaptophysin-like protein	protein-coding
mm_8255.1	chr1	138847388	138847399	-	1	NA	intron (NM_010714, intron 1 of 6)	CpG	186	NM_010714	16876	Mm.250732	NM_010714	ENSMUSG00000019230	Lhx9	3110009O07Rik|BB104635|LH2B	LIM homeobox protein 9	protein-coding
mm_163739.1	chr13	119699929	119699954	+	1	NA	exon (NM_001291439, exon 2 of 10)	exon (NM_001291439, exon 2 of 10)	9590	NM_001291439	208715	Mm.61526	NM_145942	ENSMUSG00000093930	Hmgcs1	B130032C06Rik	3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1	protein-coding
mm_166542.1	chr6	34289907	34289912	-	1	NA	Intergenic	Intergenic	27534	NR_037965	626009	Mm.451	NR_028277		Gm6644	Akr1b3p|EG626009	Akr1b3 pseudogene	pseudo
mm_45583.1	chr5	74065663	74065675	-	1	NA	intron (NM_177561, intron 1 of 8)	intron (NM_177561, intron 1 of 8)	2742	NM_177561	69727	Mm.48795	NM_177561	ENSMUSG00000054814	Usp46	1190009E20Rik|2410018I08Rik|AI451644	ubiquitin specific peptidase 46	protein-coding
mm_147492.1	chr18	47368859	47368878	-	1	NA	promoter-TSS (NM_018744)	promoter-TSS (NM_018744)	0	NM_018744	20358	Mm.40909	NM_018744	ENSMUSG00000019647	Sema6a	A730020P05Rik|AI851735|Sema6A-1|Semaq|VIa	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A	protein-coding
mm_94617.1	chr11	16758912	16758916	+	1	NA	intron (NM_207655, intron 1 of 27)	intron (NM_207655, intron 1 of 27)	6711	NM_007912	13649	Mm.8534	NM_007912	ENSMUSG00000020122	Egfr	9030024J15Rik|AI552599|Erbb|Errb1|Errp|Wa5|wa-2|wa2	epidermal growth factor receptor	protein-coding
mm_90338.1	chr10	127084727	127084746	+	1	NA	intron (NM_001033263, intron 5 of 18)	intron (NM_001033263, intron 5 of 18)	5829	NM_001033263	216439	Mm.336761	NM_001033263	ENSMUSG00000025422	Agap2	AGAP-2|Centg1|PIKE|cnt-g1|mKIAA0167	ArfGAP with GTPase domain, ankyrin repeat and PH domain 2	protein-coding
mm_66421.1	chr7	44534278	44534288	-	1	NA	intron (NM_011131, intron 22 of 26)	intron (NM_011131, intron 22 of 26)	-2212	NM_019866	272382	Mm.8012	NM_019866	ENSMUSG00000008193	Spib	Spi-B	Spi-B transcription factor (Spi-1/PU.1 related)	protein-coding
mm_3261.1	chr1	136259658	136259688	+	1	NA	3' UTR (NM_001101516, exon 1 of 1)	3' UTR (NM_001101516, exon 1 of 1)	1200	NM_001101516	383563	Mm.40367	NM_001101516	ENSMUSG00000052759	Gpr25	Gm1300	G protein-coupled receptor 25	protein-coding
mm_24589.1	chr3	93445056	93445058	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	2727	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_159454.1	chr3	146894068	146894068	+	1	NA	5' UTR (NM_001302958, exon 2 of 15)	5' UTR (NM_001302958, exon 2 of 15)	41701	NM_001302958	70892	Mm.187793	NM_027594	ENSMUSG00000036745	Ttll7	1110049N09Rik|4921517B04Rik|C630030B20|mTTLL7	tubulin tyrosine ligase-like family, member 7	protein-coding
mm_36868.1	chr4	107064719	107064729	-	1	NA	exon (NM_025500, exon 2 of 7)	exon (NM_025500, exon 2 of 7)	2142	NM_025500	56280	Mm.29517	NM_025500	ENSMUSG00000028622	Mrpl37	2300004O14Rik|AI132596|MRP-L2|Rpml2	mitochondrial ribosomal protein L37	protein-coding
mm_12956.1	chr2	90239479	90239501	+	1	NA	Intergenic	Intergenic	13496	NM_146984	406186	Mm.377948	NM_146984	ENSMUSG00000075063	Olfr142	K20|MOR227-2	olfactory receptor 142	protein-coding
mm_12769.1	chr2	79311753	79311795	+	1	NA	intron (NM_010576, intron 17 of 27)	intron (NM_010576, intron 17 of 27)	56348	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D|Itga4B	integrin alpha 4	protein-coding
mm_56988.1	chr6	120822665	120822675	-	1	NA	promoter-TSS (NM_007510)	promoter-TSS (NM_007510)	15	NM_007510	11973	Mm.29045	NM_007510	ENSMUSG00000019210	Atp6v1e1	2410029D23Rik|Atp6e|Atp6e2|Atp6v1e|D6Ertd385e|E2|P31|Vma4	ATPase, H+ transporting, lysosomal V1 subunit E1	protein-coding
mm_45846.1	chr5	87699399	87699400	-	1	NA	promoter-TSS (NM_001286023)	promoter-TSS (NM_001286023)	26	NM_001286020	12991	Mm.268737	NM_009972	ENSMUSG00000063157	Csn2	Csnb	casein beta	protein-coding
mm_96802.1	chr11	69981461	69981471	+	1	NA	promoter-TSS (NM_018740)	promoter-TSS (NM_018740)	-231	NM_018740	54351	Mm.13430	NM_018740	ENSMUSG00000018565	Elp5	Derp6|Rai12	elongator acetyltransferase complex subunit 5	protein-coding
mm_126294.1	chr15	79347631	79347644	+	1	NA	promoter-TSS (NM_001304832)	promoter-TSS (NM_001304832)	117	NM_010755	17133	Mm.86646	NM_010755	ENSMUSG00000042622	Maff	-	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein F (avian)	protein-coding
mm_60717.1	chr7	45325030	45325066	+	1	NA	promoter-TSS (NR_110499)	promoter-TSS (NR_110499)	90	NR_110499	100040970	Mm.289810	NR_110499	ENSMUSG00000046721	Rpl14-ps1	ENSMUSG00000046721|Gm9811	ribosomal protein L14, pseudogene 1	pseudo
mm_151760.1	chr19	5118346	5118358	-	1	NA	promoter-TSS (NM_008451)	promoter-TSS (NM_008451)	56	NR_045528	16594	Mm.271648	NM_008451	ENSMUSG00000024862	Klc2	8030455F02Rik|AW212649|KLC 2|KLC-2	kinesin light chain 2	protein-coding
mm_147611.1	chr18	56975334	56975376	-	1	NA	promoter-TSS (NM_029909)	promoter-TSS (NM_029909)	24	NM_029909	77422	Mm.256874	NM_029909	ENSMUSG00000024592	C330018D20Rik	AU018666	RIKEN cDNA C330018D20 gene	protein-coding
mm_97209.1	chr11	75619522	75619538	+	1	NA	exon (NM_008850, exon 9 of 12)	exon (NM_008850, exon 9 of 12)	-11490	NM_008916	19062	Mm.1458	NM_008916	ENSMUSG00000006127	Inpp5k	C62|Pps|SKIP	inositol polyphosphate 5-phosphatase K	protein-coding
mm_163826.1	chr14	19417354	19417379	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	185221	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_57564.1	chr6	127125802	127125818	-	1	NA	3' UTR (NM_009829, exon 5 of 5)	3' UTR (NM_009829, exon 5 of 5)	-16258	NM_177003	319801	Mm.101836	NM_177003	ENSMUSG00000038028	Tigar	9630033F20Rik|AA793651|AI595337|C79710|C85509	Trp53 induced glycolysis repulatory phosphatase	protein-coding
mm_18667.1	chr2	70825485	70825524	-	1	NA	promoter-TSS (NM_172664)	promoter-TSS (NM_172664)	-24	NM_172664	228012	Mm.136511	NM_172664	ENSMUSG00000041997	Tlk1	4930545J15Rik	tousled-like kinase 1	protein-coding
mm_75815.1	chr8	70331941	70331944	-	1	NA	TTS (NM_001163282)	TTS (NM_001163282)	2177	NM_008107	14559	Mm.258280	NM_008107	ENSMUSG00000087408	Gdf1	AI385651|Gdf-1	growth differentiation factor 1	protein-coding
mm_4586.1	chr1	178319143	178319171	+	1	NA	promoter-TSS (NM_025511)	promoter-TSS (NM_025511)	4	NM_025511	66359	Mm.489720	NM_025511	ENSMUSG00000026500	Cox20	2310005N03Rik|Fam36a	COX20 Cox2 chaperone	protein-coding
mm_57057.1	chr6	122486358	122486426	-	1	NA	promoter-TSS (NM_027664)	promoter-TSS (NM_027664)	-87	NM_027664	108653	Mm.277939	NM_027664	ENSMUSG00000040649	Rimklb	4931417E21Rik|4933426K21Rik|AA097693|AI325948|AU015629|Naags	ribosomal modification protein rimK-like family member B	protein-coding
mm_170668.1	chr2	118554986	118555005	+	1	NA	Intergenic	IAPLTR2_Mm|LTR|ERVK	-5309	NM_138313	171543	Mm.210125	NM_138313	ENSMUSG00000040093	Bmf	AW260063|AW411872	BCL2 modifying factor	protein-coding
mm_76339.1	chr8	84721700	84721713	-	1	NA	exon (NM_010906, exon 7 of 9)	exon (NM_010906, exon 7 of 9)	20249	NM_008535	17095	Mm.4925	NM_008535	ENSMUSG00000034041	Lyl1	Lyl-1|bHLHa18	lymphoblastomic leukemia 1	protein-coding
mm_118650.1	chr14	21741580	21741593	+	1	NA	intron (NM_001007268, intron 5 of 7)	intron (NM_001007268, intron 5 of 7)	1293	NM_013849	27389	Mm.390674	NM_013849	ENSMUSG00000021768	Dusp13	DUSP13A|DUSP13B|Gm1203|LMW-DSP6|MDSP|TMDP|TS-DSP6	dual specificity phosphatase 13	protein-coding
mm_89671.1	chr10	97506661	97506670	+	1	NA	exon (NM_007833, exon 4 of 8)	exon (NM_007833, exon 4 of 8)	24334	NM_007833	13179	Mm.56769	NM_007833	ENSMUSG00000019929	Dcn	DC|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding
mm_138902.1	chr17	43568707	43568743	+	1	NA	5' UTR (NM_013737, exon 1 of 12)	5' UTR (NM_013737, exon 1 of 12)	274	NM_013737	27226	Mm.9277	NM_013737	ENSMUSG00000023913	Pla2g7	PAF-AH|R75400	phospholipase A2, group VII (platelet-activating factor acetylhydrolase, plasma)	protein-coding
mm_156107.1	chrX	114284648	114284658	+	1	NA	Intergenic	Intergenic	-189680	NM_001290478	237010	Mm.132583	NM_172781	ENSMUSG00000025597	Klhl4	B130014A11|C130018J01Rik	kelch-like 4	protein-coding
mm_42568.1	chr5	117160463	117160467	+	1	NA	intron (NM_001081308, intron 1 of 19)	MTE2b|LTR|ERVL-MaLR	26877	NM_183306	330177	Mm.24343	NM_183306	ENSMUSG00000061288	Taok3	2900006A08Rik|A130052D22|A430105I05Rik	TAO kinase 3	protein-coding
mm_132888.1	chr16	48842609	48842631	+	1	NA	promoter-TSS (NM_020509)	promoter-TSS (NM_020509)	68	NM_020509	57262	Mm.441868	NM_020509	ENSMUSG00000061100	Retnla	1810019L16Rik|Fizz-1|Fizz1|HIMF|RELM-alpha|RELMa|RELMalpha|Xcp2	resistin like alpha	protein-coding
mm_87303.1	chr10	42535097	42535120	+	1	NA	3' UTR (NM_017472, exon 4 of 4)	3' UTR (NM_017472, exon 4 of 4)	33054	NM_017472	54198	Mm.277870	NM_017472	ENSMUSG00000019804	Snx3	SDP3	sorting nexin 3	protein-coding
mm_166250.1	chr5	78704097	78704100	+	1	NA	Intergenic	Intergenic	811806	NR_035474	100316701		NR_035474	ENSMUSG00000089570	Mir669m-1	mmu-mir-669m-1	microRNA 669m-1	ncRNA
mm_31879.1	chr4	81442427	81442444	+	1	NA	intron (NM_010820, intron 1 of 46)	CpG	380	NM_010820	17475	Mm.153039	NM_010820	ENSMUSG00000028402	Mpdz	AI225843|B930003D11Rik|MUPP1	multiple PDZ domain protein	protein-coding
mm_129101.1	chr15	76013623	76013627	-	1	NA	intron (NM_134087, intron 1 of 4)	intron (NM_134087, intron 1 of 4)	711	NM_134087	105732	Mm.267178	NM_134087	ENSMUSG00000046761	Fam83h	AA409316	family with sequence similarity 83, member H	protein-coding
mm_86568.1	chr10	11343388	11343506	+	1	NA	promoter-TSS (NM_010146)	promoter-TSS (NM_010146)	2	NM_010146	13853	Mm.89946	NM_010146	ENSMUSG00000055493	Epm2a	TG-B|Tg(TcraK,TcrbK)TG-BFlv	epilepsy, progressive myoclonic epilepsy, type 2 gene alpha	protein-coding
mm_27882.1	chr3	79173257	79173259	-	1	NA	Intergenic	Intergenic	-27383	NM_001099624	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_122035.1	chr14	29968159	29968240	-	1	NA	promoter-TSS (NM_019979)	promoter-TSS (NM_019979)	-181	NM_019979	80795	Mm.104491	NM_019979	ENSMUSG00000042682	Selenok	1110001C03Rik|AA673253|HSPC030|Hsp30|Selk	selenoprotein K	protein-coding
mm_19958.1	chr2	117342916	117342928	-	1	NA	promoter-TSS (NM_011246)	promoter-TSS (NM_011246)	-45	NM_011246	19419	Mm.42150	NM_011246	ENSMUSG00000027347	Rasgrp1	Rasgrp	RAS guanyl releasing protein 1	protein-coding
mm_144152.1	chr18	5591869	5591902	+	1	NA	promoter-TSS (NM_011546)	promoter-TSS (NM_011546)	25	NM_011546	21417	Mm.3929	NM_011546	ENSMUSG00000024238	Zeb1	3110032K11Rik|AREB6|BZP|MEB1|Nil2|TCF-8|Tcf18|Tcf8|Tw|ZEB|Zfhep|Zfhx1a|Zfx1a|Zfx1ha|[delta]EF1	zinc finger E-box binding homeobox 1	protein-coding
mm_123207.1	chr14	59365466	59365487	-	1	NA	promoter-TSS (NM_199015)	promoter-TSS (NM_199015)	14	NM_199015	219132	Mm.479285	NM_199015	ENSMUSG00000068245	Phf11d	D14Ertd668e|Phf11|Phf11l	PHD finger protein 11D	protein-coding
mm_17594.1	chr2	30720023	30720033	-	1	NA	Intergenic	Intergenic	-1182	NR_037272	100526499		NR_037272	ENSMUSG00000093091	Mir3089	mir-3089|mmu-mir-3089	microRNA 3089	ncRNA
mm_132686.1	chr16	43072223	43072233	+	1	NA	intron (NM_001285805, intron 2 of 10)	intron (NM_001285805, intron 2 of 10)	116648	NR_002445	170658	Mm.375824	NR_002445		BC002163	-	NADH dehydrogenase Fe-S protein 5 pseudogene	pseudo
mm_163743.1	chr13	119728414	119728420	-	1	NA	5' UTR (NM_175538, exon 2 of 4)	5' UTR (NM_175538, exon 2 of 4)	27465	NM_175538	245269	Mm.403943	NM_175538	ENSMUSG00000095930	Nim1k	E130304F04Rik|Nim1	NIM1 serine/threonine protein kinase	protein-coding
mm_17736.1	chr2	32694100	32694106	-	1	NA	promoter-TSS (NM_010236)	promoter-TSS (NM_010236)	72	NM_010236	14287	Mm.3830	NM_010236	ENSMUSG00000009566	Fpgs	AA408187	folylpolyglutamyl synthetase	protein-coding
mm_136160.1	chr16	88506957	88506965	-	1	NA	promoter-TSS (NM_181490)	promoter-TSS (NM_181490)	17	NM_181490	239931	Mm.126860	NM_181490	ENSMUSG00000055811	Cldn17	-	claudin 17	protein-coding
mm_47441.1	chr5	123182705	123182731	-	1	NA	promoter-TSS (NM_008277)	promoter-TSS (NM_008277)	-32	NM_008277	15445	Mm.439709	NM_008277	ENSMUSG00000029445	Hpd	Fla|Flp|Hppd|Laf	4-hydroxyphenylpyruvic acid dioxygenase	protein-coding
mm_137344.1	chr17	25139929	25139938	+	1	NA	intron (NM_001317404, intron 1 of 24)	intron (NM_001317404, intron 1 of 24)	3302	NM_001317404	26373	Mm.270587	NM_011930	ENSMUSG00000036636	Clcn7	ClC-7|D17Wsu51e	chloride channel, voltage-sensitive 7	protein-coding
mm_108851.1	chr12	98420184	98420204	+	1	NA	Intergenic	Intergenic	-103650	NR_136759	105245437	Mm.446375	NR_136759		Gm40893	-	predicted gene, 40893	ncRNA
mm_38948.1	chr4	150556502	150556518	-	1	NA	intron (NM_001085492, intron 11 of 22)	intron (NM_001085492, intron 11 of 22)	95664	NM_173774	242773	Mm.29280	NM_173774	ENSMUSG00000039838	Slc45a1	C230078B22|Dnb5	solute carrier family 45, member 1	protein-coding
mm_55999.1	chr6	86472165	86472175	-	1	NA	non-coding (NR_131125, exon 5 of 5)	non-coding (NR_131125, exon 5 of 5)	8660	NR_131125	320486	Mm.391625	NR_131125	ENSMUSG00000085589	A430078I02Rik	T25621	RIKEN cDNA A430078I02 gene	ncRNA
mm_104807.1	chr11	98775344	98775354	-	1	NA	promoter-TSS (NM_145434)	promoter-TSS (NM_145434)	28	NM_145434	217166	Mm.390397	NM_145434	ENSMUSG00000020889	Nr1d1	A530070C09Rik|R75201	nuclear receptor subfamily 1, group D, member 1	protein-coding
mm_34441.1	chr4	147940860	147940920	+	1	NA	promoter-TSS (NM_029841)	promoter-TSS (NM_029841)	-5	NM_029841	77034	Mm.183076	NM_029841	ENSMUSG00000044496	2510039O18Rik	Kiaa2013	RIKEN cDNA 2510039O18 gene	protein-coding
mm_170767.1	chr2	161109094	161109102	-	1	NA	promoter-TSS (NM_173368)	promoter-TSS (NM_173368)	-12	NR_126509	71389	Mm.122738	NM_173368	ENSMUSG00000057133	Chd6	5430439G14Rik|6330406J24Rik|CHD-6	chromodomain helicase DNA binding protein 6	protein-coding
mm_23785.1	chr3	79345337	79345349	+	1	NA	promoter-TSS (NM_001142953)	promoter-TSS (NM_001142953)	-33	NM_001142953	100233207	Mm.373801	NM_001142953	ENSMUSG00000091685	Gm17359	-	predicted gene, 17359	protein-coding
mm_32273.1	chr4	102698286	102698291	+	1	NA	Intergenic	RLTR8|LTR|ERVK	-61847	NM_001285860	73094	Mm.54201	NM_144906	ENSMUSG00000028524	Sgip1	3110007P09Rik|SGIP1alpha|gag	SH3-domain GRB2-like (endophilin) interacting protein 1	protein-coding
mm_18709.1	chr2	72075080	72075087	-	1	NA	intron (NM_001204166, intron 1 of 27)	MLT1G3|LTR|ERVL-MaLR	20466	NM_001204166	56508	Mm.196153	NM_019688	ENSMUSG00000049044	Rapgef4	1300003D15Rik|5730402K07Rik|6330581N18Rik|EPAC 2|Epac-2|Epac2|mKIAA4040	Rap guanine nucleotide exchange factor (GEF) 4	protein-coding
mm_137857.1	chr17	31114530	31114533	+	1	NA	3' UTR (NM_009593, exon 15 of 15)	3' UTR (NM_009593, exon 15 of 15)	15080	NM_011575	21786	Mm.4641	NM_011575	ENSMUSG00000024029	Tff3	ITF|mITF	trefoil factor 3, intestinal	protein-coding
mm_73365.1	chr8	105605023	105605040	+	1	NA	promoter-TSS (NM_001081241)	promoter-TSS (NM_001081241)	-198	NM_001081241	75687	Mm.41261	NM_001081241	ENSMUSG00000038604	Fam65a	2310066E14Rik|AI837433	family with sequence similarity 65, member A	protein-coding
mm_48441.1	chr5	140636019	140636033	-	1	NA	exon (NM_175274, exon 2 of 14)	exon (NM_175274, exon 2 of 14)	13005	NM_001308040	78339	Mm.28947	NM_175274	ENSMUSG00000036565	Ttyh3	2900029G13Rik|AI414930|TTY3|mTTY3	tweety family member 3	protein-coding
mm_81974.1	chr9	121297562	121297574	+	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	-20396	NM_177589	209012	Mm.371804	NM_177589	ENSMUSG00000040936	Ulk4	4932415A06Rik|A730098P15	unc-51-like kinase 4	protein-coding
mm_101889.1	chr11	48997117	48997128	-	1	NA	Intergenic	Intergenic	-4876	NM_011579	21822	Mm.15793	NM_011579	ENSMUSG00000078922	Tgtp1	Gtp2|Irgb6|Mg21|Tgtp	T cell specific GTPase 1	protein-coding
mm_57447.1	chr6	125009602	125009637	-	1	NA	promoter-TSS (NM_175557)	promoter-TSS (NM_175557)	-50	NM_175557	269800	Mm.108677	NM_175557	ENSMUSG00000038346	Zfp384	BB163993|C130073D16Rik|Ciz|NP|Nmp4	zinc finger protein 384	protein-coding
mm_33678.1	chr4	133251354	133251388	+	1	NA	exon (NM_016693, exon 24 of 29)	exon (NM_016693, exon 24 of 29)	10553	NM_016693	53608	Mm.36640	NM_016693	ENSMUSG00000028862	Map3k6	Ask2|MAPKKK6|MEKK6	mitogen-activated protein kinase kinase kinase 6	protein-coding
mm_148357.1	chr18	84951452	84951462	-	1	NA	promoter-TSS (NM_025969)	promoter-TSS (NM_025969)	67	NM_025969	67105	Mm.250617	NM_025969	ENSMUSG00000024645	Timm21	1700034H14Rik|2700002I20Rik	tranlocase of inner mitochondrial membrane 21	protein-coding
mm_126305.1	chr15	79519810	79519813	+	1	NA	intron (NM_134090, intron 1 of 4)	intron (NM_134090, intron 1 of 4)	3403	NM_134090	105785	Mm.298199	NM_134090	ENSMUSG00000010830	Kdelr3	AI173274	KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 3	protein-coding
mm_137420.1	chr17	26159673	26159674	+	1	NA	intron (NM_001159598, intron 2 of 9)	B2_Mm1t|SINE|B2	20987	NM_001159598	12005	Mm.23684	NM_009733	ENSMUSG00000024182	Axin1	AI316800|Axin|Fu|Kb|Ki|fused|kinky|knobbly	axin 1	protein-coding
mm_99347.1	chr11	101582237	101582312	+	1	NA	promoter-TSS (NM_144830)	promoter-TSS (NM_144830)	32	NM_144830	217203	Mm.280559	NM_144830	ENSMUSG00000034947	Tmem106a	0610008L10Rik|AI043106|BC022145	transmembrane protein 106A	protein-coding
mm_57941.1	chr6	134792471	134792479	-	1	NA	5' UTR (NM_130447, exon 1 of 7)	5' UTR (NM_130447, exon 1 of 7)	153	NM_130447	70686	Mm.491182	NM_130447	ENSMUSG00000030203	Dusp16	3830417M17Rik|AW558566|D6Ertd213e|MKP-7|MKP7|Mkpm	dual specificity phosphatase 16	protein-coding
mm_23143.1	chr3	38902006	38902008	+	1	NA	intron (NM_183221, intron 1 of 16)	intron (NM_183221, intron 1 of 16)	15067	NM_183221	329628	Mm.316210	NM_183221	ENSMUSG00000046743	Fat4	6030410K14Rik|9430004M15	FAT atypical cadherin 4	protein-coding
mm_23890.1	chr3	83031387	83031415	+	1	NA	exon (NM_010196, exon 5 of 5)	exon (NM_010196, exon 5 of 5)	5248	NM_001111048	14161	Mm.88793	NM_010196	ENSMUSG00000028001	Fga	ENSMUSG00000059807|Fib	fibrinogen alpha chain	protein-coding
mm_50206.1	chr6	42247409	42247471	+	1	NA	intron (NM_029555, intron 3 of 7)	intron (NM_029555, intron 3 of 7)	1505	NM_029555	76263	Mm.267014	NM_029555	ENSMUSG00000029864	Gstk1	0610025I19Rik|AW260476|DsbA-L	glutathione S-transferase kappa 1	protein-coding
mm_162463.1	chr1	130629579	130629581	-	1	NA	promoter-TSS (NM_009581)	promoter-TSS (NM_009581)	26	NM_009581	22789	Mm.4644	NM_009581	ENSMUSG00000042554	Zp3r	AV264399|SP56	zona pellucida 3 receptor	protein-coding
mm_53049.1	chr6	124739185	124739232	+	1	NA	promoter-TSS (NM_001077705)	promoter-TSS (NM_001077705)	-499	NM_001077705	15170	Mm.271799	NM_013545	ENSMUSG00000004266	Ptpn6	70Z-SHP|Hcph|PTPTY-42|Ptp1C|SH-PTP1|SHP-1|hcp|me	protein tyrosine phosphatase, non-receptor type 6	protein-coding
mm_99991.1	chr11	114727441	114727460	+	1	NA	promoter-TSS (NM_001034878)	promoter-TSS (NM_001034878)	38	NM_001034878	432611	Mm.212764	NM_001034878	ENSMUSG00000034706	Dnaic2	C030015H18Rik|Dnai2|Gm728	dynein, axonemal, intermediate chain 2	protein-coding
mm_88361.1	chr10	75936405	75936417	+	1	NA	exon (NM_175329, exon 2 of 4)	exon (NM_175329, exon 2 of 4)	838	NM_175329	103172	Mm.333849	NM_175329	ENSMUSG00000049422	Chchd10	1620401E04Rik|AI267078|Ndg2	coiled-coil-helix-coiled-coil-helix domain containing 10	protein-coding
mm_30.1	chr1	6214829	6214838	+	1	NA	5' UTR (NM_009826, exon 1 of 24)	5' UTR (NM_009826, exon 1 of 24)	171	NM_009826	12421	Mm.293811	NM_009826	ENSMUSG00000025907	Rb1cc1	2900055E04Rik|5930404L04Rik|Cc1|FIP200|LaXp180	RB1-inducible coiled-coil 1	protein-coding
mm_129065.1	chr15	75616404	75616445	-	1	NA	promoter-TSS (NM_011759)	promoter-TSS (NM_011759)	-260	NM_001044718	22701	Mm.87210	NM_011759	ENSMUSG00000047003	Zfp41	CTfin92|Zfp-41	zinc finger protein 41	protein-coding
mm_15895.1	chr2	164947742	164947748	+	1	NA	promoter-TSS (NM_013599)	promoter-TSS (NM_013599)	-474	NM_013599	17395	Mm.4406	NM_013599	ENSMUSG00000017737	Mmp9	AW743869|B/MMP9|Clg4b|Gel B|MMP-9|pro-MMP-9	matrix metallopeptidase 9	protein-coding
mm_128200.1	chr15	35913192	35913192	-	1	NA	intron (NM_177151, intron 56 of 61)	intron (NM_177151, intron 56 of 61)	25054	NM_053071	12864	Mm.548	NM_053071	ENSMUSG00000014313	Cox6c	-	cytochrome c oxidase subunit VIc	protein-coding
mm_13127.1	chr2	91730128	91730197	+	1	NA	promoter-TSS (NM_001080754)	promoter-TSS (NM_001080754)	24	NM_001080754	228361	Mm.436667	NM_172669	ENSMUSG00000040506	Ambra1	2310079H06Rik|A130023A14|AA474864|AV021921|D030051N19Rik|mKIAA1736	autophagy/beclin 1 regulator 1	protein-coding
mm_49333.1	chr6	21233445	21233447	+	1	NA	intron (NM_019697, intron 1 of 5)	L1Md_T|LINE|L1	17337	NM_019697	16508	Mm.425316	NM_019697	ENSMUSG00000060882	Kcnd2	AI839615|AW555701|Kv4.2|R75121|mKIAA1044	potassium voltage-gated channel, Shal-related family, member 2	protein-coding
mm_4637.1	chr1	179846055	179846062	+	1	NA	Intergenic	MTEa|LTR|ERVL-MaLR	-42043	NM_026375	226747	Mm.128165	NM_026375	ENSMUSG00000026491	Ahctf1	6230412P20Rik|AV011447|Elys	AT hook containing transcription factor 1	protein-coding
mm_86544.1	chr10	9336657	9336682	+	1	NA	Intergenic	Intergenic	338539	NM_177271	320825	Mm.101115	NM_177271	ENSMUSG00000060487	Samd5	E130306M17Rik	sterile alpha motif domain containing 5	protein-coding
mm_4136.1	chr1	170644524	170644570	+	1	NA	promoter-TSS (NM_177068)	promoter-TSS (NM_177068)	15	NM_177068	320078	Mm.287131	NM_177068	ENSMUSG00000038463	Olfml2b	1110018N05Rik|4832415H08Rik|AI467542	olfactomedin-like 2B	protein-coding
mm_113898.1	chr13	49197028	49197033	+	1	NA	TTS (NM_013610)	TTS (NM_013610)	9483	NM_013610	18081	Mm.18503	NM_013610	ENSMUSG00000037966	Ninj1	AU024536	ninjurin 1	protein-coding
mm_83034.1	chr9	37255647	37255665	-	1	NA	promoter-TSS (NM_001145960)	promoter-TSS (NM_001145960)	82	NM_020258	56857	Mm.440037	NM_020258	ENSMUSG00000032122	Slc37a2	G3PP|Slc37a1|cI-2|ci2	solute carrier family 37 (glycerol-3-phosphate transporter), member 2	protein-coding
mm_29617.1	chr3	121283097	121283103	-	1	NA	Intergenic	Intergenic	-8717	NM_024178	66789	Mm.269881	NM_024178	ENSMUSG00000039887	Alg14	5430428G01Rik|AI854024	asparagine-linked glycosylation 14	protein-coding
mm_10109.1	chr2	3686323	3686356	+	1	NA	Intergenic	Intergenic	-27119	NM_025626	66540	Mm.277864	NM_025626	ENSMUSG00000026655	Fam107b	3110001A13Rik|AA589595|AA959793|AI132312	family with sequence similarity 107, member B	protein-coding
mm_37034.1	chr4	115486891	115486902	-	1	NA	3' UTR (NM_007822, exon 12 of 12)	3' UTR (NM_007822, exon 12 of 12)	9245	NM_007822	13119	Mm.250901	NM_007822	ENSMUSG00000028715	Cyp4a14	AI314743	cytochrome P450, family 4, subfamily a, polypeptide 14	protein-coding
mm_24886.1	chr3	96104817	96104827	+	1	NA	intron (NM_001025614, intron 1 of 11)	CpG	295	NM_001025614	229603	Mm.272336	NM_001025613	ENSMUSG00000038495	Otud7b	2900060B22Rik|4930463P07Rik|AI462125|CEZANNE|Trabid2|Za20d1	OTU domain containing 7B	protein-coding
mm_49894.1	chr6	38918997	38919029	+	1	NA	promoter-TSS (NM_011539)	promoter-TSS (NM_011539)	27	NM_011539	21391	Mm.4054	NM_011539	ENSMUSG00000029925	Tbxas1	CYP5|CYP5A1|THAS|TS|TXAS|TXS	thromboxane A synthase 1, platelet	protein-coding
mm_76105.1	chr8	80395153	80395165	-	1	NA	Intergenic	Intergenic	-98886	NM_010369	14934	Mm.13123	NM_010369	ENSMUSG00000051839	Gypa	AI853584|CD235a|GPA	glycophorin A	protein-coding
mm_57594.1	chr6	127769428	127769456	-	1	NA	promoter-TSS (NM_201371)	promoter-TSS (NM_201371)	-283	NM_201371	381813	Mm.39750	NM_201371	ENSMUSG00000030350	Prmt8	Hrmt1l3|Hrmt1l4	protein arginine N-methyltransferase 8	protein-coding
mm_167192.1	chr7	142577244	142577260	+	1	NA	promoter-TSS (NR_030416)	promoter-TSS (NR_030416)	-105	NR_030416	735280		NR_030416	ENSMUSG00000076275	Mir675	Mirn675|mir-675|mmu-mir-675	microRNA 675	ncRNA
mm_99786.1	chr11	107353137	107353145	+	1	NA	intron (NM_145823, intron 1 of 9)	C-rich|Low_complexity|Low_complexity	117579	NM_145823	71795	Mm.397413	NM_145823	ENSMUSG00000040430	Pitpnc1	1110020B03Rik|5830436L09Rik|AI662802|AI851387|C330017I21Rik|Dnr411|RDGBB|RDGBB1|rdgB-beta	phosphatidylinositol transfer protein, cytoplasmic 1	protein-coding
mm_69957.1	chr7	142376060	142376064	-	1	NA	3' UTR (NM_009983, exon 9 of 9)	3' UTR (NM_009983, exon 9 of 9)	-2316	NM_001347541	320802	Mm.154486	NM_177265	ENSMUSG00000045777	Ifitm10	6330512M04Rik|AI848576|DSPA3	interferon induced transmembrane protein 10	protein-coding
mm_17441.1	chr2	28325474	28325481	-	1	NA	Intergenic	Intergenic	119788	NM_019498	56177	Mm.43278	NM_019498	ENSMUSG00000026833	Olfm1	AMY|AW742568|Noe1|OlfA|Pancortin|Pancortin3	olfactomedin 1	protein-coding
mm_103899.1	chr11	83575470	83575483	-	1	NA	exon (NM_011338, exon 4 of 4)	exon (NM_011338, exon 4 of 4)	3160	NM_011338	20308	Mm.416125	NM_011338	ENSMUSG00000019122	Ccl9	CCF18|MRP-2|Scya10|Scya9	chemokine (C-C motif) ligand 9	protein-coding
mm_7793.1	chr1	131514225	131514238	-	1	NA	intron (NM_001081011, intron 2 of 22)	intron (NM_001081011, intron 2 of 22)	13130	NM_001081011	14270	Mm.276259	NM_019520	ENSMUSG00000026425	Srgap2	9930124L22Rik|AI448945|FBP2|Fnbp2|srGAP3	SLIT-ROBO Rho GTPase activating protein 2	protein-coding
mm_117649.1	chr13	92794983	92795000	-	1	NA	promoter-TSS (NM_011582)	promoter-TSS (NM_011582)	-173	NM_011582	21828	Mm.20865	NM_011582	ENSMUSG00000021702	Thbs4	TSP4	thrombospondin 4	protein-coding
mm_9699.1	chr1	178406416	178406439	-	1	NA	intron (NM_026626, intron 1 of 6)	CpG	546	NM_026626	68226	Mm.252132	NM_026626	ENSMUSG00000026495	Efcab2	1700073K01Rik|D830011E08Rik	EF-hand calcium binding domain 2	protein-coding
mm_152810.1	chr19	23058174	23058184	-	1	NA	Intergenic	Intergenic	-83047	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_89065.1	chr10	82897235	82897265	+	1	NA	3' UTR (NM_001042523, exon 15 of 15)	3' UTR (NM_001042523, exon 15 of 15)	30624	NM_025499	66341	Mm.443284	NM_025499	ENSMUSG00000109864	Eid3	1700027M21Rik|NS4EB	EP300 interacting inhibitor of differentiation 3	protein-coding
mm_26537.1	chr3	146122230	146122234	+	1	NA	intron (NM_134160, intron 1 of 11)	B1_Mur1|SINE|Alu	441	NM_134160	171166	Mm.114683	NM_134160	ENSMUSG00000036853	Mcoln3	6720490O21Rik|TRPML3|Va	mucolipin 3	protein-coding
mm_135661.1	chr16	52406725	52406736	-	1	NA	intron (NM_009655, intron 1 of 15)	intron (NM_009655, intron 1 of 15)	46351	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_106648.1	chr11	121063302	121063319	-	1	NA	intron (NM_026907, intron 1 of 4)	intron (NM_026907, intron 1 of 4)	259	NM_026907	58210	Mm.116986	NM_026907	ENSMUSG00000039364	Sectm1b	1810003C24Rik|K12|Sectm1	secreted and transmembrane 1B	protein-coding
mm_97324.1	chr11	76945703	76945713	+	1	NA	promoter-TSS (NM_178645)	promoter-TSS (NM_178645)	52	NM_178645	104184	Mm.399785	NM_178645	ENSMUSG00000020840	Blmh	AI035728|Bh|Bmh	bleomycin hydrolase	protein-coding
mm_86185.1	chr9	119322422	119322449	-	1	NA	promoter-TSS (NM_133985)	promoter-TSS (NM_133985)	-8	NM_133985	108737	Mm.293565	NM_133985	ENSMUSG00000036737	Oxsr1	2210022N24Rik|2810422B09Rik|AI462649|AW209236|Osr1|mKIAA1101	oxidative-stress responsive 1	protein-coding
mm_43545.1	chr5	137553531	137553600	+	1	NA	promoter-TSS (NM_031404)	promoter-TSS (NM_031404)	10	NM_031404	83766	Mm.31646	NM_031404	ENSMUSG00000029712	Actl6b	Actl6|ArpNa|Baf53b	actin-like 6B	protein-coding
mm_166916.1	chr7	30423345	30423348	+	1	NA	promoter-TSS (NM_172142)	promoter-TSS (NM_172142)	42	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_71644.1	chr8	57651743	57651793	+	1	NA	promoter-TSS (NR_040698)	promoter-TSS (NR_040698)	15	NR_040698	100502619	Mm.393851	NR_040698		AW046200	-	expressed sequence AW046200	ncRNA
mm_30511.1	chr3	158036546	158036565	-	1	NA	promoter-TSS (NM_001289525)	promoter-TSS (NM_001289525)	84	NM_001093752	69207	Mm.223946	NM_026989	ENSMUSG00000055436	Srsf11	0610009J05Rik|2610019N13Rik|BF642805|Sfrs11	serine/arginine-rich splicing factor 11	protein-coding
mm_90701.1	chr10	130354470	130354473	+	1	NA	intron (NM_183264, intron 3 of 8)	intron (NM_183264, intron 3 of 8)	31619	NM_183264	67596	Mm.131264	NM_183264	ENSMUSG00000034833	Tespa1	5830405N20Rik|A430001F24Rik|AI450549	thymocyte expressed, positive selection associated 1	protein-coding
mm_55006.1	chr6	48836307	48836321	-	1	NA	exon (NM_001164209, exon 4 of 8)	exon (NM_001164209, exon 4 of 8)	4674	NM_023056	65963	Mm.28385	NM_023056	ENSMUSG00000029810	Tmem176b	1810009M01Rik|Clast1|Lr8	transmembrane protein 176B	protein-coding
mm_121981.1	chr14	25857206	25857236	-	1	NA	intron (NM_013469, intron 1 of 14)	intron (NM_013469, intron 1 of 14)	15066	NM_013469	11744	Mm.294083	NM_013469	ENSMUSG00000021866	Anxa11	A830099O17Rik|Anx11	annexin A11	protein-coding
mm_4106.1	chr1	167598390	167598411	+	1	NA	promoter-TSS (NM_009107)	promoter-TSS (NM_009107)	38	NM_009107	20183	Mm.3475	NM_009107	ENSMUSG00000015843	Rxrg	Nr2b3	retinoid X receptor gamma	protein-coding
mm_66789.1	chr7	47091412	47091418	-	1	NA	exon (NM_001163565, exon 3 of 14)	exon (NM_001163565, exon 3 of 14)	-8191	NR_106023	102465639		NR_106023	ENSMUSG00000098960	Mir7056	Gm27696|mmu-mir-7056	microRNA 7056	ncRNA
mm_139681.1	chr17	57415156	57415166	+	1	NA	intron (NM_010130, intron 10 of 21)	L1_Mur2|LINE|L1	56475	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_70832.1	chr8	23153264	23153276	+	1	NA	promoter-TSS (NM_029002)	promoter-TSS (NM_029002)	-1	NM_029002	74561	Mm.290028	NM_029002	ENSMUSG00000063672	Nkx6-3	9130417I07Rik|Nkx6.3	NK6 homeobox 3	protein-coding
mm_120454.1	chr14	65969742	65969792	+	1	NA	intron (NM_013492, intron 1 of 8)	MER5A|DNA|hAT-Charlie	1284	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_29650.1	chr3	122245303	122245332	-	1	NA	promoter-TSS (NM_008129)	promoter-TSS (NM_008129)	-240	NM_008129	14630	Mm.292676	NM_008129	ENSMUSG00000028124	Gclm	AI649393|Gcmc|Glclr	glutamate-cysteine ligase, modifier subunit	protein-coding
mm_152776.1	chr19	21170965	21170994	-	1	NA	Intergenic	Intergenic	66269	NR_126458	75354	Mm.243873	NR_126458		4930554I06Rik	-	RIKEN cDNA 4930554I06 gene	ncRNA
mm_92642.1	chr10	80348588	80348611	-	1	NA	promoter-TSS (NM_001285435)	promoter-TSS (NM_001285435)	-151	NR_104340	66548	Mm.71891	NM_025629	ENSMUSG00000043822	Adamtsl5	2010109H09Rik|Thsd6	ADAMTS-like 5	protein-coding
mm_67874.1	chr7	99182682	99182728	-	1	NA	promoter-TSS (NM_026384)	promoter-TSS (NM_026384)	8	NM_026384	67800	Mm.180189	NM_026384	ENSMUSG00000030747	Dgat2	0610010B06Rik|ARAT|DGAT-2	diacylglycerol O-acyltransferase 2	protein-coding
mm_143669.1	chr17	79895996	79896019	-	1	NA	exon (NM_019717, exon 1 of 13)	exon (NM_019717, exon 1 of 13)	116	NM_178050	56298	Mm.175403	NM_019717	ENSMUSG00000059811	Atl2	2010110I21Rik|AA407293|AV334690|Aip-2|Arl6ip2	atlastin GTPase 2	protein-coding
mm_86324.1	chr9	123051424	123051445	-	1	NA	exon (NM_177911, exon 8 of 14)	exon (NM_177911, exon 8 of 14)	16693	NM_177911	331046	Mm.195309	NM_177911	ENSMUSG00000025787	Tgm4	9530008N10Rik|Eapa1|TGP	transglutaminase 4 (prostate)	protein-coding
mm_133150.1	chr16	70314120	70314149	+	1	NA	5' UTR (NM_028803, exon 1 of 16)	5' UTR (NM_028803, exon 1 of 16)	185	NM_028803	74185	Mm.396102	NM_028803	ENSMUSG00000022707	Gbe1	2310045H19Rik|2810426P10Rik|D16Ertd536e	glucan (1,4-alpha-), branching enzyme 1	protein-coding
mm_109371.1	chr12	109646550	109646553	+	1	NA	non-coding (NR_028261, exon 11 of 21)	non-coding (NR_028261, exon 11 of 21)	-3066	NR_046304	100861570		NR_046304	ENSMUSG00000084549	DQ267100	-	snoRNA DQ267100	snoRNA
mm_163759.1	chr13	119791226	119791257	+	1	NA	promoter-TSS (NM_028245)	promoter-TSS (NM_028245)	-119	NM_001302550	72465	Mm.139115	NM_028245	ENSMUSG00000094870	Zfp131	2610109I01Rik|AW558871|Znf131	zinc finger protein 131	protein-coding
mm_67456.1	chr7	80402709	80402731	-	1	NA	promoter-TSS (NM_011046)	promoter-TSS (NM_011046)	92	NM_011046	18550	Mm.5241	NM_011046	ENSMUSG00000030530	Furin	9130404I01Rik|Fur|PACE|Pcsk3|SPC1	furin (paired basic amino acid cleaving enzyme)	protein-coding
mm_20816.1	chr2	144527502	144527512	-	1	NA	promoter-TSS (NM_029763)	promoter-TSS (NM_029763)	-109	NM_172859	241688	Mm.442156	NM_172859	ENSMUSG00000037259	Dzank1	2810039F03Rik|6330439K17Rik|6430408C01|AI851115|Ankrd64	double zinc ribbon and ankyrin repeat domains 1	protein-coding
mm_6373.1	chr1	72537132	72537145	-	1	NA	promoter-TSS (NM_001045533)	promoter-TSS (NM_001045533)	-574	NM_001045533	381270	Mm.337023	NM_001045533	ENSMUSG00000039372	March4	BC056494|mKIAA1399	membrane-associated ring finger (C3HC4) 4	protein-coding
mm_11680.1	chr2	35558453	35558487	+	1	NA	promoter-TSS (NM_001114125)	promoter-TSS (NM_001114125)	12	NM_001114125	69601	Mm.29629	NM_001001602	ENSMUSG00000026883	Dab2ip	2310011D08Rik|AI480459|Aip1|mKIAA1743	disabled 2 interacting protein	protein-coding
mm_105408.1	chr11	103567881	103567881	-	1	NA	intron (NM_001033434, intron 7 of 13)	MYSERV6-int|LTR|ERVK	46858	NM_001033434	380730	Mm.380214	NM_001033434	ENSMUSG00000034239	Gm884	LRRC37	predicted gene 884	protein-coding
mm_117784.1	chr13	97030604	97030638	-	1	NA	intron (NR_104276, intron 1 of 2)	RLTR51A_Mm|LTR|ERVK?	3741	NM_025585	66479	Mm.390629	NM_025585	ENSMUSG00000052075	1700029F12Rik	-	RIKEN cDNA 1700029F12 gene	protein-coding
mm_160084.1	chr7	13837410	13837410	-	1	NA	promoter-TSS (NM_001111296)	promoter-TSS (NM_001111296)	0	NM_001111296	20859	Mm.260026	NM_001111296	ENSMUSG00000078798	Sult2a1	ST2A1|Std|Sth1|mSTa1	sulfotransferase family 2A, dehydroepiandrosterone (DHEA)-preferring, member 1	protein-coding
mm_15037.1	chr2	152757059	152757071	+	1	NA	exon (NM_053091, exon 3 of 5)	exon (NM_053091, exon 3 of 5)	2892	NM_053091	84682	Mm.196668	NM_053091	ENSMUSG00000009876	Cox4i2	Cox4b|CoxIV-2	cytochrome c oxidase subunit IV isoform 2	protein-coding
mm_85595.1	chr9	107338306	107338351	-	1	NA	promoter-TSS (NM_133984)	promoter-TSS (NM_133984)	22	NM_133984	69536	Mm.259467	NM_133984	ENSMUSG00000032579	Hemk1	2310008M14Rik|AW049265	HemK methyltransferase family member 1	protein-coding
mm_22071.1	chr2	168741899	168741973	-	1	NA	promoter-TSS (NM_015731)	promoter-TSS (NM_015731)	-136	NM_015731	11981	Mm.330819	NM_015731	ENSMUSG00000027546	Atp9a	IIa	ATPase, class II, type 9A	protein-coding
mm_19457.1	chr2	92371040	92371062	-	1	NA	promoter-TSS (NM_001290775)	promoter-TSS (NM_001290775)	6	NM_001290774	228366	Mm.31158	NM_172670	ENSMUSG00000040434	Large2	5730485C17Rik|AI891893|Gyltl1b|Largel|mKIAA4105	LARGE xylosyl- and glucuronyltransferase 2	protein-coding
mm_114713.1	chr13	83575140	83575143	+	1	NA	intron (NM_001347577, intron 1 of 10)	intron (NM_001347577, intron 1 of 10)	1534	NM_001347569	17260	Mm.24001	NM_025282	ENSMUSG00000005583	Mef2c	5430401D19Rik|9930028G15Rik|AV011172|Mef2	myocyte enhancer factor 2C	protein-coding
mm_28328.1	chr3	89355560	89355584	-	1	NA	intron (NM_029974, intron 9 of 15)	intron (NM_029974, intron 9 of 15)	-5544	NM_009614	11490	Mm.274049	NM_009614	ENSMUSG00000028041	Adam15	AD56|MDC15	a disintegrin and metallopeptidase domain 15 (metargidin)	protein-coding
mm_65258.1	chr7	19887947	19887962	-	1	NA	promoter-TSS (NM_177036)	promoter-TSS (NM_177036)	11	NM_177036	319930	Mm.215839	NM_177036	ENSMUSG00000049848	Ceacam19	C130022P09Rik|CEAL1	carcinoembryonic antigen-related cell adhesion molecule 19	protein-coding
mm_44984.1	chr5	37336935	37336945	-	1	NA	promoter-TSS (NM_021292)	promoter-TSS (NM_021292)	-59	NM_021292	59056	Mm.479678	NM_021292	ENSMUSG00000029122	Evc	-	Ellis van Creveld gene syndrome	protein-coding
mm_91832.1	chr10	56982159	56982168	-	1	NA	Intergenic	Intergenic	504190	NR_045353	74928	Mm.416643	NR_045353	ENSMUSG00000097370	4930467K11Rik	-	RIKEN cDNA 4930467K11 gene	ncRNA
mm_84463.1	chr9	66592946	66592969	-	1	NA	5' UTR (NM_144937, exon 1 of 15)	5' UTR (NM_144937, exon 1 of 15)	158	NM_144937	235441	Mm.32465	NM_144937	ENSMUSG00000032376	Usp3	AA409661|BC017156	ubiquitin specific peptidase 3	protein-coding
mm_41823.1	chr5	104046789	104046810	+	1	NA	promoter-TSS (NM_028794)	promoter-TSS (NM_028794)	-65	NM_028794	74167	Mm.241484	NM_028794	ENSMUSG00000029310	Nudt9	1190002C07Rik|ADPR-PPase|AI462474	nudix (nucleoside diphosphate linked moiety X)-type motif 9	protein-coding
mm_84328.1	chr9	64021923	64021942	-	1	NA	5' UTR (NM_008542, exon 1 of 4)	5' UTR (NM_008542, exon 1 of 4)	127	NM_008542	17130	Mm.325757	NM_008542	ENSMUSG00000036867	Smad6	Madh6|b2b390Clo	SMAD family member 6	protein-coding
mm_40393.1	chr5	52787146	52787152	+	1	NA	intron (NM_001308144, intron 3 of 12)	RLTR31D_MM|LTR|ERVK	4094	NM_030185	78796	Mm.266886	NM_030185	ENSMUSG00000029179	Zcchc4	4930449I23Rik	zinc finger, CCHC domain containing 4	protein-coding
mm_36983.1	chr4	109665308	109665320	-	1	NA	promoter-TSS (NM_007671)	promoter-TSS (NM_007671)	58	NM_007671	12580	Mm.1912	NM_007671	ENSMUSG00000028551	Cdkn2c	C77269|INK4c|p18|p18-INK4c|p18-INK6|p18INK4c	cyclin-dependent kinase inhibitor 2C (p18, inhibits CDK4)	protein-coding
mm_140813.1	chr17	22864162	22864164	-	1	NA	intron (NM_177358, intron 2 of 5)	intron (NM_177358, intron 2 of 5)	2971	NM_177358	240041	Mm.328828	NM_177358	ENSMUSG00000059142	Zfp945	A630033E08Rik|C730040L01Rik	zinc finger protein 945	protein-coding
mm_114974.1	chr13	97241253	97241268	+	1	NA	5' UTR (NM_007930, exon 1 of 3)	5' UTR (NM_007930, exon 1 of 3)	155	NM_007930	13803	Mm.241073	NM_007930	ENSMUSG00000041773	Enc1	Nrpb|PIG10	ectodermal-neural cortex 1	protein-coding
mm_114952.1	chr13	96924657	96924659	+	1	NA	promoter-TSS (NM_001166065)	promoter-TSS (NM_001166065)	-31	NM_001166065	218476	Mm.483490	NM_001166065	ENSMUSG00000091387	Gcnt4	C2gnt3|Gm279|Gm73	glucosaminyl (N-acetyl) transferase 4, core 2 (beta-1,6-N-acetylglucosaminyltransferase)	protein-coding
mm_166954.1	chr7	44476350	44476354	+	1	NA	Intergenic	L1MEd|LINE|L1	6005	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_88161.1	chr10	69706230	69706266	+	1	NA	intron (NM_170730, intron 1 of 17)	intron (NM_170730, intron 1 of 17)	172540	NM_146005	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_87528.1	chr10	53343872	53343881	+	1	NA	exon (NM_001141927, exon 3 of 3)	exon (NM_001141927, exon 3 of 3)	6190	NM_001141927	18821	Mm.34145	NM_023129	ENSMUSG00000038583	Pln	Plb	phospholamban	protein-coding
mm_143794.1	chr17	81838492	81838522	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-100120	NM_011406	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_94822.1	chr11	23257457	23257464	+	1	NA	intron (NM_001035226, intron 2 of 25)	intron (NM_001035226, intron 2 of 25)	1419	NM_134014	103573	Mm.217547	NM_134014	ENSMUSG00000020290	Xpo1	AA420417|Crm1|Exp1	exportin 1	protein-coding
mm_47486.1	chr5	123879993	123880012	-	1	NA	promoter-TSS (NM_175520)	promoter-TSS (NM_175520)	18	NM_175520	243270	Mm.33362	NM_175520	ENSMUSG00000049241	Hcar1	Gpr81	hydrocarboxylic acid receptor 1	protein-coding
mm_44890.1	chr5	35094908	35094918	-	1	NA	exon (NM_013587, exon 7 of 8)	exon (NM_013587, exon 7 of 8)	10784	NM_013587	16976	Mm.277661	NM_013587	ENSMUSG00000029103	Lrpap1	AA617339|AI790446|AU042172|C77774|HBP44|RAP	low density lipoprotein receptor-related protein associated protein 1	protein-coding
mm_150402.1	chr19	36554775	36554793	+	1	NA	exon (NM_001163471, exon 1 of 21)	exon (NM_001163471, exon 1 of 21)	145	NM_172637	226098	Mm.61107	NM_172637	ENSMUSG00000041180	Hectd2	4921524L07|A630025O09Rik|AW212605	HECT domain containing 2	protein-coding
mm_138947.1	chr17	44107840	44107843	+	1	NA	Intergenic	Intergenic	-2033	NM_199016	224794	Mm.255971	NM_199016	ENSMUSG00000023961	Enpp4	4933413N07Rik|AA986363|AI195364|E-NPP 4|Gm90|mKIAA0879	ectonucleotide pyrophosphatase/phosphodiesterase 4	protein-coding
mm_5012.1	chr1	192813039	192813040	+	1	NA	Intergenic	Intergenic	-28666	NR_040468	73455	Mm.414869	NR_040468		1700065J18Rik	-	RIKEN cDNA 1700065J18 gene	ncRNA
mm_112834.1	chr13	20825271	20825274	+	1	NA	intron (NM_012054, intron 2 of 20)	ORR1C2|LTR|ERVL-MaLR	31159	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_78027.1	chr9	13766786	13766797	+	1	NA	intron (NR_024025, intron 1 of 15)	intron (NR_024025, intron 1 of 15)	17610	NR_024025	77116	Mm.210405	NM_023858	ENSMUSG00000031918	Mtmr2	6030445P13Rik	myotubularin related protein 2	protein-coding
mm_124096.1	chr14	79243616	79243625	-	1	NA	intron (NM_001033215, intron 1 of 2)	RCHARR1|DNA|hAT-Charlie	3747	NM_001033215	105590	Mm.486536	NM_001033215	ENSMUSG00000071262	Zfp957	AU017455	zinc finger protein 957	protein-coding
mm_162123.1	chrX	70394770	70394770	-	1	NA	promoter-TSS (NM_001033807)	promoter-TSS (NM_001033807)	-30	NM_001033807	619303	Mm.388146	NM_001033807	ENSMUSG00000073141	4930567H17Rik	-	RIKEN cDNA 4930567H17 gene	protein-coding
mm_33607.1	chr4	132581145	132581165	+	1	NA	3' UTR (NM_001081211, exon 2 of 2)	3' UTR (NM_001081211, exon 2 of 2)	17088	NM_001081211	19204	Mm.89389	NM_001081211	ENSMUSG00000056529	Ptafr	PAFR	platelet-activating factor receptor	protein-coding
mm_169265.1	chr13	8441717	8441717	-	1	NA	intron (NR_110345, intron 1 of 10)	LTRIS2|LTR|ERV1	238851	NM_052977	94191	Mm.425794	NM_052977	ENSMUSG00000052551	Adarb2	Adar3|RED2	adenosine deaminase, RNA-specific, B2	protein-coding
mm_126541.1	chr15	82022955	82022965	+	1	NA	exon (NM_010247, exon 5 of 13)	exon (NM_010247, exon 5 of 13)	6591	NM_010247	14375	Mm.288809	NM_010247	ENSMUSG00000022471	Xrcc6	70kDa|G22p1|Ku70	X-ray repair complementing defective repair in Chinese hamster cells 6	protein-coding
mm_103594.1	chr11	78301471	78301478	-	1	NA	promoter-TSS (NM_017407)	promoter-TSS (NM_017407)	-117	NM_017407	54141	Mm.24250	NM_017407	ENSMUSG00000002055	Spag5	AI874642|D11Bhm180e|Deepest|MAP126|Mastrin|S17	sperm associated antigen 5	protein-coding
mm_96345.1	chr11	66956509	66956525	+	1	NA	promoter-TSS (NR_130315)	promoter-TSS (NR_130315)	-121	NR_130645	71576	Mm.340077	NR_130315	ENSMUSG00000085683	9130409J20Rik	-	RIKEN cDNA 9130409J20 gene	ncRNA
mm_72417.1	chr8	81871566	81871572	+	1	NA	intron (NM_001024617, intron 8 of 24)	intron (NM_001024617, intron 8 of 24)	529007	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_134233.1	chr16	11633172	11633177	-	1	NA	intron (NM_001290148, intron 9 of 13)	intron (NM_001290148, intron 9 of 13)	-146528	NR_126430	73761	Mm.39183	NR_126430		4833415N18Rik	-	RIKEN cDNA 4833415N18 gene	ncRNA
mm_111537.1	chr12	100887871	100887887	-	1	NA	5' UTR (NM_175493, exon 2 of 3)	5' UTR (NM_175493, exon 2 of 3)	11645	NM_001177674	238377	Mm.32160	NM_175493	ENSMUSG00000047415	Gpr68	BB131428|Ogr1	G protein-coupled receptor 68	protein-coding
mm_99818.1	chr11	108606248	108606278	+	1	NA	exon (NM_029606, exon 21 of 28)	exon (NM_029606, exon 21 of 28)	-76346	NM_145688	76380	Mm.344071	NM_029586	ENSMUSG00000020728	Cep112	1700001M19Rik|1700029K01Rik|8430407H02Rik|AV043680|AV207351|Ccdc46|Macoco	centrosomal protein 112	protein-coding
mm_33506.1	chr4	130913180	130913194	+	1	NA	promoter-TSS (NM_010686)	promoter-TSS (NM_010686)	-147	NM_010686	16792	Mm.271868	NM_010686	ENSMUSG00000028581	Laptm5	E3	lysosomal-associated protein transmembrane 5	protein-coding
mm_68018.1	chr7	100959651	100959694	-	1	NA	intron (NM_183168, intron 1 of 2)	MIRb|SINE|MIR	4694	NM_183168	233571	Mm.235193	NM_183168	ENSMUSG00000048779	P2ry6	2010204J23Rik|P2Y6	pyrimidinergic receptor P2Y, G-protein coupled, 6	protein-coding
mm_105581.1	chr11	106674650	106674671	-	1	NA	intron (NM_001305157, intron 13 of 15)	intron (NM_001305157, intron 13 of 15)	40621	NM_001305158	18613	Mm.343951	NM_008816	ENSMUSG00000020717	Pecam1	C85791|Cd31|PECAM-1|Pecam	platelet/endothelial cell adhesion molecule 1	protein-coding
mm_173197.1	chrX	62776720	62776738	-	1	NA	Intergenic	Intergenic	-249718	NR_045442	75545	Mm.391270	NR_045442	ENSMUSG00000085757	1700019B21Rik	-	RIKEN cDNA 1700019B21 gene	ncRNA
mm_140853.1	chr17	23684330	23684340	-	1	NA	promoter-TSS (NM_020293)	promoter-TSS (NM_020293)	-309	NM_020293	56863	Mm.491368	NM_020293	ENSMUSG00000066720	Cldn9	nmf329	claudin 9	protein-coding
mm_135919.1	chr16	67620881	67620922	-	1	NA	promoter-TSS (NM_178721)	promoter-TSS (NM_178721)	7	NM_001347247	239857	Mm.394300	NM_178721	ENSMUSG00000064115	Cadm2	2900078E11Rik|9330131D06|A830029E02Rik|Igdf4d|Igsf4d|NECL3|SynCAM 2|SynCAM2	cell adhesion molecule 2	protein-coding
mm_168249.1	chr10	82629860	82629861	+	1	NA	promoter-TSS (NR_037190)	promoter-TSS (NR_037190)	18	NR_037190	624784	Mm.284252	NR_037190		Gm9855	ENSMUSG00000051559	thymine DNA glycosylase pseudogene	pseudo
mm_92076.1	chr10	62664039	62664079	-	1	NA	exon (NM_001033260, exon 3 of 4)	exon (NM_001033260, exon 3 of 4)	-12861	NM_053183	94213	Mm.114116	NM_053183	ENSMUSG00000020076	Ddx50	4933429B04Rik|8430408E17Rik|GU2|RH-II	DEAD (Asp-Glu-Ala-Asp) box polypeptide 50	protein-coding
mm_166799.1	chr7	3497805	3497811	-	1	NA	intron (NM_177363, intron 2 of 5)	B4|SINE|B4	4744	NM_177363	245126	Mm.245747	NM_177363	ENSMUSG00000053338	Tarm1	9930022N03Rik|ENSMUSG00000053338|Gm9904|OLT-2	T cell-interacting, activating receptor on myeloid cells 1	protein-coding
mm_8257.1	chr1	138848589	138848603	-	1	NA	Intergenic	Intergenic	-1017	NM_010714	16876	Mm.250732	NM_010714	ENSMUSG00000019230	Lhx9	3110009O07Rik|BB104635|LH2B	LIM homeobox protein 9	protein-coding
mm_139336.1	chr17	49454781	49454794	+	1	NA	exon (NM_020042, exon 11 of 11)	exon (NM_020042, exon 11 of 11)	26423	NM_020042	56738	Mm.22256	NM_020042	ENSMUSG00000064120	Mocs1	3110045D15Rik|AI043170|AW536397	molybdenum cofactor synthesis 1	protein-coding
mm_103302.1	chr11	72550256	72550264	-	1	NA	promoter-TSS (NM_029932)	promoter-TSS (NM_029932)	-14	NM_029932	77577	Mm.46185	NM_029932	ENSMUSG00000020798	Spns3	9830002I17Rik	spinster homolog 3	protein-coding
mm_112173.1	chr12	113421160	113421174	-	1	NA	Intergenic	Intergenic	-68398	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_87423.1	chr10	50773365	50773372	+	1	NA	intron (NM_198007, intron 36 of 41)	AT_rich|Low_complexity|Low_complexity	-122283	NM_011376	20464	Mm.4774	NM_011376	ENSMUSG00000019913	Sim1	bHLHe14|mSIM1	single-minded homolog 1 (Drosophila)	protein-coding
mm_74183.1	chr8	123492708	123492712	+	1	NA	intron (NM_054070, intron 9 of 16)	intron (NM_054070, intron 9 of 16)	14848	NR_028260	114896	Mm.287475	NM_054070	ENSMUSG00000031967	Afg3l1	1700047G05Rik|3110061K15Rik	AFG3-like AAA ATPase 1	protein-coding
mm_71448.1	chr8	46521563	46521582	+	1	NA	intron (NM_001302163, intron 11 of 20)	intron (NM_001302163, intron 11 of 20)	-30497	NM_027973	71876	Mm.22108	NM_027973	ENSMUSG00000031629	Cenpu	1700029A22Rik|Mlf1ip	centromere protein U	protein-coding
mm_9267.1	chr1	171632846	171632856	-	1	NA	3' UTR (NM_144539, exon 8 of 8)	3' UTR (NM_144539, exon 8 of 8)	9049	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_120437.1	chr14	65835149	65835157	+	1	NA	Intergenic	MMERGLN_LTR|LTR|ERV1	-1184	NM_028039	71988	Mm.249280	NM_028039	ENSMUSG00000022034	Esco2	2410004I17Rik|D030072L07Rik	establishment of sister chromatid cohesion N-acetyltransferase 2	protein-coding
mm_9523.1	chr1	173766946	173766979	-	1	NA	promoter-TSS (NM_008329)	promoter-TSS (NM_008329)	-43	NM_008329	15951	Mm.261270	NM_008329	ENSMUSG00000073489	Ifi204	Ifi16|p204	interferon activated gene 204	protein-coding
mm_28897.1	chr3	97994939	97994963	-	1	NA	Intergenic	Intergenic	-18587	NM_010928	18129	Mm.485843	NM_010928	ENSMUSG00000027878	Notch2	AI853703|N2	notch 2	protein-coding
mm_142179.1	chr17	36271355	36271365	-	1	NA	promoter-TSS (NM_178281)	promoter-TSS (NM_178281)	73	NM_178281	79263	Mm.40624	NM_024468	ENSMUSG00000045409	Trim39	1100001D15Rik|E130103K13Rik|RBCC-B30.2|Rnf23|mKIAA4179|tfp	tripartite motif-containing 39	protein-coding
mm_145218.1	chr18	50053395	50053404	+	1	NA	5' UTR (NM_134131, exon 1 of 2)	5' UTR (NM_134131, exon 1 of 2)	117	NM_134131	106869	Mm.27740	NM_134131	ENSMUSG00000062210	Tnfaip8	AA987150|E130304C20Rik|ENSMUSG00000073567|Gg2-1|Gm10539|Nded|Ssc-2|Tipe	tumor necrosis factor, alpha-induced protein 8	protein-coding
mm_35246.1	chr4	19877596	19877613	-	1	NA	3' UTR (NM_175406, exon 8 of 8)	3' UTR (NM_175406, exon 8 of 8)	44962	NM_175406	242341	Mm.19298	NM_175406	ENSMUSG00000028238	Atp6v0d2	1620401A02Rik|AI324824|V-ATPase	ATPase, H+ transporting, lysosomal V0 subunit D2	protein-coding
mm_77436.1	chr8	121578672	121578682	-	1	NA	exon (NM_133765, exon 1 of 9)	exon (NM_133765, exon 1 of 9)	129	NM_133765	76454	Mm.24829	NM_133765	ENSMUSG00000052934	Fbxo31	1110003O08Rik|2310046N15Rik|Fbx14|Fbxo14	F-box protein 31	protein-coding
mm_147607.1	chr18	56921286	56921295	-	1	NA	intron (NM_177115, intron 1 of 4)	intron (NM_177115, intron 1 of 4)	4258	NM_177115	320253	Mm.312623	NM_177115	ENSMUSG00000032656	March3	6330411I15Rik|A530081L18Rik|AI843639|MARCH-III	membrane-associated ring finger (C3HC4) 3	protein-coding
mm_159530.1	chr4	64020592	64020592	-	1	NA	exon (NM_011607, exon 2 of 26)	exon (NM_011607, exon 2 of 26)	26423	NM_011607	21923	Mm.980	NM_011607	ENSMUSG00000028364	Tnc	AI528729|C130033P17Rik|Hxb|TN|TN-C|Ten|cytotactin|tenascin-C	tenascin C	protein-coding
mm_115078.1	chr13	102295286	102295292	+	1	NA	Intergenic	MTEa|LTR|ERVL-MaLR	-398269	NM_008533	17079	Mm.373974	NM_008533	ENSMUSG00000021624	Cd180	F630107B15|Ly78|RP105	CD180 antigen	protein-coding
mm_34359.1	chr4	144892675	144892683	+	1	NA	promoter-TSS (NM_001172424)	promoter-TSS (NM_001172424)	-148	NM_001172424	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding
mm_98886.1	chr11	97830133	97830143	+	1	NA	intron (NM_010688, intron 4 of 6)	intron (NM_010688, intron 4 of 6)	-10642	NM_001080935	68127	Mm.110270	NM_001080935	ENSMUSG00000050538	B230217C12Rik	AI840637	RIKEN cDNA B230217C12 gene	protein-coding
mm_40567.1	chr5	62858748	62858758	+	1	NA	intron (NM_001170705, intron 7 of 8)	intron (NM_001170705, intron 7 of 8)	44930	NM_001170705	100322896	Mm.479821	NM_001170705	ENSMUSG00000090326	Dthd1	Gm17384	death domain containing 1	protein-coding
mm_88988.1	chr10	81565664	81565687	+	1	NA	exon (NM_010347, exon 7 of 7)	exon (NM_010347, exon 7 of 7)	6231	NM_001276288	14797	Mm.180013	NM_010347	ENSMUSG00000054452	Aes	AL024115|Esp1|Grg|Grg-5|Grg5|Tle5	amino-terminal enhancer of split	protein-coding
mm_106244.1	chr11	117782183	117782203	-	1	NA	promoter-TSS (NM_181856)	promoter-TSS (NM_181856)	-104	NM_001195090	217356	Mm.116675	NM_181856	ENSMUSG00000050106	Tmc8	EVIN2|Ever2|mFLJ00400	transmembrane channel-like gene family 8	protein-coding
mm_58930.1	chr7	17973562	17973570	+	1	NA	exon (NM_023289, exon 2 of 4)	exon (NM_023289, exon 2 of 4)	1399	NM_023289	66996	Mm.36666	NM_023289	ENSMUSG00000030368	Ceacam11	1600015D01Rik	carcinoembryonic antigen-related cell adhesion molecule 11	protein-coding
mm_57425.1	chr6	124914054	124914057	-	1	NA	3' UTR (NM_026988, exon 5 of 5)	3' UTR (NM_026988, exon 5 of 5)	-2350	NM_008479	16768	Mm.4528	NM_008479	ENSMUSG00000030124	Lag3	CD223|LAG-3|Ly66	lymphocyte-activation gene 3	protein-coding
mm_30422.1	chr3	152667965	152667976	-	1	NA	5' UTR (NM_001081277, exon 1 of 14)	5' UTR (NM_001081277, exon 1 of 14)	170	NM_001081277	229949	Mm.207057	NM_001081277	ENSMUSG00000039058	Ak5	-	adenylate kinase 5	protein-coding
mm_108803.1	chr12	91757024	91757036	+	1	NA	intron (NM_175367, intron 1 of 6)	intron (NM_175367, intron 1 of 6)	29406	NM_175367	108800	Mm.23125	NM_175367	ENSMUSG00000020961	Ston2	4933401N24Rik|AI425999|AW544599	stonin 2	protein-coding
mm_3390.1	chr1	140572074	140572078	+	1	NA	intron (NR_040604, intron 3 of 3)	intron (NR_040604, intron 3 of 3)	84326	NR_040604	75910	Mm.483845	NR_040604	ENSMUSG00000102368	4930590L20Rik	-	RIKEN cDNA 4930590L20 gene	ncRNA
mm_70933.1	chr8	25849611	25849617	+	1	NA	promoter-TSS (NM_008432)	promoter-TSS (NM_008432)	-9	NM_008432	16532	Mm.289679	NM_008432	ENSMUSG00000031576	Kcnu1	Kcnma3|Slo3|mSlo3	potassium channel, subfamily U, member 1	protein-coding
mm_31713.1	chr4	62634367	62634388	+	1	NA	intron (NM_134257, intron 6 of 15)	intron (NM_134257, intron 6 of 15)	14705	NM_134257	50780	Mm.286753	NM_019492	ENSMUSG00000059810	Rgs3	4930506N09Rik|C2PA-RGS3|C2pa|PDZ-RGS3|RGS3S	regulator of G-protein signaling 3	protein-coding
mm_156994.1	chrX	7422950	7422974	-	1	NA	promoter-TSS (NR_027924)	promoter-TSS (NR_027924)	26	NR_027924	68355	Mm.45111	NR_027924		2010204K13Rik	0610010M13Rik|Cip7	RIKEN cDNA 2010204K13 gene	ncRNA
mm_6178.1	chr1	65100673	65100683	-	1	NA	exon (NM_007774, exon 3 of 3)	exon (NM_007774, exon 3 of 3)	2685	NM_007774	12964	Mm.26904	NM_007774	ENSMUSG00000044429	Cryga	Cryg-4|DGcry-4	crystallin, gamma A	protein-coding
mm_116749.1	chr13	51798534	51798558	-	1	NA	Intergenic	Intergenic	-4799	NM_013660	20354	Mm.33903	NM_013660	ENSMUSG00000021451	Sema4d	CD100|Semacl2|Semaj|Semcl2|coll-4	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D	protein-coding
mm_63101.1	chr7	122627619	122627623	+	1	NA	intron (NM_001316672, intron 16 of 16)	intron (NM_001316672, intron 16 of 16)	-44123	NM_019430	54376	Mm.444212	NM_019430	ENSMUSG00000066189	Cacng3	-	calcium channel, voltage-dependent, gamma subunit 3	protein-coding
mm_131430.1	chr16	15637845	15637884	+	1	NA	promoter-TSS (NM_011159)	promoter-TSS (NM_011159)	-2	NM_011159	19090	Mm.71	NM_011159	ENSMUSG00000022672	Prkdc	AI326420|AU019811|DNA-PKcs|DNAPDcs|DNAPK|DNPK1|DOXNPH|HYRC1|XRCC7|dxnph|p460|scid|slip	protein kinase, DNA activated, catalytic polypeptide	protein-coding
mm_144550.1	chr18	30322422	30322423	+	1	NA	intron (NM_181414, intron 19 of 24)	intron (NM_181414, intron 19 of 24)	49526	NM_181414	225326	Mm.194127	NM_181414	ENSMUSG00000033628	Pik3c3	5330434F23Rik|Vps34	phosphoinositide-3-kinase, class 3	protein-coding
mm_96518.1	chr11	68495396	68495407	+	1	NA	exon (NM_177320, exon 17 of 19)	exon (NM_177320, exon 17 of 19)	-7618	NM_001004435	104709	Mm.234573	NM_001004435	ENSMUSG00000046207	Pik3r6	BB220380|p84|p84 PIKAP|p87(PIKAP)|p87PIKAP	phosphoinositide-3-kinase, regulatory subunit 6	protein-coding
mm_6958.1	chr1	86021837	86021850	-	1	NA	promoter-TSS (NM_001122732)	promoter-TSS (NM_001122732)	-99	NM_001122732	70060	Mm.196313	NM_027029	ENSMUSG00000026226	Spata3	1700011N12Rik|1700029H01Rik|4930424D10Rik|Mtsarg1|Tsarg1	spermatogenesis associated 3	protein-coding
mm_48702.1	chr5	147042665	147042673	-	1	NA	intron (NM_080795, intron 1 of 9)	intron (NM_080795, intron 1 of 9)	33903	NM_080795	140887	Mm.272203	NM_080795	ENSMUSG00000016520	Lnx2	9630046H24|AW209022	ligand of numb-protein X 2	protein-coding
mm_8553.1	chr1	155232591	155232595	-	1	NA	Intergenic	Intergenic	73890	NM_021433	58244	Mm.66264	NM_021433	ENSMUSG00000026470	Stx6	2310039E05Rik|2410005I16Rik|AA437559|AI415714|AI845861	syntaxin 6	protein-coding
mm_134140.1	chr16	10700281	10700285	-	1	NA	intron (NM_001204229, intron 21 of 22)	intron (NM_001204229, intron 21 of 22)	85253	NM_009896	12703	Mm.130	NM_009896	ENSMUSG00000038037	Socs1	Cish1|Cish7|JAB|SOCS-1|SSI-1	suppressor of cytokine signaling 1	protein-coding
mm_59984.1	chr7	30515146	30515156	+	1	NA	promoter-TSS (NR_036630)	promoter-TSS (NR_036630)	29	NR_036630	100504207	Mm.297831	NM_001004161	ENSMUSG00000062132	Arhgap33os	Gm1082	Rho GTPase activating protein 33, opposite strand	ncRNA
mm_56986.1	chr6	120493937	120494017	-	1	NA	promoter-TSS (NM_033567)	promoter-TSS (NM_033567)	-170	NM_033567	94047	Mm.23088	NM_033567	ENSMUSG00000094626	Cecr6	AW048664	cat eye syndrome chromosome region, candidate 6	protein-coding
mm_16146.1	chr2	172100612	172100627	+	1	NA	Intergenic	Intergenic	-57153	NM_175631	228942	Mm.40555	NM_175631	ENSMUSG00000067578	Cbln4	AI848962	cerebellin 4 precursor protein	protein-coding
mm_89742.1	chr10	99107071	99107132	+	1	NA	promoter-TSS (NM_027740)	promoter-TSS (NM_027740)	-70	NM_027740	382406	Mm.440656	NM_027740	ENSMUSG00000019952	Poc1b	4933430F16Rik|Wdr51b	POC1 centriolar protein B	protein-coding
mm_158712.1	chrX	162552741	162552757	-	1	NA	intron (NM_178256, intron 3 of 17)	intron (NM_178256, intron 3 of 17)	90909	NM_001290633	194590	Mm.442441	NM_178256	ENSMUSG00000040855	Reps2	POB1	RALBP1 associated Eps domain containing protein 2	protein-coding
mm_101934.1	chr11	50207203	50207242	-	1	NA	exon (NM_011018, exon 4 of 8)	exon (NM_011018, exon 4 of 8)	3598	NM_001290769	18412	Mm.40828	NM_011018	ENSMUSG00000015837	Sqstm1	A170|OSF-6|Osi|STAP|STONE14|p62	sequestosome 1	protein-coding
mm_149760.1	chr19	22816745	22816748	+	1	NA	intron (NM_001035243, intron 8 of 23)	Lx6|LINE|L1	66141	NR_029591	387200		NR_029591	ENSMUSG00000065507	Mir204	Mirn204|mir-204|mmu-mir-204	microRNA 204	ncRNA
mm_126022.1	chr15	76691239	76691258	+	1	NA	intron (NM_033371, intron 2 of 10)	intron (NM_033371, intron 2 of 10)	-5478	NM_182805	76282	Mm.30130	NM_182805	ENSMUSG00000022546	Gpt	1300007J06Rik|2310022B03Rik|ALT|ALT1|Gpt-1|Gpt1	glutamic pyruvic transaminase, soluble	protein-coding
mm_27532.1	chr3	57542762	57542762	-	1	NA	intron (NM_001168281, intron 2 of 6)	ID4_|SINE|ID	33114	NM_133784	97064	Mm.405029	NM_133784	ENSMUSG00000027803	Wwtr1	2310058J06Rik|2610021I22Rik|C78399|Taz	WW domain containing transcription regulator 1	protein-coding
mm_81364.1	chr9	108739707	108739710	+	1	NA	intron (NM_008924, intron 6 of 10)	PB1D11|SINE|Alu	47565	NM_008924	19087	Mm.253102	NM_008924	ENSMUSG00000032601	Prkar2a	1110061A24Rik|AI317181|AI836829|RII(alpha)	protein kinase, cAMP dependent regulatory, type II alpha	protein-coding
mm_34550.1	chr4	149586515	149586548	+	1	NA	promoter-TSS (NM_023051)	promoter-TSS (NM_023051)	63	NM_023051	65945	Mm.38993	NM_023051	ENSMUSG00000039953	Clstn1	1810034E21Rik|Cst-1|Cstn1	calsyntenin 1	protein-coding
mm_121601.1	chr14	8004037	8004045	-	1	NA	intron (NM_001331064, intron 1 of 8)	intron (NM_001331064, intron 1 of 8)	1075	NM_001331064	66082	Mm.181473	NM_025341	ENSMUSG00000025277	Abhd6	0610041D24Rik|AA673485|AV065425	abhydrolase domain containing 6	protein-coding
mm_156495.1	chrX	144336189	144336197	+	1	NA	non-coding (NR_037145, exon 4 of 27)	non-coding (NR_037145, exon 4 of 27)	18227	NM_026247	67574	Mm.249084	NM_026247	ENSMUSG00000041718	Alg13	2810046O15Rik|4833435D08Rik|Glt28d1|MDS031|OTTMUSG00000018917	asparagine-linked glycosylation 13	protein-coding
mm_149298.1	chr19	10699337	10699349	+	1	NA	intron (NM_181403, intron 1 of 4)	intron (NM_181403, intron 1 of 4)	10528	NM_181403	107305	Mm.19091	NM_181403	ENSMUSG00000048832	Vps37c	5730409F24Rik|AU042646	vacuolar protein sorting 37C	protein-coding
mm_147129.1	chr18	36068612	36068621	-	1	NA	intron (NM_001167891, intron 1 of 9)	CpG	-37587	NR_015571	74966	Mm.379238	NM_030089		4930471G03Rik	1700007N01Rik	RIKEN cDNA 4930471G03 gene	ncRNA
mm_112300.1	chr12	114709131	114709135	-	1	NA	Intergenic	Intergenic	-195439	NR_106063	102465664		NR_106063	ENSMUSG00000098357	Mir7094-2	Gm27508|mmu-mir-7094-2	microRNA 7094-2	ncRNA
mm_38225.1	chr4	135987183	135987269	-	1	NA	promoter-TSS (NM_025411)	promoter-TSS (NM_025411)	18	NM_025411	66193	Mm.29131	NM_025411	ENSMUSG00000028669	Pithd1	1110049F12Rik|AA408179|Trp26	PITH (C-terminal proteasome-interacting domain of thioredoxin-like) domain containing 1	protein-coding
mm_19300.1	chr2	90471146	90471177	-	1	NA	exon (NM_008982, exon 3 of 24)	exon (NM_008982, exon 3 of 24)	8013	NM_001135657	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_115381.1	chr13	113098348	113098359	+	1	NA	exon (NM_010370, exon 2 of 5)	exon (NM_010370, exon 2 of 5)	2628	NM_010370	14938	Mm.15510	NM_010370	ENSMUSG00000023132	Gzma	AW494114|Ctla-3|Ctla3|Hf|Hf1|SE1|TSP-1|TSP1	granzyme A	protein-coding
mm_100713.1	chr11	3805211	3805252	-	1	NA	intron (NM_152818, intron 2 of 13)	intron (NM_152818, intron 2 of 13)	58672	NM_152818	74309	Mm.61022	NM_152818	ENSMUSG00000020435	Osbp2	1700095P05Rik|C630001G20Rik|Gm244|ORP-4|OSBPL1	oxysterol binding protein 2	protein-coding
mm_74477.1	chr8	4275887	4275915	-	1	NA	promoter-TSS (NM_011592)	promoter-TSS (NM_011592)	4	NM_011592	21856	Mm.195249	NM_011592	ENSMUSG00000002949	Timm44	0710005E20Rik|D8Ertd118e|Mimt44|Tim44	translocase of inner mitochondrial membrane 44	protein-coding
mm_4640.1	chr1	179959985	179960080	+	1	NA	promoter-TSS (NM_001346804)	promoter-TSS (NM_001346804)	-728	NM_001346804	226751	Mm.259655	NM_001033285	ENSMUSG00000026490	Cdc42bpa	A930014J19Rik|DMPK-like	CDC42 binding protein kinase alpha	protein-coding
mm_137384.1	chr17	25786567	25786584	+	1	NA	promoter-TSS (NM_001165929)	promoter-TSS (NM_001165929)	-5	NM_001165929	381077	Mm.328867	NM_001165929	ENSMUSG00000071202	Ccdc78	Gm938|Gm950	coiled-coil domain containing 78	protein-coding
mm_131755.1	chr16	22857848	22857914	+	1	NA	promoter-TSS (NM_001190805)	promoter-TSS (NM_001190805)	36	NM_001190804	67838	Mm.37516	NM_026400	ENSMUSG00000004460	Dnajb11	1810031F23Rik|ABBP-2|AL024055|Dj9|ERdj3|ERj3p	DnaJ heat shock protein family (Hsp40) member B11	protein-coding
mm_171650.1	chr4	40596317	40596336	+	1	NA	Intergenic	MMETn-int|LTR|ERVK	-70778	NR_040644	71293	Mm.399556	NR_040644	ENSMUSG00000086355	4933428C19Rik	-	RIKEN cDNA 4933428C19 gene	ncRNA
mm_13170.1	chr2	92848719	92848723	+	1	NA	Intergenic	B4A|SINE|B4	-66380	NM_030725	80976	Mm.33490	NM_030725	ENSMUSG00000027220	Syt13	5730409J20Rik|AI549909|mKIAA1427	synaptotagmin XIII	protein-coding
mm_124315.1	chr14	103219033	103219043	-	1	NA	intron (NM_207215, intron 33 of 84)	RSINE1|SINE|B4	-119472	NM_001347600	50789	Mm.214746	NM_015822	ENSMUSG00000022124	Fbxl3	AU041772|AW212966|FBK|Fbl3a|Fbxl3a|Ovtm|Play68	F-box and leucine-rich repeat protein 3	protein-coding
mm_106694.1	chr12	3438356	3438358	+	1	NA	intron (NM_001270988, intron 1 of 11)	intron (NM_001270988, intron 1 of 11)	11500	NM_172421	75302	Mm.120475	NM_172421	ENSMUSG00000037486	Asxl2	4930556B16Rik|mKIAA1685	additional sex combs like 2 (Drosophila)	protein-coding
mm_52526.1	chr6	115675945	115675956	+	1	NA	intron (NM_029780, intron 1 of 16)	intron (NM_029780, intron 1 of 16)	685	NM_029780	110157	Mm.184163	NM_029780	ENSMUSG00000000441	Raf1	6430402F14Rik|AA990557|BB129353|Craf1|D830050J10Rik|Raf-1|c-Raf|v-Raf	v-raf-leukemia viral oncogene 1	protein-coding
mm_49141.1	chr6	10789732	10789754	+	1	NA	Intergenic	Intergenic	184635	NR_033776	57866	Mm.4397	NR_033776		AA545190	-	EST AA545190	ncRNA
mm_71516.1	chr8	46846561	46846575	+	1	NA	3' UTR (NM_008391, exon 9 of 9)	3' UTR (NM_008391, exon 9 of 9)	106823	NM_008391	16363	Mm.1149	NM_008391	ENSMUSG00000031627	Irf2	9830146E22Rik|AI646973|Irf-2	interferon regulatory factor 2	protein-coding
mm_131615.1	chr16	19760337	19760394	+	1	NA	5' UTR (NM_001159407, exon 1 of 6)	5' UTR (NM_001159407, exon 1 of 6)	131	NM_001159407	108105	Mm.33935	NM_054052	ENSMUSG00000022686	B3gnt5	beta3GnT5	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5	protein-coding
mm_100407.1	chr11	119418239	119418256	+	1	NA	Intergenic	Intergenic	27775	NR_035453	100316690		NR_035453	ENSMUSG00000088015	Mir1932	mir-1932|mmu-mir-1932	microRNA 1932	ncRNA
mm_85131.1	chr9	95614732	95614751	-	1	NA	Intergenic	Intergenic	-22887	NM_029620	76477	Mm.46016	NM_029620	ENSMUSG00000015354	Pcolce2	2400001O18Rik|Pcpe2	procollagen C-endopeptidase enhancer 2	protein-coding
mm_167596.1	chr9	49222173	49222176	+	1	NA	Intergenic	Intergenic	-28357	NM_177701	235327	Mm.246604	NM_177701	ENSMUSG00000054156	Gm4894	A430041E03|EG235327	predicted gene 4894	protein-coding
mm_48593.1	chr5	143992608	143992616	-	1	NA	exon (NM_177682, exon 12 of 15)	exon (NM_177682, exon 12 of 15)	22241	NM_177682	231874	Mm.320432	NM_177682	ENSMUSG00000029617	Ccz1	AU022870	CCZ1 vacuolar protein trafficking and biogenesis associated	protein-coding
mm_32572.1	chr4	109978005	109978048	+	1	NA	promoter-TSS (NM_172296)	promoter-TSS (NM_172296)	1	NM_172296	242620	Mm.32825	NM_172296	ENSMUSG00000047143	Dmrta2	Dmrt5	doublesex and mab-3 related transcription factor like family A2	protein-coding
mm_13388.1	chr2	103969574	103969597	+	1	NA	promoter-TSS (NM_008505)	promoter-TSS (NM_008505)	28	NM_001142336	16909	Mm.29266	NM_008505	ENSMUSG00000032698	Lmo2	Rbtn-2|Rbtn2|Rhom-2|Ttg2	LIM domain only 2	protein-coding
mm_151076.1	chr19	47579689	47579714	+	1	NA	promoter-TSS (NM_001164639)	promoter-TSS (NM_001164639)	-318	NM_009289	20874	Mm.281011	NM_009289	ENSMUSG00000025060	Slk	9A2|AV021402|AW411554|Etk4|SMAK|Stk2|mKIAA0204|mSLK	STE20-like kinase	protein-coding
mm_36887.1	chr4	107253514	107253524	-	1	NA	promoter-TSS (NM_029985)	promoter-TSS (NM_029985)	14	NM_029985	77809	Mm.29681	NM_029985	ENSMUSG00000028617	Lrrc42	A930011F22Rik|AA536996	leucine rich repeat containing 42	protein-coding
mm_53608.1	chr6	138727885	138727887	+	1	NA	Intergenic	Intergenic	-69442	NM_015777	50540	Mm.84043	NM_015777	ENSMUSG00000046717	Igbp1b	alpha4-b	immunoglobulin (CD79A) binding protein 1b	protein-coding
mm_15369.1	chr2	156421130	156421143	+	1	NA	5' UTR (NM_001291121, exon 1 of 22)	5' UTR (NM_001291121, exon 1 of 22)	227	NM_001291123	13821	Mm.20852	NM_013510	ENSMUSG00000027624	Epb41l1	4.1N|Epb4.1l1|NBL1|mKIAA0338	erythrocyte membrane protein band 4.1 like 1	protein-coding
mm_100418.1	chr11	119434748	119434795	+	1	NA	Intergenic	Intergenic	44299	NR_035453	100316690		NR_035453	ENSMUSG00000088015	Mir1932	mir-1932|mmu-mir-1932	microRNA 1932	ncRNA
mm_96280.1	chr11	62951179	62951185	+	1	NA	promoter-TSS (NM_025496)	promoter-TSS (NM_025496)	-11	NM_025496	66338	Mm.46166	NM_025496	ENSMUSG00000042200	Cdrt4	1700019I23Rik	CMT1A duplicated region transcript 4	protein-coding
mm_69190.1	chr7	127274009	127274036	-	1	NA	promoter-TSS (NM_009266)	promoter-TSS (NM_009266)	37	NM_009266	20768	Mm.20294	NM_009266	ENSMUSG00000049091	Sephs2	Sps2|Ysg3	selenophosphate synthetase 2	protein-coding
mm_6381.1	chr1	72769612	72769627	-	1	NA	Intergenic	Intergenic	-54861	NM_008342	16008	Mm.141936	NM_008342	ENSMUSG00000039323	Igfbp2	AI255832|IBP-2|Igfbp-2|mIGFBP-2	insulin-like growth factor binding protein 2	protein-coding
mm_96405.1	chr11	67251700	67251735	+	1	NA	exon (NM_010855, exon 23 of 40)	exon (NM_010855, exon 23 of 40)	13905	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_6733.1	chr1	82827008	82827011	-	1	NA	Intergenic	Intergenic	-12451	NM_001310713	15463	Mm.392569	NM_010472	ENSMUSG00000026159	Agfg1	AU045498|C130049H11Rik|C85612|D730048C23Rik|Hrb|RAB|Rip	ArfGAP with FG repeats 1	protein-coding
mm_140431.1	chr17	88112610	88112648	+	1	NA	Intergenic	Intergenic	-12883	NM_001190356	225058	Mm.312053	NM_001190356		Gm4832	EG225058	predicted gene 4832	protein-coding
mm_157680.1	chrX	59568069	59568094	-	1	NA	intron (NM_001290414, intron 1 of 6)	CpG	17491	NM_001290414	14168	Mm.7995	NM_010200	ENSMUSG00000031137	Fgf13	Fhf2	fibroblast growth factor 13	protein-coding
mm_152561.1	chr19	11586441	11586480	-	1	NA	TTS (NM_026835)	TTS (NM_026835)	18344	NM_026835	68774	Mm.290390	NM_026835	ENSMUSG00000024679	Ms4a6d	1110058E16Rik|AI447446|Ms4a11	membrane-spanning 4-domains, subfamily A, member 6D	protein-coding
mm_138003.1	chr17	33817807	33817834	+	1	NA	exon (NM_030697, exon 3 of 11)	exon (NM_030697, exon 3 of 11)	6678	NM_016844	54127	Mm.352374	NM_016844	ENSMUSG00000067288	Rps28	-	ribosomal protein S28	protein-coding
mm_54040.1	chr6	13461996	13461996	-	1	NA	Intergenic	Intergenic	48659	NR_038149	69413	Mm.177847	NR_038149	ENSMUSG00000101894	1700016P04Rik	-	RIKEN cDNA 1700016P04 gene	ncRNA
mm_12646.1	chr2	74727250	74727270	+	1	NA	5' UTR (NM_010469, exon 5 of 6)	5' UTR (NM_010469, exon 5 of 6)	1190	NR_029566	387144		NR_029566	ENSMUSG00000065500	Mir10b	Mirn10b|mir-10b|mmu-mir-10b	microRNA 10b	ncRNA
mm_117245.1	chr13	64363852	64363862	-	1	NA	3' UTR (NM_009984, exon 8 of 8)	3' UTR (NM_009984, exon 8 of 8)	6663	NM_009984	13039	Mm.930	NM_009984	ENSMUSG00000021477	Ctsl	1190035F06Rik|CatL|Ctsl1|MEP|fs|nkt	cathepsin L	protein-coding
mm_95299.1	chr11	46086666	46086674	+	1	NA	intron (NM_001291890, intron 3 of 22)	intron (NM_001291890, intron 3 of 22)	-15600	NR_106177	102465996		NR_106177	ENSMUSG00000098942	Mir8100	Gm27638|mmu-mir-8100	microRNA 8100	ncRNA
mm_11780.1	chr2	39005302	39005319	+	1	NA	promoter-TSS (NM_025592)	promoter-TSS (NM_025592)	-179	NM_025592	66489	Mm.345333	NM_025592	ENSMUSG00000062997	Rpl35	2410039E09Rik	ribosomal protein L35	protein-coding
mm_152845.1	chr19	23652781	23652820	-	1	NA	promoter-TSS (NM_026188)	promoter-TSS (NM_026188)	12	NM_026188	67483	Mm.443287	NM_026188	ENSMUSG00000033053	1700028P14Rik	AV209940	RIKEN cDNA 1700028P14 gene	protein-coding
mm_94934.1	chr11	29704278	29704284	+	1	NA	intron (NM_194051, intron 1 of 8)	intron (NM_194051, intron 1 of 8)	10507	NM_194051	68585	Mm.192580	NM_024226	ENSMUSG00000020458	Rtn4	1110020G17Rik|AA407876|AA409940|AA960376|ASY|C130026I10Rik|NOGO|NSP-CL|NgA|Nogo-A|Nogo-B|Nogo-C|mKIAA0886|mKIAA4153	reticulon 4	protein-coding
mm_11884.1	chr2	49621872	49621874	+	1	NA	intron (NM_008449, intron 1 of 25)	intron (NM_008449, intron 1 of 25)	2559	NM_008449	16574	Mm.256342	NM_008449	ENSMUSG00000026764	Kif5c	KINN|Khc|NKHC|NKHC2	kinesin family member 5C	protein-coding
mm_122678.1	chr14	52009652	52009663	-	1	NA	exon (NM_001253694, exon 4 of 6)	exon (NM_001253694, exon 4 of 6)	4901	NM_001253695	69890	Mm.475652	NM_027248	ENSMUSG00000049295	Zfp219	2010302A17Rik	zinc finger protein 219	protein-coding
mm_46338.1	chr5	101851508	101851517	-	1	NA	intron (NM_172882, intron 59 of 66)	intron (NM_172882, intron 59 of 66)	86382	NM_173370	74596	Mm.46764	NM_173370	ENSMUSG00000029330	Cds1	4833409J18Rik|AI314024|AW125888	CDP-diacylglycerol synthase 1	protein-coding
mm_165767.1	chr3	121570994	121571007	+	1	NA	Intergenic	Intergenic	-38656	NM_145394	213603	Mm.33062	NM_145394	ENSMUSG00000039865	Slc44a3	BC010552	solute carrier family 44, member 3	protein-coding
mm_161203.1	chr13	58402629	58402629	+	1	NA	promoter-TSS (NM_025279)	promoter-TSS (NM_025279)	32	NM_001168248	74386	Mm.85289	NM_028904	ENSMUSG00000035367	Rmi1	4932432N11Rik|C79893	RecQ mediated genome instability 1	protein-coding
mm_141637.1	chr17	33068003	33068007	-	1	NA	promoter-TSS (NM_001009544)	promoter-TSS (NM_001009544)	53	NM_001009544	74042	Mm.84774	NM_001009544	ENSMUSG00000023350	4921501E09Rik	PHF8	RIKEN cDNA 4921501E09 gene	protein-coding
mm_87776.1	chr10	60294960	60294986	+	1	NA	exon (NM_011179, exon 6 of 15)	exon (NM_011179, exon 6 of 15)	10512	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_105730.1	chr11	109231014	109231032	-	1	NA	3' UTR (NM_001165934, exon 17 of 17)	3' UTR (NM_001165934, exon 17 of 17)	67158	NM_001165934	19739	Mm.38548	NM_011268	ENSMUSG00000020599	Rgs9	RGS9-1|Rgs9-2	regulator of G-protein signaling 9	protein-coding
mm_25564.1	chr3	116563052	116563063	+	1	NA	promoter-TSS (NM_175413)	promoter-TSS (NM_175413)	84	NM_175413	109245	Mm.216027	NM_027321	ENSMUSG00000027961	Lrrc39	2010005E21Rik|9430028I06Rik|Myomasp	leucine rich repeat containing 39	protein-coding
mm_78627.1	chr9	38730703	38730704	+	1	NA	intron (NM_172767, intron 11 of 19)	Lx8|LINE|L1	12435	NM_172767	67776	Mm.290950	NM_172767	ENSMUSG00000023186	Vwa5a	5830475I06Rik|AW552491|BCSC-1|E130119J22|Loh11cr2a	von Willebrand factor A domain containing 5A	protein-coding
mm_164535.1	chr17	6659054	6659083	+	1	NA	Intergenic	Intergenic	-3129	NM_001166627	100040531	Mm.457987	NM_001166627	ENSMUSG00000095677	Dynlt1f	100040631|Dynlt1e	dynein light chain Tctex-type 1F	protein-coding
mm_158604.1	chrX	152295478	152295479	-	1	NA	non-coding (NR_040269, exon 3 of 3)	non-coding (NR_040269, exon 3 of 3)	32015	NR_040269	72997	Mm.254833	NR_040269		Kantr	2810454L23Rik|2900056M20Rik|Spasm	Kdm5c adjacent non-coding transcript	ncRNA
mm_124963.1	chr15	15099349	15099352	+	1	NA	Intergenic	Intergenic	-1678751	NM_009869	12565	Mm.439758	NM_009869	ENSMUSG00000025370	Cdh9	-	cadherin 9	protein-coding
mm_56231.1	chr6	90661753	90661770	-	1	NA	3' UTR (NM_001134384, exon 14 of 14)	3' UTR (NM_001134384, exon 14 of 14)	42515	NM_001037493	71699	Mm.272633	NM_027868	ENSMUSG00000030089	Slc41a3	1010001P06Rik|AI480742|SLC41A1-L2	solute carrier family 41, member 3	protein-coding
mm_22384.1	chr2	181156944	181156954	-	1	NA	promoter-TSS (NM_007906)	promoter-TSS (NM_007906)	66	NM_007906	13628	Mm.2645	NM_007906	ENSMUSG00000016349	Eef1a2	Eef1a|S1|wasted|wst	eukaryotic translation elongation factor 1 alpha 2	protein-coding
mm_145505.1	chr18	60391529	60391535	+	1	NA	3' UTR (NM_001146275, exon 3 of 3)	3' UTR (NM_001146275, exon 3 of 3)	15503	NM_001146275	60440	Mm.261140	NM_021792	ENSMUSG00000054072	Iigp1	2900074L10Rik|AI046432|AW111922|Ifgga1|Iigp|Irga6	interferon inducible GTPase 1	protein-coding
mm_135201.1	chr16	36532240	36532261	-	1	NA	intron (NM_013803, intron 1 of 6)	intron (NM_013803, intron 1 of 6)	29884	NM_013803	12374	Mm.103619	NM_013803	ENSMUSG00000051980	Casr	CaR|Gprc2a	calcium-sensing receptor	protein-coding
mm_169552.1	chr15	103242684	103242689	+	1	NA	exon (NM_010447, exon 7 of 10)	exon (NM_010447, exon 7 of 10)	2232	NR_002883	434858	Mm.391346	NR_002883		Gm5643	EG434858	heterogeneous nuclear ribonucleoprotein A1 pseudogene	pseudo
mm_137128.1	chr17	22878121	22878132	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-10992	NM_001110254	240041	Mm.328828	NM_177358	ENSMUSG00000059142	Zfp945	A630033E08Rik|C730040L01Rik	zinc finger protein 945	protein-coding
mm_4085.1	chr1	167001040	167001071	+	1	NA	promoter-TSS (NM_175461)	promoter-TSS (NM_175461)	-362	NM_175461	226610	Mm.389217	NM_175461	ENSMUSG00000060568	Fam78b	C030014K22Rik|C030020L09Rik	family with sequence similarity 78, member B	protein-coding
mm_16212.1	chr2	173073190	173073202	+	1	NA	Intergenic	Intergenic	46329	NM_001081387	664799	Mm.389396	NM_001081387	ENSMUSG00000070495	Ctcfl	Boris|OTTMUSG00000016680	CCCTC-binding factor (zinc finger protein)-like	protein-coding
mm_16447.1	chr2	180456235	180456246	+	1	NA	Intergenic	Intergenic	-4738	NM_148933	108115	Mm.133687	NM_148933	ENSMUSG00000038963	Slco4a1	OATP-E|Slc21a12	solute carrier organic anion transporter family, member 4a1	protein-coding
mm_79948.1	chr9	66040473	66040499	+	1	NA	3' UTR (NM_173185, exon 14 of 14)	3' UTR (NM_173185, exon 14 of 14)	-19683	NM_011149	19035	Mm.335249	NM_011149	ENSMUSG00000032383	Ppib	AA408962|AA553318|AI844835|Cphn-2|Cphn2|CyP-20b	peptidylprolyl isomerase B	protein-coding
mm_19993.1	chr2	118723517	118723534	-	1	NA	exon (NM_177568, exon 5 of 32)	exon (NM_177568, exon 5 of 32)	4913	NM_177568	18796	Mm.215156	NM_177568	ENSMUSG00000040061	Plcb2	AI550384|B230205M18Rik|B230399N12	phospholipase C, beta 2	protein-coding
mm_11353.1	chr2	30901628	30901634	+	1	NA	intron (NM_022415, intron 1 of 2)	intron (NM_022415, intron 1 of 2)	1666	NM_022415	64292	Mm.28768	NM_022415	ENSMUSG00000050737	Ptges	2410099E23Rik|D2Ertd369e|Pges|mPGES|mPGES-1	prostaglandin E synthase	protein-coding
mm_55489.1	chr6	69417442	69417456	-	1	NA	Intergenic	Intergenic	-90275	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_136217.1	chr16	89960775	89960789	-	1	NA	promoter-TSS (NM_009384)	promoter-TSS (NM_009384)	45	NM_009384	21844	Mm.310902	NM_009384	ENSMUSG00000002489	Tiam1	AI847750|D16Ium10|D16Ium10e	T cell lymphoma invasion and metastasis 1	protein-coding
mm_120628.1	chr14	70462902	70462904	+	1	NA	intron (NM_145981, intron 2 of 4)	intron (NM_145981, intron 2 of 4)	5386	NM_145981	105653	Mm.192598	NM_145981	ENSMUSG00000003469	Phyhip	AW049870|C630010D02Rik|Lnap1ip|PAHX-AP#1|PAHX-AP1	phytanoyl-CoA hydroxylase interacting protein	protein-coding
mm_107392.1	chr12	33314334	33314368	+	1	NA	intron (NM_001033436, intron 1 of 7)	intron (NM_001033436, intron 1 of 7)	11836	NM_001033436	380753	Mm.41540	NM_028139	ENSMUSG00000020564	Atxn7l1	2810423G08Rik|Atxn7l4	ataxin 7-like 1	protein-coding
mm_157876.1	chrX	75764637	75764654	-	1	NA	promoter-TSS (NR_029443)	promoter-TSS (NR_029443)	54	NR_029443	74396	Mm.162493	NR_029443	ENSMUSG00000087396	4933407K13Rik	A130080L05Rik	RIKEN cDNA 4933407K13 gene	ncRNA
mm_119521.1	chr14	47489789	47489793	+	1	NA	intron (NM_030236, intron 1 of 1)	intron (NM_030236, intron 1 of 1)	17230	NM_001146085	78938	Mm.11935	NM_030236	ENSMUSG00000037536	Fbxo34	2900057B08Rik|5830426G16Rik	F-box protein 34	protein-coding
mm_71557.1	chr8	49370918	49370922	+	1	NA	Intergenic	Intergenic	-696230	NM_011857	23965	Mm.42191	NM_011857	ENSMUSG00000031561	Tenm3	2610100B16Rik|Odz1|Odz3|Ten-m3|mKIAA1455	teneurin transmembrane protein 3	protein-coding
mm_148987.1	chr19	8594072	8594127	+	1	NA	exon (NM_001164634, exon 2 of 11)	exon (NM_001164634, exon 2 of 11)	917	NM_001164635	19879	Mm.285294	NM_031194	ENSMUSG00000063796	Slc22a8	Oat3|Roct	solute carrier family 22 (organic anion transporter), member 8	protein-coding
mm_150777.1	chr19	44294297	44294304	+	1	NA	5' UTR (NM_009128, exon 1 of 6)	5' UTR (NM_009128, exon 1 of 6)	624	NM_009128	20250	Mm.487021	NM_009128	ENSMUSG00000025203	Scd2	Mir5114|Scd-2|mir-5114|swty	stearoyl-Coenzyme A desaturase 2	protein-coding
mm_37881.1	chr4	132422485	132422497	-	1	NA	promoter-TSS (NM_175306)	promoter-TSS (NM_175306)	-45	NM_175306	100169	Mm.158361	NM_175306	ENSMUSG00000066043	Phactr4	3110001B12Rik|AI527228|AW495572|C330013F19Rik|N28169|mKIAA4120	phosphatase and actin regulator 4	protein-coding
mm_106103.1	chr11	116274103	116274138	-	1	NA	promoter-TSS (NM_146032)	promoter-TSS (NM_146032)	97	NM_146032	217337	Mm.29655	NM_146032	ENSMUSG00000020780	Srp68	2610024I03Rik	signal recognition particle 68	protein-coding
mm_105711.1	chr11	108343550	108343568	-	1	NA	exon (NM_011101, exon 1 of 17)	exon (NM_011101, exon 1 of 17)	329	NM_011101	18750	Mm.222178	NM_011101	ENSMUSG00000050965	Prkca	AI875142|Pkca	protein kinase C, alpha	protein-coding
mm_78391.1	chr9	28645851	28645853	+	1	NA	intron (NM_177906, intron 2 of 7)	intron (NM_177906, intron 2 of 7)	854583	NM_177906	330908	Mm.379474	NM_177906	ENSMUSG00000062257	Opcml	2900075O15Rik|3732419F12|AI844366|B930023M13Rik|C230027C17|Gm181|Obcam	opioid binding protein/cell adhesion molecule-like	protein-coding
mm_7008.1	chr1	86487406	86487450	-	1	NA	Intergenic	CpG	-39308	NM_008972	19231	Mm.19187	NM_008972	ENSMUSG00000026238	Ptma	Thym	prothymosin alpha	protein-coding
mm_30598.1	chr4	6382598	6382608	+	1	NA	intron (NM_016807, intron 4 of 8)	intron (NM_016807, intron 4 of 8)	16923	NM_001098227	53378	Mm.247473	NM_016807	ENSMUSG00000028249	Sdcbp	MDA-9|Sycl|syntenin-1	syndecan binding protein	protein-coding
mm_121744.1	chr14	18816901	18816912	-	1	NA	intron (NM_144839, intron 3 of 5)	intron (NM_144839, intron 3 of 5)	76721	NM_144839	218793	Mm.23551	NM_144839	ENSMUSG00000058317	Ube2e2	BC016265	ubiquitin-conjugating enzyme E2E 2	protein-coding
mm_124270.1	chr14	103007765	103007771	-	1	NA	intron (NR_045657, intron 2 of 2)	Lx10|LINE|L1	-25131	NM_177715	239217	Mm.246466	NM_177715	ENSMUSG00000098557	Kctd12	AU046135|AW538430|Pfet1|Pfetin	potassium channel tetramerisation domain containing 12	protein-coding
mm_38581.1	chr4	141819328	141819365	-	1	NA	intron (NM_007919, intron 5 of 7)	intron (NM_007919, intron 5 of 7)	6659	NM_007919	13706	Mm.45316	NM_007919	ENSMUSG00000058579	Cela2a	Ela-2|Ela2|Ela2a	chymotrypsin-like elastase family, member 2A	protein-coding
mm_18598.1	chr2	66785008	66785023	-	1	NA	promoter-TSS (NM_009135)	promoter-TSS (NM_009135)	-105	NM_009135	20272	Mm.38127	NM_009135	ENSMUSG00000034810	Scn7a	1110034K09Rik|AI642000|NaG|Nav2|Nav2.3|Nax|Scn6a	sodium channel, voltage-gated, type VII, alpha	protein-coding
mm_60368.1	chr7	44462122	44462165	+	1	NA	exon (NM_198250, exon 3 of 3)	exon (NM_198250, exon 3 of 3)	-3292	NM_026690	68352	Mm.88478	NM_026690	ENSMUSG00000038704	Aspdh	0610012D14Rik	aspartate dehydrogenase domain containing	protein-coding
mm_104096.1	chr11	86688781	86688785	-	1	NA	intron (NM_175004, intron 2 of 2)	intron (NM_175004, intron 2 of 2)	4702	NM_001098810	217057	Mm.24868	NM_175004	ENSMUSG00000072582	Ptrh2	A230072I16Rik|Bit1|CGI-147	peptidyl-tRNA hydrolase 2	protein-coding
mm_141803.1	chr17	34518640	34518672	-	1	NA	Intergenic	Intergenic	-1304	NM_030747	624681	Mm.471592	NM_030747	ENSMUSG00000092618	Btnl6	EG624681|Gm6519|NG13	butyrophilin-like 6	protein-coding
mm_131953.1	chr16	24448083	24448153	+	1	NA	promoter-TSS (NM_001145952)	promoter-TSS (NM_001145952)	27	NM_001145952	210126	Mm.209385	NM_178665	ENSMUSG00000033306	Lpp	9430020K16Rik|AA959454|AU024130|B130055L10Rik|C79715|D630048H16	LIM domain containing preferred translocation partner in lipoma	protein-coding
mm_102073.1	chr11	52263802	52263810	-	1	NA	intron (NM_001313981, intron 3 of 10)	L2|LINE|L2	18789	NM_009331	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_36211.1	chr4	62468908	62468923	-	1	NA	5' UTR (NM_023597, exon 2 of 11)	5' UTR (NM_023597, exon 2 of 11)	1980	NM_001290522	71354	Mm.155573	NM_023597	ENSMUSG00000028391	Wdr31	5430402I10Rik|spWD	WD repeat domain 31	protein-coding
mm_95266.1	chr11	44962937	44962946	+	1	NA	intron (NM_007897, intron 10 of 15)	intron (NM_007897, intron 10 of 15)	153987	NR_045100	100504255	Mm.123608	NR_045100	ENSMUSG00000084773	Gm12159	OTTMUSG00000005475	predicted gene 12159	ncRNA
mm_13714.1	chr2	117179305	117179321	+	1	NA	3' UTR (NM_033524, exon 7 of 7)	3' UTR (NM_033524, exon 7 of 7)	-5814	NR_030440	732489		NR_030440	ENSMUSG00000076376	Mir674	Mirn674|mir-674|mmu-mir-674	microRNA 674	ncRNA
mm_33320.1	chr4	129082833	129082846	+	1	NA	exon (NM_029219, exon 8 of 9)	exon (NM_029219, exon 8 of 9)	-22691	NM_025452	66260	Mm.25295	NM_025452	ENSMUSG00000028786	Tmem54	1810017F10Rik|AI507302	transmembrane protein 54	protein-coding
mm_142504.1	chr17	46073711	46073753	-	1	NA	Intergenic	Intergenic	-37272	NM_026768	68565	Mm.287443	NM_026768	ENSMUSG00000023967	Mrps18a	1110004O20Rik|C79712	mitochondrial ribosomal protein S18A	protein-coding
mm_122305.1	chr14	34936107	34936109	-	1	NA	intron (NM_008166, intron 2 of 15)	intron (NM_008166, intron 2 of 15)	41499	NR_029774	723847		NR_029774	ENSMUSG00000065481	Mir346	Mirn346|mir-346|mmu-mir-346	microRNA 346	ncRNA
mm_113810.1	chr13	46609545	46609574	+	1	NA	intron (NM_026056, intron 4 of 12)	intron (NM_026056, intron 4 of 12)	-59963	NM_001033192	97863	Mm.275934	NM_001033192	ENSMUSG00000069237	Fam8a1	C78339	family with sequence similarity 8, member A1	protein-coding
mm_35607.1	chr4	43046175	43046188	-	1	NA	promoter-TSS (NM_172691)	promoter-TSS (NM_172691)	39	NR_045567	230088	Mm.260162	NM_172691	ENSMUSG00000036002	Fam214b	B230312A22Rik	family with sequence similarity 214, member B	protein-coding
mm_10342.1	chr2	11654036	11654046	+	1	NA	intron (NM_008367, intron 1 of 7)	B4A|SINE|B4	11249	NM_008367	16184	Mm.915	NM_008367	ENSMUSG00000026770	Il2ra	CD25|Il2r|Ly-43	interleukin 2 receptor, alpha chain	protein-coding
mm_121717.1	chr14	16447090	16447105	-	1	NA	intron (NM_011243, intron 3 of 7)	intron (NM_011243, intron 3 of 7)	81891	NM_009409	21974	Mm.130362	NM_009409	ENSMUSG00000017485	Top2b	D230016L12Rik|Top-2	topoisomerase (DNA) II beta	protein-coding
mm_120543.1	chr14	67256521	67256523	+	1	NA	intron (NM_010095, intron 7 of 16)	intron (NM_010095, intron 7 of 16)	23230	NM_001276387	13592	Mm.319947	NM_010095	ENSMUSG00000022053	Ebf2	D14Ggc1e|EBF-2|Mmot1|O/E-3|OE-3	early B cell factor 2	protein-coding
mm_36465.1	chr4	82506433	82506474	-	1	NA	promoter-TSS (NM_001113209)	promoter-TSS (NM_001113209)	-674	NM_008687	18028	Mm.317947	NM_008687	ENSMUSG00000008575	Nfib	6720429L07Rik|CTF|E030026I10Rik|NF-I/B|NF1-B|NFI-B	nuclear factor I/B	protein-coding
mm_98124.1	chr11	87216485	87216499	+	1	NA	exon (NM_197987, exon 23 of 24)	exon (NM_197987, exon 23 of 24)	89417	NM_197987	68729	Mm.17436	NM_197987	ENSMUSG00000018548	Trim37	1110032A10Rik|2810004E07Rik|AI848587|AU043018|MUL|TEF3|mKIAA0898	tripartite motif-containing 37	protein-coding
mm_102658.1	chr11	63922300	63922342	-	1	NA	promoter-TSS (NM_018805)	promoter-TSS (NM_018805)	-37	NM_018805	54710	Mm.274426	NM_018805	ENSMUSG00000070407	Hs3st3b1	3-OST-3B|3OST3B1|3Ost3b|AU041882|AW536289|Hs3st3b|m3-OST-3B	heparan sulfate (glucosamine) 3-O-sulfotransferase 3B1	protein-coding
mm_112623.1	chr13	15648094	15648097	+	1	NA	intron (NM_008130, intron 6 of 14)	intron (NM_008130, intron 6 of 14)	154535	NR_045507	71071	Mm.380845	NR_045507		4933412O06Rik	-	RIKEN cDNA 4933412O06 gene	ncRNA
mm_18880.1	chr2	76360448	76360463	-	1	NA	promoter-TSS (NM_009989)	promoter-TSS (NM_009989)	-2	NM_009989	13067	Mm.4872	NM_009989	ENSMUSG00000056436	Cyct	T-Cc	cytochrome c, testis	protein-coding
mm_141086.1	chr17	25942822	25942856	-	1	NA	promoter-TSS (NM_011822)	promoter-TSS (NM_011822)	-850	NM_011822	14755	Mm.362054	NM_011822	ENSMUSG00000025728	Pigq	Gpi1|Gpi1h|Gpi1p|Gpih	phosphatidylinositol glycan anchor biosynthesis, class Q	protein-coding
mm_10805.1	chr2	24349823	24349831	+	1	NA	3' UTR (NM_031167, exon 5 of 5)	3' UTR (NM_031167, exon 5 of 5)	4456	NM_001039701	16181	Mm.882	NM_031167	ENSMUSG00000026981	Il1rn	F630041P17Rik|IL-1ra	interleukin 1 receptor antagonist	protein-coding
mm_9262.1	chr1	171630420	171630425	-	1	NA	Intergenic	(TCCC)n|Simple_repeat|Simple_repeat	11478	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_63849.1	chr7	135653931	135653952	+	1	NA	exon (NM_011212, exon 6 of 21)	exon (NM_011212, exon 6 of 21)	-1627	NR_015548	67765	Mm.445272	NR_015548	ENSMUSG00000097471	5830432E09Rik	-	RIKEN cDNA 5830432E09 gene	ncRNA
mm_106785.1	chr12	4769128	4769138	+	1	NA	promoter-TSS (NM_028376)	promoter-TSS (NM_028376)	134	NM_175431	207921	Mm.184898	NM_175431	ENSMUSG00000050545	Fam228b	A830093I24Rik	family with sequence similarity 228, member B	protein-coding
mm_152556.1	chr19	11484643	11484660	-	1	NA	Intergenic	Intergenic	-7387	NM_001164202	666926	Mm.486382	NM_001164202	ENSMUSG00000058470	Gm8369	EG666926	predicted gene 8369	protein-coding
mm_141280.1	chr17	27904632	27904637	-	1	NA	intron (NM_026836, intron 2 of 4)	intron (NM_026836, intron 2 of 4)	3090	NM_026836	68776	Mm.267998	NM_026836	ENSMUSG00000024218	Taf11	1110038O14Rik|28kDa|AI115401|AL024207|AW552398|PRO214|TAF2I|TAFII28	TATA-box binding protein associated factor 11	protein-coding
mm_3283.1	chr1	136626095	136626139	+	1	NA	exon (NM_001160251, exon 2 of 2)	exon (NM_001160251, exon 2 of 2)	1216	NM_001160251	226442	Mm.62521	NM_177643	ENSMUSG00000041483	Zfp281	Znf281	zinc finger protein 281	protein-coding
mm_172973.1	chr9	90537833	90537847	-	1	NA	Intergenic	MMVL30-int|LTR|ERV1	-267071	NM_194334	67016	Mm.335347	NM_194334	ENSMUSG00000037410	Tbc1d2b	1810061M12Rik|AI480956|AV021536|AV023399|AW491493|mKIAA1055	TBC1 domain family, member 2B	protein-coding
mm_76857.1	chr8	105413460	105413465	-	1	NA	promoter-TSS (NM_177791)	promoter-TSS (NM_177791)	40	NM_177791	279499	Mm.67628	NM_177791	ENSMUSG00000051648	Kctd19	4922504H04Rik	potassium channel tetramerisation domain containing 19	protein-coding
mm_11867.1	chr2	48949563	48949617	+	1	NA	promoter-TSS (NM_001177313)	promoter-TSS (NM_001177313)	82	NM_029924	109241	Mm.440436	NM_029924	ENSMUSG00000036792	Mbd5	9430004D19Rik|AA536666|AI426407|C030040A15Rik|Gm1630|OTTMUSG00000012483	methyl-CpG binding domain protein 5	protein-coding
mm_55722.1	chr6	73469578	73469647	-	1	NA	promoter-TSS (NM_025737)	promoter-TSS (NM_025737)	55	NM_025737	66740	Mm.440760	NM_025737	ENSMUSG00000056197	4931417E11Rik	-	RIKEN cDNA 4931417E11 gene	protein-coding
mm_168589.1	chr1	173599287	173599289	-	1	NA	promoter-TSS (NM_001177350)	promoter-TSS (NM_001177350)	-14	NM_001177350	623121	Mm.138449	NM_001033384	ENSMUSG00000073491	Ifi213	E030037K03Rik|E430029J22Rik|Pydc4|Pyr-A	interferon activated gene 213	protein-coding
mm_29991.1	chr3	135440372	135440376	-	1	NA	intron (NM_025356, intron 2 of 7)	intron (NM_025356, intron 2 of 7)	1615	NM_025356	66105	Mm.49884	NM_025356	ENSMUSG00000078578	Ube2d3	1100001F19Rik|9430029A22Rik|AA414951	ubiquitin-conjugating enzyme E2D 3	protein-coding
mm_48435.1	chr5	140623317	140623333	-	1	NA	3' UTR (NM_175274, exon 14 of 14)	3' UTR (NM_175274, exon 14 of 14)	15984	NM_008494	16848	Mm.12834	NM_008494	ENSMUSG00000029570	Lfng	AW061165	LFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	protein-coding
mm_22540.1	chr3	8746961	8746989	+	1	NA	Intergenic	Intergenic	-79937	NM_010423	15213	Mm.29581	NM_010423	ENSMUSG00000040289	Hey1	AI316788|AI414254|CHF2|HRT1|Herp2|Hesr1|bHLHb31|hesr-1	hairy/enhancer-of-split related with YRPW motif 1	protein-coding
mm_69199.1	chr7	127375998	127376020	-	1	NA	promoter-TSS (NM_175560)	promoter-TSS (NM_175560)	41	NM_175560	269997	Mm.221270	NM_175560	ENSMUSG00000054381	Zfp747	6430604K15Rik	zinc finger protein 747	protein-coding
mm_58749.1	chr7	13303193	13303216	+	1	NA	exon (NM_010715, exon 20 of 29)	exon (NM_010715, exon 20 of 29)	-22463	NM_001168504	232889	Mm.223639	NM_001004762	ENSMUSG00000033847	Pla2g4c	D7Ertd445e	phospholipase A2, group IVC (cytosolic, calcium-independent)	protein-coding
mm_123814.1	chr14	70523434	70523444	-	1	NA	intron (NM_011359, intron 1 of 5)	RSINE1|SINE|B4	642	NM_011359	20389	Mm.24040	NM_011359	ENSMUSG00000022097	Sftpc	Bricd6|SP-C|SP5|SPC|Sftp-2|Sftp2|pro-SpC	surfactant associated protein C	protein-coding
mm_48790.1	chr5	148652721	148652769	-	1	NA	Intergenic	Intergenic	-89095	NR_028285	70138	Mm.417834	NR_028285	ENSMUSG00000086494	2210417A02Rik	AV081004	RIKEN cDNA 2210417A02 gene	ncRNA
mm_38164.1	chr4	135216794	135216813	-	1	NA	3' UTR (NM_013885, exon 6 of 6)	3' UTR (NM_013885, exon 6 of 6)	55957	NM_013885	29876	Mm.257765	NM_013885	ENSMUSG00000037242	Clic4	D0Jmb3|TU-74|mc3s5|mtCLIC	chloride intracellular channel 4 (mitochondrial)	protein-coding
mm_116331.1	chr13	38037084	38037158	-	1	NA	promoter-TSS (NM_027724)	promoter-TSS (NM_027724)	132	NM_024242	71340	Mm.297130	NM_024242	ENSMUSG00000021428	Riok1	3110046C13Rik|5430416A05Rik|Ad034	RIO kinase 1 (yeast)	protein-coding
mm_7523.1	chr1	124100242	124100259	-	1	NA	Intergenic	Intergenic	-54691	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_22885.1	chr3	30602057	30602096	+	1	NA	promoter-TSS (NM_030557)	promoter-TSS (NM_030557)	-11	NM_001289623	80732	Mm.200378	NM_030557	ENSMUSG00000037730	Mynn	2810011C24Rik|AA415053|AI661031|AW049392|Mynr|SBBIZ1	myoneurin	protein-coding
mm_99127.1	chr11	100317651	100317658	+	1	NA	Intergenic	B3|SINE|B2	-2295	NM_011508	20918	Mm.13886	NM_011508	ENSMUSG00000035530	Eif1	Sui1-rs1	eukaryotic translation initiation factor 1	protein-coding
mm_95473.1	chr11	50793933	50793982	+	1	NA	intron (NM_175643, intron 19 of 21)	intron (NM_175643, intron 19 of 21)	33774	NM_013922	30944	Mm.103674	NM_013922	ENSMUSG00000044807	Zfp354c	5330421P20Rik|AJ18|AW743325|Kid3|Tcf17l2|Znf354c|mKIAA4218	zinc finger protein 354C	protein-coding
mm_156211.1	chrX	134685118	134685149	+	1	NA	non-coding (NR_045454, exon 3 of 3)	non-coding (NR_045454, exon 3 of 3)	1329	NR_045454	77983	Mm.153204	NR_045454	ENSMUSG00000087024	B230119M05Rik	-	RIKEN cDNA B230119M05 gene	ncRNA
mm_60329.1	chr7	44246778	44246796	+	1	NA	promoter-TSS (NM_025880)	promoter-TSS (NM_025880)	65	NM_025880	668661	Mm.274492	NM_025880	ENSMUSG00000045411	2410002F23Rik	-	RIKEN cDNA 2410002F23 gene	protein-coding
mm_152763.1	chr19	20384532	20384560	-	1	NA	exon (NM_010730, exon 3 of 13)	exon (NM_010730, exon 3 of 13)	6125	NM_010730	16952	Mm.248360	NM_010730	ENSMUSG00000024659	Anxa1	Anx-1|Anx-A1|C430014K04Rik|Lpc-1|Lpc1	annexin A1	protein-coding
mm_113417.1	chr13	34037582	34037587	+	1	NA	promoter-TSS (NM_026512)	promoter-TSS (NM_026512)	-57	NM_026512	68021	Mm.140243	NM_026512	ENSMUSG00000038286	Bphl	2010012D11Rik|5730533B08Rik|AI115341	biphenyl hydrolase-like (serine hydrolase, breast epithelial mucin-associated antigen)	protein-coding
mm_8449.1	chr1	152902737	152902750	-	1	NA	promoter-TSS (NM_001160256)	promoter-TSS (NM_001160256)	-97	NM_001005507	226517	Mm.270775	NM_001005507	ENSMUSG00000042772	Smg7	9430023P16Rik|mKIAA0250	Smg-7 homolog, nonsense mediated mRNA decay factor (C. elegans)	protein-coding
mm_4185.1	chr1	171160357	171160359	+	1	NA	3' UTR (NM_008623, exon 8 of 8)	3' UTR (NM_008623, exon 8 of 8)	4840	NM_001315500	17528	Mm.9986	NM_008623	ENSMUSG00000056569	Mpz	Mpp|P-zero|P0	myelin protein zero	protein-coding
mm_103931.1	chr11	83648599	83648605	-	1	NA	exon (NM_011337, exon 2 of 3)	exon (NM_011337, exon 2 of 3)	776	NM_011337	20302	Mm.1282	NM_011337	ENSMUSG00000000982	Ccl3	AI323804|G0S19-1|LD78alpha|MIP-1alpha|MIP1-(a)|MIP1-alpha|Mip1a|Scya3	chemokine (C-C motif) ligand 3	protein-coding
mm_142987.1	chr17	56287926	56287954	-	1	NA	intron (NM_025836, intron 1 of 7)	intron (NM_025836, intron 1 of 7)	2571	NM_025836	66905	Mm.311696	NM_025836	ENSMUSG00000024197	Plin3	1300012C15Rik|M6prbp1|Tip47	perilipin 3	protein-coding
mm_153035.1	chr19	31910440	31910454	-	1	NA	intron (NM_001081074, intron 3 of 11)	intron (NM_001081074, intron 3 of 11)	41686	NM_001081074	69865	Mm.87538	NM_001081074	ENSMUSG00000052595	A1cf	1810073H04Rik|ACF64|ACF65|ASP|Acf|MCM|MerCreMer|Tg(Myh6-cre/Esr1*)1Jmk|mer	APOBEC1 complementation factor	protein-coding
mm_69549.1	chr7	135697872	135697882	-	1	NA	exon (NM_001081117, exon 12 of 14)	exon (NM_001081117, exon 12 of 14)	18502	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_64739.1	chr7	4752164	4752178	-	1	NA	non-coding (NR_110411, exon 3 of 4)	non-coding (NR_110411, exon 3 of 4)	731	NM_183406	333182	Mm.29625	NM_183405	ENSMUSG00000051811	Cox6b2	1700067P11Rik|BC048670|COXVIB2	cytochrome c oxidase subunit VIb polypeptide 2	protein-coding
mm_32142.1	chr4	99656130	99656154	+	1	NA	promoter-TSS (NM_010425)	promoter-TSS (NM_010425)	-157	NM_010425	15221	Mm.4758	NM_010425	ENSMUSG00000067261	Foxd3	CWH3|Genesis|Hfh2	forkhead box D3	protein-coding
mm_79704.1	chr9	61054638	61054651	+	1	NA	Intergenic	Intergenic	37575	NR_040767	330956	Mm.207985	NR_040767	ENSMUSG00000111290	Gm5122	A430102L10	predicted gene 5122	ncRNA
mm_140351.1	chr17	86831293	86831299	+	1	NA	3' UTR (NM_010137, exon 16 of 16)	3' UTR (NM_010137, exon 16 of 16)	77432	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_8723.1	chr1	160047499	160047508	-	1	NA	intron (NM_001162896, intron 1 of 2)	intron (NM_001162896, intron 1 of 2)	3123	NM_001162896	67647	Mm.171518	NM_001024470	ENSMUSG00000090394	4930523C07Rik	-	RIKEN cDNA 4930523C07 gene	protein-coding
mm_68508.1	chr7	111082609	111082631	-	1	NA	intron (NM_001040131, intron 1 of 20)	CpG	410	NM_001040131	13690	Mm.185453	NM_013507	ENSMUSG00000005610	Eif4g2	DAP-5|E130105L11Rik|Nat1|Natm1|p97	eukaryotic translation initiation factor 4, gamma 2	protein-coding
mm_103064.1	chr11	69837767	69837776	-	1	NA	promoter-TSS (NM_026982)	promoter-TSS (NM_026982)	-754	NM_026982	69186	Mm.248772	NM_026982	ENSMUSG00000070394	Tmem256	1810027O10Rik|3110009M16Rik	transmembrane protein 256	protein-coding
mm_16421.1	chr2	180235137	180235150	+	1	NA	Intergenic	Intergenic	-9284	NM_001081171	16776	Mm.4339	NM_001081171	ENSMUSG00000015647	Lama5	AA408760|AA408762|AI853660|[a]5|laminin-511|mKIAA0533	laminin, alpha 5	protein-coding
mm_63284.1	chr7	126776940	126777004	+	1	NA	promoter-TSS (NM_026875)	promoter-TSS (NM_026875)	-3	NM_026875	66090	Mm.27114	NM_025347	ENSMUSG00000042675	Ypel3	0610043B10Rik|1190001G19Rik|Suap	yippee-like 3 (Drosophila)	protein-coding
mm_161588.1	chr16	32735871	32735871	+	1	NA	promoter-TSS (NM_080457)	promoter-TSS (NM_080457)	-15	NM_080457	140474	Mm.214599	NM_080457	ENSMUSG00000079620	Muc4	4933405I11Rik|Asgp	mucin 4	protein-coding
mm_105613.1	chr11	106787546	106787575	-	1	NA	intron (NM_007840, intron 1 of 12)	CpG	934	NM_007840	13207	Mm.491096	NM_007840	ENSMUSG00000020719	Ddx5	2600009A06Rik|G17P1|HUMP68|Hlr1|p68	DEAD (Asp-Glu-Ala-Asp) box polypeptide 5	protein-coding
mm_84918.1	chr9	80067717	80067761	-	1	NA	intron (NM_001311110, intron 1 of 23)	CpG	836	NM_146003	215351	Mm.28232	NM_146003	ENSMUSG00000034252	Senp6	2810017C20Rik|E130319N12Rik|Susp1|mKIAA0797	SUMO/sentrin specific peptidase 6	protein-coding
mm_13145.1	chr2	92185468	92185494	+	1	NA	promoter-TSS (NM_001109691)	promoter-TSS (NM_001109691)	-2	NM_001109691	192285	Mm.330408	NM_138755	ENSMUSG00000058318	Phf21a	80kDa|Bhc|Bhc80|D030065N23Rik|PFTF1	PHD finger protein 21A	protein-coding
mm_120469.1	chr14	65973317	65973327	+	1	NA	intron (NM_013492, intron 2 of 8)	intron (NM_013492, intron 2 of 8)	4839	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_60690.1	chr7	45163940	45163955	+	1	NA	promoter-TSS (NM_182993)	promoter-TSS (NM_182993)	26	NM_182993	72961	Mm.255631	NM_182993	ENSMUSG00000070570	Slc17a7	2900052E22Rik|AI851913|Vglut1	solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 7	protein-coding
mm_84926.1	chr9	81633513	81633564	-	1	NA	promoter-TSS (NM_010482)	promoter-TSS (NM_010482)	-986	NM_010482	15551	Mm.445308	NM_010482	ENSMUSG00000049511	Htr1b	-	5-hydroxytryptamine (serotonin) receptor 1B	protein-coding
mm_78072.1	chr9	15432165	15432175	+	1	NA	Intergenic	RLTR9A|LTR|ERVK	-73325	NM_133214	170748	Mm.86572	NM_133214	ENSMUSG00000058173	Smco4	Fn5	single-pass membrane protein with coiled-coil domains 4	protein-coding
mm_160383.1	chr8	44950220	44950220	+	1	NA	promoter-TSS (NM_001081286)	promoter-TSS (NM_001081286)	12	NM_001081286	14107	Mm.27365	NM_001081286	ENSMUSG00000070047	Fat1	2310038E12Rik|AU023433|Fath|mFat1	FAT atypical cadherin 1	protein-coding
mm_105575.1	chr11	106613014	106613024	-	1	NA	promoter-TSS (NM_198292)	promoter-TSS (NM_198292)	-89	NM_198292	21763	Mm.102407	NM_198292	ENSMUSG00000040548	Tex2	4930568E07Rik|AI553404|Def-5|Taz4	testis expressed gene 2	protein-coding
mm_36434.1	chr4	82294783	82294793	-	1	NA	3' UTR (NM_001113209, exon 12 of 12)	3' UTR (NM_001113209, exon 12 of 12)	210991	NM_001286127	18028	Mm.317947	NM_008687	ENSMUSG00000008575	Nfib	6720429L07Rik|CTF|E030026I10Rik|NF-I/B|NF1-B|NFI-B	nuclear factor I/B	protein-coding
mm_60128.1	chr7	36739858	36739859	+	1	NA	intron (NM_172298, intron 1 of 1)	intron (NM_172298, intron 1 of 1)	41740	NM_172298	243931	Mm.44141	NM_172298	ENSMUSG00000021217	Tshz3	A630038G13Rik|Tsh3|Zfp537|mKIAA1474|teashirt3	teashirt zinc finger family member 3	protein-coding
mm_59294.1	chr7	25077520	25077535	+	1	NA	intron (NM_175477, intron 1 of 1)	CpG	281	NM_175477	232976	Mm.41568	NM_175477	ENSMUSG00000045252	Zfp574	A630056B21Rik|Znf574	zinc finger protein 574	protein-coding
mm_18152.1	chr2	45085439	45085451	-	1	NA	intron (NM_001289521, intron 1 of 8)	intron (NM_001289521, intron 1 of 8)	24832	NM_001289521	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_23116.1	chr3	37639929	37639943	+	1	NA	promoter-TSS (NM_011896)	promoter-TSS (NM_011896)	-11	NM_001305441	24063	Mm.330986	NM_011896	ENSMUSG00000037211	Spry1	sprouty1|spry-1	sprouty homolog 1 (Drosophila)	protein-coding
mm_34981.1	chr4	156014696	156014708	+	1	NA	intron (NM_011659, intron 2 of 6)	intron (NM_011659, intron 2 of 6)	1007	NM_011659	22163	Mm.13885	NM_011659	ENSMUSG00000029075	Tnfrsf4	ACT35|CD134|Ly-70|Ox40|TXGP1L|Txgp1	tumor necrosis factor receptor superfamily, member 4	protein-coding
mm_53271.1	chr6	128438789	128438842	+	1	NA	promoter-TSS (NM_010219)	promoter-TSS (NM_010219)	58	NR_028592	791299	Mm.297516	NR_028592	ENSMUSG00000059659	Gm10069	ENSMUSG00000059659	predicted gene 10069	ncRNA
mm_123972.1	chr14	75131576	75131582	-	1	NA	promoter-TSS (NM_027581)	promoter-TSS (NM_027581)	456	NM_001247984	18826	Mm.153911	NM_008879	ENSMUSG00000021998	Lcp1	AW536232|D14Ertd310e|LCP-1|Pls2|pp65	lymphocyte cytosolic protein 1	protein-coding
mm_111553.1	chr12	101040071	101040090	-	1	NA	3' UTR (NM_001160214, exon 15 of 15)	3' UTR (NM_001160214, exon 15 of 15)	-11097	NM_026681	68339	Mm.156217	NM_026681	ENSMUSG00000021182	Ccdc88c	0610010D24Rik|AV000935|AW324073|Daple|mKIAA1509	coiled-coil domain containing 88C	protein-coding
mm_45027.1	chr5	38684744	38684813	-	1	NA	promoter-TSS (NM_001177902)	promoter-TSS (NM_001177902)	48	NM_001177902	100515	Mm.38277	NM_001081144	ENSMUSG00000046572	Zfp518b	6820424L24Rik|AA410078|AI661722|Znf518b	zinc finger protein 518B	protein-coding
mm_168527.1	chr1	160206627	160206640	-	1	NA	exon (NM_009786, exon 3 of 6)	exon (NM_009786, exon 3 of 6)	6259	NM_009786	12301	Mm.10702	NM_009786	ENSMUSG00000014226	Cacybp	SIP	calcyclin binding protein	protein-coding
mm_50970.1	chr6	60944473	60944489	+	1	NA	5' UTR (NM_001163507, exon 1 of 8)	5' UTR (NM_001163507, exon 1 of 8)	164	NM_001163507	70945	Mm.389770	NM_027613	ENSMUSG00000054641	Mmrn1	4921530G03Rik|Emilin4|Mmrn	multimerin 1	protein-coding
mm_63205.1	chr7	125872678	125872720	+	1	NA	exon (NM_001081022, exon 26 of 28)	exon (NM_001081022, exon 26 of 28)	164823	NM_001081022	233865	Mm.274389	NM_001081022	ENSMUSG00000032743	D430042O09Rik	Kiaa0556	RIKEN cDNA D430042O09 gene	protein-coding
mm_121125.1	chr14	101840756	101840768	+	1	NA	5' UTR (NM_001347628, exon 1 of 27)	5' UTR (NM_001347628, exon 1 of 27)	139	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_82223.1	chr9	3024776	3024789	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	13961	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_125084.1	chr15	26974235	26974241	+	1	NA	Intergenic	ORR1A0|LTR|ERVL-MaLR	-78674	NM_176959	448987	Mm.253378	NM_176959	ENSMUSG00000043556	Fbxl7	AL023057|D230018M15Rik|FBL7|Fbl6	F-box and leucine-rich repeat protein 7	protein-coding
mm_18106.1	chr2	44988872	44988895	-	1	NA	exon (NM_015753, exon 10 of 10)	exon (NM_015753, exon 10 of 10)	34294	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_9010.1	chr1	166002614	166002647	-	1	NA	promoter-TSS (NM_198932)	promoter-TSS (NM_198932)	4	NM_198932	18986	Mm.245261	NM_011137	ENSMUSG00000026565	Pou2f1	2810482H01Rik|NF-A1|Oct-1|Oct1|Otf-1|Otf1	POU domain, class 2, transcription factor 1	protein-coding
mm_123616.1	chr14	68120816	68120842	-	1	NA	exon (NM_008691, exon 3 of 3)	exon (NM_008691, exon 3 of 3)	-2923	NR_045897	100043072	Mm.242832	NR_045897		A230070E04Rik	Gm4210	RIKEN cDNA A230070E04 gene	ncRNA
mm_6854.1	chr1	84258213	84258242	-	1	NA	intron (NM_001003948, intron 1 of 2)	intron (NM_001003948, intron 1 of 2)	26418	NM_001003948	98496	Mm.187470	NM_001003948	ENSMUSG00000045658	Pid1	5033414K04Rik|NYGGF4	phosphotyrosine interaction domain containing 1	protein-coding
mm_135095.1	chr16	34958845	34958863	-	1	NA	promoter-TSS (NR_045722)	promoter-TSS (NR_045722)	10	NR_045722	278725	Mm.436927	NR_045722		E130310I04Rik	A930019C19Rik	RIKEN cDNA E130310I04 gene	ncRNA
mm_81055.1	chr9	105658499	105658505	+	1	NA	exon (NM_001081309, exon 7 of 20)	exon (NM_001081309, exon 7 of 20)	15507	NM_001081309	75669	Mm.274830	NM_029380	ENSMUSG00000032571	Pik3r4	2210010O15Rik|C730038E05Rik|C85833|D9Ertd418e	phosphatidylinositol 3 kinase, regulatory subunit, polypeptide 4, p150	protein-coding
mm_112918.1	chr13	20923395	20923406	+	1	NA	intron (NM_012054, intron 11 of 20)	Lx8b|LINE|L1	129287	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_147516.1	chr18	52518738	52518741	-	1	NA	3' UTR (NM_010728, exon 7 of 7)	3' UTR (NM_010728, exon 7 of 7)	10982	NM_001286181	16948	Mm.172	NM_010728	ENSMUSG00000024529	Lox	AI893619|TSC-160|rrg	lysyl oxidase	protein-coding
mm_143561.1	chr17	74192037	74192042	-	1	NA	Intergenic	Intergenic	102824	NM_133771	76890	Mm.311874	NM_133771	ENSMUSG00000058704	Memo1	0610016J10Rik|D930048L02Rik	mediator of cell motility 1	protein-coding
mm_155566.1	chrX	76264282	76264312	+	1	NA	promoter-TSS (NM_001013760)	promoter-TSS (NM_001013760)	-9	NM_001013760	238829	Mm.292319	NM_001013760	ENSMUSG00000071738	Cldn34b3	EG238829|Gm4937	claudin 34B3	protein-coding
mm_109454.1	chr12	111152019	111152019	+	1	NA	Intergenic	Intergenic	-14351	NM_001286122	22031	Mm.27431	NM_011632	ENSMUSG00000021277	Traf3	AI528849|CAP-1|CD40bp|CRAF1|LAP1|T-BAM|amn	TNF receptor-associated factor 3	protein-coding
mm_150866.1	chr19	45018155	45018197	+	1	NA	promoter-TSS (NM_001130526)	promoter-TSS (NM_001130526)	41	NM_001130526	226154	Mm.28204	NM_145503	ENSMUSG00000035342	Lzts2	BC014695|LAPSER1|mKIAA1813	leucine zipper, putative tumor suppressor 2	protein-coding
mm_50063.1	chr6	41188217	41188242	+	1	NA	Intergenic	Intergenic	-114043	NM_011646	22074	Mm.383263	NM_011646	ENSMUSG00000054106	Try4	0910001B19Rik|Td	trypsin 4	protein-coding
mm_11032.1	chr2	26916361	26916396	+	1	NA	promoter-TSS (NM_013678)	promoter-TSS (NM_013678)	-43	NM_013678	20931	Mm.389260	NM_013678	ENSMUSG00000014873	Surf2	Surf-2	surfeit gene 2	protein-coding
mm_168385.1	chr1	123857205	123857207	+	1	NA	intron (NM_199021, intron 2 of 25)	L1Md_T|LINE|L1	188353	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_86952.1	chr10	24915621	24915637	+	1	NA	exon (NM_007482, exon 8 of 8)	exon (NM_007482, exon 8 of 8)	4965	NR_105870	102465545		NR_105870	ENSMUSG00000099181	Mir6905	Gm27879|mmu-mir-6905	microRNA 6905	ncRNA
mm_34440.1	chr4	147936814	147936852	+	1	NA	promoter-TSS (NM_011122)	promoter-TSS (NM_011122)	-57	NM_011122	18822	Mm.23951	NM_011122	ENSMUSG00000019055	Plod1	2410042F05Rik|AI854890|AV007929|Lh1|Plod	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1	protein-coding
mm_37905.1	chr4	132734826	132734836	-	1	NA	intron (NM_133888, intron 7 of 7)	intron (NM_133888, intron 7 of 7)	-2285	NM_201368	381560	Mm.44558	NM_201368	ENSMUSG00000037752	Xkr8	4931440N07Rik|AI597014|Gm1031|XRG8|mXkr8	X-linked Kx blood group related 8	protein-coding
mm_20047.1	chr2	120207224	120207238	-	1	NA	intron (NM_177845, intron 1 of 19)	intron (NM_177845, intron 1 of 19)	38104	NM_177845	329502	Mm.330505	NM_177845	ENSMUSG00000050211	Pla2g4e	2310026J01Rik|C230096D22|Pla2epsilon	phospholipase A2, group IVE	protein-coding
mm_8008.1	chr1	134803424	134803434	-	1	NA	non-coding (NR_015606, exon 1 of 2)	non-coding (NR_015606, exon 1 of 2)	292	NR_015606	329251	Mm.188709	NM_001081307	ENSMUSG00000073557	Ppp1r12b	1810037O03Rik|9530009M10Rik|AI132431|Mypt2	protein phosphatase 1, regulatory (inhibitor) subunit 12B	protein-coding
mm_84722.1	chr9	73969100	73969109	-	1	NA	Intergenic	Intergenic	-35537	NM_001081153	208898	Mm.41035	NM_001081153	ENSMUSG00000062151	Unc13c	1500037O19Rik|AU019458|D9Ertd414e|Munc13-3|Unc13h3	unc-13 homolog C (C. elegans)	protein-coding
mm_168838.1	chr12	23189689	23189690	-	1	NA	Intergenic	CpG	-179446	NR_015504	69732	Mm.391403	NM_028362	ENSMUSG00000073164	2410018L13Rik	2810480C08Rik	RIKEN cDNA 2410018L13 gene	ncRNA
mm_160764.1	chr10	94944340	94944340	-	1	NA	exon (NM_018797, exon 1 of 31)	exon (NM_018797, exon 1 of 31)	238	NM_018797	54712	Mm.256712	NM_018797	ENSMUSG00000074785	Plxnc1	2510048K12Rik|AW742158|CD232|Vespr	plexin C1	protein-coding
mm_29290.1	chr3	107753812	107753839	-	1	NA	exon (NM_007778, exon 4 of 9)	exon (NM_007778, exon 4 of 9)	6644	NM_001113530	12977	Mm.795	NM_007778	ENSMUSG00000014599	Csf1	C87615|Csfm|MCSF|op	colony stimulating factor 1 (macrophage)	protein-coding
mm_98272.1	chr11	89010894	89010909	+	1	NA	exon (NM_009546, exon 4 of 9)	exon (NM_009546, exon 4 of 9)	11498	NM_009546	217069	Mm.248445	NM_009546	ENSMUSG00000000275	Trim25	AA960166|AL022677|EFP|Zfp147	tripartite motif-containing 25	protein-coding
mm_156405.1	chrX	140277743	140277755	+	1	NA	Intergenic	CpG	-33199	NR_037208	100499512		NR_037208	ENSMUSG00000093102	Mir3475	mir-3475|mmu-mir-3475	microRNA 3475	ncRNA
mm_112731.1	chr13	19210315	19210330	+	1	NA	Intergenic	Intergenic	185491	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_167274.1	chr8	33844775	33844811	-	1	NA	intron (NM_001042674, intron 4 of 7)	intron (NM_001042674, intron 4 of 7)	85070	NM_019733	19663	Mm.323997	NM_019733	ENSMUSG00000031586	Rbpms	2010300K22Rik|2700019M19Rik|AU017537|RBP-MS|hermes	RNA binding protein gene with multiple splicing	protein-coding
mm_97005.1	chr11	70879413	70879426	+	1	NA	intron (NM_001291143, intron 3 of 18)	intron (NM_001291143, intron 3 of 18)	34658	NM_001291142	54189	Mm.7087	NM_019400	ENSMUSG00000020817	Rabep1	Rab5ep|rabaptin-5|rabaptin-5alpha	rabaptin, RAB GTPase binding effector protein 1	protein-coding
mm_48263.1	chr5	137871780	137871790	-	1	NA	promoter-TSS (NM_001024932)	promoter-TSS (NM_001024932)	-27	NM_001024932	545812	Mm.332769	NM_001024932	ENSMUSG00000066682	Pilrb2	EG545812	paired immunoglobin-like type 2 receptor beta 2	protein-coding
mm_170802.1	chr2	175640353	175640372	+	1	NA	promoter-TSS (NM_001177543).3	promoter-TSS (NM_001177543).3	-29	NM_001177543	100039060	Mm.289463	NM_001177543	ENSMUSG00000078886	0610010B08Rik	Gm2026	RIKEN cDNA 0610010B08 gene	protein-coding
mm_23485.1	chr3	60500758	60500795	+	1	NA	promoter-TSS (NM_001253711)	promoter-TSS (NM_001253711)	-403	NM_001253711	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_30581.1	chr4	5536822	5536825	+	1	NA	Intergenic	Intergenic	-95505	NR_038183	73872	Mm.427301	NR_038183	ENSMUSG00000086066	4930423M02Rik	-	RIKEN cDNA 4930423M02 gene	ncRNA
mm_83072.1	chr9	37657156	37657164	-	1	NA	5' UTR (NM_025289, exon 1 of 9)	5' UTR (NM_025289, exon 1 of 9)	152	NM_025289	21376	Mm.28689	NM_025289	ENSMUSG00000011114	Tbrg1	AA408552|AA409675|Niam|Tb-5|mFLJ00213	transforming growth factor beta regulated gene 1	protein-coding
mm_84708.1	chr9	72985338	72985342	-	1	NA	promoter-TSS (NM_001286546)	promoter-TSS (NM_001286546)	36	NM_001198789	546143	Mm.260946	NM_001198789	ENSMUSG00000086158	Ccpg1os	EG546143|Gm5918	cell cycle progression 1, opposite strand	protein-coding
mm_41243.1	chr5	88765213	88765223	+	1	NA	5' UTR (NM_007832, exon 1 of 7)	5' UTR (NM_007832, exon 1 of 7)	205	NM_007832	13178	Mm.298892	NM_007832	ENSMUSG00000029366	Dck	-	deoxycytidine kinase	protein-coding
mm_13287.1	chr2	101649732	101649749	+	1	NA	promoter-TSS (NM_009019)	promoter-TSS (NM_009019)	-208	NM_009019	19373	Mm.828	NM_009019	ENSMUSG00000061311	Rag1	Rag-1	recombination activating gene 1	protein-coding
mm_64544.1	chr7	144284465	144284506	+	1	NA	promoter-TSS (NM_001081370)	promoter-TSS (NM_001081370)	100	NM_001081370	210274	Mm.483624	NM_001081370	ENSMUSG00000037541	Shank2	ProSAP1|mKIAA1022	SH3/ankyrin domain gene 2	protein-coding
mm_90672.1	chr10	128896248	128896258	+	1	NA	Intergenic	Intergenic	-4535	NM_010272	14561	Mm.299218	NM_010272	ENSMUSG00000025352	Gdf11	BMP-11|Bmp11	growth differentiation factor 11	protein-coding
mm_8872.1	chr1	162859873	162859883	-	1	NA	5' UTR (NM_001330291, exon 1 of 9)	5' UTR (NM_001330291, exon 1 of 9)	122	NM_001330291	14261	Mm.976	NM_010231	ENSMUSG00000040181	Fmo1	-	flavin containing monooxygenase 1	protein-coding
mm_101253.1	chr11	20831061	20831074	-	1	NA	promoter-TSS (NM_173752)	promoter-TSS (NM_173752)	41	NM_173752	216551	Mm.76694	NM_173752	ENSMUSG00000042363	Lgalsl	1110067D22Rik|A530071M23|Grpa|Hspc159|Lgalsla	lectin, galactoside binding-like	protein-coding
mm_63204.1	chr7	125829654	125829668	+	1	NA	intron (NM_001081022, intron 13 of 27)	intron (NM_001081022, intron 13 of 27)	121785	NM_001081022	233865	Mm.274389	NM_001081022	ENSMUSG00000032743	D430042O09Rik	Kiaa0556	RIKEN cDNA D430042O09 gene	protein-coding
mm_16101.1	chr2	169632497	169632514	+	1	NA	Intergenic	Intergenic	-1141	NM_080455	228911	Mm.315789	NM_080455	ENSMUSG00000047907	Tshz2	2900073F20Rik|B830045G17|Mtsh2|Sdccag33l|Tsh2|Zfp218|mKIAA4248|teashirt2	teashirt zinc finger family member 2	protein-coding
mm_21635.1	chr2	164278327	164278336	-	1	NA	promoter-TSS (NM_009300)	promoter-TSS (NM_009300)	-24	NM_009300	20941	Mm.1286	NM_009300	ENSMUSG00000016998	Svs4	SVS-IV|Svp-2|Svp-4|Svp2|Svp4	seminal vesicle secretory protein 4	protein-coding
mm_3369.1	chr1	138960156	138960175	+	1	NA	Intergenic	Intergenic	-3544	NM_001166501	329260	Mm.337604	NM_181347	ENSMUSG00000056268	Dennd1b	4632404N19Rik|4930467M19Rik|6820401H01Rik|F730008N07Rik	DENN/MADD domain containing 1B	protein-coding
mm_10491.1	chr2	14824096	14824119	+	1	NA	promoter-TSS (NM_001252533)	promoter-TSS (NM_001252533)	15	NM_001252533	12296	Mm.313930	NM_023116	ENSMUSG00000057914	Cacnb2	AW060387|CAB2|Cavbeta2|Cchb2	calcium channel, voltage-dependent, beta 2 subunit	protein-coding
mm_26346.1	chr3	142547462	142547481	+	1	NA	3' UTR (NM_001083312, exon 11 of 11)	3' UTR (NM_001083312, exon 11 of 11)	-12581	NM_018734	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_89693.1	chr10	97568062	97568091	+	1	NA	intron (NM_008524, intron 1 of 2)	intron (NM_008524, intron 1 of 2)	2575	NM_008524	17022	Mm.18888	NM_008524	ENSMUSG00000036446	Lum	Ldc|SLRR2D	lumican	protein-coding
mm_63627.1	chr7	128344732	128344739	+	1	NA	Intergenic	Intergenic	-46604	NM_145590	233913	Mm.220880	NM_145590	ENSMUSG00000030780	BC017158	-	cDNA sequence BC017158	protein-coding
mm_25722.1	chr3	122729871	122729894	+	1	NA	intron (NM_153422, intron 1 of 20)	CpG	724	NM_153422	242202	Mm.134911	NM_153422	ENSMUSG00000053965	Pde5a	Cgbpde|Cn5n|PDE5a2|Pde5|Pde5a1	phosphodiesterase 5A, cGMP-specific	protein-coding
mm_3293.1	chr1	136680457	136680476	+	1	NA	Intergenic	Intergenic	-2930	NR_045324	100503460	Mm.30630	NR_045324	ENSMUSG00000097113	Gm19705	-	predicted gene, 19705	ncRNA
mm_155529.1	chrX	74282779	74282812	+	1	NA	promoter-TSS (NM_001242616)	promoter-TSS (NM_001242616)	77	NM_001242615	66826	Mm.268483	NM_181516	ENSMUSG00000009995	Taz	5031411C02Rik|9130012G04Rik|AW107266|AW552613|G4.5	tafazzin	protein-coding
mm_166854.1	chr7	19697656	19697665	-	1	NA	intron (NM_001305843, intron 3 of 4)	intron (NM_001305843, intron 3 of 4)	738	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_44668.1	chr5	29378338	29378401	-	1	NA	promoter-TSS (NM_020295)	promoter-TSS (NM_020295)	21	NM_020295	56873	Mm.41572	NM_020295	ENSMUSG00000010721	Lmbr1	1110048D14Rik|AU017641	limb region 1	protein-coding
mm_82925.1	chr9	35116976	35116986	-	1	NA	promoter-TSS (NM_009178)	promoter-TSS (NM_009178)	-171	NM_009178	20443	Mm.275973	NM_009178	ENSMUSG00000032038	St3gal4	Siat4c	ST3 beta-galactoside alpha-2,3-sialyltransferase 4	protein-coding
mm_48778.1	chr5	148552211	148552221	-	1	NA	5' UTR (NM_011908, exon 1 of 5)	5' UTR (NM_011908, exon 1 of 5)	572	NM_011908	24109	Mm.21846	NM_011908	ENSMUSG00000001687	Ubl3	AW108023|HCG	ubiquitin-like 3	protein-coding
mm_128111.1	chr15	28025927	28025950	-	1	NA	promoter-TSS (NM_001081302)	promoter-TSS (NM_001081302)	-90	NM_001081302	223435	Mm.485422	NM_001081302	ENSMUSG00000022263	Trio	6720464I07Rik|AA408740|Solo	triple functional domain (PTPRF interacting)	protein-coding
mm_75279.1	chr8	41015801	41015831	-	1	NA	intron (NM_001005863, intron 6 of 13)	intron (NM_001005863, intron 6 of 13)	-1652	NR_015457	78849	Mm.440930	NR_015457	ENSMUSG00000084960	B430010I23Rik	-	RIKEN cDNA B430010I23 gene	ncRNA
mm_113867.1	chr13	48491061	48491065	+	1	NA	exon (NM_026450, exon 5 of 5)	exon (NM_026450, exon 5 of 5)	22347	NM_001164575	67911	Mm.251375	NM_026450	ENSMUSG00000050954	Zfp169	1700025J14Rik|4930429A13Rik|BE688704	zinc finger protein 169	protein-coding
mm_82816.1	chr9	31004180	31004227	-	1	NA	Intergenic	Intergenic	-26441	NM_001115130	235132	Mm.239355	NM_172765	ENSMUSG00000047412	Zbtb44	6030404E16Rik|Btbd15|E230011F09	zinc finger and BTB domain containing 44	protein-coding
mm_146793.1	chr18	20114911	20114915	-	1	NA	promoter-TSS (NM_001291804)	promoter-TSS (NM_001291804)	-140	NM_013504	13505	Mm.33740	NM_013504	ENSMUSG00000044322	Dsc1	1110020A10Rik|AI507491	desmocollin 1	protein-coding
mm_73564.1	chr8	109575781	109575797	+	1	NA	exon (NM_017370, exon 5 of 5)	exon (NM_017370, exon 5 of 5)	3383	NM_017370	15439	Mm.26730	NM_017370	ENSMUSG00000031722	Hp	HP-1|preHP2	haptoglobin	protein-coding
mm_111089.1	chr12	80436408	80436456	-	1	NA	5' UTR (NM_177267, exon 1 of 9)	5' UTR (NM_177267, exon 1 of 9)	169	NM_177267	320808	Mm.220310	NM_177267	ENSMUSG00000049106	Dcaf5	9430020B07Rik|AI325023|AI430035|AI848110|AW124614|BCRG2|BCRP2|Wdr22	DDB1 and CUL4 associated factor 5	protein-coding
mm_132483.1	chr16	36880059	36880073	+	1	NA	TTS (NR_040476)	TTS (NR_040476)	-4945	NM_030035	224139	Mm.244815	NM_030035	ENSMUSG00000034243	Golgb1	4930428L02Rik|628101|6330407A06Rik|AU042952|C130074L01Rik|F730017E11Rik|Gm6840|mKIAA4151	golgi autoantigen, golgin subfamily b, macrogolgin 1	protein-coding
mm_24299.1	chr3	89366278	89366292	+	1	NA	Intergenic	Intergenic	-1032	NM_029974	77772	Mm.164013	NM_029974	ENSMUSG00000042672	Dcst1	A330106H01Rik	DC-STAMP domain containing 1	protein-coding
mm_112830.1	chr13	20818820	20818845	+	1	NA	intron (NM_012054, intron 2 of 20)	L1MC5|LINE|L1	24719	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_108462.1	chr12	83520468	83520484	+	1	NA	promoter-TSS (NM_030246)	promoter-TSS (NM_030246)	10	NM_030246	73828	Mm.38238	NM_030246	ENSMUSG00000021222	Dcaf4	1110018E21Rik|Wdr21	DDB1 and CUL4 associated factor 4	protein-coding
mm_156412.1	chrX	140664566	140664601	+	1	NA	Intergenic	Intergenic	-13445	NM_011845	23947	Mm.131097	NM_011845	ENSMUSG00000000266	Mid2	FXY2|Trim1	midline 2	protein-coding
mm_103620.1	chr11	78690010	78690013	-	1	NA	intron (NM_008702, intron 1 of 10)	intron (NM_008702, intron 1 of 10)	7414	NM_008702	18099	Mm.9001	NM_008702	ENSMUSG00000017376	Nlk	AI194375	nemo like kinase	protein-coding
mm_155663.1	chrX	87238371	87238377	+	1	NA	intron (NM_001160403, intron 5 of 10)	intron (NM_001160403, intron 5 of 10)	877249	NM_001160403	331461	Mm.121680	NM_001160403	ENSMUSG00000052372	Il1rapl1	6330532G10Rik|C030039N24|IL1R8|IL1RAPL|MRX34|OPHN4|TIGIRR-2	interleukin 1 receptor accessory protein-like 1	protein-coding
mm_82477.1	chr9	16502431	16502441	-	1	NA	Intergenic	Intergenic	-124205	NM_001080814	270120	Mm.195010	NM_001080814	ENSMUSG00000074505	Fat3	9430076A06Rik|D430038H04Rik|Gm1132|Gm510|MFAT3F	FAT atypical cadherin 3	protein-coding
mm_132194.1	chr16	32471497	32471530	+	1	NA	3' UTR (NM_009981, exon 9 of 9)	3' UTR (NM_009981, exon 9 of 9)	16366	NM_145932	106407	Mm.476915	NM_145932	ENSMUSG00000035699	Slc51a	AV001382|AW261577|D630035O19Rik|OSTalpha|Osta	solute carrier family 51, alpha subunit	protein-coding
mm_60465.1	chr7	44477890	44477916	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-6614	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_91617.1	chr10	41634143	41634151	-	1	NA	Intergenic	Intergenic	-27552	NM_001303469	75973	Mm.228517	NM_029493	ENSMUSG00000075225	Ccdc162	5033413D22Rik|Ccdc162p|Gm29096|Gm61|Gm6976	coiled-coil domain containing 162	protein-coding
mm_62631.1	chr7	107604028	107604039	+	1	NA	intron (NM_008905, intron 1 of 24)	intron (NM_008905, intron 1 of 24)	-2811	NM_001163557	19024	Mm.2817	NM_008905	ENSMUSG00000036528	Ppfibp2	Cclp1	PTPRF interacting protein, binding protein 2 (liprin beta 2)	protein-coding
mm_59723.1	chr7	28787774	28787786	+	1	NA	exon (NM_001122766, exon 12 of 13)	exon (NM_001122766, exon 12 of 13)	-1189	NM_177158	320435	Mm.74632	NM_177158	ENSMUSG00000051735	Rinl	5830482F20Rik|9930116N10Rik	Ras and Rab interactor-like	protein-coding
mm_35928.1	chr4	53032295	53032305	-	1	NA	3' UTR (NM_013454, exon 50 of 50)	3' UTR (NM_013454, exon 50 of 50)	20420	NM_025623	66536	Mm.38244	NM_025623	ENSMUSG00000015247	Nipsnap3b	2700063N13Rik|Nipsnap3a	nipsnap homolog 3B (C. elegans)	protein-coding
mm_95363.1	chr11	48902287	48902299	+	1	NA	promoter-TSS (NM_001024230)	promoter-TSS (NM_001024230)	-141	NM_001024230	432555	Mm.338931	NM_001024230	ENSMUSG00000058163	Gm5431	EG432555|Irgb9b8	predicted gene 5431	protein-coding
mm_105497.1	chr11	106159943	106159956	-	1	NA	intron (NM_172397, intron 1 of 4)	CpG	193	NM_172397	67803	Mm.21687	NM_172397	ENSMUSG00000040699	Limd2	0610025L06Rik|AI413966	LIM domain containing 2	protein-coding
mm_67794.1	chr7	97737612	97737631	-	1	NA	exon (NM_175105, exon 1 of 3)	exon (NM_175105, exon 1 of 3)	626	NM_175105	66333	Mm.29756	NM_175105	ENSMUSG00000042797	Aqp11	1700015P13Rik|AI648923|sjds	aquaporin 11	protein-coding
mm_50946.1	chr6	58596699	58596710	+	1	NA	promoter-TSS (NM_011920)	promoter-TSS (NM_011920)	32	NM_011920	26357	Mm.333096	NM_011920	ENSMUSG00000029802	Abcg2	ABC15|ABCP|AI428558|BCRP|Bcrp1|MXR|MXR1	ATP-binding cassette, sub-family G (WHITE), member 2	protein-coding
mm_134705.1	chr16	22857515	22857576	-	1	NA	promoter-TSS (NM_001190805)	promoter-TSS (NM_001190805)	124	NM_001081368	70573	Mm.68291	NM_001081368	ENSMUSG00000004462	Tbccd1	5730478M09Rik|AU015083|BB165076	TBCC domain containing 1	protein-coding
mm_36406.1	chr4	77916025	77916048	-	1	NA	intron (NM_011211, intron 2 of 39)	intron (NM_011211, intron 2 of 39)	295859	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding
mm_23792.1	chr3	79591357	79591430	+	1	NA	promoter-TSS (NM_026352)	promoter-TSS (NM_026352)	4	NM_026352	67738	Mm.295252	NM_026352	ENSMUSG00000027804	Ppid	4930564J03Rik|CYP-40|Ppidl|Ppif	peptidylprolyl isomerase D (cyclophilin D)	protein-coding
mm_95129.1	chr11	34299707	34299720	+	1	NA	intron (NM_033374, intron 30 of 51)	intron (NM_033374, intron 30 of 51)	-15109	NM_001025382	574403	Mm.444796	NM_001025382	ENSMUSG00000069911	Fam196b	EG574403|Gm6041	family with sequence similarity 196, member B	protein-coding
mm_130434.1	chr15	98170455	98170467	-	1	NA	TTS (NM_177716)	TTS (NM_177716)	2655	NM_177716	239650	Mm.54140	NM_177716	ENSMUSG00000029875	Ccdc184	5630400A08|AI836003	coiled-coil domain containing 184	protein-coding
mm_36237.1	chr4	63154791	63154830	-	1	NA	promoter-TSS (NM_007443)	promoter-TSS (NM_007443)	-638	NM_007443	11699	Mm.2197	NM_007443	ENSMUSG00000028356	Ambp	AI194774|ASPI|HI-30|Intin4|Itil|UTI	alpha 1 microglobulin/bikunin	protein-coding
mm_36275.1	chr4	63730450	63730459	-	1	NA	intron (NM_177371, intron 3 of 3)	intron (NM_177371, intron 3 of 3)	14659	NM_177371	326623	Mm.208152	NM_177371	ENSMUSG00000050395	Tnfsf15	Tl1|Tl1a|Tnlg1b|Vegi	tumor necrosis factor (ligand) superfamily, member 15	protein-coding
mm_11011.1	chr2	26581067	26581069	+	1	NA	promoter-TSS (NM_178444)	promoter-TSS (NM_178444)	12	NM_178444	353156	Mm.268933	NM_178444	ENSMUSG00000026921	Egfl7	VE-statin|Zneu1	EGF-like domain 7	protein-coding
mm_137199.1	chr17	23868079	23868125	+	1	NA	promoter-TSS (NM_020487)	promoter-TSS (NM_020487)	30	NM_020487	57256	Mm.386785	NM_020487	ENSMUSG00000024116	Prss21	1700023E12Rik|TESP5|mT4|testisin	protease, serine 21	protein-coding
mm_98994.1	chr11	98776019	98776021	+	1	NA	promoter-TSS (NM_145434)	promoter-TSS (NM_145434)	-643	NM_145434	217166	Mm.390397	NM_145434	ENSMUSG00000020889	Nr1d1	A530070C09Rik|R75201	nuclear receptor subfamily 1, group D, member 1	protein-coding
mm_172294.1	chr6	96969621	96969625	+	1	NA	intron (NM_177233, intron 3 of 5)	MusHAL1|LINE|L1	90788	NM_177233	320701	Mm.131700	NM_177233	ENSMUSG00000046500	Fam19a4	C130034I18Rik|Fam19a4 Tafa-4|Tafa-4	family with sequence similarity 19, member A4	protein-coding
mm_101627.1	chr11	36007713	36007726	-	1	NA	3' UTR (NM_001290702, exon 28 of 28)	3' UTR (NM_001290702, exon 28 of 28)	-27630	NM_170779	211652	Mm.31267	NM_170779	ENSMUSG00000018849	Wwc1	AA408228|AU017197|BC037006|Kibra|mKIAA0869	WW, C2 and coiled-coil domain containing 1	protein-coding
mm_112112.1	chr12	112797086	112797134	-	1	NA	Intergenic	Intergenic	-11865	NM_145450	217887	Mm.186678	NM_145450	ENSMUSG00000037594	BC022687	AW050009|C130001I08Rik|Flj20080	cDNA sequence BC022687	protein-coding
mm_52841.1	chr6	121732972	121732972	+	1	NA	Intergenic	Intergenic	96799	NM_175628	232345	Mm.30151	NM_175628	ENSMUSG00000030111	A2m	A2mp	alpha-2-macroglobulin	protein-coding
mm_12356.1	chr2	69749638	69749650	+	1	NA	exon (NM_001081086, exon 14 of 14)	exon (NM_001081086, exon 14 of 14)	26556	NM_001081086	228005	Mm.11815	NM_001081086	ENSMUSG00000042133	Ppig	AU019516|AU022200|B230312B02Rik|CYP|SRCyp	peptidyl-prolyl isomerase G (cyclophilin G)	protein-coding
mm_129531.1	chr15	79285471	79285498	-	1	NA	promoter-TSS (NM_177580)	promoter-TSS (NM_177580)	25	NM_177580	207495	Mm.309647	NM_177580	ENSMUSG00000018126	Baiap2l2	BC048937	BAI1-associated protein 2-like 2	protein-coding
mm_5407.1	chr1	33813243	33813290	-	1	NA	intron (NM_001290699, intron 2 of 12)	intron (NM_001290699, intron 2 of 12)	1329	NM_133817	98403	Mm.289103	NM_133817	ENSMUSG00000042197	Zfp451	4930515K21Rik|4933435G09Rik|AI596398|COASTER|Kiaa0576-hp|Znf451|mKIAA1702	zinc finger protein 451	protein-coding
mm_86882.1	chr10	22058867	22058881	+	1	NA	Intergenic	Intergenic	9205	NM_053264	114671	Mm.288194	NM_053264	ENSMUSG00000069712	4930444G20Rik	-	RIKEN cDNA 4930444G20 gene	protein-coding
mm_158669.1	chrX	157579773	157579785	-	1	NA	intron (NM_172307, intron 3 of 10)	ORR1A2|LTR|ERVL-MaLR	-10794	NM_001098723	100073351	Mm.491276	NM_001098723	ENSMUSG00000046873	Yy2	-	Yy2 transcription factor	protein-coding
mm_46450.1	chr5	105116771	105116801	-	1	NA	3' UTR (NM_001256005, exon 11 of 11)	3' UTR (NM_001256005, exon 11 of 11)	-6494	NM_172777	236573	Mm.425261	NM_172777	ENSMUSG00000029298	Gbp9	-	guanylate-binding protein 9	protein-coding
mm_169381.1	chr14	40184431	40184435	+	1	NA	Intergenic	L1Md_T|LINE|L1	528770	NR_045936	73591	Mm.65499	NR_045936	ENSMUSG00000101261	1700109I08Rik	-	RIKEN cDNA 1700109I08 gene	ncRNA
mm_20179.1	chr2	122594982	122594989	-	1	NA	3' UTR (NM_025961, exon 9 of 9)	3' UTR (NM_025961, exon 9 of 9)	16292	NM_025961	67092	Mm.29975	NM_025961	ENSMUSG00000027199	Gatm	1810003P21Rik|AI314789|AT	glycine amidinotransferase (L-arginine:glycine amidinotransferase)	protein-coding
mm_142109.1	chr17	35835971	35836000	-	1	NA	exon (NM_011655, exon 4 of 4)	exon (NM_011655, exon 4 of 4)	2316	NM_011655	22154	Mm.273538	NM_011655	ENSMUSG00000001525	Tubb5	AA408537|AI596182|B130022C14Rik|M(beta)5	tubulin, beta 5 class I	protein-coding
mm_63179.1	chr7	125487661	125487665	+	1	NA	intron (NM_026330, intron 1 of 7)	B1_Mur1|SINE|Alu	3879	NM_026330	67711	Mm.4467	NM_026330	ENSMUSG00000030750	Nsmce1	2510027N19Rik	NSE1 homolog, SMC5-SMC6 complex component	protein-coding
mm_143662.1	chr17	79715035	79715047	-	1	NA	promoter-TSS (NM_009994)	promoter-TSS (NM_009994)	0	NM_009994	13078	Mm.214016	NM_009994	ENSMUSG00000024087	Cyp1b1	CP1B|P4501b1	cytochrome P450, family 1, subfamily b, polypeptide 1	protein-coding
mm_134616.1	chr16	21063124	21063139	-	1	NA	Intergenic	Intergenic	90813	NM_025634	66561	Mm.422867	NM_025634	ENSMUSG00000090356	Teddm3	2310042E22Rik	transmembrane epididymal family member 3	protein-coding
mm_84461.1	chr9	66590673	66590675	-	1	NA	intron (NM_001302116, intron 1 of 13)	intron (NM_001302116, intron 1 of 13)	2441	NM_144937	235441	Mm.32465	NM_144937	ENSMUSG00000032376	Usp3	AA409661|BC017156	ubiquitin specific peptidase 3	protein-coding
mm_41821.1	chr5	103982932	103982935	+	1	NA	Intergenic	Intergenic	-5545	NM_001163486	243168	Mm.284944	NM_198030	ENSMUSG00000034528	Hsd17b13	AI047820|PAN1B-like|Pan1b	hydroxysteroid (17-beta) dehydrogenase 13	protein-coding
mm_123232.1	chr14	60087348	60087353	-	1	NA	promoter-TSS (NM_015803)	promoter-TSS (NM_015803)	-516	NM_015803	50769	Mm.319599	NM_015803	ENSMUSG00000021983	Atp8a2	AI415030|Atpc1b|agil|wl	ATPase, aminophospholipid transporter-like, class I, type 8A, member 2	protein-coding
mm_78113.1	chr9	20642870	20642898	+	1	NA	promoter-TSS (NM_013911)	promoter-TSS (NM_013911)	-78	NM_013911	30843	Mm.24608	NM_013911	ENSMUSG00000066892	Fbxl12	3110048D16Rik|Fbl12	F-box and leucine-rich repeat protein 12	protein-coding
mm_171006.1	chr2	80838292	80838299	+	1	NA	Intergenic	Intergenic	199031	NM_001190179	69482	Mm.29200	NM_027091	ENSMUSG00000026999	Nup35	2310006I24Rik|35kDa|5330402E05Rik|MP44|NO44	nucleoporin 35	protein-coding
mm_149463.1	chr19	11530933	11530941	+	1	NA	TTS (NM_027209)	TTS (NM_027209)	-5912	NM_025658	66607	Mm.441056	NM_025658	ENSMUSG00000024678	Ms4a4d	2210417J23Rik	membrane-spanning 4-domains, subfamily A, member 4D	protein-coding
mm_38615.1	chr4	141933081	141933095	-	1	NA	intron (NM_177868, intron 15 of 31)	intron (NM_177868, intron 15 of 31)	-49904	NR_040672	545691	Mm.332015	NR_040672	ENSMUSG00000085424	Fhad1os1	Gm13037|OTTMUSG00000010113	forkhead-associated (FHA) phosphopeptide binding domain 1, opposite strand 1	ncRNA
mm_81470.1	chr9	109931493	109931515	+	1	NA	promoter-TSS (NM_008633)	promoter-TSS (NM_008633)	-270	NM_001205331	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_13681.1	chr2	116914272	116914277	+	1	NA	Intergenic	Intergenic	14122	NR_040335	320975	Mm.132509	NR_040335	ENSMUSG00000085316	D330050G23Rik	-	RIKEN cDNA D330050G23 gene	ncRNA
mm_85159.1	chr9	96333551	96333561	-	1	NA	exon (NM_007502, exon 7 of 7)	exon (NM_007502, exon 7 of 7)	30743	NM_007502	11933	Mm.424	NM_007502	ENSMUSG00000032412	Atp1b3	AA409958|AI664000|AW212096	ATPase, Na+/K+ transporting, beta 3 polypeptide	protein-coding
mm_20350.1	chr2	127788855	127788900	-	1	NA	promoter-TSS (NM_016902)	promoter-TSS (NM_016902)	14	NM_016902	53885	Mm.210766	NM_016902	ENSMUSG00000027378	Nphp1	-	nephronophthisis 1 (juvenile) homolog (human)	protein-coding
mm_141010.1	chr17	25014307	25014334	-	1	NA	intron (NM_020608, intron 1 of 20)	CpG	910	NM_020608	57354	Mm.328854	NM_020608	ENSMUSG00000038002	Cramp1l	5830477H08Rik|AI256853|AI790734|Cramp1|Tce4|mKIAA1426	Crm, cramped-like (Drosophila)	protein-coding
mm_89736.1	chr10	99013281	99013288	+	1	NA	intron (NM_026482, intron 15 of 20)	intron (NM_026482, intron 15 of 20)	-93887	NM_027740	382406	Mm.440656	NM_027740	ENSMUSG00000019952	Poc1b	4933430F16Rik|Wdr51b	POC1 centriolar protein B	protein-coding
mm_27315.1	chr3	50366789	50366799	-	1	NA	3' UTR (NM_011990, exon 12 of 12)	3' UTR (NM_011990, exon 12 of 12)	76819	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_128767.1	chr15	66286804	66286821	-	1	NA	promoter-TSS (NM_152923)	promoter-TSS (NM_152923)	-588	NM_152923	110862	Mm.255585	NM_152923	ENSMUSG00000056258	Kcnq3	-	potassium voltage-gated channel, subfamily Q, member 3	protein-coding
mm_60941.1	chr7	46919994	46920029	+	1	NA	promoter-TSS (NM_021884)	promoter-TSS (NM_021884)	-81	NM_021884	22088	Mm.241334	NM_021884	ENSMUSG00000014402	Tsg101	AI255943|CC2	tumor susceptibility gene 101	protein-coding
mm_65203.1	chr7	19696982	19697035	-	1	NA	exon (NM_009696, exon 4 of 4)	exon (NM_009696, exon 4 of 4)	1390	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_90797.1	chr10	7212223	7212247	-	1	NA	promoter-TSS (NM_172546)	promoter-TSS (NM_172546)	2	NM_172546	215748	Mm.37984	NM_172546	ENSMUSG00000015202	Cnksr3	6820402C05|BC024086|Magi1	Cnksr family member 3	protein-coding
mm_49418.1	chr6	28981491	28981526	+	1	NA	Intergenic	CpG	-41111	NR_029567	387237		NR_029567	ENSMUSG00000065469	Mir129-1	Mirn129-1|Mirn129b|miR-129b|mir-129-1	microRNA 129-1	ncRNA
mm_161991.1	chr19	34599351	34599351	-	1	NA	promoter-TSS (NM_001110517)	promoter-TSS (NM_001110517)	76	NM_001110517	667373	Mm.371956	NM_001101605	ENSMUSG00000079339	Ifit1bl1	Gm14446|Ifit1c|OTTMUSG00000016644	interferon induced protein with tetratricpeptide repeats 1B like 1	protein-coding
mm_110579.1	chr12	56521341	56521351	-	1	NA	intron (NR_045082, intron 1 of 6)	intron (NR_045082, intron 1 of 6)	8074	NR_045082	104798	Mm.310950	NR_045082		E030019B13Rik	AI413669	RIKEN cDNA E030019B13 gene	ncRNA
mm_158107.1	chrX	102071227	102071239	-	1	NA	promoter-TSS (NM_001278534)	promoter-TSS (NM_001278534)	74	NM_001278534	331474	Mm.23297	NM_183318	ENSMUSG00000049191	Rgag4	6430402L03Rik|Mar5|Mart5|mKIAA2001	retrotransposon gag domain containing 4	protein-coding
mm_75043.1	chr8	32819772	32819782	-	1	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	130249	NM_001177589	100042715	Mm.291093	NM_001177589		Gm3985	-	predicted gene 3985	protein-coding
mm_69447.1	chr7	133015314	133015329	-	1	NA	promoter-TSS (NM_001170744)	promoter-TSS (NM_001170744)	-74	NM_001170744	13017	Mm.246240	NM_009980	ENSMUSG00000030970	Ctbp2	AA407280|D7Ertd45e|Gtrgeo6|Ribeye	C-terminal binding protein 2	protein-coding
mm_7457.1	chr1	120435723	120435727	-	1	NA	Intergenic	Intergenic	69359	NM_010766	17167	Mm.1856	NM_010766	ENSMUSG00000026390	Marco	AI323439|Ly112|Scara2	macrophage receptor with collagenous structure	protein-coding
mm_37363.1	chr4	120810410	120810413	-	1	NA	intron (NM_001048168, intron 1 of 9)	B3|SINE|B2	15330	NM_001277095	18046	Mm.435590	NM_008692	ENSMUSG00000032897	Nfyc	-	nuclear transcription factor-Y gamma	protein-coding
mm_30369.1	chr3	152193724	152193734	-	1	NA	5' UTR (NM_025926, exon 1 of 3)	5' UTR (NM_025926, exon 1 of 3)	116	NM_025926	67035	Mm.46746	NM_025926	ENSMUSG00000028035	Dnajb4	1700029A20Rik|2010306G19Rik|5730460G06Rik	DnaJ heat shock protein family (Hsp40) member B4	protein-coding
mm_44575.1	chr5	24842358	24842453	-	1	NA	promoter-TSS (NM_053075)	promoter-TSS (NM_053075)	-44	NM_053075	19744	Mm.319175	NM_053075	ENSMUSG00000028945	Rheb	Rheb1	Ras homolog enriched in brain	protein-coding
mm_103451.1	chr11	76217491	76217591	-	1	NA	promoter-TSS (NM_177367)	promoter-TSS (NM_177367)	31	NM_177367	276919	Mm.482713	NM_177367	ENSMUSG00000049396	Gemin4	4932415L08Rik|AU015359	gem (nuclear organelle) associated protein 4	protein-coding
mm_91321.1	chr10	24959945	24959968	-	1	NA	Intergenic	MT2B1|LTR|ERVL	-32486	NM_007482	11846	Mm.154144	NM_007482	ENSMUSG00000019987	Arg1	AI|AI256583|Arg-1|PGIF	arginase, liver	protein-coding
mm_31885.1	chr4	82315937	82315968	+	1	NA	intron (NM_001286131, intron 8 of 9)	intron (NM_001286131, intron 8 of 9)	189827	NM_001286127	18028	Mm.317947	NM_008687	ENSMUSG00000008575	Nfib	6720429L07Rik|CTF|E030026I10Rik|NF-I/B|NF1-B|NFI-B	nuclear factor I/B	protein-coding
mm_62449.1	chr7	101384889	101384911	+	1	NA	promoter-TSS (NM_027180)	promoter-TSS (NM_027180)	-626	NM_027180	69710	Mm.277687	NM_027180	ENSMUSG00000032812	Arap1	2410002L19Rik|Centd2|mKIAA0782	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	protein-coding
mm_96174.1	chr11	61578994	61579035	+	1	NA	intron (NM_001252188, intron 1 of 10)	CpG	673	NM_010148	13855	Mm.139695	NM_010148	ENSMUSG00000001036	Epn2	9530051D10Rik|AA536924|Ibp2	epsin 2	protein-coding
mm_49085.1	chr6	6863552	6863570	+	1	NA	TTS (NR_002839)	TTS (NR_002839)	227	NM_010057	13396	Mm.439763	NM_010057	ENSMUSG00000029754	Dlx6	-	distal-less homeobox 6	protein-coding
mm_54672.1	chr6	39241673	39241691	-	1	NA	Intergenic	Intergenic	-34909	NM_001033430	338523	Mm.293175	NM_001033430	ENSMUSG00000042599	Kdm7a	A630082K20Rik|BB041802|ENSMUSG00000073143|Jhdm1d|mKIAA1718	lysine (K)-specific demethylase 7A	protein-coding
mm_71763.1	chr8	66397678	66397682	+	1	NA	intron (NM_175188, intron 5 of 7)	intron (NM_175188, intron 5 of 7)	11379	NM_001166375	72925	Mm.380457	NM_175188	ENSMUSG00000036469	March1	2900024D24Rik|BB085186	membrane-associated ring finger (C3HC4) 1	protein-coding
mm_20863.1	chr2	148438441	148438453	-	1	NA	3' UTR (NM_010740, exon 2 of 2)	3' UTR (NM_010740, exon 2 of 2)	5088	NM_010740	17064	Mm.681	NM_010740	ENSMUSG00000027435	Cd93	6030404G09Rik|AA145088|AA4.1|AW555904|C1qr1|C1qrp|Ly68	CD93 antigen	protein-coding
mm_58801.1	chr7	16295839	16295857	+	1	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	-9053	NM_001136471	243846	Mm.482401	NM_172297	ENSMUSG00000041375	Ccdc9	2600011L02Rik	coiled-coil domain containing 9	protein-coding
mm_111406.1	chr12	91110253	91110255	-	1	NA	promoter-TSS (NR_030473)	promoter-TSS (NR_030473)	25	NR_030473	735273		NR_030473	ENSMUSG00000076118	Mir669c	Mirn669c|Mirn669c-1	microRNA 669c	ncRNA
mm_92220.1	chr10	68277316	68277328	-	1	NA	intron (NM_023598, intron 2 of 9)	intron (NM_023598, intron 2 of 9)	1404	NM_023598	71371	Mm.440357	NM_023598	ENSMUSG00000019947	Arid5b	4930580B11|5430435G07Rik|AI467247|Desrt|Mrf2|Mrf2alpha|Mrf2beta	AT rich interactive domain 5B (MRF1-like)	protein-coding
mm_84676.1	chr9	72084749	72084752	-	1	NA	intron (NM_001253862, intron 3 of 19)	(A)n|Simple_repeat|Simple_repeat	26451	NM_001253862	21406	Mm.171615	NM_011544	ENSMUSG00000032228	Tcf12	A130037E08Rik|ALF1|HEB|HEBAlt|HTF-4|HTF4|ME1|REB|bHLHb20	transcription factor 12	protein-coding
mm_137758.1	chr17	29487446	29487456	+	1	NA	Intergenic	Intergenic	-3594	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_102600.1	chr11	62389765	62389800	-	1	NA	exon (NM_001252313, exon 13 of 45)	exon (NM_001252313, exon 13 of 45)	48733	NM_001252313	20185	Mm.271814	NM_011308	ENSMUSG00000018501	Ncor1	5730405M06Rik|A230020K14Rik|N-CoR|RIP13|Rxrip13|mKIAA1047	nuclear receptor co-repressor 1	protein-coding
mm_147923.1	chr18	65890749	65890762	-	1	NA	Intergenic	ERVB7_2-LTR_MM|LTR|ERVK	17269	NM_175012	225642	Mm.20298	NM_175012	ENSMUSG00000024517	Grp	BLP	gastrin releasing peptide	protein-coding
mm_79912.1	chr9	65462539	65462542	+	1	NA	intron (NM_138584, intron 1 of 8)	intron (NM_138584, intron 1 of 8)	1603	NM_138584	27965	Mm.272475	NM_138584	ENSMUSG00000032388	Spg21	ACP33|BM-019|C78576|D9Wsu18e|GL010|MAST	spastic paraplegia 21 homolog (human)	protein-coding
mm_22781.1	chr3	21955082	21955088	+	1	NA	Intergenic	Intergenic	-121567	NM_030732	81004	Mm.202966	NM_030732	ENSMUSG00000027630	Tbl1xr1	8030499H02Rik|A630076E03Rik|AW539987|C21|C230089I12Rik|DC42|Ira1|TBLR1	transducin (beta)-like 1X-linked receptor 1	protein-coding
mm_41515.1	chr5	92387771	92387779	+	1	NA	promoter-TSS (NM_181728)	promoter-TSS (NM_181728)	-359	NM_181728	109979	Mm.263514	NM_181728	ENSMUSG00000034842	Art3	4930569O04Rik|ARTC3	ADP-ribosyltransferase 3	protein-coding
mm_56682.1	chr6	113910447	113910451	-	1	NA	intron (NM_001347365, intron 2 of 23)	intron (NM_001347365, intron 2 of 23)	-18910	NM_001036684	11941	Mm.321755	NM_009723	ENSMUSG00000030302	Atp2b2	D6Abb2e|Gena300|PMCA2|Tmy|dfw|jog|wms|wri	ATPase, Ca++ transporting, plasma membrane 2	protein-coding
mm_148480.1	chr19	4125947	4125999	+	1	NA	promoter-TSS (NM_016666)	promoter-TSS (NM_016666)	13	NM_025889	66990	Mm.276255	NM_025889		Tmem134	2410001H17Rik|AI463452	transmembrane protein 134	protein-coding
mm_45109.1	chr5	45450122	45450139	-	1	NA	promoter-TSS (NM_024236)	promoter-TSS (NM_024236)	99	NM_024236	110391	Mm.30204	NM_024236	ENSMUSG00000015806	Qdpr	2610008L04Rik|D5Ertd371e|Dhpr|PKU2	quinoid dihydropteridine reductase	protein-coding
mm_130460.1	chr15	98607484	98607494	-	1	NA	5' UTR (NM_007405, exon 1 of 22)	5' UTR (NM_007405, exon 1 of 22)	144	NM_007405	11512	Mm.157091	NM_007405	ENSMUSG00000022994	Adcy6	AC6|mKIAA0422	adenylate cyclase 6	protein-coding
mm_73736.1	chr8	113644155	113644159	+	1	NA	3' UTR (NM_001048143, exon 6 of 6)	3' UTR (NM_001048143, exon 6 of 6)	944	NM_001048145	668110	Mm.390078	NM_029139	ENSMUSG00000033409	Syce1l	4930481F22Rik|MMRP|PSESS|mmrp2	synaptonemal complex central element protein 1 like	protein-coding
mm_35107.1	chr4	9643623	9643633	-	1	NA	promoter-TSS (NM_001177853)	promoter-TSS (NM_001177853)	89	NM_001177853	65973	Mm.222206	NM_023066	ENSMUSG00000028207	Asph	2310005F16Rik|3110001L23Rik|AI848629|AW261690|AW561901|BAH|C79816|cI-37	aspartate-beta-hydroxylase	protein-coding
mm_12293.1	chr2	69036069	69036089	+	1	NA	intron (NM_172856, intron 4 of 9)	intron (NM_172856, intron 4 of 9)	-99721	NM_181547	329416	Mm.90047	NM_181547	ENSMUSG00000034738	Nostrin	Daip2|mDaIP2	nitric oxide synthase trafficker	protein-coding
mm_11026.1	chr2	26903064	26903094	+	1	NA	promoter-TSS (NM_009298)	promoter-TSS (NM_009298)	-192	NM_009298	20935	Mm.245577	NM_009298	ENSMUSG00000036160	Surf6	D2Wsu129e|Surf-6	surfeit gene 6	protein-coding
mm_89159.1	chr10	86068191	86068201	+	1	NA	intron (NM_013722, intron 10 of 13)	intron (NM_013722, intron 10 of 13)	-27658	NR_038024	78170	Mm.444790	NR_038024		4930486F22Rik	-	RIKEN cDNA 4930486F22 gene	ncRNA
mm_154591.1	chrX	7579750	7579760	+	1	NA	promoter-TSS (NM_054039)	promoter-TSS (NM_054039)	79	NM_054039	20371	Mm.182291	NM_054039	ENSMUSG00000039521	Foxp3	JM2|scurfin|sf	forkhead box P3	protein-coding
mm_81651.1	chr9	110953790	110953807	+	1	NA	intron (NM_028838, intron 1 of 8)	CpG	2253	NM_028838	74249	Mm.307615	NM_028838	ENSMUSG00000032495	Lrrc2	2400002D05Rik|4933431K03Rik	leucine rich repeat containing 2	protein-coding
mm_142840.1	chr17	51795603	51795632	-	1	NA	intron (NM_009122, intron 5 of 10)	A-rich|Low_complexity|Low_complexity	16437	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_23633.1	chr3	66401148	66401161	+	1	NA	Intergenic	Intergenic	-104317	NM_145820	72789	Mm.443526	NM_028357	ENSMUSG00000027831	Veph1	2810471M23Rik|Veph	ventricular zone expressed PH domain-containing 1	protein-coding
mm_161795.1	chr17	48400785	48400785	-	1	NA	promoter-TSS (NM_001347402)	promoter-TSS (NM_001347402)	-205	NM_001347401	18044	Mm.4929	NM_010913	ENSMUSG00000023994	Nfya	AA407810|Cbf-b|SEZ-10|SEZ10	nuclear transcription factor-Y alpha	protein-coding
mm_80539.1	chr9	80310717	80310720	+	1	NA	3' UTR (NM_001039546, exon 33 of 33)	3' UTR (NM_001039546, exon 33 of 33)	145684	NM_001039546	17920	Mm.4040	NM_008662	ENSMUSG00000033577	Myo6	BC029719|Tlc|sv	myosin VI	protein-coding
mm_137503.1	chr17	27017993	27018003	+	1	NA	promoter-TSS (NM_001251881)	promoter-TSS (NM_001251881)	-37	NM_001251881	70772	Mm.440437	NM_027544	ENSMUSG00000048731	Ggnbp1	0610031G08Rik|mdf	gametogenetin binding protein 1	protein-coding
mm_105974.1	chr11	115514375	115514393	-	1	NA	promoter-TSS (NM_008258)	promoter-TSS (NM_008258)	-14	NM_008258	15374	Mm.1775	NM_008258	ENSMUSG00000020737	Hn1	-	hematological and neurological expressed sequence 1	protein-coding
mm_91747.1	chr10	49710634	49710639	-	1	NA	intron (NM_001111268, intron 2 of 16)	intron (NM_001111268, intron 2 of 16)	78118	NM_010349	14806	Mm.332838	NM_010349	ENSMUSG00000056073	Grik2	AW124492|GluK2|Glur-6|Glur6|Glurbeta2	glutamate receptor, ionotropic, kainate 2 (beta 2)	protein-coding
mm_84728.1	chr9	74927542	74927542	-	1	NA	Intergenic	MLT1G3|LTR|ERVL-MaLR	-25511	NM_001113283	235493	Mm.208955	NM_153584	ENSMUSG00000034858	Fam214a	6330415I01Rik|AI553555|C130047D21Rik|Kiaa1370|mKIAA1370	family with sequence similarity 214, member A	protein-coding
mm_122000.1	chr14	26669627	26669691	-	1	NA	promoter-TSS (NR_106132)	promoter-TSS (NR_106132)	-51	NR_106132	102465773		NR_106132	ENSMUSG00000098751	Mir7672	Gm27314|mmu-mir-7672	microRNA 7672	ncRNA
mm_23003.1	chr3	34069394	34069402	+	1	NA	TTS (NM_001113188)	TTS (NM_001113188)	11956	NM_001286972	67713	Mm.274266	NM_026332	ENSMUSG00000027679	Dnajc19	1810055D05Rik|AA959924|Tim14	DnaJ heat shock protein family (Hsp40) member C19	protein-coding
mm_123303.1	chr14	61656813	61656816	-	1	NA	intron (NR_028264, intron 1 of 6)	RLTR25B|LTR|ERVK	-24704	NR_029733	387174		NR_029733	ENSMUSG00000093007	Mir15a	Mirn15a|mir-15a|mmu-mir-15a	microRNA 15a	ncRNA
mm_133272.1	chr16	77375328	77375365	+	1	NA	intron (NR_015543, intron 2 of 4)	intron (NR_015543, intron 2 of 4)	46018	NR_015543	77994	Mm.394688	NR_015543	ENSMUSG00000090386	Mir99ahg	2810055G20Rik|D730043B02Rik	Mir99a and Mirlet7c-1 host gene (non-protein coding)	ncRNA
mm_2774.1	chr1	130732104	130732135	+	1	NA	5' UTR (NM_177604, exon 1 of 4)	5' UTR (NM_177604, exon 1 of 4)	143	NM_177604	212439	Mm.268547	NM_177604	ENSMUSG00000042510	AA986860	E030025M07|Sarg	expressed sequence AA986860	protein-coding
mm_167317.1	chr8	66386397	66386414	+	1	NA	exon (NM_001166375, exon 1 of 4)	exon (NM_001166375, exon 1 of 4)	104	NM_001166375	72925	Mm.380457	NM_175188	ENSMUSG00000036469	March1	2900024D24Rik|BB085186	membrane-associated ring finger (C3HC4) 1	protein-coding
mm_8669.1	chr1	156669613	156669637	-	1	NA	exon (NM_023141, exon 3 of 6)	exon (NM_023141, exon 3 of 6)	4714	NM_023141	30935	Mm.206737	NM_023141	ENSMUSG00000060519	Tor3a	Adir	torsin family 3, member A	protein-coding
mm_44167.1	chr5	150764820	150764826	+	1	NA	intron (NM_001346503, intron 17 of 34)	intron (NM_001346503, intron 17 of 34)	90996	NM_001346503	100710	Mm.32959	NM_175310	ENSMUSG00000034021	Pds5b	AI646570|AS3|AW212954|Aprin|Tg(Wap-ERBB2)229Wzw|WAP-Her-2|mKIAA0979	PDS5 cohesin associated factor B	protein-coding
mm_12600.1	chr2	74675093	74675102	+	1	NA	promoter-TSS (NM_008274)	promoter-TSS (NM_008274)	84	NM_008274	15432	Mm.57124	NM_008274	ENSMUSG00000001823	Hoxd12	Hox-4.7|Hox-5.6	homeobox D12	protein-coding
mm_142131.1	chr17	35908908	35908924	-	1	NA	exon (NM_028476, exon 5 of 10)	exon (NM_028476, exon 5 of 10)	1152	NM_001142745	73242	Mm.273155	NM_028476	ENSMUSG00000024426	Atat1	0610011P08Rik|2610008K08Rik|2610110G12Rik|3110080J08Rik|Mec17|TAT	alpha tubulin acetyltransferase 1	protein-coding
mm_171168.1	chr3	27642987	27643000	-	1	NA	exon (NM_173182, exon 2 of 26)	exon (NM_173182, exon 2 of 26)	-57998	NR_037275	100526525		NR_037275	ENSMUSG00000092695	Mir3092	mir-3092|mmu-mir-3092	microRNA 3092	ncRNA
mm_123979.1	chr14	75180744	75180758	-	1	NA	intron (NM_008879, intron 2 of 16)	intron (NM_008879, intron 2 of 16)	44326	NM_008879	18826	Mm.153911	NM_008879	ENSMUSG00000021998	Lcp1	AW536232|D14Ertd310e|LCP-1|Pls2|pp65	lymphocyte cytosolic protein 1	protein-coding
mm_100380.1	chr11	119274881	119274911	+	1	NA	exon (NM_008064, exon 7 of 20)	exon (NM_008064, exon 7 of 20)	6933	NM_008064	14387	Mm.4793	NM_008064	ENSMUSG00000025579	Gaa	E430018M07Rik	glucosidase, alpha, acid	protein-coding
mm_3985.1	chr1	164278104	164278126	+	1	NA	intron (NM_029115, intron 1 of 5)	intron (NM_029115, intron 1 of 5)	2517	NM_029115	74895	Mm.167258	NM_029115	ENSMUSG00000026578	Ccdc181	4930455F23Rik|AI427889	coiled-coil domain containing 181	protein-coding
mm_128210.1	chr15	36140437	36140467	-	1	NA	promoter-TSS (NM_001195748)	promoter-TSS (NM_001195748)	-52	NM_001195748	626596	Mm.321798	NM_001195748	ENSMUSG00000037627	Rgs22	-	regulator of G-protein signalling 22	protein-coding
mm_92537.1	chr10	79614154	79614193	-	1	NA	promoter-TSS (NM_198614)	promoter-TSS (NM_198614)	-148	NM_001168624	237397	Mm.334207	NM_198614	ENSMUSG00000045912	C2cd4c	4932409I22Rik|Fam148c|Gm238	C2 calcium-dependent domain containing 4C	protein-coding
mm_18174.1	chr2	45110168	45110183	-	1	NA	promoter-TSS (NR_110572)	promoter-TSS (NR_110572)	102	NM_001289521	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_9072.1	chr1	168370091	168370095	-	1	NA	intron (NM_008783, intron 2 of 7)	intron (NM_008783, intron 2 of 7)	62076	NM_001291508	18514	Mm.43358	NM_008783	ENSMUSG00000052534	Pbx1	2310056B04Rik|D230003C07Rik|Pbx-1	pre B cell leukemia homeobox 1	protein-coding
mm_72207.1	chr8	72586158	72586194	+	1	NA	3' UTR (NM_144534, exon 6 of 6)	3' UTR (NM_144534, exon 6 of 6)	14073	NM_144534	74166	Mm.212927	NM_144534	ENSMUSG00000031791	Tmem38a	1110001E17Rik|AI413399|TRIC-A|mg33a	transmembrane protein 38A	protein-coding
mm_116742.1	chr13	51763431	51763478	-	1	NA	intron (NM_013660, intron 1 of 15)	intron (NM_013660, intron 1 of 15)	30293	NM_001281880	20354	Mm.33903	NM_013660	ENSMUSG00000021451	Sema4d	CD100|Semacl2|Semaj|Semcl2|coll-4	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D	protein-coding
mm_102059.1	chr11	52253720	52253750	-	1	NA	3' UTR (NM_009331, exon 10 of 10)	3' UTR (NM_009331, exon 10 of 10)	21740	NM_011543	21402	Mm.42944	NM_011543	ENSMUSG00000036309	Skp1a	15kDa|2610043E24Rik|2610206H23Rik|EMC19|OCP-II|OCP2|SKP1|Tceb1l|p19A|p19Skp1	S-phase kinase-associated protein 1A	protein-coding
mm_73951.1	chr8	120228489	120228503	+	1	NA	promoter-TSS (NR_110496)	promoter-TSS (NR_110496)	-266	NR_110496	434353	Mm.411793	NR_110496	ENSMUSG00000097960	A330074K22Rik	-	RIKEN cDNA A330074K22 gene	ncRNA
mm_85923.1	chr9	111523220	111523242	-	1	NA	Intergenic	RLTR16C_MM|LTR|ERVK	84150	NM_172928	245038	Mm.26361	NM_172928	ENSMUSG00000032500	Dclk3	BC056929|C730036H08|Dcamkl3	doublecortin-like kinase 3	protein-coding
mm_5822.1	chr1	52727458	52727474	-	1	NA	promoter-TSS (NM_133829)	promoter-TSS (NM_133829)	-148	NM_133829	98682	Mm.491173	NM_133829	ENSMUSG00000041439	Mfsd6	2210010L05Rik|9630025I22Rik|AI836200|AW212394|MMR2	major facilitator superfamily domain containing 6	protein-coding
mm_168920.1	chr12	59066884	59066885	+	1	NA	promoter-TSS (NM_008891)	promoter-TSS (NM_008891)	-35	NM_008891	18949	Mm.22347	NM_008891	ENSMUSG00000020994	Pnn	AU045199|D12Ertd512e	pinin	protein-coding
mm_166646.1	chr6	85374425	85374445	-	1	NA	exon (NM_177466, exon 1 of 5)	exon (NM_177466, exon 1 of 5)	199	NM_177466	52055	Mm.220334	NM_177466	ENSMUSG00000051343	Rab11fip5	9130206P09Rik|C75969|D6Ertd32e|GAF1|RIP11	RAB11 family interacting protein 5 (class I)	protein-coding
mm_30403.1	chr3	152253122	152253134	-	1	NA	exon (NM_199465, exon 3 of 13)	exon (NM_199465, exon 3 of 13)	13192	NM_199465	68810	Mm.200188	NM_199465	ENSMUSG00000039103	Nexn	1110046H09Rik|AA553326|NELIN	nexilin	protein-coding
mm_21359.1	chr2	157129983	157129992	-	1	NA	intron (NM_018851, intron 1 of 15)	intron (NM_018851, intron 1 of 15)	5235	NM_001139520	56045	Mm.248478	NM_018851	ENSMUSG00000027639	Samhd1	E330031J07Rik|Mg11	SAM domain and HD domain, 1	protein-coding
mm_79761.1	chr9	62421310	62421326	+	1	NA	exon (NM_175484, exon 12 of 12)	exon (NM_175484, exon 12 of 12)	79975	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	protein-coding
mm_124103.1	chr14	79301053	79301062	-	1	NA	intron (NM_025427, intron 1 of 4)	CpG	578	NM_025427	66214	Mm.29811	NM_025427	ENSMUSG00000022018	Rgcc	1190002H23Rik|Rgc-32|Rgc32	regulator of cell cycle	protein-coding
mm_120255.1	chr14	63011751	63011763	+	1	NA	promoter-TSS (NM_001039121)	promoter-TSS (NM_001039121)	-14	NM_001039121	654458	Mm.390737	NM_001039121	ENSMUSG00000075572	Defb43	BD-43|EG654458|mBD-43	defensin beta 43	protein-coding
mm_56563.1	chr6	101377255	101377267	-	1	NA	exon (NM_018884, exon 1 of 10)	exon (NM_018884, exon 1 of 10)	636	NM_018884	55983	Mm.321654	NM_018884	ENSMUSG00000035357	Pdzrn3	1110020C07Rik|AI429718|AL023082|LNX3|SEMACAP3|Semcap3	PDZ domain containing RING finger 3	protein-coding
mm_171577.1	chr4	147443383	147443399	+	1	NA	intron (NM_001039209, intron 1 of 2)	CpG	-109886	NM_001014397	433804	Mm.332047	NM_001014397	ENSMUSG00000065999	Zfp985	Gm13154|OTTMUSG00000010673	zinc finger protein 985	protein-coding
mm_20677.1	chr2	132385393	132385434	-	1	NA	promoter-TSS (NM_144944)	promoter-TSS (NM_144944)	34	NM_144944	246313	Mm.283777	NM_144944	ENSMUSG00000050558	Prokr2	B830005M06Rik|EG-VEGRF2|Gpcr73l1|Gpr73l1|PKR2	prokineticin receptor 2	protein-coding
mm_137216.1	chr17	24169811	24169822	+	1	NA	promoter-TSS (NM_009729)	promoter-TSS (NM_009729)	-387	NM_009729	11984	Mm.30155	NM_009729	ENSMUSG00000024121	Atp6v0c	Atp6c|Atp6c2|Atp6l|Atpl|Atpl-rs1|PL16|VATL|Vma3	ATPase, H+ transporting, lysosomal V0 subunit C	protein-coding
mm_132015.1	chr16	25871283	25871284	+	1	NA	intron (NM_001127259, intron 10 of 13)	intron (NM_001127259, intron 10 of 13)	69367	NM_001127264	22061	Mm.20894	NM_011641	ENSMUSG00000022510	Trp63	AI462811|Ket|P51/P63|P63|P73l|Tp63|Trp53rp1	transformation related protein 63	protein-coding
mm_125646.1	chr15	62250554	62250556	+	1	NA	non-coding (NR_003368, exon 9 of 9)	non-coding (NR_003368, exon 9 of 9)	-31104	NR_003523	67552	Mm.484027	NM_026230		H2afy3	4933432H23Rik	H2A histone family, member Y3	pseudo
mm_154867.1	chrX	20678692	20678719	+	1	NA	exon (NM_009457, exon 18 of 26)	exon (NM_009457, exon 18 of 26)	-9249	NM_001310456	18555	Mm.102574	NM_011049	ENSMUSG00000031065	Cdk16	Crk5|Pctaire1|Pctk1	cyclin-dependent kinase 16	protein-coding
mm_141753.1	chr17	34261614	34261627	-	1	NA	Intergenic	Intergenic	-1607	NM_207105	14961	Mm.254067	NM_207105	ENSMUSG00000073421	H2-Ab1	AI845868|Abeta|H-2Ab|H2-Ab|I-Abeta|IAb|Ia-2|Ia2|Rmcs1	histocompatibility 2, class II antigen A, beta 1	protein-coding
mm_109514.1	chr12	111454286	111454297	+	1	NA	3' UTR (NM_009396, exon 12 of 12)	3' UTR (NM_009396, exon 12 of 12)	11630	NM_009396	21928	Mm.255332	NM_009396	ENSMUSG00000021281	Tnfaip2	B94|Exoc3l3|M-sec|Tnfip2|tnfb94	tumor necrosis factor, alpha-induced protein 2	protein-coding
mm_98357.1	chr11	93885885	93885924	+	1	NA	promoter-TSS (NM_134012)	promoter-TSS (NM_134012)	-138	NM_001013375	217109	Mm.379350	NM_001013375	ENSMUSG00000054079	Utp18	6230425C22Rik|6430513M13|Wdr50	UTP18 small subunit processome component	protein-coding
mm_42867.1	chr5	122232367	122232387	+	1	NA	intron (NM_028752, intron 2 of 6)	RLTR40|LTR|ERVK	22090	NM_028752	74096	Mm.28804	NM_028752	ENSMUSG00000064267	Hvcn1	0610039P13Rik|AI450555|BTS|HV1|Vsop.|mVSOP	hydrogen voltage-gated channel 1	protein-coding
mm_7027.1	chr1	87098878	87098904	-	1	NA	exon (NM_001081082, exon 11 of 11)	exon (NM_001081082, exon 11 of 11)	2715	NM_001081082	76768	Mm.58068	NM_001081082	ENSMUSG00000079440	Alpi	2010001C14Rik|Akp6|gIAP	alkaline phosphatase, intestinal	protein-coding
mm_112121.1	chr12	112860887	112860967	-	1	NA	promoter-TSS (NM_019925)	promoter-TSS (NM_019925)	-11	NM_019925	56696	Mm.20455	NM_019925	ENSMUSG00000021298	Gpr132	G2a	G protein-coupled receptor 132	protein-coding
mm_81870.1	chr9	119052864	119052893	+	1	NA	promoter-TSS (NM_011700)	promoter-TSS (NM_011700)	100	NM_001164567	22351	Mm.83817	NM_011700	ENSMUSG00000038775	Vill	Villp	villin-like	protein-coding
mm_87069.1	chr10	29144130	29144164	+	1	NA	5' UTR (NM_026138, exon 1 of 7)	5' UTR (NM_026138, exon 1 of 7)	151	NM_026138	67412	Mm.390264	NM_026138	ENSMUSG00000038916	Soga3	6330407J23Rik	SOGA family member 3	protein-coding
mm_59547.1	chr7	28070946	28070949	+	1	NA	promoter-TSS (NM_001122603)	promoter-TSS (NM_001122603)	-289	NM_001122603	215384	Mm.292276	NM_175444	ENSMUSG00000047730	Fcgbp	A430096B05Rik	Fc fragment of IgG binding protein	protein-coding
mm_85410.1	chr9	103424916	103424924	-	1	NA	TTS (NM_001002896)	TTS (NM_001002896)	1342	NR_040466	100529079	Mm.437003	NR_040466	ENSMUSG00000086236	5830418P13Rik	-	RIKEN cDNA 5830418P13 gene	ncRNA
mm_159976.1	chr6	113105023	113105023	+	1	NA	promoter-TSS (NM_173005)	promoter-TSS (NM_173005)	88	NM_173005	72895	Mm.367159	NM_028385	ENSMUSG00000034269	Setd5	2900045N06Rik|C330007C20|C85544|mKIAA1757	SET domain containing 5	protein-coding
mm_37631.1	chr4	127358105	127358107	-	1	NA	promoter-TSS (NM_010291)	promoter-TSS (NM_010291)	58	NM_010291	14622	Mm.26859	NM_010291	ENSMUSG00000042357	Gjb5	Cnx31.1|Cx31.1|Gjb-5	gap junction protein, beta 5	protein-coding
mm_1769.1	chr1	77522369	77522386	+	1	NA	Intergenic	Intergenic	-7289	NM_007936	13838	Mm.400747	NM_007936	ENSMUSG00000026235	Epha4	2900005C20Rik|AI385584|Cek8|Hek8|Sek|Sek1|Tyro1|rb	Eph receptor A4	protein-coding
mm_85347.1	chr9	103209041	103209050	-	1	NA	exon (NM_133977, exon 17 of 17)	exon (NM_133977, exon 17 of 17)	-6980	NM_009275	20818	Mm.273053	NM_009275	ENSMUSG00000032553	Srprb	AA409543	signal recognition particle receptor, B subunit	protein-coding
mm_160528.1	chr9	37621670	37621670	+	1	NA	intron (NM_011734, intron 2 of 9)	intron (NM_011734, intron 2 of 9)	7823	NM_011734	22619	Mm.196345	NM_011734	ENSMUSG00000001942	Siae	LSE|Ysg2	sialic acid acetylesterase	protein-coding
mm_139652.1	chr17	57401150	57401160	+	1	NA	intron (NM_010130, intron 2 of 21)	L1VL2|LINE|L1	42469	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_32628.1	chr4	114909845	114909848	+	1	NA	promoter-TSS (NM_008593)	promoter-TSS (NM_008593)	557	NR_030721	100040736	Mm.231287	NR_030721	ENSMUSG00000085399	Foxd2os	9130206I24Rik	forkhead box D2, opposite strand	ncRNA
mm_11889.1	chr2	49743835	49743851	+	1	NA	intron (NM_008449, intron 19 of 25)	intron (NM_008449, intron 19 of 25)	-43843	NM_027990	71897	Mm.41381	NM_027990	ENSMUSG00000026765	Lypd6b	2310010M24Rik|AW049525	LY6/PLAUR domain containing 6B	protein-coding
mm_137165.1	chr17	23807132	23807167	+	1	NA	intron (NM_175229, intron 1 of 13)	CpG	3962	NM_175229	75956	Mm.5222	NM_175229	ENSMUSG00000039218	Srrm2	5033413A03Rik|AA410130|SRm300|mKIAA0324	serine/arginine repetitive matrix 2	protein-coding
mm_157795.1	chrX	73880741	73880815	-	1	NA	promoter-TSS (NM_008478)	promoter-TSS (NM_008478)	56	NM_008478	16728	Mm.260568	NM_008478	ENSMUSG00000031391	L1cam	CD171|L1|N-CAM-L1|NCAM-L1	L1 cell adhesion molecule	protein-coding
mm_23552.1	chr3	62159098	62159103	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-179677	NM_001081295	622434	Mm.153974	NM_001081295	ENSMUSG00000036885	Arhgef26	4631416L12Rik|8430436L14Rik|AI303572|AW491953|SGEF	Rho guanine nucleotide exchange factor (GEF) 26	protein-coding
mm_114892.1	chr13	94359454	94359467	+	1	NA	promoter-TSS (NR_045619)	promoter-TSS (NR_045619)	500	NM_009680	11774	Mm.21185	NM_009680	ENSMUSG00000021686	Ap3b1	AP-3|AU015684|C78395|Hps2|beta3A|pe|pearl|rim2	adaptor-related protein complex 3, beta 1 subunit	protein-coding
mm_24503.1	chr3	92456814	92456841	+	1	NA	exon (NM_011478, exon 2 of 2)	exon (NM_011478, exon 2 of 2)	1893	NM_001204427	20766	Mm.57092	NM_011478	ENSMUSG00000045539	Sprr3	SPR3	small proline-rich protein 3	protein-coding
mm_22942.1	chr3	31954792	31954798	+	1	NA	intron (NM_028231, intron 2 of 5)	intron (NM_028231, intron 2 of 5)	52092	NM_028231	72413	Mm.64790	NM_028231	ENSMUSG00000037610	Kcnmb2	2700049B16Rik|3110031N04Rik	potassium large conductance calcium-activated channel, subfamily M, beta member 2	protein-coding
mm_73860.1	chr8	118283745	118283767	+	1	NA	5' UTR (NM_019707, exon 1 of 14)	5' UTR (NM_019707, exon 1 of 14)	145	NM_019707	12554	Mm.334841	NM_019707	ENSMUSG00000031841	Cdh13	4932416G01Rik|Cdht|Tcad	cadherin 13	protein-coding
mm_119661.1	chr14	52141047	52141066	+	1	NA	intron (NM_023879, intron 13 of 24)	intron (NM_023879, intron 13 of 24)	30153	NM_023879	77945	Mm.21662	NM_023879	ENSMUSG00000057132	Rpgrip1	0610005A07Rik|4930401L23Rik|4930505G06Rik|A930002K18Rik|AA415034|nmf247	retinitis pigmentosa GTPase regulator interacting protein 1	protein-coding
mm_126135.1	chr15	78342032	78342069	+	1	NA	intron (NM_007780, intron 8 of 13)	B4|SINE|B4	-6549	NR_106137	102465776		NR_106137	ENSMUSG00000098996	Mir7676-1	Gm27600|mmu-mir-7676-1	microRNA 7676-1	ncRNA
mm_15508.1	chr2	158258066	158258109	+	1	NA	promoter-TSS (NM_177850)	promoter-TSS (NM_177850)	-154	NM_177850	329547	Mm.260883	NM_177850	ENSMUSG00000052922	Bpi	9230105K17Rik|Bpifd1	bactericidal permeablility increasing protein	protein-coding
mm_76202.1	chr8	83086903	83086914	-	1	NA	3' UTR (NM_177378, exon 7 of 7)	3' UTR (NM_177378, exon 7 of 7)	-78444	NM_001111304	71310	Mm.24031	NM_027758	ENSMUSG00000031709	Tbc1d9	4933431N12Rik|AI847101|AW490653|C76116	TBC1 domain family, member 9	protein-coding
mm_14637.1	chr2	136781838	136781842	+	1	NA	3' UTR (NM_001291056, exon 8 of 8)	3' UTR (NM_001291056, exon 8 of 8)	68390	NM_001291056	20614	Mm.45953	NM_011428	ENSMUSG00000027273	Snap25	Bdr|GENA70|SNAP-25|SUP|sp	synaptosomal-associated protein 25	protein-coding
mm_30987.1	chr4	35224402	35224412	+	1	NA	intron (NM_001081343, intron 1 of 10)	MER44B|DNA|TcMar-Tigger	1473	NM_001081343	73205	Mm.331544	NM_001081343	ENSMUSG00000028300	3110043O21Rik	AI840585	RIKEN cDNA 3110043O21 gene	protein-coding
mm_32725.1	chr4	116557152	116557164	+	1	NA	promoter-TSS (NM_029868)	promoter-TSS (NM_029868)	-569	NM_029868	77110	Mm.41715	NM_029868	ENSMUSG00000034042	Gpbp1l1	5330440M15Rik|BC002292	GC-rich promoter binding protein 1-like 1	protein-coding
mm_107189.1	chr12	25098998	25099028	+	1	NA	Intergenic	CpG	-2921	NM_010496	15902	Mm.34871	NM_010496	ENSMUSG00000020644	Id2	AI255428|C78922|Idb2|bHLHb26	inhibitor of DNA binding 2	protein-coding
mm_14445.1	chr2	130933150	130933158	+	1	NA	intron (NM_009730, intron 1 of 28)	RLTR31D_MM|LTR|ERVK	26659	NM_009730	11990	Mm.119936	NM_009730	ENSMUSG00000027312	Atrn	AW558010|Mgca|mg	attractin	protein-coding
mm_158263.1	chrX	109013461	109013471	-	1	NA	promoter-TSS (NM_016710)	promoter-TSS (NM_016710)	-86	NM_016710	50887	Mm.298443	NM_016710	ENSMUSG00000031245	Hmgn5	GARP45|NBP-45|Nsbp1	high-mobility group nucleosome binding domain 5	protein-coding
mm_1972.1	chr1	86522666	86522683	+	1	NA	Intergenic	Intergenic	-4062	NM_008972	19231	Mm.19187	NM_008972	ENSMUSG00000026238	Ptma	Thym	prothymosin alpha	protein-coding
mm_36129.1	chr4	59117834	59117843	-	1	NA	Intergenic	Intergenic	-71712	NM_011673	22234	Mm.198803	NM_011673	ENSMUSG00000028381	Ugcg	AU043821|C80537|Epcs21|GlcT-1|Ugcgl	UDP-glucose ceramide glucosyltransferase	protein-coding
mm_159901.1	chr6	39419705	39419705	-	1	NA	promoter-TSS (NM_001311109)	promoter-TSS (NM_001311109)	71	NM_001311109	54484	Mm.270484	NM_018810	ENSMUSG00000029922	Mkrn1	RFP	makorin, ring finger protein, 1	protein-coding
mm_170004.1	chr1	71653131	71653131	-	1	NA	promoter-TSS (NR_040308)	promoter-TSS (NR_040308)	103	NM_010233	14268	Mm.193099	NM_010233	ENSMUSG00000026193	Fn1	E330027I09|Fn|Fn-1	fibronectin 1	protein-coding
mm_157716.1	chrX	69606288	69606293	-	1	NA	intron (NM_008032, intron 3 of 19)	intron (NM_008032, intron 3 of 19)	245959	NM_008032	14266	Mm.466576	NM_008032	ENSMUSG00000031189	Aff2	FMR2P|Fmr2|Ox19|Oxh	AF4/FMR2 family, member 2	protein-coding
mm_92680.1	chr10	80586549	80586587	-	1	NA	exon (NM_145421, exon 2 of 5)	exon (NM_145421, exon 2 of 5)	3773	NM_145421	216169	Mm.29802	NM_145421	ENSMUSG00000003346	Abhd17a	1700013O15Rik|BC005632|D10Bwg1364e|Fam108a	abhydrolase domain containing 17A	protein-coding
mm_90857.1	chr10	8839772	8839782	-	1	NA	intron (NM_175155, intron 2 of 19)	RSINE1|SINE|B4	46293	NM_175155	70097	Mm.338275	NM_175155	ENSMUSG00000015305	Sash1	1100001C18Rik|2500002E12Rik|A330076K04Rik|mKIAA0790	SAM and SH3 domain containing 1	protein-coding
mm_74546.1	chr8	10484008	10484016	-	1	NA	intron (NM_001319151, intron 23 of 34)	MTEa|LTR|ERVL-MaLR	330101	NM_001319151	244281	Mm.422761	NM_001081397	ENSMUSG00000039057	Myo16	BM140241|C230040D10Rik|Gm1105|NYAP3|mKIAA0865	myosin XVI	protein-coding
mm_28429.1	chr3	90464666	90464676	-	1	NA	intron (NM_008727, intron 1 of 21)	intron (NM_008727, intron 1 of 21)	1195	NM_008727	18160	Mm.4627	NM_008727	ENSMUSG00000027931	Npr1	AI893888|GC-A|NPR-A|NPRA|Pndr	natriuretic peptide receptor 1	protein-coding
mm_148360.1	chr18	85697954	85697976	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-696987	NM_144946	246317	Mm.329578	NM_144946	ENSMUSG00000050321	Neto1	AI851453|Btcl1|C130005O10Rik	neuropilin (NRP) and tolloid (TLL)-like 1	protein-coding
mm_476.1	chr1	36506859	36506862	+	1	NA	3' UTR (NM_033570, exon 7 of 7)	3' UTR (NM_033570, exon 7 of 7)	-5007	NM_001331209	94218	Mm.256323	NM_053186	ENSMUSG00000001138	Cnnm3	Acdp3|Clp3|mACDP3	cyclin M3	protein-coding
mm_72781.1	chr8	86745591	86745601	+	1	NA	promoter-TSS (NR_027829)	promoter-TSS (NR_027829)	-103	NR_027829	666945	Mm.391806	NR_027829		Gm10638	ENSMUSG00000074178	predicted gene 10638	ncRNA
mm_28742.1	chr3	95738089	95738117	-	1	NA	exon (NM_007899, exon 3 of 11)	exon (NM_007899, exon 3 of 11)	1466	NM_007899	13601	Mm.3433	NM_007899	ENSMUSG00000028108	Ecm1	AI663821|p85	extracellular matrix protein 1	protein-coding
mm_56811.1	chr6	116668402	116668415	-	1	NA	intron (NM_178045, intron 1 of 10)	MIRc|SINE|MIR	5428	NM_178045	213391	Mm.257931	NM_178045	ENSMUSG00000042129	Rassf4	3830411C14Rik|AD037|AI586137	Ras association (RalGDS/AF-6) domain family member 4	protein-coding
mm_37226.1	chr4	117929727	117929739	-	1	NA	promoter-TSS (NM_001284191)	promoter-TSS (NM_001284191)	30	NM_001284191	11876	Mm.56897	NM_009711	ENSMUSG00000028539	Artn	neublastin	artemin	protein-coding
mm_59622.1	chr7	28154577	28154579	+	1	NA	exon (NM_001164655, exon 13 of 20)	exon (NM_001164655, exon 13 of 20)	-15170	NM_007991	14113	Mm.4595	NM_007991	ENSMUSG00000046865	Fbl	AL022665|FIB|FLRN|RNU3IP1	fibrillarin	protein-coding
mm_146480.1	chr18	89206101	89206106	+	1	NA	intron (NM_001039149, intron 1 of 5)	L2a|LINE|L2	8676	NM_001039149	225825	Mm.139293	NM_178687	ENSMUSG00000034028	Cd226	BC051526|DNAM-1|DNAM1|Pta1|TLiSA1	CD226 antigen	protein-coding
mm_141620.1	chr17	32877926	32877946	-	1	NA	Intergenic	Intergenic	13667	NM_207245	240066	Mm.26636	NM_207245	ENSMUSG00000095325	Zfp870	AI173952	zinc finger protein 870	protein-coding
mm_80305.1	chr9	73219451	73219456	+	1	NA	Intergenic	Intergenic	105984	NM_198609	225215	Mm.379366	NM_198609	ENSMUSG00000032215	Rsl24d1	2410159K22Rik	ribosomal L24 domain containing 1	protein-coding
mm_107311.1	chr12	31264266	31264290	+	1	NA	Intergenic	Intergenic	-1016	NM_008482	16777	Mm.172674	NM_008482	ENSMUSG00000002900	Lamb1	C77966|C80098|C81607|D130003D08Rik|Lamb-1|Lamb1-1	laminin B1	protein-coding
mm_134977.1	chr16	32078082	32078085	-	1	NA	intron (NM_177326, intron 1 of 14)	intron (NM_177326, intron 1 of 14)	1259	NM_177326	224105	Mm.234204	NM_177326	ENSMUSG00000022781	Pak2	5330420P17Rik|A130002K10Rik|AI836325|D16Ertd269e|PAK-2|mKIAA4182	p21 protein (Cdc42/Rac)-activated kinase 2	protein-coding
mm_118262.1	chr13	112463890	112463905	-	1	NA	promoter-TSS (NM_010560)	promoter-TSS (NM_010560)	-173	NM_010560	16195	Mm.4364	NM_010560	ENSMUSG00000021756	Il6st	5133400A03Rik|AA389424|BB405851|CD130|D13Ertd699e|gp130	interleukin 6 signal transducer	protein-coding
mm_83428.1	chr9	44980440	44980455	-	1	NA	promoter-TSS (NM_009850)	promoter-TSS (NM_009850)	-16	NM_009850	12502	Mm.335106	NM_009850	ENSMUSG00000002033	Cd3g	Ctg-3|Ctg3|T3g	CD3 antigen, gamma polypeptide	protein-coding
mm_23756.1	chr3	70007641	70007644	+	1	NA	promoter-TSS (NM_001018031)	promoter-TSS (NM_001018031)	29	NM_001018031	229389	Mm.331071	NM_001018031	ENSMUSG00000027788	Otol1	Gm414	otolin 1	protein-coding
mm_161846.1	chr18	9212971	9212971	+	1	NA	exon (NM_008058, exon 1 of 1)	exon (NM_008058, exon 1 of 1)	115	NM_008058	14370	Mm.184289	NM_008058	ENSMUSG00000036904	Fzd8	Fz8	frizzled class receptor 8	protein-coding
mm_165904.1	chr4	49536813	49536815	-	1	NA	exon (NM_144903, exon 9 of 9)	exon (NM_144903, exon 9 of 9)	12732	NM_144903	230163	Mm.482116	NM_144903	ENSMUSG00000028307	Aldob	Aldo-2|Aldo2|BC016435	aldolase B, fructose-bisphosphate	protein-coding
mm_88324.1	chr10	75566220	75566241	+	1	NA	Intergenic	Intergenic	-2432	NM_001305992	14598	Mm.4559	NM_008116	ENSMUSG00000006345	Ggt1	CD224|GGT|GGT 1|GGT-1|Ggtp|dwg	gamma-glutamyltransferase 1	protein-coding
mm_18653.1	chr2	69781991	69782003	-	1	NA	exon (NM_001077684, exon 3 of 9)	exon (NM_001077684, exon 3 of 9)	7489	NM_001077684	75051	Mm.195726	NM_001077684	ENSMUSG00000070883	Ccdc173	4930525K21Rik|4930578N16Rik	coiled-coil domain containing 173	protein-coding
mm_85909.1	chr9	111056901	111056915	-	1	NA	5' UTR (NM_017466, exon 1 of 2)	5' UTR (NM_017466, exon 1 of 2)	336	NM_001302377	54199	Mm.7336	NM_017466	ENSMUSG00000043953	Ccrl2	1810047I05Rik|Ackr5|CCR11|Cmkbr1l2|E01|L-CCR	chemokine (C-C motif) receptor-like 2	protein-coding
mm_96274.1	chr11	62847091	62847103	+	1	NA	promoter-TSS (NM_001291441)	promoter-TSS (NM_001291441)	-26	NM_001033669	213980	Mm.482259	NM_001033669	ENSMUSG00000090173	Fbxw10	Fbw10|HREP|SM25H2|SM2SH2	F-box and WD-40 domain protein 10	protein-coding
mm_109145.1	chr12	107141559	107141568	+	1	NA	Intergenic	Intergenic	-425239	NR_015512	71033	Mm.159404	NR_015512	ENSMUSG00000085820	4933406K04Rik	4930426M03Rik|4930485I22Rik|4933427G14Rik	RIKEN cDNA 4933406K04 gene	ncRNA
mm_172473.1	chr7	44815275	44815279	+	1	NA	promoter-TSS (NM_053074)	promoter-TSS (NM_053074)	381	NM_030693	107503	Mm.389890	NM_030693	ENSMUSG00000038539	Atf5	AFTA|Atf7|Atfx|ODA-10	activating transcription factor 5	protein-coding
mm_27700.1	chr3	66981590	66981612	-	1	NA	promoter-TSS (NM_001302359)	promoter-TSS (NM_001302359)	170	NM_013665	20429	Mm.39093	NM_013665	ENSMUSG00000027833	Shox2	6330543G17Rik|OG12|Og12x|Prx3|SHOT	short stature homeobox 2	protein-coding
mm_127809.1	chr15	5045996	5046000	-	1	NA	intron (NM_001243837, intron 5 of 17)	intron (NM_001243837, intron 5 of 17)	17775	NM_001243837	109828	Mm.208034	NM_001243837	ENSMUSG00000079105	C7	A530026G17|Gm1238	complement component 7	protein-coding
mm_154662.1	chrX	7873864	7873879	+	1	NA	exon (NM_001290536, exon 8 of 9)	exon (NM_001290536, exon 8 of 9)	-4435	NM_138606	18715	Mm.347478	NM_138606	ENSMUSG00000031155	Pim2	DXCch3|Pim-2	proviral integration site 2	protein-coding
mm_134748.1	chr16	23108135	23108143	-	1	NA	promoter-TSS (NR_030705)	promoter-TSS (NR_030705)	671	NR_110335	13682	Mm.260084	NM_013506	ENSMUSG00000022884	Eif4a2	4833432N07Rik|BM-010|Ddx2b|Eif4|eIF-4A-II|eIF4A-II	eukaryotic translation initiation factor 4A2	protein-coding
mm_73323.1	chr8	105272072	105272088	+	1	NA	intron (NR_045689, intron 6 of 12)	intron (NR_045689, intron 6 of 12)	2279	NM_001256044	26386	Mm.89204	NM_011939	ENSMUSG00000033249	Hsf4	HSF 4|HSTF 4|HSTF4|ldis1|mHSF4	heat shock transcription factor 4	protein-coding
mm_11673.1	chr2	35292655	35292686	+	1	NA	exon (NM_001206369, exon 5 of 17)	exon (NM_001206369, exon 5 of 17)	10290	NM_146120	227753	Mm.443	NM_146120	ENSMUSG00000026879	Gsn	ADF	gelsolin	protein-coding
mm_69352.1	chr7	130266217	130266225	-	1	NA	5' UTR (NM_010207, exon 1 of 18)	5' UTR (NM_010207, exon 1 of 18)	587	NM_010207	14183	Mm.16340	NM_010207	ENSMUSG00000030849	Fgfr2	AU043015|AW556123|Bek|Fgfr-2|Fgfr-7|Fgfr7|KGFR|KGFRTr|svs	fibroblast growth factor receptor 2	protein-coding
mm_135906.1	chr16	67278269	67278272	-	1	NA	intron (NM_178721, intron 1 of 9)	RMER6D|LTR|ERVK	342638	NM_001347247	239857	Mm.394300	NM_178721	ENSMUSG00000064115	Cadm2	2900078E11Rik|9330131D06|A830029E02Rik|Igdf4d|Igsf4d|NECL3|SynCAM 2|SynCAM2	cell adhesion molecule 2	protein-coding
mm_119769.1	chr14	54174601	54174626	+	1	NA	Intergenic	Intergenic	79316	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_154361.1	chrM	6363	6378	+	1	NA	NA	Intergenic	NA	NA								
mm_21267.1	chr2	156839791	156839858	-	1	NA	promoter-TSS (NM_001291124)	promoter-TSS (NM_001291124)	-183	NM_001291124	228839	Mm.315625	NM_173396	ENSMUSG00000062175	Tgif2	4921501K24|5730599O09Rik|C80753|C81206	TGFB-induced factor homeobox 2	protein-coding
mm_140905.1	chr17	24150943	24150950	-	1	NA	promoter-TSS (NM_001286662)	promoter-TSS (NM_001286662)	-24	NM_001286662	18607	Mm.10504	NM_011062	ENSMUSG00000024122	Pdpk1	Pdk1	3-phosphoinositide dependent protein kinase 1	protein-coding
mm_19730.1	chr2	104494384	104494395	-	1	NA	promoter-TSS (NM_001145824)	promoter-TSS (NM_001145824)	100	NM_010434	15259	Mm.257925	NM_010434	ENSMUSG00000027177	Hipk3	DYRK6|FIST3|PKY|mir-1902	homeodomain interacting protein kinase 3	protein-coding
mm_13102.1	chr2	91313003	91313003	+	1	NA	intron (NM_001311144, intron 3 of 8)	intron (NM_001311144, intron 3 of 8)	47888	NM_023854	77038	Mm.43636	NM_023854	ENSMUSG00000027255	Arfgap2	2310032E02Rik|Zfp289	ADP-ribosylation factor GTPase activating protein 2	protein-coding
mm_135477.1	chr16	45953566	45953603	-	1	NA	Intergenic	Intergenic	56829	NM_001134480	433022	Mm.380993	NM_001134480	ENSMUSG00000087141	Plcxd2	AW494639|EG433022	phosphatidylinositol-specific phospholipase C, X domain containing 2	protein-coding
mm_42523.1	chr5	115575149	115575207	+	1	NA	exon (NM_172719, exon 4 of 58)	exon (NM_172719, exon 4 of 58)	-5771	NR_105996	102466790		NR_105996	ENSMUSG00000099047	Mir7029	Gm27293|mmu-mir-7029	microRNA 7029	ncRNA
mm_74495.1	chr8	5105327	5105337	-	1	NA	promoter-TSS (NM_011388)	promoter-TSS (NM_011388)	-45	NM_011388	20494	Mm.3500	NM_011388	ENSMUSG00000023073	Slc10a2	9130221J18Rik|AI605518|ASBT|IBAT|ISBT	solute carrier family 10, member 2	protein-coding
mm_31551.1	chr4	56057787	56057794	+	1	NA	Intergenic	Intergenic	-525315	NM_010637	16600	Mm.4325	NM_010637	ENSMUSG00000003032	Klf4	EZF|Gklf|Zie	Kruppel-like factor 4 (gut)	protein-coding
mm_110879.1	chr12	74803969	74803971	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	373362	NM_172805	238271	Mm.44465	NM_172805	ENSMUSG00000034402	Kcnh5	Eag2	potassium voltage-gated channel, subfamily H (eag-related), member 5	protein-coding
mm_80078.1	chr9	70007156	70007171	+	1	NA	3' UTR (NM_016787, exon 11 of 11)	3' UTR (NM_016787, exon 11 of 11)	-5385	NM_001282084	235459	Mm.293117	NM_199151	ENSMUSG00000033543	Gtf2a2	TFIIA-gamma|TfIIg|Tfiia2	general transcription factor II A, 2	protein-coding
mm_39266.1	chr5	3578208	3578223	+	1	NA	intron (NM_029843, intron 3 of 5)	(T)n|Simple_repeat|Simple_repeat	6499	NM_029843	77036	Mm.389069	NM_029843	ENSMUSG00000008307	1700109H08Rik	-	RIKEN cDNA 1700109H08 gene	protein-coding
mm_13260.1	chr2	98666267	98666276	+	1	NA	Intergenic	SYNREP_MM|Satellite|Satellite	1198614	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_24252.1	chr3	89177554	89177592	+	1	NA	TTS (NM_007712)	TTS (NM_007712)	182	NM_001309909	24045	Mm.257052	NM_011886	ENSMUSG00000028049	Scamp3	Sc3	secretory carrier membrane protein 3	protein-coding
mm_118893.1	chr14	26634747	26634750	+	1	NA	TTS (NM_001285466)	TTS (NM_001285466)	-3449	NM_007479	11843	Mm.297768	NM_007479	ENSMUSG00000021877	Arf4	AA407803	ADP-ribosylation factor 4	protein-coding
mm_110984.1	chr12	77108557	77108559	-	1	NA	Intergenic	Intergenic	-129546	NM_001252614	53618	Mm.35628	NM_016893	ENSMUSG00000021065	Fut8	-	fucosyltransferase 8	protein-coding
mm_65460.1	chr7	25466400	25466422	-	1	NA	exon (NM_001039186, exon 6 of 8)	exon (NM_001039186, exon 6 of 8)	11214	NM_001039185	26365	Mm.322502	NM_011926	ENSMUSG00000074272	Ceacam1	Bgp|Bgp1|C-CAM|CD66a|Cc1|Cea-1|Cea-7|Cea1|Cea7|Hv-2|Hv2|MHVR|MHVR1|Mhv-1|bb-1|mCEA1|mmCGM1|mmCGM1a|mmCGM2	carcinoembryonic antigen-related cell adhesion molecule 1	protein-coding
mm_132973.1	chr16	52032558	52032572	+	1	NA	intron (NM_001033238, intron 1 of 17)	intron (NM_001033238, intron 1 of 17)	1016	NM_001033238	208650	Mm.328206	NM_001033238	ENSMUSG00000022637	Cblb	AI429560|AI851073|Cbl-b	Casitas B-lineage lymphoma b	protein-coding
mm_154977.1	chrX	37827008	37827010	+	1	NA	promoter-TSS (NM_008955)	promoter-TSS (NM_008955)	-46	NM_008955	19202	Mm.10105	NM_008955	ENSMUSG00000006200	Rhox6	AV213605|AW548842|Psx1	reproductive homeobox 6	protein-coding
mm_141872.1	chr17	34836870	34836959	-	1	NA	promoter-TSS (NM_019442)	promoter-TSS (NM_019442)	-11	NM_019442	54402	Mm.440064	NM_019442	ENSMUSG00000061207	Stk19	G11|RP1	serine/threonine kinase 19	protein-coding
mm_97295.1	chr11	76407166	76407201	+	1	NA	promoter-TSS (NM_019818)	promoter-TSS (NM_019818)	40	NM_019818	56322	Mm.18803	NM_019818	ENSMUSG00000020843	Timm22	Tim22	translocase of inner mitochondrial membrane 22	protein-coding
mm_79255.1	chr9	50751842	50751852	+	1	NA	intron (NM_024441, intron 1 of 1)	intron (NM_024441, intron 1 of 1)	507	NM_001164708	69253	Mm.1980	NM_024441	ENSMUSG00000038086	Hspb2	27kDa|2810021G24Rik|HSP27|MKBP	heat shock protein 2	protein-coding
mm_55732.1	chr6	77349498	77349535	-	1	NA	intron (NM_001109764, intron 8 of 19)	intron (NM_001109764, intron 8 of 19)	32959	NR_045141	70753	Mm.490700	NR_045141	ENSMUSG00000108077	6330415B21Rik	-	RIKEN cDNA 6330415B21 gene	ncRNA
mm_131411.1	chr16	14473619	14473647	+	1	NA	3' UTR (NM_008576, exon 31 of 31)	3' UTR (NM_008576, exon 31 of 31)	-88684	NR_033556	545280	Mm.123679	NR_033556	ENSMUSG00000075395	A630010A05Rik	-	RIKEN cDNA A630010A05 gene	ncRNA
mm_71700.1	chr8	61742550	61742578	+	1	NA	intron (NM_001081390, intron 2 of 19)	intron (NM_001081390, intron 2 of 19)	17534	NM_001293773	72333	Mm.29933	NM_001081390	ENSMUSG00000058056	Palld	2410003B16Rik|6030492A02	palladin, cytoskeletal associated protein	protein-coding
mm_136544.1	chr16	97962187	97962198	-	1	NA	intron (NM_175428, intron 1 of 2)	CpG	430	NM_001081685	114565	Mm.474489	NM_175428	ENSMUSG00000046962	Zbtb21	5430437K12Rik|B430213I24Rik|Zfp295|Znf295|mKIAA1227	zinc finger and BTB domain containing 21	protein-coding
mm_57612.1	chr6	128126683	128126696	-	1	NA	intron (NM_175414, intron 1 of 8)	intron (NM_175414, intron 1 of 8)	16889	NM_175414	109246	Mm.21814	NM_175414	ENSMUSG00000030352	Tspan9	6720474K14Rik|9430079M16Rik|AU018597	tetraspanin 9	protein-coding
mm_131140.1	chr16	6348733	6348770	+	1	NA	intron (NM_021477, intron 2 of 16)	intron (NM_021477, intron 2 of 16)	373164	NR_045799	68238	Mm.434605	NR_045799	ENSMUSG00000101481	1700123O21Rik	-	RIKEN cDNA 1700123O21 gene	ncRNA
mm_158527.1	chrX	143861150	143861160	-	1	NA	3' UTR (NM_010025, exon 7 of 7)	3' UTR (NM_010025, exon 7 of 7)	-33743	NM_007603	12338	Mm.30290	NM_007603	ENSMUSG00000067276	Capn6	-	calpain 6	protein-coding
mm_79152.1	chr9	47740156	47740160	+	1	NA	intron (NM_001025600, intron 1 of 8)	intron (NM_001025600, intron 1 of 8)	78050	NR_046048	100038460	Mm.447649	NR_046048		Gm10677	ENSMUSG00000074363	predicted gene 10677	ncRNA
mm_67366.1	chr7	79839454	79839498	-	1	NA	exon (NM_008486, exon 4 of 20)	exon (NM_008486, exon 4 of 20)	2876	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_50001.1	chr6	41048353	41048353	+	1	NA	Intergenic	Intergenic	-12844	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_20726.1	chr2	136512016	136512062	-	1	NA	Intergenic	B3|SINE|B2	-20282	NM_175667	319196	Mm.477841	NM_175667	ENSMUSG00000074771	Ankef1	AV276460|Ankrd5	ankyrin repeat and EF-hand domain containing 1	protein-coding
mm_119083.1	chr14	30886522	30886532	+	1	NA	promoter-TSS (NM_001289633)	promoter-TSS (NM_001289633)	51	NM_001289632	16427	Mm.34819	NM_018746	ENSMUSG00000021922	Itih4	ITI-HC4|Itih-4|PK-120	inter alpha-trypsin inhibitor, heavy chain 4	protein-coding
mm_100047.1	chr11	115163375	115163383	+	1	NA	promoter-TSS (NM_012030)	promoter-TSS (NM_012030)	38	NM_012030	26941	Mm.27842	NM_012030	ENSMUSG00000020733	Slc9a3r1	EBP-50|NHE-RF|NHERF-1|NHERF1	solute carrier family 9 (sodium/hydrogen exchanger), member 3 regulator 1	protein-coding
mm_151474.1	chr19	58673145	58673158	+	1	NA	exon (NM_026925, exon 4 of 13)	exon (NM_026925, exon 4 of 13)	2786	NM_026925	69060	Mm.20407	NM_026925	ENSMUSG00000046008	Pnlip	1810007A24Rik|PL|PTL	pancreatic lipase	protein-coding
mm_118903.1	chr14	26655887	26655964	+	1	NA	exon (NM_007479, exon 6 of 6)	exon (NM_007479, exon 6 of 6)	13683	NR_106132	102465773		NR_106132	ENSMUSG00000098751	Mir7672	Gm27314|mmu-mir-7672	microRNA 7672	ncRNA
mm_131517.1	chr16	17531156	17531190	+	1	NA	promoter-TSS (NM_026909)	promoter-TSS (NM_026909)	-121	NM_026909	69009	Mm.10174	NM_026909	ENSMUSG00000022760	Thap7	1810004B07Rik	THAP domain containing 7	protein-coding
mm_38369.1	chr4	138367967	138368008	-	1	NA	promoter-TSS (NM_028176)	promoter-TSS (NM_028176)	-32	NM_028176	72269	Mm.46182	NM_028176	ENSMUSG00000028755	Cda	2210401N16Rik	cytidine deaminase	protein-coding
mm_129616.1	chr15	80013990	80014018	-	1	NA	5' UTR (NM_011057, exon 1 of 7)	5' UTR (NM_011057, exon 1 of 7)	804	NM_011057	18591	Mm.144089	NM_011057	ENSMUSG00000000489	Pdgfb	PDGF-B|Sis	platelet derived growth factor, B polypeptide	protein-coding
mm_136641.1	chr17	5799661	5799678	+	1	NA	non-coding (NR_045079, exon 1 of 3)	non-coding (NR_045079, exon 1 of 3)	179	NR_045080	78512	Mm.23696	NR_045079	ENSMUSG00000096965	3300005D01Rik	-	RIKEN cDNA 3300005D01 gene	ncRNA
mm_164819.1	chr18	35034141	35034149	+	1	NA	Intergenic	Intergenic	-79794	NM_010481	15526	Mm.209419	NM_010481	ENSMUSG00000024359	Hspa9	74kDa|Csa|Grp75|Hsc74|Hsp74|Hsp74a|Hspa9a|Mortalin|Mot-2|Mot2|Mthsp70|Pbp74	heat shock protein 9	protein-coding
mm_21998.1	chr2	167743867	167743935	-	1	NA	Intergenic	Intergenic	52724	NR_015500	329562	Mm.123101	NM_177851	ENSMUSG00000006462	A530013C23Rik	-	RIKEN cDNA A530013C23 gene	ncRNA
mm_26327.1	chr3	142541558	142541569	+	1	NA	exon (NM_001083312, exon 6 of 11)	exon (NM_001083312, exon 6 of 11)	11227	NM_145545	229900	Mm.45740	NM_145545	ENSMUSG00000040253	Gbp7	9830147J24Rik	guanylate binding protein 7	protein-coding
mm_98146.1	chr11	87583938	87583951	+	1	NA	exon (NM_011129, exon 3 of 12)	exon (NM_011129, exon 3 of 12)	2883	NM_001284392	18952	Mm.2214	NM_011129	ENSMUSG00000020486	Sept4	ARTS|Bh5|OTTMUSG00000001265|Pnutl2	septin 4	protein-coding
mm_32080.1	chr4	98114832	98114835	+	1	NA	3' UTR (NM_001122953, exon 10 of 10)	3' UTR (NM_001122953, exon 10 of 10)	268432	NM_053157	94043	Mm.331719	NM_053157	ENSMUSG00000028563	Tm2d1	2310026L18Rik|AA990549|Bbp	TM2 domain containing 1	protein-coding
mm_24860.1	chr3	95893954	95893974	+	1	NA	promoter-TSS (NM_146104)	promoter-TSS (NM_146104)	43	NM_146134	226548	Mm.306954	NM_146104	ENSMUSG00000015750	Aph1a	6530402N02Rik|APH-1a	aph1 homolog A, gamma secretase subunit	protein-coding
mm_140762.1	chr17	17624437	17624455	-	1	NA	promoter-TSS (NM_172827)	promoter-TSS (NM_172827)	43	NM_172827	240028	Mm.328807	NM_172827	ENSMUSG00000023845	Lnpep	2010309L07Rik|4732490P18Rik|CAP|IRAP|PLAP|gp160|vp165	leucyl/cystinyl aminopeptidase	protein-coding
mm_142969.1	chr17	56133760	56133780	-	1	NA	promoter-TSS (NM_013662)	promoter-TSS (NM_013662)	82	NM_013662	20359	Mm.8029	NM_013662	ENSMUSG00000001227	Sema6b	Sema|Seman|VIb|semaZ	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B	protein-coding
mm_51026.1	chr6	65150796	65150813	+	1	NA	Intergenic	ORR1B1-int|LTR|ERVL-MaLR	-6074	NM_019455	54486	Mm.410688	NM_019455	ENSMUSG00000029919	Hpgds	H-PGDS|Ptgds2	hematopoietic prostaglandin D synthase	protein-coding
mm_39447.1	chr5	17574455	17574465	+	1	NA	promoter-TSS (NM_013657)	promoter-TSS (NM_013657)	-356	NM_013657	20348	Mm.5071	NM_013657	ENSMUSG00000028780	Sema3c	1110036B02Rik|SemE|Semae	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	protein-coding
mm_89466.1	chr10	93453403	93453470	+	1	NA	promoter-TSS (NM_008517)	promoter-TSS (NM_008517)	40	NM_008517	16993	Mm.271071	NM_008517	ENSMUSG00000015889	Lta4h	-	leukotriene A4 hydrolase	protein-coding
mm_44054.1	chr5	147959359	147959369	+	1	NA	intron (NM_029920, intron 1 of 14)	intron (NM_029920, intron 1 of 14)	2044	NM_029920	77521	Mm.244177	NM_029920	ENSMUSG00000029651	Mtus2	5730592G18Rik|A730013O20Rik|AU067634|C130038G02Rik|Cazip|Gm763|mKIAA0774	microtubule associated tumor suppressor candidate 2	protein-coding
mm_148426.1	chr19	3941588	3941601	+	1	NA	exon (NM_019449, exon 4 of 11)	exon (NM_019449, exon 4 of 11)	6408	NM_001161428	54445	Mm.262094	NM_019449	ENSMUSG00000036908	Unc93b1	Unc-93B1|Unc93b	unc-93 homolog B1 (C. elegans)	protein-coding
mm_70725.1	chr8	18595129	18595141	+	1	NA	promoter-TSS (NM_173189)	promoter-TSS (NM_173189)	-38	NM_173189	244329	Mm.235296	NM_173189	ENSMUSG00000039842	Mcph1	5430437K10Rik|BRIT1|D030046N04Rik|MCT	microcephaly, primary autosomal recessive 1	protein-coding
mm_103619.1	chr11	78657066	78657069	-	1	NA	intron (NM_008702, intron 1 of 10)	intron (NM_008702, intron 1 of 10)	40358	NM_008702	18099	Mm.9001	NM_008702	ENSMUSG00000017376	Nlk	AI194375	nemo like kinase	protein-coding
mm_112614.1	chr13	15463664	15463711	+	1	NA	promoter-TSS (NM_008130)	promoter-TSS (NM_008130)	-36	NM_008130	14634	Mm.5098	NM_008130	ENSMUSG00000021318	Gli3	AI854843|AU023367|Bph|GLI3-190|GLI3FL|Pdn|Xt|add	GLI-Kruppel family member GLI3	protein-coding
mm_54665.1	chr6	39206669	39206685	-	1	NA	promoter-TSS (NM_001033430)	promoter-TSS (NM_001033430)	96	NM_001033430	338523	Mm.293175	NM_001033430	ENSMUSG00000042599	Kdm7a	A630082K20Rik|BB041802|ENSMUSG00000073143|Jhdm1d|mKIAA1718	lysine (K)-specific demethylase 7A	protein-coding
mm_169030.1	chr13	119756071	119756072	+	1	NA	promoter-TSS (NM_175538)	promoter-TSS (NM_175538)	-189	NM_175538	245269	Mm.403943	NM_175538	ENSMUSG00000095930	Nim1k	E130304F04Rik|Nim1	NIM1 serine/threonine protein kinase	protein-coding
mm_150154.1	chr19	31951055	31951072	+	1	NA	Intergenic	Intergenic	82302	NM_001081074	69865	Mm.87538	NM_001081074	ENSMUSG00000052595	A1cf	1810073H04Rik|ACF64|ACF65|ASP|Acf|MCM|MerCreMer|Tg(Myh6-cre/Esr1*)1Jmk|mer	APOBEC1 complementation factor	protein-coding
mm_69288.1	chr7	128206019	128206027	-	1	NA	TTS (NM_001029872)	TTS (NM_001029872)	343	NM_009943	12862	Mm.43824	NM_009943	ENSMUSG00000030785	Cox6a2	CoxVIaH|VIaH	cytochrome c oxidase subunit VIa polypeptide 2	protein-coding
mm_128959.1	chr15	74799858	74799871	-	1	NA	5' UTR (NM_029627, exon 1 of 4)	5' UTR (NM_029627, exon 1 of 4)	104	NM_029627	76486	Mm.273319	NM_029627	ENSMUSG00000044678	Ly6k	2410015A16Rik|3110035B01Rik|mLy-6K	lymphocyte antigen 6 complex, locus K	protein-coding
mm_114240.1	chr13	56614255	56614274	+	1	NA	exon (NM_009369, exon 2 of 17)	exon (NM_009369, exon 2 of 17)	4661	NM_009369	21810	Mm.14455	NM_009369	ENSMUSG00000035493	Tgfbi	68kDa|AI181842|AI747162|Beta-ig|big-h3	transforming growth factor, beta induced	protein-coding
mm_160926.1	chr11	87405033	87405033	+	1	NA	promoter-TSS (NM_001291440)	promoter-TSS (NM_001291440)	-32	NM_031386	83560	Mm.440758	NM_031386	ENSMUSG00000010342	Tex14	C85585	testis expressed gene 14	protein-coding
mm_39564.1	chr5	23314347	23314356	+	1	NA	Intergenic	(AGTTG)n|Simple_repeat|Simple_repeat	120002	NR_040469	269630	Mm.425231	NR_040469	ENSMUSG00000073147	5031425E22Rik	-	RIKEN cDNA 5031425E22 gene	ncRNA
mm_81309.1	chr9	108374366	108374367	+	1	NA	intron (NM_001311157, intron 12 of 20)	intron (NM_001311157, intron 12 of 20)	-18468	NM_053216	112418	Mm.78287	NM_053216	ENSMUSG00000032611	1700102P08Rik	AI593206	RIKEN cDNA 1700102P08 gene	protein-coding
mm_109156.1	chr12	108179134	108179134	+	1	NA	promoter-TSS (NM_009832)	promoter-TSS (NM_009832)	150	NM_028262	52690	Mm.159185	NM_028262	ENSMUSG00000056770	Setd3	2610102I01Rik|2610305M23Rik|6030490B17Rik|D12Ertd771e	SET domain containing 3	protein-coding
mm_46544.1	chr5	106457944	106457954	-	1	NA	5' UTR (NM_001005477, exon 1 of 3)	5' UTR (NM_001005477, exon 1 of 3)	217	NM_001005477	104382	Mm.271593	NM_001005477	ENSMUSG00000034384	Barhl2	E130309B19Rik|MBH1	BarH-like 2 (Drosophila)	protein-coding
mm_38660.1	chr4	144403622	144403640	-	1	NA	intron (NM_029948, intron 1 of 3)	RMER17C|LTR|ERVK	4833	NM_029948	77632	Mm.31283	NM_029948	ENSMUSG00000028591	Pramef12	4930569K13Rik|AU023001|C86578	PRAME family member 12	protein-coding
mm_12564.1	chr2	72828865	72828905	+	1	NA	Intergenic	Intergenic	-15168	NR_102349	76218	Mm.75260	NR_102348	ENSMUSG00000085427	6430710C18Rik	5033406J01Rik	RIKEN cDNA 6430710C18 gene	ncRNA
mm_25524.1	chr3	114118013	114118013	+	1	NA	intron (NM_007729, intron 24 of 66)	intron (NM_007729, intron 24 of 66)	87473	NM_007729	12814	Mm.209715	NM_007729	ENSMUSG00000027966	Col11a1	C530001D20Rik|cho	collagen, type XI, alpha 1	protein-coding
mm_168382.1	chr11	23268981	23268990	+	1	NA	intron (NM_001035226, intron 4 of 25)	intron (NM_001035226, intron 4 of 25)	12944	NM_134014	103573	Mm.217547	NM_134014	ENSMUSG00000020290	Xpo1	AA420417|Crm1|Exp1	exportin 1	protein-coding
mm_28862.1	chr3	97297807	97297833	-	1	NA	Intergenic	Intergenic	-11436	NR_105813	102465206		NR_105813	ENSMUSG00000099036	Mir378c	Gm27930|mmu-mir-378c	microRNA 378c	ncRNA
mm_16190.1	chr2	172977759	172977789	+	1	NA	Intergenic	Intergenic	-2068	NM_012046	26972	Mm.23495	NM_012046	ENSMUSG00000005883	Spo11	AI449549|Spo11a|Spo11b	SPO11 meiotic protein covalently bound to DSB	protein-coding
mm_119992.1	chr14	55591726	55591785	+	1	NA	promoter-TSS (NM_011190)	promoter-TSS (NM_011190)	-35	NM_194346	268749	Mm.23748	NM_194346	ENSMUSG00000047098	Rnf31	AL033293|BC031509|Flj10111|HOIP|Paul|mFLJ00217	ring finger protein 31	protein-coding
mm_150782.1	chr19	44295027	44295044	+	1	NA	exon (NM_009128, exon 2 of 6)	exon (NM_009128, exon 2 of 6)	1359	NM_009128	20250	Mm.487021	NM_009128	ENSMUSG00000025203	Scd2	Mir5114|Scd-2|mir-5114|swty	stearoyl-Coenzyme A desaturase 2	protein-coding
mm_150856.1	chr19	45006623	45006668	+	1	NA	promoter-TSS (NM_153796)	promoter-TSS (NM_153796)	87	NM_153796	226153	Mm.105585	NM_153796	ENSMUSG00000025209	Twnk	D19Ertd626e|PEO|Peo1|Twinl	twinkle mtDNA helicase	protein-coding
mm_3531.1	chr1	150179917	150179930	+	1	NA	Intergenic	Intergenic	-14975	NR_110420	102639566	Mm.417208	NR_110420	ENSMUSG00000097754	Ptgs2os2	Gm26687|Linc-cox2|Lincrna-cox2	prostaglandin-endoperoxide synthase 2, opposite strand 2	ncRNA
mm_5219.1	chr1	13898468	13898470	-	1	NA	Intergenic	Lx5c|LINE|L1	-111540	NR_004447	433273	Mm.304088	NR_004447	ENSMUSG00000097711	Gm5523	EG433273	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_75828.1	chr8	70506120	70506143	-	1	NA	intron (NM_025577, intron 2 of 4)	intron (NM_025577, intron 2 of 4)	608	NM_025577	66462	Mm.28242	NM_025577	ENSMUSG00000058833	2810428I15Rik	-	RIKEN cDNA 2810428I15 gene	protein-coding
mm_39900.1	chr5	31240887	31240941	+	1	NA	promoter-TSS (NM_147201)	promoter-TSS (NM_147201)	-4	NM_147201	192292	Mm.292040	NM_147201	ENSMUSG00000029148	Nrbp1	B230344L17Rik|Nrbp	nuclear receptor binding protein 1	protein-coding
mm_31226.1	chr4	44106537	44106560	+	1	NA	Intergenic	Intergenic	-15345	NR_040414	623796	Mm.490409	NR_040414	ENSMUSG00000084274	Gm12504	OTTMUSG00000007209	prothymosin alpha pseudogene	pseudo
mm_143019.1	chr17	56512423	56512434	-	1	NA	promoter-TSS (NM_011483)	promoter-TSS (NM_011483)	55	NM_011483	20834	Mm.76862	NM_011483	ENSMUSG00000044526	Znrf4	1700094M01Rik|Ssrzf1|spzn	zinc and ring finger 4	protein-coding
mm_140639.1	chr17	12674804	12674807	-	1	NA	intron (NM_009202, intron 1 of 10)	intron (NM_009202, intron 1 of 10)	1033	NM_009202	20517	Mm.594	NM_009202	ENSMUSG00000023829	Slc22a1	Lx1|Oct1|Orct|Orct1	solute carrier family 22 (organic cation transporter), member 1	protein-coding
mm_4557.1	chr1	177444732	177444742	+	1	NA	promoter-TSS (NM_001012330)	promoter-TSS (NM_001012330)	76	NM_001012330	30928	Mm.330700	NM_013915	ENSMUSG00000063659	Zbtb18	RP58|Zfp238|Znf238	zinc finger and BTB domain containing 18	protein-coding
mm_165566.1	chr3	16597880	16597880	+	1	NA	Intergenic	Intergenic	414697	NM_001145919	229096	Mm.23834	NM_172677	ENSMUSG00000047213	Ythdf3	9130022A11Rik	YTH domain family 3	protein-coding
mm_3163.1	chr1	135232878	135232899	+	1	NA	Intergenic	Intergenic	25584	NM_001163131	13710	Mm.441439	NM_007921	ENSMUSG00000003051	Elf3	ESE-1|ESX|jen	E74-like factor 3	protein-coding
mm_152210.1	chr19	7802670	7802680	-	1	NA	promoter-TSS (NM_146232)	promoter-TSS (NM_146232)	-8	NM_146232	236149	Mm.207060	NM_146232	ENSMUSG00000053303	Slc22a26	-	solute carrier family 22 (organic cation transporter), member 26	protein-coding
mm_169199.1	chr13	66291383	66291385	-	1	NA	Intergenic	Intergenic	149734	NM_183119	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
mm_25991.1	chr3	134200143	134200152	+	1	NA	Intergenic	Intergenic	-36348	NM_001004367	319478	Mm.224814	NM_001004367	ENSMUSG00000044365	Cxxc4	9330210J02Rik|C030003J12Rik|Idax	CXXC finger 4	protein-coding
mm_109236.1	chr12	108865450	108865460	+	1	NA	intron (NM_011710, intron 8 of 10)	intron (NM_011710, intron 8 of 10)	14326	NM_001012310	104910	Mm.202653	NM_001012310	ENSMUSG00000048856	Slc25a47	AI132487|AI876593|HDMCP	solute carrier family 25, member 47	protein-coding
mm_68705.1	chr7	119760796	119760838	-	1	NA	promoter-TSS (NM_016870)	promoter-TSS (NM_016870)	-106	NM_212441	20216	Mm.334199	NM_016870	ENSMUSG00000030935	Acsm3	Sa|Sah	acyl-CoA synthetase medium-chain family member 3	protein-coding
mm_82417.1	chr9	14902561	14902571	-	1	NA	intron (NM_022888, intron 1 of 4)	intron (NM_022888, intron 1 of 4)	1385	NM_176807	64931	Mm.86738	NM_022888	ENSMUSG00000031933	Izumo1r	0910001L11Rik|C86255|Folbp3|Folr4|Juno	IZUMO1 receptor, JUNO	protein-coding
mm_65031.1	chr7	18532226	18532242	-	1	NA	promoter-TSS (NM_054060)	promoter-TSS (NM_054060)	-7	NM_054060	114868	Mm.389809	NM_054060	ENSMUSG00000070798	Psg25	cea13	pregnancy-specific glycoprotein 25	protein-coding
mm_53692.1	chr6	142683464	142683470	+	1	NA	intron (NM_001310143, intron 8 of 38)	intron (NM_001310143, intron 8 of 38)	18807	NM_021041	20928	Mm.35670	NM_011511	ENSMUSG00000030249	Abcc9	AI414027|AI449286|SUR2A|SUR2B|Sur2	ATP-binding cassette, sub-family C (CFTR/MRP), member 9	protein-coding
mm_1749.1	chr1	75505739	75505749	+	1	NA	exon (NM_178884, exon 1 of 20)	exon (NM_178884, exon 1 of 20)	708	NM_178884	98733	Mm.236454	NM_178884	ENSMUSG00000026211	Obsl1	AW822216	obscurin-like 1	protein-coding
mm_111008.1	chr12	78980591	78980600	-	1	NA	intron (NM_178745, intron 1 of 2)	intron (NM_178745, intron 1 of 2)	2883	NM_001170401	268567	Mm.341747	NM_178745	ENSMUSG00000046157	Tmem229b	6330442E10Rik|9830138K24|AU019070	transmembrane protein 229B	protein-coding
mm_45062.1	chr5	43044045	43044070	-	1	NA	Intergenic	MLT1A0|LTR|ERVL-MaLR	-189406	NM_175937	231207	Mm.7233	NM_175937	ENSMUSG00000039782	Cpeb2	A630055H10Rik|Cpe-bp2	cytoplasmic polyadenylation element binding protein 2	protein-coding
mm_86150.1	chr9	117252451	117252489	-	1	NA	promoter-TSS (NM_001172126)	promoter-TSS (NM_001172126)	13	NM_001172123	207181	Mm.326411	NM_178660	ENSMUSG00000039607	Rbms3	6720477E09Rik|8430436O14Rik	RNA binding motif, single stranded interacting protein	protein-coding
mm_43510.1	chr5	137030276	137030290	+	1	NA	promoter-TSS (NM_001039385)	promoter-TSS (NM_001039385)	-12	NM_001039385	381677	Mm.389697	NM_001039385	ENSMUSG00000037428	Vgf	Gm1052	VGF nerve growth factor inducible	protein-coding
mm_129623.1	chr15	80088898	80088903	-	1	NA	Intergenic	B3|SINE|B2	-2434	NM_009303	20972	Mm.230301	NM_009303	ENSMUSG00000022415	Syngr1	R75468|Syngr1b|p29	synaptogyrin 1	protein-coding
mm_162427.1	chr1	93343683	93343691	+	1	NA	promoter-TSS (NM_080850)	promoter-TSS (NM_080850)	42	NM_023200	66385	Mm.88704	NM_023200	ENSMUSG00000026275	Ppp1r7	2310014J01Rik|SDS22	protein phosphatase 1, regulatory (inhibitor) subunit 7	protein-coding
mm_38991.1	chr4	151108455	151108546	-	1	NA	intron (NM_001081557, intron 11 of 23)	CpG	18930	NM_001308446	105704528	Mm.415128	NM_001308446	ENSMUSG00000078491	Gm13090	OTTMUSG00000010356	predicted gene 13090	protein-coding
mm_22722.1	chr3	19508647	19508657	+	1	NA	promoter-TSS (NM_001163536)	promoter-TSS (NM_001163536)	57	NM_025489	66326	Mm.45615	NM_025489	ENSMUSG00000027606	Dnajc5b	1700008A05Rik	DnaJ heat shock protein family (Hsp40) member C5 beta	protein-coding
mm_142051.1	chr17	35637854	35637857	-	1	NA	exon (NM_001033366, exon 2 of 3)	exon (NM_001033366, exon 2 of 3)	5840	NM_001033366	268949	Mm.296301	NM_001033366	ENSMUSG00000073408	Dpcr1	Gm630	diffuse panbronchiolitis critical region 1 (human)	protein-coding
mm_97782.1	chr11	82388895	82388949	+	1	NA	promoter-TSS (NM_001304439)	promoter-TSS (NM_001304439)	22	NM_001304439	270893	Mm.341593	NM_023438	ENSMUSG00000020701	Tmem132e	Gm644	transmembrane protein 132E	protein-coding
mm_101376.1	chr11	23770934	23770942	-	1	NA	promoter-TSS (NM_009044)	promoter-TSS (NM_009044)	32	NM_009044	19696	Mm.4869	NM_009044	ENSMUSG00000020275	Rel	c-Rel	reticuloendotheliosis oncogene	protein-coding
mm_19027.1	chr2	76968477	76968502	-	1	NA	exon (NM_011652, exon 9 of 313)	exon (NM_011652, exon 9 of 313)	14058	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_144773.1	chr18	35828854	35828868	+	1	NA	promoter-TSS (NM_133687)	promoter-TSS (NM_133687)	-957	NM_133687	67393	Mm.94560	NM_133687	ENSMUSG00000046668	Cxxc5	4930415K17Rik	CXXC finger 5	protein-coding
mm_40887.1	chr5	74979879	74979906	+	1	NA	Intergenic	Intergenic	30698	NR_045866	619945	Mm.359372	NM_001037908	ENSMUSG00000072874	Gm6116	EG619945	predicted gene 6116	ncRNA
mm_122455.1	chr14	45318557	45318579	-	1	NA	promoter-TSS (NM_015774)	promoter-TSS (NM_015774)	4	NM_015774	50527	Mm.387108	NM_015774	ENSMUSG00000021831	Ero1l	ERO1-L|Ero1a	ERO1-like (S. cerevisiae)	protein-coding
mm_92942.1	chr10	85003641	85003665	-	1	NA	intron (NM_183172, intron 9 of 9)	intron (NM_183172, intron 9 of 9)	86040	NM_183172	237422	Mm.18936	NM_183172	ENSMUSG00000035620	Ric8b	BC051080|Ric-8|Ric-8b	RIC8 guanine nucleotide exchange factor B	protein-coding
mm_61155.1	chr7	58658421	58658431	+	1	NA	5' UTR (NM_009728, exon 1 of 21)	5' UTR (NM_009728, exon 1 of 21)	224	NM_009728	11982	Mm.135129	NM_009728	ENSMUSG00000025324	Atp10a	Atp10c|pfatp	ATPase, class V, type 10A	protein-coding
mm_50886.1	chr6	56714822	56714853	+	1	NA	promoter-TSS (NM_030235)	promoter-TSS (NM_030235)	-68	NM_030235	78937	Mm.105343	NM_030235	ENSMUSG00000029787	Avl9	5830411G16Rik|D730049P16Rik|mKIAA0241	AVL9 cell migration associated	protein-coding
mm_29568.1	chr3	116968629	116968633	-	1	NA	5' UTR (NM_023245, exon 1 of 8)	5' UTR (NM_023245, exon 1 of 8)	321	NM_023245	114301	Mm.253736	NM_023245	ENSMUSG00000033377	Palmd	4631423C22Rik|PALML	palmdelphin	protein-coding
mm_161714.1	chr17	25497105	25497105	-	1	NA	intron (NM_011425, intron 1 of 2)	intron (NM_011425, intron 1 of 2)	183	NM_011425	20609	Mm.353282	NM_011425	ENSMUSG00000050824	Sstr5	Smstr5|sst5	somatostatin receptor 5	protein-coding
mm_154347.1	chrM	5723	5731	+	1	NA	NA	Intergenic	NA	NA								
mm_53953.1	chr6	5298398	5298408	-	1	NA	promoter-TSS (NM_183308)	promoter-TSS (NM_183308)	-30	NM_183308	330260	Mm.126984	NM_183308	ENSMUSG00000032667	Pon2	6330405I24Rik|AI481612	paraoxonase 2	protein-coding
mm_27403.1	chr3	51277471	51277485	-	1	NA	promoter-TSS (NM_001291063)	promoter-TSS (NM_001291063)	36	NM_001291062	69257	Mm.131038	NM_023502	ENSMUSG00000037174	Elf2	2610036A20Rik|A230104O07Rik|AW111824|BB183398|EU32|NERF|NERF-1A|NERF-1B|NERF-2	E74-like factor 2	protein-coding
mm_129644.1	chr15	80565135	80565147	-	1	NA	Intergenic	Intergenic	-4671	NM_001163189	383075	Mm.297626	NM_001163189	ENSMUSG00000050439	Enthd1	Gm1242|Gm86	ENTH domain containing 1	protein-coding
mm_70847.1	chr8	23446890	23446909	+	1	NA	3' UTR (NM_013834, exon 3 of 3)	3' UTR (NM_013834, exon 3 of 3)	35397	NM_013834	20377	Mm.281691	NM_013834	ENSMUSG00000031548	Sfrp1	2210415K03Rik|AW011917|AW107218|AW742929|sFRP-1	secreted frizzled-related protein 1	protein-coding
mm_155165.1	chrX	53008664	53008693	+	1	NA	exon (NM_013556, exon 4 of 9)	exon (NM_013556, exon 4 of 9)	20600	NM_013556	15452	Mm.299381	NM_013556	ENSMUSG00000025630	Hprt	C81579|HPGRT|Hprt1	hypoxanthine guanine phosphoribosyl transferase	protein-coding
mm_76436.1	chr8	84986067	84986080	-	1	NA	Intergenic	CpG	-4522	NM_133255	170833	Mm.247775	NM_133255	ENSMUSG00000052566	Hook2	A630054I03Rik	hook microtubule tethering protein 2	protein-coding
mm_154235.1	chr19	60575808	60575811	-	1	NA	intron (NM_030197, intron 1 of 8)	intron (NM_030197, intron 1 of 8)	5214	NM_001172097	78832	Mm.259026	NM_030197	ENSMUSG00000033417	Cacul1	2700078E11Rik|2810417M16Rik|9830127L17Rik|AI450346|D130033C15Rik	CDK2 associated, cullin domain 1	protein-coding
mm_47071.1	chr5	116545046	116545055	-	1	NA	intron (NM_026886, intron 1 of 12)	RSINE1|SINE|B4	46767	NM_026886	68955	Mm.146779	NM_026886	ENSMUSG00000063919	Srrm4	1500001A10Rik|B230202K19Rik|bv|mKIAA1853|nSR100	serine/arginine repetitive matrix 4	protein-coding
mm_55469.1	chr6	68755632	68755636	-	1	NA	Intergenic	Intergenic	571540	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_106589.1	chr11	120729815	120729822	-	1	NA	exon (NM_007621, exon 8 of 8)	exon (NM_007621, exon 8 of 8)	2203	NM_007621	12409	Mm.21454	NM_007621	ENSMUSG00000025150	Cbr2	MLCR	carbonyl reductase 2	protein-coding
mm_156026.1	chrX	107149581	107149605	+	1	NA	promoter-TSS (NM_175442)	promoter-TSS (NM_175442)	-22	NM_175442	213438	Mm.265244	NM_175442	ENSMUSG00000054293	A630033H20Rik	AI662791|P2ry10	RIKEN cDNA A630033H20 gene	protein-coding
mm_168462.1	chr11	45726038	45726056	+	1	NA	Intergenic	L1Md_T|LINE|L1	-82036	NR_045876	100009664	Mm.415439	NR_045876		F630206G17Rik	-	RIKEN cDNA F630206G17 gene	ncRNA
mm_45279.1	chr5	64899020	64899032	-	1	NA	Intergenic	Intergenic	33673	NM_030682	21897	Mm.273024	NM_030682	ENSMUSG00000044827	Tlr1	-	toll-like receptor 1	protein-coding
mm_150924.1	chr19	46152524	46152566	+	1	NA	promoter-TSS (NM_178930)	promoter-TSS (NM_178930)	-13	NM_178930	107338	Mm.271620	NM_178930	ENSMUSG00000025224	Gbf1	1700083E03Rik|AI035702|AW049900|mKIAA0248	golgi-specific brefeldin A-resistance factor 1	protein-coding
mm_150283.1	chr19	34292403	34292406	+	1	NA	intron (NM_007987, intron 1 of 8)	intron (NM_007987, intron 1 of 8)	1745	NM_001146708	14102	Mm.1626	NM_007987	ENSMUSG00000024778	Fas	AI196731|APO1|APT1|CD95|TNFR6|Tnfrsf6|lpr	Fas (TNF receptor superfamily member 6)	protein-coding
mm_87907.1	chr10	62253048	62253057	+	1	NA	exon (NM_009314, exon 1 of 5)	exon (NM_009314, exon 1 of 5)	614	NM_009314	21337	Mm.8054	NM_009314	ENSMUSG00000020081	Tacr2	Nk2r|Skr|Tac2r	tachykinin receptor 2	protein-coding
mm_60190.1	chr7	43408188	43408211	+	1	NA	promoter-TSS (NM_172900)	promoter-TSS (NM_172900)	-81	NM_172900	243958	Mm.24444	NM_172900	ENSMUSG00000030468	Siglecg	9830164H23|A630096C01Rik|Siglec-G|Siglec10|mSiglec-G	sialic acid binding Ig-like lectin G	protein-coding
mm_170844.1	chr2	177464749	177464758	+	1	NA	promoter-TSS (NM_001177568)	promoter-TSS (NM_001177568)	11	NM_001177568	628308	Mm.460436	NM_001177568	ENSMUSG00000078866	Zfp970	Gm14420|OTTMUSG00000016588	zinc finger protein 970	protein-coding
mm_45815.1	chr5	87678068	87678083	-	1	NA	exon (NM_007784, exon 29 of 34)	exon (NM_007784, exon 29 of 34)	11867	NM_001286016	12990	Mm.427467	NM_007784	ENSMUSG00000070702	Csn1s1	AA959832|AW212882|Csna	casein alpha s1	protein-coding
mm_145469.1	chr18	60300006	60300008	+	1	NA	exon (NM_001101475, exon 2 of 2)	exon (NM_001101475, exon 2 of 2)	6627	NM_001101475	240328	Mm.329461	NM_001101475	ENSMUSG00000090942	F830016B08Rik	Ifgga4	RIKEN cDNA F830016B08 gene	protein-coding
mm_111299.1	chr12	85485956	85485966	-	1	NA	Intergenic	Intergenic	12060	NM_010234	14281	Mm.246513	NM_010234	ENSMUSG00000021250	Fos	D12Rfj1|c-fos|cFos	FBJ osteosarcoma oncogene	protein-coding
mm_86907.1	chr10	22645122	22645137	+	1	NA	5' UTR (NM_178934, exon 1 of 5)	5' UTR (NM_178934, exon 1 of 5)	118	NM_178934	353169	Mm.473705	NM_178934	ENSMUSG00000037490	Slc2a12	GLUT-12|Glut12	solute carrier family 2 (facilitated glucose transporter), member 12	protein-coding
mm_19868.1	chr2	114047386	114047442	-	1	NA	3' UTR (NM_009608, exon 7 of 7)	3' UTR (NM_009608, exon 7 of 7)	5461	NM_009608	11464	Mm.686	NM_009608	ENSMUSG00000068614	Actc1	Actc-1	actin, alpha, cardiac muscle 1	protein-coding
mm_2743.1	chr1	128591278	128591290	+	1	NA	intron (NM_009911, intron 1 of 1)	CpG	1015	NM_009911	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding
mm_128610.1	chr15	58823466	58823468	-	1	NA	promoter-TSS (NM_175212)	promoter-TSS (NM_175212)	-40	NM_175212	74868	Mm.293754	NM_175212	ENSMUSG00000062373	Tmem65	2610029O13Rik|4930438D12Rik	transmembrane protein 65	protein-coding
mm_115209.1	chr13	109260370	109260375	+	1	NA	intron (NM_011056, intron 3 of 16)	intron (NM_011056, intron 3 of 16)	-64372	NR_030644	100124489		NR_030644	ENSMUSG00000076946	Mir582	Mirn582|mir-582|mmu-mir-582	microRNA 582	ncRNA
mm_141300.1	chr17	28080306	28080316	-	1	NA	intron (NM_001085555, intron 1 of 9)	intron (NM_001085555, intron 1 of 9)	273	NM_013687	21463	Mm.29758	NM_013687	ENSMUSG00000062859	Tcp11	D17Ken1|Tcp-11	t-complex protein 11	protein-coding
mm_386.1	chr1	34077228	34077245	+	1	NA	intron (NM_133833, intron 1 of 92)	intron (NM_133833, intron 1 of 92)	-40123	NR_105861	102466987		NR_105861	ENSMUSG00000105982	Mir6896	mmu-mir-6896	microRNA 6896	ncRNA
mm_78323.1	chr9	24625192	24625201	+	1	NA	promoter-TSS (NM_001039942)	promoter-TSS (NM_001039942)	-8	NM_001039944	664726	Mm.437189	NM_001039944		Cypt10	-	cysteine-rich perinuclear theca 10	protein-coding
mm_99845.1	chr11	109362030	109362045	+	1	NA	promoter-TSS (NM_010303)	promoter-TSS (NM_010303)	-757	NM_010303	14674	Mm.193925	NM_010303	ENSMUSG00000020611	Gna13	AU024132|AU043124|Galpha13	guanine nucleotide binding protein, alpha 13	protein-coding
mm_73538.1	chr8	108703839	108703893	+	1	NA	Intergenic	Intergenic	-10778	NM_007496	11906	Mm.416972	NM_007496	ENSMUSG00000038872	Zfhx3	A230102L03Rik|Atbf1|Sci|WBP9|mKIAA4228	zinc finger homeobox 3	protein-coding
mm_121938.1	chr14	24004488	24004530	-	1	NA	promoter-TSS (NM_001253365)	promoter-TSS (NM_001253365)	-304	NM_001253374	16531	Mm.343607	NM_010610	ENSMUSG00000063142	Kcnma1	5730414M22Rik|BKCa|MaxiK|Slo|Slo1|mSlo|mSlo1	potassium large conductance calcium-activated channel, subfamily M, alpha member 1	protein-coding
mm_88987.1	chr10	81565538	81565563	+	1	NA	exon (NM_010347, exon 7 of 7)	exon (NM_010347, exon 7 of 7)	6106	NM_001276288	14797	Mm.180013	NM_010347	ENSMUSG00000054452	Aes	AL024115|Esp1|Grg|Grg-5|Grg5|Tle5	amino-terminal enhancer of split	protein-coding
mm_159347.1	chr3	63773540	63773540	-	1	NA	intron (NM_001177733, intron 4 of 23)	intron (NM_001177733, intron 4 of 23)	77451	NM_001177733	269437	Mm.316391	NM_183191	ENSMUSG00000036834	Plch1	BC042549|PLC-eta-1|PLCeta1|Plcl3	phospholipase C, eta 1	protein-coding
mm_124184.1	chr14	94086171	94086178	-	1	NA	Intergenic	Intergenic	-195495	NM_001346722	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding
mm_82424.1	chr9	14903911	14903921	-	1	NA	promoter-TSS (NM_176807)	promoter-TSS (NM_176807)	35	NM_176807	64931	Mm.86738	NM_022888	ENSMUSG00000031933	Izumo1r	0910001L11Rik|C86255|Folbp3|Folr4|Juno	IZUMO1 receptor, JUNO	protein-coding
mm_133380.1	chr16	84714986	84714988	+	1	NA	TTS (NR_029565)	TTS (NR_029565)	847	NR_029565	387173		NR_029565	ENSMUSG00000065397	Mir155	Mirn155|mir-155|mmu-mir-155	microRNA 155	ncRNA
mm_83979.1	chr9	57265790	57265790	-	1	NA	Intergenic	Intergenic	-3191	NM_028820	74211	Mm.428905	NM_028820	ENSMUSG00000032300	1700017B05Rik	AA682102|D9Ertd278e	RIKEN cDNA 1700017B05 gene	protein-coding
mm_18979.1	chr2	76849007	76849017	-	1	NA	exon (NM_011652, exon 137 of 313)	exon (NM_011652, exon 137 of 313)	133535	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_169159.1	chr13	65348591	65348594	-	1	NA	Intergenic	Intergenic	69738	NM_178364	170936	Mm.151546	NM_178364	ENSMUSG00000021514	Zfp369	B930030B22Rik|D230020H11Rik|NRIF2	zinc finger protein 369	protein-coding
mm_63933.1	chr7	139538112	139538139	+	1	NA	intron (NM_183144, intron 8 of 15)	intron (NM_183144, intron 8 of 15)	44672	NM_183248	14912	Mm.28308	NM_183248	ENSMUSG00000041309	Nkx6-2	Gtx|Nkx6.2	NK6 homeobox 2	protein-coding
mm_13063.1	chr2	91115523	91115554	+	1	NA	3' UTR (NM_011355, exon 5 of 5)	3' UTR (NM_011355, exon 5 of 5)	-2606	NM_008653	17868	Mm.10728	NM_008653	ENSMUSG00000002100	Mybpc3	-	myosin binding protein C, cardiac	protein-coding
mm_143241.1	chr17	63500631	63500641	-	1	NA	promoter-TSS (NM_015794)	promoter-TSS (NM_015794)	-56	NM_015794	50758	Mm.136366	NM_015794	ENSMUSG00000023965	Fbxl17	6330576B01Rik|AI452053|BB073797|C130023C01Rik|Fbx13|Fbxo13	F-box and leucine-rich repeat protein 17	protein-coding
mm_160034.1	chr6	132656911	132656911	+	1	NA	promoter-TSS (NM_207023)	promoter-TSS (NM_207023)	-46	NM_207023	387348	Mm.377910	NM_207023	ENSMUSG00000059382	Tas2r120	T2R20|Tas2r20|mGR20|mt2r47	taste receptor, type 2, member 120	protein-coding
mm_19428.1	chr2	91935795	91935821	-	1	NA	intron (NM_001166597, intron 26 of 31)	intron (NM_001166597, intron 26 of 31)	-3511	NM_010784	17242	Mm.906	NM_010784	ENSMUSG00000027239	Mdk	MK|Mek	midkine	protein-coding
mm_33994.1	chr4	137905139	137905148	+	1	NA	5' UTR (NM_199307, exon 2 of 20)	5' UTR (NM_199307, exon 2 of 20)	42906	NM_199307	230857	Mm.401062	NM_199307	ENSMUSG00000057530	Ece1	AW322500|ECE-1|ECE-1a|ECE-1b|ECE-1d	endothelin converting enzyme 1	protein-coding
mm_5483.1	chr1	36800111	36800116	-	1	NA	intron (NM_018872, intron 33 of 40)	intron (NM_018872, intron 33 of 40)	21129	NM_001289612	22637	Mm.8038	NM_009539	ENSMUSG00000026117	Zap70	Srk|ZAP-70|mrtle|mur	zeta-chain (TCR) associated protein kinase	protein-coding
mm_169218.1	chr13	66729822	66729838	+	1	NA	Intergenic	RLTR27|LTR|ERVK	175520	NM_026219	67530	Mm.379136	NM_026219	ENSMUSG00000021520	Uqcrb	2210415M14Rik|QP-C|QPC|UQBC|UQBP|UQPC	ubiquinol-cytochrome c reductase binding protein	protein-coding
mm_30470.1	chr3	154594194	154594198	-	1	NA	intron (NM_001168358, intron 2 of 4)	intron (NM_001168358, intron 2 of 4)	-2515	NM_009968	12972	Mm.374855	NM_009968	ENSMUSG00000028199	Cryz	Sez9	crystallin, zeta	protein-coding
mm_115027.1	chr13	99184734	99184755	+	1	NA	promoter-TSS (NM_001004149)	promoter-TSS (NM_001004149)	-79	NM_001004149	238803	Mm.343207	NM_001004149	ENSMUSG00000050919	Zfp366	DC-SCRIPT|Znf366	zinc finger protein 366	protein-coding
mm_48296.1	chr5	138255543	138255600	-	1	NA	promoter-TSS (NM_001081108)	promoter-TSS (NM_001081108)	89	NM_001081108	66096	Mm.206901	NM_001081108	ENSMUSG00000050552	Lamtor4	0910001L09Rik|AV006840	late endosomal/lysosomal adaptor, MAPK and MTOR activator 4	protein-coding
mm_161997.1	chr19	39007020	39007020	+	1	NA	promoter-TSS (NM_028089)	promoter-TSS (NM_028089)	1	NM_028089	72082	Mm.142581	NM_028089	ENSMUSG00000025002	Cyp2c55	2010318C06Rik	cytochrome P450, family 2, subfamily c, polypeptide 55	protein-coding
mm_16305.1	chr2	174289785	174289856	+	1	NA	intron (NR_002846, intron 1 of 4)	(CA)n|Simple_repeat|Simple_repeat	5500	NM_022000	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_17282.1	chr2	26138277	26138278	-	1	NA	3' UTR (NM_001256522, exon 2 of 2)	3' UTR (NM_001256522, exon 2 of 2)	1266	NM_001256522	109299	Mm.389259	NM_001256521		C330006A16Rik	AI551216	RIKEN cDNA C330006A16 gene	protein-coding
mm_110400.1	chr12	44210179	44210185	-	1	NA	promoter-TSS (NM_013760)	promoter-TSS (NM_013760)	-114	NM_013760	27362	Mm.27432	NM_013760	ENSMUSG00000014905	Dnajb9	AA408011|AA673251|AA673481|AW556981|ERdj4|Mdg1|mDj7	DnaJ heat shock protein family (Hsp40) member B9	protein-coding
mm_89723.1	chr10	98915182	98915192	+	1	NA	promoter-TSS (NM_026482)	promoter-TSS (NM_026482)	35	NM_026482	67972	Mm.166944	NM_026482	ENSMUSG00000019943	Atp2b1	2810442I22Rik|E130111D10Rik|Pmca1	ATPase, Ca++ transporting, plasma membrane 1	protein-coding
mm_81071.1	chr9	106206790	106206804	+	1	NA	intron (NM_011876, intron 1 of 8)	intron (NM_011876, intron 1 of 8)	3689	NM_011876	23999	Mm.274346	NM_011876	ENSMUSG00000023277	Twf2	A6-related|AU014993|Ptk9l|Ptk9r	twinfilin actin binding protein 2	protein-coding
mm_116080.1	chr13	28419995	28420008	-	1	NA	Intergenic	Intergenic	277517	NM_023746	28078	Mm.155058	NM_023746	ENSMUSG00000017064	Prl5a1	1600013P04Rik|D13Wsu14e|Ghd24|PLP-L|Prlpl	prolactin family 5, subfamily a, member 1	protein-coding
mm_165810.1	chr3	145758699	145758701	+	1	NA	promoter-TSS (NM_026993)	promoter-TSS (NM_026993)	8	NM_026993	69219	Mm.234247	NM_026993	ENSMUSG00000028194	Ddah1	2410006N07Rik|2510015N06Rik|AI987801|AW050362	dimethylarginine dimethylaminohydrolase 1	protein-coding
mm_132206.1	chr16	32608843	32608853	+	1	NA	promoter-TSS (NM_011638)	promoter-TSS (NM_011638)	-48	NM_011638	22042	Mm.28683	NM_011638	ENSMUSG00000022797	Tfrc	2610028K12Rik|CD71|E430033M20Rik|Mtvr1|TFR|TFR1|TR|Trfr|p90	transferrin receptor	protein-coding
mm_30993.1	chr4	38263872	38263876	+	1	NA	Intergenic	Intergenic	-1186419	NM_001081095	75471	Mm.23522	NM_001081095	ENSMUSG00000028287	1700009N14Rik	AI429145	RIKEN cDNA 1700009N14 gene	protein-coding
mm_77532.1	chr8	123023626	123023629	-	1	NA	intron (NM_001081379, intron 1 of 12)	B2_Mm1a|SINE|B2	18657	NR_037865	77087	Mm.31567	NM_001081379	ENSMUSG00000035569	Ankrd11	2410104C19Rik|3010027A04Rik|6330578C09Rik|9530048I21Rik|AA930108|Gm176|Yod	ankyrin repeat domain 11	protein-coding
mm_97475.1	chr11	78323088	78323112	+	1	NA	promoter-TSS (NM_001303423)	promoter-TSS (NM_001303423)	27	NM_001303423	11676	Mm.7729	NM_009657	ENSMUSG00000017390	Aldoc	AI847350|AU040929|Aldo3|Scrg2	aldolase C, fructose-bisphosphate	protein-coding
mm_170951.1	chr2	53696848	53696861	-	1	NA	Intergenic	Intergenic	388698	NM_023396	67874	Mm.27086	NM_023396	ENSMUSG00000075334	Rprm	2410012A13Rik|Reprimo	reprimo, TP53 dependent G2 arrest mediator candidate	protein-coding
mm_143785.1	chr17	81731250	81731261	-	1	NA	intron (NR_104580, intron 1 of 8)	intron (NR_104580, intron 1 of 8)	7132	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_33460.1	chr4	130792514	130792667	+	1	NA	promoter-TSS (NM_011520)	promoter-TSS (NM_011520)	53	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_130879.1	chr15	102246338	102246363	-	1	NA	5' UTR (NM_001042727, exon 1 of 8)	5' UTR (NM_001042727, exon 1 of 8)	150	NM_001042727	19411	Mm.1273	NM_011244	ENSMUSG00000001288	Rarg	Nr1b3|RAR-gamma|RARD|RARgamma2	retinoic acid receptor, gamma	protein-coding
mm_159465.1	chr4	3872100	3872100	-	1	NA	promoter-TSS (NM_020021)	promoter-TSS (NM_020021)	5	NM_020021	17451	Mm.459300	NM_020021	ENSMUSG00000078365	Mos	c-mos	Moloney sarcoma oncogene	protein-coding
mm_136725.1	chr17	8236108	8236118	+	1	NA	promoter-TSS (NM_001190333)	promoter-TSS (NM_001190333)	70	NM_001190333	12458	Mm.8007	NM_009835	ENSMUSG00000040899	Ccr6	CC-CKR-6|CCR-6|Cmkbr6|KY411	chemokine (C-C motif) receptor 6	protein-coding
mm_83608.1	chr9	48605105	48605116	-	1	NA	promoter-TSS (NM_001311062)	promoter-TSS (NM_001311062)	13	NM_001311062	18113	Mm.8362	NM_010924	ENSMUSG00000032271	Nnmt	-	nicotinamide N-methyltransferase	protein-coding
mm_114544.1	chr13	73829896	73829902	+	1	NA	intron (NM_001347535, intron 2 of 8)	intron (NM_001347535, intron 2 of 8)	17732	NM_028186	72293	Mm.45506	NM_028186	ENSMUSG00000021567	Nkd2	2210403L10Rik|AW212591|mNkd2	naked cuticle 2 homolog (Drosophila)	protein-coding
mm_808.1	chr1	45402095	45402106	+	1	NA	exon (NM_007737, exon 30 of 54)	exon (NM_007737, exon 30 of 54)	90562	NM_009930	12825	Mm.249555	NM_009930	ENSMUSG00000026043	Col3a1	AW550625|Col3a-1|Tsk-2|Tsk2	collagen, type III, alpha 1	protein-coding
mm_102786.1	chr11	68401088	68401104	-	1	NA	Intergenic	Intergenic	-14270	NM_008744	18208	Mm.39095	NM_008744	ENSMUSG00000020902	Ntn1	AI561871|BC019633|Netrin-1	netrin 1	protein-coding
mm_96715.1	chr11	69664213	69664219	+	1	NA	TTS (NR_110993)	TTS (NR_110993)	1173	NR_035455	100316840		NR_035455	ENSMUSG00000088752	Mir1934	mir-1934|mmu-mir-1934	microRNA 1934	ncRNA
mm_31928.1	chr4	85514351	85514364	+	1	NA	Intergenic	CpG	308901	NM_019535	20404	Mm.143603	NM_019535	ENSMUSG00000028488	Sh3gl2	9530001L19Rik|AI120490|AW555077|B930049H17Rik|EEN-B1|SH3PA|Sh3d2a	SH3-domain GRB2-like 2	protein-coding
mm_6111.1	chr1	64107189	64107193	-	1	NA	intron (NM_033563, intron 1 of 3)	intron (NM_033563, intron 1 of 3)	14198	NM_033563	93691	Mm.29466	NM_033563	ENSMUSG00000025959	Klf7	9830124P08Rik	Kruppel-like factor 7 (ubiquitous)	protein-coding
mm_153742.1	chr19	44696883	44696890	-	1	NA	Intergenic	Intergenic	-60508	NM_011037	18504	Mm.192158	NM_011037	ENSMUSG00000004231	Pax2	Opdc|Pax-2	paired box 2	protein-coding
mm_153242.1	chr19	36119283	36119303	-	1	NA	exon (NM_013468, exon 2 of 9)	exon (NM_013468, exon 2 of 9)	551	NM_013468	107765	Mm.10279	NM_013468	ENSMUSG00000024803	Ankrd1	Alrp|CARP|Crap|MARP1	ankyrin repeat domain 1 (cardiac muscle)	protein-coding
mm_155847.1	chrX	101274024	101274034	+	1	NA	promoter-TSS (NM_021521)	promoter-TSS (NM_021521)	-62	NM_021521	59024	Mm.20873	NM_021521	ENSMUSG00000079487	Med12	230kDa|Mopa|OPA-1|Tnrc11|Trap230	mediator complex subunit 12	protein-coding
mm_170344.1	chr1	85012089	85012089	+	1	NA	Intergenic	Intergenic	-77006	NM_027921	71781	Mm.158754	NM_027921	ENSMUSG00000026220	Slc16a14	1110004H10Rik	solute carrier family 16 (monocarboxylic acid transporters), member 14	protein-coding
mm_127013.1	chr15	95864093	95864117	+	1	NA	intron (NM_001253813, intron 2 of 20)	intron (NM_001253813, intron 2 of 20)	73262	NM_001253813	105722	Mm.38087	NM_175344	ENSMUSG00000064210	Ano6	2900059G15Rik|AA407480|AW554778|F730003B03Rik|Tmem16f	anoctamin 6	protein-coding
mm_63432.1	chr7	127478944	127478967	+	1	NA	Intergenic	CpG	-6266	NM_010183	14123	Mm.323505	NM_010183	ENSMUSG00000042423	Fbrs	Fbs|Fbs1	fibrosin	protein-coding
mm_68929.1	chr7	126492299	126492318	-	1	NA	3' UTR (NM_001347658, exon 22 of 22)	3' UTR (NM_001347658, exon 22 of 22)	4953	NM_001163713	233870	Mm.197829	NM_172745	ENSMUSG00000073838	Tufm	2300002G02Rik|C76308|C76389|EF-TuMT|EFTU	Tu translation elongation factor, mitochondrial	protein-coding
mm_38488.1	chr4	140814139	140814168	-	1	NA	non-coding (NR_045944, exon 2 of 3)	non-coding (NR_045944, exon 2 of 3)	3160	NR_045944	100049161	Mm.20854	NR_045944	ENSMUSG00000085918	Gm13032	OTTMUSG00000010086	predicted gene 13032	ncRNA
mm_18245.1	chr2	52189655	52189672	-	1	NA	exon (NM_010889, exon 120 of 157)	exon (NM_010889, exon 120 of 157)	-101339	NR_040620	78049	Mm.243883	NR_040620		4930573O16Rik	-	RIKEN cDNA 4930573O16 gene	ncRNA
mm_33027.1	chr4	122673788	122673797	+	1	NA	Intergenic	L2|LINE|L2	-15467	NM_023865	77432	Mm.491436	NM_023865	ENSMUSG00000023263	9530002B09Rik	Aump|Vpp1|Vppl	RIKEN cDNA 9530002B09 gene	protein-coding
mm_5552.1	chr1	38664923	38664933	-	1	NA	Intergenic	Intergenic	-37684	NM_001290814	16764	Mm.336679	NM_010678	ENSMUSG00000037138	Aff3	3222402O04Rik|A730046J16|LAF-4|Laf4	AF4/FMR2 family, member 3	protein-coding
mm_56597.1	chr6	108659803	108659823	-	1	NA	promoter-TSS (NM_011498)	promoter-TSS (NM_011498)	-816	NM_011498	20893	Mm.2436	NM_011498	ENSMUSG00000030103	Bhlhe40	Bhlhb2|C130042M06Rik|CR8|Clast5|Dec1|Sharp2|Stra13|Stra14	basic helix-loop-helix family, member e40	protein-coding
mm_46925.1	chr5	114670072	114670112	-	1	NA	3' UTR (NM_019821, exon 5 of 5)	3' UTR (NM_019821, exon 5 of 5)	-11671	NM_022017	63873	Mm.266450	NM_022017	ENSMUSG00000014158	Trpv4	0610033B08Rik|OTRPC4|Trp12|VR-OAC|VRL-2|VROAC	transient receptor potential cation channel, subfamily V, member 4	protein-coding
mm_19886.1	chr2	114050359	114050365	-	1	NA	exon (NM_009608, exon 3 of 7)	exon (NM_009608, exon 3 of 7)	2513	NM_009608	11464	Mm.686	NM_009608	ENSMUSG00000068614	Actc1	Actc-1	actin, alpha, cardiac muscle 1	protein-coding
mm_137359.1	chr17	25366281	25366312	+	1	NA	promoter-TSS (NM_010781)	promoter-TSS (NM_010781)	-37	NM_010781	17229	Mm.7409	NM_010781	ENSMUSG00000033825	Tpsb2	AV011504|MMCP-6|Mcp-6|Mcp6|Mcpt6	tryptase beta 2	protein-coding
mm_135040.1	chr16	32877688	32877715	-	1	NA	promoter-TSS (NM_001159349)	promoter-TSS (NM_001159349)	-83	NM_027226	69823	Mm.12831	NM_027226	ENSMUSG00000022800	Fyttd1	2010005M05Rik|3830411L18Rik|3830421F13Rik|4933423A17Rik|AI098218|AW539567|C85190	forty-two-three domain containing 1	protein-coding
mm_120322.1	chr14	63142938	63142962	+	1	NA	3' UTR (NM_007798, exon 10 of 10)	3' UTR (NM_007798, exon 10 of 10)	20488	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_81568.1	chr9	110420112	110420117	+	1	NA	intron (NM_008694, intron 1 of 3)	ID_B1|SINE|B4	306	NM_008694	18054	Mm.236225	NM_008694	ENSMUSG00000032484	Ngp	bectenecin	neutrophilic granule protein	protein-coding
mm_104091.1	chr11	86648232	86648245	-	1	NA	intron (NM_029478, intron 5 of 11)	intron (NM_029478, intron 5 of 11)	-7833	NR_106195	102465902		NR_106195	ENSMUSG00000099324	Mir8115	Gm28012|mmu-mir-8115	microRNA 8115	ncRNA
mm_7601.1	chr1	126090478	126090479	-	1	NA	intron (NM_001081756, intron 10 of 16)	intron (NM_001081756, intron 10 of 16)	-177550	NM_001311089	72585	Mm.490405	NM_145100	ENSMUSG00000026344	Lypd1	2700050C12Rik|AI853408|C530008O16Rik|Lynx2|Lypdc1	Ly6/Plaur domain containing 1	protein-coding
mm_101919.1	chr11	50200720	50200734	-	1	NA	TTS (NM_026543)	TTS (NM_026543)	10093	NM_001290769	18412	Mm.40828	NM_011018	ENSMUSG00000015837	Sqstm1	A170|OSF-6|Osi|STAP|STONE14|p62	sequestosome 1	protein-coding
mm_106383.1	chr11	118495497	118495512	-	1	NA	intron (NM_001039168, intron 12 of 14)	intron (NM_001039168, intron 12 of 14)	18544	NM_172573	217364	Mm.473963	NM_172573	ENSMUSG00000033857	Engase	C130099A03|D230014K01Rik	endo-beta-N-acetylglucosaminidase	protein-coding
mm_132985.1	chr16	52206800	52206837	+	1	NA	3' UTR (NM_001033238, exon 18 of 18)	3' UTR (NM_001033238, exon 18 of 18)	175269	NM_001033238	208650	Mm.328206	NM_001033238	ENSMUSG00000022637	Cblb	AI429560|AI851073|Cbl-b	Casitas B-lineage lymphoma b	protein-coding
mm_93382.1	chr10	105574422	105574433	-	1	NA	promoter-TSS (NM_177368)	promoter-TSS (NM_177368)	52	NM_177368	278279	Mm.25225	NM_177368	ENSMUSG00000036019	Tmtc2	8430438D04Rik|D330034A10Rik	transmembrane and tetratricopeptide repeat containing 2	protein-coding
mm_156284.1	chrX	136837282	136837295	+	1	NA	3' UTR (NM_011123, exon 7 of 7)	3' UTR (NM_011123, exon 7 of 7)	14542	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_4145.1	chr1	170985371	170985378	+	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-9303	NM_010187	14130	Mm.425062	NM_010187	ENSMUSG00000026656	Fcgr2b	AI528646|CD32|F630109E10Rik|Fc[g]RII|FcgRII|Fcgr2|Fcgr2a|Fcr-2|Fcr-3|Ly-17|Ly-m20|LyM-1|Lym-1|fcRII	Fc receptor, IgG, low affinity IIb	protein-coding
mm_10802.1	chr2	24349706	24349719	+	1	NA	3' UTR (NM_031167, exon 5 of 5)	3' UTR (NM_031167, exon 5 of 5)	4341	NM_001039701	16181	Mm.882	NM_031167	ENSMUSG00000026981	Il1rn	F630041P17Rik|IL-1ra	interleukin 1 receptor antagonist	protein-coding
mm_13058.1	chr2	91114316	91114343	+	1	NA	exon (NM_011355, exon 4 of 5)	exon (NM_011355, exon 4 of 5)	-3815	NM_008653	17868	Mm.10728	NM_008653	ENSMUSG00000002100	Mybpc3	-	myosin binding protein C, cardiac	protein-coding
mm_69040.1	chr7	126800038	126800054	-	1	NA	promoter-TSS (NM_001177307)	promoter-TSS (NM_001177307)	401	NM_001177308	11674	Mm.275831	NM_007438	ENSMUSG00000030695	Aldoa	Aldo-1|Aldo1	aldolase A, fructose-bisphosphate	protein-coding
mm_115528.1	chr13	5864374	5864403	-	1	NA	intron (NM_011803, intron 1 of 3)	intron (NM_011803, intron 1 of 3)	2899	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_115133.1	chr13	104398387	104398388	+	1	NA	intron (NR_136938, intron 14 of 26)	intron (NR_136938, intron 14 of 26)	110552	NM_001081020	108154	Mm.208125	NM_175496	ENSMUSG00000046169	Adamts6	A930019D11Rik|ADAM-TS6|b2b1879.1Clo|b2b2029Clo|b2b2182Clo|b2b2187.1Clo|b2b2228Clo	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 6	protein-coding
mm_26531.1	chr3	146117528	146117540	+	1	NA	Intergenic	Intergenic	-4257	NM_134160	171166	Mm.114683	NM_134160	ENSMUSG00000036853	Mcoln3	6720490O21Rik|TRPML3|Va	mucolipin 3	protein-coding
mm_102451.1	chr11	59787637	59787683	-	1	NA	promoter-TSS (NR_110894)	promoter-TSS (NR_110894)	-3	NM_001290283	194908	Mm.344651	NM_183139	ENSMUSG00000043648	Pld6	4933433K01Rik|Gm10|Zuc|mZuc|mitoPLD	phospholipase D family, member 6	protein-coding
mm_62800.1	chr7	112853154	112853158	+	1	NA	intron (NM_001166585, intron 3 of 10)	intron (NM_001166585, intron 3 of 10)	93772	NM_001166585	21676	Mm.24685	NM_009346	ENSMUSG00000055320	Tead1	2610024B07Rik|B230114H05Rik|Gtrgeo5|TEAD-1|TEF-1|Tcf13|mTEF-1	TEA domain family member 1	protein-coding
mm_148543.1	chr19	4711154	4711258	+	1	NA	promoter-TSS (NM_021287)	promoter-TSS (NM_021287)	-17	NM_021287	20743	Mm.329668	NM_021287	ENSMUSG00000067889	Sptbn2	Spnb3|mKIAA0302	spectrin beta, non-erythrocytic 2	protein-coding
mm_9277.1	chr1	171634286	171634311	-	1	NA	3' UTR (NM_144539, exon 8 of 8)	3' UTR (NM_144539, exon 8 of 8)	7602	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_15774.1	chr2	164332819	164332821	+	1	NA	promoter-TSS (NM_009301)	promoter-TSS (NM_009301)	55	NM_009301	20944	Mm.140154	NM_009301	ENSMUSG00000017004	Svs5	BB115186|Semg1|Svp-1|Svp1|Svp5	seminal vesicle secretory protein 5	protein-coding
mm_78405.1	chr9	29014046	29014066	+	1	NA	intron (NM_172290, intron 5 of 7)	intron (NM_172290, intron 5 of 7)	949073	NM_172290	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding
mm_118001.1	chr13	100552599	100552656	-	1	NA	promoter-TSS (NM_008756)	promoter-TSS (NM_008756)	-129	NM_008756	18260	Mm.4807	NM_008756	ENSMUSG00000021638	Ocln	AI503564|Ocl	occludin	protein-coding
mm_168829.1	chr12	22745626	22745630	-	1	NA	Intergenic	CpG	264615	NR_015504	69732	Mm.391403	NM_028362	ENSMUSG00000073164	2410018L13Rik	2810480C08Rik	RIKEN cDNA 2410018L13 gene	ncRNA
mm_32927.1	chr4	119195417	119195426	+	1	NA	promoter-TSS (NM_001038998)	promoter-TSS (NM_001038998)	-104	NM_001038998	69216	Mm.36697	NM_024462	ENSMUSG00000028643	Svbp	2410005K17Rik|AI851162|Ccdc23	small vasohibin binding protein	protein-coding
mm_36393.1	chr4	77701074	77701100	-	1	NA	intron (NM_011211, intron 2 of 39)	intron (NM_011211, intron 2 of 39)	510808	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding
mm_70923.1	chr8	25808653	25808661	+	1	NA	intron (NM_011485, intron 1 of 6)	intron (NM_011485, intron 1 of 6)	183	NM_011485	20845	Mm.293314	NM_011485	ENSMUSG00000031574	Star	AV363654|D8Ertd419e|stARD1	steroidogenic acute regulatory protein	protein-coding
mm_67542.1	chr7	81489803	81489815	-	1	NA	intron (NM_021492, intron 1 of 25)	intron (NM_021492, intron 1 of 25)	4116	NM_021492	11775	Mm.322894	NM_021492	ENSMUSG00000062444	Ap3b2	AI549966|AU042881|Naptb|[b]-NAP|beta-NAP|beta3B	adaptor-related protein complex 3, beta 2 subunit	protein-coding
mm_20902.1	chr2	149798808	149798824	-	1	NA	Intergenic	Intergenic	-31967	NM_001085521	433485	Mm.330649	NM_001085521	ENSMUSG00000074736	Syndig1	AW123113|DSPC2|Gm14134|H2C20orf39|OTTMUSG00000015750|Tmem90b	synapse differentiation inducing 1	protein-coding
mm_118287.1	chr13	112927357	112927390	-	1	NA	promoter-TSS (NM_172594)	promoter-TSS (NM_172594)	7	NM_028151	72198	Mm.291029	NM_028151	ENSMUSG00000016018	Skiv2l2	2610528A15Rik|mKIAA0052	superkiller viralicidic activity 2-like 2 (S. cerevisiae)	protein-coding
mm_32201.1	chr4	101496546	101496598	+	1	NA	promoter-TSS (NM_198412)	promoter-TSS (NM_198412)	-76	NM_198412	72685	Mm.76494	NM_198412	ENSMUSG00000028528	Dnajc6	2810027M23Rik|mKIAA0473	DnaJ heat shock protein family (Hsp40) member C6	protein-coding
mm_146658.1	chr18	11858040	11858040	-	1	NA	intron (NM_022021, intron 1 of 8)	intron (NM_022021, intron 1 of 8)	-17602	NR_035447	100316686		NR_035447	ENSMUSG00000084565	Mir1901	Mirn1901|mmu-mir-1901	microRNA 1901	ncRNA
mm_8223.1	chr1	138172153	138172166	-	1	NA	intron (NM_001111316, intron 1 of 31)	intron (NM_001111316, intron 1 of 31)	2967	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_29904.1	chr3	131470978	131470988	-	1	NA	Intergenic	Intergenic	-93785	NM_001289479	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_136637.1	chr17	5720857	5720879	+	1	NA	intron (NM_146073, intron 5 of 8)	intron (NM_146073, intron 5 of 8)	-77789	NR_045081	78512	Mm.23696	NR_045079	ENSMUSG00000096965	3300005D01Rik	-	RIKEN cDNA 3300005D01 gene	ncRNA
mm_56489.1	chr6	99176360	99176367	-	1	NA	intron (NM_001347345, intron 4 of 19)	intron (NM_001347345, intron 4 of 19)	90152	NM_001197321	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_37410.1	chr4	122859278	122859311	-	1	NA	TTS (NM_008917)	TTS (NM_008917)	23067	NM_008917	19063	Mm.277719	NM_008917	ENSMUSG00000028657	Ppt1	9530043G02Rik|AA960502|C77813|CLN1|D4Ertd184e|INCL|PPT	palmitoyl-protein thioesterase 1	protein-coding
mm_46720.1	chr5	110653349	110653422	-	1	NA	promoter-TSS (NM_027156)	promoter-TSS (NM_027156)	-3	NM_153570	100608	Mm.29960	NM_153570	ENSMUSG00000033294	Noc4l	AI326906	NOC4 like	protein-coding
mm_91325.1	chr10	25200223	25200245	-	1	NA	promoter-TSS (NM_001347460)	promoter-TSS (NM_001347460)	-64	NM_001347460	432442	Mm.485937	NM_018747	ENSMUSG00000039166	Akap7	6430401D08|AI662165|AKAP15|Akap18|BB170514	A kinase (PRKA) anchor protein 7	protein-coding
mm_106788.1	chr12	4769341	4769360	+	1	NA	promoter-TSS (NM_175431)	promoter-TSS (NM_175431)	55	NM_028376	382562	Mm.251575	NM_028376	ENSMUSG00000020639	Pfn4	2900024P18Rik	profilin family, member 4	protein-coding
mm_64434.1	chr7	142578061	142578069	+	1	NA	promoter-TSS (NR_130974)	promoter-TSS (NR_130974)	81	NR_130974	14955	Mm.14802	NR_001592	ENSMUSG00000000031	H19	AI747191	H19, imprinted maternally expressed transcript	ncRNA
mm_134304.1	chr16	15637278	15637385	-	1	NA	promoter-TSS (NM_011159)	promoter-TSS (NM_011159)	69	NM_008565	17217	Mm.1500	NM_008565	ENSMUSG00000022673	Mcm4	19G|AI325074|AU045576|Cdc21|Mcmd4|mKIAA4003|mcdc21	minichromosome maintenance complex component 4	protein-coding
mm_106942.1	chr12	8739678	8739704	+	1	NA	intron (NM_001160220, intron 13 of 20)	L1M5|LINE|L1	-31705	NM_011519	20969	Mm.2580	NM_011519	ENSMUSG00000020592	Sdc1	AA408134|AA409076|CD138|Sstn|Synd|Synd1|syn-1	syndecan 1	protein-coding
mm_171551.1	chr4	147131995	147131996	+	1	NA	Intergenic	Intergenic	-43871	NM_001039209	195531	Mm.270762	NM_001039209	ENSMUSG00000078496	Zfp982	Gm13152|OTTMUSG00000010671	zinc finger protein 982	protein-coding
mm_58397.1	chr7	3213876	3213886	+	1	NA	Intergenic	Intergenic	-4745	NR_029640	100049710		NR_029640	ENSMUSG00000077815	Mir290a	Mir290|Mirn290|mir-290a|mmu-miR-290|mmu-mir-290a	microRNA 290a	ncRNA
mm_3358.1	chr1	138172714	138172731	+	1	NA	intron (NM_001111316, intron 1 of 31)	intron (NM_001111316, intron 1 of 31)	2404	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_93713.1	chr10	118869160	118869185	-	1	NA	promoter-TSS (NM_001014390)	promoter-TSS (NM_001014390)	-269	NM_001014390	69181	Mm.45565	NM_001014390	ENSMUSG00000028630	Dyrk2	1810038L18Rik	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 2	protein-coding
mm_3934.1	chr1	163762160	163762174	+	1	NA	Intergenic	Intergenic	-17416	NM_001305643	16579	Mm.4651	NM_010629	ENSMUSG00000026585	Kifap3	KAP-3|KAP3|SMAP	kinesin-associated protein 3	protein-coding
mm_18138.1	chr2	45036475	45036516	-	1	NA	intron (NM_001289521, intron 1 of 8)	intron (NM_001289521, intron 1 of 8)	-13318	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_162290.1	chr1	27716302	27716304	+	1	NA	Intergenic	Intergenic	-1028843	NM_001033764	210940	Mm.297614	NM_001033764	ENSMUSG00000073722	4931408C20Rik	-	RIKEN cDNA 4931408C20 gene	protein-coding
mm_66021.1	chr7	30603804	30603812	-	1	NA	exon (NM_026815, exon 7 of 8)	exon (NM_026815, exon 7 of 8)	8926	NM_026815	109637	Mm.25471	NM_026815	ENSMUSG00000006313	Upk1a	1110031P12Rik|AU019298|C87192|Tspan21|Upk1	uroplakin 1A	protein-coding
mm_159280.1	chr2	165875787	165875787	-	1	NA	intron (NM_027230, intron 1 of 23)	intron (NM_027230, intron 1 of 23)	2650	NM_001291158	228880	Mm.227598	NM_027230	ENSMUSG00000039671	Zmynd8	1110013E22Rik|2010005I16Rik|3632413B07Rik|AI316811|AL024039|Prkcbp1|RACK7	zinc finger, MYND-type containing 8	protein-coding
mm_99646.1	chr11	105452966	105452983	+	1	NA	intron (NM_172568, intron 2 of 11)	intron (NM_172568, intron 2 of 11)	3761	NM_172568	632687	Mm.121570	NM_172568	ENSMUSG00000078627	March10	4933417C16Rik|AV039223|OTTMUSG00000002847|Rnf190	membrane-associated ring finger (C3HC4) 10	protein-coding
mm_1618.1	chr1	74391688	74391716	+	1	NA	promoter-TSS (NM_153088)	promoter-TSS (NM_153088)	93	NM_153088	227292	Mm.165042	NM_153088	ENSMUSG00000026176	Ctdsp1	GIP|NLIIF|Nif3|SCP1	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 1	protein-coding
mm_39464.1	chr5	19226743	19226800	+	1	NA	promoter-TSS (NR_102342)	promoter-TSS (NR_102342)	-216	NR_102342	70832	Mm.398993	NR_102341	ENSMUSG00000097626	4921504A21Rik	-	RIKEN cDNA 4921504A21 gene	ncRNA
mm_121873.1	chr14	21038444	21038447	-	1	NA	intron (NM_018829, intron 6 of 8)	intron (NM_018829, intron 6 of 8)	13997	NM_018829	55946	Mm.376269	NM_018829	ENSMUSG00000021824	Ap3m1	1200013D09Rik|C78982|R75378	adaptor-related protein complex 3, mu 1 subunit	protein-coding
mm_90035.1	chr10	115570010	115570035	+	1	NA	promoter-TSS (NM_029982)	promoter-TSS (NM_029982)	36	NM_029982	77798	Mm.446685	NM_029982	ENSMUSG00000092210	A930009A15Rik	-	RIKEN cDNA A930009A15 gene	protein-coding
mm_141658.1	chr17	33718696	33718712	-	1	NA	promoter-TSS (NM_001252480)	promoter-TSS (NM_001252480)	-27	NR_045522	224703	Mm.311439	NM_145486	ENSMUSG00000079557	March2	9530046H09Rik|MARCH-II	membrane-associated ring finger (C3HC4) 2	protein-coding
mm_143779.1	chr17	81725592	81725595	-	1	NA	intron (NR_104580, intron 1 of 8)	Lx8|LINE|L1	12794	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_163776.1	chr13	120019187	120019192	+	1	NA	Intergenic	B2_Mm1a|SINE|B2	33015	NM_001302966	100861753	Mm.165042	NM_001302966	ENSMUSG00000095609	Gm21188	-	predicted gene, 21188	protein-coding
mm_80726.1	chr9	92542256	92542272	+	1	NA	promoter-TSS (NM_011961)	promoter-TSS (NM_011961)	41	NM_001142916	26432	Mm.79983	NM_011961	ENSMUSG00000032374	Plod2	D530025C14Rik|LH2|Plod-2	procollagen lysine, 2-oxoglutarate 5-dioxygenase 2	protein-coding
mm_112865.1	chr13	20847832	20847850	+	1	NA	intron (NM_012054, intron 3 of 20)	L1M2|LINE|L1	53728	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_162526.1	chr1	163313019	163313023	-	1	NA	5' UTR (NM_175686, exon 1 of 5)	5' UTR (NM_175686, exon 1 of 5)	629	NM_011127	18933	Mm.288642	NM_011127	ENSMUSG00000026586	Prrx1	A230024N07Rik|AA755424|AI385634|AI843499|K-2|Pmx|Pmx1|Prx1|mHox	paired related homeobox 1	protein-coding
mm_25802.1	chr3	127789224	127789247	+	1	NA	promoter-TSS (NM_145133)	promoter-TSS (NM_145133)	-678	NM_145133	211550	Mm.31852	NM_145133	ENSMUSG00000046688	Tifa	T2bp	TRAF-interacting protein with forkhead-associated domain	protein-coding
mm_165760.1	chr3	116927267	116927275	-	1	NA	exon (NM_023245, exon 6 of 8)	exon (NM_023245, exon 6 of 8)	-40996	NR_040596	74654	Mm.410820	NR_040596	ENSMUSG00000080907	4930455H04Rik	-	RIKEN cDNA 4930455H04 gene	ncRNA
mm_36161.1	chr4	59960660	59960668	-	1	NA	promoter-TSS (NM_008648)	promoter-TSS (NM_008648)	1	NM_008648	17843	Mm.457982	NM_008648	ENSMUSG00000041333	Mup4	Mup-4|Mup1	major urinary protein 4	protein-coding
mm_141534.1	chr17	31850055	31850074	-	1	NA	exon (NM_010831, exon 8 of 14)	exon (NM_010831, exon 8 of 14)	5728	NM_010831	17691	Mm.290941	NM_010831	ENSMUSG00000024042	Sik1	Msk|Sik|Snf1lk	salt inducible kinase 1	protein-coding
mm_22680.1	chr3	16183209	16183280	+	1	NA	promoter-TSS (NM_001145919)	promoter-TSS (NM_001145919)	61	NM_001145919	229096	Mm.23834	NM_172677	ENSMUSG00000047213	Ythdf3	9130022A11Rik	YTH domain family 3	protein-coding
mm_113532.1	chr13	37837628	37837666	+	1	NA	intron (NM_001039188, intron 1 of 9)	intron (NM_001039188, intron 1 of 9)	10254	NM_001039188	68750	Mm.491109	NM_026830	ENSMUSG00000039087	Rreb1	1110037N09Rik|AA414966|B930013M22Rik	ras responsive element binding protein 1	protein-coding
mm_107855.1	chr12	69538189	69538193	+	1	NA	Intergenic	Intergenic	44837	NM_001033236	207965	Mm.102487	NM_001033236	ENSMUSG00000049882	Vcpkmt	Gm71|Mettl21d|Mettl221d|VCP-KMT	valosin containing protein lysine (K) methyltransferase	protein-coding
mm_460.1	chr1	36307746	36307763	+	1	NA	promoter-TSS (NM_001290727)	promoter-TSS (NM_001290727)	21	NM_001172205	214855	Mm.34316	NM_145996	ENSMUSG00000037447	Arid5a	D430024K22Rik|Mrf1	AT rich interactive domain 5A (MRF1-like)	protein-coding
mm_29785.1	chr3	127499096	127499137	-	1	NA	promoter-TSS (NM_001327938)	promoter-TSS (NM_001327938)	-1	NM_001327938	109676	Mm.220242	NM_178655	ENSMUSG00000032826	Ank2	100043364|AI835472|AW491075|Ank-2|Gm4392	ankyrin 2, brain	protein-coding
mm_35535.1	chr4	41314798	41314802	-	1	NA	5' UTR (NM_026893, exon 1 of 9)	5' UTR (NM_026893, exon 1 of 9)	101	NM_026893	68970	Mm.28891	NM_026893	ENSMUSG00000028436	Dcaf12	1500001L20Rik|5830424K06Rik|AA420338|AI851081|Wdr40a	DDB1 and CUL4 associated factor 12	protein-coding
mm_68365.1	chr7	106814084	106814089	-	1	NA	promoter-TSS (NM_028910)	promoter-TSS (NM_028910)	-58	NM_028910	66786	Mm.159186	NM_028910	ENSMUSG00000036744	Olfr701	4932441H21Rik|4933433E02Rik|MOR283-1	olfactory receptor 701	protein-coding
mm_97781.1	chr11	82387558	82387568	+	1	NA	Intergenic	CpG	-1337	NM_001304439	270893	Mm.341593	NM_023438	ENSMUSG00000020701	Tmem132e	Gm644	transmembrane protein 132E	protein-coding
mm_93009.1	chr10	87058322	87058349	-	1	NA	intron (NM_029685, intron 1 of 5)	intron (NM_029685, intron 1 of 5)	289	NM_029685	76640	Mm.78423	NM_029685	ENSMUSG00000047129	1700113H08Rik	-	RIKEN cDNA 1700113H08 gene	protein-coding
mm_159448.1	chr3	137552622	137552622	-	1	NA	promoter-TSS (NM_177665)	promoter-TSS (NM_177665)	0	NM_177665	229862	Mm.246591	NM_177665	ENSMUSG00000055138	Gm4861	9230109N16|EG229862	predicted gene 4861	protein-coding
mm_29824.1	chr3	129678000	129678006	-	1	NA	3' UTR (NM_010113, exon 24 of 24)	3' UTR (NM_010113, exon 24 of 24)	47083	NM_001310737	13645	Mm.252481	NM_010113	ENSMUSG00000028017	Egf	AI790464	epidermal growth factor	protein-coding
mm_85769.1	chr9	108991564	108991583	-	1	NA	promoter-TSS (NM_173019)	promoter-TSS (NM_173019)	-329	NM_173019	270198	Mm.132391	NM_173019	ENSMUSG00000025648	Pfkfb4	C230090D14	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4	protein-coding
mm_42198.1	chr5	112292226	112292261	+	1	NA	intron (NM_001326590, intron 1 of 5)	intron (NM_001326590, intron 1 of 5)	15552	NM_009419	22022	Mm.250631	NM_009419	ENSMUSG00000029344	Tpst2	AI448750|D5Ucla3|Tango13b|grm|grt	protein-tyrosine sulfotransferase 2	protein-coding
mm_80856.1	chr9	98425307	98425330	+	1	NA	intron (NM_011254, intron 1 of 3)	intron (NM_011254, intron 1 of 3)	2357	NM_011254	19659	Mm.279741	NM_011254	ENSMUSG00000046402	Rbp1	CRBPI|Crbp|Rbp-1	retinol binding protein 1, cellular	protein-coding
mm_142235.1	chr17	37481144	37481168	-	1	NA	3' UTR (NM_008204, exon 4 of 4)	3' UTR (NM_008204, exon 4 of 4)	2373	NM_008204	14990	Mm.329041	NM_008204	ENSMUSG00000016283	H2-M2	H-2M2|Thy19.4	histocompatibility 2, M region locus 2	protein-coding
mm_132457.1	chr16	36103704	36103710	+	1	NA	Intergenic	Intergenic	22432	NM_001159422	381045	Mm.310434	NM_198645	ENSMUSG00000075229	Ccdc58	A930007B11Rik|AI413631	coiled-coil domain containing 58	protein-coding
mm_18663.1	chr2	70753319	70753323	-	1	NA	intron (NM_172664, intron 5 of 19)	intron (NM_172664, intron 5 of 19)	72159	NM_172664	228012	Mm.136511	NM_172664	ENSMUSG00000041997	Tlk1	4930545J15Rik	tousled-like kinase 1	protein-coding
mm_160402.1	chr8	70863486	70863486	-	1	NA	Intergenic	Intergenic	-6478	NM_032397	84036	Mm.32074	NM_032397	ENSMUSG00000002908	Kcnn1	AI854248|KCa2.1|SK1	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 1	protein-coding
mm_138811.1	chr17	39846561	39846573	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	3570	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_49577.1	chr6	30641794	30641841	+	1	NA	exon (NM_025350, exon 6 of 10)	exon (NM_025350, exon 6 of 10)	2599	NM_025350	109697	Mm.25377	NM_025350	ENSMUSG00000054446	Cpa1	0910001L12Rik|Cpa	carboxypeptidase A1, pancreatic	protein-coding
mm_6060.1	chr1	60504793	60504801	-	1	NA	intron (NM_001045513, intron 4 of 13)	intron (NM_001045513, intron 4 of 13)	61968	NM_001045513	77300	Mm.440325	NM_001045513	ENSMUSG00000026014	Raph1	9430025M21Rik|C730009O10Rik|Lpd	Ras association (RalGDS/AF-6) and pleckstrin homology domains 1	protein-coding
mm_139881.1	chr17	70756012	70756025	+	1	NA	intron (NM_001347411, intron 9 of 14)	intron (NM_001347411, intron 9 of 14)	90759	NM_001164077	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_60349.1	chr7	44358590	44358613	+	1	NA	TTS (NM_001034115)	TTS (NM_001034115)	16429	NM_027049	69349	Mm.358922	NM_027049	ENSMUSG00000008028	1700008O03Rik	-	RIKEN cDNA 1700008O03 gene	protein-coding
mm_163013.1	chr11	44658986	44659001	+	1	NA	intron (NM_007897, intron 6 of 15)	intron (NM_007897, intron 6 of 15)	40893	NM_001290710	13591	Mm.439662	NM_007897	ENSMUSG00000057098	Ebf1	Ebf|O/E-1|OE-1|Olf-1|Olf1	early B cell factor 1	protein-coding
mm_134719.1	chr16	22896569	22896599	-	1	NA	exon (NM_001276450, exon 5 of 7)	exon (NM_001276450, exon 5 of 7)	-2198	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_37876.1	chr4	132397527	132397529	-	1	NA	intron (NM_001161797, intron 2 of 12)	intron (NM_001161797, intron 2 of 12)	24918	NM_001161797	100169	Mm.158361	NM_175306	ENSMUSG00000066043	Phactr4	3110001B12Rik|AI527228|AW495572|C330013F19Rik|N28169|mKIAA4120	phosphatase and actin regulator 4	protein-coding
mm_111782.1	chr12	104473237	104473254	-	1	NA	promoter-TSS (NM_010351)	promoter-TSS (NM_010351)	-9	NM_010351	14836	Mm.129	NM_010351	ENSMUSG00000021095	Gsc	-	goosecoid homeobox	protein-coding
mm_62140.1	chr7	97098468	97098490	+	1	NA	intron (NM_001162477, intron 1 of 9)	B1_Mur2|SINE|Alu	16728	NM_010248	14389	Mm.42033	NM_010248	ENSMUSG00000004508	Gab2	AI463667|D130058I17Rik|p97	growth factor receptor bound protein 2-associated protein 2	protein-coding
mm_146687.1	chr18	12862611	12862621	-	1	NA	promoter-TSS (NM_001252492)	promoter-TSS (NM_001252492)	97	NM_001252493	64291	Mm.259470	NM_020573	ENSMUSG00000044252	Osbpl1a	G430090F17Rik|Gm753|ORP-1|Osbpl1b	oxysterol binding protein-like 1A	protein-coding
mm_90245.1	chr10	121488979	121488997	+	1	NA	Intergenic	Intergenic	-12738	NM_138956	192678	Mm.41265	NM_138956	ENSMUSG00000025795	Rassf3	AW212023|AW322379	Ras association (RalGDS/AF-6) domain family member 3	protein-coding
mm_52535.1	chr6	115887213	115887226	+	1	NA	intron (NM_001167763, intron 9 of 28)	intron (NM_001167763, intron 9 of 28)	33691	NM_031177	81896	Mm.333335	NM_031177	ENSMUSG00000030323	Ift122	C86139|Wdr10|sopb	intraflagellar transport 122	protein-coding
mm_157556.1	chrX	52052518	52052532	-	1	NA	TTS (NM_008150)	TTS (NM_008150)	-79753	NM_028851	74279	Mm.159154	NM_028851	ENSMUSG00000031118	1700080O16Rik	-	RIKEN cDNA 1700080O16 gene	protein-coding
mm_144181.1	chr18	6765283	6765297	+	1	NA	exon (NM_181070, exon 1 of 7)	exon (NM_181070, exon 1 of 7)	123	NM_001278447	19330	Mm.132802	NM_181070	ENSMUSG00000073639	Rab18	AA959686	RAB18, member RAS oncogene family	protein-coding
mm_106687.1	chr12	3350267	3350277	+	1	NA	Intergenic	MIRc|SINE|MIR	-14860	NM_008445	16570	Mm.7688	NM_008445	ENSMUSG00000020668	Kif3c	mKIAA4058	kinesin family member 3C	protein-coding
mm_43897.1	chr5	144190285	144190334	+	1	NA	promoter-TSS (NM_010800)	promoter-TSS (NM_010800)	23	NM_010800	17341	Mm.386767	NM_010800	ENSMUSG00000052271	Bhlha15	1810009C13Rik|Bhlhb8|MIST-1|Mist1	basic helix-loop-helix family, member a15	protein-coding
mm_168367.1	chr11	17221454	17221464	+	1	NA	intron (NM_178909, intron 2 of 7)	LSU-rRNA_Hsa|rRNA|rRNA	9566	NM_178909	103784	Mm.298132	NM_178909	ENSMUSG00000078970	Wdr92	AI553587|HZGJ	WD repeat domain 92	protein-coding
mm_145491.1	chr18	60389843	60389864	+	1	NA	exon (NM_001146275, exon 3 of 3)	exon (NM_001146275, exon 3 of 3)	13824	NM_001146275	60440	Mm.261140	NM_021792	ENSMUSG00000054072	Iigp1	2900074L10Rik|AI046432|AW111922|Ifgga1|Iigp|Irga6	interferon inducible GTPase 1	protein-coding
mm_50132.1	chr6	41542565	41542581	+	1	NA	Intergenic	Intergenic	20797	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_133655.1	chr16	91807363	91807384	+	1	NA	intron (NM_001110275, intron 8 of 28)	intron (NM_001110275, intron 8 of 28)	78002	NM_010587	16443	Mm.40546	NM_010587	ENSMUSG00000022957	Itsn1	AA517634|AA545208|AI316805|AI839402|AI848451|Ehsh1|Ese1|Itsn|Sh3p17	intersectin 1 (SH3 domain protein 1A)	protein-coding
mm_73184.1	chr8	95320441	95320466	+	1	NA	intron (NM_199455, intron 4 of 7)	intron (NM_199455, intron 4 of 7)	8855	NM_199455	73407	Mm.472783	NM_028532	ENSMUSG00000090206	Tepp	1700055M20Rik	testis, prostate and placenta expressed	protein-coding
mm_15568.1	chr2	158614378	158614391	+	1	NA	exon (NM_009508, exon 2 of 2)	exon (NM_009508, exon 2 of 2)	3626	NM_009508	22348	Mm.143404	NM_009508	ENSMUSG00000037771	Slc32a1	R75019|VGAT|Viaat	solute carrier family 32 (GABA vesicular transporter), member 1	protein-coding
mm_124327.1	chr14	103843474	103843484	-	1	NA	5' UTR (NM_001136061, exon 2 of 8)	5' UTR (NM_001136061, exon 2 of 8)	222	NM_007904	13618	Mm.229532	NM_007904	ENSMUSG00000022122	Ednrb	ET-B|ET-BR|ETR-b|ETb|Sox10m1	endothelin receptor type B	protein-coding
mm_151936.1	chr19	5800732	5800741	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	1936	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_137813.1	chr17	30007656	30007664	+	1	NA	intron (NM_148926, intron 1 of 4)	intron (NM_148926, intron 1 of 4)	2573	NM_148926	21769	Mm.220972	NM_148926	ENSMUSG00000044477	Zfand3	AW539211|TEG-27|Tex27	zinc finger, AN1-type domain 3	protein-coding
mm_173139.1	chrX	21334795	21334813	-	1	NA	promoter-TSS (NR_033482)	promoter-TSS (NR_033482)	-77	NR_033482	629024	Mm.391230	NR_033482	ENSMUSG00000087586	Gm6938	EG629024	predicted gene 6938	ncRNA
mm_129645.1	chr15	80565151	80565167	-	1	NA	Intergenic	Intergenic	-4689	NM_001163189	383075	Mm.297626	NM_001163189	ENSMUSG00000050439	Enthd1	Gm1242|Gm86	ENTH domain containing 1	protein-coding
mm_101191.1	chr11	18327045	18327067	-	1	NA	Intergenic	(CAT)n|Simple_repeat|Simple_repeat	231070	NR_131129	327872		NR_131129	ENSMUSG00000085453	Gm12018	OTTMUSG00000005202	predicted gene 12018	ncRNA
mm_83081.1	chr9	40032502	40032506	-	1	NA	Intergenic	Intergenic	10109	NM_146286	258283	Mm.377413	NM_146286	ENSMUSG00000046678	Olfr981	MOR223-8	olfactory receptor 981	protein-coding
mm_37057.1	chr4	116052187	116052192	-	1	NA	intron (NM_028142, intron 1 of 5)	intron (NM_028142, intron 1 of 5)	1687	NM_028142	72181	Mm.282560	NM_028142	ENSMUSG00000028706	Nsun4	2310010O12Rik|2810405F18Rik|AI507900|Shtap	NOL1/NOP2/Sun domain family, member 4	protein-coding
mm_168620.1	chr11	78248066	78248077	+	1	NA	intron (NM_009143, intron 1 of 2)	RLTR12E|LTR|ERVK	2325	NM_009143	20316	Mm.20755	NM_009143	ENSMUSG00000002064	Sdf2	AI853825	stromal cell derived factor 2	protein-coding
mm_48991.1	chr6	4756387	4756395	+	1	NA	exon (NM_130877, exon 2 of 2)	exon (NM_130877, exon 2 of 2)	9085	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_11467.1	chr2	32288318	32288353	+	1	NA	promoter-TSS (NM_133852)	promoter-TSS (NM_133852)	82	NM_001080968	99412	Mm.106376	NM_133852	ENSMUSG00000002546	Golga2	AW555139|GM130|mKIAA4150	golgi autoantigen, golgin subfamily a, 2	protein-coding
mm_113499.1	chr13	37482382	37482392	+	1	NA	Intergenic	Intergenic	137042	NM_010745	17084	Mm.2639	NM_010745	ENSMUSG00000021423	Ly86	MD-1|MD1|ly86_tv2	lymphocyte antigen 86	protein-coding
mm_116024.1	chr13	25020105	25020113	-	1	NA	exon (NM_001013389, exon 1 of 11)	exon (NM_001013389, exon 1 of 11)	208	NM_001013389	380836	Mm.387097	NM_001013389	ENSMUSG00000021339	Mrs2	Gm902|HPT|Mrs2l|RPT	MRS2 magnesium transporter	protein-coding
mm_156813.1	chrX	164090237	164090249	+	1	NA	promoter-TSS (NM_020626)	promoter-TSS (NM_020626)	56	NM_020626	57394	Mm.143766	NM_020626	ENSMUSG00000015401	Tmem27	0610008J07Rik|NX-17|NX17	transmembrane protein 27	protein-coding
mm_50109.1	chr6	41533767	41533787	+	1	NA	Intergenic	Intergenic	12001	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_49429.1	chr6	29272465	29272502	+	1	NA	promoter-TSS (NM_001190461)	promoter-TSS (NM_001190461)	-5	NM_001190461	69573	Mm.45161	NM_023516	ENSMUSG00000043421	Hilpda	2310016C08Rik|AW049004|Hig2	hypoxia inducible lipid droplet associated	protein-coding
mm_142110.1	chr17	35836002	35836033	-	1	NA	exon (NM_011655, exon 4 of 4)	exon (NM_011655, exon 4 of 4)	2284	NM_011655	22154	Mm.273538	NM_011655	ENSMUSG00000001525	Tubb5	AA408537|AI596182|B130022C14Rik|M(beta)5	tubulin, beta 5 class I	protein-coding
mm_47863.1	chr5	134614954	134615029	-	1	NA	promoter-TSS (NM_022964)	promoter-TSS (NM_022964)	34	NM_022964	56743	Mm.391375	NM_020044	ENSMUSG00000040751	Lat2	AW125574|LAB|NTAL|WSCR5|Wbscr15|Wbscr5	linker for activation of T cells family, member 2	protein-coding
mm_146210.1	chr18	76930022	76930101	+	1	NA	promoter-TSS (NM_025409)	promoter-TSS (NM_025409)	34	NM_025409	66191	Mm.28593	NM_025409	ENSMUSG00000090000	Ier3ip1	1110057H19Rik|AI644142|AL022842|AL022863|AV026606	immediate early response 3 interacting protein 1	protein-coding
mm_43772.1	chr5	141241555	141241569	+	1	NA	promoter-TSS (NM_177879)	promoter-TSS (NM_177879)	28	NM_177879	330222	Mm.151931	NM_177879	ENSMUSG00000039683	Sdk1	5330440E10|6720466O15Rik	sidekick cell adhesion molecule 1	protein-coding
mm_56634.1	chr6	113076318	113076327	-	1	NA	intron (NR_027009, intron 1 of 1)	CpG	922	NR_027010	14910	Mm.280950	NR_027008	ENSMUSG00000086429	Gt(ROSA)26Sor	AV258896|Gtrgeo26|Gtrosa26|R26|ROSA26|Thumpd3as1	gene trap ROSA 26, Philippe Soriano	ncRNA
mm_49271.1	chr6	17519700	17519730	+	1	NA	intron (NM_008591, intron 4 of 21)	intron (NM_008591, intron 4 of 21)	55758	NM_008591	17295	Mm.86844	NM_008591	ENSMUSG00000009376	Met	AI838057|HGF|HGFR|Par4|c-Met	met proto-oncogene	protein-coding
mm_55589.1	chr6	71440624	71440645	-	1	NA	promoter-TSS (NM_024288)	promoter-TSS (NM_024288)	3	NM_024288	68477	Mm.28474	NM_024288	ENSMUSG00000002222	Rmnd5a	1110007A06Rik|AJ237586|AW125795|Gid2|MTA.D02.090	required for meiotic nuclear division 5 homolog A	protein-coding
mm_50192.1	chr6	41851866	41851868	+	1	NA	exon (NM_008843, exon 4 of 4)	exon (NM_008843, exon 4 of 4)	4318	NM_008843	18716	Mm.214755	NM_008843	ENSMUSG00000058499	Pip	GCDFP-15|GP17|mSMGP	prolactin induced protein	protein-coding
mm_121994.1	chr14	26523031	26523031	-	1	NA	intron (NM_001310445, intron 1 of 22)	intron (NM_001310445, intron 1 of 22)	11593	NM_032008	83997	Mm.36769	NM_032008	ENSMUSG00000021870	Slmap	D330001L02Rik|Miranda|Slap|mKIAA1601	sarcolemma associated protein	protein-coding
mm_103650.1	chr11	78973017	78973040	-	1	NA	exon (NM_010708, exon 3 of 11)	exon (NM_010708, exon 3 of 11)	11896	NM_001159301	16859	Mm.341434	NM_010708	ENSMUSG00000001123	Lgals9	AA407335|AI194909|AI265545|LGALS35|Lgals5|gal-9|galectin-9	lectin, galactose binding, soluble 9	protein-coding
mm_114917.1	chr13	95176687	95176692	+	1	NA	intron (NM_001170669, intron 1 of 18)	intron (NM_001170669, intron 1 of 18)	46361	NM_001170669	218461	Mm.100167	NM_172263	ENSMUSG00000021684	Pde8b	B230331L10Rik|C030047E14Rik	phosphodiesterase 8B	protein-coding
mm_124901.1	chr15	10714840	10714881	+	1	NA	promoter-TSS (NM_001166408)	promoter-TSS (NM_001166408)	19	NR_045064	75259	Mm.33928	NR_045063	ENSMUSG00000097058	4930556M19Rik	1700009D01Rik|C130022M03Rik	RIKEN cDNA 4930556M19 gene	ncRNA
mm_99689.1	chr11	106066042	106066054	+	1	NA	promoter-TSS (NM_027346)	promoter-TSS (NM_027346)	-59	NM_027346	70207	Mm.343857	NM_027346	ENSMUSG00000001983	Taco1	2310066I18Rik|Ccdc44	translational activator of mitochondrially encoded cytochrome c oxidase I	protein-coding
mm_98416.1	chr11	94565040	94565056	+	1	NA	promoter-TSS (NM_007689)	promoter-TSS (NM_007689)	-26	NM_007689	12643	Mm.440523	NM_007689	ENSMUSG00000039084	Chad	SLRR4A	chondroadherin	protein-coding
mm_155840.1	chrX	101087388	101087393	+	1	NA	Intergenic	Intergenic	-1985	NM_007515	11989	Mm.5140	NM_007515	ENSMUSG00000031297	Slc7a3	Atrc3|CAT-3|CAT3|SLC7A1|SLC7A2	solute carrier family 7 (cationic amino acid transporter, y+ system), member 3	protein-coding
mm_114499.1	chr13	70028357	70028362	+	1	NA	promoter-TSS (NR_045965)	promoter-TSS (NR_045965)	-11	NR_045965	74280	Mm.273343	NR_045965	ENSMUSG00000099639	1700084F23Rik	1700003E18Rik|4930589D02Rik	RIKEN cDNA 1700084F23 gene	ncRNA
mm_54642.1	chr6	38863599	38863602	-	1	NA	intron (NM_001294144, intron 1 of 14)	intron (NM_001294144, intron 1 of 14)	12590	NM_010433	15258	Mm.23790	NM_010433	ENSMUSG00000061436	Hipk2	1110014O20Rik|B230339E18Rik|Stank	homeodomain interacting protein kinase 2	protein-coding
mm_124409.1	chr14	115477641	115477647	-	1	NA	intron (NM_175500, intron 5 of 7)	intron (NM_175500, intron 5 of 7)	-68092	NR_045761	75088	Mm.444706	NR_045761	ENSMUSG00000093551	4930505G20Rik	-	RIKEN cDNA 4930505G20 gene	ncRNA
mm_74627.1	chr8	13167888	13167916	-	1	NA	exon (NM_010684, exon 4 of 9)	exon (NM_010684, exon 4 of 9)	8741	NM_010684	16783	Mm.16716	NM_010684	ENSMUSG00000031447	Lamp1	CD107a|LGP-120|LGP-A|Lamp-1|P2B	lysosomal-associated membrane protein 1	protein-coding
mm_25822.1	chr3	127930580	127930597	+	1	NA	intron (NR_040552, intron 3 of 4)	intron (NR_040552, intron 3 of 4)	14417	NR_040552	329753	Mm.119720	NR_040552	ENSMUSG00000104763	9830132P13Rik	9830132P13	RIKEN cDNA 9830132P13 gene	ncRNA
mm_119708.1	chr14	53806498	53806520	+	1	NA	Intergenic	Intergenic	447420	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_80360.1	chr9	75221027	75221059	+	1	NA	3' UTR (NM_010864, exon 41 of 41)	3' UTR (NM_010864, exon 41 of 41)	-10971	NM_001081322	208943	Mm.41339	NM_001081322	ENSMUSG00000033590	Myo5c	9130003O20Rik|BB085560|C330029I24	myosin VC	protein-coding
mm_94913.1	chr11	29456534	29456550	+	1	NA	exon (NM_176841, exon 12 of 32)	exon (NM_176841, exon 12 of 32)	58491	NM_026465	67939	Mm.251087	NM_026465	ENSMUSG00000032673	Prorsd1	2010316F05Rik|Ncrna00117|Prdxdd1	prolyl-tRNA synthetase domain containing 1	protein-coding
mm_161245.1	chr13	98749439	98749439	-	1	NA	intron (NM_172591, intron 16 of 25)	intron (NM_172591, intron 16 of 25)	-54608	NM_001025606	380863	Mm.28264	NM_001025606	ENSMUSG00000052485	Tmem171	Gm905	transmembrane protein 171	protein-coding
mm_49197.1	chr6	15197063	15197074	+	1	NA	exon (NM_001286607, exon 2 of 17)	exon (NM_001286607, exon 2 of 17)	11562	NM_001286607	114142	Mm.332919	NM_053242	ENSMUSG00000029563	Foxp2	2810043D05Rik|AI449000|CAG-16|D0Kist7	forkhead box P2	protein-coding
mm_66150.1	chr7	31137426	31137443	-	1	NA	intron (NM_027898, intron 11 of 18)	B3A|SINE|B2	-10411	NM_011322	20266	Mm.1418	NM_011322	ENSMUSG00000019194	Scn1b	-	sodium channel, voltage-gated, type I, beta	protein-coding
mm_113312.1	chr13	30761620	30761630	+	1	NA	intron (NM_001347508, intron 8 of 8)	intron (NM_001347508, intron 8 of 8)	12392	NM_013674	16364	Mm.4677	NM_013674	ENSMUSG00000021356	Irf4	AI385587|IRF-4|LSIRF|NF-EM5|Spip	interferon regulatory factor 4	protein-coding
mm_97825.1	chr11	83039860	83039874	+	1	NA	non-coding (NR_073523, exon 1 of 5)	non-coding (NR_073523, exon 1 of 5)	175	NR_073523	237887	Mm.341645	NM_181542	ENSMUSG00000072621	Slfn10-ps	Slfn10|mFLJ00257	schlafen 10, pseudogene	pseudo
mm_112555.1	chr13	12565892	12565914	+	1	NA	promoter-TSS (NM_026184)	promoter-TSS (NM_026184)	20	NM_026184	67475	Mm.358706	NM_026184	ENSMUSG00000057069	Ero1lb	1300013B24Rik|1700065B09Rik|AI447560|Ero1b|ero1-beta	ERO1-like beta (S. cerevisiae)	protein-coding
mm_55693.1	chr6	72840991	72841001	-	1	NA	TTS (NM_019715)	TTS (NM_019715)	-51951	NM_009332	21415	Mm.440067	NM_009332	ENSMUSG00000055799	Tcf7l1	Tcf-3|Tcf3|bHLHb21	transcription factor 7 like 1 (T cell specific, HMG box)	protein-coding
mm_34544.1	chr4	149539643	149539659	+	1	NA	intron (NM_023465, intron 1 of 4)	intron (NM_023465, intron 1 of 4)	1788	NR_049189	100885828		NR_049189	ENSMUSG00000093403	Mir5616	Gm25191|mir-5616|mmu-mir-5616	microRNA 5616	ncRNA
mm_108347.1	chr12	80463205	80463257	+	1	NA	5' UTR (NM_133798, exon 1 of 9)	5' UTR (NM_133798, exon 1 of 9)	136	NM_133798	97827	Mm.206631	NM_133798	ENSMUSG00000032705	Exd2	4930539P14Rik|C85658|Exdl2	exonuclease 3'-5' domain containing 2	protein-coding
mm_166387.1	chr5	133140791	133140794	+	1	NA	Intergenic	Intergenic	-598449	NM_177047	319974	Mm.409595	NM_177047	ENSMUSG00000029673	Auts2	2700063G02Rik|A730011F23Rik|D830032G16Rik	autism susceptibility candidate 2	protein-coding
mm_147600.1	chr18	56789285	56789287	-	1	NA	intron (NM_177115, intron 3 of 4)	intron (NM_177115, intron 3 of 4)	81473	NM_010721	16906	Mm.4105	NM_010721	ENSMUSG00000024590	Lmnb1	-	lamin B1	protein-coding
mm_90816.1	chr10	7919801	7919816	-	1	NA	exon (NM_138667, exon 3 of 7)	exon (NM_138667, exon 3 of 7)	36315	NM_138667	68652	Mm.193041	NM_138667	ENSMUSG00000015755	Tab2	1110030N06Rik|A530078N03Rik|Map3k7ip2|mKIAA0733	TGF-beta activated kinase 1/MAP3K7 binding protein 2	protein-coding
mm_126700.1	chr15	85132062	85132078	+	1	NA	promoter-TSS (NM_080470)	promoter-TSS (NM_080470)	-29	NM_026357	67747	Mm.158173	NM_026357	ENSMUSG00000022431	Ribc2	4930579A10Rik|Trib	RIB43A domain with coiled-coils 2	protein-coding
mm_122340.1	chr14	37135231	37135241	-	1	NA	promoter-TSS (NM_001199122)	promoter-TSS (NM_001199122)	86	NM_078478	66092	Mm.182912	NM_078478	ENSMUSG00000041028	Ghitm	1010001P14Rik|C77840|MICS1|PTD010|Tmbim5	growth hormone inducible transmembrane protein	protein-coding
mm_139473.1	chr17	55986467	55986491	+	1	NA	promoter-TSS (NM_183178)	promoter-TSS (NM_183178)	-32	NM_183178	240121	Mm.270660	NM_183178	ENSMUSG00000011589	Fsd1	-	fibronectin type 3 and SPRY domain-containing protein	protein-coding
mm_130274.1	chr15	96698911	96698914	-	1	NA	intron (NM_175121, intron 1 of 15)	CpG	786	NM_175121	67760	Mm.46754	NM_175121	ENSMUSG00000022462	Slc38a2	5033402L14Rik|AI316867|ATA2|SAT2|mKIAA1382	solute carrier family 38, member 2	protein-coding
mm_40480.1	chr5	54053907	54053913	+	1	NA	intron (NM_001081103, intron 2 of 11)	intron (NM_001081103, intron 2 of 11)	55387	NM_001081103	116873	Mm.265985	NM_054083	ENSMUSG00000039156	Stim2	-	stromal interaction molecule 2	protein-coding
mm_172075.1	chr6	140746904	140746923	+	1	NA	Intergenic	Intergenic	120028	NM_001309436	11569	Mm.86453	NM_009637	ENSMUSG00000030232	Aebp2	AU023766|B230313N05Rik	AE binding protein 2	protein-coding
mm_83521.1	chr9	46230009	46230026	-	1	NA	exon (NM_009692, exon 4 of 4)	exon (NM_009692, exon 4 of 4)	1387	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2|apo-AI|apoA-I	apolipoprotein A-I	protein-coding
mm_50872.1	chr6	55452216	55452226	+	1	NA	5' UTR (NM_001025372, exon 1 of 16)	5' UTR (NM_001025372, exon 1 of 16)	243	NM_007407	11517	Mm.44245	NM_007407	ENSMUSG00000029778	Adcyap1r1	2900024I10Rik|AI846590|PAC1|PAC1R|PACAP1-R	adenylate cyclase activating polypeptide 1 receptor 1	protein-coding
mm_96227.1	chr11	62512421	62512426	+	1	NA	intron (NM_001039536, intron 6 of 6)	intron (NM_001039536, intron 6 of 6)	26838	NM_028448	73139	Mm.390409	NM_028448	ENSMUSG00000018509	Cenpv	3110013H01Rik|AA671303|Prr6	centromere protein V	protein-coding
mm_173212.1	chrX	73175057	73175064	-	1	NA	TTS (NM_001243002)	TTS (NM_001243002)	1929	NM_001243002	100504429	Mm.307966	NM_001243002	ENSMUSG00000079566	Spin2d	4930408F14Rik	spindlin family, member 2D	protein-coding
mm_44346.1	chr5	17782931	17782945	-	1	NA	3' UTR (NM_001159558, exon 16 of 16)	3' UTR (NM_001159558, exon 16 of 16)	52958	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_64075.1	chr7	140920897	140920911	+	1	NA	promoter-TSS (NM_133946)	promoter-TSS (NM_133946)	2	NM_133946	101613	Mm.386833	NM_133946	ENSMUSG00000038745	Nlrp6	AI504961|Avr|Nalp6|Navr|Navr/Avr|Non-AVR|Pypaf5	NLR family, pyrin domain containing 6	protein-coding
mm_15427.1	chr2	157087043	157087054	+	1	NA	promoter-TSS (NM_001177439)	promoter-TSS (NM_001177439)	-7	NM_001177439	383766	Mm.480305	NM_001177439	ENSMUSG00000074628	Tldc2	Gm1332	TBC/LysM associated domain containing 2	protein-coding
mm_53762.1	chr6	145746840	145746869	+	1	NA	Intergenic	(CCCCG)n|Simple_repeat|Simple_repeat	-61529	NM_027760	71323	Mm.158669	NM_027760	ENSMUSG00000030259	Rassf8	5133400D11Rik|AA815821|AW123240|Hoj1|mHoj-1	Ras association (RalGDS/AF-6) domain family (N-terminal) member 8	protein-coding
mm_142479.1	chr17	45686811	45686829	-	1	NA	promoter-TSS (NM_198167)	promoter-TSS (NM_198167)	448	NM_026732	68463	Mm.379158	NM_026732	ENSMUSG00000023939	Mrpl14	1110006I11Rik|AI846816|MRP-L32|Rpml32	mitochondrial ribosomal protein L14	protein-coding
mm_114128.1	chr13	55211520	55211561	+	1	NA	intron (NM_008739, intron 1 of 22)	CpG	1758	NM_008739	18193	Mm.12964	NM_008739	ENSMUSG00000021488	Nsd1	AI528500|KMT3B	nuclear receptor-binding SET-domain protein 1	protein-coding
mm_116725.1	chr13	51703150	51703162	-	1	NA	exon (NM_001281880, exon 17 of 17)	exon (NM_001281880, exon 17 of 17)	51448	NM_029279	75420	Mm.275981	NM_029279	ENSMUSG00000035139	Secisbp2	2210413N07Rik|2810012K13Rik|SBP2	SECIS binding protein 2	protein-coding
mm_52672.1	chr6	117907174	117907184	+	1	NA	promoter-TSS (NM_001166429)	intron (NM_133834, intron 1 of 3)	397	NM_133834	98758	Mm.422979	NM_133834	ENSMUSG00000042079	Hnrnpf	4833420I20Rik|AA407306|Hnrpf	heterogeneous nuclear ribonucleoprotein F	protein-coding
mm_45551.1	chr5	73131433	73131437	-	1	NA	intron (NM_028194, intron 7 of 62)	L1M4c|LINE|L1	124531	NM_173403	231290	Mm.491387	NM_173403	ENSMUSG00000029219	Slc10a4	E130304D01	solute carrier family 10 (sodium/bile acid cotransporter family), member 4	protein-coding
mm_32611.1	chr4	112232347	112232386	+	1	NA	promoter-TSS (NM_001102474)	promoter-TSS (NM_001102474)	-55	NM_001102474	195564	Mm.259652	NM_177578	ENSMUSG00000070868	Skint3	A430090E18Rik|Skint-3	selection and upkeep of intraepithelial T cells 3	protein-coding
mm_171707.1	chr4	75511584	75511584	-	1	NA	Intergenic	L1Md_F2|LINE|L1	-233298	NM_025849	66928	Mm.24332	NM_025849	ENSMUSG00000028398	Tmem261	1700027K24Rik|3110001D03Rik	transmembrane protein 261	protein-coding
mm_65332.1	chr7	24978391	24978400	-	1	NA	3' UTR (NM_001290469, exon 23 of 23)	3' UTR (NM_001290469, exon 23 of 23)	-5667	NM_010261	14470	Mm.22473	NM_010261	ENSMUSG00000003380	Rabac1	2310040I06Rik|Gbpap1|PRA1|prenylin	Rab acceptor 1 (prenylated)	protein-coding
mm_77423.1	chr8	121083086	121083153	-	1	NA	promoter-TSS (NR_045471)	promoter-TSS (NR_045471)	-9	NR_130109	68790	Mm.246916	NR_045471	ENSMUSG00000097336	Fendrr	1110050K14Rik|LL66|linc-Foxf1a|lincFoxf1	Foxf1 adjacent non-coding developmental regulatory RNA	ncRNA
mm_137700.1	chr17	29090696	29090725	+	1	NA	promoter-TSS (NM_001111099)	promoter-TSS (NM_001111099)	-269	NM_001111099	12575	Mm.195663	NM_007669	ENSMUSG00000023067	Cdkn1a	CAP20|CDKI|CIP1|Cdkn1|P21|SDI1|Waf1|mda6|p21Cip1|p21WAF	cyclin-dependent kinase inhibitor 1A (P21)	protein-coding
mm_85268.1	chr9	99436471	99436533	-	1	NA	5' UTR (NM_008624, exon 1 of 6)	5' UTR (NM_008624, exon 1 of 6)	210	NM_008624	17532	Mm.2045	NM_008624	ENSMUSG00000032470	Mras	2900078C09Rik|AI326250	muscle and microspikes RAS	protein-coding
mm_137634.1	chr17	28329443	28329486	+	1	NA	exon (NM_011287, exon 4 of 6)	exon (NM_011287, exon 4 of 6)	993	NM_011287	19896	Mm.336955	NM_011287	ENSMUSG00000037805	Rpl10a	CsA-19|Nedd6	ribosomal protein L10A	protein-coding
mm_121506.1	chr14	121939125	121939134	+	1	NA	intron (NM_026861, intron 4 of 8)	intron (NM_026861, intron 4 of 8)	-23355	NM_182806	110168	Mm.37405	NM_182806	ENSMUSG00000050350	Gpr18	-	G protein-coupled receptor 18	protein-coding
mm_99664.1	chr11	105922947	105922958	+	1	NA	exon (NM_181071, exon 26 of 26)	exon (NM_181071, exon 26 of 26)	21195	NM_007805	13056	Mm.149403	NM_007805	ENSMUSG00000019590	Cyb561	-	cytochrome b-561	protein-coding
mm_56696.1	chr6	114659195	114659196	-	1	NA	intron (NM_001253718, intron 2 of 19)	MT2B1|LTR|ERVL	16098	NM_001253717	74244	Mm.275332	NM_028835	ENSMUSG00000030314	Atg7	1810013K23Rik|Agp7|Apg7l|Atg7l|Gm21553	autophagy related 7	protein-coding
mm_103161.1	chr11	70455195	70455211	-	1	NA	3' UTR (NM_023158, exon 5 of 5)	3' UTR (NM_023158, exon 5 of 5)	3272	NM_025397	66172	Mm.46424	NM_025397	ENSMUSG00000018923	Med11	1110030J09Rik|AI465144|AW545069	mediator complex subunit 11	protein-coding
mm_103086.1	chr11	69917700	69917734	-	1	NA	exon (NM_001166592, exon 5 of 7)	exon (NM_001166592, exon 5 of 7)	2913	NM_001166590	276770	Mm.18026	NM_181582	ENSMUSG00000078812	Eif5a	AA410058|D19Wsu54e|Eif4d|Eif5a1|eIF-4D|eIF-5A|eIF-5A-1|eIF-5A1	eukaryotic translation initiation factor 5A	protein-coding
mm_80769.1	chr9	95559916	95559960	+	1	NA	5' UTR (NM_198414, exon 1 of 1)	5' UTR (NM_198414, exon 1 of 1)	121	NM_198414	75552	Mm.151485	NM_198414	ENSMUSG00000064225	Paqr9	1700020G04Rik	progestin and adipoQ receptor family member IX	protein-coding
mm_16919.1	chr2	13574553	13574569	-	1	NA	exon (NM_011701, exon 1 of 9)	exon (NM_011701, exon 1 of 9)	250	NM_011701	22352	Mm.268000	NM_011701	ENSMUSG00000026728	Vim	-	vimentin	protein-coding
mm_90083.1	chr10	116808799	116808811	+	1	NA	intron (NM_001033333, intron 13 of 24)	ORR1B2|LTR|ERVL-MaLR	79552	NR_131036	75878	Mm.370607	NR_131036		4930579P08Rik	-	RIKEN cDNA 4930579P08 gene	ncRNA
mm_111973.1	chr12	110019957	110019964	-	1	NA	Intergenic	Intergenic	138113	NR_045466	67280	Mm.390495	NR_045466		3110009F21Rik	-	RIKEN cDNA 3110009F21 gene	ncRNA
mm_115486.1	chr13	3610983	3610998	-	1	NA	5' UTR (NM_134063, exon 1 of 20)	5' UTR (NM_134063, exon 1 of 20)	118	NM_134063	105203	Mm.221609	NM_134063	ENSMUSG00000033799	Fam208b	AI645998|Pap20|mKIAA2006	family with sequence similarity 208, member B	protein-coding
mm_158742.1	chrX	164250377	164250382	-	1	NA	intron (NM_009759, intron 1 of 18)	intron (NM_009759, intron 1 of 18)	7814	NM_009759	12169	Mm.504	NM_009759	ENSMUSG00000031377	Bmx	Etk|Etk/Bmx|Tyro8	BMX non-receptor tyrosine kinase	protein-coding
mm_75023.1	chr8	31168748	31168769	-	1	NA	promoter-TSS (NM_026453)	promoter-TSS (NM_026453)	-34	NM_026453	67920	Mm.289818	NM_026453	ENSMUSG00000031578	Mak16	2600016B03Rik|AI314911|Rbm13	MAK16 homolog	protein-coding
mm_132571.1	chr16	38143297	38143312	+	1	NA	intron (NM_001347232, intron 1 of 11)	intron (NM_001347232, intron 1 of 11)	-54044	NR_033221	414072	Mm.483602	NR_033221		BC031361	-	cDNA sequence BC031361	ncRNA
mm_107320.1	chr12	31390811	31390823	+	1	NA	Intergenic	L2a|LINE|L2	-39346	NM_007861	13382	Mm.3131	NM_007861	ENSMUSG00000020664	Dld	-	dihydrolipoamide dehydrogenase	protein-coding
mm_22227.1	chr2	174428731	174428743	-	1	NA	exon (NM_022325, exon 5 of 6)	exon (NM_022325, exon 5 of 6)	10302	NM_022325	64138	Mm.156919	NM_022325	ENSMUSG00000016256	Ctsz	AI787083|AU019819|CTSX|D2Wsu143e	cathepsin Z	protein-coding
mm_140412.1	chr17	87648343	87648345	+	1	NA	intron (NM_008532, intron 8 of 9)	intron (NM_008532, intron 8 of 9)	12365	NM_008532	17075	Mm.4259	NM_008532	ENSMUSG00000045394	Epcam	CD326|EGP|EGP-2|Egp314|Ep-CAM|EpCAM1|GA733-2|Ly74|TROP1|Tacsd1|Tacstd1|gp40	epithelial cell adhesion molecule	protein-coding
mm_160294.1	chr7	130728655	130728655	+	1	NA	exon (NM_021314, exon 3 of 18)	exon (NM_021314, exon 3 of 18)	36099	NM_021314	57752	Mm.86322	NM_021314	ENSMUSG00000030852	Tacc2	mKIAA4180	transforming, acidic coiled-coil containing protein 2	protein-coding
mm_150377.1	chr19	36083697	36083736	+	1	NA	promoter-TSS (NM_019428)	promoter-TSS (NM_019428)	0	NM_019428	54364	Mm.277891	NM_019428	ENSMUSG00000024800	Rpp30	Rnasep2|TSG15	ribonuclease P/MRP 30 subunit	protein-coding
mm_89113.1	chr10	84652601	84652601	+	1	NA	intron (NM_027423, intron 10 of 27)	intron (NM_027423, intron 10 of 27)	30164	NM_027423	70428	Mm.335007	NM_027423	ENSMUSG00000034453	Polr3b	2700078H01Rik|A330032P03Rik|C85372|RPC2	polymerase (RNA) III (DNA directed) polypeptide B	protein-coding
mm_124625.1	chr15	3291107	3291145	+	1	NA	intron (NM_001166063, intron 5 of 8)	(CA)n|Simple_repeat|Simple_repeat	12400	NM_001166063	100039139	Mm.455610	NM_001166063	ENSMUSG00000091119	Ccdc152	ENSMUSG00000071814	coiled-coil domain containing 152	protein-coding
mm_112791.1	chr13	20185417	20185427	+	1	NA	5' UTR (NM_080288, exon 2 of 22)	5' UTR (NM_080288, exon 2 of 22)	94915	NM_080288	140580	Mm.342392	NM_080288	ENSMUSG00000041112	Elmo1	6330578D22Rik|C230095H21Rik|CED-12	engulfment and cell motility 1	protein-coding
mm_80633.1	chr9	89211234	89211253	+	1	NA	promoter-TSS (NM_026829)	promoter-TSS (NM_026829)	53	NM_026829	107885	Mm.486274	NM_026829	ENSMUSG00000066442	Mthfs	1110034I12Rik|2310020H23Rik|AI119695	5, 10-methenyltetrahydrofolate synthetase	protein-coding
mm_137447.1	chr17	26532896	26532900	+	1	NA	Intergenic	Intergenic	-24426	NM_013642	19252	Mm.239041	NM_013642	ENSMUSG00000024190	Dusp1	3CH134|MKP1|Ptpn16|U19515|erp|mkp-1	dual specificity phosphatase 1	protein-coding
mm_99500.1	chr11	102925273	102925288	+	1	NA	promoter-TSS (NM_197959)	promoter-TSS (NM_197959)	-156	NM_197959	70218	Mm.32084	NM_197959	ENSMUSG00000051378	Kif18b	3000004C01Rik	kinesin family member 18B	protein-coding
mm_154500.1	chrM	11746	11761	-	1	NA	NA	Intergenic	NA	NA								
mm_163888.1	chr14	25869643	25869647	+	1	NA	intron (NM_013469, intron 2 of 14)	intron (NM_013469, intron 2 of 14)	27490	NM_013469	11744	Mm.294083	NM_013469	ENSMUSG00000021866	Anxa11	A830099O17Rik|Anx11	annexin A11	protein-coding
mm_86162.1	chr9	118467062	118467065	-	1	NA	Intergenic	U4|snRNA|snRNA	-11126	NM_001164789	13813	Mm.200692	NM_010136	ENSMUSG00000032446	Eomes	C77258|TBR-2|Tbr2	eomesodermin	protein-coding
mm_43522.1	chr5	137151984	137152002	+	1	NA	Intergenic	Intergenic	-35786	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_170112.1	chr17	39845435	39845436	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	2438	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_158963.1	chr1	92619787	92619787	+	1	NA	promoter-TSS (NM_206896)	promoter-TSS (NM_206896)	-94	NM_206896	257890	Mm.337259	NM_206896	ENSMUSG00000061616	Olfr12	MOR208-5	olfactory receptor 12	protein-coding
mm_67154.1	chr7	73539261	73539273	-	1	NA	TTS (NR_037569)	TTS (NR_037569)	2479	NM_001081345	244059	Mm.34539	NM_001081345	ENSMUSG00000078671	Chd2	2810013C04Rik|2810040A01Rik|5630401D06Rik|AI851092|BC029703|CHD-2	chromodomain helicase DNA binding protein 2	protein-coding
mm_20514.1	chr2	130642823	130642844	-	1	NA	promoter-TSS (NM_001291028)	promoter-TSS (NM_001291028)	11	NM_197945	241638	Mm.440130	NM_197945	ENSMUSG00000037703	Lzts3	Prosapip1	leucine zipper, putative tumor suppressor family member 3	protein-coding
mm_155845.1	chrX	101260173	101260179	+	1	NA	3' UTR (NM_018789, exon 3 of 3)	3' UTR (NM_018789, exon 3 of 3)	3816	NM_001033362	245536	Mm.212463	NM_001033362	ENSMUSG00000090141	Gm614	-	predicted gene 614	protein-coding
mm_49793.1	chr6	35252693	35252717	+	1	NA	promoter-TSS (NR_015608)	promoter-TSS (NR_015608)	6	NR_015608	67705	Mm.228046	NR_015608	ENSMUSG00000073155	1810058I24Rik	AI414869|AI848234	RIKEN cDNA 1810058I24 gene	ncRNA
mm_55200.1	chr6	52204388	52204408	-	1	NA	5' UTR (NM_010453, exon 1 of 2)	5' UTR (NM_010453, exon 1 of 2)	189	NM_010453	15402	Mm.173	NM_010453	ENSMUSG00000038253	Hoxa5	Hox-1.3	homeobox A5	protein-coding
mm_112485.1	chr13	5871601	5871609	+	1	NA	Intergenic	Intergenic	10116	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_109146.1	chr12	107157337	107157372	+	1	NA	Intergenic	B3|SINE|B2	-441030	NR_015512	71033	Mm.159404	NR_015512	ENSMUSG00000085820	4933406K04Rik	4930426M03Rik|4930485I22Rik|4933427G14Rik	RIKEN cDNA 4933406K04 gene	ncRNA
mm_109629.1	chr12	112767516	112767543	+	1	NA	exon (NM_178911, exon 8 of 11)	exon (NM_178911, exon 8 of 11)	6874	NM_178911	104759	Mm.203915	NM_178911	ENSMUSG00000052160	Pld4	AI132321|thss	phospholipase D family, member 4	protein-coding
mm_1423.1	chr1	67174365	67174373	+	1	NA	exon (NM_001080809, exon 19 of 38)	exon (NM_001080809, exon 19 of 38)	51342	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_142546.1	chr17	46556205	46556220	-	1	NA	promoter-TSS (NM_020493)	promoter-TSS (NM_020493)	-50	NM_020493	20807	Mm.45044	NM_020493	ENSMUSG00000015605	Srf	AW049942|AW240594	serum response factor	protein-coding
mm_85627.1	chr9	107616180	107616218	-	1	NA	exon (NM_008138, exon 7 of 9)	exon (NM_008138, exon 7 of 9)	-6958	NM_001291539	20347	Mm.4083	NM_009153	ENSMUSG00000057969	Sema3b	SemA|Semaa|sema5|semaV	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B	protein-coding
mm_80319.1	chr9	74866497	74866511	+	1	NA	intron (NM_008262, intron 1 of 1)	intron (NM_008262, intron 1 of 1)	4583	NM_008262	15379	Mm.303355	NM_008262	ENSMUSG00000043013	Onecut1	D9Ertd423e|HNF-6|Hfh12|Hnf6|Hnf6b|OC-1|Oc1	one cut domain, family member 1	protein-coding
mm_48645.1	chr5	145805863	145805876	-	1	NA	promoter-TSS (NM_177380)	promoter-TSS (NM_177380)	5	NM_177380	337924	Mm.425301	NM_177380	ENSMUSG00000054417	Cyp3a44	-	cytochrome P450, family 3, subfamily a, polypeptide 44	protein-coding
mm_127175.1	chr15	98934627	98934689	+	1	NA	promoter-TSS (NM_011654)	promoter-TSS (NM_011654)	-268	NM_011654	22143	Mm.392113	NM_011654	ENSMUSG00000023004	Tuba1b	Tuba2	tubulin, alpha 1B	protein-coding
mm_60257.1	chr7	43797545	43797566	+	1	NA	promoter-TSS (NM_008940)	promoter-TSS (NM_008940)	-22	NM_001324398	259277	Mm.458023	NM_008940	ENSMUSG00000064023	Klk8	BSP1|NP|Nrpn|Prss19	kallikrein related-peptidase 8	protein-coding
mm_142429.1	chr17	45569620	45569647	-	1	NA	exon (NM_008302, exon 7 of 11)	exon (NM_008302, exon 7 of 11)	3628	NM_008302	15516	Mm.2180	NM_008302	ENSMUSG00000023944	Hsp90ab1	90kDa|AL022974|C81438|Hsp84|Hsp84-1|Hsp90|Hspcb	heat shock protein 90 alpha (cytosolic), class B member 1	protein-coding
mm_8623.1	chr1	156270689	156270699	-	1	NA	exon (NM_001277730, exon 13 of 18)	exon (NM_001277730, exon 13 of 18)	32654	NM_001134741	214575	Mm.252800	NM_001134741	ENSMUSG00000060985	Tdrd5	Gm103	tudor domain containing 5	protein-coding
mm_121584.1	chr14	4948114	4948116	-	1	NA	Intergenic	RLTR1F_Mm|LTR|ERVK	76959	NM_001242945	100041306	Mm.396155	NM_001242945	ENSMUSG00000094132	Gm3264	-	predicted gene 3264	protein-coding
mm_99031.1	chr11	98944200	98944243	+	1	NA	intron (NM_001177303, intron 1 of 8)	intron (NM_001177303, intron 1 of 8)	4510	NM_001177303	19401	Mm.439744	NM_009024	ENSMUSG00000037992	Rara	Nr1b1|RAR|RARalpha1	retinoic acid receptor, alpha	protein-coding
mm_139458.1	chr17	55952792	55952796	+	1	NA	5' UTR (NM_015766, exon 1 of 5)	5' UTR (NM_015766, exon 1 of 5)	171	NM_015766	50498	Mm.256798	NM_015766	ENSMUSG00000003206	Ebi3	EBI-3|IL-27	Epstein-Barr virus induced gene 3	protein-coding
mm_29312.1	chr3	107986398	107986399	-	1	NA	promoter-TSS (NM_008183)	promoter-TSS (NM_008183)	38	NM_008183	14863	Mm.440086	NM_008183	ENSMUSG00000040562	Gstm2	Gstb-2|Gstb2	glutathione S-transferase, mu 2	protein-coding
mm_66002.1	chr7	30562742	30562770	-	1	NA	promoter-TSS (NM_170760)	promoter-TSS (NM_170760)	428	NM_025498	66340	Mm.86557	NM_025498	ENSMUSG00000036835	Psenen	1700023M09Rik|Pen-2	presenilin enhancer gamma secretase subunit	protein-coding
mm_37934.1	chr4	132922548	132922563	-	1	NA	promoter-TSS (NM_145553)	promoter-TSS (NM_145553)	-4	NM_001163792	230789	Mm.11473	NM_145553	ENSMUSG00000028878	Fam76a	-	family with sequence similarity 76, member A	protein-coding
mm_12878.1	chr2	84678397	84678450	+	1	NA	promoter-TSS (NM_001290751)	promoter-TSS (NM_001290751)	21	NM_025885	381379	Mm.219643	NM_025885	ENSMUSG00000027080	Med19	2410018M14Rik|3110040A13Rik|LCMR1	mediator complex subunit 19	protein-coding
mm_104290.1	chr11	90388208	90388237	-	1	NA	intron (NM_172563, intron 1 of 3)	intron (NM_172563, intron 1 of 3)	2695	NM_172563	217082	Mm.158903	NM_172563	ENSMUSG00000003949	Hlf	E230015K02Rik	hepatic leukemia factor	protein-coding
mm_75282.1	chr8	41016750	41016767	-	1	NA	promoter-TSS (NR_015457)	promoter-TSS (NR_015457)	-710	NR_015457	78849	Mm.440930	NR_015457	ENSMUSG00000084960	B430010I23Rik	-	RIKEN cDNA B430010I23 gene	ncRNA
mm_17453.1	chr2	28556113	28556121	-	1	NA	exon (NM_009885, exon 11 of 11)	exon (NM_009885, exon 11 of 11)	7286	NM_009885	12613	Mm.236017	NM_009885	ENSMUSG00000026818	Cel	1810036E18Rik|BAL	carboxyl ester lipase	protein-coding
mm_120770.1	chr14	73552752	73552776	+	1	NA	promoter-TSS (NM_011506)	promoter-TSS (NM_011506)	-22	NM_011506	20916	Mm.38951	NM_011506	ENSMUSG00000022110	Sucla2	4930547K18Rik|A-SCS	succinate-Coenzyme A ligase, ADP-forming, beta subunit	protein-coding
mm_63537.1	chr7	127989088	127989100	+	1	NA	Intergenic	B3A|SINE|B2	4773	NM_023258	66824	Mm.24163	NM_023258	ENSMUSG00000030793	Pycard	9130417A21Rik|Asc|CARD5|TMS-1|TNS1|masc	PYD and CARD domain containing	protein-coding
mm_105551.1	chr11	106388067	106388105	-	1	NA	Intergenic	Intergenic	-5305	NM_010494	15896	Mm.394	NM_010494	ENSMUSG00000001029	Icam2	CD102|Icam-2|Ly-60	intercellular adhesion molecule 2	protein-coding
mm_70897.1	chr8	25601563	25601574	+	1	NA	promoter-TSS (NM_001308482)	promoter-TSS (NM_001308482)	-33	NM_001308481	234135	Mm.217337	NM_001001735	ENSMUSG00000054823	Whsc1l1	6720429E03|A530023P05|AI528490|NSD3|WHISTLE	Wolf-Hirschhorn syndrome candidate 1-like 1 (human)	protein-coding
mm_110700.1	chr12	69228168	69228184	-	1	NA	promoter-TSS (NM_011133)	promoter-TSS (NM_011133)	14	NM_011133	18974	Mm.9199	NM_011133	ENSMUSG00000020974	Pole2	-	polymerase (DNA directed), epsilon 2 (p59 subunit)	protein-coding
mm_132596.1	chr16	38458888	38458911	+	1	NA	promoter-TSS (NM_009855)	promoter-TSS (NM_009855)	-34	NM_009855	12519	Mm.89474	NM_009855	ENSMUSG00000075122	Cd80	B71|Cd28l|Ly-53|Ly53|MIC17|TSA1	CD80 antigen	protein-coding
mm_50545.1	chr6	49046259	49046271	+	1	NA	intron (NM_053110, intron 4 of 10)	intron (NM_053110, intron 4 of 10)	9747	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_117314.1	chr13	67609635	67609664	-	1	NA	promoter-TSS (NM_001163246)	promoter-TSS (NM_001163246)	58	NM_001163246	100416706	Mm.478045	NM_001163246	ENSMUSG00000058093	Zfp729b	AA987127	zinc finger protein 729b	protein-coding
mm_95306.1	chr11	46222603	46222626	+	1	NA	exon (NM_001252459, exon 25 of 31)	exon (NM_001252459, exon 25 of 31)	-9521	NR_105955	102465598		NR_105955	ENSMUSG00000099230	Mir6989	Gm27885|mmu-mir-6989	microRNA 6989	ncRNA
mm_159575.1	chr4	116877488	116877488	+	1	NA	promoter-TSS (NM_001029912)	promoter-TSS (NM_001029912)	86	NM_001029912	74464	Mm.218946	NM_001029912	ENSMUSG00000033948	Zswim5	4933426E21Rik|AI503093|mKIAA1511	zinc finger SWIM-type containing 5	protein-coding
mm_11330.1	chr2	30441979	30442004	+	1	NA	intron (NM_138748, intron 8 of 9)	intron (NM_138748, intron 8 of 9)	25941	NM_138748	110854	Mm.275393	NM_138748	ENSMUSG00000039515	Ptpa	2610042B21Rik|C77440|N28142|PR53|Ppp2r4	protein phosphatase 2 protein activator	protein-coding
mm_102545.1	chr11	61296571	61296573	-	1	NA	Intergenic	RMER21B|LTR|ERV1	-29044	NR_138545	11671	Mm.398221	NM_007437	ENSMUSG00000010025	Aldh3a2	AI194803|Ahd-3|Ahd-3r|Ahd3|Ahd3-r|Aldh4|Aldh4-r|FALDH	aldehyde dehydrogenase family 3, subfamily A2	protein-coding
mm_100493.1	chr11	120467656	120467719	+	1	NA	promoter-TSS (NM_008244)	promoter-TSS (NM_008244)	52	NM_001159328	15239	Mm.7919	NM_008244	ENSMUSG00000025793	Hgs	Hgr|Hrs|ZFYVE8|tn	HGF-regulated tyrosine kinase substrate	protein-coding
mm_155236.1	chrX	57212059	57212069	+	1	NA	promoter-TSS (NM_011616)	promoter-TSS (NM_011616)	-79	NM_011616	21947	Mm.4861	NM_011616	ENSMUSG00000031132	Cd40lg	CD154|CD40-L|Cd40l|HIGM1|IGM|IMD3|Ly-62|Ly62|T-BAM|TRAP|Tnfsf5|Tnlg8b|gp39	CD40 ligand	protein-coding
mm_8051.1	chr1	135373469	135373483	-	1	NA	intron (NM_175259, intron 2 of 4)	intron (NM_175259, intron 2 of 4)	1587	NM_175259	77552	Mm.41407	NM_175259	ENSMUSG00000041889	Shisa4	9330132O05Rik|Tmem58|mShisa4	shisa family member 4	protein-coding
mm_46748.1	chr5	111594241	111594249	-	1	NA	Intergenic	L1MD1|LINE|L1	12684	NR_015546	330164	Mm.193276	NM_177875	ENSMUSG00000052848	C130026L21Rik	-	RIKEN cDNA C130026L21 gene	ncRNA
mm_114440.1	chr13	66007874	66007883	+	1	NA	Intergenic	Intergenic	-105575	NM_001177832	628709	Mm.390595	NM_001177832	ENSMUSG00000095909	Gm10324	ENSMUSG00000071302	predicted gene 10324	protein-coding
mm_112950.1	chr13	21041199	21041235	+	1	NA	Intergenic	Lx10|LINE|L1	32082	NM_146535	258528	Mm.377554	NM_146535	ENSMUSG00000042869	Olfr1370	MOR256-14	olfactory receptor 1370	protein-coding
mm_74420.1	chr8	3625542	3625548	-	1	NA	promoter-TSS (NM_001129804)	promoter-TSS (NM_001129804)	0	NM_001129803	18545	Mm.440882	NM_008790	ENSMUSG00000004630	Pcp2	L7|Pcp-2	Purkinje cell protein 2 (L7)	protein-coding
mm_60964.1	chr7	47727356	47727359	+	1	NA	Intergenic	Intergenic	-125985	NM_153067	233222	Mm.240142	NM_153067	ENSMUSG00000078698	Mrgpra3	Mrga3	MAS-related GPR, member A3	protein-coding
mm_55303.1	chr6	54934460	54934475	-	1	NA	exon (NM_172729, exon 8 of 12)	exon (NM_172729, exon 8 of 12)	37194	NM_001171007	107607	Mm.28498	NM_172729	ENSMUSG00000038058	Nod1	C230079P11|Card4|F830007N14Rik|Nlrc1	nucleotide-binding oligomerization domain containing 1	protein-coding
mm_118619.1	chr14	21076137	21076147	+	1	NA	promoter-TSS (NM_001243041)	promoter-TSS (NM_001243041)	-10	NM_001243041	11534	Mm.188734	NM_134079	ENSMUSG00000039197	Adk	2310026J05Rik|5033405D03Rik|AI255373|AI987814|Ak	adenosine kinase	protein-coding
mm_108081.1	chr12	73961083	73961088	+	1	NA	Intergenic	Intergenic	-3445	NM_178392	75627	Mm.25937	NM_178392	ENSMUSG00000021113	Snapc1	2700033G17Rik|AU015787	small nuclear RNA activating complex, polypeptide 1	protein-coding
mm_28002.1	chr3	83008666	83008702	-	1	NA	exon (NM_133862, exon 4 of 10)	exon (NM_133862, exon 4 of 10)	960	NM_001317105	99571	Mm.16422	NM_133862	ENSMUSG00000033860	Fgg	3010002H13Rik|AI256424	fibrinogen gamma chain	protein-coding
mm_129473.1	chr15	78710775	78710793	-	1	NA	intron (NM_183141, intron 1 of 1)	intron (NM_183141, intron 1 of 1)	7329	NM_183141	207393	Mm.323188	NM_183141	ENSMUSG00000043460	Elfn2	6330514E13|AW048948|BC094219|Lrrc62|Ppp1r29	leucine rich repeat and fibronectin type III, extracellular 2	protein-coding
mm_68841.1	chr7	126355953	126355971	-	1	NA	Intergenic	Intergenic	12083	NR_106025	102466797		NR_106025	ENSMUSG00000099017	Mir7058	Gm27766|mmu-mir-7058	microRNA 7058	ncRNA
mm_75522.1	chr8	56474417	56474425	-	1	NA	intron (NR_131020, intron 1 of 2)	RMER17C2|LTR|ERVK	10547	NR_131020	75123	Mm.72666	NR_131020	ENSMUSG00000110310	4930518J21Rik	-	RIKEN cDNA 4930518J21 gene	ncRNA
mm_65996.1	chr7	30554778	30554830	-	1	NA	TTS (NM_001290569)	TTS (NM_001290569)	1502	NM_001012401	243912	Mm.34885	NM_001012401	ENSMUSG00000036854	Hspb6	AA387366|Gm479|Hsp20	heat shock protein, alpha-crystallin-related, B6	protein-coding
mm_79158.1	chr9	47810082	47810093	+	1	NA	exon (NM_018770, exon 6 of 10)	exon (NM_018770, exon 6 of 10)	8121	NR_046048	100038460	Mm.447649	NR_046048		Gm10677	ENSMUSG00000074363	predicted gene 10677	ncRNA
mm_95323.1	chr11	46479984	46479995	+	1	NA	3' UTR (NM_134250, exon 7 of 7)	3' UTR (NM_134250, exon 7 of 7)	25058	NM_134250	171285	Mm.72168	NM_134250	ENSMUSG00000020399	Havcr2	TIM-3|Tim3|Timd3	hepatitis A virus cellular receptor 2	protein-coding
mm_86289.1	chr9	121915176	121915184	-	1	NA	exon (NM_010012, exon 1 of 1)	exon (NM_010012, exon 1 of 1)	1125	NM_010012	13124	Mm.20889	NM_010012	ENSMUSG00000050445	Cyp8b1	-	cytochrome P450, family 8, subfamily b, polypeptide 1	protein-coding
mm_43649.1	chr5	138280493	138280504	+	1	NA	promoter-TSS (NM_016964)	promoter-TSS (NM_016964)	-11	NM_016964	50878	Mm.285609	NM_016964	ENSMUSG00000036928	Stag3	SA-2	stromal antigen 3	protein-coding
mm_122634.1	chr14	51145909	51145923	-	1	NA	5' UTR (NM_011271, exon 2 of 2)	5' UTR (NM_011271, exon 2 of 2)	851	NM_011271	19752	Mm.235538	NM_011271	ENSMUSG00000035896	Rnase1	AI574248|Rib-1|Rib1	ribonuclease, RNase A family, 1 (pancreatic)	protein-coding
mm_131180.1	chr16	7149768	7149795	+	1	NA	intron (NM_183188, intron 1 of 12)	intron (NM_183188, intron 1 of 12)	79946	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_128031.1	chr15	25363699	25363709	-	1	NA	3' UTR (NM_027395, exon 2 of 2)	3' UTR (NM_027395, exon 2 of 2)	50060	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	brain abundant, membrane attached signal protein 1	protein-coding
mm_171692.1	chr4	65990180	65990193	-	1	NA	intron (NM_019514, intron 5 of 21)	L1Md_T|LINE|L1	385200	NM_001161782	69807	Mm.22786	NM_053084	ENSMUSG00000051675	Trim32	1810045E12Rik|3f3|BBS11|Zfp117	tripartite motif-containing 32	protein-coding
mm_134833.1	chr16	26106195	26106202	-	1	NA	promoter-TSS (NM_173379)	promoter-TSS (NM_173379)	-414	NM_173379	210530	Mm.326869	NM_173379	ENSMUSG00000038168	P3h2	4832416N06|AW553532|Leprel1|Mlat4	prolyl 3-hydroxylase 2	protein-coding
mm_112571.1	chr13	13590317	13590338	+	1	NA	promoter-TSS (NM_010748)	promoter-TSS (NM_010748)	-82	NM_010748	17101	Mm.342337	NM_010748	ENSMUSG00000019726	Lyst	D13Sfk13|beige|bg	lysosomal trafficking regulator	protein-coding
mm_59657.1	chr7	28180227	28180266	+	1	NA	promoter-TSS (NM_001271370)	promoter-TSS (NM_001271370)	-70	NM_001271370	13549	Mm.57249	NM_010092	ENSMUSG00000002409	Dyrk1b	Mirk	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1b	protein-coding
mm_127441.1	chr15	101270397	101270426	+	1	NA	exon (NM_010444, exon 2 of 7)	exon (NM_010444, exon 2 of 7)	3565	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_124008.1	chr14	76104762	76104765	-	1	NA	intron (NM_026177, intron 3 of 7)	Lx7|LINE|L1	6052	NM_026177	67467	Mm.260767	NM_026177	ENSMUSG00000022008	Gpalpp1	1200011I18Rik|Kiaa1704	GPALPP motifs containing 1	protein-coding
mm_81867.1	chr9	119035019	119035020	+	1	NA	intron (NM_133710, intron 6 of 7)	intron (NM_133710, intron 6 of 7)	3223	NR_029742	387218		NR_029742	ENSMUSG00000065513	Mir26a-1	Mirn26a|Mirn26a-1|miR-26a|mir-26a-1	microRNA 26a-1	ncRNA
mm_113062.1	chr13	23739829	23739935	+	1	NA	TTS (NM_015786)	TTS (NM_015786)	1075	NM_015786	50708	Mm.193539	NM_015786	ENSMUSG00000036181	Hist1h1c	0610008C09Rik|H1.2|H1c|H1f2|H1var1|His1a	histone cluster 1, H1c	protein-coding
mm_88659.1	chr10	79996543	79996551	+	1	NA	intron (NR_038088, intron 1 of 4)	intron (NR_038088, intron 1 of 4)	-1061	NM_001347081	27403	Mm.103351	NM_013850	ENSMUSG00000035722	Abca7	ABCX|Abc51	ATP-binding cassette, sub-family A (ABC1), member 7	protein-coding
mm_152042.1	chr19	6128209	6128289	-	1	NA	promoter-TSS (NM_026912)	promoter-TSS (NM_026912)	-34	NM_026912	69024	Mm.329629	NM_026912	ENSMUSG00000024787	Snx15	1500032B08Rik|E130013C21Rik	sorting nexin 15	protein-coding
mm_85312.1	chr9	101187782	101187785	-	1	NA	intron (NM_001161362, intron 3 of 13)	intron (NM_001161362, intron 3 of 13)	11290	NM_172144	235542	Mm.335386	NM_172144	ENSMUSG00000043154	Ppp2r3a	3222402P14Rik|A730042E07	protein phosphatase 2, regulatory subunit B'', alpha	protein-coding
mm_127043.1	chr15	96641668	96641747	+	1	NA	5' UTR (NM_134086, exon 1 of 16)	5' UTR (NM_134086, exon 1 of 16)	255	NM_134086	105727	Mm.103568	NM_134086	ENSMUSG00000023169	Slc38a1	AA408026|AA409865|AL022800|AU015942|NAT2	solute carrier family 38, member 1	protein-coding
mm_123907.1	chr14	73322437	73322452	-	1	NA	intron (NM_009029, intron 1 of 26)	intron (NM_009029, intron 1 of 26)	3347	NM_009029	19645	Mm.273862	NM_009029	ENSMUSG00000022105	Rb1	Rb|Rb-1|pRb	retinoblastoma 1	protein-coding
mm_47051.1	chr5	116083290	116083297	-	1	NA	promoter-TSS (NM_001101546)	promoter-TSS (NM_001101546)	-47	NM_001101546	545798	Mm.483995	NM_001101546	ENSMUSG00000079278	Tmem233	DSPB2|Gm13843|OTTMUSG00000014722	transmembrane protein 233	protein-coding
mm_79010.1	chr9	45500345	45500356	+	1	NA	intron (NM_001081270, intron 3 of 32)	intron (NM_001081270, intron 3 of 32)	-69118	NR_040732	74602	Mm.394117	NR_040732	ENSMUSG00000097074	4833428L15Rik	-	RIKEN cDNA 4833428L15 gene	ncRNA
mm_88693.1	chr10	80141554	80141575	+	1	NA	promoter-TSS (NM_025313)	promoter-TSS (NM_025313)	-711	NM_001347092	66043	Mm.278560	NM_025313	ENSMUSG00000003072	Atp5d	0610008F14Rik|1500000I11Rik|AA960090|AI876556|AU020773|C85518	ATP synthase, H+ transporting, mitochondrial F1 complex, delta subunit	protein-coding
mm_55054.1	chr6	49046336	49046408	-	1	NA	intron (NM_053110, intron 4 of 10)	RLTR20A4|LTR|ERVK	9854	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_171498.1	chr4	146224754	146224765	-	1	NA	Intergenic	CpG	-45626	NM_001083918	666532	Mm.392861	NM_001083918	ENSMUSG00000067916	Zfp991	Gm13139|OTTMUSG00000010657	zinc finger protein 991	protein-coding
mm_136242.1	chr16	90934764	90934779	-	1	NA	promoter-TSS (NM_026502)	promoter-TSS (NM_026502)	78	NM_026502	68001	Mm.45374	NM_026502	ENSMUSG00000022972	1110004E09Rik	-	RIKEN cDNA 1110004E09 gene	protein-coding
mm_96359.1	chr11	67064751	67064771	+	1	NA	3' UTR (NM_001040026, exon 6 of 6)	3' UTR (NM_001040026, exon 6 of 6)	12091	NM_001040026	52892	Mm.129731	NM_001040026	ENSMUSG00000069844	Sco1	2610001C07Rik|D11Bwg1310e	SCO1 cytochrome c oxidase assembly protein	protein-coding
mm_13739.1	chr2	118114685	118114716	+	1	NA	exon (NM_011580, exon 5 of 22)	exon (NM_011580, exon 5 of 22)	2824	NM_001313914	21825	Mm.4159	NM_011580	ENSMUSG00000040152	Thbs1	TSP-1|TSP1|Thbs-1|tbsp1	thrombospondin 1	protein-coding
mm_85702.1	chr9	108110777	108110790	-	1	NA	exon (NM_007567, exon 5 of 12)	exon (NM_007567, exon 5 of 12)	-16303	NM_146226	235606	Mm.219639	NM_146226	ENSMUSG00000032590	Apeh	-	acylpeptide hydrolase	protein-coding
mm_8856.1	chr1	162714377	162714384	-	1	NA	exon (NM_001081290, exon 10 of 35)	exon (NM_001081290, exon 10 of 35)	26176	NM_001081290	226562	Mm.245446	NM_001081290	ENSMUSG00000040225	Prrc2c	1810043M20Rik|9630039I18Rik|A630006J20|Bat2d|Bat2d1|Bat2l2|E130112L15Rik|Prrc3|mKIAA1096	proline-rich coiled-coil 2C	protein-coding
mm_72655.1	chr8	84842740	84842785	+	1	NA	exon (NM_007591, exon 9 of 9)	exon (NM_007591, exon 9 of 9)	-2097	NM_009010	19358	Mm.255539	NM_009010	ENSMUSG00000003813	Rad23a	2310040P19Rik|AL024030|HR23A|mHR23A	RAD23 homolog A, nucleotide excision repair protein	protein-coding
mm_152372.1	chr19	10203881	10203948	-	1	NA	promoter-TSS (NM_001271614)	promoter-TSS (NM_001271614)	29	NM_007999	14156	Mm.2952	NM_007999	ENSMUSG00000024742	Fen1	AW538437|FEN-1	flap structure specific endonuclease 1	protein-coding
mm_26535.1	chr3	146121656	146121683	+	1	NA	promoter-TSS (NM_134160)	promoter-TSS (NM_134160)	-122	NM_134160	171166	Mm.114683	NM_134160	ENSMUSG00000036853	Mcoln3	6720490O21Rik|TRPML3|Va	mucolipin 3	protein-coding
mm_92980.1	chr10	86693479	86693509	-	1	NA	exon (NM_011631, exon 14 of 18)	exon (NM_011631, exon 14 of 18)	7967	NR_015572	66263	Mm.392261	NR_015572		1810014B01Rik	-	RIKEN cDNA 1810014B01 gene	pseudo
mm_171566.1	chr4	147305624	147305624	+	1	NA	intron (NM_001039209, intron 1 of 2)	intron (NM_001039209, intron 1 of 2)	129758	NM_001039209	195531	Mm.270762	NM_001039209	ENSMUSG00000078496	Zfp982	Gm13152|OTTMUSG00000010671	zinc finger protein 982	protein-coding
mm_129744.1	chr15	82244375	82244426	-	1	NA	promoter-TSS (NM_001080158)	promoter-TSS (NM_001080158)	-64	NM_001080158	66570	Mm.23596	NM_025639	ENSMUSG00000068101	Cenpm	2610019I03Rik|AI853711|Pane1	centromere protein M	protein-coding
mm_149299.1	chr19	10699366	10699376	+	1	NA	intron (NM_181403, intron 1 of 4)	intron (NM_181403, intron 1 of 4)	10556	NM_181403	107305	Mm.19091	NM_181403	ENSMUSG00000048832	Vps37c	5730409F24Rik|AU042646	vacuolar protein sorting 37C	protein-coding
mm_168119.1	chr10	18023106	18023108	-	1	NA	5' UTR (NM_028440, exon 1 of 3)	5' UTR (NM_028440, exon 1 of 3)	145	NM_028440	73112	Mm.276041	NM_028440	ENSMUSG00000078453	Abracl	1700028I04Rik|3110003A17Rik	ABRA C-terminal like	protein-coding
mm_161466.1	chr15	78305625	78305625	-	1	NA	promoter-TSS (NM_007781)	promoter-TSS (NM_007781)	96	NM_007781	12984	Mm.1940	NM_007781	ENSMUSG00000071714	Csf2rb2	AIC2A|BetaIl3|Bil3|Csfgmrb|Il3r|Il3rb|Il3rb2	colony stimulating factor 2 receptor, beta 2, low-affinity (granulocyte-macrophage)	protein-coding
mm_81404.1	chr9	109051091	109051104	+	1	NA	intron (NM_025858, intron 2 of 5)	L1M3|LINE|L1	-3769	NM_026381	66940	Mm.196533	NM_025858	ENSMUSG00000025647	Shisa5	2310008D10Rik|6430628I05Rik|Scotin|mShisa5	shisa family member 5	protein-coding
mm_113890.1	chr13	49190353	49190358	+	1	NA	intron (NM_013610, intron 1 of 3)	intron (NM_013610, intron 1 of 3)	2808	NM_013610	18081	Mm.18503	NM_013610	ENSMUSG00000037966	Ninj1	AU024536	ninjurin 1	protein-coding
mm_69107.1	chr7	127021167	127021189	-	1	NA	promoter-TSS (NM_001102563)	promoter-TSS (NM_001102563)	33	NM_001102563	69017	Mm.392047	NM_001102563	ENSMUSG00000045114	Prrt2	1500031I19Rik|AI195361|DSPB3	proline-rich transmembrane protein 2	protein-coding
mm_25397.1	chr3	107230609	107230617	+	1	NA	promoter-TSS (NM_001256174)	promoter-TSS (NM_001256174)	-1	NM_001256174	319929	Mm.30453	NM_001256174	ENSMUSG00000094613	A630076J17Rik	-	RIKEN cDNA A630076J17 gene	protein-coding
mm_145843.1	chr18	65448175	65448200	+	1	NA	exon (NM_172833, exon 5 of 16)	exon (NM_172833, exon 5 of 16)	17190	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_156516.1	chrX	150566602	150566629	+	1	NA	exon (NM_009653, exon 10 of 11)	exon (NM_009653, exon 10 of 11)	-19170	NR_106147	102465782		NR_106147	ENSMUSG00000099172	Mir3620	Gm27984|mmu-mir-3620	microRNA 3620	ncRNA
mm_72011.1	chr8	70703479	70703499	+	1	NA	Intergenic	Intergenic	5750	NM_001286944	16478	Mm.419851	NM_010592	ENSMUSG00000071076	Jund	Jund1	jun D proto-oncogene	protein-coding
mm_150626.1	chr19	41336987	41336997	+	1	NA	intron (NM_031376, intron 2 of 16)	intron (NM_031376, intron 2 of 16)	48078	NM_031376	83490	Mm.222266	NM_031376	ENSMUSG00000025017	Pik3ap1	1810044J04Rik|BCAP	phosphoinositide-3-kinase adaptor protein 1	protein-coding
mm_143366.1	chr17	67354499	67354520	-	1	NA	promoter-TSS (NM_008984)	promoter-TSS (NM_008984)	-50	NM_008984	19274	Mm.311809	NM_008984	ENSMUSG00000033278	Ptprm	RPTPmu|mKIAA4044	protein tyrosine phosphatase, receptor type, M	protein-coding
mm_170115.1	chr17	39845688	39845689	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	2691	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_32983.1	chr4	120136253	120136269	+	1	NA	TTS (NM_010657)	TTS (NM_010657)	-24945	NM_007902	13615	Mm.284855	NM_007902	ENSMUSG00000028635	Edn2	ET-2|PPET2|VIC	endothelin 2	protein-coding
mm_160279.1	chr7	121391879	121391879	+	1	NA	promoter-TSS (NM_001081327)	promoter-TSS (NM_001081327)	-417	NM_001081327	195646	Mm.247449	NM_177575	ENSMUSG00000046321	Hs3st2	6430516N12Rik|A830061E14Rik|AW491345	heparan sulfate (glucosamine) 3-O-sulfotransferase 2	protein-coding
mm_135370.1	chr16	44065360	44065379	-	1	NA	Intergenic	MLT1F|LTR|ERVL-MaLR	-37424	NM_001172107	207798	Mm.19316	NM_153528	ENSMUSG00000036292	Gramd1c	4921521N14Rik	GRAM domain containing 1C	protein-coding
mm_152187.1	chr19	7432495	7432512	-	1	NA	exon (NM_053076, exon 3 of 7)	exon (NM_053076, exon 3 of 7)	9930	NR_105957	102466781		NR_105957	ENSMUSG00000098293	Mir6991	Gm27966|mmu-mir-6991	microRNA 6991	ncRNA
mm_101419.1	chr11	29526344	29526379	-	1	NA	promoter-TSS (NM_001282119)	promoter-TSS (NM_001282119)	-36	NM_001282120	76784	Mm.285429	NM_133767	ENSMUSG00000020459	Mtif2	2310038D14Rik|2410112O06Rik|IF-2(Mt)|IF-2mt|IF2(mt)	mitochondrial translational initiation factor 2	protein-coding
mm_48543.1	chr5	142905407	142905418	-	1	NA	exon (NM_007393, exon 3 of 6)	exon (NM_007393, exon 3 of 6)	1342	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_7157.1	chr1	91458274	91458289	-	1	NA	intron (NM_011066, intron 1 of 22)	intron (NM_011066, intron 1 of 22)	1047	NM_011066	18627	Mm.482463	NM_011066	ENSMUSG00000055866	Per2	mKIAA0347|mPer2	period circadian clock 2	protein-coding
mm_55224.1	chr6	52233484	52233487	-	1	NA	intron (NM_001122950, intron 1 of 1)	CpG	1454	NM_008263	15395	Mm.5	NM_008263	ENSMUSG00000000938	Hoxa10	Hox-1.8|Hoxa-10	homeobox A10	protein-coding
mm_131219.1	chr16	8839527	8839529	+	1	NA	intron (NM_001081400, intron 2 of 3)	B1F1|SINE|Alu	9428	NM_001081400	69053	Mm.390868	NM_001081400	ENSMUSG00000022507	1810013L24Rik	1110017P05Rik|3010002C02Rik|AA792997|AW124177|Gm19906|R74903	RIKEN cDNA 1810013L24 gene	protein-coding
mm_168136.1	chr10	29699349	29699353	-	1	NA	Intergenic	CpG	-163484	NM_028351	72780	Mm.45191	NM_028351	ENSMUSG00000019880	Rspo3	2810459H04Rik|AW742308|Cristin1|Thsd2	R-spondin 3	protein-coding
mm_135740.1	chr16	55838828	55838853	-	1	NA	promoter-TSS (NM_030612)	promoter-TSS (NM_030612)	-199	NM_001159395	80859	Mm.247272	NM_030612	ENSMUSG00000035356	Nfkbiz	AA408868|INAP|Mail	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, zeta	protein-coding
mm_166564.1	chr6	48747664	48747679	-	1	NA	intron (NM_175035, intron 1 of 2)	intron (NM_175035, intron 1 of 2)	1474	NM_175035	317757	Mm.455917	NM_175035	ENSMUSG00000043505	Gimap5	D630024P16|E230026N22Rik	GTPase, IMAP family member 5	protein-coding
mm_112390.1	chr12	119238486	119238494	-	1	NA	promoter-TSS (NM_177290)	promoter-TSS (NM_177290)	-214	NM_177290	320910	Mm.217000	NM_177290	ENSMUSG00000025321	Itgb8	4832412O06Rik	integrin beta 8	protein-coding
mm_109200.1	chr12	108652946	108652975	+	1	NA	exon (NM_007965, exon 3 of 13)	exon (NM_007965, exon 3 of 13)	-5660	NR_029771	723909		NR_029771	ENSMUSG00000065436	Mir342	Mirn342|mmu-mir-342	microRNA 342	ncRNA
mm_81798.1	chr9	115311167	115311169	+	1	NA	promoter-TSS (NM_024222)	promoter-TSS (NM_024222)	-747	NM_024222	68292	Mm.296158	NM_024222	ENSMUSG00000032437	Stt3b	1300006C19Rik|Simp	STT3, subunit of the oligosaccharyltransferase complex, homolog B (S. cerevisiae)	protein-coding
mm_10600.1	chr2	18698971	18698977	+	1	NA	promoter-TSS (NM_001001334)	promoter-TSS (NM_001001334)	-48	NM_001001334	381350	Mm.330024	NM_001001334	ENSMUSG00000037708	Spag6	Spag6l	sperm associated antigen 6	protein-coding
mm_19901.1	chr2	114147043	114147054	-	1	NA	intron (NM_001290788, intron 12 of 33)	intron (NM_001290788, intron 12 of 33)	3522	NR_105968	102465982		NR_105968	ENSMUSG00000098464	Mir7002	Gm27429|mmu-mir-7002	microRNA 7002	ncRNA
mm_151804.1	chr19	5424907	5425026	-	1	NA	promoter-TSS (NM_024176)	promoter-TSS (NM_024176)	13	NM_024176	66556	Mm.275446	NM_024176	ENSMUSG00000024914	Drap1	2310074H19Rik|NC2-alpha	Dr1 associated protein 1 (negative cofactor 2 alpha)	protein-coding
mm_26290.1	chr3	142506817	142506832	+	1	NA	exon (NM_153564, exon 8 of 11)	exon (NM_153564, exon 8 of 11)	9890	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_72604.1	chr8	84416550	84416555	+	1	NA	intron (NM_001252061, intron 1 of 46)	intron (NM_001252061, intron 1 of 46)	1188	NM_001252061	12286	Mm.334658	NM_007578	ENSMUSG00000034656	Cacna1a	APCA|BI|Caca1a|Cacnl1a4|Cav2.1|Ccha1a|EA2|FHM|HPCA|MHP|MHP1|SCA6|alpha1A|la|nmf352|rkr|smrl|tg	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	protein-coding
mm_140341.1	chr17	86823691	86823705	+	1	NA	exon (NM_010137, exon 8 of 16)	exon (NM_010137, exon 8 of 16)	69834	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_5721.1	chr1	44102342	44102344	-	1	NA	promoter-TSS (NM_029368)	promoter-TSS (NM_029368)	45	NM_029368	75623	Mm.348017	NM_029368	ENSMUSG00000026049	Tex30	1700029F09Rik|3110030D08Rik	testis expressed 30	protein-coding
mm_23455.1	chr3	60472221	60472233	+	1	NA	promoter-TSS (NM_001253713)	promoter-TSS (NM_001253713)	-603	NM_001253713	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_94431.1	chr11	6292054	6292067	+	1	NA	promoter-TSS (NM_001252288)	promoter-TSS (NM_001252288)	463	NM_001252283	18293	Mm.276348	NM_010956	ENSMUSG00000020456	Ogdh	2210403E04Rik|2210412K19Rik|AA409584|d1401|mKIAA4192	oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)	protein-coding
mm_55545.1	chr6	70951295	70951302	-	1	NA	Intergenic	Intergenic	-5308	NM_001101464	232077	Mm.297656	NM_001101464	ENSMUSG00000055874	Foxi3	-	forkhead box I3	protein-coding
mm_63961.1	chr7	139943814	139943875	+	1	NA	promoter-TSS (NM_009482)	promoter-TSS (NM_009482)	-12	NM_009482	22286	Mm.10205	NM_009482	ENSMUSG00000047751	Utf1	AI505934	undifferentiated embryonic cell transcription factor 1	protein-coding
mm_45061.1	chr5	41844233	41844329	-	1	NA	promoter-TSS (NM_001081422)	promoter-TSS (NM_001081422)	34	NM_001310601	665775	Mm.158726	NM_001081422	ENSMUSG00000061755	Bod1l	A230054D04Rik|AI853319|FAM44A|mKIAA1327	biorientation of chromosomes in cell division 1-like	protein-coding
mm_74866.1	chr8	24955230	24955235	-	1	NA	intron (NM_001270996, intron 21 of 21)	intron (NM_001270996, intron 21 of 21)	-6428	NM_153397	353188	Mm.269223	NM_153397	ENSMUSG00000037437	Adam32	-	a disintegrin and metallopeptidase domain 32	protein-coding
mm_45769.1	chr5	86917468	86917483	-	1	NA	3' UTR (NM_152811, exon 6 of 6)	3' UTR (NM_152811, exon 6 of 6)	9028	NM_152811	71773	Mm.26741	NM_152811	ENSMUSG00000035836	Ugt2b1	1300012D20Rik	UDP glucuronosyltransferase 2 family, polypeptide B1	protein-coding
mm_149943.1	chr19	27321760	27321763	+	1	NA	promoter-TSS (NM_183179)	promoter-TSS (NM_183179)	-858	NM_183179	240595	Mm.269759	NM_183179	ENSMUSG00000047298	Kcnv2	KV11.1	potassium channel, subfamily V, member 2	protein-coding
mm_104099.1	chr11	86695327	86695347	-	1	NA	3' UTR (NM_001003908, exon 32 of 32)	3' UTR (NM_001003908, exon 32 of 32)	11256	NM_001098810	217057	Mm.24868	NM_175004	ENSMUSG00000072582	Ptrh2	A230072I16Rik|Bit1|CGI-147	peptidyl-tRNA hydrolase 2	protein-coding
mm_34711.1	chr4	152116393	152116402	+	1	NA	promoter-TSS (NM_033042)	promoter-TSS (NM_033042)	54	NM_033042	85030	Mm.101198	NM_033042	ENSMUSG00000024793	Tnfrsf25	APO-3|DDR3|DR3|LARD|TR3|TRAMP|Tnfrsf12|WSL-1|WSL-LR|Wsl	tumor necrosis factor receptor superfamily, member 25	protein-coding
mm_9134.1	chr1	170845788	170845800	-	1	NA	intron (NM_001081304, intron 4 of 15)	intron (NM_001081304, intron 4 of 15)	21977	NM_001081304	226641	Mm.377046	NM_001081304	ENSMUSG00000026663	Atf6	9130025P16Rik|9630036G24|AA789574|Atf6alpha|ESTM49	activating transcription factor 6	protein-coding
mm_21.1	chr1	5094137	5094140	+	1	NA	intron (NM_001310442, intron 4 of 12)	intron (NM_001310442, intron 4 of 12)	11052	NM_001310442	108664	Mm.27082	NM_133826	ENSMUSG00000033793	Atp6v1h	0710001F19Rik|AU022349|CGI-11|SFD|SFDalpha|SFDbeta|VMA13	ATPase, H+ transporting, lysosomal V1 subunit H	protein-coding
mm_62984.1	chr7	120203973	120203985	+	1	NA	promoter-TSS (NM_026458)	promoter-TSS (NM_026458)	15	NM_026458	67928	Mm.158178	NM_026458	ENSMUSG00000062017	Abca14	1700110B15Rik|4930539G24Rik	ATP-binding cassette, sub-family A (ABC1), member 14	protein-coding
mm_22659.1	chr3	14871701	14871705	+	1	NA	3' UTR (NM_007606, exon 7 of 7)	3' UTR (NM_007606, exon 7 of 7)	8165	NM_007606	12350	Mm.300	NM_007606	ENSMUSG00000027559	Car3	BB219044|Ca3|Car-3	carbonic anhydrase 3	protein-coding
mm_135943.1	chr16	74411416	74411430	-	1	NA	promoter-TSS (NM_175549)	promoter-TSS (NM_175549)	-511	NM_175549	268902	Mm.171736	NM_175549	ENSMUSG00000052516	Robo2	2600013A04Rik|9430089E08Rik|BB097918|D230004I22Rik|mKIAA1568	roundabout guidance receptor 2	protein-coding
mm_59865.1	chr7	30184161	30184181	+	1	NA	promoter-TSS (NM_009944)	promoter-TSS (NM_009944)	0	NM_009944	12865	Mm.423030	NM_009944	ENSMUSG00000074218	Cox7a1	COX7A|COX7AH|COX7AM	cytochrome c oxidase subunit VIIa 1	protein-coding
mm_146919.1	chr18	31609894	31609927	-	1	NA	promoter-TSS (NM_026165)	promoter-TSS (NM_026165)	-8	NM_026165	67453	Mm.23896	NM_026165	ENSMUSG00000024259	Slc25a46	1200007B05Rik|AI325987	solute carrier family 25, member 46	protein-coding
mm_9527.1	chr1	173782986	173782994	-	1	NA	Intergenic	Intergenic	-16071	NM_008329	15951	Mm.261270	NM_008329	ENSMUSG00000073489	Ifi204	Ifi16|p204	interferon activated gene 204	protein-coding
mm_154659.1	chrX	7842068	7842128	+	1	NA	promoter-TSS (NM_001290537)	promoter-TSS (NM_001290537)	16	NM_001290537	54644	Mm.142827	NM_138604	ENSMUSG00000031154	Otud5	AA407879|AI553596|BB114028|DUBA|DXImx46e|Sfc7	OTU domain containing 5	protein-coding
mm_49361.1	chr6	22875523	22875537	+	1	NA	promoter-TSS (NM_001311064)	promoter-TSS (NM_001311064)	28	NM_001081306	19283	Mm.41639	NM_011219	ENSMUSG00000068748	Ptprz1	AI850339|DSD-1-PG|PTPbeta|PTPzeta|Ptprz|Ptpz|R-PTP-zeta|RPTPz|Rptpbeta	protein tyrosine phosphatase, receptor type Z, polypeptide 1	protein-coding
mm_90827.1	chr10	7956064	7956147	-	1	NA	promoter-TSS (NM_138667)	promoter-TSS (NM_138667)	18	NM_138667	68652	Mm.193041	NM_138667	ENSMUSG00000015755	Tab2	1110030N06Rik|A530078N03Rik|Map3k7ip2|mKIAA0733	TGF-beta activated kinase 1/MAP3K7 binding protein 2	protein-coding
mm_59004.1	chr7	19181212	19181221	+	1	NA	promoter-TSS (NR_029763)	promoter-TSS (NR_029763)	46	NM_028153	72205	Mm.154121	NM_028153	ENSMUSG00000040811	Eml2	1600029N02Rik|EMAP-2	echinoderm microtubule associated protein like 2	protein-coding
mm_169148.1	chr13	62558622	62558641	-	1	NA	promoter-TSS (NM_001162911)	promoter-TSS (NM_001162911)	-32	NM_001162911	77117	Mm.470091	NM_175252	ENSMUSG00000074865	Zfp934	6720457D02Rik	zinc finger protein 934	protein-coding
mm_166677.1	chr6	97827314	97827316	+	1	NA	intron (NM_001113198, intron 1 of 9)	intron (NM_001113198, intron 1 of 9)	20257	NM_001113198	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_58430.1	chr7	3297507	3297527	+	1	NA	exon (NM_016969, exon 3 of 3)	exon (NM_016969, exon 3 of 3)	4489	NM_001093766	50918	Mm.29874	NM_016969	ENSMUSG00000068566	Myadm	D7Wsu62e	myeloid-associated differentiation marker	protein-coding
mm_42989.1	chr5	123310500	123310522	+	1	NA	Intergenic	Intergenic	-33937	NM_029850	77045	Mm.151960	NM_029850	ENSMUSG00000029438	Bcl7a	4432415N06Rik|AI448316	B cell CLL/lymphoma 7A	protein-coding
mm_158363.1	chrX	134806650	134806681	-	1	NA	exon (NM_001166397, exon 6 of 6)	exon (NM_001166397, exon 6 of 6)	2556	NM_001166397	67416	Mm.285969	NM_026139	ENSMUSG00000033436	Armcx2	3230401N03Rik|AI043003|ALEX2	armadillo repeat containing, X-linked 2	protein-coding
mm_115398.1	chr13	113794647	113794671	+	1	NA	exon (NM_172595, exon 1 of 5)	exon (NM_172595, exon 1 of 5)	151	NM_172595	218639	Mm.79837	NM_172595	ENSMUSG00000042348	Arl15	A430036I03|Arfrp2|C230032K13Rik	ADP-ribosylation factor-like 15	protein-coding
mm_129700.1	chr15	81697257	81697298	-	1	NA	promoter-TSS (NM_001164320)	promoter-TSS (NM_001164320)	10	NM_001164320	214685	Mm.393287	NM_001164320	ENSMUSG00000063765	Chadl	AY100452|D930017K21Rik	chondroadherin-like	protein-coding
mm_140733.1	chr17	15564323	15564359	-	1	NA	Intergenic	CpG	-1018	NM_144809	213389	Mm.215162	NM_144809	ENSMUSG00000051977	Prdm9	BC012016|Dsbc1|G1-419-29|Meisetz|PRDM9-B|Rcr1|repro7	PR domain containing 9	protein-coding
mm_137993.1	chr17	33638090	33638110	+	1	NA	promoter-TSS (NR_028279)	promoter-TSS (NR_028279)	5	NR_028279	378460	Mm.272606	NM_001002842	ENSMUSG00000032739	Pram1	AY665714	PML-RAR alpha-regulated adaptor molecule 1	protein-coding
mm_83827.1	chr9	53975353	53975363	-	1	NA	promoter-TSS (NM_177769)	promoter-TSS (NM_177769)	-57	NM_177769	270162	Mm.259791	NM_177769	ENSMUSG00000041986	Elmod1	4831417L10|AI428506|AI834991	ELMO/CED-12 domain containing 1	protein-coding
mm_112675.1	chr13	16027621	16027642	+	1	NA	3' UTR (NM_008380, exon 5 of 5)	3' UTR (NM_008380, exon 5 of 5)	15780	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_83324.1	chr9	44196494	44196515	-	1	NA	intron (NM_007619, intron 2 of 15)	L1MB5|LINE|L1	37542	NM_007619	12402	Mm.266871	NM_007619	ENSMUSG00000034342	Cbl	4732447J05Rik|Cbl-2|c-Cbl|cbl	Casitas B-lineage lymphoma	protein-coding
mm_74749.1	chr8	19026559	19026573	-	1	NA	promoter-TSS (NM_183036)	promoter-TSS (NM_183036)	-37	NM_183036	360212	Mm.271558	NM_183036	ENSMUSG00000053790	Defb38	BD-38	defensin beta 38	protein-coding
mm_106445.1	chr11	119863411	119863457	-	1	NA	intron (NM_028898, intron 20 of 33)	intron (NM_028898, intron 20 of 33)	-18855	NR_039557	100628577		NR_039557	ENSMUSG00000093061	Mir5098	mmu-mir-5098|mu-mir-5098	microRNA 5098	ncRNA
mm_9982.1	chr1	191239600	191239608	-	1	NA	Intergenic	Intergenic	-56271	NM_007498	11910	Mm.2706	NM_007498	ENSMUSG00000026628	Atf3	LRG-21	activating transcription factor 3	protein-coding
mm_144832.1	chr18	36366564	36366587	+	1	NA	exon (NM_001081365, exon 2 of 3)	exon (NM_001081365, exon 2 of 3)	17951	NM_001081365	66060	Mm.272527	NM_001081365	ENSMUSG00000046727	Cystm1	0610010O12Rik	cysteine-rich transmembrane module containing 1	protein-coding
mm_147098.1	chr18	35654342	35654349	-	1	NA	exon (NM_001270646, exon 1 of 1)	exon (NM_001270646, exon 1 of 1)	854	NM_001270646	381148	Mm.297784	NM_001270646	ENSMUSG00000073600	Prob1	Gm1614	proline rich basic protein 1	protein-coding
mm_113659.1	chr13	42681562	42681564	+	1	NA	intron (NM_001302635, intron 1 of 13)	intron (NM_001302635, intron 1 of 13)	764	NM_001302635	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding
mm_72010.1	chr8	70703436	70703473	+	1	NA	Intergenic	Intergenic	5715	NM_001286944	16478	Mm.419851	NM_010592	ENSMUSG00000071076	Jund	Jund1	jun D proto-oncogene	protein-coding
mm_74593.1	chr8	11557992	11557997	-	1	NA	promoter-TSS (NM_001302459)	promoter-TSS (NM_001302459)	-416	NM_001302459	26356	Mm.25709	NM_011919	ENSMUSG00000045969	Ing1	2610028J21Rik|AA407184|AI875420|mING1h|p33Ing1|p37Ing1b	inhibitor of growth family, member 1	protein-coding
mm_128558.1	chr15	55906918	55906957	-	1	NA	promoter-TSS (NM_016667)	promoter-TSS (NM_016667)	12	NM_016667	20649	Mm.309425	NM_016667	ENSMUSG00000060429	Sntb1	-	syntrophin, basic 1	protein-coding
mm_24339.1	chr3	89735690	89735716	+	1	NA	exon (NM_001146296, exon 2 of 15)	exon (NM_001146296, exon 2 of 15)	4985	NM_019655	56417	Mm.316628	NM_019655	ENSMUSG00000027951	Adar	AV242451|Adar1|Adar1p110|Adar1p150|mZaADAR	adenosine deaminase, RNA-specific	protein-coding
mm_99733.1	chr11	106306031	106306040	+	1	NA	Intergenic	Intergenic	-4139	NM_008117	14599	Mm.343934	NM_008117	ENSMUSG00000020713	Gh	Gh1|Ghb1	growth hormone	protein-coding
mm_35095.1	chr4	8673721	8673729	-	1	NA	Intergenic	Intergenic	-16681	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_31884.1	chr4	82065925	82065935	+	1	NA	non-coding (NR_040659, exon 1 of 3)	non-coding (NR_040659, exon 1 of 3)	550	NR_040659	545641	Mm.216028	NR_040659	ENSMUSG00000085022	Gm5860	EG545641	predicted gene 5860	ncRNA
mm_134366.1	chr16	17111205	17111255	-	1	NA	promoter-TSS (NM_144954)	promoter-TSS (NM_144954)	22	NM_001252445	66053	Mm.253614	NM_144954	ENSMUSG00000022771	Ppil2	0610009L05Rik|1700016N17Rik|4921520K19Rik|4930511F14Rik|AA589416|C130078A06Rik|CYC4	peptidylprolyl isomerase (cyclophilin)-like 2	protein-coding
mm_3152.1	chr1	135154402	135154451	+	1	NA	exon (NM_026823, exon 5 of 7)	exon (NM_026823, exon 5 of 7)	7592	NM_026823	68724	Mm.174998	NM_026823	ENSMUSG00000026426	Arl8a	1110033P22Rik|Arl10b|gie2	ADP-ribosylation factor-like 8A	protein-coding
mm_53545.1	chr6	136827800	136827811	+	1	NA	intron (NM_021714, intron 1 of 11)	CpG	411	NM_021714	60321	Mm.141197	NM_021714	ENSMUSG00000030216	Wbp11	2510026P17Rik|D6Wsu113e|Npwbp|SIPP1	WW domain binding protein 11	protein-coding
mm_37581.1	chr4	126325642	126325653	-	1	NA	promoter-TSS (NM_011902)	promoter-TSS (NM_011902)	-448	NM_011902	24084	Mm.23895	NM_011902	ENSMUSG00000028845	Tekt2	AU014974|tektin-t	tektin 2	protein-coding
mm_31071.1	chr4	41355867	41355872	+	1	NA	intron (NM_023305, intron 1 of 6)	B3|SINE|B2	6873	NM_023305	67123	Mm.289795	NM_023305	ENSMUSG00000028437	Ubap1	2700092A01Rik|NAG20|UBAP-1|Ubap	ubiquitin-associated protein 1	protein-coding
mm_8917.1	chr1	163313662	163313677	-	1	NA	promoter-TSS (NM_175686)	promoter-TSS (NM_175686)	-19	NM_175686	18933	Mm.288642	NM_011127	ENSMUSG00000026586	Prrx1	A230024N07Rik|AA755424|AI385634|AI843499|K-2|Pmx|Pmx1|Prx1|mHox	paired related homeobox 1	protein-coding
mm_72624.1	chr8	84650366	84650373	+	1	NA	Intergenic	Intergenic	12483	NM_010499	15936	Mm.399	NM_010499	ENSMUSG00000053560	Ier2	AI317238|Ch1|Pip92	immediate early response 2	protein-coding
mm_30924.1	chr4	32750692	32750695	+	1	NA	intron (NM_001081392, intron 80 of 101)	intron (NM_001081392, intron 80 of 101)	-49566	NM_175364	108755	Mm.1182	NM_175364	ENSMUSG00000045854	Lyrm2	2610208E05Rik	LYR motif containing 2	protein-coding
mm_135313.1	chr16	38713236	38713304	-	1	NA	promoter-TSS (NM_020260)	promoter-TSS (NM_020260)	-235	NM_020260	12549	Mm.370848	NM_020260	ENSMUSG00000022799	Arhgap31	5830477L08Rik|AU041750|Cdgap|D330026I07Rik	Rho GTPase activating protein 31	protein-coding
mm_90637.1	chr10	128498958	128498996	+	1	NA	promoter-TSS (NM_172259)	promoter-TSS (NM_172259)	-270	NR_131150	654440	Mm.441262	NR_131150	ENSMUSG00000097353	A430046D13Rik	-	Riken cDNA A430046D13 gene	ncRNA
mm_105051.1	chr11	100650712	100650749	-	1	NA	promoter-TSS (NM_177790)	promoter-TSS (NM_177790)	-37	NM_177790	278304	Mm.274734	NM_177790	ENSMUSG00000014198	Zfp385c	A930006D11Rik|Znf385c	zinc finger protein 385C	protein-coding
mm_17039.1	chr2	20671712	20671725	-	1	NA	intron (NM_029895, intron 4 of 18)	intron (NM_029895, intron 4 of 18)	152205	NM_001177631	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding
mm_150617.1	chr19	40993197	40993210	+	1	NA	intron (NM_008528, intron 1 of 16)	intron (NM_008528, intron 1 of 16)	1332	NM_008528	17060	Mm.9749	NM_008528	ENSMUSG00000061132	Blnk	BASH|Bca|Ly-57|Ly57|Lyw-57|SLP-65	B cell linker	protein-coding
mm_142605.1	chr17	46812157	46812173	-	1	NA	intron (NM_001100452, intron 5 of 10)	B1_Mur1|SINE|Alu	19248	NM_001100452	210982	Mm.37642	NM_001100452	ENSMUSG00000036568	Gltscr1l	mKIAA0240	GLTSCR1-like	protein-coding
mm_98447.1	chr11	94943740	94943777	+	1	NA	exon (NM_007742, exon 25 of 51)	exon (NM_007742, exon 25 of 51)	7534	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_91595.1	chr10	40350112	40350120	-	1	NA	intron (NM_001291816, intron 1 of 11)	CpG	808	NM_001291816	78334	Mm.200924	NM_198164	ENSMUSG00000038481	Cdk19	2700084L06Rik|AI845279|AW228747|CDK11|Cdc2l6|mKIAA1028	cyclin-dependent kinase 19	protein-coding
mm_87680.1	chr10	59223512	59223524	+	1	NA	exon (NM_172939, exon 1 of 1)	exon (NM_172939, exon 1 of 1)	1596	NM_172939	268301	Mm.3036	NM_172939	ENSMUSG00000098188	Sowahc	4921515A04Rik|9430099J10Rik|Ankrd57|C820004L04Rik	sosondowah ankyrin repeat domain family member C	protein-coding
mm_31168.1	chr4	43452427	43452473	+	1	NA	exon (NM_001110320, exon 5 of 9)	exon (NM_001110320, exon 5 of 9)	2176	NM_001110320	12517	Mm.188157	NM_007654	ENSMUSG00000028459	Cd72	CD72c|Ly-19|Ly-32|Ly-m19|Lyb-2	CD72 antigen	protein-coding
mm_20788.1	chr2	143990178	143990221	-	1	NA	exon (NM_133626, exon 2 of 3)	exon (NM_133626, exon 2 of 3)	21064	NM_133626	81910	Mm.13705	NM_024281	ENSMUSG00000027422	Rrbp1	1700087N07Rik|5730465C04Rik|ES/130|mKIAA1398|mRRp0|mRRp1.8|mRRp10|mRRp15a|mRRp15b|mRRp16.8|mRRp2|mRRp41|mRRp47|mRRp5.4|p180	ribosome binding protein 1	protein-coding
mm_44337.1	chr5	15883815	15883833	-	1	NA	promoter-TSS (NR_045974)	promoter-TSS (NR_045974)	-58	NR_045974	75058	Mm.183467	NR_045974	ENSMUSG00000105185	4930519H02Rik	-	RIKEN cDNA 4930519H02 gene	ncRNA
mm_31530.1	chr4	55044901	55044910	+	1	NA	intron (NM_172867, intron 7 of 12)	intron (NM_172867, intron 7 of 12)	96960	NM_172867	242466	Mm.102904	NM_172867	ENSMUSG00000060206	Zfp462	6030417H05|9430078C22Rik|Gt4-2|Zfpip	zinc finger protein 462	protein-coding
mm_146755.1	chr18	16768823	16768824	-	1	NA	intron (NM_007664, intron 2 of 15)	intron (NM_007664, intron 2 of 15)	40423	NM_007664	12558	Mm.257437	NM_007664	ENSMUSG00000024304	Cdh2	CDHN|N-CAD|Ncad	cadherin 2	protein-coding
mm_118972.1	chr14	27876394	27876420	+	1	NA	intron (NM_177814, intron 3 of 15)	intron (NM_177814, intron 3 of 15)	254000	NM_177814	238988	Mm.318004	NM_177814	ENSMUSG00000040640	Erc2	6430531D06|CAST|CAST1/ERC2|D14Ertd171e|ELKS2alpha	ELKS/RAB6-interacting/CAST family member 2	protein-coding
mm_68089.1	chr7	101903784	101903786	-	1	NA	promoter-TSS (NM_001282088)	promoter-TSS (NM_001282088)	0	NM_001282088	791260	Mm.475469	NM_001081679	ENSMUSG00000078630	Tomt	Comt2|F930017I19Rik	transmembrane O-methyltransferase	protein-coding
mm_24055.1	chr3	87906914	87906933	+	1	NA	promoter-TSS (NM_001331051)	promoter-TSS (NM_001331051)	73	NM_001331052	15191	Mm.292208	NM_008231	ENSMUSG00000004897	Hdgf	AI118077|D3Ertd299e	hepatoma-derived growth factor	protein-coding
mm_11192.1	chr2	29122756	29122764	+	1	NA	Intergenic	Lx8|LINE|L1	-2232	NM_198033	269254	Mm.41867	NM_198033	ENSMUSG00000043535	Setx	A130090N03|A930037J23Rik|AOA2|AW060766|Als4|SCAR1|Sen1|mKIAA0625	senataxin	protein-coding
mm_136614.1	chr17	5343973	5343978	+	1	NA	3' UTR (NM_001085355, exon 20 of 20)	3' UTR (NM_001085355, exon 20 of 20)	74792	NM_175349	106557	Mm.432764	NM_175349	ENSMUSG00000101959	Ldhal6b	4933402O15Rik|AI326310|LDHL|Ldhal	lactate dehydrogenase A-like 6B	protein-coding
mm_110811.1	chr12	72236667	72236684	-	1	NA	promoter-TSS (NR_104446)	promoter-TSS (NR_104446)	52	NM_001007596	104001	Mm.221275	NM_153457	ENSMUSG00000021087	Rtn1	Nsp	reticulon 1	protein-coding
mm_150295.1	chr19	34524728	34524775	+	1	NA	exon (NM_021460, exon 2 of 10)	exon (NM_021460, exon 2 of 10)	2723	NM_001111100	16889	Mm.157545	NM_021460	ENSMUSG00000024781	Lipa	AA960673|Lal|Lip-1|Lip1	lysosomal acid lipase A	protein-coding
mm_119349.1	chr14	41106849	41106858	+	1	NA	intron (NM_133653, intron 2 of 9)	MER20|DNA|hAT-Charlie	1820	NM_133653	11720	Mm.14064	NM_133653	ENSMUSG00000037798	Mat1a	AI046368|AdoMet|Ams|MAT|MATA1|SAMS|SAMS1	methionine adenosyltransferase I, alpha	protein-coding
mm_9244.1	chr1	171345401	171345443	-	1	NA	promoter-TSS (NM_011070)	promoter-TSS (NM_011070)	223	NM_001242580	27045	Mm.12915	NM_012049	ENSMUSG00000013997	Nit1	AI255805|ESTM30|W57327	nitrilase 1	protein-coding
mm_59127.1	chr7	19946124	19946140	+	1	NA	intron (NM_027308, intron 1 of 4)	intron (NM_027308, intron 1 of 4)	4611	NM_027308	70080	Mm.98583	NM_027308	ENSMUSG00000040498	Igsf23	2210010C17Rik	immunoglobulin superfamily, member 23	protein-coding
mm_112672.1	chr13	16027547	16027561	+	1	NA	3' UTR (NM_008380, exon 5 of 5)	3' UTR (NM_008380, exon 5 of 5)	15703	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_74419.1	chr8	3625290	3625297	-	1	NA	promoter-TSS (NM_001129804)	promoter-TSS (NM_001129804)	-11	NM_008790	18545	Mm.440882	NM_008790	ENSMUSG00000004630	Pcp2	L7|Pcp-2	Purkinje cell protein 2 (L7)	protein-coding
mm_122288.1	chr14	34503353	34503371	-	1	NA	promoter-TSS (NM_009758)	promoter-TSS (NM_009758)	-816	NM_009758	12166	Mm.237825	NM_009758	ENSMUSG00000021796	Bmpr1a	1110037I22Rik|ALK3|AU045487|BMPR-IA|Bmpr	bone morphogenetic protein receptor, type 1A	protein-coding
mm_107787.1	chr12	61586188	61586204	+	1	NA	intron (NM_178714, intron 1 of 3)	intron (NM_178714, intron 1 of 3)	63029	NM_001310586	238205	Mm.28802	NM_178714	ENSMUSG00000035653	Lrfn5	AI427653|AI604817|C130061B21|mKIAA4208	leucine rich repeat and fibronectin type III domain containing 5	protein-coding
mm_129384.1	chr15	78191627	78191627	-	1	NA	3' UTR (NM_001330686, exon 4 of 4)	3' UTR (NM_001330686, exon 4 of 4)	12610	NM_001330686	19293	Mm.2766	NM_013645	ENSMUSG00000005716	Pvalb	PV|Parv|Pva	parvalbumin	protein-coding
mm_30232.1	chr3	145924910	145924923	-	1	NA	intron (NM_009740, intron 1 of 2)	CpG	654	NM_009740	12042	Mm.239141	NM_009740	ENSMUSG00000028191	Bcl10	AI132454|BCL-10|C81403|CARMEN|CIPER|CLAP|ME10|cE10	B cell leukemia/lymphoma 10	protein-coding
mm_171507.1	chr4	146270421	146270421	+	1	NA	promoter-TSS (NM_001083918).2	promoter-TSS (NM_001083918).2	36	NM_001083918	666532	Mm.392861	NM_001083918	ENSMUSG00000067916	Zfp991	Gm13139|OTTMUSG00000010657	zinc finger protein 991	protein-coding
mm_104516.1	chr11	96006984	96007019	-	1	NA	Intergenic	CpG-2488	-1057	NM_009951	140486	Mm.294769	NM_009951	ENSMUSG00000013415	Igf2bp1	AL024068|AW549074|CRD-BP|Crdbp|D030026A21Rik|D11Moh40e|D11Moh45|IMP-1|IMP1|Neilsen|ZBP-1|Zbp1|mir-3063	insulin-like growth factor 2 mRNA binding protein 1	protein-coding
mm_125437.1	chr15	44619150	44619192	+	1	NA	promoter-TSS (NM_019480)	promoter-TSS (NM_019480)	-470	NM_019480	55960	Mm.287896	NM_019480	ENSMUSG00000022339	Ebag9	AI835379|Rcas1	estrogen receptor-binding fragment-associated gene 9	protein-coding
mm_128159.1	chr15	33073557	33073562	-	1	NA	Intergenic	LTRIS2|LTR|ERV1	-9570	NM_018755	54381	Mm.158251	NM_018755	ENSMUSG00000039007	Cpq	1190003P12Rik|2610034C17Rik|Hls2|Lal-1|Pgcp	carboxypeptidase Q	protein-coding
mm_73788.1	chr8	117256660	117256724	+	1	NA	promoter-TSS (NM_001163262)	promoter-TSS (NM_001163262)	-327	NM_001163262	74440	Mm.233181	NM_028941	ENSMUSG00000034390	Cmip	4933407C03Rik|5830471E12Rik|AI314065|AI464126	c-Maf inducing protein	protein-coding
mm_109384.1	chr12	109734970	109734973	+	1	NA	promoter-TSS (NR_030253)	promoter-TSS (NR_030253)	-10	NR_028265	100040724	Mm.260543	NR_028265	ENSMUSG00000097391	Mirg	2810474H01Rik|AI852992|Gm2928|Meg9|mir-410	miRNA containing gene	ncRNA
mm_32808.1	chr4	117124934	117124981	+	1	NA	intron (NR_024078, intron 1 of 6)	intron (NR_024078, intron 1 of 6)	768	NR_024078	78611	Mm.446227	NM_001033187		Btbd19	9530048O09Rik|BB115071	BTB (POZ) domain containing 19	ncRNA
mm_95759.1	chr11	54906777	54906781	+	1	NA	intron (NM_001329860, intron 1 of 5)	intron (NM_001329860, intron 1 of 5)	3925	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_2633.1	chr1	121486944	121486948	+	1	NA	intron (NM_001025156, intron 18 of 23)	B3A|SINE|B2	41519	NM_010483	15564	Mm.4833	NM_010483	ENSMUSG00000050534	Htr5b	5-Ht5b	5-hydroxytryptamine (serotonin) receptor 5B	protein-coding
mm_21415.1	chr2	158124286	158124298	-	1	NA	exon (NM_009373, exon 10 of 13)	exon (NM_009373, exon 10 of 13)	22100	NM_009373	21817	Mm.330731	NM_009373	ENSMUSG00000037820	Tgm2	G[a]h|TG2|TGase2|tTG|tTGas	transglutaminase 2, C polypeptide	protein-coding
mm_3001.1	chr1	133255245	133255248	+	1	NA	intron (NR_037984, intron 3 of 3)	intron (NR_037984, intron 3 of 3)	9149	NM_182930	240753	Mm.253559	NM_182930	ENSMUSG00000041757	Plekha6	9530028L01Rik|AU042621|Pepp3	pleckstrin homology domain containing, family A member 6	protein-coding
mm_68499.1	chr7	111078557	111078568	-	1	NA	intron (NM_001040131, intron 5 of 20)	intron (NM_001040131, intron 5 of 20)	4468	NM_001040131	13690	Mm.185453	NM_013507	ENSMUSG00000005610	Eif4g2	DAP-5|E130105L11Rik|Nat1|Natm1|p97	eukaryotic translation initiation factor 4, gamma 2	protein-coding
mm_155346.1	chrX	68678643	68678667	+	1	NA	promoter-TSS (NR_033481)	promoter-TSS (NR_033481)	114	NM_001290424	14265	Mm.3451	NM_008031	ENSMUSG00000000838	Fmr1	FMRP|Fmr-1	fragile X mental retardation syndrome 1	protein-coding
mm_51197.1	chr6	71284098	71284106	+	1	NA	exon (NM_145568, exon 4 of 4)	exon (NM_145568, exon 4 of 4)	12083	NM_145568	57896	Mm.250569	NM_145568	ENSMUSG00000053012	Krcc1	AA792894	lysine-rich coiled-coil 1	protein-coding
mm_121041.1	chr14	80021281	80021291	+	1	NA	exon (NM_001030294, exon 7 of 7)	exon (NM_001030294, exon 7 of 7)	20984	NM_001030294	380924	Mm.26456	NM_001030294	ENSMUSG00000022026	Olfm4	GC1|GW112|Gm296|Gm913|OlfD|pPD4	olfactomedin 4	protein-coding
mm_114918.1	chr13	95323603	95323606	+	1	NA	promoter-TSS (NM_001302538)	promoter-TSS (NM_001302538)	-1	NM_001302538	72114	Mm.3774	NM_028106	ENSMUSG00000041995	Zbed3	0610037K01Rik|2610005H11Rik|AU018975|AU024588	zinc finger, BED type containing 3	protein-coding
mm_49865.1	chr6	38551787	38551851	+	1	NA	5' UTR (NM_001170849, exon 1 of 8)	5' UTR (NM_001170849, exon 1 of 8)	485	NM_001170848	192196	Mm.276133	NM_138680	ENSMUSG00000029823	Luc7l2	4930471C18Rik|AA522013|AU015269|CGI59|Cgi74	LUC7-like 2 (S. cerevisiae)	protein-coding
mm_127847.1	chr15	7398234	7398323	-	1	NA	5' UTR (NM_001289498, exon 1 of 23)	5' UTR (NM_001289498, exon 1 of 23)	112	NM_001289496	268780	Mm.203208	NM_178748	ENSMUSG00000042961	Egflam	5930412K08|AU040377	EGF-like, fibronectin type III and laminin G domains	protein-coding
mm_25432.1	chr3	107895917	107895931	+	1	NA	promoter-TSS (NM_010360)	promoter-TSS (NM_010360)	70	NM_010360	14866	Mm.282351	NM_010360	ENSMUSG00000004032	Gstm5	-	glutathione S-transferase, mu 5	protein-coding
mm_66440.1	chr7	44816955	44816966	-	1	NA	promoter-TSS (NR_033136)	promoter-TSS (NR_033136)	-302	NR_033136	107503	Mm.389890	NM_030693	ENSMUSG00000038539	Atf5	AFTA|Atf7|Atfx|ODA-10	activating transcription factor 5	protein-coding
mm_90569.1	chr10	128231744	128231754	+	1	NA	promoter-TSS (NM_001136082)	promoter-TSS (NM_001136082)	-314	NM_001164080	21853	Mm.6458	NM_011589	ENSMUSG00000039994	Timeless	C77407|Debt69|tim	timeless circadian clock 1	protein-coding
mm_15718.1	chr2	164047668	164047676	+	1	NA	intron (NM_001114079, intron 12 of 13)	intron (NM_001114079, intron 12 of 13)	22448	NM_001114079	381404	Mm.82301	NM_001114079	ENSMUSG00000054582	Pabpc1l	1810053B01Rik|Epab	poly(A) binding protein, cytoplasmic 1-like	protein-coding
mm_151615.1	chr19	3900857	3900867	-	1	NA	intron (NM_001167784, intron 10 of 19)	intron (NM_001167784, intron 10 of 19)	4368	NM_016921	27060	Mm.271689	NM_016921	ENSMUSG00000001750	Tcirg1	ATP6N1C|ATP6a3|Atp6i|OC-116|OPTB1|Stv1|TIRC7|Vph1|oc	T cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 protein A3	protein-coding
mm_106432.1	chr11	119392111	119392123	-	1	NA	Intergenic	Intergenic	1645	NR_035453	100316690		NR_035453	ENSMUSG00000088015	Mir1932	mir-1932|mmu-mir-1932	microRNA 1932	ncRNA
mm_106725.1	chr12	3873085	3873101	+	1	NA	intron (NM_007872, intron 5 of 22)	intron (NM_007872, intron 5 of 22)	-10849	NR_045884	100038522	Mm.417270	NR_045884	ENSMUSG00000073242	Dnmt3aos	ENSMUSG00000073242|Gm10485	DNA methyltransferase 3A, opposite strand	ncRNA
mm_159104.1	chr2	37443086	37443086	-	1	NA	promoter-TSS (NM_146121)	promoter-TSS (NM_146121)	35	NM_199025	320633	Mm.383299	NM_199025	ENSMUSG00000050714	Zbtb26	A630026F21Rik	zinc finger and BTB domain containing 26	protein-coding
mm_87413.1	chr10	46526193	46526193	+	1	NA	Intergenic	BGLII_Mus|LTR|ERVK	281444	NR_028276	108637		NR_028276	ENSMUSG00000096263	Snord14c	Gm23107|Rnu14|U14	small nucleolar RNA, C/D box 14C	snoRNA
mm_127810.1	chr15	5046045	5046058	-	1	NA	intron (NM_001243837, intron 5 of 17)	intron (NM_001243837, intron 5 of 17)	17722	NM_001243837	109828	Mm.208034	NM_001243837	ENSMUSG00000079105	C7	A530026G17|Gm1238	complement component 7	protein-coding
mm_158682.1	chrX	160138376	160138435	-	1	NA	promoter-TSS (NM_008810)	promoter-TSS (NM_008810)	25	NM_008810	18597	Mm.34775	NM_008810	ENSMUSG00000031299	Pdha1	Pdha-1	pyruvate dehydrogenase E1 alpha 1	protein-coding
mm_138079.1	chr17	33956068	33956108	+	1	NA	promoter-TSS (NM_011296)	promoter-TSS (NM_011296)	206	NM_172620	224705	Mm.448614	NM_172620	ENSMUSG00000024319	Vps52	ARE1|D130068D18|D430041K17Rik|SAC2|Sacm2l|tclw5	VPS52 GARP complex subunit	protein-coding
mm_121474.1	chr14	121035195	121035208	+	1	NA	promoter-TSS (NM_134082)	promoter-TSS (NM_134082)	-373	NM_134082	223254	Mm.223980	NM_134082	ENSMUSG00000025555	Farp1	AW228844|BC030329|Cdep	FERM, RhoGEF (Arhgef) and pleckstrin domain protein 1 (chondrocyte-derived)	protein-coding
mm_124825.1	chr15	9073184	9073187	+	1	NA	intron (NM_001040395, intron 1 of 12)	intron (NM_001040395, intron 1 of 12)	1925	NM_001040395	68646	Mm.244226	NM_001040395	ENSMUSG00000022253	Nadk2	MNADK|Nadkd1	NAD kinase 2, mitochondrial	protein-coding
mm_173061.1	chrX	128714741	128714741	-	1	NA	Intergenic	Intergenic	-336783	NR_045441	75274	Mm.108718	NR_045441	ENSMUSG00000086244	4930558G05Rik	-	RIKEN cDNA 4930558G05 gene	ncRNA
mm_109993.1	chr12	15814740	15814752	-	1	NA	intron (NM_144551, intron 1 of 2)	intron (NM_144551, intron 1 of 2)	2039	NM_144551	217410	Mm.491136	NM_144551	ENSMUSG00000020601	Trib2	AW319517|TRB-2|TRB2	tribbles pseudokinase 2	protein-coding
mm_75831.1	chr8	70510323	70510422	-	1	NA	promoter-TSS (NM_019883)	promoter-TSS (NM_019883)	-5	NM_019883	22186	Mm.297372	NM_019883	ENSMUSG00000090137	Uba52	D8Ertd21e|Gm1863|Rps27a|Ubb|Ubc	ubiquitin A-52 residue ribosomal protein fusion product 1	protein-coding
mm_70217.1	chr7	144939812	144939822	-	1	NA	5' UTR (NM_007631, exon 1 of 5)	5' UTR (NM_007631, exon 1 of 5)	108	NM_007631	12443	Mm.273049	NM_007631	ENSMUSG00000070348	Ccnd1	AI327039|CycD1|Cyl-1|PRAD1|bcl-1|cD1	cyclin D1	protein-coding
mm_139396.1	chr17	52304500	52304515	+	1	NA	Intergenic	Intergenic	-298202	NM_001031811	211468	Mm.399068	NM_001031811	ENSMUSG00000035580	Kcnh8	C130090D05Rik|ELK|ELK1|ELK3|Kv12.1	potassium voltage-gated channel, subfamily H (eag-related), member 8	protein-coding
mm_86918.1	chr10	23851455	23851489	+	1	NA	promoter-TSS (NM_011979)	promoter-TSS (NM_011979)	10	NM_011979	26464	Mm.27334	NM_011979	ENSMUSG00000020010	Vnn3	-	vanin 3	protein-coding
mm_88553.1	chr10	78596565	78596569	+	1	NA	Intergenic	RMER19B|LTR|ERVK	-4603	NM_027875	71709	Mm.86439	NM_027875	ENSMUSG00000032714	Syde1	1200008N06Rik|BB043000|mSYD1A	synapse defective 1, Rho GTPase, homolog 1 (C. elegans)	protein-coding
mm_24905.1	chr3	96219781	96219789	+	1	NA	promoter-TSS (NM_178213)	promoter-TSS (NM_178213)	-131	NM_178213	621893		NM_178213	ENSMUSG00000063689	Hist2h2ab	EG621893|H2a-613a	histone cluster 2, H2ab	protein-coding
mm_37382.1	chr4	120975605	120975616	-	1	NA	intron (NM_133716, intron 5 of 9)	intron (NM_133716, intron 5 of 9)	-2288	NR_105982	102465614		NR_105982	ENSMUSG00000106436	Mir7015	mmu-mir-7015	microRNA 7015	ncRNA
mm_114179.1	chr13	55635003	55635036	+	1	NA	promoter-TSS (NM_001282055)	promoter-TSS (NM_001282055)	20	NM_001282055	212880	Mm.202725	NM_145975	ENSMUSG00000021500	Ddx46	2200005K02Rik|8430438J23Rik|AI325430|AI957095|mKIAA0801	DEAD (Asp-Glu-Ala-Asp) box polypeptide 46	protein-coding
mm_57162.1	chr6	122779967	122779970	-	1	NA	Intergenic	Intergenic	-37223	NM_011401	20527	Mm.395108	NM_011401	ENSMUSG00000003153	Slc2a3	AA408729|AL023014|AL024341|AU040424|C78366|Glut-3|Glut3	solute carrier family 2 (facilitated glucose transporter), member 3	protein-coding
mm_38658.1	chr4	143457999	143458000	-	1	NA	Intergenic	Intergenic	-7675	NM_001347238	242737	Mm.148643	NM_173773	ENSMUSG00000047799	Oog4	E330017M15	oogenesin 4	protein-coding
mm_26690.1	chr3	156666556	156666558	+	1	NA	intron (NM_177274, intron 1 of 6)	intron (NM_177274, intron 1 of 6)	104763	NM_001039094	320840	Mm.317293	NM_177274	ENSMUSG00000040037	Negr1	5330422G01Rik|KILON|Ntra	neuronal growth regulator 1	protein-coding
mm_12663.1	chr2	75659057	75659091	+	1	NA	promoter-TSS (NM_198090)	promoter-TSS (NM_198090)	-185	NM_146130	229279	Mm.316306	NM_053263	ENSMUSG00000059005	Hnrnpa3	2410013L13Rik|2610209F03Rik|2610510D13Rik|Hnrpa3	heterogeneous nuclear ribonucleoprotein A3	protein-coding
mm_107825.1	chr12	69168809	69168839	+	1	NA	promoter-TSS (NM_001081406)	promoter-TSS (NM_001081406)	10	NM_001081406	69706	Mm.28847	NM_027178	ENSMUSG00000034883	Lrr1	2410005L11Rik|AU021780|LRR-1|Ppil5	leucine rich repeat protein 1	protein-coding
mm_58821.1	chr7	16615608	16615620	+	1	NA	promoter-TSS (NM_172739)	promoter-TSS (NM_172739)	-621	NM_172739	232906	Mm.28646	NM_172739	ENSMUSG00000058230	Arhgap35	6430596G11Rik|AI841135|Grlf1|mKIAA1722|p190A|p190RhoGAP	Rho GTPase activating protein 35	protein-coding
mm_113758.1	chr13	44741483	44741487	+	1	NA	intron (NM_001205044, intron 2 of 18)	B2_Mm2|SINE|B2	10214	NM_001205043	16468	Mm.25059	NM_021878	ENSMUSG00000038518	Jarid2	Jmj|jumonji	jumonji, AT rich interactive domain 2	protein-coding
mm_153308.1	chr19	38024331	38024346	-	1	NA	intron (NM_001302140, intron 2 of 53)	intron (NM_001302140, intron 2 of 53)	19239	NM_001099634	226101	Mm.34674	NM_177035	ENSMUSG00000048612	Myof	2310004N10Rik|2310051D19Rik|E030042N20Rik|Fer1l3	myoferlin	protein-coding
mm_33040.1	chr4	122933248	122933279	+	1	NA	Intergenic	Intergenic	27925	NM_029662	76574	Mm.331842	NM_029662	ENSMUSG00000028655	Mfsd2a	1700018O18Rik|Mfsd2|NLS1	major facilitator superfamily domain containing 2A	protein-coding
mm_119554.1	chr14	48655307	48655318	+	1	NA	Intergenic	Intergenic	7560	NM_144841	18424	Mm.134516	NM_144841	ENSMUSG00000021848	Otx2	E130306E05Rik	orthodenticle homeobox 2	protein-coding
mm_79110.1	chr9	46269909	46269923	+	1	NA	exon (NM_080434, exon 4 of 4)	exon (NM_080434, exon 4 of 4)	1308	NM_080434	66113	Mm.29738	NM_080434	ENSMUSG00000032079	Apoa5	1300007O05Rik|Apoav|RAP3	apolipoprotein A-V	protein-coding
mm_39122.1	chr4	155019384	155019391	-	1	NA	Intergenic	(CTAG)n|Simple_repeat|Simple_repeat	-8403	NM_001113360	269615	Mm.379458	NM_175556	ENSMUSG00000029055	Plch2	A930027K05Rik|PLCeta2|Plc-eta2|Plcl4	phospholipase C, eta 2	protein-coding
mm_49869.1	chr6	38560217	38560236	+	1	NA	intron (NM_001331223, intron 2 of 12)	intron (NM_001331223, intron 2 of 12)	4503	NM_001331223	192196	Mm.276133	NM_138680	ENSMUSG00000029823	Luc7l2	4930471C18Rik|AA522013|AU015269|CGI59|Cgi74	LUC7-like 2 (S. cerevisiae)	protein-coding
mm_120166.1	chr14	60763785	60763788	+	1	NA	3' UTR (NM_001033272, exon 13 of 13)	3' UTR (NM_001033272, exon 13 of 13)	-4348	NM_183175	239126	Mm.319636	NM_183175	ENSMUSG00000071347	C1qtnf9	9130217G22Rik|CTRP9|Ciqtnf9	C1q and tumor necrosis factor related protein 9	protein-coding
mm_60095.1	chr7	35119286	35119301	+	1	NA	promoter-TSS (NM_001287514)	promoter-TSS (NM_001287514)	0	NM_001287521	12606	Mm.349667	NM_007678	ENSMUSG00000034957	Cebpa	C/ebpalpha|CBF-A|Cebp	CCAAT/enhancer binding protein (C/EBP), alpha	protein-coding
mm_24862.1	chr3	95929280	95929298	+	1	NA	promoter-TSS (NM_001253757)	promoter-TSS (NM_001253757)	32	NM_023210	66471	Mm.218657	NM_023210	ENSMUSG00000015749	Anp32e	2810018A15Rik|AI047746|AI326868|CPD1|LANP-L|LANPL|mLANP-L	acidic (leucine-rich) nuclear phosphoprotein 32 family, member E	protein-coding
mm_150654.1	chr19	41932828	41932844	+	1	NA	promoter-TSS (NM_023740)	promoter-TSS (NM_023740)	478	NM_001164561	66583	Mm.289086	NM_025644	ENSMUSG00000034321	Exosc1	2610035C18Rik|2610104C07Rik|2610312F07Rik|AI447561	exosome component 1	protein-coding
mm_172920.1	chr9	67049291	67049291	-	1	NA	promoter-TSS (NM_001164251)	promoter-TSS (NM_001164251)	-78	NM_001164251	22003	Mm.121878	NM_024427	ENSMUSG00000032366	Tpm1	AA986836|AI854628|TM2|Tm3|Tmpa|Tpm-1|alpha-TM	tropomyosin 1, alpha	protein-coding
mm_44850.1	chr5	34215147	34215150	-	1	NA	intron (NM_001015039, intron 8 of 12)	L1MB7|LINE|L1	-27438	NM_010753	17122	Mm.259260	NM_010753	ENSMUSG00000037235	Mxd4	2810410A03Rik|Mad4|bHLHc12	Max dimerization protein 4	protein-coding
mm_40846.1	chr5	73306665	73306677	+	1	NA	exon (NM_001159889, exon 7 of 7)	exon (NM_001159889, exon 7 of 7)	13877	NM_001159888	68095	Mm.247039	NM_023429	ENSMUSG00000029152	Ociad1	6030432N09Rik|AI481327|AW557942|Asrij|B230209J16Rik|BB021357|Emi2|Imi2|OCIA|TPA018	OCIA domain containing 1	protein-coding
mm_22146.1	chr2	172370515	172370540	-	1	NA	promoter-TSS (NM_001291185)	promoter-TSS (NM_001291185)	43	NM_001291185	20878	Mm.249363	NM_011497	ENSMUSG00000027496	Aurka	AIRK1|ARK-1|AU019385|AW539821|Ark1|Aurora-A|Ayk1|IAK|IAK1|Stk6	aurora kinase A	protein-coding
mm_15411.1	chr2	156775444	156775469	+	1	NA	promoter-TSS (NM_172118)	promoter-TSS (NM_172118)	-8	NM_172118	98932	Mm.271770	NM_172118	ENSMUSG00000067818	Myl9	AI327049|MLC20|Mylc2c|RLC-C	myosin, light polypeptide 9, regulatory	protein-coding
mm_69532.1	chr7	135693448	135693458	-	1	NA	exon (NM_001081117, exon 13 of 14)	exon (NM_001081117, exon 13 of 14)	22926	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_143514.1	chr17	72939921	72939934	-	1	NA	3' UTR (NM_029999, exon 3 of 3)	3' UTR (NM_029999, exon 3 of 3)	21622	NM_029999	77889	Mm.154109	NM_029999	ENSMUSG00000024063	Lbh	1810009F10Rik|6720416L16Rik	limb-bud and heart	protein-coding
mm_136123.1	chr16	85900604	85900633	-	1	NA	5' UTR (NM_011782, exon 1 of 8)	5' UTR (NM_011782, exon 1 of 8)	507	NM_011782	23794	Mm.112933	NM_011782	ENSMUSG00000022894	Adamts5	9530092O11Rik|ADAM-TS5|ADAMTS1|ADAMTS11|ADMP-2|AI481094|ASMP-2	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)	protein-coding
mm_131540.1	chr16	17763901	17763903	+	1	NA	intron (NM_145479, intron 1 of 6)	B1_Mus1|SINE|Alu	4281	NM_145479	224023	Mm.282807	NM_145479	ENSMUSG00000022750	Klhl22	2610318I18Rik|Kelchl	kelch-like 22	protein-coding
mm_107283.1	chr12	29783626	29783642	+	1	NA	exon (NM_001093776, exon 6 of 25)	exon (NM_001093776, exon 6 of 25)	-97189	NR_046080	328075	Mm.447832	NR_046080		C630031E19Rik	C630031E19	RIKEN cDNA C630031E19 gene	ncRNA
mm_42687.1	chr5	119835096	119835104	+	1	NA	5' UTR (NM_011537, exon 1 of 9)	5' UTR (NM_011537, exon 1 of 9)	437	NM_011537	21388	Mm.103636	NM_011537	ENSMUSG00000018263	Tbx5	-	T-box 5	protein-coding
mm_48433.1	chr5	140623065	140623083	-	1	NA	3' UTR (NM_175274, exon 14 of 14)	3' UTR (NM_175274, exon 14 of 14)	15733	NM_008494	16848	Mm.12834	NM_008494	ENSMUSG00000029570	Lfng	AW061165	LFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	protein-coding
mm_2474.1	chr1	105780694	105780762	+	1	NA	promoter-TSS (NM_009399)	promoter-TSS (NM_009399)	5	NM_009399	21934	Mm.6251	NM_009399	ENSMUSG00000026321	Tnfrsf11a	Ly109|ODFR|OFE|Rank|TRANCE-R|mRANK	tumor necrosis factor receptor superfamily, member 11a, NFKB activator	protein-coding
mm_20065.1	chr2	120368793	120368795	-	1	NA	intron (NM_001110496, intron 15 of 19)	RLTR28|LTR|ERVL	-15661	NR_027618	269338	Mm.246131	NM_147153	ENSMUSG00000027291	Vps39	A230065P22Rik|AW743070|Vam6|Vam6P|mVam6	VPS39 HOPS complex subunit	protein-coding
mm_163114.1	chr11	72540552	72540558	-	1	NA	intron (NM_029932, intron 2 of 11)	intron (NM_029932, intron 2 of 11)	9691	NM_029932	77577	Mm.46185	NM_029932	ENSMUSG00000020798	Spns3	9830002I17Rik	spinster homolog 3	protein-coding
mm_147570.1	chr18	55131257	55131261	-	1	NA	Intergenic	Intergenic	-141079	NM_175751	269023	Mm.192984	NM_175751	ENSMUSG00000052713	Zfp608	4932417D18Rik|D430007A19Rik|Znf608	zinc finger protein 608	protein-coding
mm_27642.1	chr3	63862819	63862820	-	1	NA	Intergenic	Intergenic	-11828	NM_001177732	269437	Mm.316391	NM_183191	ENSMUSG00000036834	Plch1	BC042549|PLC-eta-1|PLCeta1|Plcl3	phospholipase C, eta 1	protein-coding
mm_151343.1	chr19	55895491	55895497	+	1	NA	5' UTR (NM_001142924, exon 1 of 12)	5' UTR (NM_001142924, exon 1 of 12)	173	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_8411.1	chr1	152053213	152053231	-	1	NA	intron (NM_197990, intron 1 of 5)	intron (NM_197990, intron 1 of 5)	37098	NM_197990	69399	Mm.278031	NM_197990	ENSMUSG00000032666	1700025G04Rik	2610510E02Rik|2900042O04Rik|ENSMUSG00000073540	RIKEN cDNA 1700025G04 gene	protein-coding
mm_11963.1	chr2	53191467	53191480	+	1	NA	promoter-TSS (NM_018785)	promoter-TSS (NM_018785)	-286	NM_018785	56194	Mm.257474	NM_018785	ENSMUSG00000061136	Prpf40a	2810012K09Rik|FBP-11|FBP11|Fnbp11|Fnbp3	pre-mRNA processing factor 40A	protein-coding
mm_100737.1	chr11	4095334	4095336	-	1	NA	promoter-TSS (NM_026443)	promoter-TSS (NM_026443)	96	NM_026443	67900	Mm.41719	NM_026443	ENSMUSG00000004748	Mtfp1	1700020C11Rik|2610507A21Rik|AV005788|Mtp18	mitochondrial fission process 1	protein-coding
mm_40915.1	chr5	75640939	75640967	+	1	NA	intron (NM_021099, intron 11 of 20)	intron (NM_021099, intron 11 of 20)	65962	NM_021099	16590	Mm.247073	NM_021099	ENSMUSG00000005672	Kit	Bs|CD117|Fdc|Gsfsco1|Gsfsco5|Gsfsow3|SCO1|SCO5|SOW3|Ssm|Tr-kit|W|c-KIT	KIT proto-oncogene receptor tyrosine kinase	protein-coding
mm_80032.1	chr9	68737022	68737026	+	1	NA	intron (NM_013646, intron 1 of 10)	intron (NM_013646, intron 1 of 10)	-28322	NR_033299	320440	Mm.483129	NM_177159		9530091C08Rik	-	RIKEN cDNA 9530091C08 gene	ncRNA
mm_46381.1	chr5	103977340	103977356	-	1	NA	promoter-TSS (NM_001163486)	promoter-TSS (NM_001163486)	40	NM_198030	243168	Mm.284944	NM_198030	ENSMUSG00000034528	Hsd17b13	AI047820|PAN1B-like|Pan1b	hydroxysteroid (17-beta) dehydrogenase 13	protein-coding
mm_25033.1	chr3	98160641	98160651	+	1	NA	promoter-TSS (NM_027665)	promoter-TSS (NM_027665)	12	NM_027665	71078	Mm.50711	NM_027665	ENSMUSG00000043468	Adam30	4933424D07Rik|svph4	a disintegrin and metallopeptidase domain 30	protein-coding
mm_91521.1	chr10	37138781	37138794	-	1	NA	5' UTR (NM_008538, exon 1 of 2)	5' UTR (NM_008538, exon 1 of 2)	139	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_89015.1	chr10	82048105	82048146	+	1	NA	promoter-TSS (NM_001319203)	promoter-TSS (NM_001319203)	2	NM_001319203	408062	Mm.391409	NM_001024626	ENSMUSG00000061371	Zfp873	-	zinc finger protein 873	protein-coding
mm_48224.1	chr5	137645666	137645676	-	1	NA	promoter-TSS (NM_010571)	promoter-TSS (NM_010571)	43	NM_010571	16369	Mm.24486	NM_010571	ENSMUSG00000047182	Irs3	AA408304	insulin receptor substrate 3	protein-coding
mm_47038.1	chr5	116021733	116021745	-	1	NA	intron (NM_031869, intron 1 of 6)	intron (NM_031869, intron 1 of 6)	2689	NM_031869	19079	Mm.458152	NM_031869	ENSMUSG00000029513	Prkab1	1300015D22Rik|AU021155|E430008F22	protein kinase, AMP-activated, beta 1 non-catalytic subunit	protein-coding
mm_42151.1	chr5	111429218	111429267	+	1	NA	intron (NM_001081235, intron 1 of 1)	intron (NM_001081235, intron 1 of 1)	11076	NM_001081235	433938	Mm.332576	NM_001081235	ENSMUSG00000070576	Mn1	AA003644|AA009236	meningioma 1	protein-coding
mm_165303.1	chr2	94412661	94412675	-	1	NA	TTS (NR_027831)	TTS (NR_027831)	5961	NR_027831	66457	Mm.402557	NR_027831		2810002D19Rik	-	RIKEN cDNA 2810002D19 gene	ncRNA
mm_35621.1	chr4	43454538	43454547	-	1	NA	promoter-TSS (NM_001110320)	promoter-TSS (NM_001110320)	84	NM_001110320	12517	Mm.188157	NM_007654	ENSMUSG00000028459	Cd72	CD72c|Ly-19|Ly-32|Ly-m19|Lyb-2	CD72 antigen	protein-coding
mm_134484.1	chr16	18626424	18626461	-	1	NA	intron (NM_213614, intron 2 of 11)	CpG	3496	NM_213614	18951	Mm.20365	NM_213614	ENSMUSG00000072214	Sept5	Cdcrel-1|Cdcrel1|Pnutl1	septin 5	protein-coding
mm_153664.1	chr19	44395813	44395821	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	11892	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_121612.1	chr14	8258980	8258991	-	1	NA	promoter-TSS (NM_053115)	promoter-TSS (NM_053115)	34	NM_053115	93732	Mm.28700	NM_053115	ENSMUSG00000021751	Acox2	THCCox	acyl-Coenzyme A oxidase 2, branched chain	protein-coding
mm_81976.1	chr9	121298777	121298800	+	1	NA	Intergenic	Intergenic	-21616	NM_177589	209012	Mm.371804	NM_177589	ENSMUSG00000040936	Ulk4	4932415A06Rik|A730098P15	unc-51-like kinase 4	protein-coding
mm_57605.1	chr6	128025691	128025713	-	1	NA	intron (NM_175414, intron 3 of 8)	intron (NM_175414, intron 3 of 8)	117876	NM_175414	109246	Mm.21814	NM_175414	ENSMUSG00000030352	Tspan9	6720474K14Rik|9430079M16Rik|AU018597	tetraspanin 9	protein-coding
mm_95710.1	chr11	54496036	54496039	+	1	NA	intron (NM_173753, intron 10 of 17)	intron (NM_173753, intron 10 of 17)	-26808	NM_001252494	192786	Mm.254404	NM_175258	ENSMUSG00000037533	Rapgef6	A530068K01|AI844632|BB085664|C030018K18Rik|PDZ-GEF2|Pdzgef2|RA-GEF-2|Ragef2|mKIAA4052	Rap guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_166721.1	chr6	120465234	120465259	+	1	NA	intron (NM_008359, intron 1 of 12)	B1_Mus1|SINE|Alu	2049	NM_008359	16172	Mm.4481	NM_008359	ENSMUSG00000002897	Il17ra	AW538159|Cdw217|Il17r|VDw217	interleukin 17 receptor A	protein-coding
mm_127825.1	chr15	6429903	6429949	-	1	NA	exon (NM_023118, exon 10 of 15)	exon (NM_023118, exon 10 of 15)	-15407	NM_013485	12279	Mm.29095	NM_013485	ENSMUSG00000022149	C9	-	complement component 9	protein-coding
mm_109535.1	chr12	111543660	111543692	+	1	NA	intron (NM_173363, intron 11 of 11)	intron (NM_173363, intron 11 of 11)	2730	NR_033168	100316932	Mm.484709	NR_033168	ENSMUSG00000064493	Snora28	MBI-13	small nucleolar RNA, H/ACA box 28	snoRNA
mm_63876.1	chr7	136353359	136353369	+	1	NA	Intergenic	Intergenic	-3949	NR_040459	330664	Mm.127762	NR_040459	ENSMUSG00000109633	C230079O03Rik	C230079O03	RIKEN cDNA C230079O03 gene	ncRNA
mm_90228.1	chr10	121365079	121365158	+	1	NA	promoter-TSS (NM_029364)	promoter-TSS (NM_029364)	28	NM_029364	75612	Mm.207683	NM_029364	ENSMUSG00000034707	Gns	2610016K11Rik|AU042285|C87209|G6S|N28088	glucosamine (N-acetyl)-6-sulfatase	protein-coding
mm_7717.1	chr1	130661492	130661511	-	1	NA	5' UTR (NM_007576, exon 1 of 10)	5' UTR (NM_007576, exon 1 of 10)	117	NM_007576	12269	Mm.306720	NM_007576	ENSMUSG00000026405	C4bp	AI195242|C4bpa	complement component 4 binding protein	protein-coding
mm_123443.1	chr14	64949815	64949820	-	1	NA	promoter-TSS (NM_001253731)	promoter-TSS (NM_001253731)	40	NM_177338	219150	Mm.344074	NM_177338	ENSMUSG00000021972	Hmbox1	AI451877|AI604847|F830020C16Rik	homeobox containing 1	protein-coding
mm_94578.1	chr11	11690268	11690280	+	1	NA	promoter-TSS (NM_001301865)	promoter-TSS (NM_001301865)	97	NM_001301863	22778	Mm.103545	NM_009578	ENSMUSG00000018654	Ikzf1	5832432G11Rik|Ikaros|LyF-1|Zfpn1a1|Znfn1a1|hlk-1|mKIAA4227	IKAROS family zinc finger 1	protein-coding
mm_7666.1	chr1	128561619	128561621	-	1	NA	Intergenic	Intergenic	30679	NM_009911	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding
mm_152468.1	chr19	10949239	10949277	-	1	NA	promoter-TSS (NM_023731)	promoter-TSS (NM_023731)	8	NM_023731	108673	Mm.294908	NM_023731	ENSMUSG00000024732	Ccdc86	4933411H20Rik|6720480F16Rik|D19Ertd678e	coiled-coil domain containing 86	protein-coding
mm_59434.1	chr7	27130371	27130404	+	1	NA	exon (NM_007817, exon 7 of 10)	exon (NM_007817, exon 7 of 10)	10432	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_124428.1	chr14	118236639	118236663	-	1	NA	non-coding (NR_131969, exon 1 of 3)	non-coding (NR_131969, exon 1 of 3)	379	NM_177753	223227	Mm.70950	NM_177753	ENSMUSG00000061517	Sox21	Sox25	SRY (sex determining region Y)-box 21	protein-coding
mm_147185.1	chr18	36783147	36783191	-	1	NA	promoter-TSS (NM_080636)	promoter-TSS (NM_080636)	36	NM_008214	15115	Mm.10528	NM_008214	ENSMUSG00000001380	Hars	MMHRS	histidyl-tRNA synthetase	protein-coding
mm_122718.1	chr14	52279024	52279038	-	1	NA	promoter-TSS (NM_023434)	promoter-TSS (NM_023434)	-115	NM_023434	268741	Mm.246237	NM_023434	ENSMUSG00000016831	Tox4	5730589K01Rik|A630040M18|AA410149|LCP1	TOX high mobility group box family member 4	protein-coding
mm_113264.1	chr13	28951437	28951477	+	1	NA	3' UTR (NM_009238, exon 1 of 1)	3' UTR (NM_009238, exon 1 of 1)	2225	NM_009238	20677	Mm.240627	NM_009238	ENSMUSG00000076431	Sox4	AA682046|Sox-4	SRY (sex determining region Y)-box 4	protein-coding
mm_40125.1	chr5	34989727	34989776	+	1	NA	intron (NM_173402, intron 3 of 16)	intron (NM_173402, intron 3 of 16)	-9327	NM_001163512	71729	Mm.196208	NM_173402	ENSMUSG00000029101	Rgs12	1200016K18Rik|4632412M04Rik|AI481290|E130309H11	regulator of G-protein signaling 12	protein-coding
mm_24872.1	chr3	95977411	95977442	+	1	NA	Intergenic	Intergenic	-8084	NR_045872	668224	Mm.357766	NR_045872		Gm9054	EG668224	predicted gene 9054	ncRNA
mm_55769.1	chr6	78467546	78467575	-	1	NA	exon (NM_011260, exon 4 of 6)	exon (NM_011260, exon 4 of 6)	1314	NM_011260	19695	Mm.252385	NM_011260	ENSMUSG00000030017	Reg3g	AI449515|REG-3-gamma|reg III-gamma	regenerating islet-derived 3 gamma	protein-coding
mm_77762.1	chr9	3000191	3000216	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	38540	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_15851.1	chr2	164777520	164777534	+	1	NA	exon (NM_009394, exon 5 of 6)	exon (NM_009394, exon 5 of 6)	2207	NM_009394	21925	Mm.1716	NM_009394	ENSMUSG00000017300	Tnnc2	Tncs	troponin C2, fast	protein-coding
mm_95994.1	chr11	59204625	59204672	+	1	NA	exon (NM_026035, exon 3 of 4)	exon (NM_026035, exon 3 of 4)	2162	NM_001302336	67212	Mm.282694	NM_026035	ENSMUSG00000036860	Mrpl55	2810038N09Rik|L55mt|MRP-L55	mitochondrial ribosomal protein L55	protein-coding
mm_70430.1	chr8	11555846	11555879	+	1	NA	promoter-TSS (NM_001302457)	promoter-TSS (NM_001302457)	100	NM_001302458	26356	Mm.25709	NM_011919	ENSMUSG00000045969	Ing1	2610028J21Rik|AA407184|AI875420|mING1h|p33Ing1|p37Ing1b	inhibitor of growth family, member 1	protein-coding
mm_66747.1	chr7	46712126	46712126	-	1	NA	exon (NM_011315, exon 4 of 4)	exon (NM_011315, exon 4 of 4)	-1475	NM_030233	78935	Mm.289866	NM_030233	ENSMUSG00000006763	Saal1	5031425D22Rik|SPACIA1	serum amyloid A-like 1	protein-coding
mm_64399.1	chr7	142500261	142500333	+	1	NA	intron (NM_001347548, intron 1 of 14)	intron (NM_001347548, intron 1 of 14)	1461	NM_001347551	21957	Mm.389992	NM_011620	ENSMUSG00000061723	Tnnt3	fTnT	troponin T3, skeletal, fast	protein-coding
mm_162891.1	chr10	110455915	110455921	-	1	NA	Intergenic	CpG	-144732	NR_028438	109335	Mm.367727	NR_028438		9230102K24Rik	-	RIKEN cDNA 9230102K24 gene	ncRNA
mm_98823.1	chr11	97362321	97362332	+	1	NA	promoter-TSS (NM_138657)	promoter-TSS (NM_138657)	-225	NM_138657	192157	Mm.34339	NM_138657	ENSMUSG00000038485	Socs7	2310063P06Rik|C85125|Nap4	suppressor of cytokine signaling 7	protein-coding
mm_7412.1	chr1	119422200	119422211	-	1	NA	promoter-TSS (NM_008381)	promoter-TSS (NM_008381)	43	NM_008381	16324	Mm.3092	NM_008381	ENSMUSG00000037035	Inhbb	-	inhibin beta-B	protein-coding
mm_35667.1	chr4	43562398	43562430	-	1	NA	promoter-TSS (NM_013497)	promoter-TSS (NM_013497)	169	NM_011602	21894	Mm.208601	NM_011602	ENSMUSG00000028465	Tln1	Tln	talin 1	protein-coding
mm_110098.1	chr12	25241990	25242024	-	1	NA	Intergenic	Intergenic	112833	NR_045844	432641	Mm.112955	NR_045844		Gm17746	-	predicted gene, 17746	ncRNA
mm_79291.1	chr9	51214478	51214507	+	1	NA	intron (NM_011136, intron 1 of 4)	intron (NM_011136, intron 1 of 4)	802	NM_011136	18985	Mm.897	NM_011136	ENSMUSG00000032053	Pou2af1	BOB.1|Bob-1|Bob1|OBF-1|OBF.1|OCA-B|OCAB	POU domain, class 2, associating factor 1	protein-coding
mm_33420.1	chr4	129984894	129984896	+	1	NA	promoter-TSS (NM_173071)	promoter-TSS (NM_173071)	25	NM_001290714	230775	Mm.262241	NM_173071	ENSMUSG00000028782	Adgrb2	Bai2	adhesion G protein-coupled receptor B2	protein-coding
mm_66249.1	chr7	35585542	35585550	-	1	NA	promoter-TSS (NM_178263)	promoter-TSS (NM_178263)	36	NM_145840	243923	Mm.222680	NM_145840	ENSMUSG00000056043	Rgs9bp	R9AP|Rgs9-1bp	regulator of G-protein signalling 9 binding protein	protein-coding
mm_99607.1	chr11	104577048	104577054	+	1	NA	intron (NM_010858, intron 2 of 8)	intron (NM_010858, intron 2 of 8)	-14853	NR_130177	100415912	Mm.446786	NR_130177		Gm11665	Gm11664|OTTMUSG00000003182|OTTMUSG00000003183	predicted gene 11665	ncRNA
mm_65846.1	chr7	29248458	29248468	-	1	NA	promoter-TSS (NM_028179)	promoter-TSS (NM_028179)	4	NM_028179	72275	Mm.441142	NM_028179	ENSMUSG00000030587	2200002D01Rik	2010005J02Rik|H2RSP|IMUP|IMUP-1|IMUP-2	RIKEN cDNA 2200002D01 gene	protein-coding
mm_101302.1	chr11	22287070	22287090	-	1	NA	promoter-TSS (NM_153078)	promoter-TSS (NM_153078)	-285	NM_001252515	216565	Mm.491265	NM_153078	ENSMUSG00000042302	Ehbp1	AF424697|Flj21950|NACSIN	EH domain binding protein 1	protein-coding
mm_10901.1	chr2	25288168	25288175	+	1	NA	promoter-TSS (NM_030055)	promoter-TSS (NM_030055)	26	NM_030055	78217	Mm.160057	NM_030055	ENSMUSG00000026963	Tmem210	4930571C24Rik	transmembrane protein 210	protein-coding
mm_31882.1	chr4	82065856	82065876	+	1	NA	non-coding (NR_040659, exon 1 of 3)	non-coding (NR_040659, exon 1 of 3)	486	NR_040659	545641	Mm.216028	NR_040659	ENSMUSG00000085022	Gm5860	EG545641	predicted gene 5860	ncRNA
mm_146879.1	chr18	25679454	25679501	-	1	NA	exon (NM_001146295, exon 2 of 2)	exon (NM_001146295, exon 2 of 2)	74506	NM_133195	108013	Mm.266435	NM_133195	ENSMUSG00000024268	Celf4	A230070D14Rik|BRUNOL-4|Brul4|Brunol4|C130060B05Rik	CUGBP, Elav-like family member 4	protein-coding
mm_125575.1	chr15	59374290	59374302	+	1	NA	promoter-TSS (NM_026746)	promoter-TSS (NM_026746)	98	NM_001164604	68501	Mm.27762	NM_026746	ENSMUSG00000059586	Nsmce2	1110014D18Rik|AI661537	NSE2/MMS21 homolog, SMC5-SMC6 complex SUMO ligase	protein-coding
mm_74988.1	chr8	27156337	27156373	-	1	NA	exon (NM_001080813, exon 2 of 6)	exon (NM_001080813, exon 2 of 6)	13445	NR_045840	71082	Mm.395259	NR_045840		4933416M07Rik	-	RIKEN cDNA 4933416M07 gene	ncRNA
mm_24289.1	chr3	89245879	89245919	+	1	NA	promoter-TSS (NM_025327)	promoter-TSS (NM_025327)	-2	NM_183037	360213	Mm.331156	NM_183037	ENSMUSG00000042766	Trim46	TRIFIC	tripartite motif-containing 46	protein-coding
mm_154292.1	chr19	61140749	61140769	-	1	NA	promoter-TSS (NM_001309216)	promoter-TSS (NM_001309216)	81	NR_131956	414758	Mm.100056	NM_001001737	ENSMUSG00000074733	Zfp950	5830428H23Rik|AU016073|BC055757|Gm34518|Zfp826|mszf84	zinc finger protein 950	protein-coding
mm_145893.1	chr18	65587463	65587476	+	1	NA	intron (NM_207255, intron 2 of 5)	intron (NM_207255, intron 2 of 5)	7239	NM_207255	328977	Mm.286232	NM_207255	ENSMUSG00000042439	Zfp532	C530030I18Rik|Znf532|mKIAA1629	zinc finger protein 532	protein-coding
mm_13806.1	chr2	119047130	119047159	+	1	NA	promoter-TSS (NM_029617)	promoter-TSS (NM_029617)	25	NM_029617	76464	Mm.202518	NM_029617	ENSMUSG00000027326	Knl1	2310043D08Rik|5730505K17Rik|Casc5	kinetochore scaffold 1	protein-coding
mm_36076.1	chr4	58206324	58206334	-	1	NA	exon (NM_022814, exon 1 of 48)	exon (NM_022814, exon 1 of 48)	267	NM_022814	64817	Mm.261024	NM_022814	ENSMUSG00000028369	Svep1	1110021D17Rik|4833413O10Rik|AA387071|D430029O09Rik|Polydom	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	protein-coding
mm_85919.1	chr9	111119287	111119301	-	1	NA	intron (NM_027742, intron 1 of 13)	intron (NM_027742, intron 1 of 13)	1183	NM_001164838	71268	Mm.302287	NM_027742	ENSMUSG00000032497	Lrrfip2	5133400F20Rik|AI850587	leucine rich repeat (in FLII) interacting protein 2	protein-coding
mm_56412.1	chr6	97221741	97221772	-	1	NA	intron (NM_022992, intron 1 of 2)	intron (NM_022992, intron 1 of 2)	10964	NM_022992	65106	Mm.291014	NM_022992	ENSMUSG00000035199	Arl6ip5	5930404D22Rik|AV001879|Aip-5|Gtrap3-18|addiscin	ADP-ribosylation factor-like 6 interacting protein 5	protein-coding
mm_60587.1	chr7	44482776	44482789	+	1	NA	Intergenic	Intergenic	-1735	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_34798.1	chr4	154637547	154637564	+	1	NA	promoter-TSS (NM_027504)	promoter-TSS (NM_027504)	-682	NM_027504	70673	Mm.257785	NM_027504	ENSMUSG00000039410	Prdm16	5730557K01Rik|csp1|mel1	PR domain containing 16	protein-coding
mm_23230.1	chr3	50415776	50415805	+	1	NA	intron (NM_011990, intron 6 of 11)	intron (NM_011990, intron 6 of 11)	27823	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_17774.1	chr2	32847200	32847214	-	1	NA	promoter-TSS (NM_001113569)	promoter-TSS (NM_001113569)	25	NM_009295	20910	Mm.278865	NM_009295	ENSMUSG00000026797	Stxbp1	AI317162|AI326233|MMS10-G|Ms10g|Munc-18a|Munc18-1|N-sec1|Rb-sec1|Sxtbp1|Unc18-1|Unc18h|nsec1	syntaxin binding protein 1	protein-coding
mm_172573.1	chr8	11312825	11312828	+	1	NA	promoter-TSS (NM_009932)	promoter-TSS (NM_009932)	0	NR_133670	12826	Mm.738	NM_009931	ENSMUSG00000031502	Col4a1	Bru|Col4a-1|Raw|Svc	collagen, type IV, alpha 1	protein-coding
mm_111031.1	chr12	79172610	79172672	-	1	NA	promoter-TSS (NM_016800)	promoter-TSS (NM_016800)	-183	NM_016800	53612	Mm.265929	NM_016800	ENSMUSG00000021124	Vti1b	AU015348|GES30|MVti1b|SNARE|Vti1-rp1	vesicle transport through interaction with t-SNAREs 1B	protein-coding
mm_76838.1	chr8	105283214	105283236	-	1	NA	exon (NM_028888, exon 6 of 8)	exon (NM_028888, exon 6 of 8)	6303	NM_001166394	74356	Mm.204876	NM_028888	ENSMUSG00000014837	4931428F04Rik	AI426165|Kiaa0895l	RIKEN cDNA 4931428F04 gene	protein-coding
mm_69480.1	chr7	133776712	133776734	-	1	NA	promoter-TSS (NM_025850)	promoter-TSS (NM_025850)	80	NM_001286032	101437	Mm.199223	NM_133941	ENSMUSG00000030986	Dhx32	3110079L04Rik|4732469F02Rik|AA408140|Ddx32	DEAH (Asp-Glu-Ala-His) box polypeptide 32	protein-coding
mm_156257.1	chrX	136788462	136788504	+	1	NA	intron (NR_033324, intron 8 of 9)	ORR1D1|LTR|ERVL-MaLR	-8762	NM_010297	14657	Mm.215168	NM_010297	ENSMUSG00000018595	Glra4	-	glycine receptor, alpha 4 subunit	protein-coding
mm_79035.1	chr9	46127234	46127237	+	1	NA	intron (NM_027498, intron 3 of 24)	intron (NM_027498, intron 3 of 24)	-101395	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2|apo-AI|apoA-I	apolipoprotein A-I	protein-coding
mm_36375.1	chr4	76570348	76570351	-	1	NA	intron (NM_011211, intron 10 of 39)	intron (NM_011211, intron 10 of 39)	-1292063	NM_025849	66928	Mm.24332	NM_025849	ENSMUSG00000028398	Tmem261	1700027K24Rik|3110001D03Rik	transmembrane protein 261	protein-coding
mm_15573.1	chr2	158666659	158666672	+	1	NA	promoter-TSS (NM_001159662)	promoter-TSS (NM_001159662)	-68	NM_153089	228852	Mm.150540	NM_153089	ENSMUSG00000037754	Ppp1r16b	ANKRD4|C130078N17Rik|TIMAP|Wdt4	protein phosphatase 1, regulatory (inhibitor) subunit 16B	protein-coding
mm_139228.1	chr17	47730721	47730728	+	1	NA	exon (NM_025973, exon 5 of 9)	exon (NM_025973, exon 5 of 9)	3882	NM_025973	109820	Mm.22957	NM_025973	ENSMUSG00000023987	Pgc	2210410L06Rik|Upg-1|Upg1	progastricsin (pepsinogen C)	protein-coding
mm_41174.1	chr5	88002580	88002583	+	1	NA	promoter-TSS (NM_011422)	promoter-TSS (NM_011422)	56	NM_011422	20599	Mm.261199	NM_011422	ENSMUSG00000029280	Smr3a	AA589601|MSG1|MSG3|Smr1|Smr3	submaxillary gland androgen regulated protein 3A	protein-coding
mm_171420.1	chr4	13378093	13378095	+	1	NA	Intergenic	L1VL1|LINE|L1	-365208	NM_001111026	12395	Mm.4909	NM_009822	ENSMUSG00000006586	Runx1t1	Cbfa2t1h|ETO|MTG8	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	protein-coding
mm_120964.1	chr14	77904366	77904441	+	1	NA	5' UTR (NM_029495, exon 1 of 12)	5' UTR (NM_029495, exon 1 of 12)	164	NM_029495	108670	Mm.68134	NM_029495	ENSMUSG00000022014	Epsti1	2310046K10Rik|5033415K03Rik|BRESI1	epithelial stromal interaction 1 (breast)	protein-coding
mm_104667.1	chr11	97657313	97657323	-	1	NA	Intergenic	MT2B2|LTR|ERVL	-6094	NM_139311	246198	Mm.23685	NM_139311	ENSMUSG00000038437	Mllt6	AI315037|Af17	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 6	protein-coding
mm_112332.1	chr12	115912817	115912839	-	1	NA	Intergenic	Intergenic	-134896	NM_001004066	56220	Mm.254997	NM_019565	ENSMUSG00000042063	Zfp386	Kzf1|mKIAA4205	zinc finger protein 386 (Kruppel-like)	protein-coding
mm_82014.1	chr9	121719288	121719305	+	1	NA	intron (NM_010918, intron 1 of 16)	CpG	115	NM_010918	18087	Mm.32842	NM_010918	ENSMUSG00000032525	Nktr	5330401F18Rik|D9Wsu172e	natural killer tumor recognition sequence	protein-coding
mm_26814.1	chr3	10254214	10254262	-	1	NA	intron (NM_029310, intron 2 of 5)	intron (NM_029310, intron 2 of 5)	-45662	NM_024406	11770	Mm.582	NM_024406	ENSMUSG00000062515	Fabp4	422/aP2|ALBP/Ap2|Ap2|Lbpl	fatty acid binding protein 4, adipocyte	protein-coding
mm_114649.1	chr13	77135514	77135583	+	1	NA	promoter-TSS (NM_134071)	promoter-TSS (NM_134071)	12	NM_001145676	72371	Mm.81475	NM_028215	ENSMUSG00000071252	2210408I21Rik	-	RIKEN cDNA 2210408I21 gene	protein-coding
mm_143777.1	chr17	81712908	81712913	-	1	NA	intron (NR_104580, intron 1 of 8)	intron (NR_104580, intron 1 of 8)	25477	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_92026.1	chr10	62449739	62449757	-	1	NA	promoter-TSS (NM_181423)	promoter-TSS (NM_181423)	-55	NM_181423	338359	Mm.235898	NM_181423	ENSMUSG00000020079	Supv3l1	6330443E10Rik	suppressor of var1, 3-like 1 (S. cerevisiae)	protein-coding
mm_110756.1	chr12	70111259	70111274	-	1	NA	intron (NM_001286079, intron 1 of 28)	CpG	363	NR_104398	18080	Mm.244047	NM_008697	ENSMUSG00000021068	Nin	3110068G20Rik|AI385615|AU024711|mKIAA1565	ninein	protein-coding
mm_131601.1	chr16	19063295	19063331	+	1	NA	Intergenic	Intergenic	186563	NM_010435	15260	Mm.15694	NM_010435	ENSMUSG00000022702	Hira	AA138857|D16Ertd95e|Gm15797|N28177|OTTMUSG00000026264|Tuple1	histone cell cycle regulator	protein-coding
mm_1227.1	chr1	62758264	62758279	+	1	NA	intron (NM_001077405, intron 7 of 15)	B1F|SINE|Alu	36461	NR_040601	74992	Mm.401979	NR_040601		4930487H11Rik	-	RIKEN cDNA 4930487H11 gene	ncRNA
mm_135300.1	chr16	38678408	38678418	-	1	NA	intron (NM_020260, intron 1 of 11)	RCHARR1|DNA|hAT-Charlie	34622	NM_020260	12549	Mm.370848	NM_020260	ENSMUSG00000022799	Arhgap31	5830477L08Rik|AU041750|Cdgap|D330026I07Rik	Rho GTPase activating protein 31	protein-coding
mm_42015.1	chr5	108132886	108132896	+	1	NA	promoter-TSS (NM_028481)	promoter-TSS (NM_028481)	-23	NM_028481	73254	Mm.441231	NM_028481	ENSMUSG00000056531	Ccdc18	1700021E15Rik|4932411G06Rik|NY-SAR-41	coiled-coil domain containing 18	protein-coding
mm_72715.1	chr8	84997849	84997858	+	1	NA	intron (NM_133255, intron 14 of 21)	intron (NM_133255, intron 14 of 21)	7258	NM_001167991	170833	Mm.247775	NM_133255	ENSMUSG00000052566	Hook2	A630054I03Rik	hook microtubule tethering protein 2	protein-coding
mm_163269.1	chr11	115163357	115163371	+	1	NA	promoter-TSS (NM_012030)	promoter-TSS (NM_012030)	23	NM_012030	26941	Mm.27842	NM_012030	ENSMUSG00000020733	Slc9a3r1	EBP-50|NHE-RF|NHERF-1|NHERF1	solute carrier family 9 (sodium/hydrogen exchanger), member 3 regulator 1	protein-coding
mm_172373.1	chr7	126324972	126324972	-	1	NA	Intergenic	Intergenic	43073	NR_106025	102466797		NR_106025	ENSMUSG00000099017	Mir7058	Gm27766|mmu-mir-7058	microRNA 7058	ncRNA
mm_152328.1	chr19	9954199	9954222	-	1	NA	Intergenic	B4A|SINE|B4	-26390	NR_073181	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
mm_145891.1	chr18	65582391	65582399	+	1	NA	intron (NM_207255, intron 1 of 5)	intron (NM_207255, intron 1 of 5)	2165	NM_207255	328977	Mm.286232	NM_207255	ENSMUSG00000042439	Zfp532	C530030I18Rik|Znf532|mKIAA1629	zinc finger protein 532	protein-coding
mm_64008.1	chr7	140203779	140203788	+	1	NA	Intergenic	Intergenic	-1015	NM_001011814	258055	Mm.377339	NM_001011814	ENSMUSG00000050366	Olfr524	MOR103-14P	olfactory receptor 524	protein-coding
mm_45657.1	chr5	77114873	77114886	-	1	NA	5' UTR (NM_175606, exon 1 of 3)	5' UTR (NM_175606, exon 1 of 3)	244	NM_175606	74318	Mm.181852	NM_175606	ENSMUSG00000059325	Hopx	1110018K11Rik|1200015P04Rik|2300002F06Rik|AI848177|AW490897|Cameo|Hdop|Hod|Hop|Ob1|Obl|Toto	HOP homeobox	protein-coding
mm_33226.1	chr4	126756549	126756580	+	1	NA	intron (NM_133886, intron 1 of 20)	MIR3|SINE|MIR	2794	NM_001035526	100317	Mm.206206	NM_133886	ENSMUSG00000028830	AU040320	A730047D20Rik|AAVR|Kiaa0319l	expressed sequence AU040320	protein-coding
mm_57232.1	chr6	123282810	123282827	-	1	NA	3' UTR (NM_019948, exon 6 of 6)	3' UTR (NM_019948, exon 6 of 6)	7053	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_131260.1	chr16	10791584	10791591	+	1	NA	promoter-TSS (NM_013638)	promoter-TSS (NM_013638)	518	NM_008933	19119	Mm.325769	NM_008933	ENSMUSG00000038015	Prm2	AI528784|Prm-2	protamine 2	protein-coding
mm_127051.1	chr15	96700085	96700093	+	1	NA	promoter-TSS (NM_175121)	promoter-TSS (NM_175121)	-391	NM_175121	67760	Mm.46754	NM_175121	ENSMUSG00000022462	Slc38a2	5033402L14Rik|AI316867|ATA2|SAT2|mKIAA1382	solute carrier family 38, member 2	protein-coding
mm_120960.1	chr14	77520173	77520204	+	1	NA	intron (NM_001253759, intron 7 of 19)	RLTR25A|LTR|ERVK	-13320	NR_033141	629678	Mm.390721	NM_001037935	ENSMUSG00000067973	Gm6994	EG629678	predicted gene 6994	ncRNA
mm_52021.1	chr6	94680943	94680952	+	1	NA	intron (NM_008377, intron 1 of 18)	intron (NM_008377, intron 1 of 18)	19198	NM_008377	16206	Mm.245210	NM_008377	ENSMUSG00000030029	Lrig1	D6Bwg0781e|Img|LIG-1	leucine-rich repeats and immunoglobulin-like domains 1	protein-coding
mm_172842.1	chr9	3258928	3258935	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-59118	NR_027988	114673	Mm.422774	NM_053265	ENSMUSG00000042360	4930433N12Rik	-	RIKEN cDNA 4930433N12 gene	ncRNA
mm_73430.1	chr8	106135870	106135889	+	1	NA	intron (NR_040344, intron 1 of 4)	intron (NR_040344, intron 1 of 4)	479	NR_040346	69771	Mm.393274	NR_040344		1810019D21Rik	-	RIKEN cDNA 1810019D21 gene	ncRNA
mm_43882.1	chr5	143817787	143817818	+	1	NA	Intergenic	CpG	-54060	NM_013557	15467	Mm.389709	NM_013557	ENSMUSG00000029613	Eif2ak1	HCR|Hri	eukaryotic translation initiation factor 2 alpha kinase 1	protein-coding
mm_2454.1	chr1	101302415	101302426	+	1	NA	Intergenic	L1Md_T|LINE|L1	146652	NR_037989	100504525	Mm.87065	NR_037989	ENSMUSG00000100684	Gm20268	-	predicted gene, 20268	ncRNA
mm_27107.1	chr3	30647794	30647876	-	1	NA	promoter-TSS (NM_001290510)	promoter-TSS (NM_001290510)	-17	NM_027941	71827	Mm.45373	NM_027941	ENSMUSG00000027702	Lrrc34	1700007J06Rik|SPATA34	leucine rich repeat containing 34	protein-coding
mm_136485.1	chr16	96082390	96082481	-	1	NA	promoter-TSS (NM_145125)	promoter-TSS (NM_145125)	-7	NM_145125	93871	Mm.240871	NM_145125	ENSMUSG00000022914	Brwd1	5330419I02Rik|D530019K20Rik|G1-403-16|Wdr9|repro5	bromodomain and WD repeat domain containing 1	protein-coding
mm_16032.1	chr2	167642599	167642616	+	1	NA	TTS (NM_145538)	TTS (NM_145538)	-10602	NM_023230	66589	Mm.278783	NM_023230	ENSMUSG00000078923	Ube2v1	0610011J09Rik|AI256840|CROC-1|CROC1|D7Bwg1382e|UEV-1	ubiquitin-conjugating enzyme E2 variant 1	protein-coding
mm_137421.1	chr17	26202947	26203016	+	1	NA	promoter-TSS (NM_001081069)	promoter-TSS (NM_001081069)	19	NM_001081069	50782	Mm.109840	NM_001081069	ENSMUSG00000024186	Rgs11	C78048	regulator of G-protein signaling 11	protein-coding
mm_134990.1	chr16	32144510	32144520	-	1	NA	exon (NM_001347181, exon 3 of 3)	exon (NM_001347181, exon 3 of 3)	20961	NM_146069	224109	Mm.33498	NM_146069	ENSMUSG00000052384	Nrros	E430025L02Rik|Lrcc33|Lrrc33	negative regulator of reactive oxygen species	protein-coding
mm_170397.1	chr1	86359011	86359014	-	1	NA	promoter-TSS (NR_015507)	promoter-TSS (NR_015507)	443	NM_010880	17975	Mm.154378	NM_010880	ENSMUSG00000026234	Ncl	B530004O11Rik|C23|D0Nds28|D1Nds28|Nucl	nucleolin	protein-coding
mm_10886.1	chr2	25262557	25262563	+	1	NA	promoter-TSS (NM_175286)	promoter-TSS (NM_175286)	-38	NM_175286	97031	Mm.308539	NM_175286	ENSMUSG00000048707	Tprn	C430004E15Rik|C87750	taperin	protein-coding
mm_127467.1	chr15	101272767	101272773	+	1	NA	exon (NM_010444, exon 5 of 7)	exon (NM_010444, exon 5 of 7)	5924	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_28633.1	chr3	95193737	95193738	-	1	NA	intron (NM_029885, intron 7 of 9)	intron (NM_029885, intron 7 of 9)	-23720	NR_108026	100504029	Mm.478537	NR_108026	ENSMUSG00000097167	Gm16740	-	predicted gene, 16740	ncRNA
mm_59262.1	chr7	24884658	24884681	+	1	NA	promoter-TSS (NM_023133)	promoter-TSS (NM_023133)	-45	NM_023133	20085	Mm.300281	NM_023133	ENSMUSG00000040952	Rps19	Dsk3	ribosomal protein S19	protein-coding
mm_59103.1	chr7	19701310	19701329	+	1	NA	TTS (NM_001109748)	TTS (NM_001109748)	-2131	NM_009696	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_116007.1	chr13	24604790	24604795	-	1	NA	promoter-TSS (NR_024599)	promoter-TSS (NR_024599)	-25	NR_024599	76024	Mm.440710	NR_024599		Gm11346	5830431A10Rik|AI447617|Gm11347|OTTMUSG00000000601|OTTMUSG00000000602	X-linked lymphocyte-regulated 5 pseudogene	pseudo
mm_62233.1	chr7	98563228	98563236	+	1	NA	Intergenic	Intergenic	69010	NM_001113379	434215	Mm.323057	NM_001113379	ENSMUSG00000090958	Lrrc32	AI426318|D11S833Eh|D7H11S833E|EG434215|Garp	leucine rich repeat containing 32	protein-coding
mm_107191.1	chr12	25099827	25099836	+	1	NA	Intergenic	Intergenic	-3739	NM_010496	15902	Mm.34871	NM_010496	ENSMUSG00000020644	Id2	AI255428|C78922|Idb2|bHLHb26	inhibitor of DNA binding 2	protein-coding
mm_112151.1	chr12	113260218	113260232	-	1	NA	Intergenic	Intergenic	74322	NM_153776	69195	Mm.313244	NM_153776	ENSMUSG00000049036	Tmem121	2410008J05Rik|Hole	transmembrane protein 121	protein-coding
mm_86753.1	chr10	19598389	19598393	+	1	NA	intron (NM_010511, intron 2 of 6)	MRLTR33|LTR|ERVK	6442	NM_010511	15979	Mm.549	NM_010511	ENSMUSG00000020009	Ifngr1	CD119|IFN-gammaR|Ifgr|Ifngr|Nktar	interferon gamma receptor 1	protein-coding
mm_157952.1	chrX	87238376	87238416	-	1	NA	intron (NM_001160403, intron 5 of 10)	intron (NM_001160403, intron 5 of 10)	877227	NM_001160403	331461	Mm.121680	NM_001160403	ENSMUSG00000052372	Il1rapl1	6330532G10Rik|C030039N24|IL1R8|IL1RAPL|MRX34|OPHN4|TIGIRR-2	interleukin 1 receptor accessory protein-like 1	protein-coding
mm_114126.1	chr13	55210401	55210470	+	1	NA	intron (NM_008739, intron 1 of 22)	CpG	653	NM_008739	18193	Mm.12964	NM_008739	ENSMUSG00000021488	Nsd1	AI528500|KMT3B	nuclear receptor-binding SET-domain protein 1	protein-coding
mm_6333.1	chr1	71627280	71627333	-	1	NA	exon (NM_001276413, exon 18 of 44)	exon (NM_001276413, exon 18 of 44)	25928	NM_010233	14268	Mm.193099	NM_010233	ENSMUSG00000026193	Fn1	E330027I09|Fn|Fn-1	fibronectin 1	protein-coding
mm_139107.1	chr17	47314011	47314037	+	1	NA	5' UTR (NM_172622, exon 3 of 17)	5' UTR (NM_172622, exon 3 of 17)	-54863	NM_001146212	64657	Mm.216250	NM_183086	ENSMUSG00000034729	Mrps10	1110038B19Rik|AW743084|Rpms10	mitochondrial ribosomal protein S10	protein-coding
mm_163849.1	chr14	19418225	19418245	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	184352	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_89253.1	chr10	87859234	87859244	+	1	NA	5' UTR (NM_010512, exon 1 of 5)	5' UTR (NM_010512, exon 1 of 5)	187	NM_010512	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_155906.1	chrX	101695834	101695841	+	1	NA	Intergenic	CpG	38310	NM_009910	12766	Mm.12876	NM_009910	ENSMUSG00000050232	Cxcr3	Cd183|Cmkar3	chemokine (C-X-C motif) receptor 3	protein-coding
mm_77811.1	chr9	3038014	3038034	+	1	NA	TTS (NR_039546)	TTS (NR_039546)	719	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_95088.1	chr11	33529949	33529985	+	1	NA	Intergenic	MIR3|SINE|MIR	-16221	NM_023146	66011	Mm.383775	NM_023146	ENSMUSG00000040594	Ranbp17	-	RAN binding protein 17	protein-coding
mm_63843.1	chr7	135651926	135651944	+	1	NA	promoter-TSS (NM_001316681)	promoter-TSS (NM_001316681)	36	NM_001316681	19267	Mm.945	NM_011212	ENSMUSG00000041836	Ptpre	PTPe|PTPepsilon|RPTPepsilon	protein tyrosine phosphatase, receptor type, E	protein-coding
mm_66077.1	chr7	30944020	30944035	-	1	NA	promoter-TSS (NM_032541)	promoter-TSS (NM_032541)	2	NM_032541	84506	Mm.439939	NM_032541	ENSMUSG00000050440	Hamp	Hamp1|Hepc|Hepc1	hepcidin antimicrobial peptide	protein-coding
mm_10927.1	chr2	25431239	25431254	+	1	NA	intron (NM_007379, intron 1 of 47)	intron (NM_007379, intron 1 of 47)	2572	NM_007379	11305	Mm.2210	NM_007379	ENSMUSG00000026944	Abca2	AI413825|Abc2|D2H0S1474E|mKIAA1062	ATP-binding cassette, sub-family A (ABC1), member 2	protein-coding
mm_6493.1	chr1	74194654	74194658	-	1	NA	promoter-TSS (NM_178241)	promoter-TSS (NM_178241)	-25	NM_178241	227288	Mm.337035	NM_178241	ENSMUSG00000048480	Cxcr1	Il8ra	chemokine (C-X-C motif) receptor 1	protein-coding
mm_24783.1	chr3	95541608	95541623	+	1	NA	intron (NM_001267695, intron 3 of 7)	intron (NM_001267695, intron 3 of 7)	14829	NM_001267695	13040	Mm.3619	NM_021281	ENSMUSG00000038642	Ctss	Cats	cathepsin S	protein-coding
mm_145656.1	chr18	61130551	61130577	+	1	NA	TTS (NM_178277)	TTS (NM_178277)	13096	NR_105949	102466212		NR_105949	ENSMUSG00000098389	Mir6983	Gm27496|mmu-mir-6983	microRNA 6983	ncRNA
mm_92142.1	chr10	67011238	67011254	-	1	NA	3' UTR (NM_001204915, exon 9 of 9)	3' UTR (NM_001204915, exon 9 of 9)	6171	NR_110511	102634101	Mm.445258	NR_110511		Gm31763	-	predicted gene, 31763	ncRNA
mm_120157.1	chr14	60709346	60709358	+	1	NA	intron (NM_001033272, intron 3 of 12)	intron (NM_001033272, intron 3 of 12)	-23552	NM_001310594	219140	Mm.149776	NM_001033272	ENSMUSG00000021990	Spata13	C79050|ESTM11|X83327|mFLJ00298	spermatogenesis associated 13	protein-coding
mm_104935.1	chr11	100096238	100096242	-	1	NA	promoter-TSS (NM_016880)	promoter-TSS (NM_016880)	-16	NM_016880	53617	Mm.37952	NM_016880	ENSMUSG00000048013	Krt35	AI662400|Ha5|Krt1-24|Krtha5	keratin 35	protein-coding
mm_96067.1	chr11	59740259	59740278	+	1	NA	promoter-TSS (NR_045476)	promoter-TSS (NR_045476)	-114	NR_045476	69320	Mm.443242	NR_045476	ENSMUSG00000086330	1700007J10Rik	4930573L17Rik	RIKEN cDNA 1700007J10 gene	ncRNA
mm_55230.1	chr6	52240658	52240668	-	1	NA	5' UTR (NM_001122950, exon 1 of 2)	5' UTR (NM_001122950, exon 1 of 2)	191	NM_001122950	15395	Mm.5	NM_008263	ENSMUSG00000000938	Hoxa10	Hox-1.8|Hoxa-10	homeobox A10	protein-coding
mm_86215.1	chr9	120023559	120023574	-	1	NA	promoter-TSS (NM_011724)	promoter-TSS (NM_011724)	32	NM_011724	22437	Mm.10117	NM_011724	ENSMUSG00000079243	Xirp1	AI415219|Cmya1	xin actin-binding repeat containing 1	protein-coding
mm_22283.1	chr2	180104444	180104454	-	1	NA	promoter-TSS (NM_133849)	promoter-TSS (NM_133849)	-42	NM_133849	99296	Mm.285360	NM_133849	ENSMUSG00000039059	Hrh3	AW049250|H3R|HH3R	histamine receptor H3	protein-coding
mm_16318.1	chr2	174304362	174304372	+	1	NA	intron (NM_001310085, intron 2 of 12)	RMER12C|LTR|ERVK	6508	NM_001310085	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_78472.1	chr9	32652503	32652510	+	1	NA	Intergenic	B3A|SINE|B2	-43536	NM_011808	23871	Mm.292415	NM_011808	ENSMUSG00000032035	Ets1	AI196000|AI448617|D230050P06|Ets-1|Tpl1|vs	E26 avian leukemia oncogene 1, 5' domain	protein-coding
mm_5126.1	chr1	9631150	9631173	-	1	NA	promoter-TSS (NR_015470)	promoter-TSS (NR_015470)	-69	NR_015470	72481	Mm.279818	NR_015470	ENSMUSG00000079671	2610203C22Rik	2310007M24Rik	RIKEN cDNA 2610203C22 gene	ncRNA
mm_4412.1	chr1	172496274	172496293	+	1	NA	exon (NM_001145800, exon 17 of 21)	exon (NM_001145800, exon 17 of 21)	-3963	NM_178598	21346	Mm.271711	NM_178598	ENSMUSG00000026547	Tagln2	2700094C18Rik|SM22beta|Sm22B|Sm22a	transgelin 2	protein-coding
mm_17804.1	chr2	33371401	33371484	-	1	NA	promoter-TSS (NM_175211)	promoter-TSS (NM_175211)	52	NM_001290570	241308	Mm.274249	NM_175211	ENSMUSG00000038831	Ralgps1	5830418G11Rik|AI853783|AI854138|RALGEF2|RALGPS1A|RalGEF 2|mKIAA0351	Ral GEF with PH domain and SH3 binding motif 1	protein-coding
mm_159769.1	chr5	100039358	100039358	-	1	NA	promoter-TSS (NM_016690)	promoter-TSS (NM_016690)	-136	NM_016690	50926	Mm.389579	NM_016690	ENSMUSG00000029328	Hnrnpdl	AA407431|AA959857|D5Ertd650e|D5Wsu145e|Hnrnpdl1|Hnrpdl|JKTBP|hnRNP DL|hnRNP-DL	heterogeneous nuclear ribonucleoprotein D-like	protein-coding
mm_146287.1	chr18	78476863	78476871	+	1	NA	intron (NM_030683, intron 2 of 11)	intron (NM_030683, intron 2 of 11)	120083	NM_207651	27411	Mm.44158	NM_030683	ENSMUSG00000024552	Slc14a2	UT-A1|UT-A3	solute carrier family 14 (urea transporter), member 2	protein-coding
mm_151947.1	chr19	5801072	5801074	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	1599	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_159874.1	chr5	149528670	149528670	+	1	NA	promoter-TSS (NM_029440)	promoter-TSS (NM_029440)	-9	NM_029440	381693	Mm.136919	NM_029440	ENSMUSG00000029658	Wdr95	4930434E21Rik	WD40 repeat domain 95	protein-coding
mm_127040.1	chr15	96641056	96641070	+	1	NA	5' UTR (NM_134086, exon 1 of 16)	5' UTR (NM_134086, exon 1 of 16)	899	NM_134086	105727	Mm.103568	NM_134086	ENSMUSG00000023169	Slc38a1	AA408026|AA409865|AL022800|AU015942|NAT2	solute carrier family 38, member 1	protein-coding
mm_24920.1	chr3	96402119	96402121	+	1	NA	Intergenic	CpG	12713	NR_001579	21748		NR_001579	ENSMUSG00000064796	Terc	mTER|mTR	telomerase RNA component	ncRNA
mm_117549.1	chr13	84055921	84055923	-	1	NA	intron (NR_131220, intron 1 of 1)	intron (NR_131220, intron 1 of 1)	8852	NR_131220	553095	Mm.39702	NR_131220	ENSMUSG00000098087	Gm17750	-	predicted gene, 17750	ncRNA
mm_133482.1	chr16	90219662	90219686	+	1	NA	Intergenic	L1_Mus1|LINE|L1	-1068	NM_011434	20655	Mm.276325	NM_011434	ENSMUSG00000022982	Sod1	B430204E11Rik|Cu/Zn-SOD|CuZnSOD|Ipo-1|Ipo1|SODC|Sod-1	superoxide dismutase 1, soluble	protein-coding
mm_115727.1	chr13	17215512	17215550	-	1	NA	intron (NM_138654, intron 12 of 13)	intron (NM_138654, intron 12 of 13)	479234	NM_138654	192136	Mm.364180	NM_138654	ENSMUSG00000055137	Sugct	5033411D12Rik|D17907	succinyl-CoA glutarate-CoA transferase	protein-coding
mm_134945.1	chr16	31275282	31275290	-	1	NA	promoter-TSS (NM_025800)	promoter-TSS (NM_025800)	-9	NM_025800	66849	Mm.291593	NM_025800	ENSMUSG00000047714	Ppp1r2	0610025N14Rik|2310007G06Rik|4930440J04Rik|5430408E15Rik|D16Ertd248e|IPP-2	protein phosphatase 1, regulatory (inhibitor) subunit 2	protein-coding
mm_81859.1	chr9	118776505	118776507	+	1	NA	intron (NM_001113514, intron 2 of 13)	intron (NM_001113514, intron 2 of 13)	64814	NM_001113514	104099	Mm.335520	NM_133721	ENSMUSG00000039115	Itga9	(alpha)9|2610002H11Rik|6720458D17Rik|AI461869|D130073C02|D9Ertd428e	integrin alpha 9	protein-coding
mm_162159.1	chrX	92490004	92490004	+	1	NA	promoter-TSS (NM_001034103)	promoter-TSS (NM_001034103)	55	NM_001034103	546347	Mm.380183	NM_001034103	ENSMUSG00000071726	Gm5941	EG546347	predicted gene 5941	protein-coding
mm_52229.1	chr6	103574600	103574602	+	1	NA	intron (NM_007697, intron 2 of 26)	intron (NM_007697, intron 2 of 26)	63725	NM_007697	12661	Mm.251288	NM_007697	ENSMUSG00000030077	Chl1	A530023M13Rik|AI465420|CALL|LICAM2	cell adhesion molecule L1-like	protein-coding
mm_19561.1	chr2	98667333	98667341	-	1	NA	Intergenic	Intergenic	1199680	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_173355.1	chrY	90814763	90814764	+	1	NA	intron (NM_133362, intron 2 of 3)	IMPB_01|Satellite|Satellite	24643	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_23766.1	chr3	73397556	73397559	+	1	NA	intron (NR_040547, intron 2 of 7)	intron (NR_040547, intron 2 of 7)	84094	NR_040547	74693	Mm.292227	NR_040547	ENSMUSG00000102362	4930509J09Rik	-	RIKEN cDNA 4930509J09 gene	ncRNA
mm_92097.1	chr10	62887462	62887473	-	1	NA	Intergenic	Intergenic	-7453	NM_001253857	52463	Mm.17774	NM_027384	ENSMUSG00000047146	Tet1	2510010B09Rik|AA517754|BB001228|Cxxc6|D10Ertd17e|LCX|mKIAA1676	tet methylcytosine dioxygenase 1	protein-coding
mm_86803.1	chr10	20312956	20312976	+	1	NA	intron (NM_001025392, intron 1 of 12)	CpG	497	NM_001025393	72567	Mm.294783	NM_153787	ENSMUSG00000037608	Bclaf1	2610102K23Rik|2700025J07Rik|2810454G14Rik|5730534O06Rik|AI450190|AW556225|Btf|mKIAA0164	BCL2-associated transcription factor 1	protein-coding
mm_38932.1	chr4	150192574	150192585	-	1	NA	exon (NM_009802, exon 6 of 8)	exon (NM_009802, exon 6 of 8)	8556	NM_009802	12353	Mm.232523	NM_009802	ENSMUSG00000028972	Car6	Ca6|DOC1	carbonic anhydrase 6	protein-coding
mm_102175.1	chr11	53980355	53980384	-	1	NA	promoter-TSS (NM_019723)	promoter-TSS (NM_019723)	-342	NM_019723	56517	Mm.154284	NM_019723	ENSMUSG00000063652	Slc22a21	Octn3|Slc22a9	solute carrier family 22 (organic cation transporter), member 21	protein-coding
mm_13230.1	chr2	97526137	97526140	+	1	NA	intron (NM_001289744, intron 1 of 1)	MIRb|SINE|MIR	58481	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_157034.1	chrX	7947764	7947776	-	1	NA	5' UTR (NM_010413, exon 1 of 29)	5' UTR (NM_010413, exon 1 of 29)	119	NM_001130416	15185	Mm.29854	NM_010413	ENSMUSG00000031161	Hdac6	Hd6|Hdac5|Sfc6|mHDA2	histone deacetylase 6	protein-coding
mm_51315.1	chr6	72314476	72314496	+	1	NA	TTS (NM_001282071)	TTS (NM_001282071)	9876	NM_147779	20388	Mm.46033	NM_147779	ENSMUSG00000056370	Sftpb	AI562151|SF-B|SP-B|Sftp-3|Sftp3	surfactant associated protein B	protein-coding
mm_118122.1	chr13	104178169	104178181	-	1	NA	promoter-TSS (NM_030731)	promoter-TSS (NM_030731)	291	NM_025879	66975	Mm.272541	NM_025879	ENSMUSG00000021711	Trappc13	2410002O22Rik|2610524F24Rik|AI451892|AU017229	trafficking protein particle complex 13	protein-coding
mm_144613.1	chr18	32816898	32816942	+	1	NA	promoter-TSS (NR_033206)	promoter-TSS (NR_033206)	60	NR_033206	53603	Mm.143716	NM_021367	ENSMUSG00000024379	Tslp	-	thymic stromal lymphopoietin	protein-coding
mm_44480.1	chr5	23434308	23434359	-	1	NA	promoter-TSS (NM_026984)	promoter-TSS (NM_026984)	20	NR_040469	269630	Mm.425231	NR_040469	ENSMUSG00000073147	5031425E22Rik	-	RIKEN cDNA 5031425E22 gene	ncRNA
mm_9766.1	chr1	180989852	180989862	-	1	NA	exon (NM_010145, exon 9 of 9)	exon (NM_010145, exon 9 of 9)	27712	NM_010145	13849	Mm.9075	NM_010145	ENSMUSG00000038776	Ephx1	EH|Eph-1|Eph1|Epxh1|mEH	epoxide hydrolase 1, microsomal	protein-coding
mm_140257.1	chr17	84511833	84511913	+	1	NA	promoter-TSS (NM_177606)	promoter-TSS (NM_177606)	-22	NM_177606	213556	Mm.215159	NM_177606	ENSMUSG00000040852	Plekhh2	AI256725|E030001K05|mKIAA2028	pleckstrin homology domain containing, family H (with MyTH4 domain) member 2	protein-coding
mm_94483.1	chr11	6588980	6588980	+	1	NA	intron (NM_146014, intron 4 of 9)	intron (NM_146014, intron 4 of 9)	17074	NM_001081652	192950	Mm.337771	NM_001081652	ENSMUSG00000041073	Nacad	D230024G13Rik|mKIAA0363	NAC alpha domain containing	protein-coding
mm_87146.1	chr10	34484847	34484850	+	1	NA	intron (NM_010237, intron 2 of 8)	intron (NM_010237, intron 2 of 8)	1448	NM_010237	14302	Mm.332432	NM_010237	ENSMUSG00000019779	Frk	BSK|BSK/IYK|C85044|GTK|RAK	fyn-related kinase	protein-coding
mm_104199.1	chr11	87984277	87984279	-	1	NA	intron (NM_001168471, intron 1 of 2)	B1_Mur3|SINE|Alu	2307	NM_001168472	68097	Mm.246436	NM_026556	ENSMUSG00000020483	Dynll2	1700064A15Rik|6720463E02Rik|C87222|DLC8|DLC8b|Dlc2	dynein light chain LC8-type 2	protein-coding
mm_151298.1	chr19	55514245	55514255	+	1	NA	intron (NM_001293686, intron 7 of 7)	intron (NM_001293686, intron 7 of 7)	187954	NR_045318	77594	Mm.329924	NR_045318	ENSMUSG00000097632	4930552P12Rik	-	RIKEN cDNA 4930552P12 gene	ncRNA
mm_103842.1	chr11	83045004	83045029	-	1	NA	Intergenic	MTB|LTR|ERVL-MaLR	-4483	NR_073524	237887	Mm.341645	NM_181542	ENSMUSG00000072621	Slfn10-ps	Slfn10|mFLJ00257	schlafen 10, pseudogene	pseudo
mm_50634.1	chr6	51326914	51326917	+	1	NA	Intergenic	MER5A|DNA|hAT-Charlie	-52795	NR_110455	625167	Mm.389772	NR_110455	ENSMUSG00000107660	Gm6559	EG625167	predicted gene 6559	ncRNA
mm_56702.1	chr6	114969930	114969940	-	1	NA	Intergenic	CpG	-48183	NM_177683	232334	Mm.268357	NM_177683	ENSMUSG00000030315	Vgll4	BC048841|VGL-4	vestigial like family member 4	protein-coding
mm_90681.1	chr10	128909870	128909873	+	1	NA	promoter-TSS (NM_007653)	promoter-TSS (NM_007653)	5	NM_007653	12512	Mm.371552	NM_007653	ENSMUSG00000025351	Cd63	C75951|ME491|Tspan30	CD63 antigen	protein-coding
mm_142826.1	chr17	51766755	51766767	-	1	NA	intron (NM_009122, intron 9 of 10)	intron (NM_009122, intron 9 of 10)	45293	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_13902.1	chr2	120476912	120476924	+	1	NA	promoter-TSS (NM_001109761)	promoter-TSS (NM_001109761)	9	NM_001109761	12335	Mm.458021	NM_007601	ENSMUSG00000079110	Capn3	AI323605|Capa-3|Capa3|Lp82|p94	calpain 3	protein-coding
mm_152310.1	chr19	9891120	9891122	-	1	NA	intron (NM_016692, intron 4 of 17)	intron (NM_016692, intron 4 of 17)	8412	NM_016692	16319	Mm.29755	NM_016692	ENSMUSG00000024660	Incenp	2700067E22Rik|AU019509|C130081E20|C77457	inner centromere protein	protein-coding
mm_77451.1	chr8	121829507	121829515	-	1	NA	promoter-TSS (NM_145605)	promoter-TSS (NM_145605)	58	NM_145605	234825	Mm.209329	NM_145605	ENSMUSG00000040263	Klhdc4	AA408426|AV352552|BC012312|G430025P05Rik	kelch domain containing 4	protein-coding
mm_146232.1	chr18	77137321	77137334	+	1	NA	intron (NM_008602, intron 11 of 13)	intron (NM_008602, intron 11 of 13)	-48520	NM_153124	225742	Mm.365178	NM_013666	ENSMUSG00000025425	St8sia5	ST8SiaV|Siat8e	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 5	protein-coding
mm_125107.1	chr15	27796798	27796824	+	1	NA	intron (NM_001081302, intron 34 of 56)	intron (NM_001081302, intron 34 of 56)	-115269	NM_001242423	223433	Mm.266485	NM_198301	ENSMUSG00000056069	Fam105a	9830126M18	family with sequence similarity 105, member A	protein-coding
mm_63727.1	chr7	130865802	130865812	+	1	NA	promoter-TSS (NM_133942)	promoter-TSS (NM_133942)	83	NM_001346515	101476	Mm.323554	NM_133942	ENSMUSG00000040268	Plekha1	AA960558|C920009D07Rik|TAPP1	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 1	protein-coding
mm_129347.1	chr15	77905383	77905399	-	1	NA	Intergenic	Intergenic	23603	NM_019913	56551	Mm.291917	NM_019913	ENSMUSG00000005354	Txn2	2510006J11Rik|AI788873|Trx2	thioredoxin 2	protein-coding
mm_54823.1	chr6	42358392	42358393	-	1	NA	TTS (NM_023580)	TTS (NM_023580)	8564	NM_001289619	22793	Mm.282303	NM_011777	ENSMUSG00000029860	Zyx	9530098H06Rik|R75157	zyxin	protein-coding
mm_101845.1	chr11	48816937	48816961	-	1	NA	5' UTR (NM_145377, exon 1 of 6)	5' UTR (NM_145377, exon 1 of 6)	442	NM_145377	211007	Mm.794	NM_145377	ENSMUSG00000040365	Trim41	AW552703|BC020156|R75223|RINCK	tripartite motif-containing 41	protein-coding
mm_19548.1	chr2	98664045	98664074	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	1196402	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_27200.1	chr3	35666194	35666201	-	1	NA	promoter-TSS (NR_040748)	promoter-TSS (NR_040748)	-34	NR_040748	625963	Mm.251506	NR_040748	ENSMUSG00000105662	Gm6639	-	predicted gene 6639	ncRNA
mm_115388.1	chr13	113209967	113209980	+	1	NA	exon (NM_023612, exon 1 of 3)	exon (NM_023612, exon 1 of 3)	314	NM_023612	71690	Mm.38929	NM_023612	ENSMUSG00000042379	Esm1	0610042H23Rik|AV004503|ESM-1	endothelial cell-specific molecule 1	protein-coding
mm_3383.1	chr1	139501680	139501690	+	1	NA	promoter-TSS (NM_031164)	promoter-TSS (NM_031164)	-22	NM_031164	14060	Mm.30105	NM_031164	ENSMUSG00000026368	F13b	Cf-13b|Cf13b	coagulation factor XIII, beta subunit	protein-coding
mm_6553.1	chr1	75136589	75136601	-	1	NA	exon (NM_026977, exon 9 of 9)	exon (NM_026977, exon 9 of 9)	-2705	NM_194333	22626	Mm.68157	NM_194333	ENSMUSG00000026205	Slc23a3	SVCT3|Yspl1	solute carrier family 23 (nucleobase transporters), member 3	protein-coding
mm_143195.1	chr17	62627931	62627935	-	1	NA	intron (NM_010109, intron 2 of 3)	RSINE1|SINE|B4	253384	NM_207654	13640	Mm.7978	NM_010109	ENSMUSG00000048915	Efna5	AL-1|AV158822|EFL-5|Ephrin-A5|Epl7|LERK-7|RAGS	ephrin A5	protein-coding
mm_171087.1	chr3	124385701	124385708	+	1	NA	Intergenic	Intergenic	40324	NM_027939	71824	Mm.331353	NM_027939	ENSMUSG00000027973	1700006A11Rik	-	RIKEN cDNA 1700006A11 gene	protein-coding
mm_74626.1	chr8	13167844	13167869	-	1	NA	exon (NM_010684, exon 4 of 9)	exon (NM_010684, exon 4 of 9)	8695	NM_010684	16783	Mm.16716	NM_010684	ENSMUSG00000031447	Lamp1	CD107a|LGP-120|LGP-A|Lamp-1|P2B	lysosomal-associated membrane protein 1	protein-coding
mm_89938.1	chr10	111270561	111270589	+	1	NA	exon (NM_001003717, exon 9 of 23)	exon (NM_001003717, exon 9 of 23)	-28104	NM_027914	71769	Mm.45256	NM_027914	ENSMUSG00000035759	Bbs10	1300007O09Rik|AI452285	Bardet-Biedl syndrome 10 (human)	protein-coding
mm_140911.1	chr17	24168750	24168767	-	1	NA	intron (NR_037854, intron 1 of 2)	intron (NR_037854, intron 1 of 2)	637	NR_037854	100039636	Mm.30155	NR_037854		Atp6v0c-ps2	Atp6l-ps2|Gm15487	ATPase, H+ transporting, lysosomal V0 subunit C, pseudogene 2	pseudo
mm_111554.1	chr12	101040130	101040133	-	1	NA	3' UTR (NM_001160214, exon 15 of 15)	3' UTR (NM_001160214, exon 15 of 15)	-11148	NM_026681	68339	Mm.156217	NM_026681	ENSMUSG00000021182	Ccdc88c	0610010D24Rik|AV000935|AW324073|Daple|mKIAA1509	coiled-coil domain containing 88C	protein-coding
mm_77985.1	chr9	7873146	7873169	+	1	NA	promoter-TSS (NM_007464)	promoter-TSS (NM_007464)	13	NM_007464	11796	Mm.2026	NM_007464	ENSMUSG00000032000	Birc3	AW107670|Api1|Api2|Birc2|C-IAP2|HIAP2|IAP1|IAP2|MIAP1|MIAP2|MIHB|MIHC|RNF49|cIAP-1|cIAP-2|cIAP1|cIAP2	baculoviral IAP repeat-containing 3	protein-coding
mm_155594.1	chrX	81094573	81094591	+	1	NA	exon (NM_138751, exon 3 of 3)	exon (NM_138751, exon 3 of 3)	23938	NM_138751	192216	Mm.490421	NM_138751	ENSMUSG00000025666	Tmem47	3010015F07Rik|AI115536|BCMP1|Tm4sf10	transmembrane protein 47	protein-coding
mm_11304.1	chr2	30237681	30237747	+	1	NA	promoter-TSS (NM_177725)	promoter-TSS (NM_177725)	-55	NM_177725	241296	Mm.389232	NM_177725	ENSMUSG00000007476	Lrrc8a	Lrrc8|mKIAA1437	leucine rich repeat containing 8A	protein-coding
mm_48253.1	chr5	137827810	137827820	-	1	NA	intron (NM_153510, intron 3 of 6)	B3|SINE|B2	8463	NM_153510	231805	Mm.379385	NM_153510	ENSMUSG00000046245	Pilra	AV021745|FDF03	paired immunoglobin-like type 2 receptor alpha	protein-coding
mm_163466.1	chr12	102283079	102283098	-	1	NA	promoter-TSS (NM_001161365)	promoter-TSS (NM_001161365)	14	NM_177620	217835	Mm.24145	NM_177620	ENSMUSG00000044456	Rin3	6430500K07|C86933	Ras and Rab interactor 3	protein-coding
mm_149909.1	chr19	25672409	25672420	+	1	NA	promoter-TSS (NM_145831)	promoter-TSS (NM_145831)	3	NM_145831	226049	Mm.275572	NM_145831	ENSMUSG00000048138	Dmrt2	Terra	doublesex and mab-3 related transcription factor 2	protein-coding
mm_70965.1	chr8	27023794	27023810	+	1	NA	promoter-TSS (NM_153592)	promoter-TSS (NM_153592)	3	NM_153592	244373	Mm.277699	NM_153592	ENSMUSG00000031483	Erlin2	BC036333|C87251|Spfh2	ER lipid raft associated 2	protein-coding
mm_36597.1	chr4	88722503	88722515	-	1	NA	promoter-TSS (NM_172871)	promoter-TSS (NM_172871)	-1	NM_172871	242521	Mm.260601	NM_172871	ENSMUSG00000070923	Klhl9	8030469P05|C530050O22Rik|ENSMUSG00000070923|mKIAA1354	kelch-like 9	protein-coding
mm_161126.1	chr12	111406836	111406836	+	1	NA	promoter-TSS (NM_001101503)	promoter-TSS (NM_001101503)	27	NM_001101503	380787	Mm.125602	NM_001101503	ENSMUSG00000087075	A230065H16Rik	Gm898|Lbh2	RIKEN cDNA A230065H16 gene	protein-coding
mm_142359.1	chr17	43667166	43667198	-	1	NA	promoter-TSS (NM_001285948)	promoter-TSS (NM_001285948)	-167	NM_028711	74011	Mm.288697	NM_028711	ENSMUSG00000023912	Slc25a27	3632410G24Rik|9430092A03Rik|D530043E16Rik|Ucp4	solute carrier family 25, member 27	protein-coding
mm_93575.1	chr10	116582124	116582139	-	1	NA	promoter-TSS (NM_028082)	promoter-TSS (NM_028082)	-620	NM_001037846	72068	Mm.351553	NM_028082	ENSMUSG00000020166	Cnot2	2600016M12Rik|2810470K03Rik|AA537049|AA959607|AW557563|C79650	CCR4-NOT transcription complex, subunit 2	protein-coding
mm_26900.1	chr3	19265097	19265109	-	1	NA	promoter-TSS (NM_008802)	promoter-TSS (NM_008802)	-95	NM_008802	18583	Mm.355614	NM_008802	ENSMUSG00000069094	Pde7a	AU015378|AW047537	phosphodiesterase 7A	protein-coding
mm_144994.1	chr18	38296827	38296837	+	1	NA	promoter-TSS (NM_001164621)	promoter-TSS (NM_001164621)	27	NM_001164621	56736	Mm.228903	NM_020012	ENSMUSG00000060450	Rnf14	2310075C09Rik|2610005D23Rik|AA986456|AU041447|D18Ertd188e|D7Bwg0165e|Triad2	ring finger protein 14	protein-coding
mm_56568.1	chr6	102553897	102553900	-	1	NA	Intergenic	L1MA8|LINE|L1	-89231	NM_008779	18488	Mm.435479	NM_008779	ENSMUSG00000030075	Cntn3	Pang	contactin 3	protein-coding
mm_31790.1	chr4	63729010	63729027	+	1	NA	3' UTR (NM_177371, exon 4 of 4)	3' UTR (NM_177371, exon 4 of 4)	16095	NM_177371	326623	Mm.208152	NM_177371	ENSMUSG00000050395	Tnfsf15	Tl1|Tl1a|Tnlg1b|Vegi	tumor necrosis factor (ligand) superfamily, member 15	protein-coding
mm_121712.1	chr14	16172493	16172509	-	1	NA	Intergenic	Intergenic	-76813	NM_021504	59007	Mm.258381	NM_021504	ENSMUSG00000021785	Ngly1	1110002C09Rik|PNGase|Png1	N-glycanase 1	protein-coding
mm_23438.1	chr3	59431235	59431239	+	1	NA	Intergenic	L1_Mus2|LINE|L1	-86981	NM_001162884	242050	Mm.228086	NM_001162884	ENSMUSG00000036334	Igsf10	6530405F15Rik|9030224D03|AA409708|AA536958|AI414626|Adlican2|CMF608	immunoglobulin superfamily, member 10	protein-coding
mm_342.1	chr1	30875009	30875040	+	1	NA	Intergenic	Intergenic	-11768	NM_001081080	213109	Mm.194486	NM_025871	ENSMUSG00000048874	Phf3	2310061N19Rik|mKIAA0244	PHD finger protein 3	protein-coding
mm_148286.1	chr18	82554686	82554697	-	1	NA	exon (NM_010777, exon 4 of 7)	exon (NM_010777, exon 4 of 7)	183	NM_001025254	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_40594.1	chr5	64230397	64230452	+	1	NA	promoter-TSS (NM_001289514)	promoter-TSS (NM_001289514)	67	NM_001289514	57915	Mm.286353	NM_019636	ENSMUSG00000029174	Tbc1d1	1110062G02Rik|AI385682|AW555803|Nob1|Nobq1|Tbc1|mKIAA1108	TBC1 domain family, member 1	protein-coding
mm_149737.1	chr19	22321644	22321647	+	1	NA	intron (NM_001035243, intron 1 of 23)	L2b|LINE|L2	-126563	NM_177341	226025	Mm.131943	NM_177341	ENSMUSG00000052387	Trpm3	6330504P12Rik|9330180E14|AU018608|B930001P07Rik|LTRPC3|MLSN2	transient receptor potential cation channel, subfamily M, member 3	protein-coding
mm_148307.1	chr18	83488832	83488836	-	1	NA	Intergenic	Intergenic	-162950	NR_045361	70960	Mm.410834	NR_045361		4921531P14Rik	1700108N05Rik	RIKEN cDNA 4921531P14 gene	ncRNA
mm_141452.1	chr17	30389369	30389370	-	1	NA	intron (NM_172618, intron 6 of 11)	intron (NM_172618, intron 6 of 11)	6811	NR_030688	623169	Mm.440508	NR_030688		Gm6402	EG623169	ribosomal protein S17 pseudogene	pseudo
mm_139408.1	chr17	52602243	52602284	+	1	NA	promoter-TSS (NM_001031811)	promoter-TSS (NM_001031811)	-446	NM_001031811	211468	Mm.399068	NM_001031811	ENSMUSG00000035580	Kcnh8	C130090D05Rik|ELK|ELK1|ELK3|Kv12.1	potassium voltage-gated channel, subfamily H (eag-related), member 8	protein-coding
mm_167289.1	chr8	44935430	44935439	+	1	NA	Intergenic	CpG	-14774	NM_001081286	14107	Mm.27365	NM_001081286	ENSMUSG00000070047	Fat1	2310038E12Rik|AU023433|Fath|mFat1	FAT atypical cadherin 1	protein-coding
mm_166687.1	chr6	103511923	103511941	+	1	NA	intron (NM_007697, intron 1 of 26)	intron (NM_007697, intron 1 of 26)	1056	NM_007697	12661	Mm.251288	NM_007697	ENSMUSG00000030077	Chl1	A530023M13Rik|AI465420|CALL|LICAM2	cell adhesion molecule L1-like	protein-coding
mm_95095.1	chr11	34009400	34009439	+	1	NA	Intergenic	Intergenic	-16226	NM_001190886	70357	Mm.252514	NM_027398	ENSMUSG00000053519	Kcnip1	KCHIP1|Kchip1.2	Kv channel-interacting protein 1	protein-coding
mm_5653.1	chr1	40580640	40580677	-	1	NA	exon (NM_177084, exon 1 of 12)	exon (NM_177084, exon 1 of 12)	431	NM_177084	110895	Mm.108602	NM_177084	ENSMUSG00000026065	Slc9a4	AW990558|D730009J23Rik|NHE4	solute carrier family 9 (sodium/hydrogen exchanger), member 4	protein-coding
mm_82553.1	chr9	20976672	20976719	-	1	NA	promoter-TSS (NM_010333)	promoter-TSS (NM_010333)	98	NM_010333	14739	Mm.46493	NM_010333	ENSMUSG00000043895	S1pr2	1100001A16Rik|Edg5|Gpcr13|H218|LPb2|S1P2	sphingosine-1-phosphate receptor 2	protein-coding
mm_71897.1	chr8	70001409	70001419	+	1	NA	Intergenic	Intergenic	-5030	NM_145596	234366	Mm.270044	NM_145596	ENSMUSG00000036180	Gatad2a	1110066C11Rik|BC031407|C80248	GATA zinc finger domain containing 2A	protein-coding
mm_165168.1	chr2	26204645	26204648	-	1	NA	intron (NM_010711, intron 1 of 5)	intron (NM_010711, intron 1 of 5)	1929	NM_001039653	16871	Mm.386765	NM_010711	ENSMUSG00000026934	Lhx3	Lim3|P-LIM|mLIM3|mLim-3	LIM homeobox protein 3	protein-coding
mm_15698.1	chr2	163721235	163721249	+	1	NA	exon (NM_001039391, exon 3 of 4)	exon (NM_001039391, exon 3 of 4)	27205	NM_011106	18769	Mm.10091	NM_011106	ENSMUSG00000035268	Pkig	PKIgamma	protein kinase inhibitor, gamma	protein-coding
mm_78746.1	chr9	42138815	42138819	+	1	NA	Intergenic	MTC|LTR|ERVL-MaLR	-14528	NM_011436	20660	Mm.121920	NM_011436	ENSMUSG00000049313	Sorl1	2900010L19Rik|AI596264|AW261561|LR11|SorLA|gp250|mSorLA	sortilin-related receptor, LDLR class A repeats-containing	protein-coding
mm_115647.1	chr13	12291773	12291806	-	1	NA	exon (NM_033268, exon 10 of 21)	exon (NM_033268, exon 10 of 21)	-33676	NM_001081128	238505	Mm.40335	NM_001081128	ENSMUSG00000021311	Mtr	AI894170|D830038K18Rik|MS	5-methyltetrahydrofolate-homocysteine methyltransferase	protein-coding
mm_154005.1	chr19	53038535	53038646	-	1	NA	promoter-TSS (NM_133216)	promoter-TSS (NM_133216)	64	NM_133216	170750	Mm.99776	NM_133216	ENSMUSG00000025027	Xpnpep1	D230045I08Rik|sAMP	X-prolyl aminopeptidase (aminopeptidase P) 1, soluble	protein-coding
mm_31412.1	chr4	48048276	48048283	+	1	NA	intron (NM_015743, intron 1 of 7)	intron (NM_015743, intron 1 of 7)	-2967	NM_001307989	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_136909.1	chr17	13016666	13016683	+	1	NA	3' UTR (NM_013671, exon 5 of 5)	3' UTR (NM_013671, exon 5 of 5)	8835	NM_013671	20656	Mm.290876	NM_013671	ENSMUSG00000006818	Sod2	MnSOD|Sod-2	superoxide dismutase 2, mitochondrial	protein-coding
mm_4211.1	chr1	171270376	171270386	+	1	NA	promoter-TSS (NM_020579)	promoter-TSS (NM_020579)	53	NM_020579	57370	Mm.274011	NM_020579	ENSMUSG00000052423	B4galt3	9530061M23Rik|AA104562|AW125175|ESTM26|ESTM6|R74981	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 3	protein-coding
mm_32253.1	chr4	102570520	102570544	+	1	NA	5' UTR (NM_001177980, exon 1 of 10)	5' UTR (NM_001177980, exon 1 of 10)	472	NM_001177980	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_29755.1	chr3	127161923	127161934	-	1	NA	intron (NR_105029, intron 2 of 3)	intron (NR_105029, intron 2 of 3)	623	NR_105029	100862268	Mm.444603	NR_105029	ENSMUSG00000097456	LOC100862268	-	uncharacterized LOC100862268	ncRNA
mm_122189.1	chr14	31641206	31641272	-	1	NA	promoter-TSS (NM_019975)	promoter-TSS (NM_019975)	182	NM_025295	26363	Mm.282679	NM_025295	ENSMUSG00000021900	Btd	-	biotinidase	protein-coding
mm_16311.1	chr2	174298730	174298741	+	1	NA	exon (NM_001077507, exon 1 of 11)	exon (NM_001077507, exon 1 of 11)	876	NM_001310085	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_37746.1	chr4	129614262	129614280	-	1	NA	promoter-TSS (NM_001195730)	promoter-TSS (NM_001195730)	-14	NM_001195730	100504491	Mm.482597	NM_001195730	ENSMUSG00000078552	Dcdc2b	Gm12964|Gm1366|OTTMUSG00000009523	doublecortin domain containing 2b	protein-coding
mm_95192.1	chr11	42939631	42939634	+	1	NA	Intergenic	Intergenic	-210245	NM_176999	319767	Mm.252339	NM_176999	ENSMUSG00000055415	Atp10b	5930426O13Rik|9030605H24Rik	ATPase, class V, type 10B	protein-coding
mm_133010.1	chr16	56075400	56075492	+	1	NA	promoter-TSS (NM_001304503)	promoter-TSS (NM_001304503)	-34	NM_001304503	66315	Mm.255784	NM_025483	ENSMUSG00000052917	Senp7	2410152H17Rik|2810413I22Rik|2900036C23Rik|6030449K19Rik|AI790676	SUMO1/sentrin specific peptidase 7	protein-coding
mm_116208.1	chr13	32776465	32776477	-	1	NA	intron (NM_001166030, intron 1 of 11)	intron (NM_001166030, intron 1 of 11)	5308	NM_001166030	238564	Mm.60041	NM_001166030	ENSMUSG00000044951	Mylk4	EG238564	myosin light chain kinase family, member 4	protein-coding
mm_85897.1	chr9	111055710	111055729	-	1	NA	exon (NM_017466, exon 2 of 2)	exon (NM_017466, exon 2 of 2)	1525	NM_001302377	54199	Mm.7336	NM_017466	ENSMUSG00000043953	Ccrl2	1810047I05Rik|Ackr5|CCR11|Cmkbr1l2|E01|L-CCR	chemokine (C-C motif) receptor-like 2	protein-coding
mm_34193.1	chr4	140702082	140702150	+	1	NA	intron (NM_173867, intron 1 of 12)	CpG	643	NM_173867	108911	Mm.253	NM_173867	ENSMUSG00000040945	Rcc2	2610510H01Rik|2610529N02Rik|AA536646|AA675016|Td60|mKIAA1470	regulator of chromosome condensation 2	protein-coding
mm_23377.1	chr3	55537177	55537185	+	1	NA	3' UTR (NM_001111052, exon 14 of 14)	3' UTR (NM_001111052, exon 14 of 14)	75423	NM_001195540	13175	Mm.393242	NM_019978	ENSMUSG00000027797	Dclk1	1700113D08Rik|2810480F11Rik|AI836758|Click-I|Cpg16|Dcamkl1|Dcl|Dclk|mKIAA0369	doublecortin-like kinase 1	protein-coding
mm_61735.1	chr7	82173799	82173808	+	1	NA	Intergenic	Intergenic	-86105	NM_001277955	20408	Mm.736	NM_017400	ENSMUSG00000030638	Sh3gl3	EEN-B2|SH3P13|Sh3d2c|Sh3d2c2	SH3-domain GRB2-like 3	protein-coding
mm_137609.1	chr17	28236926	28236968	+	1	NA	intron (NM_011145, intron 1 of 7)	intron (NM_011145, intron 1 of 7)	4193	NM_011145	19015	Mm.328914	NM_011145	ENSMUSG00000002250	Ppard	NUC-1|NUC1|Nr1c2|PPAR-beta|PPAR-delta|PPAR[b]|PPARdelta|Pparb|Pparb/d	peroxisome proliferator activator receptor delta	protein-coding
mm_89218.1	chr10	86779076	86779095	+	1	NA	promoter-TSS (NM_175331)	promoter-TSS (NM_175331)	80	NM_175331	103466	Mm.200446	NM_175331	ENSMUSG00000054027	Nt5dc3	AU040402|AW540062|C630002B14Rik|TU12B1-TY	5'-nucleotidase domain containing 3	protein-coding
mm_81145.1	chr9	106877938	106877939	+	1	NA	intron (NM_001015507, intron 22 of 22)	intron (NM_001015507, intron 22 of 22)	9062	NM_175402	109095	Mm.431589	NM_175402	ENSMUSG00000074102	Rbm15b	1810017N16Rik	RNA binding motif protein 15B	protein-coding
mm_21734.1	chr2	164745917	164745940	-	1	NA	promoter-TSS (NM_133763)	promoter-TSS (NM_133763)	-87	NM_133763	76233	Mm.440009	NM_133763	ENSMUSG00000017299	Dnttip1	6430706C13Rik	deoxynucleotidyltransferase, terminal, interacting protein 1	protein-coding
mm_66560.1	chr7	45239069	45239103	-	1	NA	promoter-TSS (NM_007645)	promoter-TSS (NM_007645)	29	NM_001290802	12493	Mm.3689	NM_007645	ENSMUSG00000030798	Cd37	Tspan26	CD37 antigen	protein-coding
mm_166623.1	chr6	72544325	72544349	-	1	NA	promoter-TSS (NM_007599)	promoter-TSS (NM_007599)	-54	NM_007599	12332	Mm.18626	NM_007599	ENSMUSG00000056737	Capg	gCap39|mbh1	capping protein (actin filament), gelsolin-like	protein-coding
mm_86239.1	chr9	120866541	120866549	-	1	NA	Intergenic	Intergenic	48705	NR_040742	76402	Mm.436588	NR_040742	ENSMUSG00000100146	1700020M21Rik	-	RIKEN cDNA 1700020M21 gene	ncRNA
mm_16956.1	chr2	17390911	17390943	-	1	NA	intron (NM_028757, intron 4 of 6)	intron (NM_028757, intron 4 of 6)	-172587	NR_105847	102465964		NR_105847	ENSMUSG00000099161	Mir6419	Gm27713|mmu-mir-6419	microRNA 6419	ncRNA
mm_6879.1	chr1	84363797	84363808	-	1	NA	Intergenic	Intergenic	-79157	NM_001003948	98496	Mm.187470	NM_001003948	ENSMUSG00000045658	Pid1	5033414K04Rik|NYGGF4	phosphotyrosine interaction domain containing 1	protein-coding
mm_21466.1	chr2	160950667	160950670	-	1	NA	intron (NR_126509, intron 35 of 35)	AT_rich|Low_complexity|Low_complexity	-38329	NM_182840	280635	Mm.330747	NM_182840	ENSMUSG00000050700	Emilin3	1110013O17Rik|EMILIN-3|EMILIN-5|EMILIN-T|Emilin5	elastin microfibril interfacer 3	protein-coding
mm_80085.1	chr9	70207376	70207387	+	1	NA	promoter-TSS (NM_181072)	promoter-TSS (NM_181072)	31	NM_181072	71602	Mm.249311	NM_181072	ENSMUSG00000032220	Myo1e	2310020N23Rik|9130023P14Rik|AA407778|myosin-1e|myr 3	myosin IE	protein-coding
mm_19423.1	chr2	91931697	91931723	-	1	NA	promoter-TSS (NM_001291481)	promoter-TSS (NM_001291481)	-8	NM_001012335	17242	Mm.906	NM_010784	ENSMUSG00000027239	Mdk	MK|Mek	midkine	protein-coding
mm_143228.1	chr17	63333886	63333889	-	1	NA	intron (NM_015794, intron 6 of 8)	intron (NM_015794, intron 6 of 8)	-20914	NR_130176	414079	Mm.444282	NR_130176	ENSMUSG00000090565	4930405O22Rik	-	RIKEN cDNA 4930405O22 gene	ncRNA
mm_161248.1	chr13	100452886	100452886	-	1	NA	promoter-TSS (NM_008670)	promoter-TSS (NM_008670)	-22	NM_008670	17940	Mm.6898	NM_008670	ENSMUSG00000021640	Naip1	AV364616|Birc1a|D13Lsd1|Naip|Naip-rs1	NLR family, apoptosis inhibitory protein 1	protein-coding
mm_39411.1	chr5	14669053	14669086	+	1	NA	exon (NM_011995, exon 4 of 25)	exon (NM_011995, exon 4 of 25)	154151	NM_001110796	26875	Mm.146275	NM_011995	ENSMUSG00000061601	Pclo	Acz|Pico	piccolo (presynaptic cytomatrix protein)	protein-coding
mm_32091.1	chr4	98437323	98437346	+	1	NA	exon (NM_172696, exon 12 of 44)	exon (NM_172696, exon 12 of 44)	41508	NM_172696	12695	Mm.90218	NM_007704	ENSMUSG00000061859	Patj	Cipp|Inadl	PATJ, crumbs cell polarity complex component	protein-coding
mm_85426.1	chr9	103499293	103499299	-	1	NA	exon (NM_178638, exon 4 of 6)	exon (NM_178638, exon 4 of 6)	-18968	NM_001002896	107993	Mm.335403	NM_001002896	ENSMUSG00000032556	Bfsp2	AI448593|CP49	beaded filament structural protein 2, phakinin	protein-coding
mm_99944.1	chr11	111073718	111073739	+	1	NA	3' UTR (NM_008425, exon 2 of 2)	3' UTR (NM_008425, exon 2 of 2)	7564	NM_008425	16518	Mm.4951	NM_008425	ENSMUSG00000041695	Kcnj2	IRK1|Kcnf1|Kir2.1	potassium inwardly-rectifying channel, subfamily J, member 2	protein-coding
mm_157358.1	chrX	37085241	37085246	-	1	NA	promoter-TSS (NM_026055)	promoter-TSS (NM_026055)	-21	NM_026055	67248	Mm.30478	NM_026055	ENSMUSG00000079641	Rpl39	2810465O16Rik	ribosomal protein L39	protein-coding
mm_150595.1	chr19	40679679	40679685	+	1	NA	intron (NM_009848, intron 1 of 9)	Lx5|LINE|L1	19912	NM_009848	12495	Mm.2824	NM_009848	ENSMUSG00000048120	Entpd1	2610206B08Rik|AA408691|Cd39|NTPDase-1	ectonucleoside triphosphate diphosphohydrolase 1	protein-coding
mm_73991.1	chr8	120672733	120672762	+	1	NA	exon (NM_009941, exon 3 of 5)	exon (NM_009941, exon 3 of 5)	4427	NM_001293559	12857	Mm.386758	NM_009941	ENSMUSG00000031818	Cox4i1	AL024441|COX|COX IV-1|COXIV|Cox4|Cox4a|IV-1	cytochrome c oxidase subunit IV isoform 1	protein-coding
mm_152459.1	chr19	10871927	10871938	-	1	NA	exon (NM_134142, exon 4 of 4)	exon (NM_134142, exon 4 of 4)	-2153	NM_133804	98170	Mm.490254	NM_133804	ENSMUSG00000024736	Tmem132a	6720481D13Rik|Hspa5bp1|Orai1|R74613	transmembrane protein 132A	protein-coding
mm_113893.1	chr13	49193726	49193760	+	1	NA	exon (NM_013610, exon 2 of 4)	exon (NM_013610, exon 2 of 4)	6196	NM_013610	18081	Mm.18503	NM_013610	ENSMUSG00000037966	Ninj1	AU024536	ninjurin 1	protein-coding
mm_48599.1	chr5	144209532	144209535	-	1	NA	intron (NM_027410, intron 10 of 24)	B4|SINE|B4	14045	NM_027410	70381	Mm.239412	NM_027410	ENSMUSG00000066621	Tecpr1	2210010N04Rik|mKIAA1358	tectonin beta-propeller repeat containing 1	protein-coding
mm_97651.1	chr11	79504187	79504210	+	1	NA	promoter-TSS (NM_019409)	promoter-TSS (NM_019409)	-116	NM_019409	18377	Mm.93335	NM_019409	ENSMUSG00000049612	Omg	-	oligodendrocyte myelin glycoprotein	protein-coding
mm_39908.1	chr5	31297552	31297586	+	1	NA	promoter-TSS (NM_144909)	promoter-TSS (NM_144909)	-12	NM_144909	231103	Mm.100043	NM_144909	ENSMUSG00000059434	Gckr	GKRP	glucokinase regulatory protein	protein-coding
mm_37756.1	chr4	129647492	129647518	-	1	NA	3' UTR (NM_008468, exon 14 of 14)	3' UTR (NM_008468, exon 14 of 14)	-6440	NM_001199695	109658	Mm.268863	NM_001005506	ENSMUSG00000053841	Txlna	2600010N21Rik|AI425952|AW209241|Il14|Txln	taxilin alpha	protein-coding
mm_148774.1	chr19	6106123	6106133	+	1	NA	exon (NM_001009546, exon 2 of 18)	exon (NM_001009546, exon 2 of 18)	330	NM_001009546	381204	Mm.359041	NM_001009546	ENSMUSG00000054999	Naaladl1	Gm964|Naaladasel	N-acetylated alpha-linked acidic dipeptidase-like 1	protein-coding
mm_50137.1	chr6	41543067	41543077	+	1	NA	Intergenic	Intergenic	21296	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_32400.1	chr4	106867208	106867218	+	1	NA	Intergenic	Intergenic	-44257	NM_198438	72475	Mm.195635	NM_023672	ENSMUSG00000061887	Ssbp3	2610021L12Rik|2610200M23Rik|5730488C10Rik|AI854733|AW551939|LAST|SSDP1	single-stranded DNA binding protein 3	protein-coding
mm_161788.1	chr17	46025050	46025050	-	1	NA	5' UTR (NM_001110267, exon 1 of 4)	5' UTR (NM_001110267, exon 1 of 4)	113	NM_001110267	22339	Mm.282184	NM_009505	ENSMUSG00000023951	Vegfa	Vegf|Vpf	vascular endothelial growth factor A	protein-coding
mm_39293.1	chr5	5420058	5420069	+	1	NA	Intergenic	Intergenic	-39812	NM_011074	18647	Mm.389061	NM_011074	ENSMUSG00000028926	Cdk14	Pftk1|mKIAA0834	cyclin-dependent kinase 14	protein-coding
mm_146575.1	chr18	7273579	7273587	-	1	NA	intron (NM_001081393, intron 7 of 20)	intron (NM_001081393, intron 7 of 20)	24318	NM_001081393	74934	Mm.107918	NM_001081393	ENSMUSG00000061802	Armc4	4930463I21Rik|b2b227.1Clo|b2b643Clo	armadillo repeat containing 4	protein-coding
mm_114913.1	chr13	94976456	94976475	+	1	NA	5' UTR (NM_172590, exon 1 of 13)	5' UTR (NM_172590, exon 1 of 13)	121	NM_172590	218460	Mm.33856	NM_172590	ENSMUSG00000042015	Wdr41	B830029I03Rik|MSTP048	WD repeat domain 41	protein-coding
mm_170625.1	chr1	9726971	9726971	+	1	NA	intron (NM_173443, intron 2 of 2)	B1_Mus1|SINE|Alu	-20677	NR_040462	73331	Mm.460470	NR_040462		1700034P13Rik	-	RIKEN cDNA 1700034P13 gene	ncRNA
mm_111501.1	chr12	99412597	99412611	-	1	NA	intron (NM_183186, intron 1 of 5)	intron (NM_183186, intron 1 of 5)	37470	NM_183186	71375	Mm.341972	NM_183186	ENSMUSG00000033713	Foxn3	5430426H20Rik|AA589593|AW556347|Ches1|Ches1l|HTLFL1	forkhead box N3	protein-coding
mm_46270.1	chr5	99978849	99978859	-	1	NA	promoter-TSS (NM_007516)	promoter-TSS (NM_007516)	84	NM_001077266	11991	Mm.150231	NM_007516	ENSMUSG00000000568	Hnrnpd	Auf1|Hnrpd	heterogeneous nuclear ribonucleoprotein D	protein-coding
mm_19865.1	chr2	114013621	114013638	-	1	NA	promoter-TSS (NM_010290)	promoter-TSS (NM_010290)	-10	NM_010290	14617	Mm.389394	NM_010290	ENSMUSG00000068615	Gjd2	Gja9|connexin36|cx36	gap junction protein, delta 2	protein-coding
mm_155453.1	chrX	73495608	73495630	+	1	NA	3' UTR (NM_007542, exon 8 of 8)	3' UTR (NM_007542, exon 8 of 8)	-7467	NM_001310537	320707	Mm.210095	NM_177236	ENSMUSG00000031376	Atp2b3	6430519O13Rik|Pmca3	ATPase, Ca++ transporting, plasma membrane 3	protein-coding
mm_169315.1	chr14	10609026	10609027	+	1	NA	intron (NM_010210, intron 3 of 8)	L1Md_T|LINE|L1	-129527	NR_131139	547334	Mm.434606	NR_131139	ENSMUSG00000089833	Fhitos	Gm16542	fragile histidine triad gene, opposite strand	ncRNA
mm_122803.1	chr14	54554380	54554398	-	1	NA	promoter-TSS (NM_145462)	promoter-TSS (NM_145462)	-28	NM_145462	219072	Mm.202152	NM_145462	ENSMUSG00000022177	Haus4	9430093H08Rik|AU016300|D14Ertd500e	HAUS augmin-like complex, subunit 4	protein-coding
mm_99654.1	chr11	105655535	105655544	+	1	NA	intron (NM_181071, intron 2 of 25)	intron (NM_181071, intron 2 of 25)	65553	NM_181071	77097	Mm.22501	NM_175492	ENSMUSG00000053580	Tanc2	3526402J09Rik|5730590C14Rik	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2	protein-coding
mm_135009.1	chr16	32402916	32402937	-	1	NA	intron (NM_001160402, intron 1 of 4)	intron (NM_001160402, intron 1 of 4)	2420	NM_001160402	277203	Mm.484240	NM_001160402	ENSMUSG00000079625	Tm4sf19	EG277203	transmembrane 4 L six family member 19	protein-coding
mm_135028.1	chr16	32797373	32797377	-	1	NA	promoter-TSS (NM_146071)	promoter-TSS (NM_146071)	60	NM_146071	224116	Mm.153301	NM_146071	ENSMUSG00000035638	Muc20	BC026367	mucin 20	protein-coding
mm_50396.1	chr6	48718626	48718633	+	1	NA	promoter-TSS (NM_146167)	promoter-TSS (NM_146167)	8	NM_146167	231932	Mm.30479	NM_146167	ENSMUSG00000043931	Gimap7	IAN7|Ian3	GTPase, IMAP family member 7	protein-coding
mm_71368.1	chr8	45748955	45748959	+	1	NA	intron (NM_172752, intron 6 of 22)	intron (NM_172752, intron 6 of 22)	70340	NR_045739	319940	Mm.441720	NR_045739	ENSMUSG00000085440	Sorbs2os	D330022K07Rik	sorbin and SH3 domain containing 2, opposite strand	ncRNA
mm_25876.1	chr3	130201346	130201350	+	1	NA	intron (NM_029838, intron 2 of 37)	intron (NM_029838, intron 2 of 37)	20503	NM_001244952	77018	Mm.91728	NM_029838	ENSMUSG00000058897	Col25a1	2700062B08Rik|CLAC-P	collagen, type XXV, alpha 1	protein-coding
mm_27061.1	chr3	27695862	27695894	-	1	NA	intron (NM_173182, intron 1 of 25)	intron (NM_173182, intron 1 of 25)	14561	NM_173182	72007	Mm.38832	NM_173182	ENSMUSG00000039286	Fndc3b	1600019O04Rik|AW550168|Fad104|mKIAA4164	fibronectin type III domain containing 3B	protein-coding
mm_173132.1	chrX	19347130	19347140	+	1	NA	Intergenic	RLTR13D6|LTR|ERVK	-200164	NR_029807	723828		NR_029807	ENSMUSG00000065471	Mir222	Mirn222|mir-222|mmu-mir-222	microRNA 222	ncRNA
mm_63803.1	chr7	133005990	133006025	+	1	NA	intron (NM_001347623, intron 1 of 8)	intron (NM_001347623, intron 1 of 8)	9240	NM_001170744	13017	Mm.246240	NM_009980	ENSMUSG00000030970	Ctbp2	AA407280|D7Ertd45e|Gtrgeo6|Ribeye	C-terminal binding protein 2	protein-coding
mm_59807.1	chr7	29155745	29155754	+	1	NA	exon (NM_001146023, exon 3 of 8)	exon (NM_001146023, exon 3 of 8)	461	NM_001146023	73833	Mm.260890	NM_028661	ENSMUSG00000030590	Fam98c	1110006G06Rik|AI836081|AV026483|B230110F21Rik	family with sequence similarity 98, member C	protein-coding
mm_1512.1	chr1	72536697	72536721	+	1	NA	promoter-TSS (NM_001045533)	promoter-TSS (NM_001045533)	-145	NM_001045533	381270	Mm.337023	NM_001045533	ENSMUSG00000039372	March4	BC056494|mKIAA1399	membrane-associated ring finger (C3HC4) 4	protein-coding
mm_28595.1	chr3	94472870	94472887	-	1	NA	exon (NM_025506, exon 3 of 7)	exon (NM_025506, exon 3 of 7)	713	NM_025506	66353	Mm.46405	NM_025506	ENSMUSG00000028139	Riiad1	2310007A19Rik|Ncrna00166	regulatory subunit of type II PKA R-subunit (RIIa) domain containing 1	protein-coding
mm_123141.1	chr14	56694086	56694117	-	1	NA	intron (NM_023773, intron 11 of 13)	LSU-rRNA_Hsa|rRNA|rRNA	6899	NR_046209	100503823	Mm.474486	NR_046209		Gm16973	-	predicted gene, 16973	ncRNA
mm_158897.1	chr1	24030415	24030415	-	1	NA	exon (NM_026604, exon 14 of 21)	exon (NM_026604, exon 14 of 21)	-24775	NM_026503	68002	Mm.250424	NM_026503	ENSMUSG00000026154	Sdhaf4	1110058L19Rik|1700001E18Rik|C6orf57	succinate dehydrogenase complex assembly factor 4	protein-coding
mm_157705.1	chrX	62670259	62670285	-	1	NA	Intergenic	Intergenic	-143261	NR_045442	75545	Mm.391270	NR_045442	ENSMUSG00000085757	1700019B21Rik	-	RIKEN cDNA 1700019B21 gene	ncRNA
mm_139995.1	chr17	72938343	72938349	+	1	NA	intron (NM_029999, intron 2 of 2)	intron (NM_029999, intron 2 of 2)	20041	NM_029999	77889	Mm.154109	NM_029999	ENSMUSG00000024063	Lbh	1810009F10Rik|6720416L16Rik	limb-bud and heart	protein-coding
mm_27563.1	chr3	58577378	58577420	-	1	NA	intron (NM_001040396, intron 1 of 5)	intron (NM_001040396, intron 1 of 5)	741	NM_001040396	69227	Mm.270950	NM_001040396	ENSMUSG00000075700	Selenot	2810407C02Rik|5730408P04Rik|Selt	selenoprotein T	protein-coding
mm_83184.1	chr9	40984502	40984502	-	1	NA	intron (NM_001281954, intron 5 of 9)	intron (NM_001281954, intron 5 of 9)	20126	NM_001281954	54698	Mm.42791	NM_019465	ENSMUSG00000032021	Crtam	-	cytotoxic and regulatory T cell molecule	protein-coding
mm_142510.1	chr17	46160411	46160417	-	1	NA	promoter-TSS (NM_019581)	promoter-TSS (NM_019581)	-618	NM_019581	56055	Mm.22147	NM_019581	ENSMUSG00000023952	Gtpbp2	nmf205	GTP binding protein 2	protein-coding
mm_129378.1	chr15	78173828	78173840	-	1	NA	5' UTR (NM_025931, exon 1 of 7)	5' UTR (NM_025931, exon 1 of 7)	274	NM_025931	67042	Mm.30191	NM_025931	ENSMUSG00000016637	Ift27	2600013G09Rik|Rabl4	intraflagellar transport 27	protein-coding
mm_19928.1	chr2	116064734	116064749	-	1	NA	promoter-TSS (NM_001346038)	promoter-TSS (NM_001346038)	-122	NM_001159570	17536	Mm.247566	NM_010825	ENSMUSG00000027210	Meis2	A430109D20Rik|Mrg1|Stra10	Meis homeobox 2	protein-coding
mm_136552.1	chr17	3084223	3084251	+	1	NA	promoter-TSS (NR_003519)	promoter-TSS (NR_003519)	-54	NR_003519	328734	Mm.335641	NR_003519		Pisd-ps2	D030013I16Rik	phosphatidylserine decarboxylase, pseudogene 2	pseudo
mm_108726.1	chr12	87264649	87264672	+	1	NA	promoter-TSS (NM_134044)	promoter-TSS (NM_134044)	-416	NM_134044	104799	Mm.208750	NM_134044	ENSMUSG00000021038	Vipas39	6720456H09Rik|9330175H22Rik|AI413782|SPE-39|Spe39|Vipar|hSPE-39	VPS33B interacting protein, apical-basolateral polarity regulator, spe-39 homolog	protein-coding
mm_121657.1	chr14	11981226	11981232	-	1	NA	intron (NM_008981, intron 4 of 29)	intron (NM_008981, intron 4 of 29)	-208714	NM_001347593	19270	Mm.431266	NM_008981	ENSMUSG00000021745	Ptprg	5430405N12Rik|AW046354|AW549872|RPTPgamma	protein tyrosine phosphatase, receptor type, G	protein-coding
mm_108522.1	chr12	84053440	84053450	+	1	NA	5' UTR (NM_134246, exon 2 of 4)	5' UTR (NM_134246, exon 2 of 4)	1294	NM_134246	171281	Mm.202331	NM_134246	ENSMUSG00000021228	Acot3	AW108394|PTE-Ia|Pte2a	acyl-CoA thioesterase 3	protein-coding
mm_108286.1	chr12	79135980	79136007	+	1	NA	intron (NM_009705, intron 2 of 7)	(TTTTG)n|Simple_repeat|Simple_repeat	5205	NM_009705	11847	Mm.3506	NM_009705	ENSMUSG00000021125	Arg2	AII|AU022422	arginase type II	protein-coding
mm_59428.1	chr7	27129708	27129720	+	1	NA	intron (NM_007817, intron 5 of 9)	intron (NM_007817, intron 5 of 9)	9759	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_100577.1	chr11	120767097	120767109	+	1	NA	Intergenic	Intergenic	17101	NM_009053	19719	Mm.871	NM_009053	ENSMUSG00000025158	Rfng	-	RFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	protein-coding
mm_101315.1	chr11	22837169	22837179	-	1	NA	exon (NM_001169114, exon 2 of 2)	exon (NM_001169114, exon 2 of 2)	22561	NM_016888	53625	Mm.395495	NM_016888	ENSMUSG00000051650	B3gnt2	AA408337|AA409404|AW260308|B3Galt6|B3gnt1|BGnT-1|BGnT-2|BGnT1|BGnT2|Beta3gnt	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 2	protein-coding
mm_135667.1	chr16	52407759	52407769	-	1	NA	intron (NM_009655, intron 1 of 15)	B4A|SINE|B4	45317	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_122875.1	chr14	54925855	54925888	-	1	NA	5' UTR (NM_010112, exon 1 of 6)	5' UTR (NM_010112, exon 1 of 6)	917	NM_010112	13644	Mm.236438	NM_010112	ENSMUSG00000022203	Efs	-	embryonal Fyn-associated substrate	protein-coding
mm_37630.1	chr4	127354210	127354219	-	1	NA	promoter-TSS (NM_008127)	promoter-TSS (NM_008127)	-133	NM_008127	14621	Mm.56906	NM_008127	ENSMUSG00000046623	Gjb4	Cnx30.3|Cx30.3|Gjb-4	gap junction protein, beta 4	protein-coding
mm_64060.1	chr7	140856328	140856370	+	1	NA	promoter-TSS (NM_018742)	promoter-TSS (NM_018742)	34	NM_018742	54399	Mm.155696	NM_018742	ENSMUSG00000025484	Bet1l	2610021K23Rik|Gs15	Bet1 golgi vesicular membrane trafficking protein like	protein-coding
mm_26786.1	chr3	9610091	9610124	-	1	NA	promoter-TSS (NM_133218)	promoter-TSS (NM_133218)	-22	NM_133218	170753	Mm.212908	NM_133218	ENSMUSG00000040209	Zfp704	C030026M03|C030034L19Rik|Gig1|Znf704	zinc finger protein 704	protein-coding
mm_154353.1	chrM	5996	6020	+	1	NA	NA	Intergenic	NA	NA								
mm_30445.1	chr3	153721045	153721057	-	1	NA	intron (NM_011372, intron 1 of 4)	intron (NM_011372, intron 1 of 4)	4082	NM_011372	20447	Mm.296453	NM_011372	ENSMUSG00000052544	St6galnac3	Siat7c	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 3	protein-coding
mm_74368.1	chr8	128418763	128418782	+	1	NA	exon (NM_008737, exon 3 of 17)	exon (NM_008737, exon 3 of 17)	59531	NR_035436	100316680		NR_035436	ENSMUSG00000084523	Mir1903	Mirn1903|mmu-mir-1903	microRNA 1903	ncRNA
mm_76022.1	chr8	75085047	75085074	-	1	NA	Intergenic	Intergenic	-8558	NM_010442	15368	Mm.276389	NM_010442	ENSMUSG00000005413	Hmox1	D8Wsu38e|HO-1|HO1|Hemox|Hmox|Hsp32	heme oxygenase 1	protein-coding
mm_47135.1	chr5	120503594	120503627	-	1	NA	promoter-TSS (NM_023625)	promoter-TSS (NM_023625)	13	NM_023625	71772	Mm.100065	NM_023625	ENSMUSG00000029598	Plbd2	1300012G16Rik|AU019810|P76	phospholipase B domain containing 2	protein-coding
mm_141735.1	chr17	34120970	34120991	-	1	NA	intron (NM_001204973, intron 1 of 12)	CpG-6274	767	NM_010238	14312	Mm.3444	NM_010238	ENSMUSG00000024335	Brd2	AW228947|D17H6S113E|Frg-1|Fsrg-1|Fsrg1|Nat|Ring3|Rnf3|mKIAA4005	bromodomain containing 2	protein-coding
mm_142736.1	chr17	48388149	48388162	-	1	NA	3' UTR (NM_010913, exon 9 of 9)	3' UTR (NM_010913, exon 9 of 9)	12425	NM_001347402	18044	Mm.4929	NM_010913	ENSMUSG00000023994	Nfya	AA407810|Cbf-b|SEZ-10|SEZ10	nuclear transcription factor-Y alpha	protein-coding
mm_88332.1	chr10	75571554	75571586	+	1	NA	intron (NM_001305992, intron 1 of 13)	intron (NM_001305992, intron 1 of 13)	-1925	NM_008116	14598	Mm.4559	NM_008116	ENSMUSG00000006345	Ggt1	CD224|GGT|GGT 1|GGT-1|Ggtp|dwg	gamma-glutamyltransferase 1	protein-coding
mm_59889.1	chr7	30306857	30306879	+	1	NA	3' UTR (NM_001081114, exon 14 of 14)	3' UTR (NM_001081114, exon 14 of 14)	-1885	NM_198027	233065	Mm.276277	NM_198027	ENSMUSG00000042831	Alkbh6	AI839550|Abh6|C130099A02	alkB homolog 6	protein-coding
mm_42225.1	chr5	113490516	113490548	+	1	NA	Intergenic	CpG	-59888	NM_177292	320916	Mm.102783	NM_177292	ENSMUSG00000063430	Wscd2	4933413A10Rik|C530024P05Rik|Gm450	WSC domain containing 2	protein-coding
mm_149984.1	chr19	29159983	29159993	+	1	NA	Intergenic	Intergenic	24709	NR_029778	724062		NR_029778	ENSMUSG00000065556	Mir101b	Mirn101b|mir-101b	microRNA 101b	ncRNA
mm_101733.1	chr11	43232263	43232279	-	1	NA	intron (NM_176999, intron 16 of 22)	intron (NM_176999, intron 16 of 22)	82394	NM_176999	319767	Mm.252339	NM_176999	ENSMUSG00000055415	Atp10b	5930426O13Rik|9030605H24Rik	ATPase, class V, type 10B	protein-coding
mm_47755.1	chr5	131307255	131307294	-	1	NA	5' UTR (NM_145218, exon 1 of 11)	5' UTR (NM_145218, exon 1 of 11)	248	NM_145218	212996	Mm.299204	NM_145218	ENSMUSG00000034040	Wbscr17	AA388321|E330012B09Rik	Williams-Beuren syndrome chromosome region 17 homolog (human)	protein-coding
mm_122582.1	chr14	50836452	50836464	-	1	NA	exon (NM_009351, exon 40 of 55)	exon (NM_009351, exon 40 of 55)	28512	NM_009632	11546	Mm.281482	NM_009632	ENSMUSG00000036023	Parp2	ARTD2|Adprt2|Adprtl2|Aspartl2|C78626|PARP-2	poly (ADP-ribose) polymerase family, member 2	protein-coding
mm_28984.1	chr3	101283158	101283161	-	1	NA	exon (NM_013486, exon 3 of 5)	exon (NM_013486, exon 3 of 5)	4780	NM_013486	12481	Mm.22842	NM_013486	ENSMUSG00000027863	Cd2	LFA-2|Ly-37|Ly37	CD2 antigen	protein-coding
mm_102680.1	chr11	65261886	65261893	-	1	NA	intron (NM_146386, intron 1 of 12)	intron (NM_146386, intron 1 of 12)	8100	NM_145136	214384	Mm.32257	NM_145136	ENSMUSG00000020542	Myocd	BSAC2A|Srfcp	myocardin	protein-coding
mm_45672.1	chr5	77216219	77216221	-	1	NA	Intergenic	Lx8|LINE|L1	-4749	NM_001289768	69982	Mm.46106	NM_183284	ENSMUSG00000053030	Spink2	1700007F22Rik|AV038945|HUSI-II	serine peptidase inhibitor, Kazal type 2	protein-coding
mm_55946.1	chr6	85126126	85126132	-	1	NA	promoter-TSS (NM_001034902)	promoter-TSS (NM_001034902)	-35	NM_001034902	545861	Mm.321419	NM_001034902	ENSMUSG00000072952	Gm5878	EG545861	predicted gene 5878	protein-coding
mm_161978.1	chr19	13619103	13619103	+	1	NA	promoter-TSS (NM_146636)	promoter-TSS (NM_146636)	-61	NM_146636	258629	Mm.271479	NM_146636	ENSMUSG00000094846	Olfr1487	MOR202-18	olfactory receptor 1487	protein-coding
mm_87745.1	chr10	60266984	60267026	+	1	NA	Intergenic	Intergenic	-10623	NM_001146123	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_166941.1	chr7	43432087	43432091	+	1	NA	intron (NM_177693, intron 2 of 4)	(CAGG)n|Simple_repeat|Simple_repeat	1988	NM_177693	233187	Mm.267027	NM_177693	ENSMUSG00000004613	Lim2	19kDa|4833403J20|MP19|To3	lens intrinsic membrane protein 2	protein-coding
mm_113988.1	chr13	52582793	52582804	+	1	NA	promoter-TSS (NM_001198977)	promoter-TSS (NM_001198977)	-639	NM_001198977	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_78730.1	chr9	41581248	41581260	+	1	NA	promoter-TSS (NR_029822)	promoter-TSS (NR_029822)	1	NR_015483	73144	Mm.38166	NM_001033153	ENSMUSG00000074415	3110039I08Rik	2610203C20Rik|AI848448|D230004N17Rik|D3Mgi9|Mir100hg	RIKEN cDNA 3110039I08 gene	ncRNA
mm_23636.1	chr3	66985681	66985692	+	1	NA	promoter-TSS (NM_025822)	promoter-TSS (NM_025822)	14	NM_025822	66880	Mm.316418	NM_025822	ENSMUSG00000034544	Rsrc1	1200013F24Rik|SRrp53	arginine/serine-rich coiled-coil 1	protein-coding
mm_144298.1	chr18	12256290	12256296	+	1	NA	intron (NM_001190371, intron 9 of 9)	intron (NM_001190371, intron 9 of 9)	-19907	NM_008720	18145	Mm.3484	NM_008720	ENSMUSG00000024413	Npc1	A430089E03Rik|C85354|D18Ertd139e|D18Ertd723e|lcsd|nmf164|spm	Niemann-Pick type C1	protein-coding
mm_161866.1	chr18	35214904	35214904	+	1	NA	5' UTR (NM_178005, exon 1 of 2)	5' UTR (NM_178005, exon 1 of 2)	120	NM_178005	107065	Mm.39900	NM_178005	ENSMUSG00000071862	Lrrtm2	AI851755|BB129880|C630011A14Rik|mKIAA0416	leucine rich repeat transmembrane neuronal 2	protein-coding
mm_37213.1	chr4	117887293	117887353	-	1	NA	promoter-TSS (NM_033617)	promoter-TSS (NM_033617)	6	NM_033617	114143	Mm.207052	NM_033617	ENSMUSG00000033379	Atp6v0b	2310024H13Rik|Atp6f|VMA16	ATPase, H+ transporting, lysosomal V0 subunit B	protein-coding
mm_40428.1	chr5	53555774	53555784	+	1	NA	promoter-TSS (NM_001080928)	promoter-TSS (NM_001080928)	0	NM_001080928	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_47438.1	chr5	123181496	123181500	-	1	NA	exon (NM_008277, exon 4 of 14)	exon (NM_008277, exon 4 of 14)	1188	NM_008277	15445	Mm.439709	NM_008277	ENSMUSG00000029445	Hpd	Fla|Flp|Hppd|Laf	4-hydroxyphenylpyruvic acid dioxygenase	protein-coding
mm_139755.1	chr17	64078900	64078919	+	1	NA	exon (NM_001286415, exon 15 of 18)	exon (NM_001286415, exon 15 of 18)	-28237	NR_130982	68771	Mm.443351	NR_130982		1110058D11Rik	-	RIKEN cDNA 1110058D11 gene	ncRNA
mm_163195.1	chr11	95611282	95611287	+	1	NA	Intergenic	Intergenic	-23586	NM_033217	18053	Mm.283893	NM_033217	ENSMUSG00000000120	Ngfr	LNGFR|Tnfrsf16|p75|p75NGFR|p75NTR	nerve growth factor receptor (TNFR superfamily, member 16)	protein-coding
mm_91873.1	chr10	59582967	59582984	-	1	NA	intron (NM_001033259, intron 1 of 7)	intron (NM_001033259, intron 1 of 7)	33717	NM_001033259	215999	Mm.296470	NM_001033259	ENSMUSG00000009647	Mcu	2010012O16Rik|AV064928|C10orf42|Ccdc109a|D130073L02Rik|Gm64	mitochondrial calcium uniporter	protein-coding
mm_136588.1	chr17	4994905	4994953	+	1	NA	promoter-TSS (NM_001085355)	promoter-TSS (NM_001085355)	-145	NM_001085355	239985	Mm.133401	NM_001085355	ENSMUSG00000069729	Arid1b	8030481M12|9330189K18Rik|AI836955|Ardi1b|B230217J03Rik|mKIAA1235	AT rich interactive domain 1B (SWI-like)	protein-coding
mm_103966.1	chr11	84491530	84491534	-	1	NA	intron (NM_019816, intron 5 of 12)	intron (NM_019816, intron 5 of 12)	21969	NM_019816	56321	Mm.257482	NM_019816	ENSMUSG00000018697	Aatf	4933415H02Rik|5830465M17Rik|Che-1|Trb	apoptosis antagonizing transcription factor	protein-coding
mm_150263.1	chr19	34217196	34217227	+	1	NA	intron (NM_029682, intron 1 of 10)	MLT1N2|LTR|ERVL-MaLR	24941	NM_029682	76630	Mm.130952	NM_029682	ENSMUSG00000024776	Stambpl1	1700095N21Rik|8230401J17Rik|ALMalpha|AMSH-FP	STAM binding protein like 1	protein-coding
mm_48716.1	chr5	147307265	147307281	-	1	NA	promoter-TSS (NM_007673)	promoter-TSS (NM_007673)	-24	NM_007673	12591	Mm.20358	NM_007673	ENSMUSG00000029646	Cdx2	Cdx-2	caudal type homeobox 2	protein-coding
mm_153581.1	chr19	43500284	43500292	-	1	NA	3' UTR (NM_010324, exon 9 of 9)	3' UTR (NM_010324, exon 9 of 9)	24317	NM_010324	14718	Mm.19039	NM_010324	ENSMUSG00000025190	Got1	AI789014|Got-1|cAspAT|cCAT	glutamic-oxaloacetic transaminase 1, soluble	protein-coding
mm_5000.1	chr1	191911690	191911692	+	1	NA	3' UTR (NM_009579, exon 2 of 2)	3' UTR (NM_009579, exon 2 of 2)	-4164	NR_030669	98736	Mm.379232	NM_001024489	ENSMUSG00000055833	1700034H15Rik	4930557M11Rik|BB016121	RIKEN cDNA 1700034H15 gene	ncRNA
mm_11146.1	chr2	28513129	28513149	+	1	NA	promoter-TSS (NM_009058)	promoter-TSS (NM_009058)	-28	NM_009058	19730	Mm.5236	NM_009058	ENSMUSG00000026821	Ralgds	Gnds|Rgds|mKIAA1308	ral guanine nucleotide dissociation stimulator	protein-coding
mm_22015.1	chr2	167833643	167833648	-	1	NA	Intergenic	Intergenic	-98682	NM_011201	19246	Mm.277916	NM_011201	ENSMUSG00000027540	Ptpn1	PTP-1B|PTP-HA2|PTP1B	protein tyrosine phosphatase, non-receptor type 1	protein-coding
mm_123988.1	chr14	75754446	75754462	-	1	NA	promoter-TSS (NM_177381)	promoter-TSS (NM_177381)	39	NM_177381	338337	Mm.86507	NM_177381	ENSMUSG00000034893	Cog3	E430004N23	component of oligomeric golgi complex 3	protein-coding
mm_34152.1	chr4	139380602	139380656	+	1	NA	promoter-TSS (NM_001160319)	promoter-TSS (NM_001160319)	-30	NM_001160319	69116	Mm.271956	NM_001160319	ENSMUSG00000066036	Ubr4	1810009A16Rik|A930005E13Rik|D930005K06Rik|Gm1032|Gm1666|N28143|RBAF600|Zubr1|mKIAA0462|p600	ubiquitin protein ligase E3 component n-recognin 4	protein-coding
mm_31566.1	chr4	57568145	57568160	+	1	NA	promoter-TSS (NM_172868)	promoter-TSS (NM_172868)	-96	NM_001304544	677884	Mm.331630	NM_001304544	ENSMUSG00000089945	Pakap	AF064781|Gm20459|Palm2-Akap2|Palm2Akap2|Palm2akap2	paralemmin A kinase anchor protein	protein-coding
mm_9009.1	chr1	166002592	166002609	-	1	NA	promoter-TSS (NM_198932)	promoter-TSS (NM_198932)	34	NM_198932	18986	Mm.245261	NM_011137	ENSMUSG00000026565	Pou2f1	2810482H01Rik|NF-A1|Oct-1|Oct1|Otf-1|Otf1	POU domain, class 2, transcription factor 1	protein-coding
mm_13727.1	chr2	117449021	117449025	+	1	NA	Intergenic	Intergenic	-106146	NM_011246	19419	Mm.42150	NM_011246	ENSMUSG00000027347	Rasgrp1	Rasgrp	RAS guanyl releasing protein 1	protein-coding
mm_81439.1	chr9	109102790	109102802	+	1	NA	intron (NM_172775, intron 5 of 37)	intron (NM_172775, intron 5 of 37)	7360	NM_172775	235611	Mm.53862	NM_172775	ENSMUSG00000053646	Plxnb1	2900002G15Rik|AU042020|mKIAA0407	plexin B1	protein-coding
mm_62248.1	chr7	99267398	99267406	+	1	NA	promoter-TSS (NM_001043355)	promoter-TSS (NM_001043355)	-45	NM_010837	17760	Mm.154087	NM_010837	ENSMUSG00000055407	Map6	2810411E12Rik|Map-6|Mtap6|STOP	microtubule-associated protein 6	protein-coding
mm_11024.1	chr2	26630505	26630528	+	1	NA	intron (NM_019833, intron 1 of 4)	RMER21B|LTR|ERV1	2059	NM_019833	56279	Mm.279863	NM_019833	ENSMUSG00000036186	Fam69b	AB030186|AW209000|B230317C12Rik|PIP49	family with sequence similarity 69, member B	protein-coding
mm_84205.1	chr9	60687878	60687946	-	1	NA	promoter-TSS (NM_001146047)	promoter-TSS (NM_001146047)	222	NM_145616	102747	Mm.269413	NM_145616	ENSMUSG00000047766	Lrrc49	AI430817|AW050057|D430025H09Rik|PGs4|p79	leucine rich repeat containing 49	protein-coding
mm_154870.1	chrX	20681158	20681171	+	1	NA	exon (NM_009457, exon 22 of 26)	exon (NM_009457, exon 22 of 26)	-6790	NM_001310456	18555	Mm.102574	NM_011049	ENSMUSG00000031065	Cdk16	Crk5|Pctaire1|Pctk1	cyclin-dependent kinase 16	protein-coding
mm_17036.1	chr2	20669305	20669319	-	1	NA	intron (NM_029895, intron 4 of 18)	RLTR41C|LTR|ERV1	149799	NM_001177631	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding
mm_99678.1	chr11	105989248	105989256	+	1	NA	3' UTR (NM_001281819, exon 24 of 24)	3' UTR (NM_001281819, exon 24 of 24)	-3558	NR_104047	100379610	Mm.754	NR_104047	ENSMUSG00000085297	Gm11651	OTTMUSG00000003114	predicted gene 11651	ncRNA
mm_44461.1	chr5	22550280	22550386	-	1	NA	promoter-TSS (NM_011959)	promoter-TSS (NM_011959)	-2	NM_011959	26429	Mm.412217	NM_011959	ENSMUSG00000029012	Orc5	AL033327|MmORC5|Orc5l	origin recognition complex, subunit 5	protein-coding
mm_62837.1	chr7	113766120	113766199	+	1	NA	5' UTR (NM_145584, exon 1 of 16)	5' UTR (NM_145584, exon 1 of 16)	161	NM_145584	233744	Mm.334160	NM_145584	ENSMUSG00000038156	Spon1	AI666765|AW455831|BC020531|D330035F22Rik|FSP	spondin 1, (f-spondin) extracellular matrix protein	protein-coding
mm_116096.1	chr13	28809691	28809694	-	1	NA	intron (NR_045053, intron 2 of 8)	intron (NR_045053, intron 2 of 8)	75730	NR_045054	72518	Mm.37454	NR_045053		2610307P16Rik	AI666457	RIKEN cDNA 2610307P16 gene	ncRNA
mm_119436.1	chr14	46387471	46387484	+	1	NA	intron (NM_007554, intron 1 of 3)	CpG	3192	NM_001316360	12159	Mm.6813	NM_007554	ENSMUSG00000021835	Bmp4	Bmp-4|Bmp2b|Bmp2b-1|Bmp2b1	bone morphogenetic protein 4	protein-coding
mm_63991.1	chr7	140097054	140097080	+	1	NA	TTS (NR_104415)	TTS (NR_104415)	3671	NM_009475	22264	Mm.439707	NM_009475	ENSMUSG00000025467	Prap1	Upa	proline-rich acidic protein 1	protein-coding
mm_123429.1	chr14	64440814	64440820	-	1	NA	exon (NM_026322, exon 6 of 11)	exon (NM_026322, exon 6 of 11)	209	NM_001253715	110265	Mm.26713	NM_026322	ENSMUSG00000054733	Msra	2310045J23Rik|6530413P12Rik|MSR-A	methionine sulfoxide reductase A	protein-coding
mm_50977.1	chr6	62050816	62050842	+	1	NA	intron (NM_001164316, intron 10 of 10)	ID_B1|SINE|B4	-870019	NR_040287	100504262	Mm.438066	NR_040287		A730020E08Rik	-	RIKEN cDNA A730020E08 gene	ncRNA
mm_3242.1	chr1	136018064	136018068	+	1	NA	promoter-TSS (NM_001160146)	promoter-TSS (NM_001160146)	65	NM_025439	66241	Mm.41773	NM_025439	ENSMUSG00000026411	Tmem9	1500015G18Rik|AW545782	transmembrane protein 9	protein-coding
mm_85092.1	chr9	92227270	92227285	-	1	NA	Intergenic	Intergenic	-22917	NM_011636	22038	Mm.421956	NM_011636	ENSMUSG00000032369	Plscr1	MmTRA1a|MmTRA1b|Nor1|Tra1|Tra1a|Tra1b|Tras1|Tras2	phospholipid scramblase 1	protein-coding
mm_38317.1	chr4	137320528	137320543	-	1	NA	3' UTR (NM_009861, exon 6 of 6)	3' UTR (NM_009861, exon 6 of 6)	37224	NM_009861	12540	Mm.1022	NM_009861	ENSMUSG00000006699	Cdc42	AI747189|AU018915	cell division cycle 42	protein-coding
mm_166471.1	chr5	142906010	142906031	-	1	NA	intron (NM_007393, intron 1 of 5)	CpG	734	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_154192.1	chr19	58860949	58860970	-	1	NA	promoter-TSS (NM_175199)	promoter-TSS (NM_175199)	25	NM_175199	73442	Mm.39739	NM_175199	ENSMUSG00000025092	Hspa12a	1700063D12Rik|AI118035|AI840429|AW048913|AW556406|D5Mgi40|Gm19925|mKIAA0417	heat shock protein 12A	protein-coding
mm_74390.1	chr8	128732926	128732937	+	1	NA	3' UTR (NM_010578, exon 16 of 16)	3' UTR (NM_010578, exon 16 of 16)	47277	NM_010578	16412	Mm.263396	NM_010578	ENSMUSG00000025809	Itgb1	4633401G24Rik|AA409975|AA960159|CD29|ENSMUSG00000051907|Fnrb|Gm9863|gpIIa	integrin beta 1 (fibronectin receptor beta)	protein-coding
mm_136676.1	chr17	6256838	6256858	+	1	NA	Intergenic	CpG	-13622	NM_001033178	77106	Mm.381893	NM_001033178	ENSMUSG00000038141	Tmem181a	5930418K15Rik|C76977|Gpr178|Tmem181|mKIAA1423	transmembrane protein 181A	protein-coding
mm_24125.1	chr3	88200608	88200629	+	1	NA	Intergenic	CpG	-14553	NR_037276	100526540		NR_037276	ENSMUSG00000092988	Mir3093	mir-3093|mmu-mir-3093	microRNA 3093	ncRNA
mm_125594.1	chr15	59648551	59648561	+	1	NA	promoter-TSS (NM_144549)	promoter-TSS (NM_144549)	-98	NM_144549	211770	Mm.40298	NM_144549	ENSMUSG00000032501	Trib1	A530090O15Rik|TRB-1|Trb1	tribbles pseudokinase 1	protein-coding
mm_76592.1	chr8	89042816	89042829	-	1	NA	intron (NM_021390, intron 1 of 3)	CpG-14342	1340	NM_021390	58198	Mm.214361	NM_021390	ENSMUSG00000031665	Sall1	Msal-3	sal-like 1 (Drosophila)	protein-coding
mm_86641.1	chr10	14117516	14117520	+	1	NA	intron (NM_010437, intron 2 of 8)	PB1D7|SINE|Alu	151139	NM_010437	15273	Mm.42157	NM_010437	ENSMUSG00000015501	Hivep2	Gm20114|MIBP1|Schnurri-2|Shn-2	human immunodeficiency virus type I enhancer binding protein 2	protein-coding
mm_51174.1	chr6	70726661	70726677	+	1	NA	Intergenic	Intergenic	65506	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_47884.1	chr5	134703369	134703383	-	1	NA	3' UTR (NM_007925, exon 37 of 37)	3' UTR (NM_007925, exon 37 of 37)	-14786	NM_010717	16885	Mm.15409	NM_010717	ENSMUSG00000029674	Limk1	KIZ-1|LIMK-1|Limk	LIM-domain containing, protein kinase	protein-coding
mm_21183.1	chr2	155074457	155074502	-	1	NA	promoter-TSS (NM_016661)	promoter-TSS (NM_016661)	18	NM_016661	269378	Mm.330692	NM_016661	ENSMUSG00000027597	Ahcy	AA987153|AL024110|CuBP|SAHH	S-adenosylhomocysteine hydrolase	protein-coding
mm_110033.1	chr12	16894685	16894725	-	1	NA	promoter-TSS (NM_009072)	promoter-TSS (NM_009072)	-273	NM_009072	19878	Mm.276024	NM_009072	ENSMUSG00000020580	Rock2	B230113H15Rik|ROKalpha|Rho-kinase|Rock-II|Rock2m|mKIAA0619	Rho-associated coiled-coil containing protein kinase 2	protein-coding
mm_103820.1	chr11	83003750	83003760	-	1	NA	exon (NM_181545, exon 6 of 6)	exon (NM_181545, exon 6 of 6)	-11925	NM_172796	237886	Mm.270253	NM_172796	ENSMUSG00000069793	Slfn9	9830137M10Rik	schlafen 9	protein-coding
mm_38892.1	chr4	149774083	149774113	-	1	NA	5' UTR (NM_027460, exon 1 of 7)	5' UTR (NM_027460, exon 1 of 7)	169	NM_027460	70556	Mm.41877	NM_027460	ENSMUSG00000028982	Slc25a33	5730438N18Rik|Pnc1	solute carrier family 25, member 33	protein-coding
mm_89979.1	chr10	111595924	111595935	+	1	NA	Intergenic	Intergenic	-1656	NR_045344	71321	Mm.410785	NR_045344	ENSMUSG00000097082	4933440J02Rik	-	RIKEN cDNA 4933440J02 gene	ncRNA
mm_142590.1	chr17	46752058	46752058	-	1	NA	exon (NM_001305988, exon 1 of 5)	exon (NM_001305988, exon 1 of 5)	156	NM_001305989	72029	Mm.240325	NM_028065	ENSMUSG00000023973	Cnpy3	1600025D17Rik|2410050O22Rik|AI413153|CAG4A|ERDA5|PRAT4A|Tnrc5	canopy FGF signaling regulator 3	protein-coding
mm_23107.1	chr3	37420342	37420356	+	1	NA	promoter-TSS (NM_001291044)	promoter-TSS (NM_001291044)	399	NM_021343	57815	Mm.172679	NM_021343	ENSMUSG00000027722	Spata5	2510048F20Rik|C78064|Spaf	spermatogenesis associated 5	protein-coding
mm_46346.1	chr5	102072136	102072204	-	1	NA	Intergenic	Intergenic	-2249	NM_172882	72145	Mm.332522	NM_172882	ENSMUSG00000043940	Wdfy3	2610509D04Rik|ALFY|AW319683|B930017C24|BWF1|Bchs|D5Ertd66e|Ggtb3|ZFYVE25|mKIAA0993	WD repeat and FYVE domain containing 3	protein-coding
mm_50691.1	chr6	51589354	51589395	+	1	NA	3' UTR (NM_001127349, exon 7 of 7)	3' UTR (NM_001127349, exon 7 of 7)	44851	NM_001127348	71982	Mm.294166	NM_028035	ENSMUSG00000038301	Snx10	2410004M09Rik	sorting nexin 10	protein-coding
mm_101137.1	chr11	12557810	12557822	-	1	NA	Intergenic	Intergenic	-92856	NM_001282993	12808	Mm.22847	NM_172496	ENSMUSG00000020173	Cobl	-	cordon-bleu WH2 repeat	protein-coding
mm_87405.1	chr10	45685996	45685997	+	1	NA	intron (NM_172473, intron 19 of 23)	intron (NM_172473, intron 19 of 23)	108167	NM_172473	209462	Mm.458633	NM_172473	ENSMUSG00000038822	Hace1	1700042J16Rik|A730034A22Rik|BC025474	HECT domain and ankyrin repeat containing, E3 ubiquitin protein ligase 1	protein-coding
mm_87883.1	chr10	61715281	61715328	+	1	NA	promoter-TSS (NM_178058)	promoter-TSS (NM_178058)	41	NM_001284300	71361	Mm.286309	NM_153779	ENSMUSG00000020085	Aifm2	5430437E11Rik|Amid|D730001I10Rik|PRG3	apoptosis-inducing factor, mitochondrion-associated 2	protein-coding
mm_85659.1	chr9	107668968	107668995	-	1	NA	promoter-TSS (NM_001199218)	promoter-TSS (NM_001199218)	-13	NM_001199218	76257	Mm.296560	NM_023805	ENSMUSG00000010064	Slc38a3	0610012J02Rik|D9Ucla2|Nat1|Slc38-3|Sn1|Snat3|mNAT	solute carrier family 38, member 3	protein-coding
mm_35315.1	chr4	25615680	25615690	-	1	NA	3' UTR (NM_010243, exon 3 of 3)	3' UTR (NM_010243, exon 3 of 3)	184318	NM_010243	14348	Mm.39101	NM_010243	ENSMUSG00000055373	Fut9	AI746471|AU067636|mFUT9|mFuc-TIX	fucosyltransferase 9	protein-coding
mm_147050.1	chr18	34931994	34932004	-	1	NA	promoter-TSS (NM_144866)	promoter-TSS (NM_144866)	4	NM_144866	225363	Mm.329353	NM_144866	ENSMUSG00000024360	Etf1	AI463371|D6Ertd109e|ERF|ERF1|SUP45L1|TB3-1	eukaryotic translation termination factor 1	protein-coding
mm_53360.1	chr6	129359760	129359766	+	1	NA	intron (NM_177686, intron 5 of 5)	AT_rich|Low_complexity|Low_complexity	9519	NM_177686	232413	Mm.90241	NM_177686	ENSMUSG00000053063	Clec12a	CLL-1|D230024O04|KLRL1|Micl	C-type lectin domain family 12, member a	protein-coding
mm_15833.1	chr2	164685052	164685056	+	1	NA	promoter-TSS (NM_001012704)	promoter-TSS (NM_001012704)	-53	NM_001012704	408190	Mm.376205	NM_001012704	ENSMUSG00000067704	Wfdc13	Wfdc13l1	WAP four-disulfide core domain 13	protein-coding
mm_162570.1	chr1	173975047	173975056	-	1	NA	exon (NM_011940, exon 3 of 7)	exon (NM_011940, exon 3 of 7)	7793	NM_008327	26388	Mm.218770	NM_008327	ENSMUSG00000026535	Ifi202b	Ifbip-1|Ifi202|Ifi202a|p202	interferon activated gene 202B	protein-coding
mm_20496.1	chr2	130284423	130284451	-	1	NA	promoter-TSS (NM_130884)	promoter-TSS (NM_130884)	14	NM_130884	170718	Mm.29590	NM_130884	ENSMUSG00000027406	Idh3b	C78231	isocitrate dehydrogenase 3 (NAD+) beta	protein-coding
mm_151064.1	chr19	47253418	47253447	+	1	NA	exon (NM_021360, exon 4 of 6)	exon (NM_021360, exon 4 of 6)	20157	NR_105961	102466782		NR_105961	ENSMUSG00000098786	Mir6995	Gm27576|mmu-mir-6995	microRNA 6995	ncRNA
mm_147199.1	chr18	37874348	37874380	-	1	NA	intron (NM_007858, intron 16 of 26)	intron (NM_007858, intron 16 of 26)	-19704	NR_105945	102465592		NR_105945	ENSMUSG00000098706	Mir6979	Gm27524|mmu-mir-6979	microRNA 6979	ncRNA
mm_39832.1	chr5	30853789	30853794	+	1	NA	intron (NM_133350, intron 1 of 6)	intron (NM_133350, intron 1 of 6)	-8016	NM_001310516	100732	Mm.332295	NM_133350	ENSMUSG00000029166	Mapre3	AI790651|EB2|EB3|EBF3|RP3	microtubule-associated protein, RP/EB family, member 3	protein-coding
mm_134526.1	chr16	19236861	19236866	-	1	NA	Intergenic	RMER17B|LTR|ERVK	49878	NM_146451	258443	Mm.377506	NM_146451	ENSMUSG00000050742	Olfr164	MOR279-2	olfactory receptor 164	protein-coding
mm_117367.1	chr13	70841791	70841810	-	1	NA	promoter-TSS (NR_137640)	promoter-TSS (NR_137640)	11	NM_172053	271127	Mm.115970	NM_172053	ENSMUSG00000049538	Adamts16	-	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 16	protein-coding
mm_24298.1	chr3	89365306	89365355	+	1	NA	promoter-TSS (NM_029974)	promoter-TSS (NM_029974)	-77	NM_029974	77772	Mm.164013	NM_029974	ENSMUSG00000042672	Dcst1	A330106H01Rik	DC-STAMP domain containing 1	protein-coding
mm_51257.1	chr6	71936009	71936040	+	1	NA	intron (NM_009088, intron 12 of 33)	intron (NM_009088, intron 12 of 33)	26971	NM_009088	20019	Mm.135581	NM_009088	ENSMUSG00000049553	Polr1a	194kDa|3010014K16Rik|RPA194|Rpo1-4|mRPA1	polymerase (RNA) I polypeptide A	protein-coding
mm_19390.1	chr2	91333227	91333230	-	1	NA	intron (NM_001311144, intron 3 of 8)	B1_Mur1|SINE|Alu	68113	NM_023854	77038	Mm.43636	NM_023854	ENSMUSG00000027255	Arfgap2	2310032E02Rik|Zfp289	ADP-ribosylation factor GTPase activating protein 2	protein-coding
mm_70241.1	chr8	3353631	3353686	+	1	NA	5' UTR (NM_001033378, exon 1 of 11)	5' UTR (NM_001033378, exon 1 of 11)	243	NM_001033378	319493	Mm.234565	NM_001033378	ENSMUSG00000074497	A430078G23Rik	-	RIKEN cDNA A430078G23 gene	protein-coding
mm_63251.1	chr7	126622905	126622905	+	1	NA	TTS (NM_019738)	TTS (NM_019738)	2565	NM_019738	56312	Mm.18742	NM_019738	ENSMUSG00000030717	Nupr1	2310032H04Rik|Com1|p8	nuclear protein transcription regulator 1	protein-coding
mm_52901.1	chr6	122707593	122707608	+	1	NA	promoter-TSS (NM_001289830)	promoter-TSS (NM_001289830)	35	NM_001289828	71950	Mm.6047	NM_028016	ENSMUSG00000012396	Nanog	2410002E02Rik|ENK|ecat4	Nanog homeobox	protein-coding
mm_17818.1	chr2	33745026	33745028	-	1	NA	intron (NM_175184, intron 9 of 9)	Lx9|LINE|L1	-60789	NR_045729	320482	Mm.442057	NR_045729	ENSMUSG00000086484	Nron	A630071L07Rik|Gm24353	non-protein coding RNA, repressor of NFAT	ncRNA
mm_108294.1	chr12	79208884	79208888	+	1	NA	promoter-TSS (NM_030017)	promoter-TSS (NM_030017)	-27	NM_001313971	77974	Mm.274373	NM_030017	ENSMUSG00000021123	Rdh12	-	retinol dehydrogenase 12	protein-coding
mm_83058.1	chr9	37545255	37545273	-	1	NA	3' UTR (NM_022029, exon 4 of 4)	3' UTR (NM_022029, exon 4 of 4)	6009	NM_020518	57276	Mm.27478	NM_020518	ENSMUSG00000001943	Vsig2	1190004B15Rik|2210413P10Rik|AU040484|CTX|Ctm	V-set and immunoglobulin domain containing 2	protein-coding
mm_122151.1	chr14	31251195	31251348	-	1	NA	promoter-TSS (NM_027088)	promoter-TSS (NM_027088)	-53	NM_027949	71838	Mm.5348	NM_027949	ENSMUSG00000021902	Phf7	1700006H01Rik|1700010P14Rik|AI427892|AW555949	PHD finger protein 7	protein-coding
mm_169010.1	chr13	107121802	107121805	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	99233	NR_015471	100040322	Mm.133867	NR_015471		3830408C21Rik	-	RIKEN cDNA 3830408C21 gene	ncRNA
mm_1137.1	chr1	60609223	60609229	+	1	NA	Intergenic	Intergenic	-42461	NM_001045513	77300	Mm.440325	NM_001045513	ENSMUSG00000026014	Raph1	9430025M21Rik|C730009O10Rik|Lpd	Ras association (RalGDS/AF-6) and pleckstrin homology domains 1	protein-coding
mm_39218.1	chr4	156192577	156192617	-	1	NA	intron (NM_021604, intron 2 of 35)	intron (NM_021604, intron 2 of 35)	4891	NM_021604	11603	Mm.273098	NM_021604	ENSMUSG00000041936	Agrn	Agrin|nmf380	agrin	protein-coding
mm_11335.1	chr2	30636550	30636562	+	1	NA	Intergenic	Intergenic	41455	NR_136917	665635	Mm.450149	NR_136917		Gm14486	OTTMUSG00000016802	predicted gene 14486	ncRNA
mm_66518.1	chr7	45103973	45103992	-	1	NA	promoter-TSS (NM_010189)	promoter-TSS (NM_010189)	-160	NM_010189	14132	Mm.3303	NM_010189	ENSMUSG00000003420	Fcgrt	FcRn	Fc receptor, IgG, alpha chain transporter	protein-coding
mm_93603.1	chr10	117234022	117234027	-	1	NA	3' UTR (NM_029906, exon 4 of 4)	3' UTR (NM_029906, exon 4 of 4)	4657	NM_029906	77397	Mm.118350	NM_029906	ENSMUSG00000020177	9530003J23Rik	Lyzf1	RIKEN cDNA 9530003J23 gene	protein-coding
mm_66770.1	chr7	46742980	46742980	-	1	NA	promoter-TSS (NM_009117)	promoter-TSS (NM_009117)	0	NM_009117	20208	Mm.148800	NM_009117	ENSMUSG00000074115	Saa1	Saa-1|Saa2	serum amyloid A 1	protein-coding
mm_167706.1	chr9	95805434	95805436	-	1	NA	intron (NM_001033210, intron 1 of 15)	intron (NM_001033210, intron 1 of 15)	39844	NM_001033210	102502	Mm.11869	NM_001033210	ENSMUSG00000049493	Pls1	AI427122	plastin 1 (I-isoform)	protein-coding
mm_122602.1	chr14	51041924	51041928	-	1	NA	promoter-TSS (NM_183032)	promoter-TSS (NM_183032)	-59	NM_183032	328401	Mm.99528	NM_183032	ENSMUSG00000052382	Rnase9	ESRL|Rak1	ribonuclease, RNase A family, 9 (non-active)	protein-coding
mm_84312.1	chr9	63711984	63711994	-	1	NA	intron (NM_016769, intron 1 of 8)	intron (NM_016769, intron 1 of 8)	46005	NM_016769	17127	Mm.7320	NM_016769	ENSMUSG00000032402	Smad3	AU022421|Madh3	SMAD family member 3	protein-coding
mm_70244.1	chr8	3360805	3360809	+	1	NA	intron (NM_001033378, intron 1 of 10)	intron (NM_001033378, intron 1 of 10)	7392	NM_001033378	319493	Mm.234565	NM_001033378	ENSMUSG00000074497	A430078G23Rik	-	RIKEN cDNA A430078G23 gene	protein-coding
mm_93829.1	chr10	121585874	121585883	-	1	NA	intron (NM_019786, intron 1 of 20)	intron (NM_019786, intron 1 of 20)	916	NM_019786	56480	Mm.34580	NM_019786	ENSMUSG00000020115	Tbk1	1200008B05Rik|AI462036|AW048562	TANK-binding kinase 1	protein-coding
mm_2070.1	chr1	87626681	87626690	+	1	NA	intron (NM_010566, intron 1 of 26)	intron (NM_010566, intron 1 of 26)	6373	NM_001110193	16331	Mm.15105	NM_010566	ENSMUSG00000026288	Inpp5d	SHIP|SHIP-1|SHIP1|SIP-145|p150Ship|s-SHIP	inositol polyphosphate-5-phosphatase D	protein-coding
mm_6734.1	chr1	82832492	82832494	-	1	NA	Intergenic	Intergenic	-6967	NM_001310713	15463	Mm.392569	NM_010472	ENSMUSG00000026159	Agfg1	AU045498|C130049H11Rik|C85612|D730048C23Rik|Hrb|RAB|Rip	ArfGAP with FG repeats 1	protein-coding
mm_138300.1	chr17	34631093	34631147	+	1	NA	exon (NM_030890, exon 2 of 4)	exon (NM_030890, exon 2 of 4)	1434	NM_030890	260297	Mm.390965	NM_030890	ENSMUSG00000015476	Prrt1	Bat-4|Bat4|D17H6S54E|DSPD1|G5b|NG5|ORF31	proline-rich transmembrane protein 1	protein-coding
mm_74187.1	chr8	123653792	123653805	+	1	NA	promoter-TSS (NM_133955)	promoter-TSS (NM_133955)	-131	NM_133955	69581	Mm.168257	NM_133955	ENSMUSG00000039960	Rhou	2310026M05Rik|AI182090|Arhu|CDC42L1|G28K|WRCH-1|WRCH1|mG28K	ras homolog family member U	protein-coding
mm_118121.1	chr13	104109621	104109640	-	1	NA	promoter-TSS (NM_029447)	promoter-TSS (NM_029447)	-16	NM_029447	75805	Mm.127692	NM_029447	ENSMUSG00000021710	Nln	4930472G13Rik|C79345	neurolysin (metallopeptidase M3 family)	protein-coding
mm_161878.1	chr18	37355124	37355124	+	1	NA	promoter-TSS (NM_053133)	promoter-TSS (NM_053133)	-147	NM_053133	93879	Mm.348052	NM_053133	ENSMUSG00000045876	Pcdhb8	Pcdhb5C|PcdhbH	protocadherin beta 8	protein-coding
mm_58280.1	chr6	145862197	145862224	-	1	NA	3' UTR (NM_001271768, exon 5 of 5)	3' UTR (NM_001271768, exon 5 of 5)	3210	NM_001271768	79362	Mm.154529	NM_024469	ENSMUSG00000030256	Bhlhe41	6430520M22Rik|Bhlhb2l|Bhlhb3|DEC2|Sharp1	basic helix-loop-helix family, member e41	protein-coding
mm_64641.1	chr7	4008107	4008117	-	1	NA	3' UTR (NM_178611, exon 7 of 7)	3' UTR (NM_178611, exon 7 of 7)	55092	NM_001302677	52855	Mm.290880	NM_178611	ENSMUSG00000055541	Lair1	5133400O11Rik|BB115266|D7Bwg0421e|Lair-1	leukocyte-associated Ig-like receptor 1	protein-coding
mm_105645.1	chr11	107131890	107131900	-	1	NA	promoter-TSS (NM_176850)	promoter-TSS (NM_176850)	27	NM_176850	207165	Mm.343986	NM_176850	ENSMUSG00000040481	Bptf	9430093H17Rik|Falz	bromodomain PHD finger transcription factor	protein-coding
mm_51450.1	chr6	80458747	80458747	+	1	NA	intron (NM_001347261, intron 2 of 2)	intron (NM_001347261, intron 2 of 2)	439104	NM_178731	243499	Mm.483425	NM_178731	ENSMUSG00000052581	Lrrtm4	7530419J18Rik|A230052N11	leucine rich repeat transmembrane neuronal 4	protein-coding
mm_82177.1	chr9	123851384	123851431	+	1	NA	TTS (NM_011798)	TTS (NM_011798)	254	NM_148925	17281	Mm.252941	NM_148925	ENSMUSG00000025241	Fyco1	2810409M01Rik|Mem2|RUFY3|ZFYVE7	FYVE and coiled-coil domain containing 1	protein-coding
mm_166060.1	chr4	133686303	133686307	+	1	NA	exon (NM_001080819, exon 17 of 20)	exon (NM_001080819, exon 17 of 20)	-13658	NM_001145956	230801	Mm.217004	NM_178698	ENSMUSG00000043257	Pigv	B330013B03|D430024F16Rik	phosphatidylinositol glycan anchor biosynthesis, class V	protein-coding
mm_111276.1	chr12	85341608	85341620	-	1	NA	3' UTR (NM_026775, exon 5 of 5)	3' UTR (NM_026775, exon 5 of 5)	-2252	NM_145138	217718	Mm.29071	NM_145138	ENSMUSG00000034290	Nek9	C130021H08Rik	NIMA (never in mitosis gene a)-related expressed kinase 9	protein-coding
mm_33947.1	chr4	137296887	137296905	+	1	NA	3' UTR (NM_009523, exon 5 of 5)	3' UTR (NM_009523, exon 5 of 5)	19261	NM_009523	22417	Mm.20355	NM_009523	ENSMUSG00000036856	Wnt4	Wnt-4	wingless-type MMTV integration site family, member 4	protein-coding
mm_40358.1	chr5	48001399	48001412	+	1	NA	intron (NR_111900, intron 4 of 35)	intron (NR_111900, intron 4 of 35)	18250	NM_001291228	20563	Mm.289739	NM_178804	ENSMUSG00000031558	Slit2	Drad-1|E030015M03Rik|E130320P19Rik|Slil3|mKIAA4141|slit-2	slit homolog 2 (Drosophila)	protein-coding
mm_37712.1	chr4	129491109	129491119	-	1	NA	promoter-TSS (NM_080442)	promoter-TSS (NM_080442)	-76	NM_001085491	68233	Mm.424983	NM_001085491	ENSMUSG00000078554	Fam229a	1700125D06Rik	family with sequence similarity 229, member A	protein-coding
mm_91794.1	chr10	53379817	53379858	-	1	NA	promoter-TSS (NM_001204983)	promoter-TSS (NM_001204983)	14	NM_001204983	100038725	Mm.441403	NM_001204983	ENSMUSG00000038594	Cep85l	ENSMUSG00000038594|Gm9766	centrosomal protein 85-like	protein-coding
mm_123694.1	chr14	69688570	69688579	-	1	NA	intron (NM_033325, intron 10 of 13)	ORR1G|LTR|ERVL-MaLR	-3674	NR_105915	102465573		NR_105915	ENSMUSG00000098666	Mir6950	Gm27586|mmu-mir-6950	microRNA 6950	ncRNA
mm_8386.1	chr1	151344377	151344386	-	1	NA	promoter-TSS (NM_001039512)	promoter-TSS (NM_001039512)	-117	NM_001039512	117198	Mm.33764	NM_028582	ENSMUSG00000023150	Ivns1abp	1190004M08Rik|1700126I16Rik|AA960440|HSPC068|ND1|NS-1|NS1-BP|Nd1-L|Nd1-S|mKIAA0850	influenza virus NS1A binding protein	protein-coding
mm_52114.1	chr6	97915187	97915201	+	1	NA	intron (NM_001113198, intron 1 of 9)	intron (NM_001113198, intron 1 of 9)	-14623	NM_001178049	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_83146.1	chr9	40455838	40455844	-	1	NA	promoter-TSS (NM_172768)	promoter-TSS (NM_172768)	-77	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_2450.1	chr1	100252649	100252658	+	1	NA	intron (NM_172851, intron 11 of 23)	intron (NM_172851, intron 11 of 23)	479888	NM_172851	241175	Mm.251301	NM_172851	ENSMUSG00000067028	Cntnap5b	C230078M14Rik|Caspr5-2	contactin associated protein-like 5B	protein-coding
mm_132976.1	chr16	52049682	52049689	+	1	NA	intron (NM_001033238, intron 3 of 17)	intron (NM_001033238, intron 3 of 17)	18136	NM_001033238	208650	Mm.328206	NM_001033238	ENSMUSG00000022637	Cblb	AI429560|AI851073|Cbl-b	Casitas B-lineage lymphoma b	protein-coding
mm_38594.1	chr4	141825583	141825601	-	1	NA	exon (NM_007919, exon 2 of 8)	exon (NM_007919, exon 2 of 8)	413	NM_007919	13706	Mm.45316	NM_007919	ENSMUSG00000058579	Cela2a	Ela-2|Ela2|Ela2a	chymotrypsin-like elastase family, member 2A	protein-coding
mm_18260.1	chr2	52289691	52289708	-	1	NA	exon (NM_010889, exon 35 of 157)	exon (NM_010889, exon 35 of 157)	-1303	NR_040620	78049	Mm.243883	NR_040620		4930573O16Rik	-	RIKEN cDNA 4930573O16 gene	ncRNA
mm_35023.1	chr4	3973596	3973607	-	1	NA	Intergenic	Intergenic	34177	NR_104356	66433	Mm.27406	NM_181391	ENSMUSG00000042198	Chchd7	1810049H20Rik	coiled-coil-helix-coiled-coil-helix domain containing 7	protein-coding
mm_86645.1	chr10	14705582	14705595	+	1	NA	promoter-TSS (NM_025418)	promoter-TSS (NM_025418)	-21	NR_045824	69412	Mm.259735	NR_045824	ENSMUSG00000019865	1700016L04Rik	-	RIKEN cDNA 1700016L04 gene	ncRNA
mm_96697.1	chr11	69632928	69633002	+	1	NA	promoter-TSS (NM_011814)	promoter-TSS (NM_011814)	-6	NM_011814	23879	Mm.41930	NM_011814	ENSMUSG00000018765	Fxr2	Fxr2h	fragile X mental retardation, autosomal homolog 2	protein-coding
mm_52936.1	chr6	122933984	122934003	+	1	NA	3' UTR (NM_199311, exon 6 of 6)	3' UTR (NM_199311, exon 6 of 6)	12145	NM_199311	269799	Mm.297275	NM_199311	ENSMUSG00000049037	Clec4a1	BC049354|Dcir4	C-type lectin domain family 4, member a1	protein-coding
mm_149657.1	chr19	18713166	18713187	+	1	NA	promoter-TSS (NM_177640)	promoter-TSS (NM_177640)	-60	NM_177640	225995	Mm.28101	NM_177640	ENSMUSG00000047044	D030056L22Rik	-	RIKEN cDNA D030056L22 gene	protein-coding
mm_1488.1	chr1	71714153	71714162	+	1	NA	Intergenic	Intergenic	60822	NR_040308	100042814	Mm.405775	NR_040308	ENSMUSG00000073652	Apol7d	ENSMUSG00000073652|Gm15456|OTTMUSG00000022136	apolipoprotein L 7d	ncRNA
mm_102671.1	chr11	65178090	65178096	-	1	NA	3' UTR (NM_145136, exon 14 of 14)	3' UTR (NM_145136, exon 14 of 14)	-15132	NM_175003	216831	Mm.134338	NM_175003	ENSMUSG00000033389	Arhgap44	6330543G20|AI840762|AU040829|AW493732|Rich2	Rho GTPase activating protein 44	protein-coding
mm_152212.1	chr19	7961169	7961170	-	1	NA	intron (NM_134256, intron 1 of 10)	intron (NM_134256, intron 1 of 10)	4858	NM_134256	171405	Mm.326517	NM_134256	ENSMUSG00000067656	Slc22a27	Oat9|mOAT6-L|mOAT6-S	solute carrier family 22, member 27	protein-coding
mm_56585.1	chr6	106800052	106800095	-	1	NA	promoter-TSS (NM_021449)	promoter-TSS (NM_021449)	14	NM_021449	58799	Mm.290085	NM_021449	ENSMUSG00000005362	Crbn	2610203G15Rik|2900045O07Rik|AF229032|AW108261|piL	cereblon	protein-coding
mm_166444.1	chr5	137264360	137264372	+	1	NA	Intergenic	Intergenic	-23888	NM_009599	11423	Mm.255464	NM_009599	ENSMUSG00000023328	Ache	-	acetylcholinesterase	protein-coding
mm_134674.1	chr16	22402655	22402674	-	1	NA	intron (NM_023794, intron 7 of 12)	intron (NM_023794, intron 7 of 12)	36906	NM_023794	104156	Mm.155708	NM_023794	ENSMUSG00000013089	Etv5	1110005E01Rik|8430401F14Rik|ERM	ets variant 5	protein-coding
mm_87100.1	chr10	33139193	33139212	+	1	NA	exon (NM_029726, exon 2 of 38)	exon (NM_029726, exon 2 of 38)	55719	NM_029726	76757	Mm.338508	NM_029726	ENSMUSG00000019787	Trdn	2310045H21Rik|EG432451|TDN	triadin	protein-coding
mm_12268.1	chr2	68970846	68970853	+	1	NA	intron (NM_172856, intron 3 of 9)	intron (NM_172856, intron 3 of 9)	109408	NM_001347161	241447	Mm.222222	NM_172856	ENSMUSG00000027035	Cers6	4732462C07Rik|AW544719|Lass6|T1L	ceramide synthase 6	protein-coding
mm_45268.1	chr5	64467951	64467955	-	1	NA	promoter-TSS (NR_040681)	promoter-TSS (NR_040681)	-11	NR_040681	69999	Mm.261413	NR_040681	ENSMUSG00000100911	1700027F09Rik	-	RIKEN cDNA 1700027F09 gene	ncRNA
mm_137932.1	chr17	32658967	32658977	+	1	NA	promoter-TSS (NM_001101588)	promoter-TSS (NM_001101588)	-511	NM_001101588	631304	Mm.328950	NM_001101588	ENSMUSG00000090700	Cyp4f40	EG631304	cytochrome P450, family 4, subfamily f, polypeptide 40	protein-coding
mm_81292.1	chr9	108336789	108336831	+	1	NA	exon (NM_016802, exon 6 of 6)	exon (NM_016802, exon 6 of 6)	-2270	NM_008160	14775	Mm.1090	NM_008160	ENSMUSG00000063856	Gpx1	AI195024|AL033363|CGPx|GPx-1|GSHPx-1|Gpx	glutathione peroxidase 1	protein-coding
mm_42251.1	chr5	114003679	114003693	+	1	NA	promoter-TSS (NM_001286397)	promoter-TSS (NM_001286397)	-49	NM_010018	13142	Mm.20115	NM_010018	ENSMUSG00000042096	Dao	AI987963|DAAO|DAMOX|Dao-1|Dao1	D-amino acid oxidase	protein-coding
mm_91281.1	chr10	24711934	24711949	-	1	NA	exon (NM_008813, exon 1 of 25)	exon (NM_008813, exon 1 of 25)	218	NM_001308327	18605	Mm.27254	NM_008813	ENSMUSG00000037370	Enpp1	4833416E15Rik|AI428932|C76301|CD203c|E-NPP 1|E-NPP1|Ly-41|M6S1|NPP1|Npps|PC-1|Pca|Pca-1|Pdnp1|ttw|twy	ectonucleotide pyrophosphatase/phosphodiesterase 1	protein-coding
mm_16175.1	chr2	172551029	172551043	+	1	NA	promoter-TSS (NM_001159696)	promoter-TSS (NM_001159696)	45	NM_001159696	21420	Mm.3629	NM_009335	ENSMUSG00000028640	Tfap2c	AA409384|AP2gamma|Ap-2.2|Stra2|Tcfap2c	transcription factor AP-2, gamma	protein-coding
mm_92485.1	chr10	78297916	78297986	-	1	NA	intron (NM_053014, intron 2 of 9)	intron (NM_053014, intron 2 of 9)	42256	NR_106119	102465765		NR_106119	ENSMUSG00000098885	Mir7659	Gm27433|mmu-mir-7659	microRNA 7659	ncRNA
mm_83881.1	chr9	55283662	55283672	-	1	NA	promoter-TSS (NM_032002)	promoter-TSS (NM_032002)	-42	NM_032002	83961	Mm.443874	NM_032002	ENSMUSG00000032311	Nrg4	AI552600	neuregulin 4	protein-coding
mm_74256.1	chr8	124863102	124863114	+	1	NA	promoter-TSS (NM_025615)	promoter-TSS (NM_025615)	75	NM_010322	14712	Mm.29114	NM_010322	ENSMUSG00000031985	Gnpat	AU019525|D1Ertd819e|DHAPAT	glyceronephosphate O-acyltransferase	protein-coding
mm_80017.1	chr9	67880428	67880450	+	1	NA	intron (NM_177184, intron 12 of 84)	intron (NM_177184, intron 12 of 84)	40043	NM_177184	320528	Mm.241454	NM_177184	ENSMUSG00000035284	Vps13c	AI552542|AV026040|C230055H22Rik|W51662|chorein	vacuolar protein sorting 13C	protein-coding
mm_76717.1	chr8	94711401	94711422	-	1	NA	Intergenic	Intergenic	-15169	NM_026385	67801	Mm.279977	NM_026385	ENSMUSG00000031775	Pllp	0610010I06Rik|AV001002|Plapi|Tm4sf11	plasma membrane proteolipid	protein-coding
mm_13151.1	chr2	92382912	92382924	+	1	NA	promoter-TSS (NM_183112)	promoter-TSS (NM_183112)	0	NM_183112	75641	Mm.330409	NM_183112	ENSMUSG00000044916	1700029I15Rik	1700021K07Rik	RIKEN cDNA 1700029I15 gene	protein-coding
mm_108461.1	chr12	83520437	83520447	+	1	NA	promoter-TSS (NM_030246)	promoter-TSS (NM_030246)	-24	NM_030246	73828	Mm.38238	NM_030246	ENSMUSG00000021222	Dcaf4	1110018E21Rik|Wdr21	DDB1 and CUL4 associated factor 4	protein-coding
mm_80109.1	chr9	70399421	70399431	+	1	NA	3' UTR (NM_181072, exon 28 of 28)	3' UTR (NM_181072, exon 28 of 28)	6327	NR_049200	100885839		NR_049200	ENSMUSG00000093763	Mir5626	Gm25590|mir-5626|mmu-mir-5626	microRNA 5626	ncRNA
mm_31372.1	chr4	47367248	47367273	+	1	NA	intron (NM_001312868, intron 1 of 8)	B3|SINE|B2	14038	NM_009370	21812	Mm.197552	NM_009370	ENSMUSG00000007613	Tgfbr1	ALK5|AU017191|Alk-5|ESK2|TGFR-1|TbetaR-I|TbetaRI	transforming growth factor, beta receptor I	protein-coding
mm_150880.1	chr19	45076685	45076702	+	1	NA	exon (NM_178929, exon 2 of 5)	exon (NM_178929, exon 2 of 5)	554	NM_178929	107250	Mm.24417	NM_178929	ENSMUSG00000025213	Kazald1	AI842353|Bono1|IGFBP-rP10	Kazal-type serine peptidase inhibitor domain 1	protein-coding
mm_101598.1	chr11	34737823	34737829	-	1	NA	intron (NM_033374, intron 2 of 51)	intron (NM_033374, intron 2 of 51)	46079	NM_033374	94176	Mm.380679	NM_033374	ENSMUSG00000020143	Dock2	AI662014|AW122239|CED-5|Hch|MBC	dedicator of cyto-kinesis 2	protein-coding
mm_106229.1	chr11	117267499	117267511	-	1	NA	intron (NM_001113487, intron 1 of 10)	intron (NM_001113487, intron 1 of 10)	1259	NM_001113487	53860	Mm.38450	NM_017380	ENSMUSG00000059248	Sept9	MSF1|Msf|PNUTL4|Sint1	septin 9	protein-coding
mm_79604.1	chr9	58582259	58582269	+	1	NA	promoter-TSS (NM_009145)	promoter-TSS (NM_009145)	24	NM_009145	20320	Mm.15125	NM_009145	ENSMUSG00000032336	Nptn	AW554172|SDR-1|Sdfr1	neuroplastin	protein-coding
mm_123912.1	chr14	73325947	73325982	-	1	NA	promoter-TSS (NM_009029)	promoter-TSS (NM_009029)	-173	NM_009029	19645	Mm.273862	NM_009029	ENSMUSG00000022105	Rb1	Rb|Rb-1|pRb	retinoblastoma 1	protein-coding
mm_107264.1	chr12	29123297	29123338	+	1	NA	Intergenic	Intergenic	371489	NM_201357	380752	Mm.273724	NM_201357	ENSMUSG00000036613	Tssc1	D12Ertd604e|Eipr1	tumor suppressing subtransferable candidate 1	protein-coding
mm_147642.1	chr18	60269730	60269738	-	1	NA	3' UTR (NM_001034859, exon 2 of 2)	3' UTR (NM_001034859, exon 2 of 2)	3533	NM_001034859	225594	Mm.329460	NM_001034859	ENSMUSG00000068606	Gm4841	EG225594|Ifgga3	predicted gene 4841	protein-coding
mm_112742.1	chr13	19339868	19339876	+	1	NA	Intergenic	Intergenic	55941	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_97323.1	chr11	76945661	76945671	+	1	NA	promoter-TSS (NM_178645)	promoter-TSS (NM_178645)	10	NM_178645	104184	Mm.399785	NM_178645	ENSMUSG00000020840	Blmh	AI035728|Bh|Bmh	bleomycin hydrolase	protein-coding
mm_75002.1	chr8	27228530	27228556	-	1	NA	5' UTR (NM_013462, exon 2 of 4)	5' UTR (NM_013462, exon 2 of 4)	1045	NM_013462	11556	Mm.278475	NM_013462	ENSMUSG00000031489	Adrb3	Adrb-3	adrenergic receptor, beta 3	protein-coding
mm_27174.1	chr3	34019798	34019812	-	1	NA	promoter-TSS (NM_001113188)	promoter-TSS (NM_001113188)	-274	NM_001113189	14359	Mm.259021	NM_008053	ENSMUSG00000027680	Fxr1	1110050J02Rik|9530073J07Rik|AI851072|Fxr1h|Fxr1p	fragile X mental retardation gene 1, autosomal homolog	protein-coding
mm_166381.1	chr5	131011293	131011297	+	1	NA	intron (NM_145218, intron 5 of 10)	B4A|SINE|B4	296227	NM_145218	212996	Mm.299204	NM_145218	ENSMUSG00000034040	Wbscr17	AA388321|E330012B09Rik	Williams-Beuren syndrome chromosome region 17 homolog (human)	protein-coding
mm_98506.1	chr11	94952142	94952152	+	1	NA	3' UTR (NM_007742, exon 51 of 51)	3' UTR (NM_007742, exon 51 of 51)	-15446	NM_018792	54388	Mm.30482	NM_018792	ENSMUSG00000038994	Hils1	H1.9|TISP64	histone H1-like protein in spermatids 1	protein-coding
mm_90538.1	chr10	128091125	128091135	+	1	NA	TTS (NM_016774)	TTS (NM_016774)	-1653	NM_054078	116848	Mm.252213	NM_054078	ENSMUSG00000040054	Baz2a	AA415431|C030005G16Rik|C78388|Tip5|Walp3|mKIAA0314	bromodomain adjacent to zinc finger domain, 2A	protein-coding
mm_168968.1	chr12	82789664	82789666	-	1	NA	intron (NM_001310478, intron 2 of 17)	intron (NM_001310478, intron 2 of 17)	149490	NR_046045	74283	Mm.398247	NR_046045	ENSMUSG00000100890	1700085C21Rik	-	RIKEN cDNA 1700085C21 gene	ncRNA
mm_19155.1	chr2	80581464	80581479	-	1	NA	promoter-TSS (NM_001290745)	promoter-TSS (NM_001290745)	-289	NM_016965	50884	Mm.25203	NM_016965	ENSMUSG00000027002	Nckap1	C79304|H19|Hem-2|Hem2|Nap1|mKIAA0587|mh19|p125Nap1	NCK-associated protein 1	protein-coding
mm_16929.1	chr2	13793818	13793879	-	1	NA	promoter-TSS (NM_145838)	promoter-TSS (NM_145838)	-328	NM_145838	241230	Mm.330004	NM_145838	ENSMUSG00000003418	St8sia6	1700007J08Rik|AI314453|AI875066|ST8SiaVI|Siat8f	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 6	protein-coding
mm_149650.1	chr19	18631980	18632008	+	1	NA	promoter-TSS (NM_017375)	promoter-TSS (NM_017375)	-22	NM_145497	225994	Mm.211595	NM_145497	ENSMUSG00000037847	Nmrk1	AA408380|D630020N23Rik|Nrk1	nicotinamide riboside kinase 1	protein-coding
mm_143289.1	chr17	65868107	65868128	-	1	NA	intron (NM_009067, intron 1 of 9)	B1F1|SINE|Alu	16806	NM_001198949	19765	Mm.17009	NM_009067	ENSMUSG00000024096	Ralbp1	RLIP76|Rip1	ralA binding protein 1	protein-coding
mm_79453.1	chr9	56123255	56123265	+	1	NA	intron (NM_011193, intron 6 of 14)	intron (NM_011193, intron 6 of 14)	33284	NM_011193	19200	Mm.2534	NM_011193	ENSMUSG00000032322	Pstpip1	CD2BP1|def-2	proline-serine-threonine phosphatase-interacting protein 1	protein-coding
mm_46050.1	chr5	92083668	92083726	-	1	NA	promoter-TSS (NM_011816)	promoter-TSS (NM_011816)	47	NM_011816	23881	Mm.290530	NM_011816	ENSMUSG00000029405	G3bp2	AA409541|E430034L04Rik|G3BP|mKIAA0660	GTPase activating protein (SH3 domain) binding protein 2	protein-coding
mm_2895.1	chr1	131919010	131919022	+	1	NA	exon (NM_001145804, exon 2 of 7)	exon (NM_001145804, exon 2 of 7)	8558	NM_001145804	98415	Mm.246869	NM_175294	ENSMUSG00000026434	Nucks1	2700010L10Rik|8430423A01Rik|AI647518|C78391|Nucks	nuclear casein kinase and cyclin-dependent kinase substrate 1	protein-coding
mm_53512.1	chr6	135714007	135714023	+	1	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	55102	NR_126088	75024	Mm.399147	NR_126088	ENSMUSG00000107396	4930425L21Rik	4930473P14Rik	RIKEN cDNA 4930425L21 gene	ncRNA
mm_164797.1	chr18	20745400	20745405	+	1	NA	exon (NM_019737, exon 1 of 9)	exon (NM_019737, exon 1 of 9)	1002	NM_019737	56386	Mm.393827	NM_019737	ENSMUSG00000056124	B4galt6	AA536803|AU022389	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 6	protein-coding
mm_133267.1	chr16	77362442	77362459	+	1	NA	intron (NR_015543, intron 2 of 4)	intron (NR_015543, intron 2 of 4)	33122	NR_015543	77994	Mm.394688	NR_015543	ENSMUSG00000090386	Mir99ahg	2810055G20Rik|D730043B02Rik	Mir99a and Mirlet7c-1 host gene (non-protein coding)	ncRNA
mm_4710.1	chr1	180942360	180942368	+	1	NA	promoter-TSS (NM_144794)	promoter-TSS (NM_144794)	-154	NM_144794	208795	Mm.185518	NM_144794	ENSMUSG00000026519	Tmem63a	BC014795|Tmem64a	transmembrane protein 63a	protein-coding
mm_133427.1	chr16	87495984	87496062	+	1	NA	promoter-TSS (NM_009840)	promoter-TSS (NM_009840)	-50	NR_040375	414095	Mm.166361	NR_040375	ENSMUSG00000093606	B130034C11Rik	-	RIKEN cDNA B130034C11 gene	ncRNA
mm_167298.1	chr8	52830564	52830564	-	1	NA	Intergenic	MYSERV16_I-int|LTR|ERVK	-681138	NM_001205054	11593	Mm.334535	NM_001005847	ENSMUSG00000031521	Aga	AW060726	aspartylglucosaminidase	protein-coding
mm_58328.1	chr6	146577431	146577472	-	1	NA	promoter-TSS (NM_026218)	promoter-TSS (NM_026218)	384	NM_138757	71177	Mm.271774	NM_138757	ENSMUSG00000040250	Asun	4933424B01Rik|Spata30	asunder, spermatogenesis regulator	protein-coding
mm_29021.1	chr3	101924469	101924492	-	1	NA	promoter-TSS (NM_001039371)	promoter-TSS (NM_001039371)	-27	NM_001039371	242126	Mm.90204	NM_001039371	ENSMUSG00000033147	Slc22a15	2610034P21Rik|4930477M19|A530052I06Rik|BB219042	solute carrier family 22 (organic anion/cation transporter), member 15	protein-coding
mm_62772.1	chr7	112354560	112354572	+	1	NA	TTS (NM_001193305)	TTS (NM_001193305)	-13742	NM_027587	100504195	Mm.291129	NM_027587	ENSMUSG00000030771	Micalcl	4921517J23Rik	MICAL C-terminal like	protein-coding
mm_9295.1	chr1	171637242	171637268	-	1	NA	intron (NM_001347184, intron 4 of 5)	intron (NM_001347184, intron 4 of 5)	4645	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_38689.1	chr4	145195000	145195044	-	1	NA	promoter-TSS (NM_001276465)	promoter-TSS (NM_001276465)	-17	NM_001276465	230895	Mm.240310	NM_001033190	ENSMUSG00000020220	Vps13d	-	vacuolar protein sorting 13D	protein-coding
mm_124445.1	chr14	118876662	118876665	-	1	NA	non-coding (NR_130725, exon 21 of 21)	non-coding (NR_130725, exon 21 of 21)	21713	NM_001160099	58187	Mm.390755	NM_021386	ENSMUSG00000022132	Cldn10	6720456I16Rik|Cldn10a|Cldn10b|D14Ertd728e	claudin 10	protein-coding
mm_4058.1	chr1	165841670	165841682	+	1	NA	intron (NM_001113391, intron 1 of 7)	intron (NM_001113391, intron 1 of 7)	52995	NM_001113392	12503	Mm.217308	NM_031162	ENSMUSG00000005763	Cd247	4930549J05Rik|A430104F18Rik|AW552088|Cd3|Cd3-eta|Cd3-zeta|Cd3h|Cd3z|Cd3zeta|T3z|Tcrk|Tcrz	CD247 antigen	protein-coding
mm_47369.1	chr5	122949234	122949248	-	1	NA	intron (NM_001003953, intron 6 of 22)	intron (NM_001003953, intron 6 of 22)	39858	NM_001003953	30841	Mm.86406	NM_013910	ENSMUSG00000029475	Kdm2b	Cxxc2|Fbl10|Fbxl10|Jhdm1b|PCCX2	lysine (K)-specific demethylase 2B	protein-coding
mm_110689.1	chr12	69184026	69184051	-	1	NA	promoter-TSS (NM_025589)	promoter-TSS (NM_025589)	29	NM_025589	66483	Mm.379115	NM_025589	ENSMUSG00000049751	Rpl36al	2410038A03Rik|RPL36A	ribosomal protein L36A-like	protein-coding
mm_2512.1	chr1	106230804	106230815	+	1	NA	intron (NM_133821, intron 1 of 16)	RMER19A|LTR|ERVK	58940	NM_133821	98432	Mm.24115	NM_133821	ENSMUSG00000044340	Phlpp1	AI836256|Phlpp|Plekhe1|SCOP|mKIAA0606	PH domain and leucine rich repeat protein phosphatase 1	protein-coding
mm_77327.1	chr8	119426581	119426593	-	1	NA	Intergenic	Intergenic	-10575	NM_027950	71839	Mm.272357	NM_027950	ENSMUSG00000074063	Osgin1	1700012B18Rik|Okl38	oxidative stress induced growth inhibitor 1	protein-coding
mm_37584.1	chr4	126338613	126338616	-	1	NA	Intergenic	Intergenic	-13415	NM_011902	24084	Mm.23895	NM_011902	ENSMUSG00000028845	Tekt2	AU014974|tektin-t	tektin 2	protein-coding
mm_142193.1	chr17	36951587	36951601	-	1	NA	5' UTR (NM_029632, exon 1 of 3)	5' UTR (NM_029632, exon 1 of 3)	198	NM_029632	76497	Mm.46176	NM_029632	ENSMUSG00000036398	Ppp1r11	1500041B02Rik|AV117883|Hcgv|Tcte5|Tctex-5|Tctex5	protein phosphatase 1, regulatory (inhibitor) subunit 11	protein-coding
mm_154667.1	chrX	7878743	7878755	+	1	NA	exon (NM_138606, exon 2 of 6)	exon (NM_138606, exon 2 of 6)	443	NM_138606	18715	Mm.347478	NM_138606	ENSMUSG00000031155	Pim2	DXCch3|Pim-2	proviral integration site 2	protein-coding
mm_67671.1	chr7	88299493	88299506	-	1	NA	exon (NM_009982, exon 4 of 7)	exon (NM_009982, exon 4 of 7)	21414	NM_001311790	13032	Mm.89295	NM_009982	ENSMUSG00000030560	Ctsc	AI047818|CatC|DPP1|DPPI	cathepsin C	protein-coding
mm_114537.1	chr13	73699950	73699963	+	1	NA	5' UTR (NM_027780, exon 1 of 2)	5' UTR (NM_027780, exon 1 of 2)	130	NM_027780	71390	Mm.105251	NM_027780		Slc6a19os	5430425J12Rik	solute carrier family 6 (neurotransmitter transporter), member 19, opposite strand	protein-coding
mm_100839.1	chr11	5707659	5707708	-	1	NA	promoter-TSS (NM_026080)	promoter-TSS (NM_026080)	16	NM_026080	64660	Mm.7328	NM_026080	ENSMUSG00000020477	Mrps24	3110030K20Rik|AI414579|Rpms24	mitochondrial ribosomal protein S24	protein-coding
mm_8080.1	chr1	135585709	135585719	-	1	NA	promoter-TSS (NM_173437)	promoter-TSS (NM_173437)	-359	NM_173437	215690	Mm.34977	NM_173437	ENSMUSG00000009418	Nav1	9530089B19|9930003A20Rik|C230080M11Rik|Pomfil3|Unc53h1|mKIAA1151|steerin-1	neuron navigator 1	protein-coding
mm_3888.1	chr1	161150985	161150988	+	1	NA	exon (NM_028664, exon 2 of 7)	exon (NM_028664, exon 2 of 7)	8274	NM_028664	73844	Mm.38830	NM_028664	ENSMUSG00000044835	Ankrd45	4933409K03Rik	ankyrin repeat domain 45	protein-coding
mm_93386.1	chr10	106007465	106007473	-	1	NA	Intergenic	RLTR17|LTR|ERVK	165990	NM_025602	52713	Mm.339224	NM_025602	ENSMUSG00000019897	Ccdc59	2300004H16Rik|D10Ertd718e	coiled-coil domain containing 59	protein-coding
mm_14134.1	chr2	126035696	126035724	+	1	NA	5' UTR (NM_008008, exon 2 of 4)	5' UTR (NM_008008, exon 2 of 4)	1052	NM_008008	14178	Mm.330557	NM_008008	ENSMUSG00000027208	Fgf7	Kgf	fibroblast growth factor 7	protein-coding
mm_44033.1	chr5	147432014	147432017	+	1	NA	intron (NM_028291, intron 1 of 18)	intron (NM_028291, intron 1 of 18)	1435	NM_028291	72587	Mm.320469	NM_028291	ENSMUSG00000029647	Pan3	2700050F09Rik|A430027N15Rik|AU014670	PAN3 poly(A) specific ribonuclease subunit	protein-coding
mm_13401.1	chr2	103970365	103970374	+	1	NA	promoter-TSS (NM_008505)	promoter-TSS (NM_008505)	82	NM_001142335	16909	Mm.29266	NM_008505	ENSMUSG00000032698	Lmo2	Rbtn-2|Rbtn2|Rhom-2|Ttg2	LIM domain only 2	protein-coding
mm_162494.1	chr1	136247455	136247461	-	1	NA	Intergenic	Intergenic	-13178	NM_028872	67313	Mm.36763	NM_028872	ENSMUSG00000041605	5730559C18Rik	1700034M08Rik|4933426C09Rik|AI586180|D1Mgi54	RIKEN cDNA 5730559C18 gene	protein-coding
mm_24580.1	chr3	93444776	93444782	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	2449	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_157379.1	chrX	37901351	37901365	-	1	NA	exon (NM_023894, exon 2 of 4)	exon (NM_023894, exon 2 of 4)	412	NM_023894	104384	Mm.156958	NM_023894	ENSMUSG00000068048	Rhox9	1600026O01Rik|Gpbox|Psx2	reproductive homeobox 9	protein-coding
mm_93955.1	chr10	127263316	127263345	-	1	NA	promoter-TSS (NM_001039000)	promoter-TSS (NM_001039000)	33	NM_008447	16572	Mm.30355	NM_008447	ENSMUSG00000074657	Kif5a	D10Bwg0738e|Khc|Kif5|Kns|mKIAA4086	kinesin family member 5A	protein-coding
mm_82790.1	chr9	29179087	29179093	-	1	NA	exon (NM_172290, exon 3 of 8)	exon (NM_172290, exon 3 of 8)	784039	NM_172290	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding
mm_113865.1	chr13	48491007	48491011	+	1	NA	exon (NM_026450, exon 5 of 5)	exon (NM_026450, exon 5 of 5)	22401	NM_001164575	67911	Mm.251375	NM_026450	ENSMUSG00000050954	Zfp169	1700025J14Rik|4930429A13Rik|BE688704	zinc finger protein 169	protein-coding
mm_106508.1	chr11	120458039	120458082	-	1	NA	promoter-TSS (NM_025560)	promoter-TSS (NM_025560)	3	NM_025560	66431	Mm.45063	NM_025560	ENSMUSG00000039670	Oxld1	1810049H13Rik	oxidoreductase like domain containing 1	protein-coding
mm_53913.1	chr6	3988947	3988964	-	1	NA	promoter-TSS (NR_138566)	promoter-TSS (NR_138566)	-97	NR_138566	21789	Mm.25612	NM_009364	ENSMUSG00000029664	Tfpi2	AV000670|PP5/TFPI-2	tissue factor pathway inhibitor 2	protein-coding
mm_148237.1	chr18	80554781	80554797	-	1	NA	Intergenic	Intergenic	-10243	NR_028424	100039348	Mm.254722	NR_028424		Gm2176	A430076E10Rik	glucosamine-6-phosphate deaminase 1 pseudogene	pseudo
mm_77836.1	chr9	5298000	5298001	+	1	NA	promoter-TSS (NM_009807)	promoter-TSS (NM_009807)	-517	NM_009807	12362	Mm.1051	NM_009807	ENSMUSG00000025888	Casp1	ICE|Il1bc	caspase 1	protein-coding
mm_144468.1	chr18	23771714	23771738	+	1	NA	intron (NM_001162941, intron 1 of 7)	intron (NM_001162941, intron 1 of 7)	3263	NR_105778	102465185		NR_105778	ENSMUSG00000098607	Mir6360	Gm27296|mmu-mir-6360	microRNA 6360	ncRNA
mm_142182.1	chr17	36272245	36272248	-	1	NA	promoter-TSS (NM_024468)	promoter-TSS (NM_024468)	-242	NM_024468	79263	Mm.40624	NM_024468	ENSMUSG00000045409	Trim39	1100001D15Rik|E130103K13Rik|RBCC-B30.2|Rnf23|mKIAA4179|tfp	tripartite motif-containing 39	protein-coding
mm_80546.1	chr9	81863782	81863842	+	1	NA	promoter-TSS (NM_175213)	promoter-TSS (NM_175213)	68	NM_175213	75033	Mm.335329	NM_175213	ENSMUSG00000043289	Mei4	4930486G11Rik	meiotic double-stranded break formation protein 4	protein-coding
mm_63940.1	chr7	139834149	139834167	+	1	NA	promoter-TSS (NM_177469)	promoter-TSS (NM_177469)	-16	NM_177469	52389	Mm.39863	NM_177469	ENSMUSG00000025475	Adgra1	2900059M17Rik|D7Ertd680e|Gpr123	adhesion G protein-coupled receptor A1	protein-coding
mm_11590.1	chr2	33216091	33216106	+	1	NA	5' UTR (NM_011923, exon 1 of 5)	5' UTR (NM_011923, exon 1 of 5)	137	NM_011923	26360	Mm.208919	NM_011923	ENSMUSG00000004105	Angptl2	AI593246|AW260363|Arp2	angiopoietin-like 2	protein-coding
mm_122099.1	chr14	30914127	30914151	-	1	NA	intron (NM_008407, intron 14 of 20)	intron (NM_008407, intron 14 of 20)	9448	NM_008407	16426	Mm.4517	NM_008407	ENSMUSG00000006522	Itih3	AW108094|ITI-HC3|Intin3|Itih-3	inter-alpha trypsin inhibitor, heavy chain 3	protein-coding
mm_142134.1	chr17	35910001	35910029	-	1	NA	promoter-TSS (NM_028476)	promoter-TSS (NM_028476)	53	NM_001142745	73242	Mm.273155	NM_028476	ENSMUSG00000024426	Atat1	0610011P08Rik|2610008K08Rik|2610110G12Rik|3110080J08Rik|Mec17|TAT	alpha tubulin acetyltransferase 1	protein-coding
mm_132699.1	chr16	43363078	43363129	+	1	NA	intron (NM_181058, intron 2 of 6)	LFSINE_Vert|SINE|tRNA	57093	NR_046026	626693	Mm.447083	NR_046026	ENSMUSG00000085499	Gm15713	OTTMUSG00000025617	predicted gene 15713	ncRNA
mm_120813.1	chr14	75131227	75131241	+	1	NA	promoter-TSS (NM_027581)	promoter-TSS (NM_027581)	111	NM_001247984	18826	Mm.153911	NM_008879	ENSMUSG00000021998	Lcp1	AW536232|D14Ertd310e|LCP-1|Pls2|pp65	lymphocyte cytosolic protein 1	protein-coding
mm_2951.1	chr1	132417410	132417464	+	1	NA	promoter-TSS (NM_172516)	promoter-TSS (NM_172516)	-16	NM_172516	213452	Mm.257120	NM_172516	ENSMUSG00000042046	Dstyk	A930019K20Rik|C430014H23Rik|C820013G01|Ripk5	dual serine/threonine and tyrosine protein kinase	protein-coding
mm_92324.1	chr10	75668050	75668101	-	1	NA	intron (NM_172549, intron 29 of 36)	CpG	-24067	NM_027890	71733	Mm.247956	NM_027890	ENSMUSG00000006342	Susd2	1200011D11Rik	sushi domain containing 2	protein-coding
mm_106032.1	chr11	116077563	116077596	-	1	NA	TTS (NM_016852)	TTS (NM_016852)	382	NM_001009573	70450	Mm.259460	NM_001009573	ENSMUSG00000057948	Unc13d	2610108D09Rik|Jinx|Munc13-4|mFLJ00067	unc-13 homolog D (C. elegans)	protein-coding
mm_62556.1	chr7	102571497	102571505	+	1	NA	Intergenic	Intergenic	-6019	NM_009277	20821	Mm.321227	NM_009277	ENSMUSG00000030966	Trim21	Ro52|Ssa1	tripartite motif-containing 21	protein-coding
mm_34228.1	chr4	141013800	141013820	+	1	NA	exon (NM_008546, exon 3 of 9)	exon (NM_008546, exon 3 of 9)	3173	NM_008546	17150	Mm.7386	NM_008546	ENSMUSG00000060572	Mfap2	AI893631|Magp|Magp1	microfibrillar-associated protein 2	protein-coding
mm_96497.1	chr11	68122671	68122685	+	1	NA	intron (NM_018768, intron 7 of 7)	intron (NM_018768, intron 7 of 7)	-98214	NR_105833	102465219		NR_105833	ENSMUSG00000099174	Mir6406	Gm27981|mmu-mir-6406	microRNA 6406	ncRNA
mm_21585.1	chr2	164237327	164237340	-	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	1008	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_14527.1	chr2	132695925	132695931	+	1	NA	intron (NM_028637, intron 2 of 2)	intron (NM_028637, intron 2 of 2)	5645	NM_028637	73747	Mm.284114	NM_028637	ENSMUSG00000044991	1110034G24Rik	-	RIKEN cDNA 1110034G24 gene	protein-coding
mm_21038.1	chr2	152511707	152511718	-	1	NA	promoter-TSS (NM_001039120)	promoter-TSS (NM_001039120)	24	NM_001039120	654457	Mm.389363	NM_001039120	ENSMUSG00000074680	Defb26	EG654457	defensin beta 26	protein-coding
mm_122729.1	chr14	52316334	52316344	-	1	NA	promoter-TSS (NM_001244916)	promoter-TSS (NM_001244916)	-16	NM_001244916	50524	Mm.39487	NM_015772	ENSMUSG00000049532	Sall2	AI225809|AW559097|Msal-2|Sal-2|mKIAA0360|p150(Sal2)	sal-like 2 (Drosophila)	protein-coding
mm_168583.1	chr11	73469654	73469657	+	1	NA	Intergenic	L1_Mus3|LINE|L1	-15445	NM_147025	259027	Mm.223412	NM_147025	ENSMUSG00000072709	Olfr380	MOR135-1	olfactory receptor 380	protein-coding
mm_151513.1	chr19	58736995	58737027	+	1	NA	exon (NM_018874, exon 9 of 13)	exon (NM_018874, exon 9 of 13)	8124	NM_018874	18946	Mm.10753	NM_018874	ENSMUSG00000042179	Pnliprp1	Plrp1	pancreatic lipase related protein 1	protein-coding
mm_98206.1	chr11	87797429	87797445	+	1	NA	exon (NM_010824, exon 8 of 14)	exon (NM_010824, exon 8 of 14)	3653	NM_010824	17523	Mm.4668	NM_010824	ENSMUSG00000009350	Mpo	mKIAA4033	myeloperoxidase	protein-coding
mm_48430.1	chr5	140621294	140621308	-	1	NA	3' UTR (NM_175274, exon 14 of 14)	3' UTR (NM_175274, exon 14 of 14)	13960	NM_008494	16848	Mm.12834	NM_008494	ENSMUSG00000029570	Lfng	AW061165	LFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	protein-coding
mm_145706.1	chr18	62744570	62744594	+	1	NA	Intergenic	Intergenic	-3195	NM_001168423	100038417	Mm.387557	NM_001168423	ENSMUSG00000073551	Spink13	ENSMUSG00000073551|Gm10534|Spink5l3	serine peptidase inhibitor, Kazal type 13	protein-coding
mm_155081.1	chrX	47912446	47912464	+	1	NA	promoter-TSS (NM_177215)	promoter-TSS (NM_177215)	-1	NM_177215	320634	Mm.210343	NM_177215	ENSMUSG00000001173	Ocrl	9530014D17Rik|BB143339|OCRL1	oculocerebrorenal syndrome of Lowe	protein-coding
mm_115842.1	chr13	21287337	21287349	-	1	NA	3' UTR (NM_010343, exon 5 of 5)	3' UTR (NM_010343, exon 5 of 5)	5343	NM_010343	14780	Mm.1332	NM_010343	ENSMUSG00000004344	Gpx5	AV379049|Arep	glutathione peroxidase 5	protein-coding
mm_58329.1	chr6	146577589	146577592	-	1	NA	promoter-TSS (NM_026218)	promoter-TSS (NM_026218)	245	NM_138757	71177	Mm.271774	NM_138757	ENSMUSG00000040250	Asun	4933424B01Rik|Spata30	asunder, spermatogenesis regulator	protein-coding
mm_34148.1	chr4	139363566	139363575	+	1	NA	intron (NM_001039200, intron 12 of 22)	intron (NM_001039200, intron 12 of 22)	10983	NM_146157	230866	Mm.394288	NM_146157	ENSMUSG00000078517	Emc1	2700016F22Rik	ER membrane protein complex subunit 1	protein-coding
mm_81960.1	chr9	120929241	120929251	+	1	NA	intron (NR_040753, intron 2 of 2)	intron (NR_040753, intron 2 of 2)	1556	NR_040753	78060	Mm.463884	NR_040753	ENSMUSG00000086365	4930593C16Rik	-	RIKEN cDNA 4930593C16 gene	ncRNA
mm_164811.1	chr18	32162992	32162992	+	1	NA	promoter-TSS (NM_011946)	promoter-TSS (NM_011946)	-97	NM_011946	26405	Mm.211762	NM_011946	ENSMUSG00000024383	Map3k2	9630061B06Rik|AI585793|Mekk2|Mekk2b	mitogen-activated protein kinase kinase kinase 2	protein-coding
mm_171145.1	chr3	153360052	153360061	-	1	NA	intron (NM_011372, intron 3 of 4)	ORR1A2|LTR|ERVL-MaLR	-61407	NR_126464	75489	Mm.443252	NR_126464	ENSMUSG00000105023	1700012D16Rik	-	RIKEN cDNA 1700012D16 gene	ncRNA
mm_147173.1	chr18	36726778	36726782	-	1	NA	promoter-TSS (NM_009841)	promoter-TSS (NM_009841)	35	NM_009841	12475	Mm.3460	NM_009841	ENSMUSG00000051439	Cd14	-	CD14 antigen	protein-coding
mm_146459.1	chr18	86601966	86601976	+	1	NA	Intergenic	Intergenic	-109139	NM_001302356	12405	Mm.70775	NM_172633	ENSMUSG00000024647	Cbln2	6330593N19Rik|A730004O05	cerebellin 2 precursor protein	protein-coding
mm_173317.1	chrY	90736333	90736336	+	1	NA	Intergenic	IMPB_01|Satellite|Satellite	18716	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_79995.1	chr9	67035986	67036005	+	1	NA	exon (NM_001164251, exon 3 of 10)	exon (NM_001164251, exon 3 of 10)	7876	NM_001164252	22003	Mm.121878	NM_024427	ENSMUSG00000032366	Tpm1	AA986836|AI854628|TM2|Tm3|Tmpa|Tpm-1|alpha-TM	tropomyosin 1, alpha	protein-coding
mm_145058.1	chr18	40308206	40308229	+	1	NA	intron (NM_026135, intron 1 of 1)	intron (NM_026135, intron 1 of 1)	49856	NM_026135	383348	Mm.76366	NM_026135	ENSMUSG00000051401	Kctd16	4930434H12Rik|Gm1267	potassium channel tetramerisation domain containing 16	protein-coding
mm_170799.1	chr2	175470025	175470031	+	1	NA	promoter-TSS (NM_001242944)	promoter-TSS (NM_001242944)	3	NM_001242944	100503949	Mm.484023	NM_001242944	ENSMUSG00000078896	Zfp965	668009|Gm8923	zinc finger protein 965	protein-coding
mm_129557.1	chr15	79529658	79529661	-	1	NA	3' UTR (NM_001040187, exon 13 of 13)	3' UTR (NM_001040187, exon 13 of 13)	3258	NM_152806	67040	Mm.29644	NM_152806	ENSMUSG00000055065	Ddx17	2610007K22Rik|A430025E01Rik|AI047725|C80929|Gm926|p72	DEAD (Asp-Glu-Ala-Asp) box polypeptide 17	protein-coding
mm_89904.1	chr10	111164823	111164868	+	1	NA	promoter-TSS (NM_001003717)	promoter-TSS (NM_001003717)	43	NM_175489	237542	Mm.220204	NM_175489	ENSMUSG00000020189	Osbpl8	AA536976|AA536995|C730029P18Rik|D330025H14Rik|ORP-8	oxysterol binding protein-like 8	protein-coding
mm_148775.1	chr19	6106405	6106428	+	1	NA	exon (NM_001009546, exon 3 of 18)	exon (NM_001009546, exon 3 of 18)	618	NM_001009546	381204	Mm.359041	NM_001009546	ENSMUSG00000054999	Naaladl1	Gm964|Naaladasel	N-acetylated alpha-linked acidic dipeptidase-like 1	protein-coding
mm_43862.1	chr5	143471116	143471126	+	1	NA	intron (NM_144915, intron 2 of 14)	RSINE1|SINE|B4	6628	NM_144915	231871	Mm.469963	NM_144915	ENSMUSG00000039206	Daglb	E330036I19Rik	diacylglycerol lipase, beta	protein-coding
mm_122442.1	chr14	45285354	45285366	-	1	NA	3' UTR (NM_015774, exon 16 of 16)	3' UTR (NM_015774, exon 16 of 16)	33212	NM_015774	50527	Mm.387108	NM_015774	ENSMUSG00000021831	Ero1l	ERO1-L|Ero1a	ERO1-like (S. cerevisiae)	protein-coding
mm_16158.1	chr2	172393949	172393964	+	1	NA	5' UTR (NM_001276423, exon 1 of 6)	5' UTR (NM_001276423, exon 1 of 6)	162	NM_001276423	320664	Mm.210195	NM_001033538	ENSMUSG00000074570	Cass4	F730031O20Rik	Cas scaffolding protein family member 4	protein-coding
mm_149063.1	chr19	8840520	8840549	+	1	NA	promoter-TSS (NM_001290823)	promoter-TSS (NM_001290823)	31	NM_001290823	14705	Mm.345134	NM_008144	ENSMUSG00000071657	Bscl2	2900097C17Rik|AI046355|Gng3lg	Berardinelli-Seip congenital lipodystrophy 2 (seipin)	protein-coding
mm_130371.1	chr15	97820987	97821022	-	1	NA	intron (NM_001204275, intron 1 of 24)	URR1B|DNA|hAT-Charlie	-6141	NM_001204281	56233	Mm.384027	NM_019572	ENSMUSG00000022475	Hdac7	5830434K02Rik|HD7|HD7a|Hdac7a|mFLJ00062	histone deacetylase 7	protein-coding
mm_91318.1	chr10	24959478	24959480	-	1	NA	Intergenic	MLT1B|LTR|ERVL-MaLR	-32009	NM_007482	11846	Mm.154144	NM_007482	ENSMUSG00000019987	Arg1	AI|AI256583|Arg-1|PGIF	arginase, liver	protein-coding
mm_10066.1	chr1	193510125	193510133	-	1	NA	Intergenic	Intergenic	-2599	NR_029592	387201		NR_029592	ENSMUSG00000065533	Mir205	Mirn205|mir-205|mmu-mir-205	microRNA 205	ncRNA
mm_169066.1	chr1	32685857	32685869	-	1	NA	Intergenic	RLTR9D|LTR|ERVK	-138570	NM_001164286	408191	Mm.479439	NM_001164286	ENSMUSG00000091318	Gm5415	EG408191|Senp14	predicted gene 5415	protein-coding
mm_159107.1	chr2	38784491	38784491	-	1	NA	promoter-TSS (NM_001159549)	promoter-TSS (NM_001159549)	24	NM_001159548	14536	Mm.439703	NM_010264	ENSMUSG00000063972	Nr6a1	1700113M01Rik|Gcnf|NCNF|RTR	nuclear receptor subfamily 6, group A, member 1	protein-coding
mm_144522.1	chr18	25016048	25016084	+	1	NA	intron (NM_001289654, intron 10 of 24)	intron (NM_001289654, intron 10 of 24)	149899	NM_001142697	66648	Mm.263189	NM_001004361	ENSMUSG00000024269	Tpgs2	5730437P09Rik|5730494M16Rik|AI666318|Pgs2	tubulin polyglutamylase complex subunit 2	protein-coding
mm_71238.1	chr8	40908406	40908420	+	1	NA	exon (NM_007514, exon 7 of 12)	exon (NM_007514, exon 7 of 12)	-17820	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_150203.1	chr19	32765103	32765107	+	1	NA	intron (NM_008960, intron 1 of 8)	intron (NM_008960, intron 1 of 8)	7528	NM_008960	19211	Mm.245395	NM_008960	ENSMUSG00000013663	Pten	2310035O07Rik|A130070J02Rik|AI463227|B430203M17Rik|MMAC1|TEP1	phosphatase and tensin homolog	protein-coding
mm_42819.1	chr5	122061438	122061448	+	1	NA	Intergenic	Intergenic	-11592	NM_001312908	13048	Mm.156172	NM_007804	ENSMUSG00000042589	Cux2	1700051K22Rik|Cutl2|Cux-2|ENSMUSG00000072641	cut-like homeobox 2	protein-coding
mm_14034.1	chr2	122152969	122153001	+	1	NA	TTS (NM_009735)	TTS (NM_009735)	5298	NM_009735	12010	Mm.163	NM_009735	ENSMUSG00000060802	B2m	Ly-m11|beta2-m|beta2m	beta-2 microglobulin	protein-coding
mm_28151.1	chr3	87744268	87744269	-	1	NA	intron (NM_028971, intron 5 of 14)	intron (NM_028971, intron 5 of 14)	4355	NM_028971	74485	Mm.474494	NM_028971	ENSMUSG00000023084	Lrrc71	4933430H15Rik	leucine rich repeat containing 71	protein-coding
mm_155562.1	chrX	75514303	75514316	+	1	NA	promoter-TSS (NM_011692)	promoter-TSS (NM_011692)	12	NM_011692	22327	Mm.8294	NM_011692	ENSMUSG00000031197	Vbp1	VBP-1	von Hippel-Lindau binding protein 1	protein-coding
mm_59391.1	chr7	26764390	26764397	+	1	NA	intron (NM_007814, intron 6 of 8)	intron (NM_007814, intron 6 of 8)	7251	NM_007814	13090	Mm.14098	NM_007814	ENSMUSG00000066704	Cyp2b19	CYPIIB19	cytochrome P450, family 2, subfamily b, polypeptide 19	protein-coding
mm_28340.1	chr3	89393295	89393336	-	1	NA	promoter-TSS (NM_009565)	promoter-TSS (NM_009565)	-112	NM_009565	22724	Mm.262184	NM_009565	ENSMUSG00000028042	Zbtb7b	Thpok|Zfp67|c-Krox	zinc finger and BTB domain containing 7B	protein-coding
mm_66461.1	chr7	44901284	44901305	-	1	NA	TTS (NM_027376)	TTS (NM_027376)	5215	NM_027376	70300	Mm.276298	NM_027376	ENSMUSG00000011658	Fuz	2600013E07Rik|b2b1273Clo	fuzzy planar cell polarity protein	protein-coding
mm_168656.1	chr11	8884163	8884182	+	1	NA	Intergenic	Intergenic	127019	NM_001303610	15574	Mm.42201	NM_008316	ENSMUSG00000020413	Hus1	-	HUS1 checkpoint clamp component	protein-coding
mm_3836.1	chr1	160044056	160044084	+	1	NA	promoter-TSS (NR_028111)	promoter-TSS (NR_028111)	-310	NR_028111	67647	Mm.171518	NM_001024470	ENSMUSG00000090394	4930523C07Rik	-	RIKEN cDNA 4930523C07 gene	protein-coding
mm_153291.1	chr19	37353621	37353654	-	1	NA	Intergenic	Intergenic	-22766	NM_010615	16551	Mm.42203	NM_010615	ENSMUSG00000012443	Kif11	Eg5|Kif8|Kifl1|Knsl1	kinesin family member 11	protein-coding
mm_77890.1	chr9	7347405	7347410	+	1	NA	promoter-TSS (NM_008605)	promoter-TSS (NM_008605)	33	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_54043.1	chr6	13654131	13654157	-	1	NA	intron (NM_175312, intron 2 of 4)	MLT2B4|LTR|ERVL	23822	NM_175312	101148	Mm.354863	NM_175312	ENSMUSG00000042742	Bmt2	AI666701|B630005N14Rik	base methyltransferase of 25S rRNA 2	protein-coding
mm_57126.1	chr6	122600379	122600382	-	1	NA	intron (NM_001134391, intron 1 of 7)	MRLTR33|LTR|ERVK	2064	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_28711.1	chr3	95652395	95652409	-	1	NA	Intergenic	Intergenic	-6319	NM_008562	17210	Mm.1639	NM_008562	ENSMUSG00000038612	Mcl1	AW556805|Mcl-1	myeloid cell leukemia sequence 1	protein-coding
mm_54267.1	chr6	28696565	28696565	-	1	NA	intron (NM_019776, intron 12 of 23)	intron (NM_019776, intron 12 of 23)	135182	NM_138682	192198	Mm.443660	NM_138682	ENSMUSG00000049939	Lrrc4	MBAG1|NGL-2|NGL2|NLG-2|Nag14	leucine rich repeat containing 4	protein-coding
mm_49485.1	chr6	29536029	29536064	+	1	NA	exon (NM_001252382, exon 7 of 9)	exon (NM_001252382, exon 7 of 9)	6764	NM_001252382	27056	Mm.6479	NM_012057	ENSMUSG00000029771	Irf5	AW491843|mirf5	interferon regulatory factor 5	protein-coding
mm_151554.1	chr19	59458940	59458980	+	1	NA	promoter-TSS (NR_002863)	promoter-TSS (NR_002863)	270	NM_010132	13797	Mm.245394	NM_010132	ENSMUSG00000043969	Emx2	Pdo	empty spiracles homeobox 2	protein-coding
mm_65281.1	chr7	24399859	24399919	-	1	NA	5' UTR (NM_028047, exon 1 of 14)	5' UTR (NM_028047, exon 1 of 14)	261	NM_028047	71997	Mm.150977	NM_028047	ENSMUSG00000002210	Smg9	1500002O20Rik|AI429693|N28092	smg-9 homolog, nonsense mediated mRNA decay factor (C. elegans)	protein-coding
mm_88974.1	chr10	81453220	81453226	+	1	NA	Intergenic	Intergenic	19908	NM_001311127	319586	Mm.152689	NM_176954	ENSMUSG00000034818	Celf5	4930565A21Rik|Brunol5	CUGBP, Elav-like family member 5	protein-coding
mm_53074.1	chr6	124934304	124934333	+	1	NA	exon (NM_001170341, exon 6 of 9)	exon (NM_001170341, exon 6 of 9)	2930	NM_001170341	30853	Mm.29737	NM_145385	ENSMUSG00000030120	Mlf2	AI256856|AU018944|C77284	myeloid leukemia factor 2	protein-coding
mm_78335.1	chr9	25255256	25255280	+	1	NA	intron (NM_001205367, intron 1 of 12)	Lx9|LINE|L1	2829	NM_001205367	235072	Mm.270259	NM_009859	ENSMUSG00000001833	Sept7	Cdc10|E430034N22	septin 7	protein-coding
mm_70700.1	chr8	15034160	15034166	+	1	NA	TTS (NM_029116)	TTS (NM_029116)	11915	NR_037972	434285	Mm.334425	NM_001007591	ENSMUSG00000049008	BB014433	-	expressed sequence BB014433	ncRNA
mm_35655.1	chr4	43556266	43556289	-	1	NA	intron (NM_011602, intron 3 of 56)	intron (NM_011602, intron 3 of 56)	6306	NM_011602	21894	Mm.208601	NM_011602	ENSMUSG00000028465	Tln1	Tln	talin 1	protein-coding
mm_123221.1	chr14	59557073	59557079	-	1	NA	Intergenic	Intergenic	40883	NM_001168537	71891	Mm.439850	NM_027986	ENSMUSG00000021982	Cdadc1	2310010M10Rik|AI449174|AI463398|BB130816|NYD-SP15	cytidine and dCMP deaminase domain containing 1	protein-coding
mm_117256.1	chr13	64367883	64367951	-	1	NA	exon (NM_009984, exon 4 of 8)	exon (NM_009984, exon 4 of 8)	2603	NM_009984	13039	Mm.930	NM_009984	ENSMUSG00000021477	Ctsl	1190035F06Rik|CatL|Ctsl1|MEP|fs|nkt	cathepsin L	protein-coding
mm_38705.1	chr4	145215407	145215440	-	1	NA	3' UTR (NM_011610, exon 10 of 10)	3' UTR (NM_011610, exon 10 of 10)	-20418	NM_001276465	230895	Mm.240310	NM_001033190	ENSMUSG00000020220	Vps13d	-	vacuolar protein sorting 13D	protein-coding
mm_99480.1	chr11	102604756	102604792	+	1	NA	exon (NM_020510, exon 1 of 1)	exon (NM_020510, exon 1 of 1)	343	NM_020510	57265	Mm.36416	NM_020510	ENSMUSG00000050288	Fzd2	AL033370|AW456835|Fz10|Fzd10|Mfz10|Mfz10a	frizzled class receptor 2	protein-coding
mm_161289.1	chr14	26206542	26206542	-	1	NA	promoter-TSS (NM_001270496)	promoter-TSS (NM_001270496)	-12	NM_001270496	100039257	Mm.33344	NM_001270495	ENSMUSG00000021867	Tmem254b	ENSMUSG00000021867|Gm9746	transmembrane protein 254b	protein-coding
mm_25344.1	chr3	106722133	106722139	+	1	NA	intron (NM_028081, intron 1 of 2)	CpG	454	NM_001286685	321000	Mm.259638	NM_028081	ENSMUSG00000056260	Lrif1	2010012G17Rik|4933421E11Rik|AI450568	ligand dependent nuclear receptor interacting factor 1	protein-coding
mm_165466.1	chr2	163547254	163547289	+	1	NA	5' UTR (NM_008261, exon 1 of 10)	5' UTR (NM_008261, exon 1 of 10)	116	NM_008261	15378	Mm.202383	NM_008261	ENSMUSG00000017950	Hnf4a	HNF-4|Hnf4|Hnf4alpha|MODY1|Nr2a1|TCF-14|Tcf14	hepatic nuclear factor 4, alpha	protein-coding
mm_59849.1	chr7	29859967	29860053	+	1	NA	promoter-TSS (NM_172740)	promoter-TSS (NM_172740)	31	NM_172740	233058	Mm.297657	NM_172740	ENSMUSG00000058402	Zfp420	B230119D13|B230312I18Rik|mszf59-1|mszf70	zinc finger protein 420	protein-coding
mm_111444.1	chr12	98249347	98249351	-	1	NA	intron (NM_008079, intron 5 of 16)	intron (NM_008079, intron 5 of 16)	10110	NM_008079	14420	Mm.5120	NM_008079	ENSMUSG00000021003	Galc	2310068B06Rik|A930008M05Rik|AW212969|AW413532|Gacy|twi|twitcher	galactosylceramidase	protein-coding
mm_123073.1	chr14	55721262	55721275	-	1	NA	intron (NM_019519, intron 2 of 15)	intron (NM_019519, intron 2 of 15)	908	NM_019519	56187	Mm.87216	NM_019519	ENSMUSG00000040472	Rabggta	gm	Rab geranylgeranyl transferase, a subunit	protein-coding
mm_119654.1	chr14	52110911	52110932	+	1	NA	promoter-TSS (NM_001168515)	promoter-TSS (NM_001168515)	18	NM_023879	77945	Mm.21662	NM_023879	ENSMUSG00000057132	Rpgrip1	0610005A07Rik|4930401L23Rik|4930505G06Rik|A930002K18Rik|AA415034|nmf247	retinitis pigmentosa GTPase regulator interacting protein 1	protein-coding
mm_6353.1	chr1	71652177	71652179	-	1	NA	intron (NM_001276409, intron 1 of 44)	B1F|SINE|Alu	1056	NM_010233	14268	Mm.193099	NM_010233	ENSMUSG00000026193	Fn1	E330027I09|Fn|Fn-1	fibronectin 1	protein-coding
mm_105198.1	chr11	102097322	102097326	-	1	NA	Intergenic	Intergenic	3976	NM_008918	19064	Mm.1269	NM_008918	ENSMUSG00000017316	Ppy	AV061413|IGSPP|PP	pancreatic polypeptide	protein-coding
mm_101192.1	chr11	18327257	18327259	-	1	NA	Intergenic	Intergenic	231272	NR_131129	327872		NR_131129	ENSMUSG00000085453	Gm12018	OTTMUSG00000005202	predicted gene 12018	ncRNA
mm_83218.1	chr9	42124269	42124275	-	1	NA	promoter-TSS (NM_011436)	promoter-TSS (NM_011436)	17	NM_011436	20660	Mm.121920	NM_011436	ENSMUSG00000049313	Sorl1	2900010L19Rik|AI596264|AW261561|LR11|SorLA|gp250|mSorLA	sortilin-related receptor, LDLR class A repeats-containing	protein-coding
mm_46484.1	chr5	105131997	105132015	-	1	NA	intron (NM_008620, intron 3 of 10)	L1MA6|LINE|L1	7546	NM_008620	17472	Mm.440525	NM_008620	ENSMUSG00000079363	Gbp4	AW228052|Mag-2|Mpa-2|Mpa2	guanylate binding protein 4	protein-coding
mm_26688.1	chr3	156643704	156643707	+	1	NA	intron (NM_177274, intron 1 of 6)	intron (NM_177274, intron 1 of 6)	81911	NM_001039094	320840	Mm.317293	NM_177274	ENSMUSG00000040037	Negr1	5330422G01Rik|KILON|Ntra	neuronal growth regulator 1	protein-coding
mm_162275.1	chr1	12992329	12992356	-	1	NA	Intergenic	CpG	-1207	NM_172841	240726	Mm.24481	NM_172841	ENSMUSG00000025938	Slco5a1	4732454B15|A630033C23Rik|AA407151	solute carrier organic anion transporter family, member 5A1	protein-coding
mm_71994.1	chr8	70617913	70617970	+	1	NA	exon (NM_153074, exon 2 of 3)	exon (NM_153074, exon 2 of 3)	1097	NM_153074	211228	Mm.132939	NM_153074	ENSMUSG00000049988	Lrrc25	Mapa	leucine rich repeat containing 25	protein-coding
mm_95298.1	chr11	46060904	46060912	+	1	NA	intron (NM_001291891, intron 1 of 22)	intron (NM_001291891, intron 1 of 22)	4924	NM_001291891	11492	Mm.89940	NM_009616	ENSMUSG00000011256	Adam19	AL024287|MADDAM|MTLNB|Mltnb	a disintegrin and metallopeptidase domain 19 (meltrin beta)	protein-coding
mm_128682.1	chr15	60824885	60824895	-	1	NA	5' UTR (NM_001162926, exon 1 of 2)	5' UTR (NM_001162926, exon 1 of 2)	190	NM_001162926	399603	Mm.411968	NM_207269	ENSMUSG00000072568	Fam84b	BF642811|D330050I23Rik	family with sequence similarity 84, member B	protein-coding
mm_128293.1	chr15	37233293	37233332	-	1	NA	5' UTR (NM_026496, exon 1 of 16)	5' UTR (NM_026496, exon 1 of 16)	276	NM_026496	252973	Mm.244612	NM_026496	ENSMUSG00000022286	Grhl2	0610015A08Rik|BOM|Tcfcp2l3|clft3	grainyhead-like 2 (Drosophila)	protein-coding
mm_19387.1	chr2	91256034	91256047	-	1	NA	promoter-TSS (NM_030880)	promoter-TSS (NM_030880)	-125	NM_001289677	80708	Mm.236650	NM_028733	ENSMUSG00000027257	Pacsin3	4921507A02Rik|6330413E15Rik|AW413130	protein kinase C and casein kinase substrate in neurons 3	protein-coding
mm_27869.1	chr3	79159904	79159915	-	1	NA	Intergenic	Intergenic	-14034	NM_001099624	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_58755.1	chr7	13398116	13398127	+	1	NA	promoter-TSS (NM_013877)	promoter-TSS (NM_013877)	-34	NM_013877	29865	Mm.103669	NM_013877	ENSMUSG00000005649	Cabp5	-	calcium binding protein 5	protein-coding
mm_48757.1	chr5	148329997	148330019	-	1	NA	3' UTR (NM_007513, exon 13 of 13)	3' UTR (NM_007513, exon 13 of 13)	62807	NM_001301424	11987	Mm.275489	NM_007513	ENSMUSG00000041313	Slc7a1	4831426K01Rik|AI447493|Atrc-1|Atrc1|Cat1|Rec-1|Rev-1|mCAT-1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 1	protein-coding
mm_110939.1	chr12	76597401	76597412	-	1	NA	intron (NM_013675, intron 32 of 35)	intron (NM_013675, intron 32 of 35)	-49481	NR_046044	100504549	Mm.440349	NR_046044		AI463170	-	expressed sequence AI463170	ncRNA
mm_169951.1	chr16	78350831	78350837	+	1	NA	intron (NM_009988, intron 7 of 7)	L1Md_T|LINE|L1	25923	NR_002700	654432	Mm.458574	NR_002700	ENSMUSG00000044645	Gm7334	EG654432	B-cell translocation gene 3 pseudogene	pseudo
mm_15661.1	chr2	163314494	163314498	+	1	NA	exon (NM_001098799, exon 4 of 9)	exon (NM_001098799, exon 4 of 9)	83477	NM_021566	59091	Mm.34459	NM_021566	ENSMUSG00000017817	Jph2	1110002E14Rik|JP-2|Jp2	junctophilin 2	protein-coding
mm_109207.1	chr12	108676294	108676296	+	1	NA	intron (NM_001163394, intron 7 of 13)	intron (NM_001163394, intron 7 of 13)	17675	NR_029771	723909		NR_029771	ENSMUSG00000065436	Mir342	Mirn342|mmu-mir-342	microRNA 342	ncRNA
mm_70779.1	chr8	22227323	22227357	+	1	NA	promoter-TSS (NM_001293688)	promoter-TSS (NM_001293688)	37	NM_001293688	56229	Mm.32067	NM_019576	ENSMUSG00000031480	Thsd1	4833423O18Rik|Tmtsp	thrombospondin, type I, domain 1	protein-coding
mm_83299.1	chr9	43239947	43239955	-	1	NA	promoter-TSS (NM_178644)	promoter-TSS (NM_178644)	-135	NM_178644	102644	Mm.246479	NM_178644	ENSMUSG00000032014	Oaf	AL024221|D130038B21Rik|D9Ucla1	out at first homolog	protein-coding
mm_98528.1	chr11	94991375	94991388	+	1	NA	5' UTR (NM_172261, exon 1 of 10)	5' UTR (NM_172261, exon 1 of 10)	169	NM_172261	217124	Mm.229087	NM_172261	ENSMUSG00000038976	Ppp1r9b	SPL|Spn	protein phosphatase 1, regulatory subunit 9B	protein-coding
mm_145338.1	chr18	56432178	56432194	+	1	NA	promoter-TSS (NM_026240)	promoter-TSS (NM_026240)	54	NM_026240	107022	Mm.24356	NM_026240	ENSMUSG00000001700	Gramd3	9030613F08Rik|9130427A09Rik|AW061306|NS3TP2	GRAM domain containing 3	protein-coding
mm_44848.1	chr5	34196463	34196476	-	1	NA	intron (NM_001015039, intron 12 of 12)	intron (NM_001015039, intron 12 of 12)	-8759	NM_010753	17122	Mm.259260	NM_010753	ENSMUSG00000037235	Mxd4	2810410A03Rik|Mad4|bHLHc12	Max dimerization protein 4	protein-coding
mm_91490.1	chr10	37135669	37135676	-	1	NA	3' UTR (NM_008538, exon 2 of 2)	3' UTR (NM_008538, exon 2 of 2)	3254	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_157828.1	chrX	74244029	74244037	-	1	NA	intron (NM_010227, intron 1 of 45)	intron (NM_010227, intron 1 of 45)	2501	NM_010227	192176	Mm.295533	NM_010227	ENSMUSG00000031328	Flna	ABP-280|Dilp2|F730004A14Rik|Fln1|GENA 379|filamin-1	filamin, alpha	protein-coding
mm_24212.1	chr3	88626512	88626539	+	1	NA	intron (NM_001198912, intron 1 of 21)	intron (NM_001198912, intron 1 of 21)	5131	NM_001198912	16800	Mm.239329	NM_008487	ENSMUSG00000028059	Arhgef2	AA408978|GEF|GEF-H1|GEFH1|LFP40|Lbcl1|Lfc|P40|mKIAA0651	rho/rac guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_84073.1	chr9	58201706	58201725	-	1	NA	promoter-TSS (NM_001161540)	promoter-TSS (NM_001161540)	0	NM_001161535	320563	Mm.186499	NM_177193	ENSMUSG00000051243	Islr2	B930052A04Rik|Linx|Mbu-3|mKIAA1465	immunoglobulin superfamily containing leucine-rich repeat 2	protein-coding
mm_37608.1	chr4	126753667	126753680	-	1	NA	promoter-TSS (NM_001035526)	promoter-TSS (NM_001035526)	-97	NM_133886	100317	Mm.206206	NM_133886	ENSMUSG00000028830	AU040320	A730047D20Rik|AAVR|Kiaa0319l	expressed sequence AU040320	protein-coding
mm_136034.1	chr16	77421591	77421606	-	1	NA	intron (NR_015543, intron 2 of 4)	intron (NR_015543, intron 2 of 4)	92270	NR_015543	77994	Mm.394688	NR_015543	ENSMUSG00000090386	Mir99ahg	2810055G20Rik|D730043B02Rik	Mir99a and Mirlet7c-1 host gene (non-protein coding)	ncRNA
mm_97578.1	chr11	78940946	78940977	+	1	NA	intron (NM_001313921, intron 10 of 25)	RSINE1|SINE|B4	15670	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_96328.1	chr11	64800741	64800757	+	1	NA	Intergenic	Intergenic	-178286	NM_023479	68626	Mm.157711	NM_023479	ENSMUSG00000020549	Elac2	1110017O07Rik|D11Wsu80e|Hpc2	elaC ribonuclease Z 2	protein-coding
mm_38284.1	chr4	136890284	136890294	-	1	NA	exon (NM_007574, exon 3 of 3)	exon (NM_007574, exon 3 of 3)	2625	NM_007574	12262	Mm.439732	NM_007574	ENSMUSG00000036896	C1qc	AI385742|C1qg|Ciqc	complement component 1, q subcomponent, C chain	protein-coding
mm_166230.1	chr5	66082305	66082311	-	1	NA	intron (NM_178446, intron 2 of 6)	intron (NM_178446, intron 2 of 6)	15871	NM_139065	245945	Mm.36863	NM_139065	ENSMUSG00000070780	Rbm47	9530077J19Rik	RNA binding motif protein 47	protein-coding
mm_57875.1	chr6	130337509	130337525	-	1	NA	5' UTR (NM_010648, exon 1 of 7)	5' UTR (NM_010648, exon 1 of 7)	109	NM_001289605	16634	Mm.425338	NM_010648	ENSMUSG00000067591	Klra3	5E6|Ly49c|NK-2.1|Nk-2|Nk2|Nk2.1	killer cell lectin-like receptor, subfamily A, member 3	protein-coding
mm_72771.1	chr8	85840972	85841028	+	1	NA	promoter-TSS (NM_199446)	promoter-TSS (NM_199446)	-2	NM_199446	102093	Mm.237296	NM_199446	ENSMUSG00000036879	Phkb	AI463271	phosphorylase kinase beta	protein-coding
mm_144991.1	chr18	38296725	38296734	+	1	NA	promoter-TSS (NM_020012)	promoter-TSS (NM_020012)	-76	NM_001164621	56736	Mm.228903	NM_020012	ENSMUSG00000060450	Rnf14	2310075C09Rik|2610005D23Rik|AA986456|AU041447|D18Ertd188e|D7Bwg0165e|Triad2	ring finger protein 14	protein-coding
mm_99906.1	chr11	109736644	109736645	+	1	NA	Intergenic	MLT1D|LTR|ERVL-MaLR	-14388	NM_153782	208659	Mm.208662	NM_153782	ENSMUSG00000020614	Fam20a	AI606893	family with sequence similarity 20, member A	protein-coding
mm_96997.1	chr11	70702364	70702376	+	1	NA	intron (NM_153103, intron 1 of 22)	intron (NM_153103, intron 1 of 22)	1822	NM_153103	16562	Mm.99996	NM_153103	ENSMUSG00000020821	Kif1c	B430105J22Rik|D11Bwg1349e|Ltxs1|Orch3	kinesin family member 1C	protein-coding
mm_83999.1	chr9	57468981	57469014	-	1	NA	promoter-TSS (NM_020270)	promoter-TSS (NM_020270)	-937	NM_001301635	56807	Mm.102278	NM_020270	ENSMUSG00000040722	Scamp5	Sc5	secretory carrier membrane protein 5	protein-coding
mm_49241.1	chr6	17307041	17307085	+	1	NA	promoter-TSS (NM_001243064)	promoter-TSS (NM_001243064)	-577	NM_001243064	12389	Mm.28278	NM_007616	ENSMUSG00000007655	Cav1	Cav|Cav-1	caveolin 1, caveolae protein	protein-coding
mm_11261.1	chr2	29965670	29965688	+	1	NA	5' UTR (NM_001177668, exon 1 of 56)	5' UTR (NM_001177668, exon 1 of 56)	119	NM_001309460	20740	Mm.204969	NM_001076554	ENSMUSG00000057738	Sptan1	2610027H02Rik|Spna-2|Spna2	spectrin alpha, non-erythrocytic 1	protein-coding
mm_16263.1	chr2	173522589	173522618	+	1	NA	promoter-TSS (NM_028158)	promoter-TSS (NM_028158)	11	NM_028158	72221	Mm.46132	NM_028158	ENSMUSG00000027518	1700021F07Rik	-	RIKEN cDNA 1700021F07 gene	protein-coding
mm_16822.1	chr2	11473965	11473980	-	1	NA	3' UTR (NM_001177754, exon 16 of 16)	3' UTR (NM_001177754, exon 16 of 16)	28118	NM_001177754	170768	Mm.19669	NM_133232	ENSMUSG00000026773	Pfkfb3	E330010H22Rik|iPFK-2|uPFK-2	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	protein-coding
mm_43046.1	chr5	124076002	124076009	+	1	NA	intron (NM_019875, intron 9 of 11)	intron (NM_019875, intron 9 of 11)	19793	NM_019875	56325	Mm.254839	NM_019875	ENSMUSG00000029408	Abcb9	TAPL|mKIAA1520	ATP-binding cassette, sub-family B (MDR/TAP), member 9	protein-coding
mm_77240.1	chr8	115705218	115705235	-	1	NA	3' UTR (NM_001025577, exon 1 of 1)	3' UTR (NM_001025577, exon 1 of 1)	1668	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_139513.1	chr17	56584823	56584827	+	1	NA	promoter-TSS (NM_001163300)	promoter-TSS (NM_001163300)	-157	NM_001163300	224903	Mm.255066	NM_001163300	ENSMUSG00000071054	Safb	3110021E02Rik|5330423C17Rik|AU018122|D18386|E130307D12|HAP|HET|SAF-B1|SAFB1	scaffold attachment factor B	protein-coding
mm_132741.1	chr16	44123567	44123575	+	1	NA	intron (NM_007508, intron 1 of 14)	intron (NM_007508, intron 1 of 14)	15448	NM_007508	11964	Mm.217787	NM_007508	ENSMUSG00000052459	Atp6v1a	AI647066|Atp6a1|Atp6a2|Atp6v1a1|VA68|VPP2	ATPase, H+ transporting, lysosomal V1 subunit A	protein-coding
mm_159872.1	chr5	146585223	146585223	-	1	NA	promoter-TSS (NM_008151)	promoter-TSS (NM_008151)	16	NM_001010941	14738	Mm.153539	NM_008151	ENSMUSG00000041468	Gpr12	Gpcr01|Gpcr12|Gpcr20|Gpcr21	G-protein coupled receptor 12	protein-coding
mm_43027.1	chr5	123914987	123914992	+	1	NA	intron (NM_026603, intron 2 of 7)	intron (NM_026603, intron 2 of 7)	7714	NM_026603	68184	Mm.28549	NM_026603	ENSMUSG00000023106	Denr	1500003K04Rik	density-regulated protein	protein-coding
mm_57762.1	chr6	129233954	129233960	-	1	NA	intron (NR_040265, intron 1 of 2)	intron (NR_040265, intron 1 of 2)	4088	NR_040265	76432	Mm.261738	NR_040265	ENSMUSG00000097354	2310001H17Rik	AI646108	RIKEN cDNA 2310001H17 gene	ncRNA
mm_147417.1	chr18	46161744	46161752	-	1	NA	Intergenic	BGLII_C|LTR|ERVK	37070	NM_001170855	28105	Mm.277382	NM_178872	ENSMUSG00000033949	Trim36	D18Wsu100e|haprin	tripartite motif-containing 36	protein-coding
mm_107924.1	chr12	71074961	71074996	+	1	NA	exon (NM_001081195, exon 20 of 24)	exon (NM_001081195, exon 20 of 24)	-36450	NM_029227	75266	Mm.402075	NM_029227	ENSMUSG00000021078	Tomm20l	4930553D19Rik	translocase of outer mitochondrial membrane 20 homolog (yeast)-like	protein-coding
mm_55523.1	chr6	70435504	70435508	-	1	NA	Intergenic	Intergenic	356669	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_44274.1	chr5	5694500	5694539	-	1	NA	promoter-TSS (NM_001103156)	promoter-TSS (NM_001103156)	49	NM_028734	74051	Mm.274956	NM_028734	ENSMUSG00000015653	Steap2	4921538B17Rik|AI930049|AW045895|IPCA-1|IPCA1|PCANAP1|STAMP1|STMP	six transmembrane epithelial antigen of prostate 2	protein-coding
mm_65065.1	chr7	18910353	18910376	-	1	NA	promoter-TSS (NM_001033314)	promoter-TSS (NM_001033314)	40	NM_001033314	232933	Mm.333624	NM_001033314	ENSMUSG00000074358	Ccdc61	C530028I08Rik|Gm159	coiled-coil domain containing 61	protein-coding
mm_136058.1	chr16	79091079	79091107	-	1	NA	promoter-TSS (NM_178855)	promoter-TSS (NM_178855)	4	NM_008941	19146	Mm.5184	NM_008941	ENSMUSG00000022857	Tmprss15	Entk|Prss7	transmembrane protease, serine 15	protein-coding
mm_58199.1	chr6	143162359	143162359	-	1	NA	Intergenic	Intergenic	-4871	NM_029250	75320	Mm.272548	NM_029250	ENSMUSG00000030275	Etnk1	1110061E11Rik|4930555L11Rik|AI195356|AI841245|C80956|D6Ertd3e|EKI1	ethanolamine kinase 1	protein-coding
mm_147620.1	chr18	57552369	57552415	-	1	NA	promoter-TSS (NR_015494)	promoter-TSS (NR_015494)	3	NR_027944	75084	Mm.243841	NR_015494	ENSMUSG00000086607	4930511M06Rik	-	RIKEN cDNA 4930511M06 gene	ncRNA
mm_164972.1	chr19	7483153	7483164	-	1	NA	5' UTR (NM_053076, exon 1 of 7)	5' UTR (NM_053076, exon 1 of 7)	133	NM_001271486	20168	Mm.246990	NM_053076	ENSMUSG00000024758	Rtn3	RTN3-A1	reticulon 3	protein-coding
mm_95916.1	chr11	58220517	58220528	+	1	NA	exon (NM_019440, exon 2 of 2)	exon (NM_019440, exon 2 of 2)	5545	NM_019440	54396	Mm.458517	NM_019440	ENSMUSG00000069874	Irgm2	AI481100|GTPI|Ifggd2|Iigp2	immunity-related GTPase family M member 2	protein-coding
mm_60915.1	chr7	46797834	46797837	+	1	NA	intron (NM_001291075, intron 2 of 15)	intron (NM_001291075, intron 2 of 15)	1164	NM_001291075	14884	Mm.22700	NM_008186	ENSMUSG00000006599	Gtf2h1	62kDa|AW743425|AW822074|BTF2 p62|C77871|p62	general transcription factor II H, polypeptide 1	protein-coding
mm_38130.1	chr4	134661586	134661589	-	1	NA	intron (NM_207237, intron 1 of 11)	intron (NM_207237, intron 1 of 11)	42703	NM_207237	230815	Mm.18905	NM_207237	ENSMUSG00000037306	Man1c1	AI593348	mannosidase, alpha, class 1C, member 1	protein-coding
mm_106182.1	chr11	116695230	116695242	-	1	NA	promoter-TSS (NM_009180)	promoter-TSS (NM_009180)	-576	NM_009180	20446	Mm.3947	NM_009180	ENSMUSG00000057286	St6galnac2	II|ST6GalNAc|Siat7|Siat7b	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2	protein-coding
mm_96511.1	chr11	68468530	68468570	+	1	NA	intron (NM_177320, intron 1 of 18)	intron (NM_177320, intron 1 of 18)	-34469	NM_001004435	104709	Mm.234573	NM_001004435	ENSMUSG00000046207	Pik3r6	BB220380|p84|p84 PIKAP|p87(PIKAP)|p87PIKAP	phosphoinositide-3-kinase, regulatory subunit 6	protein-coding
mm_24509.1	chr3	92584386	92584393	+	1	NA	exon (NM_008574, exon 2 of 2)	exon (NM_008574, exon 2 of 2)	4635	NM_008574	17235	Mm.331192	NM_008574		Smcp	Mcs|Mcsp	sperm mitochondria-associated cysteine-rich protein	protein-coding
mm_30404.1	chr3	152253681	152253690	-	1	NA	intron (NM_199465, intron 2 of 12)	intron (NM_199465, intron 2 of 12)	12635	NM_199465	68810	Mm.200188	NM_199465	ENSMUSG00000039103	Nexn	1110046H09Rik|AA553326|NELIN	nexilin	protein-coding
mm_150112.1	chr19	29606220	29606223	+	1	NA	TTS (NM_001081319)	TTS (NM_001081319)	42199	NM_001081213	226090	Mm.267131	NM_146098	ENSMUSG00000046324	Ermp1	D19Ertd410e|D19Wsu12e|Fxna|mKIAA1815	endoplasmic reticulum metallopeptidase 1	protein-coding
mm_67344.1	chr7	79822349	79822366	-	1	NA	exon (NM_008486, exon 20 of 20)	exon (NM_008486, exon 20 of 20)	11630	NM_008589	17293	Mm.31472	NM_008589	ENSMUSG00000030543	Mesp2	bHLHc6	mesoderm posterior 2	protein-coding
mm_20704.1	chr2	132945876	132945884	-	1	NA	5' UTR (NM_198029, exon 1 of 15)	5' UTR (NM_198029, exon 1 of 15)	156	NM_198029	241639	Mm.209784	NM_198029	ENSMUSG00000027356	Fermt1	5830467P10Rik|Kindlin-1	fermitin family member 1	protein-coding
mm_94780.1	chr11	21572222	21572232	+	1	NA	promoter-TSS (NM_001316675)	promoter-TSS (NM_001316675)	-54	NM_145425	216560	Mm.138090	NM_145425	ENSMUSG00000020319	Wdpcp	AV249152	WD repeat containing planar cell polarity effector	protein-coding
mm_101421.1	chr11	29547804	29547812	-	1	NA	promoter-TSS (NM_028504)	promoter-TSS (NM_028504)	-142	NM_028504	73324	Mm.69388	NM_028504	ENSMUSG00000020461	Clhc1	1700034F02Rik	clathrin heavy chain linker domain containing 1	protein-coding
mm_32378.1	chr4	106316123	106316139	+	1	NA	promoter-TSS (NM_183225)	promoter-TSS (NM_183225)	-82	NM_183225	329908	Mm.234544	NM_183225	ENSMUSG00000028514	Usp24	2700066K03Rik|2810030C21Rik|AI414051|B130021E18|C79851	ubiquitin specific peptidase 24	protein-coding
mm_24347.1	chr3	89831396	89831406	+	1	NA	promoter-TSS (NM_172530)	promoter-TSS (NM_172530)	31	NM_172530	214547	Mm.225	NM_172530	ENSMUSG00000046280	She	9430022A14	src homology 2 domain-containing transforming protein E	protein-coding
mm_3266.1	chr1	136365058	136365063	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-18956	NM_001347110	67886	Mm.144143	NM_001081360	ENSMUSG00000041570	Camsap2	1600013L13Rik|4930541M15Rik|Camsap1l1|mKIAA1078	calmodulin regulated spectrin-associated protein family, member 2	protein-coding
mm_24986.1	chr3	96975393	96975399	+	1	NA	Intergenic	Intergenic	-49345	NM_008123	14616	Mm.258183	NM_008123	ENSMUSG00000049908	Gja8	Aey5|Cnx50|Cx50|Lop10	gap junction protein, alpha 8	protein-coding
mm_121368.1	chr14	117527480	117527497	+	1	NA	intron (NM_001079844, intron 3 of 9)	intron (NM_001079844, intron 3 of 9)	426359	NR_105747	102465148		NR_105747	ENSMUSG00000098648	Mir6239	Gm28025|mmu-mir-6239	microRNA 6239	ncRNA
mm_21750.1	chr2	164828480	164828499	-	1	NA	promoter-TSS (NM_029370)	promoter-TSS (NM_029370)	45	NM_029370	75642	Mm.159541	NM_029370	ENSMUSG00000017767	Spata25	1700020C07Rik|Tsg23	spermatogenesis associated 25	protein-coding
mm_53416.1	chr6	133115278	133115291	+	1	NA	Intergenic	B4A|SINE|B4	10045	NR_073368	381820	Mm.291762	NM_001163445	ENSMUSG00000072704	Smim10l1	2700089E24Rik|AI662692	small integral membrane protein 10 like 1	protein-coding
mm_148076.1	chr18	72351030	72351073	-	1	NA	promoter-TSS (NM_007831)	promoter-TSS (NM_007831)	18	NM_007831	13176	Mm.167882	NM_007831	ENSMUSG00000060534	Dcc	C030036D22Rik|Igdcc1	deleted in colorectal carcinoma	protein-coding
mm_71566.1	chr8	53605199	53605209	+	1	NA	intron (NM_146208, intron 6 of 9)	intron (NM_146208, intron 6 of 9)	33861	NM_146208	234258	Mm.281749	NM_146208	ENSMUSG00000039396	Neil3	AI449477|BC034753|C85903	nei like 3 (E. coli)	protein-coding
mm_127010.1	chr15	95830418	95830430	+	1	NA	intron (NM_175344, intron 1 of 19)	intron (NM_175344, intron 1 of 19)	39581	NM_001253813	105722	Mm.38087	NM_175344	ENSMUSG00000064210	Ano6	2900059G15Rik|AA407480|AW554778|F730003B03Rik|Tmem16f	anoctamin 6	protein-coding
mm_116364.1	chr13	40730782	40730798	-	1	NA	promoter-TSS (NM_001122948)	promoter-TSS (NM_001122948)	-333	NM_001122948	21418	Mm.85544	NM_011547	ENSMUSG00000021359	Tfap2a	AP-2|AP2alpha|Ap-2 (a)|Ap2|Ap2tf|Tcfap2a	transcription factor AP-2, alpha	protein-coding
mm_73547.1	chr8	108839054	108839062	+	1	NA	intron (NM_007496, intron 3 of 9)	AT_rich|Low_complexity|Low_complexity	-97802	NR_037295	100526511		NR_037295	ENSMUSG00000093241	Mir3108	mir-3108|mmu-mir-3108	microRNA 3108	ncRNA
mm_66957.1	chr7	62423247	62423255	-	1	NA	Intergenic	Intergenic	-3112	NM_011746	22652	Mm.146	NM_011746	ENSMUSG00000070527	Mkrn3	D7H15S9-1|Zfp127	makorin, ring finger protein, 3	protein-coding
mm_10036.1	chr1	192855574	192855606	-	1	NA	5' UTR (NM_198247, exon 1 of 4)	5' UTR (NM_198247, exon 1 of 4)	162	NM_198247	214791	Mm.22806	NM_198247	ENSMUSG00000016262	Sertad4	4833404A09|C130018M11Rik	SERTA domain containing 4	protein-coding
mm_130361.1	chr15	97770190	97770200	-	1	NA	Intergenic	Intergenic	-2529	NM_001177811	223864	Mm.24028	NM_144850	ENSMUSG00000022469	Rapgef3	2310016P22Rik|9330170P05Rik|Epac|Epac1	Rap guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_152679.1	chr19	15959202	15959204	-	1	NA	intron (NM_198019, intron 14 of 14)	intron (NM_198019, intron 14 of 14)	25786	NM_198019	208518	Mm.105652	NM_198019	ENSMUSG00000041491	Cep78	5730599I05Rik|D030027P05	centrosomal protein 78	protein-coding
mm_83972.1	chr9	57261495	57261524	-	1	NA	intron (NM_028820, intron 1 of 2)	intron (NM_028820, intron 1 of 2)	1090	NM_028820	74211	Mm.428905	NM_028820	ENSMUSG00000032300	1700017B05Rik	AA682102|D9Ertd278e	RIKEN cDNA 1700017B05 gene	protein-coding
mm_7973.1	chr1	134063316	134063331	-	1	NA	Intergenic	Intergenic	15832	NM_007570	12227	Mm.392646	NM_007570	ENSMUSG00000020423	Btg2	AA959598|APRO1|Pc3|TIS21	B cell translocation gene 2, anti-proliferative	protein-coding
mm_45133.1	chr5	48813516	48813526	-	1	NA	intron (NM_001199244, intron 1 of 7)	intron (NM_001199244, intron 1 of 7)	76036	NM_030265	80334	Mm.160172	NM_030265	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding
mm_14865.1	chr2	148798850	148798870	+	1	NA	promoter-TSS (NM_009978)	promoter-TSS (NM_009978)	21	NM_009978	13012	Mm.20435	NM_009978	ENSMUSG00000027442	Cst8	Cres|Cst-rs1	cystatin 8 (cystatin-related epididymal spermatogenic)	protein-coding
mm_27576.1	chr3	58810553	58810570	-	1	NA	Intergenic	Intergenic	74651	NM_153386	229320	Mm.131502	NM_153384	ENSMUSG00000043850	Clrn1	A130002D11Rik|USH3|Ush3a|clarin-1	clarin 1	protein-coding
mm_145722.1	chr18	63757799	63757809	+	1	NA	intron (NM_001014981, intron 13 of 27)	L1_Rod|LINE|L1	49109	NM_001014981	104082	Mm.30850	NM_001014981	ENSMUSG00000040560	Wdr7	AI462727|TRAG|mKIAA0541	WD repeat domain 7	protein-coding
mm_56422.1	chr6	97253125	97253152	-	1	NA	promoter-TSS (NM_001081157)	promoter-TSS (NM_001081157)	-358	NM_001081157	320502	Mm.68163	NM_001081157	ENSMUSG00000044086	Lmod3	5430424A14Rik	leiomodin 3 (fetal)	protein-coding
mm_21857.1	chr2	165884409	165884454	-	1	NA	intron (NM_027230, intron 1 of 23)	intron (NM_027230, intron 1 of 23)	407	NM_001252584	228880	Mm.227598	NM_027230	ENSMUSG00000039671	Zmynd8	1110013E22Rik|2010005I16Rik|3632413B07Rik|AI316811|AL024039|Prkcbp1|RACK7	zinc finger, MYND-type containing 8	protein-coding
mm_37234.1	chr4	118029200	118029238	-	1	NA	intron (NM_009176, intron 4 of 11)	intron (NM_009176, intron 4 of 11)	-99456	NM_001284192	11876	Mm.56897	NM_009711	ENSMUSG00000028539	Artn	neublastin	artemin	protein-coding
mm_138498.1	chr17	35200852	35200872	+	1	NA	exon (NM_013693, exon 3 of 4)	exon (NM_013693, exon 3 of 4)	1145	NM_013693	21926	Mm.1293	NM_013693	ENSMUSG00000024401	Tnf	DIF|TNF-a|TNF-alpha|TNFSF2|TNFalpha|Tnfa|Tnfsf1a|Tnlg1f	tumor necrosis factor	protein-coding
mm_5023.1	chr1	193156766	193156813	+	1	NA	intron (NM_016851, intron 1 of 7)	intron (NM_016851, intron 1 of 7)	3677	NM_016851	54139	Mm.273695	NM_016851	ENSMUSG00000026638	Irf6	AI876454|E230028I05Rik|mirf6	interferon regulatory factor 6	protein-coding
mm_63016.1	chr7	121032756	121032767	+	1	NA	Intergenic	Intergenic	-1684	NM_021554	59052	Mm.29122	NM_021554	ENSMUSG00000030876	Mettl9	0610012D09Rik|AA517660|Drev|MNCb-5680	methyltransferase like 9	protein-coding
mm_54360.1	chr6	31113474	31113482	-	1	NA	intron (NR_110471, intron 3 of 3)	intron (NR_110471, intron 3 of 3)	-50385	NR_029532	387223		NR_029532	ENSMUSG00000065604	Mir29b-1	Mirn29b|Mirn29b-1|mir-29b-1	microRNA 29b-1	ncRNA
mm_12536.1	chr2	72285792	72285802	+	1	NA	promoter-TSS (NM_178084)	promoter-TSS (NM_178084)	96	NM_178084	65964	Mm.304143	NM_023057	ENSMUSG00000004085	Map3k20	AV006891|B230120H23Rik|MLTK|MLTKalpha|MLTKbeta|Zak	mitogen-activated protein kinase kinase kinase 20	protein-coding
mm_10459.1	chr2	14294863	14294880	+	1	NA	exon (NM_008625, exon 15 of 30)	exon (NM_008625, exon 15 of 30)	33868	NR_030609	100124488		NR_030609	ENSMUSG00000077897	Mir511	Mirn511|mir-511|mmu-mir-511	microRNA 511	ncRNA
mm_6309.1	chr1	71586927	71586946	-	1	NA	exon (NM_001276413, exon 43 of 44)	exon (NM_001276413, exon 43 of 44)	29780	NM_026195	108147	Mm.38010	NM_026195	ENSMUSG00000026192	Atic	2610509C24Rik|AA536954|AW212393	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	protein-coding
mm_133860.1	chr16	96281012	96281026	+	1	NA	promoter-TSS (NM_033149)	promoter-TSS (NM_033149)	-13	NM_033149	93961	Mm.154783	NM_033149	ENSMUSG00000074892	B3galt5	1190002B21Rik|AU045265|b3Galt-V	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 5	protein-coding
mm_88278.1	chr10	75060824	75060848	+	1	NA	promoter-TSS (NM_001081412)	promoter-TSS (NM_001081412)	-60	NM_001081412	110279	Mm.333722	NM_001081412	ENSMUSG00000009681	Bcr	5133400C09Rik|AI561783|AI853148|mKIAA3017	breakpoint cluster region	protein-coding
mm_90848.1	chr10	8762289	8762314	-	1	NA	intron (NM_175155, intron 8 of 19)	intron (NM_175155, intron 8 of 19)	123769	NM_175155	70097	Mm.338275	NM_175155	ENSMUSG00000015305	Sash1	1100001C18Rik|2500002E12Rik|A330076K04Rik|mKIAA0790	SAM and SH3 domain containing 1	protein-coding
mm_10345.1	chr2	11666408	11666413	+	1	NA	intron (NM_008367, intron 1 of 7)	intron (NM_008367, intron 1 of 7)	23618	NM_008367	16184	Mm.915	NM_008367	ENSMUSG00000026770	Il2ra	CD25|Il2r|Ly-43	interleukin 2 receptor, alpha chain	protein-coding
mm_132331.1	chr16	33819178	33819189	+	1	NA	3' UTR (NM_010739, exon 13 of 13)	3' UTR (NM_010739, exon 13 of 13)	-10482	NM_010580	16419	Mm.6424	NM_010580	ENSMUSG00000022817	Itgb5	AA475909|AI874634|ESTM23|[b]-5|[b]5|[b]5A|[b]5B|beta-5|beta5	integrin beta 5	protein-coding
mm_139295.1	chr17	48316192	48316213	+	1	NA	promoter-TSS (NM_177083)	promoter-TSS (NM_177083)	40	NM_177083	320148	Mm.123455	NM_177083	ENSMUSG00000043740	B430306N03Rik	Treml6	RIKEN cDNA B430306N03 gene	protein-coding
mm_49664.1	chr6	31220344	31220364	+	1	NA	promoter-TSS (NR_040262)	promoter-TSS (NR_040262)	3	NR_040261	73652	Mm.441297	NR_040257	ENSMUSG00000087380	2210408F21Rik	-	RIKEN cDNA 2210408F21 gene	ncRNA
mm_32866.1	chr4	118429682	118429690	+	1	NA	promoter-TSS (NM_001039176)	promoter-TSS (NM_001039176)	-15	NM_001039176	54325	Mm.282096	NM_019422	ENSMUSG00000006390	Elovl1	AA407424|BB151133|Ssc1	elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 1	protein-coding
mm_40643.1	chr5	64961433	64961439	+	1	NA	Intergenic	Intergenic	-1402	NM_011604	21899	Mm.42146	NM_011604	ENSMUSG00000051498	Tlr6	-	toll-like receptor 6	protein-coding
mm_167105.1	chr7	111692815	111692852	-	1	NA	intron (NM_173739, intron 1 of 10)	intron (NM_173739, intron 1 of 10)	87144	NM_173739	233733	Mm.323322	NM_173739	ENSMUSG00000038296	Galnt18	2900011G21Rik|BC024988|Galntl4	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 18	protein-coding
mm_87122.1	chr10	33359328	33359329	+	1	NA	intron (NM_029726, intron 20 of 37)	Lx5c|LINE|L1	-102971	NR_040657	442820	Mm.490725	NR_040657		D830005E20Rik	-	RIKEN cDNA D830005E20 gene	ncRNA
mm_61046.1	chr7	49778440	49778452	+	1	NA	promoter-TSS (NM_133740)	promoter-TSS (NM_133740)	88	NM_133740	71974	Mm.33202	NM_133740	ENSMUSG00000030505	Prmt3	2010005E20Rik|2410018A17Rik|AL033309|Hrmt1l3	protein arginine N-methyltransferase 3	protein-coding
mm_148607.1	chr19	5328001	5328017	+	1	NA	Intergenic	Intergenic	-7732	NM_139301	225865	Mm.87321	NM_139301	ENSMUSG00000038498	Catsper1	Catsper|KSper	cation channel, sperm associated 1	protein-coding
mm_86347.1	chr9	123632385	123632387	-	1	NA	5' UTR (NM_011731, exon 1 of 11)	5' UTR (NM_011731, exon 1 of 11)	179	NM_011731	22599	Mm.41963	NM_011731	ENSMUSG00000025243	Slc6a20b	AA986306|Sit1|Slc6a20|XT3|Xtrp3	solute carrier family 6 (neurotransmitter transporter), member 20B	protein-coding
mm_43707.1	chr5	139354242	139354260	+	1	NA	exon (NM_001160265, exon 3 of 9)	exon (NM_001160265, exon 3 of 9)	1634	NM_001160265	545817	Mm.482474	NM_001160265	ENSMUSG00000029541	Cyp2w1	Gm455	cytochrome P450, family 2, subfamily w, polypeptide 1	protein-coding
mm_152725.1	chr19	18631749	18631753	-	1	NA	promoter-TSS (NM_017375)	promoter-TSS (NM_017375)	62	NM_017375	20409	Mm.172222	NM_017375	ENSMUSG00000024725	Ostf1	C78236|SH3P2|Sh3d3	osteoclast stimulating factor 1	protein-coding
mm_112722.1	chr13	19192217	19192219	+	1	NA	Intergenic	Intergenic	203595	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_8936.1	chr1	164307444	164307503	-	1	NA	promoter-TSS (NM_001160209)	promoter-TSS (NM_001160209)	11	NM_001160209	66352	Mm.33285	NM_025505	ENSMUSG00000026577	Blzf1	1700030G05Rik|Blzf1l|Golgin-45|Jem-1	basic leucine zipper nuclear factor 1	protein-coding
mm_10499.1	chr2	15055275	15055379	+	1	NA	promoter-TSS (NM_001165941)	promoter-TSS (NM_001165941)	-35	NM_029466	75869	Mm.174068	NM_029466	ENSMUSG00000017418	Arl5b	4930587A11Rik|AW146430|Arl8	ADP-ribosylation factor-like 5B	protein-coding
mm_93565.1	chr10	116545820	116545823	-	1	NA	intron (NM_001037846, intron 2 of 15)	intron (NM_001037846, intron 2 of 15)	35690	NM_001037848	72068	Mm.351553	NM_028082	ENSMUSG00000020166	Cnot2	2600016M12Rik|2810470K03Rik|AA537049|AA959607|AW557563|C79650	CCR4-NOT transcription complex, subunit 2	protein-coding
mm_86401.1	chr9	123978298	123978299	-	1	NA	exon (NM_007718, exon 1 of 1)	exon (NM_007718, exon 1 of 1)	110	NM_007718	12770	Mm.423532	NM_007718	ENSMUSG00000064039	Ccr1l1	Cmkbr1l1	chemokine (C-C motif) receptor 1-like 1	protein-coding
mm_37397.1	chr4	121109185	121109193	-	1	NA	promoter-TSS (NM_001081312)	promoter-TSS (NM_001081312)	37	NM_001081312	69469	Mm.481120	NM_001081312	ENSMUSG00000078577	Tmco2	1700028F16Rik	transmembrane and coiled-coil domains 2	protein-coding
mm_23362.1	chr3	55242587	55242645	+	1	NA	promoter-TSS (NM_001195538)	promoter-TSS (NM_001195538)	90	NM_001195538	13175	Mm.393242	NM_019978	ENSMUSG00000027797	Dclk1	1700113D08Rik|2810480F11Rik|AI836758|Click-I|Cpg16|Dcamkl1|Dcl|Dclk|mKIAA0369	doublecortin-like kinase 1	protein-coding
mm_44642.1	chr5	28165464	28165474	-	1	NA	promoter-TSS (NM_010134)	promoter-TSS (NM_010134)	-227	NM_010134	13799	Mm.4298	NM_010134	ENSMUSG00000039095	En2	BB131122|En-2	engrailed 2	protein-coding
mm_61974.1	chr7	90519538	90519541	+	1	NA	Intergenic	L2|LINE|L2	-43544	NM_026734	68472	Mm.289791	NM_026734	ENSMUSG00000030614	Tmem126b	1110001A23Rik	transmembrane protein 126B	protein-coding
mm_96769.1	chr11	69935696	69935703	+	1	NA	promoter-TSS (NM_016875)	promoter-TSS (NM_016875)	-200	NM_016875	53422	Mm.29286	NM_016875	ENSMUSG00000018554	Ybx2	Msy2	Y box protein 2	protein-coding
mm_131843.1	chr16	22961295	22961301	+	1	NA	exon (NM_053176, exon 7 of 7)	exon (NM_053176, exon 7 of 7)	10226	NM_053176	94175	Mm.358794	NM_053176	ENSMUSG00000022877	Hrg	AI265597|AW413091|D16jh2|D18020|Hprg|Hrgp	histidine-rich glycoprotein	protein-coding
mm_160508.1	chr9	20300420	20300420	+	1	NA	exon (NM_146561, exon 1 of 1)	exon (NM_146561, exon 1 of 1)	209	NM_146561	258554	Mm.334991	NM_146561	ENSMUSG00000049028	Olfr873	MOR145-2	olfactory receptor 873	protein-coding
mm_154989.1	chrX	38316149	38316165	+	1	NA	promoter-TSS (NM_001290389)	promoter-TSS (NM_001290389)	35	NM_133690	67821	Mm.60134	NM_133690	ENSMUSG00000016327	Atp1b4	1110020B02Rik	ATPase, (Na+)/K+ transporting, beta 4 polypeptide	protein-coding
mm_37494.1	chr4	123664726	123664805	-	1	NA	intron (NM_001199136, intron 1 of 97)	CpG	-1116	NR_136925	102633214	Mm.399387	NR_136925		Gm12925	OTTMUSG00000009214	predicted gene 12925	ncRNA
mm_154480.1	chrM	4387	4452	-	1	NA	NA	Intergenic	NA	NA								
mm_19172.1	chr2	84345224	84345230	-	1	NA	exon (NM_018782, exon 12 of 16)	exon (NM_018782, exon 12 of 16)	80039	NM_018782	54598	Mm.75467	NM_018782	ENSMUSG00000059588	Calcrl	AV071593|CRLR	calcitonin receptor-like	protein-coding
mm_117606.1	chr13	90886757	90886761	-	1	NA	exon (NM_001145879, exon 6 of 7)	exon (NM_001145879, exon 6 of 7)	18596	NM_001145879	435376	Mm.292579	NM_001145879	ENSMUSG00000078958	Atp6ap1l	EG435376	ATPase, H+ transporting, lysosomal accessory protein 1-like	protein-coding
mm_88268.1	chr10	74547865	74547888	+	1	NA	intron (NM_001142740, intron 25 of 31)	intron (NM_001142740, intron 25 of 31)	-419355	NM_010311	14687	Mm.32595	NM_010311	ENSMUSG00000040009	Gnaz	AI847979|Gz	guanine nucleotide binding protein, alpha z subunit	protein-coding
mm_89768.1	chr10	100098575	100098591	+	1	NA	3' UTR (NM_013598, exon 10 of 10)	3' UTR (NM_013598, exon 10 of 10)	82762	NM_013598	17311	Mm.45124	NM_013598	ENSMUSG00000019966	Kitl	Clo|Con|Gb|Kitlg|Mgf|SCF|SF|SLF|Sl|blz|contrasted	kit ligand	protein-coding
mm_37481.1	chr4	123572867	123572877	-	1	NA	intron (NM_001199136, intron 1 of 97)	intron (NM_001199136, intron 1 of 97)	-43548	NR_105824	102465214		NR_105824	ENSMUSG00000099005	Mir6398	Gm27657|mmu-mir-6398	microRNA 6398	ncRNA
mm_1484.1	chr1	71642992	71643021	+	1	NA	exon (NM_001276413, exon 7 of 44)	exon (NM_001276413, exon 7 of 44)	10228	NM_010233	14268	Mm.193099	NM_010233	ENSMUSG00000026193	Fn1	E330027I09|Fn|Fn-1	fibronectin 1	protein-coding
mm_32014.1	chr4	94739566	94739587	+	1	NA	5' UTR (NM_001290551, exon 1 of 22)	5' UTR (NM_001290551, exon 1 of 22)	287	NM_001290551	21687	Mm.14313	NM_013690	ENSMUSG00000006386	Tek	AA517024|Cd202b|Hyk|STK1|Tie-2|Tie2	endothelial-specific receptor tyrosine kinase	protein-coding
mm_93269.1	chr10	95768070	95768087	-	1	NA	Intergenic	Intergenic	-172585	NM_001001932	216238	Mm.210035	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding
mm_23466.1	chr3	60475410	60475431	+	1	NA	intron (NM_001253713, intron 2 of 9)	intron (NM_001253713, intron 2 of 9)	2590	NM_001253713	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_75852.1	chr8	70659824	70659839	-	1	NA	promoter-TSS (NM_023217)	promoter-TSS (NM_023217)	-93	NM_023217	66522	Mm.154906	NM_023217	ENSMUSG00000056204	Pgpep1	2810003H13Rik|Gm19458|PAP-I|PGP|PGP-I|PGPI|Pcp	pyroglutamyl-peptidase I	protein-coding
mm_16090.1	chr2	168956233	168956256	+	1	NA	promoter-TSS (NM_009564)	promoter-TSS (NM_009564)	-657	NM_009564	22722	Mm.2095	NM_009564	ENSMUSG00000027551	Zfp64	-	zinc finger protein 64	protein-coding
mm_86773.1	chr10	20141883	20141888	+	1	NA	3' UTR (NM_008580, exon 30 of 30)	3' UTR (NM_008580, exon 30 of 30)	-7035	NM_008635	17761	Mm.20928	NM_008635	ENSMUSG00000019996	Map7	E-MAP-115|MAP-7|Mtap7|R75000|mshi|mste|ste	microtubule-associated protein 7	protein-coding
mm_49309.1	chr6	18169815	18169833	+	1	NA	promoter-TSS (NM_021050)	promoter-TSS (NM_021050)	-863	NM_021050	12638	Mm.15621	NM_021050	ENSMUSG00000041301	Cftr	AW495489|Abcc7	cystic fibrosis transmembrane conductance regulator	protein-coding
mm_24093.1	chr3	88030840	88030850	+	1	NA	Intergenic	Intergenic	-3334	NM_022031	73940	Mm.294467	NM_022031	ENSMUSG00000004894	Hapln2	4930401E20Rik|Bral1	hyaluronan and proteoglycan link protein 2	protein-coding
mm_91675.1	chr10	43373950	43373954	-	1	NA	intron (NM_027772, intron 4 of 7)	intron (NM_027772, intron 4 of 7)	-105188	NM_199028	331623	Mm.490388	NM_199028	ENSMUSG00000038214	Bend3	mKIAA1553	BEN domain containing 3	protein-coding
mm_80892.1	chr9	99612546	99612557	+	1	NA	promoter-TSS (NM_001077424)	promoter-TSS (NM_001077424)	49	NM_001077424	333424	Mm.297753	NM_001077424	ENSMUSG00000037953	A4gnt	AV080780|Alpha4gnt|Gm798	alpha-1,4-N-acetylglucosaminyltransferase	protein-coding
mm_79109.1	chr9	46269070	46269084	+	1	NA	intron (NM_080434, intron 1 of 3)	intron (NM_080434, intron 1 of 3)	469	NM_080434	66113	Mm.29738	NM_080434	ENSMUSG00000032079	Apoa5	1300007O05Rik|Apoav|RAP3	apolipoprotein A-V	protein-coding
mm_44460.1	chr5	22550251	22550261	-	1	NA	promoter-TSS (NM_011959)	promoter-TSS (NM_011959)	75	NM_011959	26429	Mm.412217	NM_011959	ENSMUSG00000029012	Orc5	AL033327|MmORC5|Orc5l	origin recognition complex, subunit 5	protein-coding
mm_80174.1	chr9	72274874	72274886	+	1	NA	promoter-TSS (NM_146224)	promoter-TSS (NM_146224)	-8	NM_146224	235469	Mm.242791	NM_146224	ENSMUSG00000038535	Zfp280d	A930005F02Rik|BC027163|Suhw4|ZNF634|Znf280d	zinc finger protein 280D	protein-coding
mm_53670.1	chr6	141671880	141671889	+	1	NA	intron (NM_020495, intron 11 of 15)	intron (NM_020495, intron 11 of 15)	42366	NM_020495	28253	Mm.272223	NM_020495	ENSMUSG00000030236	Slco1b2	7330442B20Rik|OATP-C|OATP2|Oatp1b2|Oatp4|Slc21a10|Slc21a6|lst-1|mlst-1	solute carrier organic anion transporter family, member 1b2	protein-coding
mm_145104.1	chr18	44104475	44104481	+	1	NA	promoter-TSS (NM_030061)	promoter-TSS (NM_030061)	-45	NM_030061	78242	Mm.99782	NM_030061	ENSMUSG00000061144	Spink12	9230117E20Rik	serine peptidase inhibitor, Kazal type 12	protein-coding
mm_172756.1	chr8	85607211	85607215	-	1	NA	Intergenic	RLTR31C_MM|LTR|ERVK	-51942	NM_019794	56445	Mm.475573	NM_019794	ENSMUSG00000031701	Dnaja2	1500017M13Rik|2010206B19Rik|DNAJ|DNJ3|Dnaj3|HIRIP4|PRO3015|mDj3	DnaJ heat shock protein family (Hsp40) member A2	protein-coding
mm_10538.1	chr2	16457337	16457347	+	1	NA	intron (NM_026162, intron 1 of 13)	intron (NM_026162, intron 1 of 13)	101038	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding
mm_150567.1	chr19	40089641	40089656	+	1	NA	promoter-TSS (NM_001167877)	promoter-TSS (NM_001167877)	-31	NM_134144	107141	Mm.474575	NM_134144	ENSMUSG00000054827	Cyp2c50	AI266900	cytochrome P450, family 2, subfamily c, polypeptide 50	protein-coding
mm_133607.1	chr16	91489695	91489707	+	1	NA	exon (NM_010508, exon 2 of 11)	exon (NM_010508, exon 2 of 11)	4486	NM_010508	15975	Mm.502	NM_010508	ENSMUSG00000022967	Ifnar1	CD118|Ifar|Ifnar|Ifrc|Infar	interferon (alpha and beta) receptor 1	protein-coding
mm_50089.1	chr6	41524010	41524033	+	1	NA	exon (NM_009430, exon 3 of 5)	exon (NM_009430, exon 3 of 5)	2245	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_86599.1	chr10	13499535	13499548	+	1	NA	Intergenic	Intergenic	-1487	NM_001330198	66848	Mm.26625	NM_025799	ENSMUSG00000019810	Fuca2	0610025O11Rik|5530401P20Rik	fucosidase, alpha-L- 2, plasma	protein-coding
mm_131440.1	chr16	16072782	16072792	+	1	NA	intron (NM_146068, intron 5 of 19)	intron (NM_146068, intron 5 of 19)	74064	NM_146068	224008	Mm.244703	NM_146068	ENSMUSG00000041974	Spidr	2310008H04Rik|Kiaa0146	scaffolding protein involved in DNA repair	protein-coding
mm_4979.1	chr1	191575722	191575792	+	1	NA	promoter-TSS (NM_001305233)	promoter-TSS (NM_001305233)	121	NM_001306204	77065	Mm.338175	NM_178632	ENSMUSG00000037461	Ints7	5930412E23Rik|int7	integrator complex subunit 7	protein-coding
mm_122542.1	chr14	47568428	47568436	-	1	NA	promoter-TSS (NM_172599)	promoter-TSS (NM_172599)	2	NM_172599	100504663	Mm.287279	NM_172599	ENSMUSG00000037526	Atg14	4832427M01|Atg14L|D14Ertd114e|D14Ertd436e	autophagy related 14	protein-coding
mm_3027.1	chr1	133664445	133664464	+	1	NA	Intergenic	Intergenic	-3055	NM_144530	70579	Mm.245357	NM_144530	ENSMUSG00000102976	Zc3h11a	1110003F06Rik|5730454B08Rik|G630041M05Rik|Zc3hdc11a|Zc3hh11a|mKIAA0663	zinc finger CCCH type containing 11A	protein-coding
mm_34510.1	chr4	148853537	148853538	+	1	NA	intron (NM_027195, intron 2 of 15)	intron (NM_027195, intron 2 of 15)	49145	NM_027195	69743	Mm.233879	NM_027195	ENSMUSG00000028977	Casz1	2410019P08Rik|AV096627|BC040081|Cst|D4Ertd432e	castor zinc finger 1	protein-coding
mm_73002.1	chr8	93810808	93810814	+	1	NA	promoter-TSS (NM_010308)	promoter-TSS (NM_010308)	-27	NM_010308	14681	Mm.251445	NM_010308	ENSMUSG00000031748	Gnao1	AW050213|Galphao|Gnao|alphaO	guanine nucleotide binding protein, alpha O	protein-coding
mm_47552.1	chr5	124354757	124354777	-	1	NA	promoter-TSS (NM_013812)	promoter-TSS (NM_013812)	-139	NM_013812	13445	Mm.391838	NM_013812	ENSMUSG00000029394	Cdk2ap1	Apc10|Cdkap1|DORC1|Doc1|ST19|doc-1|p12	CDK2 (cyclin-dependent kinase 2)-associated protein 1	protein-coding
mm_122055.1	chr14	30278028	30278030	-	1	NA	intron (NM_001302637, intron 3 of 48)	intron (NM_001302637, intron 3 of 48)	75457	NM_001302637	12289	Mm.9772	NM_028981	ENSMUSG00000015968	Cacna1d	8430418G19Rik|C79217|Cach3|Cacn4|Cacnl1a2|Cav1.3|Cchl1a|Cchl1a2|D-LTCC	calcium channel, voltage-dependent, L type, alpha 1D subunit	protein-coding
mm_60882.1	chr7	46376449	46376459	+	1	NA	promoter-TSS (NM_010866)	promoter-TSS (NM_010866)	-20	NM_010866	17927	Mm.1526	NM_010866	ENSMUSG00000009471	Myod1	AI503393|MYF3|MyoD|Myod-1|bHLHc1	myogenic differentiation 1	protein-coding
mm_76999.1	chr8	107293202	107293204	-	1	NA	promoter-TSS (NM_018823)	promoter-TSS (NM_018823)	-267	NM_018823	54446	Mm.390057	NM_018823	ENSMUSG00000003847	Nfat5	AI225870|B130038B15Rik|CAG-8|CAG80|NFATL1|OREBP|TonEBP|mKIAA0827|nfatz	nuclear factor of activated T cells 5	protein-coding
mm_137611.1	chr17	28252539	28252581	+	1	NA	intron (NM_011145, intron 2 of 7)	intron (NM_011145, intron 2 of 7)	-19148	NR_045427	69050	Mm.486938	NR_045427	ENSMUSG00000002250	1810013A23Rik	-	RIKEN cDNA 1810013A23 gene	ncRNA
mm_47004.1	chr5	115436509	115436531	-	1	NA	intron (NM_008629, intron 6 of 14)	CpG	6835	NM_008629	17690	Mm.5077	NM_008629	ENSMUSG00000054256	Msi1	Msi1h|Musahi1|m-Msi-1	musashi RNA-binding protein 1	protein-coding
mm_41574.1	chr5	93172765	93172778	+	1	NA	3' UTR (NM_001009818, exon 10 of 10)	3' UTR (NM_001009818, exon 10 of 10)	33724	NM_017367	12453	Mm.250419	NM_017367	ENSMUSG00000063015	Ccni	-	cyclin I	protein-coding
mm_137799.1	chr17	29717116	29717147	+	1	NA	promoter-TSS (NM_026782)	promoter-TSS (NM_026782)	-114	NM_001163741	68597	Mm.390979	NM_026782	ENSMUSG00000024018	Ccdc167	1110021J02Rik	coiled-coil domain containing 167	protein-coding
mm_31938.1	chr4	86575784	86575794	+	1	NA	5' UTR (NM_178376, exon 1 of 1)	5' UTR (NM_178376, exon 1 of 1)	116	NM_178376	68441	Mm.31178	NM_178376	ENSMUSG00000070934	Rraga	1300010C19Rik|AI255374|FIP-1|RAGA	Ras-related GTP binding A	protein-coding
mm_157319.1	chrX	21680577	21680584	-	1	NA	Intergenic	L1_Mur3|LINE|L1	-34320	NM_020049	56774	Mm.253984	NM_020049	ENSMUSG00000031089	Slc6a14	1110007A17Rik|9030613J17Rik|ATB0plus|CATB0plus	solute carrier family 6 (neurotransmitter transporter), member 14	protein-coding
mm_85543.1	chr9	106682237	106682249	-	1	NA	intron (NM_001286498, intron 2 of 5)	intron (NM_001286498, intron 2 of 5)	3573	NM_011573	21767	Mm.22266	NM_011573	ENSMUSG00000040813	Tex264	TEG-264	testis expressed gene 264	protein-coding
mm_159957.1	chr6	87914175	87914175	+	1	NA	TTS (NM_017477)	TTS (NM_017477)	199	NM_173737	232210	Mm.246241	NM_173737	ENSMUSG00000030060	Hmces	8430410A17Rik|C85376	5-hydroxymethylcytosine (hmC) binding, ES cell specific	protein-coding
mm_125598.1	chr15	59650725	59650757	+	1	NA	intron (NM_144549, intron 1 of 2)	intron (NM_144549, intron 1 of 2)	2087	NM_144549	211770	Mm.40298	NM_144549	ENSMUSG00000032501	Trib1	A530090O15Rik|TRB-1|Trb1	tribbles pseudokinase 1	protein-coding
mm_138345.1	chr17	34914460	34914476	+	1	NA	promoter-TSS (NM_023557)	promoter-TSS (NM_023557)	2	NM_023557	70129	Mm.183126	NM_023557	ENSMUSG00000007034	Slc44a4	2210409B01Rik|NG22	solute carrier family 44, member 4	protein-coding
mm_50375.1	chr6	48682509	48682537	+	1	NA	Intergenic	Intergenic	-2055	NM_001243200	107526	Mm.333048	NM_174990	ENSMUSG00000054435	Gimap4	AU019574|E430007K16Rik|Ian-1|Ian1|Imap4	GTPase, IMAP family member 4	protein-coding
mm_47703.1	chr5	129879039	129879094	-	1	NA	promoter-TSS (NM_011079)	promoter-TSS (NM_011079)	17	NM_011079	18682	Mm.3159	NM_011079	ENSMUSG00000025537	Phkg1	Phkg	phosphorylase kinase gamma 1	protein-coding
mm_110654.1	chr12	59053853	59053867	-	1	NA	intron (NM_030057, intron 1 of 5)	intron (NM_030057, intron 1 of 5)	7612	NM_001306218	78232	Mm.290070	NM_030057	ENSMUSG00000020993	Trappc6b	5830498C14Rik|C79212	trafficking protein particle complex 6B	protein-coding
mm_65986.1	chr7	30524422	30524426	-	1	NA	exon (NM_001289670, exon 20 of 21)	exon (NM_001289670, exon 20 of 21)	9302	NR_036630	100504207	Mm.297831	NM_001004161	ENSMUSG00000062132	Arhgap33os	Gm1082	Rho GTPase activating protein 33, opposite strand	ncRNA
mm_44277.1	chr5	5749318	5749340	-	1	NA	promoter-TSS (NM_027399)	promoter-TSS (NM_027399)	-12	NM_027399	70358	Mm.85429	NM_027399	ENSMUSG00000015652	Steap1	2410007B19Rik|Prss24|Steap	six transmembrane epithelial antigen of the prostate 1	protein-coding
mm_92737.1	chr10	80918183	80918209	-	1	NA	promoter-TSS (NM_010722)	promoter-TSS (NM_010722)	49	NM_010722	16907	Mm.7362	NM_010722	ENSMUSG00000062075	Lmnb2	-	lamin B2	protein-coding
mm_75741.1	chr8	69749939	69749970	-	1	NA	promoter-TSS (NM_001200023)	promoter-TSS (NM_001200023)	8	NM_001200023	620419	Mm.460423	NM_001200023	ENSMUSG00000092260	Zfp963	-	zinc finger protein 963	protein-coding
mm_50912.1	chr6	57582802	57582826	+	1	NA	intron (NM_025992, intron 1 of 22)	intron (NM_025992, intron 1 of 22)	1822	NM_025992	67138	Mm.297393	NM_025992	ENSMUSG00000029798	Herc6	1700121D12Rik|2510038N07Rik|4930427L17Rik|AI451296|CEB1|Herc5	hect domain and RLD 6	protein-coding
mm_28497.1	chr3	92484608	92484616	-	1	NA	exon (NM_009264, exon 2 of 2)	exon (NM_009264, exon 2 of 2)	1269	NM_009264	20753	Mm.331191	NM_009264	ENSMUSG00000050359	Sprr1a	AI528815|SPR1a|mSPRR1A	small proline-rich protein 1A	protein-coding
mm_163294.1	chr11	118992938	118992950	+	1	NA	TTS (NM_001030291)	TTS (NM_001030291)	4756	NM_001030291	238011	Mm.244114	NM_001030291	ENSMUSG00000046697	Enpp7	Alk-SMase|Gm254	ectonucleotide pyrophosphatase/phosphodiesterase 7	protein-coding
mm_92134.1	chr10	66698088	66698096	-	1	NA	Intergenic	Intergenic	222292	NR_138560	68488	Mm.338835	NR_138560		1110002J07Rik	-	RIKEN cDNA 1110002J07 gene	ncRNA
mm_66397.1	chr7	44304864	44304900	-	1	NA	exon (NM_009131, exon 4 of 4)	exon (NM_009131, exon 4 of 4)	2077	NM_009131	20256	Mm.20428	NM_009131	ENSMUSG00000004473	Clec11a	AW457320|Clecsf3|Scgf	C-type lectin domain family 11, member a	protein-coding
mm_32817.1	chr4	117367721	117367730	+	1	NA	intron (NM_025739, intron 2 of 14)	intron (NM_025739, intron 2 of 14)	7736	NM_001310729	66743	Mm.318331	NM_025739	ENSMUSG00000028677	Rnf220	4732477A13|4931406I20Rik|5730503K05Rik|AV302541	ring finger protein 220	protein-coding
mm_12774.1	chr2	79327577	79327588	+	1	NA	3' UTR (NM_010576, exon 28 of 28)	3' UTR (NM_010576, exon 28 of 28)	72156	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D|Itga4B	integrin alpha 4	protein-coding
mm_125854.1	chr15	74989613	74989623	+	1	NA	Intergenic	Intergenic	-6188	NM_020498	57248	Mm.358339	NM_020498	ENSMUSG00000022586	Ly6i	AI789751|Ly-6I|Ly-6M	lymphocyte antigen 6 complex, locus I	protein-coding
mm_166570.1	chr6	48988658	48988660	+	1	NA	exon (NM_172888, exon 1 of 5)	exon (NM_172888, exon 1 of 5)	1798	NM_172888	243377	Mm.446302	NM_172888	ENSMUSG00000039215	Svs1	9530003A11	seminal vesicle secretory protein 1	protein-coding
mm_6326.1	chr1	71612502	71612525	-	1	NA	exon (NM_001276413, exon 25 of 44)	exon (NM_001276413, exon 25 of 44)	40721	NM_010233	14268	Mm.193099	NM_010233	ENSMUSG00000026193	Fn1	E330027I09|Fn|Fn-1	fibronectin 1	protein-coding
mm_113313.1	chr13	30761663	30761671	+	1	NA	intron (NM_001347508, intron 8 of 8)	intron (NM_001347508, intron 8 of 8)	12434	NM_013674	16364	Mm.4677	NM_013674	ENSMUSG00000021356	Irf4	AI385587|IRF-4|LSIRF|NF-EM5|Spip	interferon regulatory factor 4	protein-coding
mm_6939.1	chr1	85727085	85727099	-	1	NA	intron (NM_177055, intron 1 of 5)	intron (NM_177055, intron 1 of 5)	9514	NM_177055	319997	Mm.116691	NM_177055	ENSMUSG00000052760	A630001G21Rik	-	RIKEN cDNA A630001G21 gene	protein-coding
mm_108991.1	chr12	102899256	102899263	+	1	NA	promoter-TSS (NM_001039049)	promoter-TSS (NM_001039049)	-47	NM_001039049	75483	Mm.660	NM_001039049	ENSMUSG00000043319	Cox8c	1700007F21Rik|COX8-3|COXVIII-3	cytochrome c oxidase subunit VIIIc	protein-coding
mm_94924.1	chr11	29508601	29508613	+	1	NA	3' UTR (NM_176841, exon 32 of 32)	3' UTR (NM_176841, exon 32 of 32)	6426	NM_026465	67939	Mm.251087	NM_026465	ENSMUSG00000032673	Prorsd1	2010316F05Rik|Ncrna00117|Prdxdd1	prolyl-tRNA synthetase domain containing 1	protein-coding
mm_163224.1	chr11	102097494	102097498	+	1	NA	Intergenic	Intergenic	3804	NM_008918	19064	Mm.1269	NM_008918	ENSMUSG00000017316	Ppy	AV061413|IGSPP|PP	pancreatic polypeptide	protein-coding
mm_85617.1	chr9	107614681	107614723	-	1	NA	3' UTR (NM_008138, exon 9 of 9)	3' UTR (NM_008138, exon 9 of 9)	-5461	NM_001291539	20347	Mm.4083	NM_009153	ENSMUSG00000057969	Sema3b	SemA|Semaa|sema5|semaV	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B	protein-coding
mm_171591.1	chr4	147642511	147642514	-	1	NA	promoter-TSS (NM_145078)	promoter-TSS (NM_145078)	-4	NM_145078	112422	Mm.327194	NM_145078	ENSMUSG00000066000	Zfp979	2610305D13Rik|Ssm1b	zinc finger protein 979	protein-coding
mm_102727.1	chr11	67242835	67242837	-	1	NA	exon (NM_010855, exon 8 of 40)	exon (NM_010855, exon 8 of 40)	5024	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_46067.1	chr5	92278218	92278222	-	1	NA	promoter-TSS (NM_001163687)	promoter-TSS (NM_001163687)	-39	NM_025972	67111	Mm.28890	NM_025972	ENSMUSG00000029413	Naaa	2210023K21Rik|3830414F09Rik|Asahl	N-acylethanolamine acid amidase	protein-coding
mm_137249.1	chr17	24528244	24528264	+	1	NA	promoter-TSS (NR_045289)	promoter-TSS (NR_045289)	3	NR_045289	75614	Mm.440235	NR_045289	ENSMUSG00000093565	Rab26os	2610019E17Rik	RAB26, member RAS oncogene family, opposite strand	ncRNA
mm_118256.1	chr13	112424713	112424724	-	1	NA	Intergenic	Intergenic	-39352	NM_010560	16195	Mm.4364	NM_010560	ENSMUSG00000021756	Il6st	5133400A03Rik|AA389424|BB405851|CD130|D13Ertd699e|gp130	interleukin 6 signal transducer	protein-coding
mm_109169.1	chr12	108334342	108334406	+	1	NA	promoter-TSS (NM_010010)	promoter-TSS (NM_010010)	-7	NM_010010	13116	Mm.41911	NM_010010	ENSMUSG00000021259	Cyp46a1	Cyp46	cytochrome P450, family 46, subfamily a, polypeptide 1	protein-coding
mm_15003.1	chr2	152477033	152477038	+	1	NA	promoter-TSS (NM_176950)	promoter-TSS (NM_176950)	-28	NM_176950	319579	Mm.190454	NM_176950	ENSMUSG00000049560	Defb20	9230107O10Rik|BD-20|mBD-20	defensin beta 20	protein-coding
mm_94963.1	chr11	30786717	30786720	+	1	NA	intron (NM_134013, intron 1 of 46)	intron (NM_134013, intron 1 of 46)	14943	NM_134013	103554	Mm.240066	NM_134013	ENSMUSG00000040850	Psme4	AA409398|AU041366|TEMO|mKIAA0077	proteasome (prosome, macropain) activator subunit 4	protein-coding
mm_101438.1	chr11	30138829	30138841	-	1	NA	exon (NM_009260, exon 13 of 31)	exon (NM_009260, exon 13 of 31)	59422	NM_009260	20742	Mm.123110	NM_009260	ENSMUSG00000020315	Sptbn1	9930031C03Rik|AL033301|SPTB2|Spnb-2|Spnb2|elf1|elf3|mKIAA4049	spectrin beta, non-erythrocytic 1	protein-coding
mm_60170.1	chr7	40902619	40902637	+	1	NA	exon (NM_021387, exon 4 of 5)	exon (NM_021387, exon 4 of 5)	3350	NM_021387	58188	Mm.150675	NM_021387	ENSMUSG00000039257	Vstm2b	2900093B09Rik|AB030198	V-set and transmembrane domain containing 2B	protein-coding
mm_40823.1	chr5	72647780	72647801	+	1	NA	promoter-TSS (NM_001081205)	promoter-TSS (NM_001081205)	-6	NM_001081205	70701	Mm.38884	NM_001081205	ENSMUSG00000067219	Nipal1	3830408G10Rik|Npal1	NIPA-like domain containing 1	protein-coding
mm_134855.1	chr16	28323549	28323571	-	1	NA	intron (NM_001276419, intron 3 of 4)	MTD|LTR|ERVL-MaLR	122515	NM_183064	14167	Mm.7996	NM_010199	ENSMUSG00000022523	Fgf12	AV114868|B230343J05Rik|FGF-12|FHF-1|Fhf1	fibroblast growth factor 12	protein-coding
mm_74038.1	chr8	121907828	121907877	+	1	NA	promoter-TSS (NM_011404)	promoter-TSS (NM_011404)	19	NM_001033485	407789	Mm.436576	NM_001033485		BC048644	-	cDNA sequence BC048644	protein-coding
mm_31259.1	chr4	45130448	45130450	+	1	NA	Intergenic	Intergenic	-22336	NM_001099675	68512	Mm.282081	NM_001099675	ENSMUSG00000078713	Tomm5	1110019J04Rik|Tom5	translocase of outer mitochondrial membrane 5 homolog (yeast)	protein-coding
mm_90667.1	chr10	128821888	128821913	+	1	NA	promoter-TSS (NM_024180)	promoter-TSS (NM_024180)	129	NM_025364	66118	Mm.235562	NM_025364	ENSMUSG00000078427	Sarnp	1110005A23Rik|Cip29	SAP domain containing ribonucleoprotein	protein-coding
mm_17618.1	chr2	30967821	30967830	-	1	NA	promoter-TSS (NM_144884)	promoter-TSS (NM_144884)	93	NM_144884	30931	Mm.154994	NM_144884	ENSMUSG00000026849	Tor1a	DQ2|Dyt1|torsinA	torsin family 1, member A (torsin A)	protein-coding
mm_146421.1	chr18	84720872	84720889	+	1	NA	intron (NM_173770, intron 1 of 4)	intron (NM_173770, intron 1 of 4)	638	NM_173770	240479	Mm.472378	NM_173770	ENSMUSG00000047992	Fam69c	B230399E16Rik	family with sequence similarity 69, member C	protein-coding
mm_80023.1	chr9	67996525	67996538	+	1	NA	TTS (NM_177184)	TTS (NM_177184)	29183	NR_045745	434412	Mm.490707	NR_045745	ENSMUSG00000111841	Gm20745	-	predicted gene, 20745	ncRNA
mm_45994.1	chr5	90506600	90506607	-	1	NA	exon (NM_007423, exon 12 of 15)	exon (NM_007423, exon 12 of 15)	-12346	NM_145146	280662	Mm.348786	NM_145146	ENSMUSG00000029369	Afm	Alf|alpha-Alb	afamin	protein-coding
mm_121134.1	chr14	101884047	101884125	+	1	NA	intron (NM_001347628, intron 4 of 26)	intron (NM_001347628, intron 4 of 26)	43463	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_159871.1	chr5	146231560	146231560	+	1	NA	promoter-TSS (NM_153599)	promoter-TSS (NM_153599)	-115	NM_153599	264064	Mm.260576	NM_153599	ENSMUSG00000029635	Cdk8	-	cyclin-dependent kinase 8	protein-coding
mm_171852.1	chr5	16941329	16941333	+	1	NA	Intergenic	L1Md_T|LINE|L1	387430	NM_001289461	15234	Mm.267078	NM_010427	ENSMUSG00000028864	Hgf	C230052L06Rik|HGF/SF|NK1|NK2|SF|SF/HGF	hepatocyte growth factor	protein-coding
mm_126647.1	chr15	84123117	84123117	+	1	NA	promoter-TSS (NM_029427)	promoter-TSS (NM_029427)	58	NM_029427	75772	Mm.159565	NM_029427	ENSMUSG00000018868	Pnpla5	4833426H19Rik|GS2L	patatin-like phospholipase domain containing 5	protein-coding
mm_89779.1	chr10	100820895	100820895	+	1	NA	Intergenic	RLTR44D|LTR|ERVK	228509	NM_001081246	66605	Mm.72646	NM_001081246	ENSMUSG00000056912	1700017N19Rik	-	RIKEN cDNA 1700017N19 gene	protein-coding
mm_84113.1	chr9	58370452	58370458	-	1	NA	promoter-TSS (NR_040727)	promoter-TSS (NR_040727)	-49	NR_040727	73529	Mm.490924	NR_040727	ENSMUSG00000100487	1700072B07Rik	-	RIKEN cDNA 1700072B07 gene	ncRNA
mm_11569.1	chr2	32897877	32897883	+	1	NA	intron (NM_146119, intron 1 of 13)	intron (NM_146119, intron 1 of 13)	21746	NM_146119	227737	Mm.301646	NM_146119	ENSMUSG00000026796	Fam129b	9130404D14Rik	family with sequence similarity 129, member B	protein-coding
mm_53407.1	chr6	132439540	132439542	+	1	NA	Intergenic	L1MDb|LINE|L1	-75406	NM_053251	114600	Mm.428480	NM_053251		Gm4736	EG114600|Mp4|Mp6	predicted gene 4736	protein-coding
mm_12144.1	chr2	61804639	61804645	+	1	NA	5' UTR (NM_009322, exon 1 of 6)	5' UTR (NM_009322, exon 1 of 6)	189	NM_009322	21375	Mm.308525	NM_009322	ENSMUSG00000035033	Tbr1	-	T-box brain gene 1	protein-coding
mm_52347.1	chr6	110946953	110946984	+	1	NA	intron (NM_001346640, intron 2 of 10)	RLTR12E|LTR|ERVK	301370	NM_177328	108073	Mm.240881	NM_177328	ENSMUSG00000056755	Grm7	6330570A01Rik|BB176677|C030018L03|E130018M02Rik|Gpr1g|Gprc1g|SMN2|Tg(SMN2)89Ahmb|mGluR7	glutamate receptor, metabotropic 7	protein-coding
mm_125465.1	chr15	52712483	52712491	+	1	NA	promoter-TSS (NM_027212)	promoter-TSS (NM_027212)	42	NM_027212	69790	Mm.195562	NM_027212	ENSMUSG00000038622	Med30	1810038N03Rik|2510044J04Rik|TRAP25|Thrap6	mediator complex subunit 30	protein-coding
mm_12809.1	chr2	80302329	80302331	+	1	NA	Intergenic	Intergenic	9860	NM_177256	320769	Mm.60992	NM_177256	ENSMUSG00000050114	Prdx6b	1-cysPrx-P1|4930414C22Rik|Aop2-rs1|Prdx5-rs1|Prdx6-ps1|Prdx6-rs1|Prdx6-rs1-ps	peroxiredoxin 6B	protein-coding
mm_257.1	chr1	20670067	20670081	+	1	NA	intron (NR_131249, intron 1 of 2)	intron (NR_131249, intron 1 of 2)	192	NR_131249	105661730	Mm.137893	NR_131249		Linc-md1	-	long intergenic non-coding RNA muscle differentiation 1	ncRNA
mm_29555.1	chr3	116807904	116807914	-	1	NA	intron (NM_001081326, intron 1 of 33)	intron (NM_001081326, intron 1 of 33)	257	NM_001081326	77559	Mm.237099	NM_001081326	ENSMUSG00000033400	Agl	1110061O17Rik|9430004C13Rik|9630046L06Rik|AI850929|C77197	amylo-1,6-glucosidase, 4-alpha-glucanotransferase	protein-coding
mm_104829.1	chr11	99089297	99089318	-	1	NA	promoter-TSS (NM_172564)	promoter-TSS (NM_172564)	-1	NM_172564	217169	Mm.262067	NM_172564	ENSMUSG00000017607	Tns4	9930017A07Rik|AA589547|AU016405|Cten	tensin 4	protein-coding
mm_51448.1	chr6	80314452	80314460	+	1	NA	intron (NM_001347261, intron 2 of 2)	intron (NM_001347261, intron 2 of 2)	294813	NM_178731	243499	Mm.483425	NM_178731	ENSMUSG00000052581	Lrrtm4	7530419J18Rik|A230052N11	leucine rich repeat transmembrane neuronal 4	protein-coding
mm_136864.1	chr17	12859061	12859069	+	1	NA	intron (NM_008552, intron 3 of 8)	MTD|LTR|ERVL-MaLR	9078	NM_008552	17171	Mm.425994	NM_008552	ENSMUSG00000068037	Mas1	Mas-1|Mgra	MAS1 oncogene	protein-coding
mm_120698.1	chr14	70890661	70890711	+	1	NA	5' UTR (NM_008115, exon 1 of 9)	5' UTR (NM_008115, exon 1 of 9)	579	NM_001302094	14586	Mm.32619	NM_008115	ENSMUSG00000022103	Gfra2	-	glial cell line derived neurotrophic factor family receptor alpha 2	protein-coding
mm_34015.1	chr4	137994032	137994106	+	1	NA	5' UTR (NM_001256198, exon 2 of 33)	5' UTR (NM_001256198, exon 2 of 33)	613	NM_172703	230861	Mm.268903	NM_172703	ENSMUSG00000028760	Eif4g3	1500002J22Rik|4930523M17Rik|G1-419-52|eIF4GII|repro8	eukaryotic translation initiation factor 4 gamma, 3	protein-coding
mm_73506.1	chr8	107344436	107344438	+	1	NA	intron (NM_133957, intron 5 of 15)	intron (NM_133957, intron 5 of 15)	50967	NM_133957	54446	Mm.390057	NM_018823	ENSMUSG00000003847	Nfat5	AI225870|B130038B15Rik|CAG-8|CAG80|NFATL1|OREBP|TonEBP|mKIAA0827|nfatz	nuclear factor of activated T cells 5	protein-coding
mm_30374.1	chr3	152210018	152210028	-	1	NA	promoter-TSS (NM_027287)	promoter-TSS (NM_027287)	60	NM_027287	67035	Mm.46746	NM_025926	ENSMUSG00000028035	Dnajb4	1700029A20Rik|2010306G19Rik|5730460G06Rik	DnaJ heat shock protein family (Hsp40) member B4	protein-coding
mm_3206.1	chr1	135818905	135818981	+	1	NA	5' UTR (NM_133664, exon 1 of 10)	5' UTR (NM_133664, exon 1 of 10)	345	NM_133664	16763	Mm.36726	NM_133664	ENSMUSG00000041782	Lad1	-	ladinin	protein-coding
mm_120901.1	chr14	75955051	75955063	+	1	NA	promoter-TSS (NM_026214)	promoter-TSS (NM_026214)	54	NM_026214	67516	Mm.390712	NM_026214	ENSMUSG00000046523	Kctd4	2210017A09Rik|AU017169	potassium channel tetramerisation domain containing 4	protein-coding
mm_102105.1	chr11	53255632	53255637	-	1	NA	Intergenic	Intergenic	44845	NM_008300	15525	Mm.239865	NM_008300	ENSMUSG00000020361	Hspa4	70kDa|AI317151|APG-2|Hsp110|Hsp70RY|mKIAA4025	heat shock protein 4	protein-coding
mm_21510.1	chr2	163625113	163625126	-	1	NA	3' UTR (NM_012032, exon 10 of 10)	3' UTR (NM_012032, exon 10 of 10)	17907	NM_001305803	76080	Mm.89828	NM_029512	ENSMUSG00000017679	Ttpal	3110080A02Rik|5830472M02Rik	tocopherol (alpha) transfer protein-like	protein-coding
mm_116921.1	chr13	55529341	55529367	-	1	NA	promoter-TSS (NM_013739)	promoter-TSS (NM_013739)	-816	NM_013739	27261	Mm.33910	NM_013739	ENSMUSG00000035711	Dok3	AI450713|Dokl	docking protein 3	protein-coding
mm_112050.1	chr12	111712947	111712958	-	1	NA	promoter-TSS (NM_026511)	promoter-TSS (NM_026511)	1	NM_001324481	70369	Mm.44239	NM_027404	ENSMUSG00000049792	Bag5	1600025G07Rik|4930405J06Rik|Bag-5	BCL2-associated athanogene 5	protein-coding
mm_502.1	chr1	37029348	37029357	+	1	NA	Intergenic	CpG	-89825	NM_018872	56030	Mm.186943	NM_018872	ENSMUSG00000026116	Tmem131	2610524E03Rik|CC28|D1Bwg0491e|Neg|RW1|YR-23|mKIAA0257	transmembrane protein 131	protein-coding
mm_74284.1	chr8	125685612	125685635	+	1	NA	Intergenic	Intergenic	15805	NM_028908	74393	Mm.41709	NM_028908	ENSMUSG00000050930	Map10	4933403G14Rik|AI835009|mKIAA1383	microtubule-associated protein 10	protein-coding
mm_10050.1	chr1	193201138	193201158	-	1	NA	intron (NM_153137, intron 1 of 15)	intron (NM_153137, intron 1 of 15)	398	NM_153137	215243	Mm.261259	NM_153137	ENSMUSG00000037318	Traf3ip3	6030423D04Rik|AI115021|T3jam	TRAF3 interacting protein 3	protein-coding
mm_86614.1	chr10	13965259	13965279	+	1	NA	Intergenic	CpG	-1110	NM_010437	15273	Mm.42157	NM_010437	ENSMUSG00000015501	Hivep2	Gm20114|MIBP1|Schnurri-2|Shn-2	human immunodeficiency virus type I enhancer binding protein 2	protein-coding
mm_130871.1	chr15	102224494	102224503	-	1	NA	intron (NM_013566, intron 3 of 14)	intron (NM_013566, intron 3 of 14)	7437	NM_013566	16421	Mm.58	NM_013566	ENSMUSG00000001281	Itgb7	Ly69	integrin beta 7	protein-coding
mm_43019.1	chr5	123907563	123907571	+	1	NA	intron (NM_026603, intron 1 of 7)	intron (NM_026603, intron 1 of 7)	292	NM_026603	68184	Mm.28549	NM_026603	ENSMUSG00000023106	Denr	1500003K04Rik	density-regulated protein	protein-coding
mm_92437.1	chr10	77201198	77201214	-	1	NA	Intergenic	Intergenic	-34676	NM_009929	12822	Mm.4352	NM_009929	ENSMUSG00000001435	Col18a1	-	collagen, type XVIII, alpha 1	protein-coding
mm_68677.1	chr7	118984039	118984069	-	1	NA	exon (NM_001195774, exon 2 of 4)	exon (NM_001195774, exon 2 of 4)	11157	NM_022420	64297	Mm.103439	NM_022420	ENSMUSG00000008734	Gprc5b	AW125761|Raig2	G protein-coupled receptor, family C, group 5, member B	protein-coding
mm_29318.1	chr3	108017432	108017441	-	1	NA	intron (NM_010358, intron 1 of 7)	intron (NM_010358, intron 1 of 7)	537	NM_010358	14862	Mm.37199	NM_010358	ENSMUSG00000058135	Gstm1	Gstb-1|Gstb1	glutathione S-transferase, mu 1	protein-coding
mm_23306.1	chr3	52736459	52736462	+	1	NA	Intergenic	MTEb|LTR|ERVL-MaLR	-3264	NR_038079	329639	Mm.131245	NR_038079	ENSMUSG00000102785	Gm2447	100039832|A530017F20	predicted gene 2447	ncRNA
mm_4318.1	chr1	171849829	171849845	+	1	NA	intron (NM_001289470, intron 2 of 8)	intron (NM_001289470, intron 2 of 8)	10140	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_8756.1	chr1	160351865	160351934	-	1	NA	promoter-TSS (NM_001038621)	promoter-TSS (NM_001038621)	-328	NM_001038621	29809	Mm.25833	NM_013862	ENSMUSG00000026721	Rabgap1l	5830411O09Rik|8430421H08Rik|9630005B12Rik|AW049894|HHL|Hh1|mKIAA0471	RAB GTPase activating protein 1-like	protein-coding
mm_108368.1	chr12	80816688	80816696	+	1	NA	intron (NM_001242419, intron 1 of 6)	intron (NM_001242419, intron 1 of 6)	26160	NM_001242419	217684	Mm.341776	NM_178682	ENSMUSG00000021133	Susd6	4933426M11Rik|mKIAA0247	sushi domain containing 6	protein-coding
mm_63013.1	chr7	120982522	120982546	+	1	NA	promoter-TSS (NM_007672)	promoter-TSS (NM_007672)	25	NM_028955	74466	Mm.189707	NM_028955	ENSMUSG00000030877	Mfsd13b	4933427G17Rik	major facilitator superfamily domain containing 13B	protein-coding
mm_113727.1	chr13	43804928	43804935	+	1	NA	Intergenic	MTEa|LTR|ERVL-MaLR	19819	NM_001289915	12522	Mm.57175	NM_009856	ENSMUSG00000015396	Cd83	-	CD83 antigen	protein-coding
mm_143663.1	chr17	79715052	79715103	-	1	NA	promoter-TSS (NM_009994)	promoter-TSS (NM_009994)	-36	NM_009994	13078	Mm.214016	NM_009994	ENSMUSG00000024087	Cyp1b1	CP1B|P4501b1	cytochrome P450, family 1, subfamily b, polypeptide 1	protein-coding
mm_53329.1	chr6	129230596	129230598	+	1	NA	Intergenic	RMER17C-int|LTR|ERVK	7448	NR_040265	76432	Mm.261738	NR_040265	ENSMUSG00000097354	2310001H17Rik	AI646108	RIKEN cDNA 2310001H17 gene	ncRNA
mm_154483.1	chrM	4579	4619	-	1	NA	NA	Intergenic	NA	NA								
mm_52751.1	chr6	120666389	120666424	+	1	NA	promoter-TSS (NM_001128151)	promoter-TSS (NM_001128151)	-15	NM_001128151	330409	Mm.333357	NM_001128151	ENSMUSG00000071226	Cecr2	2610101O16Rik|2810409N01Rik|Gtl4|mKIAA1740	cat eye syndrome chromosome region, candidate 2	protein-coding
mm_55963.1	chr6	85502981	85503034	-	1	NA	promoter-TSS (NM_001289674)	promoter-TSS (NM_001289674)	-13	NM_001289675	330369	Mm.38777	NM_001001160	ENSMUSG00000047013	Fbxo41	9630017H13|D6Ertd538e	F-box protein 41	protein-coding
mm_54116.1	chr6	18030345	18030389	-	1	NA	promoter-TSS (NM_023653)	promoter-TSS (NM_023653)	78	NM_023653	22413	Mm.33653	NM_023653	ENSMUSG00000010797	Wnt2	2610510E18Rik|Int1l1|Irp|Mirp|Wnt-2|Wnt2a	wingless-type MMTV integration site family, member 2	protein-coding
mm_168138.1	chr10	30216004	30216012	+	1	NA	Intergenic	L1_Mus3|LINE|L1	-15468	NM_001109747	66311	Mm.251779	NM_001109747	ENSMUSG00000075266	Cenpw	2610036L11Rik|Cug2	centromere protein W	protein-coding
mm_110465.1	chr12	51802626	51802652	-	1	NA	exon (NM_144788, exon 5 of 43)	exon (NM_144788, exon 5 of 43)	26897	NM_144788	207304	Mm.249391	NM_144788	ENSMUSG00000035247	Hectd1	A630086P08Rik|AI844876|b2b327Clo|opm	HECT domain containing 1	protein-coding
mm_92923.1	chr10	84440624	84440630	-	1	NA	promoter-TSS (NM_001004363)	promoter-TSS (NM_001004363)	-156	NM_001004363	77976	Mm.25874	NM_001004363	ENSMUSG00000020032	Nuak1	AU014801|AW494241|B230104P22Rik|Omphk1	NUAK family, SNF1-like kinase, 1	protein-coding
mm_63312.1	chr7	126862631	126862684	+	1	NA	exon (NM_172746, exon 2 of 7)	exon (NM_172746, exon 2 of 7)	685	NM_172746	233876	Mm.363427	NM_172746	ENSMUSG00000042606	Hirip3	B130036O03|C86302	HIRA interacting protein 3	protein-coding
mm_131770.1	chr16	22894249	22894271	+	1	NA	intron (NR_075099, intron 1 of 5)	intron (NR_075099, intron 1 of 5)	126	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_131865.1	chr16	23146581	23146621	+	1	NA	promoter-TSS (NM_009605)	promoter-TSS (NM_009605)	65	NM_009605	11450	Mm.3969	NM_009605	ENSMUSG00000022878	Adipoq	30kDa|APN|Acdc|Acrp30|Ad|GBP28|adipo|apM1	adiponectin, C1Q and collagen domain containing	protein-coding
mm_25161.1	chr3	103056975	103057007	+	1	NA	3' UTR (NM_001310693, exon 18 of 18)	3' UTR (NM_001310693, exon 18 of 18)	-1294	NM_010937	18176	Mm.400954	NM_010937	ENSMUSG00000027852	Nras	AV095280|N-ras	neuroblastoma ras oncogene	protein-coding
mm_22239.1	chr2	174464040	174464050	-	1	NA	promoter-TSS (NM_025983)	promoter-TSS (NM_025983)	56	NM_025983	67126	Mm.20841	NM_025983	ENSMUSG00000016252	Atp5e	2410043G19Rik|ATPE|AV000645	ATP synthase, H+ transporting, mitochondrial F1 complex, epsilon subunit	protein-coding
mm_139994.1	chr17	72921157	72921171	+	1	NA	intron (NM_029999, intron 1 of 2)	intron (NM_029999, intron 1 of 2)	2859	NM_029999	77889	Mm.154109	NM_029999	ENSMUSG00000024063	Lbh	1810009F10Rik|6720416L16Rik	limb-bud and heart	protein-coding
mm_114367.1	chr13	62263614	62263624	+	1	NA	Intergenic	Intergenic	119555	NM_001162910	100041979	Mm.445930	NM_001162910	ENSMUSG00000094942	Gm3604	-	predicted gene 3604	protein-coding
mm_12548.1	chr2	72405253	72405264	+	1	NA	3' UTR (NM_001164791, exon 12 of 12)	3' UTR (NM_001164791, exon 12 of 12)	-70961	NM_025866	66953	Mm.270676	NM_025866	ENSMUSG00000055612	Cdca7	2310021G01Rik|AU044109|JPO1	cell division cycle associated 7	protein-coding
mm_152434.1	chr19	10719419	10719430	-	1	NA	intron (NM_007650, intron 10 of 10)	intron (NM_007650, intron 10 of 10)	19550	NM_007650	12507	Mm.779	NM_007650	ENSMUSG00000024669	Cd5	Ly-1|Ly-12|Ly-A|Lyt-1	CD5 antigen	protein-coding
mm_113981.1	chr13	52180262	52180266	+	1	NA	Intergenic	Intergenic	83523	NR_045061	74050	Mm.84860	NR_045061		4921525O09Rik	-	RIKEN cDNA 4921525O09 gene	ncRNA
mm_111432.1	chr12	91788334	91788343	-	1	NA	Intergenic	MT2A|LTR|ERVL	-1902	NM_175367	108800	Mm.23125	NM_175367	ENSMUSG00000020961	Ston2	4933401N24Rik|AI425999|AW544599	stonin 2	protein-coding
mm_146433.1	chr18	84877815	84877833	+	1	NA	intron (NM_025797, intron 3 of 4)	intron (NM_025797, intron 3 of 4)	26410	NM_025797	109672	Mm.31018	NM_025797	ENSMUSG00000024646	Cyb5a	0610009N12Rik|Cyb5	cytochrome b5 type A (microsomal)	protein-coding
mm_28349.1	chr3	89458755	89458774	-	1	NA	promoter-TSS (NM_026784)	promoter-TSS (NM_026784)	-354	NM_026784	68603	Mm.34242	NM_026784	ENSMUSG00000027952	Pmvk	1110011E12Rik|2900002L22Rik|AV001327|PMK|PMKA|PMKASE	phosphomevalonate kinase	protein-coding
mm_56017.1	chr6	86526165	86526187	-	1	NA	promoter-TSS (NM_011865)	promoter-TSS (NM_011865)	-11	NM_011865	23983	Mm.274146	NM_011865	ENSMUSG00000051695	Pcbp1	WBP17|[a]CP-1|alphaCP-1|hnRNP E1	poly(rC) binding protein 1	protein-coding
mm_144851.1	chr18	36638575	36638585	+	1	NA	exon (NM_175375, exon 22 of 34)	exon (NM_175375, exon 22 of 34)	-25480	NM_201256	108112	Mm.24790	NM_201256	ENSMUSG00000090264	Eif4ebp3	4e-bp3	eukaryotic translation initiation factor 4E binding protein 3	protein-coding
mm_98118.1	chr11	87127053	87127105	+	1	NA	promoter-TSS (NM_197987)	promoter-TSS (NM_197987)	4	NM_197987	68729	Mm.17436	NM_197987	ENSMUSG00000018548	Trim37	1110032A10Rik|2810004E07Rik|AI848587|AU043018|MUL|TEF3|mKIAA0898	tripartite motif-containing 37	protein-coding
mm_118874.1	chr14	25857610	25857618	+	1	NA	intron (NM_013469, intron 1 of 14)	intron (NM_013469, intron 1 of 14)	15459	NM_013469	11744	Mm.294083	NM_013469	ENSMUSG00000021866	Anxa11	A830099O17Rik|Anx11	annexin A11	protein-coding
mm_168658.1	chr11	88890316	88890323	-	1	NA	Intergenic	RLTR4_Mm|LTR|ERV1	-15609	NR_045955	73921	Mm.439148	NR_045955	ENSMUSG00000087338	Scpep1os	4930405P13Rik	serine carboxypeptidase 1, opposite strand	ncRNA
mm_87407.1	chr10	45807559	45807569	+	1	NA	promoter-TSS (NR_040624)	promoter-TSS (NR_040624)	-140	NR_040624	320363	Mm.123343	NR_040624	ENSMUSG00000110874	D030045P18Rik	-	RIKEN cDNA D030045P18 gene	ncRNA
mm_61532.1	chr7	79053216	79053234	+	1	NA	promoter-TSS (NM_007424)	promoter-TSS (NM_007424)	98	NR_132432	102633600	Mm.382916	NR_132432	ENSMUSG00000097441	Gm26633	-	predicted gene, 26633	ncRNA
mm_115799.1	chr13	19356177	19356182	-	1	NA	Intergenic	Intergenic	39634	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_76135.1	chr8	81014788	81014795	-	1	NA	5' UTR (NM_027554, exon 1 of 10)	5' UTR (NM_027554, exon 1 of 10)	115	NM_027554	74841	Mm.246018	NM_027554	ENSMUSG00000038250	Usp38	4631402N15Rik|4833420O05Rik|AA536967|AU044701|AW544820|mKIAA1891	ubiquitin specific peptidase 38	protein-coding
mm_48715.1	chr5	147307234	147307256	-	1	NA	promoter-TSS (NM_007673)	promoter-TSS (NM_007673)	4	NM_007673	12591	Mm.20358	NM_007673	ENSMUSG00000029646	Cdx2	Cdx-2	caudal type homeobox 2	protein-coding
mm_171504.1	chr4	146270359	146270363	+	1	NA	promoter-TSS (NM_001083918).2	promoter-TSS (NM_001083918).2	-24	NM_001083918	666532	Mm.392861	NM_001083918	ENSMUSG00000067916	Zfp991	Gm13139|OTTMUSG00000010657	zinc finger protein 991	protein-coding
mm_152768.1	chr19	20727534	20727568	-	1	NA	promoter-TSS (NM_011921)	promoter-TSS (NM_011921)	5	NM_011921	26358	Mm.14609	NM_011921	ENSMUSG00000024747	Aldh1a7	AI987940|Ahd2-like|Aldh-pb|Aldh1a4|Aldhpb	aldehyde dehydrogenase family 1, subfamily A7	protein-coding
mm_38216.1	chr4	135971895	135971908	-	1	NA	intron (NM_011942, intron 1 of 9)	intron (NM_011942, intron 1 of 9)	693	NM_011942	26394	Mm.34302	NM_011942	ENSMUSG00000028670	Lypla2	LysoII	lysophospholipase 2	protein-coding
mm_95296.1	chr11	46056166	46056175	+	1	NA	exon (NM_009616, exon 1 of 23)	exon (NM_009616, exon 1 of 23)	186	NM_001291891	11492	Mm.89940	NM_009616	ENSMUSG00000011256	Adam19	AL024287|MADDAM|MTLNB|Mltnb	a disintegrin and metallopeptidase domain 19 (meltrin beta)	protein-coding
mm_63953.1	chr7	139894988	139895048	+	1	NA	5' UTR (NM_177261, exon 1 of 31)	5' UTR (NM_177261, exon 1 of 31)	322	NM_177261	76484	Mm.44442	NM_177261	ENSMUSG00000066129	Kndc1	2410012C07Rik|B830014K08Rik|VKIND|very-kind	kinase non-catalytic C-lobe domain (KIND) containing 1	protein-coding
mm_47501.1	chr5	124034596	124034607	-	1	NA	Intergenic	Intergenic	-2341	NM_177876	330192	Mm.4079	NM_177876	ENSMUSG00000066278	Vps37b	2300007F24Rik|AI415429|BC026744	vacuolar protein sorting 37B	protein-coding
mm_133170.1	chr16	72027508	72027526	+	1	NA	Intergenic	Intergenic	206810	NR_131116	319533	Mm.373754	NR_131115		8030451O07Rik	-	RIKEN cDNA 8030451O07 gene	ncRNA
mm_25776.1	chr3	126596962	126596986	+	1	NA	promoter-TSS (NM_001293663)	promoter-TSS (NM_001293663)	23	NM_023813	108058	Mm.255822	NM_023813	ENSMUSG00000053819	Camk2d	2810011D23Rik|8030469K03Rik|CaMK II|[d]-CaMKII	calcium/calmodulin-dependent protein kinase II, delta	protein-coding
mm_42487.1	chr5	115471982	115472003	+	1	NA	intron (NM_011107, intron 2 of 3)	intron (NM_011107, intron 2 of 3)	5726	NM_011107	18778	Mm.20190	NM_011107	ENSMUSG00000029522	Pla2g1b	Pla2a|sPLA2IB	phospholipase A2, group IB, pancreas	protein-coding
mm_33249.1	chr4	127126035	127126081	+	1	NA	promoter-TSS (NM_001099319)	promoter-TSS (NM_001099319)	15	NM_001099319	100039968	Mm.392655	NM_001099319	ENSMUSG00000070737	Tmem35b	Gm12942|OTTMUSG00000009332|Zmym6nb	transmembrane protein 35B	protein-coding
mm_147117.1	chr18	35740068	35740074	-	1	NA	intron (NM_028261, intron 1 of 7)	intron (NM_028261, intron 1 of 7)	483	NM_001289592	72512	Mm.45995	NM_028261	ENSMUSG00000024349	Tmem173	2610307O08Rik|ERIS|MPYS|Mita|STING	transmembrane protein 173	protein-coding
mm_38569.1	chr4	141790630	141790698	-	1	NA	promoter-TSS (NM_172338)	promoter-TSS (NM_172338)	-20	NM_172338	214063	Mm.39102	NM_172338	ENSMUSG00000040697	Dnajc16	2900037O03Rik|4732437J24Rik|D030060M24|mKIAA0962	DnaJ heat shock protein family (Hsp40) member C16	protein-coding
mm_145493.1	chr18	60390182	60390190	+	1	NA	exon (NM_001146275, exon 3 of 3)	exon (NM_001146275, exon 3 of 3)	14157	NM_001146275	60440	Mm.261140	NM_021792	ENSMUSG00000054072	Iigp1	2900074L10Rik|AI046432|AW111922|Ifgga1|Iigp|Irga6	interferon inducible GTPase 1	protein-coding
mm_12867.1	chr2	83812740	83812751	+	1	NA	promoter-TSS (NM_175514)	promoter-TSS (NM_175514)	17	NM_175514	241520	Mm.330351	NM_175514	ENSMUSG00000048388	Fam171b	D430039N05Rik	family with sequence similarity 171, member B	protein-coding
mm_10481.1	chr2	14739220	14739242	+	1	NA	intron (NM_023116, intron 2 of 13)	intron (NM_023116, intron 2 of 13)	18589	NR_028497	625342	Mm.484784	NR_028497		Gm13315	OTTMUSG00000011384	lactate dehydrogenase A pseudogene	pseudo
mm_169006.1	chr13	104916655	104916659	-	1	NA	Intergenic	LTRIS2|LTR|ERV1	-52764	NM_029984	77803	Mm.159995	NM_029984	ENSMUSG00000042655	Fam159b	A930021C24Rik	family with sequence similarity 159, member B	protein-coding
mm_100142.1	chr11	115992942	115992990	+	1	NA	intron (NM_001005608, intron 23 of 39)	intron (NM_001005608, intron 23 of 39)	18241	NM_133663	192897	Mm.213873	NM_133663	ENSMUSG00000020758	Itgb4	AA407042|C230078O20|CD104	integrin beta 4	protein-coding
mm_106554.1	chr11	120617860	120617881	-	1	NA	promoter-TSS (NM_024229)	promoter-TSS (NM_024229)	20	NM_024229	68671	Mm.21439	NM_024229	ENSMUSG00000025137	Pcyt2	1110033E03Rik|ET	phosphate cytidylyltransferase 2, ethanolamine	protein-coding
mm_120610.1	chr14	70205172	70205180	+	1	NA	promoter-TSS (NM_001271408)	promoter-TSS (NM_001271408)	-553	NM_001271408	20410	Mm.5068	NM_011366	ENSMUSG00000022091	Sorbs3	SCAM-1|SH3P3|Sh3d4|vinexin-g	sorbin and SH3 domain containing 3	protein-coding
mm_62189.1	chr7	97579561	97579609	+	1	NA	promoter-TSS (NM_183251)	promoter-TSS (NM_183251)	-88	NM_001177947	66273	Mm.41583	NM_183251	ENSMUSG00000035642	Aamdc	1810020D17Rik|1810037D19Rik|LI2	adipogenesis associated Mth938 domain containing	protein-coding
mm_23162.1	chr3	40708860	40708906	+	1	NA	promoter-TSS (NM_178386)	promoter-TSS (NM_178386)	12	NM_178386	73333	Mm.78691	NM_178386	ENSMUSG00000069041	Slc25a31	1700034J06Rik|Ant4|Sfec	solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 31	protein-coding
mm_94977.1	chr11	31672023	31672050	+	1	NA	promoter-TSS (NM_001024919)	promoter-TSS (NM_001024919)	-174	NM_001024919	69556	Mm.34183	NM_001024919	ENSMUSG00000044502	Bod1	2310022M17Rik|BOD2.1|Fam44b	biorientation of chromosomes in cell division 1	protein-coding
mm_2901.1	chr1	131962942	131962969	+	1	NA	promoter-TSS (NM_001177628)	promoter-TSS (NM_001177628)	40	NM_001177628	212980	Mm.200307	NM_145977	ENSMUSG00000026435	Slc45a3	2210413P12Rik|AU023994|AU043764|IPCA-6|PRST|Pcanap6	solute carrier family 45, member 3	protein-coding
mm_43781.1	chr5	142367779	142367813	+	1	NA	Intergenic	CpG	-33701	NM_199068	17425	Mm.24214	NM_010812	ENSMUSG00000056493	Foxk1	A630048H08Rik|AI463295|ENSMUSG00000075577|Gm10868|Mnf	forkhead box K1	protein-coding
mm_161525.1	chr15	100870596	100870596	+	1	NA	promoter-TSS (NM_001077499)	promoter-TSS (NM_001077499)	-49	NM_001077499	20273	Mm.385012	NM_011323	ENSMUSG00000023033	Scn8a	AI853486|C630029C19Rik|NaCh6|Nav1.6|dmu|med|mnd-2|mnd2|nmf2|nmf335|nmf58|nur14|seal	sodium channel, voltage-gated, type VIII, alpha	protein-coding
mm_75769.1	chr8	69978306	69978309	-	1	NA	intron (NM_145596, intron 1 of 12)	B1F1|SINE|Alu	-3924	NM_001113346	234366	Mm.270044	NM_145596	ENSMUSG00000036180	Gatad2a	1110066C11Rik|BC031407|C80248	GATA zinc finger domain containing 2A	protein-coding
mm_108500.1	chr12	83947522	83947552	+	1	NA	Intergenic	Intergenic	-3071	NM_023633	71952	Mm.251483	NM_023633	ENSMUSG00000046791	2410016O06Rik	MAPJD|NO66	RIKEN cDNA 2410016O06 gene	protein-coding
mm_150772.1	chr19	44294159	44294168	+	1	NA	5' UTR (NM_009128, exon 1 of 6)	5' UTR (NM_009128, exon 1 of 6)	487	NM_009128	20250	Mm.487021	NM_009128	ENSMUSG00000025203	Scd2	Mir5114|Scd-2|mir-5114|swty	stearoyl-Coenzyme A desaturase 2	protein-coding
mm_94251.1	chr11	3330833	3330843	+	1	NA	5' UTR (NM_178149, exon 1 of 6)	5' UTR (NM_178149, exon 1 of 6)	107	NM_178149	216505	Mm.390323	NM_178149	ENSMUSG00000034614	Pik3ip1	1500004A08Rik|5830455E04Rik|Crkd|Hgfl	phosphoinositide-3-kinase interacting protein 1	protein-coding
mm_162697.1	chr10	20175306	20175310	-	1	NA	intron (NM_001198635, intron 1 of 17)	intron (NM_001198635, intron 1 of 17)	26388	NM_001198635	17761	Mm.20928	NM_008635	ENSMUSG00000019996	Map7	E-MAP-115|MAP-7|Mtap7|R75000|mshi|mste|ste	microtubule-associated protein 7	protein-coding
mm_14202.1	chr2	127221849	127221869	+	1	NA	exon (NM_177214, exon 15 of 45)	exon (NM_177214, exon 15 of 45)	13455	NM_177214	320632	Mm.215860	NM_177214	ENSMUSG00000003660	Snrnp200	A330064G03Rik|Ascc3l1|BC011390|HELIC2|U5-200-KD|U5-200KD	small nuclear ribonucleoprotein 200 (U5)	protein-coding
mm_55478.1	chr6	68910949	68910962	-	1	NA	Intergenic	Intergenic	416219	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_4039.1	chr1	165774477	165774483	+	1	NA	3' UTR (NM_011804, exon 4 of 4)	3' UTR (NM_011804, exon 4 of 4)	10700	NM_011804	433375	Mm.294885	NM_011804	ENSMUSG00000040713	Creg1	AA755314|Creg	cellular repressor of E1A-stimulated genes 1	protein-coding
mm_111924.1	chr12	108882773	108882779	-	1	NA	exon (NM_001164488, exon 3 of 10)	exon (NM_001164488, exon 3 of 10)	10422	NM_001164488	22375	Mm.38433	NM_011710	ENSMUSG00000021266	Wars	TrpRS|WRS	tryptophanyl-tRNA synthetase	protein-coding
mm_55698.1	chr6	72899723	72899811	-	1	NA	promoter-TSS (NM_001347231)	promoter-TSS (NM_001347231)	212	NM_019715	74287	Mm.29194	NM_019715	ENSMUSG00000055239	Kcmf1	1700094M07Rik|Debt91|Pmcf	potassium channel modulatory factor 1	protein-coding
mm_106607.1	chr11	120784211	120784230	-	1	NA	promoter-TSS (NM_145370)	promoter-TSS (NM_145370)	-16	NM_009053	19719	Mm.871	NM_009053	ENSMUSG00000025158	Rfng	-	RFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	protein-coding
mm_147415.1	chr18	46141575	46141599	-	1	NA	Intergenic	MTC-int|LTR|ERVL-MaLR	57231	NM_001170855	28105	Mm.277382	NM_178872	ENSMUSG00000033949	Trim36	D18Wsu100e|haprin	tripartite motif-containing 36	protein-coding
mm_53620.1	chr6	140424155	140424166	+	1	NA	promoter-TSS (NM_144920)	promoter-TSS (NM_144920)	61	NM_144920	109135	Mm.247670	NM_144920	ENSMUSG00000030231	Plekha5	2810431N21Rik|AI428202|AK129423|AMH-Cre|Ayu21-9|Gt(pU21)9Imeg|Pepp2|Tg(AMH-cre)1Flor	pleckstrin homology domain containing, family A member 5	protein-coding
mm_57178.1	chr6	122848371	122848379	-	1	NA	3' UTR (NM_009779, exon 2 of 2)	3' UTR (NM_009779, exon 2 of 2)	7782	NM_009779	12267	Mm.2408	NM_009779	ENSMUSG00000040552	C3ar1	AZ3B|C3AR|HNFAG09	complement component 3a receptor 1	protein-coding
mm_25074.1	chr3	99885449	99885488	+	1	NA	promoter-TSS (NM_028892)	promoter-TSS (NM_028892)	51	NM_028892	74362	Mm.55847	NM_028892	ENSMUSG00000027867	Spag17	4931427F14Rik|PF6|Spag17-ps	sperm associated antigen 17	protein-coding
mm_69342.1	chr7	129769839	129769868	-	1	NA	Intergenic	Intergenic	177990	NM_172255	207425	Mm.229323	NM_172255	ENSMUSG00000042055	Wdr11	2900055P10Rik|AW489876|Brwd2|mKIAA1351	WD repeat domain 11	protein-coding
mm_65748.1	chr7	28547044	28547087	-	1	NA	exon (NM_001081115, exon 1 of 6)	exon (NM_001081115, exon 1 of 6)	189	NM_001081115	233038	Mm.224815	NM_001081115	ENSMUSG00000047586	Nccrp1	1190020J12Rik|Gm163|NCCRP-1	non-specific cytotoxic cell receptor protein 1 homolog (zebrafish)	protein-coding
mm_106569.1	chr11	120648105	120648137	-	1	NA	5' UTR (NM_026751, exon 1 of 1)	5' UTR (NM_026751, exon 1 of 1)	216	NM_026751	68515	Mm.194594	NM_026751	ENSMUSG00000025141	Myadml2	1110012N22Rik	myeloid-associated differentiation marker-like 2	protein-coding
mm_62951.1	chr7	119596766	119596770	+	1	NA	3' UTR (NM_146197, exon 14 of 14)	3' UTR (NM_146197, exon 14 of 14)	-21060	NM_054094	117147	Mm.427560	NM_054094	ENSMUSG00000033533	Acsm1	Acas3|Bucs1|Macs	acyl-CoA synthetase medium-chain family member 1	protein-coding
mm_87284.1	chr10	42274081	42274098	+	1	NA	intron (NM_019740, intron 2 of 3)	intron (NM_019740, intron 2 of 3)	2653	NM_019740	56484	Mm.338613	NM_019740	ENSMUSG00000048756	Foxo3	1110048B16Rik|2010203A17Rik|C76856|FKHRL1|Fkhr2|Foxo3a	forkhead box O3	protein-coding
mm_150588.1	chr19	40661289	40661304	+	1	NA	intron (NM_009848, intron 1 of 9)	intron (NM_009848, intron 1 of 9)	1526	NM_009848	12495	Mm.2824	NM_009848	ENSMUSG00000048120	Entpd1	2610206B08Rik|AA408691|Cd39|NTPDase-1	ectonucleoside triphosphate diphosphohydrolase 1	protein-coding
mm_120275.1	chr14	63129287	63129296	+	1	NA	intron (NM_007798, intron 1 of 9)	intron (NM_007798, intron 1 of 9)	6829	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_11990.1	chr2	55437525	55437535	+	1	NA	exon (NM_001304810, exon 2 of 3)	exon (NM_001304810, exon 2 of 3)	1560	NM_008426	16519	Mm.5127	NM_008426	ENSMUSG00000026824	Kcnj3	GIRK-1|GIRK1|Kcnf3|Kir3.1	potassium inwardly-rectifying channel, subfamily J, member 3	protein-coding
mm_138354.1	chr17	34981848	34981897	+	1	NA	promoter-TSS (NM_001110101)	promoter-TSS (NM_001110101)	18	NM_001204274	27756	Mm.165735	NM_030597	ENSMUSG00000007050	Lsm2	D17H6S56E-2|D17H6S56E2|Dmapl|Dmpkap|G7b|Sm-X5|SmX5|snRNP	LSM2 homolog, U6 small nuclear RNA and mRNA degradation associated	protein-coding
mm_135684.1	chr16	52424578	52424581	-	1	NA	intron (NM_009655, intron 1 of 15)	intron (NM_009655, intron 1 of 15)	28502	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_74796.1	chr8	22398484	22398497	-	1	NA	promoter-TSS (NR_045473)	promoter-TSS (NR_045473)	131	NM_181325	18408	Mm.200907	NM_181325	ENSMUSG00000031482	Slc25a15	D630044L02Rik|Ornt1	solute carrier family 25 (mitochondrial carrier ornithine transporter), member 15	protein-coding
mm_160002.1	chr6	121838534	121838534	+	1	NA	promoter-TSS (NM_008645)	promoter-TSS (NM_008645)	-7	NM_008645	17836	Mm.1311	NM_008645	ENSMUSG00000059908	Mug1	-	murinoglobulin 1	protein-coding
mm_93136.1	chr10	92162754	92162765	-	1	NA	intron (NR_028262, intron 2 of 12)	intron (NR_028262, intron 2 of 12)	2419	NR_028262	110333	Mm.429764	NR_028262		Rmst	100041799|AI853140|C230053E11Rik|D930049J19Rik|Dmt2|Gm3515|M2|Ncrms	rhabdomyosarcoma 2 associated transcript (non-coding RNA)	ncRNA
mm_84027.1	chr9	57761939	57761956	-	1	NA	intron (NM_007713, intron 1 of 12)	intron (NM_007713, intron 1 of 12)	3913	NM_007713	102414	Mm.25720	NM_007713	ENSMUSG00000032316	Clk3	AI256811	CDC-like kinase 3	protein-coding
mm_72337.1	chr8	79225927	79225939	+	1	NA	intron (NM_026315, intron 2 of 5)	MTEa|LTR|ERVL-MaLR	22650	NM_026315	67687	Mm.178707	NM_026315	ENSMUSG00000031682	1700011L22Rik	-	RIKEN cDNA 1700011L22 gene	protein-coding
mm_81988.1	chr9	121415970	121415985	+	1	NA	intron (NM_175114, intron 2 of 15)	intron (NM_175114, intron 2 of 15)	49019	NM_175114	67095	Mm.491112	NM_175114	ENSMUSG00000032536	Trak1	2310001H13Rik|AI413908|AI467545|hyrt|mKIAA1042	trafficking protein, kinesin binding 1	protein-coding
mm_46911.1	chr5	114380449	114380454	-	1	NA	promoter-TSS (NM_001159941)	promoter-TSS (NM_001159941)	54	NM_001159941	330171	Mm.238285	NM_026145	ENSMUSG00000001098	Kctd10	AW536343|C87062|mBACURD3	potassium channel tetramerisation domain containing 10	protein-coding
mm_46756.1	chr5	112229068	112229087	-	1	NA	promoter-TSS (NR_033657)	promoter-TSS (NR_033657)	-129	NR_003718	330166	Mm.44854	NR_003718	ENSMUSG00000097767	Miat	3632434I06|A230057G18Rik|Rncr2|gomafu	myocardial infarction associated transcript (non-protein coding)	ncRNA
mm_112944.1	chr13	20999960	21000005	+	1	NA	exon (NM_012054, exon 16 of 21)	exon (NM_012054, exon 16 of 21)	73317	NM_146535	258528	Mm.377554	NM_146535	ENSMUSG00000042869	Olfr1370	MOR256-14	olfactory receptor 1370	protein-coding
mm_22523.1	chr3	7646912	7646921	+	1	NA	Intergenic	Intergenic	-33156	NM_001313888	16196	Mm.3825	NM_008371	ENSMUSG00000040329	Il7	A630026I06Rik|Il-7|hlb368	interleukin 7	protein-coding
mm_144116.1	chr18	4396776	4396781	+	1	NA	3' UTR (NM_026157, exon 9 of 9)	3' UTR (NM_026157, exon 9 of 9)	21186	NM_026157	67440	Mm.49826	NM_026157	ENSMUSG00000024234	Mtpap	0610027A18Rik|AW551379|Papd1	mitochondrial poly(A) polymerase	protein-coding
mm_93413.1	chr10	108498303	108498311	-	1	NA	3' UTR (NM_001252342, exon 11 of 11)	3' UTR (NM_001252342, exon 11 of 11)	166118	NM_054056	114774	Mm.391419	NM_054056	ENSMUSG00000035873	Pawr	2310001G03Rik|PAR4|Par-4	PRKC, apoptosis, WT1, regulator	protein-coding
mm_172890.1	chr9	5548625	5548639	-	1	NA	Intergenic	ERVB4_2-LTR_MM|LTR|ERVK	203156	NM_009808	12364	Mm.42163	NM_009808	ENSMUSG00000025887	Casp12	-	caspase 12	protein-coding
mm_24370.1	chr3	90104155	90104165	+	1	NA	promoter-TSS (NM_029937)	promoter-TSS (NM_029937)	28	NM_029937	77595	Mm.159949	NM_029937	ENSMUSG00000027939	Nup210l	4930548O11Rik|R26-EGFP|Tg(Gt(ROSA)26Sor-EGFP)130910Eps	nucleoporin 210-like	protein-coding
mm_17315.1	chr2	26440969	26440971	-	1	NA	exon (NM_153125, exon 2 of 30)	exon (NM_153125, exon 2 of 30)	4246	NM_153125	227648	Mm.206371	NM_153125	ENSMUSG00000026924	Sec16a	AU024582|C230052J16Rik	SEC16 homolog A, endoplasmic reticulum export factor	protein-coding
mm_141965.1	chr17	35121353	35121368	-	1	NA	promoter-TSS (NM_009975)	promoter-TSS (NM_009975)	-68	NM_009975	13001	Mm.378901	NM_009975	ENSMUSG00000024387	Csnk2b	CK II beta	casein kinase 2, beta polypeptide	protein-coding
mm_40493.1	chr5	57717481	57717525	+	1	NA	promoter-TSS (NM_001310606)	promoter-TSS (NM_001310606)	416	NR_015588	319216	Mm.332387	NR_015588	ENSMUSG00000097216	4932441J04Rik	-	RIKEN cDNA 4932441J04 gene	ncRNA
mm_162579.1	chr1	177796688	177796690	-	1	NA	promoter-TSS (NM_007422)	promoter-TSS (NM_007422)	-180	NM_007422	11566	Mm.338021	NM_007422	ENSMUSG00000015961	Adss	AI314886|AS|Adss2	adenylosuccinate synthetase, non muscle	protein-coding
mm_82474.1	chr9	16502171	16502181	-	1	NA	Intergenic	CpG	-123945	NM_001080814	270120	Mm.195010	NM_001080814	ENSMUSG00000074505	Fat3	9430076A06Rik|D430038H04Rik|Gm1132|Gm510|MFAT3F	FAT atypical cadherin 3	protein-coding
mm_2556.1	chr1	111833268	111833275	+	1	NA	Intergenic	Intergenic	31647	NM_001081316	319901	Mm.103468	NM_001081316	ENSMUSG00000038702	Dsel	9330132E09Rik|DS-epi2	dermatan sulfate epimerase-like	protein-coding
mm_153234.1	chr19	35858380	35858381	-	1	NA	Intergenic	Intergenic	198980	NM_001347442	15566	Mm.254266	NM_008315	ENSMUSG00000024798	Htr7	5-HT7	5-hydroxytryptamine (serotonin) receptor 7	protein-coding
mm_17105.1	chr2	24048858	24048868	-	1	NA	intron (NM_080462, intron 1 of 6)	intron (NM_080462, intron 1 of 6)	516	NM_080462	140483	Mm.33120	NM_080462	ENSMUSG00000026986	Hnmt	1500031F01Rik|AI788969	histamine N-methyltransferase	protein-coding
mm_112310.1	chr12	114851672	114851678	-	1	NA	Intergenic	Intergenic	-337981	NR_106063	102465664		NR_106063	ENSMUSG00000098357	Mir7094-2	Gm27508|mmu-mir-7094-2	microRNA 7094-2	ncRNA
mm_115877.1	chr13	21753456	21753470	-	1	NA	promoter-TSS (NM_178201)	promoter-TSS (NM_178201)	449	NM_178183	319169	Mm.370338	NM_178183	ENSMUSG00000063021	Hist1h2ak	-	histone cluster 1, H2ak	protein-coding
mm_163245.1	chr11	106066767	106066787	+	1	NA	intron (NM_027346, intron 1 of 4)	intron (NM_027346, intron 1 of 4)	670	NM_027346	70207	Mm.343857	NM_027346	ENSMUSG00000001983	Taco1	2310066I18Rik|Ccdc44	translational activator of mitochondrially encoded cytochrome c oxidase I	protein-coding
mm_62372.1	chr7	100640561	100640583	+	1	NA	3' UTR (NM_024287, exon 8 of 8)	3' UTR (NM_024287, exon 8 of 8)	16393	NM_001163187	27276	Mm.491216	NM_013746	ENSMUSG00000030701	Plekhb1	AI315628|PHR1|Phret1|evt-1	pleckstrin homology domain containing, family B (evectins) member 1	protein-coding
mm_59184.1	chr7	24470304	24470305	+	1	NA	intron (NM_011113, intron 3 of 6)	PB1D10|SINE|Alu	7821	NM_011113	18793	Mm.1359	NM_011113	ENSMUSG00000046223	Plaur	Cd87|u-PAR|uPAR	plasminogen activator, urokinase receptor	protein-coding
mm_156763.1	chrX	160529704	160529716	+	1	NA	intron (NM_172783, intron 4 of 32)	intron (NM_172783, intron 4 of 32)	27276	NM_001177878	110094	Mm.350712	NM_172783	ENSMUSG00000031295	Phka2	6330505C01Rik|D330034O08|Phk	phosphorylase kinase alpha 2	protein-coding
mm_145780.1	chr18	65076033	65076061	+	1	NA	intron (NM_001114386, intron 3 of 30)	intron (NM_001114386, intron 3 of 30)	52520	NM_031881	83814	Mm.98668	NM_031881	ENSMUSG00000024589	Nedd4l	1300012C07Rik|Nedd4-2|Nedd4b	neural precursor cell expressed, developmentally down-regulated gene 4-like	protein-coding
mm_97720.1	chr11	80209903	80209905	+	1	NA	intron (NM_021536, intron 1 of 18)	intron (NM_021536, intron 1 of 18)	849	NM_021536	59040	Mm.489674	NM_021536	ENSMUSG00000017686	Rhot1	2210403N23Rik|AA415293|AF244542|AI834919|Arht1|C430039G08Rik|Miro1	ras homolog family member T1	protein-coding
mm_59776.1	chr7	28835897	28835922	+	1	NA	exon (NM_010707, exon 3 of 9)	exon (NM_010707, exon 3 of 9)	1739	NM_010707	16857	Mm.210336	NM_010707		Lgals6	galectin-6	lectin, galactose binding, soluble 6	protein-coding
mm_124252.1	chr14	101841663	101841667	-	1	NA	intron (NM_001347628, intron 1 of 26)	intron (NM_001347628, intron 1 of 26)	1042	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_162610.1	chr1	183297266	183297305	-	1	NA	promoter-TSS (NM_027861)	promoter-TSS (NM_027861)	225	NM_181732	108909	Mm.290502	NM_145626	ENSMUSG00000042901	Aida	2610208M17Rik|BC004835	axin interactor, dorsalization associated	protein-coding
mm_100623.1	chr11	121702394	121702404	+	1	NA	promoter-TSS (NM_144797)	promoter-TSS (NM_144797)	-28	NM_144797	210029	Mm.153566	NM_144797	ENSMUSG00000039208	Metrnl	9430048M07Rik|BC019776	meteorin, glial cell differentiation regulator-like	protein-coding
mm_21977.1	chr2	167358383	167358395	-	1	NA	Intergenic	RMER5|LTR|ERV1	-9211	NM_019835	56336	Mm.200886	NM_019835	ENSMUSG00000017929	B4galt5	9430078I07Rik|AW049941|AW539721	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 5	protein-coding
mm_101779.1	chr11	45752944	45752976	-	1	NA	Intergenic	Intergenic	-55123	NR_045876	100009664	Mm.415439	NR_045876		F630206G17Rik	-	RIKEN cDNA F630206G17 gene	ncRNA
mm_157450.1	chrX	42149028	42149041	-	1	NA	promoter-TSS (NM_001077712)	promoter-TSS (NM_001077712)	-378	NM_001077712	20843	Mm.290422	NM_021465	ENSMUSG00000025862	Stag2	9230105L23Rik|B230112I07Rik|SA-2|SAP2	stromal antigen 2	protein-coding
mm_44686.1	chr5	30144260	30144308	-	1	NA	exon (NM_178878, exon 5 of 20)	exon (NM_178878, exon 5 of 20)	10696	NM_178878	97212	Mm.200497	NM_178878	ENSMUSG00000025745	Hadha	C77020|Mtpa	hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), alpha subunit	protein-coding
mm_37805.1	chr4	130818690	130818709	-	1	NA	exon (NM_011520, exon 3 of 5)	exon (NM_011520, exon 3 of 5)	26162	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_35819.1	chr4	46991843	46991916	-	1	NA	promoter-TSS (NM_001081141)	promoter-TSS (NM_001081141)	-165	NM_001081141	242425	Mm.101909	NM_001081141	ENSMUSG00000039809	Gabbr2	GABABR2|Gb2|Gm425|Gpr51	gamma-aminobutyric acid (GABA) B receptor, 2	protein-coding
mm_2033.1	chr1	87205800	87205817	+	1	NA	promoter-TSS (NM_009604)	promoter-TSS (NM_009604)	-3	NM_009604	11449	Mm.2810	NM_009604	ENSMUSG00000026253	Chrng	Achr-3|Acrg	cholinergic receptor, nicotinic, gamma polypeptide	protein-coding
mm_116170.1	chr13	30792298	30792304	-	1	NA	Intergenic	Intergenic	43068	NM_013674	16364	Mm.4677	NM_013674	ENSMUSG00000021356	Irf4	AI385587|IRF-4|LSIRF|NF-EM5|Spip	interferon regulatory factor 4	protein-coding
mm_163099.1	chr11	69735274	69735276	-	1	NA	exon (NM_001291068, exon 29 of 29)	exon (NM_001291068, exon 29 of 29)	23358	NM_001291068	20020	Mm.16533	NM_009089	ENSMUSG00000005198	Polr2a	220kDa|Rpb1|Rpo2-1	polymerase (RNA) II (DNA directed) polypeptide A	protein-coding
mm_95737.1	chr11	54691450	54691452	+	1	NA	exon (NM_001252494, exon 27 of 29)	exon (NM_001252494, exon 27 of 29)	95305	NM_001252497	192786	Mm.254404	NM_175258	ENSMUSG00000037533	Rapgef6	A530068K01|AI844632|BB085664|C030018K18Rik|PDZ-GEF2|Pdzgef2|RA-GEF-2|Ragef2|mKIAA4052	Rap guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_160132.1	chr7	30586799	30586799	-	1	NA	exon (NM_001290573, exon 3 of 37)	exon (NM_001290573, exon 3 of 37)	1927	NM_001290573	75410	Mm.168688	NM_029274	ENSMUSG00000006307	Kmt2b	2610014H22Rik|Mll2|Wbp7|mKIAA0304	lysine (K)-specific methyltransferase 2B	protein-coding
mm_129811.1	chr15	82998575	82998610	-	1	NA	3' UTR (NM_028728, exon 6 of 6)	3' UTR (NM_028728, exon 6 of 6)	24546	NM_028728	74039	Mm.32584	NM_028728	ENSMUSG00000058099	Nfam1	4921501M20Rik|Cnaip	Nfat activating molecule with ITAM motif 1	protein-coding
mm_172300.1	chr7	103106056	103106061	+	1	NA	Intergenic	L1Md_T|LINE|L1	8315	NM_147087	259091	Mm.377835	NM_147087	ENSMUSG00000078080	Olfr585	MOR14-4	olfactory receptor 585	protein-coding
mm_78736.1	chr9	41585392	41585398	+	1	NA	intron (NR_015483, intron 1 of 1)	intron (NR_015483, intron 1 of 1)	3469	NR_029822	387236		NR_029822	ENSMUSG00000093354	Mir125b-1	Mirn125b|Mirn125b-1|mir-125b-1	microRNA 125b-1	ncRNA
mm_63097.1	chr7	122377404	122377417	+	1	NA	intron (NM_001316672, intron 2 of 16)	(CAGA)n|Simple_repeat|Simple_repeat	88285	NM_008855	18751	Mm.207496	NM_008855	ENSMUSG00000052889	Prkcb	PKC-B|PKC-Beta|Pkcb|Prkcb1|Prkcb2	protein kinase C, beta	protein-coding
mm_81733.1	chr9	113756392	113756447	+	1	NA	intron (NM_001286599, intron 1 of 10)	SSU-rRNA_Hsa|rRNA|rRNA	14946	NM_001114347	76499	Mm.222272	NM_029633	ENSMUSG00000033392	Clasp2	1500004F14Rik|8030404L10Rik|C77448|CLASP2beta|mKIAA0627	CLIP associating protein 2	protein-coding
mm_95768.1	chr11	54908560	54908604	+	1	NA	exon (NM_008161, exon 3 of 5)	exon (NM_008161, exon 3 of 5)	5728	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_71429.1	chr8	46492858	46492868	+	1	NA	exon (NM_007981, exon 2 of 21)	exon (NM_007981, exon 2 of 21)	1897	NM_001302163	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_4493.1	chr1	173641404	173641420	+	1	NA	intron (NM_175026, intron 4 of 6)	MTD|LTR|ERVL-MaLR	10553	NM_175026	236312	Mm.447	NM_175026	ENSMUSG00000043263	Ifi209	4930422C14|AI447904|Ifix|Pyhin-1|Pyhin1	interferon activated gene 209	protein-coding
mm_16815.1	chr2	11333376	11333398	-	1	NA	Intergenic	Intergenic	-6102	NR_040369	100503147	Mm.91961	NR_040369	ENSMUSG00000086006	Gm13293	OTTMUSG00000011311	predicted gene 13293	ncRNA
mm_120199.1	chr14	61648415	61648430	+	1	NA	intron (NR_028264, intron 1 of 6)	CpG	-16312	NR_029733	387174		NR_029733	ENSMUSG00000093007	Mir15a	Mirn15a|mir-15a|mmu-mir-15a	microRNA 15a	ncRNA
mm_159486.1	chr4	42158092	42158092	+	1	NA	promoter-TSS (NM_001199959)	promoter-TSS (NM_001199959)	0	NM_001199959	100040048	Mm.6660	NM_001199959	ENSMUSG00000096826	Ccl27b	Ctack|ENSMUSG00000066202|Scya27b	chemokine (C-C motif) ligand 27b	protein-coding
mm_19953.1	chr2	117338478	117338488	-	1	NA	intron (NM_011246, intron 1 of 16)	intron (NM_011246, intron 1 of 16)	4394	NM_011246	19419	Mm.42150	NM_011246	ENSMUSG00000027347	Rasgrp1	Rasgrp	RAS guanyl releasing protein 1	protein-coding
mm_34738.1	chr4	152199997	152200039	+	1	NA	intron (NM_001146058, intron 1 of 8)	intron (NM_001146058, intron 1 of 8)	174	NM_001146058	70025	Mm.296191	NM_133348	ENSMUSG00000028937	Acot7	2410041A17Rik|Ach1|Act|Bach|CTE-IIa|Cte-II|Lach1	acyl-CoA thioesterase 7	protein-coding
mm_142248.1	chr17	37483246	37483252	-	1	NA	intron (NM_001347387, intron 1 of 4)	intron (NM_001347387, intron 1 of 4)	280	NM_008204	14990	Mm.329041	NM_008204	ENSMUSG00000016283	H2-M2	H-2M2|Thy19.4	histocompatibility 2, M region locus 2	protein-coding
mm_80904.1	chr9	100597687	100597724	+	1	NA	Intergenic	Intergenic	-26620	NM_001101483	245020	Mm.236289	NM_001101483	ENSMUSG00000070287	Slc35g2	Gm519|Tmem22	solute carrier family 35, member G2	protein-coding
mm_23806.1	chr3	79885153	79885168	+	1	NA	promoter-TSS (NM_133187)	promoter-TSS (NM_133187)	-770	NM_133187	68659	Mm.427274	NM_133187	ENSMUSG00000027955	Fam198b	1110032E23Rik|2210419I08Rik|AV011458|Ened	family with sequence similarity 198, member B	protein-coding
mm_162524.1	chr1	157526066	157526076	+	1	NA	promoter-TSS (NM_001159986)	promoter-TSS (NM_001159986)	-99	NM_001159986	89867	Mm.87114	NM_033354	ENSMUSG00000026589	Sec16b	Lztr2|Rgpr|Rgpr-p117	SEC16 homolog B (S. cerevisiae)	protein-coding
mm_160930.1	chr11	89538535	89538535	-	1	NA	exon (NM_001327810, exon 3 of 20)	exon (NM_001327810, exon 3 of 20)	-119587	NM_172534	382543	Mm.60997	NM_172534	ENSMUSG00000047773	Ankfn1	4932411E22Rik|Gm1175|nmf9	ankyrin-repeat and fibronectin type III domain containing 1	protein-coding
mm_57457.1	chr6	125168987	125169000	-	1	NA	intron (NM_146171, intron 29 of 31)	intron (NM_146171, intron 29 of 31)	-2526	NM_001289726	14433	Mm.304088	NM_008084	ENSMUSG00000057666	Gapdh	Gapd	glyceraldehyde-3-phosphate dehydrogenase	protein-coding
mm_143217.1	chr17	62882843	62882895	-	1	NA	Intergenic	CpG-6536	-1552	NM_010109	13640	Mm.7978	NM_010109	ENSMUSG00000048915	Efna5	AL-1|AV158822|EFL-5|Ephrin-A5|Epl7|LERK-7|RAGS	ephrin A5	protein-coding
mm_103542.1	chr11	77513336	77513348	-	1	NA	promoter-TSS (NM_001024920)	promoter-TSS (NM_001024920)	-69	NM_001024920	216964	Mm.341211	NM_001024920	ENSMUSG00000044328	Trp53i13	2410019G02Rik|Tp53i13	transformation related protein 53 inducible protein 13	protein-coding
mm_125198.1	chr15	32920838	32920848	+	1	NA	5' UTR (NM_008304, exon 1 of 5)	5' UTR (NM_008304, exon 1 of 5)	120	NM_008304	15529	Mm.234266	NM_008304	ENSMUSG00000022261	Sdc2	4833414L08Rik|AA960457|Hspg1|Synd2|syndecan-2	syndecan 2	protein-coding
mm_1909.1	chr1	85904584	85904586	+	1	NA	intron (NM_022417, intron 2 of 5)	B1_Mus1|SINE|Alu	10075	NM_022417	64294	Mm.29870	NM_022417	ENSMUSG00000026223	Itm2c	3110038L02Rik|BRI3|Bricd2c|E25|E25C|ITM3	integral membrane protein 2C	protein-coding
mm_126808.1	chr15	87652040	87652049	+	1	NA	intron (NM_134096, intron 1 of 3)	intron (NM_134096, intron 1 of 3)	26814	NM_134096	106014	Mm.244319	NM_134096	ENSMUSG00000054863	Fam19a5	TAFA5|Tafa-5|Tara-5	family with sequence similarity 19, member A5	protein-coding
mm_73898.1	chr8	119437093	119437133	+	1	NA	promoter-TSS (NM_027950)	promoter-TSS (NM_027950)	-49	NM_027950	71839	Mm.272357	NM_027950	ENSMUSG00000074063	Osgin1	1700012B18Rik|Okl38	oxidative stress induced growth inhibitor 1	protein-coding
mm_4243.1	chr1	171389147	171389157	+	1	NA	TTS (NM_027893)	TTS (NM_027893)	192	NM_001005508	226652	Mm.251048	NM_001005508	ENSMUSG00000048865	Arhgap30	6030405P05Rik|Gm102|mFLJ00267	Rho GTPase activating protein 30	protein-coding
mm_156786.1	chrX	162500379	162500397	+	1	NA	intron (NM_178256, intron 13 of 17)	L1M5|LINE|L1	143270	NM_001290633	194590	Mm.442441	NM_178256	ENSMUSG00000040855	Reps2	POB1	RALBP1 associated Eps domain containing protein 2	protein-coding
mm_164285.1	chr15	103014338	103014368	+	1	NA	promoter-TSS (NR_030526)	promoter-TSS (NR_030526)	345	NM_175730	15424	Mm.103825	NM_175730	ENSMUSG00000022485	Hoxc5	AI181837|Hox-3.4|Hox-6.2	homeobox C5	protein-coding
mm_58706.1	chr7	12965832	12965894	+	1	NA	promoter-TSS (NM_178732)	promoter-TSS (NM_178732)	-1	NM_178732	243834	Mm.133086	NM_178732	ENSMUSG00000004500	Zfp324	A930002M05|D430030K24Rik|ZF5128	zinc finger protein 324	protein-coding
mm_154148.1	chr19	58454436	58454473	-	1	NA	non-coding (NR_104342, exon 2 of 12)	non-coding (NR_104342, exon 2 of 12)	944	NM_001285457	14585	Mm.88367	NM_010279	ENSMUSG00000025089	Gfra1	AU042498	glial cell line derived neurotrophic factor family receptor alpha 1	protein-coding
mm_123217.1	chr14	59441303	59441307	-	1	NA	promoter-TSS (NM_001320721)	promoter-TSS (NM_001320721)	324	NM_026908	69008	Mm.179091	NM_026908	ENSMUSG00000021981	Cab39l	1500031K13Rik|2810425O13Rik|4930520C08Rik|AA589432|MO2L	calcium binding protein 39-like	protein-coding
mm_97956.1	chr11	83711225	83711232	+	1	NA	3' UTR (NM_007969, exon 3 of 3)	3' UTR (NM_007969, exon 3 of 3)	2224	NM_007969	14038	Mm.1650	NM_007969	ENSMUSG00000000983	Wfdc18	Expi|Kal1|WDNM1	WAP four-disulfide core domain 18	protein-coding
mm_115015.1	chr13	98354982	98354997	+	1	NA	exon (NM_008242, exon 1 of 1)	exon (NM_008242, exon 1 of 1)	744	NM_008242	15229	Mm.347441	NM_008242	ENSMUSG00000078302	Foxd1	AI385632|BF-2|FREAC4|Hfh10|Hfhbf2	forkhead box D1	protein-coding
mm_149800.1	chr19	23687386	23687408	+	1	NA	promoter-TSS (NM_028208)	promoter-TSS (NM_028208)	-3	NM_028208	72351	Mm.474795	NM_028208	ENSMUSG00000074925	Ptar1	1700084D09Rik|2010013L17Rik|4930428J16Rik|AI449677	protein prenyltransferase alpha subunit repeat containing 1	protein-coding
mm_29349.1	chr3	108416012	108416050	-	1	NA	promoter-TSS (NM_017392)	promoter-TSS (NM_017392)	-537	NM_001004177	53883	Mm.39728	NM_017392	ENSMUSG00000068740	Celsr2	Adgrc2|EGFL2|Flamingo1|flamingo|mKIAA0279|mfmi1	cadherin, EGF LAG seven-pass G-type receptor 2	protein-coding
mm_97614.1	chr11	78952806	78952826	+	1	NA	exon (NM_010927, exon 22 of 27)	exon (NM_010927, exon 22 of 27)	27525	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_73469.1	chr8	106668813	106668828	+	1	NA	3' UTR (NM_009864, exon 16 of 16)	3' UTR (NM_009864, exon 16 of 16)	-14248	NM_173037	272538	Mm.87151	NM_173037	ENSMUSG00000041949	Tango6	AW413431|E330010G16|Tmco7	transport and golgi organization 6	protein-coding
mm_74971.1	chr8	27043051	27043061	-	1	NA	intron (NM_001039077, intron 1 of 4)	CpG	501	NM_054057	114863	Mm.277501	NM_054057	ENSMUSG00000031485	Prosc	1700024N20Rik|2200002F22Rik	proline synthetase co-transcribed	protein-coding
mm_123171.1	chr14	57398514	57398530	-	1	NA	promoter-TSS (NM_030004)	promoter-TSS (NM_030004)	-39	NM_030004	68631	Mm.25539	NM_030004	ENSMUSG00000021947	Cryl1	1110025H08Rik|A230106J09Rik|C85932|gul3dh	crystallin, lambda 1	protein-coding
mm_2177.1	chr1	88453378	88453402	+	1	NA	Intergenic	L2b|LINE|L2	46380	NM_029269	75396	Mm.173058	NM_029269	ENSMUSG00000026295	Spp2	0610038O04Rik|pp-24|spp24	secreted phosphoprotein 2	protein-coding
mm_48635.1	chr5	145167011	145167028	-	1	NA	promoter-TSS (NM_178576)	promoter-TSS (NM_178576)	85	NM_133735	71799	Mm.277413	NM_133735	ENSMUSG00000029624	Ptcd1	1110069M14Rik	pentatricopeptide repeat domain 1	protein-coding
mm_134488.1	chr16	18629865	18629951	-	1	NA	promoter-TSS (NM_213614)	promoter-TSS (NM_213614)	30	NM_213614	18951	Mm.20365	NM_213614	ENSMUSG00000072214	Sept5	Cdcrel-1|Cdcrel1|Pnutl1	septin 5	protein-coding
mm_91338.1	chr10	26078855	26078865	-	1	NA	non-coding (NR_028030, exon 1 of 1)	non-coding (NR_028030, exon 1 of 1)	192	NM_029881	77220	Mm.266260	NM_029881	ENSMUSG00000049420	Tmem200a	C030003D03Rik	transmembrane protein 200A	protein-coding
mm_2971.1	chr1	133068482	133068494	+	1	NA	intron (NM_001099276, intron 2 of 32)	intron (NM_001099276, intron 2 of 32)	22476	NM_001099276	240752	Mm.387308	NM_001099276	ENSMUSG00000026447	Pik3c2b	C330011J12Rik|Gm199|PI3K-C2beta|PI3KC2beta	phosphoinositide-3-kinase, class 2, beta polypeptide	protein-coding
mm_8979.1	chr1	165634452	165634576	-	1	NA	promoter-TSS (NM_001083897)	promoter-TSS (NM_001083897)	27	NM_001001880	68481	Mm.46438	NM_001001880	ENSMUSG00000026566	Mpzl1	1110007A10Rik|PZR	myelin protein zero-like 1	protein-coding
mm_149567.1	chr19	12801361	12801374	+	1	NA	intron (NM_134152, intron 1 of 8)	intron (NM_134152, intron 1 of 8)	2758	NM_134152	107321	Mm.313136	NM_134152	ENSMUSG00000024696	Lpxn	4933402K05Rik|A530083L21Rik|AV278559|LDPL	leupaxin	protein-coding
mm_150206.1	chr19	32787068	32787071	+	1	NA	intron (NM_008960, intron 2 of 8)	MTC|LTR|ERVL-MaLR	29492	NM_008960	19211	Mm.245395	NM_008960	ENSMUSG00000013663	Pten	2310035O07Rik|A130070J02Rik|AI463227|B430203M17Rik|MMAC1|TEP1	phosphatase and tensin homolog	protein-coding
mm_130543.1	chr15	98953588	98953591	-	1	NA	promoter-TSS (NM_011653)	promoter-TSS (NM_011653)	-88	NM_011653	22142	Mm.405359	NM_011653	ENSMUSG00000072235	Tuba1a	Tuba-1|Tuba1	tubulin, alpha 1A	protein-coding
mm_101738.1	chr11	43375958	43375982	-	1	NA	Intergenic	B3A|SINE|B2	-1509	NR_029558	387164		NR_029558	ENSMUSG00000065601	Mir146	Mirn146|miR-146a|mmu-mir-146	microRNA 146	ncRNA
mm_75987.1	chr8	72361452	72361462	-	1	NA	intron (NM_007944, intron 21 of 23)	MTC|LTR|ERVL-MaLR	42395	NM_008452	16598	Mm.26938	NM_008452	ENSMUSG00000055148	Klf2	Lklf	Kruppel-like factor 2 (lung)	protein-coding
mm_16237.1	chr2	173156331	173156359	+	1	NA	intron (NM_011044, intron 6 of 9)	RSINE1|SINE|B4	3272	NM_011044	18534	Mm.266867	NM_011044	ENSMUSG00000027513	Pck1	AI265463|PEPCK|Pck-1	phosphoenolpyruvate carboxykinase 1, cytosolic	protein-coding
mm_125433.1	chr15	44457446	44457486	+	1	NA	promoter-TSS (NM_138674)	promoter-TSS (NM_138674)	-87	NM_138674	192190	Mm.211494	NM_138674	ENSMUSG00000038725	Pkhd1l1	AB055648|PKHDL1	polycystic kidney and hepatic disease 1-like 1	protein-coding
mm_26272.1	chr3	142504347	142504375	+	1	NA	exon (NM_153564, exon 6 of 11)	exon (NM_153564, exon 6 of 11)	7427	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_117578.1	chr13	86054215	86054227	-	1	NA	Intergenic	ERVB7_2B-LTR_MM|LTR|ERVK	-7426	NM_007749	12867	Mm.378898	NM_007749	ENSMUSG00000017778	Cox7c	COXVIIc|Cox7c1	cytochrome c oxidase subunit VIIc	protein-coding
mm_169808.1	chr16	18533308	18533308	-	1	NA	intron (NR_104347, intron 2 of 8)	SSU-rRNA_Hsa|rRNA|rRNA	34437	NR_104347	13972	Mm.236139	NM_023120	ENSMUSG00000000884	Gnb1l	ESTM55|Gm16314|Me49f07|OTTMUSG00000033458|Wdr14|Wdvcf	guanine nucleotide binding protein (G protein), beta polypeptide 1-like	protein-coding
mm_47171.1	chr5	120744227	120744243	-	1	NA	intron (NM_001347448, intron 3 of 11)	L1M5|LINE|L1	5613	NM_145227	246728	Mm.260926	NM_145227	ENSMUSG00000032690	Oas2	Oasl11	2'-5' oligoadenylate synthetase 2	protein-coding
mm_97809.1	chr11	82961836	82961849	+	1	NA	3' UTR (NM_183201, exon 6 of 6)	3' UTR (NM_183201, exon 6 of 6)	-1161	NR_045932	76392	Mm.295205	NR_045932	ENSMUSG00000086327	Slfn5os	1700003F17Rik	schlafen 5, opposite strand	ncRNA
mm_9935.1	chr1	190144208	190144210	-	1	NA	intron (NM_008937, intron 4 of 4)	RMER12C|LTR|ERVK	26471	NM_008937	19130	Mm.132579	NM_008937	ENSMUSG00000010175	Prox1	A230003G05Rik	prospero homeobox 1	protein-coding
mm_130525.1	chr15	98892189	98892192	-	1	NA	3' UTR (NM_007857, exon 3 of 3)	3' UTR (NM_007857, exon 3 of 3)	6350	NM_007857	13363	Mm.324688	NM_007857	ENSMUSG00000023000	Dhh	C78960	desert hedgehog	protein-coding
mm_168498.1	chr11	52358666	52358666	-	1	NA	Intergenic	Intergenic	-2196	NM_011694	22333	Mm.3555	NM_011694	ENSMUSG00000020402	Vdac1	AL033343|Vdac5|mVDAC1|mVDAC5	voltage-dependent anion channel 1	protein-coding
mm_99165.1	chr11	100713918	100713938	+	1	NA	promoter-TSS (NM_029307)	promoter-TSS (NM_029307)	78	NM_029307	75482	Mm.46175	NM_029307	ENSMUSG00000017832	Hspb9	1700007H20Rik	heat shock protein, alpha-crystallin-related, B9	protein-coding
mm_106084.1	chr11	116175246	116175261	-	1	NA	exon (NM_015729, exon 10 of 14)	exon (NM_015729, exon 10 of 14)	-7075	NM_172571	217335	Mm.35241	NM_172571	ENSMUSG00000020776	Fbf1	1110033G01Rik|5930413D20|mKIAA1863	Fas (TNFRSF6) binding factor 1	protein-coding
mm_11973.1	chr2	54854675	54854712	+	1	NA	exon (NM_173030, exon 5 of 13)	exon (NM_173030, exon 5 of 13)	418306	NM_173030	271786	Mm.330227	NM_173030	ENSMUSG00000060988	Galnt13	A230002A12|A230020F20|BB182356	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13	protein-coding
mm_94598.1	chr11	11821826	11821847	+	1	NA	intron (NM_001190448, intron 12 of 14)	RMER10B|LTR|ERVL	-12874	NM_001163360	60530	Mm.236114	NM_021891	ENSMUSG00000035455	Fignl1	-	fidgetin-like 1	protein-coding
mm_26884.1	chr3	17789608	17789651	-	1	NA	promoter-TSS (NR_033490)	promoter-TSS (NR_033490)	-292	NR_033490	70441	Mm.458192	NR_033490	ENSMUSG00000100252	Mir124-2hg	100040120|2610100L16Rik|6430547I21Rik|A930005K07Rik|AW125202|Gm2612	Mir124-2 host gene (non-protein coding)	ncRNA
mm_31299.1	chr4	45998956	45998966	+	1	NA	intron (NM_146142, intron 6 of 16)	intron (NM_146142, intron 6 of 16)	26664	NM_146142	100121	Mm.275413	NM_146142	ENSMUSG00000035517	Tdrd7	5730495N10Rik|AI447470|PCTAIRE2BP	tudor domain containing 7	protein-coding
mm_134369.1	chr16	17121772	17121795	-	1	NA	intron (NM_183287, intron 2 of 7)	intron (NM_183287, intron 2 of 7)	2359	NR_029659	723816		NR_029659	ENSMUSG00000065572	Mir130b	Mirn130b|mir-130b	microRNA 130b	ncRNA
mm_130241.1	chr15	96615412	96615424	-	1	NA	intron (NM_001166458, intron 3 of 15)	Lx5c|LINE|L1	26544	NM_134086	105727	Mm.103568	NM_134086	ENSMUSG00000023169	Slc38a1	AA408026|AA409865|AL022800|AU015942|NAT2	solute carrier family 38, member 1	protein-coding
mm_41523.1	chr5	92555036	92555070	+	1	NA	Intergenic	Intergenic	-16484	NM_001033478	384198	Mm.76757	NM_001033478	ENSMUSG00000057068	Fam47e	C730043O17|Gm1381	family with sequence similarity 47, member E	protein-coding
mm_157903.1	chrX	77853475	77853504	-	1	NA	promoter-TSS (NM_017471)	promoter-TSS (NM_017471)	11	NM_017471	54192	Mm.8034	NM_017471	ENSMUSG00000000003	Pbsn	PB|Prbs	probasin	protein-coding
mm_119560.1	chr14	48760864	48760866	+	1	NA	intron (NR_029384, intron 4 of 4)	RCHARR1|DNA|hAT-Charlie	91577	NR_029384	606497	Mm.165199	NR_029384	ENSMUSG00000098682	Otx2os1	-	orthodenticle homeobox 2 opposite strand 1	ncRNA
mm_29283.1	chr3	107674179	107674202	-	1	NA	intron (NM_145542, intron 3 of 16)	intron (NM_145542, intron 3 of 16)	22358	NM_145542	229709	Mm.220328	NM_145542	ENSMUSG00000027893	Ahcyl1	1110034F20Rik|AA409031|AA414901|Ahcy-rs3|DCAL|Irbit	S-adenosylhomocysteine hydrolase-like 1	protein-coding
mm_113156.1	chr13	24802858	24802867	+	1	NA	5' UTR (NM_024473, exon 1 of 5)	5' UTR (NM_024473, exon 1 of 5)	1205	NM_024473	79555	Mm.266668	NM_024473	ENSMUSG00000019132	BC005537	8030460C05Rik|C78201	cDNA sequence BC005537	protein-coding
mm_13275.1	chr2	101550385	101550395	+	1	NA	Intergenic	Intergenic	-74358	NM_009020	19374	Mm.4988	NM_009020	ENSMUSG00000032864	Rag2	Rag-2	recombination activating gene 2	protein-coding
mm_145225.1	chr18	50075811	50075816	+	1	NA	intron (NM_134131, intron 1 of 1)	intron (NM_134131, intron 1 of 1)	22531	NM_134131	106869	Mm.27740	NM_134131	ENSMUSG00000062210	Tnfaip8	AA987150|E130304C20Rik|ENSMUSG00000073567|Gg2-1|Gm10539|Nded|Ssc-2|Tipe	tumor necrosis factor, alpha-induced protein 8	protein-coding
mm_8933.1	chr1	164307182	164307192	-	1	NA	promoter-TSS (NM_001293313)	promoter-TSS (NM_001293313)	297	NM_001160209	66352	Mm.33285	NM_025505	ENSMUSG00000026577	Blzf1	1700030G05Rik|Blzf1l|Golgin-45|Jem-1	basic leucine zipper nuclear factor 1	protein-coding
mm_85809.1	chr9	110387586	110387596	-	1	NA	exon (NM_001081043, exon 20 of 25)	exon (NM_001081043, exon 20 of 25)	20619	NM_001081043	104831	Mm.335477	NM_001081043	ENSMUSG00000036057	Ptpn23	AI462446|PTP-TD14	protein tyrosine phosphatase, non-receptor type 23	protein-coding
mm_19204.1	chr2	84501405	84501417	-	1	NA	non-coding (NR_046046, exon 3 of 3)	non-coding (NR_046046, exon 3 of 3)	5462	NR_046046	672763	Mm.491046	NR_046046	ENSMUSG00000087362	Gm13710	OTTMUSG00000013441	predicted gene 13710	ncRNA
mm_122059.1	chr14	30353469	30353535	-	1	NA	promoter-TSS (NM_001083616)	promoter-TSS (NM_001083616)	-16	NM_001083616	12289	Mm.9772	NM_028981	ENSMUSG00000015968	Cacna1d	8430418G19Rik|C79217|Cach3|Cacn4|Cacnl1a2|Cav1.3|Cchl1a|Cchl1a2|D-LTCC	calcium channel, voltage-dependent, L type, alpha 1D subunit	protein-coding
mm_52744.1	chr6	120472952	120472977	+	1	NA	exon (NM_008359, exon 3 of 13)	exon (NM_008359, exon 3 of 13)	9767	NM_008359	16172	Mm.4481	NM_008359	ENSMUSG00000002897	Il17ra	AW538159|Cdw217|Il17r|VDw217	interleukin 17 receptor A	protein-coding
mm_18574.1	chr2	65567466	65567495	-	1	NA	promoter-TSS (NM_018732)	promoter-TSS (NM_018732)	12	NM_018732	20269	Mm.330256	NM_018732	ENSMUSG00000057182	Scn3a	Gm1000|Nav1.3	sodium channel, voltage-gated, type III, alpha	protein-coding
mm_56983.1	chr6	120364345	120364374	-	1	NA	promoter-TSS (NR_045558)	promoter-TSS (NR_045558)	10	NR_045558	67200	Mm.45767	NM_026028	ENSMUSG00000030177	Ccdc77	2400002C23Rik|2700091N06Rik|AV168274	coiled-coil domain containing 77	protein-coding
mm_95034.1	chr11	32058890	32058900	+	1	NA	3' UTR (NM_008741, exon 5 of 5)	3' UTR (NM_008741, exon 5 of 5)	42333	NR_130637	104692	Mm.414035	NR_130637	ENSMUSG00000086386	Gm12108	BB052462|OTTMUSG00000005365	predicted gene 12108	ncRNA
mm_150241.1	chr19	34085297	34085307	+	1	NA	TTS (NM_027340)	TTS (NM_027340)	-15641	NM_023903	78753	Mm.195937	NM_023903	ENSMUSG00000056078	Lipm	4632427C23Rik|AW227514|Lipl3	lipase, family member M	protein-coding
mm_19321.1	chr2	90566756	90566767	-	1	NA	intron (NM_008982, intron 1 of 23)	intron (NM_008982, intron 1 of 23)	13886	NM_008982	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_89317.1	chr10	87930688	87930697	+	1	NA	exon (NM_010512, exon 5 of 5)	exon (NM_010512, exon 5 of 5)	-35979	NR_000040	22172	Mm.391420	NR_000040		Tyms-ps	-	thymidylate synthase, pseudogene	pseudo
mm_2612.1	chr1	120479337	120479368	+	1	NA	exon (NM_010766, exon 13 of 17)	exon (NM_010766, exon 13 of 17)	25732	NM_010766	17167	Mm.1856	NM_010766	ENSMUSG00000026390	Marco	AI323439|Ly112|Scara2	macrophage receptor with collagenous structure	protein-coding
mm_79763.1	chr9	62677849	62677863	+	1	NA	promoter-TSS (NM_176922)	promoter-TSS (NM_176922)	1	NM_176922	319480	Mm.34883	NM_176922	ENSMUSG00000032243	Itga11	4732459H24Rik	integrin alpha 11	protein-coding
mm_30926.1	chr4	32759112	32759123	+	1	NA	exon (NM_001081392, exon 88 of 102)	exon (NM_001081392, exon 88 of 102)	-41142	NM_175364	108755	Mm.1182	NM_175364	ENSMUSG00000045854	Lyrm2	2610208E05Rik	LYR motif containing 2	protein-coding
mm_135641.1	chr16	52356138	52356186	-	1	NA	intron (NM_009655, intron 1 of 15)	B4|SINE|B4	96919	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_13426.1	chr2	104596338	104596340	+	1	NA	intron (NM_001037326, intron 1 of 1)	AT_rich|Low_complexity|Low_complexity	5855	NM_001037326	228410	Mm.259876	NM_145529	ENSMUSG00000027176	Cstf3	4732468G05Rik|C79532|CstF-77	cleavage stimulation factor, 3' pre-RNA, subunit 3	protein-coding
mm_106034.1	chr11	116077757	116077797	-	1	NA	TTS (NM_016852)	TTS (NM_016852)	184	NM_001009573	70450	Mm.259460	NM_001009573	ENSMUSG00000057948	Unc13d	2610108D09Rik|Jinx|Munc13-4|mFLJ00067	unc-13 homolog D (C. elegans)	protein-coding
mm_96054.1	chr11	59566155	59566177	+	1	NA	exon (NM_145827, exon 10 of 10)	exon (NM_145827, exon 10 of 10)	5572	NM_001011789	257962	Mm.377316	NM_001011789	ENSMUSG00000059610	Olfr222	MOR256-45P	olfactory receptor 222	protein-coding
mm_64442.1	chr7	142653734	142653744	+	1	NA	3' UTR (NM_010514, exon 4 of 4)	3' UTR (NM_010514, exon 4 of 4)	1257	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_96394.1	chr11	67250314	67250338	+	1	NA	exon (NM_010855, exon 20 of 40)	exon (NM_010855, exon 20 of 40)	12514	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_134898.1	chr16	29998242	29998269	-	1	NA	Intergenic	B3A|SINE|B2	-10412	NR_033631	100043102	Mm.30797	NR_033631	ENSMUSG00000097184	4632428C04Rik	Gm4231	RIKEN cDNA 4632428C04 gene	ncRNA
mm_16017.1	chr2	167451012	167451030	+	1	NA	intron (NM_001304540, intron 7 of 16)	intron (NM_001304540, intron 7 of 16)	29311	NM_001304542	77031	Mm.278924	NM_148929	ENSMUSG00000039463	Slc9a8	1200006P13Rik|6430709P13Rik|AI182282|NHE-8|NHE8	solute carrier family 9 (sodium/hydrogen exchanger), member 8	protein-coding
mm_18339.1	chr2	58139332	58139336	-	1	NA	intron (NM_139200, intron 6 of 7)	intron (NM_139200, intron 6 of 7)	20788	NM_139200	227929	Mm.273905	NM_139200	ENSMUSG00000026832	Cytip	A130053M09Rik|AI462064|C80816|Cbp|Cybr|Pscdbp	cytohesin 1 interacting protein	protein-coding
mm_83188.1	chr9	41004600	41004632	-	1	NA	promoter-TSS (NM_019465)	promoter-TSS (NM_019465)	12	NM_001281954	54698	Mm.42791	NM_019465	ENSMUSG00000032021	Crtam	-	cytotoxic and regulatory T cell molecule	protein-coding
mm_142772.1	chr17	49676481	49676486	-	1	NA	intron (NM_177052, intron 5 of 22)	intron (NM_177052, intron 5 of 22)	61311	NM_177052	319991	Mm.441340	NM_177052	ENSMUSG00000023999	Kif6	D130004B10Rik|D130084M03Rik	kinesin family member 6	protein-coding
mm_118343.1	chr13	114458940	114458960	-	1	NA	promoter-TSS (NM_008046)	promoter-TSS (NM_008046)	1	NM_001301373	14313	Mm.4913	NM_008046	ENSMUSG00000021765	Fst	AL033346|FS	follistatin	protein-coding
mm_160624.1	chr9	98842739	98842739	+	1	NA	exon (NM_001134660, exon 1 of 1)	exon (NM_001134660, exon 1 of 1)	152	NM_001134660	623166	Mm.390211	NM_001134660	ENSMUSG00000091080	Prr23a1	EG623166|Gm6400|Prr23a	proline rich 23A, member 1	protein-coding
mm_112525.1	chr13	9276640	9276661	+	1	NA	5' UTR (NM_001081426, exon 1 of 37)	5' UTR (NM_001081426, exon 1 of 37)	125	NM_001081426	208440	Mm.217326	NM_172459	ENSMUSG00000048264	Dip2c	2900024P20Rik|9630044M06|mKIAA0934	disco interacting protein 2 homolog C	protein-coding
mm_140850.1	chr17	23677478	23677484	-	1	NA	promoter-TSS (NM_013749)	promoter-TSS (NM_013749)	-32	NM_013749	27279	Mm.28518	NM_013749	ENSMUSG00000023905	Tnfrsf12a	AI255180|C87282|Fn14|HPIP|TWEAK-R|TweakR	tumor necrosis factor receptor superfamily, member 12a	protein-coding
mm_69868.1	chr7	141455834	141455853	-	1	NA	intron (NM_001163689, intron 1 of 8)	intron (NM_001163689, intron 1 of 8)	655	NM_001163689	66853	Mm.29998	NM_025802	ENSMUSG00000025509	Pnpla2	0610039C21Rik|1110001C14Rik|Atgl|TTS-2.2	patatin-like phospholipase domain containing 2	protein-coding
mm_148146.1	chr18	77065073	77065119	-	1	NA	promoter-TSS (NM_001164168)	promoter-TSS (NM_001164168)	-112	NM_008602	17344	Mm.6370	NM_008602	ENSMUSG00000025423	Pias2	6330408K17Rik|AI462206|ARIP3|AU018068|Dib|Miz1|PIASxalpha|PIASxb|PIASxbeta|SIZ2	protein inhibitor of activated STAT 2	protein-coding
mm_119406.1	chr14	44988193	44988203	+	1	NA	promoter-TSS (NM_008964)	promoter-TSS (NM_008964)	87	NM_008964	19217	Mm.4630	NM_008964	ENSMUSG00000037759	Ptger2	EP2|Ptgerep2	prostaglandin E receptor 2 (subtype EP2)	protein-coding
mm_150829.1	chr19	44746690	44746700	+	1	NA	Intergenic	CpG	-10699	NM_011037	18504	Mm.192158	NM_011037	ENSMUSG00000004231	Pax2	Opdc|Pax-2	paired box 2	protein-coding
mm_172393.1	chr7	14087418	14087422	-	1	NA	intron (NM_001101586, intron 3 of 5)	L1Md_T|LINE|L1	35573	NM_001101586	629203	Mm.482066	NM_001101586	ENSMUSG00000074375	Sult2a3	EG629203|Gm6955	sulfotransferase family 2A, dehydroepiandrosterone (DHEA)-preferring, member 3	protein-coding
mm_142587.1	chr17	46727357	46727372	-	1	NA	exon (NM_010321, exon 2 of 6)	exon (NM_010321, exon 2 of 6)	1801	NM_010321	14711	Mm.29395	NM_010321	ENSMUSG00000002769	Gnmt	-	glycine N-methyltransferase	protein-coding
mm_44818.1	chr5	33652340	33652356	-	1	NA	TTS (NM_026698)	TTS (NM_026698)	226	NM_001289725	20492	Mm.4172	NM_009193	ENSMUSG00000004642	Slbp	-	stem-loop binding protein	protein-coding
mm_90337.1	chr10	127084657	127084673	+	1	NA	intron (NM_001033263, intron 5 of 18)	(CA)n|Simple_repeat|Simple_repeat	5758	NM_001033263	216439	Mm.336761	NM_001033263	ENSMUSG00000025422	Agap2	AGAP-2|Centg1|PIKE|cnt-g1|mKIAA0167	ArfGAP with GTPase domain, ankyrin repeat and PH domain 2	protein-coding
mm_71256.1	chr8	40917545	40917571	+	1	NA	3' UTR (NM_001044740, exon 12 of 12)	3' UTR (NM_001044740, exon 12 of 12)	-8675	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_126544.1	chr15	82028090	82028094	+	1	NA	intron (NM_010247, intron 7 of 12)	intron (NM_010247, intron 7 of 12)	11723	NM_010247	14375	Mm.288809	NM_010247	ENSMUSG00000022471	Xrcc6	70kDa|G22p1|Ku70	X-ray repair complementing defective repair in Chinese hamster cells 6	protein-coding
mm_51340.1	chr6	72439035	72439065	+	1	NA	non-coding (NR_046011, exon 1 of 1)	non-coding (NR_046011, exon 1 of 1)	367	NR_046011	78108	Mm.440743	NR_046011	ENSMUSG00000108591	Particl	4930414L22Rik|AI449819	promoter of Mat2a antisense radiation induced circulating long non-coding RNA	ncRNA
mm_21540.1	chr2	163736267	163736278	-	1	NA	intron (NM_007398, intron 2 of 11)	intron (NM_007398, intron 2 of 11)	13967	NM_007398	11486	Mm.388	NM_007398	ENSMUSG00000017697	Ada	-	adenosine deaminase	protein-coding
mm_27986.1	chr3	81975860	81975861	-	1	NA	promoter-TSS (NM_019911)	promoter-TSS (NM_019911)	-132	NM_019911	56720	Mm.258622	NM_019911	ENSMUSG00000028011	Tdo2	AA407491|TDO|TO|chky	tryptophan 2,3-dioxygenase	protein-coding
mm_152066.1	chr19	6532373	6532391	-	1	NA	3' UTR (NM_020253, exon 23 of 23)	3' UTR (NM_020253, exon 23 of 23)	10688	NM_009203	20521	Mm.391146	NM_009203	ENSMUSG00000061742	Slc22a12	AI987855|OAT4L|Rst|Slc22al2|URAT1	solute carrier family 22 (organic anion/cation transporter), member 12	protein-coding
mm_115635.1	chr13	12228392	12228409	-	1	NA	intron (NM_001081128, intron 14 of 32)	intron (NM_001081128, intron 14 of 32)	29713	NM_001081128	238505	Mm.40335	NM_001081128	ENSMUSG00000021311	Mtr	AI894170|D830038K18Rik|MS	5-methyltetrahydrofolate-homocysteine methyltransferase	protein-coding
mm_99290.1	chr11	101323034	101323064	+	1	NA	3' UTR (NM_011192, exon 11 of 11)	3' UTR (NM_011192, exon 11 of 11)	-2014	NM_178932	237940	Mm.302277	NM_178932	ENSMUSG00000078651	Aoc2	RAO	amine oxidase, copper containing 2 (retina-specific)	protein-coding
mm_55763.1	chr6	78466513	78466528	-	1	NA	exon (NM_011260, exon 6 of 6)	exon (NM_011260, exon 6 of 6)	2354	NM_011260	19695	Mm.252385	NM_011260	ENSMUSG00000030017	Reg3g	AI449515|REG-3-gamma|reg III-gamma	regenerating islet-derived 3 gamma	protein-coding
mm_61211.1	chr7	64205890	64205892	+	1	NA	promoter-TSS (NR_029805)	promoter-TSS (NR_029805)	85	NR_029805	387207		NR_029805	ENSMUSG00000065585	Mir211	Mirn211|mir-211|mmu-mir-211	microRNA 211	ncRNA
mm_59788.1	chr7	28931716	28931717	+	1	NA	intron (NM_021895, intron 1 of 20)	intron (NM_021895, intron 1 of 20)	30564	NM_021895	60595	Mm.81144	NM_021895	ENSMUSG00000054808	Actn4	C77391	actinin alpha 4	protein-coding
mm_34398.1	chr4	145209920	145209930	+	1	NA	Intergenic	Intergenic	-14920	NM_001276465	230895	Mm.240310	NM_001033190	ENSMUSG00000020220	Vps13d	-	vacuolar protein sorting 13D	protein-coding
mm_152345.1	chr19	9984586	9984619	-	1	NA	TTS (NM_011913)	TTS (NM_011913)	1956	NM_010239	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
mm_43346.1	chr5	135132332	135132343	+	1	NA	exon (NM_021455, exon 9 of 17)	exon (NM_021455, exon 9 of 17)	-17374	NM_013763	27368	Mm.36746	NM_013763	ENSMUSG00000005374	Tbl2	C76179|WS-bTRP	transducin (beta)-like 2	protein-coding
mm_25642.1	chr3	121291852	121291862	+	1	NA	promoter-TSS (NM_024178)	promoter-TSS (NM_024178)	40	NM_024178	66789	Mm.269881	NM_024178	ENSMUSG00000039887	Alg14	5430428G01Rik|AI854024	asparagine-linked glycosylation 14	protein-coding
mm_62694.1	chr7	110122254	110122295	+	1	NA	5' UTR (NM_009516, exon 1 of 11)	5' UTR (NM_009516, exon 1 of 11)	215	NM_009516	22390	Mm.287173	NM_009516	ENSMUSG00000031016	Wee1	Wee1A	WEE 1 homolog 1 (S. pombe)	protein-coding
mm_51569.1	chr6	83716647	83716649	+	1	NA	intron (NM_011912, intron 1 of 2)	intron (NM_011912, intron 1 of 2)	-4447	NR_002871	574519	Mm.487605	NR_002871	ENSMUSG00000085794	Vax2os	Vas2os|Vax2os1|Vax2os2	ventral anterior homeobox 2, opposite strand	ncRNA
mm_170698.1	chr2	134763641	134763655	-	1	NA	Intergenic	Intergenic	-22516	NM_019677	18795	Mm.330607	NM_019677	ENSMUSG00000051177	Plcb1	3110043I21Rik|AI132408|Plcb|mKIAA0581	phospholipase C, beta 1	protein-coding
mm_29716.1	chr3	124300738	124300746	-	1	NA	Intergenic	RMER17B|LTR|ERVK	-20295	NM_146140	229801	Mm.165810	NM_146140	ENSMUSG00000044528	Tram1l1	A830091N21Rik	translocation associated membrane protein 1-like 1	protein-coding
mm_164234.1	chr15	91633121	91633149	-	1	NA	Intergenic	Intergenic	-40089	NM_025730	66725	Mm.37558	NM_025730	ENSMUSG00000036273	Lrrk2	4921513O20Rik|9330188B09Rik|AW561911|D630001M17Rik|Gm927|cI-46	leucine-rich repeat kinase 2	protein-coding
mm_93762.1	chr10	120193781	120193803	-	1	NA	intron (NM_028679, intron 1 of 11)	intron (NM_028679, intron 1 of 11)	7745	NM_028679	73914	Mm.146194	NM_028679	ENSMUSG00000020227	Irak3	4833428C18Rik|AI563835|IRAK-M	interleukin-1 receptor-associated kinase 3	protein-coding
mm_172379.1	chr7	130264015	130264024	-	1	NA	intron (NM_001347638, intron 1 of 15)	intron (NM_001347638, intron 1 of 15)	2789	NM_010207	14183	Mm.16340	NM_010207	ENSMUSG00000030849	Fgfr2	AU043015|AW556123|Bek|Fgfr-2|Fgfr-7|Fgfr7|KGFR|KGFRTr|svs	fibroblast growth factor receptor 2	protein-coding
mm_34404.1	chr4	145224848	145224874	+	1	NA	exon (NM_011610, exon 5 of 10)	exon (NM_011610, exon 5 of 10)	22009	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_147454.1	chr18	46574320	46574328	-	1	NA	5' UTR (NM_173394, exon 1 of 3)	5' UTR (NM_173394, exon 1 of 3)	209	NM_173394	225471	Mm.149280	NM_173394	ENSMUSG00000056130	Ticam2	B430113A10|TICAM-2|TRAM|Tirp|Trif	toll-like receptor adaptor molecule 2	protein-coding
mm_144798.1	chr18	36106181	36106222	+	1	NA	promoter-TSS (NR_015571)	promoter-TSS (NR_015571)	-2	NR_015571	74966	Mm.379238	NM_030089		4930471G03Rik	1700007N01Rik	RIKEN cDNA 4930471G03 gene	ncRNA
mm_77146.1	chr8	111562525	111562552	-	1	NA	intron (NM_001168623, intron 1 of 4)	MIRb|SINE|MIR	24195	NM_001168623	170737	Mm.271578	NM_133206	ENSMUSG00000033545	Znrf1	B830022L21Rik|Rnf42|Zrfp1|nin283	zinc and ring finger 1	protein-coding
mm_41531.1	chr5	92684838	92684841	+	1	NA	intron (NM_015756, intron 1 of 10)	intron (NM_015756, intron 1 of 10)	1404	NM_015756	27428	Mm.46014	NM_015756	ENSMUSG00000029381	Shroom3	AL022960|D5Ertd287e|Shrm|Shrm3	shroom family member 3	protein-coding
mm_17978.1	chr2	37703068	37703094	-	1	NA	Intergenic	CpG	-55796	NM_009261	20744	Mm.237095	NM_009261	ENSMUSG00000026915	Strbp	6430510M02Rik|AI852513|C230082I21Rik|C86322|Spnr	spermatid perinuclear RNA binding protein	protein-coding
mm_132788.1	chr16	45016714	45016733	+	1	NA	Intergenic	Intergenic	73045	NM_001128132	74603	Mm.297337	NM_027578	ENSMUSG00000036172	Cd200r3	4733401I18Rik|4833409J19Rik|AI505817|BB106877|mCD200RLb	CD200 receptor 3	protein-coding
mm_172737.1	chr8	78490011	78490018	+	1	NA	Intergenic	BGLII|LTR|ERVK	18914	NM_001252089	19656	Mm.24718	NM_009033	ENSMUSG00000037070	Rbmxl1	Hnrpg|Rbmx|Rbmxrt	RNA binding motif protein, X-linked like-1	protein-coding
mm_86121.1	chr9	116170396	116170400	-	1	NA	intron (NM_009371, intron 1 of 7)	URR1A|DNA|hAT-Charlie	4965	NM_029575	21813	Mm.172346	NM_009371	ENSMUSG00000032440	Tgfbr2	1110020H15Rik|AU042018|DNIIR|RIIDN|TBR-II|TbetaR-II|TbetaRII	transforming growth factor, beta receptor II	protein-coding
mm_2897.1	chr1	131932046	131932052	+	1	NA	3' UTR (NM_001145804, exon 7 of 7)	3' UTR (NM_001145804, exon 7 of 7)	21591	NM_001145804	98415	Mm.246869	NM_175294	ENSMUSG00000026434	Nucks1	2700010L10Rik|8430423A01Rik|AI647518|C78391|Nucks	nuclear casein kinase and cyclin-dependent kinase substrate 1	protein-coding
mm_12669.1	chr2	75715045	75715049	+	1	NA	Intergenic	Intergenic	-10384	NM_010902	18024	Mm.1025	NM_010902	ENSMUSG00000015839	Nfe2l2	Nrf2	nuclear factor, erythroid derived 2, like 2	protein-coding
mm_96947.1	chr11	70540912	70540918	+	1	NA	exon (NM_001302476, exon 2 of 10)	exon (NM_001302476, exon 2 of 10)	643	NM_001302476	18806	Mm.260177	NM_008876	ENSMUSG00000020828	Pld2	PLD1C	phospholipase D2	protein-coding
mm_151797.1	chr19	5423801	5423821	-	1	NA	TTS (NR_015545)	TTS (NR_015545)	1168	NM_024176	66556	Mm.275446	NM_024176	ENSMUSG00000024914	Drap1	2310074H19Rik|NC2-alpha	Dr1 associated protein 1 (negative cofactor 2 alpha)	protein-coding
mm_22873.1	chr3	29154219	29154226	+	1	NA	intron (NM_001167748, intron 4 of 12)	intron (NM_001167748, intron 4 of 12)	71645	NM_029412	75740	Mm.330948	NM_029412	ENSMUSG00000063600	Egfem1	6130401L20Rik|Efcab11	EGF-like and EMI domain containing 1	protein-coding
mm_4657.1	chr1	180356427	180356431	+	1	NA	intron (NM_001081175, intron 2 of 7)	intron (NM_001081175, intron 2 of 7)	-25880	NR_003623	277333	Mm.389223	NM_199472		Gm5069	EG277333	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_88528.1	chr10	78298311	78298317	+	1	NA	intron (NM_053014, intron 2 of 9)	intron (NM_053014, intron 2 of 9)	41893	NR_106119	102465765		NR_106119	ENSMUSG00000098885	Mir7659	Gm27433|mmu-mir-7659	microRNA 7659	ncRNA
mm_103997.1	chr11	84870189	84870230	-	1	NA	promoter-TSS (NR_131197)	promoter-TSS (NR_131197)	204	NR_131201	102635561	Mm.341797	NR_131197		Ggnbp2os	-	gametogenetin binding protein 2, opposite strand	ncRNA
mm_58977.1	chr7	19052313	19052348	+	1	NA	intron (NM_026605, intron 22 of 26)	intron (NM_026605, intron 22 of 26)	-2357	NM_031255	83434	Mm.84435	NM_031255	ENSMUSG00000040866	Rsph6a	RSP4|Rshl1	radial spoke head 6 homolog A (Chlamydomonas)	protein-coding
mm_170295.1	chr18	3040298	3040302	+	1	NA	Intergenic	IAPLTR4|LTR|ERVK	83112	NM_001167539	100312476	Mm.480293	NM_001167539	ENSMUSG00000091539	Vmn1r238	-	vomeronasal 1 receptor, 238	protein-coding
mm_40189.1	chr5	36465159	36465196	+	1	NA	promoter-TSS (NM_024478)	promoter-TSS (NM_024478)	-8	NM_024478	17713	Mm.21535	NM_024478	ENSMUSG00000029198	Grpel1	AA408748|mt-GrpE#1|mt-Grpel1	GrpE-like 1, mitochondrial	protein-coding
mm_5574.1	chr1	39478735	39478760	-	1	NA	promoter-TSS (NM_018775)	promoter-TSS (NM_018775)	0	NM_018775	54610	Mm.387293	NM_018775	ENSMUSG00000003134	Tbc1d8	AD3|HBLP1|VRP	TBC1 domain family, member 8	protein-coding
mm_83488.1	chr9	45945091	45945123	-	1	NA	intron (NM_172257, intron 15 of 25)	intron (NM_172257, intron 15 of 25)	-5517	NR_106055	102465659		NR_106055	ENSMUSG00000098327	Mir7087	Gm27273|mmu-mir-7087	microRNA 7087	ncRNA
mm_69891.1	chr7	141637363	141637369	-	1	NA	intron (NM_001330001, intron 31 of 33)	intron (NM_001330001, intron 31 of 33)	16665	NR_106030	102466798		NR_106030	ENSMUSG00000098759	Mir7063	Gm27654|mmu-mir-7063	microRNA 7063	ncRNA
mm_133780.1	chr16	94969300	94969304	+	1	NA	intron (NM_001025584, intron 1 of 4)	intron (NM_001025584, intron 1 of 4)	28394	NM_001025584	16522	Mm.328720	NM_010606	ENSMUSG00000043301	Kcnj6	BIR1|GIRK2|KATP2|KCNJ7|Kir3.2|weaver|wv	potassium inwardly-rectifying channel, subfamily J, member 6	protein-coding
mm_128754.1	chr15	64921611	64921688	-	1	NA	5' UTR (NM_009623, exon 1 of 18)	5' UTR (NM_009623, exon 1 of 18)	647	NM_001331075	11514	Mm.1425	NM_009623	ENSMUSG00000022376	Adcy8	AC8|AW060868	adenylate cyclase 8	protein-coding
mm_62911.1	chr7	117486708	117486754	+	1	NA	intron (NM_175645, intron 2 of 11)	intron (NM_175645, intron 2 of 11)	105752	NM_175645	233781	Mm.461427	NM_175645	ENSMUSG00000030657	Xylt1	8030490L12	xylosyltransferase 1	protein-coding
mm_169031.1	chr13	120304672	120304683	-	1	NA	intron (NM_001037925, intron 3 of 4)	intron (NM_001037925, intron 3 of 4)	4285	NM_001037925	625360	Mm.327506	NM_001037925	ENSMUSG00000094796	BC147527	-	cDNA sequence BC147527	protein-coding
mm_2627.1	chr1	121035278	121035286	+	1	NA	Intergenic	L1M5|LINE|L1	-52123	NR_038008	98452	Mm.131017	NR_038008	ENSMUSG00000097881	Celrr	AI848258|B230209K01Rik|Celr|Gm818	cerebellum expressed regulatory RNA	ncRNA
mm_165317.1	chr2	103605866	103605867	-	1	NA	intron (NM_178890, intron 1 of 16)	MIR|SINE|MIR	39556	NM_178890	99382	Mm.35850	NM_178890	ENSMUSG00000032724	Abtb2	AW539457|BPOZ-2	ankyrin repeat and BTB (POZ) domain containing 2	protein-coding
mm_162032.1	chr19	53944266	53944266	+	1	NA	promoter-TSS (NM_019658)	promoter-TSS (NM_019658)	-40	NM_001168505	56392	Mm.228669	NM_019658	ENSMUSG00000024976	Shoc2	AU017287|Sur8|mKIAA0862	soc-2 (suppressor of clear) homolog (C. elegans)	protein-coding
mm_65131.1	chr7	19508293	19508304	-	1	NA	promoter-TSS (NM_177692)	promoter-TSS (NM_177692)	33	NM_177692	232946	Mm.64557	NM_177692	ENSMUSG00000057667	Bloc1s3	BC043666|Blos3|E230011O18|rp	biogenesis of lysosomal organelles complex-1, subunit 3	protein-coding
mm_112237.1	chr12	113482401	113482405	-	1	NA	Intergenic	Intergenic	-7162	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_32822.1	chr4	117550306	117550316	+	1	NA	promoter-TSS (NM_080469)	promoter-TSS (NM_080469)	-13	NM_001285902	140546	Mm.235891	NM_080469	ENSMUSG00000033423	Eri3	PINT1|Prnpip1	exoribonuclease 3	protein-coding
mm_5703.1	chr1	43397318	43397325	-	1	NA	Intergenic	Intergenic	-48430	NM_010879	17974	Mm.389903	NM_010879	ENSMUSG00000066877	Nck2	4833426I10Rik|Grb4|NCKbeta|Nck-2	non-catalytic region of tyrosine kinase adaptor protein 2	protein-coding
mm_77989.1	chr9	8095702	8095703	+	1	NA	intron (NM_001045524, intron 6 of 10)	intron (NM_001045524, intron 6 of 10)	38592	NM_001045524	234915	Mm.101341	NM_001045524	ENSMUSG00000040729	Cep126	Kiaa1377|mKIAA1377	centrosomal protein 126	protein-coding
mm_80481.1	chr9	78209277	78209299	+	1	NA	TTS (NM_010357)	TTS (NM_010357)	17322	NM_010357	14860	Mm.2662	NM_010357	ENSMUSG00000032348	Gsta4	GST5.7|mGsta4	glutathione S-transferase, alpha 4	protein-coding
mm_60510.1	chr7	44479597	44479599	+	1	NA	Intergenic	L1MC4|LINE|L1	-4919	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_106715.1	chr12	3834818	3834843	+	1	NA	intron (NM_001271753, intron 1 of 22)	intron (NM_001271753, intron 1 of 22)	27414	NR_045884	100038522	Mm.417270	NR_045884	ENSMUSG00000073242	Dnmt3aos	ENSMUSG00000073242|Gm10485	DNA methyltransferase 3A, opposite strand	ncRNA
mm_77652.1	chr8	124564347	124564361	-	1	NA	exon (NM_007428, exon 2 of 5)	exon (NM_007428, exon 2 of 5)	5353	NM_007428	11606	Mm.301626	NM_007428	ENSMUSG00000031980	Agt	AI265500|AngI|AngII|Aogen|Serpina8	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	protein-coding
mm_100866.1	chr11	5898529	5898541	-	1	NA	exon (NM_022879, exon 2 of 7)	exon (NM_022879, exon 2 of 7)	247	NM_022879	17898	Mm.46514	NM_022879	ENSMUSG00000020469	Myl7	MLC-2alpha|MLC2a|MYL2A|Mylc2a|RLC-A	myosin, light polypeptide 7, regulatory	protein-coding
mm_24142.1	chr3	88297148	88297193	+	1	NA	promoter-TSS (NM_009836)	promoter-TSS (NM_009836)	35	NM_009836	12462	Mm.256034	NM_009836	ENSMUSG00000001416	Cct3	AL024092|Cctg|Tcp1-rs3|TriC-P5	chaperonin containing Tcp1, subunit 3 (gamma)	protein-coding
mm_99682.1	chr11	106020116	106020167	+	1	NA	exon (NM_001037712, exon 7 of 13)	exon (NM_001037712, exon 7 of 13)	11938	NM_001037712	192775	Mm.343850	NM_001037712	ENSMUSG00000001901	Kcnh6	m-erg2	potassium voltage-gated channel, subfamily H (eag-related), member 6	protein-coding
mm_70316.1	chr8	4248189	4248219	+	1	NA	promoter-TSS (NM_001195258)	promoter-TSS (NM_001195258)	-10	NM_001195258	100044509	Mm.439193	NM_001195258	ENSMUSG00000089736	Tgfbr3l	Gm14378|OTTMUSG00000016477	transforming growth factor, beta receptor III-like	protein-coding
mm_115837.1	chr13	21287197	21287203	-	1	NA	3' UTR (NM_010343, exon 5 of 5)	3' UTR (NM_010343, exon 5 of 5)	5486	NM_010343	14780	Mm.1332	NM_010343	ENSMUSG00000004344	Gpx5	AV379049|Arep	glutathione peroxidase 5	protein-coding
mm_88377.1	chr10	76345443	76345457	+	1	NA	promoter-TSS (NM_001081419)	promoter-TSS (NM_001081419)	-159	NM_001081419	64451	Mm.33183	NM_001081419	ENSMUSG00000020231	Dip2a	4931420H10Rik|AI426328|Dip2|Kiaa0184-hp|mKIAA0184	disco interacting protein 2 homolog A	protein-coding
mm_131490.1	chr16	17266391	17266393	+	1	NA	Intergenic	PB1D9|SINE|Alu	-9908	NM_177473	224019	Mm.246388	NM_177473	ENSMUSG00000055692	Tmem191c	4933405M22Rik|D16Bwg1494e|MNCb-4137	transmembrane protein 191C	protein-coding
mm_95725.1	chr11	54596102	54596128	+	1	NA	promoter-TSS (NM_001252498)	promoter-TSS (NM_001252498)	-31	NM_001252498	192786	Mm.254404	NM_175258	ENSMUSG00000037533	Rapgef6	A530068K01|AI844632|BB085664|C030018K18Rik|PDZ-GEF2|Pdzgef2|RA-GEF-2|Ragef2|mKIAA4052	Rap guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_92296.1	chr10	73202470	73202477	-	1	NA	Intergenic	Intergenic	-115768	NR_040646	327768	Mm.417745	NR_040646		A330049N07Rik	-	RIKEN cDNA A330049N07 gene	ncRNA
mm_20022.1	chr2	119418460	119418464	-	1	NA	intron (NM_026574, intron 24 of 35)	A-rich|Low_complexity|Low_complexity	59167	NM_026574	68142	Mm.330496	NM_026574	ENSMUSG00000034154	Ino80	2310079N15Rik|4632409L19Rik|Inoc1	INO80 complex subunit	protein-coding
mm_6457.1	chr1	74016720	74016728	-	1	NA	intron (NM_027884, intron 3 of 34)	intron (NM_027884, intron 3 of 34)	107723	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_165491.1	chr2	164613731	164613738	+	1	NA	promoter-TSS (NM_001080550)	promoter-TSS (NM_001080550)	34	NM_001012725	433502	Mm.376157	NM_001012725	ENSMUSG00000070531	Wfdc6b	WAP6b|Wfdc6	WAP four-disulfide core domain 6B	protein-coding
mm_160305.1	chr7	140507430	140507430	-	1	NA	promoter-TSS (NM_146520)	promoter-TSS (NM_146520)	-112	NM_146520	258513	Mm.261779	NM_146520	ENSMUSG00000052508	Olfr536	MOR252-1|MOR252-4	olfactory receptor 536	protein-coding
mm_59679.1	chr7	28436090	28436098	+	1	NA	promoter-TSS (NM_175021)	promoter-TSS (NM_175021)	97	NM_175021	233033	Mm.54120	NM_175021	ENSMUSG00000109336	Samd4b	BC042901	sterile alpha motif domain containing 4B	protein-coding
mm_30261.1	chr3	146769956	146770019	-	1	NA	5' UTR (NM_001164198, exon 1 of 10)	5' UTR (NM_001164198, exon 1 of 10)	251	NM_001164198	18749	Mm.16766	NM_011100	ENSMUSG00000005034	Prkacb	CbPKA|Pkacb	protein kinase, cAMP dependent, catalytic, beta	protein-coding
mm_96163.1	chr11	61487998	61488011	+	1	NA	TTS (NM_001291037)	TTS (NM_001291037)	2560	NM_029568	76293	Mm.272278	NM_029568	ENSMUSG00000042436	Mfap4	1110007F23Rik	microfibrillar-associated protein 4	protein-coding
mm_158407.1	chrX	136868519	136868534	-	1	NA	promoter-TSS (NM_176971)	promoter-TSS (NM_176971)	14	NM_176971	319642	Mm.44557	NM_176971	ENSMUSG00000043463	Rab9b	9330195C02Rik	RAB9B, member RAS oncogene family	protein-coding
mm_150688.1	chr19	42117561	42117564	+	1	NA	intron (NM_145501, intron 8 of 8)	B1_Mur4|SINE|Alu	11431	NM_027106	69534	Mm.30060	NM_027106	ENSMUSG00000018821	Avpi1	2310008N12Rik|AA410041|VIT32|esu|mVIT32	arginine vasopressin-induced 1	protein-coding
mm_34559.1	chr4	149637401	149637404	+	1	NA	intron (NM_001290989, intron 8 of 17)	B1F2|SINE|Alu	18165	NR_105990	102465983		NR_105990	ENSMUSG00000098580	Mir7023	Gm27912|mmu-mir-7023	microRNA 7023	ncRNA
mm_97224.1	chr11	75650554	75650570	+	1	NA	promoter-TSS (NM_008659)	promoter-TSS (NM_008659)	-947	NM_008659	17913	Mm.234502	NM_008659	ENSMUSG00000017774	Myo1c	C80397|MMIb|MYO1E|NMI|mm1beta|myr2	myosin IC	protein-coding
mm_134842.1	chr16	26526726	26526738	-	1	NA	promoter-TSS (NM_001101640)	promoter-TSS (NM_001101640)	39	NM_001101640	100043057	Mm.295917	NM_001101640	ENSMUSG00000091972	Tmem207	Gm540	transmembrane protein 207	protein-coding
mm_71024.1	chr8	33536579	33536587	+	1	NA	Intergenic	Intergenic	-33961	NM_031374	104271	Mm.280624	NM_031374	ENSMUSG00000009628	Tex15	2210014E14Rik|AL022622|AU022940	testis expressed gene 15	protein-coding
mm_26047.1	chr3	135689121	135689131	+	1	NA	intron (NM_008689, intron 1 of 24)	intron (NM_008689, intron 1 of 24)	2421	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_18401.1	chr2	60284099	60284159	-	1	NA	5' UTR (NM_025422, exon 1 of 5)	5' UTR (NM_025422, exon 1 of 5)	355	NM_025422	66205	Mm.227281	NM_025422	ENSMUSG00000060703	Cd302	1110055L24Rik|AI159627	CD302 antigen	protein-coding
mm_14334.1	chr2	129592793	129592803	+	1	NA	promoter-TSS (NM_001291022)	promoter-TSS (NM_001291022)	-41	NM_001291020	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_68740.1	chr7	121064219	121064223	-	1	NA	3' UTR (NM_030691, exon 6 of 6)	3' UTR (NM_030691, exon 6 of 6)	10309	NM_030691	80719	Mm.160384	NM_030691	ENSMUSG00000035004	Igsf6	-	immunoglobulin superfamily, member 6	protein-coding
mm_155001.1	chrX	40712887	40712888	+	1	NA	Intergenic	L1_Rod|LINE|L1	-688414	NM_016886	53623	Mm.327681	NM_016886	ENSMUSG00000001986	Gria3	2900064I19Rik|GluA3|GluR-C|GluR-K3|Glur-3|Glur3|Gluralpha3	glutamate receptor, ionotropic, AMPA3 (alpha 3)	protein-coding
mm_119673.1	chr14	52622525	52622535	+	1	NA	Intergenic	Intergenic	-126835	NM_001170918	57269	Mm.88822	NM_020512	ENSMUSG00000059887	Olfr1507	MOR244-1|Mor28|Or28	olfactory receptor 1507	protein-coding
mm_29872.1	chr3	130730497	130730506	-	1	NA	promoter-TSS (NM_001287581)	promoter-TSS (NM_001287581)	-103	NM_001005859	68436	Mm.140568	NM_026724	ENSMUSG00000062006	Rpl34	1100001I22Rik	ribosomal protein L34	protein-coding
mm_129177.1	chr15	76273883	76273914	-	1	NA	intron (NM_028852, intron 1 of 4)	intron (NM_028852, intron 1 of 4)	-4059	NR_045747	100038659	Mm.448549	NR_045747		Mirt2	ENSMUSG00000075583|Gm10872|Gm24562	myocardial infraction associated transcript 2	ncRNA
mm_169624.1	chr1	54026425	54026426	+	1	NA	intron (NM_001001883, intron 2 of 28)	L1Md_T|LINE|L1	168609	NM_001001883	329152	Mm.132150	NM_172655	ENSMUSG00000042807	Hecw2	A730039N16Rik|D030049F17Rik|Gm971|Nedl2|mKIAA1301	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2	protein-coding
mm_89721.1	chr10	98914640	98914721	+	1	NA	promoter-TSS (NM_026482)	promoter-TSS (NM_026482)	-472	NM_026482	67972	Mm.166944	NM_026482	ENSMUSG00000019943	Atp2b1	2810442I22Rik|E130111D10Rik|Pmca1	ATPase, Ca++ transporting, plasma membrane 1	protein-coding
mm_158739.1	chrX	164076483	164076511	-	1	NA	promoter-TSS (NM_009173)	promoter-TSS (NM_009173)	-4	NM_001308385	20438	Mm.37215	NM_009173	ENSMUSG00000040749	Siah1b	AA960570|Sinh1b|siah-1b	seven in absentia 1B	protein-coding
mm_36143.1	chr4	59472896	59472918	-	1	NA	3' UTR (NM_144904, exon 15 of 15)	3' UTR (NM_144904, exon 15 of 15)	-34274	NM_001163288	634731	Mm.483589	NM_001163288	ENSMUSG00000038578	Susd1	A530080P10|Gm12528|OTTMUSG00000007332	sushi domain containing 1	protein-coding
mm_139252.1	chr17	47734359	47734405	+	1	NA	TTS (NM_025973)	TTS (NM_025973)	-2655	NM_001161722	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_96283.1	chr11	63046738	63046770	+	1	NA	intron (NR_105772, intron 5 of 6)	intron (NR_105772, intron 5 of 6)	-14905	NM_027660	71062	Mm.23534	NM_027660	ENSMUSG00000042189	Tekt3	4933407G07Rik	tektin 3	protein-coding
mm_66341.1	chr7	43465564	43465590	-	1	NA	intron (NM_001290316, intron 4 of 9)	intron (NM_001290316, intron 4 of 9)	2344	NM_001290316	75690	Mm.30200	NM_001290316	ENSMUSG00000070604	Vsig10l	-	V-set and immunoglobulin domain containing 10 like	protein-coding
mm_142998.1	chr17	56412993	56412997	-	1	NA	3' UTR (NM_001252453, exon 29 of 29)	3' UTR (NM_001252453, exon 29 of 29)	5914	NR_105943	102465590		NR_105943	ENSMUSG00000098339	Mir6977	Gm27922|mmu-mir-6977	microRNA 6977	ncRNA
mm_36841.1	chr4	106678644	106678654	-	1	NA	promoter-TSS (NM_001172073)	promoter-TSS (NM_001172073)	37	NM_001172073	72354	Mm.25806	NM_028209	ENSMUSG00000025413	Ttc4	2810002P21Rik|AF007005|L62	tetratricopeptide repeat domain 4	protein-coding
mm_105120.1	chr11	101119890	101119900	-	1	NA	promoter-TSS (NM_134024)	promoter-TSS (NM_134024)	-52	NM_028933	67998	Mm.33881	NM_026501	ENSMUSG00000017802	Fam134c	1300010M03Rik|4933404C01Rik|AI551748	family with sequence similarity 134, member C	protein-coding
mm_21309.1	chr2	157079635	157079679	-	1	NA	promoter-TSS (NM_001164663)	promoter-TSS (NM_001164663)	-392	NM_001164663	320706	Mm.79466	NM_001164663	ENSMUSG00000055485	Soga1	9830001H06Rik|AI426038|D430036N24Rik|Soga	suppressor of glucose, autophagy associated 1	protein-coding
mm_107664.1	chr12	52854668	52854715	+	1	NA	intron (NM_198111, intron 2 of 13)	intron (NM_198111, intron 2 of 13)	155308	NM_198111	238161	Mm.310822	NM_198111	ENSMUSG00000061603	Akap6	AI482140|Akapalpha|Akapbeta|PRKA	A kinase (PRKA) anchor protein 6	protein-coding
mm_57746.1	chr6	129097330	129097338	-	1	NA	intron (NM_153506, intron 2 of 4)	intron (NM_153506, intron 2 of 4)	3569	NM_153506	232409	Mm.30870	NM_153506	ENSMUSG00000030155	Clec2e	Clra|clr-a	C-type lectin domain family 2, member e	protein-coding
mm_75820.1	chr8	70476912	70476969	-	1	NA	promoter-TSS (NM_001122830)	promoter-TSS (NM_001122830)	3	NM_001122830	234378	Mm.187090	NM_172052	ENSMUSG00000055707	Klhl26	C630013N10Rik|Klkl26	kelch-like 26	protein-coding
mm_135924.1	chr16	69863719	69863731	-	1	NA	promoter-TSS (NM_173069)	promoter-TSS (NM_173069)	19	NM_173069	224318	Mm.212743	NM_173069	ENSMUSG00000063163	Speer2	SPEER-2	spermatogenesis associated glutamate (E)-rich protein 2	protein-coding
mm_79654.1	chr9	59618269	59618272	+	1	NA	intron (NR_038074, intron 1 of 22)	intron (NR_038074, intron 1 of 22)	986	NR_038074	67287	Mm.439943	NM_029922	ENSMUSG00000025237	Parp6	1700119G14Rik|2310028P13Rik|3110038K10Rik|ARTD17|C030013N01Rik|PARP-6	poly (ADP-ribose) polymerase family, member 6	protein-coding
mm_15031.1	chr2	152695508	152695518	+	1	NA	exon (NM_001159551, exon 10 of 13)	exon (NM_001159551, exon 10 of 13)	8365	NM_025543	66405	Mm.440291	NM_025543	ENSMUSG00000042814	Mcts2	2400002F11Rik|MCT-2	malignant T cell amplified sequence 2	protein-coding
mm_157969.1	chrX	92680024	92680054	-	1	NA	Intergenic	RMER15|LTR|ERVL	-80467	NM_173783	215641	Mm.327999	NM_173783	ENSMUSG00000067649	Mageb18	B430216B18Rik	melanoma antigen family B, 18	protein-coding
mm_137072.1	chr17	20957021	20957043	+	1	NA	exon (NM_016891, exon 6 of 15)	exon (NM_016891, exon 6 of 15)	11578	NM_016891	51792	Mm.294138	NM_016891	ENSMUSG00000007564	Ppp2r1a	6330556D22Rik|PP2A|PR65	protein phosphatase 2, regulatory subunit A, alpha	protein-coding
mm_115118.1	chr13	104228984	104228990	+	1	NA	promoter-TSS (NM_021790)	promoter-TSS (NM_021790)	-143	NM_172807	238831	Mm.98910	NM_172807	ENSMUSG00000021713	Ppwd1	4632422M10Rik|A330090G21Rik	peptidylprolyl isomerase domain and WD repeat containing 1	protein-coding
mm_62110.1	chr7	96532701	96532707	+	1	NA	intron (NM_001310762, intron 4 of 32)	intron (NM_001310762, intron 4 of 32)	-190740	NR_046043	670727	Mm.421352	NR_046043	ENSMUSG00000085751	Gm15412	OTTMUSG00000021245	predicted gene 15412	ncRNA
mm_168828.1	chr12	22623379	22623389	-	1	NA	Intergenic	CpG	386859	NR_015504	69732	Mm.391403	NM_028362	ENSMUSG00000073164	2410018L13Rik	2810480C08Rik	RIKEN cDNA 2410018L13 gene	ncRNA
mm_22503.1	chr3	7407356	7407369	+	1	NA	intron (NM_008862, intron 1 of 2)	intron (NM_008862, intron 1 of 2)	40758	NM_008862	18767	Mm.3193	NM_008862	ENSMUSG00000027499	Pkia	AI415001|PKIalpha	protein kinase inhibitor, alpha	protein-coding
mm_5281.1	chr1	20617974	20617990	-	1	NA	promoter-TSS (NM_153179)	promoter-TSS (NM_153179)	75	NM_153179	241035	Mm.249253	NM_153179	ENSMUSG00000043760	Pkhd1	AI118496|AI182499|FPC|Tigm1	polycystic kidney and hepatic disease 1	protein-coding
mm_77788.1	chr9	3026478	3026495	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	12257	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_124099.1	chr14	79300927	79300931	-	1	NA	intron (NM_025427, intron 1 of 4)	CpG	706	NM_025427	66214	Mm.29811	NM_025427	ENSMUSG00000022018	Rgcc	1190002H23Rik|Rgc-32|Rgc32	regulator of cell cycle	protein-coding
mm_92610.1	chr10	80136472	80136484	-	1	NA	exon (NM_001195268, exon 4 of 9)	exon (NM_001195268, exon 4 of 9)	909	NM_001195268	100503659	Mm.485395	NM_015761	ENSMUSG00000035640	Cbarp	9630008F14|Dos|R29144/1	calcium channel, voltage-dependent, beta subunit associated regulatory protein	protein-coding
mm_137138.1	chr17	23604691	23604706	+	1	NA	intron (NM_001289482, intron 1 of 3)	ID_B1|SINE|B4	3872	NM_001289482	332221	Mm.270315	NM_001033425	ENSMUSG00000023902	Zscan10	BC068284|Zfp206|Zkscan10|Znf206	zinc finger and SCAN domain containing 10	protein-coding
mm_2483.1	chr1	105984422	105984463	+	1	NA	Intergenic	Intergenic	-5964	NM_001122676	227449	Mm.210188	NM_001122675	ENSMUSG00000038866	Zcchc2	9930114B20Rik|AW212015	zinc finger, CCHC domain containing 2	protein-coding
mm_24156.1	chr3	88446792	88446805	+	1	NA	intron (NM_001163491, intron 10 of 14)	HAL1|LINE|L1	-5847	NR_105978	102465611		NR_105978	ENSMUSG00000098655	Mir7011	Gm27677|mmu-mir-7011	microRNA 7011	ncRNA
mm_11133.1	chr2	28446960	28446992	+	1	NA	promoter-TSS (NM_001005420)	promoter-TSS (NM_001005420)	-965	NM_001005420	241289	Mm.330095	NM_001005420	ENSMUSG00000035829	Ppp1r26	Gm347|Kiaa0649|mKIAA0649	protein phosphatase 1, regulatory subunit 26	protein-coding
mm_94054.1	chr10	128186085	128186113	-	1	NA	Intergenic	B3|SINE|B2	-5802	NM_001039080	56516	Mm.42247	NM_019711	ENSMUSG00000040043	Rbms2	2610315E04Rik|Scr3	RNA binding motif, single stranded interacting protein 2	protein-coding
mm_85043.1	chr9	89177884	89177888	-	1	NA	Intergenic	Intergenic	-21387	NM_007534	12045	Mm.479217	NM_007534	ENSMUSG00000089929	Bcl2a1b	A1-b	B cell leukemia/lymphoma 2 related protein A1b	protein-coding
mm_57821.1	chr6	129462803	129462814	-	1	NA	non-coding (NR_132130, exon 6 of 6)	non-coding (NR_132130, exon 6 of 6)	9971	NM_001309637	56644	Mm.239516	NM_020008	ENSMUSG00000079293	Clec7a	BGR|Clecsf12|beta-GR	C-type lectin domain family 7, member a	protein-coding
mm_62259.1	chr7	99323186	99323191	+	1	NA	intron (NM_010837, intron 3 of 3)	intron (NM_010837, intron 3 of 3)	30051	NM_009825	12406	Mm.22708	NM_009825	ENSMUSG00000070436	Serpinh1	BERF-1|Cbp1|Cbp2|Hsp47|J6|Serpinh2|gp46	serine (or cysteine) peptidase inhibitor, clade H, member 1	protein-coding
mm_20328.1	chr2	127511110	127511120	-	1	NA	intron (NR_110989, intron 1 of 8)	intron (NR_110989, intron 1 of 8)	10277	NM_001291005	56461	Mm.315292	NM_019789	ENSMUSG00000079056	Kcnip3	4933407H12Rik|AI413860|Csen|DREAM|KChIP3|R74849	Kv channel interacting protein 3, calsenilin	protein-coding
mm_162434.1	chr1	101608392	101608397	+	1	NA	Intergenic	Lx4A|LINE|L1	452626	NR_037989	100504525	Mm.87065	NR_037989	ENSMUSG00000100684	Gm20268	-	predicted gene, 20268	ncRNA
mm_92196.1	chr10	68135290	68135301	-	1	NA	intron (NM_023598, intron 4 of 9)	intron (NM_023598, intron 4 of 9)	143431	NM_023598	71371	Mm.440357	NM_023598	ENSMUSG00000019947	Arid5b	4930580B11|5430435G07Rik|AI467247|Desrt|Mrf2|Mrf2alpha|Mrf2beta	AT rich interactive domain 5B (MRF1-like)	protein-coding
mm_50867.1	chr6	55451739	55451763	+	1	NA	promoter-TSS (NM_001025372)	promoter-TSS (NM_001025372)	-227	NM_001025372	11517	Mm.44245	NM_007407	ENSMUSG00000029778	Adcyap1r1	2900024I10Rik|AI846590|PAC1|PAC1R|PACAP1-R	adenylate cyclase activating polypeptide 1 receptor 1	protein-coding
mm_129495.1	chr15	78837817	78837817	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-4830	NM_027219	104445	Mm.307488	NM_027219	ENSMUSG00000049521	Cdc42ep1	1810058K22Rik|AA980734|Borg5|CEP1|MSE55	CDC42 effector protein (Rho GTPase binding) 1	protein-coding
mm_76453.1	chr8	85119680	85119694	-	1	NA	5' UTR (NM_001037745, exon 2 of 5)	5' UTR (NM_001037745, exon 2 of 5)	3408	NM_001037745	244556	Mm.334682	NM_001037745	ENSMUSG00000074194	Zfp791	EG244556	zinc finger protein 791	protein-coding
mm_144520.1	chr18	24941409	24941429	+	1	NA	intron (NM_175276, intron 5 of 26)	intron (NM_175276, intron 5 of 26)	224546	NM_001142697	66648	Mm.263189	NM_001004361	ENSMUSG00000024269	Tpgs2	5730437P09Rik|5730494M16Rik|AI666318|Pgs2	tubulin polyglutamylase complex subunit 2	protein-coding
mm_110614.1	chr12	56613271	56613291	-	1	NA	promoter-TSS (NM_008701)	promoter-TSS (NM_008701)	3	NM_008701	18094	Mm.129420	NM_008701	ENSMUSG00000058669	Nkx2-9	Nkx-2.9|Nkx2-8|Nkx2.9|tinman	NK2 homeobox 9	protein-coding
mm_72690.1	chr8	84969657	84969679	+	1	NA	promoter-TSS (NM_011563)	promoter-TSS (NM_011563)	46	NM_011563	21672	Mm.347009	NM_011563	ENSMUSG00000005161	Prdx2	AL022839|Band-8|NkefB|PRP|PrxII|TDX1|TPx|TPx-B|TR|TSA|Tdpx1|Torin	peroxiredoxin 2	protein-coding
mm_5674.1	chr1	43098626	43098686	-	1	NA	promoter-TSS (NM_001013025)	promoter-TSS (NM_001013025)	-34	NM_001013025	73122	Mm.246069	NM_001013025	ENSMUSG00000070939	Tgfbrap1	3110018K12Rik|AU024090|AU042859|AW742551|Trap1	transforming growth factor, beta receptor associated protein 1	protein-coding
mm_130953.1	chr15	103255428	103255432	-	1	NA	promoter-TSS (NM_008685)	promoter-TSS (NM_008685)	9	NM_008685	18022	Mm.457989	NM_008685	ENSMUSG00000058794	Nfe2	NF-E2|NF-E2/P45|p45|p45NFE2|p45nf-e2	nuclear factor, erythroid derived 2	protein-coding
mm_157715.1	chrX	68044852	68044861	-	1	NA	Intergenic	Intergenic	-34677	NR_030575	100124449		NR_030575	ENSMUSG00000106233	Mir509	Mirn509|mmu-mir-509	microRNA 509	ncRNA
mm_49422.1	chr6	29246035	29246065	+	1	NA	Intergenic	ORR1D2|LTR|ERVL-MaLR	-26438	NM_001190461	69573	Mm.45161	NM_023516	ENSMUSG00000043421	Hilpda	2310016C08Rik|AW049004|Hig2	hypoxia inducible lipid droplet associated	protein-coding
mm_166085.1	chr4	138836447	138836456	-	1	NA	intron (NM_001122954, intron 1 of 5)	intron (NM_001122954, intron 1 of 5)	4575	NM_001082531	18780	Mm.4675	NM_011108	ENSMUSG00000058908	Pla2g2a	EF|Mom1|Pla2|sPLA2|sPla2-IIA	phospholipase A2, group IIA (platelets, synovial fluid)	protein-coding
mm_154095.1	chr19	56952149	56952151	-	1	NA	intron (NM_001177797, intron 1 of 18)	intron (NM_001177797, intron 1 of 18)	56425	NM_146102	226250	Mm.226284	NM_146102	ENSMUSG00000025083	Afap1l2	AU041783|C86904|mKIAA1914	actin filament associated protein 1-like 2	protein-coding
mm_139310.1	chr17	48351705	48351720	+	1	NA	exon (NM_001272078, exon 4 of 5)	exon (NM_001272078, exon 4 of 5)	5311	NM_001272078	83433	Mm.261623	NM_031254	ENSMUSG00000023992	Trem2	TREM-2|Trem2a|Trem2b|Trem2c	triggering receptor expressed on myeloid cells 2	protein-coding
mm_140226.1	chr17	83985668	83985670	+	1	NA	Intergenic	Intergenic	-12883	NR_130994	78148	Mm.243918	NR_130994		8430430B14Rik	-	RIKEN cDNA 8430430B14 gene	ncRNA
mm_114057.1	chr13	54371424	54371428	+	1	NA	promoter-TSS (NM_009946)	promoter-TSS (NM_009946)	77	NM_009946	12890	Mm.268902	NM_009946	ENSMUSG00000025867	Cplx2	921-L|AI413745|AW492120	complexin 2	protein-coding
mm_95487.1	chr11	51584760	51584821	+	1	NA	promoter-TSS (NM_028398)	promoter-TSS (NM_028398)	33	NM_028398	72947	Mm.256875	NM_028398	ENSMUSG00000020359	Phykpl	2900006B13Rik|Agxt2l2	5-phosphohydroxy-L-lysine phospholyase	protein-coding
mm_51374.1	chr6	72956690	72956709	+	1	NA	TTS (NM_025284)	TTS (NM_025284)	1533	NM_001039392	19240	Mm.3532	NM_025284	ENSMUSG00000079523	Tmsb10	Ptmb10|Tb10	thymosin, beta 10	protein-coding
mm_61465.1	chr7	75610039	75610080	+	1	NA	exon (NM_029332, exon 7 of 37)	exon (NM_029332, exon 7 of 37)	154525	NM_029332	75547	Mm.216107	NM_029332	ENSMUSG00000066406	Akap13	1700026G02Rik|5730522G15Rik|5830460E08Rik|AKAP-13|AKAP-Lbc|BRX|Ht31|LBC|PROTO-LB|PROTO-LBC	A kinase (PRKA) anchor protein 13	protein-coding
mm_116484.1	chr13	44018573	44018604	-	1	NA	Intergenic	Intergenic	-102579	NR_045285	328235	Mm.188356	NR_045285	ENSMUSG00000089815	Gm5083	A730030A06	predicted gene 5083	ncRNA
mm_148054.1	chr18	71996532	71996532	-	1	NA	intron (NM_007831, intron 1 of 28)	intron (NM_007831, intron 1 of 28)	354537	NM_007831	13176	Mm.167882	NM_007831	ENSMUSG00000060534	Dcc	C030036D22Rik|Igdcc1	deleted in colorectal carcinoma	protein-coding
mm_167923.1	chrX	102707851	102707858	+	1	NA	promoter-TSS (NM_001039116)	promoter-TSS (NM_001039116)	-27	NM_001039116	632708	Mm.297715	NM_001039116	ENSMUSG00000073027	Dmrtc1b	Dmrt8.2|Gm714	DMRT-like family C1b	protein-coding
mm_146229.1	chr18	77082183	77082188	+	1	NA	intron (NM_001164170, intron 1 of 12)	L1MD|LINE|L1	16505	NM_001164168	17344	Mm.6370	NM_008602	ENSMUSG00000025423	Pias2	6330408K17Rik|AI462206|ARIP3|AU018068|Dib|Miz1|PIASxalpha|PIASxb|PIASxbeta|SIZ2	protein inhibitor of activated STAT 2	protein-coding
mm_164199.1	chr15	79761724	79761724	+	1	NA	3' UTR (NM_017470, exon 4 of 4)	3' UTR (NM_017470, exon 4 of 4)	12743	NM_017470	54152	Mm.288159	NM_017470	ENSMUSG00000022420	Dnal4	D15Ertd424e|Dnalc4	dynein, axonemal, light chain 4	protein-coding
mm_93454.1	chr10	110126890	110126895	-	1	NA	Intergenic	Lx7|LINE|L1	-126673	NM_001081035	260315	Mm.225050	NM_177797	ENSMUSG00000020181	Nav3	4732483H20Rik|9630020C08Rik|POMFIL1|Pomfil1p|mKIAA0938|unc53H3	neuron navigator 3	protein-coding
mm_159306.1	chr2	180027993	180027993	+	1	NA	exon (NM_177727, exon 3 of 9)	exon (NM_177727, exon 3 of 9)	3006	NM_177727	241846	Mm.21577	NM_177727	ENSMUSG00000039108	Lsm14b	9430078B04|BC040823	LSM family member 14B	protein-coding
mm_28253.1	chr3	88548265	88548311	-	1	NA	promoter-TSS (NM_016899)	promoter-TSS (NM_016899)	-9	NM_016899	53868	Mm.26994	NM_016899	ENSMUSG00000008601	Rab25	AV012978	RAB25, member RAS oncogene family	protein-coding
mm_125600.1	chr15	59653412	59653423	+	1	NA	intron (NM_144549, intron 2 of 2)	intron (NM_144549, intron 2 of 2)	4763	NM_144549	211770	Mm.40298	NM_144549	ENSMUSG00000032501	Trib1	A530090O15Rik|TRB-1|Trb1	tribbles pseudokinase 1	protein-coding
mm_88450.1	chr10	77550886	77550916	+	1	NA	intron (NM_008404, intron 7 of 15)	intron (NM_008404, intron 7 of 15)	20553	NM_008404	16414	Mm.1137	NM_008404	ENSMUSG00000000290	Itgb2	2E6|AI528527|Cd18|LAD|LCAMB|Lfa1|MF17	integrin beta 2	protein-coding
mm_84569.1	chr9	68969520	68969540	-	1	NA	intron (NM_013646, intron 1 of 10)	intron (NM_013646, intron 1 of 10)	204184	NR_033299	320440	Mm.483129	NM_177159		9530091C08Rik	-	RIKEN cDNA 9530091C08 gene	ncRNA
mm_74697.1	chr8	15327265	15327305	-	1	NA	Intergenic	RMER17A2|LTR|ERVK	269632	NM_008664	17930	Mm.272115	NM_008664	ENSMUSG00000031461	Myom2	AW146149	myomesin 2	protein-coding
mm_41929.1	chr5	105699946	105700041	+	1	NA	promoter-TSS (NM_178701)	promoter-TSS (NM_178701)	24	NM_001122768	231549	Mm.23837	NM_178701	ENSMUSG00000046079	Lrrc8d	2810473G09Rik|4930525N13Rik|A930019F03|Lrrc5	leucine rich repeat containing 8D	protein-coding
mm_143955.1	chr17	86880441	86880446	-	1	NA	Intergenic	Intergenic	-36905	NM_001277980	78469	Mm.67234	NM_030104	ENSMUSG00000037689	Tmem247	1700090G07Rik	transmembrane protein 247	protein-coding
mm_53589.1	chr6	137754530	137754599	+	1	NA	promoter-TSS (NM_172733)	promoter-TSS (NM_172733)	-13	NM_172733	232449	Mm.29181	NM_172733	ENSMUSG00000030225	Dera	2010002D22Rik|2500002K03Rik|DEOC	deoxyribose-phosphate aldolase (putative)	protein-coding
mm_45805.1	chr5	87569068	87569074	-	1	NA	promoter-TSS (NM_016771)	promoter-TSS (NM_016771)	-65	NM_016771	53315	Mm.6824	NM_016771	ENSMUSG00000029273	Sult1d1	5033411P13Rik|AI987815|ST1d1|SULT-N|Sultn	sulfotransferase family 1D, member 1	protein-coding
mm_97153.1	chr11	75463794	75463797	+	1	NA	promoter-TSS (NR_029739)	promoter-TSS (NR_029739)	79	NR_029739	387141		NR_029739	ENSMUSG00000065529	Mir22	Mirn22|mmu-mir-22	microRNA 22	ncRNA
mm_80903.1	chr9	100504588	100504589	+	1	NA	intron (NM_010878, intron 2 of 3)	intron (NM_010878, intron 2 of 3)	2268	NM_001324530	17973	Mm.181485	NM_010878	ENSMUSG00000032475	Nck1	6330586M15Rik|D230010O13Rik|Nck|Nck-1	non-catalytic region of tyrosine kinase adaptor protein 1	protein-coding
mm_32833.1	chr4	117673995	117674025	+	1	NA	TTS (NM_023178)	TTS (NM_023178)	8215	NM_023178	66233	Mm.29142	NM_023178	ENSMUSG00000009640	Dmap1	1500016M21Rik|DNMAP1|DNMTAP1|Dmtap1|mKIAA1425	DNA methyltransferase 1-associated protein 1	protein-coding
mm_30950.1	chr4	33209238	33209254	+	1	NA	exon (NM_177774, exon 1 of 3)	exon (NM_177774, exon 1 of 3)	255	NM_177774	272009	Mm.156636	NM_177774	ENSMUSG00000054679	Srsf12	B830039L16|Sfrs13b|Srrp|Srsf13b	serine/arginine-rich splicing factor 12	protein-coding
mm_95146.1	chr11	35544523	35544565	+	1	NA	intron (NM_011412, intron 5 of 35)	intron (NM_011412, intron 5 of 35)	-72272	NR_029799	723924		NR_029799	ENSMUSG00000065583	Mir218-2	Mirn218-2|mir-218-2	microRNA 218-2	ncRNA
mm_165223.1	chr2	50066522	50066528	+	1	NA	promoter-TSS (NM_177139)	promoter-TSS (NM_177139)	96	NM_177139	320343	Mm.130607	NM_177139	ENSMUSG00000050447	Lypd6	E130115E03Rik	LY6/PLAUR domain containing 6	protein-coding
mm_64477.1	chr7	143053518	143053543	+	1	NA	non-coding (NR_015529, exon 1 of 4)	non-coding (NR_015529, exon 1 of 4)	156	NR_110355	97423	Mm.5250	NM_133790	ENSMUSG00000059277	R74862	-	expressed sequence R74862	ncRNA
mm_58044.1	chr6	136827767	136827769	-	1	NA	intron (NM_021714, intron 1 of 11)	CpG	448	NM_021714	60321	Mm.141197	NM_021714	ENSMUSG00000030216	Wbp11	2510026P17Rik|D6Wsu113e|Npwbp|SIPP1	WW domain binding protein 11	protein-coding
mm_167367.1	chr8	88243973	88243986	+	1	NA	intron (NM_001164498, intron 3 of 12)	intron (NM_001164498, intron 3 of 12)	-28424	NM_007406	11513	Mm.288206	NM_007406	ENSMUSG00000031659	Adcy7	AA407758	adenylate cyclase 7	protein-coding
mm_28108.1	chr3	86548478	86548484	-	1	NA	promoter-TSS (NM_011839)	promoter-TSS (NM_011839)	-198	NM_011839	23937	Mm.389466	NM_011839	ENSMUSG00000057777	Mab21l2	-	mab-21-like 2 (C. elegans)	protein-coding
mm_160019.1	chr6	129740528	129740528	-	1	NA	promoter-TSS (NM_177155)	promoter-TSS (NM_177155)	-44	NM_177155	320407	Mm.123265	NM_177155	ENSMUSG00000043932	Klri2	A530090P03Rik	killer cell lectin-like receptor family I member 2	protein-coding
mm_149954.1	chr19	28578189	28578202	+	1	NA	intron (NM_175459, intron 2 of 10)	MLT1C|LTR|ERVL-MaLR	-100029	NR_045330	320176	Mm.406716	NR_045330	ENSMUSG00000097735	D930032P07Rik	-	RIKEN cDNA D930032P07 gene	ncRNA
mm_1938.1	chr1	86154753	86154821	+	1	NA	promoter-TSS (NM_027456)	promoter-TSS (NM_027456)	7	NM_001310702	78795	Mm.379264	NM_027456	ENSMUSG00000062590	Armc9	3830422A13Rik|4831423D23Rik|4930438O05Rik|5730415N24Rik	armadillo repeat containing 9	protein-coding
mm_142948.1	chr17	56109745	56109755	-	1	NA	promoter-TSS (NM_020568)	promoter-TSS (NM_020568)	52	NM_020568	57435	Mm.12966	NM_020568	ENSMUSG00000002831	Plin4	S3-12|mKIAA1881	perilipin 4	protein-coding
mm_101867.1	chr11	48891639	48891645	-	1	NA	intron (NM_001024230, intron 4 of 4)	RMER17C|LTR|ERVK	10510	NM_001024230	432555	Mm.338931	NM_001024230	ENSMUSG00000058163	Gm5431	EG432555|Irgb9b8	predicted gene 5431	protein-coding
mm_147685.1	chr18	60723699	60723714	-	1	NA	Intergenic	Intergenic	-10317	NM_008306	15531	Mm.181862	NM_008306	ENSMUSG00000054008	Ndst1	1200015G06Rik|HSNST|HSNST 1|Hsst|N-HSST|N-HSST 1|NDST-1|b2b2230Clo	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 1	protein-coding
mm_40128.1	chr5	34999112	34999117	+	1	NA	promoter-TSS (NM_001163512)	promoter-TSS (NM_001163512)	36	NM_001163512	71729	Mm.196208	NM_173402	ENSMUSG00000029101	Rgs12	1200016K18Rik|4632412M04Rik|AI481290|E130309H11	regulator of G-protein signaling 12	protein-coding
mm_61948.1	chr7	90194337	90194339	+	1	NA	intron (NM_001252520, intron 18 of 20)	intron (NM_001252520, intron 18 of 20)	64106	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_50130.1	chr6	41542046	41542079	+	1	NA	Intergenic	Intergenic	20286	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_145365.1	chr18	56707942	56707988	+	1	NA	5' UTR (NM_010721, exon 1 of 11)	5' UTR (NM_010721, exon 1 of 11)	152	NM_010721	16906	Mm.4105	NM_010721	ENSMUSG00000024590	Lmnb1	-	lamin B1	protein-coding
mm_24279.1	chr3	89225073	89225084	+	1	NA	intron (NM_013691, intron 20 of 22)	intron (NM_013691, intron 20 of 22)	2120	NR_030579	100124470		NR_030579	ENSMUSG00000076255	Mir92b	Mirn92b|mir-92b|mmu-mir-92b	microRNA 92b	ncRNA
mm_120379.1	chr14	64588279	64588289	+	1	NA	intron (NR_040709, intron 1 of 3)	intron (NR_040709, intron 1 of 3)	169	NR_040709	268755	Mm.194050	NR_040709	ENSMUSG00000097545	Mir124a-1hg	A930011O12Rik|Rncr3|mir-124-1|mir-3078	Mir124-1 host gene (non-protein coding)	ncRNA
mm_108332.1	chr12	80109885	80109907	+	1	NA	exon (NM_007564, exon 2 of 2)	exon (NM_007564, exon 2 of 2)	3117	NM_007564	12192	Mm.235132	NM_007564	ENSMUSG00000021127	Zfp36l1	AW742437|AW743212|Berg36|Brf1|D530020L18Rik|ERF1|TIS11b|cMG1	zinc finger protein 36, C3H type-like 1	protein-coding
mm_165639.1	chr3	74588596	74588596	+	1	NA	Intergenic	Intergenic	555176	NM_001310529	213234	Mm.80075	NM_172515	ENSMUSG00000034151	Zbbx	4931432L23	zinc finger, B-box domain containing	protein-coding
mm_80426.1	chr9	77920401	77920403	+	1	NA	intron (NM_134255, intron 1 of 7)	ID_B1|SINE|B4	3037	NM_134255	68801	Mm.430736	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	ELOVL family member 5, elongation of long chain fatty acids (yeast)	protein-coding
mm_78658.1	chr9	40457684	40457713	+	1	NA	Intergenic	Intergenic	-1934	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_101633.1	chr11	36432605	36432622	-	1	NA	intron (NM_011856, intron 2 of 28)	intron (NM_011856, intron 2 of 28)	-452524	NM_170779	211652	Mm.31267	NM_170779	ENSMUSG00000018849	Wwc1	AA408228|AU017197|BC037006|Kibra|mKIAA0869	WW, C2 and coiled-coil domain containing 1	protein-coding
mm_157295.1	chrX	20920912	20920927	-	1	NA	promoter-TSS (NM_013680)	promoter-TSS (NM_013680)	-1	NM_013680	20964	Mm.439844	NM_013680	ENSMUSG00000037217	Syn1	Syn-1|Syn1-S	synapsin I	protein-coding
mm_87256.1	chr10	41519494	41519516	+	1	NA	promoter-TSS (NM_016898)	promoter-TSS (NM_016898)	5	NM_016898	53599	Mm.269815	NM_016898	ENSMUSG00000019818	Cd164	A115|A24|AA589639|AW540279|MGC-24|MSSP	CD164 antigen	protein-coding
mm_52704.1	chr6	119349727	119349731	+	1	NA	intron (NM_001347427, intron 36 of 36)	intron (NM_001347427, intron 36 of 36)	-18963	NM_172492	211187	Mm.121498	NM_172492	ENSMUSG00000055003	Lrtm2	A230084J22|AI841794	leucine-rich repeats and transmembrane domains 2	protein-coding
mm_164519.1	chr16	97004120	97004121	+	1	NA	intron (NM_031174, intron 3 of 32)	intron (NM_031174, intron 3 of 32)	166615	NM_031174	13508	Mm.102437	NM_031174	ENSMUSG00000050272	Dscam	4932410A21Rik	Down syndrome cell adhesion molecule	protein-coding
mm_19385.1	chr2	91236926	91236965	-	1	NA	promoter-TSS (NR_015464)	promoter-TSS (NR_015464)	121	NM_028119	107986	Mm.389334	NM_028119	ENSMUSG00000002109	Ddb2	2610043A19Rik	damage specific DNA binding protein 2	protein-coding
mm_52017.1	chr6	94592347	94592359	+	1	NA	intron (NM_026255, intron 6 of 9)	intron (NM_026255, intron 6 of 9)	14062	NR_106008	102466992		NR_106008	ENSMUSG00000098531	Mir7041	Gm27872|mmu-mir-7041	microRNA 7041	ncRNA
mm_96026.1	chr11	59548650	59548686	+	1	NA	exon (NM_145827, exon 4 of 10)	exon (NM_145827, exon 4 of 10)	5982	NM_145827	216799	Mm.54174	NM_145827	ENSMUSG00000032691	Nlrp3	AGTAVPRL|AII/AVP|Cias1|FCAS|FCU|MWS|Mmig1|NALP3|Pypaf1	NLR family, pyrin domain containing 3	protein-coding
mm_110460.1	chr12	51692076	51692092	-	1	NA	promoter-TSS (NM_001172098)	promoter-TSS (NM_001172098)	-170	NM_052973	94186	Mm.65979	NM_052973	ENSMUSG00000020954	Strn3	Gs2na|SG2NA	striatin, calmodulin binding protein 3	protein-coding
mm_89251.1	chr10	87859181	87859195	+	1	NA	5' UTR (NM_010512, exon 1 of 5)	5' UTR (NM_010512, exon 1 of 5)	136	NM_010512	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_89477.1	chr10	93551830	93551830	+	1	NA	intron (NM_175488, intron 4 of 15)	intron (NM_175488, intron 4 of 15)	11198	NM_175488	237465	Mm.477086	NM_175488	ENSMUSG00000036168	Ccdc38	4933417K05Rik	coiled-coil domain containing 38	protein-coding
mm_96190.1	chr11	61956781	61956791	+	1	NA	promoter-TSS (NM_001281818)	promoter-TSS (NM_001281818)	23	NM_001310526	432572	Mm.438022	NM_001029936	ENSMUSG00000042331	Specc1	2810012G08Rik|B230396K10Rik|Cytsb	sperm antigen with calponin homology and coiled-coil domains 1	protein-coding
mm_170751.1	chr2	156348030	156348030	-	1	NA	intron (NM_001316755, intron 8 of 9)	intron (NM_001316755, intron 8 of 9)	-35326	NM_020255	19018	Mm.389346	NM_020255	ENSMUSG00000046229	Scand1	2310003H23Rik|Leap1|PGC-2|Ppargc2	SCAN domain-containing 1	protein-coding
mm_6891.1	chr1	84696107	84696122	-	1	NA	TTS (NR_039588)	TTS (NR_039588)	107	NM_152915	227325	Mm.292560	NM_152915	ENSMUSG00000036766	Dner	A930026D19Rik|BET|Bret	delta/notch-like EGF repeat containing	protein-coding
mm_12288.1	chr2	69022962	69022979	+	1	NA	intron (NM_172856, intron 4 of 9)	intron (NM_172856, intron 4 of 9)	-112830	NM_181547	329416	Mm.90047	NM_181547	ENSMUSG00000034738	Nostrin	Daip2|mDaIP2	nitric oxide synthase trafficker	protein-coding
mm_170308.1	chr18	34952464	34952466	-	1	NA	exon (NM_010481, exon 3 of 17)	exon (NM_010481, exon 3 of 17)	1886	NM_010481	15526	Mm.209419	NM_010481	ENSMUSG00000024359	Hspa9	74kDa|Csa|Grp75|Hsc74|Hsp74|Hsp74a|Hspa9a|Mortalin|Mot-2|Mot2|Mthsp70|Pbp74	heat shock protein 9	protein-coding
mm_128613.1	chr15	58823585	58823602	-	1	NA	promoter-TSS (NM_175212)	promoter-TSS (NM_175212)	-166	NM_175212	74868	Mm.293754	NM_175212	ENSMUSG00000062373	Tmem65	2610029O13Rik|4930438D12Rik	transmembrane protein 65	protein-coding
mm_168569.1	chr11	69671311	69671319	-	1	NA	intron (NM_001159375, intron 1 of 10)	CpG	1108	NM_144958	13681	Mm.26680	NM_144958	ENSMUSG00000059796	Eif4a1	BM-010|Ddx2a|Eif4	eukaryotic translation initiation factor 4A1	protein-coding
mm_157573.1	chrX	52613898	52613910	-	1	NA	promoter-TSS (NM_016697)	promoter-TSS (NM_016697)	70	NM_016697	14734	Mm.22515	NM_016697	ENSMUSG00000055653	Gpc3	OCI-5	glypican 3	protein-coding
mm_102118.1	chr11	53300374	53300515	-	1	NA	promoter-TSS (NM_008300)	promoter-TSS (NM_008300)	35	NM_008300	15525	Mm.239865	NM_008300	ENSMUSG00000020361	Hspa4	70kDa|AI317151|APG-2|Hsp110|Hsp70RY|mKIAA4025	heat shock protein 4	protein-coding
mm_113139.1	chr13	24638485	24638510	+	1	NA	promoter-TSS (NM_001080381)	promoter-TSS (NM_001080381)	-151	NM_001080381	193385	Mm.217319	NM_029679	ENSMUSG00000036006	Fam65b	-	family with sequence similarity 65, member B	protein-coding
mm_2304.1	chr1	91540026	91540051	+	1	NA	promoter-TSS (NM_001039126)	promoter-TSS (NM_001039126)	-527	NM_001039126	65247	Mm.234152	NM_023046	ENSMUSG00000026311	Asb1	1700029O08Rik|1700054C17Rik|AI426616|AI851378|mKIAA1146	ankyrin repeat and SOCS box-containing 1	protein-coding
mm_41206.1	chr5	88531966	88531975	+	1	NA	Intergenic	Intergenic	-4073	NM_152839	16069	Mm.1192	NM_152839	ENSMUSG00000067149	Jchain	9530090F24Rik|AI323815|Igj|Jch	immunoglobulin joining chain	protein-coding
mm_96373.1	chr11	67237801	67237818	+	1	NA	promoter-TSS (NM_010855)	promoter-TSS (NM_010855)	-3	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_55526.1	chr6	70718866	70718889	-	1	NA	Intergenic	Intergenic	73298	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_157175.1	chrX	9655162	9655191	-	1	NA	3' UTR (NM_025975, exon 5 of 5)	3' UTR (NM_025975, exon 5 of 5)	7807	NM_025975	67117	Mm.29150	NM_025975	ENSMUSG00000031176	Dynlt3	2310075M16Rik|AU042796|Tcte1l	dynein light chain Tctex-type 3	protein-coding
mm_171010.1	chr2	83430666	83430669	+	1	NA	Intergenic	L1Md_T|LINE|L1	-213911	NM_026934	69082	Mm.27804	NM_026934	ENSMUSG00000027091	Zc3h15	1700006A17Rik|1810012H02Rik|2610312B22Rik|FM22|Ierepo4	zinc finger CCCH-type containing 15	protein-coding
mm_69912.1	chr7	141691392	141691399	-	1	NA	exon (NM_023566, exon 2 of 46)	exon (NM_023566, exon 2 of 46)	1055	NM_023566	17831	Mm.2041	NM_023566		Muc2	2010015E03Rik|MCM|wnn	mucin 2	protein-coding
mm_167021.1	chr7	65624003	65624003	-	1	NA	Intergenic	L1ME4b|LINE|L1	-20895	NM_172310	272396	Mm.35127	NM_172310	ENSMUSG00000030515	Tarsl2	A530046H20Rik	threonyl-tRNA synthetase-like 2	protein-coding
mm_83295.1	chr9	43225085	43225108	-	1	NA	intron (NM_178644, intron 1 of 3)	intron (NM_178644, intron 1 of 3)	14720	NM_178644	102644	Mm.246479	NM_178644	ENSMUSG00000032014	Oaf	AL024221|D130038B21Rik|D9Ucla1	out at first homolog	protein-coding
mm_54912.1	chr6	47788179	47788188	-	1	NA	Intergenic	Intergenic	15469	NR_030485	735289		NR_030485	ENSMUSG00000076060	Mir704	Mirn704|mir-704|mmu-mir-704	microRNA 704	ncRNA
mm_139376.1	chr17	51833021	51833037	+	1	NA	promoter-TSS (NM_009122)	promoter-TSS (NM_009122)	261	NM_001163632	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_29512.1	chr3	116423485	116423519	-	1	NA	5' UTR (NM_001173553, exon 1 of 14)	5' UTR (NM_001173553, exon 1 of 14)	530	NM_001080818	229776	Mm.17647	NM_001080818	ENSMUSG00000033502	Cdc14a	A830059A17Rik|CDC14A2|CDC14a1|Cdc14	CDC14 cell division cycle 14A	protein-coding
mm_138523.1	chr17	35241767	35241774	+	1	NA	promoter-TSS (NM_019693)	promoter-TSS (NM_019693)	24	NM_019693	53817	Mm.439827	NM_019693	ENSMUSG00000019432	Ddx39b	0610030D10Rik|AI428441|Bat-1|Bat1|Bat1a|D17H6S81E|D17H6S81E-1|D6S81Eh	DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B	protein-coding
mm_79498.1	chr9	57130743	57130793	+	1	NA	promoter-TSS (NM_028636)	promoter-TSS (NM_028636)	-9	NM_028636	73744	Mm.30110	NM_028636	ENSMUSG00000032295	Man2c1	1110025H24Rik	mannosidase, alpha, class 2C, member 1	protein-coding
mm_74071.1	chr8	122436881	122436889	+	1	NA	intron (NR_028354, intron 8 of 10)	intron (NR_028354, intron 8 of 10)	-3945	NM_007806	13057	Mm.271671	NM_007806	ENSMUSG00000006519	Cyba	b558|nmf333|p22-phox|p22phox	cytochrome b-245, alpha polypeptide	protein-coding
mm_77487.1	chr8	122567707	122567715	-	1	NA	promoter-TSS (NM_026014)	promoter-TSS (NM_026014)	-304	NM_026014	67177	Mm.21873	NM_026014	ENSMUSG00000006585	Cdt1	2610318F11Rik|AW545653|C76791|Ris2	chromatin licensing and DNA replication factor 1	protein-coding
mm_1591.1	chr1	74351971	74351989	+	1	NA	3' UTR (NM_019999, exon 9 of 9)	3' UTR (NM_019999, exon 9 of 9)	-10128	NM_001033345	241112	Mm.310460	NM_001033345	ENSMUSG00000073650	Catip	Gm216	ciliogenesis associated TTC17 interacting protein	protein-coding
mm_48385.1	chr5	139808502	139808525	-	1	NA	exon (NM_001161548, exon 3 of 9)	exon (NM_001161548, exon 3 of 9)	4730	NM_144914	231832	Mm.482655	NM_144914	ENSMUSG00000036687	Tmem184a	Sdmg1	transmembrane protein 184a	protein-coding
mm_136134.1	chr16	86806508	86806520	-	1	NA	Intergenic	LTR10_RN|LTR|ERVK	-547671	NM_001159331	67768	Mm.296532	NM_026366	ENSMUSG00000044442	N6amt1	5830445C04Rik|Hemk2|Pred28	N-6 adenine-specific DNA methyltransferase 1 (putative)	protein-coding
mm_54266.1	chr6	28421681	28421741	-	1	NA	promoter-TSS (NM_028900)	promoter-TSS (NM_028900)	13	NM_028900	74375	Mm.332950	NM_028900	ENSMUSG00000029708	Gcc1	4932417P04Rik	golgi coiled coil 1	protein-coding
mm_138663.1	chr17	35873827	35873838	+	1	NA	exon (NM_001146711, exon 3 of 4)	exon (NM_001146711, exon 3 of 4)	-5946	NM_026987	69192	Mm.390986	NM_026987	ENSMUSG00000024422	Dhx16	2410006N22Rik|DBP2|Ddx16|mKIAA0577	DEAH (Asp-Glu-Ala-His) box polypeptide 16	protein-coding
mm_168463.1	chr1	145965770	145965774	-	1	NA	Intergenic	L1Md_A|LINE|L1	-529894	NM_153539	215378	Mm.441817	NM_153539	ENSMUSG00000035131	Brinp3	B830045N13Rik|Fam5c	bone morphogenetic protein/retinoic acid inducible neural specific 3	protein-coding
mm_135889.1	chr16	64852522	64852543	-	1	NA	promoter-TSS (NM_001347245)	promoter-TSS (NM_001347245)	447	NM_178647	106143	Mm.10160	NM_178647	ENSMUSG00000054604	Cggbp1	AA960172|AL023996|AW045841	CGG triplet repeat binding protein 1	protein-coding
mm_7131.1	chr1	91052835	91052846	-	1	NA	promoter-TSS (NM_008515)	promoter-TSS (NM_008515)	-604	NM_001310732	16978	Mm.45039	NM_008515	ENSMUSG00000026305	Lrrfip1	AU024550|Fliiap1	leucine rich repeat (in FLII) interacting protein 1	protein-coding
mm_103412.1	chr11	75460475	75460485	-	1	NA	Intergenic	Intergenic	-1059	NR_030711	100042498	Mm.482242	NR_030711	ENSMUSG00000085148	Mir22hg	2210403K04Rik|mir-22	Mir22 host gene (non-protein coding)	ncRNA
mm_3037.1	chr1	134037535	134037552	+	1	NA	promoter-TSS (NM_021355)	promoter-TSS (NM_021355)	28	NM_021355	14264	Mm.287146	NM_021355	ENSMUSG00000041559	Fmod	AI131919|AU041740|SLRR2E	fibromodulin	protein-coding
mm_69467.1	chr7	133702488	133702509	-	1	NA	promoter-TSS (NM_001302087)	promoter-TSS (NM_001302087)	2	NM_001302087	22276	Mm.3160	NM_009479	ENSMUSG00000030979	Uros	AI415298|UROIIIS|Uros3	uroporphyrinogen III synthase	protein-coding
mm_37389.1	chr4	121017148	121017199	-	1	NA	promoter-TSS (NM_133716)	promoter-TSS (NM_133716)	74	NM_133716	69780	Mm.271819	NM_133716	ENSMUSG00000032870	Smap2	1810031K02Rik|AA408614|Smap1l	small ArfGAP 2	protein-coding
mm_28588.1	chr3	94388153	94388164	-	1	NA	intron (NR_121656, intron 3 of 9)	intron (NR_121656, intron 3 of 9)	10726	NR_121656	19885	Mm.4372	NM_011281	ENSMUSG00000028150	Rorc	Nr1f3|RORgamma|TOR|Thor	RAR-related orphan receptor gamma	protein-coding
mm_85989.1	chr9	112187876	112187878	-	1	NA	promoter-TSS (NM_001177620)	promoter-TSS (NM_001177620)	49	NM_001177615	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_7864.1	chr1	132617009	132617012	-	1	NA	intron (NM_001160318, intron 10 of 26)	intron (NM_001160318, intron 10 of 26)	25848	NM_001160316	269116	Mm.326702	NM_182716	ENSMUSG00000026442	Nfasc	AA387016|D430023G06Rik|NF|mKIAA0756	neurofascin	protein-coding
mm_21580.1	chr2	164237233	164237239	-	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	1105	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_122354.1	chr14	38898195	38898199	-	1	NA	promoter-TSS (NR_045713)	promoter-TSS (NR_045713)	-105	NR_045713	75170	Mm.372967	NR_045713	ENSMUSG00000093528	Nrg3os	4930529F24Rik	neuregulin 3, opposite strand	ncRNA
mm_80560.1	chr9	83548343	83548357	+	1	NA	promoter-TSS (NM_172507)	promoter-TSS (NM_172507)	12	NM_172507	212531	Mm.491246	NM_172507	ENSMUSG00000032261	Sh3bgrl2	A930014C21Rik|AA408038|B930089I21	SH3 domain binding glutamic acid-rich protein like 2	protein-coding
mm_113200.1	chr13	24943596	24943606	+	1	NA	5' UTR (NM_008156, exon 2 of 26)	5' UTR (NM_008156, exon 2 of 26)	449	NM_008156	14756	Mm.291831	NM_008156	ENSMUSG00000021340	Gpld1	6330541J12Rik|AW546131	glycosylphosphatidylinositol specific phospholipase D1	protein-coding
mm_67594.1	chr7	83697564	83697568	-	1	NA	intron (NM_010551, intron 2 of 18)	B4|SINE|B4	37924	NM_010551	16170	Mm.10137	NM_010551	ENSMUSG00000001741	Il16	mKIAA4048	interleukin 16	protein-coding
mm_54969.1	chr6	48737112	48737123	-	1	NA	Intergenic	Intergenic	-1930	NM_175860	16205	Mm.252599	NM_008376	ENSMUSG00000090019	Gimap1	IAP38|Imap38|imap	GTPase, IMAP family member 1	protein-coding
mm_49083.1	chr6	6862989	6863002	+	1	NA	promoter-TSS (NM_010057)	promoter-TSS (NM_010057)	-339	NM_010057	13396	Mm.439763	NM_010057	ENSMUSG00000029754	Dlx6	-	distal-less homeobox 6	protein-coding
mm_20954.1	chr2	151741173	151741177	-	1	NA	5' UTR (NM_001305244, exon 1 of 5)	5' UTR (NM_001305244, exon 1 of 5)	135	NM_212446	228769	Mm.146984	NM_144889	ENSMUSG00000032869	Psmf1	AW048666|BC012260|PI31	proteasome (prosome, macropain) inhibitor subunit 1	protein-coding
mm_839.1	chr1	51585414	51585438	+	1	NA	Intergenic	LTR82B|LTR|ERVL	-107027	NM_001310549	109019	Mm.196290	NM_028696	ENSMUSG00000026107	Nabp1	4930434H03Rik|4930442A21Rik|4930488J04Rik|4933440J18Rik|5830411E10Rik|AI852561|Nbp1|Obfc2a|Ssb2	nucleic acid binding protein 1	protein-coding
mm_84844.1	chr9	78378661	78378705	-	1	NA	promoter-TSS (NM_026480)	promoter-TSS (NM_026480)	-95	NM_026480	67968	Mm.26883	NM_026480	ENSMUSG00000032346	Ooep	2410146L05Rik|Floped|Moep19|Sddr	oocyte expressed protein	protein-coding
mm_49201.1	chr6	15364487	15364495	+	1	NA	intron (NM_053242, intron 5 of 18)	intron (NM_053242, intron 5 of 18)	178985	NM_001286607	114142	Mm.332919	NM_053242	ENSMUSG00000029563	Foxp2	2810043D05Rik|AI449000|CAG-16|D0Kist7	forkhead box P2	protein-coding
mm_155250.1	chrX	57223764	57223776	+	1	NA	3' UTR (NM_011616, exon 5 of 5)	3' UTR (NM_011616, exon 5 of 5)	11627	NM_011616	21947	Mm.4861	NM_011616	ENSMUSG00000031132	Cd40lg	CD154|CD40-L|Cd40l|HIGM1|IGM|IMD3|Ly-62|Ly62|T-BAM|TRAP|Tnfsf5|Tnlg8b|gp39	CD40 ligand	protein-coding
mm_61224.1	chr7	64501688	64501702	+	1	NA	promoter-TSS (NM_001291167)	promoter-TSS (NM_001291167)	-11	NM_007461	11784	Mm.4657	NM_007461	ENSMUSG00000030519	Apba2	X11-like|X11L|XllL|mXllL	amyloid beta (A4) precursor protein-binding, family A, member 2	protein-coding
mm_11376.1	chr2	31143413	31143443	+	1	NA	Intergenic	Intergenic	-1420	NM_001038700	14269	Mm.52297	NM_019406	ENSMUSG00000075415	Fnbp1	1110057E06Rik|2210010H06Rik|FBP1|Fbp17	formin binding protein 1	protein-coding
mm_118919.1	chr14	26766443	26766456	+	1	NA	Intergenic	Intergenic	-96603	NM_178668	211948	Mm.290758	NM_178668	ENSMUSG00000043702	Pde12	2'-PDE|E430028B21Rik	phosphodiesterase 12	protein-coding
mm_82077.1	chr9	122999177	122999181	+	1	NA	exon (NM_010620, exon 21 of 35)	exon (NM_010620, exon 21 of 35)	-22147	NM_025339	66079	Mm.482265	NM_025339	ENSMUSG00000066233	Tmem42	0610027O18Rik|4933429E06Rik|AV003444|D9Ertd662e	transmembrane protein 42	protein-coding
mm_120055.1	chr14	56672460	56672473	+	1	NA	exon (NM_023773, exon 2 of 14)	exon (NM_023773, exon 2 of 14)	4218	NM_023773	75339	Mm.152466	NM_023773	ENSMUSG00000079184	Mphosph8	1500035L22Rik|4930548G07Rik|AU040635	M-phase phosphoprotein 8	protein-coding
mm_113389.1	chr13	33039972	33040005	+	1	NA	3' UTR (NM_011452, exon 7 of 7)	3' UTR (NM_011452, exon 7 of 7)	12574	NM_011452	20706	Mm.45371	NM_011452	ENSMUSG00000021403	Serpinb9b	1600019A21Rik|R86|SPI-CI|Spi10|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 9b	protein-coding
mm_80025.1	chr9	68640576	68640623	+	1	NA	Intergenic	Intergenic	-13187	NM_001289917	19883	Mm.378450	NM_013646	ENSMUSG00000032238	Rora	9530021D13Rik|Nr1f1|ROR1|ROR2|ROR3|nmf267|sg|staggerer|tmgc26	RAR-related orphan receptor alpha	protein-coding
mm_143204.1	chr17	62815105	62815112	-	1	NA	intron (NM_010109, intron 1 of 3)	(A)n|Simple_repeat|Simple_repeat	66209	NM_207654	13640	Mm.7978	NM_010109	ENSMUSG00000048915	Efna5	AL-1|AV158822|EFL-5|Ephrin-A5|Epl7|LERK-7|RAGS	ephrin A5	protein-coding
mm_14022.1	chr2	122150990	122151001	+	1	NA	exon (NM_009735, exon 2 of 4)	exon (NM_009735, exon 2 of 4)	3308	NM_009735	12010	Mm.163	NM_009735	ENSMUSG00000060802	B2m	Ly-m11|beta2-m|beta2m	beta-2 microglobulin	protein-coding
mm_67908.1	chr7	99695859	99695871	-	1	NA	promoter-TSS (NM_001252531)	promoter-TSS (NM_001252531)	-56	NM_001252531	101488	Mm.11249	NM_175316	ENSMUSG00000030737	Slco2b1	AI060904|AI852653|OATP-B|Slc21a9	solute carrier organic anion transporter family, member 2b1	protein-coding
mm_18046.1	chr2	39065439	39065503	-	1	NA	promoter-TSS (NR_110968)	promoter-TSS (NR_110968)	70	NR_110968	76899	Mm.131098	NM_029793	ENSMUSG00000026754	Golga1	0710001G09Rik|2210418B03Rik|AW107649|Golgi97|awag|golgin-97	golgi autoantigen, golgin subfamily a, 1	protein-coding
mm_120829.1	chr14	75176590	75176605	+	1	NA	intron (NM_008879, intron 1 of 16)	intron (NM_008879, intron 1 of 16)	40172	NM_008879	18826	Mm.153911	NM_008879	ENSMUSG00000021998	Lcp1	AW536232|D14Ertd310e|LCP-1|Pls2|pp65	lymphocyte cytosolic protein 1	protein-coding
mm_88039.1	chr10	67537210	67537213	+	1	NA	promoter-TSS (NM_010118)	promoter-TSS (NM_010118)	-658	NM_010118	13654	Mm.290421	NM_010118	ENSMUSG00000037868	Egr2	Egr-2|Krox-20|Krox20|NGF1-B|Zfp-25|Zfp-6	early growth response 2	protein-coding
mm_168366.1	chr11	17221336	17221336	+	1	NA	intron (NM_178909, intron 2 of 7)	LSU-rRNA_Hsa|rRNA|rRNA	9443	NM_178909	103784	Mm.298132	NM_178909	ENSMUSG00000078970	Wdr92	AI553587|HZGJ	WD repeat domain 92	protein-coding
mm_74790.1	chr8	22185822	22185840	-	1	NA	promoter-TSS (NM_001004140)	promoter-TSS (NM_001004140)	-12	NM_001004140	80986	Mm.22448	NM_001004140	ENSMUSG00000037725	Ckap2	AI461656|AW228814|LB1	cytoskeleton associated protein 2	protein-coding
mm_39211.1	chr4	156053914	156053915	-	1	NA	promoter-TSS (NR_029958)	promoter-TSS (NR_029958)	73	NR_029958	723865		NR_029958	ENSMUSG00000065427	Mir429	Mirn429|mir-429|mmu-mir-429	microRNA 429	ncRNA
mm_23091.1	chr3	37063043	37063049	+	1	NA	promoter-TSS (NM_009350)	promoter-TSS (NM_009350)	-610	NM_009350	21744	Mm.8122	NM_009350	ENSMUSG00000027719	Adad1	Tenr	adenosine deaminase domain containing 1 (testis specific)	protein-coding
mm_129493.1	chr15	78803016	78803050	-	1	NA	promoter-TSS (NM_130859)	promoter-TSS (NM_130859)	9	NM_130859	105844	Mm.17629	NM_130859	ENSMUSG00000033170	Card10	AI449026|Bimp1|Carma3	caspase recruitment domain family, member 10	protein-coding
mm_164391.1	chr16	33169758	33169788	+	1	NA	Intergenic	RMER19B|LTR|ERVK	-15298	NM_176840	106326	Mm.486405	NM_176840	ENSMUSG00000022807	Osbpl11	9430097N02Rik|AI132306|AU019795|ORP-11	oxysterol binding protein-like 11	protein-coding
mm_24885.1	chr3	96104499	96104571	+	1	NA	promoter-TSS (NM_001025614)	promoter-TSS (NM_001025614)	8	NM_001025614	229603	Mm.272336	NM_001025613	ENSMUSG00000038495	Otud7b	2900060B22Rik|4930463P07Rik|AI462125|CEZANNE|Trabid2|Za20d1	OTU domain containing 7B	protein-coding
mm_90930.1	chr10	12868191	12868227	-	1	NA	Intergenic	Intergenic	-6474	NM_011682	22288	Mm.331784	NM_011682	ENSMUSG00000019820	Utrn	AA589569|DRP|Dmdl	utrophin	protein-coding
mm_59399.1	chr7	26766709	26766719	+	1	NA	intron (NM_007814, intron 6 of 8)	intron (NM_007814, intron 6 of 8)	9572	NM_007814	13090	Mm.14098	NM_007814	ENSMUSG00000066704	Cyp2b19	CYPIIB19	cytochrome P450, family 2, subfamily b, polypeptide 19	protein-coding
mm_170218.1	chr17	76296766	76296785	+	1	NA	Intergenic	RLTR9E|LTR|ERVK	435752	NR_033456	100043885	Mm.127562	NR_033456		Gm4710	-	predicted gene 4710	ncRNA
mm_155587.1	chrX	79904359	79904363	+	1	NA	Intergenic	Intergenic	-232926	NM_028025	71967	Mm.379207	NM_028025	ENSMUSG00000046942	Mageb16	2410003J06Rik	melanoma antigen family B, 16	protein-coding
mm_54194.1	chr6	24528026	24528034	-	1	NA	promoter-TSS (NM_001311068)	promoter-TSS (NM_001311068)	-114	NM_080847	78910	Mm.160150	NM_080847	ENSMUSG00000029685	Asb15	4930400E23Rik|Asb-15	ankyrin repeat and SOCS box-containing 15	protein-coding
mm_47846.1	chr5	134386216	134386219	-	1	NA	intron (NM_001347488, intron 14 of 27)	PB1D10|SINE|Alu	70045	NM_001081465	57080	Mm.332735	NM_020331	ENSMUSG00000023079	Gtf2ird1	1700012P16Rik|BEN|Cream1|ESTM9|GTF3|Gtf2il|MusTRD1|Tg(Alb1-Myc)166.8Sst|WBSCR11|X83320	general transcription factor II I repeat domain-containing 1	protein-coding
mm_151309.1	chr19	55743410	55743437	+	1	NA	intron (NR_138565, intron 3 of 15)	intron (NR_138565, intron 3 of 15)	1613	NM_001142923	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_46473.1	chr5	105131328	105131332	-	1	NA	intron (NM_008620, intron 3 of 10)	intron (NM_008620, intron 3 of 10)	8222	NM_008620	17472	Mm.440525	NM_008620	ENSMUSG00000079363	Gbp4	AW228052|Mag-2|Mpa-2|Mpa2	guanylate binding protein 4	protein-coding
mm_91743.1	chr10	49231891	49231897	-	1	NA	intron (NM_001111268, intron 14 of 16)	intron (NM_001111268, intron 14 of 16)	-136051	NR_046212	100418235	Mm.185993	NR_046212		C130030K03Rik	-	proteasome (prosome, macropain) subunit, alpha type 6 pseudogene	pseudo
mm_22728.1	chr3	19644577	19644589	+	1	NA	5' UTR (NM_001081281, exon 1 of 10)	5' UTR (NM_001081281, exon 1 of 10)	123	NM_001081281	381485	Mm.35419	NM_001081281	ENSMUSG00000060913	Trim55	D830041C10Rik|Murf2|Rnf29	tripartite motif-containing 55	protein-coding
mm_60550.1	chr7	44480957	44480973	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-3552	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_36153.1	chr4	59549315	59549325	-	1	NA	promoter-TSS (NM_144904)	promoter-TSS (NM_144904)	44	NM_178164	230257	Mm.331640	NM_144904	ENSMUSG00000028382	Ptbp3	5830471K22Rik|AA407443|AI462022|AW107884|C86549|Rod1	polypyrimidine tract binding protein 3	protein-coding
mm_134325.1	chr16	16358513	16358523	-	1	NA	promoter-TSS (NM_001276341)	promoter-TSS (NM_001276341)	57	NM_001276341	74006	Mm.218820	NM_152816	ENSMUSG00000022789	Dnm1l	6330417M19Rik|AI450666|Dlp1|Dnmlp1|Drp1|python	dynamin 1-like	protein-coding
mm_90836.1	chr10	8511622	8511627	-	1	NA	intron (NM_177387, intron 1 of 7)	intron (NM_177387, intron 1 of 7)	7201	NM_177387	338362	Mm.41163	NM_177387	ENSMUSG00000047712	Ust	D930010O20Rik|UA2OST	uronyl-2-sulfotransferase	protein-coding
mm_133094.1	chr16	64851955	64851959	+	1	NA	promoter-TSS (NM_178647)	promoter-TSS (NM_178647)	-128	NM_178647	106143	Mm.10160	NM_178647	ENSMUSG00000054604	Cggbp1	AA960172|AL023996|AW045841	CGG triplet repeat binding protein 1	protein-coding
mm_76686.1	chr8	94098343	94098388	-	1	NA	5' UTR (NM_026116, exon 1 of 17)	5' UTR (NM_026116, exon 1 of 17)	446	NM_026116	67378	Mm.292107	NM_026116	ENSMUSG00000031755	Bbs2	2410125H22Rik|AI447581	Bardet-Biedl syndrome 2 (human)	protein-coding
mm_162226.1	chrX	147993109	147993109	+	1	NA	intron (NM_011022, intron 1 of 6)	intron (NM_011022, intron 1 of 6)	116	NM_001122734	100039934	Mm.474426	NM_001122734	ENSMUSG00000095621	Gm15085	OTTMUSG00000018973	predicted gene 15085	protein-coding
mm_21384.1	chr2	157501330	157501336	-	1	NA	Intergenic	Intergenic	-58745	NM_001291129	18111	Mm.34330	NM_010923	ENSMUSG00000067786	Nnat	5730414I02Rik|AW107673|Peg5	neuronatin	protein-coding
mm_170146.1	chr17	45442062	45442081	+	1	NA	non-coding (NR_130961, exon 3 of 3)	non-coding (NR_130961, exon 3 of 3)	8240	NR_130961	105246278	Mm.206588	NR_130960	ENSMUSG00000097119	B230354K17Rik	-	RIKEN cDNA B230354K17 gene	ncRNA
mm_45309.1	chr5	65428355	65428365	-	1	NA	intron (NM_009466, intron 1 of 11)	intron (NM_009466, intron 1 of 11)	7482	NM_009466	22235	Mm.344831	NM_009466	ENSMUSG00000029201	Ugdh	Udpgdh	UDP-glucose dehydrogenase	protein-coding
mm_44137.1	chr5	150118627	150118684	+	1	NA	Intergenic	CpG	99980	NM_001289566	140498	Mm.444643	NM_080468	ENSMUSG00000053368	Rxfp2	Gpr106|Great|Lgr8	relaxin/insulin-like family peptide receptor 2	protein-coding
mm_99288.1	chr11	101322573	101322591	+	1	NA	3' UTR (NM_011192, exon 11 of 11)	3' UTR (NM_011192, exon 11 of 11)	-2481	NM_178932	237940	Mm.302277	NM_178932	ENSMUSG00000078651	Aoc2	RAO	amine oxidase, copper containing 2 (retina-specific)	protein-coding
mm_14925.1	chr2	151488602	151488606	+	1	NA	Intergenic	RLTR17D_Mm|LTR|ERVK	-5578	NM_001291074	386649	Mm.419479	NM_198326	ENSMUSG00000027455	Nsfl1c	Munc-18c|Stxbp3a|p47	NSFL1 (p97) cofactor (p47)	protein-coding
mm_142210.1	chr17	36995493	36995527	-	1	NA	Intergenic	B3|SINE|B2	-5653	NM_001168502	22715	Mm.305561	NM_009559	ENSMUSG00000036036	Zfp57	G19|Zfp-57	zinc finger protein 57	protein-coding
mm_114888.1	chr13	94301455	94301483	+	1	NA	Intergenic	Intergenic	-15638	NM_001346609	107767	Mm.201455	NM_029153	ENSMUSG00000021687	Scamp1	4930505M11Rik|AI415563|AW122395	secretory carrier membrane protein 1	protein-coding
mm_26114.1	chr3	137626631	137626636	+	1	NA	3' UTR (NM_030143, exon 3 of 3)	3' UTR (NM_030143, exon 3 of 3)	2961	NM_030143	73284	Mm.250841	NM_030143	ENSMUSG00000046818	Ddit4l	1700037B15Rik|1700108M02Rik|REDD2|RTP801L|Smhs1	DNA-damage-inducible transcript 4-like	protein-coding
mm_137321.1	chr17	24896489	24896530	+	1	NA	promoter-TSS (NM_019730)	promoter-TSS (NM_019730)	9	NM_019730	79059	Mm.430765	NM_019730	ENSMUSG00000073435	Nme3	1810009F08Rik|AI413736|DR-nm23|Ndk3|Nm23-DR|Nm23-M3	NME/NM23 nucleoside diphosphate kinase 3	protein-coding
mm_121482.1	chr14	121035806	121035826	+	1	NA	5' UTR (NM_134082, exon 1 of 27)	5' UTR (NM_134082, exon 1 of 27)	242	NM_134082	223254	Mm.223980	NM_134082	ENSMUSG00000025555	Farp1	AW228844|BC030329|Cdep	FERM, RhoGEF (Arhgef) and pleckstrin domain protein 1 (chondrocyte-derived)	protein-coding
mm_12626.1	chr2	74704533	74704545	+	1	NA	promoter-TSS (NM_001290730)	promoter-TSS (NM_001290730)	-76	NM_001290731	15437	Mm.280673	NM_008276	ENSMUSG00000027102	Hoxd8	4921540P06Rik|AI047735|Hox-4.3|Hox-5.4	homeobox D8	protein-coding
mm_145127.1	chr18	44539467	44539469	+	1	NA	intron (NM_001085373, intron 3 of 18)	intron (NM_001085373, intron 3 of 18)	-122197	NR_026853	626275	Mm.427116	NR_026853	ENSMUSG00000097610	A930012L18Rik	-	RIKEN cDNA A930012L18 gene	ncRNA
mm_121004.1	chr14	79515715	79515732	+	1	NA	promoter-TSS (NM_001286412)	promoter-TSS (NM_001286412)	49	NM_001286411	13709	Mm.20938	NM_007920	ENSMUSG00000036461	Elf1	Elf-1|Sts1|mElf-1|p70	E74-like factor 1	protein-coding
mm_99299.1	chr11	101348013	101348019	+	1	NA	Intergenic	RMER5|LTR|ERV1	17410	NM_009675	11754	Mm.67281	NM_009675	ENSMUSG00000019326	Aoc3	SSAO|VAP1	amine oxidase, copper containing 3	protein-coding
mm_30119.1	chr3	141211765	141211817	-	1	NA	5' UTR (NM_008811, exon 1 of 1)	5' UTR (NM_008811, exon 1 of 1)	564	NM_008811	18598	Mm.4223	NM_008811	ENSMUSG00000047674	Pdha2	Pdhal	pyruvate dehydrogenase E1 alpha 2	protein-coding
mm_56409.1	chr6	97205550	97205572	-	1	NA	promoter-TSS (NM_011666)	promoter-TSS (NM_011666)	86	NM_001301858	22200	Mm.277626	NM_011666	ENSMUSG00000030061	Uba3	A830034N06Rik|AI256736|AI848246|AW546539|Ube1c	ubiquitin-like modifier activating enzyme 3	protein-coding
mm_26033.1	chr3	135462960	135463008	+	1	NA	exon (NM_025356, exon 7 of 8)	exon (NM_025356, exon 7 of 8)	-22627	NM_027288	110173	Mm.280536	NM_027288	ENSMUSG00000028164	Manba	2410030O07Rik|B930014J03Rik|Bmn	mannosidase, beta A, lysosomal	protein-coding
mm_114787.1	chr13	89227468	89227473	+	1	NA	intron (NM_010103, intron 8 of 9)	intron (NM_010103, intron 8 of 9)	-313166	NM_013500	12950	Mm.266790	NM_013500	ENSMUSG00000021613	Hapln1	BB099155|CLP|Crtl1|Crtl1l|LP|LP-1	hyaluronan and proteoglycan link protein 1	protein-coding
mm_96881.1	chr11	70238011	70238031	+	1	NA	promoter-TSS (NM_001177601)	promoter-TSS (NM_001177601)	-107	NM_145758	104457	Mm.30016	NM_026757	ENSMUSG00000020831	0610010K14Rik	1110020A23Rik|AL033328|AU045833|Bap18	RIKEN cDNA 0610010K14 gene	protein-coding
mm_85022.1	chr9	88438886	88438892	-	1	NA	promoter-TSS (NM_172926)	promoter-TSS (NM_172926)	62	NM_172926	244962	Mm.439873	NM_172926	ENSMUSG00000032422	Snx14	B830022K16|C330035N22Rik|YR-14	sorting nexin 14	protein-coding
mm_102450.1	chr11	59787314	59787322	-	1	NA	promoter-TSS (NR_110894)	promoter-TSS (NR_110894)	-96	NR_110894	194908	Mm.344651	NM_183139	ENSMUSG00000043648	Pld6	4933433K01Rik|Gm10|Zuc|mZuc|mitoPLD	phospholipase D family, member 6	protein-coding
mm_58839.1	chr7	16838125	16838141	+	1	NA	intron (NM_133789, intron 14 of 17)	intron (NM_133789, intron 14 of 17)	-4769	NM_001252458	101540	Mm.1881	NM_178900	ENSMUSG00000041187	Prkd2	AI325941|PKD2	protein kinase D2	protein-coding
mm_36489.1	chr4	83203777	83203777	-	1	NA	Intergenic	MT2A|LTR|ERVL	120412	NM_027238	69863	Mm.5540	NM_025782	ENSMUSG00000038172	Ttc39b	1810054D07Rik|9130422G05Rik|AI450603|AV103077|AW215585	tetratricopeptide repeat domain 39B	protein-coding
mm_119109.1	chr14	31001603	31001628	+	1	NA	promoter-TSS (NM_026911)	promoter-TSS (NM_026911)	51	NM_026911	69019	Mm.28852	NM_026911	ENSMUSG00000021917	Spcs1	1810004F21Rik	signal peptidase complex subunit 1 homolog (S. cerevisiae)	protein-coding
mm_108885.1	chr12	99965928	99965946	+	1	NA	5' UTR (NM_001164426, exon 2 of 3)	5' UTR (NM_001164426, exon 2 of 3)	1438	NM_001164427	217826	Mm.312335	NM_146037	ENSMUSG00000045404	Kcnk13	BB085247|F730021E22Rik|Gm1570|Gm1685	potassium channel, subfamily K, member 13	protein-coding
mm_27349.1	chr3	50414965	50414972	-	1	NA	intron (NM_011990, intron 6 of 11)	intron (NM_011990, intron 6 of 11)	28645	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_163386.1	chr12	54374354	54374358	+	1	NA	Intergenic	Intergenic	16962	NR_033689	665239	Mm.26856	NR_033689		Gm7550	EG665239|Gm666	predicted gene 7550	ncRNA
mm_20255.1	chr2	126598034	126598047	-	1	NA	intron (NM_008230, intron 9 of 11)	intron (NM_008230, intron 9 of 11)	20638	NM_008230	15186	Mm.18603	NM_008230	ENSMUSG00000027360	Hdc	AW108189|Hdc-a|Hdc-c|Hdc-e|Hdc-s	histidine decarboxylase	protein-coding
mm_66573.1	chr7	45333734	45333751	-	1	NA	promoter-TSS (NM_175130)	promoter-TSS (NM_175130)	38	NM_175130	68667	Mm.439890	NM_175130	ENSMUSG00000038260	Trpm4	1110030C19Rik|AW047689|LTRPC4|LTrpC-4|TRPM4B	transient receptor potential cation channel, subfamily M, member 4	protein-coding
mm_65284.1	chr7	24435463	24435469	-	1	NA	intron (NM_199013, intron 2 of 2)	intron (NM_199013, intron 2 of 2)	10216	NM_199013	210145	Mm.33811	NM_199013	ENSMUSG00000062028	Irgc1	F630044M05Rik|Gm1102|Gm474|Ifgge|Iigp5|Irgc	immunity-related GTPase family, cinema 1	protein-coding
mm_41140.1	chr5	87887476	87887490	+	1	NA	exon (NM_027128, exon 4 of 10)	exon (NM_027128, exon 4 of 10)	1788	NM_027128	69592	Mm.389652	NM_027128	ENSMUSG00000009580	Odam	2310011G06Rik|APIN	odontogenic, ameloblast asssociated	protein-coding
mm_4569.1	chr1	177711246	177711251	+	1	NA	Intergenic	RLTR25B|LTR|ERVK	-18566	NM_027077	69428	Mm.84467	NM_027077	ENSMUSG00000015962	1700016C15Rik	-	RIKEN cDNA 1700016C15 gene	protein-coding
mm_13961.1	chr2	121413934	121413959	+	1	NA	promoter-TSS (NM_007952)	promoter-TSS (NM_007952)	44	NM_007952	14827	Mm.263177	NM_007952	ENSMUSG00000027248	Pdia3	58kDa|ERp57|ERp60|ERp61|Erp|Grp58|PDI|PDI-Q2|PI-PLC|PLC[a]|Plca	protein disulfide isomerase associated 3	protein-coding
mm_124875.1	chr15	10223810	10223826	+	1	NA	promoter-TSS (NM_001253781)	promoter-TSS (NM_001253781)	-88	NM_001253781	19116	Mm.10516	NM_011169	ENSMUSG00000005268	Prlr	AI987712|Pr-1|Pr-3|Prlr-rs1	prolactin receptor	protein-coding
mm_169357.1	chr14	27141852	27141852	+	1	NA	Intergenic	Intergenic	-2141	NM_001289686	71704	Mm.248606	NM_027871	ENSMUSG00000021895	Arhgef3	1200004I24Rik|9830169H03Rik|C76747|Xpln	Rho guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_27802.1	chr3	75956250	75956260	-	1	NA	exon (NM_175193, exon 1 of 15)	exon (NM_175193, exon 1 of 15)	694	NM_175193	73124	Mm.249232	NM_175193	ENSMUSG00000034109	Golim4	3110027H23Rik|GIMPC|GPP130|Golph4|P138	golgi integral membrane protein 4	protein-coding
mm_172565.1	chr8	110846745	110846747	-	1	NA	promoter-TSS (NM_133973)	promoter-TSS (NM_133973)	57	NM_133953	101943	Mm.236123	NM_133953	ENSMUSG00000033732	Sf3b3	1810061H24Rik|5730409A01Rik|AA409318|D8Ertd633e|RSE1|SAP130|mKIAA0017	splicing factor 3b, subunit 3	protein-coding
mm_137114.1	chr17	22424262	22424276	+	1	NA	promoter-TSS (NM_001331197)	promoter-TSS (NM_001331197)	67	NM_001331198	74149	Mm.30767	NM_198003	ENSMUSG00000071266	Zfp946	1300003B13Rik	zinc finger protein 946	protein-coding
mm_111703.1	chr12	103694033	103694049	-	1	NA	intron (NM_026687, intron 2 of 5)	intron (NM_026687, intron 2 of 5)	648	NM_001164742	68348	Mm.20149	NM_026687	ENSMUSG00000021081	Serpina1f	0610012A11Rik|AI327419|Serpina2|epserin	serine (or cysteine) peptidase inhibitor, clade A, member 1F	protein-coding
mm_136171.1	chr16	88627659	88627667	-	1	NA	promoter-TSS (NM_027173)	promoter-TSS (NM_027173)	3	NM_027173	69699	Mm.158296	NM_027173	ENSMUSG00000045331	2310079G19Rik	-	RIKEN cDNA 2310079G19 gene	protein-coding
mm_56457.1	chr6	98342644	98342656	-	1	NA	5' UTR (NM_001128092, exon 1 of 4)	5' UTR (NM_001128092, exon 1 of 4)	104	NM_001128092	330390	Mm.484161	NM_001128092	ENSMUSG00000090667	Gm765	-	predicted gene 765	protein-coding
mm_78207.1	chr9	21484563	21484566	+	1	NA	intron (NM_007871, intron 11 of 19)	B2_Mm2|SINE|B2	12000	NR_029585	387194		NR_029585	ENSMUSG00000065547	Mir199a-1	Mirn199|Mirn199a-1|mir-199a-1	microRNA 199a-1	ncRNA
mm_156654.1	chrX	157702869	157702878	+	1	NA	intron (NR_045569, intron 1 of 6)	intron (NR_045569, intron 1 of 6)	3900	NR_103722	66106	Mm.140340	NM_025357	ENSMUSG00000041476	Smpx	1010001C09Rik|Csl	small muscle protein, X-linked	protein-coding
mm_62476.1	chr7	101863782	101863793	+	1	NA	intron (NM_001252552, intron 4 of 6)	intron (NM_001252552, intron 4 of 6)	-6597	NM_001303239	14276	Mm.439666	NM_008035	ENSMUSG00000032725	Folr2	FBP2|FR-P3|FR-beta|Folbp-2|Folbp2	folate receptor 2 (fetal)	protein-coding
mm_170043.1	chr17	24589168	24589177	-	1	NA	intron (NM_013630, intron 34 of 45)	B1_Mus1|SINE|Alu	39222	NM_013630	18763	Mm.30435	NM_013630	ENSMUSG00000032855	Pkd1	PC1|mFLJ00285	polycystic kidney disease 1 homolog	protein-coding
mm_90852.1	chr10	8814004	8814010	-	1	NA	intron (NM_175155, intron 4 of 19)	intron (NM_175155, intron 4 of 19)	72063	NM_175155	70097	Mm.338275	NM_175155	ENSMUSG00000015305	Sash1	1100001C18Rik|2500002E12Rik|A330076K04Rik|mKIAA0790	SAM and SH3 domain containing 1	protein-coding
mm_136684.1	chr17	6746310	6746316	+	1	NA	intron (NM_009510, intron 7 of 12)	intron (NM_009510, intron 7 of 12)	36467	NM_009510	22350	Mm.277812	NM_009510	ENSMUSG00000052397	Ezr	AW146364|R75297|Vil2|p81	ezrin	protein-coding
mm_109003.1	chr12	103314945	103314962	+	1	NA	promoter-TSS (NM_001195726)	promoter-TSS (NM_001195726)	-6	NM_001195726	100504156	Mm.425749	NM_001195726	ENSMUSG00000096753	Fam181a	EG544888	family with sequence similarity 181, member A	protein-coding
mm_78439.1	chr9	32095792	32095825	+	1	NA	Intergenic	Intergenic	-20328	NM_001195632	330914	Mm.46683	NM_177379	ENSMUSG00000041444	Arhgap32	3426406O18Rik|Gc-gap|Grit|Px-rics|Rics|mKIAA0712|p200Rhogap|p250Gap	Rho GTPase activating protein 32	protein-coding
mm_157420.1	chrX	38564191	38564207	-	1	NA	exon (NM_028288, exon 4 of 23)	exon (NM_028288, exon 4 of 23)	11997	NM_028288	72584	Mm.327675	NM_028288	ENSMUSG00000031095	Cul4b	2700050M05Rik|AA409770|CUL-4B|mKIAA0695	cullin 4B	protein-coding
mm_162204.1	chrX	135494617	135494617	+	1	NA	promoter-TSS (NM_001099321).2	promoter-TSS (NM_001099321).2	11	NM_001099321	100040635	Mm.336240	NM_001099321	ENSMUSG00000079432	Gm15023	OTTMUSG00000018782	predicted gene 15023	protein-coding
mm_169733.1	chr15	82249697	82249698	-	1	NA	Intergenic	B1_Mus1|SINE|Alu	-2700	NR_037697	76505	Mm.23023	NR_037697	ENSMUSG00000068099	1500009C09Rik	-	RIKEN cDNA 1500009C09 gene	ncRNA
mm_11787.1	chr2	42530666	42530668	+	1	NA	intron (NM_053011, intron 1 of 90)	intron (NM_053011, intron 1 of 90)	-83099	NR_105754	102465171		NR_105754	ENSMUSG00000098660	Mir6336	Gm27584|mmu-mir-6336	microRNA 6336	ncRNA
mm_97127.1	chr11	74926865	74926887	+	1	NA	intron (NM_001002764, intron 1 of 18)	intron (NM_001002764, intron 1 of 18)	1004	NM_001002764	103677	Mm.288460	NM_001002764	ENSMUSG00000038290	Smg6	AI317223|AU041178	Smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans)	protein-coding
mm_166577.1	chr6	52233989	52233996	-	1	NA	exon (NM_008263, exon 1 of 2)	exon (NM_008263, exon 1 of 2)	947	NM_008263	15395	Mm.5	NM_008263	ENSMUSG00000000938	Hoxa10	Hox-1.8|Hoxa-10	homeobox A10	protein-coding
mm_44973.1	chr5	36816174	36816188	-	1	NA	exon (NM_008550, exon 10 of 19)	exon (NM_008550, exon 10 of 19)	14468	NM_008550	17160	Mm.761	NM_008550	ENSMUSG00000029119	Man2b2	mKIAA0935	mannosidase 2, alpha B2	protein-coding
mm_67215.1	chr7	74430249	74430257	-	1	NA	intron (NM_001038643, intron 2 of 10)	RSINE1|SINE|B4	124527	NM_023908	108116	Mm.425467	NM_023908	ENSMUSG00000025790	Slco3a1	5830414C08Rik|Anr1|MJAM|OATP-D|R75096|Slc21a11	solute carrier organic anion transporter family, member 3a1	protein-coding
mm_172470.1	chr7	43607165	43607183	+	1	NA	promoter-TSS (NM_028913)	promoter-TSS (NM_028913)	5	NM_028913	74400	Mm.159188	NM_028913	ENSMUSG00000055102	Zfp819	4930427I11Rik|4933405K07Rik	zinc finger protein 819	protein-coding
mm_158599.1	chrX	151520987	151520997	-	1	NA	5' UTR (NM_001113354, exon 1 of 22)	5' UTR (NM_001113354, exon 1 of 22)	320	NM_001113354	320595	Mm.17156	NM_177201	ENSMUSG00000041229	Phf8	9830141C09Rik|mKIAA1111	PHD finger protein 8	protein-coding
mm_143131.1	chr17	57215148	57215178	-	1	NA	exon (NM_009778, exon 25 of 41)	exon (NM_009778, exon 25 of 41)	2065	NR_105944	102465591		NR_105944	ENSMUSG00000099066	Mir6978	Gm27858|mmu-mir-6978	microRNA 6978	ncRNA
mm_6835.1	chr1	84230235	84230247	-	1	NA	intron (NM_001003948, intron 1 of 2)	RSINE1|SINE|B4	-11280	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_121037.1	chr14	80000293	80000309	+	1	NA	promoter-TSS (NM_001030294)	promoter-TSS (NM_001030294)	-1	NM_001030294	380924	Mm.26456	NM_001030294	ENSMUSG00000022026	Olfm4	GC1|GW112|Gm296|Gm913|OlfD|pPD4	olfactomedin 4	protein-coding
mm_107954.1	chr12	72441951	72441970	+	1	NA	promoter-TSS (NM_001142728)	promoter-TSS (NM_001142728)	94	NM_030070	78257	Mm.266280	NM_030070	ENSMUSG00000021090	Lrrc9	4921529O18Rik|4930432K16Rik	leucine rich repeat containing 9	protein-coding
mm_25720.1	chr3	122729710	122729735	+	1	NA	intron (NM_153422, intron 1 of 20)	CpG	564	NM_153422	242202	Mm.134911	NM_153422	ENSMUSG00000053965	Pde5a	Cgbpde|Cn5n|PDE5a2|Pde5|Pde5a1	phosphodiesterase 5A, cGMP-specific	protein-coding
mm_139098.1	chr17	46910489	46910499	+	1	NA	promoter-TSS (NM_008938)	promoter-TSS (NM_008938)	9	NM_008938	19133	Mm.291370	NM_008938	ENSMUSG00000023978	Prph2	AOFMD|AVMD|Nmf193|PRPH|RP7|Rd-2|Rd2|Rds|Tspan22|rds	peripherin 2	protein-coding
mm_83764.1	chr9	51974808	51974812	-	1	NA	Intergenic	Intergenic	-11208	NM_001301728	14148	Mm.1061	NM_007996	ENSMUSG00000032051	Fdx1	-	ferredoxin 1	protein-coding
mm_155092.1	chrX	48146550	48146560	+	1	NA	5' UTR (NM_028773, exon 1 of 8)	5' UTR (NM_028773, exon 1 of 8)	119	NM_028773	74131	Mm.276131	NM_028773	ENSMUSG00000031101	Sash3	1200013B08Rik|AW413946|SLY1	SAM and SH3 domain containing 3	protein-coding
mm_96896.1	chr11	70437929	70437949	+	1	NA	promoter-TSS (NR_106064)	promoter-TSS (NR_106064)	-316	NR_106064	102465670		NR_106064	ENSMUSG00000099109	Mir7115	Gm27902|mmu-mir-7115	microRNA 7115	ncRNA
mm_111103.1	chr12	80924411	80924425	-	1	NA	promoter-TSS (NR_033786)	promoter-TSS (NR_033786)	29	NR_033786	67340	Mm.386790	NR_033786	ENSMUSG00000101912	1700052I22Rik	-	RIKEN cDNA 1700052I22 gene	ncRNA
mm_90734.1	chr10	5309405	5309451	-	1	NA	exon (NM_001347711, exon 46 of 146)	exon (NM_001347711, exon 46 of 146)	-114721	NM_001079686	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_62405.1	chr7	101163030	101163037	+	1	NA	intron (NM_199012, intron 3 of 20)	intron (NM_199012, intron 3 of 20)	54258	NM_199012	207278	Mm.263041	NM_199012	ENSMUSG00000030691	Fchsd2	BC034086|R74866|Sh3md3|mKIAA0769	FCH and double SH3 domains 2	protein-coding
mm_79185.1	chr9	48403955	48403963	+	1	NA	Intergenic	Intergenic	41918	NM_172921	244853	Mm.325522	NM_172921	ENSMUSG00000044229	Nxpe4	C130036J11|D930028F11Rik|Fam55d	neurexophilin and PC-esterase domain family, member 4	protein-coding
mm_32157.1	chr4	99960377	99960388	+	1	NA	intron (NM_028132, intron 1 of 10)	intron (NM_028132, intron 1 of 10)	30931	NM_028132	72157	Mm.217764	NM_028132	ENSMUSG00000025791	Pgm2	2610020G18Rik|AA407108|AI098105|Pgm-2|Pgm1	phosphoglucomutase 2	protein-coding
mm_144318.1	chr18	12652023	12652084	+	1	NA	intron (NM_028341, intron 1 of 13)	intron (NM_028341, intron 1 of 13)	8520	NM_028341	72747	Mm.52526	NM_028341	ENSMUSG00000024424	Ttc39c	1700008N02Rik|2810439F02Rik	tetratricopeptide repeat domain 39C	protein-coding
mm_58070.1	chr6	136924036	136924089	-	1	NA	3' UTR (NM_007486, exon 6 of 6)	3' UTR (NM_007486, exon 6 of 6)	-1882	NM_026983	69187	Mm.33692	NM_026983	ENSMUSG00000030219	Erp27	1810033M07Rik|1810047B09Rik	endoplasmic reticulum protein 27	protein-coding
mm_39992.1	chr5	32492321	32492333	+	1	NA	3' UTR (NM_172707, exon 8 of 8)	3' UTR (NM_172707, exon 8 of 8)	33357	NM_172707	19046	Mm.241931	NM_172707	ENSMUSG00000014956	Ppp1cb	1200010B19	protein phosphatase 1, catalytic subunit, beta isoform	protein-coding
mm_115303.1	chr13	112188754	112188758	+	1	NA	Intergenic	Intergenic	-99695	NM_001168403	77318	Mm.159895	NM_029898	ENSMUSG00000049985	Ankrd55	C030011J08Rik	ankyrin repeat domain 55	protein-coding
mm_30475.1	chr3	154711049	154711069	-	1	NA	promoter-TSS (NM_175176)	promoter-TSS (NM_175176)	-74	NM_175176	209601	Mm.331454	NM_175176	ENSMUSG00000078161	Erich3	1700013E18Rik|4922501L14Rik|5031409G23Rik|AI596448|Gm133	glutamate rich 3	protein-coding
mm_170656.1	chr2	104874643	104874660	+	1	NA	Intergenic	(GAA)n|Simple_repeat|Simple_repeat	-11673	NM_177600	211936	Mm.416538	NM_177600	ENSMUSG00000045106	Ccdc73	2210415I11Rik|4931417A20|AV080665|BC095976	coiled-coil domain containing 73	protein-coding
mm_130028.1	chr15	88900632	88900634	-	1	NA	Intergenic	Intergenic	38439	NM_145478	223775	Mm.400129	NM_145478	ENSMUSG00000035828	Pim3	BC026639|Kid1	proviral integration site 3	protein-coding
mm_115164.1	chr13	107890641	107890658	+	1	NA	promoter-TSS (NM_145456)	promoter-TSS (NM_145456)	-585	NM_145456	67263	Mm.490418	NM_145456	ENSMUSG00000032846	Zswim6	2900036G02Rik|mKIAA1577	zinc finger SWIM-type containing 6	protein-coding
mm_53130.1	chr6	125145260	125145278	+	1	NA	promoter-TSS (NM_001039669)	promoter-TSS (NM_001039669)	45	NM_001302779	320678	Mm.129415	NM_178787	ENSMUSG00000038271	Iffo1	4733401N06Rik|A930037G23Rik|HOM-TES-103|Iffo	intermediate filament family orphan 1	protein-coding
mm_21063.1	chr2	152781942	152781966	-	1	NA	3' UTR (NM_009743, exon 3 of 3)	3' UTR (NM_009743, exon 3 of 3)	27781	NM_053091	84682	Mm.196668	NM_053091	ENSMUSG00000009876	Cox4i2	Cox4b|CoxIV-2	cytochrome c oxidase subunit IV isoform 2	protein-coding
mm_46268.1	chr5	99967247	99967276	-	1	NA	exon (NM_007516, exon 3 of 8)	exon (NM_007516, exon 3 of 8)	11677	NM_001077266	11991	Mm.150231	NM_007516	ENSMUSG00000000568	Hnrnpd	Auf1|Hnrpd	heterogeneous nuclear ribonucleoprotein D	protein-coding
mm_119285.1	chr14	34378765	34378779	+	1	NA	intron (NM_153127, intron 1 of 6)	intron (NM_153127, intron 1 of 6)	3268	NM_153127	105450	Mm.272673	NM_153127	ENSMUSG00000041445	Mmrn2	AA986839|ENDOGLYX1|Emilin3|EndoGlyx-1	multimerin 2	protein-coding
mm_118790.1	chr14	24118928	24118965	+	1	NA	Intergenic	Intergenic	30069	NR_106069	102465697		NR_106069	ENSMUSG00000105723	Mir7210	mir-7210|mmu-mir-7210	microRNA 7210	ncRNA
mm_155729.1	chrX	96163430	96163457	+	1	NA	exon (NM_010833, exon 9 of 13)	exon (NM_010833, exon 9 of 13)	67398	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_161719.1	chr17	26069013	26069013	-	1	NA	exon (NM_001162868, exon 1 of 14)	exon (NM_001162868, exon 1 of 14)	164	NM_001162868	215445	Mm.41191	NM_153140	ENSMUSG00000037098	Rab11fip3	Cart1|D030060O14Rik|Rab11-FIP3|mKIAA0665	RAB11 family interacting protein 3 (class II)	protein-coding
mm_152028.1	chr19	6077184	6077229	-	1	NA	promoter-TSS (NM_001081041)	promoter-TSS (NM_001081041)	-19	NM_001081041	68505	Mm.227361	NM_001081041	ENSMUSG00000024797	Vps51	1110014N23Rik|3110057M17Rik|AI837850|Ffr	VPS51 GARP complex subunit	protein-coding
mm_140184.1	chr17	80997896	80997899	+	1	NA	intron (NM_026516, intron 3 of 3)	intron (NM_026516, intron 3 of 3)	53265	NM_026516	68027	Mm.357108	NM_026516	ENSMUSG00000024245	Tmem178	2810417M05Rik|Tmem178a	transmembrane protein 178	protein-coding
mm_79120.1	chr9	46618759	46618762	+	1	NA	Intergenic	Intergenic	-294843	NR_015605	73040	Mm.265384	NR_015605	ENSMUSG00000099696	2900052N01Rik	AU067665	RIKEN cDNA 2900052N01 gene	ncRNA
mm_127772.1	chr15	3279316	3279324	-	1	NA	exon (NM_009155, exon 5 of 5)	exon (NM_009155, exon 5 of 5)	8343	NM_009155	20363	Mm.392203	NM_009155	ENSMUSG00000064373	Selenop	AU018766|D15Ucla1|Se-P|Sepp1|selp	selenoprotein P	protein-coding
mm_106626.1	chr11	120856233	120856251	-	1	NA	intron (NM_027745, intron 18 of 18)	intron (NM_027745, intron 18 of 18)	-31695	NM_007988	14104	Mm.236443	NM_007988	ENSMUSG00000025153	Fasn	A630082H08Rik|FAS	fatty acid synthase	protein-coding
mm_65928.1	chr7	30314175	30314185	-	1	NA	promoter-TSS (NM_153577)	promoter-TSS (NM_153577)	-636	NM_001290565	233066	Mm.227325	NM_153577	ENSMUSG00000019737	Syne4	0610012K07Rik|AI428936|Nesp4	spectrin repeat containing, nuclear envelope family member 4	protein-coding
mm_111073.1	chr12	80135744	80135750	-	1	NA	Intergenic	Intergenic	-2903	NR_033514	69548	Mm.269712	NR_033514	ENSMUSG00000097729	2310015A10Rik	5330419I17Rik	RIKEN cDNA 2310015A10 gene	ncRNA
mm_4886.1	chr1	188261982	188261992	+	1	NA	promoter-TSS (NM_021408)	promoter-TSS (NM_021408)	-851	NM_021408	22283	Mm.331238	NM_021408	ENSMUSG00000026609	Ush2a	A930011D15Rik|A930037M10Rik|Gm676|Gm983|Mush2a|Usherin|Ushrn	Usher syndrome 2A	protein-coding
mm_152058.1	chr19	6307837	6307845	-	1	NA	intron (NM_001033342, intron 1 of 36)	intron (NM_001033342, intron 1 of 36)	1384	NM_001033342	240505	Mm.329622	NM_001033342	ENSMUSG00000024769	Cdc42bpg	BC046418|MRCKgamma	CDC42 binding protein kinase gamma (DMPK-like)	protein-coding
mm_100216.1	chr11	116966732	116966735	+	1	NA	exon (NM_172948, exon 9 of 17)	exon (NM_172948, exon 9 of 17)	47870	NM_172948	268510	Mm.35141	NM_172948	ENSMUSG00000043857	Mgat5b	C330018B01|GnT-IX|mGnTVB	mannoside acetylglucosaminyltransferase 5, isoenzyme B	protein-coding
mm_169716.1	chr15	77767498	77767513	-	1	NA	exon (NM_022410, exon 32 of 41)	exon (NM_022410, exon 32 of 41)	-12276	NM_001081970	239552	Mm.125650	NM_001081970	ENSMUSG00000056656	Apol8	9830006J20Rik|APOL-II|Apol2	apolipoprotein L 8	protein-coding
mm_143379.1	chr17	67950909	67950983	-	1	NA	promoter-TSS (NM_001347410)	promoter-TSS (NM_001347410)	-6	NM_001347410	268970	Mm.9935	NM_172964	ENSMUSG00000024043	Arhgap28	AU044757|AW550892|E130310N06	Rho GTPase activating protein 28	protein-coding
mm_122977.1	chr14	54983284	54983308	-	1	NA	exon (NM_080728, exon 25 of 41)	exon (NM_080728, exon 25 of 41)	-7520	NR_030607	100124433		NR_030607	ENSMUSG00000077928	Mir208b	Mirn208b|mir-208b	microRNA 208b	ncRNA
mm_3376.1	chr1	139172061	139172072	+	1	NA	3' UTR (NM_001166501, exon 22 of 22)	3' UTR (NM_001166501, exon 22 of 22)	194409	NR_108103	78229	Mm.437838	NR_108103	ENSMUSG00000104900	4930596I21Rik	-	RIKEN cDNA 4930596I21 gene	ncRNA
mm_12363.1	chr2	69750514	69750527	+	1	NA	3' UTR (NM_001081086, exon 14 of 14)	3' UTR (NM_001081086, exon 14 of 14)	27432	NM_001081086	228005	Mm.11815	NM_001081086	ENSMUSG00000042133	Ppig	AU019516|AU022200|B230312B02Rik|CYP|SRCyp	peptidyl-prolyl isomerase G (cyclophilin G)	protein-coding
mm_132724.1	chr16	43618945	43618965	+	1	NA	3' UTR (NM_019778, exon 9 of 9)	3' UTR (NM_019778, exon 9 of 9)	-21700	NR_030576	100124467		NR_030576	ENSMUSG00000076372	Mir568	Mirn568|mmu-mir-568	microRNA 568	ncRNA
mm_110929.1	chr12	76369692	76369698	-	1	NA	promoter-TSS (NM_001172104)	promoter-TSS (NM_001172104)	-135	NM_028356	109929	Mm.41880	NM_028356	ENSMUSG00000056459	Zbtb25	2810462M08Rik|2900064P18Rik|AI842128|Kup|Zfp-50|Zfp50	zinc finger and BTB domain containing 25	protein-coding
mm_43763.1	chr5	140705007	140705037	+	1	NA	promoter-TSS (NM_181066)	promoter-TSS (NM_181066)	11	NR_074085	231841	Mm.271932	NM_172724	ENSMUSG00000000148	Brat1	AA881470|Baat1	BRCA1-associated ATM activator 1	protein-coding
mm_23873.1	chr3	83029198	83029215	+	1	NA	exon (NM_010196, exon 3 of 5)	exon (NM_010196, exon 3 of 5)	3053	NM_001111048	14161	Mm.88793	NM_010196	ENSMUSG00000028001	Fga	ENSMUSG00000059807|Fib	fibrinogen alpha chain	protein-coding
mm_15981.1	chr2	166793785	166793813	+	1	NA	promoter-TSS (NM_023815)	promoter-TSS (NM_023815)	32	NM_023815	76367	Mm.330796	NM_023815	ENSMUSG00000042854	Trp53rkb	2810408M09Rik|4933401B08Rik|5630401H01Rik|Nori-2|PRPK|Tp53rk|Trp53rk|Trp53tk|mNori-2p	transformation related protein 53 regulating kinase B	protein-coding
mm_98732.1	chr11	96352865	96352881	+	1	NA	intron (NM_134032, intron 1 of 1)	intron (NM_134032, intron 1 of 1)	1241	NM_134032	103889	Mm.281153	NM_134032	ENSMUSG00000075588	Hoxb2	AI894218|Hox-2.8|Hoxbes2	homeobox B2	protein-coding
mm_1415.1	chr1	67159383	67159393	+	1	NA	intron (NM_001080809, intron 11 of 37)	intron (NM_001080809, intron 11 of 37)	36361	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_102524.1	chr11	60913776	60913816	-	1	NA	promoter-TSS (NM_025294)	promoter-TSS (NM_025294)	-4	NM_025294	24083	Mm.22780	NM_025294	ENSMUSG00000018931	Natd1	AI256713|F3-2|Gm16515|Gtlf3b	N-acetyltransferase domain containing 1	protein-coding
mm_115465.1	chr13	119429266	119429272	+	1	NA	intron (NM_145457, intron 1 of 10)	CpG	367	NM_145457	218693	Mm.490243	NM_145457	ENSMUSG00000025451	Paip1	PAIP-1	polyadenylate binding protein-interacting protein 1	protein-coding
mm_14318.1	chr2	129310082	129310109	+	1	NA	promoter-TSS (NM_010554)	promoter-TSS (NM_010554)	-123	NM_010554	16175	Mm.15534	NM_010554	ENSMUSG00000027399	Il1a	Il-1a	interleukin 1 alpha	protein-coding
mm_149910.1	chr19	25675218	25675220	+	1	NA	intron (NM_145831, intron 2 of 3)	intron (NM_145831, intron 2 of 3)	2808	NM_145831	226049	Mm.275572	NM_145831	ENSMUSG00000048138	Dmrt2	Terra	doublesex and mab-3 related transcription factor 2	protein-coding
mm_99876.1	chr11	109425609	109425622	+	1	NA	promoter-TSS (NM_025275)	promoter-TSS (NM_025275)	-331	NM_025275	13929	Mm.211850	NM_025275	ENSMUSG00000020610	Amz2	AA408420|ESTM12|X83328	archaelysin family metallopeptidase 2	protein-coding
mm_39441.1	chr5	16870244	16870254	+	1	NA	Intergenic	Intergenic	316348	NM_001289461	15234	Mm.267078	NM_010427	ENSMUSG00000028864	Hgf	C230052L06Rik|HGF/SF|NK1|NK2|SF|SF/HGF	hepatocyte growth factor	protein-coding
mm_14198.1	chr2	127183018	127183068	+	1	NA	Intergenic	Intergenic	25237	NM_198630	329509	Mm.120738	NM_198630	ENSMUSG00000044145	1810024B03Rik	-	RIKEN cDNA 1810024B03 gene	protein-coding
mm_97405.1	chr11	77879580	77879595	+	1	NA	Intergenic	MIRc|SINE|MIR	14285	NM_008952	19193	Mm.8543	NM_008952	ENSMUSG00000017453	Pipox	LPIPOX|Pso	pipecolic acid oxidase	protein-coding
mm_97711.1	chr11	80178852	80178858	+	1	NA	TTS (NM_172133)	TTS (NM_172133)	-5017	NM_028019	71956	Mm.22985	NM_028019	ENSMUSG00000020707	Rnf135	0610037N03Rik|2410006N06Rik	ring finger protein 135	protein-coding
mm_125254.1	chr15	35296119	35296134	+	1	NA	promoter-TSS (NM_054049)	promoter-TSS (NM_054049)	14	NM_054049	107587	Mm.46336	NM_054049	ENSMUSG00000022330	Osr2	5430409I15Rik|Osr2A|Osr2B	odd-skipped related 2	protein-coding
mm_85723.1	chr9	108306158	108306161	-	1	NA	promoter-TSS (NM_133986)	promoter-TSS (NM_133986)	0	NM_133986	102791	Mm.24670	NM_133986	ENSMUSG00000039461	Tcta	9130410M22Rik|AW553637|C85065|Tctal	T cell leukemia translocation altered gene	protein-coding
mm_72329.1	chr8	79027970	79027978	+	1	NA	promoter-TSS (NM_178267)	promoter-TSS (NM_178267)	-463	NM_001294279	622675	Mm.48724	NM_178267	ENSMUSG00000071064	Zfp827	2810449M09Rik|D630040G17Rik|Znf827	zinc finger protein 827	protein-coding
mm_22845.1	chr3	27984636	27984639	+	1	NA	intron (NM_008875, intron 1 of 25)	intron (NM_008875, intron 1 of 25)	466	NM_008875	18805	Mm.212039	NM_008875	ENSMUSG00000027695	Pld1	AA536939|C85393|Pld1a|Pld1b|mPLD1	phospholipase D1	protein-coding
mm_85432.1	chr9	103729368	103729403	-	1	NA	intron (NM_178638, intron 2 of 5)	L2|LINE|L2	32452	NM_178638	81907	Mm.384704	NM_178638	ENSMUSG00000042757	Tmem108	AI462967|B130017P16Rik|R74726	transmembrane protein 108	protein-coding
mm_133755.1	chr16	94442582	94442599	+	1	NA	exon (NM_009441, exon 33 of 46)	exon (NM_009441, exon 33 of 46)	-71575	NM_001159617	56176	Mm.474449	NM_019543	ENSMUSG00000022940	Pigp	Dcrc|Dscr5	phosphatidylinositol glycan anchor biosynthesis, class P	protein-coding
mm_107965.1	chr12	72757383	72757410	+	1	NA	Intergenic	Intergenic	-3815	NM_008910	19042	Mm.261045	NM_008910	ENSMUSG00000021096	Ppm1a	2310003C21Rik|2900017D14Rik|AI427932|AU017636|MMPa-2|MPPa-1	protein phosphatase 1A, magnesium dependent, alpha isoform	protein-coding
mm_107711.1	chr12	55836318	55836330	+	1	NA	promoter-TSS (NM_001037756)	promoter-TSS (NM_001037756)	-42	NM_001037756	52592	Mm.24761	NM_027867	ENSMUSG00000012076	Brms1l	0710008O11Rik|AI159718|BRMS1|D12Ertd407e	breast cancer metastasis-suppressor 1-like	protein-coding
mm_162645.1	chr1	194744122	194744124	+	1	NA	intron (NM_008882, intron 4 of 31)	intron (NM_008882, intron 4 of 31)	124294	NM_008882	18845	Mm.2251	NM_008882	ENSMUSG00000026640	Plxna2	2810428A13Rik|AA589422|AW457381|OCT|PlexA2|Plxn2|mKIAA0463	plexin A2	protein-coding
mm_119428.1	chr14	45543676	45543692	+	1	NA	promoter-TSS (NR_045809)	promoter-TSS (NR_045809)	-26	NR_045809	67651	Mm.55930	NR_045809		4930527F14Rik	-	RIKEN cDNA 4930527F14 gene	ncRNA
mm_115314.1	chr13	112363418	112363436	+	1	NA	exon (NM_029898, exon 8 of 11)	exon (NM_029898, exon 8 of 11)	74909	NM_001168404	77318	Mm.159895	NM_029898	ENSMUSG00000049985	Ankrd55	C030011J08Rik	ankyrin repeat domain 55	protein-coding
mm_111075.1	chr12	80139337	80139341	-	1	NA	Intergenic	Intergenic	-6495	NR_033514	69548	Mm.269712	NR_033514	ENSMUSG00000097729	2310015A10Rik	5330419I17Rik	RIKEN cDNA 2310015A10 gene	ncRNA
mm_157407.1	chrX	38435543	38435560	-	1	NA	exon (NM_001017959, exon 4 of 9)	exon (NM_001017959, exon 4 of 9)	20909	NM_010685	16784	Mm.486	NM_010685	ENSMUSG00000016534	Lamp2	CD107b|LGP-B|Lamp II|Lamp-2|Lamp-2a|Lamp-2b|Lamp-2c|Mac3	lysosomal-associated membrane protein 2	protein-coding
mm_125319.1	chr15	38299358	38299366	+	1	NA	intron (NM_001289471, intron 1 of 4)	CpG	1349	NM_013692	21847	Mm.4292	NM_013692	ENSMUSG00000037465	Klf10	AI115143|EGR[a]|Egral|Gdnfif|TIEG-1|Tieg|Tieg1|mGIF	Kruppel-like factor 10	protein-coding
mm_88392.1	chr10	76531594	76531635	+	1	NA	promoter-TSS (NM_146006)	promoter-TSS (NM_146006)	9	NM_146006	16987	Mm.55075	NM_146006	ENSMUSG00000033105	Lss	2810025N20Rik|D10Ertd116e|Osc	lanosterol synthase	protein-coding
mm_11615.1	chr2	34608466	34608479	+	1	NA	intron (NM_001290626, intron 9 of 10)	MLT1F2|LTR|ERVL-MaLR	146760	NM_025709	66691	Mm.156452	NM_025709	ENSMUSG00000026867	Gapvd1	2010005B09Rik|4432404J10Rik|AW108497|Gapex-5|RAP6|RME-6|mKIAA1521	GTPase activating protein and VPS9 domains 1	protein-coding
mm_86112.1	chr9	115438606	115438606	-	1	NA	Intergenic	Intergenic	56787	NR_130329	100316675		NR_130329	ENSMUSG00000080409	Mir467h	Mirn467h|mmu-mir-467h	microRNA 467h	ncRNA
mm_30025.1	chr3	135665546	135665555	-	1	NA	intron (NM_008689, intron 3 of 24)	intron (NM_008689, intron 3 of 24)	25997	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_86275.1	chr9	121792417	121792426	-	1	NA	promoter-TSS (NM_029095)	promoter-TSS (NM_029095)	86	NM_029095	74770	Mm.44195	NM_029095	ENSMUSG00000032523	Hhatl	1110011D13Rik|Gup1|Mg56	hedgehog acyltransferase-like	protein-coding
mm_43635.1	chr5	138229769	138229779	+	1	NA	5' UTR (NM_001013773, exon 2 of 6)	5' UTR (NM_001013773, exon 2 of 6)	3870	NM_001013773	381680	Mm.156846	NM_001013773	ENSMUSG00000047592	Nxpe5	-	neurexophilin and PC-esterase domain family, member 5	protein-coding
mm_30764.1	chr4	15976403	15976422	+	1	NA	intron (NM_013752, intron 9 of 15)	Lx9|LINE|L1	18445	NM_013752	27354	Mm.20866	NM_013752	ENSMUSG00000028224	Nbn	Nbs1	nibrin	protein-coding
mm_63606.1	chr7	128150180	128150203	+	1	NA	exon (NM_021334, exon 30 of 30)	exon (NM_021334, exon 30 of 30)	20623	NM_021334	16411	Mm.22378	NM_021334	ENSMUSG00000030789	Itgax	AI449405|Cd11c|Cr4|N418	integrin alpha X	protein-coding
mm_122208.1	chr14	32085279	32085328	-	1	NA	promoter-TSS (NM_145460)	promoter-TSS (NM_145460)	-17	NR_104305	105638	Mm.2519	NM_172254	ENSMUSG00000021905	Dph3	DELGIP1|DelgipP1|Desr1|KTI11|Zcsl2	diphthamine biosynthesis 3	protein-coding
mm_35031.1	chr4	4019669	4019675	-	1	NA	promoter-TSS (NM_181989)	promoter-TSS (NM_181989)	-9	NM_181989	242285	Mm.98096	NM_181989	ENSMUSG00000028236	Sdr16c5	Rdhe2|Scdr9	short chain dehydrogenase/reductase family 16C, member 5	protein-coding
mm_69411.1	chr7	132570191	132570232	-	1	NA	intron (NM_016978, intron 1 of 9)	intron (NM_016978, intron 1 of 9)	6187	NM_016978	18242	Mm.13694	NM_016978	ENSMUSG00000030934	Oat	AI194874|rhg	ornithine aminotransferase	protein-coding
mm_18308.1	chr2	53191971	53191985	-	1	NA	promoter-TSS (NM_018785)	promoter-TSS (NM_018785)	-106	NM_022989	65103	Mm.37623	NM_022989	ENSMUSG00000026960	Arl6ip6	2310057C01Rik|2610529A11Rik|Aip-6	ADP-ribosylation factor-like 6 interacting protein 6	protein-coding
mm_92334.1	chr10	75797761	75797776	-	1	NA	intron (NM_008185, intron 1 of 4)	intron (NM_008185, intron 1 of 4)	816	NM_008185	14871	Mm.2746	NM_008185	ENSMUSG00000001663	Gstt1	AI255817|Gstt1-1	glutathione S-transferase, theta 1	protein-coding
mm_136053.1	chr16	78576800	78576806	-	1	NA	promoter-TSS (NM_001252440)	promoter-TSS (NM_001252440)	-115	NM_025967	67102	Mm.37332	NM_025967	ENSMUSG00000022864	D16Ertd472e	1700010I10Rik|2310009O17Rik|E330003K22Rik|Eurl	DNA segment, Chr 16, ERATO Doi 472, expressed	protein-coding
mm_131746.1	chr16	22230335	22230384	+	1	NA	Intergenic	Intergenic	35646	NM_001330554	20462	Mm.210352	NM_009186	ENSMUSG00000022858	Tra2b	5730405G21Rik|D16Ertd266e|SIG-41|Sfrs10|Silg41|TRA2beta	transformer 2 beta homolog (Drosophila)	protein-coding
mm_122774.1	chr14	54409423	54409434	-	1	NA	promoter-TSS (NM_001253680)	promoter-TSS (NM_001253680)	44	NM_001253680	20540	Mm.142455	NM_011405	ENSMUSG00000000958	Slc7a7	AI790233|my+lat1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 7	protein-coding
mm_123822.1	chr14	70617715	70617719	-	1	NA	intron (NM_001252665, intron 2 of 12)	intron (NM_001252665, intron 2 of 12)	852	NM_001252666	13829	Mm.210863	NM_013514	ENSMUSG00000022099	Dmtn	AI325486|Epb4.9|Epb49|dematin	dematin actin binding protein	protein-coding
mm_104969.1	chr11	100203220	100203248	-	1	NA	TTS (NM_016958)	TTS (NM_016958)	2796	NM_001313957	16664	Mm.439898	NM_016958	ENSMUSG00000045545	Krt14	AI626930|CK-14|K14|Krt-1.14|Krt1-14	keratin 14	protein-coding
mm_117180.1	chr13	63398282	63398299	-	1	NA	intron (NM_001347514, intron 3 of 15)	intron (NM_001347514, intron 3 of 15)	33455	NM_001347515	14088	Mm.126106	NM_007985	ENSMUSG00000021461	Fancc	Facc	Fanconi anemia, complementation group C	protein-coding
mm_72323.1	chr8	78509407	78509417	+	1	NA	promoter-TSS (NM_001282108)	promoter-TSS (NM_001282108)	84	NM_001282108	76775	Mm.334631	NM_029736	ENSMUSG00000031684	Slc10a7	2410193C02Rik|P7	solute carrier family 10 (sodium/bile acid cotransporter family), member 7	protein-coding
mm_164537.1	chr17	6743278	6743288	+	1	NA	intron (NM_009510, intron 7 of 12)	intron (NM_009510, intron 7 of 12)	37453	NM_183368	83672	Mm.442201	NM_031395	ENSMUSG00000041831	Sytl3	A430092N21|Slp3|Slp3-a|Slp3-b|mFLJ00307	synaptotagmin-like 3	protein-coding
mm_168857.1	chr12	27418565	27418579	-	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	-75854	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding
mm_80366.1	chr9	75314236	75314265	+	1	NA	non-coding (NR_073186, exon 1 of 12)	non-coding (NR_073186, exon 1 of 12)	182	NM_138719	14697	Mm.17604	NM_010313	ENSMUSG00000032192	Gnb5	GBS|Gbeta5|flr	guanine nucleotide binding protein (G protein), beta 5	protein-coding
mm_157831.1	chrX	74246401	74246438	-	1	NA	exon (NM_010227, exon 1 of 46)	exon (NM_010227, exon 1 of 46)	115	NM_010227	192176	Mm.295533	NM_010227	ENSMUSG00000031328	Flna	ABP-280|Dilp2|F730004A14Rik|Fln1|GENA 379|filamin-1	filamin, alpha	protein-coding
mm_8159.1	chr1	136949471	136949497	-	1	NA	intron (NM_030676, intron 2 of 8)	intron (NM_030676, intron 2 of 8)	4146	NM_001159769	26424	Mm.16794	NM_030676	ENSMUSG00000026398	Nr5a2	AU020803|D1Ertd308e|Ftf|LRH-1|UF2-H3B	nuclear receptor subfamily 5, group A, member 2	protein-coding
mm_70116.1	chr7	142899986	142900002	-	1	NA	promoter-TSS (NM_009377)	promoter-TSS (NM_009377)	-28	NM_009377	21823	Mm.1292	NM_009377	ENSMUSG00000000214	Th	-	tyrosine hydroxylase	protein-coding
mm_17979.1	chr2	37703280	37703290	-	1	NA	Intergenic	CpG	-56000	NM_009261	20744	Mm.237095	NM_009261	ENSMUSG00000026915	Strbp	6430510M02Rik|AI852513|C230082I21Rik|C86322|Spnr	spermatid perinuclear RNA binding protein	protein-coding
mm_32567.1	chr4	109731410	109731413	+	1	NA	intron (NM_007983, intron 4 of 18)	B1_Mus1|SINE|Alu	54784	NM_007983	14084	Mm.318259	NM_007983	ENSMUSG00000010517	Faf1	AA408698|Dffrx|Fam	Fas-associated factor 1	protein-coding
mm_36048.1	chr4	57300325	57300358	-	1	NA	intron (NM_011207, intron 1 of 25)	CpG	1496	NM_011207	545622	Mm.246552	NM_011207	ENSMUSG00000038764	Ptpn3	9530011I20Rik|PTP-H1|PTPCL	protein tyrosine phosphatase, non-receptor type 3	protein-coding
mm_79658.1	chr9	59656592	59656599	+	1	NA	5' UTR (NM_011099, exon 1 of 11)	5' UTR (NM_011099, exon 1 of 11)	227	NM_001253883	18746	Mm.326167	NM_011099	ENSMUSG00000032294	Pkm	AA414905|AL024370|AL024424|Pk-2|Pk-3|Pk3|Pkm2	pyruvate kinase, muscle	protein-coding
mm_77932.1	chr9	7354099	7354128	+	1	NA	intron (NM_001320077, intron 7 of 10)	B4A|SINE|B4	6739	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_55294.1	chr6	54593140	54593217	-	1	NA	promoter-TSS (NM_153573)	promoter-TSS (NM_153573)	-50	NM_153573	231997	Mm.274693	NM_153573	ENSMUSG00000038074	Fkbp14	BC029109|FKBP-14|FKBP22	FK506 binding protein 14	protein-coding
mm_135843.1	chr16	58616974	58616979	-	1	NA	promoter-TSS (NM_001033404)	promoter-TSS (NM_001033404)	2	NM_001033404	328695	Mm.293308	NM_001033404	ENSMUSG00000075002	Gm813	Gm1781	predicted gene 813	protein-coding
mm_664.1	chr1	40442588	40442606	+	1	NA	intron (NM_001025602, intron 4 of 10)	intron (NM_001025602, intron 4 of 10)	2968	NM_010743	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_164069.1	chr14	118787960	118787962	+	1	NA	promoter-TSS (NM_001160098)	promoter-TSS (NM_001160098)	90	NM_001160097	58187	Mm.390755	NM_021386	ENSMUSG00000022132	Cldn10	6720456I16Rik|Cldn10a|Cldn10b|D14Ertd728e	claudin 10	protein-coding
mm_43481.1	chr5	136701004	136701009	+	1	NA	TTS (NM_021611)	TTS (NM_021611)	6829	NM_001085387	59310	Mm.5178	NM_021611	ENSMUSG00000005474	Myl10	1700027I08Rik|Mylc2pl|PLRLC	myosin, light chain 10, regulatory	protein-coding
mm_36693.1	chr4	96642730	96642732	-	1	NA	intron (NM_010007, intron 4 of 8)	intron (NM_010007, intron 4 of 8)	21388	NM_010007	13109	Mm.12838	NM_010007	ENSMUSG00000052520	Cyp2j5	-	cytochrome P450, family 2, subfamily j, polypeptide 5	protein-coding
mm_34203.1	chr4	140924239	140924258	+	1	NA	intron (NM_008812, intron 3 of 15)	intron (NM_008812, intron 3 of 15)	17888	NM_008812	18600	Mm.2296	NM_008812	ENSMUSG00000028927	Padi2	Pdi|Pdi2|mKIAA0994	peptidyl arginine deiminase, type II	protein-coding
mm_147107.1	chr18	35703071	35703081	-	1	NA	promoter-TSS (NM_029669)	promoter-TSS (NM_029669)	68	NM_029669	76594	Mm.108596	NM_029669	ENSMUSG00000024350	Dnajc18	2700075B01Rik|AU041129	DnaJ heat shock protein family (Hsp40) member C18	protein-coding
mm_69140.1	chr7	127050527	127050539	-	1	NA	exon (NM_026918, exon 3 of 3)	exon (NM_026918, exon 3 of 3)	1444	NM_026918	69036	Mm.21835	NM_026918	ENSMUSG00000049350	Zg16	1810010M01Rik|AI593689|ZG16p	zymogen granule protein 16	protein-coding
mm_36150.1	chr4	59505898	59505907	-	1	NA	intron (NM_178164, intron 4 of 13)	B1F1|SINE|Alu	43462	NM_178164	230257	Mm.331640	NM_144904	ENSMUSG00000028382	Ptbp3	5830471K22Rik|AA407443|AI462022|AW107884|C86549|Rod1	polypyrimidine tract binding protein 3	protein-coding
mm_3370.1	chr1	138960177	138960187	+	1	NA	Intergenic	Intergenic	-3527	NM_001166501	329260	Mm.337604	NM_181347	ENSMUSG00000056268	Dennd1b	4632404N19Rik|4930467M19Rik|6820401H01Rik|F730008N07Rik	DENN/MADD domain containing 1B	protein-coding
mm_113000.1	chr13	21787481	21787494	+	1	NA	promoter-TSS (NM_001290466)	promoter-TSS (NM_001290466)	-1	NM_178202	319188	Mm.264645	NM_178202	ENSMUSG00000069308	Hist1h2bp	-	histone cluster 1, H2bp	protein-coding
mm_151807.1	chr19	5447771	5447773	-	1	NA	promoter-TSS (NM_010235)	promoter-TSS (NM_010235)	74	NM_010235	14283	Mm.6215	NM_010235	ENSMUSG00000024912	Fosl1	AW538199|Fra1|fra-1	fos-like antigen 1	protein-coding
mm_98779.1	chr11	96807686	96807719	+	1	NA	intron (NM_007622, intron 5 of 5)	intron (NM_007622, intron 5 of 5)	-9546	NR_033523	629750	Mm.390396	NR_033523		Gm11517	OTTMUSG00000001634	ubiquitin A-52 residue ribosomal protein fusion product 1 pseudogene	pseudo
mm_19764.1	chr2	105399356	105399358	-	1	NA	promoter-TSS (NM_009037)	promoter-TSS (NM_009037)	-38	NM_009037	19672	Mm.4876	NM_009037	ENSMUSG00000005973	Rcn1	Rcn	reticulocalbin 1	protein-coding
mm_3547.1	chr1	150407488	150407499	+	1	NA	exon (NM_133780, exon 10 of 52)	exon (NM_133780, exon 10 of 52)	-14438	NM_145511	226499	Mm.222093	NM_145511	ENSMUSG00000006010	BC003331	1810053E15Rik|Odr4|odr-4	cDNA sequence BC003331	protein-coding
mm_88846.1	chr10	80930072	80930075	+	1	NA	promoter-TSS (NM_008655)	promoter-TSS (NM_008655)	-18	NM_008655	17873	Mm.1360	NM_008655	ENSMUSG00000015312	Gadd45b	AI323528|Myd118	growth arrest and DNA-damage-inducible 45 beta	protein-coding
mm_94825.1	chr11	23284656	23284669	+	1	NA	exon (NM_134014, exon 15 of 26)	exon (NM_134014, exon 15 of 26)	-22233	NM_001190401	17847	Mm.119155	NM_001190401	ENSMUSG00000056342	Usp34	A530081C03Rik|Murr2	ubiquitin specific peptidase 34	protein-coding
mm_86675.1	chr10	18085719	18085719	+	1	NA	intron (NM_009048, intron 1 of 19)	RLTRETN_Mm|LTR|ERVK	29779	NM_001111065	19707	Mm.4479	NM_009048	ENSMUSG00000019854	Reps1	BB161292	RalBP1 associated Eps domain containing protein	protein-coding
mm_127014.1	chr15	95943559	95943561	+	1	NA	intron (NM_175344, intron 12 of 19)	intron (NM_175344, intron 12 of 19)	135993	NR_126493	402773	Mm.210567	NM_001033483	ENSMUSG00000078925	D030018L15Rik	-	nuclear receptor coactivator 2 pseudogene	pseudo
mm_12607.1	chr2	74682287	74682326	+	1	NA	promoter-TSS (NM_008273)	promoter-TSS (NM_008273)	-17	NM_008273	15431	Mm.207763	NM_008273	ENSMUSG00000042499	Hoxd11	E230017H14Rik|Hox-4.6|Hox-5.4|Hox-5.5	homeobox D11	protein-coding
mm_27048.1	chr3	27194125	27194158	-	1	NA	intron (NM_178772, intron 1 of 4)	L3|LINE|CR1	11137	NM_178772	320024	Mm.24576	NM_178772	ENSMUSG00000027698	Nceh1	Aadacl1|B230106I24Rik|CPO-BP|Nceh	neutral cholesterol ester hydrolase 1	protein-coding
mm_173337.1	chrY	90811302	90811309	+	1	NA	intron (NM_133362, intron 2 of 3)	RLTR40|LTR|ERVK	25863	NM_133362	170942	Mm.76062	NM_133362	ENSMUSG00000096768	Erdr1	edr	erythroid differentiation regulator 1	protein-coding
mm_78636.1	chr9	40148157	40148165	+	1	NA	promoter-TSS (NM_029379)	promoter-TSS (NM_029379)	39	NM_029379	75667	Mm.45821	NM_029379	ENSMUSG00000040541	Tmem225	1700030E15Rik|Tnen225	transmembrane protein 225	protein-coding
mm_64218.1	chr7	141558496	141558498	+	1	NA	Intergenic	Intergenic	-3683	NM_007459	11772	Mm.253090	NM_007459	ENSMUSG00000002957	Ap2a2	2410074K14Rik|AF006990|AW146353|Adtab|C78001|L25	adaptor-related protein complex 2, alpha 2 subunit	protein-coding
mm_141931.1	chr17	35029841	35029870	-	1	NA	intron (NM_013600, intron 21 of 23)	intron (NM_013600, intron 21 of 23)	-1839	NM_023893	78376	Mm.390966	NM_023893	ENSMUSG00000036185	Sapcd1	2810436B06Rik|G7d|Ng23	suppressor APC domain containing 1	protein-coding
mm_163686.1	chr13	95918496	95918504	-	1	NA	Intergenic	Intergenic	-26578	NM_027711	544963	Mm.38878	NM_027711	ENSMUSG00000021676	Iqgap2	4933417J23Rik|A630053O10|AI788777	IQ motif containing GTPase activating protein 2	protein-coding
mm_12269.1	chr2	68979190	68979209	+	1	NA	intron (NM_172856, intron 3 of 9)	intron (NM_172856, intron 3 of 9)	117758	NM_001347161	241447	Mm.222222	NM_172856	ENSMUSG00000027035	Cers6	4732462C07Rik|AW544719|Lass6|T1L	ceramide synthase 6	protein-coding
mm_124139.1	chr14	87004800	87004811	-	1	NA	intron (NM_019670, intron 7 of 27)	intron (NM_019670, intron 7 of 27)	136309	NM_019670	56419	Mm.440585	NM_019670	ENSMUSG00000022021	Diaph3	4930417P13Rik|Dia2|Diap3|Drf3|mDia2|mKIAA4117|p134MDia2	diaphanous related formin 3	protein-coding
mm_42488.1	chr5	115472009	115472015	+	1	NA	exon (NM_011107, exon 3 of 4)	exon (NM_011107, exon 3 of 4)	5746	NM_011107	18778	Mm.20190	NM_011107	ENSMUSG00000029522	Pla2g1b	Pla2a|sPLA2IB	phospholipase A2, group IB, pancreas	protein-coding
mm_24034.1	chr3	87629488	87629496	+	1	NA	intron (NM_001003912, intron 1 of 39)	MYSERV6-int|LTR|ERVK	10741	NM_001003912	213498	Mm.287267	NM_001003912	ENSMUSG00000041977	Arhgef11	B930073M02|E130307F09|PDZ-RhoGEF|Prg|RhoGEF|mKIAA0380	Rho guanine nucleotide exchange factor (GEF) 11	protein-coding
mm_45816.1	chr5	87679047	87679050	-	1	NA	exon (NM_007784, exon 30 of 34)	exon (NM_007784, exon 30 of 34)	12840	NM_001286016	12990	Mm.427467	NM_007784	ENSMUSG00000070702	Csn1s1	AA959832|AW212882|Csna	casein alpha s1	protein-coding
mm_2328.1	chr1	92774279	92774307	+	1	NA	Intergenic	Intergenic	-57393	NM_016696	14733	Mm.297976	NM_016696	ENSMUSG00000034220	Gpc1	AI462976	glypican 1	protein-coding
mm_157839.1	chrX	74353577	74353622	-	1	NA	promoter-TSS (NM_025410)	promoter-TSS (NM_025410)	19	NM_025410	66192	Mm.21705	NM_025410	ENSMUSG00000015289	Lage3	1110049G11Rik|Eso3|Itba2	L antigen family, member 3	protein-coding
mm_36677.1	chr4	96348651	96348677	-	1	NA	promoter-TSS (NM_001004141)	promoter-TSS (NM_001004141)	16	NM_001004141	100066	Mm.26915	NM_001004141	ENSMUSG00000066097	Cyp2j11	AI314783|Cyp2j11-ps	cytochrome P450, family 2, subfamily j, polypeptide 11	protein-coding
mm_27302.1	chr3	49435821	49435848	-	1	NA	Intergenic	Intergenic	321482	NM_130448	73173	Mm.87246	NM_130448	ENSMUSG00000037892	Pcdh18	3110038E07Rik|BB095589|PCDH68L	protocadherin 18	protein-coding
mm_142711.1	chr17	47888224	47888234	-	1	NA	intron (NM_001110824, intron 2 of 16)	intron (NM_001110824, intron 2 of 16)	36403	NM_028767	74123	Mm.240062	NM_028767	ENSMUSG00000023991	Foxp4	1200010K03Rik|2310007G05Rik|mFKHLA	forkhead box P4	protein-coding
mm_90089.1	chr10	116914281	116914303	+	1	NA	intron (NM_001003950, intron 6 of 9)	intron (NM_001003950, intron 6 of 9)	-17413	NM_001033333	237558	Mm.336386	NM_001033333	ENSMUSG00000034057	Myrfl	Gm239	myelin regulatory factor-like	protein-coding
mm_5480.1	chr1	36702159	36702185	-	1	NA	exon (NM_146107, exon 5 of 11)	exon (NM_146107, exon 5 of 11)	7753	NM_146107	226977	Mm.28521	NM_146107	ENSMUSG00000037351	Actr1b	2310066K23Rik|AA960180|AI851923|Arp1b	ARP1 actin-related protein 1B, centractin beta	protein-coding
mm_79294.1	chr9	51273824	51273836	+	1	NA	intron (NM_001195681, intron 3 of 4)	intron (NM_001195681, intron 3 of 4)	4724	NM_001195681	100502940	Mm.235705	NM_001195681	ENSMUSG00000079559	Gm684	-	predicted gene 684	protein-coding
mm_61553.1	chr7	79399134	79399145	+	1	NA	exon (NM_145946, exon 3 of 38)	exon (NM_145946, exon 3 of 38)	6801	NM_145946	208836	Mm.349493	NM_145946	ENSMUSG00000039187	Fanci	-	Fanconi anemia, complementation group I	protein-coding
mm_33293.1	chr4	128960977	128960992	+	1	NA	intron (NM_172875, intron 3 of 10)	intron (NM_172875, intron 3 of 10)	1471	NM_172875	242669	Mm.215814	NM_172875	ENSMUSG00000028789	Azin2	4933429I20Rik|Adc|Azi2|B930082O19|ODC-p|Odcp	antizyme inhibitor 2	protein-coding
mm_104178.1	chr11	87749459	87749487	-	1	NA	Intergenic	Intergenic	-7391	NR_029555	387160		NR_029555	ENSMUSG00000105196	Mir142	Mirn142|miR-142|mir-142a|mmu-mir-142|mmu-mir-142a	microRNA 142	ncRNA
mm_71806.1	chr8	68793941	68794016	+	1	NA	promoter-TSS (NM_001293792)	promoter-TSS (NM_001293792)	49	NM_001293792	70885	Mm.252421	NM_027590	ENSMUSG00000031864	Ints10	4921521J11Rik|AI462004	integrator complex subunit 10	protein-coding
mm_52763.1	chr6	120870038	120870041	+	1	NA	intron (NM_153516, intron 4 of 6)	B1_Mus2|SINE|Alu	33809	NM_153516	94044	Mm.27990	NM_153516	ENSMUSG00000009112	Bcl2l13	BCL-RAMBO|E430016C20Rik|Mil-1|Mil1	BCL2-like 13 (apoptosis facilitator)	protein-coding
mm_93323.1	chr10	99132403	99132430	-	1	NA	intron (NM_027740, intron 4 of 11)	intron (NM_027740, intron 4 of 11)	24281	NM_015737	14426	Mm.314	NM_015737	ENSMUSG00000090035	Galnt4	AV011803	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 4	protein-coding
mm_39658.1	chr5	24985841	24985862	+	1	NA	intron (NM_145401, intron 3 of 15)	intron (NM_145401, intron 3 of 15)	9902	NM_001310480	108099	Mm.33649	NM_145401	ENSMUSG00000028944	Prkag2	2410051C13Rik|AAKG|AAKG2|AI854673|H91620p|WPWS	protein kinase, AMP-activated, gamma 2 non-catalytic subunit	protein-coding
mm_70597.1	chr8	13288284	13288290	+	1	NA	promoter-TSS (NM_001042649)	promoter-TSS (NM_001042649)	-161	NM_001042650	102323	Mm.368890	NM_001024504	ENSMUSG00000038506	Dcun1d2	AW495713|mFLJ10704	DCN1, defective in cullin neddylation 1, domain containing 2 (S. cerevisiae)	protein-coding
mm_117144.1	chr13	61037747	61037754	-	1	NA	exon (NM_029636, exon 5 of 8)	exon (NM_029636, exon 5 of 8)	2847	NM_029636	104002	Mm.46088	NM_029636	ENSMUSG00000021439	Ctsq	1600010J02Rik	cathepsin Q	protein-coding
mm_105041.1	chr11	100591502	100591519	-	1	NA	exon (NM_019795, exon 7 of 14)	exon (NM_019795, exon 7 of 14)	15619	NM_001146318	12799	Mm.15711	NM_009923	ENSMUSG00000006782	Cnp	CNPase|Cnp-1|Cnp1	2',3'-cyclic nucleotide 3' phosphodiesterase	protein-coding
mm_134301.1	chr16	15594510	15594531	-	1	NA	promoter-TSS (NM_001159351)	promoter-TSS (NM_001159351)	-2	NM_023585	70620	Mm.235407	NM_023585	ENSMUSG00000022674	Ube2v2	1110021H13Rik|4632410D19Rik|5730524P06Rik|6820402M05|AI848315|C81524|MMS2	ubiquitin-conjugating enzyme E2 variant 2	protein-coding
mm_128416.1	chr15	44788017	44788031	-	1	NA	promoter-TSS (NM_176998)	promoter-TSS (NM_176998)	39	NM_176998	319613	Mm.207715	NM_176998	ENSMUSG00000022340	Sybu	Golsyn	syntabulin (syntaxin-interacting)	protein-coding
mm_161893.1	chr18	42301839	42301839	+	1	NA	exon (NM_172626, exon 7 of 20)	exon (NM_172626, exon 7 of 20)	26486	NM_172626	225432	Mm.329400	NM_172626	ENSMUSG00000024491	Rbm27	A730010I06|AI043120|Psc1|mKIAA1311	RNA binding motif protein 27	protein-coding
mm_141605.1	chr17	32788265	32788283	-	1	NA	promoter-TSS (NM_172458)	promoter-TSS (NM_172458)	13	NM_172458	208292	Mm.38813	NM_172458	ENSMUSG00000024298	Zfp871	4732483N19|9030612M13Rik|AI118577|AI265322|mKIAA3006	zinc finger protein 871	protein-coding
mm_37142.1	chr4	116992562	116992564	-	1	NA	intron (NM_009478, intron 6 of 9)	intron (NM_009478, intron 6 of 9)	1850	NM_009478	22275	Mm.46484	NM_009478	ENSMUSG00000028684	Urod	AI323803|UPD|Uro-d	uroporphyrinogen decarboxylase	protein-coding
mm_155922.1	chrX	103356421	103356433	+	1	NA	promoter-TSS (NM_009767)	promoter-TSS (NM_009767)	-49	NM_009767	12212	Mm.42223	NM_009767	ENSMUSG00000031327	Chic1	Brx|ENSMUSG00000073019|Gm10454	cysteine-rich hydrophobic domain 1	protein-coding
mm_75659.1	chr8	66480384	66480417	-	1	NA	exon (NM_025465, exon 5 of 7)	exon (NM_025465, exon 5 of 7)	6107	NM_025465	66282	Mm.294985	NM_025465	ENSMUSG00000025591	Tma16	1810029B16Rik	translation machinery associated 16	protein-coding
mm_8740.1	chr1	160247616	160247637	-	1	NA	intron (NM_001038621, intron 3 of 8)	intron (NM_001038621, intron 3 of 8)	-34734	NM_009786	12301	Mm.10702	NM_009786	ENSMUSG00000014226	Cacybp	SIP	calcyclin binding protein	protein-coding
mm_80548.1	chr9	82829932	82829942	+	1	NA	5' UTR (NM_001168240, exon 1 of 3)	5' UTR (NM_001168240, exon 1 of 3)	131	NM_022986	65099	Mm.41415	NM_022986	ENSMUSG00000032251	Irak1bp1	4921528N06Rik|AI851240|Aabp3|Aip70|Simpl	interleukin-1 receptor-associated kinase 1 binding protein 1	protein-coding
mm_94326.1	chr11	4264301	4264313	+	1	NA	intron (NM_008501, intron 1 of 3)	intron (NM_008501, intron 1 of 3)	-2489	NM_001039537	16878	Mm.4964	NM_008501	ENSMUSG00000034394	Lif	-	leukemia inhibitory factor	protein-coding
mm_78626.1	chr9	38719025	38719055	+	1	NA	intron (NM_001145957, intron 1 of 18)	intron (NM_001145957, intron 1 of 18)	772	NM_172767	67776	Mm.290950	NM_172767	ENSMUSG00000023186	Vwa5a	5830475I06Rik|AW552491|BCSC-1|E130119J22|Loh11cr2a	von Willebrand factor A domain containing 5A	protein-coding
mm_108994.1	chr12	102949203	102949233	+	1	NA	5' UTR (NM_001081017, exon 1 of 49)	5' UTR (NM_001081017, exon 1 of 49)	359	NM_001081017	217843	Mm.387073	NM_177621	ENSMUSG00000021198	Unc79	9030205A07Rik|Mlca3	unc-79 homolog (C. elegans)	protein-coding
mm_155546.1	chrX	74313015	74313109	+	1	NA	promoter-TSS (NM_138607)	promoter-TSS (NM_138607)	29	NM_138607	108160	Mm.4370	NM_138607	ENSMUSG00000001962	Fam50a	D0HXS9928E|XAP-5	family with sequence similarity 50, member A	protein-coding
mm_9.1	chr1	4808247	4808287	+	1	NA	intron (NM_008866, intron 1 of 8)	intron (NM_008866, intron 1 of 8)	374	NM_008866	18777	Mm.299955	NM_008866	ENSMUSG00000025903	Lypla1	Pla1a	lysophospholipase 1	protein-coding
mm_88651.1	chr10	79991575	79991583	+	1	NA	intron (NM_007725, intron 2 of 6)	intron (NM_007725, intron 2 of 6)	2979	NM_007725	12798	Mm.157770	NM_007725	ENSMUSG00000004665	Cnn2	AA408047|AI324678|Calpo2	calponin 2	protein-coding
mm_22737.1	chr3	19894856	19894894	+	1	NA	promoter-TSS (NR_027985)	promoter-TSS (NR_027985)	4	NR_027985	70808	Mm.427103	NR_027985	ENSMUSG00000048106	4632415L05Rik	AI662792	RRS1 ribosome biogenesis regulator homolog pseudogene	pseudo
mm_83361.1	chr9	44407345	44407372	-	1	NA	promoter-TSS (NM_024266)	promoter-TSS (NM_024266)	190	NM_021789	60409	Mm.29814	NM_021789	ENSMUSG00000032112	Trappc4	1500017G03Rik|AI303617|HSPC172|PTD009|Sbd|Sbdn|Sdcbp2|TRS23	trafficking protein particle complex 4	protein-coding
mm_172985.1	chrM	102	102	+	1	NA	NA	Intergenic	NA	NA								
mm_100464.1	chr11	119913424	119913434	+	1	NA	promoter-TSS (NM_001085498)	promoter-TSS (NM_001085498)	-381	NM_001085498	208092	Mm.306673	NM_001085498	ENSMUSG00000025371	Chmp6	2400004G01Rik	charged multivesicular body protein 6	protein-coding
mm_10944.1	chr2	25501861	25501874	+	1	NA	promoter-TSS (NM_001271777)	promoter-TSS (NM_001271777)	-148	NM_001271777	69379	Mm.24596	NM_027062	ENSMUSG00000015083	C8g	-	complement component 8, gamma polypeptide	protein-coding
mm_114583.1	chr13	75707548	75707561	+	1	NA	promoter-TSS (NM_138953)	promoter-TSS (NM_138953)	70	NM_138953	192657	Mm.21288	NM_138953	ENSMUSG00000001542	Ell2	-	elongation factor RNA polymerase II 2	protein-coding
mm_80133.1	chr9	70658533	70658537	+	1	NA	Intergenic	Intergenic	-1361	NM_172772	235461	Mm.170855	NM_172772	ENSMUSG00000042444	Fam63b	AI465301|B230380D07Rik|mKIAA1164	family with sequence similarity 63, member B	protein-coding
mm_105448.1	chr11	104442333	104442380	-	1	NA	promoter-TSS (NM_001081045)	promoter-TSS (NM_001081045)	-65	NM_001081045	76719	Mm.136418	NM_001081045	ENSMUSG00000018412	Kansl1	1700081L11Rik|9430041J06Rik|mKIAA1267	KAT8 regulatory NSL complex subunit 1	protein-coding
mm_120587.1	chr14	69840360	69840378	+	1	NA	promoter-TSS (NM_028526)	promoter-TSS (NM_028526)	-38	NM_028560	73523	Mm.23509	NM_028526	ENSMUSG00000022085	Pebp4	PEBP-4	phosphatidylethanolamine binding protein 4	protein-coding
mm_108066.1	chr12	73940584	73940595	+	1	NA	exon (NM_010431, exon 10 of 15)	exon (NM_010431, exon 10 of 15)	-23941	NM_178392	75627	Mm.25937	NM_178392	ENSMUSG00000021113	Snapc1	2700033G17Rik|AU015787	small nuclear RNA activating complex, polypeptide 1	protein-coding
mm_30773.1	chr4	17853635	17853648	+	1	NA	5' UTR (NM_019724, exon 1 of 10)	5' UTR (NM_019724, exon 1 of 10)	183	NM_019724	17389	Mm.187315	NM_019724	ENSMUSG00000028226	Mmp16	MT-MMP 3|MT3-MMP|Mt3mmp	matrix metallopeptidase 16	protein-coding
mm_61033.1	chr7	49553877	49553902	+	1	NA	intron (NM_175272, intron 16 of 37)	intron (NM_175272, intron 16 of 37)	82946	NM_001005232	13172	Mm.307176	NM_001005232	ENSMUSG00000030507	Dbx1	AI426026|Dbx	developing brain homeobox 1	protein-coding
mm_137119.1	chr17	22501525	22501527	+	1	NA	Intergenic	L1VL2|LINE|L1	71747	NM_001104573	210876	Mm.390947	NM_001104573	ENSMUSG00000095093	Vmn2r111	EG210876|V2rp2	vomeronasal 2, receptor 111	protein-coding
mm_167129.1	chr7	126777158	126777178	+	1	NA	5' UTR (NM_026875, exon 1 of 5)	5' UTR (NM_026875, exon 1 of 5)	193	NM_025347	66090	Mm.27114	NM_025347	ENSMUSG00000042675	Ypel3	0610043B10Rik|1190001G19Rik|Suap	yippee-like 3 (Drosophila)	protein-coding
mm_25789.1	chr3	126810613	126810644	+	1	NA	intron (NM_001346636, intron 15 of 20)	intron (NM_001346636, intron 15 of 20)	132758	NM_001034168	109676	Mm.220242	NM_178655	ENSMUSG00000032826	Ank2	100043364|AI835472|AW491075|Ank-2|Gm4392	ankyrin 2, brain	protein-coding
mm_120970.1	chr14	77931241	77931282	+	1	NA	exon (NM_029495, exon 4 of 12)	exon (NM_029495, exon 4 of 12)	27022	NM_029495	108670	Mm.68134	NM_029495	ENSMUSG00000022014	Epsti1	2310046K10Rik|5033415K03Rik|BRESI1	epithelial stromal interaction 1 (breast)	protein-coding
mm_68039.1	chr7	101354432	101354446	-	1	NA	intron (NM_001040111, intron 1 of 33)	intron (NM_001040111, intron 1 of 33)	6370	NM_001040111	69710	Mm.277687	NM_027180	ENSMUSG00000032812	Arap1	2410002L19Rik|Centd2|mKIAA0782	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	protein-coding
mm_127139.1	chr15	98168664	98168679	+	1	NA	exon (NM_177716, exon 1 of 1)	exon (NM_177716, exon 1 of 1)	865	NM_177716	239650	Mm.54140	NM_177716	ENSMUSG00000029875	Ccdc184	5630400A08|AI836003	coiled-coil domain containing 184	protein-coding
mm_76551.1	chr8	88354712	88354742	-	1	NA	exon (NM_012047, exon 5 of 17)	exon (NM_012047, exon 5 of 17)	7464	NM_012047	26992	Mm.5400	NM_012047	ENSMUSG00000031660	Brd7	BP75|CELTIX1|Ptpn13ip	bromodomain containing 7	protein-coding
mm_18649.1	chr2	69713462	69713477	-	1	NA	promoter-TSS (NM_177244)	promoter-TSS (NM_177244)	-863	NM_177244	320720	Mm.289566	NM_177244	ENSMUSG00000027086	Fastkd1	5330408N05Rik|mKIAA1800	FAST kinase domains 1	protein-coding
mm_71962.1	chr8	70528021	70528038	+	1	NA	5' UTR (NM_001199631, exon 1 of 9)	5' UTR (NM_001199631, exon 1 of 9)	183	NM_001199631	14232	Mm.141864	NM_010223	ENSMUSG00000019428	Fkbp8	38kDa|FKBP-38|FKBP-8|Fkbp38	FK506 binding protein 8	protein-coding
mm_173107.1	chrX	156931742	156931744	+	1	NA	Intergenic	Intergenic	392260	NR_033598	74941	Mm.484588	NR_033598		4930503H13Rik	-	gem (nuclear organelle) associated protein 8 pseudogene	pseudo
mm_39058.1	chr4	154023766	154023777	-	1	NA	exon (NM_001163722, exon 3 of 4)	exon (NM_001163722, exon 3 of 4)	2273	NM_001163722	68859	Mm.477488	NM_001033144	ENSMUSG00000078350	Smim1	0610011H04Rik|1190007F08Rik|2700009I11Rik	small integral membrane protein 1	protein-coding
mm_172750.1	chr8	84687137	84687146	-	1	NA	intron (NM_025788, intron 1 of 5)	intron (NM_025788, intron 1 of 5)	721	NM_025788	66830	Mm.289698	NM_025788	ENSMUSG00000001910	Nacc1	2010001H03Rik|4930511N13Rik|Btbd14b|Nac1	nucleus accumbens associated 1, BEN and BTB (POZ) domain containing	protein-coding
mm_35046.1	chr4	4576404	4576415	-	1	NA	Intergenic	Intergenic	-46951	NM_001277919	622019	Mm.246123	NM_001277919		Gm11780	OTTMUSG00000004194	predicted gene 11780	protein-coding
mm_83084.1	chr9	40239873	40239885	-	1	NA	Intergenic	RMER16A3|LTR|ERVK	-29337	NM_001083917	235281	Mm.290083	NM_153522	ENSMUSG00000049281	Scn3b	1110001K16Rik|4833414B02Rik|Scnb3	sodium channel, voltage-gated, type III, beta	protein-coding
mm_40458.1	chr5	53604342	53604386	+	1	NA	intron (NM_001277116, intron 3 of 12)	Lx7|LINE|L1	13878	NM_001080927	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_57984.1	chr6	135733666	135733672	-	1	NA	exon (NM_008171, exon 15 of 15)	exon (NM_008171, exon 15 of 15)	74756	NR_126088	75024	Mm.399147	NR_126088	ENSMUSG00000107396	4930425L21Rik	4930473P14Rik	RIKEN cDNA 4930425L21 gene	ncRNA
mm_26591.1	chr3	151437891	151437914	+	1	NA	promoter-TSS (NM_133222)	promoter-TSS (NM_133222)	20	NM_133222	170757	Mm.317261	NM_133222	ENSMUSG00000039167	Adgrl4	1110033N21Rik|ETL1|Eltd1|Etl	adhesion G protein-coupled receptor L4	protein-coding
mm_111819.1	chr12	106034385	106034423	-	1	NA	intron (NM_001029843, intron 1 of 13)	intron (NM_001029843, intron 1 of 13)	24141	NM_001029843	22367	Mm.2981	NM_011705	ENSMUSG00000021115	Vrk1	51PK	vaccinia related kinase 1	protein-coding
mm_11255.1	chr2	29903569	29903596	+	1	NA	intron (NM_013615, intron 7 of 16)	intron (NM_013615, intron 7 of 16)	13519	NM_013615	18286	Mm.330116	NM_013615	ENSMUSG00000026790	Odf2	AI848335|MMTEST29	outer dense fiber of sperm tails 2	protein-coding
mm_16031.1	chr2	167629086	167629098	+	1	NA	intron (NM_001311146, intron 1 of 2)	intron (NM_001311146, intron 1 of 2)	2913	NM_001311146	66589	Mm.278783	NM_023230	ENSMUSG00000078923	Ube2v1	0610011J09Rik|AI256840|CROC-1|CROC1|D7Bwg1382e|UEV-1	ubiquitin-conjugating enzyme E2 variant 1	protein-coding
mm_139485.1	chr17	56079629	56079643	+	1	NA	promoter-TSS (NM_001304785)	promoter-TSS (NM_001304785)	5	NM_001304785	15193	Mm.12966	NM_008233	ENSMUSG00000002833	Hdgfrp2	HRP-2	hepatoma-derived growth factor, related protein 2	protein-coding
mm_48422.1	chr5	140389189	140389254	-	1	NA	promoter-TSS (NM_172277)	promoter-TSS (NM_172277)	87	NM_172277	231834	Mm.27098	NM_172277	ENSMUSG00000029560	Snx8	B130023O14Rik	sorting nexin 8	protein-coding
mm_34689.1	chr4	151933721	151933755	+	1	NA	promoter-TSS (NM_172704)	promoter-TSS (NM_172704)	18	NM_172704	230935	Mm.21353	NM_172704	ENSMUSG00000039768	Dnajc11	E030019A03Rik	DnaJ heat shock protein family (Hsp40) member C11	protein-coding
mm_41018.1	chr5	81418115	81418119	+	1	NA	intron (NM_001347371, intron 4 of 23)	intron (NM_001347371, intron 4 of 23)	396524	NM_198702	319387	Mm.273631	NM_198702	ENSMUSG00000037605	Adgrl3	5430402I23Rik|CIRL-3|D130075K09Rik|Gm1379|LEC3|Lphn3|mKIAA0768	adhesion G protein-coupled receptor L3	protein-coding
mm_148458.1	chr19	4003409	4003418	+	1	NA	promoter-TSS (NM_021791)	promoter-TSS (NM_021791)	28	NM_021791	60425	Mm.266972	NM_021791	ENSMUSG00000024871	Doc2g	D830013O18Rik	double C2, gamma	protein-coding
mm_116930.1	chr13	55784464	55784473	-	1	NA	promoter-TSS (NM_001252487)	promoter-TSS (NM_001252487)	-111	NM_029772	76856	Mm.159795	NM_029772	ENSMUSG00000021499	Catsper3	4921522D01Rik|CACRC	cation channel, sperm associated 3	protein-coding
mm_63510.1	chr7	127848388	127848398	+	1	NA	exon (NM_009294, exon 9 of 11)	exon (NM_009294, exon 9 of 11)	6585	NM_009294	20909	Mm.24867	NM_009294	ENSMUSG00000030805	Stx4a	Stx4|Syn-4|Syn4	syntaxin 4A (placental)	protein-coding
mm_75755.1	chr8	69908883	69908906	-	1	NA	3' UTR (NM_001113346, exon 13 of 13)	3' UTR (NM_001113346, exon 13 of 13)	-6336	NM_023312	67184	Mm.21162	NM_023312	ENSMUSG00000036199	Ndufa13	2700054G14Rik|AU022060|CDA016|CGI-39|GRIM-19|Grim19	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 13	protein-coding
mm_134089.1	chr16	8792367	8792377	-	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	-37728	NM_001081400	69053	Mm.390868	NM_001081400	ENSMUSG00000022507	1810013L24Rik	1110017P05Rik|3010002C02Rik|AA792997|AW124177|Gm19906|R74903	RIKEN cDNA 1810013L24 gene	protein-coding
mm_149121.1	chr19	8989278	8989295	+	1	NA	promoter-TSS (NM_001286518)	promoter-TSS (NM_001286518)	2	NM_001286518	66395	Mm.203866	NM_009643	ENSMUSG00000069833	Ahnak	DY6	AHNAK nucleoprotein (desmoyokin)	protein-coding
mm_35913.1	chr4	52197212	52197217	-	1	NA	Intergenic	RMER19B|LTR|ERVK	-146104	NR_040668	329844	Mm.128934	NR_040668	ENSMUSG00000085515	C630028M04Rik	-	RIKEN cDNA C630028M04 gene	ncRNA
mm_25321.1	chr3	106547698	106547714	+	1	NA	promoter-TSS (NM_026013)	promoter-TSS (NM_026013)	-92	NM_001286986	67171	Mm.290488	NM_026013	ENSMUSG00000027900	Dram2	2010305N14Rik|2610318G18Rik|AI647667|Tmem77	DNA-damage regulated autophagy modulator 2	protein-coding
mm_43799.1	chr5	142818995	142819003	+	1	NA	Intergenic	Intergenic	-1612	NM_001122730	231861	Mm.354649	NM_178242	ENSMUSG00000039477	Tnrc18	BC025631|EG381742|Zfp469	trinucleotide repeat containing 18	protein-coding
mm_94161.1	chr10	128745479	128745499	-	1	NA	Intergenic	Intergenic	-1433	NM_016811	13139	Mm.291235	NM_016811	ENSMUSG00000025357	Dgka	80kDa|AW146112|Dagk1	diacylglycerol kinase, alpha	protein-coding
mm_69979.1	chr7	142377615	142377652	-	1	NA	intron (NM_009983, intron 5 of 8)	intron (NM_009983, intron 5 of 8)	-3887	NM_001347541	320802	Mm.154486	NM_177265	ENSMUSG00000045777	Ifitm10	6330512M04Rik|AI848576|DSPA3	interferon induced transmembrane protein 10	protein-coding
mm_9099.1	chr1	169747635	169747649	-	1	NA	promoter-TSS (NM_009062)	promoter-TSS (NM_009062)	0	NM_009062	19736	Mm.41642	NM_009062	ENSMUSG00000038530	Rgs4	AA004315|AA597169|ESTM48|ESTM50	regulator of G-protein signaling 4	protein-coding
mm_54335.1	chr6	30642323	30642359	-	1	NA	exon (NM_025350, exon 7 of 10)	exon (NM_025350, exon 7 of 10)	3123	NM_025350	109697	Mm.25377	NM_025350	ENSMUSG00000054446	Cpa1	0910001L12Rik|Cpa	carboxypeptidase A1, pancreatic	protein-coding
mm_147832.1	chr18	62548683	62548717	-	1	NA	promoter-TSS (NM_177829)	promoter-TSS (NM_177829)	43	NM_134136	107035	Mm.21295	NM_134136	ENSMUSG00000042211	Fbxo38	6030410I24Rik|AU044865|AW214031|Moka|SP329	F-box protein 38	protein-coding
mm_137885.1	chr17	31636029	31636030	+	1	NA	intron (NM_178224, intron 1 of 15)	intron (NM_178224, intron 1 of 15)	1176	NM_144855	12411	Mm.206417	NM_144855	ENSMUSG00000024039	Cbs	AI047524|AI303044|HIP4	cystathionine beta-synthase	protein-coding
mm_74523.1	chr8	9414847	9414859	-	1	NA	intron (NM_001347127, intron 1 of 3)	intron (NM_001347127, intron 1 of 3)	270184	NR_073360	74688	Mm.159298	NR_073360	ENSMUSG00000109215	4930453L07Rik	-	RIKEN cDNA 4930453L07 gene	ncRNA
mm_134985.1	chr16	32130310	32130336	-	1	NA	Intergenic	Intergenic	30521	NM_025892	66994	Mm.22990	NM_025892	ENSMUSG00000035790	Cep19	1500031L02Rik|AI428934|AL022620	centrosomal protein 19	protein-coding
mm_8584.1	chr1	155973206	155973259	-	1	NA	promoter-TSS (NM_001039184)	promoter-TSS (NM_001039184)	23	NM_001039184	74081	Mm.260247	NM_001039184	ENSMUSG00000033671	Cep350	4933409L06Rik|6430546F08Rik	centrosomal protein 350	protein-coding
mm_90487.1	chr10	127961526	127961549	+	1	NA	Intergenic	Intergenic	45971	NM_013786	27400	Mm.26719	NM_013786	ENSMUSG00000025396	Hsd17b6	17betaHSD9|Hsd17b9|Rdh8	hydroxysteroid (17-beta) dehydrogenase 6	protein-coding
mm_53727.1	chr6	145075399	145075416	+	1	NA	intron (NM_007532, intron 1 of 10)	intron (NM_007532, intron 1 of 10)	750	NM_007532	12035	Mm.4606	NM_007532	ENSMUSG00000030268	Bcat1	BCATc|Eca39	branched chain aminotransferase 1, cytosolic	protein-coding
mm_49805.1	chr6	36388040	36388053	+	1	NA	promoter-TSS (NM_203491)	promoter-TSS (NM_203491)	-38	NM_203491	243764	Mm.448632	NM_203491	ENSMUSG00000045613	Chrm2	AChR-M2|Chrm-2|M2	cholinergic receptor, muscarinic 2, cardiac	protein-coding
mm_76296.1	chr8	84203669	84203671	-	1	NA	Intergenic	Intergenic	-4848	NR_029740	387216		NR_029740	ENSMUSG00000065611	Mir23a	Mirn23a|mir-23a|mmu-mir-23a	microRNA 23a	ncRNA
mm_30154.1	chr3	142623863	142623891	-	1	NA	promoter-TSS (NR_105802)	promoter-TSS (NR_105802)	69	NR_105802	102465200		NR_105802	ENSMUSG00000098871	Mir6381	Gm27963|mmu-mir-6381	microRNA 6381	ncRNA
mm_76206.1	chr8	83389725	83389735	-	1	NA	promoter-TSS (NM_001329627)	promoter-TSS (NM_001329627)	-112	NM_001329627	12745	Mm.358581	NM_009904	ENSMUSG00000002190	Clgn	4930459O04Rik|A2/6|AI528775|Cln	calmegin	protein-coding
mm_76552.1	chr8	88361704	88361717	-	1	NA	exon (NM_012047, exon 2 of 17)	exon (NM_012047, exon 2 of 17)	481	NM_012047	26992	Mm.5400	NM_012047	ENSMUSG00000031660	Brd7	BP75|CELTIX1|Ptpn13ip	bromodomain containing 7	protein-coding
mm_66161.1	chr7	31155958	31155981	-	1	NA	Intergenic	Intergenic	-4919	NM_027898	52857	Mm.27366	NM_027898	ENSMUSG00000001248	Gramd1a	1300003M23Rik|AI415002|AW547240|D7Bwg0611e	GRAM domain containing 1A	protein-coding
mm_33817.1	chr4	135337799	135337805	+	1	NA	intron (NM_016799, intron 9 of 17)	intron (NM_016799, intron 9 of 17)	15412	NM_016799	51796	Mm.1963	NM_016799	ENSMUSG00000028809	Srrm1	AA407769|POP101|Srm160	serine/arginine repetitive matrix 1	protein-coding
mm_393.1	chr1	34121175	34121187	+	1	NA	intron (NM_001276764, intron 8 of 102)	intron (NM_001276764, intron 8 of 102)	3822	NR_105861	102466987		NR_105861	ENSMUSG00000105982	Mir6896	mmu-mir-6896	microRNA 6896	ncRNA
mm_39379.1	chr5	12719820	12719867	+	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	336677	NM_028882	108151	Mm.89313	NM_028882	ENSMUSG00000040254	Sema3d	4631426B19Rik	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D	protein-coding
mm_69126.1	chr7	127026525	127026541	-	1	NA	promoter-TSS (NM_010772)	promoter-TSS (NM_010772)	-54	NM_010772	17188	Mm.378964	NM_010772	ENSMUSG00000030678	Maz	MAZI|PUR1|Pur-1|SAF-1|SAF-2	MYC-associated zinc finger protein (purine-binding transcription factor)	protein-coding
mm_31121.1	chr4	42957423	42957432	+	1	NA	exon (NM_019874, exon 3 of 3)	exon (NM_019874, exon 3 of 3)	4333	NM_019874	56323	Mm.20437	NM_019874	ENSMUSG00000036052	Dnajb5	1110058L06Rik|AI462558|Hsc40|Hsp40-3	DnaJ heat shock protein family (Hsp40) member B5	protein-coding
mm_53055.1	chr6	124809725	124809760	+	1	NA	TTS (NM_009415)	TTS (NM_009415)	824	NM_001306053	14794	Mm.261906	NM_013539	ENSMUSG00000038451	Spsb2	AI461677|C9|Grcc9|SSB2	splA/ryanodine receptor domain and SOCS box containing 2	protein-coding
mm_126680.1	chr15	84720054	84720092	+	1	NA	promoter-TSS (NM_001164628)	promoter-TSS (NM_001164628)	21	NM_001205334	73167	Mm.128411	NM_028455	ENSMUSG00000078954	Arhgap8	3110043J09Rik	Rho GTPase activating protein 8	protein-coding
mm_26126.1	chr3	137867860	137867876	+	1	NA	TTS (NM_016750)	TTS (NM_016750)	193	NM_001033155	70604	Mm.256488	NM_001033155	ENSMUSG00000074212	Dnajb14	5730496F10Rik	DnaJ heat shock protein family (Hsp40) member B14	protein-coding
mm_20279.1	chr2	126890878	126890896	-	1	NA	3' UTR (NM_023220, exon 15 of 15)	3' UTR (NM_023220, exon 15 of 15)	11498	NR_106202	102466258		NR_106202	ENSMUSG00000098896	Mir3473g	Gm27751|mmu-mir-3473g	microRNA 3473g	ncRNA
mm_139303.1	chr17	48347502	48347531	+	1	NA	intron (NM_001272078, intron 1 of 4)	intron (NM_001272078, intron 1 of 4)	1115	NM_001272078	83433	Mm.261623	NM_031254	ENSMUSG00000023992	Trem2	TREM-2|Trem2a|Trem2b|Trem2c	triggering receptor expressed on myeloid cells 2	protein-coding
mm_102919.1	chr11	69600153	69600169	-	1	NA	3' UTR (NM_013415, exon 7 of 7)	3' UTR (NM_013415, exon 7 of 7)	5799	NM_013415	11932	Mm.235204	NM_013415	ENSMUSG00000041329	Atp1b2	Amog|Atpb-2	ATPase, Na+/K+ transporting, beta 2 polypeptide	protein-coding
mm_82706.1	chr9	22772822	22772848	-	1	NA	intron (NM_178415, intron 19 of 22)	U4|snRNA|snRNA	297120	NM_178415	319845	Mm.176725	NM_178415	ENSMUSG00000035919	Bbs9	E130103I17Rik	Bardet-Biedl syndrome 9 (human)	protein-coding
mm_10866.1	chr2	25180738	25180764	+	1	NA	promoter-TSS (NM_025980)	promoter-TSS (NM_025980)	-7	NM_025980	67122	Mm.46539	NM_025980	ENSMUSG00000078202	Nrarp	2700054M22Rik	Notch-regulated ankyrin repeat protein	protein-coding
mm_62421.1	chr7	101321704	101321790	+	1	NA	5' UTR (NM_019990, exon 2 of 7)	5' UTR (NM_019990, exon 2 of 7)	428	NM_019990	56018	Mm.28896	NM_019990	ENSMUSG00000030688	Stard10	AV048538|CGI-52|NY-C0-28|PC-TP2|PCTP2|Pctpl|Sdccag28|SdccagG28|TISP-81	START domain containing 10	protein-coding
mm_102714.1	chr11	67113439	67113474	-	1	NA	non-coding (NR_038055, exon 5 of 5)	non-coding (NR_038055, exon 5 of 5)	6624	NR_038055	74184	Mm.162554	NR_038055	ENSMUSG00000087410	2310065F04Rik	linc-Myh	RIKEN cDNA 2310065F04 gene	ncRNA
mm_89971.1	chr10	111506429	111506435	+	1	NA	exon (NM_009344, exon 1 of 2)	exon (NM_009344, exon 1 of 2)	146	NM_009344	21664	Mm.3117	NM_009344	ENSMUSG00000020205	Phlda1	DT1P1B11|TDAG51|Tdag	pleckstrin homology like domain, family A, member 1	protein-coding
mm_167003.1	chr7	49703580	49703582	-	1	NA	Intergenic	Intergenic	-55525	NM_001146053	53415	Mm.20801	NM_016865	ENSMUSG00000039745	Htatip2	AW111545|Cc3|Tip30	HIV-1 Tat interactive protein 2	protein-coding
mm_65213.1	chr7	19698083	19698093	-	1	NA	intron (NM_001305843, intron 3 of 4)	intron (NM_001305843, intron 3 of 4)	310	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_3989.1	chr1	164373261	164373275	+	1	NA	intron (NM_138314, intron 9 of 13)	intron (NM_138314, intron 9 of 13)	65596	NM_178071	171567	Mm.219428	NM_138314	ENSMUSG00000026575	Nme7	D530024H21Rik|Nm23-M7|Nm23-r7	NME/NM23 family member 7	protein-coding
mm_106114.1	chr11	116335385	116335399	-	1	NA	promoter-TSS (NM_008240)	promoter-TSS (NM_008240)	-38	NM_008240	15223	Mm.378938	NM_008240	ENSMUSG00000034227	Foxj1	FKHL-13|HFH-4|Hfh4	forkhead box J1	protein-coding
mm_58651.1	chr7	6286590	6286622	+	1	NA	promoter-TSS (NM_001024928)	promoter-TSS (NM_001024928)	26	NM_001024928	384763	Mm.276279	NM_001024928	ENSMUSG00000054893	Zfp667	A830025F02Rik|Mip1|ZNF667	zinc finger protein 667	protein-coding
mm_117984.1	chr13	100174434	100174444	-	1	NA	intron (NM_010872, intron 8 of 15)	IMPB_01|Satellite|Satellite	27683	NM_001126182	17948	Mm.89961	NM_010872	ENSMUSG00000078945	Naip2	Birc1b|Naip-rs6	NLR family, apoptosis inhibitory protein 2	protein-coding
mm_48687.1	chr5	146749514	146749519	-	1	NA	intron (NM_011669, intron 6 of 8)	RMER6A|LTR|ERVK	45440	NM_011669	22217	Mm.167971	NM_011669	ENSMUSG00000029640	Usp12	Ubh1	ubiquitin specific peptidase 12	protein-coding
mm_3014.1	chr1	133363690	133363696	+	1	NA	5' UTR (NM_175443, exon 1 of 8)	5' UTR (NM_175443, exon 1 of 8)	121	NM_175443	214253	Mm.52111	NM_175443	ENSMUSG00000070644	Etnk2	4933417N20Rik|AI197444|EKI 2|Eki2|Tuc1	ethanolamine kinase 2	protein-coding
mm_149429.1	chr19	11469407	11469419	+	1	NA	promoter-TSS (NM_028595)	promoter-TSS (NM_028595)	45	NM_028595	73656	Mm.440719	NM_028595	ENSMUSG00000079419	Ms4a6c	2200009H22Rik|2210417N07Rik	membrane-spanning 4-domains, subfamily A, member 6C	protein-coding
mm_37328.1	chr4	119492564	119492618	-	1	NA	promoter-TSS (NM_177572)	promoter-TSS (NM_177572)	7	NM_177572	194237	Mm.206201	NM_177572	ENSMUSG00000048899	Rimkla	B930030J24|NAAGS|NAAGS-II|Rimk	ribosomal modification protein rimK-like family member A	protein-coding
mm_5120.1	chr1	7397073	7397076	-	1	NA	Intergenic	Intergenic	308154	NM_183028	319263	Mm.21539	NM_183028	ENSMUSG00000051285	Pcmtd1	8430411F12Rik|A030012M09Rik	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding
mm_8309.1	chr1	144177186	144177196	-	1	NA	intron (NM_153171, intron 1 of 5)	intron (NM_153171, intron 1 of 5)	181	NM_153171	246709	Mm.38271	NM_153171	ENSMUSG00000051079	Rgs13	-	regulator of G-protein signaling 13	protein-coding
mm_113291.1	chr13	30336382	30336415	+	1	NA	promoter-TSS (NM_177322)	promoter-TSS (NM_177322)	42	NM_177322	11607	Mm.35062	NM_177322	ENSMUSG00000049115	Agtr1a	1810074K20Rik|AG2S|AI551199|AT1|AT1a|AT2R1|AT2R1A|Agtr-1a|Agtr1|Angtr-1a	angiotensin II receptor, type 1a	protein-coding
mm_158636.1	chrX	155214105	155214138	-	1	NA	exon (NM_009121, exon 4 of 6)	exon (NM_009121, exon 4 of 6)	2328	NM_009121	20229	Mm.2734	NM_009121	ENSMUSG00000025283	Sat1	AA617398|SSAT|Sat	spermidine/spermine N1-acetyl transferase 1	protein-coding
mm_41238.1	chr5	88765037	88765054	+	1	NA	promoter-TSS (NM_007832)	promoter-TSS (NM_007832)	32	NM_007832	13178	Mm.298892	NM_007832	ENSMUSG00000029366	Dck	-	deoxycytidine kinase	protein-coding
mm_48302.1	chr5	138272734	138272743	-	1	NA	promoter-TSS (NM_001033416)	promoter-TSS (NM_001033416)	16	NM_001033416	330217	Mm.332774	NM_001033416	ENSMUSG00000075593	Gal3st4	1500031A01Rik	galactose-3-O-sulfotransferase 4	protein-coding
mm_140261.1	chr17	84613232	84613252	+	1	NA	intron (NM_177606, intron 27 of 29)	intron (NM_177606, intron 27 of 29)	-13257	NM_172256	213575	Mm.246119	NM_172256	ENSMUSG00000024253	Dync2li1	4933404O11Rik|CGI-60|D2lic|LIC3|mD2LIC	dynein cytoplasmic 2 light intermediate chain 1	protein-coding
mm_11203.1	chr2	29159916	29159919	+	1	NA	intron (NM_198033, intron 15 of 25)	(T)n|Simple_repeat|Simple_repeat	34925	NM_198033	269254	Mm.41867	NM_198033	ENSMUSG00000043535	Setx	A130090N03|A930037J23Rik|AOA2|AW060766|Als4|SCAR1|Sen1|mKIAA0625	senataxin	protein-coding
mm_145513.1	chr18	60443117	60443126	+	1	NA	Intergenic	MER73|LTR|ERVL	58862	NM_134133	106878	Mm.273197	NM_134133	ENSMUSG00000038059	Smim3	2010002N04Rik|AI195350|AW561905|Nid67|cI-41	small integral membrane protein 3	protein-coding
mm_80646.1	chr9	89826949	89826957	+	1	NA	non-coding (NR_040735, exon 1 of 6)	non-coding (NR_040735, exon 1 of 6)	434	NR_040735	74700	Mm.159306	NR_040735	ENSMUSG00000098627	4930524O08Rik	-	RIKEN cDNA 4930524O08 gene	ncRNA
mm_141588.1	chr17	32409516	32409520	-	1	NA	Intergenic	Intergenic	-5936	NM_001347343	320484	Mm.122284	NM_178785	ENSMUSG00000052142	Rasal3	A430107D22Rik	RAS protein activator like 3	protein-coding
mm_8672.1	chr1	156674291	156674344	-	1	NA	promoter-TSS (NM_023141)	promoter-TSS (NM_023141)	22	NM_023141	30935	Mm.206737	NM_023141	ENSMUSG00000060519	Tor3a	Adir	torsin family 3, member A	protein-coding
mm_42784.1	chr5	121452690	121452714	+	1	NA	promoter-TSS (NM_029912)	promoter-TSS (NM_029912)	-7	NM_029912	77462	Mm.358781	NM_029912	ENSMUSG00000029452	Tmem116	4930406A18Rik|4930513P12Rik|C030022K24Rik	transmembrane protein 116	protein-coding
mm_85696.1	chr9	108083331	108083370	-	1	NA	exon (NM_008243, exon 11 of 18)	exon (NM_008243, exon 11 of 18)	1852	NR_106056	102466914		NR_106056	ENSMUSG00000098787	Mir7088	Gm27577|mmu-mir-7088	microRNA 7088	ncRNA
mm_48240.1	chr5	137741416	137741454	-	1	NA	promoter-TSS (NM_001347505)	promoter-TSS (NM_001347505)	-267	NM_001347505	243300	Mm.74750	NM_175521	ENSMUSG00000045348	Nyap1	6430598A04Rik	neuronal tyrosine-phosphorylated phosphoinositide 3-kinase adaptor 1	protein-coding
mm_134956.1	chr16	31311094	31311109	-	1	NA	exon (NM_007470, exon 3 of 6)	exon (NM_007470, exon 3 of 6)	3707	NM_001301353	11815	Mm.2082	NM_007470	ENSMUSG00000022548	Apod	-	apolipoprotein D	protein-coding
mm_171091.1	chr3	127772021	127772022	+	1	NA	intron (NM_027808, intron 1 of 13)	L1Md_A|LINE|L1	8506	NM_027808	71481	Mm.158704	NM_027808	ENSMUSG00000028028	Alpk1	8430410J10Rik|LAK	alpha-kinase 1	protein-coding
mm_169396.1	chr14	45570411	45570411	-	1	NA	Intergenic	Intergenic	26701	NR_045809	67651	Mm.55930	NR_045809		4930527F14Rik	-	RIKEN cDNA 4930527F14 gene	ncRNA
mm_24079.1	chr3	87932166	87932184	+	1	NA	exon (NM_177663, exon 2 of 4)	exon (NM_177663, exon 2 of 4)	1861	NM_177663	229504	Mm.45744	NM_177663	ENSMUSG00000048039	Isg20l2	4930429N24|C80587	interferon stimulated exonuclease gene 20-like 2	protein-coding
mm_74607.1	chr8	12458017	12458024	-	1	NA	Intergenic	Intergenic	62501	NM_009233	20664	Mm.39088	NM_009233	ENSMUSG00000096014	Sox1	BB176347|Sox-1	SRY (sex determining region Y)-box 1	protein-coding
mm_19014.1	chr2	76905825	76905835	-	1	NA	intron (NM_011652, intron 46 of 312)	B1_Mur4|SINE|Alu	76717	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_46501.1	chr5	105133993	105134003	-	1	NA	intron (NM_008620, intron 3 of 10)	B3A|SINE|B2	5554	NM_008620	17472	Mm.440525	NM_008620	ENSMUSG00000079363	Gbp4	AW228052|Mag-2|Mpa-2|Mpa2	guanylate binding protein 4	protein-coding
mm_101109.1	chr11	11933373	11933406	-	1	NA	3' UTR (NM_010345, exon 17 of 17)	3' UTR (NM_010345, exon 17 of 17)	-35245	NM_001190448	13195	Mm.12906	NM_016672	ENSMUSG00000020182	Ddc	Aadc	dopa decarboxylase	protein-coding
mm_3589.1	chr1	151358071	151358073	+	1	NA	intron (NM_054102, intron 8 of 14)	intron (NM_054102, intron 8 of 14)	13574	NM_001039511	117198	Mm.33764	NM_028582	ENSMUSG00000023150	Ivns1abp	1190004M08Rik|1700126I16Rik|AA960440|HSPC068|ND1|NS-1|NS1-BP|Nd1-L|Nd1-S|mKIAA0850	influenza virus NS1A binding protein	protein-coding
mm_40687.1	chr5	65763548	65763570	+	1	NA	promoter-TSS (NM_001024917)	promoter-TSS (NM_001024917)	38	NM_001024917	333789	Mm.332398	NM_001024917	ENSMUSG00000037795	N4bp2	B3bp|E430014I16|Gm1791|Gm868	NEDD4 binding protein 2	protein-coding
mm_6385.1	chr1	72849159	72849173	-	1	NA	exon (NM_008342, exon 2 of 4)	exon (NM_008342, exon 2 of 4)	23779	NM_001310659	16008	Mm.141936	NM_008342	ENSMUSG00000039323	Igfbp2	AI255832|IBP-2|Igfbp-2|mIGFBP-2	insulin-like growth factor binding protein 2	protein-coding
mm_59802.1	chr7	29134926	29134957	+	1	NA	promoter-TSS (NM_001174155)	promoter-TSS (NM_001174155)	8	NR_045676	233046	Mm.465324	NM_145149	ENSMUSG00000030589	Rasgrp4	-	RAS guanyl releasing protein 4	protein-coding
mm_40778.1	chr5	67260926	67260970	+	1	NA	5' UTR (NM_001285452, exon 1 of 7)	5' UTR (NM_001285452, exon 1 of 7)	383	NM_030108	67878	Mm.23217	NM_028975	ENSMUSG00000037720	Tmem33	1110006G02Rik|1600019D15Rik|2410089A21Rik|2700052H22Rik|5430406L04Rik|AA388285|AI314185|AI426615|db83	transmembrane protein 33	protein-coding
mm_166547.1	chr6	38921506	38921513	+	1	NA	intron (NM_011539, intron 1 of 12)	intron (NM_011539, intron 1 of 12)	2523	NM_011539	21391	Mm.4054	NM_011539	ENSMUSG00000029925	Tbxas1	CYP5|CYP5A1|THAS|TS|TXAS|TXS	thromboxane A synthase 1, platelet	protein-coding
mm_154208.1	chr19	59075611	59075644	-	1	NA	5' UTR (NM_001114312, exon 1 of 17)	5' UTR (NM_001114312, exon 1 of 17)	442	NM_175172	71653	Mm.37338	NM_175172	ENSMUSG00000041362	Shtn1	4930506M07Rik|Kiaa1598|Shootin1|mKIAA1598	shootin 1	protein-coding
mm_164793.1	chr18	16746244	16746264	-	1	NA	intron (NM_007664, intron 2 of 15)	intron (NM_007664, intron 2 of 15)	62992	NM_007664	12558	Mm.257437	NM_007664	ENSMUSG00000024304	Cdh2	CDHN|N-CAD|Ncad	cadherin 2	protein-coding
mm_15044.1	chr2	152830598	152830638	+	1	NA	promoter-TSS (NM_001289716)	promoter-TSS (NM_001289716)	99	NM_001289716	12048	Mm.238213	NM_009743	ENSMUSG00000007659	Bcl2l1	Bcl(X)L|Bcl-XL|Bcl2l|BclX|bcl-x|bcl2-L-1	BCL2-like 1	protein-coding
mm_33558.1	chr4	131873519	131873535	+	1	NA	promoter-TSS (NM_020587)	promoter-TSS (NM_020587)	-112	NM_020587	57317	Mm.2478	NM_020587	ENSMUSG00000028911	Srsf4	5730499P16Rik|AW550192|MNCb-2616|SRp75|Sfrs4	serine/arginine-rich splicing factor 4	protein-coding
mm_88066.1	chr10	67693879	67693893	+	1	NA	Intergenic	Intergenic	-144931	NM_001005419	211488	Mm.297250	NM_001005419	ENSMUSG00000057134	Ado	Gm237	2-aminoethanethiol (cysteamine) dioxygenase	protein-coding
mm_51948.1	chr6	91726208	91726229	+	1	NA	exon (NM_009320, exon 5 of 15)	exon (NM_009320, exon 5 of 15)	42151	NM_009320	21366	Mm.395650	NM_009320	ENSMUSG00000030096	Slc6a6	AA589629|C80501|Taut	solute carrier family 6 (neurotransmitter transporter, taurine), member 6	protein-coding
mm_35225.1	chr4	19687875	19687890	-	1	NA	non-coding (NR_074090, exon 2 of 25)	non-coding (NR_074090, exon 2 of 25)	21122	NM_177327	107568	Mm.78312	NM_177327	ENSMUSG00000041058	Wwp1	8030445B08Rik|AIP5|SDRP1|Tiul1	WW domain containing E3 ubiquitin protein ligase 1	protein-coding
mm_155033.1	chrX	42068451	42068472	+	1	NA	promoter-TSS (NR_125870)	promoter-TSS (NR_125870)	63	NR_125870	11798	Mm.259879	NM_009688	ENSMUSG00000025860	Xiap	1110015C02Rik|Aipa|Api3|Birc4|IAP3|ILP-1|MIHA	X-linked inhibitor of apoptosis	protein-coding
mm_77286.1	chr8	116799974	116799990	-	1	NA	intron (NR_046193, intron 2 of 3)	MT2B|LTR|ERVL	1430	NR_046193	78213	Mm.402039	NR_046193		4930563M20Rik	-	RIKEN cDNA 4930563M20 gene	ncRNA
mm_16690.1	chr2	6884909	6884919	-	1	NA	promoter-TSS (NM_001110228)	promoter-TSS (NM_001110228)	82	NM_010160	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_127967.1	chr15	12010065	12010067	-	1	NA	Intergenic	B3A|SINE|B2	-14059	NM_011294	20024	Mm.41746	NM_011294	ENSMUSG00000022205	Sub1	AI842364|P15|P9|Pc4|Rpo2tc1	SUB1 homolog (S. cerevisiae)	protein-coding
mm_118713.1	chr14	22185946	22185952	+	1	NA	intron (NM_028275, intron 2 of 6)	ID_B1|SINE|B4	166237	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_122464.1	chr14	45529551	45529621	-	1	NA	5' UTR (NM_146054, exon 2 of 15)	5' UTR (NM_146054, exon 2 of 15)	479	NM_146054	218952	Mm.210018	NM_146054	ENSMUSG00000037712	Fermt2	AA960555|Kindlin-2|Mig2|Plekhc1	fermitin family member 2	protein-coding
mm_8050.1	chr1	135373428	135373455	-	1	NA	intron (NM_175259, intron 2 of 4)	intron (NM_175259, intron 2 of 4)	1622	NM_175259	77552	Mm.41407	NM_175259	ENSMUSG00000041889	Shisa4	9330132O05Rik|Tmem58|mShisa4	shisa family member 4	protein-coding
mm_49757.1	chr6	34755690	34755726	+	1	NA	exon (NM_145575, exon 5 of 12)	exon (NM_145575, exon 5 of 12)	-24724	NM_001289657	76223	Mm.150047	NM_178630	ENSMUSG00000038836	Agbl3	2900053G10Rik|4930431N21Rik|6530406M24Rik|CCP3	ATP/GTP binding protein-like 3	protein-coding
mm_159521.1	chr4	61519606	61519606	-	1	NA	promoter-TSS (NM_001134644).2	promoter-TSS (NM_001134644).2	-120	NM_001199936	100039177	Mm.422695	NM_001199936	ENSMUSG00000078675	Mup16	Mup6	major urinary protein 16	protein-coding
mm_17506.1	chr2	28917985	28918007	-	1	NA	Intergenic	CpG	-1556	NM_001164186	54422	Mm.21390	NM_019446	ENSMUSG00000026805	Barhl1	Dres115|MBH2	BarH-like 1 (Drosophila)	protein-coding
mm_9283.1	chr1	171634626	171634638	-	1	NA	3' UTR (NM_144539, exon 8 of 8)	3' UTR (NM_144539, exon 8 of 8)	7268	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_167650.1	chr9	65700394	65700401	+	1	NA	intron (NM_172536, intron 6 of 9)	L2b|LINE|L2	23849	NM_001301307	18247	Mm.116749	NM_010952	ENSMUSG00000040652	Oaz2	AZ-2|AZ2|Oaz2-ps|Sez15	ornithine decarboxylase antizyme 2	protein-coding
mm_57311.1	chr6	124723615	124723654	-	1	NA	intron (NM_001077705, intron 11 of 15)	intron (NM_001077705, intron 11 of 15)	-5244	NR_029792	723944		NR_029792	ENSMUSG00000065462	Mir200c	Mirn200c|mir-200c	microRNA 200c	ncRNA
mm_17298.1	chr2	26294551	26294561	-	1	NA	promoter-TSS (NM_177841)	promoter-TSS (NM_177841)	1	NM_177841	329366	Mm.77712	NM_177841	ENSMUSG00000048038	Ccdc187	4932418E24Rik	coiled-coil domain containing 187	protein-coding
mm_31872.1	chr4	80834287	80834295	+	1	NA	promoter-TSS (NM_031202)	promoter-TSS (NM_031202)	78	NM_001282015	22178	Mm.30438	NM_031202	ENSMUSG00000005994	Tyrp1	Oca3|TRP-1|TRP1|Tyrp|b|brown|isa	tyrosinase-related protein 1	protein-coding
mm_7417.1	chr1	119504685	119504724	-	1	NA	promoter-TSS (NM_022327)	promoter-TSS (NM_022327)	78	NM_022327	64143	Mm.27832	NM_022327	ENSMUSG00000004451	Ralb	5730472O18Rik	v-ral simian leukemia viral oncogene B	protein-coding
mm_84648.1	chr9	71554980	71554983	-	1	NA	intron (NM_001033208, intron 6 of 12)	intron (NM_001033208, intron 6 of 12)	37379	NM_001033208	102371	Mm.27585	NM_001033208	ENSMUSG00000041361	Myzap	AA407270|AV006038|Gcom1|Gm640|Grinl1a7|Myozap	myocardial zonula adherens protein	protein-coding
mm_54073.1	chr6	14755097	14755134	-	1	NA	exon (NM_080464, exon 1 of 4)	exon (NM_080464, exon 1 of 4)	159	NM_080464	140491	Mm.209429	NM_080464	ENSMUSG00000042717	Ppp1r3a	GM|RG1|RGL	protein phosphatase 1, regulatory (inhibitor) subunit 3A	protein-coding
mm_42672.1	chr5	119671684	119671699	+	1	NA	5' UTR (NM_011535, exon 1 of 8)	5' UTR (NM_011535, exon 1 of 8)	458	NM_011535	21386	Mm.219139	NM_011535	ENSMUSG00000018604	Tbx3	D5Ertd189e	T-box 3	protein-coding
mm_32803.1	chr4	117120593	117120606	+	1	NA	non-coding (NR_024078, exon 7 of 7)	non-coding (NR_024078, exon 7 of 7)	5126	NR_024078	78611	Mm.446227	NM_001033187		Btbd19	9530048O09Rik|BB115071	BTB (POZ) domain containing 19	ncRNA
mm_68610.1	chr7	116381686	116381689	-	1	NA	intron (NM_011083, intron 8 of 32)	intron (NM_011083, intron 8 of 32)	-47497	NM_026533	68052	Mm.14798	NM_026533	ENSMUSG00000090862	Rps13	2700063M04Rik	ribosomal protein S13	protein-coding
mm_29251.1	chr3	107219010	107219056	-	1	NA	intron (NM_001111143, intron 2 of 8)	intron (NM_001111143, intron 2 of 8)	2699	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_27872.1	chr3	79163779	79163780	-	1	NA	Intergenic	Lx|LINE|L1	-17904	NM_001099624	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_156300.1	chrX	136837893	136837895	+	1	NA	3' UTR (NM_011123, exon 7 of 7)	3' UTR (NM_011123, exon 7 of 7)	15148	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_90742.1	chr10	5368374	5368399	-	1	NA	intron (NM_001347732, intron 13 of 145)	intron (NM_001347732, intron 13 of 145)	119928	NM_001347711	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_152868.1	chr19	24225064	24225074	-	1	NA	promoter-TSS (NM_011597)	promoter-TSS (NM_011597)	-43	NM_011597	21873	Mm.104744	NM_011597	ENSMUSG00000024812	Tjp2	ZO-2	tight junction protein 2	protein-coding
mm_97687.1	chr11	80136576	80136584	+	1	NA	TTS (NM_183275)	TTS (NM_183275)	5573	NM_183275	68550	Mm.18466	NM_183275	ENSMUSG00000046909	Tefm	1110002N22Rik	transcription elongation factor, mitochondrial	protein-coding
mm_17812.1	chr2	33718727	33718737	-	1	NA	Intergenic	Intergenic	77539	NR_046275	100504399	Mm.72070	NM_177842		C130021I20Rik	-	Riken cDNA C130021I20 gene	ncRNA
mm_157877.1	chrX	75764663	75764708	-	1	NA	promoter-TSS (NR_029443)	promoter-TSS (NR_029443)	14	NR_029443	74396	Mm.162493	NR_029443	ENSMUSG00000087396	4933407K13Rik	A130080L05Rik	RIKEN cDNA 4933407K13 gene	ncRNA
mm_2270.1	chr1	91214556	91214579	+	1	NA	intron (NM_016894, intron 2 of 2)	intron (NM_016894, intron 2 of 2)	34745	NM_001168392	51801	Mm.3272	NM_016894	ENSMUSG00000034353	Ramp1	9130218E19Rik	receptor (calcitonin) activity modifying protein 1	protein-coding
mm_139662.1	chr17	57406940	57406952	+	1	NA	exon (NM_010130, exon 6 of 22)	exon (NM_010130, exon 6 of 22)	48260	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_167840.1	chr9	124441579	124441612	+	1	NA	Intergenic	Intergenic	17808	NR_015516	75135	Mm.476814	NR_015516		4930526I15Rik	1600027J15Rik	RIKEN cDNA 4930526I15 gene	ncRNA
mm_68820.1	chr7	126082475	126082485	-	1	NA	promoter-TSS (NM_001101488)	promoter-TSS (NM_001101488)	-69	NM_001101488	269994	Mm.39599	NM_001101488	ENSMUSG00000046182	Gsg1l	AI852434|C230098I05Rik|G630023A01Rik|Gm637|g1l	GSG1-like	protein-coding
mm_79344.1	chr9	53405281	53405323	+	1	NA	promoter-TSS (NM_029247)	promoter-TSS (NM_029247)	16	NM_029247	75311	Mm.26078	NM_029247	ENSMUSG00000005131	4930550C14Rik	AU017961	RIKEN cDNA 4930550C14 gene	protein-coding
mm_132068.1	chr16	30064352	30064363	+	1	NA	promoter-TSS (NM_008235)	promoter-TSS (NM_008235)	-1000	NM_008235	15205	Mm.390859	NM_008235	ENSMUSG00000022528	Hes1	Hry|bHLHb39	hairy and enhancer of split 1 (Drosophila)	protein-coding
mm_1425.1	chr1	67174508	67174518	+	1	NA	intron (NM_001080809, intron 19 of 37)	intron (NM_001080809, intron 19 of 37)	51486	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_33367.1	chr4	129513433	129513444	+	1	NA	promoter-TSS (NM_010807)	promoter-TSS (NM_010807)	-143	NM_010807	17357	Mm.424974	NM_010807	ENSMUSG00000047945	Marcksl1	AL022768|AW215397|AW536807|D4Bc1|F52|MacMARCKS|Macs2|Macs3|Mlp|Mrp	MARCKS-like 1	protein-coding
mm_11630.1	chr2	34775596	34775645	+	1	NA	exon (NM_001163434, exon 9 of 9)	exon (NM_001163434, exon 9 of 9)	3530	NM_022310	14828	Mm.330160	NM_022310	ENSMUSG00000026864	Hspa5	AL022860|AU019543|Bip|D2Wsu141e|D2Wsu17e|Grp78|Hsce70|SEZ-7|Sez7|baffled|mBiP	heat shock protein 5	protein-coding
mm_110289.1	chr12	32123824	32123830	-	1	NA	Intergenic	Intergenic	-62548	NM_011158	19088	Mm.25594	NM_011158	ENSMUSG00000002997	Prkar2b	AI451071|AW061005|PKARIIbeta|Pkarb2|RII(beta)	protein kinase, cAMP dependent regulatory, type II beta	protein-coding
mm_158716.1	chrX	162643576	162643622	-	1	NA	promoter-TSS (NM_001290633)	promoter-TSS (NM_001290633)	59	NM_001290633	194590	Mm.442441	NM_178256	ENSMUSG00000040855	Reps2	POB1	RALBP1 associated Eps domain containing protein 2	protein-coding
mm_99658.1	chr11	105731759	105731781	+	1	NA	intron (NM_181071, intron 4 of 25)	intron (NM_181071, intron 4 of 25)	141784	NM_181071	77097	Mm.22501	NM_175492	ENSMUSG00000053580	Tanc2	3526402J09Rik|5730590C14Rik	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2	protein-coding
mm_79437.1	chr9	56089938	56089949	+	1	NA	promoter-TSS (NM_011193)	promoter-TSS (NM_011193)	-33	NM_011193	19200	Mm.2534	NM_011193	ENSMUSG00000032322	Pstpip1	CD2BP1|def-2	proline-serine-threonine phosphatase-interacting protein 1	protein-coding
mm_156268.1	chrX	136833270	136833282	+	1	NA	exon (NM_011123, exon 4 of 7)	exon (NM_011123, exon 4 of 7)	10530	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_144238.1	chr18	10715049	10715050	+	1	NA	Intergenic	Intergenic	8189	NR_045379	75370	Mm.159511	NR_045379	ENSMUSG00000097387	4930563E18Rik	-	RIKEN cDNA 4930563E18 gene	ncRNA
mm_44309.1	chr5	9145939	9145961	-	1	NA	intron (NM_011806, intron 4 of 17)	intron (NM_011806, intron 4 of 17)	15826	NM_001110327	23857	Mm.22480	NM_011806	ENSMUSG00000042508	Dmtf1	Dimp|Dmp1	cyclin D binding myb-like transcription factor 1	protein-coding
mm_129660.1	chr15	81104990	81104994	-	1	NA	promoter-TSS (NM_153049)	promoter-TSS (NM_153049)	55	NM_153049	223701	Mm.439814	NM_153049	ENSMUSG00000042292	Mkl1	AMKL|Bsac|Mal|Mrtf-A	MKL (megakaryoblastic leukemia)/myocardin-like 1	protein-coding
mm_62396.1	chr7	101108520	101108546	+	1	NA	promoter-TSS (NM_001146010)	promoter-TSS (NM_001146010)	-242	NM_001146010	207278	Mm.263041	NM_199012	ENSMUSG00000030691	Fchsd2	BC034086|R74866|Sh3md3|mKIAA0769	FCH and double SH3 domains 2	protein-coding
mm_65723.1	chr7	28380928	28380936	-	1	NA	Intergenic	Intergenic	-1704	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_82813.1	chr9	30781408	30781427	-	1	NA	Intergenic	Intergenic	139533	NM_001329420	235130	Mm.65867	NM_001024139	ENSMUSG00000033453	Adamts15	-	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 15	protein-coding
mm_153627.1	chr19	44013657	44013667	-	1	NA	exon (NM_001167905, exon 6 of 8)	exon (NM_001167905, exon 6 of 8)	15585	NM_001001446	226143	Mm.329866	NM_001001446	ENSMUSG00000025197	Cyp2c44	AW107714|BC034834|b2b386Clo	cytochrome P450, family 2, subfamily c, polypeptide 44	protein-coding
mm_90530.1	chr10	128086133	128086167	+	1	NA	TTS (NR_030442)	TTS (NR_030442)	864	NR_030442	751518		NR_030442	ENSMUSG00000093245	Mir677	Mirn677|mir-677|mmu-mir-677	microRNA 677	ncRNA
mm_97937.1	chr11	83648633	83648648	+	1	NA	exon (NM_011337, exon 2 of 3)	exon (NM_011337, exon 2 of 3)	738	NM_011337	20302	Mm.1282	NM_011337	ENSMUSG00000000982	Ccl3	AI323804|G0S19-1|LD78alpha|MIP-1alpha|MIP1-(a)|MIP1-alpha|Mip1a|Scya3	chemokine (C-C motif) ligand 3	protein-coding
mm_138075.1	chr17	33951521	33951527	+	1	NA	promoter-TSS (NM_019420)	promoter-TSS (NM_019420)	-36	NM_019420	54218	Mm.11132	NM_019420	ENSMUSG00000067370	B3galt4	Gal-T2|Galt2	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 4	protein-coding
mm_126098.1	chr15	78163632	78163645	+	1	NA	intron (NM_025931, intron 6 of 6)	intron (NM_025931, intron 6 of 6)	10470	NM_025931	67042	Mm.30191	NM_025931	ENSMUSG00000016637	Ift27	2600013G09Rik|Rabl4	intraflagellar transport 27	protein-coding
mm_48507.1	chr5	142818933	142818933	-	1	NA	Intergenic	Intergenic	-1546	NM_001122730	231861	Mm.354649	NM_178242	ENSMUSG00000039477	Tnrc18	BC025631|EG381742|Zfp469	trinucleotide repeat containing 18	protein-coding
mm_114676.1	chr13	80885686	80885711	+	1	NA	intron (NM_001042591, intron 1 of 7)	CpG	2276	NM_001042591	105171	Mm.423137	NM_001042591	ENSMUSG00000074794	Arrdc3	AI450344|mKIAA1376	arrestin domain containing 3	protein-coding
mm_77749.1	chr8	127441192	127441227	-	1	NA	intron (NM_001309391, intron 20 of 24)	intron (NM_001309391, intron 20 of 24)	141557	NM_001013580	93742	Mm.299254	NM_033620	ENSMUSG00000025812	Pard3	AA960621|AI256638|Asip|D8Ertd580e|Par-3|Par3|Pard-3|Pard3a|Phip	par-3 family cell polarity regulator	protein-coding
mm_69289.1	chr7	128206294	128206337	-	1	NA	promoter-TSS (NM_009943)	promoter-TSS (NM_009943)	51	NM_009943	12862	Mm.43824	NM_009943	ENSMUSG00000030785	Cox6a2	CoxVIaH|VIaH	cytochrome c oxidase subunit VIa polypeptide 2	protein-coding
mm_336.1	chr1	29969218	29969223	+	1	NA	Intergenic	Intergenic	547732	NR_105760	102465174		NR_105760	ENSMUSG00000099257	Mir6342	Gm27268|mmu-mir-6342	microRNA 6342	ncRNA
mm_115195.1	chr13	108864392	108864401	+	1	NA	intron (NM_011056, intron 2 of 16)	(T)n|Simple_repeat|Simple_repeat	210219	NM_011056	238871	Mm.434429	NM_011056	ENSMUSG00000021699	Pde4d	9630011N22Rik|Dpde3	phosphodiesterase 4D, cAMP specific	protein-coding
mm_107979.1	chr12	72945691	72945697	+	1	NA	TTS (NM_011384)	TTS (NM_011384)	5812	NM_011384	20476	Mm.57138	NM_011384	ENSMUSG00000021099	Six6	Optx2|Six9	sine oculis-related homeobox 6	protein-coding
mm_164318.1	chr16	3714806	3714834	-	1	NA	intron (NM_019453, intron 2 of 9)	intron (NM_019453, intron 2 of 9)	3304	NM_001161790	54483	Mm.143718	NM_019453	ENSMUSG00000022534	Mefv	FMF|TRIM20|pyrin	Mediterranean fever	protein-coding
mm_98488.1	chr11	94951290	94951324	+	1	NA	exon (NM_007742, exon 50 of 51)	exon (NM_007742, exon 50 of 51)	15083	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_79675.1	chr9	59709460	59709468	+	1	NA	exon (NM_001033498, exon 2 of 11)	exon (NM_001033498, exon 2 of 11)	1700	NM_001033498	546134	Mm.297580	NM_001033498	ENSMUSG00000074259	Gramd2	BC064463	GRAM domain containing 2	protein-coding
mm_35830.1	chr4	48034456	48034498	-	1	NA	Intergenic	Intergenic	-10828	NM_015743	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_84270.1	chr9	62790873	62790878	-	1	NA	TTS (NM_010193)	TTS (NM_010193)	20773	NM_010193	14155	Mm.24069	NM_010193	ENSMUSG00000032244	Fem1b	mKIAA0396	feminization 1 homolog b (C. elegans)	protein-coding
mm_41630.1	chr5	97006514	97006522	+	1	NA	intron (NM_080708, intron 1 of 15)	intron (NM_080708, intron 1 of 15)	8829	NM_080708	140780	Mm.281490	NM_080708	ENSMUSG00000034663	Bmp2k	4933417M22Rik|AA673486|AV128808|BIKE	BMP2 inducible kinase	protein-coding
mm_39681.1	chr5	25759988	25760044	+	1	NA	promoter-TSS (NM_001004365)	promoter-TSS (NM_001004365)	43	NM_001004365	242894	Mm.150319	NM_001004365	ENSMUSG00000056367	Actr3b	9630005C02|ARP11|AW047569|Arp3b|Arp3beta	ARP3 actin-related protein 3B	protein-coding
mm_104640.1	chr11	97525465	97525474	-	1	NA	exon (NM_018873, exon 16 of 20)	exon (NM_018873, exon 16 of 20)	-25129	NM_001289118	100141474	Mm.482426	NM_001289118	ENSMUSG00000047988	4933428G20Rik	-	RIKEN cDNA 4933428G20 gene	protein-coding
mm_151074.1	chr19	47579412	47579425	+	1	NA	promoter-TSS (NM_001164639)	promoter-TSS (NM_001164639)	-601	NM_009289	20874	Mm.281011	NM_009289	ENSMUSG00000025060	Slk	9A2|AV021402|AW411554|Etk4|SMAK|Stk2|mKIAA0204|mSLK	STE20-like kinase	protein-coding
mm_136218.1	chr16	89960808	89960814	-	1	NA	promoter-TSS (NM_009384)	promoter-TSS (NM_009384)	16	NM_009384	21844	Mm.310902	NM_009384	ENSMUSG00000002489	Tiam1	AI847750|D16Ium10|D16Ium10e	T cell lymphoma invasion and metastasis 1	protein-coding
mm_42601.1	chr5	117509943	117509954	+	1	NA	intron (NM_001312914, intron 3 of 19)	intron (NM_001312914, intron 3 of 19)	95946	NM_001312914	333050	Mm.437947	NM_001034873	ENSMUSG00000061578	Ksr2	-	kinase suppressor of ras 2	protein-coding
mm_124443.1	chr14	118853145	118853156	-	1	NA	intron (NM_001160097, intron 1 of 3)	intron (NM_001160097, intron 1 of 3)	-1800	NM_021386	58187	Mm.390755	NM_021386	ENSMUSG00000022132	Cldn10	6720456I16Rik|Cldn10a|Cldn10b|D14Ertd728e	claudin 10	protein-coding
mm_134801.1	chr16	24380306	24380326	-	1	NA	Intergenic	Intergenic	-13034	NM_178665	210126	Mm.209385	NM_178665	ENSMUSG00000033306	Lpp	9430020K16Rik|AA959454|AU024130|B130055L10Rik|C79715|D630048H16	LIM domain containing preferred translocation partner in lipoma	protein-coding
mm_172188.1	chr6	50566511	50566511	-	1	NA	promoter-TSS (NM_007808)	promoter-TSS (NM_007808)	-37	NM_007808	13063	Mm.35389	NM_007808	ENSMUSG00000063694	Cycs	-	cytochrome c, somatic	protein-coding
mm_96918.1	chr11	70468112	70468136	+	1	NA	Intergenic	Intergenic	-8140	NM_023158	66102	Mm.425692	NM_023158	ENSMUSG00000018920	Cxcl16	0910001K24Rik|AV290116|BB024863|CXCL16v1|CXCL16v2|SR-PSOX|Zmynd15|b2b498Clo	chemokine (C-X-C motif) ligand 16	protein-coding
mm_123669.1	chr14	69248897	69248941	-	1	NA	intron (NM_026331, intron 2 of 3)	intron (NM_026331, intron 2 of 3)	36184	NM_026331	67712	Mm.293635	NM_026331	ENSMUSG00000034248	Slc25a37	1700020E22Rik|4930513O14Rik|4930526G11Rik|AI848481|C330015G08Rik|Mfrn|Mfrn1|Mscp|frascati|mitoferrin	solute carrier family 25, member 37	protein-coding
mm_12330.1	chr2	69412789	69412804	+	1	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	32334	NM_175512	241452	Mm.211655	NM_175512	ENSMUSG00000027068	Dhrs9	C730025I08Rik|Rdh15	dehydrogenase/reductase (SDR family) member 9	protein-coding
mm_4326.1	chr1	171852052	171852056	+	1	NA	exon (NM_013489, exon 3 of 9)	exon (NM_013489, exon 3 of 9)	12357	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_135696.1	chr16	52442365	52442375	-	1	NA	intron (NM_009655, intron 1 of 15)	intron (NM_009655, intron 1 of 15)	10711	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_64114.1	chr7	141078189	141078207	+	1	NA	promoter-TSS (NM_001162924)	promoter-TSS (NM_001162924)	-31	NM_001162924	56460	Mm.350037	NM_019762	ENSMUSG00000054065	Pkp3	2310056L12Rik	plakophilin 3	protein-coding
mm_11887.1	chr2	49721782	49721803	+	1	NA	intron (NM_008449, intron 11 of 25)	intron (NM_008449, intron 11 of 25)	-65894	NM_027990	71897	Mm.41381	NM_027990	ENSMUSG00000026765	Lypd6b	2310010M24Rik|AW049525	LY6/PLAUR domain containing 6B	protein-coding
mm_125990.1	chr15	76351348	76351372	+	1	NA	promoter-TSS (NM_026859)	promoter-TSS (NM_026859)	66	NM_026859	68877	Mm.289680	NM_026859	ENSMUSG00000022553	Maf1	1110068E11Rik|AU042856	MAF1 homolog, negative regulator of RNA polymerase III	protein-coding
mm_114229.1	chr13	56522521	56522540	+	1	NA	promoter-TSS (NM_178674)	promoter-TSS (NM_178674)	22	NM_178674	213311	Mm.233904	NM_178674	ENSMUSG00000035509	Fbxl21	D630045D17Rik|FBL3B|FBXL3B|Psttm	F-box and leucine-rich repeat protein 21	protein-coding
mm_85657.1	chr9	107667257	107667264	-	1	NA	5' UTR (NM_023805, exon 1 of 16)	5' UTR (NM_023805, exon 1 of 16)	139	NM_023805	76257	Mm.296560	NM_023805	ENSMUSG00000010064	Slc38a3	0610012J02Rik|D9Ucla2|Nat1|Slc38-3|Sn1|Snat3|mNAT	solute carrier family 38, member 3	protein-coding
mm_124699.1	chr15	6445321	6445353	+	1	NA	promoter-TSS (NM_013485)	promoter-TSS (NM_013485)	4	NM_013485	12279	Mm.29095	NM_013485	ENSMUSG00000022149	C9	-	complement component 9	protein-coding
mm_1563.1	chr1	74155642	74155669	+	1	NA	intron (NM_009909, intron 1 of 1)	intron (NM_009909, intron 1 of 1)	1661	NM_009909	12765	Mm.234466	NM_009909	ENSMUSG00000026180	Cxcr2	CD128|CDw128|Cmkar2|Gpcr16|IL-8Rh|IL-8rb|IL8RA|Il8rb|mIL-8RH	chemokine (C-X-C motif) receptor 2	protein-coding
mm_142251.1	chr17	37527617	37527627	-	1	NA	Intergenic	Intergenic	-2335	NM_001005485	545205	Mm.383371	NM_001005485	ENSMUSG00000090675	Olfr111	-	olfactory receptor 111	protein-coding
mm_103153.1	chr11	70381960	70381963	-	1	NA	Intergenic	HAL1|LINE|L1	28070	NM_029231	75273	Mm.340601	NM_029231	ENSMUSG00000018921	Pelp1	4930563C04Rik|MNAR	proline, glutamic acid and leucine rich protein 1	protein-coding
mm_90025.1	chr10	115401262	115401268	+	1	NA	intron (NM_001033261, intron 4 of 34)	AT_rich|Low_complexity|Low_complexity	16306	NM_001033261	216345	Mm.207621	NM_001033261	ENSMUSG00000034163	Zfc3h1	BC033596|Ccdc131|Psrc2	zinc finger, C3H1-type containing	protein-coding
mm_168584.1	chr11	73470277	73470296	+	1	NA	Intergenic	L1Md_T|LINE|L1	-16076	NM_147025	259027	Mm.223412	NM_147025	ENSMUSG00000072709	Olfr380	MOR135-1	olfactory receptor 380	protein-coding
mm_77740.1	chr8	126945842	126945862	-	1	NA	promoter-TSS (NM_024214)	promoter-TSS (NM_024214)	69	NM_024214	67952	Mm.6932	NM_024214	ENSMUSG00000093904	Tomm20	1810060K07Rik|BB284719|Gm19268|MAS20|MOM19|TOM20|mKIAA0016	translocase of outer mitochondrial membrane 20 homolog (yeast)	protein-coding
mm_117827.1	chr13	98206152	98206186	-	1	NA	promoter-TSS (NM_012026)	promoter-TSS (NM_012026)	-4	NM_012026	110596	Mm.252718	NM_012026	ENSMUSG00000021662	Arhgef28	9230110L08Rik|AI323540|D13Bwg1089e|RIP2|Rgnef|RhoGEF|Rhoip2|p190RhoGEF	Rho guanine nucleotide exchange factor (GEF) 28	protein-coding
mm_110764.1	chr12	70227623	70227639	-	1	NA	promoter-TSS (NR_045174)	promoter-TSS (NR_045174)	52	NM_133198	110095	Mm.256926	NM_133198	ENSMUSG00000021069	Pygl	-	liver glycogen phosphorylase	protein-coding
mm_145080.1	chr18	42338963	42338966	+	1	NA	3' UTR (NM_172626, exon 20 of 20)	3' UTR (NM_172626, exon 20 of 20)	-55633	NM_138945	18998	Mm.488204	NM_138945	ENSMUSG00000024497	Pou4f3	Brn3.1|Brn3c|ddl|dreidel	POU domain, class 4, transcription factor 3	protein-coding
mm_78220.1	chr9	21546760	21546832	+	1	NA	promoter-TSS (NM_021531)	promoter-TSS (NM_021531)	-98	NM_021531	59035	Mm.178115	NM_021531	ENSMUSG00000032185	Carm1	Prmt4	coactivator-associated arginine methyltransferase 1	protein-coding
mm_132957.1	chr16	50044239	50044258	+	1	NA	intron (NR_045935, intron 2 of 3)	B3A|SINE|B2	28604	NR_045935	224180	Mm.146439	NM_175010		Gm4827	B130050K08|EG224180	predicted gene 4827	ncRNA
mm_118202.1	chr13	108158585	108158630	-	1	NA	promoter-TSS (NM_001127346)	promoter-TSS (NM_001127346)	18	NM_001127346	75597	Mm.276040	NM_001127346	ENSMUSG00000068184	Ndufaf2	1810058I14Rik|C86051|Ndufa12l|mimitin	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, assembly factor 2	protein-coding
mm_165504.1	chr2	167775671	167775695	+	1	NA	Intergenic	B4|SINE|B4	84506	NR_015500	329562	Mm.123101	NM_177851	ENSMUSG00000006462	A530013C23Rik	-	RIKEN cDNA A530013C23 gene	ncRNA
mm_6754.1	chr1	84037440	84037463	-	1	NA	3' UTR (NM_001003948, exon 3 of 3)	3' UTR (NM_001003948, exon 3 of 3)	181510	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_2090.1	chr1	87701086	87701093	+	1	NA	intron (NM_010566, intron 15 of 26)	intron (NM_010566, intron 15 of 26)	-54922	NM_029846	77040	Mm.272972	NM_029846	ENSMUSG00000026289	Atg16l1	1500009K01Rik|Apg16l|Atg16l|WDR30	autophagy related 16-like 1 (S. cerevisiae)	protein-coding
mm_74814.1	chr8	22701531	22701579	-	1	NA	intron (NM_001159774, intron 2 of 21)	Lx8b|LINE|L1	5028	NM_010546	16150	Mm.277886	NM_010546	ENSMUSG00000031537	Ikbkb	AI132552|IKK-2|IKK-beta|IKK2|IKK[b]|IKKbeta	inhibitor of kappaB kinase beta	protein-coding
mm_109096.1	chr12	104865377	104865400	+	1	NA	promoter-TSS (NR_104437)	promoter-TSS (NR_104437)	-312	NR_104435	94040	Mm.244078	NM_053155	ENSMUSG00000021097	Clmn	9330188N17Rik|AI428889|AI788815|mKIAA1188	calmin	protein-coding
mm_18300.1	chr2	53138108	53138120	-	1	NA	TTS (NM_018785)	TTS (NM_018785)	53073	NM_018785	56194	Mm.257474	NM_018785	ENSMUSG00000061136	Prpf40a	2810012K09Rik|FBP-11|FBP11|Fnbp11|Fnbp3	pre-mRNA processing factor 40A	protein-coding
mm_102146.1	chr11	53632111	53632126	-	1	NA	exon (NM_008355, exon 4 of 4)	exon (NM_008355, exon 4 of 4)	2584	NM_008355	16163	Mm.1284	NM_008355	ENSMUSG00000020383	Il13	Il-13	interleukin 13	protein-coding
mm_111917.1	chr12	108875521	108875529	-	1	NA	intron (NM_011710, intron 5 of 10)	intron (NM_011710, intron 5 of 10)	17673	NM_001164488	22375	Mm.38433	NM_011710	ENSMUSG00000021266	Wars	TrpRS|WRS	tryptophanyl-tRNA synthetase	protein-coding
mm_162422.1	chr1	91611357	91611367	+	1	NA	Intergenic	Intergenic	70282	NM_023046	65247	Mm.234152	NM_023046	ENSMUSG00000026311	Asb1	1700029O08Rik|1700054C17Rik|AI426616|AI851378|mKIAA1146	ankyrin repeat and SOCS box-containing 1	protein-coding
mm_96442.1	chr11	67384804	67384805	+	1	NA	Intergenic	Intergenic	57701	NM_001081250	544791	Mm.461064	NM_001081250	ENSMUSG00000060180	Myh13	MyHC-eo	myosin, heavy polypeptide 13, skeletal muscle	protein-coding
mm_161745.1	chr17	33824604	33824604	+	1	NA	promoter-TSS (NM_023202)	promoter-TSS (NM_023202)	32	NR_103516	66416	Mm.29513	NM_023202	ENSMUSG00000041881	Ndufa7	14.5kDa|2400007M02Rik|CI-B14.5a	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 7 (B14.5a)	protein-coding
mm_16416.1	chr2	180120644	180120648	+	1	NA	intron (NM_144500, intron 1 of 13)	intron (NM_144500, intron 1 of 13)	1280	NM_144500	228983	Mm.253578	NM_144500	ENSMUSG00000039050	Osbpl2	C130070J12Rik|ORP-2|Orp2|mKIAA0772	oxysterol binding protein-like 2	protein-coding
mm_18383.1	chr2	60098766	60098782	-	1	NA	intron (NM_001001182, intron 1 of 35)	intron (NM_001001182, intron 1 of 35)	26966	NM_001001182	407823	Mm.228071	NM_001001182	ENSMUSG00000026987	Baz2b	5830435C13Rik|BC053917|D2Ertd794e	bromodomain adjacent to zinc finger domain, 2B	protein-coding
mm_92113.1	chr10	63203883	63203887	-	1	NA	promoter-TSS (NM_182992)	promoter-TSS (NM_182992)	67	NM_182992	68802	Mm.259767	NM_182992	ENSMUSG00000020067	Mypn	1110056A04Rik|9830112J03|AI853556|mKIAA4170	myopalladin	protein-coding
mm_1248.1	chr1	62810093	62810111	+	1	NA	intron (NM_010939, intron 15 of 15)	intron (NM_010939, intron 15 of 15)	-15370	NR_040601	74992	Mm.401979	NR_040601		4930487H11Rik	-	RIKEN cDNA 4930487H11 gene	ncRNA
mm_104882.1	chr11	99521337	99521340	-	1	NA	promoter-TSS (NM_213730)	promoter-TSS (NM_213730)	-80	NM_213730	237934	Mm.484091	NM_213730	ENSMUSG00000064165	Krt39	4732494G06Rik|Ka35	keratin 39	protein-coding
mm_267.1	chr1	20951607	20951635	+	1	NA	promoter-TSS (NM_027974)	promoter-TSS (NM_027974)	-5	NM_027974	71877	Mm.29178	NM_027974	ENSMUSG00000041809	Efhc1	1700029F22Rik|mRib72-1|myoclonin1	EF-hand domain (C-terminal) containing 1	protein-coding
mm_159599.1	chr4	127053180	127053180	-	1	NA	intron (NM_026670, intron 4 of 7)	B1_Mur1|SINE|Alu	7952	NM_026670	68310	Mm.273806	NM_026670	ENSMUSG00000043872	Zmym1	5830412B09Rik|AW209050	zinc finger, MYM domain containing 1	protein-coding
mm_151113.1	chr19	47864441	47864488	+	1	NA	3' UTR (NM_010362, exon 6 of 6)	3' UTR (NM_010362, exon 6 of 6)	-1081	NM_030051	68214	Mm.63791	NM_026619	ENSMUSG00000025069	Gsto2	1700020F09Rik|4930425C18Rik|GSTO 2-2	glutathione S-transferase omega 2	protein-coding
mm_149622.1	chr19	16956065	16956075	+	1	NA	promoter-TSS (NM_181348)	promoter-TSS (NM_181348)	-48	NM_181348	353211	Mm.257354	NM_181348	ENSMUSG00000039126	Prune2	6330414G02Rik|A230083H22Rik|A330102H22Rik|Bmcc1|mKIAA0367	prune homolog 2	protein-coding
mm_147541.1	chr18	53744671	53744692	-	1	NA	promoter-TSS (NM_178686)	promoter-TSS (NM_178686)	-134	NM_178686	225523	Mm.193678	NM_178686	ENSMUSG00000048799	Cep120	A230075C01|AU016693|Ccdc100	centrosomal protein 120	protein-coding
mm_57959.1	chr6	135241352	135241404	-	1	NA	exon (NM_010352, exon 5 of 7)	exon (NM_010352, exon 5 of 7)	6506	NM_001080552	14840	Mm.272306	NM_010352	ENSMUSG00000030206	Gsg1	-	germ cell associated 1	protein-coding
mm_50231.1	chr6	42351041	42351061	+	1	NA	exon (NM_001289618, exon 3 of 10)	exon (NM_001289618, exon 3 of 10)	1223	NM_001289619	22793	Mm.282303	NM_011777	ENSMUSG00000029860	Zyx	9530098H06Rik|R75157	zyxin	protein-coding
mm_166913.1	chr7	30100842	30100843	+	1	NA	intron (NM_011981, intron 2 of 2)	B1_Mur4|SINE|Alu	5766	NM_011981	26466	Mm.195092	NM_011981	ENSMUSG00000049421	Zfp260	AI480997|Ozrf1|PEX1|Zfp63|Znf260	zinc finger protein 260	protein-coding
mm_34192.1	chr4	140701937	140701962	+	1	NA	intron (NM_173867, intron 1 of 12)	CpG	476	NM_173867	108911	Mm.253	NM_173867	ENSMUSG00000040945	Rcc2	2610510H01Rik|2610529N02Rik|AA536646|AA675016|Td60|mKIAA1470	regulator of chromosome condensation 2	protein-coding
mm_162994.1	chr11	28853793	28853798	+	1	NA	intron (NM_146015, intron 1 of 10)	intron (NM_146015, intron 1 of 10)	590	NM_146015	216616	Mm.44176	NM_146015	ENSMUSG00000020467	Efemp1	-	epidermal growth factor-containing fibulin-like extracellular matrix protein 1	protein-coding
mm_16990.1	chr2	18219483	18219492	-	1	NA	exon (NM_001190817, exon 11 of 13)	exon (NM_001190817, exon 11 of 13)	154902	NM_001252561	17354	Mm.209175	NM_010804	ENSMUSG00000026743	Mllt10	Af10|B130021D15Rik|D630001B22Rik|mKIAA4140	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 10	protein-coding
mm_70097.1	chr7	142660978	142660988	-	1	NA	non-coding (NR_002855, exon 1 of 4)	non-coding (NR_002855, exon 1 of 4)	288	NM_001122736	16002	Mm.3862	NM_010514	ENSMUSG00000048583	Igf2	AL033362|Igf-2|Igf-II|M6pr|Mpr|Peg2	insulin-like growth factor 2	protein-coding
mm_129534.1	chr15	79328127	79328150	-	1	NA	5' UTR (NM_001199024, exon 1 of 16)	5' UTR (NM_001199024, exon 1 of 16)	233	NM_016915	53357	Mm.155620	NM_016915	ENSMUSG00000042632	Pla2g6	BB112799|PNPLA9|iPLA(2)beta|iPLA2|iPLA2beta	phospholipase A2, group VI	protein-coding
mm_90170.1	chr10	119502132	119502169	+	1	NA	intron (NM_133442, intron 1 of 21)	intron (NM_133442, intron 1 of 21)	48116	NM_001277293	74053	Mm.196692	NM_028736	ENSMUSG00000034813	Grip1	4931400F03Rik|GRIP|eb	glutamate receptor interacting protein 1	protein-coding
mm_37502.1	chr4	123718199	123718209	-	1	NA	promoter-TSS (NR_002445).2	promoter-TSS (NR_002445).2	-18	NM_001030274	595136	Mm.42805	NM_001030274	ENSMUSG00000028648	Ndufs5	AI256693	NADH dehydrogenase (ubiquinone) Fe-S protein 5	protein-coding
mm_18399.1	chr2	60263548	60263565	-	1	NA	intron (NM_001290660, intron 2 of 5)	MTC|LTR|ERVL-MaLR	20928	NM_025422	66205	Mm.227281	NM_025422	ENSMUSG00000060703	Cd302	1110055L24Rik|AI159627	CD302 antigen	protein-coding
mm_90550.1	chr10	128096909	128096909	+	1	NA	intron (NM_054078, intron 2 of 29)	CpG	4126	NM_054078	116848	Mm.252213	NM_054078	ENSMUSG00000040054	Baz2a	AA415431|C030005G16Rik|C78388|Tip5|Walp3|mKIAA0314	bromodomain adjacent to zinc finger domain, 2A	protein-coding
mm_141995.1	chr17	35186966	35187006	-	1	NA	exon (NM_010734, exon 2 of 4)	exon (NM_010734, exon 2 of 4)	1454	NM_010734	16988	Mm.19379	NM_010734	ENSMUSG00000073412	Lst1	B144	leukocyte specific transcript 1	protein-coding
mm_26460.1	chr3	143017150	143017168	+	1	NA	Intergenic	Intergenic	-135155	NM_178654	109333	Mm.244236	NM_178654	ENSMUSG00000004591	Pkn2	6030436C20Rik|AI507382|PRK2|Prkcl2|Stk7	protein kinase N2	protein-coding
mm_169816.1	chr16	20537692	20537701	+	1	NA	exon (NM_009679, exon 2 of 11)	exon (NM_009679, exon 2 of 11)	2216	NM_009679	11773	Mm.18946	NM_009679	ENSMUSG00000022841	Ap2m1	-	adaptor-related protein complex 2, mu 1 subunit	protein-coding
mm_148219.1	chr18	80236870	80236888	-	1	NA	5' UTR (NM_001136181, exon 2 of 5)	5' UTR (NM_001136181, exon 2 of 5)	10223	NM_001136181	66255	Mm.272341	NM_001136181	ENSMUSG00000078963	Hsbp1l1	1810005K13Rik	heat shock factor binding protein 1-like 1	protein-coding
mm_108281.1	chr12	79040461	79040497	+	1	NA	intron (NM_181073, intron 1 of 28)	intron (NM_181073, intron 1 of 28)	11316	NM_181073	211945	Mm.478321	NM_181073	ENSMUSG00000060716	Plekhh1	AV308913|C77772|D630024D12Rik|mKIAA1200	pleckstrin homology domain containing, family H (with MyTH4 domain) member 1	protein-coding
mm_150062.1	chr19	29385615	29385625	+	1	NA	3' UTR (NM_021893, exon 7 of 7)	3' UTR (NM_021893, exon 7 of 7)	18182	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_94256.1	chr11	3332462	3332484	+	1	NA	intron (NM_178149, intron 3 of 5)	CpG-1656	1742	NM_178149	216505	Mm.390323	NM_178149	ENSMUSG00000034614	Pik3ip1	1500004A08Rik|5830455E04Rik|Crkd|Hgfl	phosphoinositide-3-kinase interacting protein 1	protein-coding
mm_40623.1	chr5	64810219	64810262	+	1	NA	intron (NM_008453, intron 1 of 5)	PB1D9|SINE|Alu	6717	NM_008453	16599	Mm.392759	NM_008453	ENSMUSG00000029178	Klf3	9930027G08Rik|AL024007|Bklf|Tef-2	Kruppel-like factor 3 (basic)	protein-coding
mm_101485.1	chr11	31369884	31369911	-	1	NA	5' UTR (NM_011491, exon 1 of 4)	5' UTR (NM_011491, exon 1 of 4)	164	NM_011491	20856	Mm.32506	NM_011491	ENSMUSG00000020303	Stc2	AW125853|Stc2l|mustc2	stanniocalcin 2	protein-coding
mm_92135.1	chr10	66698099	66698148	-	1	NA	Intergenic	Intergenic	222261	NR_138560	68488	Mm.338835	NR_138560		1110002J07Rik	-	RIKEN cDNA 1110002J07 gene	ncRNA
mm_29190.1	chr3	106547727	106547781	-	1	NA	promoter-TSS (NM_026013)	promoter-TSS (NM_026013)	-44	NM_001286986	67171	Mm.290488	NM_026013	ENSMUSG00000027900	Dram2	2010305N14Rik|2610318G18Rik|AI647667|Tmem77	DNA-damage regulated autophagy modulator 2	protein-coding
mm_87310.1	chr10	42761541	42761607	+	1	NA	promoter-TSS (NM_153055)	promoter-TSS (NM_153055)	78	NM_153055	140740	Mm.214344	NM_153055	ENSMUSG00000019802	Sec63	5730478J10Rik|AI649014|AW319215	SEC63-like (S. cerevisiae)	protein-coding
mm_89089.1	chr10	83971356	83971374	+	1	NA	Intergenic	(GA)n|Simple_repeat|Simple_repeat	248500	NM_001145198	69784	Mm.271188	NM_001145198	ENSMUSG00000087651	1500009L16Rik	2700050C19Rik|OCC-1	RIKEN cDNA 1500009L16 gene	protein-coding
mm_35057.1	chr4	6355492	6355506	-	1	NA	Intergenic	Intergenic	-10181	NM_016807	53378	Mm.247473	NM_016807	ENSMUSG00000028249	Sdcbp	MDA-9|Sycl|syntenin-1	syndecan binding protein	protein-coding
mm_16743.1	chr2	9593990	9594002	-	1	NA	Intergenic	Intergenic	284604	NM_008091	14462	Mm.313866	NM_008091	ENSMUSG00000015619	Gata3	Gata-3|jal	GATA binding protein 3	protein-coding
mm_88322.1	chr10	75564585	75564601	+	1	NA	Intergenic	Intergenic	-4069	NM_001305992	14598	Mm.4559	NM_008116	ENSMUSG00000006345	Ggt1	CD224|GGT|GGT 1|GGT-1|Ggtp|dwg	gamma-glutamyltransferase 1	protein-coding
mm_134261.1	chr16	13750791	13750805	-	1	NA	Intergenic	RCHARR1|DNA|hAT-Charlie	-20314	NM_011987	26565	Mm.4214	NM_011987	ENSMUSG00000022683	Pla2g10	GX sPLA2|PLA2GX|sPLA2-X	phospholipase A2, group X	protein-coding
mm_23590.1	chr3	64949212	64949219	+	1	NA	Intergenic	Intergenic	-104472	NR_003962	319210	Mm.246646	NM_175670	ENSMUSG00000097538	Vmn2r-ps11	4930518C23Rik	vomeronasal 2, receptor, pseudogene 11	pseudo
mm_73883.1	chr8	119344933	119344973	+	1	NA	exon (NM_024219, exon 2 of 4)	exon (NM_024219, exon 2 of 4)	415	NM_024219	68196	Mm.358714	NM_024219	ENSMUSG00000031839	Hsbp1	0610007A03Rik|AA408769|Hsp25	heat shock factor binding protein 1	protein-coding
mm_27178.1	chr3	34351675	34351682	-	1	NA	Intergenic	Intergenic	-208703	NR_015580	320478	Mm.444063	NR_015580	ENSMUSG00000105265	Sox2ot	B230215L15Rik	SOX2 overlapping transcript (non-protein coding)	ncRNA
mm_26148.1	chr3	138107240	138107273	+	1	NA	exon (NM_001163457, exon 14 of 20)	exon (NM_001163457, exon 14 of 20)	24121	NM_008642	17777	Mm.2941	NM_008642	ENSMUSG00000028158	Mttp	1810043K16Rik|MTP	microsomal triglyceride transfer protein	protein-coding
mm_169971.1	chr17	13998961	13998966	-	1	NA	Intergenic	(CTG)n|Simple_repeat|Simple_repeat	50590	NM_001122977	635895	Mm.388844	NM_001122977	ENSMUSG00000067941	Gm7168	EG635895	predicted gene 7168	protein-coding
mm_134490.1	chr16	18630094	18630139	-	1	NA	promoter-TSS (NM_213614)	promoter-TSS (NM_213614)	-178	NM_213614	18951	Mm.20365	NM_213614	ENSMUSG00000072214	Sept5	Cdcrel-1|Cdcrel1|Pnutl1	septin 5	protein-coding
mm_131767.1	chr16	22892843	22892845	+	1	NA	intron (NR_075099, intron 1 of 5)	T-rich|Low_complexity|Low_complexity	829	NM_001276449	11625	Mm.197554	NM_013465	ENSMUSG00000022868	Ahsg	-	alpha-2-HS-glycoprotein	protein-coding
mm_119186.1	chr14	32321988	32322042	+	1	NA	promoter-TSS (NM_001081130)	promoter-TSS (NM_001081130)	-4	NM_001081130	239017	Mm.318302	NM_001081130	ENSMUSG00000021913	Ogdhl	-	oxoglutarate dehydrogenase-like	protein-coding
mm_5955.1	chr1	56971314	56971329	-	1	NA	promoter-TSS (NR_024325)	promoter-TSS (NR_024325)	13	NM_139146	212712	Mm.145599	NM_139146	ENSMUSG00000038331	Satb2	mKIAA1034	special AT-rich sequence binding protein 2	protein-coding
mm_134579.1	chr16	20405548	20405575	-	1	NA	intron (NM_176839, intron 3 of 6)	intron (NM_176839, intron 3 of 6)	20833	NM_013790	27416	Mm.20845	NM_013790	ENSMUSG00000022822	Abcc5	2900011L11Rik|AI132311|Abcc5a|Abcc5b|Mrp5	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	protein-coding
mm_70846.1	chr8	23446870	23446881	+	1	NA	3' UTR (NM_013834, exon 3 of 3)	3' UTR (NM_013834, exon 3 of 3)	35373	NM_013834	20377	Mm.281691	NM_013834	ENSMUSG00000031548	Sfrp1	2210415K03Rik|AW011917|AW107218|AW742929|sFRP-1	secreted frizzled-related protein 1	protein-coding
mm_152640.1	chr19	12526382	12526392	-	1	NA	Intergenic	Intergenic	-24391	NM_172442	207521	Mm.247695	NM_172442	ENSMUSG00000039982	Dtx4	AI449438|BC044798|D930042H13|RNF155	deltex 4, E3 ubiquitin ligase	protein-coding
mm_18381.1	chr2	60049295	60049297	-	1	NA	intron (NM_001001182, intron 2 of 35)	intron (NM_001001182, intron 2 of 35)	76444	NM_001001182	407823	Mm.228071	NM_001001182	ENSMUSG00000026987	Baz2b	5830435C13Rik|BC053917|D2Ertd794e	bromodomain adjacent to zinc finger domain, 2B	protein-coding
mm_139289.1	chr17	48300402	48300436	+	1	NA	5' UTR (NM_001033405, exon 1 of 5)	5' UTR (NM_001033405, exon 1 of 5)	381	NM_001033405	328833	Mm.329104	NM_001033405	ENSMUSG00000071068	Treml2	AW049306|Gm750|Tlt2	triggering receptor expressed on myeloid cells-like 2	protein-coding
mm_121105.1	chr14	101117159	101117160	+	1	NA	Intergenic	Lx5b|LINE|L1	82910	NM_029680	76627	Mm.31415	NM_029680	ENSMUSG00000042888	Prr30	1700110M21Rik	proline rich 30	protein-coding
mm_112472.1	chr13	5868512	5868523	+	1	NA	3' UTR (NM_011803, exon 4 of 4)	3' UTR (NM_011803, exon 4 of 4)	7028	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_80987.1	chr9	103226833	103226843	+	1	NA	exon (NM_133977, exon 3 of 17)	exon (NM_133977, exon 3 of 17)	3448	NM_133977	22041	Mm.37214	NM_133977	ENSMUSG00000032554	Trf	AI266983|Cd176|HP|Tf|Tfn|hpx	transferrin	protein-coding
mm_53835.1	chr6	148212216	148212237	+	1	NA	promoter-TSS (NR_015615)	promoter-TSS (NR_015615)	-62	NR_015615	320737	Mm.137858	NR_015615		4732416N19Rik	-	RIKEN cDNA 4732416N19 gene	ncRNA
mm_82315.1	chr9	7873017	7873046	-	1	NA	5' UTR (NM_007464, exon 1 of 9)	5' UTR (NM_007464, exon 1 of 9)	139	NM_007464	11796	Mm.2026	NM_007464	ENSMUSG00000032000	Birc3	AW107670|Api1|Api2|Birc2|C-IAP2|HIAP2|IAP1|IAP2|MIAP1|MIAP2|MIHB|MIHC|RNF49|cIAP-1|cIAP-2|cIAP1|cIAP2	baculoviral IAP repeat-containing 3	protein-coding
mm_56131.1	chr6	87672143	87672179	-	1	NA	promoter-TSS (NM_001170489)	promoter-TSS (NM_001170489)	7	NM_024251	72103	Mm.31770	NM_024251	ENSMUSG00000030051	Aplf	2010301N04Rik|AI452191	aprataxin and PNKP like factor	protein-coding
mm_129563.1	chr15	79546542	79546566	-	1	NA	promoter-TSS (NM_199079)	promoter-TSS (NM_199079)	5	NM_199079	67040	Mm.29644	NM_152806	ENSMUSG00000055065	Ddx17	2610007K22Rik|A430025E01Rik|AI047725|C80929|Gm926|p72	DEAD (Asp-Glu-Ala-Asp) box polypeptide 17	protein-coding
mm_10966.1	chr2	25702482	25702506	+	1	NA	intron (NM_153558, intron 5 of 6)	intron (NM_153558, intron 5 of 6)	2420	NM_153558	227627	Mm.44630	NM_153558	ENSMUSG00000062061	Obp2a	BC027556|Lcn13	odorant binding protein 2A	protein-coding
mm_38194.1	chr4	135380766	135380779	-	1	NA	5' UTR (NM_001243306, exon 2 of 6)	5' UTR (NM_001243306, exon 2 of 6)	4900	NM_001168498	230822	Mm.35548	NM_145555	ENSMUSG00000043924	Ncmap	A330049M08Rik|AA545175|Mp11	noncompact myelin associated protein	protein-coding
mm_9674.1	chr1	178331123	178331137	-	1	NA	exon (NM_016805, exon 10 of 14)	exon (NM_016805, exon 10 of 14)	6654	NM_016805	51810	Mm.86589	NM_016805	ENSMUSG00000039630	Hnrnpu	AA408410|AI256620|AL024194|AL024437|AW557595|C86794|Hnrpu|SAFA|Sp120|hnRNP U	heterogeneous nuclear ribonucleoprotein U	protein-coding
mm_42081.1	chr5	110176812	110176820	+	1	NA	promoter-TSS (NR_040431)	promoter-TSS (NR_040431)	115	NM_008146	269682	Mm.9392	NM_008146	ENSMUSG00000029502	Golga3	5330413L04|5430416E01Rik|AI449376|AW490576|G1-499-14|Mea-2|Mea2|repro27	golgi autoantigen, golgin subfamily a, 3	protein-coding
mm_21052.1	chr2	152623077	152623088	-	1	NA	promoter-TSS (NM_001039122)	promoter-TSS (NM_001039122)	-29	NM_001039122	654459	Mm.358531	NM_001039122	ENSMUSG00000074678	Defb25	BD-25|OTTMUSG00000015862|mBD-25	defensin beta 25	protein-coding
mm_105692.1	chr11	107794643	107794657	-	1	NA	promoter-TSS (NM_019431)	promoter-TSS (NM_019431)	-186	NM_019431	54377	Mm.103724	NM_019431	ENSMUSG00000020723	Cacng4	AI413107|AW491861	calcium channel, voltage-dependent, gamma subunit 4	protein-coding
mm_152506.1	chr19	11196701	11196742	-	1	NA	promoter-TSS (NR_045317)	promoter-TSS (NR_045317)	2	NM_198224	73466	Mm.272723	NM_198224	ENSMUSG00000057240	Ms4a13	1700060E18Rik|Tetm4.2	membrane-spanning 4-domains, subfamily A, member 13	protein-coding
mm_170261.1	chr18	15011217	15011234	+	1	NA	intron (NM_134112, intron 1 of 4)	intron (NM_134112, intron 1 of 4)	22230	NR_045372	74456	Mm.391075	NR_045372		4933424G05Rik	-	RIKEN cDNA 4933424G05 gene	ncRNA
mm_2256.1	chr1	91107308	91107318	+	1	NA	exon (NM_008515, exon 15 of 23)	exon (NM_008515, exon 15 of 23)	-37790	NM_001033408	329207	Mm.295940	NM_001033408	ENSMUSG00000070732	Rbm44	Gm817	RNA binding motif protein 44	protein-coding
mm_100261.1	chr11	117332380	117332388	+	1	NA	promoter-TSS (NM_001113488)	promoter-TSS (NM_001113488)	71	NM_001113488	53860	Mm.38450	NM_017380	ENSMUSG00000059248	Sept9	MSF1|Msf|PNUTL4|Sint1	septin 9	protein-coding
mm_43957.1	chr5	145236045	145236076	+	1	NA	intron (NM_001083958, intron 4 of 4)	intron (NM_001083958, intron 4 of 4)	4301	NM_028298	72611	Mm.206555	NM_028298	ENSMUSG00000007812	Zfp655	2700038I16Rik|9030409O18Rik|mKIAA4222	zinc finger protein 655	protein-coding
mm_146425.1	chr18	84851332	84851348	+	1	NA	promoter-TSS (NM_025797)	promoter-TSS (NM_025797)	-74	NM_025797	109672	Mm.31018	NM_025797	ENSMUSG00000024646	Cyb5a	0610009N12Rik|Cyb5	cytochrome b5 type A (microsomal)	protein-coding
mm_60313.1	chr7	44198108	44198138	+	1	NA	promoter-TSS (NM_008693)	promoter-TSS (NM_008693)	-68	NM_008693	18050	Mm.439740	NM_008693	ENSMUSG00000066515	Klk1b3	Ngfg|gamma-NGF|mGk-3	kallikrein 1-related peptidase b3	protein-coding
mm_39375.1	chr5	12383342	12383351	+	1	NA	5' UTR (NM_028882, exon 1 of 18)	5' UTR (NM_028882, exon 1 of 18)	180	NM_028882	108151	Mm.89313	NM_028882	ENSMUSG00000040254	Sema3d	4631426B19Rik	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D	protein-coding
mm_98043.1	chr11	85549593	85549595	+	1	NA	intron (NM_138681, intron 18 of 25)	B4A|SINE|B4	170150	NR_045875	71489	Mm.442482	NR_045875	ENSMUSG00000086199	Bcas3os1	8430403D17Rik	breast carcinoma amplified sequence 3, opposite strand 1	ncRNA
mm_165673.1	chr3	89402598	89402609	-	1	NA	promoter-TSS (NM_020517)	promoter-TSS (NM_020517)	47	NM_020517	57275	Mm.482283	NM_020517	ENSMUSG00000078173	Lenep	AU018355|Lep503	lens epithelial protein	protein-coding
mm_115225.1	chr13	109837778	109837786	+	1	NA	intron (NM_011056, intron 7 of 16)	intron (NM_011056, intron 7 of 16)	-66027	NR_035442	100316683		NR_035442	ENSMUSG00000084651	Mir1904	Mirn1904|mmu-mir-1904	microRNA 1904	ncRNA
mm_10114.1	chr2	3713518	3713528	+	1	NA	promoter-TSS (NM_025626)	promoter-TSS (NM_025626)	65	NM_025626	66540	Mm.277864	NM_025626	ENSMUSG00000026655	Fam107b	3110001A13Rik|AA589595|AA959793|AI132312	family with sequence similarity 107, member B	protein-coding
mm_32600.1	chr4	111972834	111972854	+	1	NA	promoter-TSS (NM_177818)	promoter-TSS (NM_177818)	-83	NM_177818	328505	Mm.226771	NM_177818	ENSMUSG00000049214	Skint7	C130057D23Rik	selection and upkeep of intraepithelial T cells 7	protein-coding
mm_169404.1	chr14	50785497	50785515	-	1	NA	promoter-TSS (NM_001080949)	promoter-TSS (NM_001080949)	14	NM_177625	219022	Mm.276362	NM_177625	ENSMUSG00000006288	Ttc5	-	tetratricopeptide repeat domain 5	protein-coding
mm_135118.1	chr16	35841179	35841198	-	1	NA	exon (NM_001039530, exon 14 of 17)	exon (NM_001039530, exon 14 of 17)	30194	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_121223.1	chr14	103055378	103055382	+	1	NA	exon (NM_008392, exon 5 of 5)	exon (NM_008392, exon 5 of 5)	8368	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_51574.1	chr6	83758769	83758779	+	1	NA	TTS (NM_134157)	TTS (NM_134157)	3734	NR_105027	67934	Mm.126190	NR_105027	ENSMUSG00000099354	1700124L16Rik	-	RIKEN cDNA 1700124L16 gene	ncRNA
mm_15397.1	chr2	156721632	156721646	+	1	NA	promoter-TSS (NR_040505)	promoter-TSS (NR_040505)	360	NM_001042487	228836	Mm.22094	NM_146128	ENSMUSG00000061689	Dlgap4	AI225853|BC024558|DAP-4|DAP4|SAPAP-4|Sapap4|WBP16	discs, large homolog-associated protein 4 (Drosophila)	protein-coding
mm_141007.1	chr17	24960621	24960654	-	1	NA	promoter-TSS (NM_198937)	promoter-TSS (NM_198937)	-14	NM_198937	52009	Mm.371601	NM_198937	ENSMUSG00000024165	Hn1l	2810430B18Rik|AL022629|C16orf34|D17Ertd441e	hematological and neurological expressed 1-like	protein-coding
mm_53501.1	chr6	135362705	135362760	+	1	NA	promoter-TSS (NM_001288628)	promoter-TSS (NM_001288628)	-199	NM_010128	13730	Mm.182785	NM_010128	ENSMUSG00000030208	Emp1	I-8-09|TMP	epithelial membrane protein 1	protein-coding
mm_57704.1	chr6	128543313	128543321	-	1	NA	exon (NM_001001179, exon 32 of 36)	exon (NM_001001179, exon 32 of 36)	-16597	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_3423.1	chr1	146495688	146495693	+	1	NA	promoter-TSS (NM_153539)	promoter-TSS (NM_153539)	24	NM_153539	215378	Mm.441817	NM_153539	ENSMUSG00000035131	Brinp3	B830045N13Rik|Fam5c	bone morphogenetic protein/retinoic acid inducible neural specific 3	protein-coding
mm_18023.1	chr2	38613728	38613750	-	1	NA	intron (NM_011187, intron 5 of 7)	intron (NM_011187, intron 5 of 7)	30167	NM_011187	19177	Mm.389251	NM_011187	ENSMUSG00000026750	Psmb7	AU020723|MC14	proteasome (prosome, macropain) subunit, beta type 7	protein-coding
mm_65757.1	chr7	28629753	28629763	-	1	NA	intron (NM_175319, intron 1 of 12)	intron (NM_175319, intron 1 of 12)	1257	NM_175319	101744	Mm.26022	NM_175319	ENSMUSG00000037469	Acp7	AU017076|C330005M16Rik|Papl	acid phosphatase 7, tartrate resistant	protein-coding
mm_91324.1	chr10	25200208	25200218	-	1	NA	promoter-TSS (NM_001347460)	promoter-TSS (NM_001347460)	-43	NM_001347460	432442	Mm.485937	NM_018747	ENSMUSG00000039166	Akap7	6430401D08|AI662165|AKAP15|Akap18|BB170514	A kinase (PRKA) anchor protein 7	protein-coding
mm_200.1	chr1	16105371	16105379	+	1	NA	promoter-TSS (NM_133832)	promoter-TSS (NM_133832)	-507	NM_133832	98711	Mm.274376	NM_133832	ENSMUSG00000025921	Rdh10	3110069K09Rik|4921506A21Rik|AI875664|AW549993|D1Ertd762e|m366Asp	retinol dehydrogenase 10 (all-trans)	protein-coding
mm_97272.1	chr11	75765390	75765415	+	1	NA	3' UTR (NM_009536, exon 6 of 6)	3' UTR (NM_009536, exon 6 of 6)	-30407	NR_136933	102641247	Mm.411386	NR_136932		Gm12339	OTTMUSG00000006218	predicted gene 12339	ncRNA
mm_160641.1	chr9	108826174	108826174	+	1	NA	promoter-TSS (NM_080437)	promoter-TSS (NM_080437)	-146	NM_080437	107934	Mm.39945	NM_080437	ENSMUSG00000023473	Celsr3	Adgrc3|Fmi1|flamingo|mKIAA0812	cadherin, EGF LAG seven-pass G-type receptor 3	protein-coding
mm_124762.1	chr15	6656538	6656563	+	1	NA	intron (NM_011815, intron 15 of 17)	(T)n|Simple_repeat|Simple_repeat	-51831	NM_030168	78757	Mm.275811	NM_030168	ENSMUSG00000050310	Rictor	4921505C17Rik|6030405M08Rik|AVO3|AW492497|D530039E11Rik	RPTOR independent companion of MTOR, complex 2	protein-coding
mm_138807.1	chr17	39501970	39501975	+	1	NA	Intergenic	L1_Mm|LINE|L1	-34170	NM_001255977	100043300	Mm.27927	NM_001255977	ENSMUSG00000096345	Esp16	Gm4345	exocrine gland secreted peptide 16	protein-coding
mm_79168.1	chr9	47850639	47850685	+	1	NA	3' UTR (NM_018770, exon 10 of 10)	3' UTR (NM_018770, exon 10 of 10)	-32454	NR_046048	100038460	Mm.447649	NR_046048		Gm10677	ENSMUSG00000074363	predicted gene 10677	ncRNA
mm_37607.1	chr4	126753631	126753644	-	1	NA	promoter-TSS (NM_001035526)	promoter-TSS (NM_001035526)	82	NM_001035525	100317	Mm.206206	NM_133886	ENSMUSG00000028830	AU040320	A730047D20Rik|AAVR|Kiaa0319l	expressed sequence AU040320	protein-coding
mm_124748.1	chr15	6619710	6619726	+	1	NA	exon (NM_001278269, exon 2 of 17)	exon (NM_001278269, exon 2 of 17)	39871	NM_011815	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_49081.1	chr6	6560404	6560418	+	1	NA	exon (NM_009169, exon 2 of 3)	exon (NM_009169, exon 2 of 3)	18247	NM_009169	20422	Mm.2469	NM_009169	ENSMUSG00000042541	Shfm1	DSS1|Shfdg1|Shfg	split hand/foot malformation (ectrodactyly) type 1	protein-coding
mm_145781.1	chr18	65076071	65076101	+	1	NA	intron (NM_001114386, intron 3 of 30)	intron (NM_001114386, intron 3 of 30)	52559	NM_031881	83814	Mm.98668	NM_031881	ENSMUSG00000024589	Nedd4l	1300012C07Rik|Nedd4-2|Nedd4b	neural precursor cell expressed, developmentally down-regulated gene 4-like	protein-coding
mm_136987.1	chr17	17294438	17294461	+	1	NA	promoter-TSS (NM_001324550)	promoter-TSS (NM_001324550)	6	NM_001324550	100862203	Mm.484235	NM_001324550		Gm6712	EG626854	predicted gene 6712	protein-coding
mm_81449.1	chr9	109816589	109816615	+	1	NA	promoter-TSS (NM_183136)	promoter-TSS (NM_183136)	-25	NM_183136	78709	Mm.99613	NM_183136	ENSMUSG00000050074	Spink8	C630041L24Rik	serine peptidase inhibitor, Kazal type 8	protein-coding
mm_45107.1	chr5	44799918	44799950	-	1	NA	promoter-TSS (NM_010698)	promoter-TSS (NM_010698)	-188	NM_001077398	16826	Mm.25785	NM_010698	ENSMUSG00000039706	Ldb2	AI035351|AW146358|CLIM1|CLP-36|Ldb3	LIM domain binding 2	protein-coding
mm_127049.1	chr15	96654950	96655014	+	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	-12069	NM_001166458	105727	Mm.103568	NM_134086	ENSMUSG00000023169	Slc38a1	AA408026|AA409865|AL022800|AU015942|NAT2	solute carrier family 38, member 1	protein-coding
mm_161110.1	chr12	104112724	104112724	+	1	NA	promoter-TSS (NM_028740)	promoter-TSS (NM_028740)	0	NM_028740	74069	Mm.159128	NM_028740	ENSMUSG00000041536	Serpina3a	-	serine (or cysteine) peptidase inhibitor, clade A, member 3A	protein-coding
mm_84521.1	chr9	67043833	67043843	-	1	NA	promoter-TSS (NM_001164256)	promoter-TSS (NM_001164256)	33	NM_001164252	22003	Mm.121878	NM_024427	ENSMUSG00000032366	Tpm1	AA986836|AI854628|TM2|Tm3|Tmpa|Tpm-1|alpha-TM	tropomyosin 1, alpha	protein-coding
mm_47469.1	chr5	123684276	123684286	-	1	NA	promoter-TSS (NM_019765)	promoter-TSS (NM_019765)	80	NM_019765	56430	Mm.241109	NM_019765	ENSMUSG00000049550	Clip1	1110007I12Rik|4631429H07Rik|AV017631|C81039|CLIP-170|CLIP170|CYLN1|Clip50|Rsn|mKIAA4046|restin	CAP-GLY domain containing linker protein 1	protein-coding
mm_170252.1	chr1	80967839	80967840	+	1	NA	Intergenic	RLTR10D2|LTR|ERVK	-109478	NM_172849	241134	Mm.313904	NM_172849	ENSMUSG00000054976	Nyap2	9430031J16Rik|Jr6|Kiaa1486	neuronal tyrosine-phophorylated phosphoinositide 3-kinase adaptor 2	protein-coding
mm_64861.1	chr7	13037834	13037951	-	1	NA	promoter-TSS (NM_145578)	promoter-TSS (NM_145578)	86	NM_145578	22192	Mm.196580	NM_145578	ENSMUSG00000005575	Ube2m	2510040H03Rik|UBC12|Ubc-rs2	ubiquitin-conjugating enzyme E2M	protein-coding
mm_138282.1	chr17	34610010	34610019	+	1	NA	intron (NM_018862, intron 1 of 6)	intron (NM_018862, intron 1 of 6)	1000	NM_018862	55979	Mm.8684	NM_018862	ENSMUSG00000034254	Agpat1	1-AGP|1-AGPAT|AW047140	1-acylglycerol-3-phosphate O-acyltransferase 1 (lysophosphatidic acid acyltransferase, alpha)	protein-coding
mm_67030.1	chr7	66689475	66689491	-	1	NA	promoter-TSS (NR_003961)	promoter-TSS (NR_003961)	78	NM_080443	117589	Mm.34785	NM_080443	ENSMUSG00000030509	Asb7	AI449039|Asb-7|D030055C23Rik	ankyrin repeat and SOCS box-containing 7	protein-coding
mm_147810.1	chr18	61719319	61719332	-	1	NA	intron (NM_021296, intron 2 of 3)	L3|LINE|CR1	7006	NM_021296	17714	Mm.269657	NM_021296	ENSMUSG00000024580	Grpel2	mt-GrpE#2|mt-Grpel2	GrpE-like 2, mitochondrial	protein-coding
mm_124668.1	chr15	6386861	6386874	+	1	NA	5' UTR (NM_001102400, exon 1 of 13)	5' UTR (NM_001102400, exon 1 of 13)	119	NM_001310446	13132	Mm.240830	NM_023118	ENSMUSG00000022150	Dab2	5730435J12Rik|AA960054|AI957090|D15Wsu122e|D630005B22Rik|Doc-2|Doc2|p96	disabled 2, mitogen-responsive phosphoprotein	protein-coding
mm_80221.1	chr9	72570796	72570809	+	1	NA	intron (NM_001033536, intron 1 of 8)	L1Md_A|LINE|L1	38562	NM_001033536	319758	Mm.32081	NM_001033536	ENSMUSG00000037674	Rfx7	2510005N23Rik|9930116O05Rik|D130086K05Rik|Rfxdc2	regulatory factor X, 7	protein-coding
mm_67790.1	chr7	97721516	97721518	-	1	NA	TTS (NM_023671)	TTS (NM_023671)	16730	NM_175105	66333	Mm.29756	NM_175105	ENSMUSG00000042797	Aqp11	1700015P13Rik|AI648923|sjds	aquaporin 11	protein-coding
mm_168105.1	chr10	14567391	14567409	-	1	NA	Intergenic	Intergenic	-22364	NM_001002268	215798	Mm.440142	NM_001002268	ENSMUSG00000039116	Adgrg6	1190004A11Rik|AI449247|AW045736|DREG|Gm222|Gpr126	adhesion G protein-coupled receptor G6	protein-coding
mm_131062.1	chr16	4558698	4558741	+	1	NA	intron (NM_031182, intron 1 of 6)	CpG	1001	NM_031182	83383	Mm.273210	NM_031182	ENSMUSG00000005718	Tfap4	AI642933|AP-4|D930048N17Rik|Tcfap4|bHLHc41	transcription factor AP4	protein-coding
mm_155787.1	chrX	96713487	96713497	+	1	NA	promoter-TSS (NM_029536)	promoter-TSS (NM_029536)	24	NM_029536	76206	Mm.256065	NM_029536	ENSMUSG00000031210	Gpr165	6530406P05Rik	G protein-coupled receptor 165	protein-coding
mm_35164.1	chr4	14621495	14621506	-	1	NA	intron (NM_145947, intron 1 of 18)	intron (NM_145947, intron 1 of 18)	278	NM_145947	208890	Mm.483839	NM_145947	ENSMUSG00000040569	Slc26a7	-	solute carrier family 26, member 7	protein-coding
mm_59216.1	chr7	24593861	24593878	+	1	NA	5' UTR (NM_023154, exon 2 of 8)	5' UTR (NM_023154, exon 2 of 8)	-6228	NM_001033205	101544	Mm.20117	NM_001033205	ENSMUSG00000066721	Zfp575	AI326876|Znf575	zinc finger protein 575	protein-coding
mm_84209.1	chr9	60688129	60688184	-	1	NA	promoter-TSS (NM_001146047)	promoter-TSS (NM_001146047)	-22	NM_001146046	102747	Mm.269413	NM_145616	ENSMUSG00000047766	Lrrc49	AI430817|AW050057|D430025H09Rik|PGs4|p79	leucine rich repeat containing 49	protein-coding
mm_55310.1	chr6	54972629	54972643	-	1	NA	promoter-TSS (NM_172729)	promoter-TSS (NM_172729)	-24	NM_172729	107607	Mm.28498	NM_172729	ENSMUSG00000038058	Nod1	C230079P11|Card4|F830007N14Rik|Nlrc1	nucleotide-binding oligomerization domain containing 1	protein-coding
mm_162301.1	chr1	36325806	36325815	-	1	NA	Intergenic	Intergenic	18077	NM_001172205	214855	Mm.34316	NM_145996	ENSMUSG00000037447	Arid5a	D430024K22Rik|Mrf1	AT rich interactive domain 5A (MRF1-like)	protein-coding
mm_90793.1	chr10	7064276	7064280	-	1	NA	Intergenic	Intergenic	-41093	NM_001033391	320495	Mm.331674	NM_001033391	ENSMUSG00000064065	Ipcef1	A130090K04Rik	interaction protein for cytohesin exchange factors 1	protein-coding
mm_82102.1	chr9	123062391	123062405	+	1	NA	exon (NM_177911, exon 12 of 14)	exon (NM_177911, exon 12 of 14)	27657	NM_177911	331046	Mm.195309	NM_177911	ENSMUSG00000025787	Tgm4	9530008N10Rik|Eapa1|TGP	transglutaminase 4 (prostate)	protein-coding
mm_36290.1	chr4	63997130	63997143	-	1	NA	intron (NM_011607, intron 12 of 25)	B4A|SINE|B4	49879	NM_011607	21923	Mm.980	NM_011607	ENSMUSG00000028364	Tnc	AI528729|C130033P17Rik|Hxb|TN|TN-C|Ten|cytotactin|tenascin-C	tenascin C	protein-coding
mm_70640.1	chr8	13907828	13907837	+	1	NA	promoter-TSS (NM_025785)	promoter-TSS (NM_025785)	26	NM_025785	66822	Mm.37950	NM_025785	ENSMUSG00000038365	Fbxo25	9130015I06Rik|AI649137|Fbx25	F-box protein 25	protein-coding
mm_104800.1	chr11	98775008	98775018	-	1	NA	5' UTR (NM_145434, exon 1 of 8)	5' UTR (NM_145434, exon 1 of 8)	364	NM_145434	217166	Mm.390397	NM_145434	ENSMUSG00000020889	Nr1d1	A530070C09Rik|R75201	nuclear receptor subfamily 1, group D, member 1	protein-coding
mm_165846.1	chr4	8625734	8625735	+	1	NA	Intergenic	MT2A|LTR|ERVL	-64672	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_71092.1	chr8	34820128	34820142	+	1	NA	TTS (NM_176933)	TTS (NM_176933)	12525	NM_176933	319520	Mm.170276	NM_176933	ENSMUSG00000031530	Dusp4	2700078F24Rik|AI844617|BB104621|E130306H24Rik|MKP2	dual specificity phosphatase 4	protein-coding
mm_17809.1	chr2	33640867	33640890	-	1	NA	promoter-TSS (NM_010725)	promoter-TSS (NM_010725)	-315	NR_046275	100504399	Mm.72070	NM_177842		C130021I20Rik	-	Riken cDNA C130021I20 gene	ncRNA
mm_35520.1	chr4	41206285	41206300	-	1	NA	exon (NM_026872, exon 15 of 29)	exon (NM_026872, exon 15 of 29)	68843	NM_026872	68926	Mm.41864	NM_026872	ENSMUSG00000028433	Ubap2	1190005K07Rik|AA408600|AU045235|UBAP-2|mKIAA1491	ubiquitin-associated protein 2	protein-coding
mm_171228.1	chr3	65643352	65643358	+	1	NA	Intergenic	RLTR11B|LTR|ERVK	-15933	NR_106200	102465905		NR_106200	ENSMUSG00000098944	Mir8120	Gm27637|mmu-mir-8120	microRNA 8120	ncRNA
mm_14077.1	chr2	124609882	124609904	+	1	NA	promoter-TSS (NM_199238)	promoter-TSS (NM_199238)	-403	NM_199238	214968	Mm.330536	NM_172537	ENSMUSG00000027200	Sema6d	1110067B02Rik|AA409156|D330011G23|mKIAA1479	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	protein-coding
mm_146773.1	chr18	20059290	20059298	-	1	NA	5' UTR (NM_013505, exon 1 of 17)	5' UTR (NM_013505, exon 1 of 17)	260	NM_013505	13506	Mm.280547	NM_013505	ENSMUSG00000024331	Dsc2	AW228162	desmocollin 2	protein-coding
mm_23079.1	chr3	36552601	36552677	+	1	NA	promoter-TSS (NM_019393)	promoter-TSS (NM_019393)	33	NM_019393	50911	Mm.116711	NM_019393	ENSMUSG00000027714	Exosc9	PM/Scl-75|Pmscl1|RRP45|p5|p6	exosome component 9	protein-coding
mm_56719.1	chr6	115592494	115592503	-	1	NA	promoter-TSS (NM_001101431)	promoter-TSS (NM_001101431)	78	NM_001101431	70291	Mm.133694	NM_001101431	ENSMUSG00000068011	Mkrn2os	2510049J12Rik	makorin, ring finger protein 2, opposite strand	protein-coding
mm_132588.1	chr16	38443400	38443450	+	1	NA	Intergenic	Intergenic	9264	NM_007414	11544	Mm.20047	NM_007414	ENSMUSG00000002844	Adprh	Arh1	ADP-ribosylarginine hydrolase	protein-coding
mm_155059.1	chrX	42432485	42432485	+	1	NA	Intergenic	Intergenic	-70080	NM_011364	20400	Mm.441197	NM_011364	ENSMUSG00000005696	Sh2d1a	Gm686|SAP	SH2 domain containing 1A	protein-coding
mm_60973.1	chr7	48877978	48877980	+	1	NA	exon (NM_001013368, exon 4 of 13)	exon (NM_001013368, exon 4 of 13)	3062	NM_001013368	108961	Mm.240566	NM_001013368	ENSMUSG00000046179	E2f8	4432406C08Rik|AA410048	E2F transcription factor 8	protein-coding
mm_30587.1	chr4	5644269	5644279	+	1	NA	promoter-TSS (NM_173426)	promoter-TSS (NM_173426)	95	NM_173426	242297	Mm.331470	NM_173426	ENSMUSG00000049119	Fam110b	1700012H17Rik|5031405P22|AW049855	family with sequence similarity 110, member B	protein-coding
mm_38612.1	chr4	141875312	141875322	-	1	NA	promoter-TSS (NM_025994)	promoter-TSS (NM_025994)	-397	NM_025994	27984	Mm.395598	NM_025994	ENSMUSG00000040659	Efhd2	2600015J22Rik|AA408606|D4Wsu27e	EF hand domain containing 2	protein-coding
mm_99302.1	chr11	101370714	101370723	+	1	NA	exon (NM_008061, exon 2 of 5)	exon (NM_008061, exon 2 of 5)	3002	NM_008061	14377	Mm.18064	NM_008061	ENSMUSG00000078650	G6pc	AW107337|G6Pase|G6pt|Glc-6-Pase	glucose-6-phosphatase, catalytic	protein-coding
mm_142142.1	chr17	35979792	35979831	-	1	NA	promoter-TSS (NM_001282025)	promoter-TSS (NM_001282025)	14	NM_001282013	75210	Mm.40036	NM_145487	ENSMUSG00000038500	Prr3	4930540G07Rik|Cat56	proline-rich polypeptide 3	protein-coding
mm_74465.1	chr8	4217134	4217168	-	1	NA	5' UTR (NM_207203, exon 1 of 7)	5' UTR (NM_207203, exon 1 of 7)	161	NM_207203	73072	Mm.477379	NM_207203	ENSMUSG00000064125	Prr36	-	proline rich 36	protein-coding
mm_149812.1	chr19	23893507	23893536	+	1	NA	exon (NM_177034, exon 2 of 13)	exon (NM_177034, exon 2 of 13)	134645	NM_177034	319924	Mm.22879	NM_177034	ENSMUSG00000024897	Apba1	6430513E09Rik|Lin-10|Mint|Mint1|Urop11|X11|X11alpha	amyloid beta (A4) precursor protein binding, family A, member 1	protein-coding
mm_39586.1	chr5	23485334	23485345	+	1	NA	intron (NM_026984, intron 12 of 25)	intron (NM_026984, intron 12 of 25)	50910	NM_026984	69188	Mm.205190	NM_026984	ENSMUSG00000029004	Kmt2e	1810033J14Rik|9530077A04Rik|D230038D11Rik|Mll5|NKp44L	lysine (K)-specific methyltransferase 2E	protein-coding
mm_94577.1	chr11	11690203	11690213	+	1	NA	promoter-TSS (NM_001301865)	promoter-TSS (NM_001301865)	31	NM_001301863	22778	Mm.103545	NM_009578	ENSMUSG00000018654	Ikzf1	5832432G11Rik|Ikaros|LyF-1|Zfpn1a1|Znfn1a1|hlk-1|mKIAA4227	IKAROS family zinc finger 1	protein-coding
mm_152870.1	chr19	24280552	24280615	-	1	NA	promoter-TSS (NM_008044)	promoter-TSS (NM_008044)	3	NM_008044	14297	Mm.7319	NM_008044	ENSMUSG00000059363	Fxn	FA|FARR|Frda|X25	frataxin	protein-coding
mm_76701.1	chr8	94434143	94434170	-	1	NA	intron (NR_015514, intron 2 of 2)	intron (NR_015514, intron 2 of 2)	947	NR_015514	320377	Mm.486022	NR_015514		9330175E14Rik	A630085K21	RIKEN cDNA 9330175E14 gene	ncRNA
mm_30349.1	chr3	151748533	151748572	-	1	NA	intron (NM_133871, intron 2 of 7)	B1_Mur4|SINE|Alu	1407	NM_133871	99899	Mm.30756	NM_133871	ENSMUSG00000028037	Ifi44	A430056A10Rik|AW261460|MTAP44|p44	interferon-induced protein 44	protein-coding
mm_22950.1	chr3	32365307	32365326	+	1	NA	promoter-TSS (NR_027966)	promoter-TSS (NR_027966)	-173	NR_027966	67576	Mm.435324	NR_027966		4930429B21Rik	-	RIKEN cDNA 4930429B21 gene	ncRNA
mm_29067.1	chr3	103792548	103792571	-	1	NA	promoter-TSS (NR_125731)	promoter-TSS (NR_125731)	-996	NM_001301304	15257	Mm.20827	NM_010432	ENSMUSG00000008730	Hipk1	1110062K04Rik|Myak	homeodomain interacting protein kinase 1	protein-coding
mm_73433.1	chr8	106138409	106138421	+	1	NA	non-coding (NR_040346, exon 4 of 4)	non-coding (NR_040346, exon 4 of 4)	-1441	NM_176838	77411	Mm.183003	NM_176838	ENSMUSG00000084128	Esrp2	9530027K23Rik|Rbm35b	epithelial splicing regulatory protein 2	protein-coding
mm_109640.1	chr12	112796038	112796081	+	1	NA	Intergenic	Intergenic	-12916	NM_145450	217887	Mm.186678	NM_145450	ENSMUSG00000037594	BC022687	AW050009|C130001I08Rik|Flj20080	cDNA sequence BC022687	protein-coding
mm_33455.1	chr4	130783734	130783734	+	1	NA	Intergenic	Intergenic	-8803	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_11206.1	chr2	29191646	29191654	+	1	NA	Intergenic	Intergenic	56449	NM_001305805	171171	Mm.442448	NM_133500	ENSMUSG00000035513	Ntng2	2610016D08Rik|Lmnt2	netrin G2	protein-coding
mm_97671.1	chr11	79694907	79694910	+	1	NA	TTS (NM_175543)	TTS (NM_175543)	-17061	NR_029579	387188		NR_029579	ENSMUSG00000065395	Mir193a	Mir193|Mirn193|mir-193a|mmu-mir-193|mmu-mir-193a	microRNA 193a	ncRNA
mm_172353.1	chr7	114706205	114706206	-	1	NA	Intergenic	Intergenic	-12438	NM_054084	116903	Mm.273838	NM_054084	ENSMUSG00000030666	Calcb	CGRP2|Calc2	calcitonin-related polypeptide, beta	protein-coding
mm_151404.1	chr19	56548255	56548283	+	1	NA	promoter-TSS (NM_018831)	promoter-TSS (NM_018831)	8	NM_025811	66866	Mm.46346	NM_025811	ENSMUSG00000025078	Nhlrc2	1200003G01Rik|AI835049|AV002846|AW496455	NHL repeat containing 2	protein-coding
mm_134394.1	chr16	17467767	17467771	-	1	NA	intron (NM_001277231, intron 1 of 1)	intron (NM_001277231, intron 1 of 1)	15784	NM_007764	12929	Mm.21048	NM_007764	ENSMUSG00000006134	Crkl	1110025F07Rik|AA589403|AI325100|Crkol	v-crk avian sarcoma virus CT10 oncogene homolog-like	protein-coding
mm_148791.1	chr19	6164479	6164511	+	1	NA	promoter-TSS (NM_028967)	promoter-TSS (NM_028967)	37	NM_028967	74481	Mm.159219	NM_028967	ENSMUSG00000039699	Batf2	4933430F08Rik	basic leucine zipper transcription factor, ATF-like 2	protein-coding
mm_75420.1	chr8	46765059	46765063	-	1	NA	intron (NM_008391, intron 1 of 8)	intron (NM_008391, intron 1 of 8)	25316	NM_008391	16363	Mm.1149	NM_008391	ENSMUSG00000031627	Irf2	9830146E22Rik|AI646973|Irf-2	interferon regulatory factor 2	protein-coding
mm_160757.1	chr10	82985778	82985778	+	1	NA	5' UTR (NM_021439, exon 1 of 3)	5' UTR (NM_021439, exon 1 of 3)	281	NM_021439	58250	Mm.360747	NM_021439	ENSMUSG00000034612	Chst11	1110020P09Rik|C4ST|C4ST-1|C4ST1|C4s	carbohydrate sulfotransferase 11	protein-coding
mm_161852.1	chr18	15400021	15400021	-	1	NA	intron (NM_001308641, intron 1 of 4)	intron (NM_001308641, intron 1 of 4)	2978	NM_001308647	11829	Mm.250786	NM_009700	ENSMUSG00000024411	Aqp4	WCH4	aquaporin 4	protein-coding
mm_133841.1	chr16	96200571	96200587	+	1	NA	5' UTR (NM_015825, exon 1 of 8)	5' UTR (NM_015825, exon 1 of 8)	109	NM_015825	50795	Mm.28638	NM_015825	ENSMUSG00000040666	Sh3bgr	5430437A18Rik	SH3-binding domain glutamic acid-rich protein	protein-coding
mm_53954.1	chr6	5298463	5298476	-	1	NA	promoter-TSS (NM_183308)	promoter-TSS (NM_183308)	-96	NM_183308	330260	Mm.126984	NM_183308	ENSMUSG00000032667	Pon2	6330405I24Rik|AI481612	paraoxonase 2	protein-coding
mm_69348.1	chr7	130242273	130242276	-	1	NA	intron (NM_010207, intron 3 of 17)	intron (NM_010207, intron 3 of 17)	24534	NM_010207	14183	Mm.16340	NM_010207	ENSMUSG00000030849	Fgfr2	AU043015|AW556123|Bek|Fgfr-2|Fgfr-7|Fgfr7|KGFR|KGFRTr|svs	fibroblast growth factor receptor 2	protein-coding
mm_91520.1	chr10	37138758	37138761	-	1	NA	5' UTR (NM_008538, exon 1 of 2)	5' UTR (NM_008538, exon 1 of 2)	167	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_97228.1	chr11	75651505	75651537	+	1	NA	promoter-TSS (NM_001080774)	promoter-TSS (NM_001080774)	12	NM_008659	17913	Mm.234502	NM_008659	ENSMUSG00000017774	Myo1c	C80397|MMIb|MYO1E|NMI|mm1beta|myr2	myosin IC	protein-coding
mm_31440.1	chr4	48540420	48540502	+	1	NA	promoter-TSS (NM_028137)	promoter-TSS (NM_028137)	-38	NM_028137	66665	Mm.140749	NM_028137	ENSMUSG00000039693	Msantd3	2410046L14Rik|2810429P03Rik|5730528L13Rik|Mysantd3	Myb/SANT-like DNA-binding domain containing 3	protein-coding
mm_56311.1	chr6	92183973	92184038	-	1	NA	promoter-TSS (NM_025578)	promoter-TSS (NM_025578)	18	NM_025578	64658	Mm.87062	NM_025578	ENSMUSG00000014551	Mrps25	2810429N01Rik|Rpms25	mitochondrial ribosomal protein S25	protein-coding
mm_172790.1	chr9	108560460	108560472	+	1	NA	promoter-TSS (NM_011830)	promoter-TSS (NM_011830)	-35	NM_011830	23918	Mm.6065	NM_011830	ENSMUSG00000062867	Impdh2	IMPD	inosine 5'-phosphate dehydrogenase 2	protein-coding
mm_115454.1	chr13	118732825	118732827	+	1	NA	intron (NM_008002, intron 1 of 2)	intron (NM_008002, intron 1 of 2)	18127	NM_008002	14165	Mm.317323	NM_008002	ENSMUSG00000021732	Fgf10	AEY17|BB213776|Fgf-10|Gsfaey17	fibroblast growth factor 10	protein-coding
mm_77644.1	chr8	124434443	124434505	-	1	NA	promoter-TSS (NM_171824)	promoter-TSS (NM_171824)	-538	NM_171824	209966	Mm.234233	NM_171824	ENSMUSG00000050751	Pgbd5	2900019M05Rik|AI854313	piggyBac transposable element derived 5	protein-coding
mm_137027.1	chr17	17887094	17887135	+	1	NA	promoter-TSS (NM_008039)	promoter-TSS (NM_008039)	-710	NM_008039	14289	Mm.378918	NM_008039	ENSMUSG00000052270	Fpr2	E330010I07Rik|Fpr-rs2	formyl peptide receptor 2	protein-coding
mm_68021.1	chr7	100964349	100964369	-	1	NA	promoter-TSS (NM_183168)	promoter-TSS (NM_183168)	7	NM_183168	233571	Mm.235193	NM_183168	ENSMUSG00000048779	P2ry6	2010204J23Rik|P2Y6	pyrimidinergic receptor P2Y, G-protein coupled, 6	protein-coding
mm_135345.1	chr16	43628854	43628861	-	1	NA	Intergenic	Intergenic	-11798	NR_030576	100124467		NR_030576	ENSMUSG00000076372	Mir568	Mirn568|mmu-mir-568	microRNA 568	ncRNA
mm_75343.1	chr8	43307021	43307035	-	1	NA	promoter-TSS (NM_009556)	promoter-TSS (NM_009556)	-19	NM_009556	22702	Mm.285848	NM_009556	ENSMUSG00000051176	Zfp42	Rex-1|Rex1|Zfp-42	zinc finger protein 42	protein-coding
mm_166515.1	chr6	15745302	15745303	-	1	NA	intron (NM_175088, intron 3 of 4)	intron (NM_175088, intron 3 of 4)	24641	NM_175088	16543	Mm.1314	NM_175088	ENSMUSG00000041390	Mdfic	Kdt1|Mdfid	MyoD family inhibitor domain containing	protein-coding
mm_95913.1	chr11	58207314	58207340	+	1	NA	3' UTR (NM_018738, exon 3 of 3)	3' UTR (NM_018738, exon 3 of 3)	-7650	NM_019440	54396	Mm.458517	NM_019440	ENSMUSG00000069874	Irgm2	AI481100|GTPI|Ifggd2|Iigp2	immunity-related GTPase family M member 2	protein-coding
mm_118733.1	chr14	22258839	22258871	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	239143	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_117386.1	chr13	73346962	73346976	-	1	NA	non-coding (NR_045293, exon 2 of 3)	non-coding (NR_045293, exon 2 of 3)	415	NR_045293	432777	Mm.415319	NR_045293		D630045M09Rik	AU019512	RIKEN cDNA D630045M09 gene	ncRNA
mm_158120.1	chrX	102252155	102252172	-	1	NA	promoter-TSS (NM_001276466)	promoter-TSS (NM_001276466)	18	NM_001276466	12705	Mm.2390	NM_007709	ENSMUSG00000051159	Cited1	AI316840|AU019144|Msg1	Cbp/p300-interacting transactivator with Glu/Asp-rich carboxy-terminal domain 1	protein-coding
mm_26632.1	chr3	152921153	152921155	+	1	NA	intron (NM_012028, intron 2 of 4)	B4A|SINE|B4	61053	NM_012028	26938	Mm.40915	NM_012028	ENSMUSG00000039037	St6galnac5	AI851940|Siat7e	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 5	protein-coding
mm_133515.1	chr16	90741211	90741211	+	1	NA	intron (NM_029844, intron 1 of 2)	intron (NM_029844, intron 1 of 2)	2887	NM_029844	77037	Mm.22455	NM_029844	ENSMUSG00000039956	Mrap	1110025G12Rik|Falp|ORF61	melanocortin 2 receptor accessory protein	protein-coding
mm_147435.1	chr18	46476842	46476849	-	1	NA	Intergenic	MIR|SINE|MIR	-11029	NR_045438	72076	Mm.82766	NM_028086		Mospd4	2010013H21Rik	motile sperm domain containing 4	pseudo
mm_130216.1	chr15	95759245	95759248	-	1	NA	Intergenic	Intergenic	-7655	NR_131148	629300	Mm.247258	NR_131148		Gm6961	EG629300	predicted gene 6961	ncRNA
mm_44482.1	chr5	23506739	23506760	-	1	NA	3' UTR (NM_009274, exon 15 of 15)	3' UTR (NM_009274, exon 15 of 15)	72320	NM_026984	69188	Mm.205190	NM_026984	ENSMUSG00000029004	Kmt2e	1810033J14Rik|9530077A04Rik|D230038D11Rik|Mll5|NKp44L	lysine (K)-specific methyltransferase 2E	protein-coding
mm_153443.1	chr19	40994279	40994289	-	1	NA	5' UTR (NM_008528, exon 1 of 17)	5' UTR (NM_008528, exon 1 of 17)	251	NM_008528	17060	Mm.9749	NM_008528	ENSMUSG00000061132	Blnk	BASH|Bca|Ly-57|Ly57|Lyw-57|SLP-65	B cell linker	protein-coding
mm_84159.1	chr9	59539990	59540005	-	1	NA	intron (NM_010421, intron 1 of 13)	CpG	457	NM_010421	15211	Mm.2284	NM_010421	ENSMUSG00000025232	Hexa	Hex-1	hexosaminidase A	protein-coding
mm_142217.1	chr17	37168661	37168670	-	1	NA	Intergenic	Intergenic	-16695	NM_001011813	258051	Mm.233576	NM_001011813	ENSMUSG00000091601	Olfr93	MOR256-39P	olfactory receptor 93	protein-coding
mm_100209.1	chr11	116853458	116853481	+	1	NA	promoter-TSS (NM_178620)	promoter-TSS (NM_178620)	-375	NM_011358	20382	Mm.21841	NM_011358	ENSMUSG00000034120	Srsf2	D11Wsu175e|MRF-1|Pr264|SC35|Sfrs10|Sfrs2	serine/arginine-rich splicing factor 2	protein-coding
mm_109348.1	chr12	109605027	109605029	+	1	NA	intron (NR_028261, intron 1 of 20)	intron (NR_028261, intron 1 of 20)	1083	NR_028261	75745	Mm.293263	NR_028261		Rian	5530401N18Rik|C130089L09Rik|Meg8	RNA imprinted and accumulated in nucleus	ncRNA
mm_173065.1	chrX	134054480	134054480	-	1	NA	Intergenic	Intergenic	-4696	NM_001290398	108062	Mm.67938	NM_133196	ENSMUSG00000031256	Cstf2	C630034J23Rik|Cstf64|mir-3112	cleavage stimulation factor, 3' pre-RNA subunit 2	protein-coding
mm_1572.1	chr1	74261121	74261136	+	1	NA	intron (NM_029711, intron 6 of 9)	intron (NM_029711, intron 6 of 9)	-17472	NM_174985	227289	Mm.246587	NM_174985	ENSMUSG00000064272	Gpbar1	BG37|GPCR|GPR131|M-BAR|TGR5	G protein-coupled bile acid receptor 1	protein-coding
mm_6763.1	chr1	84105654	84105669	-	1	NA	intron (NM_001003948, intron 2 of 2)	ORR1F|LTR|ERVL-MaLR	113300	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_132252.1	chr16	32751562	32751605	+	1	NA	exon (NM_080457, exon 2 of 27)	exon (NM_080457, exon 2 of 27)	15697	NM_080457	140474	Mm.214599	NM_080457	ENSMUSG00000079620	Muc4	4933405I11Rik|Asgp	mucin 4	protein-coding
mm_6482.1	chr1	74093582	74093583	-	1	NA	intron (NM_027884, intron 1 of 34)	intron (NM_027884, intron 1 of 34)	30865	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_57768.1	chr6	129236202	129236214	-	1	NA	intron (NR_040265, intron 1 of 2)	intron (NR_040265, intron 1 of 2)	1837	NR_040265	76432	Mm.261738	NR_040265	ENSMUSG00000097354	2310001H17Rik	AI646108	RIKEN cDNA 2310001H17 gene	ncRNA
mm_9153.1	chr1	170927541	170927566	-	1	NA	promoter-TSS (NM_001160215)	promoter-TSS (NM_001160215)	30	NM_001160215	98752	Mm.1850	NM_145141	ENSMUSG00000038421	Fcrla	BB219290|FCRL|FCRL1|FREB|Fcrlm1|Fcrx|Freb1|mFREB|mFcrX	Fc receptor-like A	protein-coding
mm_14745.1	chr2	144466332	144466333	+	1	NA	non-coding (NR_038065, exon 1 of 1)	non-coding (NR_038065, exon 1 of 1)	1156	NR_038065	171588	Mm.450554	NR_038065	ENSMUSG00000083674	Gm38402	-	zinc finger protein pseudogene	pseudo
mm_110946.1	chr12	76643729	76643743	-	1	NA	intron (NM_013675, intron 2 of 35)	intron (NM_013675, intron 2 of 35)	66811	NM_013675	20741	Mm.32881	NM_013675	ENSMUSG00000021061	Sptb	AI842465|D330027P03Rik|Gm1301|Spnb-1|Spnb1|ja|jaundiced|mKIAA4219	spectrin beta, erythrocytic	protein-coding
mm_98583.1	chr11	95748550	95748556	+	1	NA	promoter-TSS (NM_201609)	promoter-TSS (NM_201609)	-514	NM_201609	268469	Mm.389038	NM_201609	ENSMUSG00000075595	Zfp652	9530033F24Rik|ZNF652	zinc finger protein 652	protein-coding
mm_68260.1	chr7	105592181	105592213	-	1	NA	exon (NM_017371, exon 9 of 10)	exon (NM_017371, exon 9 of 10)	7919	NM_017371	15458	Mm.3485	NM_017371	ENSMUSG00000030895	Hpx	Hpxn|hx	hemopexin	protein-coding
mm_126043.1	chr15	76904635	76904648	+	1	NA	exon (NM_012053, exon 3 of 6)	exon (NM_012053, exon 3 of 6)	570	NM_012053	26961	Mm.30066	NM_012053	ENSMUSG00000003970	Rpl8	-	ribosomal protein L8	protein-coding
mm_158769.1	chrX	166585680	166585737	-	1	NA	promoter-TSS (NM_019397)	promoter-TSS (NM_019397)	8	NM_019397	54156	Mm.37707	NM_019397	ENSMUSG00000000402	Egfl6	Maeg	EGF-like-domain, multiple 6	protein-coding
mm_19872.1	chr2	114048154	114048171	-	1	NA	exon (NM_009608, exon 6 of 7)	exon (NM_009608, exon 6 of 7)	4713	NM_009608	11464	Mm.686	NM_009608	ENSMUSG00000068614	Actc1	Actc-1	actin, alpha, cardiac muscle 1	protein-coding
mm_5004.1	chr1	191977394	191977400	+	1	NA	promoter-TSS (NM_001303132)	promoter-TSS (NM_001303132)	27	NM_023727	74023	Mm.274393	NM_023727	ENSMUSG00000049353	Rd3	3322402L07Rik|rd-3|rd3	retinal degeneration 3	protein-coding
mm_85190.1	chr9	96719550	96719564	-	1	NA	intron (NM_175537, intron 1 of 2)	CpG	12118	NM_175537	245007	Mm.485954	NM_175537	ENSMUSG00000040433	Zbtb38	A930014K01Rik|CIBZ	zinc finger and BTB domain containing 38	protein-coding
mm_166843.1	chr7	19517741	19517749	+	1	NA	promoter-TSS (NM_027116)	promoter-TSS (NM_027116)	-986	NM_027116	69547	Mm.77325	NM_027116	ENSMUSG00000060621	Nkpd1	2310015G09Rik	NTPase, KAP family P-loop domain containing 1	protein-coding
mm_105846.1	chr11	113708953	113708972	-	1	NA	intron (NM_029794, intron 1 of 6)	intron (NM_029794, intron 1 of 6)	564	NM_026682	52670	Mm.229207	NM_026682	ENSMUSG00000018727	Cpsf4l	0610010C04Rik|1500000C01Rik|D11Ertd636e	cleavage and polyadenylation specific factor 4-like	protein-coding
mm_39986.1	chr5	32459995	32459998	+	1	NA	intron (NM_172707, intron 1 of 7)	intron (NM_172707, intron 1 of 7)	1026	NM_172707	19046	Mm.241931	NM_172707	ENSMUSG00000014956	Ppp1cb	1200010B19	protein phosphatase 1, catalytic subunit, beta isoform	protein-coding
mm_129491.1	chr15	78802871	78802884	-	1	NA	exon (NM_130859, exon 1 of 21)	exon (NM_130859, exon 1 of 21)	165	NM_130859	105844	Mm.17629	NM_130859	ENSMUSG00000033170	Card10	AI449026|Bimp1|Carma3	caspase recruitment domain family, member 10	protein-coding
mm_38185.1	chr4	135325172	135325188	-	1	NA	exon (NM_001130477, exon 15 of 18)	exon (NM_001130477, exon 15 of 18)	28034	NM_016799	51796	Mm.1963	NM_016799	ENSMUSG00000028809	Srrm1	AA407769|POP101|Srm160	serine/arginine repetitive matrix 1	protein-coding
mm_131268.1	chr16	10835521	10835534	+	1	NA	intron (NM_001162932, intron 1 of 1)	intron (NM_001162932, intron 1 of 1)	468	NM_001162932	223970	Mm.325777	NM_001033278	ENSMUSG00000037991	Rmi2	A630055G03Rik|Gm537|Gm929	RecQ mediated genome instability 2	protein-coding
mm_67363.1	chr7	79838937	79838954	-	1	NA	exon (NM_008486, exon 6 of 20)	exon (NM_008486, exon 6 of 20)	3407	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_20723.1	chr2	136387805	136387820	-	1	NA	5' UTR (NM_172858, exon 1 of 10)	5' UTR (NM_172858, exon 1 of 10)	155	NM_172858	241656	Mm.131572	NM_172858	ENSMUSG00000039913	Pak7	2900083L08Rik|6430627N20|Pak5	p21 protein (Cdc42/Rac)-activated kinase 7	protein-coding
mm_146606.1	chr18	9619437	9619452	-	1	NA	promoter-TSS (NM_007593)	promoter-TSS (NM_007593)	25	NM_007593	26369	Mm.195831	NM_007593	ENSMUSG00000050996	Cetn1	caltractin	centrin 1	protein-coding
mm_93056.1	chr10	88683022	88683025	-	1	NA	promoter-TSS (NM_011461)	promoter-TSS (NM_011461)	0	NM_011461	20728	Mm.21642	NM_011461	ENSMUSG00000004359	Spic	AU019198|C76795|Prf|Spi-C	Spi-C transcription factor (Spi-1/PU.1 related)	protein-coding
mm_89698.1	chr10	97607251	97607261	+	1	NA	promoter-TSS (NM_008438)	promoter-TSS (NM_008438)	51	NM_008438	16545	Mm.6228	NM_008438	ENSMUSG00000019932	Kera	CNA2|SLRR2B	keratocan	protein-coding
mm_40113.1	chr5	34898693	34898698	+	1	NA	intron (NM_010414, intron 58 of 66)	intron (NM_010414, intron 58 of 66)	-17220	NM_207277	403174	Mm.291225	NM_207277	ENSMUSG00000051246	Msantd1	A930005I04Rik|Gm144	Myb/SANT-like DNA-binding domain containing 1	protein-coding
mm_29621.1	chr3	121427473	121427490	-	1	NA	intron (NM_028044, intron 1 of 6)	CpG	940	NM_028044	71994	Mm.275555	NM_028044	ENSMUSG00000053931	Cnn3	1600014M03Rik|C85854|Calpo3	calponin 3, acidic	protein-coding
mm_124340.1	chr14	103844301	103844305	-	1	NA	promoter-TSS (NM_001276296)	promoter-TSS (NM_001276296)	173	NM_001136061	13618	Mm.229532	NM_007904	ENSMUSG00000022122	Ednrb	ET-B|ET-BR|ETR-b|ETb|Sox10m1	endothelin receptor type B	protein-coding
mm_62681.1	chr7	109958275	109958279	+	1	NA	intron (NM_021494, intron 1 of 22)	intron (NM_021494, intron 1 of 22)	2145	NM_021494	19347	Mm.21904	NM_021494	ENSMUSG00000035901	Dennd5a	1500012B19Rik|AJ245569|AW496491|ORF37|Rab6ip1|mKIAA1091	DENN/MADD domain containing 5A	protein-coding
mm_136430.1	chr16	94317880	94317919	-	1	NA	Intergenic	MT2A|LTR|ERVL	-10523	NM_133229	170765	Mm.42604	NM_133229	ENSMUSG00000022941	Ripply3	Dscr6	ripply transcriptional repressor 3	protein-coding
mm_134401.1	chr16	17561241	17561254	-	1	NA	promoter-TSS (NM_001145435)	promoter-TSS (NM_001145435)	0	NM_029053	74685	Mm.38634	NM_029053	ENSMUSG00000022759	Lrrc74b	4930451C15Rik|mCG12354|mCP17390	leucine rich repeat containing 74B	protein-coding
mm_16852.1	chr2	11634904	11634908	-	1	NA	Intergenic	Intergenic	-7886	NM_008367	16184	Mm.915	NM_008367	ENSMUSG00000026770	Il2ra	CD25|Il2r|Ly-43	interleukin 2 receptor, alpha chain	protein-coding
mm_166699.1	chr6	114316248	114316256	+	1	NA	3' UTR (NM_178703, exon 16 of 16)	3' UTR (NM_178703, exon 16 of 16)	33617	NM_178703	232333	Mm.5260	NM_178703	ENSMUSG00000030310	Slc6a1	A730043E01|GABATHG|GABATR|GAT-1|Gabt|Gabt1|Gat1|XT-1|Xtrp1	solute carrier family 6 (neurotransmitter transporter, GABA), member 1	protein-coding
mm_50269.1	chr6	45060184	45060247	+	1	NA	5' UTR (NM_001004357, exon 1 of 24)	5' UTR (NM_001004357, exon 1 of 24)	154	NM_001004357	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding
mm_68286.1	chr7	105633461	105633477	-	1	NA	TTS (NM_029802)	TTS (NM_029802)	102	NM_018880	55992	Mm.29290	NM_018880	ENSMUSG00000036989	Trim3	BERP1|HAC1|Rnf22	tripartite motif-containing 3	protein-coding
mm_41217.1	chr5	88583508	88583523	+	1	NA	promoter-TSS (NM_027530)	promoter-TSS (NM_027530)	2	NM_027530	52822	Mm.270469	NM_027530	ENSMUSG00000029291	Rufy3	2810428M05Rik|6330416M07Rik|AW455998|AW538594|D5Bwg0860e|Ripx|Rpipx	RUN and FYVE domain containing 3	protein-coding
mm_38579.1	chr4	141818281	141818286	-	1	NA	intron (NM_007919, intron 6 of 7)	AT_rich|Low_complexity|Low_complexity	7722	NM_007919	13706	Mm.45316	NM_007919	ENSMUSG00000058579	Cela2a	Ela-2|Ela2|Ela2a	chymotrypsin-like elastase family, member 2A	protein-coding
mm_157541.1	chrX	51205774	51205839	-	1	NA	5' UTR (NM_134163, exon 1 of 8)	5' UTR (NM_134163, exon 1 of 8)	184	NM_001310515	171170	Mm.295324	NM_134163	ENSMUSG00000036109	Mbnl3	A530038J18Rik|AI661274|CHCR|E430034C16Rik|MBLX|MBLX39|MBXL	muscleblind-like 3 (Drosophila)	protein-coding
mm_119439.1	chr14	46390783	46390793	+	1	NA	promoter-TSS (NM_007554)	promoter-TSS (NM_007554)	-119	NM_007554	12159	Mm.6813	NM_007554	ENSMUSG00000021835	Bmp4	Bmp-4|Bmp2b|Bmp2b-1|Bmp2b1	bone morphogenetic protein 4	protein-coding
mm_157075.1	chrX	8892913	8892930	-	1	NA	non-coding (NR_045448, exon 1 of 1)	non-coding (NR_045448, exon 1 of 1)	568	NR_045448	102941	Mm.41588	NM_175327	ENSMUSG00000052364	B630019K06Rik	AI843180	novel protein similar to F-box and leucine-rich repeat protein 17 (Fbxl17)	pseudo
mm_56525.1	chr6	99521213	99521225	-	1	NA	promoter-TSS (NM_001347345)	promoter-TSS (NM_001347345)	-226	NM_001347345	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_164542.1	chr17	8283851	8283861	+	1	NA	promoter-TSS (NM_018819)	promoter-TSS (NM_018819)	43	NM_018819	55951	Mm.288510	NM_018819	ENSMUSG00000023861	Mpc1	0610006G08Rik|3830411I18Rik|Brp44l	mitochondrial pyruvate carrier 1	protein-coding
mm_108142.1	chr12	76255291	76255307	+	1	NA	promoter-TSS (NM_138745)	promoter-TSS (NM_138745)	67	NM_138745	108156	Mm.29584	NM_138745	ENSMUSG00000021048	Mthfd1	Dcs|E430024A07Rik|Mthfd	methylenetetrahydrofolate dehydrogenase (NADP+ dependent), methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthase	protein-coding
mm_42410.1	chr5	115082261	115082278	+	1	NA	exon (NM_029012, exon 4 of 11)	exon (NM_029012, exon 4 of 11)	25693	NM_001271591	100502825	Mm.361657	NM_001271590		Rpl37rt	Gm13826|OTTMUSG00000014624	ribosomal protein L37, retrotransposed	protein-coding
mm_5051.1	chr1	194938871	194938968	+	1	NA	promoter-TSS (NM_133654)	promoter-TSS (NM_133654)	98	NM_001111059	12490	Mm.29798	NM_133654	ENSMUSG00000016494	Cd34	AU040960	CD34 antigen	protein-coding
mm_119543.1	chr14	48120959	48120967	+	1	NA	promoter-TSS (NM_033602)	promoter-TSS (NM_033602)	94	NM_033602	93834	Mm.296457	NM_033602	ENSMUSG00000021846	Peli2	AW047589|BB129927	pellino 2	protein-coding
mm_38512.1	chr4	141394610	141394638	-	1	NA	intron (NM_001146307, intron 6 of 18)	intron (NM_001146307, intron 6 of 18)	3475	NM_001146307	12733	Mm.167900	NM_024412	ENSMUSG00000033770	Clcnka	C75963|CLC-K1|Clcnk1	chloride channel, voltage-sensitive Ka	protein-coding
mm_144529.1	chr18	25066081	25066092	+	1	NA	intron (NM_175276, intron 15 of 26)	intron (NM_175276, intron 15 of 26)	99879	NM_001142697	66648	Mm.263189	NM_001004361	ENSMUSG00000024269	Tpgs2	5730437P09Rik|5730494M16Rik|AI666318|Pgs2	tubulin polyglutamylase complex subunit 2	protein-coding
mm_70468.1	chr8	11952681	11952690	+	1	NA	Intergenic	B3|SINE|B2	112164	NM_029326	75528	Mm.440342	NM_029326	ENSMUSG00000031512	Tex29	1700018L24Rik	testis expressed 29	protein-coding
mm_98102.1	chr11	86684035	86684089	+	1	NA	promoter-TSS (NM_001098810)	promoter-TSS (NM_001098810)	-19	NM_001098810	217057	Mm.24868	NM_175004	ENSMUSG00000072582	Ptrh2	A230072I16Rik|Bit1|CGI-147	peptidyl-tRNA hydrolase 2	protein-coding
mm_29764.1	chr3	127204842	127204845	-	1	NA	intron (NM_001327938, intron 1 of 47)	intron (NM_001327938, intron 1 of 47)	43538	NR_105029	100862268	Mm.444603	NR_105029	ENSMUSG00000097456	LOC100862268	-	uncharacterized LOC100862268	ncRNA
mm_164467.1	chr16	61056393	61056402	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-450866	NM_007938	13840	Mm.455790	NM_007938	ENSMUSG00000055540	Epha6	Ehk2|Hek12|m-ehk2	Eph receptor A6	protein-coding
mm_123281.1	chr14	61420838	61420840	-	1	NA	intron (NM_008466, intron 1 of 16)	intron (NM_008466, intron 1 of 16)	19108	NM_008466	16648	Mm.25548	NM_008466	ENSMUSG00000021929	Kpna3	IPOA4	karyopherin (importin) alpha 3	protein-coding
mm_142638.1	chr17	47422540	47422554	-	1	NA	promoter-TSS (NM_001347584)	promoter-TSS (NM_001347584)	-667	NM_001347584	75462	Mm.46129	NM_029296	ENSMUSG00000047150	1700001C19Rik	-	RIKEN cDNA 1700001C19 gene	protein-coding
mm_57028.1	chr6	122282947	122282955	-	1	NA	promoter-TSS (NM_016970)	promoter-TSS (NM_016970)	-118	NM_016970	50928	Mm.20434	NM_016970	ENSMUSG00000030114	Klrg1	2F1-Ag|MAFA|MAFA-L	killer cell lectin-like receptor subfamily G, member 1	protein-coding
mm_71091.1	chr8	34818656	34818677	+	1	NA	exon (NM_176933, exon 4 of 4)	exon (NM_176933, exon 4 of 4)	11056	NM_176933	319520	Mm.170276	NM_176933	ENSMUSG00000031530	Dusp4	2700078F24Rik|AI844617|BB104621|E130306H24Rik|MKP2	dual specificity phosphatase 4	protein-coding
mm_136082.1	chr16	84835464	84835481	-	1	NA	promoter-TSS (NM_001302216)	promoter-TSS (NM_001302216)	153	NM_016755	11957	Mm.353	NM_016755	ENSMUSG00000022890	Atp5j	CF6	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit F	protein-coding
mm_67862.1	chr7	99116758	99116762	-	1	NA	intron (NM_178635, intron 2 of 14)	intron (NM_178635, intron 2 of 14)	24384	NM_178635	78610	Mm.323072	NM_178635	ENSMUSG00000035354	Uvrag	9530039D02Rik|AI648770|BB124205|Uvrag1|Uvragl	UV radiation resistance associated gene	protein-coding
mm_98724.1	chr11	96340804	96340813	+	1	NA	intron (NM_001079869, intron 1 of 3)	CpG	-2961	NM_010458	15410	Mm.342481	NM_010458	ENSMUSG00000048763	Hoxb3	Hox-2.7	homeobox B3	protein-coding
mm_163244.1	chr11	105985789	105985792	+	1	NA	promoter-TSS (NR_104047)	promoter-TSS (NR_104047)	-96	NR_104047	100379610	Mm.754	NR_104047	ENSMUSG00000085297	Gm11651	OTTMUSG00000003114	predicted gene 11651	ncRNA
mm_87184.1	chr10	39369018	39369051	+	1	NA	promoter-TSS (NM_008054)	promoter-TSS (NM_008054)	-765	NM_001122892	14360	Mm.4848	NM_008054	ENSMUSG00000019843	Fyn	AI448320|AW552119	Fyn proto-oncogene	protein-coding
mm_157572.1	chrX	52582922	52582951	-	1	NA	exon (NM_016697, exon 2 of 8)	exon (NM_016697, exon 2 of 8)	7093	NR_045367	100504594	Mm.447008	NR_045367	ENSMUSG00000055110	A630012P03Rik	-	RIKEN cDNA A630012P03 gene	ncRNA
mm_168179.1	chr10	56497606	56497608	+	1	NA	Intergenic	Intergenic	120307	NM_010288	14609	Mm.378921	NM_010288	ENSMUSG00000050953	Gja1	AU042049|AW546267|Cnx43|Cx43|Cx43alpha1|Gja-1|Npm1|connexin43	gap junction protein, alpha 1	protein-coding
mm_46755.1	chr5	112228935	112228975	-	1	NA	promoter-TSS (NR_033657)	promoter-TSS (NR_033657)	-7	NR_003718	330166	Mm.44854	NR_003718	ENSMUSG00000097767	Miat	3632434I06|A230057G18Rik|Rncr2|gomafu	myocardial infarction associated transcript (non-protein coding)	ncRNA
mm_73843.1	chr8	117498294	117498318	+	1	NA	promoter-TSS (NM_172285)	promoter-TSS (NM_172285)	31	NM_172285	234779	Mm.192699	NM_172285	ENSMUSG00000034330	Plcg2	PLC-gamma-2|PLCgamma2|Plcg-2	phospholipase C, gamma 2	protein-coding
mm_64219.1	chr7	141562163	141562192	+	1	NA	promoter-TSS (NM_007459)	promoter-TSS (NM_007459)	-3	NM_007459	11772	Mm.253090	NM_007459	ENSMUSG00000002957	Ap2a2	2410074K14Rik|AF006990|AW146353|Adtab|C78001|L25	adaptor-related protein complex 2, alpha 2 subunit	protein-coding
mm_125811.1	chr15	74931688	74931733	+	1	NA	Intergenic	Intergenic	-23341	NM_001164039	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_3779.1	chr1	156615878	156615886	+	1	NA	intron (NM_001136104, intron 1 of 12)	intron (NM_001136104, intron 1 of 12)	57095	NM_001136104	11352	Mm.329515	NM_009595	ENSMUSG00000026596	Abl2	AA536808|Abll|Arg	v-abl Abelson murine leukemia viral oncogene 2 (arg, Abelson-related gene)	protein-coding
mm_58301.1	chr6	146081036	146081051	-	1	NA	Intergenic	Intergenic	146896	NM_010656	16651	Mm.49689	NM_010656	ENSMUSG00000030255	Sspn	Krag	sarcospan	protein-coding
mm_45731.1	chr5	86327744	86327757	-	1	NA	intron (NM_145561, intron 5 of 9)	intron (NM_145561, intron 5 of 9)	-38442	NM_001030297	435845	Mm.359654	NM_001030297	ENSMUSG00000061184	Tmprss11c	Tmprss13	transmembrane protease, serine 11c	protein-coding
mm_119391.1	chr14	41137609	41137633	+	1	NA	Intergenic	Lx9|LINE|L1	5833	NM_023134	20387	Mm.46062	NM_023134	ENSMUSG00000021789	Sftpa1	SP-A|Sftp-1|Sftp1	surfactant associated protein A1	protein-coding
mm_115833.1	chr13	21287003	21287032	-	1	NA	3' UTR (NM_010343, exon 5 of 5)	3' UTR (NM_010343, exon 5 of 5)	5669	NM_010343	14780	Mm.1332	NM_010343	ENSMUSG00000004344	Gpx5	AV379049|Arep	glutathione peroxidase 5	protein-coding
mm_129488.1	chr15	78773441	78773451	-	1	NA	promoter-TSS (NM_008595)	promoter-TSS (NM_008595)	-1	NM_008595	17305	Mm.149235	NM_008595	ENSMUSG00000018169	Mfng	AW546563	MFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	protein-coding
mm_36772.1	chr4	102572163	102572176	-	1	NA	intron (NM_019840, intron 6 of 14)	intron (NM_019840, intron 6 of 14)	2109	NM_001177980	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_140338.1	chr17	86809601	86809630	+	1	NA	exon (NM_010137, exon 6 of 16)	exon (NM_010137, exon 6 of 16)	55751	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_89212.1	chr10	86705857	86705878	+	1	NA	promoter-TSS (NM_011631)	promoter-TSS (NM_011631)	56	NM_001003939	103220	Mm.440762	NM_153595	ENSMUSG00000044937	Ttc41	AI449705|AU041509|Gnn	tetratricopeptide repeat domain 41	protein-coding
mm_53012.1	chr6	123275858	123275862	+	1	NA	TTS (NM_010819)	TTS (NM_010819)	13753	NM_010819	17474	Mm.441101	NM_010819	ENSMUSG00000030144	Clec4d	Clecsf8|Mpcl|mcl	C-type lectin domain family 4, member d	protein-coding
mm_24764.1	chr3	95499274	95499289	+	1	NA	promoter-TSS (NM_007802)	promoter-TSS (NM_007802)	71	NM_007802	13038	Mm.272085	NM_007802	ENSMUSG00000028111	Ctsk	AI323530|MMS10-Q|Ms10q|catK	cathepsin K	protein-coding
mm_59516.1	chr7	27591706	27591778	+	1	NA	5' UTR (NM_001110208, exon 1 of 14)	5' UTR (NM_001110208, exon 1 of 14)	190	NM_001110208	11652	Mm.177194	NM_007434	ENSMUSG00000004056	Akt2	2410016A19Rik|AW554154|PKB|PKBbeta	thymoma viral proto-oncogene 2	protein-coding
mm_71976.1	chr8	70594376	70594396	+	1	NA	promoter-TSS (NM_023627)	promoter-TSS (NM_023627)	-95	NM_023627	71780	Mm.29357	NM_023627	ENSMUSG00000019139	Isyna1	1300017C10Rik|AU018670	myo-inositol 1-phosphate synthase A1	protein-coding
mm_42508.1	chr5	115519660	115519679	+	1	NA	intron (NM_133915, intron 1 of 11)	B3|SINE|B2	12993	NM_133915	19303	Mm.18714	NM_011223	ENSMUSG00000029528	Pxn	AW108311|AW123232|Pax	paxillin	protein-coding
mm_77172.1	chr8	111690364	111690382	-	1	NA	promoter-TSS (NR_106044)	promoter-TSS (NR_106044)	637	NM_025583	66473	Mm.34374	NM_025583	ENSMUSG00000031957	Ctrb1	2200008D09Rik|AI504462|Ctrb|Prt-2	chymotrypsinogen B1	protein-coding
mm_145866.1	chr18	65462750	65462760	+	1	NA	exon (NM_172833, exon 10 of 16)	exon (NM_172833, exon 10 of 16)	31758	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_36894.1	chr4	107680876	107680887	-	1	NA	intron (NM_019872, intron 1 of 3)	intron (NM_019872, intron 1 of 3)	3281	NM_019872	56296	Mm.141324	NM_019872	ENSMUSG00000028610	Dmrtb1	Dmrt6|Prp13	DMRT-like family B with proline-rich C-terminal, 1	protein-coding
mm_172216.1	chr6	62407113	62407114	+	1	NA	Intergenic	RLTR10D2|LTR|ERVK	-849744	NM_008167	14804	Mm.439651	NM_008167	ENSMUSG00000071424	Grid2	B230104L07Rik|GluD2|GluRdelta2|Lc|Lc<J>|MMS10-AC|Ms10ac|cpr|ho|nmf408|tpr	glutamate receptor, ionotropic, delta 2	protein-coding
mm_108686.1	chr12	86836944	86836946	+	1	NA	Intergenic	Intergenic	47869	NM_145836	238330	Mm.248358	NM_145836	ENSMUSG00000034168	Irf2bpl	6430527G18Rik|Eap1	interferon regulatory factor 2 binding protein-like	protein-coding
mm_66498.1	chr7	45061746	45061756	-	1	NA	promoter-TSS (NM_025533)	promoter-TSS (NM_025533)	-99	NM_022999	65116	Mm.379098	NM_022999	ENSMUSG00000007837	Prrg2	1600014G02Rik|2510041M06Rik|N4WBP1	proline-rich Gla (G-carboxyglutamic acid) polypeptide 2	protein-coding
mm_112976.1	chr13	21293861	21293899	+	1	NA	Intergenic	Intergenic	-1194	NM_010343	14780	Mm.1332	NM_010343	ENSMUSG00000004344	Gpx5	AV379049|Arep	glutathione peroxidase 5	protein-coding
mm_171793.1	chr5	115845302	115845303	+	1	NA	promoter-TSS (NM_007708)	promoter-TSS (NM_007708)	-354	NM_007708	12704	Mm.8321	NM_007708	ENSMUSG00000029516	Cit	C030025P15Rik|CRIK|CRIK-SK|Cit-k	citron	protein-coding
mm_98937.1	chr11	98358686	98358725	+	1	NA	promoter-TSS (NR_045477)	promoter-TSS (NR_045477)	337	NM_021547	59045	Mm.265546	NM_021547	ENSMUSG00000018167	Stard3	Mln64|es64	START domain containing 3	protein-coding
mm_86251.1	chr9	121490000	121490010	-	1	NA	3' UTR (NM_001284508, exon 4 of 4)	3' UTR (NM_001284508, exon 4 of 4)	5689	NM_001284508	12424	Mm.2619	NM_031161	ENSMUSG00000032532	Cck	-	cholecystokinin	protein-coding
mm_43611.1	chr5	137989742	137989753	+	1	NA	exon (NM_013478, exon 4 of 4)	exon (NM_013478, exon 4 of 4)	8226	NM_013478	12007	Mm.30061	NM_013478	ENSMUSG00000037053	Azgp1	Zag	alpha-2-glycoprotein 1, zinc	protein-coding
mm_63426.1	chr7	127475202	127475217	+	1	NA	exon (NM_145589, exon 7 of 11)	exon (NM_145589, exon 7 of 11)	3595	NM_145589	233895	Mm.44183	NM_145589	ENSMUSG00000030822	Prr14	BC006909	proline rich 14	protein-coding
mm_47303.1	chr5	122372013	122372070	-	1	NA	promoter-TSS (NM_026883)	promoter-TSS (NM_026883)	-78	NM_026883	68948	Mm.474469	NM_026883	ENSMUSG00000029463	Fam216a	1500011H22Rik	family with sequence similarity 216, member A	protein-coding
mm_89839.1	chr10	106879294	106879305	+	1	NA	intron (NM_001205341, intron 21 of 31)	intron (NM_001205341, intron 21 of 31)	244365	NM_001142804	380660	Mm.336072	NM_198636	ENSMUSG00000035948	Acss3	8430416H19Rik|Gm874	acyl-CoA synthetase short-chain family member 3	protein-coding
mm_169897.1	chr16	48601749	48601769	-	1	NA	intron (NM_010816, intron 20 of 26)	BGLII|LTR|ERVK	170197	NM_198297	77647	Mm.167298	NM_198297	ENSMUSG00000030775	Trat1	C030046M14Rik|Tcrim|Trim	T cell receptor associated transmembrane adaptor 1	protein-coding
mm_37209.1	chr4	117884498	117884528	-	1	NA	3' UTR (NM_033617, exon 8 of 8)	3' UTR (NM_033617, exon 8 of 8)	-1037	NM_001253381	53418	Mm.123843	NM_017377	ENSMUSG00000028541	B4galt2	Ggtb2	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 2	protein-coding
mm_153587.1	chr19	43511630	43511677	-	1	NA	intron (NM_010324, intron 2 of 8)	intron (NM_010324, intron 2 of 8)	12952	NM_010324	14718	Mm.19039	NM_010324	ENSMUSG00000025190	Got1	AI789014|Got-1|cAspAT|cCAT	glutamic-oxaloacetic transaminase 1, soluble	protein-coding
mm_116270.1	chr13	34652884	34652896	-	1	NA	promoter-TSS (NR_105041)	promoter-TSS (NR_105041)	-33	NR_105041	101056149	Mm.421309	NR_105041	ENSMUSG00000086786	Gm15908	OTTMUSG00000027716	predicted gene 15908	ncRNA
mm_23265.1	chr3	51483970	51483999	+	1	NA	promoter-TSS (NM_016858)	promoter-TSS (NM_016858)	18	NM_016858	19338	Mm.1664	NM_016858	ENSMUSG00000027739	Rab33b	-	RAB33B, member RAS oncogene family	protein-coding
mm_156078.1	chrX	109196773	109196794	+	1	NA	promoter-TSS (NM_001037917)	promoter-TSS (NM_001037917)	27	NM_001037917	622976	Mm.482747	NM_001037917	ENSMUSG00000048621	Gm6377	EG622976	predicted gene 6377	protein-coding
mm_60522.1	chr7	44480011	44480019	+	1	NA	Intergenic	(TCC)n|Simple_repeat|Simple_repeat	-4502	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_142012.1	chr17	35200414	35200422	-	1	NA	exon (NM_013693, exon 4 of 4)	exon (NM_013693, exon 4 of 4)	1589	NM_013693	21926	Mm.1293	NM_013693	ENSMUSG00000024401	Tnf	DIF|TNF-a|TNF-alpha|TNFSF2|TNFalpha|Tnfa|Tnfsf1a|Tnlg1f	tumor necrosis factor	protein-coding
mm_120951.1	chr14	76780838	76780840	+	1	NA	Intergenic	Intergenic	103271	NR_015485	73272	Mm.116804	NR_015485	ENSMUSG00000101009	1700108F19Rik	1700020I02Rik|BB065030	RIKEN cDNA 1700108F19 gene	ncRNA
mm_79525.1	chr9	57645262	57645279	+	1	NA	5' UTR (NM_007783, exon 1 of 13)	5' UTR (NM_007783, exon 1 of 13)	383	NM_007783	12988	Mm.21974	NM_007783	ENSMUSG00000032312	Csk	AW212630|p50CSK	c-src tyrosine kinase	protein-coding
mm_18175.1	chr2	45110199	45110207	-	1	NA	promoter-TSS (NM_001289521)	promoter-TSS (NM_001289521)	74	NM_001289521	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_152527.1	chr19	11324153	11324174	-	1	NA	intron (NM_001025610, intron 4 of 5)	intron (NM_001025610, intron 4 of 5)	10532	NM_001276398	109225	Mm.491251	NM_027836	ENSMUSG00000024672	Ms4a7	9130422I10Rik|A430103C15Rik|CD20l4|CFFMA	membrane-spanning 4-domains, subfamily A, member 7	protein-coding
mm_44399.1	chr5	17835973	17835986	-	1	NA	promoter-TSS (NM_001159555)	promoter-TSS (NM_001159555)	-83	NM_007643	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_136273.1	chr16	91056503	91056513	-	1	NA	intron (NM_001163695, intron 1 of 1)	intron (NM_001163695, intron 1 of 1)	-12129	NM_026110	67367	Mm.347	NM_026110	ENSMUSG00000022974	Paxbp1	1810007M14Rik|C21orf66|Gcfc|Gcfc1|Pax3/7bp	PAX3 and PAX7 binding protein 1	protein-coding
mm_23234.1	chr3	50606186	50606190	+	1	NA	Intergenic	Intergenic	-162575	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_73537.1	chr8	108703742	108703772	+	1	NA	Intergenic	Intergenic	-10887	NM_007496	11906	Mm.416972	NM_007496	ENSMUSG00000038872	Zfhx3	A230102L03Rik|Atbf1|Sci|WBP9|mKIAA4228	zinc finger homeobox 3	protein-coding
mm_32582.1	chr4	110652621	110652626	+	1	NA	intron (NM_001048189, intron 3 of 12)	intron (NM_001048189, intron 3 of 12)	254925	NM_030231	78933	Mm.435620	NM_030231	ENSMUSG00000061298	Agbl4	4930578N11Rik|4931433A01Rik	ATP/GTP binding protein-like 4	protein-coding
mm_20223.1	chr2	125782713	125782730	-	1	NA	5' UTR (NM_177608, exon 1 of 18)	5' UTR (NM_177608, exon 1 of 18)	149	NM_177608	70354	Mm.138091	NM_133725	ENSMUSG00000035093	Secisbp2l	3110001I20Rik|AI504340|C630011I23	SECIS binding protein 2-like	protein-coding
mm_103728.1	chr11	79623121	79623125	-	1	NA	promoter-TSS (NR_003283)	promoter-TSS (NR_003283)	40	NR_003283	790912	Mm.447313	NR_003283	ENSMUSG00000087434	Rab11fip4os1	Gm11202|OTTMUSG00000000185	RAB11 family interacting protein 4 (class II), opposite strand 1	ncRNA
mm_106503.1	chr11	120437634	120437654	-	1	NA	promoter-TSS (NM_001195023)	promoter-TSS (NM_001195023)	56	NM_001195023	217365	Mm.309520	NM_199469	ENSMUSG00000039703	Nploc4	AK129375|Npl4|mKIAA1499	NPL4 homolog, ubiquitin recognition factor	protein-coding
mm_42085.1	chr5	110181032	110181032	+	1	NA	intron (NM_001347389, intron 1 of 23)	intron (NM_001347389, intron 1 of 23)	4331	NM_008146	269682	Mm.9392	NM_008146	ENSMUSG00000029502	Golga3	5330413L04|5430416E01Rik|AI449376|AW490576|G1-499-14|Mea-2|Mea2|repro27	golgi autoantigen, golgin subfamily a, 3	protein-coding
mm_15953.1	chr2	165983374	165983377	+	1	NA	Intergenic	Intergenic	-9262	NM_008679	17979	Mm.469663	NM_008679	ENSMUSG00000027678	Ncoa3	2010305B15Rik|AW321064|Actr|Aib1|KAT13B|Rac3|Src3|Tram-1|Tram1|bHLHe42|p/Cip|pCip	nuclear receptor coactivator 3	protein-coding
mm_121528.1	chr14	122181706	122181725	+	1	NA	promoter-TSS (NM_029556)	promoter-TSS (NM_029556)	21	NM_029556	69634	Mm.34608	NM_029556	ENSMUSG00000025545	Clybl	0610033J05Rik|2310014M14Rik|AI256068|Clb	citrate lyase beta like	protein-coding
mm_169471.1	chr14	68932759	68932768	+	1	NA	Intergenic	(TAGA)n|Simple_repeat|Simple_repeat	-96526	NM_009285	20855	Mm.20911	NM_009285	ENSMUSG00000014813	Stc1	Stc	stanniocalcin 1	protein-coding
mm_78428.1	chr9	31281226	31281269	+	1	NA	Intergenic	CpG	9846	NM_001101597	638580	Mm.373655	NM_001101597		Gm7244	EG638580	predicted gene 7244	protein-coding
mm_81906.1	chr9	119983977	119983987	+	1	NA	intron (NM_153287, intron 1 of 4)	CpG	676	NM_153287	215418	Mm.491094	NM_153287	ENSMUSG00000032515	Csrnp1	4931429D10Rik|Axud1|CSRNP-1|URAX1|taip-3	cysteine-serine-rich nuclear protein 1	protein-coding
mm_129727.1	chr15	82016175	82016202	-	1	NA	promoter-TSS (NM_010247)	promoter-TSS (NM_010247)	-48	NM_134095	28075	Mm.474453	NM_134095	ENSMUSG00000022472	Desi1	AI427858|AI850401|D15Wsu75e|DeSI-1|Fam152b|Pppde2	desumoylating isopeptidase 1	protein-coding
mm_77707.1	chr8	126591704	126591740	-	1	NA	exon (NM_001164598, exon 2 of 2)	exon (NM_001164598, exon 2 of 2)	1714	NM_001164598	270110	Mm.334918	NM_001164598	ENSMUSG00000051495	Irf2bp2	E130305N23Rik|IRF-2BP2	interferon regulatory factor 2 binding protein 2	protein-coding
mm_16050.1	chr2	167754244	167754260	+	1	NA	Intergenic	Intergenic	63075	NR_015500	329562	Mm.123101	NM_177851	ENSMUSG00000006462	A530013C23Rik	-	RIKEN cDNA A530013C23 gene	ncRNA
mm_14756.1	chr2	144714846	144714859	+	1	NA	intron (NM_025314, intron 4 of 5)	RMER13B|LTR|ERVK	-108814	NM_025490	66328	Mm.45377	NM_025490	ENSMUSG00000027431	Scp2d1	1700010M22Rik	SCP2 sterol-binding domain containing 1	protein-coding
mm_89919.1	chr10	111190376	111190395	+	1	NA	intron (NM_175489, intron 1 of 23)	intron (NM_175489, intron 1 of 23)	25583	NM_175489	237542	Mm.220204	NM_175489	ENSMUSG00000020189	Osbpl8	AA536976|AA536995|C730029P18Rik|D330025H14Rik|ORP-8	oxysterol binding protein-like 8	protein-coding
mm_99352.1	chr11	101583723	101583733	+	1	NA	exon (NM_144830, exon 3 of 9)	exon (NM_144830, exon 3 of 9)	1486	NM_144830	217203	Mm.280559	NM_144830	ENSMUSG00000034947	Tmem106a	0610008L10Rik|AI043106|BC022145	transmembrane protein 106A	protein-coding
mm_5068.1	chr1	195034187	195034227	+	1	NA	non-coding (NR_015566, exon 8 of 8)	non-coding (NR_015566, exon 8 of 8)	-2833	NR_029809	723963		NR_029809	ENSMUSG00000065412	Mir29b-2	Mirn29b-2|mir-29b-2	microRNA 29b-2	ncRNA
mm_74922.1	chr8	25589520	25589555	-	1	NA	intron (NM_173012, intron 4 of 10)	intron (NM_173012, intron 4 of 10)	7950	NM_173012	270035	Mm.268349	NM_173012	ENSMUSG00000037363	Letm2	6030453H13|D030041N04Rik	leucine zipper-EF-hand containing transmembrane protein 2	protein-coding
mm_22029.1	chr2	168050409	168050428	-	1	NA	Intergenic	CpG	-30586	NM_021409	58220	Mm.292834	NM_021409	ENSMUSG00000044641	Pard6b	AV025615|Par6b	par-6 family cell polarity regulator beta	protein-coding
mm_68801.1	chr7	125491372	125491383	-	1	NA	intron (NM_026330, intron 1 of 7)	CpG	165	NM_026330	67711	Mm.4467	NM_026330	ENSMUSG00000030750	Nsmce1	2510027N19Rik	NSE1 homolog, SMC5-SMC6 complex component	protein-coding
mm_159843.1	chr5	135353271	135353271	+	1	NA	promoter-TSS (NM_178240)	promoter-TSS (NM_178240)	-24	NM_001346745	215061	Mm.261834	NM_178240	ENSMUSG00000053388	Trim50	-	tripartite motif-containing 50	protein-coding
mm_17079.1	chr2	22895499	22895559	-	1	NA	promoter-TSS (NM_019501)	promoter-TSS (NM_019501)	7	NM_019501	56075	Mm.249752	NM_019501	ENSMUSG00000026784	Pdss1	2610203G20Rik|2700031G06Rik|TPT|TPT 1|Tprt|mDLP1|mSPS1	prenyl (solanesyl) diphosphate synthase, subunit 1	protein-coding
mm_120963.1	chr14	77904350	77904360	+	1	NA	5' UTR (NM_029495, exon 1 of 12)	5' UTR (NM_029495, exon 1 of 12)	116	NM_029495	108670	Mm.68134	NM_029495	ENSMUSG00000022014	Epsti1	2310046K10Rik|5033415K03Rik|BRESI1	epithelial stromal interaction 1 (breast)	protein-coding
mm_100457.1	chr11	119835579	119835601	+	1	NA	intron (NM_028898, intron 13 of 33)	intron (NM_028898, intron 13 of 33)	-1225	NR_045312	319454	Mm.442144	NR_045312	ENSMUSG00000085081	Rptoros	A430071A18Rik	regulatory associated protein of MTOR, complex 1, opposite strand	ncRNA
mm_65665.1	chr7	28146847	28146857	-	1	NA	exon (NM_001164655, exon 8 of 20)	exon (NM_001164655, exon 8 of 20)	17386	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_72349.1	chr8	79640177	79640187	+	1	NA	intron (NM_001081164, intron 1 of 20)	CpG	506	NM_001081164	73945	Mm.34348	NM_001081164	ENSMUSG00000036990	Otud4	4930431L18Rik|AI449692|D8Ertd69e|mKIAA1046	OTU domain containing 4	protein-coding
mm_20258.1	chr2	126602299	126602310	-	1	NA	intron (NM_008230, intron 7 of 11)	intron (NM_008230, intron 7 of 11)	16374	NM_008230	15186	Mm.18603	NM_008230	ENSMUSG00000027360	Hdc	AW108189|Hdc-a|Hdc-c|Hdc-e|Hdc-s	histidine decarboxylase	protein-coding
mm_17605.1	chr2	30897519	30897543	-	1	NA	intron (NM_022415, intron 2 of 2)	intron (NM_022415, intron 2 of 2)	5766	NM_022415	64292	Mm.28768	NM_022415	ENSMUSG00000050737	Ptges	2410099E23Rik|D2Ertd369e|Pges|mPGES|mPGES-1	prostaglandin E synthase	protein-coding
mm_13190.1	chr2	93192407	93192420	+	1	NA	intron (NM_001025246, intron 1 of 7)	intron (NM_001025246, intron 1 of 7)	4829	NM_001025246	277414	Mm.41033	NM_001025246	ENSMUSG00000068735	Trp53i11	Tp53i11	transformation related protein 53 inducible protein 11	protein-coding
mm_24486.1	chr3	92170213	92170222	+	1	NA	Intergenic	Intergenic	-27463	NM_027042	69332	Mm.120271	NM_027042	ENSMUSG00000027927	Lelp1	1700012F11Rik	late cornified envelope-like proline-rich 1	protein-coding
mm_7411.1	chr1	119422182	119422196	-	1	NA	promoter-TSS (NM_008381)	promoter-TSS (NM_008381)	59	NM_008381	16324	Mm.3092	NM_008381	ENSMUSG00000037035	Inhbb	-	inhibin beta-B	protein-coding
mm_117655.1	chr13	93192194	93192200	-	1	NA	promoter-TSS (NM_133905)	promoter-TSS (NM_133905)	86	NM_133905	100715	Mm.242865	NM_133905	ENSMUSG00000042167	Papd4	8030446C20Rik|AI649009|GLD-2|Gld2	PAP associated domain containing 4	protein-coding
mm_173211.1	chrX	73082456	73082460	-	1	NA	promoter-TSS (NM_001081642)	promoter-TSS (NM_001081642)	49	NM_001081642	434794	Mm.104764	NM_001081642	ENSMUSG00000079845	Xlr4a	-	X-linked lymphocyte-regulated 4A	protein-coding
mm_3400.1	chr1	143739552	143739566	+	1	NA	promoter-TSS (NM_023505)	promoter-TSS (NM_023505)	-9	NM_001038592	69367	Mm.272727	NM_023505	ENSMUSG00000018196	Glrx2	1700010P22Rik|AI645710|Grx2	glutaredoxin 2 (thioltransferase)	protein-coding
mm_97998.1	chr11	84173292	84173304	+	1	NA	Intergenic	Intergenic	-5822	NM_001037932	628813	Mm.390389	NM_001037932	ENSMUSG00000051452	Gm11437	AI463690|OTTMUSG00000000997	predicted gene 11437	protein-coding
mm_29382.1	chr3	108840544	108840553	-	1	NA	promoter-TSS (NM_011504)	promoter-TSS (NM_011504)	-46	NM_011504	20912	Mm.316894	NM_011504	ENSMUSG00000027882	Stxbp3	Munc-18c|Stxbp3a|Sxtbp3|Unc18-3	syntaxin binding protein 3	protein-coding
mm_61488.1	chr7	75703236	75703243	+	1	NA	intron (NM_029332, intron 16 of 36)	intron (NM_029332, intron 16 of 36)	-145099	NM_001122780	207952	Mm.206223	NM_029652	ENSMUSG00000055652	Klhl25	2810402K13Rik|BC027373|Enc-1	kelch-like 25	protein-coding
mm_96126.1	chr11	60777576	60777589	+	1	NA	promoter-TSS (NM_001085440)	promoter-TSS (NM_001085440)	57	NM_175491	237782	Mm.57726	NM_175491	ENSMUSG00000049323	Smcr8	2310076G09Rik|AI642055|D030073L15Rik	Smith-Magenis syndrome chromosome region, candidate 8 homolog (human)	protein-coding
mm_160346.1	chr8	19729568	19729568	+	1	NA	promoter-TSS (NM_001270553)	promoter-TSS (NM_001270553)	-8	NM_001270553	100861668	Mm.491087	NM_001270553	ENSMUSG00000095294	Gm21119	-	predicted gene, 21119	protein-coding
mm_55018.1	chr6	48841019	48841035	-	1	NA	promoter-TSS (NM_025326)	promoter-TSS (NM_025326)	-39	NM_023056	65963	Mm.28385	NM_023056	ENSMUSG00000029810	Tmem176b	1810009M01Rik|Clast1|Lr8	transmembrane protein 176B	protein-coding
mm_9977.1	chr1	191224977	191224987	-	1	NA	Intergenic	Intergenic	-41649	NM_007498	11910	Mm.2706	NM_007498	ENSMUSG00000026628	Atf3	LRG-21	activating transcription factor 3	protein-coding
mm_114475.1	chr13	68582214	68582270	+	1	NA	promoter-TSS (NR_131892)	promoter-TSS (NR_131892)	32	NR_138478	69577	Mm.23670	NM_027123	ENSMUSG00000021532	Fastkd3	2310010B21Rik|AW048587	FAST kinase domains 3	protein-coding
mm_6541.1	chr1	75124937	75124950	-	1	NA	TTS (NM_194333)	TTS (NM_194333)	8947	NM_194333	22626	Mm.68157	NM_194333	ENSMUSG00000026205	Slc23a3	SVCT3|Yspl1	solute carrier family 23 (nucleobase transporters), member 3	protein-coding
mm_100565.1	chr11	120730743	120730755	+	1	NA	exon (NM_007621, exon 3 of 8)	exon (NM_007621, exon 3 of 8)	1272	NM_007621	12409	Mm.21454	NM_007621	ENSMUSG00000025150	Cbr2	MLCR	carbonyl reductase 2	protein-coding
mm_143819.1	chr17	83846763	83846765	-	1	NA	promoter-TSS (NM_025325)	promoter-TSS (NM_025325)	26	NM_025325	107766	Mm.30100	NM_025325	ENSMUSG00000000673	Haao	0610007K21Rik|0610012J07Rik|3-HAO|3-HAOxase|3HAO	3-hydroxyanthranilate 3,4-dioxygenase	protein-coding
mm_80742.1	chr9	94743529	94743545	+	1	NA	intron (NM_177909, intron 4 of 15)	intron (NM_177909, intron 4 of 15)	-8292	NR_106116	102465763		NR_106116	ENSMUSG00000098251	Mir7656	Gm27614|mmu-mir-7656	microRNA 7656	ncRNA
mm_31456.1	chr4	48663503	48663525	+	1	NA	promoter-TSS (NM_026509)	promoter-TSS (NM_026509)	0	NM_026509	68016	Mm.133444	NM_026509	ENSMUSG00000028348	Murc	2310039E09Rik	muscle-related coiled-coil protein	protein-coding
mm_124967.1	chr15	18818665	18818691	+	1	NA	promoter-TSS (NM_001316758)	promoter-TSS (NM_001316758)	-269	NM_001316758	320873	Mm.117794	NM_009865	ENSMUSG00000022321	Cdh10	A830016G23Rik|C030003B10Rik|C030011H18Rik	cadherin 10	protein-coding
mm_33539.1	chr4	130934481	130934483	+	1	NA	exon (NM_010686, exon 8 of 8)	exon (NM_010686, exon 8 of 8)	-9903	NM_010769	17180	Mm.271796	NM_010769	ENSMUSG00000040533	Matn1	CMP|Crtm|Mat1|matrilin-1	matrilin 1, cartilage matrix protein	protein-coding
mm_6573.1	chr1	75209430	75209476	-	1	NA	5' UTR (NM_029010, exon 2 of 17)	5' UTR (NM_029010, exon 2 of 17)	1325	NM_029010	74577	Mm.458319	NM_029010	ENSMUSG00000026200	Glb1l	4833408P15Rik	galactosidase, beta 1-like	protein-coding
mm_40953.1	chr5	76856754	76856770	+	1	NA	exon (NM_001163793, exon 6 of 9)	exon (NM_001163793, exon 6 of 9)	16163	NM_001163793	320827	Mm.101504	NM_001163793	ENSMUSG00000036377	C530008M17Rik	2810489J07Rik|4930529A19Rik|4931405B09Rik|Kiaa1211|mKIAA1211	RIKEN cDNA C530008M17 gene	protein-coding
mm_27549.1	chr3	57848081	57848098	-	1	NA	promoter-TSS (NM_019410)	promoter-TSS (NM_019410)	-332	NM_019410	18645	Mm.271744	NM_019410	ENSMUSG00000027805	Pfn2	Pfn	profilin 2	protein-coding
mm_115448.1	chr13	118556163	118556173	+	1	NA	promoter-TSS (NR_045982)	promoter-TSS (NR_045982)	0	NR_045982	75890	Mm.141235	NR_045982	ENSMUSG00000100727	1700003P14Rik	1700030O10Rik|4930584L06Rik	RIKEN cDNA 1700003P14 gene	ncRNA
mm_105063.1	chr11	100718569	100718587	-	1	NA	exon (NM_001305003, exon 3 of 6)	exon (NM_001305003, exon 3 of 6)	4728	NM_029307	75482	Mm.46175	NM_029307	ENSMUSG00000017832	Hspb9	1700007H20Rik	heat shock protein, alpha-crystallin-related, B9	protein-coding
mm_120864.1	chr14	75229569	75229579	+	1	NA	3' UTR (NM_001247984, exon 16 of 16)	3' UTR (NM_001247984, exon 16 of 16)	-12713	NM_019775	56373	Mm.24242	NM_019775	ENSMUSG00000021999	Cpb2	1110032P04Rik|4930405E17Rik|AI255929|CPR|Cpu|TAFI	carboxypeptidase B2 (plasma)	protein-coding
mm_50365.1	chr6	48659457	48659466	+	1	NA	3' UTR (NM_001286629, exon 5 of 5)	3' UTR (NM_001286629, exon 5 of 5)	12100	NM_212486	243374	Mm.86514	NM_212486	ENSMUSG00000064262	Gimap8	Gm457|IAN9|IMAP8	GTPase, IMAP family member 8	protein-coding
mm_77839.1	chr9	5299175	5299216	+	1	NA	intron (NM_009807, intron 1 of 9)	intron (NM_009807, intron 1 of 9)	678	NM_009807	12362	Mm.1051	NM_009807	ENSMUSG00000025888	Casp1	ICE|Il1bc	caspase 1	protein-coding
mm_106005.1	chr11	115708539	115708614	-	1	NA	promoter-TSS (NM_008163)	promoter-TSS (NM_008163)	21	NM_008163	14784	Mm.439649	NM_008163	ENSMUSG00000059923	Grb2	AA408164|Ash	growth factor receptor bound protein 2	protein-coding
mm_49245.1	chr6	17307660	17307744	+	1	NA	promoter-TSS (NM_001243064)	promoter-TSS (NM_001243064)	62	NM_001243064	12389	Mm.28278	NM_007616	ENSMUSG00000007655	Cav1	Cav|Cav-1	caveolin 1, caveolae protein	protein-coding
mm_18944.1	chr2	76766377	76766392	-	1	NA	exon (NM_011652, exon 253 of 313)	exon (NM_011652, exon 253 of 313)	91069	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_151767.1	chr19	5273008	5273037	-	1	NA	promoter-TSS (NM_153129)	promoter-TSS (NM_153129)	97	NM_153129	107975	Mm.234923	NM_153129	ENSMUSG00000024855	Pacs1	AI325977	phosphofurin acidic cluster sorting protein 1	protein-coding
mm_1780.1	chr1	78511866	78511896	+	1	NA	5' UTR (NM_026713, exon 2 of 7)	5' UTR (NM_026713, exon 2 of 7)	821	NM_026713	68393	Mm.41325	NM_026713	ENSMUSG00000012187	Mogat1	0610030A14Rik|1110064N14Rik|Dgat2l|Dgat2l1|MGAT1|WI1-2612I11.1|mDC2	monoacylglycerol O-acyltransferase 1	protein-coding
mm_88074.1	chr10	67979570	67979575	+	1	NA	promoter-TSS (NM_001081346)	promoter-TSS (NM_001081346)	-26	NM_001081346	170799	Mm.209844	NM_133244	ENSMUSG00000037846	Rtkn2	B130039D23Rik|Mbf|Plekhk1	rhotekin 2	protein-coding
mm_13356.1	chr2	103412075	103412099	+	1	NA	promoter-TSS (NM_001145813)	promoter-TSS (NM_001145813)	-11	NM_001145813	13711	Mm.20888	NM_010125	ENSMUSG00000027186	Elf5	ESE-2|ESE-5|ESE-5.	E74-like factor 5	protein-coding
mm_44128.1	chr5	149678209	149678221	+	1	NA	promoter-TSS (NM_001081204)	promoter-TSS (NM_001081204)	-42	NM_001081204	381694	Mm.45060	NM_001081204	ENSMUSG00000051950	B3glct	B3galtl|Gm1057	beta-3-glucosyltransferase	protein-coding
mm_94539.1	chr11	9131625	9131631	+	1	NA	intron (NM_001159401, intron 4 of 8)	intron (NM_001159401, intron 4 of 8)	13121	NM_001159402	22271	Mm.4610	NM_009477	ENSMUSG00000020407	Upp1	AI325217|UPase|UdRPase|Up|Upp	uridine phosphorylase 1	protein-coding
mm_84995.1	chr9	86695839	86695854	-	1	NA	promoter-TSS (NM_008615)	promoter-TSS (NM_008615)	68	NM_008615	17436	Mm.148155	NM_008615	ENSMUSG00000032418	Me1	D9Ertd267e|Mdh-1|Mod-1|Mod1	malic enzyme 1, NADP(+)-dependent, cytosolic	protein-coding
mm_112884.1	chr13	20859254	20859263	+	1	NA	intron (NM_012054, intron 4 of 20)	L2b|LINE|L2	65145	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_42232.1	chr5	113550879	113550891	+	1	NA	5' UTR (NM_177292, exon 1 of 8)	5' UTR (NM_177292, exon 1 of 8)	465	NM_177292	320916	Mm.102783	NM_177292	ENSMUSG00000063430	Wscd2	4933413A10Rik|C530024P05Rik|Gm450	WSC domain containing 2	protein-coding
mm_25536.1	chr3	115674070	115674077	+	1	NA	Intergenic	Intergenic	40982	NM_007901	13609	Mm.982	NM_007901	ENSMUSG00000045092	S1pr1	AI849002|Edg1|Lpb1|S1p|S1p1	sphingosine-1-phosphate receptor 1	protein-coding
mm_57927.1	chr6	134558733	134558737	-	1	NA	intron (NM_008514, intron 1 of 22)	intron (NM_008514, intron 1 of 22)	8178	NM_008514	16974	Mm.321990	NM_008514	ENSMUSG00000030201	Lrp6	C030016K15Rik|Cd|Gw|ska26|ska<m26Jus>|skax26	low density lipoprotein receptor-related protein 6	protein-coding
mm_148620.1	chr19	5414889	5414912	+	1	NA	intron (NR_027938, intron 1 of 3)	intron (NR_027938, intron 1 of 3)	8085	NR_027938	74931	Mm.388511	NR_015545	ENSMUSG00000086938	4930481A15Rik	-	RIKEN cDNA 4930481A15 gene	ncRNA
mm_129031.1	chr15	74959200	74959218	-	1	NA	3' UTR (NM_001164036, exon 4 of 4)	3' UTR (NM_001164036, exon 4 of 4)	4103	NM_001164040	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_46169.1	chr5	96739213	96739222	-	1	NA	exon (NM_175473, exon 55 of 74)	exon (NM_175473, exon 55 of 74)	-54168	NM_013470	11745	Mm.7214	NM_013470	ENSMUSG00000029484	Anxa3	Anx3	annexin A3	protein-coding
mm_119657.1	chr14	52136478	52136507	+	1	NA	intron (NM_023879, intron 10 of 24)	intron (NM_023879, intron 10 of 24)	25589	NM_023879	77945	Mm.21662	NM_023879	ENSMUSG00000057132	Rpgrip1	0610005A07Rik|4930401L23Rik|4930505G06Rik|A930002K18Rik|AA415034|nmf247	retinitis pigmentosa GTPase regulator interacting protein 1	protein-coding
mm_51457.1	chr6	82041708	82041719	+	1	NA	promoter-TSS (NM_145570)	promoter-TSS (NM_145570)	85	NM_145570	232146	Mm.489683	NM_145570	ENSMUSG00000035104	Eva1a	BC014699|Fam176a|Tmem166	eva-1 homolog A (C. elegans)	protein-coding
mm_169436.1	chr14	55885112	55885114	+	1	NA	promoter-TSS (NM_019820)	promoter-TSS (NM_019820)	171	NR_138134	219094	Mm.37592	NM_027143	ENSMUSG00000047153	Khnyn	6330555F21|9130227C08Rik|AI605259|Kiaa0323|mKIAA0323	KH and NYN domain containing	protein-coding
mm_54807.1	chr6	42040143	42040153	-	1	NA	exon (NM_009299, exon 2 of 4)	exon (NM_009299, exon 2 of 4)	1754	NM_009299	20939	Mm.4119	NM_009299	ENSMUSG00000023289	Sva	-	seminal vesicle antigen	protein-coding
mm_133065.1	chr16	58662095	58662112	+	1	NA	Intergenic	Intergenic	-8105	NM_007757	12892	Mm.291519	NM_007757	ENSMUSG00000022742	Cpox	CPX|Cpo|HCP|cac|nct	coproporphyrinogen oxidase	protein-coding
mm_130956.1	chr15	103310403	103310413	-	1	NA	promoter-TSS (NM_030720)	promoter-TSS (NM_030720)	30	NM_030720	80910	Mm.160369	NM_030720	ENSMUSG00000063234	Gpr84	EX33	G protein-coupled receptor 84	protein-coding
mm_44213.1	chr5	4115095	4115113	-	1	NA	Intergenic	Intergenic	-10407	NM_020010	13121	Mm.140158	NM_020010	ENSMUSG00000001467	Cyp51	AI426508|CYPLI|Cyp51a1|Ldm|P450-14DM|P450LI	cytochrome P450, family 51	protein-coding
mm_152844.1	chr19	23448412	23448425	-	1	NA	promoter-TSS (NM_174857)	promoter-TSS (NM_174857)	-96	NM_174857	71738	Mm.50841	NM_174857	ENSMUSG00000033207	Mamdc2	1200015L10Rik|AI591564|mamcan	MAM domain containing 2	protein-coding
mm_18380.1	chr2	60037349	60037398	-	1	NA	intron (NM_001001182, intron 2 of 35)	intron (NM_001001182, intron 2 of 35)	88367	NM_001001182	407823	Mm.228071	NM_001001182	ENSMUSG00000026987	Baz2b	5830435C13Rik|BC053917|D2Ertd794e	bromodomain adjacent to zinc finger domain, 2B	protein-coding
mm_128825.1	chr15	67131563	67131568	-	1	NA	intron (NM_009177, intron 2 of 8)	intron (NM_009177, intron 2 of 8)	45317	NM_009177	20442	Mm.248334	NM_009177	ENSMUSG00000013846	St3gal1	5330418N22Rik|AI467004|ST3GalI|Siat4|Siat4a|St3gal-1	ST3 beta-galactoside alpha-2,3-sialyltransferase 1	protein-coding
mm_33771.1	chr4	134470747	134470772	+	1	NA	exon (NM_019641, exon 3 of 5)	exon (NM_019641, exon 3 of 5)	2439	NM_019641	16765	Mm.378957	NM_019641	ENSMUSG00000028832	Stmn1	19k|Lag|Lap18|Op18|P18|P19|Pig|Pp17|Pp18|Pp19|Pr22|Smn	stathmin 1	protein-coding
mm_129634.1	chr15	80235378	80235392	-	1	NA	intron (NM_178719, intron 1 of 5)	intron (NM_178719, intron 1 of 5)	1305	NM_178719	239555	Mm.307163	NM_178719	ENSMUSG00000022412	Mief1	A230016E22|AI452372|Smcr7l	mitochondrial elongation factor 1	protein-coding
mm_29151.1	chr3	105959253	105959280	-	1	NA	promoter-TSS (NM_027432)	promoter-TSS (NM_027432)	-232	NM_027432	70465	Mm.5110	NM_027432	ENSMUSG00000000561	Wdr77	2610003I18Rik|2610312E17Rik|C79984|p44/MEP50	WD repeat domain 77	protein-coding
mm_138086.1	chr17	33997060	33997071	+	1	NA	exon (NM_001001892, exon 5 of 8)	exon (NM_001001892, exon 5 of 8)	3268	NM_001001892	14972	Mm.422886	NM_001001892	ENSMUSG00000061232	H2-K1	H-2K|H-2K(d)|H2-K|K-f	histocompatibility 2, K1, K region	protein-coding
mm_34991.1	chr4	156028946	156028956	+	1	NA	TTS (NM_009400)	TTS (NM_009400)	2609	NM_021985	21936	Mm.3180	NM_009400	ENSMUSG00000041954	Tnfrsf18	AITR|Gitr	tumor necrosis factor receptor superfamily, member 18	protein-coding
mm_127488.1	chr15	101293467	101293480	+	1	NA	non-coding (NR_033803, exon 1 of 2)	non-coding (NR_033803, exon 1 of 2)	261	NR_033803	77717	Mm.391998	NR_033803	ENSMUSG00000075408	6030408B16Rik	AI225877	RIKEN cDNA 6030408B16 gene	ncRNA
mm_144867.1	chr18	36727622	36727628	+	1	NA	promoter-TSS (NM_009841)	promoter-TSS (NM_009841)	-810	NM_009841	12475	Mm.3460	NM_009841	ENSMUSG00000051439	Cd14	-	CD14 antigen	protein-coding
mm_159723.1	chr5	35389320	35389320	+	1	NA	exon (NM_010445, exon 1 of 2)	exon (NM_010445, exon 1 of 2)	203	NM_010445	15371	Mm.358606	NM_010445	ENSMUSG00000067438	Hmx1	Nkx5-3	H6 homeobox 1	protein-coding
mm_22660.1	chr3	14871710	14871717	+	1	NA	3' UTR (NM_007606, exon 7 of 7)	3' UTR (NM_007606, exon 7 of 7)	8175	NM_007606	12350	Mm.300	NM_007606	ENSMUSG00000027559	Car3	BB219044|Ca3|Car-3	carbonic anhydrase 3	protein-coding
mm_49379.1	chr6	24597811	24597821	+	1	NA	promoter-TSS (NM_053098)	promoter-TSS (NM_053098)	45	NM_053098	93677	Mm.332941	NM_053098	ENSMUSG00000029683	Lmod2	C-Lmod	leiomodin 2 (cardiac)	protein-coding
mm_125846.1	chr15	74958947	74958958	+	1	NA	3' UTR (NM_001164036, exon 4 of 4)	3' UTR (NM_001164036, exon 4 of 4)	3846	NM_001164040	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_172742.1	chr8	79700977	79700984	-	1	NA	exon (NM_015751, exon 7 of 18)	exon (NM_015751, exon 7 of 18)	10760	NM_015751	24015	Mm.5831	NM_015751	ENSMUSG00000058355	Abce1	C79080|Oabp|RLI|RNS41|Rnaseli	ATP-binding cassette, sub-family E (OABP), member 1	protein-coding
mm_54290.1	chr6	29272493	29272506	-	1	NA	promoter-TSS (NM_001190461)	promoter-TSS (NM_001190461)	11	NM_001190461	69573	Mm.45161	NM_023516	ENSMUSG00000043421	Hilpda	2310016C08Rik|AW049004|Hig2	hypoxia inducible lipid droplet associated	protein-coding
mm_509.1	chr1	37246710	37246717	+	1	NA	intron (NM_009918, intron 3 of 5)	ORR1B1|LTR|ERVL-MaLR	27508	NM_009918	12790	Mm.214224	NM_009918	ENSMUSG00000026114	Cnga3	CNG3	cyclic nucleotide gated channel alpha 3	protein-coding
mm_140607.1	chr17	10631124	10631164	-	1	NA	intron (NM_027032, intron 2 of 4)	intron (NM_027032, intron 2 of 4)	174928	NR_077238	319750	Mm.383485	NR_077237	ENSMUSG00000089633	A230009B12Rik	-	RIKEN cDNA A230009B12 gene	ncRNA
mm_142942.1	chr17	56040214	56040231	-	1	NA	promoter-TSS (NM_013733)	promoter-TSS (NM_013733)	-194	NM_013733	27221	Mm.391010	NM_013733	ENSMUSG00000002835	Chaf1a	AL023013|AL024058|CAF-1|Cac1p	chromatin assembly factor 1, subunit A (p150)	protein-coding
mm_143480.1	chr17	71263030	71263033	-	1	NA	intron (NM_145158, intron 4 of 7)	RLTR20A2B_MM|LTR|ERVK	47934	NM_145158	246707	Mm.23462	NM_145158	ENSMUSG00000024053	Emilin2	FOAP-10	elastin microfibril interfacer 2	protein-coding
mm_47651.1	chr5	125391682	125391718	-	1	NA	Intergenic	Intergenic	-1683	NM_019639	22190	Mm.331	NM_019639	ENSMUSG00000008348	Ubc	2700054O04Rik|AI194771|Rps27a|TI-225|Uba52|Ubb	ubiquitin C	protein-coding
mm_140200.1	chr17	83706171	83706200	+	1	NA	promoter-TSS (NM_001171052)	promoter-TSS (NM_001171052)	22	NM_001171052	116871	Mm.277668	NM_054082	ENSMUSG00000055817	Mta3	1110002J22Rik|mKIAA1266	metastasis associated 3	protein-coding
mm_37767.1	chr4	129742181	129742189	-	1	NA	non-coding (NR_045036, exon 1 of 12)	non-coding (NR_045036, exon 1 of 12)	118	NM_011317	20218	Mm.8256	NM_011317	ENSMUSG00000028790	Khdrbs1	Sam68|p62|p68	KH domain containing, RNA binding, signal transduction associated 1	protein-coding
mm_72476.1	chr8	83608227	83608280	+	1	NA	promoter-TSS (NM_018808)	promoter-TSS (NM_018808)	78	NM_018808	81489	Mm.282092	NM_018808	ENSMUSG00000005483	Dnajb1	0610007I11Rik|DjB1|HSPF1|Hdj1|Hsp40	DnaJ heat shock protein family (Hsp40) member B1	protein-coding
mm_46636.1	chr5	108520031	108520055	-	1	NA	3' UTR (NM_007756, exon 4 of 4)	3' UTR (NM_007756, exon 4 of 4)	29984	NM_007756	12889	Mm.5195	NM_007756	ENSMUSG00000033615	Cplx1	921-S	complexin 1	protein-coding
mm_96853.1	chr11	70054335	70054360	+	1	NA	promoter-TSS (NM_009714)	promoter-TSS (NM_009714)	-8	NM_009714	11889	Mm.6559	NM_009714	ENSMUSG00000020884	Asgr1	ASGPR1|Asgr|Asgr-1|HL-1	asialoglycoprotein receptor 1	protein-coding
mm_168329.1	chr11	116394541	116394547	+	1	NA	intron (NM_027258, intron 2 of 18)	IAPLTR1_Mm|LTR|ERVK	18488	NM_027258	217340	Mm.426344	NM_027258	ENSMUSG00000052949	Rnf157	2610036E23Rik|A130073L17Rik|mKIAA1917	ring finger protein 157	protein-coding
mm_43682.1	chr5	138807248	138807265	+	1	NA	exon (NM_030565, exon 7 of 10)	exon (NM_030565, exon 7 of 10)	-12824	NM_001195128	384244	Mm.485002	NM_001195128	ENSMUSG00000094504	Gm5294	EG384244	predicted gene 5294	protein-coding
mm_20048.1	chr2	120245056	120245071	-	1	NA	5' UTR (NM_177845, exon 1 of 20)	5' UTR (NM_177845, exon 1 of 20)	272	NM_177845	329502	Mm.330505	NM_177845	ENSMUSG00000050211	Pla2g4e	2310026J01Rik|C230096D22|Pla2epsilon	phospholipase A2, group IVE	protein-coding
mm_116026.1	chr13	25020290	25020346	-	1	NA	promoter-TSS (NM_001013389)	promoter-TSS (NM_001013389)	-1	NM_001013389	380836	Mm.387097	NM_001013389	ENSMUSG00000021339	Mrs2	Gm902|HPT|Mrs2l|RPT	MRS2 magnesium transporter	protein-coding
mm_96561.1	chr11	69016074	69016135	+	1	NA	5' UTR (NM_001281465, exon 1 of 23)	5' UTR (NM_001281465, exon 1 of 23)	193	NM_001013256	68964	Mm.285785	NM_001013256	ENSMUSG00000020898	Ctc1	1500010J02Rik|AAF-132|AAF132	CTS telomere maintenance complex component 1	protein-coding
mm_148189.1	chr18	78963334	78963338	-	1	NA	intron (NM_053099, intron 2 of 5)	intron (NM_053099, intron 2 of 5)	146055	NM_053099	240427	Mm.312871	NM_053099	ENSMUSG00000024548	Setbp1	C130092E12|Seb|mKIAA0437	SET binding protein 1	protein-coding
mm_106865.1	chr12	8009425	8009461	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	31766	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_67850.1	chr7	98665348	98665348	-	1	NA	Intergenic	Intergenic	-8779	NM_172280	233545	Mm.387819	NM_172280	ENSMUSG00000035401	Emsy	2210018M11Rik|2310016L09Rik|AU019521|AU019557	EMSY, BRCA2-interacting transcriptional repressor	protein-coding
mm_50885.1	chr6	56369703	56369717	+	1	NA	promoter-TSS (NM_001159957)	promoter-TSS (NM_001159957)	-76	NM_001159955	18575	Mm.5145	NM_011054	ENSMUSG00000004347	Pde1c	-	phosphodiesterase 1C	protein-coding
mm_6737.1	chr1	83038412	83038422	-	1	NA	promoter-TSS (NM_030556)	promoter-TSS (NM_030556)	31	NM_030556	80721	Mm.261542	NM_030556	ENSMUSG00000038496	Slc19a3	A230084E24Rik|AI788884|ThTr2	solute carrier family 19, member 3	protein-coding
mm_2073.1	chr1	87637508	87637512	+	1	NA	intron (NM_010566, intron 2 of 26)	intron (NM_010566, intron 2 of 26)	17198	NM_001110193	16331	Mm.15105	NM_010566	ENSMUSG00000026288	Inpp5d	SHIP|SHIP-1|SHIP1|SIP-145|p150Ship|s-SHIP	inositol polyphosphate-5-phosphatase D	protein-coding
mm_101221.1	chr11	20153775	20153777	-	1	NA	Intergenic	RMER16-int|LTR|ERVK	-40825	NM_146243	66713	Mm.259045	NM_146243	ENSMUSG00000020152	Actr2	4921510D23Rik|AA409782|Arp2|D6Ertd746e	ARP2 actin-related protein 2	protein-coding
mm_123904.1	chr14	73239779	73239786	-	1	NA	3' UTR (NM_175116, exon 1 of 1)	3' UTR (NM_175116, exon 1 of 1)	1891	NM_175116	67168	Mm.390681	NM_175116	ENSMUSG00000033446	Lpar6	2610302I02Rik|P2ry5|P2y5	lysophosphatidic acid receptor 6	protein-coding
mm_141212.1	chr17	27133880	27133897	-	1	NA	promoter-TSS (NM_026063)	promoter-TSS (NM_026063)	3	NM_026063	67267	Mm.272389	NM_026063	ENSMUSG00000024208	Uqcc2	2900010M23Rik|Cbp6|M19|Mnf1	ubiquinol-cytochrome c reductase complex assembly factor 2	protein-coding
mm_101719.1	chr11	42182308	42182333	-	1	NA	5' UTR (NM_010250, exon 1 of 10)	5' UTR (NM_010250, exon 1 of 10)	610	NM_010250	14394	Mm.439668	NM_010250	ENSMUSG00000010803	Gabra1	Gabra-1	gamma-aminobutyric acid (GABA) A receptor, subunit alpha 1	protein-coding
mm_99413.1	chr11	102276806	102276833	+	1	NA	exon (NM_148953, exon 3 of 5)	exon (NM_148953, exon 3 of 5)	7996	NM_148953	217217	Mm.216432	NM_148953	ENSMUSG00000034768	Asb16	-	ankyrin repeat and SOCS box-containing 16	protein-coding
mm_48596.1	chr5	144014859	144014918	-	1	NA	promoter-TSS (NM_177682)	promoter-TSS (NM_177682)	-35	NM_177682	231874	Mm.320432	NM_177682	ENSMUSG00000029617	Ccz1	AU022870	CCZ1 vacuolar protein trafficking and biogenesis associated	protein-coding
mm_36837.1	chr4	106492307	106492340	-	1	NA	promoter-TSS (NM_080458)	promoter-TSS (NM_080458)	-80	NM_080458	140475	Mm.135448	NM_080458	ENSMUSG00000025418	Bsnd	-	Bartter syndrome, infantile, with sensorineural deafness (Barttin)	protein-coding
mm_140667.1	chr17	12916003	12916044	-	1	NA	promoter-TSS (NM_013686)	promoter-TSS (NM_013686)	68	NM_026310	67681	Mm.290166	NM_026310	ENSMUSG00000057388	Mrpl18	1010001C05Rik|C79879|HSPC071|MRP-L18	mitochondrial ribosomal protein L18	protein-coding
mm_69336.1	chr7	129420929	129420956	-	1	NA	Intergenic	Intergenic	163848	NM_001080963	381925	Mm.39184	NM_001080963	ENSMUSG00000070366	Plpp4	C030048B12Rik|Gm1090|Ppapdc1a	phospholipid phosphatase 4	protein-coding
mm_119424.1	chr14	45351178	45351209	+	1	NA	promoter-TSS (NM_019637)	promoter-TSS (NM_019637)	7	NM_019637	56291	Mm.202561	NM_019637	ENSMUSG00000053205	Styx	0610039A20Rik|hStyxb	serine/threonine/tyrosine interaction protein	protein-coding
mm_85822.1	chr9	110420862	110420874	-	1	NA	exon (NM_008694, exon 2 of 4)	exon (NM_008694, exon 2 of 4)	1060	NM_008694	18054	Mm.236225	NM_008694	ENSMUSG00000032484	Ngp	bectenecin	neutrophilic granule protein	protein-coding
mm_115603.1	chr13	11905430	11905434	-	1	NA	intron (NM_023868, intron 3 of 104)	intron (NM_023868, intron 3 of 104)	201513	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding
mm_52406.1	chr6	113380714	113380747	+	1	NA	exon (NM_026552, exon 2 of 6)	exon (NM_026552, exon 2 of 6)	2617	NM_001170485	68089	Mm.289306	NM_026552	ENSMUSG00000079426	Arpc4	20kDa|5330419I20Rik|AI327076|p20-Arc	actin related protein 2/3 complex, subunit 4	protein-coding
mm_18866.1	chr2	75713021	75713039	-	1	NA	Intergenic	Intergenic	-8367	NM_010902	18024	Mm.1025	NM_010902	ENSMUSG00000015839	Nfe2l2	Nrf2	nuclear factor, erythroid derived 2, like 2	protein-coding
mm_111682.1	chr12	103391554	103391557	-	1	NA	intron (NM_026580, intron 1 of 5)	MLT1C|LTR|ERVL-MaLR	2873	NM_001177841	68149	Mm.127378	NM_026580	ENSMUSG00000021203	Otub2	2010015L18Rik|4930586I02Rik|AI413508|AW557219|OTB2|OTU2	OTU domain, ubiquitin aldehyde binding 2	protein-coding
mm_91041.1	chr10	18545848	18545858	-	1	NA	5' UTR (NM_019487, exon 1 of 4)	5' UTR (NM_019487, exon 1 of 4)	223	NM_019487	56016	Mm.35551	NM_019487	ENSMUSG00000019853	Hebp2	SOUL	heme binding protein 2	protein-coding
mm_36849.1	chr4	106738015	106738027	-	1	NA	intron (NM_146149, intron 2 of 7)	intron (NM_146149, intron 2 of 7)	4106	NM_146149	230579	Mm.222956	NM_146149	ENSMUSG00000034871	Fam151a	2010309H15Rik	family with sequence simliarity 151, member A	protein-coding
mm_149402.1	chr19	11392664	11392679	+	1	NA	exon (NM_001310331, exon 7 of 7)	exon (NM_001310331, exon 7 of 7)	-14990	NM_029499	64380	Mm.440715	NM_029499	ENSMUSG00000024675	Ms4a4c	5830413L19Rik|AI449185|Ms4a9	membrane-spanning 4-domains, subfamily A, member 4C	protein-coding
mm_141453.1	chr17	30396056	30396060	-	1	NA	non-coding (NR_030688, exon 1 of 1)	non-coding (NR_030688, exon 1 of 1)	122	NR_030688	623169	Mm.440508	NR_030688		Gm6402	EG623169	ribosomal protein S17 pseudogene	pseudo
mm_73017.1	chr8	93968937	93968953	+	1	NA	3' UTR (NM_010308, exon 9 of 9)	3' UTR (NM_010308, exon 9 of 9)	43695	NM_011787	23802	Mm.34641	NM_011787	ENSMUSG00000031751	Amfr	gp78	autocrine motility factor receptor	protein-coding
mm_49380.1	chr6	24603324	24603341	+	1	NA	exon (NM_053098, exon 2 of 3)	exon (NM_053098, exon 2 of 3)	5561	NM_053098	93677	Mm.332941	NM_053098	ENSMUSG00000029683	Lmod2	C-Lmod	leiomodin 2 (cardiac)	protein-coding
mm_133229.1	chr16	76814521	76814524	+	1	NA	Intergenic	Intergenic	196359	NR_040573	76601	Mm.396217	NR_040573	ENSMUSG00000100857	1700041M19Rik	-	RIKEN cDNA 1700041M19 gene	ncRNA
mm_1585.1	chr1	74295664	74295672	+	1	NA	intron (NM_027154, intron 1 of 11)	intron (NM_027154, intron 1 of 11)	8668	NM_027154	69660	Mm.261182	NM_027154	ENSMUSG00000006301	Tmbim1	2310061B02Rik|AA960455|AU024746|C78899|RECS1|Tmbib1|mKIAA4161	transmembrane BAX inhibitor motif containing 1	protein-coding
mm_130089.1	chr15	89379265	89379300	-	1	NA	promoter-TSS (NM_001013022)	promoter-TSS (NM_001013022)	-28	NM_001013022	70113	Mm.247273	NM_001013022	ENSMUSG00000047394	Odf3b	2010001J22Rik	outer dense fiber of sperm tails 3B	protein-coding
mm_154849.1	chrX	20483467	20483467	+	1	NA	intron (NM_199317, intron 6 of 12)	L1MDa|LINE|L1	57779	NM_001289684	382207	Mm.281517	NM_199317	ENSMUSG00000037315	Jade3	5730598B06|AI851988|AW544806|Phf16|mKIAA0215	jade family PHD finger 3	protein-coding
mm_40239.1	chr5	37735527	37735545	+	1	NA	promoter-TSS (NM_001081106)	promoter-TSS (NM_001081106)	17	NM_001081106	231162	Mm.76407	NM_001081106	ENSMUSG00000062329	Cytl1	4930443F05Rik|4Cytl1|C17|Cyt1|Gm147	cytokine-like 1	protein-coding
mm_166803.1	chr7	4170938	4170941	+	1	NA	Intergenic	RLTR48A|LTR|ERV1	-6240	NM_021454	58804	Mm.34268	NM_021454	ENSMUSG00000063838	Cdc42ep5	1700027J19Rik|2010007O02Rik|Borg3|C85526|CEP5	CDC42 effector protein (Rho GTPase binding) 5	protein-coding
mm_129089.1	chr15	75909544	75909567	-	1	NA	promoter-TSS (NM_001285431)	promoter-TSS (NM_001285431)	1	NM_001285431	66656	Mm.258927	NM_023240	ENSMUSG00000055762	Eef1d	EF-1-delta	eukaryotic translation elongation factor 1 delta (guanine nucleotide exchange protein)	protein-coding
mm_85106.1	chr9	95402239	95402242	-	1	NA	3' UTR (NM_018763, exon 2 of 2)	3' UTR (NM_018763, exon 2 of 2)	5030	NM_018763	54371	Mm.212446	NM_018763	ENSMUSG00000033350	Chst2	AI428561|AW121776|C130041E03Rik|Chts2|GST-2|GlcNAc6ST|Gn6st	carbohydrate sulfotransferase 2	protein-coding
mm_170048.1	chr17	25514355	25514359	-	1	NA	Intergenic	RMER19B|LTR|ERVK	-17069	NM_001191008	20609	Mm.353282	NM_011425	ENSMUSG00000050824	Sstr5	Smstr5|sst5	somatostatin receptor 5	protein-coding
mm_93361.1	chr10	103144969	103144979	-	1	NA	intron (NM_001163559, intron 20 of 25)	intron (NM_001163559, intron 20 of 25)	91348	NM_001163559	74978	Mm.483817	NM_029134	ENSMUSG00000019892	Lrriq1	4930503E15Rik|Gm1557	leucine-rich repeats and IQ motif containing 1	protein-coding
mm_83744.1	chr9	51103982	51103994	-	1	NA	promoter-TSS (NR_029655)	promoter-TSS (NR_029655)	-343	NR_029655	723849		NR_029655	ENSMUSG00000065492	Mir34b	Mirn34b|mir-34b|mmu-mir-34b	microRNA 34b	ncRNA
mm_24653.1	chr3	94399273	94399333	+	1	NA	promoter-TSS (NM_177250)	promoter-TSS (NM_177250)	84	NM_177250	320747	Mm.213001	NM_177250	ENSMUSG00000044505	Lingo4	A530050P17Rik|LERN4|Lrrn6d	leucine rich repeat and Ig domain containing 4	protein-coding
mm_17688.1	chr2	32323464	32323492	-	1	NA	intron (NM_001301737, intron 12 of 21)	intron (NM_001301737, intron 12 of 21)	5018	NR_029811	387239		NR_029811	ENSMUSG00000092807	Mir199b	Mirn199b|mir-199b	microRNA 199b	ncRNA
mm_43142.1	chr5	125441619	125441667	+	1	NA	promoter-TSS (NM_029752)	promoter-TSS (NM_029752)	75	NM_029752	76809	Mm.290720	NM_029752	ENSMUSG00000037905	Bri3bp	2410150I18Rik|AI841257|AW742481	Bri3 binding protein	protein-coding
mm_44615.1	chr5	25498775	25498812	-	1	NA	promoter-TSS (NM_001081383)	promoter-TSS (NM_001081383)	-10	NM_001081383	231051	Mm.332268	NM_001081383	ENSMUSG00000038056	Kmt2c	E330008K23Rik|HALR|Mll3|mKIAA1506	lysine (K)-specific methyltransferase 2C	protein-coding
mm_89884.1	chr10	108434177	108434194	+	1	NA	Intergenic	Intergenic	101996	NM_054056	114774	Mm.391419	NM_054056	ENSMUSG00000035873	Pawr	2310001G03Rik|PAR4|Par-4	PRKC, apoptosis, WT1, regulator	protein-coding
mm_69136.1	chr7	127042394	127042414	-	1	NA	promoter-TSS (NM_145588)	promoter-TSS (NM_145588)	16	NM_145588	110033	Mm.286488	NM_145588	ENSMUSG00000030677	Kif22	AU021460|C81217|Kid|Kif22a	kinesin family member 22	protein-coding
mm_63276.1	chr7	126763134	126763148	+	1	NA	exon (NM_011952, exon 3 of 9)	exon (NM_011952, exon 3 of 9)	-3273	NM_024228	68616	Mm.246881	NM_024228	ENSMUSG00000030703	Gdpd3	1110015E22Rik	glycerophosphodiester phosphodiesterase domain containing 3	protein-coding
mm_129584.1	chr15	79742494	79742511	-	1	NA	promoter-TSS (NM_194342)	promoter-TSS (NM_194342)	34	NM_194342	223697	Mm.202715	NM_194342	ENSMUSG00000042524	Sun2	B230369L08Rik|C030011B15|Unc84b	Sad1 and UNC84 domain containing 2	protein-coding
mm_120926.1	chr14	76476914	76476930	+	1	NA	intron (NM_001310646, intron 3 of 4)	intron (NM_001310646, intron 3 of 4)	-11514	NM_001177751	21807	Mm.153272	NM_009366	ENSMUSG00000022010	Tsc22d1	AA589566|AW105905|Egr5|TSC-22|Tgfb1i4|Tsc|Tsc22	TSC22 domain family, member 1	protein-coding
mm_65034.1	chr7	18556813	18556825	-	1	NA	3' UTR (NM_001037168, exon 5 of 5)	3' UTR (NM_001037168, exon 5 of 5)	10486	NM_001037168	545925	Mm.440302	NM_001037168	ENSMUSG00000070797	Psg27	EG545925|cea15	pregnancy-specific glycoprotein 27	protein-coding
mm_42381.1	chr5	114932959	114932971	+	1	NA	intron (NM_145209, intron 5 of 6)	intron (NM_145209, intron 5 of 6)	-9237	NM_028211	72357	Mm.292672	NM_028211	ENSMUSG00000029559	2210016L21Rik	-	RIKEN cDNA 2210016L21 gene	protein-coding
mm_92809.1	chr10	81385245	81385250	-	1	NA	intron (NM_133964, intron 1 of 4)	intron (NM_133964, intron 1 of 4)	819	NM_133964	102115	Mm.294975	NM_133964	ENSMUSG00000078440	Dohh	1110033C18Rik|AI585913|AL022869|Hlrc1	deoxyhypusine hydroxylase/monooxygenase	protein-coding
mm_96272.1	chr11	62842756	62842760	+	1	NA	3' UTR (NM_053169, exon 6 of 6)	3' UTR (NM_053169, exon 6 of 6)	-4365	NM_001033669	213980	Mm.482259	NM_001033669	ENSMUSG00000090173	Fbxw10	Fbw10|HREP|SM25H2|SM2SH2	F-box and WD-40 domain protein 10	protein-coding
mm_173303.1	chrY	68824337	68824337	-	1	NA	Intergenic	Intergenic	-1484290	NM_001160135	100039574	Mm.458579	NM_001160135	ENSMUSG00000094739	Gm20806	-	predicted gene, 20806	protein-coding
mm_45996.1	chr5	90639649	90639662	-	1	NA	intron (NM_001310656, intron 1 of 10)	intron (NM_001310656, intron 1 of 10)	872	NM_028478	73246	Mm.30172	NM_028478	ENSMUSG00000029370	Rassf6	1600016B17Rik	Ras association (RalGDS/AF-6) domain family member 6	protein-coding
mm_128693.1	chr15	62039160	62039172	-	1	NA	promoter-TSS (NR_132746)	promoter-TSS (NR_132746)	-91	NR_132746	19296	Mm.4608	NM_011222	ENSMUSG00000097039	Pvt1	Ayu21-84Imeg|Gt(pU21)84Imeg|Mis-1|Mlvi-1|Pvt-1	plasmacytoma variant translocation 1	ncRNA
mm_101716.1	chr11	42182094	42182104	-	1	NA	intron (NM_010250, intron 1 of 9)	intron (NM_010250, intron 1 of 9)	831	NM_010250	14394	Mm.439668	NM_010250	ENSMUSG00000010803	Gabra1	Gabra-1	gamma-aminobutyric acid (GABA) A receptor, subunit alpha 1	protein-coding
mm_61495.1	chr7	75752593	75752605	+	1	NA	3' UTR (NM_029332, exon 37 of 37)	3' UTR (NM_029332, exon 37 of 37)	-95739	NM_001122780	207952	Mm.206223	NM_029652	ENSMUSG00000055652	Klhl25	2810402K13Rik|BC027373|Enc-1	kelch-like 25	protein-coding
mm_12253.1	chr2	68905870	68905885	+	1	NA	intron (NM_172856, intron 1 of 9)	intron (NM_172856, intron 1 of 9)	44436	NM_001347161	241447	Mm.222222	NM_172856	ENSMUSG00000027035	Cers6	4732462C07Rik|AW544719|Lass6|T1L	ceramide synthase 6	protein-coding
mm_19371.1	chr2	91183842	91183899	-	1	NA	promoter-TSS (NM_145527)	promoter-TSS (NM_145527)	-823	NM_145527	228355	Mm.36410	NM_145527	ENSMUSG00000040687	Madd	9630059K23Rik|IG20	MAP-kinase activating death domain	protein-coding
mm_71141.1	chr8	39046074	39046082	+	1	NA	intron (NM_030254, intron 1 of 7)	intron (NM_030254, intron 1 of 7)	40211	NM_030254	80286	Mm.272722	NM_030254	ENSMUSG00000039530	Tusc3	AU022242|BC003311|N33	tumor suppressor candidate 3	protein-coding
mm_121263.1	chr14	103073346	103073359	+	1	NA	exon (NM_001033242, exon 3 of 4)	exon (NM_001033242, exon 3 of 4)	3136	NM_001033242	211286	Mm.295289	NM_001033242	ENSMUSG00000022125	Cln5	A730075N08Rik	ceroid-lipofuscinosis, neuronal 5	protein-coding
mm_7048.1	chr1	87127125	87127128	-	1	NA	exon (NM_007432, exon 9 of 11)	exon (NM_007432, exon 9 of 11)	2118	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_56853.1	chr6	118139095	118139158	-	1	NA	promoter-TSS (NM_030165)	promoter-TSS (NM_030165)	14	NM_030165	78752	Mm.300317	NM_030165	ENSMUSG00000042042	Csgalnact2	4632415D10Rik|Galnact2	chondroitin sulfate N-acetylgalactosaminyltransferase 2	protein-coding
mm_150447.1	chr19	38055059	38055075	+	1	NA	promoter-TSS (NM_001164362)	promoter-TSS (NM_001164362)	25	NM_001164362	74107	Mm.9916	NM_028293	ENSMUSG00000024989	Cep55	1200008O12Rik|2700032M20Rik	centrosomal protein 55	protein-coding
mm_13929.1	chr2	120977149	120977185	+	1	NA	5' UTR (NM_175285, exon 1 of 14)	5' UTR (NM_175285, exon 1 of 14)	105	NM_175285	96957	Mm.315212	NM_175285	ENSMUSG00000054484	Tmem62	B830009D23Rik|C77355	transmembrane protein 62	protein-coding
mm_11088.1	chr2	27886385	27886395	+	1	NA	promoter-TSS (NM_015734)	promoter-TSS (NM_015734)	-35	NM_015734	12831	Mm.7281	NM_015734	ENSMUSG00000026837	Col5a1	AI413331	collagen, type V, alpha 1	protein-coding
mm_150589.1	chr19	40665214	40665225	+	1	NA	intron (NM_009848, intron 1 of 9)	B1_Mus2|SINE|Alu	5449	NM_009848	12495	Mm.2824	NM_009848	ENSMUSG00000048120	Entpd1	2610206B08Rik|AA408691|Cd39|NTPDase-1	ectonucleoside triphosphate diphosphohydrolase 1	protein-coding
mm_89969.1	chr10	111485348	111485358	+	1	NA	intron (NM_001146707, intron 1 of 13)	intron (NM_001146707, intron 1 of 13)	4736	NM_001146707	53605	Mm.290407	NM_015781	ENSMUSG00000058799	Nap1l1	AA407126|AI256722|D10Ertd68e|NAP-1	nucleosome assembly protein 1-like 1	protein-coding
mm_24175.1	chr3	88575826	88575852	+	1	NA	Intergenic	RLTR11A2|LTR|ERVK	-3832	NM_025448	66256	Mm.7091	NM_025448	ENSMUSG00000041355	Ssr2	1500032E05Rik|AI315033|AU020133|TLAP|TRAPB|TRAPbeta	signal sequence receptor, beta	protein-coding
mm_13116.1	chr2	91650170	91650237	+	1	NA	promoter-TSS (NM_001145902)	promoter-TSS (NM_001145902)	85	NR_027371	228359	Mm.22413	NM_146124	ENSMUSG00000027247	Arhgap1	B230365D05Rik|C76222|Cdc42GAP|p50rhoGAP	Rho GTPase activating protein 1	protein-coding
mm_110210.1	chr12	28552394	28552404	-	1	NA	Intergenic	Intergenic	-4062	NM_001177964	68511	Mm.310284	NM_001177964	ENSMUSG00000020633	Dcdc2c	1110015M06Rik	doublecortin domain containing 2C	protein-coding
mm_72629.1	chr8	84660404	84660422	+	1	NA	TTS (NM_010499)	TTS (NM_010499)	2439	NM_010499	15936	Mm.399	NM_010499	ENSMUSG00000053560	Ier2	AI317238|Ch1|Pip92	immediate early response 2	protein-coding
mm_137204.1	chr17	23942370	23942374	+	1	NA	intron (NM_011321, intron 1 of 3)	intron (NM_011321, intron 1 of 3)	376	NM_011321	20234	Mm.390958	NM_011321	ENSMUSG00000024128	Sbp	AV082137|AV082259|p25	spermine binding protein	protein-coding
mm_154565.1	chrX	6415726	6415730	+	1	NA	promoter-TSS (NM_001313764)	promoter-TSS (NM_001313764)	-14	NM_001313764	208431	Mm.23208	NM_001040459	ENSMUSG00000068270	Shroom4	D430043L16Rik|Gm724|Shrm4	shroom family member 4	protein-coding
mm_38803.1	chr4	148159809	148159819	-	1	NA	promoter-TSS (NM_176848)	promoter-TSS (NM_176848)	-225	NM_001161851	230903	Mm.220327	NM_173401	ENSMUSG00000029001	Fbxo44	5730411K09|AV001623|FBG3|FBX30|Fbx6a|Fbxo6a	F-box protein 44	protein-coding
mm_34344.1	chr4	144519815	144519835	+	1	NA	promoter-TSS (NM_198662)	promoter-TSS (NM_198662)	3	NM_198662	381572	Mm.184290	NM_198662	ENSMUSG00000028593	9430007A20Rik	Aadacl4|Gm1034	RIKEN cDNA 9430007A20 gene	protein-coding
mm_143644.1	chr17	79354990	79355000	-	1	NA	promoter-TSS (NM_026514)	promoter-TSS (NM_026514)	96	NM_026514	260409	Mm.140601	NM_026514	ENSMUSG00000036533	Cdc42ep3	3200001F04Rik|AA986861|Borg2|Cep3|UB1	CDC42 effector protein (Rho GTPase binding) 3	protein-coding
mm_27002.1	chr3	25840879	25840882	-	1	NA	intron (NM_001163387, intron 3 of 5)	intron (NM_001163387, intron 3 of 5)	312427	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_83970.1	chr9	57158289	57158338	-	1	NA	promoter-TSS (NM_025417)	promoter-TSS (NM_025417)	-14	NM_025417	66199	Mm.41687	NM_025417	ENSMUSG00000032299	Commd4	1110039H05Rik	COMM domain containing 4	protein-coding
mm_105019.1	chr11	100441059	100441110	-	1	NA	promoter-TSS (NM_001102650)	promoter-TSS (NM_001102650)	5	NM_026561	68106	Mm.28738	NM_026561	ENSMUSG00000017176	Nt5c3b	2610037D24Rik|AI841843|C330027I04Rik|Nt5c3l	5'-nucleotidase, cytosolic IIIB	protein-coding
mm_35390.1	chr4	33290134	33290169	-	1	NA	Intergenic	Intergenic	-20160	NM_011884	24018	Mm.240024	NM_011884	ENSMUSG00000028274	Rngtt	AU020997|HCE|MCE1	RNA guanylyltransferase and 5'-phosphatase	protein-coding
mm_126673.1	chr15	84538947	84538955	+	1	NA	Intergenic	Intergenic	18872	NM_177630	223732	Mm.6471	NM_177630	ENSMUSG00000055745	Ldoc1l	BC058638|Mar6|Mart6	leucine zipper, down-regulated in cancer 1-like	protein-coding
mm_131959.1	chr16	24488475	24488479	+	1	NA	intron (NM_001145952, intron 2 of 11)	intron (NM_001145952, intron 2 of 11)	40386	NM_001145952	210126	Mm.209385	NM_178665	ENSMUSG00000033306	Lpp	9430020K16Rik|AA959454|AU024130|B130055L10Rik|C79715|D630048H16	LIM domain containing preferred translocation partner in lipoma	protein-coding
mm_23433.1	chr3	59103564	59103581	+	1	NA	intron (NM_177855, intron 15 of 43)	intron (NM_177855, intron 15 of 43)	-1751	NM_173398	229323	Mm.123648	NM_173398	ENSMUSG00000050075	Gpr171	A630006E05|F730001G15Rik|H963	G protein-coupled receptor 171	protein-coding
mm_16259.1	chr2	173276684	173276711	+	1	NA	promoter-TSS (NM_022995)	promoter-TSS (NM_022995)	-164	NM_022995	65112	Mm.73682	NM_022995	ENSMUSG00000038400	Pmepa1	2210418I02Rik|AW455466|Erg1.2|N4wbp4|Stag1|Tmepai	prostate transmembrane protein, androgen induced 1	protein-coding
mm_9431.1	chr1	172501616	172501617	-	1	NA	intron (NM_178598, intron 1 of 4)	intron (NM_178598, intron 1 of 4)	1370	NM_178598	21346	Mm.271711	NM_178598	ENSMUSG00000026547	Tagln2	2700094C18Rik|SM22beta|Sm22B|Sm22a	transgelin 2	protein-coding
mm_2456.1	chr1	104768511	104768526	+	1	NA	promoter-TSS (NM_011800)	promoter-TSS (NM_011800)	-301	NM_011800	23836	Mm.103640	NM_011800	ENSMUSG00000050840	Cdh20	Cdh7	cadherin 20	protein-coding
mm_16515.1	chr2	181377557	181377571	+	1	NA	intron (NM_001048148, intron 1 of 5)	intron (NM_001048148, intron 1 of 5)	-3671	NM_023684	72699	Mm.440138	NM_023684	ENSMUSG00000090077	Lime1	2810038K19Rik|LIME	Lck interacting transmembrane adaptor 1	protein-coding
mm_73346.1	chr8	105373266	105373277	+	1	NA	Intergenic	Intergenic	-2110	NM_001081333	102075	Mm.32034	NM_175321	ENSMUSG00000014782	Plekhg4	4931414L13Rik|AI448583|mFLJ00068	pleckstrin homology domain containing, family G (with RhoGef domain) member 4	protein-coding
mm_77147.1	chr8	111599915	111599921	-	1	NA	intron (NM_001168623, intron 1 of 4)	intron (NM_001168623, intron 1 of 4)	30404	NM_027570	52815	Mm.27589	NM_027570	ENSMUSG00000031958	Ldhd	4733401P21Rik|D8Bwg1320e	lactate dehydrogenase D	protein-coding
mm_157971.1	chrX	93796291	93796294	-	1	NA	intron (NM_145630, intron 5 of 11)	intron (NM_145630, intron 5 of 11)	35803	NM_145630	236900	Mm.12775	NM_145630	ENSMUSG00000035232	Pdk3	2610001M10Rik|AI035637	pyruvate dehydrogenase kinase, isoenzyme 3	protein-coding
mm_37346.1	chr4	119962534	119962543	-	1	NA	intron (NM_010657, intron 1 of 8)	(ATGGTG)n|Simple_repeat|Simple_repeat	147860	NM_010657	16656	Mm.302758	NM_010657	ENSMUSG00000028634	Hivep3	2900056N03Rik|A130075N07|AI848000|E030045D18Rik|KBP-1|KBP1|Krc|Rc|Schnurri-3|Shn3|Zas3	human immunodeficiency virus type I enhancer binding protein 3	protein-coding
mm_98786.1	chr11	96926181	96926188	+	1	NA	Intergenic	Intergenic	-3140	NM_146026	217138	Mm.342551	NM_146026	ENSMUSG00000047040	Prr15l	Atad4|BC022765|E230006A12Rik	proline rich 15-like	protein-coding
mm_104259.1	chr11	88924633	88924643	-	1	NA	3' UTR (NM_029023, exon 13 of 13)	3' UTR (NM_029023, exon 13 of 13)	18710	NR_045955	73921	Mm.439148	NR_045955	ENSMUSG00000087338	Scpep1os	4930405P13Rik	serine carboxypeptidase 1, opposite strand	ncRNA
mm_79900.1	chr9	65371674	65371686	+	1	NA	exon (NM_001111145, exon 3 of 7)	exon (NM_001111145, exon 3 of 7)	10620	NM_001111145	208080	Mm.291862	NM_001111145	ENSMUSG00000086228	Ubap1l	Gm514	ubiquitin-associated protein 1-like	protein-coding
mm_69369.1	chr7	130646888	130646892	-	1	NA	intron (NM_001004468, intron 3 of 21)	intron (NM_001004468, intron 3 of 21)	-45666	NM_001347637	57752	Mm.86322	NM_021314	ENSMUSG00000030852	Tacc2	mKIAA4180	transforming, acidic coiled-coil containing protein 2	protein-coding
mm_75232.1	chr8	39629246	39629257	-	1	NA	intron (NM_001113326, intron 3 of 9)	ID_B1|SINE|B4	13427	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_105855.1	chr11	113751252	113751294	-	1	NA	promoter-TSS (NM_020006)	promoter-TSS (NM_020006)	-113	NM_020006	56699	Mm.293378	NM_020006	ENSMUSG00000041598	Cdc42ep4	1500041M20Rik|Borg4|CEP4	CDC42 effector protein (Rho GTPase binding) 4	protein-coding
mm_83413.1	chr9	44865403	44865405	-	1	NA	intron (NM_001081049, intron 1 of 35)	intron (NM_001081049, intron 1 of 35)	15870	NM_001081049	214162	Mm.2389	NM_001081049	ENSMUSG00000002028	Kmt2a	6430520K01|ALL-1|All1|Cxxc7|HRX|HTRX1|Mll|Mll1|mKIAA4050	lysine (K)-specific methyltransferase 2A	protein-coding
mm_109441.1	chr12	110738088	110738099	+	1	NA	exon (NM_027149, exon 1 of 3)	exon (NM_027149, exon 1 of 3)	161	NM_001347428	69641	Mm.475762	NM_027149	ENSMUSG00000037957	Wdr20	2310040A13Rik|AI549910|Wdr20a	WD repeat domain 20	protein-coding
mm_109886.1	chr12	5367919	5367921	-	1	NA	intron (NM_001164493, intron 1 of 13)	intron (NM_001164493, intron 1 of 13)	7762	NM_001164493	208439	Mm.388281	NM_001164493	ENSMUSG00000020627	Klhl29	A230106N14Rik|Gm68|Kbtbd9|mKIAA1921	kelch-like 29	protein-coding
mm_2345.1	chr1	92894899	92894901	+	1	NA	intron (NM_001347091, intron 4 of 17)	intron (NM_001347091, intron 4 of 17)	8006	NM_172850	241158	Mm.108280	NM_172850	ENSMUSG00000034212	Ankmy1	4930483I10Rik|ZMYND13	ankyrin repeat and MYND domain containing 1	protein-coding
mm_163046.1	chr11	55678211	55678211	+	1	NA	Intergenic	Intergenic	-70013	NM_020492	14654	Mm.89320	NM_020492	ENSMUSG00000000263	Glra1	nmf11|oscillator|ot|spasmodic|spd	glycine receptor, alpha 1 subunit	protein-coding
mm_32321.1	chr4	103619581	103619592	+	1	NA	Intergenic	Intergenic	237086	NR_040673	622167	Mm.244115	NR_040673	ENSMUSG00000086136	Gm12718	OTTMUSG00000008109	predicted gene 12718	ncRNA
mm_68349.1	chr7	106509212	106509226	-	1	NA	Intergenic	Intergenic	-68146	NR_003967	209380	Mm.461779	NM_001001318		Gm4759	EG209380	GTPase, very large interferon inducible 1 pseudogene	pseudo
mm_168342.1	chr11	120598173	120598183	-	1	NA	promoter-TSS (NM_025389)	promoter-TSS (NM_025389)	187	NM_011568	21681	Mm.1886	NM_011568	ENSMUSG00000025134	Alyref	ALY|REF1|Refbp1|Thoc4	Aly/REF export factor	protein-coding
mm_71272.1	chr8	40919518	40919529	+	1	NA	3' UTR (NM_001044740, exon 12 of 12)	3' UTR (NM_001044740, exon 12 of 12)	-6710	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_3835.1	chr1	159992573	159992574	+	1	NA	Intergenic	Intergenic	-51807	NR_028111	67647	Mm.171518	NM_001024470	ENSMUSG00000090394	4930523C07Rik	-	RIKEN cDNA 4930523C07 gene	protein-coding
mm_146191.1	chr18	76111845	76111854	+	1	NA	intron (NM_145356, intron 3 of 4)	intron (NM_145356, intron 3 of 4)	-13378	NR_045365	73009	Mm.443541	NR_045365		2900057B20Rik	-	RIKEN cDNA 2900057B20 gene	ncRNA
mm_22084.1	chr2	168767037	168767045	-	1	NA	5' UTR (NM_201396, exon 1 of 3)	5' UTR (NM_201396, exon 1 of 3)	160	NM_201395	99377	Mm.434054	NM_175303	ENSMUSG00000027547	Sall4	5730441M18Rik|AA407717|AL022809|AW536104|C330011P20Rik|C78083|C78563|Tex20	sal-like 4 (Drosophila)	protein-coding
mm_166631.1	chr6	78467530	78467534	-	1	NA	exon (NM_011260, exon 4 of 6)	exon (NM_011260, exon 4 of 6)	1342	NM_011260	19695	Mm.252385	NM_011260	ENSMUSG00000030017	Reg3g	AI449515|REG-3-gamma|reg III-gamma	regenerating islet-derived 3 gamma	protein-coding
mm_39814.1	chr5	30711578	30711586	+	1	NA	promoter-TSS (NM_023047)	promoter-TSS (NM_023047)	-313	NM_023047	65254	Mm.27732	NM_023047	ENSMUSG00000029168	Dpysl5	CRAM|CRMP-5|Crmp5	dihydropyrimidinase-like 5	protein-coding
mm_148425.1	chr19	3941549	3941557	+	1	NA	exon (NM_019449, exon 4 of 11)	exon (NM_019449, exon 4 of 11)	6367	NM_001161428	54445	Mm.262094	NM_019449	ENSMUSG00000036908	Unc93b1	Unc-93B1|Unc93b	unc-93 homolog B1 (C. elegans)	protein-coding
mm_114595.1	chr13	75764041	75764060	+	1	NA	exon (NM_138953, exon 8 of 12)	exon (NM_138953, exon 8 of 12)	56566	NM_138953	192657	Mm.21288	NM_138953	ENSMUSG00000001542	Ell2	-	elongation factor RNA polymerase II 2	protein-coding
mm_89775.1	chr10	100589111	100589131	+	1	NA	5' UTR (NM_175128, exon 1 of 7)	5' UTR (NM_175128, exon 1 of 7)	138	NM_175128	68281	Mm.268474	NM_175128	ENSMUSG00000046567	4930430F08Rik	4930571E09Rik|A730088G13Rik|AW551239|C430008C19Rik	RIKEN cDNA 4930430F08 gene	protein-coding
mm_151268.1	chr19	54513530	54513534	+	1	NA	Intergenic	MLT1A|LTR|ERVL-MaLR	468350	NM_007417	11551	Mm.235195	NM_007417	ENSMUSG00000033717	Adra2a	AW122659|Adra-2|Adra-2a|alpha(2A)AR|alpha2-C10|alpha2A|alpha2A-AR	adrenergic receptor, alpha 2a	protein-coding
mm_14818.1	chr2	146838989	146839001	+	1	NA	Intergenic	Intergenic	-16894	NM_001033298	228730	Mm.292352	NM_001033298	ENSMUSG00000074749	Kiz	Gm114|Ncrna00153|Plk1s1	kizuna centrosomal protein	protein-coding
mm_73252.1	chr8	104322379	104322389	+	1	NA	exon (NM_028524, exon 1 of 4)	exon (NM_028524, exon 1 of 4)	157	NM_028524	75502	Mm.232593	NM_028524	ENSMUSG00000035785	Cmtm2b	1700013O04Rik|Cklfsf22|Cklfsf2b	CKLF-like MARVEL transmembrane domain containing 2B	protein-coding
mm_33858.1	chr4	135895415	135895476	+	1	NA	5' UTR (NM_009924, exon 1 of 2)	5' UTR (NM_009924, exon 1 of 2)	256	NM_009924	12802	Mm.297251	NM_009924	ENSMUSG00000062585	Cnr2	CB-2|CB2|CB2-R	cannabinoid receptor 2 (macrophage)	protein-coding
mm_73411.1	chr8	106052722	106052748	+	1	NA	intron (NM_001301176, intron 13 of 14)	B1_Mus1|SINE|Alu	-6868	NM_010901	18021	Mm.383185	NM_010901	ENSMUSG00000031902	Nfatc3	C80703|D8Ertd281e|NFAT4|NFATx	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 3	protein-coding
mm_70567.1	chr8	13140129	13140149	+	1	NA	intron (NM_146207, intron 15 of 19)	intron (NM_146207, intron 15 of 19)	4067	NR_106032	102465645		NR_106032	ENSMUSG00000098532	Mir7065	Gm27871|mmu-mir-7065	microRNA 7065	ncRNA
mm_85807.1	chr9	110307717	110307725	-	1	NA	intron (NM_001081381, intron 1 of 6)	intron (NM_001081381, intron 1 of 6)	2529	NM_001081381	72341	Mm.374250	NM_001081381	ENSMUSG00000054836	Elp6	2610001P13Rik|2610002I17Rik|AV159994|Tmem103	elongator acetyltransferase complex subunit 6	protein-coding
mm_143599.1	chr17	75551791	75551834	-	1	NA	5' UTR (NM_133747, exon 1 of 8)	5' UTR (NM_133747, exon 1 of 8)	134	NM_133747	72722	Mm.24641	NM_133747	ENSMUSG00000002017	Fam98a	2810405J04Rik|AL024114	family with sequence similarity 98, member A	protein-coding
mm_122012.1	chr14	27271423	27271429	-	1	NA	intron (NM_001289686, intron 4 of 12)	intron (NM_001289686, intron 4 of 12)	33416	NM_027871	71704	Mm.248606	NM_027871	ENSMUSG00000021895	Arhgef3	1200004I24Rik|9830169H03Rik|C76747|Xpln	Rho guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_162508.1	chr1	150748617	150748618	+	1	NA	intron (NM_001024720, intron 21 of 106)	intron (NM_001024720, intron 21 of 106)	244818	NM_001024720	545370	Mm.379425	NM_001024720	ENSMUSG00000066842	Hmcn1	EG545370|FIBL-6|Gm201	hemicentin 1	protein-coding
mm_4103.1	chr1	167598303	167598325	+	1	NA	promoter-TSS (NM_009107)	promoter-TSS (NM_009107)	-48	NM_009107	20183	Mm.3475	NM_009107	ENSMUSG00000015843	Rxrg	Nr2b3	retinoid X receptor gamma	protein-coding
mm_46644.1	chr5	108550176	108550208	-	1	NA	promoter-TSS (NM_007756)	promoter-TSS (NM_007756)	-165	NM_007756	12889	Mm.5195	NM_007756	ENSMUSG00000033615	Cplx1	921-S	complexin 1	protein-coding
mm_50636.1	chr6	51329853	51329865	+	1	NA	Intergenic	Intergenic	-49851	NR_110455	625167	Mm.389772	NR_110455	ENSMUSG00000107660	Gm6559	EG625167	predicted gene 6559	ncRNA
mm_30880.1	chr4	32239450	32239470	+	1	NA	Intergenic	CpG	-177975	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_169480.1	chr1	47086822	47086824	-	1	NA	Intergenic	Intergenic	-233314	NM_172653	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|mKIAA1265	solute carrier family 39 (zinc transporter), member 10	protein-coding
mm_94059.1	chr10	128337961	128337977	-	1	NA	intron (NM_026444, intron 1 of 10)	CpG	242	NM_026444	12974	Mm.58836	NM_026444	ENSMUSG00000005683	Cs	2610511A05Rik|9030605P22Rik|Ahl4|BB234005|Cis	citrate synthase	protein-coding
mm_66703.1	chr7	45920831	45920883	-	1	NA	promoter-TSS (NM_001146346)	promoter-TSS (NM_001146346)	-8	NM_001146346	13732	Mm.20829	NM_010129	ENSMUSG00000040212	Emp3	H-4|H4|HNMP-1|MI-35|Ymp	epithelial membrane protein 3	protein-coding
mm_76501.1	chr8	86764654	86764684	-	1	NA	Intergenic	LTR40b|LTR|ERVL	-18663	NM_009172	20437	Mm.324553	NM_009172	ENSMUSG00000036840	Siah1a	AA982064|AI853500|Sinh1a	seven in absentia 1A	protein-coding
mm_27087.1	chr3	30013350	30013369	-	1	NA	promoter-TSS (NM_007963)	promoter-TSS (NM_007963)	-155	NM_007963	14013	Mm.56965	NM_007963	ENSMUSG00000027684	Mecom	D630039M04Rik|Evi-1|Evi1|Jbo|Mds|Mds1|Mds1-Evi1|Prdm3|Znfpr1b1	MDS1 and EVI1 complex locus	protein-coding
mm_79624.1	chr9	59291549	59291555	+	1	NA	promoter-TSS (NM_028121)	promoter-TSS (NM_028121)	-20	NM_028121	72141	Mm.22456	NM_028121	ENSMUSG00000025236	Adpgk	2610017G09Rik|Adp-gk|C77577	ADP-dependent glucokinase	protein-coding
mm_168394.1	chr1	128267058	128267058	-	1	NA	intron (NM_026390, intron 9 of 12)	RLTRETN_Mm|LTR|ERVK	22877	NM_026390	67812	Mm.293321	NM_026390	ENSMUSG00000026353	Ubxn4	1300013G12Rik|Ubxd2|mKIAA0242	UBX domain protein 4	protein-coding
mm_31904.1	chr4	84429455	84429472	+	1	NA	intron (NM_172870, intron 2 of 5)	intron (NM_172870, intron 2 of 5)	245623	NM_172870	242509	Mm.190774	NM_172870	ENSMUSG00000028487	Bnc2	5031434M05Rik|8430420F16Rik	basonuclin 2	protein-coding
mm_112807.1	chr13	20748348	20748348	+	1	NA	Intergenic	Intergenic	-45765	NM_001281854	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_154330.1	chrM	3065	3075	+	1	NA	NA	Intergenic	NA	NA								
mm_82337.1	chr9	10412301	10412303	-	1	NA	intron (NM_001170787, intron 3 of 24)	intron (NM_001170787, intron 3 of 24)	492424	NM_001033359	244682	Mm.187021	NM_001033359	ENSMUSG00000039488	Cntn5	6720426O10Rik|A830025P08Rik|Gm507|NB-2	contactin 5	protein-coding
mm_5460.1	chr1	36369095	36369107	-	1	NA	promoter-TSS (NM_172652)	promoter-TSS (NM_172652)	80	NM_172652	226976	Mm.24734	NM_172652	ENSMUSG00000010453	Kansl3	4632411B12Rik|4932435K23|AI431067|AI647574|C85723|Kiaa1310|mKIAA1310	KAT8 regulatory NSL complex subunit 3	protein-coding
mm_9665.1	chr1	177796675	177796677	-	1	NA	promoter-TSS (NM_007422)	promoter-TSS (NM_007422)	-167	NM_007422	11566	Mm.338021	NM_007422	ENSMUSG00000015961	Adss	AI314886|AS|Adss2	adenylosuccinate synthetase, non muscle	protein-coding
mm_140923.1	chr17	24220618	24220641	-	1	NA	intron (NM_028056, intron 1 of 9)	CpG-6044	140	NM_028056	72016	Mm.23881	NM_028056	ENSMUSG00000024118	1600002H07Rik	-	RIKEN cDNA 1600002H07 gene	protein-coding
mm_23129.1	chr3	37714709	37714709	+	1	NA	exon (NM_198657, exon 3 of 3)	exon (NM_198657, exon 3 of 3)	9651	NM_198657	381438	Mm.490549	NM_198657	ENSMUSG00000058174	Gm5148	EG381438	predicted gene 5148	protein-coding
mm_171763.1	chr5	107289493	107289495	-	1	NA	5' UTR (NM_011578, exon 1 of 17)	5' UTR (NM_011578, exon 1 of 17)	101	NM_011578	21814	Mm.200775	NM_011578	ENSMUSG00000029287	Tgfbr3	1110036H20Rik|AU015626|AW215636|TBRIII	transforming growth factor, beta receptor III	protein-coding
mm_63896.1	chr7	138848511	138848533	+	1	NA	intron (NM_026391, intron 2 of 8)	intron (NM_026391, intron 2 of 8)	2136	NM_026391	52432	Mm.258739	NM_026391	ENSMUSG00000041769	Ppp2r2d	1300017E19Rik|D7Ertd753e|MDS026	protein phosphatase 2, regulatory subunit B, delta	protein-coding
mm_38874.1	chr4	149682984	149682985	-	1	NA	intron (NM_001029837, intron 1 of 23)	MTB_Mm|LTR|ERVL-MaLR	-6895	NM_001164051	18707	Mm.229108	NM_008840	ENSMUSG00000039936	Pik3cd	2410099E07Rik|2610208K16Rik|AW545373|p110delta	phosphatidylinositol 3-kinase catalytic delta polypeptide	protein-coding
mm_64390.1	chr7	142488996	142489007	+	1	NA	intron (NM_001271508, intron 5 of 10)	intron (NM_001271508, intron 5 of 10)	-9835	NM_001347549	21957	Mm.389992	NM_011620	ENSMUSG00000061723	Tnnt3	fTnT	troponin T3, skeletal, fast	protein-coding
mm_68483.1	chr7	110982170	110982180	-	1	NA	5' UTR (NM_194464, exon 1 of 21)	5' UTR (NM_194464, exon 1 of 21)	286	NM_194464	17540	Mm.250023	NM_010826	ENSMUSG00000005611	Mrvi1	BB115629|Irag|Ris1	MRV integration site 1	protein-coding
mm_130833.1	chr15	101846994	101847002	-	1	NA	exon (NM_008473, exon 7 of 9)	exon (NM_008473, exon 7 of 9)	3788	NM_008473	16678	Mm.183137	NM_008473	ENSMUSG00000046834	Krt1	Krt-2.1|Krt2-1|Krt86	keratin 1	protein-coding
mm_113253.1	chr13	27849340	27849342	+	1	NA	promoter-TSS (NM_001045532)	promoter-TSS (NM_001045532)	-1	NM_001045532	666317		NM_001045532	ENSMUSG00000062551	Prl2c1	Ghd22	Prolactin family 2, subfamily c, member 1	protein-coding
mm_80197.1	chr9	72400344	72400352	+	1	NA	Intergenic	Intergenic	-38181	NM_008613	17427	Mm.387671	NM_008613	ENSMUSG00000032221	Mns1	AW546487	meiosis-specific nuclear structural protein 1	protein-coding
mm_3903.1	chr1	161766042	161766069	+	1	NA	Intergenic	Intergenic	22440	NM_001205243	14103	Mm.3355	NM_010177	ENSMUSG00000000817	Fasl	APT1LG1|CD178|CD95-L|CD95L|Fas-L|Faslg|Tnfsf6|Tnlg1a|gld	Fas ligand (TNF superfamily, member 6)	protein-coding
mm_83464.1	chr9	45264218	45264234	-	1	NA	intron (NR_136903, intron 4 of 5)	intron (NR_136903, intron 4 of 5)	2481	NR_106054	102466803		NR_106054	ENSMUSG00000098361	Mir7086	Gm27643|mmu-mir-7086	microRNA 7086	ncRNA
mm_158370.1	chrX	135025308	135025344	-	1	NA	non-coding (NR_040282, exon 4 of 4)	non-coding (NR_040282, exon 4 of 4)	11276	NR_040281	320606	Mm.439072	NR_040281	ENSMUSG00000089759	3632454L22Rik	-	RIKEN cDNA 3632454L22 gene	ncRNA
mm_28132.1	chr3	87112464	87112469	-	1	NA	intron (NM_001170985, intron 2 of 15)	intron (NM_001170985, intron 2 of 15)	62281	NM_001170985	170643	Mm.89552	NM_130867	ENSMUSG00000041734	Kirrel	6720469N11Rik|Kirrel1|Neph1	kin of IRRE like (Drosophila)	protein-coding
mm_75318.1	chr8	41400848	41400869	-	1	NA	exon (NM_013522, exon 6 of 9)	exon (NM_013522, exon 6 of 9)	16260	NM_013522	14300	Mm.217312	NM_013522	ENSMUSG00000031590	Frg1	-	FSHD region gene 1	protein-coding
mm_154327.1	chrM	2744	2761	+	1	NA	NA	Intergenic	NA	NA								
mm_42299.1	chr5	114597854	114597854	+	1	NA	intron (NM_001004180, intron 2 of 2)	B4|SINE|B4	29603	NM_001004180	433940	Mm.194212	NM_001004180	ENSMUSG00000041930	Fam222a	-	family with sequence similarity 222, member A	protein-coding
mm_11584.1	chr2	33176785	33176806	+	1	NA	intron (NM_001290572, intron 8 of 17)	intron (NM_001290572, intron 8 of 17)	-39166	NM_011923	26360	Mm.208919	NM_011923	ENSMUSG00000004105	Angptl2	AI593246|AW260363|Arp2	angiopoietin-like 2	protein-coding
mm_156219.1	chrX	134717944	134718018	+	1	NA	promoter-TSS (NM_030066)	promoter-TSS (NM_030066)	43	NM_001166379	78248	Mm.458522	NM_030066	ENSMUSG00000033460	Armcx1	3010033I09Rik|ALEX1	armadillo repeat containing, X-linked 1	protein-coding
mm_112080.1	chr12	112671181	112671198	-	1	NA	intron (NM_001331107, intron 2 of 13)	intron (NM_001331107, intron 2 of 13)	3087	NM_001165894	11651	Mm.6645	NM_009652	ENSMUSG00000001729	Akt1	Akt|LTR-akt|PKB|PKB/Akt|PKBalpha|Rac	thymoma viral proto-oncogene 1	protein-coding
mm_92451.1	chr10	77767351	77767358	-	1	NA	intron (NM_001287074, intron 1 of 11)	RMER17C|LTR|ERVK	3971	NM_001101630	100041261	Mm.477434	NM_001101630	ENSMUSG00000095817	Gm3238	-	predicted gene 3238	protein-coding
mm_42056.1	chr5	108683539	108683552	+	1	NA	3' UTR (NM_008325, exon 15 of 15)	3' UTR (NM_008325, exon 15 of 15)	-8180	NM_174870	231583	Mm.440571	NM_174870	ENSMUSG00000046959	Slc26a1	Sat1	solute carrier family 26 (sulfate transporter), member 1	protein-coding
mm_126288.1	chr15	79327584	79327594	+	1	NA	intron (NM_016915, intron 1 of 15)	intron (NM_016915, intron 1 of 15)	782	NM_016915	53357	Mm.155620	NM_016915	ENSMUSG00000042632	Pla2g6	BB112799|PNPLA9|iPLA(2)beta|iPLA2|iPLA2beta	phospholipase A2, group VI	protein-coding
mm_86203.1	chr9	119982861	119982869	-	1	NA	intron (NM_153287, intron 1 of 4)	intron (NM_153287, intron 1 of 4)	1793	NM_153287	215418	Mm.491094	NM_153287	ENSMUSG00000032515	Csrnp1	4931429D10Rik|Axud1|CSRNP-1|URAX1|taip-3	cysteine-serine-rich nuclear protein 1	protein-coding
mm_86104.1	chr9	115310286	115310296	-	1	NA	5' UTR (NM_024222, exon 1 of 16)	5' UTR (NM_024222, exon 1 of 16)	130	NM_024222	68292	Mm.296158	NM_024222	ENSMUSG00000032437	Stt3b	1300006C19Rik|Simp	STT3, subunit of the oligosaccharyltransferase complex, homolog B (S. cerevisiae)	protein-coding
mm_64942.1	chr7	16313970	16313987	-	1	NA	intron (NM_133234, intron 3 of 3)	CpG	4395	NM_133234	170770	Mm.7660	NM_133234	ENSMUSG00000002083	Bbc3	PUMA|PUMA/JFY1	BCL2 binding component 3	protein-coding
mm_21891.1	chr2	166155495	166155517	-	1	NA	promoter-TSS (NM_001252578)	promoter-TSS (NM_001252578)	177	NM_001252579	72043	Mm.1011	NM_028072	ENSMUSG00000006800	Sulf2	2010004N24Rik|AU020235|MSulf-2|mKIAA1247	sulfatase 2	protein-coding
mm_46980.1	chr5	115272884	115272903	-	1	NA	promoter-TSS (NM_016698)	promoter-TSS (NM_016698)	2	NM_001302448	50849	Mm.30051	NM_016698	ENSMUSG00000041740	Rnf10	AA675014|RIE2|mKIAA0262	ring finger protein 10	protein-coding
mm_121731.1	chr14	18239054	18239098	-	1	NA	promoter-TSS (NM_011584)	promoter-TSS (NM_011584)	30	NM_011584	353187	Mm.26587	NM_011584	ENSMUSG00000021775	Nr1d2	RVR|Rev-erb	nuclear receptor subfamily 1, group D, member 2	protein-coding
mm_23519.1	chr3	60603736	60603751	+	1	NA	exon (NM_001253711, exon 3 of 8)	exon (NM_001253711, exon 3 of 8)	102564	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_46612.1	chr5	107987004	107987055	-	1	NA	promoter-TSS (NM_026062)	promoter-TSS (NM_026062)	48	NM_026062	67266	Mm.277897	NM_026062	ENSMUSG00000029270	Fam69a	2900024C23Rik|AI315274	family with sequence similarity 69, member A	protein-coding
mm_130853.1	chr15	102004306	102004321	-	1	NA	promoter-TSS (NM_031170)	promoter-TSS (NM_031170)	29	NM_031170	16691	Mm.358618	NM_031170	ENSMUSG00000049382	Krt8	AA960620|AL022697|AU019895|Card2|EndoA|K8|Krt-2.8|Krt2-8	keratin 8	protein-coding
mm_103808.1	chr11	82991741	82991782	-	1	NA	promoter-TSS (NM_172796)	promoter-TSS (NM_172796)	69	NM_172796	237886	Mm.270253	NM_172796	ENSMUSG00000069793	Slfn9	9830137M10Rik	schlafen 9	protein-coding
mm_161862.1	chr18	32139570	32139570	-	1	NA	promoter-TSS (NM_001042767)	promoter-TSS (NM_001042767)	0	NM_001042767	19123	Mm.2786	NM_008934	ENSMUSG00000024386	Proc	PC	protein C	protein-coding
mm_76929.1	chr8	105936998	105937025	-	1	NA	intron (NM_013640, intron 4 of 7)	intron (NM_013640, intron 4 of 7)	1381	NM_013640	19171	Mm.787	NM_013640	ENSMUSG00000031897	Psmb10	Mecl-1|Mecl1	proteasome (prosome, macropain) subunit, beta type 10	protein-coding
mm_140702.1	chr17	14665627	14665630	-	1	NA	3' UTR (NM_011581, exon 22 of 22)	3' UTR (NM_011581, exon 22 of 22)	28634	NM_011581	21826	Mm.26688	NM_011581	ENSMUSG00000023885	Thbs2	TSP2|Thbs-2	thrombospondin 2	protein-coding
mm_172581.1	chr8	121379557	121379562	-	1	NA	Intergenic	RLTR15|LTR|ERVK	162395	NM_029597	76405	Mm.165697	NM_029597	ENSMUSG00000031809	1700018B08Rik	1700084O22Rik	RIKEN cDNA 1700018B08 gene	protein-coding
mm_10989.1	chr2	26294727	26294740	+	1	NA	promoter-TSS (NM_177841)	promoter-TSS (NM_177841)	-176	NM_177841	329366	Mm.77712	NM_177841	ENSMUSG00000048038	Ccdc187	4932418E24Rik	coiled-coil domain containing 187	protein-coding
mm_78450.1	chr9	32224458	32224497	+	1	NA	5' UTR (NM_177379, exon 1 of 13)	5' UTR (NM_177379, exon 1 of 13)	228	NM_177379	330914	Mm.46683	NM_177379	ENSMUSG00000041444	Arhgap32	3426406O18Rik|Gc-gap|Grit|Px-rics|Rics|mKIAA0712|p200Rhogap|p250Gap	Rho GTPase activating protein 32	protein-coding
mm_72325.1	chr8	78589400	78589401	+	1	NA	intron (NM_001009981, intron 5 of 10)	intron (NM_001009981, intron 5 of 10)	80072	NM_001282108	76775	Mm.334631	NM_029736	ENSMUSG00000031684	Slc10a7	2410193C02Rik|P7	solute carrier family 10 (sodium/bile acid cotransporter family), member 7	protein-coding
mm_26187.1	chr3	138415461	138415468	+	1	NA	promoter-TSS (NM_011996)	promoter-TSS (NM_011996)	-33	NM_011996	26876	Mm.158750	NM_011996	ENSMUSG00000037797	Adh4	Adh2	alcohol dehydrogenase 4 (class II), pi polypeptide	protein-coding
mm_60356.1	chr7	44384804	44384844	+	1	NA	5' UTR (NM_016663, exon 2 of 11)	5' UTR (NM_016663, exon 2 of 11)	698	NM_016663	20981	Mm.4824	NM_016663	ENSMUSG00000030731	Syt3	AI385753|sytIII	synaptotagmin III	protein-coding
mm_38182.1	chr4	135272782	135272792	-	1	NA	promoter-TSS (NM_013885)	promoter-TSS (NM_013885)	-27	NM_013885	29876	Mm.257765	NM_013885	ENSMUSG00000037242	Clic4	D0Jmb3|TU-74|mc3s5|mtCLIC	chloride intracellular channel 4 (mitochondrial)	protein-coding
mm_18749.1	chr2	73386331	73386343	-	1	NA	5' UTR (NM_001276443, exon 1 of 17)	5' UTR (NM_001276443, exon 1 of 17)	143	NM_001276443	68526	Mm.451014	NM_001080707	ENSMUSG00000041762	Gpr155	1110017O10Rik|DEPDC3|F730029F15Rik|PGR22	G protein-coupled receptor 155	protein-coding
mm_110974.1	chr12	76962160	76962172	-	1	NA	promoter-TSS (NM_001146176)	promoter-TSS (NM_001146176)	82	NM_008558	17187	Mm.268548	NM_008558	ENSMUSG00000059436	Max	AA960152|AI875693|bHLHd4|bHLHd5|bHLHd6|bHLHd7|bHLHd8	Max protein	protein-coding
mm_26980.1	chr3	25590391	25590398	-	1	NA	intron (NM_001163387, intron 3 of 5)	intron (NM_001163387, intron 3 of 5)	562913	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_97666.1	chr11	79660638	79660648	+	1	NA	intron (NM_175543, intron 3 of 14)	CpG	14443	NR_045898	72218	Mm.443271	NR_045898	ENSMUSG00000086569	Rab11fip4os2	1700020F10Rik|4930542H20Rik|Rab11fib4os2	RAB11 family interacting protein 4 (class II), opposite strand 2	ncRNA
mm_28438.1	chr3	90490718	90490767	-	1	NA	intron (NM_133854, intron 1 of 3)	intron (NM_133854, intron 1 of 3)	271	NM_133854	20615	Mm.331182	NM_133854	ENSMUSG00000001018	Snapin	25kDa|AA407989|AV026596|Bloc1s7|Snap25bp|Snapap	SNAP-associated protein	protein-coding
mm_94527.1	chr11	9049099	9049110	+	1	NA	promoter-TSS (NM_001290520)	promoter-TSS (NM_001290520)	-113	NM_177576	194974	Mm.79210	NM_177576	ENSMUSG00000040985	Sun3	Sunc1	Sad1 and UNC84 domain containing 3	protein-coding
mm_55807.1	chr6	82939560	82939587	-	1	NA	exon (NM_011350, exon 1 of 14)	exon (NM_011350, exon 1 of 14)	196	NM_001308374	20355	Mm.270543	NM_011350	ENSMUSG00000000627	Sema4f	Sema W	sema domain, immunoglobulin domain (Ig), TM domain, and short cytoplasmic domain	protein-coding
mm_11308.1	chr2	30266570	30266592	+	1	NA	promoter-TSS (NM_001281829)	promoter-TSS (NM_001281829)	-140	NM_001281829	227696	Mm.297949	NM_172267	ENSMUSG00000079484	Phyhd1	-	phytanoyl-CoA dioxygenase domain containing 1	protein-coding
mm_159722.1	chr5	34915694	34915694	+	1	NA	promoter-TSS (NM_207277)	promoter-TSS (NM_207277)	-221	NM_207277	403174	Mm.291225	NM_207277	ENSMUSG00000051246	Msantd1	A930005I04Rik|Gm144	Myb/SANT-like DNA-binding domain containing 1	protein-coding
mm_40602.1	chr5	64320213	64320214	+	1	NA	intron (NM_001310611, intron 16 of 21)	intron (NM_001310611, intron 16 of 21)	89856	NM_001289514	57915	Mm.286353	NM_019636	ENSMUSG00000029174	Tbc1d1	1110062G02Rik|AI385682|AW555803|Nob1|Nobq1|Tbc1|mKIAA1108	TBC1 domain family, member 1	protein-coding
mm_124750.1	chr15	6632863	6632883	+	1	NA	intron (NM_011815, intron 5 of 17)	intron (NM_011815, intron 5 of 17)	53026	NM_011815	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_76758.1	chr8	95576246	95576256	-	1	NA	promoter-TSS (NM_001310539)	promoter-TSS (NM_001310539)	-644	NM_001310539	70993	Mm.486561	NM_027640	ENSMUSG00000048400	Prss54	4931432M23Rik|Klkbl4	protease, serine 54	protein-coding
mm_124045.1	chr14	77036980	77036988	-	1	NA	promoter-TSS (NM_172488)	promoter-TSS (NM_172488)	212	NM_001310649	108811	Mm.102168	NM_175369	ENSMUSG00000034795	Ccdc122	4933415L06Rik	coiled-coil domain containing 122	protein-coding
mm_132778.1	chr16	44786679	44786695	+	1	NA	intron (NM_021325, intron 1 of 6)	Lx7|LINE|L1	20951	NM_021325	57781	Mm.416152	NM_021325	ENSMUSG00000022667	Cd200r1	CD200R|Mox2r|OX2R	CD200 receptor 1	protein-coding
mm_34649.1	chr4	150852723	150852730	+	1	NA	intron (NR_040649, intron 1 of 3)	intron (NR_040649, intron 1 of 3)	2223	NR_040649	73348	Mm.396218	NR_040649	ENSMUSG00000078492	1700045H11Rik	-	RIKEN cDNA 1700045H11 gene	ncRNA
mm_102541.1	chr11	61267142	61267154	-	1	NA	promoter-TSS (NM_007437)	promoter-TSS (NM_007437)	38	NM_001331114	11671	Mm.398221	NM_007437	ENSMUSG00000010025	Aldh3a2	AI194803|Ahd-3|Ahd-3r|Ahd3|Ahd3-r|Aldh4|Aldh4-r|FALDH	aldehyde dehydrogenase family 3, subfamily A2	protein-coding
mm_72423.1	chr8	82774235	82774263	+	1	NA	promoter-TSS (NM_145600)	promoter-TSS (NM_145600)	-123	NM_145600	30932	Mm.269248	NM_145600	ENSMUSG00000031711	Zfp330	BC008086|Noa36|Znf330	zinc finger protein 330	protein-coding
mm_41261.1	chr5	89027999	89028012	+	1	NA	intron (NM_001197147, intron 3 of 25)	intron (NM_001197147, intron 3 of 25)	140745	NM_018760	54403	Mm.41044	NM_018760	ENSMUSG00000060961	Slc4a4	AI835705|NBC|NBC1	solute carrier family 4 (anion exchanger), member 4	protein-coding
mm_166485.1	chr5	146706622	146706624	+	1	NA	Intergenic	Intergenic	88333	NM_011669	22217	Mm.167971	NM_011669	ENSMUSG00000029640	Usp12	Ubh1	ubiquitin specific peptidase 12	protein-coding
mm_116494.1	chr13	44869688	44869714	-	1	NA	intron (NM_001205044, intron 4 of 18)	LSU-rRNA_Hsa|rRNA|rRNA	132395	NM_025772	94245	Mm.352311	NM_025772	ENSMUSG00000057531	Dtnbp1	5430437B18Rik|AW048963|Bloc1s8|dysbindin|sdy	dystrobrevin binding protein 1	protein-coding
mm_22613.1	chr3	14533908	14533920	+	1	NA	5' UTR (NM_028915, exon 1 of 19)	5' UTR (NM_028915, exon 1 of 19)	126	NM_028915	71710	Mm.257449	NM_028915	ENSMUSG00000027550	Lrrcc1	1200008A14Rik|4932441F23Rik|AI195358|AI447421	leucine rich repeat and coiled-coil domain containing 1	protein-coding
mm_148965.1	chr19	7494504	7494506	+	1	NA	promoter-TSS (NM_146091)	promoter-TSS (NM_146091)	67	NM_146091	109168	Mm.264016	NM_146091	ENSMUSG00000024759	Atl3	4633402C03Rik|5730596K20Rik|AI465397|AW228836	atlastin GTPase 3	protein-coding
mm_9777.1	chr1	181144134	181144183	-	1	NA	promoter-TSS (NM_026171)	promoter-TSS (NM_026171)	46	NM_026171	67459	Mm.263464	NM_026171	ENSMUSG00000026516	Nvl	1200009I24Rik	nuclear VCP-like	protein-coding
mm_155026.1	chrX	42067877	42067887	+	1	NA	promoter-TSS (NR_125870)	promoter-TSS (NR_125870)	46	NM_009688	11798	Mm.259879	NM_009688	ENSMUSG00000025860	Xiap	1110015C02Rik|Aipa|Api3|Birc4|IAP3|ILP-1|MIHA	X-linked inhibitor of apoptosis	protein-coding
mm_156747.1	chrX	159973686	159973700	+	1	NA	non-coding (NR_110970, exon 17 of 17)	non-coding (NR_110970, exon 17 of 17)	-14740	NM_001163085	270672	Mm.386889	NM_001163085	ENSMUSG00000031303	Map3k15	BC031147|MEKK15	mitogen-activated protein kinase kinase kinase 15	protein-coding
mm_4729.1	chr1	181352650	181352664	+	1	NA	promoter-TSS (NM_001160212)	promoter-TSS (NM_001160212)	29	NM_001160211	72978	Mm.338083	NM_028408	ENSMUSG00000026514	Cnih3	2900075G08Rik|CNIH-3	cornichon family AMPA receptor auxiliary protein 3	protein-coding
mm_157626.1	chrX	56597881	56597971	-	1	NA	promoter-TSS (NM_146234)	promoter-TSS (NM_146234)	-7	NM_146234	236792	Mm.291824	NM_146234	ENSMUSG00000061273	Mmgt1	9630048L06Rik|BC032271|Emc5|Mir5116|Tmem32|mir-5116	membrane magnesium transporter 1	protein-coding
mm_133151.1	chr16	70314478	70314498	+	1	NA	intron (NM_028803, intron 1 of 15)	CpG	539	NM_028803	74185	Mm.396102	NM_028803	ENSMUSG00000022707	Gbe1	2310045H19Rik|2810426P10Rik|D16Ertd536e	glucan (1,4-alpha-), branching enzyme 1	protein-coding
mm_147119.1	chr18	35740205	35740240	-	1	NA	intron (NM_028261, intron 1 of 7)	intron (NM_028261, intron 1 of 7)	332	NM_001289592	72512	Mm.45995	NM_028261	ENSMUSG00000024349	Tmem173	2610307O08Rik|ERIS|MPYS|Mita|STING	transmembrane protein 173	protein-coding
mm_105493.1	chr11	106159401	106159451	-	1	NA	5' UTR (NM_172397, exon 2 of 5)	5' UTR (NM_172397, exon 2 of 5)	716	NM_172397	67803	Mm.21687	NM_172397	ENSMUSG00000040699	Limd2	0610025L06Rik|AI413966	LIM domain containing 2	protein-coding
mm_25569.1	chr3	116629263	116629266	+	1	NA	3' UTR (NM_001289571, exon 16 of 16)	3' UTR (NM_001289571, exon 16 of 16)	-14677	NM_030016	229780	Mm.259648	NM_030016	ENSMUSG00000033439	Trmt13	4631408H19Rik|A330067P21|A930028L21Rik|Ccdc76	tRNA methyltransferase 13	protein-coding
mm_55893.1	chr6	83536470	83536476	-	1	NA	promoter-TSS (NM_009610)	promoter-TSS (NM_009610)	-222	NM_009610	11468	Mm.292865	NM_009610	ENSMUSG00000059430	Actg2	ACTA3|Act-4|Act4|SMGA	actin, gamma 2, smooth muscle, enteric	protein-coding
mm_77344.1	chr8	119574523	119574533	-	1	NA	promoter-TSS (NM_026648)	promoter-TSS (NM_026648)	672	NM_175185	72552	Mm.36756	NM_175185	ENSMUSG00000034189	Hsdl1	2700067E09Rik	hydroxysteroid dehydrogenase like 1	protein-coding
mm_170174.1	chr1	75715842	75715847	-	1	NA	Intergenic	B4A|SINE|B4	169578	NM_009208	20536	Mm.5053	NM_009208	ENSMUSG00000006576	Slc4a3	A930038D23Rik|Ae3	solute carrier family 4 (anion exchanger), member 3	protein-coding
mm_105831.1	chr11	113209634	113209654	-	1	NA	promoter-TSS (NR_040276)	promoter-TSS (NR_040276)	25	NR_040276	319871	Mm.383743	NR_040276	ENSMUSG00000085421	4732490B19Rik	-	RIKEN cDNA 4732490B19 gene	ncRNA
mm_5777.1	chr1	51478391	51478406	-	1	NA	promoter-TSS (NM_001310549)	promoter-TSS (NM_001310549)	1	NM_028696	109019	Mm.196290	NM_028696	ENSMUSG00000026107	Nabp1	4930434H03Rik|4930442A21Rik|4930488J04Rik|4933440J18Rik|5830411E10Rik|AI852561|Nbp1|Obfc2a|Ssb2	nucleic acid binding protein 1	protein-coding
mm_170476.1	chr19	11518562	11518572	+	1	NA	promoter-TSS (NM_027209)	promoter-TSS (NM_027209)	8	NM_027209	69774	Mm.436639	NM_027209	ENSMUSG00000024677	Ms4a6b	1810027D10Rik	membrane-spanning 4-domains, subfamily A, member 6B	protein-coding
mm_60180.1	chr7	43078032	43078040	+	1	NA	Intergenic	Intergenic	59238	NM_001105061	668612	Mm.469896	NM_001105061	ENSMUSG00000091528	Gm9268	EG668612|Vmn2r64	predicted gene 9268	protein-coding
mm_34363.1	chr4	144892814	144892835	+	1	NA	promoter-TSS (NM_001172424)	promoter-TSS (NM_001172424)	-3	NM_001172424	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding
mm_481.1	chr1	36761339	36761363	+	1	NA	promoter-TSS (NM_009539)	promoter-TSS (NM_009539)	-447	NM_009539	22637	Mm.8038	NM_009539	ENSMUSG00000026117	Zap70	Srk|ZAP-70|mrtle|mur	zeta-chain (TCR) associated protein kinase	protein-coding
mm_86864.1	chr10	21993878	21993886	+	1	NA	promoter-TSS (NM_011361)	promoter-TSS (NM_011361)	-8	NM_001161850	20393	Mm.28405	NM_011361	ENSMUSG00000019970	Sgk1	Sgk	serum/glucocorticoid regulated kinase 1	protein-coding
mm_12717.1	chr2	77725754	77725767	+	1	NA	intron (NM_178723, intron 1 of 9)	intron (NM_178723, intron 1 of 9)	-22488	NM_001113399	241494	Mm.490320	NM_178723	ENSMUSG00000027016	Zfp385b	B830010L13Rik|C130013B13Rik|Zfp533|Znf385b	zinc finger protein 385B	protein-coding
mm_34728.1	chr4	152178174	152178208	+	1	NA	promoter-TSS (NM_133348)	promoter-TSS (NM_133348)	91	NM_133348	70025	Mm.296191	NM_133348	ENSMUSG00000028937	Acot7	2410041A17Rik|Ach1|Act|Bach|CTE-IIa|Cte-II|Lach1	acyl-CoA thioesterase 7	protein-coding
mm_16452.1	chr2	180464042	180464065	+	1	NA	exon (NM_148933, exon 2 of 12)	exon (NM_148933, exon 2 of 12)	3075	NM_148933	108115	Mm.133687	NM_148933	ENSMUSG00000038963	Slco4a1	OATP-E|Slc21a12	solute carrier organic anion transporter family, member 4a1	protein-coding
mm_137208.1	chr17	24038237	24038249	+	1	NA	promoter-TSS (NM_175440)	promoter-TSS (NM_175440)	0	NM_175440	213171	Mm.133083	NM_175440	ENSMUSG00000050762	Prss27	CAPH2|Mpn|marapsin	protease, serine 27	protein-coding
mm_166904.1	chr7	28810965	28810972	+	1	NA	promoter-TSS (NM_177301)	promoter-TSS (NM_177301)	78	NM_177301	15388	Mm.9043	NM_177301	ENSMUSG00000015165	Hnrnpl	C79783|D830027H13Rik|Hnrpl	heterogeneous nuclear ribonucleoprotein L	protein-coding
mm_72152.1	chr8	72152563	72152584	+	1	NA	3' UTR (NM_001001491, exon 8 of 8)	3' UTR (NM_001001491, exon 8 of 8)	-8627	NM_023126	17274	Mm.162811	NM_023126	ENSMUSG00000003037	Rab8a	AA409338|Mel	RAB8A, member RAS oncogene family	protein-coding
mm_56248.1	chr6	90754282	90754292	-	1	NA	intron (NM_001134384, intron 1 of 13)	intron (NM_001134384, intron 1 of 13)	-37758	NM_001134383	232227	Mm.196943	NM_182784	ENSMUSG00000034312	Iqsec1	AW561907|BC026481|BRAG2|D6Ertd349e|cI-43	IQ motif and Sec7 domain 1	protein-coding
mm_54493.1	chr6	35510057	35510068	-	1	NA	3' UTR (NM_008098, exon 4 of 4)	3' UTR (NM_008098, exon 4 of 4)	29826	NM_008098	14489	Mm.182746	NM_008098	ENSMUSG00000029840	Mtpn	5033418D15Rik|Gcdp|V1	myotrophin	protein-coding
mm_73029.1	chr8	94173354	94173394	+	1	NA	exon (NM_008630, exon 3 of 3)	exon (NM_008630, exon 3 of 3)	756	NM_008630	17750	Mm.147226	NM_008630	ENSMUSG00000031762	Mt2	AA409533|MT-II|Mt-2	metallothionein 2	protein-coding
mm_28892.1	chr3	97888687	97888819	-	1	NA	promoter-TSS (NM_001289701)	promoter-TSS (NM_001289701)	-46	NM_001289701	83679	Mm.129840	NM_031401	ENSMUSG00000038170	Pde4dip	4732458A06Rik|9430063L05Rik|C87016|D130016K21Rik|D3Bwg1078e|Usmg4|mKIAA0454	phosphodiesterase 4D interacting protein (myomegalin)	protein-coding
mm_87519.1	chr10	52800219	52800221	+	1	NA	intron (NM_178675, intron 1 of 7)	intron (NM_178675, intron 1 of 7)	109719	NM_178675	215085	Mm.338690	NM_178675	ENSMUSG00000038602	Slc35f1	Duf6|E130016L02	solute carrier family 35, member F1	protein-coding
mm_71163.1	chr8	40511790	40511862	+	1	NA	promoter-TSS (NM_001271543)	promoter-TSS (NM_001271543)	43	NM_033560	52348	Mm.489696	NM_033560	ENSMUSG00000031600	Vps37a	2210018P21Rik|4930592A21Rik|AW261445|D8Ertd531e	vacuolar protein sorting 37A	protein-coding
mm_28377.1	chr3	89960563	89960617	-	1	NA	intron (NM_001081182, intron 2 of 27)	CpG	2742	NM_001081182	54667	Mm.30455	NM_001081182	ENSMUSG00000060671	Atp8b2	Id	ATPase, class I, type 8B, member 2	protein-coding
mm_133061.1	chr16	58465487	58465487	+	1	NA	exon (NM_028523, exon 16 of 16)	exon (NM_028523, exon 16 of 16)	56952	NM_028523	73379	Mm.373589	NM_028523	ENSMUSG00000035107	Dcbld2	1700055P21Rik|AW146002|CLCP1|Esdn	discoidin, CUB and LCCL domain containing 2	protein-coding
mm_83169.1	chr9	40531292	40531306	-	1	NA	Intergenic	CpG	-75535	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_151202.1	chr19	53539508	53539520	+	1	NA	intron (NM_001085390, intron 3 of 3)	intron (NM_001085390, intron 3 of 3)	10196	NM_001085390	240672	Mm.482424	NM_001085390	ENSMUSG00000034765	Dusp5	Gm337	dual specificity phosphatase 5	protein-coding
mm_124359.1	chr14	105176873	105176918	-	1	NA	5' UTR (NM_134077, exon 1 of 21)	5' UTR (NM_134077, exon 1 of 21)	432	NM_134077	74213	Mm.474531	NM_134077	ENSMUSG00000022119	Rbm26	1700009P03Rik|AI447318|C230097K14Rik|C86225|MLZ-393|Pro1777|Se70-2	RNA binding motif protein 26	protein-coding
mm_104082.1	chr11	86602224	86602251	-	1	NA	intron (NM_029478, intron 9 of 11)	intron (NM_029478, intron 9 of 11)	-18079	NR_029738	387140		NR_029738	ENSMUSG00000065455	Mir21a	Mir21|Mirn21|mmu-mir-21|mmu-mir-21a	microRNA 21a	ncRNA
mm_56308.1	chr6	91843877	91843915	-	1	NA	Intergenic	CpG	-34157	NM_172730	232236	Mm.234879	NM_172730	ENSMUSG00000034083	Ccdc174	C130022K22Rik	coiled-coil domain containing 174	protein-coding
mm_134604.1	chr16	20622325	20622335	-	1	NA	intron (NM_177940, intron 2 of 18)	CpG-5611	-1052	NM_028420	73047	Mm.425977	NM_028420	ENSMUSG00000051146	Camk2n2	2900075A18Rik	calcium/calmodulin-dependent protein kinase II inhibitor 2	protein-coding
mm_101231.1	chr11	20332655	20332688	-	1	NA	promoter-TSS (NM_018861)	promoter-TSS (NM_018861)	42	NM_018861	55963	Mm.6379	NM_018861	ENSMUSG00000020142	Slc1a4	ASCT-1|ASCT1|AW045657|SATT	solute carrier family 1 (glutamate/neutral amino acid transporter), member 4	protein-coding
mm_21030.1	chr2	152414840	152414861	-	1	NA	promoter-TSS (NM_177656)	promoter-TSS (NM_177656)	194	NM_175126	67917	Mm.391810	NM_175126	ENSMUSG00000074682	Zcchc3	2810406K24Rik	zinc finger, CCHC domain containing 3	protein-coding
mm_140214.1	chr17	83810761	83810775	+	1	NA	intron (NM_054082, intron 16 of 16)	B3|SINE|B2	36022	NM_025325	107766	Mm.30100	NM_025325	ENSMUSG00000000673	Haao	0610007K21Rik|0610012J07Rik|3-HAO|3-HAOxase|3HAO	3-hydroxyanthranilate 3,4-dioxygenase	protein-coding
mm_121109.1	chr14	101653981	101654048	+	1	NA	promoter-TSS (NM_016723)	promoter-TSS (NM_016723)	47	NM_016723	50933	Mm.275970	NM_016723	ENSMUSG00000022111	Uchl3	-	ubiquitin carboxyl-terminal esterase L3 (ubiquitin thiolesterase)	protein-coding
mm_161504.1	chr15	97731396	97731396	-	1	NA	promoter-TSS (NM_001168693)	promoter-TSS (NM_001168693)	9	NM_001168693	19011	Mm.1001	NM_008902	ENSMUSG00000022468	Endou	Pp11r|Tcl-30	endonuclease, polyU-specific	protein-coding
mm_30910.1	chr4	32426687	32426699	+	1	NA	intron (NM_001109661, intron 1 of 4)	intron (NM_001109661, intron 1 of 4)	9258	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_157377.1	chrX	37878828	37878848	-	1	NA	exon (NM_001004193, exon 1 of 4)	exon (NM_001004193, exon 1 of 4)	106	NM_001004193	434768	Mm.336025	NM_001004193	ENSMUSG00000064137	Rhox8	Tox	reproductive homeobox 8	protein-coding
mm_4768.1	chr1	182484226	182484241	+	1	NA	exon (NM_009794, exon 10 of 21)	exon (NM_009794, exon 10 of 21)	33250	NM_009794	12334	Mm.19306	NM_009794	ENSMUSG00000026509	Capn2	AI326419|Capa-2|Capa2|m-calpain|m-calpin	calpain 2	protein-coding
mm_67428.1	chr7	80370784	80370790	-	1	NA	5' UTR (NM_172903, exon 2 of 24)	5' UTR (NM_172903, exon 2 of 24)	588	NM_172903	140481	Mm.269245	NM_172903	ENSMUSG00000038886	Man2a2	1700052O22Rik|4931438M07Rik|AI480988|MX|Man IIx	mannosidase 2, alpha 2	protein-coding
mm_54300.1	chr6	29478398	29478407	-	1	NA	Intergenic	Intergenic	6965	NM_001145360	668210	Mm.420607	NM_001145360	ENSMUSG00000090685	Gm9047	EG668210	predicted gene 9047	protein-coding
mm_41764.1	chr5	103425203	103425231	+	1	NA	promoter-TSS (NM_011204)	promoter-TSS (NM_011204)	25	NM_011204	19249	Mm.3414	NM_011204	ENSMUSG00000034573	Ptpn13	AI324989|PTP-BL|PTPL1|Ptpri|RIP	protein tyrosine phosphatase, non-receptor type 13	protein-coding
mm_170459.1	chr1	89096890	89096894	-	1	NA	intron (NM_133816, intron 1 of 5)	ERVB7_1-LTR_MM|LTR|ERVK	26430	NM_133816	98402	Mm.170983	NM_133816	ENSMUSG00000036206	Sh3bp4	AI594717|AW227605|BOG25	SH3-domain binding protein 4	protein-coding
mm_61628.1	chr7	80246370	80246371	+	1	NA	promoter-TSS (NM_177765)	promoter-TSS (NM_177765)	-6	NM_177765	269954	Mm.276780	NM_177765	ENSMUSG00000045467	Ttll13	1700111A04Rik|4921538O11|BC024578	tubulin tyrosine ligase-like family, member 13	protein-coding
mm_151875.1	chr19	5798373	5798383	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	-2397	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_69954.1	chr7	142372742	142372775	-	1	NA	promoter-TSS (NM_177265)	promoter-TSS (NM_177265)	-431	NM_001347542	320802	Mm.154486	NM_177265	ENSMUSG00000045777	Ifitm10	6330512M04Rik|AI848576|DSPA3	interferon induced transmembrane protein 10	protein-coding
mm_125453.1	chr15	51877743	51877746	+	1	NA	intron (NM_030132, intron 1 of 2)	CpG	303	NM_030132	78581	Mm.176347	NM_030132	ENSMUSG00000022313	Utp23	1700010I21Rik|AI662478|BB238373|D530033C11Rik	UTP23 small subunit processome component	protein-coding
mm_29308.1	chr3	107943684	107943699	-	1	NA	promoter-TSS (NM_008184)	promoter-TSS (NM_008184)	58	NM_008184	14867	Mm.458154	NM_008184	ENSMUSG00000068762	Gstm6	-	glutathione S-transferase, mu 6	protein-coding
mm_9272.1	chr1	171634075	171634084	-	1	NA	3' UTR (NM_144539, exon 8 of 8)	3' UTR (NM_144539, exon 8 of 8)	7821	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_115873.1	chr13	21721796	21721811	-	1	NA	promoter-TSS (NM_178200)	promoter-TSS (NM_178200)	-241	NM_178200	319186	Mm.277425	NM_178200	ENSMUSG00000096807	Hist1h2bm	H2b-291b	histone cluster 1, H2bm	protein-coding
mm_80361.1	chr9	75232014	75232033	+	1	NA	promoter-TSS (NM_001081322)	promoter-TSS (NM_001081322)	9	NM_001081322	208943	Mm.41339	NM_001081322	ENSMUSG00000033590	Myo5c	9130003O20Rik|BB085560|C330029I24	myosin VC	protein-coding
mm_167400.1	chr8	95434839	95434853	-	1	NA	promoter-TSS (NM_008187)	promoter-TSS (NM_008187)	23	NM_008187	14894	Mm.2080	NM_008187	ENSMUSG00000031796	Cfap20	2600014O15Rik|AL024127|Gtl3|T10-2A2	cilia and flagella associated protein 20	protein-coding
mm_58125.1	chr6	140101154	140101160	-	1	NA	Intergenic	Intergenic	59632	NM_007605	12344	Mm.12817	NM_007605	ENSMUSG00000041791	Capza3	510-4|Cappa3|Gsg3|Tex8|repro32	capping protein (actin filament) muscle Z-line, alpha 3	protein-coding
mm_33150.1	chr4	125176572	125176598	+	1	NA	Intergenic	Intergenic	-48704	NM_153159	230738	Mm.402	NM_153159	ENSMUSG00000042677	Zc3h12a	BC036563|MCPIP|MCPIP-1|Mcpip1|Reg1	zinc finger CCCH type containing 12A	protein-coding
mm_96508.1	chr11	68451674	68451686	+	1	NA	intron (NM_177320, intron 1 of 18)	intron (NM_177320, intron 1 of 18)	19555	NM_177320	320207	Mm.244960	NM_177320	ENSMUSG00000020901	Pik3r5	AV230647|F730038I15Rik	phosphoinositide-3-kinase, regulatory subunit 5, p101	protein-coding
mm_95409.1	chr11	49983068	49983094	+	1	NA	Intergenic	L1M4b|LINE|L1	-42250	NM_021540	59044	Mm.359004	NM_021540	ENSMUSG00000020376	Rnf130	2510042A13Rik|G1RZFP|G1rp|GOLIATH|GP	ring finger protein 130	protein-coding
mm_158089.1	chrX	101332504	101332549	-	1	NA	Intergenic	Intergenic	33347	NM_172932	245537	Mm.121508	NM_172932	ENSMUSG00000031302	Nlgn3	A230085M13Rik|HNL3|NL3	neuroligin 3	protein-coding
mm_24602.1	chr3	93445453	93445462	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	3127	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_147504.1	chr18	50053649	50053662	-	1	NA	intron (NM_134131, intron 1 of 1)	CpG	373	NM_134131	106869	Mm.27740	NM_134131	ENSMUSG00000062210	Tnfaip8	AA987150|E130304C20Rik|ENSMUSG00000073567|Gg2-1|Gm10539|Nded|Ssc-2|Tipe	tumor necrosis factor, alpha-induced protein 8	protein-coding
mm_112723.1	chr13	19192236	19192251	+	1	NA	Intergenic	Intergenic	203570	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_166295.1	chr5	104108481	104108485	+	1	NA	intron (NM_010097, intron 1 of 10)	intron (NM_010097, intron 1 of 10)	5605	NM_010097	13602	Mm.29027	NM_010097	ENSMUSG00000029309	Sparcl1	Ecm2|Sc1|hevin|mast9	SPARC-like 1	protein-coding
mm_93431.1	chr10	109010622	109010685	-	1	NA	5' UTR (NM_001252342, exon 1 of 11)	5' UTR (NM_001252342, exon 1 of 11)	322	NM_009306	20979	Mm.289702	NM_009306	ENSMUSG00000035864	Syt1	AW124717|G630098F17Rik|SytI	synaptotagmin I	protein-coding
mm_158216.1	chrX	105928540	105928542	-	1	NA	intron (NM_009530, intron 1 of 34)	CpG	831	NM_009530	22589	Mm.10141	NM_009530	ENSMUSG00000031229	Atrx	4833408C14Rik|AI447451|ATR2|DXHXS6677E|HP1-BP38|Hp1bp2|Hp1bp38|MRXS3|RAD54L|Rad54|XH2|Xnp|ZNF-HX	alpha thalassemia/mental retardation syndrome X-linked	protein-coding
mm_60263.1	chr7	43824494	43824517	+	1	NA	promoter-TSS (NM_011177)	promoter-TSS (NM_011177)	-39	NM_001164697	19144	Mm.3944	NM_011177	ENSMUSG00000050063	Klk6	AI849898|BSP|Bssp|Klk29|MSP|Prss18|Prss9|neurosin	kallikrein related-peptidase 6	protein-coding
mm_41463.1	chr5	90935088	90935105	+	1	NA	intron (NM_026788, intron 1 of 7)	(TC)n|Simple_repeat|Simple_repeat	3900	NM_026788	665563	Mm.153030	NM_026788	ENSMUSG00000029376	Mthfd2l	1110019K23Rik|C630010D07Rik	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2-like	protein-coding
mm_39177.1	chr4	155784023	155784030	-	1	NA	3' UTR (NM_001033394, exon 2 of 2)	3' UTR (NM_001033394, exon 2 of 2)	1848	NM_001033394	320587	Mm.384382	NM_001033394	ENSMUSG00000073680	Tmem88b	A230069A22Rik	transmembrane protein 88B	protein-coding
mm_89816.1	chr10	104422569	104422570	+	1	NA	Intergenic	RMER19B|LTR|ERVK	135300	NR_105838	102465222		NR_105838	ENSMUSG00000099264	Mir6411	Gm27767|mmu-mir-6411	microRNA 6411	ncRNA
mm_52795.1	chr6	121270539	121270550	+	1	NA	3' UTR (NM_011909, exon 11 of 11)	3' UTR (NM_011909, exon 11 of 11)	24638	NM_011909	24110	Mm.326911	NM_011909	ENSMUSG00000030107	Usp18	1110058H21Rik|AW047653|UBP43|Ubp15	ubiquitin specific peptidase 18	protein-coding
mm_113058.1	chr13	23710649	23710668	+	1	NA	exon (NM_001347493, exon 1 of 5)	exon (NM_001347493, exon 1 of 5)	196	NM_001347493	15216	Mm.2681	NM_010424	ENSMUSG00000006611	Hfe	MR2	hemochromatosis	protein-coding
mm_67482.1	chr7	80712936	80712974	-	1	NA	3' UTR (NM_016721, exon 38 of 38)	3' UTR (NM_016721, exon 38 of 38)	-24078	NM_173863	70461	Mm.392175	NM_173863	ENSMUSG00000030527	Crtc3	2610312F20Rik|6332415K15Rik|AI429792|BC011210|TORC3	CREB regulated transcription coactivator 3	protein-coding
mm_20842.1	chr2	148022033	148022050	-	1	NA	Intergenic	Intergenic	23423	NM_001291067	15376	Mm.938	NM_010446	ENSMUSG00000037025	Foxa2	HNF3-beta|HNF3beta|Hnf-3b|Hnf3b|Tcf-3b|Tcf3b	forkhead box A2	protein-coding
mm_80514.1	chr9	80004213	80004238	+	1	NA	Intergenic	Intergenic	-26343	NM_001081243	70598	Mm.23049	NM_001081243	ENSMUSG00000034898	Filip1	5730485H21Rik|AI843021	filamin A interacting protein 1	protein-coding
mm_135320.1	chr16	38783514	38783525	-	1	NA	intron (NM_178924, intron 5 of 7)	intron (NM_178924, intron 5 of 7)	16684	NM_178924	22268	Mm.130793	NM_178924	ENSMUSG00000049436	Upk1b	AI413235|Tspan20|UPIb|Upk1	uroplakin 1B	protein-coding
mm_92938.1	chr10	84551965	84551992	-	1	NA	intron (NR_040658, intron 2 of 3)	ORR1B1|LTR|ERVL-MaLR	1360	NR_040658	442847	Mm.128292	NR_040658	ENSMUSG00000097076	Platr7	C330046G13Rik	pluripotency associated transcript 7	ncRNA
mm_164343.1	chr16	15301396	15301405	-	1	NA	Intergenic	Intergenic	293118	NM_001159351	70620	Mm.235407	NM_023585	ENSMUSG00000022674	Ube2v2	1110021H13Rik|4632410D19Rik|5730524P06Rik|6820402M05|AI848315|C81524|MMS2	ubiquitin-conjugating enzyme E2 variant 2	protein-coding
mm_160218.1	chr7	100176911	100176911	+	1	NA	intron (NM_001190869, intron 1 of 4)	B1_Mus2|SINE|Alu	241	NM_001190869	57442	Mm.282386	NM_020574	ENSMUSG00000035165	Kcne3	2210017H05Rik|MiRP2	potassium voltage-gated channel, Isk-related subfamily, gene 3	protein-coding
mm_118258.1	chr13	112439988	112440001	-	1	NA	Intergenic	Intergenic	-24076	NM_010560	16195	Mm.4364	NM_010560	ENSMUSG00000021756	Il6st	5133400A03Rik|AA389424|BB405851|CD130|D13Ertd699e|gp130	interleukin 6 signal transducer	protein-coding
mm_161254.1	chr13	105443669	105443669	+	1	NA	promoter-TSS (NM_008308)	promoter-TSS (NM_008308)	-24	NM_008308	15550	Mm.4716	NM_008308	ENSMUSG00000021721	Htr1a	Gpcr18	5-hydroxytryptamine (serotonin) receptor 1A	protein-coding
mm_53923.1	chr6	4531273	4531294	-	1	NA	exon (NM_007743, exon 37 of 52)	exon (NM_007743, exon 37 of 52)	25665	NM_007743	12843	Mm.277792	NM_007743	ENSMUSG00000029661	Col1a2	AA960264|AI325291|Col1a-2|Cola-2|Cola2|oim	collagen, type I, alpha 2	protein-coding
mm_69529.1	chr7	135652274	135652302	-	1	NA	promoter-TSS (NR_015548)	promoter-TSS (NR_015548)	26	NR_015548	67765	Mm.445272	NR_015548	ENSMUSG00000097471	5830432E09Rik	-	RIKEN cDNA 5830432E09 gene	ncRNA
mm_112766.1	chr13	19357522	19357540	+	1	NA	TTS (NM_024270)	TTS (NM_024270)	38282	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_42507.1	chr5	115506669	115506753	+	1	NA	promoter-TSS (NM_011223)	promoter-TSS (NM_011223)	35	NM_133915	19303	Mm.18714	NM_011223	ENSMUSG00000029528	Pxn	AW108311|AW123232|Pax	paxillin	protein-coding
mm_146448.1	chr18	86394773	86394782	+	1	NA	promoter-TSS (NM_144946)	promoter-TSS (NM_144946)	-175	NM_144946	246317	Mm.329578	NM_144946	ENSMUSG00000050321	Neto1	AI851453|Btcl1|C130005O10Rik	neuropilin (NRP) and tolloid (TLL)-like 1	protein-coding
mm_100624.1	chr11	121702419	121702434	+	1	NA	promoter-TSS (NM_144797)	promoter-TSS (NM_144797)	-1	NM_144797	210029	Mm.153566	NM_144797	ENSMUSG00000039208	Metrnl	9430048M07Rik|BC019776	meteorin, glial cell differentiation regulator-like	protein-coding
mm_126892.1	chr15	89498014	89498046	+	1	NA	Intergenic	Intergenic	-1827	NM_021423	58234	Mm.146855	NM_021423	ENSMUSG00000022623	Shank3	AI841104|SHANK3c-3|SHANK3c-4|Shank3b	SH3/ankyrin domain gene 3	protein-coding
mm_58405.1	chr7	3219527	3219559	+	1	NA	promoter-TSS (NR_106140)	promoter-TSS (NR_106140)	61	NR_030276	100124471		NR_030276	ENSMUSG00000078032	Mir291b	Mirn291b|mir-291b|mmu-mir-291b	microRNA 291b	ncRNA
mm_28215.1	chr3	88395955	88395998	-	1	NA	exon (NM_025928, exon 4 of 5)	exon (NM_025928, exon 4 of 5)	-11510	NM_007541	12096	Mm.389459	NM_007541	ENSMUSG00000074483	Bglap	BGP|Bglap1|OC|OG1|mOC-A	bone gamma carboxyglutamate protein	protein-coding
mm_133981.1	chr16	4549407	4549436	-	1	NA	exon (NM_031182, exon 5 of 7)	exon (NM_031182, exon 5 of 7)	10299	NM_031182	83383	Mm.273210	NM_031182	ENSMUSG00000005718	Tfap4	AI642933|AP-4|D930048N17Rik|Tcfap4|bHLHc41	transcription factor AP4	protein-coding
mm_54115.1	chr6	17694696	17694714	-	1	NA	intron (NM_001289624, intron 1 of 15)	CpG	711	NM_001289625	64213	Mm.12051	NM_022332	ENSMUSG00000029534	St7	9430001H04Rik|Fam4a2|HELG|RAY1|SEN4|TSG7	suppression of tumorigenicity 7	protein-coding
mm_8635.1	chr1	156420900	156420914	-	1	NA	promoter-TSS (NM_001346967)	promoter-TSS (NM_001346967)	8	NM_001346967	77352	Mm.428709	NM_001033180	ENSMUSG00000026601	Axdnd1	9430070O13Rik|Gm979	axonemal dynein light chain domain containing 1	protein-coding
mm_4371.1	chr1	172121721	172121743	+	1	NA	exon (NM_009938, exon 33 of 33)	exon (NM_009938, exon 33 of 33)	-5023	NM_001159525	19298	Mm.247764	NM_023041	ENSMUSG00000003464	Pex19	Pxf	peroxisomal biogenesis factor 19	protein-coding
mm_134405.1	chr16	17654680	17654686	-	1	NA	intron (NM_033609, intron 13 of 17)	intron (NM_033609, intron 13 of 17)	8213	NM_001166164	72315	Mm.297777	NM_001166164	ENSMUSG00000041617	Ccdc74a	2310015A05Rik	coiled-coil domain containing 74A	protein-coding
mm_101910.1	chr11	49679126	49679127	-	1	NA	intron (NM_212484, intron 10 of 11)	intron (NM_212484, intron 10 of 11)	15531	NM_170727	68662	Mm.22802	NM_054037	ENSMUSG00000064057	Scgb3a1	HIN-1|LuLeu2|Pnsp2|UGRP2|Utgrp2	secretoglobin, family 3A, member 1	protein-coding
mm_154447.1	chrM	1643	1653	-	1	NA	NA	Intergenic	NA	NA								
mm_81405.1	chr9	109051154	109051219	+	1	NA	intron (NM_025858, intron 2 of 5)	L1M3|LINE|L1	-3680	NM_026381	66940	Mm.196533	NM_025858	ENSMUSG00000025647	Shisa5	2310008D10Rik|6430628I05Rik|Scotin|mShisa5	shisa family member 5	protein-coding
mm_80001.1	chr9	67191622	67191662	+	1	NA	Intergenic	Intergenic	45084	NR_029576	387185		NR_029576	ENSMUSG00000076379	Mir190a	Mir190|Mirn190|mir-190|mir-190a|mmu-mir-190|mmu-mir-190a	microRNA 190a	ncRNA
mm_36549.1	chr4	86672559	86672563	-	1	NA	Intergenic	Intergenic	-2502	NM_007408	11520	Mm.381	NM_007408	ENSMUSG00000028494	Plin2	AA407157|ADPH|Adfp|Adrp	perilipin 2	protein-coding
mm_63977.1	chr7	139972374	139972382	+	1	NA	TTS (NM_001033465)	TTS (NM_001033465)	6377	NM_001347614	381933	Mm.440431	NM_001033465	ENSMUSG00000073795	6430531B16Rik	Gm1093	RIKEN cDNA 6430531B16 gene	protein-coding
mm_82245.1	chr9	4635268	4635271	-	1	NA	intron (NM_019691, intron 4 of 16)	intron (NM_019691, intron 4 of 16)	160965	NM_001113180	14802	Mm.209263	NM_019691	ENSMUSG00000025892	Gria4	GluA4|GluR-D|Glur-4|Glur4|Gluralpha4|spkw1	glutamate receptor, ionotropic, AMPA4 (alpha 4)	protein-coding
mm_171424.1	chr4	134103941	134103941	-	1	NA	intron (NR_045571, intron 1 of 13)	B2_Mm1a|SINE|B2	1358	NM_026257	67586	Mm.282029	NM_026257	ENSMUSG00000012126	Ubxn11	4930506L07Rik|D4Bwg1540e|Soc|Soci|Ubxd5	UBX domain protein 11	protein-coding
mm_40883.1	chr5	74572494	74572510	+	1	NA	exon (NM_001159573, exon 12 of 18)	exon (NM_001159573, exon 12 of 18)	37020	NM_001159574	66899	Mm.272468	NM_024183	ENSMUSG00000029227	Fip1l1	1300019H17Rik|Rje	FIP1 like 1 (S. cerevisiae)	protein-coding
mm_103900.1	chr11	83575864	83575910	-	1	NA	exon (NM_011338, exon 3 of 4)	exon (NM_011338, exon 3 of 4)	2749	NM_011338	20308	Mm.416125	NM_011338	ENSMUSG00000019122	Ccl9	CCF18|MRP-2|Scya10|Scya9	chemokine (C-C motif) ligand 9	protein-coding
mm_67056.1	chr7	67372847	67372857	-	1	NA	promoter-TSS (NM_001291196)	promoter-TSS (NM_001291196)	6	NM_001291192	17258	Mm.132788	NM_001033713	ENSMUSG00000030557	Mef2a	A430079H05Rik	myocyte enhancer factor 2A	protein-coding
mm_153822.1	chr19	46304627	46304640	-	1	NA	promoter-TSS (NM_001177369)	promoter-TSS (NM_001177369)	-104	NM_001177369	18034	Mm.102365	NM_019408	ENSMUSG00000025225	Nfkb2	NF-kappaB2|lyt|p49|p49/p100|p50B|p52	nuclear factor of kappa light polypeptide gene enhancer in B cells 2, p49/p100	protein-coding
mm_30246.1	chr3	146571781	146571803	-	1	NA	Intergenic	ID4_|SINE|ID	-25357	NM_009474	22262	Mm.10865	NM_009474	ENSMUSG00000028186	Uox	AI663847	urate oxidase	protein-coding
mm_111000.1	chr12	78846800	78846802	-	1	NA	intron (NM_023721, intron 7 of 8)	L1_Mus3|LINE|L1	14837	NM_023721	73834	Mm.311549	NM_023721	ENSMUSG00000021114	Atp6v1d	1110004P10Rik|Atp6m|VATD|Vma8	ATPase, H+ transporting, lysosomal V1 subunit D	protein-coding
mm_95881.1	chr11	58102863	58102874	+	1	NA	Intergenic	Intergenic	-1285	NM_026949	69125	Mm.28910	NM_026949	ENSMUSG00000020515	Cnot8	1500015I04Rik|1810022F04Rik|AA536816|AU015770|AU043059	CCR4-NOT transcription complex, subunit 8	protein-coding
mm_50477.1	chr6	48988062	48988070	+	1	NA	exon (NM_172888, exon 1 of 5)	exon (NM_172888, exon 1 of 5)	1205	NM_172888	243377	Mm.446302	NM_172888	ENSMUSG00000039215	Svs1	9530003A11	seminal vesicle secretory protein 1	protein-coding
mm_143676.1	chr17	80029233	80029236	-	1	NA	TTS (NM_144802)	TTS (NM_144802)	33034	NM_144802	72692	Mm.64579	NM_144802	ENSMUSG00000024095	Hnrnpll	2510028H02Rik|2810036L13Rik|AI256697|AI852082|Hnrpll	heterogeneous nuclear ribonucleoprotein L-like	protein-coding
mm_138729.1	chr17	36958559	36958569	+	1	NA	promoter-TSS (NM_029602)	promoter-TSS (NM_029602)	-28	NM_029602	76416	Mm.26684	NM_029602	ENSMUSG00000036214	Znrd1as	1700022C21Rik|AI746295|Znrd1-as	zinc ribbon domain containing 1, antisense	protein-coding
mm_133789.1	chr16	95258210	95258244	+	1	NA	non-coding (NR_073406, exon 2 of 6)	non-coding (NR_073406, exon 2 of 6)	669	NM_001271690	16516	Mm.272239	NM_019664	ENSMUSG00000062609	Kcnj15	4930414N08Rik|AI182284|AI267127|IRKK|Kir4.2	potassium inwardly-rectifying channel, subfamily J, member 15	protein-coding
mm_118924.1	chr14	27000667	27000679	+	1	NA	5' UTR (NM_010420, exon 1 of 4)	5' UTR (NM_010420, exon 1 of 4)	311	NM_010420	15209	Mm.4802	NM_010420	ENSMUSG00000040726	Hesx1	HES-1|Rpx	homeobox gene expressed in ES cells	protein-coding
mm_65916.1	chr7	30195564	30195569	-	1	NA	promoter-TSS (NM_009795)	promoter-TSS (NM_009795)	-518	NM_009795	12336	Mm.439782	NM_009795	ENSMUSG00000001794	Capns1	Capa-4|Capa4|Capn4|D7Ertd146e	calpain, small subunit 1	protein-coding
mm_36378.1	chr4	76854317	76854320	-	1	NA	intron (NM_011211, intron 8 of 39)	intron (NM_011211, intron 8 of 39)	1357577	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding
mm_29235.1	chr3	107214279	107214316	-	1	NA	exon (NM_001111143, exon 6 of 9)	exon (NM_001111143, exon 6 of 9)	7435	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_128797.1	chr15	66812717	66812732	-	1	NA	5' UTR (NM_009192, exon 2 of 9)	5' UTR (NM_009192, exon 2 of 9)	19105	NM_001029841	20491	Mm.7601	NM_009192	ENSMUSG00000022372	Sla	Slap|Slap-1	src-like adaptor	protein-coding
mm_145812.1	chr18	65430109	65430111	+	1	NA	promoter-TSS (NM_172833)	promoter-TSS (NM_172833)	-887	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_118592.1	chr14	20674299	20674307	+	1	NA	promoter-TSS (NM_172596)	promoter-TSS (NM_172596)	-18	NM_172596	218811	Mm.173119	NM_172596	ENSMUSG00000039367	Sec24c	2610204K03Rik|mKIAA0079	Sec24 related gene family, member C (S. cerevisiae)	protein-coding
mm_38552.1	chr4	141606104	141606112	-	1	NA	promoter-TSS (NM_133754)	promoter-TSS (NM_133754)	-56	NM_133754	74202	Mm.490327	NM_133754	ENSMUSG00000006219	Fblim1	2410043F08Rik|Cal|Fblp1|Gt10|migfilin|migfilin(s)	filamin binding LIM protein 1	protein-coding
mm_88476.1	chr10	77606696	77606718	+	1	NA	5' UTR (NM_001301671, exon 1 of 4)	5' UTR (NM_001301671, exon 1 of 4)	109	NM_001301671	20610	Mm.24433	NM_019929	ENSMUSG00000020265	Sumo3	2810014B19Rik|D10Ertd345e|SMT3A|SUMO-3|Smt3h1	small ubiquitin-like modifier 3	protein-coding
mm_764.1	chr1	43985043	43985046	+	1	NA	intron (NM_001310540, intron 23 of 28)	intron (NM_001310540, intron 23 of 28)	34962	NM_001013799	433294	Mm.123621	NM_001013799	ENSMUSG00000047343	Mettl21c	A530098C11Rik	methyltransferase like 21C	protein-coding
mm_119772.1	chr14	54175975	54175982	+	1	NA	Intergenic	Intergenic	77951	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_78487.1	chr9	32699812	32699821	+	1	NA	intron (NM_011808, intron 1 of 7)	intron (NM_011808, intron 1 of 7)	3774	NM_001038642	23871	Mm.292415	NM_011808	ENSMUSG00000032035	Ets1	AI196000|AI448617|D230050P06|Ets-1|Tpl1|vs	E26 avian leukemia oncogene 1, 5' domain	protein-coding
mm_71001.1	chr8	31090148	31090160	+	1	NA	intron (NM_025869, intron 1 of 4)	intron (NM_025869, intron 1 of 4)	492	NM_025869	66959	Mm.23916	NM_025869	ENSMUSG00000039661	Dusp26	2310043K02Rik|Skrp3	dual specificity phosphatase 26 (putative)	protein-coding
mm_138844.1	chr17	40520031	40520044	+	1	NA	promoter-TSS (NM_001177584)	promoter-TSS (NM_001177584)	15	NM_001177584	100126778	Mm.422023	NM_001177584	ENSMUSG00000090747	Esp8	Gm17495	exocrine gland secreted peptide 8	protein-coding
mm_102364.1	chr11	58386823	58386836	-	1	NA	exon (NM_001083884, exon 6 of 7)	exon (NM_001083884, exon 6 of 7)	6183	NM_001330197	70163	Mm.24119	NM_027339	ENSMUSG00000013643	Lypd8	2210415F13Rik	LY6/PLAUR domain containing 8	protein-coding
mm_48182.1	chr5	137333562	137333575	-	1	NA	promoter-TSS (NM_031406)	promoter-TSS (NM_031406)	14	NM_031406	83704	Mm.235625	NM_031406	ENSMUSG00000037344	Slc12a9	CIP1	solute carrier family 12 (potassium/chloride transporters), member 9	protein-coding
mm_153749.1	chr19	45006386	45006450	-	1	NA	promoter-TSS (NM_153796)	promoter-TSS (NM_153796)	24	NM_053164	94067	Mm.44174	NM_053164	ENSMUSG00000025208	Mrpl43	4930442D21Rik|bMRP36a	mitochondrial ribosomal protein L43	protein-coding
mm_61185.1	chr7	62377000	62377015	+	1	NA	promoter-TSS (NM_013779)	promoter-TSS (NM_013779)	28	NM_013779	27385	Mm.45207	NM_013779	ENSMUSG00000056972	Magel2	Mage-l2|NDNL1|nM15|ns7	melanoma antigen, family L, 2	protein-coding
mm_135539.1	chr16	49771682	49771694	-	1	NA	Intergenic	Intergenic	72394	NM_028680	73916	Mm.241276	NM_028680	ENSMUSG00000032965	Ift57	4833420A15Rik|Esrrbl1|Hippi|MHS4R2	intraflagellar transport 57	protein-coding
mm_25381.1	chr3	107212797	107212811	+	1	NA	exon (NM_001111143, exon 8 of 9)	exon (NM_001111143, exon 8 of 9)	8928	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_150788.1	chr19	44301352	44301398	+	1	NA	exon (NM_009128, exon 5 of 6)	exon (NM_009128, exon 5 of 6)	-1796	NR_039574	100628619		NR_039574	ENSMUSG00000093315	Mir5114	mmu-mir-5114|mu-mir-5114	microRNA 5114	ncRNA
mm_17005.1	chr2	18800015	18800045	-	1	NA	non-coding (NR_131254, exon 1 of 1)	non-coding (NR_131254, exon 1 of 1)	1788	NR_131254	66774	Mm.87075	NR_131254	ENSMUSG00000097638	Carlr	4933439G12Rik|Carl	cardiac and apoptosis-related long non-coding RNA	ncRNA
mm_123984.1	chr14	75593022	75593041	-	1	NA	promoter-TSS (NM_001164139)	promoter-TSS (NM_001164139)	85	NM_001164140	67926	Mm.23361	NM_026457	ENSMUSG00000034913	Spert	1700086N05Rik|AI596460|Nurit	spermatid associated	protein-coding
mm_144803.1	chr18	36281070	36281151	+	1	NA	promoter-TSS (NM_008989)	promoter-TSS (NM_008989)	-52	NM_008989	19290	Mm.231802	NM_008989	ENSMUSG00000043991	Pura	CAGER-1|Pur-alpha|ssCRE-BP	purine rich element binding protein A	protein-coding
mm_124263.1	chr14	102978664	102978675	-	1	NA	3' UTR (NM_177715, exon 1 of 1)	3' UTR (NM_177715, exon 1 of 1)	3963	NR_039592	100628599		NR_039592	ENSMUSG00000092901	Mir5130	mir-5130|mmu-mir-5130|mu-mir-5130	microRNA 5130	ncRNA
mm_24540.1	chr3	93293060	93293066	+	1	NA	Intergenic	Intergenic	-26686	NM_133698	68723	Mm.208047	NM_133698	ENSMUSG00000041991	Hrnr	1110033K19Rik|A530063N20Rik|S100a18	hornerin	protein-coding
mm_139606.1	chr17	57303918	57303951	+	1	NA	exon (NM_001163815, exon 16 of 28)	exon (NM_001163815, exon 16 of 28)	24834	NM_001163815	22324	Mm.248172	NM_011691	ENSMUSG00000034116	Vav1	Vav|vav-T	vav 1 oncogene	protein-coding
mm_73885.1	chr8	119345426	119345435	+	1	NA	intron (NM_024219, intron 2 of 3)	intron (NM_024219, intron 2 of 3)	892	NM_024219	68196	Mm.358714	NM_024219	ENSMUSG00000031839	Hsbp1	0610007A03Rik|AA408769|Hsp25	heat shock factor binding protein 1	protein-coding
mm_94562.1	chr11	11684968	11685027	+	1	NA	promoter-TSS (NM_009578)	promoter-TSS (NM_009578)	-928	NM_009578	22778	Mm.103545	NM_009578	ENSMUSG00000018654	Ikzf1	5832432G11Rik|Ikaros|LyF-1|Zfpn1a1|Znfn1a1|hlk-1|mKIAA4227	IKAROS family zinc finger 1	protein-coding
mm_136583.1	chr17	4794705	4794727	+	1	NA	Intergenic	Intergenic	159736	NR_130984	75117	Mm.429393	NR_130984		4930517M08Rik	-	RIKEN cDNA 4930517M08 gene	ncRNA
mm_76974.1	chr8	106337930	106337980	-	1	NA	promoter-TSS (NM_021491)	promoter-TSS (NM_021491)	33	NM_021491	58994	Mm.23298	NM_021491	ENSMUSG00000031906	Smpd3	4631433G07Rik|AI427456|AW537966|fro|nSMase2	sphingomyelin phosphodiesterase 3, neutral	protein-coding
mm_39387.1	chr5	13398705	13398726	+	1	NA	promoter-TSS (NM_009152)	promoter-TSS (NM_009152)	-282	NM_001243073	20346	Mm.372039	NM_009152	ENSMUSG00000028883	Sema3a	Hsema-I|SEMA1|SemD|Semad|coll-1	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	protein-coding
mm_33627.1	chr4	132795038	132795042	+	1	NA	intron (NM_001033308, intron 1 of 5)	intron (NM_001033308, intron 1 of 5)	1324	NM_001033308	230787	Mm.290912	NM_001033308	ENSMUSG00000037731	Themis2	ICB-1	thymocyte selection associated family member 2	protein-coding
mm_64608.1	chr7	3249712	3249755	-	1	NA	promoter-TSS (NM_001033431)	promoter-TSS (NM_001033431)	7	NM_001033431	378425	Mm.277152	NM_001033431	ENSMUSG00000078817	Nlrp12	Nalp12|PYPAF7	NLR family, pyrin domain containing 12	protein-coding
mm_102585.1	chr11	61855027	61855069	-	1	NA	promoter-TSS (NM_013881)	promoter-TSS (NM_013881)	44	NM_013881	29869	Mm.162025	NM_013881	ENSMUSG00000004798	Ulk2	A830085I22Rik|AU015340|Unc51.2|mKIAA0623	unc-51 like kinase 2	protein-coding
mm_166519.1	chr6	18169839	18169844	+	1	NA	promoter-TSS (NM_021050)	promoter-TSS (NM_021050)	-846	NM_021050	12638	Mm.15621	NM_021050	ENSMUSG00000041301	Cftr	AW495489|Abcc7	cystic fibrosis transmembrane conductance regulator	protein-coding
mm_150019.1	chr19	29370262	29370274	+	1	NA	intron (NM_021893, intron 1 of 6)	MER20|DNA|hAT-Charlie	2830	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_141457.1	chr17	30538103	30538107	-	1	NA	intron (NM_172618, intron 1 of 11)	intron (NM_172618, intron 1 of 11)	38182	NM_172618	224671	Mm.41220	NM_027060	ENSMUSG00000062202	Btbd9	1700023F20Rik|4930402L05|AI464421	BTB (POZ) domain containing 9	protein-coding
mm_118086.1	chr13	103758258	103758281	-	1	NA	exon (NM_172592, exon 5 of 10)	exon (NM_172592, exon 5 of 10)	6313	NM_172592	218543	Mm.458176	NM_172592	ENSMUSG00000032621	Srek1	8430401B01|AI450757|AI462342|SRrp508|SRrp86|Sfrs12|Srsf12	splicing regulatory glutamine/lysine-rich protein 1	protein-coding
mm_51397.1	chr6	78371791	78371826	+	1	NA	exon (NM_011036, exon 3 of 6)	exon (NM_011036, exon 3 of 6)	923	NM_011036	18489	Mm.2553	NM_011036	ENSMUSG00000071356	Reg3b	HIP|PAP1|Pap|REG-III	regenerating islet-derived 3 beta	protein-coding
mm_66696.1	chr7	45920157	45920193	-	1	NA	intron (NM_001146346, intron 2 of 4)	G-rich|Low_complexity|Low_complexity	674	NM_001146346	13732	Mm.20829	NM_010129	ENSMUSG00000040212	Emp3	H-4|H4|HNMP-1|MI-35|Ymp	epithelial membrane protein 3	protein-coding
mm_135735.1	chr16	55838592	55838600	-	1	NA	promoter-TSS (NM_030612)	promoter-TSS (NM_030612)	45	NM_030612	80859	Mm.247272	NM_030612	ENSMUSG00000035356	Nfkbiz	AA408868|INAP|Mail	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, zeta	protein-coding
mm_120536.1	chr14	67233903	67233910	+	1	NA	5' UTR (NM_001276387, exon 1 of 17)	5' UTR (NM_001276387, exon 1 of 17)	614	NM_001276387	13592	Mm.319947	NM_010095	ENSMUSG00000022053	Ebf2	D14Ggc1e|EBF-2|Mmot1|O/E-3|OE-3	early B cell factor 2	protein-coding
mm_2727.1	chr1	128197673	128197676	+	1	NA	intron (NM_181750, intron 19 of 26)	intron (NM_181750, intron 19 of 26)	-4687	NR_029543	387147		NR_029543	ENSMUSG00000065520	Mir128-1	Mirn128|Mirn128-1|Mirn128a|mir-128-1	microRNA 128-1	ncRNA
mm_161441.1	chr15	72546086	72546086	-	1	NA	exon (NM_001033876, exon 1 of 2)	exon (NM_001033876, exon 1 of 2)	193	NM_001033876	223604	Mm.386856	NM_001033876	ENSMUSG00000036760	Kcnk9	Task3	potassium channel, subfamily K, member 9	protein-coding
mm_14081.1	chr2	124649343	124649348	+	1	NA	intron (NM_001291000, intron 1 of 18)	RMER15|LTR|ERVL	-4236	NM_199240	214968	Mm.330536	NM_172537	ENSMUSG00000027200	Sema6d	1110067B02Rik|AA409156|D330011G23|mKIAA1479	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	protein-coding
mm_83529.1	chr9	46230227	46230262	-	1	NA	exon (NM_009692, exon 4 of 4)	exon (NM_009692, exon 4 of 4)	1614	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2|apo-AI|apoA-I	apolipoprotein A-I	protein-coding
mm_48696.1	chr5	146832833	146832863	-	1	NA	promoter-TSS (NM_019647)	promoter-TSS (NM_019647)	-42	NM_019647	19933	Mm.316592	NM_019647	ENSMUSG00000041453	Rpl21	8430440E03Rik|L21	ribosomal protein L21	protein-coding
mm_167510.1	chr9	13514681	13514695	+	1	NA	Intergenic	Intergenic	83327	NR_028271	18689	Mm.41972	NM_008835	ENSMUSG00000031802	Phxr4	Sp5	per-hexamer repeat gene 4	ncRNA
mm_127476.1	chr15	101273974	101273983	+	1	NA	intron (NM_010444, intron 6 of 6)	intron (NM_010444, intron 6 of 6)	7132	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_70413.1	chr8	11448496	11448557	+	1	NA	3' UTR (NM_009932, exon 48 of 48)	3' UTR (NM_009932, exon 48 of 48)	-29403	NR_126558	102132	Mm.37632	NR_126558	ENSMUSG00000096957	E230013L22Rik	AI645545	RIKEN cDNA E230013L22 gene	ncRNA
mm_131313.1	chr16	11632082	11632085	+	1	NA	intron (NM_001290148, intron 9 of 13)	intron (NM_001290148, intron 9 of 13)	-147619	NR_126430	73761	Mm.39183	NR_126430		4833415N18Rik	-	RIKEN cDNA 4833415N18 gene	ncRNA
mm_20228.1	chr2	125788359	125788364	-	1	NA	Intergenic	Intergenic	-5491	NM_177608	70354	Mm.138091	NM_133725	ENSMUSG00000035093	Secisbp2l	3110001I20Rik|AI504340|C630011I23	SECIS binding protein 2-like	protein-coding
mm_66158.1	chr7	31151428	31151448	-	1	NA	promoter-TSS (NM_027898)	promoter-TSS (NM_027898)	-388	NM_027898	52857	Mm.27366	NM_027898	ENSMUSG00000001248	Gramd1a	1300003M23Rik|AI415002|AW547240|D7Bwg0611e	GRAM domain containing 1A	protein-coding
mm_57990.1	chr6	136172180	136172245	-	1	NA	intron (NM_008171, intron 2 of 14)	intron (NM_008171, intron 2 of 14)	1299	NM_008171	14812	Mm.436649	NM_008171	ENSMUSG00000030209	Grin2b	AW490526|GluN2B|NR2B|Nmdar2b	glutamate receptor, ionotropic, NMDA2B (epsilon 2)	protein-coding
mm_60423.1	chr7	44476493	44476521	+	1	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	6160	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_11162.1	chr2	28556752	28556760	+	1	NA	exon (NM_009885, exon 10 of 11)	exon (NM_009885, exon 10 of 11)	6647	NM_009885	12613	Mm.236017	NM_009885	ENSMUSG00000026818	Cel	1810036E18Rik|BAL	carboxyl ester lipase	protein-coding
mm_17164.1	chr2	25272337	25272376	-	1	NA	promoter-TSS (NM_175300)	promoter-TSS (NM_175300)	62	NM_023464	68475	Mm.21444	NM_023464	ENSMUSG00000026966	Ssna1	1110003H09Rik|1190004J23Rik|AA934184|N14|NA14	SS nuclear autoantigen 1	protein-coding
mm_73549.1	chr8	108948159	108948169	+	1	NA	exon (NM_007496, exon 9 of 10)	exon (NM_007496, exon 9 of 10)	11304	NR_037295	100526511		NR_037295	ENSMUSG00000093241	Mir3108	mir-3108|mmu-mir-3108	microRNA 3108	ncRNA
mm_157243.1	chrX	18147090	18147101	-	1	NA	TTS (NM_028568)	TTS (NM_028568)	1225	NM_028568	73547	Mm.159027	NM_028568	ENSMUSG00000025043	Dusp21	1700094E07Rik|DSP21	dual specificity phosphatase 21	protein-coding
mm_21978.1	chr2	167367262	167367265	-	1	NA	Intergenic	Intergenic	-18085	NM_019835	56336	Mm.200886	NM_019835	ENSMUSG00000017929	B4galt5	9430078I07Rik|AW049941|AW539721	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 5	protein-coding
mm_15455.1	chr2	157424218	157424252	+	1	NA	promoter-TSS (NM_001025395)	promoter-TSS (NM_001025395)	-58	NM_009271	20779	Mm.22845	NM_009271	ENSMUSG00000027646	Src	AW259666|pp60c-src	Rous sarcoma oncogene	protein-coding
mm_102561.1	chr11	61453993	61454019	-	1	NA	promoter-TSS (NM_009548)	promoter-TSS (NM_009548)	-14	NM_001291024	22671	Mm.89201	NM_009548	ENSMUSG00000010086	Rnf112	ZNF179|Zfp179|bfp|neurolastin	ring finger protein 112	protein-coding
mm_88518.1	chr10	78052065	78052070	+	1	NA	exon (NM_019448, exon 6 of 13)	exon (NM_019448, exon 6 of 13)	2108	NM_001284197	54427	Mm.13433	NM_019448	ENSMUSG00000000730	Dnmt3l	D6Ertd14e|ecat7	DNA (cytosine-5-)-methyltransferase 3-like	protein-coding
mm_3609.1	chr1	151755410	151755441	+	1	NA	promoter-TSS (NM_001039644)	promoter-TSS (NM_001039644)	51	NM_001311166	66967	Mm.337691	NM_001039644	ENSMUSG00000043019	Edem3	2310050N11Rik	ER degradation enhancer, mannosidase alpha-like 3	protein-coding
mm_77729.1	chr8	126852703	126852740	-	1	NA	Intergenic	Intergenic	93200	NM_024214	67952	Mm.6932	NM_024214	ENSMUSG00000093904	Tomm20	1810060K07Rik|BB284719|Gm19268|MAS20|MOM19|TOM20|mKIAA0016	translocase of outer mitochondrial membrane 20 homolog (yeast)	protein-coding
mm_169980.1	chr17	14991417	14991418	+	1	NA	3' UTR (NM_001123370, exon 12 of 12)	3' UTR (NM_001123370, exon 12 of 12)	12553	NM_001123370	100041574	Mm.393767	NM_001123370	ENSMUSG00000036552	9030025P20Rik	D17Zt9e	RIKEN cDNA 9030025P20 gene	protein-coding
mm_134576.1	chr16	20403321	20403338	-	1	NA	intron (NM_176839, intron 5 of 6)	intron (NM_176839, intron 5 of 6)	23065	NM_013790	27416	Mm.20845	NM_013790	ENSMUSG00000022822	Abcc5	2900011L11Rik|AI132311|Abcc5a|Abcc5b|Mrp5	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	protein-coding
mm_128841.1	chr15	68401608	68401624	-	1	NA	Intergenic	MLTR11B|LTR|ERVK	-60327	NR_029718	387228		NR_029718	ENSMUSG00000065437	Mir30d	Mirn30d|mir-30d|mmu-mir-30d	microRNA 30d	ncRNA
mm_95458.1	chr11	50377758	50377779	+	1	NA	promoter-TSS (NM_021510)	promoter-TSS (NM_021510)	49	NM_001347487	59013	Mm.21740	NM_021510	ENSMUSG00000007850	Hnrnph1	AI642080|E430005G16Rik|Hnrnph|Hnrph1	heterogeneous nuclear ribonucleoprotein H1	protein-coding
mm_23556.1	chr3	62338942	62339012	+	1	NA	5' UTR (NM_001081295, exon 1 of 14)	5' UTR (NM_001081295, exon 1 of 14)	200	NM_001081295	622434	Mm.153974	NM_001081295	ENSMUSG00000036885	Arhgef26	4631416L12Rik|8430436L14Rik|AI303572|AW491953|SGEF	Rho guanine nucleotide exchange factor (GEF) 26	protein-coding
mm_114811.1	chr13	91496245	91496245	+	1	NA	intron (NM_024272, intron 1 of 16)	intron (NM_024272, intron 1 of 16)	35148	NM_024186	66970	Mm.343095	NM_024186	ENSMUSG00000003992	Ssbp2	1500004K09Rik|2310079I02Rik|9330163K02Rik|A830008M03Rik|AU067692|AW558684|Hspc116|SSDP2	single-stranded DNA binding protein 2	protein-coding
mm_173018.1	chrX	101085357	101085380	-	1	NA	promoter-TSS (NM_007515)	promoter-TSS (NM_007515)	37	NM_001301840	11989	Mm.5140	NM_007515	ENSMUSG00000031297	Slc7a3	Atrc3|CAT-3|CAT3|SLC7A1|SLC7A2	solute carrier family 7 (cationic amino acid transporter, y+ system), member 3	protein-coding
mm_76268.1	chr8	84066433	84066450	-	1	NA	promoter-TSS (NM_009055)	promoter-TSS (NM_009055)	-395	NM_009055	19724	Mm.7892	NM_009055	ENSMUSG00000031706	Rfx1	AI047719|AI385641	regulatory factor X, 1 (influences HLA class II expression)	protein-coding
mm_162623.1	chr1	183418521	183418529	+	1	NA	promoter-TSS (NM_030175)	promoter-TSS (NM_030175)	55	NM_030175	78772	Mm.29003	NM_030175	ENSMUSG00000053461	Hhipl2	4930507C10Rik|AW208802|Hhip3	hedgehog interacting protein-like 2	protein-coding
mm_153761.1	chr19	45591634	45591638	-	1	NA	intron (NM_013907, intron 6 of 8)	intron (NM_013907, intron 6 of 8)	31021	NM_172639	226162	Mm.21978	NM_172639	ENSMUSG00000041035	Dpcd	5330431N19Rik|Ndac	deleted in primary ciliary dyskinesia	protein-coding
mm_138693.1	chr17	35979932	35980009	+	1	NA	promoter-TSS (NM_001282025)	promoter-TSS (NM_001282025)	15	NM_008136	14670	Mm.335754	NM_008136	ENSMUSG00000024429	Gnl1	Gna-rs1|Gnal1	guanine nucleotide binding protein-like 1	protein-coding
mm_1256.1	chr1	63114400	63114411	+	1	NA	promoter-TSS (NM_001114609)	promoter-TSS (NM_001114609)	-66	NR_045915	100380944	Mm.392955	NR_045914	ENSMUSG00000084799	Ino80dos	Gm11602|OTTMUSG00000002611	INO80 complex subunit D, opposite strand	ncRNA
mm_123398.1	chr14	63419540	63419567	-	1	NA	Intergenic	Intergenic	-2366	NM_007549	12143	Mm.3962	NM_007549	ENSMUSG00000014453	Blk	-	B lymphoid kinase	protein-coding
mm_5132.1	chr1	9696864	9696874	-	1	NA	intron (NM_008651, intron 1 of 15)	B1F|SINE|Alu	3340	NM_001290397	17864	Mm.479	NM_008651	ENSMUSG00000025912	Mybl1	A-myb|G1-419-6|repro9	myeloblastosis oncogene-like 1	protein-coding
mm_71253.1	chr8	40917153	40917157	+	1	NA	3' UTR (NM_001044740, exon 12 of 12)	3' UTR (NM_001044740, exon 12 of 12)	-9078	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_58331.1	chr6	146577809	146577824	-	1	NA	promoter-TSS (NM_026218)	promoter-TSS (NM_026218)	19	NM_138757	71177	Mm.271774	NM_138757	ENSMUSG00000040250	Asun	4933424B01Rik|Spata30	asunder, spermatogenesis regulator	protein-coding
mm_114215.1	chr13	56181788	56181810	+	1	NA	Intergenic	Intergenic	-2914	NM_001168615	212937	Mm.116697	NM_145976	ENSMUSG00000049625	Tifab	-	TRAF-interacting protein with forkhead-associated domain, family member B	protein-coding
mm_70271.1	chr8	3598316	3598325	+	1	NA	intron (NM_001347112, intron 2 of 17)	intron (NM_001347112, intron 2 of 17)	10870	NM_001347111	69697	Mm.390010	NM_027171	ENSMUSG00000044433	Camsap3	2310057J16Rik|Kiaa1543|Nezha	calmodulin regulated spectrin-associated protein family, member 3	protein-coding
mm_12916.1	chr2	84936612	84936712	+	1	NA	promoter-TSS (NM_021398)	promoter-TSS (NM_021398)	16	NM_021398	58207	Mm.290729	NM_021398	ENSMUSG00000027074	Slc43a3	Eeg1|SEEEG-1	solute carrier family 43, member 3	protein-coding
mm_78624.1	chr9	38718282	38718326	+	1	NA	promoter-TSS (NM_001145957)	promoter-TSS (NM_001145957)	36	NM_172767	67776	Mm.290950	NM_172767	ENSMUSG00000023186	Vwa5a	5830475I06Rik|AW552491|BCSC-1|E130119J22|Loh11cr2a	von Willebrand factor A domain containing 5A	protein-coding
mm_112254.1	chr12	113807774	113807779	-	1	NA	Intergenic	Intergenic	263868	NM_174885	238406	Mm.188683	NM_174885	ENSMUSG00000043945	Adam6a	Adam6|tMDCIV	a disintegrin and metallopeptidase domain 6A	protein-coding
mm_35302.1	chr4	22835481	22835499	-	1	NA	Intergenic	Intergenic	344942	NR_131335	105500046		NR_131335	ENSMUSG00000107859	Gm30731	Pnky|lnc-pou3f2	predicted gene, 30731	ncRNA
mm_75668.1	chr8	67693514	67693516	-	1	NA	3' UTR (NM_027626, exon 8 of 8)	3' UTR (NM_027626, exon 8 of 8)	124780	NM_027626	234353	Mm.32525	NM_027626	ENSMUSG00000030465	Psd3	4931420C21Rik|AI661273|BC003498|D430018P08|EFA6D	pleckstrin and Sec7 domain containing 3	protein-coding
mm_132811.1	chr16	45162560	45162565	+	1	NA	intron (NM_026402, intron 2 of 11)	intron (NM_026402, intron 2 of 11)	3733	NM_026402	67841	Mm.41775	NM_026402	ENSMUSG00000022663	Atg3	2610016C12Rik|APG3|Apg3l|Atg3l|PC3-96	autophagy related 3	protein-coding
mm_29515.1	chr3	116424008	116424020	-	1	NA	promoter-TSS (NM_001173553)	promoter-TSS (NM_001173553)	18	NM_001080818	229776	Mm.17647	NM_001080818	ENSMUSG00000033502	Cdc14a	A830059A17Rik|CDC14A2|CDC14a1|Cdc14	CDC14 cell division cycle 14A	protein-coding
mm_154420.1	chrM	16130	16146	+	1	NA	NA	Intergenic	NA	NA								
mm_36686.1	chr4	96553590	96553596	-	1	NA	promoter-TSS (NM_010008)	promoter-TSS (NM_010008)	58	NM_010008	13110	Mm.98200	NM_010008	ENSMUSG00000052914	Cyp2j6	-	cytochrome P450, family 2, subfamily j, polypeptide 6	protein-coding
mm_167579.1	chr9	45293244	45293244	+	1	NA	Intergenic	Intergenic	-24095	NM_001324486	16154	Mm.379327	NM_008348	ENSMUSG00000032089	Il10ra	AW553859|CDw210|CDw210a|IL-10R1|IL-10RA|Il10r|mIL-10R	interleukin 10 receptor, alpha	protein-coding
mm_79908.1	chr9	65435798	65435845	+	1	NA	promoter-TSS (NM_027134)	promoter-TSS (NM_027134)	39	NM_027134	69606	Mm.287956	NM_027134	ENSMUSG00000059183	Mtfmt	2310020P08Rik	mitochondrial methionyl-tRNA formyltransferase	protein-coding
mm_83581.1	chr9	48340695	48340697	-	1	NA	5' UTR (NM_030069, exon 1 of 6)	5' UTR (NM_030069, exon 1 of 6)	202	NM_030069	78252	Mm.31626	NM_030069	ENSMUSG00000032028	Nxpe2	4432416J03Rik|AI323362|Fam55b	neurexophilin and PC-esterase domain family, member 2	protein-coding
mm_111599.1	chr12	101976898	101976914	-	1	NA	intron (NM_016856, intron 1 of 14)	intron (NM_016856, intron 1 of 14)	932	NM_016856	51786	Mm.716	NM_016856	ENSMUSG00000041781	Cpsf2	100kDa|2610024B04Rik|AI662483|Cpsf|MCPSF|mKIAA1367	cleavage and polyadenylation specific factor 2	protein-coding
mm_72454.1	chr8	83170670	83170690	+	1	NA	intron (NM_027758, intron 1 of 17)	(T)n|Simple_repeat|Simple_repeat	5328	NM_027758	71310	Mm.24031	NM_027758	ENSMUSG00000031709	Tbc1d9	4933431N12Rik|AI847101|AW490653|C76116	TBC1 domain family, member 9	protein-coding
mm_126813.1	chr15	87715543	87715569	+	1	NA	intron (NM_134096, intron 2 of 3)	intron (NM_134096, intron 2 of 3)	80387	NR_105817	102465209		NR_105817	ENSMUSG00000098938	Mir6393	Gm27424|mmu-mir-6393	microRNA 6393	ncRNA
mm_102035.1	chr11	51834079	51834084	-	1	NA	intron (NM_199299, intron 4 of 11)	ID_B1|SINE|B4	23400	NM_199299	76901	Mm.259996	NM_199299	ENSMUSG00000020387	Jade2	1200017K05Rik|AI480685|Phf15|mKIAA0239	jade family PHD finger 2	protein-coding
mm_85141.1	chr9	95815297	95815307	-	1	NA	intron (NM_001033210, intron 1 of 15)	intron (NM_001033210, intron 1 of 15)	29977	NM_001033210	102502	Mm.11869	NM_001033210	ENSMUSG00000049493	Pls1	AI427122	plastin 1 (I-isoform)	protein-coding
mm_164326.1	chr16	6349110	6349116	+	1	NA	intron (NM_021477, intron 2 of 16)	CpG	373526	NR_045799	68238	Mm.434605	NR_045799	ENSMUSG00000101481	1700123O21Rik	-	RIKEN cDNA 1700123O21 gene	ncRNA
mm_125072.1	chr15	25971980	25971991	+	1	NA	exon (NM_001277316, exon 7 of 7)	exon (NM_001277316, exon 7 of 7)	-12381	NM_144523	52521	Mm.29145	NM_144523	ENSMUSG00000052253	Zfp622	1110033B05Rik|D15Ertd806e|ZPR9|Znf622	zinc finger protein 622	protein-coding
mm_52211.1	chr6	103314633	103314649	+	1	NA	Intergenic	(TCTG)n|Simple_repeat|Simple_repeat	-196235	NM_007697	12661	Mm.251288	NM_007697	ENSMUSG00000030077	Chl1	A530023M13Rik|AI465420|CALL|LICAM2	cell adhesion molecule L1-like	protein-coding
mm_27443.1	chr3	51814016	51814023	-	1	NA	intron (NM_001004176, intron 2 of 4)	intron (NM_001004176, intron 2 of 4)	152840	NM_001310482	211666	Mm.24679	NM_174995	ENSMUSG00000074604	Mgst2	GST2|MGST-II	microsomal glutathione S-transferase 2	protein-coding
mm_42260.1	chr5	114100309	114100369	+	1	NA	promoter-TSS (NM_001033202)	promoter-TSS (NM_001033202)	6	NM_001033202	100756	Mm.240421	NM_001033202	ENSMUSG00000029592	Usp30	6330590F17Rik|AI851327|D5Ertd483e	ubiquitin specific peptidase 30	protein-coding
mm_145732.1	chr18	64265039	64265067	+	1	NA	intron (NM_009182, intron 2 of 5)	intron (NM_009182, intron 2 of 5)	10694	NM_009182	20451	Mm.252110	NM_009182	ENSMUSG00000056812	St8sia3	AI847333|ST8SiaIII|Siat8c	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3	protein-coding
mm_68825.1	chr7	126197997	126198008	-	1	NA	intron (NM_001311143, intron 1 of 23)	L1MB2|LINE|L1	2406	NM_028816	74204	Mm.235663	NM_028816	ENSMUSG00000000131	Xpo6	2610005L19Rik|AL022631|C230091E20Rik|R75304|Ranbp20|mKIAA0370	exportin 6	protein-coding
mm_104351.1	chr11	94297784	94297819	-	1	NA	exon (NM_026313, exon 7 of 11)	exon (NM_026313, exon 7 of 11)	24110	NM_026313	67684	Mm.30927	NM_026313	ENSMUSG00000020863	Luc7l3	3300001P08Rik|Luc7a	LUC7-like 3 (S. cerevisiae)	protein-coding
mm_80002.1	chr9	67205062	67205093	+	1	NA	Intergenic	Intergenic	31649	NR_029576	387185		NR_029576	ENSMUSG00000076379	Mir190a	Mir190|Mirn190|mir-190|mir-190a|mmu-mir-190|mmu-mir-190a	microRNA 190a	ncRNA
mm_83788.1	chr9	52168793	52168806	-	1	NA	promoter-TSS (NM_001162921)	promoter-TSS (NM_001162921)	-688	NM_001162921	244871	Mm.295686	NM_001162921	ENSMUSG00000035164	Zc3h12c	A230108E06|C230027N18Rik|mKIAA1726	zinc finger CCCH type containing 12C	protein-coding
mm_164715.1	chr17	56103246	56103263	-	1	NA	exon (NM_020568, exon 7 of 9)	exon (NM_020568, exon 7 of 9)	6548	NM_020568	57435	Mm.12966	NM_020568	ENSMUSG00000002831	Plin4	S3-12|mKIAA1881	perilipin 4	protein-coding
mm_11726.1	chr2	36715187	36715196	+	1	NA	Intergenic	Intergenic	-19132	NM_146943	258945	Mm.377764	NM_146943	ENSMUSG00000111863	Olfr347	MOR136-9	olfactory receptor 347	protein-coding
mm_11578.1	chr2	32924506	32924527	+	1	NA	TTS (NM_199302)	TTS (NM_199302)	36739	NM_199302	227738	Mm.248037	NM_199302	ENSMUSG00000026792	Lrsam1	-	leucine rich repeat and sterile alpha motif containing 1	protein-coding
mm_146906.1	chr18	31316983	31316991	-	1	NA	5' UTR (NM_009065, exon 1 of 5)	5' UTR (NM_009065, exon 1 of 5)	141	NM_009065	19762	Mm.5163	NM_009065	ENSMUSG00000057455	Rit2	RIBA|Rin|Roc2	Ras-like without CAAX 2	protein-coding
mm_74060.1	chr8	122376612	122376652	+	1	NA	promoter-TSS (NM_001310650)	promoter-TSS (NM_001310650)	16	NM_001029993	76014	Mm.241489	NM_001029993	ENSMUSG00000017478	Zc3h18	1190001B23Rik|5830416A07Rik|Nhn1	zinc finger CCCH-type containing 18	protein-coding
mm_32199.1	chr4	101420154	101420196	+	1	NA	intron (NM_001177605, intron 2 of 5)	CpG	472	NM_009647	11639	Mm.42040	NM_009647	ENSMUSG00000028527	Ak4	AK 4|Ak-3|Ak-4|Ak3|Ak3l1|D4Ertd274e	adenylate kinase 4	protein-coding
mm_118999.1	chr14	28526180	28526195	+	1	NA	TTS (NM_009524)	TTS (NM_009524)	14782	NM_001256224	22418	Mm.287544	NM_009524	ENSMUSG00000021994	Wnt5a	8030457G12Rik|Wnt-5a	wingless-type MMTV integration site family, member 5A	protein-coding
mm_65905.1	chr7	30193099	30193108	-	1	NA	intron (NM_009795, intron 2 of 10)	intron (NM_009795, intron 2 of 10)	1945	NM_009795	12336	Mm.439782	NM_009795	ENSMUSG00000001794	Capns1	Capa-4|Capa4|Capn4|D7Ertd146e	calpain, small subunit 1	protein-coding
mm_114167.1	chr13	55471681	55471707	+	1	NA	intron (NM_001030296, intron 1 of 2)	CpG	6082	NR_105909	102465569		NR_105909	ENSMUSG00000098341	Mir6944	Gm27710|mmu-mir-6944	microRNA 6944	ncRNA
mm_96416.1	chr11	67255645	67255653	+	1	NA	exon (NM_010855, exon 32 of 40)	exon (NM_010855, exon 32 of 40)	17837	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_100718.1	chr11	3895111	3895136	-	1	NA	promoter-TSS (NM_026150)	promoter-TSS (NM_026150)	3	NM_026150	67430	Mm.347950	NM_026150	ENSMUSG00000020434	4921536K21Rik	AV043724	RIKEN cDNA 4921536K21 gene	protein-coding
mm_129995.1	chr15	86185680	86185766	-	1	NA	5' UTR (NM_145475, exon 1 of 13)	5' UTR (NM_145475, exon 1 of 13)	418	NM_145475	223753	Mm.222685	NM_145475	ENSMUSG00000035891	Cerk	AI848610|D330016D08Rik|mKIAA1646	ceramide kinase	protein-coding
mm_61171.1	chr7	59306556	59306561	+	1	NA	3' UTR (NM_001033962, exon 11 of 11)	3' UTR (NM_001033962, exon 11 of 11)	17591	NR_015479	330544	Mm.9002	NR_015479	ENSMUSG00000100826	C230091D08Rik	-	RIKEN cDNA C230091D08 gene	ncRNA
mm_145408.1	chr18	57468670	57468691	+	1	NA	5' UTR (NM_001134697, exon 1 of 2)	5' UTR (NM_001134697, exon 1 of 2)	194	NM_001134697	629147	Mm.57415	NM_001134697	ENSMUSG00000069372	Ctxn3	ENSMUSG00000069372	cortexin 3	protein-coding
mm_26097.1	chr3	136935251	136935261	+	1	NA	3' UTR (NM_001293622, exon 13 of 13)	3' UTR (NM_001293622, exon 13 of 13)	265190	NM_001293622	19055	Mm.331389	NM_008913	ENSMUSG00000028161	Ppp3ca	2900074D19Rik|CN|Caln|Calna|CnA	protein phosphatase 3, catalytic subunit, alpha isoform	protein-coding
mm_59710.1	chr7	28735959	28735969	+	1	NA	intron (NM_001310687, intron 5 of 6)	intron (NM_001310687, intron 5 of 6)	5817	NM_011885	24030	Mm.358650	NM_011885	ENSMUSG00000045948	Mrps12	AI327385|Rpms12|rps12	mitochondrial ribosomal protein S12	protein-coding
mm_32446.1	chr4	107314364	107314397	+	1	NA	promoter-TSS (NM_001205156)	promoter-TSS (NM_001205156)	17	NM_001205156	230584	Mm.29118	NM_145550	ENSMUSG00000057375	Yipf1	C030002N13Rik	Yip1 domain family, member 1	protein-coding
mm_73192.1	chr8	95411974	95411998	+	1	NA	Intergenic	Intergenic	22883	NM_008187	14894	Mm.2080	NM_008187	ENSMUSG00000031796	Cfap20	2600014O15Rik|AL024127|Gtl3|T10-2A2	cilia and flagella associated protein 20	protein-coding
mm_327.1	chr1	24733802	24733805	+	1	NA	intron (NM_001310483, intron 9 of 15)	intron (NM_001310483, intron 9 of 15)	54885	NM_001310483	68421	Mm.336563	NM_026719	ENSMUSG00000073725	Lmbrd1	0910001K20Rik|AV347960	LMBR1 domain containing 1	protein-coding
mm_30746.1	chr4	14864179	14864195	+	1	NA	promoter-TSS (NM_028264)	promoter-TSS (NM_028264)	-32	NM_028264	72519	Mm.279158	NM_028264	ENSMUSG00000028221	Tmem55a	2610319K07Rik|AI315591|AV001360	transmembrane protein 55A	protein-coding
mm_64140.1	chr7	141215853	141215967	+	1	NA	promoter-TSS (NM_025886)	promoter-TSS (NM_025886)	50	NM_025886	66985	Mm.21202	NM_025886	ENSMUSG00000038618	Rassf7	2400009B11Rik|AW210608	Ras association (RalGDS/AF-6) domain family (N-terminal) member 7	protein-coding
mm_121665.1	chr14	12345810	12345833	-	1	NA	promoter-TSS (NM_080433)	promoter-TSS (NM_080433)	44	NM_080433	54713	Mm.34644	NM_080433	ENSMUSG00000021743	Fezf2	AI451466|AI852056|Fez|Fezl|Zfp312	Fez family zinc finger 2	protein-coding
mm_1693.1	chr1	75142503	75142519	+	1	NA	promoter-TSS (NM_026977)	promoter-TSS (NM_026977)	-143	NM_026977	69171	Mm.28193	NM_026977	ENSMUSG00000033159	Cnppd1	1810031K17Rik|AU043960	cyclin Pas1/PHO80 domain containing 1	protein-coding
mm_148525.1	chr19	4510481	4510487	+	1	NA	promoter-TSS (NM_001162946)	promoter-TSS (NM_001162946)	12	NM_001162946	18563	Mm.1845	NM_008797	ENSMUSG00000024892	Pcx	Pc|Pcb	pyruvate carboxylase	protein-coding
mm_156685.1	chrX	159372292	159372300	+	1	NA	5' UTR (NM_025437, exon 1 of 7)	5' UTR (NM_025437, exon 1 of 7)	101	NM_025437	66235	Mm.294623	NM_025437	ENSMUSG00000067194	Eif1ax	1500010B24Rik|AI426898|Eif1ay	eukaryotic translation initiation factor 1A, X-linked	protein-coding
mm_143054.1	chr17	57004419	57004433	-	1	NA	exon (NM_133801, exon 9 of 13)	exon (NM_133801, exon 9 of 13)	-4321	NM_008954	19197	Mm.86487	NM_008954	ENSMUSG00000002664	Pspn	PSP	persephin	protein-coding
mm_6773.1	chr1	84131759	84131770	-	1	NA	intron (NM_001003948, intron 2 of 2)	MLT1F2|LTR|ERVL-MaLR	87197	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_127284.1	chr15	99972907	99972925	+	1	NA	non-coding (NR_028124, exon 1 of 1)	non-coding (NR_028124, exon 1 of 1)	136	NM_001284523	207214	Mm.28811	NM_001024526	ENSMUSG00000023025	Larp4	DXErtd793|DXErtd793e	La ribonucleoprotein domain family, member 4	protein-coding
mm_80113.1	chr9	70542394	70542416	+	1	NA	promoter-TSS (NM_025690)	promoter-TSS (NM_025690)	-373	NM_026337	66660	Mm.22379	NM_025690	ENSMUSG00000032212	Sltm	5730455C01Rik|5730555F13Rik|9130215G10Rik|Met	SAFB-like, transcription modulator	protein-coding
mm_167498.1	chr9	13296682	13296736	+	1	NA	Intergenic	Intergenic	49753	NM_025534	66396	Mm.290620	NM_025534	ENSMUSG00000079084	Ccdc82	2310043N13Rik	coiled-coil domain containing 82	protein-coding
mm_72367.1	chr8	80933604	80933608	+	1	NA	Intergenic	Intergenic	-53087	NM_001301298	14388	Mm.277409	NM_021356	ENSMUSG00000031714	Gab1	AA408973|AW107238	growth factor receptor bound protein 2-associated protein 1	protein-coding
mm_171348.1	chr4	109117972	109117972	-	1	NA	promoter-TSS (NM_173350)	promoter-TSS (NM_173350)	64	NM_173350	100273	Mm.366315	NM_133885	ENSMUSG00000028559	Osbpl9	2600011I06Rik|AU015843|Orp-9	oxysterol binding protein-like 9	protein-coding
mm_43467.1	chr5	136693597	136693612	+	1	NA	promoter-TSS (NM_001303021)	promoter-TSS (NM_001303021)	-72	NM_001303021	59310	Mm.5178	NM_021611	ENSMUSG00000005474	Myl10	1700027I08Rik|Mylc2pl|PLRLC	myosin, light chain 10, regulatory	protein-coding
mm_13169.1	chr2	92609594	92609604	+	1	NA	intron (NM_023850, intron 1 of 2)	MLTR31C_MM|LTR|ERVK	9892	NM_023850	76969	Mm.38021	NM_023850	ENSMUSG00000027221	Chst1	2610008E20Rik|AW125896|C6ST|GST-1|Gst1|KSGAL6ST	carbohydrate (keratan sulfate Gal-6) sulfotransferase 1	protein-coding
mm_166919.1	chr7	30671645	30671649	-	1	NA	promoter-TSS (NR_027849)	promoter-TSS (NR_027849)	-42	NR_027848	74927	Mm.87326	NM_183108	ENSMUSG00000049761	Pmis2	1700071L20Rik|4930479M11Rik	Pmis2, sperm specific protein	ncRNA
mm_85075.1	chr9	91361699	91361718	-	1	NA	exon (NM_009573, exon 3 of 3)	exon (NM_009573, exon 3 of 3)	4091	NM_009573	22771	Mm.335350	NM_009573	ENSMUSG00000032368	Zic1	ZIC|ZNF201	zinc finger protein of the cerebellum 1	protein-coding
mm_171263.1	chr3	84889493	84889503	-	1	NA	intron (NM_001177773, intron 3 of 13)	ORR1A1|LTR|ERVL-MaLR	25353	NM_001177774	50754	Mm.196475	NM_080428	ENSMUSG00000028086	Fbxw7	1110001A17Rik|AGO|Cdc4|Fbw7|Fbwd6|Fbx30|Fbxo30|Fbxw6|SEL-10	F-box and WD-40 domain protein 7	protein-coding
mm_127249.1	chr15	99670404	99670419	+	1	NA	promoter-TSS (NM_009597)	promoter-TSS (NM_009597)	-307	NM_009597	11419	Mm.440107	NM_009597	ENSMUSG00000023017	Asic1	AI843610|ASIC|ASIC1a|Accn2|B530003N02Rik|BNaC2	acid-sensing (proton-gated) ion channel 1	protein-coding
mm_119506.1	chr14	47381583	47381609	+	1	NA	exon (NM_010705, exon 4 of 6)	exon (NM_010705, exon 4 of 6)	7736	NM_001145953	16854	Mm.248615	NM_010705	ENSMUSG00000050335	Lgals3	GBP|L-34|Mac-2|gal3	lectin, galactose binding, soluble 3	protein-coding
mm_46060.1	chr5	92262782	92262788	-	1	NA	intron (NM_025972, intron 7 of 10)	intron (NM_025972, intron 7 of 10)	-9626	NM_011148	19023	Mm.87155	NM_011148	ENSMUSG00000029410	Ppef2	-	protein phosphatase, EF hand calcium-binding domain 2	protein-coding
mm_143963.1	chr17	87101056	87101059	-	1	NA	Intergenic	Intergenic	-6622	NM_019654	56468	Mm.126885	NM_019654	ENSMUSG00000037104	Socs5	1810018L08Rik|Cish5|mKIAA0671	suppressor of cytokine signaling 5	protein-coding
mm_134544.1	chr16	19883783	19883806	-	1	NA	non-coding (NR_015488, exon 1 of 2)	non-coding (NR_015488, exon 1 of 2)	480	NR_027896	68162	Mm.35159	NR_015488		A930003A15Rik	AI853191	RIKEN cDNA A930003A15 gene	ncRNA
mm_110557.1	chr12	55491701	55491715	-	1	NA	TTS (NR_035430)	TTS (NR_035430)	939	NM_010907	18035	Mm.170515	NM_010907	ENSMUSG00000021025	Nfkbia	AI462015|Nfkbi	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, alpha	protein-coding
mm_15274.1	chr2	155236530	155236599	+	1	NA	promoter-TSS (NM_025947)	promoter-TSS (NM_025947)	31	NM_025947	67068	Mm.23693	NM_025947	ENSMUSG00000047459	Dynlrb1	2010012N15Rik|2010320M17Rik|9430076K19Rik|AV124457|DNLC2A|Dncl2a|km23-1	dynein light chain roadblock-type 1	protein-coding
mm_46302.1	chr5	100500601	100500616	-	1	NA	promoter-TSS (NM_172714)	promoter-TSS (NM_172714)	31	NM_172714	231506	Mm.212568	NM_172714	ENSMUSG00000035310	Lin54	AI461788	lin-54 homolog (C. elegans)	protein-coding
mm_123140.1	chr14	56668022	56668039	-	1	NA	promoter-TSS (NM_023773)	promoter-TSS (NM_023773)	-218	NM_023773	75339	Mm.152466	NM_023773	ENSMUSG00000079184	Mphosph8	1500035L22Rik|4930548G07Rik|AU040635	M-phase phosphoprotein 8	protein-coding
mm_135435.1	chr16	45382964	45382974	-	1	NA	3' UTR (NM_010818, exon 6 of 6)	3' UTR (NM_010818, exon 6 of 6)	26084	NM_010818	17470	Mm.245851	NM_010818	ENSMUSG00000022661	Cd200	Mox2|OX2	CD200 antigen	protein-coding
mm_25216.1	chr3	103846895	103846902	+	1	NA	intron (NM_001142960, intron 3 of 3)	intron (NM_001142960, intron 3 of 3)	-12897	NR_104070	19260	Mm.395	NM_008979	ENSMUSG00000027843	Ptpn22	70zpep|PEP|Ptpn8	protein tyrosine phosphatase, non-receptor type 22 (lymphoid)	protein-coding
mm_170552.1	chr1	94150828	94150840	+	1	NA	Intergenic	L1Md_F2|LINE|L1	-98281	NM_008798	18566	Mm.5024	NM_008798	ENSMUSG00000026285	Pdcd1	Ly101|PD-1|Pdc1	programmed cell death 1	protein-coding
mm_77816.1	chr9	3199945	3199951	+	1	NA	promoter-TSS (NR_027988)	promoter-TSS (NR_027988)	-135	NR_027988	114673	Mm.422774	NM_053265	ENSMUSG00000042360	4930433N12Rik	-	RIKEN cDNA 4930433N12 gene	ncRNA
mm_12649.1	chr2	74745685	74745693	+	1	NA	intron (NM_010468, intron 2 of 2)	intron (NM_010468, intron 2 of 2)	-6995	NR_110447	102634401	Mm.235021	NR_110447	ENSMUSG00000085015	LOC102634401	-	uncharacterized LOC102634401	ncRNA
mm_35152.1	chr4	12087849	12087859	-	1	NA	non-coding (NR_110955, exon 1 of 29)	non-coding (NR_110955, exon 1 of 29)	103	NM_177861	329795	Mm.475125	NM_177861	ENSMUSG00000049488	Tmem67	5330408M12Rik|B230117O07|b2b1163.1Clo|b2b1291.1Clo	transmembrane protein 67	protein-coding
mm_165051.1	chr19	40740945	40740945	-	1	NA	3' UTR (NM_009848, exon 10 of 10)	3' UTR (NM_009848, exon 10 of 10)	81175	NM_009848	12495	Mm.2824	NM_009848	ENSMUSG00000048120	Entpd1	2610206B08Rik|AA408691|Cd39|NTPDase-1	ectonucleoside triphosphate diphosphohydrolase 1	protein-coding
mm_170590.1	chr19	5800864	5800865	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	1808	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_158551.1	chrX	145602327	145602328	-	1	NA	Intergenic	Intergenic	-114688	NM_153319	27494	Mm.100068	NM_153319	ENSMUSG00000041688	Amot	CAG-2|D0Kist1|Sii6	angiomotin	protein-coding
mm_73504.1	chr8	107324932	107324936	+	1	NA	intron (NM_001286260, intron 2 of 12)	AT_rich|Low_complexity|Low_complexity	31464	NM_133957	54446	Mm.390057	NM_018823	ENSMUSG00000003847	Nfat5	AI225870|B130038B15Rik|CAG-8|CAG80|NFATL1|OREBP|TonEBP|mKIAA0827|nfatz	nuclear factor of activated T cells 5	protein-coding
mm_21069.1	chr2	152825755	152825762	-	1	NA	intron (NM_001289717, intron 2 of 2)	intron (NM_001289717, intron 2 of 2)	4959	NM_001289716	12048	Mm.238213	NM_009743	ENSMUSG00000007659	Bcl2l1	Bcl(X)L|Bcl-XL|Bcl2l|BclX|bcl-x|bcl2-L-1	BCL2-like 1	protein-coding
mm_110494.1	chr12	54141912	54141923	-	1	NA	Intergenic	Intergenic	61957	NM_028133	112407	Mm.133037	NM_028133	ENSMUSG00000035105	Egln3	2610021G09Rik|AI505553|AI648162|Hif-p4h-3|Phd3|SM-20	egl-9 family hypoxia-inducible factor 3	protein-coding
mm_154429.1	chrM	571	581	-	1	NA	NA	Intergenic	NA	NA								
mm_81276.1	chr9	108264069	108264086	+	1	NA	promoter-TSS (NM_001276486)	promoter-TSS (NM_001276486)	-119	NM_001276486	13138	Mm.7524	NM_010017	ENSMUSG00000039952	Dag1	D9Wsu13e|DG|Dp427|Dp71	dystroglycan 1	protein-coding
mm_70804.1	chr8	22974847	22974882	+	1	NA	promoter-TSS (NM_001110783)	promoter-TSS (NM_001110783)	28	NM_001277280	11733	Mm.334444	NM_031158	ENSMUSG00000031543	Ank1	Ank-1|nb|pale	ankyrin 1, erythroid	protein-coding
mm_121554.1	chr14	122479416	122479420	+	1	NA	3' UTR (NM_009574, exon 3 of 3)	3' UTR (NM_009574, exon 3 of 3)	4034	NM_009574	22772	Mm.308936	NM_009574	ENSMUSG00000061524	Zic2	HPE5|Ku	zinc finger protein of the cerebellum 2	protein-coding
mm_29397.1	chr3	108904557	108904563	-	1	NA	exon (NM_025845, exon 6 of 6)	exon (NM_025845, exon 6 of 6)	7144	NM_025845	66921	Mm.51049	NM_025845	ENSMUSG00000027881	Prpf38b	1110021E09Rik|AU018955	PRP38 pre-mRNA processing factor 38 (yeast) domain containing B	protein-coding
mm_22130.1	chr2	170406502	170406518	-	1	NA	exon (NM_001164369, exon 4 of 12)	exon (NM_001164369, exon 4 of 12)	21335	NM_001164369	76960	Mm.240850	NM_029815	ENSMUSG00000013523	Bcas1	2210416M21Rik|9030223A09Rik|AI841227|NABC1	breast carcinoma amplified sequence 1	protein-coding
mm_32745.1	chr4	116651509	116651535	+	1	NA	5' UTR (NM_021473, exon 1 of 9)	5' UTR (NM_021473, exon 1 of 9)	152	NM_021473	58810	Mm.30085	NM_021473	ENSMUSG00000028692	Akr1a1	2610201A18Rik|Akr1a4	aldo-keto reductase family 1, member A1 (aldehyde reductase)	protein-coding
mm_5016.1	chr1	192892876	192892880	+	1	NA	3' UTR (NM_181546, exon 8 of 8)	3' UTR (NM_181546, exon 8 of 8)	-37126	NM_198247	214791	Mm.22806	NM_198247	ENSMUSG00000016262	Sertad4	4833404A09|C130018M11Rik	SERTA domain containing 4	protein-coding
mm_62567.1	chr7	104219405	104219410	+	1	NA	intron (NM_001013616, intron 1 of 7)	intron (NM_001013616, intron 1 of 7)	612	NM_001013616	94088	Mm.274843	NM_001013616	ENSMUSG00000072244	Trim6	C430046K18Rik|D7Ertd684e	tripartite motif-containing 6	protein-coding
mm_55868.1	chr6	83459106	83459112	-	1	NA	Intergenic	Intergenic	-2717	NM_001347313	194388	Mm.211030	NM_183138	ENSMUSG00000034832	Tet3	B430006D22Rik|BC037432|D230004J03Rik	tet methylcytosine dioxygenase 3	protein-coding
mm_51086.1	chr6	67036641	67036676	+	1	NA	promoter-TSS (NR_040278)	promoter-TSS (NR_040278)	59	NR_040278	320172	Mm.449039	NR_040278	ENSMUSG00000087231	E230016M11Rik	-	RIKEN cDNA E230016M11 gene	ncRNA
mm_32180.1	chr4	100819435	100819459	+	1	NA	intron (NM_198037, intron 1 of 26)	intron (NM_198037, intron 1 of 26)	42768	NM_198037	320508	Mm.151962	NM_198037	ENSMUSG00000028532	Cachd1	1190007F10Rik|AI852726|B430218L07Rik|Vwcd1|mKIAA1573	cache domain containing 1	protein-coding
mm_17585.1	chr2	30415635	30415708	-	1	NA	promoter-TSS (NM_007760)	promoter-TSS (NM_007760)	77	NM_007760	12908	Mm.20396	NM_007760	ENSMUSG00000026853	Crat	AW107812|CARAT	carnitine acetyltransferase	protein-coding
mm_83647.1	chr9	49505434	49505458	-	1	NA	exon (NM_001311065, exon 18 of 18)	exon (NM_001311065, exon 18 of 18)	-12842	NR_029465	100036537	Mm.437541	NR_029465	ENSMUSG00000079564	Gm11149	ENSMUSG00000060603|ENSMUSG00000079564	predicted gene 11149	ncRNA
mm_33502.1	chr4	130826214	130826231	+	1	NA	TTS (NM_011520)	TTS (NM_011520)	33685	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_167946.1	chrX	137537616	137537618	-	1	NA	Intergenic	Intergenic	-33137	NM_030688	60367	Mm.328321	NM_030688	ENSMUSG00000059203	Il1rapl2	-	interleukin 1 receptor accessory protein-like 2	protein-coding
mm_114925.1	chr13	95531915	95531923	+	1	NA	Intergenic	Intergenic	-6679	NM_007974	14063	Mm.1614	NM_007974	ENSMUSG00000021678	F2rl1	Gpcr11|PAR-2|Par2	coagulation factor II (thrombin) receptor-like 1	protein-coding
mm_158426.1	chrX	139796371	139796399	-	1	NA	Intergenic	Intergenic	-4423	NM_016675	12738	Mm.117068	NM_016675	ENSMUSG00000047230	Cldn2	AL022813	claudin 2	protein-coding
mm_44147.1	chr5	150259923	150259936	+	1	NA	promoter-TSS (NM_172887)	promoter-TSS (NM_172887)	-1	NM_172887	320365	Mm.216590	NM_172887	ENSMUSG00000056602	Fry	13CDNA73|9330186A19Rik|AF346502|AI462658|C87180|D930046M03|cg003|mKIAA4143	FRY microtubule binding protein	protein-coding
mm_11167.1	chr2	28557977	28558017	+	1	NA	exon (NM_009885, exon 8 of 11)	exon (NM_009885, exon 8 of 11)	5406	NM_009885	12613	Mm.236017	NM_009885	ENSMUSG00000026818	Cel	1810036E18Rik|BAL	carboxyl ester lipase	protein-coding
mm_132021.1	chr16	26463466	26463478	+	1	NA	5' UTR (NM_053241, exon 1 of 5)	5' UTR (NM_053241, exon 1 of 5)	337	NM_053241	114141	Mm.275205	NM_053241	ENSMUSG00000038148	Cldn16	PCLN1|claudin-16	claudin 16	protein-coding
mm_78785.1	chr9	44032171	44032181	+	1	NA	Intergenic	Intergenic	-11208	NM_009382	21838	Mm.3951	NM_009382	ENSMUSG00000032011	Thy1	CD90|T25|Thy-1|Thy-1.2|Thy1.1|Thy1.2	thymus cell antigen 1, theta	protein-coding
mm_56739.1	chr6	115762347	115762380	-	1	NA	5' UTR (NM_001168257, exon 1 of 11)	5' UTR (NM_001168257, exon 1 of 11)	103	NM_001168256	94346	Mm.29739	NM_144805	ENSMUSG00000059900	Tmem40	9030407H20Rik|AV091463|W64236	transmembrane protein 40	protein-coding
mm_17292.1	chr2	26206536	26206580	-	1	NA	promoter-TSS (NM_001039653)	promoter-TSS (NM_001039653)	17	NM_001039653	16871	Mm.386765	NM_010711	ENSMUSG00000026934	Lhx3	Lim3|P-LIM|mLIM3|mLim-3	LIM homeobox protein 3	protein-coding
mm_42394.1	chr5	114937389	114937401	+	1	NA	exon (NM_145209, exon 7 of 7)	exon (NM_145209, exon 7 of 7)	-4807	NM_028211	72357	Mm.292672	NM_028211	ENSMUSG00000029559	2210016L21Rik	-	RIKEN cDNA 2210016L21 gene	protein-coding
mm_118220.1	chr13	110357137	110357195	-	1	NA	promoter-TSS (NM_177713)	promoter-TSS (NM_177713)	6	NM_177713	238875	Mm.30533	NM_177713	ENSMUSG00000046006	Gapt	9830130M13Rik	Grb2-binding adaptor, transmembrane	protein-coding
mm_3417.1	chr1	144967619	144967619	+	1	NA	Intergenic	RMER1B|Other|Other	-192198	NM_022881	64214	Mm.253927	NM_022881	ENSMUSG00000026357	Rgs18	-	regulator of G-protein signaling 18	protein-coding
mm_118786.1	chr14	24104178	24104193	+	1	NA	Intergenic	Intergenic	15308	NR_106069	102465697		NR_106069	ENSMUSG00000105723	Mir7210	mir-7210|mmu-mir-7210	microRNA 7210	ncRNA
mm_155829.1	chrX	100730127	100730141	+	1	NA	promoter-TSS (NM_001305941)	promoter-TSS (NM_001305941)	-52	NM_001305941	71584	Mm.283495	NM_023608	ENSMUSG00000019359	Gdpd2	9130017L10Rik|Gde3|Obdpf	glycerophosphodiester phosphodiesterase domain containing 2	protein-coding
mm_14496.1	chr2	131951012	131951028	+	1	NA	promoter-TSS (NM_001278520)	promoter-TSS (NM_001278520)	-17	NM_001278520	26434	Mm.180750	NM_023043	ENSMUSG00000027338	Prnd	AI450264|Dpl|PrPLP|doppel	prion protein dublet	protein-coding
mm_75526.1	chr8	57306414	57306444	-	1	NA	intron (NR_110474, intron 3 of 4)	B1_Mur4|SINE|Alu	14430	NR_110474	102636514		NR_110474	ENSMUSG00000100510	Uph	-	upperhand	ncRNA
mm_160439.1	chr8	95110376	95110376	-	1	NA	intron (NM_001145831, intron 6 of 21)	intron (NM_001145831, intron 6 of 21)	2966	NM_001145832	16582	Mm.378951	NM_010631	ENSMUSG00000031788	Kifc3	AI325457|BB123200	kinesin family member C3	protein-coding
mm_2339.1	chr1	92848709	92848727	+	1	NA	intron (NM_016696, intron 1 of 8)	CpG	-1660	NR_029559	387167		NR_029559	ENSMUSG00000065470	Mir149	Mirn149|mir-149|mmu-mir-149	microRNA 149	ncRNA
mm_125700.1	chr15	66909290	66909300	+	1	NA	intron (NM_018865, intron 2 of 4)	intron (NM_018865, intron 2 of 4)	17902	NM_018865	22402	Mm.10222	NM_018865	ENSMUSG00000005124	Wisp1	AW146261|CCN4|Elm1	WNT1 inducible signaling pathway protein 1	protein-coding
mm_156447.1	chrX	142681884	142681900	+	1	NA	5' UTR (NM_001199360, exon 1 of 7)	5' UTR (NM_001199360, exon 1 of 7)	166	NM_001199360	209497	Mm.249648	NM_177592	ENSMUSG00000047045	Tmem164	AI316850|AI852450|AW547186|F730011B02	transmembrane protein 164	protein-coding
mm_87812.1	chr10	60301919	60301939	+	1	NA	TTS (NM_001252635)	TTS (NM_001252635)	17468	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_88263.1	chr10	73845349	73845352	+	1	NA	intron (NM_001142740, intron 1 of 31)	intron (NM_001142740, intron 1 of 31)	23483	NM_001142735	11994	Mm.338933	NM_023115	ENSMUSG00000052613	Pcdh15	BB078305|ENSMUSG00000046980|Gm9815|Ush1f|av|nmf19|roda	protocadherin 15	protein-coding
mm_47122.1	chr5	119691257	119691266	-	1	NA	promoter-TSS (NR_040416)	promoter-TSS (NR_040416)	-43	NR_040416	433944	Mm.491053	NR_040416	ENSMUSG00000086847	Tbx3os2	Gm16065|OTTMUSG00000029666	T-box 3, opposite strand 2	ncRNA
mm_46071.1	chr5	92322811	92322826	-	1	NA	3' UTR (NM_008599, exon 4 of 4)	3' UTR (NM_008599, exon 4 of 4)	5261	NM_008599	17329	Mm.766	NM_008599	ENSMUSG00000029417	Cxcl9	BB139920|CMK|Mig|MuMIG|Scyb9|crg-10	chemokine (C-X-C motif) ligand 9	protein-coding
mm_27309.1	chr3	50366518	50366527	-	1	NA	3' UTR (NM_011990, exon 12 of 12)	3' UTR (NM_011990, exon 12 of 12)	77091	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_141951.1	chr17	35085610	35085615	-	1	NA	promoter-TSS (NM_001163192)	promoter-TSS (NM_001163192)	-17	NM_001163192	433099	Mm.328993	NM_001163192	ENSMUSG00000034923	Ly6g6f	CJ068215	lymphocyte antigen 6 complex, locus G6F	protein-coding
mm_100453.1	chr11	119680994	119681030	+	1	NA	intron (NM_028898, intron 3 of 33)	intron (NM_028898, intron 3 of 33)	78107	NM_028898	74370	Mm.209933	NM_028898	ENSMUSG00000025583	Rptor	4932417H02Rik|Rap|Raptor|mKIAA1303	regulatory associated protein of MTOR, complex 1	protein-coding
mm_173361.1	chrY	90819532	90819536	+	1	NA	Intergenic	IMPB_01|Satellite|Satellite	19872	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_153925.1	chr19	47314819	47314829	-	1	NA	intron (NM_001164717, intron 7 of 13)	intron (NM_001164717, intron 7 of 13)	-41235	NR_105961	102466782		NR_105961	ENSMUSG00000098786	Mir6995	Gm27576|mmu-mir-6995	microRNA 6995	ncRNA
mm_144599.1	chr18	32377295	32377317	+	1	NA	promoter-TSS (NM_009668)	promoter-TSS (NM_009668)	89	NM_009668	30948	Mm.4383	NM_009668	ENSMUSG00000024381	Bin1	ALP-1|Amphl|BRAMP-2|SH3P9	bridging integrator 1	protein-coding
mm_151735.1	chr19	4926956	4926967	-	1	NA	exon (NM_133803, exon 2 of 18)	exon (NM_133803, exon 2 of 18)	1326	NM_133803	75221	Mm.234769	NM_133803	ENSMUSG00000063904	Dpp3	4930533O14Rik|C86324	dipeptidylpeptidase 3	protein-coding
mm_86793.1	chr10	20208436	20208446	+	1	NA	promoter-TSS (NM_001101561)	promoter-TSS (NM_001101561)	2	NM_001101561	621697	Mm.440587	NM_001101561		Rpl32l	EG621697|Gm6251	ribosomal protein L32-like	protein-coding
mm_87977.1	chr10	63655189	63655194	+	1	NA	intron (NM_177612, intron 5 of 17)	Lx7|LINE|L1	-165864	NM_001164519	216033	Mm.444692	NM_177612	ENSMUSG00000060843	Ctnna3	4930429L08Rik|4933408A16|Catna3|Vr22	catenin (cadherin associated protein), alpha 3	protein-coding
mm_68163.1	chr7	103812550	103812572	-	1	NA	TTS (NM_016956)	TTS (NM_016956)	1362	NM_016956	15130	Mm.288567	NM_016956		Hbb-b2	AI036344|Hbb2|Hbbt2|beta2	hemoglobin, beta adult minor chain	protein-coding
mm_3473.1	chr1	150104946	150104998	+	1	NA	exon (NM_011198, exon 9 of 10)	exon (NM_011198, exon 9 of 10)	4941	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_52883.1	chr6	122513644	122513668	+	1	NA	promoter-TSS (NM_015776)	promoter-TSS (NM_015776)	-20	NM_015776	50530	Mm.41931	NM_015776	ENSMUSG00000030116	Mfap5	MAGP-2|MFAP-5	microfibrillar associated protein 5	protein-coding
mm_101672.1	chr11	37236142	37236189	-	1	NA	Intergenic	Intergenic	-291924	NM_011856	23964	Mm.439889	NM_011856	ENSMUSG00000049336	Tenm2	Odz2|Odz3|Ten-2|Ten-m2	teneurin transmembrane protein 2	protein-coding
mm_115806.1	chr13	19358319	19358367	-	1	NA	intron (NM_024270, intron 8 of 8)	intron (NM_024270, intron 8 of 8)	37470	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_9682.1	chr1	178333027	178333040	-	1	NA	exon (NM_016805, exon 6 of 14)	exon (NM_016805, exon 6 of 14)	4751	NM_016805	51810	Mm.86589	NM_016805	ENSMUSG00000039630	Hnrnpu	AA408410|AI256620|AL024194|AL024437|AW557595|C86794|Hnrpu|SAFA|Sp120|hnRNP U	heterogeneous nuclear ribonucleoprotein U	protein-coding
mm_38438.1	chr4	139622626	139622675	-	1	NA	promoter-TSS (NM_175438)	promoter-TSS (NM_175438)	-244	NM_175438	212647	Mm.273571	NM_175438	ENSMUSG00000028737	Aldh4a1	A930035F14Rik|Ahd-1|Ahd1|Aldh4|Aldh5a1|E330022C09|P5cd|P5cdh|P5cdhl|P5cdhs|Ssdh1	aldehyde dehydrogenase 4 family, member A1	protein-coding
mm_152155.1	chr19	7241163	7241199	-	1	NA	promoter-TSS (NM_027643)	promoter-TSS (NM_027643)	41	NM_027643	70999	Mm.329605	NM_027643	ENSMUSG00000024764	Naa40	4931433E08Rik|AU023197|Nat11	N(alpha)-acetyltransferase 40, NatD catalytic subunit	protein-coding
mm_172567.1	chr8	111310236	111310236	-	1	NA	Intergenic	Intergenic	-10014	NM_146218	234736	Mm.334816	NM_146218	ENSMUSG00000033596	Rfwd3	BC027246	ring finger and WD repeat domain 3	protein-coding
mm_18872.1	chr2	76215025	76215049	-	1	NA	intron (NM_001081033, intron 3 of 19)	intron (NM_001081033, intron 3 of 19)	123616	NM_001081033	241489	Mm.246613	NM_001081033	ENSMUSG00000075270	Pde11a	6330414F14Rik|A630086N24Rik|Gm350|PDE11A1	phosphodiesterase 11A	protein-coding
mm_132238.1	chr16	32750689	32750707	+	1	NA	exon (NM_080457, exon 2 of 27)	exon (NM_080457, exon 2 of 27)	14812	NM_080457	140474	Mm.214599	NM_080457	ENSMUSG00000079620	Muc4	4933405I11Rik|Asgp	mucin 4	protein-coding
mm_54030.1	chr6	12315264	12315280	-	1	NA	3' UTR (NM_001164805, exon 27 of 27)	3' UTR (NM_001164805, exon 27 of 27)	-205692	NR_003631	625347	Mm.389084	NM_001039041	ENSMUSG00000057223	Gm6578	EG625347	mitochondrial ribosomal protein L32 pseudogene	pseudo
mm_53060.1	chr6	124830194	124830209	+	1	NA	promoter-TSS (NM_013538)	promoter-TSS (NM_013538)	25	NM_013538	14793	Mm.285723	NM_013538	ENSMUSG00000023505	Cdca3	2410005A12Rik|C8|Grcc8|Tome-1	cell division cycle associated 3	protein-coding
mm_73007.1	chr8	93810991	93811007	+	1	NA	TTS (NR_026888)	TTS (NR_026888)	161	NM_001113384	14681	Mm.251445	NM_010308	ENSMUSG00000031748	Gnao1	AW050213|Galphao|Gnao|alphaO	guanine nucleotide binding protein, alpha O	protein-coding
mm_43277.1	chr5	130836765	130836768	+	1	NA	intron (NM_021371, intron 5 of 5)	intron (NM_021371, intron 5 of 5)	387974	NM_021371	140904	Mm.40875	NM_021371	ENSMUSG00000060371	Caln1	9630012C17Rik|Cabp8|MNCb-0849	calneuron 1	protein-coding
mm_150543.1	chr19	39315481	39315488	+	1	NA	intron (NM_007815, intron 5 of 8)	MurERV4-int|LTR|ERVK	28399	NM_007815	13095	Mm.20764	NM_007815	ENSMUSG00000003053	Cyp2c29	AHOH|AHOHase|AI159681|AI196010|Ah-2|Ahh-1|Cyp2c|P450-2C	cytochrome P450, family 2, subfamily c, polypeptide 29	protein-coding
mm_923.1	chr1	55131318	55131331	+	1	NA	promoter-TSS (NM_025283)	promoter-TSS (NM_025283)	79	NM_025283	19070	Mm.291037	NM_025283	ENSMUSG00000025979	Mob4	2610109B12Rik|Mobkl3|Phocn|Prei3	MOB family member 4, phocein	protein-coding
mm_129497.1	chr15	78850978	78850995	-	1	NA	TTS (NM_027219)	TTS (NM_027219)	4543	NM_025622	107753	Mm.390793	NM_025622	ENSMUSG00000043501	Lgals2	2200008F12Rik|AI324147	lectin, galactose-binding, soluble 2	protein-coding
mm_125138.1	chr15	30496803	30496808	+	1	NA	intron (NM_008729, intron 3 of 22)	(T)n|Simple_repeat|Simple_repeat	324212	NM_008729	18163	Mm.321648	NM_008729	ENSMUSG00000022240	Ctnnd2	Catnd2|Nprap|neurojugin	catenin (cadherin associated protein), delta 2	protein-coding
mm_81909.1	chr9	120013043	120013077	+	1	NA	TTS (NM_011724)	TTS (NM_011724)	10538	NM_011724	22437	Mm.10117	NM_011724	ENSMUSG00000079243	Xirp1	AI415219|Cmya1	xin actin-binding repeat containing 1	protein-coding
mm_151861.1	chr19	5797259	5797268	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	-1282	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_15719.1	chr2	164074103	164074117	+	1	NA	promoter-TSS (NM_021420)	promoter-TSS (NM_021420)	-68	NM_021420	58231	Mm.234472	NM_021420	ENSMUSG00000018209	Stk4	AI447339|AU020804|Kas-2|Mst1|Ysk3	serine/threonine kinase 4	protein-coding
mm_54268.1	chr6	28831942	28831977	-	1	NA	promoter-TSS (NM_138682)	promoter-TSS (NM_138682)	-212	NM_138682	192198	Mm.443660	NM_138682	ENSMUSG00000049939	Lrrc4	MBAG1|NGL-2|NGL2|NLG-2|Nag14	leucine rich repeat containing 4	protein-coding
mm_23875.1	chr3	83030243	83030259	+	1	NA	exon (NM_010196, exon 4 of 5)	exon (NM_010196, exon 4 of 5)	4098	NM_001111048	14161	Mm.88793	NM_010196	ENSMUSG00000028001	Fga	ENSMUSG00000059807|Fib	fibrinogen alpha chain	protein-coding
mm_124322.1	chr14	103651376	103651384	-	1	NA	intron (NM_198014, intron 1 of 6)	intron (NM_198014, intron 1 of 6)	1137	NM_198014	105439	Mm.27548	NM_198014	ENSMUSG00000055717	Slain1	9630044O09Rik|AA675320|AW742596	SLAIN motif family, member 1	protein-coding
mm_121867.1	chr14	20734318	20734361	-	1	NA	TTS (NM_178597)	TTS (NM_178597)	223	NM_010811	17423	Mm.4084	NM_010811	ENSMUSG00000039308	Ndst2	Mndns|NDST-2	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 2	protein-coding
mm_767.1	chr1	44119452	44119519	+	1	NA	promoter-TSS (NM_144558)	promoter-TSS (NM_144558)	-483	NM_144558	246229	Mm.386883	NM_144558	ENSMUSG00000041684	Bivm	AI854267	basic, immunoglobulin-like variable motif containing	protein-coding
mm_45095.1	chr5	44226656	44226664	-	1	NA	promoter-TSS (NM_173764)	promoter-TSS (NM_173764)	-54	NM_173764	231225	Mm.30688	NM_173764	ENSMUSG00000046985	Tapt1	4932414K18Rik	transmembrane anterior posterior transformation 1	protein-coding
mm_29130.1	chr3	105687422	105687457	-	1	NA	5' UTR (NM_017397, exon 1 of 11)	5' UTR (NM_017397, exon 1 of 11)	132	NM_017397	53975	Mm.272826	NM_017397	ENSMUSG00000027905	Ddx20	GEMIN3|dp103	DEAD (Asp-Glu-Ala-Asp) box polypeptide 20	protein-coding
mm_161080.1	chr12	83688550	83688550	+	1	NA	promoter-TSS (NM_008943)	promoter-TSS (NM_008943)	-13	NM_008943	19164	Mm.998	NM_008943	ENSMUSG00000019969	Psen1	Ad3h|PS-1|PS1|S182	presenilin 1	protein-coding
mm_93940.1	chr10	127191545	127191556	-	1	NA	exon (NM_030714, exon 5 of 6)	exon (NM_030714, exon 5 of 6)	-1496	NM_028027	52666	Mm.272230	NM_028027	ENSMUSG00000019467	Arhgef25	2410008H17Rik|D10Ertd610e|GEFT	Rho guanine nucleotide exchange factor (GEF) 25	protein-coding
mm_79400.1	chr9	54950839	54950852	+	1	NA	promoter-TSS (NM_011966)	promoter-TSS (NM_011966)	-14	NM_011966	26441	Mm.30270	NM_011966	ENSMUSG00000032301	Psma4	C9	proteasome (prosome, macropain) subunit, alpha type 4	protein-coding
mm_16877.1	chr2	12419428	12419448	-	1	NA	promoter-TSS (NM_024185)	promoter-TSS (NM_024185)	22	NM_024185	66960	Mm.34059	NM_024185	ENSMUSG00000026767	Fam188a	1810041E18Rik|2310047O13Rik|5830410F13Rik|AI447827|AW111958	family with sequence similarity 188, member A	protein-coding
mm_130354.1	chr15	97767051	97767073	-	1	NA	intron (NM_144850, intron 1 of 27)	intron (NM_144850, intron 1 of 27)	604	NM_001177810	223864	Mm.24028	NM_144850	ENSMUSG00000022469	Rapgef3	2310016P22Rik|9330170P05Rik|Epac|Epac1	Rap guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_157784.1	chrX	73824406	73824423	-	1	NA	5' UTR (NM_001290540, exon 1 of 6)	5' UTR (NM_001290540, exon 1 of 6)	555	NM_001029868	245469	Mm.103782	NM_001029868	ENSMUSG00000002006	Pdzd4	B230341P03|D130075J17Rik|Kiaa1444-hp|LU1|PDZRN4L|Pdzk4|Pdzrnk4l|Xlu	PDZ domain containing 4	protein-coding
mm_125479.1	chr15	54571471	54571507	+	1	NA	5' UTR (NM_178920, exon 1 of 4)	5' UTR (NM_178920, exon 1 of 4)	123	NM_178920	105853	Mm.410994	NM_178920	ENSMUSG00000024479	Mal2	AI461653	mal, T cell differentiation protein 2	protein-coding
mm_25899.1	chr3	131111196	131111216	+	1	NA	5' UTR (NM_001276402, exon 1 of 10)	5' UTR (NM_001276402, exon 1 of 10)	909	NM_001276402	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_157488.1	chrX	48256659	48256673	-	1	NA	promoter-TSS (NM_028276)	promoter-TSS (NM_028276)	-268	NM_028276	72554	Mm.336045	NM_028276	ENSMUSG00000063785	Utp14a	2700066J21Rik|JsdX|NY-CO-16|SDCCAG16|T25628|mKIAA0266	UTP14A small subunit processome component	protein-coding
mm_120057.1	chr14	56674624	56674626	+	1	NA	exon (NM_023773, exon 3 of 14)	exon (NM_023773, exon 3 of 14)	6377	NM_023773	75339	Mm.152466	NM_023773	ENSMUSG00000079184	Mphosph8	1500035L22Rik|4930548G07Rik|AU040635	M-phase phosphoprotein 8	protein-coding
mm_108549.1	chr12	84409138	84409152	+	1	NA	promoter-TSS (NM_028377)	promoter-TSS (NM_028377)	77	NM_028377	72873	Mm.440428	NM_028377	ENSMUSG00000057265	Bbof1	2900006K08Rik|AI427784|Ccdc176	basal body orientation factor 1	protein-coding
mm_78077.1	chr9	15709716	15709748	+	1	NA	promoter-TSS (NM_172289)	promoter-TSS (NM_172289)	-37	NM_172289	234967	Mm.138815	NM_172289	ENSMUSG00000043885	Slc36a4	6330573I15Rik|PAT4	solute carrier family 36 (proton/amino acid symporter), member 4	protein-coding
mm_18597.1	chr2	66784923	66784949	-	1	NA	promoter-TSS (NM_009135)	promoter-TSS (NM_009135)	-26	NM_009135	20272	Mm.38127	NM_009135	ENSMUSG00000034810	Scn7a	1110034K09Rik|AI642000|NaG|Nav2|Nav2.3|Nax|Scn6a	sodium channel, voltage-gated, type VII, alpha	protein-coding
mm_160952.1	chr11	97699310	97699310	-	1	NA	promoter-TSS (NM_001163307)	promoter-TSS (NM_001163307)	74	NM_001163307	22658	Mm.2418	NM_009545	ENSMUSG00000018537	Pcgf2	Mel18|Rnf110|Zfp144|mel-18	polycomb group ring finger 2	protein-coding
mm_89559.1	chr10	95318458	95318467	+	1	NA	intron (NM_009950, intron 2 of 2)	intron (NM_009950, intron 2 of 2)	5247	NM_001330138	12905	Mm.473739	NM_009950	ENSMUSG00000045867	Cradd	RAIDD	CASP2 and RIPK1 domain containing adaptor with death domain	protein-coding
mm_104489.1	chr11	95831802	95831823	-	1	NA	3' UTR (NM_001163464, exon 8 of 8)	3' UTR (NM_001163464, exon 8 of 8)	7312	NM_153104	237928	Mm.133075	NM_153104	ENSMUSG00000050860	Phospho1	D11Moh36|Phospo1	phosphatase, orphan 1	protein-coding
mm_15910.1	chr2	165059292	165059304	+	1	NA	intron (NM_170702, intron 1 of 7)	B3A|SINE|B2	3662	NM_011611	21939	Mm.271833	NM_011611	ENSMUSG00000017652	Cd40	AI326936|Bp50|GP39|HIGM1|IGM|IMD3|T-BAM|TRAP|Tnfrsf5|p50	CD40 antigen	protein-coding
mm_10679.1	chr2	21509084	21509085	+	1	NA	intron (NM_001004761, intron 2 of 10)	L1ME3A|LINE|L1	141517	NM_001004761	241263	Mm.166647	NM_175706	ENSMUSG00000045967	Gpr158	5330427M13Rik|mKIAA1136	G protein-coupled receptor 158	protein-coding
mm_149066.1	chr19	8841206	8841239	+	1	NA	exon (NM_008144, exon 2 of 11)	exon (NM_008144, exon 2 of 11)	719	NM_001290823	14705	Mm.345134	NM_008144	ENSMUSG00000071657	Bscl2	2900097C17Rik|AI046355|Gng3lg	Berardinelli-Seip congenital lipodystrophy 2 (seipin)	protein-coding
mm_141003.1	chr17	24936970	24937002	-	1	NA	promoter-TSS (NM_001163447)	promoter-TSS (NM_001163447)	-9	NM_013931	30957	Mm.43081	NM_013931	ENSMUSG00000024163	Mapk8ip3	BB120594|D17Wsu15e|JIP-3|JSAP1|JSAP1a|JSAP1b|JSAP1c|JSAP1d|Jip3|Syd2|mKIAA1066	mitogen-activated protein kinase 8 interacting protein 3	protein-coding
mm_33258.1	chr4	127169132	127169230	+	1	NA	promoter-TSS (NM_198618)	promoter-TSS (NM_198618)	-23	NM_198618	242667	Mm.331885	NM_198618	ENSMUSG00000042388	Dlgap3	BC058433|DAP-3|DAP3|Prpl8|Sapap3	discs, large (Drosophila) homolog-associated protein 3	protein-coding
mm_41326.1	chr5	90474559	90474682	+	1	NA	exon (NM_009654, exon 13 of 15)	exon (NM_009654, exon 13 of 15)	13750	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_116328.1	chr13	38031945	38031951	-	1	NA	intron (NM_027724, intron 2 of 12)	intron (NM_027724, intron 2 of 12)	4989	NM_027724	71213	Mm.314688	NM_027724	ENSMUSG00000044566	Cage1	4933427I01Rik|Ctag3	cancer antigen 1	protein-coding
mm_36798.1	chr4	103120208	103120224	-	1	NA	intron (NM_001039081, intron 1 of 12)	ID4|SINE|ID	826	NM_001039081	71148	Mm.288721	NM_027696	ENSMUSG00000028522	Mier1	4933425I22Rik|5830411K19Rik|er1	MEIR1 treanscription regulator	protein-coding
mm_15519.1	chr2	158324588	158324594	+	1	NA	exon (NM_008489, exon 10 of 15)	exon (NM_008489, exon 10 of 15)	18098	NM_008489	16803	Mm.218846	NM_008489	ENSMUSG00000016024	Lbp	Bpifd2|Ly88	lipopolysaccharide binding protein	protein-coding
mm_151481.1	chr19	58676251	58676263	+	1	NA	exon (NM_026925, exon 7 of 13)	exon (NM_026925, exon 7 of 13)	5892	NM_026925	69060	Mm.20407	NM_026925	ENSMUSG00000046008	Pnlip	1810007A24Rik|PL|PTL	pancreatic lipase	protein-coding
mm_4379.1	chr1	172148111	172148176	+	1	NA	5' UTR (NM_153555, exon 1 of 14)	5' UTR (NM_153555, exon 1 of 14)	128	NM_153555	98193	Mm.159915	NM_153555	ENSMUSG00000026554	Dcaf8	AA408877|AA433120|AA792214|AU018973|C76055|D1Dau35e|D1Ucla4|H326|Wdr42a	DDB1 and CUL4 associated factor 8	protein-coding
mm_77810.1	chr9	3037331	3037355	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	1400	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_166826.1	chr7	18524765	18524793	-	1	NA	exon (NM_054060, exon 4 of 5)	exon (NM_054060, exon 4 of 5)	7448	NM_054060	114868	Mm.389809	NM_054060	ENSMUSG00000070798	Psg25	cea13	pregnancy-specific glycoprotein 25	protein-coding
mm_21551.1	chr2	164071125	164071146	-	1	NA	promoter-TSS (NM_001291155)	promoter-TSS (NM_001291155)	-33	NM_025996	67145	Mm.23173	NM_025996	ENSMUSG00000018322	Tomm34	2610100K07Rik|TOM34	translocase of outer mitochondrial membrane 34	protein-coding
mm_14773.1	chr2	145786325	145786335	+	1	NA	5' UTR (NM_028724, exon 2 of 13)	5' UTR (NM_028724, exon 2 of 13)	214	NM_028724	74030	Mm.228799	NM_028724	ENSMUSG00000001768	Rin2	2010003K16Rik|4632403N06Rik|AW821980|RASSF4	Ras and Rab interactor 2	protein-coding
mm_10392.1	chr2	13481071	13481101	+	1	NA	intron (NM_001081084, intron 6 of 66)	intron (NM_001081084, intron 6 of 66)	10790	NM_001081084	65969	Mm.313915	NM_001081084	ENSMUSG00000026726	Cubn	AA408369|AL022750|D2Wsu88e	cubilin (intrinsic factor-cobalamin receptor)	protein-coding
mm_144703.1	chr18	34863249	34863259	+	1	NA	exon (NM_007913, exon 2 of 2)	exon (NM_007913, exon 2 of 2)	2047	NM_007913	13653	Mm.181959	NM_007913	ENSMUSG00000038418	Egr1	A530045N19Rik|ETR103|Egr-1|Krox-1|Krox-24|Krox24|NGF1-A|NGFI-A|NGFIA|TIS8|Zenk|Zfp-6|Zif268|egr	early growth response 1	protein-coding
mm_144580.1	chr18	31931276	31931283	+	1	NA	promoter-TSS (NM_144862)	promoter-TSS (NM_144862)	-228	NM_144862	225341	Mm.24551	NM_144862	ENSMUSG00000024395	Lims2	PINCH2	LIM and senescent cell antigen like domains 2	protein-coding
mm_113044.1	chr13	23575754	23575773	+	1	NA	promoter-TSS (NM_178204)	promoter-TSS (NM_178204)	0	NM_178204	319149	Mm.347699	NM_178204	ENSMUSG00000099583	Hist1h3d	H3-b	histone cluster 1, H3d	protein-coding
mm_33437.1	chr4	130107610	130107620	+	1	NA	promoter-TSS (NM_026441)	promoter-TSS (NM_026441)	59	NM_026441	67898	Mm.20818	NM_026441	ENSMUSG00000028779	Pef1	2600002E23Rik|Peflin	penta-EF hand domain containing 1	protein-coding
mm_25963.1	chr3	132684160	132684191	+	1	NA	promoter-TSS (NM_007926)	promoter-TSS (NM_007926)	31	NM_001163455	271981	Mm.257864	NM_173032	ENSMUSG00000028030	Tbck	1700120J03Rik|9430001M19|A630047E20Rik|C030007I09Rik|Tbckl	TBC1 domain containing kinase	protein-coding
mm_87649.1	chr10	58418421	58418447	+	1	NA	exon (NM_201242, exon 9 of 10)	exon (NM_201242, exon 9 of 10)	24061	NM_001346676	110829	Mm.57734	NM_026148	ENSMUSG00000019920	Lims1	2310016J22Rik|4921524A02Rik|AI507642|AU021743|AW551584|C430041B13Rik|Lims1l|PINCH|PINCH1	LIM and senescent cell antigen-like domains 1	protein-coding
mm_114735.1	chr13	83731379	83731394	+	1	NA	intron (NR_015561, intron 2 of 3)	CpG	3280	NR_015561	320203	Mm.245636	NM_177100	ENSMUSG00000050334	C130071C03Rik	2810449C10Rik	RIKEN cDNA C130071C03 gene	ncRNA
mm_9891.1	chr1	186704994	186705023	-	1	NA	5' UTR (NM_009367, exon 1 of 7)	5' UTR (NM_009367, exon 1 of 7)	981	NM_009367	21808	Mm.18213	NM_009367	ENSMUSG00000039239	Tgfb2	BB105277|Tgf-beta2|Tgfb-2	transforming growth factor, beta 2	protein-coding
mm_4218.1	chr1	171329377	171329404	+	1	NA	5' UTR (NM_001128609, exon 1 of 6)	5' UTR (NM_001128609, exon 1 of 6)	245	NM_011615	21945	Mm.270139	NM_011615	ENSMUSG00000013973	Dedd	CASP8IP1|DEFT|Dedpro1|FLDED1|KE05	death effector domain-containing	protein-coding
mm_21561.1	chr2	164182668	164182686	-	1	NA	promoter-TSS (NM_145369)	promoter-TSS (NM_145369)	65	NM_145369	209232	Mm.218273	NM_145369	ENSMUSG00000040154	Wfdc5	BC019734|Prg5|Wap1	WAP four-disulfide core domain 5	protein-coding
mm_110666.1	chr12	64474886	64474911	-	1	NA	promoter-TSS (NM_001163271)	promoter-TSS (NM_001163271)	0	NM_001163271	623046	Mm.189552	NM_001163271	ENSMUSG00000043060	Fscb	EG623046	fibrous sheath CABYR binding protein	protein-coding
mm_37043.1	chr4	115781091	115781104	-	1	NA	promoter-TSS (NM_029196)	promoter-TSS (NM_029196)	-63	NM_029196	75173	Mm.331798	NM_029196	ENSMUSG00000044556	Tex38	4930544O15Rik|Theg4	testis expressed 38	protein-coding
mm_132933.1	chr16	49855120	49855130	+	1	NA	promoter-TSS (NM_010581)	promoter-TSS (NM_010581)	-529	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_101494.1	chr11	31821284	31821311	-	1	NA	intron (NR_102310, intron 2 of 3)	MLT1A0|LTR|ERVL-MaLR	3250	NR_102310	414116	Mm.150222	NR_102310	ENSMUSG00000085772	D630024D03Rik	-	RIKEN cDNA D630024D03 gene	ncRNA
mm_131537.1	chr16	17759602	17759610	+	1	NA	promoter-TSS (NM_145479)	promoter-TSS (NM_145479)	-15	NM_145479	224023	Mm.282807	NM_145479	ENSMUSG00000022750	Klhl22	2610318I18Rik|Kelchl	kelch-like 22	protein-coding
mm_98307.1	chr11	90033522	90033576	+	1	NA	intron (NM_026433, intron 1 of 2)	intron (NM_026433, intron 1 of 2)	3201	NM_026433	67888	Mm.212428	NM_026433	ENSMUSG00000069763	Tmem100	1810057C19Rik|AV011897	transmembrane protein 100	protein-coding
mm_148732.1	chr19	5878133	5878162	+	1	NA	promoter-TSS (NM_134154)	promoter-TSS (NM_134154)	-319	NM_134154	107375	Mm.5323	NM_134154	ENSMUSG00000024818	Slc25a45	AW491445	solute carrier family 25, member 45	protein-coding
mm_120090.1	chr14	57878416	57878422	+	1	NA	intron (NM_029492, intron 2 of 12)	intron (NM_029492, intron 2 of 12)	11843	NM_029492	75965	Mm.29044	NM_029492	ENSMUSG00000021969	Zdhhc20	4930542A17Rik|5033406L14Rik|AI448102|B230110O18Rik|ENSMUSG00000055956|HK11	zinc finger, DHHC domain containing 20	protein-coding
mm_9724.1	chr1	180193476	180193492	-	1	NA	promoter-TSS (NM_001163290)	promoter-TSS (NM_001163290)	1	NM_001163290	67426	Mm.38330	NM_023341	ENSMUSG00000026489	Coq8a	4632432J16Rik|AI462003|Adck3|Cabc1|mKIAA0451	coenzyme Q8A	protein-coding
mm_21744.1	chr2	164804687	164804733	-	1	NA	promoter-TSS (NM_178375)	promoter-TSS (NM_178375)	171	NM_133240	170789	Mm.277878	NM_133240	ENSMUSG00000017307	Acot8	PTE-2|Pte1	acyl-CoA thioesterase 8	protein-coding
mm_145801.1	chr18	65352407	65352412	+	1	NA	intron (NM_001037294, intron 3 of 12)	B3|SINE|B2	41479	NM_001037294	225638	Mm.296528	NM_001037294	ENSMUSG00000032845	Alpk2	Gm549|Hak	alpha-kinase 2	protein-coding
mm_163119.1	chr11	75630806	75630811	+	1	NA	promoter-TSS (NM_008916)	promoter-TSS (NM_008916)	-212	NM_008916	19062	Mm.1458	NM_008916	ENSMUSG00000006127	Inpp5k	C62|Pps|SKIP	inositol polyphosphate 5-phosphatase K	protein-coding
mm_56661.1	chr6	113501878	113501949	-	1	NA	promoter-TSS (NM_172487)	promoter-TSS (NM_172487)	18	NM_001289699	210673	Mm.133060	NM_172487	ENSMUSG00000045009	Prrt3	6330505P20|B230206N24Rik	proline-rich transmembrane protein 3	protein-coding
mm_106532.1	chr11	120573303	120573329	-	1	NA	promoter-TSS (NM_011032)	promoter-TSS (NM_011032)	-380	NM_011032	18453	Mm.16660	NM_011032	ENSMUSG00000025130	P4hb	ERp59|PDI|Pdia1|Thbp	prolyl 4-hydroxylase, beta polypeptide	protein-coding
mm_46875.1	chr5	113832717	113832739	-	1	NA	Intergenic	Intergenic	-2227	NM_009151	20345	Mm.332590	NM_009151	ENSMUSG00000048163	Selplg	CD162|Psgl-1|Psgl1|Selp1|Selpl	selectin, platelet (p-selectin) ligand	protein-coding
mm_149246.1	chr19	10206461	10206479	+	1	NA	exon (NM_001163431, exon 2 of 4)	exon (NM_001163431, exon 2 of 4)	437	NM_001163431	69038	Mm.375100	NM_026919	ENSMUSG00000036372	Tmem258	1810006K21Rik	transmembrane protein 258	protein-coding
mm_148070.1	chr18	72349857	72349872	-	1	NA	intron (NM_007831, intron 1 of 28)	intron (NM_007831, intron 1 of 28)	1205	NM_007831	13176	Mm.167882	NM_007831	ENSMUSG00000060534	Dcc	C030036D22Rik|Igdcc1	deleted in colorectal carcinoma	protein-coding
mm_145245.1	chr18	51117755	51117765	+	1	NA	promoter-TSS (NM_001081224)	promoter-TSS (NM_001081224)	-138	NM_001081224	71373	Mm.63546	NM_001081224	ENSMUSG00000073565	Prr16	5430406M13Rik|AI607429	proline rich 16	protein-coding
mm_146783.1	chr18	20105983	20105985	-	1	NA	intron (NM_013504, intron 5 of 16)	intron (NM_013504, intron 5 of 16)	8789	NM_001291804	13505	Mm.33740	NM_013504	ENSMUSG00000044322	Dsc1	1110020A10Rik|AI507491	desmocollin 1	protein-coding
mm_33244.1	chr4	127030168	127030178	+	1	NA	3' UTR (NM_023603, exon 10 of 10)	3' UTR (NM_023603, exon 10 of 10)	8872	NM_023603	71514	Mm.257276	NM_023603	ENSMUSG00000028820	Sfpq	1110004P21Rik|2810416M14Rik|5730453G22Rik|9030402K04Rik|AU021830|D4Ertd314e|Gm12940|OTTMUSG00000009329|PSF|REP1	splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)	protein-coding
mm_152934.1	chr19	28561067	28561083	-	1	NA	intron (NM_175459, intron 2 of 10)	intron (NM_175459, intron 2 of 10)	-117149	NR_045330	320176	Mm.406716	NR_045330	ENSMUSG00000097735	D930032P07Rik	-	RIKEN cDNA D930032P07 gene	ncRNA
mm_5226.1	chr1	14309812	14309814	-	1	NA	5' UTR (NM_001252192, exon 1 of 17)	5' UTR (NM_001252192, exon 1 of 17)	386	NM_001310459	14048	Mm.250185	NM_010164	ENSMUSG00000025932	Eya1	bor	EYA transcriptional coactivator and phosphatase 1	protein-coding
mm_107991.1	chr12	73261503	73261507	+	1	NA	intron (NM_008612, intron 7 of 7)	L1VL2|LINE|L1	25206	NM_029580	76357	Mm.311344	NM_029580	ENSMUSG00000034442	Trmt5	2610027O18Rik|mKIAA1393	TRM5 tRNA methyltransferase 5	protein-coding
mm_62627.1	chr7	107595033	107595060	+	1	NA	promoter-TSS (NM_008905)	promoter-TSS (NM_008905)	-5	NM_008905	19024	Mm.2817	NM_008905	ENSMUSG00000036528	Ppfibp2	Cclp1	PTPRF interacting protein, binding protein 2 (liprin beta 2)	protein-coding
mm_56188.1	chr6	88518736	88518757	-	1	NA	promoter-TSS (NM_016906)	promoter-TSS (NM_016906)	54	NM_016906	53421	Mm.28375	NM_016906	ENSMUSG00000030082	Sec61a1	AA408394|AA410007|Sec61a	Sec61 alpha 1 subunit (S. cerevisiae)	protein-coding
mm_129969.1	chr15	85711606	85711612	-	1	NA	Intergenic	MIR3|SINE|MIR	4290	NR_029727	387245		NR_029727	ENSMUSG00000065564	Mirlet7b	Mirnlet7b|let-7b|mmu-let-7b	microRNA let7b	ncRNA
mm_132914.1	chr16	49057400	49057413	+	1	NA	promoter-TSS (NM_001166210)	promoter-TSS (NM_001166210)	-80	NM_001166210	667772	Mm.301387	NM_001166210	ENSMUSG00000092009	Myh15	EG667772	myosin, heavy chain 15	protein-coding
mm_171186.1	chr3	40894035	40894051	-	1	NA	promoter-TSS (NM_026622)	promoter-TSS (NM_026622)	-234	NM_026622	269423	Mm.32373	NM_026622	ENSMUSG00000037818	Abhd18	2310068E01Rik|3110057O12Rik|AI645591	abhydrolase domain containing 18	protein-coding
mm_55612.1	chr6	72042538	72042540	-	1	NA	promoter-TSS (NR_046180)	promoter-TSS (NR_046180)	-11	NR_046180	330350	Mm.246787	NR_046180	ENSMUSG00000108356	9130221F21Rik	9130221F21	RIKEN cDNA 9130221F21 gene	ncRNA
mm_13067.1	chr2	91118911	91118921	+	1	NA	intron (NM_008653, intron 1 of 31)	intron (NM_008653, intron 1 of 31)	772	NM_008653	17868	Mm.10728	NM_008653	ENSMUSG00000002100	Mybpc3	-	myosin binding protein C, cardiac	protein-coding
mm_45451.1	chr5	67619422	67619425	-	1	NA	3' UTR (NM_009727, exon 36 of 36)	3' UTR (NM_009727, exon 36 of 36)	11540	NM_001033415	330096	Mm.442747	NM_001033415	ENSMUSG00000050010	Shisa3	D830007B15Rik	shisa family member 3	protein-coding
mm_27310.1	chr3	50366530	50366541	-	1	NA	3' UTR (NM_011990, exon 12 of 12)	3' UTR (NM_011990, exon 12 of 12)	77078	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_33361.1	chr4	129491193	129491220	+	1	NA	promoter-TSS (NM_080442)	promoter-TSS (NM_080442)	16	NM_001085491	68233	Mm.424983	NM_001085491	ENSMUSG00000078554	Fam229a	1700125D06Rik	family with sequence similarity 229, member A	protein-coding
mm_117642.1	chr13	92530789	92530802	-	1	NA	promoter-TSS (NM_173392)	promoter-TSS (NM_173392)	15	NM_173392	218441	Mm.259585	NM_173392	ENSMUSG00000021706	Zfyve16	AI035632|B130024H06Rik|B130031L15|mKIAA0305	zinc finger, FYVE domain containing 16	protein-coding
mm_55557.1	chr6	71322201	71322238	-	1	NA	promoter-TSS (NM_009858)	promoter-TSS (NM_009858)	-593	NM_009858	12526	Mm.333148	NM_009858	ENSMUSG00000053044	Cd8b1	Cd8b|Ly-3|Ly-C|Lyt-3	CD8 antigen, beta chain 1	protein-coding
mm_35848.1	chr4	48468792	48468819	-	1	NA	exon (NM_172304, exon 4 of 16)	exon (NM_172304, exon 4 of 16)	4617	NM_172304	269536	Mm.272025	NM_172304	ENSMUSG00000028345	Tex10	2610206N19Rik|2810462N03Rik|BC006867	testis expressed gene 10	protein-coding
mm_99474.1	chr11	102436521	102436534	+	1	NA	TTS (NM_199200)	TTS (NM_199200)	6205	NM_008175	14824	Mm.1568	NM_008175	ENSMUSG00000034708	Grn	Pgrn|epithelin	granulin	protein-coding
mm_101286.1	chr11	21684074	21684105	-	1	NA	intron (NM_145425, intron 6 of 17)	intron (NM_145425, intron 6 of 17)	111808	NM_145425	216560	Mm.138090	NM_145425	ENSMUSG00000020319	Wdpcp	AV249152	WD repeat containing planar cell polarity effector	protein-coding
mm_26392.1	chr3	142572726	142572736	+	1	NA	3' UTR (NM_018734, exon 11 of 11)	3' UTR (NM_018734, exon 11 of 11)	12235	NM_001289493	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_18351.1	chr2	58160652	58160664	-	1	NA	promoter-TSS (NM_139200)	promoter-TSS (NM_139200)	-536	NM_139200	227929	Mm.273905	NM_139200	ENSMUSG00000026832	Cytip	A130053M09Rik|AI462064|C80816|Cbp|Cybr|Pscdbp	cytohesin 1 interacting protein	protein-coding
mm_71032.1	chr8	33600640	33600642	+	1	NA	intron (NM_017374, intron 1 of 6)	intron (NM_017374, intron 1 of 6)	1020	NM_017374	19053	Mm.29301	NM_017374	ENSMUSG00000009630	Ppp2cb	AI115466|D8Ertd766e|PP2Ac	protein phosphatase 2 (formerly 2A), catalytic subunit, beta isoform	protein-coding
mm_52408.1	chr6	113389036	113389059	+	1	NA	promoter-TSS (NM_001142732)	promoter-TSS (NM_001142732)	-213	NM_001142732	101100	Mm.388573	NM_133923	ENSMUSG00000030276	Ttll3	4833441J24Rik|AI450050	tubulin tyrosine ligase-like family, member 3	protein-coding
mm_172107.1	chr6	3200794	3200794	+	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	-87725	NR_036696	667335	Mm.380219	NR_036696	ENSMUSG00000106779	Gm8579	EG667335	spermatogenesis associated glutamate (E)-rich protein 4a pseudogene	pseudo
mm_45420.1	chr5	66543911	66543931	-	1	NA	intron (NM_001310626, intron 1 of 15)	intron (NM_001310626, intron 1 of 15)	74896	NM_009686	11787	Mm.5159	NM_009686	ENSMUSG00000029207	Apbb2	2310007D03Rik|FE65L1|Rirl1|TR2L|Zfra	amyloid beta (A4) precursor protein-binding, family B, member 2	protein-coding
mm_15161.1	chr2	154009809	154009830	+	1	NA	exon (NM_008953, exon 3 of 9)	exon (NM_008953, exon 3 of 9)	1543	NM_008953	19194	Mm.29197	NM_008953	ENSMUSG00000042459	Bpifa2	Bpifa2e|Psp	BPI fold containing family A, member 2	protein-coding
mm_46691.1	chr5	110086301	110086307	-	1	NA	Intergenic	Intergenic	-13665	NM_207279	403178	Mm.297057	NM_207279	ENSMUSG00000064247	Plcxd1	A330045H12Rik|Gm576	phosphatidylinositol-specific phospholipase C, X domain containing 1	protein-coding
mm_101759.1	chr11	43426193	43426258	-	1	NA	promoter-TSS (NM_001131054)	promoter-TSS (NM_001131054)	23	NM_001131054	30939	Mm.6856	NM_013917	ENSMUSG00000020415	Pttg1	AW555095|C87862|Pttg|Pttg3	pituitary tumor-transforming gene 1	protein-coding
mm_167882.1	chrX	48010417	48010431	+	1	NA	Intergenic	Intergenic	24429	NM_013912	30878	Mm.29262	NM_013912	ENSMUSG00000037010	Apln	6030430G11Rik|Apel	apelin	protein-coding
mm_163275.1	chr11	115699279	115699281	-	1	NA	5' UTR (NM_008163, exon 2 of 6)	5' UTR (NM_008163, exon 2 of 6)	254	NM_001313937	14784	Mm.439649	NM_008163	ENSMUSG00000059923	Grb2	AA408164|Ash	growth factor receptor bound protein 2	protein-coding
mm_16494.1	chr2	181187376	181187419	+	1	NA	promoter-TSS (NM_025598)	promoter-TSS (NM_025598)	54	NM_025598	66496	Mm.213943	NM_025598	ENSMUSG00000016344	Ppdpf	0610012G23Rik|2610317A05Rik|2700038C09Rik|3110053G12Rik	pancreatic progenitor cell differentiation and proliferation factor	protein-coding
mm_86119.1	chr9	116089548	116089566	-	1	NA	3' UTR (NM_029575, exon 7 of 7)	3' UTR (NM_029575, exon 7 of 7)	85806	NM_029575	21813	Mm.172346	NM_009371	ENSMUSG00000032440	Tgfbr2	1110020H15Rik|AU042018|DNIIR|RIIDN|TBR-II|TbetaR-II|TbetaRII	transforming growth factor, beta receptor II	protein-coding
mm_151314.1	chr19	55837829	55837831	+	1	NA	intron (NR_138565, intron 4 of 15)	intron (NR_138565, intron 4 of 15)	-57491	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_32537.1	chr4	109001055	109001065	+	1	NA	exon (NM_146150, exon 1 of 31)	exon (NM_146150, exon 1 of 31)	255	NM_146150	230598	Mm.274950	NM_146150	ENSMUSG00000053510	Nrd1	2600011I06Rik|AI875733|NRD-C|Nrdc	nardilysin, N-arginine dibasic convertase, NRD convertase 1	protein-coding
mm_98216.1	chr11	87853208	87853249	+	1	NA	promoter-TSS (NM_001039684)	promoter-TSS (NM_001039684)	3	NM_001039684	380718	Mm.24404	NM_001039684	ENSMUSG00000034121	Mks1	AK190930|B8d3	Meckel syndrome, type 1	protein-coding
mm_36446.1	chr4	82475067	82475070	-	1	NA	intron (NM_001113210, intron 2 of 11)	intron (NM_001113210, intron 2 of 11)	30711	NM_001286127	18028	Mm.317947	NM_008687	ENSMUSG00000008575	Nfib	6720429L07Rik|CTF|E030026I10Rik|NF-I/B|NF1-B|NFI-B	nuclear factor I/B	protein-coding
mm_14685.1	chr2	140170642	140170701	+	1	NA	promoter-TSS (NM_001081090)	promoter-TSS (NM_001081090)	25	NM_027093	69487	Mm.287921	NM_027093	ENSMUSG00000027384	Ndufaf5	2310003L22Rik	NADH dehydrogenase (ubiquinone) complex I, assembly factor 5	protein-coding
mm_95830.1	chr11	55469725	55469742	+	1	NA	promoter-TSS (NM_013716)	promoter-TSS (NM_013716)	-19	NM_013716	27041	Mm.39631	NM_013716	ENSMUSG00000018583	G3bp1	AI849976|B430204O07|C87777|G3bp|mKIAA4115	GTPase activating protein (SH3 domain) binding protein 1	protein-coding
mm_137419.1	chr17	26138662	26138769	+	1	NA	promoter-TSS (NM_009733)	promoter-TSS (NM_009733)	29	NM_001159598	12005	Mm.23684	NM_009733	ENSMUSG00000024182	Axin1	AI316800|Axin|Fu|Kb|Ki|fused|kinky|knobbly	axin 1	protein-coding
mm_11711.1	chr2	36230633	36230707	+	1	NA	exon (NM_008969, exon 2 of 11)	exon (NM_008969, exon 2 of 11)	244	NM_008969	19224	Mm.275434	NM_008969	ENSMUSG00000047250	Ptgs1	COX1|Cox-1|Cox-3|PGHS-1|PHS 1|Pghs1	prostaglandin-endoperoxide synthase 1	protein-coding
mm_146377.1	chr18	82585019	82585036	+	1	NA	3' UTR (NM_010777, exon 7 of 7)	3' UTR (NM_010777, exon 7 of 7)	30519	NM_001025254	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_157124.1	chrX	9446073	9446083	-	1	NA	intron (NM_007807, intron 9 of 12)	intron (NM_007807, intron 9 of 12)	23246	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_67962.1	chr7	100539590	100539598	-	1	NA	3' UTR (NM_183270, exon 2 of 2)	3' UTR (NM_183270, exon 2 of 2)	2494	NM_183270	68185	Mm.228995	NM_183270	ENSMUSG00000044881	Coa4	5330414O08Rik|AI115477|AW047259|Chchd8|E2ig2	cytochrome c oxidase assembly factor 4	protein-coding
mm_2417.1	chr1	94075169	94075173	+	1	NA	Intergenic	RLTR19B|LTR|ERVK	-22618	NM_008798	18566	Mm.5024	NM_008798	ENSMUSG00000026285	Pdcd1	Ly101|PD-1|Pdc1	programmed cell death 1	protein-coding
mm_101266.1	chr11	21239332	21239353	-	1	NA	5' UTR (NM_001290628, exon 1 of 23)	5' UTR (NM_001290628, exon 1 of 23)	310	NM_001290628	245944	Mm.170103	NM_139061	ENSMUSG00000020128	Vps54	Hcc8|Vps54l|mSLP8|wr	VPS54 GARP complex subunit	protein-coding
mm_134523.1	chr16	19236256	19236264	-	1	NA	Intergenic	L1_Mur2|LINE|L1	50481	NM_146451	258443	Mm.377506	NM_146451	ENSMUSG00000050742	Olfr164	MOR279-2	olfactory receptor 164	protein-coding
mm_68458.1	chr7	110123002	110123029	-	1	NA	intron (NM_009516, intron 1 of 10)	CpG	956	NM_009516	22390	Mm.287173	NM_009516	ENSMUSG00000031016	Wee1	Wee1A	WEE 1 homolog 1 (S. pombe)	protein-coding
mm_163091.1	chr11	69734721	69734727	-	1	NA	exon (NM_001291068, exon 29 of 29)	exon (NM_001291068, exon 29 of 29)	23909	NM_001291068	20020	Mm.16533	NM_009089	ENSMUSG00000005198	Polr2a	220kDa|Rpb1|Rpo2-1	polymerase (RNA) II (DNA directed) polypeptide A	protein-coding
mm_41383.1	chr5	90744418	90744420	+	1	NA	Intergenic	Intergenic	-14879	NM_009141	20311	Mm.4660	NM_009141	ENSMUSG00000029371	Cxcl5	AMCF-II|Cxcl6|ENA-78|GCP-2|LIX|Scyb5|Scyb6	chemokine (C-X-C motif) ligand 5	protein-coding
mm_67337.1	chr7	79793061	79793073	-	1	NA	exon (NM_008588, exon 1 of 2)	exon (NM_008588, exon 1 of 2)	523	NM_008588	17292	Mm.1404	NM_008588	ENSMUSG00000030544	Mesp1	bHLHc5	mesoderm posterior 1	protein-coding
mm_107971.1	chr12	72792294	72792295	+	1	NA	intron (NM_008910, intron 4 of 5)	intron (NM_008910, intron 4 of 5)	31083	NM_008910	19042	Mm.261045	NM_008910	ENSMUSG00000021096	Ppm1a	2310003C21Rik|2900017D14Rik|AI427932|AU017636|MMPa-2|MPPa-1	protein phosphatase 1A, magnesium dependent, alpha isoform	protein-coding
mm_165553.1	chr3	13472634	13472670	+	1	NA	intron (NM_001163328, intron 1 of 8)	intron (NM_001163328, intron 1 of 8)	997	NM_001163328	76897	Mm.422625	NM_178631	ENSMUSG00000039717	Ralyl	0710005M24Rik	RALY RNA binding protein-like	protein-coding
mm_117739.1	chr13	95671539	95671584	-	1	NA	intron (NM_027711, intron 20 of 35)	intron (NM_027711, intron 20 of 35)	-25359	NM_010170	14064	Mm.440952	NM_010170	ENSMUSG00000021675	F2rl2	F730031A08|PAR3	coagulation factor II (thrombin) receptor-like 2	protein-coding
mm_38576.1	chr4	141817900	141817937	-	1	NA	exon (NM_007919, exon 7 of 8)	exon (NM_007919, exon 7 of 8)	8087	NM_007919	13706	Mm.45316	NM_007919	ENSMUSG00000058579	Cela2a	Ela-2|Ela2|Ela2a	chymotrypsin-like elastase family, member 2A	protein-coding
mm_108860.1	chr12	98771051	98771064	+	1	NA	promoter-TSS (NM_001160108)	promoter-TSS (NM_001160108)	35	NM_001160108	75553	Mm.25549	NM_029334	ENSMUSG00000021012	Zc3h14	1010001P15Rik|1700016A15Rik|2700069A02Rik|AU014748	zinc finger CCCH type containing 14	protein-coding
mm_106933.1	chr12	8637265	8637303	+	1	NA	Intergenic	Intergenic	-36850	NM_001160221	80913	Mm.341243	NM_030723	ENSMUSG00000020594	Pum2	5730503J23Rik|Pumm2	pumilio RNA-binding family member 2	protein-coding
mm_54614.1	chr6	38354548	38354565	-	1	NA	promoter-TSS (NM_028421)	promoter-TSS (NM_028421)	47	NM_028864	78781	Mm.25243	NM_028421	ENSMUSG00000029826	Zc3hav1	1200014N16Rik|2900058M19Rik|9130009D18Rik|9830115L13Rik|ARTD13|D6Bwg1452e|ZAP	zinc finger CCCH type, antiviral 1	protein-coding
mm_51056.1	chr6	65631941	65631962	+	1	NA	3' UTR (NM_001001495, exon 8 of 8)	3' UTR (NM_001001495, exon 8 of 8)	-39660	NM_172399	68169	Mm.52392	NM_172399	ENSMUSG00000049001	Ndnf	A930038C07Rik|epidermacan	neuron-derived neurotrophic factor	protein-coding
mm_160920.1	chr11	84195604	84195604	+	1	NA	exon (NM_133360, exon 1 of 54)	exon (NM_133360, exon 1 of 54)	166	NM_133360	107476	Mm.31374	NM_133360	ENSMUSG00000020532	Acaca	A530025K05Rik|Acac|Acc1|Gm738	acetyl-Coenzyme A carboxylase alpha	protein-coding
mm_99683.1	chr11	106033585	106033602	+	1	NA	intron (NM_001037712, intron 12 of 12)	intron (NM_001037712, intron 12 of 12)	-3279	NM_027946	71833	Mm.307455	NM_027946	ENSMUSG00000049354	Dcaf7	1700012F10Rik|2610037L01Rik|C86529|HAN11|Wdr68	DDB1 and CUL4 associated factor 7	protein-coding
mm_145839.1	chr18	65445567	65445575	+	1	NA	intron (NM_172833, intron 3 of 15)	intron (NM_172833, intron 3 of 15)	14574	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_118561.1	chr14	17981868	17981876	+	1	NA	5' UTR (NM_009380, exon 1 of 7)	5' UTR (NM_009380, exon 1 of 7)	228	NM_009380	21834	Mm.32563	NM_009380	ENSMUSG00000021779	Thrb	Nr1a2|T3R[b]|T3Rbeta|Thrb1|Thrb2|c-erbAbeta	thyroid hormone receptor beta	protein-coding
mm_2349.1	chr1	92910759	92910769	+	1	NA	promoter-TSS (NM_181405)	promoter-TSS (NM_181405)	0	NR_138578	75995	Mm.46179	NR_138577	ENSMUSG00000097251	5033417F24Rik	6330419D11Rik	RIKEN cDNA 5033417F24 gene	ncRNA
mm_171167.1	chr3	27155078	27155087	-	1	NA	intron (NR_040548, intron 2 of 2)	intron (NR_040548, intron 2 of 2)	1056	NR_040548	76657	Mm.417839	NR_040548	ENSMUSG00000097584	1700125G22Rik	-	RIKEN cDNA 1700125G22 gene	ncRNA
mm_113679.1	chr13	42790592	42790608	+	1	NA	intron (NM_001005740, intron 1 of 12)	L1_Mus1|LINE|L1	-75647	NM_001302636	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding
mm_115751.1	chr13	19182357	19182369	-	1	NA	Intergenic	Intergenic	213450	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_160083.1	chr7	13733506	13733506	+	1	NA	promoter-TSS (NM_009286)	promoter-TSS (NM_009286)	0	NM_009286	100043194	Mm.457986	NM_009286	ENSMUSG00000070811	Sult2a2	C730007P19Rik|ST|ST2A2|Sth2|mSTa2	sulfotransferase family 2A, dehydroepiandrosterone (DHEA)-preferring, member 2	protein-coding
mm_28467.1	chr3	90695707	90695721	-	1	NA	promoter-TSS (NM_001281852)	promoter-TSS (NM_001281852)	7	NM_001281852	20202	Mm.2128	NM_009114	ENSMUSG00000056071	S100a9	60B8Ag|AW546964|BEE22|Cagb|GAGB|L1Ag|MRP14|p14	S100 calcium binding protein A9 (calgranulin B)	protein-coding
mm_151051.1	chr19	47090749	47090800	+	1	NA	promoter-TSS (NM_011053)	promoter-TSS (NM_011053)	8	NM_011053	18572	Mm.41166	NM_011053	ENSMUSG00000025047	Pdcd11	1110021I22Rik|ALG-4|Pdcd7|mKIAA0185	programmed cell death 11	protein-coding
mm_139333.1	chr17	49428360	49428445	+	1	NA	promoter-TSS (NM_020042)	promoter-TSS (NM_020042)	38	NM_020042	56738	Mm.22256	NM_020042	ENSMUSG00000064120	Mocs1	3110045D15Rik|AI043170|AW536397	molybdenum cofactor synthesis 1	protein-coding
mm_170942.1	chr2	4959737	4959755	-	1	NA	Intergenic	Intergenic	-16376	NM_001311208	68527	Mm.27791	NM_026754	ENSMUSG00000026668	Ucma	1110017I16Rik|AW121955|Grp	upper zone of growth plate and cartilage matrix associated	protein-coding
mm_79478.1	chr9	56952748	56952751	+	1	NA	intron (NM_178374, intron 1 of 8)	ID_B1|SINE|B4	1825	NM_178374	66069	Mm.220984	NM_178374	ENSMUSG00000055334	Snupn	0610031A09Rik|Rnut1|Snupn1	snurportin 1	protein-coding
mm_54254.1	chr6	28262455	28262465	-	1	NA	promoter-TSS (NM_001081678)	promoter-TSS (NM_001081678)	-859	NM_001081678	627049	Mm.84441	NM_001081678	ENSMUSG00000039841	Zfp800	AA407452|Znf800	zinc finger protein 800	protein-coding
mm_11710.1	chr2	36230493	36230545	+	1	NA	promoter-TSS (NM_008969)	promoter-TSS (NM_008969)	93	NM_008969	19224	Mm.275434	NM_008969	ENSMUSG00000047250	Ptgs1	COX1|Cox-1|Cox-3|PGHS-1|PHS 1|Pghs1	prostaglandin-endoperoxide synthase 1	protein-coding
mm_148784.1	chr19	6114449	6114456	+	1	NA	exon (NM_001009546, exon 14 of 18)	exon (NM_001009546, exon 14 of 18)	4134	NM_133678	66406	Mm.303924	NM_133678	ENSMUSG00000024790	Sac3d1	2410004C24Rik|AU015683|shd1	SAC3 domain containing 1	protein-coding
mm_56937.1	chr6	119848121	119848168	-	1	NA	promoter-TSS (NM_178085)	promoter-TSS (NM_178085)	6	NM_053204	111173	Mm.288860	NM_053204	ENSMUSG00000030172	Erc1	4930404L01Rik|5033405M01Rik|9630025C19Rik|B430107L16Rik|CAST2|ELKS|Elks1|RAB6IP2A|RAB6IP2B|Rab6ip2|mKIAA1081	ELKS/RAB6-interacting/CAST family member 1	protein-coding
mm_111761.1	chr12	103989920	103989946	-	1	NA	promoter-TSS (NM_001166350)	promoter-TSS (NM_001166350)	10	NM_199314	380780	Mm.201338	NM_199314	ENSMUSG00000063232	Serpina11	Gm895	serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 11	protein-coding
mm_47431.1	chr5	123175923	123175969	-	1	NA	exon (NM_008277, exon 11 of 14)	exon (NM_008277, exon 11 of 14)	6740	NM_008277	15445	Mm.439709	NM_008277	ENSMUSG00000029445	Hpd	Fla|Flp|Hppd|Laf	4-hydroxyphenylpyruvic acid dioxygenase	protein-coding
mm_38719.1	chr4	145234772	145234786	-	1	NA	intron (NM_011610, intron 1 of 9)	intron (NM_011610, intron 1 of 9)	12091	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_123752.1	chr14	70195986	70195996	-	1	NA	intron (NM_001271408, intron 5 of 20)	intron (NM_001271408, intron 5 of 20)	-3745	NM_001271409	20410	Mm.5068	NM_011366	ENSMUSG00000022091	Sorbs3	SCAM-1|SH3P3|Sh3d4|vinexin-g	sorbin and SH3 domain containing 3	protein-coding
mm_120381.1	chr14	64588546	64588559	+	1	NA	intron (NR_040709, intron 1 of 3)	intron (NR_040709, intron 1 of 3)	437	NR_040709	268755	Mm.194050	NR_040709	ENSMUSG00000097545	Mir124a-1hg	A930011O12Rik|Rncr3|mir-124-1|mir-3078	Mir124-1 host gene (non-protein coding)	ncRNA
mm_119667.1	chr14	52427932	52427952	+	1	NA	Intergenic	Intergenic	-17015	NM_146431	258423	Mm.377492	NM_146431	ENSMUSG00000063106	Olfr1510	MOR223-6	olfactory receptor 1510	protein-coding
mm_47232.1	chr5	121385573	121385590	-	1	NA	promoter-TSS (NM_001163470)	promoter-TSS (NM_001163470)	34	NM_001163470	231712	Mm.20488	NM_172275	ENSMUSG00000042726	Trafd1	1110008K06Rik|Fln29	TRAF type zinc finger domain containing 1	protein-coding
mm_75592.1	chr8	61612411	61612413	-	1	NA	intron (NM_001293772, intron 10 of 21)	intron (NM_001293772, intron 10 of 21)	-21243	NM_001293774	72333	Mm.29933	NM_001081390	ENSMUSG00000058056	Palld	2410003B16Rik|6030492A02	palladin, cytoskeletal associated protein	protein-coding
mm_152687.1	chr19	16657782	16657785	-	1	NA	intron (NM_173028, intron 53 of 71)	B1_Mur2|SINE|Alu	123150	NM_173028	271564	Mm.211963	NM_173028	ENSMUSG00000046230	Vps13a	4930425F11|4930516E05Rik|4930543C13Rik|9930023P20|Chac|Chorein|D330038K10Rik|mKIAA0986	vacuolar protein sorting 13A	protein-coding
mm_112222.1	chr12	113429491	113429502	-	1	NA	Intergenic	Intergenic	-60069	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_148841.1	chr19	6364579	6364668	+	1	NA	intron (NM_011750, intron 1 of 12)	intron (NM_011750, intron 1 of 12)	933	NR_122118	22668	Mm.256422	NM_011750	ENSMUSG00000024949	Sf1	BBP|MZFM|WBP4|Zfp162	splicing factor 1	protein-coding
mm_62261.1	chr7	99348915	99348931	+	1	NA	exon (NM_009825, exon 2 of 5)	exon (NM_009825, exon 2 of 5)	4316	NM_009825	12406	Mm.22708	NM_009825	ENSMUSG00000070436	Serpinh1	BERF-1|Cbp1|Cbp2|Hsp47|J6|Serpinh2|gp46	serine (or cysteine) peptidase inhibitor, clade H, member 1	protein-coding
mm_72446.1	chr8	83165555	83165571	+	1	NA	5' UTR (NM_001111304, exon 1 of 21)	5' UTR (NM_001111304, exon 1 of 21)	211	NM_027758	71310	Mm.24031	NM_027758	ENSMUSG00000031709	Tbc1d9	4933431N12Rik|AI847101|AW490653|C76116	TBC1 domain family, member 9	protein-coding
mm_134851.1	chr16	28159870	28159874	-	1	NA	3' UTR (NM_010199, exon 6 of 6)	3' UTR (NM_010199, exon 6 of 6)	286203	NM_183064	14167	Mm.7996	NM_010199	ENSMUSG00000022523	Fgf12	AV114868|B230343J05Rik|FGF-12|FHF-1|Fhf1	fibroblast growth factor 12	protein-coding
mm_5772.1	chr1	51474018	51474046	-	1	NA	intron (NM_001310548, intron 3 of 5)	LFSINE_Vert|SINE|tRNA	4367	NM_028696	109019	Mm.196290	NM_028696	ENSMUSG00000026107	Nabp1	4930434H03Rik|4930442A21Rik|4930488J04Rik|4933440J18Rik|5830411E10Rik|AI852561|Nbp1|Obfc2a|Ssb2	nucleic acid binding protein 1	protein-coding
mm_149453.1	chr19	11497558	11497571	+	1	NA	intron (NM_001164202, intron 1 of 4)	intron (NM_001164202, intron 1 of 4)	5526	NM_001164202	666926	Mm.486382	NM_001164202	ENSMUSG00000058470	Gm8369	EG666926	predicted gene 8369	protein-coding
mm_25415.1	chr3	107368420	107368429	+	1	NA	Intergenic	Intergenic	-35135	NM_001045807	229700	Mm.27966	NM_001045807	ENSMUSG00000048109	Rbm15	C230088J01Rik|mKIAA1438	RNA binding motif protein 15	protein-coding
mm_109275.1	chr12	109546334	109546398	+	1	NA	non-coding (NR_003633, exon 1 of 5)	non-coding (NR_003633, exon 1 of 5)	968	NR_003633	17263	Mm.289645	NM_144513	ENSMUSG00000021268	Meg3	2900016C05Rik|3110050O07Rik|6330408G06Rik|AI425946|AW108224|D12Bwg1266e|Gtl2|R74756|R75394	maternally expressed 3	ncRNA
mm_73406.1	chr8	105932639	105932654	+	1	NA	TTS (NM_173432)	TTS (NM_173432)	1216	NM_023182	109660	Mm.2745	NM_023182	ENSMUSG00000031896	Ctrl	0910001G08Rik|1810004D15Rik|AV005227|Ctra-1|Ctra1|chymopasin|mFLJ00366	chymotrypsin-like	protein-coding
mm_20058.1	chr2	120328682	120328698	-	1	NA	exon (NM_178851, exon 12 of 25)	exon (NM_178851, exon 12 of 25)	-14525	NM_001024145	271844	Mm.24880	NM_001024145	ENSMUSG00000046971	Pla2g4f	4732472I07Rik|Gm647|Pla2zeta	phospholipase A2, group IVF	protein-coding
mm_40611.1	chr5	64626853	64626860	+	1	NA	Intergenic	Intergenic	-16157	NR_045078	100042198	Mm.25191	NR_045078	ENSMUSG00000105402	Gm3716	Gm1683	predicted gene 3716	ncRNA
mm_38755.1	chr4	147814672	147814675	-	1	NA	Intergenic	Intergenic	-4885	NM_001127189	100041677	Mm.327194	NM_001127189	ENSMUSG00000078495	Zfp984	Gm13157|OTTMUSG00000010679	zinc finger protein 984	protein-coding
mm_26475.1	chr3	144570688	144570721	+	1	NA	promoter-TSS (NM_011828)	promoter-TSS (NM_011828)	277	NM_053102	93684	Mm.29812	NM_053102	ENSMUSG00000037072	Selenof	9430015P09Rik|Sep15	selenoprotein F	protein-coding
mm_172870.1	chr9	42423680	42423680	+	1	NA	intron (NM_173038, intron 7 of 7)	B1_Mus2|SINE|Alu	-23751	NM_001324548	21683	Mm.42209	NM_009347	ENSMUSG00000037705	Tecta	Tctna	tectorin alpha	protein-coding
mm_60315.1	chr7	44198195	44198216	+	1	NA	promoter-TSS (NM_008693)	promoter-TSS (NM_008693)	14	NM_008693	18050	Mm.439740	NM_008693	ENSMUSG00000066515	Klk1b3	Ngfg|gamma-NGF|mGk-3	kallikrein 1-related peptidase b3	protein-coding
mm_128886.1	chr15	73156558	73156604	-	1	NA	intron (NM_153178, intron 1 of 18)	intron (NM_153178, intron 1 of 18)	28366	NM_153178	239528	Mm.23095	NM_153178	ENSMUSG00000036698	Ago2	1110029L17Rik|2310051F07Rik|AI225898|AL022874|AW546247|ENSMUSG00000072493|Eif2c2|Gerp95|Gm10365|mKIAA4215	argonaute RISC catalytic subunit 2	protein-coding
mm_101182.1	chr11	17002929	17002951	-	1	NA	intron (NM_019549, intron 1 of 9)	intron (NM_019549, intron 1 of 9)	5778	NM_019549	56193	Mm.98232	NM_019549	ENSMUSG00000020120	Plek	2010300B13Rik	pleckstrin	protein-coding
mm_140808.1	chr17	22314795	22314809	-	1	NA	Intergenic	Intergenic	46598	NM_176962	319615	Mm.442162	NM_176962	ENSMUSG00000033972	Zfp944	6330416L07Rik	zinc finger protein 944	protein-coding
mm_166716.1	chr6	118374750	118374758	+	1	NA	Intergenic	Intergenic	44663	NM_194339	213895	Mm.25269	NM_194339	ENSMUSG00000030138	Bms1	AA408648|AU020092|AU043373|BB007109|BC030906|Bms1l|mKIAA0187	BMS1, ribosome biogenesis factor	protein-coding
mm_42603.1	chr5	117659904	117659919	+	1	NA	intron (NM_001312914, intron 5 of 19)	intron (NM_001312914, intron 5 of 19)	-206928	NM_008712	18125	Mm.44249	NM_008712	ENSMUSG00000029361	Nos1	2310005C01Rik|N-NOS|NC-NOS|NO|NOS|NOS-I|Nos-1|bNOS|nNOS	nitric oxide synthase 1, neuronal	protein-coding
mm_48737.1	chr5	147637300	147637314	-	1	NA	intron (NM_010228, intron 13 of 29)	intron (NM_010228, intron 13 of 29)	88681	NM_010228	14254	Mm.389712	NM_010228	ENSMUSG00000029648	Flt1	AI323757|Flt-1|VEGFR-1|VEGFR1|sFlt1	FMS-like tyrosine kinase 1	protein-coding
mm_4097.1	chr1	167350152	167350162	+	1	NA	5' UTR (NM_019993, exon 1 of 11)	5' UTR (NM_019993, exon 1 of 11)	166	NM_019993	56752	Mm.292539	NM_019993	ENSMUSG00000026687	Aldh9a1	AA139417|Abaldh|ESTM40|TMABA-DH|Tmabadh	aldehyde dehydrogenase 9, subfamily A1	protein-coding
mm_117678.1	chr13	93674324	93674326	-	1	NA	promoter-TSS (NM_022884)	promoter-TSS (NM_022884)	-23	NM_022884	64918	Mm.29981	NM_022884	ENSMUSG00000042118	Bhmt2	C81077|D13Ucla2	betaine-homocysteine methyltransferase 2	protein-coding
mm_81336.1	chr9	108517685	108517706	+	1	NA	intron (NM_175143, intron 1 of 9)	CpG	608	NM_175143	69232	Mm.335449	NM_175143	ENSMUSG00000006673	Qrich1	2610028H07Rik	glutamine-rich 1	protein-coding
mm_57015.1	chr6	121245743	121245755	-	1	NA	promoter-TSS (NM_011909)	promoter-TSS (NM_011909)	-157	NM_011909	24110	Mm.326911	NM_011909	ENSMUSG00000030107	Usp18	1110058H21Rik|AW047653|UBP43|Ubp15	ubiquitin specific peptidase 18	protein-coding
mm_156872.1	chrX	164506349	164506370	+	1	NA	intron (NM_027027, intron 1 of 7)	intron (NM_027027, intron 1 of 7)	8456	NM_027027	69299	Mm.79031	NM_027027	ENSMUSG00000031384	Asb9	1700011M07Rik	ankyrin repeat and SOCS box-containing 9	protein-coding
mm_154367.1	chrM	8943	8953	+	1	NA	NA	Intergenic	NA	NA								
mm_36492.1	chr4	83266039	83266081	-	1	NA	intron (NM_027238, intron 3 of 19)	intron (NM_027238, intron 3 of 19)	58129	NM_027238	69863	Mm.5540	NM_025782	ENSMUSG00000038172	Ttc39b	1810054D07Rik|9130422G05Rik|AI450603|AV103077|AW215585	tetratricopeptide repeat domain 39B	protein-coding
mm_33962.1	chr4	137560671	137560679	+	1	NA	intron (NM_008305, intron 81 of 96)	intron (NM_008305, intron 81 of 96)	14505	NM_001033979	435811	Mm.359646	NM_001033979	ENSMUSG00000094035	Ldlrad2	-	low density lipoprotein receptor A domain containing 2	protein-coding
mm_165001.1	chr19	21461318	21461329	-	1	NA	intron (NM_010266, intron 1 of 13)	L1MB5|LINE|L1	11338	NM_010266	14544	Mm.45054	NM_010266	ENSMUSG00000058624	Gda	AU015411|AW047581|GAH	guanine deaminase	protein-coding
mm_17191.1	chr2	25465883	25465894	-	1	NA	TTS (NM_008963)	TTS (NM_008963)	3861	NM_008963	19215	Mm.1008	NM_008963	ENSMUSG00000015090	Ptgds	21kDa|L-PGDS|PGD2|PGDS|PGDS2|Ptgs3	prostaglandin D2 synthase (brain)	protein-coding
mm_53306.1	chr6	129180976	129181013	+	1	NA	intron (NM_053109, intron 1 of 4)	intron (NM_053109, intron 1 of 4)	379	NM_053109	93694	Mm.197536	NM_053109	ENSMUSG00000030157	Clec2d	Clr-b|Clrb|Ocil	C-type lectin domain family 2, member d	protein-coding
mm_27584.1	chr3	59115642	59115653	-	1	NA	exon (NM_001287124, exon 2 of 2)	exon (NM_001287124, exon 2 of 2)	-13826	NM_173398	229323	Mm.123648	NM_173398	ENSMUSG00000050075	Gpr171	A630006E05|F730001G15Rik|H963	G protein-coupled receptor 171	protein-coding
mm_13508.1	chr2	109693602	109693624	+	1	NA	promoter-TSS (NM_001048142)	promoter-TSS (NM_001048142)	50	NM_001048142	12064	Mm.1442	NM_007540	ENSMUSG00000048482	Bdnf	-	brain derived neurotrophic factor	protein-coding
mm_82481.1	chr9	17675671	17675695	-	1	NA	Intergenic	Intergenic	-616584	NM_025844	66917	Mm.103534	NM_025844	ENSMUSG00000001774	Chordc1	1110001O09Rik|AA409036|Chp-1|morgana	cysteine and histidine-rich domain (CHORD)-containing, zinc-binding protein 1	protein-coding
mm_28460.1	chr3	90694955	90694973	-	1	NA	intron (NM_009114, intron 2 of 2)	intron (NM_009114, intron 2 of 2)	757	NM_001281852	20202	Mm.2128	NM_009114	ENSMUSG00000056071	S100a9	60B8Ag|AW546964|BEE22|Cagb|GAGB|L1Ag|MRP14|p14	S100 calcium binding protein A9 (calgranulin B)	protein-coding
mm_45914.1	chr5	89438266	89438274	-	1	NA	exon (NM_008096, exon 8 of 13)	exon (NM_008096, exon 8 of 13)	19628	NM_008096	14473	Mm.196595	NM_008096	ENSMUSG00000035540	Gc	DBP|VDB	group specific component	protein-coding
mm_126153.1	chr15	78409740	78409748	+	1	NA	intron (NM_138670, intron 1 of 2)	intron (NM_138670, intron 1 of 2)	2640	NM_138670	246221	Mm.294215	NM_138670	ENSMUSG00000071711	Mpst	Mst	mercaptopyruvate sulfurtransferase	protein-coding
mm_100450.1	chr11	119671260	119671282	+	1	NA	intron (NM_028898, intron 2 of 33)	intron (NM_028898, intron 2 of 33)	68366	NM_028898	74370	Mm.209933	NM_028898	ENSMUSG00000025583	Rptor	4932417H02Rik|Rap|Raptor|mKIAA1303	regulatory associated protein of MTOR, complex 1	protein-coding
mm_31420.1	chr4	48051380	48051396	+	1	NA	exon (NM_015743, exon 3 of 8)	exon (NM_015743, exon 3 of 8)	142	NM_001307989	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_160098.1	chr7	18484188	18484188	-	1	NA	promoter-TSS (NM_001029893)	promoter-TSS (NM_001029893)	-39	NM_001029893	574429	Mm.296754	NM_001029893	ENSMUSG00000070799	Psg26	EG574429|cea14	pregnancy-specific glycoprotein 26	protein-coding
mm_95559.1	chr11	52318760	52318770	+	1	NA	Intergenic	Intergenic	-35751	NM_001313981	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_78882.1	chr9	44579618	44579630	+	1	NA	Intergenic	Intergenic	-25268	NM_001110826	13209	Mm.267061	NM_007841	ENSMUSG00000032097	Ddx6	1110001P04Rik|E230023J21Rik|HLR2|mRCK/P54|p54|rck	DEAD (Asp-Glu-Ala-Asp) box polypeptide 6	protein-coding
mm_136396.1	chr16	93354074	93354086	-	1	NA	promoter-TSS (NR_040490)	promoter-TSS (NR_040490)	-9	NR_040488	69857	Mm.81192	NR_040486	ENSMUSG00000100277	1810053B23Rik	1810008L18Rik|1810056K14Rik	RIKEN cDNA 1810053B23 gene	ncRNA
mm_118721.1	chr14	22214210	22214214	+	1	NA	intron (NM_028275, intron 2 of 6)	L1Md_F2|LINE|L1	194500	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_31046.1	chr4	41135685	41135714	+	1	NA	promoter-TSS (NM_026275)	promoter-TSS (NM_026275)	-322	NM_026275	67615	Mm.389540	NM_026275	ENSMUSG00000036241	Ube2r2	1200003M11Rik|Cdc34b|Ubc3b	ubiquitin-conjugating enzyme E2R 2	protein-coding
mm_13051.1	chr2	91099693	91099704	+	1	NA	intron (NM_011355, intron 2 of 4)	intron (NM_011355, intron 2 of 4)	3020	NM_011355	20375	Mm.1302	NM_011355	ENSMUSG00000002111	Spi1	Dis-1|Dis1|PU.1|Sfpi-1|Sfpi1|Spi-1|Tcfpu1|Tfpu.1	spleen focus forming virus (SFFV) proviral integration oncogene	protein-coding
mm_159543.1	chr4	88835457	88835457	+	1	NA	promoter-TSS (NM_010505)	promoter-TSS (NM_010505)	-68	NM_010505	15968	Mm.377089	NM_010505	ENSMUSG00000096682	Ifna5	Ifa5	interferon alpha 5	protein-coding
mm_123634.1	chr14	68533763	68533781	-	1	NA	promoter-TSS (NM_007402)	promoter-TSS (NM_007402)	-83	NM_007402	11500	Mm.261495	NM_007402	ENSMUSG00000022056	Adam7	ADAM 7|EAP1|EAPI	a disintegrin and metallopeptidase domain 7	protein-coding
mm_138529.1	chr17	35242996	35243017	+	1	NA	intron (NM_001252457, intron 1 of 10)	intron (NM_001252457, intron 1 of 10)	189	NM_001252457	53817	Mm.439827	NM_019693	ENSMUSG00000019432	Ddx39b	0610030D10Rik|AI428441|Bat-1|Bat1|Bat1a|D17H6S81E|D17H6S81E-1|D6S81Eh	DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B	protein-coding
mm_71159.1	chr8	40431588	40431590	+	1	NA	intron (NM_178395, intron 1 of 12)	intron (NM_178395, intron 1 of 12)	7774	NM_178395	70546	Mm.34326	NM_178395	ENSMUSG00000039470	Zdhhc2	5730415P04Rik|6430583A19Rik	zinc finger, DHHC domain containing 2	protein-coding
mm_80697.1	chr9	92193102	92193118	+	1	NA	5' UTR (NM_001195693, exon 1 of 7)	5' UTR (NM_001195693, exon 1 of 7)	174	NM_001195693	100504689	Mm.464262	NM_001195693	ENSMUSG00000095654	Plscr5	331000	phospholipid scramblase family, member 5	protein-coding
mm_64596.1	chr7	3203999	3204010	-	1	NA	Intergenic	Intergenic	-14622	NR_029640	100049710		NR_029640	ENSMUSG00000077815	Mir290a	Mir290|Mirn290|mir-290a|mmu-miR-290|mmu-mir-290a	microRNA 290a	ncRNA
mm_56697.1	chr6	114859933	114859935	-	1	NA	3' UTR (NM_028835, exon 19 of 19)	3' UTR (NM_028835, exon 19 of 19)	61818	NM_177683	232334	Mm.268357	NM_177683	ENSMUSG00000030315	Vgll4	BC048841|VGL-4	vestigial like family member 4	protein-coding
mm_94756.1	chr11	21140644	21140672	+	1	NA	exon (NM_023324, exon 3 of 7)	exon (NM_023324, exon 3 of 7)	49334	NM_023324	67245	Mm.28957	NM_023324	ENSMUSG00000020134	Peli1	2810468L03Rik|A930031K15Rik|AA409794|AI586297|D11Ertd676e	pellino 1	protein-coding
mm_104331.1	chr11	93995782	93995814	-	1	NA	promoter-TSS (NM_001199204)	promoter-TSS (NM_001199204)	-293	NM_001199203	70834	Mm.260737	NM_027569	ENSMUSG00000020859	Spag9	3110018C07Rik|4733401I23Rik|4831406C20Rik|AW552012|JLP|JSAP2|JSAP2a|Jip4|Mapk8ip4|syd1	sperm associated antigen 9	protein-coding
mm_170918.1	chr2	37261808	37261808	-	1	NA	Intergenic	MMERVK9C_I-int|LTR|ERVK	-5143	NM_001081010	545417	Mm.379955	NM_001081010		Olfr367-ps	EG545417|MOR128-1|ORL1283|OTTMUSG00000012147|Olfr367	olfactory receptor 367, pseudogene	protein-coding
mm_146266.1	chr18	77870231	77870260	+	1	NA	intron (NM_013831, intron 6 of 14)	intron (NM_013831, intron 6 of 14)	-68222	NM_001195633	100502841	Mm.297782	NM_001195633	ENSMUSG00000039840	Epg5	4732475F16|5430411K18Rik|AI661957|AW456499|mKIAA1632	ectopic P-granules autophagy protein 5 homolog (C. elegans)	protein-coding
mm_119564.1	chr14	48878913	48878923	+	1	NA	promoter-TSS (NR_033783)	promoter-TSS (NR_033783)	45	NR_033783	66770	Mm.136954	NR_033783		4933429O19Rik	1700031B11Rik	RIKEN cDNA 4933429O19 gene	ncRNA
mm_106849.1	chr12	8008068	8008076	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	30395	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_82986.1	chr9	36532175	36532180	-	1	NA	TTS (NM_001033783)	TTS (NM_001033783)	9786	NM_001033783	434396	Mm.118836	NM_001033783	ENSMUSG00000074448	Gm5615	EG434396|Pate-H|Pate9	predicted gene 5615	protein-coding
mm_118810.1	chr14	25459322	25459332	+	1	NA	5' UTR (NM_183208, exon 1 of 24)	5' UTR (NM_183208, exon 1 of 24)	142	NM_183208	328365	Mm.227484	NM_183208	ENSMUSG00000007817	Zmiz1	BC065120|E330020C23|ENSMUSG00000072684|Gm10397|I920194n01|Rai17|Zimp10	zinc finger, MIZ-type containing 1	protein-coding
mm_152759.1	chr19	20375272	20375355	-	1	NA	exon (NM_010730, exon 12 of 13)	exon (NM_010730, exon 12 of 13)	15358	NM_010730	16952	Mm.248360	NM_010730	ENSMUSG00000024659	Anxa1	Anx-1|Anx-A1|C430014K04Rik|Lpc-1|Lpc1	annexin A1	protein-coding
mm_50432.1	chr6	48845159	48845177	+	1	NA	3' UTR (NM_025326, exon 7 of 7)	3' UTR (NM_025326, exon 7 of 7)	3512	NM_001098271	66058	Mm.27061	NM_025326	ENSMUSG00000023367	Tmem176a	0610011I04Rik|AU040201|AU041743|Keg2	transmembrane protein 176A	protein-coding
mm_127176.1	chr15	98953052	98953074	+	1	NA	intron (NM_011653, intron 1 of 3)	CpG	438	NM_011653	22142	Mm.405359	NM_011653	ENSMUSG00000072235	Tuba1a	Tuba-1|Tuba1	tubulin, alpha 1A	protein-coding
mm_143945.1	chr17	86710545	86710594	-	1	NA	Intergenic	Intergenic	-43295	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_68134.1	chr7	102239493	102239512	-	1	NA	TTS (NM_145583)	TTS (NM_145583)	10616	NM_019566	56212	Mm.259795	NM_019566	ENSMUSG00000073982	Rhog	2810426G09Rik|Arhg|Sid10750	ras homolog family member G	protein-coding
mm_136496.1	chr16	96192223	96192262	-	1	NA	promoter-TSS (NM_001001492)	promoter-TSS (NM_001001492)	15	NM_001001492	385668	Mm.24626	NM_001001492	ENSMUSG00000045275	Lca5l	4921526F01Rik|Lcca5l	Leber congenital amaurosis 5-like	protein-coding
mm_132323.1	chr16	33794114	33794122	+	1	NA	promoter-TSS (NM_010739)	promoter-TSS (NM_010739)	81	NM_010739	17063	Mm.3177	NM_010739	ENSMUSG00000022824	Muc13	114/A10|14/A10|AI159736|Lrrp|Ly64|NJ-1	mucin 13, epithelial transmembrane	protein-coding
mm_122691.1	chr14	52020681	52020694	-	1	NA	promoter-TSS (NM_001253694)	promoter-TSS (NM_001253694)	46	NM_001253696	69890	Mm.475652	NM_027248	ENSMUSG00000049295	Zfp219	2010302A17Rik	zinc finger protein 219	protein-coding
mm_104526.1	chr11	96075656	96075677	-	1	NA	promoter-TSS (NM_001161419)	promoter-TSS (NM_001161419)	28	NM_007506	11951	Mm.258	NM_007506	ENSMUSG00000006057	Atp5g1	-	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit C1 (subunit 9)	protein-coding
mm_12384.1	chr2	69867491	69867528	+	1	NA	exon (NM_001110145, exon 6 of 12)	exon (NM_001110145, exon 6 of 12)	5947	NM_009278	20823	Mm.10508	NM_009278	ENSMUSG00000068882	Ssb	SS-B	Sjogren syndrome antigen B	protein-coding
mm_21906.1	chr2	166446672	166446674	-	1	NA	promoter-TSS (NR_015558)	promoter-TSS (NR_015558)	-778	NR_015558	319684	Mm.399746	NR_015558		5031425F14Rik	-	RIKEN cDNA 5031425F14 gene	ncRNA
mm_8577.1	chr1	155812806	155812857	-	1	NA	promoter-TSS (NM_023268)	promoter-TSS (NM_023268)	68	NM_023268	104009	Mm.27035	NM_023268	ENSMUSG00000033684	Qsox1	1300003H02Rik|QSOX|Qscn6|SOx	quiescin Q6 sulfhydryl oxidase 1	protein-coding
mm_129237.1	chr15	76617326	76617374	-	1	NA	promoter-TSS (NM_028064)	promoter-TSS (NM_028064)	-498	NM_028064	72027	Mm.276829	NM_028064	ENSMUSG00000063354	Slc39a4	1600025H15Rik|AU041686|AWMS2|ZIP4	solute carrier family 39 (zinc transporter), member 4	protein-coding
mm_54925.1	chr6	47830510	47830584	-	1	NA	promoter-TSS (NM_177882)	promoter-TSS (NM_177882)	-42	NM_177882	330301	Mm.128149	NM_177882	ENSMUSG00000051499	Zfp786	A730012O14Rik|Znf786	zinc finger protein 786	protein-coding
mm_130907.1	chr15	102510815	102510825	-	1	NA	intron (NM_001163643, intron 1 of 15)	CpG	6184	NM_001163643	26404	Mm.172897	NM_009582	ENSMUSG00000023050	Map3k12	DLK|MUK|Zpk	mitogen-activated protein kinase kinase kinase 12	protein-coding
mm_88397.1	chr10	76576399	76576419	+	1	NA	intron (NM_080845, intron 1 of 13)	intron (NM_080845, intron 1 of 13)	761	NM_080845	14317	Mm.36278	NM_080845	ENSMUSG00000001155	Ftcd	-	formiminotransferase cyclodeaminase	protein-coding
mm_114697.1	chr13	83504138	83504159	+	1	NA	5' UTR (NM_025282, exon 1 of 11)	5' UTR (NM_025282, exon 1 of 11)	114	NM_001347564	17260	Mm.24001	NM_025282	ENSMUSG00000005583	Mef2c	5430401D19Rik|9930028G15Rik|AV011172|Mef2	myocyte enhancer factor 2C	protein-coding
mm_100238.1	chr11	117232399	117232413	+	1	NA	intron (NM_001113486, intron 2 of 11)	AT_rich|Low_complexity|Low_complexity	32745	NM_001113486	53860	Mm.38450	NM_017380	ENSMUSG00000059248	Sept9	MSF1|Msf|PNUTL4|Sint1	septin 9	protein-coding
mm_42938.1	chr5	122989291	122989315	+	1	NA	promoter-TSS (NM_001003953)	promoter-TSS (NM_001003953)	-51	NR_045820	109202	Mm.30769	NM_175405	ENSMUSG00000056735	A930024E05Rik	-	RIKEN cDNA A930024E05 gene	ncRNA
mm_152931.1	chr19	28486292	28486294	-	1	NA	intron (NM_001305671, intron 3 of 9)	intron (NM_001305671, intron 3 of 9)	-191931	NR_045330	320176	Mm.406716	NR_045330	ENSMUSG00000097735	D930032P07Rik	-	RIKEN cDNA D930032P07 gene	ncRNA
mm_152831.1	chr19	23207527	23207550	-	1	NA	3' UTR (NM_001252685, exon 24 of 24)	3' UTR (NM_001252685, exon 24 of 24)	58107	NR_035423	100316672		NR_035423	ENSMUSG00000080626	Mir1192	Mirn1192|mmu-mir-1192	microRNA 1192	ncRNA
mm_76269.1	chr8	84067284	84067288	-	1	NA	intron (NM_009055, intron 1 of 20)	CpG	450	NM_009055	19724	Mm.7892	NM_009055	ENSMUSG00000031706	Rfx1	AI047719|AI385641	regulatory factor X, 1 (influences HLA class II expression)	protein-coding
mm_55398.1	chr6	60788516	60788537	-	1	NA	intron (NM_009221, intron 4 of 5)	intron (NM_009221, intron 4 of 5)	40478	NM_001042451	20617	Mm.17484	NM_009221	ENSMUSG00000025889	Snca	NACP|alphaSYN	synuclein, alpha	protein-coding
mm_165684.1	chr3	90695123	90695154	+	1	NA	exon (NM_001281852, exon 2 of 3)	exon (NM_001281852, exon 2 of 3)	583	NM_001281852	20202	Mm.2128	NM_009114	ENSMUSG00000056071	S100a9	60B8Ag|AW546964|BEE22|Cagb|GAGB|L1Ag|MRP14|p14	S100 calcium binding protein A9 (calgranulin B)	protein-coding
mm_141343.1	chr17	28558330	28558393	-	1	NA	TTS (NR_105935)	TTS (NR_105935)	140	NR_105935	102465585		NR_105935	ENSMUSG00000099152	Mir6969	Gm27305|mmu-mir-6969	microRNA 6969	ncRNA
mm_161360.1	chr14	56887788	56887788	+	1	NA	promoter-TSS (NM_029498)	promoter-TSS (NM_029498)	-7	NM_029498	76007	Mm.31417	NM_029498	ENSMUSG00000021945	Zmym2	5830413P05Rik|FIM|MYM|RAMP|SCLL|Zfp198|Znf198	zinc finger, MYM-type 2	protein-coding
mm_109211.1	chr12	108677728	108677737	+	1	NA	intron (NM_001163394, intron 7 of 13)	RLTR21|LTR|ERVK	19112	NR_029771	723909		NR_029771	ENSMUSG00000065436	Mir342	Mirn342|mmu-mir-342	microRNA 342	ncRNA
mm_88194.1	chr10	70096827	70096859	+	1	NA	promoter-TSS (NM_001111121)	promoter-TSS (NM_001111121)	-278	NM_001111121	76551	Mm.281741	NM_001111121	ENSMUSG00000048701	Ccdc6	2810012H18Rik|AA536681|AA960498|AW061011	coiled-coil domain containing 6	protein-coding
mm_90077.1	chr10	116418140	116418148	+	1	NA	promoter-TSS (NR_028107)	promoter-TSS (NR_028107)	23	NR_028107	67342	Mm.245800	NM_026098	ENSMUSG00000020164	Kcnmb4os1	1700058G18Rik	potassium large conductance calcium-activated channel, subfamily M, beta member 4, opposite strand 1	ncRNA
mm_9741.1	chr1	180334688	180334700	-	1	NA	intron (NM_001081175, intron 2 of 7)	intron (NM_001081175, intron 2 of 7)	-4145	NR_003623	277333	Mm.389223	NM_199472		Gm5069	EG277333	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_96073.1	chr11	59848041	59848102	+	1	NA	promoter-TSS (NM_134029)	promoter-TSS (NM_134029)	-2	NM_134029	103850	Mm.41761	NM_134029	ENSMUSG00000032615	Nt5m	2010013E09Rik|AI846937|dNT-2	5',3'-nucleotidase, mitochondrial	protein-coding
mm_153778.1	chr19	45783222	45783246	-	1	NA	promoter-TSS (NM_023799)	promoter-TSS (NM_023799)	57	NM_023799	76055	Mm.122725	NM_023799	ENSMUSG00000025220	Mgea5	2810009A20Rik|4833427O07Rik|5830447M11Rik|AA408215|Hy5|Ncoat|OGA|mKIAA0679	meningioma expressed antigen 5 (hyaluronidase)	protein-coding
mm_146789.1	chr18	20114768	20114782	-	1	NA	promoter-TSS (NM_001291804)	promoter-TSS (NM_001291804)	-2	NM_013504	13505	Mm.33740	NM_013504	ENSMUSG00000044322	Dsc1	1110020A10Rik|AI507491	desmocollin 1	protein-coding
mm_98612.1	chr11	95842725	95842739	+	1	NA	promoter-TSS (NM_001284397)	promoter-TSS (NM_001284397)	64	NM_001038664	14710	Mm.46299	NM_023121	ENSMUSG00000038811	Gngt2	AV096488	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 2	protein-coding
mm_138479.1	chr17	35195041	35195050	+	1	NA	promoter-TSS (NR_105939)	promoter-TSS (NR_105939)	73	NR_105939	102465588		NR_105939	ENSMUSG00000098291	Mir6973a	Gm27967|mmu-mir-6973a	microRNA 6973a	ncRNA
mm_61091.1	chr7	51724304	51724314	+	1	NA	Intergenic	MER44D|DNA|TcMar-Tigger	102479	NM_080853	140919	Mm.256618	NM_080853	ENSMUSG00000030500	Slc17a6	2900073D12Rik|DNPI|VGLUT2	solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 6	protein-coding
mm_143717.1	chr17	80933823	80933831	-	1	NA	TTS (NR_131127)	TTS (NR_131127)	-10805	NM_026516	68027	Mm.357108	NM_026516	ENSMUSG00000024245	Tmem178	2810417M05Rik|Tmem178a	transmembrane protein 178	protein-coding
mm_170084.1	chr17	35445870	35445887	+	1	NA	Intergenic	Intergenic	6711	NM_001201460	110558	Mm.431282	NM_001201460		H2-Q9	H-2Q9|Ped|Qa-2|Qa-9|Qa9	histocompatibility 2, Q region locus 9	protein-coding
mm_99864.1	chr11	109397277	109397286	+	1	NA	3' UTR (NM_010303, exon 4 of 4)	3' UTR (NM_010303, exon 4 of 4)	-28665	NM_025275	13929	Mm.211850	NM_025275	ENSMUSG00000020610	Amz2	AA408420|ESTM12|X83328	archaelysin family metallopeptidase 2	protein-coding
mm_57609.1	chr6	128124313	128124323	-	1	NA	intron (NM_175414, intron 1 of 8)	intron (NM_175414, intron 1 of 8)	19260	NM_175414	109246	Mm.21814	NM_175414	ENSMUSG00000030352	Tspan9	6720474K14Rik|9430079M16Rik|AU018597	tetraspanin 9	protein-coding
mm_133144.1	chr16	70254443	70254446	+	1	NA	Intergenic	Intergenic	-59505	NM_028803	74185	Mm.396102	NM_028803	ENSMUSG00000022707	Gbe1	2310045H19Rik|2810426P10Rik|D16Ertd536e	glucan (1,4-alpha-), branching enzyme 1	protein-coding
mm_130248.1	chr15	96641161	96641252	-	1	NA	5' UTR (NM_134086, exon 1 of 16)	5' UTR (NM_134086, exon 1 of 16)	756	NM_134086	105727	Mm.103568	NM_134086	ENSMUSG00000023169	Slc38a1	AA408026|AA409865|AL022800|AU015942|NAT2	solute carrier family 38, member 1	protein-coding
mm_443.1	chr1	34849951	34850010	+	1	NA	promoter-TSS (NM_145516)	promoter-TSS (NM_145516)	21	NM_145516	226971	Mm.292751	NM_145516	ENSMUSG00000026123	Plekhb2	2310009M15Rik|AU018239|Evt2|Phdc|evt-2	pleckstrin homology domain containing, family B (evectins) member 2	protein-coding
mm_29205.1	chr3	106788079	106788118	-	1	NA	intron (NM_007651, intron 1 of 7)	intron (NM_007651, intron 1 of 7)	2051	NM_007651	12508	Mm.316861	NM_007651	ENSMUSG00000040747	Cd53	AI323659|Ox-44|Tspan25	CD53 antigen	protein-coding
mm_28083.1	chr3	84641483	84641486	-	1	NA	Intergenic	RMER19B|LTR|ERVK	-24708	NM_177260	320782	Mm.107370	NM_177260	ENSMUSG00000056498	Tmem154	9930117H01Rik	transmembrane protein 154	protein-coding
mm_69710.1	chr7	140102385	140102428	-	1	NA	promoter-TSS (NR_104415)	promoter-TSS (NR_104415)	35	NM_001286217	69064	Mm.41915	NM_026928	ENSMUSG00000025466	Fuom	Fucu|Le51	fucose mutarotase	protein-coding
mm_59549.1	chr7	28071199	28071213	+	1	NA	promoter-TSS (NM_001122603)	promoter-TSS (NM_001122603)	-30	NM_001122603	215384	Mm.292276	NM_175444	ENSMUSG00000047730	Fcgbp	A430096B05Rik	Fc fragment of IgG binding protein	protein-coding
mm_150687.1	chr19	42106162	42106180	+	1	NA	intron (NM_145501, intron 4 of 8)	intron (NM_145501, intron 4 of 8)	15736	NM_145501	84095	Mm.117037	NM_145501	ENSMUSG00000025178	Pi4k2a	Pi4k2	phosphatidylinositol 4-kinase type 2 alpha	protein-coding
mm_93694.1	chr10	117845088	117845094	-	1	NA	intron (NM_024457, intron 1 of 7)	intron (NM_024457, intron 1 of 7)	883	NM_024457	215449	Mm.233009	NM_024457	ENSMUSG00000052681	Rap1b	2810443E11Rik	RAS related protein 1b	protein-coding
mm_90840.1	chr10	8721917	8721922	-	1	NA	TTS (NM_175155)	TTS (NM_175155)	164151	NM_175155	70097	Mm.338275	NM_175155	ENSMUSG00000015305	Sash1	1100001C18Rik|2500002E12Rik|A330076K04Rik|mKIAA0790	SAM and SH3 domain containing 1	protein-coding
mm_104152.1	chr11	87108657	87108719	-	1	NA	promoter-TSS (NM_175563)	promoter-TSS (NM_175563)	26	NM_175563	270906	Mm.132381	NM_175563	ENSMUSG00000020493	Prr11	B930067F20Rik	proline rich 11	protein-coding
mm_76377.1	chr8	84835522	84835549	-	1	NA	TTS (NM_183358)	TTS (NM_183358)	3253	NM_183358	102060	Mm.489649	NM_183358	ENSMUSG00000033751	Gadd45gip1	2310040G17Rik|AI425883|Crif1|MRP-L59|Plinp1	growth arrest and DNA-damage-inducible, gamma interacting protein 1	protein-coding
mm_16036.1	chr2	167688767	167688793	+	1	NA	promoter-TSS (NM_009883)	promoter-TSS (NM_009883)	-135	NM_009883	12608	Mm.439656	NM_009883	ENSMUSG00000056501	Cebpb	C/EBPbeta|CRP2|IL-6DBP|LAP|LIP|NF-IL6|NF-M|Nfil6	CCAAT/enhancer binding protein (C/EBP), beta	protein-coding
mm_87540.1	chr10	53596816	53596826	+	1	NA	promoter-TSS (NM_025541)	promoter-TSS (NM_025541)	-140	NM_025541	66403	Mm.272989	NM_025541	ENSMUSG00000019857	Asf1a	2310079C17Rik|C79052	anti-silencing function 1A histone chaperone	protein-coding
mm_115798.1	chr13	19345770	19345799	-	1	NA	Intergenic	Intergenic	50029	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_12569.1	chr2	72979955	72979976	+	1	NA	promoter-TSS (NM_001098425)	promoter-TSS (NM_001098425)	481	NM_001018042	20687	Mm.124328	NM_011450	ENSMUSG00000027109	Sp3	D130027J01Rik	trans-acting transcription factor 3	protein-coding
mm_94515.1	chr11	8605083	8605093	+	1	NA	intron (NM_001083587, intron 2 of 30)	intron (NM_001083587, intron 2 of 30)	59447	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_42441.1	chr5	115429760	115429770	+	1	NA	promoter-TSS (NM_008629)	promoter-TSS (NM_008629)	80	NM_008629	17690	Mm.5077	NM_008629	ENSMUSG00000054256	Msi1	Msi1h|Musahi1|m-Msi-1	musashi RNA-binding protein 1	protein-coding
mm_7564.1	chr1	124756406	124756415	-	1	NA	Intergenic	B3A|SINE|B2	679317	NM_023735	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding
mm_169603.1	chr15	35938144	35938144	-	1	NA	5' UTR (NM_053071, exon 1 of 4)	5' UTR (NM_053071, exon 1 of 4)	102	NM_053071	12864	Mm.548	NM_053071	ENSMUSG00000014313	Cox6c	-	cytochrome c oxidase subunit VIc	protein-coding
mm_9850.1	chr1	184732497	184732525	-	1	NA	promoter-TSS (NM_008250)	promoter-TSS (NM_008250)	-18	NM_008250	15284	Mm.1347	NM_008250	ENSMUSG00000039377	Hlx	Hlx1	H2.0-like homeobox	protein-coding
mm_53157.1	chr6	125314002	125314054	+	1	NA	promoter-TSS (NM_010736)	promoter-TSS (NM_010736)	-158	NM_010736	17000	Mm.3122	NM_010736	ENSMUSG00000030339	Ltbr	AI256028|CD18|LTbetaR|Ltar|TNF-R-III|TNFCR|TNFR-RP|TNFR2-RP|TNFRrp|Tnfbr|Tnfrsf3	lymphotoxin B receptor	protein-coding
mm_118865.1	chr14	25850664	25850671	+	1	NA	intron (NM_013469, intron 1 of 14)	intron (NM_013469, intron 1 of 14)	8512	NM_013469	11744	Mm.294083	NM_013469	ENSMUSG00000021866	Anxa11	A830099O17Rik|Anx11	annexin A11	protein-coding
mm_19945.1	chr2	116999654	116999657	-	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	99503	NR_040335	320975	Mm.132509	NR_040335	ENSMUSG00000085316	D330050G23Rik	-	RIKEN cDNA D330050G23 gene	ncRNA
mm_102461.1	chr11	59839829	59839843	-	1	NA	promoter-TSS (NM_011991)	promoter-TSS (NM_011991)	-69	NM_011991	26572	Mm.40	NM_011991	ENSMUSG00000019373	Cops3	Csn3|Sgn3	COP9 signalosome subunit 3	protein-coding
mm_154059.1	chr19	55127167	55127179	-	1	NA	Intergenic	Intergenic	-27726	NM_008149	14732	Mm.210196	NM_008149	ENSMUSG00000024978	Gpam	GPAT|GPAT1	glycerol-3-phosphate acyltransferase, mitochondrial	protein-coding
mm_121406.1	chr14	119304073	119304075	+	1	NA	intron (NM_015820, intron 1 of 1)	intron (NM_015820, intron 1 of 1)	165809	NM_015820	50787	Mm.445777	NM_015820	ENSMUSG00000053465	Hs6st3	6OST3|HS6ST-3	heparan sulfate 6-O-sulfotransferase 3	protein-coding
mm_67452.1	chr7	80401462	80401473	-	1	NA	intron (NM_001081454, intron 1 of 15)	intron (NM_001081454, intron 1 of 15)	1345	NM_011046	18550	Mm.5241	NM_011046	ENSMUSG00000030530	Furin	9130404I01Rik|Fur|PACE|Pcsk3|SPC1	furin (paired basic amino acid cleaving enzyme)	protein-coding
mm_20812.1	chr2	144474872	144474882	-	1	NA	3' UTR (NM_172859, exon 21 of 21)	3' UTR (NM_172859, exon 21 of 21)	9701	NR_038065	171588	Mm.450554	NR_038065	ENSMUSG00000083674	Gm38402	-	zinc finger protein pseudogene	pseudo
mm_126722.1	chr15	85402097	85402121	+	1	NA	intron (NM_016843, intron 9 of 11)	intron (NM_016843, intron 9 of 11)	65728	NM_016843	54138	Mm.248906	NM_016843	ENSMUSG00000016541	Atxn10	AI325283|C77170|E46|Sca10|TEG-169|Tex169	ataxin 10	protein-coding
mm_147343.1	chr18	43321702	43321713	-	1	NA	3' UTR (NM_001291455, exon 14 of 14)	3' UTR (NM_001291455, exon 14 of 14)	51565	NM_001136086	22240	Mm.8180	NM_009468	ENSMUSG00000024501	Dpysl3	CRMP-4|DRP-3|TUC4|ULIP-1|Ulip|Ulip1	dihydropyrimidinase-like 3	protein-coding
mm_112453.1	chr13	5863882	5863896	+	1	NA	intron (NM_011803, intron 1 of 3)	intron (NM_011803, intron 1 of 3)	2400	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_6422.1	chr1	73928505	73928529	-	1	NA	intron (NM_001289895, intron 22 of 32)	intron (NM_001289895, intron 22 of 32)	-64051	NR_045311	109198	Mm.359721	NR_045311	ENSMUSG00000100301	6030407O03Rik	-	RIKEN cDNA 6030407O03 gene	ncRNA
mm_98150.1	chr11	87593590	87593593	+	1	NA	intron (NM_133215, intron 2 of 18)	intron (NM_133215, intron 2 of 18)	1374	NM_133215	170749	Mm.399376	NM_133215	ENSMUSG00000018401	Mtmr4	AA596759|ESTM44|FYVE-DSP2|ZFYVE11|mKIAA0647	myotubularin related protein 4	protein-coding
mm_83149.1	chr9	40456153	40456176	-	1	NA	promoter-TSS (NM_172768)	promoter-TSS (NM_172768)	-400	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_29289.1	chr3	107749075	107749096	-	1	NA	exon (NM_007778, exon 6 of 9)	exon (NM_007778, exon 6 of 9)	11384	NM_001113530	12977	Mm.795	NM_007778	ENSMUSG00000014599	Csf1	C87615|Csfm|MCSF|op	colony stimulating factor 1 (macrophage)	protein-coding
mm_132377.1	chr16	34921481	34921491	+	1	NA	intron (NM_139300, intron 15 of 31)	intron (NM_139300, intron 15 of 31)	17843	NR_040536	76649	Mm.420532	NR_040536	ENSMUSG00000100593	1700119H24Rik	-	RIKEN cDNA 1700119H24 gene	ncRNA
mm_2656.1	chr1	125677132	125677142	+	1	NA	5' UTR (NM_027677, exon 1 of 2)	5' UTR (NM_027677, exon 1 of 2)	141	NM_027677	71111	Mm.32727	NM_027677	ENSMUSG00000026343	Gpr39	4933415E13Rik	G protein-coupled receptor 39	protein-coding
mm_31287.1	chr4	45890359	45890364	+	1	NA	promoter-TSS (NM_198660)	promoter-TSS (NM_198660)	58	NM_198660	381522	Mm.54220	NM_198660	ENSMUSG00000035539	Ccdc180	E230008N13Rik|Gm1025	coiled-coil domain containing 180	protein-coding
mm_26421.1	chr3	142614800	142614810	+	1	NA	intron (NM_010259, intron 10 of 10)	L1_Mur2|LINE|L1	-5858	NM_010260	14469	Mm.24038	NM_010260	ENSMUSG00000028270	Gbp2	-	guanylate binding protein 2	protein-coding
mm_146581.1	chr18	7610600	7610604	-	1	NA	intron (NM_001081287, intron 1 of 16)	ORR1E|LTR|ERVL-MaLR	16261	NM_001081287	75739	Mm.133293	NM_001081287	ENSMUSG00000057440	Mpp7	1110068J02Rik|2810038M04Rik|5430426E14Rik|AI415104|Gm955	membrane protein, palmitoylated 7 (MAGUK p55 subfamily member 7)	protein-coding
mm_168407.1	chr1	130195967	130195986	+	1	NA	intron (NM_172485, intron 26 of 27)	intron (NM_172485, intron 26 of 27)	227067	NM_007827	13137	Mm.436759	NM_007827	ENSMUSG00000026401	Cd55b	AI323748|Daf|Daf-TM|Daf2|TM-DAF	CD55 molecule, decay accelerating factor for complement B	protein-coding
mm_167960.1	chrX	142692077	142692085	+	1	NA	intron (NM_001199360, intron 2 of 6)	intron (NM_001199360, intron 2 of 6)	10355	NM_001199360	209497	Mm.249648	NM_177592	ENSMUSG00000047045	Tmem164	AI316850|AI852450|AW547186|F730011B02	transmembrane protein 164	protein-coding
mm_54007.1	chr6	7818022	7818037	-	1	NA	Intergenic	Intergenic	-27195	NM_052993	94192	Mm.102752	NM_052993	ENSMUSG00000042460	C1galt1	2210410E06Rik|AV284120|T-synthase	core 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase, 1	protein-coding
mm_45274.1	chr5	64805322	64805328	-	1	NA	intron (NM_008453, intron 1 of 5)	intron (NM_008453, intron 1 of 5)	1802	NM_008453	16599	Mm.392759	NM_008453	ENSMUSG00000029178	Klf3	9930027G08Rik|AL024007|Bklf|Tef-2	Kruppel-like factor 3 (basic)	protein-coding
mm_156079.1	chrX	109196803	109196818	+	1	NA	promoter-TSS (NM_001037917)	promoter-TSS (NM_001037917)	54	NM_001037917	622976	Mm.482747	NM_001037917	ENSMUSG00000048621	Gm6377	EG622976	predicted gene 6377	protein-coding
mm_146531.1	chr18	5334365	5334410	-	1	NA	promoter-TSS (NM_178722)	promoter-TSS (NM_178722)	52	NM_178722	240186	Mm.118257	NM_178722	ENSMUSG00000050945	Zfp438	9430031G09|9430091M14Rik|B830013J05Rik	zinc finger protein 438	protein-coding
mm_36390.1	chr4	77454110	77454120	-	1	NA	intron (NM_011211, intron 4 of 39)	intron (NM_011211, intron 4 of 39)	757780	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding
mm_68731.1	chr7	120670257	120670263	-	1	NA	promoter-TSS (NM_001040137)	promoter-TSS (NM_001040137)	-10	NM_001040137	67983	Mm.394441	NM_001040136	ENSMUSG00000030887	Pdzd9	4930408O21Rik	PDZ domain containing 9	protein-coding
mm_142395.1	chr17	45020690	45020735	-	1	NA	intron (NM_178652, intron 6 of 11)	B1F|SINE|Alu	-139827	NM_029257	75341	Mm.386821	NM_029257		4930564C03Rik	-	RIKEN cDNA 4930564C03 gene	protein-coding
mm_120641.1	chr14	70521430	70521447	+	1	NA	exon (NM_011359, exon 5 of 6)	exon (NM_011359, exon 5 of 6)	-1178	NR_033241	12153	Mm.27757	NM_009755	ENSMUSG00000022098	Bmp1	Pcp|Tld	bone morphogenetic protein 1	protein-coding
mm_72816.1	chr8	88115985	88115996	+	1	NA	Intergenic	L1M2|LINE|L1	-2769	NM_029074	382030	Mm.216574	NM_029074	ENSMUSG00000036810	Cnep1r1	5033428A16Rik|NEP1-R1|Tmem188	CTD nuclear envelope phosphatase 1 regulatory subunit 1	protein-coding
mm_96521.1	chr11	68496527	68496552	+	1	NA	3' UTR (NM_177320, exon 19 of 19)	3' UTR (NM_177320, exon 19 of 19)	-6480	NM_001004435	104709	Mm.234573	NM_001004435	ENSMUSG00000046207	Pik3r6	BB220380|p84|p84 PIKAP|p87(PIKAP)|p87PIKAP	phosphoinositide-3-kinase, regulatory subunit 6	protein-coding
mm_34635.1	chr4	150614509	150614525	+	1	NA	exon (NM_001085492, exon 18 of 23)	exon (NM_001085492, exon 18 of 23)	37657	NM_173774	242773	Mm.29280	NM_173774	ENSMUSG00000039838	Slc45a1	C230078B22|Dnb5	solute carrier family 45, member 1	protein-coding
mm_143562.1	chr17	74224983	74224985	-	1	NA	intron (NM_133771, intron 6 of 8)	intron (NM_133771, intron 6 of 8)	69879	NM_133771	76890	Mm.311874	NM_133771	ENSMUSG00000058704	Memo1	0610016J10Rik|D930048L02Rik	mediator of cell motility 1	protein-coding
mm_154425.1	chrM	406	410	-	1	NA	NA	Intergenic	NA	NA								
mm_53700.1	chr6	142756968	142756974	+	1	NA	exon (NM_009908, exon 1 of 8)	exon (NM_009908, exon 1 of 8)	285	NM_009908	12764	Mm.3820	NM_009908	ENSMUSG00000030282	Cmas	AW208911|CMPNeu5Ac|D6Bwg0250e	cytidine monophospho-N-acetylneuraminic acid synthetase	protein-coding
mm_145814.1	chr18	65430770	65430782	+	1	NA	promoter-TSS (NM_172833)	promoter-TSS (NM_172833)	-221	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_159893.1	chr6	29471398	29471398	+	1	NA	promoter-TSS (NM_001145360)	promoter-TSS (NM_001145360)	-39	NM_001145360	668210	Mm.420607	NM_001145360	ENSMUSG00000090685	Gm9047	EG668210	predicted gene 9047	protein-coding
mm_127074.1	chr15	97377181	97377196	+	1	NA	intron (NM_172293, intron 5 of 5)	intron (NM_172293, intron 5 of 5)	-129901	NM_001164602	105827	Mm.24005	NM_178114	ENSMUSG00000048218	Amigo2	AI415330|AMIGO-2|AW208913|Ali1	adhesion molecule with Ig like domain 2	protein-coding
mm_52000.1	chr6	92816490	92816498	+	1	NA	exon (NM_175314, exon 20 of 30)	exon (NM_175314, exon 20 of 30)	84947	NM_175314	101401	Mm.158235	NM_175314	ENSMUSG00000030022	Adamts9	1810011L16Rik|8430403M15Rik|AW743315|E030027K14Rik	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 9	protein-coding
mm_108815.1	chr12	95692330	95692344	+	1	NA	5' UTR (NM_201518, exon 1 of 2)	5' UTR (NM_201518, exon 1 of 2)	111	NM_201518	399558	Mm.341948	NM_201518	ENSMUSG00000047414	Flrt2	-	fibronectin leucine rich transmembrane protein 2	protein-coding
mm_83776.1	chr9	52127865	52127877	-	1	NA	intron (NM_001162921, intron 2 of 5)	A-rich|Low_complexity|Low_complexity	12248	NR_105750	102465150		NR_105750	ENSMUSG00000099311	Mir6244	Gm27368|mmu-mir-6244	microRNA 6244	ncRNA
mm_150281.1	chr19	34290654	34290668	+	1	NA	promoter-TSS (NM_001146708)	promoter-TSS (NM_001146708)	2	NM_001146708	14102	Mm.1626	NM_007987	ENSMUSG00000024778	Fas	AI196731|APO1|APT1|CD95|TNFR6|Tnfrsf6|lpr	Fas (TNF receptor superfamily member 6)	protein-coding
mm_123331.1	chr14	63049874	63049882	-	1	NA	Intergenic	Intergenic	2887	NM_001034910	619548	Mm.387101	NM_001034910	ENSMUSG00000054763	Defb42	BD-42|Defb44|mBD-42	defensin beta 42	protein-coding
mm_24878.1	chr3	95994032	95994042	+	1	NA	intron (NM_023320, intron 2 of 5)	intron (NM_023320, intron 2 of 5)	1802	NM_023320	67220	Mm.458147	NM_023320	ENSMUSG00000015745	Plekho1	2810052M02Rik|CKIP-1|Ckip1|JZA-20|Jza2	pleckstrin homology domain containing, family O member 1	protein-coding
mm_172510.1	chr7	7130721	7130727	-	1	NA	TTS (NM_029584)	TTS (NM_029584)	6031	NM_029584	76373	Mm.159732	NM_029584	ENSMUSG00000063535	Zfp773	2810409K11Rik	zinc finger protein 773	protein-coding
mm_33855.1	chr4	135876928	135876940	+	1	NA	Intergenic	Intergenic	-3088	NM_026383	52830	Mm.29159	NM_026383	ENSMUSG00000028675	Pnrc2	0610011E17Rik|D4Bwg0593e	proline-rich nuclear receptor coactivator 2	protein-coding
mm_105512.1	chr11	106255781	106255837	-	1	NA	promoter-TSS (NM_025310)	promoter-TSS (NM_025310)	-7	NM_025310	56095	Mm.29795	NM_025310	ENSMUSG00000020706	Ftsj3	AA537063|AU045295|C79843|D11Ertd400e|Epcs3	FtsJ RNA methyltransferase homolog 3 (E. coli)	protein-coding
mm_97082.1	chr11	73047855	73047902	+	1	NA	promoter-TSS (NM_025818)	promoter-TSS (NM_025818)	11	NM_025818	66874	Mm.41903	NM_025818	ENSMUSG00000020783	Ncbp3	1200014J11Rik|C130061O14Rik|C78393	nuclear cap binding subunit 3	protein-coding
mm_101336.1	chr11	23498050	23498061	-	1	NA	promoter-TSS (NM_172391)	promoter-TSS (NM_172391)	-16	NM_172391	268390	Mm.13148	NM_172391	ENSMUSG00000020288	Ahsa2	-	AHA1, activator of heat shock protein ATPase 2	protein-coding
mm_82631.1	chr9	21927566	21927576	-	1	NA	promoter-TSS (NM_178577)	promoter-TSS (NM_178577)	-36	NM_001253870	235043	Mm.253329	NM_178577	ENSMUSG00000040883	Tmem205	-	transmembrane protein 205	protein-coding
mm_91763.1	chr10	51494835	51494848	-	1	NA	exon (NM_013532, exon 7 of 9)	exon (NM_013532, exon 7 of 9)	3943	NM_013532	14728	Mm.34408	NM_013532	ENSMUSG00000062593	Lilrb4a	CD85K|Gp49b|HM18|ILT3|LIR-5|Lilrb4|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4A	protein-coding
mm_84635.1	chr9	71163089	71163100	-	1	NA	promoter-TSS (NM_001271843)	promoter-TSS (NM_001271843)	195	NR_073483	64008	Mm.449427	NM_022026	ENSMUSG00000032204	Aqp9	1700020I22Rik|AI266899|AQP-9	aquaporin 9	protein-coding
mm_160601.1	chr9	77544092	77544092	-	1	NA	promoter-TSS (NM_172528)	promoter-TSS (NM_172528)	-33	NM_172528	214345	Mm.28534	NM_172528	ENSMUSG00000032352	Lrrc1	A430093J20Rik|AU016091|D030059I21|mKIAA4018	leucine rich repeat containing 1	protein-coding
mm_59152.1	chr7	24370097	24370121	+	1	NA	promoter-TSS (NM_001163510)	promoter-TSS (NM_001163510)	-154	NM_001163510	16534	Mm.9911	NM_008433	ENSMUSG00000054342	Kcnn4	IK1|IKCA1|KCA4|KCa3.1|SK4|SKCas|mIKCa1	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4	protein-coding
mm_142148.1	chr17	36006628	36006652	-	1	NA	3' UTR (NM_008207, exon 6 of 6)	3' UTR (NM_008207, exon 6 of 6)	12136	NR_015618	77810	Mm.483143	NR_015618		A930015D03Rik	-	RIKEN cDNA A930015D03 gene	ncRNA
mm_151251.1	chr19	53907367	53907376	+	1	NA	intron (NM_001168491, intron 1 of 11)	intron (NM_001168491, intron 1 of 11)	4020	NM_001168491	18569	Mm.1605	NM_011050	ENSMUSG00000024975	Pdcd4	D19Ucla1|Ma3|Tis	programmed cell death 4	protein-coding
mm_45124.1	chr5	46007571	46007581	-	1	NA	Intergenic	Intergenic	-75167	NR_110478	78106	Mm.243807	NR_110478	ENSMUSG00000106602	4930405L22Rik	-	RIKEN cDNA 4930405L22 gene	ncRNA
mm_166697.1	chr6	114249680	114249691	+	1	NA	3' UTR (NM_172890, exon 14 of 14)	3' UTR (NM_172890, exon 14 of 14)	-32950	NM_178703	232333	Mm.5260	NM_178703	ENSMUSG00000030310	Slc6a1	A730043E01|GABATHG|GABATR|GAT-1|Gabt|Gabt1|Gat1|XT-1|Xtrp1	solute carrier family 6 (neurotransmitter transporter, GABA), member 1	protein-coding
mm_94613.1	chr11	16752204	16752215	+	1	NA	promoter-TSS (NM_007912)	promoter-TSS (NM_007912)	6	NM_007912	13649	Mm.8534	NM_007912	ENSMUSG00000020122	Egfr	9030024J15Rik|AI552599|Erbb|Errb1|Errp|Wa5|wa-2|wa2	epidermal growth factor receptor	protein-coding
mm_91678.1	chr10	43533165	43533169	-	1	NA	intron (NM_026411, intron 1 of 3)	intron (NM_026411, intron 1 of 3)	7827	NM_026411	67851	Mm.209953	NM_026411	ENSMUSG00000019797	1700021F05Rik	-	RIKEN cDNA 1700021F05 gene	protein-coding
mm_35576.1	chr4	41739488	41739505	-	1	NA	exon (NM_001286542, exon 2 of 2)	exon (NM_001286542, exon 2 of 2)	1863	NM_001286540	18391	Mm.425181	NM_011014	ENSMUSG00000036078	Sigmar1	Oprs1|Sig1R|sigma1R	sigma non-opioid intracellular receptor 1	protein-coding
mm_107874.1	chr12	69946170	69946193	+	1	NA	intron (NM_178628, intron 7 of 14)	intron (NM_178628, intron 7 of 14)	-17228	NR_036607	100040999	Mm.394588	NR_036607	ENSMUSG00000079076	Gm3086	-	RuvB-like protein 1 pseudogene	pseudo
mm_169036.1	chr13	13437600	13437601	+	1	NA	promoter-TSS (NM_010917)	promoter-TSS (NM_010917)	-2	NM_010917	18073	Mm.4691	NM_010917	ENSMUSG00000005397	Nid1	A630025O17|Nid|entactin|entactin-1|nidogen-1	nidogen 1	protein-coding
mm_100802.1	chr11	4992567	4992597	-	1	NA	intron (NM_007454, intron 1 of 20)	L2b|LINE|L2	5758	NM_007454	11764	Mm.274816	NM_007454	ENSMUSG00000009090	Ap1b1	Adtb1|b2b1660Clo	adaptor protein complex AP-1, beta 1 subunit	protein-coding
mm_158580.1	chrX	150657393	150657407	-	1	NA	promoter-TSS (NM_019548)	promoter-TSS (NM_019548)	36	NM_019548	56191	Mm.3597	NM_019548	ENSMUSG00000025272	Tro	AA409408|Maged3|Maged3l|Tnn|Trol|magphinin	trophinin	protein-coding
mm_78060.1	chr9	14903495	14903501	+	1	NA	intron (NM_022888, intron 1 of 4)	intron (NM_022888, intron 1 of 4)	453	NM_176807	64931	Mm.86738	NM_022888	ENSMUSG00000031933	Izumo1r	0910001L11Rik|C86255|Folbp3|Folr4|Juno	IZUMO1 receptor, JUNO	protein-coding
mm_145294.1	chr18	53252405	53252416	+	1	NA	intron (NM_029394, intron 1 of 6)	intron (NM_029394, intron 1 of 6)	6748	NM_029394	69226	Mm.32414	NM_029394	ENSMUSG00000024535	Snx24	2810011K15Rik|5730433I16Rik|AI451341	sorting nexing 24	protein-coding
mm_66027.1	chr7	30613862	30613865	-	1	NA	Intergenic	Intergenic	-1129	NM_026815	109637	Mm.25471	NM_026815	ENSMUSG00000006313	Upk1a	1110031P12Rik|AU019298|C87192|Tspan21|Upk1	uroplakin 1A	protein-coding
mm_41484.1	chr5	92083430	92083441	+	1	NA	promoter-TSS (NM_001080797)	promoter-TSS (NM_001080797)	163	NM_001080794	23881	Mm.290530	NM_011816	ENSMUSG00000029405	G3bp2	AA409541|E430034L04Rik|G3BP|mKIAA0660	GTPase activating protein (SH3 domain) binding protein 2	protein-coding
mm_155247.1	chrX	57223654	57223666	+	1	NA	3' UTR (NM_011616, exon 5 of 5)	3' UTR (NM_011616, exon 5 of 5)	11517	NM_011616	21947	Mm.4861	NM_011616	ENSMUSG00000031132	Cd40lg	CD154|CD40-L|Cd40l|HIGM1|IGM|IMD3|Ly-62|Ly62|T-BAM|TRAP|Tnfsf5|Tnlg8b|gp39	CD40 ligand	protein-coding
mm_43159.1	chr5	127027373	127027379	+	1	NA	Intergenic	Intergenic	-3413	NR_040685	71247	Mm.399586	NR_040685	ENSMUSG00000105490	4933438B17Rik	-	RIKEN cDNA 4933438B17 gene	ncRNA
mm_103026.1	chr11	69735233	69735244	-	1	NA	exon (NM_001291068, exon 29 of 29)	exon (NM_001291068, exon 29 of 29)	23395	NM_001291068	20020	Mm.16533	NM_009089	ENSMUSG00000005198	Polr2a	220kDa|Rpb1|Rpo2-1	polymerase (RNA) II (DNA directed) polypeptide A	protein-coding
mm_21900.1	chr2	166156188	166156198	-	1	NA	promoter-TSS (NM_028072)	promoter-TSS (NM_028072)	-510	NM_028072	72043	Mm.1011	NM_028072	ENSMUSG00000006800	Sulf2	2010004N24Rik|AU020235|MSulf-2|mKIAA1247	sulfatase 2	protein-coding
mm_152543.1	chr19	11336075	11336087	-	1	NA	promoter-TSS (NM_027836)	promoter-TSS (NM_027836)	65	NM_001025610	109225	Mm.491251	NM_027836	ENSMUSG00000024672	Ms4a7	9130422I10Rik|A430103C15Rik|CD20l4|CFFMA	membrane-spanning 4-domains, subfamily A, member 7	protein-coding
mm_28228.1	chr3	88454821	88454831	-	1	NA	5' UTR (NM_001163490, exon 2 of 15)	5' UTR (NM_001163490, exon 2 of 15)	935	NM_013658	20351	Mm.439752	NM_013658	ENSMUSG00000028064	Sema4a	AI132332|SemB|Semab	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A	protein-coding
mm_83015.1	chr9	36784554	36784581	-	1	NA	exon (NM_001199494, exon 8 of 11)	exon (NM_001199494, exon 8 of 11)	12501	NM_007915	13663	Mm.4337	NM_007915	ENSMUSG00000062762	Ei24	AA536736|AI115355|PIG8	etoposide induced 2.4 mRNA	protein-coding
mm_49074.1	chr6	5959290	5959291	+	1	NA	intron (NM_001191027, intron 9 of 15)	intron (NM_001191027, intron 9 of 15)	18103	NR_040255	72249	Mm.443268	NR_040255	ENSMUSG00000085416	1700019G24Rik	-	RIKEN cDNA 1700019G24 gene	ncRNA
mm_52705.1	chr6	119386656	119386681	+	1	NA	intron (NM_197985, intron 1 of 7)	intron (NM_197985, intron 1 of 7)	30815	NM_197985	68465	Mm.291826	NM_197985	ENSMUSG00000030168	Adipor2	1110001I14Rik|ADCR2|AI115388|AW554121|D6Ucla1e|Paqr2	adiponectin receptor 2	protein-coding
mm_11589.1	chr2	33216052	33216084	+	1	NA	5' UTR (NM_011923, exon 1 of 5)	5' UTR (NM_011923, exon 1 of 5)	107	NM_011923	26360	Mm.208919	NM_011923	ENSMUSG00000004105	Angptl2	AI593246|AW260363|Arp2	angiopoietin-like 2	protein-coding
mm_141837.1	chr17	34638065	34638082	-	1	NA	Intergenic	Intergenic	-6810	NM_019873	56299	Mm.10025	NM_019873	ENSMUSG00000033739	Fkbpl	DIR1|NG7|Ppiase-X|Wisp39	FK506 binding protein-like	protein-coding
mm_10364.1	chr2	11705460	11705464	+	1	NA	promoter-TSS (NM_001271500)	promoter-TSS (NM_001271500)	169	NM_001271497	16169	Mm.200196	NM_008358	ENSMUSG00000023206	Il15ra	AA690181|IL-15RA	interleukin 15 receptor, alpha chain	protein-coding
mm_26353.1	chr3	142548925	142548933	+	1	NA	3' UTR (NM_001083312, exon 11 of 11)	3' UTR (NM_001083312, exon 11 of 11)	-11123	NM_018734	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_11161.1	chr2	28555879	28555909	+	1	NA	TTS (NM_009885)	TTS (NM_009885)	7509	NM_009885	12613	Mm.236017	NM_009885	ENSMUSG00000026818	Cel	1810036E18Rik|BAL	carboxyl ester lipase	protein-coding
mm_24616.1	chr3	93505049	93505092	+	1	NA	Intergenic	Looper|DNA|PiggyBac	-15426	NM_016740	20195	Mm.280038	NM_016740	ENSMUSG00000027907	S100a11	EMAPI|Emap1|S100a14|S100c|cal	S100 calcium binding protein A11	protein-coding
mm_18581.1	chr2	66165381	66165386	-	1	NA	Intergenic	RMER19C|LTR|ERVK	-40590	NM_015736	14425	Mm.439760	NM_015736	ENSMUSG00000026994	Galnt3	-	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 3	protein-coding
mm_14944.1	chr2	151827441	151827441	+	1	NA	Intergenic	Intergenic	-15486	NM_001040689	228770	Mm.159868	NM_001040689	ENSMUSG00000032852	Rspo4	A730099F22|A930029K19Rik	R-spondin 4	protein-coding
mm_69894.1	chr7	141637733	141637744	-	1	NA	intron (NM_001330001, intron 31 of 33)	intron (NM_001330001, intron 31 of 33)	17037	NR_106030	102466798		NR_106030	ENSMUSG00000098759	Mir7063	Gm27654|mmu-mir-7063	microRNA 7063	ncRNA
mm_112143.1	chr12	113153875	113153877	-	1	NA	TTS (NM_007763)	TTS (NM_007763)	1864	NM_007763	12925	Mm.272368	NM_007763	ENSMUSG00000006360	Crip1	CRHP|CRP1|Crip	cysteine-rich protein 1 (intestinal)	protein-coding
mm_107310.1	chr12	31168846	31168870	+	1	NA	promoter-TSS (NR_102715)	promoter-TSS (NR_102715)	-4	NR_102715	100043065	Mm.479482	NM_001034058		6030469F06Rik	-	RIKEN cDNA 6030469F06 gene	ncRNA
mm_11158.1	chr2	28549464	28549476	+	1	NA	exon (NM_009058, exon 16 of 18)	exon (NM_009058, exon 16 of 18)	13933	NM_009885	12613	Mm.236017	NM_009885	ENSMUSG00000026818	Cel	1810036E18Rik|BAL	carboxyl ester lipase	protein-coding
mm_115846.1	chr13	21287409	21287409	-	1	NA	exon (NM_010343, exon 5 of 5)	exon (NM_010343, exon 5 of 5)	5277	NM_010343	14780	Mm.1332	NM_010343	ENSMUSG00000004344	Gpx5	AV379049|Arep	glutathione peroxidase 5	protein-coding
mm_166898.1	chr7	28382896	28382906	-	1	NA	Intergenic	Intergenic	-3673	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_3249.1	chr1	136131412	136131441	+	1	NA	promoter-TSS (NM_001039472)	promoter-TSS (NM_001039472)	25	NM_001039472	16565	Mm.276135	NM_019962	ENSMUSG00000041642	Kif21b	2610511N21Rik|mKIAA0449	kinesin family member 21B	protein-coding
mm_149832.1	chr19	24673999	24674017	+	1	NA	promoter-TSS (NM_183160)	promoter-TSS (NM_183160)	0	NM_183160	226040	Mm.391170	NM_183160	ENSMUSG00000048572	Tmem252	E030010A14Rik	transmembrane protein 252	protein-coding
mm_61800.1	chr7	84233002	84233014	+	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	-81115	NM_133722	70178	Mm.23914	NM_133722	ENSMUSG00000038459	Abhd17c	2210412D01Rik|AL023007|Fam108c|Fam108c1	abhydrolase domain containing 17C	protein-coding
mm_63552.1	chr7	128070911	128070926	+	1	NA	exon (NM_008401, exon 5 of 30)	exon (NM_008401, exon 5 of 30)	8278	NM_008401	16409	Mm.262106	NM_008401	ENSMUSG00000030786	Itgam	CD11b/CD18|CR3|CR3A|Cd11b|F730045J24Rik|Ly-40|MAC1|Mac-1|Mac-1a	integrin alpha M	protein-coding
mm_44724.1	chr5	30961373	30961386	-	1	NA	Intergenic	MER21C|LTR|ERVL	-1052	NM_016703	50907	Mm.272414	NM_016703	ENSMUSG00000045302	Preb	C85705	prolactin regulatory element binding	protein-coding
mm_5565.1	chr1	38897925	38897961	-	1	NA	5' UTR (NM_145142, exon 1 of 7)	5' UTR (NM_145142, exon 1 of 7)	217	NM_145142	98388	Mm.260054	NM_145142	ENSMUSG00000026080	Chst10	AI507003|AU041319|Hnk-1st|ST	carbohydrate sulfotransferase 10	protein-coding
mm_84845.1	chr9	78396097	78396116	-	1	NA	exon (NM_001191044, exon 1 of 17)	exon (NM_001191044, exon 1 of 17)	329	NM_001191044	100048658	Mm.158166	NM_001191044	ENSMUSG00000070291	Ddx43	ENSMUSG00000070291|OTTMUSG00000019690	DEAD (Asp-Glu-Ala-Asp) box polypeptide 43	protein-coding
mm_113592.1	chr13	40944372	40944384	+	1	NA	intron (NM_133219, intron 1 of 2)	RMER10A|LTR|ERVL	26744	NM_133219	14538	Mm.314757	NM_008105	ENSMUSG00000021360	Gcnt2	5330430K10Rik|IGnT|IGnTA|IGnTB|IGnTC	glucosaminyl (N-acetyl) transferase 2, I-branching enzyme	protein-coding
mm_60752.1	chr7	45486339	45486339	+	1	NA	promoter-TSS (NM_001290999)	promoter-TSS (NM_001290999)	76	NM_001290999	56734	Mm.439742	NM_008807	ENSMUSG00000023467	Tulp2	Pdet	tubby-like protein 2	protein-coding
mm_143749.1	chr17	81568702	81568706	-	1	NA	intron (NR_104580, intron 2 of 8)	intron (NR_104580, intron 2 of 8)	169683	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_124198.1	chr14	98169314	98169342	-	1	NA	5' UTR (NM_001038610, exon 1 of 11)	5' UTR (NM_001038610, exon 1 of 11)	437	NM_001038610	13134	Mm.320593	NM_007826	ENSMUSG00000055639	Dach1	Dac|Dach	dachshund 1 (Drosophila)	protein-coding
mm_130791.1	chr15	101680282	101680298	-	1	NA	promoter-TSS (NM_010669)	promoter-TSS (NM_010669)	-1	NM_010669	16688	Mm.441891	NM_010669	ENSMUSG00000023041	Krt6b	BB144589|Krt2-6b|mK6[b]	keratin 6B	protein-coding
mm_81743.1	chr9	113812548	113812621	+	1	NA	promoter-TSS (NM_001286601)	promoter-TSS (NM_001286601)	-2	NM_001286601	76499	Mm.222272	NM_029633	ENSMUSG00000033392	Clasp2	1500004F14Rik|8030404L10Rik|C77448|CLASP2beta|mKIAA0627	CLIP associating protein 2	protein-coding
mm_57359.1	chr6	124761284	124761293	-	1	NA	3' UTR (NM_013509, exon 12 of 12)	3' UTR (NM_013509, exon 12 of 12)	-4801	NM_007881	13498	Mm.333380	NM_007881	ENSMUSG00000004263	Atn1	Atr1|Drpla|atrophin-1	atrophin 1	protein-coding
mm_10692.1	chr2	22622420	22622430	+	1	NA	promoter-TSS (NM_008078)	promoter-TSS (NM_008078)	98	NM_008078	14417	Mm.4784	NM_008078	ENSMUSG00000026787	Gad2	6330404F12Rik|GAD(65)|GAD65|Gad-2	glutamic acid decarboxylase 2	protein-coding
mm_157955.1	chrX	87763750	87763772	-	1	NA	intron (NM_001160403, intron 2 of 10)	intron (NM_001160403, intron 2 of 10)	351862	NM_001160403	331461	Mm.121680	NM_001160403	ENSMUSG00000052372	Il1rapl1	6330532G10Rik|C030039N24|IL1R8|IL1RAPL|MRX34|OPHN4|TIGIRR-2	interleukin 1 receptor accessory protein-like 1	protein-coding
mm_45557.1	chr5	73180199	73180201	-	1	NA	intron (NM_028194, intron 3 of 62)	intron (NM_028194, intron 3 of 62)	76418	NM_028194	72313	Mm.260594	NM_028194	ENSMUSG00000070733	Fryl	2010313D22Rik|2310004H21Rik|2510002A14Rik|9030227G01Rik|mKIAA0826	FRY like transcription coactivator	protein-coding
mm_19034.1	chr2	76969814	76969825	-	1	NA	exon (NM_011652, exon 7 of 313)	exon (NM_011652, exon 7 of 313)	12728	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_134021.1	chr16	4880448	4880479	-	1	NA	promoter-TSS (NM_145359)	promoter-TSS (NM_145359)	-612	NM_145359	207740	Mm.268895	NM_145359	ENSMUSG00000039568	Ubald1	1500031H01Rik|BC013706|Fam100a	UBA-like domain containing 1	protein-coding
mm_5902.1	chr1	54907165	54907175	-	1	NA	intron (NM_001081433, intron 1 of 27)	intron (NM_001081433, intron 1 of 27)	19217	NM_001081433	329154	Mm.397910	NM_001081433	ENSMUSG00000052331	Ankrd44	4930444A19Rik|A130096K20|E130014H08Rik|PP6-ARS-B	ankyrin repeat domain 44	protein-coding
mm_133193.1	chr16	72777048	72777052	+	1	NA	intron (NM_019413, intron 2 of 28)	intron (NM_019413, intron 2 of 28)	113901	NM_019413	19876	Mm.310772	NM_019413	ENSMUSG00000022883	Robo1	AW494633|AW742721|DUTT1|Gm310	roundabout guidance receptor 1	protein-coding
mm_131682.1	chr16	20675727	20675739	+	1	NA	exon (NM_145941, exon 6 of 33)	exon (NM_145941, exon 6 of 33)	3006	NM_001304432	208643	Mm.260256	NM_145941	ENSMUSG00000045983	Eif4g1	E030015G23Rik|eIF-4-gamma 1|eIF-4G 1|eIF-4G1|eIF4GI	eukaryotic translation initiation factor 4, gamma 1	protein-coding
mm_151139.1	chr19	53038842	53038849	+	1	NA	promoter-TSS (NM_133216)	promoter-TSS (NM_133216)	-191	NM_133216	170750	Mm.99776	NM_133216	ENSMUSG00000025027	Xpnpep1	D230045I08Rik|sAMP	X-prolyl aminopeptidase (aminopeptidase P) 1, soluble	protein-coding
mm_84425.1	chr9	65827545	65827576	-	1	NA	promoter-TSS (NM_172536)	promoter-TSS (NM_172536)	4	NM_172536	214812	Mm.139231	NM_172536	ENSMUSG00000040524	Zfp609	9830165N24|BC016271|Znf609|mKIAA0295	zinc finger protein 609	protein-coding
mm_131144.1	chr16	6460423	6460446	+	1	NA	intron (NM_021477, intron 2 of 16)	intron (NM_021477, intron 2 of 16)	484847	NR_045799	68238	Mm.434605	NR_045799	ENSMUSG00000101481	1700123O21Rik	-	RIKEN cDNA 1700123O21 gene	ncRNA
mm_83926.1	chr9	56635099	56635135	-	1	NA	5' UTR (NM_001311076, exon 1 of 2)	5' UTR (NM_001311076, exon 1 of 2)	531	NM_001311076	235402	Mm.246605	NM_181074	ENSMUSG00000049556	Lingo1	4930471K13Rik|AV148400|LERN1|LINGO-1|Lrrn6a|UNQ201	leucine rich repeat and Ig domain containing 1	protein-coding
mm_51960.1	chr6	91757919	91757925	+	1	NA	3' UTR (NM_009320, exon 15 of 15)	3' UTR (NM_009320, exon 15 of 15)	49471	NM_001159507	243547	Mm.333264	NM_001033353	ENSMUSG00000030098	Grip2	-	glutamate receptor interacting protein 2	protein-coding
mm_118011.1	chr13	100724881	100724883	-	1	NA	intron (NM_009874, intron 2 of 11)	MERVK26-int|LTR|ERVK	6060	NM_009874	12572	Mm.259718	NM_009874	ENSMUSG00000069089	Cdk7	AI323415|AI528512|C230069N13|Cdkn7|Crk4	cyclin-dependent kinase 7	protein-coding
mm_80143.1	chr9	70779539	70779560	+	1	NA	3' UTR (NM_007399, exon 16 of 16)	3' UTR (NM_007399, exon 16 of 16)	100567	NM_007399	11487	Mm.3037	NM_007399	ENSMUSG00000054693	Adam10	1700031C13Rik|MADM|kuz|kuzbanian	a disintegrin and metallopeptidase domain 10	protein-coding
mm_65539.1	chr7	26188043	26188045	-	1	NA	intron (NM_010000, intron 4 of 8)	A-rich|Low_complexity|Low_complexity	14635	NM_010000	13094	Mm.14413	NM_010000	ENSMUSG00000040660	Cyp2b9	Cyp2b	cytochrome P450, family 2, subfamily b, polypeptide 9	protein-coding
mm_161464.1	chr15	77756941	77756941	-	1	NA	Intergenic	Intergenic	-1712	NM_001081970	239552	Mm.125650	NM_001081970	ENSMUSG00000056656	Apol8	9830006J20Rik|APOL-II|Apol2	apolipoprotein L 8	protein-coding
mm_124650.1	chr15	5179749	5179765	+	1	NA	3' UTR (NM_001013367, exon 9 of 9)	3' UTR (NM_001013367, exon 9 of 9)	-5803	NM_026213	67515	Mm.254979	NM_026213	ENSMUSG00000022151	Ttc33	2410099M07Rik|2900001O04Rik|AI507072|AW538342|Osrf	tetratricopeptide repeat domain 33	protein-coding
mm_144193.1	chr18	7869876	7869898	+	1	NA	intron (NM_153085, intron 1 of 13)	CpG	690	NM_153085	225131	Mm.204524	NM_153085	ENSMUSG00000024283	Wac	1110067P07Rik|A230035H12Rik|AI256735|AI256776|Wwp4	WW domain containing adaptor with coiled-coil	protein-coding
mm_4146.1	chr1	170986020	170986023	+	1	NA	Intergenic	Intergenic	-9950	NM_010187	14130	Mm.425062	NM_010187	ENSMUSG00000026656	Fcgr2b	AI528646|CD32|F630109E10Rik|Fc[g]RII|FcgRII|Fcgr2|Fcgr2a|Fcr-2|Fcr-3|Ly-17|Ly-m20|LyM-1|Lym-1|fcRII	Fc receptor, IgG, low affinity IIb	protein-coding
mm_17436.1	chr2	27570948	27570958	-	1	NA	Intergenic	Intergenic	55806	NM_080848	140858	Mm.28265	NM_080848	ENSMUSG00000026917	Wdr5	2410008O07Rik|AA408785|AA960360|Big|Big-3	WD repeat domain 5	protein-coding
mm_147111.1	chr18	35708416	35708422	-	1	NA	Intergenic	Intergenic	-5275	NM_029669	76594	Mm.108596	NM_029669	ENSMUSG00000024350	Dnajc18	2700075B01Rik|AU041129	DnaJ heat shock protein family (Hsp40) member C18	protein-coding
mm_122538.1	chr14	47418167	47418191	-	1	NA	5' UTR (NM_144553, exon 1 of 19)	5' UTR (NM_144553, exon 1 of 19)	228	NM_144553	218977	Mm.240543	NM_144553	ENSMUSG00000037544	Dlgap5	C77459|C86398|Dap-5|Dlg7|Hurp|mKIAA0008	discs, large (Drosophila) homolog-associated protein 5	protein-coding
mm_74543.1	chr8	9977651	9977690	-	1	NA	promoter-TSS (NM_026868)	promoter-TSS (NM_026868)	-47	NM_001081119	68904	Mm.142570	NM_026868	ENSMUSG00000040396	Abhd13	1110065L07Rik|AI463703|AI788994	abhydrolase domain containing 13	protein-coding
mm_19738.1	chr2	104712123	104712180	-	1	NA	promoter-TSS (NM_177190)	promoter-TSS (NM_177190)	11	NM_177190	320554	Mm.249065	NM_177190	ENSMUSG00000027175	Tcp11l1	C130096D04Rik	t-complex 11 like 1	protein-coding
mm_23406.1	chr3	58414779	58414794	+	1	NA	promoter-TSS (NM_001347233)	promoter-TSS (NM_001347233)	66	NM_001081229	72033	Mm.218409	NM_001081229	ENSMUSG00000027806	Tsc22d2	1810043J12Rik|5530402M19Rik	TSC22 domain family, member 2	protein-coding
mm_120149.1	chr14	60489845	60489846	+	1	NA	Intergenic	Intergenic	111559	NM_001164705	72125	Mm.275499	NM_028113	ENSMUSG00000021986	Amer2	2600011E07Rik|Fam123a	APC membrane recruitment 2	protein-coding
mm_29635.1	chr3	121814305	121814327	-	1	NA	intron (NM_008991, intron 1 of 22)	intron (NM_008991, intron 1 of 22)	899	NM_008991	19299	Mm.399042	NM_008991	ENSMUSG00000028127	Abcd3	AI313901|AU018866|AW146054|PMP68|PMP70|Pxmp1	ATP-binding cassette, sub-family D (ALD), member 3	protein-coding
mm_158882.1	chr1	8470465	8470465	-	1	NA	intron (NM_027671, intron 15 of 20)	RMER17A2|LTR|ERVK	829412	NM_001290390	71096	Mm.336395	NM_027671	ENSMUSG00000025909	Sntg1	4933426D16Rik|G1SYN|SYN4	syntrophin, gamma 1	protein-coding
mm_161770.1	chr17	36981208	36981208	-	1	NA	promoter-TSS (NM_029747)	promoter-TSS (NM_029747)	29	NM_029747	76797	Mm.159787	NM_029747	ENSMUSG00000064308	2410137M14Rik	-	RIKEN cDNA 2410137M14 gene	protein-coding
mm_89935.1	chr10	111253596	111253609	+	1	NA	intron (NM_175489, intron 4 of 23)	B3|SINE|B2	-45077	NM_027914	71769	Mm.45256	NM_027914	ENSMUSG00000035759	Bbs10	1300007O09Rik|AI452285	Bardet-Biedl syndrome 10 (human)	protein-coding
mm_8209.1	chr1	138136454	138136466	-	1	NA	intron (NM_001111316, intron 1 of 31)	intron (NM_001111316, intron 1 of 31)	38666	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_98982.1	chr11	98741806	98741816	+	1	NA	promoter-TSS (NM_001313983)	promoter-TSS (NM_001313983)	26	NM_001313983	21833	Mm.265917	NM_178060	ENSMUSG00000058756	Thra	6430529J03Rik|AW259572|Erba|Nr1a1|Rvr|T3R[a]|T3Ralpha|Thra1|Thra2|c-erbA-1|c-erbA-alpha|c-erbAalpha	thyroid hormone receptor alpha	protein-coding
mm_165610.1	chr3	52972739	52972743	+	1	NA	Intergenic	Intergenic	44482	NM_026225	67542	Mm.249548	NM_026225	ENSMUSG00000027742	Cog6	4933405E16Rik|AU018618|mKIAA1134	component of oligomeric golgi complex 6	protein-coding
mm_139880.1	chr17	70751405	70751419	+	1	NA	intron (NM_001347411, intron 9 of 14)	intron (NM_001347411, intron 9 of 14)	95365	NM_001164077	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_101361.1	chr11	23741119	23741130	-	1	NA	TTS (NM_009044)	TTS (NM_009044)	29846	NM_009044	19696	Mm.4869	NM_009044	ENSMUSG00000020275	Rel	c-Rel	reticuloendotheliosis oncogene	protein-coding
mm_141161.1	chr17	26508865	26508882	-	1	NA	promoter-TSS (NM_013642)	promoter-TSS (NM_013642)	-401	NM_013642	19252	Mm.239041	NM_013642	ENSMUSG00000024190	Dusp1	3CH134|MKP1|Ptpn16|U19515|erp|mkp-1	dual specificity phosphatase 1	protein-coding
mm_59674.1	chr7	28381393	28381403	+	1	NA	Intergenic	Intergenic	-2170	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_148067.1	chr18	72330604	72330626	-	1	NA	intron (NM_007831, intron 1 of 28)	intron (NM_007831, intron 1 of 28)	20454	NM_007831	13176	Mm.167882	NM_007831	ENSMUSG00000060534	Dcc	C030036D22Rik|Igdcc1	deleted in colorectal carcinoma	protein-coding
mm_146268.1	chr18	77875337	77875373	+	1	NA	intron (NM_013831, intron 11 of 14)	ORR1F|LTR|ERVL-MaLR	-63112	NM_001195633	100502841	Mm.297782	NM_001195633	ENSMUSG00000039840	Epg5	4732475F16|5430411K18Rik|AI661957|AW456499|mKIAA1632	ectopic P-granules autophagy protein 5 homolog (C. elegans)	protein-coding
mm_104185.1	chr11	87797426	87797447	-	1	NA	exon (NM_010824, exon 8 of 14)	exon (NM_010824, exon 8 of 14)	3652	NM_010824	17523	Mm.4668	NM_010824	ENSMUSG00000009350	Mpo	mKIAA4033	myeloperoxidase	protein-coding
mm_150891.1	chr19	45364190	45364204	+	1	NA	intron (NM_009771, intron 1 of 13)	intron (NM_009771, intron 1 of 13)	463	NM_001037758	12234	Mm.119717	NM_009771	ENSMUSG00000025217	Btrc	Beta-Trcp1|E3RS-IkappaB|E3RSIkappaB|FWD1|Fbw1a|HOS|Slimb|b-TrCP|beta-TrCP	beta-transducin repeat containing protein	protein-coding
mm_129754.1	chr15	82354281	82354291	-	1	NA	promoter-TSS (NM_025987)	promoter-TSS (NM_025987)	5	NM_025987	67130	Mm.27570	NM_025987	ENSMUSG00000022450	Ndufa6	14kDa|2700038D15Rik|B230217P19Rik	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 6 (B14)	protein-coding
mm_141446.1	chr17	29888571	29888593	-	1	NA	promoter-TSS (NM_001081160)	promoter-TSS (NM_001081160)	-700	NM_001081160	74762	Mm.40901	NM_001081160	ENSMUSG00000043557	Mdga1	1200011I03Rik|GPIM|Mamdc3	MAM domain containing glycosylphosphatidylinositol anchor 1	protein-coding
mm_100658.1	chr11	3198518	3198561	-	1	NA	Intergenic	RMER6B|LTR|ERVK	-3814	NM_001166548	74203	Mm.255649	NM_023743	ENSMUSG00000020454	Eif4enif1	2610509L04Rik|A930019J01Rik|AA410001|AU021239|Clast4|D11Ertd166e	eukaryotic translation initiation factor 4E nuclear import factor 1	protein-coding
mm_63924.1	chr7	139389073	139389161	+	1	NA	promoter-TSS (NM_001127363)	promoter-TSS (NM_001127363)	8	NM_001127363	212111	Mm.28308	NM_183144	ENSMUSG00000025477	Inpp5a	-	inositol polyphosphate-5-phosphatase A	protein-coding
mm_14560.1	chr2	134845530	134845540	+	1	NA	intron (NM_019677, intron 2 of 32)	intron (NM_019677, intron 2 of 32)	59371	NM_001145830	18795	Mm.330607	NM_019677	ENSMUSG00000051177	Plcb1	3110043I21Rik|AI132408|Plcb|mKIAA0581	phospholipase C, beta 1	protein-coding
mm_121631.1	chr14	8367247	8367257	-	1	NA	intron (NM_146050, intron 1 of 9)	intron (NM_146050, intron 1 of 9)	11511	NM_146050	18300	Mm.25351	NM_146050	ENSMUSG00000021749	Oit1	2310076N21Rik|AV067083|EF-7|Fam3d	oncoprotein induced transcript 1	protein-coding
mm_44042.1	chr5	147546595	147546600	+	1	NA	3' UTR (NM_028291, exon 19 of 19)	3' UTR (NM_028291, exon 19 of 19)	116017	NM_028291	72587	Mm.320469	NM_028291	ENSMUSG00000029647	Pan3	2700050F09Rik|A430027N15Rik|AU014670	PAN3 poly(A) specific ribonuclease subunit	protein-coding
mm_12837.1	chr2	80837084	80837094	+	1	NA	Intergenic	Intergenic	197825	NM_001190179	69482	Mm.29200	NM_027091	ENSMUSG00000026999	Nup35	2310006I24Rik|35kDa|5330402E05Rik|MP44|NO44	nucleoporin 35	protein-coding
mm_161674.1	chr17	14978711	14978711	-	1	NA	promoter-TSS (NM_001123370)	promoter-TSS (NM_001123370)	101	NM_001123368	100041586	Mm.440445	NM_001123368	ENSMUSG00000079710	Gm3417	-	predicted gene 3417	protein-coding
mm_112762.1	chr13	19350301	19350328	+	1	NA	Intergenic	Intergenic	45499	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_9000.1	chr1	165775300	165775304	-	1	NA	TTS (NM_011804)	TTS (NM_011804)	11522	NM_011804	433375	Mm.294885	NM_011804	ENSMUSG00000040713	Creg1	AA755314|Creg	cellular repressor of E1A-stimulated genes 1	protein-coding
mm_42349.1	chr5	114911383	114911406	+	1	NA	3' UTR (NM_011854, exon 6 of 6)	3' UTR (NM_011854, exon 6 of 6)	-11846	NM_145209	231655	Mm.95479	NM_145209	ENSMUSG00000041827	Oasl1	7530414C13Rik|oasl9	2'-5' oligoadenylate synthetase-like 1	protein-coding
mm_150733.1	chr19	43731779	43731799	+	1	NA	3' UTR (NM_053103, exon 13 of 13)	3' UTR (NM_053103, exon 13 of 13)	21211	NM_144874	226139	Mm.248237	NM_144874	ENSMUSG00000040018	Cox15	2900026G05Rik	cytochrome c oxidase assembly protein 15	protein-coding
mm_125240.1	chr15	34306667	34306757	+	1	NA	promoter-TSS (NM_016762)	promoter-TSS (NM_016762)	31	NM_016762	17181	Mm.396856	NM_016762	ENSMUSG00000022324	Matn2	Crtm2|matrilin-2	matrilin 2	protein-coding
mm_42428.1	chr5	115341226	115341270	+	1	NA	promoter-TSS (NM_026933)	promoter-TSS (NM_026933)	1	NM_026933	69076	Mm.27951	NM_026933	ENSMUSG00000029535	Triap1	1810015M01Rik|AU020874|AU043831|P53csv|Wf-1	TP53 regulated inhibitor of apoptosis 1	protein-coding
mm_114023.1	chr13	52632958	52632986	+	1	NA	exon (NM_011518, exon 9 of 14)	exon (NM_011518, exon 9 of 14)	36090	NM_011518	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_171764.1	chr5	10763898	10763914	+	1	NA	Intergenic	RLTR9D|LTR|ERVK	-101123	NR_003596	623849	Mm.335888	NR_003596	ENSMUSG00000091422	Gm6455	EG623849	predicted gene 6455	pseudo
mm_169707.1	chr15	75841906	75841907	-	1	NA	promoter-TSS (NM_172121)	promoter-TSS (NM_172121)	2	NM_172121	223642	Mm.209800	NM_172121	ENSMUSG00000075600	Zc3h3	BC049953|Kiaa0150|Smicl|Zc3hdc3	zinc finger CCCH type containing 3	protein-coding
mm_112648.1	chr13	16017620	16017633	+	1	NA	exon (NM_008380, exon 4 of 5)	exon (NM_008380, exon 4 of 5)	5775	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_86342.1	chr9	123260815	123260822	-	1	NA	promoter-TSS (NM_001002267)	promoter-TSS (NM_001002267)	-29	NM_001002267	72309	Mm.8569	NM_001002267	ENSMUSG00000054871	Tmem158	2310037P21Rik|Ris1	transmembrane protein 158	protein-coding
mm_43702.1	chr5	139252723	139252787	+	1	NA	promoter-TSS (NM_001163316)	promoter-TSS (NM_001163316)	431	NM_026269	67604	Mm.270137	NM_026269	ENSMUSG00000025858	Get4	1110007L15Rik|AW412535|Cee	golgi to ER traffic protein 4	protein-coding
mm_76458.1	chr8	85299757	85299791	-	1	NA	promoter-TSS (NM_022997)	promoter-TSS (NM_022997)	142	NR_028268	56452	Mm.29709	NM_019716	ENSMUSG00000031697	Orc6	6720420I10Rik|Orc6l	origin recognition complex, subunit 6	protein-coding
mm_4407.1	chr1	172481766	172481792	+	1	NA	promoter-TSS (NM_001145800)	promoter-TSS (NM_001145800)	-434	NM_001145800	93842	Mm.214530	NM_033608	ENSMUSG00000037995	Igsf9	644ETD8|Dasm1|Kiaa1355-hp|NRT1|Ncaml|mKIAA1355	immunoglobulin superfamily, member 9	protein-coding
mm_2413.1	chr1	93859847	93859866	+	1	NA	Intergenic	(TCTCTG)n|Simple_repeat|Simple_repeat	-1488	NM_199366	381334	Mm.482878	NM_199366	ENSMUSG00000094651	Gal3st2	GP3ST|Gm988	galactose-3-O-sulfotransferase 2	protein-coding
mm_35166.1	chr4	14621793	14621797	-	1	NA	promoter-TSS (NM_145947)	promoter-TSS (NM_145947)	-17	NM_145947	208890	Mm.483839	NM_145947	ENSMUSG00000040569	Slc26a7	-	solute carrier family 26, member 7	protein-coding
mm_78879.1	chr9	44498229	44498237	+	1	NA	promoter-TSS (NM_030256)	promoter-TSS (NM_030256)	-903	NM_030256	80288	Mm.370270	NM_030256	ENSMUSG00000063382	Bcl9l	B9L|BC003321|BCL9-2|DLNB11	B cell CLL/lymphoma 9-like	protein-coding
mm_115996.1	chr13	24414799	24414814	-	1	NA	promoter-TSS (NM_001284520)	promoter-TSS (NM_001284520)	-316	NM_007717	12763	Mm.8396	NM_007717	ENSMUSG00000016756	Cmah	-	cytidine monophospho-N-acetylneuraminic acid hydroxylase	protein-coding
mm_154117.1	chr19	57182294	57182315	-	1	NA	intron (NM_001290813, intron 1 of 20)	intron (NM_001290813, intron 1 of 20)	15327	NM_001103177	226251	Mm.217161	NM_178688	ENSMUSG00000025085	Ablim1	2210411C18Rik|2610209L21Rik|4833406P10Rik|9330196J19Rik|AV079770|AW060987|AW215784|Limab1|mKIAA0059	actin-binding LIM protein 1	protein-coding
mm_27662.1	chr3	65302652	65302662	-	1	NA	promoter-TSS (NR_126080)	promoter-TSS (NR_126080)	28	NR_126080	102637797	Mm.446731	NR_126080	ENSMUSG00000104093	A330015K06Rik	-	RIKEN cDNA A330015K06 gene	ncRNA
mm_13453.1	chr2	105425994	105425999	+	1	NA	Intergenic	Intergenic	-26677	NM_009037	19672	Mm.4876	NM_009037	ENSMUSG00000005973	Rcn1	Rcn	reticulocalbin 1	protein-coding
mm_147803.1	chr18	61658267	61658280	-	1	NA	intron (NR_045402, intron 1 of 4)	intron (NR_045402, intron 1 of 4)	7265	NR_045402	328968	Mm.392305	NR_045402		Carmn	Carmen|E330013P06|Gm16908|Mir143hg	cardiac mesoderm enhancer-associated non-coding RNA	ncRNA
mm_76445.1	chr8	85060439	85060468	-	1	NA	promoter-TSS (NR_110582)	promoter-TSS (NR_110582)	7	NR_110582	320466	Mm.401371	NR_110581	ENSMUSG00000087026	A230103J11Rik	-	RIKEN cDNA A230103J11 gene	ncRNA
mm_145494.1	chr18	60390193	60390213	+	1	NA	exon (NM_001146275, exon 3 of 3)	exon (NM_001146275, exon 3 of 3)	14174	NM_001146275	60440	Mm.261140	NM_021792	ENSMUSG00000054072	Iigp1	2900074L10Rik|AI046432|AW111922|Ifgga1|Iigp|Irga6	interferon inducible GTPase 1	protein-coding
mm_53367.1	chr6	129403602	129403616	+	1	NA	exon (NM_019985, exon 5 of 6)	exon (NM_019985, exon 5 of 6)	-5253	NM_001205363	232414	Mm.391518	NM_172732	ENSMUSG00000046080	Clec9a	9830005G06Rik|DNGR-1	C-type lectin domain family 9, member a	protein-coding
mm_121387.1	chr14	118953514	118953536	+	1	NA	intron (NM_008929, intron 2 of 11)	B3A|SINE|B2	15593	NM_008929	100037258	Mm.12616	NM_008929	ENSMUSG00000022136	Dnajc3	AA408985|AU067833|Dnajc3a|Dnajc3b|Prkri|mp58|p58|p58IPK	DnaJ heat shock protein family (Hsp40) member C3	protein-coding
mm_140684.1	chr17	13008303	13008354	-	1	NA	exon (NM_013671, exon 2 of 5)	exon (NM_013671, exon 2 of 5)	489	NM_013671	20656	Mm.290876	NM_013671	ENSMUSG00000006818	Sod2	MnSOD|Sod-2	superoxide dismutase 2, mitochondrial	protein-coding
mm_41542.1	chr5	92877688	92877691	+	1	NA	intron (NM_001077595, intron 1 of 9)	B1_Mur1|SINE|Alu	-20304	NM_001077596	27428	Mm.46014	NM_015756	ENSMUSG00000029381	Shroom3	AL022960|D5Ertd287e|Shrm|Shrm3	shroom family member 3	protein-coding
mm_162071.1	chrX	16911556	16911556	-	1	NA	5' UTR (NM_010883, exon 1 of 3)	5' UTR (NM_010883, exon 1 of 3)	218	NM_010883	17986	Mm.5014	NM_010883	ENSMUSG00000040138	Ndp	ND|Ndph	Norrie disease (pseudoglioma) (human)	protein-coding
mm_97379.1	chr11	77713671	77713674	+	1	NA	3' UTR (NM_001024205, exon 4 of 4)	3' UTR (NM_001024205, exon 4 of 4)	11621	NM_001313933	12957	Mm.22830	NM_009965	ENSMUSG00000000724	Cryba1	BA3/A1|Cryb	crystallin, beta A1	protein-coding
mm_64522.1	chr7	143847351	143847379	+	1	NA	exon (NM_007856, exon 9 of 9)	exon (NM_007856, exon 9 of 9)	24198	NM_007856	13360	Mm.249342	NM_007856	ENSMUSG00000058454	Dhcr7	AA409147	7-dehydrocholesterol reductase	protein-coding
mm_60132.1	chr7	37320981	37321013	+	1	NA	Intergenic	Intergenic	448755	NM_172385	243937	Mm.322505	NM_172385	ENSMUSG00000043456	Zfp536	9630010P11Rik|Znf536|mKIAA0390	zinc finger protein 536	protein-coding
mm_123635.1	chr14	68533784	68533794	-	1	NA	promoter-TSS (NM_007402)	promoter-TSS (NM_007402)	-100	NM_007402	11500	Mm.261495	NM_007402	ENSMUSG00000022056	Adam7	ADAM 7|EAP1|EAPI	a disintegrin and metallopeptidase domain 7	protein-coding
mm_52249.1	chr6	106771696	106771703	+	1	NA	intron (NM_001242360, intron 2 of 5)	intron (NM_001242360, intron 2 of 5)	2561	NM_001242358	70047	Mm.196332	NM_027296	ENSMUSG00000013736	Trnt1	2410043H24Rik|2610044E04Rik|9830143O18Rik|AA408384|C76540|CGI-47|mt-Trat	tRNA nucleotidyl transferase, CCA-adding, 1	protein-coding
mm_111255.1	chr12	84959559	84959561	-	1	NA	intron (NM_178065, intron 1 of 19)	B3|SINE|B2	11326	NM_178065	68497	Mm.24446	NM_178065	ENSMUSG00000042350	Arel1	1110018G07Rik|AI649076|AW610792|Kiaa0317|mKIAA0317	apoptosis resistant E3 ubiquitin protein ligase 1	protein-coding
mm_66990.1	chr7	64058679	64058720	-	1	NA	Intergenic	Intergenic	-95136	NM_001039104	17364	Mm.38875	NM_018752	ENSMUSG00000030523	Trpm1	4732499L03Rik|AI606771|Ltrpc1|Mlsn1	transient receptor potential cation channel, subfamily M, member 1	protein-coding
mm_64225.1	chr7	141625441	141625451	+	1	NA	intron (NM_007459, intron 15 of 21)	intron (NM_007459, intron 15 of 21)	4745	NR_106030	102466798		NR_106030	ENSMUSG00000098759	Mir7063	Gm27654|mmu-mir-7063	microRNA 7063	ncRNA
mm_139922.1	chr17	70988482	70988487	+	1	NA	intron (NM_023402, intron 1 of 3)	MIR|SINE|MIR	2032	NM_023402	67938	Mm.261329	NM_023402	ENSMUSG00000034868	Myl12b	1500001M02Rik|C77744|Mylc2b|RLC-B	myosin, light chain 12B, regulatory	protein-coding
mm_89507.1	chr10	94114715	94114728	+	1	NA	intron (NM_053072, intron 8 of 20)	intron (NM_053072, intron 8 of 20)	-33210	NM_011629	22025	Mm.107483	NM_011629	ENSMUSG00000005897	Nr2c1	4831444H07Rik|80.3|Eenr|TR2|Tr2-11	nuclear receptor subfamily 2, group C, member 1	protein-coding
mm_119666.1	chr14	52328108	52328112	+	1	NA	exon (NM_015772, exon 1 of 2)	exon (NM_015772, exon 1 of 2)	560	NM_015772	50524	Mm.39487	NM_015772	ENSMUSG00000049532	Sall2	AI225809|AW559097|Msal-2|Sal-2|mKIAA0360|p150(Sal2)	sal-like 2 (Drosophila)	protein-coding
mm_103723.1	chr11	79530503	79530513	-	1	NA	5' UTR (NM_010161, exon 1 of 2)	5' UTR (NM_010161, exon 1 of 2)	101	NM_146023	101488212	Mm.439665	NM_146023	ENSMUSG00000070354	Gm21975	Evi2a-evi2b	predicted gene 21975	protein-coding
mm_124939.1	chr15	12248801	12248804	+	1	NA	intron (NM_172958, intron 7 of 15)	intron (NM_172958, intron 7 of 15)	43708	NM_172958	268783	Mm.54460	NM_172958	ENSMUSG00000039458	Mtmr12	3Pap|4932703C11|C730015A02Rik|Pip3ap|mKIAA1682	myotubularin related protein 12	protein-coding
mm_10975.1	chr2	25737006	25737008	+	1	NA	promoter-TSS (NM_001099301)	promoter-TSS (NM_001099301)	-2	NM_001099301	383678	Mm.464561	NM_001099301	ENSMUSG00000079539	Obp2b	Lcn14|OTTMUSG00000012631	odorant binding protein 2B	protein-coding
mm_145574.1	chr18	60925613	60925639	+	1	NA	promoter-TSS (NM_177407)	promoter-TSS (NM_177407)	-6	NM_177407	12322	Mm.131530	NM_009792	ENSMUSG00000024617	Camk2a	CaMKII|R74975|mKIAA0968	calcium/calmodulin-dependent protein kinase II alpha	protein-coding
mm_143568.1	chr17	74295018	74295028	-	1	NA	promoter-TSS (NM_133771)	promoter-TSS (NM_133771)	-160	NM_133771	76890	Mm.311874	NM_133771	ENSMUSG00000058704	Memo1	0610016J10Rik|D930048L02Rik	mediator of cell motility 1	protein-coding
mm_140822.1	chr17	23599539	23599547	-	1	NA	promoter-TSS (NM_011747)	promoter-TSS (NM_011747)	-56	NM_011747	22654	Mm.40326	NM_011747	ENSMUSG00000062012	Zfp13	4933429B21|AI835008|Krox-8|Rhit|Zfp-13	zinc finger protein 13	protein-coding
mm_93754.1	chr10	120173673	120173700	-	1	NA	intron (NM_028679, intron 5 of 11)	intron (NM_028679, intron 5 of 11)	27851	NM_028679	73914	Mm.146194	NM_028679	ENSMUSG00000020227	Irak3	4833428C18Rik|AI563835|IRAK-M	interleukin-1 receptor-associated kinase 3	protein-coding
mm_18273.1	chr2	52372510	52372532	-	1	NA	Intergenic	Intergenic	-33723	NM_010889	17996	Mm.389247	NM_010889	ENSMUSG00000026950	Neb	AI595938	nebulin	protein-coding
mm_167216.1	chr8	8914782	8914783	+	1	NA	Intergenic	Intergenic	217506	NR_045854	71249	Mm.158635	NR_045854	ENSMUSG00000108848	4933430N04Rik	-	RIKEN cDNA 4933430N04 gene	ncRNA
mm_30777.1	chr4	19122654	19122681	+	1	NA	Intergenic	Lx2A1|LINE|L1	-158183	NM_013927	30952	Mm.445778	NM_013927	ENSMUSG00000056494	Cngb3	CCNC2|CNG6|Cngbeta2	cyclic nucleotide gated channel beta 3	protein-coding
mm_57250.1	chr6	123283423	123283446	-	1	NA	3' UTR (NM_019948, exon 6 of 6)	3' UTR (NM_019948, exon 6 of 6)	6437	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_29783.1	chr3	127499050	127499071	-	1	NA	promoter-TSS (NM_001327938)	promoter-TSS (NM_001327938)	55	NM_001327938	109676	Mm.220242	NM_178655	ENSMUSG00000032826	Ank2	100043364|AI835472|AW491075|Ank-2|Gm4392	ankyrin 2, brain	protein-coding
mm_25617.1	chr3	118433934	118433942	+	1	NA	promoter-TSS (NR_029551)	promoter-TSS (NR_029551)	81	NR_029551	387155		NR_029551	ENSMUSG00000065569	Mir137	Mirn137|mir-137|mmu-mir-137	microRNA 137	ncRNA
mm_71865.1	chr8	69096235	69096248	+	1	NA	exon (NM_007509, exon 2 of 14)	exon (NM_007509, exon 2 of 14)	-7019	NM_153054	110877	Mm.19301	NM_153054	ENSMUSG00000036330	Slc18a1	4832416I10Rik|Vat1|Vmat1	solute carrier family 18 (vesicular monoamine), member 1	protein-coding
mm_159488.1	chr4	42273298	42273298	+	1	NA	intron (NR_033123, intron 2 of 4).2	intron (NR_033123, intron 2 of 4).2	17567	NM_011335	100042493	Mm.407493	NM_011335	ENSMUSG00000095675	Ccl21b	6CKBAC1|6Ckine|AI159701|CKb9|SLC|Scya21|Scya21a|TCA4	chemokine (C-C motif) ligand 21B (leucine)	protein-coding
mm_135849.1	chr16	59495771	59495780	-	1	NA	intron (NM_174848, intron 16 of 18)	(A)n|Simple_repeat|Simple_repeat	24000	NM_025910	67014	Mm.289150	NM_025910	ENSMUSG00000022724	Mina	1810047J07Rik|2410057H13Rik|3830408E23Rik|AI449204	myc induced nuclear antigen	protein-coding
mm_128198.1	chr15	35155759	35155793	-	1	NA	promoter-TSS (NM_019635)	promoter-TSS (NM_019635)	30	NM_019635	56274	Mm.262330	NM_019635	ENSMUSG00000022329	Stk3	0610042I06Rik|MST|Mst2|Mst3|Ste20|mess1	serine/threonine kinase 3	protein-coding
mm_172675.1	chr8	48070673	48070673	-	1	NA	Intergenic	Intergenic	-28419	NM_001161516	320685	Mm.121549	NM_178788	ENSMUSG00000031562	Dctd	6030466N05Rik	dCMP deaminase	protein-coding
mm_87637.1	chr10	58351988	58351990	+	1	NA	intron (NM_026148, intron 1 of 9)	intron (NM_026148, intron 1 of 9)	-19465	NM_201242	110829	Mm.57734	NM_026148	ENSMUSG00000019920	Lims1	2310016J22Rik|4921524A02Rik|AI507642|AU021743|AW551584|C430041B13Rik|Lims1l|PINCH|PINCH1	LIM and senescent cell antigen-like domains 1	protein-coding
mm_167789.1	chr9	123104520	123104535	-	1	NA	intron (NM_026917, intron 1 of 6)	intron (NM_026917, intron 1 of 6)	8678	NM_026917	69035	Mm.28300	NM_026917	ENSMUSG00000025786	Zdhhc3	1110020O22Rik|1810006O10Rik|2210017C02Rik|DHHC-3|GODZ|Gramp1|Zfp373	zinc finger, DHHC domain containing 3	protein-coding
mm_53596.1	chr6	138140522	138140581	+	1	NA	promoter-TSS (NM_019946)	promoter-TSS (NM_019946)	14	NM_019946	56615	Mm.14796	NM_019946	ENSMUSG00000008540	Mgst1	1500002K10Rik|Gst	microsomal glutathione S-transferase 1	protein-coding
mm_29281.1	chr3	107667699	107667706	-	1	NA	exon (NM_145542, exon 14 of 17)	exon (NM_145542, exon 14 of 17)	28846	NM_145542	229709	Mm.220328	NM_145542	ENSMUSG00000027893	Ahcyl1	1110034F20Rik|AA409031|AA414901|Ahcy-rs3|DCAL|Irbit	S-adenosylhomocysteine hydrolase-like 1	protein-coding
mm_159478.1	chr4	34050190	34050190	-	1	NA	promoter-TSS (NM_026293)	promoter-TSS (NM_026293)	-123	NM_026293	67652	Mm.55848	NM_026293	ENSMUSG00000028264	Spaca1	1700124L11Rik|4930540L03Rik	sperm acrosome associated 1	protein-coding
mm_62923.1	chr7	118597296	118597342	+	1	NA	promoter-TSS (NM_001105252)	promoter-TSS (NM_001105252)	22	NM_001105252	74424	Mm.11068	NM_028930	ENSMUSG00000030650	Tmc5	4932443L08Rik|AU016085	transmembrane channel-like gene family 5	protein-coding
mm_40644.1	chr5	64970070	64970089	+	1	NA	promoter-TSS (NR_030577)	promoter-TSS (NR_030577)	4	NM_026667	68303	Mm.258545	NM_026667	ENSMUSG00000029185	Fam114a1	1190001N04Rik|9130005N14Rik|Noxp20	family with sequence similarity 114, member A1	protein-coding
mm_120747.1	chr14	73238011	73238021	+	1	NA	5' UTR (NM_175116, exon 1 of 1)	5' UTR (NM_175116, exon 1 of 1)	125	NM_175116	67168	Mm.390681	NM_175116	ENSMUSG00000033446	Lpar6	2610302I02Rik|P2ry5|P2y5	lysophosphatidic acid receptor 6	protein-coding
mm_1540.1	chr1	72852085	72852095	+	1	NA	exon (NM_008342, exon 4 of 4)	exon (NM_008342, exon 4 of 4)	22775	NM_010518	16011	Mm.405761	NM_010518	ENSMUSG00000026185	Igfbp5	AI256729|AW208790|IGFBP-5|IGFBP-5P	insulin-like growth factor binding protein 5	protein-coding
mm_97376.1	chr11	77710449	77710451	+	1	NA	3' UTR (NM_001024205, exon 4 of 4)	3' UTR (NM_001024205, exon 4 of 4)	14843	NM_001313933	12957	Mm.22830	NM_009965	ENSMUSG00000000724	Cryba1	BA3/A1|Cryb	crystallin, beta A1	protein-coding
mm_78427.1	chr9	31280926	31280934	+	1	NA	Intergenic	CpG	9529	NM_001101597	638580	Mm.373655	NM_001101597		Gm7244	EG638580	predicted gene 7244	protein-coding
mm_53839.1	chr6	148354778	148354802	+	1	NA	non-coding (NR_003634, exon 1 of 1)	non-coding (NR_003634, exon 1 of 1)	134	NR_003634	66184	Mm.391542	NM_025405	ENSMUSG00000063171	Rps4l	1110033J19Rik|AA407494|Rps4y2	ribosomal protein S4-like	pseudo
mm_165057.1	chr19	41900807	41900809	-	1	NA	Intergenic	Intergenic	-4655	NM_199447	107094	Mm.276044	NM_199447	ENSMUSG00000035049	Rrp12	AA408556|AA536972|mKIAA0690	ribosomal RNA processing 12 homolog (S. cerevisiae)	protein-coding
mm_122827.1	chr14	54686606	54686647	-	1	NA	exon (NM_023190, exon 1 of 19)	exon (NM_023190, exon 1 of 19)	305	NM_001085473	56215	Mm.297078	NM_019567	ENSMUSG00000022185	Acin1	2610036I19Rik|2610510L13Rik|Acinus|Acn|C79325|acinusL|acinusS|mKIAA0670	apoptotic chromatin condensation inducer 1	protein-coding
mm_87094.1	chr10	33083204	33083214	+	1	NA	promoter-TSS (NM_029726)	promoter-TSS (NM_029726)	-274	NM_029726	76757	Mm.338508	NM_029726	ENSMUSG00000019787	Trdn	2310045H21Rik|EG432451|TDN	triadin	protein-coding
mm_142720.1	chr17	48146199	48146209	-	1	NA	5' UTR (NM_177824, exon 1 of 3)	5' UTR (NM_177824, exon 1 of 3)	103	NM_001177897	328829	Mm.466999	NM_177824	ENSMUSG00000073386	9830107B12Rik	Trem5	RIKEN cDNA 9830107B12 gene	protein-coding
mm_58142.1	chr6	141946828	141946836	-	1	NA	5' UTR (NM_013797, exon 1 of 14)	5' UTR (NM_013797, exon 1 of 14)	130	NM_013797	28248	Mm.103665	NM_013797	ENSMUSG00000041698	Slco1a1	A530084B21|OATP-1|Oatp1|Oatp1a1|Slc21a1	solute carrier organic anion transporter family, member 1a1	protein-coding
mm_125425.1	chr15	42638821	42638832	+	1	NA	intron (NM_009640, intron 1 of 8)	intron (NM_009640, intron 1 of 8)	38151	NM_001286062	11600	Mm.309336	NM_009640	ENSMUSG00000022309	Angpt1	1110046O21Rik|Ang-1|Ang1	angiopoietin 1	protein-coding
mm_62572.1	chr7	104250304	104250306	+	1	NA	intron (NM_030684, intron 4 of 7)	T-rich|Low_complexity|Low_complexity	5848	NM_030684	94094	Mm.326945	NM_030684	ENSMUSG00000056144	Trim34a	Trim34|Trim34-1	tripartite motif-containing 34A	protein-coding
mm_12402.1	chr2	70475956	70475969	+	1	NA	intron (NM_022435, intron 1 of 1)	CpG	1039	NM_022435	64406	Mm.423397	NM_022435	ENSMUSG00000075304	Sp5	-	trans-acting transcription factor 5	protein-coding
mm_129188.1	chr15	76350497	76350526	-	1	NA	promoter-TSS (NM_026859)	promoter-TSS (NM_026859)	599	NM_025340	106025	Mm.41463	NM_025340	ENSMUSG00000022552	Sharpin	0610041B22Rik|AW121341|RBCKL1|SIPL1|cpdm	SHANK-associated RH domain interacting protein	protein-coding
mm_96203.1	chr11	62107538	62107542	+	1	NA	intron (NM_001029936, intron 1 of 12)	intron (NM_001029936, intron 1 of 12)	30516	NM_001029936	432572	Mm.438022	NM_001029936	ENSMUSG00000042331	Specc1	2810012G08Rik|B230396K10Rik|Cytsb	sperm antigen with calponin homology and coiled-coil domains 1	protein-coding
mm_4952.1	chr1	191225047	191225062	+	1	NA	Intergenic	Intergenic	-41721	NM_007498	11910	Mm.2706	NM_007498	ENSMUSG00000026628	Atf3	LRG-21	activating transcription factor 3	protein-coding
mm_79502.1	chr9	57175270	57175280	+	1	NA	promoter-TSS (NR_033784)	promoter-TSS (NR_033784)	0	NR_033784	67319	Mm.234187	NR_033784	ENSMUSG00000100282	1700041C23Rik	-	RIKEN cDNA 1700041C23 gene	ncRNA
mm_150638.1	chr19	41691353	41691369	+	1	NA	intron (NM_015748, intron 4 of 36)	intron (NM_015748, intron 4 of 36)	52495	NM_015748	20562	Mm.39155	NM_015748	ENSMUSG00000025020	Slit1	Slil1|mKIAA0813	slit homolog 1 (Drosophila)	protein-coding
mm_136086.1	chr16	84835656	84835669	-	1	NA	promoter-TSS (NM_016755)	promoter-TSS (NM_016755)	-37	NM_001302213	11957	Mm.353	NM_016755	ENSMUSG00000022890	Atp5j	CF6	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit F	protein-coding
mm_162980.1	chr11	20830779	20830801	-	1	NA	intron (NM_173752, intron 1 of 4)	CpG	318	NM_173752	216551	Mm.76694	NM_173752	ENSMUSG00000042363	Lgalsl	1110067D22Rik|A530071M23|Grpa|Hspc159|Lgalsla	lectin, galactoside binding-like	protein-coding
mm_151660.1	chr19	4127267	4127286	-	1	NA	intron (NM_025889, intron 3 of 6)	intron (NM_025889, intron 3 of 6)	1316	NM_025889	66990	Mm.276255	NM_025889		Tmem134	2410001H17Rik|AI463452	transmembrane protein 134	protein-coding
mm_46837.1	chr5	113324313	113324349	-	1	NA	TTS (NR_106088)	TTS (NR_106088)	214	NR_106088	102465709		NR_106088	ENSMUSG00000105778	Mir7229	mmu-mir-7229	microRNA 7229	ncRNA
mm_105757.1	chr11	109473657	109473666	-	1	NA	promoter-TSS (NM_001029842)	promoter-TSS (NM_001029842)	-65	NM_001029842	104681	Mm.265874	NM_134038	ENSMUSG00000041920	Slc16a6	AW743111|ESTM12|MCT 6|MCT 7|MCT6	solute carrier family 16 (monocarboxylic acid transporters), member 6	protein-coding
mm_124906.1	chr15	10981748	10981765	+	1	NA	promoter-TSS (NM_008537)	promoter-TSS (NM_008537)	0	NM_008537	17117	Mm.2787	NM_008537	ENSMUSG00000022244	Amacr	Macr1	alpha-methylacyl-CoA racemase	protein-coding
mm_111895.1	chr12	108639122	108639149	-	1	NA	intron (NM_001163396, intron 2 of 14)	L2|LINE|L2	3382	NM_001163396	14026	Mm.238841	NM_007965	ENSMUSG00000021262	Evl	AI528774	Ena-vasodilator stimulated phosphoprotein	protein-coding
mm_169098.1	chr1	34113969	34113978	+	1	NA	exon (NM_134448, exon 3 of 98)	exon (NM_134448, exon 3 of 98)	-3386	NR_105861	102466987		NR_105861	ENSMUSG00000105982	Mir6896	mmu-mir-6896	microRNA 6896	ncRNA
mm_158248.1	chrX	107403632	107403651	-	1	NA	promoter-TSS (NM_008409)	promoter-TSS (NM_008409)	-281	NM_008409	16431	Mm.193	NM_008409	ENSMUSG00000031239	Itm2a	AW108051|Bricd2a|E25|Itm2	integral membrane protein 2A	protein-coding
mm_150210.1	chr19	32815479	32815499	+	1	NA	exon (NM_008960, exon 7 of 9)	exon (NM_008960, exon 7 of 9)	57912	NM_008960	19211	Mm.245395	NM_008960	ENSMUSG00000013663	Pten	2310035O07Rik|A130070J02Rik|AI463227|B430203M17Rik|MMAC1|TEP1	phosphatase and tensin homolog	protein-coding
mm_123405.1	chr14	63543883	63543890	-	1	NA	promoter-TSS (NM_177594)	promoter-TSS (NM_177594)	67	NM_177594	210376	Mm.441613	NM_177594	ENSMUSG00000035078	Mtmr9	9430075G12Rik|AA516943|AF073881|LIP-STYX|MTMR8|mMTMH3	myotubularin related protein 9	protein-coding
mm_111345.1	chr12	86885861	86885886	-	1	NA	Intergenic	Intergenic	-1059	NM_145836	238330	Mm.248358	NM_145836	ENSMUSG00000034168	Irf2bpl	6430527G18Rik|Eap1	interferon regulatory factor 2 binding protein-like	protein-coding
mm_15742.1	chr2	164237332	164237339	+	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	1006	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_125521.1	chr15	57694915	57694979	+	1	NA	5' UTR (NM_199449, exon 1 of 4)	5' UTR (NM_199449, exon 1 of 4)	280	NM_199449	387609	Mm.36557	NM_199449	ENSMUSG00000071757	Zhx2	Afr-1|Afr1|Raf|mKIAA0854	zinc fingers and homeoboxes 2	protein-coding
mm_60704.1	chr7	45217309	45217335	+	1	NA	exon (NM_001285498, exon 2 of 12)	exon (NM_001285498, exon 2 of 12)	1569	NM_001285498	21677	Mm.3019	NM_011565	ENSMUSG00000030796	Tead2	ETF|Etdf|TEAD-2|TEF-4|TEF4	TEA domain family member 2	protein-coding
mm_111143.1	chr12	81790890	81790898	-	1	NA	Intergenic	Intergenic	-9724	NM_001174107	338372	Mm.35284	NM_177395	ENSMUSG00000042724	Map3k9	E130314H24Rik|Mlk1|Prke1	mitogen-activated protein kinase kinase kinase 9	protein-coding
mm_107779.1	chr12	61523113	61523184	+	1	NA	promoter-TSS (NM_001310586)	promoter-TSS (NM_001310586)	-19	NM_178714	238205	Mm.28802	NM_178714	ENSMUSG00000035653	Lrfn5	AI427653|AI604817|C130061B21|mKIAA4208	leucine rich repeat and fibronectin type III domain containing 5	protein-coding
mm_8802.1	chr1	161852783	161852786	-	1	NA	intron (NM_172645, intron 8 of 23)	intron (NM_172645, intron 8 of 23)	23877	NM_172645	226551	Mm.170002	NM_172645	ENSMUSG00000040297	Suco	4732491B11|AI848100|AU016931|Opt	SUN domain containing ossification factor	protein-coding
mm_52053.1	chr6	97222605	97222619	+	1	NA	intron (NM_022992, intron 1 of 2)	intron (NM_022992, intron 1 of 2)	11820	NM_022992	65106	Mm.291014	NM_022992	ENSMUSG00000035199	Arl6ip5	5930404D22Rik|AV001879|Aip-5|Gtrap3-18|addiscin	ADP-ribosylation factor-like 6 interacting protein 5	protein-coding
mm_64378.1	chr7	142466789	142466834	+	1	NA	intron (NM_001271510, intron 1 of 10)	(TGGG)n|Simple_repeat|Simple_repeat	-5032	NM_001271508	16985	Mm.234003	NM_019391	ENSMUSG00000018819	Lsp1	Lsp-1|WP34|p50|pp52	lymphocyte specific 1	protein-coding
mm_121647.1	chr14	9560884	9560905	-	1	NA	intron (NM_001308286, intron 6 of 6)	intron (NM_001308286, intron 6 of 6)	-323201	NR_030680	100042415	Mm.235938	NR_030680		Mnd1-ps	Gm3833	Mnd1 retrotransposed pseudogene	pseudo
mm_83809.1	chr9	53536758	53536769	-	1	NA	promoter-TSS (NM_001081152)	promoter-TSS (NM_001081152)	-92	NM_007499	11920	Mm.5088	NM_007499	ENSMUSG00000034218	Atm	AI256621|C030026E19Rik	ataxia telangiectasia mutated	protein-coding
mm_64074.1	chr7	140920858	140920881	+	1	NA	promoter-TSS (NM_133946)	promoter-TSS (NM_133946)	-33	NM_133946	101613	Mm.386833	NM_133946	ENSMUSG00000038745	Nlrp6	AI504961|Avr|Nalp6|Navr|Navr/Avr|Non-AVR|Pypaf5	NLR family, pyrin domain containing 6	protein-coding
mm_72074.1	chr8	71543177	71543214	+	1	NA	exon (NM_028617, exon 2 of 9)	exon (NM_028617, exon 2 of 9)	265	NM_028617	73711	Mm.307770	NM_028617	ENSMUSG00000031813	Mvb12a	1110012M11Rik|Fam125a	multivesicular body subunit 12A	protein-coding
mm_20881.1	chr2	148771490	148771503	-	1	NA	promoter-TSS (NM_030059)	promoter-TSS (NM_030059)	1	NM_030059	78240	Mm.99424	NM_030059	ENSMUSG00000036958	Cst11	9230101F08Rik|BB067629|CRES2|mCSTE1	cystatin 11	protein-coding
mm_133983.1	chr16	4559609	4559681	-	1	NA	promoter-TSS (NM_031182)	promoter-TSS (NM_031182)	75	NM_031182	83383	Mm.273210	NM_031182	ENSMUSG00000005718	Tfap4	AI642933|AP-4|D930048N17Rik|Tcfap4|bHLHc41	transcription factor AP4	protein-coding
mm_85698.1	chr9	108094528	108094542	-	1	NA	promoter-TSS (NM_146226)	promoter-TSS (NM_146226)	-55	NM_146226	235606	Mm.219639	NM_146226	ENSMUSG00000032590	Apeh	-	acylpeptide hydrolase	protein-coding
mm_120317.1	chr14	63142798	63142813	+	1	NA	3' UTR (NM_007798, exon 10 of 10)	3' UTR (NM_007798, exon 10 of 10)	20343	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_44212.1	chr5	4104655	4104792	-	1	NA	promoter-TSS (NM_020010)	promoter-TSS (NM_020010)	-26	NM_020010	13121	Mm.140158	NM_020010	ENSMUSG00000001467	Cyp51	AI426508|CYPLI|Cyp51a1|Ldm|P450-14DM|P450LI	cytochrome P450, family 51	protein-coding
mm_148925.1	chr19	6996115	6996136	+	1	NA	promoter-TSS (NM_153597)	promoter-TSS (NM_153597)	-6	NM_153597	107328	Mm.391161	NM_153597	ENSMUSG00000047656	Trpt1	AU079016|AW045591|Tpt1|Tpt1h	tRNA phosphotransferase 1	protein-coding
mm_42141.1	chr5	111417318	111417319	+	1	NA	promoter-TSS (NM_001081235)	promoter-TSS (NM_001081235)	-848	NM_001081235	433938	Mm.332576	NM_001081235	ENSMUSG00000070576	Mn1	AA003644|AA009236	meningioma 1	protein-coding
mm_113451.1	chr13	35785197	35785200	+	1	NA	intron (NM_001123386, intron 1 of 6)	intron (NM_001123386, intron 1 of 6)	43796	NM_001123386	12593	Mm.29002	NM_009881	ENSMUSG00000059288	Cdyl	AI325931	chromodomain protein, Y chromosome-like	protein-coding
mm_138826.1	chr17	39847891	39847895	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	4896	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_45552.1	chr5	73132949	73132967	-	1	NA	intron (NM_028194, intron 6 of 62)	(A)n|Simple_repeat|Simple_repeat	123660	NM_028194	72313	Mm.260594	NM_028194	ENSMUSG00000070733	Fryl	2010313D22Rik|2310004H21Rik|2510002A14Rik|9030227G01Rik|mKIAA0826	FRY like transcription coactivator	protein-coding
mm_39045.1	chr4	152448768	152448789	-	1	NA	promoter-TSS (NM_001252656)	promoter-TSS (NM_001252656)	77	NM_001252655	16498	Mm.388924	NM_010598	ENSMUSG00000028931	Kcnab2	F5|I2rf5|Kcnb3|kv-beta-2	potassium voltage-gated channel, shaker-related subfamily, beta member 2	protein-coding
mm_160992.1	chr11	106365483	106365483	+	1	NA	Intergenic	Intergenic	-9343	NM_029345	75573	Mm.159539	NM_029345	ENSMUSG00000009210	Prr29	2310007L24Rik	proline rich 29	protein-coding
mm_16991.1	chr2	18219708	18219719	-	1	NA	exon (NM_001190817, exon 11 of 13)	exon (NM_001190817, exon 11 of 13)	155128	NM_001252561	17354	Mm.209175	NM_010804	ENSMUSG00000026743	Mllt10	Af10|B130021D15Rik|D630001B22Rik|mKIAA4140	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 10	protein-coding
mm_84017.1	chr9	57653465	57653479	-	1	NA	5' UTR (NM_001304761, exon 1 of 15)	5' UTR (NM_001304761, exon 1 of 15)	159	NM_001304761	12988	Mm.21974	NM_007783	ENSMUSG00000032312	Csk	AW212630|p50CSK	c-src tyrosine kinase	protein-coding
mm_67637.1	chr7	84409963	84410002	-	1	NA	promoter-TSS (NM_007488)	promoter-TSS (NM_007488)	56	NM_007488	11864	Mm.38594	NM_007488	ENSMUSG00000015709	Arnt2	Hif-2b|bHLHe1|mKIAA0307	aryl hydrocarbon receptor nuclear translocator 2	protein-coding
mm_63114.1	chr7	122671318	122671324	+	1	NA	promoter-TSS (NM_019430)	promoter-TSS (NM_019430)	-423	NM_019430	54376	Mm.444212	NM_019430	ENSMUSG00000066189	Cacng3	-	calcium channel, voltage-dependent, gamma subunit 3	protein-coding
mm_43343.1	chr5	135123735	135123760	+	1	NA	exon (NM_021455, exon 6 of 17)	exon (NM_021455, exon 6 of 17)	16856	NM_021455	58805	Mm.34213	NM_021455	ENSMUSG00000005373	Mlxipl	ChREBP|Mlx|WS-bHLH|Wbscr14|bHLHd14	MLX interacting protein-like	protein-coding
mm_107723.1	chr12	56695629	56695700	+	1	NA	5' UTR (NM_011041, exon 1 of 4)	5' UTR (NM_011041, exon 1 of 4)	193	NM_011041	18511	Mm.5035	NM_011041	ENSMUSG00000001497	Pax9	Pax-9	paired box 9	protein-coding
mm_167183.1	chr7	141808559	141808561	+	1	NA	intron (NM_010844, intron 31 of 49)	intron (NM_010844, intron 31 of 49)	19549	NM_010844	17833	Mm.334332	NM_010844	ENSMUSG00000037974	Muc5ac	2210005L13Rik|MGM	mucin 5, subtypes A and C, tracheobronchial/gastric	protein-coding
mm_152069.1	chr19	6543020	6543039	-	1	NA	promoter-TSS (NM_009203)	promoter-TSS (NM_009203)	41	NM_009203	20521	Mm.391146	NM_009203	ENSMUSG00000061742	Slc22a12	AI987855|OAT4L|Rst|Slc22al2|URAT1	solute carrier family 22 (organic anion/cation transporter), member 12	protein-coding
mm_88980.1	chr10	81559525	81559583	+	1	NA	non-coding (NR_074087, exon 1 of 7)	non-coding (NR_074087, exon 1 of 7)	110	NM_001276288	14797	Mm.180013	NM_010347	ENSMUSG00000054452	Aes	AL024115|Esp1|Grg|Grg-5|Grg5|Tle5	amino-terminal enhancer of split	protein-coding
mm_143022.1	chr17	56554383	56554426	-	1	NA	promoter-TSS (NR_130128)	promoter-TSS (NR_130128)	-17	NR_130128	100504425	Mm.384143	NR_130128	ENSMUSG00000110218	Gm20219	Tincr	predicted gene, 20219	ncRNA
mm_129027.1	chr15	74958822	74958839	-	1	NA	3' UTR (NM_001164036, exon 4 of 4)	3' UTR (NM_001164036, exon 4 of 4)	3724	NM_001164040	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_61184.1	chr7	62349438	62349456	+	1	NA	3' UTR (NM_010882, exon 1 of 1)	3' UTR (NM_010882, exon 1 of 1)	1170	NM_010882	17984	Mm.400253	NM_010882	ENSMUSG00000033585	Ndn	AI528698|Peg6	necdin	protein-coding
mm_119562.1	chr14	48878582	48878603	+	1	NA	promoter-TSS (NR_033783)	promoter-TSS (NR_033783)	-281	NR_033783	66770	Mm.136954	NR_033783		4933429O19Rik	1700031B11Rik	RIKEN cDNA 4933429O19 gene	ncRNA
mm_91740.1	chr10	47102735	47102752	-	1	NA	Intergenic	Intergenic	857994	NR_028276	108637		NR_028276	ENSMUSG00000096263	Snord14c	Gm23107|Rnu14|U14	small nucleolar RNA, C/D box 14C	snoRNA
mm_157199.1	chrX	12160456	12160479	-	1	NA	promoter-TSS (NM_001168321)	promoter-TSS (NM_001168321)	-112	NM_001168321	71458	Mm.196328	NM_029510	ENSMUSG00000040363	Bcor	2900008C10Rik|5830466J11Rik|8430401K06Rik|BcorR|D930024N20Rik|mKIAA1575	BCL6 interacting corepressor	protein-coding
mm_145415.1	chr18	58146368	58146368	+	1	NA	intron (NM_010181, intron 7 of 64)	intron (NM_010181, intron 7 of 64)	63558	NM_010181	14119	Mm.20271	NM_010181	ENSMUSG00000024598	Fbn2	BC063774|Fib-2|mKIAA4226|sne|sy	fibrillin 2	protein-coding
mm_163318.1	chr12	7854080	7854081	-	1	NA	Intergenic	Intergenic	-123597	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_41373.1	chr5	90583252	90583255	+	1	NA	intron (NM_001252661, intron 10 of 13)	MER67C|LTR|ERV1	22044	NM_001252661	622307	Mm.389654	NM_001252661	ENSMUSG00000070690	5830473C10Rik	Arg|Gm17754	RIKEN cDNA 5830473C10 gene	protein-coding
mm_106095.1	chr11	116198702	116198836	-	1	NA	promoter-TSS (NM_027107)	promoter-TSS (NM_027107)	-86	NM_027107	69535	Mm.390347	NM_027107	ENSMUSG00000020778	Ten1	2310004N24Rik	TEN1 telomerase capping complex subunit	protein-coding
mm_72873.1	chr8	88693467	88693472	+	1	NA	Intergenic	Intergenic	-3559	NM_001128170	74256	Mm.490395	NM_173369	ENSMUSG00000036712	Cyld	2010013M14Rik|2900009M21Rik|C130039D01Rik|CDMT|CYLD1|EAC|mKIAA0849	CYLD lysine 63 deubiquitinase	protein-coding
mm_33494.1	chr4	130823512	130823524	+	1	NA	3' UTR (NM_011520, exon 5 of 5)	3' UTR (NM_011520, exon 5 of 5)	30981	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_137300.1	chr17	24850516	24850591	+	1	NA	promoter-TSS (NM_024284)	promoter-TSS (NM_024284)	63	NM_024284	14651	Mm.43784	NM_024284	ENSMUSG00000024158	Hagh	BC019817|Glo-2|Glo2|Rsp29	hydroxyacyl glutathione hydrolase	protein-coding
mm_143692.1	chr17	80290067	80290183	-	1	NA	promoter-TSS (NM_194269)	promoter-TSS (NM_194269)	-87	NM_194269	378462	Mm.45208	NM_194269	ENSMUSG00000045257	Morn2	Mopt	MORN repeat containing 2	protein-coding
mm_87668.1	chr10	58812338	58812352	+	1	NA	Intergenic	CpG	-1014	NM_172788	237353	Mm.333078	NM_172788	ENSMUSG00000037990	Sh3rf3	4831416G18Rik|Igfbp5-ip|Sh3md4|Sh3rf31	SH3 domain containing ring finger 3	protein-coding
mm_79674.1	chr9	59680190	59680207	+	1	NA	TTS (NM_011099)	TTS (NM_011099)	23830	NM_001253883	18746	Mm.326167	NM_011099	ENSMUSG00000032294	Pkm	AA414905|AL024370|AL024424|Pk-2|Pk-3|Pk3|Pkm2	pyruvate kinase, muscle	protein-coding
mm_126691.1	chr15	85017139	85017141	+	1	NA	promoter-TSS (NM_023478)	promoter-TSS (NM_023478)	-1	NM_023478	22270	Mm.46214	NM_023478	ENSMUSG00000022435	Upk3a	1110017C07Rik|UP3a|UPIII|Upk3	uroplakin 3A	protein-coding
mm_75402.1	chr8	46209057	46209122	-	1	NA	exon (NM_007450, exon 2 of 4)	exon (NM_007450, exon 2 of 4)	1920	NM_007450	11739	Mm.16228	NM_007450	ENSMUSG00000031633	Slc25a4	AU019225|Ant1	solute carrier family 25 (mitochondrial carrier, adenine nucleotide translocator), member 4	protein-coding
mm_11343.1	chr2	30803786	30803796	+	1	NA	promoter-TSS (NR_028487)	promoter-TSS (NR_028487)	-127	NR_028487	73598	Mm.34166	NM_198000	ENSMUSG00000044320	1700001O22Rik	1700113K14Rik|4930549G18Rik	RIKEN cDNA 1700001O22 gene	protein-coding
mm_132400.1	chr16	35001325	35001340	+	1	NA	3' UTR (NM_139300, exon 32 of 32)	3' UTR (NM_139300, exon 32 of 32)	-21089	NM_023587	70757	Mm.27286	NM_023587	ENSMUSG00000035376	Hacd2	6330408J20Rik|AI255777|AI481689|Hcad2|Ptplb	3-hydroxyacyl-CoA dehydratase 2	protein-coding
mm_822.1	chr1	46894632	46894658	+	1	NA	Intergenic	ORR1D2|LTR|ERVL-MaLR	-41136	NM_172653	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|mKIAA1265	solute carrier family 39 (zinc transporter), member 10	protein-coding
mm_19386.1	chr2	91236968	91236989	-	1	NA	promoter-TSS (NM_028119)	promoter-TSS (NM_028119)	88	NM_028119	107986	Mm.389334	NM_028119	ENSMUSG00000002109	Ddb2	2610043A19Rik	damage specific DNA binding protein 2	protein-coding
mm_86540.1	chr10	8866596	8866603	+	1	NA	intron (NM_175155, intron 1 of 19)	intron (NM_175155, intron 1 of 19)	19471	NM_175155	70097	Mm.338275	NM_175155	ENSMUSG00000015305	Sash1	1100001C18Rik|2500002E12Rik|A330076K04Rik|mKIAA0790	SAM and SH3 domain containing 1	protein-coding
mm_86787.1	chr10	20185425	20185425	+	1	NA	intron (NM_001198635, intron 1 of 17)	intron (NM_001198635, intron 1 of 17)	16429	NR_045350	73811	Mm.55644	NR_045350	ENSMUSG00000110754	4930405J17Rik	-	RIKEN cDNA 4930405J17 gene	ncRNA
mm_20967.1	chr2	151972950	151972958	-	1	NA	intron (NM_146127, intron 1 of 1)	intron (NM_146127, intron 1 of 1)	440	NM_001289151	73847	Mm.272444	NM_028666	ENSMUSG00000027459	Fam110a	1700008J10Rik|5430432M24Rik|AI747080	family with sequence similarity 110, member A	protein-coding
mm_154125.1	chr19	57239266	57239301	-	1	NA	Intergenic	Intergenic	-23251	NM_178688	226251	Mm.217161	NM_178688	ENSMUSG00000025085	Ablim1	2210411C18Rik|2610209L21Rik|4833406P10Rik|9330196J19Rik|AV079770|AW060987|AW215784|Limab1|mKIAA0059	actin-binding LIM protein 1	protein-coding
mm_26011.1	chr3	135307712	135307750	+	1	NA	promoter-TSS (NM_178877)	promoter-TSS (NM_178877)	31	NM_178877	97086	Mm.441764	NM_178877	ENSMUSG00000037994	Slc9b2	C80638|NHA2|NHE10|Nhedc2|nha-oc|nhaoc	solute carrier family 9, subfamily B (NHA2, cation proton antiporter 2), member 2	protein-coding
mm_74111.1	chr8	123041374	123041389	+	1	NA	intron (NM_001081379, intron 1 of 12)	CpG	903	NR_037865	77087	Mm.31567	NM_001081379	ENSMUSG00000035569	Ankrd11	2410104C19Rik|3010027A04Rik|6330578C09Rik|9530048I21Rik|AA930108|Gm176|Yod	ankyrin repeat domain 11	protein-coding
mm_50027.1	chr6	41122005	41122013	+	1	NA	Intergenic	Intergenic	-86500	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_131978.1	chr16	25011202	25011205	+	1	NA	Intergenic	Intergenic	-48436	NR_040374	319487	Mm.137341	NR_040374	ENSMUSG00000096960	A230028O05Rik	-	RIKEN cDNA A230028O05 gene	ncRNA
mm_59862.1	chr7	30099558	30099614	+	1	NA	5' UTR (NM_011981, exon 2 of 3)	5' UTR (NM_011981, exon 2 of 3)	4510	NM_011981	26466	Mm.195092	NM_011981	ENSMUSG00000049421	Zfp260	AI480997|Ozrf1|PEX1|Zfp63|Znf260	zinc finger protein 260	protein-coding
mm_29074.1	chr3	103862635	103862646	-	1	NA	intron (NR_104070, intron 3 of 22)	intron (NR_104070, intron 3 of 22)	2363	NM_008979	19260	Mm.395	NM_008979	ENSMUSG00000027843	Ptpn22	70zpep|PEP|Ptpn8	protein tyrosine phosphatase, non-receptor type 22 (lymphoid)	protein-coding
mm_99433.1	chr11	102430464	102430523	+	1	NA	5' UTR (NM_008175, exon 1 of 13)	5' UTR (NM_008175, exon 1 of 13)	171	NM_008175	14824	Mm.1568	NM_008175	ENSMUSG00000034708	Grn	Pgrn|epithelin	granulin	protein-coding
mm_108873.1	chr12	99645225	99645255	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-17266	NR_045288	73457	Mm.383439	NR_045288	ENSMUSG00000100211	1700064M15Rik	-	RIKEN cDNA 1700064M15 gene	ncRNA
mm_30811.1	chr4	20042153	20042171	+	1	NA	5' UTR (NM_010281, exon 1 of 9)	5' UTR (NM_010281, exon 1 of 9)	110	NM_010281	14590	Mm.20461	NM_010281	ENSMUSG00000073987	Ggh	gamma-GH	gamma-glutamyl hydrolase	protein-coding
mm_69355.1	chr7	130462695	130462705	-	1	NA	intron (NM_001029895, intron 10 of 11)	(A)n|Simple_repeat|Simple_repeat	56880	NM_001136054	11907	Mm.216321	NM_013799	ENSMUSG00000030850	Ate1	AI225793|AW547406	arginyltransferase 1	protein-coding
mm_86532.1	chr10	7832508	7832520	+	1	NA	promoter-TSS (NM_172785)	promoter-TSS (NM_172785)	44	NM_172785	237256	Mm.140055	NM_172785	ENSMUSG00000039981	Zc3h12d	D730019B10Rik|TFL	zinc finger CCCH type containing 12D	protein-coding
mm_55965.1	chr6	85513587	85513591	-	1	NA	promoter-TSS (NM_020596)	promoter-TSS (NM_020596)	-47	NM_020596	13656	Mm.44137	NM_020596	ENSMUSG00000071341	Egr4	NGF1-C|NGFI-C|NGFIC|pAT133	early growth response 4	protein-coding
mm_169283.1	chr13	97099310	97099342	-	1	NA	intron (NM_001146045, intron 5 of 12)	intron (NM_001146045, intron 5 of 12)	27683	NM_001100458	320557	Mm.458280	NM_001100458	ENSMUSG00000041817	Fam169a	B230112C05Rik|SLAP75	family with sequence similarity 169, member A	protein-coding
mm_85684.1	chr9	107872826	107872844	-	1	NA	promoter-TSS (NM_029169)	promoter-TSS (NM_029169)	-16	NM_029169	19654	Mm.139926	NM_011251	ENSMUSG00000032582	Rbm6	4930506F14Rik|Def-3|NY-LU-12|g16|mKIAA4015	RNA binding motif protein 6	protein-coding
mm_33652.1	chr4	133068270	133068273	+	1	NA	intron (NM_146155, intron 6 of 6)	Tigger19a|DNA|TcMar-Tigger	56765	NM_146155	230793	Mm.31816	NM_146155	ENSMUSG00000037692	Ahdc1	D030015G18Rik	AT hook, DNA binding motif, containing 1	protein-coding
mm_153799.1	chr19	46039443	46039455	-	1	NA	5' UTR (NM_010697, exon 1 of 11)	5' UTR (NM_010697, exon 1 of 11)	172	NM_010697	16825	Mm.327442	NM_010697	ENSMUSG00000025223	Ldb1	CLIM2|NLI	LIM domain binding 1	protein-coding
mm_169140.1	chr13	62006625	62006643	+	1	NA	Intergenic	Intergenic	-123256	NM_001039239	630579	Mm.440905	NM_001039239	ENSMUSG00000074867	Zfp808	EG630579|Gm7036	zinc finger protein 80	protein-coding
mm_154950.1	chrX	36598200	36598214	+	1	NA	promoter-TSS (NM_016783)	promoter-TSS (NM_016783)	14	NM_016783	53328	Mm.9052	NM_016783	ENSMUSG00000006373	Pgrmc1	AA415812|HPR6.6|PPMR|Vema	progesterone receptor membrane component 1	protein-coding
mm_34408.1	chr4	145241955	145241967	+	1	NA	intron (NM_011610, intron 1 of 9)	MIR3|SINE|MIR	4909	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_10338.1	chr2	11645495	11645506	+	1	NA	intron (NM_008367, intron 1 of 7)	intron (NM_008367, intron 1 of 7)	2708	NM_008367	16184	Mm.915	NM_008367	ENSMUSG00000026770	Il2ra	CD25|Il2r|Ly-43	interleukin 2 receptor, alpha chain	protein-coding
mm_19998.1	chr2	118728579	118728630	-	1	NA	promoter-TSS (NM_177568)	promoter-TSS (NM_177568)	-166	NM_001290790	18796	Mm.215156	NM_177568	ENSMUSG00000040061	Plcb2	AI550384|B230205M18Rik|B230399N12	phospholipase C, beta 2	protein-coding
mm_96061.1	chr11	59566488	59566501	+	1	NA	3' UTR (NM_145827, exon 10 of 10)	3' UTR (NM_145827, exon 10 of 10)	5244	NM_001011789	257962	Mm.377316	NM_001011789	ENSMUSG00000059610	Olfr222	MOR256-45P	olfactory receptor 222	protein-coding
mm_86487.1	chr10	5185280	5185282	+	1	NA	intron (NM_001347711, intron 94 of 145)	intron (NM_001347711, intron 94 of 145)	9426	NM_001079686	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_153632.1	chr19	44021764	44021775	-	1	NA	intron (NM_001001446, intron 1 of 8)	intron (NM_001001446, intron 1 of 8)	7478	NM_001001446	226143	Mm.329866	NM_001001446	ENSMUSG00000025197	Cyp2c44	AW107714|BC034834|b2b386Clo	cytochrome P450, family 2, subfamily c, polypeptide 44	protein-coding
mm_75628.1	chr8	64692981	64692994	-	1	NA	5' UTR (NM_013494, exon 1 of 9)	5' UTR (NM_013494, exon 1 of 9)	122	NM_013494	12876	Mm.31395	NM_013494	ENSMUSG00000037852	Cpe	CPH|Cph-1|Cph1|R74677|fat	carboxypeptidase E	protein-coding
mm_98056.1	chr11	85821952	85821958	+	1	NA	intron (NR_077059, intron 1 of 4)	intron (NR_077059, intron 1 of 4)	10433	NR_077059	69909	Mm.440214	NR_077059	ENSMUSG00000087013	2610027K06Rik	-	RIKEN cDNA 2610027K06 gene	ncRNA
mm_38107.1	chr4	134517902	134517912	-	1	NA	intron (NM_001081099, intron 1 of 2)	intron (NM_001081099, intron 1 of 2)	6908	NM_001081099	69885	Mm.141592	NM_001081099	ENSMUSG00000078521	Aunip	2610002D18Rik|Clhc1	aurora kinase A and ninein interacting protein	protein-coding
mm_111636.1	chr12	102623379	102623404	-	1	NA	exon (NM_172584, exon 3 of 10)	exon (NM_172584, exon 3 of 10)	61629	NR_035457	100316812		NR_035457	ENSMUSG00000089324	Mir1936	mir-1936|mmu-mir-1936	microRNA 1936	ncRNA
mm_12491.1	chr2	71786924	71786945	+	1	NA	promoter-TSS (NM_008397)	promoter-TSS (NM_008397)	-5	NM_008397	16403	Mm.225096	NM_008397	ENSMUSG00000027111	Itga6	5033401O05Rik|AI115430|Cd49f|VLA-6	integrin alpha 6	protein-coding
mm_144585.1	chr18	31954831	31954872	+	1	NA	intron (NM_144862, intron 5 of 9)	intron (NM_144862, intron 5 of 9)	-5215	NM_001025381	574402	Mm.391108	NM_001025381	ENSMUSG00000052229	Gpr17	AI853548	G protein-coupled receptor 17	protein-coding
mm_35610.1	chr4	43383316	43383338	-	1	NA	intron (NM_001037709, intron 1 of 11)	intron (NM_001037709, intron 1 of 11)	1345	NM_001037709	100213	Mm.235730	NM_199057	ENSMUSG00000035969	Rusc2	AI840675|mKIAA0375	RUN and SH3 domain containing 2	protein-coding
mm_151106.1	chr19	47863376	47863386	+	1	NA	exon (NM_010362, exon 5 of 6)	exon (NM_010362, exon 5 of 6)	-2164	NM_030051	68214	Mm.63791	NM_026619	ENSMUSG00000025069	Gsto2	1700020F09Rik|4930425C18Rik|GSTO 2-2	glutathione S-transferase omega 2	protein-coding
mm_12746.1	chr2	79126663	79126685	+	1	NA	Intergenic	Intergenic	-128752	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D|Itga4B	integrin alpha 4	protein-coding
mm_103206.1	chr11	70652878	70652914	-	1	NA	exon (NM_011072, exon 2 of 3)	exon (NM_011072, exon 2 of 3)	1754	NM_011072	18643	Mm.2647	NM_011072	ENSMUSG00000018293	Pfn1	Pfn	profilin 1	protein-coding
mm_163030.1	chr11	51644326	51644328	+	1	NA	exon (NM_145974, exon 4 of 5)	exon (NM_145974, exon 4 of 5)	-6627	NR_027958	97775	Mm.220299	NM_175289	ENSMUSG00000052563	D930048N14Rik	AI315703|R75254	RIKEN cDNA D930048N14 gene	ncRNA
mm_87772.1	chr10	60294586	60294592	+	1	NA	exon (NM_011179, exon 5 of 15)	exon (NM_011179, exon 5 of 15)	10128	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_33515.1	chr4	130928678	130928688	+	1	NA	exon (NM_010686, exon 4 of 8)	exon (NM_010686, exon 4 of 8)	15349	NM_010686	16792	Mm.271868	NM_010686	ENSMUSG00000028581	Laptm5	E3	lysosomal-associated protein transmembrane 5	protein-coding
mm_86601.1	chr10	13501047	13501070	+	1	NA	promoter-TSS (NM_001330198)	promoter-TSS (NM_001330198)	30	NM_025799	66848	Mm.26625	NM_025799	ENSMUSG00000019810	Fuca2	0610025O11Rik|5530401P20Rik	fucosidase, alpha-L- 2, plasma	protein-coding
mm_38050.1	chr4	133984831	133984833	-	1	NA	intron (NM_026144, intron 6 of 8)	PB1D10|SINE|Alu	16032	NM_026144	67422	Mm.100290	NM_026144	ENSMUSG00000012117	Dhdds	3222401G21Rik|CIT|DS|HDS|W91638	dehydrodolichyl diphosphate synthase	protein-coding
mm_120700.1	chr14	70941881	70941908	+	1	NA	intron (NM_001302094, intron 3 of 7)	intron (NM_001302094, intron 3 of 7)	51787	NM_001302094	14586	Mm.32619	NM_008115	ENSMUSG00000022103	Gfra2	-	glial cell line derived neurotrophic factor family receptor alpha 2	protein-coding
mm_162252.1	chrX	164497877	164497877	+	1	NA	promoter-TSS (NM_027027)	promoter-TSS (NM_027027)	-26	NM_027027	69299	Mm.79031	NM_027027	ENSMUSG00000031384	Asb9	1700011M07Rik	ankyrin repeat and SOCS box-containing 9	protein-coding
mm_143414.1	chr17	70834802	70834827	-	1	NA	Intergenic	Intergenic	11963	NM_001164077	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_113529.1	chr13	37826816	37826832	+	1	NA	promoter-TSS (NM_001039188)	promoter-TSS (NM_001039188)	-88	NM_001177868	68750	Mm.491109	NM_026830	ENSMUSG00000039087	Rreb1	1110037N09Rik|AA414966|B930013M22Rik	ras responsive element binding protein 1	protein-coding
mm_5379.1	chr1	30949757	30949757	-	1	NA	promoter-TSS (NR_002688)	promoter-TSS (NR_002688)	-2	NM_011200	19243	Mm.491181	NM_011200	ENSMUSG00000026064	Ptp4a1	AA415290|AU019864|C130021B01|Prl-1	protein tyrosine phosphatase 4a1	protein-coding
mm_93855.1	chr10	122096466	122096468	-	1	NA	intron (NM_153059, intron 1 of 5)	intron (NM_153059, intron 1 of 5)	635	NM_153059	216395	Mm.236764	NM_153059	ENSMUSG00000034620	Tmem5	6330415D21Rik	transmembrane protein 5	protein-coding
mm_154082.1	chr19	56617708	56617718	-	1	NA	Intergenic	B1F|SINE|Alu	69452	NM_025811	66866	Mm.46346	NM_025811	ENSMUSG00000025078	Nhlrc2	1200003G01Rik|AI835049|AV002846|AW496455	NHL repeat containing 2	protein-coding
mm_98012.1	chr11	84525673	84525689	+	1	NA	promoter-TSS (NM_008498)	promoter-TSS (NM_008498)	21	NR_038057	78365	Mm.260345	NR_038057	ENSMUSG00000087211	Lhx1os	1500016L03Rik|Lhx1as	LIM homeobox 1, opposite strand	ncRNA
mm_47217.1	chr5	121010086	121010126	-	1	NA	promoter-TSS (NM_011286)	promoter-TSS (NM_011286)	-14	NM_001302344	19894	Mm.181166	NM_011286	ENSMUSG00000029608	Rph3a	2900002P20Rik|AU022689|AW108370	rabphilin 3A	protein-coding
mm_158279.1	chrX	111531164	111531176	-	1	NA	intron (NM_025949, intron 1 of 24)	intron (NM_025949, intron 1 of 24)	6789	NM_025949	67071	Mm.37617	NM_025949	ENSMUSG00000025665	Rps6ka6	2610524K04Rik|RSK4|S6K-alpha-6	ribosomal protein S6 kinase polypeptide 6	protein-coding
mm_139154.1	chr17	47540444	47540459	+	1	NA	intron (NM_001081635, intron 1 of 6)	intron (NM_001081635, intron 1 of 6)	35400	NM_001081635	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_84231.1	chr9	61990724	61990729	-	1	NA	intron (NM_028748, intron 1 of 7)	intron (NM_028748, intron 1 of 7)	36064	NM_028748	74090	Mm.273267	NM_028748	ENSMUSG00000032278	Paqr5	0610010I15Rik|AV002411|BB115488|mPRg	progestin and adipoQ receptor family member V	protein-coding
mm_18387.1	chr2	60125587	60125598	-	1	NA	5' UTR (NM_001001182, exon 1 of 36)	5' UTR (NM_001001182, exon 1 of 36)	148	NM_001001182	407823	Mm.228071	NM_001001182	ENSMUSG00000026987	Baz2b	5830435C13Rik|BC053917|D2Ertd794e	bromodomain adjacent to zinc finger domain, 2B	protein-coding
mm_106998.1	chr12	11279635	11279648	+	1	NA	exon (NM_025695, exon 5 of 27)	exon (NM_025695, exon 5 of 27)	13755	NM_025695	67241	Mm.173953	NM_025695	ENSMUSG00000020608	Smc6	2810489L22Rik|3830418C19Rik|AA990493|AU018782|AW742439|SMC-6|Smc6l1|mKIAA4103	structural maintenance of chromosomes 6	protein-coding
mm_157327.1	chrX	23296398	23296417	-	1	NA	intron (NM_026167, intron 3 of 8)	intron (NM_026167, intron 3 of 8)	-10848	NM_001290476	67455	Mm.224306	NM_026167	ENSMUSG00000036782	Klhl13	1200009K10Rik|AI451128|Bklhd2|D130072F20Rik	kelch-like 13	protein-coding
mm_166350.1	chr5	119684531	119684545	+	1	NA	TTS (NR_040416)	TTS (NR_040416)	6680	NR_040416	433944	Mm.491053	NR_040416	ENSMUSG00000086847	Tbx3os2	Gm16065|OTTMUSG00000029666	T-box 3, opposite strand 2	ncRNA
mm_157114.1	chrX	9438319	9438336	-	1	NA	exon (NM_007807, exon 13 of 13)	exon (NM_007807, exon 13 of 13)	30997	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_104587.1	chr11	97026137	97026147	-	1	NA	non-coding (NR_133649, exon 1 of 2)	non-coding (NR_133649, exon 1 of 2)	276	NR_133649	100127433	Mm.156282	NR_133649	ENSMUSG00000087067	Gm11532	OTTMUSG00000001860|Sp6os	predicted gene 11532	ncRNA
mm_15453.1	chr2	157423914	157423944	+	1	NA	promoter-TSS (NM_001025395)	promoter-TSS (NM_001025395)	-364	NM_009271	20779	Mm.22845	NM_009271	ENSMUSG00000027646	Src	AW259666|pp60c-src	Rous sarcoma oncogene	protein-coding
mm_90961.1	chr10	13324222	13324242	-	1	NA	promoter-TSS (NM_001195096)	promoter-TSS (NM_001195096)	-72	NM_001033257	215789	Mm.283359	NM_001033257	ENSMUSG00000062866	Phactr2	AV158170|BC012871	phosphatase and actin regulator 2	protein-coding
mm_113197.1	chr13	24943543	24943562	+	1	NA	5' UTR (NM_008156, exon 2 of 26)	5' UTR (NM_008156, exon 2 of 26)	400	NM_008156	14756	Mm.291831	NM_008156	ENSMUSG00000021340	Gpld1	6330541J12Rik|AW546131	glycosylphosphatidylinositol specific phospholipase D1	protein-coding
mm_85499.1	chr9	106158135	106158141	-	1	NA	promoter-TSS (NM_174846)	promoter-TSS (NM_174846)	0	NM_001039586	235582	Mm.335420	NM_174846	ENSMUSG00000020258	Glyctk	6230410P16Rik|C430006L12	glycerate kinase	protein-coding
mm_147695.1	chr18	60749009	60749021	-	1	NA	Intergenic	Intergenic	-25581	NM_020600	20044	Mm.43778	NM_020600	ENSMUSG00000024608	Rps14	2600014J02Rik|AL023078	ribosomal protein S14	protein-coding
mm_140975.1	chr17	24696506	24696536	-	1	NA	promoter-TSS (NM_023040)	promoter-TSS (NM_023040)	287	NM_027988	71893	Mm.390971	NM_027988	ENSMUSG00000019320	Noxo1	2310034C04Rik|P41NOX|P41NOXA|P41NOXB|P41NOXC|Snx28|hslt	NADPH oxidase organizer 1	protein-coding
mm_63061.1	chr7	122067393	122067460	+	1	NA	promoter-TSS (NM_026140)	promoter-TSS (NM_026140)	228	NM_138589	28018	Mm.282122	NM_138589	ENSMUSG00000030870	Ubfd1	AI467302|D7Wsu105e|D7Wsu128e|Ubph	ubiquitin family domain containing 1	protein-coding
mm_30016.1	chr3	135665217	135665271	-	1	NA	intron (NM_008689, intron 3 of 24)	intron (NM_008689, intron 3 of 24)	26303	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_23515.1	chr3	60567550	60567565	+	1	NA	intron (NM_001310514, intron 2 of 8)	intron (NM_001310514, intron 2 of 8)	66378	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_87911.1	chr10	62338896	62338921	+	1	NA	intron (NM_010438, intron 4 of 21)	intron (NM_010438, intron 4 of 21)	1513	NM_001146100	15275	Mm.196605	NM_010438	ENSMUSG00000037012	Hk1	BB404130|Hk-1|Hk1-s|dea|mHk1-s	hexokinase 1	protein-coding
mm_1034.1	chr1	58756267	58756281	+	1	NA	3' UTR (NM_207653, exon 10 of 10)	3' UTR (NM_207653, exon 10 of 10)	25722	NM_001293805	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_124989.1	chr15	21489829	21489832	+	1	NA	intron (NM_001008420, intron 4 of 11)	intron (NM_001008420, intron 4 of 11)	378378	NM_001008420	215654	Mm.300909	NM_001008420	ENSMUSG00000040452	Cdh12	Cdhb	cadherin 12	protein-coding
mm_139855.1	chr17	69969192	69969202	+	1	NA	5' UTR (NM_001347412, exon 1 of 14)	5' UTR (NM_001347412, exon 1 of 14)	124	NM_001347411	224997	Mm.311840	NM_027712	ENSMUSG00000003279	Dlgap1	4933422O14Rik|9630002F18|AI845682|AI848168|BB075781|D17Bwg0511e|GKAP/SAPAP|GKPA/SAPAP|Gkap|Sapap1|mKIAA4162	discs, large (Drosophila) homolog-associated protein 1	protein-coding
mm_31838.1	chr4	73790917	73790940	+	1	NA	promoter-TSS (NR_046042)	promoter-TSS (NR_046042)	-316	NR_046042	667768	Mm.244966	NR_046041	ENSMUSG00000085034	Gm11240	OTTMUSG00000000286	predicted gene 11240	ncRNA
mm_111140.1	chr12	81765128	81765130	-	1	NA	intron (NM_001174107, intron 2 of 10)	MTD|LTR|ERVL-MaLR	16041	NM_177395	338372	Mm.35284	NM_177395	ENSMUSG00000042724	Map3k9	E130314H24Rik|Mlk1|Prke1	mitogen-activated protein kinase kinase kinase 9	protein-coding
mm_86260.1	chr9	121592067	121592082	-	1	NA	intron (NR_040740, intron 1 of 3)	intron (NR_040740, intron 1 of 3)	5054	NR_040740	75384	Mm.445955	NR_040740	ENSMUSG00000084995	Lyzl4os	4930589B17Rik|4930596M17Rik	lysozyme-like 4, opposite strand	ncRNA
mm_64768.1	chr7	4971835	4971884	-	1	NA	promoter-TSS (NM_001200041)	promoter-TSS (NM_001200041)	-898	NM_001200041	381835	Mm.297828	NM_001200041	ENSMUSG00000085272	Sbk3	Gm1078|Sgk110	SH3 domain binding kinase family, member 3	protein-coding
mm_43620.1	chr5	138161084	138161116	+	1	NA	promoter-TSS (NM_012002)	promoter-TSS (NM_012002)	-2	NM_012002	26893	Mm.3981	NM_012002	ENSMUSG00000019494	Cops6	Sgn3|VIP/MOV34	COP9 signalosome subunit 6	protein-coding
mm_26883.1	chr3	17786835	17786845	-	1	NA	Intergenic	CpG	-3081	NR_033490	70441	Mm.458192	NR_033490	ENSMUSG00000100252	Mir124-2hg	100040120|2610100L16Rik|6430547I21Rik|A930005K07Rik|AW125202|Gm2612	Mir124-2 host gene (non-protein coding)	ncRNA
mm_173292.1	chrY	37699587	37699587	-	1	NA	Intergenic	Intergenic	-258224	NM_001160143	100040031	Mm.463839	NM_001160143	ENSMUSG00000093950	Gm20823	-	predicted gene, 20823	protein-coding
mm_164079.1	chr14	122712188	122712190	+	1	NA	intron (NM_144844, intron 17 of 23)	intron (NM_144844, intron 17 of 23)	177861	NM_144844	110821	Mm.23876	NM_144844	ENSMUSG00000041650	Pcca	C79630	propionyl-Coenzyme A carboxylase, alpha polypeptide	protein-coding
mm_62392.1	chr7	101052963	101052964	+	1	NA	Intergenic	L1MB8|LINE|L1	-40910	NM_001302346	18442	Mm.3000	NM_008773	ENSMUSG00000032860	P2ry2	P2U1|P2Y2	purinergic receptor P2Y, G-protein coupled 2	protein-coding
mm_151213.1	chr19	53623150	53623186	+	1	NA	exon (NM_007790, exon 11 of 29)	exon (NM_007790, exon 11 of 29)	22772	NM_007790	13006	Mm.14910	NM_007790	ENSMUSG00000024974	Smc3	Bamacan|Cspg6|HCAP|Mmip1|SMC-3|SmcD	structural maintenance of chromosomes 3	protein-coding
mm_119396.1	chr14	41137875	41137883	+	1	NA	Intergenic	Intergenic	6091	NM_023134	20387	Mm.46062	NM_023134	ENSMUSG00000021789	Sftpa1	SP-A|Sftp-1|Sftp1	surfactant associated protein A1	protein-coding
mm_67190.1	chr7	73940523	73940532	-	1	NA	3' UTR (NM_009181, exon 6 of 6)	3' UTR (NM_009181, exon 6 of 6)	73155	NM_009181	20450	Mm.4954	NM_009181	ENSMUSG00000025789	St8sia2	AI323367|ST8SiaII|STX|Siat8b	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 2	protein-coding
mm_20550.1	chr2	131069007	131069015	-	1	NA	TTS (NM_011426)	TTS (NM_011426)	-5197	NM_001163529	110751	Mm.108550	NM_033615	ENSMUSG00000027318	Adam33	Adaml	a disintegrin and metallopeptidase domain 33	protein-coding
mm_61223.1	chr7	64501651	64501683	+	1	NA	promoter-TSS (NM_001291167)	promoter-TSS (NM_001291167)	-39	NM_007461	11784	Mm.4657	NM_007461	ENSMUSG00000030519	Apba2	X11-like|X11L|XllL|mXllL	amyloid beta (A4) precursor protein-binding, family A, member 2	protein-coding
mm_68849.1	chr7	126369401	126369411	-	1	NA	TTS (NM_023712)	TTS (NM_023712)	162	NM_010689	16797	Mm.10280	NM_010689	ENSMUSG00000030742	Lat	p36-38|pp36	linker for activation of T cells	protein-coding
mm_109141.1	chr12	106585870	106585877	+	1	NA	Intergenic	Intergenic	130451	NR_015512	71033	Mm.159404	NR_015512	ENSMUSG00000085820	4933406K04Rik	4930426M03Rik|4930485I22Rik|4933427G14Rik	RIKEN cDNA 4933406K04 gene	ncRNA
mm_13232.1	chr2	97630798	97630818	+	1	NA	exon (NM_178725, exon 3 of 3)	exon (NM_178725, exon 3 of 3)	163151	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_3402.1	chr1	143777264	143777327	+	1	NA	promoter-TSS (NM_001159866)	promoter-TSS (NM_001159866)	17	NM_019562	56207	Mm.261004	NM_019562	ENSMUSG00000018189	Uchl5	5830413B11Rik|Uch37	ubiquitin carboxyl-terminal esterase L5	protein-coding
mm_138629.1	chr17	35841882	35841889	+	1	NA	intron (NM_001010833, intron 1 of 15)	intron (NM_001010833, intron 1 of 15)	387	NM_001010833	240087	Mm.218511	NM_001010833	ENSMUSG00000061607	Mdc1	6820401C03|AA413496|Nfbd1|mKIAA0170	mediator of DNA damage checkpoint 1	protein-coding
mm_61085.1	chr7	51622392	51622441	+	1	NA	5' UTR (NM_080853, exon 1 of 12)	5' UTR (NM_080853, exon 1 of 12)	586	NM_080853	140919	Mm.256618	NM_080853	ENSMUSG00000030500	Slc17a6	2900073D12Rik|DNPI|VGLUT2	solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 6	protein-coding
mm_113301.1	chr13	30748715	30748721	+	1	NA	promoter-TSS (NM_013674)	promoter-TSS (NM_013674)	-515	NM_001347508	16364	Mm.4677	NM_013674	ENSMUSG00000021356	Irf4	AI385587|IRF-4|LSIRF|NF-EM5|Spip	interferon regulatory factor 4	protein-coding
mm_171654.1	chr4	40724041	40724045	+	1	NA	exon (NM_001164672, exon 3 of 9)	exon (NM_001164672, exon 3 of 9)	1113	NM_001164672	15502	Mm.27897	NM_008298	ENSMUSG00000028410	Dnaja1	HSJ-2|Hsj2|Nedd7	DnaJ heat shock protein family (Hsp40) member A1	protein-coding
mm_139032.1	chr17	46163076	46163121	+	1	NA	intron (NM_019581, intron 1 of 11)	intron (NM_019581, intron 1 of 11)	2066	NM_001145979	56055	Mm.22147	NM_019581	ENSMUSG00000023952	Gtpbp2	nmf205	GTP binding protein 2	protein-coding
mm_173255.1	chrX	94702996	94702997	-	1	NA	Intergenic	IAP1-MM_LTR|LTR|ERVK	-21573	NM_001081473	668166	Mm.426145	NM_001081473	ENSMUSG00000073062	Zxdb	Zxda	zinc finger, X-linked, duplicated B	protein-coding
mm_55890.1	chr6	83536216	83536230	-	1	NA	promoter-TSS (NM_009610)	promoter-TSS (NM_009610)	28	NM_009610	11468	Mm.292865	NM_009610	ENSMUSG00000059430	Actg2	ACTA3|Act-4|Act4|SMGA	actin, gamma 2, smooth muscle, enteric	protein-coding
mm_25920.1	chr3	131156459	131156470	+	1	NA	intron (NM_001276403, intron 3 of 11)	intron (NM_001276403, intron 3 of 11)	43673	NM_001276403	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_75543.1	chr8	57487692	57487700	-	1	NA	promoter-TSS (NR_126555)	promoter-TSS (NR_126555)	164	NM_021788	60406	Mm.118	NM_021788	ENSMUSG00000031609	Sap30	30kDa	sin3 associated polypeptide	protein-coding
mm_126656.1	chr15	84192290	84192305	+	1	NA	promoter-TSS (NM_178614)	promoter-TSS (NM_178614)	64	NM_178614	68653	Mm.290725	NM_178614	ENSMUSG00000022437	Samm50	1110030L07Rik	SAMM50 sorting and assembly machinery component	protein-coding
mm_68762.1	chr7	121589855	121589863	-	1	NA	promoter-TSS (NR_131051)	promoter-TSS (NR_131051)	-23	NR_102286	75793	Mm.23397	NR_102286		4933432K03Rik	1700001C18Rik|4930433G11Rik|AI428127	RIKEN cDNA 4933432K03 gene	ncRNA
mm_103299.1	chr11	72502437	72502451	-	1	NA	intron (NM_029932, intron 9 of 11)	intron (NM_029932, intron 9 of 11)	-12524	NM_153060	216892	Mm.212812	NM_153060	ENSMUSG00000040447	Spns2	-	spinster homolog 2	protein-coding
mm_156232.1	chrX	135885861	135885897	+	1	NA	promoter-TSS (NM_198161)	promoter-TSS (NM_198161)	28	NM_198161	70237	Mm.440847	NM_198161	ENSMUSG00000072964	Bhlhb9	2700087I09Rik	basic helix-loop-helix domain containing, class B9	protein-coding
mm_147750.1	chr18	61196547	61196557	-	1	NA	TTS (NM_007885)	TTS (NM_007885)	15044	NM_007885	13521	Mm.24803	NM_007885	ENSMUSG00000034320	Slc26a2	Dtd|ST-OB	solute carrier family 26 (sulfate transporter), member 2	protein-coding
mm_144569.1	chr18	31780712	31780739	+	1	NA	exon (NM_001242430, exon 8 of 8)	exon (NM_001242430, exon 8 of 8)	-8434	NM_027002	69241	Mm.279898	NM_027002	ENSMUSG00000024258	Polr2d	2310002G05Rik|2610028L19Rik|HSRBP4|RBP4	polymerase (RNA) II (DNA directed) polypeptide D	protein-coding
mm_152978.1	chr19	29486990	29487004	-	1	NA	Intergenic	Intergenic	34990	NR_015567	77779	Mm.458738	NR_015567	ENSMUSG00000097855	A930007I19Rik	-	RIKEN cDNA A930007I19 gene	ncRNA
mm_149001.1	chr19	8664396	8664419	+	1	NA	5' UTR (NM_007698, exon 1 of 2)	5' UTR (NM_007698, exon 1 of 2)	402	NM_001112697	12669	Mm.240607	NM_007698	ENSMUSG00000032773	Chrm1	Chrm-1|M1|M1R	cholinergic receptor, muscarinic 1, CNS	protein-coding
mm_146646.1	chr18	11048668	11048685	-	1	NA	intron (NR_105023, intron 3 of 5)	intron (NR_105023, intron 3 of 5)	-3834	NM_010258	14465	Mm.329287	NM_010258	ENSMUSG00000005836	Gata6	AA410133|GATA-6	GATA binding protein 6	protein-coding
mm_72123.1	chr8	71690219	71690229	+	1	NA	exon (NM_013564, exon 2 of 2)	exon (NM_013564, exon 2 of 2)	972	NM_013564	16336	Mm.476857	NM_013564	ENSMUSG00000079019	Insl3	Rlf|Rlnl	insulin-like 3	protein-coding
mm_172488.1	chr7	53805850	53805851	-	1	NA	Intergenic	RLTR10D2|LTR|ERVK	86039	NR_105746	102466619		NR_105746	ENSMUSG00000099176	Mir6238	Gm27982|mmu-mir-6238	microRNA 6238	ncRNA
mm_55714.1	chr6	73138948	73138951	-	1	NA	intron (NM_001164669, intron 30 of 76)	intron (NM_001164669, intron 30 of 76)	82682	NM_001164669	330355	Mm.333166	NM_001164669	ENSMUSG00000052861	Dnah6	9830168K20|A730004I20Rik|Dnahc6|mKIAA1697|mdhc6	dynein, axonemal, heavy chain 6	protein-coding
mm_5929.1	chr1	55248679	55248683	-	1	NA	Intergenic	Intergenic	11504	NM_175439	212679	Mm.19223	NM_175439	ENSMUSG00000046994	Mars2	C730026E21Rik|MetRS	methionine-tRNA synthetase 2 (mitochondrial)	protein-coding
mm_117452.1	chr13	74808560	74808572	-	1	NA	promoter-TSS (NM_009817)	promoter-TSS (NM_009817)	194	NM_001301153	12380	Mm.29163	NM_009817	ENSMUSG00000021585	Cast	-	calpastatin	protein-coding
mm_117178.1	chr13	63325018	63325021	-	1	NA	non-coding (NR_110521, exon 6 of 6)	non-coding (NR_110521, exon 6 of 6)	-23736	NR_037235	100526474		NR_037235	ENSMUSG00000092741	Mir3074-1	mmu-mir-3074-1	microRNA 3074-1	ncRNA
mm_71720.1	chr8	61952011	61952047	+	1	NA	intron (NM_001293783, intron 8 of 37)	intron (NM_001293783, intron 8 of 37)	23942	NM_001293783	234311	Mm.275233	NM_144928	ENSMUSG00000037921	Ddx60	9830118M07	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	protein-coding
mm_141700.1	chr17	33996489	33996499	-	1	NA	exon (NM_001001892, exon 8 of 8)	exon (NM_001001892, exon 8 of 8)	3839	NM_001001892	14972	Mm.422886	NM_001001892	ENSMUSG00000061232	H2-K1	H-2K|H-2K(d)|H2-K|K-f	histocompatibility 2, K1, K region	protein-coding
mm_157152.1	chrX	9462763	9462795	-	1	NA	intron (NM_007807, intron 3 of 12)	intron (NM_007807, intron 3 of 12)	6545	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_156815.1	chrX	164120018	164120020	+	1	NA	Intergenic	BC1_Mm|scRNA|scRNA	-19323	NM_001130513	70008	Mm.13451	NM_027286	ENSMUSG00000015405	Ace2	2010305L05Rik	angiotensin I converting enzyme (peptidyl-dipeptidase A) 2	protein-coding
mm_126583.1	chr15	82293937	82293975	+	1	NA	3' UTR (NM_011889, exon 10 of 10)	3' UTR (NM_011889, exon 10 of 10)	-5028	NM_029066	74716	Mm.159315	NM_029066	ENSMUSG00000022455	Wbp2nl	4930521I23Rik|PAWP	WBP2 N-terminal like	protein-coding
mm_29915.1	chr3	131489748	131489757	-	1	NA	Intergenic	Intergenic	-75016	NM_001289479	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_13960.1	chr2	121363662	121363670	+	1	NA	TTS (NM_080459)	TTS (NM_080459)	5025	NM_009897	12716	Mm.252145	NM_009897	ENSMUSG00000000308	Ckmt1	Mt-CK|ScCKmit|UbCKmit|mi-CK	creatine kinase, mitochondrial 1, ubiquitous	protein-coding
mm_111876.1	chr12	108003643	108003663	-	1	NA	promoter-TSS (NM_021399)	promoter-TSS (NM_021399)	-239	NM_021399	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_91716.1	chr10	44458570	44458584	-	1	NA	5' UTR (NM_007548, exon 1 of 7)	5' UTR (NM_007548, exon 1 of 7)	171	NM_007548	12142	Mm.4800	NM_007548	ENSMUSG00000038151	Prdm1	Blimp-1|Blimp1|PRDI-BF1|ZNFPR1A1|b2b1765Clo	PR domain containing 1, with ZNF domain	protein-coding
mm_162842.1	chr10	85927979	85927981	+	1	NA	promoter-TSS (NM_001163614)	promoter-TSS (NM_001163614)	-511	NM_001163614	67341	Mm.382315	NM_001163614	ENSMUSG00000085111	Ascl4	1700054F16Rik|bHLHa44	achaete-scute family bHLH transcription factor 4	protein-coding
mm_68057.1	chr7	101837777	101837832	-	1	NA	promoter-TSS (NM_001122739)	promoter-TSS (NM_001122739)	20	NM_001122739	16332	Mm.476000	NM_010567	ENSMUSG00000032737	Inppl1	51C|SHIP2	inositol polyphosphate phosphatase-like 1	protein-coding
mm_33195.1	chr4	126273959	126273968	+	1	NA	exon (NM_013718, exon 4 of 5)	exon (NM_013718, exon 4 of 5)	11558	NM_013718	27096	Mm.8392	NM_013718	ENSMUSG00000028847	Trappc3	1110058K12Rik|AI835942|AU019197|Bet3	trafficking protein particle complex 3	protein-coding
mm_89032.1	chr10	82707960	82707964	+	1	NA	intron (NM_001081218, intron 3 of 14)	ID_B1|SINE|B4	8955	NM_001081218	67933	Mm.127405	NM_026462	ENSMUSG00000020246	Hcfc2	1700129L13Rik|AU019838	host cell factor C2	protein-coding
mm_119258.1	chr14	33941073	33941084	+	1	NA	promoter-TSS (NM_019506)	promoter-TSS (NM_019506)	39	NM_019506	12165	Mm.422844	NM_019506	ENSMUSG00000072625	Gdf2	Bmp9	growth differentiation factor 2	protein-coding
mm_4069.1	chr1	166130469	166130479	+	1	NA	promoter-TSS (NM_021610)	promoter-TSS (NM_021610)	14	NM_021610	59290	Mm.46357	NM_021610	ENSMUSG00000000544	Gpa33	2010310L10Rik|2210401D16Rik|BB116197	glycoprotein A33 (transmembrane)	protein-coding
mm_24823.1	chr3	95650919	95650937	+	1	NA	Intergenic	Intergenic	-7793	NM_008562	17210	Mm.1639	NM_008562	ENSMUSG00000038612	Mcl1	AW556805|Mcl-1	myeloid cell leukemia sequence 1	protein-coding
mm_114244.1	chr13	56625723	56625763	+	1	NA	exon (NM_009369, exon 5 of 17)	exon (NM_009369, exon 5 of 17)	16140	NM_009369	21810	Mm.14455	NM_009369	ENSMUSG00000035493	Tgfbi	68kDa|AI181842|AI747162|Beta-ig|big-h3	transforming growth factor, beta induced	protein-coding
mm_59174.1	chr7	24445791	24445797	+	1	NA	promoter-TSS (NM_199013)	promoter-TSS (NM_199013)	-112	NM_199013	210145	Mm.33811	NM_199013	ENSMUSG00000062028	Irgc1	F630044M05Rik|Gm1102|Gm474|Ifgge|Iigp5|Irgc	immunity-related GTPase family, cinema 1	protein-coding
mm_29931.1	chr3	131491438	131491448	-	1	NA	Intergenic	Intergenic	-73325	NM_001289479	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_93137.1	chr10	92163032	92163040	-	1	NA	intron (NR_028262, intron 2 of 12)	intron (NR_028262, intron 2 of 12)	2142	NR_028262	110333	Mm.429764	NR_028262		Rmst	100041799|AI853140|C230053E11Rik|D930049J19Rik|Dmt2|Gm3515|M2|Ncrms	rhabdomyosarcoma 2 associated transcript (non-coding RNA)	ncRNA
mm_67447.1	chr7	80391224	80391243	-	1	NA	exon (NM_001081454, exon 16 of 16)	exon (NM_001081454, exon 16 of 16)	-3287	NM_010194	14159	Mm.48757	NM_010194	ENSMUSG00000053158	Fes	AI586313|BB137047|FPS|c-fes	feline sarcoma oncogene	protein-coding
mm_20807.1	chr2	144331356	144331367	-	1	NA	promoter-TSS (NM_152947)	promoter-TSS (NM_152947)	1	NM_152947	107586	Mm.252750	NM_026924	ENSMUSG00000037279	Ovol2	1700108N11Rik|1810007D21Rik|M-OVO|M-OVO-A|M-OVO-B|MOVO|Ovo2|Zfp339|movo2	ovo like zinc finger 2	protein-coding
mm_54728.1	chr6	40585784	40585811	-	1	NA	promoter-TSS (NM_021364)	promoter-TSS (NM_021364)	8	NM_021364	23845	Mm.103765	NM_021364	ENSMUSG00000029915	Clec5a	Clecsf5|Ly100|MDL-1|Mdl1	C-type lectin domain family 5, member a	protein-coding
mm_11030.1	chr2	26912850	26912851	+	1	NA	TTS (NM_013677)	TTS (NM_013677)	2043	NM_013721	27176	Mm.328601	NM_013721	ENSMUSG00000062647	Rpl7a	Surf3	ribosomal protein L7A	protein-coding
mm_169987.1	chr17	15041611	15041630	+	1	NA	promoter-TSS (NM_001039552)	promoter-TSS (NM_001039552)	8	NM_001039552	381062	Mm.393767	NM_183133	ENSMUSG00000036552	Ermard	2210404J11Rik|2410011O22Rik|AI448938	ER membrane associated RNA degradation	protein-coding
mm_133037.1	chr16	57353272	57353284	+	1	NA	promoter-TSS (NM_001040397)	promoter-TSS (NM_001040397)	1	NM_001040397	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding
mm_21424.1	chr2	158211786	158211794	-	1	NA	intron (NM_001131021, intron 5 of 15)	intron (NM_001131021, intron 5 of 15)	17434	NM_001131021	228846	Mm.187574	NM_177657	ENSMUSG00000037813	D630003M21Rik	-	RIKEN cDNA D630003M21 gene	protein-coding
mm_70331.1	chr8	4493421	4493435	+	1	NA	promoter-TSS (NM_026058)	promoter-TSS (NM_026058)	23	NM_026058	67260	Mm.35511	NM_026058	ENSMUSG00000008206	Cers4	2900019C14Rik|Lass4|Trh1	ceramide synthase 4	protein-coding
mm_14676.1	chr2	139546018	139546020	+	1	NA	intron (NM_175467, intron 3 of 12)	ID_B1|SINE|B4	52099	NM_175467	228677	Mm.100450	NM_175467	ENSMUSG00000039092	Sptlc3	C130053K05Rik	serine palmitoyltransferase, long chain base subunit 3	protein-coding
mm_8321.1	chr1	144954801	144954801	-	1	NA	Intergenic	Intergenic	-179380	NM_022881	64214	Mm.253927	NM_022881	ENSMUSG00000026357	Rgs18	-	regulator of G-protein signaling 18	protein-coding
mm_109775.1	chr12	118851240	118851241	+	1	NA	3' UTR (NM_177082, exon 3 of 3)	3' UTR (NM_177082, exon 3 of 3)	4911	NM_177082	320145	Mm.51682	NM_177082	ENSMUSG00000048562	Sp8	D930049B17Rik|mBtd	trans-acting transcription factor 8	protein-coding
mm_129605.1	chr15	79893118	79893137	-	1	NA	promoter-TSS (NR_030675)	promoter-TSS (NR_030675)	11	NR_030675	109361	Mm.394656	NR_030675		D730005E14Rik	-	RIKEN cDNA D730005E14 gene	ncRNA
mm_87667.1	chr10	58696726	58696754	+	1	NA	promoter-TSS (NR_033565)	promoter-TSS (NR_033565)	-5	NR_033565	103505	Mm.50261	NR_033565		BB019430	-	expressed sequence BB019430	ncRNA
mm_23710.1	chr3	68869564	68869589	+	1	NA	promoter-TSS (NM_001167996)	promoter-TSS (NM_001167996)	-10	NM_001167996	68725	Mm.45741	NM_001167996	ENSMUSG00000046999	1110032F04Rik	AI115547	RIKEN cDNA 1110032F04 gene	protein-coding
mm_39676.1	chr5	25529830	25529873	+	1	NA	promoter-TSS (NR_027388)	promoter-TSS (NR_027388)	-167	NR_027388	73571	Mm.105263	NR_027388	ENSMUSG00000101856	1700096K18Rik	-	RIKEN cDNA 1700096K18 gene	ncRNA
mm_61981.1	chr7	90954725	90954751	+	1	NA	Intergenic	Intergenic	-136048	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_25175.1	chr3	103171715	103171725	+	1	NA	promoter-TSS (NM_026602)	promoter-TSS (NM_026602)	9	NM_026602	68183	Mm.104919	NM_026602	ENSMUSG00000005687	Bcas2	6430539P16Rik|AI132645|C76366|C80030	breast carcinoma amplified sequence 2	protein-coding
mm_84122.1	chr9	58556140	58556155	-	1	NA	Intergenic	Intergenic	-15207	NM_133983	102657	Mm.5356	NM_133983	ENSMUSG00000035914	Cd276	6030411F23Rik|AU016588|B7RP-2|B7h3	CD276 antigen	protein-coding
mm_82255.1	chr9	4796161	4796195	-	1	NA	promoter-TSS (NM_001113181)	promoter-TSS (NM_001113181)	56	NM_001113180	14802	Mm.209263	NM_019691	ENSMUSG00000025892	Gria4	GluA4|GluR-D|Glur-4|Glur4|Gluralpha4|spkw1	glutamate receptor, ionotropic, AMPA4 (alpha 4)	protein-coding
mm_81025.1	chr9	104566696	104566706	+	1	NA	Intergenic	Intergenic	-3087	NM_028719	74020	Mm.326240	NM_028719	ENSMUSG00000032564	Cpne4	3632411M23Rik|4933406O10Rik	copine IV	protein-coding
mm_87278.1	chr10	41893968	41893978	+	1	NA	intron (NM_001013370, intron 1 of 9)	intron (NM_001013370, intron 1 of 9)	6534	NM_001013370	140742	Mm.139418	NM_001013370	ENSMUSG00000038332	Sesn1	1110002G11Rik|AU044290|Pa26|Sest1	sestrin 1	protein-coding
mm_126939.1	chr15	91899375	91899384	+	1	NA	exon (NM_207243, exon 27 of 44)	exon (NM_207243, exon 27 of 44)	61051	NM_198927	223809	Mm.486225	NM_198927	ENSMUSG00000047295	Smgc	2310010P21Rik|DXImx49e|Muc19|Muc19/Smgc|Sfc21	submandibular gland protein C	protein-coding
mm_15784.1	chr2	164403203	164403219	+	1	NA	promoter-TSS (NM_009036)	promoter-TSS (NM_009036)	17	NM_009036	19668	Mm.473794	NM_009036	ENSMUSG00000017007	Rbpjl	RBP-L|Rbpsuhl	recombination signal binding protein for immunoglobulin kappa J region-like	protein-coding
mm_65462.1	chr7	25471921	25471971	-	1	NA	exon (NM_001039186, exon 5 of 8)	exon (NM_001039186, exon 5 of 8)	5679	NM_001039185	26365	Mm.322502	NM_011926	ENSMUSG00000074272	Ceacam1	Bgp|Bgp1|C-CAM|CD66a|Cc1|Cea-1|Cea-7|Cea1|Cea7|Hv-2|Hv2|MHVR|MHVR1|Mhv-1|bb-1|mCEA1|mmCGM1|mmCGM1a|mmCGM2	carcinoembryonic antigen-related cell adhesion molecule 1	protein-coding
mm_163447.1	chr12	87109326	87109330	+	1	NA	intron (NM_153415, intron 20 of 20)	intron (NM_153415, intron 20 of 20)	-6789	NM_001294308	64242	Mm.41395	NM_022414	ENSMUSG00000021032	Ngb	-	neuroglobin	protein-coding
mm_111455.1	chr12	98385931	98385934	-	1	NA	Intergenic	Intergenic	117297	NM_008152	14744	Mm.378924	NM_008152	ENSMUSG00000021886	Gpr65	Dig1|Gpcr25|TDAG8	G-protein coupled receptor 65	protein-coding
mm_55889.1	chr6	83536028	83536034	-	1	NA	intron (NM_009610, intron 1 of 8)	intron (NM_009610, intron 1 of 8)	220	NM_009610	11468	Mm.292865	NM_009610	ENSMUSG00000059430	Actg2	ACTA3|Act-4|Act4|SMGA	actin, gamma 2, smooth muscle, enteric	protein-coding
mm_79817.1	chr9	64321699	64321708	+	1	NA	intron (NM_001001295, intron 7 of 16)	L2|LINE|L2	18754	NM_172519	213550	Mm.268341	NM_172519	ENSMUSG00000032396	Dis3l	AV340375	DIS3 like exosome 3'-5' exoribonuclease	protein-coding
mm_133579.1	chr16	91407056	91407075	+	1	NA	intron (NM_008349, intron 1 of 6)	intron (NM_008349, intron 1 of 6)	830	NM_008349	16155	Mm.4154	NM_008349	ENSMUSG00000022969	Il10rb	6620401D04Rik|AI528744|CRF2-4|Crfb4|D16H21S58|D21S58h|IL-10R2|Il10r2	interleukin 10 receptor, beta	protein-coding
mm_56559.1	chr6	101256826	101256826	-	1	NA	intron (NM_018884, intron 3 of 9)	ID_B1|SINE|B4	121071	NM_018884	55983	Mm.321654	NM_018884	ENSMUSG00000035357	Pdzrn3	1110020C07Rik|AI429718|AL023082|LNX3|SEMACAP3|Semcap3	PDZ domain containing RING finger 3	protein-coding
mm_140496.1	chr17	3557786	3557797	-	1	NA	promoter-TSS (NR_045303)	promoter-TSS (NR_045303)	-33	NR_045303	68230	Mm.431352	NR_045302		1700102H20Rik	-	RIKEN cDNA 1700102H20 gene	ncRNA
mm_163115.1	chr11	73085290	73085297	+	1	NA	Intergenic	Intergenic	-5302	NM_172944	16407	Mm.96	NM_008399	ENSMUSG00000005947	Itgae	A530055J10|CD103|aM290|alpha-E1|alpha-M290	integrin alpha E, epithelial-associated	protein-coding
mm_93332.1	chr10	99461581	99461605	-	1	NA	Intergenic	Intergenic	-147578	NR_038019	100504202	Mm.403801	NR_038019		Gm20110	-	predicted gene, 20110	ncRNA
mm_33317.1	chr4	129080495	129080506	+	1	NA	exon (NM_029219, exon 7 of 9)	exon (NM_029219, exon 7 of 9)	22229	NM_029219	75234	Mm.259672	NM_029219	ENSMUSG00000028793	Rnf19b	4930534K13Rik|4930555L03Rik|Ibrdc3	ring finger protein 19B	protein-coding
mm_72646.1	chr8	84708626	84708645	+	1	NA	3' UTR (NM_010906, exon 9 of 9)	3' UTR (NM_010906, exon 9 of 9)	7178	NM_008535	17095	Mm.4925	NM_008535	ENSMUSG00000034041	Lyl1	Lyl-1|bHLHa18	lymphoblastomic leukemia 1	protein-coding
mm_55640.1	chr6	72345122	72345132	-	1	NA	promoter-TSS (NM_138592)	promoter-TSS (NM_138592)	48	NM_138592	28035	Mm.281900	NM_138592	ENSMUSG00000056305	Usp39	AA408960|AI894154|CGI-21|D6Wsu157e|SAD1	ubiquitin specific peptidase 39	protein-coding
mm_146553.1	chr18	6222828	6222866	-	1	NA	exon (NM_008448, exon 11 of 26)	exon (NM_008448, exon 11 of 26)	18677	NM_008448	16573	Mm.223744	NM_008448	ENSMUSG00000006740	Kif5b	AL022807|Khc|Khcs|Kns1|Ukhc	kinesin family member 5B	protein-coding
mm_90317.1	chr10	127063600	127063655	+	1	NA	promoter-TSS (NM_009870)	promoter-TSS (NM_009870)	24	NM_009870	12567	Mm.6839	NM_009870	ENSMUSG00000006728	Cdk4	Crk3	cyclin-dependent kinase 4	protein-coding
mm_13911.1	chr2	120501308	120501335	+	1	NA	exon (NM_007601, exon 16 of 24)	exon (NM_007601, exon 16 of 24)	24412	NM_001109761	12335	Mm.458021	NM_007601	ENSMUSG00000079110	Capn3	AI323605|Capa-3|Capa3|Lp82|p94	calpain 3	protein-coding
mm_145350.1	chr18	56503877	56503901	+	1	NA	TTS (NM_026240)	TTS (NM_026240)	-34250	NR_106160	102465790		NR_106160	ENSMUSG00000099196	Mir1258	Gm27371|mmu-mir-1258	microRNA 1258	ncRNA
mm_127735.1	chr15	103297881	103297900	+	1	NA	exon (NM_019817, exon 8 of 9)	exon (NM_019817, exon 8 of 9)	12548	NM_030720	80910	Mm.160369	NM_030720	ENSMUSG00000063234	Gpr84	EX33	G protein-coupled receptor 84	protein-coding
mm_109625.1	chr12	112766777	112766795	+	1	NA	exon (NM_178911, exon 7 of 11)	exon (NM_178911, exon 7 of 11)	6131	NM_178911	104759	Mm.203915	NM_178911	ENSMUSG00000052160	Pld4	AI132321|thss	phospholipase D family, member 4	protein-coding
mm_32610.1	chr4	112232267	112232274	+	1	NA	promoter-TSS (NM_177578)	promoter-TSS (NM_177578)	25	NM_177578	195564	Mm.259652	NM_177578	ENSMUSG00000070868	Skint3	A430090E18Rik|Skint-3	selection and upkeep of intraepithelial T cells 3	protein-coding
mm_148757.1	chr19	6061177	6061235	+	1	NA	promoter-TSS (NM_013859)	promoter-TSS (NM_013859)	-1	NM_013859	29805	Mm.2310	NM_013859	ENSMUSG00000075227	Znhit2	C11orf5|Fon|ORF6|Znhit2-ps	zinc finger, HIT domain containing 2	protein-coding
mm_925.1	chr1	55204904	55204912	+	1	NA	intron (NM_028713, intron 4 of 8)	intron (NM_028713, intron 4 of 8)	21874	NM_028713	74013	Mm.292050	NM_028713	ENSMUSG00000025978	Rftn2	2700010E02Rik|3222401M22Rik	raftlin family member 2	protein-coding
mm_132715.1	chr16	43507066	43507075	+	1	NA	intron (NM_181058, intron 3 of 6)	intron (NM_181058, intron 3 of 6)	-86874	NR_046026	626693	Mm.447083	NR_046026	ENSMUSG00000085499	Gm15713	OTTMUSG00000025617	predicted gene 15713	ncRNA
mm_135008.1	chr16	32247153	32247179	-	1	NA	promoter-TSS (NM_026898)	promoter-TSS (NM_026898)	-61	NM_001185162	68980	Mm.159860	NM_026898	ENSMUSG00000022787	Wdr53	1500002B03Rik|AI848860	WD repeat domain 53	protein-coding
mm_56989.1	chr6	120822681	120822707	-	1	NA	promoter-TSS (NM_007510)	promoter-TSS (NM_007510)	-9	NM_007510	11973	Mm.29045	NM_007510	ENSMUSG00000019210	Atp6v1e1	2410029D23Rik|Atp6e|Atp6e2|Atp6v1e|D6Ertd385e|E2|P31|Vma4	ATPase, H+ transporting, lysosomal V1 subunit E1	protein-coding
mm_6509.1	chr1	74304387	74304407	-	1	NA	promoter-TSS (NM_027154)	promoter-TSS (NM_027154)	-61	NM_027154	69660	Mm.261182	NM_027154	ENSMUSG00000006301	Tmbim1	2310061B02Rik|AA960455|AU024746|C78899|RECS1|Tmbib1|mKIAA4161	transmembrane BAX inhibitor motif containing 1	protein-coding
mm_148244.1	chr18	80673857	80673860	-	1	NA	intron (NM_198429, intron 3 of 9)	intron (NM_198429, intron 3 of 9)	34315	NM_001164111	18018	Mm.329560	NM_016791	ENSMUSG00000033016	Nfatc1	2210017P03Rik|AI449492|AV076380|NF-ATc|NFAT2|NFATc|Nfatcb	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 1	protein-coding
mm_17590.1	chr2	30556583	30556617	-	1	NA	Intergenic	Intergenic	-38444	NM_030137	78617	Mm.40413	NM_030137	ENSMUSG00000047363	Cstad	9530039B02Rik	CSA-conditional, T cell activation-dependent protein	protein-coding
mm_113584.1	chr13	40886938	40886944	+	1	NA	5' UTR (NM_008105, exon 1 of 3)	5' UTR (NM_008105, exon 1 of 3)	183	NM_008105	14538	Mm.314757	NM_008105	ENSMUSG00000021360	Gcnt2	5330430K10Rik|IGnT|IGnTA|IGnTB|IGnTC	glucosaminyl (N-acetyl) transferase 2, I-branching enzyme	protein-coding
mm_25713.1	chr3	122690755	122690755	+	1	NA	Intergenic	Intergenic	-38403	NM_153422	242202	Mm.134911	NM_153422	ENSMUSG00000053965	Pde5a	Cgbpde|Cn5n|PDE5a2|Pde5|Pde5a1	phosphodiesterase 5A, cGMP-specific	protein-coding
mm_43911.1	chr5	144256137	144256154	+	1	NA	intron (NM_018772, intron 2 of 2)	intron (NM_018772, intron 2 of 2)	920	NM_018772	55950	Mm.38011	NM_018772	ENSMUSG00000047843	Bri3	I3	brain protein I3	protein-coding
mm_19233.1	chr2	84710869	84710883	-	1	NA	5' UTR (NM_144887, exon 2 of 12)	5' UTR (NM_144887, exon 2 of 12)	4288	NM_144887	228136	Mm.288508	NM_144887	ENSMUSG00000034075	Zdhhc5	1110032A17Rik|AI451382|Zisp	zinc finger, DHHC domain containing 5	protein-coding
mm_121287.1	chr14	105258687	105258697	+	1	NA	promoter-TSS (NM_029561)	promoter-TSS (NM_029561)	19	NM_001190989	76273	Mm.290669	NM_029561	ENSMUSG00000053253	Ndfip2	0710001O20Rik|2810436B12Rik|9130207N19Rik|N4wbp5a|mKIAA1165	Nedd4 family interacting protein 2	protein-coding
mm_23303.1	chr3	52648149	52648151	+	1	NA	Intergenic	Intergenic	-91574	NR_038079	329639	Mm.131245	NR_038079	ENSMUSG00000102785	Gm2447	100039832|A530017F20	predicted gene 2447	ncRNA
mm_150359.1	chr19	34649142	34649157	+	1	NA	3' UTR (NM_008331, exon 2 of 2)	3' UTR (NM_008331, exon 2 of 2)	8260	NM_008331	15957	Mm.439751	NM_008331	ENSMUSG00000034459	Ifit1	ISG56|Ifi56|P56	interferon-induced protein with tetratricopeptide repeats 1	protein-coding
mm_35676.1	chr4	43653561	43653583	-	1	NA	promoter-TSS (NM_001290462)	promoter-TSS (NM_001290462)	22	NM_001290462	433700	Mm.331569	NM_001007463	ENSMUSG00000066196	Spag8	MH-SPAG8|SMP-1	sperm associated antigen 8	protein-coding
mm_11456.1	chr2	32163038	32163045	+	1	NA	intron (NM_172661, intron 1 of 29)	intron (NM_172661, intron 1 of 29)	11893	NM_001159634	227723	Mm.25504	NM_172661	ENSMUSG00000039262	Prrc2b	5830434P21Rik|AI173903|Bat2l|Bat2l1|D430039P21|mKIAA0515	proline-rich coiled-coil 2B	protein-coding
mm_90502.1	chr10	128035626	128035635	+	1	NA	5' UTR (NM_013608, exon 1 of 8)	5' UTR (NM_013608, exon 1 of 8)	284	NM_001113199	17938	Mm.3746	NM_013608	ENSMUSG00000061315	Naca	AL022831|AL024382|Gm1878|mKIAA0363|skNAC	nascent polypeptide-associated complex alpha polypeptide	protein-coding
mm_45232.1	chr5	53594231	53594241	-	1	NA	intron (NM_001080927, intron 1 of 10)	PB1D10|SINE|Alu	3750	NM_001080927	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_37330.1	chr4	119540014	119540014	-	1	NA	intron (NM_172699, intron 1 of 12)	CpG	353	NM_172699	230700	Mm.259227	NM_172699	ENSMUSG00000032998	Foxj3	C330039G02Rik|Fhd6	forkhead box J3	protein-coding
mm_152389.1	chr19	10462308	10462312	-	1	NA	Intergenic	Intergenic	-4863	NM_001111140	278795	Mm.490638	NM_001111140	ENSMUSG00000090291	Lrrc10b	Gm705|SerdinR	leucine rich repeat containing 10B	protein-coding
mm_66157.1	chr7	31151391	31151414	-	1	NA	promoter-TSS (NM_027898)	promoter-TSS (NM_027898)	-352	NM_027898	52857	Mm.27366	NM_027898	ENSMUSG00000001248	Gramd1a	1300003M23Rik|AI415002|AW547240|D7Bwg0611e	GRAM domain containing 1A	protein-coding
mm_36337.1	chr4	72199072	72199108	-	1	NA	intron (NM_001285530, intron 2 of 17)	intron (NM_001285530, intron 2 of 17)	1803	NM_011599	21885	Mm.278444	NM_011599	ENSMUSG00000008305	Tle1	C230057C06Rik|Estm14|Grg-1|Grg1|Tle4l	transducin-like enhancer of split 1	protein-coding
mm_14109.1	chr2	125791696	125791706	+	1	NA	Intergenic	Intergenic	-8831	NM_177608	70354	Mm.138091	NM_133725	ENSMUSG00000035093	Secisbp2l	3110001I20Rik|AI504340|C630011I23	SECIS binding protein 2-like	protein-coding
mm_57007.1	chr6	121110103	121110171	-	1	NA	intron (NM_001270475, intron 1 of 31)	(CGG)n|Simple_repeat|Simple_repeat	20885	NM_001270475	194401	Mm.122399	NM_153396	ENSMUSG00000051586	Mical3	C130040D16Rik|Mical-3|mKIAA1364	microtubule associated monooxygenase, calponin and LIM domain containing 3	protein-coding
mm_129773.1	chr15	82791084	82791093	-	1	NA	exon (NM_029562, exon 7 of 9)	exon (NM_029562, exon 7 of 9)	3157	NM_029562	76279	Mm.439931	NM_029562	ENSMUSG00000022445	Cyp2d26	1300006E06Rik	cytochrome P450, family 2, subfamily d, polypeptide 26	protein-coding
mm_153437.1	chr19	40977077	40977088	-	1	NA	intron (NM_008528, intron 1 of 16)	RLTR21|LTR|ERVK	17453	NM_008528	17060	Mm.9749	NM_008528	ENSMUSG00000061132	Blnk	BASH|Bca|Ly-57|Ly57|Lyw-57|SLP-65	B cell linker	protein-coding
mm_55334.1	chr6	56362109	56362125	-	1	NA	5' UTR (NM_001159953, exon 1 of 19)	5' UTR (NM_001159953, exon 1 of 19)	275	NM_001159952	18575	Mm.5145	NM_011054	ENSMUSG00000004347	Pde1c	-	phosphodiesterase 1C	protein-coding
mm_165462.1	chr2	160364883	160364895	-	1	NA	3' UTR (NM_010658, exon 1 of 1)	3' UTR (NM_010658, exon 1 of 1)	2176	NM_010658	16658	Mm.330745	NM_010658	ENSMUSG00000074622	Mafb	Kreisler|Krml|Krml1|kr	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein B (avian)	protein-coding
mm_145088.1	chr18	42519081	42519087	+	1	NA	intron (NR_110344, intron 1 of 22)	intron (NR_110344, intron 1 of 22)	7597	NR_110344	56070	Mm.270511	NM_001039474	ENSMUSG00000024498	Tcerg1	2410022J09Rik|2900090C16Rik|AI428505|CA150b|FBP23|FBP28|Taf2s|ca150|p144	transcription elongation regulator 1 (CA150)	protein-coding
mm_102502.1	chr11	60695876	60695890	-	1	NA	Intergenic	MT2C_Mm|LTR|ERVL	-3807	NM_001159405	16897	Mm.285453	NM_008502	ENSMUSG00000020536	Llgl1	AI325176|Lgl1|Llglh|Mgl1	lethal giant larvae homolog 1 (Drosophila)	protein-coding
mm_146926.1	chr18	31949715	31949742	-	1	NA	promoter-TSS (NM_001025381)	promoter-TSS (NM_001025381)	-92	NM_001025381	574402	Mm.391108	NM_001025381	ENSMUSG00000052229	Gpr17	AI853548	G protein-coupled receptor 17	protein-coding
mm_57155.1	chr6	122732402	122732422	-	1	NA	exon (NM_011401, exon 8 of 10)	exon (NM_011401, exon 8 of 10)	10333	NM_011401	20527	Mm.395108	NM_011401	ENSMUSG00000003153	Slc2a3	AA408729|AL023014|AL024341|AU040424|C78366|Glut-3|Glut3	solute carrier family 2 (facilitated glucose transporter), member 3	protein-coding
mm_41497.1	chr5	92323838	92323846	+	1	NA	exon (NM_008599, exon 4 of 4)	exon (NM_008599, exon 4 of 4)	4237	NM_008599	17329	Mm.766	NM_008599	ENSMUSG00000029417	Cxcl9	BB139920|CMK|Mig|MuMIG|Scyb9|crg-10	chemokine (C-X-C motif) ligand 9	protein-coding
mm_106458.1	chr11	120020235	120020237	-	1	NA	intron (NM_001198787, intron 2 of 13)	intron (NM_001198787, intron 2 of 13)	-5374	NR_029767	723844		NR_029767	ENSMUSG00000065600	Mir338	Mirn338|mir-338|mmu-mir-338	microRNA 338	ncRNA
mm_114726.1	chr13	83715353	83715361	+	1	NA	Intergenic	Intergenic	-12749	NR_015561	320203	Mm.245636	NM_177100	ENSMUSG00000050334	C130071C03Rik	2810449C10Rik	RIKEN cDNA C130071C03 gene	ncRNA
mm_35569.1	chr4	41640354	41640364	-	1	NA	promoter-TSS (NM_027147)	promoter-TSS (NM_027147)	-57	NM_027147	69638	Mm.372459	NM_027147	ENSMUSG00000028445	Enho	1110065P19Rik|2310040A07Rik	energy homeostasis associated	protein-coding
mm_95422.1	chr11	50132003	50132029	+	1	NA	intron (NM_001290760, intron 1 of 21)	intron (NM_001290760, intron 1 of 21)	656	NM_029745	76795	Mm.290975	NM_029745	ENSMUSG00000036644	Tbc1d9b	-	TBC1 domain family, member 9B	protein-coding
mm_161443.1	chr15	73596421	73596421	-	1	NA	5' UTR (NM_001168255, exon 1 of 7)	5' UTR (NM_001168255, exon 1 of 7)	105	NM_001168255	106068	Mm.212813	NM_001033219	ENSMUSG00000079020	Slc45a4	9330175B01Rik|AW552276	solute carrier family 45, member 4	protein-coding
mm_73143.1	chr8	94984350	94984361	+	1	NA	promoter-TSS (NM_018882)	promoter-TSS (NM_018882)	-44	NM_018882	14766	Mm.290834	NM_018882	ENSMUSG00000031785	Adgrg1	Cyt28|Gpr56|TM7LN4|TM7XN1	adhesion G protein-coupled receptor G1	protein-coding
mm_17476.1	chr2	28560659	28560679	-	1	NA	exon (NM_009885, exon 4 of 11)	exon (NM_009885, exon 4 of 11)	2734	NM_009885	12613	Mm.236017	NM_009885	ENSMUSG00000026818	Cel	1810036E18Rik|BAL	carboxyl ester lipase	protein-coding
mm_163977.1	chr14	55765707	55765709	-	1	NA	promoter-TSS (NM_008519)	promoter-TSS (NM_008519)	-254	NM_008519	16995	Mm.20853	NM_008519	ENSMUSG00000046908	Ltb4r1	BLT1|BLTR|Ltb4r|mBLTR	leukotriene B4 receptor 1	protein-coding
mm_49928.1	chr6	39381387	39381411	+	1	NA	promoter-TSS (NM_011226)	promoter-TSS (NM_011226)	-29	NM_011226	19331	Mm.123866	NM_011226	ENSMUSG00000029923	Rab19	-	RAB19, member RAS oncogene family	protein-coding
mm_48270.1	chr5	137962956	137962967	-	1	NA	promoter-TSS (NM_080450)	promoter-TSS (NM_080450)	-2	NM_080450	118446	Mm.332771	NM_080450	ENSMUSG00000056966	Gjc3	Cx29|Gje1	gap junction protein, gamma 3	protein-coding
mm_22971.1	chr3	32708746	32708756	+	1	NA	5' UTR (NM_019673, exon 1 of 14)	5' UTR (NM_019673, exon 1 of 14)	205	NM_019673	56456	Mm.41077	NM_019673	ENSMUSG00000027671	Actl6a	2810432C06Rik|AI851094|ARP4|Actl6|Baf53a|C79802	actin-like 6A	protein-coding
mm_59609.1	chr7	28142414	28142422	+	1	NA	exon (NM_001164655, exon 6 of 20)	exon (NM_001164655, exon 6 of 20)	12952	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_20412.1	chr2	129300246	129300262	-	1	NA	3' UTR (NM_010554, exon 7 of 7)	3' UTR (NM_010554, exon 7 of 7)	2884	NR_040371	100503468	Mm.446943	NR_040371	ENSMUSG00000085498	Gm14023	OTTMUSG00000015408	predicted gene 14023	ncRNA
mm_117682.1	chr13	94245574	94245585	-	1	NA	intron (NM_001346609, intron 2 of 8)	intron (NM_001346609, intron 2 of 8)	39702	NM_029153	107767	Mm.201455	NM_029153	ENSMUSG00000021687	Scamp1	4930505M11Rik|AI415563|AW122395	secretory carrier membrane protein 1	protein-coding
mm_12865.1	chr2	83812568	83812643	+	1	NA	promoter-TSS (NM_175514)	promoter-TSS (NM_175514)	-123	NM_175514	241520	Mm.330351	NM_175514	ENSMUSG00000048388	Fam171b	D430039N05Rik	family with sequence similarity 171, member B	protein-coding
mm_77885.1	chr9	7282316	7282336	+	1	NA	3' UTR (NM_008607, exon 10 of 10)	3' UTR (NM_008607, exon 10 of 10)	9812	NM_008607	17386	Mm.5022	NM_008607	ENSMUSG00000050578	Mmp13	Clg|MMP-13|Mmp1	matrix metallopeptidase 13	protein-coding
mm_58812.1	chr7	16400108	16400118	+	1	NA	Intergenic	CpG	-1083	NM_198631	330474	Mm.333594	NM_198631	ENSMUSG00000059273	Zc3h4	Bwq1|Gm768|Kiaa1064-hp|mKIAA1064	zinc finger CCCH-type containing 4	protein-coding
mm_34836.1	chr4	155250284	155250294	+	1	NA	non-coding (NR_033802, exon 1 of 3)	non-coding (NR_033802, exon 1 of 3)	323	NR_033802	67513	Mm.10374	NM_001190445	ENSMUSG00000073684	Faap20	2610002J02Rik	Fanconi anemia core complex associated protein 20	protein-coding
mm_100557.1	chr11	120729538	120729548	+	1	NA	TTS (NM_007621)	TTS (NM_007621)	-2259	NM_001347608	67880	Mm.231091	NM_026428	ENSMUSG00000039450	Dcxr	0610038K04Rik|1810027P18Rik|XR	dicarbonyl L-xylulose reductase	protein-coding
mm_130524.1	chr15	98881389	98881410	-	1	NA	promoter-TSS (NM_026967)	promoter-TSS (NM_026967)	15	NM_026967	69159	Mm.259708	NM_026967	ENSMUSG00000023755	Rhebl1	1810036J22Rik|Rheb2	Ras homolog enriched in brain like 1	protein-coding
mm_138532.1	chr17	35243153	35243176	+	1	NA	promoter-TSS (NR_105941)	promoter-TSS (NR_105941)	347	NM_001252457	53817	Mm.439827	NM_019693	ENSMUSG00000019432	Ddx39b	0610030D10Rik|AI428441|Bat-1|Bat1|Bat1a|D17H6S81E|D17H6S81E-1|D6S81Eh	DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B	protein-coding
mm_17730.1	chr2	32453185	32453190	-	1	NA	intron (NM_194335, intron 1 of 1)	L2c|LINE|L2	-1717	NM_146118	227731	Mm.37395	NM_146118	ENSMUSG00000026819	Slc25a25	1110030N17Rik|MCSC|mKIAA1896	solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 25	protein-coding
mm_79002.1	chr9	45410076	45410086	+	1	NA	non-coding (NR_028499, exon 6 of 6)	non-coding (NR_028499, exon 6 of 6)	4004	NM_007503	11936	Mm.22742	NM_007503	ENSMUSG00000059412	Fxyd2	Atp1g1	FXYD domain-containing ion transport regulator 2	protein-coding
mm_64989.1	chr7	16916887	16916915	-	1	NA	3' UTR (NM_007590, exon 6 of 6)	3' UTR (NM_007590, exon 6 of 6)	7131	NM_007590	12315	Mm.288630	NM_007590	ENSMUSG00000019370	Calm3	CaMA|R75142	calmodulin 3	protein-coding
mm_77013.1	chr8	107588231	107588241	-	1	NA	intron (NM_010817, intron 1 of 6)	CpG	246	NM_010817	17463	Mm.18347	NM_010817	ENSMUSG00000039067	Psmd7	AW107203|Mov-34|Mov34	proteasome (prosome, macropain) 26S subunit, non-ATPase, 7	protein-coding
mm_117708.1	chr13	95165644	95165646	-	1	NA	intron (NM_001170669, intron 1 of 18)	intron (NM_001170669, intron 1 of 18)	57405	NM_001170669	218461	Mm.100167	NM_172263	ENSMUSG00000021684	Pde8b	B230331L10Rik|C030047E14Rik	phosphodiesterase 8B	protein-coding
mm_118626.1	chr14	21194480	21194485	+	1	NA	intron (NM_001243041, intron 4 of 10)	MER76|LTR|ERVL	118330	NM_001243041	11534	Mm.188734	NM_134079	ENSMUSG00000039197	Adk	2310026J05Rik|5033405D03Rik|AI255373|AI987814|Ak	adenosine kinase	protein-coding
mm_20774.1	chr2	143860471	143860479	-	1	NA	intron (NM_009751, intron 1 of 7)	intron (NM_009751, intron 1 of 7)	2698	NM_009751	12075	Mm.275937	NM_009751	ENSMUSG00000027420	Bfsp1	CP95	beaded filament structural protein 1, in lens-CP94	protein-coding
mm_151075.1	chr19	47579603	47579681	+	1	NA	promoter-TSS (NM_001164639)	promoter-TSS (NM_001164639)	-377	NM_009289	20874	Mm.281011	NM_009289	ENSMUSG00000025060	Slk	9A2|AV021402|AW411554|Etk4|SMAK|Stk2|mKIAA0204|mSLK	STE20-like kinase	protein-coding
mm_2863.1	chr1	131712716	131712725	+	1	NA	3' UTR (NM_145509, exon 6 of 6)	3' UTR (NM_145509, exon 6 of 6)	24025	NM_001311096	226421	Mm.44508	NM_145509	ENSMUSG00000052688	Rab7b	5430435G22Rik	RAB7B, member RAS oncogene family	protein-coding
mm_149184.1	chr19	9899701	9899722	+	1	NA	promoter-TSS (NM_016692)	promoter-TSS (NM_016692)	-178	NM_016692	16319	Mm.29755	NM_016692	ENSMUSG00000024660	Incenp	2700067E22Rik|AU019509|C130081E20|C77457	inner centromere protein	protein-coding
mm_35039.1	chr4	4138433	4138480	-	1	NA	promoter-TSS (NM_001002927)	promoter-TSS (NM_001002927)	-11	NM_001002927	18619	Mm.475097	NM_001002927	ENSMUSG00000045573	Penk	AI326464|ENK|PPA|Penk1	preproenkephalin	protein-coding
mm_151873.1	chr19	5798311	5798323	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	-2336	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_133947.1	chr16	3959477	3959511	-	1	NA	intron (NM_175547, intron 1 of 14)	intron (NM_175547, intron 1 of 14)	17138	NM_175547	268857	Mm.215994	NM_175547	ENSMUSG00000049871	Nlrc3	CLR16.2|D230007K08Rik|mFLJ00348	NLR family, CARD domain containing 3	protein-coding
mm_102569.1	chr11	61515494	61515497	-	1	NA	Intergenic	Intergenic	10351	NM_001330781	27078	Mm.261226	NM_013717	ENSMUSG00000001039	B9d1	AW045994|B9|Eppb9	B9 protein domain 1	protein-coding
mm_135569.1	chr16	50262451	50262485	-	1	NA	exon (NM_027444, exon 7 of 17)	exon (NM_027444, exon 7 of 17)	169921	NM_027444	70508	Mm.28940	NM_027444	ENSMUSG00000022641	Bbx	5530401J07Rik|5730403O13Rik	bobby sox HMG box containing	protein-coding
mm_90134.1	chr10	117721713	117721733	+	1	NA	Intergenic	Intergenic	-10965	NM_001288586	17246	Mm.22670	NM_010786	ENSMUSG00000020184	Mdm2	1700007J15Rik|AA415488|Mdm-2	transformed mouse 3T3 cell double minute 2	protein-coding
mm_6613.1	chr1	75479390	75479404	-	1	NA	promoter-TSS (NM_001001566)	promoter-TSS (NM_001001566)	74	NM_001001565	74241	Mm.260577	NM_001001565	ENSMUSG00000032997	Chpf	1700028N03Rik|AI414328|D1Bwg1363e	chondroitin polymerizing factor	protein-coding
mm_70833.1	chr8	23153295	23153305	+	1	NA	promoter-TSS (NM_029002)	promoter-TSS (NM_029002)	29	NM_029002	74561	Mm.290028	NM_029002	ENSMUSG00000063672	Nkx6-3	9130417I07Rik|Nkx6.3	NK6 homeobox 3	protein-coding
mm_92397.1	chr10	76614491	76614506	-	1	NA	exon (NM_146007, exon 3 of 28)	exon (NM_146007, exon 3 of 28)	8906	NM_146007	12834	Mm.1949	NM_146007	ENSMUSG00000020241	Col6a2	Col6a-2	collagen, type VI, alpha 2	protein-coding
mm_6442.1	chr1	73998527	73998533	-	1	NA	intron (NM_027884, intron 6 of 34)	intron (NM_027884, intron 6 of 34)	125917	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_107761.1	chr12	59072272	59072284	+	1	NA	exon (NM_008891, exon 9 of 9)	exon (NM_008891, exon 9 of 9)	5359	NM_008891	18949	Mm.22347	NM_008891	ENSMUSG00000020994	Pnn	AU045199|D12Ertd512e	pinin	protein-coding
mm_133022.1	chr16	57121683	57121701	+	1	NA	promoter-TSS (NM_138599)	promoter-TSS (NM_138599)	-22	NM_138599	28185	Mm.196933	NM_138599	ENSMUSG00000022752	Tomm70a	2610044B22Rik|D16Ium22|D16Ium22e|D16Wsu109e|Tom70|Tomm70|mKIAA0719	translocase of outer mitochondrial membrane 70 homolog A (yeast)	protein-coding
mm_79090.1	chr9	46242669	46242711	+	1	NA	exon (NM_007468, exon 3 of 3)	exon (NM_007468, exon 3 of 3)	1846	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_105703.1	chr11	108262842	108262852	-	1	NA	intron (NM_011101, intron 2 of 16)	B1_Mur1|SINE|Alu	81041	NM_011101	18750	Mm.222178	NM_011101	ENSMUSG00000050965	Prkca	AI875142|Pkca	protein kinase C, alpha	protein-coding
mm_54607.1	chr6	38341856	38341869	-	1	NA	intron (NM_001347122, intron 1 of 12)	intron (NM_001347122, intron 1 of 12)	12741	NM_028864	78781	Mm.25243	NM_028421	ENSMUSG00000029826	Zc3hav1	1200014N16Rik|2900058M19Rik|9130009D18Rik|9830115L13Rik|ARTD13|D6Bwg1452e|ZAP	zinc finger CCCH type, antiviral 1	protein-coding
mm_31506.1	chr4	53566587	53566592	+	1	NA	intron (NM_133891, intron 15 of 15)	intron (NM_133891, intron 15 of 15)	-64882	NM_176966	319636	Mm.103464	NM_176966	ENSMUSG00000054752	Fsd1l	A230072O16Rik|Ccdc10|Csdufd1|Fsd1nl|OTTMUSG00000007002	fibronectin type III and SPRY domain containing 1-like	protein-coding
mm_138222.1	chr17	34325659	34325679	+	1	NA	promoter-TSS (NM_001033978)	promoter-TSS (NM_001033978)	-6	NM_001033978	381091	Mm.139204	NM_001033978	ENSMUSG00000067341	H2-Eb2	A130038H09Rik|H-2Eb2|Ia-5|Ia5|Iebeta2	histocompatibility 2, class II antigen E beta2	protein-coding
mm_45153.1	chr5	49334945	49334948	-	1	NA	Intergenic	Intergenic	-49287	NM_001199244	80334	Mm.160172	NM_030265	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding
mm_121585.1	chr14	6287327	6287344	-	1	NA	promoter-TSS (NM_001270812)	promoter-TSS (NM_001270812)	-85	NM_001270812	100861615	Mm.488431	NM_001270812	ENSMUSG00000079396	LOC100861615	-	alpha takusan-like	protein-coding
mm_82970.1	chr9	35790076	35790090	-	1	NA	promoter-TSS (NM_026593)	promoter-TSS (NM_026593)	29	NM_026593	68171	Mm.99495	NM_026593	ENSMUSG00000032108	D730048I06Rik	Pate-C|Pate6|mANLP2	RIKEN cDNA D730048I06 gene	protein-coding
mm_30969.1	chr4	34485735	34485766	+	1	NA	Intergenic	Intergenic	-64865	NM_001007589	433693	Mm.389532	NM_026019	ENSMUSG00000028291	Akirin2	2700059D21Rik|AA114675|AA522011|AU019887|Akirin-2	akirin 2	protein-coding
mm_22389.1	chr2	181197036	181197062	-	1	NA	exon (NM_009184, exon 6 of 8)	exon (NM_009184, exon 6 of 8)	5740	NM_009184	20459	Mm.4497	NM_009184	ENSMUSG00000038751	Ptk6	BRK|Sik|Tksk|tks	PTK6 protein tyrosine kinase 6	protein-coding
mm_96586.1	chr11	69089744	69089764	+	1	NA	exon (NM_009497, exon 3 of 5)	exon (NM_009497, exon 3 of 5)	1226	NM_009497	22318	Mm.28643	NM_009497	ENSMUSG00000020894	Vamp2	Syb-2|Syb2|sybII	vesicle-associated membrane protein 2	protein-coding
mm_87539.1	chr10	53596796	53596808	+	1	NA	promoter-TSS (NM_025541)	promoter-TSS (NM_025541)	-159	NM_025541	66403	Mm.272989	NM_025541	ENSMUSG00000019857	Asf1a	2310079C17Rik|C79052	anti-silencing function 1A histone chaperone	protein-coding
mm_14278.1	chr2	128792374	128792392	+	1	NA	intron (NM_008587, intron 16 of 18)	intron (NM_008587, intron 16 of 18)	-25920	NM_028248	72477	Mm.259688	NM_028248	ENSMUSG00000014353	Tmem87b	2610301K12Rik|2810431I02Rik|AU014804	transmembrane protein 87B	protein-coding
mm_135748.1	chr16	55923987	55923992	-	1	NA	TTS (NM_001159365)	TTS (NM_001159365)	10859	NM_001159364	74201	Mm.178427	NM_028815	ENSMUSG00000022604	Cep97	2810403B08Rik|4932439K18Rik|AA437768|E130116N02Rik|Lrriq2	centrosomal protein 97	protein-coding
mm_127721.1	chr15	103135815	103135827	+	1	NA	intron (NR_045743, intron 3 of 6)	intron (NR_045743, intron 3 of 6)	11007	NR_045743	432989	Mm.383979	NR_045743	ENSMUSG00000097003	D930007P13Rik	-	Riken cDNA D930007P13 gene	ncRNA
mm_154546.1	chrM	14785	14824	-	1	NA	NA	Intergenic	NA	NA								
mm_57329.1	chr6	124740985	124741093	-	1	NA	promoter-TSS (NM_013535)	promoter-TSS (NM_013535)	40	NM_013535	14790	Mm.439877	NM_013535	ENSMUSG00000072772	Grcc10	2310033H05Rik|C10	gene rich cluster, C10 gene	protein-coding
mm_149523.1	chr19	12442834	12442841	+	1	NA	Intergenic	RMER1C|Other|Other	14932	NM_019540	56093	Mm.285849	NM_019540	ENSMUSG00000040065	Pfpl	Epcs5|Epcs50	pore forming protein-like	protein-coding
mm_11599.1	chr2	33641268	33641322	+	1	NA	promoter-TSS (NM_010725)	promoter-TSS (NM_010725)	102	NR_046275	100504399	Mm.72070	NM_177842		C130021I20Rik	-	Riken cDNA C130021I20 gene	ncRNA
mm_137563.1	chr17	27702716	27702741	+	1	NA	exon (NM_001286743, exon 3 of 10)	exon (NM_001286743, exon 3 of 10)	17489	NM_178365	23969	Mm.4926	NM_011861	ENSMUSG00000040276	Pacsin1	A830061D09Rik|H74|mKIAA1379|syndapin	protein kinase C and casein kinase substrate in neurons 1	protein-coding
mm_127711.1	chr15	103010128	103010140	+	1	NA	intron (NM_010465, intron 1 of 1)	intron (NM_010465, intron 1 of 1)	572	NM_010465	15425	Mm.4444	NM_010465	ENSMUSG00000001661	Hoxc6	Hox-3.3|Hox-6.1	homeobox C6	protein-coding
mm_130811.1	chr15	101734415	101734419	-	1	NA	3' UTR (NM_019956, exon 9 of 9)	3' UTR (NM_019956, exon 9 of 9)	8680	NM_019956	56735	Mm.358677	NM_019956	ENSMUSG00000051879	Krt71	AA589543|Ca|Cal4|Cu|Krt2-6g|mK6irs|mK6irs1	keratin 71	protein-coding
mm_128428.1	chr15	49981452	49981452	-	1	NA	Intergenic	U2|snRNA|snRNA	907597	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_92406.1	chr10	76709684	76709733	-	1	NA	exon (NM_009933, exon 35 of 35)	exon (NM_009933, exon 35 of 35)	16336	NM_009933	12833	Mm.2509	NM_009933	ENSMUSG00000001119	Col6a1	AI747156|Col6a-1	collagen, type VI, alpha 1	protein-coding
mm_95489.1	chr11	51606331	51606355	+	1	NA	exon (NM_010448, exon 2 of 7)	exon (NM_010448, exon 2 of 7)	538	NM_001048061	15384	Mm.256875	NM_010448	ENSMUSG00000020358	Hnrnpab	3010025C11Rik|CBF-A|Cgbfa|Hnrpab	heterogeneous nuclear ribonucleoprotein A/B	protein-coding
mm_162191.1	chrX	112093456	112093456	+	1	NA	promoter-TSS (NM_031382)	promoter-TSS (NM_031382)	-64	NM_031382	83556	Mm.190608	NM_031382	ENSMUSG00000034555	Tex16	OTTMUSG00000018437	testis expressed gene 16	protein-coding
mm_331.1	chr1	26616985	26616993	+	1	NA	Intergenic	RLTR16|LTR|ERVK	70471	NM_001033764	210940	Mm.297614	NM_001033764	ENSMUSG00000073722	4931408C20Rik	-	RIKEN cDNA 4931408C20 gene	protein-coding
mm_98605.1	chr11	95837794	95837795	+	1	NA	intron (NM_001163464, intron 1 of 7)	intron (NM_001163464, intron 1 of 7)	-4501	NM_023121	14710	Mm.46299	NM_023121	ENSMUSG00000038811	Gngt2	AV096488	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 2	protein-coding
mm_68534.1	chr7	113368812	113368839	-	1	NA	intron (NM_133700, intron 2 of 10)	intron (NM_133700, intron 2 of 10)	514	NM_133700	68815	Mm.238034	NM_133700	ENSMUSG00000038187	Btbd10	1110056N09Rik|Gmrp1	BTB (POZ) domain containing 10	protein-coding
mm_45250.1	chr5	59986005	59986037	-	1	NA	promoter-TSS (NR_040683)	promoter-TSS (NR_040683)	-19	NR_040682	71057	Mm.50817	NR_040682	ENSMUSG00000106013	4933402J10Rik	-	RIKEN cDNA 4933402J10 gene	ncRNA
mm_156263.1	chrX	136831145	136831156	+	1	NA	exon (NM_011123, exon 2 of 7)	exon (NM_011123, exon 2 of 7)	8404	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_43696.1	chr5	139167078	139167083	+	1	NA	intron (NM_001081265, intron 7 of 12)	intron (NM_001081265, intron 7 of 12)	16857	NM_001081265	433956	Mm.5547	NM_001081265	ENSMUSG00000025857	Dnaaf5	BC053401|C76907|Heatr2	dynein, axonemal assembly factor 5	protein-coding
mm_165799.1	chr3	141465655	141465664	+	1	NA	promoter-TSS (NM_009472)	promoter-TSS (NM_009472)	95	NM_001293561	22253	Mm.24430	NM_009472	ENSMUSG00000059921	Unc5c	B130051O18Rik|Unc5h3|rcm	unc-5 netrin receptor C	protein-coding
mm_161235.1	chr13	93637780	93637780	-	1	NA	promoter-TSS (NM_016668)	promoter-TSS (NM_016668)	-22	NM_016668	12116	Mm.329582	NM_016668	ENSMUSG00000074768	Bhmt	-	betaine-homocysteine methyltransferase	protein-coding
mm_106257.1	chr11	117873434	117873460	-	1	NA	promoter-TSS (NM_027919)	promoter-TSS (NM_027919)	79	NM_027919	71776	Mm.3200	NM_027919	ENSMUSG00000017713	Tha1	1300017K07Rik|GLY1	threonine aldolase 1	protein-coding
mm_153445.1	chr19	41000487	41000487	-	1	NA	Intergenic	Intergenic	-5952	NM_008528	17060	Mm.9749	NM_008528	ENSMUSG00000061132	Blnk	BASH|Bca|Ly-57|Ly57|Lyw-57|SLP-65	B cell linker	protein-coding
mm_18027.1	chr2	38623546	38623610	-	1	NA	intron (NM_011187, intron 5 of 7)	MIR3|SINE|MIR	20328	NM_011187	19177	Mm.389251	NM_011187	ENSMUSG00000026750	Psmb7	AU020723|MC14	proteasome (prosome, macropain) subunit, beta type 7	protein-coding
mm_154693.1	chrX	8050743	8050787	+	1	NA	Intergenic	RLTR12E|LTR|ERVK	23548	NM_001290716	20937	Mm.9244	NM_011514	ENSMUSG00000039231	Suv39h1	AI852103|AL022883|DXHXS7466e|H3-K9-HMTase 1|KMT1A|mIS6	suppressor of variegation 3-9 homolog 1 (Drosophila)	protein-coding
mm_64286.1	chr7	141845373	141845377	+	1	NA	exon (NM_028801, exon 9 of 49)	exon (NM_028801, exon 9 of 49)	6303	NM_028801	74180	Mm.200752	NM_028801	ENSMUSG00000066108	Muc5b	2300002I04Rik|A130042M24|AV085033|MUC5|MUC9|mucin 5b	mucin 5, subtype B, tracheobronchial	protein-coding
mm_99849.1	chr11	109362772	109362854	+	1	NA	promoter-TSS (NM_010303)	promoter-TSS (NM_010303)	19	NM_010303	14674	Mm.193925	NM_010303	ENSMUSG00000020611	Gna13	AU024132|AU043124|Galpha13	guanine nucleotide binding protein, alpha 13	protein-coding
mm_99023.1	chr11	98937154	98937170	+	1	NA	promoter-TSS (NM_009024)	promoter-TSS (NM_009024)	-534	NM_009024	19401	Mm.439744	NM_009024	ENSMUSG00000037992	Rara	Nr1b1|RAR|RARalpha1	retinoic acid receptor, alpha	protein-coding
mm_171380.1	chr4	119293761	119293766	-	1	NA	exon (NM_011732, exon 2 of 8)	exon (NM_011732, exon 2 of 8)	750	NM_011732	22608	Mm.258204	NM_011732	ENSMUSG00000028639	Ybx1	1700102N10Rik|C79409|EF1A|MSY1|Nsep1|YB-1|dbpB|mYB-1a	Y box protein 1	protein-coding
mm_108201.1	chr12	76902145	76902155	+	1	NA	intron (NM_145927, intron 7 of 11)	ORR1C2|LTR|ERVL-MaLR	60098	NM_008558	17187	Mm.268548	NM_008558	ENSMUSG00000059436	Max	AA960152|AI875693|bHLHd4|bHLHd5|bHLHd6|bHLHd7|bHLHd8	Max protein	protein-coding
mm_70234.1	chr8	3248641	3248643	+	1	NA	intron (NM_010568, intron 2 of 20)	MTE2a|LTR|ERVL-MaLR	30975	NM_010568	16337	Mm.268003	NM_010568	ENSMUSG00000005534	Insr	4932439J01Rik|CD220|D630014A15Rik|IR|IR-A|IR-B	insulin receptor	protein-coding
mm_63186.1	chr7	125552309	125552311	+	1	NA	promoter-TSS (NM_001008700)	promoter-TSS (NM_001008700)	28	NM_001008700	16190	Mm.233802	NM_010557	ENSMUSG00000030748	Il4ra	CD124|Il4r	interleukin 4 receptor, alpha	protein-coding
mm_153712.1	chr19	44400166	44400182	-	1	NA	exon (NM_009127, exon 5 of 6)	exon (NM_009127, exon 5 of 6)	7535	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_124904.1	chr15	10952204	10952214	+	1	NA	promoter-TSS (NM_030888)	promoter-TSS (NM_030888)	-123	NM_030888	81799	Mm.280158	NM_030888	ENSMUSG00000058914	C1qtnf3	2310005P21Rik|CORS-26|CORS26|CTRP3|Corcs|Cors	C1q and tumor necrosis factor related protein 3	protein-coding
mm_73037.1	chr8	94222948	94222949	+	1	NA	intron (NM_172410, intron 2 of 22)	intron (NM_172410, intron 2 of 22)	8347	NM_172410	71805	Mm.458170	NM_172410	ENSMUSG00000032939	Nup93	2410008G02Rik	nucleoporin 93	protein-coding
mm_66688.1	chr7	45867481	45867493	-	1	NA	promoter-TSS (NM_008172)	promoter-TSS (NM_008172)	-806	NM_008172	14814	Mm.322594	NM_008172	ENSMUSG00000002771	Grin2d	GluN2D|NMDAR2D|NR2D	glutamate receptor, ionotropic, NMDA2D (epsilon 4)	protein-coding
mm_90404.1	chr10	127380592	127380702	+	1	NA	Intergenic	CpG	-9664	NM_001168292	71750	Mm.29342	NM_027900	ENSMUSG00000025404	R3hdm2	1300003K24Rik|AU041262|mKIAA1002	R3H domain containing 2	protein-coding
mm_26160.1	chr3	138277490	138277495	+	1	NA	promoter-TSS (NM_007409)	promoter-TSS (NM_007409)	-153	NM_007409	11522	Mm.2409	NM_007409	ENSMUSG00000074207	Adh1	ADH-AA|AI194826|Adh-1|Adh-1-t|Adh-1e|Adh-1t|Adh-3e|Adh1-e|Adh1-t|Adh1tl|Adh3-e	alcohol dehydrogenase 1 (class I)	protein-coding
mm_119497.1	chr14	47380131	47380141	+	1	NA	exon (NM_010705, exon 3 of 6)	exon (NM_010705, exon 3 of 6)	6276	NM_001145953	16854	Mm.248615	NM_010705	ENSMUSG00000050335	Lgals3	GBP|L-34|Mac-2|gal3	lectin, galactose binding, soluble 3	protein-coding
mm_161587.1	chr16	32668330	32668330	+	1	NA	promoter-TSS (NR_033493)	promoter-TSS (NR_033493)	-133	NR_033493	675921	Mm.404316	NR_033493	ENSMUSG00000075265	Tnk2os	ENSMUSG00000075265|Gm10818	tyrosine kinase, non-receptor 2, opposite strand	ncRNA
mm_85228.1	chr9	97111163	97111175	-	1	NA	promoter-TSS (NM_138756)	promoter-TSS (NM_138756)	-128	NM_138756	192287	Mm.228067	NM_138756	ENSMUSG00000032449	Slc25a36	C330005L02Rik	solute carrier family 25, member 36	protein-coding
mm_54558.1	chr6	37299951	37299981	-	1	NA	promoter-TSS (NM_001081206)	promoter-TSS (NM_001081206)	10	NM_001081206	320127	Mm.119469	NM_001081206	ENSMUSG00000038665	Dgki	C130010K08Rik	diacylglycerol kinase, iota	protein-coding
mm_159571.1	chr4	115298945	115298945	+	1	NA	promoter-TSS (NM_177406)	promoter-TSS (NM_177406)	-101	NM_177406	277753	Mm.276106	NM_177406	ENSMUSG00000066071	Cyp4a12a	BC025936|Cyp4a12	cytochrome P450, family 4, subfamily a, polypeptide 12a	protein-coding
mm_97155.1	chr11	75463986	75464010	+	1	NA	TTS (NR_029739)	TTS (NR_029739)	282	NR_029739	387141		NR_029739	ENSMUSG00000065529	Mir22	Mirn22|mmu-mir-22	microRNA 22	ncRNA
mm_157490.1	chrX	48314691	48314716	-	1	NA	Intergenic	CpG	-26655	NM_178782	320376	Mm.210146	NM_178782	ENSMUSG00000036959	Bcorl1	6720425J07Rik|B930011H20Rik	BCL6 co-repressor-like 1	protein-coding
mm_100753.1	chr11	4237527	4237547	-	1	NA	intron (NM_001013365, intron 1 of 2)	intron (NM_001013365, intron 1 of 2)	752	NM_001013365	18413	Mm.131422	NM_001013365	ENSMUSG00000058755	Osm	OncoM	oncostatin M	protein-coding
mm_17067.1	chr2	22744574	22744595	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-29743	NM_019456	54519	Mm.14255	NM_019456	ENSMUSG00000026786	Apbb1ip	9930118P07Rik|Prp48	amyloid beta (A4) precursor protein-binding, family B, member 1 interacting protein	protein-coding
mm_123554.1	chr14	66846433	66846474	-	1	NA	intron (NM_009955, intron 3 of 13)	intron (NM_009955, intron 3 of 13)	22147	NM_009955	12934	Mm.352648	NM_009955	ENSMUSG00000022048	Dpysl2	AI851130|Crmp2|DRP2|Musunc33|TOAD-64|Ulip2	dihydropyrimidinase-like 2	protein-coding
mm_118860.1	chr14	25842175	25842193	+	1	NA	promoter-TSS (NM_013469)	promoter-TSS (NM_013469)	29	NM_013469	11744	Mm.294083	NM_013469	ENSMUSG00000021866	Anxa11	A830099O17Rik|Anx11	annexin A11	protein-coding
mm_155976.1	chrX	106126805	106126825	+	1	NA	3' UTR (NM_009726, exon 23 of 23)	3' UTR (NM_009726, exon 23 of 23)	-16460	NM_205820	279572	Mm.336203	NM_205820	ENSMUSG00000033777	Tlr13	AI666735|Gm713	toll-like receptor 13	protein-coding
mm_138414.1	chr17	35068905	35068922	+	1	NA	exon (NM_023463, exon 2 of 3)	exon (NM_023463, exon 2 of 3)	1588	NM_023463	68468	Mm.215096	NM_023463	ENSMUSG00000092586	Ly6g6c	1110003M04Rik|AU016360|G6c|NG24	lymphocyte antigen 6 complex, locus G6C	protein-coding
mm_154697.1	chrX	8252759	8252793	+	1	NA	promoter-TSS (NM_001290430)	promoter-TSS (NM_001290430)	-370	NM_001290430	54632	Mm.327529	NM_133991	ENSMUSG00000031171	Ftsj1	AI931847|Ftsj|Ftsjl|Sfc12	FtsJ RNA methyltransferase homolog 1 (E. coli)	protein-coding
mm_93142.1	chr10	92165160	92165177	-	1	NA	promoter-TSS (NR_028262)	promoter-TSS (NR_028262)	10	NR_028262	110333	Mm.429764	NR_028262		Rmst	100041799|AI853140|C230053E11Rik|D930049J19Rik|Dmt2|Gm3515|M2|Ncrms	rhabdomyosarcoma 2 associated transcript (non-coding RNA)	ncRNA
mm_25938.1	chr3	131471206	131471222	+	1	NA	Intergenic	Intergenic	-93554	NM_001289479	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_21001.1	chr2	152343943	152343951	-	1	NA	5' UTR (NM_175093, exon 1 of 4)	5' UTR (NM_175093, exon 1 of 4)	113	NM_175093	228775	Mm.276018	NM_144554	ENSMUSG00000032715	Trib3	Ifld2|Nipk|SINK|SKIP3|TRB-3|Trb3	tribbles pseudokinase 3	protein-coding
mm_68528.1	chr7	112688511	112688520	-	1	NA	intron (NM_009346, intron 1 of 12)	intron (NM_009346, intron 1 of 12)	9195	NM_009346	21676	Mm.24685	NM_009346	ENSMUSG00000055320	Tead1	2610024B07Rik|B230114H05Rik|Gtrgeo5|TEAD-1|TEF-1|Tcf13|mTEF-1	TEA domain family member 1	protein-coding
mm_67199.1	chr7	74284345	74284356	-	1	NA	exon (NM_023908, exon 10 of 10)	exon (NM_023908, exon 10 of 10)	270430	NM_023908	108116	Mm.425467	NM_023908	ENSMUSG00000025790	Slco3a1	5830414C08Rik|Anr1|MJAM|OATP-D|R75096|Slc21a11	solute carrier organic anion transporter family, member 3a1	protein-coding
mm_20559.1	chr2	131074429	131074446	-	1	NA	exon (NM_011426, exon 14 of 21)	exon (NM_011426, exon 14 of 21)	-10623	NM_001163529	110751	Mm.108550	NM_033615	ENSMUSG00000027318	Adam33	Adaml	a disintegrin and metallopeptidase domain 33	protein-coding
mm_114846.1	chr13	92775021	92775029	+	1	NA	intron (NM_011582, intron 6 of 21)	intron (NM_011582, intron 6 of 21)	19793	NM_011582	21828	Mm.20865	NM_011582	ENSMUSG00000021702	Thbs4	TSP4	thrombospondin 4	protein-coding
mm_100003.1	chr11	114851616	114851646	+	1	NA	promoter-TSS (NM_147217)	promoter-TSS (NM_147217)	91	NM_001110338	70355	Mm.242413	NM_147217	ENSMUSG00000051043	Gprc5c	1110028I06Rik|3200002M13Rik|Raig3	G protein-coupled receptor, family C, group 5, member C	protein-coding
mm_48495.1	chr5	142774185	142774199	-	1	NA	intron (NM_178242, intron 8 of 15)	intron (NM_178242, intron 8 of 15)	43195	NM_178242	231861	Mm.354649	NM_178242	ENSMUSG00000039477	Tnrc18	BC025631|EG381742|Zfp469	trinucleotide repeat containing 18	protein-coding
mm_100918.1	chr11	6292132	6292149	-	1	NA	promoter-TSS (NM_001252288)	promoter-TSS (NM_001252288)	-418	NM_001252288	18293	Mm.276348	NM_010956	ENSMUSG00000020456	Ogdh	2210403E04Rik|2210412K19Rik|AA409584|d1401|mKIAA4192	oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)	protein-coding
mm_46619.1	chr5	108132578	108132588	-	1	NA	promoter-TSS (NM_028481)	promoter-TSS (NM_028481)	8	NM_001347383	73130	Mm.363960	NM_028876	ENSMUSG00000063406	Tmed5	3110020O18Rik|4432412D15Rik	transmembrane p24 trafficking protein 5	protein-coding
mm_7057.1	chr1	87180961	87180969	-	1	NA	Intergenic	MLT1B|LTR|ERVL-MaLR	-2349	NM_027084	69453	Mm.84618	NM_027084	ENSMUSG00000036480	Prss56	1700027L20Rik	protease, serine 56	protein-coding
mm_96792.1	chr11	69976653	69976668	+	1	NA	intron (NM_018740, intron 4 of 8)	intron (NM_018740, intron 4 of 8)	3670	NM_001253700	54351	Mm.13430	NM_018740	ENSMUSG00000018565	Elp5	Derp6|Rai12	elongator acetyltransferase complex subunit 5	protein-coding
mm_92880.1	chr10	82662627	82662661	-	1	NA	intron (NM_029102, intron 4 of 9)	intron (NM_029102, intron 4 of 9)	28006	NM_029102	74782	Mm.191281	NM_029102	ENSMUSG00000020251	Glt8d2	1110021D20Rik	glycosyltransferase 8 domain containing 2	protein-coding
mm_74795.1	chr8	22398471	22398471	-	1	NA	promoter-TSS (NR_045473)	promoter-TSS (NR_045473)	150	NM_181325	18408	Mm.200907	NM_181325	ENSMUSG00000031482	Slc25a15	D630044L02Rik|Ornt1	solute carrier family 25 (mitochondrial carrier ornithine transporter), member 15	protein-coding
mm_56781.1	chr6	116633815	116633828	-	1	NA	3' UTR (NM_178045, exon 11 of 11)	3' UTR (NM_178045, exon 11 of 11)	-4822	NM_026057	67255	Mm.18810	NM_026057	ENSMUSG00000059878	Zfp422	2900028O21Rik|AU041373|KOX15|Krox-25-2|Krox-26|Krox25|Krox26|Znf22	zinc finger protein 422	protein-coding
mm_96898.1	chr11	70440315	70440338	+	1	NA	3' UTR (NM_001271358, exon 15 of 15)	3' UTR (NM_001271358, exon 15 of 15)	2071	NR_106064	102465670		NR_106064	ENSMUSG00000099109	Mir7115	Gm27902|mmu-mir-7115	microRNA 7115	ncRNA
mm_5505.1	chr1	37430011	37430015	-	1	NA	promoter-TSS (NM_026123)	promoter-TSS (NM_026123)	90	NM_198006	76178	Mm.28085	NM_198006	ENSMUSG00000026112	Coa5	1700001A24Rik|6330578E17Rik|Pet191	cytochrome C oxidase assembly factor 5	protein-coding
mm_156364.1	chrX	139563319	139563339	+	1	NA	promoter-TSS (NM_001254761)	promoter-TSS (NM_001254761)	-11	NM_001254761	66889	Mm.27764	NM_023270	ENSMUSG00000031438	Rnf128	1300002C13Rik|AI987883|GRAIL|Greul1	ring finger protein 128	protein-coding
mm_98066.1	chr11	85832968	85832986	+	1	NA	promoter-TSS (NR_077059)	promoter-TSS (NR_077059)	362	NM_009324	21385	Mm.287052	NM_009324	ENSMUSG00000000093	Tbx2	-	T-box 2	protein-coding
mm_112573.1	chr13	13590403	13590456	+	1	NA	promoter-TSS (NM_010748)	promoter-TSS (NM_010748)	20	NM_010748	17101	Mm.342337	NM_010748	ENSMUSG00000019726	Lyst	D13Sfk13|beige|bg	lysosomal trafficking regulator	protein-coding
mm_22570.1	chr3	10186689	10186691	+	1	NA	Intergenic	Intergenic	-2805	NM_001030305	18857	Mm.371777	NM_001030305	ENSMUSG00000052468	Pmp2	P2	peripheral myelin protein 2	protein-coding
mm_115504.1	chr13	4150660	4150673	-	1	NA	promoter-TSS (NM_134066)	promoter-TSS (NM_134066)	-20	NM_001346535	105349	Mm.41337	NM_134066	ENSMUSG00000021214	Akr1c18	AW146047	aldo-keto reductase family 1, member C18	protein-coding
mm_76181.1	chr8	82401809	82401855	-	1	NA	intron (NM_001254747, intron 1 of 7)	intron (NM_001254747, intron 1 of 7)	754	NM_001254747	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_147201.1	chr18	37887955	37887956	-	1	NA	intron (NM_007858, intron 16 of 26)	B1_Mus1|SINE|Alu	-33295	NR_105945	102465592		NR_105945	ENSMUSG00000098706	Mir6979	Gm27524|mmu-mir-6979	microRNA 6979	ncRNA
mm_26524.1	chr3	145962673	145962678	+	1	NA	Intergenic	RMER17C|LTR|ERVK	24643	NM_025555	66421	Mm.25137	NM_025555	ENSMUSG00000036873	2410004B18Rik	4930572C24Rik	RIKEN cDNA 2410004B18 gene	protein-coding
mm_5267.1	chr1	17097840	17097872	-	1	NA	promoter-TSS (NM_020604)	promoter-TSS (NM_020604)	33	NM_020604	57339	Mm.143761	NM_020604	ENSMUSG00000042686	Jph1	ENSMUSG00000054314|JP-1|Jp1	junctophilin 1	protein-coding
mm_30273.1	chr3	146812926	146812946	-	1	NA	promoter-TSS (NM_011100)	promoter-TSS (NM_011100)	10	NM_011100	18749	Mm.16766	NM_011100	ENSMUSG00000005034	Prkacb	CbPKA|Pkacb	protein kinase, cAMP dependent, catalytic, beta	protein-coding
mm_163890.1	chr14	26965887	26965890	-	1	NA	intron (NM_145221, intron 1 of 21)	AT_rich|Low_complexity|Low_complexity	4663	NM_145221	72993	Mm.202322	NM_145221	ENSMUSG00000040760	Appl1	2900057D21Rik|7330406P05Rik|AI585782|AW209077|BB022931|C88264|DIP13	adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 1	protein-coding
mm_108030.1	chr12	73731782	73731785	+	1	NA	intron (NM_001313977, intron 11 of 14)	intron (NM_001313977, intron 11 of 14)	146987	NM_008856	18755	Mm.341677	NM_008856	ENSMUSG00000021108	Prkch	Pkch	protein kinase C, eta	protein-coding
mm_148305.1	chr18	83238602	83238602	-	1	NA	Intergenic	Intergenic	87282	NR_045361	70960	Mm.410834	NR_045361		4921531P14Rik	1700108N05Rik	RIKEN cDNA 4921531P14 gene	ncRNA
mm_38253.1	chr4	136695616	136695628	-	1	NA	intron (NM_001290753, intron 4 of 15)	intron (NM_001290753, intron 4 of 15)	73001	NM_001243262	242707	Mm.448979	NM_001243262	ENSMUSG00000070683	Lactbl1	-	lactamase, beta-like 1	protein-coding
mm_65259.1	chr7	19888068	19888091	-	1	NA	promoter-TSS (NM_177036)	promoter-TSS (NM_177036)	-114	NM_177036	319930	Mm.215839	NM_177036	ENSMUSG00000049848	Ceacam19	C130022P09Rik|CEAL1	carcinoembryonic antigen-related cell adhesion molecule 19	protein-coding
mm_66121.1	chr7	31053075	31053090	-	1	NA	intron (NM_052991, intron 4 of 7)	intron (NM_052991, intron 4 of 7)	-1628	NM_022007	57780	Mm.41770	NM_022007	ENSMUSG00000036578	Fxyd7	1110035I01Rik	FXYD domain-containing ion transport regulator 7	protein-coding
mm_147299.1	chr18	39519254	39519262	-	1	NA	Intergenic	Intergenic	-32013	NM_008173	14815	Mm.129481	NM_008173	ENSMUSG00000024431	Nr3c1	GR|Grl-1|Grl1	nuclear receptor subfamily 3, group C, member 1	protein-coding
mm_48257.1	chr5	137831274	137831282	-	1	NA	exon (NM_153510, exon 3 of 7)	exon (NM_153510, exon 3 of 7)	5000	NM_153510	231805	Mm.379385	NM_153510	ENSMUSG00000046245	Pilra	AV021745|FDF03	paired immunoglobin-like type 2 receptor alpha	protein-coding
mm_165421.1	chr2	148851208	148851213	-	1	NA	promoter-TSS (NM_029960)	promoter-TSS (NM_029960)	-276	NM_029960	77705	Mm.159975	NM_029960	ENSMUSG00000027446	9230104L09Rik	mCST E2	RIKEN cDNA 9230104L09 gene	protein-coding
mm_106493.1	chr11	120347432	120347459	-	1	NA	promoter-TSS (NR_105900)	promoter-TSS (NR_105900)	-32	NR_105900	102465564		NR_105900	ENSMUSG00000098955	Mir6935	Gm27344|mmu-mir-6935	microRNA 6935	ncRNA
mm_13775.1	chr2	118745739	118745773	+	1	NA	promoter-TSS (NM_001301269)	promoter-TSS (NM_001301269)	-2	NM_001301269	100043272	Mm.398072	NM_001301269	ENSMUSG00000074918	Inafm2	5430417L22Rik|ENSMUSG00000074918	InaF motif containing 2	protein-coding
mm_132229.1	chr16	32670788	32670788	+	1	NA	intron (NM_016788, intron 6 of 15)	intron (NM_016788, intron 6 of 15)	-2366	NM_001347185	51789	Mm.251115	NM_016788	ENSMUSG00000022791	Tnk2	Ack|Ack-1|Ack1|Cdgip|Pyk1	tyrosine kinase, non-receptor, 2	protein-coding
mm_105742.1	chr11	109363182	109363213	-	1	NA	exon (NM_010303, exon 1 of 4)	exon (NM_010303, exon 1 of 4)	403	NM_010303	14674	Mm.193925	NM_010303	ENSMUSG00000020611	Gna13	AU024132|AU043124|Galpha13	guanine nucleotide binding protein, alpha 13	protein-coding
mm_17355.1	chr2	26608671	26608675	-	1	NA	Intergenic	MTE2b|LTR|ERVL-MaLR	-4256	NM_026212	67512	Mm.24244	NM_026212	ENSMUSG00000026922	Agpat2	2510002J07Rik|AV000834|BSCL|BSCL1|LPAAB|LPAAT-beta	1-acylglycerol-3-phosphate O-acyltransferase 2 (lysophosphatidic acid acyltransferase, beta)	protein-coding
mm_26084.1	chr3	136684887	136684901	+	1	NA	intron (NM_008913, intron 1 of 13)	intron (NM_008913, intron 1 of 13)	14828	NM_001293622	19055	Mm.331389	NM_008913	ENSMUSG00000028161	Ppp3ca	2900074D19Rik|CN|Caln|Calna|CnA	protein phosphatase 3, catalytic subunit, alpha isoform	protein-coding
mm_116089.1	chr13	28663380	28663383	-	1	NA	intron (NR_045053, intron 5 of 8)	intron (NR_045053, intron 5 of 8)	47492	NR_105787	102466635		NR_105787	ENSMUSG00000099158	Mir6368	Gm27800|mmu-mir-6368	microRNA 6368	ncRNA
mm_30207.1	chr3	144760795	144760809	-	1	NA	non-coding (NR_130895, exon 1 of 13)	non-coding (NR_130895, exon 1 of 13)	175	NR_130895	12722	Mm.454553	NM_009899	ENSMUSG00000056025	Clca3a1	Cacc|Clca1	chloride channel accessory 3A1	protein-coding
mm_154507.1	chrM	12062	12098	-	1	NA	NA	Intergenic	NA	NA								
mm_87735.1	chr10	60134778	60134810	+	1	NA	TTS (NM_052994)	TTS (NM_052994)	8018	NR_105871	102465546		NR_105871	ENSMUSG00000105468	Mir6906	mmu-mir-6906	microRNA 6906	ncRNA
mm_163086.1	chr11	69600696	69600704	-	1	NA	3' UTR (NM_013415, exon 7 of 7)	3' UTR (NM_013415, exon 7 of 7)	5260	NM_013415	11932	Mm.235204	NM_013415	ENSMUSG00000041329	Atp1b2	Amog|Atpb-2	ATPase, Na+/K+ transporting, beta 2 polypeptide	protein-coding
mm_22159.1	chr2	172940014	172940049	-	1	NA	exon (NM_007557, exon 1 of 7)	exon (NM_007557, exon 1 of 7)	290	NM_007557	12162	Mm.595	NM_007557	ENSMUSG00000008999	Bmp7	OP1	bone morphogenetic protein 7	protein-coding
mm_49836.1	chr6	37900478	37900487	+	1	NA	promoter-TSS (NM_001272076)	promoter-TSS (NM_001272076)	-5	NM_001272076	21848	Mm.41063	NM_145076	ENSMUSG00000029833	Trim24	A130082H20Rik|AI447469|D430004I05Rik|TIF1|TIF1-alpha|TIF1alpha|Tif1a	tripartite motif-containing 24	protein-coding
mm_3307.1	chr1	137898655	137898664	+	1	NA	Intergenic	Intergenic	-67796	NR_029795	735252		NR_029795	ENSMUSG00000065565	Mir181a-1	Mirn181a-1|Mirn213|miR-213|mir-181a-1|mmu-mir-213	microRNA 181a-1	ncRNA
mm_48112.1	chr5	137116178	137116219	-	1	NA	promoter-TSS (NM_201373)	promoter-TSS (NM_201373)	9	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_157578.1	chrX	52743892	52743918	-	1	NA	non-coding (NR_003188, exon 1 of 1)	non-coding (NR_003188, exon 1 of 1)	688	NR_003188	751866	Mm.381916	NR_003188		Kis2	Kis2-T1|Kis2-T2|Kis2-T3|Kis2-T4|Kis2-T5|Platr24|Xpcl1	Kaplan integration site 2	ncRNA
mm_79825.1	chr9	64544928	64544930	+	1	NA	intron (NM_001134399, intron 5 of 24)	intron (NM_001134399, intron 5 of 24)	159303	NM_001134399	214058	Mm.127721	NM_172522	ENSMUSG00000036466	Megf11	2410080H04Rik|D130061K05	multiple EGF-like-domains 11	protein-coding
mm_66467.1	chr7	44929529	44929537	-	1	NA	promoter-TSS (NM_001077264)	promoter-TSS (NM_001077264)	-43	NM_001077264	11771	Mm.6877	NM_007458	ENSMUSG00000060279	Ap2a1	Adtaa	adaptor-related protein complex 2, alpha 1 subunit	protein-coding
mm_16145.1	chr2	172006932	172006964	+	1	NA	Intergenic	Intergenic	36518	NM_175631	228942	Mm.40555	NM_175631	ENSMUSG00000067578	Cbln4	AI848962	cerebellin 4 precursor protein	protein-coding
mm_153091.1	chr19	32485824	32485841	-	1	NA	promoter-TSS (NM_010799)	promoter-TSS (NM_010799)	63	NM_010799	17330	Mm.255116	NM_010799	ENSMUSG00000024896	Minpp1	AA408516	multiple inositol polyphosphate histidine phosphatase 1	protein-coding
mm_1858.1	chr1	84839834	84839875	+	1	NA	promoter-TSS (NM_025386)	promoter-TSS (NM_025386)	13	NM_025386	66153	Mm.381192	NM_025386	ENSMUSG00000073633	Fbxo36	0610008D19Rik|1110020F21Rik|2410002G19Rik|D1Ertd757e	F-box protein 36	protein-coding
mm_36831.1	chr4	106316213	106316223	-	1	NA	promoter-TSS (NM_183225)	promoter-TSS (NM_183225)	5	NM_183225	329908	Mm.234544	NM_183225	ENSMUSG00000028514	Usp24	2700066K03Rik|2810030C21Rik|AI414051|B130021E18|C79851	ubiquitin specific peptidase 24	protein-coding
mm_149137.1	chr19	9003062	9003101	+	1	NA	exon (NM_009643, exon 5 of 5)	exon (NM_009643, exon 5 of 5)	13797	NM_001286518	66395	Mm.203866	NM_009643	ENSMUSG00000069833	Ahnak	DY6	AHNAK nucleoprotein (desmoyokin)	protein-coding
mm_162752.1	chr10	60062494	60062502	+	1	NA	exon (NM_001199187, exon 8 of 11)	exon (NM_001199187, exon 8 of 11)	-43759	NM_052994	94214	Mm.153429	NM_052994	ENSMUSG00000058297	Spock2	AA407235|Gcap26|mKIAA0275	sparc/osteonectin, cwcv and kazal-like domains proteoglycan 2	protein-coding
mm_132786.1	chr16	44943738	44943752	+	1	NA	promoter-TSS (NM_029018)	promoter-TSS (NM_029018)	67	NM_001128132	74603	Mm.297337	NM_027578	ENSMUSG00000036172	Cd200r3	4733401I18Rik|4833409J19Rik|AI505817|BB106877|mCD200RLb	CD200 receptor 3	protein-coding
mm_37522.1	chr4	124693569	124693606	-	1	NA	promoter-TSS (NM_026031)	promoter-TSS (NM_026031)	-33	NM_026031	67205	Mm.259121	NM_026031	ENSMUSG00000028907	Utp11l	2700082D03Rik|CGI-94|Cgi94|Utp11	UTP11-like, U3 small nucleolar ribonucleoprotein, (yeast)	protein-coding
mm_114928.1	chr13	95696933	95696979	+	1	NA	promoter-TSS (NM_010170)	promoter-TSS (NM_010170)	36	NM_010170	14064	Mm.440952	NM_010170	ENSMUSG00000021675	F2rl2	F730031A08|PAR3	coagulation factor II (thrombin) receptor-like 2	protein-coding
mm_64891.1	chr7	15945785	15945808	-	1	NA	intron (NM_133831, intron 1 of 12)	CpG	312	NM_133831	68077	Mm.277634	NM_133831	ENSMUSG00000041560	Gltscr2	5330430H08Rik|9430097C02Rik|AU041936|AW536441|PICT-1|R74911	glioma tumor suppressor candidate region gene 2	protein-coding
mm_121122.1	chr14	101840588	101840598	+	1	NA	promoter-TSS (NM_001347628)	promoter-TSS (NM_001347628)	-30	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_135465.1	chr16	45801781	45801790	-	1	NA	intron (NM_001252442, intron 4 of 18)	intron (NM_001252442, intron 4 of 18)	42593	NM_153412	208177	Mm.211477	NM_153412	ENSMUSG00000033149	Phldb2	AV253284|C820004H04Rik|LL5b|LL5beta	pleckstrin homology like domain, family B, member 2	protein-coding
mm_80131.1	chr9	70656249	70656261	+	1	NA	intron (NM_172772, intron 1 of 8)	intron (NM_172772, intron 1 of 8)	919	NM_172772	235461	Mm.170855	NM_172772	ENSMUSG00000042444	Fam63b	AI465301|B230380D07Rik|mKIAA1164	family with sequence similarity 63, member B	protein-coding
mm_51152.1	chr6	70703532	70703555	+	1	NA	Intergenic	Intergenic	88632	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_139131.1	chr17	47505192	47505205	+	1	NA	5' UTR (NM_001081636, exon 1 of 7)	5' UTR (NM_001081636, exon 1 of 7)	147	NM_001081635	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_110529.1	chr12	54986346	54986362	-	1	NA	promoter-TSS (NM_013815)	promoter-TSS (NM_013815)	-18	NM_013815	217578	Mm.479583	NM_013815	ENSMUSG00000035021	Baz1a	Acf1|B930060C03|BC065123|Gtl5|Wcrf180|cbp146	bromodomain adjacent to zinc finger domain 1A	protein-coding
mm_103552.1	chr11	77718782	77718814	-	1	NA	TTS (NM_001024205)	TTS (NM_001024205)	6495	NM_001313933	12957	Mm.22830	NM_009965	ENSMUSG00000000724	Cryba1	BA3/A1|Cryb	crystallin, beta A1	protein-coding
mm_38542.1	chr4	141598210	141598229	-	1	NA	intron (NM_133754, intron 1 of 8)	intron (NM_133754, intron 1 of 8)	1705	NM_001163256	74202	Mm.490327	NM_133754	ENSMUSG00000006219	Fblim1	2410043F08Rik|Cal|Fblp1|Gt10|migfilin|migfilin(s)	filamin binding LIM protein 1	protein-coding
mm_85155.1	chr9	96333178	96333199	-	1	NA	3' UTR (NM_007502, exon 7 of 7)	3' UTR (NM_007502, exon 7 of 7)	31111	NM_007502	11933	Mm.424	NM_007502	ENSMUSG00000032412	Atp1b3	AA409958|AI664000|AW212096	ATPase, Na+/K+ transporting, beta 3 polypeptide	protein-coding
mm_69176.1	chr7	127218399	127218465	-	1	NA	promoter-TSS (NM_017461)	promoter-TSS (NM_017461)	13	NM_017461	54204	Mm.18	NM_017461	ENSMUSG00000000486	Sept1	Diff6|Pnutl3	septin 1	protein-coding
mm_155767.1	chrX	96239936	96239948	+	1	NA	promoter-TSS (NR_030718)	promoter-TSS (NR_030718)	16	NR_030718	100038363	Mm.30815	NR_030718	ENSMUSG00000078122	F630028O10Rik	ENSMUSG00000065522|Gm14924|OTTMUSG00000018496|mir-223	RIKEN cDNA F630028O10 gene	ncRNA
mm_68822.1	chr7	126112022	126112025	-	1	NA	intron (NM_001311143, intron 17 of 23)	intron (NM_001311143, intron 17 of 23)	-29612	NM_001101488	269994	Mm.39599	NM_001101488	ENSMUSG00000046182	Gsg1l	AI852434|C230098I05Rik|G630023A01Rik|Gm637|g1l	GSG1-like	protein-coding
mm_149945.1	chr19	27322540	27322592	+	1	NA	promoter-TSS (NM_183179)	promoter-TSS (NM_183179)	-53	NM_183179	240595	Mm.269759	NM_183179	ENSMUSG00000047298	Kcnv2	KV11.1	potassium channel, subfamily V, member 2	protein-coding
mm_2978.1	chr1	133129413	133129448	+	1	NA	Intergenic	Intergenic	-1736	NM_133819	108954	Mm.293628	NM_133819	ENSMUSG00000046062	Ppp1r15b	1810033K10Rik|AI606441|C530022L24Rik|CReP	protein phosphatase 1, regulatory (inhibitor) subunit 15b	protein-coding
mm_113033.1	chr13	23531843	23531853	+	1	NA	TTS (NM_153173)	TTS (NM_153173)	804	NM_153173	69386	Mm.158272	NM_153173	ENSMUSG00000060981	Hist1h4h	1700024H08Rik	histone cluster 1, H4h	protein-coding
mm_26117.1	chr3	137838495	137838499	+	1	NA	Intergenic	RLTR19B|LTR|ERVK	-25990	NM_001316995	51788	Mm.117541	NM_016750	ENSMUSG00000037894	H2afz	H2A.Z|H2a.z-1	H2A histone family, member Z	protein-coding
mm_116162.1	chr13	30684643	30684673	-	1	NA	intron (NM_001037955, intron 3 of 6)	intron (NM_001037955, intron 3 of 6)	24599	NM_134068	105352	Mm.289646	NM_134068	ENSMUSG00000069255	Dusp22	JKAP|JSP1|LMW-DSP2|MKPX	dual specificity phosphatase 22	protein-coding
mm_132458.1	chr16	36156802	36156813	+	1	NA	promoter-TSS (NM_173869)	promoter-TSS (NM_173869)	-4	NM_173869	268885	Mm.187847	NM_173869	ENSMUSG00000059657	Stfa2l1	-	stefin A2 like 1	protein-coding
mm_134839.1	chr16	26371782	26371792	-	1	NA	promoter-TSS (NM_016674)	promoter-TSS (NM_016674)	52	NM_016674	12737	Mm.289441	NM_016674	ENSMUSG00000022512	Cldn1	AI596271	claudin 1	protein-coding
mm_49514.1	chr6	29870296	29870300	+	1	NA	intron (NM_001347084, intron 3 of 17)	intron (NM_001347084, intron 3 of 17)	10702	NM_001171001	74340	Mm.210899	NM_021414	ENSMUSG00000029772	Ahcyl2	4631427C17Rik|AI227036|Adohcyase3|mKIAA0828	S-adenosylhomocysteine hydrolase-like 2	protein-coding
mm_57725.1	chr6	128891106	128891178	-	1	NA	promoter-TSS (NM_001254946)	promoter-TSS (NM_001254946)	-18	NM_001254946	232406	Mm.30745	NM_001254946	ENSMUSG00000090164	BC035044	-	cDNA sequence BC035044	protein-coding
mm_49382.1	chr6	24733242	24733248	+	1	NA	promoter-TSS (NM_028920)	promoter-TSS (NM_028920)	0	NM_028920	74409	Mm.87331	NM_028920	ENSMUSG00000029679	Hyal6	4932701A20Rik|Hyal-ps1|Hyalp1	hyaluronoglucosaminidase 6	protein-coding
mm_34822.1	chr4	154961464	154961474	+	1	NA	exon (NM_010419, exon 3 of 3)	exon (NM_010419, exon 3 of 3)	546	NM_010419	15208	Mm.137268	NM_010419	ENSMUSG00000048001	Hes5	bHLHb38	hairy and enhancer of split 5 (Drosophila)	protein-coding
mm_21749.1	chr2	164821096	164821109	-	1	NA	exon (NM_178375, exon 2 of 2)	exon (NM_178375, exon 2 of 2)	-1584	NM_028028	71971	Mm.161149	NM_028028	ENSMUSG00000017764	Zswim1	2410003H12Rik|AI850991|BB046916	zinc finger SWIM-type containing 1	protein-coding
mm_164965.1	chr19	6393861	6393900	+	1	NA	exon (NM_011224, exon 17 of 20)	exon (NM_011224, exon 17 of 20)	-6703	NM_011242	19395	Mm.77017	NM_011242	ENSMUSG00000032946	Rasgrp2	CDC25L|Caldaggef1	RAS, guanyl releasing protein 2	protein-coding
mm_155859.1	chrX	101321242	101321246	+	1	NA	3' UTR (NM_172932, exon 7 of 7)	3' UTR (NM_172932, exon 7 of 7)	22065	NM_172932	245537	Mm.121508	NM_172932	ENSMUSG00000031302	Nlgn3	A230085M13Rik|HNL3|NL3	neuroligin 3	protein-coding
mm_121364.1	chr14	117350333	117350339	+	1	NA	intron (NM_001079844, intron 2 of 9)	intron (NM_001079844, intron 2 of 9)	425039	NM_011821	23888	Mm.440025	NM_011821	ENSMUSG00000058571	Gpc6	-	glypican 6	protein-coding
mm_10799.1	chr2	24349617	24349630	+	1	NA	exon (NM_031167, exon 5 of 5)	exon (NM_031167, exon 5 of 5)	4252	NM_001039701	16181	Mm.882	NM_031167	ENSMUSG00000026981	Il1rn	F630041P17Rik|IL-1ra	interleukin 1 receptor antagonist	protein-coding
mm_118547.1	chr14	17659279	17659296	+	1	NA	Intergenic	Intergenic	-1673	NM_001113417	21834	Mm.32563	NM_009380	ENSMUSG00000021779	Thrb	Nr1a2|T3R[b]|T3Rbeta|Thrb1|Thrb2|c-erbAbeta	thyroid hormone receptor beta	protein-coding
mm_89136.1	chr10	85538584	85538627	+	1	NA	intron (NM_028709, intron 1 of 16)	L2a|LINE|L2	-59806	NM_001017525	74007	Mm.36544	NM_028709	ENSMUSG00000020042	Btbd11	6330404E16Rik	BTB (POZ) domain containing 11	protein-coding
mm_29558.1	chr3	116807983	116807998	-	1	NA	intron (NM_001081326, intron 1 of 33)	CpG	176	NM_001081326	77559	Mm.237099	NM_001081326	ENSMUSG00000033400	Agl	1110061O17Rik|9430004C13Rik|9630046L06Rik|AI850929|C77197	amylo-1,6-glucosidase, 4-alpha-glucanotransferase	protein-coding
mm_152548.1	chr19	11372926	11372949	-	1	NA	Intergenic	L1M2a|LINE|L1	-2551	NM_001310331	666907		NM_001310331	ENSMUSG00000101389	Ms4a4a	EG666907	membrane-spanning 4-domains, subfamily A, member 4A	protein-coding
mm_165195.1	chr2	32387028	32387065	+	1	NA	exon (NM_008491, exon 2 of 6)	exon (NM_008491, exon 2 of 6)	693	NM_008491	16819	Mm.9537	NM_008491	ENSMUSG00000026822	Lcn2	24p3|AW212229|NRL|Sip24	lipocalin 2	protein-coding
mm_151626.1	chr19	3911771	3911790	-	1	NA	intron (NM_001271443, intron 1 of 6)	intron (NM_001271443, intron 1 of 6)	994	NM_144870	225887	Mm.44227	NM_144870	ENSMUSG00000059734	Ndufs8	BC021616|CI-23kD|TYKY	NADH dehydrogenase (ubiquinone) Fe-S protein 8	protein-coding
mm_26166.1	chr3	138280458	138280470	+	1	NA	exon (NM_007409, exon 3 of 9)	exon (NM_007409, exon 3 of 9)	2819	NM_007409	11522	Mm.2409	NM_007409	ENSMUSG00000074207	Adh1	ADH-AA|AI194826|Adh-1|Adh-1-t|Adh-1e|Adh-1t|Adh-3e|Adh1-e|Adh1-t|Adh1tl|Adh3-e	alcohol dehydrogenase 1 (class I)	protein-coding
mm_121167.1	chr14	103014427	103014462	+	1	NA	intron (NR_045657, intron 2 of 2)	RMER1B|Other|Other	19359	NR_045657	71264	Mm.399572	NR_045657		4933432I03Rik	-	RIKEN cDNA 4933432I03 gene	ncRNA
mm_117743.1	chr13	95889374	95889377	-	1	NA	intron (NM_027711, intron 1 of 35)	intron (NM_027711, intron 1 of 35)	2547	NM_027711	544963	Mm.38878	NM_027711	ENSMUSG00000021676	Iqgap2	4933417J23Rik|A630053O10|AI788777	IQ motif containing GTPase activating protein 2	protein-coding
mm_38625.1	chr4	142084198	142084219	-	1	NA	promoter-TSS (NM_145402)	promoter-TSS (NM_145402)	-90	NR_027137	100038693	Mm.402714	NR_027137	ENSMUSG00000073728	Tmem51os1	ENSMUSG00000073728|Gm10565|Tmem51as1	Tmem51 opposite strand 1	ncRNA
mm_94618.1	chr11	16759514	16759524	+	1	NA	intron (NM_207655, intron 1 of 27)	intron (NM_207655, intron 1 of 27)	7316	NM_007912	13649	Mm.8534	NM_007912	ENSMUSG00000020122	Egfr	9030024J15Rik|AI552599|Erbb|Errb1|Errp|Wa5|wa-2|wa2	epidermal growth factor receptor	protein-coding
mm_31414.1	chr4	48049081	48049092	+	1	NA	5' UTR (NM_015743, exon 2 of 8)	5' UTR (NM_015743, exon 2 of 8)	-2160	NM_001307989	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_65285.1	chr7	24435483	24435488	-	1	NA	intron (NM_199013, intron 2 of 2)	intron (NM_199013, intron 2 of 2)	10197	NM_199013	210145	Mm.33811	NM_199013	ENSMUSG00000062028	Irgc1	F630044M05Rik|Gm1102|Gm474|Ifgge|Iigp5|Irgc	immunity-related GTPase family, cinema 1	protein-coding
mm_105147.1	chr11	101462233	101462250	-	1	NA	exon (NM_012037, exon 4 of 6)	exon (NM_012037, exon 4 of 6)	3958	NM_012037	26949	Mm.29210	NM_012037	ENSMUSG00000034993	Vat1	VAT-1	vesicle amine transport 1	protein-coding
mm_147989.1	chr18	67631660	67631663	-	1	NA	intron (NM_001081073, intron 6 of 11)	RLTR31B2|LTR|ERVK	9675	NM_001081073	225659	Mm.111928	NM_001081073	ENSMUSG00000073542	Cep76	6230425F05Rik|9630013E05	centrosomal protein 76	protein-coding
mm_106189.1	chr11	116807681	116807758	-	1	NA	3' UTR (NM_001347633, exon 5 of 5)	3' UTR (NM_001347633, exon 5 of 5)	20327	NM_026280	67622	Mm.64962	NM_026280	ENSMUSG00000020814	Mxra7	1810057P16Rik|E130302J09Rik	matrix-remodelling associated 7	protein-coding
mm_125751.1	chr15	73748417	73748418	+	1	NA	5' UTR (NM_008975, exon 1 of 6)	5' UTR (NM_008975, exon 1 of 6)	391	NM_008975	19245	Mm.390807	NM_008975	ENSMUSG00000059895	Ptp4a3	AV088979|Prl-3|pPtp4a3	protein tyrosine phosphatase 4a3	protein-coding
mm_38325.1	chr4	137356311	137356318	-	1	NA	intron (NM_009861, intron 1 of 5)	PB1D9|SINE|Alu	1445	NM_009861	12540	Mm.1022	NM_009861	ENSMUSG00000006699	Cdc42	AI747189|AU018915	cell division cycle 42	protein-coding
mm_5631.1	chr1	40425328	40425332	-	1	NA	Intergenic	RMER12B|LTR|ERVK	-4240	NM_001294171	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_10716.1	chr2	22804628	22804639	+	1	NA	intron (NM_019456, intron 1 of 13)	intron (NM_019456, intron 1 of 13)	30306	NM_019456	54519	Mm.14255	NM_019456	ENSMUSG00000026786	Apbb1ip	9930118P07Rik|Prp48	amyloid beta (A4) precursor protein-binding, family B, member 1 interacting protein	protein-coding
mm_114668.1	chr13	78211472	78211479	+	1	NA	intron (NR_045195, intron 1 of 2)	intron (NR_045195, intron 1 of 2)	-12602	NM_010151	13865	Mm.439653	NM_010151	ENSMUSG00000069171	Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR-3|EAR3|Erbal3|SVP44|Tcfcoup1	nuclear receptor subfamily 2, group F, member 1	protein-coding
mm_142426.1	chr17	45569347	45569381	-	1	NA	exon (NM_008302, exon 8 of 11)	exon (NM_008302, exon 8 of 11)	3897	NM_008302	15516	Mm.2180	NM_008302	ENSMUSG00000023944	Hsp90ab1	90kDa|AL022974|C81438|Hsp84|Hsp84-1|Hsp90|Hspcb	heat shock protein 90 alpha (cytosolic), class B member 1	protein-coding
mm_94106.1	chr10	128583758	128583800	-	1	NA	TTS (NR_105882)	TTS (NR_105882)	718	NR_105882	102465553		NR_105882	ENSMUSG00000098592	Mir6917	Gm27633|mmu-mir-6917	microRNA 6917	ncRNA
mm_173067.1	chrX	134541621	134541621	-	1	NA	promoter-TSS (NM_013898).2	promoter-TSS (NM_013898).2	49	NM_013898	30058	Mm.214504	NM_013898	ENSMUSG00000048007	Timm8a1	DXHXS1274E|Ddp1|Fci-12|Tim8a|Timm8a	translocase of inner mitochondrial membrane 8A1	protein-coding
mm_96123.1	chr11	60776873	60776890	+	1	NA	promoter-TSS (NM_001085440)	promoter-TSS (NM_001085440)	484	NM_009410	21975	Mm.10708	NM_009410	ENSMUSG00000002814	Top3a	-	topoisomerase (DNA) III alpha	protein-coding
mm_37005.1	chr4	111880599	111880614	-	1	NA	intron (NM_145551, intron 13 of 14)	intron (NM_145551, intron 13 of 14)	22190	NM_145551	230612	Mm.26630	NM_145551	ENSMUSG00000028544	Slc5a9	AI159731|SGLT4	solute carrier family 5 (sodium/glucose cotransporter), member 9	protein-coding
mm_173021.1	chrX	102208364	102208381	+	1	NA	Intergenic	Intergenic	-18981	NM_009094	20102	Mm.66	NM_009094	ENSMUSG00000031320	Rps4x	Rps4|Rps4-1	ribosomal protein S4, X-linked	protein-coding
mm_46441.1	chr5	105082751	105082783	-	1	NA	exon (NM_172777, exon 8 of 11)	exon (NM_172777, exon 8 of 11)	27525	NM_172777	236573	Mm.425261	NM_172777	ENSMUSG00000029298	Gbp9	-	guanylate-binding protein 9	protein-coding
mm_117588.1	chr13	89694926	89694931	-	1	NA	intron (NM_019389, intron 6 of 13)	intron (NM_019389, intron 6 of 13)	47584	NM_001081249	13003	Mm.158700	NM_019389	ENSMUSG00000021614	Vcan	5430420N07Rik|9430051N09|Cspg2|DPEAAE|NG2|PG-M|PG-M(V0)|PG-M(V1)|hdf	versican	protein-coding
mm_47912.1	chr5	134951119	134951145	-	1	NA	Intergenic	Intergenic	-4198	NM_009903	12740	Mm.7339	NM_009903	ENSMUSG00000047501	Cldn4	Cep-r|Cpetr|Cpetr1	claudin 4	protein-coding
mm_17259.1	chr2	25946081	25946091	-	1	NA	intron (NM_001276359, intron 5 of 16)	intron (NM_001276359, intron 5 of 16)	37196	NM_001276360	227634	Mm.36834	NM_001115076	ENSMUSG00000026933	Camsap1	9530003A05Rik|C77823|PRO2405	calmodulin regulated spectrin-associated protein 1	protein-coding
mm_122984.1	chr14	54984733	54984749	-	1	NA	exon (NM_080728, exon 23 of 41)	exon (NM_080728, exon 23 of 41)	-8965	NR_030607	100124433		NR_030607	ENSMUSG00000077928	Mir208b	Mirn208b|mir-208b	microRNA 208b	ncRNA
mm_170066.1	chr17	31054157	31054168	+	1	NA	Intergenic	ERVB3_1-LTR_MM|LTR|ERVK	-3532	NM_009593	11307	Mm.15691	NM_009593	ENSMUSG00000024030	Abcg1	AW413978|Abc8|White	ATP-binding cassette, sub-family G (WHITE), member 1	protein-coding
mm_37215.1	chr4	117904589	117904615	-	1	NA	intron (NM_146152, intron 6 of 19)	intron (NM_146152, intron 6 of 19)	10397	NM_146152	230673	Mm.287810	NM_146152	ENSMUSG00000033365	Ipo13	Imp13|Kap13|Ranbp13	importin 13	protein-coding
mm_130017.1	chr15	88706404	88706431	-	1	NA	intron (NM_001033274, intron 7 of 12)	intron (NM_001033274, intron 7 of 12)	27802	NM_001033274	223770	Mm.254438	NM_001033274	ENSMUSG00000022387	Brd1	1110059H06Rik|AI316859|mKIAA4191	bromodomain containing 1	protein-coding
mm_122917.1	chr14	54958707	54958728	-	1	NA	exon (NM_010856, exon 15 of 39)	exon (NM_010856, exon 15 of 39)	7890	NM_001164171	17888	Mm.290003	NM_010856	ENSMUSG00000040752	Myh6	A830009F23Rik|AA517445|Myhc-a|Myhca|alpha-MHC	myosin, heavy polypeptide 6, cardiac muscle, alpha	protein-coding
mm_170971.1	chr2	63911919	63911933	-	1	NA	Intergenic	BGLII|LTR|ERVK	186112	NM_001267846	60344	Mm.130769	NM_021716	ENSMUSG00000075324	Fign	fi|fidget	fidgetin	protein-coding
mm_125006.1	chr15	25364721	25364745	+	1	NA	exon (NM_027395, exon 2 of 2)	exon (NM_027395, exon 2 of 2)	49031	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	brain abundant, membrane attached signal protein 1	protein-coding
mm_75322.1	chr8	41835309	41835315	-	1	NA	intron (NR_045497, intron 1 of 5)	intron (NR_045497, intron 1 of 5)	8045	NR_045497	69966	Mm.416903	NR_045497	ENSMUSG00000102046	2810404M03Rik	-	RIKEN cDNA 2810404M03 gene	ncRNA
mm_66085.1	chr7	30957343	30957375	-	1	NA	promoter-TSS (NM_011680)	promoter-TSS (NM_011680)	-556	NM_011680	22282	Mm.322453	NM_011680	ENSMUSG00000058239	Usf2	Usf-2|bHLHb12	upstream transcription factor 2	protein-coding
mm_18756.1	chr2	73437524	73437541	-	1	NA	exon (NM_153138, exon 5 of 8)	exon (NM_153138, exon 5 of 8)	16357	NM_001289722	215280	Mm.223504	NM_153138	ENSMUSG00000075284	Wipf1	AI115543|D2Ertd120e|WIP|Waspip	WAS/WASL interacting protein family, member 1	protein-coding
mm_150414.1	chr19	37207529	37207587	+	1	NA	promoter-TSS (NM_027314)	promoter-TSS (NM_027314)	13	NM_001164336	69104	Mm.175989	NM_027314	ENSMUSG00000023307	March5	1810015H18Rik|2310008I22Rik|2700055A20Rik|5730499H23Rik|E130202O05Rik|MARCH-V|MITOL|Marchv|Rnf153	membrane-associated ring finger (C3HC4) 5	protein-coding
mm_86881.1	chr10	21997436	21997449	+	1	NA	intron (NM_001161848, intron 9 of 11)	intron (NM_001161848, intron 9 of 11)	2776	NM_011361	20393	Mm.28405	NM_011361	ENSMUSG00000019970	Sgk1	Sgk	serum/glucocorticoid regulated kinase 1	protein-coding
mm_62301.1	chr7	100172456	100172457	+	1	NA	Intergenic	B1_Mur2|SINE|Alu	-4214	NM_001190869	57442	Mm.282386	NM_020574	ENSMUSG00000035165	Kcne3	2210017H05Rik|MiRP2	potassium voltage-gated channel, Isk-related subfamily, gene 3	protein-coding
mm_58346.1	chr6	147263859	147263874	-	1	NA	5' UTR (NM_008970, exon 1 of 4)	5' UTR (NM_008970, exon 1 of 4)	147	NM_008970	19227	Mm.28440	NM_008970	ENSMUSG00000048776	Pthlh	PLP|PTH-like|Pthrp	parathyroid hormone-like peptide	protein-coding
mm_21175.1	chr2	154871552	154871575	-	1	NA	3' UTR (NM_026030, exon 9 of 9)	3' UTR (NM_026030, exon 9 of 9)	21343	NM_026030	67204	Mm.377134	NM_026030	ENSMUSG00000074656	Eif2s2	2810026E11Rik|38kDa|AA408636|AA571381|AA986487|AW822225|D2Ertd303e|EIF2|EIF2B	eukaryotic translation initiation factor 2, subunit 2 (beta)	protein-coding
mm_143619.1	chr17	78835327	78835373	-	1	NA	promoter-TSS (NM_181649)	promoter-TSS (NM_181649)	31	NM_001081179	320473	Mm.46309	NM_028084	ENSMUSG00000039414	Heatr5b	2010013B10Rik|A230048G03Rik|AV071430|D330050P16Rik|mKIAA1414	HEAT repeat containing 5B	protein-coding
mm_139510.1	chr17	56372439	56372448	+	1	NA	exon (NM_172132, exon 7 of 23)	exon (NM_172132, exon 7 of 23)	46393	NM_172132	193796	Mm.45047	NM_172132	ENSMUSG00000024201	Kdm4b	4732474L06Rik|Jmjd2b|mKIAA0876	lysine (K)-specific demethylase 4B	protein-coding
mm_6088.1	chr1	63176654	63176707	-	1	NA	promoter-TSS (NM_018796)	promoter-TSS (NM_018796)	142	NM_145518	227197	Mm.290791	NM_145518	ENSMUSG00000025968	Ndufs1	5830412M15Rik|9930026A05Rik	NADH dehydrogenase (ubiquinone) Fe-S protein 1	protein-coding
mm_147509.1	chr18	50568722	50568730	-	1	NA	promoter-TSS (NM_026108)	promoter-TSS (NM_026108)	-27	NM_026108	67365	Mm.158150	NM_026108	ENSMUSG00000048875	Hdhd1a	1700121L12Rik|GS1|Hdhd1|Pudp	haloacid dehalogenase-like hydrolase domain containing 1A	protein-coding
mm_142524.1	chr17	46327991	46328001	-	1	NA	promoter-TSS (NM_170680)	promoter-TSS (NM_170680)	27	NM_001347396	224814	Mm.76543	NM_145140	ENSMUSG00000032842	Abcc10	Mrp7|mFLJ00002	ATP-binding cassette, sub-family C (CFTR/MRP), member 10	protein-coding
mm_11846.1	chr2	45197756	45197778	+	1	NA	Intergenic	Intergenic	-84488	NM_015753	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_128727.1	chr15	64060677	64060690	-	1	NA	promoter-TSS (NM_144846)	promoter-TSS (NM_144846)	-235	NM_144846	223601	Mm.246108	NM_144846	ENSMUSG00000022378	Fam49b	0910001A06Rik|AW122079	family with sequence similarity 49, member B	protein-coding
mm_85188.1	chr9	96713754	96713755	-	1	NA	intron (NM_175537, intron 2 of 2)	L1MD|LINE|L1	17921	NM_175537	245007	Mm.485954	NM_175537	ENSMUSG00000040433	Zbtb38	A930014K01Rik|CIBZ	zinc finger and BTB domain containing 38	protein-coding
mm_54531.1	chr6	36715481	36715492	-	1	NA	TTS (NM_008973)	TTS (NM_008973)	95875	NM_008973	19242	Mm.279690	NM_008973	ENSMUSG00000029838	Ptn	HARP|HB-GAM|HBBN|HBGF-8|HBNF|OSF|Osf-1|Osf1	pleiotrophin	protein-coding
mm_146685.1	chr18	12862342	12862426	-	1	NA	5' UTR (NM_001252492, exon 1 of 14)	5' UTR (NM_001252492, exon 1 of 14)	329	NM_001252493	64291	Mm.259470	NM_020573	ENSMUSG00000044252	Osbpl1a	G430090F17Rik|Gm753|ORP-1|Osbpl1b	oxysterol binding protein-like 1A	protein-coding
mm_13812.1	chr2	119174484	119174527	+	1	NA	promoter-TSS (NM_001039223)	promoter-TSS (NM_001039223)	-4	NM_001039223	623781	Mm.389344	NM_001039223	ENSMUSG00000055926	Gm14137	OTTMUSG00000015762	predicted gene 14137	protein-coding
mm_60692.1	chr7	45172293	45172305	+	1	NA	intron (NM_182993, intron 9 of 11)	intron (NM_182993, intron 9 of 11)	-1004	NR_106022	102465638		NR_106022	ENSMUSG00000106470	Mir7055	mmu-mir-7055	microRNA 7055	ncRNA
mm_140519.1	chr17	6106279	6106307	-	1	NA	promoter-TSS (NM_001103181)	promoter-TSS (NM_001103181)	-537	NM_001103181	68842	Mm.449307	NM_054040	ENSMUSG00000034377	Tulp4	1110057P05Rik|2210038L17Rik|Tusp	tubby like protein 4	protein-coding
mm_94951.1	chr11	29742349	29742406	+	1	NA	TTS (NM_146016)	TTS (NM_146016)	23814	NM_024226	68585	Mm.192580	NM_024226	ENSMUSG00000020458	Rtn4	1110020G17Rik|AA407876|AA409940|AA960376|ASY|C130026I10Rik|NOGO|NSP-CL|NgA|Nogo-A|Nogo-B|Nogo-C|mKIAA0886|mKIAA4153	reticulon 4	protein-coding
mm_96533.1	chr11	68594054	68594064	+	1	NA	intron (NM_177779, intron 4 of 6)	intron (NM_177779, intron 4 of 6)	7022	NM_177779	276920	Mm.123046	NM_177779	ENSMUSG00000045915	Ccdc42	A530001H01Rik	coiled-coil domain containing 42	protein-coding
mm_167795.1	chr9	123924827	123924847	-	1	NA	Intergenic	CpG	43855	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_113375.1	chr13	33004564	33004578	+	1	NA	promoter-TSS (NM_009256)	promoter-TSS (NM_009256)	30	NM_009256	20723	Mm.245041	NM_009256	ENSMUSG00000045827	Serpinb9	BB283241|CAP-3|CAP3|PI-9|PI9|Spi6|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 9	protein-coding
mm_90694.1	chr10	130322828	130322842	+	1	NA	promoter-TSS (NM_183264)	promoter-TSS (NM_183264)	-17	NM_183264	67596	Mm.131264	NM_183264	ENSMUSG00000034833	Tespa1	5830405N20Rik|A430001F24Rik|AI450549	thymocyte expressed, positive selection associated 1	protein-coding
mm_96397.1	chr11	67250545	67250563	+	1	NA	exon (NM_010855, exon 21 of 40)	exon (NM_010855, exon 21 of 40)	12742	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_56353.1	chr6	93717490	93717517	-	1	NA	intron (NM_001083321, intron 11 of 21)	intron (NM_001083321, intron 11 of 21)	195460	NR_104594	14924	Mm.217216	NM_010367	ENSMUSG00000045095	Magi1	AIP3|BAP1|Baiap1|Gukmi1|MAGI1c|Magi-1|TNRC19|WWP3|mKIAA4129	membrane associated guanylate kinase, WW and PDZ domain containing 1	protein-coding
mm_82141.1	chr9	123769197	123769215	+	1	NA	intron (NM_009913, intron 1 of 2)	intron (NM_009913, intron 1 of 2)	1995	NM_001166625	12769	Mm.440604	NM_009913	ENSMUSG00000029530	Ccr9	A130091K22Rik|Cmkbr10|GPR-9-6	chemokine (C-C motif) receptor 9	protein-coding
mm_58793.1	chr7	16160185	16160194	+	1	NA	3' UTR (NM_148946, exon 10 of 10)	3' UTR (NM_148946, exon 10 of 10)	-15206	NM_001277988	17537	Mm.360516	NM_008627	ENSMUSG00000041420	Meis3	AI573393|Mrg2	Meis homeobox 3	protein-coding
mm_106863.1	chr12	8009339	8009349	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	31667	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_85715.1	chr9	108209088	108209103	-	1	NA	exon (NM_001276486, exon 4 of 4)	exon (NM_001276486, exon 4 of 4)	-18712	NM_007567	12217	Mm.20425	NM_007567	ENSMUSG00000032589	Bsn	-	bassoon	protein-coding
mm_52965.1	chr6	123124541	123124564	+	1	NA	intron (NM_011999, intron 1 of 5)	B1F2|SINE|Alu	1236	NM_001170333	26888	Mm.47384	NM_011999	ENSMUSG00000030148	Clec4a2	Clec4a|Clecsf6|DCIR|Dcir1	C-type lectin domain family 4, member a2	protein-coding
mm_51982.1	chr6	91978958	91978983	+	1	NA	promoter-TSS (NM_172731)	promoter-TSS (NM_172731)	5	NM_172731	232237	Mm.295740	NM_172731	ENSMUSG00000034037	Fgd5	C330025N11Rik|ZFYVE23|mFLJ00274	FYVE, RhoGEF and PH domain containing 5	protein-coding
mm_127887.1	chr15	9136120	9136123	-	1	NA	intron (NM_001285980, intron 2 of 9)	B1F1|SINE|Alu	4333	NM_013787	27401	Mm.35584	NM_013787	ENSMUSG00000054115	Skp2	4930500A04Rik|FBXL1|FWD1|p45	S-phase kinase-associated protein 2 (p45)	protein-coding
mm_73319.1	chr8	105226819	105226822	+	1	NA	intron (NM_145604, intron 1 of 15)	intron (NM_145604, intron 1 of 15)	1632	NM_145604	234678	Mm.27186	NM_145604	ENSMUSG00000031889	D230025D16Rik	BC006874|Lin10	RIKEN cDNA D230025D16 gene	protein-coding
mm_70616.1	chr8	13435505	13435518	+	1	NA	promoter-TSS (NM_001143672)	promoter-TSS (NM_001143672)	52	NM_001143672	272465	Mm.250502	NM_001143671	ENSMUSG00000038457	Tmem255b	Fam70b|Gm687	transmembrane protein 255B	protein-coding
mm_131264.1	chr16	10827922	10827944	+	1	NA	Intergenic	B4|SINE|B4	-7126	NM_001162932	223970	Mm.325777	NM_001033278	ENSMUSG00000037991	Rmi2	A630055G03Rik|Gm537|Gm929	RecQ mediated genome instability 2	protein-coding
mm_71992.1	chr8	70617722	70617740	+	1	NA	exon (NM_153074, exon 2 of 3)	exon (NM_153074, exon 2 of 3)	887	NM_153074	211228	Mm.132939	NM_153074	ENSMUSG00000049988	Lrrc25	Mapa	leucine rich repeat containing 25	protein-coding
mm_39261.1	chr5	3557741	3557753	+	1	NA	exon (NM_001042501, exon 3 of 11)	exon (NM_001042501, exon 3 of 11)	13914	NM_001042501	68152	Mm.240265	NM_026583	ENSMUSG00000058503	Fam133b	2900022K02Rik|5830415L20Rik	family with sequence similarity 133, member B	protein-coding
mm_167680.1	chr9	78532728	78532756	+	1	NA	Intergenic	Intergenic	-51018	NM_010106	13627	Mm.138471	NM_010106	ENSMUSG00000037742	Eef1a1	-	eukaryotic translation elongation factor 1 alpha 1	protein-coding
mm_14146.1	chr2	126552812	126552820	+	1	NA	promoter-TSS (NM_011978)	promoter-TSS (NM_011978)	-208	NM_011978	26458	Mm.290044	NM_011978	ENSMUSG00000027359	Slc27a2	ACSVL1|FATP2|VLCS|Vlac|Vlacs	solute carrier family 27 (fatty acid transporter), member 2	protein-coding
mm_4137.1	chr1	170644573	170644586	+	1	NA	promoter-TSS (NM_177068)	promoter-TSS (NM_177068)	47	NM_177068	320078	Mm.287131	NM_177068	ENSMUSG00000038463	Olfml2b	1110018N05Rik|4832415H08Rik|AI467542	olfactomedin-like 2B	protein-coding
mm_88570.1	chr10	79669482	79669492	+	1	NA	promoter-TSS (NM_148934)	promoter-TSS (NM_148934)	77	NM_148934	110012	Mm.22623	NM_148934	ENSMUSG00000020308	Tpgs1	AV005629|Gm16517|Gtrgeo22|PGs1	tubulin polyglutamylase complex subunit 1	protein-coding
mm_82037.1	chr9	122117381	122117391	+	1	NA	5' UTR (NM_133741, exon 1 of 7)	5' UTR (NM_133741, exon 1 of 7)	120	NM_133741	20623	Mm.257989	NM_133741	ENSMUSG00000038145	Snrk	2010012F07Rik|AI448042|AW547029|E030034B15|R74830|mKIAA0096	SNF related kinase	protein-coding
mm_24248.1	chr3	89146146	89146154	+	1	NA	TTS (NM_008227)	TTS (NM_008227)	9527	NM_001099779	18770	Mm.383180	NM_013631	ENSMUSG00000041237	Pklr	Pk-1|Pk1|R-PK	pyruvate kinase liver and red blood cell	protein-coding
mm_14609.1	chr2	136532244	136532259	+	1	NA	promoter-TSS (NM_175667)	promoter-TSS (NM_175667)	-70	NM_175667	319196	Mm.477841	NM_175667	ENSMUSG00000074771	Ankef1	AV276460|Ankrd5	ankyrin repeat and EF-hand domain containing 1	protein-coding
mm_93404.1	chr10	107912278	107912284	-	1	NA	promoter-TSS (NM_001177567)	promoter-TSS (NM_001177567)	-147	NM_001177567	628870	Mm.336090	NM_001177567	ENSMUSG00000091455	Otogl	EG628870|Gm6924	otogelin-like	protein-coding
mm_19821.1	chr2	110840056	110840062	-	1	NA	intron (NM_001128103, intron 4 of 26)	intron (NM_001128103, intron 4 of 26)	110185	NM_001128103	228432	Mm.483325	NM_001081556	ENSMUSG00000074968	Ano3	AI838058|B230324K02Rik|Tmem16c	anoctamin 3	protein-coding
mm_128067.1	chr15	26895579	26895585	-	1	NA	promoter-TSS (NM_176959)	promoter-TSS (NM_176959)	-18	NM_176959	448987	Mm.253378	NM_176959	ENSMUSG00000043556	Fbxl7	AL023057|D230018M15Rik|FBL7|Fbl6	F-box and leucine-rich repeat protein 7	protein-coding
mm_90410.1	chr10	127420385	127420395	+	1	NA	promoter-TSS (NM_001168293)	promoter-TSS (NM_001168293)	-477	NM_027900	71750	Mm.29342	NM_027900	ENSMUSG00000025404	R3hdm2	1300003K24Rik|AU041262|mKIAA1002	R3H domain containing 2	protein-coding
mm_90452.1	chr10	127706795	127706806	+	1	NA	intron (NM_001081219, intron 3 of 26)	intron (NM_001081219, intron 3 of 26)	1544	NM_001081219	432516	Mm.90450	NM_001081219	ENSMUSG00000025401	Myo1a	BBM-I|Myhl	myosin IA	protein-coding
mm_58093.1	chr6	137519742	137519742	-	1	NA	intron (NM_001271595, intron 8 of 20)	B4A|SINE|B4	153	NM_001271589	13860	Mm.235346	NM_007945	ENSMUSG00000015766	Eps8	AW261790	epidermal growth factor receptor pathway substrate 8	protein-coding
mm_48611.1	chr5	144358104	144358123	-	1	NA	promoter-TSS (NM_025833)	promoter-TSS (NM_025833)	-1	NM_025833	66898	Mm.18814	NM_025833	ENSMUSG00000038859	Baiap2l1	1300006M19Rik|AI585895|IRTKS	BAI1-associated protein 2-like 1	protein-coding
mm_34474.1	chr4	148193051	148193054	+	1	NA	Intergenic	Intergenic	32384	NM_176848	230904	Mm.262287	NM_176848	ENSMUSG00000041556	Fbxo2	FBG1|FBX2|Fbs1|Fbs2|NFB42|Prpl4	F-box protein 2	protein-coding
mm_26943.1	chr3	20266298	20266330	-	1	NA	exon (NM_029706, exon 5 of 11)	exon (NM_029706, exon 5 of 11)	9419	NM_029706	76703	Mm.34692	NM_029706	ENSMUSG00000011463	Cpb1	0910001A18Rik|1810063F02Rik|2210008M23Rik|AI504870	carboxypeptidase B1 (tissue)	protein-coding
mm_7090.1	chr1	88584784	88584790	-	1	NA	Intergenic	Intergenic	33270	NR_037971	100503197	Mm.99352	NR_037971	ENSMUSG00000100798	Gm19589	-	predicted gene, 19589	ncRNA
mm_72181.1	chr8	72319827	72319877	+	1	NA	exon (NM_008452, exon 2 of 3)	exon (NM_008452, exon 2 of 3)	790	NM_008452	16598	Mm.26938	NM_008452	ENSMUSG00000055148	Klf2	Lklf	Kruppel-like factor 2 (lung)	protein-coding
mm_86141.1	chr9	116980673	116980676	-	1	NA	intron (NM_001172122, intron 3 of 13)	intron (NM_001172122, intron 3 of 13)	271809	NM_001172123	207181	Mm.326411	NM_178660	ENSMUSG00000039607	Rbms3	6720477E09Rik|8430436O14Rik	RNA binding motif, single stranded interacting protein	protein-coding
mm_43501.1	chr5	136978077	136978078	+	1	NA	Intergenic	Intergenic	8827	NM_001310747	70103	Mm.273147	NM_027318	ENSMUSG00000059518	Znhit1	2700001K05Rik|ZNFN4A1	zinc finger, HIT domain containing 1	protein-coding
mm_49883.1	chr6	38663020	38663060	+	1	NA	promoter-TSS (NM_001101507)	promoter-TSS (NM_001101507)	-29	NM_001101507	665180	Mm.349066	NM_001101507	ENSMUSG00000079598	Clec2l	AI414054|AW122724|Gm1064	C-type lectin domain family 2, member L	protein-coding
mm_143364.1	chr17	67354267	67354282	-	1	NA	5' UTR (NM_008984, exon 1 of 31)	5' UTR (NM_008984, exon 1 of 31)	185	NM_008984	19274	Mm.311809	NM_008984	ENSMUSG00000033278	Ptprm	RPTPmu|mKIAA4044	protein tyrosine phosphatase, receptor type, M	protein-coding
mm_139130.1	chr17	47505175	47505182	+	1	NA	5' UTR (NM_001081636, exon 1 of 7)	5' UTR (NM_001081636, exon 1 of 7)	127	NM_001081635	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_137517.1	chr17	27115981	27115994	+	1	NA	exon (NM_080553, exon 48 of 58)	exon (NM_080553, exon 48 of 58)	17904	NM_026063	67267	Mm.272389	NM_026063	ENSMUSG00000024208	Uqcc2	2900010M23Rik|Cbp6|M19|Mnf1	ubiquinol-cytochrome c reductase complex assembly factor 2	protein-coding
mm_138439.1	chr17	35122755	35122764	+	1	NA	promoter-TSS (NM_032460)	promoter-TSS (NM_032460)	-193	NM_032460	81845	Mm.7405	NM_032460	ENSMUSG00000092417	Gpank1	Bat-4|Bat4|D17H6S54E|G5	G patch domain and ankyrin repeats 1	protein-coding
mm_113581.1	chr13	40860157	40860187	+	1	NA	5' UTR (NM_023887, exon 1 of 3)	5' UTR (NM_023887, exon 1 of 3)	404	NM_023887	14538	Mm.314757	NM_008105	ENSMUSG00000021360	Gcnt2	5330430K10Rik|IGnT|IGnTA|IGnTB|IGnTC	glucosaminyl (N-acetyl) transferase 2, I-branching enzyme	protein-coding
mm_108071.1	chr12	73941970	73941996	+	1	NA	exon (NM_010431, exon 12 of 15)	exon (NM_010431, exon 12 of 15)	-22547	NM_178392	75627	Mm.25937	NM_178392	ENSMUSG00000021113	Snapc1	2700033G17Rik|AU015787	small nuclear RNA activating complex, polypeptide 1	protein-coding
mm_99043.1	chr11	98964865	98964883	+	1	NA	intron (NM_001176528, intron 1 of 7)	intron (NM_001176528, intron 1 of 7)	4403	NM_001176528	19401	Mm.439744	NM_009024	ENSMUSG00000037992	Rara	Nr1b1|RAR|RARalpha1	retinoic acid receptor, alpha	protein-coding
mm_9661.1	chr1	177796536	177796546	-	1	NA	promoter-TSS (NM_007422)	promoter-TSS (NM_007422)	-32	NM_007422	11566	Mm.338021	NM_007422	ENSMUSG00000015961	Adss	AI314886|AS|Adss2	adenylosuccinate synthetase, non muscle	protein-coding
mm_157787.1	chrX	73824902	73824914	-	1	NA	promoter-TSS (NM_001290540)	promoter-TSS (NM_001290540)	61	NM_001029868	245469	Mm.103782	NM_001029868	ENSMUSG00000002006	Pdzd4	B230341P03|D130075J17Rik|Kiaa1444-hp|LU1|PDZRN4L|Pdzk4|Pdzrnk4l|Xlu	PDZ domain containing 4	protein-coding
mm_35724.1	chr4	44704463	44704495	-	1	NA	non-coding (NR_073462, exon 1 of 1)	non-coding (NR_073462, exon 1 of 1)	1679	NR_073462	70602	Mm.491142	NR_073462	ENSMUSG00000103995	5730488B01Rik	-	RIKEN cDNA 5730488B01 gene	ncRNA
mm_61743.1	chr7	82535772	82535778	+	1	NA	intron (NM_001190374, intron 15 of 29)	intron (NM_001190374, intron 15 of 29)	112753	NM_177894	330577	Mm.222812	NM_177894	ENSMUSG00000038570	Saxo2	1700129I04Rik|D030069K18|Fam154b	stabilizer of axonemal microtubules 2	protein-coding
mm_67943.1	chr7	100371774	100371788	-	1	NA	promoter-TSS (NM_001017985)	promoter-TSS (NM_001017985)	115	NM_028292	72590	Mm.177502	NM_028292	ENSMUSG00000030718	Ppme1	1110069N17Rik|2700017M01Rik|PME-1|Pme1	protein phosphatase methylesterase 1	protein-coding
mm_29736.1	chr3	126922741	126922751	-	1	NA	3' UTR (NM_178655, exon 25 of 25)	3' UTR (NM_178655, exon 25 of 25)	20640	NM_001034168	109676	Mm.220242	NM_178655	ENSMUSG00000032826	Ank2	100043364|AI835472|AW491075|Ank-2|Gm4392	ankyrin 2, brain	protein-coding
mm_37.1	chr1	6453819	6453830	+	1	NA	Intergenic	Intergenic	-33407	NM_001244693	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding
mm_107573.1	chr12	44329193	44329209	+	1	NA	intron (NM_001146031, intron 1 of 27)	CpG	316	NM_001146031	319504	Mm.208439	NM_176930	ENSMUSG00000020598	Nrcam	Bravo|C030017F07Rik|C130076O07Rik|mKIAA0343	neuronal cell adhesion molecule	protein-coding
mm_150550.1	chr19	39321623	39321626	+	1	NA	exon (NM_007815, exon 6 of 9)	exon (NM_007815, exon 6 of 9)	34539	NM_007815	13095	Mm.20764	NM_007815	ENSMUSG00000003053	Cyp2c29	AHOH|AHOHase|AI159681|AI196010|Ah-2|Ahh-1|Cyp2c|P450-2C	cytochrome P450, family 2, subfamily c, polypeptide 29	protein-coding
mm_130218.1	chr15	95772645	95772655	-	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-18193	NM_175344	105722	Mm.38087	NM_175344	ENSMUSG00000064210	Ano6	2900059G15Rik|AA407480|AW554778|F730003B03Rik|Tmem16f	anoctamin 6	protein-coding
mm_103853.1	chr11	83192175	83192214	-	1	NA	intron (NM_011409, intron 1 of 2)	intron (NM_011409, intron 1 of 2)	864	NM_011409	20557	Mm.290922	NM_011409	ENSMUSG00000018986	Slfn3	-	schlafen 3	protein-coding
mm_57951.1	chr6	135117983	135117985	-	1	NA	intron (NM_053118, intron 1 of 2)	intron (NM_053118, intron 1 of 2)	299	NM_053118	93746	Mm.49902	NM_053118	ENSMUSG00000030205	Gprc5d	-	G protein-coupled receptor, family C, group 5, member D	protein-coding
mm_84493.1	chr9	66847668	66847682	-	1	NA	3' UTR (NM_173413, exon 8 of 8)	3' UTR (NM_173413, exon 8 of 8)	-12969	NM_026674	68318	Mm.284229	NM_026674	ENSMUSG00000053040	Aph1c	0610008A10Rik|APH-1b|Aph1b	aph1 homolog C, gamma secretase subunit	protein-coding
mm_41853.1	chr5	104439499	104439519	+	1	NA	exon (NM_001204203, exon 6 of 7)	exon (NM_001204203, exon 6 of 7)	3317	NM_001204233	20750	Mm.288474	NM_009263	ENSMUSG00000029304	Spp1	2AR|Apl-1|BNSP|BSPI|Bsp|ETA-1|Eta|OP|Opn|Opnl|Ric|Spp-1	secreted phosphoprotein 1	protein-coding
mm_67427.1	chr7	80368980	80368982	-	1	NA	intron (NM_172903, intron 3 of 23)	intron (NM_172903, intron 3 of 23)	2394	NM_172903	140481	Mm.269245	NM_172903	ENSMUSG00000038886	Man2a2	1700052O22Rik|4931438M07Rik|AI480988|MX|Man IIx	mannosidase 2, alpha 2	protein-coding
mm_161129.1	chr12	112732439	112732439	+	1	NA	promoter-TSS (NR_105905)	promoter-TSS (NR_105905)	-883	NR_105905	102466989		NR_105905	ENSMUSG00000099165	Mir6940	Gm27655|mmu-mir-6940	microRNA 6940	ncRNA
mm_93777.1	chr10	120476255	120476310	-	1	NA	5' UTR (NM_010441, exon 1 of 5)	5' UTR (NM_010441, exon 1 of 5)	187	NM_001347170	15364	Mm.157190	NM_010441	ENSMUSG00000056758	Hmga2	9430083A20Rik|HMGI-C|Hmgic|pg|pygmy	high mobility group AT-hook 2	protein-coding
mm_133537.1	chr16	91056766	91056775	+	1	NA	intron (NM_001163695, intron 1 of 1)	intron (NM_001163695, intron 1 of 1)	12375	NM_001163695	74387	Mm.236220	NM_028905	ENSMUSG00000039851	4932438H23Rik	4931406G06Rik|AI550392	RIKEN cDNA 4932438H23 gene	protein-coding
mm_36284.1	chr4	63861101	63861122	-	1	NA	5' UTR (NM_009403, exon 1 of 4)	5' UTR (NM_009403, exon 1 of 4)	173	NM_009403	21949	Mm.4664	NM_009403	ENSMUSG00000028362	Tnfsf8	CD153|CD30LG|Cd30l|Tnlg3a	tumor necrosis factor (ligand) superfamily, member 8	protein-coding
mm_137718.1	chr17	29100324	29100340	+	1	NA	3' UTR (NM_007669, exon 3 of 3)	3' UTR (NM_007669, exon 3 of 3)	6563	NM_007669	12575	Mm.195663	NM_007669	ENSMUSG00000023067	Cdkn1a	CAP20|CDKI|CIP1|Cdkn1|P21|SDI1|Waf1|mda6|p21Cip1|p21WAF	cyclin-dependent kinase inhibitor 1A (P21)	protein-coding
mm_131326.1	chr16	13109683	13109693	+	1	NA	promoter-TSS (NM_015769)	promoter-TSS (NM_015769)	-48	NM_015769	50505	Mm.287837	NM_015769	ENSMUSG00000022545	Ercc4	AI606920|Xpf	excision repair cross-complementing rodent repair deficiency, complementation group 4	protein-coding
mm_127315.1	chr15	100269184	100269190	+	1	NA	Intergenic	MTC|LTR|ERVL-MaLR	-11650	NM_183109	75002	Mm.261400	NM_183109	ENSMUSG00000045631	Tmprss12	4930478A21Rik	transmembrane (C-terminal) protease, serine 12	protein-coding
mm_119279.1	chr14	34310817	34310830	+	1	NA	promoter-TSS (NM_008133)	promoter-TSS (NM_008133)	96	NM_008133	14661	Mm.10600	NM_008133	ENSMUSG00000021794	Glud1	AI118167|Gdh-X|Glud|Gludl	glutamate dehydrogenase 1	protein-coding
mm_51027.1	chr6	65432467	65432515	+	1	NA	intron (NM_175524, intron 1 of 5)	intron (NM_175524, intron 1 of 5)	51197	NM_175524	243407	Mm.389758	NM_175524	ENSMUSG00000029917	C130060K24Rik	-	RIKEN cDNA C130060K24 gene	protein-coding
mm_33228.1	chr4	126757007	126757013	+	1	NA	exon (NM_001035526, exon 2 of 24)	exon (NM_001035526, exon 2 of 24)	3240	NM_001035526	100317	Mm.206206	NM_133886	ENSMUSG00000028830	AU040320	A730047D20Rik|AAVR|Kiaa0319l	expressed sequence AU040320	protein-coding
mm_144768.1	chr18	35773802	35773805	+	1	NA	intron (NM_019912, intron 1 of 6)	B1_Mur1|SINE|Alu	2244	NM_019912	56550	Mm.180052	NM_019912	ENSMUSG00000091896	Ube2d2a	1500034D03Rik|Ubc2e|Ube2d2|ubc4	ubiquitin-conjugating enzyme E2D 2A	protein-coding
mm_168642.1	chr1	185076732	185076732	-	1	NA	Intergenic	RLTR1B|LTR|ERV1	-77183	NM_145515	226778	Mm.7445	NM_145515	ENSMUSG00000026620	Mark1	AW491150|B930025N23Rik|Emk3|Par-1c|mKIAA1477|mPar-1c	MAP/microtubule affinity regulating kinase 1	protein-coding
mm_155120.1	chrX	48870415	48870424	+	1	NA	intron (NM_001085499, intron 8 of 20)	B3A|SINE|B2	7294	NM_001085499	209005	Mm.336054	NM_001085499	ENSMUSG00000079606	Gm595	-	predicted gene 595	protein-coding
mm_101115.1	chr11	11967559	11967609	-	1	NA	exon (NM_010345, exon 4 of 17)	exon (NM_010345, exon 4 of 17)	60387	NM_001177629	14783	Mm.273117	NM_010345	ENSMUSG00000020176	Grb10	5730571D09Rik|AI325020|Meg1|mKIAA0207	growth factor receptor bound protein 10	protein-coding
mm_35408.1	chr4	34756235	34756267	-	1	NA	promoter-TSS (NM_001033255)	promoter-TSS (NM_001033255)	8	NM_001033255	214568	Mm.297405	NM_001033255	ENSMUSG00000071015	Gm136	-	predicted gene 136	protein-coding
mm_128557.1	chr15	55906883	55906903	-	1	NA	promoter-TSS (NM_016667)	promoter-TSS (NM_016667)	56	NM_016667	20649	Mm.309425	NM_016667	ENSMUSG00000060429	Sntb1	-	syntrophin, basic 1	protein-coding
mm_172356.1	chr7	116084594	116084600	-	1	NA	intron (NR_029433, intron 3 of 3)	intron (NR_029433, intron 3 of 3)	8552	NR_029433	69350	Mm.440425	NR_029433	ENSMUSG00000087621	1700003G18Rik	2610312K03Rik	RIKEN cDNA 1700003G18 gene	ncRNA
mm_36531.1	chr4	86611988	86612001	-	1	NA	promoter-TSS (NM_173400)	promoter-TSS (NM_173400)	28	NM_173400	230376	Mm.74730	NM_173400	ENSMUSG00000038047	Haus6	6230416J20Rik|9830144E06|D4Ertd27e|mKIAA1574	HAUS augmin-like complex, subunit 6	protein-coding
mm_14289.1	chr2	128819503	128819506	+	1	NA	intron (NM_028248, intron 1 of 18)	intron (NM_028248, intron 1 of 18)	1201	NM_028248	72477	Mm.259688	NM_028248	ENSMUSG00000014353	Tmem87b	2610301K12Rik|2810431I02Rik|AU014804	transmembrane protein 87B	protein-coding
mm_12984.1	chr2	90847208	90847294	+	1	NA	promoter-TSS (NM_001317241)	promoter-TSS (NM_001317241)	96	NM_001317242	56428	Mm.28023	NM_019758	ENSMUSG00000027282	Mtch2	2310034D24Rik|4930539J07Rik|HSPC032	mitochondrial carrier 2	protein-coding
mm_134360.1	chr16	16863875	16863885	-	1	NA	exon (NM_001190325, exon 1 of 3)	exon (NM_001190325, exon 1 of 3)	105	NM_001190325	16136	Mm.184441	NM_001190325	ENSMUSG00000075370	Igll1	BB139905|Igl-5|Igll|Lambda5	immunoglobulin lambda-like polypeptide 1	protein-coding
mm_39166.1	chr4	155653185	155653236	-	1	NA	promoter-TSS (NM_001320235)	promoter-TSS (NM_001320235)	80	NM_001320235	26561	Mm.29373	NM_011985	ENSMUSG00000029061	Mmp23	CA-MMP	matrix metallopeptidase 23	protein-coding
mm_74196.1	chr8	123805961	123805990	+	1	NA	promoter-TSS (NM_009003)	promoter-TSS (NM_009003)	-21	NM_009003	19341	Mm.9221	NM_009003	ENSMUSG00000019478	Rab4a	AI848268|Rab4	RAB4A, member RAS oncogene family	protein-coding
mm_31399.1	chr4	48045381	48045389	+	1	NA	promoter-TSS (NM_015743)	promoter-TSS (NM_015743)	80	NM_015743	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_23014.1	chr3	34560213	34560224	+	1	NA	promoter-TSS (NR_015580)	promoter-TSS (NR_015580)	-163	NR_015580	320478	Mm.444063	NR_015580	ENSMUSG00000105265	Sox2ot	B230215L15Rik	SOX2 overlapping transcript (non-protein coding)	ncRNA
mm_86649.1	chr10	17723221	17723229	+	1	NA	promoter-TSS (NM_010828)	promoter-TSS (NM_010828)	-3	NM_010828	17684	Mm.272321	NM_010828	ENSMUSG00000039910	Cited2	AI835299|ER154-like|Mrg1|Msg2|p35srj	Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 2	protein-coding
mm_152417.1	chr19	10669587	10669612	-	1	NA	exon (NM_021453, exon 7 of 9)	exon (NM_021453, exon 7 of 9)	8472	NM_021453	58803	Mm.34037	NM_021453	ENSMUSG00000024738	Pga5	1110035E17Rik|Pepf	pepsinogen 5, group I	protein-coding
mm_142047.1	chr17	35533952	35533962	-	1	NA	exon (NM_020576, exon 2 of 2)	exon (NM_020576, exon 2 of 2)	756	NM_020576	57390	Mm.34201	NM_020576	ENSMUSG00000024409	Psors1c2	AI448740|Pcg|SPR1	psoriasis susceptibility 1 candidate 2 (human)	protein-coding
mm_172133.1	chr6	34191040	34191043	-	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	-13987	NM_021435	58246	Mm.245527	NM_021435	ENSMUSG00000018999	Slc35b4	4930474D06Rik|AB041549|AW494345	solute carrier family 35, member B4	protein-coding
mm_61106.1	chr7	52010706	52010707	+	1	NA	TTS (NM_001195601)	TTS (NM_001195601)	-4688	NM_001160345	75744	Mm.386823	NM_001160345	ENSMUSG00000074093	Svip	1700006C13Rik|6620401M08Rik	small VCP/p97-interacting protein	protein-coding
mm_118574.1	chr14	19708018	19708053	+	1	NA	Intergenic	Intergenic	-43222	NM_008695	18074	Mm.20348	NM_008695	ENSMUSG00000021806	Nid2	AW547149|Ly111|NID-2|entactin-2|nidogen-2	nidogen 2	protein-coding
mm_113983.1	chr13	52582660	52582677	+	1	NA	promoter-TSS (NM_001198977)	promoter-TSS (NM_001198977)	-769	NM_001198977	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_55067.1	chr6	49050514	49050517	-	1	NA	intron (NM_053110, intron 7 of 10)	intron (NM_053110, intron 7 of 10)	13997	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_72302.1	chr8	76899853	76899864	+	1	NA	intron (NR_028579, intron 1 of 1)	CpG	315	NR_028579	100039211	Mm.367571	NR_028579	ENSMUSG00000074235	Gm10649	ENSMUSG00000074235	predicted gene 10649	ncRNA
mm_39776.1	chr5	30105178	30105219	+	1	NA	promoter-TSS (NM_001167879)	promoter-TSS (NM_001167879)	2	NM_001167879	242915	Mm.332287	NM_001167879	ENSMUSG00000044576	Garem2	Fam59b|Gareml|Gm444	GRB2 associated regulator of MAPK1 subtype 2	protein-coding
mm_10620.1	chr2	19381359	19381365	+	1	NA	intron (NM_029619, intron 2 of 4)	intron (NM_029619, intron 2 of 4)	9726	NM_029619	76467	Mm.27166	NM_029619	ENSMUSG00000023094	Msrb2	2310050L06Rik|Mrsb|Msrb|Pilb	methionine sulfoxide reductase B2	protein-coding
mm_79443.1	chr9	56090211	56090238	+	1	NA	5' UTR (NM_011193, exon 1 of 15)	5' UTR (NM_011193, exon 1 of 15)	248	NM_011193	19200	Mm.2534	NM_011193	ENSMUSG00000032322	Pstpip1	CD2BP1|def-2	proline-serine-threonine phosphatase-interacting protein 1	protein-coding
mm_3788.1	chr1	157388889	157388890	+	1	NA	intron (NM_177644, intron 1 of 17)	RMER17C|LTR|ERVK	-23463	NR_027984	69953	Mm.286863	NM_027274	ENSMUSG00000049881	2810025M15Rik	AI429618	RIKEN cDNA 2810025M15 gene	ncRNA
mm_65361.1	chr7	25005877	25005887	-	1	NA	promoter-TSS (NM_001290469)	promoter-TSS (NM_001290469)	55	NM_001290469	232975	Mm.44101	NM_144921	ENSMUSG00000040907	Atp1a3	Atpa-2	ATPase, Na+/K+ transporting, alpha 3 polypeptide	protein-coding
mm_43697.1	chr5	139200632	139200678	+	1	NA	promoter-TSS (NM_001256117)	promoter-TSS (NM_001256117)	18	NM_001256117	77053	Mm.210845	NM_024451	ENSMUSG00000036817	Sun1	4632417G13Rik|5730434D03Rik|Unc84a|mKIAA0810	Sad1 and UNC84 domain containing 1	protein-coding
mm_61475.1	chr7	75629616	75629620	+	1	NA	intron (NM_029332, intron 8 of 36)	B4A|SINE|B4	174084	NM_029332	75547	Mm.216107	NM_029332	ENSMUSG00000066406	Akap13	1700026G02Rik|5730522G15Rik|5830460E08Rik|AKAP-13|AKAP-Lbc|BRX|Ht31|LBC|PROTO-LB|PROTO-LBC	A kinase (PRKA) anchor protein 13	protein-coding
mm_112349.1	chr12	118301260	118301289	-	1	NA	5' UTR (NM_009239, exon 1 of 6)	5' UTR (NM_009239, exon 1 of 6)	166	NM_009239	20688	Mm.34699	NM_009239	ENSMUSG00000025323	Sp4	5730497N03Rik|HF-1b|HF1-b	trans-acting transcription factor 4	protein-coding
mm_65130.1	chr7	19506687	19506694	-	1	NA	3' UTR (NM_177692, exon 2 of 2)	3' UTR (NM_177692, exon 2 of 2)	1641	NM_177692	232946	Mm.64557	NM_177692	ENSMUSG00000057667	Bloc1s3	BC043666|Blos3|E230011O18|rp	biogenesis of lysosomal organelles complex-1, subunit 3	protein-coding
mm_1808.1	chr1	81077275	81077327	+	1	NA	promoter-TSS (NM_172849)	promoter-TSS (NM_172849)	-16	NM_172849	241134	Mm.313904	NM_172849	ENSMUSG00000054976	Nyap2	9430031J16Rik|Jr6|Kiaa1486	neuronal tyrosine-phophorylated phosphoinositide 3-kinase adaptor 2	protein-coding
mm_46242.1	chr5	99229448	99229473	-	1	NA	intron (NM_145839, intron 8 of 13)	intron (NM_145839, intron 8 of 13)	23467	NM_181318	320292	Mm.259074	NM_145839	ENSMUSG00000089809	Rasgef1b	4732452O09Rik|GPIgamma4|Gpig4	RasGEF domain family, member 1B	protein-coding
mm_157919.1	chrX	78583800	78583810	-	1	NA	promoter-TSS (NM_001289683)	promoter-TSS (NM_001289683)	0	NM_001164275	546336	Mm.211712	NM_027322	ENSMUSG00000047996	Prrg1	2010007L08Rik	proline rich Gla (G-carboxyglutamic acid) 1	protein-coding
mm_29939.1	chr3	132717502	132717504	-	1	NA	intron (NM_001163455, intron 6 of 25)	intron (NM_001163455, intron 6 of 25)	33359	NM_001163455	271981	Mm.257864	NM_173032	ENSMUSG00000028030	Tbck	1700120J03Rik|9430001M19|A630047E20Rik|C030007I09Rik|Tbckl	TBC1 domain containing kinase	protein-coding
mm_17060.1	chr2	22416717	22416725	-	1	NA	intron (NM_148413, intron 19 of 19)	Lx6|LINE|L1	189218	NM_148413	667663	Mm.330033	NM_148413	ENSMUSG00000025716	Myo3a	9030416P08Rik	myosin IIIA	protein-coding
mm_130698.1	chr15	100684612	100684711	-	1	NA	exon (NM_033612, exon 4 of 8)	exon (NM_033612, exon 4 of 8)	3259	NM_033612	109901	Mm.2131	NM_033612	ENSMUSG00000023031	Cela1	1810009A17Rik|1810062B19Rik|Ela-1|Ela1|PC-TsF	chymotrypsin-like elastase family, member 1	protein-coding
mm_117871.1	chr13	98890975	98891035	-	1	NA	promoter-TSS (NM_001048267)	promoter-TSS (NM_001048267)	37	NM_001048267	238799	Mm.173286	NM_178716	ENSMUSG00000009470	Tnpo1	AU021749|D13Ertd688e|IPO2|Kpnb2|MIP|MIP1|TRN	transportin 1	protein-coding
mm_24124.1	chr3	88200324	88200348	+	1	NA	Intergenic	Intergenic	-14835	NR_037276	100526540		NR_037276	ENSMUSG00000092988	Mir3093	mir-3093|mmu-mir-3093	microRNA 3093	ncRNA
mm_61125.1	chr7	55794226	55794238	+	1	NA	promoter-TSS (NM_146190)	promoter-TSS (NM_146190)	84	NM_146190	233276	Mm.284306	NM_146190	ENSMUSG00000033790	Tubgcp5	B130010C12Rik|GCP5|mKIAA1899	tubulin, gamma complex associated protein 5	protein-coding
mm_79015.1	chr9	45839882	45839896	+	1	NA	intron (NM_011792, intron 1 of 8)	intron (NM_011792, intron 1 of 8)	1344	NM_011792	23821	Mm.24044	NM_011792	ENSMUSG00000032086	Bace1	ASP2|Bace|C76936	beta-site APP cleaving enzyme 1	protein-coding
mm_58703.1	chr7	12928307	12928328	+	1	NA	exon (NM_029809, exon 2 of 2)	exon (NM_029809, exon 2 of 2)	901	NM_029809	381845	Mm.439896	NM_029809	ENSMUSG00000033967	Rnf225	2310014L17Rik|AV237412|C77118	ring finger protein 225	protein-coding
mm_107683.1	chr12	54656809	54656813	+	1	NA	promoter-TSS (NM_134054)	promoter-TSS (NM_134054)	-239	NM_134054	104725	Mm.485026	NM_134054	ENSMUSG00000044408	Sptssa	1110002B05Rik|AA407909|AA409588|AU041967|Ssspta	serine palmitoyltransferase, small subunit A	protein-coding
mm_27639.1	chr3	62924258	62924266	-	1	NA	Intergenic	Intergenic	-319122	NM_177346	229357	Mm.95181	NM_177346	ENSMUSG00000043441	Gpr149	9630018L10Rik|Ieda|PGR10|R35	G protein-coupled receptor 149	protein-coding
mm_135829.1	chr16	58523303	58523342	-	1	NA	promoter-TSS (NM_018784)	promoter-TSS (NM_018784)	-10	NM_018784	54613	Mm.212742	NM_018784	ENSMUSG00000022747	St3gal6	1700023B24Rik|AI930218|AW552396|Siat10|St3galVI	ST3 beta-galactoside alpha-2,3-sialyltransferase 6	protein-coding
mm_81225.1	chr9	107635124	107635146	+	1	NA	exon (NM_008138, exon 1 of 9)	exon (NM_008138, exon 1 of 9)	207	NM_008138	14678	Mm.196464	NM_008138	ENSMUSG00000032562	Gnai2	C76432|Galphai2|Gia|Gnai-2	guanine nucleotide binding protein (G protein), alpha inhibiting 2	protein-coding
mm_129383.1	chr15	78191554	78191562	-	1	NA	3' UTR (NM_001330686, exon 4 of 4)	3' UTR (NM_001330686, exon 4 of 4)	12679	NM_001330686	19293	Mm.2766	NM_013645	ENSMUSG00000005716	Pvalb	PV|Parv|Pva	parvalbumin	protein-coding
mm_586.1	chr1	39449506	39449528	+	1	NA	intron (NM_018775, intron 1 of 19)	intron (NM_018775, intron 1 of 19)	29230	NM_018775	54610	Mm.387293	NM_018775	ENSMUSG00000003134	Tbc1d8	AD3|HBLP1|VRP	TBC1 domain family, member 8	protein-coding
mm_89622.1	chr10	96185957	96185968	+	1	NA	Intergenic	Intergenic	-40245	NR_110448	74881	Mm.410819	NR_110448		4930459C07Rik	-	RIKEN cDNA 4930459C07 gene	ncRNA
mm_150326.1	chr19	34574596	34574629	+	1	NA	3' UTR (NM_008332, exon 3 of 3)	3' UTR (NM_008332, exon 3 of 3)	-8917	NM_010501	15959	Mm.426079	NM_010501	ENSMUSG00000074896	Ifit3	Ifi49|P49	interferon-induced protein with tetratricopeptide repeats 3	protein-coding
mm_85133.1	chr9	95750336	95750368	-	1	NA	promoter-TSS (NM_011643)	promoter-TSS (NM_011643)	6	NM_001311123	22063	Mm.149633	NM_011643	ENSMUSG00000032839	Trpc1	Mtrp1|Trp1|Trrp1	transient receptor potential cation channel, subfamily C, member 1	protein-coding
mm_167675.1	chr9	75538251	75538254	+	1	NA	intron (NM_016963, intron 1 of 9)	RMER10B|LTR|ERVL	21405	NM_016963	50875	Mm.38445	NM_016963	ENSMUSG00000058587	Tmod3	U-Tmod|UTMOD	tropomodulin 3	protein-coding
mm_165741.1	chr3	107216222	107216225	-	1	NA	intron (NM_001111143, intron 4 of 8)	intron (NM_001111143, intron 4 of 8)	5509	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_80507.1	chr9	78615822	78615832	+	1	NA	5' UTR (NM_153098, exon 1 of 33)	5' UTR (NM_153098, exon 1 of 33)	281	NM_153098	235505	Mm.32955	NM_153098	ENSMUSG00000046186	Cd109	9930012E15Rik|AI480638|GARP	CD109 antigen	protein-coding
mm_28298.1	chr3	89102018	89102020	-	1	NA	promoter-TSS (NM_001253751)	promoter-TSS (NM_001253751)	-52	NM_001253751	110196	Mm.39472	NM_134469	ENSMUSG00000059743	Fdps	6030492I17Rik|AI256750|Fdpsl1|mKIAA1293	farnesyl diphosphate synthetase	protein-coding
mm_55203.1	chr6	52208646	52208678	-	1	NA	promoter-TSS (NM_010454)	promoter-TSS (NM_010454)	-38	NM_010454	15403	Mm.222030	NM_010454	ENSMUSG00000043219	Hoxa6	Hox-1.2	homeobox A6	protein-coding
mm_140360.1	chr17	86831619	86831621	+	1	NA	3' UTR (NM_010137, exon 16 of 16)	3' UTR (NM_010137, exon 16 of 16)	77756	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_115346.1	chr13	112660672	112660682	+	1	NA	promoter-TSS (NM_178746)	promoter-TSS (NM_178746)	-89	NM_178746	268706	Mm.40834	NM_175376	ENSMUSG00000047789	Slc38a9	4833412L08Rik|6720411P22Rik|9130023D20Rik|9430067K09Rik|A730092C09	solute carrier family 38, member 9	protein-coding
mm_165288.1	chr2	85260100	85260110	+	1	NA	Intergenic	Lx5|LINE|L1	-63406	NM_001033346	241528	Mm.291095	NM_001033346	ENSMUSG00000075224	Lrrc55	A330097E02Rik|Gm351	leucine rich repeat containing 55	protein-coding
mm_34014.1	chr4	137993921	137993933	+	1	NA	intron (NM_172703, intron 1 of 34)	intron (NM_172703, intron 1 of 34)	471	NM_172703	230861	Mm.268903	NM_172703	ENSMUSG00000028760	Eif4g3	1500002J22Rik|4930523M17Rik|G1-419-52|eIF4GII|repro8	eukaryotic translation initiation factor 4 gamma, 3	protein-coding
mm_61017.1	chr7	49397773	49397808	+	1	NA	intron (NM_175272, intron 3 of 37)	intron (NM_175272, intron 3 of 37)	151601	NM_175272	78286	Mm.333881	NM_175272	ENSMUSG00000052512	Nav2	5330421F07Rik|AU067780|BQ960892|HELAD1|POMFIL2|RAINB1|RAINB2|Unc53H2|mKIAA3015	neuron navigator 2	protein-coding
mm_165889.1	chr4	43791625	43791635	+	1	NA	Intergenic	L1M3|LINE|L1	-9303	NR_033638	29848	Mm.424497	NR_033638	ENSMUSG00000111338	Olfr29-ps1	MOR262-11|MTPCR52|Olfr158|Olfr29|Olfr37d|mOR37d	olfactory receptor 29, pseudogene 1	pseudo
mm_144067.1	chr17	90980321	90980323	-	1	NA	intron (NM_001346957, intron 3 of 18)	intron (NM_001346957, intron 3 of 18)	109283	NM_001346957	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_86886.1	chr10	22158567	22158584	+	1	NA	promoter-TSS (NM_009016)	promoter-TSS (NM_009016)	-34	NM_009016	19368	Mm.458004	NM_009016		Raet1a	RAE-1alpha|Rae1alpha|Raet1	retinoic acid early transcript 1, alpha	protein-coding
mm_151911.1	chr19	5799628	5799645	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	3036	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_80858.1	chr9	98486068	98486106	+	1	NA	Intergenic	Intergenic	-4450	NM_009034	19660	Mm.12825	NM_009034	ENSMUSG00000032454	Rbp2	Crbp-2|CrbpII|Rbp-2	retinol binding protein 2, cellular	protein-coding
mm_44115.1	chr5	149439669	149439689	+	1	NA	promoter-TSS (NM_029464)	promoter-TSS (NM_029464)	19	NM_001310765	75860	Mm.159605	NM_029464	ENSMUSG00000029660	Tex26	4930588N13Rik	testis expressed 26	protein-coding
mm_134333.1	chr16	16473977	16473987	-	1	NA	intron (NM_001301817, intron 7 of 16)	intron (NM_001301817, intron 7 of 16)	53429	NM_001301818	224014	Mm.256131	NM_139232	ENSMUSG00000022788	Fgd4	9030023J02Rik|9330209B17Rik|Frabp|ZFYVE6	FYVE, RhoGEF and PH domain containing 4	protein-coding
mm_129467.1	chr15	78670478	78670480	-	1	NA	3' UTR (NM_183141, exon 2 of 2)	3' UTR (NM_183141, exon 2 of 2)	47634	NM_183141	207393	Mm.323188	NM_183141	ENSMUSG00000043460	Elfn2	6330514E13|AW048948|BC094219|Lrrc62|Ppp1r29	leucine rich repeat and fibronectin type III, extracellular 2	protein-coding
mm_8929.1	chr1	164086912	164086922	-	1	NA	Intergenic	Intergenic	24841	NM_001164059	20343	Mm.1461	NM_011346	ENSMUSG00000026581	Sell	AI528707|CD62L|L-selectin|LECAM-1|Lnhr|Ly-22|Ly-m22|Lyam-1|Lyam1	selectin, lymphocyte	protein-coding
mm_14724.1	chr2	144033078	144033110	+	1	NA	promoter-TSS (NM_207275)	promoter-TSS (NM_207275)	-8	NM_001044750	403171	Mm.389362	NM_207275	ENSMUSG00000037307	Banf2	4930517K23Rik|Baf-L|Baf-like|Gm115	barrier to autointegration factor 2	protein-coding
mm_65311.1	chr7	24766016	24766020	-	1	NA	Intergenic	Intergenic	-5707	NM_026862	68891	Mm.292848	NM_026862	ENSMUSG00000052212	Cd177	1190003K14Rik|Pdp3	CD177 antigen	protein-coding
mm_161844.1	chr18	7297932	7297932	-	1	NA	promoter-TSS (NM_001081393)	promoter-TSS (NM_001081393)	-31	NM_001081393	74934	Mm.107918	NM_001081393	ENSMUSG00000061802	Armc4	4930463I21Rik|b2b227.1Clo|b2b643Clo	armadillo repeat containing 4	protein-coding
mm_76231.1	chr8	83573502	83573512	-	1	NA	intron (NM_134118, intron 3 of 12)	intron (NM_134118, intron 3 of 12)	6749	NM_025843	66916	Mm.29683	NM_025843	ENSMUSG00000033938	Ndufb7	1110002H15Rik	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 7	protein-coding
mm_11180.1	chr2	28840472	28840482	+	1	NA	promoter-TSS (NM_001166033)	promoter-TSS (NM_001166033)	71	NM_001033294	227674	Mm.44179	NM_001033294	ENSMUSG00000026806	Ddx31	5830444G11Rik|Gm997	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 31	protein-coding
mm_134495.1	chr16	18811585	18811609	-	1	NA	promoter-TSS (NM_001161623)	promoter-TSS (NM_001161623)	42	NM_001161623	12544	Mm.1248	NM_009862	ENSMUSG00000000028	Cdc45	Cdc45l	cell division cycle 45	protein-coding
mm_104805.1	chr11	98775255	98775260	-	1	NA	5' UTR (NM_145434, exon 1 of 8)	5' UTR (NM_145434, exon 1 of 8)	120	NM_145434	217166	Mm.390397	NM_145434	ENSMUSG00000020889	Nr1d1	A530070C09Rik|R75201	nuclear receptor subfamily 1, group D, member 1	protein-coding
mm_27894.1	chr3	79287308	79287318	-	1	NA	Intergenic	CpG	-58063	NM_001142953	100233207	Mm.373801	NM_001142953	ENSMUSG00000091685	Gm17359	-	predicted gene, 17359	protein-coding
mm_93824.1	chr10	121476308	121476327	-	1	NA	promoter-TSS (NM_138956)	promoter-TSS (NM_138956)	-67	NM_138956	192678	Mm.41265	NM_138956	ENSMUSG00000025795	Rassf3	AW212023|AW322379	Ras association (RalGDS/AF-6) domain family member 3	protein-coding
mm_76742.1	chr8	95202836	95202844	-	1	NA	Intergenic	Intergenic	-60300	NM_001145831	16582	Mm.378951	NM_010631	ENSMUSG00000031788	Kifc3	AI325457|BB123200	kinesin family member C3	protein-coding
mm_151915.1	chr19	5799744	5799756	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	2922	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_25495.1	chr3	109340755	109340787	+	1	NA	promoter-TSS (NM_020505)	promoter-TSS (NM_020505)	88	NM_020505	57257	Mm.282257	NM_020505	ENSMUSG00000033721	Vav3	A530094I06Rik|AA986410|Idd18.1	vav 3 oncogene	protein-coding
mm_52064.1	chr6	97439543	97439557	+	1	NA	intron (NM_145148, intron 2 of 23)	intron (NM_145148, intron 2 of 23)	19736	NM_001346639	232288	Mm.27789	NM_145148	ENSMUSG00000030064	Frmd4b	6030440G05Rik|C87375|GOBLIN|GRSP1|R74720	FERM domain containing 4B	protein-coding
mm_8360.1	chr1	150455960	150455970	-	1	NA	exon (NM_021400, exon 7 of 13)	exon (NM_021400, exon 7 of 13)	10200	NM_021400	96875	Mm.174256	NM_021400	ENSMUSG00000006014	Prg4	CACP|DOL54|JCAP|MSF|SZP|lubricin	proteoglycan 4 (megakaryocyte stimulating factor, articular superficial zone protein)	protein-coding
mm_93060.1	chr10	88765583	88765598	-	1	NA	intron (NM_175158, intron 43 of 61)	intron (NM_175158, intron 43 of 61)	34176	NM_025859	104303	Mm.291247	NM_025859	ENSMUSG00000060904	Arl1	2310008D22Rik|AU019749	ADP-ribosylation factor-like 1	protein-coding
mm_97801.1	chr11	82954557	82954575	+	1	NA	intron (NM_183201, intron 1 of 5)	MER89|LTR|ERV1	2464	NM_183201	327978	Mm.42147	NM_183201	ENSMUSG00000054404	Slfn5	AI956840	schlafen 5	protein-coding
mm_135050.1	chr16	33380697	33380713	-	1	NA	promoter-TSS (NM_011749)	promoter-TSS (NM_011749)	31	NR_045709	100502742	Mm.217880	NR_045709	ENSMUSG00000097318	1700007L15Rik	linc-Iqcg|linc1609	RIKEN cDNA 1700007L15 gene	ncRNA
mm_9354.1	chr1	172147924	172147965	-	1	NA	promoter-TSS (NM_153555)	promoter-TSS (NM_153555)	-71	NM_153555	98193	Mm.159915	NM_153555	ENSMUSG00000026554	Dcaf8	AA408877|AA433120|AA792214|AU018973|C76055|D1Dau35e|D1Ucla4|H326|Wdr42a	DDB1 and CUL4 associated factor 8	protein-coding
mm_62711.1	chr7	110768139	110768156	+	1	NA	promoter-TSS (NM_001276301)	promoter-TSS (NM_001276301)	-59	NM_001276301	11717	Mm.3238	NM_009667	ENSMUSG00000005686	Ampd3	-	adenosine monophosphate deaminase 3	protein-coding
mm_1100.1	chr1	59763419	59763462	+	1	NA	promoter-TSS (NM_007561)	promoter-TSS (NM_007561)	-839	NM_007561	12168	Mm.7106	NM_007561	ENSMUSG00000067336	Bmpr2	2610024H22Rik|AL117858|AW546137|BB189135|BMP-2|BMPR-2|BMPR-II|BMPRII|BRK-3|Gm20272	bone morphogenetic protein receptor, type II (serine/threonine kinase)	protein-coding
mm_6895.1	chr1	84696183	84696202	-	1	NA	promoter-TSS (NM_152915)	promoter-TSS (NM_152915)	29	NM_152915	227325	Mm.292560	NM_152915	ENSMUSG00000036766	Dner	A930026D19Rik|BET|Bret	delta/notch-like EGF repeat containing	protein-coding
mm_82375.1	chr9	14615429	14615438	-	1	NA	promoter-TSS (NM_001081395)	promoter-TSS (NM_001081395)	-433	NM_001081395	75723	Mm.159552	NM_001081395	ENSMUSG00000013076	Amotl1	2310010G08Rik|2310067L22Rik|4932416D09Rik|JEAP|mFLJ00155	angiomotin-like 1	protein-coding
mm_139496.1	chr17	56241741	56241751	+	1	NA	Intergenic	Intergenic	-1242	NR_029827	723883		NR_029827	ENSMUSG00000065491	Mir7b	Mirn7b|mir-7b|mmu-mir-7b	microRNA 7b	ncRNA
mm_143923.1	chr17	85618549	85618553	-	1	NA	promoter-TSS (NR_015387)	promoter-TSS (NR_015387)	-155	NR_038082	100043902	Mm.150838	NR_015385	ENSMUSG00000093460	Six3os1	D17Mgi26|E130112H22Rik|Rncr1|Six3os	SIX homeobox 3, opposite strand 1	ncRNA
mm_136151.1	chr16	87634948	87634952	-	1	NA	Intergenic	RMER4B|LTR|ERVK	-64004	NM_007520	12013	Mm.26147	NM_007520	ENSMUSG00000025612	Bach1	6230421P05Rik|AI323795	BTB and CNC homology 1, basic leucine zipper transcription factor 1	protein-coding
mm_120001.1	chr14	55618139	55618183	+	1	NA	promoter-TSS (NM_020002)	promoter-TSS (NM_020002)	-5	NM_020002	56739	Mm.23149	NM_020002	ENSMUSG00000002324	Rec8	Rec8L1|mrec	REC8 meiotic recombination protein	protein-coding
mm_24211.1	chr3	88625572	88625576	+	1	NA	intron (NM_001198912, intron 1 of 21)	B2_Mm2|SINE|B2	4180	NM_001198912	16800	Mm.239329	NM_008487	ENSMUSG00000028059	Arhgef2	AA408978|GEF|GEF-H1|GEFH1|LFP40|Lbcl1|Lfc|P40|mKIAA0651	rho/rac guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_132485.1	chr16	36913712	36913750	+	1	NA	exon (NM_030035, exon 13 of 22)	exon (NM_030035, exon 13 of 22)	-16542	NR_040476	68306	Mm.399193	NR_040476	ENSMUSG00000084834	4930565N06Rik	4930428L02Rik	RIKEN cDNA 4930565N06 gene	ncRNA
mm_80562.1	chr9	83587975	83587987	+	1	NA	intron (NM_172507, intron 2 of 3)	intron (NM_172507, intron 2 of 3)	39643	NM_172507	212531	Mm.491246	NM_172507	ENSMUSG00000032261	Sh3bgrl2	A930014C21Rik|AA408038|B930089I21	SH3 domain binding glutamic acid-rich protein like 2	protein-coding
mm_94454.1	chr11	6389577	6389596	+	1	NA	Intergenic	(CGG)n|Simple_repeat|Simple_repeat	-5539	NM_001005867	52915	Mm.1144	NM_028601	ENSMUSG00000041164	Zmiz2	Zimp7	zinc finger, MIZ-type containing 2	protein-coding
mm_79603.1	chr9	58489818	58489834	+	1	NA	5' UTR (NM_176921, exon 2 of 3)	5' UTR (NM_176921, exon 2 of 3)	1223	NM_176921	319477	Mm.153674	NM_176921	ENSMUSG00000066607	6030419C18Rik	-	RIKEN cDNA 6030419C18 gene	protein-coding
mm_90662.1	chr10	128805795	128805806	+	1	NA	intron (NM_028873, intron 1 of 6)	intron (NM_028873, intron 1 of 6)	124	NM_028873	74330	Mm.296915	NM_028873	ENSMUSG00000025354	Dnajc14	5730551F12Rik|DNAJ|DRIP78|HDJ3|LIP6	DnaJ heat shock protein family (Hsp40) member C14	protein-coding
mm_11226.1	chr2	29788309	29788320	+	1	NA	promoter-TSS (NM_178693)	promoter-TSS (NM_178693)	51	NM_178693	227683	Mm.245948	NM_178693	ENSMUSG00000026798	Coq4	A330041N06|D2Ertd97e	coenzyme Q4	protein-coding
mm_65168.1	chr7	19677948	19677952	-	1	NA	promoter-TSS (NM_001277944)	promoter-TSS (NM_001277944)	-9	NM_001277944	11813	Mm.28394	NM_001277944	ENSMUSG00000002992	Apoc2	apo-CII|apoC-II	apolipoprotein C-II	protein-coding
mm_19504.1	chr2	93744622	93744626	-	1	NA	intron (NM_010163, intron 8 of 13)	intron (NM_010163, intron 8 of 13)	77944	NM_010163	14043	Mm.4336	NM_010163	ENSMUSG00000027198	Ext2	AI893565	exostoses (multiple) 2	protein-coding
mm_161782.1	chr17	43426956	43426956	+	1	NA	exon (NM_001081178, exon 8 of 21)	exon (NM_001081178, exon 8 of 21)	37490	NM_001081178	224792	Mm.23478	NM_001081178	ENSMUSG00000056492	Adgrf5	8430401C09Rik|9330185D23|AI528491|Gpr116|mKIAA0758	adhesion G protein-coupled receptor F5	protein-coding
mm_120229.1	chr14	62862514	62862517	+	1	NA	intron (NM_175546, intron 1 of 11)	intron (NM_175546, intron 1 of 11)	-3027	NR_105860	102465311		NR_105860	ENSMUSG00000098858	Mir6541	Gm27311|mmu-mir-6541	microRNA 6541	ncRNA
mm_216.1	chr1	16688508	16688518	+	1	NA	promoter-TSS (NM_001159711)	promoter-TSS (NM_001159711)	57	NM_016923	17087	Mm.116844	NM_016923	ENSMUSG00000025779	Ly96	ESOP-1|MD-2|MD2	lymphocyte antigen 96	protein-coding
mm_152256.1	chr19	8773568	8773595	-	1	NA	promoter-TSS (NR_015538)	promoter-TSS (NR_015538)	886	NR_028419	67706	Mm.45155	NM_026325	ENSMUSG00000003680	Tmem179b	0610031L02Rik|1500003K22Rik|1810059G22Rik	transmembrane protein 179B	protein-coding
mm_134756.1	chr16	23225269	23225278	-	1	NA	promoter-TSS (NM_001252505)	promoter-TSS (NM_001252505)	533	NM_145933	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_147023.1	chr18	34651682	34651692	-	1	NA	promoter-TSS (NM_178347)	promoter-TSS (NM_178347)	49	NM_178347	52563	Mm.196638	NM_178347	ENSMUSG00000024370	Cdc23	6030435O18|D18Ertd243e	CDC23 cell division cycle 23	protein-coding
mm_87599.1	chr10	57645903	57645912	+	1	NA	promoter-TSS (NM_001039053)	promoter-TSS (NM_001039053)	38	NM_001039053	18768	Mm.262135	NM_008863	ENSMUSG00000019876	Pkib	Pkibeta|Prkacn2	protein kinase inhibitor beta, cAMP dependent, testis specific	protein-coding
mm_102710.1	chr11	67011723	67011739	-	1	NA	Intergenic	RLTR9A3B|LTR|ERVK	-13423	NM_001291042	338369	Mm.128138	NM_177392	ENSMUSG00000050270	Tmem220	-	transmembrane protein 220	protein-coding
mm_55695.1	chr6	72851277	72851281	-	1	NA	intron (NM_001347231, intron 3 of 6)	ORR1B1|LTR|ERVL-MaLR	48013	NM_001347231	74287	Mm.29194	NM_019715	ENSMUSG00000055239	Kcmf1	1700094M07Rik|Debt91|Pmcf	potassium channel modulatory factor 1	protein-coding
mm_48208.1	chr5	137600780	137600790	-	1	NA	promoter-TSS (NM_001254762)	promoter-TSS (NM_001254762)	-77	NM_001254762	68929	Mm.41355	NM_030037	ENSMUSG00000037221	Mospd3	1190005J19Rik|5133401H10Rik|Gtig2|R124	motile sperm domain containing 3	protein-coding
mm_78633.1	chr9	40050389	40050409	+	1	NA	promoter-TSS (NR_033613)	promoter-TSS (NR_033613)	-159	NR_033613	72224	Mm.235535	NR_033613	ENSMUSG00000101963	1700001J11Rik	-	ring finger protein 19A pseudogene	pseudo
mm_126515.1	chr15	81835881	81835906	+	1	NA	Intergenic	Intergenic	22433	NM_020507	57259	Mm.323595	NM_020507	ENSMUSG00000048546	Tob2	2900090N22Rik|4930545K18Rik|AV071822|mKIAA1663	transducer of ERBB2, 2	protein-coding
mm_90378.1	chr10	127266257	127266292	+	1	NA	promoter-TSS (NM_027151)	promoter-TSS (NM_027151)	12	NM_001190453	69654	Mm.167537	NM_027151	ENSMUSG00000025410	Dctn2	2310042E05Rik|C130077D06Rik|C87049|DCTN-50|GMP23-48K|RBP50|p50	dynactin 2	protein-coding
mm_144225.1	chr18	9958148	9958186	+	1	NA	promoter-TSS (NM_153552)	promoter-TSS (NM_153552)	-13	NM_153552	225160	Mm.219648	NM_153552	ENSMUSG00000024287	Thoc1	3110002N20Rik|AW107452|NMP-84	THO complex 1	protein-coding
mm_94883.1	chr11	26387195	26387211	+	1	NA	non-coding (NR_102382, exon 1 of 12)	non-coding (NR_102382, exon 1 of 12)	119	NR_102382	67030	Mm.18875	NM_025923	ENSMUSG00000004018	Fancl	2010322C19Rik|AW554273|B230118H11Rik|Phf9|Pog|gcd	Fanconi anemia, complementation group L	protein-coding
mm_106847.1	chr12	8007909	8007913	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	30234	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_52340.1	chr6	110714082	110714084	+	1	NA	intron (NM_001346640, intron 1 of 10)	intron (NM_001346640, intron 1 of 10)	68485	NM_177328	108073	Mm.240881	NM_177328	ENSMUSG00000056755	Grm7	6330570A01Rik|BB176677|C030018L03|E130018M02Rik|Gpr1g|Gprc1g|SMN2|Tg(SMN2)89Ahmb|mGluR7	glutamate receptor, metabotropic 7	protein-coding
mm_39432.1	chr5	16553780	16553795	+	1	NA	promoter-TSS (NM_001289461)	promoter-TSS (NM_001289461)	-114	NM_001289461	15234	Mm.267078	NM_010427	ENSMUSG00000028864	Hgf	C230052L06Rik|HGF/SF|NK1|NK2|SF|SF/HGF	hepatocyte growth factor	protein-coding
mm_153294.1	chr19	37693079	37693121	-	1	NA	exon (NM_001105201, exon 6 of 6)	exon (NM_001105201, exon 6 of 6)	-4708	NM_007811	13082	Mm.42230	NM_007811	ENSMUSG00000024987	Cyp26a1	Cyp26|P450RA|P450RAI|RAH	cytochrome P450, family 26, subfamily a, polypeptide 1	protein-coding
mm_75319.1	chr8	41407688	41407700	-	1	NA	exon (NM_013522, exon 5 of 9)	exon (NM_013522, exon 5 of 9)	9424	NM_013522	14300	Mm.217312	NM_013522	ENSMUSG00000031590	Frg1	-	FSHD region gene 1	protein-coding
mm_69658.1	chr7	139978688	139978698	-	1	NA	promoter-TSS (NM_001033465)	promoter-TSS (NM_001033465)	62	NM_001347614	381933	Mm.440431	NM_001033465	ENSMUSG00000073795	6430531B16Rik	Gm1093	RIKEN cDNA 6430531B16 gene	protein-coding
mm_46448.1	chr5	105116691	105116700	-	1	NA	3' UTR (NM_001256005, exon 11 of 11)	3' UTR (NM_001256005, exon 11 of 11)	-6403	NM_172777	236573	Mm.425261	NM_172777	ENSMUSG00000029298	Gbp9	-	guanylate-binding protein 9	protein-coding
mm_147256.1	chr18	38634543	38634554	-	1	NA	Intergenic	Intergenic	-33280	NM_011898	24066	Mm.42038	NM_011898	ENSMUSG00000024427	Spry4	A030006O18Rik|sprouty4	sprouty homolog 4 (Drosophila)	protein-coding
mm_27592.1	chr3	59130681	59130691	-	1	NA	promoter-TSS (NM_001287124)	promoter-TSS (NM_001287124)	76	NM_001008497	140795	Mm.439021	NM_133200	ENSMUSG00000036381	P2ry14	A330108O13Rik|Gpr105|P2Y14	purinergic receptor P2Y, G-protein coupled, 14	protein-coding
mm_64126.1	chr7	141132479	141132501	+	1	NA	intron (NM_013782, intron 1 of 11)	intron (NM_013782, intron 1 of 11)	1204	NM_013782	27388	Mm.293591	NM_013782	ENSMUSG00000025495	Ptdss2	AI481134|AI988017|PSS2	phosphatidylserine synthase 2	protein-coding
mm_129335.1	chr15	77829605	77829608	-	1	NA	intron (NM_022410, intron 1 of 40)	intron (NM_022410, intron 1 of 40)	12569	NM_022410	17886	Mm.29677	NM_022410	ENSMUSG00000022443	Myh9	Fltn|Myhn-1|Myhn1|NMHCIIA|NMMHC-A|NMMHC-IIA|TU72.6	myosin, heavy polypeptide 9, non-muscle	protein-coding
mm_97837.1	chr11	83065093	83065109	+	1	NA	promoter-TSS (NM_011408)	promoter-TSS (NM_011408)	-11	NM_011408	20556	Mm.278689	NM_011408	ENSMUSG00000072620	Slfn2	Shlf2	schlafen 2	protein-coding
mm_118143.1	chr13	105054581	105054630	-	1	NA	5' UTR (NM_029879, exon 1 of 6)	5' UTR (NM_029879, exon 1 of 6)	325	NM_029879	52882	Mm.100348	NM_029879	ENSMUSG00000021719	Rgs7bp	A930030I01Rik|AI842293|D13Bwg1146e|R7bp	regulator of G-protein signalling 7 binding protein	protein-coding
mm_126434.1	chr15	80597866	80597875	+	1	NA	intron (NM_001289442, intron 1 of 7)	ID_B1|SINE|B4	25273	NM_001289442	17444	Mm.12947	NM_010815	ENSMUSG00000042351	Grap2	GRAP-2|GRB2L|GRBLG|GRID|Gads|GrbX|Grf40|GrpL|Mona|P38	GRB2-related adaptor protein 2	protein-coding
mm_77893.1	chr9	7347532	7347540	+	1	NA	exon (NM_008605, exon 1 of 10)	exon (NM_008605, exon 1 of 10)	162	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_138856.1	chr17	42316664	42316683	+	1	NA	exon (NM_028474, exon 2 of 4)	exon (NM_028474, exon 2 of 4)	726	NM_028474	627626	Mm.390999	NM_028474	ENSMUSG00000042256	Ptchd4	3110082D06Rik|Gm321	patched domain containing 4	protein-coding
mm_120349.1	chr14	63899743	63899791	+	1	NA	intron (NM_028228, intron 6 of 6)	intron (NM_028228, intron 6 of 6)	39455	NM_028228	72400	Mm.379214	NM_028228	ENSMUSG00000021958	Pinx1	2210403I16Rik|2610028A01Rik|67-11-3|AU024023|LPTS|LPTS1	PIN2/TERF1 interacting, telomerase inhibitor 1	protein-coding
mm_159031.1	chr1	175766798	175766798	+	1	NA	intron (NM_029453, intron 11 of 27)	intron (NM_029453, intron 11 of 27)	68205	NM_029453	75820	Mm.50361	NM_029453	ENSMUSG00000026523	Wdr64	4930415O10Rik|4930511H01Rik	WD repeat domain 64	protein-coding
mm_7741.1	chr1	130911553	130911564	-	1	NA	promoter-TSS (NM_021380)	promoter-TSS (NM_021380)	-262	NM_021380	58181	Mm.103794	NM_021380	ENSMUSG00000026416	Il20	Zcyto10	interleukin 20	protein-coding
mm_110673.1	chr12	65172542	65172552	-	1	NA	promoter-TSS (NM_172578)	promoter-TSS (NM_172578)	33	NM_172578	217653	Mm.21144	NM_172578	ENSMUSG00000047534	Mis18bp1	6720403H11|C79407|Knl2|mKIAA1903	MIS18 binding protein 1	protein-coding
mm_129008.1	chr15	74883110	74883119	-	1	NA	Intergenic	Intergenic	-1410	NM_025929	67038	Mm.154566	NM_025929	ENSMUSG00000063522	2010109I03Rik	Ly6m	RIKEN cDNA 2010109I03 gene	protein-coding
mm_107048.1	chr12	16170449	16170458	+	1	NA	Intergenic	Intergenic	-353668	NM_144551	217410	Mm.491136	NM_144551	ENSMUSG00000020601	Trib2	AW319517|TRB-2|TRB2	tribbles pseudokinase 2	protein-coding
mm_129659.1	chr15	81070944	81070948	-	1	NA	intron (NM_001082536, intron 2 of 13)	intron (NM_001082536, intron 2 of 13)	34101	NM_153049	223701	Mm.439814	NM_153049	ENSMUSG00000042292	Mkl1	AMKL|Bsac|Mal|Mrtf-A	MKL (megakaryoblastic leukemia)/myocardin-like 1	protein-coding
mm_114930.1	chr13	95711166	95711166	+	1	NA	intron (NM_027711, intron 12 of 35)	intron (NM_027711, intron 12 of 35)	14246	NM_010170	14064	Mm.440952	NM_010170	ENSMUSG00000021675	F2rl2	F730031A08|PAR3	coagulation factor II (thrombin) receptor-like 2	protein-coding
mm_9733.1	chr1	180230017	180230034	-	1	NA	intron (NM_001128605, intron 7 of 10)	intron (NM_001128605, intron 7 of 10)	15925	NM_011183	19165	Mm.330850	NM_011183	ENSMUSG00000010609	Psen2	ALG-3|Ad4h|Alg3|PS-2|PS2|Psnl2|STM2	presenilin 2	protein-coding
mm_17757.1	chr2	32775379	32775398	-	1	NA	promoter-TSS (NM_001290566)	promoter-TSS (NM_001290566)	-49	NM_001290566	338348	Mm.475130	NM_177384	ENSMUSG00000039021	Ttc16	1200002K10Rik	tetratricopeptide repeat domain 16	protein-coding
mm_73605.1	chr8	109999302	109999310	+	1	NA	3' UTR (NM_146214, exon 12 of 12)	3' UTR (NM_146214, exon 12 of 12)	8870	NM_146214	234724	Mm.28110	NM_146214	ENSMUSG00000001670	Tat	-	tyrosine aminotransferase	protein-coding
mm_82012.1	chr9	121719155	121719166	+	1	NA	promoter-TSS (NM_010918)	promoter-TSS (NM_010918)	-21	NM_010918	18087	Mm.32842	NM_010918	ENSMUSG00000032525	Nktr	5330401F18Rik|D9Wsu172e	natural killer tumor recognition sequence	protein-coding
mm_134897.1	chr16	29946500	29946532	-	1	NA	Intergenic	Intergenic	32608	NR_037689	328657	Mm.425982	NM_001033403		Gm1968	-	predicted gene 1968	ncRNA
mm_88971.1	chr10	81414086	81414099	+	1	NA	intron (NM_026756, intron 2 of 8)	intron (NM_026756, intron 2 of 8)	2205	NR_106141	102465778		NR_106141	ENSMUSG00000105379	Mir1191b	mmu-mir-1191b	microRNA 1191b	ncRNA
mm_125483.1	chr15	54600892	54600910	+	1	NA	3' UTR (NM_178920, exon 4 of 4)	3' UTR (NM_178920, exon 4 of 4)	29535	NM_178920	105853	Mm.410994	NM_178920	ENSMUSG00000024479	Mal2	AI461653	mal, T cell differentiation protein 2	protein-coding
mm_169661.1	chr15	58933774	58933774	+	1	NA	promoter-TSS (NM_023172)	promoter-TSS (NM_023172)	-36	NM_023172	66218	Mm.322294	NM_023172	ENSMUSG00000022354	Ndufb9	1190008J14Rik	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 9	protein-coding
mm_73255.1	chr8	104340349	104340379	+	1	NA	promoter-TSS (NM_024217)	promoter-TSS (NM_024217)	-230	NM_024217	68119	Mm.390108	NM_024217	ENSMUSG00000031875	Cmtm3	9430096L06Rik|AI413895|BNAS2|Cklfsf3	CKLF-like MARVEL transmembrane domain containing 3	protein-coding
mm_64748.1	chr7	4783845	4783853	-	1	NA	promoter-TSS (NM_001290423)	promoter-TSS (NM_001290423)	909	NM_030028	78052	Mm.160043	NM_030028	ENSMUSG00000013091	Tmem190	4930572D21Rik	transmembrane protein 190	protein-coding
mm_92223.1	chr10	68278829	68278867	-	1	NA	promoter-TSS (NM_023598)	promoter-TSS (NM_023598)	-122	NM_023598	71371	Mm.440357	NM_023598	ENSMUSG00000019947	Arid5b	4930580B11|5430435G07Rik|AI467247|Desrt|Mrf2|Mrf2alpha|Mrf2beta	AT rich interactive domain 5B (MRF1-like)	protein-coding
mm_137195.1	chr17	23829244	23829268	+	1	NA	promoter-TSS (NM_026305)	promoter-TSS (NM_026305)	-147	NM_026305	67673	Mm.153758	NM_026305	ENSMUSG00000055839	Elob	0610040H15Rik|Tceb2	elongin B	protein-coding
mm_145687.1	chr18	61725721	61725734	+	1	NA	promoter-TSS (NR_029432)	promoter-TSS (NR_029432)	604	NM_021296	17714	Mm.269657	NM_021296	ENSMUSG00000024580	Grpel2	mt-GrpE#2|mt-Grpel2	GrpE-like 2, mitochondrial	protein-coding
mm_89037.1	chr10	82812200	82812209	+	1	NA	promoter-TSS (NR_038042)	promoter-TSS (NR_038042)	81	NR_038042	70003	Mm.48789	NR_038042	ENSMUSG00000056821	1700028I16Rik	-	RIKEN cDNA 1700028I16 gene	ncRNA
mm_136701.1	chr17	7576143	7576154	+	1	NA	Intergenic	Intergenic	-190843	NM_001142539	667055	Mm.327371	NM_001142539	ENSMUSG00000056133	Gm9992	ENSMUSG00000056133	predicted gene 9992	protein-coding
mm_100936.1	chr11	6520873	6520891	-	1	NA	promoter-TSS (NM_178440)	promoter-TSS (NM_178440)	76	NM_178440	246177	Mm.239554	NM_178440	ENSMUSG00000020437	Myo1g	E430002D17Rik	myosin IG	protein-coding
mm_9522.1	chr1	173766902	173766928	-	1	NA	promoter-TSS (NM_008329)	promoter-TSS (NM_008329)	4	NM_008329	15951	Mm.261270	NM_008329	ENSMUSG00000073489	Ifi204	Ifi16|p204	interferon activated gene 204	protein-coding
mm_25847.1	chr3	129474721	129474729	+	1	NA	Intergenic	RLTR17|LTR|ERVK	41052	NR_033594	435755	Mm.430561	NR_033594	ENSMUSG00000105712	Pou5f1-rs4	EG435755|Gm5712|Oct4P1|Otf3-rs4|Otf3d	POU domain, class 5, transcription factor 1, related sequence 4	pseudo
mm_91977.1	chr10	61648459	61648504	-	1	NA	promoter-TSS (NM_026438)	promoter-TSS (NM_026438)	-140	NM_026438	67895	Mm.28897	NM_026438	ENSMUSG00000020089	Ppa1	2010317E03Rik|Pyp	pyrophosphatase (inorganic) 1	protein-coding
mm_117068.1	chr13	59084231	59084244	-	1	NA	intron (NM_001025074, intron 16 of 17)	intron (NM_001025074, intron 16 of 17)	276540	NM_001025074	18212	Mm.130054	NM_008745	ENSMUSG00000055254	Ntrk2	GP145-TrkB/GP95-TrkB|Tkrb|trk-B|trkB	neurotrophic tyrosine kinase, receptor, type 2	protein-coding
mm_37728.1	chr4	129558831	129558841	-	1	NA	promoter-TSS (NM_010693)	promoter-TSS (NM_010693)	-464	NM_010693	16818	Mm.293753	NM_010693	ENSMUSG00000000409	Lck	Hck-3|Lsk|Lskt|p56<lck>|p56Lck	lymphocyte protein tyrosine kinase	protein-coding
mm_130151.1	chr15	91172188	91172192	-	1	NA	intron (NM_011994, intron 6 of 9)	intron (NM_011994, intron 6 of 9)	19617	NM_011994	26874	Mm.295456	NM_011994	ENSMUSG00000055782	Abcd2	ABC39|ALDL1|ALDR|ALDRP	ATP-binding cassette, sub-family D (ALD), member 2	protein-coding
mm_67589.1	chr7	83653339	83653342	-	1	NA	intron (NM_010551, intron 13 of 18)	intron (NM_010551, intron 13 of 18)	21323	NM_023377	170460	Mm.357953	NM_023377	ENSMUSG00000046027	Stard5	2310058G22Rik|AI607880|D7Ertd152e	StAR-related lipid transfer (START) domain containing 5	protein-coding
mm_20949.1	chr2	151670579	151670613	-	1	NA	Intergenic	Intergenic	-2063	NM_001276400	668929	Mm.473683	NM_001114677	ENSMUSG00000074704	Rad21l	Gm14160|MeiRAD21L|Rad21l1	RAD21-like (S. pombe)	protein-coding
mm_54921.1	chr6	47807482	47807493	-	1	NA	intron (NM_009787, intron 2 of 9)	intron (NM_009787, intron 2 of 9)	-3835	NR_030485	735289		NR_030485	ENSMUSG00000076060	Mir704	Mirn704|mir-704|mmu-mir-704	microRNA 704	ncRNA
mm_125125.1	chr15	30172944	30172970	+	1	NA	5' UTR (NM_008729, exon 1 of 23)	5' UTR (NM_008729, exon 1 of 23)	364	NM_008729	18163	Mm.321648	NM_008729	ENSMUSG00000022240	Ctnnd2	Catnd2|Nprap|neurojugin	catenin (cadherin associated protein), delta 2	protein-coding
mm_73981.1	chr8	120537473	120537501	+	1	NA	promoter-TSS (NM_001145896)	promoter-TSS (NM_001145896)	78	NM_001145896	382034	Mm.334856	NM_198671	ENSMUSG00000031822	Gse1	2210013I18Rik|mKIAA0182	genetic suppressor element 1, coiled-coil protein	protein-coding
mm_155408.1	chrX	73358346	73358357	+	1	NA	3' UTR (NM_031494, exon 6 of 6)	3' UTR (NM_031494, exon 6 of 6)	15730	NM_001160229	27081	Mm.26595	NM_031494	ENSMUSG00000031365	Zfp275	5430431L06Rik|AI593314|DXBay20|DXHXS52|DXPas8	zinc finger protein 275	protein-coding
mm_114355.1	chr13	60940213	60940223	+	1	NA	exon (NM_009411, exon 3 of 5)	exon (NM_009411, exon 3 of 5)	1717	NM_009411	21984	Mm.2372	NM_009411	ENSMUSG00000033834	Tpbpa	AV033951|Tb-1|Tb1|Tpbp|b2b1247Clo	trophoblast specific protein alpha	protein-coding
mm_52287.1	chr6	108662771	108662778	+	1	NA	intron (NM_011498, intron 4 of 4)	intron (NM_011498, intron 4 of 4)	-1840	NR_104577	75394	Mm.395061	NR_040757	ENSMUSG00000087341	0610040F04Rik	-	RIKEN cDNA 0610040F04 gene	ncRNA
mm_102171.1	chr11	53979888	53979940	-	1	NA	5' UTR (NM_019723, exon 1 of 10)	5' UTR (NM_019723, exon 1 of 10)	113	NM_019723	56517	Mm.154284	NM_019723	ENSMUSG00000063652	Slc22a21	Octn3|Slc22a9	solute carrier family 22 (organic cation transporter), member 21	protein-coding
mm_151365.1	chr19	55925934	55925947	+	1	NA	intron (NM_009333, intron 12 of 12)	CT-rich|Low_complexity|Low_complexity	30619	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_114472.1	chr13	67863352	67863372	+	1	NA	promoter-TSS (NM_001001185)	promoter-TSS (NM_001001185)	36	NM_001001185	408058	Mm.177840	NM_001001185	ENSMUSG00000064063	BC048507	-	cDNA sequence BC048507	protein-coding
mm_13620.1	chr2	113440897	113440952	+	1	NA	promoter-TSS (NM_001285459)	promoter-TSS (NM_001285459)	-140	NM_001285459	14260	Mm.4938	NM_010230	ENSMUSG00000044042	Fmn1	Fmn|formin-1|ld	formin 1	protein-coding
mm_97994.1	chr11	84129650	84129705	+	1	NA	promoter-TSS (NM_172562)	promoter-TSS (NM_172562)	-109	NM_172562	217031	Mm.45159	NM_172562	ENSMUSG00000018651	Tada2a	AV319371|D030022J10Rik|Tada2l	transcriptional adaptor 2A	protein-coding
mm_53980.1	chr6	6861679	6861685	-	1	NA	intron (NR_015388, intron 1 of 1)	intron (NR_015388, intron 1 of 1)	-1652	NM_010057	13396	Mm.439763	NM_010057	ENSMUSG00000029754	Dlx6	-	distal-less homeobox 6	protein-coding
mm_35171.1	chr4	14826545	14826555	-	1	NA	promoter-TSS (NM_152812)	promoter-TSS (NM_152812)	37	NM_152812	72201	Mm.387724	NM_152812	ENSMUSG00000040550	Otud6b	2600013N14Rik|AU015433	OTU domain containing 6B	protein-coding
mm_92813.1	chr10	81407661	81407683	-	1	NA	exon (NM_008688, exon 6 of 10)	exon (NM_008688, exon 6 of 10)	8625	NR_106141	102465778		NR_106141	ENSMUSG00000105379	Mir1191b	mmu-mir-1191b	microRNA 1191b	ncRNA
mm_33966.1	chr4	137594150	137594274	+	1	NA	promoter-TSS (NM_130879)	promoter-TSS (NM_130879)	23	NM_130879	170707	Mm.218478	NM_130879	ENSMUSG00000043411	Usp48	2810449C13Rik|AI115503|BC021769|D330022K21Rik|Usp31	ubiquitin specific peptidase 48	protein-coding
mm_5860.1	chr1	53773471	53773475	-	1	NA	intron (NM_133810, intron 2 of 7)	intron (NM_133810, intron 2 of 7)	11742	NM_133810	98267	Mm.25559	NM_133810	ENSMUSG00000026094	Stk17b	3110009A03Rik|AI120141|Drak2	serine/threonine kinase 17b (apoptosis-inducing)	protein-coding
mm_34832.1	chr4	155246861	155246872	+	1	NA	Intergenic	Intergenic	-3100	NM_001190445	67513	Mm.10374	NM_001190445	ENSMUSG00000073684	Faap20	2610002J02Rik	Fanconi anemia core complex associated protein 20	protein-coding
mm_46420.1	chr5	104113589	104113599	-	1	NA	5' UTR (NM_010097, exon 1 of 11)	5' UTR (NM_010097, exon 1 of 11)	494	NM_010097	13602	Mm.29027	NM_010097	ENSMUSG00000029309	Sparcl1	Ecm2|Sc1|hevin|mast9	SPARC-like 1	protein-coding
mm_31880.1	chr4	81628271	81628275	+	1	NA	Intergenic	Intergenic	-141260	NR_030570	100124446		NR_030570	ENSMUSG00000077941	Mir466h	Mirn466h	microRNA 466h	ncRNA
mm_54929.1	chr6	48064564	48064591	-	1	NA	exon (NM_001163475, exon 7 of 7)	exon (NM_001163475, exon 7 of 7)	-16463	NM_001081382	72306	Mm.381553	NM_001081382	ENSMUSG00000071477	Zfp777	2500002G23Rik	zinc finger protein 777	protein-coding
mm_154816.1	chrX	14680514	14680537	+	1	NA	Intergenic	RLTR17|LTR|ERVK	430964	NR_033171	67395	Mm.50369	NM_026128	ENSMUSG00000045217	Ppp1r2-ps9	4930403L05Rik	protein phosphatase 1, regulatory (inhibitor) subunit 2, pseudogene 9	pseudo
mm_171841.1	chr5	151655749	151655755	+	1	NA	Intergenic	L1Md_T|LINE|L1	-4544	NM_027009	69263	Mm.12553	NM_027009	ENSMUSG00000033970	Rfc3	2810416I22Rik|38kDa|AU022547|Recc3	replication factor C (activator 1) 3	protein-coding
mm_145798.1	chr18	65248925	65248925	+	1	NA	promoter-TSS (NR_029600)	promoter-TSS (NR_029600)	64	NR_029600	387231		NR_029600	ENSMUSG00000065402	Mir122	Mir122a|Mirn122a|mir-122|mmu-mir-122	microRNA 122	ncRNA
mm_163615.1	chr13	53161157	53161158	+	1	NA	intron (NM_013846, intron 1 of 8)	Lx8|LINE|L1	124952	NM_013846	26564	Mm.342774	NM_013846	ENSMUSG00000021464	Ror2	Ntrkr2|mRor2	receptor tyrosine kinase-like orphan receptor 2	protein-coding
mm_90202.1	chr10	120364135	120364176	+	1	NA	3' UTR (NM_010441, exon 5 of 5)	3' UTR (NM_010441, exon 5 of 5)	-25368	NR_040626	320626	Mm.446091	NR_040626	ENSMUSG00000090191	9230105E05Rik	-	RIKEN cDNA 9230105E05 gene	ncRNA
mm_101367.1	chr11	23748456	23748462	-	1	NA	intron (NM_009044, intron 5 of 9)	B1_Mur2|SINE|Alu	22511	NM_009044	19696	Mm.4869	NM_009044	ENSMUSG00000020275	Rel	c-Rel	reticuloendotheliosis oncogene	protein-coding
mm_61959.1	chr7	90283796	90283801	+	1	NA	Intergenic	Intergenic	-18366	NR_111924	75338	Mm.487222	NM_029256	ENSMUSG00000030617	Ccdc83	4930549K11Rik|4930554C01Rik|4932423M01Rik	coiled-coil domain containing 83	protein-coding
mm_44252.1	chr5	5380546	5380556	-	1	NA	promoter-TSS (NM_011074)	promoter-TSS (NM_011074)	-300	NM_011074	18647	Mm.389061	NM_011074	ENSMUSG00000028926	Cdk14	Pftk1|mKIAA0834	cyclin-dependent kinase 14	protein-coding
mm_38836.1	chr4	149158064	149158084	-	1	NA	exon (NM_001081274, exon 7 of 13)	exon (NM_001081274, exon 7 of 13)	8633	NM_001081274	110208	Mm.252080	NM_025801	ENSMUSG00000028961	Pgd	0610042A05Rik|AU019875|C78335	phosphogluconate dehydrogenase	protein-coding
mm_20091.1	chr2	120850599	120850603	-	1	NA	promoter-TSS (NM_001024856)	promoter-TSS (NM_001024856)	-17	NM_080788	140810	Mm.275698	NM_080788	ENSMUSG00000090100	Ttbk2	2610507N02Rik|AI326283|B930008N24Rik|TTK|Ttbk|Ttbk1|mKIAA0847	tau tubulin kinase 2	protein-coding
mm_28918.1	chr3	98857921	98857931	-	1	NA	exon (NM_001304800, exon 2 of 4)	exon (NM_001304800, exon 2 of 4)	1868	NM_001304800	15492	Mm.140811	NM_008293	ENSMUSG00000027871	Hsd3b1	3-beta-HSD I|D3Ertd383e	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1	protein-coding
mm_123352.1	chr14	63142462	63142465	-	1	NA	3' UTR (NM_007798, exon 10 of 10)	3' UTR (NM_007798, exon 10 of 10)	20001	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_155360.1	chrX	70385948	70385963	+	1	NA	promoter-TSS (NM_026787)	promoter-TSS (NM_026787)	42	NM_026787	68618	Mm.293255	NM_026787	ENSMUSG00000045237	1110012L19Rik	-	RIKEN cDNA 1110012L19 gene	protein-coding
mm_148143.1	chr18	77047269	77047279	-	1	NA	promoter-TSS (NM_027721)	promoter-TSS (NM_027721)	22	NM_027721	71206	Mm.35803	NM_027721	ENSMUSG00000025420	Katnal2	3110023G01Rik|4933439B08Rik	katanin p60 subunit A-like 2	protein-coding
mm_52458.1	chr6	113695966	113695982	+	1	NA	TTS (NM_172161)	TTS (NM_172161)	-1076	NM_001347356	381801	Mm.333322	NM_001033463	ENSMUSG00000056952	Tatdn2	AI646012|mKIAA0218	TatD DNase domain containing 2	protein-coding
mm_115967.1	chr13	23967139	23967145	-	1	NA	intron (NM_145399, intron 6 of 10)	intron (NM_145399, intron 6 of 10)	24072	NM_145399	214189	Mm.255667	NM_145399	ENSMUSG00000021337	Scgn	-	secretagogin, EF-hand calcium binding protein	protein-coding
mm_34745.1	chr4	152296201	152296221	+	1	NA	Intergenic	RMER17C2|LTR|ERVK	-1003	NR_037908	57295	Mm.277464	NM_133788	ENSMUSG00000039662	Icmt	1700008E11Rik|C80758|Gm13095|HSTE14|OTTMUSG00000010406|PPMT|STE14|pcCMT	isoprenylcysteine carboxyl methyltransferase	protein-coding
mm_163207.1	chr11	99389076	99389084	+	1	NA	exon (NM_010660, exon 1 of 8)	exon (NM_010660, exon 1 of 8)	284	NM_010660	16661	Mm.22662	NM_010660	ENSMUSG00000019761	Krt10	D130054E02Rik|K10|K1C1|Krt-1.10|Krt1-10	keratin 10	protein-coding
mm_134296.1	chr16	14291356	14291371	-	1	NA	promoter-TSS (NM_013607)	promoter-TSS (NM_013607)	45	NM_001161775	17880	Mm.250705	NM_013607	ENSMUSG00000018830	Myh11	AV071570|SM1|SM2|smMHC	myosin, heavy polypeptide 11, smooth muscle	protein-coding
mm_21220.1	chr2	155826454	155826464	-	1	NA	5' UTR (NM_010579, exon 1 of 6)	5' UTR (NM_010579, exon 1 of 6)	466	NM_010579	16418	Mm.271674	NM_010579	ENSMUSG00000027613	Eif6	1110004P11|AA408895|CAB|Itgb4bp|eIF-6|imc-415|p27(BBP)|p27BBP	eukaryotic translation initiation factor 6	protein-coding
mm_16630.1	chr2	5714342	5714402	-	1	NA	5' UTR (NM_001290375, exon 1 of 11)	5' UTR (NM_001290375, exon 1 of 11)	390	NM_001290374	227541	Mm.191949	NM_177343	ENSMUSG00000039145	Camk1d	A630059D12Rik|CKLiK|CaMKIdelta|E030025C11Rik|mCKLiK	calcium/calmodulin-dependent protein kinase ID	protein-coding
mm_55918.1	chr6	83831684	83831702	-	1	NA	promoter-TSS (NM_146169)	promoter-TSS (NM_146169)	48	NM_146169	232164	Mm.404420	NM_146169	ENSMUSG00000045896	Paip2b	-	poly(A) binding protein interacting protein 2B	protein-coding
mm_106602.1	chr11	120731984	120731998	-	1	NA	promoter-TSS (NM_007621)	promoter-TSS (NM_007621)	30	NM_007621	12409	Mm.21454	NM_007621	ENSMUSG00000025150	Cbr2	MLCR	carbonyl reductase 2	protein-coding
mm_145464.1	chr18	60247276	60247289	+	1	NA	3' UTR (NM_001033767, exon 3 of 3)	3' UTR (NM_001033767, exon 3 of 3)	25985	NM_001034859	225594	Mm.329460	NM_001034859	ENSMUSG00000068606	Gm4841	EG225594|Ifgga3	predicted gene 4841	protein-coding
mm_72869.1	chr8	88660010	88660027	+	1	NA	intron (NM_145857, intron 2 of 12)	intron (NM_145857, intron 2 of 12)	12671	NM_145857	257632	Mm.222633	NM_145857	ENSMUSG00000055994	Nod2	ACUG|BLAU|CD|Card15|F830032C23Rik|IBD1|Nlrc2	nucleotide-binding oligomerization domain containing 2	protein-coding
mm_86273.1	chr9	121791084	121791090	-	1	NA	promoter-TSS (NR_027967)	promoter-TSS (NR_027967)	33	NR_027967	74770	Mm.44195	NM_029095	ENSMUSG00000032523	Hhatl	1110011D13Rik|Gup1|Mg56	hedgehog acyltransferase-like	protein-coding
mm_43633.1	chr5	138219734	138219740	+	1	NA	Intergenic	U4|snRNA|snRNA	-6167	NM_001013773	381680	Mm.156846	NM_001013773	ENSMUSG00000047592	Nxpe5	-	neurexophilin and PC-esterase domain family, member 5	protein-coding
mm_27857.1	chr3	79157368	79157391	-	1	NA	Intergenic	L1_Mur3|LINE|L1	-11504	NM_001099624	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_19382.1	chr2	91236841	91236855	-	1	NA	promoter-TSS (NR_015464)	promoter-TSS (NR_015464)	218	NM_028119	107986	Mm.389334	NM_028119	ENSMUSG00000002109	Ddb2	2610043A19Rik	damage specific DNA binding protein 2	protein-coding
mm_57078.1	chr6	122581467	122581502	-	1	NA	exon (NM_031159, exon 6 of 8)	exon (NM_031159, exon 6 of 8)	20960	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_107368.1	chr12	32850633	32850656	+	1	NA	3' UTR (NM_021524, exon 11 of 11)	3' UTR (NM_021524, exon 11 of 11)	26528	NR_045032	100504486	Mm.440246	NR_045032		Gdap10	Gdap-ps	ganglioside-induced differentiation-associated-protein 10	ncRNA
mm_84070.1	chr9	58201552	58201618	-	1	NA	5' UTR (NM_001161537, exon 1 of 3)	5' UTR (NM_001161537, exon 1 of 3)	130	NM_001161535	320563	Mm.186499	NM_177193	ENSMUSG00000051243	Islr2	B930052A04Rik|Linx|Mbu-3|mKIAA1465	immunoglobulin superfamily containing leucine-rich repeat 2	protein-coding
mm_101731.1	chr11	42321075	42321083	-	1	NA	promoter-TSS (NM_008068)	promoter-TSS (NM_008068)	-7	NM_001099641	14399	Mm.4915	NM_008068	ENSMUSG00000020428	Gabra6	GABA-ARalpha6|Gabra-6|alpha6	gamma-aminobutyric acid (GABA) A receptor, subunit alpha 6	protein-coding
mm_55290.1	chr6	54566447	54566453	-	1	NA	promoter-TSS (NM_027268)	promoter-TSS (NM_027268)	-68	NM_027268	69938	Mm.41557	NM_027268	ENSMUSG00000019124	Scrn1	2810019K23Rik|6330535A03Rik|AI852905|SES1|mKIAA0193	secernin 1	protein-coding
mm_46172.1	chr5	96921163	96921178	-	1	NA	promoter-TSS (NR_131152)	promoter-TSS (NR_131152)	-102	NR_131152	666266	Mm.32442	NR_131152	ENSMUSG00000106357	Gm8013	EG666266	predicted gene 8013	ncRNA
mm_54522.1	chr6	35989017	35989027	-	1	NA	Intergenic	Intergenic	-399062	NM_203491	243764	Mm.448632	NM_203491	ENSMUSG00000045613	Chrm2	AChR-M2|Chrm-2|M2	cholinergic receptor, muscarinic 2, cardiac	protein-coding
mm_8072.1	chr1	135510394	135510407	-	1	NA	intron (NM_173437, intron 3 of 28)	intron (NM_173437, intron 3 of 28)	-55717	NR_049188	100885827		NR_049188	ENSMUSG00000093515	Mir1231	Gm23720|mir-1231|mmu-mir-1231	microRNA 1231	ncRNA
mm_77253.1	chr8	115706100	115706119	-	1	NA	exon (NM_001025577, exon 1 of 1)	exon (NM_001025577, exon 1 of 1)	785	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_111204.1	chr12	84361783	84361797	-	1	NA	promoter-TSS (NM_172581)	promoter-TSS (NM_172581)	31	NM_172581	217705	Mm.259468	NM_172581	ENSMUSG00000021234	Fam161b	9330169D17|9830169C18Rik	family with sequence similarity 161, member B	protein-coding
mm_173070.1	chrX	136068111	136068111	-	1	NA	5' UTR (NM_009749, exon 1 of 3)	5' UTR (NM_009749, exon 1 of 3)	125	NM_009749	12069	Mm.94160	NM_009749	ENSMUSG00000042750	Bex2	AL024066|Bex1	brain expressed X-linked 2	protein-coding
mm_158446.1	chrX	140542992	140542994	-	1	NA	promoter-TSS (NR_122039)	promoter-TSS (NR_122039)	194	NM_010286	14605	Mm.22216	NM_010286	ENSMUSG00000031431	Tsc22d3	DIP|Dsip1|Gilz|TSC-22R|Tilz3	TSC22 domain family, member 3	protein-coding
mm_124768.1	chr15	6708373	6708396	+	1	NA	promoter-TSS (NM_030168)	promoter-TSS (NM_030168)	3	NM_030168	78757	Mm.275811	NM_030168	ENSMUSG00000050310	Rictor	4921505C17Rik|6030405M08Rik|AVO3|AW492497|D530039E11Rik	RPTOR independent companion of MTOR, complex 2	protein-coding
mm_6612.1	chr1	75479285	75479358	-	1	NA	promoter-TSS (NM_177056)	promoter-TSS (NM_177056)	150	NM_001001565	74241	Mm.260577	NM_001001565	ENSMUSG00000032997	Chpf	1700028N03Rik|AI414328|D1Bwg1363e	chondroitin polymerizing factor	protein-coding
mm_42255.1	chr5	114004782	114004809	+	1	NA	promoter-TSS (NM_001286396)	promoter-TSS (NM_001286396)	-13	NM_001286396	13142	Mm.20115	NM_010018	ENSMUSG00000042096	Dao	AI987963|DAAO|DAMOX|Dao-1|Dao1	D-amino acid oxidase	protein-coding
mm_3091.1	chr1	134415389	134415395	+	1	NA	promoter-TSS (NM_001306069)	promoter-TSS (NM_001306069)	14	NM_028320	72674	Mm.259976	NM_028320	ENSMUSG00000026457	Adipor1	2810031L11Rik|ACDCR1|CGI-45|Paqr1	adiponectin receptor 1	protein-coding
mm_4114.1	chr1	167689203	167689217	+	1	NA	promoter-TSS (NM_033652)	promoter-TSS (NM_033652)	-348	NM_033652	110648	Mm.330081	NM_033652	ENSMUSG00000026686	Lmx1a	Lmx1.1|dr|dreher|sst	LIM homeobox transcription factor 1 alpha	protein-coding
mm_126000.1	chr15	76512383	76512405	+	1	NA	promoter-TSS (NM_010046)	promoter-TSS (NM_010046)	-576	NM_010046	13350	Mm.22633	NM_010046	ENSMUSG00000022555	Dgat1	ARAT|C75990|D15Ertd23e|Dgat	diacylglycerol O-acyltransferase 1	protein-coding
mm_13216.1	chr2	96318015	96318057	+	1	NA	promoter-TSS (NM_001289742)	promoter-TSS (NM_001289742)	-133	NM_001289742	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_86292.1	chr9	122051212	122051218	-	1	NA	Intergenic	Intergenic	-55189	NM_153540	215494	Mm.402151	NM_153540	ENSMUSG00000066235	Pomgnt2	Ago61|C85492|Gtdc2	protein O-linked mannose beta 1,4-N-acetylglucosaminyltransferase 2	protein-coding
mm_43652.1	chr5	138341924	138341936	+	1	NA	Intergenic	Intergenic	61421	NM_016964	50878	Mm.285609	NM_016964	ENSMUSG00000036928	Stag3	SA-2	stromal antigen 3	protein-coding
mm_135162.1	chr16	35866258	35866299	-	1	NA	exon (NM_001039530, exon 2 of 17)	exon (NM_001039530, exon 2 of 17)	5104	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_4159.1	chr1	171029304	171029315	+	1	NA	exon (NM_144559, exon 5 of 5)	exon (NM_144559, exon 5 of 5)	10383	NM_144559	246256	Mm.251254	NM_144559	ENSMUSG00000059089	Fcgr4	4833442P21Rik|CD16-2|FcgRIV|FcgammaRIV|Fcgr3a|Fcrl3	Fc receptor, IgG, low affinity IV	protein-coding
mm_162894.1	chr10	111754035	111754037	-	1	NA	Intergenic	Intergenic	120340	NR_046029	629206	Mm.391444	NR_046029		Gm20758	-	predicted gene, 20758	ncRNA
mm_155518.1	chrX	74254783	74254872	+	1	NA	5' UTR (NM_007927, exon 1 of 6)	5' UTR (NM_007927, exon 1 of 6)	140	NM_007927	13726	Mm.18892	NM_007927	ENSMUSG00000001964	Emd	AW550900|Sta	emerin	protein-coding
mm_134436.1	chr16	18213867	18213882	-	1	NA	promoter-TSS (NR_027843)	promoter-TSS (NR_027843)	-11	NR_015575	66779	Mm.387525	NR_015575		4933432I09Rik	-	RIKEN cDNA 4933432I09 gene	ncRNA
mm_107980.1	chr12	72945701	72945710	+	1	NA	TTS (NM_011384)	TTS (NM_011384)	5823	NM_011384	20476	Mm.57138	NM_011384	ENSMUSG00000021099	Six6	Optx2|Six9	sine oculis-related homeobox 6	protein-coding
mm_90364.1	chr10	127166486	127166503	+	1	NA	intron (NR_045166, intron 2 of 9)	intron (NR_045166, intron 2 of 9)	663	NM_001244618	14421	Mm.386762	NM_008080	ENSMUSG00000006731	B4galnt1	4933429D13Rik|Gal-NAc-T|GalNAc-T|GalNAcT|Galgt1|Ggm-2|Ggm2	beta-1,4-N-acetyl-galactosaminyl transferase 1	protein-coding
mm_108535.1	chr12	84226656	84226675	+	1	NA	Intergenic	Intergenic	-7784	NM_001163501	238317	Mm.31256	NM_001163501	ENSMUSG00000042507	Elmsan1	9430029N19Rik|C130039O16Rik|Gm260	ELM2 and Myb/SANT-like domain containing 1	protein-coding
mm_56462.1	chr6	98928027	98928043	-	1	NA	3' UTR (NM_053202, exon 19 of 19)	3' UTR (NM_053202, exon 19 of 19)	100263	NM_001197322	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_45383.1	chr5	66133712	66133745	-	1	NA	intron (NM_001127382, intron 2 of 7)	intron (NM_001127382, intron 2 of 7)	17250	NM_001291226	245945	Mm.36863	NM_139065	ENSMUSG00000070780	Rbm47	9530077J19Rik	RNA binding motif protein 47	protein-coding
mm_123558.1	chr14	66865894	66865895	-	1	NA	intron (NM_009955, intron 1 of 13)	intron (NM_009955, intron 1 of 13)	2706	NM_009955	12934	Mm.352648	NM_009955	ENSMUSG00000022048	Dpysl2	AI851130|Crmp2|DRP2|Musunc33|TOAD-64|Ulip2	dihydropyrimidinase-like 2	protein-coding
mm_163212.1	chr11	100397884	100397913	-	1	NA	promoter-TSS (NM_010593)	promoter-TSS (NM_010593)	-108	NM_010593	16480	Mm.299774	NM_010593	ENSMUSG00000001552	Jup	Ctnng|D930025P04Rik|PG	junction plakoglobin	protein-coding
mm_167929.1	chrX	104040542	104040544	+	1	NA	Intergenic	RLTR9A3B|LTR|ERVK	-59259	NM_011276	19820	Mm.427762	NM_011276	ENSMUSG00000056537	Rlim	AL022832|AW743871|Ha1r|Rlim1|Rnf12	ring finger protein, LIM domain interacting	protein-coding
mm_34514.1	chr4	148896313	148896350	+	1	NA	intron (NM_027195, intron 3 of 15)	intron (NM_027195, intron 3 of 15)	91939	NM_027195	69743	Mm.233879	NM_027195	ENSMUSG00000028977	Casz1	2410019P08Rik|AV096627|BC040081|Cst|D4Ertd432e	castor zinc finger 1	protein-coding
mm_165360.1	chr2	122771286	122771327	+	1	NA	promoter-TSS (NR_027888)	promoter-TSS (NR_027888)	-407	NR_027888	59010	Mm.28986	NM_021507	ENSMUSG00000005803	Sqrdl	0610039J17Rik|4930557M22Rik|SQOR	sulfide quinone reductase-like (yeast)	protein-coding
mm_118040.1	chr13	101692625	101692638	-	1	NA	promoter-TSS (NM_001024955)	promoter-TSS (NM_001024955)	-1	NM_001024955	18708	Mm.259333	NM_001024955	ENSMUSG00000041417	Pik3r1	PI3K|p50alpha|p55alpha|p85alpha	phosphatidylinositol 3-kinase, regulatory subunit, polypeptide 1 (p85 alpha)	protein-coding
mm_141210.1	chr17	27133621	27133642	-	1	NA	intron (NM_026063, intron 1 of 3)	CpG	260	NM_026063	67267	Mm.272389	NM_026063	ENSMUSG00000024208	Uqcc2	2900010M23Rik|Cbp6|M19|Mnf1	ubiquinol-cytochrome c reductase complex assembly factor 2	protein-coding
mm_134469.1	chr16	18460048	18460081	-	1	NA	intron (NM_013711, intron 11 of 17)	intron (NM_013711, intron 11 of 17)	-33348	NM_001111062	12846	Mm.100940	NM_007744	ENSMUSG00000000326	Comt	Comt1|D16Wsu103e|D330014B15Rik	catechol-O-methyltransferase	protein-coding
mm_168531.1	chr1	161035498	161035508	+	1	NA	non-coding (NR_002840, exon 1 of 4)	non-coding (NR_002840, exon 1 of 4)	337	NR_002840	14455	Mm.270065	NR_002840	ENSMUSG00000053332	Gas5	Gas-5|Mir5117|Snhg2	growth arrest specific 5	ncRNA
mm_64313.1	chr7	141864700	141864709	+	1	NA	exon (NM_028801, exon 31 of 49)	exon (NM_028801, exon 31 of 49)	25632	NM_028801	74180	Mm.200752	NM_028801	ENSMUSG00000066108	Muc5b	2300002I04Rik|A130042M24|AV085033|MUC5|MUC9|mucin 5b	mucin 5, subtype B, tracheobronchial	protein-coding
mm_48903.1	chr6	3498400	3498439	+	1	NA	promoter-TSS (NM_024260)	promoter-TSS (NM_024260)	26	NM_001167750	73288	Mm.45539	NM_024260	ENSMUSG00000001376	Vps50	1700034M03Rik|8430415E05Rik|BLM|C87205|Ccdc132|mKIAA1861	VPS50 EARP/GARPII complex subunit	protein-coding
mm_145144.1	chr18	45559819	45559881	+	1	NA	promoter-TSS (NM_080465)	promoter-TSS (NM_080465)	-304	NM_080465	140492	Mm.411614	NM_080465	ENSMUSG00000054477	Kcnn2	KCa2.2|SK2|SKCA2|bc|fri	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2	protein-coding
mm_69872.1	chr7	141475329	141475367	-	1	NA	promoter-TSS (NM_025593)	promoter-TSS (NM_025593)	112	NM_053082	64540	Mm.489619	NM_053082	ENSMUSG00000025511	Tspan4	AI325509|AI746565|D130042I01Rik|NAG-2|Tm4sf7|Tspan-4	tetraspanin 4	protein-coding
mm_137896.1	chr17	31681505	31681512	+	1	NA	3' UTR (NM_001278570, exon 3 of 3)	3' UTR (NM_001278570, exon 3 of 3)	3577	NM_001278570	12954	Mm.1228	NM_013501	ENSMUSG00000024041	Cryaa	Acry-1|Crya-1|Crya1|DAcry-1|lop18	crystallin, alpha A	protein-coding
mm_93625.1	chr10	117278028	117278062	-	1	NA	3' UTR (NM_017372, exon 4 of 4)	3' UTR (NM_017372, exon 4 of 4)	4227	NM_017372	17105	Mm.45436	NM_017372	ENSMUSG00000069516	Lyz2	AI326280|Lys|Lysm|Lyzf2|Lyzs|Lzm|Lzm-s1|Lzp	lysozyme 2	protein-coding
mm_55874.1	chr6	83506890	83506894	-	1	NA	promoter-TSS (NM_001162521)	promoter-TSS (NM_001162521)	77	NM_013764	27369	Mm.42234	NM_013764	ENSMUSG00000014554	Dguok	dGK|dGK1|dGK2|dGK3	deoxyguanosine kinase	protein-coding
mm_117130.1	chr13	60936444	60936471	-	1	NA	intron (NM_007796, intron 1 of 4)	intron (NM_007796, intron 1 of 4)	109	NM_001145799	13024	Mm.482089	NM_007796	ENSMUSG00000044258	Ctla2a	Ctla-2a	cytotoxic T lymphocyte-associated protein 2 alpha	protein-coding
mm_165134.1	chr2	11172141	11172145	+	1	NA	promoter-TSS (NM_008859)	promoter-TSS (NM_008859)	-239	NM_008859	18761	Mm.329993	NM_008859	ENSMUSG00000026778	Prkcq	A130035A12Rik|AW494342|PKC-0|PKC-theta|PKCtheta|Pkcq	protein kinase C, theta	protein-coding
mm_8343.1	chr1	150165053	150165080	-	1	NA	promoter-TSS (NR_110420)	promoter-TSS (NR_110420)	-118	NR_110420	102639566	Mm.417208	NR_110420	ENSMUSG00000097754	Ptgs2os2	Gm26687|Linc-cox2|Lincrna-cox2	prostaglandin-endoperoxide synthase 2, opposite strand 2	ncRNA
mm_74263.1	chr8	124898104	124898154	+	1	NA	promoter-TSS (NM_198103)	promoter-TSS (NM_198103)	243	NM_001111141	244666	Mm.482915	NM_001111141	ENSMUSG00000031986	Sprtn	Gm505	SprT-like N-terminal domain	protein-coding
mm_156238.1	chrX	136139449	136139451	+	1	NA	intron (NM_212457, intron 1 of 2)	CpG	405	NM_212457	406217	Mm.336245	NM_212457	ENSMUSG00000047844	Bex4	-	brain expressed X-linked 4	protein-coding
mm_112043.1	chr12	111671482	111671492	-	1	NA	exon (NM_021273, exon 3 of 8)	exon (NM_021273, exon 3 of 8)	851	NM_021273	12709	Mm.16831	NM_021273	ENSMUSG00000001270	Ckb	B-CK|Bck|Ck-3|Ck3|Ckbb	creatine kinase, brain	protein-coding
mm_164900.1	chr18	67065252	67065254	-	1	NA	Intergenic	Intergenic	-23045	NM_177137	14680	Mm.440746	NM_010307	ENSMUSG00000024524	Gnal	2610011C15Rik|9630020G10Rik|Galphaolf|Gna10|Golf	guanine nucleotide binding protein, alpha stimulating, olfactory type	protein-coding
mm_3535.1	chr1	150392865	150392877	+	1	NA	promoter-TSS (NM_133780)	promoter-TSS (NM_133780)	33	NM_133780	108989	Mm.174256	NM_133780	ENSMUSG00000006005	Tpr	2610029M07Rik|C77892	translocated promoter region, nuclear basket protein	protein-coding
mm_131665.1	chr16	20629973	20629983	+	1	NA	5' UTR (NM_139293, exon 1 of 19)	5' UTR (NM_139293, exon 1 of 19)	127	NM_139293	107522	Mm.263319	NM_025462	ENSMUSG00000022842	Ece2	1810009K13Rik|6330509A19Rik|9630025D12Rik|BB127715|Ece-2	endothelin converting enzyme 2	protein-coding
mm_9693.1	chr1	178337292	178337319	-	1	NA	exon (NM_016805, exon 1 of 14)	exon (NM_016805, exon 1 of 14)	479	NM_016805	51810	Mm.86589	NM_016805	ENSMUSG00000039630	Hnrnpu	AA408410|AI256620|AL024194|AL024437|AW557595|C86794|Hnrpu|SAFA|Sp120|hnRNP U	heterogeneous nuclear ribonucleoprotein U	protein-coding
mm_132827.1	chr16	45224978	45224988	+	1	NA	intron (NM_177584, intron 1 of 5)	intron (NM_177584, intron 1 of 5)	646	NM_177584	208154	Mm.38199	NM_177584	ENSMUSG00000052013	Btla	A630002H24	B and T lymphocyte associated	protein-coding
mm_114067.1	chr13	54381775	54381786	+	1	NA	3' UTR (NM_009946, exon 4 of 4)	3' UTR (NM_009946, exon 4 of 4)	10431	NM_009946	12890	Mm.268902	NM_009946	ENSMUSG00000025867	Cplx2	921-L|AI413745|AW492120	complexin 2	protein-coding
mm_165752.1	chr3	108257139	108257141	+	1	NA	5' UTR (NM_011967, exon 1 of 9)	5' UTR (NM_011967, exon 1 of 9)	214	NM_011967	26442	Mm.208883	NM_011967	ENSMUSG00000068749	Psma5	ZETA	proteasome (prosome, macropain) subunit, alpha type 5	protein-coding
mm_132498.1	chr16	36948617	36948636	+	1	NA	exon (NM_008225, exon 5 of 14)	exon (NM_008225, exon 5 of 14)	13643	NM_008225	15163	Mm.4091	NM_008225	ENSMUSG00000022831	Hcls1	AW213261|HS1	hematopoietic cell specific Lyn substrate 1	protein-coding
mm_58946.1	chr7	18565106	18565111	+	1	NA	exon (NM_001037168, exon 2 of 5)	exon (NM_001037168, exon 2 of 5)	2197	NM_001037168	545925	Mm.440302	NM_001037168	ENSMUSG00000070797	Psg27	EG545925|cea15	pregnancy-specific glycoprotein 27	protein-coding
mm_124890.1	chr15	10314074	10314079	+	1	NA	intron (NM_001253781, intron 2 of 9)	intron (NM_001253781, intron 2 of 9)	20425	NM_001253782	19116	Mm.10516	NM_011169	ENSMUSG00000005268	Prlr	AI987712|Pr-1|Pr-3|Prlr-rs1	prolactin receptor	protein-coding
mm_97558.1	chr11	78931665	78931679	+	1	NA	exon (NM_010927, exon 5 of 27)	exon (NM_010927, exon 5 of 27)	6381	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_140407.1	chr17	87646140	87646152	+	1	NA	exon (NM_008532, exon 8 of 10)	exon (NM_008532, exon 8 of 10)	10167	NM_008532	17075	Mm.4259	NM_008532	ENSMUSG00000045394	Epcam	CD326|EGP|EGP-2|Egp314|Ep-CAM|EpCAM1|GA733-2|Ly74|TROP1|Tacsd1|Tacstd1|gp40	epithelial cell adhesion molecule	protein-coding
mm_114302.1	chr13	59579057	59579059	+	1	NA	Intergenic	RMER4B|LTR|ERVK	6165	NR_045633	319469	Mm.437992	NR_045633	ENSMUSG00000021557	A230056J06Rik	-	RIKEN cDNA A230056J06 gene	ncRNA
mm_160701.1	chr10	43174688	43174688	+	1	NA	promoter-TSS (NR_102361)	promoter-TSS (NR_102361)	-11	NR_102361	74530	Mm.415375	NM_172419	ENSMUSG00000045008	9030612E09Rik	-	RIKEN cDNA 9030612E09 gene	ncRNA
mm_132803.1	chr16	45158726	45158810	+	1	NA	promoter-TSS (NM_028756)	promoter-TSS (NM_028756)	-61	NM_026402	67841	Mm.41775	NM_026402	ENSMUSG00000022663	Atg3	2610016C12Rik|APG3|Apg3l|Atg3l|PC3-96	autophagy related 3	protein-coding
mm_74145.1	chr8	123280930	123280950	+	1	NA	intron (NM_016925, intron 30 of 42)	intron (NM_016925, intron 30 of 42)	-26718	NM_028200	72325	Mm.276193	NM_028200	ENSMUSG00000001062	Vps9d1	1300018I17Rik|2410004N05Rik|5DOS1|Vsp9d1	VPS9 domain containing 1	protein-coding
mm_105791.1	chr11	109987017	109987027	-	1	NA	intron (NM_013851, intron 1 of 38)	B4|SINE|B4	8794	NM_013851	27404	Mm.341004	NM_013851	ENSMUSG00000020620	Abca8b	Abca8	ATP-binding cassette, sub-family A (ABC1), member 8b	protein-coding
mm_45605.1	chr5	75044563	75044662	-	1	NA	promoter-TSS (NM_028850)	promoter-TSS (NM_028850)	29	NM_028850	74277	Mm.239814	NM_028850	ENSMUSG00000029229	Chic2	1700081B18Rik|4930502K01Rik|BTL	cysteine-rich hydrophobic domain 2	protein-coding
mm_5709.1	chr1	43811903	43811904	-	1	NA	intron (NM_026430, intron 1 of 14)	ORR1D2|LTR|ERVL-MaLR	15805	NM_026430	67883	Mm.387202	NM_026430	ENSMUSG00000057363	Uxs1	1600025I13Rik|AI451869|AI649125|AW550562	UDP-glucuronate decarboxylase 1	protein-coding
mm_117251.1	chr13	64366163	64366188	-	1	NA	intron (NM_009984, intron 6 of 7)	RSINE1|SINE|B4	4345	NM_009984	13039	Mm.930	NM_009984	ENSMUSG00000021477	Ctsl	1190035F06Rik|CatL|Ctsl1|MEP|fs|nkt	cathepsin L	protein-coding
mm_35385.1	chr4	33248484	33248489	-	1	NA	5' UTR (NM_001033225, exon 1 of 2)	5' UTR (NM_001033225, exon 1 of 2)	301	NM_001033225	108767	Mm.27769	NM_001033225	ENSMUSG00000040128	Pnrc1	5730463C12Rik|B4-2|PRR2|Prol2	proline-rich nuclear receptor coactivator 1	protein-coding
mm_29709.1	chr3	123508916	123508929	-	1	NA	promoter-TSS (NR_028574)	promoter-TSS (NR_028574)	-586	NR_028574	69895	Mm.260791	NR_028574	ENSMUSG00000104960	Snhg8	1110065M07Rik|2010109N14Rik	small nucleolar RNA host gene 8	ncRNA
mm_169294.1	chr1	40324545	40324548	+	1	NA	promoter-TSS (NM_133193)	promoter-TSS (NM_133193)	-81	NM_133193	107527	Mm.155583	NM_133193	ENSMUSG00000070942	Il1rl2	AI481289|AW551444|IL-1Rrp2	interleukin 1 receptor-like 2	protein-coding
mm_164937.1	chr18	86121687	86121689	+	1	NA	Intergenic	Lx8|LINE|L1	-273264	NM_144946	246317	Mm.329578	NM_144946	ENSMUSG00000050321	Neto1	AI851453|Btcl1|C130005O10Rik	neuropilin (NRP) and tolloid (TLL)-like 1	protein-coding
mm_86105.1	chr9	115310401	115310407	-	1	NA	promoter-TSS (NM_024222)	promoter-TSS (NM_024222)	17	NM_024222	68292	Mm.296158	NM_024222	ENSMUSG00000032437	Stt3b	1300006C19Rik|Simp	STT3, subunit of the oligosaccharyltransferase complex, homolog B (S. cerevisiae)	protein-coding
mm_46618.1	chr5	108132542	108132570	-	1	NA	promoter-TSS (NM_028481)	promoter-TSS (NM_028481)	35	NM_001347383	73130	Mm.363960	NM_028876	ENSMUSG00000063406	Tmed5	3110020O18Rik|4432412D15Rik	transmembrane p24 trafficking protein 5	protein-coding
mm_89420.1	chr10	90877322	90877325	+	1	NA	intron (NM_001347053, intron 1 of 8)	intron (NM_001347053, intron 1 of 8)	47480	NM_001347053	77531	Mm.440605	NM_181398	ENSMUSG00000058589	Anks1b	AIDA-1b|C030032C09Rik|E530015N03Rik|ENSMUSG00000078431|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding
mm_107128.1	chr12	21111721	21111776	+	1	NA	promoter-TSS (NM_001098168)	promoter-TSS (NM_001098168)	-8	NM_001004364	211914	Mm.358946	NM_001004364	ENSMUSG00000052632	Asap2	6530401G17Rik|Ddef2|Gm1523|Gm592|PAG3|PAP	ArfGAP with SH3 domain, ankyrin repeat and PH domain 2	protein-coding
mm_97278.1	chr11	76000017	76000023	+	1	NA	5' UTR (NM_198637, exon 1 of 2)	5' UTR (NM_198637, exon 1 of 2)	108	NM_198637	74230	Mm.271247	NM_198637	ENSMUSG00000053783	1700016K19Rik	Liat1	RIKEN cDNA 1700016K19 gene	protein-coding
mm_74861.1	chr8	24824017	24824045	-	1	NA	5' UTR (NM_007401, exon 1 of 21)	5' UTR (NM_007401, exon 1 of 21)	338	NM_001272058	11499	Mm.143889	NM_007401	ENSMUSG00000031554	Adam5	tMDC II|tMDCII	a disintegrin and metallopeptidase domain 5	protein-coding
mm_88696.1	chr10	80142335	80142353	+	1	NA	promoter-TSS (NM_025313)	promoter-TSS (NM_025313)	29	NM_025313	66043	Mm.278560	NM_025313	ENSMUSG00000003072	Atp5d	0610008F14Rik|1500000I11Rik|AA960090|AI876556|AU020773|C85518	ATP synthase, H+ transporting, mitochondrial F1 complex, delta subunit	protein-coding
mm_18042.1	chr2	39005559	39005563	-	1	NA	promoter-TSS (NM_025592)	promoter-TSS (NM_025592)	-430	NM_025592	66489	Mm.345333	NM_025592	ENSMUSG00000062997	Rpl35	2410039E09Rik	ribosomal protein L35	protein-coding
mm_122247.1	chr14	33646339	33646345	-	1	NA	Intergenic	RMER1C|Other|Other	57072	NM_008978	19256	Mm.8019	NM_008978	ENSMUSG00000021940	Ptpn20	typ	protein tyrosine phosphatase, non-receptor type 20	protein-coding
mm_135496.1	chr16	46183589	46183621	-	1	NA	Intergenic	RMER17B|LTR|ERVK	-28528	NM_001304528	11615	Mm.330692	NM_001304528	ENSMUSG00000048087	Gm4737	AL024110|EG11615|ENSMUSG00000048087	predicted gene 4737	protein-coding
mm_6513.1	chr1	74394045	74394084	-	1	NA	promoter-TSS (NR_029743)	promoter-TSS (NR_029743)	-246	NR_029743	387219		NR_029743	ENSMUSG00000065468	Mir26b	Mirn26b|mir-26b|mmu-mir-26b	microRNA 26b	ncRNA
mm_42515.1	chr5	115544220	115544254	+	1	NA	intron (NM_133915, intron 1 of 11)	intron (NM_133915, intron 1 of 11)	-15230	NM_007475	11837	Mm.5286	NM_007475	ENSMUSG00000067274	Rplp0	36B4|Arbp|L10E	ribosomal protein, large, P0	protein-coding
mm_138864.1	chr17	43016523	43016535	+	1	NA	promoter-TSS (NM_178589)	promoter-TSS (NM_178589)	-26	NM_178589	94185	Mm.200792	NM_178589	ENSMUSG00000023915	Tnfrsf21	AA959878|DR6|R74815|TR7	tumor necrosis factor receptor superfamily, member 21	protein-coding
mm_170849.1	chr2	177759238	177759238	+	1	NA	promoter-TSS (NM_001243903)	promoter-TSS (NM_001243903)	-50	NM_001243903	626802	Mm.386029	NM_001243903	ENSMUSG00000078864	Gm14322	OTTMUSG00000016321	predicted gene 14322	protein-coding
mm_69349.1	chr7	130244561	130244605	-	1	NA	intron (NM_010207, intron 2 of 17)	L2a|LINE|L2	22225	NM_010207	14183	Mm.16340	NM_010207	ENSMUSG00000030849	Fgfr2	AU043015|AW556123|Bek|Fgfr-2|Fgfr-7|Fgfr7|KGFR|KGFRTr|svs	fibroblast growth factor receptor 2	protein-coding
mm_119855.1	chr14	54442323	54442338	+	1	NA	3' UTR (NM_008608, exon 10 of 10)	3' UTR (NM_008608, exon 10 of 10)	10732	NM_008608	17387	Mm.280175	NM_008608	ENSMUSG00000000957	Mmp14	AI325305|MMP-X1|MT-MMP-1|MT1-MMP|sabe	matrix metallopeptidase 14 (membrane-inserted)	protein-coding
mm_13848.1	chr2	119594289	119594332	+	1	NA	promoter-TSS (NR_027832)	promoter-TSS (NR_027832)	14	NR_015473	66602	Mm.379181	NR_015473	ENSMUSG00000085438	1700020I14Rik	1190006L01Rik|4933437I03Rik|AI451541|AI585852|AW538376|AW558897|Cyrano	RIKEN cDNA 1700020I14 gene	ncRNA
mm_127768.1	chr15	3275705	3275769	-	1	NA	exon (NM_009155, exon 3 of 5)	exon (NM_009155, exon 3 of 5)	4760	NM_009155	20363	Mm.392203	NM_009155	ENSMUSG00000064373	Selenop	AU018766|D15Ucla1|Se-P|Sepp1|selp	selenoprotein P	protein-coding
mm_19869.1	chr2	114047449	114047468	-	1	NA	3' UTR (NM_009608, exon 7 of 7)	3' UTR (NM_009608, exon 7 of 7)	5417	NM_009608	11464	Mm.686	NM_009608	ENSMUSG00000068614	Actc1	Actc-1	actin, alpha, cardiac muscle 1	protein-coding
mm_139499.1	chr17	56265828	56265831	+	1	NA	Intergenic	B2_Mm2|SINE|B2	9036	NM_010192	14154	Mm.290813	NM_010192	ENSMUSG00000043683	Fem1a	AW611390|Fem1aa	feminization 1 homolog a (C. elegans)	protein-coding
mm_86552.1	chr10	10343098	10343101	+	1	NA	intron (NM_001127353, intron 34 of 36)	intron (NM_001127353, intron 34 of 36)	129215	NM_001127353	215772	Mm.246573	NM_172547	ENSMUSG00000050994	Adgb	9130014G24Rik	androglobin	protein-coding
mm_39759.1	chr5	29736452	29736460	+	1	NA	promoter-TSS (NR_028426)	promoter-TSS (NR_028426)	-520	NR_028426	332993	Mm.473746	NR_028426		Gm5129	EG332993|ENSMUSG00000053121	predicted gene 5129	ncRNA
mm_58623.1	chr7	5069190	5069202	+	1	NA	intron (NM_133671, intron 5 of 11)	intron (NM_133671, intron 5 of 11)	7053	NM_001205231	22185	Mm.360389	NM_133671	ENSMUSG00000030435	U2af2	65kDa	U2 small nuclear ribonucleoprotein auxiliary factor (U2AF) 2	protein-coding
mm_38326.1	chr4	137357662	137357710	-	1	NA	promoter-TSS (NM_001243769)	promoter-TSS (NM_001243769)	73	NM_009861	12540	Mm.1022	NM_009861	ENSMUSG00000006699	Cdc42	AI747189|AU018915	cell division cycle 42	protein-coding
mm_119167.1	chr14	32085726	32085747	+	1	NA	promoter-TSS (NM_001284346)	promoter-TSS (NM_001284346)	8	NM_145460	218885	Mm.202257	NM_145460	ENSMUSG00000021906	Oxnad1	2410002F01Rik|AW492292|BC019806	oxidoreductase NAD-binding domain containing 1	protein-coding
mm_112592.1	chr13	13954615	13954691	+	1	NA	promoter-TSS (NM_178640)	promoter-TSS (NM_178640)	-21	NM_178640	97884	Mm.21686	NM_178640	ENSMUSG00000039242	B3galnt2	A930105D20Rik|C80633|D230016N13Rik	UDP-GalNAc:betaGlcNAc beta 1,3-galactosaminyltransferase, polypeptide 2	protein-coding
mm_132911.1	chr16	48873310	48873343	+	1	NA	intron (NM_181596, intron 2 of 3)	B2_Mm2|SINE|B2	718	NM_181596	245195	Mm.231288	NM_181596	ENSMUSG00000022651	Retnlg	Fizz3|Relmg|Xcp1	resistin like gamma	protein-coding
mm_141473.1	chr17	30875032	30875036	-	1	NA	exon (NM_013811, exon 93 of 93)	exon (NM_013811, exon 93 of 93)	-26833	NM_021332	14652	Mm.390969	NM_021332	ENSMUSG00000024027	Glp1r	GLP-1R|GLP1Rc	glucagon-like peptide 1 receptor	protein-coding
mm_22161.1	chr2	172940300	172940349	-	1	NA	promoter-TSS (NM_007557)	promoter-TSS (NM_007557)	-3	NM_007557	12162	Mm.595	NM_007557	ENSMUSG00000008999	Bmp7	OP1	bone morphogenetic protein 7	protein-coding
mm_61399.1	chr7	73375586	73375597	+	1	NA	promoter-TSS (NM_177740)	promoter-TSS (NM_177740)	71	NM_177740	244058	Mm.333943	NM_177740	ENSMUSG00000070509	Rgma	BC059072|C230063O06	repulsive guidance molecule family member A	protein-coding
mm_161270.1	chr14	7315051	7315051	-	1	NA	Intergenic	CpG	17344	NM_001025085	545013	Mm.422841	NM_001025085	ENSMUSG00000072726	Gm5797	EG545013	predicted gene 5797	protein-coding
mm_78869.1	chr9	44407164	44407185	+	1	NA	promoter-TSS (NM_024266)	promoter-TSS (NM_024266)	374	NM_021789	60409	Mm.29814	NM_021789	ENSMUSG00000032112	Trappc4	1500017G03Rik|AI303617|HSPC172|PTD009|Sbd|Sbdn|Sdcbp2|TRS23	trafficking protein particle complex 4	protein-coding
mm_103173.1	chr11	70459802	70459812	-	1	NA	5' UTR (NM_001029929, exon 1 of 14)	5' UTR (NM_001029929, exon 1 of 14)	177	NM_023158	66102	Mm.425692	NM_023158	ENSMUSG00000018920	Cxcl16	0910001K24Rik|AV290116|BB024863|CXCL16v1|CXCL16v2|SR-PSOX|Zmynd15|b2b498Clo	chemokine (C-X-C motif) ligand 16	protein-coding
mm_164449.1	chr16	49913537	49913556	+	1	NA	Intergenic	Intergenic	57892	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_42423.1	chr5	115327275	115327283	+	1	NA	non-coding (NR_036616, exon 1 of 5)	non-coding (NR_036616, exon 1 of 5)	102	NR_036616	108014	Mm.287826	NM_025573	ENSMUSG00000029538	Srsf9	25kDa|2610029M16Rik|SRp30c|Sfrs9	serine/arginine-rich splicing factor 9	protein-coding
mm_64530.1	chr7	144130465	144130467	+	1	NA	intron (NR_037302, intron 1 of 5)	intron (NR_037302, intron 1 of 5)	-45054	NM_001113373	210274	Mm.483624	NM_001081370	ENSMUSG00000037541	Shank2	ProSAP1|mKIAA1022	SH3/ankyrin domain gene 2	protein-coding
mm_27629.1	chr3	60963519	60963520	-	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-39266	NM_008772	18441	Mm.281452	NM_008772	ENSMUSG00000027765	P2ry1	P2Y1	purinergic receptor P2Y, G-protein coupled 1	protein-coding
mm_147352.1	chr18	43354782	43354803	-	1	NA	exon (NM_001291455, exon 5 of 14)	exon (NM_001291455, exon 5 of 14)	18480	NM_001136086	22240	Mm.8180	NM_009468	ENSMUSG00000024501	Dpysl3	CRMP-4|DRP-3|TUC4|ULIP-1|Ulip|Ulip1	dihydropyrimidinase-like 3	protein-coding
mm_22346.1	chr2	180893409	180893422	-	1	NA	promoter-TSS (NR_029538)	promoter-TSS (NR_029538)	-625	NR_029538	723951		NR_029538	ENSMUSG00000065454	Mir124a-3	Mirn124a-3|mir-124-3|mir-124a-3	microRNA 124a-3	ncRNA
mm_14839.1	chr2	147373948	147373955	+	1	NA	3' UTR (NM_008780, exon 5 of 5)	3' UTR (NM_008780, exon 5 of 5)	8957	NM_008780	18503	Mm.315502	NM_008780	ENSMUSG00000037034	Pax1	Pax-1|hbs|hunchback|un|undulated|wt	paired box 1	protein-coding
mm_50203.1	chr6	42245896	42245903	+	1	NA	promoter-TSS (NM_029555)	promoter-TSS (NM_029555)	-36	NM_029555	76263	Mm.267014	NM_029555	ENSMUSG00000029864	Gstk1	0610025I19Rik|AW260476|DsbA-L	glutathione S-transferase kappa 1	protein-coding
mm_147972.1	chr18	67248805	67248829	-	1	NA	Intergenic	LTR73|LTR|ERV1	-2987	NM_172630	225651	Mm.235792	NM_172630	ENSMUSG00000062526	Mppe1	A530095G11	metallophosphoesterase 1	protein-coding
mm_68476.1	chr7	110862922	110862938	-	1	NA	promoter-TSS (NM_053247)	promoter-TSS (NM_053247)	23	NM_053247	114332	Mm.396078	NM_053247	ENSMUSG00000030787	Lyve1	1200012G08Rik|Crsbp-1|Lyve-1|Xlkd1	lymphatic vessel endothelial hyaluronan receptor 1	protein-coding
mm_87131.1	chr10	34283496	34283510	+	1	NA	3' UTR (NM_009433, exon 1 of 1)	3' UTR (NM_009433, exon 1 of 1)	1313	NM_009433	22110	Mm.20445	NM_009433	ENSMUSG00000047514	Tspyl1	Tspyl	testis-specific protein, Y-encoded-like 1	protein-coding
mm_76847.1	chr8	105322347	105322351	-	1	NA	intron (NM_177449, intron 2 of 4)	intron (NM_177449, intron 2 of 4)	3927	NM_177449	234684	Mm.381717	NM_177449	ENSMUSG00000041679	Lrrc29	A630024J02Rik|FBL9|FBXL9	leucine rich repeat containing 29	protein-coding
mm_60982.1	chr7	48984350	48984352	+	1	NA	intron (NM_001111016, intron 2 of 38)	intron (NM_001111016, intron 2 of 38)	25278	NM_001111016	78286	Mm.333881	NM_175272	ENSMUSG00000052512	Nav2	5330421F07Rik|AU067780|BQ960892|HELAD1|POMFIL2|RAINB1|RAINB2|Unc53H2|mKIAA3015	neuron navigator 2	protein-coding
mm_127180.1	chr15	98983705	98983732	+	1	NA	Intergenic	Intergenic	-2247	NR_045991	75951	Mm.441657	NR_045991	ENSMUSG00000097587	4930578M01Rik	3010001K12Rik	RIKEN cDNA 4930578M01 gene	ncRNA
mm_51436.1	chr6	80018906	80018945	+	1	NA	promoter-TSS (NM_178731)	promoter-TSS (NM_178731)	48	NM_001134743	243499	Mm.483425	NM_178731	ENSMUSG00000052581	Lrrtm4	7530419J18Rik|A230052N11	leucine rich repeat transmembrane neuronal 4	protein-coding
mm_153973.1	chr19	47863402	47863426	-	1	NA	exon (NM_010362, exon 5 of 6)	exon (NM_010362, exon 5 of 6)	-2131	NM_030051	68214	Mm.63791	NM_026619	ENSMUSG00000025069	Gsto2	1700020F09Rik|4930425C18Rik|GSTO 2-2	glutathione S-transferase omega 2	protein-coding
mm_156870.1	chrX	164506228	164506264	+	1	NA	intron (NM_027027, intron 1 of 7)	intron (NM_027027, intron 1 of 7)	8343	NM_027027	69299	Mm.79031	NM_027027	ENSMUSG00000031384	Asb9	1700011M07Rik	ankyrin repeat and SOCS box-containing 9	protein-coding
mm_5874.1	chr1	53791444	53791454	-	1	NA	Intergenic	Intergenic	-6234	NM_133810	98267	Mm.25559	NM_133810	ENSMUSG00000026094	Stk17b	3110009A03Rik|AI120141|Drak2	serine/threonine kinase 17b (apoptosis-inducing)	protein-coding
mm_47098.1	chr5	118155380	118155469	-	1	NA	promoter-TSS (NM_172721)	promoter-TSS (NM_172721)	34	NM_172721	231672	Mm.221769	NM_172721	ENSMUSG00000032867	Fbxw8	4930438M06Rik|FBW6|FBW8|FBXO29|Fbx29	F-box and WD-40 domain protein 8	protein-coding
mm_89360.1	chr10	88379218	88379299	+	1	NA	promoter-TSS (NM_001004164)	promoter-TSS (NM_001004164)	-154	NM_001004164	432486	Mm.335190	NM_001004164	ENSMUSG00000035311	Gnptab	EG432486|mKIAA1208	N-acetylglucosamine-1-phosphate transferase, alpha and beta subunits	protein-coding
mm_28904.1	chr3	98352177	98352184	-	1	NA	Intergenic	Intergenic	-12211	NM_016966	236539	Mm.16898	NM_016966	ENSMUSG00000053398	Phgdh	3-PGDH|3PGDH|4930479N23|A10|PGAD|PGD|PGDH|SERA	3-phosphoglycerate dehydrogenase	protein-coding
mm_104183.1	chr11	87797346	87797370	-	1	NA	exon (NM_010824, exon 8 of 14)	exon (NM_010824, exon 8 of 14)	3574	NM_010824	17523	Mm.4668	NM_010824	ENSMUSG00000009350	Mpo	mKIAA4033	myeloperoxidase	protein-coding
mm_1028.1	chr1	58754983	58754993	+	1	NA	3' UTR (NM_207653, exon 10 of 10)	3' UTR (NM_207653, exon 10 of 10)	24436	NM_001293805	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_110224.1	chr12	28635892	28635905	-	1	NA	promoter-TSS (NM_011300)	promoter-TSS (NM_011300)	55	NM_011300	20115	Mm.279839	NM_011300	ENSMUSG00000061477	Rps7	Mtu|Rps7A|S7	ribosomal protein S7	protein-coding
mm_53198.1	chr6	125552934	125552938	+	1	NA	promoter-TSS (NM_011708)	promoter-TSS (NM_011708)	-12	NM_011708	22371	Mm.22339	NM_011708	ENSMUSG00000001930	Vwf	6820430P06Rik|AI551257|B130011O06Rik|C630030D09|F8VWF|VWD	Von Willebrand factor	protein-coding
mm_162497.1	chr1	138175619	138175625	-	1	NA	promoter-TSS (NM_001268286)	promoter-TSS (NM_001268286)	-317	NM_001268286	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_74353.1	chr8	128166387	128166396	+	1	NA	Intergenic	Intergenic	111834	NR_105822	102465212		NR_105822	ENSMUSG00000099326	Mir21c	Gm28013|mmu-mir-21c	microRNA 21c	ncRNA
mm_149360.1	chr19	11121352	11121370	+	1	NA	intron (NM_027058, intron 1 of 6)	intron (NM_027058, intron 1 of 6)	9517	NM_027058	69369	Mm.391200	NM_027058	ENSMUSG00000024729	1700017D01Rik	-	RIKEN cDNA 1700017D01 gene	protein-coding
mm_127621.1	chr15	102461338	102461368	+	1	NA	intron (NM_001170911, intron 3 of 3)	intron (NM_001170911, intron 3 of 3)	2183	NM_025385	66151	Mm.393955	NM_025385	ENSMUSG00000023048	Prr13	1110020C13Rik|2010324E22Rik	proline rich 13	protein-coding
mm_154670.1	chrX	7882195	7882219	+	1	NA	exon (NM_138606, exon 5 of 6)	exon (NM_138606, exon 5 of 6)	-2037	NM_001083937	22232	Mm.214976	NM_078484	ENSMUSG00000031156	Slc35a2	AI327289|Had-1|Had1|Sfc8|UGT|Ugalt	solute carrier family 35 (UDP-galactose transporter), member A2	protein-coding
mm_129552.1	chr15	79442010	79442065	-	1	NA	promoter-TSS (NM_013767)	promoter-TSS (NM_013767)	20	NM_001289898	27373	Mm.30199	NM_013767	ENSMUSG00000022433	Csnk1e	AI426939|AI551861|AW457082|CK1epsilon|CKIe|KC1epsilon|tau	casein kinase 1, epsilon	protein-coding
mm_26625.1	chr3	152763374	152763415	+	1	NA	intron (NM_178016, intron 10 of 11)	Lx8|LINE|L1	49294	NM_025662	329777	Mm.331447	NM_025662	ENSMUSG00000039047	Pigk	3000001O05Rik	phosphatidylinositol glycan anchor biosynthesis, class K	protein-coding
mm_55970.1	chr6	85831826	85831859	-	1	NA	promoter-TSS (NM_023455)	promoter-TSS (NM_023455)	48	NM_023455	68396	Mm.154782	NM_023455	ENSMUSG00000030004	Nat8	0610037O16Rik|CCNAT|Cml4	N-acetyltransferase 8 (GCN5-related)	protein-coding
mm_31096.1	chr4	41755568	41755583	+	1	NA	promoter-TSS (NM_001302511)	promoter-TSS (NM_001302511)	347	NM_016658	14430	Mm.439669	NM_016658	ENSMUSG00000036073	Galt	AW553376	galactose-1-phosphate uridyl transferase	protein-coding
mm_19087.1	chr2	79254690	79254720	-	1	NA	promoter-TSS (NM_010576)	promoter-TSS (NM_010576)	-721	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D|Itga4B	integrin alpha 4	protein-coding
mm_140577.1	chr17	10079829	10079838	-	1	NA	Intergenic	RMER10A|LTR|ERVL	239528	NM_021881	19317	Mm.130694	NM_021881	ENSMUSG00000062078	Qk	1110003F05Rik|1500005P18|QkI|l(17)-1Wis|l17Wis1	quaking	protein-coding
mm_67738.1	chr7	90265371	90265374	-	1	NA	promoter-TSS (NM_183293)	promoter-TSS (NM_183293)	60	NM_029256	75338	Mm.487222	NM_029256	ENSMUSG00000030617	Ccdc83	4930549K11Rik|4930554C01Rik|4932423M01Rik	coiled-coil domain containing 83	protein-coding
mm_112733.1	chr13	19214281	19214283	+	1	NA	Intergenic	Intergenic	181531	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_51223.1	chr6	71371409	71371420	+	1	NA	Intergenic	B4A|SINE|B4	-2013	NM_009857	12525	Mm.1858	NM_009857	ENSMUSG00000053977	Cd8a	BB154331|Ly-2|Ly-35|Ly-B|Lyt-2	CD8 antigen, alpha chain	protein-coding
mm_11489.1	chr2	32451090	32451090	+	1	NA	exon (NM_001164357, exon 1 of 10)	exon (NM_001164357, exon 1 of 10)	380	NM_001164357	227731	Mm.37395	NM_146118	ENSMUSG00000026819	Slc25a25	1110030N17Rik|MCSC|mKIAA1896	solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 25	protein-coding
mm_12302.1	chr2	69109523	69109539	+	1	NA	3' UTR (NM_001347161, exon 11 of 11)	3' UTR (NM_001347161, exon 11 of 11)	-26269	NM_181547	329416	Mm.90047	NM_181547	ENSMUSG00000034738	Nostrin	Daip2|mDaIP2	nitric oxide synthase trafficker	protein-coding
mm_23521.1	chr3	60614422	60614434	+	1	NA	intron (NM_001253709, intron 4 of 8)	intron (NM_001253709, intron 4 of 8)	113249	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_160721.1	chr10	67538030	67538030	+	1	NA	promoter-TSS (NM_001347458)	promoter-TSS (NM_001347458)	100	NM_001347458	13654	Mm.290421	NM_010118	ENSMUSG00000037868	Egr2	Egr-2|Krox-20|Krox20|NGF1-B|Zfp-25|Zfp-6	early growth response 2	protein-coding
mm_57291.1	chr6	124433523	124433534	-	1	NA	intron (NM_001346656, intron 16 of 17)	intron (NM_001346656, intron 16 of 17)	-18461	NM_001277805	19305	Mm.22418	NM_008995	ENSMUSG00000005069	Pex5	AW212715|ESTM1|PTS1R|Pxr1|X83306	peroxisomal biogenesis factor 5	protein-coding
mm_148890.1	chr19	6877799	6877802	+	1	NA	Intergenic	RLTR19-int|LTR|ERVK	-19589	NM_001081291	78317	Mm.329596	NM_198008	ENSMUSG00000047810	Ccdc88b	2610041P08Rik|Ccdc88	coiled-coil domain containing 88B	protein-coding
mm_151680.1	chr19	4257624	4257644	-	1	NA	Intergenic	Intergenic	6244	NR_105951	102465595		NR_105951	ENSMUSG00000099290	Mir6985	Gm27719|mmu-mir-6985	microRNA 6985	ncRNA
mm_130192.1	chr15	94404340	94404371	-	1	NA	promoter-TSS (NM_001164785)	promoter-TSS (NM_001164785)	-5	NM_001164786	223838	Mm.214132	NM_177431	ENSMUSG00000022449	Adamts20	Adamst20|bt	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 20	protein-coding
mm_158822.1	chrX	167382748	167382760	-	1	NA	promoter-TSS (NM_001313758)	promoter-TSS (NM_001313758)	-5	NM_001313758	110639	Mm.272955	NM_026662	ENSMUSG00000025742	Prps2	2610101M19Rik|AA589463|AI464149|Prps-2	phosphoribosyl pyrophosphate synthetase 2	protein-coding
mm_139891.1	chr17	70850158	70850187	+	1	NA	promoter-TSS (NM_001164076)	promoter-TSS (NM_001164076)	-382	NM_001164076	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_97588.1	chr11	78945870	78945879	+	1	NA	exon (NM_010927, exon 15 of 27)	exon (NM_010927, exon 15 of 27)	20583	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_55281.1	chr6	54409317	54409343	-	1	NA	intron (NR_033635, intron 1 of 13)	intron (NR_033635, intron 1 of 13)	20891	NR_033635	100042056	Mm.448157	NM_198118	ENSMUSG00000073067	9130019P16Rik	6430501H15Rik|OTTMUSG00000023151	RIKEN cDNA 9130019P16 gene	ncRNA
mm_133734.1	chr16	93864448	93864451	+	1	NA	intron (NM_001045529, intron 12 of 16)	B4A|SINE|B4	-19452	NM_028083	110749	Mm.274222	NM_028083	ENSMUSG00000022945	Chaf1b	2600017H24Rik|C76145|CAF-I p60|CAF-Ip60|CAF1|CAF1A|CAF1P60|MPHOSPH7	chromatin assembly factor 1, subunit B (p60)	protein-coding
mm_143781.1	chr17	81730906	81730923	-	1	NA	intron (NR_104580, intron 1 of 8)	B4|SINE|B4	7473	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_106023.1	chr11	116027392	116027401	-	1	NA	Intergenic	Intergenic	-2892	NM_008211	15081	Mm.18516	NM_008211	ENSMUSG00000016559	H3f3b	9430068D06Rik|H3.3B	H3 histone, family 3B	protein-coding
mm_124059.1	chr14	78088978	78088993	-	1	NA	promoter-TSS (NM_177629)	promoter-TSS (NM_177629)	22	NM_177629	219170	Mm.320428	NM_177629	ENSMUSG00000045655	Fam216b	9330158N17|AU021034	family with sequence similarity 216, member B	protein-coding
mm_166156.1	chr5	15507060	15507070	-	1	NA	Intergenic	IAPEY4_LTR|LTR|ERVK	22157	NM_001310449	100861755	Mm.382859	NM_001310449	ENSMUSG00000106445	Gm21190	-	predicted gene, 21190	protein-coding
mm_156017.1	chrX	107089665	107089680	+	1	NA	5' UTR (NM_172435, exon 2 of 3)	5' UTR (NM_172435, exon 2 of 3)	337	NM_172435	78826	Mm.74639	NM_172435	ENSMUSG00000050921	P2ry10	5830408N17Rik|Lypsr2|P2Y10	purinergic receptor P2Y, G-protein coupled 10	protein-coding
mm_108794.1	chr12	91401025	91401038	+	1	NA	promoter-TSS (NM_001113404)	promoter-TSS (NM_001113404)	38	NM_011648	22095	Mm.173847	NM_011648	ENSMUSG00000020963	Tshr	AI481368|hypothroid|hyt|pet	thyroid stimulating hormone receptor	protein-coding
mm_109895.1	chr12	7555366	7555366	-	1	NA	Intergenic	Intergenic	-175036	NR_045045	73575	Mm.179463	NR_045045	ENSMUSG00000102096	1700101O22Rik	-	RIKEN cDNA 1700101O22 gene	ncRNA
mm_8260.1	chr1	139214803	139214805	-	1	NA	intron (NM_133239, intron 11 of 11)	intron (NM_133239, intron 11 of 11)	162272	NM_133239	170788	Mm.95700	NM_133239	ENSMUSG00000063681	Crb1	7530426H14Rik|A930008G09Rik	crumbs family member 1, photoreceptor morphogenesis associated	protein-coding
mm_165688.1	chr3	92621151	92621154	-	1	NA	5' UTR (NM_001166172, exon 2 of 3)	5' UTR (NM_001166172, exon 2 of 3)	508	NM_001166172	78382	Mm.235474	NM_001166172	ENSMUSG00000086848	Lce6a	2210420J11Rik	late cornified envelope 6A	protein-coding
mm_126455.1	chr15	80930518	80930527	+	1	NA	3' UTR (NM_177124, exon 22 of 22)	3' UTR (NM_177124, exon 22 of 22)	-9517	NR_039573	100628612		NR_039573	ENSMUSG00000092868	Mir5113	mir-5113|mmu-mir-5113|mu-mir-5113	microRNA 5113	ncRNA
mm_161364.1	chr14	58075081	58075081	+	1	NA	intron (NM_013518, intron 1 of 2)	CpG	2395	NM_013518	14180	Mm.8846	NM_013518	ENSMUSG00000021974	Fgf9	Eks	fibroblast growth factor 9	protein-coding
mm_77498.1	chr8	122611359	122611411	-	1	NA	promoter-TSS (NM_021502)	promoter-TSS (NM_021502)	102	NM_001193645	50917	Mm.1786	NM_016722	ENSMUSG00000015027	Galns	mFLJ00319	galactosamine (N-acetyl)-6-sulfate sulfatase	protein-coding
mm_167758.1	chr9	110422527	110422538	-	1	NA	3' UTR (NM_008694, exon 4 of 4)	3' UTR (NM_008694, exon 4 of 4)	2724	NM_008694	18054	Mm.236225	NM_008694	ENSMUSG00000032484	Ngp	bectenecin	neutrophilic granule protein	protein-coding
mm_147176.1	chr18	36744496	36744499	-	1	NA	promoter-TSS (NM_011879)	promoter-TSS (NM_011879)	90	NM_010885	17991	Mm.29867	NM_010885	ENSMUSG00000014294	Ndufa2	AV000592|B8|C1-B8|CI-B8	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 2	protein-coding
mm_139660.1	chr17	57405272	57405291	+	1	NA	intron (NM_010130, intron 5 of 21)	Lx4B|LINE|L1	46595	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_1032.1	chr1	58755324	58755340	+	1	NA	3' UTR (NM_207653, exon 10 of 10)	3' UTR (NM_207653, exon 10 of 10)	24780	NM_001293805	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_90124.1	chr10	117531039	117531045	+	1	NA	Intergenic	Intergenic	-98458	NM_027468	70574	Mm.339332	NM_027468	ENSMUSG00000020183	Cpm	1110060I01Rik|5730456K23Rik|AA589379|E030045M14Rik	carboxypeptidase M	protein-coding
mm_146299.1	chr18	80206776	80206881	+	1	NA	promoter-TSS (NM_025299)	promoter-TSS (NM_025299)	-18	NM_178604	27366	Mm.172411	NM_025299	ENSMUSG00000057130	Txnl4a	D18Wsu98e|Dim1|ENSMUSG00000057130|Txnl4|U5-15kD|U5-15kDa	thioredoxin-like 4A	protein-coding
mm_17051.1	chr2	20968988	20968999	-	1	NA	non-coding (NR_033225, exon 1 of 2)	non-coding (NR_033225, exon 1 of 2)	119	NR_033225	433408	Mm.386941	NR_033225		Gm13375	OTTMUSG00000011664	predicted gene 13375	ncRNA
mm_157232.1	chrX	16817381	16817403	-	1	NA	promoter-TSS (NM_172778)	promoter-TSS (NM_172778)	-26	NM_172778	109731	Mm.241656	NM_172778	ENSMUSG00000040147	Maob	6330414K01Rik|MAO-B	monoamine oxidase B	protein-coding
mm_107752.1	chr12	59066941	59067001	+	1	NA	promoter-TSS (NM_008891)	promoter-TSS (NM_008891)	52	NM_008891	18949	Mm.22347	NM_008891	ENSMUSG00000020994	Pnn	AU045199|D12Ertd512e	pinin	protein-coding
mm_159313.1	chr3	7613408	7613408	-	1	NA	promoter-TSS (NM_001313890)	promoter-TSS (NM_001313890)	352	NM_008371	16196	Mm.3825	NM_008371	ENSMUSG00000040329	Il7	A630026I06Rik|Il-7|hlb368	interleukin 7	protein-coding
mm_141025.1	chr17	25184405	25184468	-	1	NA	promoter-TSS (NM_183150)	promoter-TSS (NM_183150)	-125	NM_183150	214489	Mm.274433	NM_183150	ENSMUSG00000067722	BC003965	Ccsmst1	cDNA sequence BC003965	protein-coding
mm_135005.1	chr16	32243853	32243855	-	1	NA	intron (NM_173439, intron 1 of 2)	intron (NM_173439, intron 1 of 2)	3171	NM_173439	268882	Mm.256137	NM_173439	ENSMUSG00000035764	Fbxo45	2610017J04Rik|AI463119|BC026799	F-box protein 45	protein-coding
mm_113844.1	chr13	47194062	47194070	+	1	NA	promoter-TSS (NM_001170643)	promoter-TSS (NM_001170643)	63	NM_001170643	218215	Mm.287609	NM_146042	ENSMUSG00000038068	Rnf144b	BC025007|E130105P19Rik|Ibrdc2|Pir2	ring finger protein 144B	protein-coding
mm_57032.1	chr6	122325491	122325519	-	1	NA	exon (NM_001271579, exon 7 of 15)	exon (NM_001271579, exon 7 of 15)	14152	NM_001042623	13619	Mm.6822	NM_007905	ENSMUSG00000040669	Phc1	AW557034|Edr|Edr1|Mph1|Rae-28|rae28	polyhomeotic-like 1 (Drosophila)	protein-coding
mm_78094.1	chr9	18478348	18478350	+	1	NA	promoter-TSS (NM_028557)	promoter-TSS (NM_028557)	-46	NM_028557	73503	Mm.160088	NM_028557	ENSMUSG00000038691	Mbd3l1	1700070G05Rik|1700095H13Rik|Mbd3l	methyl-CpG binding domain protein 3-like 1	protein-coding
mm_131479.1	chr16	17144601	17144622	+	1	NA	promoter-TSS (NM_029779)	promoter-TSS (NM_029779)	-188	NM_029779	76872	Mm.101656	NM_029779	ENSMUSG00000022768	Ccdc116	4930432J16Rik	coiled-coil domain containing 116	protein-coding
mm_127026.1	chr15	96287271	96287280	+	1	NA	promoter-TSS (NM_175251)	promoter-TSS (NM_175251)	-247	NM_175251	77044	Mm.17166	NM_175251	ENSMUSG00000033237	Arid2	1700124K17Rik|4432409D24Rik|zipzap/p200	AT rich interactive domain 2 (ARID, RFX-like)	protein-coding
mm_82214.1	chr9	3002365	3002386	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	36368	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_169029.1	chr13	119188768	119188768	+	1	NA	Intergenic	L1Md_A|LINE|L1	220243	NM_008710	18115	Mm.132584	NM_008710	ENSMUSG00000025453	Nnt	4930423F13Rik|AI323702|BB168308	nicotinamide nucleotide transhydrogenase	protein-coding
mm_78615.1	chr9	37545940	37545947	+	1	NA	intron (NM_022029, intron 2 of 3)	intron (NM_022029, intron 2 of 3)	6688	NM_020518	57276	Mm.27478	NM_020518	ENSMUSG00000001943	Vsig2	1190004B15Rik|2210413P10Rik|AU040484|CTX|Ctm	V-set and immunoglobulin domain containing 2	protein-coding
mm_165614.1	chr3	55740605	55740609	+	1	NA	intron (NM_030595, intron 41 of 57)	intron (NM_030595, intron 41 of 57)	-41903	NM_010750	17116	Mm.440209	NM_010750	ENSMUSG00000056947	Mab21l1	AW047968	mab-21-like 1 (C. elegans)	protein-coding
mm_18815.1	chr2	74576595	74576607	-	1	NA	intron (NM_001110209, intron 1 of 13)	intron (NM_001110209, intron 1 of 13)	2347	NM_001110209	69605	Mm.156113	NM_027133	ENSMUSG00000009207	Lnpk	2310011O18Rik|4921514L11Rik|9530051D01Rik|AI666268|Lnp|Lnpk1|Ul|ulnaless	lunapark, ER junction formation factor	protein-coding
mm_38578.1	chr4	141817976	141817999	-	1	NA	exon (NM_007919, exon 7 of 8)	exon (NM_007919, exon 7 of 8)	8018	NM_007919	13706	Mm.45316	NM_007919	ENSMUSG00000058579	Cela2a	Ela-2|Ela2|Ela2a	chymotrypsin-like elastase family, member 2A	protein-coding
mm_105249.1	chr11	102350182	102350199	-	1	NA	3' UTR (NM_011403, exon 20 of 20)	3' UTR (NM_011403, exon 20 of 20)	15091	NM_011403	20533	Mm.7248	NM_011403	ENSMUSG00000006574	Slc4a1	Ae1|CD233|Empb3|l11Jus51	solute carrier family 4 (anion exchanger), member 1	protein-coding
mm_25373.1	chr3	107211293	107211302	+	1	NA	TTS (NM_001111143)	TTS (NM_001111143)	10435	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_156472.1	chrX	143664334	143664354	+	1	NA	intron (NM_008778, intron 1 of 14)	intron (NM_008778, intron 1 of 14)	-1401	NM_001195049	18481	Mm.40035	NM_008778	ENSMUSG00000031284	Pak3	PAK-3|Pak65alpha|Pak65beta|Stk4	p21 protein (Cdc42/Rac)-activated kinase 3	protein-coding
mm_151470.1	chr19	58671730	58671779	+	1	NA	exon (NM_026925, exon 3 of 13)	exon (NM_026925, exon 3 of 13)	1389	NM_026925	69060	Mm.20407	NM_026925	ENSMUSG00000046008	Pnlip	1810007A24Rik|PL|PTL	pancreatic lipase	protein-coding
mm_168732.1	chr12	114141174	114141185	-	1	NA	Intergenic	Intergenic	328287	NR_106062	102465663		NR_106062	ENSMUSG00000105438	Mir7094-1	mmu-mir-7094-1	microRNA 7094-1	ncRNA
mm_75796.1	chr8	70110210	70110220	-	1	NA	exon (NM_007789, exon 7 of 15)	exon (NM_007789, exon 7 of 15)	-7629	NR_106033	102465646		NR_106033	ENSMUSG00000099042	Mir7066	Gm27290|mmu-mir-7066	microRNA 7066	ncRNA
mm_26758.1	chr3	8666964	8666978	-	1	NA	promoter-TSS (NM_010423)	promoter-TSS (NM_010423)	67	NM_010423	15213	Mm.29581	NM_010423	ENSMUSG00000040289	Hey1	AI316788|AI414254|CHF2|HRT1|Herp2|Hesr1|bHLHb31|hesr-1	hairy/enhancer-of-split related with YRPW motif 1	protein-coding
mm_89303.1	chr10	87914393	87914413	+	1	NA	intron (NM_001314010, intron 4 of 4)	intron (NM_001314010, intron 4 of 4)	-52268	NR_000040	22172	Mm.391420	NR_000040		Tyms-ps	-	thymidylate synthase, pseudogene	pseudo
mm_93943.1	chr10	127195714	127195739	-	1	NA	promoter-TSS (NM_030714)	promoter-TSS (NM_030714)	-17	NM_030714	80904	Mm.271724	NM_030714	ENSMUSG00000040415	Dtx3	Deltex3|mg310	deltex 3, E3 ubiquitin ligase	protein-coding
mm_26550.1	chr3	146404632	146404738	+	1	NA	promoter-TSS (NM_001253768)	promoter-TSS (NM_001253768)	43	NM_138744	99167	Mm.200783	NM_138744	ENSMUSG00000036825	Ssx2ip	AU014939|AU042321|Adip	synovial sarcoma, X 2 interacting protein	protein-coding
mm_16840.1	chr2	11502033	11502049	-	1	NA	promoter-TSS (NM_001177754)	promoter-TSS (NM_001177754)	49	NM_001177754	170768	Mm.19669	NM_133232	ENSMUSG00000026773	Pfkfb3	E330010H22Rik|iPFK-2|uPFK-2	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	protein-coding
mm_57193.1	chr6	122850041	122850053	-	1	NA	exon (NM_009779, exon 2 of 2)	exon (NM_009779, exon 2 of 2)	6110	NM_009779	12267	Mm.2408	NM_009779	ENSMUSG00000040552	C3ar1	AZ3B|C3AR|HNFAG09	complement component 3a receptor 1	protein-coding
mm_165126.1	chr2	5394173	5394173	+	1	NA	intron (NR_030601, intron 1 of 1)	Lx8|LINE|L1	14783	NR_030601	100124465		NR_030601	ENSMUSG00000078031	Mir466d	Mirn466d	microRNA 466d	ncRNA
mm_13360.1	chr2	103424796	103424806	+	1	NA	intron (NM_010125, intron 1 of 6)	intron (NM_010125, intron 1 of 6)	733	NM_010125	13711	Mm.20888	NM_010125	ENSMUSG00000027186	Elf5	ESE-2|ESE-5|ESE-5.	E74-like factor 5	protein-coding
mm_70513.1	chr8	12940929	12940945	+	1	NA	intron (NM_178076, intron 1 of 30)	intron (NM_178076, intron 1 of 30)	-7004	NR_128567	104797311		NR_128567	ENSMUSG00000105030	Gm38671	Mir9768|mmu-mir-9768	predicted gene, 38671	ncRNA
mm_19876.1	chr2	114049202	114049242	-	1	NA	exon (NM_009608, exon 5 of 7)	exon (NM_009608, exon 5 of 7)	3653	NM_009608	11464	Mm.686	NM_009608	ENSMUSG00000068614	Actc1	Actc-1	actin, alpha, cardiac muscle 1	protein-coding
mm_111651.1	chr12	102757751	102757759	-	1	NA	promoter-TSS (NM_001142939)	promoter-TSS (NM_001142939)	55	NM_001142939	100859931	Mm.291222	NM_001142939	ENSMUSG00000041716	Gm20604	AK010878-Moap1	predicted gene 20604	protein-coding
mm_10749.1	chr2	23156509	23156527	+	1	NA	promoter-TSS (NM_013771)	promoter-TSS (NM_013771)	13	NM_013771	27377	Mm.23335	NM_013771	ENSMUSG00000026775	Yme1l1	FtsH1|Ftsh	YME1-like 1 (S. cerevisiae)	protein-coding
mm_129352.1	chr15	77915722	77915739	-	1	NA	3' UTR (NM_019913, exon 4 of 4)	3' UTR (NM_019913, exon 4 of 4)	13264	NM_019913	56551	Mm.291917	NM_019913	ENSMUSG00000005354	Txn2	2510006J11Rik|AI788873|Trx2	thioredoxin 2	protein-coding
mm_47059.1	chr5	116382704	116382707	-	1	NA	Intergenic	RLTR13C3|LTR|ERVK	40159	NM_030704	80888	Mm.21549	NM_030704	ENSMUSG00000041548	Hspb8	AU018630|AW413033|Cryac|D5Ucla4|E2IG1|H11|H11K|HSP20-like|HSP22	heat shock protein 8	protein-coding
mm_96829.1	chr11	69999317	69999330	+	1	NA	exon (NM_030064, exon 5 of 5)	exon (NM_030064, exon 5 of 5)	-1303	NM_007888	13543	Mm.5114	NM_007888	ENSMUSG00000020888	Dvl2	-	dishevelled segment polarity protein 2	protein-coding
mm_11185.1	chr2	29060240	29060287	+	1	NA	promoter-TSS (NM_009442)	promoter-TSS (NM_009442)	0	NM_009442	22130	Mm.252195	NM_009442	ENSMUSG00000026803	Ttf1	AV245725|TTF-1|TTF-I	transcription termination factor, RNA polymerase I	protein-coding
mm_133053.1	chr16	57572305	57572332	+	1	NA	exon (NM_001040397, exon 5 of 5)	exon (NM_001040397, exon 5 of 5)	23076	NM_001177871	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding
mm_78169.1	chr9	21032095	21032107	+	1	NA	promoter-TSS (NM_008319)	promoter-TSS (NM_008319)	63	NM_008319	15898	Mm.4629	NM_008319	ENSMUSG00000032174	Icam5	CD50|ICAM-3|Icam3|TLN|Tlcn	intercellular adhesion molecule 5, telencephalin	protein-coding
mm_144358.1	chr18	17773373	17773374	+	1	NA	Intergenic	Intergenic	-192383	NR_045374	75162	Mm.60874	NR_045374		4930545E07Rik	-	RIKEN cDNA 4930545E07 gene	ncRNA
mm_4447.1	chr1	172579306	172579308	+	1	NA	Intergenic	Intergenic	11261	NM_029084	74748	Mm.179812	NM_029084	ENSMUSG00000053318	Slamf8	5830408F06Rik|Blame|SBBI42	SLAM family member 8	protein-coding
mm_1215.1	chr1	62727023	62727072	+	1	NA	intron (NM_001077405, intron 2 of 15)	(CA)n|Simple_repeat|Simple_repeat	23730	NM_001077405	18187	Mm.266341	NM_010939	ENSMUSG00000025969	Nrp2	1110048P06Rik|Np-2|Np2|Npn-2|Npn2	neuropilin 2	protein-coding
mm_128112.1	chr15	28025953	28025965	-	1	NA	promoter-TSS (NM_001081302)	promoter-TSS (NM_001081302)	-111	NM_001081302	223435	Mm.485422	NM_001081302	ENSMUSG00000022263	Trio	6720464I07Rik|AA408740|Solo	triple functional domain (PTPRF interacting)	protein-coding
mm_75685.1	chr8	68121621	68121637	-	1	NA	Intergenic	Intergenic	-147055	NM_177698	234353	Mm.32525	NM_027626	ENSMUSG00000030465	Psd3	4931420C21Rik|AI661273|BC003498|D430018P08|EFA6D	pleckstrin and Sec7 domain containing 3	protein-coding
mm_148662.1	chr19	5568414	5568447	+	1	NA	5' UTR (NM_001033448, exon 1 of 2)	5' UTR (NM_001033448, exon 1 of 2)	356	NM_001033448	381201	Mm.441906	NM_001033448	ENSMUSG00000049562	Ap5b1	Gm962	adaptor-related protein complex 5, beta 1 subunit	protein-coding
mm_143355.1	chr17	67143619	67143630	-	1	NA	intron (NM_008984, intron 2 of 30)	ORR1B1|LTR|ERVL-MaLR	-117389	NR_049205	100885844		NR_049205	ENSMUSG00000093508	Mir5709	Gm22041|mir-5709|mmu-mir-5709	microRNA 5709	ncRNA
mm_141766.1	chr17	34282916	34282926	-	1	NA	3' UTR (NM_010378, exon 5 of 5)	3' UTR (NM_010378, exon 5 of 5)	4850	NM_010378	14960	Mm.235338	NM_010378	ENSMUSG00000036594	H2-Aa	Aalpha|H-2Aa|H2Aa|I-Aalpha|IAalpha|Ia-1|Ia1	histocompatibility 2, class II antigen A, alpha	protein-coding
mm_92195.1	chr10	68135269	68135284	-	1	NA	intron (NM_023598, intron 4 of 9)	intron (NM_023598, intron 4 of 9)	143450	NM_023598	71371	Mm.440357	NM_023598	ENSMUSG00000019947	Arid5b	4930580B11|5430435G07Rik|AI467247|Desrt|Mrf2|Mrf2alpha|Mrf2beta	AT rich interactive domain 5B (MRF1-like)	protein-coding
mm_133402.1	chr16	84834944	84834955	+	1	NA	promoter-TSS (NM_001302216)	promoter-TSS (NM_001302216)	49	NM_001302216	11957	Mm.353	NM_016755	ENSMUSG00000022890	Atp5j	CF6	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit F	protein-coding
mm_6903.1	chr1	84814881	84814895	-	1	NA	exon (NM_133975, exon 2 of 41)	exon (NM_133975, exon 2 of 41)	24416	NM_133975	14897	Mm.209265	NM_133975	ENSMUSG00000026219	Trip12	1110036I07Rik|6720416K24Rik|AA410158|Gtl6|TRIP-12	thyroid hormone receptor interactor 12	protein-coding
mm_70873.1	chr8	25068582	25068616	+	1	NA	intron (NM_031257, intron 3 of 11)	intron (NM_031257, intron 3 of 11)	-29637	NM_001081187	330723	Mm.334452	NM_001081187	ENSMUSG00000037406	Htra4	B430206E18Rik	HtrA serine peptidase 4	protein-coding
mm_67633.1	chr7	84372413	84372446	-	1	NA	intron (NM_007488, intron 1 of 18)	intron (NM_007488, intron 1 of 18)	37609	NM_007488	11864	Mm.38594	NM_007488	ENSMUSG00000015709	Arnt2	Hif-2b|bHLHe1|mKIAA0307	aryl hydrocarbon receptor nuclear translocator 2	protein-coding
mm_18847.1	chr2	75633581	75633594	-	1	NA	Intergenic	RMER20B|LTR|ERVK	-25672	NM_146130	229279	Mm.316306	NM_053263	ENSMUSG00000059005	Hnrnpa3	2410013L13Rik|2610209F03Rik|2610510D13Rik|Hnrpa3	heterogeneous nuclear ribonucleoprotein A3	protein-coding
mm_138666.1	chr17	35874974	35874999	+	1	NA	3' UTR (NM_001146711, exon 4 of 4)	3' UTR (NM_001146711, exon 4 of 4)	-4792	NM_026987	69192	Mm.390986	NM_026987	ENSMUSG00000024422	Dhx16	2410006N22Rik|DBP2|Ddx16|mKIAA0577	DEAH (Asp-Glu-Ala-His) box polypeptide 16	protein-coding
mm_13976.1	chr2	121437906	121437946	+	1	NA	3' UTR (NM_007952, exon 13 of 13)	3' UTR (NM_007952, exon 13 of 13)	4675	NM_145973	269344	Mm.330522	NM_145973	ENSMUSG00000027246	Ell3	A930015D22Rik	elongation factor RNA polymerase II-like 3	protein-coding
mm_140602.1	chr17	10319325	10319380	-	1	NA	promoter-TSS (NM_001159517)	promoter-TSS (NM_001159517)	9	NM_021881	19317	Mm.130694	NM_021881	ENSMUSG00000062078	Qk	1110003F05Rik|1500005P18|QkI|l(17)-1Wis|l17Wis1	quaking	protein-coding
mm_168534.1	chr1	161035952	161035953	+	1	NA	non-coding (NR_002840, exon 1 of 4)	non-coding (NR_002840, exon 1 of 4)	786	NR_002840	14455	Mm.270065	NR_002840	ENSMUSG00000053332	Gas5	Gas-5|Mir5117|Snhg2	growth arrest specific 5	ncRNA
mm_64671.1	chr7	4461253	4461269	-	1	NA	Intergenic	Intergenic	-3474	NM_026146	67425	Mm.360392	NM_026146	ENSMUSG00000006154	Eps8l1	2310051G19Rik|4632407K17Rik|AW060268|DRC3|EPS8R1	EPS8-like 1	protein-coding
mm_67817.1	chr7	98164979	98165012	-	1	NA	intron (NM_007602, intron 1 of 12)	B3|SINE|B2	-2653	NM_001301250	12337	Mm.326847	NM_007602	ENSMUSG00000035547	Capn5	nCL-3	calpain 5	protein-coding
mm_125123.1	chr15	30172742	30172768	+	1	NA	5' UTR (NM_008729, exon 1 of 23)	5' UTR (NM_008729, exon 1 of 23)	162	NM_008729	18163	Mm.321648	NM_008729	ENSMUSG00000022240	Ctnnd2	Catnd2|Nprap|neurojugin	catenin (cadherin associated protein), delta 2	protein-coding
mm_36131.1	chr4	59315796	59315813	-	1	NA	exon (NM_001163288, exon 16 of 17)	exon (NM_001163288, exon 16 of 17)	55753	NR_105031	101055769	Mm.421401	NR_105031		Gm12596	OTTMUSG00000007649	predicted gene 12596	ncRNA
mm_44006.1	chr5	146948764	146948774	+	1	NA	5' UTR (NM_025652, exon 1 of 9)	5' UTR (NM_025652, exon 1 of 9)	112	NM_025652	66596	Mm.196528	NM_025652	ENSMUSG00000016503	Gtf3a	2010015D03Rik|2610111I01Rik|5330403M05Rik	general transcription factor III A	protein-coding
mm_33283.1	chr4	128747125	128747144	+	1	NA	exon (NM_018774, exon 13 of 15)	exon (NM_018774, exon 13 of 15)	-12124	NM_001009819	215493	Mm.300900	NM_001009819	ENSMUSG00000028794	A3galt2	Gm433|iGb3|iGb3S	alpha 1,3-galactosyltransferase 2 (isoglobotriaosylceramide synthase)	protein-coding
mm_148520.1	chr19	4300615	4300625	+	1	NA	intron (NM_001290818, intron 1 of 20)	intron (NM_001290818, intron 1 of 20)	5602	NM_130863	110355	Mm.254144	NM_130863	ENSMUSG00000024858	Grk2	Adrbk-1|Adrbk1|Bark-1|beta ARK|betaARK1	G protein-coupled receptor kinase 2	protein-coding
mm_97525.1	chr11	78501823	78501839	+	1	NA	exon (NM_011707, exon 7 of 8)	exon (NM_011707, exon 7 of 8)	-1682	NM_008759	18292	Mm.134360	NM_008759	ENSMUSG00000001103	Sebox	OG9|Og9x	SEBOX homeobox	protein-coding
mm_82453.1	chr9	15619607	15619615	-	1	NA	promoter-TSS (NR_040746)	promoter-TSS (NR_040746)	-246	NR_040746	78025	Mm.55983	NR_040746	ENSMUSG00000111299	4930540M03Rik	-	RIKEN cDNA 4930540M03 gene	ncRNA
mm_111742.1	chr12	103897065	103897095	-	1	NA	exon (NM_009245, exon 3 of 5)	exon (NM_009245, exon 3 of 5)	7870	NM_009245	20702	Mm.439692	NM_009245	ENSMUSG00000079015	Serpina1c	Pi3|Pi6|Skalp|Spi1-3|Spi1-6|Wap3	serine (or cysteine) peptidase inhibitor, clade A, member 1C	protein-coding
mm_49975.1	chr6	40891197	40891207	+	1	NA	intron (NR_035473, intron 2 of 3)	intron (NR_035473, intron 2 of 3)	-3708	NM_139296	194357	Mm.207087	NM_139296	ENSMUSG00000029885	Moxd2	Dbhl1	monooxygenase, DBH-like 2	protein-coding
mm_84584.1	chr9	69760866	69760879	-	1	NA	promoter-TSS (NR_040765)	promoter-TSS (NR_040765)	68	NM_022378	64290	Mm.440890	NM_022378	ENSMUSG00000059246	Foxb1	C43|Fkh5|Foxb1a|Foxb1b|Hfh-e5.1|Mf3|Twh	forkhead box B1	protein-coding
mm_41944.1	chr5	105731830	105731847	+	1	NA	intron (NM_178701, intron 1 of 2)	intron (NM_178701, intron 1 of 2)	31028	NM_178701	231549	Mm.23837	NM_178701	ENSMUSG00000046079	Lrrc8d	2810473G09Rik|4930525N13Rik|A930019F03|Lrrc5	leucine rich repeat containing 8D	protein-coding
mm_11611.1	chr2	34406962	34406972	+	1	NA	5' UTR (NM_177345, exon 1 of 12)	5' UTR (NM_177345, exon 1 of 12)	116	NM_001290626	227743	Mm.270866	NM_177345	ENSMUSG00000038696	Mapkap1	AI591529|D230039K05Rik|Sin1	mitogen-activated protein kinase associated protein 1	protein-coding
mm_85930.1	chr9	112092635	112092649	-	1	NA	intron (NM_001177618, intron 17 of 18)	intron (NM_001177618, intron 17 of 18)	26069	NR_029823	723815		NR_029823	ENSMUSG00000065441	Mir128-2	Mirn128-2|Mirn128b|mir-128-2|mir-128b	microRNA 128-2	ncRNA
mm_171502.1	chr4	146270309	146270309	+	1	NA	promoter-TSS (NM_001083918).2	promoter-TSS (NM_001083918).2	-76	NM_001083918	666532	Mm.392861	NM_001083918	ENSMUSG00000067916	Zfp991	Gm13139|OTTMUSG00000010657	zinc finger protein 991	protein-coding
mm_106437.1	chr11	119541446	119541465	-	1	NA	3' UTR (NM_008730, exon 5 of 5)	3' UTR (NM_008730, exon 5 of 5)	6365	NM_008730	18164	Mm.5142	NM_008730	ENSMUSG00000025582	Nptx1	D11Bwg1004e|Np1	neuronal pentraxin 1	protein-coding
mm_143629.1	chr17	78895140	78895150	-	1	NA	intron (NM_001163625, intron 3 of 6)	intron (NM_001163625, intron 3 of 6)	11847	NM_001163625	73671	Mm.45514	NM_001163625	ENSMUSG00000038045	Sult6b1	2410078J06Rik|AV101767|ST6B1	sulfotransferase family, cytosolic, 6B, member 1	protein-coding
mm_40882.1	chr5	74535642	74535691	+	1	NA	5' UTR (NM_001159573, exon 1 of 18)	5' UTR (NM_001159573, exon 1 of 18)	184	NM_001159574	66899	Mm.272468	NM_024183	ENSMUSG00000029227	Fip1l1	1300019H17Rik|Rje	FIP1 like 1 (S. cerevisiae)	protein-coding
mm_126257.1	chr15	79081865	79081879	+	1	NA	exon (NM_145139, exon 7 of 13)	exon (NM_145139, exon 7 of 13)	6649	NM_145139	223691	Mm.206404	NM_145139	ENSMUSG00000033047	Eif3l	0610011H21Rik|D15N1e|Eif3eip|Eif3ip|Eif3s6ip|HSP-66Y|PAF67	eukaryotic translation initiation factor 3, subunit L	protein-coding
mm_17480.1	chr2	28561265	28561277	-	1	NA	exon (NM_009885, exon 2 of 11)	exon (NM_009885, exon 2 of 11)	2132	NM_009885	12613	Mm.236017	NM_009885	ENSMUSG00000026818	Cel	1810036E18Rik|BAL	carboxyl ester lipase	protein-coding
mm_150234.1	chr19	34008285	34008295	+	1	NA	promoter-TSS (NM_172837)	promoter-TSS (NM_172837)	36	NM_001205349	240633	Mm.58924	NM_172837	ENSMUSG00000024771	Lipk	9930115F20|BC055815|Lipl2	lipase, family member K	protein-coding
mm_89988.1	chr10	111996760	111996800	+	1	NA	intron (NM_028608, intron 1 of 5)	intron (NM_028608, intron 1 of 5)	484	NM_028608	73690	Mm.173790	NM_028608	ENSMUSG00000056888	Glipr1	2410114O14Rik|RTVP-1|RTVP1|mRTVP-1	GLI pathogenesis-related 1 (glioma)	protein-coding
mm_47644.1	chr5	125389178	125389208	-	1	NA	intron (NM_019639, intron 1 of 1)	intron (NM_019639, intron 1 of 1)	824	NM_019639	22190	Mm.331	NM_019639	ENSMUSG00000008348	Ubc	2700054O04Rik|AI194771|Rps27a|TI-225|Uba52|Ubb	ubiquitin C	protein-coding
mm_53931.1	chr6	4747019	4747030	-	1	NA	promoter-TSS (NM_130877)	promoter-TSS (NM_130877)	180	NM_001130188	20392	Mm.8739	NM_011360	ENSMUSG00000004631	Sgce	e-SG	sarcoglycan, epsilon	protein-coding
mm_9999.1	chr1	191445804	191445818	-	1	NA	Intergenic	ORR1D2|LTR|ERVL-MaLR	-48770	NM_144880	226849	Mm.205569	NM_144880	ENSMUSG00000026626	Ppp2r5a	PR61alpha	protein phosphatase 2, regulatory subunit B', alpha	protein-coding
mm_132870.1	chr16	48611789	48611808	+	1	NA	intron (NM_010816, intron 20 of 26)	intron (NM_010816, intron 20 of 26)	160158	NM_198297	77647	Mm.167298	NM_198297	ENSMUSG00000030775	Trat1	C030046M14Rik|Tcrim|Trim	T cell receptor associated transmembrane adaptor 1	protein-coding
mm_47062.1	chr5	116408841	116408865	-	1	NA	3' UTR (NM_030704, exon 3 of 3)	3' UTR (NM_030704, exon 3 of 3)	14011	NM_030704	80888	Mm.21549	NM_030704	ENSMUSG00000041548	Hspb8	AU018630|AW413033|Cryac|D5Ucla4|E2IG1|H11|H11K|HSP20-like|HSP22	heat shock protein 8	protein-coding
mm_17198.1	chr2	25468857	25468868	-	1	NA	exon (NM_008963, exon 3 of 7)	exon (NM_008963, exon 3 of 7)	887	NM_008963	19215	Mm.1008	NM_008963	ENSMUSG00000015090	Ptgds	21kDa|L-PGDS|PGD2|PGDS|PGDS2|Ptgs3	prostaglandin D2 synthase (brain)	protein-coding
mm_73869.1	chr8	118799387	118799394	+	1	NA	intron (NM_019707, intron 4 of 13)	intron (NM_019707, intron 4 of 13)	515779	NM_019707	12554	Mm.334841	NM_019707	ENSMUSG00000031841	Cdh13	4932416G01Rik|Cdht|Tcad	cadherin 13	protein-coding
mm_140148.1	chr17	80095494	80095501	+	1	NA	Intergenic	RMER17C|LTR|ERVK	-31974	NM_176963	319625	Mm.29098	NM_176963	ENSMUSG00000035473	Galm	A530057M15Rik|AU015645|AU020959	galactose mutarotase	protein-coding
mm_129786.1	chr15	82794873	82794906	-	1	NA	promoter-TSS (NM_029562)	promoter-TSS (NM_029562)	-644	NM_029562	76279	Mm.439931	NM_029562	ENSMUSG00000022445	Cyp2d26	1300006E06Rik	cytochrome P450, family 2, subfamily d, polypeptide 26	protein-coding
mm_24415.1	chr3	90514919	90514976	+	1	NA	promoter-TSS (NM_011309)	promoter-TSS (NM_011309)	512	NM_009113	20196	Mm.6523	NM_009113	ENSMUSG00000042312	S100a13	-	S100 calcium binding protein A13	protein-coding
mm_140664.1	chr17	12909882	12909897	-	1	NA	exon (NM_001034866, exon 1 of 19)	exon (NM_001034866, exon 1 of 19)	111	NM_001034866	240023	Mm.242315	NM_001034866	ENSMUSG00000073460	Pnldc1	Gm313	poly(A)-specific ribonuclease (PARN)-like domain containing 1	protein-coding
mm_41392.1	chr5	90769851	90769859	+	1	NA	3' UTR (NM_023785, exon 3 of 3)	3' UTR (NM_023785, exon 3 of 3)	1337	NM_023785	57349	Mm.293614	NM_023785	ENSMUSG00000029372	Ppbp	2400003M24Rik|AI854500|CTAP3|CTAPIII|Cxcl7|LA-PF4|LDGF|MDGF|NAP-2|NAP-2-L1|Scyb7|TGB|TGB1|THBGB1|b-TG1|beta-TG	pro-platelet basic protein	protein-coding
mm_34423.1	chr4	145281522	145281558	+	1	NA	intron (NM_009401, intron 10 of 12)	PB1D9|SINE|Alu	33607	NM_009401	21941	Mm.12810	NM_009401	ENSMUSG00000028602	Tnfrsf8	Cd30|D1S166E|Ki|Ki-1	tumor necrosis factor receptor superfamily, member 8	protein-coding
mm_168592.1	chr1	173880175	173880175	-	1	NA	promoter-TSS (NM_001170853)	promoter-TSS (NM_001170853)	12	NM_001170853	100040462	Mm.463437	NM_001170853	ENSMUSG00000090272	Mndal	Gm2785|Ifi212	myeloid nuclear differentiation antigen like	protein-coding
mm_114209.1	chr13	56152060	56152100	+	1	NA	Intergenic	Intergenic	-16530	NM_001159513	26914	Mm.283802	NM_012015	ENSMUSG00000015937	H2afy	H2AF12M|mH2a1|macroH2A1	H2A histone family, member Y	protein-coding
mm_156922.1	chrX	169150263	169150275	+	1	NA	intron (NM_001287530, intron 1 of 12)	Lx5c|LINE|L1	36940	NM_001290371	11704	Mm.391342	NM_009666	ENSMUSG00000031354	Amelx	ALGN|AMGL|AMGX|Amel|Amg|LRAP|Rgsc888	amelogenin, X-linked	protein-coding
mm_57220.1	chr6	123260256	123260262	-	1	NA	Intergenic	Intergenic	-1848	NM_001163161	17474	Mm.441101	NM_010819	ENSMUSG00000030144	Clec4d	Clecsf8|Mpcl|mcl	C-type lectin domain family 4, member d	protein-coding
mm_128742.1	chr15	64312605	64312630	-	1	NA	promoter-TSS (NM_001276463)	promoter-TSS (NM_001276463)	56	NM_001276462	13196	Mm.277236	NM_010026	ENSMUSG00000022377	Asap1	AV239055|DEF-1|Ddef1|PAP|mKIAA1249|s19	ArfGAP with SH3 domain, ankyrin repeat and PH domain1	protein-coding
mm_106579.1	chr11	120727315	120727321	-	1	NA	promoter-TSS (NM_026428)	promoter-TSS (NM_026428)	-34	NM_001347608	67880	Mm.231091	NM_026428	ENSMUSG00000039450	Dcxr	0610038K04Rik|1810027P18Rik|XR	dicarbonyl L-xylulose reductase	protein-coding
mm_85238.1	chr9	98873927	98873930	-	1	NA	Intergenic	Intergenic	9161	NM_028033	71979	Mm.140843	NM_028033	ENSMUSG00000090470	Prr23a3	2410012M07Rik	proline rich 23A, member 3	protein-coding
mm_164165.1	chr15	73723157	73723159	+	1	NA	promoter-TSS (NM_001166390)	promoter-TSS (NM_001166390)	13	NM_001166389	19245	Mm.390807	NM_008975	ENSMUSG00000059895	Ptp4a3	AV088979|Prl-3|pPtp4a3	protein tyrosine phosphatase 4a3	protein-coding
mm_101304.1	chr11	22342286	22342296	-	1	NA	Intergenic	Intergenic	-55496	NM_001252515	216565	Mm.491265	NM_153078	ENSMUSG00000042302	Ehbp1	AF424697|Flj21950|NACSIN	EH domain binding protein 1	protein-coding
mm_95709.1	chr11	54486422	54486424	+	1	NA	intron (NM_173753, intron 6 of 17)	intron (NM_173753, intron 6 of 17)	-36422	NM_001252494	192786	Mm.254404	NM_175258	ENSMUSG00000037533	Rapgef6	A530068K01|AI844632|BB085664|C030018K18Rik|PDZ-GEF2|Pdzgef2|RA-GEF-2|Ragef2|mKIAA4052	Rap guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_128358.1	chr15	39964257	39964260	-	1	NA	non-coding (NR_045719, exon 2 of 3)	non-coding (NR_045719, exon 2 of 3)	1609	NR_045719	105976	Mm.394885	NR_045719		AU022793	-	expressed sequence AU022793	ncRNA
mm_111786.1	chr12	104751901	104751937	-	1	NA	promoter-TSS (NM_148948)	promoter-TSS (NM_148948)	33	NM_148948	192119	Mm.21135	NM_148948	ENSMUSG00000041415	Dicer1	1110006F08Rik|D12Ertd7e|mKIAA0928	dicer 1, ribonuclease type III	protein-coding
mm_146936.1	chr18	32136512	32136514	-	1	NA	intron (NM_001042767, intron 1 of 8)	intron (NM_001042767, intron 1 of 8)	1692	NM_008934	19123	Mm.2786	NM_008934	ENSMUSG00000024386	Proc	PC	protein C	protein-coding
mm_92803.1	chr10	81365808	81365825	-	1	NA	promoter-TSS (NM_001014836)	promoter-TSS (NM_001014836)	4	NM_001014836	432479	Mm.440450	NM_001014836	ENSMUSG00000020234	4930404N11Rik	2210409H10Rik|5730551K18Rik|AI854616	RIKEN cDNA 4930404N11 gene	protein-coding
mm_164570.1	chr17	21535451	21535511	-	1	NA	promoter-TSS (NM_144515)	promoter-TSS (NM_144515)	-58	NM_144515	22710	Mm.296100	NM_144515	ENSMUSG00000051341	Zfp52	KRAB11|Zfp-52|Zfp76|mszf23-2|mszf24|mszf34|mszf75|zfec29	zinc finger protein 52	protein-coding
mm_8131.1	chr1	136234039	136234051	-	1	NA	exon (NM_028872, exon 1 of 10)	exon (NM_028872, exon 1 of 10)	235	NM_028872	67313	Mm.36763	NM_028872	ENSMUSG00000041605	5730559C18Rik	1700034M08Rik|4933426C09Rik|AI586180|D1Mgi54	RIKEN cDNA 5730559C18 gene	protein-coding
mm_8507.1	chr1	154394586	154394590	-	1	NA	3' UTR (NM_009782, exon 47 of 47)	3' UTR (NM_009782, exon 47 of 47)	-137682	NR_040629	78112	Mm.401935	NR_040629	ENSMUSG00000099933	4930452N14Rik	-	RIKEN cDNA 4930452N14 gene	ncRNA
mm_135231.1	chr16	36895860	36895871	-	1	NA	intron (NM_030035, intron 8 of 21)	intron (NM_030035, intron 8 of 21)	1324	NR_040476	68306	Mm.399193	NR_040476	ENSMUSG00000084834	4930565N06Rik	4930428L02Rik	RIKEN cDNA 4930565N06 gene	ncRNA
mm_118090.1	chr13	103774467	103774572	-	1	NA	Intergenic	CpG	-9937	NM_172592	218543	Mm.458176	NM_172592	ENSMUSG00000032621	Srek1	8430401B01|AI450757|AI462342|SRrp508|SRrp86|Sfrs12|Srsf12	splicing regulatory glutamine/lysine-rich protein 1	protein-coding
mm_131212.1	chr16	8829997	8830021	+	1	NA	promoter-TSS (NM_001081400)	promoter-TSS (NM_001081400)	-91	NM_001081400	69053	Mm.390868	NM_001081400	ENSMUSG00000022507	1810013L24Rik	1110017P05Rik|3010002C02Rik|AA792997|AW124177|Gm19906|R74903	RIKEN cDNA 1810013L24 gene	protein-coding
mm_53007.1	chr6	123270848	123270858	+	1	NA	intron (NM_001163161, intron 5 of 5)	B1F|SINE|Alu	8746	NM_010819	17474	Mm.441101	NM_010819	ENSMUSG00000030144	Clec4d	Clecsf8|Mpcl|mcl	C-type lectin domain family 4, member d	protein-coding
mm_34476.1	chr4	148333480	148333485	+	1	NA	Intergenic	Intergenic	-45517	NM_001083342	242748	Mm.33873	NM_001083342	ENSMUSG00000041544	Ptchd2	Disp3|G630052C06Rik|RNDEu-2	patched domain containing 2	protein-coding
mm_74467.1	chr8	4217262	4217301	-	1	NA	promoter-TSS (NM_207203)	promoter-TSS (NM_207203)	31	NM_207203	73072	Mm.477379	NM_207203	ENSMUSG00000064125	Prr36	-	proline rich 36	protein-coding
mm_135109.1	chr16	35769362	35769384	-	1	NA	promoter-TSS (NM_153550)	promoter-TSS (NM_153550)	-17	NM_153550	224132	Mm.24094	NM_153550	ENSMUSG00000022848	Dirc2	RCC4	disrupted in renal carcinoma 2 (human)	protein-coding
mm_161708.1	chr17	24887485	24887485	+	1	NA	promoter-TSS (NM_027141)	promoter-TSS (NM_027141)	4	NM_027141	79043	Mm.274794	NM_027141	ENSMUSG00000024160	Spsb3	2310012N15Rik|3300001M01Rik|SSB3|Tce1|mKIAA4204	splA/ryanodine receptor domain and SOCS box containing 3	protein-coding
mm_629.1	chr1	40250970	40250995	+	1	NA	intron (NM_008362, intron 1 of 10)	intron (NM_008362, intron 1 of 10)	-15604	NM_001123382	16177	Mm.896	NM_008362	ENSMUSG00000026072	Il1r1	CD121a|CD121b|IL-1R1|IL-iR|Il1r-1	interleukin 1 receptor, type I	protein-coding
mm_150299.1	chr19	34551195	34551210	+	1	NA	intron (NM_008332, intron 1 of 2)	intron (NM_008332, intron 1 of 2)	508	NM_008332	15958	Mm.2036	NM_008332	ENSMUSG00000045932	Ifit2	AV302338|Ifi54|P54	interferon-induced protein with tetratricopeptide repeats 2	protein-coding
mm_56288.1	chr6	91490018	91490030	-	1	NA	3' UTR (NM_009531, exon 16 of 16)	3' UTR (NM_009531, exon 16 of 16)	16273	NM_028766	74122	Mm.38801	NM_028766	ENSMUSG00000030095	Tmem43	1200015A22Rik|LUMA	transmembrane protein 43	protein-coding
mm_33093.1	chr4	124696002	124696014	+	1	NA	Intergenic	Intergenic	-2454	NM_026031	67205	Mm.259121	NM_026031	ENSMUSG00000028907	Utp11l	2700082D03Rik|CGI-94|Cgi94|Utp11	UTP11-like, U3 small nucleolar ribonucleoprotein, (yeast)	protein-coding
mm_133964.1	chr16	4092325	4092358	-	1	NA	exon (NM_001025432, exon 27 of 31)	exon (NM_001025432, exon 27 of 31)	-14531	NM_026508	68015	Mm.123366	NM_026508	ENSMUSG00000005981	Trap1	2410002K23Rik|HSP75	TNF receptor-associated protein 1	protein-coding
mm_48417.1	chr5	140340467	140340473	-	1	NA	3' UTR (NM_172277, exon 11 of 11)	3' UTR (NM_172277, exon 11 of 11)	8548	NM_008637	17766	Mm.118846	NM_008637	ENSMUSG00000036639	Nudt1	Mth1	nudix (nucleoside diphosphate linked moiety X)-type motif 1	protein-coding
mm_85911.1	chr9	111057236	111057252	-	1	NA	promoter-TSS (NM_017466)	promoter-TSS (NM_017466)	0	NM_001302377	54199	Mm.7336	NM_017466	ENSMUSG00000043953	Ccrl2	1810047I05Rik|Ackr5|CCR11|Cmkbr1l2|E01|L-CCR	chemokine (C-C motif) receptor-like 2	protein-coding
mm_125745.1	chr15	73723165	73723174	+	1	NA	promoter-TSS (NM_001166390)	promoter-TSS (NM_001166390)	24	NM_001166389	19245	Mm.390807	NM_008975	ENSMUSG00000059895	Ptp4a3	AV088979|Prl-3|pPtp4a3	protein tyrosine phosphatase 4a3	protein-coding
mm_62873.1	chr7	114745686	114745718	+	1	NA	promoter-TSS (NM_173767)	promoter-TSS (NM_173767)	-64	NM_173767	233752	Mm.83037	NM_173767	ENSMUSG00000048782	Insc	3830422K02Rik|C730020D23	inscuteable homolog (Drosophila)	protein-coding
mm_77995.1	chr9	8899829	8899855	+	1	NA	promoter-TSS (NM_008829)	promoter-TSS (NM_008829)	9	NM_008829	18667	Mm.12798	NM_008829	ENSMUSG00000031870	Pgr	9930019P03Rik|BB114106|ENSMUSG00000074510|NR3C3|PR|PR-A|PR-B	progesterone receptor	protein-coding
mm_2520.1	chr1	106369900	106369901	+	1	NA	intron (NM_133821, intron 12 of 16)	intron (NM_133821, intron 12 of 16)	176731	NR_106164	102466254		NR_106164	ENSMUSG00000098344	Mir3473f	Gm27846|mmu-mir-3473f	microRNA 3473f	ncRNA
mm_71965.1	chr8	70529599	70529640	+	1	NA	exon (NM_001199631, exon 2 of 9)	exon (NM_001199631, exon 2 of 9)	1773	NM_001199631	14232	Mm.141864	NM_010223	ENSMUSG00000019428	Fkbp8	38kDa|FKBP-38|FKBP-8|Fkbp38	FK506 binding protein 8	protein-coding
mm_28117.1	chr3	86899434	86899438	-	1	NA	intron (NM_001195497, intron 2 of 15)	intron (NM_001195497, intron 2 of 15)	21448	NM_001195496	70762	Mm.44490	NM_027539	ENSMUSG00000028078	Dclk2	6330415M09Rik|AU044875|CL2|CLICK2|Click-II|Dcamkl2	doublecortin-like kinase 2	protein-coding
mm_17439.1	chr2	27714232	27714239	-	1	NA	intron (NM_001290482, intron 1 of 9)	intron (NM_001290482, intron 1 of 9)	3652	NM_001290482	20181	Mm.24624	NM_011305	ENSMUSG00000015846	Rxra	9530071D11Rik|Nr2b1|RXRalpha1	retinoid X receptor alpha	protein-coding
mm_31135.1	chr4	43257769	43257777	+	1	NA	intron (NM_001310758, intron 30 of 38)	intron (NM_001310758, intron 30 of 38)	-9386	NM_177195	320571	Mm.74465	NM_177195	ENSMUSG00000028457	Atp8b5	4930417M19Rik|Feta	ATPase, class I, type 8B, member 5	protein-coding
mm_98934.1	chr11	98357039	98357079	+	1	NA	exon (NM_001313970, exon 7 of 7)	exon (NM_001313970, exon 7 of 7)	1224	NR_045477	69338	Mm.398308	NR_045477	ENSMUSG00000085944	1700003D09Rik	-	RIKEN cDNA 1700003D09 gene	ncRNA
mm_169719.1	chr15	77777770	77777788	-	1	NA	exon (NM_022410, exon 19 of 41)	exon (NM_022410, exon 19 of 41)	-22550	NM_001081970	239552	Mm.125650	NM_001081970	ENSMUSG00000056656	Apol8	9830006J20Rik|APOL-II|Apol2	apolipoprotein L 8	protein-coding
mm_84740.1	chr9	75387227	75387247	-	1	NA	3' UTR (NM_015806, exon 6 of 6)	3' UTR (NM_015806, exon 6 of 6)	22122	NM_027418	50772	Mm.480076	NM_015806	ENSMUSG00000042688	Mapk6	2610021I23Rik|D130053K17Rik|Erk3|Mapk4|Mapk63|Prkm4|Prkm6	mitogen-activated protein kinase 6	protein-coding
mm_134385.1	chr16	17214195	17214209	-	1	NA	TTS (NM_001033338)	TTS (NM_001033338)	6067	NM_001033338	239731	Mm.86671	NM_001033338	ENSMUSG00000071636	Rimbp3	Gm1759|Gm603|RIM-BP3|mKIAA1666	RIMS binding protein 3	protein-coding
mm_113487.1	chr13	37376925	37376945	+	1	NA	exon (NM_010745, exon 3 of 5)	exon (NM_010745, exon 3 of 5)	31590	NM_010745	17084	Mm.2639	NM_010745	ENSMUSG00000021423	Ly86	MD-1|MD1|ly86_tv2	lymphocyte antigen 86	protein-coding
mm_68432.1	chr7	109840913	109840922	-	1	NA	intron (NM_020052, intron 7 of 21)	ID_B1|SINE|B4	24762	NM_020052	56788	Mm.40447	NM_020052	ENSMUSG00000007279	Scube2	4932442O19Rik|Cegf1|Cegp1	signal peptide, CUB domain, EGF-like 2	protein-coding
mm_137458.1	chr17	26571103	26571124	+	1	NA	intron (NM_026170, intron 1 of 9)	intron (NM_026170, intron 1 of 9)	9601	NM_026170	67458	Mm.30496	NM_026170	ENSMUSG00000001576	Ergic1	1200007D18Rik|maa-136	endoplasmic reticulum-golgi intermediate compartment (ERGIC) 1	protein-coding
mm_151168.1	chr19	53198021	53198025	+	1	NA	intron (NM_013758, intron 1 of 15)	intron (NM_013758, intron 1 of 15)	54026	NM_013758	27360	Mm.426080	NM_013758	ENSMUSG00000025026	Add3	AI463285|R75380	adducin 3 (gamma)	protein-coding
mm_106730.1	chr12	3891309	3891358	+	1	NA	promoter-TSS (NM_153743)	promoter-TSS (NM_153743)	-411	NM_153743	13435	Mm.5001	NM_007872	ENSMUSG00000020661	Dnmt3a	MmuIIIA	DNA methyltransferase 3A	protein-coding
mm_13069.1	chr2	91118974	91118980	+	1	NA	intron (NM_008653, intron 1 of 31)	intron (NM_008653, intron 1 of 31)	833	NM_008653	17868	Mm.10728	NM_008653	ENSMUSG00000002100	Mybpc3	-	myosin binding protein C, cardiac	protein-coding
mm_143752.1	chr17	81582167	81582184	-	1	NA	intron (NR_104580, intron 2 of 8)	intron (NR_104580, intron 2 of 8)	156212	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_143649.1	chr17	79451636	79451644	-	1	NA	Intergenic	Intergenic	26245	NR_033463	74622	Mm.311921	NR_033463		4930429F11Rik	-	RIKEN cDNA 4930429F11 gene	ncRNA
mm_43574.1	chr5	137745968	137746027	+	1	NA	promoter-TSS (NM_023910)	promoter-TSS (NM_023910)	28	NM_029805	78829	Mm.286399	NM_023910	ENSMUSG00000029723	Tsc22d4	0610009M14Rik|1700023B23Rik|AI415410|Thg-1pit|Tilz2	TSC22 domain family, member 4	protein-coding
mm_136488.1	chr16	96082730	96082740	-	1	NA	promoter-TSS (NM_145125)	promoter-TSS (NM_145125)	-307	NM_145125	93871	Mm.240871	NM_145125	ENSMUSG00000022914	Brwd1	5330419I02Rik|D530019K20Rik|G1-403-16|Wdr9|repro5	bromodomain and WD repeat domain containing 1	protein-coding
mm_23713.1	chr3	69004970	69005021	+	1	NA	promoter-TSS (NM_133786)	promoter-TSS (NM_133786)	23	NM_133786	70099	Mm.206841	NM_133786	ENSMUSG00000034349	Smc4	2500002A22Rik|C79747|SMC-4|Smc4l1	structural maintenance of chromosomes 4	protein-coding
mm_167476.1	chr8	128418812	128418836	+	1	NA	exon (NM_008737, exon 3 of 17)	exon (NM_008737, exon 3 of 17)	59583	NR_035436	100316680		NR_035436	ENSMUSG00000084523	Mir1903	Mirn1903|mmu-mir-1903	microRNA 1903	ncRNA
mm_96929.1	chr11	70511091	70511101	+	1	NA	TTS (NM_029360)	TTS (NM_029360)	3520	NM_001013607	327956	Mm.244514	NM_001013607	ENSMUSG00000020830	Vmo1	Gm741	vitelline membrane outer layer 1 homolog (chicken)	protein-coding
mm_163277.1	chr11	116021248	116021251	-	1	NA	TTS (NM_008211)	TTS (NM_008211)	3255	NM_008211	15081	Mm.18516	NM_008211	ENSMUSG00000016559	H3f3b	9430068D06Rik|H3.3B	H3 histone, family 3B	protein-coding
mm_33436.1	chr4	130107601	130107606	+	1	NA	promoter-TSS (NM_026441)	promoter-TSS (NM_026441)	47	NM_026441	67898	Mm.20818	NM_026441	ENSMUSG00000028779	Pef1	2600002E23Rik|Peflin	penta-EF hand domain containing 1	protein-coding
mm_142483.1	chr17	45733844	45733848	-	1	NA	promoter-TSS (NM_028164)	promoter-TSS (NM_028164)	-2	NM_028164	72240	Mm.482897	NM_028164	ENSMUSG00000094690	1600014C23Rik	-	RIKEN cDNA 1600014C23 gene	protein-coding
mm_954.1	chr1	57774843	57774932	+	1	NA	promoter-TSS (NM_144882)	promoter-TSS (NM_144882)	26	NM_144882	67198	Mm.159989	NM_144882	ENSMUSG00000038305	Spats2l	2810022L02Rik|A230104H11Rik|AA987173|AI480531|AI842453|AW413586	spermatogenesis associated, serine-rich 2-like	protein-coding
mm_33998.1	chr4	137913548	137913564	+	1	NA	intron (NM_199307, intron 2 of 19)	CpG	51319	NM_199307	230857	Mm.401062	NM_199307	ENSMUSG00000057530	Ece1	AW322500|ECE-1|ECE-1a|ECE-1b|ECE-1d	endothelin converting enzyme 1	protein-coding
mm_67290.1	chr7	78783027	78783057	-	1	NA	promoter-TSS (NM_026498)	promoter-TSS (NM_026498)	47	NM_023331	67308	Mm.193181	NM_023331	ENSMUSG00000030612	Mrpl46	3110052F15Rik|C15orf4|C80107|LIECG2|P2ECSL	mitochondrial ribosomal protein L46	protein-coding
mm_20650.1	chr2	132055928	132055944	-	1	NA	3' UTR (NM_018824, exon 16 of 16)	3' UTR (NM_018824, exon 16 of 16)	-25948	NM_175445	215653	Mm.204737	NM_175445	ENSMUSG00000027339	Rassf2	3830431H01Rik|9030412M04Rik|AI852669|AW495050	Ras association (RalGDS/AF-6) domain family member 2	protein-coding
mm_44301.1	chr5	8996619	8996632	-	1	NA	intron (NM_023733, intron 1 of 17)	intron (NM_023733, intron 1 of 17)	521	NM_023733	74114	Mm.28197	NM_023733	ENSMUSG00000003623	Crot	1200003H03Rik	carnitine O-octanoyltransferase	protein-coding
mm_68333.1	chr7	106504316	106504344	-	1	NA	Intergenic	L1_Mus1|LINE|L1	-63257	NR_003967	209380	Mm.461779	NM_001001318		Gm4759	EG209380	GTPase, very large interferon inducible 1 pseudogene	pseudo
mm_51934.1	chr6	91684062	91684132	+	1	NA	promoter-TSS (NM_009320)	promoter-TSS (NM_009320)	30	NM_009320	21366	Mm.395650	NM_009320	ENSMUSG00000030096	Slc6a6	AA589629|C80501|Taut	solute carrier family 6 (neurotransmitter transporter, taurine), member 6	protein-coding
mm_34807.1	chr4	154869643	154869658	+	1	NA	promoter-TSS (NM_013783)	promoter-TSS (NM_013783)	65	NM_013783	27390	Mm.116944	NM_013783	ENSMUSG00000058183	Mmel1	Mell1|NEP2|NEPII|Nl1|SEP	membrane metallo-endopeptidase-like 1	protein-coding
mm_38057.1	chr4	134004586	134004597	-	1	NA	3' UTR (NM_145833, exon 4 of 4)	3' UTR (NM_145833, exon 4 of 4)	-3727	NM_026144	67422	Mm.100290	NM_026144	ENSMUSG00000012117	Dhdds	3222401G21Rik|CIT|DS|HDS|W91638	dehydrodolichyl diphosphate synthase	protein-coding
mm_156156.1	chrX	129957282	129957304	+	1	NA	exon (NM_172493, exon 12 of 27)	exon (NM_172493, exon 12 of 27)	207551	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diaph2	Dia3|Diap2|Drf2|E430022I22Rik	diaphanous related formin 2	protein-coding
mm_84163.1	chr9	59565097	59565108	-	1	NA	TTS (NM_010421)	TTS (NM_010421)	-13235	NM_175235	76183	Mm.265415	NM_175235	ENSMUSG00000032297	Celf6	6330569O16Rik|Brunol6	CUGBP, Elav-like family member 6	protein-coding
mm_17654.1	chr2	32063246	32063259	-	1	NA	Intergenic	Intergenic	12306	NR_106135	102466844		NR_106135	ENSMUSG00000099075	Mir7674	Gm27563|mmu-mir-7674	microRNA 7674	ncRNA
mm_130209.1	chr15	95528578	95528640	-	1	NA	promoter-TSS (NM_001289653)	promoter-TSS (NM_001289653)	-357	NM_001289653	54003	Mm.3959	NM_016743	ENSMUSG00000022454	Nell2	A330108N19Rik|R75516|mel91	NEL-like 2	protein-coding
mm_43972.1	chr5	146079255	146079258	+	1	NA	promoter-TSS (NM_001105160)	promoter-TSS (NM_001105160)	-2	NM_001105160	100041449	Mm.301900	NM_001105160	ENSMUSG00000061292	Cyp3a59	ENSMUSG00000061292	cytochrome P450, family 3, subfamily a, polypeptide 59	protein-coding
mm_114525.1	chr13	73467349	73467349	+	1	NA	promoter-TSS (NM_145376)	promoter-TSS (NM_145376)	-34	NM_145376	210992	Mm.284649	NM_145376	ENSMUSG00000021608	Lpcat1	2900035H07Rik|Aytl2|BB137372|BC005662|C87117|LPCAT|rd11	lysophosphatidylcholine acyltransferase 1	protein-coding
mm_148491.1	chr19	4153705	4153773	+	1	NA	promoter-TSS (NM_016933)	promoter-TSS (NM_016933)	-907	NM_016933	19265	Mm.271937	NM_016933	ENSMUSG00000045826	Ptprcap	AI605264|CD-45-AP|LPAP|LSM-1	protein tyrosine phosphatase, receptor type, C polypeptide-associated protein	protein-coding
mm_78333.1	chr9	25252911	25252930	+	1	NA	intron (NM_001205367, intron 1 of 12)	CpG	481	NM_001205367	235072	Mm.270259	NM_009859	ENSMUSG00000001833	Sept7	Cdc10|E430034N22	septin 7	protein-coding
mm_55184.1	chr6	52164823	52164829	-	1	NA	promoter-TSS (NM_010451)	promoter-TSS (NM_010451)	5	NM_010451	15399	Mm.131	NM_010451	ENSMUSG00000014704	Hoxa2	AI324701|HOX1.11|Hox-1.11	homeobox A2	protein-coding
mm_23743.1	chr3	69340490	69340493	+	1	NA	intron (NM_178726, intron 1 of 3)	intron (NM_178726, intron 1 of 3)	23573	NM_178726	242083	Mm.40577	NM_178726	ENSMUSG00000027784	Ppm1l	3222401G13|5930404J21Rik|AI481720|AW045850|PP2C|PP2Cepsilon|Pp2ce|Ppp2ce|mKIAA4175	protein phosphatase 1 (formerly 2C)-like	protein-coding
mm_60358.1	chr7	44428791	44428816	+	1	NA	Intergenic	(TCC)n|Simple_repeat|Simple_repeat	-13684	NM_198250	272381	Mm.44173	NM_198250	ENSMUSG00000047085	Lrrc4b	A830007M12|Lrig4	leucine rich repeat containing 4B	protein-coding
mm_35144.1	chr4	11559192	11559202	-	1	NA	intron (NM_001039556, intron 1 of 14)	intron (NM_001039556, intron 1 of 14)	277	NM_001256145	623474	Mm.491200	NM_177285	ENSMUSG00000078773	Rad54b	E130016E03Rik	RAD54 homolog B (S. cerevisiae)	protein-coding
mm_153329.1	chr19	38124554	38124574	-	1	NA	exon (NM_011255, exon 2 of 6)	exon (NM_011255, exon 2 of 6)	247	NM_011255	19662	Mm.2605	NM_011255	ENSMUSG00000024990	Rbp4	Rbp-4	retinol binding protein 4, plasma	protein-coding
mm_72063.1	chr8	71469187	71469222	+	1	NA	promoter-TSS (NM_025600)	promoter-TSS (NM_025600)	10	NR_122114	66498	Mm.260360	NM_025600	ENSMUSG00000074247	Dda1	1500034J01Rik|1700095J19Rik|R74921	DET1 and DDB1 associated 1	protein-coding
mm_144055.1	chr17	90607072	90607083	-	1	NA	intron (NM_001346957, intron 9 of 18)	AT_rich|Low_complexity|Low_complexity	-151197	NM_001346959	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_166171.1	chr5	25181471	25181475	+	1	NA	promoter-TSS (NM_026449)	promoter-TSS (NM_026449)	-7	NM_026449	67909	Mm.141471	NM_026449	ENSMUSG00000028938	Galntl5	1700021B12Rik|Galnt15	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 5	protein-coding
mm_132113.1	chr16	31663842	31663912	+	1	NA	promoter-TSS (NM_001252434)	promoter-TSS (NM_001252434)	-58	NM_001252433	13383	Mm.382	NM_007862	ENSMUSG00000022770	Dlg1	B130052P05Rik|Dlgh1|E-dlg/SAP97|SAP-97|SAP97|mKIAA4187	discs, large homolog 1 (Drosophila)	protein-coding
mm_170464.1	chr1	89455396	89455415	+	1	NA	5' UTR (NM_178119, exon 1 of 18)	5' UTR (NM_178119, exon 1 of 18)	594	NM_001037136	347722	Mm.291135	NM_178119	ENSMUSG00000055013	Agap1	Centg2|Ggap1|R75364|mKIAA1099	ArfGAP with GTPase domain, ankyrin repeat and PH domain 1	protein-coding
mm_156919.1	chrX	169106660	169106709	+	1	NA	intron (NR_109847, intron 1 of 14)	intron (NR_109847, intron 1 of 14)	-6194	NM_001287530	11856	Mm.441810	NM_009707	ENSMUSG00000031355	Arhgap6	AI504284|RhoGAPX-1	Rho GTPase activating protein 6	protein-coding
mm_32584.1	chr4	111252533	111252533	+	1	NA	intron (NM_001048189, intron 5 of 12)	intron (NM_001048189, intron 5 of 12)	-162473	NR_033793	67621	Mm.45533	NM_026279	ENSMUSG00000028545	Bend5	2310026E23Rik	BEN domain containing 5	protein-coding
mm_155419.1	chrX	73490972	73490995	+	1	NA	exon (NM_007542, exon 2 of 8)	exon (NM_007542, exon 2 of 8)	7382	NM_007542	12111	Mm.2608	NM_007542	ENSMUSG00000031375	Bgn	BG|DSPG1|PG-S1|PGI|SLRR1A	biglycan	protein-coding
mm_100594.1	chr11	120990559	120990575	+	1	NA	intron (NM_027874, intron 1 of 9)	C-rich|Low_complexity|Low_complexity	766	NM_139059	104318	Mm.216227	NM_027874	ENSMUSG00000025162	Csnk1d	1200006A05Rik|AA409348|D930010H05Rik	casein kinase 1, delta	protein-coding
mm_25993.1	chr3	134236484	134236500	+	1	NA	promoter-TSS (NM_001004367)	promoter-TSS (NM_001004367)	-3	NM_001004367	319478	Mm.224814	NM_001004367	ENSMUSG00000044365	Cxxc4	9330210J02Rik|C030003J12Rik|Idax	CXXC finger 4	protein-coding
mm_132584.1	chr16	38362180	38362196	+	1	NA	promoter-TSS (NM_022318)	promoter-TSS (NM_022318)	-2	NM_001081984	64082	Mm.390856	NM_022318	ENSMUSG00000022803	Popdc2	AV006127|Pop2	popeye domain containing 2	protein-coding
mm_125088.1	chr15	27466701	27466721	+	1	NA	promoter-TSS (NM_020332)	promoter-TSS (NM_020332)	34	NM_020332	11732	Mm.265264	NM_020332	ENSMUSG00000022265	Ank	Ankh|D15Ertd221e|ank|mKIAA1581	progressive ankylosis	protein-coding
mm_150549.1	chr19	39321577	39321606	+	1	NA	exon (NM_007815, exon 6 of 9)	exon (NM_007815, exon 6 of 9)	34506	NM_007815	13095	Mm.20764	NM_007815	ENSMUSG00000003053	Cyp2c29	AHOH|AHOHase|AI159681|AI196010|Ah-2|Ahh-1|Cyp2c|P450-2C	cytochrome P450, family 2, subfamily c, polypeptide 29	protein-coding
mm_10023.1	chr1	192092421	192092425	-	1	NA	5' UTR (NM_011633, exon 1 of 10)	5' UTR (NM_011633, exon 1 of 10)	176	NM_011633	22033	Mm.380491	NM_011633		Traf5	-	TNF receptor-associated factor 5	protein-coding
mm_21360.1	chr2	157130020	157130034	-	1	NA	intron (NM_018851, intron 1 of 15)	intron (NM_018851, intron 1 of 15)	5195	NM_001139520	56045	Mm.248478	NM_018851	ENSMUSG00000027639	Samhd1	E330031J07Rik|Mg11	SAM domain and HD domain, 1	protein-coding
mm_62504.1	chr7	102065486	102065527	+	1	NA	promoter-TSS (NR_104582)	promoter-TSS (NR_104582)	15	NM_001286689	102443350	Mm.292904	NM_001286689	ENSMUSG00000070425	Xndc1	Xndr	Xrcc1 N-terminal domain containing 1	protein-coding
mm_53891.1	chr6	3377108	3377142	-	1	NA	exon (NM_010156, exon 2 of 2)	exon (NM_010156, exon 2 of 2)	22446	NM_010156	209086	Mm.196013	NM_010156	ENSMUSG00000047735	Samd9l	AA175286|ESTM25|mKIAA2005	sterile alpha motif domain containing 9-like	protein-coding
mm_68108.1	chr7	102019526	102019540	-	1	NA	TTS (NM_029211)	TTS (NM_029211)	-1378	NM_010531	16068	Mm.422756	NM_010531	ENSMUSG00000070427	Il18bp	IL-18BP|Igifbp|MC54L	interleukin 18 binding protein	protein-coding
mm_99555.1	chr11	103649499	103649521	+	1	NA	promoter-TSS (NM_001033212)	promoter-TSS (NM_001033212)	1	NM_001033212	104582	Mm.44618	NM_001033212	ENSMUSG00000046215	Rprml	AW049332	reprimo-like	protein-coding
mm_165456.1	chr2	158146344	158146352	-	1	NA	promoter-TSS (NM_009373)	promoter-TSS (NM_009373)	44	NM_009373	21817	Mm.330731	NM_009373	ENSMUSG00000037820	Tgm2	G[a]h|TG2|TGase2|tTG|tTGas	transglutaminase 2, C polypeptide	protein-coding
mm_113045.1	chr13	23575783	23575793	+	1	NA	promoter-TSS (NM_178204)	promoter-TSS (NM_178204)	25	NM_178204	319149	Mm.347699	NM_178204	ENSMUSG00000099583	Hist1h3d	H3-b	histone cluster 1, H3d	protein-coding
mm_118472.1	chr14	11570040	11570051	+	1	NA	intron (NM_008981, intron 1 of 29)	intron (NM_008981, intron 1 of 29)	16492	NM_008981	19270	Mm.431266	NM_008981	ENSMUSG00000021745	Ptprg	5430405N12Rik|AW046354|AW549872|RPTPgamma	protein tyrosine phosphatase, receptor type, G	protein-coding
mm_87123.1	chr10	33364351	33364352	+	1	NA	intron (NM_029726, intron 21 of 37)	intron (NM_029726, intron 21 of 37)	-107994	NR_040657	442820	Mm.490725	NR_040657		D830005E20Rik	-	RIKEN cDNA D830005E20 gene	ncRNA
mm_93719.1	chr10	119076181	119076192	-	1	NA	Intergenic	Intergenic	-16719	NR_045348	73400	Mm.416864	NR_045348	ENSMUSG00000100681	1700064J06Rik	-	RIKEN cDNA 1700064J06 gene	ncRNA
mm_142647.1	chr17	47502277	47502296	-	1	NA	promoter-TSS (NM_022015)	promoter-TSS (NM_022015)	1	NM_022015	63856	Mm.275901	NM_022015	ENSMUSG00000023980	Taf8	AW260255|Tbn	TATA-box binding protein associated factor 8	protein-coding
mm_5893.1	chr1	54439004	54439014	-	1	NA	promoter-TSS (NM_001033194)	promoter-TSS (NM_001033194)	17	NM_001033194	98488	Mm.25856	NM_001033194	ENSMUSG00000041303	Gtf3c3	TF3C-gamma|TFIIIC102	general transcription factor IIIC, polypeptide 3	protein-coding
mm_63509.1	chr7	127841948	127841962	+	1	NA	5' UTR (NM_009294, exon 1 of 11)	5' UTR (NM_009294, exon 1 of 11)	147	NM_009294	20909	Mm.24867	NM_009294	ENSMUSG00000030805	Stx4a	Stx4|Syn-4|Syn4	syntaxin 4A (placental)	protein-coding
mm_32662.1	chr4	115093583	115093608	+	1	NA	3' UTR (NM_001164557, exon 4 of 4)	3' UTR (NM_001164557, exon 4 of 4)	4887	NM_001164557	67182	Mm.30181	NM_026018	ENSMUSG00000028716	Pdzk1ip1	0610007F13Rik|2700030M23Rik|AU046042|Map17	PDZK1 interacting protein 1	protein-coding
mm_148285.1	chr18	82527787	82527791	-	1	NA	intron (NM_001025245, intron 3 of 3)	intron (NM_001025245, intron 3 of 3)	-26674	NM_001025256	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_73432.1	chr8	106137059	106137074	+	1	NA	promoter-TSS (NM_176838)	promoter-TSS (NM_176838)	-92	NM_176838	77411	Mm.183003	NM_176838	ENSMUSG00000084128	Esrp2	9530027K23Rik|Rbm35b	epithelial splicing regulatory protein 2	protein-coding
mm_141793.1	chr17	34342989	34343003	-	1	NA	exon (NM_010381, exon 3 of 4)	exon (NM_010381, exon 3 of 4)	1649	NM_010381	100504404	Mm.15680	NM_010381		H2-Ea-ps	AI323765|E-alpha-f|H-2Ea|H2-Ea|I-Ealpha|Ia-3|Ia3|MHC-H2-Ea	histocompatibility 2, class II antigen E alpha, pseudogene	protein-coding
mm_101247.1	chr11	20741848	20741908	-	1	NA	promoter-TSS (NM_001252503)	promoter-TSS (NM_001252503)	-322	NM_181411	216549	Mm.356580	NM_181411	ENSMUSG00000049659	Aftph	-	aftiphilin	protein-coding
mm_22400.1	chr2	181240693	181240710	-	1	NA	exon (NM_183162, exon 2 of 19)	exon (NM_183162, exon 2 of 19)	1326	NM_183162	229003	Mm.315872	NM_183162	ENSMUSG00000027580	Helz2	PDIP1|Pric285|mKIAA1769|mPDIP1	helicase with zinc finger 2, transcriptional coactivator	protein-coding
mm_58432.1	chr7	3297577	3297583	+	1	NA	exon (NM_016969, exon 3 of 3)	exon (NM_016969, exon 3 of 3)	4552	NM_001093766	50918	Mm.29874	NM_016969	ENSMUSG00000068566	Myadm	D7Wsu62e	myeloid-associated differentiation marker	protein-coding
mm_25408.1	chr3	107279067	107279071	+	1	NA	exon (NM_026774, exon 1 of 4)	exon (NM_026774, exon 1 of 4)	211	NM_026774	68576	Mm.290035	NM_026774	ENSMUSG00000087260	Lamtor5	1110003H18Rik|Hbxip|XIP	late endosomal/lysosomal adaptor, MAPK and MTOR activator 5	protein-coding
mm_53828.1	chr6	147531441	147531450	+	1	NA	intron (NM_025911, intron 3 of 12)	intron (NM_025911, intron 3 of 12)	55574	NM_025911	67015	Mm.209774	NM_025911	ENSMUSG00000030301	Ccdc91	1700086G08Rik|1810060J02Rik|AU045683|AW555238|p56	coiled-coil domain containing 91	protein-coding
mm_154829.1	chrX	18145883	18145883	+	1	NA	promoter-TSS (NM_028568)	promoter-TSS (NM_028568)	13	NM_028568	73547	Mm.159027	NM_028568	ENSMUSG00000025043	Dusp21	1700094E07Rik|DSP21	dual specificity phosphatase 21	protein-coding
mm_51903.1	chr6	91156716	91156738	+	1	NA	promoter-TSS (NM_144919)	promoter-TSS (NM_144919)	-88	NM_144919	232232	Mm.206218	NM_144919	ENSMUSG00000034245	Hdac11	-	histone deacetylase 11	protein-coding
mm_138790.1	chr17	37276056	37276094	+	1	NA	Intergenic	B3|SINE|B2	4343	NM_146515	258508	Mm.377544	NM_146515	ENSMUSG00000061972	Olfr99	MOR156-1	olfactory receptor 99	protein-coding
mm_103256.1	chr11	70992541	70992570	-	1	NA	intron (NM_178367, intron 9 of 11)	intron (NM_178367, intron 9 of 11)	-9529	NM_007573	12261	Mm.30049	NM_007573	ENSMUSG00000018446	C1qbp	AA407365|AA986492|D11Wsu182e|HABP1|P32|gC1qBP	complement component 1, q subcomponent binding protein	protein-coding
mm_120917.1	chr14	76414978	76414996	+	1	NA	promoter-TSS (NM_207652)	promoter-TSS (NM_207652)	26	NM_001310646	21807	Mm.153272	NM_009366	ENSMUSG00000022010	Tsc22d1	AA589566|AW105905|Egr5|TSC-22|Tgfb1i4|Tsc|Tsc22	TSC22 domain family, member 1	protein-coding
mm_111888.1	chr12	108275195	108275217	-	1	NA	5' UTR (NM_001159910, exon 1 of 6)	5' UTR (NM_001159910, exon 1 of 6)	211	NM_001159910	668158	Mm.482792	NM_001159910	ENSMUSG00000084883	Ccdc85c	EG668158|Gm265|Gm9010	coiled-coil domain containing 85C	protein-coding
mm_154831.1	chrX	18162665	18162682	+	1	NA	promoter-TSS (NM_009483)	promoter-TSS (NM_009483)	98	NM_001310444	22289	Mm.257498	NM_009483	ENSMUSG00000037369	Kdm6a	Utx	lysine (K)-specific demethylase 6A	protein-coding
mm_171806.1	chr5	129128547	129128548	-	1	NA	intron (NM_001347486, intron 5 of 24)	intron (NM_001347486, intron 5 of 24)	31797	NM_001347486	243277	Mm.440501	NM_177734	ENSMUSG00000044017	Adgrd1	E230012M21Rik|Gpr133	adhesion G protein-coupled receptor D1	protein-coding
mm_22646.1	chr3	14866854	14866871	+	1	NA	exon (NM_007606, exon 3 of 7)	exon (NM_007606, exon 3 of 7)	3324	NM_007606	12350	Mm.300	NM_007606	ENSMUSG00000027559	Car3	BB219044|Ca3|Car-3	carbonic anhydrase 3	protein-coding
mm_166886.1	chr7	28085346	28085358	-	1	NA	exon (NM_001122603, exon 4 of 20)	exon (NM_001122603, exon 4 of 20)	14116	NM_001122603	215384	Mm.292276	NM_175444	ENSMUSG00000047730	Fcgbp	A430096B05Rik	Fc fragment of IgG binding protein	protein-coding
mm_119032.1	chr14	30485072	30485087	+	1	NA	intron (NM_133761, intron 3 of 9)	intron (NM_133761, intron 3 of 9)	5514	NM_133761	75901	Mm.28733	NM_133761	ENSMUSG00000021962	Dcp1a	1110066A22Rik|4930568L04Rik|AU019772|D14Ertd817e|Mitc1|SMIF	decapping mRNA 1A	protein-coding
mm_20427.1	chr2	129304814	129304855	-	1	NA	exon (NM_010554, exon 5 of 7)	exon (NM_010554, exon 5 of 7)	5138	NM_010554	16175	Mm.15534	NM_010554	ENSMUSG00000027399	Il1a	Il-1a	interleukin 1 alpha	protein-coding
mm_135226.1	chr16	36784933	36784971	-	1	NA	promoter-TSS (NM_021301)	promoter-TSS (NM_021301)	10	NM_001145899	57738	Mm.281804	NM_021301	ENSMUSG00000022899	Slc15a2	8430408C16Rik|C78862|Pept2	solute carrier family 15 (H+/peptide transporter), member 2	protein-coding
mm_169456.1	chr14	63193856	63193869	-	1	NA	promoter-TSS (NM_201610)	promoter-TSS (NM_201610)	-337	NM_201610	382913	Mm.239490	NM_201610	ENSMUSG00000035121	Neil2	Gm1212|NEH2	nei like 2 (E. coli)	protein-coding
mm_61254.1	chr7	65862127	65862140	+	1	NA	promoter-TSS (NM_001291184)	promoter-TSS (NM_001291184)	-3	NM_001291184	18553	Mm.294007	NM_011048	ENSMUSG00000030513	Pcsk6	C86343|Pace4|SPC4	proprotein convertase subtilisin/kexin type 6	protein-coding
mm_60193.1	chr7	43408263	43408273	+	1	NA	promoter-TSS (NM_172900)	promoter-TSS (NM_172900)	-12	NM_172900	243958	Mm.24444	NM_172900	ENSMUSG00000030468	Siglecg	9830164H23|A630096C01Rik|Siglec-G|Siglec10|mSiglec-G	sialic acid binding Ig-like lectin G	protein-coding
mm_130477.1	chr15	98728121	98728187	-	1	NA	promoter-TSS (NM_024169)	promoter-TSS (NM_024169)	44	NM_024169	66120	Mm.30729	NM_024169	ENSMUSG00000003355	Fkbp11	1110002O23Rik|FKBP-11	FK506 binding protein 11	protein-coding
mm_20668.1	chr2	132145340	132145368	-	1	NA	promoter-TSS (NM_018824)	promoter-TSS (NM_018824)	-246	NM_018824	54338	Mm.103581	NM_018824	ENSMUSG00000027340	Slc23a2	AI844736|NBTL1|SVCT2|Slc23a1|YSPL2|YSPL3|mKIAA0238	solute carrier family 23 (nucleobase transporters), member 2	protein-coding
mm_87145.1	chr10	34483631	34483644	+	1	NA	5' UTR (NM_001159544, exon 1 of 8)	5' UTR (NM_001159544, exon 1 of 8)	237	NM_010237	14302	Mm.332432	NM_010237	ENSMUSG00000019779	Frk	BSK|BSK/IYK|C85044|GTK|RAK	fyn-related kinase	protein-coding
mm_173356.1	chrY	90819314	90819316	+	1	NA	Intergenic	(CAGAGA)n|Simple_repeat|Simple_repeat	20091	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_172057.1	chr6	129059796	129059809	+	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	13901	NR_024263	232408	Mm.259262	NM_153094	ENSMUSG00000030154	Klrb1f	A630024B12Rik|Nkr-p1f|Nkrp1-f|Nkrp1f	killer cell lectin-like receptor subfamily B member 1F	protein-coding
mm_9033.1	chr1	166946417	166946417	-	1	NA	Intergenic	Intergenic	53313	NR_037988	100503962	Mm.216842	NR_037988	ENSMUSG00000102548	Gm16701	-	predicted gene, 16701	ncRNA
mm_87866.1	chr10	61297800	61297808	+	1	NA	promoter-TSS (NM_011073)	promoter-TSS (NM_011073)	-32	NM_011073	18646	Mm.240313	NM_011073	ENSMUSG00000037202	Prf1	Pfn|Pfp|Prf-1	perforin 1 (pore forming protein)	protein-coding
mm_97871.1	chr11	83176049	83176056	+	1	NA	intron (NM_011410, intron 3 of 7)	T-rich|Low_complexity|Low_complexity	866	NM_001302559	20558	Mm.38192	NM_011410	ENSMUSG00000000204	Slfn4	AI450778	schlafen 4	protein-coding
mm_76952.1	chr8	105991742	105991752	-	1	NA	promoter-TSS (NM_001301204)	promoter-TSS (NM_001301204)	26	NM_001301204	319446	Mm.248357	NM_176913	ENSMUSG00000053687	Dpep2	F630103D06Rik|MBD-2	dipeptidase 2	protein-coding
mm_30225.1	chr3	145648711	145648728	-	1	NA	exon (NM_010516, exon 3 of 5)	exon (NM_010516, exon 3 of 5)	1266	NM_010516	16007	Mm.1231	NM_010516	ENSMUSG00000028195	Cyr61	AI325051|CCN1|Igfbp10	cysteine rich protein 61	protein-coding
mm_73150.1	chr8	94994239	94994327	+	1	NA	intron (NM_018882, intron 1 of 13)	intron (NM_018882, intron 1 of 13)	9884	NM_018882	14766	Mm.290834	NM_018882	ENSMUSG00000031785	Adgrg1	Cyt28|Gpr56|TM7LN4|TM7XN1	adhesion G protein-coupled receptor G1	protein-coding
mm_96553.1	chr11	68888595	68888605	+	1	NA	promoter-TSS (NM_177060)	promoter-TSS (NM_177060)	47	NM_177060	320040	Mm.305696	NM_177060	ENSMUSG00000046490	Rnf222	9930039A11Rik	ring finger protein 222	protein-coding
mm_14657.1	chr2	137194355	137194357	+	1	NA	Intergenic	Intergenic	-77836	NM_013822	16449	Mm.22398	NM_013822	ENSMUSG00000027276	Jag1	ABE2|Gsfabe2|Htu|Ozz|Ser-1	jagged 1	protein-coding
mm_120703.1	chr14	70977264	70977273	+	1	NA	exon (NM_008115, exon 8 of 9)	exon (NM_008115, exon 8 of 9)	87161	NM_001302094	14586	Mm.32619	NM_008115	ENSMUSG00000022103	Gfra2	-	glial cell line derived neurotrophic factor family receptor alpha 2	protein-coding
mm_145892.1	chr18	65583183	65583194	+	1	NA	intron (NM_207255, intron 2 of 5)	intron (NM_207255, intron 2 of 5)	2958	NM_207255	328977	Mm.286232	NM_207255	ENSMUSG00000042439	Zfp532	C530030I18Rik|Znf532|mKIAA1629	zinc finger protein 532	protein-coding
mm_140328.1	chr17	86754085	86754093	+	1	NA	5' UTR (NM_010137, exon 1 of 16)	5' UTR (NM_010137, exon 1 of 16)	225	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_172231.1	chr6	67625954	67625980	-	1	NA	Intergenic	L1Md_T|LINE|L1	-60268	NR_003100	75070	Mm.463364	NR_003100		4930515G16Rik	-	myc induced nuclear antigen pseudogene	pseudo
mm_94276.1	chr11	3923759	3923773	+	1	NA	exon (NM_001130458, exon 6 of 10)	exon (NM_001130458, exon 6 of 10)	8195	NM_001130459	21452	Mm.20948	NM_015749	ENSMUSG00000020432	Tcn2	AW208754|Tcn-2	transcobalamin 2	protein-coding
mm_169460.1	chr1	46416310	46416326	+	1	NA	Intergenic	Intergenic	-9200	NM_001310335	100101919	Mm.383402	NM_001310335	ENSMUSG00000101337	Dnah7c	Dnahc7c	dynein, axonemal, heavy chain 7C	protein-coding
mm_15366.1	chr2	156421076	156421076	+	1	NA	5' UTR (NM_001291121, exon 1 of 22)	5' UTR (NM_001291121, exon 1 of 22)	167	NM_001291123	13821	Mm.20852	NM_013510	ENSMUSG00000027624	Epb41l1	4.1N|Epb4.1l1|NBL1|mKIAA0338	erythrocyte membrane protein band 4.1 like 1	protein-coding
mm_32724.1	chr4	116557122	116557141	+	1	NA	promoter-TSS (NM_029868)	promoter-TSS (NM_029868)	-596	NM_029868	77110	Mm.41715	NM_029868	ENSMUSG00000034042	Gpbp1l1	5330440M15Rik|BC002292	GC-rich promoter binding protein 1-like 1	protein-coding
mm_74772.1	chr8	21702710	21702729	-	1	NA	exon (NM_001007582, exon 2 of 2)	exon (NM_001007582, exon 2 of 2)	928	NM_001007582	382000	Mm.14269	NM_001007582	ENSMUSG00000058618	AY761184	CRS1C-3|CRS1C-6	cDNA sequence AY761184	protein-coding
mm_67247.1	chr7	75309278	75309289	-	1	NA	promoter-TSS (NM_153579)	promoter-TSS (NM_153579)	-21	NM_153579	64176	Mm.273082	NM_153579	ENSMUSG00000053025	Sv2b	A830038F04Rik|AI850768|mKIAA0735	synaptic vesicle glycoprotein 2 b	protein-coding
mm_20607.1	chr2	131562489	131562502	-	1	NA	promoter-TSS (NM_013460)	promoter-TSS (NM_013460)	-210	NM_013460	11550	Mm.389380	NM_013460	ENSMUSG00000027335	Adra1d	Adra-1|Adra1|Adra1a|Gpcr8|Spr8|[a]1d|alpha1D-AR	adrenergic receptor, alpha 1d	protein-coding
mm_50342.1	chr6	48540489	48540500	+	1	NA	exon (NM_001347164, exon 3 of 3)	exon (NM_001347164, exon 3 of 3)	2925	NM_133764	76252	Mm.30214	NM_133764	ENSMUSG00000039347	Atp6v0e2	0610006O14Rik|NM9.2	ATPase, H+ transporting, lysosomal V0 subunit E2	protein-coding
mm_97660.1	chr11	79579145	79579154	+	1	NA	3' UTR (NM_010897, exon 58 of 58)	3' UTR (NM_010897, exon 58 of 58)	-12063	NM_175543	268451	Mm.130656	NM_175543	ENSMUSG00000017639	Rab11fip4	A730072L08Rik|RAB11-FIP4|mKIAA1821	RAB11 family interacting protein 4 (class II)	protein-coding
mm_72589.1	chr8	84338676	84338681	+	1	NA	Intergenic	Intergenic	-68276	NM_026350	67736	Mm.30095	NM_026350	ENSMUSG00000004994	Ccdc130	4930527D15Rik|C77430	coiled-coil domain containing 130	protein-coding
mm_78473.1	chr9	32679746	32679755	+	1	NA	Intergenic	L1MB8|LINE|L1	-16292	NM_011808	23871	Mm.292415	NM_011808	ENSMUSG00000032035	Ets1	AI196000|AI448617|D230050P06|Ets-1|Tpl1|vs	E26 avian leukemia oncogene 1, 5' domain	protein-coding
mm_1238.1	chr1	62796033	62796078	+	1	NA	3' UTR (NM_001077407, exon 16 of 16)	3' UTR (NM_001077407, exon 16 of 16)	-1323	NR_040601	74992	Mm.401979	NR_040601		4930487H11Rik	-	RIKEN cDNA 4930487H11 gene	ncRNA
mm_93581.1	chr10	116919640	116919658	-	1	NA	exon (NM_001003950, exon 4 of 10)	exon (NM_001003950, exon 4 of 10)	-22770	NM_001033333	237558	Mm.336386	NM_001033333	ENSMUSG00000034057	Myrfl	Gm239	myelin regulatory factor-like	protein-coding
mm_57287.1	chr6	124431602	124431610	-	1	NA	exon (NM_153508, exon 18 of 18)	exon (NM_153508, exon 18 of 18)	-16539	NM_001277805	19305	Mm.22418	NM_008995	ENSMUSG00000005069	Pex5	AW212715|ESTM1|PTS1R|Pxr1|X83306	peroxisomal biogenesis factor 5	protein-coding
mm_144229.1	chr18	10324918	10324950	+	1	NA	promoter-TSS (NM_001083628)	promoter-TSS (NM_001083628)	-245	NM_001083628	381157	Mm.261535	NM_001083628	ENSMUSG00000042942	Greb1l	mKIAA4095	growth regulation by estrogen in breast cancer-like	protein-coding
mm_132639.1	chr16	39984546	39984556	+	1	NA	Intergenic	CpG	1082206	NM_170599	207683	Mm.245564	NM_170599	ENSMUSG00000022790	Igsf11	1700025L02Rik|BT-IgSF|Igsf13	immunoglobulin superfamily, member 11	protein-coding
mm_62927.1	chr7	118600209	118600234	+	1	NA	5' UTR (NM_001105252, exon 2 of 22)	5' UTR (NM_001105252, exon 2 of 22)	2924	NM_001105252	74424	Mm.11068	NM_028930	ENSMUSG00000030650	Tmc5	4932443L08Rik|AU016085	transmembrane channel-like gene family 5	protein-coding
mm_56758.1	chr6	116101830	116101838	-	1	NA	intron (NM_177412, intron 3 of 5)	intron (NM_177412, intron 3 of 5)	91540	NM_177412	330401	Mm.425352	NM_177412	ENSMUSG00000030126	Tmcc1	3632431M01Rik|mKIAA0779	transmembrane and coiled coil domains 1	protein-coding
mm_119466.1	chr14	47277041	47277045	+	1	NA	promoter-TSS (NM_080843)	promoter-TSS (NM_080843)	-100	NM_080843	67296	Mm.23957	NM_080843	ENSMUSG00000048379	Socs4	3110032M18Rik|A730004F22Rik|AI427843|AU015727|AU015859|Socs7	suppressor of cytokine signaling 4	protein-coding
mm_112008.1	chr12	110889774	110889804	-	1	NA	promoter-TSS (NM_026048)	promoter-TSS (NM_026048)	525	NM_001081057	104859	Mm.35583	NM_175336	ENSMUSG00000021275	Tecpr2	4930573I19Rik|AI604920|mKIAA0297	tectonin beta-propeller repeat containing 2	protein-coding
mm_36066.1	chr4	57916312	57916324	-	1	NA	promoter-TSS (NM_178727)	promoter-TSS (NM_178727)	-54	NM_178727	242484	Mm.23214	NM_178727	ENSMUSG00000052117	D630039A03Rik	-	RIKEN cDNA D630039A03 gene	protein-coding
mm_140779.1	chr17	17877536	17877552	-	1	NA	exon (NM_013521, exon 2 of 2)	exon (NM_013521, exon 2 of 2)	6395	NM_013521	14293	Mm.56951	NM_013521	ENSMUSG00000045551	Fpr1	FPR|LXA4R|fMLF-R	formyl peptide receptor 1	protein-coding
mm_93805.1	chr10	120899068	120899076	-	1	NA	promoter-TSS (NM_177092)	promoter-TSS (NM_177092)	-101	NM_177092	320183	Mm.169755	NM_177092	ENSMUSG00000051236	Msrb3	D430026P16Rik|I-8-23|MsrB2	methionine sulfoxide reductase B3	protein-coding
mm_5790.1	chr1	51896036	51896045	-	1	NA	intron (NM_001290982, intron 1 of 28)	intron (NM_001290982, intron 1 of 28)	19938	NM_001290982	17912	Mm.3390	NM_010863	ENSMUSG00000018417	Myo1b	AA406997|MIH-L|MMIa	myosin IB	protein-coding
mm_7636.1	chr1	127859030	127859045	-	1	NA	Intergenic	Intergenic	-9736	NM_178690	226407	Mm.489713	NM_178690	ENSMUSG00000036104	Rab3gap1	1700003B17Rik|4732493F09Rik|AL117896|Rab3gap|p130	RAB3 GTPase activating protein subunit 1	protein-coding
mm_168645.1	chr1	185172154	185172159	-	1	NA	Intergenic	RLTR1B|LTR|ERV1	-32012	NM_001163754	98732	Mm.275841	NM_172649	ENSMUSG00000039318	Rab3gap2	1110059F07Rik|2010002H18Rik|5830469C09|AI851069|AW743433|RAB3-GAP150|mKIAA0839	RAB3 GTPase activating protein subunit 2	protein-coding
mm_66840.1	chr7	48881642	48881671	-	1	NA	promoter-TSS (NM_001013368)	promoter-TSS (NM_001013368)	-615	NM_001013368	108961	Mm.240566	NM_001013368	ENSMUSG00000046179	E2f8	4432406C08Rik|AA410048	E2F transcription factor 8	protein-coding
mm_103274.1	chr11	72135738	72135775	-	1	NA	5' UTR (NM_001081641, exon 1 of 19)	5' UTR (NM_001081641, exon 1 of 19)	133	NM_001024927	327958	Mm.351793	NM_001024927	ENSMUSG00000040543	Pitpnm3	A330068P14Rik|AI848332|Ackr6|Gm880	PITPNM family member 3	protein-coding
mm_155956.1	chrX	105120362	105120429	+	1	NA	promoter-TSS (NM_053201)	promoter-TSS (NM_053201)	17	NM_053201	107528	Mm.24341	NM_053201	ENSMUSG00000031227	Magee1	AI847422|DAMAGE|mMage-e1	melanoma antigen, family E, 1	protein-coding
mm_73001.1	chr8	93810791	93810801	+	1	NA	promoter-TSS (NM_010308)	promoter-TSS (NM_010308)	-42	NM_010308	14681	Mm.251445	NM_010308	ENSMUSG00000031748	Gnao1	AW050213|Galphao|Gnao|alphaO	guanine nucleotide binding protein, alpha O	protein-coding
mm_146306.1	chr18	80256250	80256297	+	1	NA	promoter-TSS (NM_001164424)	promoter-TSS (NM_001164424)	-33	NM_025861	66943	Mm.29247	NM_025861	ENSMUSG00000034006	Pqlc1	2310009N05Rik|4933425L21Rik|5730564E11Rik|C78974	PQ loop repeat containing 1	protein-coding
mm_82756.1	chr9	26860879	26860894	-	1	NA	promoter-TSS (NM_001113323)	promoter-TSS (NM_001113323)	-63	NM_001113323	70893	Mm.78118	NM_001113323	ENSMUSG00000031966	Glb1l3	4921509F24Rik	galactosidase, beta 1 like 3	protein-coding
mm_52473.1	chr6	114248377	114248402	+	1	NA	3' UTR (NM_172890, exon 14 of 14)	3' UTR (NM_172890, exon 14 of 14)	-34246	NM_178703	232333	Mm.5260	NM_178703	ENSMUSG00000030310	Slc6a1	A730043E01|GABATHG|GABATR|GAT-1|Gabt|Gabt1|Gat1|XT-1|Xtrp1	solute carrier family 6 (neurotransmitter transporter, GABA), member 1	protein-coding
mm_38127.1	chr4	134563444	134563454	-	1	NA	3' UTR (NM_207237, exon 12 of 12)	3' UTR (NM_207237, exon 12 of 12)	4402	NR_105829	102465216		NR_105829	ENSMUSG00000099289	Mir6403	Gm27992|mmu-mir-6403	microRNA 6403	ncRNA
mm_52442.1	chr6	113624668	113624678	+	1	NA	intron (NM_009507, intron 1 of 2)	intron (NM_009507, intron 1 of 2)	652	NM_009507	22346	Mm.29407	NM_009507	ENSMUSG00000033933	Vhl	Vhlh	von Hippel-Lindau tumor suppressor	protein-coding
mm_147958.1	chr18	67061330	67061335	-	1	NA	Intergenic	AT_rich|Low_complexity|Low_complexity	-26966	NM_177137	14680	Mm.440746	NM_010307	ENSMUSG00000024524	Gnal	2610011C15Rik|9630020G10Rik|Galphaolf|Gna10|Golf	guanine nucleotide binding protein, alpha stimulating, olfactory type	protein-coding
mm_163742.1	chr13	119727778	119727787	-	1	NA	exon (NM_175538, exon 2 of 4)	exon (NM_175538, exon 2 of 4)	28100	NM_175538	245269	Mm.403943	NM_175538	ENSMUSG00000095930	Nim1k	E130304F04Rik|Nim1	NIM1 serine/threonine protein kinase	protein-coding
mm_158108.1	chrX	102071301	102071322	-	1	NA	promoter-TSS (NM_001278534)	promoter-TSS (NM_001278534)	-4	NM_001278534	331474	Mm.23297	NM_183318	ENSMUSG00000049191	Rgag4	6430402L03Rik|Mar5|Mart5|mKIAA2001	retrotransposon gag domain containing 4	protein-coding
mm_85966.1	chr9	112141398	112141401	-	1	NA	intron (NM_001177617, intron 10 of 14)	intron (NM_001177617, intron 10 of 14)	-22688	NR_029823	723815		NR_029823	ENSMUSG00000065441	Mir128-2	Mirn128-2|Mirn128b|mir-128-2|mir-128b	microRNA 128-2	ncRNA
mm_53225.1	chr6	127130229	127130241	+	1	NA	3' UTR (NM_009829, exon 5 of 5)	3' UTR (NM_009829, exon 5 of 5)	-19154	NR_040274	77558	Mm.358918	NR_040273	ENSMUSG00000097166	9330179D12Rik	-	RIKEN cDNA 9330179D12 gene	ncRNA
mm_140142.1	chr17	79999877	79999887	+	1	NA	Intergenic	Intergenic	62386	NM_144802	72692	Mm.64579	NM_144802	ENSMUSG00000024095	Hnrnpll	2510028H02Rik|2810036L13Rik|AI256697|AI852082|Hnrpll	heterogeneous nuclear ribonucleoprotein L-like	protein-coding
mm_99853.1	chr11	109362927	109362977	+	1	NA	5' UTR (NM_010303, exon 1 of 4)	5' UTR (NM_010303, exon 1 of 4)	158	NM_010303	14674	Mm.193925	NM_010303	ENSMUSG00000020611	Gna13	AU024132|AU043124|Galpha13	guanine nucleotide binding protein, alpha 13	protein-coding
mm_51469.1	chr6	82960210	82960218	+	1	NA	intron (NM_033079, intron 2 of 9)	MLT1F1|LTR|ERVL-MaLR	13292	NM_033079	110958	Mm.100652	NM_033079	ENSMUSG00000030041	M1ap	D6Mm5e	meiosis 1 associated protein	protein-coding
mm_131364.1	chr16	13780771	13780781	+	1	NA	promoter-TSS (NM_001039521)	promoter-TSS (NM_001039521)	77	NM_001039521	106298	Mm.288606	NM_001039521	ENSMUSG00000022682	Rrn3	AL023001|E130302O19Rik|R75565|TIF-1A|Tif1a	RRN3 RNA polymerase I transcription factor homolog (yeast)	protein-coding
mm_33716.1	chr4	134019440	134019450	+	1	NA	promoter-TSS (NM_145833)	promoter-TSS (NM_145833)	-629	NM_145833	83557	Mm.302567	NM_145833	ENSMUSG00000050966	Lin28a	AL024421|ENSMUSG00000070700|Gm10299|Lin-28|Lin28|Tex17|lin-28A	lin-28 homolog A (C. elegans)	protein-coding
mm_55277.1	chr6	54241894	54241912	-	1	NA	intron (NM_001163640, intron 6 of 12)	intron (NM_001163640, intron 6 of 12)	-22955	NM_001311133	69993	Mm.321147	NM_023543	ENSMUSG00000004633	Chn2	1700026N20Rik|4930557O16Rik|ARHGAP3|Bch	chimerin 2	protein-coding
mm_90533.1	chr10	128086326	128086349	+	1	NA	TTS (NR_030442)	TTS (NR_030442)	1051	NR_030442	751518		NR_030442	ENSMUSG00000093245	Mir677	Mirn677|mir-677|mmu-mir-677	microRNA 677	ncRNA
mm_157072.1	chrX	8206476	8206547	-	1	NA	promoter-TSS (NM_145907)	promoter-TSS (NM_145907)	14	NM_145907	53627	Mm.443425	NM_016913	ENSMUSG00000031169	Porcn	2410004O13Rik|AW045557|DXHXS7465e|Mg61|Mporc|Ppn|mMg61|porc	porcupine homolog (Drosophila)	protein-coding
mm_80611.1	chr9	88286796	88286815	+	1	NA	Intergenic	Intergenic	-40804	NM_011851	23959	Mm.244235	NM_011851	ENSMUSG00000032420	Nt5e	2210401F01Rik|5'-NT|AI447961|CD73|NT|Nt5|eNT	5' nucleotidase, ecto	protein-coding
mm_34205.1	chr4	140924289	140924311	+	1	NA	intron (NM_008812, intron 3 of 15)	intron (NM_008812, intron 3 of 15)	17940	NM_008812	18600	Mm.2296	NM_008812	ENSMUSG00000028927	Padi2	Pdi|Pdi2|mKIAA0994	peptidyl arginine deiminase, type II	protein-coding
mm_73435.1	chr8	106150360	106150417	+	1	NA	promoter-TSS (NM_133792)	promoter-TSS (NM_133792)	-11	NM_133792	192654	Mm.284770	NM_133792	ENSMUSG00000031903	Pla2g15	ACS|C87498|LLPL|Lpla2|Lypla3	phospholipase A2, group XV	protein-coding
mm_151411.1	chr19	56593686	56593696	+	1	NA	exon (NM_025811, exon 9 of 11)	exon (NM_025811, exon 9 of 11)	45430	NM_025811	66866	Mm.46346	NM_025811	ENSMUSG00000025078	Nhlrc2	1200003G01Rik|AI835049|AV002846|AW496455	NHL repeat containing 2	protein-coding
mm_66801.1	chr7	47133646	47133656	-	1	NA	promoter-TSS (NM_013643)	promoter-TSS (NM_013643)	33	NM_013643	19259	Mm.4654	NM_013643	ENSMUSG00000030854	Ptpn5	Step	protein tyrosine phosphatase, non-receptor type 5	protein-coding
mm_48268.1	chr5	137962912	137962931	-	1	NA	promoter-TSS (NM_080450)	promoter-TSS (NM_080450)	38	NM_080450	118446	Mm.332771	NM_080450	ENSMUSG00000056966	Gjc3	Cx29|Gje1	gap junction protein, gamma 3	protein-coding
mm_138705.1	chr17	36023853	36023875	+	1	NA	intron (NR_015618, intron 1 of 1)	intron (NR_015618, intron 1 of 1)	-3304	NM_008207	15042	Mm.439654	NM_008207	ENSMUSG00000053835	H2-T24	H-2T24	histocompatibility 2, T region locus 24	protein-coding
mm_39478.1	chr5	20497090	20497090	+	1	NA	intron (NM_001170746, intron 10 of 22)	intron (NM_001170746, intron 10 of 22)	385034	NM_172992	68770	Mm.86410	NM_172992	ENSMUSG00000039987	Phtf2	1110054G21Rik|9530062N20Rik|AI447096|C77923	putative homeodomain transcription factor 2	protein-coding
mm_121747.1	chr14	18893624	18893647	-	1	NA	promoter-TSS (NM_144839)	promoter-TSS (NM_144839)	-8	NM_144839	218793	Mm.23551	NM_144839	ENSMUSG00000058317	Ube2e2	BC016265	ubiquitin-conjugating enzyme E2E 2	protein-coding
mm_112551.1	chr13	12460671	12460697	+	1	NA	intron (NM_018886, intron 1 of 9)	intron (NM_018886, intron 1 of 9)	1054	NM_001291060	56048	Mm.474138	NM_018886	ENSMUSG00000057554	Lgals8	1200015E08Rik|AI326142|D13Ertd524e|Lgals-8	lectin, galactose binding, soluble 8	protein-coding
mm_69655.1	chr7	139958038	139958040	-	1	NA	promoter-TSS (NR_029589)	promoter-TSS (NR_029589)	-279	NR_029589	387198		NR_029589	ENSMUSG00000065502	Mir202	Mirn202|mir-202|mmu-mir-202	microRNA 202	ncRNA
mm_101237.1	chr11	20656880	20656905	-	1	NA	Intergenic	Intergenic	24915	NM_001038625	58172	Mm.339676	NM_021372	ENSMUSG00000049800	Sertad2	AB041541|AU021878|Kiaa0127|MNCb-1504|SEI-2|Sei2|TRIP-Br2|mKIAA0127	SERTA domain containing 2	protein-coding
mm_2217.1	chr1	89866397	89866401	+	1	NA	intron (NM_001037136, intron 15 of 16)	intron (NM_001037136, intron 15 of 16)	64777	NM_010262	14472	Mm.204730	NM_010262	ENSMUSG00000034486	Gbx2	D130058E05Rik|Gbx-2|MMoxA|Stra7	gastrulation brain homeobox 2	protein-coding
mm_158666.1	chrX	157518584	157518600	-	1	NA	Intergenic	Intergenic	-22212	NR_040420	625253	Mm.463485	NR_040420		Gm6568	EG625253	DnaJ (Hsp40) homolog, subfamily B, member 9 pseudogene	pseudo
mm_15804.1	chr2	164486068	164486095	+	1	NA	promoter-TSS (NM_001048227)	promoter-TSS (NM_001048227)	-59	NM_001048227	52840	Mm.256927	NM_026797	ENSMUSG00000017734	Dbndd2	1110017A21Rik|2900022J10Rik|AU041050|AW048677|D2Bwg0891e|Nkip|R74724	dysbindin (dystrobrevin binding protein 1) domain containing 2	protein-coding
mm_63180.1	chr7	125489006	125489010	+	1	NA	intron (NM_026330, intron 1 of 7)	L1ME3E|LINE|L1	2534	NM_026330	67711	Mm.4467	NM_026330	ENSMUSG00000030750	Nsmce1	2510027N19Rik	NSE1 homolog, SMC5-SMC6 complex component	protein-coding
mm_156215.1	chrX	134686549	134686569	+	1	NA	promoter-TSS (NR_045454)	promoter-TSS (NR_045454)	40	NM_001202500	100503043	Mm.31961	NM_001202500	ENSMUSG00000049804	Armcx4	AI448196|Gm195	armadillo repeat containing, X-linked 4	protein-coding
mm_133660.1	chr16	91835435	91835437	+	1	NA	intron (NM_001110275, intron 16 of 28)	intron (NM_001110275, intron 16 of 28)	96194	NM_138597	28080	Mm.41	NM_138597	ENSMUSG00000022956	Atp5o	ATPO|D12Wsu28e|OSCP	ATP synthase, H+ transporting, mitochondrial F1 complex, O subunit	protein-coding
mm_129613.1	chr15	79971122	79971129	-	1	NA	Intergenic	Intergenic	27901	NR_106072	102465699		NR_106072	ENSMUSG00000099222	Mir7213	Gm27377|mmu-mir-7213	microRNA 7213	ncRNA
mm_156207.1	chrX	134585709	134585717	+	1	NA	promoter-TSS (NM_019865)	promoter-TSS (NM_019865)	59	NM_019865	19982	Mm.286408	NM_019865	ENSMUSG00000079435	Rpl36a	L44L|Rpl44	ribosomal protein L36A	protein-coding
mm_116624.1	chr13	48880673	48880689	-	1	NA	3' UTR (NM_001033268, exon 18 of 18)	3' UTR (NM_001033268, exon 18 of 18)	-9796	NM_011078	18676	Mm.486213	NM_011078	ENSMUSG00000038025	Phf2	GRC5	PHD finger protein 2	protein-coding
mm_23991.1	chr3	86312203	86312210	+	1	NA	intron (NM_001077687, intron 13 of 50)	intron (NM_001077687, intron 13 of 50)	87516	NM_001077687	80877	Mm.439825	NM_030695	ENSMUSG00000028080	Lrba	C80285|D3Ertd775e|Lab300|Lba	LPS-responsive beige-like anchor	protein-coding
mm_76503.1	chr8	86841793	86841820	-	1	NA	3' UTR (NM_030563, exon 7 of 7)	3' UTR (NM_030563, exon 7 of 7)	43452	NM_030563	80750	Mm.25117	NM_030563	ENSMUSG00000031652	N4bp1	AI481586|C81621	NEDD4 binding protein 1	protein-coding
mm_13128.1	chr2	91730934	91730938	+	1	NA	intron (NM_172669, intron 1 of 17)	intron (NM_172669, intron 1 of 17)	798	NM_001080754	228361	Mm.436667	NM_172669	ENSMUSG00000040506	Ambra1	2310079H06Rik|A130023A14|AA474864|AV021921|D030051N19Rik|mKIAA1736	autophagy/beclin 1 regulator 1	protein-coding
mm_121936.1	chr14	24004208	24004258	-	1	NA	promoter-TSS (NM_001253365)	promoter-TSS (NM_001253365)	-28	NM_001253374	16531	Mm.343607	NM_010610	ENSMUSG00000063142	Kcnma1	5730414M22Rik|BKCa|MaxiK|Slo|Slo1|mSlo|mSlo1	potassium large conductance calcium-activated channel, subfamily M, alpha member 1	protein-coding
mm_94309.1	chr11	4218221	4218249	+	1	NA	promoter-TSS (NM_028022)	promoter-TSS (NM_028022)	-16	NM_028022	71962	Mm.7852	NM_028022	ENSMUSG00000020424	Gatsl3	2410008K03Rik	GATS protein-like 3	protein-coding
mm_75643.1	chr8	65037103	65037132	-	1	NA	5' UTR (NM_001297554, exon 2 of 4)	5' UTR (NM_001297554, exon 2 of 4)	219	NM_001297554	100038489	Mm.58847	NM_001297554	ENSMUSG00000079042	Apela	ENSMUSG00000074303|Ela|Ende|Gm10664	apelin receptor early endogenous ligand	protein-coding
mm_47926.1	chr5	135012858	135012868	-	1	NA	TTS (NM_001190437)	TTS (NM_001190437)	294	NR_026688	69812	Mm.18422	NR_026688	ENSMUSG00000085042	Abhd11os	2010001M06Rik|AI462243|Wbscr26|Wnscr26	abhydrolase domain containing 11, opposite strand	ncRNA
mm_48292.1	chr5	138195634	138195658	-	1	NA	TTS (NM_177878)	TTS (NM_177878)	1332	NM_177878	330216	Mm.19719	NM_177878	ENSMUSG00000049285	Mblac1	-	metallo-beta-lactamase domain containing 1	protein-coding
mm_107158.1	chr12	24572579	24572589	+	1	NA	intron (NM_001161406, intron 1 of 15)	CpG	297	NM_001161406	195733	Mm.263068	NM_145890	ENSMUSG00000020656	Grhl1	LBP-32|MGR|Tcfcp2l2	grainyhead-like 1 (Drosophila)	protein-coding
mm_95016.1	chr11	32000419	32000445	+	1	NA	promoter-TSS (NM_008741)	promoter-TSS (NM_008741)	13	NM_008741	18197	Mm.3304	NM_008741	ENSMUSG00000020297	Nsg2	-	neuron specific gene family member 2	protein-coding
mm_171548.1	chr4	147025130	147025146	+	1	NA	intron (NM_001177767, intron 2 of 4)	intron (NM_001177767, intron 2 of 4)	3288	NM_001177767	100043034	Mm.422606	NM_001177767	ENSMUSG00000067919	Rex2	Gm13138|OTTMUSG00000010655	reduced expression 2	protein-coding
mm_71568.1	chr8	54077165	54077183	+	1	NA	promoter-TSS (NM_009506)	promoter-TSS (NM_009506)	-358	NM_009506	22341	Mm.1402	NM_009506	ENSMUSG00000031520	Vegfc	AW228853|VEGF-C	vascular endothelial growth factor C	protein-coding
mm_148382.1	chr19	3323328	3323339	+	1	NA	promoter-TSS (NM_013495)	promoter-TSS (NM_013495)	32	NM_013495	12894	Mm.18522	NM_013495	ENSMUSG00000024900	Cpt1a	C730027G07|CPTI|Cpt1	carnitine palmitoyltransferase 1a, liver	protein-coding
mm_65496.1	chr7	25718685	25718723	-	1	NA	intron (NM_028771, intron 1 of 4)	intron (NM_028771, intron 1 of 4)	349	NM_028771	52132	Mm.278798	NM_028771	ENSMUSG00000002608	Ccdc97	1200014H14Rik|2810446P04Rik|AA545218|D7Ertd462e	coiled-coil domain containing 97	protein-coding
mm_21451.1	chr2	160656223	160656238	-	1	NA	intron (NM_009408, intron 2 of 20)	RLTR12E|LTR|ERVK	10333	NM_009408	21969	Mm.217233	NM_009408	ENSMUSG00000070544	Top1	AI467334|D130064I21Rik|Top-1	topoisomerase (DNA) I	protein-coding
mm_124118.1	chr14	79521857	79521869	-	1	NA	intron (NM_001286411, intron 1 of 8)	intron (NM_001286411, intron 1 of 8)	6189	NM_001286411	13709	Mm.20938	NM_007920	ENSMUSG00000036461	Elf1	Elf-1|Sts1|mElf-1|p70	E74-like factor 1	protein-coding
mm_69477.1	chr7	133760081	133760100	-	1	NA	5' UTR (NM_001286030, exon 1 of 12)	5' UTR (NM_001286030, exon 1 of 12)	179	NM_001286030	101437	Mm.199223	NM_133941	ENSMUSG00000030986	Dhx32	3110079L04Rik|4732469F02Rik|AA408140|Ddx32	DEAH (Asp-Glu-Ala-His) box polypeptide 32	protein-coding
mm_107969.1	chr12	72761268	72761316	+	1	NA	promoter-TSS (NM_008910)	promoter-TSS (NM_008910)	81	NM_008910	19042	Mm.261045	NM_008910	ENSMUSG00000021096	Ppm1a	2310003C21Rik|2900017D14Rik|AI427932|AU017636|MMPa-2|MPPa-1	protein phosphatase 1A, magnesium dependent, alpha isoform	protein-coding
mm_33915.1	chr4	136462583	136462623	+	1	NA	Intergenic	CpG	-7158	NM_024452	269593	Mm.485824	NM_024452	ENSMUSG00000001089	Luzp1	2700072H04Rik|AI266952|Luzp|mFLJ00226	leucine zipper protein 1	protein-coding
mm_15491.1	chr2	157566931	157566941	+	1	NA	promoter-TSS (NM_016916)	promoter-TSS (NM_016916)	-575	NM_016916	53619	Mm.480461	NM_016916	ENSMUSG00000067787	Blcap	AI462828|Bc10	bladder cancer associated protein	protein-coding
mm_130470.1	chr15	98677452	98677467	-	1	NA	promoter-TSS (NM_172612)	promoter-TSS (NM_172612)	2	NM_172612	223881	Mm.274010	NM_172612	ENSMUSG00000054855	Rnd1	A830014L09Rik|Arhs	Rho family GTPase 1	protein-coding
mm_118215.1	chr13	110280104	110280213	-	1	NA	promoter-TSS (NM_023852)	promoter-TSS (NM_023852)	48	NM_023852	67295	Mm.151600	NM_023852	ENSMUSG00000021700	Rab3c	2700062I01Rik|3110015B08Rik|3110037E15Rik|AI850886	RAB3C, member RAS oncogene family	protein-coding
mm_69963.1	chr7	142376605	142376621	-	1	NA	exon (NM_009983, exon 9 of 9)	exon (NM_009983, exon 9 of 9)	-2867	NM_001347541	320802	Mm.154486	NM_177265	ENSMUSG00000045777	Ifitm10	6330512M04Rik|AI848576|DSPA3	interferon induced transmembrane protein 10	protein-coding
mm_151252.1	chr19	53929261	53929276	+	1	NA	TTS (NM_001195338)	TTS (NM_001195338)	-15038	NM_001168505	56392	Mm.228669	NM_019658	ENSMUSG00000024976	Shoc2	AU017287|Sur8|mKIAA0862	soc-2 (suppressor of clear) homolog (C. elegans)	protein-coding
mm_151884.1	chr19	5798570	5798580	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	-2594	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_128679.1	chr15	60820138	60820179	-	1	NA	3' UTR (NM_001162926, exon 2 of 2)	3' UTR (NM_001162926, exon 2 of 2)	-2807	NR_030696	320469	Mm.230853	NM_177166		9930014A18Rik	-	RIKEN cDNA 9930014A18 gene	ncRNA
mm_43094.1	chr5	124451213	124451223	+	1	NA	intron (NM_001310725, intron 3 of 6)	intron (NM_001310725, intron 3 of 6)	4514	NM_001310727	67956	Mm.137966	NM_030241	ENSMUSG00000049327	Kmt5a	2410195B05Rik|AA617402|AW536475|PR-SET7|PR/SET07|Setd8	lysine methyltransferase 5A	protein-coding
mm_170520.1	chr19	31944394	31944395	-	1	NA	intron (NM_001081074, intron 9 of 11)	(CCCTAA)n|Simple_repeat|Simple_repeat	75633	NM_001081074	69865	Mm.87538	NM_001081074	ENSMUSG00000052595	A1cf	1810073H04Rik|ACF64|ACF65|ASP|Acf|MCM|MerCreMer|Tg(Myh6-cre/Esr1*)1Jmk|mer	APOBEC1 complementation factor	protein-coding
mm_156630.1	chrX	155622650	155622665	+	1	NA	intron (NM_001093750, intron 1 of 2)	intron (NM_001093750, intron 1 of 2)	670	NM_001093750	211612	Mm.218811	NM_001093750	ENSMUSG00000041552	Ptchd1	9630036J22Rik|AI848149|Gm387	patched domain containing 1	protein-coding
mm_134214.1	chr16	11203260	11203312	-	1	NA	promoter-TSS (NM_025546)	promoter-TSS (NM_025546)	6	NM_025546	66409	Mm.28291	NM_025546	ENSMUSG00000005846	Rsl1d1	2410005K20Rik|C76439|pBK1	ribosomal L1 domain containing 1	protein-coding
mm_91275.1	chr10	24645388	24645400	-	1	NA	exon (NM_008813, exon 24 of 25)	exon (NM_008813, exon 24 of 25)	49952	NM_010217	14219	Mm.390287	NM_010217	ENSMUSG00000019997	Ctgf	Ccn2|Fisp12|Hcs24|fisp-12	connective tissue growth factor	protein-coding
mm_1370.1	chr1	66467913	66467994	+	1	NA	promoter-TSS (NM_175510)	promoter-TSS (NM_175510)	-494	NM_175510	329178	Mm.44798	NM_175510	ENSMUSG00000055567	Unc80	C030018G13Rik|C230061B10Rik|UNC-80	unc-80, NALCN activator	protein-coding
mm_9902.1	chr1	187143058	187143060	-	1	NA	intron (NM_028848, intron 5 of 9)	intron (NM_028848, intron 5 of 9)	17921	NR_040554	69308	Mm.490882	NR_040554	ENSMUSG00000089730	1700007P06Rik	-	RIKEN cDNA 1700007P06 gene	ncRNA
mm_134260.1	chr16	13750014	13750042	-	1	NA	Intergenic	RLTR9A|LTR|ERVK	-19544	NM_011987	26565	Mm.4214	NM_011987	ENSMUSG00000022683	Pla2g10	GX sPLA2|PLA2GX|sPLA2-X	phospholipase A2, group X	protein-coding
mm_53780.1	chr6	146502311	146502332	+	1	NA	promoter-TSS (NM_019923)	promoter-TSS (NM_019923)	-98	NM_019923	16439	Mm.7800	NM_010586	ENSMUSG00000030287	Itpr2	AI649341|InsP3R-2|InsP3R-5|Ip3r2|Itpr5|insP3R2	inositol 1,4,5-triphosphate receptor 2	protein-coding
mm_124722.1	chr15	6580017	6580027	+	1	NA	exon (NM_001278269, exon 1 of 17)	exon (NM_001278269, exon 1 of 17)	175	NM_011815	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_134100.1	chr16	9995001	9995012	-	1	NA	Intergenic	CpG	-2473	NM_008170	14811	Mm.2953	NM_008170	ENSMUSG00000059003	Grin2a	GluN2A|NMDAR2A|NR2A	glutamate receptor, ionotropic, NMDA2A (epsilon 1)	protein-coding
mm_159007.1	chr1	162698126	162698126	-	1	NA	exon (NM_001081290, exon 19 of 35)	exon (NM_001081290, exon 19 of 35)	-39907	NM_001177581	100038657	Mm.416999	NM_001177581	ENSMUSG00000091060	7420461P10Rik	ENSMUSG00000073516	RIKEN cDNA 7420461P10 gene	protein-coding
mm_36646.1	chr4	94533306	94533310	-	1	NA	intron (NM_026368, intron 4 of 5)	intron (NM_026368, intron 4 of 5)	23488	NM_026368	67770	Mm.35170	NM_026368	ENSMUSG00000028578	Caap1	5830433M19Rik|AI536248|CAAP	caspase activity and apoptosis inhibitor 1	protein-coding
mm_69961.1	chr7	142376496	142376518	-	1	NA	3' UTR (NM_009983, exon 9 of 9)	3' UTR (NM_009983, exon 9 of 9)	-2761	NM_001347541	320802	Mm.154486	NM_177265	ENSMUSG00000045777	Ifitm10	6330512M04Rik|AI848576|DSPA3	interferon induced transmembrane protein 10	protein-coding
mm_116627.1	chr13	48949142	48949157	-	1	NA	exon (NM_001033268, exon 2 of 18)	exon (NM_001033268, exon 2 of 18)	18679	NM_001033268	218236	Mm.426571	NM_001033268	ENSMUSG00000038014	Fam120a	C9orf10|Ossa	family with sequence similarity 120, member A	protein-coding
mm_89942.1	chr10	111278723	111278763	+	1	NA	intron (NM_175489, intron 15 of 23)	intron (NM_175489, intron 15 of 23)	-19936	NM_027914	71769	Mm.45256	NM_027914	ENSMUSG00000035759	Bbs10	1300007O09Rik|AI452285	Bardet-Biedl syndrome 10 (human)	protein-coding
mm_167336.1	chr8	71575910	71575913	+	1	NA	intron (NM_011977, intron 3 of 13)	B1_Mur2|SINE|Alu	6984	NM_011977	26457	Mm.38165	NM_011977	ENSMUSG00000031808	Slc27a1	FATP1|Fatp	solute carrier family 27 (fatty acid transporter), member 1	protein-coding
mm_68722.1	chr7	120201383	120201406	-	1	NA	intron (NM_016669, intron 1 of 7)	intron (NM_016669, intron 1 of 7)	594	NM_016669	12971	Mm.9114	NM_016669	ENSMUSG00000030905	Crym	-	crystallin, mu	protein-coding
mm_2099.1	chr1	87776937	87776941	+	1	NA	intron (NM_001205391, intron 10 of 18)	intron (NM_001205391, intron 10 of 18)	-7632	NR_028519	100217415	Mm.453537	NR_028519	ENSMUSG00000089281	Scarna6	MBI-46	small Cajal body-specific RNA 6	ncRNA
mm_83987.1	chr9	57434922	57434932	-	1	NA	exon (NM_176831, exon 3 of 7)	exon (NM_176831, exon 3 of 7)	5187	NM_176831	66812	Mm.250508	NM_176831	ENSMUSG00000063849	Ppcdc	1810057I13Rik|8430432M10Rik	phosphopantothenoylcysteine decarboxylase	protein-coding
mm_138245.1	chr17	34587643	34587679	+	1	NA	exon (NM_010929, exon 30 of 30)	exon (NM_010929, exon 30 of 30)	-2145	NM_134116	106512	Mm.26584	NM_134116	ENSMUSG00000034786	Gpsm3	AA960287|AGS4	G-protein signalling modulator 3 (AGS3-like, C. elegans)	protein-coding
mm_160935.1	chr11	93886946	93886946	+	1	NA	intron (NM_134012, intron 1 of 15)	intron (NM_134012, intron 1 of 15)	727	NM_134012	103537	Mm.210334	NM_134012	ENSMUSG00000059474	Mbtd1	AA408199|AI194990|hemp	mbt domain containing 1	protein-coding
mm_32786.1	chr4	116711902	116711905	+	1	NA	intron (NM_026714, intron 6 of 9)	B1_Mur2|SINE|Alu	2973	NM_026714	68394	Mm.425201	NM_026714	ENSMUSG00000028689	Ccdc163	0610037D15Rik|4933430J04Rik	coiled-coil domain containing 163	protein-coding
mm_80201.1	chr9	72408566	72408574	+	1	NA	Intergenic	Intergenic	-29959	NM_008613	17427	Mm.387671	NM_008613	ENSMUSG00000032221	Mns1	AW546487	meiosis-specific nuclear structural protein 1	protein-coding
mm_135603.1	chr16	52142955	52142963	-	1	NA	intron (NM_001033238, intron 9 of 17)	intron (NM_001033238, intron 9 of 17)	111410	NM_001033238	208650	Mm.328206	NM_001033238	ENSMUSG00000022637	Cblb	AI429560|AI851073|Cbl-b	Casitas B-lineage lymphoma b	protein-coding
mm_167842.1	chrM	12510	12520	-	1	NA	NA	Intergenic	NA	NA								
mm_93442.1	chr10	109903815	109903829	-	1	NA	exon (NM_001081035, exon 2 of 39)	exon (NM_001081035, exon 2 of 39)	96397	NM_001081035	260315	Mm.225050	NM_177797	ENSMUSG00000020181	Nav3	4732483H20Rik|9630020C08Rik|POMFIL1|Pomfil1p|mKIAA0938|unc53H3	neuron navigator 3	protein-coding
mm_46975.1	chr5	115194259	115194274	-	1	NA	5' UTR (NM_001310712, exon 1 of 6)	5' UTR (NM_001310712, exon 1 of 6)	115	NM_001310712	29867	Mm.38551	NM_013879	ENSMUSG00000029544	Cabp1	caldendrin	calcium binding protein 1	protein-coding
mm_27666.1	chr3	65380932	65380948	-	1	NA	3' UTR (NM_026155, exon 5 of 5)	3' UTR (NM_026155, exon 5 of 5)	11613	NM_026155	67437	Mm.232728	NM_026155	ENSMUSG00000027828	Ssr3	0610038P07Rik|AL022999|AU022074|AW553833|TRAPG	signal sequence receptor, gamma	protein-coding
mm_165309.1	chr2	102568957	102568960	-	1	NA	intron (NM_173749, intron 1 of 10)	intron (NM_173749, intron 1 of 10)	18937	NM_173749	210622	Mm.28649	NM_173749	ENSMUSG00000027188	Pamr1	5930437L24|E430002G05Rik|Ramp	peptidase domain containing associated with muscle regeneration 1	protein-coding
mm_150957.1	chr19	46395354	46395365	+	1	NA	intron (NM_016860, intron 1 of 10)	CpG	376	NM_016860	54130	Mm.3118	NM_016860	ENSMUSG00000025228	Actr1a	Arp1|alpha-Arp1	ARP1 actin-related protein 1A, centractin alpha	protein-coding
mm_105920.1	chr11	115004187	115004202	-	1	NA	Intergenic	Intergenic	-2314	NM_134158	140497	Mm.2699	NM_134158	ENSMUSG00000044811	Cd300c2	CLM4|Cd300c|Cd300d|DIgR1|Igsf7|Lmir2|MAIR-II	CD300C molecule 2	protein-coding
mm_80144.1	chr9	70835119	70835126	+	1	NA	intron (NM_001324473, intron 1 of 8)	RSINE1|SINE|B4	99686	NM_008280	15450	Mm.390187	NM_008280	ENSMUSG00000032207	Lipc	AI256194|HL|Hpl	lipase, hepatic	protein-coding
mm_112439.1	chr13	5803830	5803847	+	1	NA	Intergenic	Intergenic	54254	NR_045891	71867	Mm.179181	NR_045891	ENSMUSG00000100625	1700016G22Rik	-	RIKEN cDNA 1700016G22 gene	ncRNA
mm_36676.1	chr4	96348626	96348636	-	1	NA	promoter-TSS (NM_001004141)	promoter-TSS (NM_001004141)	49	NM_001004141	100066	Mm.26915	NM_001004141	ENSMUSG00000066097	Cyp2j11	AI314783|Cyp2j11-ps	cytochrome P450, family 2, subfamily j, polypeptide 11	protein-coding
mm_102650.1	chr11	63271012	63271020	-	1	NA	intron (NR_105772, intron 4 of 6)	intron (NR_105772, intron 4 of 6)	115053	NR_105772	102466632		NR_105772	ENSMUSG00000098829	Mir6354	Gm27282|mmu-mir-6354	microRNA 6354	ncRNA
mm_95805.1	chr11	55109836	55109846	+	1	NA	3' UTR (NM_010299, exon 4 of 4)	3' UTR (NM_010299, exon 4 of 4)	11856	NM_010299	14667	Mm.287807	NM_010299	ENSMUSG00000000594	Gm2a	AA408702|AW215435|GM2-AP|SAP-3	GM2 ganglioside activator protein	protein-coding
mm_161491.1	chr15	85821873	85821873	-	1	NA	promoter-TSS (NM_011105)	promoter-TSS (NM_011105)	-140	NM_011105	18766	Mm.89965	NM_011105	ENSMUSG00000052496	Pkdrej	-	polycystin (PKD) family receptor for egg jelly	protein-coding
mm_14564.1	chr2	134992013	134992040	+	1	NA	intron (NM_019677, intron 3 of 32)	PB1D7|SINE|Alu	205862	NM_001145830	18795	Mm.330607	NM_019677	ENSMUSG00000051177	Plcb1	3110043I21Rik|AI132408|Plcb|mKIAA0581	phospholipase C, beta 1	protein-coding
mm_49026.1	chr6	4759619	4759629	+	1	NA	3' UTR (NM_130877, exon 2 of 2)	3' UTR (NM_130877, exon 2 of 2)	12318	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_17339.1	chr2	26601639	26601645	-	1	NA	intron (NM_026212, intron 1 of 5)	intron (NM_026212, intron 1 of 5)	2775	NM_026212	67512	Mm.24244	NM_026212	ENSMUSG00000026922	Agpat2	2510002J07Rik|AV000834|BSCL|BSCL1|LPAAB|LPAAT-beta	1-acylglycerol-3-phosphate O-acyltransferase 2 (lysophosphatidic acid acyltransferase, beta)	protein-coding
mm_37387.1	chr4	121014620	121014640	-	1	NA	intron (NM_133716, intron 1 of 9)	intron (NM_133716, intron 1 of 9)	2617	NM_133716	69780	Mm.271819	NM_133716	ENSMUSG00000032870	Smap2	1810031K02Rik|AA408614|Smap1l	small ArfGAP 2	protein-coding
mm_130825.1	chr15	101845934	101845953	-	1	NA	exon (NM_008473, exon 9 of 9)	exon (NM_008473, exon 9 of 9)	4843	NM_008473	16678	Mm.183137	NM_008473	ENSMUSG00000046834	Krt1	Krt-2.1|Krt2-1|Krt86	keratin 1	protein-coding
mm_18590.1	chr2	66634684	66634741	-	1	NA	5' UTR (NM_001290675, exon 1 of 27)	5' UTR (NM_001290675, exon 1 of 27)	250	NM_001290674	20274	Mm.440889	NM_018852	ENSMUSG00000075316	Scn9a	Nav1.7|PN1|mKIAA4197	sodium channel, voltage-gated, type IX, alpha	protein-coding
mm_173052.1	chrX	122405576	122405576	+	1	NA	Intergenic	ERVB7_1-LTR_MM|LTR|ERVK	-8191	NM_138742	54561	Mm.490573	NM_138742	ENSMUSG00000055733	Nap1l3	MB20	nucleosome assembly protein 1-like 3	protein-coding
mm_93689.1	chr10	117817372	117817422	-	1	NA	exon (NM_024457, exon 7 of 8)	exon (NM_024457, exon 7 of 8)	-24692	NM_134010	103468	Mm.12568	NM_134010	ENSMUSG00000052798	Nup107	AW541137|C76801	nucleoporin 107	protein-coding
mm_26310.1	chr3	142519281	142519291	+	1	NA	intron (NM_153564, intron 10 of 10)	intron (NM_153564, intron 10 of 10)	-11050	NM_001083312	229900	Mm.45740	NM_145545	ENSMUSG00000040253	Gbp7	9830147J24Rik	guanylate binding protein 7	protein-coding
mm_79055.1	chr9	46230002	46230022	+	1	NA	exon (NM_009692, exon 4 of 4)	exon (NM_009692, exon 4 of 4)	1382	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2|apo-AI|apoA-I	apolipoprotein A-I	protein-coding
mm_117816.1	chr13	97967635	97967667	-	1	NA	intron (NM_012026, intron 18 of 35)	intron (NM_012026, intron 18 of 35)	238514	NM_012026	110596	Mm.252718	NM_012026	ENSMUSG00000021662	Arhgef28	9230110L08Rik|AI323540|D13Bwg1089e|RIP2|Rgnef|RhoGEF|Rhoip2|p190RhoGEF	Rho guanine nucleotide exchange factor (GEF) 28	protein-coding
mm_107486.1	chr12	38780105	38780117	+	1	NA	promoter-TSS (NM_007960)	promoter-TSS (NM_007960)	29	NM_007960	14009	Mm.4866	NM_007960	ENSMUSG00000004151	Etv1	ER81|Etsrp81	ets variant 1	protein-coding
mm_32810.1	chr4	117126777	117126797	+	1	NA	promoter-TSS (NM_175030)	promoter-TSS (NM_175030)	-26	NM_175030	242646	Mm.358914	NM_175030	ENSMUSG00000047671	Tctex1d4	4833401D15Rik	Tctex1 domain containing 4	protein-coding
mm_123863.1	chr14	72539201	72539219	-	1	NA	3' UTR (NM_207636, exon 26 of 26)	3' UTR (NM_207636, exon 26 of 26)	170793	NM_207636	319448	Mm.205421	NM_207636	ENSMUSG00000033487	Fndc3a	1700094E19Rik|D14Ertd453e|F730017H24Rik|Fndc3|sys	fibronectin type III domain containing 3A	protein-coding
mm_94752.1	chr11	21116869	21116879	+	1	NA	intron (NM_023324, intron 1 of 6)	intron (NM_023324, intron 1 of 6)	25550	NM_023324	67245	Mm.28957	NM_023324	ENSMUSG00000020134	Peli1	2810468L03Rik|A930031K15Rik|AA409794|AI586297|D11Ertd676e	pellino 1	protein-coding
mm_145381.1	chr18	57095083	57095086	+	1	NA	Intergenic	Intergenic	-38006	NM_001001979	70417	Mm.297863	NM_001001979	ENSMUSG00000024593	Megf10	3000002B06Rik|Gm331	multiple EGF-like-domains 10	protein-coding
mm_153516.1	chr19	41665979	41665979	-	1	NA	intron (NM_015748, intron 4 of 36)	intron (NM_015748, intron 4 of 36)	77328	NR_106166	102465884		NR_106166	ENSMUSG00000098286	Mir8091	Gm27575|mmu-mir-8091	microRNA 8091	ncRNA
mm_119473.1	chr14	47310540	47310564	+	1	NA	exon (NM_178684, exon 3 of 4)	exon (NM_178684, exon 3 of 4)	12238	NM_178684	218975	Mm.212297	NM_178684	ENSMUSG00000021840	Mapk1ip1l	9130202B12|C130032J12Rik	mitogen-activated protein kinase 1 interacting protein 1-like	protein-coding
mm_67298.1	chr7	79149016	79149029	-	1	NA	promoter-TSS (NM_008594)	promoter-TSS (NM_008594)	38	NM_001045489	17304	Mm.1451	NM_008594	ENSMUSG00000030605	Mfge8	AA408458|AI325141|MFG-E8|MP47|Mfgm|P47|SED1|lactadherin	milk fat globule-EGF factor 8 protein	protein-coding
mm_20658.1	chr2	132111468	132111478	-	1	NA	intron (NM_018824, intron 1 of 15)	intron (NM_018824, intron 1 of 15)	33635	NM_018824	54338	Mm.103581	NM_018824	ENSMUSG00000027340	Slc23a2	AI844736|NBTL1|SVCT2|Slc23a1|YSPL2|YSPL3|mKIAA0238	solute carrier family 23 (nucleobase transporters), member 2	protein-coding
mm_46915.1	chr5	114443956	114443978	-	1	NA	promoter-TSS (NM_029956)	promoter-TSS (NM_029956)	60	NM_029956	77697	Mm.105182	NM_029956	ENSMUSG00000029575	Mmab	9130222L19Rik|ATR	methylmalonic aciduria (cobalamin deficiency) cblB type homolog (human)	protein-coding
mm_167930.1	chrX	104670844	104670858	-	1	NA	5' UTR (NM_175358, exon 1 of 12)	5' UTR (NM_175358, exon 1 of 12)	213	NM_175358	108672	Mm.30574	NM_175358	ENSMUSG00000033906	Zdhhc15	6030457O13Rik	zinc finger, DHHC domain containing 15	protein-coding
mm_104034.1	chr11	86257580	86257590	-	1	NA	promoter-TSS (NM_027421)	promoter-TSS (NM_027421)	-17	NM_027421	70422	Mm.171304	NM_027421	ENSMUSG00000018068	Ints2	2810417D08Rik|AA408260|AI987735|mKIAA1287	integrator complex subunit 2	protein-coding
mm_57826.1	chr6	129463122	129463145	-	1	NA	exon (NM_020008, exon 6 of 6)	exon (NM_020008, exon 6 of 6)	9646	NM_001309637	56644	Mm.239516	NM_020008	ENSMUSG00000079293	Clec7a	BGR|Clecsf12|beta-GR	C-type lectin domain family 7, member a	protein-coding
mm_107948.1	chr12	72212298	72212320	+	1	NA	non-coding (NR_104446, exon 7 of 7)	non-coding (NR_104446, exon 7 of 7)	23437	NR_104446	104001	Mm.221275	NM_153457	ENSMUSG00000021087	Rtn1	Nsp	reticulon 1	protein-coding
mm_80010.1	chr9	67840387	67840429	+	1	NA	promoter-TSS (NM_177184)	promoter-TSS (NM_177184)	12	NM_177184	320528	Mm.241454	NM_177184	ENSMUSG00000035284	Vps13c	AI552542|AV026040|C230055H22Rik|W51662|chorein	vacuolar protein sorting 13C	protein-coding
mm_42093.1	chr5	110327644	110327652	+	1	NA	intron (NM_011132, intron 39 of 48)	intron (NM_011132, intron 39 of 48)	15387	NM_153400	231602	Mm.55948	NM_153400	ENSMUSG00000029503	P2rx2	P2X2a|P2x2	purinergic receptor P2X, ligand-gated ion channel, 2	protein-coding
mm_22974.1	chr3	32708969	32709010	+	1	NA	intron (NM_019673, intron 1 of 13)	CpG	443	NM_019673	56456	Mm.41077	NM_019673	ENSMUSG00000027671	Actl6a	2810432C06Rik|AI851094|ARP4|Actl6|Baf53a|C79802	actin-like 6A	protein-coding
mm_45260.1	chr5	63968808	63968840	-	1	NA	promoter-TSS (NM_145923)	promoter-TSS (NM_145923)	73	NM_145923	100532	Mm.243632	NM_145923	ENSMUSG00000047881	Rell1	AA536743	RELT-like 1	protein-coding
mm_10735.1	chr2	23068218	23068241	+	1	NA	promoter-TSS (NM_001102438)	promoter-TSS (NM_001102438)	28	NM_001102436	74159	Mm.181973	NM_028793	ENSMUSG00000026781	Acbd5	1300014E15Rik	acyl-Coenzyme A binding domain containing 5	protein-coding
mm_138193.1	chr17	34282753	34282766	+	1	NA	TTS (NM_010378)	TTS (NM_010378)	5012	NM_010378	14960	Mm.235338	NM_010378	ENSMUSG00000036594	H2-Aa	Aalpha|H-2Aa|H2Aa|I-Aalpha|IAalpha|Ia-1|Ia1	histocompatibility 2, class II antigen A, alpha	protein-coding
mm_51427.1	chr6	78428485	78428497	+	1	NA	3' UTR (NM_009042, exon 6 of 6)	3' UTR (NM_009042, exon 6 of 6)	2508	NM_009042	19692	Mm.142731	NM_009042	ENSMUSG00000059654	Reg1	-	regenerating islet-derived 1	protein-coding
mm_171346.1	chr4	108193074	108193088	+	1	NA	intron (NM_001167936, intron 6 of 13)	MLTR31A_MM|LTR|ERVK	24841	NM_001167936	230590	Mm.301798	NM_001167936	ENSMUSG00000034645	Zyg11a	BC022150	zyg-11 family member A, cell cycle regulator	protein-coding
mm_114232.1	chr13	56609282	56609300	+	1	NA	promoter-TSS (NM_009369)	promoter-TSS (NM_009369)	-312	NM_009369	21810	Mm.14455	NM_009369	ENSMUSG00000035493	Tgfbi	68kDa|AI181842|AI747162|Beta-ig|big-h3	transforming growth factor, beta induced	protein-coding
mm_120531.1	chr14	67176876	67176877	+	1	NA	Intergenic	Intergenic	-56416	NM_010095	13592	Mm.319947	NM_010095	ENSMUSG00000022053	Ebf2	D14Ggc1e|EBF-2|Mmot1|O/E-3|OE-3	early B cell factor 2	protein-coding
mm_85531.1	chr9	106476373	106476384	-	1	NA	promoter-TSS (NM_145620)	promoter-TSS (NM_145620)	571	NM_001311150	235587	Mm.273659	NM_145619	ENSMUSG00000023249	Parp3	A930002C11Rik|AW990611|Adprt3|Adprtl3|PARP-3|pADPRT-3	poly (ADP-ribose) polymerase family, member 3	protein-coding
mm_40565.1	chr5	62811651	62811688	+	1	NA	Intergenic	Intergenic	-2154	NM_001170705	100322896	Mm.479821	NM_001170705	ENSMUSG00000090326	Dthd1	Gm17384	death domain containing 1	protein-coding
mm_32042.1	chr4	95967323	95967381	+	1	NA	promoter-TSS (NR_045777)	promoter-TSS (NR_045777)	-27	NM_030014	77963	Mm.49994	NM_030014	ENSMUSG00000028572	Hook1	A930033L17Rik|azh	hook microtubule tethering protein 1	protein-coding
mm_114855.1	chr13	93303775	93303788	+	1	NA	promoter-TSS (NM_011982)	promoter-TSS (NM_011982)	24	NM_011982	26556	Mm.37533	NM_011982	ENSMUSG00000007617	Homer1	PSD-Zip45|SYN47|Ves-1|homer-1|vesl-1	homer scaffolding protein 1	protein-coding
mm_108336.1	chr12	80130892	80130909	+	1	NA	intron (NR_033514, intron 2 of 2)	intron (NR_033514, intron 2 of 2)	1944	NR_033514	69548	Mm.269712	NR_033514	ENSMUSG00000097729	2310015A10Rik	5330419I17Rik	RIKEN cDNA 2310015A10 gene	ncRNA
mm_58747.1	chr7	13278877	13278900	+	1	NA	promoter-TSS (NM_010715)	promoter-TSS (NM_010715)	62	NM_010715	16881	Mm.288179	NM_010715	ENSMUSG00000056394	Lig1	AL033288|LigI	ligase I, DNA, ATP-dependent	protein-coding
mm_125981.1	chr15	76331289	76331361	+	1	NA	promoter-TSS (NM_010331)	promoter-TSS (NM_010331)	31	NM_010331	14731	Mm.5903	NM_010331	ENSMUSG00000022561	Gpaa1	C80044|mGAA1	GPI anchor attachment protein 1	protein-coding
mm_152591.1	chr19	11604829	11604833	-	1	NA	promoter-TSS (NM_026835)	promoter-TSS (NM_026835)	-27	NM_026835	68774	Mm.290390	NM_026835	ENSMUSG00000024679	Ms4a6d	1110058E16Rik|AI447446|Ms4a11	membrane-spanning 4-domains, subfamily A, member 6D	protein-coding
mm_104198.1	chr11	87980941	87980957	-	1	NA	3' UTR (NM_001168471, exon 3 of 3)	3' UTR (NM_001168471, exon 3 of 3)	5636	NM_001168472	68097	Mm.246436	NM_026556	ENSMUSG00000020483	Dynll2	1700064A15Rik|6720463E02Rik|C87222|DLC8|DLC8b|Dlc2	dynein light chain LC8-type 2	protein-coding
mm_71498.1	chr8	46793503	46793522	+	1	NA	exon (NM_008391, exon 2 of 9)	exon (NM_008391, exon 2 of 9)	53767	NM_008391	16363	Mm.1149	NM_008391	ENSMUSG00000031627	Irf2	9830146E22Rik|AI646973|Irf-2	interferon regulatory factor 2	protein-coding
mm_136168.1	chr16	88563167	88563200	-	1	NA	promoter-TSS (NM_018778)	promoter-TSS (NM_018778)	0	NM_018778	54420	Mm.25836	NM_018778	ENSMUSG00000050520	Cldn8	AI648025	claudin 8	protein-coding
mm_5627.1	chr1	40397474	40397503	-	1	NA	Intergenic	Intergenic	-32082	NM_001294171	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_166511.1	chr6	11341311	11341315	+	1	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	-366935	NR_033776	57866	Mm.4397	NR_033776		AA545190	-	EST AA545190	ncRNA
mm_141980.1	chr17	35164577	35164663	-	1	NA	intron (NM_001199044, intron 1 of 30)	CpG	257	NM_001199044	53761	Mm.272462	NM_020027	ENSMUSG00000024393	Prrc2a	3110039B05Rik|Bat-2|Bat2|D17H6S51E|G2|Wbp12|mKIAA4178	proline-rich coiled-coil 2A	protein-coding
mm_150803.1	chr19	44333368	44333380	+	1	NA	promoter-TSS (NM_183216)	promoter-TSS (NM_183216)	48	NM_183216	329065	Mm.313583	NM_183216	ENSMUSG00000050195	Scd4	ACOD4	stearoyl-coenzyme A desaturase 4	protein-coding
mm_114049.1	chr13	54302515	54302671	+	1	NA	Intergenic	Intergenic	-68756	NM_009946	12890	Mm.268902	NM_009946	ENSMUSG00000025867	Cplx2	921-L|AI413745|AW492120	complexin 2	protein-coding
mm_32033.1	chr4	95579464	95579499	+	1	NA	promoter-TSS (NM_029347)	promoter-TSS (NM_029347)	60	NM_029347	75578	Mm.276098	NM_029347	ENSMUSG00000028573	Fggy	2310009E04Rik	FGGY carbohydrate kinase domain containing	protein-coding
mm_77230.1	chr8	115704157	115704183	-	1	NA	3' UTR (NM_001025577, exon 1 of 1)	3' UTR (NM_001025577, exon 1 of 1)	2724	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_18430.1	chr2	60781896	60781915	-	1	NA	exon (NM_001141932, exon 5 of 15)	exon (NM_001141932, exon 5 of 15)	-59302	NM_001159564	16420	Mm.98193	NM_021359	ENSMUSG00000026971	Itgb6	2210409C20Rik|4831415H04Rik	integrin beta 6	protein-coding
mm_107177.1	chr12	24973807	24973813	+	1	NA	Intergenic	Intergenic	-1122	NM_001081378	77480	Mm.250641	NM_001081378	ENSMUSG00000036333	Kidins220	3110039L19Rik|AI194387|AI316525|C330002I19Rik|mKIAA1250	kinase D-interacting substrate 220	protein-coding
mm_160200.1	chr7	80309433	80309433	+	1	NA	exon (NM_145150, exon 9 of 14)	exon (NM_145150, exon 9 of 14)	14982	NM_001285998	233406	Mm.227274	NM_145150	ENSMUSG00000038943	Prc1	D7Ertd348e	protein regulator of cytokinesis 1	protein-coding
mm_33695.1	chr4	133553371	133553393	+	1	NA	promoter-TSS (NM_011850)	promoter-TSS (NM_011850)	6	NM_011850	23957	Mm.346759	NM_011850	ENSMUSG00000037583	Nr0b2	SHP|SHP-1|Shp1	nuclear receptor subfamily 0, group B, member 2	protein-coding
mm_23605.1	chr3	65339540	65339542	+	1	NA	intron (NR_040390, intron 2 of 3)	intron (NR_040390, intron 2 of 3)	9888	NR_040390	319798	Mm.445698	NR_040390		A730090N16Rik	-	RIKEN cDNA A730090N16 gene	ncRNA
mm_54548.1	chr6	36810100	36810126	-	1	NA	5' UTR (NM_008973, exon 1 of 5)	5' UTR (NM_008973, exon 1 of 5)	1248	NM_008973	19242	Mm.279690	NM_008973	ENSMUSG00000029838	Ptn	HARP|HB-GAM|HBBN|HBGF-8|HBNF|OSF|Osf-1|Osf1	pleiotrophin	protein-coding
mm_47547.1	chr5	124351184	124351224	-	1	NA	intron (NM_013812, intron 1 of 3)	intron (NM_013812, intron 1 of 3)	3424	NM_013812	13445	Mm.391838	NM_013812	ENSMUSG00000029394	Cdk2ap1	Apc10|Cdkap1|DORC1|Doc1|ST19|doc-1|p12	CDK2 (cyclin-dependent kinase 2)-associated protein 1	protein-coding
mm_118376.1	chr13	117024141	117024172	-	1	NA	intron (NM_001081009, intron 3 of 26)	intron (NM_001081009, intron 3 of 26)	1360	NM_001081009	52552	Mm.274466	NM_027272	ENSMUSG00000021725	Parp8	2810430O08Rik|ARTD16|D13Ertd275e	poly (ADP-ribose) polymerase family, member 8	protein-coding
mm_142437.1	chr17	45571069	45571073	-	1	NA	exon (NM_008302, exon 4 of 11)	exon (NM_008302, exon 4 of 11)	2190	NM_008302	15516	Mm.2180	NM_008302	ENSMUSG00000023944	Hsp90ab1	90kDa|AL022974|C81438|Hsp84|Hsp84-1|Hsp90|Hspcb	heat shock protein 90 alpha (cytosolic), class B member 1	protein-coding
mm_27126.1	chr3	32340561	32340585	-	1	NA	3' UTR (NM_009517, exon 6 of 6)	3' UTR (NM_009517, exon 6 of 6)	-24916	NR_027966	67576	Mm.435324	NR_027966		4930429B21Rik	-	RIKEN cDNA 4930429B21 gene	ncRNA
mm_155482.1	chrX	73675541	73675547	+	1	NA	intron (NM_001142810, intron 1 of 12)	intron (NM_001142810, intron 1 of 12)	2411	NM_001142809	102857	Mm.274553	NM_133987	ENSMUSG00000019558	Slc6a8	AA589632|CRT|CRTR|CT1|CTR5|Creat	solute carrier family 6 (neurotransmitter transporter, creatine), member 8	protein-coding
mm_104170.1	chr11	87566583	87566602	-	1	NA	Intergenic	Intergenic	-11797	NM_001284398	18952	Mm.2214	NM_011129	ENSMUSG00000020486	Sept4	ARTS|Bh5|OTTMUSG00000001265|Pnutl2	septin 4	protein-coding
mm_44503.1	chr5	23871361	23871365	-	1	NA	intron (NR_037304, intron 3 of 4)	MERV1_LTR|LTR|ERV1	19130	NR_028536	100217436		NR_028536		Snord93	Gm22397|MBII-336	small nucleolar RNA, C/D box 93	snoRNA
mm_93959.1	chr10	127286252	127286263	-	1	NA	exon (NM_001347171, exon 6 of 13)	exon (NM_001347171, exon 6 of 13)	2761	NM_001347171	110962	Mm.372826	NM_033072	ENSMUSG00000025409	Mbd6	D10Wsu93e	methyl-CpG binding domain protein 6	protein-coding
mm_100190.1	chr11	116751045	116751081	+	1	NA	Intergenic	Intergenic	-1104	NR_003364	193217	Mm.100084	NR_003364		BC018473	-	cDNA sequence BC018473	ncRNA
mm_110348.1	chr12	36627396	36627413	-	1	NA	intron (NM_178629, intron 9 of 9)	Lx9|LINE|L1	-188801	NR_039558	100628578		NR_039558	ENSMUSG00000092998	Mir5099	mmu-mir-5099|mu-mir-5099	microRNA 5099	ncRNA
mm_122581.1	chr14	50836385	50836399	-	1	NA	exon (NM_009351, exon 40 of 55)	exon (NM_009351, exon 40 of 55)	28446	NM_009632	11546	Mm.281482	NM_009632	ENSMUSG00000036023	Parp2	ARTD2|Adprt2|Adprtl2|Aspartl2|C78626|PARP-2	poly (ADP-ribose) polymerase family, member 2	protein-coding
mm_71877.1	chr8	69797788	69797808	+	1	NA	exon (NM_133224, exon 8 of 26)	exon (NM_133224, exon 8 of 26)	6635	NM_133224	170759	Mm.186066	NM_133224	ENSMUSG00000031862	Atp13a1	Atp13a|Cgi152|catp	ATPase type 13A1	protein-coding
mm_117927.1	chr13	99434251	99434274	-	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-21436	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_169378.1	chr14	37261143	37261161	-	1	NA	Intergenic	L1Md_T|LINE|L1	-125830	NM_078478	66092	Mm.182912	NM_078478	ENSMUSG00000041028	Ghitm	1010001P14Rik|C77840|MICS1|PTD010|Tmbim5	growth hormone inducible transmembrane protein	protein-coding
mm_86529.1	chr10	7832327	7832367	+	1	NA	promoter-TSS (NM_172785)	promoter-TSS (NM_172785)	-123	NM_172785	237256	Mm.140055	NM_172785	ENSMUSG00000039981	Zc3h12d	D730019B10Rik|TFL	zinc finger CCCH type containing 12D	protein-coding
mm_65002.1	chr7	17027854	17027921	-	1	NA	promoter-TSS (NM_011155)	promoter-TSS (NM_011155)	27	NM_011155	19060	Mm.3294	NM_011155	ENSMUSG00000003099	Ppp5c	AU020526|PP5	protein phosphatase 5, catalytic subunit	protein-coding
mm_76804.1	chr8	104310053	104310102	-	1	NA	promoter-TSS (NM_181990)	promoter-TSS (NM_181990)	68	NM_181990	100504164	Mm.443302	NM_181990	ENSMUSG00000110430	Cmtm1	CHLFH1a|CKLFH|CKLFH1|Cklfsf1	CKLF-like MARVEL transmembrane domain containing 1	protein-coding
mm_128486.1	chr15	50890125	50890138	-	1	NA	promoter-TSS (NM_032000)	promoter-TSS (NM_032000)	-90	NM_032000	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_102261.1	chr11	55336481	55336520	-	1	NA	Intergenic	Intergenic	-24243	NM_001029988	245827	Mm.339363	NM_001029988	ENSMUSG00000055333	Fat2	EMI2|Fath2|Gm523|mKIAA0811	FAT atypical cadherin 2	protein-coding
mm_110964.1	chr12	76822466	76822508	-	1	NA	promoter-TSS (NM_134050)	promoter-TSS (NM_134050)	37	NM_134050	104886	Mm.172847	NM_134050	ENSMUSG00000021062	Rab15	2310012G06Rik|AI840042	RAB15, member RAS oncogene family	protein-coding
mm_126510.1	chr15	81802774	81802785	+	1	NA	5' UTR (NM_153484, exon 1 of 4)	5' UTR (NM_153484, exon 1 of 4)	106	NM_153484	21685	Mm.270278	NM_017376	ENSMUSG00000022389	Tef	2310028D20Rik	thyrotroph embryonic factor	protein-coding
mm_121978.1	chr14	25850547	25850593	-	1	NA	intron (NM_013469, intron 1 of 14)	intron (NM_013469, intron 1 of 14)	8415	NM_013469	11744	Mm.294083	NM_013469	ENSMUSG00000021866	Anxa11	A830099O17Rik|Anx11	annexin A11	protein-coding
mm_84576.1	chr9	69295795	69295797	-	1	NA	intron (NM_001289916, intron 1 of 9)	intron (NM_001289916, intron 1 of 9)	5955	NM_001289916	19883	Mm.378450	NM_013646	ENSMUSG00000032238	Rora	9530021D13Rik|Nr1f1|ROR1|ROR2|ROR3|nmf267|sg|staggerer|tmgc26	RAR-related orphan receptor alpha	protein-coding
mm_41936.1	chr5	105701411	105701416	+	1	NA	intron (NM_178701, intron 1 of 2)	intron (NM_178701, intron 1 of 2)	603	NM_178701	231549	Mm.23837	NM_178701	ENSMUSG00000046079	Lrrc8d	2810473G09Rik|4930525N13Rik|A930019F03|Lrrc5	leucine rich repeat containing 8D	protein-coding
mm_129331.1	chr15	77813152	77813167	-	1	NA	exon (NM_022410, exon 2 of 41)	exon (NM_022410, exon 2 of 41)	29016	NM_022410	17886	Mm.29677	NM_022410	ENSMUSG00000022443	Myh9	Fltn|Myhn-1|Myhn1|NMHCIIA|NMMHC-A|NMMHC-IIA|TU72.6	myosin, heavy polypeptide 9, non-muscle	protein-coding
mm_94892.1	chr11	28853190	28853259	+	1	NA	promoter-TSS (NM_146015)	promoter-TSS (NM_146015)	19	NM_146015	216616	Mm.44176	NM_146015	ENSMUSG00000020467	Efemp1	-	epidermal growth factor-containing fibulin-like extracellular matrix protein 1	protein-coding
mm_42295.1	chr5	114444325	114444342	+	1	NA	promoter-TSS (NM_029956)	promoter-TSS (NM_029956)	64	NM_023556	17855	Mm.28088	NM_023556	ENSMUSG00000041939	Mvk	2310010A05Rik|AI256848|AI414037|MK	mevalonate kinase	protein-coding
mm_67124.1	chr7	70361798	70361810	-	1	NA	intron (NM_183261, intron 1 of 2)	intron (NM_183261, intron 1 of 2)	-1211	NM_009697	11819	Mm.158143	NM_009697	ENSMUSG00000030551	Nr2f2	2700033K02Rik|9430015G03Rik|ARP-1|Aporp1|COUP-TF2|COUP-TFII|COUPTFB|EAR3|SVP40|Tcfcoup2	nuclear receptor subfamily 2, group F, member 2	protein-coding
mm_31484.1	chr4	52465929	52465941	+	1	NA	exon (NM_008017, exon 16 of 25)	exon (NM_008017, exon 16 of 25)	26714	NM_001301412	14211	Mm.2999	NM_008017	ENSMUSG00000028312	Smc2	5730502P04Rik|AI255214|AW545314|CAP-E|CAPE|Fin16|SMC-2|Smc2l1	structural maintenance of chromosomes 2	protein-coding
mm_53.1	chr1	6528093	6528108	+	1	NA	intron (NM_001244693, intron 2 of 22)	intron (NM_001244693, intron 2 of 22)	40869	NM_001244692	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding
mm_46652.1	chr5	108660745	108660778	-	1	NA	promoter-TSS (NM_199011)	promoter-TSS (NM_199011)	8	NM_199011	110524	Mm.260921	NM_199011	ENSMUSG00000004815	Dgkq	110kDa|DAGK|DAGK7|Dagk4|Dgkd	diacylglycerol kinase, theta	protein-coding
mm_50421.1	chr6	48771040	48771065	+	1	NA	promoter-TSS (NM_031247)	promoter-TSS (NM_031247)	-201	NM_031247	83408	Mm.333050	NM_031247	ENSMUSG00000039264	Gimap3	2010110D23Rik|Gimap5|Ian4	GTPase, IMAP family member 3	protein-coding
mm_160697.1	chr10	40302185	40302185	-	1	NA	promoter-TSS (NM_009665)	promoter-TSS (NM_009665)	1	NM_007444	100041585	Mm.476925	NM_007444	ENSMUSG00000063953	Amd2	AdoMetDC|Amd1|Amd3|ENSMUSG00000063953	S-adenosylmethionine decarboxylase 2	protein-coding
mm_57401.1	chr6	124864124	124864149	-	1	NA	promoter-TSS (NM_013533)	promoter-TSS (NM_013533)	-219	NM_013533	14788	Mm.2514	NM_013533	ENSMUSG00000038390	Gpr162	A-2|BC031437|Grca	G protein-coupled receptor 162	protein-coding
mm_99550.1	chr11	103425241	103425270	+	1	NA	Intergenic	Intergenic	-12591	NM_183034	353047	Mm.18556	NM_183034	ENSMUSG00000034247	Plekhm1	AP162|B2|BC038943|D330036J23Rik	pleckstrin homology domain containing, family M (with RUN domain) member 1	protein-coding
mm_131455.1	chr16	16870956	16870969	+	1	NA	5' UTR (NM_011624, exon 1 of 18)	5' UTR (NM_011624, exon 1 of 18)	226	NM_011624	21976	Mm.326089	NM_011624	ENSMUSG00000022779	Top3b	-	topoisomerase (DNA) III beta	protein-coding
mm_58734.1	chr7	13030127	13030143	+	1	NA	exon (NM_011588, exon 14 of 17)	exon (NM_011588, exon 14 of 17)	4642	NM_026885	68953	Mm.295670	NM_026885	ENSMUSG00000033916	Chmp2a	1500016L11Rik	charged multivesicular body protein 2A	protein-coding
mm_171210.1	chr3	5860456	5860460	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-284210	NM_001163305	19302	Mm.132336	NM_008994	ENSMUSG00000040374	Pex2	D3Ertd138e|PAF-1|PMP35|Pxmp3	peroxisomal biogenesis factor 2	protein-coding
mm_136767.1	chr17	8924110	8924128	+	1	NA	intron (NM_001347321, intron 3 of 21)	MTE2b|LTR|ERVL-MaLR	-64214	NM_025851	66931	Mm.67591	NM_025851	ENSMUSG00000023873	1700010I14Rik	-	RIKEN cDNA 1700010I14 gene	protein-coding
mm_52360.1	chr6	112489096	112489129	+	1	NA	exon (NM_001081147, exon 1 of 2)	exon (NM_001081147, exon 1 of 2)	696	NM_001081147	18430	Mm.333310	NM_001081147	ENSMUSG00000049112	Oxtr	OTR	oxytocin receptor	protein-coding
mm_117558.1	chr13	85127394	85127414	-	1	NA	Intergenic	Intergenic	-61981	NM_001347587	66671	Mm.18474	NM_023243	ENSMUSG00000021548	Ccnh	6330408H09Rik|AI661354|AV102684|AW538719	cyclin H	protein-coding
mm_33333.1	chr4	129136921	129136941	+	1	NA	promoter-TSS (NM_027402)	promoter-TSS (NM_027402)	-68	NM_027402	384061	Mm.44075	NM_027402	ENSMUSG00000001334	Fndc5	1500001L03Rik|AI836596|C87088|PeP|Pxp	fibronectin type III domain containing 5	protein-coding
mm_63446.1	chr7	127490294	127490310	+	1	NA	TTS (NR_106027)	TTS (NR_106027)	1051	NR_106027	102465642		NR_106027	ENSMUSG00000098267	Mir7060	Gm27515|mmu-mir-7060	microRNA 7060	ncRNA
mm_42305.1	chr5	114775943	114775952	+	1	NA	promoter-TSS (NR_027872)	promoter-TSS (NR_027872)	807	NM_026718	68420	Mm.275554	NM_026718	ENSMUSG00000041870	Ankrd13a	1100001D10Rik|ANKRD13|AU046136	ankyrin repeat domain 13a	protein-coding
mm_109800.1	chr12	3309552	3309674	-	1	NA	5' UTR (NM_016676, exon 1 of 6)	5' UTR (NM_016676, exon 1 of 6)	356	NM_016676	19325	Mm.378993	NM_016676	ENSMUSG00000020671	Rab10	AW107754	RAB10, member RAS oncogene family	protein-coding
mm_111466.1	chr12	98574540	98574558	-	1	NA	5' UTR (NM_001316665, exon 1 of 7)	5' UTR (NM_001316665, exon 1 of 7)	163	NM_001316666	72258	Mm.196158	NM_029911	ENSMUSG00000033854	Kcnk10	1700024D23Rik|3010005K24Rik|Trek2	potassium channel, subfamily K, member 10	protein-coding
mm_116163.1	chr13	30749417	30749421	-	1	NA	intron (NM_001347508, intron 1 of 8)	intron (NM_001347508, intron 1 of 8)	186	NM_013674	16364	Mm.4677	NM_013674	ENSMUSG00000021356	Irf4	AI385587|IRF-4|LSIRF|NF-EM5|Spip	interferon regulatory factor 4	protein-coding
mm_162774.1	chr10	68136808	68136834	-	1	NA	intron (NM_023598, intron 4 of 9)	intron (NM_023598, intron 4 of 9)	141905	NM_023598	71371	Mm.440357	NM_023598	ENSMUSG00000019947	Arid5b	4930580B11|5430435G07Rik|AI467247|Desrt|Mrf2|Mrf2alpha|Mrf2beta	AT rich interactive domain 5B (MRF1-like)	protein-coding
mm_27603.1	chr3	59153582	59153592	-	1	NA	promoter-TSS (NR_045641)	promoter-TSS (NR_045641)	41	NR_045641	320463	Mm.484506	NR_045641	ENSMUSG00000036381	F630111L10Rik	-	RIKEN cDNA F630111L10 gene	ncRNA
mm_19444.1	chr2	91982689	91982750	-	1	NA	3' UTR (NM_011957, exon 12 of 12)	3' UTR (NM_011957, exon 12 of 12)	-19156	NM_138306	104418	Mm.314923	NM_138306	ENSMUSG00000040479	Dgkz	E130307B02Rik|ENSMUSG00000075035|F730209L11Rik|mDGK[z]	diacylglycerol kinase zeta	protein-coding
mm_16288.1	chr2	174111094	174111102	+	1	NA	exon (NM_213733, exon 2 of 12)	exon (NM_213733, exon 2 of 12)	747	NM_213733	228961	Mm.295629	NM_213733	ENSMUSG00000039263	Npepl1	BC023239|C85514|mKIAA1974	aminopeptidase-like 1	protein-coding
mm_157421.1	chrX	38564288	38564334	-	1	NA	intron (NM_001110142, intron 3 of 22)	G-rich|Low_complexity|Low_complexity	11885	NM_028288	72584	Mm.327675	NM_028288	ENSMUSG00000031095	Cul4b	2700050M05Rik|AA409770|CUL-4B|mKIAA0695	cullin 4B	protein-coding
mm_48717.1	chr5	147322247	147322276	-	1	NA	exon (NM_001039678, exon 1 of 2)	exon (NM_001039678, exon 1 of 2)	179	NM_001039678	231903	Mm.291286	NM_001039678	ENSMUSG00000075543	Urad	EG231903|Prhoxnb	ureidoimidazoline (2-oxo-4-hydroxy-4-carboxy-5) decarboxylase	protein-coding
mm_133028.1	chr16	57191364	57191380	+	1	NA	intron (NM_026254, intron 10 of 17)	intron (NM_026254, intron 10 of 17)	-24040	NM_023175	52633	Mm.383203	NM_023175	ENSMUSG00000022751	Nit2	1190017B19Rik|D16Ertd502e	nitrilase family, member 2	protein-coding
mm_97079.1	chr11	73009750	73009798	+	1	NA	intron (NM_008771, intron 6 of 11)	intron (NM_008771, intron 6 of 11)	-9234	NM_018883	55984	Mm.9998	NM_018883	ENSMUSG00000020785	Camkk1	AI846603|CaMKKalpha|Camkk	calcium/calmodulin-dependent protein kinase kinase 1, alpha	protein-coding
mm_154242.1	chr19	60766369	60766385	-	1	NA	exon (NM_010123, exon 19 of 22)	exon (NM_010123, exon 19 of 22)	8008	NR_034047	100217439		NR_034047		Snora19	MBI-51	small nucleolar RNA, H/ACA box 19	snoRNA
mm_171915.1	chr5	5782147	5782151	-	1	NA	Intergenic	Intergenic	-32832	NM_027399	70358	Mm.85429	NM_027399	ENSMUSG00000015652	Steap1	2410007B19Rik|Prss24|Steap	six transmembrane epithelial antigen of the prostate 1	protein-coding
mm_113634.1	chr13	42051843	42051875	+	1	NA	promoter-TSS (NM_007772)	promoter-TSS (NM_007772)	-162	NM_007772	110521	Mm.4808	NM_007772	ENSMUSG00000021366	Hivep1	Cryabp1	human immunodeficiency virus type I enhancer binding protein 1	protein-coding
mm_45213.1	chr5	52994166	52994178	-	1	NA	Intergenic	Intergenic	-1880	NR_040413	75954	Mm.258937	NR_040413	ENSMUSG00000106352	5033403H07Rik	-	RIKEN cDNA 5033403H07 gene	ncRNA
mm_104235.1	chr11	88702292	88702292	-	1	NA	intron (NM_001201341, intron 5 of 7)	intron (NM_001201341, intron 5 of 7)	15937	NM_054043	76626	Mm.400451	NM_054043	ENSMUSG00000069769	Msi2	1700105C15Rik|AI451722|AI563628|AW489193|Msi2h	musashi RNA-binding protein 2	protein-coding
mm_153779.1	chr19	45783486	45783496	-	1	NA	promoter-TSS (NM_023799)	promoter-TSS (NM_023799)	-200	NM_023799	76055	Mm.122725	NM_023799	ENSMUSG00000025220	Mgea5	2810009A20Rik|4833427O07Rik|5830447M11Rik|AA408215|Hy5|Ncoat|OGA|mKIAA0679	meningioma expressed antigen 5 (hyaluronidase)	protein-coding
mm_24819.1	chr3	95645593	95645603	+	1	NA	Intergenic	Intergenic	-13123	NM_008562	17210	Mm.1639	NM_008562	ENSMUSG00000038612	Mcl1	AW556805|Mcl-1	myeloid cell leukemia sequence 1	protein-coding
mm_125416.1	chr15	41794485	41794489	+	1	NA	intron (NM_130885, intron 1 of 14)	intron (NM_130885, intron 1 of 14)	4972	NM_130885	170719	Mm.254267	NM_130885	ENSMUSG00000022307	Oxr1	2210416C20Rik|C7|C7B	oxidation resistance 1	protein-coding
mm_129013.1	chr15	74923546	74923560	-	1	NA	Intergenic	Intergenic	-31498	NM_001164039	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_77939.1	chr9	7355397	7355439	+	1	NA	exon (NM_008605, exon 8 of 10)	exon (NM_008605, exon 8 of 10)	8044	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_73044.1	chr8	94329627	94329653	+	1	NA	intron (NM_019415, intron 1 of 24)	intron (NM_019415, intron 1 of 24)	432	NM_001205311	20497	Mm.25804	NM_019415	ENSMUSG00000031766	Slc12a3	AI035291|NCC|NCCT|TSC	solute carrier family 12, member 3	protein-coding
mm_6963.1	chr1	86111975	86111984	-	1	NA	promoter-TSS (NM_008311)	promoter-TSS (NM_008311)	-9	NM_008311	15559	Mm.439747	NM_008311	ENSMUSG00000026228	Htr2b	5-HT2B|AJ012488|AV377389	5-hydroxytryptamine (serotonin) receptor 2B	protein-coding
mm_52231.1	chr6	103691982	103691984	+	1	NA	intron (NM_007697, intron 12 of 26)	intron (NM_007697, intron 12 of 26)	181107	NM_007697	12661	Mm.251288	NM_007697	ENSMUSG00000030077	Chl1	A530023M13Rik|AI465420|CALL|LICAM2	cell adhesion molecule L1-like	protein-coding
mm_16102.1	chr2	169632693	169632747	+	1	NA	promoter-TSS (NM_080455)	promoter-TSS (NM_080455)	-926	NM_080455	228911	Mm.315789	NM_080455	ENSMUSG00000047907	Tshz2	2900073F20Rik|B830045G17|Mtsh2|Sdccag33l|Tsh2|Zfp218|mKIAA4248|teashirt2	teashirt zinc finger family member 2	protein-coding
mm_149866.1	chr19	25147345	25147357	+	1	NA	exon (NM_028785, exon 25 of 48)	exon (NM_028785, exon 25 of 48)	-89851	NM_181404	107351	Mm.260722	NM_181404	ENSMUSG00000032702	Kank1	A930031B09Rik|AU015049|AW121052|Ankrd15|D330024H06Rik|mKIAA0172	KN motif and ankyrin repeat domains 1	protein-coding
mm_11210.1	chr2	29619693	29619825	+	1	NA	promoter-TSS (NM_054050)	promoter-TSS (NM_054050)	39	NM_001039086	107746	Mm.298274	NM_054050	ENSMUSG00000039844	Rapgef1	4932418O06Rik|C3G|Grf2	Rap guanine nucleotide exchange factor (GEF) 1	protein-coding
mm_132145.1	chr16	32099782	32099857	+	1	NA	promoter-TSS (NM_025892)	promoter-TSS (NM_025892)	17	NM_025892	66994	Mm.22990	NM_025892	ENSMUSG00000035790	Cep19	1500031L02Rik|AI428934|AL022620	centrosomal protein 19	protein-coding
mm_110606.1	chr12	56536663	56536678	-	1	NA	5' UTR (NM_009385, exon 1 of 3)	5' UTR (NM_009385, exon 1 of 3)	238	NM_009385	21869	Mm.89972	NM_009385	ENSMUSG00000001496	Nkx2-1	AV026640|Nkx2.1|T/EBP|Titf1|Ttf-1	NK2 homeobox 1	protein-coding
mm_92977.1	chr10	86691699	86691755	-	1	NA	exon (NM_011631, exon 17 of 18)	exon (NM_011631, exon 17 of 18)	6200	NR_015572	66263	Mm.392261	NR_015572		1810014B01Rik	-	RIKEN cDNA 1810014B01 gene	pseudo
mm_159094.1	chr2	33640637	33640637	-	1	NA	promoter-TSS (NM_010725)	promoter-TSS (NM_010725)	-126	NM_010725	16917	Mm.39825	NM_010725	ENSMUSG00000038765	Lmx1b	Icst|LMX1.1|LMX1.2	LIM homeobox transcription factor 1 beta	protein-coding
mm_151743.1	chr19	5001790	5001814	-	1	NA	Intergenic	CpG	-11831	NM_153553	225872	Mm.287867	NM_153553	ENSMUSG00000045903	Npas4	LE-PAS|Nxf	neuronal PAS domain protein 4	protein-coding
mm_113164.1	chr13	24806928	24806932	+	1	NA	intron (NM_024473, intron 3 of 4)	intron (NM_024473, intron 3 of 4)	5273	NM_024473	79555	Mm.266668	NM_024473	ENSMUSG00000019132	BC005537	8030460C05Rik|C78201	cDNA sequence BC005537	protein-coding
mm_162663.1	chr10	5550852	5550868	-	1	NA	promoter-TSS (NM_153399)	promoter-TSS (NM_153399)	-168	NM_001347732	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_54417.1	chr6	32897023	32897033	-	1	NA	intron (NM_025336, intron 4 of 7)	intron (NM_025336, intron 4 of 7)	163124	NM_025336	66075	Mm.21501	NM_025336	ENSMUSG00000053768	Chchd3	0610041L09Rik|1700039J09Rik|AW558177	coiled-coil-helix-coiled-coil-helix domain containing 3	protein-coding
mm_134559.1	chr16	20301788	20301808	-	1	NA	intron (NM_001005767, intron 1 of 9)	intron (NM_001005767, intron 1 of 9)	564	NM_001005767	381038	Mm.371737	NM_001005767	ENSMUSG00000033918	Parl	D16Ertd607e|PRO2207|PSARL1|PSENIP2|Psarl	presenilin associated, rhomboid-like	protein-coding
mm_152174.1	chr19	7341849	7341863	-	1	NA	promoter-TSS (NM_001080388)	promoter-TSS (NM_001080388)	4	NM_001080389	13728	Mm.258986	NM_007928	ENSMUSG00000024969	Mark2	EMK-1|Emk|Par-1|Par-1b	MAP/microtubule affinity regulating kinase 2	protein-coding
mm_31062.1	chr4	41314923	41314970	+	1	NA	promoter-TSS (NM_026893)	promoter-TSS (NM_026893)	-45	NM_026893	68970	Mm.28891	NM_026893	ENSMUSG00000028436	Dcaf12	1500001L20Rik|5830424K06Rik|AA420338|AI851081|Wdr40a	DDB1 and CUL4 associated factor 12	protein-coding
mm_71602.1	chr8	55059153	55059164	+	1	NA	3' UTR (NM_001253754, exon 7 of 7)	3' UTR (NM_001253754, exon 7 of 7)	104430	NM_001253756	234267	Mm.241700	NM_153581	ENSMUSG00000031517	Gpm6a	Gpm6|M6A	glycoprotein m6a	protein-coding
mm_70942.1	chr8	26119462	26119539	+	1	NA	promoter-TSS (NM_207659)	promoter-TSS (NM_207659)	120	NM_029965	77733	Mm.291906	NM_029965	ENSMUSG00000013878	Rnf170	6720407G21Rik|AI481227	ring finger protein 170	protein-coding
mm_12818.1	chr2	80316828	80316841	+	1	NA	intron (NM_024181, intron 1 of 22)	intron (NM_024181, intron 1 of 22)	1368	NM_024181	66861	Mm.21762	NM_024181	ENSMUSG00000027006	Dnajc10	1200006L06Rik|D2Ertd706e|ERdj5|JPDI	DnaJ heat shock protein family (Hsp40) member C10	protein-coding
mm_19894.1	chr2	114051994	114052027	-	1	NA	exon (NM_009608, exon 2 of 7)	exon (NM_009608, exon 2 of 7)	865	NM_009608	11464	Mm.686	NM_009608	ENSMUSG00000068614	Actc1	Actc-1	actin, alpha, cardiac muscle 1	protein-coding
mm_53264.1	chr6	128362755	128362774	+	1	NA	promoter-TSS (NM_008021)	promoter-TSS (NM_008021)	58	NM_001326583	72440	Mm.143908	NM_197981	ENSMUSG00000048668	Rhno1	2510047L19Rik|5930416I19Rik	RAD9-HUS1-RAD1 interacting nuclear orphan 1	protein-coding
mm_135044.1	chr16	33056390	33056429	-	1	NA	promoter-TSS (NM_021338)	promoter-TSS (NM_021338)	-44	NM_001130485	57808	Mm.19355	NM_021338	ENSMUSG00000060636	Rpl35a	2810431L15Rik|Rpl35	ribosomal protein L35A	protein-coding
mm_36410.1	chr4	78060414	78060418	-	1	NA	intron (NM_011211, intron 1 of 39)	L1_Mus3|LINE|L1	151479	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding
mm_127655.1	chr15	102498528	102498563	+	1	NA	3' UTR (NM_001163643, exon 16 of 16)	3' UTR (NM_001163643, exon 16 of 16)	18459	NM_001163643	26404	Mm.172897	NM_009582	ENSMUSG00000023050	Map3k12	DLK|MUK|Zpk	mitogen-activated protein kinase kinase kinase 12	protein-coding
mm_125431.1	chr15	44428074	44428174	+	1	NA	promoter-TSS (NM_175009)	promoter-TSS (NM_175009)	13	NM_175009	223527	Mm.291828	NM_175009	ENSMUSG00000022338	Eny2	1810057B09Rik|6720481I12|DC6|Ey2	enhancer of yellow 2 homolog (Drosophila)	protein-coding
mm_116619.1	chr13	48878657	48878669	-	1	NA	TTS (NM_001033268)	TTS (NM_001033268)	-7778	NM_011078	18676	Mm.486213	NM_011078	ENSMUSG00000038025	Phf2	GRC5	PHD finger protein 2	protein-coding
mm_64209.1	chr7	141475460	141475462	+	1	NA	promoter-TSS (NM_025593)	promoter-TSS (NM_025593)	225	NM_053082	64540	Mm.489619	NM_053082	ENSMUSG00000025511	Tspan4	AI325509|AI746565|D130042I01Rik|NAG-2|Tm4sf7|Tspan-4	tetraspanin 4	protein-coding
mm_3653.1	chr1	153093951	153093990	+	1	NA	intron (NM_175460, intron 7 of 10)	intron (NM_175460, intron 7 of 10)	92477	NM_008485	16782	Mm.329272	NM_008485	ENSMUSG00000026479	Lamc2	AA589349	laminin, gamma 2	protein-coding
mm_63623.1	chr7	128266338	128266348	+	1	NA	intron (NM_133254, intron 1 of 13)	intron (NM_133254, intron 1 of 13)	646	NM_133254	246787	Mm.38870	NM_133254	ENSMUSG00000030781	Slc5a2	Sglt2	solute carrier family 5 (sodium/glucose cotransporter), member 2	protein-coding
mm_135004.1	chr16	32179676	32179688	-	1	NA	promoter-TSS (NM_001033539)	promoter-TSS (NM_001033539)	-118	NM_001033539	328660	Mm.441006	NM_001033539	ENSMUSG00000075269	Bex6	B020003O03Rik	brain expressed family member 6	protein-coding
mm_38168.1	chr4	135217061	135217091	-	1	NA	3' UTR (NM_013885, exon 6 of 6)	3' UTR (NM_013885, exon 6 of 6)	55684	NM_013885	29876	Mm.257765	NM_013885	ENSMUSG00000037242	Clic4	D0Jmb3|TU-74|mc3s5|mtCLIC	chloride intracellular channel 4 (mitochondrial)	protein-coding
mm_43909.1	chr5	144256084	144256112	+	1	NA	intron (NM_018772, intron 2 of 2)	intron (NM_018772, intron 2 of 2)	873	NM_018772	55950	Mm.38011	NM_018772	ENSMUSG00000047843	Bri3	I3	brain protein I3	protein-coding
mm_23173.1	chr3	40783122	40783141	+	1	NA	intron (NM_011020, intron 14 of 18)	intron (NM_011020, intron 14 of 18)	-16820	NM_173169	20873	Mm.3794	NM_011495	ENSMUSG00000025758	Plk4	1700028H20|AI385771|Sak|Stk18	polo-like kinase 4	protein-coding
mm_20307.1	chr2	127208245	127208273	-	1	NA	promoter-TSS (NM_177214)	promoter-TSS (NM_177214)	21	NM_198630	329509	Mm.120738	NM_198630	ENSMUSG00000044145	1810024B03Rik	-	RIKEN cDNA 1810024B03 gene	protein-coding
mm_79981.1	chr9	66946058	66946143	+	1	NA	promoter-TSS (NM_026467)	promoter-TSS (NM_026467)	24	NM_026467	67941	Mm.30120	NM_026467	ENSMUSG00000036781	Rps27l	1810034D23Rik	ribosomal protein S27-like	protein-coding
mm_39412.1	chr5	14677451	14677452	+	1	NA	exon (NM_011995, exon 5 of 25)	exon (NM_011995, exon 5 of 25)	162533	NM_001110796	26875	Mm.146275	NM_011995	ENSMUSG00000061601	Pclo	Acz|Pico	piccolo (presynaptic cytomatrix protein)	protein-coding
mm_119155.1	chr14	31575494	31575502	+	1	NA	intron (NM_009937, intron 1 of 16)	L2b|LINE|L2	1885	NM_009937	382864	Mm.239821	NM_009937	ENSMUSG00000057606	Colq	A130034K24Rik	collagen-like tail subunit (single strand of homotrimer) of asymmetric acetylcholinesterase	protein-coding
mm_54900.1	chr6	47455052	47455069	-	1	NA	intron (NM_012042, intron 1 of 21)	CpG	736	NM_012042	26965	Mm.87611	NM_012042	ENSMUSG00000029686	Cul1	-	cullin 1	protein-coding
mm_8230.1	chr1	138175627	138175644	-	1	NA	promoter-TSS (NM_001268286)	promoter-TSS (NM_001268286)	-330	NM_001268286	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_7138.1	chr1	91062516	91062527	-	1	NA	intron (NM_001310732, intron 1 of 24)	intron (NM_001310732, intron 1 of 24)	9077	NM_008515	16978	Mm.45039	NM_008515	ENSMUSG00000026305	Lrrfip1	AU024550|Fliiap1	leucine rich repeat (in FLII) interacting protein 1	protein-coding
mm_2967.1	chr1	133046144	133046162	+	1	NA	5' UTR (NM_001099276, exon 1 of 33)	5' UTR (NM_001099276, exon 1 of 33)	141	NM_001099276	240752	Mm.387308	NM_001099276	ENSMUSG00000026447	Pik3c2b	C330011J12Rik|Gm199|PI3K-C2beta|PI3KC2beta	phosphoinositide-3-kinase, class 2, beta polypeptide	protein-coding
mm_116579.1	chr13	47105734	47105747	-	1	NA	intron (NM_025900, intron 1 of 10)	CpG	481	NM_025900	110052	Mm.131150	NM_025900	ENSMUSG00000021377	Dek	1810019E15Rik|D13H6S231E	DEK oncogene (DNA binding)	protein-coding
mm_47264.1	chr5	121836811	121836845	-	1	NA	promoter-TSS (NM_001306128)	promoter-TSS (NM_001306128)	31	NM_001306128	16923	Mm.65493	NM_008507	ENSMUSG00000042594	Sh2b3	AI429800|Lnk	SH2B adaptor protein 3	protein-coding
mm_153570.1	chr19	42752460	42752517	-	1	NA	5' UTR (NM_029011, exon 1 of 16)	5' UTR (NM_029011, exon 1 of 16)	287	NM_029011	74580	Mm.329858	NM_029011	ENSMUSG00000060224	Pyroxd2	3830409H07Rik|4833409A17Rik	pyridine nucleotide-disulphide oxidoreductase domain 2	protein-coding
mm_70936.1	chr8	25849661	25849665	+	1	NA	promoter-TSS (NM_008432)	promoter-TSS (NM_008432)	40	NM_008432	16532	Mm.289679	NM_008432	ENSMUSG00000031576	Kcnu1	Kcnma3|Slo3|mSlo3	potassium channel, subfamily U, member 1	protein-coding
mm_168550.1	chr11	63846940	63846950	-	1	NA	Intergenic	Intergenic	75339	NM_018805	54710	Mm.274426	NM_018805	ENSMUSG00000070407	Hs3st3b1	3-OST-3B|3OST3B1|3Ost3b|AU041882|AW536289|Hs3st3b|m3-OST-3B	heparan sulfate (glucosamine) 3-O-sulfotransferase 3B1	protein-coding
mm_127121.1	chr15	98093671	98093681	+	1	NA	promoter-TSS (NM_144851)	promoter-TSS (NM_144851)	-107	NM_144851	223870	Mm.384023	NM_144851	ENSMUSG00000033075	Senp1	2310046A20Rik|D15Ertd528e|E330036L07Rik|suPr-2	SUMO1/sentrin specific peptidase 1	protein-coding
mm_109310.1	chr12	109560850	109560858	+	1	NA	non-coding (NR_003633, exon 5 of 5)	non-coding (NR_003633, exon 5 of 5)	-2838	NR_030427	791079		NR_030427	ENSMUSG00000076451	Mir770	Mirn770|mir-770|mmu-mir-770	microRNA 770	ncRNA
mm_55240.1	chr6	52313499	52313510	-	1	NA	promoter-TSS (NM_007966)	promoter-TSS (NM_007966)	6	NM_007966	14028	Mm.389754	NM_007966	ENSMUSG00000005503	Evx1	Evx-1	even-skipped homeobox 1	protein-coding
mm_1771.1	chr1	77951433	77951439	+	1	NA	Intergenic	Intergenic	245700	NM_008781	18505	Mm.1371	NM_008781	ENSMUSG00000004872	Pax3	Pax-3|Sp|Splchl2|splotch	paired box 3	protein-coding
mm_152651.1	chr19	12765419	12765443	-	1	NA	5' UTR (NM_170786, exon 1 of 2)	5' UTR (NM_170786, exon 1 of 2)	201	NM_170786	12803	Mm.290924	NM_053007	ENSMUSG00000079415	Cntf	AI429687	ciliary neurotrophic factor	protein-coding
mm_68456.1	chr7	110122891	110122903	-	1	NA	exon (NM_009516, exon 1 of 11)	exon (NM_009516, exon 1 of 11)	838	NM_009516	22390	Mm.287173	NM_009516	ENSMUSG00000031016	Wee1	Wee1A	WEE 1 homolog 1 (S. pombe)	protein-coding
mm_23628.1	chr3	66219910	66219927	+	1	NA	promoter-TSS (NM_008987)	promoter-TSS (NM_008987)	31	NM_008987	19288	Mm.276776	NM_008987	ENSMUSG00000027832	Ptx3	AI607804|TSG-14	pentraxin related gene	protein-coding
mm_160520.1	chr9	31163343	31163343	-	1	NA	intron (NM_001102455, intron 9 of 16)	intron (NM_001102455, intron 9 of 16)	-31544	NM_011176	19143	Mm.243926	NM_011176	ENSMUSG00000031995	St14	Epithin|MT-SP1|Prss14|Tmprss14|mCAP3|matriptase	suppression of tumorigenicity 14 (colon carcinoma)	protein-coding
mm_164223.1	chr15	85354251	85354252	-	1	NA	intron (NM_016843, intron 1 of 11)	intron (NM_016843, intron 1 of 11)	17870	NM_016843	54138	Mm.248906	NM_016843	ENSMUSG00000016541	Atxn10	AI325283|C77170|E46|Sca10|TEG-169|Tex169	ataxin 10	protein-coding
mm_161217.1	chr13	67278456	67278456	-	1	NA	promoter-TSS (NR_033540)	promoter-TSS (NR_033540)	-138	NR_033540	100038627	Mm.387089	NR_033540		F630042J09Rik	ENSMUSG00000074823	RIKEN cDNA F630042J09 gene	ncRNA
mm_166121.1	chr4	152065505	152065508	+	1	NA	Intergenic	ID_B1|SINE|B4	-21357	NR_104381	269608	Mm.332102	NM_001004156	ENSMUSG00000039713	Plekhg5	BC023181|Syx	pleckstrin homology domain containing, family G (with RhoGef domain) member 5	protein-coding
mm_134922.1	chr16	30388807	30388858	-	1	NA	promoter-TSS (NM_001128094)	promoter-TSS (NM_001128094)	-302	NM_001128096	224088	Mm.8924	NM_001128094	ENSMUSG00000022533	Atp13a3	AU022875|Gm1745|Gm541|Gm542	ATPase type 13A3	protein-coding
mm_112749.1	chr13	19341929	19341941	+	1	NA	Intergenic	Intergenic	53878	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_39198.1	chr4	156016597	156016611	-	1	NA	TTS (NM_011659)	TTS (NM_011659)	2909	NM_011659	22163	Mm.13885	NM_011659	ENSMUSG00000029075	Tnfrsf4	ACT35|CD134|Ly-70|Ox40|TXGP1L|Txgp1	tumor necrosis factor receptor superfamily, member 4	protein-coding
mm_125263.1	chr15	35371499	35371593	+	1	NA	promoter-TSS (NM_177151)	promoter-TSS (NM_177151)	0	NM_177151	666173	Mm.309250	NM_177151	ENSMUSG00000037646	Vps13b	1810042B05Rik|2310042E16Rik|4732488H20|C330002D13Rik|C87206|Coh1|D230005K13|mKIAA0532|mKIAA5032	vacuolar protein sorting 13B	protein-coding
mm_95753.1	chr11	54902889	54902894	+	1	NA	promoter-TSS (NM_008161)	promoter-TSS (NM_008161)	37	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_48002.1	chr5	136161293	136161310	-	1	NA	intron (NM_178751, intron 2 of 2)	RSINE1|SINE|B4	9355	NM_178751	269717	Mm.308396	NM_178751	ENSMUSG00000039747	Orai2	A730041O15Rik|Tmem142b	ORAI calcium release-activated calcium modulator 2	protein-coding
mm_128069.1	chr15	27518762	27518767	-	1	NA	intron (NM_020332, intron 1 of 11)	B4|SINE|B4	52087	NM_020332	11732	Mm.265264	NM_020332	ENSMUSG00000022265	Ank	Ankh|D15Ertd221e|ank|mKIAA1581	progressive ankylosis	protein-coding
mm_96450.1	chr11	67533076	67533091	+	1	NA	promoter-TSS (NM_008088)	promoter-TSS (NM_008088)	85	NM_008088	14457	Mm.40338	NM_008088	ENSMUSG00000033066	Gas7	AW124766|B230343A10Rik|Gas7-cb	growth arrest specific 7	protein-coding
mm_147474.1	chr18	46864032	46864047	-	1	NA	intron (NM_029008, intron 1 of 19)	intron (NM_029008, intron 1 of 19)	14000	NM_029008	74574	Mm.26379	NM_029008	ENSMUSG00000024481	Lvrn	4833403I15Rik|APQ|Aqpep	laeverin	protein-coding
mm_88200.1	chr10	70110269	70110296	+	1	NA	intron (NM_001111121, intron 1 of 8)	intron (NM_001111121, intron 1 of 8)	13161	NM_001111121	76551	Mm.281741	NM_001111121	ENSMUSG00000048701	Ccdc6	2810012H18Rik|AA536681|AA960498|AW061011	coiled-coil domain containing 6	protein-coding
mm_38440.1	chr4	139833525	139833535	-	1	NA	promoter-TSS (NM_011039)	promoter-TSS (NM_011039)	-562	NM_011039	18509	Mm.218760	NM_011039	ENSMUSG00000028736	Pax7	Pax-7	paired box 7	protein-coding
mm_112194.1	chr12	113425680	113425694	-	1	NA	Intergenic	(CAGCT)n|Simple_repeat|Simple_repeat	-63878	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_158207.1	chrX	105855945	105855967	-	1	NA	exon (NM_009530, exon 12 of 35)	exon (NM_009530, exon 12 of 35)	73416	NM_009530	22589	Mm.10141	NM_009530	ENSMUSG00000031229	Atrx	4833408C14Rik|AI447451|ATR2|DXHXS6677E|HP1-BP38|Hp1bp2|Hp1bp38|MRXS3|RAD54L|Rad54|XH2|Xnp|ZNF-HX	alpha thalassemia/mental retardation syndrome X-linked	protein-coding
mm_47908.1	chr5	134946256	134946271	-	1	NA	exon (NM_009903, exon 1 of 1)	exon (NM_009903, exon 1 of 1)	671	NM_009903	12740	Mm.7339	NM_009903	ENSMUSG00000047501	Cldn4	Cep-r|Cpetr|Cpetr1	claudin 4	protein-coding
mm_15835.1	chr2	164687329	164687335	+	1	NA	3' UTR (NM_001012704, exon 2 of 2)	3' UTR (NM_001012704, exon 2 of 2)	2225	NM_001012704	408190	Mm.376205	NM_001012704	ENSMUSG00000067704	Wfdc13	Wfdc13l1	WAP four-disulfide core domain 13	protein-coding
mm_85880.1	chr9	110990571	110990599	-	1	NA	promoter-TSS (NM_153100)	promoter-TSS (NM_153100)	-872	NM_153100	235636	Mm.441138	NM_153100	ENSMUSG00000066319	Rtp3	Tmem7	receptor transporter protein 3	protein-coding
mm_109841.1	chr12	4477139	4477196	-	1	NA	promoter-TSS (NM_010881)	promoter-TSS (NM_010881)	15	NM_010881	17977	Mm.301039	NM_010881	ENSMUSG00000020647	Ncoa1	KAT13A|NCoA-1|NRC-1|SRC-1|SRC-a|SRC1|bHLHe74|mNRC-1	nuclear receptor coactivator 1	protein-coding
mm_43962.1	chr5	145260177	145260179	+	1	NA	Intergenic	MuRRS4-int|LTR|ERV1	-23165	NM_001081431	666311	Mm.260773	NM_001081431	ENSMUSG00000070420	Zscan25	EG666311|Zfp498	zinc finger and SCAN domain containing 25	protein-coding
mm_120489.1	chr14	65979725	65979779	+	1	NA	exon (NM_013492, exon 7 of 9)	exon (NM_013492, exon 7 of 9)	11269	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_84096.1	chr9	58249630	58249640	-	1	NA	exon (NM_008884, exon 1 of 8)	exon (NM_008884, exon 1 of 8)	151	NM_178087	18854	Mm.392123	NM_008884	ENSMUSG00000036986	Pml	1200009E24Rik|AI661194|Trim19	promyelocytic leukemia	protein-coding
mm_90965.1	chr10	13375359	13375374	-	1	NA	intron (NM_001195065, intron 1 of 12)	RSINE1|SINE|B4	13604	NM_001195066	215789	Mm.283359	NM_001033257	ENSMUSG00000062866	Phactr2	AV158170|BC012871	phosphatase and actin regulator 2	protein-coding
mm_170785.1	chr2	174980968	174980983	-	1	NA	Intergenic	Intergenic	86794	NM_001085546	664987		NM_001085546	ENSMUSG00000078905	Gm14393	OTTMUSG00000016546	predicted gene 14393	protein-coding
mm_59621.1	chr7	28153416	28153426	+	1	NA	exon (NM_001164655, exon 12 of 20)	exon (NM_001164655, exon 12 of 20)	-16327	NM_007991	14113	Mm.4595	NM_007991	ENSMUSG00000046865	Fbl	AL022665|FIB|FLRN|RNU3IP1	fibrillarin	protein-coding
mm_115280.1	chr13	111807276	111807292	+	1	NA	intron (NM_011945, intron 1 of 19)	intron (NM_011945, intron 1 of 19)	1699	NM_011945	26401	Mm.15918	NM_011945	ENSMUSG00000021754	Map3k1	MAPKKK1|MEKK1|Mekk	mitogen-activated protein kinase kinase kinase 1	protein-coding
mm_58717.1	chr7	13016851	13016858	+	1	NA	Intergenic	B1_Mur4|SINE|Alu	-7054	NM_001024699	232879	Mm.279272	NM_001024699	ENSMUSG00000049600	Zbtb45	BB161562|Gm157|Zfp499	zinc finger and BTB domain containing 45	protein-coding
mm_58230.1	chr6	144781908	144781988	-	1	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	109080	NR_040519	66760	Mm.233631	NR_040519	ENSMUSG00000085785	Sox5os3	4933425H06Rik	SRY (sex determining region Y)-box 5, opposite strand 3	ncRNA
mm_68470.1	chr7	110648818	110648833	-	1	NA	Intergenic	Intergenic	21156	NM_009627	11535	Mm.1408	NM_009627	ENSMUSG00000030790	Adm	AM	adrenomedullin	protein-coding
mm_58252.1	chr6	145075939	145075954	-	1	NA	5' UTR (NM_007532, exon 1 of 11)	5' UTR (NM_007532, exon 1 of 11)	211	NM_007532	12035	Mm.4606	NM_007532	ENSMUSG00000030268	Bcat1	BCATc|Eca39	branched chain aminotransferase 1, cytosolic	protein-coding
mm_134080.1	chr16	8721697	8721699	-	1	NA	intron (NM_001003918, intron 1 of 30)	intron (NM_001003918, intron 1 of 30)	16644	NM_001003918	252870	Mm.295330	NM_001003918	ENSMUSG00000022710	Usp7	2210010O09Rik|AA409944|AA617399|AU019296|AW548146|C80752|Hausp	ubiquitin specific peptidase 7	protein-coding
mm_104053.1	chr11	86358285	86358322	-	1	NA	promoter-TSS (NM_001080931)	promoter-TSS (NM_001080931)	-778	NM_001080931	327987	Mm.341886	NM_001080931	ENSMUSG00000034297	Med13	1110067M05Rik|D030023K18|Thrap1|Trap240	mediator complex subunit 13	protein-coding
mm_39305.1	chr5	7960260	7960288	+	1	NA	promoter-TSS (NM_054098)	promoter-TSS (NM_054098)	-198	NM_054098	117167	Mm.31403	NM_054098	ENSMUSG00000012428	Steap4	1110021O17Rik|AI481214|Tiarp|Tnfaip9	STEAP family member 4	protein-coding
mm_172018.1	chr6	113378192	113378192	+	1	NA	promoter-TSS (NM_026552)	promoter-TSS (NM_026552)	79	NM_001170485	68089	Mm.289306	NM_026552	ENSMUSG00000079426	Arpc4	20kDa|5330419I20Rik|AI327076|p20-Arc	actin related protein 2/3 complex, subunit 4	protein-coding
mm_124102.1	chr14	79301041	79301043	-	1	NA	intron (NM_025427, intron 1 of 4)	CpG	593	NM_025427	66214	Mm.29811	NM_025427	ENSMUSG00000022018	Rgcc	1190002H23Rik|Rgc-32|Rgc32	regulator of cell cycle	protein-coding
mm_118877.1	chr14	25868785	25868809	+	1	NA	intron (NM_013469, intron 1 of 14)	intron (NM_013469, intron 1 of 14)	26642	NM_013469	11744	Mm.294083	NM_013469	ENSMUSG00000021866	Anxa11	A830099O17Rik|Anx11	annexin A11	protein-coding
mm_137050.1	chr17	17917863	17917868	+	1	NA	Intergenic	Intergenic	30041	NM_008039	14289	Mm.378918	NM_008039	ENSMUSG00000052270	Fpr2	E330010I07Rik|Fpr-rs2	formyl peptide receptor 2	protein-coding
mm_77809.1	chr9	3036399	3036401	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	2343	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_17664.1	chr2	32083651	32083751	-	1	NA	promoter-TSS (NM_175511)	promoter-TSS (NM_175511)	4	NM_175511	241303	Mm.250441	NM_175511	ENSMUSG00000050592	Fam78a	A130092J06Rik	family with sequence similarity 78, member A	protein-coding
mm_1191.1	chr1	62703429	62703439	+	1	NA	5' UTR (NM_001077407, exon 1 of 16)	5' UTR (NM_001077407, exon 1 of 16)	117	NM_001077405	18187	Mm.266341	NM_010939	ENSMUSG00000025969	Nrp2	1110048P06Rik|Np-2|Np2|Npn-2|Npn2	neuropilin 2	protein-coding
mm_107013.1	chr12	12262140	12262157	+	1	NA	promoter-TSS (NM_001146119)	promoter-TSS (NM_001146119)	9	NM_001146119	76820	Mm.440802	NM_029758	ENSMUSG00000020589	Fam49a	2410157M17Rik|9630047E15|D12Ertd553e	family with sequence similarity 49, member A	protein-coding
mm_72533.1	chr8	83995474	83995480	+	1	NA	3' UTR (NM_008854, exon 10 of 10)	3' UTR (NM_008854, exon 10 of 10)	-2195	NM_001081415	666704	Mm.298091	NM_001081415	ENSMUSG00000079003	Samd1	AA589507	sterile alpha motif domain containing 1	protein-coding
mm_141606.1	chr17	32788285	32788297	-	1	NA	promoter-TSS (NM_172458)	promoter-TSS (NM_172458)	-4	NM_172458	208292	Mm.38813	NM_172458	ENSMUSG00000024298	Zfp871	4732483N19|9030612M13Rik|AI118577|AI265322|mKIAA3006	zinc finger protein 871	protein-coding
mm_171075.1	chr3	120105604	120105613	+	1	NA	Intergenic	L1Md_T|LINE|L1	-322220	NM_019550	56195	Mm.29966	NM_019550	ENSMUSG00000028134	Ptbp2	Ptb2|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding
mm_40136.1	chr5	35046484	35046493	+	1	NA	intron (NM_019447, intron 10 of 13)	intron (NM_019447, intron 10 of 13)	4979	NM_019447	54426	Mm.27369	NM_019447	ENSMUSG00000029102	Hgfac	HGFA	hepatocyte growth factor activator	protein-coding
mm_32308.1	chr4	103170953	103170980	+	1	NA	TTS (NM_177732)	TTS (NM_177732)	43918	NM_177732	242585	Mm.281800	NM_177732	ENSMUSG00000028521	Slc35d1	AI834976|C330011J09|UGTREL7|mKIAA0260	solute carrier family 35 (UDP-glucuronic acid/UDP-N-acetylgalactosamine dual transporter), member D1	protein-coding
mm_5253.1	chr1	16619438	16619446	-	1	NA	promoter-TSS (NM_001271017)	promoter-TSS (NM_001271017)	-104	NM_001271017	66799	Mm.122430	NM_025773	ENSMUSG00000025939	Ube2w	6130401J04Rik	ubiquitin-conjugating enzyme E2W (putative)	protein-coding
mm_33753.1	chr4	134324898	134324910	+	1	NA	intron (NM_001039048, intron 5 of 8)	intron (NM_001039048, intron 5 of 8)	9784	NM_001039048	433766	Mm.331961	NM_001039048	ENSMUSG00000028834	Trim63	MuRF1|RF1|Rnf28	tripartite motif-containing 63	protein-coding
mm_151468.1	chr19	58670434	58670461	+	1	NA	promoter-TSS (NM_026925)	promoter-TSS (NM_026925)	82	NM_026925	69060	Mm.20407	NM_026925	ENSMUSG00000046008	Pnlip	1810007A24Rik|PL|PTL	pancreatic lipase	protein-coding
mm_169385.1	chr14	41586726	41586729	+	1	NA	Intergenic	BGLII|LTR|ERVK	185677	NM_001244671	100042055	Mm.429109	NM_001244671	ENSMUSG00000095226	Gm10377	ENSMUSG00000072606	predicted gene 10377	protein-coding
mm_62177.1	chr7	97400169	97400178	+	1	NA	5' UTR (NM_024220, exon 1 of 3)	5' UTR (NM_024220, exon 1 of 3)	170	NM_024220	68197	Mm.334031	NM_024220	ENSMUSG00000030647	Ndufc2	1810004I06Rik|2010300P09Rik|G1|R75094	NADH dehydrogenase (ubiquinone) 1, subcomplex unknown, 2	protein-coding
mm_117613.1	chr13	91388102	91388110	-	1	NA	promoter-TSS (NR_045161)	promoter-TSS (NR_045161)	-21	NR_045161	320297	Mm.375866	NR_045161	ENSMUSG00000097182	A830009L08Rik	-	RIKEN cDNA A830009L08 gene	ncRNA
mm_159569.1	chr4	112616508	112616508	+	1	NA	intron (NM_001285963, intron 1 of 7)	intron (NM_001285963, intron 1 of 7)	2768	NM_001285963	329919	Mm.259806	NM_177865	ENSMUSG00000034359	Skint2	A430070M19|B7S3|OTTMUSG00000008540|Skint-2	selection and upkeep of intraepithelial T cells 2	protein-coding
mm_126339.1	chr15	79900272	79900288	+	1	NA	intron (NM_001160415, intron 5 of 8)	MIRb|SINE|MIR	5257	NM_001347041	80287	Mm.284059	NM_030255	ENSMUSG00000009585	Apobec3	Apobec|Arp3|BC003314|Cem15|Rfv3	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 3	protein-coding
mm_66712.1	chr7	46030282	46030307	-	1	NA	promoter-TSS (NM_018795)	promoter-TSS (NM_018795)	-8	NM_018795	27421	Mm.63514	NM_018795	ENSMUSG00000030834	Abcc6	Abcc1b|DCC|Dyscalc1|Mrp6|dyscalc	ATP-binding cassette, sub-family C (CFTR/MRP), member 6	protein-coding
mm_66586.1	chr7	45395183	45395203	-	1	NA	intron (NM_009224, intron 1 of 9)	intron (NM_009224, intron 1 of 9)	549	NM_009224	20637	Mm.216386	NM_009224	ENSMUSG00000063511	Snrnp70	2700022N21Rik|3200002N22Rik|AI325098|R74807|Rnu1p70|Rnulp70|Snrp70|Srnp70|U1-70|U1-70K	small nuclear ribonucleoprotein 70 (U1)	protein-coding
mm_121527.1	chr14	122171265	122171307	+	1	NA	Intergenic	Intergenic	-10408	NM_029556	69634	Mm.34608	NM_029556	ENSMUSG00000025545	Clybl	0610033J05Rik|2310014M14Rik|AI256068|Clb	citrate lyase beta like	protein-coding
mm_120208.1	chr14	62292476	62292496	+	1	NA	intron (NM_173419, intron 1 of 1)	intron (NM_173419, intron 1 of 1)	493	NM_173419	239133	Mm.127330	NM_173419	ENSMUSG00000048281	Dleu7	BC038059	deleted in lymphocytic leukemia, 7	protein-coding
mm_53174.1	chr6	125349700	125349775	+	1	NA	promoter-TSS (NM_011609)	promoter-TSS (NM_011609)	14	NM_011609	21937	Mm.1258	NM_011609	ENSMUSG00000030341	Tnfrsf1a	CD120a|FPF|TNF-R|TNF-R-I|TNF-R1|TNF-R55|TNF-alphaR1|TNFAR|TNFR60|TNFRI|TNFRp55|TNFalpha-R1|Tnfr-2|Tnfr1|p55|p55-R	tumor necrosis factor receptor superfamily, member 1a	protein-coding
mm_84695.1	chr9	72403641	72403654	-	1	NA	Intergenic	Intergenic	-34882	NM_008613	17427	Mm.387671	NM_008613	ENSMUSG00000032221	Mns1	AW546487	meiosis-specific nuclear structural protein 1	protein-coding
mm_94570.1	chr11	11687748	11687756	+	1	NA	intron (NM_001025597, intron 1 of 7)	intron (NM_001025597, intron 1 of 7)	1827	NM_001025597	22778	Mm.103545	NM_009578	ENSMUSG00000018654	Ikzf1	5832432G11Rik|Ikaros|LyF-1|Zfpn1a1|Znfn1a1|hlk-1|mKIAA4227	IKAROS family zinc finger 1	protein-coding
mm_100470.1	chr11	119996981	119997006	+	1	NA	exon (NM_001037755, exon 9 of 14)	exon (NM_001037755, exon 9 of 14)	-17774	NR_037225	100526518		NR_037225	ENSMUSG00000105524	Mir3065	mir-3065|mmu-mir-3065	microRNA 3065	ncRNA
mm_14102.1	chr2	125256435	125256445	+	1	NA	intron (NM_023595, intron 3 of 5)	intron (NM_023595, intron 3 of 5)	8925	NM_023595	110074	Mm.282499	NM_023595	ENSMUSG00000027203	Dut	5031412I06Rik|5133400F09Rik|D2Bwg0749e|Dutp|dUTPase	deoxyuridine triphosphatase	protein-coding
mm_118008.1	chr13	100650982	100651085	-	1	NA	promoter-TSS (NM_001015889)	promoter-TSS (NM_001015889)	28	NM_001044371	19356	Mm.248489	NM_011233	ENSMUSG00000021635	Rad17	MmRad24	RAD17 checkpoint clamp loader component	protein-coding
mm_46376.1	chr5	103795186	103795190	-	1	NA	intron (NM_001080798, intron 3 of 19)	intron (NM_001080798, intron 3 of 19)	40615	NM_001080798	17355	Mm.6949	NM_133919	ENSMUSG00000029313	Aff1	9630032B01Rik|AW319193|Af4|Mllt2h|Rob	AF4/FMR2 family, member 1	protein-coding
mm_18379.1	chr2	60010565	60010566	-	1	NA	intron (NM_001001182, intron 2 of 35)	intron (NM_001001182, intron 2 of 35)	115175	NM_001001182	407823	Mm.228071	NM_001001182	ENSMUSG00000026987	Baz2b	5830435C13Rik|BC053917|D2Ertd794e	bromodomain adjacent to zinc finger domain, 2B	protein-coding
mm_8446.1	chr1	152880270	152880273	-	1	NA	intron (NM_001005507, intron 1 of 21)	intron (NM_001005507, intron 1 of 21)	-2103	NM_001160257	226517	Mm.270775	NM_001005507	ENSMUSG00000042772	Smg7	9430023P16Rik|mKIAA0250	Smg-7 homolog, nonsense mediated mRNA decay factor (C. elegans)	protein-coding
mm_4182.1	chr1	171160060	171160076	+	1	NA	exon (NM_001315500, exon 6 of 6)	exon (NM_001315500, exon 6 of 6)	4550	NM_001315500	17528	Mm.9986	NM_008623	ENSMUSG00000056569	Mpz	Mpp|P-zero|P0	myelin protein zero	protein-coding
mm_71267.1	chr8	40919021	40919031	+	1	NA	3' UTR (NM_001044740, exon 12 of 12)	3' UTR (NM_001044740, exon 12 of 12)	-7207	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_1745.1	chr1	75479530	75479593	+	1	NA	promoter-TSS (NM_001001566)	promoter-TSS (NM_001001566)	29	NM_177056	319998	Mm.44401	NM_177056	ENSMUSG00000051703	Tmem198	A230078I05Rik|Tmem198-1|Tmem198a	transmembrane protein 198	protein-coding
mm_31590.1	chr4	57849157	57849160	+	1	NA	intron (NM_009649, intron 1 of 2)	B3|SINE|B2	3910	NM_001035532	11641	Mm.467752	NM_009649	ENSMUSG00000038729	Akap2	AA959716|AI649048|Akap-2|Akap-kl|B230340M18Rik|Prka2	A kinase (PRKA) anchor protein 2	protein-coding
mm_54533.1	chr6	36715569	36715573	-	1	NA	TTS (NM_008973)	TTS (NM_008973)	95790	NM_008973	19242	Mm.279690	NM_008973	ENSMUSG00000029838	Ptn	HARP|HB-GAM|HBBN|HBGF-8|HBNF|OSF|Osf-1|Osf1	pleiotrophin	protein-coding
mm_157528.1	chrX	51017968	51018009	-	1	NA	promoter-TSS (NM_172413)	promoter-TSS (NM_172413)	30	NM_172413	72065	Mm.43152	NM_172413	ENSMUSG00000050029	Rap2c	2010200P20Rik|AI194294|AL022976	RAP2C, member of RAS oncogene family	protein-coding
mm_122400.1	chr14	41004268	41004283	-	1	NA	intron (NM_001316735, intron 1 of 5)	intron (NM_001316735, intron 1 of 5)	2645	NM_001316739	70564	Mm.27227	NM_027464	ENSMUSG00000021792	Fam213a	5730469M10Rik|AU040822|Adrx|Pamm	family with sequence similarity 213, member A	protein-coding
mm_17983.1	chr2	37801213	37801226	-	1	NA	exon (NM_146122, exon 22 of 22)	exon (NM_146122, exon 22 of 22)	24970	NM_001163566	241324	Mm.392369	NM_001163566	ENSMUSG00000035403	Crb2	5930402A21|BC043114	crumbs family member 2	protein-coding
mm_5440.1	chr1	34842988	34843039	-	1	NA	promoter-TSS (NM_001160236)	promoter-TSS (NM_001160236)	37	NM_001160235	214469	Mm.120151	NM_174997	ENSMUSG00000037503	Fam168b	mKIAA4042	family with sequence similarity 168, member B	protein-coding
mm_78793.1	chr9	44046607	44046617	+	1	NA	intron (NM_009382, intron 2 of 3)	intron (NM_009382, intron 2 of 3)	3228	NM_009382	21838	Mm.3951	NM_009382	ENSMUSG00000032011	Thy1	CD90|T25|Thy-1|Thy-1.2|Thy1.1|Thy1.2	thymus cell antigen 1, theta	protein-coding
mm_23057.1	chr3	35762274	35762323	+	1	NA	intron (NM_029570, intron 1 of 29)	Lx8b|LINE|L1	8160	NM_029570	76295	Mm.239416	NM_029570	ENSMUSG00000037400	Atp11b	1110019I14Rik|ATPIF|ATPIR|mKIAA0956	ATPase, class VI, type 11B	protein-coding
mm_95616.1	chr11	53519872	53519917	+	1	NA	5' UTR (NM_001252332, exon 1 of 10)	5' UTR (NM_001252332, exon 1 of 10)	158	NM_001347496	20362	Mm.274399	NM_033144	ENSMUSG00000018398	Sept8	AW046166|Sepl	septin 8	protein-coding
mm_11194.1	chr2	29122806	29122811	+	1	NA	Intergenic	Lx8|LINE|L1	-2184	NM_198033	269254	Mm.41867	NM_198033	ENSMUSG00000043535	Setx	A130090N03|A930037J23Rik|AOA2|AW060766|Als4|SCAR1|Sen1|mKIAA0625	senataxin	protein-coding
mm_102831.1	chr11	69098748	69098752	-	1	NA	promoter-TSS (NM_011065)	promoter-TSS (NM_011065)	-206	NM_011065	18626	Mm.7373	NM_011065	ENSMUSG00000020893	Per1	Hftm|Per|m-rigui|mPer1	period circadian clock 1	protein-coding
mm_171044.1	chr2	98663735	98663735	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	1196078	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_87376.1	chr10	44468840	44468848	+	1	NA	Intergenic	Intergenic	-10096	NM_007548	12142	Mm.4800	NM_007548	ENSMUSG00000038151	Prdm1	Blimp-1|Blimp1|PRDI-BF1|ZNFPR1A1|b2b1765Clo	PR domain containing 1, with ZNF domain	protein-coding
mm_87827.1	chr10	60357985	60358037	+	1	NA	exon (NM_001159572, exon 2 of 7)	exon (NM_001159572, exon 2 of 7)	11160	NM_028732	74048	Mm.273584	NM_028732	ENSMUSG00000020101	Vsir	4632428N05Rik|Dies1|PD-1H|VISTA	V-set immunoregulatory receptor	protein-coding
mm_147200.1	chr18	37877761	37877772	-	1	NA	intron (NM_007858, intron 16 of 26)	intron (NM_007858, intron 16 of 26)	-23106	NR_105945	102465592		NR_105945	ENSMUSG00000098706	Mir6979	Gm27524|mmu-mir-6979	microRNA 6979	ncRNA
mm_155955.1	chrX	105120354	105120354	+	1	NA	promoter-TSS (NM_053201)	promoter-TSS (NM_053201)	-24	NM_053201	107528	Mm.24341	NM_053201	ENSMUSG00000031227	Magee1	AI847422|DAMAGE|mMage-e1	melanoma antigen, family E, 1	protein-coding
mm_104395.1	chr11	94498194	94498207	-	1	NA	intron (NM_027984, intron 1 of 9)	intron (NM_027984, intron 1 of 9)	1774	NM_027984	71889	Mm.248620	NM_027984	ENSMUSG00000010080	Epn3	2310022G12Rik	epsin 3	protein-coding
mm_120827.1	chr14	75174958	75174978	+	1	NA	intron (NM_008879, intron 1 of 16)	intron (NM_008879, intron 1 of 16)	38543	NM_008879	18826	Mm.153911	NM_008879	ENSMUSG00000021998	Lcp1	AW536232|D14Ertd310e|LCP-1|Pls2|pp65	lymphocyte cytosolic protein 1	protein-coding
mm_35887.1	chr4	49542592	49542601	-	1	NA	intron (NM_144903, intron 4 of 8)	ID2|SINE|ID	6950	NM_144903	230163	Mm.482116	NM_144903	ENSMUSG00000028307	Aldob	Aldo-2|Aldo2|BC016435	aldolase B, fructose-bisphosphate	protein-coding
mm_62755.1	chr7	112023470	112023566	+	1	NA	promoter-TSS (NM_177249)	promoter-TSS (NM_177249)	12	NM_177249	74996	Mm.16974	NM_133758	ENSMUSG00000059263	Usp47	4930502N04Rik|A630020C16Rik	ubiquitin specific peptidase 47	protein-coding
mm_139063.1	chr17	46520759	46520782	+	1	NA	intron (NM_001081335, intron 23 of 40)	intron (NM_001081335, intron 23 of 40)	23981	NM_207161	381101	Mm.35801	NM_207161	ENSMUSG00000040658	Dnph1	C76683|Rcl	2'-deoxynucleoside 5'-phosphate N-hydrolase 1	protein-coding
mm_139196.1	chr17	47629891	47629968	+	1	NA	promoter-TSS (NM_198421)	promoter-TSS (NM_198421)	-761	NM_198421	224836	Mm.59393	NM_198421	ENSMUSG00000090115	Usp49	C330046L10Rik|Gm545	ubiquitin specific peptidase 49	protein-coding
mm_50926.1	chr6	57636624	57636631	+	1	NA	intron (NM_025992, intron 13 of 22)	Lx9|LINE|L1	55451	NM_025574	66459	Mm.44201	NM_025574	ENSMUSG00000043162	Pyurf	2610022G08Rik|AI847956|Prey	Pigy upstream reading frame	protein-coding
mm_72820.1	chr8	88137907	88137919	+	1	NA	promoter-TSS (NR_106039)	promoter-TSS (NR_106039)	28	NM_172757	234549	Mm.36291	NM_172757	ENSMUSG00000031657	Heatr3	C030036P15Rik	HEAT repeat containing 3	protein-coding
mm_22330.1	chr2	180701153	180701167	-	1	NA	intron (NM_177852, intron 1 of 14)	intron (NM_177852, intron 1 of 14)	942	NM_011805	23856	Mm.253836	NM_011805	ENSMUSG00000038914	Dido1	6720461J16Rik|D130048F08Rik|DATF-1|DIO-1|Datf1|dido	death inducer-obliterator 1	protein-coding
mm_164694.1	chr17	48314682	48314684	+	1	NA	Intergenic	LTR16A|LTR|ERVL	-1479	NM_177083	320148	Mm.123455	NM_177083	ENSMUSG00000043740	B430306N03Rik	Treml6	RIKEN cDNA B430306N03 gene	protein-coding
mm_114862.1	chr13	93461738	93461778	+	1	NA	intron (NM_021310, intron 3 of 10)	intron (NM_021310, intron 3 of 10)	38050	NM_021310	57748	Mm.100273	NM_021310	ENSMUSG00000021690	Jmy	-	junction-mediating and regulatory protein	protein-coding
mm_133322.1	chr16	78217158	78217188	+	1	NA	Intergenic	Intergenic	38281	NR_045698	100503619	Mm.387531	NR_045698	ENSMUSG00000109841	E330011O21Rik	-	RIKEN cDNA E330011O21 gene	ncRNA
mm_170287.1	chr1	82948920	82948922	+	1	NA	Intergenic	RLTR17|LTR|ERVK	89527	NM_030556	80721	Mm.261542	NM_030556	ENSMUSG00000038496	Slc19a3	A230084E24Rik|AI788884|ThTr2	solute carrier family 19, member 3	protein-coding
mm_73382.1	chr8	105685988	105686001	+	1	NA	Intergenic	Intergenic	-4912	NM_001033320	234695	Mm.471640	NM_001033320	ENSMUSG00000050357	Carmil2	CG1399-PB|D130029J02Rik|Gm585|Rltpr	capping protein regulator and myosin 1 linker 2	protein-coding
mm_129366.1	chr15	77970751	77970824	-	1	NA	promoter-TSS (NM_018749)	promoter-TSS (NM_018749)	37	NM_018749	55944	Mm.3955	NM_018749	ENSMUSG00000016554	Eif3d	66/67kDa|AA407891|Eif3s7|eIF3p66	eukaryotic translation initiation factor 3, subunit D	protein-coding
mm_62722.1	chr7	110773619	110773641	+	1	NA	intron (NM_009667, intron 1 of 14)	intron (NM_009667, intron 1 of 14)	1026	NM_009667	11717	Mm.3238	NM_009667	ENSMUSG00000005686	Ampd3	-	adenosine monophosphate deaminase 3	protein-coding
mm_86329.1	chr9	123061816	123061822	-	1	NA	exon (NM_177911, exon 11 of 14)	exon (NM_177911, exon 11 of 14)	27078	NM_177911	331046	Mm.195309	NM_177911	ENSMUSG00000025787	Tgm4	9530008N10Rik|Eapa1|TGP	transglutaminase 4 (prostate)	protein-coding
mm_131512.1	chr16	17508923	17508926	+	1	NA	promoter-TSS (NM_001331226)	promoter-TSS (NM_001331226)	241	NM_025808	66863	Mm.161726	NM_025808	ENSMUSG00000022761	Lztr1	1200003E21Rik|AI591627|AW550890	leucine-zipper-like transcriptional regulator, 1	protein-coding
mm_133266.1	chr16	77361519	77361526	+	1	NA	intron (NR_015543, intron 2 of 4)	intron (NR_015543, intron 2 of 4)	32194	NR_015543	77994	Mm.394688	NR_015543	ENSMUSG00000090386	Mir99ahg	2810055G20Rik|D730043B02Rik	Mir99a and Mirlet7c-1 host gene (non-protein coding)	ncRNA
mm_55841.1	chr6	83156404	83156414	-	1	NA	promoter-TSS (NM_023790)	promoter-TSS (NM_023790)	5	NM_027948	71837	Mm.17621	NM_027948	ENSMUSG00000030030	1700003E16Rik	AU041756	RIKEN cDNA 1700003E16 gene	protein-coding
mm_104247.1	chr11	88851463	88851522	-	1	NA	promoter-TSS (NR_126433)	promoter-TSS (NR_126433)	11	NM_009648	11640	Mm.2969	NM_009648	ENSMUSG00000018428	Akap1	AKAP121|AKAP84|Akap|C76494|C81186|DAKAP1|S-AKAP84	A kinase (PRKA) anchor protein 1	protein-coding
mm_172614.1	chr8	19694948	19694951	+	1	NA	Intergenic	B3A|SINE|B2	-34627	NM_001270553	100861668	Mm.491087	NM_001270553	ENSMUSG00000095294	Gm21119	-	predicted gene, 21119	protein-coding
mm_164989.1	chr19	11279405	11279417	-	1	NA	intron (NM_183190, intron 1 of 4)	intron (NM_183190, intron 1 of 4)	4402	NM_183190	269063	Mm.268940	NM_183190	ENSMUSG00000054523	Ms4a5	-	membrane-spanning 4-domains, subfamily A, member 5	protein-coding
mm_128858.1	chr15	72806226	72806245	-	1	NA	non-coding (NR_002864, exon 1 of 1)	non-coding (NR_002864, exon 1 of 1)	4089	NR_002864	353342	Mm.440245	NR_002864	ENSMUSG00000106847	Peg13	-	paternally expressed 13	ncRNA
mm_64627.1	chr7	3685918	3685984	-	1	NA	exon (NM_029934, exon 6 of 8)	exon (NM_029934, exon 6 of 8)	7574	NM_029934	77582	Mm.397541	NM_029934	ENSMUSG00000035596	Mboat7	5730589L02Rik|BB1|Leng4|Lpiat|Lpiat1|mBB1	membrane bound O-acyltransferase domain containing 7	protein-coding
mm_117291.1	chr13	66932917	66932927	-	1	NA	promoter-TSS (NM_008959)	promoter-TSS (NM_008959)	92	NM_008959	19210	Mm.281464	NM_008959	ENSMUSG00000021518	Ptdss1	AU044268|AW539008|PSS-1|mKIAA0024	phosphatidylserine synthase 1	protein-coding
mm_48683.1	chr5	146655550	146655583	-	1	NA	Intergenic	Intergenic	-70327	NM_001010941	14738	Mm.153539	NM_008151	ENSMUSG00000041468	Gpr12	Gpcr01|Gpcr12|Gpcr20|Gpcr21	G-protein coupled receptor 12	protein-coding
mm_6282.1	chr1	69684292	69684313	-	1	NA	intron (NM_011770, intron 1 of 7)	intron (NM_011770, intron 1 of 7)	1658	NM_011770	22779	Mm.106343	NM_011770	ENSMUSG00000025997	Ikzf2	A730095J18Rik|Helios|Zfpn1a2|Znfn1a2	IKAROS family zinc finger 2	protein-coding
mm_9293.1	chr1	171636667	171636691	-	1	NA	intron (NM_001347184, intron 4 of 5)	intron (NM_001347184, intron 4 of 5)	5221	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_107377.1	chr12	32954180	32954278	+	1	NA	promoter-TSS (NM_198710)	promoter-TSS (NM_198710)	43	NM_198710	19027	Mm.246304	NM_013635	ENSMUSG00000020570	Sypl	AI314763|AI604763|D12Ertd446e|PanI|Pphn|Sypl1	synaptophysin-like protein	protein-coding
mm_775.1	chr1	44551561	44551566	+	1	NA	promoter-TSS (NM_028450)	promoter-TSS (NM_028450)	-108	NM_028450	70676	Mm.133132	NM_027506	ENSMUSG00000056870	Gulp1	3110030A04Rik|5730529O06Rik|CED-6|Ced6|GULP|Gulp-2	GULP, engulfment adaptor PTB domain containing 1	protein-coding
mm_15744.1	chr2	164237438	164237444	+	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	900	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_167940.1	chrX	116448928	116448931	+	1	NA	promoter-TSS (NM_001033471)	promoter-TSS (NM_001033471)	-15	NM_001033471	382239	Mm.336224	NM_001033471	ENSMUSG00000072995	Cpxcr1	Gm1143	CPX chromosome region, candidate 1	protein-coding
mm_50308.1	chr6	47835729	47835739	+	1	NA	promoter-TSS (NM_027477)	promoter-TSS (NM_027477)	73	NM_027477	272347	Mm.169059	NM_027477	ENSMUSG00000062519	Zfp398	5730513I23Rik	zinc finger protein 398	protein-coding
mm_127870.1	chr15	8444165	8444209	-	1	NA	5' UTR (NM_027707, exon 1 of 47)	5' UTR (NM_027707, exon 1 of 47)	276	NM_027707	71175	Mm.240329	NM_027707	ENSMUSG00000022141	Nipbl	Idn3	Nipped-B homolog (Drosophila)	protein-coding
mm_152317.1	chr19	9914175	9914209	-	1	NA	Intergenic	Intergenic	-14659	NM_016692	16319	Mm.29755	NM_016692	ENSMUSG00000024660	Incenp	2700067E22Rik|AU019509|C130081E20|C77457	inner centromere protein	protein-coding
mm_109213.1	chr12	108677782	108677797	+	1	NA	intron (NM_001163394, intron 7 of 13)	RLTR21|LTR|ERVK	19169	NR_029771	723909		NR_029771	ENSMUSG00000065436	Mir342	Mirn342|mmu-mir-342	microRNA 342	ncRNA
mm_173332.1	chrY	90785047	90785052	+	1	NA	promoter-TSS (NR_137282)	promoter-TSS (NR_137282)	-393	NR_137282	170942	Mm.76062	NM_133362	ENSMUSG00000096768	Erdr1	edr	erythroid differentiation regulator 1	protein-coding
mm_5536.1	chr1	38112150	38112153	-	1	NA	intron (NM_019570, intron 1 of 22)	L1MB2|LINE|L1	17511	NM_019570	56210	Mm.389103	NM_019570	ENSMUSG00000026082	Rev1	1110027I23Rik|AU022044|Rev1l	REV1, DNA directed polymerase	protein-coding
mm_92103.1	chr10	63023735	63023741	-	1	NA	promoter-TSS (NM_026085)	promoter-TSS (NM_026085)	111	NM_001079824	432467	Mm.274784	NM_001079824	ENSMUSG00000020069	Hnrnph3	AA693301|AI666703|Hnrph3	heterogeneous nuclear ribonucleoprotein H3	protein-coding
mm_40169.1	chr5	35814425	35814453	+	1	NA	intron (NM_001177696, intron 6 of 21)	intron (NM_001177696, intron 6 of 21)	56559	NM_001177698	231148	Mm.254446	NM_177678	ENSMUSG00000029095	Ablim2	AI606905|C230091L11	actin-binding LIM protein 2	protein-coding
mm_123627.1	chr14	68124495	68124499	-	1	NA	exon (NM_008691, exon 1 of 3)	exon (NM_008691, exon 1 of 3)	507	NM_008691	18040	Mm.242832	NM_008691	ENSMUSG00000022054	Nefm	NF-M|NF160|NF165|Nef3|Nfm	neurofilament, medium polypeptide	protein-coding
mm_15080.1	chr2	153161322	153161339	+	1	NA	promoter-TSS (NM_133847)	promoter-TSS (NM_133847)	29	NM_133847	99237	Mm.330674	NM_133847	ENSMUSG00000068040	Tm9sf4	AA986553|AU045326|B930079E06|mKIAA0255	transmembrane 9 superfamily protein member 4	protein-coding
mm_111464.1	chr12	98528753	98528764	-	1	NA	intron (NM_029911, intron 1 of 6)	intron (NM_029911, intron 1 of 6)	4914	NR_136759	105245437	Mm.446375	NR_136759		Gm40893	-	predicted gene, 40893	ncRNA
mm_81729.1	chr9	113369004	113369004	+	1	NA	Intergenic	Intergenic	218148	NR_040760	102688	Mm.394901	NR_040760	ENSMUSG00000109890	AU023762	-	expressed sequence AU023762	ncRNA
mm_104498.1	chr11	95842455	95842483	-	1	NA	promoter-TSS (NM_001284397)	promoter-TSS (NM_001284397)	7	NM_001163464	66610	Mm.485545	NM_025659	ENSMUSG00000018381	Abi3	2210414K06Rik|AI987680|NESH	ABI gene family, member 3	protein-coding
mm_125101.1	chr15	27681665	27681676	+	1	NA	promoter-TSS (NM_198301)	promoter-TSS (NM_198301)	-128	NM_001242423	223433	Mm.266485	NM_198301	ENSMUSG00000056069	Fam105a	9830126M18	family with sequence similarity 105, member A	protein-coding
mm_47957.1	chr5	135573037	135573051	-	1	NA	promoter-TSS (NM_019577)	promoter-TSS (NM_019577)	-1	NM_019577	56221	Mm.31505	NM_019577	ENSMUSG00000004814	Ccl24	CKb-6|MPIF-2|Scya24	chemokine (C-C motif) ligand 24	protein-coding
mm_52088.1	chr6	97829672	97829682	+	1	NA	intron (NM_001113198, intron 1 of 9)	intron (NM_001113198, intron 1 of 9)	22619	NM_001113198	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_85619.1	chr9	107614848	107614858	-	1	NA	3' UTR (NM_008138, exon 9 of 9)	3' UTR (NM_008138, exon 9 of 9)	-5612	NM_001291539	20347	Mm.4083	NM_009153	ENSMUSG00000057969	Sema3b	SemA|Semaa|sema5|semaV	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B	protein-coding
mm_169959.1	chr1	6916543	6916554	+	1	NA	Intergenic	Intergenic	-172372	NM_183028	319263	Mm.21539	NM_183028	ENSMUSG00000051285	Pcmtd1	8430411F12Rik|A030012M09Rik	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding
mm_61821.1	chr7	87584348	87584451	+	1	NA	5' UTR (NM_001081414, exon 1 of 10)	5' UTR (NM_001081414, exon 1 of 10)	231	NM_001143834	108071	Mm.235018	NM_001033224	ENSMUSG00000049583	Grm5	6430542K11Rik|AI850523|Glu5R|Gprc1e|mGluR5|mGluR5b	glutamate receptor, metabotropic 5	protein-coding
mm_43252.1	chr5	130204932	130204938	+	1	NA	intron (NM_001199059, intron 4 of 8)	B1_Mur1|SINE|Alu	-14809	NM_001081394	71667	Mm.258508	NM_027854	ENSMUSG00000053094	Tmem248	0610007L01Rik|A930023A16Rik|AW557951|G430067H08Rik	transmembrane protein 248	protein-coding
mm_32151.1	chr4	99929432	99929438	+	1	NA	promoter-TSS (NM_028132)	promoter-TSS (NM_028132)	-16	NM_028132	72157	Mm.217764	NM_028132	ENSMUSG00000025791	Pgm2	2610020G18Rik|AA407108|AI098105|Pgm-2|Pgm1	phosphoglucomutase 2	protein-coding
mm_59564.1	chr7	28086526	28086543	+	1	NA	exon (NM_001122603, exon 5 of 20)	exon (NM_001122603, exon 5 of 20)	15298	NM_001122603	215384	Mm.292276	NM_175444	ENSMUSG00000047730	Fcgbp	A430096B05Rik	Fc fragment of IgG binding protein	protein-coding
mm_24385.1	chr3	90254242	90254252	+	1	NA	promoter-TSS (NM_028881)	promoter-TSS (NM_028881)	-34	NM_028881	74343	Mm.35627	NM_028881	ENSMUSG00000027936	Crtc2	4632407F12Rik|Torc2|mTORC2	CREB regulated transcription coactivator 2	protein-coding
mm_26624.1	chr3	152714095	152714137	+	1	NA	promoter-TSS (NM_025662)	promoter-TSS (NM_025662)	16	NM_025662	329777	Mm.331447	NM_025662	ENSMUSG00000039047	Pigk	3000001O05Rik	phosphatidylinositol glycan anchor biosynthesis, class K	protein-coding
mm_34596.1	chr4	150236686	150236767	+	1	NA	promoter-TSS (NM_001025388).2	promoter-TSS (NM_001025388).2	-471	NM_023119	13806	Mm.70666	NM_023119	ENSMUSG00000063524	Eno1	0610008I15|AL022784|Eno-1|MBP-1	enolase 1, alpha non-neuron	protein-coding
mm_34156.1	chr4	139431069	139431075	+	1	NA	intron (NM_001160319, intron 48 of 105)	ID_B1|SINE|B4	50413	NM_001160319	69116	Mm.271956	NM_001160319	ENSMUSG00000066036	Ubr4	1810009A16Rik|A930005E13Rik|D930005K06Rik|Gm1032|Gm1666|N28143|RBAF600|Zubr1|mKIAA0462|p600	ubiquitin protein ligase E3 component n-recognin 4	protein-coding
mm_69052.1	chr7	126862351	126862393	-	1	NA	promoter-TSS (NM_153580)	promoter-TSS (NM_153580)	400	NM_172746	233876	Mm.363427	NM_172746	ENSMUSG00000042606	Hirip3	B130036O03|C86302	HIRA interacting protein 3	protein-coding
mm_146049.1	chr18	69593547	69593557	+	1	NA	intron (NM_013685, intron 8 of 19)	intron (NM_013685, intron 8 of 19)	247831	NM_001083967	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding
mm_132429.1	chr16	35770399	35770427	+	1	NA	promoter-TSS (NM_175111)	promoter-TSS (NM_175111)	27	NM_175111	66667	Mm.45272	NM_175111	ENSMUSG00000022849	Hspbap1	3830421G21Rik	Hspb associated protein 1	protein-coding
mm_751.1	chr1	43730641	43730654	+	1	NA	promoter-TSS (NM_024283)	promoter-TSS (NM_024283)	45	NM_024283	78896	Mm.50109	NM_024283	ENSMUSG00000026051	1500015O10Rik	Ecrg4	RIKEN cDNA 1500015O10 gene	protein-coding
mm_72697.1	chr8	84976747	84976757	+	1	NA	TTS (NM_008416)	TTS (NM_008416)	1996	NM_008416	16477	Mm.1167	NM_008416	ENSMUSG00000052837	Junb	-	jun B proto-oncogene	protein-coding
mm_85303.1	chr9	100546055	100546092	-	1	NA	promoter-TSS (NM_010878)	promoter-TSS (NM_010878)	61	NM_010878	17973	Mm.181485	NM_010878	ENSMUSG00000032475	Nck1	6330586M15Rik|D230010O13Rik|Nck|Nck-1	non-catalytic region of tyrosine kinase adaptor protein 1	protein-coding
mm_144291.1	chr18	12147266	12147268	+	1	NA	intron (NM_024182, intron 7 of 12)	intron (NM_024182, intron 7 of 12)	18417	NM_024182	66878	Mm.28551	NM_024182	ENSMUSG00000024404	Riok3	1200013N13Rik|D18Ertd331e|E130306C24Rik|Sudd	RIO kinase 3	protein-coding
mm_68995.1	chr7	126649557	126649580	-	1	NA	intron (NM_029339, intron 1 of 9)	CpG	259	NM_029339	75565	Mm.45686	NM_029339	ENSMUSG00000030714	Sgf29	1700023O11Rik|9530025I05Rik|Ccdc101	SAGA complex associated factor 29	protein-coding
mm_30168.1	chr3	144200928	144200943	-	1	NA	intron (NM_001161770, intron 1 of 3)	intron (NM_001161770, intron 1 of 3)	1397	NM_001161770	16911	Mm.29187	NM_010723	ENSMUSG00000028266	Lmo4	A730077C12Rik|Crp3|Etohi4	LIM domain only 4	protein-coding
mm_88128.1	chr10	69325203	69325214	+	1	NA	Intergenic	Intergenic	27704	NM_007659	12534	Mm.281367	NM_007659	ENSMUSG00000019942	Cdk1	Cdc2|Cdc2a|p34<CDC2>	cyclin-dependent kinase 1	protein-coding
mm_25436.1	chr3	108086030	108086055	+	1	NA	promoter-TSS (NM_001289720)	promoter-TSS (NM_001289720)	-616	NM_001289720	109674	Mm.274335	NM_028779	ENSMUSG00000027889	Ampd2	1200014F01Rik|AI552571|Ampd-2|m4521Dajl	adenosine monophosphate deaminase 2	protein-coding
mm_52027.1	chr6	95117902	95117960	+	1	NA	promoter-TSS (NM_001102670)	promoter-TSS (NM_001102670)	51	NM_001008785	243574	Mm.333275	NM_001008785	ENSMUSG00000030031	Kbtbd8	AU040152|SSEC-51|SSEC51|Takrp|mKIAA1842	kelch repeat and BTB (POZ) domain containing 8	protein-coding
mm_72389.1	chr8	81766538	81766581	+	1	NA	intron (NM_001297593, intron 4 of 23)	intron (NM_001297593, intron 4 of 23)	423997	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_75958.1	chr8	71702607	71702634	-	1	NA	promoter-TSS (NM_028189)	promoter-TSS (NM_028189)	-820	NM_028189	72297	Mm.290837	NM_028189	ENSMUSG00000031803	B3gnt3	2210008L19Rik	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 3	protein-coding
mm_38637.1	chr4	143133820	143133842	-	1	NA	exon (NM_001081355, exon 8 of 10)	exon (NM_001081355, exon 8 of 10)	2331	NR_105988	102465618		NR_105988	ENSMUSG00000106597	Mir7021	mmu-mir-7021	microRNA 7021	ncRNA
mm_163944.1	chr14	51172723	51172734	+	1	NA	Intergenic	B3|SINE|B2	10468	NM_019398	54159	Mm.377125	NM_019398	ENSMUSG00000059606	Rnase2b	Ear5|Raf4|mR5	ribonuclease, RNase A family, 2B (liver, eosinophil-derived neurotoxin)	protein-coding
mm_23655.1	chr3	67603205	67603216	+	1	NA	3' UTR (NM_025813, exon 16 of 16)	3' UTR (NM_025813, exon 16 of 16)	20442	NM_025813	66868	Mm.491153	NM_025813	ENSMUSG00000027775	Mfsd1	1200003O06Rik	major facilitator superfamily domain containing 1	protein-coding
mm_60226.1	chr7	43579774	43579787	+	1	NA	intron (NM_172482, intron 1 of 3)	intron (NM_172482, intron 1 of 3)	194	NM_172482	210105	Mm.234422	NM_172482	ENSMUSG00000030469	Zfp719	8030458J18|9430094P17Rik|C630016O21Rik|mszf6	zinc finger protein 719	protein-coding
mm_24940.1	chr3	96576979	96576992	+	1	NA	TTS (NM_027241)	TTS (NM_027241)	-10184	NR_040409	100038464	Mm.475126	NR_040409	ENSMUSG00000074398	Gm15441	ENSMUSG00000074398|OTTMUSG00000021867	predicted gene 15441	ncRNA
mm_121607.1	chr14	8258069	8258098	-	1	NA	intron (NM_053115, intron 1 of 14)	intron (NM_053115, intron 1 of 14)	756	NM_001161667	93732	Mm.28700	NM_053115	ENSMUSG00000021751	Acox2	THCCox	acyl-Coenzyme A oxidase 2, branched chain	protein-coding
mm_3224.1	chr1	135848035	135848044	+	1	NA	exon (NM_001130176, exon 7 of 13)	exon (NM_001130176, exon 7 of 13)	7178	NM_001130176	21956	Mm.247470	NM_011619	ENSMUSG00000026414	Tnnt2	Tnt|cTnT	troponin T2, cardiac	protein-coding
mm_162488.1	chr1	135766190	135766201	+	1	NA	5' UTR (NM_013750, exon 1 of 2)	5' UTR (NM_013750, exon 1 of 2)	110	NM_013750	27280	Mm.34346	NM_013750	ENSMUSG00000041801	Phlda3	Tih1	pleckstrin homology like domain, family A, member 3	protein-coding
mm_62450.1	chr7	101385524	101385552	+	1	NA	promoter-TSS (NM_027180)	promoter-TSS (NM_027180)	12	NM_027180	69710	Mm.277687	NM_027180	ENSMUSG00000032812	Arap1	2410002L19Rik|Centd2|mKIAA0782	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	protein-coding
mm_48570.1	chr5	143315295	143315311	-	1	NA	promoter-TSS (NM_172726)	promoter-TSS (NM_172726)	57	NM_172726	231868	Mm.440105	NM_172726	ENSMUSG00000039244	E130309D02Rik	A630028N22	RIKEN cDNA E130309D02 gene	protein-coding
mm_19153.1	chr2	80581235	80581266	-	1	NA	promoter-TSS (NM_001290745)	promoter-TSS (NM_001290745)	-68	NM_016965	50884	Mm.25203	NM_016965	ENSMUSG00000027002	Nckap1	C79304|H19|Hem-2|Hem2|Nap1|mKIAA0587|mh19|p125Nap1	NCK-associated protein 1	protein-coding
mm_81267.1	chr9	108053155	108053165	+	1	NA	promoter-TSS (NM_177275)	promoter-TSS (NM_177275)	1	NM_177275	320844	Mm.449806	NM_177275	ENSMUSG00000032593	Amigo3	E430002N15Rik|ali3|mKIAA1851	adhesion molecule with Ig like domain 3	protein-coding
mm_100841.1	chr11	5739367	5739369	-	1	NA	intron (NM_001077661, intron 1 of 5)	intron (NM_001077661, intron 1 of 5)	1808	NM_178623	72046	Mm.271657	NM_178623	ENSMUSG00000049680	Urgcp	2010005J08Rik|9130001I21Rik|AW060359|Urg4|mKIAA1507	upregulator of cell proliferation	protein-coding
mm_56237.1	chr6	90662869	90662885	-	1	NA	exon (NM_001134384, exon 14 of 14)	exon (NM_001134384, exon 14 of 14)	43631	NM_001037493	71699	Mm.272633	NM_027868	ENSMUSG00000030089	Slc41a3	1010001P06Rik|AI480742|SLC41A1-L2	solute carrier family 41, member 3	protein-coding
mm_130193.1	chr15	94543473	94543514	-	1	NA	promoter-TSS (NM_029926)	promoter-TSS (NM_029926)	14	NM_172437	78895	Mm.34344	NM_172437	ENSMUSG00000033356	Pus7l	3000003F02Rik	pseudouridylate synthase 7-like	protein-coding
mm_156328.1	chrX	138914446	138914460	+	1	NA	promoter-TSS (NM_013724)	promoter-TSS (NM_013724)	23	NM_013724	27206	Mm.482319	NM_013724	ENSMUSG00000052854	Nrk	AA407323|AA409510|AI225895|AV168563|AW538185|Nesk	Nik related kinase	protein-coding
mm_151712.1	chr19	4625085	4625123	-	1	NA	TTS (NM_001033447)	TTS (NM_001033447)	513	NM_023131	19671	Mm.391143	NM_023131	ENSMUSG00000024889	Rce1	D19Ertd283e|D19Ertd98e	Ras converting CAAX endopeptidase 1	protein-coding
mm_8153.1	chr1	136789573	136789573	-	1	NA	Intergenic	Intergenic	93362	NR_037986	100503474	Mm.428276	NR_037986		Platr22	Gm16880	pluripotency associated transcript 22	ncRNA
mm_59998.1	chr7	30565411	30565432	+	1	NA	promoter-TSS (NM_145580)	promoter-TSS (NM_145580)	-6	NM_145580	101883	Mm.333757	NM_145580	ENSMUSG00000036826	Igflr1	F630003I17Rik|Tmem149	IGF-like family receptor 1	protein-coding
mm_110113.1	chr12	26443695	26443701	-	1	NA	3' UTR (NM_021384, exon 6 of 6)	3' UTR (NM_021384, exon 6 of 6)	12754	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_5545.1	chr1	38615539	38615542	-	1	NA	intron (NM_001290814, intron 1 of 21)	intron (NM_001290814, intron 1 of 21)	11704	NM_001290814	16764	Mm.336679	NM_010678	ENSMUSG00000037138	Aff3	3222402O04Rik|A730046J16|LAF-4|Laf4	AF4/FMR2 family, member 3	protein-coding
mm_99201.1	chr11	101022685	101022692	+	1	NA	intron (NM_001243050, intron 5 of 20)	intron (NM_001243050, intron 5 of 20)	-7652	NR_105893	102466767		NR_105893	ENSMUSG00000098415	Mir6928	Gm27728|mmu-mir-6928	microRNA 6928	ncRNA
mm_99590.1	chr11	104309809	104309813	+	1	NA	intron (NM_001038609, intron 7 of 11)	intron (NM_001038609, intron 7 of 11)	78375	NM_001285454	17762	Mm.1287	NM_010838	ENSMUSG00000018411	Mapt	AI413597|AW045860|Mtapt|Tau	microtubule-associated protein tau	protein-coding
mm_59846.1	chr7	29768644	29768650	+	1	NA	promoter-TSS (NM_023750)	promoter-TSS (NM_023750)	95	NM_023750	74352	Mm.251083	NM_023750	ENSMUSG00000046185	Zfp84	2210410P13Rik|4633401C23Rik|AI415447|BB081605|C86188|KRAB18|Zfp69	zinc finger protein 84	protein-coding
mm_35286.1	chr4	21722993	21723023	-	1	NA	Intergenic	RLTR17|LTR|ERVK	-4693	NM_001290422	51813	Mm.278584	NM_016746	ENSMUSG00000028252	Ccnc	AI451004|AU020987|CG1C	cyclin C	protein-coding
mm_112591.1	chr13	13954540	13954555	+	1	NA	promoter-TSS (NM_178640)	promoter-TSS (NM_178640)	-127	NM_178640	97884	Mm.21686	NM_178640	ENSMUSG00000039242	B3galnt2	A930105D20Rik|C80633|D230016N13Rik	UDP-GalNAc:betaGlcNAc beta 1,3-galactosaminyltransferase, polypeptide 2	protein-coding
mm_78372.1	chr9	27349025	27349031	+	1	NA	3' UTR (NM_001326702, exon 20 of 20)	3' UTR (NM_001326702, exon 20 of 20)	-3657	NR_027907	235086	Mm.48719	NM_001033323	ENSMUSG00000034275	Igsf9b	AI414108|AI854107|Gm508|mKIAA1030	immunoglobulin superfamily, member 9B	protein-coding
mm_4971.1	chr1	191290716	191290750	+	1	NA	Intergenic	ORR1D2|LTR|ERVL-MaLR	27385	NM_025424	66208	Mm.46444	NM_025424	ENSMUSG00000037499	Nenf	1110060M21Rik|SCIRP10|Spuf	neuron derived neurotrophic factor	protein-coding
mm_104384.1	chr11	94474325	94474347	-	1	NA	promoter-TSS (NM_001177890)	promoter-TSS (NM_001177890)	-138	NM_001112813	12291	Mm.29585	NM_009783	ENSMUSG00000020866	Cacna1g	Cav3.1d|[a]1G|a1G|alpha-1G|mKIAA1123	calcium channel, voltage-dependent, T type, alpha 1G subunit	protein-coding
mm_67784.1	chr7	97417512	97417539	-	1	NA	promoter-TSS (NM_009381)	promoter-TSS (NM_009381)	25	NM_009381	21835	Mm.28585	NM_009381	ENSMUSG00000035686	Thrsp	S14|SPOT14	thyroid hormone responsive	protein-coding
mm_23137.1	chr3	38885684	38885702	+	1	NA	Intergenic	CpG	-1247	NM_183221	329628	Mm.316210	NM_183221	ENSMUSG00000046743	Fat4	6030410K14Rik|9430004M15	FAT atypical cadherin 4	protein-coding
mm_164155.1	chr15	65947347	65947347	+	1	NA	intron (NM_001145096, intron 8 of 16)	intron (NM_001145096, intron 8 of 16)	29457	NM_001145096	654498	Mm.364550	NM_001145096	ENSMUSG00000072511	Hhla1	F930104E18Rik	HERV-H LTR-associating 1	protein-coding
mm_70110.1	chr7	142666205	142666221	-	1	NA	intron (NR_002855, intron 2 of 3)	intron (NR_002855, intron 2 of 3)	603	NM_001315488	16002	Mm.3862	NM_010514	ENSMUSG00000048583	Igf2	AL033362|Igf-2|Igf-II|M6pr|Mpr|Peg2	insulin-like growth factor 2	protein-coding
mm_127933.1	chr15	10485891	10485951	-	1	NA	promoter-TSS (NM_011232)	promoter-TSS (NM_011232)	16	NM_026396	67832	Mm.28057	NM_026396	ENSMUSG00000022247	Brix1	1110064N10Rik|Bxdc2|C76935	BRX1, biogenesis of ribosomes	protein-coding
mm_158627.1	chrX	153037452	153037471	-	1	NA	promoter-TSS (NR_040272)	promoter-TSS (NR_040272)	102	NM_023788	75625	Mm.6890	NM_023788	ENSMUSG00000047238	Mageh1	2010107K23Rik|APR-1|APR1	melanoma antigen, family H, 1	protein-coding
mm_35038.1	chr4	4138218	4138231	-	1	NA	5' UTR (NM_001002927, exon 1 of 2)	5' UTR (NM_001002927, exon 1 of 2)	221	NM_001002927	18619	Mm.475097	NM_001002927	ENSMUSG00000045573	Penk	AI326464|ENK|PPA|Penk1	preproenkephalin	protein-coding
mm_137999.1	chr17	33760031	33760054	+	1	NA	intron (NM_008997, intron 1 of 4)	CpG	444	NM_008997	19326	Mm.387587	NM_008997	ENSMUSG00000077450	Rab11b	A730055L17Rik	RAB11B, member RAS oncogene family	protein-coding
mm_101870.1	chr11	48891885	48891895	-	1	NA	intron (NM_001024230, intron 4 of 4)	intron (NM_001024230, intron 4 of 4)	10262	NM_001024230	432555	Mm.338931	NM_001024230	ENSMUSG00000058163	Gm5431	EG432555|Irgb9b8	predicted gene 5431	protein-coding
mm_85776.1	chr9	109054784	109054796	-	1	NA	promoter-TSS (NM_026381)	promoter-TSS (NM_026381)	-76	NM_026381	66940	Mm.196533	NM_025858	ENSMUSG00000025647	Shisa5	2310008D10Rik|6430628I05Rik|Scotin|mShisa5	shisa family member 5	protein-coding
mm_8091.1	chr1	135688819	135688852	-	1	NA	Intergenic	Intergenic	-40362	NM_007791	13007	Mm.196484	NM_007791	ENSMUSG00000026421	Csrp1	AA408841|AA959891|AW545626|CRP1|Csrp	cysteine and glycine-rich protein 1	protein-coding
mm_148718.1	chr19	5842300	5842311	+	1	NA	TTS (NR_003513)	TTS (NR_003513)	3173	NR_131212	66961	Mm.281895	NR_003513	ENSMUSG00000092274	Neat1	2310043N10Rik|VINC	nuclear paraspeckle assembly transcript 1 (non-protein coding)	ncRNA
mm_145082.1	chr18	42394473	42394481	+	1	NA	promoter-TSS (NM_138945)	promoter-TSS (NM_138945)	-120	NM_138945	18998	Mm.488204	NM_138945	ENSMUSG00000024497	Pou4f3	Brn3.1|Brn3c|ddl|dreidel	POU domain, class 4, transcription factor 3	protein-coding
mm_73047.1	chr8	94355047	94355089	+	1	NA	intron (NM_019415, intron 21 of 24)	intron (NM_019415, intron 21 of 24)	25860	NM_001205311	20497	Mm.25804	NM_019415	ENSMUSG00000031766	Slc12a3	AI035291|NCC|NCCT|TSC	solute carrier family 12, member 3	protein-coding
mm_35366.1	chr4	32571664	32571686	-	1	NA	promoter-TSS (NR_026843)	promoter-TSS (NR_026843)	-13	NR_026843	414068	Mm.389550	NR_026843	ENSMUSG00000086150	Bach2os	-	BTB and CNC homology 2, opposite strand	ncRNA
mm_8717.1	chr1	159168686	159168689	-	1	NA	Intergenic	Intergenic	-63639	NM_011931	26374	Mm.328135	NM_011931	ENSMUSG00000040782	Rfwd2	AI316802|C80879|Cop1	ring finger and WD repeat domain 2	protein-coding
mm_13142.1	chr2	92184312	92184325	+	1	NA	5' UTR (NM_138755, exon 1 of 18)	5' UTR (NM_138755, exon 1 of 18)	136	NM_001346704	192285	Mm.330408	NM_138755	ENSMUSG00000058318	Phf21a	80kDa|Bhc|Bhc80|D030065N23Rik|PFTF1	PHD finger protein 21A	protein-coding
mm_26297.1	chr3	142507925	142507949	+	1	NA	exon (NM_153564, exon 10 of 11)	exon (NM_153564, exon 10 of 11)	11003	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_132513.1	chr16	37384496	37384500	+	1	NA	intron (NM_001114611, intron 1 of 25)	CpG	460	NM_001114613	207227	Mm.80170	NM_172440	ENSMUSG00000022829	Stxbp5l	9430094L02|A830015P08Rik|LLGL4|T2dm1|t2md1|tomosyn-2	syntaxin binding protein 5-like	protein-coding
mm_133995.1	chr16	4719079	4719126	-	1	NA	5' UTR (NM_001290761, exon 1 of 5)	5' UTR (NM_001290761, exon 1 of 5)	254	NM_001290763	67824	Mm.28451	NM_026393	ENSMUSG00000063445	Nmral1	1110025F24Rik|AI256624	NmrA-like family domain containing 1	protein-coding
mm_133207.1	chr16	74620041	74620050	+	1	NA	Intergenic	Intergenic	-209133	NM_175549	268902	Mm.171736	NM_175549	ENSMUSG00000052516	Robo2	2600013A04Rik|9430089E08Rik|BB097918|D230004I22Rik|mKIAA1568	roundabout guidance receptor 2	protein-coding
mm_116365.1	chr13	40730821	40730825	-	1	NA	promoter-TSS (NM_001122948)	promoter-TSS (NM_001122948)	-366	NM_001122948	21418	Mm.85544	NM_011547	ENSMUSG00000021359	Tfap2a	AP-2|AP2alpha|Ap-2 (a)|Ap2|Ap2tf|Tcfap2a	transcription factor AP-2, alpha	protein-coding
mm_26797.1	chr3	9833654	9833668	-	1	NA	promoter-TSS (NM_053182)	promoter-TSS (NM_053182)	18	NM_053182	94212	Mm.23897	NM_053182	ENSMUSG00000027508	Pag1	Cbp|F730007C19Rik|Pag	phosphoprotein associated with glycosphingolipid microdomains 1	protein-coding
mm_142419.1	chr17	45568382	45568415	-	1	NA	TTS (NM_028662)	TTS (NM_028662)	4246	NM_028662	73836	Mm.289716	NM_028662	ENSMUSG00000037089	Slc35b2	1110003M08Rik|AA407792|AI842275|PAPST1|Slc35b1	solute carrier family 35, member B2	protein-coding
mm_121016.1	chr14	79536337	79536341	+	1	NA	5' UTR (NM_007920, exon 2 of 9)	5' UTR (NM_007920, exon 2 of 9)	20665	NM_001286411	13709	Mm.20938	NM_007920	ENSMUSG00000036461	Elf1	Elf-1|Sts1|mElf-1|p70	E74-like factor 1	protein-coding
mm_31374.1	chr4	47387155	47387158	+	1	NA	intron (NM_001312869, intron 1 of 7)	L1_Mus3|LINE|L1	940	NM_001312869	21812	Mm.197552	NM_009370	ENSMUSG00000007613	Tgfbr1	ALK5|AU017191|Alk-5|ESK2|TGFR-1|TbetaR-I|TbetaRI	transforming growth factor, beta receptor I	protein-coding
mm_2920.1	chr1	132030769	132030793	+	1	NA	intron (NM_172510, intron 9 of 10)	B3A|SINE|B2	23176	NM_007923	13714	Mm.254233	NM_007923	ENSMUSG00000026436	Elk4	2310011G17Rik|A130026I01Rik|BB162516|SAP-1|Sap1	ELK4, member of ETS oncogene family	protein-coding
mm_97714.1	chr11	80179354	80179368	+	1	NA	TTS (NM_172133)	TTS (NM_172133)	-4511	NM_028019	71956	Mm.22985	NM_028019	ENSMUSG00000020707	Rnf135	0610037N03Rik|2410006N06Rik	ring finger protein 135	protein-coding
mm_132095.1	chr16	31297334	31297344	+	1	NA	3' UTR (NM_007470, exon 6 of 6)	3' UTR (NM_007470, exon 6 of 6)	17469	NM_001301353	11815	Mm.2082	NM_007470	ENSMUSG00000022548	Apod	-	apolipoprotein D	protein-coding
mm_169051.1	chr1	32074587	32074590	-	1	NA	Intergenic	Intergenic	-98218	NM_133235	170771	Mm.336594	NM_133235	ENSMUSG00000026058	Khdrbs2	6330586C16Rik|Slim1|Slm-1|Slm1|mSLM-1	KH domain containing, RNA binding, signal transduction associated 2	protein-coding
mm_97459.1	chr11	78245511	78245519	+	1	NA	promoter-TSS (NM_009143)	promoter-TSS (NM_009143)	188	NM_009297	20926	Mm.20755	NM_009297	ENSMUSG00000002052	Supt6	5131400N11Rik|AI132449|SPT6|Supt6h|mKIAA0162	suppressor of Ty 6	protein-coding
mm_70100.1	chr7	142661189	142661206	-	1	NA	promoter-TSS (NM_001122736)	promoter-TSS (NM_001122736)	74	NM_001122736	16002	Mm.3862	NM_010514	ENSMUSG00000048583	Igf2	AL033362|Igf-2|Igf-II|M6pr|Mpr|Peg2	insulin-like growth factor 2	protein-coding
mm_8576.1	chr1	155779097	155779101	-	1	NA	3' UTR (NM_001024945, exon 12 of 12)	3' UTR (NM_001024945, exon 12 of 12)	33800	NM_023268	104009	Mm.27035	NM_023268	ENSMUSG00000033684	Qsox1	1300003H02Rik|QSOX|Qscn6|SOx	quiescin Q6 sulfhydryl oxidase 1	protein-coding
mm_106334.1	chr11	118355497	118355497	-	1	NA	promoter-TSS (NM_011594)	promoter-TSS (NM_011594)	-86	NM_011594	21858	Mm.206505	NM_011594	ENSMUSG00000017466	Timp2	D11Bwg1104e|Timp-2	tissue inhibitor of metalloproteinase 2	protein-coding
mm_34118.1	chr4	139228823	139228850	+	1	NA	intron (NM_001271405, intron 1 of 8)	intron (NM_001271405, intron 1 of 8)	34725	NM_001271405	12345	Mm.2945	NM_009798	ENSMUSG00000028745	Capzb	1700120C01Rik|AI325129|CPB1|CPB2|CPbeat2|CPbeta1|CPbeta2|Cappb1	capping protein (actin filament) muscle Z-line, beta	protein-coding
mm_97301.1	chr11	76547950	76547997	+	1	NA	intron (NM_198894, intron 1 of 22)	intron (NM_198894, intron 1 of 22)	23411	NM_198895	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_120290.1	chr14	63135533	63135543	+	1	NA	intron (NM_007798, intron 3 of 9)	intron (NM_007798, intron 3 of 9)	13076	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_79275.1	chr9	50768229	50768271	+	1	NA	promoter-TSS (NM_198675)	promoter-TSS (NM_198675)	12	NM_198675	382137	Mm.390169	NM_198675	ENSMUSG00000037845	Fdxacb1	D630004A14Rik	ferredoxin-fold anticodon binding domain containing 1	protein-coding
mm_22739.1	chr3	19895097	19895124	+	1	NA	non-coding (NR_027985, exon 1 of 1)	non-coding (NR_027985, exon 1 of 1)	239	NR_027985	70808	Mm.427103	NR_027985	ENSMUSG00000048106	4632415L05Rik	AI662792	RRS1 ribosome biogenesis regulator homolog pseudogene	pseudo
mm_168716.1	chr12	105685370	105685376	+	1	NA	promoter-TSS (NM_178613)	promoter-TSS (NM_178613)	21	NM_178613	66787	Mm.248019	NM_178613	ENSMUSG00000044715	Gskip	4933433P14Rik	GSK3B interacting protein	protein-coding
mm_127324.1	chr15	100304212	100304222	+	1	NA	promoter-TSS (NM_027334)	promoter-TSS (NM_027334)	-600	NM_027334	70152	Mm.488086	NM_027334	ENSMUSG00000054619	Mettl7a1	2210414H16Rik|3300001H21Rik|Aam-B|Mettl7a|UbiE1	methyltransferase like 7A1	protein-coding
mm_65725.1	chr7	28380971	28380981	-	1	NA	Intergenic	Intergenic	-1748	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_78133.1	chr9	20868843	20868880	+	1	NA	5' UTR (NM_175687, exon 1 of 8)	5' UTR (NM_175687, exon 1 of 8)	219	NM_175687	319278	Mm.249932	NM_175687	ENSMUSG00000038884	A230050P20Rik	RyDEN	RIKEN cDNA A230050P20 gene	protein-coding
mm_164852.1	chr18	47368964	47368970	-	1	NA	promoter-TSS (NM_018744)	promoter-TSS (NM_018744)	-97	NM_001311097	20358	Mm.40909	NM_018744	ENSMUSG00000019647	Sema6a	A730020P05Rik|AI851735|Sema6A-1|Semaq|VIa	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A	protein-coding
mm_96617.1	chr11	69101021	69101027	+	1	NA	exon (NM_001159367, exon 3 of 23)	exon (NM_001159367, exon 3 of 23)	866	NM_001159367	18626	Mm.7373	NM_011065	ENSMUSG00000020893	Per1	Hftm|Per|m-rigui|mPer1	period circadian clock 1	protein-coding
mm_45688.1	chr5	77370809	77370812	-	1	NA	intron (NM_008048, intron 1 of 4)	intron (NM_008048, intron 1 of 4)	37235	NM_001159518	29817	Mm.233470	NM_008048	ENSMUSG00000036256	Igfbp7	AGM|Fstl2|Mac25	insulin-like growth factor binding protein 7	protein-coding
mm_123750.1	chr14	70192820	70192831	-	1	NA	promoter-TSS (NM_001271409)	promoter-TSS (NM_001271409)	-579	NM_001271409	20410	Mm.5068	NM_011366	ENSMUSG00000022091	Sorbs3	SCAM-1|SH3P3|Sh3d4|vinexin-g	sorbin and SH3 domain containing 3	protein-coding
mm_29486.1	chr3	115714855	115714863	-	1	NA	5' UTR (NM_007901, exon 1 of 2)	5' UTR (NM_007901, exon 1 of 2)	196	NM_007901	13609	Mm.982	NM_007901	ENSMUSG00000045092	S1pr1	AI849002|Edg1|Lpb1|S1p|S1p1	sphingosine-1-phosphate receptor 1	protein-coding
mm_50307.1	chr6	47835651	47835725	+	1	NA	promoter-TSS (NM_027477)	promoter-TSS (NM_027477)	27	NM_027477	272347	Mm.169059	NM_027477	ENSMUSG00000062519	Zfp398	5730513I23Rik	zinc finger protein 398	protein-coding
mm_128002.1	chr15	12823810	12823812	-	1	NA	intron (NM_001166360, intron 1 of 2)	intron (NM_001166360, intron 1 of 2)	846	NM_029998	77877	Mm.207311	NM_029998	ENSMUSG00000022195	6030458C11Rik	-	RIKEN cDNA 6030458C11 gene	protein-coding
mm_100134.1	chr11	115974870	115974876	+	1	NA	5' UTR (NM_133663, exon 1 of 39)	5' UTR (NM_133663, exon 1 of 39)	148	NM_133663	192897	Mm.213873	NM_133663	ENSMUSG00000020758	Itgb4	AA407042|C230078O20|CD104	integrin beta 4	protein-coding
mm_63804.1	chr7	133124019	133124032	+	1	NA	promoter-TSS (NM_009980)	promoter-TSS (NM_009980)	-542	NM_009980	13017	Mm.246240	NM_009980	ENSMUSG00000030970	Ctbp2	AA407280|D7Ertd45e|Gtrgeo6|Ribeye	C-terminal binding protein 2	protein-coding
mm_92531.1	chr10	79555089	79555126	-	1	NA	promoter-TSS (NM_027422)	promoter-TSS (NM_027422)	21	NM_001316699	70427	Mm.334193	NM_027422	ENSMUSG00000042570	Mier2	2700087H15Rik|mKIAA1193	MIER family member 2	protein-coding
mm_153434.1	chr19	40955605	40955627	-	1	NA	intron (NM_008528, intron 6 of 16)	ID_B1|SINE|B4	38919	NM_008528	17060	Mm.9749	NM_008528	ENSMUSG00000061132	Blnk	BASH|Bca|Ly-57|Ly57|Lyw-57|SLP-65	B cell linker	protein-coding
mm_114887.1	chr13	94295262	94295272	+	1	NA	Intergenic	B4A|SINE|B4	-9436	NM_001346609	107767	Mm.201455	NM_029153	ENSMUSG00000021687	Scamp1	4930505M11Rik|AI415563|AW122395	secretory carrier membrane protein 1	protein-coding
mm_52378.1	chr6	113107614	113107619	+	1	NA	intron (NM_173005, intron 1 of 20)	BC1_Mm|scRNA|scRNA	2681	NM_173005	72895	Mm.367159	NM_028385	ENSMUSG00000034269	Setd5	2900045N06Rik|C330007C20|C85544|mKIAA1757	SET domain containing 5	protein-coding
mm_59314.1	chr7	25289378	25289389	+	1	NA	intron (NM_001302811, intron 11 of 20)	intron (NM_001302811, intron 11 of 20)	7204	NM_027882	71722	Mm.28833	NM_027882	ENSMUSG00000005442	Cic	1200010B10Rik|mKIAA0306	capicua transcriptional repressor	protein-coding
mm_77917.1	chr9	7351104	7351116	+	1	NA	intron (NM_001320077, intron 5 of 10)	intron (NM_001320077, intron 5 of 10)	3736	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_115146.1	chr13	104849646	104849654	+	1	NA	intron (NM_029984, intron 2 of 2)	MTD|LTR|ERVL-MaLR	14243	NM_029984	77803	Mm.159995	NM_029984	ENSMUSG00000042655	Fam159b	A930021C24Rik	family with sequence similarity 159, member B	protein-coding
mm_87425.1	chr10	50779484	50779492	+	1	NA	intron (NM_198007, intron 36 of 41)	Lx8|LINE|L1	-116163	NM_011376	20464	Mm.4774	NM_011376	ENSMUSG00000019913	Sim1	bHLHe14|mSIM1	single-minded homolog 1 (Drosophila)	protein-coding
mm_156536.1	chrX	151072355	151072363	+	1	NA	intron (NM_008001, intron 7 of 17)	intron (NM_008001, intron 7 of 17)	24184	NM_001164578	69499	Mm.8142	NM_175146	ENSMUSG00000025264	Tsr2	2310007F12Rik	TSR2 20S rRNA accumulation	protein-coding
mm_157622.1	chrX	56549693	56549703	-	1	NA	promoter-TSS (NM_001033372)	promoter-TSS (NM_001033372)	-92	NM_001033372	270599	Mm.424438	NM_001033372	ENSMUSG00000064016	Gm648	-	predicted gene 648	protein-coding
mm_95797.1	chr11	55103545	55103562	+	1	NA	intron (NM_010299, intron 1 of 3)	intron (NM_010299, intron 1 of 3)	5568	NM_010299	14667	Mm.287807	NM_010299	ENSMUSG00000000594	Gm2a	AA408702|AW215435|GM2-AP|SAP-3	GM2 ganglioside activator protein	protein-coding
mm_44669.1	chr5	29478579	29478597	-	1	NA	promoter-TSS (NM_019944)	promoter-TSS (NM_019944)	-118	NM_019944	15285	Mm.103760	NM_019944	ENSMUSG00000001566	Mnx1	HB9|Hlxb9|MNR2	motor neuron and pancreas homeobox 1	protein-coding
mm_67376.1	chr7	79842006	79842016	-	1	NA	exon (NM_008486, exon 1 of 20)	exon (NM_008486, exon 1 of 20)	341	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_20736.1	chr2	137116396	137116406	-	1	NA	5' UTR (NM_013822, exon 1 of 26)	5' UTR (NM_013822, exon 1 of 26)	119	NM_013822	16449	Mm.22398	NM_013822	ENSMUSG00000027276	Jag1	ABE2|Gsfabe2|Htu|Ozz|Ser-1	jagged 1	protein-coding
mm_46813.1	chr5	113138080	113138097	-	1	NA	5' UTR (NM_001347397, exon 1 of 8)	5' UTR (NM_001347397, exon 1 of 8)	497	NM_001347397	243219	Mm.160131	NM_172884	ENSMUSG00000051339	2900026A02Rik	8430408O14Rik|A530094D01|AW539426|Gm449|Kiaa1671|mKIAA1671	RIKEN cDNA 2900026A02 gene	protein-coding
mm_170348.1	chr18	51003008	51003024	+	1	NA	Intergenic	CpG	-114882	NM_001081224	71373	Mm.63546	NM_001081224	ENSMUSG00000073565	Prr16	5430406M13Rik|AI607429	proline rich 16	protein-coding
mm_25234.1	chr3	103885940	103885976	+	1	NA	exon (NM_008979, exon 13 of 21)	exon (NM_008979, exon 13 of 21)	25681	NM_008979	19260	Mm.395	NM_008979	ENSMUSG00000027843	Ptpn22	70zpep|PEP|Ptpn8	protein tyrosine phosphatase, non-receptor type 22 (lymphoid)	protein-coding
mm_17877.1	chr2	34958608	34958632	-	1	NA	intron (NM_009421, intron 3 of 10)	MIR3|SINE|MIR	3152	NM_009421	22029	Mm.239514	NM_009421	ENSMUSG00000026875	Traf1	4732496E14Rik	TNF receptor-associated factor 1	protein-coding
mm_1328.1	chr1	65186676	65186722	+	1	NA	promoter-TSS (NM_001310624)	promoter-TSS (NM_001310624)	14	NM_001310624	18711	Mm.38370	NM_011086	ENSMUSG00000025949	Pikfyve	5230400C17Rik|Pip5k|Pip5k3|Pipk5k3|PipkIII|p235	phosphoinositide kinase, FYVE finger containing	protein-coding
mm_31581.1	chr4	57781166	57781170	+	1	NA	intron (NM_001304544, intron 6 of 8)	intron (NM_001304544, intron 6 of 8)	-64080	NM_009649	11641	Mm.467752	NM_009649	ENSMUSG00000038729	Akap2	AA959716|AI649048|Akap-2|Akap-kl|B230340M18Rik|Prka2	A kinase (PRKA) anchor protein 2	protein-coding
mm_106611.1	chr11	120809157	120809176	-	1	NA	exon (NM_007988, exon 39 of 43)	exon (NM_007988, exon 39 of 43)	-12771	NM_026824	68730	Mm.180622	NM_026824	ENSMUSG00000025155	Dus1l	1110032N12Rik	dihydrouridine synthase 1-like (S. cerevisiae)	protein-coding
mm_155647.1	chrX	85614610	85614626	+	1	NA	exon (NM_025729, exon 4 of 9)	exon (NM_025729, exon 4 of 9)	40596	NM_025729	66724	Mm.119646	NM_025729	ENSMUSG00000035476	Tab3	4921526G09Rik|Map3k7ip3|mKIAA4135	TGF-beta activated kinase 1/MAP3K7 binding protein 3	protein-coding
mm_154621.1	chrX	7723050	7723061	+	1	NA	intron (NM_001290794, intron 1 of 10)	intron (NM_001290794, intron 1 of 10)	128	NM_001290794	54636	Mm.305725	NM_172372	ENSMUSG00000039382	Wdr45	C79260|DXImx38e|JM5|Sfc19|WIPI-4|Wdrx1	WD repeat domain 45	protein-coding
mm_154198.1	chr19	58982936	58982949	-	1	NA	intron (NM_175172, intron 14 of 14)	L1Md_T|LINE|L1	-39270	NM_001327998	73442	Mm.39739	NM_175199	ENSMUSG00000025092	Hspa12a	1700063D12Rik|AI118035|AI840429|AW048913|AW556406|D5Mgi40|Gm19925|mKIAA0417	heat shock protein 12A	protein-coding
mm_124403.1	chr14	115207538	115207546	-	1	NA	intron (NM_175500, intron 2 of 7)	RMER17C|LTR|ERVK	115327	NM_175500	103978	Mm.320791	NM_175500	ENSMUSG00000022112	Gpc5	A230034F01Rik	glypican 5	protein-coding
mm_94732.1	chr11	20917295	20917310	+	1	NA	Intergenic	Intergenic	-86194	NM_173752	216551	Mm.76694	NM_173752	ENSMUSG00000042363	Lgalsl	1110067D22Rik|A530071M23|Grpa|Hspc159|Lgalsla	lectin, galactoside binding-like	protein-coding
mm_112747.1	chr13	19341817	19341827	+	1	NA	Intergenic	Intergenic	53991	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_129655.1	chr15	81045452	81045465	-	1	NA	intron (NM_001082536, intron 2 of 13)	intron (NM_001082536, intron 2 of 13)	59589	NM_153049	223701	Mm.439814	NM_153049	ENSMUSG00000042292	Mkl1	AMKL|Bsac|Mal|Mrtf-A	MKL (megakaryoblastic leukemia)/myocardin-like 1	protein-coding
mm_132559.1	chr16	38089072	38089103	+	1	NA	promoter-TSS (NM_019827)	promoter-TSS (NM_019827)	86	NM_019827	56637	Mm.394930	NM_019827	ENSMUSG00000022812	Gsk3b	7330414F15Rik|8430431H08Rik|C86142|GSK-3|GSK-3beta|GSK3	glycogen synthase kinase 3 beta	protein-coding
mm_151632.1	chr19	3929724	3929765	-	1	NA	promoter-TSS (NM_026316)	promoter-TSS (NM_026316)	-28	NM_026316	67689	Mm.109341	NM_026316	ENSMUSG00000024885	Aldh3b1	1700001N19Rik|ALDH4|ALDH7	aldehyde dehydrogenase 3 family, member B1	protein-coding
mm_18643.1	chr2	69522640	69522647	-	1	NA	intron (NM_001081088, intron 13 of 78)	(A)n|Simple_repeat|Simple_repeat	63424	NM_001081088	14725	Mm.23847	NM_001081088	ENSMUSG00000027070	Lrp2	AI315343|AW536255|D230004K18Rik|Gp330|Megalin|b2b1625.2Clo	low density lipoprotein receptor-related protein 2	protein-coding
mm_96220.1	chr11	62509320	62509326	+	1	NA	intron (NM_001039536, intron 4 of 6)	MTD|LTR|ERVL-MaLR	29938	NM_028448	73139	Mm.390409	NM_028448	ENSMUSG00000018509	Cenpv	3110013H01Rik|AA671303|Prr6	centromere protein V	protein-coding
mm_106962.1	chr12	8922062	8922117	+	1	NA	exon (NM_008640, exon 1 of 7)	exon (NM_008640, exon 1 of 7)	782	NM_008640	17775	Mm.30071	NM_008640	ENSMUSG00000020585	Laptm4a	AA286466|LAPTM4|MTP|Mtrp|mKIAA0108	lysosomal-associated protein transmembrane 4A	protein-coding
mm_50917.1	chr6	57602868	57602879	+	1	NA	intron (NM_025992, intron 5 of 22)	B3|SINE|B2	21881	NM_025992	67138	Mm.297393	NM_025992	ENSMUSG00000029798	Herc6	1700121D12Rik|2510038N07Rik|4930427L17Rik|AI451296|CEB1|Herc5	hect domain and RLD 6	protein-coding
mm_41105.1	chr5	87775300	87775309	+	1	NA	intron (NM_007785, intron 1 of 13)	intron (NM_007785, intron 1 of 13)	854	NM_007785	12993	Mm.4908	NM_007785	ENSMUSG00000061937	Csn1s2a	Csng|PP22	casein alpha s2-like A	protein-coding
mm_39897.1	chr5	31203252	31203272	+	1	NA	promoter-TSS (NM_175311)	promoter-TSS (NM_175311)	-959	NM_175311	101023	Mm.45033	NM_175311	ENSMUSG00000043059	Zfp513	AW990386|D430028M17Rik|Znf513	zinc finger protein 513	protein-coding
mm_1432.1	chr1	67193281	67193298	+	1	NA	intron (NM_001080809, intron 21 of 37)	intron (NM_001080809, intron 21 of 37)	70262	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_58175.1	chr6	142757175	142757186	-	1	NA	intron (NM_009908, intron 1 of 7)	intron (NM_009908, intron 1 of 7)	494	NM_009908	12764	Mm.3820	NM_009908	ENSMUSG00000030282	Cmas	AW208911|CMPNeu5Ac|D6Bwg0250e	cytidine monophospho-N-acetylneuraminic acid synthetase	protein-coding
mm_37797.1	chr4	130520214	130520224	-	1	NA	Intergenic	Intergenic	53817	NM_025998	67149	Mm.423029	NM_025998	ENSMUSG00000078532	Nkain1	2610200G18Rik|2810426C15Rik	Na+/K+ transporting ATPase interacting 1	protein-coding
mm_88193.1	chr10	70095352	70095353	+	1	NA	Intergenic	Intergenic	-1769	NM_001111121	76551	Mm.281741	NM_001111121	ENSMUSG00000048701	Ccdc6	2810012H18Rik|AA536681|AA960498|AW061011	coiled-coil domain containing 6	protein-coding
mm_13908.1	chr2	120500055	120500066	+	1	NA	intron (NM_007601, intron 15 of 23)	intron (NM_007601, intron 15 of 23)	23151	NM_001109761	12335	Mm.458021	NM_007601	ENSMUSG00000079110	Capn3	AI323605|Capa-3|Capa3|Lp82|p94	calpain 3	protein-coding
mm_105457.1	chr11	104550411	104550419	-	1	NA	promoter-TSS (NM_010858)	promoter-TSS (NM_010858)	205	NM_001285990	217232	Mm.89845	NM_145436	ENSMUSG00000020687	Cdc27	AI452358|APC3|BC023187	cell division cycle 27	protein-coding
mm_121699.1	chr14	14294655	14294689	-	1	NA	Intergenic	Intergenic	-33441	NM_147027	18330	Mm.484338	NM_147027	ENSMUSG00000072707	Olfr31	MOR274-1|MTPCR53	olfactory receptor 31	protein-coding
mm_9499.1	chr1	173730089	173730119	-	1	NA	exon (NM_001204910, exon 5 of 8)	exon (NM_001204910, exon 5 of 8)	11705	NM_001204910	226691	Mm.440876	NM_001204910	ENSMUSG00000073490	Ifi207	AI607873|Pyhin-A	interferon activated gene 207	protein-coding
mm_155157.1	chrX	52927005	52927015	+	1	NA	intron (NM_027642, intron 3 of 10)	intron (NM_027642, intron 3 of 10)	14796	NM_001290546	70998	Mm.26870	NM_027642	ENSMUSG00000025626	Phf6	2700007B13Rik|4931428F02Rik|mKIAA1823	PHD finger protein 6	protein-coding
mm_56155.1	chr6	87845695	87845707	-	1	NA	exon (NM_013493, exon 2 of 5)	exon (NM_013493, exon 2 of 5)	5405	NM_001109746	12785	Mm.290251	NM_013493	ENSMUSG00000030057	Cnbp	AA408710|Cnbp1|Znf9	cellular nucleic acid binding protein	protein-coding
mm_120912.1	chr14	76251563	76251569	+	1	NA	Intergenic	Intergenic	140675	NM_013745	27275	Mm.21138	NM_013745	ENSMUSG00000022009	Nufip1	Nufip	nuclear fragile X mental retardation protein interacting protein 1	protein-coding
mm_48360.1	chr5	139406112	139406138	-	1	NA	promoter-TSS (NM_177000)	promoter-TSS (NM_177000)	-262	NM_177000	319772	Mm.440271	NM_177000	ENSMUSG00000044092	C130050O18Rik	-	RIKEN cDNA C130050O18 gene	protein-coding
mm_112324.1	chr12	115372461	115372488	-	1	NA	Intergenic	Intergenic	323320	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
mm_144235.1	chr18	10617847	10617855	+	1	NA	promoter-TSS (NM_009226)	promoter-TSS (NM_009226)	55	NM_009226	20641	Mm.603	NM_009226	ENSMUSG00000002477	Snrpd1	AA407109|AL023031|SMD1	small nuclear ribonucleoprotein D1	protein-coding
mm_40597.1	chr5	64237960	64237964	+	1	NA	intron (NM_001289514, intron 1 of 18)	intron (NM_001289514, intron 1 of 18)	7605	NM_001289514	57915	Mm.286353	NM_019636	ENSMUSG00000029174	Tbc1d1	1110062G02Rik|AI385682|AW555803|Nob1|Nobq1|Tbc1|mKIAA1108	TBC1 domain family, member 1	protein-coding
mm_25192.1	chr3	103575276	103575286	+	1	NA	promoter-TSS (NM_018800)	promoter-TSS (NM_018800)	-1	NM_001276679	54524	Mm.88818	NM_018800	ENSMUSG00000027849	Syt6	3110037A08Rik|AW048930|sytVI	synaptotagmin VI	protein-coding
mm_162709.1	chr10	24553330	24553378	+	1	NA	Intergenic	Intergenic	-42088	NM_010217	14219	Mm.390287	NM_010217	ENSMUSG00000019997	Ctgf	Ccn2|Fisp12|Hcs24|fisp-12	connective tissue growth factor	protein-coding
mm_135036.1	chr16	32868326	32868368	-	1	NA	promoter-TSS (NM_001200038)	promoter-TSS (NM_001200038)	19	NM_001200038	100502698	Mm.327319	NM_172615	ENSMUSG00000035629	Rubcn	1700021K19Rik|5330403K09|Kiaa0226|Rubicon|mKIAA0226	RUN domain and cysteine-rich domain containing, Beclin 1-interacting protein	protein-coding
mm_46602.1	chr5	107868975	107868990	-	1	NA	intron (NM_007964, intron 1 of 17)	CpG	6125	NM_007964	14020	Mm.35796	NM_007964	ENSMUSG00000011831	Evi5	NB4S	ecotropic viral integration site 5	protein-coding
mm_8227.1	chr1	138175182	138175198	-	1	NA	promoter-TSS (NM_001111316)	promoter-TSS (NM_001111316)	-64	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_62931.1	chr7	118649148	118649194	+	1	NA	intron (NM_001105252, intron 10 of 21)	intron (NM_001105252, intron 10 of 21)	15435	NM_028930	74424	Mm.11068	NM_028930	ENSMUSG00000030650	Tmc5	4932443L08Rik|AU016085	transmembrane channel-like gene family 5	protein-coding
mm_172535.1	chr7	94395042	94395046	-	1	NA	Intergenic	L1Md_T|LINE|L1	1315165	NM_021427	58238	Mm.113787	NM_021427	ENSMUSG00000051515	Fam181b	A830059I20Rik|AB041569	family with sequence similarity 181, member B	protein-coding
mm_51400.1	chr6	78372098	78372138	+	1	NA	exon (NM_011036, exon 4 of 6)	exon (NM_011036, exon 4 of 6)	1233	NM_011036	18489	Mm.2553	NM_011036	ENSMUSG00000071356	Reg3b	HIP|PAP1|Pap|REG-III	regenerating islet-derived 3 beta	protein-coding
mm_89093.1	chr10	84308848	84308858	+	1	NA	Intergenic	Intergenic	131618	NM_001004363	77976	Mm.25874	NM_001004363	ENSMUSG00000020032	Nuak1	AU014801|AW494241|B230104P22Rik|Omphk1	NUAK family, SNF1-like kinase, 1	protein-coding
mm_89972.1	chr10	111506543	111506563	+	1	NA	exon (NM_009344, exon 1 of 2)	exon (NM_009344, exon 1 of 2)	267	NM_009344	21664	Mm.3117	NM_009344	ENSMUSG00000020205	Phlda1	DT1P1B11|TDAG51|Tdag	pleckstrin homology like domain, family A, member 1	protein-coding
mm_170662.1	chr2	113920533	113920533	-	1	NA	Intergenic	Intergenic	-71872	NM_181416	228482	Mm.45753	NM_181416	ENSMUSG00000041219	Arhgap11a	6530401L14Rik|mKIAA0013	Rho GTPase activating protein 11A	protein-coding
mm_73257.1	chr8	104340618	104340622	+	1	NA	promoter-TSS (NM_024217)	promoter-TSS (NM_024217)	26	NM_024217	68119	Mm.390108	NM_024217	ENSMUSG00000031875	Cmtm3	9430096L06Rik|AI413895|BNAS2|Cklfsf3	CKLF-like MARVEL transmembrane domain containing 3	protein-coding
mm_29024.1	chr3	101924630	101924640	-	1	NA	promoter-TSS (NM_001039371)	promoter-TSS (NM_001039371)	-182	NM_001039371	242126	Mm.90204	NM_001039371	ENSMUSG00000033147	Slc22a15	2610034P21Rik|4930477M19|A530052I06Rik|BB219042	solute carrier family 22 (organic anion/cation transporter), member 15	protein-coding
mm_120163.1	chr14	60750160	60750171	+	1	NA	intron (NM_001310594, intron 5 of 9)	intron (NM_001310594, intron 5 of 9)	17261	NM_001310594	219140	Mm.149776	NM_001033272	ENSMUSG00000021990	Spata13	C79050|ESTM11|X83327|mFLJ00298	spermatogenesis associated 13	protein-coding
mm_8461.1	chr1	153249102	153249147	-	1	NA	exon (NM_010683, exon 11 of 28)	exon (NM_010683, exon 11 of 28)	-62677	NM_008485	16782	Mm.329272	NM_008485	ENSMUSG00000026479	Lamc2	AA589349	laminin, gamma 2	protein-coding
mm_67713.1	chr7	89980602	89980625	-	1	NA	5' UTR (NM_021876, exon 1 of 12)	5' UTR (NM_021876, exon 1 of 12)	363	NM_021876	13626	Mm.380914	NM_021876	ENSMUSG00000030619	Eed	ENSMUSG00000039373|l(7)5Rn|l7Rn5|lusk	embryonic ectoderm development	protein-coding
mm_93914.1	chr10	127060339	127060387	-	1	NA	promoter-TSS (NM_001033262)	promoter-TSS (NM_001033262)	-179	NM_001033262	216438	Mm.37892	NM_001033262	ENSMUSG00000040502	March9	AI608492|BC019560	membrane-associated ring finger (C3HC4) 9	protein-coding
mm_47811.1	chr5	134176708	134176716	-	1	NA	promoter-TSS (NM_033572)	promoter-TSS (NM_033572)	55	NM_033572	94254	Mm.29508	NM_033572	ENSMUSG00000061979	Rcc1l	5730496C04Rik|AU019812|Wbscr16	reculator of chromosome condensation 1 like	protein-coding
mm_46531.1	chr5	105693977	105693999	-	1	NA	Intergenic	RMER15|LTR|ERVL	-5981	NM_001122768	231549	Mm.23837	NM_178701	ENSMUSG00000046079	Lrrc8d	2810473G09Rik|4930525N13Rik|A930019F03|Lrrc5	leucine rich repeat containing 8D	protein-coding
mm_170703.1	chr2	138035309	138035325	+	1	NA	Intergenic	IAPLTR1_Mm|LTR|ERVK	-221267	NM_001025431	228662	Mm.153405	NM_145534	ENSMUSG00000062098	Btbd3	mKIAA0952	BTB (POZ) domain containing 3	protein-coding
mm_90007.1	chr10	113272835	113272839	+	1	NA	Intergenic	IAPLTR2a2_Mm|LTR|ERVK	-313741	NR_035418	100316831		NR_035418	ENSMUSG00000080594	Mir669h	Mirn669h|mir-669h|mmu-mir-669h	microRNA 669h	ncRNA
mm_23317.1	chr3	53260819	53260854	+	1	NA	3' UTR (NM_175386, exon 4 of 4)	3' UTR (NM_175386, exon 4 of 4)	202422	NM_172501	212114	Mm.85744	NM_172501	ENSMUSG00000042997	Nhlrc3	4833441N19|8030451K01Rik|mKIAA4083	NHL repeat containing 3	protein-coding
mm_18809.1	chr2	73912433	73912466	-	1	NA	Intergenic	ORR1B2|LTR|ERVL-MaLR	-1123	NM_001301722	228033	Mm.2966	NM_175015	ENSMUSG00000018770	Atp5g3	6030447M23	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit C3 (subunit 9)	protein-coding
mm_163333.1	chr12	11436476	11436487	-	1	NA	5' UTR (NM_012038, exon 1 of 4)	5' UTR (NM_012038, exon 1 of 4)	168	NM_012038	26950	Mm.27005	NM_012038	ENSMUSG00000054459	Vsnl1	VILIP|Vnsl1	visinin-like 1	protein-coding
mm_144711.1	chr18	35034097	35034134	+	1	NA	Intergenic	Intergenic	-79764	NM_010481	15526	Mm.209419	NM_010481	ENSMUSG00000024359	Hspa9	74kDa|Csa|Grp75|Hsc74|Hsp74|Hsp74a|Hspa9a|Mortalin|Mot-2|Mot2|Mthsp70|Pbp74	heat shock protein 9	protein-coding
mm_141439.1	chr17	29658305	29658334	-	1	NA	intron (NR_132314, intron 7 of 27)	intron (NR_132314, intron 7 of 27)	-2276	NM_028791	74157	Mm.390979	NM_028791	ENSMUSG00000024019	Cmtr1	1300018I05Rik|AI451264|Ftsjd2|MTr1	cap methyltransferase 1	protein-coding
mm_117257.1	chr13	64367973	64368021	-	1	NA	exon (NM_009984, exon 4 of 8)	exon (NM_009984, exon 4 of 8)	2523	NM_009984	13039	Mm.930	NM_009984	ENSMUSG00000021477	Ctsl	1190035F06Rik|CatL|Ctsl1|MEP|fs|nkt	cathepsin L	protein-coding
mm_97424.1	chr11	78037960	78038042	+	1	NA	promoter-TSS (NM_001284227)	promoter-TSS (NM_001284227)	60	NM_008028	14252	Mm.130227	NM_008028	ENSMUSG00000061981	Flot2	AI573412|Esa|reggie-2	flotillin 2	protein-coding
mm_169871.1	chr16	36072098	36072098	+	1	NA	promoter-TSS (NM_027342)	promoter-TSS (NM_027342)	438	NM_001159421	381045	Mm.310434	NM_198645	ENSMUSG00000075229	Ccdc58	A930007B11Rik|AI413631	coiled-coil domain containing 58	protein-coding
mm_105235.1	chr11	102317788	102317816	-	1	NA	promoter-TSS (NM_001044383)	promoter-TSS (NM_001044383)	-515	NM_001044383	21429	Mm.2845	NM_011551	ENSMUSG00000020923	Ubtf	A930005G04Rik|NOR-90|Tcfubf|UBF|UBF-1|UBF1	upstream binding transcription factor, RNA polymerase I	protein-coding
mm_55694.1	chr6	72842849	72842898	-	1	NA	exon (NM_019715, exon 7 of 7)	exon (NM_019715, exon 7 of 7)	-53828	NM_009332	21415	Mm.440067	NM_009332	ENSMUSG00000055799	Tcf7l1	Tcf-3|Tcf3|bHLHb21	transcription factor 7 like 1 (T cell specific, HMG box)	protein-coding
mm_126393.1	chr15	80193001	80193014	+	1	NA	intron (NM_010795, intron 1 of 1)	intron (NM_010795, intron 1 of 1)	19286	NM_010795	17309	Mm.299693	NM_010795	ENSMUSG00000042428	Mgat3	1110038J12Rik|AI848272|GnT-III	mannoside acetylglucosaminyltransferase 3	protein-coding
mm_97389.1	chr11	77801155	77801166	+	1	NA	promoter-TSS (NM_001291215)	promoter-TSS (NM_001291215)	-138	NM_001291214	360013	Mm.341248	NM_011586	ENSMUSG00000000631	Myo18a	MAJN|MyoPDZ|MysPDZ|SP-R210	myosin XVIIIA	protein-coding
mm_14063.1	chr2	122704218	122704224	+	1	NA	Intergenic	MLT1F|LTR|ERVL-MaLR	-1558	NM_001290993	22785	Mm.27801	NM_011774	ENSMUSG00000005802	Slc30a4	Znt4|lm|znT-4	solute carrier family 30 (zinc transporter), member 4	protein-coding
mm_20096.1	chr2	120970707	120970761	-	1	NA	promoter-TSS (NM_009461)	promoter-TSS (NM_009461)	-19	NM_009461	22222	Mm.389330	NM_009461	ENSMUSG00000027272	Ubr1	AI504731	ubiquitin protein ligase E3 component n-recognin 1	protein-coding
mm_25826.1	chr3	128528692	128528694	+	1	NA	Intergenic	Intergenic	-297088	NR_045704	402774	Mm.209170	NR_045704	ENSMUSG00000105816	D030025E07Rik	-	RIKEN cDNA D030025E07 gene	ncRNA
mm_127228.1	chr15	99402122	99402143	+	1	NA	exon (NM_026669, exon 3 of 10)	exon (NM_026669, exon 3 of 10)	8913	NM_001171035	110213	Mm.16769	NM_026669	ENSMUSG00000023010	Tmbim6	5031406P05Rik|Bi1|Tegt	transmembrane BAX inhibitor motif containing 6	protein-coding
mm_99724.1	chr11	106300411	106300439	+	1	NA	exon (NM_008117, exon 5 of 5)	exon (NM_008117, exon 5 of 5)	1471	NM_008117	14599	Mm.343934	NM_008117	ENSMUSG00000020713	Gh	Gh1|Ghb1	growth hormone	protein-coding
mm_23983.1	chr3	86040806	86040825	+	1	NA	Intergenic	Intergenic	-38324	NM_001001650	368202	Mm.253822	NM_001001650	ENSMUSG00000049013	Prss48	Esspl|Gm1019	protease, serine 48	protein-coding
mm_150057.1	chr19	29383614	29383632	+	1	NA	intron (NM_021893, intron 5 of 6)	intron (NM_021893, intron 5 of 6)	16185	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_107360.1	chr12	32835392	32835394	+	1	NA	intron (NM_021524, intron 4 of 10)	ID4_|SINE|ID	11277	NR_045032	100504486	Mm.440246	NR_045032		Gdap10	Gdap-ps	ganglioside-induced differentiation-associated-protein 10	ncRNA
mm_32350.1	chr4	104936274	104936278	+	1	NA	intron (NM_001285953, intron 1 of 19)	intron (NM_001285953, intron 1 of 19)	22820	NM_001285952	242594	Mm.65181	NM_001162980	ENSMUSG00000078612	1700024P16Rik	C1orf168|Gm620	RIKEN cDNA 1700024P16 gene	protein-coding
mm_125502.1	chr15	55264974	55264981	+	1	NA	Intergenic	RMER10B|LTR|ERVL	-42773	NM_181277	12818	Mm.297859	NM_181277	ENSMUSG00000022371	Col14a1	5730412L22Rik|AW108078	collagen, type XIV, alpha 1	protein-coding
mm_74220.1	chr8	124021520	124021530	+	1	NA	promoter-TSS (NM_133966)	promoter-TSS (NM_133966)	-216	NM_133966	102162	Mm.291777	NM_133966	ENSMUSG00000038697	Taf5l	1110005N04Rik|AI849020	TATA-box binding protein associated factor 5 like	protein-coding
mm_54544.1	chr6	36809982	36810000	-	1	NA	5' UTR (NM_008973, exon 1 of 5)	5' UTR (NM_008973, exon 1 of 5)	1370	NM_008973	19242	Mm.279690	NM_008973	ENSMUSG00000029838	Ptn	HARP|HB-GAM|HBBN|HBGF-8|HBNF|OSF|Osf-1|Osf1	pleiotrophin	protein-coding
mm_27760.1	chr3	69599213	69599231	-	1	NA	promoter-TSS (NM_020026)	promoter-TSS (NM_020026)	-262	NM_020026	26879	Mm.153710	NM_020026	ENSMUSG00000043300	B3galnt1	B3galt3|b3GT3	UDP-GalNAc:betaGlcNAc beta 1,3-galactosaminyltransferase, polypeptide 1	protein-coding
mm_69921.1	chr7	141840488	141840490	-	1	NA	intron (NM_028801, intron 1 of 48)	intron (NM_028801, intron 1 of 48)	1417	NM_028801	74180	Mm.200752	NM_028801	ENSMUSG00000066108	Muc5b	2300002I04Rik|A130042M24|AV085033|MUC5|MUC9|mucin 5b	mucin 5, subtype B, tracheobronchial	protein-coding
mm_151722.1	chr19	4828637	4828642	-	1	NA	intron (NM_016892, intron 5 of 7)	intron (NM_016892, intron 5 of 7)	10683	NM_016892	12460	Mm.434411	NM_016892	ENSMUSG00000034108	Ccs	Ccsd	copper chaperone for superoxide dismutase	protein-coding
mm_107993.1	chr12	73286824	73286864	+	1	NA	promoter-TSS (NM_029580)	promoter-TSS (NM_029580)	-4	NM_001037717	625098	Mm.32075	NM_001037717	ENSMUSG00000044712	Slc38a6	AW322671|EG625098	solute carrier family 38, member 6	protein-coding
mm_135657.1	chr16	52400634	52400650	-	1	NA	intron (NM_009655, intron 1 of 15)	intron (NM_009655, intron 1 of 15)	52439	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_50495.1	chr6	48990226	48990238	+	1	NA	exon (NM_172888, exon 2 of 5)	exon (NM_172888, exon 2 of 5)	3371	NM_172888	243377	Mm.446302	NM_172888	ENSMUSG00000039215	Svs1	9530003A11	seminal vesicle secretory protein 1	protein-coding
mm_25328.1	chr3	106569344	106569360	+	1	NA	intron (NM_001025582, intron 5 of 6)	Lx7|LINE|L1	-21550	NM_133869	99712	Mm.429443	NM_133869	ENSMUSG00000040774	Cept1	9930118K05Rik|mCEPT1	choline/ethanolaminephosphotransferase 1	protein-coding
mm_121094.1	chr14	99301982	99302028	+	1	NA	exon (NM_009769, exon 2 of 4)	exon (NM_009769, exon 2 of 4)	3314	NM_009769	12224	Mm.30262	NM_009769	ENSMUSG00000005148	Klf5	4930520J07Rik|Bteb2|CKLF|IKLF	Kruppel-like factor 5	protein-coding
mm_122161.1	chr14	31398063	31398091	-	1	NA	intron (NM_011894, intron 3 of 8)	intron (NM_011894, intron 3 of 8)	19600	NM_001347585	24056	Mm.383198	NM_011894	ENSMUSG00000021892	Sh3bp5	AI606498|SH3BP-5|Sab	SH3-domain binding protein 5 (BTK-associated)	protein-coding
mm_165604.1	chr3	50414999	50415001	-	1	NA	intron (NM_011990, intron 6 of 11)	intron (NM_011990, intron 6 of 11)	28613	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_133093.1	chr16	62867081	62867107	+	1	NA	intron (NM_011173, intron 1 of 14)	intron (NM_011173, intron 1 of 14)	12787	NM_011173	19128	Mm.127156	NM_011173	ENSMUSG00000022912	Pros1	AW214361	protein S (alpha)	protein-coding
mm_77622.1	chr8	123953751	123953753	-	1	NA	3' UTR (NM_019552, exon 13 of 13)	3' UTR (NM_019552, exon 13 of 13)	-4487	NM_172288	234865	Mm.267812	NM_172288	ENSMUSG00000039509	Nup133	mermaid	nucleoporin 133	protein-coding
mm_138336.1	chr17	34898464	34898501	+	1	NA	promoter-TSS (NM_001286575)	promoter-TSS (NM_001286575)	-10	NM_001286575	110147	Mm.35345	NM_145830	ENSMUSG00000013787	Ehmt2	Bat8|D17Ertd710e|G9a|KMT1C|NG36	euchromatic histone lysine N-methyltransferase 2	protein-coding
mm_170446.1	chr18	83700870	83700876	+	1	NA	Intergenic	IAPLTR1_Mm|LTR|ERVK	-374989	NR_045361	70960	Mm.410834	NR_045361		4921531P14Rik	1700108N05Rik	RIKEN cDNA 4921531P14 gene	ncRNA
mm_77427.1	chr8	121108302	121108359	-	1	NA	promoter-TSS (NM_001166482)	promoter-TSS (NM_001166482)	49	NM_172761	234814	Mm.31690	NM_172761	ENSMUSG00000031816	Mthfsd	AW049977|BC052066|C920004D05	methenyltetrahydrofolate synthetase domain containing	protein-coding
mm_137785.1	chr17	29495636	29495657	+	1	NA	TTS (NM_008842)	TTS (NM_008842)	4601	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_39683.1	chr5	25774966	25774968	+	1	NA	intron (NM_001310504, intron 1 of 10)	RLTR17B_Mm|LTR|ERVK	14994	NM_001004365	242894	Mm.150319	NM_001004365	ENSMUSG00000056367	Actr3b	9630005C02|ARP11|AW047569|Arp3b|Arp3beta	ARP3 actin-related protein 3B	protein-coding
mm_137751.1	chr17	29398465	29398487	+	1	NA	Intergenic	Intergenic	37562	NM_001159538	26382	Mm.279187	NM_013710	ENSMUSG00000024013	Fgd2	Tcd-2|Tcd2|ZFYVE4|tcs-2|tcs2	FYVE, RhoGEF and PH domain containing 2	protein-coding
mm_54277.1	chr6	29165004	29165008	-	1	NA	promoter-TSS (NM_133925)	promoter-TSS (NM_133925)	-282	NM_133925	68272	Mm.40802	NM_026650	ENSMUSG00000029701	Rbm28	2810480G15Rik|AI503051	RNA binding motif protein 28	protein-coding
mm_167088.1	chr7	104472049	104472059	-	1	NA	exon (NM_001167828, exon 7 of 7)	exon (NM_001167828, exon 7 of 7)	-6861	NM_009099	20128	Mm.295578	NM_009099	ENSMUSG00000030921	Trim30a	Rpt-1|Rpt1|Trim30	tripartite motif-containing 30A	protein-coding
mm_153365.1	chr19	40271637	40271698	-	1	NA	promoter-TSS (NM_016861)	promoter-TSS (NM_016861)	-51	NM_016861	54132	Mm.5567	NM_016861	ENSMUSG00000055044	Pdlim1	CLP36|Clim1|mClim1	PDZ and LIM domain 1 (elfin)	protein-coding
mm_94595.1	chr11	11809091	11809103	+	1	NA	promoter-TSS (NM_021891)	promoter-TSS (NM_021891)	-135	NM_001163360	60530	Mm.236114	NM_021891	ENSMUSG00000035455	Fignl1	-	fidgetin-like 1	protein-coding
mm_37214.1	chr4	117891995	117892040	-	1	NA	promoter-TSS (NM_026344)	promoter-TSS (NM_026344)	-14	NM_026344	67728	Mm.13823	NM_026344	ENSMUSG00000028540	Dph2	9130020C19Rik|AI467389|Dph2l2	DPH2 homolog	protein-coding
mm_56034.1	chr6	86649427	86649429	-	1	NA	3' UTR (NM_010751, exon 6 of 6)	3' UTR (NM_010751, exon 6 of 6)	19731	NM_010751	17119	Mm.279580	NM_010751	ENSMUSG00000001156	Mxd1	AW122478|Mad|Mad1	MAX dimerization protein 1	protein-coding
mm_60675.1	chr7	45073529	45073530	+	1	NA	exon (NM_025533, exon 2 of 9)	exon (NM_025533, exon 2 of 9)	11100	NM_025533	66394	Mm.272139	NM_025533	ENSMUSG00000003421	Nosip	2310061K06Rik|CGI-25	nitric oxide synthase interacting protein	protein-coding
mm_159507.1	chr4	47386091	47386091	+	1	NA	promoter-TSS (NM_001312869)	promoter-TSS (NM_001312869)	-125	NM_001312869	21812	Mm.197552	NM_009370	ENSMUSG00000007613	Tgfbr1	ALK5|AU017191|Alk-5|ESK2|TGFR-1|TbetaR-I|TbetaRI	transforming growth factor, beta receptor I	protein-coding
mm_125728.1	chr15	73155586	73155590	+	1	NA	intron (NM_153178, intron 1 of 18)	intron (NM_153178, intron 1 of 18)	29359	NM_153178	239528	Mm.23095	NM_153178	ENSMUSG00000036698	Ago2	1110029L17Rik|2310051F07Rik|AI225898|AL022874|AW546247|ENSMUSG00000072493|Eif2c2|Gerp95|Gm10365|mKIAA4215	argonaute RISC catalytic subunit 2	protein-coding
mm_134971.1	chr16	32017824	32017827	-	1	NA	3' UTR (NM_177326, exon 15 of 15)	3' UTR (NM_177326, exon 15 of 15)	-14538	NM_177103	320213	Mm.152890	NM_023801	ENSMUSG00000022772	Senp5	6230429P13Rik|A730063F07Rik|AI851888|BB189556|SMT3IP3	SUMO/sentrin specific peptidase 5	protein-coding
mm_87831.1	chr10	60367576	60367642	+	1	NA	intron (NM_028732, intron 4 of 6)	intron (NM_028732, intron 4 of 6)	20758	NM_028732	74048	Mm.273584	NM_028732	ENSMUSG00000020101	Vsir	4632428N05Rik|Dies1|PD-1H|VISTA	V-set immunoregulatory receptor	protein-coding
mm_79244.1	chr9	50554834	50554848	+	1	NA	intron (NM_133217, intron 1 of 11)	intron (NM_133217, intron 1 of 11)	297	NM_133217	170752	Mm.390149	NM_133217	ENSMUSG00000032066	Bco2	B-diox-II|Bcdo2|Bcmo2|CMO2	beta-carotene oxygenase 2	protein-coding
mm_18461.1	chr2	62343671	62343701	-	1	NA	intron (NM_001159543, intron 23 of 24)	intron (NM_001159543, intron 23 of 24)	68545	NM_010074	13482	Mm.1151	NM_010074	ENSMUSG00000035000	Dpp4	Cd26|Dpp-4|THAM	dipeptidylpeptidase 4	protein-coding
mm_71895.1	chr8	69902179	69902194	+	1	NA	promoter-TSS (NM_032004)	promoter-TSS (NM_032004)	2	NM_032004	83984	Mm.432504	NM_032004	ENSMUSG00000047654	Tssk6	Sstk|TSK-6|TSSK-6	testis-specific serine kinase 6	protein-coding
mm_33012.1	chr4	120854787	120854843	+	1	NA	Intergenic	CpG	-23054	NM_182929	242662	Mm.192502	NM_182929	ENSMUSG00000032890	Rims3	A730060M23Rik|Nim3|Rim3|mKIAA0237	regulating synaptic membrane exocytosis 3	protein-coding
mm_86290.1	chr9	121916289	121916315	-	1	NA	promoter-TSS (NM_010012)	promoter-TSS (NM_010012)	3	NM_010012	13124	Mm.20889	NM_010012	ENSMUSG00000050445	Cyp8b1	-	cytochrome P450, family 8, subfamily b, polypeptide 1	protein-coding
mm_43650.1	chr5	138280517	138280537	+	1	NA	promoter-TSS (NM_016964)	promoter-TSS (NM_016964)	18	NM_016964	50878	Mm.285609	NM_016964	ENSMUSG00000036928	Stag3	SA-2	stromal antigen 3	protein-coding
mm_88609.1	chr10	79822618	79822679	+	1	NA	intron (NM_030218, intron 1 of 4)	intron (NM_030218, intron 1 of 4)	1627	NM_030218	78906	Mm.33087	NM_030218	ENSMUSG00000035852	Misp	9130017N09Rik	mitotic spindle positioning	protein-coding
mm_68545.1	chr7	114234997	114235009	-	1	NA	exon (NM_033370, exon 12 of 22)	exon (NM_033370, exon 12 of 22)	19677	NM_033370	70349	Mm.277024	NM_033370	ENSMUSG00000030754	Copb1	2610019B04Rik	coatomer protein complex, subunit beta 1	protein-coding
mm_161081.1	chr12	84069368	84069368	+	1	NA	promoter-TSS (NM_001347417)	promoter-TSS (NM_001347417)	43	NM_145444	217698	Mm.484019	NM_145444	ENSMUSG00000042540	Acot5	BC016076|PTE-Ic	acyl-CoA thioesterase 5	protein-coding
mm_38781.1	chr4	148075444	148075452	-	1	NA	Intergenic	Intergenic	12616	NM_009642	11610	Mm.46247	NM_009642	ENSMUSG00000029007	Agtrap	3300002E14Rik|AT1R|Atrap|D4Wsu124e	angiotensin II, type I receptor-associated protein	protein-coding
mm_102867.1	chr11	69406756	69406770	-	1	NA	exon (NM_001017426, exon 9 of 23)	exon (NM_001017426, exon 9 of 23)	6912	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_10817.1	chr2	24350421	24350427	+	1	NA	3' UTR (NM_031167, exon 5 of 5)	3' UTR (NM_031167, exon 5 of 5)	5053	NM_001039701	16181	Mm.882	NM_031167	ENSMUSG00000026981	Il1rn	F630041P17Rik|IL-1ra	interleukin 1 receptor antagonist	protein-coding
mm_1507.1	chr1	72307492	72307502	+	1	NA	promoter-TSS (NM_009533)	promoter-TSS (NM_009533)	76	NM_009533	22596	Mm.246952	NM_009533	ENSMUSG00000026187	Xrcc5	AI314015|Ku80|Ku86	X-ray repair complementing defective repair in Chinese hamster cells 5	protein-coding
mm_134862.1	chr16	28446988	28447010	-	1	NA	promoter-TSS (NM_183064)	promoter-TSS (NM_183064)	-924	NM_001276420	14167	Mm.7996	NM_010199	ENSMUSG00000022523	Fgf12	AV114868|B230343J05Rik|FGF-12|FHF-1|Fhf1	fibroblast growth factor 12	protein-coding
mm_60077.1	chr7	34021545	34021557	+	1	NA	promoter-TSS (NM_009596)	promoter-TSS (NM_009596)	-16	NM_009596	11354	Mm.8025	NM_009596	ENSMUSG00000066583	Scgb1b27	Abp|Abpa|Abpa27|Sal-1|Tcp	secretoglobin, family 1B, member 27	protein-coding
mm_114134.1	chr13	55220656	55220668	+	1	NA	intron (NM_008739, intron 2 of 22)	B1_Mur3|SINE|Alu	10880	NM_008739	18193	Mm.12964	NM_008739	ENSMUSG00000021488	Nsd1	AI528500|KMT3B	nuclear receptor-binding SET-domain protein 1	protein-coding
mm_86830.1	chr10	21192175	21192184	+	1	NA	Intergenic	Intergenic	-31195	NM_010848	17863	Mm.52109	NM_010848	ENSMUSG00000019982	Myb	AI550390|M16449|c-myb	myeloblastosis oncogene	protein-coding
mm_88167.1	chr10	69747015	69747030	+	1	NA	intron (NM_170730, intron 1 of 17)	intron (NM_170730, intron 1 of 17)	-178510	NM_170687	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_61596.1	chr7	80026162	80026192	+	1	NA	promoter-TSS (NM_175433)	promoter-TSS (NM_175433)	-51	NM_175433	209225	Mm.290925	NM_175433	ENSMUSG00000048897	Zfp710	5430400N05Rik|9830165K13|AI324798|Znf710	zinc finger protein 710	protein-coding
mm_164044.1	chr14	94124099	94124102	+	1	NA	Intergenic	Intergenic	-233421	NM_001346722	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding
mm_142679.1	chr17	47732480	47732488	-	1	NA	exon (NM_025973, exon 6 of 9)	exon (NM_025973, exon 6 of 9)	-4553	NM_001161722	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_31218.1	chr4	44004439	44004455	+	1	NA	Intergenic	Intergenic	-8196	NM_016760	12757	Mm.298875	NM_016760	ENSMUSG00000028478	Clta	AV026556|Lca	clathrin, light polypeptide (Lca)	protein-coding
mm_47608.1	chr5	125106320	125106350	-	1	NA	intron (NM_011424, intron 5 of 46)	intron (NM_011424, intron 5 of 46)	72879	NM_001253905	20602	Mm.278646	NM_011424	ENSMUSG00000029478	Ncor2	N-CoR|SMRT|SMRTe	nuclear receptor co-repressor 2	protein-coding
mm_74642.1	chr8	13254247	13254269	-	1	NA	promoter-TSS (NM_172750)	promoter-TSS (NM_172750)	-96	NM_172750	234072	Mm.132785	NM_172750	ENSMUSG00000031448	Adprhl1	Arh2|D330008N11Rik	ADP-ribosylhydrolase like 1	protein-coding
mm_27417.1	chr3	51408926	51408984	-	1	NA	promoter-TSS (NM_025523)	promoter-TSS (NM_025523)	0	NM_025523	66377	Mm.331007	NM_025523	ENSMUSG00000037152	Ndufc1	2310016K22Rik|KFYI	NADH dehydrogenase (ubiquinone) 1, subcomplex unknown, 1	protein-coding
mm_168277.1	chr1	103419885	103419886	-	1	NA	Intergenic	Intergenic	-1348934	NM_011800	23836	Mm.103640	NM_011800	ENSMUSG00000050840	Cdh20	Cdh7	cadherin 20	protein-coding
mm_86708.1	chr10	18845076	18845082	+	1	NA	promoter-TSS (NM_022032)	promoter-TSS (NM_022032)	8	NM_022032	64058	Mm.28209	NM_022032	ENSMUSG00000019851	Perp	1110017A08Rik|KCP1|KRTCAP1|PIGPC1|THW	PERP, TP53 apoptosis effector	protein-coding
mm_57640.1	chr6	128362862	128362926	-	1	NA	promoter-TSS (NM_008021)	promoter-TSS (NM_008021)	17	NM_001326585	72440	Mm.143908	NM_197981	ENSMUSG00000048668	Rhno1	2510047L19Rik|5930416I19Rik	RAD9-HUS1-RAD1 interacting nuclear orphan 1	protein-coding
mm_41325.1	chr5	90472580	90472605	+	1	NA	exon (NM_009654, exon 12 of 15)	exon (NM_009654, exon 12 of 15)	11722	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_141468.1	chr17	30602303	30602343	-	1	NA	intron (NM_025374, intron 2 of 5)	intron (NM_025374, intron 2 of 5)	10336	NM_025374	109801	Mm.261984	NM_025374	ENSMUSG00000024026	Glo1	0610009E22Rik|1110008E19Rik|2510049H23Rik|AW550643|GLY1|Glo-1|Glo-1r|Glo-1s|Glo1-r|Glo1-s|Qglo	glyoxalase 1	protein-coding
mm_3876.1	chr1	161001827	161001830	+	1	NA	intron (NM_080844, intron 7 of 7)	intron (NM_080844, intron 7 of 7)	23222	NM_080844	11905	Mm.260770	NM_080844	ENSMUSG00000026715	Serpinc1	AI114908|ATIII|At-3|At3	serine (or cysteine) peptidase inhibitor, clade C (antithrombin), member 1	protein-coding
mm_145049.1	chr18	40256871	40256882	+	1	NA	promoter-TSS (NR_045177)	promoter-TSS (NR_045177)	-86	NR_045177	73001	Mm.428647	NR_045177	ENSMUSG00000071860	2900055J20Rik	-	RIKEN cDNA 2900055J20 gene	ncRNA
mm_6014.1	chr1	59014097	59014104	-	1	NA	Intergenic	Intergenic	40529	NM_172656	227154	Mm.286006	NM_172656	ENSMUSG00000026027	Stradb	AA792893|Als2cr2|B830008M19|D1Ucla2|ILPIP|ILPIPA|PRO1038|Papk|Syradb	STE20-related kinase adaptor beta	protein-coding
mm_112776.1	chr13	20090297	20090310	+	1	NA	promoter-TSS (NM_080288)	promoter-TSS (NM_080288)	-204	NM_080288	140580	Mm.342392	NM_080288	ENSMUSG00000041112	Elmo1	6330578D22Rik|C230095H21Rik|CED-12	engulfment and cell motility 1	protein-coding
mm_109175.1	chr12	108410626	108410662	+	1	NA	promoter-TSS (NM_001043336)	promoter-TSS (NM_001043336)	11	NM_001286347	68519	Mm.236645	NM_001043335	ENSMUSG00000058070	Eml1	1110008N23Rik|A930030P13Rik|AA171013|AI847476|AI853955|ELP79|EMAP|EMAPL|heco	echinoderm microtubule associated protein like 1	protein-coding
mm_14686.1	chr2	140171017	140171043	+	1	NA	promoter-TSS (NM_001081090)	promoter-TSS (NM_001081090)	384	NM_027093	69487	Mm.287921	NM_027093	ENSMUSG00000027384	Ndufaf5	2310003L22Rik	NADH dehydrogenase (ubiquinone) complex I, assembly factor 5	protein-coding
mm_135688.1	chr16	52427519	52427538	-	1	NA	intron (NM_009655, intron 1 of 15)	Lx8|LINE|L1	25553	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_150277.1	chr19	34248498	34248508	+	1	NA	exon (NM_007392, exon 4 of 9)	exon (NM_007392, exon 4 of 9)	6870	NM_007392	11475	Mm.213025	NM_007392	ENSMUSG00000035783	Acta2	0610041G09Rik|Actvs|SMalphaA|a-SMA|alphaSMA	actin, alpha 2, smooth muscle, aorta	protein-coding
mm_39988.1	chr5	32490993	32491017	+	1	NA	exon (NM_172707, exon 8 of 8)	exon (NM_172707, exon 8 of 8)	32035	NM_172707	19046	Mm.241931	NM_172707	ENSMUSG00000014956	Ppp1cb	1200010B19	protein phosphatase 1, catalytic subunit, beta isoform	protein-coding
mm_86002.1	chr9	112232408	112232422	-	1	NA	promoter-TSS (NM_001177616)	promoter-TSS (NM_001177616)	86	NM_001177616	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_46818.1	chr5	113138545	113138561	-	1	NA	promoter-TSS (NM_001347397)	promoter-TSS (NM_001347397)	32	NM_001347397	243219	Mm.160131	NM_172884	ENSMUSG00000051339	2900026A02Rik	8430408O14Rik|A530094D01|AW539426|Gm449|Kiaa1671|mKIAA1671	RIKEN cDNA 2900026A02 gene	protein-coding
mm_27431.1	chr3	51559621	51559633	-	1	NA	promoter-TSS (NR_033624)	promoter-TSS (NR_033624)	-130	NR_033624	100039684	Mm.387178	NR_033624		5031434O11Rik	AI481280|Gm2370	RIKEN cDNA 5031434O11 gene	ncRNA
mm_18114.1	chr2	44996463	44996486	-	1	NA	exon (NM_015753, exon 8 of 10)	exon (NM_015753, exon 8 of 10)	26703	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_95901.1	chr11	58202528	58202539	+	1	NA	intron (NM_018738, intron 2 of 2)	PB1D9|SINE|Alu	2977	NM_018738	16145	Mm.33902	NM_018738	ENSMUSG00000078853	Igtp	AW558444|Irgm3	interferon gamma induced GTPase	protein-coding
mm_4376.1	chr1	172148038	172148048	+	1	NA	promoter-TSS (NM_153555)	promoter-TSS (NM_153555)	28	NM_153555	98193	Mm.159915	NM_153555	ENSMUSG00000026554	Dcaf8	AA408877|AA433120|AA792214|AU018973|C76055|D1Dau35e|D1Ucla4|H326|Wdr42a	DDB1 and CUL4 associated factor 8	protein-coding
mm_122838.1	chr14	54724039	54724049	-	1	NA	3' UTR (NM_016972, exon 11 of 11)	3' UTR (NM_016972, exon 11 of 11)	-11870	NM_207131	110794	Mm.236223	NM_207131	ENSMUSG00000052435	Cebpe	C/EBPe|CRP1|Gm294	CCAAT/enhancer binding protein (C/EBP), epsilon	protein-coding
mm_32943.1	chr4	119520957	119520957	+	1	NA	Intergenic	Intergenic	17812	NM_001004178	433752	Mm.425205	NM_001004178	ENSMUSG00000087385	AA415398	-	expressed sequence AA415398	protein-coding
mm_73026.1	chr8	94153023	94153033	+	1	NA	exon (NM_013603, exon 2 of 3)	exon (NM_013603, exon 2 of 3)	421	NM_013603	17751	Mm.2064	NM_013603	ENSMUSG00000031760	Mt3	Mt-3	metallothionein 3	protein-coding
mm_37752.1	chr4	129640615	129640660	-	1	NA	5' UTR (NM_001005506, exon 1 of 10)	5' UTR (NM_001005506, exon 1 of 10)	168	NM_001005506	109658	Mm.268863	NM_001005506	ENSMUSG00000053841	Txlna	2600010N21Rik|AI425952|AW209241|Il14|Txln	taxilin alpha	protein-coding
mm_53955.1	chr6	5325269	5325294	-	1	NA	Intergenic	RLTR9D2|LTR|ERVK	-26908	NM_183308	330260	Mm.126984	NM_183308	ENSMUSG00000032667	Pon2	6330405I24Rik|AI481612	paraoxonase 2	protein-coding
mm_161628.1	chr16	84834911	84834911	-	1	NA	promoter-TSS (NM_001302216)	promoter-TSS (NM_001302216)	87	NM_001302216	11957	Mm.353	NM_016755	ENSMUSG00000022890	Atp5j	CF6	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit F	protein-coding
mm_171071.1	chr3	115915908	115915908	+	1	NA	intron (NM_027193, intron 5 of 7)	intron (NM_027193, intron 5 of 7)	27725	NM_027193	69740	Mm.5915	NM_027193	ENSMUSG00000033554	Dph5	2410012M04Rik|AU045680|C80186	diphthamide biosynthesis 5	protein-coding
mm_97088.1	chr11	73138359	73138372	+	1	NA	promoter-TSS (NM_010353)	promoter-TSS (NM_010353)	-71	NM_010353	14841	Mm.42045	NM_010353	ENSMUSG00000050107	Gsg2	Haspin	germ cell associated 2, haspin	protein-coding
mm_160714.1	chr10	61299745	61299745	+	1	NA	intron (NM_011073, intron 1 of 2)	intron (NM_011073, intron 1 of 2)	1909	NM_011073	18646	Mm.240313	NM_011073	ENSMUSG00000037202	Prf1	Pfn|Pfp|Prf-1	perforin 1 (pore forming protein)	protein-coding
mm_172297.1	chr7	100987201	100987201	+	1	NA	Intergenic	Intergenic	-22835	NM_183168	233571	Mm.235193	NM_183168	ENSMUSG00000048779	P2ry6	2010204J23Rik|P2Y6	pyrimidinergic receptor P2Y, G-protein coupled, 6	protein-coding
mm_16394.1	chr2	179414950	179414958	+	1	NA	promoter-TSS (NM_026596)	promoter-TSS (NM_026596)	18	NM_026596	68175	Mm.158187	NM_026596		4930591A17Rik	-	RIKEN cDNA 4930591A17 gene	protein-coding
mm_5579.1	chr1	39551994	39552004	-	1	NA	3' UTR (NM_001033135, exon 7 of 7)	3' UTR (NM_001033135, exon 7 of 7)	-3159	NR_028555	100217461		NR_028555	ENSMUSG00000077704	Snord89	MBII-289	small nucleolar RNA, C/D box 89	snoRNA
mm_168175.1	chr10	56377270	56377277	+	1	NA	promoter-TSS (NM_010288)	promoter-TSS (NM_010288)	-27	NM_010288	14609	Mm.378921	NM_010288	ENSMUSG00000050953	Gja1	AU042049|AW546267|Cnx43|Cx43|Cx43alpha1|Gja-1|Npm1|connexin43	gap junction protein, alpha 1	protein-coding
mm_94320.1	chr11	4236862	4236868	+	1	NA	promoter-TSS (NM_001013365)	promoter-TSS (NM_001013365)	80	NM_001013365	18413	Mm.131422	NM_001013365	ENSMUSG00000058755	Osm	OncoM	oncostatin M	protein-coding
mm_120509.1	chr14	66344314	66344316	+	1	NA	promoter-TSS (NM_019675)	promoter-TSS (NM_019675)	19	NM_019675	56471	Mm.35474	NM_019675	ENSMUSG00000022044	Stmn4	Lagl|R75359|RB3	stathmin-like 4	protein-coding
mm_85385.1	chr9	103227994	103228040	-	1	NA	exon (NM_133977, exon 2 of 17)	exon (NM_133977, exon 2 of 17)	2269	NM_133977	22041	Mm.37214	NM_133977	ENSMUSG00000032554	Trf	AI266983|Cd176|HP|Tf|Tfn|hpx	transferrin	protein-coding
mm_66997.1	chr7	64392215	64392259	-	1	NA	promoter-TSS (NM_026483)	promoter-TSS (NM_026483)	-1	NM_026483	67973	Mm.26973	NM_026483	ENSMUSG00000030521	Mphosph10	2810453H10Rik|5730405D16Rik|AI326008	M-phase phosphoprotein 10 (U3 small nucleolar ribonucleoprotein)	protein-coding
mm_54840.1	chr6	42586405	42586407	-	1	NA	TTS (NM_203396)	TTS (NM_203396)	10966	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_9018.1	chr1	166127906	166127920	-	1	NA	promoter-TSS (NM_001160049)	promoter-TSS (NM_001160049)	-15	NM_001160049	240892	Mm.35315	NM_001033344	ENSMUSG00000026564	Dusp27	C130085G02Rik|Gm209	dual specificity phosphatase 27 (putative)	protein-coding
mm_2023.1	chr1	87128199	87128207	+	1	NA	TTS (NM_007432)	TTS (NM_007432)	3195	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_24294.1	chr3	89293895	89293905	+	1	NA	Intergenic	B1F|SINE|Alu	-12949	NM_001162425	13636	Mm.15675	NM_010107	ENSMUSG00000027954	Efna1	AI325262|B61|Efl1|Epl1|Eplg1|Lerk1	ephrin A1	protein-coding
mm_80819.1	chr9	96705805	96705835	+	1	NA	intron (NM_175537, intron 2 of 2)	intron (NM_175537, intron 2 of 2)	25855	NM_175537	245007	Mm.485954	NM_175537	ENSMUSG00000040433	Zbtb38	A930014K01Rik|CIBZ	zinc finger and BTB domain containing 38	protein-coding
mm_105534.1	chr11	106301201	106301216	-	1	NA	exon (NM_008117, exon 3 of 5)	exon (NM_008117, exon 3 of 5)	688	NM_008117	14599	Mm.343934	NM_008117	ENSMUSG00000020713	Gh	Gh1|Ghb1	growth hormone	protein-coding
mm_73759.1	chr8	115134424	115134427	+	1	NA	intron (NM_019573, intron 8 of 8)	B1_Mus1|SINE|Alu	572469	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_116758.1	chr13	52531270	52531285	-	1	NA	promoter-TSS (NM_001024474)	promoter-TSS (NM_001024474)	-441	NM_001024474	68203	Mm.29362	NM_001024474	ENSMUSG00000047842	Diras2	2900052J15Rik|AI414999	DIRAS family, GTP-binding RAS-like 2	protein-coding
mm_84078.1	chr9	58202027	58202051	-	1	NA	promoter-TSS (NM_001161540)	promoter-TSS (NM_001161540)	-240	NM_001161540	320563	Mm.186499	NM_177193	ENSMUSG00000051243	Islr2	B930052A04Rik|Linx|Mbu-3|mKIAA1465	immunoglobulin superfamily containing leucine-rich repeat 2	protein-coding
mm_35000.1	chr4	156199519	156199541	+	1	NA	3' UTR (NM_015783, exon 2 of 2)	3' UTR (NM_015783, exon 2 of 2)	1288	NM_015783	100038882	Mm.4950	NM_015783	ENSMUSG00000035692	Isg15	G1p2|IGI15|IP17|Irfp|UCRP	ISG15 ubiquitin-like modifier	protein-coding
mm_87328.1	chr10	42897920	42897931	+	1	NA	intron (NM_172938, intron 1 of 8)	intron (NM_172938, intron 1 of 8)	37413	NM_172938	268297	Mm.98731	NM_172938	ENSMUSG00000044770	Scml4	9330161D17|mFLJ00197	sex comb on midleg-like 4 (Drosophila)	protein-coding
mm_26852.1	chr3	14778453	14778466	-	1	NA	promoter-TSS (NM_001083957)	promoter-TSS (NM_001083957)	1	NM_001083957	12346	Mm.273195	NM_009799	ENSMUSG00000027556	Car1	AW555628|Ca1|Car-1	carbonic anhydrase 1	protein-coding
mm_112371.1	chr12	119197216	119197254	-	1	NA	intron (NM_177290, intron 3 of 13)	intron (NM_177290, intron 3 of 13)	41041	NM_177290	320910	Mm.217000	NM_177290	ENSMUSG00000025321	Itgb8	4832412O06Rik	integrin beta 8	protein-coding
mm_45607.1	chr5	75044698	75044708	-	1	NA	promoter-TSS (NM_028850)	promoter-TSS (NM_028850)	-62	NM_028850	74277	Mm.239814	NM_028850	ENSMUSG00000029229	Chic2	1700081B18Rik|4930502K01Rik|BTL	cysteine-rich hydrophobic domain 2	protein-coding
mm_65312.1	chr7	24780902	24780931	-	1	NA	exon (NM_007675, exon 3 of 4)	exon (NM_007675, exon 3 of 4)	3712	NM_007675	26366	Mm.30300	NM_007675	ENSMUSG00000054169	Ceacam10	Bgp3|Cea10	carcinoembryonic antigen-related cell adhesion molecule 10	protein-coding
mm_127486.1	chr15	101293197	101293209	+	1	NA	promoter-TSS (NR_033803)	promoter-TSS (NR_033803)	-9	NR_033803	77717	Mm.391998	NR_033803	ENSMUSG00000075408	6030408B16Rik	AI225877	RIKEN cDNA 6030408B16 gene	ncRNA
mm_40658.1	chr5	65154980	65154990	+	1	NA	intron (NM_001347355, intron 5 of 10)	intron (NM_001347355, intron 5 of 10)	23754	NM_175174	71778	Mm.10281	NM_175174	ENSMUSG00000054920	Klhl5	1300013C10Rik	kelch-like 5	protein-coding
mm_152498.1	chr19	11130779	11130784	-	1	NA	promoter-TSS (NM_027058)	promoter-TSS (NM_027058)	97	NM_027058	69369	Mm.391200	NM_027058	ENSMUSG00000024729	1700017D01Rik	-	RIKEN cDNA 1700017D01 gene	protein-coding
mm_157819.1	chrX	74059367	74059370	-	1	NA	intron (NM_001081979, intron 1 of 2)	intron (NM_001081979, intron 1 of 2)	26322	NM_010788	17257	Mm.131408	NM_010788	ENSMUSG00000031393	Mecp2	1500041B07Rik|D630021H01Rik|Mbd5|WBP10	methyl CpG binding protein 2	protein-coding
mm_138177.1	chr17	34264999	34265008	+	1	NA	exon (NM_207105, exon 2 of 6)	exon (NM_207105, exon 2 of 6)	1776	NM_207105	14961	Mm.254067	NM_207105	ENSMUSG00000073421	H2-Ab1	AI845868|Abeta|H-2Ab|H2-Ab|I-Abeta|IAb|Ia-2|Ia2|Rmcs1	histocompatibility 2, class II antigen A, beta 1	protein-coding
mm_143216.1	chr17	62882712	62882723	-	1	NA	Intergenic	CpG-6536	-1400	NM_010109	13640	Mm.7978	NM_010109	ENSMUSG00000048915	Efna5	AL-1|AV158822|EFL-5|Ephrin-A5|Epl7|LERK-7|RAGS	ephrin A5	protein-coding
mm_100797.1	chr11	4943924	4943934	-	1	NA	exon (NM_010904, exon 3 of 4)	exon (NM_010904, exon 3 of 4)	-3592	NM_001243043	11764	Mm.274816	NM_007454	ENSMUSG00000009090	Ap1b1	Adtb1|b2b1660Clo	adaptor protein complex AP-1, beta 1 subunit	protein-coding
mm_46892.1	chr5	113992407	113992412	-	1	NA	intron (NM_198109, intron 1 of 14)	L1MB8|LINE|L1	1348	NM_198109	231637	Mm.389682	NM_198109	ENSMUSG00000042121	Ssh1	AW551225|Gm1394|Gm1395|SSH-1|SSH-1L	slingshot homolog 1 (Drosophila)	protein-coding
mm_124868.1	chr15	10177624	10177654	+	1	NA	5' UTR (NM_011169, exon 1 of 10)	5' UTR (NM_011169, exon 1 of 10)	401	NM_011169	19116	Mm.10516	NM_011169	ENSMUSG00000005268	Prlr	AI987712|Pr-1|Pr-3|Prlr-rs1	prolactin receptor	protein-coding
mm_41488.1	chr5	92127340	92127349	+	1	NA	Intergenic	Intergenic	-10594	NM_019490	56041	Mm.15868	NM_019490	ENSMUSG00000029407	Uso1	115kDa|TAP|Vdp	USO1 vesicle docking factor	protein-coding
mm_33167.1	chr4	126024507	126024550	+	1	NA	promoter-TSS (NM_007782)	promoter-TSS (NM_007782)	-131	NR_045561	12986	Mm.271701	NM_007782	ENSMUSG00000028859	Csf3r	Cd114|Csfgr|G-CSF-R|G-CSFR	colony stimulating factor 3 receptor (granulocyte)	protein-coding
mm_121884.1	chr14	21714571	21714584	-	1	NA	promoter-TSS (NM_001013826)	promoter-TSS (NM_001013826)	-1	NM_001013826	435391	Mm.295860	NM_001013826	ENSMUSG00000063821	Dupd1	EG435391	dual specificity phosphatase and pro isomerase domain containing 1	protein-coding
mm_52277.1	chr6	108659665	108659667	+	1	NA	promoter-TSS (NM_011498)	promoter-TSS (NM_011498)	-963	NM_011498	20893	Mm.2436	NM_011498	ENSMUSG00000030103	Bhlhe40	Bhlhb2|C130042M06Rik|CR8|Clast5|Dec1|Sharp2|Stra13|Stra14	basic helix-loop-helix family, member e40	protein-coding
mm_44268.1	chr5	5664184	5664192	-	1	NA	promoter-TSS (NM_172447)	promoter-TSS (NM_172447)	44	NM_172447	207686	Mm.319007	NM_172447	ENSMUSG00000040473	Cfap69	4921525K03|A330021E22Rik|AI427898	cilia and flagella associated protein 69	protein-coding
mm_89472.1	chr10	93504334	93504342	+	1	NA	intron (NM_010401, intron 16 of 19)	intron (NM_010401, intron 16 of 19)	15570	NM_010401	15109	Mm.13000	NM_010401	ENSMUSG00000020017	Hal	Hsd|his|histidase	histidine ammonia lyase	protein-coding
mm_146126.1	chr18	74489261	74489264	+	1	NA	intron (NM_201600, intron 1 of 38)	intron (NM_201600, intron 1 of 38)	41862	NR_045368	73606	Mm.444734	NR_045368		1700120E14Rik	-	RIKEN cDNA 1700120E14 gene	ncRNA
mm_536.1	chr1	37998006	37998014	+	1	NA	promoter-TSS (NM_172054)	promoter-TSS (NM_172054)	0	NM_198303	226982	Mm.260943	NM_198303	ENSMUSG00000026083	Eif5b	A030003E17Rik|BC018347|IF2	eukaryotic translation initiation factor 5B	protein-coding
mm_35100.1	chr4	8926734	8926758	-	1	NA	Intergenic	Intergenic	236340	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_25794.1	chr3	127553463	127553512	+	1	NA	promoter-TSS (NM_138593)	promoter-TSS (NM_138593)	-2	NM_197997	71643	Mm.274884	NM_197997	ENSMUSG00000051278	Zgrf1	4930422G04Rik|AI448607	zinc finger, GRF-type containing 1	protein-coding
mm_154773.1	chrX	12652273	12652286	+	1	NA	5' UTR (NM_001101484, exon 1 of 1)	5' UTR (NM_001101484, exon 1 of 1)	396	NM_001101484	245347	Mm.327568	NM_001101484		Gm4984	AI428901|EG245347	predicted pseudogene 4984	protein-coding
mm_168408.1	chr11	30699167	30699183	-	1	NA	Intergenic	BGLII|LTR|ERVK	-49779	NM_029344	75572	Mm.390319	NM_029344	ENSMUSG00000060923	Acyp2	2310004B09Rik	acylphosphatase 2, muscle type	protein-coding
mm_5734.1	chr1	45334787	45334816	-	1	NA	exon (NM_009930, exon 26 of 51)	exon (NM_009930, exon 26 of 51)	23263	NM_009930	12825	Mm.249555	NM_009930	ENSMUSG00000026043	Col3a1	AW550625|Col3a-1|Tsk-2|Tsk2	collagen, type III, alpha 1	protein-coding
mm_232.1	chr1	19103032	19103043	+	1	NA	promoter-TSS (NM_153154)	promoter-TSS (NM_153154)	15	NM_153154	226896	Mm.244858	NM_153154	ENSMUSG00000042596	Tfap2d	Tcfap2d	transcription factor AP-2, delta	protein-coding
mm_24806.1	chr3	95556303	95556325	+	1	NA	TTS (NM_021281)	TTS (NM_021281)	-3363	NM_026489	67981	Mm.179050	NM_026489	ENSMUSG00000028109	Hormad1	4921522K05Rik|Nohma	HORMA domain containing 1	protein-coding
mm_157269.1	chrX	19237842	19237860	-	1	NA	Intergenic	Intergenic	-90880	NR_029807	723828		NR_029807	ENSMUSG00000065471	Mir222	Mirn222|mir-222|mmu-mir-222	microRNA 222	ncRNA
mm_32230.1	chr4	102235549	102235558	+	1	NA	Intergenic	Intergenic	-19189	NM_001177983	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_138937.1	chr17	43953046	43953063	+	1	NA	promoter-TSS (NM_030598)	promoter-TSS (NM_030598)	55	NM_001286654	53901	Mm.251242	NM_030598	ENSMUSG00000039601	Rcan2	Csp2|Dscr1l1|MCIP2|ZAKI-4	regulator of calcineurin 2	protein-coding
mm_95270.1	chr11	45673199	45673200	+	1	NA	Intergenic	Intergenic	-134884	NR_045876	100009664	Mm.415439	NR_045876		F630206G17Rik	-	RIKEN cDNA F630206G17 gene	ncRNA
mm_67563.1	chr7	81863312	81863326	-	1	NA	intron (NR_111910, intron 2 of 7)	intron (NR_111910, intron 2 of 7)	632	NM_001291282	107769	Mm.221412	NM_145375	ENSMUSG00000038623	Tm6sf1	AI428514|BC023123|C630016D09Rik	transmembrane 6 superfamily member 1	protein-coding
mm_20923.1	chr2	150842366	150842387	-	1	NA	intron (NM_024465, intron 5 of 12)	intron (NM_024465, intron 5 of 12)	55580	NM_153781	110078	Mm.222584	NM_153781	ENSMUSG00000033059	Pygb	-	brain glycogen phosphorylase	protein-coding
mm_97980.1	chr11	83882731	83882760	+	1	NA	exon (NM_001291268, exon 5 of 9)	exon (NM_001291268, exon 5 of 9)	29785	NM_001291269	21410	Mm.7226	NM_009330	ENSMUSG00000020679	Hnf1b	HNF-1-beta|HNF-1B|HNF-1Beta|Hnf1beta|LFB3|Tcf-2|Tcf2|vHNF1	HNF1 homeobox B	protein-coding
mm_17288.1	chr2	26204578	26204590	-	1	NA	intron (NM_010711, intron 1 of 5)	intron (NM_010711, intron 1 of 5)	1991	NM_001039653	16871	Mm.386765	NM_010711	ENSMUSG00000026934	Lhx3	Lim3|P-LIM|mLIM3|mLim-3	LIM homeobox protein 3	protein-coding
mm_74581.1	chr8	11267618	11267659	-	1	NA	exon (NM_009931, exon 2 of 52)	exon (NM_009931, exon 2 of 52)	-45167	NM_009932	12827	Mm.181021	NM_009932	ENSMUSG00000031503	Col4a2	Col4a-2	collagen, type IV, alpha 2	protein-coding
mm_72351.1	chr8	79640224	79640241	+	1	NA	intron (NM_001081164, intron 1 of 20)	CpG	556	NM_001081164	73945	Mm.34348	NM_001081164	ENSMUSG00000036990	Otud4	4930431L18Rik|AI449692|D8Ertd69e|mKIAA1046	OTU domain containing 4	protein-coding
mm_24639.1	chr3	94377410	94377423	+	1	NA	promoter-TSS (NM_001293734)	promoter-TSS (NM_001293734)	-16	NM_001293734	19885	Mm.4372	NM_011281	ENSMUSG00000028150	Rorc	Nr1f3|RORgamma|TOR|Thor	RAR-related orphan receptor gamma	protein-coding
mm_36741.1	chr4	99829181	99829191	-	1	NA	promoter-TSS (NM_145549)	promoter-TSS (NM_145549)	-68	NM_026348	67733	Mm.257094	NM_026348	ENSMUSG00000028549	Itgb3bp	4930471O16Rik|AU022583	integrin beta 3 binding protein (beta3-endonexin)	protein-coding
mm_60789.1	chr7	45567081	45567096	+	1	NA	TTS (NR_038166)	TTS (NR_038166)	-3065	NM_009737	12036	Mm.24210	NM_009737	ENSMUSG00000030826	Bcat2	Bcat-2|Eca40	branched chain aminotransferase 2, mitochondrial	protein-coding
mm_148114.1	chr18	74778741	74778816	-	1	NA	promoter-TSS (NR_028560)	promoter-TSS (NR_028560)	-323	NR_028560	100217466		NR_028560		Scarna17	MBII-119	small Cajal body-specific RNA 17	ncRNA
mm_24231.1	chr3	88950430	88950446	+	1	NA	promoter-TSS (NM_022994)	promoter-TSS (NM_022994)	-156	NM_001164533	65111	Mm.29028	NM_022994	ENSMUSG00000068921	Dap3	4921514D13Rik|DAP-3|MRP-S29|S29mt	death associated protein 3	protein-coding
mm_35795.1	chr4	46536135	46536143	-	1	NA	promoter-TSS (NM_029077)	promoter-TSS (NM_029077)	2	NM_029077	74735	Mm.240252	NM_029077	ENSMUSG00000039853	Trim14	5830400N10Rik|pub	tripartite motif-containing 14	protein-coding
mm_97461.1	chr11	78245984	78246011	+	1	NA	promoter-TSS (NM_009297)	promoter-TSS (NM_009297)	251	NM_009143	20316	Mm.20755	NM_009143	ENSMUSG00000002064	Sdf2	AI853825	stromal cell derived factor 2	protein-coding
mm_16565.1	chr2	3366569	3366571	-	1	NA	promoter-TSS (NM_145921)	promoter-TSS (NM_145921)	-1	NM_145921	99035	Mm.13808	NM_145921	ENSMUSG00000026645	Olah	AI607300|E230009B14Rik|Thedc1	oleoyl-ACP hydrolase	protein-coding
mm_172179.1	chr6	49236493	49236496	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-21540	NM_023670	140488	Mm.281018	NM_023670	ENSMUSG00000029814	Igf2bp3	2610101N11Rik|AA522010|AL022933|AU045931|IMP-3|IMP3|Koc13|Neilsen|mimp3	insulin-like growth factor 2 mRNA binding protein 3	protein-coding
mm_67485.1	chr7	80713544	80713598	-	1	NA	3' UTR (NM_016721, exon 38 of 38)	3' UTR (NM_016721, exon 38 of 38)	-24694	NM_173863	70461	Mm.392175	NM_173863	ENSMUSG00000030527	Crtc3	2610312F20Rik|6332415K15Rik|AI429792|BC011210|TORC3	CREB regulated transcription coactivator 3	protein-coding
mm_34823.1	chr4	154964118	154964147	+	1	NA	promoter-TSS (NM_172990)	promoter-TSS (NM_172990)	9	NR_131230	269614	Mm.30042	NM_172990	ENSMUSG00000029056	Pank4	D030031I12Rik|R75150	pantothenate kinase 4	protein-coding
mm_20845.1	chr2	148040197	148040211	-	1	NA	Intergenic	Intergenic	5260	NM_001291067	15376	Mm.938	NM_010446	ENSMUSG00000037025	Foxa2	HNF3-beta|HNF3beta|Hnf-3b|Hnf3b|Tcf-3b|Tcf3b	forkhead box A2	protein-coding
mm_38121.1	chr4	134548215	134548228	-	1	NA	intron (NM_029100, intron 2 of 11)	MIRc|SINE|MIR	3945	NM_029100	74777	Mm.29773	NM_029100	ENSMUSG00000050989	Selenon	1110019I12Rik|AI414492|SelN|Sepn1	selenoprotein N	protein-coding
mm_123360.1	chr14	63142961	63142971	-	1	NA	3' UTR (NM_007798, exon 10 of 10)	3' UTR (NM_007798, exon 10 of 10)	20504	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_99586.1	chr11	104296464	104296468	+	1	NA	intron (NM_001038609, intron 5 of 11)	intron (NM_001038609, intron 5 of 11)	65030	NM_001285454	17762	Mm.1287	NM_010838	ENSMUSG00000018411	Mapt	AI413597|AW045860|Mtapt|Tau	microtubule-associated protein tau	protein-coding
mm_42268.1	chr5	114143471	114143482	+	1	NA	Intergenic	Intergenic	12320	NM_011677	22256	Mm.1393	NM_011677	ENSMUSG00000029591	Ung	UNG1|UNG2	uracil DNA glycosylase	protein-coding
mm_133621.1	chr16	91561723	91561752	+	1	NA	exon (NM_008338, exon 6 of 7)	exon (NM_008338, exon 6 of 7)	14643	NM_008338	15980	Mm.249364	NM_008338	ENSMUSG00000022965	Ifngr2	Ifgr2|Ifgt	interferon gamma receptor 2	protein-coding
mm_123651.1	chr14	69171853	69171861	-	1	NA	promoter-TSS (NM_010920)	promoter-TSS (NM_010920)	-14	NR_045931	73554	Mm.320005	NR_045931	ENSMUSG00000092499	1700092C10Rik	-	RIKEN cDNA 1700092C10 gene	ncRNA
mm_57183.1	chr6	122848717	122848758	-	1	NA	3' UTR (NM_009779, exon 2 of 2)	3' UTR (NM_009779, exon 2 of 2)	7420	NM_009779	12267	Mm.2408	NM_009779	ENSMUSG00000040552	C3ar1	AZ3B|C3AR|HNFAG09	complement component 3a receptor 1	protein-coding
mm_34779.1	chr4	154026023	154026059	+	1	NA	promoter-TSS (NM_001163722)	promoter-TSS (NM_001163722)	3	NM_001163722	68859	Mm.477488	NM_001033144	ENSMUSG00000078350	Smim1	0610011H04Rik|1190007F08Rik|2700009I11Rik	small integral membrane protein 1	protein-coding
mm_122706.1	chr14	52197151	52197173	-	1	NA	promoter-TSS (NM_033618)	promoter-TSS (NM_033618)	77	NM_033618	114741	Mm.21662	NM_033618	ENSMUSG00000035726	Supt16	Cdc68|Fact140|Spt16|Supt16h	suppressor of Ty 16	protein-coding
mm_53617.1	chr6	140423912	140423960	+	1	NA	promoter-TSS (NM_144920)	promoter-TSS (NM_144920)	-163	NM_144920	109135	Mm.247670	NM_144920	ENSMUSG00000030231	Plekha5	2810431N21Rik|AI428202|AK129423|AMH-Cre|Ayu21-9|Gt(pU21)9Imeg|Pepp2|Tg(AMH-cre)1Flor	pleckstrin homology domain containing, family A member 5	protein-coding
mm_15210.1	chr2	154214065	154214075	+	1	NA	exon (NM_153418, exon 11 of 16)	exon (NM_153418, exon 11 of 16)	-9672	NM_144890	228802	Mm.167411	NM_144890	ENSMUSG00000038572	Bpifb5	Lplunc5	BPI fold containing family B, member 5	protein-coding
mm_49769.1	chr6	34865090	34865095	+	1	NA	intron (NM_197986, intron 1 of 1)	intron (NM_197986, intron 1 of 1)	1946	NM_197986	68487	Mm.248440	NM_197986	ENSMUSG00000057137	Tmem140	1110007F12Rik	transmembrane protein 140	protein-coding
mm_93029.1	chr10	88135825	88135829	-	1	NA	intron (NM_029249, intron 3 of 10)	intron (NM_029249, intron 3 of 10)	11114	NM_029249	75317	Mm.179378	NM_029249	ENSMUSG00000035365	Parpbp	4930547N16Rik|AI503644|PARI	PARP1 binding protein	protein-coding
mm_33380.1	chr4	129556813	129556816	+	1	NA	TTS (NR_106199)	TTS (NR_106199)	997	NR_106199	102465997		NR_106199	ENSMUSG00000099070	Mir8119	Gm27567|mmu-mir-8119	microRNA 8119	ncRNA
mm_136961.1	chr17	15500145	15500183	+	1	NA	intron (NM_013684, intron 1 of 7)	CpG	276	NM_013684	21374	Mm.244820	NM_013684	ENSMUSG00000014767	Tbp	GTF2D1|Gtf2d|SCA17|TFIID	TATA box binding protein	protein-coding
mm_6928.1	chr1	84868960	84868996	-	1	NA	intron (NM_025386, intron 1 of 3)	intron (NM_025386, intron 1 of 3)	29137	NM_025386	66153	Mm.381192	NM_025386	ENSMUSG00000073633	Fbxo36	0610008D19Rik|1110020F21Rik|2410002G19Rik|D1Ertd757e	F-box protein 36	protein-coding
mm_57921.1	chr6	134045630	134045652	-	1	NA	intron (NM_007961, intron 1 of 7)	intron (NM_007961, intron 1 of 7)	9941	NM_007961	14011	Mm.269995	NM_007961	ENSMUSG00000030199	Etv6	AW123102|AW557856|Tel	ets variant 6	protein-coding
mm_73880.1	chr8	119344541	119344551	+	1	NA	promoter-TSS (NM_024219)	promoter-TSS (NM_024219)	8	NM_024219	68196	Mm.358714	NM_024219	ENSMUSG00000031839	Hsbp1	0610007A03Rik|AA408769|Hsp25	heat shock factor binding protein 1	protein-coding
mm_96194.1	chr11	61984592	61984609	+	1	NA	intron (NM_001310526, intron 1 of 7)	B1F1|SINE|Alu	27837	NM_001310526	432572	Mm.438022	NM_001029936	ENSMUSG00000042331	Specc1	2810012G08Rik|B230396K10Rik|Cytsb	sperm antigen with calponin homology and coiled-coil domains 1	protein-coding
mm_54910.1	chr6	47780682	47780688	-	1	NA	Intergenic	B2_Mm2|SINE|B2	22967	NR_030485	735289		NR_030485	ENSMUSG00000076060	Mir704	Mirn704|mir-704|mmu-mir-704	microRNA 704	ncRNA
mm_44599.1	chr5	25100221	25100232	-	1	NA	promoter-TSS (NR_027851)	promoter-TSS (NR_027851)	416	NM_145401	108099	Mm.33649	NM_145401	ENSMUSG00000028944	Prkag2	2410051C13Rik|AAKG|AAKG2|AI854673|H91620p|WPWS	protein kinase, AMP-activated, gamma 2 non-catalytic subunit	protein-coding
mm_169653.1	chr15	55644859	55644869	-	1	NA	intron (NM_016667, intron 5 of 6)	MTA_Mm|LTR|ERVL-MaLR	87456	NM_001168250	105837	Mm.390829	NM_134092	ENSMUSG00000022369	Mtbp	AI429604|MDM2BP	Mdm2, transformed 3T3 cell double minute p53 binding protein	protein-coding
mm_12579.1	chr2	73274732	73274749	+	1	NA	3' UTR (NM_001005343, exon 2 of 2)	3' UTR (NM_001005343, exon 2 of 2)	2814	NM_001005343	381373	Mm.330293	NM_001005343	ENSMUSG00000068859	Sp9	-	trans-acting transcription factor 9	protein-coding
mm_167668.1	chr9	73125256	73125261	+	1	NA	Intergenic	Intergenic	11789	NM_198609	225215	Mm.379366	NM_198609	ENSMUSG00000032215	Rsl24d1	2410159K22Rik	ribosomal L24 domain containing 1	protein-coding
mm_16633.1	chr2	5714491	5714538	-	1	NA	5' UTR (NM_001290375, exon 1 of 11)	5' UTR (NM_001290375, exon 1 of 11)	248	NM_001290374	227541	Mm.191949	NM_177343	ENSMUSG00000039145	Camk1d	A630059D12Rik|CKLiK|CaMKIdelta|E030025C11Rik|mCKLiK	calcium/calmodulin-dependent protein kinase ID	protein-coding
mm_116900.1	chr13	55415217	55415251	-	1	NA	promoter-TSS (NM_029303)	promoter-TSS (NM_029303)	-2	NM_029303	75477	Mm.432537	NM_029303	ENSMUSG00000044444	Pfn3	1700012P12Rik	profilin 3	protein-coding
mm_116383.1	chr13	41079601	41079622	-	1	NA	promoter-TSS (NM_001145803)	promoter-TSS (NM_001145803)	95	NM_001145803	17152	Mm.8149	NM_008547	ENSMUSG00000021363	Mak	A930010O05Rik	male germ cell-associated kinase	protein-coding
mm_163588.1	chr13	38191791	38191806	-	1	NA	exon (NM_023842, exon 23 of 24)	exon (NM_023842, exon 23 of 24)	-13141	NM_026382	67797	Mm.250783	NM_026382	ENSMUSG00000021431	Snrnp48	1110050F08Rik|6530403A03Rik|C6orf151	small nuclear ribonucleoprotein 48 (U11/U12)	protein-coding
mm_80193.1	chr9	72396260	72396279	+	1	NA	Intergenic	Intergenic	-42260	NM_008613	17427	Mm.387671	NM_008613	ENSMUSG00000032221	Mns1	AW546487	meiosis-specific nuclear structural protein 1	protein-coding
mm_62860.1	chr7	114717280	114717290	+	1	NA	Intergenic	Intergenic	-1358	NM_054084	116903	Mm.273838	NM_054084	ENSMUSG00000030666	Calcb	CGRP2|Calc2	calcitonin-related polypeptide, beta	protein-coding
mm_41598.1	chr5	96160758	96160765	+	1	NA	intron (NM_144910, intron 1 of 11)	intron (NM_144910, intron 1 of 11)	786	NM_001285511	231464	Mm.28374	NM_144910	ENSMUSG00000034724	Cnot6l	4932442K20Rik	CCR4-NOT transcription complex, subunit 6-like	protein-coding
mm_149097.1	chr19	8939557	8939559	+	1	NA	intron (NM_144872, intron 19 of 21)	intron (NM_144872, intron 19 of 21)	-2362	NM_011842	23942	Mm.25339	NM_011842	ENSMUSG00000071646	Mta2	AW550797|Mata1l1|Mta1l1|mmta2	metastasis-associated gene family, member 2	protein-coding
mm_136302.1	chr16	91549745	91549767	-	1	NA	intron (NM_008338, intron 1 of 6)	intron (NM_008338, intron 1 of 6)	2662	NM_008338	15980	Mm.249364	NM_008338	ENSMUSG00000022965	Ifngr2	Ifgr2|Ifgt	interferon gamma receptor 2	protein-coding
mm_146653.1	chr18	11051546	11051556	-	1	NA	promoter-TSS (NM_010258)	promoter-TSS (NM_010258)	-959	NM_010258	14465	Mm.329287	NM_010258	ENSMUSG00000005836	Gata6	AA410133|GATA-6	GATA binding protein 6	protein-coding
mm_140143.1	chr17	79999907	79999921	+	1	NA	Intergenic	Intergenic	62354	NM_144802	72692	Mm.64579	NM_144802	ENSMUSG00000024095	Hnrnpll	2510028H02Rik|2810036L13Rik|AI256697|AI852082|Hnrpll	heterogeneous nuclear ribonucleoprotein L-like	protein-coding
mm_123647.1	chr14	68655805	68655817	-	1	NA	promoter-TSS (NM_010082)	promoter-TSS (NM_010082)	31	NM_010082	13522	Mm.117450	NM_010082	ENSMUSG00000014725	Adam28	C130072N01Rik|D430033C21Rik|Dtgn1|MDC-L|MDCL|TECADAM|eMDCII	a disintegrin and metallopeptidase domain 28	protein-coding
mm_160464.1	chr8	110725757	110725757	+	1	NA	promoter-TSS (NM_001310591)	promoter-TSS (NM_001310591)	31	NM_001310591	244654	Mm.490385	NM_198625	ENSMUSG00000033763	Mtss1l	ABBA	metastasis suppressor 1-like	protein-coding
mm_65618.1	chr7	27535310	27535336	-	1	NA	intron (NM_001317355, intron 11 of 13)	intron (NM_001317355, intron 11 of 13)	12062	NM_001033315	233020	Mm.429716	NM_001033315	ENSMUSG00000040424	Hipk4	Gm162	homeodomain interacting protein kinase 4	protein-coding
mm_26206.1	chr3	138550618	138550627	+	1	NA	intron (NM_001313980, intron 5 of 7)	intron (NM_001313980, intron 5 of 7)	23354	NM_001313980	13684	Mm.3941	NM_007917	ENSMUSG00000028156	Eif4e	EG668879|Eif4e-ps|If4e|eIF-4E	eukaryotic translation initiation factor 4E	protein-coding
mm_73329.1	chr8	105289984	105290009	+	1	NA	promoter-TSS (NM_028888)	promoter-TSS (NM_028888)	-468	NM_028888	74356	Mm.204876	NM_028888	ENSMUSG00000014837	4931428F04Rik	AI426165|Kiaa0895l	RIKEN cDNA 4931428F04 gene	protein-coding
mm_77005.1	chr8	107425030	107425056	-	1	NA	promoter-TSS (NM_026277)	promoter-TSS (NM_026277)	-5	NM_026277	67619	Mm.36817	NM_026277	ENSMUSG00000003848	Nob1	1700021I09Rik|ART-4|Nob1p|Psmd8bp1	NIN1/RPN12 binding protein 1 homolog	protein-coding
mm_152612.1	chr19	11965137	11965150	-	1	NA	promoter-TSS (NM_001033174)	promoter-TSS (NM_001033174)	-701	NM_001033174	76303	Mm.291279	NM_001033174	ENSMUSG00000024687	Osbp	1110018F06Rik|AW559088|mKIAA4220	oxysterol binding protein	protein-coding
mm_139287.1	chr17	48300345	48300375	+	1	NA	5' UTR (NM_001033405, exon 1 of 5)	5' UTR (NM_001033405, exon 1 of 5)	322	NM_001033405	328833	Mm.329104	NM_001033405	ENSMUSG00000071068	Treml2	AW049306|Gm750|Tlt2	triggering receptor expressed on myeloid cells-like 2	protein-coding
mm_95247.1	chr11	44618125	44618135	+	1	NA	promoter-TSS (NM_001290711)	promoter-TSS (NM_001290711)	30	NM_001290710	13591	Mm.439662	NM_007897	ENSMUSG00000057098	Ebf1	Ebf|O/E-1|OE-1|Olf-1|Olf1	early B cell factor 1	protein-coding
mm_156998.1	chrX	7567564	7567577	-	1	NA	intron (NM_138605, intron 1 of 3)	intron (NM_138605, intron 1 of 3)	-6030	NR_029473	78185	Mm.160055	NR_029473	ENSMUSG00000039545	Ppp1r3fos	4930524L23Rik	protein phosphatase 1, regulatory subunit 3F, opposite strand	ncRNA
mm_28573.1	chr3	93445274	93445332	-	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	2973	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_36765.1	chr4	101356792	101356793	-	1	NA	promoter-TSS (NR_040708)	promoter-TSS (NR_040708)	-544	NR_040708	77866	Mm.137053	NR_040708	ENSMUSG00000086782	E130102H24Rik	-	RIKEN cDNA E130102H24 gene	ncRNA
mm_88483.1	chr10	77630141	77630147	+	1	NA	intron (NM_019803, intron 1 of 5)	intron (NM_019803, intron 1 of 5)	7823	NM_019803	22213	Mm.458125	NM_019803	ENSMUSG00000009293	Ube2g2	1110003O05Rik|D10Xrf369|UBC7|Ubc7p	ubiquitin-conjugating enzyme E2G 2	protein-coding
mm_14674.1	chr2	139494119	139494175	+	1	NA	5' UTR (NM_175467, exon 2 of 13)	5' UTR (NM_175467, exon 2 of 13)	227	NM_175467	228677	Mm.100450	NM_175467	ENSMUSG00000039092	Sptlc3	C130053K05Rik	serine palmitoyltransferase, long chain base subunit 3	protein-coding
mm_103724.1	chr11	79530518	79530532	-	1	NA	promoter-TSS (NM_010161)	promoter-TSS (NM_010161)	84	NM_146023	101488212	Mm.439665	NM_146023	ENSMUSG00000070354	Gm21975	Evi2a-evi2b	predicted gene 21975	protein-coding
mm_55671.1	chr6	72522578	72522585	-	1	NA	Intergenic	MLT1B|LTR|ERVL-MaLR	-21810	NM_007599	12332	Mm.18626	NM_007599	ENSMUSG00000056737	Capg	gCap39|mbh1	capping protein (actin filament), gelsolin-like	protein-coding
mm_131503.1	chr16	17419336	17419348	+	1	NA	exon (NM_023348, exon 2 of 5)	exon (NM_023348, exon 2 of 5)	-13028	NM_001001983	224020	Mm.5718	NM_001001983	ENSMUSG00000041720	Pi4ka	Pik4ca	phosphatidylinositol 4-kinase, catalytic, alpha polypeptide	protein-coding
mm_133849.1	chr16	96206351	96206369	+	1	NA	intron (NM_015825, intron 1 of 7)	intron (NM_015825, intron 1 of 7)	5890	NM_015825	50795	Mm.28638	NM_015825	ENSMUSG00000040666	Sh3bgr	5430437A18Rik	SH3-binding domain glutamic acid-rich protein	protein-coding
mm_170730.1	chr2	151353042	151353042	+	1	NA	Intergenic	Intergenic	51003	NR_040747	74660	Mm.170672	NR_040747	ENSMUSG00000087609	4930442J19Rik	1700029E19Rik|Gm14152|OTTMUSG00000015807	RIKEN cDNA 4930442J19 gene	ncRNA
mm_20871.1	chr2	148443544	148443582	-	1	NA	promoter-TSS (NM_010740)	promoter-TSS (NM_010740)	-28	NM_010740	17064	Mm.681	NM_010740	ENSMUSG00000027435	Cd93	6030404G09Rik|AA145088|AA4.1|AW555904|C1qr1|C1qrp|Ly68	CD93 antigen	protein-coding
mm_332.1	chr1	26617025	26617031	+	1	NA	Intergenic	RLTR16|LTR|ERVK	70432	NM_001033764	210940	Mm.297614	NM_001033764	ENSMUSG00000073722	4931408C20Rik	-	RIKEN cDNA 4931408C20 gene	protein-coding
mm_15790.1	chr2	164425772	164425794	+	1	NA	3' UTR (NM_011521, exon 5 of 5)	3' UTR (NM_011521, exon 5 of 5)	17405	NM_011521	20971	Mm.3815	NM_011521	ENSMUSG00000017009	Sdc4	AA959608|AW108331|S4|Synd4|ryudocan|syndecan-4	syndecan 4	protein-coding
mm_134779.1	chr16	23981198	23981204	-	1	NA	intron (NM_009744, intron 1 of 9)	intron (NM_009744, intron 1 of 9)	7411	NM_009744	12053	Mm.347398	NM_009744	ENSMUSG00000022508	Bcl6	Bcl5	B cell leukemia/lymphoma 6	protein-coding
mm_145333.1	chr18	56400318	56400362	+	1	NA	Intergenic	Intergenic	-31792	NM_026240	107022	Mm.24356	NM_026240	ENSMUSG00000001700	Gramd3	9030613F08Rik|9130427A09Rik|AW061306|NS3TP2	GRAM domain containing 3	protein-coding
mm_70056.1	chr7	142651389	142651391	-	1	NA	3' UTR (NM_010514, exon 4 of 4)	3' UTR (NM_010514, exon 4 of 4)	3606	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_94885.1	chr11	26816300	26816304	+	1	NA	Intergenic	Intergenic	31194	NR_002890	654472	Mm.347777	NR_002890		Gm12070	OTTMUSG00000005300	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_74240.1	chr8	124722146	124722187	+	1	NA	promoter-TSS (NM_026855)	promoter-TSS (NM_026855)	27	NM_026855	68865	Mm.22779	NM_026855	ENSMUSG00000031982	Arv1	1110067L22Rik|AI461928|AW121084	ARV1 homolog, fatty acid homeostasis modulator	protein-coding
mm_61431.1	chr7	73772045	73772046	+	1	NA	intron (NM_001162532, intron 2 of 2)	intron (NM_001162532, intron 2 of 2)	31738	NM_001162532	100038347	Mm.425464	NM_001162532	ENSMUSG00000078670	Fam174b	-	family with sequence similarity 174, member B	protein-coding
mm_83395.1	chr9	44718776	44718778	-	1	NA	intron (NM_153537, intron 4 of 21)	MIRc|SINE|MIR	16421	NM_153537	102693	Mm.28639	NM_153537	ENSMUSG00000048537	Phldb1	AU041016|D330037A14Rik|Ll5a	pleckstrin homology like domain, family B, member 1	protein-coding
mm_53102.1	chr6	125067689	125067699	+	1	NA	promoter-TSS (NM_001163269)	promoter-TSS (NM_001163269)	-226	NM_001163269	381810	Mm.333386	NM_001163268	ENSMUSG00000067714	Lpar5	GPR93|Gm1072|Gpr92|LPA5	lysophosphatidic acid receptor 5	protein-coding
mm_40456.1	chr5	53604146	53604174	+	1	NA	intron (NM_001277116, intron 3 of 12)	intron (NM_001277116, intron 3 of 12)	13674	NM_001080927	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_1847.1	chr1	83015350	83015382	+	1	NA	intron (NM_030556, intron 5 of 6)	intron (NM_030556, intron 5 of 6)	23082	NM_030556	80721	Mm.261542	NM_030556	ENSMUSG00000038496	Slc19a3	A230084E24Rik|AI788884|ThTr2	solute carrier family 19, member 3	protein-coding
mm_141331.1	chr17	28486109	28486149	-	1	NA	promoter-TSS (NM_010220)	promoter-TSS (NM_010220)	20	NM_010220	14229	Mm.276405	NM_010220	ENSMUSG00000024222	Fkbp5	D17Ertd592e|Dit1|FKBP-5|FKBP51	FK506 binding protein 5	protein-coding
mm_110317.1	chr12	34528910	34528927	-	1	NA	promoter-TSS (NM_024124)	promoter-TSS (NM_024124)	-29	NM_024124	79221	Mm.310551	NM_024124	ENSMUSG00000004698	Hdac9	AV022454|D030072B18Rik|HD7B|HD9|HDRP|Hdac7b|Mitr|mKIAA0744	histone deacetylase 9	protein-coding
mm_155342.1	chrX	68678542	68678554	+	1	NA	promoter-TSS (NM_008031)	promoter-TSS (NM_008031)	7	NM_001290424	14265	Mm.3451	NM_008031	ENSMUSG00000000838	Fmr1	FMRP|Fmr-1	fragile X mental retardation syndrome 1	protein-coding
mm_151329.1	chr19	55894338	55894378	+	1	NA	promoter-TSS (NM_001142924)	promoter-TSS (NM_001142924)	-963	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_94567.1	chr11	11686298	11686322	+	1	NA	5' UTR (NM_009578, exon 1 of 7)	5' UTR (NM_009578, exon 1 of 7)	385	NM_001025597	22778	Mm.103545	NM_009578	ENSMUSG00000018654	Ikzf1	5832432G11Rik|Ikaros|LyF-1|Zfpn1a1|Znfn1a1|hlk-1|mKIAA4227	IKAROS family zinc finger 1	protein-coding
mm_16534.1	chr2	181579509	181579525	+	1	NA	promoter-TSS (NR_027290)	promoter-TSS (NR_027290)	-15	NR_027290	100271841	Mm.438007	NR_027289	ENSMUSG00000010492	Uckl1os	Gm16119|OTTMUSG00000030649	uridine-cytidine kinase 1-like 1, opposite strand	ncRNA
mm_100417.1	chr11	119430283	119430294	+	1	NA	Intergenic	Intergenic	39816	NR_035453	100316690		NR_035453	ENSMUSG00000088015	Mir1932	mir-1932|mmu-mir-1932	microRNA 1932	ncRNA
mm_35605.1	chr4	43046137	43046154	-	1	NA	promoter-TSS (NM_172691)	promoter-TSS (NM_172691)	75	NR_045567	230088	Mm.260162	NM_172691	ENSMUSG00000036002	Fam214b	B230312A22Rik	family with sequence similarity 214, member B	protein-coding
mm_6774.1	chr1	84131822	84131831	-	1	NA	intron (NM_001003948, intron 2 of 2)	MLT1F2|LTR|ERVL-MaLR	87135	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_51728.1	chr6	87009231	87009253	+	1	NA	promoter-TSS (NM_020045)	promoter-TSS (NM_020045)	-594	NM_001170591	56748	Mm.23809	NM_020045	ENSMUSG00000029993	Nfu1	0610006G17Rik|CGI-33|Hirip5	NFU1 iron-sulfur cluster scaffold	protein-coding
mm_37604.1	chr4	126752988	126753054	-	1	NA	promoter-TSS (NM_001035526)	promoter-TSS (NM_001035526)	408	NM_011986	26562	Mm.206206	NM_011986	ENSMUSG00000028833	Ncdn	AU042419|MMS10-AE|Ms10ae|mKIAA0607|norbin	neurochondrin	protein-coding
mm_53260.1	chr6	127913711	127913732	+	1	NA	intron (NM_026743, intron 2 of 7)	intron (NM_026743, intron 2 of 7)	26099	NM_026743	68498	Mm.174368	NM_026743	ENSMUSG00000030351	Tspan11	1110014F12Rik|AU067806	tetraspanin 11	protein-coding
mm_146384.1	chr18	82669161	82669170	+	1	NA	intron (NM_177832, intron 5 of 29)	intron (NM_177832, intron 5 of 29)	23569	NM_177832	329002	Mm.34438	NM_177832	ENSMUSG00000041258	Zfp236	AI447957|Gm335	zinc finger protein 236	protein-coding
mm_95274.1	chr11	45851956	45851996	+	1	NA	promoter-TSS (NM_001045520)	promoter-TSS (NM_001045520)	12	NM_001045520	216705	Mm.169673	NM_001045520	ENSMUSG00000006169	Clint1	AI642036|AW537616|C530049I24Rik|Enth|Epn4|F630206G17Rik|mKIAA0171	clathrin interactor 1	protein-coding
mm_49521.1	chr6	29917006	29917028	+	1	NA	promoter-TSS (NM_177204)	promoter-TSS (NM_177204)	4	NR_104576	320609	Mm.56097	NM_177204	ENSMUSG00000039629	Strip2	D330017J20Rik|Fam40b	striatin interacting protein 2	protein-coding
mm_65429.1	chr7	25297968	25298005	-	1	NA	promoter-TSS (NM_008776)	promoter-TSS (NM_008776)	-31	NM_008776	18476	Mm.597	NM_008776	ENSMUSG00000005447	Pafah1b3	Pafahg|mus[g]	platelet-activating factor acetylhydrolase, isoform 1b, subunit 3	protein-coding
mm_33697.1	chr4	133584338	133584348	+	1	NA	promoter-TSS (NM_001290742)	promoter-TSS (NM_001290742)	-30	NM_001290742	100210	Mm.274001	NM_133884	ENSMUSG00000028848	Gpn2	AI838661|Atpbd1b|R74630	GPN-loop GTPase 2	protein-coding
mm_4149.1	chr1	171018897	171018908	+	1	NA	promoter-TSS (NM_144559)	promoter-TSS (NM_144559)	-24	NM_144559	246256	Mm.251254	NM_144559	ENSMUSG00000059089	Fcgr4	4833442P21Rik|CD16-2|FcgRIV|FcgammaRIV|Fcgr3a|Fcrl3	Fc receptor, IgG, low affinity IV	protein-coding
mm_44000.1	chr5	146845115	146845123	+	1	NA	promoter-TSS (NM_026864)	promoter-TSS (NM_026864)	48	NM_026864	68895	Mm.266978	NM_026864	ENSMUSG00000029641	Rasl11a	1110065D03Rik|AI852031	RAS-like, family 11, member A	protein-coding
mm_81059.1	chr9	106148693	106148712	+	1	NA	Intergenic	Intergenic	-5422	NR_029549	387153		NR_029549	ENSMUSG00000065407	Mir135a-1	Mir135a01|Mirn135|Mirn135a-1|mir-135a-1	microRNA 135a-1	ncRNA
mm_120905.1	chr14	76026089	76026128	+	1	NA	Intergenic	RLTR18|LTR|ERVK	-15243	NM_026816	68705	Mm.20415	NM_026816	ENSMUSG00000067995	Gtf2f2	1110031C13Rik|AI326315	general transcription factor IIF, polypeptide 2	protein-coding
mm_7451.1	chr1	120265248	120265304	-	1	NA	promoter-TSS (NM_133186)	promoter-TSS (NM_133186)	4	NM_133186	68428	Mm.181033	NM_133186	ENSMUSG00000026389	Steap3	1010001D01Rik|Tsap6|pHyde	STEAP family member 3	protein-coding
mm_165653.1	chr3	83863027	83863037	-	1	NA	Intergenic	Intergenic	-21424	NM_011905	24088	Mm.87596	NM_011905	ENSMUSG00000027995	Tlr2	Ly105	toll-like receptor 2	protein-coding
mm_121375.1	chr14	118543244	118543247	+	1	NA	intron (NM_001033336, intron 20 of 30)	intron (NM_001033336, intron 20 of 30)	49227	NR_105815	102465208		NR_105815	ENSMUSG00000098433	Mir6391	Gm27914|mmu-mir-6391	microRNA 6391	ncRNA
mm_2603.1	chr1	120055250	120055259	+	1	NA	intron (NM_001311077, intron 9 of 12)	intron (NM_001311077, intron 9 of 12)	18526	NM_019432	170706	Mm.24750	NM_019432	ENSMUSG00000050777	Tmem37	AI173373|AW540203|Pr|Pr1	transmembrane protein 37	protein-coding
mm_115265.1	chr13	110683670	110683674	+	1	NA	Intergenic	Intergenic	-219827	NR_131193	75139	Mm.490931	NR_131193		Gm38397	-	predicted gene, 38397	ncRNA
mm_145131.1	chr18	44662114	44662124	+	1	NA	non-coding (NR_026853, exon 1 of 5)	non-coding (NR_026853, exon 1 of 5)	147	NM_001085374	328949	Mm.312511	NM_001033406	ENSMUSG00000071856	Mcc	D18Ertd451e|E330037C19	mutated in colorectal cancers	protein-coding
mm_123494.1	chr14	66163905	66163921	-	1	NA	intron (NM_001162366, intron 22 of 29)	intron (NM_001162366, intron 22 of 29)	22953	NM_144803	110902	Mm.57350	NM_144803	ENSMUSG00000022041	Chrna2	Acra-2|Acra2|BC011490	cholinergic receptor, nicotinic, alpha polypeptide 2 (neuronal)	protein-coding
mm_173150.1	chrX	32209420	32209422	+	1	NA	Intergenic	RLTR1B|LTR|ERV1	-68973	NM_001168334	100040482	Mm.479861	NM_001168334	ENSMUSG00000096194	Btbd35f2	Gm2799	BTB domain containing 35, family member 2	protein-coding
mm_131671.1	chr16	20672888	20672892	+	1	NA	intron (NM_001304432, intron 1 of 31)	CpG	163	NM_001304432	208643	Mm.260256	NM_145941	ENSMUSG00000045983	Eif4g1	E030015G23Rik|eIF-4-gamma 1|eIF-4G 1|eIF-4G1|eIF4GI	eukaryotic translation initiation factor 4, gamma 1	protein-coding
mm_65465.1	chr7	25476407	25476426	-	1	NA	exon (NM_001039186, exon 2 of 8)	exon (NM_001039186, exon 2 of 8)	1209	NM_001039185	26365	Mm.322502	NM_011926	ENSMUSG00000074272	Ceacam1	Bgp|Bgp1|C-CAM|CD66a|Cc1|Cea-1|Cea-7|Cea1|Cea7|Hv-2|Hv2|MHVR|MHVR1|Mhv-1|bb-1|mCEA1|mmCGM1|mmCGM1a|mmCGM2	carcinoembryonic antigen-related cell adhesion molecule 1	protein-coding
mm_2169.1	chr1	88259377	88259387	+	1	NA	3' UTR (NM_198652, exon 8 of 8)	3' UTR (NM_198652, exon 8 of 8)	10026	NR_040291	78605	Mm.384762	NR_040291		6430706D22Rik	-	RIKEN cDNA 6430706D22 gene	ncRNA
mm_116229.1	chr13	33158363	33158374	-	1	NA	promoter-TSS (NM_011453)	promoter-TSS (NM_011453)	-17	NM_011453	20707	Mm.219429	NM_011453	ENSMUSG00000021404	Serpinb9c	3830421J05Rik|Nk9|Spi11	serine (or cysteine) peptidase inhibitor, clade B, member 9c	protein-coding
mm_79796.1	chr9	64092336	64092343	+	1	NA	Intergenic	Intergenic	11578	NR_040743	76814	Mm.243771	NR_040743		Scarletltr	2600006L11Rik	Scarletltr, erythroid developmental long intergenic non-protein coding transcript	ncRNA
mm_52928.1	chr6	122923677	122923726	+	1	NA	intron (NM_199311, intron 1 of 5)	intron (NM_199311, intron 1 of 5)	1853	NM_199311	269799	Mm.297275	NM_199311	ENSMUSG00000049037	Clec4a1	BC049354|Dcir4	C-type lectin domain family 4, member a1	protein-coding
mm_168760.1	chr12	118683414	118683414	+	1	NA	Intergenic	Intergenic	-153221	NR_045947	100384890	Mm.484658	NR_045947		D230030E09Rik	Npe	Riken cDNA D230030E09 gene	ncRNA
mm_121260.1	chr14	103070236	103070256	+	1	NA	promoter-TSS (NM_001033242)	promoter-TSS (NM_001033242)	30	NM_001033242	211286	Mm.295289	NM_001033242	ENSMUSG00000022125	Cln5	A730075N08Rik	ceroid-lipofuscinosis, neuronal 5	protein-coding
mm_115634.1	chr13	12200481	12200500	-	1	NA	intron (NM_001081128, intron 24 of 32)	intron (NM_001081128, intron 24 of 32)	-14002	NR_045170	328186	Mm.188154	NM_183202		Gm10336	B330003H21|ENSMUSG00000071543	predicted gene 10336	ncRNA
mm_88198.1	chr10	70097265	70097301	+	1	NA	5' UTR (NM_001111121, exon 1 of 9)	5' UTR (NM_001111121, exon 1 of 9)	162	NM_001111121	76551	Mm.281741	NM_001111121	ENSMUSG00000048701	Ccdc6	2810012H18Rik|AA536681|AA960498|AW061011	coiled-coil domain containing 6	protein-coding
mm_127702.1	chr15	102990973	102990986	+	1	NA	exon (NM_010466, exon 1 of 2)	exon (NM_010466, exon 1 of 2)	440	NM_010466	15426	Mm.6167	NM_010466	ENSMUSG00000001657	Hoxc8	D130011F21Rik|Hox-3.1	homeobox C8	protein-coding
mm_122618.1	chr14	51145429	51145434	-	1	NA	3' UTR (NM_011271, exon 2 of 2)	3' UTR (NM_011271, exon 2 of 2)	1336	NM_011271	19752	Mm.235538	NM_011271	ENSMUSG00000035896	Rnase1	AI574248|Rib-1|Rib1	ribonuclease, RNase A family, 1 (pancreatic)	protein-coding
mm_172237.1	chr6	68251710	68251725	+	1	NA	Intergenic	RLTR3_Mm|LTR|ERVK	-686018	NR_003100	75070	Mm.463364	NR_003100		4930515G16Rik	-	myc induced nuclear antigen pseudogene	pseudo
mm_140120.1	chr17	78989328	78989338	+	1	NA	intron (NM_001171004, intron 2 of 18)	Lx8|LINE|L1	19172	NM_001171005	75292	Mm.252776	NM_029239	ENSMUSG00000024070	Prkd3	4930557O20Rik|5730497N19Rik|PKD3|Pkcnu|Prkcn	protein kinase D3	protein-coding
mm_167598.1	chr9	50494049	50494057	+	1	NA	promoter-TSS (NM_029639)	promoter-TSS (NM_029639)	-472	NM_029639	76509	Mm.29959	NM_029639	ENSMUSG00000032068	Plet1	0610037B23Rik|1600029D21Rik|AA407923|AU043048	placenta expressed transcript 1	protein-coding
mm_7034.1	chr1	87100182	87100192	-	1	NA	exon (NM_001081082, exon 6 of 11)	exon (NM_001081082, exon 6 of 11)	1419	NM_001081082	76768	Mm.58068	NM_001081082	ENSMUSG00000079440	Alpi	2010001C14Rik|Akp6|gIAP	alkaline phosphatase, intestinal	protein-coding
mm_42087.1	chr5	110230976	110231099	+	1	NA	promoter-TSS (NM_001253814)	promoter-TSS (NM_001253814)	33	NM_027922	71782	Mm.288442	NM_027922	ENSMUSG00000029501	Ankle2	1110001J12Rik|AI661024|D5Ertd585e	ankyrin repeat and LEM domain containing 2	protein-coding
mm_146457.1	chr18	86408535	86408542	+	1	NA	intron (NM_144946, intron 4 of 10)	B1_Mur3|SINE|Alu	13586	NM_144946	246317	Mm.329578	NM_144946	ENSMUSG00000050321	Neto1	AI851453|Btcl1|C130005O10Rik	neuropilin (NRP) and tolloid (TLL)-like 1	protein-coding
mm_160656.1	chr9	118150122	118150122	-	1	NA	promoter-TSS (NM_026442)	promoter-TSS (NM_026442)	74	NM_026442	67899	Mm.9953	NM_026442	ENSMUSG00000039163	Cmc1	2010110K16Rik|2010312P05Rik|AI596001	COX assembly mitochondrial protein 1	protein-coding
mm_150428.1	chr19	37439773	37439789	+	1	NA	exon (NM_008245, exon 4 of 4)	exon (NM_008245, exon 4 of 4)	4940	NM_008245	15242	Mm.33896	NM_008245	ENSMUSG00000024986	Hhex	Hex|Hex1|Hhex-rs2|Prh|Prhx	hematopoietically expressed homeobox	protein-coding
mm_12178.1	chr2	62968195	62968203	+	1	NA	intron (NM_133207, intron 2 of 15)	intron (NM_133207, intron 2 of 15)	216088	NM_133207	170738	Mm.242532	NM_133207	ENSMUSG00000059742	Kcnh7	9330137I11Rik|Kv11.3|erg3	potassium voltage-gated channel, subfamily H (eag-related), member 7	protein-coding
mm_105363.1	chr11	103174897	103174907	-	1	NA	intron (NM_019679, intron 1 of 26)	intron (NM_019679, intron 1 of 26)	3764	NM_019679	57778	Mm.138913	NM_019679	ENSMUSG00000055805	Fmnl1	8030453N10Rik|AI553564|Fmnl|Fnrl|Frls	formin-like 1	protein-coding
mm_104709.1	chr11	98026657	98026683	-	1	NA	promoter-TSS (NM_001159483)	promoter-TSS (NM_001159483)	-40	NM_001159483	19921	Mm.10247	NM_009078	ENSMUSG00000017404	Rpl19	-	ribosomal protein L19	protein-coding
mm_90552.1	chr10	128099441	128099444	+	1	NA	intron (NM_054078, intron 2 of 29)	B2_Mm2|SINE|B2	6659	NM_054078	116848	Mm.252213	NM_054078	ENSMUSG00000040054	Baz2a	AA415431|C030005G16Rik|C78388|Tip5|Walp3|mKIAA0314	bromodomain adjacent to zinc finger domain, 2A	protein-coding
mm_23235.1	chr3	50616037	50616060	+	1	NA	Intergenic	Intergenic	-172435	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_57626.1	chr6	128297090	128297107	-	1	NA	intron (NM_011567, intron 1 of 11)	intron (NM_011567, intron 1 of 11)	3715	NM_001080979	21679	Mm.14774	NM_011567	ENSMUSG00000030353	Tead4	ETFR-2|Etfr2|FR-19|Rtef1|TEAD-4|TEF-3|Tcf13r1|Tef3|Tefr|Tefr1|Tefr1a	TEA domain family member 4	protein-coding
mm_115360.1	chr13	112853232	112853252	+	1	NA	intron (NM_008903, intron 2 of 5)	RSINE1|SINE|B4	52465	NM_008247	19012	Mm.291029	NM_008247	ENSMUSG00000021759	Plpp1	Hic53|Hpic53|LPP-1|LPP1|PAP-2a|PAP2-alpha|PAP2a|Ppap2a|mPAP	phospholipid phosphatase 1	protein-coding
mm_8780.1	chr1	161241662	161241680	-	1	NA	non-coding (NR_130150, exon 4 of 4)	non-coding (NR_130150, exon 4 of 4)	9539	NR_130150	11758	Mm.186185	NM_007453	ENSMUSG00000026701	Prdx6	1-Cys Prx|1-cysPrx|9430088D19Rik|AA690119|Aop2|Brp-12|CP-3|GPx|Ltw-4|Ltw4|Lvtw-4|NSGPx|ORF06|Prdx5|aiPLA2	peroxiredoxin 6	protein-coding
mm_26647.1	chr3	153973492	153973520	+	1	NA	promoter-TSS (NM_001081263)	promoter-TSS (NM_001081263)	70	NM_001081263	242259	Mm.239962	NM_001081263	ENSMUSG00000028360	Slc44a5	AA117069|Gm422	solute carrier family 44, member 5	protein-coding
mm_30379.1	chr3	152243853	152243861	-	1	NA	exon (NM_199465, exon 9 of 13)	exon (NM_199465, exon 9 of 13)	22463	NM_199465	68810	Mm.200188	NM_199465	ENSMUSG00000039103	Nexn	1110046H09Rik|AA553326|NELIN	nexilin	protein-coding
mm_138225.1	chr17	34347802	34347805	+	1	NA	Intergenic	Intergenic	-3158	NM_010381	100504404	Mm.15680	NM_010381		H2-Ea-ps	AI323765|E-alpha-f|H-2Ea|H2-Ea|I-Ealpha|Ia-3|Ia3|MHC-H2-Ea	histocompatibility 2, class II antigen E alpha, pseudogene	protein-coding
mm_7745.1	chr1	131056511	131056534	-	1	NA	exon (NM_008551, exon 7 of 10)	exon (NM_008551, exon 7 of 10)	36677	NM_010548	16153	Mm.874	NM_010548	ENSMUSG00000016529	Il10	CSIF|Il-10	interleukin 10	protein-coding
mm_117540.1	chr13	83609211	83609219	-	1	NA	intron (NM_001347569, intron 3 of 10)	intron (NM_001347569, intron 3 of 10)	35608	NM_001347569	17260	Mm.24001	NM_025282	ENSMUSG00000005583	Mef2c	5430401D19Rik|9930028G15Rik|AV011172|Mef2	myocyte enhancer factor 2C	protein-coding
mm_68434.1	chr7	109894011	109894027	-	1	NA	3' UTR (NM_021494, exon 23 of 23)	3' UTR (NM_021494, exon 23 of 23)	-28340	NM_020052	56788	Mm.40447	NM_020052	ENSMUSG00000007279	Scube2	4932442O19Rik|Cegf1|Cegp1	signal peptide, CUB domain, EGF-like 2	protein-coding
mm_153641.1	chr19	44135817	44135881	-	1	NA	promoter-TSS (NM_001081077)	promoter-TSS (NM_001081077)	27	NM_001081077	72502	Mm.276109	NM_001081077	ENSMUSG00000025200	Cwf19l1	2610528C06Rik|AI854304|AV336991	CWF19-like 1, cell cycle control (S. pombe)	protein-coding
mm_1404.1	chr1	67147901	67147902	+	1	NA	intron (NM_001080809, intron 5 of 37)	intron (NM_001080809, intron 5 of 37)	24874	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_7796.1	chr1	131525170	131525232	-	1	NA	5' UTR (NM_001081011, exon 2 of 23)	5' UTR (NM_001081011, exon 2 of 23)	2160	NM_001081011	14270	Mm.276259	NM_019520	ENSMUSG00000026425	Srgap2	9930124L22Rik|AI448945|FBP2|Fnbp2|srGAP3	SLIT-ROBO Rho GTPase activating protein 2	protein-coding
mm_152693.1	chr19	16781066	16781075	-	1	NA	promoter-TSS (NM_173028)	promoter-TSS (NM_173028)	-137	NM_173028	271564	Mm.211963	NM_173028	ENSMUSG00000046230	Vps13a	4930425F11|4930516E05Rik|4930543C13Rik|9930023P20|Chac|Chorein|D330038K10Rik|mKIAA0986	vacuolar protein sorting 13A	protein-coding
mm_152602.1	chr19	11774941	11774945	-	1	NA	TTS (NM_025606)	TTS (NM_025606)	4528	NM_025606	94063	Mm.203928	NM_025606	ENSMUSG00000024683	Mrpl16	2310039D06Rik	mitochondrial ribosomal protein L16	protein-coding
mm_108707.1	chr12	87021376	87021382	+	1	NA	Intergenic	Intergenic	-5185	NM_172583	217733	Mm.110032	NM_172583	ENSMUSG00000034145	Tmem63c	4932420N09|9330187M14Rik	transmembrane protein 63c	protein-coding
mm_7349.1	chr1	106515529	106515543	-	1	NA	Intergenic	5S|rRNA|rRNA	31095	NR_106164	102466254		NR_106164	ENSMUSG00000098344	Mir3473f	Gm27846|mmu-mir-3473f	microRNA 3473f	ncRNA
mm_122172.1	chr14	31494961	31494985	-	1	NA	promoter-TSS (NM_025907)	promoter-TSS (NM_025907)	4	NM_025907	67011	Mm.291731	NM_025907	ENSMUSG00000021891	Mettl6	1600013P15Rik|AI467521|AU020711	methyltransferase like 6	protein-coding
mm_111518.1	chr12	99883430	99883460	-	1	NA	promoter-TSS (NM_030172)	promoter-TSS (NM_030172)	-3	NM_030172	78767	Mm.235920	NM_030172	ENSMUSG00000021176	Efcab11	2610021K21Rik|2610110A13Rik	EF-hand calcium binding domain 11	protein-coding
mm_105242.1	chr11	102319826	102319859	-	1	NA	promoter-TSS (NM_001302954)	promoter-TSS (NM_001302954)	-746	NM_011551	21429	Mm.2845	NM_011551	ENSMUSG00000020923	Ubtf	A930005G04Rik|NOR-90|Tcfubf|UBF|UBF-1|UBF1	upstream binding transcription factor, RNA polymerase I	protein-coding
mm_77538.1	chr8	123042233	123042243	-	1	NA	promoter-TSS (NR_045268)	promoter-TSS (NR_045268)	46	NR_037865	77087	Mm.31567	NM_001081379	ENSMUSG00000035569	Ankrd11	2410104C19Rik|3010027A04Rik|6330578C09Rik|9530048I21Rik|AA930108|Gm176|Yod	ankyrin repeat domain 11	protein-coding
mm_7243.1	chr1	93635622	93635632	-	1	NA	promoter-TSS (NM_021537)	promoter-TSS (NM_021537)	100	NM_021537	59041	Mm.28761	NM_021537	ENSMUSG00000026277	Stk25	1500019J11Rik|AU018434|C86992|Ste20-like|Ysk1	serine/threonine kinase 25 (yeast)	protein-coding
mm_125120.1	chr15	30172571	30172600	+	1	NA	promoter-TSS (NM_008729)	promoter-TSS (NM_008729)	-8	NM_008729	18163	Mm.321648	NM_008729	ENSMUSG00000022240	Ctnnd2	Catnd2|Nprap|neurojugin	catenin (cadherin associated protein), delta 2	protein-coding
mm_75569.1	chr8	60891448	60891469	-	1	NA	intron (NM_028299, intron 1 of 7)	intron (NM_028299, intron 1 of 7)	1007	NM_028299	72612	Mm.25263	NM_028299	ENSMUSG00000038005	Hpf1	2700029M09Rik|C230006B22Rik|C4orf27	histone PARylation factor 1	protein-coding
mm_56146.1	chr6	87811772	87811802	-	1	NA	promoter-TSS (NM_001039394)	promoter-TSS (NM_001039394)	-8	NM_001039394	69834	Mm.37380	NM_133717	ENSMUSG00000030055	Rab43	1810048P08Rik|2500004H21Rik|AW490415	RAB43, member RAS oncogene family	protein-coding
mm_85865.1	chr9	110874100	110874124	-	1	NA	intron (NM_146260, intron 2 of 5)	intron (NM_146260, intron 2 of 5)	5971	NM_146260	20776	Mm.390229	NM_146260	ENSMUSG00000049555	Tmie	5131400L21Rik|Mm.87012|sr	transmembrane inner ear	protein-coding
mm_11491.1	chr2	32452309	32452317	+	1	NA	promoter-TSS (NM_001164357)	promoter-TSS (NM_001164357)	-843	NM_146118	227731	Mm.37395	NM_146118	ENSMUSG00000026819	Slc25a25	1110030N17Rik|MCSC|mKIAA1896	solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 25	protein-coding
mm_118616.1	chr14	21051835	21051839	+	1	NA	promoter-TSS (NM_134079)	promoter-TSS (NM_134079)	605	NM_018829	55946	Mm.376269	NM_018829	ENSMUSG00000021824	Ap3m1	1200013D09Rik|C78982|R75378	adaptor-related protein complex 3, mu 1 subunit	protein-coding
mm_5324.1	chr1	22806238	22806272	-	1	NA	promoter-TSS (NM_001012625)	promoter-TSS (NM_001012625)	-531	NM_001012624	116837	Mm.60061	NM_053270	ENSMUSG00000041670	Rims1	C030033M19Rik|RIM1|RIM1a|RIM1alpha|Rab3ip1|Rim|Serg1|mKIAA0340	regulating synaptic membrane exocytosis 1	protein-coding
mm_80148.1	chr9	70914321	70914325	+	1	NA	intron (NM_001324473, intron 1 of 8)	PB1D10|SINE|Alu	20485	NM_008280	15450	Mm.390187	NM_008280	ENSMUSG00000032207	Lipc	AI256194|HL|Hpl	lipase, hepatic	protein-coding
mm_153689.1	chr19	44397011	44397028	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	10690	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_31309.1	chr4	46078948	46078952	+	1	NA	intron (NM_021883, intron 3 of 9)	intron (NM_021883, intron 3 of 9)	39728	NM_021883	21916	Mm.249594	NM_021883	ENSMUSG00000028328	Tmod1	E-Tmod|Tmod	tropomodulin 1	protein-coding
mm_113886.1	chr13	49188203	49188216	+	1	NA	intron (NM_013610, intron 1 of 3)	intron (NM_013610, intron 1 of 3)	662	NM_013610	18081	Mm.18503	NM_013610	ENSMUSG00000037966	Ninj1	AU024536	ninjurin 1	protein-coding
mm_21022.1	chr2	152398117	152398136	-	1	NA	promoter-TSS (NM_011438)	promoter-TSS (NM_011438)	-80	NM_011438	20667	Mm.28424	NM_011438	ENSMUSG00000051817	Sox12	2010205A02Rik	SRY (sex determining region Y)-box 12	protein-coding
mm_27567.1	chr3	58622810	58622810	-	1	NA	intron (NM_001081262, intron 10 of 13)	intron (NM_001081262, intron 10 of 13)	14397	NM_001081262	545527	Mm.357722	NM_001081262	ENSMUSG00000070471	Erich6	4932431H17Rik|Fam194a	glutamate rich 6	protein-coding
mm_17602.1	chr2	30828229	30828311	-	1	NA	promoter-TSS (NM_133346)	promoter-TSS (NM_133346)	30	NM_133346	72323	Mm.27656	NM_133346	ENSMUSG00000039483	Asb6	2510004M11Rik|AA409356	ankyrin repeat and SOCS box-containing 6	protein-coding
mm_20376.1	chr2	128466469	128466478	-	1	NA	Intergenic	Intergenic	-37122	NR_028590	100043424	Mm.297222	NR_028589		Gm14005	OTTMUSG00000015351	predicted gene 14005	ncRNA
mm_142001.1	chr17	35199412	35199433	-	1	NA	TTS (NM_013693)	TTS (NM_013693)	2585	NM_013693	21926	Mm.1293	NM_013693	ENSMUSG00000024401	Tnf	DIF|TNF-a|TNF-alpha|TNFSF2|TNFalpha|Tnfa|Tnfsf1a|Tnlg1f	tumor necrosis factor	protein-coding
mm_166795.1	chr6	149401668	149401685	+	1	NA	Intergenic	Intergenic	-7308	NM_001112796	12121	Mm.177181	NM_009753	ENSMUSG00000003452	Bicd1	B830009D06Rik|bic-D 1	bicaudal D homolog 1 (Drosophila)	protein-coding
mm_83661.1	chr9	49568470	49568505	-	1	NA	TTS (NR_029465)	TTS (NR_029465)	50199	NR_029465	100036537	Mm.437541	NR_029465	ENSMUSG00000079564	Gm11149	ENSMUSG00000060603|ENSMUSG00000079564	predicted gene 11149	ncRNA
mm_129126.1	chr15	76180668	76180689	-	1	NA	exon (NM_201393, exon 31 of 32)	exon (NM_201393, exon 31 of 32)	15032	NM_201394	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
mm_84200.1	chr9	60649750	60649790	-	1	NA	intron (NM_001311095, intron 7 of 15)	intron (NM_001311095, intron 7 of 15)	37764	NM_001311095	102747	Mm.269413	NM_145616	ENSMUSG00000047766	Lrrc49	AI430817|AW050057|D430025H09Rik|PGs4|p79	leucine rich repeat containing 49	protein-coding
mm_143501.1	chr17	71526820	71526837	-	1	NA	promoter-TSS (NM_023294)	promoter-TSS (NM_023294)	29	NM_023294	67052	Mm.225956	NM_023294	ENSMUSG00000024056	Ndc80	2610020P18Rik|AV139730|HEC|HEC1|Kntc2	NDC80 kinetochore complex component	protein-coding
mm_95828.1	chr11	55469649	55469659	+	1	NA	promoter-TSS (NM_013716)	promoter-TSS (NM_013716)	-98	NM_013716	27041	Mm.39631	NM_013716	ENSMUSG00000018583	G3bp1	AI849976|B430204O07|C87777|G3bp|mKIAA4115	GTPase activating protein (SH3 domain) binding protein 1	protein-coding
mm_9984.1	chr1	191253739	191253752	-	1	NA	Intergenic	B1_Mur1|SINE|Alu	64373	NM_025424	66208	Mm.46444	NM_025424	ENSMUSG00000037499	Nenf	1110060M21Rik|SCIRP10|Spuf	neuron derived neurotrophic factor	protein-coding
mm_65525.1	chr7	25787050	25787062	-	1	NA	intron (NM_009465, intron 2 of 19)	intron (NM_009465, intron 2 of 19)	1677	NM_001190974	26362	Mm.4128	NM_009465	ENSMUSG00000002602	Axl	AI323647|Ark|Tyro7|Ufo	AXL receptor tyrosine kinase	protein-coding
mm_171477.1	chr4	145864032	145864032	+	1	NA	Intergenic	Intergenic	26813	NR_033612	236069	Mm.276881	NR_033612	ENSMUSG00000096233	Gm13238	OTTMUSG00000011065	carnitine deficiency-associated gene expressed in ventricle 3 pseudogene	pseudo
mm_45821.1	chr5	87692791	87692798	-	1	NA	3' UTR (NM_001286023, exon 7 of 7)	3' UTR (NM_001286023, exon 7 of 7)	6631	NM_001286020	12991	Mm.268737	NM_009972	ENSMUSG00000063157	Csn2	Csnb	casein beta	protein-coding
mm_172860.1	chr9	40803211	40803216	+	1	NA	exon (NM_031165, exon 5 of 9)	exon (NM_031165, exon 5 of 9)	1940	NM_031165	15481	Mm.290774	NM_031165	ENSMUSG00000015656	Hspa8	2410008N15Rik|Hsc70|Hsc71|Hsc73|Hsp73|Hspa10	heat shock protein 8	protein-coding
mm_70757.1	chr8	21134611	21134627	+	1	NA	promoter-TSS (NM_001177485)	promoter-TSS (NM_001177485)	-31	NM_001177485	100038927	Mm.426552	NM_001177485	ENSMUSG00000074444	Defa30	Gm15284|OTTMUSG00000019742	defensin, alpha, 30	protein-coding
mm_7500.1	chr1	121430990	121431012	-	1	NA	promoter-TSS (NM_029955)	promoter-TSS (NM_029955)	-66	NM_029955	70829	Mm.25788	NM_027567	ENSMUSG00000026339	Ccdc93	4633402D15Rik|9230102M16Rik	coiled-coil domain containing 93	protein-coding
mm_107741.1	chr12	58212292	58212309	+	1	NA	5' UTR (NM_009216, exon 2 of 2)	5' UTR (NM_009216, exon 2 of 2)	496	NM_009216	20605	Mm.278336	NM_009216	ENSMUSG00000035431	Sstr1	SRIF-2|SS-1-R|SS1-R|SS1R|Smstr-1|Smstr1|sst1	somatostatin receptor 1	protein-coding
mm_27798.1	chr3	75655775	75655802	-	1	NA	promoter-TSS (NR_040539)	promoter-TSS (NR_040539)	-57	NR_040539	69193	Mm.374088	NR_040539	ENSMUSG00000099370	Platr10	2410007B07Rik	pluripotency associated transcript 10	ncRNA
mm_60092.1	chr7	34969336	34969372	+	1	NA	intron (NM_008820, intron 7 of 14)	intron (NM_008820, intron 7 of 14)	56947	NM_008820	18624	Mm.69751	NM_008820	ENSMUSG00000063931	Pepd	Pep-4|Pep4|dal	peptidase D	protein-coding
mm_56074.1	chr6	87136505	87136516	-	1	NA	3' UTR (NM_054041, exon 18 of 18)	3' UTR (NM_054041, exon 18 of 18)	31764	NM_001167937	52372	Mm.282851	NM_001167937	ENSMUSG00000090891	D6Ertd527e	AU043841	DNA segment, Chr 6, ERATO Doi 527, expressed	protein-coding
mm_13724.1	chr2	117417792	117417802	+	1	NA	Intergenic	Intergenic	-74920	NM_011246	19419	Mm.42150	NM_011246	ENSMUSG00000027347	Rasgrp1	Rasgrp	RAS guanyl releasing protein 1	protein-coding
mm_34457.1	chr4	148130743	148130772	+	1	NA	promoter-TSS (NM_027426)	promoter-TSS (NM_027426)	-59	NM_027426	70433	Mm.275288	NM_027426	ENSMUSG00000029005	Draxin	2610109H07Rik|neucrin	dorsal inhibitory axon guidance protein	protein-coding
mm_26558.1	chr3	146499829	146499843	+	1	NA	promoter-TSS (NM_001316756)	promoter-TSS (NM_001316756)	0	NM_010318	14707	Mm.140804	NM_010318	ENSMUSG00000068523	Gng5	G(y)5	guanine nucleotide binding protein (G protein), gamma 5	protein-coding
mm_66501.1	chr7	45083164	45083176	-	1	NA	3' UTR (NM_026555, exon 7 of 7)	3' UTR (NM_026555, exon 7 of 7)	9043	NM_026555	52377	Mm.29997	NM_026555	ENSMUSG00000019539	Rcn3	6030455P07Rik|D530026G20Rik|D7Ertd671e|RLP49	reticulocalbin 3, EF-hand calcium binding domain	protein-coding
mm_57432.1	chr6	124914437	124914458	-	1	NA	exon (NM_026988, exon 4 of 5)	exon (NM_026988, exon 4 of 5)	-2742	NM_008479	16768	Mm.4528	NM_008479	ENSMUSG00000030124	Lag3	CD223|LAG-3|Ly66	lymphocyte-activation gene 3	protein-coding
mm_77841.1	chr9	5299268	5299283	+	1	NA	intron (NM_009807, intron 1 of 9)	intron (NM_009807, intron 1 of 9)	758	NM_009807	12362	Mm.1051	NM_009807	ENSMUSG00000025888	Casp1	ICE|Il1bc	caspase 1	protein-coding
mm_39637.1	chr5	24482770	24482774	+	1	NA	3' UTR (NM_001256431, exon 9 of 9)	3' UTR (NM_001256431, exon 9 of 9)	30595	NM_139153	213990	Mm.250703	NM_139153	ENSMUSG00000023353	Agap3	AGAP-3|AV028425|Centg3|Crag|Crag.|MRIP-1|cnt-g3	ArfGAP with GTPase domain, ankyrin repeat and PH domain 3	protein-coding
mm_149923.1	chr19	26623402	26623418	+	1	NA	intron (NM_011416, intron 2 of 32)	intron (NM_011416, intron 2 of 32)	18250	NM_011416	67155	Mm.342988	NM_011416	ENSMUSG00000024921	Smarca2	2610209L14Rik|SNF2alpha|Snf2l2|brahma|brm	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	protein-coding
mm_38026.1	chr4	133815806	133815816	-	1	NA	Intergenic	Intergenic	58920	NM_001285506	20111	Mm.301827	NM_009097	ENSMUSG00000003644	Rps6ka1	Mapkapk-1a|Rsk|Rsk-1|Rsk1|S6K-alpha-1|p90-Rsk1|p90Rsk1|p90S6K|p90rsk	ribosomal protein S6 kinase polypeptide 1	protein-coding
mm_152250.1	chr19	8716006	8716021	-	1	NA	intron (NM_001161413, intron 1 of 9)	RSINE1|SINE|B4	-2116	NM_008577	17254	Mm.4114	NM_008577	ENSMUSG00000010095	Slc3a2	4F2|4F2HC|AI314110|Cd98|Ly-10|Ly-m10|Ly10|Mdu1|Mgp-2hc|NACAE	solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2	protein-coding
mm_62272.1	chr7	99570545	99570588	+	1	NA	intron (NM_177231, intron 1 of 15)	intron (NM_177231, intron 1 of 15)	18297	NR_029760	723840		NR_029760	ENSMUSG00000065571	Mir326	Mirn326|mir-326|mmu-mir-326	microRNA 326	ncRNA
mm_134685.1	chr16	22436551	22436565	-	1	NA	5' UTR (NM_023794, exon 2 of 13)	5' UTR (NM_023794, exon 2 of 13)	3012	NM_023794	104156	Mm.155708	NM_023794	ENSMUSG00000013089	Etv5	1110005E01Rik|8430401F14Rik|ERM	ets variant 5	protein-coding
mm_113399.1	chr13	33484785	33484787	+	1	NA	promoter-TSS (NM_011455)	promoter-TSS (NM_011455)	-4	NM_011455	93806	Mm.202781	NM_011455	ENSMUSG00000057726	Serpinb9g	1600002F03Rik|AW545779|NK21B	serine (or cysteine) peptidase inhibitor, clade B, member 9g	protein-coding
mm_3020.1	chr1	133365148	133365156	+	1	NA	intron (NM_175443, intron 1 of 7)	intron (NM_175443, intron 1 of 7)	1580	NM_175443	214253	Mm.52111	NM_175443	ENSMUSG00000070644	Etnk2	4933417N20Rik|AI197444|EKI 2|Eki2|Tuc1	ethanolamine kinase 2	protein-coding
mm_114389.1	chr13	63271452	63271457	+	1	NA	intron (NR_110520, intron 2 of 5)	intron (NR_110520, intron 2 of 5)	25693	NR_045794	100504114	Mm.437070	NR_045794	ENSMUSG00000097242	Gm16907	-	predicted gene, 16907	ncRNA
mm_45433.1	chr5	67099174	67099182	-	1	NA	promoter-TSS (NM_008888)	promoter-TSS (NM_008888)	-52	NM_008888	18935	Mm.62505	NM_008888	ENSMUSG00000012520	Phox2b	Dilp1|NBPhox|Pmx2b|Px2b	paired-like homeobox 2b	protein-coding
mm_145110.1	chr18	44200807	44200810	+	1	NA	Intergenic	Intergenic	-4631	NM_001048217	433181	Mm.117440	NM_001048217	ENSMUSG00000073573	Spink11	9230112K01Rik	serine peptidase inhibitor, Kazal type 11	protein-coding
mm_38423.1	chr4	139192665	139192718	-	1	NA	promoter-TSS (NM_009798)	promoter-TSS (NM_009798)	-208	NM_009798	12345	Mm.2945	NM_009798	ENSMUSG00000028745	Capzb	1700120C01Rik|AI325129|CPB1|CPB2|CPbeat2|CPbeta1|CPbeta2|Cappb1	capping protein (actin filament) muscle Z-line, beta	protein-coding
mm_136378.1	chr16	92825836	92825846	-	1	NA	intron (NM_001111022, intron 1 of 6)	intron (NM_001111022, intron 1 of 6)	233	NM_001111021	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_92975.1	chr10	86498873	86498909	-	1	NA	promoter-TSS (NM_013722)	promoter-TSS (NM_013722)	5	NM_001164495	27204	Mm.394931	NM_013722	ENSMUSG00000059602	Syn3	-	synapsin III	protein-coding
mm_157614.1	chrX	53776404	53776407	-	1	NA	promoter-TSS (NM_001009549)	promoter-TSS (NM_001009549)	-11	NM_001009549	333473	Mm.327378	NM_001009549	ENSMUSG00000059334	Zfp36l3	AY661338	zinc finger protein 36, C3H type-like 3	protein-coding
mm_101241.1	chr11	20712221	20712238	-	1	NA	exon (NM_001252503, exon 3 of 8)	exon (NM_001252503, exon 3 of 8)	29327	NM_001290545	216549	Mm.356580	NM_181411	ENSMUSG00000049659	Aftph	-	aftiphilin	protein-coding
mm_115012.1	chr13	98354441	98354451	+	1	NA	5' UTR (NM_008242, exon 1 of 1)	5' UTR (NM_008242, exon 1 of 1)	201	NM_008242	15229	Mm.347441	NM_008242	ENSMUSG00000078302	Foxd1	AI385632|BF-2|FREAC4|Hfh10|Hfhbf2	forkhead box D1	protein-coding
mm_59059.1	chr7	19414984	19415008	+	1	NA	exon (NM_007710, exon 3 of 8)	exon (NM_007710, exon 3 of 8)	3902	NM_007710	12715	Mm.2375	NM_007710	ENSMUSG00000030399	Ckm	Ckmm|M-CK|MCK	creatine kinase, muscle	protein-coding
mm_59176.1	chr7	24457994	24458013	+	1	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	-4480	NM_011113	18793	Mm.1359	NM_011113	ENSMUSG00000046223	Plaur	Cd87|u-PAR|uPAR	plasminogen activator, urokinase receptor	protein-coding
mm_116731.1	chr13	51734616	51734626	-	1	NA	intron (NM_001281880, intron 2 of 16)	intron (NM_001281880, intron 2 of 16)	59126	NM_001281880	20354	Mm.33903	NM_013660	ENSMUSG00000021451	Sema4d	CD100|Semacl2|Semaj|Semcl2|coll-4	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D	protein-coding
mm_12731.1	chr2	78869153	78869163	+	1	NA	5' UTR (NM_009454, exon 1 of 6)	5' UTR (NM_009454, exon 1 of 6)	111	NM_009454	22193	Mm.1485	NM_009454	ENSMUSG00000027011	Ube2e3	Ubce4|ubcM2	ubiquitin-conjugating enzyme E2E 3	protein-coding
mm_48970.1	chr6	4747611	4747613	+	1	NA	promoter-TSS (NM_001130188)	promoter-TSS (NM_001130188)	306	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_147767.1	chr18	61375425	61375437	-	1	NA	intron (NM_133249, intron 1 of 11)	intron (NM_133249, intron 1 of 11)	25000	NM_133249	170826	Mm.415302	NM_133249	ENSMUSG00000033871	Ppargc1b	4631412G21Rik|Perc	peroxisome proliferative activated receptor, gamma, coactivator 1 beta	protein-coding
mm_110989.1	chr12	77166909	77166914	-	1	NA	Intergenic	RMER19B|LTR|ERVK	-71193	NM_001252614	53618	Mm.35628	NM_016893	ENSMUSG00000021065	Fut8	-	fucosyltransferase 8	protein-coding
mm_130744.1	chr15	101256230	101256240	-	1	NA	Intergenic	Intergenic	-10611	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_19250.1	chr2	84773339	84773371	-	1	NA	exon (NM_009776, exon 3 of 8)	exon (NM_009776, exon 3 of 8)	2074	NM_009776	12258	Mm.38888	NM_009776	ENSMUSG00000023224	Serping1	C1INH|C1nh	serine (or cysteine) peptidase inhibitor, clade G, member 1	protein-coding
mm_5570.1	chr1	39439068	39439083	-	1	NA	intron (NM_018775, intron 1 of 19)	RMER15|LTR|ERVL	39672	NM_018775	54610	Mm.387293	NM_018775	ENSMUSG00000003134	Tbc1d8	AD3|HBLP1|VRP	TBC1 domain family, member 8	protein-coding
mm_135925.1	chr16	69863793	69863807	-	1	NA	promoter-TSS (NM_173069)	promoter-TSS (NM_173069)	-56	NM_173069	224318	Mm.212743	NM_173069	ENSMUSG00000063163	Speer2	SPEER-2	spermatogenesis associated glutamate (E)-rich protein 2	protein-coding
mm_19805.1	chr2	110305731	110305755	-	1	NA	promoter-TSS (NM_130452)	promoter-TSS (NM_130452)	-18	NM_130452	170442	Mm.27335	NM_130452	ENSMUSG00000041660	Bbox1	AI874739	butyrobetaine (gamma), 2-oxoglutarate dioxygenase 1 (gamma-butyrobetaine hydroxylase)	protein-coding
mm_72601.1	chr8	84415410	84415424	+	1	NA	promoter-TSS (NM_001252060)	promoter-TSS (NM_001252060)	53	NM_001252061	12286	Mm.334658	NM_007578	ENSMUSG00000034656	Cacna1a	APCA|BI|Caca1a|Cacnl1a4|Cav2.1|Ccha1a|EA2|FHM|HPCA|MHP|MHP1|SCA6|alpha1A|la|nmf352|rkr|smrl|tg	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	protein-coding
mm_96866.1	chr11	70166697	70166707	+	1	NA	promoter-TSS (NM_010796)	promoter-TSS (NM_010796)	79	NM_010796	17312	Mm.252405	NM_010796	ENSMUSG00000000318	Clec10a	CD301a|M-ASGP-BP-1|Mgl|Mgl1	C-type lectin domain family 10, member A	protein-coding
mm_45793.1	chr5	87538174	87538186	-	1	NA	promoter-TSS (NM_019878)	promoter-TSS (NM_019878)	15	NM_019878	56362	Mm.23502	NM_019878	ENSMUSG00000029269	Sult1b1	ST1B1|St2b2	sulfotransferase family 1B, member 1	protein-coding
mm_10541.1	chr2	16512153	16512164	+	1	NA	exon (NM_026162, exon 2 of 14)	exon (NM_026162, exon 2 of 14)	155854	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding
mm_74429.1	chr8	3717548	3717558	-	1	NA	exon (NM_029465, exon 7 of 9)	exon (NM_029465, exon 7 of 9)	3098	NM_029465	75863	Mm.109183	NM_029465	ENSMUSG00000074491	Clec4g	4930572L20Rik	C-type lectin domain family 4, member g	protein-coding
mm_59945.1	chr7	30425524	30425548	+	1	NA	exon (NM_172142, exon 5 of 11)	exon (NM_172142, exon 5 of 11)	2232	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_42144.1	chr5	111418222	111418233	+	1	NA	promoter-TSS (NM_001081235)	promoter-TSS (NM_001081235)	61	NM_001081235	433938	Mm.332576	NM_001081235	ENSMUSG00000070576	Mn1	AA003644|AA009236	meningioma 1	protein-coding
mm_171651.1	chr4	40722600	40722602	+	1	NA	promoter-TSS (NM_001164672)	promoter-TSS (NM_001164672)	133	NM_008298	15502	Mm.27897	NM_008298	ENSMUSG00000028410	Dnaja1	HSJ-2|Hsj2|Nedd7	DnaJ heat shock protein family (Hsp40) member A1	protein-coding
mm_121517.1	chr14	122034661	122034677	+	1	NA	promoter-TSS (NM_001037744)	promoter-TSS (NM_001037744)	-5	NM_001037744	223262	Mm.297637	NM_001037744	ENSMUSG00000071229	Timm8a2	-	translocase of inner mitochondrial membrane 8A2	protein-coding
mm_158811.1	chrX	167307812	167307844	-	1	NA	exon (NM_001290758, exon 4 of 4)	exon (NM_001290758, exon 4 of 4)	22743	NM_001290757	170743	Mm.23979	NM_133211	ENSMUSG00000044583	Tlr7	-	toll-like receptor 7	protein-coding
mm_70919.1	chr8	25785290	25785319	+	1	NA	promoter-TSS (NM_026032)	promoter-TSS (NM_026032)	-95	NM_026121	67384	Mm.118400	NM_026121	ENSMUSG00000037316	Bag4	2410112I15Rik|SODD	BCL2-associated athanogene 4	protein-coding
mm_19591.1	chr2	102057496	102057499	-	1	NA	intron (NM_001290784, intron 4 of 5)	intron (NM_001290784, intron 4 of 5)	128963	NM_178886	241576	Mm.489740	NM_178886	ENSMUSG00000048058	Ldlrad3	6430500P08|AI194318|Lrad3	low density lipoprotein receptor class A domain containing 3	protein-coding
mm_75289.1	chr8	41041855	41041863	-	1	NA	promoter-TSS (NM_001005865)	promoter-TSS (NM_001005865)	72	NM_001005865	102103	Mm.149438	NM_001005863	ENSMUSG00000045636	Mtus1	AI481402|ATBP135|Atip1|B430010I23Rik|B430305I03Rik|C85752|Cctsg1-440|MD44|MTSG1|mKIAA1288	mitochondrial tumor suppressor 1	protein-coding
mm_64685.1	chr7	4514538	4514550	-	1	NA	intron (NM_011618, intron 1 of 13)	intron (NM_011618, intron 1 of 13)	1431	NM_001277903	21955	Mm.358643	NM_011618	ENSMUSG00000064179	Tnnt1	AW146156|Tnt|sTnT|ssTnT	troponin T1, skeletal, slow	protein-coding
mm_132155.1	chr16	32177579	32177589	+	1	NA	Intergenic	Intergenic	-2216	NM_001033539	328660	Mm.441006	NM_001033539	ENSMUSG00000075269	Bex6	B020003O03Rik	brain expressed family member 6	protein-coding
mm_132028.1	chr16	27388950	27388966	+	1	NA	promoter-TSS (NM_001289436)	promoter-TSS (NM_001289436)	2	NM_001289436	67501	Mm.258985	NM_026202	ENSMUSG00000038127	Ccdc50	C3orf6	coiled-coil domain containing 50	protein-coding
mm_39121.1	chr4	155011007	155011026	-	1	NA	promoter-TSS (NM_175556)	promoter-TSS (NM_175556)	-32	NM_001113360	269615	Mm.379458	NM_175556	ENSMUSG00000029055	Plch2	A930027K05Rik|PLCeta2|Plc-eta2|Plcl4	phospholipase C, eta 2	protein-coding
mm_106517.1	chr11	120550938	120550963	-	1	NA	exon (NM_026814, exon 1 of 3)	exon (NM_026814, exon 1 of 3)	182	NM_026814	68701	Mm.46477	NM_026814	ENSMUSG00000025129	Ppp1r27	1110033I14Rik|Dysfip1|toonin	protein phosphatase 1, regulatory subunit 27	protein-coding
mm_82650.1	chr9	22022287	22022327	-	1	NA	intron (NM_010487, intron 6 of 6)	ID_B1|SINE|B4	19319	NM_008925	19089	Mm.214593	NM_008925	ENSMUSG00000003402	Prkcsh	80K-H|PKCSH	protein kinase C substrate 80K-H	protein-coding
mm_32966.1	chr4	119911860	119911867	+	1	NA	intron (NM_010657, intron 1 of 8)	intron (NM_010657, intron 1 of 8)	97185	NM_010657	16656	Mm.302758	NM_010657	ENSMUSG00000028634	Hivep3	2900056N03Rik|A130075N07|AI848000|E030045D18Rik|KBP-1|KBP1|Krc|Rc|Schnurri-3|Shn3|Zas3	human immunodeficiency virus type I enhancer binding protein 3	protein-coding
mm_108566.1	chr12	84773263	84773319	+	1	NA	promoter-TSS (NM_028863)	promoter-TSS (NM_028863)	21	NM_028863	74316	Mm.25719	NM_028863	ENSMUSG00000021241	Isca2	0710001C05Rik|5730594E03Rik|Hbld1	iron-sulfur cluster assembly 2	protein-coding
mm_90761.1	chr10	5550709	5550735	-	1	NA	promoter-TSS (NM_153399)	promoter-TSS (NM_153399)	-30	NM_001347732	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_79191.1	chr9	48450296	48450324	+	1	NA	Intergenic	Intergenic	-4034	NR_026561	667933	Mm.491076	NR_026561		Gm8884	EG667933	predicted gene 8884	ncRNA
mm_134200.1	chr16	11066142	11066165	-	1	NA	promoter-TSS (NM_009223)	promoter-TSS (NM_009223)	-145	NM_009223	20621	Mm.325800	NM_009223	ENSMUSG00000037972	Snn	2810407J07Rik|AI848521|AW547286	stannin	protein-coding
mm_129806.1	chr15	82987694	82987705	-	1	NA	Intergenic	Intergenic	-28403	NR_037241	100526477		NR_037241	ENSMUSG00000092751	Mir3080	mmu-mir-3080	microRNA 3080	ncRNA
mm_158995.1	chr1	138116636	138116636	-	1	NA	intron (NM_001268286, intron 3 of 28)	intron (NM_001268286, intron 3 of 28)	58490	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_142263.1	chr17	39845123	39845150	-	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	2139	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_8842.1	chr1	162692826	162692838	-	1	NA	exon (NM_001081290, exon 21 of 35)	exon (NM_001081290, exon 21 of 35)	-34613	NM_001177581	100038657	Mm.416999	NM_001177581	ENSMUSG00000091060	7420461P10Rik	ENSMUSG00000073516	RIKEN cDNA 7420461P10 gene	protein-coding
mm_95149.1	chr11	35768795	35768798	+	1	NA	promoter-TSS (NM_145962)	promoter-TSS (NM_145962)	-699	NM_145962	211347	Mm.255044	NM_145962	ENSMUSG00000018846	Pank3	-	pantothenate kinase 3	protein-coding
mm_89142.1	chr10	85871816	85871898	+	1	NA	promoter-TSS (NM_133993)	promoter-TSS (NM_133993)	26	NM_133993	103136	Mm.18834	NM_133993	ENSMUSG00000001785	Pwp1	2310058A11Rik|2610205J09Rik|AI098170|AL022879|AV083409|AW550690	PWP1 homolog, endonuclein	protein-coding
mm_151944.1	chr19	5801001	5801010	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	1667	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_105415.1	chr11	103638900	103638906	-	1	NA	promoter-TSS (NM_027083)	promoter-TSS (NM_027083)	-29	NM_027083	69444	Mm.275677	NM_027083	ENSMUSG00000020945	Lyzl6	1700023H08Rik|Lyc1|Lyzb	lysozyme-like 6	protein-coding
mm_74552.1	chr8	10865931	10865936	-	1	NA	Intergenic	Intergenic	16521	NR_040705	320014	Mm.403203	NR_040705	ENSMUSG00000109473	B930025P03Rik	-	RIKEN cDNA B930025P03 gene	ncRNA
mm_41473.1	chr5	91517733	91517749	+	1	NA	promoter-TSS (NM_145562)	promoter-TSS (NM_145562)	41	NM_145562	231440	Mm.5002	NM_145562	ENSMUSG00000034981	Parm1	2210012L08Rik|9130213B05Rik|W91666	prostate androgen-regulated mucin-like protein 1	protein-coding
mm_34862.1	chr4	155555065	155555081	+	1	NA	exon (NM_008142, exon 10 of 12)	exon (NM_008142, exon 10 of 12)	-7319	NM_138671	192185	Mm.28347	NM_138671	ENSMUSG00000029063	Nadk	4432404C02Rik|BC004012	NAD kinase	protein-coding
mm_112639.1	chr13	16014442	16014452	+	1	NA	intron (NM_008380, intron 2 of 4)	intron (NM_008380, intron 2 of 4)	2596	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_89125.1	chr10	84917557	84917594	+	1	NA	promoter-TSS (NM_183172)	promoter-TSS (NM_183172)	-38	NM_001013441	237422	Mm.18936	NM_183172	ENSMUSG00000035620	Ric8b	BC051080|Ric-8|Ric-8b	RIC8 guanine nucleotide exchange factor B	protein-coding
mm_72055.1	chr8	71371284	71371359	+	1	NA	promoter-TSS (NM_001293800)	promoter-TSS (NM_001293800)	23	NM_001293800	77090	Mm.440170	NM_029865	ENSMUSG00000002396	Ocel1	9430098E02Rik|AI326022|AI593544	occludin/ELL domain containing 1	protein-coding
mm_22328.1	chr2	180682633	180682636	-	1	NA	3' UTR (NM_011805, exon 6 of 6)	3' UTR (NM_011805, exon 6 of 6)	9414	NR_111965	23856	Mm.253836	NM_011805	ENSMUSG00000038914	Dido1	6720461J16Rik|D130048F08Rik|DATF-1|DIO-1|Datf1|dido	death inducer-obliterator 1	protein-coding
mm_130471.1	chr15	98727440	98727443	-	1	NA	intron (NM_024169, intron 2 of 5)	intron (NM_024169, intron 2 of 5)	757	NM_024169	66120	Mm.30729	NM_024169	ENSMUSG00000003355	Fkbp11	1110002O23Rik|FKBP-11	FK506 binding protein 11	protein-coding
mm_17233.1	chr2	25580216	25580230	-	1	NA	promoter-TSS (NM_001005424)	promoter-TSS (NM_001005424)	-124	NM_001005424	381353	Mm.379511	NM_001005424	ENSMUSG00000029419	Gm996	-	predicted gene 996	protein-coding
mm_78416.1	chr9	31030384	31030451	+	1	NA	promoter-TSS (NM_001115130)	promoter-TSS (NM_001115130)	-227	NM_001115130	235132	Mm.239355	NM_172765	ENSMUSG00000047412	Zbtb44	6030404E16Rik|Btbd15|E230011F09	zinc finger and BTB domain containing 44	protein-coding
mm_53876.1	chr6	149566068	149566116	+	1	NA	Intergenic	Intergenic	157108	NM_009753	12121	Mm.177181	NM_009753	ENSMUSG00000003452	Bicd1	B830009D06Rik|bic-D 1	bicaudal D homolog 1 (Drosophila)	protein-coding
mm_49490.1	chr6	29694205	29694250	+	1	NA	promoter-TSS (NM_001301407)	promoter-TSS (NM_001301407)	13	NM_146173	232670	Mm.225289	NM_146173	ENSMUSG00000001763	Tspan33	1300010A20Rik|Pen	tetraspanin 33	protein-coding
mm_60200.1	chr7	43409410	43409420	+	1	NA	exon (NM_172900, exon 4 of 12)	exon (NM_172900, exon 4 of 12)	1135	NM_172900	243958	Mm.24444	NM_172900	ENSMUSG00000030468	Siglecg	9830164H23|A630096C01Rik|Siglec-G|Siglec10|mSiglec-G	sialic acid binding Ig-like lectin G	protein-coding
mm_170772.1	chr2	163419478	163419492	-	1	NA	promoter-TSS (NM_025699)	promoter-TSS (NM_025699)	-15	NM_025699	66680	Mm.25119	NM_025699	ENSMUSG00000035399	Oser1	3230401D17Rik|AI256769|Perit1	oxidative stress responsive serine rich 1	protein-coding
mm_153419.1	chr19	40638767	40638775	-	1	NA	intron (NM_001304721, intron 1 of 9)	intron (NM_001304721, intron 1 of 9)	-20999	NM_009848	12495	Mm.2824	NM_009848	ENSMUSG00000048120	Entpd1	2610206B08Rik|AA408691|Cd39|NTPDase-1	ectonucleoside triphosphate diphosphohydrolase 1	protein-coding
mm_154536.1	chrM	13931	13967	-	1	NA	NA	Intergenic	NA	NA								
mm_1835.1	chr1	82820121	82820125	+	1	NA	Intergenic	Intergenic	-19337	NM_001310713	15463	Mm.392569	NM_010472	ENSMUSG00000026159	Agfg1	AU045498|C130049H11Rik|C85612|D730048C23Rik|Hrb|RAB|Rip	ArfGAP with FG repeats 1	protein-coding
mm_105264.1	chr11	102358478	102358501	-	1	NA	exon (NM_011403, exon 7 of 20)	exon (NM_011403, exon 7 of 20)	6792	NM_011403	20533	Mm.7248	NM_011403	ENSMUSG00000006574	Slc4a1	Ae1|CD233|Empb3|l11Jus51	solute carrier family 4 (anion exchanger), member 1	protein-coding
mm_33362.1	chr4	129491232	129491246	+	1	NA	promoter-TSS (NM_080442)	promoter-TSS (NM_080442)	49	NM_001085491	68233	Mm.424983	NM_001085491	ENSMUSG00000078554	Fam229a	1700125D06Rik	family with sequence similarity 229, member A	protein-coding
mm_146383.1	chr18	82585567	82585592	+	1	NA	TTS (NM_010777)	TTS (NM_010777)	31071	NM_001025254	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_94943.1	chr11	29718698	29718753	+	1	NA	5' UTR (NM_024226, exon 1 of 7)	5' UTR (NM_024226, exon 1 of 7)	162	NM_024226	68585	Mm.192580	NM_024226	ENSMUSG00000020458	Rtn4	1110020G17Rik|AA407876|AA409940|AA960376|ASY|C130026I10Rik|NOGO|NSP-CL|NgA|Nogo-A|Nogo-B|Nogo-C|mKIAA0886|mKIAA4153	reticulon 4	protein-coding
mm_57780.1	chr6	129239796	129239806	-	1	NA	Intergenic	Intergenic	-1319	NR_040266	76432	Mm.261738	NR_040265	ENSMUSG00000097354	2310001H17Rik	AI646108	RIKEN cDNA 2310001H17 gene	ncRNA
mm_117534.1	chr13	83572094	83572118	-	1	NA	intron (NM_001347566, intron 1 of 10)	intron (NM_001347566, intron 1 of 10)	-1501	NM_001347577	17260	Mm.24001	NM_025282	ENSMUSG00000005583	Mef2c	5430401D19Rik|9930028G15Rik|AV011172|Mef2	myocyte enhancer factor 2C	protein-coding
mm_84326.1	chr9	64021704	64021723	-	1	NA	5' UTR (NM_008542, exon 1 of 4)	5' UTR (NM_008542, exon 1 of 4)	346	NM_008542	17130	Mm.325757	NM_008542	ENSMUSG00000036867	Smad6	Madh6|b2b390Clo	SMAD family member 6	protein-coding
mm_51947.1	chr6	91726185	91726206	+	1	NA	exon (NM_009320, exon 5 of 15)	exon (NM_009320, exon 5 of 15)	42128	NM_009320	21366	Mm.395650	NM_009320	ENSMUSG00000030096	Slc6a6	AA589629|C80501|Taut	solute carrier family 6 (neurotransmitter transporter, taurine), member 6	protein-coding
mm_45726.1	chr5	86159304	86159316	-	1	NA	exon (NM_172712, exon 6 of 33)	exon (NM_172712, exon 6 of 33)	13433	NM_172712	231380	Mm.34012	NM_172712	ENSMUSG00000035898	Uba6	4930542H01|5730469D23Rik|AU021846|AW124799|E1-L2|Ube1l2	ubiquitin-like modifier activating enzyme 6	protein-coding
mm_161397.1	chr14	105897054	105897054	-	1	NA	promoter-TSS (NM_011897)	promoter-TSS (NM_011897)	-235	NM_011897	24064	Mm.89982	NM_011897	ENSMUSG00000022114	Spry2	sprouty2	sprouty homolog 2 (Drosophila)	protein-coding
mm_29398.1	chr3	108904565	108904584	-	1	NA	exon (NM_025845, exon 6 of 6)	exon (NM_025845, exon 6 of 6)	7130	NM_025845	66921	Mm.51049	NM_025845	ENSMUSG00000027881	Prpf38b	1110021E09Rik|AU018955	PRP38 pre-mRNA processing factor 38 (yeast) domain containing B	protein-coding
mm_27747.1	chr3	69156157	69156157	-	1	NA	intron (NR_126533, intron 2 of 2)	B4A|SINE|B4	24924	NR_126533	381452	Mm.331067	NM_001243000	ENSMUSG00000094763	Gm1647	-	predicted gene 1647	ncRNA
mm_127858.1	chr15	8350474	8350488	-	1	NA	exon (NM_027707, exon 10 of 47)	exon (NM_027707, exon 10 of 47)	93982	NM_027707	71175	Mm.240329	NM_027707	ENSMUSG00000022141	Nipbl	Idn3	Nipped-B homolog (Drosophila)	protein-coding
mm_132522.1	chr16	37777046	37777065	+	1	NA	promoter-TSS (NM_008047)	promoter-TSS (NM_008047)	0	NM_008047	14314	Mm.182434	NM_008047	ENSMUSG00000022816	Fstl1	AI316791|AW107808|Fstl|TSC-36	follistatin-like 1	protein-coding
mm_125872.1	chr15	75615118	75615130	+	1	NA	Intergenic	Intergenic	-1560	NM_001044718	22701	Mm.87210	NM_011759	ENSMUSG00000047003	Zfp41	CTfin92|Zfp-41	zinc finger protein 41	protein-coding
mm_134809.1	chr16	24895203	24895208	-	1	NA	intron (NM_001145954, intron 5 of 7)	intron (NM_001145954, intron 5 of 7)	-164434	NR_040374	319487	Mm.137341	NR_040374	ENSMUSG00000096960	A230028O05Rik	-	RIKEN cDNA A230028O05 gene	ncRNA
mm_3365.1	chr1	138303550	138303569	+	1	NA	Intergenic	Intergenic	29821	NM_177397	338375	Mm.114424	NM_177397	ENSMUSG00000026394	Atp6v1g3	-	ATPase, H+ transporting, lysosomal V1 subunit G3	protein-coding
mm_5639.1	chr1	40441658	40441704	-	1	NA	intron (NM_001025602, intron 3 of 10)	intron (NM_001025602, intron 3 of 10)	2052	NM_010743	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_148998.1	chr19	8664340	8664354	+	1	NA	5' UTR (NM_007698, exon 1 of 2)	5' UTR (NM_007698, exon 1 of 2)	342	NM_001112697	12669	Mm.240607	NM_007698	ENSMUSG00000032773	Chrm1	Chrm-1|M1|M1R	cholinergic receptor, muscarinic 1, CNS	protein-coding
mm_64408.1	chr7	142512034	142512045	+	1	NA	exon (NM_001163669, exon 13 of 17)	exon (NM_001163669, exon 13 of 17)	-5268	NR_033261	677289	Mm.350054	NR_033261	ENSMUSG00000043795	Prr33	ENSMUSG00000043795|Gm14492|OTTMUSG00000016823	proline rich 33	ncRNA
mm_101392.1	chr11	26103810	26103846	-	1	NA	intron (NR_027973, intron 1 of 5)	intron (NR_027973, intron 1 of 5)	-98412	NR_105791	102466154		NR_105791	ENSMUSG00000099015	Mir6372	Gm27358|mmu-mir-6372	microRNA 6372	ncRNA
mm_24387.1	chr3	90254345	90254363	+	1	NA	promoter-TSS (NM_028881)	promoter-TSS (NM_028881)	73	NM_028881	74343	Mm.35627	NM_028881	ENSMUSG00000027936	Crtc2	4632407F12Rik|Torc2|mTORC2	CREB regulated transcription coactivator 2	protein-coding
mm_101433.1	chr11	30100319	30100322	-	1	NA	3' UTR (NM_175836, exon 35 of 35)	3' UTR (NM_175836, exon 35 of 35)	-74287	NM_146016	237711	Mm.445271	NM_146016	ENSMUSG00000044072	Eml6	2900083P10Rik|C230094A16Rik|EMAP-6	echinoderm microtubule associated protein like 6	protein-coding
mm_52313.1	chr6	108829127	108829144	+	1	NA	exon (NM_138677, exon 1 of 12)	exon (NM_138677, exon 1 of 12)	494	NM_138677	192193	Mm.21596	NM_138677	ENSMUSG00000030104	Edem1	A130059K23Rik|EDEM|mKIAA0212	ER degradation enhancer, mannosidase alpha-like 1	protein-coding
mm_37899.1	chr4	132638886	132638904	-	1	NA	promoter-TSS (NM_010166)	promoter-TSS (NM_010166)	-151	NM_210071	14050	Mm.227733	NM_010166	ENSMUSG00000028886	Eya3	AI844637	EYA transcriptional coactivator and phosphatase 3	protein-coding
mm_144483.1	chr18	23989653	23989694	+	1	NA	promoter-TSS (NM_011755)	promoter-TSS (NM_011755)	39	NM_011755	22694	Mm.290596	NM_011755	ENSMUSG00000063281	Zfp35	Zfp-35|Znf271|mszf13|mszf20-1|mszf28|mszf68	zinc finger protein 35	protein-coding
mm_129661.1	chr15	81105000	81105069	-	1	NA	promoter-TSS (NM_153049)	promoter-TSS (NM_153049)	13	NM_153049	223701	Mm.439814	NM_153049	ENSMUSG00000042292	Mkl1	AMKL|Bsac|Mal|Mrtf-A	MKL (megakaryoblastic leukemia)/myocardin-like 1	protein-coding
mm_9811.1	chr1	182014458	182014479	-	1	NA	intron (NM_001083121, intron 1 of 13)	intron (NM_001083121, intron 1 of 13)	5512	NM_008680	13800	Mm.87759	NM_008680	ENSMUSG00000022995	Enah	Mena|NDPP-1|Ndpp1|WBP8	enabled homolog (Drosophila)	protein-coding
mm_98900.1	chr11	98000676	98000686	+	1	NA	TTS (NM_145121)	TTS (NM_145121)	-4508	NM_207231	217151	Mm.277896	NM_207231	ENSMUSG00000038352	Arl5c	Arl12|BC065791	ADP-ribosylation factor-like 5C	protein-coding
mm_162710.1	chr10	26374973	26374975	+	1	NA	promoter-TSS (NM_001347467)	promoter-TSS (NM_001347467)	245	NM_172787	237339	Mm.338439	NM_172787	ENSMUSG00000039089	L3mbtl3	AI481284|MBT-1	l(3)mbt-like 3 (Drosophila)	protein-coding
mm_62452.1	chr7	101394362	101394436	+	1	NA	promoter-TSS (NM_198096)	promoter-TSS (NM_198096)	11	NM_198096	69710	Mm.277687	NM_027180	ENSMUSG00000032812	Arap1	2410002L19Rik|Centd2|mKIAA0782	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	protein-coding
mm_65114.1	chr7	19320041	19320051	-	1	NA	Intergenic	CpG	-10001	NM_001347586	14282	Mm.248335	NM_008036	ENSMUSG00000003545	Fosb	-	FBJ osteosarcoma oncogene B	protein-coding
mm_111961.1	chr12	109598537	109598541	-	1	NA	Intergenic	Intergenic	-3136	NM_184109	353326	Mm.23062	NM_184109	ENSMUSG00000085925	Rtl1	6430411K18Rik|Mar|Mart1|Mor1|Peg11	retrotransposon-like 1	protein-coding
mm_59350.1	chr7	25659165	25659236	+	1	NA	promoter-TSS (NM_007533)	promoter-TSS (NM_007533)	47	NR_104358	27998	Mm.27853	NM_138586	ENSMUSG00000061286	Exosc5	D7Wsu180e	exosome component 5	protein-coding
mm_841.1	chr1	51594171	51594184	+	1	NA	Intergenic	Intergenic	-115778	NM_001310549	109019	Mm.196290	NM_028696	ENSMUSG00000026107	Nabp1	4930434H03Rik|4930442A21Rik|4930488J04Rik|4933440J18Rik|5830411E10Rik|AI852561|Nbp1|Obfc2a|Ssb2	nucleic acid binding protein 1	protein-coding
mm_66143.1	chr7	31126922	31126934	-	1	NA	promoter-TSS (NM_011322)	promoter-TSS (NM_011322)	95	NM_011322	20266	Mm.1418	NM_011322	ENSMUSG00000019194	Scn1b	-	sodium channel, voltage-gated, type I, beta	protein-coding
mm_22514.1	chr3	7618768	7618782	+	1	NA	Intergenic	Intergenic	-5015	NM_001313888	16196	Mm.3825	NM_008371	ENSMUSG00000040329	Il7	A630026I06Rik|Il-7|hlb368	interleukin 7	protein-coding
mm_17015.1	chr2	18952160	18952195	-	1	NA	intron (NM_008845, intron 1 of 9)	intron (NM_008845, intron 1 of 9)	45944	NM_008845	18718	Mm.313977	NM_008845	ENSMUSG00000026737	Pip4k2a	AW742916|Pip5k2a	phosphatidylinositol-5-phosphate 4-kinase, type II, alpha	protein-coding
mm_128621.1	chr15	58956505	58956515	-	1	NA	exon (NM_144800, exon 8 of 15)	exon (NM_144800, exon 8 of 15)	22700	NM_023172	66218	Mm.322294	NM_023172	ENSMUSG00000022354	Ndufb9	1190008J14Rik	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 9	protein-coding
mm_41363.1	chr5	90507871	90507897	+	1	NA	exon (NM_007423, exon 13 of 15)	exon (NM_007423, exon 13 of 15)	-11065	NM_145146	280662	Mm.348786	NM_145146	ENSMUSG00000029369	Afm	Alf|alpha-Alb	afamin	protein-coding
mm_95538.1	chr11	52265747	52265752	+	1	NA	intron (NM_001313981, intron 3 of 10)	intron (NM_001313981, intron 3 of 10)	16846	NM_009331	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_154746.1	chrX	10487824	10487831	+	1	NA	intron (NM_019634, intron 1 of 7)	L1MB8|LINE|L1	2711	NM_019634	21912	Mm.18590	NM_019634	ENSMUSG00000058254	Tspan7	1200014P11Rik|A15|AI323365|Cd231|Mxs1|PE31|R74651|TALLA|Tm4sf2	tetraspanin 7	protein-coding
mm_85496.1	chr9	106136376	106136389	-	1	NA	Intergenic	Intergenic	-17742	NR_029549	387153		NR_029549	ENSMUSG00000065407	Mir135a-1	Mir135a01|Mirn135|Mirn135a-1|mir-135a-1	microRNA 135a-1	ncRNA
mm_28994.1	chr3	101300235	101300239	-	1	NA	Intergenic	Intergenic	-12298	NM_013486	12481	Mm.22842	NM_013486	ENSMUSG00000027863	Cd2	LFA-2|Ly-37|Ly37	CD2 antigen	protein-coding
mm_94584.1	chr11	11692004	11692009	+	1	NA	intron (NM_001301866, intron 1 of 5)	intron (NM_001301866, intron 1 of 5)	1829	NM_001301863	22778	Mm.103545	NM_009578	ENSMUSG00000018654	Ikzf1	5832432G11Rik|Ikaros|LyF-1|Zfpn1a1|Znfn1a1|hlk-1|mKIAA4227	IKAROS family zinc finger 1	protein-coding
mm_105271.1	chr11	102406743	102406752	-	1	NA	intron (NM_026542, intron 1 of 11)	intron (NM_026542, intron 1 of 11)	770	NM_026542	68066	Mm.44226	NM_026542	ENSMUSG00000018677	Slc25a39	3010027G13Rik|D11Ertd333e	solute carrier family 25, member 39	protein-coding
mm_60679.1	chr7	45124598	45124623	+	1	NA	promoter-TSS (NM_013725)	promoter-TSS (NM_013725)	-221	NM_013725	27207	Mm.196538	NM_013725	ENSMUSG00000003429	Rps11	-	ribosomal protein S11	protein-coding
mm_12954.1	chr2	90188906	90188910	+	1	NA	Intergenic	Intergenic	35563	NM_001270423	100042690	Mm.271314	NM_001270423	ENSMUSG00000089859	Gm13769	Gm13766|OTTMUSG00000014164|OTTMUSG00000014278	predicted gene 13769	protein-coding
mm_120218.1	chr14	62760497	62760521	+	1	NA	promoter-TSS (NR_045503)	promoter-TSS (NR_045503)	8	NR_045503	71000	Mm.399410	NR_045503	ENSMUSG00000097775	4931440J10Rik	-	RIKEN cDNA 4931440J10 gene	ncRNA
mm_123029.1	chr14	55524210	55524223	-	1	NA	promoter-TSS (NM_008736)	promoter-TSS (NM_008736)	36	NM_008736	18185	Mm.20422	NM_008736	ENSMUSG00000040632	Nrl	D14H14S46E	neural retina leucine zipper gene	protein-coding
mm_49946.1	chr6	39879618	39879622	+	1	NA	Intergenic	Intergenic	-68684	NM_001010930	14548	Mm.377071	NM_010270	ENSMUSG00000029918	Mrps33	AI841153|CGI-139|Gdap3|MRP-S33|PTD003	mitochondrial ribosomal protein S33	protein-coding
mm_64207.1	chr7	141475305	141475315	+	1	NA	promoter-TSS (NM_025593)	promoter-TSS (NM_025593)	74	NM_053082	64540	Mm.489619	NM_053082	ENSMUSG00000025511	Tspan4	AI325509|AI746565|D130042I01Rik|NAG-2|Tm4sf7|Tspan-4	tetraspanin 4	protein-coding
mm_65759.1	chr7	28630502	28630512	-	1	NA	intron (NM_175319, intron 1 of 12)	CpG	508	NM_175319	101744	Mm.26022	NM_175319	ENSMUSG00000037469	Acp7	AU017076|C330005M16Rik|Papl	acid phosphatase 7, tartrate resistant	protein-coding
mm_87200.1	chr10	39551458	39551484	+	1	NA	exon (NM_008054, exon 13 of 14)	exon (NM_008054, exon 13 of 14)	-61463	NM_134000	103213	Mm.436686	NM_134000	ENSMUSG00000019842	Traf3ip2	AI429613|Act1|CIKS	TRAF3 interacting protein 2	protein-coding
mm_2300.1	chr1	91528033	91528036	+	1	NA	3' UTR (NM_028718, exon 15 of 15)	3' UTR (NM_028718, exon 15 of 15)	-12531	NM_001039126	65247	Mm.234152	NM_023046	ENSMUSG00000026311	Asb1	1700029O08Rik|1700054C17Rik|AI426616|AI851378|mKIAA1146	ankyrin repeat and SOCS box-containing 1	protein-coding
mm_116804.1	chr13	54106746	54106767	-	1	NA	3' UTR (NM_027324, exon 11 of 11)	3' UTR (NM_027324, exon 11 of 11)	34911	NM_027324	14057	Mm.134191	NM_027324	ENSMUSG00000021474	Sfxn1	2810002O05Rik|A930015P12Rik|f	sideroflexin 1	protein-coding
mm_109317.1	chr12	109561259	109561274	+	1	NA	non-coding (NR_003633, exon 5 of 5)	non-coding (NR_003633, exon 5 of 5)	-2426	NR_030427	791079		NR_030427	ENSMUSG00000076451	Mir770	Mirn770|mir-770|mmu-mir-770	microRNA 770	ncRNA
mm_7960.1	chr1	133930045	133930047	-	1	NA	Intergenic	Intergenic	-8645	NM_054077	116847	Mm.214514	NM_054077	ENSMUSG00000041577	Prelp	7330409J17Rik|SLRR2A	proline arginine-rich end leucine-rich repeat	protein-coding
mm_20340.1	chr2	127656183	127656196	-	1	NA	5' UTR (NM_001171187, exon 1 of 3)	5' UTR (NM_001171187, exon 1 of 3)	506	NM_010762	17153	Mm.39040	NM_010762	ENSMUSG00000027375	Mal	Mpv17|Vip17	myelin and lymphocyte protein, T cell differentiation protein	protein-coding
mm_147761.1	chr18	61353392	61353408	-	1	NA	intron (NM_133249, intron 1 of 11)	RSINE1|SINE|B4	47031	NM_133249	170826	Mm.415302	NM_133249	ENSMUSG00000033871	Ppargc1b	4631412G21Rik|Perc	peroxisome proliferative activated receptor, gamma, coactivator 1 beta	protein-coding
mm_78122.1	chr9	20644793	20644839	+	1	NA	promoter-TSS (NM_001310746)	promoter-TSS (NM_001310746)	-8	NM_001310746	66177	Mm.390165	NM_025401	ENSMUSG00000084786	Ubl5	1110030M22Rik|beacon	ubiquitin-like 5	protein-coding
mm_159734.1	chr5	62813742	62813742	+	1	NA	promoter-TSS (NM_001170705)	promoter-TSS (NM_001170705)	-81	NM_001170705	100322896	Mm.479821	NM_001170705	ENSMUSG00000090326	Dthd1	Gm17384	death domain containing 1	protein-coding
mm_166488.1	chr5	148741850	148741890	+	1	NA	promoter-TSS (NR_028285)	promoter-TSS (NR_028285)	30	NR_028285	70138	Mm.417834	NR_028285	ENSMUSG00000086494	2210417A02Rik	AV081004	RIKEN cDNA 2210417A02 gene	ncRNA
mm_92418.1	chr10	76949312	76949316	-	1	NA	intron (NM_001347216, intron 1 of 15)	L1MB5|LINE|L1	12633	NM_001347216	59093	Mm.272803	NM_021568	ENSMUSG00000001120	Pcbp3	AlphaCP-3	poly(rC) binding protein 3	protein-coding
mm_89651.1	chr10	97479604	97479617	+	1	NA	5' UTR (NM_001190451, exon 1 of 8)	5' UTR (NM_001190451, exon 1 of 8)	110	NM_001190451	13179	Mm.56769	NM_007833	ENSMUSG00000019929	Dcn	DC|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding
mm_99636.1	chr11	105181859	105181892	+	1	NA	promoter-TSS (NR_027956)	promoter-TSS (NR_027956)	348	NM_001294329	24086	Mm.126976	NM_011903	ENSMUSG00000020694	Tlk2	4933403M19Rik|PKU-alpha|PKUalpha|Tlk	tousled-like kinase 2 (Arabidopsis)	protein-coding
mm_85896.1	chr9	111055674	111055687	-	1	NA	exon (NM_017466, exon 2 of 2)	exon (NM_017466, exon 2 of 2)	1564	NM_001302377	54199	Mm.7336	NM_017466	ENSMUSG00000043953	Ccrl2	1810047I05Rik|Ackr5|CCR11|Cmkbr1l2|E01|L-CCR	chemokine (C-C motif) receptor-like 2	protein-coding
mm_46635.1	chr5	108519859	108519875	-	1	NA	3' UTR (NM_007756, exon 4 of 4)	3' UTR (NM_007756, exon 4 of 4)	30160	NM_007756	12889	Mm.5195	NM_007756	ENSMUSG00000033615	Cplx1	921-S	complexin 1	protein-coding
mm_68575.1	chr7	115846081	115846112	-	1	NA	promoter-TSS (NM_001277326)	promoter-TSS (NM_001277326)	44	NM_001277326	20679	Mm.323365	NM_011445	ENSMUSG00000051910	Sox6	AI987981|SOX-LZ	SRY (sex determining region Y)-box 6	protein-coding
mm_47228.1	chr5	121384070	121384117	-	1	NA	5' UTR (NM_001163470, exon 2 of 12)	5' UTR (NM_001163470, exon 2 of 12)	1522	NM_001163470	231712	Mm.20488	NM_172275	ENSMUSG00000042726	Trafd1	1110008K06Rik|Fln29	TRAF type zinc finger domain containing 1	protein-coding
mm_37625.1	chr4	127330548	127330626	-	1	NA	5' UTR (NM_001160012, exon 1 of 2)	5' UTR (NM_001160012, exon 1 of 2)	249	NM_001160012	14620	Mm.90003	NM_008126	ENSMUSG00000042367	Gjb3	Cnx31|Cx31|D4Wsu144e|Gjb-3	gap junction protein, beta 3	protein-coding
mm_132064.1	chr16	30010018	30010020	+	1	NA	intron (NR_033631, intron 1 of 2)	B1F|SINE|Alu	1352	NR_033631	100043102	Mm.30797	NR_033631	ENSMUSG00000097184	4632428C04Rik	Gm4231	RIKEN cDNA 4632428C04 gene	ncRNA
mm_15389.1	chr2	156721038	156721055	+	1	NA	promoter-TSS (NM_001042488)	promoter-TSS (NM_001042488)	81	NM_001042488	228836	Mm.22094	NM_146128	ENSMUSG00000061689	Dlgap4	AI225853|BC024558|DAP-4|DAP4|SAPAP-4|Sapap4|WBP16	discs, large homolog-associated protein 4 (Drosophila)	protein-coding
mm_134949.1	chr16	31300442	31300459	-	1	NA	exon (NM_007470, exon 5 of 6)	exon (NM_007470, exon 5 of 6)	14358	NM_001301353	11815	Mm.2082	NM_007470	ENSMUSG00000022548	Apod	-	apolipoprotein D	protein-coding
mm_78306.1	chr9	22655105	22655128	+	1	NA	intron (NM_178415, intron 15 of 22)	intron (NM_178415, intron 15 of 22)	179401	NM_178415	319845	Mm.176725	NM_178415	ENSMUSG00000035919	Bbs9	E130103I17Rik	Bardet-Biedl syndrome 9 (human)	protein-coding
mm_172827.1	chr9	17785820	17785830	-	1	NA	Intergenic	Intergenic	-506442	NM_025844	66917	Mm.103534	NM_025844	ENSMUSG00000001774	Chordc1	1110001O09Rik|AA409036|Chp-1|morgana	cysteine and histidine-rich domain (CHORD)-containing, zinc-binding protein 1	protein-coding
mm_156997.1	chrX	7564281	7564292	-	1	NA	exon (NM_001290574, exon 2 of 4)	exon (NM_001290574, exon 2 of 4)	-9314	NR_029473	78185	Mm.160055	NR_029473	ENSMUSG00000039545	Ppp1r3fos	4930524L23Rik	protein phosphatase 1, regulatory subunit 3F, opposite strand	ncRNA
mm_30873.1	chr4	32238471	32238493	+	1	NA	Intergenic	CpG	-178953	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_124317.1	chr14	103346350	103346365	-	1	NA	exon (NM_207215, exon 1 of 85)	exon (NM_207215, exon 1 of 85)	443	NM_207215	105689	Mm.6478	NM_207215	ENSMUSG00000033004	Mycbp2	AU023734|AW107953|AW546647|C130061D10Rik|Pam|Phr1|R75243	MYC binding protein 2	protein-coding
mm_158757.1	chrX	166478629	166478653	-	1	NA	intron (NM_019773, intron 1 of 2)	intron (NM_019773, intron 1 of 2)	1226	NM_019773	56382	Mm.25306	NM_019773	ENSMUSG00000079316	Rab9	2410064E05Rik|AI195561|Rab9a|Sid6061p	RAB9, member RAS oncogene family	protein-coding
mm_160465.1	chr8	110846478	110846478	+	1	NA	promoter-TSS (NM_133973)	promoter-TSS (NM_133973)	-122	NM_001310607	102339	Mm.272930	NM_133973	ENSMUSG00000031753	Cog4	AW554810|D8Ertd515e	component of oligomeric golgi complex 4	protein-coding
mm_37114.1	chr4	116650468	116650487	-	1	NA	intron (NM_021473, intron 1 of 8)	intron (NM_021473, intron 1 of 8)	1197	NM_021473	58810	Mm.30085	NM_021473	ENSMUSG00000028692	Akr1a1	2610201A18Rik|Akr1a4	aldo-keto reductase family 1, member A1 (aldehyde reductase)	protein-coding
mm_90882.1	chr10	9811993	9812034	-	1	NA	exon (NM_001081344, exon 13 of 26)	exon (NM_001081344, exon 13 of 26)	89027	NM_001081344	78808	Mm.331751	NM_030191	ENSMUSG00000019790	Stxbp5	0710001E20Rik|4930565N16Rik|AW742610|LGL3|mKIAA1006	syntaxin binding protein 5 (tomosyn)	protein-coding
mm_129178.1	chr15	76280950	76280955	-	1	NA	intron (NM_028852, intron 1 of 4)	ORR1D1|LTR|ERVL-MaLR	-11113	NR_045747	100038659	Mm.448549	NR_045747		Mirt2	ENSMUSG00000075583|Gm10872|Gm24562	myocardial infraction associated transcript 2	ncRNA
mm_26984.1	chr3	25685335	25685355	-	1	NA	intron (NM_001163387, intron 3 of 5)	intron (NM_001163387, intron 3 of 5)	467962	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_46066.1	chr5	92278189	92278204	-	1	NA	promoter-TSS (NM_001163687)	promoter-TSS (NM_001163687)	-15	NM_025972	67111	Mm.28890	NM_025972	ENSMUSG00000029413	Naaa	2210023K21Rik|3830414F09Rik|Asahl	N-acylethanolamine acid amidase	protein-coding
mm_38300.1	chr4	136896280	136896283	-	1	NA	exon (NM_007572, exon 3 of 3)	exon (NM_007572, exon 3 of 3)	2563	NM_007572	12259	Mm.439957	NM_007572	ENSMUSG00000036887	C1qa	AI255395|C1q	complement component 1, q subcomponent, alpha polypeptide	protein-coding
mm_67012.1	chr7	65370909	65370948	-	1	NA	5' UTR (NM_001163574, exon 1 of 27)	5' UTR (NM_001163574, exon 1 of 27)	316	NM_001163574	21872	Mm.4342	NM_009386	ENSMUSG00000030516	Tjp1	ZO1	tight junction protein 1	protein-coding
mm_78474.1	chr9	32679767	32679782	+	1	NA	Intergenic	L1MB8|LINE|L1	-16268	NM_011808	23871	Mm.292415	NM_011808	ENSMUSG00000032035	Ets1	AI196000|AI448617|D230050P06|Ets-1|Tpl1|vs	E26 avian leukemia oncogene 1, 5' domain	protein-coding
mm_93469.1	chr10	111134642	111134651	-	1	NA	Intergenic	B1_Mur2|SINE|Alu	-30156	NM_001003717	237542	Mm.220204	NM_175489	ENSMUSG00000020189	Osbpl8	AA536976|AA536995|C730029P18Rik|D330025H14Rik|ORP-8	oxysterol binding protein-like 8	protein-coding
mm_66664.1	chr7	45717620	45717676	-	1	NA	promoter-TSS (NM_009077)	promoter-TSS (NM_009077)	354	NM_203280	56632	Mm.24222	NM_020011	ENSMUSG00000057342	Sphk2	C76851	sphingosine kinase 2	protein-coding
mm_1445.1	chr1	67229411	67229428	+	1	NA	exon (NM_001080809, exon 37 of 38)	exon (NM_001080809, exon 37 of 38)	106392	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_72887.1	chr8	89776430	89776432	+	1	NA	Intergenic	Intergenic	571821	NM_172913	244579	Mm.302755	NM_172913	ENSMUSG00000043668	Tox3	500-9|BC052044|C230068E13|CAGF9|Tnrc9	TOX high mobility group box family member 3	protein-coding
mm_94020.1	chr10	127666674	127666746	-	1	NA	promoter-TSS (NM_008668)	promoter-TSS (NM_008668)	-7	NM_008668	17937	Mm.336898	NM_008668	ENSMUSG00000025402	Nab2	AI451907	Ngfi-A binding protein 2	protein-coding
mm_34665.1	chr4	150868283	150868300	+	1	NA	3' UTR (NM_133753, exon 4 of 4)	3' UTR (NM_133753, exon 4 of 4)	13200	NM_133753	74155	Mm.318841	NM_133753	ENSMUSG00000028967	Errfi1	1300002F13Rik|AI788755|Mig-6|Mig6|RALT	ERBB receptor feedback inhibitor 1	protein-coding
mm_136723.1	chr17	8236032	8236046	+	1	NA	promoter-TSS (NM_001190333)	promoter-TSS (NM_001190333)	-4	NM_001190333	12458	Mm.8007	NM_009835	ENSMUSG00000040899	Ccr6	CC-CKR-6|CCR-6|Cmkbr6|KY411	chemokine (C-C motif) receptor 6	protein-coding
mm_88540.1	chr10	78465437	78465476	+	1	NA	promoter-TSS (NM_172134)	promoter-TSS (NM_172134)	-508	NM_172134	216134	Mm.206159	NM_172134	ENSMUSG00000032788	Pdxk	2310036D04Rik|AA119688|C77999	pyridoxal (pyridoxine, vitamin B6) kinase	protein-coding
mm_16528.1	chr2	181543426	181543432	+	1	NA	intron (NM_001271585, intron 2 of 5)	PB1D7|SINE|Alu	22944	NM_001271584	13002	Mm.140761	NM_016775	ENSMUSG00000000826	Dnajc5	2610314I24Rik|AU018536|Csp	DnaJ heat shock protein family (Hsp40) member C5	protein-coding
mm_82668.1	chr9	22130142	22130147	-	1	NA	intron (NM_001102405, intron 1 of 4)	intron (NM_001102405, intron 1 of 4)	454	NM_007388	11433	Mm.46354	NM_007388	ENSMUSG00000001348	Acp5	TRACP|TRAP	acid phosphatase 5, tartrate resistant	protein-coding
mm_72517.1	chr8	83955668	83955676	+	1	NA	promoter-TSS (NM_024184)	promoter-TSS (NM_024184)	-22	NM_024184	66929	Mm.29680	NM_024184	ENSMUSG00000005470	Asf1b	1700003K02Rik|AA409591	anti-silencing function 1B histone chaperone	protein-coding
mm_114016.1	chr13	52617376	52617385	+	1	NA	intron (NM_001198977, intron 3 of 13)	intron (NM_001198977, intron 3 of 13)	20498	NM_011518	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_32951.1	chr4	119619280	119619292	+	1	NA	exon (NM_001290696, exon 7 of 12)	exon (NM_001290696, exon 7 of 12)	-18446	NM_008190	14915	Mm.2614	NM_008190	ENSMUSG00000023247	Guca2a	Guca2	guanylate cyclase activator 2a (guanylin)	protein-coding
mm_92431.1	chr10	77113929	77113993	-	1	NA	promoter-TSS (NM_001109991)	promoter-TSS (NM_001109991)	-256	NM_001109991	12822	Mm.4352	NM_009929	ENSMUSG00000001435	Col18a1	-	collagen, type XVIII, alpha 1	protein-coding
mm_146127.1	chr18	74517195	74517200	+	1	NA	intron (NR_045368, intron 3 of 3)	L1MEc|LINE|L1	13927	NR_045368	73606	Mm.444734	NR_045368		1700120E14Rik	-	RIKEN cDNA 1700120E14 gene	ncRNA
mm_3522.1	chr1	150107799	150107809	+	1	NA	3' UTR (NM_011198, exon 10 of 10)	3' UTR (NM_011198, exon 10 of 10)	7773	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_4463.1	chr1	172990316	172990337	+	1	NA	Intergenic	Intergenic	33558	NM_008763	18313	Mm.377103	NM_008763	ENSMUSG00000037924	Olfr16	MOR23|MOR26713	olfactory receptor 16	protein-coding
mm_113873.1	chr13	48662990	48663046	+	1	NA	promoter-TSS (NM_007526)	promoter-TSS (NM_007526)	-18	NM_007526	12022	Mm.42241	NM_007526	ENSMUSG00000021381	Barx1	-	BarH-like homeobox 1	protein-coding
mm_51020.1	chr6	65042709	65042719	+	1	NA	promoter-TSS (NM_007958)	promoter-TSS (NM_007958)	47	NM_007958	13990	Mm.99113	NM_007958	ENSMUSG00000029920	Smarcad1	AV081750|AW226546|D6Pas1|Etl1|mKIAA1122	SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1	protein-coding
mm_80039.1	chr9	68969144	68969160	+	1	NA	intron (NM_013646, intron 1 of 10)	MTE2b|LTR|ERVL-MaLR	203806	NR_033299	320440	Mm.483129	NM_177159		9530091C08Rik	-	RIKEN cDNA 9530091C08 gene	ncRNA
mm_135084.1	chr16	34514085	34514128	-	1	NA	promoter-TSS (NM_177357)	promoter-TSS (NM_177357)	-79	NM_177357	545156	Mm.82274	NM_177357	ENSMUSG00000061751	Kalrn	2210407G14Rik|AV235988|DUET|E530005C20Rik|Gm539|Hapip|TRAD	kalirin, RhoGEF kinase	protein-coding
mm_81683.1	chr9	111118071	111118183	+	1	NA	promoter-TSS (NM_001164838)	promoter-TSS (NM_001164838)	16	NM_001164838	71268	Mm.302287	NM_027742	ENSMUSG00000032497	Lrrfip2	5133400F20Rik|AI850587	leucine rich repeat (in FLII) interacting protein 2	protein-coding
mm_17525.1	chr2	29252963	29252997	-	1	NA	promoter-TSS (NR_029460)	promoter-TSS (NR_029460)	13	NR_029460	76220	Mm.330108	NR_029460	ENSMUSG00000079499	6530402F18Rik	mKIAA1857	RIKEN cDNA 6530402F18 gene	ncRNA
mm_36627.1	chr4	91376363	91376377	-	1	NA	5' UTR (NM_001177883, exon 1 of 7)	5' UTR (NM_001177883, exon 1 of 7)	121	NM_001347149	15569	Mm.318042	NM_010486	ENSMUSG00000008489	Elavl2	Hub|mel-N1	ELAV (embryonic lethal, abnormal vision, Drosophila)-like 2 (Hu antigen B)	protein-coding
mm_136227.1	chr16	90265002	90265005	-	1	NA	intron (NM_178923, intron 1 of 19)	intron (NM_178923, intron 1 of 19)	19500	NM_178923	224432	Mm.439811	NM_178923	ENSMUSG00000022983	Scaf4	AA517739|Sfrs15|Sra4|Srsf15	SR-related CTD-associated factor 4	protein-coding
mm_117966.1	chr13	99585665	99585667	-	1	NA	Intergenic	Intergenic	-69064	NM_008634	17755	Mm.4173	NM_008634	ENSMUSG00000052727	Map1b	A230055D22|AI843217|LC1|MAP5|Mtap-5|Mtap1b|Mtap5	microtubule-associated protein 1B	protein-coding
mm_110556.1	chr12	55491489	55491498	-	1	NA	TTS (NR_035430)	TTS (NR_035430)	1154	NM_010907	18035	Mm.170515	NM_010907	ENSMUSG00000021025	Nfkbia	AI462015|Nfkbi	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, alpha	protein-coding
mm_141282.1	chr17	27909111	27909146	-	1	NA	promoter-TSS (NM_001286041)	promoter-TSS (NM_001286041)	-178	NM_001286040	224650	Mm.32556	NM_181413	ENSMUSG00000024219	Anks1	Anks1a|mKIAA0229	ankyrin repeat and SAM domain containing 1	protein-coding
mm_172034.1	chr6	125113974	125113979	+	1	NA	exon (NM_145979, exon 24 of 39)	exon (NM_145979, exon 24 of 39)	16952	NR_106012	102466272		NR_106012	ENSMUSG00000098762	Mir7045	Gm27758|mmu-mir-7045	microRNA 7045	ncRNA
mm_34107.1	chr4	139192943	139192960	+	1	NA	promoter-TSS (NM_009798)	promoter-TSS (NM_009798)	52	NM_001037761	12345	Mm.2945	NM_009798	ENSMUSG00000028745	Capzb	1700120C01Rik|AI325129|CPB1|CPB2|CPbeat2|CPbeta1|CPbeta2|Cappb1	capping protein (actin filament) muscle Z-line, beta	protein-coding
mm_104001.1	chr11	84871735	84871738	-	1	NA	promoter-TSS (NM_153144)	promoter-TSS (NM_153144)	813	NR_131197	102635561	Mm.341797	NR_131197		Ggnbp2os	-	gametogenetin binding protein 2, opposite strand	ncRNA
mm_153854.1	chr19	46379474	46379477	-	1	NA	intron (NM_016860, intron 8 of 10)	intron (NM_016860, intron 8 of 10)	16260	NM_016860	54130	Mm.3118	NM_016860	ENSMUSG00000025228	Actr1a	Arp1|alpha-Arp1	ARP1 actin-related protein 1A, centractin alpha	protein-coding
mm_109081.1	chr12	104413604	104413616	+	1	NA	3' UTR (NM_009252, exon 5 of 5)	3' UTR (NM_009252, exon 5 of 5)	6902	NM_009252	20716	Mm.482074	NM_009252	ENSMUSG00000021091	Serpina3n	Spi2-2|Spi2.2|Spi2/eb.4	serine (or cysteine) peptidase inhibitor, clade A, member 3N	protein-coding
mm_72941.1	chr8	91619228	91619230	+	1	NA	intron (NM_011936, intron 8 of 8)	intron (NM_011936, intron 8 of 8)	182425	NM_001253822	16373	Mm.238044	NM_008393	ENSMUSG00000031734	Irx3	AI894186	Iroquois related homeobox 3	protein-coding
mm_22049.1	chr2	168262833	168262866	-	1	NA	exon (NM_001081134, exon 2 of 2)	exon (NM_001081134, exon 2 of 2)	6482	NM_001081134	241794	Mm.425102	NM_001081134	ENSMUSG00000074575	Kcng1	AW536275|OTTMUSG00000016048	potassium voltage-gated channel, subfamily G, member 1	protein-coding
mm_54580.1	chr6	38124478	38124499	-	1	NA	promoter-TSS (NM_080467)	promoter-TSS (NM_080467)	98	NM_080467	140494	Mm.462308	NM_080467	ENSMUSG00000038600	Atp6v0a4	Atp6n1b|a4	ATPase, H+ transporting, lysosomal V0 subunit A4	protein-coding
mm_74615.1	chr8	12672136	12672146	-	1	NA	promoter-TSS (NM_198031)	promoter-TSS (NM_198031)	-41	NM_198031	259279	Mm.142095	NM_198031	ENSMUSG00000000759	Tubgcp3	GCP3|Spc98p	tubulin, gamma complex associated protein 3	protein-coding
mm_73722.1	chr8	112018843	112018868	+	1	NA	3' UTR (NM_020584, exon 3 of 3)	3' UTR (NM_020584, exon 3 of 3)	7496	NM_020584	57321	Mm.213064	NM_020584	ENSMUSG00000033430	Terf2ip	Rap1	telomeric repeat binding factor 2, interacting protein	protein-coding
mm_102456.1	chr11	59839240	59839259	-	1	NA	intron (NM_011991, intron 1 of 11)	CpG	518	NM_011991	26572	Mm.40	NM_011991	ENSMUSG00000019373	Cops3	Csn3|Sgn3	COP9 signalosome subunit 3	protein-coding
mm_55888.1	chr6	83536001	83536015	-	1	NA	intron (NM_009610, intron 1 of 8)	intron (NM_009610, intron 1 of 8)	243	NM_009610	11468	Mm.292865	NM_009610	ENSMUSG00000059430	Actg2	ACTA3|Act-4|Act4|SMGA	actin, gamma 2, smooth muscle, enteric	protein-coding
mm_138675.1	chr17	35915688	35915698	+	1	NA	intron (NM_025878, intron 1 of 6)	intron (NM_025878, intron 1 of 6)	676	NM_025878	66973	Mm.29484	NM_025878	ENSMUSG00000024436	Mrps18b	2400002C15Rik	mitochondrial ribosomal protein S18B	protein-coding
mm_46119.1	chr5	92435115	92435130	-	1	NA	promoter-TSS (NM_183392)	promoter-TSS (NM_183392)	77	NM_183392	269113	Mm.275289	NM_183392	ENSMUSG00000034826	Nup54	3110079L04Rik|54kDa	nucleoporin 54	protein-coding
mm_105168.1	chr11	101784286	101784318	-	1	NA	exon (NM_001316366, exon 3 of 13)	exon (NM_001316366, exon 3 of 13)	1008	NM_008815	18612	Mm.5025	NM_008815	ENSMUSG00000017724	Etv4	AW414408|Pea-3|Pea3	ets variant 4	protein-coding
mm_14998.1	chr2	152427613	152427638	+	1	NA	non-coding (NR_110368, exon 2 of 11)	non-coding (NR_110368, exon 2 of 11)	12038	NR_110368	228778	Mm.70959	NM_177656	ENSMUSG00000032680	6820408C15Rik	-	RIKEN cDNA 6820408C15 gene	protein-coding
mm_161531.1	chr15	102204342	102204342	+	1	NA	promoter-TSS (NM_001289690)	promoter-TSS (NM_001289690)	-229	NM_001289690	68744	Mm.352945	NM_153194	ENSMUSG00000046897	Zfp740	1110034O07Rik|AW548228|Znf740	zinc finger protein 740	protein-coding
mm_90307.1	chr10	126979150	126979193	+	1	NA	5' UTR (NM_001113470, exon 1 of 8)	5' UTR (NM_001113470, exon 1 of 8)	454	NM_001113470	52468	Mm.29490	NM_146012	ENSMUSG00000078429	Ctdsp2	AI586070|D10Ertd73e|OS-4|OS4|SCP2	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 2	protein-coding
mm_136448.1	chr16	94995055	94995066	-	1	NA	intron (NM_001025584, intron 1 of 4)	intron (NM_001025584, intron 1 of 4)	2636	NM_001025584	16522	Mm.328720	NM_010606	ENSMUSG00000043301	Kcnj6	BIR1|GIRK2|KATP2|KCNJ7|Kir3.2|weaver|wv	potassium inwardly-rectifying channel, subfamily J, member 6	protein-coding
mm_78328.1	chr9	25252201	25252233	+	1	NA	promoter-TSS (NM_001205367)	promoter-TSS (NM_001205367)	-222	NM_009859	235072	Mm.270259	NM_009859	ENSMUSG00000001833	Sept7	Cdc10|E430034N22	septin 7	protein-coding
mm_134062.1	chr16	8425105	8425144	-	1	NA	promoter-TSS (NM_029070)	promoter-TSS (NM_029070)	12	NM_029070	74720	Mm.159318	NM_029070	ENSMUSG00000022715	Tmem114	4930511J11Rik|Cldn26	transmembrane protein 114	protein-coding
mm_76415.1	chr8	84966009	84966091	-	1	NA	promoter-TSS (NM_027187)	promoter-TSS (NM_027187)	-39	NM_027187	69724	Mm.182470	NM_027187	ENSMUSG00000052926	Rnaseh2a	2400006P09Rik|RNASEHI|RNHIA|RNHL	ribonuclease H2, large subunit	protein-coding
mm_130386.1	chr15	97858894	97858903	-	1	NA	exon (NM_009504, exon 9 of 10)	exon (NM_009504, exon 9 of 10)	-14396	NM_001204278	56233	Mm.384027	NM_019572	ENSMUSG00000022475	Hdac7	5830434K02Rik|HD7|HD7a|Hdac7a|mFLJ00062	histone deacetylase 7	protein-coding
mm_172344.1	chr7	11166172	11166184	-	1	NA	promoter-TSS (NM_001100186)	promoter-TSS (NM_001100186)	-30	NM_001100186	545913	Mm.380086	NM_001100186	ENSMUSG00000090714	Zscan4d	EG545913	zinc finger and SCAN domain containing 4D	protein-coding
mm_338.1	chr1	30284712	30284715	+	1	NA	Intergenic	RLTR13C2|LTR|ERVK	578543	NM_001081080	213109	Mm.194486	NM_025871	ENSMUSG00000048874	Phf3	2310061N19Rik|mKIAA0244	PHD finger protein 3	protein-coding
mm_18282.1	chr2	52470998	52471011	-	1	NA	intron (NM_001285426, intron 4 of 13)	L1Md_F2|LINE|L1	-46130	NM_182994	75423	Mm.314378	NM_182994	ENSMUSG00000036093	Arl5a	2410015N24Rik|2810410P22Rik|AA408731|AW610751|Arl5|T25534	ADP-ribosylation factor-like 5A	protein-coding
mm_74253.1	chr8	124862648	124862656	+	1	NA	promoter-TSS (NM_010322)	promoter-TSS (NM_010322)	377	NM_025615	66523	Mm.436864	NM_025615	ENSMUSG00000031984	2810004N23Rik	3110004G14Rik|Ayu21-55|Gt(pU21)55Imeg|GtAyu21-55	RIKEN cDNA 2810004N23 gene	protein-coding
mm_109093.1	chr12	104820280	104820324	+	1	NA	intron (NM_001040682, intron 1 of 12)	intron (NM_001040682, intron 1 of 12)	44774	NR_104436	94040	Mm.244078	NM_053155	ENSMUSG00000021097	Clmn	9330188N17Rik|AI428889|AI788815|mKIAA1188	calmin	protein-coding
mm_6744.1	chr1	83277229	83277242	-	1	NA	exon (NM_172430, exon 7 of 11)	exon (NM_172430, exon 7 of 11)	117473	NM_027725	71227	Mm.256482	NM_027725	ENSMUSG00000053161	Daw1	4930563E19Rik|4933429D11Rik|Wdr69|b2b1116Clo|b2b1584Clo	dynein assembly factor with WDR repeat domains 1	protein-coding
mm_2080.1	chr1	87674203	87674214	+	1	NA	intron (NM_010566, intron 5 of 26)	RLTR41|LTR|ERV1	53896	NM_001110193	16331	Mm.15105	NM_010566	ENSMUSG00000026288	Inpp5d	SHIP|SHIP-1|SHIP1|SIP-145|p150Ship|s-SHIP	inositol polyphosphate-5-phosphatase D	protein-coding
mm_40707.1	chr5	65863269	65863294	+	1	NA	promoter-TSS (NM_001081105)	promoter-TSS (NM_001081105)	-288	NM_001081105	74734	Mm.20323	NM_001081105	ENSMUSG00000029204	Rhoh	5830400A04Rik|AU019774|Arhh	ras homolog family member H	protein-coding
mm_45689.1	chr5	77381120	77381124	-	1	NA	intron (NM_008048, intron 1 of 4)	intron (NM_008048, intron 1 of 4)	26923	NM_001159518	29817	Mm.233470	NM_008048	ENSMUSG00000036256	Igfbp7	AGM|Fstl2|Mac25	insulin-like growth factor binding protein 7	protein-coding
mm_40031.1	chr5	33629950	33629964	+	1	NA	promoter-TSS (NM_178390)	promoter-TSS (NM_178390)	-322	NM_178390	74504	Mm.294695	NM_178390	ENSMUSG00000037339	Fam53a	2410018C17Rik|5430419M09Rik|Dntnp	family with sequence similarity 53, member A	protein-coding
mm_89454.1	chr10	93160825	93160894	+	1	NA	promoter-TSS (NM_146239)	promoter-TSS (NM_146239)	-17	NM_146239	237459	Mm.217404	NM_146239	ENSMUSG00000020015	Cdk17	6430598J10Rik|Pctk2	cyclin-dependent kinase 17	protein-coding
mm_84975.1	chr9	85327111	85327128	-	1	NA	promoter-TSS (NM_001160378)	promoter-TSS (NM_001160378)	5	NM_001160378	212943	Mm.74610	NM_001160378	ENSMUSG00000032265	Fam46a	BAP014|D930050G01Rik	family with sequence similarity 46, member A	protein-coding
mm_56456.1	chr6	97993159	97993203	-	1	NA	exon (NM_001178049, exon 3 of 10)	exon (NM_001178049, exon 3 of 10)	1398	NM_008601	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_59293.1	chr7	25077345	25077363	+	1	NA	5' UTR (NM_001168506, exon 1 of 2)	5' UTR (NM_001168506, exon 1 of 2)	108	NM_175477	232976	Mm.41568	NM_175477	ENSMUSG00000045252	Zfp574	A630056B21Rik|Znf574	zinc finger protein 574	protein-coding
mm_118522.1	chr14	14718776	14718789	+	1	NA	intron (NM_001033270, intron 1 of 24)	intron (NM_001033270, intron 1 of 24)	15757	NM_001033270	218756	Mm.258893	NM_001033270	ENSMUSG00000021733	Slc4a7	E430014N10Rik|NBC3|NBCn1|NBCn1-G	solute carrier family 4, sodium bicarbonate cotransporter, member 7	protein-coding
mm_1199.1	chr1	62709037	62709049	+	1	NA	intron (NM_001077405, intron 1 of 15)	intron (NM_001077405, intron 1 of 15)	5726	NM_001077405	18187	Mm.266341	NM_010939	ENSMUSG00000025969	Nrp2	1110048P06Rik|Np-2|Np2|Npn-2|Npn2	neuropilin 2	protein-coding
mm_68462.1	chr7	110293464	110293467	-	1	NA	Intergenic	Intergenic	71762	NM_009302	20947	Mm.334144	NM_009302	ENSMUSG00000031015	Swap70	70kDa|AV235546	SWA-70 protein	protein-coding
mm_5520.1	chr1	37719783	37719899	-	1	NA	promoter-TSS (NM_028096)	promoter-TSS (NM_028096)	-30	NM_028096	72097	Mm.142607	NM_028096	ENSMUSG00000026090	2010300C02Rik	-	RIKEN cDNA 2010300C02 gene	protein-coding
mm_46162.1	chr5	96162585	96162595	-	1	NA	promoter-TSS (NM_178854)	promoter-TSS (NM_178854)	-600	NM_144910	231464	Mm.28374	NM_144910	ENSMUSG00000034724	Cnot6l	4932442K20Rik	CCR4-NOT transcription complex, subunit 6-like	protein-coding
mm_48871.1	chr5	150594472	150594488	-	1	NA	promoter-TSS (NM_133898)	promoter-TSS (NM_133898)	45	NM_133898	100637	Mm.279932	NM_133898	ENSMUSG00000041132	N4bp2l1	2410024N18Rik|AI428195|B230342M21Rik	NEDD4 binding protein 2-like 1	protein-coding
mm_139847.1	chr17	69383351	69383394	+	1	NA	promoter-TSS (NM_009547)	promoter-TSS (NM_009547)	-606	NM_009547	22666	Mm.29434	NM_009547	ENSMUSG00000049672	Zbtb14	ZF5|Zfp161|b2b1982Clo	zinc finger and BTB domain containing 14	protein-coding
mm_110926.1	chr12	76369521	76369585	-	1	NA	promoter-TSS (NM_001172104)	promoter-TSS (NM_001172104)	7	NM_028356	109929	Mm.41880	NM_028356	ENSMUSG00000056459	Zbtb25	2810462M08Rik|2900064P18Rik|AI842128|Kup|Zfp-50|Zfp50	zinc finger and BTB domain containing 25	protein-coding
mm_101403.1	chr11	26593946	26593965	-	1	NA	promoter-TSS (NM_027260)	promoter-TSS (NM_027260)	-35	NM_001252447	69922	Mm.285351	NM_027260	ENSMUSG00000064090	Vrk2	2810003O05Rik|AI447698	vaccinia related kinase 2	protein-coding
mm_113530.1	chr13	37826905	37826949	+	1	NA	promoter-TSS (NM_001039188)	promoter-TSS (NM_001039188)	15	NR_033615	68750	Mm.491109	NM_026830	ENSMUSG00000039087	Rreb1	1110037N09Rik|AA414966|B930013M22Rik	ras responsive element binding protein 1	protein-coding
mm_150388.1	chr19	36349577	36349584	+	1	NA	Intergenic	Intergenic	-29487	NM_029508	76073	Mm.259180	NM_029508	ENSMUSG00000024805	Pcgf5	0610009F02Rik|1110054A01Rik|5830406C17Rik|5830443C21Rik|9530023M17Rik|AI324127	polycomb group ring finger 5	protein-coding
mm_142640.1	chr17	47433265	47433267	-	1	NA	intron (NM_029296, intron 3 of 3)	AT_rich|Low_complexity|Low_complexity	-3373	NM_145489	224833	Mm.218444	NM_145489	ENSMUSG00000034382	AI661453	-	expressed sequence AI661453	protein-coding
mm_171280.1	chr3	88835248	88835250	+	1	NA	promoter-TSS (NM_027389)	promoter-TSS (NM_027389)	18	NM_001242372	76022	Mm.126870	NM_027389	ENSMUSG00000054199	Gon4l	1500041I23Rik|2610100B20Rik|3632445O20Rik|5430404N14Rik|AA387005	gon-4-like (C.elegans)	protein-coding
mm_37063.1	chr4	116056335	116056351	-	1	NA	Intergenic	MERV1_LTR|LTR|ERV1	-2467	NM_028142	72181	Mm.282560	NM_028142	ENSMUSG00000028706	Nsun4	2310010O12Rik|2810405F18Rik|AI507900|Shtap	NOL1/NOP2/Sun domain family, member 4	protein-coding
mm_165485.1	chr2	164333593	164333600	+	1	NA	exon (NM_009301, exon 2 of 3)	exon (NM_009301, exon 2 of 3)	831	NM_009301	20944	Mm.140154	NM_009301	ENSMUSG00000017004	Svs5	BB115186|Semg1|Svp-1|Svp1|Svp5	seminal vesicle secretory protein 5	protein-coding
mm_63081.1	chr7	122288701	122288721	+	1	NA	promoter-TSS (NM_008855)	promoter-TSS (NM_008855)	-414	NM_001316672	18751	Mm.207496	NM_008855	ENSMUSG00000052889	Prkcb	PKC-B|PKC-Beta|Pkcb|Prkcb1|Prkcb2	protein kinase C, beta	protein-coding
mm_152880.1	chr19	24527449	24527452	-	1	NA	intron (NM_008846, intron 1 of 14)	intron (NM_008846, intron 1 of 14)	28377	NM_008846	18719	Mm.217214	NM_008846	ENSMUSG00000024867	Pip5k1b	PI4P5K-I[b]|PIP5K1-beta|PIP5KIbeta|Pipk5b|STM7	phosphatidylinositol-4-phosphate 5-kinase, type 1 beta	protein-coding
mm_23021.1	chr3	34599810	34599816	+	1	NA	intron (NR_015580, intron 2 of 4)	intron (NR_015580, intron 2 of 4)	-38651	NR_035433	100316679		NR_035433	ENSMUSG00000104797	Mir1897	Mirn1897|mmu-mir-1897	microRNA 1897	ncRNA
mm_89400.1	chr10	90576472	90576483	+	1	NA	promoter-TSS (NM_181398)	promoter-TSS (NM_181398)	-214	NM_001177396	77531	Mm.440605	NM_181398	ENSMUSG00000058589	Anks1b	AIDA-1b|C030032C09Rik|E530015N03Rik|ENSMUSG00000078431|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding
mm_7438.1	chr1	120067953	120067966	-	1	NA	exon (NM_019432, exon 2 of 2)	exon (NM_019432, exon 2 of 2)	5821	NM_019432	170706	Mm.24750	NM_019432	ENSMUSG00000050777	Tmem37	AI173373|AW540203|Pr|Pr1	transmembrane protein 37	protein-coding
mm_27077.1	chr3	28816265	28816275	-	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	10759	NM_026517	68028	Mm.371630	NM_026517	ENSMUSG00000039221	Rpl22l1	3110001N18Rik|AU041196	ribosomal protein L22 like 1	protein-coding
mm_157960.1	chrX	88115904	88115928	-	1	NA	promoter-TSS (NM_001160403)	promoter-TSS (NM_001160403)	-293	NM_001160403	331461	Mm.121680	NM_001160403	ENSMUSG00000052372	Il1rapl1	6330532G10Rik|C030039N24|IL1R8|IL1RAPL|MRX34|OPHN4|TIGIRR-2	interleukin 1 receptor accessory protein-like 1	protein-coding
mm_132844.1	chr16	46006512	46006553	+	1	NA	intron (NM_001134480, intron 1 of 3)	intron (NM_001134480, intron 1 of 3)	3881	NM_001134480	433022	Mm.380993	NM_001134480	ENSMUSG00000087141	Plcxd2	AW494639|EG433022	phosphatidylinositol-specific phospholipase C, X domain containing 2	protein-coding
mm_87298.1	chr10	42534810	42534828	+	1	NA	3' UTR (NM_017472, exon 4 of 4)	3' UTR (NM_017472, exon 4 of 4)	32765	NM_017472	54198	Mm.277870	NM_017472	ENSMUSG00000019804	Snx3	SDP3	sorting nexin 3	protein-coding
mm_53163.1	chr6	125321410	125321420	+	1	NA	promoter-TSS (NM_011324)	promoter-TSS (NM_011324)	75	NM_011324	20276	Mm.144114	NM_011324	ENSMUSG00000030340	Scnn1a	ENaC|SCNEA|Scnn1|mENaC	sodium channel, nonvoltage-gated 1 alpha	protein-coding
mm_158809.1	chrX	167304811	167304821	-	1	NA	TTS (NM_001290758)	TTS (NM_001290758)	25755	NM_001290757	170743	Mm.23979	NM_133211	ENSMUSG00000044583	Tlr7	-	toll-like receptor 7	protein-coding
mm_84976.1	chr9	85327138	85327157	-	1	NA	promoter-TSS (NM_001160378)	promoter-TSS (NM_001160378)	3	NM_001160379	212943	Mm.74610	NM_001160378	ENSMUSG00000032265	Fam46a	BAP014|D930050G01Rik	family with sequence similarity 46, member A	protein-coding
mm_578.1	chr1	39272908	39272911	+	1	NA	intron (NM_008719, intron 2 of 20)	intron (NM_008719, intron 2 of 20)	78637	NM_008719	18143	Mm.2380	NM_008719	ENSMUSG00000026077	Npas2	MOP4|bHLHe9	neuronal PAS domain protein 2	protein-coding
mm_29664.1	chr3	122612222	122612226	-	1	NA	intron (NM_153118, intron 1 of 13)	intron (NM_153118, intron 1 of 13)	7490	NM_001114665	214459	Mm.209491	NM_153118	ENSMUSG00000039735	Fnbp1l	2610318I01Rik|AW548221|TOCA1|toca-1	formin binding protein 1-like	protein-coding
mm_33025.1	chr4	121215292	121215302	+	1	NA	promoter-TSS (NM_001346660)	promoter-TSS (NM_001346660)	-213	NM_001346660	109263	Mm.215745	NM_001081013	ENSMUSG00000049878	Rlf	9230110M18Rik|AI195322|MommeD8	rearranged L-myc fusion sequence	protein-coding
mm_51205.1	chr6	71325838	71325842	+	1	NA	intron (NM_009858, intron 1 of 5)	ID_B1|SINE|B4	3028	NM_009858	12526	Mm.333148	NM_009858	ENSMUSG00000053044	Cd8b1	Cd8b|Ly-3|Ly-C|Lyt-3	CD8 antigen, beta chain 1	protein-coding
mm_166957.1	chr7	44477411	44477419	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	7068	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_138501.1	chr17	35210469	35210509	+	1	NA	Intergenic	Intergenic	-5138	NM_010735	16992	Mm.87787	NM_010735	ENSMUSG00000024402	Lta	LT|LT-[a]|LT-alpha|LT[a]|LTalpha|Ltx|TNF-beta|TNFSF1|Tnfb|Tnfsf1b|Tnlg1e|hlb382	lymphotoxin A	protein-coding
mm_68391.1	chr7	109518966	109519027	-	1	NA	promoter-TSS (NM_011975)	promoter-TSS (NM_011975)	-199	NM_011975	26451	Mm.305750	NM_011975	ENSMUSG00000046364	Rpl27a	L27'|L27A|L29	ribosomal protein L27A	protein-coding
mm_24447.1	chr3	90609380	90609395	+	1	NA	intron (NM_011312, intron 1 of 2)	intron (NM_011312, intron 1 of 2)	865	NM_011312	20199	Mm.19946	NM_011312	ENSMUSG00000001023	S100a5	S100D9	S100 calcium binding protein A5	protein-coding
mm_170415.1	chr18	68692179	68692181	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-47220	NR_105774	102465183		NR_105774	ENSMUSG00000099300	Mir6356	Gm27461|mmu-mir-6356	microRNA 6356	ncRNA
mm_118894.1	chr14	26638013	26638024	+	1	NA	promoter-TSS (NM_007479)	promoter-TSS (NM_007479)	-179	NM_007479	11843	Mm.297768	NM_007479	ENSMUSG00000021877	Arf4	AA407803	ADP-ribosylation factor 4	protein-coding
mm_173189.1	chrX	61258919	61258920	-	1	NA	Intergenic	Intergenic	67626	NR_033502	320247	Mm.447372	NR_033502		C030023E24Rik	-	RIKEN cDNA C030023E24 gene	ncRNA
mm_60051.1	chr7	31060096	31060143	+	1	NA	exon (NM_144556, exon 1 of 9)	exon (NM_144556, exon 1 of 9)	184	NM_144556	243914	Mm.389870	NM_144556	ENSMUSG00000036560	Lgi4	Lgil3|clp	leucine-rich repeat LGI family, member 4	protein-coding
mm_49124.1	chr6	8524170	8524170	+	1	NA	intron (NM_001286728, intron 1 of 7)	intron (NM_001286728, intron 1 of 7)	4112	NM_001286729	170772	Mm.210787	NM_133236	ENSMUSG00000029638	Glcci1	2310047L21Rik|A130036A18Rik|Fam117c|Gig18|Tssn1	glucocorticoid induced transcript 1	protein-coding
mm_23577.1	chr3	63361999	63362024	+	1	NA	exon (NM_008604, exon 18 of 23)	exon (NM_008604, exon 18 of 23)	65916	NM_001289463	17380	Mm.296022	NM_008604	ENSMUSG00000027820	Mme	6030454K05Rik|C85356|CALLA|CD10|NEP|SFE	membrane metallo endopeptidase	protein-coding
mm_27732.1	chr3	69044964	69044974	-	1	NA	promoter-TSS (NM_025863)	promoter-TSS (NM_025863)	-227	NM_025863	66949	Mm.176695	NM_025863	ENSMUSG00000034317	Trim59	2310035M22Rik|2700022F13Rik|Mrf1|TSBF1	tripartite motif-containing 59	protein-coding
mm_60631.1	chr7	44813327	44813340	+	1	NA	exon (NM_030693, exon 3 of 3)	exon (NM_030693, exon 3 of 3)	2325	NM_030693	107503	Mm.389890	NM_030693	ENSMUSG00000038539	Atf5	AFTA|Atf7|Atfx|ODA-10	activating transcription factor 5	protein-coding
mm_5425.1	chr1	34473048	34473058	-	1	NA	intron (NM_011206, intron 13 of 14)	intron (NM_011206, intron 13 of 14)	13307	NM_011206	19253	Mm.361	NM_011206	ENSMUSG00000026126	Ptpn18	FLP1|HSCF|PTP-HSCF|PTP-K1|Ptpk1	protein tyrosine phosphatase, non-receptor type 18	protein-coding
mm_32795.1	chr4	116995376	116995384	+	1	NA	promoter-TSS (NM_009478)	promoter-TSS (NM_009478)	32	NM_175244	76608	Mm.251420	NM_175244	ENSMUSG00000046861	Hectd3	1700064K09Rik|AI467540|AW743312	HECT domain containing 3	protein-coding
mm_154076.1	chr19	56544627	56544672	-	1	NA	exon (NM_018831, exon 3 of 10)	exon (NM_018831, exon 3 of 10)	3573	NM_018831	55947	Mm.2805	NM_018831	ENSMUSG00000025077	Dclre1a	2810043H12Rik|AU022226|Pso2|Smn1a|Snm1|mKIAA0086	DNA cross-link repair 1A	protein-coding
mm_96338.1	chr11	66319754	66319756	+	1	NA	intron (NM_001034874, intron 2 of 4)	intron (NM_001034874, intron 2 of 4)	-151204	NM_001099633	237806	Mm.264210	NM_001099633	ENSMUSG00000056752	Dnah9	9030022M04|A230091C01|C230051G16|D11Ertd686e|Dnahc9|mKIAA0357	dynein, axonemal, heavy chain 9	protein-coding
mm_172516.1	chr7	79790778	79790783	-	1	NA	Intergenic	Intergenic	2810	NM_008588	17292	Mm.1404	NM_008588	ENSMUSG00000030544	Mesp1	bHLHc5	mesoderm posterior 1	protein-coding
mm_50155.1	chr6	41546264	41546306	+	1	NA	Intergenic	Intergenic	24509	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_1774.1	chr1	78310296	78310375	+	1	NA	promoter-TSS (NM_001004173)	promoter-TSS (NM_001004173)	-11	NM_001004173	433323	Mm.276248	NM_001004173	ENSMUSG00000032908	Sgpp2	SPPase2|Spp2	sphingosine-1-phosphate phosphotase 2	protein-coding
mm_88848.1	chr10	80930233	80930240	+	1	NA	5' UTR (NM_008655, exon 1 of 4)	5' UTR (NM_008655, exon 1 of 4)	145	NM_008655	17873	Mm.1360	NM_008655	ENSMUSG00000015312	Gadd45b	AI323528|Myd118	growth arrest and DNA-damage-inducible 45 beta	protein-coding
mm_157078.1	chrX	9256927	9256937	-	1	NA	intron (NM_173414, intron 3 of 4)	intron (NM_173414, intron 3 of 4)	-15852	NM_023500	22439	Mm.56468	NM_023500	ENSMUSG00000015342	Xk	1810038K19Rik|XRG1|Xkh	X-linked Kx blood group	protein-coding
mm_71537.1	chr8	47093758	47093761	+	1	NA	3' UTR (NM_177304, exon 8 of 8)	3' UTR (NM_177304, exon 8 of 8)	106872	NM_177304	320981	Mm.211429	NM_177304	ENSMUSG00000038173	Enpp6	4833421B01Rik|B830047L21Rik|D8Ertd514e|E-NPP 6|GPC-Cpde|Npp6	ectonucleotide pyrophosphatase/phosphodiesterase 6	protein-coding
mm_102462.1	chr11	59848237	59848257	-	1	NA	exon (NM_134029, exon 1 of 5)	exon (NM_134029, exon 1 of 5)	174	NM_134029	103850	Mm.41761	NM_134029	ENSMUSG00000032615	Nt5m	2010013E09Rik|AI846937|dNT-2	5',3'-nucleotidase, mitochondrial	protein-coding
mm_145950.1	chr18	67401858	67401869	+	1	NA	exon (NM_026473, exon 4 of 4)	exon (NM_026473, exon 4 of 4)	11132	NM_026473	67951	Mm.181860	NM_026473	ENSMUSG00000001473	Tubb6	2310057H16Rik|BB220206	tubulin, beta 6 class V	protein-coding
mm_82595.1	chr9	21248438	21248450	-	1	NA	promoter-TSS (NM_053190)	promoter-TSS (NM_053190)	-1	NM_053190	94226	Mm.190619	NM_053190	ENSMUSG00000045087	S1pr5	Edg8|S1P5|lpB4	sphingosine-1-phosphate receptor 5	protein-coding
mm_15116.1	chr2	153677180	153677208	+	1	NA	exon (NM_010068, exon 18 of 21)	exon (NM_010068, exon 18 of 21)	27745	NM_001271747	13436	Mm.89772	NM_010068	ENSMUSG00000027478	Dnmt3b	MmuIIIB	DNA methyltransferase 3B	protein-coding
mm_7985.1	chr1	134234493	134234523	-	1	NA	5' UTR (NM_001008533, exon 1 of 2)	5' UTR (NM_001008533, exon 1 of 2)	348	NM_001291928	11539	Mm.298908	NM_009629	ENSMUSG00000042429	Adora1	A1-AR|A1AR|A1R|AA1R|AI848715|BB176431|Ri	adenosine A1 receptor	protein-coding
mm_159525.1	chr4	61674089	61674089	-	1	NA	promoter-TSS (NM_001199333)	promoter-TSS (NM_001199333)	1	NM_001134644	100048885	Mm.422695	NM_001134644		Gm2083	-	major urinary protein LOC100048885	protein-coding
mm_56143.1	chr6	87809770	87809787	-	1	NA	promoter-TSS (NM_133717)	promoter-TSS (NM_133717)	-21	NM_133717	69834	Mm.37380	NM_133717	ENSMUSG00000030055	Rab43	1810048P08Rik|2500004H21Rik|AW490415	RAB43, member RAS oncogene family	protein-coding
mm_40561.1	chr5	61806723	61806736	+	1	NA	Intergenic	Intergenic	-2114	NM_019468	14380	Mm.347430	NM_019468	ENSMUSG00000089992	G6pd2	G6pdx-ps1|Gpd-2|Gpd2	glucose-6-phosphate dehydrogenase 2	protein-coding
mm_44857.1	chr5	34243466	34243528	-	1	NA	intron (NM_001015039, intron 1 of 12)	intron (NM_001015039, intron 1 of 12)	44827	NM_001015039	231125	Mm.113388	NM_001015039	ENSMUSG00000037224	Zfyve28	9630058O20Rik|Gm146|mKIAA1643	zinc finger, FYVE domain containing 28	protein-coding
mm_29981.1	chr3	135408049	135408121	-	1	NA	3' UTR (NM_025902, exon 3 of 3)	3' UTR (NM_025902, exon 3 of 3)	15348	NM_025902	67006	Mm.269993	NM_025902	ENSMUSG00000028165	Cisd2	1500009M05Rik|1500026J14Rik|1500031D15Rik|AI848398|B630006A20Rik|Miner1|Naf-1|Noxp70|Zcd2	CDGSH iron sulfur domain 2	protein-coding
mm_68757.1	chr7	121074541	121074555	-	1	NA	promoter-TSS (NM_030691)	promoter-TSS (NM_030691)	-18	NM_030691	80719	Mm.160384	NM_030691	ENSMUSG00000035004	Igsf6	-	immunoglobulin superfamily, member 6	protein-coding
mm_152923.1	chr19	28011139	28011181	-	1	NA	promoter-TSS (NM_011265)	promoter-TSS (NM_011265)	6	NM_011265	19726	Mm.313321	NM_011265	ENSMUSG00000040929	Rfx3	C230093O12Rik|MRFX3	regulatory factor X, 3 (influences HLA class II expression)	protein-coding
mm_25898.1	chr3	131110916	131110930	+	1	NA	5' UTR (NM_001276402, exon 1 of 10)	5' UTR (NM_001276402, exon 1 of 10)	626	NM_001276402	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_86130.1	chr9	116175902	116175928	-	1	NA	promoter-TSS (NM_029575)	promoter-TSS (NM_029575)	-552	NM_009371	21813	Mm.172346	NM_009371	ENSMUSG00000032440	Tgfbr2	1110020H15Rik|AU042018|DNIIR|RIIDN|TBR-II|TbetaR-II|TbetaRII	transforming growth factor, beta receptor II	protein-coding
mm_17359.1	chr2	26640080	26640091	-	1	NA	promoter-TSS (NR_028571)	promoter-TSS (NR_028571)	159	NR_024068	72091	Mm.27103	NR_024068		Snhg7	2610002F03Rik|AI427062	small nucleolar RNA host gene 7	ncRNA
mm_57915.1	chr6	133851974	133851976	-	1	NA	exon (NM_010594, exon 2 of 4)	exon (NM_010594, exon 2 of 4)	1692	NM_010594	16483	Mm.13052	NM_010594	ENSMUSG00000032758	Kap	AW146435|FKSG22	kidney androgen regulated protein	protein-coding
mm_65037.1	chr7	18560689	18560702	-	1	NA	exon (NM_001037168, exon 4 of 5)	exon (NM_001037168, exon 4 of 5)	6610	NM_001037168	545925	Mm.440302	NM_001037168	ENSMUSG00000070797	Psg27	EG545925|cea15	pregnancy-specific glycoprotein 27	protein-coding
mm_64851.1	chr7	13034402	13034414	-	1	NA	TTS (NM_145578)	TTS (NM_145578)	369	NM_026885	68953	Mm.295670	NM_026885	ENSMUSG00000033916	Chmp2a	1500016L11Rik	charged multivesicular body protein 2A	protein-coding
mm_24053.1	chr3	87906843	87906856	+	1	NA	promoter-TSS (NM_001331051)	promoter-TSS (NM_001331051)	-1	NM_001331051	15191	Mm.292208	NM_008231	ENSMUSG00000004897	Hdgf	AI118077|D3Ertd299e	hepatoma-derived growth factor	protein-coding
mm_156949.1	chrX	169986093	169986129	+	1	NA	intron (NM_001290512, intron 8 of 9)	intron (NM_001290512, intron 8 of 9)	-7194	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_77471.1	chr8	122427708	122427711	-	1	NA	exon (NM_007806, exon 2 of 6)	exon (NM_007806, exon 2 of 6)	5231	NM_001301284	13057	Mm.271671	NM_007806	ENSMUSG00000006519	Cyba	b558|nmf333|p22-phox|p22phox	cytochrome b-245, alpha polypeptide	protein-coding
mm_26856.1	chr3	14863922	14863937	-	1	NA	intron (NM_007606, intron 1 of 6)	intron (NM_007606, intron 1 of 6)	391	NM_007606	12350	Mm.300	NM_007606	ENSMUSG00000027559	Car3	BB219044|Ca3|Car-3	carbonic anhydrase 3	protein-coding
mm_38546.1	chr4	141600873	141600887	-	1	NA	promoter-TSS (NM_001163256)	promoter-TSS (NM_001163256)	-956	NM_001163256	74202	Mm.490327	NM_133754	ENSMUSG00000006219	Fblim1	2410043F08Rik|Cal|Fblp1|Gt10|migfilin|migfilin(s)	filamin binding LIM protein 1	protein-coding
mm_155365.1	chrX	71118681	71118683	+	1	NA	exon (NM_001256048, exon 3 of 6)	exon (NM_001256048, exon 3 of 6)	68426	NM_001081354	333639	Mm.371730	NM_001081354	ENSMUSG00000059401	Mamld1	G630014P10Rik	mastermind-like domain containing 1	protein-coding
mm_59888.1	chr7	30306836	30306853	+	1	NA	exon (NM_001081114, exon 14 of 14)	exon (NM_001081114, exon 14 of 14)	-1909	NM_198027	233065	Mm.276277	NM_198027	ENSMUSG00000042831	Alkbh6	AI839550|Abh6|C130099A02	alkB homolog 6	protein-coding
mm_117490.1	chr13	78196427	78196440	-	1	NA	promoter-TSS (NM_001347539)	promoter-TSS (NM_001347539)	16	NM_001347538	13865	Mm.439653	NM_010151	ENSMUSG00000069171	Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR-3|EAR3|Erbal3|SVP44|Tcfcoup1	nuclear receptor subfamily 2, group F, member 1	protein-coding
mm_85523.1	chr9	106453655	106453708	-	1	NA	promoter-TSS (NM_021567)	promoter-TSS (NM_021567)	-157	NM_021567	59092	Mm.286394	NM_021567	ENSMUSG00000023495	Pcbp4	1200003L19Rik|AlphaCP-4	poly(rC) binding protein 4	protein-coding
mm_85763.1	chr9	108824815	108824855	-	1	NA	Intergenic	Intergenic	-1485	NM_080437	107934	Mm.39945	NM_080437	ENSMUSG00000023473	Celsr3	Adgrc3|Fmi1|flamingo|mKIAA0812	cadherin, EGF LAG seven-pass G-type receptor 3	protein-coding
mm_146228.1	chr18	77070750	77070765	+	1	NA	intron (NM_001164170, intron 1 of 12)	intron (NM_001164170, intron 1 of 12)	5077	NM_001164168	17344	Mm.6370	NM_008602	ENSMUSG00000025423	Pias2	6330408K17Rik|AI462206|ARIP3|AU018068|Dib|Miz1|PIASxalpha|PIASxb|PIASxbeta|SIZ2	protein inhibitor of activated STAT 2	protein-coding
mm_86808.1	chr10	20332161	20332194	+	1	NA	exon (NM_001025393, exon 9 of 12)	exon (NM_001025393, exon 9 of 12)	-15642	NM_027930	71804	Mm.262151	NM_027930	ENSMUSG00000019992	Mtfr2	2610016C23Rik|4933412C16Rik|Dufd1|Fam54a	mitochondrial fission regulator 2	protein-coding
mm_8689.1	chr1	157244507	157244557	-	1	NA	intron (NM_177644, intron 3 of 17)	(TG)n|Simple_repeat|Simple_repeat	-135852	NM_001305063	73435	Mm.116705	NM_028540	ENSMUSG00000026592	Tex35	1700057K13Rik	testis expressed 35	protein-coding
mm_160253.1	chr7	107606625	107606625	+	1	NA	promoter-TSS (NM_001163557)	promoter-TSS (NM_001163557)	-219	NM_001163557	19024	Mm.2817	NM_008905	ENSMUSG00000036528	Ppfibp2	Cclp1	PTPRF interacting protein, binding protein 2 (liprin beta 2)	protein-coding
mm_89402.1	chr10	90576679	90576689	+	1	NA	promoter-TSS (NM_181398)	promoter-TSS (NM_181398)	-7	NM_001177396	77531	Mm.440605	NM_181398	ENSMUSG00000058589	Anks1b	AIDA-1b|C030032C09Rik|E530015N03Rik|ENSMUSG00000078431|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding
mm_108883.1	chr12	99965754	99965788	+	1	NA	5' UTR (NM_001164426, exon 2 of 3)	5' UTR (NM_001164426, exon 2 of 3)	1272	NM_001164427	217826	Mm.312335	NM_146037	ENSMUSG00000045404	Kcnk13	BB085247|F730021E22Rik|Gm1570|Gm1685	potassium channel, subfamily K, member 13	protein-coding
mm_165743.1	chr3	107218667	107218674	+	1	NA	exon (NM_001111143, exon 3 of 9)	exon (NM_001111143, exon 3 of 9)	3062	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_151373.1	chr19	55932491	55932503	+	1	NA	non-coding (NR_138565, exon 16 of 16)	non-coding (NR_138565, exon 16 of 16)	37176	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_32513.1	chr4	108619926	108619994	+	1	NA	promoter-TSS (NM_177045)	promoter-TSS (NM_177045)	4	NM_177045	319965	Mm.151129	NM_177045	ENSMUSG00000028582	Cc2d1b	A830039B04Rik|Freud2	coiled-coil and C2 domain containing 1B	protein-coding
mm_149695.1	chr19	21274437	21274453	+	1	NA	intron (NM_009551, intron 1 of 5)	intron (NM_009551, intron 1 of 5)	2167	NM_009551	22682	Mm.292405	NM_009551	ENSMUSG00000024750	Zfand5	2310057A04Rik|5830475F03Rik|AA415485|Za20d2|Zfp216	zinc finger, AN1-type domain 5	protein-coding
mm_126734.1	chr15	85654698	85654699	+	1	NA	Intergenic	Intergenic	-49075	NR_110483	102800312	Mm.33117	NR_110483		Lncppara	Lincppara|Mirlet7bhg|linc-Ppara	long noncoding RNA near Ppara	ncRNA
mm_131761.1	chr16	22891326	22891334	+	1	NA	promoter-TSS (NM_001276450)	promoter-TSS (NM_001276450)	-685	NR_075099	11625	Mm.197554	NM_013465	ENSMUSG00000022868	Ahsg	-	alpha-2-HS-glycoprotein	protein-coding
mm_110078.1	chr12	24493697	24493738	-	1	NA	Intergenic	CpG	-4864	NM_020614	21340	Mm.39082	NM_020614	ENSMUSG00000059669	Taf1b	4930408G01Rik|A230108M10Rik|TAFI68|Tafi86|p63	TATA-box binding protein associated factor, RNA polymerase I, B	protein-coding
mm_37998.1	chr4	133672983	133673002	-	1	NA	promoter-TSS (NM_178698)	promoter-TSS (NM_178698)	-345	NM_001145956	230801	Mm.217004	NM_178698	ENSMUSG00000043257	Pigv	B330013B03|D430024F16Rik	phosphatidylinositol glycan anchor biosynthesis, class V	protein-coding
mm_72227.1	chr8	72761869	72761896	+	1	NA	5' UTR (NM_007975, exon 1 of 2)	5' UTR (NM_007975, exon 1 of 2)	223	NM_007975	14065	Mm.12948	NM_007975	ENSMUSG00000050147	F2rl3	PAR4	coagulation factor II (thrombin) receptor-like 3	protein-coding
mm_164874.1	chr18	57878292	57878309	+	1	NA	promoter-TSS (NM_009194)	promoter-TSS (NM_009194)	-378	NM_009194	20496	Mm.399997	NM_009194	ENSMUSG00000024597	Slc12a2	9330166H04Rik|Nkcc1|mBSC2|sy-ns	solute carrier family 12, member 2	protein-coding
mm_116911.1	chr13	55483701	55483753	-	1	NA	intron (NM_001177371, intron 1 of 14)	intron (NM_001177371, intron 1 of 14)	4349	NM_001177371	56320	Mm.19016	NM_019813	ENSMUSG00000034675	Dbn1	-	drebrin 1	protein-coding
mm_77237.1	chr8	115705040	115705042	-	1	NA	3' UTR (NM_001025577, exon 1 of 1)	3' UTR (NM_001025577, exon 1 of 1)	1853	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_48326.1	chr5	138996007	138996025	-	1	NA	Intergenic	CpG-11694	-1063	NM_008808	18590	Mm.2675	NM_008808	ENSMUSG00000025856	Pdgfa	-	platelet derived growth factor, alpha	protein-coding
mm_32278.1	chr4	102825449	102825451	+	1	NA	intron (NM_001285852, intron 1 of 25)	intron (NM_001285852, intron 1 of 25)	65315	NM_001285859	73094	Mm.54201	NM_144906	ENSMUSG00000028524	Sgip1	3110007P09Rik|SGIP1alpha|gag	SH3-domain GRB2-like (endophilin) interacting protein 1	protein-coding
mm_86790.1	chr10	20205250	20205282	+	1	NA	intron (NM_001198635, intron 1 of 17)	intron (NM_001198635, intron 1 of 17)	-3173	NM_001101561	621697	Mm.440587	NM_001101561		Rpl32l	EG621697|Gm6251	ribosomal protein L32-like	protein-coding
mm_18654.1	chr2	69789521	69789563	-	1	NA	promoter-TSS (NM_028521)	promoter-TSS (NM_028521)	-56	NM_001077684	75051	Mm.195726	NM_001077684	ENSMUSG00000070883	Ccdc173	4930525K21Rik|4930578N16Rik	coiled-coil domain containing 173	protein-coding
mm_129749.1	chr15	82338771	82338791	-	1	NA	promoter-TSS (NM_008669)	promoter-TSS (NM_008669)	45	NM_008669	17939	Mm.20325	NM_008669	ENSMUSG00000022453	Naga	-	N-acetyl galactosaminidase, alpha	protein-coding
mm_123314.1	chr14	62414494	62414507	-	1	NA	intron (NM_172810, intron 9 of 16)	intron (NM_172810, intron 9 of 16)	41789	NM_001204340	239134	Mm.236557	NM_172810	ENSMUSG00000021933	Gucy1b2	B930025B03|GC-SB2	guanylate cyclase 1, soluble, beta 2	protein-coding
mm_50547.1	chr6	49046711	49046721	+	1	NA	intron (NM_053110, intron 4 of 10)	intron (NM_053110, intron 4 of 10)	10198	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_92750.1	chr10	81014903	81014937	-	1	NA	promoter-TSS (NM_010319)	promoter-TSS (NM_010319)	5	NM_010319	14708	Mm.222496	NM_010319	ENSMUSG00000048240	Gng7	AI840417	guanine nucleotide binding protein (G protein), gamma 7	protein-coding
mm_106544.1	chr11	120579201	120579213	-	1	NA	3' UTR (NM_133796, exon 6 of 6)	3' UTR (NM_133796, exon 6 of 6)	2413	NM_133796	192662	Mm.30016	NM_133796	ENSMUSG00000025132	Arhgdia	5330430M07Rik|Gdi-1|Rho-GDI|RhoDGI|RhoGDI-1	Rho GDP dissociation inhibitor (GDI) alpha	protein-coding
mm_159602.1	chr4	128759129	128759129	+	1	NA	promoter-TSS (NM_001009819)	promoter-TSS (NM_001009819)	-129	NM_001009819	215493	Mm.300900	NM_001009819	ENSMUSG00000028794	A3galt2	Gm433|iGb3|iGb3S	alpha 1,3-galactosyltransferase 2 (isoglobotriaosylceramide synthase)	protein-coding
mm_169081.1	chr13	3376824	3376839	-	1	NA	Intergenic	Intergenic	-101472	NR_015522	76937	Mm.487240	NR_015522	ENSMUSG00000097709	2810429I04Rik	AI256682	RIKEN cDNA 2810429I04 gene	ncRNA
mm_55028.1	chr6	48903010	48903020	-	1	NA	intron (NM_029638, intron 1 of 4)	ERVB7_2-LTR_MM|LTR|ERVK	-1971	NM_001161622	76507	Mm.213898	NM_029638	ENSMUSG00000029811	Aoc1	1600012D06Rik|Abp1|DAO	amine oxidase, copper-containing 1	protein-coding
mm_55628.1	chr6	72314616	72314659	-	1	NA	TTS (NM_001282071)	TTS (NM_001282071)	10027	NM_147779	20388	Mm.46033	NM_147779	ENSMUSG00000056370	Sftpb	AI562151|SF-B|SP-B|Sftp-3|Sftp3	surfactant associated protein B	protein-coding
mm_166686.1	chr6	103460778	103460778	+	1	NA	Intergenic	Intergenic	-50098	NM_007697	12661	Mm.251288	NM_007697	ENSMUSG00000030077	Chl1	A530023M13Rik|AI465420|CALL|LICAM2	cell adhesion molecule L1-like	protein-coding
mm_39288.1	chr5	4023305	4023318	+	1	NA	intron (NM_194462, intron 21 of 47)	intron (NM_194462, intron 21 of 47)	81386	NM_020010	13121	Mm.140158	NM_020010	ENSMUSG00000001467	Cyp51	AI426508|CYPLI|Cyp51a1|Ldm|P450-14DM|P450LI	cytochrome P450, family 51	protein-coding
mm_110612.1	chr12	56613174	56613181	-	1	NA	5' UTR (NM_008701, exon 1 of 2)	5' UTR (NM_008701, exon 1 of 2)	107	NM_008701	18094	Mm.129420	NM_008701	ENSMUSG00000058669	Nkx2-9	Nkx-2.9|Nkx2-8|Nkx2.9|tinman	NK2 homeobox 9	protein-coding
mm_161036.1	chr12	29534929	29534929	+	1	NA	promoter-TSS (NM_001093776)	promoter-TSS (NM_001093776)	24	NM_001093776	17933	Mm.253067	NM_008666	ENSMUSG00000061911	Myt1l	2900046C06Rik|2900093J19Rik|C630034G21Rik|Nztf1|Pmng1|Png-1|mKIAA1106	myelin transcription factor 1-like	protein-coding
mm_105946.1	chr11	115276953	115276972	-	1	NA	promoter-TSS (NM_007997)	promoter-TSS (NM_007997)	7	NM_007997	14149	Mm.4719	NM_007997	ENSMUSG00000018861	Fdxr	-	ferredoxin reductase	protein-coding
mm_38982.1	chr4	150944841	150944865	-	1	NA	exon (NM_001077508, exon 7 of 7)	exon (NM_001077508, exon 7 of 7)	16854	NM_001077509	21942	Mm.244187	NM_011612	ENSMUSG00000028965	Tnfrsf9	4-1BB|A930040I11Rik|AA408498|AI325004|CDw137|Cd137|ILA|Ly63	tumor necrosis factor receptor superfamily, member 9	protein-coding
mm_152138.1	chr19	7039988	7039994	-	1	NA	promoter-TSS (NM_016737)	promoter-TSS (NM_016737)	35	NM_016737	20867	Mm.258633	NM_016737	ENSMUSG00000024966	Stip1	Hop|Sti1|p60	stress-induced phosphoprotein 1	protein-coding
mm_6057.1	chr1	60486619	60486652	-	1	NA	3' UTR (NM_001045513, exon 14 of 14)	3' UTR (NM_001045513, exon 14 of 14)	77016	NM_001198570	329165	Mm.212066	NM_198127	ENSMUSG00000026782	Abi2	8430425M24Rik|AI839867|C130078H13	abl-interactor 2	protein-coding
mm_9436.1	chr1	172526375	172526382	-	1	NA	intron (NM_027972, intron 1 of 11)	intron (NM_027972, intron 1 of 11)	5248	NM_027972	71870	Mm.78373	NM_027972	ENSMUSG00000026546	Cfap45	1700028D05Rik|Ccdc19|Nesg1	cilia and flagella associated protein 45	protein-coding
mm_69162.1	chr7	127208424	127208504	-	1	NA	promoter-TSS (NM_144522)	promoter-TSS (NM_144522)	4	NM_144522	68449	Mm.41420	NM_144522	ENSMUSG00000042492	Tbc1d10b	1110003P22Rik|C87963	TBC1 domain family, member 10b	protein-coding
mm_37390.1	chr4	121017202	121017261	-	1	NA	promoter-TSS (NM_133716)	promoter-TSS (NM_133716)	16	NM_133716	69780	Mm.271819	NM_133716	ENSMUSG00000032870	Smap2	1810031K02Rik|AA408614|Smap1l	small ArfGAP 2	protein-coding
mm_95090.1	chr11	33872446	33872451	+	1	NA	intron (NM_001190886, intron 1 of 7)	intron (NM_001190886, intron 1 of 7)	-28863	NM_001290690	70357	Mm.252514	NM_027398	ENSMUSG00000053519	Kcnip1	KCHIP1|Kchip1.2	Kv channel-interacting protein 1	protein-coding
mm_52985.1	chr6	123264041	123264082	+	1	NA	intron (NM_001163161, intron 1 of 5)	RSINE1|SINE|B4	1954	NM_010819	17474	Mm.441101	NM_010819	ENSMUSG00000030144	Clec4d	Clecsf8|Mpcl|mcl	C-type lectin domain family 4, member d	protein-coding
mm_93616.1	chr10	117277431	117277452	-	1	NA	TTS (NM_017372)	TTS (NM_017372)	4831	NM_017372	17105	Mm.45436	NM_017372	ENSMUSG00000069516	Lyz2	AI326280|Lys|Lysm|Lyzf2|Lyzs|Lzm|Lzm-s1|Lzp	lysozyme 2	protein-coding
mm_31511.1	chr4	53714143	53714199	+	1	NA	promoter-TSS (NM_139309)	promoter-TSS (NM_139309)	-11	NM_139309	246179	Mm.247210	NM_139309	ENSMUSG00000028414	Fktn	D830030O17Rik|Fcmd	fukutin	protein-coding
mm_17746.1	chr2	32714487	32714525	-	1	NA	Intergenic	Intergenic	-1534	NR_039536	100628606		NR_039536	ENSMUSG00000105841	Mir3960	mmu-mir-3960	microRNA 3960	ncRNA
mm_154686.1	chrX	7922369	7922409	+	1	NA	exon (NM_013892, exon 2 of 3)	exon (NM_013892, exon 2 of 3)	2567	NM_013892	30052	Mm.4881	NM_013892	ENSMUSG00000039278	Pcsk1n	AI848336|KEP|PEN|PEN19|PEN20|Pan3|SAAS|SAASCT|bLEN|lLEN|proSAAS	proprotein convertase subtilisin/kexin type 1 inhibitor	protein-coding
mm_51832.1	chr6	89644016	89644062	+	1	NA	promoter-TSS (NM_001178058)	promoter-TSS (NM_001178058)	51	NM_001178058	232223	Mm.229332	NM_153162	ENSMUSG00000000811	Txnrd3	AI196535|TR2|Tgr	thioredoxin reductase 3	protein-coding
mm_6592.1	chr1	75264280	75264288	-	1	NA	promoter-TSS (NM_008985)	promoter-TSS (NM_008985)	-76	NM_008985	19275	Mm.2902	NM_008985	ENSMUSG00000026204	Ptprn	IA-2|mIA-A|mKIAA4064	protein tyrosine phosphatase, receptor type, N	protein-coding
mm_9074.1	chr1	168406277	168406279	-	1	NA	intron (NM_008783, intron 2 of 7)	intron (NM_008783, intron 2 of 7)	25891	NM_001291508	18514	Mm.43358	NM_008783	ENSMUSG00000052534	Pbx1	2310056B04Rik|D230003C07Rik|Pbx-1	pre B cell leukemia homeobox 1	protein-coding
mm_74349.1	chr8	127546181	127546185	+	1	NA	intron (NM_001309391, intron 22 of 24)	intron (NM_001309391, intron 22 of 24)	246531	NM_001013580	93742	Mm.299254	NM_033620	ENSMUSG00000025812	Pard3	AA960621|AI256638|Asip|D8Ertd580e|Par-3|Par3|Pard-3|Pard3a|Phip	par-3 family cell polarity regulator	protein-coding
mm_39279.1	chr5	3927822	3927843	+	1	NA	promoter-TSS (NM_194462)	promoter-TSS (NM_194462)	-354	NM_194462	100986	Mm.46044	NM_194462	ENSMUSG00000040407	Akap9	5730481H23Rik|AKAP-9|AKAP450|AW545847|C79026|G1-448-15|PRKA9|mKIAA0803|mei2-5|repro12	A kinase (PRKA) anchor protein (yotiao) 9	protein-coding
mm_172372.1	chr7	126299944	126299944	-	1	NA	Intergenic	Intergenic	27325	NM_145587	104175	Mm.29660	NM_145587	ENSMUSG00000042978	Sbk1	Sbk	SH3-binding kinase 1	protein-coding
mm_122976.1	chr14	54978662	54978681	-	1	NA	exon (NM_080728, exon 30 of 41)	exon (NM_080728, exon 30 of 41)	-2895	NR_030607	100124433		NR_030607	ENSMUSG00000077928	Mir208b	Mirn208b|mir-208b	microRNA 208b	ncRNA
mm_168979.1	chr12	91474733	91474738	-	1	NA	intron (NM_011648, intron 1 of 9)	L1Md_T|LINE|L1	73742	NM_011648	22095	Mm.173847	NM_011648	ENSMUSG00000020963	Tshr	AI481368|hypothroid|hyt|pet	thyroid stimulating hormone receptor	protein-coding
mm_50167.1	chr6	41554516	41554523	+	1	NA	Intergenic	Intergenic	32743	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_166553.1	chr6	41544866	41544890	+	1	NA	Intergenic	MIRb|SINE|MIR	23102	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_161493.1	chr15	86033866	86033866	-	1	NA	promoter-TSS (NM_009886)	promoter-TSS (NM_009886)	-89	NM_009886	12614	Mm.22680	NM_009886	ENSMUSG00000016028	Celsr1	Adgrc1|Crsh|Scy|crash	cadherin, EGF LAG seven-pass G-type receptor 1	protein-coding
mm_90955.1	chr10	13193157	13193167	-	1	NA	promoter-TSS (NM_181470)	promoter-TSS (NM_181470)	-25	NM_181470	353258	Mm.117581	NM_181470	ENSMUSG00000019814	Ltv1	2610020N02Rik	LTV1 ribosome biogenesis factor	protein-coding
mm_149214.1	chr19	9984558	9984583	+	1	NA	TTS (NM_011913)	TTS (NM_011913)	1924	NM_010239	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
mm_5163.1	chr1	10037933	10037968	-	1	NA	promoter-TSS (NM_026493)	promoter-TSS (NM_026493)	209	NR_102282	26754	Mm.402384	NM_013715	ENSMUSG00000025917	Cops5	AI303502|CSN5|Jab1|Mov34|Sgn5	COP9 signalosome subunit 5	protein-coding
mm_87947.1	chr10	62980281	62980291	+	1	NA	promoter-TSS (NM_027425)	promoter-TSS (NM_027425)	63	NM_027425	70432	Mm.234587	NM_027425	ENSMUSG00000020070	Rufy2	2610111M19Rik|AI844453|Denn|LZ-FYVE|ZFYVE13	RUN and FYVE domain-containing 2	protein-coding
mm_14355.1	chr2	129615483	129615495	+	1	NA	exon (NM_007547, exon 3 of 8)	exon (NM_007547, exon 3 of 8)	22320	NM_001291022	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_160666.1	chr9	121641594	121641594	-	1	NA	promoter-TSS (NM_026915)	promoter-TSS (NM_026915)	-28	NM_026915	69032	Mm.33351	NM_026915	ENSMUSG00000032530	Lyzl4	1810009N24Rik|AI504271|Lyc4|Lyza	lysozyme-like 4	protein-coding
mm_77254.1	chr8	115706701	115706711	-	1	NA	exon (NM_001025577, exon 1 of 1)	exon (NM_001025577, exon 1 of 1)	188	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_155248.1	chrX	57223705	57223715	+	1	NA	3' UTR (NM_011616, exon 5 of 5)	3' UTR (NM_011616, exon 5 of 5)	11567	NM_011616	21947	Mm.4861	NM_011616	ENSMUSG00000031132	Cd40lg	CD154|CD40-L|Cd40l|HIGM1|IGM|IMD3|Ly-62|Ly62|T-BAM|TRAP|Tnfsf5|Tnlg8b|gp39	CD40 ligand	protein-coding
mm_139210.1	chr17	47728733	47728742	+	1	NA	intron (NM_025973, intron 1 of 8)	intron (NM_025973, intron 1 of 8)	1895	NM_025973	109820	Mm.22957	NM_025973	ENSMUSG00000023987	Pgc	2210410L06Rik|Upg-1|Upg1	progastricsin (pepsinogen C)	protein-coding
mm_31756.1	chr4	63362444	63362451	+	1	NA	promoter-TSS (NM_011016)	promoter-TSS (NM_011016)	-2	NM_011016	18406	Mm.14173	NM_011016	ENSMUSG00000061540	Orm2	Agp1|Orm-2	orosomucoid 2	protein-coding
mm_59292.1	chr7	25077230	25077335	+	1	NA	promoter-TSS (NM_001168506)	promoter-TSS (NM_001168506)	36	NM_175477	232976	Mm.41568	NM_175477	ENSMUSG00000045252	Zfp574	A630056B21Rik|Znf574	zinc finger protein 574	protein-coding
mm_28199.1	chr3	88254707	88254722	-	1	NA	promoter-TSS (NM_021375)	promoter-TSS (NM_021375)	-30	NM_021375	58176	Mm.103777	NM_021375	ENSMUSG00000103766	Rhbg	-	Rhesus blood group-associated B glycoprotein	protein-coding
mm_61172.1	chr7	59314328	59314341	+	1	NA	intron (NR_015479, intron 2 of 2)	intron (NR_015479, intron 2 of 2)	9815	NR_015479	330544	Mm.9002	NR_015479	ENSMUSG00000100826	C230091D08Rik	-	RIKEN cDNA C230091D08 gene	ncRNA
mm_37139.1	chr4	116821502	116821521	-	1	NA	promoter-TSS (NM_146256)	promoter-TSS (NM_146256)	-3	NM_146256	242642	Mm.279897	NM_146256	ENSMUSG00000043155	Hpdl	A830048M07Rik|BC034099|Gloxd1	4-hydroxyphenylpyruvate dioxygenase-like	protein-coding
mm_128025.1	chr15	25057110	25057113	-	1	NA	Intergenic	Lx5c|LINE|L1	356653	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	brain abundant, membrane attached signal protein 1	protein-coding
mm_105637.1	chr11	106998484	106998491	-	1	NA	intron (NM_010655, intron 1 of 10)	intron (NM_010655, intron 1 of 10)	1038	NM_010655	16647	Mm.12508	NM_010655	ENSMUSG00000018362	Kpna2	2410044B12Rik|IPOA1|PTAC58|Rch1	karyopherin (importin) alpha 2	protein-coding
mm_131282.1	chr16	11143968	11143990	+	1	NA	intron (NR_027502, intron 19 of 22)	LSU-rRNA_Hsa|rRNA|rRNA	-9447	NM_029582	106200	Mm.291015	NM_029582	ENSMUSG00000022498	Txndc11	2810408E11Rik|AI427833|EFP1|Txdc11	thioredoxin domain containing 11	protein-coding
mm_89073.1	chr10	82985474	82985504	+	1	NA	promoter-TSS (NM_021439)	promoter-TSS (NM_021439)	-8	NM_021439	58250	Mm.360747	NM_021439	ENSMUSG00000034612	Chst11	1110020P09Rik|C4ST|C4ST-1|C4ST1|C4s	carbohydrate sulfotransferase 11	protein-coding
mm_48863.1	chr5	149825338	149825347	-	1	NA	Intergenic	Intergenic	-13591	NR_077242	100861794	Mm.402054	NR_077242	ENSMUSG00000106740	Gm21221	-	predicted gene, 21221	ncRNA
mm_5438.1	chr1	34842966	34842976	-	1	NA	promoter-TSS (NM_001160236)	promoter-TSS (NM_001160236)	79	NM_001160235	214469	Mm.120151	NM_174997	ENSMUSG00000037503	Fam168b	mKIAA4042	family with sequence similarity 168, member B	protein-coding
mm_39903.1	chr5	31251679	31251728	+	1	NA	promoter-TSS (NM_027221)	promoter-TSS (NM_027221)	-3	NM_027221	69815	Mm.389609	NM_027221	ENSMUSG00000029149	Krtcap3	2010001C09Rik|AW321088|Kcp3	keratinocyte associated protein 3	protein-coding
mm_139420.1	chr17	53479430	53479448	+	1	NA	5' UTR (NM_025887, exon 1 of 6)	5' UTR (NM_025887, exon 1 of 6)	205	NM_025887	271457	Mm.329123	NM_025887	ENSMUSG00000017831	Rab5a	2410015H04Rik|AI663973|AU021172|nnyRab5a	RAB5A, member RAS oncogene family	protein-coding
mm_63857.1	chr7	135671609	135671614	+	1	NA	intron (NM_001316681, intron 12 of 17)	intron (NM_001316681, intron 12 of 17)	-19297	NR_015548	67765	Mm.445272	NR_015548	ENSMUSG00000097471	5830432E09Rik	-	RIKEN cDNA 5830432E09 gene	ncRNA
mm_14301.1	chr2	129066004	129066015	+	1	NA	promoter-TSS (NM_027192)	promoter-TSS (NM_027192)	62	NM_027192	69737	Mm.33909	NM_027192	ENSMUSG00000027394	Ttl	2410003M22Rik|2700049H19Rik|AI848570	tubulin tyrosine ligase	protein-coding
mm_13158.1	chr2	92554482	92554483	+	1	NA	Intergenic	Intergenic	-37724	NR_106080	102466819		NR_106080	ENSMUSG00000099223	Mir7221	Gm27378|mmu-mir-7221	microRNA 7221	ncRNA
mm_18832.1	chr2	74716021	74716027	-	1	NA	non-coding (NR_027899, exon 1 of 3)	non-coding (NR_027899, exon 1 of 3)	106	NR_027899	73429	Mm.443313	NR_027899		Hoxd3os1	1700064D17Rik|1700109F18Rik	homeobox D3, opposite strand 1	ncRNA
mm_125372.1	chr15	39962698	39962771	+	1	NA	promoter-TSS (NR_045719)	promoter-TSS (NR_045719)	85	NR_045719	105976	Mm.394885	NR_045719		AU022793	-	expressed sequence AU022793	ncRNA
mm_62318.1	chr7	100319095	100319105	+	1	NA	3' UTR (NM_177161, exon 13 of 13)	3' UTR (NM_177161, exon 13 of 13)	33580	NM_177161	320452	Mm.150294	NM_177161	ENSMUSG00000051048	P4ha3	D930031A02Rik	procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide III	protein-coding
mm_162448.1	chr1	120983000	120983001	+	1	NA	Intergenic	Intergenic	-104405	NR_038008	98452	Mm.131017	NR_038008	ENSMUSG00000097881	Celrr	AI848258|B230209K01Rik|Celr|Gm818	cerebellum expressed regulatory RNA	ncRNA
mm_95681.1	chr11	54141910	54141927	+	1	NA	Intergenic	Intergenic	40994	NM_011031	18452	Mm.3705	NM_011031	ENSMUSG00000018906	P4ha2	AA407196|C76437|P4hl	procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha II polypeptide	protein-coding
mm_99040.1	chr11	98960768	98960778	+	1	NA	5' UTR (NM_001176528, exon 1 of 8)	5' UTR (NM_001176528, exon 1 of 8)	302	NM_001176528	19401	Mm.439744	NM_009024	ENSMUSG00000037992	Rara	Nr1b1|RAR|RARalpha1	retinoic acid receptor, alpha	protein-coding
mm_92372.1	chr10	76237790	76237796	-	1	NA	promoter-TSS (NM_133182)	promoter-TSS (NM_133182)	72	NR_126571	15468	Mm.32020	NM_133182	ENSMUSG00000020230	Prmt2	AI504737|Hrmt1l1	protein arginine N-methyltransferase 2	protein-coding
mm_43694.1	chr5	139161802	139161851	+	1	NA	exon (NM_001081265, exon 5 of 13)	exon (NM_001081265, exon 5 of 13)	11603	NM_001081265	433956	Mm.5547	NM_001081265	ENSMUSG00000025857	Dnaaf5	BC053401|C76907|Heatr2	dynein, axonemal assembly factor 5	protein-coding
mm_168212.1	chr10	75860224	75860224	-	1	NA	promoter-TSS (NM_010798)	promoter-TSS (NM_010798)	26	NM_010798	17319	Mm.2326	NM_010798	ENSMUSG00000033307	Mif	GIF|Glif	macrophage migration inhibitory factor	protein-coding
mm_90243.1	chr10	121488851	121488861	+	1	NA	Intergenic	Intergenic	-12606	NM_138956	192678	Mm.41265	NM_138956	ENSMUSG00000025795	Rassf3	AW212023|AW322379	Ras association (RalGDS/AF-6) domain family member 3	protein-coding
mm_34631.1	chr4	150613712	150613729	+	1	NA	intron (NM_001085492, intron 15 of 22)	intron (NM_001085492, intron 15 of 22)	38454	NM_173774	242773	Mm.29280	NM_173774	ENSMUSG00000039838	Slc45a1	C230078B22|Dnb5	solute carrier family 45, member 1	protein-coding
mm_55477.1	chr6	68910444	68910457	-	1	NA	Intergenic	Intergenic	416724	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_153853.1	chr19	46378152	46378196	-	1	NA	3' UTR (NM_016860, exon 11 of 11)	3' UTR (NM_016860, exon 11 of 11)	17561	NM_016860	54130	Mm.3118	NM_016860	ENSMUSG00000025228	Actr1a	Arp1|alpha-Arp1	ARP1 actin-related protein 1A, centractin alpha	protein-coding
mm_72535.1	chr8	83995878	83995891	+	1	NA	3' UTR (NM_008854, exon 10 of 10)	3' UTR (NM_008854, exon 10 of 10)	-1788	NM_001081415	666704	Mm.298091	NM_001081415	ENSMUSG00000079003	Samd1	AA589507	sterile alpha motif domain containing 1	protein-coding
mm_15814.1	chr2	164502621	164502636	+	1	NA	exon (NM_133779, exon 9 of 12)	exon (NM_133779, exon 9 of 12)	5103	NM_133779	78928	Mm.28228	NM_133779	ENSMUSG00000017721	Pigt	2510012P17Rik|4930534E15Rik|CGI-06|NDAP|Ndap7	phosphatidylinositol glycan anchor biosynthesis, class T	protein-coding
mm_147160.1	chr18	36713360	36713363	-	1	NA	Intergenic	L1MB4|LINE|L1	13454	NM_009841	12475	Mm.3460	NM_009841	ENSMUSG00000051439	Cd14	-	CD14 antigen	protein-coding
mm_76429.1	chr8	84978452	84978463	-	1	NA	5' UTR (NM_008416, exon 1 of 1)	5' UTR (NM_008416, exon 1 of 1)	291	NM_008416	16477	Mm.1167	NM_008416	ENSMUSG00000052837	Junb	-	jun B proto-oncogene	protein-coding
mm_117583.1	chr13	89578442	89578463	-	1	NA	intron (NM_013500, intron 1 of 4)	L1Md_F2|LINE|L1	37816	NM_013500	12950	Mm.266790	NM_013500	ENSMUSG00000021613	Hapln1	BB099155|CLP|Crtl1|Crtl1l|LP|LP-1	hyaluronan and proteoglycan link protein 1	protein-coding
mm_430.1	chr1	34473264	34473296	+	1	NA	intron (NM_011206, intron 13 of 14)	intron (NM_011206, intron 13 of 14)	13534	NM_011206	19253	Mm.361	NM_011206	ENSMUSG00000026126	Ptpn18	FLP1|HSCF|PTP-HSCF|PTP-K1|Ptpk1	protein tyrosine phosphatase, non-receptor type 18	protein-coding
mm_112695.1	chr13	17695144	17695213	+	1	NA	promoter-TSS (NM_138654)	promoter-TSS (NM_138654)	-235	NM_025479	66308	Mm.291109	NM_025479	ENSMUSG00000012429	Mplkip	2810021B07Rik|C330007M08Rik|Ttdn1	M-phase specific PLK1 intereacting protein	protein-coding
mm_41584.1	chr5	93205645	93205679	+	1	NA	promoter-TSS (NM_029363)	promoter-TSS (NM_029363)	833	NM_017367	12453	Mm.250419	NM_017367	ENSMUSG00000063015	Ccni	-	cyclin I	protein-coding
mm_145189.1	chr18	49832593	49832605	+	1	NA	promoter-TSS (NM_001081371)	promoter-TSS (NM_001081371)	-398	NM_001081371	240283	Mm.257790	NM_001081371	ENSMUSG00000037416	Dmxl1	C630007L23Rik|D030030C22	Dmx-like 1	protein-coding
mm_171549.1	chr4	147087051	147087070	-	1	NA	Intergenic	CpG	-18624	NR_045446	71270	Mm.460830	NR_045446	ENSMUSG00000093617	4933438K21Rik	-	RIKEN cDNA 4933438K21 gene	ncRNA
mm_120491.1	chr14	65979819	65979838	+	1	NA	exon (NM_013492, exon 7 of 9)	exon (NM_013492, exon 7 of 9)	11345	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_25005.1	chr3	97658292	97658339	+	1	NA	5' UTR (NM_182997, exon 1 of 8)	5' UTR (NM_182997, exon 1 of 8)	103	NM_182997	108097	Mm.31175	NM_182997	ENSMUSG00000038205	Prkab2	5730553K21Rik|AW049591|BB124140	protein kinase, AMP-activated, beta 2 non-catalytic subunit	protein-coding
mm_31589.1	chr4	57845278	57845288	+	1	NA	promoter-TSS (NM_001035532)	promoter-TSS (NM_001035532)	35	NM_001035532	11641	Mm.467752	NM_009649	ENSMUSG00000038729	Akap2	AA959716|AI649048|Akap-2|Akap-kl|B230340M18Rik|Prka2	A kinase (PRKA) anchor protein 2	protein-coding
mm_99791.1	chr11	107428307	107428317	+	1	NA	intron (NM_145823, intron 1 of 9)	intron (NM_145823, intron 1 of 9)	42408	NM_145823	71795	Mm.397413	NM_145823	ENSMUSG00000040430	Pitpnc1	1110020B03Rik|5830436L09Rik|AI662802|AI851387|C330017I21Rik|Dnr411|RDGBB|RDGBB1|rdgB-beta	phosphatidylinositol transfer protein, cytoplasmic 1	protein-coding
mm_129790.1	chr15	82836579	82836582	-	1	NA	intron (NM_001114140, intron 2 of 5)	intron (NM_001114140, intron 2 of 5)	-42335	NM_029562	76279	Mm.439931	NM_029562	ENSMUSG00000022445	Cyp2d26	1300006E06Rik	cytochrome P450, family 2, subfamily d, polypeptide 26	protein-coding
mm_61533.1	chr7	79053237	79053265	+	1	NA	promoter-TSS (NM_007424)	promoter-TSS (NM_007424)	72	NR_132432	102633600	Mm.382916	NR_132432	ENSMUSG00000097441	Gm26633	-	predicted gene, 26633	ncRNA
mm_24726.1	chr3	95282588	95282605	+	1	NA	promoter-TSS (NM_133858)	promoter-TSS (NM_133858)	-339	NM_133858	75007	Mm.279287	NM_133858	ENSMUSG00000038712	Fam63a	1810005H09Rik|4930504E06Rik|AA562754|AA960384|AW561904|cI-40|mKIAA1390|ni	family with sequence similarity 63, member A	protein-coding
mm_121588.1	chr14	7808309	7808317	-	1	NA	Intergenic	RMER10A|LTR|ERVL	-9644	NM_001081427	286940	Mm.489652	NM_134080	ENSMUSG00000025278	Flnb	AL024016|Fln-b	filamin, beta	protein-coding
mm_109485.1	chr12	111437907	111437910	+	1	NA	Intergenic	Intergenic	-4753	NM_009396	21928	Mm.255332	NM_009396	ENSMUSG00000021281	Tnfaip2	B94|Exoc3l3|M-sec|Tnfip2|tnfb94	tumor necrosis factor, alpha-induced protein 2	protein-coding
mm_79474.1	chr9	56937463	56937502	+	1	NA	promoter-TSS (NM_133976)	promoter-TSS (NM_133976)	-18	NM_133976	102462	Mm.12864	NM_133976	ENSMUSG00000032288	Imp3	1190002L16Rik|AI256594	IMP3, U3 small nucleolar ribonucleoprotein	protein-coding
mm_26199.1	chr3	138526524	138526551	+	1	NA	promoter-TSS (NM_001313980)	promoter-TSS (NM_001313980)	116	NR_035481	100316706		NR_035481	ENSMUSG00000088373	Mir1956	mir-1956|mmu-mir-1956	microRNA 1956	ncRNA
mm_150986.1	chr19	46516154	46516179	+	1	NA	3' UTR (NM_053100, exon 6 of 6)	3' UTR (NM_053100, exon 6 of 6)	14518	NM_053100	93679	Mm.392177	NM_053100	ENSMUSG00000025034	Trim8	AA408830|BB006755|GERP|Rnf27	tripartite motif-containing 8	protein-coding
mm_70969.1	chr8	27042593	27042630	+	1	NA	promoter-TSS (NM_001039078)	promoter-TSS (NM_001039078)	56	NM_054057	114863	Mm.277501	NM_054057	ENSMUSG00000031485	Prosc	1700024N20Rik|2200002F22Rik	proline synthetase co-transcribed	protein-coding
mm_62291.1	chr7	99906538	99906552	+	1	NA	exon (NM_001164258, exon 12 of 19)	exon (NM_001164258, exon 12 of 19)	47327	NM_001164258	446101	Mm.440757	NM_001164258	ENSMUSG00000035211	Xrra1	AI449753	X-ray radiation resistance associated 1	protein-coding
mm_4900.1	chr1	189798527	189798538	+	1	NA	exon (NM_008976, exon 3 of 19)	exon (NM_008976, exon 3 of 19)	70264	NM_008976	19250	Mm.4498	NM_008976	ENSMUSG00000026604	Ptpn14	C130080N23Rik|OTTMUSG00000022087|PTP36	protein tyrosine phosphatase, non-receptor type 14	protein-coding
mm_166152.1	chr5	7180031	7180050	+	1	NA	intron (NM_001163223, intron 1 of 3)	intron (NM_001163223, intron 1 of 3)	-124124	NM_027603	70920	Mm.158494	NM_027603	ENSMUSG00000040514	4921511H03Rik	-	RIKEN cDNA 4921511H03 gene	protein-coding
mm_171369.1	chr4	119282231	119282236	-	1	NA	exon (NM_011732, exon 5 of 8)	exon (NM_011732, exon 5 of 8)	12280	NM_011732	22608	Mm.258204	NM_011732	ENSMUSG00000028639	Ybx1	1700102N10Rik|C79409|EF1A|MSY1|Nsep1|YB-1|dbpB|mYB-1a	Y box protein 1	protein-coding
mm_155642.1	chrX	85269490	85269504	+	1	NA	intron (NM_028046, intron 1 of 1)	intron (NM_028046, intron 1 of 1)	19820	NM_028046	71996	Mm.20201	NM_028046	ENSMUSG00000035491	Fthl17a	1600014K23Rik|AI324104	ferritin, heavy polypeptide-like 17, member A	protein-coding
mm_114141.1	chr13	55290257	55290285	+	1	NA	intron (NM_008739, intron 13 of 22)	AT_rich|Low_complexity|Low_complexity	31709	NM_009000	19336	Mm.220923	NM_009000	ENSMUSG00000034789	Rab24	6530406O07Rik	RAB24, member RAS oncogene family	protein-coding
mm_158764.1	chrX	166518576	166518582	-	1	NA	Intergenic	Intergenic	-8101	NM_001007577	245695	Mm.336318	NM_001007577	ENSMUSG00000051224	Tceanc	A630018P17Rik|Gm390	transcription elongation factor A (SII) N-terminal and central domain containing	protein-coding
mm_64724.1	chr7	4659029	4659037	-	1	NA	promoter-TSS (NM_172894)	promoter-TSS (NM_172894)	-83	NM_172894	243819	Mm.258670	NM_172894	ENSMUSG00000052296	Ppp6r1	2010309P17Rik|AI836219|B430201G11Rik|D030074N20Rik|Pp6r1|Saps1|mKIAA1115	protein phosphatase 6, regulatory subunit 1	protein-coding
mm_170692.1	chr2	132253150	132253152	-	1	NA	promoter-TSS (NM_011045)	promoter-TSS (NM_011045)	29	NM_011045	18538	Mm.7141	NM_011045	ENSMUSG00000027342	Pcna	-	proliferating cell nuclear antigen	protein-coding
mm_112942.1	chr13	20986418	20986462	+	1	NA	intron (NM_012054, intron 13 of 20)	MT2B|LTR|ERVL	86859	NM_146535	258528	Mm.377554	NM_146535	ENSMUSG00000042869	Olfr1370	MOR256-14	olfactory receptor 1370	protein-coding
mm_120582.1	chr14	69767543	69767553	+	1	NA	promoter-TSS (NM_020275)	promoter-TSS (NM_020275)	76	NM_020275	21933	Mm.193430	NM_020275	ENSMUSG00000022074	Tnfrsf10b	DR5|KILLER|Ly98|MK|TRAILR2|TRICK2A|TRICK2B|TRICKB	tumor necrosis factor receptor superfamily, member 10b	protein-coding
mm_4100.1	chr1	167350247	167350249	+	1	NA	exon (NM_019993, exon 1 of 11)	exon (NM_019993, exon 1 of 11)	257	NM_019993	56752	Mm.292539	NM_019993	ENSMUSG00000026687	Aldh9a1	AA139417|Abaldh|ESTM40|TMABA-DH|Tmabadh	aldehyde dehydrogenase 9, subfamily A1	protein-coding
mm_29672.1	chr3	122801994	122802008	-	1	NA	promoter-TSS (NR_045168)	promoter-TSS (NR_045168)	-21	NR_045168	71647	Mm.449992	NR_045168	ENSMUSG00000106583	4930447N08Rik	-	RIKEN cDNA 4930447N08 gene	ncRNA
mm_138208.1	chr17	34305042	34305062	+	1	NA	promoter-TSS (NM_010382)	promoter-TSS (NM_010382)	-815	NM_010382	14969	Mm.22564	NM_010382	ENSMUSG00000060586	H2-Eb1	Eb|H-2Eb|H2Eb|Ia-4|Ia4	histocompatibility 2, class II antigen E beta	protein-coding
mm_129598.1	chr15	79834262	79834285	-	1	NA	promoter-TSS (NM_001013360)	promoter-TSS (NM_001013360)	60	NM_001013360	504193	Mm.38438	NM_029079	ENSMUSG00000089837	Npcd	Cbx6-Nptxr	neuronal pentraxin chromo domain	protein-coding
mm_6508.1	chr1	74304346	74304377	-	1	NA	promoter-TSS (NM_027154)	promoter-TSS (NM_027154)	-25	NM_027154	69660	Mm.261182	NM_027154	ENSMUSG00000006301	Tmbim1	2310061B02Rik|AA960455|AU024746|C78899|RECS1|Tmbib1|mKIAA4161	transmembrane BAX inhibitor motif containing 1	protein-coding
mm_53331.1	chr6	129233379	129233393	+	1	NA	intron (NR_040265, intron 1 of 2)	intron (NR_040265, intron 1 of 2)	4659	NR_040265	76432	Mm.261738	NR_040265	ENSMUSG00000097354	2310001H17Rik	AI646108	RIKEN cDNA 2310001H17 gene	ncRNA
mm_29922.1	chr3	131490654	131490666	-	1	NA	Intergenic	CpG	-74108	NM_001289479	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_66921.1	chr7	60939875	60939889	-	1	NA	Intergenic	Intergenic	675445	NR_045727	319752	Mm.294476	NR_045727		B230209E15Rik	-	RIKEN cDNA B230209E15 gene	ncRNA
mm_47157.1	chr5	120683106	120683157	-	1	NA	intron (NM_008052, intron 5 of 9)	intron (NM_008052, intron 5 of 9)	28538	NM_008052	14357	Mm.1645	NM_008052	ENSMUSG00000029603	Dtx1	Fxit1|mKIAA4160	deltex 1, E3 ubiquitin ligase	protein-coding
mm_133870.1	chr16	96372686	96372708	+	1	NA	intron (NM_001177886, intron 2 of 8)	intron (NM_001177886, intron 2 of 8)	10933	NM_028078	72058	Mm.119714	NM_028078	ENSMUSG00000000159	Igsf5	2010003D20Rik|JCAM|Jam4	immunoglobulin superfamily, member 5	protein-coding
mm_161104.1	chr12	102470115	102470115	+	1	NA	intron (NM_013747, intron 1 of 12)	(TTATA)n|Simple_repeat|Simple_repeat	205	NM_013747	27277	Mm.273370	NM_013747	ENSMUSG00000021192	Golga5	Ret-II	golgi autoantigen, golgin subfamily a, 5	protein-coding
mm_163058.1	chr11	62005336	62005344	+	1	NA	intron (NM_001310526, intron 1 of 7)	intron (NM_001310526, intron 1 of 7)	48577	NM_001310526	432572	Mm.438022	NM_001029936	ENSMUSG00000042331	Specc1	2810012G08Rik|B230396K10Rik|Cytsb	sperm antigen with calponin homology and coiled-coil domains 1	protein-coding
mm_19427.1	chr2	91931995	91932008	-	1	NA	promoter-TSS (NM_001291481)	promoter-TSS (NM_001291481)	-142	NM_001291482	17242	Mm.906	NM_010784	ENSMUSG00000027239	Mdk	MK|Mek	midkine	protein-coding
mm_3717.1	chr1	154010033	154010063	+	1	NA	Intergenic	Intergenic	110119	NM_008131	14645	Mm.210745	NM_008131	ENSMUSG00000026473	Glul	GS|Glns	glutamate-ammonia ligase (glutamine synthetase)	protein-coding
mm_40923.1	chr5	75981223	75981245	+	1	NA	Intergenic	Intergenic	-2806	NM_010612	16542	Mm.285	NM_010612	ENSMUSG00000062960	Kdr	6130401C07|Flk-1|Flk1|Krd-1|Ly73|VEGFR-2|VEGFR2|sVEGFR-2	kinase insert domain protein receptor	protein-coding
mm_95334.1	chr11	46810793	46810809	+	1	NA	promoter-TSS (NM_178759)	promoter-TSS (NM_178759)	2	NM_178759	276891	Mm.69002	NM_178759	ENSMUSG00000055546	Timd4	B430010N18Rik|TIM-4|Tim4	T cell immunoglobulin and mucin domain containing 4	protein-coding
mm_131921.1	chr16	23317638	23317644	+	1	NA	5' UTR (NM_001252506, exon 2 of 7)	5' UTR (NM_001252506, exon 2 of 7)	27171	NM_001252506	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_80938.1	chr9	102717278	102717303	+	1	NA	promoter-TSS (NM_019764)	promoter-TSS (NM_019764)	-514	NM_019764	56332	Mm.21145	NM_019764	ENSMUSG00000032531	Amotl2	AW549739|C79691|Lccp|MASCOT|mKIAA0989	angiomotin-like 2	protein-coding
mm_62581.1	chr7	105375054	105375072	+	1	NA	promoter-TSS (NM_001195727)	promoter-TSS (NM_001195727)	25	NM_001329995	100503879	Mm.380109	NM_001195727	ENSMUSG00000078611	Gm5901	EG545989	predicted gene 5901	protein-coding
mm_156957.1	chrX	169989265	169989281	+	1	NA	3' UTR (NM_001290504, exon 10 of 10)	3' UTR (NM_001290504, exon 10 of 10)	-10356	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_151138.1	chr19	52613603	52613605	+	1	NA	Intergenic	Intergenic	-309577	NR_030678	100043450	Mm.145594	NR_030678		AA387883	-	expressed sequence AA387883	ncRNA
mm_6782.1	chr1	84139285	84139298	-	1	NA	intron (NM_001003948, intron 2 of 2)	L1_Mur3|LINE|L1	79670	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_48892.1	chr5	151428151	151428162	-	1	NA	non-coding (NR_131166, exon 3 of 4)	non-coding (NR_131166, exon 3 of 4)	21652	NR_131166	100042166	Mm.443286	NR_131166	ENSMUSG00000097321	Gm3704	-	predicted gene 3704	ncRNA
mm_141385.1	chr17	29090852	29090876	-	1	NA	promoter-TSS (NM_001111099)	promoter-TSS (NM_001111099)	-115	NM_001111099	12575	Mm.195663	NM_007669	ENSMUSG00000023067	Cdkn1a	CAP20|CDKI|CIP1|Cdkn1|P21|SDI1|Waf1|mda6|p21Cip1|p21WAF	cyclin-dependent kinase inhibitor 1A (P21)	protein-coding
mm_12076.1	chr2	59779489	59779506	+	1	NA	intron (NM_198294, intron 7 of 26)	intron (NM_198294, intron 7 of 26)	103109	NM_001159636	72137	Mm.288734	NM_028118	ENSMUSG00000026988	Wdsub1	1700048E19Rik|2610014F08Rik	WD repeat, SAM and U-box domain containing 1	protein-coding
mm_48084.1	chr5	136986837	136986878	-	1	NA	promoter-TSS (NM_011962)	promoter-TSS (NM_011962)	47	NM_001310747	70103	Mm.273147	NM_027318	ENSMUSG00000059518	Znhit1	2700001K05Rik|ZNFN4A1	zinc finger, HIT domain containing 1	protein-coding
mm_59322.1	chr7	25301529	25301540	+	1	NA	intron (NM_001081294, intron 1 of 2)	intron (NM_001081294, intron 1 of 2)	175	NM_001081294	623131	Mm.172160	NM_001081294	ENSMUSG00000058741	Prr19	EG623131	proline rich 19	protein-coding
mm_162223.1	chrX	144688952	144688952	+	1	NA	promoter-TSS (NM_009428)	promoter-TSS (NM_009428)	45	NM_001033795	619287	Mm.387961	NM_001033795	ENSMUSG00000071679	Zcchc16	C230031A03Rik|Mar4	zinc finger, CCHC domain containing 16	protein-coding
mm_34567.1	chr4	150029840	150029850	+	1	NA	Intergenic	Intergenic	-20822	NM_173371	100198	Mm.22183	NM_173371	ENSMUSG00000028980	H6pd	AI785303|G6pd1|Gpd-1|Gpd1	hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase)	protein-coding
mm_51663.1	chr6	86195428	86195439	+	1	NA	5' UTR (NM_031199, exon 1 of 6)	5' UTR (NM_031199, exon 1 of 6)	206	NM_031199	21802	Mm.137222	NM_031199	ENSMUSG00000029999	Tgfa	wa-1|wa1	transforming growth factor alpha	protein-coding
mm_34880.1	chr4	155582477	155582489	+	1	NA	intron (NM_138671, intron 3 of 11)	intron (NM_138671, intron 3 of 11)	18668	NM_001159637	192185	Mm.28347	NM_138671	ENSMUSG00000029063	Nadk	4432404C02Rik|BC004012	NAD kinase	protein-coding
mm_6618.1	chr1	75506463	75506490	-	1	NA	promoter-TSS (NM_178884)	promoter-TSS (NM_178884)	-24	NM_001310679	98733	Mm.236454	NM_178884	ENSMUSG00000026211	Obsl1	AW822216	obscurin-like 1	protein-coding
mm_162896.1	chr10	112399755	112399761	+	1	NA	intron (NM_001025581, intron 2 of 4)	intron (NM_001025581, intron 2 of 4)	128635	NM_001025581	268345	Mm.336242	NM_001025581	ENSMUSG00000035681	Kcnc2	AW047325|B230117I07|KShIIIA|Kv3.2	potassium voltage gated channel, Shaw-related subfamily, member 2	protein-coding
mm_101339.1	chr11	23519696	23519722	-	1	NA	promoter-TSS (NM_026105)	promoter-TSS (NM_026105)	233	NM_001110133	67358	Mm.87328	NM_026105	ENSMUSG00000020286	1700093K21Rik	-	RIKEN cDNA 1700093K21 gene	protein-coding
mm_139841.1	chr17	69262190	69262268	+	1	NA	exon (NM_013813, exon 12 of 22)	exon (NM_013813, exon 12 of 22)	14977	NR_045428	69750	Mm.439063	NR_045428	ENSMUSG00000100572	2410021H03Rik	-	RIKEN cDNA 2410021H03 gene	ncRNA
mm_33645.1	chr4	133039362	133039383	+	1	NA	intron (NM_146155, intron 2 of 6)	CpG	27866	NM_146155	230793	Mm.31816	NM_146155	ENSMUSG00000037692	Ahdc1	D030015G18Rik	AT hook, DNA binding motif, containing 1	protein-coding
mm_37304.1	chr4	119279107	119279120	-	1	NA	exon (NM_011732, exon 7 of 8)	exon (NM_011732, exon 7 of 8)	15400	NM_011732	22608	Mm.258204	NM_011732	ENSMUSG00000028639	Ybx1	1700102N10Rik|C79409|EF1A|MSY1|Nsep1|YB-1|dbpB|mYB-1a	Y box protein 1	protein-coding
mm_50344.1	chr6	48554931	48554962	+	1	NA	5' UTR (NM_177736, exon 1 of 3)	5' UTR (NM_177736, exon 1 of 3)	147	NM_177736	243371	Mm.290764	NM_177736	ENSMUSG00000073096	Lrrc61	BC027309	leucine rich repeat containing 61	protein-coding
mm_64562.1	chr7	144838591	144838614	+	1	NA	promoter-TSS (NM_008007)	promoter-TSS (NM_008007)	-10	NM_008007	14174	Mm.4947	NM_008007	ENSMUSG00000031074	Fgf3	Fgf-3|Int-2|Int-P	fibroblast growth factor 3	protein-coding
mm_125022.1	chr15	25713871	25713885	+	1	NA	intron (NM_019472, intron 3 of 40)	CpG	91328	NM_019472	17909	Mm.60590	NM_019472	ENSMUSG00000022272	Myo10	AW048724|D15Ertd600e|mKIAA0799|myosin-X	myosin X	protein-coding
mm_113043.1	chr13	23574435	23574449	+	1	NA	promoter-TSS (NM_178188)	promoter-TSS (NM_178188)	61	NM_178188	319165	Mm.390553	NM_178188	ENSMUSG00000071478	Hist1h2ad	-	histone cluster 1, H2ad	protein-coding
mm_158623.1	chrX	152769673	152769686	-	1	NA	promoter-TSS (NM_172441)	promoter-TSS (NM_172441)	-193	NM_172441	110380	Mm.40796	NM_172441	ENSMUSG00000045180	Shroom2	4832440C16|Apxl|C630003H05Rik|Shrm2	shroom family member 2	protein-coding
mm_144843.1	chr18	36563683	36563686	+	1	NA	intron (NM_175375, intron 1 of 33)	intron (NM_175375, intron 1 of 33)	3081	NM_175375	108857	Mm.482287	NM_175375	ENSMUSG00000024483	Ankhd1	1110004O12Rik|4933432B13Rik|9130019P20Rik|A530027J04Rik|A630021B20Rik|AA571404|Mask|mFLJ00246|mKIAA1085	ankyrin repeat and KH domain containing 1	protein-coding
mm_113344.1	chr13	31803850	31803853	+	1	NA	Intergenic	Intergenic	-2795	NM_008592	17300	Mm.12949	NM_008592	ENSMUSG00000050295	Foxc1	FREAC3|Fkh1|Mf1|Mf4|ch|fkh-1|frkhda	forkhead box C1	protein-coding
mm_44032.1	chr5	147431593	147431598	+	1	NA	intron (NM_028291, intron 1 of 18)	intron (NM_028291, intron 1 of 18)	1015	NM_028291	72587	Mm.320469	NM_028291	ENSMUSG00000029647	Pan3	2700050F09Rik|A430027N15Rik|AU014670	PAN3 poly(A) specific ribonuclease subunit	protein-coding
mm_41586.1	chr5	93206047	93206052	+	1	NA	promoter-TSS (NM_029363)	promoter-TSS (NM_029363)	446	NM_017367	12453	Mm.250419	NM_017367	ENSMUSG00000063015	Ccni	-	cyclin I	protein-coding
mm_165114.1	chr19	58732088	58732105	-	1	NA	exon (NM_018874, exon 5 of 13)	exon (NM_018874, exon 5 of 13)	3209	NM_018874	18946	Mm.10753	NM_018874	ENSMUSG00000042179	Pnliprp1	Plrp1	pancreatic lipase related protein 1	protein-coding
mm_30204.1	chr3	144720388	144720395	-	1	NA	promoter-TSS (NM_019464)	promoter-TSS (NM_019464)	-56	NM_001282037	54673	Mm.271775	NM_019464	ENSMUSG00000037062	Sh3glb1	AA409932|AI314629|AU015566|Bif-1|mKIAA0491	SH3-domain GRB2-like B1 (endophilin)	protein-coding
mm_74969.1	chr8	27043010	27043032	-	1	NA	intron (NM_001039077, intron 1 of 4)	CpG	466	NM_054057	114863	Mm.277501	NM_054057	ENSMUSG00000031485	Prosc	1700024N20Rik|2200002F22Rik	proline synthetase co-transcribed	protein-coding
mm_155808.1	chrX	99136181	99136183	+	1	NA	5' UTR (NM_010110, exon 1 of 5)	5' UTR (NM_010110, exon 1 of 5)	121	NM_010110	13641	Mm.3374	NM_010110	ENSMUSG00000031217	Efnb1	Cek5-L|EFL-3|Elk-L|Epl2|Eplg2|LERK-2|Lerk2|Stra1	ephrin B1	protein-coding
mm_107035.1	chr12	13501210	13501213	+	1	NA	intron (NM_027706, intron 44 of 51)	intron (NM_027706, intron 44 of 51)	126435	NR_136761	102639399	Mm.122052	NR_136761		Gm35725	-	predicted gene, 35725	ncRNA
mm_113089.1	chr13	23934435	23934439	+	1	NA	promoter-TSS (NM_175663)	promoter-TSS (NM_175663)	-25	NM_175658	319163	Mm.377876	NM_175658	ENSMUSG00000060081	Hist1h2aa	Th2a	histone cluster 1, H2aa	protein-coding
mm_108941.1	chr12	102129020	102129049	+	1	NA	promoter-TSS (NM_172152)	promoter-TSS (NM_172152)	-385	NM_172152	238384	Mm.312448	NM_172152	ENSMUSG00000041771	Slc24a4	A930002M03Rik|AW492432|NCKX4	solute carrier family 24 (sodium/potassium/calcium exchanger), member 4	protein-coding
mm_103626.1	chr11	78697586	78697605	-	1	NA	promoter-TSS (NM_008702)	promoter-TSS (NM_008702)	-170	NM_008702	18099	Mm.9001	NM_008702	ENSMUSG00000017376	Nlk	AI194375	nemo like kinase	protein-coding
mm_138660.1	chr17	35868619	35868647	+	1	NA	exon (NM_001146711, exon 2 of 4)	exon (NM_001146711, exon 2 of 4)	2018	NM_175242	76448	Mm.359982	NM_175242	ENSMUSG00000034595	Ppp1r18	2310014H01Rik|AA407849|AI450394	protein phosphatase 1, regulatory subunit 18	protein-coding
mm_134138.1	chr16	10683584	10683596	-	1	NA	intron (NM_001204229, intron 18 of 22)	L1ME3G|LINE|L1	101946	NM_009896	12703	Mm.130	NM_009896	ENSMUSG00000038037	Socs1	Cish1|Cish7|JAB|SOCS-1|SSI-1	suppressor of cytokine signaling 1	protein-coding
mm_155947.1	chrX	104947695	104947696	+	1	NA	Intergenic	Intergenic	-90428	NM_053206	272790	Mm.165776	NM_053206	ENSMUSG00000031224	Magee2	9630059J11Rik|BB131182|Mage-e2	melanoma antigen, family E, 2	protein-coding
mm_69936.1	chr7	142095221	142095231	-	1	NA	promoter-TSS (NM_008748)	promoter-TSS (NM_008748)	58	NM_008748	18218	Mm.39725	NM_008748	ENSMUSG00000037887	Dusp8	5530400B01Rik|AI593498|Nttp1	dual specificity phosphatase 8	protein-coding
mm_168456.1	chr11	43631066	43631072	-	1	NA	Intergenic	RLTR1B|LTR|ERV1	-29507	NM_008375	16204	Mm.142716	NM_008375	ENSMUSG00000020405	Fabp6	GT|I-15P|I-BABP|ILBP|ILBP3|Illbp	fatty acid binding protein 6, ileal (gastrotropin)	protein-coding
mm_9569.1	chr1	173979758	173979771	-	1	NA	intron (NM_008327, intron 1 of 6)	intron (NM_008327, intron 1 of 6)	3080	NM_008327	26388	Mm.218770	NM_008327	ENSMUSG00000026535	Ifi202b	Ifbip-1|Ifi202|Ifi202a|p202	interferon activated gene 202B	protein-coding
mm_19808.1	chr2	110314235	110314246	-	1	NA	Intergenic	Intergenic	-8515	NM_130452	170442	Mm.27335	NM_130452	ENSMUSG00000041660	Bbox1	AI874739	butyrobetaine (gamma), 2-oxoglutarate dioxygenase 1 (gamma-butyrobetaine hydroxylase)	protein-coding
mm_155378.1	chrX	71663666	71663671	+	1	NA	promoter-TSS (NM_010340)	promoter-TSS (NM_010340)	1	NM_001308501	14765	Mm.33336	NM_010340	ENSMUSG00000056380	Gpr50	H9	G-protein-coupled receptor 50	protein-coding
mm_169365.1	chr14	32201871	32201871	-	1	NA	promoter-TSS (NM_011960)	promoter-TSS (NM_011960)	20	NM_016897	53600	Mm.303703	NM_016897	ENSMUSG00000013701	Timm23	Tim23	translocase of inner mitochondrial membrane 23	protein-coding
mm_20227.1	chr2	125782835	125782845	-	1	NA	promoter-TSS (NM_177608)	promoter-TSS (NM_177608)	30	NM_177608	70354	Mm.138091	NM_133725	ENSMUSG00000035093	Secisbp2l	3110001I20Rik|AI504340|C630011I23	SECIS binding protein 2-like	protein-coding
mm_2182.1	chr1	88702276	88702296	+	1	NA	promoter-TSS (NM_177305)	promoter-TSS (NM_177305)	-95	NM_177305	320982	Mm.27968	NM_177305	ENSMUSG00000049866	Arl4c	A630084M22Rik|Arl7|LAK	ADP-ribosylation factor-like 4C	protein-coding
mm_106827.1	chr12	7992939	7992949	+	1	NA	exon (NM_009693, exon 16 of 29)	exon (NM_009693, exon 16 of 29)	15267	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_90981.1	chr10	13553141	13553153	-	1	NA	promoter-TSS (NM_019961)	promoter-TSS (NM_019961)	-5	NM_001347361	56535	Mm.282711	NM_019961	ENSMUSG00000019809	Pex3	1700014F15Rik|2810027F19Rik|2900010N04Rik	peroxisomal biogenesis factor 3	protein-coding
mm_77581.1	chr8	123751091	123751093	-	1	NA	Intergenic	RLTR17B_Mm|LTR|ERVK	17134	NR_040702	234863	Mm.246601	NR_040702	ENSMUSG00000110599	6030466F02Rik	-	RIKEN cDNA 6030466F02 gene	ncRNA
mm_53326.1	chr6	129229396	129229415	+	1	NA	Intergenic	Intergenic	8640	NR_040265	76432	Mm.261738	NR_040265	ENSMUSG00000097354	2310001H17Rik	AI646108	RIKEN cDNA 2310001H17 gene	ncRNA
mm_79265.1	chr9	50753209	50753250	+	1	NA	promoter-TSS (NM_024441)	promoter-TSS (NM_024441)	258	NM_009964	12955	Mm.178	NM_009964	ENSMUSG00000032060	Cryab	Crya-2|Crya2|HspB5|P23	crystallin, alpha B	protein-coding
mm_16051.1	chr2	167760219	167760250	+	1	NA	Intergenic	Intergenic	69057	NR_015500	329562	Mm.123101	NM_177851	ENSMUSG00000006462	A530013C23Rik	-	RIKEN cDNA A530013C23 gene	ncRNA
mm_13864.1	chr2	119742345	119742355	+	1	NA	promoter-TSS (NM_146125)	promoter-TSS (NM_146125)	13	NM_146125	228550	Mm.65337	NM_146125	ENSMUSG00000027296	Itpka	-	inositol 1,4,5-trisphosphate 3-kinase A	protein-coding
mm_57778.1	chr6	129238484	129238505	-	1	NA	promoter-TSS (NR_040268)	promoter-TSS (NR_040268)	-12	NR_040266	76432	Mm.261738	NR_040265	ENSMUSG00000097354	2310001H17Rik	AI646108	RIKEN cDNA 2310001H17 gene	ncRNA
mm_56206.1	chr6	89004168	89004170	-	1	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	-91941	NR_134978	232217	Mm.281744	NM_175017	ENSMUSG00000055403	4933427D06Rik	-	RIKEN cDNA 4933427D06 gene	ncRNA
mm_36980.1	chr4	109657820	109657846	-	1	NA	Intergenic	Intergenic	7539	NM_007671	12580	Mm.1912	NM_007671	ENSMUSG00000028551	Cdkn2c	C77269|INK4c|p18|p18-INK4c|p18-INK6|p18INK4c	cyclin-dependent kinase inhibitor 2C (p18, inhibits CDK4)	protein-coding
mm_80941.1	chr9	102717733	102717745	+	1	NA	promoter-TSS (NM_019764)	promoter-TSS (NM_019764)	-65	NM_019764	56332	Mm.21145	NM_019764	ENSMUSG00000032531	Amotl2	AW549739|C79691|Lccp|MASCOT|mKIAA0989	angiomotin-like 2	protein-coding
mm_140397.1	chr17	87636104	87636107	+	1	NA	intron (NM_008532, intron 1 of 9)	intron (NM_008532, intron 1 of 9)	126	NM_008532	17075	Mm.4259	NM_008532	ENSMUSG00000045394	Epcam	CD326|EGP|EGP-2|Egp314|Ep-CAM|EpCAM1|GA733-2|Ly74|TROP1|Tacsd1|Tacstd1|gp40	epithelial cell adhesion molecule	protein-coding
mm_46444.1	chr5	105102230	105102233	-	1	NA	intron (NM_172777, intron 3 of 10)	RLTR31C_MM|LTR|ERVK	8061	NM_172777	236573	Mm.425261	NM_172777	ENSMUSG00000029298	Gbp9	-	guanylate-binding protein 9	protein-coding
mm_46711.1	chr5	110378141	110378177	-	1	NA	exon (NM_028596, exon 4 of 12)	exon (NM_028596, exon 4 of 12)	8968	NM_028596	381668	Mm.348782	NM_028596	ENSMUSG00000043323	Fbrsl1	2410025L10Rik|AI467568|Gm1049|Gm29766|mKIAA1545	fibrosin-like 1	protein-coding
mm_102895.1	chr11	69423863	69423867	-	1	NA	exon (NM_001081330, exon 78 of 86)	exon (NM_001081330, exon 78 of 86)	-10190	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_166959.1	chr7	44479012	44479020	+	1	NA	Intergenic	Intergenic	-5501	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_32387.1	chr4	106587273	106587296	+	1	NA	3' UTR (NM_053272, exon 9 of 9)	3' UTR (NM_053272, exon 9 of 9)	26246	NM_053272	74754	Mm.133370	NM_053272	ENSMUSG00000034926	Dhcr24	2310076D10Rik|5830417J06Rik|mKIAA0018	24-dehydrocholesterol reductase	protein-coding
mm_141509.1	chr17	31654933	31654935	-	1	NA	intron (NM_001163769, intron 2 of 7)	intron (NM_001163769, intron 2 of 7)	3820	NM_024187	108121	Mm.379289	NM_024187	ENSMUSG00000061613	U2af1	2010107D16Rik|35kDa	U2 small nuclear ribonucleoprotein auxiliary factor (U2AF) 1	protein-coding
mm_70314.1	chr8	4240129	4240148	+	1	NA	promoter-TSS (NM_001291783)	promoter-TSS (NM_001291783)	33	NM_001291778	26400	Mm.3906	NM_011944	ENSMUSG00000002948	Map2k7	5930412N11Rik|JNKK 2|Jnkk2|MAPKK 7|MEK 7|Mapkk7|Mek7|Mkk7|Prkmk7|sek2	mitogen-activated protein kinase kinase 7	protein-coding
mm_35578.1	chr4	41740875	41740896	-	1	NA	exon (NM_001286551, exon 2 of 4)	exon (NM_001286551, exon 2 of 4)	474	NM_001286540	18391	Mm.425181	NM_011014	ENSMUSG00000036078	Sigmar1	Oprs1|Sig1R|sigma1R	sigma non-opioid intracellular receptor 1	protein-coding
mm_93844.1	chr10	121626453	121626513	-	1	NA	promoter-TSS (NM_001081056)	promoter-TSS (NM_001081056)	-167	NM_001081056	73192	Mm.25042	NM_001081056	ENSMUSG00000034667	Xpot	1110004L07Rik|3110065H13Rik|AI452076|C79645|EXPORTIN-T	exportin, tRNA (nuclear export receptor for tRNAs)	protein-coding
mm_100833.1	chr11	5478338	5478372	-	1	NA	Intergenic	RLTR16|LTR|ERVK	-33508	NM_001080924	407821	Mm.216313	NM_001080924	ENSMUSG00000041961	Znrf3	Gm1167	zinc and ring finger 3	protein-coding
mm_31505.1	chr4	53566193	53566198	+	1	NA	intron (NM_133891, intron 15 of 15)	intron (NM_133891, intron 15 of 15)	-65276	NM_176966	319636	Mm.103464	NM_176966	ENSMUSG00000054752	Fsd1l	A230072O16Rik|Ccdc10|Csdufd1|Fsd1nl|OTTMUSG00000007002	fibronectin type III and SPRY domain containing 1-like	protein-coding
mm_32465.1	chr4	107679422	107679439	+	1	NA	exon (NM_019872, exon 3 of 4)	exon (NM_019872, exon 3 of 4)	4732	NM_019872	56296	Mm.141324	NM_019872	ENSMUSG00000028610	Dmrtb1	Dmrt6|Prp13	DMRT-like family B with proline-rich C-terminal, 1	protein-coding
mm_78927.1	chr9	45055229	45055243	+	1	NA	promoter-TSS (NM_001093749)	promoter-TSS (NM_001093749)	55	NM_001093749	319742	Mm.49611	NM_176993	ENSMUSG00000070305	Mpzl3	5430427F17Rik|A530065I17Rik|rc	myelin protein zero-like 3	protein-coding
mm_93158.1	chr10	93161734	93161738	-	1	NA	intron (NM_146239, intron 1 of 16)	intron (NM_146239, intron 1 of 16)	860	NM_146239	237459	Mm.217404	NM_146239	ENSMUSG00000020015	Cdk17	6430598J10Rik|Pctk2	cyclin-dependent kinase 17	protein-coding
mm_159110.1	chr2	45110465	45110465	-	1	NA	promoter-TSS (NM_001289521)	promoter-TSS (NM_001289521)	-188	NM_001289521	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_56323.1	chr6	92480976	92480992	-	1	NA	5' UTR (NM_001134460, exon 1 of 8)	5' UTR (NM_001134460, exon 1 of 8)	408	NM_001134460	243548	Mm.248820	NM_001081146	ENSMUSG00000030020	Prickle2	6230400G14Rik|6720451F06Rik|mpk2	prickle planar cell polarity protein 2	protein-coding
mm_77568.1	chr8	123429596	123429599	-	1	NA	Intergenic	MuLV-int|LTR|ERV1	-13359	NM_001253784	23854	Mm.275127	NM_054046	ENSMUSG00000001482	Def8	AI449518|D8Ertd713e|DEF-8	differentially expressed in FDCP 8	protein-coding
mm_150786.1	chr19	44298061	44298127	+	1	NA	exon (NM_009128, exon 3 of 6)	exon (NM_009128, exon 3 of 6)	4418	NM_009128	20250	Mm.487021	NM_009128	ENSMUSG00000025203	Scd2	Mir5114|Scd-2|mir-5114|swty	stearoyl-Coenzyme A desaturase 2	protein-coding
mm_114221.1	chr13	56438344	56438369	+	1	NA	promoter-TSS (NM_177809)	promoter-TSS (NM_177809)	1	NM_177809	328258	Mm.482177	NM_177809	ENSMUSG00000021509	Slc25a48	AU042651|E230025K15	solute carrier family 25, member 48	protein-coding
mm_135509.1	chr16	48410121	48410150	-	1	NA	intron (NR_015373, intron 2 of 3)	ID_B1|SINE|B4	2281	NR_015373	433023	Mm.483302	NR_015373	ENSMUSG00000110573	Gm5485	EG433023	predicted gene 5485	ncRNA
mm_31964.1	chr4	86930734	86930742	+	1	NA	intron (NM_001290543, intron 5 of 5)	RLTR51A_Mm|LTR|ERVK?	56324	NM_139306	230379	Mm.45019	NM_139306	ENSMUSG00000038007	Acer2	2410116I05Rik|Asah3l|CRG-L1|maCER2	alkaline ceramidase 2	protein-coding
mm_117956.1	chr13	99444556	99444562	-	1	NA	intron (NM_008634, intron 2 of 6)	intron (NM_008634, intron 2 of 6)	-31733	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_113030.1	chr13	23493833	23493843	+	1	NA	Intergenic	Intergenic	-4981	NM_001289614	238555	Mm.129668	NM_175938	ENSMUSG00000053216	Btn2a2	Btn2|D030063K05	butyrophilin, subfamily 2, member A2	protein-coding
mm_51920.1	chr6	91252574	91252576	+	1	NA	intron (NM_007992, intron 4 of 17)	intron (NM_007992, intron 4 of 17)	39811	NM_007992	14115	Mm.249146	NM_007992	ENSMUSG00000064080	Fbln2	5730577E14Rik|FIBL-2	fibulin 2	protein-coding
mm_28491.1	chr3	92484339	92484349	-	1	NA	exon (NM_009264, exon 2 of 2)	exon (NM_009264, exon 2 of 2)	1537	NM_009264	20753	Mm.331191	NM_009264	ENSMUSG00000050359	Sprr1a	AI528815|SPR1a|mSPRR1A	small proline-rich protein 1A	protein-coding
mm_79057.1	chr9	46230086	46230099	+	1	NA	exon (NM_009692, exon 4 of 4)	exon (NM_009692, exon 4 of 4)	1462	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2|apo-AI|apoA-I	apolipoprotein A-I	protein-coding
mm_92412.1	chr10	76723462	76723517	-	1	NA	exon (NM_009933, exon 3 of 35)	exon (NM_009933, exon 3 of 35)	2555	NM_009933	12833	Mm.2509	NM_009933	ENSMUSG00000001119	Col6a1	AI747156|Col6a-1	collagen, type VI, alpha 1	protein-coding
mm_156297.1	chrX	136837591	136837625	+	1	NA	3' UTR (NM_011123, exon 7 of 7)	3' UTR (NM_011123, exon 7 of 7)	14862	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_148968.1	chr19	7536873	7536888	+	1	NA	3' UTR (NM_001163505, exon 13 of 13)	3' UTR (NM_001163505, exon 13 of 13)	-20579	NM_139269	225845	Mm.274810	NM_139269	ENSMUSG00000060675	Pla2g16	C78643|HRSL3|Hrasls3|Hrev107|MLP-3	phospholipase A2, group XVI	protein-coding
mm_39773.1	chr5	30017929	30017932	+	1	NA	intron (NM_001314054, intron 3 of 4)	intron (NM_001314054, intron 3 of 4)	4816	NM_031168	16193	Mm.1019	NM_031168	ENSMUSG00000025746	Il6	Il-6	interleukin 6	protein-coding
mm_146716.1	chr18	15063561	15063617	-	1	NA	promoter-TSS (NM_001142731)	promoter-TSS (NM_001142731)	-7	NM_001142731	106931	Mm.329299	NM_134112	ENSMUSG00000036225	Kctd1	4933402K10Rik|AI661543|AW553000	potassium channel tetramerisation domain containing 1	protein-coding
mm_12231.1	chr2	68568563	68568571	+	1	NA	Intergenic	Intergenic	-13846	NM_177651	227998	Mm.67562	NM_177651	ENSMUSG00000053896	4933409G03Rik	-	RIKEN cDNA 4933409G03 gene	protein-coding
mm_103308.1	chr11	72796758	72796766	-	1	NA	promoter-TSS (NM_001024926)	promoter-TSS (NM_001024926)	536	NM_001045536	195018	Mm.272030	NM_001045536	ENSMUSG00000055670	Zzef1	8430405D05Rik|BC051585|C130099L13Rik|C85424|NSPA|mKIAA0399	zinc finger, ZZ-type with EF hand domain 1	protein-coding
mm_76063.1	chr8	78147379	78147393	-	1	NA	Intergenic	Intergenic	-65956	NM_183096	73301	Mm.61243	NM_183096	ENSMUSG00000037101	Ttc29	1700031F13Rik	tetratricopeptide repeat domain 29	protein-coding
mm_10814.1	chr2	24350352	24350354	+	1	NA	3' UTR (NM_031167, exon 5 of 5)	3' UTR (NM_031167, exon 5 of 5)	4982	NM_001039701	16181	Mm.882	NM_031167	ENSMUSG00000026981	Il1rn	F630041P17Rik|IL-1ra	interleukin 1 receptor antagonist	protein-coding
mm_14406.1	chr2	130274425	130274435	+	1	NA	promoter-TSS (NM_024193)	promoter-TSS (NM_024193)	18	NM_024193	67134	Mm.29363	NM_024193	ENSMUSG00000027405	Nop56	2310044F10Rik|Nol5a	NOP56 ribonucleoprotein	protein-coding
mm_2769.1	chr1	130717321	130717333	+	1	NA	promoter-TSS (NM_178691)	promoter-TSS (NM_178691)	0	NM_178691	226418	Mm.106553	NM_178691	ENSMUSG00000046404	Yod1	6330564D18Rik|9930028C20Rik|Hshin7	YOD1 deubiquitinase	protein-coding
mm_158071.1	chrX	101264649	101264674	-	1	NA	promoter-TSS (NM_001317221)	promoter-TSS (NM_001317221)	-669	NM_001317221	245536	Mm.212463	NM_001033362	ENSMUSG00000090141	Gm614	-	predicted gene 614	protein-coding
mm_18458.1	chr2	61747540	61747558	-	1	NA	intron (NM_021526, intron 3 of 11)	RLTR25A|LTR|ERVK	35855	NM_021526	59029	Mm.218198	NM_021526	ENSMUSG00000026914	Psmd14	2610312C03Rik|3200001M20Rik|AA986732|Pad1|Poh1|rpm11	proteasome (prosome, macropain) 26S subunit, non-ATPase, 14	protein-coding
mm_88492.1	chr10	77814621	77814624	+	1	NA	promoter-TSS (NM_001205009)	promoter-TSS (NM_001205009)	-60	NM_001205009	100040299	Mm.486155	NM_001205009		Gm2696	-	predicted gene 2696	protein-coding
mm_20287.1	chr2	126925805	126925815	-	1	NA	exon (NM_023220, exon 5 of 15)	exon (NM_023220, exon 5 of 15)	7425	NM_023220	66552	Mm.269928	NM_023220	ENSMUSG00000027366	Sppl2a	2010106G01Rik|C130089K23Rik	signal peptide peptidase like 2A	protein-coding
mm_153544.1	chr19	42059453	42059461	-	1	NA	intron (NM_026152, intron 1 of 6)	intron (NM_026152, intron 1 of 6)	7229	NM_025752	66765	Mm.440412	NM_025752	ENSMUSG00000090369	4933411K16Rik	-	RIKEN cDNA 4933411K16 gene	protein-coding
mm_52137.1	chr6	97957034	97957038	+	1	NA	intron (NM_001113198, intron 2 of 9)	intron (NM_001113198, intron 2 of 9)	27219	NM_001178049	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_48775.1	chr5	148535201	148535202	-	1	NA	intron (NM_011908, intron 1 of 4)	intron (NM_011908, intron 1 of 4)	17587	NM_011908	24109	Mm.21846	NM_011908	ENSMUSG00000001687	Ubl3	AW108023|HCG	ubiquitin-like 3	protein-coding
mm_55040.1	chr6	48987935	48987946	-	1	NA	exon (NM_172888, exon 1 of 5)	exon (NM_172888, exon 1 of 5)	1079	NM_172888	243377	Mm.446302	NM_172888	ENSMUSG00000039215	Svs1	9530003A11	seminal vesicle secretory protein 1	protein-coding
mm_119063.1	chr14	30743804	30743808	+	1	NA	intron (NM_001166531, intron 2 of 21)	intron (NM_001166531, intron 2 of 21)	28191	NM_001166532	54650	Mm.294662	NM_019460	ENSMUSG00000006527	Sfmbt1	4930442N21Rik|9330180L21Rik|AA536974|Sfmbt|Smr	Scm-like with four mbt domains 1	protein-coding
mm_108149.1	chr12	76307063	76307074	+	1	NA	intron (NM_138745, intron 21 of 27)	intron (NM_138745, intron 21 of 27)	-17823	NM_001101471	238276	Mm.311452	NM_001101471	ENSMUSG00000021057	Akap5	3526401B18Rik|AKAP 150|AKAP-5|AKAP150|BB098886|Gm258|P150	A kinase (PRKA) anchor protein 5	protein-coding
mm_2291.1	chr1	91442878	91442905	+	1	NA	intron (NM_011066, intron 6 of 22)	MLT-int|LTR|ERVL-MaLR	16437	NM_011066	18627	Mm.482463	NM_011066	ENSMUSG00000055866	Per2	mKIAA0347|mPer2	period circadian clock 2	protein-coding
mm_3949.1	chr1	164048215	164048216	+	1	NA	promoter-TSS (NM_011345)	promoter-TSS (NM_011345)	-19	NM_011345	20339	Mm.5245	NM_011345	ENSMUSG00000026582	Sele	CD62E|E-selectin|ELAM-1|Elam|LECAM2	selectin, endothelial cell	protein-coding
mm_40763.1	chr5	66977013	66977037	+	1	NA	intron (NM_001256122, intron 3 of 20)	ORR1E|LTR|ERVL-MaLR	8609	NM_001256122	77569	Mm.374778	NM_001001980	ENSMUSG00000037736	Limch1	3732412D22Rik|mKIAA1102	LIM and calponin homology domains 1	protein-coding
mm_13703.1	chr2	117139414	117139424	+	1	NA	intron (NM_033524, intron 1 of 6)	intron (NM_033524, intron 1 of 6)	18348	NM_033524	114715	Mm.245890	NM_033524	ENSMUSG00000027351	Spred1	5730461F13Rik|AL024345|AW047647	sprouty protein with EVH-1 domain 1, related sequence	protein-coding
mm_152271.1	chr19	8819185	8819191	-	1	NA	promoter-TSS (NM_001081196)	promoter-TSS (NM_001081196)	106	NM_027412	70387	Mm.261082	NM_027412	ENSMUSG00000071660	Ttc9c	2210019E14Rik|6330408J23Rik	tetratricopeptide repeat domain 9C	protein-coding
mm_167348.1	chr8	82774079	82774087	-	1	NA	promoter-TSS (NM_145600)	promoter-TSS (NM_145600)	43	NM_145600	30932	Mm.269248	NM_145600	ENSMUSG00000031711	Zfp330	BC008086|Noa36|Znf330	zinc finger protein 330	protein-coding
mm_91506.1	chr10	37136626	37136649	-	1	NA	exon (NM_008538, exon 2 of 2)	exon (NM_008538, exon 2 of 2)	2289	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_62962.1	chr7	119760982	119760988	+	1	NA	promoter-TSS (NM_016870)	promoter-TSS (NM_016870)	62	NM_212442	20216	Mm.334199	NM_016870	ENSMUSG00000030935	Acsm3	Sa|Sah	acyl-CoA synthetase medium-chain family member 3	protein-coding
mm_80698.1	chr9	92193153	92193157	+	1	NA	5' UTR (NM_001195693, exon 1 of 7)	5' UTR (NM_001195693, exon 1 of 7)	219	NM_001195693	100504689	Mm.464262	NM_001195693	ENSMUSG00000095654	Plscr5	331000	phospholipid scramblase family, member 5	protein-coding
mm_33556.1	chr4	130944378	130944391	+	1	NA	promoter-TSS (NM_010769)	promoter-TSS (NM_010769)	-1	NM_010769	17180	Mm.271796	NM_010769	ENSMUSG00000040533	Matn1	CMP|Crtm|Mat1|matrilin-1	matrilin 1, cartilage matrix protein	protein-coding
mm_124282.1	chr14	103048426	103048436	-	1	NA	intron (NM_008392, intron 1 of 4)	intron (NM_008392, intron 1 of 4)	1419	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_4796.1	chr1	184735407	184735409	+	1	NA	Intergenic	Intergenic	-2915	NM_008250	15284	Mm.1347	NM_008250	ENSMUSG00000039377	Hlx	Hlx1	H2.0-like homeobox	protein-coding
mm_84374.1	chr9	65010746	65010793	-	1	NA	intron (NM_021345, intron 1 of 10)	intron (NM_021345, intron 1 of 10)	10948	NM_021345	57874	Mm.308180	NM_021345	ENSMUSG00000033629	Hacd3	4930523M17Rik|AW742319|B-ind1|Hcad3|Hspc121|Ptplad1	3-hydroxyacyl-CoA dehydratase 3	protein-coding
mm_41734.1	chr5	102695374	102695381	+	1	NA	intron (NM_146161, intron 2 of 8)	ORR1D2|LTR|ERVL-MaLR	-73433	NM_001286468	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding
mm_88160.1	chr10	69706195	69706215	+	1	NA	intron (NM_170730, intron 1 of 17)	intron (NM_170730, intron 1 of 17)	172497	NM_146005	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_61363.1	chr7	68979442	68979452	+	1	NA	Intergenic	Intergenic	-230209	NM_025549	66412	Mm.251199	NM_025549	ENSMUSG00000042659	Arrdc4	2410003C09Rik|AV216361	arrestin domain containing 4	protein-coding
mm_110708.1	chr12	69344155	69344190	-	1	NA	exon (NM_025441, exon 11 of 33)	exon (NM_025441, exon 11 of 33)	13004	NM_025441	66244	Mm.46705	NM_025441	ENSMUSG00000020982	Nemf	1500011I12Rik|4933405E14Rik|Sdccag1	nuclear export mediator factor	protein-coding
mm_148266.1	chr18	80987385	80987416	-	1	NA	promoter-TSS (NM_178280)	promoter-TSS (NM_178280)	-822	NM_178280	20689	Mm.215917	NM_178280	ENSMUSG00000024565	Sall3	B130022O04Rik|Msal|Msal-1|Sal|Salt|Spalt	sal-like 3 (Drosophila)	protein-coding
mm_125779.1	chr15	74714833	74714848	+	1	NA	promoter-TSS (NM_028216)	promoter-TSS (NM_028216)	1	NM_028216	72373	Mm.46395	NM_028216	ENSMUSG00000022598	Psca	2210408B04Rik	prostate stem cell antigen	protein-coding
mm_128789.1	chr15	66810141	66810143	-	1	NA	intron (NM_001029841, intron 1 of 7)	intron (NM_001029841, intron 1 of 7)	21687	NM_001029841	20491	Mm.7601	NM_009192	ENSMUSG00000022372	Sla	Slap|Slap-1	src-like adaptor	protein-coding
mm_83514.1	chr9	46012612	46012693	-	1	NA	promoter-TSS (NM_027498)	promoter-TSS (NM_027498)	-168	NM_027498	70661	Mm.219459	NM_027498	ENSMUSG00000034135	Sik3	5730525O22Rik|9030204A07Rik|AI447252|AI846254|AI849445|Qsk|SIK-3|mKIAA0999	SIK family kinase 3	protein-coding
mm_34533.1	chr4	149446677	149446723	+	1	NA	Intergenic	Intergenic	8268	NM_022020	63954	Mm.46023	NM_022020	ENSMUSG00000028996	Rbp7	1110002J23Rik|CRBP-III	retinol binding protein 7, cellular	protein-coding
mm_30197.1	chr3	144712714	144712738	-	1	NA	exon (NM_019464, exon 2 of 9)	exon (NM_019464, exon 2 of 9)	7609	NM_001282042	54673	Mm.271775	NM_019464	ENSMUSG00000037062	Sh3glb1	AA409932|AI314629|AU015566|Bif-1|mKIAA0491	SH3-domain GRB2-like B1 (endophilin)	protein-coding
mm_59581.1	chr7	28129432	28129458	+	1	NA	promoter-TSS (NM_001164655)	promoter-TSS (NM_001164655)	-21	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_74319.1	chr8	126848929	126848946	+	1	NA	Intergenic	Intergenic	96984	NM_024214	67952	Mm.6932	NM_024214	ENSMUSG00000093904	Tomm20	1810060K07Rik|BB284719|Gm19268|MAS20|MOM19|TOM20|mKIAA0016	translocase of outer mitochondrial membrane 20 homolog (yeast)	protein-coding
mm_86208.1	chr9	119984625	119984629	-	1	NA	promoter-TSS (NM_153287)	promoter-TSS (NM_153287)	31	NM_153287	215418	Mm.491094	NM_153287	ENSMUSG00000032515	Csrnp1	4931429D10Rik|Axud1|CSRNP-1|URAX1|taip-3	cysteine-serine-rich nuclear protein 1	protein-coding
mm_65215.1	chr7	19698207	19698261	-	1	NA	5' UTR (NM_009696, exon 2 of 4)	5' UTR (NM_009696, exon 2 of 4)	164	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_111634.1	chr12	102561952	102561986	-	1	NA	exon (NM_007693, exon 6 of 8)	exon (NM_007693, exon 6 of 8)	7028	NM_007693	12652	Mm.4137	NM_007693	ENSMUSG00000021194	Chga	ChrA|cgA	chromogranin A	protein-coding
mm_128471.1	chr15	50857729	50857754	-	1	NA	intron (NM_032000, intron 1 of 5)	intron (NM_032000, intron 1 of 5)	31308	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_164163.1	chr15	73487823	73487831	+	1	NA	Intergenic	Intergenic	-24733	NM_001081066	105841	Mm.322557	NM_001081066	ENSMUSG00000036661	Dennd3	AI447457|E030003N15Rik	DENN/MADD domain containing 3	protein-coding
mm_27433.1	chr3	51560802	51560809	-	1	NA	promoter-TSS (NM_080793)	promoter-TSS (NM_080793)	18	NM_080793	73251	Mm.192111	NM_080793	ENSMUSG00000037111	Setd7	1600028F23Rik|H3K4MT|KMT7|Set7|Set7/9|mKIAA1717	SET domain containing (lysine methyltransferase) 7	protein-coding
mm_103244.1	chr11	70755157	70755173	-	1	NA	Intergenic	Intergenic	-9282	NM_177565	193043	Mm.40966	NM_177565	ENSMUSG00000043602	Zfp3	AI854635|B230309J24|Fnp-1|Zfp-3	zinc finger protein 3	protein-coding
mm_112295.1	chr12	114584016	114584022	-	1	NA	Intergenic	Intergenic	-70325	NR_106063	102465664		NR_106063	ENSMUSG00000098357	Mir7094-2	Gm27508|mmu-mir-7094-2	microRNA 7094-2	ncRNA
mm_64678.1	chr7	4502201	4502240	-	1	NA	promoter-TSS (NM_029834)	promoter-TSS (NM_029834)	-540	NM_029834	232807	Mm.360391	NM_029834	ENSMUSG00000019254	Ppp1r12c	2410197A17Rik|AI839747|B430101M08|Mbs85	protein phosphatase 1, regulatory (inhibitor) subunit 12C	protein-coding
mm_149138.1	chr19	9003126	9003136	+	1	NA	exon (NM_009643, exon 5 of 5)	exon (NM_009643, exon 5 of 5)	13847	NM_001286518	66395	Mm.203866	NM_009643	ENSMUSG00000069833	Ahnak	DY6	AHNAK nucleoprotein (desmoyokin)	protein-coding
mm_158760.1	chrX	166483906	166483925	-	1	NA	Intergenic	Intergenic	-4048	NM_019773	56382	Mm.25306	NM_019773	ENSMUSG00000079316	Rab9	2410064E05Rik|AI195561|Rab9a|Sid6061p	RAB9, member RAS oncogene family	protein-coding
mm_81891.1	chr9	119408792	119408795	+	1	NA	intron (NM_001313757, intron 1 of 10)	intron (NM_001313757, intron 1 of 10)	6615	NM_007397	11481	Mm.8940	NM_007397	ENSMUSG00000061393	Acvr2b	4930516B21Rik|ActRIIB	activin receptor IIB	protein-coding
mm_88165.1	chr10	69706502	69706545	+	1	NA	intron (NM_170730, intron 1 of 17)	intron (NM_170730, intron 1 of 17)	172815	NM_146005	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_49887.1	chr6	38702815	38702854	+	1	NA	intron (NM_001294144, intron 13 of 14)	intron (NM_001294144, intron 13 of 14)	39765	NM_001101507	665180	Mm.349066	NM_001101507	ENSMUSG00000079598	Clec2l	AI414054|AW122724|Gm1064	C-type lectin domain family 2, member L	protein-coding
mm_148087.1	chr18	73703740	73703806	-	1	NA	promoter-TSS (NM_008540)	promoter-TSS (NM_008540)	-32	NM_008540	17128	Mm.100399	NM_008540	ENSMUSG00000024515	Smad4	AW743858|D18Wsu70e|DPC4|Madh4	SMAD family member 4	protein-coding
mm_49430.1	chr6	29272620	29272628	+	1	NA	promoter-TSS (NM_023516)	promoter-TSS (NM_023516)	-2	NM_023516	69573	Mm.45161	NM_023516	ENSMUSG00000043421	Hilpda	2310016C08Rik|AW049004|Hig2	hypoxia inducible lipid droplet associated	protein-coding
mm_108199.1	chr12	76887046	76887083	+	1	NA	intron (NM_145927, intron 4 of 11)	ORR1E|LTR|ERVL-MaLR	49597	NM_145927	110606	Mm.151174	NM_145927	ENSMUSG00000033373	Fntb	2010013E13Rik|AA409500	farnesyltransferase, CAAX box, beta	protein-coding
mm_163137.1	chr11	79244454	79244467	-	1	NA	intron (NM_019653, intron 5 of 8)	intron (NM_019653, intron 5 of 8)	-1436	NM_001042565	78889	Mm.307022	NM_019653	ENSMUSG00000017677	Wsb1	1110056B13Rik|2700038M07Rik	WD repeat and SOCS box-containing 1	protein-coding
mm_100056.1	chr11	115215761	115215768	+	1	NA	intron (NM_001033393, intron 8 of 9)	intron (NM_001033393, intron 8 of 9)	28277	NM_001033393	320534	Mm.260587	NM_001033393	ENSMUSG00000045980	Tmem104	C630005D06Rik|mFLJ00021	transmembrane protein 104	protein-coding
mm_73554.1	chr8	108958952	108958957	+	1	NA	3' UTR (NM_007496, exon 10 of 10)	3' UTR (NM_007496, exon 10 of 10)	22094	NR_037295	100526511		NR_037295	ENSMUSG00000093241	Mir3108	mir-3108|mmu-mir-3108	microRNA 3108	ncRNA
mm_68795.1	chr7	124186594	124186605	-	1	NA	intron (NM_001252072, intron 1 of 1)	intron (NM_001252072, intron 1 of 1)	203418	NM_001252072	628779	Mm.40210	NM_001252072	ENSMUSG00000078591	Hs3st4	EG628779|Gm6915	heparan sulfate (glucosamine) 3-O-sulfotransferase 4	protein-coding
mm_42366.1	chr5	114922542	114922565	+	1	NA	promoter-TSS (NM_145209)	promoter-TSS (NM_145209)	-687	NM_145209	231655	Mm.95479	NM_145209	ENSMUSG00000041827	Oasl1	7530414C13Rik|oasl9	2'-5' oligoadenylate synthetase-like 1	protein-coding
mm_62266.1	chr7	99535263	99535280	+	1	NA	promoter-TSS (NM_178220)	promoter-TSS (NM_178220)	-215	NM_178220	109689	Mm.260193	NM_177231	ENSMUSG00000018909	Arrb1	1200006I17Rik|AW208571|G430100A01Rik	arrestin, beta 1	protein-coding
mm_101953.1	chr11	50295942	50295956	-	1	NA	3' UTR (NM_001110500, exon 15 of 15)	3' UTR (NM_001110500, exon 15 of 15)	-3613	NM_175334	103806	Mm.51116	NM_175334	ENSMUSG00000050567	Maml1	AI644666|AW743257|D930008C07Rik|Mam-1|Mam1|mKIAA0200	mastermind like 1 (Drosophila)	protein-coding
mm_79460.1	chr9	56418625	56418681	+	1	NA	promoter-TSS (NM_025812)	promoter-TSS (NM_025812)	-193	NM_025812	66867	Mm.150856	NM_025812	ENSMUSG00000032329	Hmg20a	1200004E06Rik|5730490E10Rik|Hmgxb1|Ibraf	high mobility group 20A	protein-coding
mm_135351.1	chr16	43665000	43665035	-	1	NA	promoter-TSS (NM_001146325)	promoter-TSS (NM_001146325)	-833	NM_001146325	100043314	Mm.390896	NM_001146325	ENSMUSG00000071552	Tigit	ENSMUSG00000071552|Vstm3	T cell immunoreceptor with Ig and ITIM domains	protein-coding
mm_169309.1	chr14	104715936	104715938	-	1	NA	intron (NR_015593, intron 1 of 5)	LSU-rRNA_Hsa|rRNA|rRNA	76790	NR_015593	320249	Mm.320725	NR_015593		D130009I18Rik	-	RIKEN cDNA D130009I18 gene	ncRNA
mm_87805.1	chr10	60300776	60300802	+	1	NA	exon (NM_011179, exon 14 of 15)	exon (NM_011179, exon 14 of 15)	16328	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_80441.1	chr9	77957136	77957177	+	1	NA	exon (NM_134255, exon 2 of 8)	exon (NM_134255, exon 2 of 8)	39791	NM_134255	68801	Mm.430736	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	ELOVL family member 5, elongation of long chain fatty acids (yeast)	protein-coding
mm_141269.1	chr17	27729075	27729086	-	1	NA	promoter-TSS (NM_013891)	promoter-TSS (NM_013891)	-129	NM_013891	30051	Mm.26768	NM_013891	ENSMUSG00000024215	Spdef	PDEF|Pse	SAM pointed domain containing ets transcription factor	protein-coding
mm_115219.1	chr13	109632761	109632790	+	1	NA	intron (NM_011056, intron 3 of 16)	intron (NM_011056, intron 3 of 16)	-271034	NR_035442	100316683		NR_035442	ENSMUSG00000084651	Mir1904	Mirn1904|mmu-mir-1904	microRNA 1904	ncRNA
mm_158040.1	chrX	98890224	98890235	-	1	NA	exon (NM_052976, exon 2 of 25)	exon (NM_052976, exon 2 of 25)	796	NM_052976	94190	Mm.33536	NM_052976	ENSMUSG00000031214	Ophn1	C130037N19Rik|Wtgr	oligophrenin 1	protein-coding
mm_82612.1	chr9	21635834	21635870	-	1	NA	exon (NM_001174078, exon 4 of 34)	exon (NM_001174078, exon 4 of 34)	19683	NM_001174078	20586	Mm.286593	NM_011417	ENSMUSG00000032187	Smarca4	Brg1|HP1-BP72|SNF2beta|SW1/SNF|b2b508.1Clo|b2b692Clo	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	protein-coding
mm_101753.1	chr11	43385001	43385013	-	1	NA	Intergenic	Intergenic	-10546	NR_029558	387164		NR_029558	ENSMUSG00000065601	Mir146	Mirn146|miR-146a|mmu-mir-146	microRNA 146	ncRNA
mm_29199.1	chr3	106766479	106766501	-	1	NA	intron (NM_007651, intron 5 of 7)	B3|SINE|B2	23659	NM_007651	12508	Mm.316861	NM_007651	ENSMUSG00000040747	Cd53	AI323659|Ox-44|Tspan25	CD53 antigen	protein-coding
mm_116671.1	chr13	49210286	49210310	-	1	NA	intron (NM_026738, intron 1 of 5)	B1F2|SINE|Alu	5728	NM_026738	68480	Mm.3336	NM_026738	ENSMUSG00000037960	Card19	1110007C09Rik|AI851695|Bincard	caspase recruitment domain family, member 19	protein-coding
mm_31638.1	chr4	59579021	59579025	+	1	NA	Intergenic	RMER17A2|LTR|ERVK	-2540	NM_001301367	72479	Mm.272905	NM_024255	ENSMUSG00000028383	Hsdl2	2610207I16Rik	hydroxysteroid dehydrogenase like 2	protein-coding
mm_57061.1	chr6	122498761	122498766	-	1	NA	Intergenic	Intergenic	-12458	NM_027664	108653	Mm.277939	NM_027664	ENSMUSG00000040649	Rimklb	4931417E21Rik|4933426K21Rik|AA097693|AI325948|AU015629|Naags	ribosomal modification protein rimK-like family member B	protein-coding
mm_139968.1	chr17	71684633	71684646	+	1	NA	intron (NM_177087, intron 1 of 19)	intron (NM_177087, intron 1 of 19)	11378	NM_177087	320159	Mm.187372	NM_177087	ENSMUSG00000045761	Fam179a	4632412N22Rik	family with sequence similarity 179, member A	protein-coding
mm_88855.1	chr10	80930756	80930763	+	1	NA	intron (NM_008655, intron 2 of 3)	intron (NM_008655, intron 2 of 3)	668	NM_008655	17873	Mm.1360	NM_008655	ENSMUSG00000015312	Gadd45b	AI323528|Myd118	growth arrest and DNA-damage-inducible 45 beta	protein-coding
mm_76729.1	chr8	95020671	95020683	-	1	NA	intron (NM_173036, intron 1 of 11)	intron (NM_173036, intron 1 of 11)	2985	NM_173036	54672	Mm.27995	NM_173036	ENSMUSG00000060470	Adgrg3	A030001G24Rik|AW214383|Gpr97|Pb1|Pb99	adhesion G protein-coupled receptor G3	protein-coding
mm_120766.1	chr14	73385004	73385028	+	1	NA	exon (NM_008410, exon 1 of 6)	exon (NM_008410, exon 1 of 6)	255	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_147710.1	chr18	60812327	60812347	-	1	NA	TTS (NR_039567)	TTS (NR_039567)	261	NR_039567	100628611		NR_039567	ENSMUSG00000093327	Mir5107	mir-5107|mmu-mir-5107|mu-mir-5107	microRNA 5107	ncRNA
mm_109487.1	chr12	111442454	111442480	+	1	NA	promoter-TSS (NM_009396)	promoter-TSS (NM_009396)	-194	NM_009396	21928	Mm.255332	NM_009396	ENSMUSG00000021281	Tnfaip2	B94|Exoc3l3|M-sec|Tnfip2|tnfb94	tumor necrosis factor, alpha-induced protein 2	protein-coding
mm_49376.1	chr6	24543368	24543409	+	1	NA	intron (NM_080847, intron 1 of 9)	intron (NM_080847, intron 1 of 9)	15244	NM_080847	78910	Mm.160150	NM_080847	ENSMUSG00000029685	Asb15	4930400E23Rik|Asb-15	ankyrin repeat and SOCS box-containing 15	protein-coding
mm_153903.1	chr19	47090702	47090704	-	1	NA	promoter-TSS (NM_011053)	promoter-TSS (NM_011053)	-63	NM_011053	18572	Mm.41166	NM_011053	ENSMUSG00000025047	Pdcd11	1110021I22Rik|ALG-4|Pdcd7|mKIAA0185	programmed cell death 11	protein-coding
mm_120154.1	chr14	60702915	60702931	+	1	NA	intron (NM_001033272, intron 2 of 12)	intron (NM_001033272, intron 2 of 12)	-29981	NM_001310594	219140	Mm.149776	NM_001033272	ENSMUSG00000021990	Spata13	C79050|ESTM11|X83327|mFLJ00298	spermatogenesis associated 13	protein-coding
mm_103726.1	chr11	79530570	79530595	-	1	NA	promoter-TSS (NM_010161)	promoter-TSS (NM_010161)	27	NM_146023	101488212	Mm.439665	NM_146023	ENSMUSG00000070354	Gm21975	Evi2a-evi2b	predicted gene 21975	protein-coding
mm_133422.1	chr16	87304051	87304058	+	1	NA	Intergenic	Intergenic	-50131	NM_001159331	67768	Mm.296532	NM_026366	ENSMUSG00000044442	N6amt1	5830445C04Rik|Hemk2|Pred28	N-6 adenine-specific DNA methyltransferase 1 (putative)	protein-coding
mm_147344.1	chr18	43322262	43322291	-	1	NA	3' UTR (NM_001291455, exon 14 of 14)	3' UTR (NM_001291455, exon 14 of 14)	50996	NM_001136086	22240	Mm.8180	NM_009468	ENSMUSG00000024501	Dpysl3	CRMP-4|DRP-3|TUC4|ULIP-1|Ulip|Ulip1	dihydropyrimidinase-like 3	protein-coding
mm_56971.1	chr6	120188468	120188483	-	1	NA	intron (NM_016718, intron 1 of 3)	intron (NM_016718, intron 1 of 3)	-5348	NM_001347432	29862	Mm.103668	NM_016718	ENSMUSG00000041377	Ninj2	-	ninjurin 2	protein-coding
mm_36608.1	chr4	89126543	89126556	-	1	NA	Intergenic	MusHAL1|LINE|L1	-10821	NM_024433	66902	Mm.28500	NM_024433	ENSMUSG00000062937	Mtap	1300019I21Rik|MSAP	methylthioadenosine phosphorylase	protein-coding
mm_22298.1	chr2	180276853	180276872	-	1	NA	TTS (NM_173031)	TTS (NM_173031)	-3397	NM_145851	252966	Mm.386884	NM_145851	ENSMUSG00000038990	Cables2	ik3-2	CDK5 and Abl enzyme substrate 2	protein-coding
mm_43921.1	chr5	144768505	144768531	+	1	NA	promoter-TSS (NM_001081362)	promoter-TSS (NM_001081362)	-274	NM_001081362	100683	Mm.273570	NM_001081362	ENSMUSG00000045482	Trrap	AI481500	transformation/transcription domain-associated protein	protein-coding
mm_20450.1	chr2	129364833	129364860	-	1	NA	3' UTR (NM_008361, exon 7 of 7)	3' UTR (NM_008361, exon 7 of 7)	-5056	NR_015474	329514	Mm.207315	NM_177848	ENSMUSG00000074805	Il1bos	9430083I22|Gm14047|OTTMUSG00000015529	interleukin 1 beta, opposite strand	ncRNA
mm_59382.1	chr7	26174215	26174217	+	1	NA	intron (NM_010000, intron 1 of 8)	Lx|LINE|L1	807	NM_010000	13094	Mm.14413	NM_010000	ENSMUSG00000040660	Cyp2b9	Cyp2b	cytochrome P450, family 2, subfamily b, polypeptide 9	protein-coding
mm_84607.1	chr9	70142173	70142183	-	1	NA	promoter-TSS (NM_029784)	promoter-TSS (NM_029784)	-621	NM_029784	76886	Mm.44355	NM_029784	ENSMUSG00000032224	Fam81a	6430514L14Rik	family with sequence similarity 81, member A	protein-coding
mm_101982.1	chr11	50431102	50431131	-	1	NA	promoter-TSS (NM_172557)	promoter-TSS (NM_172557)	-5	NM_172557	216724	Mm.390400	NM_172557	ENSMUSG00000020375	Rufy1	3000002E04Rik|Rabip4|ZFYVE12	RUN and FYVE domain containing 1	protein-coding
mm_51727.1	chr6	86955224	86955230	+	1	NA	exon (NM_177762, exon 10 of 20)	exon (NM_177762, exon 10 of 20)	-54609	NM_001170591	56748	Mm.23809	NM_020045	ENSMUSG00000029993	Nfu1	0610006G17Rik|CGI-33|Hirip5	NFU1 iron-sulfur cluster scaffold	protein-coding
mm_46274.1	chr5	100038161	100038164	-	1	NA	intron (NM_016690, intron 1 of 7)	intron (NM_016690, intron 1 of 7)	1060	NM_016690	50926	Mm.389579	NM_016690	ENSMUSG00000029328	Hnrnpdl	AA407431|AA959857|D5Ertd650e|D5Wsu145e|Hnrnpdl1|Hnrpdl|JKTBP|hnRNP DL|hnRNP-DL	heterogeneous nuclear ribonucleoprotein D-like	protein-coding
mm_138388.1	chr17	35050222	35050239	+	1	NA	promoter-TSS (NM_033444)	promoter-TSS (NM_033444)	-13	NM_033444	114584	Mm.29524	NM_033444	ENSMUSG00000007041	Clic1	Clcp|G6	chloride intracellular channel 1	protein-coding
mm_62344.1	chr7	100498242	100498252	+	1	NA	exon (NM_011671, exon 5 of 8)	exon (NM_011671, exon 5 of 8)	4889	NM_011671	22228	Mm.171378	NM_011671	ENSMUSG00000033685	Ucp2	Slc25a8	uncoupling protein 2 (mitochondrial, proton carrier)	protein-coding
mm_166852.1	chr7	19696904	19696914	+	1	NA	exon (NM_009696, exon 4 of 4)	exon (NM_009696, exon 4 of 4)	1489	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_71603.1	chr8	55940411	55940451	+	1	NA	promoter-TSS (NM_080438)	promoter-TSS (NM_080438)	-394	NM_080438	110304	Mm.307061	NM_080438	ENSMUSG00000038257	Glra3	-	glycine receptor, alpha 3 subunit	protein-coding
mm_148634.1	chr19	5464058	5464108	+	1	NA	TTS (NM_009985)	TTS (NM_009985)	3476	NM_021438	58249	Mm.329656	NM_021438	ENSMUSG00000024911	Fibp	2010004G08Rik|2010005N21Rik|3010027N18Rik	fibroblast growth factor (acidic) intracellular binding protein	protein-coding
mm_159820.1	chr5	122753825	122753825	-	1	NA	exon (NM_001199676, exon 6 of 17)	exon (NM_001199676, exon 6 of 17)	25585	NM_001199676	207565	Mm.289237	NM_145358	ENSMUSG00000029471	Camkk2	6330570N16Rik|AW061083|mKIAA0787	calcium/calmodulin-dependent protein kinase kinase 2, beta	protein-coding
mm_90847.1	chr10	8762270	8762283	-	1	NA	intron (NM_175155, intron 8 of 19)	intron (NM_175155, intron 8 of 19)	123794	NM_175155	70097	Mm.338275	NM_175155	ENSMUSG00000015305	Sash1	1100001C18Rik|2500002E12Rik|A330076K04Rik|mKIAA0790	SAM and SH3 domain containing 1	protein-coding
mm_133228.1	chr16	76548744	76548785	+	1	NA	Intergenic	Intergenic	-175715	NM_173440	268903	Mm.74711	NM_173440	ENSMUSG00000048490	Nrip1	6030458L20Rik|8430438I05Rik|9630050P12|AA959574|AW456757|RIP140	nuclear receptor interacting protein 1	protein-coding
mm_62516.1	chr7	102223523	102223530	+	1	NA	intron (NR_111938, intron 2 of 4)	MIRb|SINE|MIR	498	NR_111937	233575	Mm.302013	NM_145583	ENSMUSG00000030990	Pgap2	1810006G21Rik|C76649|Frag1	post-GPI attachment to proteins 2	protein-coding
mm_96172.1	chr11	61488670	61488673	+	1	NA	TTS (NM_001291037)	TTS (NM_001291037)	3227	NM_029568	76293	Mm.272278	NM_029568	ENSMUSG00000042436	Mfap4	1110007F23Rik	microfibrillar-associated protein 4	protein-coding
mm_139716.1	chr17	57466244	57466256	+	1	NA	intron (NM_010130, intron 18 of 21)	Lx|LINE|L1	79064	NM_001104591	224916	Mm.469889	NM_001104591	ENSMUSG00000090655	Vmn2r120	EG224916	vomeronasal 2, receptor 120	protein-coding
mm_40114.1	chr5	34917519	34917545	+	1	NA	5' UTR (NM_207277, exon 1 of 3)	5' UTR (NM_207277, exon 1 of 3)	1617	NM_001310550	403174	Mm.291225	NM_207277	ENSMUSG00000051246	Msantd1	A930005I04Rik|Gm144	Myb/SANT-like DNA-binding domain containing 1	protein-coding
mm_11838.1	chr2	45111196	45111214	+	1	NA	promoter-TSS (NM_001289521)	promoter-TSS (NM_001289521)	67	NR_110572	433424	Mm.441408	NR_110571	ENSMUSG00000052248	Zeb2os	Gm13476|OTTMUSG00000012358|Zeb2nat	zinc finger E-box binding homeobox 2, opposite strand	ncRNA
mm_131407.1	chr16	14441294	14441313	+	1	NA	intron (NM_008576, intron 15 of 30)	intron (NM_008576, intron 15 of 30)	79745	NM_008576	17250	Mm.196634	NM_008576	ENSMUSG00000023088	Abcc1	Abcc1a|Abcc1b|MRP|Mdrap|Mrp1	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	protein-coding
mm_135745.1	chr16	55895356	55895410	-	1	NA	promoter-TSS (NM_001134457)	promoter-TSS (NM_001134457)	-104	NM_001134457	385658	Mm.310635	NM_001134457	ENSMUSG00000075033	Nxpe3	Fam55c|Gm1752|Gm611	neurexophilin and PC-esterase domain family, member 3	protein-coding
mm_109687.1	chr12	113142766	113142823	+	1	NA	intron (NM_001347443, intron 1 of 6)	intron (NM_001347443, intron 1 of 6)	2189	NM_001347443	68337	Mm.133825	NM_024223	ENSMUSG00000006356	Crip2	0610010I23Rik|AW743261|C77570|CRP2|CRP4|Crp|ESP1|Hlp	cysteine rich protein 2	protein-coding
mm_165334.1	chr2	114050478	114050480	-	1	NA	exon (NM_009608, exon 3 of 7)	exon (NM_009608, exon 3 of 7)	2396	NM_009608	11464	Mm.686	NM_009608	ENSMUSG00000068614	Actc1	Actc-1	actin, alpha, cardiac muscle 1	protein-coding
mm_16845.1	chr2	11513213	11513229	-	1	NA	intron (NM_001177758, intron 1 of 14)	intron (NM_001177758, intron 1 of 14)	-11131	NM_001177757	170768	Mm.19669	NM_133232	ENSMUSG00000026773	Pfkfb3	E330010H22Rik|iPFK-2|uPFK-2	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	protein-coding
mm_151675.1	chr19	4201376	4201425	-	1	NA	intron (NM_011237, intron 1 of 10)	intron (NM_011237, intron 1 of 10)	203	NM_011237	19367	Mm.277629	NM_011237	ENSMUSG00000024824	Rad9a	Rad9	RAD9 checkpoint clamp component A	protein-coding
mm_1545.1	chr1	72852240	72852244	+	1	NA	3' UTR (NM_008342, exon 4 of 4)	3' UTR (NM_008342, exon 4 of 4)	22623	NM_010518	16011	Mm.405761	NM_010518	ENSMUSG00000026185	Igfbp5	AI256729|AW208790|IGFBP-5|IGFBP-5P	insulin-like growth factor binding protein 5	protein-coding
mm_17379.1	chr2	27019998	27020017	-	1	NA	intron (NM_029862, intron 5 of 5)	intron (NM_029862, intron 5 of 5)	7991	NM_172659	227659	Mm.41203	NM_172659	ENSMUSG00000036067	Slc2a6	A330096C23|F630103L12Rik|Glut6|Glut9	solute carrier family 2 (facilitated glucose transporter), member 6	protein-coding
mm_14306.1	chr2	129123065	129123069	+	1	NA	intron (NM_009086, intron 12 of 14)	intron (NM_009086, intron 12 of 14)	-6633	NM_025395	66170	Mm.40621	NM_025395	ENSMUSG00000037938	Chchd5	1110027L01Rik|AW045710	coiled-coil-helix-coiled-coil-helix domain containing 5	protein-coding
mm_99118.1	chr11	100141525	100141567	+	1	NA	exon (NM_008471, exon 4 of 6)	exon (NM_008471, exon 4 of 6)	2153	NM_001313963	16669	Mm.439699	NM_008471	ENSMUSG00000020911	Krt19	AI663979|CK-19|EndoC|K19|Krt-1.19|Krt1-19	keratin 19	protein-coding
mm_84898.1	chr9	79830965	79830981	-	1	NA	intron (NM_001081243, intron 4 of 5)	intron (NM_001081243, intron 4 of 5)	37332	NR_040734	74633	Mm.262175	NR_040734	ENSMUSG00000086918	4930429F24Rik	-	RIKEN cDNA 4930429F24 gene	ncRNA
mm_54813.1	chr6	42340233	42340239	-	1	NA	Intergenic	RMER19C|LTR|ERVK	-9592	NM_011777	22793	Mm.282303	NM_011777	ENSMUSG00000029860	Zyx	9530098H06Rik|R75157	zyxin	protein-coding
mm_87848.1	chr10	60932339	60932365	+	1	NA	intron (NR_033616, intron 1 of 2)	intron (NR_033616, intron 1 of 2)	5780	NR_033616	73616	Mm.159038	NR_033616	ENSMUSG00000037247	Pldi	1700125F08Rik|Poldi	polymorphic derived intron containing	ncRNA
mm_19706.1	chr2	103796937	103796978	-	1	NA	5' UTR (NM_001111290, exon 1 of 18)	5' UTR (NM_001111290, exon 1 of 18)	121	NM_001111290	53872	Mm.427589	NM_016739	ENSMUSG00000027184	Caprin1	AL022980|Caprin-1|Gpiap|Gpiap1|Mmgpip137|P137|rng105	cell cycle associated protein 1	protein-coding
mm_112621.1	chr13	15606372	15606378	+	1	NA	intron (NM_008130, intron 3 of 14)	intron (NM_008130, intron 3 of 14)	142652	NM_008130	14634	Mm.5098	NM_008130	ENSMUSG00000021318	Gli3	AI854843|AU023367|Bph|GLI3-190|GLI3FL|Pdn|Xt|add	GLI-Kruppel family member GLI3	protein-coding
mm_73855.1	chr8	118283589	118283602	+	1	NA	promoter-TSS (NM_019707)	promoter-TSS (NM_019707)	-16	NM_019707	12554	Mm.334841	NM_019707	ENSMUSG00000031841	Cdh13	4932416G01Rik|Cdht|Tcad	cadherin 13	protein-coding
mm_69942.1	chr7	142144606	142144609	-	1	NA	Intergenic	Intergenic	-8524	NM_001347556	105243089		NM_001347556	ENSMUSG00000110091	Gm39115	-	predicted gene, 39115	protein-coding
mm_96831.1	chr11	70000644	70000660	+	1	NA	promoter-TSS (NM_007888)	promoter-TSS (NM_007888)	26	NM_007888	13543	Mm.5114	NM_007888	ENSMUSG00000020888	Dvl2	-	dishevelled segment polarity protein 2	protein-coding
mm_115916.1	chr13	23530918	23530943	-	1	NA	promoter-TSS (NM_153173)	promoter-TSS (NM_153173)	-114	NM_153173	69386	Mm.158272	NM_153173	ENSMUSG00000060981	Hist1h4h	1700024H08Rik	histone cluster 1, H4h	protein-coding
mm_85468.1	chr9	105560805	105560813	-	1	NA	Intergenic	MTA_Mm-int|LTR|ERVL-MaLR	-39552	NM_001253831	235574	Mm.326247	NM_175025	ENSMUSG00000032570	Atp2c1	1700121J11Rik|ATP2C1A|AW061228|BCPM|D930003G21Rik|HHD|SPCA|pmr1	ATPase, Ca++-sequestering	protein-coding
mm_23947.1	chr3	84817307	84817312	+	1	NA	intron (NM_001177773, intron 1 of 13)	intron (NM_001177773, intron 1 of 13)	1732	NM_001177773	50754	Mm.196475	NM_080428	ENSMUSG00000028086	Fbxw7	1110001A17Rik|AGO|Cdc4|Fbw7|Fbwd6|Fbx30|Fbxo30|Fbxw6|SEL-10	F-box and WD-40 domain protein 7	protein-coding
mm_56865.1	chr6	118419359	118419387	-	1	NA	promoter-TSS (NM_194339)	promoter-TSS (NM_194339)	44	NM_194339	213895	Mm.25269	NM_194339	ENSMUSG00000030138	Bms1	AA408648|AU020092|AU043373|BB007109|BC030906|Bms1l|mKIAA0187	BMS1, ribosome biogenesis factor	protein-coding
mm_33551.1	chr4	130934931	130934944	+	1	NA	3' UTR (NM_010686, exon 8 of 8)	3' UTR (NM_010686, exon 8 of 8)	-9448	NM_010769	17180	Mm.271796	NM_010769	ENSMUSG00000040533	Matn1	CMP|Crtm|Mat1|matrilin-1	matrilin 1, cartilage matrix protein	protein-coding
mm_8382.1	chr1	151252009	151252012	-	1	NA	Intergenic	RLTR8|LTR|ERVK	-92488	NM_001039512	117198	Mm.33764	NM_028582	ENSMUSG00000023150	Ivns1abp	1190004M08Rik|1700126I16Rik|AA960440|HSPC068|ND1|NS-1|NS1-BP|Nd1-L|Nd1-S|mKIAA0850	influenza virus NS1A binding protein	protein-coding
mm_67204.1	chr7	74302708	74302748	-	1	NA	intron (NM_001038643, intron 8 of 10)	B4|SINE|B4	252052	NM_023908	108116	Mm.425467	NM_023908	ENSMUSG00000025790	Slco3a1	5830414C08Rik|Anr1|MJAM|OATP-D|R75096|Slc21a11	solute carrier organic anion transporter family, member 3a1	protein-coding
mm_80275.1	chr9	72985569	72985642	+	1	NA	promoter-TSS (NM_001198789)	promoter-TSS (NM_001198789)	101	NM_028181	72278	Mm.268475	NM_028181	ENSMUSG00000034563	Ccpg1	1700030B06Rik|1810073J13Rik|9430028F23Rik|AI426686|AI875170|CPR8|D9Ertd392e	cell cycle progression 1	protein-coding
mm_109505.1	chr12	111452211	111452245	+	1	NA	intron (NM_009396, intron 11 of 11)	(TCTA)n|Simple_repeat|Simple_repeat	9567	NM_009396	21928	Mm.255332	NM_009396	ENSMUSG00000021281	Tnfaip2	B94|Exoc3l3|M-sec|Tnfip2|tnfb94	tumor necrosis factor, alpha-induced protein 2	protein-coding
mm_32730.1	chr4	116557781	116557799	+	1	NA	promoter-TSS (NM_029868)	promoter-TSS (NM_029868)	63	NM_029868	77110	Mm.41715	NM_029868	ENSMUSG00000034042	Gpbp1l1	5330440M15Rik|BC002292	GC-rich promoter binding protein 1-like 1	protein-coding
mm_79189.1	chr9	48450261	48450268	+	1	NA	Intergenic	Intergenic	-4080	NR_026561	667933	Mm.491076	NR_026561		Gm8884	EG667933	predicted gene 8884	ncRNA
mm_99600.1	chr11	104550126	104550152	+	1	NA	promoter-TSS (NM_010858)	promoter-TSS (NM_010858)	481	NM_001285990	217232	Mm.89845	NM_145436	ENSMUSG00000020687	Cdc27	AI452358|APC3|BC023187	cell division cycle 27	protein-coding
mm_33236.1	chr4	127021979	127021992	+	1	NA	exon (NM_023603, exon 1 of 10)	exon (NM_023603, exon 1 of 10)	684	NM_023603	71514	Mm.257276	NM_023603	ENSMUSG00000028820	Sfpq	1110004P21Rik|2810416M14Rik|5730453G22Rik|9030402K04Rik|AU021830|D4Ertd314e|Gm12940|OTTMUSG00000009329|PSF|REP1	splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)	protein-coding
mm_41375.1	chr5	90719117	90719162	+	1	NA	Intergenic	Lx8|LINE|L1	-40159	NM_009141	20311	Mm.4660	NM_009141	ENSMUSG00000029371	Cxcl5	AMCF-II|Cxcl6|ENA-78|GCP-2|LIX|Scyb5|Scyb6	chemokine (C-X-C motif) ligand 5	protein-coding
mm_87061.1	chr10	28844054	28844068	+	1	NA	intron (NM_001305663, intron 5 of 5)	intron (NM_001305663, intron 5 of 5)	79446	NR_033601	114676	Mm.390292	NR_033601		4930519F09Rik	-	pyruvate dehydrogenase E1 alpha 1 pseudogene	pseudo
mm_88376.1	chr10	76293149	76293163	+	1	NA	intron (NM_001081419, intron 16 of 37)	intron (NM_001081419, intron 16 of 37)	39320	NM_009115	20203	Mm.235998	NM_009115	ENSMUSG00000033208	S100b	AI850290|Bpb	S100 protein, beta polypeptide, neural	protein-coding
mm_148619.1	chr19	5406865	5406880	+	1	NA	promoter-TSS (NR_015545)	promoter-TSS (NR_015545)	57	NR_027938	74931	Mm.388511	NR_015545	ENSMUSG00000086938	4930481A15Rik	-	RIKEN cDNA 4930481A15 gene	ncRNA
mm_80609.1	chr9	87022019	87022080	+	1	NA	promoter-TSS (NM_024195)	promoter-TSS (NM_024195)	20	NM_024195	266690	Mm.30166	NM_024195	ENSMUSG00000032872	Cyb5r4	2810034J18Rik|B5+B5R|C79736|Cb5cb5r|Ncb5or|b5/b5r|b5b5r	cytochrome b5 reductase 4	protein-coding
mm_132431.1	chr16	35809070	35809083	+	1	NA	intron (NM_175111, intron 3 of 7)	MTD|LTR|ERVL-MaLR	38690	NM_175111	66667	Mm.45272	NM_175111	ENSMUSG00000022849	Hspbap1	3830421G21Rik	Hspb associated protein 1	protein-coding
mm_32303.1	chr4	103133530	103133534	+	1	NA	intron (NM_001039081, intron 3 of 12)	intron (NM_001039081, intron 3 of 12)	14142	NM_001039081	71148	Mm.288721	NM_027696	ENSMUSG00000028522	Mier1	4933425I22Rik|5830411K19Rik|er1	MEIR1 treanscription regulator	protein-coding
mm_30237.1	chr3	146153874	146153922	-	1	NA	intron (NM_001005846, intron 1 of 13)	intron (NM_001005846, intron 1 of 13)	3724	NM_001005846	68279	Mm.116862	NM_026656	ENSMUSG00000011008	Mcoln2	3300002C04Rik|AI549968|C86638|TRPML2	mucolipin 2	protein-coding
mm_18980.1	chr2	76849636	76849648	-	1	NA	intron (NM_011652, intron 135 of 312)	intron (NM_011652, intron 135 of 312)	132905	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_133879.1	chr16	96493812	96493832	+	1	NA	exon (NM_008791, exon 2 of 3)	exon (NM_008791, exon 2 of 3)	26216	NM_008791	18546	Mm.5023	NM_008791	ENSMUSG00000090223	Pcp4	P16Rimb19|Pcp-4|Pep19	Purkinje cell protein 4	protein-coding
mm_3100.1	chr1	134431996	134432024	+	1	NA	3' UTR (NM_001306069, exon 8 of 8)	3' UTR (NM_001306069, exon 8 of 8)	16346	NM_001306069	72674	Mm.259976	NM_028320	ENSMUSG00000026457	Adipor1	2810031L11Rik|ACDCR1|CGI-45|Paqr1	adiponectin receptor 1	protein-coding
mm_168952.1	chr12	7825567	7825573	-	1	NA	Intergenic	B1_Mur4|SINE|Alu	-152107	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_19892.1	chr2	114051299	114051312	-	1	NA	intron (NM_009608, intron 2 of 6)	intron (NM_009608, intron 2 of 6)	1570	NM_009608	11464	Mm.686	NM_009608	ENSMUSG00000068614	Actc1	Actc-1	actin, alpha, cardiac muscle 1	protein-coding
mm_159145.1	chr2	87136113	87136113	-	1	NA	exon (NM_146769, exon 1 of 1)	exon (NM_146769, exon 1 of 1)	206	NM_146769	258765	Mm.223196	NM_146769	ENSMUSG00000075159	Olfr1110	MOR172-4	olfactory receptor 1110	protein-coding
mm_61141.1	chr7	57419672	57419674	+	1	NA	intron (NM_176942, intron 7 of 9)	intron (NM_176942, intron 7 of 9)	32401	NR_033504	791383	Mm.403104	NR_033504	ENSMUSG00000055048	Gm9962	ENSMUSG00000055048	predicted gene 9962	ncRNA
mm_52858.1	chr6	122283004	122283025	+	1	NA	promoter-TSS (NM_016970)	promoter-TSS (NM_016970)	-181	NM_016970	50928	Mm.20434	NM_016970	ENSMUSG00000030114	Klrg1	2F1-Ag|MAFA|MAFA-L	killer cell lectin-like receptor subfamily G, member 1	protein-coding
mm_140205.1	chr17	83775508	83775516	+	1	NA	intron (NM_001171053, intron 8 of 13)	intron (NM_001171053, intron 8 of 13)	69349	NM_001171052	116871	Mm.277668	NM_054082	ENSMUSG00000055817	Mta3	1110002J22Rik|mKIAA1266	metastasis associated 3	protein-coding
mm_81136.1	chr9	106561747	106561753	+	1	NA	promoter-TSS (NM_026645)	promoter-TSS (NM_026645)	-125	NM_026645	68265	Mm.141451	NM_026645	ENSMUSG00000023577	Iqcf3	1700012F17Rik|AV040440	IQ motif containing F3	protein-coding
mm_110476.1	chr12	51847845	51847852	-	1	NA	Intergenic	Intergenic	-18312	NM_144788	207304	Mm.249391	NM_144788	ENSMUSG00000035247	Hectd1	A630086P08Rik|AI844876|b2b327Clo|opm	HECT domain containing 1	protein-coding
mm_75989.1	chr8	72386950	72386990	-	1	NA	exon (NM_007944, exon 9 of 24)	exon (NM_007944, exon 9 of 24)	34504	NM_001122832	13859	Mm.288894	NM_007944	ENSMUSG00000006276	Eps15l1	9830147J04Rik|AI593686|Eps15-rs|Eps15R	epidermal growth factor receptor pathway substrate 15-like 1	protein-coding
mm_71031.1	chr8	33599883	33599911	+	1	NA	5' UTR (NM_017374, exon 1 of 7)	5' UTR (NM_017374, exon 1 of 7)	276	NM_017374	19053	Mm.29301	NM_017374	ENSMUSG00000009630	Ppp2cb	AI115466|D8Ertd766e|PP2Ac	protein phosphatase 2 (formerly 2A), catalytic subunit, beta isoform	protein-coding
mm_26476.1	chr3	144577595	144577614	+	1	NA	exon (NM_053102, exon 2 of 5)	exon (NM_053102, exon 2 of 5)	7177	NM_053102	93684	Mm.29812	NM_053102	ENSMUSG00000037072	Selenof	9430015P09Rik|Sep15	selenoprotein F	protein-coding
mm_154497.1	chrM	11412	11545	-	1	NA	NA	Intergenic	NA	NA								
mm_19406.1	chr2	91649786	91649796	-	1	NA	promoter-TSS (NM_001145902)	promoter-TSS (NM_001145902)	0	NM_001033451	381410	Mm.330401	NM_001033451	ENSMUSG00000075040	Zfp408	Gm1011	zinc finger protein 408	protein-coding
mm_127960.1	chr15	11906157	11906182	-	1	NA	promoter-TSS (NM_001039181)	promoter-TSS (NM_001039181)	-356	NR_131059	381002	Mm.441967	NR_131059		Gm5144	-	predicted gene 5144	ncRNA
mm_80520.1	chr9	80067059	80067085	+	1	NA	5' UTR (NM_146003, exon 1 of 23)	5' UTR (NM_146003, exon 1 of 23)	169	NM_146003	215351	Mm.28232	NM_146003	ENSMUSG00000034252	Senp6	2810017C20Rik|E130319N12Rik|Susp1|mKIAA0797	SUMO/sentrin specific peptidase 6	protein-coding
mm_29166.1	chr3	106485883	106485888	-	1	NA	promoter-TSS (NM_028110)	promoter-TSS (NM_028110)	28	NR_033207	69206	Mm.14816	NM_001033146	ENSMUSG00000091575	2010016I18Rik	-	RIKEN cDNA 2010016I18 gene	ncRNA
mm_171218.1	chr3	59767212	59767216	+	1	NA	Intergenic	L1Md_F3|LINE|L1	37428	NM_001101531	433597	Mm.297801	NM_001101531	ENSMUSG00000090527	Gm5538	-	predicted gene 5538	protein-coding
mm_86446.1	chr10	4266324	4266341	+	1	NA	promoter-TSS (NM_031185)	promoter-TSS (NM_031185)	3	NM_031185	83397	Mm.27481	NM_031185	ENSMUSG00000038587	Akap12	AI317366|SSeCKS|Srcs5|Tsga12	A kinase (PRKA) anchor protein (gravin) 12	protein-coding
mm_95412.1	chr11	50025282	50025296	+	1	NA	promoter-TSS (NM_021540)	promoter-TSS (NM_021540)	-42	NM_021540	59044	Mm.359004	NM_021540	ENSMUSG00000020376	Rnf130	2510042A13Rik|G1RZFP|G1rp|GOLIATH|GP	ring finger protein 130	protein-coding
mm_78535.1	chr9	35211230	35211248	+	1	NA	promoter-TSS (NM_172291)	promoter-TSS (NM_172291)	36	NM_026130	67398	Mm.284688	NM_026130	ENSMUSG00000032042	Srpr	1300011P19Rik|D11Mgi27|Srpra	signal recognition particle receptor ('docking protein')	protein-coding
mm_53425.1	chr6	134035976	134036011	+	1	NA	5' UTR (NM_007961, exon 1 of 8)	5' UTR (NM_007961, exon 1 of 8)	293	NM_007961	14011	Mm.269995	NM_007961	ENSMUSG00000030199	Etv6	AW123102|AW557856|Tel	ets variant 6	protein-coding
mm_63530.1	chr7	127968105	127968109	+	1	NA	intron (NM_001347649, intron 1 of 14)	CpG	628	NM_139149	233908	Mm.277680	NM_139149	ENSMUSG00000030795	Fus	D430004D17Rik|D930039C12Rik|Fus1|Tls	fused in sarcoma	protein-coding
mm_17843.1	chr2	34372005	34372027	-	1	NA	promoter-TSS (NM_001290576)	promoter-TSS (NM_001290576)	29	NM_001290576	18516	Mm.239941	NM_016768	ENSMUSG00000038718	Pbx3	-	pre B cell leukemia homeobox 3	protein-coding
mm_86496.1	chr10	5664196	5664198	+	1	NA	Intergenic	MMETn-int|LTR|ERVK	24979	NM_001313969	22353	Mm.98916	NM_011702	ENSMUSG00000019772	Vip	-	vasoactive intestinal polypeptide	protein-coding
mm_96456.1	chr11	67586593	67586601	+	1	NA	promoter-TSS (NM_001109657)	promoter-TSS (NM_001109657)	97	NM_001109657	14457	Mm.40338	NM_008088	ENSMUSG00000033066	Gas7	AW124766|B230343A10Rik|Gas7-cb	growth arrest specific 7	protein-coding
mm_95951.1	chr11	58390269	58390291	+	1	NA	exon (NM_001083884, exon 7 of 7)	exon (NM_001083884, exon 7 of 7)	9634	NM_001330197	70163	Mm.24119	NM_027339	ENSMUSG00000013643	Lypd8	2210415F13Rik	LY6/PLAUR domain containing 8	protein-coding
mm_15408.1	chr2	156775164	156775209	+	1	NA	promoter-TSS (NM_172118)	promoter-TSS (NM_172118)	-278	NM_172118	98932	Mm.271770	NM_172118	ENSMUSG00000067818	Myl9	AI327049|MLC20|Mylc2c|RLC-C	myosin, light polypeptide 9, regulatory	protein-coding
mm_164546.1	chr17	12165847	12165850	+	1	NA	intron (NM_026644, intron 2 of 8)	intron (NM_026644, intron 2 of 8)	46564	NM_026644	68262	Mm.258300	NM_026644	ENSMUSG00000023827	Agpat4	1500003P24Rik	1-acylglycerol-3-phosphate O-acyltransferase 4 (lysophosphatidic acid acyltransferase, delta)	protein-coding
mm_115203.1	chr13	109116294	109116302	+	1	NA	intron (NM_011056, intron 3 of 16)	intron (NM_011056, intron 3 of 16)	-208446	NR_030644	100124489		NR_030644	ENSMUSG00000076946	Mir582	Mirn582|mir-582|mmu-mir-582	microRNA 582	ncRNA
mm_108986.1	chr12	102757783	102757798	+	1	NA	promoter-TSS (NM_001142939)	promoter-TSS (NM_001142939)	20	NM_001142939	100859931	Mm.291222	NM_001142939	ENSMUSG00000041716	Gm20604	AK010878-Moap1	predicted gene 20604	protein-coding
mm_89210.1	chr10	86703545	86703574	+	1	NA	exon (NM_011631, exon 3 of 18)	exon (NM_011631, exon 3 of 18)	1885	NM_011631	22027	Mm.87773	NM_011631	ENSMUSG00000020048	Hsp90b1	ERp99|GRP94|TA-3|Targ2|Tra-1|Tra1|endoplasmin|gp96	heat shock protein 90, beta (Grp94), member 1	protein-coding
mm_65692.1	chr7	28372598	28372610	-	1	NA	promoter-TSS (NM_001083912)	promoter-TSS (NM_001083912)	58	NM_138752	101497	Mm.235700	NM_138752	ENSMUSG00000037552	Plekhg2	AI194308|Clg|Cslg	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	protein-coding
mm_95777.1	chr11	54909699	54909760	+	1	NA	3' UTR (NM_008161, exon 5 of 5)	3' UTR (NM_008161, exon 5 of 5)	6875	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_104234.1	chr11	88694934	88694936	-	1	NA	intron (NM_001201341, intron 5 of 7)	intron (NM_001201341, intron 5 of 7)	23294	NM_054043	76626	Mm.400451	NM_054043	ENSMUSG00000069769	Msi2	1700105C15Rik|AI451722|AI563628|AW489193|Msi2h	musashi RNA-binding protein 2	protein-coding
mm_48210.1	chr5	137606903	137606921	-	1	NA	exon (NM_008788, exon 6 of 9)	exon (NM_008788, exon 6 of 9)	4492	NM_008788	18542	Mm.262345	NM_008788	ENSMUSG00000029718	Pcolce	Astt-2|Astt2|P14|PCPE-1	procollagen C-endopeptidase enhancer protein	protein-coding
mm_131818.1	chr16	22920401	22920405	+	1	NA	5' UTR (NM_021564, exon 1 of 8)	5' UTR (NM_021564, exon 1 of 8)	181	NM_001083904	59083	Mm.28461	NM_021564	ENSMUSG00000022871	Fetub	2310011O17Rik|AI255764|D17980|Gugu	fetuin beta	protein-coding
mm_11519.1	chr2	32608705	32608717	+	1	NA	intron (NM_001289549, intron 2 of 6)	intron (NM_001289549, intron 2 of 6)	1726	NR_110347	50935	Mm.88831	NM_016973	ENSMUSG00000026811	St6galnac6	ST6GalNAcVI|Siat7f	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 6	protein-coding
mm_171882.1	chr5	3293973	3293976	+	1	NA	Intergenic	BGLII_A|LTR|ERVK	-49919	NM_009873	12571	Mm.31672	NM_009873	ENSMUSG00000040274	Cdk6	AI504062|Crk2	cyclin-dependent kinase 6	protein-coding
mm_16326.1	chr2	174308446	174308522	+	1	NA	intron (NM_001310085, intron 2 of 12)	intron (NM_001310085, intron 2 of 12)	10625	NM_001310085	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_95097.1	chr11	34046923	34046958	+	1	NA	promoter-TSS (NM_010696)	promoter-TSS (NM_010696)	-261	NM_010696	16822	Mm.265350	NM_010696	ENSMUSG00000002699	Lcp2	AI323664|BB161688|SLP-76|SLP76|m1Khoe|twm	lymphocyte cytosolic protein 2	protein-coding
mm_16867.1	chr2	12111120	12111124	-	1	NA	intron (NR_138462, intron 29 of 30)	intron (NR_138462, intron 29 of 30)	-190124	NR_040353	338535	Mm.483275	NR_040353	ENSMUSG00000086843	E030013I19Rik	-	RIKEN cDNA E030013I19 gene	ncRNA
mm_113752.1	chr13	44731354	44731373	+	1	NA	promoter-TSS (NM_001205043)	promoter-TSS (NM_001205043)	92	NM_001205043	16468	Mm.25059	NM_021878	ENSMUSG00000038518	Jarid2	Jmj|jumonji	jumonji, AT rich interactive domain 2	protein-coding
mm_106254.1	chr11	117828272	117828289	-	1	NA	intron (NM_027827, intron 2 of 10)	intron (NM_027827, intron 2 of 10)	-2266	NM_009387	21877	Mm.2661	NM_009387	ENSMUSG00000025574	Tk1	D530002A18Rik|Tk-1|Tk1a|Tk1b	thymidine kinase 1	protein-coding
mm_40973.1	chr5	77001751	77001756	+	1	NA	Intergenic	GA-rich|Low_complexity|Low_complexity	-2302	NM_206935	384185	Mm.451858	NM_206935	ENSMUSG00000063820	Arl9	1700110A09Rik	ADP-ribosylation factor-like 9	protein-coding
mm_29876.1	chr3	130947316	130947339	-	1	NA	Intergenic	Intergenic	-162970	NM_010703	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_36438.1	chr4	82296251	82296268	-	1	NA	3' UTR (NM_001113209, exon 12 of 12)	3' UTR (NM_001113209, exon 12 of 12)	209520	NM_001286127	18028	Mm.317947	NM_008687	ENSMUSG00000008575	Nfib	6720429L07Rik|CTF|E030026I10Rik|NF-I/B|NF1-B|NFI-B	nuclear factor I/B	protein-coding
mm_28865.1	chr3	97546280	97546317	-	1	NA	Intergenic	ORR1D1|LTR|ERVL-MaLR	63892	NM_026539	68058	Mm.31761	NM_026539	ENSMUSG00000028089	Chd1l	4432404A22Rik|Alc1|Snf2p	chromodomain helicase DNA binding protein 1-like	protein-coding
mm_19222.1	chr2	84650715	84650749	-	1	NA	promoter-TSS (NM_001085449)	promoter-TSS (NM_001085449)	8	NM_001085449	12388	Mm.35738	NM_007615	ENSMUSG00000034101	Ctnnd1	AA409437|AU019353|Catns|Ctnnd|P120|mKIAA0384	catenin (cadherin associated protein), delta 1	protein-coding
mm_98503.1	chr11	94952056	94952064	+	1	NA	3' UTR (NM_007742, exon 51 of 51)	3' UTR (NM_007742, exon 51 of 51)	-15533	NM_018792	54388	Mm.30482	NM_018792	ENSMUSG00000038994	Hils1	H1.9|TISP64	histone H1-like protein in spermatids 1	protein-coding
mm_80205.1	chr9	72438535	72438578	+	1	NA	promoter-TSS (NM_008613)	promoter-TSS (NM_008613)	27	NM_008613	17427	Mm.387671	NM_008613	ENSMUSG00000032221	Mns1	AW546487	meiosis-specific nuclear structural protein 1	protein-coding
mm_143014.1	chr17	56462371	56462385	-	1	NA	promoter-TSS (NM_001252456)	promoter-TSS (NM_001252456)	-157	NM_001252456	19280	Mm.258771	NM_011218	ENSMUSG00000013236	Ptprs	AL022616|PTP|PTP-NU3|PTPNU-3|PTPsigma|Ptpt9|R-PTP-S|RPTPsigma	protein tyrosine phosphatase, receptor type, S	protein-coding
mm_137807.1	chr17	30004481	30004519	+	1	NA	promoter-TSS (NM_148926)	promoter-TSS (NM_148926)	-587	NM_148926	21769	Mm.220972	NM_148926	ENSMUSG00000044477	Zfand3	AW539211|TEG-27|Tex27	zinc finger, AN1-type domain 3	protein-coding
mm_89525.1	chr10	94435475	94435517	+	1	NA	Intergenic	Intergenic	-79361	NM_172051	319880	Mm.23047	NM_172051	ENSMUSG00000020023	Tmcc3	AW488095|C630016B22Rik|C88213|Tmcc1	transmembrane and coiled coil domains 3	protein-coding
mm_16904.1	chr2	13491848	13491890	-	1	NA	promoter-TSS (NM_001081084)	promoter-TSS (NM_001081084)	7	NM_001081084	65969	Mm.313915	NM_001081084	ENSMUSG00000026726	Cubn	AA408369|AL022750|D2Wsu88e	cubilin (intrinsic factor-cobalamin receptor)	protein-coding
mm_65133.1	chr7	19508381	19508389	-	1	NA	promoter-TSS (NM_177692)	promoter-TSS (NM_177692)	-54	NM_177692	232946	Mm.64557	NM_177692	ENSMUSG00000057667	Bloc1s3	BC043666|Blos3|E230011O18|rp	biogenesis of lysosomal organelles complex-1, subunit 3	protein-coding
mm_141742.1	chr17	34122636	34122646	-	1	NA	promoter-TSS (NM_001204973)	promoter-TSS (NM_001204973)	-34	NM_001204973	14312	Mm.3444	NM_010238	ENSMUSG00000024335	Brd2	AW228947|D17H6S113E|Frg-1|Fsrg-1|Fsrg1|Nat|Ring3|Rnf3|mKIAA4005	bromodomain containing 2	protein-coding
mm_4121.1	chr1	169692574	169692578	+	1	NA	3' UTR (NM_009063, exon 5 of 5)	3' UTR (NM_009063, exon 5 of 5)	37075	NM_009063	19737	Mm.20954	NM_009063	ENSMUSG00000026678	Rgs5	1110070A02Rik	regulator of G-protein signaling 5	protein-coding
mm_30541.1	chr4	3678078	3678102	+	1	NA	promoter-TSS (NM_001111096)	promoter-TSS (NM_001111096)	-31	NM_001111096	17096	Mm.317331	NM_010747	ENSMUSG00000042228	Lyn	AA407514|Hck-2|p53Lyn|p56Lyn	LYN proto-oncogene, Src family tyrosine kinase	protein-coding
mm_109736.1	chr12	117153885	117153900	+	1	NA	intron (NM_011215, intron 12 of 22)	intron (NM_011215, intron 12 of 22)	-2623	NR_033538	100038689	Mm.445351	NR_033538	ENSMUSG00000099907	Gm10421	ENSMUSG00000072792	predicted gene 10421	ncRNA
mm_172989.1	chrM	1189	1193	+	1	NA	NA	Intergenic	NA	NA								
mm_25089.1	chr3	100825453	100825467	+	1	NA	promoter-TSS (NM_178594)	promoter-TSS (NM_178594)	1	NM_178594	242122	Mm.137467	NM_178594	ENSMUSG00000051076	Vtcn1	B7h4|B7s1|B7x|BC032925	V-set domain containing T cell activation inhibitor 1	protein-coding
mm_88637.1	chr10	79918502	79918508	+	1	NA	5' UTR (NM_053244, exon 1 of 5)	5' UTR (NM_053244, exon 1 of 5)	1534	NM_053244	114229	Mm.191035	NM_053244	ENSMUSG00000035773	Kiss1r	Gpr54|KiSS-1	KISS1 receptor	protein-coding
mm_44450.1	chr5	21701526	21701535	-	1	NA	promoter-TSS (NM_178728)	promoter-TSS (NM_178728)	-185	NM_178728	242864	Mm.153292	NM_178728	ENSMUSG00000044968	Napepld	A530089G06|Mbldc1|NAPE-PLD	N-acyl phosphatidylethanolamine phospholipase D	protein-coding
mm_120987.1	chr14	79129081	79129084	+	1	NA	intron (NM_027906, intron 37 of 44)	MTC|LTR|ERVL-MaLR	118285	NM_001033215	105590	Mm.486536	NM_001033215	ENSMUSG00000071262	Zfp957	AU017455	zinc finger protein 957	protein-coding
mm_68497.1	chr7	111078122	111078139	-	1	NA	exon (NM_013507, exon 8 of 22)	exon (NM_013507, exon 8 of 22)	4900	NM_001040131	13690	Mm.185453	NM_013507	ENSMUSG00000005610	Eif4g2	DAP-5|E130105L11Rik|Nat1|Natm1|p97	eukaryotic translation initiation factor 4, gamma 2	protein-coding
mm_33935.1	chr4	136909836	136909850	+	1	NA	Intergenic	Intergenic	-10999	NM_007572	12259	Mm.439957	NM_007572	ENSMUSG00000036887	C1qa	AI255395|C1q	complement component 1, q subcomponent, alpha polypeptide	protein-coding
mm_27615.1	chr3	59220151	59220201	-	1	NA	intron (NM_027571, intron 2 of 3)	intron (NM_027571, intron 2 of 3)	-9294	NM_028808	74191	Mm.90067	NM_028808	ENSMUSG00000036362	P2ry13	2010001L06Rik|GPCR1|GPR94|Gpr86|P2Y13|P2yr13|SP174	purinergic receptor P2Y, G-protein coupled 13	protein-coding
mm_100663.1	chr11	3291610	3291630	-	1	NA	exon (NM_001253691, exon 1 of 5)	exon (NM_001253691, exon 1 of 5)	1163	NM_019574	56218	Mm.275563	NM_019574	ENSMUSG00000020453	Patz1	8430401L15Rik|AI447519|Mazr|Patz|Zfp278	POZ (BTB) and AT hook containing zinc finger 1	protein-coding
mm_107640.1	chr12	52503924	52503949	+	1	NA	Intergenic	CpG	-12141	NM_009706	11855	Mm.35059	NM_009706	ENSMUSG00000035133	Arhgap5	p190-B|p190B	Rho GTPase activating protein 5	protein-coding
mm_71561.1	chr8	50823793	50823796	+	1	NA	Intergenic	Intergenic	455682	NR_046067	100039954	Mm.400419	NR_046067	ENSMUSG00000110281	Gm2516	-	predicted gene 2516	ncRNA
mm_34138.1	chr4	139291568	139291578	+	1	NA	3' UTR (NM_001271405, exon 9 of 9)	3' UTR (NM_001271405, exon 9 of 9)	19127	NM_145384	212555	Mm.45131	NM_145384	ENSMUSG00000028744	Pqlc2	BC019216	PQ loop repeat containing 2	protein-coding
mm_112899.1	chr13	20896509	20896518	+	1	NA	intron (NM_012054, intron 4 of 20)	L1_Mur3|LINE|L1	102400	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_146243.1	chr18	77281677	77281696	+	1	NA	promoter-TSS (NM_172834)	promoter-TSS (NM_172834)	-272	NM_172834	240411	Mm.380247	NM_172834	ENSMUSG00000032818	Loxhd1	1700096C21Rik|4932417K07|sba	lipoxygenase homology domains 1	protein-coding
mm_120548.1	chr14	67716096	67716124	+	1	NA	promoter-TSS (NM_001111028)	promoter-TSS (NM_001111028)	12	NM_001285933	105440	Mm.6720	NM_134073	ENSMUSG00000034327	Kctd9	-	potassium channel tetramerisation domain containing 9	protein-coding
mm_52431.1	chr6	113483529	113483571	+	1	NA	promoter-TSS (NM_133930)	promoter-TSS (NM_133930)	-19	NM_133930	171508	Mm.41593	NM_133930	ENSMUSG00000030284	Creld1	AI843811	cysteine-rich with EGF-like domains 1	protein-coding
mm_35371.1	chr4	32987063	32987103	-	1	NA	intron (NM_027491, intron 1 of 6)	intron (NM_027491, intron 1 of 6)	4085	NM_027491	52187	Mm.300814	NM_027491	ENSMUSG00000028278	Rragd	5730543C08Rik|AI467523|C030003H22Rik|D4Ertd174e	Ras-related GTP binding D	protein-coding
mm_32799.1	chr4	117096032	117096042	+	1	NA	promoter-TSS (NM_008958)	promoter-TSS (NM_008958)	-19	NM_001312903	19207	Mm.287037	NM_008958	ENSMUSG00000028681	Ptch2	ptc2	patched 2	protein-coding
mm_130876.1	chr15	102246222	102246248	-	1	NA	5' UTR (NM_001042727, exon 1 of 8)	5' UTR (NM_001042727, exon 1 of 8)	265	NM_001042727	19411	Mm.1273	NM_011244	ENSMUSG00000001288	Rarg	Nr1b3|RAR-gamma|RARD|RARgamma2	retinoic acid receptor, gamma	protein-coding
mm_30876.1	chr4	32238936	32238946	+	1	NA	Intergenic	CpG	-178494	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_86854.1	chr10	21690363	21690373	+	1	NA	promoter-TSS (NR_045843)	promoter-TSS (NR_045843)	-477	NR_045843	432436	Mm.244553	NM_001004162		Gm5420	EG432436	predicted gene 5420	ncRNA
mm_88371.1	chr10	76032599	76032660	+	1	NA	promoter-TSS (NM_177475)	promoter-TSS (NM_177475)	17	NM_177475	64453	Mm.80609	NM_177475	ENSMUSG00000049764	Zfp280b	D10Jhu82e|Suhw2	zinc finger protein 280B	protein-coding
mm_78182.1	chr9	21220755	21220772	+	1	NA	intron (NR_106127, intron 1 of 3)	intron (NR_106127, intron 1 of 3)	5518	NR_106127	102465769		NR_106127	ENSMUSG00000098764	Mir7667	Gm27756|mmu-mir-7667	microRNA 7667	ncRNA
mm_71313.1	chr8	43307228	43307241	+	1	NA	promoter-TSS (NM_009556)	promoter-TSS (NM_009556)	-225	NM_009556	22702	Mm.285848	NM_009556	ENSMUSG00000051176	Zfp42	Rex-1|Rex1|Zfp-42	zinc finger protein 42	protein-coding
mm_130091.1	chr15	89410231	89410271	-	1	NA	promoter-TSS (NM_001162882)	promoter-TSS (NM_001162882)	12	NM_001162882	75459	Mm.45462	NM_001162880	ENSMUSG00000078938	Syce3	1700007E06Rik|TSEG-2|TSEG2	synaptonemal complex central element protein 3	protein-coding
mm_109662.1	chr12	113022366	113022384	+	1	NA	intron (NM_001291444, intron 1 of 23)	B2_Mm2|SINE|B2	7867	NM_001291444	217893	Mm.35754	NM_198165	ENSMUSG00000021143	Pacs2	6720425G15Rik|AW208651|AW489976|E230011J22|Pacs1l|mKIAA0602	phosphofurin acidic cluster sorting protein 2	protein-coding
mm_10946.1	chr2	25557847	25557851	+	1	NA	promoter-TSS (NM_021519)	promoter-TSS (NM_021519)	-51	NM_021519	59022	Mm.29945	NM_021519	ENSMUSG00000015092	Edf1	0610008L11Rik|AA409425	endothelial differentiation-related factor 1	protein-coding
mm_108205.1	chr12	76909443	76909456	+	1	NA	intron (NM_145927, intron 8 of 11)	intron (NM_145927, intron 8 of 11)	52799	NM_008558	17187	Mm.268548	NM_008558	ENSMUSG00000059436	Max	AA960152|AI875693|bHLHd4|bHLHd5|bHLHd6|bHLHd7|bHLHd8	Max protein	protein-coding
mm_84232.1	chr9	62026789	62026833	-	1	NA	promoter-TSS (NM_028748)	promoter-TSS (NM_028748)	-21	NM_028748	74090	Mm.273267	NM_028748	ENSMUSG00000032278	Paqr5	0610010I15Rik|AV002411|BB115488|mPRg	progestin and adipoQ receptor family member V	protein-coding
mm_156524.1	chrX	150594394	150594413	+	1	NA	intron (NM_008824, intron 1 of 13)	intron (NM_008824, intron 1 of 13)	4482	NM_008824	18639	Mm.249131	NM_008824	ENSMUSG00000025271	Pfkfb1	PFK/FBPase 1	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1	protein-coding
mm_141708.1	chr17	34000249	34000268	-	1	NA	promoter-TSS (NM_001001892)	promoter-TSS (NM_001001892)	75	NM_001001892	14972	Mm.422886	NM_001001892	ENSMUSG00000061232	H2-K1	H-2K|H-2K(d)|H2-K|K-f	histocompatibility 2, K1, K region	protein-coding
mm_108797.1	chr12	91588502	91588519	+	1	NA	intron (NM_175335, intron 1 of 8)	CpG	1139	NM_031391	83602	Mm.275728	NM_031391	ENSMUSG00000020962	Gtf2a1	6330549H03Rik|AA536742|AA959775|AW060250|TfIIAa/b|Tfiia1	general transcription factor II A, 1	protein-coding
mm_48267.1	chr5	137956346	137956356	-	1	NA	3' UTR (NM_080450, exon 3 of 3)	3' UTR (NM_080450, exon 3 of 3)	6608	NM_080450	118446	Mm.332771	NM_080450	ENSMUSG00000056966	Gjc3	Cx29|Gje1	gap junction protein, gamma 3	protein-coding
mm_55057.1	chr6	49047855	49047877	-	1	NA	exon (NM_053110, exon 6 of 11)	exon (NM_053110, exon 6 of 11)	11348	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_134878.1	chr16	28929983	28930008	-	1	NA	promoter-TSS (NM_177718)	promoter-TSS (NM_177718)	-297	NM_177718	239796	Mm.155887	NM_177718	ENSMUSG00000051065	Mb21d2	1600021P15Rik|A430031N04|C87006	Mab-21 domain containing 2	protein-coding
mm_130523.1	chr15	98881362	98881381	-	1	NA	promoter-TSS (NM_026967)	promoter-TSS (NM_026967)	43	NM_026967	69159	Mm.259708	NM_026967	ENSMUSG00000023755	Rhebl1	1810036J22Rik|Rheb2	Ras homolog enriched in brain like 1	protein-coding
mm_113130.1	chr13	24614577	24614583	+	1	NA	promoter-TSS (NM_001286101)	promoter-TSS (NM_001286101)	-26	NM_001286101	193385	Mm.217319	NM_029679	ENSMUSG00000036006	Fam65b	-	family with sequence similarity 65, member B	protein-coding
mm_31010.1	chr4	40269888	40269911	+	1	NA	promoter-TSS (NM_134097)	promoter-TSS (NM_134097)	-58	NM_134097	106021	Mm.251548	NM_134097	ENSMUSG00000036822	Topors	AW105885|LUN|TP53BPL|p53BP3/LUN	topoisomerase I binding, arginine/serine-rich	protein-coding
mm_149373.1	chr19	11375459	11375471	+	1	NA	promoter-TSS (NM_001310331)	promoter-TSS (NM_001310331)	-23	NM_001310331	666907		NM_001310331	ENSMUSG00000101389	Ms4a4a	EG666907	membrane-spanning 4-domains, subfamily A, member 4A	protein-coding
mm_169266.1	chr13	84691014	84691018	-	1	NA	Intergenic	Intergenic	468720	NM_175187	72745	Mm.295063	NM_175187	ENSMUSG00000035762	Tmem161b	2810446P07Rik|AI843389	transmembrane protein 161B	protein-coding
mm_24412.1	chr3	90484532	90484539	+	1	NA	exon (NM_026374, exon 8 of 14)	exon (NM_026374, exon 8 of 14)	6478	NM_133854	20615	Mm.331182	NM_133854	ENSMUSG00000001018	Snapin	25kDa|AA407989|AV026596|Bloc1s7|Snap25bp|Snapap	SNAP-associated protein	protein-coding
mm_18603.1	chr2	67573995	67573999	-	1	NA	Intergenic	Intergenic	-101460	NR_106083	102465706		NR_106083	ENSMUSG00000098299	Mir7224	Gm27971|mmu-mir-7224	microRNA 7224	ncRNA
mm_11334.1	chr2	30595038	30595048	+	1	NA	promoter-TSS (NM_030137)	promoter-TSS (NM_030137)	-1	NM_030137	78617	Mm.40413	NM_030137	ENSMUSG00000047363	Cstad	9530039B02Rik	CSA-conditional, T cell activation-dependent protein	protein-coding
mm_122925.1	chr14	54961208	54961222	-	1	NA	exon (NM_010856, exon 11 of 39)	exon (NM_010856, exon 11 of 39)	5392	NM_001164171	17888	Mm.290003	NM_010856	ENSMUSG00000040752	Myh6	A830009F23Rik|AA517445|Myhc-a|Myhca|alpha-MHC	myosin, heavy polypeptide 6, cardiac muscle, alpha	protein-coding
mm_56956.1	chr6	120037335	120037353	-	1	NA	exon (NM_001185020, exon 1 of 26)	exon (NM_001185020, exon 1 of 26)	1311	NM_001199083	232341	Mm.333349	NM_198703	ENSMUSG00000045962	Wnk1	6430573H23Rik|EG406236|Hsn2|Prkwnk1|mKIAA0344	WNK lysine deficient protein kinase 1	protein-coding
mm_5886.1	chr1	54142719	54142723	-	1	NA	intron (NM_001001883, intron 1 of 28)	intron (NM_001001883, intron 1 of 28)	52313	NM_001001883	329152	Mm.132150	NM_172655	ENSMUSG00000042807	Hecw2	A730039N16Rik|D030049F17Rik|Gm971|Nedl2|mKIAA1301	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2	protein-coding
mm_43208.1	chr5	129204328	129204332	+	1	NA	3' UTR (NM_001081342, exon 26 of 26)	3' UTR (NM_001081342, exon 26 of 26)	107580	NM_001347486	243277	Mm.440501	NM_177734	ENSMUSG00000044017	Adgrd1	E230012M21Rik|Gpr133	adhesion G protein-coupled receptor D1	protein-coding
mm_147432.1	chr18	46447641	46447642	-	1	NA	Intergenic	Intergenic	18175	NR_045438	72076	Mm.82766	NM_028086		Mospd4	2010013H21Rik	motile sperm domain containing 4	pseudo
mm_29646.1	chr3	121900537	121900564	-	1	NA	Intergenic	Intergenic	-52776	NM_172525	214137	Mm.229287	NM_172525	ENSMUSG00000039831	Arhgap29	6720461J18Rik|A830014I19|AU040217|B130017I01Rik|C76601|Parg1	Rho GTPase activating protein 29	protein-coding
mm_24759.1	chr3	95481234	95481254	+	1	NA	intron (NM_009709, intron 9 of 20)	intron (NM_009709, intron 9 of 20)	-17966	NM_007802	13038	Mm.272085	NM_007802	ENSMUSG00000028111	Ctsk	AI323530|MMS10-Q|Ms10q|catK	cathepsin K	protein-coding
mm_148689.1	chr19	5727171	5727194	+	1	NA	promoter-TSS (NM_001114597)	promoter-TSS (NM_001114597)	-865	NM_053252	114601	Mm.210447	NM_053252	ENSMUSG00000024937	Ehbp1l1	G430002G23Rik	EH domain binding protein 1-like 1	protein-coding
mm_82555.1	chr9	20976763	20976774	-	1	NA	promoter-TSS (NM_010333)	promoter-TSS (NM_010333)	25	NM_010333	14739	Mm.46493	NM_010333	ENSMUSG00000043895	S1pr2	1100001A16Rik|Edg5|Gpcr13|H218|LPb2|S1P2	sphingosine-1-phosphate receptor 2	protein-coding
mm_109632.1	chr12	112767802	112767821	+	1	NA	exon (NM_178911, exon 9 of 11)	exon (NM_178911, exon 9 of 11)	7156	NM_178911	104759	Mm.203915	NM_178911	ENSMUSG00000052160	Pld4	AI132321|thss	phospholipase D family, member 4	protein-coding
mm_103711.1	chr11	79518831	79518846	-	1	NA	intron (NM_146023, intron 3 of 3)	intron (NM_146023, intron 3 of 3)	4924	NM_001077496	216984	Mm.439665	NM_001077496	ENSMUSG00000093938	Evi2b	Evi-2|Evi2	ecotropic viral integration site 2b	protein-coding
mm_98809.1	chr11	97161527	97161539	+	1	NA	3' UTR (NM_008379, exon 22 of 22)	3' UTR (NM_008379, exon 22 of 22)	-11821	NM_198100	73174	Mm.27882	NM_198100	ENSMUSG00000038517	Tbkbp1	3110043L15Rik|ProSAPiP2|SINTBAD	TBK1 binding protein 1	protein-coding
mm_52989.1	chr6	123265319	123265364	+	1	NA	exon (NM_010819, exon 2 of 6)	exon (NM_010819, exon 2 of 6)	3234	NM_010819	17474	Mm.441101	NM_010819	ENSMUSG00000030144	Clec4d	Clecsf8|Mpcl|mcl	C-type lectin domain family 4, member d	protein-coding
mm_114303.1	chr13	59585302	59585325	+	1	NA	promoter-TSS (NM_030153)	promoter-TSS (NM_030153)	-20	NM_030153	78689	Mm.253902	NM_030153	ENSMUSG00000021555	Naa35	A330021G12Rik|A330027C19Rik|AI158944|C030004C14Rik|Mak10	N(alpha)-acetyltransferase 35, NatC auxiliary subunit	protein-coding
mm_94523.1	chr11	9048699	9048711	+	1	NA	5' UTR (NM_001037928, exon 1 of 7)	5' UTR (NM_001037928, exon 1 of 7)	113	NM_001037928	626870	Mm.369429	NM_001037928	ENSMUSG00000040978	Gm11992	OTTMUSG00000005148	predicted gene 11992	protein-coding
mm_82216.1	chr9	3004822	3004841	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	33912	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_101495.1	chr11	31824432	31824442	-	1	NA	non-coding (NR_102314, exon 1 of 4)	non-coding (NR_102314, exon 1 of 4)	110	NR_102310	414116	Mm.150222	NR_102310	ENSMUSG00000085772	D630024D03Rik	-	RIKEN cDNA D630024D03 gene	ncRNA
mm_68622.1	chr7	118116147	118116167	-	1	NA	promoter-TSS (NM_170669)	promoter-TSS (NM_170669)	-10	NM_170669	267019	Mm.288212	NM_170669	ENSMUSG00000008683	Rps15a	A630031B11Rik	ribosomal protein S15A	protein-coding
mm_143978.1	chr17	87440916	87440920	-	1	NA	intron (NM_007589, intron 2 of 5)	intron (NM_007589, intron 2 of 5)	6017	NM_007589	12314	Mm.329243	NM_007589	ENSMUSG00000036438	Calm2	1500001E21Rik|AL024017	calmodulin 2	protein-coding
mm_86284.1	chr9	121857577	121857633	-	1	NA	5' UTR (NM_019814, exon 1 of 4)	5' UTR (NM_019814, exon 1 of 4)	395	NM_019814	56295	Mm.347915	NM_019814	ENSMUSG00000038412	Higd1a	2210020B17Rik|7420700H20Rik|AI303276|AW049839|HIMP1|Hig1	HIG1 domain family, member 1A	protein-coding
mm_57764.1	chr6	129233981	129233999	-	1	NA	intron (NR_040265, intron 1 of 2)	intron (NR_040265, intron 1 of 2)	4055	NR_040265	76432	Mm.261738	NR_040265	ENSMUSG00000097354	2310001H17Rik	AI646108	RIKEN cDNA 2310001H17 gene	ncRNA
mm_43644.1	chr5	138256125	138256135	+	1	NA	intron (NM_001081108, intron 1 of 3)	intron (NM_001081108, intron 1 of 3)	648	NM_001081108	66096	Mm.206901	NM_001081108	ENSMUSG00000050552	Lamtor4	0910001L09Rik|AV006840	late endosomal/lysosomal adaptor, MAPK and MTOR activator 4	protein-coding
mm_25026.1	chr3	98127093	98127117	+	1	NA	intron (NM_010928, intron 22 of 33)	intron (NM_010928, intron 22 of 33)	-33529	NM_027665	71078	Mm.50711	NM_027665	ENSMUSG00000043468	Adam30	4933424D07Rik|svph4	a disintegrin and metallopeptidase domain 30	protein-coding
mm_113422.1	chr13	34037667	34037682	+	1	NA	promoter-TSS (NM_026512)	promoter-TSS (NM_026512)	33	NM_026512	68021	Mm.140243	NM_026512	ENSMUSG00000038286	Bphl	2010012D11Rik|5730533B08Rik|AI115341	biphenyl hydrolase-like (serine hydrolase, breast epithelial mucin-associated antigen)	protein-coding
mm_130249.1	chr15	96641460	96641474	-	1	NA	5' UTR (NM_134086, exon 1 of 16)	5' UTR (NM_134086, exon 1 of 16)	495	NM_134086	105727	Mm.103568	NM_134086	ENSMUSG00000023169	Slc38a1	AA408026|AA409865|AL022800|AU015942|NAT2	solute carrier family 38, member 1	protein-coding
mm_7445.1	chr1	120121007	120121023	-	1	NA	promoter-TSS (NM_001172074)	promoter-TSS (NM_001172074)	81	NM_007830	13167	Mm.2785	NM_007830	ENSMUSG00000026385	Dbi	ACBD1|Acbp|EP|endozepine	diazepam binding inhibitor	protein-coding
mm_52839.1	chr6	121641335	121641352	+	1	NA	exon (NM_175628, exon 6 of 36)	exon (NM_175628, exon 6 of 36)	5170	NM_175628	232345	Mm.30151	NM_175628	ENSMUSG00000030111	A2m	A2mp	alpha-2-macroglobulin	protein-coding
mm_46707.1	chr5	110286147	110286155	-	1	NA	promoter-TSS (NM_011132)	promoter-TSS (NM_011132)	17	NM_008993	19301	Mm.21853	NM_008993	ENSMUSG00000029499	Pxmp2	22kDa|PMP22	peroxisomal membrane protein 2	protein-coding
mm_1713.1	chr1	75236660	75236665	+	1	NA	promoter-TSS (NM_001159885)	promoter-TSS (NM_001159885)	-40	NM_001159885	56812	Mm.489660	NM_020266	ENSMUSG00000026203	Dnajb2	2700059H22Rik|Dnajb10|Hsj1|mDj8	DnaJ heat shock protein family (Hsp40) member B2	protein-coding
mm_19125.1	chr2	80129118	80129138	-	1	NA	promoter-TSS (NM_016744)	promoter-TSS (NM_016744)	-157	NM_016744	18573	Mm.40678	NM_016744	ENSMUSG00000059173	Pde1a	AI987702|AW125737	phosphodiesterase 1A, calmodulin-dependent	protein-coding
mm_140029.1	chr17	74016975	74017019	+	1	NA	TTS (NM_053188)	TTS (NM_053188)	30919	NM_053188	94224	Mm.38933	NM_053188	ENSMUSG00000038541	Srd5a2	5ART2|S5AR 2	steroid 5 alpha-reductase 2	protein-coding
mm_7334.1	chr1	105356659	105356714	-	1	NA	promoter-TSS (NM_001160368)	promoter-TSS (NM_001160368)	24	NM_178779	320311	Mm.389162	NM_178779	ENSMUSG00000047496	Rnf152	A930029B02Rik	ring finger protein 152	protein-coding
mm_12531.1	chr2	72207691	72207701	+	1	NA	intron (NM_001204165, intron 16 of 30)	intron (NM_001204165, intron 16 of 30)	-77941	NM_023057	65964	Mm.304143	NM_023057	ENSMUSG00000004085	Map3k20	AV006891|B230120H23Rik|MLTK|MLTKalpha|MLTKbeta|Zak	mitogen-activated protein kinase kinase kinase 20	protein-coding
mm_156663.1	chrX	157817918	157817928	+	1	NA	promoter-TSS (NM_001081667)	promoter-TSS (NM_001081667)	-512	NM_001081667	245683	Mm.295846	NM_001081667	ENSMUSG00000047485	Klhl34	Gm388	kelch-like 34	protein-coding
mm_28664.1	chr3	95266134	95266178	-	1	NA	intron (NM_173347, intron 2 of 7)	intron (NM_173347, intron 2 of 7)	-14963	NM_134253	171388	Mm.331209	NM_134253	ENSMUSG00000028115	Bnipl	1700128A13Rik|BNIP-S|BNIPL1|BNIPL2|PP73|PP753	BCL2/adenovirus E1B 19kD interacting protein like	protein-coding
mm_87130.1	chr10	34282200	34282278	+	1	NA	promoter-TSS (NM_009433)	promoter-TSS (NM_009433)	49	NM_009433	22110	Mm.20445	NM_009433	ENSMUSG00000047514	Tspyl1	Tspyl	testis-specific protein, Y-encoded-like 1	protein-coding
mm_49486.1	chr6	29537060	29537076	+	1	NA	3' UTR (NM_001252382, exon 9 of 9)	3' UTR (NM_001252382, exon 9 of 9)	7786	NM_001252382	27056	Mm.6479	NM_012057	ENSMUSG00000029771	Irf5	AW491843|mirf5	interferon regulatory factor 5	protein-coding
mm_19215.1	chr2	84643616	84643621	-	1	NA	intron (NM_007615, intron 1 of 19)	AT_rich|Low_complexity|Low_complexity	6892	NM_001085453	12388	Mm.35738	NM_007615	ENSMUSG00000034101	Ctnnd1	AA409437|AU019353|Catns|Ctnnd|P120|mKIAA0384	catenin (cadherin associated protein), delta 1	protein-coding
mm_66924.1	chr7	61311663	61311667	-	1	NA	Intergenic	Intergenic	303662	NR_045727	319752	Mm.294476	NR_045727		B230209E15Rik	-	RIKEN cDNA B230209E15 gene	ncRNA
mm_447.1	chr1	35282624	35282624	+	1	NA	Intergenic	Intergenic	432665	NM_145516	226971	Mm.292751	NM_145516	ENSMUSG00000026123	Plekhb2	2310009M15Rik|AU018239|Evt2|Phdc|evt-2	pleckstrin homology domain containing, family B (evectins) member 2	protein-coding
mm_125930.1	chr15	76247372	76247408	+	1	NA	promoter-TSS (NR_105918)	promoter-TSS (NR_105918)	583	NM_023168	66168	Mm.41665	NM_023168	ENSMUSG00000022564	Grina	1110025J15Rik|Lag|Tmbim3	glutamate receptor, ionotropic, N-methyl D-aspartate-associated protein 1 (glutamate binding)	protein-coding
mm_130313.1	chr15	97167232	97167250	-	1	NA	Intergenic	MLTR31F_MM|LTR|ERVK	-79866	NM_172293	239647	Mm.130036	NM_172293	ENSMUSG00000044250	Pced1b	Fam113b	PC-esterase domain containing 1B	protein-coding
mm_119518.1	chr14	47472629	47472640	+	1	NA	promoter-TSS (NM_030236)	promoter-TSS (NM_030236)	73	NM_001146085	78938	Mm.11935	NM_030236	ENSMUSG00000037536	Fbxo34	2900057B08Rik|5830426G16Rik	F-box protein 34	protein-coding
mm_88029.1	chr10	67229999	67230024	+	1	NA	exon (NM_001242396, exon 10 of 25)	exon (NM_001242396, exon 10 of 25)	44261	NM_001242396	108829	Mm.23846	NM_207221	ENSMUSG00000037876	Jmjd1c	5430433L24Rik|D630035I23Rik|Jmjdic|TRIP8	jumonji domain containing 1C	protein-coding
mm_33395.1	chr4	129820305	129820311	+	1	NA	promoter-TSS (NM_001164745)	promoter-TSS (NM_001164745)	-171	NM_008974	19244	Mm.193688	NM_008974	ENSMUSG00000028788	Ptp4a2	Prl-2	protein tyrosine phosphatase 4a2	protein-coding
mm_46697.1	chr5	110108131	110108150	-	1	NA	promoter-TSS (NM_145147)	promoter-TSS (NM_145147)	57	NM_145147	107999	Mm.86267	NM_145147	ENSMUSG00000033434	Gtpbp6	AV119224|Pgbpll|pgpl	GTP binding protein 6 (putative)	protein-coding
mm_109331.1	chr12	109571640	109571672	+	1	NA	promoter-TSS (NR_030438)	promoter-TSS (NR_030438)	-334	NR_030438	751547		NR_030438	ENSMUSG00000076316	Mir673	Mirn673|mir-673|mmu-mir-673	microRNA 673	ncRNA
mm_96076.1	chr11	59887216	59887219	+	1	NA	Intergenic	ORR1D1-int|LTR|ERVL-MaLR	-34282	NR_130986	69854	Mm.57859	NR_130986	ENSMUSG00000085551	1810063I02Rik	-	RIKEN cDNA 1810063I02 gene	ncRNA
mm_105157.1	chr11	101466249	101466257	-	1	NA	promoter-TSS (NM_012037)	promoter-TSS (NM_012037)	-54	NM_012037	26949	Mm.29210	NM_012037	ENSMUSG00000034993	Vat1	VAT-1	vesicle amine transport 1	protein-coding
mm_114770.1	chr13	88821583	88821591	+	1	NA	5' UTR (NM_001037987, exon 1 of 11)	5' UTR (NM_001037987, exon 1 of 11)	115	NM_001037987	13612	Mm.125580	NM_010103	ENSMUSG00000034488	Edil3	Del-1|Del1	EGF-like repeats and discoidin I-like domains 3	protein-coding
mm_151542.1	chr19	59171776	59171786	+	1	NA	Intergenic	CpG	-1752	NM_009501	22326	Mm.23801	NM_009501	ENSMUSG00000006270	Vax1	-	ventral anterior homeobox 1	protein-coding
mm_53568.1	chr6	137252481	137252503	+	1	NA	5' UTR (NM_011216, exon 1 of 27)	5' UTR (NM_011216, exon 1 of 27)	193	NM_011216	19277	Mm.186361	NM_011216	ENSMUSG00000030223	Ptpro	D28|GLEPP1|PTPBK|PTPROt|PTPU2|PTPoc|PTPphi|Ptpn15|R-PTP-O	protein tyrosine phosphatase, receptor type, O	protein-coding
mm_86445.1	chr10	4243907	4243912	+	1	NA	Intergenic	RMER17C|LTR|ERVK	-22420	NM_031185	83397	Mm.27481	NM_031185	ENSMUSG00000038587	Akap12	AI317366|SSeCKS|Srcs5|Tsga12	A kinase (PRKA) anchor protein (gravin) 12	protein-coding
mm_102844.1	chr11	69368051	69368093	-	1	NA	intron (NM_146019, intron 1 of 39)	intron (NM_146019, intron 1 of 39)	1354	NM_146019	216848	Mm.178246	NM_146019	ENSMUSG00000018474	Chd3	2600010P09Rik|AF020312|Chd7|Prp7|Prp9-1	chromodomain helicase DNA binding protein 3	protein-coding
mm_99679.1	chr11	105994618	105994624	+	1	NA	promoter-TSS (NM_001101453)	promoter-TSS (NM_001101453)	-54	NM_001101453	217246	Mm.296699	NM_001101453	ENSMUSG00000101605	Ace3	EG217246	angiotensin I converting enzyme (peptidyl-dipeptidase A) 3	protein-coding
mm_157867.1	chrX	75379787	75379791	-	1	NA	5' UTR (NM_001161373, exon 1 of 25)	5' UTR (NM_001161373, exon 1 of 25)	252	NM_007977	14069	Mm.1805	NM_007977	ENSMUSG00000031196	F8	Cf-8|Cf8|FVIII	coagulation factor VIII	protein-coding
mm_28391.1	chr3	90019198	90019212	-	1	NA	exon (NM_001165987, exon 15 of 25)	exon (NM_001165987, exon 15 of 25)	-7995	NR_106129	102465771		NR_106129	ENSMUSG00000098397	Mir7669	Gm27996|mmu-mir-7669	microRNA 7669	ncRNA
mm_10962.1	chr2	25701289	25701293	+	1	NA	intron (NM_153558, intron 3 of 6)	intron (NM_153558, intron 3 of 6)	1217	NM_153558	227627	Mm.44630	NM_153558	ENSMUSG00000062061	Obp2a	BC027556|Lcn13	odorant binding protein 2A	protein-coding
mm_3708.1	chr1	153900573	153900601	+	1	NA	TTS (NR_106194)	TTS (NR_106194)	658	NM_008131	14645	Mm.210745	NM_008131	ENSMUSG00000026473	Glul	GS|Glns	glutamate-ammonia ligase (glutamine synthetase)	protein-coding
mm_145757.1	chr18	64887815	64887829	+	1	NA	promoter-TSS (NM_001114386)	promoter-TSS (NM_001114386)	66	NM_001114386	83814	Mm.98668	NM_031881	ENSMUSG00000024589	Nedd4l	1300012C07Rik|Nedd4-2|Nedd4b	neural precursor cell expressed, developmentally down-regulated gene 4-like	protein-coding
mm_20453.1	chr2	129365003	129365025	-	1	NA	3' UTR (NM_008361, exon 7 of 7)	3' UTR (NM_008361, exon 7 of 7)	-4888	NR_015474	329514	Mm.207315	NM_177848	ENSMUSG00000074805	Il1bos	9430083I22|Gm14047|OTTMUSG00000015529	interleukin 1 beta, opposite strand	ncRNA
mm_5934.1	chr1	55363388	55363396	-	1	NA	promoter-TSS (NM_029267)	promoter-TSS (NM_029267)	77	NM_029267	75388	Mm.483408	NM_029267	ENSMUSG00000025977	Boll	4930554P13Rik|4930597B14Rik	bol, boule-like (Drosophila)	protein-coding
mm_4942.1	chr1	191183682	191183710	+	1	NA	promoter-TSS (NM_007498)	promoter-TSS (NM_007498)	-363	NM_007498	11910	Mm.2706	NM_007498	ENSMUSG00000026628	Atf3	LRG-21	activating transcription factor 3	protein-coding
mm_146927.1	chr18	31949796	31949814	-	1	NA	promoter-TSS (NM_001025381)	promoter-TSS (NM_001025381)	-169	NM_001025381	574402	Mm.391108	NM_001025381	ENSMUSG00000052229	Gpr17	AI853548	G protein-coupled receptor 17	protein-coding
mm_54058.1	chr6	13839917	13839941	-	1	NA	promoter-TSS (NM_001330667)	promoter-TSS (NM_001330667)	13	NM_001330666	64450	Mm.167625	NM_145066	ENSMUSG00000048216	Gpr85	2900026B03Rik	G protein-coupled receptor 85	protein-coding
mm_21024.1	chr2	152412921	152412925	-	1	NA	3' UTR (NM_175126, exon 1 of 1)	3' UTR (NM_175126, exon 1 of 1)	2121	NM_175126	67917	Mm.391810	NM_175126	ENSMUSG00000074682	Zcchc3	2810406K24Rik	zinc finger, CCHC domain containing 3	protein-coding
mm_144429.1	chr18	21001779	21001789	+	1	NA	promoter-TSS (NM_207623)	promoter-TSS (NM_207623)	-173	NM_001303011	56515	Mm.253542	NM_019706	ENSMUSG00000024317	Rnf138	2410015A17Rik|2810480D20Rik|STRIN|Trif|Trif-d	ring finger protein 138	protein-coding
mm_23447.1	chr3	59952136	59952167	+	1	NA	promoter-TSS (NR_037189)	promoter-TSS (NR_037189)	-158	NR_037189	676914	Mm.228502	NR_037189	ENSMUSG00000070465	Gm9696	-	arylacetamide deacetylase-like 2 pseudogene	pseudo
mm_54102.1	chr6	16884019	16884029	-	1	NA	intron (NM_031198, intron 1 of 6)	intron (NM_031198, intron 1 of 6)	14417	NM_031198	21426	Mm.36217	NM_031198	ENSMUSG00000029553	Tfec	BB107417|Tcfec|bHLHe34	transcription factor EC	protein-coding
mm_10651.1	chr2	20669686	20669704	+	1	NA	intron (NM_029895, intron 4 of 18)	RLTR41C|LTR|ERV1	150182	NM_001177631	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding
mm_60186.1	chr7	43253740	43253773	+	1	NA	Intergenic	Intergenic	39717	NM_001177525	100170401		NM_001177525		EU599041	TU7	expressed sequence EU599041	protein-coding
mm_165029.1	chr19	32757727	32757735	+	1	NA	5' UTR (NM_008960, exon 1 of 9)	5' UTR (NM_008960, exon 1 of 9)	154	NM_008960	19211	Mm.245395	NM_008960	ENSMUSG00000013663	Pten	2310035O07Rik|A130070J02Rik|AI463227|B430203M17Rik|MMAC1|TEP1	phosphatase and tensin homolog	protein-coding
mm_127712.1	chr15	103014001	103014014	+	1	NA	promoter-TSS (NM_175730)	promoter-TSS (NM_175730)	-1	NM_175730	15424	Mm.103825	NM_175730	ENSMUSG00000022485	Hoxc5	AI181837|Hox-3.4|Hox-6.2	homeobox C5	protein-coding
mm_46848.1	chr5	113614335	113614359	-	1	NA	exon (NM_008153, exon 3 of 3)	exon (NM_008153, exon 3 of 3)	36043	NM_008153	14747	Mm.5196	NM_008153	ENSMUSG00000042190	Cmklr1	ChemR23|DEZ|Gpcr27|mcmklr1	chemokine-like receptor 1	protein-coding
mm_138374.1	chr17	35004682	35004690	+	1	NA	intron (NM_011690, intron 4 of 29)	intron (NM_011690, intron 4 of 29)	3779	NM_011690	22321	Mm.28420	NM_011690	ENSMUSG00000007029	Vars	Bat6|D17H6S56E|G7a|Vars2	valyl-tRNA synthetase	protein-coding
mm_156341.1	chrX	139010069	139010091	+	1	NA	TTS (NM_013724)	TTS (NM_013724)	75156	NM_177920	331535	Mm.211704	NM_177920	ENSMUSG00000031271	Serpina7	C730040N12Rik|Tbg	serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 7	protein-coding
mm_129879.1	chr15	83447984	83447992	-	1	NA	intron (NM_001159509, intron 1 of 10)	intron (NM_001159509, intron 1 of 10)	-15138	NM_001159510	23970	Mm.23978	NM_011862	ENSMUSG00000016664	Pacsin2	AI197433	protein kinase C and casein kinase substrate in neurons 2	protein-coding
mm_50671.1	chr6	51544514	51544578	+	1	NA	promoter-TSS (NM_001127348)	promoter-TSS (NM_001127348)	23	NM_001127348	71982	Mm.294166	NM_028035	ENSMUSG00000038301	Snx10	2410004M09Rik	sorting nexin 10	protein-coding
mm_58131.1	chr6	140624660	140624666	-	1	NA	promoter-TSS (NM_001309437)	promoter-TSS (NM_001309437)	-246	NM_001309437	11569	Mm.86453	NM_009637	ENSMUSG00000030232	Aebp2	AU023766|B230313N05Rik	AE binding protein 2	protein-coding
mm_2448.1	chr1	100042784	100042784	+	1	NA	intron (NM_172851, intron 3 of 23)	intron (NM_172851, intron 3 of 23)	270019	NM_172851	241175	Mm.251301	NM_172851	ENSMUSG00000067028	Cntnap5b	C230078M14Rik|Caspr5-2	contactin associated protein-like 5B	protein-coding
mm_166770.1	chr6	135362345	135362365	+	1	NA	promoter-TSS (NM_001288628)	promoter-TSS (NM_001288628)	-576	NM_010128	13730	Mm.182785	NM_010128	ENSMUSG00000030208	Emp1	I-8-09|TMP	epithelial membrane protein 1	protein-coding
mm_39497.1	chr5	21056269	21056289	+	1	NA	promoter-TSS (NM_011203)	promoter-TSS (NM_011203)	-482	NM_011203	19248	Mm.319117	NM_011203	ENSMUSG00000028771	Ptpn12	P19-PTP|PTP-P19|PTP-PEST|PTPG1	protein tyrosine phosphatase, non-receptor type 12	protein-coding
mm_69773.1	chr7	141016839	141016850	-	1	NA	promoter-TSS (NM_001033632)	promoter-TSS (NM_001033632)	48	NM_001033632	213002	Mm.276440	NM_001033632	ENSMUSG00000059108	Ifitm6	A330075D07|Dspa2f|Fgls5|fragilis5	interferon induced transmembrane protein 6	protein-coding
mm_48888.1	chr5	151234048	151234066	-	1	NA	Intergenic	Intergenic	-43864	NM_146258	243362	Mm.209272	NM_146258	ENSMUSG00000016128	Stard13	DLC2|GT650	StAR-related lipid transfer (START) domain containing 13	protein-coding
mm_156650.1	chrX	157702764	157702778	+	1	NA	intron (NR_045569, intron 1 of 6)	intron (NR_045569, intron 1 of 6)	3798	NR_103722	66106	Mm.140340	NM_025357	ENSMUSG00000041476	Smpx	1010001C09Rik|Csl	small muscle protein, X-linked	protein-coding
mm_53054.1	chr6	124808937	124808956	+	1	NA	promoter-TSS (NM_001306053)	promoter-TSS (NM_001306053)	28	NM_001306053	14794	Mm.261906	NM_013539	ENSMUSG00000038451	Spsb2	AI461677|C9|Grcc9|SSB2	splA/ryanodine receptor domain and SOCS box containing 2	protein-coding
mm_156811.1	chrX	163958745	163958797	+	1	NA	promoter-TSS (NM_009453)	promoter-TSS (NM_009453)	-105	NM_178794	22184	Mm.426178	NM_009453	ENSMUSG00000031370	Zrsr2	35kDa|5031411E02Rik|A230052C13Rik|C77286|U2af1-rs2|URP	zinc finger (CCCH type), RNA binding motif and serine/arginine rich 2	protein-coding
mm_15110.1	chr2	153641993	153642011	+	1	NA	Intergenic	Intergenic	-7447	NM_001003963	13436	Mm.89772	NM_010068	ENSMUSG00000027478	Dnmt3b	MmuIIIB	DNA methyltransferase 3B	protein-coding
mm_151729.1	chr19	4872350	4872360	-	1	NA	exon (NM_013456, exon 3 of 21)	exon (NM_013456, exon 3 of 21)	5554	NM_013456	11474	Mm.5316	NM_013456	ENSMUSG00000006457	Actn3	-	actinin alpha 3	protein-coding
mm_138391.1	chr17	35050305	35050315	+	1	NA	promoter-TSS (NM_033444)	promoter-TSS (NM_033444)	67	NM_033444	114584	Mm.29524	NM_033444	ENSMUSG00000007041	Clic1	Clcp|G6	chloride intracellular channel 1	protein-coding
mm_127828.1	chr15	6555601	6555641	-	1	NA	Intergenic	Intergenic	-24226	NM_001278269	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_32612.1	chr4	112284802	112284813	+	1	NA	intron (NM_001102474, intron 8 of 9)	RMER3D-int|LTR|ERVK	52386	NM_001102474	195564	Mm.259652	NM_177578	ENSMUSG00000070868	Skint3	A430090E18Rik|Skint-3	selection and upkeep of intraepithelial T cells 3	protein-coding
mm_135878.1	chr16	63758451	63758452	-	1	NA	intron (NM_010140, intron 3 of 16)	intron (NM_010140, intron 3 of 16)	105706	NM_010140	13837	Mm.1977	NM_010140	ENSMUSG00000052504	Epha3	AW492086|Cek4|ETK1|End3|Hek|Hek4|Mek4|Tyro4	Eph receptor A3	protein-coding
mm_6496.1	chr1	74268181	74268212	-	1	NA	TTS (NM_029711)	TTS (NM_029711)	-10404	NM_174985	227289	Mm.246587	NM_174985	ENSMUSG00000064272	Gpbar1	BG37|GPCR|GPR131|M-BAR|TGR5	G protein-coupled bile acid receptor 1	protein-coding
mm_106409.1	chr11	119040906	119040937	-	1	NA	promoter-TSS (NM_013926)	promoter-TSS (NM_013926)	-8	NM_013926	30951	Mm.99953	NM_013926	ENSMUSG00000025578	Cbx8	Pc3	chromobox 8	protein-coding
mm_156286.1	chrX	136837370	136837381	+	1	NA	3' UTR (NM_011123, exon 7 of 7)	3' UTR (NM_011123, exon 7 of 7)	14629	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_88246.1	chr10	72658122	72658126	+	1	NA	intron (NM_001293683, intron 7 of 7)	RLTR28B|LTR|ERVL	3278	NM_001293683	52696	Mm.62876	NM_025635	ENSMUSG00000019923	Zwint	2010007E07Rik|2600001N01Rik|D10Ertd749e|Zwint-1	ZW10 interactor	protein-coding
mm_136334.1	chr16	92466082	92466187	-	1	NA	promoter-TSS (NM_001081549)	promoter-TSS (NM_001081549)	35	NM_001081549	54720	Mm.265744	NM_019466	ENSMUSG00000022951	Rcan1	Adapt78|CALP1L|CSP1|DSC1|Dscr1|MCIP1|RCN1	regulator of calcineurin 1	protein-coding
mm_38827.1	chr4	149126666	149126681	-	1	NA	promoter-TSS (NM_007745)	promoter-TSS (NM_007745)	90	NM_007745	12854	Mm.6204	NM_007745	ENSMUSG00000028971	Cort	CST|PCST	cortistatin	protein-coding
mm_625.1	chr1	40225101	40225146	+	1	NA	promoter-TSS (NM_008362)	promoter-TSS (NM_008362)	43	NM_008362	16177	Mm.896	NM_008362	ENSMUSG00000026072	Il1r1	CD121a|CD121b|IL-1R1|IL-iR|Il1r-1	interleukin 1 receptor, type I	protein-coding
mm_23702.1	chr3	68761471	68761480	+	1	NA	Intergenic	Intergenic	70051	NM_008351	16159	Mm.103783	NM_008351	ENSMUSG00000027776	Il12a	IL-12p35|Il-12a|Ll12a|p35	interleukin 12a	protein-coding
mm_113007.1	chr13	21878202	21878204	+	1	NA	Intergenic	Intergenic	18846	NR_035500	100316716		NR_035500	ENSMUSG00000088148	Mir1983	mmu-mir-1983	microRNA 1983	ncRNA
mm_106656.1	chr11	121204627	121204717	-	1	NA	promoter-TSS (NM_025402)	promoter-TSS (NM_025402)	-24	NM_025402	66179	Mm.390403	NM_025402	ENSMUSG00000025169	Ogfod3	1110031I02Rik	2-oxoglutarate and iron-dependent oxygenase domain containing 3	protein-coding
mm_55816.1	chr6	83033423	83033476	-	1	NA	promoter-TSS (NM_013586)	promoter-TSS (NM_013586)	22	NM_010070	13448	Mm.156	NM_010070	ENSMUSG00000068335	Dok1	AW557123|p62DOK	docking protein 1	protein-coding
mm_164058.1	chr14	106274762	106274769	+	1	NA	Intergenic	Intergenic	168567	NR_073203	212085	Mm.78128	NM_198601	ENSMUSG00000022113	Trim52	4921513B05Rik	tripartite motif-containing 52	protein-coding
mm_119358.1	chr14	41115149	41115157	+	1	NA	intron (NM_133653, intron 6 of 9)	(CA)n|Simple_repeat|Simple_repeat	10120	NM_133653	11720	Mm.14064	NM_133653	ENSMUSG00000037798	Mat1a	AI046368|AdoMet|Ams|MAT|MATA1|SAMS|SAMS1	methionine adenosyltransferase I, alpha	protein-coding
mm_173285.1	chrY	17151604	17151606	+	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	57726	NM_001199332	100041550	Mm.485768	NM_001199332	ENSMUSG00000095520	Gm20877	-	predicted gene, 20877	protein-coding
mm_11944.1	chr2	52882006	52882009	+	1	NA	intron (NM_172409, intron 1 of 26)	AT_rich|Low_complexity|Low_complexity	24139	NM_172409	71409	Mm.394427	NM_172409	ENSMUSG00000036053	Fmnl2	5430425K04Rik|Man	formin-like 2	protein-coding
mm_169351.1	chr14	20982671	20982673	+	1	NA	exon (NM_009502, exon 3 of 21)	exon (NM_009502, exon 3 of 21)	53239	NM_009502	22330	Mm.279361	NM_009502	ENSMUSG00000021823	Vcl	9430097D22|AA571387|AI462105|AW545629	vinculin	protein-coding
mm_83203.1	chr9	41580787	41580808	-	1	NA	promoter-TSS (NR_015483)	promoter-TSS (NR_015483)	-456	NR_015483	73144	Mm.38166	NM_001033153	ENSMUSG00000074415	3110039I08Rik	2610203C20Rik|AI848448|D230004N17Rik|D3Mgi9|Mir100hg	RIKEN cDNA 3110039I08 gene	ncRNA
mm_162841.1	chr10	85102843	85102847	+	1	NA	promoter-TSS (NM_010214)	promoter-TSS (NM_010214)	218	NM_001013028	103266	Mm.335025	NM_001013028	ENSMUSG00000060935	Tmem263	AI597468	transmembrane protein 263	protein-coding
mm_69605.1	chr7	137125753	137125777	-	1	NA	intron (NM_008598, intron 4 of 4)	intron (NM_008598, intron 4 of 4)	-108918	NR_045885	100038555	Mm.444788	NR_045885	ENSMUSG00000109722	Gm10578	ENSMUSG00000073800	predicted gene 10578	ncRNA
mm_28563.1	chr3	93444751	93444784	-	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	2437	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_110796.1	chr12	72178741	72178752	-	1	NA	intron (NM_028687, intron 2 of 20)	intron (NM_028687, intron 2 of 20)	6283	NM_028687	73936	Mm.475741	NM_028687	ENSMUSG00000021086	Ccdc175	4930403N07Rik	coiled-coil domain containing 175	protein-coding
mm_147688.1	chr18	60733115	60733157	-	1	NA	Intergenic	Intergenic	-19747	NM_008306	15531	Mm.181862	NM_008306	ENSMUSG00000054008	Ndst1	1200015G06Rik|HSNST|HSNST 1|Hsst|N-HSST|N-HSST 1|NDST-1|b2b2230Clo	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 1	protein-coding
mm_44524.1	chr5	24392491	24392494	-	1	NA	promoter-TSS (NM_001002897)	promoter-TSS (NM_001002897)	-349	NM_001002897	213948	Mm.332252	NM_001002897	ENSMUSG00000038295	Atg9b	Apg912|Apg9l2|Apgdc2|Gm574|Nos3as|eONE|sONE	autophagy related 9B	protein-coding
mm_169287.1	chr13	9806188	9806200	-	1	NA	Intergenic	RLTR9E|LTR|ERVK	-40873	NM_144516	66505	Mm.397307	NM_144516	ENSMUSG00000021156	Zmynd11	2210402G22Rik|BS69	zinc finger, MYND domain containing 11	protein-coding
mm_114359.1	chr13	61004027	61004042	+	1	NA	exon (NM_012007, exon 3 of 8)	exon (NM_012007, exon 3 of 8)	1877	NM_012007	26898	Mm.31948	NM_012007	ENSMUSG00000055298	Ctsj	CATP|CatRLP|Ctsp	cathepsin J	protein-coding
mm_92922.1	chr10	84440611	84440619	-	1	NA	promoter-TSS (NM_001004363)	promoter-TSS (NM_001004363)	-144	NM_001004363	77976	Mm.25874	NM_001004363	ENSMUSG00000020032	Nuak1	AU014801|AW494241|B230104P22Rik|Omphk1	NUAK family, SNF1-like kinase, 1	protein-coding
mm_16118.1	chr2	169915117	169915130	+	1	NA	Intergenic	ORR1A3|LTR|ERVL-MaLR	48064	NR_131974	446211	Mm.266854	NR_131974	ENSMUSG00000103935	AY702102	STDP1	cDNA sequence AY702102	ncRNA
mm_140319.1	chr17	86424182	86424211	+	1	NA	intron (NM_011104, intron 2 of 14)	intron (NM_011104, intron 2 of 14)	-137018	NR_045435	72104	Mm.443401	NR_045435	ENSMUSG00000100738	2010106C02Rik	-	RIKEN cDNA 2010106C02 gene	ncRNA
mm_117538.1	chr13	83599745	83599748	-	1	NA	intron (NM_001347569, intron 3 of 10)	intron (NM_001347569, intron 3 of 10)	26139	NM_001347569	17260	Mm.24001	NM_025282	ENSMUSG00000005583	Mef2c	5430401D19Rik|9930028G15Rik|AV011172|Mef2	myocyte enhancer factor 2C	protein-coding
mm_132943.1	chr16	49867854	49867868	+	1	NA	exon (NM_010581, exon 2 of 10)	exon (NM_010581, exon 2 of 10)	12207	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_83481.1	chr9	45906899	45906921	-	1	NA	promoter-TSS (NM_178709)	promoter-TSS (NM_178709)	1	NM_001310840	235315	Mm.3255	NM_178709	ENSMUSG00000042790	Rnf214	D130054N24Rik	ring finger protein 214	protein-coding
mm_123662.1	chr14	69244331	69244351	-	1	NA	3' UTR (NM_026331, exon 4 of 4)	3' UTR (NM_026331, exon 4 of 4)	40762	NM_026331	67712	Mm.293635	NM_026331	ENSMUSG00000034248	Slc25a37	1700020E22Rik|4930513O14Rik|4930526G11Rik|AI848481|C330015G08Rik|Mfrn|Mfrn1|Mscp|frascati|mitoferrin	solute carrier family 25, member 37	protein-coding
mm_102043.1	chr11	51997848	51997878	-	1	NA	exon (NM_009458, exon 2 of 6)	exon (NM_009458, exon 2 of 6)	2603	NM_009458	22210	Mm.384918	NM_009458	ENSMUSG00000020390	Ube2b	2610301N02Rik|E2-14k|HR6B|Rad6b|mHR6B	ubiquitin-conjugating enzyme E2B	protein-coding
mm_108393.1	chr12	80948678	80948711	+	1	NA	intron (NM_009159, intron 5 of 7)	intron (NM_009159, intron 5 of 7)	3195	NM_001347415	20384	Mm.43331	NM_009159	ENSMUSG00000021134	Srsf5	Sfrs5	serine/arginine-rich splicing factor 5	protein-coding
mm_104927.1	chr11	99993993	99993997	-	1	NA	promoter-TSS (NM_001099774)	promoter-TSS (NM_001099774)	-1	NM_001099774	77914	Mm.293692	NM_001099774	ENSMUSG00000078252	Krtap17-1	A030006P16Rik	keratin associated protein 17-1	protein-coding
mm_159078.1	chr2	26294743	26294743	-	1	NA	promoter-TSS (NM_177841)	promoter-TSS (NM_177841)	-186	NM_177841	329366	Mm.77712	NM_177841	ENSMUSG00000048038	Ccdc187	4932418E24Rik	coiled-coil domain containing 187	protein-coding
mm_67941.1	chr7	100176599	100176615	-	1	NA	promoter-TSS (NM_001190869)	promoter-TSS (NM_001190869)	-63	NM_001190869	57442	Mm.282386	NM_020574	ENSMUSG00000035165	Kcne3	2210017H05Rik|MiRP2	potassium voltage-gated channel, Isk-related subfamily, gene 3	protein-coding
mm_129980.1	chr15	86021468	86021480	-	1	NA	intron (NM_009886, intron 1 of 34)	intron (NM_009886, intron 1 of 34)	12303	NM_009886	12614	Mm.22680	NM_009886	ENSMUSG00000016028	Celsr1	Adgrc1|Crsh|Scy|crash	cadherin, EGF LAG seven-pass G-type receptor 1	protein-coding
mm_120164.1	chr14	60750208	60750222	+	1	NA	intron (NM_001310594, intron 5 of 9)	intron (NM_001310594, intron 5 of 9)	17311	NM_001310594	219140	Mm.149776	NM_001033272	ENSMUSG00000021990	Spata13	C79050|ESTM11|X83327|mFLJ00298	spermatogenesis associated 13	protein-coding
mm_122357.1	chr14	39146829	39146831	-	1	NA	intron (NM_001190187, intron 1 of 9)	intron (NM_001190187, intron 1 of 9)	248528	NR_045713	75170	Mm.372967	NR_045713	ENSMUSG00000093528	Nrg3os	4930529F24Rik	neuregulin 3, opposite strand	ncRNA
mm_5628.1	chr1	40397508	40397518	-	1	NA	Intergenic	Intergenic	-32057	NM_001294171	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_59181.1	chr7	24461563	24461569	+	1	NA	promoter-TSS (NM_011113)	promoter-TSS (NM_011113)	-917	NM_011113	18793	Mm.1359	NM_011113	ENSMUSG00000046223	Plaur	Cd87|u-PAR|uPAR	plasminogen activator, urokinase receptor	protein-coding
mm_42952.1	chr5	123015313	123015335	+	1	NA	exon (NM_175423, exon 1 of 2)	exon (NM_175423, exon 1 of 2)	250	NM_175423	109305	Mm.218582	NM_175423	ENSMUSG00000049686	Orai1	D730049H07Rik|Tmem142a|orai-1	ORAI calcium release-activated calcium modulator 1	protein-coding
mm_94753.1	chr11	21116903	21116914	+	1	NA	intron (NM_023324, intron 1 of 6)	intron (NM_023324, intron 1 of 6)	25584	NM_023324	67245	Mm.28957	NM_023324	ENSMUSG00000020134	Peli1	2810468L03Rik|A930031K15Rik|AA409794|AI586297|D11Ertd676e	pellino 1	protein-coding
mm_43388.1	chr5	135733503	135733543	+	1	NA	exon (NM_008898, exon 11 of 16)	exon (NM_008898, exon 11 of 16)	2366	NR_106001	102466791		NR_106001	ENSMUSG00000099197	Mir7034	Gm27372|mmu-mir-7034	microRNA 7034	ncRNA
mm_161790.1	chr17	46484202	46484202	-	1	NA	exon (NM_001162864, exon 2 of 15)	exon (NM_001162864, exon 2 of 15)	3473	NM_001162864	106763	Mm.297613	NM_175351	ENSMUSG00000015599	Ttbk1	AU017937|AW048023|C330008L01Rik	tau tubulin kinase 1	protein-coding
mm_132750.1	chr16	44160102	44160114	+	1	NA	3' UTR (NM_028108, exon 5 of 5)	3' UTR (NM_028108, exon 5 of 5)	-13289	NM_001029889	207806	Mm.310566	NM_001029889	ENSMUSG00000068284	Usf3	5530400K22Rik|Gm1779|Gm608|mKIAA2018	upstream transcription factor family member 3	protein-coding
mm_64324.1	chr7	141949983	141949995	+	1	NA	5' UTR (NM_029426, exon 1 of 19)	5' UTR (NM_029426, exon 1 of 19)	238	NM_001009929	75770	Mm.274868	NM_029426	ENSMUSG00000053046	Brsk2	4833424K13Rik|SAD-A|SADA	BR serine/threonine kinase 2	protein-coding
mm_131637.1	chr16	20424440	20424447	+	1	NA	intron (NM_176839, intron 1 of 6)	intron (NM_176839, intron 1 of 6)	1951	NM_013790	27416	Mm.20845	NM_013790	ENSMUSG00000022822	Abcc5	2900011L11Rik|AI132311|Abcc5a|Abcc5b|Mrp5	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	protein-coding
mm_144666.1	chr18	34408507	34408511	+	1	NA	promoter-TSS (NM_016927)	promoter-TSS (NM_016927)	-914	NM_001163004	53871	Mm.445792	NM_016927	ENSMUSG00000014503	Pkd2l2	TRPP5	polycystic kidney disease 2-like 2	protein-coding
mm_17234.1	chr2	25580240	25580254	-	1	NA	promoter-TSS (NM_001005424)	promoter-TSS (NM_001005424)	-148	NM_001005424	381353	Mm.379511	NM_001005424	ENSMUSG00000029419	Gm996	-	predicted gene 996	protein-coding
mm_73783.1	chr8	117055429	117055471	+	1	NA	intron (NM_029686, intron 13 of 42)	intron (NM_029686, intron 13 of 42)	26999	NM_029686	76645	Mm.159753	NM_029686	ENSMUSG00000034416	Pkd1l2	1700126L06Rik	polycystic kidney disease 1 like 2	protein-coding
mm_138107.1	chr17	34119884	34119933	+	1	NA	promoter-TSS (NR_037970)	promoter-TSS (NR_037970)	-8	NR_037970	14312	Mm.3444	NM_010238	ENSMUSG00000024335	Brd2	AW228947|D17H6S113E|Frg-1|Fsrg-1|Fsrg1|Nat|Ring3|Rnf3|mKIAA4005	bromodomain containing 2	protein-coding
mm_74702.1	chr8	16670230	16670236	-	1	NA	intron (NM_053171, intron 5 of 69)	intron (NM_053171, intron 5 of 69)	-501395	NR_037214	100526464		NR_037214	ENSMUSG00000093142	Mir3106	mir-3106|mmu-mir-3106	microRNA 3106	ncRNA
mm_79038.1	chr9	46207938	46207946	+	1	NA	exon (NM_027498, exon 16 of 25)	exon (NM_027498, exon 16 of 25)	-20688	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2|apo-AI|apoA-I	apolipoprotein A-I	protein-coding
mm_165239.1	chr2	62343523	62343537	-	1	NA	intron (NM_001159543, intron 23 of 24)	IMPB_01|Satellite|Satellite	68701	NM_010074	13482	Mm.1151	NM_010074	ENSMUSG00000035000	Dpp4	Cd26|Dpp-4|THAM	dipeptidylpeptidase 4	protein-coding
mm_34781.1	chr4	154082216	154082260	+	1	NA	intron (NM_011642, intron 3 of 13)	intron (NM_011642, intron 3 of 13)	14935	NM_001126330	22062	Mm.78015	NM_011642	ENSMUSG00000029026	Trp73	TAp73|Tp73|deltaNp73|p73	transformation related protein 73	protein-coding
mm_6462.1	chr1	74030825	74030846	-	1	NA	intron (NM_027884, intron 3 of 34)	L2c|LINE|L2	93612	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_67753.1	chr7	92661666	92661715	-	1	NA	exon (NM_029078, exon 5 of 16)	exon (NM_029078, exon 5 of 16)	8222	NM_029078	74737	Mm.288645	NM_029078	ENSMUSG00000041328	Pcf11	2500001H09Rik|5730417B17Rik|C77803	PCF11 cleavage and polyadenylation factor subunit	protein-coding
mm_155177.1	chrX	53688076	53688110	+	1	NA	intron (NR_102724, intron 1 of 4)	intron (NR_102724, intron 1 of 4)	1566	NR_102724	100504039		NR_102724		LOC100504039	-	uncharacterized LOC100504039	ncRNA
mm_64833.1	chr7	12926677	12926688	-	1	NA	promoter-TSS (NM_029809)	promoter-TSS (NM_029809)	-734	NM_029809	381845	Mm.439896	NM_029809	ENSMUSG00000033967	Rnf225	2310014L17Rik|AV237412|C77118	ring finger protein 225	protein-coding
mm_19919.1	chr2	115894551	115894554	-	1	NA	intron (NM_001346047, intron 10 of 13)	ID_B1|SINE|B4	170067	NM_001346044	17536	Mm.247566	NM_010825	ENSMUSG00000027210	Meis2	A430109D20Rik|Mrg1|Stra10	Meis homeobox 2	protein-coding
mm_93759.1	chr10	120193369	120193379	-	1	NA	intron (NM_028679, intron 1 of 11)	intron (NM_028679, intron 1 of 11)	8163	NM_028679	73914	Mm.146194	NM_028679	ENSMUSG00000020227	Irak3	4833428C18Rik|AI563835|IRAK-M	interleukin-1 receptor-associated kinase 3	protein-coding
mm_110020.1	chr12	16753195	16753208	-	1	NA	intron (NM_001252071, intron 1 of 32)	intron (NM_001252071, intron 1 of 32)	4038	NM_001252071	268527	Mm.428062	NM_015764	ENSMUSG00000036523	Greb1	5730583K22Rik|9130004E13|AF180470|AU023194|mKIAA0575	gene regulated by estrogen in breast cancer protein	protein-coding
mm_105929.1	chr11	115123644	115123689	-	1	NA	intron (NM_001347648, intron 2 of 5)	B3|SINE|B2	10326	NM_001347648	246746	Mm.277387	NM_145634	ENSMUSG00000047798	Cd300lf	CLIM1|CLM-1|CLM1|Digr2|F730004D16Rik|IREM1|IgSF13|LMIR3|Pigr3	CD300 molecule like family member F	protein-coding
mm_99403.1	chr11	102216762	102216804	+	1	NA	intron (NM_001284249, intron 3 of 27)	intron (NM_001284249, intron 3 of 27)	13367	NR_106179	102465892		NR_106179	ENSMUSG00000098863	Mir8101	Gm27705|mmu-mir-8101	microRNA 8101	ncRNA
mm_58302.1	chr6	146113163	146113209	-	1	NA	intron (NM_010586, intron 54 of 55)	intron (NM_010586, intron 54 of 55)	179039	NM_010656	16651	Mm.49689	NM_010656	ENSMUSG00000030255	Sspn	Krag	sarcospan	protein-coding
mm_52023.1	chr6	94698910	94698915	+	1	NA	intron (NM_008377, intron 1 of 18)	intron (NM_008377, intron 1 of 18)	1233	NM_008377	16206	Mm.245210	NM_008377	ENSMUSG00000030029	Lrig1	D6Bwg0781e|Img|LIG-1	leucine-rich repeats and immunoglobulin-like domains 1	protein-coding
mm_137202.1	chr17	23917456	23917460	+	1	NA	promoter-TSS (NM_001077633)	promoter-TSS (NM_001077633)	0	NM_001077633	620253	Mm.390964	NM_001077633	ENSMUSG00000057417	Dcpp3	Dcpp-3|EG620253|SPT-3	demilune cell and parotid protein 3	protein-coding
mm_133970.1	chr16	4320711	4320711	-	1	NA	intron (NM_001291910, intron 4 of 11)	intron (NM_001291910, intron 4 of 11)	91482	NR_003628	436332	Mm.478141	NM_001013830	ENSMUSG00000089645	Gm5766	EG436332	ribosomal protein L7a pseudogene	pseudo
mm_32804.1	chr4	117120721	117120739	+	1	NA	non-coding (NR_024078, exon 7 of 7)	non-coding (NR_024078, exon 7 of 7)	4995	NR_024078	78611	Mm.446227	NM_001033187		Btbd19	9530048O09Rik|BB115071	BTB (POZ) domain containing 19	ncRNA
mm_19389.1	chr2	91328860	91328885	-	1	NA	intron (NM_001311144, intron 3 of 8)	intron (NM_001311144, intron 3 of 8)	63757	NM_023854	77038	Mm.43636	NM_023854	ENSMUSG00000027255	Arfgap2	2310032E02Rik|Zfp289	ADP-ribosylation factor GTPase activating protein 2	protein-coding
mm_143466.1	chr17	71002398	71002404	-	1	NA	5' UTR (NM_026064, exon 1 of 4)	5' UTR (NM_026064, exon 1 of 4)	132	NM_026064	67268	Mm.489605	NM_026064	ENSMUSG00000024048	Myl12a	2900073G15Rik|AI838292|C80200	myosin, light chain 12A, regulatory, non-sarcomeric	protein-coding
mm_158106.1	chrX	102071189	102071204	-	1	NA	5' UTR (NM_001278534, exon 1 of 2)	5' UTR (NM_001278534, exon 1 of 2)	111	NM_001278534	331474	Mm.23297	NM_183318	ENSMUSG00000049191	Rgag4	6430402L03Rik|Mar5|Mart5|mKIAA2001	retrotransposon gag domain containing 4	protein-coding
mm_11618.1	chr2	34608514	34608518	+	1	NA	intron (NM_001290626, intron 9 of 10)	MLT1F2|LTR|ERVL-MaLR	146716	NM_025709	66691	Mm.156452	NM_025709	ENSMUSG00000026867	Gapvd1	2010005B09Rik|4432404J10Rik|AW108497|Gapex-5|RAP6|RME-6|mKIAA1521	GTPase activating protein and VPS9 domains 1	protein-coding
mm_81094.1	chr9	106372084	106372105	+	1	NA	intron (NM_153459, intron 2 of 2)	intron (NM_153459, intron 2 of 2)	3462	NM_153459	235584	Mm.275584	NM_153459	ENSMUSG00000053716	Dusp7	AU015694|Mkpx|Pyst2	dual specificity phosphatase 7	protein-coding
mm_47060.1	chr5	116392744	116392750	-	1	NA	Intergenic	Intergenic	30117	NM_030704	80888	Mm.21549	NM_030704	ENSMUSG00000041548	Hspb8	AU018630|AW413033|Cryac|D5Ucla4|E2IG1|H11|H11K|HSP20-like|HSP22	heat shock protein 8	protein-coding
mm_41024.1	chr5	81583210	81583227	+	1	NA	intron (NM_001347371, intron 8 of 23)	intron (NM_001347371, intron 8 of 23)	541495	NR_138557	67327	Mm.87058	NR_138557		1700031L13Rik	-	RIKEN cDNA 1700031L13 gene	ncRNA
mm_72622.1	chr8	84638751	84638776	+	1	NA	exon (NM_001252060, exon 46 of 48)	exon (NM_001252060, exon 46 of 48)	24089	NM_010499	15936	Mm.399	NM_010499	ENSMUSG00000053560	Ier2	AI317238|Ch1|Pip92	immediate early response 2	protein-coding
mm_131998.1	chr16	25286849	25286874	+	1	NA	promoter-TSS (NM_175165)	promoter-TSS (NM_175165)	44	NM_175165	71338	Mm.126851	NM_175165	ENSMUSG00000048399	Tprg	5430420C16Rik|Tprg1	transformation related protein 63 regulated	protein-coding
mm_112686.1	chr13	16030809	16030825	+	1	NA	3' UTR (NM_008380, exon 5 of 5)	3' UTR (NM_008380, exon 5 of 5)	18966	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_125023.1	chr15	25724812	25724822	+	1	NA	intron (NM_019472, intron 6 of 40)	intron (NM_019472, intron 6 of 40)	102267	NM_019472	17909	Mm.60590	NM_019472	ENSMUSG00000022272	Myo10	AW048724|D15Ertd600e|mKIAA0799|myosin-X	myosin X	protein-coding
mm_8430.1	chr1	152559744	152559748	-	1	NA	intron (NM_001346119, intron 4 of 17)	Lx8|LINE|L1	65471	NM_016846	19731	Mm.245270	NM_016846	ENSMUSG00000026482	Rgl1	Rgl|mKIAA0959	ral guanine nucleotide dissociation stimulator,-like 1	protein-coding
mm_49184.1	chr6	15185216	15185244	+	1	NA	promoter-TSS (NM_001286607)	promoter-TSS (NM_001286607)	-276	NM_212435	114142	Mm.332919	NM_053242	ENSMUSG00000029563	Foxp2	2810043D05Rik|AI449000|CAG-16|D0Kist7	forkhead box P2	protein-coding
mm_153610.1	chr19	43968544	43968563	-	1	NA	exon (NM_030703, exon 5 of 9)	exon (NM_030703, exon 5 of 9)	17967	NM_030703	93721	Mm.206774	NM_030703	ENSMUSG00000025196	Cpn1	0610011F20Rik|CPN	carboxypeptidase N, polypeptide 1	protein-coding
mm_139457.1	chr17	55952780	55952782	+	1	NA	5' UTR (NM_015766, exon 1 of 5)	5' UTR (NM_015766, exon 1 of 5)	158	NM_015766	50498	Mm.256798	NM_015766	ENSMUSG00000003206	Ebi3	EBI-3|IL-27	Epstein-Barr virus induced gene 3	protein-coding
mm_5303.1	chr1	21961479	21961509	-	1	NA	exon (NM_023872, exon 1 of 14)	exon (NM_023872, exon 1 of 14)	448	NM_001160139	226922	Mm.336519	NM_023872	ENSMUSG00000028033	Kcnq5	7730402H11|9230107O05Rik|AA589396|D1Mgi1	potassium voltage-gated channel, subfamily Q, member 5	protein-coding
mm_65951.1	chr7	30421609	30421636	-	1	NA	Intergenic	Intergenic	-1682	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_153166.1	chr19	34493356	34493358	-	1	NA	3' UTR (NM_021460, exon 10 of 10)	3' UTR (NM_021460, exon 10 of 10)	-18222	NM_009890	12642	Mm.30824	NM_009890	ENSMUSG00000050370	Ch25h	AI462618|m25OH	cholesterol 25-hydroxylase	protein-coding
mm_107515.1	chr12	40248171	40248196	+	1	NA	Intergenic	Intergenic	24819	NR_045157	629820	Mm.435540	NR_045157	ENSMUSG00000035983	Gm7008	EG629820	predicted gene 7008	ncRNA
mm_90956.1	chr10	13209935	13209937	-	1	NA	3' UTR (NM_001195065, exon 13 of 13)	3' UTR (NM_001195065, exon 13 of 13)	-16799	NM_181470	353258	Mm.117581	NM_181470	ENSMUSG00000019814	Ltv1	2610020N02Rik	LTV1 ribosome biogenesis factor	protein-coding
mm_71465.1	chr8	46534610	46534622	+	1	NA	3' UTR (NM_007981, exon 21 of 21)	3' UTR (NM_007981, exon 21 of 21)	-17453	NM_027973	71876	Mm.22108	NM_027973	ENSMUSG00000031629	Cenpu	1700029A22Rik|Mlf1ip	centromere protein U	protein-coding
mm_133745.1	chr16	94084918	94084934	+	1	NA	promoter-TSS (NM_011377)	promoter-TSS (NM_011377)	-334	NM_011377	20465	Mm.4775	NM_011377	ENSMUSG00000062713	Sim2	bHLHe15	single-minded homolog 2 (Drosophila)	protein-coding
mm_129222.1	chr15	76583970	76583978	-	1	NA	intron (NR_073123, intron 1 of 14)	intron (NR_073123, intron 1 of 14)	7615	NR_073123	268822	Mm.181624	NM_172960	ENSMUSG00000022550	Adck5	A230108P17	aarF domain containing kinase 5	protein-coding
mm_32242.1	chr4	102467055	102467055	+	1	NA	intron (NM_019840, intron 1 of 14)	Lx9|LINE|L1	-103005	NM_001177980	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_66724.1	chr7	46116079	46116089	-	1	NA	intron (NM_011510, intron 26 of 38)	intron (NM_011510, intron 26 of 38)	-15320	NM_001204411	16514	Mm.333863	NM_010602	ENSMUSG00000096146	Kcnj11	Kir6.2|mBIR	potassium inwardly rectifying channel, subfamily J, member 11	protein-coding
mm_77106.1	chr8	111081138	111081148	-	1	NA	intron (NM_181549, intron 1 of 11)	intron (NM_181549, intron 1 of 11)	565	NM_181549	353287	Mm.135495	NM_181549	ENSMUSG00000033633	Clec18a	Mrcl	C-type lectin domain family 18, member A	protein-coding
mm_43930.1	chr5	145084059	145084069	+	1	NA	intron (NM_019767, intron 1 of 9)	CpG	195	NM_019767	56443	Mm.371610	NM_019767	ENSMUSG00000029621	Arpc1a	0610010H08Rik|1110030K07Rik|41kDa|AA407347|Sid32|Sid329	actin related protein 2/3 complex, subunit 1A	protein-coding
mm_65644.1	chr7	28014124	28014183	-	1	NA	promoter-TSS (NM_001254951)	promoter-TSS (NM_001254951)	-38	NM_001254951	100043772	Mm.129275	NM_001100456	ENSMUSG00000096916	Zfp850	C130069I09Rik|Gm4636	zinc finger protein 850	protein-coding
mm_53452.1	chr6	134641020	134641097	+	1	NA	5' UTR (NM_026371, exon 1 of 4)	5' UTR (NM_026371, exon 1 of 4)	118	NM_026371	67774	Mm.41892	NM_026371	ENSMUSG00000042992	Borcs5	5830457J20Rik|AW124643|Loh12cr1	BLOC-1 related complex subunit 5	protein-coding
mm_103186.1	chr11	70615546	70615559	-	1	NA	promoter-TSS (NM_001145537)	promoter-TSS (NM_001145537)	-342	NM_001145537	668433	Mm.425687	NM_001145537	ENSMUSG00000087279	4930544D05Rik	-	RIKEN cDNA 4930544D05 gene	protein-coding
mm_102308.1	chr11	55608564	55608596	-	1	NA	promoter-TSS (NM_020492)	promoter-TSS (NM_020492)	-382	NM_020492	14654	Mm.89320	NM_020492	ENSMUSG00000000263	Glra1	nmf11|oscillator|ot|spasmodic|spd	glycine receptor, alpha 1 subunit	protein-coding
mm_86274.1	chr9	121792332	121792389	-	1	NA	5' UTR (NM_029095, exon 1 of 12)	5' UTR (NM_029095, exon 1 of 12)	147	NM_029095	74770	Mm.44195	NM_029095	ENSMUSG00000032523	Hhatl	1110011D13Rik|Gup1|Mg56	hedgehog acyltransferase-like	protein-coding
mm_43634.1	chr5	138229740	138229749	+	1	NA	5' UTR (NM_001013773, exon 2 of 6)	5' UTR (NM_001013773, exon 2 of 6)	3840	NM_001013773	381680	Mm.156846	NM_001013773	ENSMUSG00000047592	Nxpe5	-	neurexophilin and PC-esterase domain family, member 5	protein-coding
mm_138968.1	chr17	44777201	44777276	+	1	NA	promoter-TSS (NM_178652)	promoter-TSS (NM_178652)	67	NM_178652	109115	Mm.431327	NM_178652	ENSMUSG00000038954	Supt3	2310066G22Rik|AI315192|SPT3|SPT3L|Supt3h	suppressor of Ty 3	protein-coding
mm_81480.1	chr9	109945973	109945995	+	1	NA	intron (NM_001205330, intron 1 of 18)	ID_B1|SINE|B4	14210	NM_008633	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_62988.1	chr7	120328694	120328700	+	1	NA	promoter-TSS (NM_177213)	promoter-TSS (NM_177213)	13	NM_177213	320631	Mm.78330	NM_177213	ENSMUSG00000054746	Abca15	4930500I12Rik	ATP-binding cassette, sub-family A (ABC1), member 15	protein-coding
mm_37434.1	chr4	122939532	122939536	-	1	NA	Intergenic	Intergenic	21654	NM_029662	76574	Mm.331842	NM_029662	ENSMUSG00000028655	Mfsd2a	1700018O18Rik|Mfsd2|NLS1	major facilitator superfamily domain containing 2A	protein-coding
mm_146418.1	chr18	84712533	84712543	+	1	NA	Intergenic	Intergenic	-7704	NM_173770	240479	Mm.472378	NM_173770	ENSMUSG00000047992	Fam69c	B230399E16Rik	family with sequence similarity 69, member C	protein-coding
mm_38739.1	chr4	145246218	145246228	-	1	NA	intron (NM_011610, intron 1 of 9)	intron (NM_011610, intron 1 of 9)	647	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_83748.1	chr9	51165398	51165415	-	1	NA	Intergenic	Intergenic	-48284	NM_011136	18985	Mm.897	NM_011136	ENSMUSG00000032053	Pou2af1	BOB.1|Bob-1|Bob1|OBF-1|OBF.1|OCA-B|OCAB	POU domain, class 2, associating factor 1	protein-coding
mm_111330.1	chr12	86726148	86726154	-	1	NA	promoter-TSS (NR_136890)	promoter-TSS (NR_136890)	-156	NR_136890	102635405		NR_136890		Gm32755	-	predicted gene, 32755	ncRNA
mm_167107.1	chr7	112802924	112802925	+	1	NA	intron (NM_009346, intron 2 of 12)	intron (NM_009346, intron 2 of 12)	43540	NM_001166585	21676	Mm.24685	NM_009346	ENSMUSG00000055320	Tead1	2610024B07Rik|B230114H05Rik|Gtrgeo5|TEAD-1|TEF-1|Tcf13|mTEF-1	TEA domain family member 1	protein-coding
mm_111319.1	chr12	86078801	86078804	-	1	NA	5' UTR (NM_009368, exon 1 of 7)	5' UTR (NM_009368, exon 1 of 7)	239	NM_009368	21809	Mm.3992	NM_009368	ENSMUSG00000021253	Tgfb3	TGF-beta-3|Tgfb-3	transforming growth factor, beta 3	protein-coding
mm_99782.1	chr11	107337969	107337978	+	1	NA	intron (NM_145823, intron 1 of 9)	intron (NM_145823, intron 1 of 9)	132747	NM_145823	71795	Mm.397413	NM_145823	ENSMUSG00000040430	Pitpnc1	1110020B03Rik|5830436L09Rik|AI662802|AI851387|C330017I21Rik|Dnr411|RDGBB|RDGBB1|rdgB-beta	phosphatidylinositol transfer protein, cytoplasmic 1	protein-coding
mm_42925.1	chr5	122724602	122724621	+	1	NA	exon (NM_011026, exon 6 of 12)	exon (NM_011026, exon 6 of 12)	17067	NM_001310718	18438	Mm.290884	NM_011026	ENSMUSG00000029470	P2rx4	AI504491|AW555605|D5Ertd444e|P2X4	purinergic receptor P2X, ligand-gated ion channel 4	protein-coding
mm_4416.1	chr1	172499949	172499979	+	1	NA	promoter-TSS (NM_178598)	promoter-TSS (NM_178598)	-282	NM_178598	21346	Mm.271711	NM_178598	ENSMUSG00000026547	Tagln2	2700094C18Rik|SM22beta|Sm22B|Sm22a	transgelin 2	protein-coding
mm_169454.1	chr14	61325372	61325390	-	1	NA	Intergenic	Intergenic	15628	NM_177337	219144	Mm.206566	NM_177337	ENSMUSG00000043157	Arl11	ARLTS1|C730007L20Rik	ADP-ribosylation factor-like 11	protein-coding
mm_87946.1	chr10	62980234	62980261	+	1	NA	promoter-TSS (NM_027425)	promoter-TSS (NM_027425)	24	NM_027425	70432	Mm.234587	NM_027425	ENSMUSG00000020070	Rufy2	2610111M19Rik|AI844453|Denn|LZ-FYVE|ZFYVE13	RUN and FYVE domain-containing 2	protein-coding
mm_143069.1	chr17	57022089	57022150	-	1	NA	3' UTR (NM_010613, exon 18 of 18)	3' UTR (NM_010613, exon 18 of 18)	9388	NM_010613	16549	Mm.34296	NM_010613	ENSMUSG00000007670	Khsrp	6330409F21Rik|Fbp2|Fubp2|Ksrp	KH-type splicing regulatory protein	protein-coding
mm_82940.1	chr9	35305355	35305365	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	24255	NR_040715	71133	Mm.158577	NR_040715	ENSMUSG00000111746	4933422A05Rik	-	RIKEN cDNA 4933422A05 gene	ncRNA
mm_67692.1	chr7	89517577	89517587	-	1	NA	promoter-TSS (NM_029614)	promoter-TSS (NM_029614)	4	NM_029614	76453	Mm.250438	NM_029614	ENSMUSG00000039405	Prss23	2310046G15Rik|4930479H08Rik|AI790574|Spuve	protease, serine 23	protein-coding
mm_98240.1	chr11	88160580	88160587	+	1	NA	intron (NM_198013, intron 1 of 10)	intron (NM_198013, intron 1 of 10)	-8982	NM_001172099	103841	Mm.374846	NM_198013	ENSMUSG00000018378	Cuedc1	AI841487|C330016O16Rik	CUE domain containing 1	protein-coding
mm_44190.1	chr5	3461110	3461113	-	1	NA	intron (NM_009873, intron 4 of 7)	intron (NM_009873, intron 4 of 7)	-82722	NM_001042501	68152	Mm.240265	NM_026583	ENSMUSG00000058503	Fam133b	2900022K02Rik|5830415L20Rik	family with sequence similarity 133, member B	protein-coding
mm_88.1	chr1	7089102	7089117	+	1	NA	5' UTR (NM_183028, exon 1 of 6)	5' UTR (NM_183028, exon 1 of 6)	189	NM_183028	319263	Mm.21539	NM_183028	ENSMUSG00000051285	Pcmtd1	8430411F12Rik|A030012M09Rik	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding
mm_14957.1	chr2	152080899	152080906	+	1	NA	promoter-TSS (NM_001160410)	promoter-TSS (NM_001160410)	-627	NM_001160410	545474	Mm.214317	NM_001160410	ENSMUSG00000060257	Scrt2	AW060659	scratch family zinc finger 2	protein-coding
mm_141199.1	chr17	27028535	27028606	-	1	NA	promoter-TSS (NM_027544)	promoter-TSS (NM_027544)	56	NM_007523	12018	Mm.2443	NM_007523	ENSMUSG00000057789	Bak1	Bak|N-BAK1|N-Bak	BCL2-antagonist/killer 1	protein-coding
mm_54827.1	chr6	42585759	42585773	-	1	NA	Intergenic	Intergenic	11606	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_155763.1	chrX	96168024	96168034	+	1	NA	3' UTR (NM_010833, exon 13 of 13)	3' UTR (NM_010833, exon 13 of 13)	-71897	NR_030718	100038363	Mm.30815	NR_030718	ENSMUSG00000078122	F630028O10Rik	ENSMUSG00000065522|Gm14924|OTTMUSG00000018496|mir-223	RIKEN cDNA F630028O10 gene	ncRNA
mm_146058.1	chr18	69679884	69679890	+	1	NA	intron (NM_013685, intron 17 of 19)	intron (NM_013685, intron 17 of 19)	-245672	NM_201362	381175	Mm.266831	NM_201362	ENSMUSG00000038903	Ccdc68	BC046343	coiled-coil domain containing 68	protein-coding
mm_60558.1	chr7	44481221	44481293	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-3260	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_2146.1	chr1	88103230	88103249	+	1	NA	promoter-TSS (NM_201410)	promoter-TSS (NM_201410)	-18	NM_201410	394435	Mm.300095	NM_201410	ENSMUSG00000090145	Ugt1a6b	A9'|Ugt1a9	UDP glucuronosyltransferase 1 family, polypeptide A6B	protein-coding
mm_64939.1	chr7	16311313	16311335	-	1	NA	intron (NM_133234, intron 1 of 3)	intron (NM_133234, intron 1 of 3)	1741	NM_133234	170770	Mm.7660	NM_133234	ENSMUSG00000002083	Bbc3	PUMA|PUMA/JFY1	BCL2 binding component 3	protein-coding
mm_157161.1	chrX	9465401	9465411	-	1	NA	intron (NM_007807, intron 3 of 12)	intron (NM_007807, intron 3 of 12)	3918	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_171907.1	chr5	47666566	47666584	+	1	NA	Intergenic	L1Md_A|LINE|L1	-316580	NR_111900	20563	Mm.289739	NM_178804	ENSMUSG00000031558	Slit2	Drad-1|E030015M03Rik|E130320P19Rik|Slil3|mKIAA4141|slit-2	slit homolog 2 (Drosophila)	protein-coding
mm_95256.1	chr11	44643147	44643154	+	1	NA	intron (NM_007897, intron 5 of 15)	intron (NM_007897, intron 5 of 15)	25050	NM_001290710	13591	Mm.439662	NM_007897	ENSMUSG00000057098	Ebf1	Ebf|O/E-1|OE-1|Olf-1|Olf1	early B cell factor 1	protein-coding
mm_29525.1	chr3	116634991	116635024	-	1	NA	intron (NM_008246, intron 9 of 11)	intron (NM_008246, intron 9 of 11)	-20420	NM_030016	229780	Mm.259648	NM_030016	ENSMUSG00000033439	Trmt13	4631408H19Rik|A330067P21|A930028L21Rik|Ccdc76	tRNA methyltransferase 13	protein-coding
mm_102745.1	chr11	67254767	67254783	-	1	NA	exon (NM_010855, exon 30 of 40)	exon (NM_010855, exon 30 of 40)	16963	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_159450.1	chr3	142391760	142391760	-	1	NA	promoter-TSS (NM_001190857)	promoter-TSS (NM_001190857)	90	NM_022554	56376	Mm.117709	NM_019808	ENSMUSG00000028273	Pdlim5	1110001A05Rik|AI987914|C87059|Enh|Enh1|Enh2|Enh3|LIM	PDZ and LIM domain 5	protein-coding
mm_81919.1	chr9	120116238	120116246	+	1	NA	intron (NM_144793, intron 1 of 6)	intron (NM_144793, intron 1 of 6)	5843	NM_144793	208638	Mm.236656	NM_144793	ENSMUSG00000032519	Slc25a38	AV019094|BC010801|appoptosin	solute carrier family 25, member 38	protein-coding
mm_103176.1	chr11	70459880	70459919	-	1	NA	promoter-TSS (NM_023158)	promoter-TSS (NM_023158)	85	NM_023158	66102	Mm.425692	NM_023158	ENSMUSG00000018920	Cxcl16	0910001K24Rik|AV290116|BB024863|CXCL16v1|CXCL16v2|SR-PSOX|Zmynd15|b2b498Clo	chemokine (C-X-C motif) ligand 16	protein-coding
mm_66601.1	chr7	45459400	45459425	-	1	NA	intron (NM_010240, intron 1 of 3)	intron (NM_010240, intron 1 of 3)	474	NM_010240	14325	Mm.30357	NM_010240	ENSMUSG00000050708	Ftl1	Ftl|Ftl-1|L-ferritin	ferritin light polypeptide 1	protein-coding
mm_35523.1	chr4	41211859	41211900	-	1	NA	exon (NM_026872, exon 12 of 29)	exon (NM_026872, exon 12 of 29)	63256	NM_026872	68926	Mm.41864	NM_026872	ENSMUSG00000028433	Ubap2	1190005K07Rik|AA408600|AU045235|UBAP-2|mKIAA1491	ubiquitin-associated protein 2	protein-coding
mm_133129.1	chr16	65819744	65819745	+	1	NA	intron (NM_028572, intron 1 of 3)	intron (NM_028572, intron 1 of 3)	4111	NM_028572	73569	Mm.25670	NM_028572	ENSMUSG00000091243	Vgll3	1700110N18Rik|4832416J22|C80713|Vgl-3|Vito-2	vestigial like family member 3	protein-coding
mm_163549.1	chr13	23533686	23533705	-	1	NA	promoter-TSS (NM_175661)	promoter-TSS (NM_175661)	-216	NM_175661	319173	Mm.377878	NM_175661	ENSMUSG00000061991	Hist1h2af	H2a-221	histone cluster 1, H2af	protein-coding
mm_1205.1	chr1	62726016	62726034	+	1	NA	intron (NM_001077405, intron 2 of 15)	intron (NM_001077405, intron 2 of 15)	22708	NM_001077405	18187	Mm.266341	NM_010939	ENSMUSG00000025969	Nrp2	1110048P06Rik|Np-2|Np2|Npn-2|Npn2	neuropilin 2	protein-coding
mm_45224.1	chr5	53385489	53385538	-	1	NA	Intergenic	Intergenic	118407	NM_001145433	66278	Mm.27900	NM_001145433	ENSMUSG00000061461	Smim20	1110067B18Rik|1810013D10Rik|N28078	small integral membrane protein 20	protein-coding
mm_65810.1	chr7	29008771	29008817	-	1	NA	intron (NM_009109, intron 100 of 105)	intron (NM_009109, intron 100 of 105)	25940	NM_008279	26411	Mm.148278	NM_008279	ENSMUSG00000037337	Map4k1	Hpk1|mHPK1	mitogen-activated protein kinase kinase kinase kinase 1	protein-coding
mm_170474.1	chr19	11121654	11121658	+	1	NA	intron (NM_027058, intron 1 of 6)	intron (NM_027058, intron 1 of 6)	9222	NM_027058	69369	Mm.391200	NM_027058	ENSMUSG00000024729	1700017D01Rik	-	RIKEN cDNA 1700017D01 gene	protein-coding
mm_88112.1	chr10	69171750	69171758	+	1	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	-36798	NM_001252636	69288	Mm.26659	NM_001081347	ENSMUSG00000019944	Rhobtb1	1700008H16Rik|3110048G13Rik|AI173445|AI573858|AV350930	Rho-related BTB domain containing 1	protein-coding
mm_66226.1	chr7	35049546	35049570	-	1	NA	3' UTR (NM_009884, exon 2 of 2)	3' UTR (NM_009884, exon 2 of 2)	7008	NM_009884	12611	Mm.273090	NM_009884	ENSMUSG00000056216	Cebpg	C/EBP[g]|C/EBPgamma|GPE1-BP|Gpe1bp|Ig/EBP	CCAAT/enhancer binding protein (C/EBP), gamma	protein-coding
mm_116034.1	chr13	26312386	26312403	-	1	NA	promoter-TSS (NR_045933)	promoter-TSS (NR_045933)	12	NR_045933	73576	Mm.45473	NR_045933		1700092E19Rik	-	RIKEN cDNA 1700092E19 gene	ncRNA
mm_100109.1	chr11	115780738	115780756	+	1	NA	intron (NM_028014, intron 2 of 31)	intron (NM_028014, intron 2 of 31)	-15077	NR_049194	100885833		NR_049194	ENSMUSG00000093539	Mir5621	Gm22564|mir-5621|mmu-mir-5621	microRNA 5621	ncRNA
mm_170527.1	chr19	33762797	33762815	+	1	NA	promoter-TSS (NM_001322338)	promoter-TSS (NM_001322338)	-855	NM_001322338	101055671		NM_001322338	ENSMUSG00000087303	Lipo2	EG668114|Gm8981	lipase, member O2	protein-coding
mm_12257.1	chr2	68926092	68926096	+	1	NA	intron (NM_172856, intron 1 of 9)	MER5A1|DNA|hAT-Charlie	64653	NM_001347161	241447	Mm.222222	NM_172856	ENSMUSG00000027035	Cers6	4732462C07Rik|AW544719|Lass6|T1L	ceramide synthase 6	protein-coding
mm_4554.1	chr1	177444634	177444645	+	1	NA	promoter-TSS (NM_001012330)	promoter-TSS (NM_001012330)	-22	NM_001012330	30928	Mm.330700	NM_013915	ENSMUSG00000063659	Zbtb18	RP58|Zfp238|Znf238	zinc finger and BTB domain containing 18	protein-coding
mm_41457.1	chr5	90905895	90905904	+	1	NA	TTS (NM_009140)	TTS (NM_009140)	2000	NM_009140	20310	Mm.4979	NM_009140	ENSMUSG00000058427	Cxcl2	CINC-2a|GROb|Gro2|MIP-2|MIP-2a|Mgsa-b|Mip2|Scyb|Scyb2	chemokine (C-X-C motif) ligand 2	protein-coding
mm_167295.1	chr8	47289641	47289648	-	1	NA	promoter-TSS (NM_001286376)	promoter-TSS (NM_001286376)	-242	NM_001114311	71069	Mm.23973	NM_175162	ENSMUSG00000038143	Stox2	4933409N07Rik|AI449080|AI835114|mKIAA1392	storkhead box 2	protein-coding
mm_7420.1	chr1	119631668	119631668	-	1	NA	intron (NM_145506, intron 3 of 24)	intron (NM_145506, intron 3 of 24)	17332	NM_001113416	226352	Mm.253156	NM_145506	ENSMUSG00000026383	Epb41l5	1700030C16Rik|AL022914|BE37|E230025E14Rik|Epb4.1l5|Lulu1|NBL5	erythrocyte membrane protein band 4.1 like 5	protein-coding
mm_162298.1	chr1	34121364	34121372	+	1	NA	intron (NM_001276764, intron 8 of 102)	intron (NM_001276764, intron 8 of 102)	4009	NR_105861	102466987		NR_105861	ENSMUSG00000105982	Mir6896	mmu-mir-6896	microRNA 6896	ncRNA
mm_167998.1	chrX	170018115	170018123	+	1	NA	Intergenic	B2_Mm1a|SINE|B2	-39202	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_144233.1	chr18	10447816	10447850	+	1	NA	intron (NM_001083628, intron 1 of 32)	intron (NM_001083628, intron 1 of 32)	122654	NM_001083628	381157	Mm.261535	NM_001083628	ENSMUSG00000042942	Greb1l	mKIAA4095	growth regulation by estrogen in breast cancer-like	protein-coding
mm_159314.1	chr3	9250564	9250564	+	1	NA	promoter-TSS (NM_177660)	promoter-TSS (NM_177660)	-3	NM_177660	229055	Mm.103262	NM_177660	ENSMUSG00000069114	Zbtb10	4832414A18|AU021107|RINZF	zinc finger and BTB domain containing 10	protein-coding
mm_73833.1	chr8	117460732	117460757	+	1	NA	3' UTR (NM_001163262, exon 21 of 21)	3' UTR (NM_001163262, exon 21 of 21)	1479	NR_106046	102465653		NR_106046	ENSMUSG00000098483	Mir7078	Gm27386|mmu-mir-7078	microRNA 7078	ncRNA
mm_93841.1	chr10	121626319	121626334	-	1	NA	promoter-TSS (NM_001081056)	promoter-TSS (NM_001081056)	-10	NM_001081056	73192	Mm.25042	NM_001081056	ENSMUSG00000034667	Xpot	1110004L07Rik|3110065H13Rik|AI452076|C79645|EXPORTIN-T	exportin, tRNA (nuclear export receptor for tRNAs)	protein-coding
mm_51735.1	chr6	87073088	87073098	+	1	NA	intron (NM_013528, intron 11 of 18)	intron (NM_013528, intron 11 of 18)	30247	NM_013528	14583	Mm.19893	NM_013528	ENSMUSG00000029992	Gfpt1	2810423A18Rik|AI324119|AI449986|GFA|GFAT|GFAT1|GFAT1m|Gfpt	glutamine fructose-6-phosphate transaminase 1	protein-coding
mm_116054.1	chr13	27437163	27437170	-	1	NA	exon (NM_011167, exon 2 of 6)	exon (NM_011167, exon 2 of 6)	1522	NM_001271379	19112	Mm.142728	NM_011167	ENSMUSG00000021345	Prl8a6	Ghd13|PLP-C1|PLP-Ca|PLP-calpha|Prlpc|Prlpc1	prolactin family 8, subfamily a, member 6	protein-coding
mm_70875.1	chr8	25101871	25101886	+	1	NA	promoter-TSS (NM_031257)	promoter-TSS (NM_031257)	-67	NM_031257	83436	Mm.261122	NM_031257	ENSMUSG00000031557	Plekha2	6430512N22Rik|AI851530|AU041791|TAPP2|W91773	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 2	protein-coding
mm_169141.1	chr13	62015897	62015914	+	1	NA	Intergenic	Intergenic	-113985	NM_001039239	630579	Mm.440905	NM_001039239	ENSMUSG00000074867	Zfp808	EG630579|Gm7036	zinc finger protein 80	protein-coding
mm_83924.1	chr9	56621219	56621229	-	1	NA	exon (NM_181074, exon 4 of 4)	exon (NM_181074, exon 4 of 4)	14424	NM_001311076	235402	Mm.246605	NM_181074	ENSMUSG00000049556	Lingo1	4930471K13Rik|AV148400|LERN1|LINGO-1|Lrrn6a|UNQ201	leucine rich repeat and Ig domain containing 1	protein-coding
mm_72359.1	chr8	79750019	79750020	+	1	NA	intron (NM_026904, intron 4 of 4)	intron (NM_026904, intron 4 of 4)	38199	NM_026904	68999	Mm.257445	NM_026904	ENSMUSG00000036977	Anapc10	1500026N15Rik|A830003M23Rik|APC10	anaphase promoting complex subunit 10	protein-coding
mm_61391.1	chr7	73112326	73112341	+	1	NA	Intergenic	RMER15|LTR|ERVL	-10265	NR_046024	625243	Mm.261798	NR_046024	ENSMUSG00000108383	Gm6567	-	predicted gene 6567	ncRNA
mm_138477.1	chr17	35194911	35194923	+	1	NA	promoter-TSS (NR_105939)	promoter-TSS (NR_105939)	-55	NR_105939	102465588		NR_105939	ENSMUSG00000098291	Mir6973a	Gm27967|mmu-mir-6973a	microRNA 6973a	ncRNA
mm_143129.1	chr17	57214786	57214830	-	1	NA	exon (NM_009778, exon 26 of 41)	exon (NM_009778, exon 26 of 41)	2420	NR_105944	102465591		NR_105944	ENSMUSG00000099066	Mir6978	Gm27858|mmu-mir-6978	microRNA 6978	ncRNA
mm_39597.1	chr5	23502086	23502105	+	1	NA	exon (NM_026984, exon 26 of 26)	exon (NM_026984, exon 26 of 26)	67666	NM_026984	69188	Mm.205190	NM_026984	ENSMUSG00000029004	Kmt2e	1810033J14Rik|9530077A04Rik|D230038D11Rik|Mll5|NKp44L	lysine (K)-specific methyltransferase 2E	protein-coding
mm_141729.1	chr17	34116330	34116342	-	1	NA	intron (NM_010238, intron 3 of 12)	intron (NM_010238, intron 3 of 12)	3564	NR_037970	14312	Mm.3444	NM_010238	ENSMUSG00000024335	Brd2	AW228947|D17H6S113E|Frg-1|Fsrg-1|Fsrg1|Nat|Ring3|Rnf3|mKIAA4005	bromodomain containing 2	protein-coding
mm_161252.1	chr13	104179258	104179258	+	1	NA	promoter-TSS (NR_003546)	promoter-TSS (NR_003546)	160	NM_030731	81003	Mm.244190	NM_030731	ENSMUSG00000021712	Trim23	6330516O20Rik|AI450195|Arfd1	tripartite motif-containing 23	protein-coding
mm_163644.1	chr13	62968736	62968740	-	1	NA	intron (NM_001289926, intron 1 of 15)	intron (NM_001289926, intron 1 of 15)	3845	NM_001289924	72061	Mm.188105	NM_028079	ENSMUSG00000021458	2010111I01Rik	2300006M17Rik|AP-O|AW742919|Aopep|ApO|mir-23b|mir-24-1|mir-27b	RIKEN cDNA 2010111I01 gene	protein-coding
mm_40473.1	chr5	53998552	53998575	+	1	NA	promoter-TSS (NM_001081103)	promoter-TSS (NM_001081103)	40	NM_001081103	116873	Mm.265985	NM_054083	ENSMUSG00000039156	Stim2	-	stromal interaction molecule 2	protein-coding
mm_108594.1	chr12	85374280	85374304	+	1	NA	intron (NM_026775, intron 1 of 4)	CpG	425	NM_026775	68581	Mm.379159	NM_026775	ENSMUSG00000021248	Tmed10	1110014C03Rik|Tmp21|p23|p24delta1	transmembrane p24 trafficking protein 10	protein-coding
mm_118359.1	chr13	115101680	115101715	-	1	NA	5' UTR (NM_001033228, exon 1 of 29)	5' UTR (NM_001033228, exon 1 of 29)	267	NM_001033228	109700	Mm.317280	NM_001033228	ENSMUSG00000042284	Itga1	CD49A|E130012M19Rik|Vla1	integrin alpha 1	protein-coding
mm_4052.1	chr1	165790211	165790231	+	1	NA	intron (NM_001113391, intron 1 of 7)	intron (NM_001113391, intron 1 of 7)	1540	NM_001113392	12503	Mm.217308	NM_031162	ENSMUSG00000005763	Cd247	4930549J05Rik|A430104F18Rik|AW552088|Cd3|Cd3-eta|Cd3-zeta|Cd3h|Cd3z|Cd3zeta|T3z|Tcrk|Tcrz	CD247 antigen	protein-coding
mm_158172.1	chrX	103763548	103763553	-	1	NA	intron (NM_009197, intron 1 of 5)	intron (NM_009197, intron 1 of 5)	58438	NM_009197	20502	Mm.388973	NM_009197	ENSMUSG00000033965	Slc16a2	AW105741|Mct8|Xpct	solute carrier family 16 (monocarboxylic acid transporters), member 2	protein-coding
mm_131674.1	chr16	20673097	20673117	+	1	NA	intron (NM_001304432, intron 1 of 31)	CpG	380	NM_001304432	208643	Mm.260256	NM_145941	ENSMUSG00000045983	Eif4g1	E030015G23Rik|eIF-4-gamma 1|eIF-4G 1|eIF-4G1|eIF4GI	eukaryotic translation initiation factor 4, gamma 1	protein-coding
mm_104529.1	chr11	96147642	96147646	-	1	NA	intron (NM_172799, intron 9 of 14)	intron (NM_172799, intron 9 of 14)	13858	NM_172799	237930	Mm.249912	NM_172799	ENSMUSG00000038756	Ttll6	4932418K24Rik|D11Moh43e|D11Moh44e|t8130b59	tubulin tyrosine ligase-like family, member 6	protein-coding
mm_5770.1	chr1	51473426	51473467	-	1	NA	intron (NM_001310548, intron 3 of 5)	intron (NM_001310548, intron 3 of 5)	4953	NM_028696	109019	Mm.196290	NM_028696	ENSMUSG00000026107	Nabp1	4930434H03Rik|4930442A21Rik|4930488J04Rik|4933440J18Rik|5830411E10Rik|AI852561|Nbp1|Obfc2a|Ssb2	nucleic acid binding protein 1	protein-coding
mm_91961.1	chr10	61147660	61147680	-	1	NA	promoter-TSS (NM_001316673)	promoter-TSS (NM_001316673)	14	NM_009163	20397	Mm.412319	NM_009163	ENSMUSG00000020097	Sgpl1	AI428538|D10Xrf456|S1PL|Spl	sphingosine phosphate lyase 1	protein-coding
mm_75821.1	chr8	70476978	70476993	-	1	NA	promoter-TSS (NM_001122830)	promoter-TSS (NM_001122830)	-42	NM_178771	234378	Mm.187090	NM_172052	ENSMUSG00000055707	Klhl26	C630013N10Rik|Klkl26	kelch-like 26	protein-coding
mm_49492.1	chr6	29699034	29699037	+	1	NA	intron (NM_146173, intron 1 of 7)	B1_Mur3|SINE|Alu	4821	NM_146173	232670	Mm.225289	NM_146173	ENSMUSG00000001763	Tspan33	1300010A20Rik|Pen	tetraspanin 33	protein-coding
mm_80645.1	chr9	89551479	89551483	+	1	NA	Intergenic	Intergenic	71505	NM_153509	209743	Mm.242899	NM_153509	ENSMUSG00000039313	AF529169	DD1|Kiaa1024	cDNA sequence AF529169	protein-coding
mm_1271.1	chr1	63296208	63296212	+	1	NA	intron (NM_001267872, intron 5 of 5)	intron (NM_001267872, intron 5 of 5)	22941	NM_001267872	73884	Mm.86986	NM_028673	ENSMUSG00000027520	Zdbf2	4930431J08Rik|9330107J05Rik	zinc finger, DBF-type containing 2	protein-coding
mm_16332.1	chr2	174329363	174329411	+	1	NA	promoter-TSS (NM_001077510)	promoter-TSS (NM_001077510)	-683	NM_201616	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_126390.1	chr15	80189185	80189201	+	1	NA	intron (NM_010795, intron 1 of 1)	intron (NM_010795, intron 1 of 1)	15472	NM_010795	17309	Mm.299693	NM_010795	ENSMUSG00000042428	Mgat3	1110038J12Rik|AI848272|GnT-III	mannoside acetylglucosaminyltransferase 3	protein-coding
mm_61883.1	chr7	89632690	89632731	+	1	NA	promoter-TSS (NM_181407)	promoter-TSS (NM_181407)	-108	NM_181407	109264	Mm.334011	NM_181407	ENSMUSG00000030621	Me3	1700020C08Rik|B230207H15Rik	malic enzyme 3, NADP(+)-dependent, mitochondrial	protein-coding
mm_94861.1	chr11	24077801	24077810	+	1	NA	promoter-TSS (NM_001242934)	promoter-TSS (NM_001242934)	-251	NM_016707	14025	Mm.53687	NM_016707	ENSMUSG00000000861	Bcl11a	2810047E18Rik|BCL-11A|Ctip1|D930021L15Rik|Evi9|Evi9a|Evi9b|Evi9c|mKIAA1809	B cell CLL/lymphoma 11A (zinc finger protein)	protein-coding
mm_39226.1	chr4	156200825	156200833	-	1	NA	promoter-TSS (NM_015783)	promoter-TSS (NM_015783)	-11	NM_015783	100038882	Mm.4950	NM_015783	ENSMUSG00000035692	Isg15	G1p2|IGI15|IP17|Irfp|UCRP	ISG15 ubiquitin-like modifier	protein-coding
mm_24929.1	chr3	96559495	96559504	+	1	NA	intron (NM_001009935, intron 4 of 7)	intron (NM_001009935, intron 4 of 7)	1542	NM_023719	56338	Mm.410189	NM_023719	ENSMUSG00000038393	Txnip	1200008J08Rik|AA682105|Hyplip1|THIF|Tbp-2|VDUP1	thioredoxin interacting protein	protein-coding
mm_34198.1	chr4	140714319	140714357	+	1	NA	intron (NM_173867, intron 7 of 12)	intron (NM_173867, intron 7 of 12)	12865	NM_173867	108911	Mm.253	NM_173867	ENSMUSG00000040945	Rcc2	2610510H01Rik|2610529N02Rik|AA536646|AA675016|Td60|mKIAA1470	regulator of chromosome condensation 2	protein-coding
mm_50918.1	chr6	57604451	57604455	+	1	NA	intron (NM_025992, intron 6 of 22)	intron (NM_025992, intron 6 of 22)	23461	NM_025992	67138	Mm.297393	NM_025992	ENSMUSG00000029798	Herc6	1700121D12Rik|2510038N07Rik|4930427L17Rik|AI451296|CEB1|Herc5	hect domain and RLD 6	protein-coding
mm_164070.1	chr14	120277151	120277161	-	1	NA	intron (NM_175341, intron 1 of 8)	intron (NM_175341, intron 1 of 8)	1487	NM_175341	105559	Mm.238266	NM_175341	ENSMUSG00000022139	Mbnl2	1110002M11Rik|AI047808|AI837313|AI849185|AL118326|MBLL|R75232|mKIAA4072	muscleblind-like 2	protein-coding
mm_155373.1	chrX	71556065	71556071	+	1	NA	5' UTR (NM_008253, exon 1 of 5)	5' UTR (NM_008253, exon 1 of 5)	151	NM_001293625	15354	Mm.336087	NM_008253	ENSMUSG00000015217	Hmgb3	Hmg2a|Hmg4	high mobility group box 3	protein-coding
mm_136314.1	chr16	91728724	91728730	-	1	NA	promoter-TSS (NM_001110276)	promoter-TSS (NM_001110276)	75	NM_026994	66609	Mm.109823	NM_026994	ENSMUSG00000058240	Cryzl1	2210407J23Rik|2410006O11Rik|QOH-1	crystallin, zeta (quinone reductase)-like 1	protein-coding
mm_72659.1	chr8	84867144	84867150	+	1	NA	promoter-TSS (NR_106037)	promoter-TSS (NR_106037)	-800	NR_106037	102466220		NR_106037	ENSMUSG00000098331	Mir7069	Gm27777|mmu-mir-7069	microRNA 7069	ncRNA
mm_113497.1	chr13	37418764	37418793	+	1	NA	3' UTR (NM_010745, exon 5 of 5)	3' UTR (NM_010745, exon 5 of 5)	73433	NM_010745	17084	Mm.2639	NM_010745	ENSMUSG00000021423	Ly86	MD-1|MD1|ly86_tv2	lymphocyte antigen 86	protein-coding
mm_58672.1	chr7	7299062	7299075	+	1	NA	promoter-TSS (NM_001302387)	promoter-TSS (NM_001302387)	177	NR_049193	100885832		NR_049193	ENSMUSG00000093599	Mir5620	Gm23572|mir-5620|mmu-mir-5620	microRNA 5620	ncRNA
mm_155462.1	chrX	73521092	73521117	+	1	NA	intron (NM_001310537, intron 1 of 20)	intron (NM_001310537, intron 1 of 20)	18018	NM_177236	320707	Mm.210095	NM_177236	ENSMUSG00000031376	Atp2b3	6430519O13Rik|Pmca3	ATPase, Ca++ transporting, plasma membrane 3	protein-coding
mm_63964.1	chr7	139944514	139944536	+	1	NA	intron (NM_009482, intron 1 of 1)	CpG	669	NM_009482	22286	Mm.10205	NM_009482	ENSMUSG00000047751	Utf1	AI505934	undifferentiated embryonic cell transcription factor 1	protein-coding
mm_42330.1	chr5	114902630	114902668	+	1	NA	intron (NM_011854, intron 3 of 5)	B3A|SINE|B2	5715	NM_011854	23962	Mm.228363	NM_011854	ENSMUSG00000029561	Oasl2	M1204|Mmu-OASL|Oasl	2'-5' oligoadenylate synthetase-like 2	protein-coding
mm_169710.1	chr15	75909281	75909282	-	1	NA	promoter-TSS (NM_001285430)	promoter-TSS (NM_001285430)	63	NM_001285433	66656	Mm.258927	NM_023240	ENSMUSG00000055762	Eef1d	EF-1-delta	eukaryotic translation elongation factor 1 delta (guanine nucleotide exchange protein)	protein-coding
mm_55726.1	chr6	75298139	75298145	-	1	NA	Intergenic	RLTR33|LTR|ERVK	-1827121	NR_108032	73408	Mm.233629	NR_108032	ENSMUSG00000107408	1700065L07Rik	-	RIKEN cDNA 1700065L07 gene	ncRNA
mm_104895.1	chr11	99598096	99598111	-	1	NA	promoter-TSS (NM_029351)	promoter-TSS (NM_029351)	3	NM_029351	75586	Mm.75707	NM_029351	ENSMUSG00000049809	Krtap9-3	2310040M23Rik	keratin associated protein 9-3	protein-coding
mm_124945.1	chr15	12349941	12349970	+	1	NA	3' UTR (NM_025673, exon 4 of 4)	3' UTR (NM_025673, exon 4 of 4)	28459	NM_025673	66629	Mm.157655	NM_025673	ENSMUSG00000022200	Golph3	4733401N08Rik|5730410D03Rik|AW413496	golgi phosphoprotein 3	protein-coding
mm_117279.1	chr13	65112995	65113004	-	1	NA	promoter-TSS (NM_001083901)	promoter-TSS (NM_001083901)	-17	NM_133680	66631	Mm.239196	NM_133680	ENSMUSG00000038212	Mfsd14b	5730414C17Rik|AU045608|AW539692|Hiatl1	major facilitator superfamily domain containing 14B	protein-coding
mm_20366.1	chr2	128405260	128405270	-	1	NA	intron (NR_028591, intron 1 of 1)	intron (NR_028591, intron 1 of 1)	24086	NR_028591	100043424	Mm.297222	NR_028589		Gm14005	OTTMUSG00000015351	predicted gene 14005	ncRNA
mm_160275.1	chr7	119895592	119895592	-	1	NA	promoter-TSS (NM_001285961)	promoter-TSS (NM_001285961)	-134	NM_173408	233805	Mm.31539	NM_173408	ENSMUSG00000048787	Dcun1d3	1700020A13Rik|BC030335	DCN1, defective in cullin neddylation 1, domain containing 3 (S. cerevisiae)	protein-coding
mm_138685.1	chr17	35919250	35919276	+	1	NA	intron (NM_001163818, intron 1 of 18)	(T)n|Simple_repeat|Simple_repeat	1374	NR_035445	100316810		NR_035445	ENSMUSG00000084751	Mir1894	Mirn1894|mmu-mir-1894	microRNA 1894	ncRNA
mm_36477.1	chr4	82859517	82859570	-	1	NA	5' UTR (NM_026647, exon 1 of 9)	5' UTR (NM_026647, exon 1 of 9)	118	NM_026647	68268	Mm.32047	NM_026647	ENSMUSG00000028403	Zdhhc21	9130404H11Rik|AL024349|D130004H04Rik|dep	zinc finger, DHHC domain containing 21	protein-coding
mm_163894.1	chr14	27348374	27348383	+	1	NA	intron (NM_001289687, intron 1 of 9)	intron (NM_001289687, intron 1 of 9)	12341	NM_001289687	71704	Mm.248606	NM_027871	ENSMUSG00000021895	Arhgef3	1200004I24Rik|9830169H03Rik|C76747|Xpln	Rho guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_40893.1	chr5	75152317	75152367	+	1	NA	promoter-TSS (NM_011058)	promoter-TSS (NM_011058)	91	NM_001347718	18595	Mm.221403	NM_011058	ENSMUSG00000029231	Pdgfra	AI115593|CD140a|Pdgfr-2	platelet derived growth factor receptor, alpha polypeptide	protein-coding
mm_57115.1	chr6	122596516	122596526	-	1	NA	intron (NM_031159, intron 3 of 7)	intron (NM_031159, intron 3 of 7)	5923	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_137839.1	chr17	30984079	30984089	+	1	NA	exon (NM_177465, exon 9 of 22)	exon (NM_177465, exon 9 of 22)	29401	NM_177465	52020	Mm.25923	NM_177465	ENSMUSG00000054134	Umodl1	D17Ertd488e	uromodulin-like 1	protein-coding
mm_127658.1	chr15	102498768	102498778	+	1	NA	3' UTR (NM_001163643, exon 16 of 16)	3' UTR (NM_001163643, exon 16 of 16)	18231	NM_001163643	26404	Mm.172897	NM_009582	ENSMUSG00000023050	Map3k12	DLK|MUK|Zpk	mitogen-activated protein kinase kinase kinase 12	protein-coding
mm_54695.1	chr6	39557678	39557700	-	1	NA	5' UTR (NM_172477, exon 1 of 19)	5' UTR (NM_172477, exon 1 of 19)	145	NM_172477	209773	Mm.440021	NM_172477	ENSMUSG00000038456	Dennd2a	B930096L08Rik|C130031G22|mKIAA1277	DENN/MADD domain containing 2A	protein-coding
mm_145022.1	chr18	38993194	38993205	+	1	NA	promoter-TSS (NM_175164)	promoter-TSS (NM_175164)	54	NM_175164	71302	Mm.329396	NM_175164	ENSMUSG00000036452	Arhgap26	1810044B20Rik|2610010G17Rik|4933432P15Rik|AI853435|mKIAA0621	Rho GTPase activating protein 26	protein-coding
mm_143985.1	chr17	87613489	87613509	-	1	NA	Intergenic	Intergenic	-22480	NM_008532	17075	Mm.4259	NM_008532	ENSMUSG00000045394	Epcam	CD326|EGP|EGP-2|Egp314|Ep-CAM|EpCAM1|GA733-2|Ly74|TROP1|Tacsd1|Tacstd1|gp40	epithelial cell adhesion molecule	protein-coding
mm_112954.1	chr13	21179451	21179462	+	1	NA	promoter-TSS (NM_009054)	promoter-TSS (NM_009054)	-475	NM_009054	19720	Mm.314056	NM_009054	ENSMUSG00000021326	Trim27	AW538890|Gm19403|Rfp	tripartite motif-containing 27	protein-coding
mm_98739.1	chr11	96365741	96365751	+	1	NA	promoter-TSS (NM_008266)	promoter-TSS (NM_008266)	-12	NM_008266	15407	Mm.890	NM_008266	ENSMUSG00000018973	Hoxb1	Hox-2.9	homeobox B1	protein-coding
mm_62840.1	chr7	114088229	114088238	+	1	NA	intron (NM_025846, intron 1 of 5)	intron (NM_025846, intron 1 of 5)	29548	NM_025846	66922	Mm.276572	NM_025846	ENSMUSG00000055723	Rras2	2610016H24Rik|C86394|TC21	related RAS viral (r-ras) oncogene 2	protein-coding
mm_75537.1	chr8	57320844	57320871	-	1	NA	promoter-TSS (NM_010402)	promoter-TSS (NM_010402)	2	NR_110474	102636514		NR_110474	ENSMUSG00000100510	Uph	-	upperhand	ncRNA
mm_39202.1	chr4	156030749	156030764	-	1	NA	Intergenic	Intergenic	4414	NM_021985	21936	Mm.3180	NM_009400	ENSMUSG00000041954	Tnfrsf18	AITR|Gitr	tumor necrosis factor receptor superfamily, member 18	protein-coding
mm_134259.1	chr16	13739202	13739223	-	1	NA	intron (NR_040574, intron 2 of 2)	RLTR9E|LTR|ERVK	-8728	NM_011987	26565	Mm.4214	NM_011987	ENSMUSG00000022683	Pla2g10	GX sPLA2|PLA2GX|sPLA2-X	phospholipase A2, group X	protein-coding
mm_69034.1	chr7	126798504	126798518	-	1	NA	intron (NM_001177307, intron 1 of 9)	intron (NM_001177307, intron 1 of 9)	667	NM_001177307	11674	Mm.275831	NM_007438	ENSMUSG00000030695	Aldoa	Aldo-1|Aldo1	aldolase A, fructose-bisphosphate	protein-coding
mm_14252.1	chr2	128128126	128128152	+	1	NA	intron (NM_001284410, intron 1 of 3)	CpG-8520	564	NM_001284410	12125	Mm.141083	NM_009754	ENSMUSG00000027381	Bcl2l11	1500006F24Rik|Bim|Bod|bcl2-L-11	BCL2-like 11 (apoptosis facilitator)	protein-coding
mm_76674.1	chr8	93810226	93810261	-	1	NA	promoter-TSS (NM_010308)	promoter-TSS (NM_010308)	-595	NM_010308	14681	Mm.251445	NM_010308	ENSMUSG00000031748	Gnao1	AW050213|Galphao|Gnao|alphaO	guanine nucleotide binding protein, alpha O	protein-coding
mm_12577.1	chr2	73274267	73274307	+	1	NA	exon (NM_001005343, exon 2 of 2)	exon (NM_001005343, exon 2 of 2)	2361	NM_001005343	381373	Mm.330293	NM_001005343	ENSMUSG00000068859	Sp9	-	trans-acting transcription factor 9	protein-coding
mm_25048.1	chr3	98309024	98309042	+	1	NA	3' UTR (NM_008256, exon 10 of 10)	3' UTR (NM_008256, exon 10 of 10)	28602	NM_008256	15360	Mm.289131	NM_008256	ENSMUSG00000027875	Hmgcs2	1300002P16|mHS	3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2	protein-coding
mm_80116.1	chr9	70542873	70542920	+	1	NA	promoter-TSS (NM_025690)	promoter-TSS (NM_025690)	26	NM_025690	66660	Mm.22379	NM_025690	ENSMUSG00000032212	Sltm	5730455C01Rik|5730555F13Rik|9130215G10Rik|Met	SAFB-like, transcription modulator	protein-coding
mm_16958.1	chr2	17391095	17391105	-	1	NA	intron (NM_028757, intron 4 of 6)	intron (NM_028757, intron 4 of 6)	-172414	NR_105847	102465964		NR_105847	ENSMUSG00000099161	Mir6419	Gm27713|mmu-mir-6419	microRNA 6419	ncRNA
mm_142777.1	chr17	50094278	50094288	-	1	NA	intron (NM_181397, intron 3 of 9)	intron (NM_181397, intron 3 of 9)	96214	NM_181397	76438	Mm.41854	NM_181397	ENSMUSG00000039316	Rftn1	2310015N21Rik|AI853526	raftlin lipid raft linker 1	protein-coding
mm_106463.1	chr11	120047145	120047193	-	1	NA	promoter-TSS (NM_007377)	promoter-TSS (NM_007377)	-24	NM_007377	11302	Mm.6826	NM_007377	ENSMUSG00000025375	Aatk	AATYK|aatyk1|mKIAA0641	apoptosis-associated tyrosine kinase	protein-coding
mm_126216.1	chr15	78911489	78911516	+	1	NA	exon (NM_001316684, exon 18 of 18)	exon (NM_001316684, exon 18 of 18)	-2417	NM_020271	57028	Mm.263169	NM_020271	ENSMUSG00000022436	Pdxp	1600027H05Rik|AB041662|PLPP	pyridoxal (pyridoxine, vitamin B6) phosphatase	protein-coding
mm_76149.1	chr8	82353409	82353422	-	1	NA	intron (NM_008357, intron 2 of 7)	intron (NM_008357, intron 2 of 7)	49171	NM_001254747	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_40730.1	chr5	66106215	66106232	+	1	NA	intron (NM_001127382, intron 2 of 7)	intron (NM_001127382, intron 2 of 7)	-8044	NM_139065	245945	Mm.36863	NM_139065	ENSMUSG00000070780	Rbm47	9530077J19Rik	RNA binding motif protein 47	protein-coding
mm_162478.1	chr1	133801492	133801495	+	1	NA	Intergenic	Intergenic	-47746	NM_213616	381290	Mm.188617	NM_213616	ENSMUSG00000026463	Atp2b4	Pmca4	ATPase, Ca++ transporting, plasma membrane 4	protein-coding
mm_151442.1	chr19	57452929	57452947	+	1	NA	promoter-TSS (NM_029839)	promoter-TSS (NM_029839)	32	NM_028115	72133	Mm.258404	NM_028115	ENSMUSG00000025086	Trub1	2610009I02Rik|9030425C13Rik|AI448235|BB118943|C76870	TruB pseudouridine (psi) synthase family member 1	protein-coding
mm_165556.1	chr3	14808386	14808399	-	1	NA	promoter-TSS (NM_009799)	promoter-TSS (NM_009799)	-27	NM_009799	12346	Mm.273195	NM_009799	ENSMUSG00000027556	Car1	AW555628|Ca1|Car-1	carbonic anhydrase 1	protein-coding
mm_124305.1	chr14	103098956	103098970	-	1	NA	promoter-TSS (NM_001347601)	promoter-TSS (NM_001347601)	41	NM_001347601	50789	Mm.214746	NM_015822	ENSMUSG00000022124	Fbxl3	AU041772|AW212966|FBK|Fbl3a|Fbxl3a|Ovtm|Play68	F-box and leucine-rich repeat protein 3	protein-coding
mm_88118.1	chr10	69213246	69213265	+	1	NA	promoter-TSS (NM_001252638)	promoter-TSS (NM_001252638)	61	NM_001252638	69288	Mm.26659	NM_001081347	ENSMUSG00000019944	Rhobtb1	1700008H16Rik|3110048G13Rik|AI173445|AI573858|AV350930	Rho-related BTB domain containing 1	protein-coding
mm_65635.1	chr7	27674517	27674630	-	1	NA	promoter-TSS (NM_198417)	promoter-TSS (NM_198417)	8	NM_001290528	269881	Mm.389883	NM_001081292	ENSMUSG00000040390	Map3k10	BC028668|BC046514|MST|Mlk2	mitogen-activated protein kinase kinase kinase 10	protein-coding
mm_163926.1	chr14	47097749	47097752	+	1	NA	TTS (NR_126579)	TTS (NR_126579)	18411	NR_126579	100038654		NR_126579	ENSMUSG00000072589	Gm10371	ENSMUSG00000072589	predicted gene 10371	ncRNA
mm_6159.1	chr1	65048582	65048598	-	1	NA	TTS (NM_007777)	TTS (NM_007777)	2573	NM_007777	12968	Mm.258170	NM_007777	ENSMUSG00000070870	Cryge	Cryg-2|Cryg-6|DGcry-2|Elo	crystallin, gamma E	protein-coding
mm_44626.1	chr5	26492324	26492334	-	1	NA	intron (NR_029445, intron 1 of 4)	intron (NR_029445, intron 1 of 4)	985	NR_029445	75942	Mm.50087	NR_029445	ENSMUSG00000029044	4930584F24Rik	1700001J09Rik|4930522C06Rik	RIKEN cDNA 4930584F24 gene	ncRNA
mm_86996.1	chr10	26695293	26695328	+	1	NA	Intergenic	Intergenic	-20659	NR_033633	667572	Mm.482728	NR_033633	ENSMUSG00000098179	Gm8709	EG667572	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_162674.1	chr10	7473607	7473634	-	1	NA	promoter-TSS (NM_029975)	promoter-TSS (NM_029975)	-143	NM_029975	77777	Mm.442442	NM_029975	ENSMUSG00000079685	Ulbp1	A430108B07Rik|MULT1	UL16 binding protein 1	protein-coding
mm_12619.1	chr2	74695291	74695312	+	1	NA	TTS (NM_013554)	TTS (NM_013554)	-2462	NM_013555	15438	Mm.26544	NM_013555	ENSMUSG00000043342	Hoxd9	Hox-4.4|Hox-5.2	homeobox D9	protein-coding
mm_116286.1	chr13	34994104	34994148	-	1	NA	promoter-TSS (NM_001110331)	promoter-TSS (NM_001110331)	18	NM_011868	23986	Mm.491141	NM_011868	ENSMUSG00000021417	Eci2	Acbd2|Drs1|Hca88|Peci	enoyl-Coenzyme A delta isomerase 2	protein-coding
mm_11783.1	chr2	39295981	39295984	+	1	NA	Intergenic	RLTR48A|LTR|ERV1	-69644	NM_024209	67857	Mm.389242	NM_024209	ENSMUSG00000026753	Ppp6c	2310003C10Rik	protein phosphatase 6, catalytic subunit	protein-coding
mm_146816.1	chr18	20943763	20943807	-	1	NA	promoter-TSS (NM_026301)	promoter-TSS (NM_026301)	-840	NM_026301	67664	Mm.45980	NM_026301	ENSMUSG00000033107	Rnf125	4930553F04Rik	ring finger protein 125	protein-coding
mm_71932.1	chr8	70283056	70283080	+	1	NA	promoter-TSS (NM_001146153)	promoter-TSS (NM_001146153)	69	NM_001146153	26558	Mm.388127	NM_011984	ENSMUSG00000003573	Homer3	AW146114	homer scaffolding protein 3	protein-coding
mm_47800.1	chr5	132542004	132542021	-	1	NA	5' UTR (NM_177047, exon 1 of 19)	5' UTR (NM_177047, exon 1 of 19)	331	NM_177047	319974	Mm.409595	NM_177047	ENSMUSG00000029673	Auts2	2700063G02Rik|A730011F23Rik|D830032G16Rik	autism susceptibility candidate 2	protein-coding
mm_65536.1	chr7	25816566	25816568	-	1	NA	promoter-TSS (NM_028775)	promoter-TSS (NM_028775)	-37	NM_028775	74134	Mm.275188	NM_028775	ENSMUSG00000040703	Cyp2s1	1200011C15Rik|AU041727|C79779	cytochrome P450, family 2, subfamily s, polypeptide 1	protein-coding
mm_140663.1	chr17	12909872	12909877	-	1	NA	exon (NM_001034866, exon 1 of 19)	exon (NM_001034866, exon 1 of 19)	126	NM_001034866	240023	Mm.242315	NM_001034866	ENSMUSG00000073460	Pnldc1	Gm313	poly(A)-specific ribonuclease (PARN)-like domain containing 1	protein-coding
mm_7928.1	chr1	133906955	133906960	-	1	NA	exon (NM_001160422, exon 1 of 5)	exon (NM_001160422, exon 1 of 5)	216	NM_054076	269120	Mm.59985	NM_054076	ENSMUSG00000010311	Optc	-	opticin	protein-coding
mm_12739.1	chr2	78923491	78923494	+	1	NA	Intergenic	Intergenic	54445	NM_009454	22193	Mm.1485	NM_009454	ENSMUSG00000027011	Ube2e3	Ubce4|ubcM2	ubiquitin-conjugating enzyme E2E 3	protein-coding
mm_127186.1	chr15	99029867	99029913	+	1	NA	promoter-TSS (NM_009448)	promoter-TSS (NM_009448)	-1	NM_009448	22146	Mm.88212	NM_009448	ENSMUSG00000043091	Tuba1c	M[a]6|Tuba6	tubulin, alpha 1C	protein-coding
mm_19105.1	chr2	79454951	79454962	-	1	NA	exon (NM_010894, exon 2 of 2)	exon (NM_010894, exon 2 of 2)	1680	NM_010894	18012	Mm.4636	NM_010894	ENSMUSG00000034701	Neurod1	BETA2|BHF-1|Nd1|Neurod|bHLHa3	neurogenic differentiation 1	protein-coding
mm_28382.1	chr3	90000529	90000547	-	1	NA	3' UTR (NM_001165983, exon 28 of 28)	3' UTR (NM_001165983, exon 28 of 28)	1778	NR_045749	100503469	Mm.440636	NR_045749	ENSMUSG00000105552	Gm19710	-	predicted gene, 19710	ncRNA
mm_171170.1	chr3	28852109	28852119	-	1	NA	Intergenic	LTRIS2|LTR|ERV1	-40503	NM_001033479	385263	Mm.60893	NM_001033479	ENSMUSG00000074655	Gm1527	Gm1136	predicted gene 1527	protein-coding
mm_1019.1	chr1	58743548	58743550	+	1	NA	intron (NM_001293805, intron 6 of 7)	intron (NM_001293805, intron 6 of 7)	12997	NM_001293805	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_91194.1	chr10	21146487	21146494	-	1	NA	intron (NM_010848, intron 8 of 14)	intron (NM_010848, intron 8 of 14)	14494	NM_001198914	17863	Mm.52109	NM_010848	ENSMUSG00000019982	Myb	AI550390|M16449|c-myb	myeloblastosis oncogene	protein-coding
mm_137483.1	chr17	26933302	26933385	+	1	NA	TTS (NM_053173)	TTS (NM_053173)	216	NR_126158	21652	Mm.258953	NM_009343	ENSMUSG00000024193	Phf1	AW557215|D17Ertd455e|Pcl1|Phf2|Tctex3	PHD finger protein 1	protein-coding
mm_89267.1	chr10	87860145	87860159	+	1	NA	promoter-TSS (NM_001111276)	promoter-TSS (NM_001111276)	-959	NM_001111274	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_8927.1	chr1	164020989	164021012	-	1	NA	Intergenic	RLTR9E|LTR|ERVK	26055	NM_027279	69962	Mm.27284	NM_027279	ENSMUSG00000041396	Mettl18	2810422O20Rik|C78571	methyltransferase like 18	protein-coding
mm_113432.1	chr13	34739608	34739636	+	1	NA	promoter-TSS (NM_138746)	promoter-TSS (NM_138746)	-20	NM_138746	108161	Mm.41991	NM_138746	ENSMUSG00000038246	Fam50b	D0H6S2654E|X5L|XAP-5-like	family with sequence similarity 50, member B	protein-coding
mm_94818.1	chr11	23255921	23255976	+	1	NA	promoter-TSS (NM_134014)	promoter-TSS (NM_134014)	-93	NM_001035226	103573	Mm.217547	NM_134014	ENSMUSG00000020290	Xpo1	AA420417|Crm1|Exp1	exportin 1	protein-coding
mm_75028.1	chr8	31950047	31950074	-	1	NA	Intergenic	Intergenic	-31857	NM_178591	211323	Mm.153432	NM_178591	ENSMUSG00000062991	Nrg1	6030402G23Rik|ARIA|D230005F13Rik|GGF|GGFII|HRG|HRGalpha|Hgl|NDF|SMDF	neuregulin 1	protein-coding
mm_143512.1	chr17	72837470	72837502	-	1	NA	intron (NM_027166, intron 1 of 2)	CpG	782	NM_027166	383295	Mm.277533	NM_027166	ENSMUSG00000039770	Ypel5	2310076K21Rik|CGI-127	yippee-like 5 (Drosophila)	protein-coding
mm_3290.1	chr1	136677245	136677249	+	1	NA	Intergenic	Intergenic	-6149	NR_045324	100503460	Mm.30630	NR_045324	ENSMUSG00000097113	Gm19705	-	predicted gene, 19705	ncRNA
mm_7587.1	chr1	125434777	125434790	-	1	NA	intron (NM_001205385, intron 2 of 12)	intron (NM_001205385, intron 2 of 12)	944	NM_023735	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding
mm_140212.1	chr17	83804294	83804317	+	1	NA	intron (NM_054082, intron 15 of 16)	intron (NM_054082, intron 15 of 16)	42485	NM_025325	107766	Mm.30100	NM_025325	ENSMUSG00000000673	Haao	0610007K21Rik|0610012J07Rik|3-HAO|3-HAOxase|3HAO	3-hydroxyanthranilate 3,4-dioxygenase	protein-coding
mm_45023.1	chr5	38561683	38561732	-	1	NA	promoter-TSS (NM_011715)	promoter-TSS (NM_011715)	-112	NM_011715	22388	Mm.2654	NM_011715	ENSMUSG00000005103	Wdr1	Aip1|D5Wsu185e|rede	WD repeat domain 1	protein-coding
mm_1009.1	chr1	58726165	58726178	+	1	NA	intron (NM_009805, intron 1 of 4)	intron (NM_009805, intron 1 of 4)	-4381	NM_001293805	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_12828.1	chr2	80617348	80617354	+	1	NA	5' UTR (NM_024438, exon 1 of 4)	5' UTR (NM_024438, exon 1 of 4)	137	NM_024438	68082	Mm.306818	NM_024438	ENSMUSG00000027001	Dusp19	5930436K22Rik|C79103|SKRP1|TS-DSP1	dual specificity phosphatase 19	protein-coding
mm_28757.1	chr3	95855861	95855889	-	1	NA	promoter-TSS (NM_001316751)	promoter-TSS (NM_001316751)	7	NM_001316751	70767	Mm.279872	NM_027541	ENSMUSG00000015748	Prpf3	3632413F13Rik	pre-mRNA processing factor 3	protein-coding
mm_127985.1	chr15	12549263	12549285	-	1	NA	intron (NM_001081064, intron 1 of 23)	intron (NM_001081064, intron 1 of 23)	43282	NM_001081064	68070	Mm.423205	NM_001081064	ENSMUSG00000022197	Pdzd2	4930537L06Rik|A930022H17Rik|Gm21706|Gm82|Pdzk3|mKIAA0300	PDZ domain containing 2	protein-coding
mm_70777.1	chr8	22216973	22216988	+	1	NA	intron (NM_027338, intron 11 of 13)	intron (NM_027338, intron 11 of 13)	-10323	NM_001205253	56229	Mm.32067	NM_019576	ENSMUSG00000031480	Thsd1	4833423O18Rik|Tmtsp	thrombospondin, type I, domain 1	protein-coding
mm_48077.1	chr5	136812540	136812540	-	1	NA	intron (NM_001346699, intron 3 of 12)	intron (NM_001346699, intron 3 of 12)	70567	NM_024474	140709	Mm.295020	NM_024474	ENSMUSG00000004415	Col26a1	9430032K24Rik|BC002218|Col26a|Emid2|Emu2	collagen, type XXVI, alpha 1	protein-coding
mm_171310.1	chr3	94604824	94604825	-	1	NA	Intergenic	CpG	-22108	NM_029721	76742	Mm.28160	NM_029721	ENSMUSG00000028136	Snx27	5730552M22Rik|ESTM45|ESTM47|R75405	sorting nexin family member 27	protein-coding
mm_140940.1	chr17	24455239	24455257	-	1	NA	exon (NM_007893, exon 1 of 14)	exon (NM_007893, exon 1 of 14)	144	NM_001301784	13560	Mm.163132	NM_007893	ENSMUSG00000024137	E4f1	p120E4F|phi-AP3	E4F transcription factor 1	protein-coding
mm_21544.1	chr2	164054178	164054179	-	1	NA	3' UTR (NM_001291155, exon 7 of 7)	3' UTR (NM_001291155, exon 7 of 7)	16924	NM_025996	67145	Mm.23173	NM_025996	ENSMUSG00000018322	Tomm34	2610100K07Rik|TOM34	translocase of outer mitochondrial membrane 34	protein-coding
mm_95143.1	chr11	35459532	35459535	+	1	NA	intron (NM_011412, intron 4 of 35)	intron (NM_011412, intron 4 of 35)	-157283	NR_029799	723924		NR_029799	ENSMUSG00000065583	Mir218-2	Mirn218-2|mir-218-2	microRNA 218-2	ncRNA
mm_111402.1	chr12	91030071	91030103	-	1	NA	intron (NM_181815, intron 22 of 25)	intron (NM_181815, intron 22 of 25)	-15761	NR_045858	71349	Mm.442093	NR_045858		5430427M07Rik	-	RIKEN cDNA 5430427M07 gene	ncRNA
mm_64505.1	chr7	143476233	143476245	+	1	NA	exon (NM_008767, exon 2 of 11)	exon (NM_008767, exon 2 of 11)	1123	NM_001042760	18400	Mm.271740	NM_008767	ENSMUSG00000000154	Slc22a18	AW260131|BWR1A|BWSCR1A|HET|ITM|Impt1|Orctl2|Slc22a1l|TSSC5|p45-BWR1A	solute carrier family 22 (organic cation transporter), member 18	protein-coding
mm_46131.1	chr5	92675140	92675145	-	1	NA	promoter-TSS (NM_177230)	promoter-TSS (NM_177230)	-15	NM_177230	320696	Mm.209991	NM_177230	ENSMUSG00000050050	Ccdc158	4932413O14Rik	coiled-coil domain containing 158	protein-coding
mm_72451.1	chr8	83166037	83166054	+	1	NA	5' UTR (NM_001111304, exon 1 of 21)	5' UTR (NM_001111304, exon 1 of 21)	693	NM_027758	71310	Mm.24031	NM_027758	ENSMUSG00000031709	Tbc1d9	4933431N12Rik|AI847101|AW490653|C76116	TBC1 domain family, member 9	protein-coding
mm_51867.1	chr6	90550790	90550849	+	1	NA	promoter-TSS (NM_027406)	promoter-TSS (NM_027406)	-29	NM_027406	107747	Mm.30035	NM_027406	ENSMUSG00000030088	Aldh1l1	1810048F20Rik|FDH|Fthfd|Neut2	aldehyde dehydrogenase 1 family, member L1	protein-coding
mm_139409.1	chr17	52602286	52602295	+	1	NA	promoter-TSS (NM_001031811)	promoter-TSS (NM_001031811)	-419	NM_001031811	211468	Mm.399068	NM_001031811	ENSMUSG00000035580	Kcnh8	C130090D05Rik|ELK|ELK1|ELK3|Kv12.1	potassium voltage-gated channel, subfamily H (eag-related), member 8	protein-coding
mm_91576.1	chr10	40129215	40129228	-	1	NA	intron (NM_001114332, intron 1 of 5)	intron (NM_001114332, intron 1 of 5)	13033	NM_028247	72472	Mm.186778	NM_028247	ENSMUSG00000019838	Slc16a10	2610103N14Rik|9830169E08|Mct10|PRO0813|TAT1	solute carrier family 16 (monocarboxylic acid transporters), member 10	protein-coding
mm_49405.1	chr6	28427919	28427925	+	1	NA	promoter-TSS (NM_019569)	promoter-TSS (NM_019569)	21	NM_019569	56223	Mm.31708	NM_019569	ENSMUSG00000029707	Fscn3	-	fascin actin-bundling protein 3	protein-coding
mm_82454.1	chr9	15619617	15619627	-	1	NA	promoter-TSS (NR_040746)	promoter-TSS (NR_040746)	-235	NR_040746	78025	Mm.55983	NR_040746	ENSMUSG00000111299	4930540M03Rik	-	RIKEN cDNA 4930540M03 gene	ncRNA
mm_49916.1	chr6	39044400	39044411	+	1	NA	intron (NM_011539, intron 9 of 12)	B3A|SINE|B2	23181	NR_040523	69986	Mm.490941	NR_040523	ENSMUSG00000100121	1700025N23Rik	-	RIKEN cDNA 1700025N23 gene	ncRNA
mm_166500.1	chr6	3994033	3994036	+	1	NA	promoter-TSS (NM_010314)	promoter-TSS (NM_010314)	22	NM_010314	14699	Mm.95398	NM_010314	ENSMUSG00000029663	Gngt1	G(y)1|Gng1	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1	protein-coding
mm_161079.1	chr12	82340884	82340884	+	1	NA	5' UTR (NM_001167983, exon 5 of 24)	5' UTR (NM_001167983, exon 5 of 24)	29535	NM_172579	217692	Mm.261333	NM_172579	ENSMUSG00000042700	Sipa1l1	4931426N11Rik|AW213287|Spar|mKIAA0440	signal-induced proliferation-associated 1 like 1	protein-coding
mm_84083.1	chr9	58202302	58202322	-	1	NA	promoter-TSS (NM_177193)	promoter-TSS (NM_177193)	-27	NM_001161536	320563	Mm.186499	NM_177193	ENSMUSG00000051243	Islr2	B930052A04Rik|Linx|Mbu-3|mKIAA1465	immunoglobulin superfamily containing leucine-rich repeat 2	protein-coding
mm_173012.1	chrM	570	570	+	1	NA	NA	Intergenic	NA	NA								
mm_70057.1	chr7	142651394	142651404	-	1	NA	3' UTR (NM_010514, exon 4 of 4)	3' UTR (NM_010514, exon 4 of 4)	3597	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_56869.1	chr6	118562205	118562216	-	1	NA	promoter-TSS (NM_001081112)	promoter-TSS (NM_001081112)	46	NM_001081112	232339	Mm.276116	NM_001081112	ENSMUSG00000007827	Ankrd26	5730521P14Rik|BC008111|mKIAA1074	ankyrin repeat domain 26	protein-coding
mm_19802.1	chr2	110305620	110305643	-	1	NA	promoter-TSS (NM_130452)	promoter-TSS (NM_130452)	94	NM_130452	170442	Mm.27335	NM_130452	ENSMUSG00000041660	Bbox1	AI874739	butyrobetaine (gamma), 2-oxoglutarate dioxygenase 1 (gamma-butyrobetaine hydroxylase)	protein-coding
mm_73852.1	chr8	117702190	117702200	+	1	NA	exon (NM_008290, exon 1 of 5)	exon (NM_008290, exon 1 of 5)	249	NM_008290	15486	Mm.276466	NM_008290	ENSMUSG00000031844	Hsd17b2	AI194836|AI194967|AI255511	hydroxysteroid (17-beta) dehydrogenase 2	protein-coding
mm_144618.1	chr18	32837310	32837332	+	1	NA	promoter-TSS (NM_001110015)	promoter-TSS (NM_001110015)	-34	NR_045381	75795	Mm.382634	NR_045381	ENSMUSG00000097553	4930455D15Rik	-	RIKEN cDNA 4930455D15 gene	ncRNA
mm_116307.1	chr13	36734427	36734447	-	1	NA	promoter-TSS (NM_153529)	promoter-TSS (NM_153529)	40	NM_153529	68404	Mm.232930	NM_153529	ENSMUSG00000039114	Nrn1	0710008J23Rik|Cpg15|Nrn	neuritin 1	protein-coding
mm_59200.1	chr7	24507123	24507139	+	1	NA	promoter-TSS (NM_001290461)	promoter-TSS (NM_001290461)	44	NR_110958	232969	Mm.181332	NM_146183	ENSMUSG00000064264	Zfp428	2410005H09Rik|AV271806|AW047854|Znf428	zinc finger protein 428	protein-coding
mm_154445.1	chrM	1522	1544	-	1	NA	NA	Intergenic	NA	NA								
mm_78880.1	chr9	44499127	44499159	+	1	NA	promoter-TSS (NM_030256)	promoter-TSS (NM_030256)	7	NM_030256	80288	Mm.370270	NM_030256	ENSMUSG00000063382	Bcl9l	B9L|BC003321|BCL9-2|DLNB11	B cell CLL/lymphoma 9-like	protein-coding
mm_151174.1	chr19	53310496	53310552	+	1	NA	promoter-TSS (NM_001008542)	promoter-TSS (NM_001008542)	18	NM_001008542	17859	Mm.2154	NM_010847	ENSMUSG00000025025	Mxi1	ENSMUSG00000067085|Gm10197|Mad2|bHLHc11	MAX interactor 1, dimerization protein	protein-coding
mm_99882.1	chr11	109426373	109426389	+	1	NA	5' UTR (NM_001252193, exon 1 of 8)	5' UTR (NM_001252193, exon 1 of 8)	161	NM_001252193	13929	Mm.211850	NM_025275	ENSMUSG00000020610	Amz2	AA408420|ESTM12|X83328	archaelysin family metallopeptidase 2	protein-coding
mm_75101.1	chr8	34136665	34136667	-	1	NA	3' UTR (NM_026609, exon 4 of 4)	3' UTR (NM_026609, exon 4 of 4)	10073	NM_026609	68192	Mm.34212	NM_026609	ENSMUSG00000031513	Leprotl1	1110067H13Rik|1520402O14Rik|AI854296	leptin receptor overlapping transcript-like 1	protein-coding
mm_59220.1	chr7	24608380	24608393	+	1	NA	exon (NM_023154, exon 7 of 8)	exon (NM_023154, exon 7 of 8)	-2942	NM_001102613	232970	Mm.333663	NM_001102613	ENSMUSG00000074277	Phldb3	EG232970|ENSMUSG00000061511|Gm10102	pleckstrin homology like domain, family B, member 3	protein-coding
mm_149513.1	chr19	12010524	12010534	+	1	NA	Intergenic	Intergenic	26211	NM_146680	258675	Mm.271517	NM_146680	ENSMUSG00000067529	Olfr1423	MOR239-3	olfactory receptor 1423	protein-coding
mm_138019.1	chr17	33910247	33910261	+	1	NA	intron (NM_001199733, intron 1 of 7)	intron (NM_001199733, intron 1 of 7)	653	NM_001199733	13163	Mm.271809	NM_007829	ENSMUSG00000002307	Daxx	-	Fas death domain-associated protein	protein-coding
mm_89780.1	chr10	101681623	101681662	+	1	NA	5' UTR (NM_001205098, exon 1 of 8)	5' UTR (NM_001205098, exon 1 of 8)	155	NM_001205098	67569	Mm.25252	NM_026243	ENSMUSG00000019888	Mgat4c	9130411I17Rik|GntIVh	MGAT4 family, member C	protein-coding
mm_104321.1	chr11	93955901	93955930	-	1	NA	promoter-TSS (NM_001077529)	promoter-TSS (NM_001077529)	-132	NM_001077529	18103	Mm.1260	NM_008705	ENSMUSG00000020857	Nme2	NM23-H2|NM23B|nm23-M2	NME/NM23 nucleoside diphosphate kinase 2	protein-coding
mm_158293.1	chrX	112698665	112698689	-	1	NA	promoter-TSS (NM_181579)	promoter-TSS (NM_181579)	-26	NM_181579	69693	Mm.34964	NM_181579	ENSMUSG00000034607	Pof1b	2310066B14Rik	premature ovarian failure 1B	protein-coding
mm_8744.1	chr1	160251410	160251424	-	1	NA	intron (NM_001038621, intron 3 of 8)	intron (NM_001038621, intron 3 of 8)	-38525	NM_009786	12301	Mm.10702	NM_009786	ENSMUSG00000014226	Cacybp	SIP	calcyclin binding protein	protein-coding
mm_84863.1	chr9	78585150	78585173	-	1	NA	intron (NM_001276452, intron 1 of 10)	RLTR18B|LTR|ERVK	2884	NM_172773	235504	Mm.46932	NM_172773	ENSMUSG00000049624	Slc17a5	4631416G20Rik|4732491M05|AST|ISSD|NSD|SD|SIALIN|SIASD|SLD	solute carrier family 17 (anion/sugar transporter), member 5	protein-coding
mm_24226.1	chr3	88716917	88716921	+	1	NA	promoter-TSS (NM_001163310)	promoter-TSS (NM_001163310)	65	NM_001163310	19769	Mm.4009	NM_009069	ENSMUSG00000028057	Rit1	RIBB|ROC1|Rit	Ras-like without CAAX 1	protein-coding
mm_165775.1	chr3	129210017	129210024	+	1	NA	intron (NM_011098, intron 3 of 4)	intron (NM_011098, intron 3 of 4)	-3912	NM_001042502	18741	Mm.246804	NM_011098	ENSMUSG00000028023	Pitx2	9430085M16Rik|Brx1|Brx1b|Munc30|Otlx2|Ptx2|Rieg	paired-like homeodomain transcription factor 2	protein-coding
mm_133834.1	chr16	95924311	95924315	+	1	NA	intron (NR_040484, intron 1 of 3)	RMER17C|LTR|ERVK	4764	NR_040484	69776	Mm.120470	NR_040484	ENSMUSG00000086899	1600002D24Rik	-	RIKEN cDNA 1600002D24 gene	ncRNA
mm_161211.1	chr13	63015089	63015089	+	1	NA	5' UTR (NM_001289924, exon 2 of 17)	5' UTR (NM_001289924, exon 2 of 17)	50196	NM_001289924	72061	Mm.188105	NM_028079	ENSMUSG00000021458	2010111I01Rik	2300006M17Rik|AP-O|AW742919|Aopep|ApO|mir-23b|mir-24-1|mir-27b	RIKEN cDNA 2010111I01 gene	protein-coding
mm_111055.1	chr12	80110154	80110169	-	1	NA	exon (NM_007564, exon 2 of 2)	exon (NM_007564, exon 2 of 2)	2852	NM_007564	12192	Mm.235132	NM_007564	ENSMUSG00000021127	Zfp36l1	AW742437|AW743212|Berg36|Brf1|D530020L18Rik|ERF1|TIS11b|cMG1	zinc finger protein 36, C3H type-like 1	protein-coding
mm_107716.1	chr12	56253189	56253212	+	1	NA	promoter-TSS (NR_045048)	promoter-TSS (NR_045048)	-43	NR_045048	100503961	Mm.136732	NR_045048		Gm19990	-	predicted gene, 19990	ncRNA
mm_151159.1	chr19	53194285	53194297	+	1	NA	intron (NM_013758, intron 1 of 15)	intron (NM_013758, intron 1 of 15)	50294	NM_013758	27360	Mm.426080	NM_013758	ENSMUSG00000025026	Add3	AI463285|R75380	adducin 3 (gamma)	protein-coding
mm_119622.1	chr14	51129040	51129050	+	1	NA	promoter-TSS (NM_030098)	promoter-TSS (NM_030098)	-23	NM_030098	78416	Mm.103835	NM_030098	ENSMUSG00000021880	Rnase6	9530043P15Rik|BB119466	ribonuclease, RNase A family, 6	protein-coding
mm_114797.1	chr13	89739480	89739493	+	1	NA	intron (NM_172955, intron 1 of 5)	CpG	3026	NM_001081249	13003	Mm.158700	NM_019389	ENSMUSG00000021614	Vcan	5430420N07Rik|9430051N09|Cspg2|DPEAAE|NG2|PG-M|PG-M(V0)|PG-M(V1)|hdf	versican	protein-coding
mm_20272.1	chr2	126797811	126797826	-	1	NA	exon (NM_001164325, exon 34 of 39)	exon (NM_001164325, exon 34 of 39)	-14358	NM_029163	75083	Mm.389373	NM_029163	ENSMUSG00000027364	Usp50	1700086G18Rik|4930511O11Rik	ubiquitin specific peptidase 50	protein-coding
mm_26885.1	chr3	18097025	18097026	-	1	NA	intron (NM_007825, intron 3 of 5)	intron (NM_007825, intron 3 of 5)	42700	NM_021560	59058	Mm.149938	NM_021560	ENSMUSG00000025128	Bhlhe22	Beta3|Beta3a|Bhlhb5	basic helix-loop-helix family, member e22	protein-coding
mm_55712.1	chr6	72960726	72960747	-	1	NA	Intergenic	MLT1H1|LTR|ERVL-MaLR	-1988	NM_001190327	19240	Mm.3532	NM_025284	ENSMUSG00000079523	Tmsb10	Ptmb10|Tb10	thymosin, beta 10	protein-coding
mm_8770.1	chr1	160878647	160878678	-	1	NA	Intergenic	Intergenic	-27749	NM_001024952	381305	Mm.329667	NM_001024952	ENSMUSG00000040423	Rc3h1	5730557L09Rik|Gm551|N28103|mKIAA2025	RING CCCH (C3H) domains 1	protein-coding
mm_145934.1	chr18	67287824	67287826	+	1	NA	Intergenic	RMER10A|LTR|ERVL	-1398	NM_053261	114663	Mm.34079	NM_053261	ENSMUSG00000024525	Impa2	2210415D20Rik|AI326924|AW259601	inositol (myo)-1(or 4)-monophosphatase 2	protein-coding
mm_171245.1	chr3	75655178	75655180	-	1	NA	intron (NR_040539, intron 1 of 2)	MMERVK9C_I-int|LTR|ERVK	552	NR_040539	69193	Mm.374088	NR_040539	ENSMUSG00000099370	Platr10	2410007B07Rik	pluripotency associated transcript 10	ncRNA
mm_121448.1	chr14	120430690	120430786	+	1	NA	3' UTR (NM_207515, exon 8 of 8)	3' UTR (NM_207515, exon 8 of 8)	-47723	NM_029519	76108	Mm.261448	NM_029519	ENSMUSG00000051615	Rap2a	5830461H18Rik	RAS related protein 2a	protein-coding
mm_144278.1	chr18	11722649	11722667	+	1	NA	exon (NM_001081223, exon 12 of 19)	exon (NM_001081223, exon 12 of 19)	65309	NM_001081223	225182	Mm.154275	NM_175458	ENSMUSG00000041238	Rbbp8	9930104E21Rik|CtIP|RBBP-8|RIM|SAE2	retinoblastoma binding protein 8	protein-coding
mm_156764.1	chrX	160529930	160529955	+	1	NA	exon (NM_001177878, exon 5 of 33)	exon (NM_001177878, exon 5 of 33)	27508	NM_001177878	110094	Mm.350712	NM_172783	ENSMUSG00000031295	Phka2	6330505C01Rik|D330034O08|Phk	phosphorylase kinase alpha 2	protein-coding
mm_66969.1	chr7	63212515	63212531	-	1	NA	promoter-TSS (NM_007390)	promoter-TSS (NM_007390)	3	NM_007390	11441	Mm.113464	NM_007390	ENSMUSG00000030525	Chrna7	Acra7|alpha7|nAchR	cholinergic receptor, nicotinic, alpha polypeptide 7	protein-coding
mm_30870.1	chr4	32165114	32165130	+	1	NA	Intergenic	Intergenic	201015	NM_172688	26409	Mm.258589	NM_009316	ENSMUSG00000028284	Map3k7	B430101B05|C87327|Tak1	mitogen-activated protein kinase kinase kinase 7	protein-coding
mm_169469.1	chr14	67008883	67008884	-	1	NA	promoter-TSS (NM_009761)	promoter-TSS (NM_009761)	-6	NM_009761	12177	Mm.29820	NM_009761	ENSMUSG00000022051	Bnip3l	C86132|D14Ertd719e|Nip3L|Nix	BCL2/adenovirus E1B interacting protein 3-like	protein-coding
mm_44139.1	chr5	150152887	150152887	+	1	NA	Intergenic	Intergenic	-107043	NM_172887	320365	Mm.216590	NM_172887	ENSMUSG00000056602	Fry	13CDNA73|9330186A19Rik|AF346502|AI462658|C87180|D930046M03|cg003|mKIAA4143	FRY microtubule binding protein	protein-coding
mm_148044.1	chr18	70472430	70472520	-	1	NA	promoter-TSS (NM_001289649)	promoter-TSS (NM_001289649)	5	NM_172967	269033	Mm.87470	NM_172967	ENSMUSG00000044906	4930503L19Rik	9930107F24|BB148262|Lars|Las2	RIKEN cDNA 4930503L19 gene	protein-coding
mm_150264.1	chr19	34217232	34217254	+	1	NA	intron (NM_029682, intron 1 of 10)	MLT1N2|LTR|ERVL-MaLR	24973	NM_029682	76630	Mm.130952	NM_029682	ENSMUSG00000024776	Stambpl1	1700095N21Rik|8230401J17Rik|ALMalpha|AMSH-FP	STAM binding protein like 1	protein-coding
mm_93219.1	chr10	95145536	95145547	-	1	NA	intron (NR_131146, intron 1 of 3)	intron (NR_131146, intron 1 of 3)	284	NR_131146	628062		NR_131146		Gm29684	-	predicted gene, 29684	ncRNA
mm_99546.1	chr11	103347165	103347195	+	1	NA	intron (NR_045346, intron 3 of 3)	intron (NR_045346, intron 3 of 3)	2427	NR_045346	653030	Mm.440684	NR_045346	ENSMUSG00000085887	Arhgap27os3	F830206d12rik|Gm11648|OTTMUSG00000003073	Rho GTPase activating protein 27, opposite strand 3	ncRNA
mm_56505.1	chr6	99339376	99339386	-	1	NA	intron (NM_001347345, intron 2 of 19)	intron (NM_001347345, intron 2 of 19)	-72866	NM_001197321	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_170629.1	chr1	9782329	9782347	-	1	NA	Intergenic	Intergenic	-15792	NM_133220	170755	Mm.336410	NM_133220	ENSMUSG00000025915	Sgk3	2510015P22Rik|A330005P07Rik|Cisk|fy|fz	serum/glucocorticoid regulated kinase 3	protein-coding
mm_109523.1	chr12	111536042	111536046	+	1	NA	Intergenic	Intergenic	-2057	NM_178041	217869	Mm.271222	NM_173363	ENSMUSG00000021282	Eif5	2810011H21Rik|D12Ertd549e	eukaryotic translation initiation factor 5	protein-coding
mm_152821.1	chr19	23136278	23136303	-	1	NA	Intergenic	CpG	-4936	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_44617.1	chr5	25529578	25529604	-	1	NA	promoter-TSS (NR_027388)	promoter-TSS (NR_027388)	-427	NR_027388	73571	Mm.105263	NR_027388	ENSMUSG00000101856	1700096K18Rik	-	RIKEN cDNA 1700096K18 gene	ncRNA
mm_6372.1	chr1	72536985	72536999	-	1	NA	promoter-TSS (NM_001045533)	promoter-TSS (NM_001045533)	-428	NM_001045533	381270	Mm.337023	NM_001045533	ENSMUSG00000039372	March4	BC056494|mKIAA1399	membrane-associated ring finger (C3HC4) 4	protein-coding
mm_20896.1	chr2	148875605	148875616	-	1	NA	promoter-TSS (NM_009976)	promoter-TSS (NM_009976)	-98	NM_009976	13010	Mm.4263	NM_009976	ENSMUSG00000027447	Cst3	CysC	cystatin C	protein-coding
mm_115009.1	chr13	98354235	98354250	+	1	NA	promoter-TSS (NM_008242)	promoter-TSS (NM_008242)	-3	NM_008242	15229	Mm.347441	NM_008242	ENSMUSG00000078302	Foxd1	AI385632|BF-2|FREAC4|Hfh10|Hfhbf2	forkhead box D1	protein-coding
mm_21121.1	chr2	153632680	153632757	-	1	NA	promoter-TSS (NM_133850)	promoter-TSS (NM_133850)	63	NM_001195390	99311	Mm.294478	NM_133850	ENSMUSG00000056941	Commd7	2310010I22Rik|AW060956|mU3	COMM domain containing 7	protein-coding
mm_26793.1	chr3	9799353	9799376	-	1	NA	intron (NM_001195031, intron 1 of 8)	B1F|SINE|Alu	34315	NM_053182	94212	Mm.23897	NM_053182	ENSMUSG00000027508	Pag1	Cbp|F730007C19Rik|Pag	phosphoprotein associated with glycosphingolipid microdomains 1	protein-coding
mm_18793.1	chr2	73808981	73809012	-	1	NA	Intergenic	Intergenic	-33650	NM_001113246	108699	Mm.257073	NM_029716	ENSMUSG00000056486	Chn1	0610007I19Rik|0710001E19Rik|1700112L09Rik|2900046J01Rik|AI413815|ARHGAP2	chimerin 1	protein-coding
mm_107710.1	chr12	55599425	55599429	+	1	NA	5' UTR (NM_020287, exon 1 of 1)	5' UTR (NM_020287, exon 1 of 1)	510	NM_020287	56856	Mm.114886	NM_020287	ENSMUSG00000045440	Insm2	Mlt1	insulinoma-associated 2	protein-coding
mm_94461.1	chr11	6416330	6416345	+	1	NA	intron (NM_008907, intron 1 of 4)	CpG	467	NM_008907	268373	Mm.5246	NM_008907	ENSMUSG00000071866	Ppia	2700098C05|Cphn|CyP-18|CypA	peptidylprolyl isomerase A	protein-coding
mm_135314.1	chr16	38713324	38713342	-	1	NA	promoter-TSS (NM_020260)	promoter-TSS (NM_020260)	-298	NM_020260	12549	Mm.370848	NM_020260	ENSMUSG00000022799	Arhgap31	5830477L08Rik|AU041750|Cdgap|D330026I07Rik	Rho GTPase activating protein 31	protein-coding
mm_98685.1	chr11	96292454	96292508	+	1	NA	intron (NR_131758, intron 2 of 2)	intron (NR_131758, intron 2 of 2)	5835	NM_010460	15415	Mm.390366	NM_010460	ENSMUSG00000038721	Hoxb7	AI325018|Hox-2.3	homeobox B7	protein-coding
mm_97364.1	chr11	77507311	77507332	+	1	NA	TTS (NM_001024920)	TTS (NM_001024920)	5952	NM_001024920	216964	Mm.341211	NM_001024920	ENSMUSG00000044328	Trp53i13	2410019G02Rik|Tp53i13	transformation related protein 53 inducible protein 13	protein-coding
mm_57134.1	chr6	122606547	122606554	-	1	NA	exon (NM_008108, exon 2 of 2)	exon (NM_008108, exon 2 of 2)	3537	NM_008108	14562	Mm.299742	NM_008108	ENSMUSG00000030117	Gdf3	C78318|Gdf-3|Vgr-2|Vgr2|ecat9	growth differentiation factor 3	protein-coding
mm_167452.1	chr8	122903129	122903132	+	1	NA	intron (NR_037865, intron 4 of 13)	intron (NR_037865, intron 4 of 13)	54756	NM_007662	12555	Mm.1976	NM_007662	ENSMUSG00000031962	Cdh15	AI323380|Cdh14|Mcad	cadherin 15	protein-coding
mm_107703.1	chr12	55467946	55467951	+	1	NA	intron (NR_035430, intron 2 of 3)	intron (NR_035430, intron 2 of 3)	24699	NM_010907	18035	Mm.170515	NM_010907	ENSMUSG00000021025	Nfkbia	AI462015|Nfkbi	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, alpha	protein-coding
mm_162118.1	chrX	57043148	57043148	+	1	NA	promoter-TSS (NM_009766)	promoter-TSS (NM_009766)	74	NM_009766	12209	Mm.10687	NM_009766	ENSMUSG00000031130	Brs3	BRS-3	bombesin-like receptor 3	protein-coding
mm_171426.1	chr4	134164551	134164564	+	1	NA	intron (NM_144527, intron 3 of 13)	RLTR4_Mm|LTR|ERV1	22528	NM_144527	70012	Mm.26542	NM_144527	ENSMUSG00000037443	Cep85	2410030J07Rik|AI173272|AI173504|Ccdc21	centrosomal protein 85	protein-coding
mm_130514.1	chr15	98863938	98863960	-	1	NA	exon (NM_001033276, exon 11 of 55)	exon (NM_001033276, exon 11 of 55)	7256	NM_001033276	381022	Mm.264889	NM_001033276	ENSMUSG00000048154	Kmt2d	ALR|BC032281|BC058659|C430014K11Rik|KMT2B|Mll2|Mll4	lysine (K)-specific methyltransferase 2D	protein-coding
mm_7710.1	chr1	130462471	130462519	-	1	NA	intron (NM_010016, intron 1 of 9)	intron (NM_010016, intron 1 of 9)	249	NM_010016	13136	Mm.101591	NM_010016	ENSMUSG00000026399	Cd55	Daf|Daf-GPI|Daf1|GPI-DAF	CD55 molecule, decay accelerating factor for complement	protein-coding
mm_47551.1	chr5	124354540	124354554	-	1	NA	promoter-TSS (NM_013812)	promoter-TSS (NM_013812)	81	NM_013812	13445	Mm.391838	NM_013812	ENSMUSG00000029394	Cdk2ap1	Apc10|Cdkap1|DORC1|Doc1|ST19|doc-1|p12	CDK2 (cyclin-dependent kinase 2)-associated protein 1	protein-coding
mm_41581.1	chr5	93173678	93173681	+	1	NA	3' UTR (NM_001009818, exon 10 of 10)	3' UTR (NM_001009818, exon 10 of 10)	32816	NM_017367	12453	Mm.250419	NM_017367	ENSMUSG00000063015	Ccni	-	cyclin I	protein-coding
mm_137686.1	chr17	28858512	28858553	+	1	NA	5' UTR (NM_001034885, exon 1 of 10)	5' UTR (NM_001034885, exon 1 of 10)	121	NM_001034885	433091	Mm.328925	NM_001034885	ENSMUSG00000043286	Pnpla1	-	patatin-like phospholipase domain containing 1	protein-coding
mm_7391.1	chr1	111864870	111864929	-	1	NA	promoter-TSS (NM_001081316)	promoter-TSS (NM_001081316)	19	NM_001081316	319901	Mm.103468	NM_001081316	ENSMUSG00000038702	Dsel	9330132E09Rik|DS-epi2	dermatan sulfate epimerase-like	protein-coding
mm_88594.1	chr10	79777262	79777280	+	1	NA	promoter-TSS (NM_031380)	promoter-TSS (NM_031380)	-3	NM_031380	83554	Mm.251710	NM_031380	ENSMUSG00000020325	Fstl3	E030038F23Rik|Flrg	follistatin-like 3	protein-coding
mm_36345.1	chr4	73771122	73771134	-	1	NA	intron (NM_001017427, intron 3 of 17)	intron (NM_001017427, intron 3 of 17)	19474	NM_001017427	242505	Mm.389582	NM_001017427	ENSMUSG00000043003	Rasef	BC030882|RAB45	RAS and EF hand domain containing	protein-coding
mm_53077.1	chr6	124935620	124935646	+	1	NA	3' UTR (NM_001170341, exon 9 of 9)	3' UTR (NM_001170341, exon 9 of 9)	4245	NM_001170341	30853	Mm.29737	NM_145385	ENSMUSG00000030120	Mlf2	AI256856|AU018944|C77284	myeloid leukemia factor 2	protein-coding
mm_91228.1	chr10	22299445	22299484	-	1	NA	intron (NM_009018, intron 5 of 5)	intron (NM_009018, intron 5 of 5)	-7256	NR_015465	606736	Mm.387042	NR_015465	ENSMUSG00000097352	C920009B18Rik	-	RIKEN cDNA C920009B18 gene	ncRNA
mm_107109.1	chr12	17881937	17881976	+	1	NA	Intergenic	CpG	191142	NM_016677	53602	Mm.313619	NM_016677	ENSMUSG00000071379	Hpcal1	NVP-3|Nvp3|VILIP3|Vnsl3|Vsnl3	hippocalcin-like 1	protein-coding
mm_145978.1	chr18	67972340	67972351	+	1	NA	intron (NM_172631, intron 1 of 5)	intron (NM_172631, intron 1 of 5)	39088	NM_172631	52662	Mm.440183	NM_172631	ENSMUSG00000024544	Ldlrad4	8230401C20Rik|A430083H02|A430108L08Rik|C18orf1|D18Ertd653e|D330030L18Rik	low density lipoprotein receptor class A domain containing 4	protein-coding
mm_134095.1	chr16	9919756	9919768	-	1	NA	intron (NM_008170, intron 1 of 11)	ID_B1|SINE|B4	72771	NM_008170	14811	Mm.2953	NM_008170	ENSMUSG00000059003	Grin2a	GluN2A|NMDAR2A|NR2A	glutamate receptor, ionotropic, NMDA2A (epsilon 1)	protein-coding
mm_131136.1	chr16	6348506	6348521	+	1	NA	intron (NM_021477, intron 2 of 16)	intron (NM_021477, intron 2 of 16)	372926	NR_045799	68238	Mm.434605	NR_045799	ENSMUSG00000101481	1700123O21Rik	-	RIKEN cDNA 1700123O21 gene	ncRNA
mm_68105.1	chr7	102018140	102018206	-	1	NA	promoter-TSS (NM_010531)	promoter-TSS (NM_010531)	-18	NM_010531	16068	Mm.422756	NM_010531	ENSMUSG00000070427	Il18bp	IL-18BP|Igifbp|MC54L	interleukin 18 binding protein	protein-coding
mm_4601.1	chr1	178406053	178406070	+	1	NA	5' UTR (NM_026626, exon 1 of 7)	5' UTR (NM_026626, exon 1 of 7)	180	NM_026626	68226	Mm.252132	NM_026626	ENSMUSG00000026495	Efcab2	1700073K01Rik|D830011E08Rik	EF-hand calcium binding domain 2	protein-coding
mm_111283.1	chr12	85373460	85373470	-	1	NA	intron (NM_026775, intron 1 of 4)	B3|SINE|B2	1252	NM_026775	68581	Mm.379159	NM_026775	ENSMUSG00000021248	Tmed10	1110014C03Rik|Tmp21|p23|p24delta1	transmembrane p24 trafficking protein 10	protein-coding
mm_35092.1	chr4	8456558	8456558	-	1	NA	Intergenic	Intergenic	-79086	NM_021518	59021	Mm.397471	NM_021518	ENSMUSG00000047187	Rab2a	9330148M11Rik|C80220|Rab2	RAB2A, member RAS oncogene family	protein-coding
mm_85492.1	chr9	106136015	106136019	-	1	NA	Intergenic	Intergenic	-18107	NR_029549	387153		NR_029549	ENSMUSG00000065407	Mir135a-1	Mir135a01|Mirn135|Mirn135a-1|mir-135a-1	microRNA 135a-1	ncRNA
mm_32431.1	chr4	107179857	107179860	+	1	NA	intron (NM_029565, intron 1 of 7)	intron (NM_029565, intron 1 of 7)	1228	NM_029565	56374	Mm.291192	NM_029565	ENSMUSG00000028618	Tmem59	1110001M20Rik|3110046P06Rik|AI256529|D4Ertd20e|MTDCF1|ORF18	transmembrane protein 59	protein-coding
mm_50927.1	chr6	57640496	57640498	+	1	NA	intron (NM_025992, intron 13 of 22)	MYSERV-int|LTR|ERVK	51581	NM_025574	66459	Mm.44201	NM_025574	ENSMUSG00000043162	Pyurf	2610022G08Rik|AI847956|Prey	Pigy upstream reading frame	protein-coding
mm_114183.1	chr13	55647621	55647637	+	1	NA	exon (NM_001282055, exon 5 of 23)	exon (NM_001282055, exon 5 of 23)	12630	NM_001282055	212880	Mm.202725	NM_145975	ENSMUSG00000021500	Ddx46	2200005K02Rik|8430438J23Rik|AI325430|AI957095|mKIAA0801	DEAD (Asp-Glu-Ala-Asp) box polypeptide 46	protein-coding
mm_58041.1	chr6	136826094	136826096	-	1	NA	5' UTR (NM_021714, exon 2 of 12)	5' UTR (NM_021714, exon 2 of 12)	2121	NM_021714	60321	Mm.141197	NM_021714	ENSMUSG00000030216	Wbp11	2510026P17Rik|D6Wsu113e|Npwbp|SIPP1	WW domain binding protein 11	protein-coding
mm_22301.1	chr2	180334719	180334729	-	1	NA	promoter-TSS (NM_008093)	promoter-TSS (NM_008093)	-45	NM_008093	14464	Mm.388880	NM_008093	ENSMUSG00000015627	Gata5	-	GATA binding protein 5	protein-coding
mm_106424.1	chr11	119300005	119300034	-	1	NA	promoter-TSS (NM_138669)	promoter-TSS (NM_138669)	24	NM_138669	192170	Mm.197555	NM_138669	ENSMUSG00000025580	Eif4a3	2400003O03Rik|Ddx48|eIF4A-III|mKIAA0111	eukaryotic translation initiation factor 4A3	protein-coding
mm_61401.1	chr7	73375841	73375856	+	1	NA	promoter-TSS (NR_040324)	promoter-TSS (NR_040324)	-74	NR_040324	319783	Mm.349813	NR_040324	ENSMUSG00000097756	A730056A06Rik	C76391	RIKEN cDNA A730056A06 gene	ncRNA
mm_9159.1	chr1	170960090	170960100	-	1	NA	TTS (NM_001077189)	TTS (NM_001077189)	15976	NM_001077189	14130	Mm.425062	NM_010187	ENSMUSG00000026656	Fcgr2b	AI528646|CD32|F630109E10Rik|Fc[g]RII|FcgRII|Fcgr2|Fcgr2a|Fcr-2|Fcr-3|Ly-17|Ly-m20|LyM-1|Lym-1|fcRII	Fc receptor, IgG, low affinity IIb	protein-coding
mm_96457.1	chr11	67586610	67586618	+	1	NA	5' UTR (NM_001109657, exon 1 of 14)	5' UTR (NM_001109657, exon 1 of 14)	114	NM_001109657	14457	Mm.40338	NM_008088	ENSMUSG00000033066	Gas7	AW124766|B230343A10Rik|Gas7-cb	growth arrest specific 7	protein-coding
mm_36086.1	chr4	58206769	58206790	-	1	NA	promoter-TSS (NM_022814)	promoter-TSS (NM_022814)	-183	NM_022814	64817	Mm.261024	NM_022814	ENSMUSG00000028369	Svep1	1110021D17Rik|4833413O10Rik|AA387071|D430029O09Rik|Polydom	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	protein-coding
mm_61186.1	chr7	62416478	62416487	+	1	NA	Intergenic	Intergenic	3657	NM_011746	22652	Mm.146	NM_011746	ENSMUSG00000070527	Mkrn3	D7H15S9-1|Zfp127	makorin, ring finger protein, 3	protein-coding
mm_37624.1	chr4	127329099	127329155	-	1	NA	promoter-TSS (NM_008126)	promoter-TSS (NM_008126)	-2	NM_008126	14620	Mm.90003	NM_008126	ENSMUSG00000042367	Gjb3	Cnx31|Cx31|D4Wsu144e|Gjb-3	gap junction protein, beta 3	protein-coding
mm_28073.1	chr3	84304734	84304753	-	1	NA	promoter-TSS (NM_001271726)	promoter-TSS (NM_001271726)	32	NM_001271726	80890	Mm.44876	NM_030706	ENSMUSG00000027993	Trim2	mKIAA0517|narf	tripartite motif-containing 2	protein-coding
mm_25043.1	chr3	98291285	98291299	+	1	NA	exon (NM_008256, exon 2 of 10)	exon (NM_008256, exon 2 of 10)	10861	NM_008256	15360	Mm.289131	NM_008256	ENSMUSG00000027875	Hmgcs2	1300002P16|mHS	3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2	protein-coding
mm_47504.1	chr5	124035736	124035752	-	1	NA	Intergenic	Intergenic	-3484	NM_177876	330192	Mm.4079	NM_177876	ENSMUSG00000066278	Vps37b	2300007F24Rik|AI415429|BC026744	vacuolar protein sorting 37B	protein-coding
mm_111896.1	chr12	108680451	108680454	-	1	NA	intron (NM_001163394, intron 8 of 13)	intron (NM_001163394, intron 8 of 13)	21832	NR_029771	723909		NR_029771	ENSMUSG00000065436	Mir342	Mirn342|mmu-mir-342	microRNA 342	ncRNA
mm_91947.1	chr10	60938100	60938114	-	1	NA	promoter-TSS (NR_033616)	promoter-TSS (NR_033616)	25	NR_033616	73616	Mm.159038	NR_033616	ENSMUSG00000037247	Pldi	1700125F08Rik|Poldi	polymorphic derived intron containing	ncRNA
mm_85884.1	chr9	111042311	111042323	-	1	NA	3' UTR (NM_008522, exon 17 of 17)	3' UTR (NM_008522, exon 17 of 17)	14927	NM_001302377	54199	Mm.7336	NM_017466	ENSMUSG00000043953	Ccrl2	1810047I05Rik|Ackr5|CCR11|Cmkbr1l2|E01|L-CCR	chemokine (C-C motif) receptor-like 2	protein-coding
mm_30244.1	chr3	146500089	146500122	-	1	NA	promoter-TSS (NM_001316756)	promoter-TSS (NM_001316756)	269	NM_010318	14707	Mm.140804	NM_010318	ENSMUSG00000068523	Gng5	G(y)5	guanine nucleotide binding protein (G protein), gamma 5	protein-coding
mm_134622.1	chr16	21650037	21650043	-	1	NA	3' UTR (NM_001001881, exon 2 of 2)	3' UTR (NM_001001881, exon 2 of 2)	44625	NM_001001881	72190	Mm.131606	NM_001001881	ENSMUSG00000043391	2510009E07Rik	AI194952	RIKEN cDNA 2510009E07 gene	protein-coding
mm_78431.1	chr9	31906016	31906036	+	1	NA	intron (NM_013800, intron 1 of 3)	intron (NM_013800, intron 1 of 3)	7259	NM_013800	12023	Mm.261044	NM_013800	ENSMUSG00000032033	Barx2	2310006E12Rik|Barx2b	BarH-like homeobox 2	protein-coding
mm_38847.1	chr4	149247317	149247327	-	1	NA	exon (NM_001290995, exon 19 of 49)	exon (NM_001290995, exon 19 of 49)	60376	NM_207682	16561	Mm.402393	NM_008441	ENSMUSG00000063077	Kif1b	A530096N05Rik|AI448212|AI506502|D4Mil1e|KIF1Bp130|KIF1Bp204	kinesin family member 1B	protein-coding
mm_7424.1	chr1	119821313	119821316	-	1	NA	intron (NM_019933, intron 1 of 26)	B1_Mus1|SINE|Alu	15757	NM_019933	19258	Mm.458796	NM_019933	ENSMUSG00000026384	Ptpn4	PTPMEG|Ptn4|TEP|TEP/mPTPMEG|hPTP-MEG	protein tyrosine phosphatase, non-receptor type 4	protein-coding
mm_27647.1	chr3	63899411	63899432	-	1	NA	Intergenic	Intergenic	29964	NM_177856	329659	Mm.39342	NM_177856	ENSMUSG00000048581	E130311K13Rik	-	RIKEN cDNA E130311K13 gene	protein-coding
mm_52373.1	chr6	113077388	113077402	+	1	NA	promoter-TSS (NR_027008)	promoter-TSS (NR_027008)	-151	NR_027008	14910	Mm.280950	NR_027008	ENSMUSG00000086429	Gt(ROSA)26Sor	AV258896|Gtrgeo26|Gtrosa26|R26|ROSA26|Thumpd3as1	gene trap ROSA 26, Philippe Soriano	ncRNA
mm_140116.1	chr17	78916534	78916560	+	1	NA	promoter-TSS (NM_001177403)	promoter-TSS (NM_001177403)	48	NM_001177402	68554	Mm.391820	NM_001177402	ENSMUSG00000062691	Cebpzos	1110001A16Rik	CCAAT/enhancer binding protein (C/EBP), zeta, opposite strand	protein-coding
mm_100684.1	chr11	3503002	3503017	-	1	NA	exon (NM_172439, exon 2 of 13)	exon (NM_172439, exon 2 of 13)	1812	NM_172439	170835	Mm.24313	NM_172439	ENSMUSG00000034570	Inpp5j	Pib5pa|Pipp	inositol polyphosphate 5-phosphatase J	protein-coding
mm_164184.1	chr15	76280988	76281000	-	1	NA	intron (NM_028852, intron 1 of 4)	ORR1D1|LTR|ERVL-MaLR	-11155	NR_045747	100038659	Mm.448549	NR_045747		Mirt2	ENSMUSG00000075583|Gm10872|Gm24562	myocardial infraction associated transcript 2	ncRNA
mm_140990.1	chr17	24850083	24850118	-	1	NA	promoter-TSS (NM_024284)	promoter-TSS (NM_024284)	202	NM_023480	68636	Mm.347964	NM_023480	ENSMUSG00000045316	Fahd1	1110025H10Rik|AV002085	fumarylacetoacetate hydrolase domain containing 1	protein-coding
mm_27028.1	chr3	26153415	26153466	-	1	NA	promoter-TSS (NM_001163387)	promoter-TSS (NM_001163387)	-133	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_155427.1	chrX	73492741	73492797	+	1	NA	exon (NM_007542, exon 5 of 8)	exon (NM_007542, exon 5 of 8)	9168	NM_007542	12111	Mm.2608	NM_007542	ENSMUSG00000031375	Bgn	BG|DSPG1|PG-S1|PGI|SLRR1A	biglycan	protein-coding
mm_90012.1	chr10	115315032	115315054	+	1	NA	intron (NM_024454, intron 1 of 6)	intron (NM_024454, intron 1 of 6)	548	NM_024454	216344	Mm.21936	NM_024454	ENSMUSG00000020132	Rab21	9630024B22	RAB21, member RAS oncogene family	protein-coding
mm_135024.1	chr16	32520550	32520573	-	1	NA	Intergenic	Intergenic	24280	NM_199309	245308	Mm.76859	NM_199309	ENSMUSG00000052363	Zdhhc19	Gm1744|Gm616	zinc finger, DHHC domain containing 19	protein-coding
mm_78860.1	chr9	44397146	44397154	+	1	NA	promoter-TSS (NM_001293630)	promoter-TSS (NM_001293630)	55	NM_001293630	14385	Mm.30087	NM_008063	ENSMUSG00000032114	Slc37a4	100043178|G6PT|G6pt1|GSD-1b|mG6PT	solute carrier family 37 (glucose-6-phosphate transporter), member 4	protein-coding
mm_62737.1	chr7	111028738	111028750	+	1	NA	promoter-TSS (NM_009431)	promoter-TSS (NM_009431)	-207	NM_009431	22083	Mm.255858	NM_009431	ENSMUSG00000005609	Ctr9	AA409336|Sh2bp1|Tsbp|Tsp|mKIAA0155	CTR9 homolog, Paf1/RNA polymerase II complex component	protein-coding
mm_60251.1	chr7	43776267	43776298	+	1	NA	promoter-TSS (NM_019974)	promoter-TSS (NM_019974)	-47	NM_019974	56538	Mm.154276	NM_019974	ENSMUSG00000067616	Klk11	2310015I08Rik|Prss20|TLSP	kallikrein related-peptidase 11	protein-coding
mm_662.1	chr1	40441286	40441296	+	1	NA	intron (NM_001025602, intron 2 of 10)	intron (NM_001025602, intron 2 of 10)	1662	NM_010743	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_96470.1	chr11	67652480	67652495	+	1	NA	intron (NM_001109657, intron 4 of 13)	intron (NM_001109657, intron 4 of 13)	-42839	NM_009038	19674	Mm.439726	NM_009038	ENSMUSG00000020907	Rcvrn	CAR|S-modulin	recoverin	protein-coding
mm_123855.1	chr14	70994413	70994423	-	1	NA	Intergenic	Intergenic	104311	NM_001302094	14586	Mm.32619	NM_008115	ENSMUSG00000022103	Gfra2	-	glial cell line derived neurotrophic factor family receptor alpha 2	protein-coding
mm_47503.1	chr5	124035690	124035714	-	1	NA	Intergenic	Intergenic	-3442	NM_177876	330192	Mm.4079	NM_177876	ENSMUSG00000066278	Vps37b	2300007F24Rik|AI415429|BC026744	vacuolar protein sorting 37B	protein-coding
mm_59408.1	chr7	27119750	27119765	+	1	NA	promoter-TSS (NM_007817)	promoter-TSS (NM_007817)	-198	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_59014.1	chr7	19242129	19242131	+	1	NA	intron (NM_207525, intron 1 of 1)	U1|snRNA|snRNA	13741	NM_207525	403187	Mm.239583	NM_207525	ENSMUSG00000052214	Opa3	D630048P19Rik|Gm1425|Gm472	optic atrophy 3	protein-coding
mm_165607.1	chr3	51636732	51636752	+	1	NA	Intergenic	Intergenic	-24437	NM_174995	211666	Mm.24679	NM_174995	ENSMUSG00000074604	Mgst2	GST2|MGST-II	microsomal glutathione S-transferase 2	protein-coding
mm_33873.1	chr4	136143817	136143832	+	1	NA	promoter-TSS (NM_008321)	promoter-TSS (NM_008321)	2	NM_008321	15903	Mm.110	NM_008321	ENSMUSG00000007872	Id3	Hlh462|Idb3|bHLHb25	inhibitor of DNA binding 3	protein-coding
mm_13589.1	chr2	112492895	112492905	+	1	NA	promoter-TSS (NM_028844)	promoter-TSS (NM_028844)	-64	NM_028844	74268	Mm.315125	NM_028844	ENSMUSG00000003604	Aven	1700013A01Rik|1700056A21Rik|mAven-L|mAven-S	apoptosis, caspase activation inhibitor	protein-coding
mm_52888.1	chr6	122577796	122577802	+	1	NA	TTS (NM_031159)	TTS (NM_031159)	23990	NM_009645	11628	Mm.391503	NM_009645	ENSMUSG00000040627	Aicda	Aid|Arp2	activation-induced cytidine deaminase	protein-coding
mm_11894.1	chr2	49795664	49795688	+	1	NA	intron (NM_027990, intron 1 of 9)	intron (NM_027990, intron 1 of 9)	7990	NM_027990	71897	Mm.41381	NM_027990	ENSMUSG00000026765	Lypd6b	2310010M24Rik|AW049525	LY6/PLAUR domain containing 6B	protein-coding
mm_92442.1	chr10	77515776	77515818	-	1	NA	promoter-TSS (NM_133998)	promoter-TSS (NM_133998)	16	NM_133998	108707	Mm.259547	NM_133998	ENSMUSG00000032977	Fam207a	1810008A18Rik|AI303072	family with sequence similarity 207, member A	protein-coding
mm_135776.1	chr16	56839548	56839558	-	1	NA	intron (NM_019631, intron 1 of 5)	MER5A1|DNA|hAT-Charlie	-43695	NM_172825	239853	Mm.258979	NM_172825	ENSMUSG00000022755	Adgrg7	9130020O16Rik|Gpr128	adhesion G protein-coupled receptor G7	protein-coding
mm_16208.1	chr2	173063540	173063546	+	1	NA	Intergenic	RSINE1|SINE|B4	41641	NM_019547	56190	Mm.485782	NM_019547	ENSMUSG00000027510	Rbm38	Rnpc1|Seb4|Seb4l	RNA binding motif protein 38	protein-coding
mm_17246.1	chr2	25627893	25627908	-	1	NA	promoter-TSS (NM_007995)	promoter-TSS (NM_007995)	74	NM_007995	14133	Mm.10510	NM_007995	ENSMUSG00000026938	Fcna	Fcn1	ficolin A	protein-coding
mm_129263.1	chr15	76818094	76818174	-	1	NA	promoter-TSS (NM_001168288)	promoter-TSS (NM_001168288)	36	NM_001168288	223666	Mm.322931	NM_198420	ENSMUSG00000033697	Arhgap39	9530053N22|AI843066|D15Wsu169e|Kiaa1688|Porf-2	Rho GTPase activating protein 39	protein-coding
mm_16327.1	chr2	174310017	174310020	+	1	NA	intron (NM_001310085, intron 2 of 12)	intron (NM_001310085, intron 2 of 12)	12159	NM_001310085	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_98649.1	chr11	96251274	96251282	+	1	NA	promoter-TSS (NR_037977)	promoter-TSS (NR_037977)	-382	NR_037977	193022	Mm.169508	NR_037977		Gm53	-	predicted gene 53	ncRNA
mm_132473.1	chr16	36708317	36708338	+	1	NA	exon (NM_134109, exon 2 of 8)	exon (NM_134109, exon 2 of 8)	14349	NM_001285791	106347	Mm.17807	NM_134109	ENSMUSG00000022900	Ildr1	AU041483|AU044638	immunoglobulin-like domain containing receptor 1	protein-coding
mm_72856.1	chr8	88428732	88428740	+	1	NA	Intergenic	MLT1G|LTR|ERVL-MaLR	-66545	NM_012047	26992	Mm.5400	NM_012047	ENSMUSG00000031660	Brd7	BP75|CELTIX1|Ptpn13ip	bromodomain containing 7	protein-coding
mm_138420.1	chr17	35069478	35069505	+	1	NA	exon (NM_023463, exon 3 of 3)	exon (NM_023463, exon 3 of 3)	2166	NM_023463	68468	Mm.215096	NM_023463	ENSMUSG00000092586	Ly6g6c	1110003M04Rik|AU016360|G6c|NG24	lymphocyte antigen 6 complex, locus G6C	protein-coding
mm_127540.1	chr15	102104531	102104539	+	1	NA	exon (NM_153533, exon 2 of 29)	exon (NM_153533, exon 2 of 29)	1547	NM_153533	209039	Mm.29389	NM_153533	ENSMUSG00000037003	Tns2	C1-ten|Tenc1|nep|nph	tensin 2	protein-coding
mm_39316.1	chr5	8065184	8065194	+	1	NA	intron (NM_001080974, intron 7 of 7)	B4|SINE|B4	8647	NM_001080974	109552	Mm.96211	NM_025618	ENSMUSG00000003161	Sri	2210417O06Rik|2900070H08Rik|Sor	sorcin	protein-coding
mm_24941.1	chr3	96577168	96577184	+	1	NA	TTS (NM_027241)	TTS (NM_027241)	-10375	NR_040409	100038464	Mm.475126	NR_040409	ENSMUSG00000074398	Gm15441	ENSMUSG00000074398|OTTMUSG00000021867	predicted gene 15441	ncRNA
mm_118268.1	chr13	112580712	112580728	-	1	NA	promoter-TSS (NM_139299)	promoter-TSS (NM_139299)	-58	NM_139299	218624	Mm.380801	NM_139299	ENSMUSG00000050377	Il31ra	CRL3|GLM-R|GPL|Glmr|NR10	interleukin 31 receptor A	protein-coding
mm_52057.1	chr6	97232859	97232872	+	1	NA	3' UTR (NM_022992, exon 3 of 3)	3' UTR (NM_022992, exon 3 of 3)	19915	NM_001081157	320502	Mm.68163	NM_001081157	ENSMUSG00000044086	Lmod3	5430424A14Rik	leiomodin 3 (fetal)	protein-coding
mm_17578.1	chr2	30415390	30415410	-	1	NA	promoter-TSS (NM_138748)	promoter-TSS (NM_138748)	348	NM_007760	12908	Mm.20396	NM_007760	ENSMUSG00000026853	Crat	AW107812|CARAT	carnitine acetyltransferase	protein-coding
mm_13669.1	chr2	115581668	115581743	+	1	NA	promoter-TSS (NM_207264)	promoter-TSS (NM_207264)	-11	NM_207264	399568	Mm.134929	NM_207264	ENSMUSG00000040282	BC052040	-	cDNA sequence BC052040	protein-coding
mm_25055.1	chr3	98599620	98599628	+	1	NA	Intergenic	RLTR48A|LTR|ERV1	-35586	NM_008294	15495	Mm.14309	NM_008294	ENSMUSG00000095143	Hsd3b4	-	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 4	protein-coding
mm_54045.1	chr6	13677908	13677923	-	1	NA	promoter-TSS (NM_175312)	promoter-TSS (NM_175312)	51	NM_175312	101148	Mm.354863	NM_175312	ENSMUSG00000042742	Bmt2	AI666701|B630005N14Rik	base methyltransferase of 25S rRNA 2	protein-coding
mm_110044.1	chr12	17348374	17348419	-	1	NA	promoter-TSS (NM_001008421)	promoter-TSS (NM_001008421)	-97	NM_001008421	217431	Mm.27536	NM_001008421	ENSMUSG00000061458	Nol10	Gm67	nucleolar protein 10	protein-coding
mm_18029.1	chr2	38643406	38643420	-	1	NA	exon (NM_011187, exon 2 of 8)	exon (NM_011187, exon 2 of 8)	493	NM_011187	19177	Mm.389251	NM_011187	ENSMUSG00000026750	Psmb7	AU020723|MC14	proteasome (prosome, macropain) subunit, beta type 7	protein-coding
mm_132352.1	chr16	34120130	34120178	+	1	NA	intron (NM_177357, intron 33 of 59)	RSINE1|SINE|B4	-153151	NM_009471	22247	Mm.13145	NM_009471	ENSMUSG00000022814	Umps	1700095D23Rik|AA408257|AL033308|BB164745	uridine monophosphate synthetase	protein-coding
mm_19080.1	chr2	77946184	77946199	-	1	NA	5' UTR (NM_001290740, exon 1 of 20)	5' UTR (NM_001290740, exon 1 of 20)	165	NM_001290740	80744	Mm.288151	NM_030560	ENSMUSG00000027014	Cwc22	AA684037|AI173004|AL022752|B230213M24|mKIAA1604	CWC22 spliceosome-associated protein	protein-coding
mm_113022.1	chr13	22035830	22035848	+	1	NA	promoter-TSS (NM_175659)	promoter-TSS (NM_175659)	18	NM_175665	319184	Mm.358955	NM_175665	ENSMUSG00000062727	Hist1h2bk	-	histone cluster 1, H2bk	protein-coding
mm_97205.1	chr11	75601480	75601500	+	1	NA	intron (NM_008850, intron 3 of 11)	intron (NM_008850, intron 3 of 11)	-1259	NR_110477	654359	Mm.439961	NR_110477		Gm12338	OTTMUSG00000006216	cytochrome c oxidase, subunit VIIc pseudogene	pseudo
mm_121632.1	chr14	8367262	8367280	-	1	NA	intron (NM_146050, intron 1 of 9)	intron (NM_146050, intron 1 of 9)	11492	NM_146050	18300	Mm.25351	NM_146050	ENSMUSG00000021749	Oit1	2310076N21Rik|AV067083|EF-7|Fam3d	oncoprotein induced transcript 1	protein-coding
mm_126771.1	chr15	86067707	86067744	+	1	NA	intron (NM_001205353, intron 1 of 18)	intron (NM_001205353, intron 1 of 18)	8998	NM_001205353	223752	Mm.24442	NM_172611	ENSMUSG00000035900	Gramd4	9930016O13	GRAM domain containing 4	protein-coding
mm_156858.1	chrX	164402094	164402105	+	1	NA	exon (NM_010216, exon 7 of 7)	exon (NM_010216, exon 7 of 7)	-17688	NM_011081	18700	Mm.3781	NM_011081	ENSMUSG00000031381	Piga	AI194334|Pig-a	phosphatidylinositol glycan anchor biosynthesis, class A	protein-coding
mm_148422.1	chr19	3937047	3937091	+	1	NA	intron (NM_001161428, intron 3 of 9)	MTC|LTR|ERVL-MaLR	1883	NM_001161428	54445	Mm.262094	NM_019449	ENSMUSG00000036908	Unc93b1	Unc-93B1|Unc93b	unc-93 homolog B1 (C. elegans)	protein-coding
mm_117105.1	chr13	60176050	60176053	-	1	NA	exon (NM_008086, exon 1 of 1)	exon (NM_008086, exon 1 of 1)	1484	NM_008086	14451	Mm.22701	NM_008086	ENSMUSG00000052957	Gas1	AW554192|Gas-1	growth arrest specific 1	protein-coding
mm_128045.1	chr15	25413729	25413745	-	1	NA	promoter-TSS (NM_027395)	promoter-TSS (NM_027395)	27	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	brain abundant, membrane attached signal protein 1	protein-coding
mm_164530.1	chr17	6107271	6107291	+	1	NA	intron (NM_001103181, intron 1 of 13)	CpG	451	NM_001103181	68842	Mm.449307	NM_054040	ENSMUSG00000034377	Tulp4	1110057P05Rik|2210038L17Rik|Tusp	tubby like protein 4	protein-coding
mm_21190.1	chr2	155357472	155357480	-	1	NA	promoter-TSS (NM_001004721)	promoter-TSS (NM_001004721)	-52	NM_001004721	228812	Mm.5434	NM_001004721	ENSMUSG00000038383	Pigu	5430426F17Rik|BC028278|Cdc91l1	phosphatidylinositol glycan anchor biosynthesis, class U	protein-coding
mm_145822.1	chr18	65434998	65435008	+	1	NA	intron (NM_172833, intron 1 of 15)	intron (NM_172833, intron 1 of 15)	4006	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_64612.1	chr7	3502503	3502510	-	1	NA	promoter-TSS (NM_177363)	promoter-TSS (NM_177363)	46	NM_177363	245126	Mm.245747	NM_177363	ENSMUSG00000053338	Tarm1	9930022N03Rik|ENSMUSG00000053338|Gm9904|OLT-2	T cell-interacting, activating receptor on myeloid cells 1	protein-coding
mm_47128.1	chr5	120139282	120139295	-	1	NA	promoter-TSS (NR_045793)	promoter-TSS (NR_045793)	-25	NR_045793	100503427	Mm.446834	NR_045793	ENSMUSG00000097368	Gm10390	ENSMUSG00000072671	predicted gene 10390	ncRNA
mm_55038.1	chr6	48987717	48987721	-	1	NA	exon (NM_172888, exon 1 of 5)	exon (NM_172888, exon 1 of 5)	858	NM_172888	243377	Mm.446302	NM_172888	ENSMUSG00000039215	Svs1	9530003A11	seminal vesicle secretory protein 1	protein-coding
mm_155439.1	chrX	73494796	73494810	+	1	NA	3' UTR (NM_007542, exon 8 of 8)	3' UTR (NM_007542, exon 8 of 8)	-8283	NM_001310537	320707	Mm.210095	NM_177236	ENSMUSG00000031376	Atp2b3	6430519O13Rik|Pmca3	ATPase, Ca++ transporting, plasma membrane 3	protein-coding
mm_170462.1	chr18	9269613	9269613	-	1	NA	Intergenic	Intergenic	13196	NM_153086	225152	Mm.119273	NM_153086	ENSMUSG00000036855	Gjd4	9430022F06Rik|Cx39	gap junction protein, delta 4	protein-coding
mm_93533.1	chr10	115362192	115362255	-	1	NA	promoter-TSS (NM_133683)	promoter-TSS (NM_133683)	39	NM_133683	67226	Mm.29647	NM_133683	ENSMUSG00000069520	Tmem19	2810428F02Rik|AW125171	transmembrane protein 19	protein-coding
mm_155338.1	chrX	66778765	66778790	+	1	NA	Intergenic	(CAT)n|Simple_repeat|Simple_repeat	-1445	NR_030535	100124496		NR_030535	ENSMUSG00000094184	Mir743b	Mirn743b|mir-743b	microRNA 743b	ncRNA
mm_30789.1	chr4	19575597	19575612	+	1	NA	intron (NM_025476, intron 1 of 9)	B1F|SINE|Alu	538	NM_025476	66302	Mm.440686	NM_025476	ENSMUSG00000028229	Rmdn1	Fam82b|RMD-1	regulator of microtubule dynamics 1	protein-coding
mm_27776.1	chr3	73057595	73057605	-	1	NA	promoter-TSS (NM_198864)	promoter-TSS (NM_198864)	-657	NM_198864	386750	Mm.331076	NM_198864	ENSMUSG00000048304	Slitrk3	-	SLIT and NTRK-like family, member 3	protein-coding
mm_69472.1	chr7	133710431	133710447	-	1	NA	intron (NM_025392, intron 1 of 6)	L2|LINE|L2	1106	NM_025392	66165	Mm.389983	NM_025392	ENSMUSG00000030983	Bccip	1110013J05Rik|TOK-1	BRCA2 and CDKN1A interacting protein	protein-coding
mm_21724.1	chr2	164657188	164657197	-	1	NA	exon (NM_001039501, exon 2 of 2)	exon (NM_001039501, exon 2 of 2)	1146	NM_001039501	629756	Mm.189007	NM_001039501	ENSMUSG00000070529	Wfdc10	Gm120|OTTMUSG00000016289	WAP four-disulfide core domain 10	protein-coding
mm_138074.1	chr17	33949487	33949535	+	1	NA	TTS (NM_019420)	TTS (NM_019420)	1977	NM_019420	54218	Mm.11132	NM_019420	ENSMUSG00000067370	B3galt4	Gal-T2|Galt2	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 4	protein-coding
mm_11943.1	chr2	52872172	52872196	+	1	NA	intron (NM_172409, intron 1 of 26)	ID_B1|SINE|B4	14316	NM_172409	71409	Mm.394427	NM_172409	ENSMUSG00000036053	Fmnl2	5430425K04Rik|Man	formin-like 2	protein-coding
mm_160887.1	chr11	69936011	69936011	+	1	NA	promoter-TSS (NM_001347634)	promoter-TSS (NM_001347634)	112	NM_016875	53422	Mm.29286	NM_016875	ENSMUSG00000018554	Ybx2	Msy2	Y box protein 2	protein-coding
mm_108713.1	chr12	87147704	87147783	+	1	NA	promoter-TSS (NM_001252556)	promoter-TSS (NM_001252556)	36	NM_010363	14874	Mm.29652	NM_010363	ENSMUSG00000021033	Gstz1	MAAI	glutathione transferase zeta 1 (maleylacetoacetate isomerase)	protein-coding
mm_71925.1	chr8	70234614	70234628	+	1	NA	promoter-TSS (NM_133972)	promoter-TSS (NM_133972)	-199	NM_133972	76813	Mm.383251	NM_133972	ENSMUSG00000002343	Armc6	2410153K17Rik|AW554412	armadillo repeat containing 6	protein-coding
mm_51195.1	chr6	71271576	71271606	+	1	NA	promoter-TSS (NM_145568)	promoter-TSS (NM_145568)	-80	NR_106192	102465900		NR_106192	ENSMUSG00000098623	Mir8112	Gm27739|mmu-mir-8112	microRNA 8112	ncRNA
mm_1349.1	chr1	66321733	66321739	+	1	NA	promoter-TSS (NM_001310634)	promoter-TSS (NM_001310634)	12	NM_001310634	17756	Mm.256966	NM_008632	ENSMUSG00000015222	Map2	G1-397-34|MAP-2|Mtap-2|Mtap2|repro4	microtubule-associated protein 2	protein-coding
mm_65289.1	chr7	24445636	24445637	-	1	NA	promoter-TSS (NM_199013)	promoter-TSS (NM_199013)	46	NM_199013	210145	Mm.33811	NM_199013	ENSMUSG00000062028	Irgc1	F630044M05Rik|Gm1102|Gm474|Ifgge|Iigp5|Irgc	immunity-related GTPase family, cinema 1	protein-coding
mm_56163.1	chr6	87981630	87981645	-	1	NA	promoter-TSS (NR_026990)	promoter-TSS (NR_026990)	-46	NR_026990	434064	Mm.371796	NR_026990	ENSMUSG00000084950	Gm5577	EG434064	predicted gene 5577	ncRNA
mm_55859.1	chr6	83456377	83456392	-	1	NA	promoter-TSS (NM_001347313)	promoter-TSS (NM_001347313)	8	NM_001347313	194388	Mm.211030	NM_183138	ENSMUSG00000034832	Tet3	B430006D22Rik|BC037432|D230004J03Rik	tet methylcytosine dioxygenase 3	protein-coding
mm_93516.1	chr10	115287975	115287985	-	1	NA	Intergenic	Intergenic	27611	NM_024454	216344	Mm.21936	NM_024454	ENSMUSG00000020132	Rab21	9630024B22	RAB21, member RAS oncogene family	protein-coding
mm_117108.1	chr13	60177119	60177148	-	1	NA	5' UTR (NM_008086, exon 1 of 1)	5' UTR (NM_008086, exon 1 of 1)	402	NM_008086	14451	Mm.22701	NM_008086	ENSMUSG00000052957	Gas1	AW554192|Gas-1	growth arrest specific 1	protein-coding
mm_124771.1	chr15	7090609	7090615	+	1	NA	Intergenic	Intergenic	-38960	NM_001113386	16880	Mm.149720	NM_013584	ENSMUSG00000054263	Lifr	A230075M04Rik|AW061234|LIF	leukemia inhibitory factor receptor	protein-coding
mm_48653.1	chr5	145868991	145869015	-	1	NA	exon (NM_007818, exon 6 of 13)	exon (NM_007818, exon 6 of 13)	10851	NM_007818	13112	Mm.332844	NM_007818	ENSMUSG00000056035	Cyp3a11	AI256190|Cyp3a|IIIAm1|Pcn	cytochrome P450, family 3, subfamily a, polypeptide 11	protein-coding
mm_10041.1	chr1	192992454	192992466	-	1	NA	intron (NM_001301370, intron 2 of 8)	intron (NM_001301370, intron 2 of 8)	43315	NM_001301370	329324	Mm.76710	NM_181546	ENSMUSG00000016200	Syt14	B230320I09Rik|sytXIV	synaptotagmin XIV	protein-coding
mm_59465.1	chr7	27256480	27256504	+	1	NA	intron (NM_133770, intron 13 of 14)	intron (NM_133770, intron 13 of 14)	-2269	NM_010950	18223	Mm.458153	NM_010950	ENSMUSG00000063160	Numbl	nbl	numb-like	protein-coding
mm_115587.1	chr13	11826751	11826767	-	1	NA	intron (NM_023868, intron 15 of 104)	RLTR20A4|LTR|ERVK	280186	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding
mm_10087.1	chr2	3118408	3118476	+	1	NA	promoter-TSS (NM_001081161)	promoter-TSS (NM_001081161)	54	NM_001081161	269233	Mm.23044	NM_001081161	ENSMUSG00000050530	Fam171a1	9630050M13Rik|AA409679	family with sequence similarity 171, member A1	protein-coding
mm_99304.1	chr11	101374654	101374673	+	1	NA	exon (NM_008061, exon 4 of 5)	exon (NM_008061, exon 4 of 5)	6947	NM_008061	14377	Mm.18064	NM_008061	ENSMUSG00000078650	G6pc	AW107337|G6Pase|G6pt|Glc-6-Pase	glucose-6-phosphatase, catalytic	protein-coding
mm_71219.1	chr8	40899077	40899090	+	1	NA	exon (NM_001044740, exon 2 of 12)	exon (NM_001044740, exon 2 of 12)	-27150	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_54765.1	chr6	41313446	41313468	-	1	NA	exon (NM_001003405, exon 2 of 5)	exon (NM_001003405, exon 2 of 5)	1253	NM_001003405	103964	Mm.333022	NM_001003405	ENSMUSG00000036938	Try5	1810049H19Rik|Tc|Tesp4	trypsin 5	protein-coding
mm_64173.1	chr7	141457019	141457021	+	1	NA	intron (NR_028142, intron 2 of 9)	intron (NR_028142, intron 2 of 9)	1832	NM_001163689	66853	Mm.29998	NM_025802	ENSMUSG00000025509	Pnpla2	0610039C21Rik|1110001C14Rik|Atgl|TTS-2.2	patatin-like phospholipase domain containing 2	protein-coding
mm_70693.1	chr8	15027187	15027206	+	1	NA	5' UTR (NM_029116, exon 2 of 2)	5' UTR (NM_029116, exon 2 of 2)	16171	NM_029116	74901	Mm.46675	NM_029116	ENSMUSG00000055675	Kbtbd11	2900016B01Rik|4930465M17Rik|mKIAA0711	kelch repeat and BTB (POZ) domain containing 11	protein-coding
mm_129314.1	chr15	77760868	77760950	-	1	NA	3' UTR (NM_022410, exon 41 of 41)	3' UTR (NM_022410, exon 41 of 41)	-5680	NM_001081970	239552	Mm.125650	NM_001081970	ENSMUSG00000056656	Apol8	9830006J20Rik|APOL-II|Apol2	apolipoprotein L 8	protein-coding
mm_12401.1	chr2	70475112	70475127	+	1	NA	5' UTR (NM_022435, exon 1 of 2)	5' UTR (NM_022435, exon 1 of 2)	196	NM_022435	64406	Mm.423397	NM_022435	ENSMUSG00000075304	Sp5	-	trans-acting transcription factor 5	protein-coding
mm_64735.1	chr7	4724501	4724510	-	1	NA	exon (NM_177887, exon 2 of 5)	exon (NM_177887, exon 2 of 5)	577	NM_001142792	330460	Mm.361851	NM_177887	ENSMUSG00000046456	Tmem150b	A630041N19|Tmem224	transmembrane protein 150B	protein-coding
mm_135664.1	chr16	52407678	52407698	-	1	NA	intron (NM_009655, intron 1 of 15)	B4A|SINE|B4	45393	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_61442.1	chr7	75457387	75457390	+	1	NA	intron (NM_029332, intron 1 of 36)	intron (NM_029332, intron 1 of 36)	1854	NM_029332	75547	Mm.216107	NM_029332	ENSMUSG00000066406	Akap13	1700026G02Rik|5730522G15Rik|5830460E08Rik|AKAP-13|AKAP-Lbc|BRX|Ht31|LBC|PROTO-LB|PROTO-LBC	A kinase (PRKA) anchor protein 13	protein-coding
mm_137878.1	chr17	31564750	31564854	+	1	NA	promoter-TSS (NM_016670)	promoter-TSS (NM_016670)	29	NM_016670	18771	Mm.259295	NM_016670	ENSMUSG00000006705	Pknox1	D17Wsu76e|PREP1	Pbx/knotted 1 homeobox	protein-coding
mm_42392.1	chr5	114937218	114937232	+	1	NA	exon (NM_145209, exon 7 of 7)	exon (NM_145209, exon 7 of 7)	-4977	NM_028211	72357	Mm.292672	NM_028211	ENSMUSG00000029559	2210016L21Rik	-	RIKEN cDNA 2210016L21 gene	protein-coding
mm_12379.1	chr2	69861578	69861584	+	1	NA	promoter-TSS (NM_001110145)	promoter-TSS (NM_001110145)	19	NM_009278	20823	Mm.10508	NM_009278	ENSMUSG00000068882	Ssb	SS-B	Sjogren syndrome antigen B	protein-coding
mm_36538.1	chr4	86657024	86657048	-	1	NA	exon (NM_007408, exon 8 of 8)	exon (NM_007408, exon 8 of 8)	13023	NM_007408	11520	Mm.381	NM_007408	ENSMUSG00000028494	Plin2	AA407157|ADPH|Adfp|Adrp	perilipin 2	protein-coding
mm_124689.1	chr15	6435422	6435432	+	1	NA	exon (NM_001102400, exon 10 of 13)	exon (NM_001102400, exon 10 of 13)	-9906	NM_013485	12279	Mm.29095	NM_013485	ENSMUSG00000022149	C9	-	complement component 9	protein-coding
mm_13349.1	chr2	102998578	102998587	+	1	NA	Intergenic	Intergenic	74931	NM_175094	27402	Mm.315011	NM_175094	ENSMUSG00000010914	Pdhx	AI481367|E3bp|Pdx1	pyruvate dehydrogenase complex, component X	protein-coding
mm_72762.1	chr8	85515729	85515772	+	1	NA	intron (NM_173866, intron 6 of 11)	intron (NM_173866, intron 6 of 11)	23133	NM_173866	108682	Mm.200423	NM_173866	ENSMUSG00000031700	Gpt2	4631422C05Rik|ALT2|AU014768|AU041193|C87201	glutamic pyruvate transaminase (alanine aminotransferase) 2	protein-coding
mm_169193.1	chr13	66108813	66108816	+	1	NA	Intergenic	Intergenic	-4639	NM_001177832	628709	Mm.390595	NM_001177832	ENSMUSG00000095909	Gm10324	ENSMUSG00000071302	predicted gene 10324	protein-coding
mm_65901.1	chr7	30190691	30190738	-	1	NA	exon (NM_009795, exon 7 of 11)	exon (NM_009795, exon 7 of 11)	4334	NM_009795	12336	Mm.439782	NM_009795	ENSMUSG00000001794	Capns1	Capa-4|Capa4|Capn4|D7Ertd146e	calpain, small subunit 1	protein-coding
mm_28689.1	chr3	95518978	95518991	-	1	NA	Intergenic	L1MB4|LINE|L1	-7802	NM_021281	13040	Mm.3619	NM_021281	ENSMUSG00000038642	Ctss	Cats	cathepsin S	protein-coding
mm_103493.1	chr11	76571303	76571309	-	1	NA	promoter-TSS (NM_198895)	promoter-TSS (NM_198895)	78	NM_198895	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_106468.1	chr11	120086769	120086780	-	1	NA	promoter-TSS (NM_009734)	promoter-TSS (NM_009734)	53	NM_009734	12009	Mm.2556	NM_009734	ENSMUSG00000039781	Cep131	AZ1|Azi|Azi1	centrosomal protein 131	protein-coding
mm_24931.1	chr3	96559634	96559682	+	1	NA	exon (NM_023719, exon 5 of 8)	exon (NM_023719, exon 5 of 8)	1701	NM_023719	56338	Mm.410189	NM_023719	ENSMUSG00000038393	Txnip	1200008J08Rik|AA682105|Hyplip1|THIF|Tbp-2|VDUP1	thioredoxin interacting protein	protein-coding
mm_158768.1	chrX	166585641	166585653	-	1	NA	promoter-TSS (NM_019397)	promoter-TSS (NM_019397)	69	NM_019397	54156	Mm.37707	NM_019397	ENSMUSG00000000402	Egfl6	Maeg	EGF-like-domain, multiple 6	protein-coding
mm_128680.1	chr15	60822206	60822232	-	1	NA	promoter-TSS (NR_030696)	promoter-TSS (NR_030696)	-746	NR_030696	320469	Mm.230853	NM_177166		9930014A18Rik	-	RIKEN cDNA 9930014A18 gene	ncRNA
mm_100081.1	chr11	115465554	115465557	+	1	NA	intron (NM_001080934, intron 2 of 3)	intron (NM_001080934, intron 2 of 3)	3082	NM_001080934	217316	Mm.25773	NM_001080934	ENSMUSG00000045775	Slc16a5	A130015N09Rik|MCT 5|MCT 6|MCT5	solute carrier family 16 (monocarboxylic acid transporters), member 5	protein-coding
mm_151185.1	chr19	53421230	53421233	+	1	NA	Intergenic	Intergenic	-30658	NM_172429	76479	Mm.313687	NM_172429	ENSMUSG00000025024	Smndc1	2410004J23Rik|4933440I19Rik	survival motor neuron domain containing 1	protein-coding
mm_162657.1	chr10	4354242	4354256	+	1	NA	exon (NM_031185, exon 3 of 4)	exon (NM_031185, exon 3 of 4)	33859	NM_001033466	381990	Mm.262466	NM_001033466	ENSMUSG00000075327	Zbtb2	Gm1103	zinc finger and BTB domain containing 2	protein-coding
mm_56553.1	chr6	100671093	100671112	-	1	NA	promoter-TSS (NM_181590)	promoter-TSS (NM_181590)	55	NM_181590	72171	Mm.256022	NM_181590	ENSMUSG00000035378	Shq1	2810403P18Rik|Grim-1	SHQ1 homolog (S. cerevisiae)	protein-coding
mm_137584.1	chr17	28007649	28007694	+	1	NA	intron (NM_001286040, intron 11 of 24)	intron (NM_001286040, intron 11 of 24)	72913	NM_013687	21463	Mm.29758	NM_013687	ENSMUSG00000062859	Tcp11	D17Ken1|Tcp-11	t-complex protein 11	protein-coding
mm_634.1	chr1	40363830	40363838	+	1	NA	intron (NM_133193, intron 10 of 10)	intron (NM_133193, intron 10 of 10)	39207	NM_133193	107527	Mm.155583	NM_133193	ENSMUSG00000070942	Il1rl2	AI481289|AW551444|IL-1Rrp2	interleukin 1 receptor-like 2	protein-coding
mm_23784.1	chr3	79336689	79336695	+	1	NA	Intergenic	MLTR14|LTR|ERV1	-8684	NM_001142953	100233207	Mm.373801	NM_001142953	ENSMUSG00000091685	Gm17359	-	predicted gene, 17359	protein-coding
mm_137293.1	chr17	24752981	24752994	+	1	NA	promoter-TSS (NM_001012402)	promoter-TSS (NM_001012402)	-16	NM_001012402	328779	Mm.328848	NM_001012402	ENSMUSG00000039628	Hs3st6	3-OST-6	heparan sulfate (glucosamine) 3-O-sulfotransferase 6	protein-coding
mm_74327.1	chr8	126904144	126904161	+	1	NA	Intergenic	Intergenic	41769	NM_024214	67952	Mm.6932	NM_024214	ENSMUSG00000093904	Tomm20	1810060K07Rik|BB284719|Gm19268|MAS20|MOM19|TOM20|mKIAA0016	translocase of outer mitochondrial membrane 20 homolog (yeast)	protein-coding
mm_49535.1	chr6	30175278	30175282	+	1	NA	Intergenic	Intergenic	-1155	NR_126541	101447999		NR_126540		Mirc35hg	-	microRNA cluster 35, host gene	ncRNA
mm_83905.1	chr9	56202104	56202114	-	1	NA	3' UTR (NM_172924, exon 7 of 7)	3' UTR (NM_172924, exon 7 of 7)	-41039	NM_019793	56434	Mm.28484	NM_019793	ENSMUSG00000032324	Tspan3	1700055K04Rik|TM4-A|Tm4sf8	tetraspanin 3	protein-coding
mm_10104.1	chr2	3513036	3513074	+	1	NA	promoter-TSS (NR_103465)	promoter-TSS (NR_103465)	-10	NM_177647	227526	Mm.211455	NM_177647	ENSMUSG00000039496	Cdnf	9330140G23|Armetl1	cerebral dopamine neurotrophic factor	protein-coding
mm_19437.1	chr2	91963730	91963740	-	1	NA	promoter-TSS (NM_138306)	promoter-TSS (NM_138306)	-172	NM_138306	104418	Mm.314923	NM_138306	ENSMUSG00000040479	Dgkz	E130307B02Rik|ENSMUSG00000075035|F730209L11Rik|mDGK[z]	diacylglycerol kinase zeta	protein-coding
mm_14913.1	chr2	150749037	150749147	+	1	NA	promoter-TSS (NM_172117)	promoter-TSS (NM_172117)	11	NM_172117	12497	Mm.275524	NM_172117	ENSMUSG00000033068	Entpd6	2700026H11Rik|Cd39l2|NTPDase-6	ectonucleoside triphosphate diphosphohydrolase 6	protein-coding
mm_123359.1	chr14	63142932	63142936	-	1	NA	3' UTR (NM_007798, exon 10 of 10)	3' UTR (NM_007798, exon 10 of 10)	20472	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_107467.1	chr12	37242002	37242008	+	1	NA	5' UTR (NM_178767, exon 1 of 13)	5' UTR (NM_178767, exon 1 of 13)	366	NM_178767	319660	Mm.485540	NM_178767	ENSMUSG00000050103	Agmo	A530016O06Rik|AI790538|Tmem195	alkylglycerol monooxygenase	protein-coding
mm_131569.1	chr16	18217893	18217900	+	1	NA	Intergenic	Intergenic	-4033	NR_015575	66779	Mm.387525	NR_015575		4933432I09Rik	-	RIKEN cDNA 4933432I09 gene	ncRNA
mm_137933.1	chr17	32658990	32659002	+	1	NA	promoter-TSS (NM_001101588)	promoter-TSS (NM_001101588)	-487	NM_001101588	631304	Mm.328950	NM_001101588	ENSMUSG00000090700	Cyp4f40	EG631304	cytochrome P450, family 4, subfamily f, polypeptide 40	protein-coding
mm_118816.1	chr14	25481168	25481224	+	1	NA	intron (NM_001310666, intron 1 of 23)	intron (NM_001310666, intron 1 of 23)	22011	NM_183208	328365	Mm.227484	NM_183208	ENSMUSG00000007817	Zmiz1	BC065120|E330020C23|ENSMUSG00000072684|Gm10397|I920194n01|Rai17|Zimp10	zinc finger, MIZ-type containing 1	protein-coding
mm_95406.1	chr11	49846806	49846814	+	1	NA	promoter-TSS (NM_001163671)	promoter-TSS (NM_001163671)	59	NM_016961	26420	Mm.68933	NM_016961	ENSMUSG00000020366	Mapk9	AI851083|JNK2|Prkm9|p54aSAPK	mitogen-activated protein kinase 9	protein-coding
mm_67915.1	chr7	99828325	99828339	-	1	NA	promoter-TSS (NM_016720)	promoter-TSS (NM_016720)	85	NM_016720	50877	Mm.103703	NM_016720	ENSMUSG00000035239	Neu3	-	neuraminidase 3	protein-coding
mm_79202.1	chr9	48798331	48798335	+	1	NA	intron (NM_001033324, intron 2 of 6)	intron (NM_001033324, intron 2 of 6)	37612	NM_001033324	235320	Mm.457803	NM_001033324	ENSMUSG00000066687	Zbtb16	AI467657|PLZF|Zfp145|lu	zinc finger and BTB domain containing 16	protein-coding
mm_119523.1	chr14	47515302	47515321	+	1	NA	intron (NR_027414, intron 4 of 5)	intron (NR_027414, intron 4 of 5)	42750	NM_001146085	78938	Mm.11935	NM_030236	ENSMUSG00000037536	Fbxo34	2900057B08Rik|5830426G16Rik	F-box protein 34	protein-coding
mm_3089.1	chr1	134406375	134406385	+	1	NA	exon (NM_028057, exon 2 of 9)	exon (NM_028057, exon 2 of 9)	390	NM_028057	72017	Mm.280230	NM_028057	ENSMUSG00000026456	Cyb5r1	1500005G05Rik|B5R.1|C80155|Nqo3a2	cytochrome b5 reductase 1	protein-coding
mm_48909.1	chr6	3993777	3993789	+	1	NA	promoter-TSS (NM_010314)	promoter-TSS (NM_010314)	-229	NM_010314	14699	Mm.95398	NM_010314	ENSMUSG00000029663	Gngt1	G(y)1|Gng1	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1	protein-coding
mm_64305.1	chr7	141862011	141862015	+	1	NA	exon (NM_028801, exon 31 of 49)	exon (NM_028801, exon 31 of 49)	22941	NM_028801	74180	Mm.200752	NM_028801	ENSMUSG00000066108	Muc5b	2300002I04Rik|A130042M24|AV085033|MUC5|MUC9|mucin 5b	mucin 5, subtype B, tracheobronchial	protein-coding
mm_154266.1	chr19	60771697	60771707	-	1	NA	exon (NM_010123, exon 14 of 22)	exon (NM_010123, exon 14 of 22)	2683	NR_034047	100217439		NR_034047		Snora19	MBI-51	small nucleolar RNA, H/ACA box 19	snoRNA
mm_161725.1	chr17	28080734	28080734	-	1	NA	promoter-TSS (NM_013687)	promoter-TSS (NM_013687)	-95	NM_001085555	21463	Mm.29758	NM_013687	ENSMUSG00000062859	Tcp11	D17Ken1|Tcp-11	t-complex protein 11	protein-coding
mm_140924.1	chr17	24220696	24220704	-	1	NA	promoter-TSS (NM_028056)	promoter-TSS (NM_028056)	69	NM_028056	72016	Mm.23881	NM_028056	ENSMUSG00000024118	1600002H07Rik	-	RIKEN cDNA 1600002H07 gene	protein-coding
mm_28638.1	chr3	95219557	95219568	-	1	NA	3' UTR (NM_019914, exon 2 of 2)	3' UTR (NM_019914, exon 2 of 2)	-1620	NM_029885	213054	Mm.224820	NM_029885	ENSMUSG00000038766	Gabpb2	1810015F01Rik|5830427M07|9430006E19Rik|A430024B14Rik|AV050852|Gabpb2-1	GA repeat binding protein, beta 2	protein-coding
mm_155128.1	chrX	49463927	49463973	+	1	NA	Intergenic	Intergenic	-6500	NM_001081123	75404	Mm.44305	NM_001081123	ENSMUSG00000036198	Arhgap36	1100001E04Rik|rho-gap	Rho GTPase activating protein 36	protein-coding
mm_18493.1	chr2	62606304	62606321	-	1	NA	exon (NM_027835, exon 10 of 16)	exon (NM_027835, exon 10 of 16)	-32291	NM_007986	14089	Mm.41816	NM_007986	ENSMUSG00000000392	Fap	SIMP	fibroblast activation protein	protein-coding
mm_125098.1	chr15	27571597	27571616	+	1	NA	TTS (NR_106065)	TTS (NR_106065)	112	NR_106065	102466808		NR_106065	ENSMUSG00000098416	Mir7117	Gm27729|mmu-mir-7117	microRNA 7117	ncRNA
mm_65796.1	chr7	28907350	28907367	-	1	NA	intron (NM_021895, intron 8 of 20)	intron (NM_021895, intron 8 of 20)	25702	NM_001110807	60594	Mm.476990	NM_021894	ENSMUSG00000054083	Capn12	CANP 12	calpain 12	protein-coding
mm_93239.1	chr10	95415466	95415483	-	1	NA	promoter-TSS (NM_001168657)	promoter-TSS (NM_001168657)	10	NM_001168656	216233	Mm.474283	NM_007706	ENSMUSG00000020027	Socs2	8030460M17|AI527257|AW108012|CIS2|Cish2|D130043N08Rik|JAB|SOCS-2|SSI-2|hg	suppressor of cytokine signaling 2	protein-coding
mm_90495.1	chr10	128033684	128033694	+	1	NA	Intergenic	PB1D7|SINE|Alu	-1657	NM_013608	17938	Mm.3746	NM_013608	ENSMUSG00000061315	Naca	AL022831|AL024382|Gm1878|mKIAA0363|skNAC	nascent polypeptide-associated complex alpha polypeptide	protein-coding
mm_94238.1	chr11	3292939	3292962	+	1	NA	intron (NM_019574, intron 1 of 3)	intron (NM_019574, intron 1 of 3)	2493	NM_019574	56218	Mm.275563	NM_019574	ENSMUSG00000020453	Patz1	8430401L15Rik|AI447519|Mazr|Patz|Zfp278	POZ (BTB) and AT hook containing zinc finger 1	protein-coding
mm_2471.1	chr1	105675651	105675654	+	1	NA	intron (NM_173187, intron 1 of 28)	B1_Mur3|SINE|Alu	11791	NM_173187	227446	Mm.337339	NM_029349	ENSMUSG00000026319	2310035C23Rik	6430401N10|Kiaa1468|mKIAA1468	RIKEN cDNA 2310035C23 gene	protein-coding
mm_135746.1	chr16	55916844	55916851	-	1	NA	intron (NM_028815, intron 8 of 10)	RMER1B|Other|Other	18001	NM_001159364	74201	Mm.178427	NM_028815	ENSMUSG00000022604	Cep97	2810403B08Rik|4932439K18Rik|AA437768|E130116N02Rik|Lrriq2	centrosomal protein 97	protein-coding
mm_4688.1	chr1	180641331	180641374	+	1	NA	non-coding (NR_120498, exon 1 of 15)	non-coding (NR_120498, exon 1 of 15)	202	NR_120498	72568	Mm.275044	NM_175186	ENSMUSG00000058729	Lin9	2700022J23Rik|Bara|Lin-9|TGS|TGS1|mLin-9	lin-9 homolog (C. elegans)	protein-coding
mm_68065.1	chr7	101867298	101867338	-	1	NA	intron (NM_001252552, intron 3 of 6)	intron (NM_001252552, intron 3 of 6)	3470	NM_001252554	14275	Mm.2135	NM_008034	ENSMUSG00000001827	Folr1	FBP1|Folbp-1|Folbp1	folate receptor 1 (adult)	protein-coding
mm_9263.1	chr1	171632065	171632087	-	1	NA	TTS (NM_144539)	TTS (NM_144539)	9824	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_44454.1	chr5	21785116	21785232	-	1	NA	promoter-TSS (NM_009584)	promoter-TSS (NM_009584)	-9	NM_009584	22791	Mm.266312	NM_009584	ENSMUSG00000029014	Dnajc2	AU020218|MIDA1|Zrf1|Zrf2	DnaJ heat shock protein family (Hsp40) member C2	protein-coding
mm_150508.1	chr19	39023946	39023952	+	1	NA	intron (NM_028089, intron 4 of 8)	Lx9|LINE|L1	16930	NM_028089	72082	Mm.142581	NM_028089	ENSMUSG00000025002	Cyp2c55	2010318C06Rik	cytochrome P450, family 2, subfamily c, polypeptide 55	protein-coding
mm_104376.1	chr11	94375113	94375135	-	1	NA	exon (NM_029600, exon 3 of 31)	exon (NM_029600, exon 3 of 31)	17852	NM_029600	76408	Mm.23942	NM_029600	ENSMUSG00000020865	Abcc3	1700019L09Rik|ABC31|MLP2|MOAT-D|MRP3	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	protein-coding
mm_24384.1	chr3	90253123	90253124	+	1	NA	3' UTR (NM_013901, exon 4 of 4)	3' UTR (NM_013901, exon 4 of 4)	-1158	NM_028881	74343	Mm.35627	NM_028881	ENSMUSG00000027936	Crtc2	4632407F12Rik|Torc2|mTORC2	CREB regulated transcription coactivator 2	protein-coding
mm_154972.1	chrX	37178180	37178181	+	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-9338	NM_001033785	434756	Mm.471848	NM_001033785	ENSMUSG00000036551	Akap14	-	A kinase (PRKA) anchor protein 14	protein-coding
mm_43042.1	chr5	124036258	124036261	+	1	NA	Intergenic	Intergenic	-3999	NM_177876	330192	Mm.4079	NM_177876	ENSMUSG00000066278	Vps37b	2300007F24Rik|AI415429|BC026744	vacuolar protein sorting 37B	protein-coding
mm_117428.1	chr13	74493937	74493999	-	1	NA	promoter-TSS (NM_146231)	promoter-TSS (NM_146231)	-18	NM_146231	235956	Mm.296909	NM_146231	ENSMUSG00000069208	Zfp825	-	zinc finger protein 825	protein-coding
mm_50702.1	chr6	52102962	52102988	+	1	NA	promoter-TSS (NR_110440)	promoter-TSS (NR_110440)	26	NR_110440	102635415	Mm.333063	NR_110440	ENSMUSG00000085412	Halr1	Gm15055|Haunt|Linchoxa1|OTTMUSG00000018881|linc-Evx1|linc-Hoxa1|linc1547	Hoxa adjacent long noncoding RNA 1	ncRNA
mm_19720.1	chr2	104426928	104426977	-	1	NA	3' UTR (NM_001145824, exon 16 of 16)	3' UTR (NM_001145824, exon 16 of 16)	1988	NR_035432	100316678		NR_035432	ENSMUSG00000084516	Mir1902	Mirn1902|mmu-mir-1902	microRNA 1902	ncRNA
mm_50240.1	chr6	42351567	42351589	+	1	NA	exon (NM_001289618, exon 4 of 10)	exon (NM_001289618, exon 4 of 10)	1750	NM_001289619	22793	Mm.282303	NM_011777	ENSMUSG00000029860	Zyx	9530098H06Rik|R75157	zyxin	protein-coding
mm_166352.1	chr5	120029486	120029486	+	1	NA	Intergenic	Intergenic	-87027	NM_028762	74111	Mm.41022	NM_028762	ENSMUSG00000029594	Rbm19	1200009A02Rik|AV302714|NPO	RNA binding motif protein 19	protein-coding
mm_33168.1	chr4	126024702	126024737	+	1	NA	promoter-TSS (NM_007782)	promoter-TSS (NM_007782)	60	NM_001252651	12986	Mm.271701	NM_007782	ENSMUSG00000028859	Csf3r	Cd114|Csfgr|G-CSF-R|G-CSFR	colony stimulating factor 3 receptor (granulocyte)	protein-coding
mm_27391.1	chr3	50687307	50687309	-	1	NA	Intergenic	Intergenic	-243695	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_84237.1	chr9	62282137	62282143	-	1	NA	promoter-TSS (NM_025721)	promoter-TSS (NM_025721)	39	NM_025721	66712	Mm.263615	NM_025721	ENSMUSG00000046846	Spesp1	4921508E09Rik|AI428149	sperm equatorial segment protein 1	protein-coding
mm_31912.1	chr4	85205137	85205149	+	1	NA	promoter-TSS (NM_019535)	promoter-TSS (NM_019535)	-313	NM_019535	20404	Mm.143603	NM_019535	ENSMUSG00000028488	Sh3gl2	9530001L19Rik|AI120490|AW555077|B930049H17Rik|EEN-B1|SH3PA|Sh3d2a	SH3-domain GRB2-like 2	protein-coding
mm_119832.1	chr14	54363401	54363426	+	1	NA	exon (NM_026936, exon 3 of 10)	exon (NM_026936, exon 3 of 10)	2572	NM_026936	69089	Mm.182340	NM_026936	ENSMUSG00000000959	Oxa1l	1810020M02Rik|AI894287	oxidase assembly 1-like	protein-coding
mm_138326.1	chr17	34850469	34850493	+	1	NA	promoter-TSS (NM_021337)	promoter-TSS (NM_021337)	90	NM_001045864	27632	Mm.653	NM_138580	ENSMUSG00000024369	Nelfe	D17H6S45|NELF-E|RD|Rdbp	negative elongation factor complex member E, Rdbp	protein-coding
mm_94206.1	chr11	3105051	3105062	+	1	NA	Intergenic	IAPLTR4|LTR|ERVK	-18965	NR_003517	236604	Mm.247625	NM_001004146		Pisd-ps1	-	phosphatidylserine decarboxylase, pseudogene 1	pseudo
mm_105705.1	chr11	108272307	108272310	-	1	NA	intron (NM_011101, intron 2 of 16)	B4|SINE|B4	71580	NM_011101	18750	Mm.222178	NM_011101	ENSMUSG00000050965	Prkca	AI875142|Pkca	protein kinase C, alpha	protein-coding
mm_111781.1	chr12	104343101	104343113	-	1	NA	exon (NM_011458, exon 3 of 5)	exon (NM_011458, exon 3 of 5)	4621	NM_011458	20714	Mm.291569	NM_011458	ENSMUSG00000058207	Serpina3k	1300001I07Rik|D12Rp54|MMCM2|MMSpi2|RP54|Spi-2|Spi2|contrapsin	serine (or cysteine) peptidase inhibitor, clade A, member 3K	protein-coding
mm_106911.1	chr12	8208120	8208161	+	1	NA	promoter-TSS (NM_001167768)	promoter-TSS (NM_001167768)	13	NM_001167767	68832	Mm.25608	NM_172401	ENSMUSG00000037669	Ldah	1110057K04Rik|mLDAH	lipid droplet associated hydrolase	protein-coding
mm_19156.1	chr2	80581508	80581519	-	1	NA	promoter-TSS (NM_001290745)	promoter-TSS (NM_001290745)	-331	NM_016965	50884	Mm.25203	NM_016965	ENSMUSG00000027002	Nckap1	C79304|H19|Hem-2|Hem2|Nap1|mKIAA0587|mh19|p125Nap1	NCK-associated protein 1	protein-coding
mm_133670.1	chr16	92080870	92080874	+	1	NA	3' UTR (NM_017391, exon 2 of 2)	3' UTR (NM_017391, exon 2 of 2)	22536	NM_080456	121022	Mm.217354	NM_080456	ENSMUSG00000039680	Mrps6	AW046321	mitochondrial ribosomal protein S6	protein-coding
mm_173169.1	chrX	42761275	42761279	+	1	NA	intron (NM_011855, intron 12 of 32)	L1Md_F2|LINE|L1	255955	NM_001313691	20400	Mm.441197	NM_011364	ENSMUSG00000005696	Sh2d1a	Gm686|SAP	SH2 domain containing 1A	protein-coding
mm_171093.1	chr3	127837506	127837509	-	1	NA	promoter-TSS (NM_145964)	promoter-TSS (NM_145964)	-15	NM_145964	211556	Mm.403486	NM_145964	ENSMUSG00000074238	Ap1ar	AA407621|C78909|Gadkin	adaptor-related protein complex 1 associated regulatory protein	protein-coding
mm_91881.1	chr10	59733701	59733705	-	1	NA	intron (NM_001291443, intron 3 of 12)	RMER15|LTR|ERVL	31140	NM_001291443	216001	Mm.27199	NM_144822	ENSMUSG00000020111	Micu1	C730016L05Rik|Calc|Cbara1	mitochondrial calcium uptake 1	protein-coding
mm_83176.1	chr9	40784042	40784047	-	1	NA	TTS (NM_133733)	TTS (NM_133733)	-17229	NM_031165	15481	Mm.290774	NM_031165	ENSMUSG00000015656	Hspa8	2410008N15Rik|Hsc70|Hsc71|Hsc73|Hsp73|Hspa10	heat shock protein 8	protein-coding
mm_51770.1	chr6	88060880	88060889	+	1	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	-15614	NM_009005	19349	Mm.333233	NM_009005	ENSMUSG00000079477	Rab7	Rab7a	RAB7, member RAS oncogene family	protein-coding
mm_82755.1	chr9	26860850	26860868	-	1	NA	promoter-TSS (NM_001113323)	promoter-TSS (NM_001113323)	-36	NM_001113323	70893	Mm.78118	NM_001113323	ENSMUSG00000031966	Glb1l3	4921509F24Rik	galactosidase, beta 1 like 3	protein-coding
mm_99695.1	chr11	106096999	106097004	+	1	NA	exon (NM_011947, exon 2 of 16)	exon (NM_011947, exon 2 of 16)	12099	NM_011947	26406	Mm.27041	NM_011947	ENSMUSG00000020700	Map3k3	AW548911|MAPKKK3|Mekk3|mKIAA4031	mitogen-activated protein kinase kinase kinase 3	protein-coding
mm_47750.1	chr5	130949045	130949048	-	1	NA	intron (NM_145218, intron 6 of 10)	MTC|LTR|ERVL-MaLR	358476	NM_145218	212996	Mm.299204	NM_145218	ENSMUSG00000034040	Wbscr17	AA388321|E330012B09Rik	Williams-Beuren syndrome chromosome region 17 homolog (human)	protein-coding
mm_7916.1	chr1	133737987	133737990	-	1	NA	intron (NM_213616, intron 5 of 19)	intron (NM_213616, intron 5 of 19)	-11343	NR_105868	102466206		NR_105868	ENSMUSG00000098606	Mir6903	Gm27797|mmu-mir-6903	microRNA 6903	ncRNA
mm_89147.1	chr10	86021962	86021991	+	1	NA	promoter-TSS (NM_153195)	promoter-TSS (NM_153195)	47	NM_153195	69754	Mm.44236	NM_153195	ENSMUSG00000001786	Fbxo7	2410015K21Rik|A230052G17Rik|AI117679|AW260462|C85118	F-box protein 7	protein-coding
mm_140758.1	chr17	17550718	17550730	-	1	NA	intron (NM_172827, intron 11 of 17)	intron (NM_172827, intron 11 of 17)	73765	NM_172827	240028	Mm.328807	NM_172827	ENSMUSG00000023845	Lnpep	2010309L07Rik|4732490P18Rik|CAP|IRAP|PLAP|gp160|vp165	leucyl/cystinyl aminopeptidase	protein-coding
mm_83870.1	chr9	55026525	55026539	-	1	NA	promoter-TSS (NM_145129)	promoter-TSS (NM_145129)	27	NM_145129	110834	Mm.63569	NM_145129	ENSMUSG00000032303	Chrna3	(a)3|A730007P14Rik|Acra-3|Acra3	cholinergic receptor, nicotinic, alpha polypeptide 3	protein-coding
mm_92883.1	chr10	82763869	82763896	-	1	NA	intron (NM_010914, intron 1 of 7)	CpG	259	NM_010914	18045	Mm.245998	NM_010914	ENSMUSG00000020248	Nfyb	AA985999|Cbf-A	nuclear transcription factor-Y beta	protein-coding
mm_45443.1	chr5	67427587	67427593	-	1	NA	5' UTR (NM_001164806, exon 1 of 5)	5' UTR (NM_001164806, exon 1 of 5)	209	NM_001164806	666938	Mm.101339	NM_001164806	ENSMUSG00000092060	Bend4	D330027G24Rik|EG666938	BEN domain containing 4	protein-coding
mm_121197.1	chr14	103051593	103051608	+	1	NA	intron (NM_008392, intron 4 of 4)	intron (NM_008392, intron 4 of 4)	4588	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_70296.1	chr8	3676563	3676573	+	1	NA	promoter-TSS (NM_025701)	promoter-TSS (NM_025701)	91	NM_025701	66682	Mm.29090	NM_025701	ENSMUSG00000040236	Trappc5	4021401A16Rik|TRS31	trafficking protein particle complex 5	protein-coding
mm_158956.1	chr1	88269271	88269271	-	1	NA	intron (NM_172505, intron 3 of 4)	intron (NM_172505, intron 3 of 4)	137	NR_040291	78605	Mm.384762	NR_040291		6430706D22Rik	-	RIKEN cDNA 6430706D22 gene	ncRNA
mm_142147.1	chr17	36006575	36006593	-	1	NA	3' UTR (NM_008207, exon 6 of 6)	3' UTR (NM_008207, exon 6 of 6)	12080	NR_015618	77810	Mm.483143	NR_015618		A930015D03Rik	-	RIKEN cDNA A930015D03 gene	ncRNA
mm_96878.1	chr11	70215022	70215026	+	1	NA	exon (NM_153081, exon 3 of 5)	exon (NM_153081, exon 3 of 5)	1114	NM_153081	216867	Mm.289238	NM_153081	ENSMUSG00000040938	Slc16a11	AB041591|MCT 11|MNCb-2717	solute carrier family 16 (monocarboxylic acid transporters), member 11	protein-coding
mm_26684.1	chr3	156562096	156562133	+	1	NA	promoter-TSS (NR_040400)	promoter-TSS (NR_040400)	320	NM_001039094	320840	Mm.317293	NM_177274	ENSMUSG00000040037	Negr1	5330422G01Rik|KILON|Ntra	neuronal growth regulator 1	protein-coding
mm_148073.1	chr18	72350792	72350815	-	1	NA	5' UTR (NM_007831, exon 1 of 29)	5' UTR (NM_007831, exon 1 of 29)	266	NM_007831	13176	Mm.167882	NM_007831	ENSMUSG00000060534	Dcc	C030036D22Rik|Igdcc1	deleted in colorectal carcinoma	protein-coding
mm_18188.1	chr2	45112993	45113010	-	1	NA	5' UTR (NM_015753, exon 1 of 10)	5' UTR (NM_015753, exon 1 of 10)	278	NM_015753	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_164386.1	chr16	32109088	32109126	+	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	9305	NM_025892	66994	Mm.22990	NM_025892	ENSMUSG00000035790	Cep19	1500031L02Rik|AI428934|AL022620	centrosomal protein 19	protein-coding
mm_29726.1	chr3	125938607	125938617	-	1	NA	promoter-TSS (NM_011674)	promoter-TSS (NM_011674)	-62	NM_011674	22239	Mm.306021	NM_011674	ENSMUSG00000032854	Ugt8a	AI850488|AW455908|Cgt|Ugt8|mCerGT	UDP galactosyltransferase 8A	protein-coding
mm_150224.1	chr19	33964541	33964552	+	1	NA	exon (NM_026334, exon 2 of 10)	exon (NM_026334, exon 2 of 10)	3298	NM_026334	67717	Mm.329816	NM_026334	ENSMUSG00000024768	Lipf	2310051B21Rik|AV082900	lipase, gastric	protein-coding
mm_82288.1	chr9	7604175	7604188	-	1	NA	Intergenic	Intergenic	-24050	NM_013903	30800	Mm.390121	NM_013903	ENSMUSG00000018620	Mmp20	-	matrix metallopeptidase 20 (enamelysin)	protein-coding
mm_64531.1	chr7	144132896	144132904	+	1	NA	intron (NR_037302, intron 1 of 5)	intron (NR_037302, intron 1 of 5)	-42620	NM_001113373	210274	Mm.483624	NM_001081370	ENSMUSG00000037541	Shank2	ProSAP1|mKIAA1022	SH3/ankyrin domain gene 2	protein-coding
mm_161317.1	chr14	44171329	44171329	-	1	NA	promoter-TSS (NM_029131)	promoter-TSS (NM_029131)	42	NM_029131	74954	Mm.425904	NM_029131	ENSMUSG00000072595	4930503E14Rik	-	RIKEN cDNA 4930503E14 gene	protein-coding
mm_110757.1	chr12	70111291	70111301	-	1	NA	intron (NM_001286079, intron 1 of 28)	CpG	333	NR_104398	18080	Mm.244047	NM_008697	ENSMUSG00000021068	Nin	3110068G20Rik|AI385615|AU024711|mKIAA1565	ninein	protein-coding
mm_54313.1	chr6	30174077	30174079	-	1	NA	promoter-TSS (NR_126541)	promoter-TSS (NR_126541)	47	NR_126540	101447999		NR_126540		Mirc35hg	-	microRNA cluster 35, host gene	ncRNA
mm_22294.1	chr2	180262581	180262595	-	1	NA	intron (NM_145851, intron 4 of 9)	intron (NM_145851, intron 4 of 9)	5052	NR_037274	100526556		NR_037274	ENSMUSG00000092827	Mir3091	mir-3091|mmu-mir-3091	microRNA 3091	ncRNA
mm_30311.1	chr3	149445454	149445495	-	1	NA	Intergenic	Intergenic	170737	NR_040591	381482	Mm.393866	NR_040591		Gm1653	-	predicted gene 1653	ncRNA
mm_58855.1	chr7	16891756	16891800	+	1	NA	promoter-TSS (NM_010320)	promoter-TSS (NM_010320)	-8	NM_010320	14709	Mm.103770	NM_010320	ENSMUSG00000063594	Gng8	G(y)8	guanine nucleotide binding protein (G protein), gamma 8	protein-coding
mm_26693.1	chr3	156740762	156740764	+	1	NA	intron (NM_177274, intron 1 of 6)	intron (NM_177274, intron 1 of 6)	178969	NM_001039094	320840	Mm.317293	NM_177274	ENSMUSG00000040037	Negr1	5330422G01Rik|KILON|Ntra	neuronal growth regulator 1	protein-coding
mm_15948.1	chr2	165918589	165918601	+	1	NA	Intergenic	B1_Mus1|SINE|Alu	-33757	NM_001252587	228880	Mm.227598	NM_027230	ENSMUSG00000039671	Zmynd8	1110013E22Rik|2010005I16Rik|3632413B07Rik|AI316811|AL024039|Prkcbp1|RACK7	zinc finger, MYND-type containing 8	protein-coding
mm_97705.1	chr11	80178197	80178227	+	1	NA	intron (NM_172133, intron 10 of 10)	intron (NM_172133, intron 10 of 10)	-5660	NM_028019	71956	Mm.22985	NM_028019	ENSMUSG00000020707	Rnf135	0610037N03Rik|2410006N06Rik	ring finger protein 135	protein-coding
mm_72805.1	chr8	87472867	87472880	+	1	NA	promoter-TSS (NM_019626)	promoter-TSS (NM_019626)	61	NR_033430	100040294	Mm.213632	NR_033430	ENSMUSG00000097248	Gm2694	C230036H16Rik|linc1582	predicted gene 2694	ncRNA
mm_41357.1	chr5	90506529	90506539	+	1	NA	exon (NM_007423, exon 12 of 15)	exon (NM_007423, exon 12 of 15)	-12415	NM_145146	280662	Mm.348786	NM_145146	ENSMUSG00000029369	Afm	Alf|alpha-Alb	afamin	protein-coding
mm_64956.1	chr7	16497804	16497820	-	1	NA	exon (NM_172739, exon 7 of 7)	exon (NM_172739, exon 7 of 7)	-21032	NM_008718	18142	Mm.145821	NM_008718	ENSMUSG00000001988	Npas1	MOP5|bHLHe11	neuronal PAS domain protein 1	protein-coding
mm_127301.1	chr15	100227320	100227336	+	1	NA	promoter-TSS (NM_007497)	promoter-TSS (NM_007497)	-531	NM_007497	11908	Mm.676	NM_007497	ENSMUSG00000023027	Atf1	-	activating transcription factor 1	protein-coding
mm_162983.1	chr11	21370802	21370806	-	1	NA	promoter-TSS (NM_139297)	promoter-TSS (NM_139297)	-175	NM_139297	216558	Mm.28877	NM_139297	ENSMUSG00000001891	Ugp2	UDPGP|UGPase	UDP-glucose pyrophosphorylase 2	protein-coding
mm_147843.1	chr18	63386496	63386507	-	1	NA	5' UTR (NM_001039485, exon 1 of 54)	5' UTR (NM_001039485, exon 1 of 54)	682	NM_001039485	667742	Mm.158720	NM_172629	ENSMUSG00000041482	Piezo2	5930434P17|9030411M15Rik|9430028L06Rik|Fam38b|Fam38b2	piezo-type mechanosensitive ion channel component 2	protein-coding
mm_68709.1	chr7	119888321	119888324	-	1	NA	intron (NM_001163703, intron 1 of 2)	intron (NM_001163703, intron 1 of 2)	7136	NM_173408	233805	Mm.31539	NM_173408	ENSMUSG00000048787	Dcun1d3	1700020A13Rik|BC030335	DCN1, defective in cullin neddylation 1, domain containing 3 (S. cerevisiae)	protein-coding
mm_84882.1	chr9	79718836	79718842	-	1	NA	promoter-TSS (NM_001290308)	promoter-TSS (NM_001290308)	-117	NM_001290308	12816	Mm.3819	NM_007730	ENSMUSG00000032332	Col12a1	-	collagen, type XII, alpha 1	protein-coding
mm_14947.1	chr2	151962772	151962796	+	1	NA	Intergenic	Intergenic	4833	NR_035478	100316704		NR_035478	ENSMUSG00000088491	Mir1953	mir-1953|mmu-mir-1953	microRNA 1953	ncRNA
mm_137981.1	chr17	33591246	33591257	+	1	NA	intron (NM_053214, intron 16 of 27)	intron (NM_053214, intron 16 of 27)	35544	NM_053214	17916	Mm.42019	NM_053214	ENSMUSG00000024300	Myo1f	C330006B10Rik	myosin IF	protein-coding
mm_93499.1	chr10	112928828	112928845	-	1	NA	5' UTR (NM_001033474, exon 1 of 1)	5' UTR (NM_001033474, exon 1 of 1)	190	NM_001033474	382423	Mm.431239	NM_001033474	ENSMUSG00000074748	Atxn7l3b	4921506J03Rik|6230409E21Rik|AI315132|ENSMUSG00000074747	ataxin 7-like 3B	protein-coding
mm_69371.1	chr7	130792249	130792255	-	1	NA	intron (NM_001081038, intron 7 of 15)	intron (NM_001081038, intron 7 of 15)	18183	NM_001081038	330660	Mm.271550	NM_001081038	ENSMUSG00000040298	Btbd16	E330040A16Rik	BTB (POZ) domain containing 16	protein-coding
mm_163343.1	chr12	16580912	16580922	-	1	NA	intron (NM_172950, intron 1 of 19)	intron (NM_172950, intron 1 of 19)	8853	NM_015763	14245	Mm.153625	NM_015763	ENSMUSG00000020593	Lpin1	4631420P06|Kiaa0188|Lipin1|fld|mKIAA0188	lipin 1	protein-coding
mm_5687.1	chr1	43183768	43183794	-	1	NA	intron (NM_001289533, intron 1 of 5)	ORR1A4|LTR|ERVL-MaLR	12980	NM_001289533	14200	Mm.6799	NM_010212	ENSMUSG00000008136	Fhl2	FHL-2|SLIM-3|SLIM3	four and a half LIM domains 2	protein-coding
mm_78331.1	chr9	25252639	25252659	+	1	NA	exon (NM_001205367, exon 1 of 13)	exon (NM_001205367, exon 1 of 13)	210	NM_001205367	235072	Mm.270259	NM_009859	ENSMUSG00000001833	Sept7	Cdc10|E430034N22	septin 7	protein-coding
mm_144290.1	chr18	12135846	12135867	+	1	NA	exon (NM_024182, exon 2 of 13)	exon (NM_024182, exon 2 of 13)	7006	NM_024182	66878	Mm.28551	NM_024182	ENSMUSG00000024404	Riok3	1200013N13Rik|D18Ertd331e|E130306C24Rik|Sudd	RIO kinase 3	protein-coding
mm_110104.1	chr12	26413999	26414013	-	1	NA	TTS (NR_105856)	TTS (NR_105856)	1004	NR_105856	102466676		NR_105856	ENSMUSG00000098771	Mir6538	Gm27439|mmu-mir-6538	microRNA 6538	ncRNA
mm_40025.1	chr5	33371685	33371721	+	1	NA	exon (NM_021500, exon 8 of 9)	exon (NM_021500, exon 8 of 9)	-6993	NM_001081101	71101	Mm.132178	NM_001081101	ENSMUSG00000037355	Uvssa	4933407H18Rik|D330017J19Rik|Kiaa1530|mKIAA1530	UV stimulated scaffold protein A	protein-coding
mm_27088.1	chr3	30013389	30013399	-	1	NA	promoter-TSS (NM_007963)	promoter-TSS (NM_007963)	-190	NM_007963	14013	Mm.56965	NM_007963	ENSMUSG00000027684	Mecom	D630039M04Rik|Evi-1|Evi1|Jbo|Mds|Mds1|Mds1-Evi1|Prdm3|Znfpr1b1	MDS1 and EVI1 complex locus	protein-coding
mm_34449.1	chr4	148001793	148001804	+	1	NA	3' UTR (NM_008725, exon 3 of 3)	3' UTR (NM_008725, exon 3 of 3)	1076	NM_008725	230899	Mm.482123	NM_008725	ENSMUSG00000041616	Nppa	ANP|Anf|Pnd	natriuretic peptide type A	protein-coding
mm_141661.1	chr17	33760452	33760498	-	1	NA	promoter-TSS (NM_008997)	promoter-TSS (NM_008997)	11	NM_008997	19326	Mm.387587	NM_008997	ENSMUSG00000077450	Rab11b	A730055L17Rik	RAB11B, member RAS oncogene family	protein-coding
mm_5863.1	chr1	53774090	53774111	-	1	NA	intron (NM_133810, intron 2 of 7)	intron (NM_133810, intron 2 of 7)	11115	NM_133810	98267	Mm.25559	NM_133810	ENSMUSG00000026094	Stk17b	3110009A03Rik|AI120141|Drak2	serine/threonine kinase 17b (apoptosis-inducing)	protein-coding
mm_27467.1	chr3	52634485	52634491	-	1	NA	Intergenic	Intergenic	-105236	NR_038079	329639	Mm.131245	NR_038079	ENSMUSG00000102785	Gm2447	100039832|A530017F20	predicted gene 2447	ncRNA
mm_10416.1	chr2	13580104	13580115	+	1	NA	exon (NM_011701, exon 6 of 9)	exon (NM_011701, exon 6 of 9)	5798	NM_011701	22352	Mm.268000	NM_011701	ENSMUSG00000026728	Vim	-	vimentin	protein-coding
mm_62404.1	chr7	101148147	101148171	+	1	NA	intron (NM_199012, intron 3 of 20)	intron (NM_199012, intron 3 of 20)	39384	NM_199012	207278	Mm.263041	NM_199012	ENSMUSG00000030691	Fchsd2	BC034086|R74866|Sh3md3|mKIAA0769	FCH and double SH3 domains 2	protein-coding
mm_80614.1	chr9	88327628	88327630	+	1	NA	promoter-TSS (NM_011851)	promoter-TSS (NM_011851)	20	NM_011851	23959	Mm.244235	NM_011851	ENSMUSG00000032420	Nt5e	2210401F01Rik|5'-NT|AI447961|CD73|NT|Nt5|eNT	5' nucleotidase, ecto	protein-coding
mm_158638.1	chrX	155215681	155215723	-	1	NA	intron (NM_001291865, intron 2 of 6)	intron (NM_001291865, intron 2 of 6)	747	NM_009121	20229	Mm.2734	NM_009121	ENSMUSG00000025283	Sat1	AA617398|SSAT|Sat	spermidine/spermine N1-acetyl transferase 1	protein-coding
mm_2839.1	chr1	131562951	131562953	+	1	NA	Intergenic	ORR1A3|LTR|ERVL-MaLR	35049	NM_175382	108900	Mm.31278	NM_175382	ENSMUSG00000055184	Fam72a	2700049P18Rik|P17	family with sequence similarity 72, member A	protein-coding
mm_70602.1	chr8	13351652	13351657	+	1	NA	intron (NM_001291766, intron 2 of 10)	intron (NM_001291766, intron 2 of 10)	12850	NM_009361	21781	Mm.925	NM_009361	ENSMUSG00000038482	Tfdp1	Dp1|Drtf1	transcription factor Dp 1	protein-coding
mm_24360.1	chr3	90072642	90072657	+	1	NA	promoter-TSS (NM_001293748)	promoter-TSS (NM_001293748)	-2	NM_001293748	59069	Mm.240839	NM_022314	ENSMUSG00000027940	Tpm3	TM30nm|TMnm|Tm5NM|Tpm-5|Tpm5|Trop-5|gamma-TM|hTM30nm|hTMnm	tropomyosin 3, gamma	protein-coding
mm_144830.1	chr18	36365775	36365785	+	1	NA	intron (NM_001081365, intron 1 of 2)	intron (NM_001081365, intron 1 of 2)	17156	NM_001081365	66060	Mm.272527	NM_001081365	ENSMUSG00000046727	Cystm1	0610010O12Rik	cysteine-rich transmembrane module containing 1	protein-coding
mm_131424.1	chr16	14708266	14708308	+	1	NA	exon (NM_011415, exon 3 of 3)	exon (NM_011415, exon 3 of 3)	2428	NM_011415	20583	Mm.4272	NM_011415	ENSMUSG00000022676	Snai2	Slug|Slugh|Snail2	snail family zinc finger 2	protein-coding
mm_112457.1	chr13	5864771	5864803	+	1	NA	exon (NM_011803, exon 2 of 4)	exon (NM_011803, exon 2 of 4)	3298	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_79375.1	chr9	54699127	54699140	+	1	NA	promoter-TSS (NM_021422)	promoter-TSS (NM_021422)	-426	NM_021422	58233	Mm.489676	NM_021422	ENSMUSG00000032285	Dnaja4	1110021L12Rik|AV358213|Dj4|Hsj4|mmDjA4	DnaJ heat shock protein family (Hsp40) member A4	protein-coding
mm_141369.1	chr17	29007806	29007830	-	1	NA	5' UTR (NM_134115, exon 1 of 14)	5' UTR (NM_134115, exon 1 of 14)	119	NM_134115	106504	Mm.439986	NM_134115	ENSMUSG00000024006	Stk38	5830476G13Rik|9530097A09Rik|AA617404|Ndr1	serine/threonine kinase 38	protein-coding
mm_73260.1	chr8	104340710	104340723	+	1	NA	5' UTR (NM_024217, exon 1 of 5)	5' UTR (NM_024217, exon 1 of 5)	122	NM_024217	68119	Mm.390108	NM_024217	ENSMUSG00000031875	Cmtm3	9430096L06Rik|AI413895|BNAS2|Cklfsf3	CKLF-like MARVEL transmembrane domain containing 3	protein-coding
mm_62227.1	chr7	98506952	98506957	+	1	NA	Intergenic	U1|snRNA|snRNA	12732	NM_001113379	434215	Mm.323057	NM_001113379	ENSMUSG00000090958	Lrrc32	AI426318|D11S833Eh|D7H11S833E|EG434215|Garp	leucine rich repeat containing 32	protein-coding
mm_156380.1	chrX	139672123	139672154	+	1	NA	3' UTR (NM_023270, exon 7 of 7)	3' UTR (NM_023270, exon 7 of 7)	-12858	NM_001081499	245638	Mm.275869	NM_001081499	ENSMUSG00000042473	Tbc1d8b	4921505D17Rik|9030605E16Rik	TBC1 domain family, member 8B	protein-coding
mm_167360.1	chr8	84774476	84774479	-	1	NA	promoter-TSS (NM_001081981)	promoter-TSS (NM_001081981)	-108	NM_001297601	18032	Mm.9394	NM_010906	ENSMUSG00000001911	Nfix	CTF|NF-I/X|NF1-X|NFI-X	nuclear factor I/X	protein-coding
mm_104725.1	chr11	98321282	98321284	-	1	NA	Intergenic	Intergenic	8362	NM_010895	18013	Mm.4814	NM_010895	ENSMUSG00000038255	Neurod2	Ndrf|bHLHa1	neurogenic differentiation 2	protein-coding
mm_123343.1	chr14	63138416	63138434	-	1	NA	exon (NM_007798, exon 7 of 10)	exon (NM_007798, exon 7 of 10)	15963	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_123670.1	chr14	69249149	69249156	-	1	NA	intron (NM_026331, intron 2 of 3)	intron (NM_026331, intron 2 of 3)	35951	NM_026331	67712	Mm.293635	NM_026331	ENSMUSG00000034248	Slc25a37	1700020E22Rik|4930513O14Rik|4930526G11Rik|AI848481|C330015G08Rik|Mfrn|Mfrn1|Mscp|frascati|mitoferrin	solute carrier family 25, member 37	protein-coding
mm_56999.1	chr6	121003067	121003076	-	1	NA	intron (NM_001270475, intron 17 of 31)	intron (NM_001270475, intron 17 of 31)	44227	NR_138099	215458	Mm.122399	NR_138099		LOC215458	-	uncharacterized LOC215458	ncRNA
mm_80281.1	chr9	73039747	73039760	+	1	NA	promoter-TSS (NM_018889)	promoter-TSS (NM_018889)	35	NM_001308425	66364	Mm.392089	NM_001308425		2310009A05Rik	5031420N21Rik	RIKEN cDNA 2310009A05 gene	protein-coding
mm_172174.1	chr6	4747138	4747139	-	1	NA	promoter-TSS (NM_001130188)	promoter-TSS (NM_001130188)	66	NM_001130188	20392	Mm.8739	NM_011360	ENSMUSG00000004631	Sgce	e-SG	sarcoglycan, epsilon	protein-coding
mm_107166.1	chr12	24682697	24682700	+	1	NA	promoter-TSS (NM_001161807)	promoter-TSS (NM_001161807)	-903	NM_001161807	12879	Mm.52265	NM_138686	ENSMUSG00000062563	Cys1	2900006B19Rik|AV218859|Ccap|ck|cpk	cystin 1	protein-coding
mm_91709.1	chr10	44148817	44148834	-	1	NA	Intergenic	CpG	-21622	NR_001582	70365	Mm.87073	NR_001582	ENSMUSG00000091358	Speer5-ps1	1700007C10Rik|SPEER-5|Speer5-ps	spermatogenesis associated glutamate (E)-rich protein 5, pseudogene 1	pseudo
mm_57309.1	chr6	124721907	124721917	-	1	NA	exon (NM_013545, exon 13 of 16)	exon (NM_013545, exon 13 of 16)	-3522	NR_029792	723944		NR_029792	ENSMUSG00000065462	Mir200c	Mirn200c|mir-200c	microRNA 200c	ncRNA
mm_65839.1	chr7	29232538	29232610	-	1	NA	promoter-TSS (NM_001033525)	promoter-TSS (NM_001033525)	-52	NM_001033525	52150	Mm.24877	NM_001033525	ENSMUSG00000046410	Kcnk6	D7Ertd764e|Toss|Twik2	potassium inwardly-rectifying channel, subfamily K, member 6	protein-coding
mm_69567.1	chr7	135700721	135700734	-	1	NA	exon (NM_001081117, exon 12 of 14)	exon (NM_001081117, exon 12 of 14)	15652	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_124253.1	chr14	101892227	101892234	-	1	NA	intron (NM_001347628, intron 8 of 26)	intron (NM_001347628, intron 8 of 26)	51607	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_15481.1	chr2	157561773	157561783	+	1	NA	3' UTR (NM_010923, exon 3 of 3)	3' UTR (NM_010923, exon 3 of 3)	1700	NM_180960	18111	Mm.34330	NM_010923	ENSMUSG00000067786	Nnat	5730414I02Rik|AW107673|Peg5	neuronatin	protein-coding
mm_34790.1	chr4	154237578	154237608	+	1	NA	intron (NM_001162977, intron 4 of 36)	intron (NM_001162977, intron 4 of 36)	62302	NM_001112744	230972	Mm.38481	NM_001112744	ENSMUSG00000029032	Arhgef16	-	Rho guanine nucleotide exchange factor (GEF) 16	protein-coding
mm_26129.1	chr3	137868063	137868069	+	1	NA	intron (NM_001033155, intron 1 of 7)	GC_rich|Low_complexity|Low_complexity	391	NM_001033155	70604	Mm.256488	NM_001033155	ENSMUSG00000074212	Dnajb14	5730496F10Rik	DnaJ heat shock protein family (Hsp40) member B14	protein-coding
mm_76699.1	chr8	94364030	94364035	-	1	NA	intron (NM_019415, intron 24 of 24)	intron (NM_019415, intron 24 of 24)	-22468	NM_022331	64209	Mm.29151	NM_022331	ENSMUSG00000031770	Herpud1	Herp|Mifl|SUP	homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1	protein-coding
mm_8975.1	chr1	165460431	165460487	-	1	NA	promoter-TSS (NM_028759)	promoter-TSS (NM_028759)	4	NM_028759	74106	Mm.227605	NM_028759	ENSMUSG00000026571	Dcaf6	1200006M05Rik|Iqwd1|PC326	DDB1 and CUL4 associated factor 6	protein-coding
mm_30928.1	chr4	32800247	32800289	+	1	NA	promoter-TSS (NM_175364)	promoter-TSS (NM_175364)	9	NM_175364	108755	Mm.1182	NM_175364	ENSMUSG00000045854	Lyrm2	2610208E05Rik	LYR motif containing 2	protein-coding
mm_91807.1	chr10	53932833	53932833	-	1	NA	intron (NM_008548, intron 8 of 12)	intron (NM_008548, intron 8 of 12)	142963	NM_008548	17155	Mm.117294	NM_008548	ENSMUSG00000003746	Man1a	Man1a1|PCR1	mannosidase 1, alpha	protein-coding
mm_55691.1	chr6	72789192	72789238	-	1	NA	promoter-TSS (NM_009332)	promoter-TSS (NM_009332)	-170	NM_009332	21415	Mm.440067	NM_009332	ENSMUSG00000055799	Tcf7l1	Tcf-3|Tcf3|bHLHb21	transcription factor 7 like 1 (T cell specific, HMG box)	protein-coding
mm_41214.1	chr5	88581420	88581426	+	1	NA	intron (NM_001289774, intron 1 of 17)	intron (NM_001289774, intron 1 of 17)	-2090	NM_001289777	52822	Mm.270469	NM_027530	ENSMUSG00000029291	Rufy3	2810428M05Rik|6330416M07Rik|AW455998|AW538594|D5Bwg0860e|Ripx|Rpipx	RUN and FYVE domain containing 3	protein-coding
mm_58410.1	chr7	3289201	3289212	+	1	NA	5' UTR (NM_001093764, exon 1 of 3)	5' UTR (NM_001093764, exon 1 of 3)	168	NM_001093764	50918	Mm.29874	NM_016969	ENSMUSG00000068566	Myadm	D7Wsu62e	myeloid-associated differentiation marker	protein-coding
mm_151532.1	chr19	58759701	58759745	+	1	NA	promoter-TSS (NM_011128)	promoter-TSS (NM_011128)	0	NM_011128	18947	Mm.212333	NM_011128	ENSMUSG00000025091	Pnliprp2	PLRP2	pancreatic lipase-related protein 2	protein-coding
mm_127452.1	chr15	101270776	101270793	+	1	NA	exon (NM_010444, exon 2 of 7)	exon (NM_010444, exon 2 of 7)	3938	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_50210.1	chr6	42264984	42265032	+	1	NA	promoter-TSS (NM_007610)	promoter-TSS (NM_007610)	23	NM_007610	12366	Mm.3921	NM_007610	ENSMUSG00000029863	Casp2	CASP-2|ICH-1|NEDD-2|Nedd2	caspase 2	protein-coding
mm_116543.1	chr13	45940696	45940699	-	1	NA	intron (NM_001199304, intron 2 of 6)	AT_rich|Low_complexity|Low_complexity	24294	NM_001199304	20238	Mm.342683	NM_009124	ENSMUSG00000046876	Atxn1	2900016G23Rik|Atx1|C85907|ENSMUSG00000074917|Gm10786|Sca1	ataxin 1	protein-coding
mm_135594.1	chr16	50722873	50722887	-	1	NA	Intergenic	MLT1A1|LTR|ERVL-MaLR	-4252	NR_105782	102466634		NR_105782	ENSMUSG00000098482	Mir6363	Gm28026|mmu-mir-6363	microRNA 6363	ncRNA
mm_51670.1	chr6	86404221	86404240	+	1	NA	promoter-TSS (NM_011585)	promoter-TSS (NM_011585)	11	NM_001164078	21841	Mm.333219	NM_011585	ENSMUSG00000071337	Tia1	2310050N03Rik|AI256674|TIA-1|mTIA-1	cytotoxic granule-associated RNA binding protein 1	protein-coding
mm_126594.1	chr15	82354478	82354508	+	1	NA	promoter-TSS (NM_025987)	promoter-TSS (NM_025987)	-202	NM_025987	67130	Mm.27570	NM_025987	ENSMUSG00000022450	Ndufa6	14kDa|2700038D15Rik|B230217P19Rik	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 6 (B14)	protein-coding
mm_146175.1	chr18	75368032	75368035	+	1	NA	5' UTR (NM_001042660, exon 1 of 4)	5' UTR (NM_001042660, exon 1 of 4)	668	NM_001042660	17131	Mm.34407	NM_008543	ENSMUSG00000025880	Smad7	Madh7	SMAD family member 7	protein-coding
mm_110645.1	chr12	58953015	58953017	-	1	NA	Intergenic	Intergenic	59001	NM_009147	20334	Mm.491137	NM_009147	ENSMUSG00000020986	Sec23a	Msec23|Sec23r	SEC23 homolog A, COPII coat complex component	protein-coding
mm_76141.1	chr8	81823125	81823173	-	1	NA	intron (NM_001024617, intron 7 of 24)	intron (NM_001024617, intron 7 of 24)	480587	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_46670.1	chr5	108795346	108795351	-	1	NA	promoter-TSS (NM_026109)	promoter-TSS (NM_026109)	15	NM_026109	67366	Mm.46274	NM_026109	ENSMUSG00000004821	Tmed11	1810008K16Rik	transmembrane p24 trafficking protein 11	protein-coding
mm_45183.1	chr5	51872102	51872104	-	1	NA	Intergenic	Intergenic	263914	NR_105845	102466648		NR_105845	ENSMUSG00000098726	Mir6417	Gm27334|mmu-mir-6417	microRNA 6417	ncRNA
mm_24553.1	chr3	93443452	93443473	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	1132	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_33388.1	chr4	129795716	129795747	+	1	NA	Intergenic	Intergenic	-24748	NM_008974	19244	Mm.193688	NM_008974	ENSMUSG00000028788	Ptp4a2	Prl-2	protein tyrosine phosphatase 4a2	protein-coding
mm_137732.1	chr17	29308095	29308097	+	1	NA	Intergenic	Intergenic	-10786	NM_023734	74116	Mm.30950	NM_023734	ENSMUSG00000024011	Pi16	1200009H11Rik|Cripi|PI-16	peptidase inhibitor 16	protein-coding
mm_114600.1	chr13	75770779	75770799	+	1	NA	exon (NM_138953, exon 12 of 12)	exon (NM_138953, exon 12 of 12)	63305	NM_138953	192657	Mm.21288	NM_138953	ENSMUSG00000001542	Ell2	-	elongation factor RNA polymerase II 2	protein-coding
mm_71729.1	chr8	61984002	61984004	+	1	NA	intron (NM_001293783, intron 21 of 37)	intron (NM_001293783, intron 21 of 37)	55916	NM_001293783	234311	Mm.275233	NM_144928	ENSMUSG00000037921	Ddx60	9830118M07	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	protein-coding
mm_789.1	chr1	45333605	45333618	+	1	NA	exon (NM_009930, exon 22 of 51)	exon (NM_009930, exon 22 of 51)	22073	NM_009930	12825	Mm.249555	NM_009930	ENSMUSG00000026043	Col3a1	AW550625|Col3a-1|Tsk-2|Tsk2	collagen, type III, alpha 1	protein-coding
mm_47610.1	chr5	125124808	125124839	-	1	NA	exon (NM_001253905, exon 3 of 43)	exon (NM_001253905, exon 3 of 43)	54391	NM_001253905	20602	Mm.278646	NM_011424	ENSMUSG00000029478	Ncor2	N-CoR|SMRT|SMRTe	nuclear receptor co-repressor 2	protein-coding
mm_28667.1	chr3	95281763	95281793	-	1	NA	5' UTR (NM_173347, exon 1 of 8)	5' UTR (NM_173347, exon 1 of 8)	298	NM_173347	229589	Mm.14155	NM_173347	ENSMUSG00000015711	Prune1	9230112O05Rik|C130058A12|DRES-17|HTCD37|PRUNEM1|Prune|Prune-M1	prune exopolyphosphatase	protein-coding
mm_40148.1	chr5	35388845	35388882	+	1	NA	promoter-TSS (NM_010445)	promoter-TSS (NM_010445)	-254	NM_010445	15371	Mm.358606	NM_010445	ENSMUSG00000067438	Hmx1	Nkx5-3	H6 homeobox 1	protein-coding
mm_128193.1	chr15	34996084	34996119	-	1	NA	intron (NM_019635, intron 8 of 10)	B1_Mus2|SINE|Alu	158052	NM_001271704	16539	Mm.71045	NM_181317	ENSMUSG00000050963	Kcns2	E130006J24Rik|Kv9.2	K+ voltage-gated channel, subfamily S, 2	protein-coding
mm_14641.1	chr2	136891564	136891599	+	1	NA	promoter-TSS (NM_001286983)	promoter-TSS (NM_001286983)	-175	NM_001286983	59030	Mm.272570	NM_021527	ENSMUSG00000027274	Mkks	1300013E18Rik|AI463362|AI957237|Bbs6	McKusick-Kaufman syndrome	protein-coding
mm_75463.1	chr8	47818200	47818225	-	1	NA	Intergenic	Intergenic	-3931	NM_001111318	100039801	Mm.471595	NM_001111318	ENSMUSG00000061974	Cldn24	ENSMUSG00000061974|Gm10107	claudin 24	protein-coding
mm_159854.1	chr5	137858014	137858014	-	1	NA	promoter-TSS (NM_133209)	promoter-TSS (NM_133209)	35	NM_133209	170741	Mm.347593	NM_133209	ENSMUSG00000066684	Pilrb1	FDFACT|Fdact|Pilrb	paired immunoglobin-like type 2 receptor beta 1	protein-coding
mm_37949.1	chr4	133212481	133212501	-	1	NA	promoter-TSS (NM_008154)	promoter-TSS (NM_008154)	45	NM_008154	14748	Mm.4721	NM_008154	ENSMUSG00000049649	Gpr3	Gpcr20|Gpcr21|Gpcr3	G-protein coupled receptor 3	protein-coding
mm_157166.1	chrX	9467232	9467240	-	1	NA	intron (NM_007807, intron 1 of 12)	intron (NM_007807, intron 1 of 12)	2088	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_108442.1	chr12	82397379	82397389	+	1	NA	exon (NM_001167983, exon 12 of 24)	exon (NM_001167983, exon 12 of 24)	86035	NM_172579	217692	Mm.261333	NM_172579	ENSMUSG00000042700	Sipa1l1	4931426N11Rik|AW213287|Spar|mKIAA0440	signal-induced proliferation-associated 1 like 1	protein-coding
mm_27123.1	chr3	31310350	31310373	-	1	NA	promoter-TSS (NM_172861)	promoter-TSS (NM_172861)	-42	NM_172861	241919	Mm.285366	NM_172861	ENSMUSG00000069072	Slc7a14	A930013N06|BC061928	solute carrier family 7 (cationic amino acid transporter, y+ system), member 14	protein-coding
mm_63005.1	chr7	120843552	120843572	+	1	NA	promoter-TSS (NM_001267710)	promoter-TSS (NM_001267710)	-38	NM_001267710	13631	Mm.25997	NM_007908	ENSMUSG00000035064	Eef2k	C86191|eEF-2K	eukaryotic elongation factor-2 kinase	protein-coding
mm_95224.1	chr11	44469911	44469926	+	1	NA	intron (NM_024475, intron 1 of 10)	intron (NM_024475, intron 1 of 10)	630	NM_024475	79560	Mm.338784	NM_024475	ENSMUSG00000041231	Ublcp1	4930527B16Rik|8430435I17Rik|BC002236	ubiquitin-like domain containing CTD phosphatase 1	protein-coding
mm_65433.1	chr7	25368082	25368096	-	1	NA	exon (NM_028219, exon 4 of 5)	exon (NM_028219, exon 4 of 5)	1635	NM_001081375	72383	Mm.34382	NM_028219	ENSMUSG00000063651	Cnfn	2210418J09Rik	cornifelin	protein-coding
mm_53570.1	chr6	137252536	137252544	+	1	NA	5' UTR (NM_011216, exon 1 of 27)	5' UTR (NM_011216, exon 1 of 27)	241	NM_011216	19277	Mm.186361	NM_011216	ENSMUSG00000030223	Ptpro	D28|GLEPP1|PTPBK|PTPROt|PTPU2|PTPoc|PTPphi|Ptpn15|R-PTP-O	protein tyrosine phosphatase, receptor type, O	protein-coding
mm_28940.1	chr3	98882298	98882307	-	1	NA	intron (NM_019545, intron 4 of 8)	intron (NM_019545, intron 4 of 8)	10928	NM_019545	56185	Mm.281874	NM_019545	ENSMUSG00000027870	Hao2	AI325478|Hao-2|Hao3|Haox3	hydroxyacid oxidase 2	protein-coding
mm_11775.1	chr2	38931953	38931959	+	1	NA	promoter-TSS (NM_172854)	promoter-TSS (NM_172854)	-24	NM_172854	241327	Mm.103491	NM_172854	ENSMUSG00000046618	Olfml2a	4932431K08Rik|mFLJ00237	olfactomedin-like 2A	protein-coding
mm_14940.1	chr2	151561139	151561156	+	1	NA	non-coding (NR_126058, exon 4 of 4)	non-coding (NR_126058, exon 4 of 4)	-11476	NM_145535	228765	Mm.32068	NM_145535	ENSMUSG00000027456	Sdcbp2	-	syndecan binding protein (syntenin) 2	protein-coding
mm_55371.1	chr6	57825056	57825141	-	1	NA	promoter-TSS (NM_146168)	promoter-TSS (NM_146168)	27	NM_146168	232023	Mm.24642	NM_146168	ENSMUSG00000037788	Vopp1	AW146242|Ecop	vesicular, overexpressed in cancer, prosurvival protein 1	protein-coding
mm_50315.1	chr6	47877621	47877640	+	1	NA	promoter-TSS (NM_146175)	promoter-TSS (NM_146175)	75	NM_146175	101095	Mm.440186	NM_146175	ENSMUSG00000025821	Zfp282	AI449432|C81429|E430019K09Rik|HUB1	zinc finger protein 282	protein-coding
mm_144395.1	chr18	20673753	20673801	+	1	NA	3' UTR (NM_013697, exon 4 of 4)	3' UTR (NM_013697, exon 4 of 4)	8527	NM_013697	22139	Mm.2108	NM_013697	ENSMUSG00000061808	Ttr	AA408768|AI787086|D17860|prealbumin	transthyretin	protein-coding
mm_134349.1	chr16	16571479	16571497	-	1	NA	intron (NM_001301817, intron 1 of 16)	intron (NM_001301817, intron 1 of 16)	-11269	NM_139232	224014	Mm.256131	NM_139232	ENSMUSG00000022788	Fgd4	9030023J02Rik|9330209B17Rik|Frabp|ZFYVE6	FYVE, RhoGEF and PH domain containing 4	protein-coding
mm_88504.1	chr10	77862263	77862280	+	1	NA	exon (NM_001101631, exon 1 of 1)	exon (NM_001101631, exon 1 of 1)	296	NM_001101631	100041351	Mm.441672	NM_001101631		Gm3285	-	predicted gene 3285	protein-coding
mm_82145.1	chr9	123773520	123773530	+	1	NA	intron (NM_001166625, intron 2 of 3)	B3|SINE|B2	6314	NM_001166625	12769	Mm.440604	NM_009913	ENSMUSG00000029530	Ccr9	A130091K22Rik|Cmkbr10|GPR-9-6	chemokine (C-C motif) receptor 9	protein-coding
mm_63294.1	chr7	126807742	126807751	+	1	NA	Intergenic	Intergenic	-7299	NM_001177308	11674	Mm.275831	NM_007438	ENSMUSG00000030695	Aldoa	Aldo-1|Aldo1	aldolase A, fructose-bisphosphate	protein-coding
mm_108116.1	chr12	75596459	75596489	+	1	NA	promoter-TSS (NM_012024)	promoter-TSS (NM_012024)	-274	NM_012024	26932	Mm.259626	NM_012024	ENSMUSG00000021051	Ppp2r5e	4633401M22Rik|AI449017|B56beta	protein phosphatase 2, regulatory subunit B', epsilon	protein-coding
mm_94229.1	chr11	3289881	3289922	+	1	NA	promoter-TSS (NM_001253691)	promoter-TSS (NM_001253691)	-556	NM_001253690	56218	Mm.275563	NM_019574	ENSMUSG00000020453	Patz1	8430401L15Rik|AI447519|Mazr|Patz|Zfp278	POZ (BTB) and AT hook containing zinc finger 1	protein-coding
mm_32678.1	chr4	115784800	115784837	+	1	NA	promoter-TSS (NM_181040)	promoter-TSS (NM_181040)	4	NM_181040	230649	Mm.109600	NM_181040	ENSMUSG00000028710	Atpaf1	6330547J17Rik|AI593252|ATP11|ATP11p	ATP synthase mitochondrial F1 complex assembly factor 1	protein-coding
mm_155862.1	chrX	101377291	101377317	+	1	NA	promoter-TSS (NM_008124)	promoter-TSS (NM_008124)	69	NM_008124	14618	Mm.21198	NM_008124	ENSMUSG00000047797	Gjb1	Cnx32|Cx32|connexin-32	gap junction protein, beta 1	protein-coding
mm_46638.1	chr5	108525520	108525540	-	1	NA	exon (NM_007756, exon 3 of 4)	exon (NM_007756, exon 3 of 4)	24497	NM_007756	12889	Mm.5195	NM_007756	ENSMUSG00000033615	Cplx1	921-S	complexin 1	protein-coding
mm_32159.1	chr4	99971755	99971771	+	1	NA	intron (NM_028132, intron 7 of 10)	intron (NM_028132, intron 7 of 10)	42312	NM_028132	72157	Mm.217764	NM_028132	ENSMUSG00000025791	Pgm2	2610020G18Rik|AA407108|AI098105|Pgm-2|Pgm1	phosphoglucomutase 2	protein-coding
mm_16176.1	chr2	172551504	172551518	+	1	NA	exon (NM_001159696, exon 2 of 7)	exon (NM_001159696, exon 2 of 7)	520	NM_001159696	21420	Mm.3629	NM_009335	ENSMUSG00000028640	Tfap2c	AA409384|AP2gamma|Ap-2.2|Stra2|Tcfap2c	transcription factor AP-2, gamma	protein-coding
mm_73487.1	chr8	107031355	107031365	+	1	NA	promoter-TSS (NM_126165)	promoter-TSS (NM_126165)	34	NM_126165	116733	Mm.236004	NM_126165	ENSMUSG00000031913	Vps4a	4930589C15Rik|AI325971|AW553189	vacuolar protein sorting 4A	protein-coding
mm_144479.1	chr18	23954669	23954704	+	1	NA	promoter-TSS (NM_027007)	promoter-TSS (NM_027007)	-2	NM_027007	69256	Mm.218343	NM_027007	ENSMUSG00000024276	Zfp397	2810411K16Rik|6720480F11Rik|AI461664	zinc finger protein 397	protein-coding
mm_33837.1	chr4	135686456	135686496	+	1	NA	promoter-TSS (NM_174851)	promoter-TSS (NM_174851)	19	NM_174851	242700	Mm.259623	NM_174851	ENSMUSG00000062157	Ifnlr1	CRF2-12|Il28ra	interferon lambda receptor 1	protein-coding
mm_5074.1	chr1	3654896	3654899	-	1	NA	intron (NM_001011874, intron 1 of 2)	intron (NM_001011874, intron 1 of 2)	16601	NM_001011874	497097	Mm.454496	NM_001011874	ENSMUSG00000051951	Xkr4	AY534250|Gm210|XRG4|mKIAA1889	X-linked Kx blood group related 4	protein-coding
mm_33043.1	chr4	122961275	122961349	+	1	NA	promoter-TSS (NM_029662)	promoter-TSS (NM_029662)	-124	NM_029662	76574	Mm.331842	NM_029662	ENSMUSG00000028655	Mfsd2a	1700018O18Rik|Mfsd2|NLS1	major facilitator superfamily domain containing 2A	protein-coding
mm_153466.1	chr19	41264300	41264304	-	1	NA	promoter-TSS (NM_133352)	promoter-TSS (NM_133352)	-298	NM_133352	107358	Mm.246440	NM_133352	ENSMUSG00000025016	Tm9sf3	1810073M23Rik|2810031D16Rik|AI115521|AI413748|AW146116|AW549777|Smbp|mKIAA4036	transmembrane 9 superfamily member 3	protein-coding
mm_101534.1	chr11	33203601	33203611	-	1	NA	promoter-TSS (NM_019916)	promoter-TSS (NM_019916)	-18	NM_019916	27140	Mm.25362	NM_019916	ENSMUSG00000040610	Tlx3	Hox11l2|Rnx|Tlx1l2	T cell leukemia, homeobox 3	protein-coding
mm_91305.1	chr10	24917948	24917956	-	1	NA	exon (NM_007482, exon 4 of 8)	exon (NM_007482, exon 4 of 8)	7288	NR_105870	102465545		NR_105870	ENSMUSG00000099181	Mir6905	Gm27879|mmu-mir-6905	microRNA 6905	ncRNA
mm_82587.1	chr9	21237216	21237230	-	1	NA	exon (NM_016679, exon 1 of 5)	exon (NM_016679, exon 1 of 5)	2109	NM_016679	50868	Mm.248266	NM_016679	ENSMUSG00000003308	Keap1	INRF2|mKIAA0132	kelch-like ECH-associated protein 1	protein-coding
mm_125879.1	chr15	75634241	75634262	+	1	NA	Intergenic	RLTR14-int|LTR|ERV1	17567	NM_011759	22701	Mm.87210	NM_011759	ENSMUSG00000047003	Zfp41	CTfin92|Zfp-41	zinc finger protein 41	protein-coding
mm_111990.1	chr12	110682558	110682564	-	1	NA	promoter-TSS (NM_025488)	promoter-TSS (NM_025488)	58	NM_025488	66323	Mm.273316	NM_025488	ENSMUSG00000056508	1700001K19Rik	-	RIKEN cDNA 1700001K19 gene	protein-coding
mm_15876.1	chr2	164836412	164836458	+	1	NA	exon (NM_008906, exon 8 of 15)	exon (NM_008906, exon 8 of 15)	2662	NM_008906	19025	Mm.359633	NM_008906	ENSMUSG00000017760	Ctsa	AU019505|PPCA|Ppgb	cathepsin A	protein-coding
mm_79412.1	chr9	55201584	55201589	+	1	NA	intron (NM_001346657, intron 10 of 11)	B2_Mm1t|SINE|B2	-7349	NM_028049	71999	Mm.276429	NM_028049	ENSMUSG00000032309	Fbxo22	0610033L19Rik|1600016C16Rik	F-box protein 22	protein-coding
mm_79404.1	chr9	55149301	55149312	+	1	NA	promoter-TSS (NM_180600)	promoter-TSS (NM_180600)	-63	NM_180600	109161	Mm.207894	NM_180600	ENSMUSG00000032307	Ube2q2	3010021M21Rik	ubiquitin-conjugating enzyme E2Q family member 2	protein-coding
mm_85160.1	chr9	96349892	96349895	-	1	NA	intron (NM_007502, intron 1 of 6)	intron (NM_007502, intron 1 of 6)	14406	NM_007502	11933	Mm.424	NM_007502	ENSMUSG00000032412	Atp1b3	AA409958|AI664000|AW212096	ATPase, Na+/K+ transporting, beta 3 polypeptide	protein-coding
mm_53549.1	chr6	136831898	136831937	+	1	NA	intron (NM_001039558, intron 1 of 1)	intron (NM_001039558, intron 1 of 1)	3074	NM_178776	320135	Mm.386899	NM_178776	ENSMUSG00000047515	BC049715	-	cDNA sequence BC049715	protein-coding
mm_92851.1	chr10	81524272	81524285	-	1	NA	promoter-TSS (NM_010304)	promoter-TSS (NM_010304)	-53	NM_010304	14676	Mm.1546	NM_010304	ENSMUSG00000034792	Gna15	G[a]15|Galpha15	guanine nucleotide binding protein, alpha 15	protein-coding
mm_112119.1	chr12	112829487	112829504	-	1	NA	promoter-TSS (NM_028023)	promoter-TSS (NM_028023)	-106	NM_028023	71963	Mm.313185	NM_028023	ENSMUSG00000047832	Cdca4	2410018C03Rik|HEPP|SEI-3	cell division cycle associated 4	protein-coding
mm_100343.1	chr11	118394004	118394017	+	1	NA	exon (NM_011150, exon 6 of 6)	exon (NM_011150, exon 6 of 6)	7921	NM_011150	19039	Mm.3152	NM_011150	ENSMUSG00000033880	Lgals3bp	90K|CyCAP|MAC-2BP|Ppicap|Tango10b	lectin, galactoside-binding, soluble, 3 binding protein	protein-coding
mm_640.1	chr1	40399866	40399879	+	1	NA	Intergenic	Intergenic	-29698	NM_001294171	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_69423.1	chr7	132771325	132771328	-	1	NA	intron (NM_001347630, intron 2 of 3)	intron (NM_001347630, intron 2 of 3)	5590	NM_001347630	77938	Mm.225649	NM_175268	ENSMUSG00000030956	Fam53b	A930008G19Rik|mKIAA0140	family with sequence similarity 53, member B	protein-coding
mm_29782.1	chr3	127498987	127499038	-	1	NA	5' UTR (NM_001327938, exon 1 of 48)	5' UTR (NM_001327938, exon 1 of 48)	103	NM_001327938	109676	Mm.220242	NM_178655	ENSMUSG00000032826	Ank2	100043364|AI835472|AW491075|Ank-2|Gm4392	ankyrin 2, brain	protein-coding
mm_96901.1	chr11	70452231	70452250	+	1	NA	exon (NM_025397, exon 2 of 3)	exon (NM_025397, exon 2 of 3)	309	NM_025397	66172	Mm.46424	NM_025397	ENSMUSG00000018923	Med11	1110030J09Rik|AI465144|AW545069	mediator complex subunit 11	protein-coding
mm_6894.1	chr1	84696167	84696178	-	1	NA	promoter-TSS (NM_152915)	promoter-TSS (NM_152915)	49	NM_152915	227325	Mm.292560	NM_152915	ENSMUSG00000036766	Dner	A930026D19Rik|BET|Bret	delta/notch-like EGF repeat containing	protein-coding
mm_125363.1	chr15	39463095	39463098	+	1	NA	intron (NM_001256382, intron 10 of 26)	intron (NM_001256382, intron 10 of 26)	-196415	NM_001256384	116838	Mm.309296	NM_053271	ENSMUSG00000037386	Rims2	2810036I15Rik|AW048769|RIM2|Rab3ip2|Rim2(+40A)|Rim2(+44A)|Rim2(+4A)|Serg2|Syt3-rs|mKIAA0751	regulating synaptic membrane exocytosis 2	protein-coding
mm_136149.1	chr16	87612340	87612350	-	1	NA	Intergenic	Intergenic	59015	NM_144854	224419	Mm.194466	NM_144854	ENSMUSG00000025610	Map3k7cl	C21orf7|ORF63|Tak1l	Map3k7 C-terminal like	protein-coding
mm_97418.1	chr11	77985754	77985758	+	1	NA	intron (NM_174852, intron 2 of 14)	intron (NM_174852, intron 2 of 14)	2940	NM_174852	268448	Mm.274329	NM_174852	ENSMUSG00000037791	Phf12	2410142K10Rik|F630045O13|PF1|mKIAA1523	PHD finger protein 12	protein-coding
mm_98460.1	chr11	94947878	94947900	+	1	NA	exon (NM_007742, exon 40 of 51)	exon (NM_007742, exon 40 of 51)	11665	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_25181.1	chr3	103309762	103309767	+	1	NA	intron (NM_001079830, intron 1 of 18)	AT_rich|Low_complexity|Low_complexity	30471	NM_001079830	94093	Mm.195036	NM_053170	ENSMUSG00000033014	Trim33	8030451N04Rik|AI413936|Ecto|Tif1g	tripartite motif-containing 33	protein-coding
mm_126144.1	chr15	78349028	78349070	+	1	NA	TTS (NR_106138)	TTS (NR_106138)	450	NR_106138	102466845		NR_106138	ENSMUSG00000099059	Mir7676-2	Gm27790|mmu-mir-7676-2	microRNA 7676-2	ncRNA
mm_25499.1	chr3	109386670	109386681	+	1	NA	intron (NM_020505, intron 1 of 26)	intron (NM_020505, intron 1 of 26)	45992	NM_020505	57257	Mm.282257	NM_020505	ENSMUSG00000033721	Vav3	A530094I06Rik|AA986410|Idd18.1	vav 3 oncogene	protein-coding
mm_119081.1	chr14	30886459	30886483	+	1	NA	promoter-TSS (NM_001289633)	promoter-TSS (NM_001289633)	-5	NM_001159299	16427	Mm.34819	NM_018746	ENSMUSG00000021922	Itih4	ITI-HC4|Itih-4|PK-120	inter alpha-trypsin inhibitor, heavy chain 4	protein-coding
mm_146733.1	chr18	15331858	15331871	-	1	NA	Intergenic	Intergenic	71135	NM_001308647	11829	Mm.250786	NM_009700	ENSMUSG00000024411	Aqp4	WCH4	aquaporin 4	protein-coding
mm_87355.1	chr10	43610510	43610518	+	1	NA	intron (NR_033558, intron 2 of 2)	intron (NR_033558, intron 2 of 2)	17087	NR_033558	414125	Mm.244305	NR_033558	ENSMUSG00000075184	F830002L21Rik	F930017D23Rik	RIKEN cDNA F830002L21 gene	ncRNA
mm_5958.1	chr1	56971713	56971739	-	1	NA	promoter-TSS (NM_139146)	promoter-TSS (NM_139146)	257	NR_024325	329160	Mm.419039	NR_024325	ENSMUSG00000087022	9130024F11Rik	B530002L08|EG329160	RIKEN cDNA 9130024F11 gene	ncRNA
mm_148022.1	chr18	68475163	68475173	-	1	NA	Intergenic	Intergenic	-45848	NM_001271716	17200	Mm.426053	NM_008560	ENSMUSG00000045569	Mc2r	ACTH-R|ACTHR|MC2-R	melanocortin 2 receptor	protein-coding
mm_111365.1	chr12	87159948	87159948	-	1	NA	intron (NM_010363, intron 4 of 8)	intron (NM_010363, intron 4 of 8)	-4463	NR_136901	625237	Mm.390529	NR_136901		Gm6566	EG625237	predicted gene 6566	ncRNA
mm_123368.1	chr14	63171361	63171361	-	1	NA	intron (NM_010191, intron 3 of 9)	RLTR1B|LTR|ERV1	8217	NM_010191	14137	Mm.474432	NM_010191	ENSMUSG00000021273	Fdft1	SQS|SS	farnesyl diphosphate farnesyl transferase 1	protein-coding
mm_99350.1	chr11	101583574	101583593	+	1	NA	exon (NM_144830, exon 3 of 9)	exon (NM_144830, exon 3 of 9)	1341	NM_144830	217203	Mm.280559	NM_144830	ENSMUSG00000034947	Tmem106a	0610008L10Rik|AI043106|BC022145	transmembrane protein 106A	protein-coding
mm_56486.1	chr6	99173308	99173318	-	1	NA	intron (NM_001347345, intron 4 of 19)	intron (NM_001347345, intron 4 of 19)	93202	NM_001197321	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_153318.1	chr19	38116813	38116851	-	1	NA	3' UTR (NM_011255, exon 6 of 6)	3' UTR (NM_011255, exon 6 of 6)	7979	NM_011255	19662	Mm.2605	NM_011255	ENSMUSG00000024990	Rbp4	Rbp-4	retinol binding protein 4, plasma	protein-coding
mm_145785.1	chr18	65143567	65143602	+	1	NA	intron (NM_001114386, intron 5 of 30)	intron (NM_001114386, intron 5 of 30)	-105277	NR_029600	387231		NR_029600	ENSMUSG00000065402	Mir122	Mir122a|Mirn122a|mir-122|mmu-mir-122	microRNA 122	ncRNA
mm_110429.1	chr12	46819088	46819096	-	1	NA	promoter-TSS (NM_021361)	promoter-TSS (NM_021361)	-317	NM_021361	664883	Mm.247195	NM_021361	ENSMUSG00000021047	Nova1	9430099M15Rik|G630039L02|Nova-1	neuro-oncological ventral antigen 1	protein-coding
mm_135896.1	chr16	65562639	65562647	-	1	NA	promoter-TSS (NM_026879)	promoter-TSS (NM_026879)	54	NM_026879	68942	Mm.432944	NM_026879	ENSMUSG00000004843	Chmp2b	1190006E07Rik	charged multivesicular body protein 2B	protein-coding
mm_87730.1	chr10	60129676	60129681	+	1	NA	intron (NM_052994, intron 8 of 10)	intron (NM_052994, intron 8 of 10)	2902	NR_105871	102465546		NR_105871	ENSMUSG00000105468	Mir6906	mmu-mir-6906	microRNA 6906	ncRNA
mm_111606.1	chr12	102398382	102398390	-	1	NA	intron (NM_011175, intron 10 of 13)	intron (NM_011175, intron 10 of 13)	41427	NM_011175	19141	Mm.17185	NM_011175	ENSMUSG00000021190	Lgmn	AEP|AI746452|AU022324|Prsc1	legumain	protein-coding
mm_41131.1	chr5	87788699	87788708	+	1	NA	TTS (NM_001304768)	TTS (NM_001304768)	14253	NM_007785	12993	Mm.4908	NM_007785	ENSMUSG00000061937	Csn1s2a	Csng|PP22	casein alpha s2-like A	protein-coding
mm_133025.1	chr16	57121792	57121802	+	1	NA	promoter-TSS (NM_138599)	promoter-TSS (NM_138599)	83	NM_138599	28185	Mm.196933	NM_138599	ENSMUSG00000022752	Tomm70a	2610044B22Rik|D16Ium22|D16Ium22e|D16Wsu109e|Tom70|Tomm70|mKIAA0719	translocase of outer mitochondrial membrane 70 homolog A (yeast)	protein-coding
mm_47553.1	chr5	124354806	124354821	-	1	NA	promoter-TSS (NM_013812)	promoter-TSS (NM_013812)	-185	NM_013812	13445	Mm.391838	NM_013812	ENSMUSG00000029394	Cdk2ap1	Apc10|Cdkap1|DORC1|Doc1|ST19|doc-1|p12	CDK2 (cyclin-dependent kinase 2)-associated protein 1	protein-coding
mm_59537.1	chr7	27765660	27765732	+	1	NA	promoter-TSS (NR_033484)	promoter-TSS (NR_033484)	23	NR_033484	100043229	Mm.458666	NR_033484	ENSMUSG00000109143	Gm10046	ENSMUSG00000058661	predicted gene 10046	ncRNA
mm_37318.1	chr4	119359901	119359917	-	1	NA	promoter-TSS (NM_001270446)	promoter-TSS (NM_001270446)	-15	NM_001270446	73332	Mm.425204	NM_028506	ENSMUSG00000028637	Ccdc30	1700001O02Rik|1700041C02Rik|1700111D19Rik|4930445I03Rik	coiled-coil domain containing 30	protein-coding
mm_49527.1	chr6	30027197	30027200	+	1	NA	Intergenic	B1F|SINE|Alu	-20790	NM_010938	18181	Mm.259258	NM_010938	ENSMUSG00000058440	Nrf1	C87038|D6Ertd415e	nuclear respiratory factor 1	protein-coding
mm_134637.1	chr16	21762187	21762205	-	1	NA	exon (NM_023737, exon 7 of 7)	exon (NM_023737, exon 7 of 7)	25638	NM_023737	74147	Mm.28100	NM_023737	ENSMUSG00000022853	Ehhadh	1300002P22Rik|HD|L-PBE|LBFP|LBP|MFP|MFP1|PBFE	enoyl-Coenzyme A, hydratase/3-hydroxyacyl Coenzyme A dehydrogenase	protein-coding
mm_33242.1	chr4	127025850	127025914	+	1	NA	exon (NM_023603, exon 5 of 10)	exon (NM_023603, exon 5 of 10)	4581	NM_023603	71514	Mm.257276	NM_023603	ENSMUSG00000028820	Sfpq	1110004P21Rik|2810416M14Rik|5730453G22Rik|9030402K04Rik|AU021830|D4Ertd314e|Gm12940|OTTMUSG00000009329|PSF|REP1	splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)	protein-coding
mm_105633.1	chr11	106973127	106973138	-	1	NA	Intergenic	(GGA)n|Simple_repeat|Simple_repeat	26393	NM_010655	16647	Mm.12508	NM_010655	ENSMUSG00000018362	Kpna2	2410044B12Rik|IPOA1|PTAC58|Rch1	karyopherin (importin) alpha 2	protein-coding
mm_60596.1	chr7	44496708	44496710	+	1	NA	promoter-TSS (NM_197991)	promoter-TSS (NM_197991)	121	NM_028169	75538	Mm.258841	NM_028169	ENSMUSG00000051113	Fam71e1	0610007G24Rik|1700021N13Rik|1700021P22Rik|GARI-L5	family with sequence similarity 71, member E1	protein-coding
mm_34286.1	chr4	141545214	141545230	+	1	NA	promoter-TSS (NR_030695)	promoter-TSS (NR_030695)	-940	NR_030695	320456	Mm.32859	NM_177163		B330016D10Rik	-	RIKEN cDNA B330016D10 gene	ncRNA
mm_111151.1	chr12	83004497	83004517	-	1	NA	intron (NM_001310478, intron 3 of 17)	intron (NM_001310478, intron 3 of 17)	-65352	NR_046045	74283	Mm.398247	NR_046045	ENSMUSG00000100890	1700085C21Rik	-	RIKEN cDNA 1700085C21 gene	ncRNA
mm_79954.1	chr9	66126728	66126744	+	1	NA	5' UTR (NM_026635, exon 1 of 5)	5' UTR (NM_026635, exon 1 of 5)	125	NM_026635	68250	Mm.27107	NM_026635	ENSMUSG00000032381	Fam96a	5730536A07Rik	family with sequence similarity 96, member A	protein-coding
mm_12627.1	chr2	74704624	74704648	+	1	NA	promoter-TSS (NM_001290730)	promoter-TSS (NM_001290730)	21	NM_001290731	15437	Mm.280673	NM_008276	ENSMUSG00000027102	Hoxd8	4921540P06Rik|AI047735|Hox-4.3|Hox-5.4	homeobox D8	protein-coding
mm_119948.1	chr14	55001133	55001157	+	1	NA	Intergenic	Intergenic	-6596	NM_080728	140781	Mm.457983	NM_080728	ENSMUSG00000053093	Myh7	B-MHC|MyHC-I|Myhc-b|Myhcb|beta-MHC	myosin, heavy polypeptide 7, cardiac muscle, beta	protein-coding
mm_11481.1	chr2	32385491	32385501	+	1	NA	exon (NM_008491, exon 5 of 6)	exon (NM_008491, exon 5 of 6)	2243	NM_008491	16819	Mm.9537	NM_008491	ENSMUSG00000026822	Lcn2	24p3|AW212229|NRL|Sip24	lipocalin 2	protein-coding
mm_138859.1	chr17	42501492	42501496	+	1	NA	intron (NM_028474, intron 3 of 3)	RLTR13B2|LTR|ERVK	109819	NM_181753	353344	Mm.184937	NM_181753	ENSMUSG00000043972	Opn5	Gpr136|Neuropsin|PGR12|TMEM13	opsin 5	protein-coding
mm_145379.1	chr18	56925764	56925783	+	1	NA	promoter-TSS (NM_177115)	promoter-TSS (NM_177115)	-225	NM_177115	320253	Mm.312623	NM_177115	ENSMUSG00000032656	March3	6330411I15Rik|A530081L18Rik|AI843639|MARCH-III	membrane-associated ring finger (C3HC4) 3	protein-coding
mm_4912.1	chr1	190172048	190172054	+	1	NA	Intergenic	Intergenic	-1371	NM_008937	19130	Mm.132579	NM_008937	ENSMUSG00000010175	Prox1	A230003G05Rik	prospero homeobox 1	protein-coding
mm_129456.1	chr15	78570775	78570806	-	1	NA	exon (NM_009008, exon 2 of 7)	exon (NM_009008, exon 2 of 7)	1993	NM_009008	19354	Mm.1972	NM_009008	ENSMUSG00000033220	Rac2	AI323801|AI452260	RAS-related C3 botulinum substrate 2	protein-coding
mm_53925.1	chr6	4540790	4540832	-	1	NA	3' UTR (NM_007743, exon 52 of 52)	3' UTR (NM_007743, exon 52 of 52)	35193	NM_007743	12843	Mm.277792	NM_007743	ENSMUSG00000029661	Col1a2	AA960264|AI325291|Col1a-2|Cola-2|Cola2|oim	collagen, type I, alpha 2	protein-coding
mm_136367.1	chr16	92808966	92808981	-	1	NA	intron (NM_001111022, intron 2 of 6)	intron (NM_001111022, intron 2 of 6)	17101	NM_001111021	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_96087.1	chr11	60240728	60240739	+	1	NA	3' UTR (NM_001039093, exon 12 of 12)	3' UTR (NM_001039093, exon 12 of 12)	-20106	NM_001313979	20787	Mm.278701	NM_011480	ENSMUSG00000020538	Srebf1	ADD1|SREBP-1a|SREBP1|SREBP1c|bHLHd1	sterol regulatory element binding transcription factor 1	protein-coding
mm_100836.1	chr11	5542178	5542219	-	1	NA	promoter-TSS (NM_134033)	promoter-TSS (NM_134033)	19	NM_134033	104479	Mm.210403	NM_134033	ENSMUSG00000020482	Ccdc117	1110004K02Rik|1700026O03Rik|AU018638|AU042822|AV173073|BC018601	coiled-coil domain containing 117	protein-coding
mm_27939.1	chr3	79622789	79622795	-	1	NA	exon (NM_025794, exon 3 of 13)	exon (NM_025794, exon 3 of 13)	5975	NM_025794	66841	Mm.28336	NM_025794	ENSMUSG00000027809	Etfdh	0610010I20Rik|AV001013	electron transferring flavoprotein, dehydrogenase	protein-coding
mm_102756.1	chr11	67301995	67302039	-	1	NA	exon (NM_177369, exon 33 of 40)	exon (NM_177369, exon 33 of 40)	24893	NM_177369	17885	Mm.340163	NM_177369	ENSMUSG00000055775	Myh8	4832426G23Rik|AI327267|MHCp|MyHC-pn|Myhs-p|Myhsp	myosin, heavy polypeptide 8, skeletal muscle, perinatal	protein-coding
mm_83931.1	chr9	56635885	56635897	-	1	NA	promoter-TSS (NM_001311076)	promoter-TSS (NM_001311076)	-243	NM_001311076	235402	Mm.246605	NM_181074	ENSMUSG00000049556	Lingo1	4930471K13Rik|AV148400|LERN1|LINGO-1|Lrrn6a|UNQ201	leucine rich repeat and Ig domain containing 1	protein-coding
mm_140647.1	chr17	12688770	12688774	-	1	NA	intron (NM_010515, intron 43 of 47)	intron (NM_010515, intron 43 of 47)	-12934	NM_009202	20517	Mm.594	NM_009202	ENSMUSG00000023829	Slc22a1	Lx1|Oct1|Orct|Orct1	solute carrier family 22 (organic cation transporter), member 1	protein-coding
mm_126357.1	chr15	80012241	80012266	+	1	NA	intron (NM_011057, intron 1 of 6)	(CGTG)n|Simple_repeat|Simple_repeat	2555	NM_011057	18591	Mm.144089	NM_011057	ENSMUSG00000000489	Pdgfb	PDGF-B|Sis	platelet derived growth factor, B polypeptide	protein-coding
mm_68353.1	chr7	106510123	106510133	-	1	NA	Intergenic	Intergenic	-69055	NR_003967	209380	Mm.461779	NM_001001318		Gm4759	EG209380	GTPase, very large interferon inducible 1 pseudogene	pseudo
mm_39366.1	chr5	9161880	9161893	+	1	NA	promoter-TSS (NM_001110327)	promoter-TSS (NM_001110327)	-110	NM_011806	23857	Mm.22480	NM_011806	ENSMUSG00000042508	Dmtf1	Dimp|Dmp1	cyclin D binding myb-like transcription factor 1	protein-coding
mm_44554.1	chr5	24601916	24601922	-	1	NA	promoter-TSS (NM_025891)	promoter-TSS (NM_025891)	83	NM_025891	66993	Mm.436539	NM_025891	ENSMUSG00000028949	Smarcd3	1500001J14Rik|2210409C08Rik|BAF60C	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3	protein-coding
mm_123309.1	chr14	62293229	62293240	-	1	NA	promoter-TSS (NM_173419)	promoter-TSS (NM_173419)	-255	NM_173419	239133	Mm.127330	NM_173419	ENSMUSG00000048281	Dleu7	BC038059	deleted in lymphocytic leukemia, 7	protein-coding
mm_136506.1	chr16	96968934	96968935	-	1	NA	intron (NM_031174, intron 3 of 32)	(A)n|Simple_repeat|Simple_repeat	201801	NM_031174	13508	Mm.102437	NM_031174	ENSMUSG00000050272	Dscam	4932410A21Rik	Down syndrome cell adhesion molecule	protein-coding
mm_60094.1	chr7	35056753	35056759	+	1	NA	promoter-TSS (NM_009884)	promoter-TSS (NM_009884)	-190	NM_009884	12611	Mm.273090	NM_009884	ENSMUSG00000056216	Cebpg	C/EBP[g]|C/EBPgamma|GPE1-BP|Gpe1bp|Ig/EBP	CCAAT/enhancer binding protein (C/EBP), gamma	protein-coding
mm_129036.1	chr15	74995092	74995112	-	1	NA	3' UTR (NM_001271446, exon 4 of 4)	3' UTR (NM_001271446, exon 4 of 4)	2929	NM_001271417	110454	Mm.425949	NM_010738	ENSMUSG00000075602	Ly6a	Ly-6A.2|Ly-6A/E|Ly-6E.1|Sca-1|Sca1|TAP	lymphocyte antigen 6 complex, locus A	protein-coding
mm_119214.1	chr14	33194037	33194040	+	1	NA	Intergenic	Intergenic	-8972	NM_001146022	545030	Mm.318345	NM_001146022	ENSMUSG00000051506	Wdfy4	Gm18810	WD repeat and FYVE domain containing 4	protein-coding
mm_115980.1	chr13	24257802	24257804	-	1	NA	intron (NM_001311122, intron 2 of 37)	ID_B1|SINE|B4	22987	NM_001311122	68732	Mm.211047	NM_026825	ENSMUSG00000021338	Carmil1	1110037D04Rik|AI425970|CARMIL|CARML1|D130057M20|Lrrc16|Lrrc16a	capping protein regulator and myosin 1 linker 1	protein-coding
mm_32695.1	chr4	116017266	116017283	+	1	NA	intron (NM_010173, intron 1 of 14)	CpG	628	NM_010173	14073	Mm.256025	NM_010173	ENSMUSG00000034171	Faah	AW412498	fatty acid amide hydrolase	protein-coding
mm_154725.1	chrX	9436631	9436645	+	1	NA	3' UTR (NM_007807, exon 13 of 13)	3' UTR (NM_007807, exon 13 of 13)	32686	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_118182.1	chr13	107022270	107022276	-	1	NA	promoter-TSS (NM_008442)	promoter-TSS (NM_008442)	-159	NM_008442	16563	Mm.355686	NM_008442	ENSMUSG00000021693	Kif2a	C530030B14Rik|Kif2|Kns2|M-kinesin	kinesin family member 2A	protein-coding
mm_13079.1	chr2	91206026	91206046	+	1	NA	exon (NM_007387, exon 5 of 11)	exon (NM_007387, exon 5 of 11)	3124	NM_007387	11432	Mm.45570	NM_007387	ENSMUSG00000002103	Acp2	Acp-2|LAP	acid phosphatase 2, lysosomal	protein-coding
mm_21257.1	chr2	156347972	156348000	-	1	NA	intron (NM_001316755, intron 8 of 9)	intron (NM_001316755, intron 8 of 9)	-35282	NM_020255	19018	Mm.389346	NM_020255	ENSMUSG00000046229	Scand1	2310003H23Rik|Leap1|PGC-2|Ppargc2	SCAN domain-containing 1	protein-coding
mm_41328.1	chr5	90476467	90476577	+	1	NA	TTS (NM_009654)	TTS (NM_009654)	-14192	NM_007423	11576	Mm.358570	NM_007423	ENSMUSG00000054932	Afp	-	alpha fetoprotein	protein-coding
mm_124023.1	chr14	76556884	76556890	-	1	NA	promoter-TSS (NR_027699)	promoter-TSS (NR_027699)	2	NR_027699	72661	Mm.320384	NM_001160326	ENSMUSG00000052584	Serp2	2810032E02Rik	stress-associated endoplasmic reticulum protein family member 2	protein-coding
mm_90915.1	chr10	12548495	12548521	-	1	NA	intron (NM_011682, intron 50 of 73)	A-rich|Low_complexity|Low_complexity	313227	NM_011682	22288	Mm.331784	NM_011682	ENSMUSG00000019820	Utrn	AA589569|DRP|Dmdl	utrophin	protein-coding
mm_157586.1	chrX	53070568	53070578	-	1	NA	exon (NM_019538, exon 3 of 3)	exon (NM_019538, exon 3 of 3)	-13383	NR_038184	72575	Mm.59516	NR_038184		C430049B03Rik	2700063P19Rik|9430052C07Rik|mir-322|mir-351|mir-503	RIKEN cDNA C430049B03 gene	ncRNA
mm_149365.1	chr19	11333205	11333240	+	1	NA	exon (NM_001276398, exon 2 of 7)	exon (NM_001276398, exon 2 of 7)	1473	NM_001276398	109225	Mm.491251	NM_027836	ENSMUSG00000024672	Ms4a7	9130422I10Rik|A430103C15Rik|CD20l4|CFFMA	membrane-spanning 4-domains, subfamily A, member 7	protein-coding
mm_87058.1	chr10	28843946	28843954	+	1	NA	intron (NM_001305663, intron 5 of 5)	intron (NM_001305663, intron 5 of 5)	79557	NR_033601	114676	Mm.390292	NR_033601		4930519F09Rik	-	pyruvate dehydrogenase E1 alpha 1 pseudogene	pseudo
mm_29208.1	chr3	106790035	106790045	-	1	NA	5' UTR (NM_007651, exon 1 of 8)	5' UTR (NM_007651, exon 1 of 8)	109	NM_007651	12508	Mm.316861	NM_007651	ENSMUSG00000040747	Cd53	AI323659|Ox-44|Tspan25	CD53 antigen	protein-coding
mm_32089.1	chr4	98437169	98437218	+	1	NA	intron (NM_001005784, intron 11 of 19)	intron (NM_001005784, intron 11 of 19)	41367	NM_172696	12695	Mm.90218	NM_007704	ENSMUSG00000061859	Patj	Cipp|Inadl	PATJ, crumbs cell polarity complex component	protein-coding
mm_98495.1	chr11	94951668	94951672	+	1	NA	3' UTR (NM_007742, exon 51 of 51)	3' UTR (NM_007742, exon 51 of 51)	15446	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_146077.1	chr18	70580699	70580733	+	1	NA	exon (NM_010773, exon 2 of 7)	exon (NM_010773, exon 2 of 7)	12424	NM_010773	17191	Mm.322	NM_010773	ENSMUSG00000024513	Mbd2	MBD2a	methyl-CpG binding domain protein 2	protein-coding
mm_39790.1	chr5	30587394	30587406	+	1	NA	promoter-TSS (NM_010608)	promoter-TSS (NM_010608)	-770	NM_010608	16527	Mm.439936	NM_010608	ENSMUSG00000049265	Kcnk3	TASK|Task-1|cTBAK-1	potassium channel, subfamily K, member 3	protein-coding
mm_52020.1	chr6	94672713	94672725	+	1	NA	intron (NM_008377, intron 1 of 18)	intron (NM_008377, intron 1 of 18)	27426	NM_008377	16206	Mm.245210	NM_008377	ENSMUSG00000030029	Lrig1	D6Bwg0781e|Img|LIG-1	leucine-rich repeats and immunoglobulin-like domains 1	protein-coding
mm_99762.1	chr11	106788599	106788677	+	1	NA	promoter-TSS (NM_177088)	promoter-TSS (NM_177088)	-144	NM_007840	13207	Mm.491096	NM_007840	ENSMUSG00000020719	Ddx5	2600009A06Rik|G17P1|HUMP68|Hlr1|p68	DEAD (Asp-Glu-Ala-Asp) box polypeptide 5	protein-coding
mm_3346.1	chr1	138137395	138137395	+	1	NA	intron (NM_001111316, intron 1 of 31)	intron (NM_001111316, intron 1 of 31)	37731	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_124094.1	chr14	79199173	79199191	-	1	NA	intron (NM_027906, intron 44 of 44)	ORR1C2|LTR|ERVL-MaLR	48185	NM_001033215	105590	Mm.486536	NM_001033215	ENSMUSG00000071262	Zfp957	AU017455	zinc finger protein 957	protein-coding
mm_161754.1	chr17	35123037	35123037	+	1	NA	promoter-TSS (NM_032460)	promoter-TSS (NM_032460)	85	NM_032460	81845	Mm.7405	NM_032460	ENSMUSG00000092417	Gpank1	Bat-4|Bat4|D17H6S54E|G5	G patch domain and ankyrin repeats 1	protein-coding
mm_155868.1	chrX	101384444	101384454	+	1	NA	exon (NM_008124, exon 2 of 2)	exon (NM_008124, exon 2 of 2)	717	NM_001302497	14618	Mm.21198	NM_008124	ENSMUSG00000047797	Gjb1	Cnx32|Cx32|connexin-32	gap junction protein, beta 1	protein-coding
mm_31165.1	chr4	43443136	43443156	+	1	NA	5' UTR (NM_011571, exon 1 of 10)	5' UTR (NM_011571, exon 1 of 10)	869	NM_011571	21754	Mm.485441	NM_011571	ENSMUSG00000028458	Tesk1	AI326901	testis specific protein kinase 1	protein-coding
mm_1544.1	chr1	72852216	72852222	+	1	NA	3' UTR (NM_008342, exon 4 of 4)	3' UTR (NM_008342, exon 4 of 4)	22646	NM_010518	16011	Mm.405761	NM_010518	ENSMUSG00000026185	Igfbp5	AI256729|AW208790|IGFBP-5|IGFBP-5P	insulin-like growth factor binding protein 5	protein-coding
mm_40362.1	chr5	48050547	48050551	+	1	NA	intron (NR_111900, intron 4 of 35)	intron (NR_111900, intron 4 of 35)	67394	NM_001291228	20563	Mm.289739	NM_178804	ENSMUSG00000031558	Slit2	Drad-1|E030015M03Rik|E130320P19Rik|Slil3|mKIAA4141|slit-2	slit homolog 2 (Drosophila)	protein-coding
mm_26640.1	chr3	153675394	153675396	+	1	NA	intron (NM_011372, intron 1 of 4)	intron (NM_011372, intron 1 of 4)	49738	NM_011372	20447	Mm.296453	NM_011372	ENSMUSG00000052544	St6galnac3	Siat7c	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 3	protein-coding
mm_66553.1	chr7	45212116	45212143	-	1	NA	promoter-TSS (NM_015789)	promoter-TSS (NM_015789)	-246	NM_015789	50722	Mm.27287	NM_015789	ENSMUSG00000030792	Dkkl1	AI414495|SGY|SGY-1|SGY1|Soggy|mSgy	dickkopf-like 1	protein-coding
mm_143386.1	chr17	67993178	67993193	-	1	NA	intron (NM_172964, intron 1 of 17)	RCHARR1|DNA|hAT-Charlie	10923	NM_172964	268970	Mm.9935	NM_172964	ENSMUSG00000024043	Arhgap28	AU044757|AW550892|E130310N06	Rho GTPase activating protein 28	protein-coding
mm_99151.1	chr11	100575798	100575815	+	1	NA	promoter-TSS (NM_001146318)	promoter-TSS (NM_001146318)	-85	NM_001146318	12799	Mm.15711	NM_009923	ENSMUSG00000006782	Cnp	CNPase|Cnp-1|Cnp1	2',3'-cyclic nucleotide 3' phosphodiesterase	protein-coding
mm_33269.1	chr4	127968487	127968496	+	1	NA	intron (NM_001134733, intron 1 of 6)	intron (NM_001134733, intron 1 of 6)	2350	NM_001134733	635169	Mm.346755	NM_001134733	ENSMUSG00000028813	CK137956	-	cDNA sequence CK137956	protein-coding
mm_19239.1	chr2	84715264	84715275	-	1	NA	promoter-TSS (NM_144887)	promoter-TSS (NM_144887)	-105	NM_144887	228136	Mm.288508	NM_144887	ENSMUSG00000034075	Zdhhc5	1110032A17Rik|AI451382|Zisp	zinc finger, DHHC domain containing 5	protein-coding
mm_40877.1	chr5	74337703	74337709	+	1	NA	intron (NM_001286437, intron 5 of 7)	ERV3-16A3_LTR|LTR|ERVL	142380	NM_026878	68939	Mm.293316	NM_026878	ENSMUSG00000049907	Rasl11b	1190017B18Rik	RAS-like, family 11, member B	protein-coding
mm_169636.1	chr15	47540052	47540058	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	916750	NR_045811	75281	Mm.159487	NR_045811	ENSMUSG00000051198	4930548G14Rik	-	RIKEN cDNA 4930548G14 gene	ncRNA
mm_71425.1	chr8	46491087	46491120	+	1	NA	5' UTR (NM_001302163, exon 1 of 21)	5' UTR (NM_001302163, exon 1 of 21)	137	NM_001302163	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_63791.1	chr7	132633906	132633939	+	1	NA	intron (NM_029609, intron 2 of 6)	intron (NM_029609, intron 2 of 6)	23279	NM_029609	76429	Mm.276721	NM_029609	ENSMUSG00000030946	Lhpp	2310007H09Rik	phospholysine phosphohistidine inorganic pyrophosphate phosphatase	protein-coding
mm_115171.1	chr13	108045661	108045662	+	1	NA	intron (NM_001048250, intron 1 of 2)	intron (NM_001048250, intron 1 of 2)	1187	NM_001048250	75616	Mm.491164	NM_001048250	ENSMUSG00000071180	Smim15	2810008M24Rik	small integral membrane protein 15	protein-coding
mm_36228.1	chr4	62733445	62733447	-	1	NA	Intergenic	Intergenic	59472	NM_001310706	50780	Mm.286753	NM_019492	ENSMUSG00000059810	Rgs3	4930506N09Rik|C2PA-RGS3|C2pa|PDZ-RGS3|RGS3S	regulator of G-protein signaling 3	protein-coding
mm_123172.1	chr14	57525457	57525467	-	1	NA	exon (NM_145837, exon 2 of 3)	exon (NM_145837, exon 2 of 3)	633	NM_145837	239114	Mm.390726	NM_145837	ENSMUSG00000050222	Il17d	AI462269|IL-17D	interleukin 17D	protein-coding
mm_128692.1	chr15	62039139	62039154	-	1	NA	promoter-TSS (NR_132746)	promoter-TSS (NR_132746)	-111	NR_132746	19296	Mm.4608	NM_011222	ENSMUSG00000097039	Pvt1	Ayu21-84Imeg|Gt(pU21)84Imeg|Mis-1|Mlvi-1|Pvt-1	plasmacytoma variant translocation 1	ncRNA
mm_91505.1	chr10	37136586	37136600	-	1	NA	exon (NM_008538, exon 2 of 2)	exon (NM_008538, exon 2 of 2)	2333	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_56031.1	chr6	86609342	86609362	-	1	NA	Intergenic	Intergenic	-18822	NM_026414	67855	Mm.183043	NM_026414	ENSMUSG00000033508	Asprv1	2300003P22Rik|AA986851|SASP|SASPase|Taps	aspartic peptidase, retroviral-like 1	protein-coding
mm_46256.1	chr5	99327188	99327234	-	1	NA	intron (NR_030692, intron 3 of 3)	intron (NR_030692, intron 3 of 3)	-74284	NM_145839	320292	Mm.259074	NM_145839	ENSMUSG00000089809	Rasgef1b	4732452O09Rik|GPIgamma4|Gpig4	RasGEF domain family, member 1B	protein-coding
mm_13758.1	chr2	118126824	118126888	+	1	NA	3' UTR (NM_011580, exon 22 of 22)	3' UTR (NM_011580, exon 22 of 22)	14980	NM_001313914	21825	Mm.4159	NM_011580	ENSMUSG00000040152	Thbs1	TSP-1|TSP1|Thbs-1|tbsp1	thrombospondin 1	protein-coding
mm_101345.1	chr11	23633605	23633620	-	1	NA	promoter-TSS (NM_001347242)	promoter-TSS (NM_001347242)	19	NM_001347242	71675	Mm.48031	NM_027860	ENSMUSG00000042208	0610010F05Rik	Kiaa1841|mKIAA1841	RIKEN cDNA 0610010F05 gene	protein-coding
mm_27817.1	chr3	78762461	78762464	-	1	NA	Intergenic	Lx7|LINE|L1	382425	NM_001310536	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_125219.1	chr15	34083304	34083319	+	1	NA	exon (NM_026002, exon 1 of 12)	exon (NM_026002, exon 1 of 12)	592	NM_026002	67154	Mm.130883	NM_026002	ENSMUSG00000022255	Mtdh	2610103J23Rik|3D3|3D3/Lyric|AEG-1|AV353288|D8Bwg1112e|Lyric	metadherin	protein-coding
mm_114805.1	chr13	91461115	91461125	+	1	NA	promoter-TSS (NM_024186)	promoter-TSS (NM_024186)	23	NM_024186	66970	Mm.343095	NM_024186	ENSMUSG00000003992	Ssbp2	1500004K09Rik|2310079I02Rik|9330163K02Rik|A830008M03Rik|AU067692|AW558684|Hspc116|SSDP2	single-stranded DNA binding protein 2	protein-coding
mm_5133.1	chr1	9700318	9700329	-	1	NA	promoter-TSS (NM_001290397)	promoter-TSS (NM_001290397)	-114	NM_008651	17864	Mm.479	NM_008651	ENSMUSG00000025912	Mybl1	A-myb|G1-419-6|repro9	myeloblastosis oncogene-like 1	protein-coding
mm_171362.1	chr4	117202521	117202529	+	1	NA	Intergenic	Intergenic	-19901	NM_134471	73804	Mm.247651	NM_134471	ENSMUSG00000028678	Kif2c	4930402F02Rik|ESTM5|Knsl6|MCAK|X83316	kinesin family member 2C	protein-coding
mm_141376.1	chr17	29056740	29056743	-	1	NA	TTS (NR_036469)	TTS (NR_036469)	22385	NR_036469	100504267	Mm.438550	NR_036469	ENSMUSG00000085912	Trp53cor1	Gm16197|OTTMUSG00000031656|linc-p21|lincRNA-p21	tumor protein p53 pathway corepressor 1	ncRNA
mm_99604.1	chr11	104573541	104573558	+	1	NA	intron (NM_010858, intron 2 of 8)	intron (NM_010858, intron 2 of 8)	-11351	NR_130177	100415912	Mm.446786	NR_130177		Gm11665	Gm11664|OTTMUSG00000003182|OTTMUSG00000003183	predicted gene 11665	ncRNA
mm_58309.1	chr6	146213213	146213218	-	1	NA	intron (NM_010586, intron 44 of 55)	intron (NM_010586, intron 44 of 55)	279068	NM_010656	16651	Mm.49689	NM_010656	ENSMUSG00000030255	Sspn	Krag	sarcospan	protein-coding
mm_141009.1	chr17	24997852	24997881	-	1	NA	intron (NM_020608, intron 3 of 20)	intron (NM_020608, intron 3 of 20)	17364	NM_020608	57354	Mm.328854	NM_020608	ENSMUSG00000038002	Cramp1l	5830477H08Rik|AI256853|AI790734|Cramp1|Tce4|mKIAA1426	Crm, cramped-like (Drosophila)	protein-coding
mm_146486.1	chr18	90510271	90510288	+	1	NA	5' UTR (NM_198295, exon 1 of 16)	5' UTR (NM_198295, exon 1 of 16)	125	NM_198295	67988	Mm.268041	NM_198295	ENSMUSG00000024614	Tmx3	6430411B10Rik|A730024F05Rik|AV259382|Txndc10|mKIAA1830	thioredoxin-related transmembrane protein 3	protein-coding
mm_131914.1	chr16	23307915	23307934	+	1	NA	intron (NM_001252506, intron 1 of 6)	intron (NM_001252506, intron 1 of 6)	17454	NM_001252506	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_144992.1	chr18	38296740	38296750	+	1	NA	promoter-TSS (NM_001164621)	promoter-TSS (NM_001164621)	-60	NM_001164621	56736	Mm.228903	NM_020012	ENSMUSG00000060450	Rnf14	2310075C09Rik|2610005D23Rik|AA986456|AU041447|D18Ertd188e|D7Bwg0165e|Triad2	ring finger protein 14	protein-coding
mm_43932.1	chr5	145104452	145104464	+	1	NA	exon (NM_019767, exon 7 of 10)	exon (NM_019767, exon 7 of 10)	-9798	NM_023142	11867	Mm.30010	NM_023142	ENSMUSG00000029622	Arpc1b	41kDa|AA408064|AA408534|AA571392|AF007010|AW208418|L72|SOP2Hs|p41-ARC	actin related protein 2/3 complex, subunit 1B	protein-coding
mm_90685.1	chr10	128922584	128922597	+	1	NA	intron (NM_015740, intron 2 of 3)	intron (NM_015740, intron 2 of 3)	934	NM_015740	14533	Mm.30118	NM_015740	ENSMUSG00000090247	Bloc1s1	AI839753|BLOS1|Gcn5l1	biogenesis of lysosomal organelles complex-1, subunit 1	protein-coding
mm_64094.1	chr7	140976393	140976405	+	1	NA	Intergenic	ORR1D1|LTR|ERVL-MaLR	8323	NM_001112715	68713	Mm.175661	NM_026820	ENSMUSG00000025491	Ifitm1	1110036C17Rik|DSPA2a|Mil-2|Mil2	interferon induced transmembrane protein 1	protein-coding
mm_24600.1	chr3	93445379	93445385	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	3052	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_166727.1	chr6	122309058	122309071	+	1	NA	promoter-TSS (NM_010749)	promoter-TSS (NM_010749)	54	NM_010749	17113	Mm.249225	NM_010749	ENSMUSG00000007458	M6pr	CD-MPR|Mpr46	mannose-6-phosphate receptor, cation dependent	protein-coding
mm_162158.1	chrX	89752279	89752279	+	1	NA	promoter-TSS (NM_001085511)	promoter-TSS (NM_001085511)	11	NM_001085511	245509	Mm.297700	NM_001085511	ENSMUSG00000079513	4932429P05Rik	-	RIKEN cDNA 4932429P05 gene	protein-coding
mm_52506.1	chr6	115360979	115360989	+	1	NA	promoter-TSS (NM_001127330)	promoter-TSS (NM_001127330)	33	NM_001127330	19016	Mm.3020	NM_011146	ENSMUSG00000000440	Pparg	Nr1c3|PPAR-gamma|PPAR-gamma2|PPARgamma|PPARgamma2	peroxisome proliferator activated receptor gamma	protein-coding
mm_152490.1	chr19	11055634	11055669	-	1	NA	Intergenic	Lx|LINE|L1	-5085	NR_102366	107350	Mm.6381	NM_001177351	ENSMUSG00000075010	AW112010	-	expressed sequence AW112010	ncRNA
mm_109653.1	chr12	112862167	112862173	+	1	NA	Intergenic	Intergenic	-1254	NM_019925	56696	Mm.20455	NM_019925	ENSMUSG00000021298	Gpr132	G2a	G protein-coupled receptor 132	protein-coding
mm_7658.1	chr1	128404574	128404577	-	1	NA	intron (NM_177445, intron 4 of 15)	B1_Mur4|SINE|Alu	12841	NM_177445	226414	Mm.28693	NM_145507	ENSMUSG00000026356	Dars	5730439G15Rik	aspartyl-tRNA synthetase	protein-coding
mm_69870.1	chr7	141468659	141468677	-	1	NA	promoter-TSS (NM_001111050)	promoter-TSS (NM_001111050)	-121	NM_001111050	12476	Mm.30246	NM_009842	ENSMUSG00000025510	Cd151	PETA-3|SFA-1|Tspan24	CD151 antigen	protein-coding
mm_160727.1	chr10	75822414	75822414	-	1	NA	exon (NM_029472, exon 1 of 5)	exon (NM_029472, exon 1 of 5)	129	NM_029472	75886	Mm.268996	NM_029472	ENSMUSG00000009093	Gstt4	4930583C14Rik|AI507011	glutathione S-transferase, theta 4	protein-coding
mm_62808.1	chr7	112953956	112953975	+	1	NA	promoter-TSS (NM_175279)	promoter-TSS (NM_175279)	3	NM_175279	78748	Mm.349943	NM_175279	ENSMUSG00000098132	Rassf10	4632411J06Rik	Ras association (RalGDS/AF-6) domain family (N-terminal) member 10	protein-coding
mm_130472.1	chr15	98727497	98727527	-	1	NA	intron (NM_024169, intron 2 of 5)	intron (NM_024169, intron 2 of 5)	686	NM_024169	66120	Mm.30729	NM_024169	ENSMUSG00000003355	Fkbp11	1110002O23Rik|FKBP-11	FK506 binding protein 11	protein-coding
mm_138472.1	chr17	35194325	35194339	+	1	NA	promoter-TSS (NM_008518)	promoter-TSS (NM_008518)	-175	NM_008518	16994	Mm.1715	NM_008518	ENSMUSG00000024399	Ltb	AI662801|LTbeta|Tnfc|Tnfsf3|Tnlg1c|p33	lymphotoxin B	protein-coding
mm_99751.1	chr11	106688667	106688676	+	1	NA	intron (NM_001305157, intron 7 of 15)	intron (NM_001305157, intron 7 of 15)	26610	NM_001305158	18613	Mm.343951	NM_008816	ENSMUSG00000020717	Pecam1	C85791|Cd31|PECAM-1|Pecam	platelet/endothelial cell adhesion molecule 1	protein-coding
mm_160367.1	chr8	25694126	25694126	+	1	NA	intron (NM_001081269, intron 14 of 22)	intron (NM_001081269, intron 14 of 22)	-25922	NR_121642	71910	Mm.385055	NM_028000	ENSMUSG00000031570	Plpp5	1810019D05Rik|2310022A04Rik|AW045471|Ppapdc1|Ppapdc1b	phospholipid phosphatase 5	protein-coding
mm_56904.1	chr6	119196568	119196581	-	1	NA	promoter-TSS (NM_009781)	promoter-TSS (NM_009781)	-165	NM_001255999	12288	Mm.41628	NM_009781	ENSMUSG00000051331	Cacna1c	Cav1.2|Cchl1a1|D930026N18Rik|MBC|MELC-CC	calcium channel, voltage-dependent, L type, alpha 1C subunit	protein-coding
mm_55906.1	chr6	83703529	83703533	-	1	NA	non-coding (NR_002873, exon 2 of 2)	non-coding (NR_002873, exon 2 of 2)	7275	NR_075094	574519	Mm.487605	NR_002871	ENSMUSG00000085794	Vax2os	Vas2os|Vax2os1|Vax2os2	ventral anterior homeobox 2, opposite strand	ncRNA
mm_5935.1	chr1	55363433	55363443	-	1	NA	promoter-TSS (NM_029267)	promoter-TSS (NM_029267)	31	NM_029267	75388	Mm.483408	NM_029267	ENSMUSG00000025977	Boll	4930554P13Rik|4930597B14Rik	bol, boule-like (Drosophila)	protein-coding
mm_73906.1	chr8	119465277	119465305	+	1	NA	intron (NM_054095, intron 8 of 12)	intron (NM_054095, intron 8 of 12)	18572	NM_054095	117148	Mm.356184	NM_054095	ENSMUSG00000031837	Necab2	Efcbp2	N-terminal EF-hand calcium binding protein 2	protein-coding
mm_141538.1	chr17	31855830	31855838	-	1	NA	promoter-TSS (NM_010831)	promoter-TSS (NM_010831)	-42	NM_010831	17691	Mm.290941	NM_010831	ENSMUSG00000024042	Sik1	Msk|Sik|Snf1lk	salt inducible kinase 1	protein-coding
mm_99779.1	chr11	107335916	107335929	+	1	NA	intron (NM_145823, intron 2 of 9)	intron (NM_145823, intron 2 of 9)	134798	NM_145823	71795	Mm.397413	NM_145823	ENSMUSG00000040430	Pitpnc1	1110020B03Rik|5830436L09Rik|AI662802|AI851387|C330017I21Rik|Dnr411|RDGBB|RDGBB1|rdgB-beta	phosphatidylinositol transfer protein, cytoplasmic 1	protein-coding
mm_22696.1	chr3	17948437	17948450	+	1	NA	promoter-TSS (NM_029289)	promoter-TSS (NM_029289)	-1	NM_029289	75439	Mm.27023	NM_029289	ENSMUSG00000027564	Cypt12	1700001F04Rik|AV209098	cysteine-rich perinuclear theca 12	protein-coding
mm_38665.1	chr4	144463777	144463788	-	1	NA	promoter-TSS (NM_001085503)	promoter-TSS (NM_001085503)	-26	NM_001085503	230883	Mm.457844	NM_001085503	ENSMUSG00000078507	Aadacl3	Gm435	arylacetamide deacetylase-like 3	protein-coding
mm_50695.1	chr6	51597740	51597753	+	1	NA	Intergenic	Intergenic	53223	NM_001127348	71982	Mm.294166	NM_028035	ENSMUSG00000038301	Snx10	2410004M09Rik	sorting nexin 10	protein-coding
mm_97726.1	chr11	80386519	80386525	+	1	NA	intron (NM_001130171, intron 2 of 10)	B3A|SINE|B2	3243	NM_001130171	22680	Mm.401332	NM_011751	ENSMUSG00000017421	Zfp207	8430401D15Rik|BuGZ|Zep|Znf207	zinc finger protein 207	protein-coding
mm_129847.1	chr15	83166103	83166160	-	1	NA	exon (NM_029787, exon 2 of 9)	exon (NM_029787, exon 2 of 9)	6077	NM_029787	109754	Mm.22560	NM_029787	ENSMUSG00000018042	Cyb5r3	0610016L08Rik|2500002N19Rik|C85115|Dia-1|Dia1|WU:AL591952.1-001|WU:AL591952.1-002|WU:AL591952.1-003|WU:Cyb5r3	cytochrome b5 reductase 3	protein-coding
mm_54899.1	chr6	47454843	47454866	-	1	NA	intron (NM_012042, intron 1 of 21)	CpG	530	NM_012042	26965	Mm.87611	NM_012042	ENSMUSG00000029686	Cul1	-	cullin 1	protein-coding
mm_50005.1	chr6	41058395	41058417	+	1	NA	Intergenic	(TTCC)n|Simple_repeat|Simple_repeat	-22897	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_78841.1	chr9	44327028	44327038	+	1	NA	5' UTR (NM_007875, exon 1 of 9)	5' UTR (NM_007875, exon 1 of 9)	188	NM_007875	13478	Mm.18353	NM_007875	ENSMUSG00000032123	Dpagt1	AU021132|Dpagt2|GPT|Gnpta	dolichyl-phosphate (UDP-N-acetylglucosamine) acetylglucosaminephosphotransferase 1 (GlcNAc-1-P transferase)	protein-coding
mm_32320.1	chr4	103619522	103619553	+	1	NA	Intergenic	MER45R|DNA|hAT-Tip100	237037	NR_040673	622167	Mm.244115	NR_040673	ENSMUSG00000086136	Gm12718	OTTMUSG00000008109	predicted gene 12718	ncRNA
mm_103094.1	chr11	69921228	69921243	-	1	NA	promoter-TSS (NM_001166592)	promoter-TSS (NM_001166592)	40	NM_001166595	276770	Mm.18026	NM_181582	ENSMUSG00000078812	Eif5a	AA410058|D19Wsu54e|Eif4d|Eif5a1|eIF-4D|eIF-5A|eIF-5A-1|eIF-5A1	eukaryotic translation initiation factor 5A	protein-coding
mm_41158.1	chr5	87929886	87929906	+	1	NA	exon (NM_007786, exon 4 of 5)	exon (NM_007786, exon 4 of 5)	4263	NM_007786	12994	Mm.296303	NM_007786	ENSMUSG00000001622	Csn3	AW208918|CSN10|Csnk	casein kappa	protein-coding
mm_30032.1	chr3	135691266	135691271	-	1	NA	5' UTR (NM_008689, exon 1 of 25)	5' UTR (NM_008689, exon 1 of 25)	279	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_14126.1	chr2	126034558	126034573	+	1	NA	promoter-TSS (NM_008008)	promoter-TSS (NM_008008)	-93	NM_008008	14178	Mm.330557	NM_008008	ENSMUSG00000027208	Fgf7	Kgf	fibroblast growth factor 7	protein-coding
mm_116108.1	chr13	28949582	28949593	-	1	NA	Intergenic	Intergenic	4095	NM_009238	20677	Mm.240627	NM_009238	ENSMUSG00000076431	Sox4	AA682046|Sox-4	SRY (sex determining region Y)-box 4	protein-coding
mm_20462.1	chr2	129367267	129367411	-	1	NA	exon (NM_008361, exon 5 of 7)	exon (NM_008361, exon 5 of 7)	-2563	NR_015474	329514	Mm.207315	NM_177848	ENSMUSG00000074805	Il1bos	9430083I22|Gm14047|OTTMUSG00000015529	interleukin 1 beta, opposite strand	ncRNA
mm_80991.1	chr9	103367537	103367577	+	1	NA	Intergenic	Intergenic	-1777	NM_001134426	321022	Mm.261025	NM_175565	ENSMUSG00000032803	Cdv3	2510010F10Rik|C230084J24Rik|C79446|TPP36	carnitine deficiency-associated gene expressed in ventricle 3	protein-coding
mm_114939.1	chr13	96388346	96388380	+	1	NA	promoter-TSS (NM_026173)	promoter-TSS (NM_026173)	69	NM_026173	67463	Mm.86472	NM_026173	ENSMUSG00000021671	Poc5	1200014M14Rik|AV144706	POC5 centriolar protein	protein-coding
mm_50737.1	chr6	52714446	52714467	+	1	NA	intron (NM_025816, intron 1 of 17)	intron (NM_025816, intron 1 of 17)	727	NM_025816	52440	Mm.389757	NM_025816	ENSMUSG00000004535	Tax1bp1	1200003J11Rik|1700069J21Rik|AA930106|D6Ertd404e|D6Ertd772e|T6bp|TXBP151	Tax1 (human T cell leukemia virus type I) binding protein 1	protein-coding
mm_71751.1	chr8	65639361	65639371	+	1	NA	intron (NM_175188, intron 1 of 7)	B3A|SINE|B2	20841	NM_175188	72925	Mm.380457	NM_175188	ENSMUSG00000036469	March1	2900024D24Rik|BB085186	membrane-associated ring finger (C3HC4) 1	protein-coding
mm_137870.1	chr17	31386245	31386280	+	1	NA	promoter-TSS (NM_001163748)	promoter-TSS (NM_001163748)	28	NM_001163748	18585	Mm.10812	NM_008804	ENSMUSG00000041119	Pde9a	PDE9A1	phosphodiesterase 9A	protein-coding
mm_166489.1	chr5	149053215	149053230	+	1	NA	promoter-TSS (NM_010439)	promoter-TSS (NM_010439)	-165	NM_010439	15289	Mm.207047	NM_010439	ENSMUSG00000066551	Hmgb1	HMG-1|Hmg1|SBP-1|p30	high mobility group box 1	protein-coding
mm_38927.1	chr4	150189152	150189157	-	1	NA	exon (NM_009802, exon 7 of 8)	exon (NM_009802, exon 7 of 8)	11981	NM_009802	12353	Mm.232523	NM_009802	ENSMUSG00000028972	Car6	Ca6|DOC1	carbonic anhydrase 6	protein-coding
mm_50057.1	chr6	41178484	41178506	+	1	NA	Intergenic	Intergenic	-123777	NM_011646	22074	Mm.383263	NM_011646	ENSMUSG00000054106	Try4	0910001B19Rik|Td	trypsin 4	protein-coding
mm_152152.1	chr19	7232992	7232994	-	1	NA	intron (NM_027643, intron 3 of 7)	B1_Mus2|SINE|Alu	8229	NM_027643	70999	Mm.329605	NM_027643	ENSMUSG00000024764	Naa40	4931433E08Rik|AU023197|Nat11	N(alpha)-acetyltransferase 40, NatD catalytic subunit	protein-coding
mm_36283.1	chr4	63861030	63861046	-	1	NA	exon (NM_009403, exon 1 of 4)	exon (NM_009403, exon 1 of 4)	246	NM_009403	21949	Mm.4664	NM_009403	ENSMUSG00000028362	Tnfsf8	CD153|CD30LG|Cd30l|Tnlg3a	tumor necrosis factor (ligand) superfamily, member 8	protein-coding
mm_24056.1	chr3	87914919	87914945	+	1	NA	3' UTR (NM_008231, exon 6 of 6)	3' UTR (NM_008231, exon 6 of 6)	-4612	NM_026591	67707	Mm.393802	NM_026591	ENSMUSG00000019710	Mrpl24	2010005E08Rik|2810470K06Rik|6720473G22Rik|AA407670	mitochondrial ribosomal protein L24	protein-coding
mm_123883.1	chr14	72709823	72709829	-	1	NA	5' UTR (NM_207636, exon 1 of 26)	5' UTR (NM_207636, exon 1 of 26)	177	NM_207636	319448	Mm.205421	NM_207636	ENSMUSG00000033487	Fndc3a	1700094E19Rik|D14Ertd453e|F730017H24Rik|Fndc3|sys	fibronectin type III domain containing 3A	protein-coding
mm_2393.1	chr1	93635170	93635210	+	1	NA	intron (NM_021537, intron 2 of 11)	CpG	537	NM_021537	59041	Mm.28761	NM_021537	ENSMUSG00000026277	Stk25	1500019J11Rik|AU018434|C86992|Ste20-like|Ysk1	serine/threonine kinase 25 (yeast)	protein-coding
mm_119495.1	chr14	47380050	47380056	+	1	NA	exon (NM_010705, exon 3 of 6)	exon (NM_010705, exon 3 of 6)	6193	NM_001145953	16854	Mm.248615	NM_010705	ENSMUSG00000050335	Lgals3	GBP|L-34|Mac-2|gal3	lectin, galactose binding, soluble 3	protein-coding
mm_57709.1	chr6	128600064	128600067	-	1	NA	Intergenic	MT2B1|LTR|ERVL	-18459	NM_001001179	232400	Mm.259234	NM_001001179	ENSMUSG00000047228	BC048546	Ovos	cDNA sequence BC048546	protein-coding
mm_106889.1	chr12	8012192	8012200	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	34519	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_129272.1	chr15	77021950	77021971	-	1	NA	intron (NM_001164047, intron 1 of 2)	intron (NM_001164047, intron 1 of 2)	767	NM_001164048	17189	Mm.404074	NM_013593	ENSMUSG00000018893	Mb	AI325109	myoglobin	protein-coding
mm_125091.1	chr15	27466838	27466862	+	1	NA	5' UTR (NM_020332, exon 1 of 12)	5' UTR (NM_020332, exon 1 of 12)	173	NM_020332	11732	Mm.265264	NM_020332	ENSMUSG00000022265	Ank	Ankh|D15Ertd221e|ank|mKIAA1581	progressive ankylosis	protein-coding
mm_120626.1	chr14	70457610	70457618	+	1	NA	promoter-TSS (NM_145981)	promoter-TSS (NM_145981)	97	NM_145981	105653	Mm.192598	NM_145981	ENSMUSG00000003469	Phyhip	AW049870|C630010D02Rik|Lnap1ip|PAHX-AP#1|PAHX-AP1	phytanoyl-CoA hydroxylase interacting protein	protein-coding
mm_72266.1	chr8	75097235	75097245	+	1	NA	exon (NM_010442, exon 3 of 5)	exon (NM_010442, exon 3 of 5)	3622	NM_010442	15368	Mm.276389	NM_010442	ENSMUSG00000005413	Hmox1	D8Wsu38e|HO-1|HO1|Hemox|Hmox|Hsp32	heme oxygenase 1	protein-coding
mm_16461.1	chr2	180598228	180598251	+	1	NA	promoter-TSS (NM_009936)	promoter-TSS (NM_009936)	17	NM_009936	12841	Mm.141312	NM_009936	ENSMUSG00000027570	Col9a3	AV006866	collagen, type IX, alpha 3	protein-coding
mm_13575.1	chr2	112361689	112361713	+	1	NA	3' UTR (NM_133649, exon 25 of 25)	3' UTR (NM_133649, exon 25 of 25)	6326	NM_026519	68032	Mm.220942	NM_026519	ENSMUSG00000027131	Emc4	2610318K02Rik|Tmem85	ER membrane protein complex subunit 4	protein-coding
mm_159674.1	chr4	155222325	155222325	-	1	NA	exon (NM_011385, exon 1 of 7)	exon (NM_011385, exon 1 of 7)	210	NM_011385	20481	Mm.28520	NM_011385	ENSMUSG00000029050	Ski	2310012I02Rik|2610001A11Rik|AA062172|AA589460|BC004088	ski sarcoma viral oncogene homolog (avian)	protein-coding
mm_89585.1	chr10	95778949	95778955	+	1	NA	Intergenic	Intergenic	-161711	NM_001001932	216238	Mm.210035	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding
mm_45164.1	chr5	50543530	50543539	-	1	NA	Intergenic	Intergenic	290772	NR_106197	102465903		NR_106197	ENSMUSG00000099124	Mir8117	Gm27323|mmu-mir-8117	microRNA 8117	ncRNA
mm_25882.1	chr3	130817911	130817923	+	1	NA	Intergenic	Intergenic	-87519	NM_001005859	68436	Mm.140568	NM_026724	ENSMUSG00000062006	Rpl34	1100001I22Rik	ribosomal protein L34	protein-coding
mm_27133.1	chr3	32365644	32365691	-	1	NA	promoter-TSS (NM_009517)	promoter-TSS (NM_009517)	-2	NM_009517	22401	Mm.35705	NM_009517	ENSMUSG00000027663	Zmat3	Wig1	zinc finger matrin type 3	protein-coding
mm_160937.1	chr11	94443277	94443277	-	1	NA	exon (NM_001177890, exon 11 of 35)	exon (NM_001177890, exon 11 of 35)	30921	NM_001177888	12291	Mm.29585	NM_009783	ENSMUSG00000020866	Cacna1g	Cav3.1d|[a]1G|a1G|alpha-1G|mKIAA1123	calcium channel, voltage-dependent, T type, alpha 1G subunit	protein-coding
mm_85530.1	chr9	106476320	106476355	-	1	NA	promoter-TSS (NM_145620)	promoter-TSS (NM_145620)	612	NM_001311150	235587	Mm.273659	NM_145619	ENSMUSG00000023249	Parp3	A930002C11Rik|AW990611|Adprt3|Adprtl3|PARP-3|pADPRT-3	poly (ADP-ribose) polymerase family, member 3	protein-coding
mm_72884.1	chr8	89015849	89015858	+	1	NA	Intergenic	Intergenic	-8882	NR_106190	102465899		NR_106190	ENSMUSG00000099078	Mir8110	Gm27571|mmu-mir-8110	microRNA 8110	ncRNA
mm_47183.1	chr5	120753905	120753915	-	1	NA	3' UTR (NM_145226, exon 16 of 16)	3' UTR (NM_145226, exon 16 of 16)	-4062	NM_001347448	246728	Mm.260926	NM_145227	ENSMUSG00000032690	Oas2	Oasl11	2'-5' oligoadenylate synthetase 2	protein-coding
mm_154028.1	chr19	53424729	53424744	-	1	NA	Intergenic	Intergenic	-34163	NM_172429	76479	Mm.313687	NM_172429	ENSMUSG00000025024	Smndc1	2410004J23Rik|4933440I19Rik	survival motor neuron domain containing 1	protein-coding
mm_95194.1	chr11	43068413	43068418	+	1	NA	Intergenic	MT2C_Mm|LTR|ERVL	-81462	NM_176999	319767	Mm.252339	NM_176999	ENSMUSG00000055415	Atp10b	5930426O13Rik|9030605H24Rik	ATPase, class V, type 10B	protein-coding
mm_107455.1	chr12	37108617	37108631	+	1	NA	promoter-TSS (NM_008584)	promoter-TSS (NM_008584)	78	NM_008584	17286	Mm.341398	NM_008584	ENSMUSG00000036144	Meox2	AI528662|Gax|Mox-2|Mox2	mesenchyme homeobox 2	protein-coding
mm_123361.1	chr14	63143036	63143046	-	1	NA	3' UTR (NM_007798, exon 10 of 10)	3' UTR (NM_007798, exon 10 of 10)	20579	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_169189.1	chr13	66027598	66027600	+	1	NA	Intergenic	Intergenic	-85854	NM_001177832	628709	Mm.390595	NM_001177832	ENSMUSG00000095909	Gm10324	ENSMUSG00000071302	predicted gene 10324	protein-coding
mm_28518.1	chr3	92584504	92584517	-	1	NA	exon (NM_008574, exon 2 of 2)	exon (NM_008574, exon 2 of 2)	4514	NM_008574	17235	Mm.331192	NM_008574		Smcp	Mcs|Mcsp	sperm mitochondria-associated cysteine-rich protein	protein-coding
mm_142572.1	chr17	46678628	46678644	-	1	NA	intron (NM_001163729, intron 1 of 10)	intron (NM_001163729, intron 1 of 10)	-1817	NM_001277310	17256	Mm.329083	NM_010787	ENSMUSG00000002768	Mea1	Mea-1	male enhanced antigen 1	protein-coding
mm_47664.1	chr5	126504959	126504966	-	1	NA	Intergenic	Intergenic	-525827	NR_040685	71247	Mm.399586	NR_040685	ENSMUSG00000105490	4933438B17Rik	-	RIKEN cDNA 4933438B17 gene	ncRNA
mm_146982.1	chr18	33890567	33890588	-	1	NA	intron (NM_013512, intron 4 of 23)	intron (NM_013512, intron 4 of 23)	95685	NR_038151	69749	Mm.248787	NR_038151	ENSMUSG00000087590	Epb41l4aos	2410004N09Rik|Epb4.1l4aos	erythrocyte membrane protein band 4.1 like 4a, opposite strand	ncRNA
mm_120956.1	chr14	77473871	77473875	+	1	NA	intron (NM_001253759, intron 5 of 19)	intron (NM_001253759, intron 5 of 19)	32995	NR_033141	629678	Mm.390721	NM_001037935	ENSMUSG00000067973	Gm6994	EG629678	predicted gene 6994	ncRNA
mm_139084.1	chr17	46751962	46751982	+	1	NA	intron (NM_028065, intron 1 of 5)	CpG	242	NM_001305989	72029	Mm.240325	NM_028065	ENSMUSG00000023973	Cnpy3	1600025D17Rik|2410050O22Rik|AI413153|CAG4A|ERDA5|PRAT4A|Tnrc5	canopy FGF signaling regulator 3	protein-coding
mm_8035.1	chr1	135167568	135167587	-	1	NA	5' UTR (NM_134438, exon 1 of 2)	5' UTR (NM_134438, exon 1 of 2)	104	NM_134438	171469	Mm.272290	NM_134438	ENSMUSG00000026424	Gpr37l1	AW047233|CAG-18|D0Kist8	G protein-coupled receptor 37-like 1	protein-coding
mm_140484.1	chr17	3115708	3115720	-	1	NA	intron (NM_134123, intron 1 of 19)	intron (NM_134123, intron 1 of 19)	742	NM_134123	106583	Mm.124373	NM_134123	ENSMUSG00000046201	Scaf8	A630086M08Rik|A930036P18Rik|AA408306|AI447644|AI448652|AU015035|Rbm16|mKIAA1116	SR-related CTD-associated factor 8	protein-coding
mm_93302.1	chr10	96722645	96722659	-	1	NA	Intergenic	Intergenic	105651	NM_007569	12226	Mm.23811	NM_007569	ENSMUSG00000036478	Btg1	AI426953|AW546738	B cell translocation gene 1, anti-proliferative	protein-coding
mm_159295.1	chr2	175206878	175206878	-	1	NA	promoter-TSS (NM_001099308)	promoter-TSS (NM_001099308)	39	NM_001164689	626832	Mm.441314	NM_001164689	ENSMUSG00000078887	Gm6710	1600017I02Rik|2310011F05Rik|2900089K14Rik|3100002L24Rik|WF-4	predicted gene 6710	protein-coding
mm_45537.1	chr5	72763791	72763803	-	1	NA	intron (NM_001113461, intron 13 of 17)	intron (NM_001113461, intron 13 of 17)	-11020	NM_001122754	22165	Mm.3264	NM_013698	ENSMUSG00000054892	Txk	A130089B16Rik|Btkl|PTK-RL-18|PTK4|Rlk	TXK tyrosine kinase	protein-coding
mm_82160.1	chr9	123781429	123781440	+	1	NA	3' UTR (NM_001166625, exon 4 of 4)	3' UTR (NM_001166625, exon 4 of 4)	14223	NM_001166625	12769	Mm.440604	NM_009913	ENSMUSG00000029530	Ccr9	A130091K22Rik|Cmkbr10|GPR-9-6	chemokine (C-C motif) receptor 9	protein-coding
mm_6874.1	chr1	84284819	84284856	-	1	NA	promoter-TSS (NM_001003948)	promoter-TSS (NM_001003948)	-192	NM_001003948	98496	Mm.187470	NM_001003948	ENSMUSG00000045658	Pid1	5033414K04Rik|NYGGF4	phosphotyrosine interaction domain containing 1	protein-coding
mm_50204.1	chr6	42245908	42245977	+	1	NA	promoter-TSS (NM_029555)	promoter-TSS (NM_029555)	7	NM_029555	76263	Mm.267014	NM_029555	ENSMUSG00000029864	Gstk1	0610025I19Rik|AW260476|DsbA-L	glutathione S-transferase kappa 1	protein-coding
mm_54022.1	chr6	8778107	8778162	-	1	NA	5' UTR (NM_010492, exon 1 of 14)	5' UTR (NM_010492, exon 1 of 14)	350	NM_010492	15893	Mm.275683	NM_010492	ENSMUSG00000062995	Ica1	69kDa|ICA69	islet cell autoantigen 1	protein-coding
mm_86677.1	chr10	18235031	18235054	+	1	NA	promoter-TSS (NM_144820)	promoter-TSS (NM_144820)	-61	NM_144820	215814	Mm.296565	NM_144820	ENSMUSG00000059554	Ccdc28a	1700009P13Rik|AI480677	coiled-coil domain containing 28A	protein-coding
mm_27710.1	chr3	67515627	67515654	-	1	NA	promoter-TSS (NM_001164763)	promoter-TSS (NM_001164763)	-117	NM_001164763	109222	Mm.38002	NM_001164763	ENSMUSG00000049404	Rarres1	5430417P09Rik|AI662122	retinoic acid receptor responder (tazarotene induced) 1	protein-coding
mm_102767.1	chr11	68095980	68095991	-	1	NA	intron (NM_018768, intron 6 of 7)	intron (NM_018768, intron 6 of 7)	-124907	NR_105833	102465219		NR_105833	ENSMUSG00000099174	Mir6406	Gm27981|mmu-mir-6406	microRNA 6406	ncRNA
mm_65367.1	chr7	25072402	25072415	-	1	NA	promoter-TSS (NM_008168)	promoter-TSS (NM_008168)	-39	NM_008168	14809	Mm.2879	NM_008168	ENSMUSG00000003378	Grik5	GluK5|GluRgamma2|KA2	glutamate receptor, ionotropic, kainate 5 (gamma 2)	protein-coding
mm_120456.1	chr14	65970529	65970534	+	1	NA	intron (NM_013492, intron 1 of 8)	intron (NM_013492, intron 1 of 8)	2048	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_145387.1	chr18	57133374	57133422	+	1	NA	5' UTR (NM_001001979, exon 1 of 25)	5' UTR (NM_001001979, exon 1 of 25)	308	NM_001001979	70417	Mm.297863	NM_001001979	ENSMUSG00000024593	Megf10	3000002B06Rik|Gm331	multiple EGF-like-domains 10	protein-coding
mm_163950.1	chr14	52623834	52623834	+	1	NA	Intergenic	Intergenic	-128139	NM_001170918	57269	Mm.88822	NM_020512	ENSMUSG00000059887	Olfr1507	MOR244-1|Mor28|Or28	olfactory receptor 1507	protein-coding
mm_17016.1	chr2	18970477	18970488	-	1	NA	intron (NM_008845, intron 1 of 9)	intron (NM_008845, intron 1 of 9)	27639	NM_008845	18718	Mm.313977	NM_008845	ENSMUSG00000026737	Pip4k2a	AW742916|Pip5k2a	phosphatidylinositol-5-phosphate 4-kinase, type II, alpha	protein-coding
mm_145482.1	chr18	60379463	60379474	+	1	NA	intron (NM_021792, intron 1 of 1)	RLTR13D3|LTR|ERVK	3439	NM_001146275	60440	Mm.261140	NM_021792	ENSMUSG00000054072	Iigp1	2900074L10Rik|AI046432|AW111922|Ifgga1|Iigp|Irga6	interferon inducible GTPase 1	protein-coding
mm_19266.1	chr2	84887009	84887044	-	1	NA	promoter-TSS (NM_199223)	promoter-TSS (NM_199223)	-334	NM_199223	269295	Mm.86447	NM_199223	ENSMUSG00000050896	Rtn4rl2	Ngr2|Ngrh1|Ngrl3	reticulon 4 receptor-like 2	protein-coding
mm_21678.1	chr2	164426147	164426161	-	1	NA	exon (NM_011521, exon 5 of 5)	exon (NM_011521, exon 5 of 5)	17034	NM_011521	20971	Mm.3815	NM_011521	ENSMUSG00000017009	Sdc4	AA959608|AW108331|S4|Synd4|ryudocan|syndecan-4	syndecan 4	protein-coding
mm_82798.1	chr9	29412461	29412503	-	1	NA	intron (NM_172290, intron 1 of 7)	CpG	550647	NM_172290	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding
mm_143730.1	chr17	81385436	81385440	-	1	NA	non-coding (NR_104580, exon 9 of 9)	non-coding (NR_104580, exon 9 of 9)	-320353	NM_028138	72167	Mm.273257	NM_028138	ENSMUSG00000024246	Thumpd2	2810025A12Rik	THUMP domain containing 2	protein-coding
mm_57445.1	chr6	124965486	124965543	-	1	NA	promoter-TSS (NM_001164089)	promoter-TSS (NM_001164089)	15	NM_001164089	26894	Mm.244536	NM_012003	ENSMUSG00000030127	Cops7a	D6Ertd35e	COP9 signalosome subunit 7A	protein-coding
mm_14419.1	chr2	130450330	130450349	+	1	NA	promoter-TSS (NM_008980)	promoter-TSS (NM_008980)	61	NM_001163688	19262	Mm.224246	NM_008980	ENSMUSG00000027303	Ptpra	Ptpa|Ptpalpha|Rptpalpha|Rptra|Rptralpha	protein tyrosine phosphatase, receptor type, A	protein-coding
mm_145776.1	chr18	65051010	65051032	+	1	NA	intron (NM_031881, intron 1 of 29)	intron (NM_031881, intron 1 of 29)	27494	NM_031881	83814	Mm.98668	NM_031881	ENSMUSG00000024589	Nedd4l	1300012C07Rik|Nedd4-2|Nedd4b	neural precursor cell expressed, developmentally down-regulated gene 4-like	protein-coding
mm_145310.1	chr18	53862321	53862341	+	1	NA	5' UTR (NM_152809, exon 1 of 13)	5' UTR (NM_152809, exon 1 of 13)	218	NM_152809	70425	Mm.368668	NM_152809	ENSMUSG00000073563	Csnk1g3	3300002K07Rik|C330049O21Rik	casein kinase 1, gamma 3	protein-coding
mm_170212.1	chr17	70963748	70963748	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	26768	NM_023402	67938	Mm.261329	NM_023402	ENSMUSG00000034868	Myl12b	1500001M02Rik|C77744|Mylc2b|RLC-B	myosin, light chain 12B, regulatory	protein-coding
mm_4972.1	chr1	191299550	191299559	+	1	NA	Intergenic	Intergenic	18564	NM_025424	66208	Mm.46444	NM_025424	ENSMUSG00000037499	Nenf	1110060M21Rik|SCIRP10|Spuf	neuron derived neurotrophic factor	protein-coding
mm_149233.1	chr19	10182922	10182969	+	1	NA	promoter-TSS (NM_146094)	promoter-TSS (NM_146094)	57	NM_146094	76267	Mm.30158	NM_146094	ENSMUSG00000010663	Fads1	0710001O03Rik|A930006B21Rik|AI317215|DSD	fatty acid desaturase 1	protein-coding
mm_135655.1	chr16	52400533	52400570	-	1	NA	intron (NM_009655, intron 1 of 15)	intron (NM_009655, intron 1 of 15)	52530	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_120109.1	chr14	59440573	59440582	+	1	NA	promoter-TSS (NM_026908)	promoter-TSS (NM_026908)	303	NM_001320725	107303348		NM_001320725		Setdb2-phf11c	-	Setdb2-Phf11c readthrough	protein-coding
mm_82886.1	chr9	32541322	32541335	-	1	NA	5' UTR (NM_008026, exon 1 of 9)	5' UTR (NM_008026, exon 1 of 9)	124	NM_008026	14247	Mm.258908	NM_008026	ENSMUSG00000016087	Fli1	EWSR2|Fli-1|SIC-1|Sic1	Friend leukemia integration 1	protein-coding
mm_102821.1	chr11	69012448	69012458	-	1	NA	Intergenic	RLTR34C_MM|LTR|ERVK	-3458	NM_001281465	68964	Mm.285785	NM_001013256	ENSMUSG00000020898	Ctc1	1500010J02Rik|AAF-132|AAF132	CTS telomere maintenance complex component 1	protein-coding
mm_155542.1	chrX	74307184	74307196	+	1	NA	exon (NM_010273, exon 4 of 11)	exon (NM_010273, exon 4 of 11)	2178	NM_010273	14567	Mm.205830	NM_010273	ENSMUSG00000015291	Gdi1	GDIA|GDIalpha	guanosine diphosphate (GDP) dissociation inhibitor 1	protein-coding
mm_88702.1	chr10	80147847	80147855	+	1	NA	promoter-TSS (NM_001305798)	promoter-TSS (NM_001305798)	-421	NM_001305798	59090	Mm.143813	NM_021565	ENSMUSG00000035621	Midn	3000003C15Rik	midnolin	protein-coding
mm_154765.1	chrX	12136101	12136126	+	1	NA	intron (NR_045434, intron 3 of 3)	intron (NR_045434, intron 3 of 3)	24233	NR_045434	71458	Mm.196328	NM_029510	ENSMUSG00000040363	Bcor	2900008C10Rik|5830466J11Rik|8430401K06Rik|BcorR|D930024N20Rik|mKIAA1575	BCL6 interacting corepressor	protein-coding
mm_61336.1	chr7	68277531	68277539	+	1	NA	promoter-TSS (NR_040340)	promoter-TSS (NR_040340)	-941	NR_040340	100504026	Mm.426764	NR_040340	ENSMUSG00000086628	Gm16157	OTTMUSG00000031023	predicted gene 16157	ncRNA
mm_67917.1	chr7	99858301	99858303	-	1	NA	promoter-TSS (NM_001164258)	promoter-TSS (NM_001164258)	581	NM_025668	66624	Mm.30043	NM_025668	ENSMUSG00000035227	Spcs2	5730406I15Rik|AA408713|mKIAA0102	signal peptidase complex subunit 2 homolog (S. cerevisiae)	protein-coding
mm_26823.1	chr3	10335690	10335707	-	1	NA	promoter-TSS (NM_001010834)	promoter-TSS (NM_001010834)	-42	NM_001010834	241877	Mm.442146	NM_001010834	ENSMUSG00000058921	Slc10a5	Gm405|mP5	solute carrier family 10 (sodium/bile acid cotransporter family), member 5	protein-coding
mm_24017.1	chr3	87525573	87525643	+	1	NA	promoter-TSS (NM_012051)	promoter-TSS (NM_012051)	30	NM_012051	27049	Mm.219460	NM_012051	ENSMUSG00000003382	Etv3	AI414410|METS|Pe1	ets variant 3	protein-coding
mm_111563.1	chr12	101222115	101222129	-	1	NA	Intergenic	Intergenic	76513	NR_033653	74947	Mm.488905	NR_033653	ENSMUSG00000092054	Kif4-ps	4930463M05Rik|Kif4b	kinesin family member 4, pseudogene	pseudo
mm_19935.1	chr2	116065719	116065735	-	1	NA	promoter-TSS (NM_010825)	promoter-TSS (NM_010825)	-669	NM_010825	17536	Mm.247566	NM_010825	ENSMUSG00000027210	Meis2	A430109D20Rik|Mrg1|Stra10	Meis homeobox 2	protein-coding
mm_46079.1	chr5	92326791	92326800	-	1	NA	exon (NM_008599, exon 2 of 4)	exon (NM_008599, exon 2 of 4)	1284	NM_008599	17329	Mm.766	NM_008599	ENSMUSG00000029417	Cxcl9	BB139920|CMK|Mig|MuMIG|Scyb9|crg-10	chemokine (C-X-C motif) ligand 9	protein-coding
mm_108050.1	chr12	73909613	73909620	+	1	NA	intron (NM_010431, intron 1 of 14)	intron (NM_010431, intron 1 of 14)	1749	NM_001313919	15251	Mm.3879	NM_010431	ENSMUSG00000021109	Hif1a	AA959795|HIF-1-alpha|HIF1-alpha|HIF1alpha|MOP1|bHLHe78	hypoxia inducible factor 1, alpha subunit	protein-coding
mm_130206.1	chr15	95528229	95528266	-	1	NA	promoter-TSS (NM_001289653)	promoter-TSS (NM_001289653)	5	NM_001289653	54003	Mm.3959	NM_016743	ENSMUSG00000022454	Nell2	A330108N19Rik|R75516|mel91	NEL-like 2	protein-coding
mm_164700.1	chr17	49957538	49957546	+	1	NA	Intergenic	Intergenic	232955	NM_181397	76438	Mm.41854	NM_181397	ENSMUSG00000039316	Rftn1	2310015N21Rik|AI853526	raftlin lipid raft linker 1	protein-coding
mm_166487.1	chr5	147860496	147860511	-	1	NA	promoter-TSS (NM_025624)	promoter-TSS (NM_025624)	-125	NM_025624	66537	Mm.332855	NM_025624	ENSMUSG00000029649	Pomp	2510048O06Rik|Ump1	proteasome maturation protein	protein-coding
mm_83167.1	chr9	40489762	40489765	-	1	NA	Intergenic	Intergenic	-33999	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_167379.1	chr8	94102278	94102284	+	1	NA	Intergenic	Intergenic	-3470	NM_026116	67378	Mm.292107	NM_026116	ENSMUSG00000031755	Bbs2	2410125H22Rik|AI447581	Bardet-Biedl syndrome 2 (human)	protein-coding
mm_169792.1	chr16	15315386	15315390	+	1	NA	Intergenic	ERVB4_1-I_MM-int|LTR|ERVK	279130	NM_001159351	70620	Mm.235407	NM_023585	ENSMUSG00000022674	Ube2v2	1110021H13Rik|4632410D19Rik|5730524P06Rik|6820402M05|AI848315|C81524|MMS2	ubiquitin-conjugating enzyme E2 variant 2	protein-coding
mm_64249.1	chr7	141704380	141704406	+	1	NA	intron (NM_023566, intron 27 of 45)	intron (NM_023566, intron 27 of 45)	14053	NM_023566	17831	Mm.2041	NM_023566		Muc2	2010015E03Rik|MCM|wnn	mucin 2	protein-coding
mm_148822.1	chr19	6299772	6299782	+	1	NA	3' UTR (NM_010119, exon 5 of 5)	3' UTR (NM_010119, exon 5 of 5)	-6680	NM_001033342	240505	Mm.329622	NM_001033342	ENSMUSG00000024769	Cdc42bpg	BC046418|MRCKgamma	CDC42 binding protein kinase gamma (DMPK-like)	protein-coding
mm_7938.1	chr1	133914737	133914742	-	1	NA	exon (NM_054077, exon 2 of 3)	exon (NM_054077, exon 2 of 3)	6662	NM_054077	116847	Mm.214514	NM_054077	ENSMUSG00000041577	Prelp	7330409J17Rik|SLRR2A	proline arginine-rich end leucine-rich repeat	protein-coding
mm_101551.1	chr11	33755045	33755056	-	1	NA	intron (NM_001190885, intron 1 of 8)	LSU-rRNA_Hsa|rRNA|rRNA	88535	NM_027398	70357	Mm.252514	NM_027398	ENSMUSG00000053519	Kcnip1	KCHIP1|Kchip1.2	Kv channel-interacting protein 1	protein-coding
mm_26513.1	chr3	145891647	145891658	+	1	NA	3' UTR (NM_026993, exon 6 of 6)	3' UTR (NM_026993, exon 6 of 6)	-32610	NM_009740	12042	Mm.239141	NM_009740	ENSMUSG00000028191	Bcl10	AI132454|BCL-10|C81403|CARMEN|CIPER|CLAP|ME10|cE10	B cell leukemia/lymphoma 10	protein-coding
mm_98019.1	chr11	84944915	84944921	+	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	-12836	NM_007607	12351	Mm.1641	NM_007607	ENSMUSG00000000805	Car4	AW456718|Ca4	carbonic anhydrase 4	protein-coding
mm_100699.1	chr11	3533467	3533518	-	1	NA	exon (NM_001284428, exon 4 of 22)	exon (NM_001284428, exon 4 of 22)	5800	NM_013870	29856	Mm.188516	NM_013870	ENSMUSG00000020439	Smtn	smsmo	smoothelin	protein-coding
mm_61411.1	chr7	73539365	73539378	+	1	NA	TTS (NR_037569)	TTS (NR_037569)	2375	NM_001081345	244059	Mm.34539	NM_001081345	ENSMUSG00000078671	Chd2	2810013C04Rik|2810040A01Rik|5630401D06Rik|AI851092|BC029703|CHD-2	chromodomain helicase DNA binding protein 2	protein-coding
mm_138305.1	chr17	34643963	34643971	+	1	NA	promoter-TSS (NM_019873)	promoter-TSS (NM_019873)	-916	NM_019873	56299	Mm.10025	NM_019873	ENSMUSG00000033739	Fkbpl	DIR1|NG7|Ppiase-X|Wisp39	FK506 binding protein-like	protein-coding
mm_80682.1	chr9	91365960	91365969	+	1	NA	promoter-TSS (NM_009573)	promoter-TSS (NM_009573)	-165	NM_009573	22771	Mm.335350	NM_009573	ENSMUSG00000032368	Zic1	ZIC|ZNF201	zinc finger protein of the cerebellum 1	protein-coding
mm_43387.1	chr5	135733286	135733296	+	1	NA	intron (NM_008898, intron 10 of 15)	intron (NM_008898, intron 10 of 15)	2598	NR_106001	102466791		NR_106001	ENSMUSG00000099197	Mir7034	Gm27372|mmu-mir-7034	microRNA 7034	ncRNA
mm_136971.1	chr17	15745783	15745787	+	1	NA	intron (NM_007690, intron 17 of 35)	ID2|SINE|ID	40818	NM_007690	12648	Mm.8137	NM_007690	ENSMUSG00000023852	Chd1	4930525N21Rik|AI851787|AW555109	chromodomain helicase DNA binding protein 1	protein-coding
mm_151072.1	chr19	47513344	47513363	+	1	NA	non-coding (NR_045322, exon 2 of 3)	non-coding (NR_045322, exon 2 of 3)	371	NR_045322	100503104	Mm.442735	NR_045322	ENSMUSG00000097990	Gm19557	-	predicted gene, 19557	ncRNA
mm_29225.1	chr3	107212858	107212861	-	1	NA	exon (NM_001111143, exon 8 of 9)	exon (NM_001111143, exon 8 of 9)	8873	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_98618.1	chr11	95843805	95843823	+	1	NA	5' UTR (NM_001284397, exon 2 of 4)	5' UTR (NM_001284397, exon 2 of 4)	569	NM_001284397	14710	Mm.46299	NM_023121	ENSMUSG00000038811	Gngt2	AV096488	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 2	protein-coding
mm_82348.1	chr9	13826947	13826972	-	1	NA	promoter-TSS (NR_037622)	promoter-TSS (NR_037622)	94	NR_037622	74360	Mm.157212	NM_026665	ENSMUSG00000031922	Cep57	3110002L15Rik|4921510P06Rik|4931428M20Rik|AI467480|Tsp57|mKIAA0092	centrosomal protein 57	protein-coding
mm_136820.1	chr17	12410899	12410935	+	1	NA	exon (NM_008877, exon 15 of 19)	exon (NM_008877, exon 15 of 19)	32308	NM_008877	18815	Mm.971	NM_008877	ENSMUSG00000059481	Plg	AI649309|Pg	plasminogen	protein-coding
mm_45885.1	chr5	88522535	88522555	-	1	NA	exon (NM_152839, exon 3 of 4)	exon (NM_152839, exon 3 of 4)	5352	NM_152839	16069	Mm.1192	NM_152839	ENSMUSG00000067149	Jchain	9530090F24Rik|AI323815|Igj|Jch	immunoglobulin joining chain	protein-coding
mm_128433.1	chr15	50682498	50682509	-	1	NA	intron (NM_001310481, intron 4 of 5)	intron (NM_001310481, intron 4 of 5)	206546	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_154548.1	chrM	14872	14887	-	1	NA	NA	Intergenic	NA	NA								
mm_102931.1	chr11	69600859	69600863	-	1	NA	3' UTR (NM_013415, exon 7 of 7)	3' UTR (NM_013415, exon 7 of 7)	5099	NM_013415	11932	Mm.235204	NM_013415	ENSMUSG00000041329	Atp1b2	Amog|Atpb-2	ATPase, Na+/K+ transporting, beta 2 polypeptide	protein-coding
mm_13100.1	chr2	91265208	91265227	+	1	NA	TTS (NM_028733)	TTS (NM_028733)	102	NM_023854	77038	Mm.43636	NM_023854	ENSMUSG00000027255	Arfgap2	2310032E02Rik|Zfp289	ADP-ribosylation factor GTPase activating protein 2	protein-coding
mm_132085.1	chr16	30536067	30536084	+	1	NA	intron (NM_172614, intron 8 of 9)	L1MA5A|LINE|L1	14503	NM_172614	224090	Mm.241459	NM_172614	ENSMUSG00000022537	Tmem44	1700007N03Rik|9330161C17Rik|B230220N21	transmembrane protein 44	protein-coding
mm_96131.1	chr11	60837838	60837866	+	1	NA	intron (NM_001172112, intron 1 of 6)	intron (NM_001172112, intron 1 of 6)	7221	NM_145428	216820	Mm.21475	NM_145428	ENSMUSG00000042569	Dhrs7b	BC003479|C79874|C80074|PexRAP	dehydrogenase/reductase (SDR family) member 7B	protein-coding
mm_81505.1	chr9	110034667	110034679	+	1	NA	exon (NM_008633, exon 7 of 19)	exon (NM_008633, exon 7 of 19)	-17348	NM_001311163	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_132257.1	chr16	32753475	32753512	+	1	NA	exon (NM_080457, exon 3 of 27)	exon (NM_080457, exon 3 of 27)	17607	NM_080457	140474	Mm.214599	NM_080457	ENSMUSG00000079620	Muc4	4933405I11Rik|Asgp	mucin 4	protein-coding
mm_147085.1	chr18	35629824	35629836	-	1	NA	Intergenic	Intergenic	-2603	NM_011397	20522	Mm.22702	NM_011397	ENSMUSG00000024354	Slc23a1	D18Ucla2|SVCT1|Slc23a2|YSPL3	solute carrier family 23 (nucleobase transporters), member 1	protein-coding
mm_73081.1	chr8	94479877	94479907	+	1	NA	intron (NM_001033207, intron 6 of 48)	intron (NM_001033207, intron 6 of 48)	7129	NM_001033207	434341	Mm.334720	NM_001033207	ENSMUSG00000074151	Nlrc5	AI451557|AK220210|NOD27	NLR family, CARD domain containing 5	protein-coding
mm_20077.1	chr2	120604646	120604650	-	1	NA	non-coding (NR_027510, exon 6 of 6)	non-coding (NR_027510, exon 6 of 6)	4667	NM_025657	66606	Mm.428639	NM_025657	ENSMUSG00000027286	Lrrc57	2810002D13Rik|AA407405	leucine rich repeat containing 57	protein-coding
mm_168490.1	chr11	49679100	49679118	-	1	NA	intron (NM_212484, intron 10 of 11)	intron (NM_212484, intron 10 of 11)	15514	NM_170727	68662	Mm.22802	NM_054037	ENSMUSG00000064057	Scgb3a1	HIN-1|LuLeu2|Pnsp2|UGRP2|Utgrp2	secretoglobin, family 3A, member 1	protein-coding
mm_104119.1	chr11	86741720	86741720	-	1	NA	intron (NM_001003908, intron 1 of 31)	intron (NM_001003908, intron 1 of 31)	15772	NM_001003908	67300	Mm.254588	NM_001003908	ENSMUSG00000047126	Cltc	3110065L21Rik|CHC|R74732	clathrin, heavy polypeptide (Hc)	protein-coding
mm_40809.1	chr5	71699895	71699903	+	1	NA	promoter-TSS (NM_008069)	promoter-TSS (NM_008069)	-117	NM_008069	14400	Mm.38567	NM_008069	ENSMUSG00000029212	Gabrb1	AW061132|B230208N19Rik|Gabrb-1	gamma-aminobutyric acid (GABA) A receptor, subunit beta 1	protein-coding
mm_34078.1	chr4	138630541	138630543	+	1	NA	Intergenic	Intergenic	-6550	NM_029401	75718	Mm.251530	NM_029401	ENSMUSG00000028753	Vwa5b1	4931403E03Rik	von Willebrand factor A domain containing 5B1	protein-coding
mm_17628.1	chr2	31035725	31035772	-	1	NA	intron (NM_001038700, intron 13 of 14)	B4A|SINE|B4	53469	NM_028846	74270	Mm.346654	NM_028846	ENSMUSG00000026854	Usp20	1700055M05Rik|AI467231|Vdu2	ubiquitin specific peptidase 20	protein-coding
mm_6625.1	chr1	77898438	77898447	-	1	NA	Intergenic	U1|snRNA|snRNA	298694	NM_008781	18505	Mm.1371	NM_008781	ENSMUSG00000004872	Pax3	Pax-3|Sp|Splchl2|splotch	paired box 3	protein-coding
mm_102032.1	chr11	51756379	51756493	-	1	NA	5' UTR (NM_175255, exon 1 of 23)	5' UTR (NM_175255, exon 1 of 23)	398	NM_001290785	77371	Mm.33878	NM_175255	ENSMUSG00000036391	Sec24a	-	Sec24 related gene family, member A (S. cerevisiae)	protein-coding
mm_150721.1	chr19	43528361	43528373	+	1	NA	Intergenic	Intergenic	-3762	NM_010324	14718	Mm.19039	NM_010324	ENSMUSG00000025190	Got1	AI789014|Got-1|cAspAT|cCAT	glutamic-oxaloacetic transaminase 1, soluble	protein-coding
mm_52771.1	chr6	121210679	121210687	+	1	NA	promoter-TSS (NM_017379)	promoter-TSS (NM_017379)	-51	NM_017379	53857	Mm.32884	NM_017379	ENSMUSG00000030137	Tuba8	-	tubulin, alpha 8	protein-coding
mm_135343.1	chr16	42912079	42912089	-	1	NA	promoter-TSS (NR_040402)	promoter-TSS (NR_040402)	-14	NR_040402	100503040	Mm.490721	NR_040402		Gm19522	-	predicted gene, 19522	ncRNA
mm_59055.1	chr7	19414188	19414199	+	1	NA	exon (NM_007710, exon 2 of 8)	exon (NM_007710, exon 2 of 8)	3099	NM_007710	12715	Mm.2375	NM_007710	ENSMUSG00000030399	Ckm	Ckmm|M-CK|MCK	creatine kinase, muscle	protein-coding
mm_80076.1	chr9	69989469	69989539	+	1	NA	promoter-TSS (NM_016787)	promoter-TSS (NM_016787)	38	NM_001008238	12175	Mm.159777	NM_016787	ENSMUSG00000011958	Bnip2	5730523P12Rik|BNIP2beta|Nip21	BCL2/adenovirus E1B interacting protein 2	protein-coding
mm_151965.1	chr19	5801736	5801771	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	919	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_145907.1	chr18	65803596	65803599	+	1	NA	intron (NM_025468, intron 1 of 5)	intron (NM_025468, intron 1 of 5)	3019	NM_025468	66286	Mm.27800	NM_025468	ENSMUSG00000024516	Sec11c	1810029G24Rik|Sec11l3	SEC11 homolog C, signal peptidase complex subunit	protein-coding
mm_44884.1	chr5	34654008	34654018	-	1	NA	exon (NM_029278, exon 5 of 18)	exon (NM_029278, exon 5 of 18)	6135	NM_029278	75416	Mm.40292	NM_029278	ENSMUSG00000036693	Nop14	2610033H07Rik|Nol14	NOP14 nucleolar protein	protein-coding
mm_159097.1	chr2	36105185	36105185	-	1	NA	exon (NM_008500, exon 1 of 10)	exon (NM_008500, exon 1 of 10)	223	NM_001083125	16874	Mm.12881	NM_008500	ENSMUSG00000026890	Lhx6	Lhx6.1	LIM homeobox protein 6	protein-coding
mm_17280.1	chr2	26122739	26122765	-	1	NA	promoter-TSS (NM_026495)	promoter-TSS (NM_026495)	59	NM_026495	67991	Mm.131074	NM_026495	ENSMUSG00000026932	Nacc2	0610020I02Rik|AI448087|Btbd14a|C030048H19Rik	nucleus accumbens associated 2, BEN and BTB (POZ) domain containing	protein-coding
mm_133917.1	chr16	97558024	97558037	+	1	NA	intron (NM_013606, intron 12 of 13)	B3A|SINE|B2	21947	NM_013606	17858	Mm.14157	NM_013606	ENSMUSG00000023341	Mx2	AI528743|Mx-2	MX dynamin-like GTPase 2	protein-coding
mm_94547.1	chr11	11114126	11114148	+	1	NA	5' UTR (NM_177033, exon 1 of 4)	5' UTR (NM_177033, exon 1 of 4)	121	NM_177033	319922	Mm.337851	NM_177033	ENSMUSG00000050830	Vwc2	A930041G11Rik|G11|PSST739|UNQ739|cradin	von Willebrand factor C domain containing 2	protein-coding
mm_27777.1	chr3	73636695	73636707	-	1	NA	3' UTR (NM_009738, exon 4 of 4)	3' UTR (NM_009738, exon 4 of 4)	71714	NM_009738	12038	Mm.250719	NM_009738	ENSMUSG00000027792	Bche	C730038G20Rik	butyrylcholinesterase	protein-coding
mm_24274.1	chr3	89204066	89204092	+	1	NA	exon (NM_001077411, exon 3 of 11)	exon (NM_001077411, exon 3 of 11)	1154	NR_122037	14466	Mm.5031	NM_008094	ENSMUSG00000028048	Gba	GBA1|GC|GCase|GLUC|betaGC	glucosidase, beta, acid	protein-coding
mm_116730.1	chr13	51733710	51733756	-	1	NA	intron (NM_013660, intron 2 of 15)	intron (NM_013660, intron 2 of 15)	60014	NM_001281880	20354	Mm.33903	NM_013660	ENSMUSG00000021451	Sema4d	CD100|Semacl2|Semaj|Semcl2|coll-4	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D	protein-coding
mm_131392.1	chr16	14218907	14218927	+	1	NA	exon (NM_013607, exon 23 of 42)	exon (NM_013607, exon 23 of 42)	55642	NM_001114085	67203	Mm.24105	NM_023317	ENSMUSG00000022678	Nde1	2810027M15Rik|AU042936|AW822251|Nude|mNudE	nudE neurodevelopment protein 1	protein-coding
mm_1587.1	chr1	74303276	74303281	+	1	NA	intron (NM_027154, intron 1 of 11)	intron (NM_027154, intron 1 of 11)	1058	NM_027154	69660	Mm.261182	NM_027154	ENSMUSG00000006301	Tmbim1	2310061B02Rik|AA960455|AU024746|C78899|RECS1|Tmbib1|mKIAA4161	transmembrane BAX inhibitor motif containing 1	protein-coding
mm_136925.1	chr17	13846758	13846766	+	1	NA	intron (NM_010806, intron 15 of 32)	intron (NM_010806, intron 15 of 32)	-85368	NM_022311	21646	Mm.486358	NM_022311	ENSMUSG00000038347	Tcte2	AI429268|Tcte-2	t-complex-associated testis expressed 2	protein-coding
mm_127172.1	chr15	98835951	98835952	+	1	NA	intron (NM_001033276, intron 51 of 54)	intron (NM_001033276, intron 51 of 54)	-4443	NM_016781	19082	Mm.6670	NM_016781	ENSMUSG00000067713	Prkag1	AA571379|BB036179|Prkaac	protein kinase, AMP-activated, gamma 1 non-catalytic subunit	protein-coding
mm_47293.1	chr5	122241235	122241249	-	1	NA	non-coding (NR_104441, exon 13 of 13)	non-coding (NR_104441, exon 13 of 13)	23218	NR_104441	654470	Mm.28804	NM_001039153	ENSMUSG00000038593	Tctn1	G730031O11Rik|Tect1	tectonic family member 1	protein-coding
mm_55900.1	chr6	83575842	83575846	-	1	NA	intron (NR_078345, intron 2 of 7)	intron (NR_078345, intron 2 of 7)	-3340	NM_024239	70527	Mm.32801	NM_024239	ENSMUSG00000006906	Stambp	5330424L14Rik|5730422L11Rik|AW107289|Amsh|mKIAA4198	STAM binding protein	protein-coding
mm_39483.1	chr5	20882125	20882162	+	1	NA	promoter-TSS (NM_177601)	promoter-TSS (NM_177601)	-19	NM_172992	68770	Mm.86410	NM_172992	ENSMUSG00000039987	Phtf2	1110054G21Rik|9530062N20Rik|AI447096|C77923	putative homeodomain transcription factor 2	protein-coding
mm_155714.1	chrX	96097531	96097535	+	1	NA	intron (NM_010833, intron 1 of 12)	intron (NM_010833, intron 1 of 12)	1488	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_49305.1	chr6	17762882	17762885	+	1	NA	intron (NM_022332, intron 1 of 15)	intron (NM_022332, intron 1 of 15)	13713	NM_022332	64213	Mm.12051	NM_022332	ENSMUSG00000029534	St7	9430001H04Rik|Fam4a2|HELG|RAY1|SEN4|TSG7	suppression of tumorigenicity 7	protein-coding
mm_84395.1	chr9	65542347	65542367	-	1	NA	Intergenic	L1MA4|LINE|L1	37730	NM_153119	102595	Mm.247303	NM_153119	ENSMUSG00000050721	Plekho2	AI840980|Plekhq1	pleckstrin homology domain containing, family O member 2	protein-coding
mm_41755.1	chr5	102845383	102845410	+	1	NA	5' UTR (NM_001346585, exon 1 of 7)	5' UTR (NM_001346585, exon 1 of 7)	389	NM_001346585	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding
mm_76362.1	chr8	84773382	84773427	-	1	NA	5' UTR (NM_001081981, exon 1 of 11)	5' UTR (NM_001081981, exon 1 of 11)	965	NM_001081981	18032	Mm.9394	NM_010906	ENSMUSG00000001911	Nfix	CTF|NF-I/X|NF1-X|NFI-X	nuclear factor I/X	protein-coding
mm_112858.1	chr13	20842219	20842225	+	1	NA	intron (NM_012054, intron 3 of 20)	L2|LINE|L2	48109	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_23464.1	chr3	60473063	60473083	+	1	NA	5' UTR (NM_001253713, exon 2 of 10)	5' UTR (NM_001253713, exon 2 of 10)	243	NM_001253713	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_113071.1	chr13	23763661	23763674	+	1	NA	promoter-TSS (NM_030609)	promoter-TSS (NM_030609)	-1	NM_030609	80838	Mm.480242	NM_030609	ENSMUSG00000049539	Hist1h1a	H1.1|H1a|H1f1|H1var3	histone cluster 1, H1a	protein-coding
mm_170707.1	chr2	140956000	140956012	-	1	NA	intron (NM_001013802, intron 4 of 18)	intron (NM_001013802, intron 4 of 18)	-284530	NM_178382	71436	Mm.426781	NM_178382	ENSMUSG00000051379	Flrt3	5530600M07Rik|C430047I10Rik|mKIAA1469	fibronectin leucine rich transmembrane protein 3	protein-coding
mm_164134.1	chr15	50176330	50176334	+	1	NA	Intergenic	Lx5c|LINE|L1	712717	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_49431.1	chr6	29272666	29272682	+	1	NA	promoter-TSS (NM_023516)	promoter-TSS (NM_023516)	48	NM_023516	69573	Mm.45161	NM_023516	ENSMUSG00000043421	Hilpda	2310016C08Rik|AW049004|Hig2	hypoxia inducible lipid droplet associated	protein-coding
mm_876.1	chr1	52155219	52155252	+	1	NA	intron (NM_001205313, intron 23 of 24)	intron (NM_001205313, intron 23 of 24)	35613	NM_001205313	20846	Mm.277406	NM_009283	ENSMUSG00000026104	Stat1	2010005J02Rik|AA408197	signal transducer and activator of transcription 1	protein-coding
mm_159053.1	chr1	189762593	189762593	+	1	NA	intron (NM_008976, intron 1 of 18)	B4|SINE|B4	34325	NM_008976	19250	Mm.4498	NM_008976	ENSMUSG00000026604	Ptpn14	C130080N23Rik|OTTMUSG00000022087|PTP36	protein tyrosine phosphatase, non-receptor type 14	protein-coding
mm_111890.1	chr12	108275339	108275351	-	1	NA	promoter-TSS (NM_001159910)	promoter-TSS (NM_001159910)	72	NM_001159910	668158	Mm.482792	NM_001159910	ENSMUSG00000084883	Ccdc85c	EG668158|Gm265|Gm9010	coiled-coil domain containing 85C	protein-coding
mm_107974.1	chr12	72939875	72939888	+	1	NA	promoter-TSS (NM_011384)	promoter-TSS (NM_011384)	-1	NM_011384	20476	Mm.57138	NM_011384	ENSMUSG00000021099	Six6	Optx2|Six9	sine oculis-related homeobox 6	protein-coding
mm_33890.1	chr4	136180776	136180790	+	1	NA	promoter-TSS (NM_001305399)	promoter-TSS (NM_001305399)	1	NM_001305399	242705	Mm.307932	NM_177733	ENSMUSG00000018983	E2f2	E2F-2	E2F transcription factor 2	protein-coding
mm_144266.1	chr18	11053325	11053342	+	1	NA	promoter-TSS (NR_105023)	promoter-TSS (NR_105023)	-766	NR_105023	68434	Mm.57626	NR_105022	ENSMUSG00000097222	1010001N08Rik	Gata6as	RIKEN cDNA 1010001N08 gene	ncRNA
mm_121114.1	chr14	101840292	101840311	+	1	NA	promoter-TSS (NM_001347628)	promoter-TSS (NM_001347628)	-322	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_36898.1	chr4	107683577	107683592	-	1	NA	exon (NM_019872, exon 1 of 4)	exon (NM_019872, exon 1 of 4)	578	NM_019872	56296	Mm.141324	NM_019872	ENSMUSG00000028610	Dmrtb1	Dmrt6|Prp13	DMRT-like family B with proline-rich C-terminal, 1	protein-coding
mm_24786.1	chr3	95543010	95543137	+	1	NA	exon (NM_021281, exon 4 of 8)	exon (NM_021281, exon 4 of 8)	16287	NM_001267695	13040	Mm.3619	NM_021281	ENSMUSG00000038642	Ctss	Cats	cathepsin S	protein-coding
mm_24363.1	chr3	90079620	90079664	+	1	NA	5' UTR (NM_001253740, exon 1 of 8)	5' UTR (NM_001253740, exon 1 of 8)	121	NM_001293749	59069	Mm.240839	NM_022314	ENSMUSG00000027940	Tpm3	TM30nm|TMnm|Tm5NM|Tpm-5|Tpm5|Trop-5|gamma-TM|hTM30nm|hTMnm	tropomyosin 3, gamma	protein-coding
mm_157443.1	chrX	41335873	41335879	-	1	NA	Intergenic	RMER6D|LTR|ERVK	-65425	NM_016886	53623	Mm.327681	NM_016886	ENSMUSG00000001986	Gria3	2900064I19Rik|GluA3|GluR-C|GluR-K3|Glur-3|Glur3|Gluralpha3	glutamate receptor, ionotropic, AMPA3 (alpha 3)	protein-coding
mm_12958.1	chr2	90395122	90395159	+	1	NA	Intergenic	L1Md_F3|LINE|L1	-5500	NM_146263	258330	Mm.330392	NM_146263	ENSMUSG00000082980	Olfr1274-ps	GA_x5J8B7W2BV0-3116-4045|MOR228-4|MOR228-5|Olfr1274	olfactory receptor 1274, pseudogene	protein-coding
mm_16994.1	chr2	18308805	18308818	-	1	NA	exon (NM_001190817, exon 4 of 13)	exon (NM_001190817, exon 4 of 13)	84019	NM_001190817	13418	Mm.246674	NM_007869	ENSMUSG00000026740	Dnajc1	4733401K02Rik|AA960110|D230036H06Rik|Dnajl1|ERdj1|ERj1p|MTJ1	DnaJ heat shock protein family (Hsp40) member C1	protein-coding
mm_61274.1	chr7	66733594	66733624	+	1	NA	Intergenic	Intergenic	-9895	NM_001164201	545975	Mm.380104	NM_001164201	ENSMUSG00000030510	Cers3	4930550L11Rik|Gm488|Lass3|T3L	ceramide synthase 3	protein-coding
mm_156767.1	chrX	160530156	160530178	+	1	NA	intron (NM_172783, intron 5 of 32)	Lx9|LINE|L1	27733	NM_001177878	110094	Mm.350712	NM_172783	ENSMUSG00000031295	Phka2	6330505C01Rik|D330034O08|Phk	phosphorylase kinase alpha 2	protein-coding
mm_106834.1	chr12	8006082	8006091	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	28409	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_6086.1	chr1	63114283	63114345	-	1	NA	promoter-TSS (NM_001114609)	promoter-TSS (NM_001114609)	-47	NM_001114609	227195	Mm.74718	NM_001081436	ENSMUSG00000040865	Ino80d	7330405I11|A430093A21Rik|BC010584|OTTMUSG00000002594	INO80 complex subunit D	protein-coding
mm_112285.1	chr12	114456133	114456157	-	1	NA	Intergenic	Intergenic	13321	NR_106062	102465663		NR_106062	ENSMUSG00000105438	Mir7094-1	mmu-mir-7094-1	microRNA 7094-1	ncRNA
mm_15400.1	chr2	156730621	156730638	+	1	NA	intron (NM_001042487, intron 1 of 6)	intron (NM_001042487, intron 1 of 6)	9350	NM_001042487	228836	Mm.22094	NM_146128	ENSMUSG00000061689	Dlgap4	AI225853|BC024558|DAP-4|DAP4|SAPAP-4|Sapap4|WBP16	discs, large homolog-associated protein 4 (Drosophila)	protein-coding
mm_48362.1	chr5	139408494	139408506	-	1	NA	intron (NM_177000, intron 1 of 1)	intron (NM_177000, intron 1 of 1)	2113	NM_177000	319772	Mm.440271	NM_177000	ENSMUSG00000044092	C130050O18Rik	-	RIKEN cDNA C130050O18 gene	protein-coding
mm_135182.1	chr16	35983235	35983269	-	1	NA	promoter-TSS (NM_008465)	promoter-TSS (NM_008465)	-111	NM_008465	16646	Mm.3991	NM_008465	ENSMUSG00000022905	Kpna1	AW494490|IPOA5|NPI1|Rch2|mSRP1	karyopherin (importin) alpha 1	protein-coding
mm_107670.1	chr12	53252610	53252649	+	1	NA	intron (NM_013780, intron 1 of 11)	C-rich|Low_complexity|Low_complexity	3952	NM_013780	27386	Mm.247044	NM_013780	ENSMUSG00000021010	Npas3	4930423H22Rik|bHLHe12	neuronal PAS domain protein 3	protein-coding
mm_66604.1	chr7	45459840	45459881	-	1	NA	promoter-TSS (NM_010240)	promoter-TSS (NM_010240)	26	NM_010240	14325	Mm.30357	NM_010240	ENSMUSG00000050708	Ftl1	Ftl|Ftl-1|L-ferritin	ferritin light polypeptide 1	protein-coding
mm_6785.1	chr1	84139926	84139943	-	1	NA	intron (NM_001003948, intron 2 of 2)	L1_Mur3|LINE|L1	79027	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_101054.1	chr11	8664554	8664594	-	1	NA	promoter-TSS (NM_001083587)	promoter-TSS (NM_001083587)	-39	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_73924.1	chr8	119828860	119828892	+	1	NA	intron (NM_028071, intron 2 of 3)	ID_B1|SINE|B4	11703	NM_028071	72042	Mm.393405	NM_028071	ENSMUSG00000031827	Cotl1	1810074P22Rik|2010004C08Rik|Clp	coactosin-like 1 (Dictyostelium)	protein-coding
mm_46148.1	chr5	93206490	93206498	-	1	NA	promoter-TSS (NM_017367)	promoter-TSS (NM_017367)	1	NM_017367	12453	Mm.250419	NM_017367	ENSMUSG00000063015	Ccni	-	cyclin I	protein-coding
mm_17446.1	chr2	28537523	28537528	-	1	NA	intron (NM_001145836, intron 1 of 17)	intron (NM_001145836, intron 1 of 17)	4061	NM_001145836	19730	Mm.5236	NM_009058	ENSMUSG00000026821	Ralgds	Gnds|Rgds|mKIAA1308	ral guanine nucleotide dissociation stimulator	protein-coding
mm_169883.1	chr16	43143123	43143140	-	1	NA	intron (NM_001285805, intron 2 of 10)	L1Md_T|LINE|L1	-104153	NM_181058	56490	Mm.136238	NM_019778	ENSMUSG00000022708	Zbtb20	1300017A20Rik|7330412A13Rik|A930017C21Rik|D16Wsu73e|DPZF|HOF|ODA-8S|Oda8|Zfp288	zinc finger and BTB domain containing 20	protein-coding
mm_46194.1	chr5	98030571	98030616	-	1	NA	5' UTR (NM_133738, exon 1 of 17)	5' UTR (NM_133738, exon 1 of 17)	369	NM_133738	71914	Mm.24842	NM_133738	ENSMUSG00000029338	Antxr2	2310046B19Rik|AW561899|CMG-2|CMG2|cI-35	anthrax toxin receptor 2	protein-coding
mm_10414.1	chr2	13580011	13580029	+	1	NA	exon (NM_011701, exon 6 of 9)	exon (NM_011701, exon 6 of 9)	5709	NM_011701	22352	Mm.268000	NM_011701	ENSMUSG00000026728	Vim	-	vimentin	protein-coding
mm_43847.1	chr5	143240385	143240392	+	1	NA	exon (NM_001289589, exon 4 of 5)	exon (NM_001289589, exon 4 of 5)	5225	NM_177681	231866	Mm.55211	NM_177681	ENSMUSG00000029587	Zfp12	C530015C18|Krox-7|Zfp-12|Znf12	zinc finger protein 12	protein-coding
mm_55746.1	chr6	77979653	77979708	-	1	NA	promoter-TSS (NM_145732)	promoter-TSS (NM_145732)	-13	NM_009819	12386	Mm.34637	NM_009819	ENSMUSG00000063063	Ctnna2	AI481747|Catna|Catna2|cdf|chp	catenin (cadherin associated protein), alpha 2	protein-coding
mm_129070.1	chr15	75664169	75664175	-	1	NA	intron (NM_028404, intron 10 of 13)	intron (NM_028404, intron 10 of 13)	14618	NM_028404	72960	Mm.182401	NM_028404	ENSMUSG00000000934	Top1mt	2900052H09Rik	DNA topoisomerase 1, mitochondrial	protein-coding
mm_123978.1	chr14	75179258	75179272	-	1	NA	intron (NM_008879, intron 2 of 16)	intron (NM_008879, intron 2 of 16)	42840	NM_008879	18826	Mm.153911	NM_008879	ENSMUSG00000021998	Lcp1	AW536232|D14Ertd310e|LCP-1|Pls2|pp65	lymphocyte cytosolic protein 1	protein-coding
mm_171678.1	chr4	53059215	53059215	-	1	NA	intron (NM_013454, intron 34 of 49)	intron (NM_013454, intron 34 of 49)	47335	NM_025623	66536	Mm.38244	NM_025623	ENSMUSG00000015247	Nipsnap3b	2700063N13Rik|Nipsnap3a	nipsnap homolog 3B (C. elegans)	protein-coding
mm_23630.1	chr3	66219961	66219965	+	1	NA	promoter-TSS (NM_008987)	promoter-TSS (NM_008987)	76	NM_008987	19288	Mm.276776	NM_008987	ENSMUSG00000027832	Ptx3	AI607804|TSG-14	pentraxin related gene	protein-coding
mm_156276.1	chrX	136836805	136836816	+	1	NA	3' UTR (NM_011123, exon 7 of 7)	3' UTR (NM_011123, exon 7 of 7)	14064	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_144535.1	chr18	25234319	25234319	+	1	NA	intron (NM_001033532, intron 5 of 10)	MLT1A|LTR|ERVL-MaLR	65299	NM_001033532	225289	Mm.391081	NM_001033532	ENSMUSG00000033632	AW554918	4921538P22|AI461742|Kiaa1328|mKIAA1328	expressed sequence AW554918	protein-coding
mm_128187.1	chr15	34679176	34679208	-	1	NA	promoter-TSS (NM_145469)	promoter-TSS (NM_145469)	-486	NM_145469	223473	Mm.258402	NM_145469	ENSMUSG00000038879	Nipal2	9330161F08Rik|Npal2	NIPA-like domain containing 2	protein-coding
mm_167791.1	chr9	123923250	123923290	-	1	NA	Intergenic	CpG	45422	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_43850.1	chr5	143353704	143353710	+	1	NA	Intergenic	Intergenic	-3631	NM_001159321	170935	Mm.197460	NM_133355	ENSMUSG00000010825	Grid2ip	-	glutamate receptor, ionotropic, delta 2 (Grid2) interacting protein 1	protein-coding
mm_150231.1	chr19	33976470	33976478	+	1	NA	exon (NM_026334, exon 10 of 10)	exon (NM_026334, exon 10 of 10)	15226	NM_026334	67717	Mm.329816	NM_026334	ENSMUSG00000024768	Lipf	2310051B21Rik|AV082900	lipase, gastric	protein-coding
mm_156613.1	chrX	153498203	153498224	+	1	NA	promoter-TSS (NM_018798)	promoter-TSS (NM_018798)	-19	NM_018798	54609	Mm.430772	NM_018798	ENSMUSG00000050148	Ubqln2	Chap1|Dsk2|HRIHFB2157|Plic-2|Plic2	ubiquilin 2	protein-coding
mm_67488.1	chr7	80720989	80720996	-	1	NA	intron (NM_016721, intron 35 of 37)	intron (NM_016721, intron 35 of 37)	-32115	NM_173863	70461	Mm.392175	NM_173863	ENSMUSG00000030527	Crtc3	2610312F20Rik|6332415K15Rik|AI429792|BC011210|TORC3	CREB regulated transcription coactivator 3	protein-coding
mm_20848.1	chr2	148046339	148046343	-	1	NA	promoter-TSS (NM_001291067)	promoter-TSS (NM_001291067)	-393	NM_001291065	15376	Mm.938	NM_010446	ENSMUSG00000037025	Foxa2	HNF3-beta|HNF3beta|Hnf-3b|Hnf3b|Tcf-3b|Tcf3b	forkhead box A2	protein-coding
mm_14515.1	chr2	132490712	132490736	+	1	NA	promoter-TSS (NR_028286)	promoter-TSS (NR_028286)	-4	NR_028286	70371	Mm.394667	NR_028286	ENSMUSG00000086379	1700026D11Rik	-	RIKEN cDNA 1700026D11 gene	ncRNA
mm_109037.1	chr12	104101174	104101176	+	1	NA	promoter-TSS (NM_172953)	promoter-TSS (NM_172953)	62	NM_172953	268591	Mm.73172	NM_172953	ENSMUSG00000041550	Serpina5	4933415L04|PAI-3|Pci	serine (or cysteine) peptidase inhibitor, clade A, member 5	protein-coding
mm_2111.1	chr1	87853328	87853332	+	1	NA	promoter-TSS (NM_177646)	promoter-TSS (NM_177646)	43	NM_177646	227333	Mm.277217	NM_177646	ENSMUSG00000070738	Dgkd	AI841987|D330025K09|DGKdelta|dgkd-2	diacylglycerol kinase, delta	protein-coding
mm_78608.1	chr9	37545041	37545047	+	1	NA	TTS (NM_020518)	TTS (NM_020518)	5789	NM_020518	57276	Mm.27478	NM_020518	ENSMUSG00000001943	Vsig2	1190004B15Rik|2210413P10Rik|AU040484|CTX|Ctm	V-set and immunoglobulin domain containing 2	protein-coding
mm_23285.1	chr3	51765662	51765695	+	1	NA	intron (NM_001004176, intron 2 of 4)	intron (NM_001004176, intron 2 of 4)	104499	NM_001310482	211666	Mm.24679	NM_174995	ENSMUSG00000074604	Mgst2	GST2|MGST-II	microsomal glutathione S-transferase 2	protein-coding
mm_47516.1	chr5	124083098	124083129	-	1	NA	exon (NM_019875, exon 4 of 12)	exon (NM_019875, exon 4 of 12)	12685	NM_019875	56325	Mm.254839	NM_019875	ENSMUSG00000029408	Abcb9	TAPL|mKIAA1520	ATP-binding cassette, sub-family B (MDR/TAP), member 9	protein-coding
mm_169739.1	chr1	58445541	58445549	-	1	NA	promoter-TSS (NM_027351)	promoter-TSS (NM_027351)	-59	NM_001285827	70225	Mm.340195	NM_027351	ENSMUSG00000026035	Ppil3	2310076N22Rik|2510026K04Rik|Cyp10l	peptidylprolyl isomerase (cyclophilin)-like 3	protein-coding
mm_143577.1	chr17	74316288	74316305	-	1	NA	promoter-TSS (NM_001146222)	promoter-TSS (NM_001146222)	-85	NM_001146224	66310	Mm.28536	NM_024428	ENSMUSG00000024067	Dpy30	2810410M20Rik|C87842	dpy-30, histone methyltransferase complex regulatory subunit	protein-coding
mm_32672.1	chr4	115737824	115737840	+	1	NA	promoter-TSS (NM_172698)	promoter-TSS (NM_172698)	-241	NM_172698	230648	Mm.283565	NM_172698	ENSMUSG00000034210	Efcab14	4732418C07Rik	EF-hand calcium binding domain 14	protein-coding
mm_147500.1	chr18	49772576	49772585	-	1	NA	Intergenic	Intergenic	-16979	NM_001170960	68857	Mm.96010	NM_026854	ENSMUSG00000024505	Dtwd2	1190002H09Rik|8030470C17Rik|AI414673|BB115449	DTW domain containing 2	protein-coding
mm_94764.1	chr11	21238516	21238536	+	1	NA	promoter-TSS (NM_001290628)	promoter-TSS (NM_001290628)	-506	NM_139061	245944	Mm.170103	NM_139061	ENSMUSG00000020128	Vps54	Hcc8|Vps54l|mSLP8|wr	VPS54 GARP complex subunit	protein-coding
mm_87390.1	chr10	45107533	45107573	+	1	NA	intron (NM_011156, intron 6 of 14)	ORR1E|LTR|ERVL-MaLR	40339	NM_011156	19072	Mm.10281	NM_011156	ENSMUSG00000019849	Prep	AI047692|AI450383|D10Wsu136e|PEP|Pop	prolyl endopeptidase	protein-coding
mm_14216.1	chr2	127337722	127337730	+	1	NA	promoter-TSS (NM_172539)	promoter-TSS (NM_172539)	-913	NM_172539	215095	Mm.31313	NM_172539	ENSMUSG00000050468	Astl	7420700F21|C87576|Sas1b	astacin-like metalloendopeptidase (M12 family)	protein-coding
mm_29728.1	chr3	126611863	126611892	-	1	NA	intron (NM_001346636, intron 2 of 20)	(GGAA)n|Simple_repeat|Simple_repeat	14926	NM_023813	108058	Mm.255822	NM_023813	ENSMUSG00000053819	Camk2d	2810011D23Rik|8030469K03Rik|CaMK II|[d]-CaMKII	calcium/calmodulin-dependent protein kinase II, delta	protein-coding
mm_154311.1	chr19	61228397	61228454	-	1	NA	promoter-TSS (NM_009970)	promoter-TSS (NM_009970)	-7	NM_009970	12982	Mm.287228	NM_009970	ENSMUSG00000059326	Csf2ra	CD116|Csfgmra|GM-CSF-Ra|GM-CSFR	colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)	protein-coding
mm_134442.1	chr16	18248698	18248709	-	1	NA	promoter-TSS (NM_011239)	promoter-TSS (NM_011239)	-9	NM_011239	19385	Mm.235287	NM_011239	ENSMUSG00000005732	Ranbp1	Htf9a	RAN binding protein 1	protein-coding
mm_5410.1	chr1	33814408	33814468	-	1	NA	5' UTR (NM_001290700, exon 1 of 4)	5' UTR (NM_001290700, exon 1 of 4)	157	NM_133817	98403	Mm.289103	NM_133817	ENSMUSG00000042197	Zfp451	4930515K21Rik|4933435G09Rik|AI596398|COASTER|Kiaa0576-hp|Znf451|mKIAA1702	zinc finger protein 451	protein-coding
mm_50262.1	chr6	43462556	43462557	+	1	NA	intron (NR_045988, intron 1 of 2)	intron (NR_045988, intron 1 of 2)	20127	NR_045988	319812	Mm.446393	NR_045988		9430018G01Rik	-	RIKEN cDNA 9430018G01 gene	ncRNA
mm_93589.1	chr10	117063742	117063752	-	1	NA	promoter-TSS (NM_007636)	promoter-TSS (NM_007636)	67	NM_007636	12461	Mm.247788	NM_007636	ENSMUSG00000034024	Cct2	Cctb	chaperonin containing Tcp1, subunit 2 (beta)	protein-coding
mm_64955.1	chr7	16494728	16494731	-	1	NA	3' UTR (NM_172739, exon 7 of 7)	3' UTR (NM_172739, exon 7 of 7)	-17949	NM_008718	18142	Mm.145821	NM_008718	ENSMUSG00000001988	Npas1	MOP5|bHLHe11	neuronal PAS domain protein 1	protein-coding
mm_53082.1	chr6	124965621	124965633	+	1	NA	promoter-TSS (NM_001164089)	promoter-TSS (NM_001164089)	-98	NM_001164089	26894	Mm.244536	NM_012003	ENSMUSG00000030127	Cops7a	D6Ertd35e	COP9 signalosome subunit 7A	protein-coding
mm_39920.1	chr5	31527065	31527075	+	1	NA	promoter-TSS (NM_009206)	promoter-TSS (NM_009206)	75	NM_001347328	20534	Mm.352407	NM_009206	ENSMUSG00000029141	Slc4a1ap	kanadaptin	solute carrier family 4 (anion exchanger), member 1, adaptor protein	protein-coding
mm_4008.1	chr1	164960880	164960895	+	1	NA	Intergenic	MIR|SINE|MIR	-25377	NM_008510	16963	Mm.190	NM_008510	ENSMUSG00000026573	Xcl1	AI661682|ATAC|LTN|Lptn|SCM-1|SCM-1a|Scyc1	chemokine (C motif) ligand 1	protein-coding
mm_116831.1	chr13	54683688	54683719	-	1	NA	exon (NM_001146025, exon 4 of 11)	exon (NM_001146025, exon 4 of 11)	4105	NM_001146025	105239	Mm.25366	NM_134064	ENSMUSG00000034928	Rnf44	AI854545|mKIAA1100	ring finger protein 44	protein-coding
mm_52608.1	chr6	117173690	117173702	+	1	NA	3' UTR (NM_021704, exon 3 of 3)	3' UTR (NM_021704, exon 3 of 3)	5161	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_77884.1	chr9	7282202	7282216	+	1	NA	3' UTR (NM_008607, exon 10 of 10)	3' UTR (NM_008607, exon 10 of 10)	9695	NM_008607	17386	Mm.5022	NM_008607	ENSMUSG00000050578	Mmp13	Clg|MMP-13|Mmp1	matrix metallopeptidase 13	protein-coding
mm_153974.1	chr19	47863466	47863489	-	1	NA	exon (NM_010362, exon 5 of 6)	exon (NM_010362, exon 5 of 6)	-2068	NM_030051	68214	Mm.63791	NM_026619	ENSMUSG00000025069	Gsto2	1700020F09Rik|4930425C18Rik|GSTO 2-2	glutathione S-transferase omega 2	protein-coding
mm_10232.1	chr2	6471992	6472004	+	1	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	119262	NM_181399	98910	Mm.40673	NM_181399	ENSMUSG00000039046	Usp6nl	AI316785|RNTRE|TRE2NL|mKIAA0019	USP6 N-terminal like	protein-coding
mm_29211.1	chr3	106790130	106790140	-	1	NA	promoter-TSS (NM_007651)	promoter-TSS (NM_007651)	14	NM_007651	12508	Mm.316861	NM_007651	ENSMUSG00000040747	Cd53	AI323659|Ox-44|Tspan25	CD53 antigen	protein-coding
mm_23648.1	chr3	67473657	67473659	+	1	NA	intron (NM_138591, intron 16 of 17)	intron (NM_138591, intron 16 of 17)	-9751	NM_016753	17035	Mm.2632	NM_016753	ENSMUSG00000047557	Lxn	-	latexin	protein-coding
mm_110271.1	chr12	31996944	31996954	-	1	NA	intron (NM_011158, intron 2 of 10)	MamRep605|LTR?|LTR?	-46414	NM_153198	73389	Mm.390461	NM_153198	ENSMUSG00000002996	Hbp1	1700058O05Rik|BE629963|C330012F01Rik|C86454	high mobility group box transcription factor 1	protein-coding
mm_90752.1	chr10	5514121	5514124	-	1	NA	intron (NM_001347732, intron 2 of 145)	intron (NM_001347732, intron 2 of 145)	-25808	NM_001347711	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_75150.1	chr8	36172984	36172994	-	1	NA	Intergenic	Intergenic	76527	NM_001081150	244421	Mm.324032	NM_001081150	ENSMUSG00000039633	Lonrf1	-	LON peptidase N-terminal domain and ring finger 1	protein-coding
mm_23366.1	chr3	55281250	55281266	+	1	NA	intron (NM_019978, intron 3 of 16)	intron (NM_019978, intron 3 of 16)	38732	NM_001195538	13175	Mm.393242	NM_019978	ENSMUSG00000027797	Dclk1	1700113D08Rik|2810480F11Rik|AI836758|Click-I|Cpg16|Dcamkl1|Dcl|Dclk|mKIAA0369	doublecortin-like kinase 1	protein-coding
mm_66018.1	chr7	30603519	30603528	-	1	NA	3' UTR (NM_026815, exon 8 of 8)	3' UTR (NM_026815, exon 8 of 8)	9211	NM_026815	109637	Mm.25471	NM_026815	ENSMUSG00000006313	Upk1a	1110031P12Rik|AU019298|C87192|Tspan21|Upk1	uroplakin 1A	protein-coding
mm_78157.1	chr9	21027823	21027836	+	1	NA	exon (NM_010493, exon 7 of 7)	exon (NM_010493, exon 7 of 7)	-1544	NM_023892	78369	Mm.30220	NM_023892	ENSMUSG00000001014	Icam4	1810015M19Rik|Cd242|ICAM-4	intercellular adhesion molecule 4, Landsteiner-Wiener blood group	protein-coding
mm_89580.1	chr10	95730319	95730332	+	1	NA	Intergenic	Intergenic	-166158	NM_027722	71207	Mm.24397	NM_027722	ENSMUSG00000020029	Nudt4	4933436C10Rik|DIPP2|DIPP2alpha|DIPP2beta|HDCMB47P	nudix (nucleoside diphosphate linked moiety X)-type motif 4	protein-coding
mm_163305.1	chr12	3309530	3309530	-	1	NA	5' UTR (NM_016676, exon 1 of 6)	5' UTR (NM_016676, exon 1 of 6)	439	NM_016676	19325	Mm.378993	NM_016676	ENSMUSG00000020671	Rab10	AW107754	RAB10, member RAS oncogene family	protein-coding
mm_104840.1	chr11	99209512	99209537	-	1	NA	3' UTR (NM_020618, exon 11 of 11)	3' UTR (NM_020618, exon 11 of 11)	21493	NM_020618	57376	Mm.379086	NM_020618	ENSMUSG00000037935	Smarce1	2810417B20Rik|5830412H02Rik|9030408N19Rik|Baf27	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1	protein-coding
mm_77928.1	chr9	7353441	7353530	+	1	NA	exon (NM_008605, exon 6 of 10)	exon (NM_008605, exon 6 of 10)	6111	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_57894.1	chr6	131370366	131370380	-	1	NA	exon (NM_011733, exon 6 of 9)	exon (NM_011733, exon 6 of 9)	18077	NM_139117	56449	Mm.458000	NM_011733	ENSMUSG00000030189	Ybx3	Csda|Dpba|MSY3|MSY4|Yb2|dbpA|oxyR	Y box protein 3	protein-coding
mm_124348.1	chr14	104459334	104459337	-	1	NA	Intergenic	Intergenic	8664	NM_011143	18996	Mm.246550	NM_011143	ENSMUSG00000048349	Pou4f1	Brn-3|Brn-3.0|Brn3|Brn3.0|Brn3a|E130119J07Rik	POU domain, class 4, transcription factor 1	protein-coding
mm_30423.1	chr3	152668034	152668102	-	1	NA	promoter-TSS (NM_001081277)	promoter-TSS (NM_001081277)	72	NM_001081277	229949	Mm.207057	NM_001081277	ENSMUSG00000039058	Ak5	-	adenylate kinase 5	protein-coding
mm_21283.1	chr2	156953388	156953404	-	1	NA	intron (NM_013865, intron 3 of 15)	intron (NM_013865, intron 3 of 15)	38715	NM_013865	29812	Mm.279256	NM_013865	ENSMUSG00000027634	Ndrg3	4833415O14Rik|AI747193|Ndr3	N-myc downstream regulated gene 3	protein-coding
mm_149135.1	chr19	9002761	9002791	+	1	NA	exon (NM_009643, exon 5 of 5)	exon (NM_009643, exon 5 of 5)	13492	NM_001286518	66395	Mm.203866	NM_009643	ENSMUSG00000069833	Ahnak	DY6	AHNAK nucleoprotein (desmoyokin)	protein-coding
mm_87092.1	chr10	33083141	33083154	+	1	NA	promoter-TSS (NM_029726)	promoter-TSS (NM_029726)	-336	NM_029726	76757	Mm.338508	NM_029726	ENSMUSG00000019787	Trdn	2310045H21Rik|EG432451|TDN	triadin	protein-coding
mm_85371.1	chr9	103222081	103222149	-	1	NA	exon (NM_133977, exon 8 of 17)	exon (NM_133977, exon 8 of 17)	8171	NM_133977	22041	Mm.37214	NM_133977	ENSMUSG00000032554	Trf	AI266983|Cd176|HP|Tf|Tfn|hpx	transferrin	protein-coding
mm_47611.1	chr5	125128060	125128075	-	1	NA	intron (NM_011424, intron 1 of 46)	intron (NM_011424, intron 1 of 46)	51147	NM_001253905	20602	Mm.278646	NM_011424	ENSMUSG00000029478	Ncor2	N-CoR|SMRT|SMRTe	nuclear receptor co-repressor 2	protein-coding
mm_164236.1	chr15	91641860	91641866	+	1	NA	Intergenic	Intergenic	-31361	NM_025730	66725	Mm.37558	NM_025730	ENSMUSG00000036273	Lrrk2	4921513O20Rik|9330188B09Rik|AW561911|D630001M17Rik|Gm927|cI-46	leucine-rich repeat kinase 2	protein-coding
mm_46284.1	chr5	100159549	100159579	-	1	NA	5' UTR (NM_182841, exon 1 of 8)	5' UTR (NM_182841, exon 1 of 8)	244	NM_182841	231503	Mm.99790	NM_182841	ENSMUSG00000050640	Tmem150c	-	transmembrane protein 150C	protein-coding
mm_131047.1	chr16	3926246	3926252	+	1	NA	intron (NM_029738, intron 7 of 11)	intron (NM_029738, intron 7 of 11)	17240	NM_029738	76779	Mm.458921	NM_029738	ENSMUSG00000014232	Cluap1	2310030D15Rik|2610111M03Rik	clusterin associated protein 1	protein-coding
mm_4712.1	chr1	180942453	180942477	+	1	NA	promoter-TSS (NM_144794)	promoter-TSS (NM_144794)	-53	NM_144794	208795	Mm.185518	NM_144794	ENSMUSG00000026519	Tmem63a	BC014795|Tmem64a	transmembrane protein 63a	protein-coding
mm_10549.1	chr2	16660821	16660837	+	1	NA	exon (NM_026162, exon 7 of 14)	exon (NM_026162, exon 7 of 14)	304525	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding
mm_149297.1	chr19	10698531	10698565	+	1	NA	intron (NM_181403, intron 1 of 4)	intron (NM_181403, intron 1 of 4)	9733	NM_181403	107305	Mm.19091	NM_181403	ENSMUSG00000048832	Vps37c	5730409F24Rik|AU042646	vacuolar protein sorting 37C	protein-coding
mm_54752.1	chr6	41034270	41034286	-	1	NA	exon (NM_023333, exon 2 of 5)	exon (NM_023333, exon 2 of 5)	1231	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_73022.1	chr8	94037222	94037288	+	1	NA	promoter-TSS (NM_026623)	promoter-TSS (NM_026623)	57	NM_001093757	270086	Mm.251085	NM_177767	ENSMUSG00000033009	Ogfod1	4930415J21Rik|AA387199|AA939912|AW061076|mKIAA1612	2-oxoglutarate and iron-dependent oxygenase domain containing 1	protein-coding
mm_13849.1	chr2	119599960	119599964	+	1	NA	non-coding (NR_027832, exon 3 of 3)	non-coding (NR_027832, exon 3 of 3)	5666	NR_015473	66602	Mm.379181	NR_015473	ENSMUSG00000085438	1700020I14Rik	1190006L01Rik|4933437I03Rik|AI451541|AI585852|AW538376|AW558897|Cyrano	RIKEN cDNA 1700020I14 gene	ncRNA
mm_64047.1	chr7	140835266	140835291	+	1	NA	promoter-TSS (NM_029821)	promoter-TSS (NM_029821)	140	NM_001347605	76974	Mm.272359	NM_029821	ENSMUSG00000025481	Urah	1190003J15Rik|2810420C16Rik	urate (5-hydroxyiso-) hydrolase	protein-coding
mm_99159.1	chr11	100622871	100622881	+	1	NA	promoter-TSS (NM_028024)	promoter-TSS (NM_028024)	-79	NM_028024	71966	Mm.274734	NM_028024	ENSMUSG00000017837	Nkiras2	2410003M04Rik|4930527H08Rik|D630018G21Rik|KBRAS2	NFKB inhibitor interacting Ras-like protein 2	protein-coding
mm_42175.1	chr5	112261792	112261800	+	1	NA	intron (NM_023695, intron 3 of 5)	(TCCA)n|Simple_repeat|Simple_repeat	5976	NM_001312893	12960	Mm.29488	NM_023695	ENSMUSG00000029343	Crybb1	3110006K12Rik|BB1CRY	crystallin, beta B1	protein-coding
mm_33065.1	chr4	123282679	123282734	+	1	NA	promoter-TSS (NM_130881)	promoter-TSS (NM_130881)	-205	NM_130881	230721	Mm.277091	NM_130881	ENSMUSG00000011257	Pabpc4	-	poly(A) binding protein, cytoplasmic 4	protein-coding
mm_30858.1	chr4	28914143	28914145	+	1	NA	intron (NM_001290434, intron 5 of 16)	intron (NM_001290434, intron 5 of 16)	100999	NM_001122889	13841	Mm.257266	NM_010141	ENSMUSG00000028289	Epha7	Cek11|Ebk|Ehk3|Hek11|Mdk1	Eph receptor A7	protein-coding
mm_448.1	chr1	35960015	35960052	+	1	NA	Intergenic	Intergenic	-108367	NM_015818	50785	Mm.213566	NM_015818	ENSMUSG00000045216	Hs6st1	6Ost1	heparan sulfate 6-O-sulfotransferase 1	protein-coding
mm_150296.1	chr19	34550645	34550656	+	1	NA	promoter-TSS (NM_008332)	promoter-TSS (NM_008332)	-44	NM_008332	15958	Mm.2036	NM_008332	ENSMUSG00000045932	Ifit2	AV302338|Ifi54|P54	interferon-induced protein with tetratricopeptide repeats 2	protein-coding
mm_61675.1	chr7	80860910	80860972	+	1	NA	Intergenic	Intergenic	-1167	NM_009553	22691	Mm.358645	NM_009553	ENSMUSG00000038797	Zscan2	Zfp-29|Zfp29	zinc finger and SCAN domain containing 2	protein-coding
mm_31350.1	chr4	46668883	46668886	+	1	NA	intron (NM_001081141, intron 17 of 18)	intron (NM_001081141, intron 17 of 18)	-18685	NM_198664	381605	Mm.331595	NM_198664	ENSMUSG00000039813	Tbc1d2	A630005A06Rik|BC022630|Gm1037|PARIS-1|PARIS1	TBC1 domain family, member 2	protein-coding
mm_19516.1	chr2	94010719	94010727	-	1	NA	promoter-TSS (NM_026944)	promoter-TSS (NM_026944)	7	NM_026944	69113	Mm.272498	NM_026944	ENSMUSG00000040174	Alkbh3	1700108H04Rik|1810020C19Rik|Abh3|mABH3	alkB homolog 3, alpha-ketoglutarate-dependent dioxygenase	protein-coding
mm_10441.1	chr2	14258621	14258664	+	1	NA	intron (NM_008625, intron 5 of 29)	intron (NM_008625, intron 5 of 29)	-2361	NR_030609	100124488		NR_030609	ENSMUSG00000077897	Mir511	Mirn511|mir-511|mmu-mir-511	microRNA 511	ncRNA
mm_127346.1	chr15	100616277	100616305	+	1	NA	intron (NM_011873, intron 1 of 3)	intron (NM_011873, intron 1 of 3)	629	NM_011873	23994	Mm.486175	NM_011873	ENSMUSG00000000346	Dazap2	AI314727|Brbp|Gcap28|Prtb|gt6-12|mKIAA0058	DAZ associated protein 2	protein-coding
mm_158250.1	chrX	107816380	107816402	-	1	NA	promoter-TSS (NM_025921)	promoter-TSS (NM_025921)	-57	NM_025921	67028	Mm.37274	NM_025921	ENSMUSG00000031242	2610002M06Rik	8430408J07Rik|AI876413|Chmp1b2	RIKEN cDNA 2610002M06 gene	protein-coding
mm_170589.1	chr19	5800644	5800644	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	2028	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_107089.1	chr12	17542947	17542957	+	1	NA	Intergenic	Intergenic	-1921	NM_013614	18263	Mm.34102	NM_013614	ENSMUSG00000011179	Odc1	ODC	ornithine decarboxylase, structural 1	protein-coding
mm_150670.1	chr19	42051760	42051767	+	1	NA	promoter-TSS (NM_025752)	promoter-TSS (NM_025752)	-465	NM_025752	66765	Mm.440412	NM_025752	ENSMUSG00000090369	4933411K16Rik	-	RIKEN cDNA 4933411K16 gene	protein-coding
mm_64443.1	chr7	142653830	142653845	+	1	NA	exon (NM_010514, exon 4 of 4)	exon (NM_010514, exon 4 of 4)	1159	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_171679.1	chr4	54155613	54155617	-	1	NA	Intergenic	L1Md_A|LINE|L1	329570	NM_028053	52076	Mm.27184	NM_028053	ENSMUSG00000028420	Tmem38b	1600017F22Rik|AA437809|AV051057|D4Ertd89e|TRIC-B|mg33b	transmembrane protein 38B	protein-coding
mm_12264.1	chr2	68960340	68960359	+	1	NA	intron (NM_172856, intron 3 of 9)	intron (NM_172856, intron 3 of 9)	98908	NM_001347161	241447	Mm.222222	NM_172856	ENSMUSG00000027035	Cers6	4732462C07Rik|AW544719|Lass6|T1L	ceramide synthase 6	protein-coding
mm_46295.1	chr5	100416554	100416581	-	1	NA	promoter-TSS (NM_026969)	promoter-TSS (NM_026969)	-333	NM_026969	69162	Mm.18634	NM_026969	ENSMUSG00000035325	Sec31a	1810024J13Rik|ABP125|ABP130|AU042160|HSPC275|Sec31l1	Sec31 homolog A (S. cerevisiae)	protein-coding
mm_86667.1	chr10	17947497	17947511	+	1	NA	intron (NM_001033432, intron 1 of 3)	CpG	563	NM_001033432	380629	Mm.276430	NM_001033432	ENSMUSG00000039879	Heca	Gm869|HDC|HDCL	hdc homolog, cell cycle regulator	protein-coding
mm_15432.1	chr2	157201783	157201785	+	1	NA	intron (NM_011249, intron 1 of 21)	intron (NM_011249, intron 1 of 21)	2750	NM_011249	19650	Mm.244671	NM_011249	ENSMUSG00000027641	Rbl1	AW547426|PRB1|p107	retinoblastoma-like 1 (p107)	protein-coding
mm_45063.1	chr5	43232778	43232846	-	1	NA	promoter-TSS (NM_001177379)	promoter-TSS (NM_001177379)	-651	NM_175937	231207	Mm.7233	NM_175937	ENSMUSG00000039782	Cpeb2	A630055H10Rik|Cpe-bp2	cytoplasmic polyadenylation element binding protein 2	protein-coding
mm_132524.1	chr16	37777093	37777106	+	1	NA	promoter-TSS (NM_008047)	promoter-TSS (NM_008047)	44	NM_008047	14314	Mm.182434	NM_008047	ENSMUSG00000022816	Fstl1	AI316791|AW107808|Fstl|TSC-36	follistatin-like 1	protein-coding
mm_80248.1	chr9	72749013	72749034	+	1	NA	3' UTR (NM_010890, exon 29 of 29)	3' UTR (NM_010890, exon 29 of 29)	-58251	NM_175485	235472	Mm.31696	NM_175485	ENSMUSG00000036030	Prtg	A230098A12Rik|Igdcc5	protogenin	protein-coding
mm_170330.1	chr18	4403558	4403577	+	1	NA	Intergenic	RLTR34D_MM|LTR|ERVK	27975	NM_026157	67440	Mm.49826	NM_026157	ENSMUSG00000024234	Mtpap	0610027A18Rik|AW551379|Papd1	mitochondrial poly(A) polymerase	protein-coding
mm_25552.1	chr3	116007736	116007765	+	1	NA	promoter-TSS (NM_001163514)	promoter-TSS (NM_001163514)	301	NM_001163515	58193	Mm.41739	NM_021388	ENSMUSG00000027963	Extl2	3000001D04Rik|AW146439	exostoses (multiple)-like 2	protein-coding
mm_77182.1	chr8	111732079	111732084	-	1	NA	promoter-TSS (NM_001198839)	promoter-TSS (NM_001198839)	55	NM_001198839	12927	Mm.3758	NM_009954	ENSMUSG00000031955	Bcar1	AI385681|Cas|Crkas	breast cancer anti-estrogen resistance 1	protein-coding
mm_11913.1	chr2	52071510	52071531	+	1	NA	Intergenic	Intergenic	-1317	NM_175238	51869	Mm.254530	NM_175238	ENSMUSG00000036202	Rif1	5730435J01Rik|6530403D07Rik|AU016181|AW549474|D2Ertd145e	replication timing regulatory factor 1	protein-coding
mm_123935.1	chr14	73368341	73368347	-	1	NA	exon (NM_008410, exon 2 of 6)	exon (NM_008410, exon 2 of 6)	16927	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_1158.1	chr1	60900861	60900861	+	1	NA	Intergenic	ORR1A3|LTR|ERVL-MaLR	-8164	NM_009843	12477	Mm.390	NM_009843	ENSMUSG00000026011	Ctla4	Cd152|Ctla-4|Ly-56	cytotoxic T-lymphocyte-associated protein 4	protein-coding
mm_167926.1	chrX	102935589	102935593	-	1	NA	Intergenic	Intergenic	-1368	NR_026596	331480	Mm.145294	NR_026596		Gm5126	EG331480	predicted pseudogene 5126	ncRNA
mm_36383.1	chr4	77137831	77137831	-	1	NA	intron (NM_011211, intron 7 of 39)	intron (NM_011211, intron 7 of 39)	1074064	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding
mm_17769.1	chr2	32789523	32789543	-	1	NA	3' UTR (NM_001113569, exon 20 of 20)	3' UTR (NM_001113569, exon 20 of 20)	-5128	NM_025619	227736	Mm.441499	NM_025619	ENSMUSG00000038987	Cfap157	1700019L03Rik	cilia and flagella associated protein 157	protein-coding
mm_152247.1	chr19	8714364	8714364	-	1	NA	promoter-TSS (NM_008577)	promoter-TSS (NM_008577)	-467	NM_008577	17254	Mm.4114	NM_008577	ENSMUSG00000010095	Slc3a2	4F2|4F2HC|AI314110|Cd98|Ly-10|Ly-m10|Ly10|Mdu1|Mgp-2hc|NACAE	solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2	protein-coding
mm_13290.1	chr2	101886250	101886269	+	1	NA	promoter-TSS (NM_029635)	promoter-TSS (NM_029635)	-3	NM_029635	76501	Mm.330424	NM_029635	ENSMUSG00000027163	Commd9	1810029F08Rik|AA409293	COMM domain containing 9	protein-coding
mm_75412.1	chr8	46472428	46472430	-	1	NA	intron (NM_007981, intron 1 of 20)	intron (NM_007981, intron 1 of 20)	1392	NM_007981	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_90501.1	chr10	128035605	128035613	+	1	NA	5' UTR (NM_013608, exon 1 of 8)	5' UTR (NM_013608, exon 1 of 8)	263	NM_001113199	17938	Mm.3746	NM_013608	ENSMUSG00000061315	Naca	AL022831|AL024382|Gm1878|mKIAA0363|skNAC	nascent polypeptide-associated complex alpha polypeptide	protein-coding
mm_98165.1	chr11	87748955	87748969	+	1	NA	Intergenic	Intergenic	-7902	NR_029555	387160		NR_029555	ENSMUSG00000105196	Mir142	Mirn142|miR-142|mir-142a|mmu-mir-142|mmu-mir-142a	microRNA 142	ncRNA
mm_4212.1	chr1	171271628	171271629	+	1	NA	intron (NM_020579, intron 2 of 7)	(T)n|Simple_repeat|Simple_repeat	1300	NM_020579	57370	Mm.274011	NM_020579	ENSMUSG00000052423	B4galt3	9530061M23Rik|AA104562|AW125175|ESTM26|ESTM6|R74981	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 3	protein-coding
mm_75800.1	chr8	70139068	70139092	-	1	NA	promoter-TSS (NM_001145552)	promoter-TSS (NM_001145552)	117	NM_011266	19727	Mm.161167	NM_011266	ENSMUSG00000036120	Rfxank	Tvl1	regulatory factor X-associated ankyrin-containing protein	protein-coding
mm_12411.1	chr2	70509491	70509502	+	1	NA	exon (NM_025744, exon 1 of 13)	exon (NM_025744, exon 1 of 13)	677	NM_025744	66748	Mm.423014	NM_025744	ENSMUSG00000075302	Erich2	4933404M02Rik	glutamate rich 2	protein-coding
mm_75637.1	chr8	64849721	64849743	-	1	NA	5' UTR (NM_178633, exon 1 of 15)	5' UTR (NM_178633, exon 1 of 15)	192	NM_178633	77113	Mm.350347	NM_178633	ENSMUSG00000031605	Klhl2	6030411N21Rik|ABP-KELCH|AU020744|Mav	kelch-like 2, Mayven	protein-coding
mm_144933.1	chr18	37725722	37725754	+	1	NA	promoter-TSS (NM_033591)	promoter-TSS (NM_033591)	32	NM_033591	93716	Mm.247203	NM_033591	ENSMUSG00000103897	Pcdhga8	mKIAA4054	protocadherin gamma subfamily A, 8	protein-coding
mm_16638.1	chr2	5934534	5934535	-	1	NA	intron (NM_001081131, intron 1 of 16)	intron (NM_001081131, intron 1 of 16)	8258	NM_001081131	209692	Mm.222517	NM_001081131	ENSMUSG00000025815	Dhtkd1	C330018I04Rik	dehydrogenase E1 and transketolase domain containing 1	protein-coding
mm_144202.1	chr18	9485621	9485655	+	1	NA	Intergenic	Intergenic	-35488	NM_026484	67974	Mm.86523	NM_026484	ENSMUSG00000024286	Ccny	1700025H17Rik|3110050L10Rik|4631402G10Rik|5730405I09Rik	cyclin Y	protein-coding
mm_27316.1	chr3	50366843	50366866	-	1	NA	3' UTR (NM_011990, exon 12 of 12)	3' UTR (NM_011990, exon 12 of 12)	76759	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_152802.1	chr19	21674872	21674880	-	1	NA	intron (NM_146096, intron 1 of 3)	RLTR31A_Mm|LTR|ERVK	21567	NM_146096	226016	Mm.28796	NM_146096	ENSMUSG00000047368	Abhd17b	5730446C15Rik|Cgi67|Fam108b|Fam108b1	abhydrolase domain containing 17B	protein-coding
mm_122139.1	chr14	31168558	31168568	-	1	NA	promoter-TSS (NM_138672)	promoter-TSS (NM_138672)	78	NM_138672	192187	Mm.220821	NM_138672	ENSMUSG00000042286	Stab1	FEEL-1|FELE-1|MFEEL-1|MS-1|STAB-1|mKIAA0246	stabilin 1	protein-coding
mm_117357.1	chr13	69933259	69933267	-	1	NA	Intergenic	Intergenic	-26570	NR_138559	67550	Mm.158159	NR_138559		4933416O17Rik	-	RIKEN cDNA 4933416O17 gene	ncRNA
mm_171410.1	chr4	129445307	129445323	-	1	NA	Intergenic	MMVL30-int|LTR|ERV1	-4497	NM_153541	215627	Mm.428660	NM_153541	ENSMUSG00000048485	Zbtb8b	AV220464|BC023839|BOZF1|Zbtb8	zinc finger and BTB domain containing 8b	protein-coding
mm_124032.1	chr14	77029568	77029590	-	1	NA	exon (NM_172488, exon 7 of 8)	exon (NM_172488, exon 7 of 8)	7038	NM_172488	210808	Mm.89278	NM_172488	ENSMUSG00000044350	Lacc1	9030625A04Rik	laccase (multicopper oxidoreductase) domain containing 1	protein-coding
mm_3530.1	chr1	150175843	150175848	+	1	NA	Intergenic	Lx9|LINE|L1	-10897	NR_110420	102639566	Mm.417208	NR_110420	ENSMUSG00000097754	Ptgs2os2	Gm26687|Linc-cox2|Lincrna-cox2	prostaglandin-endoperoxide synthase 2, opposite strand 2	ncRNA
mm_118084.1	chr13	103467240	103467265	-	1	NA	Intergenic	Intergenic	-132760	NM_175171	328329	Mm.202606	NM_175171	ENSMUSG00000034751	Mast4	4930420O11Rik|AI642422|mKIAA0303	microtubule associated serine/threonine kinase family member 4	protein-coding
mm_20977.1	chr2	151973812	151973822	-	1	NA	promoter-TSS (NM_001289151)	promoter-TSS (NM_001289151)	164	NM_001289150	73847	Mm.272444	NM_028666	ENSMUSG00000027459	Fam110a	1700008J10Rik|5430432M24Rik|AI747080	family with sequence similarity 110, member A	protein-coding
mm_120635.1	chr14	70467613	70467619	+	1	NA	3' UTR (NM_145981, exon 5 of 5)	3' UTR (NM_145981, exon 5 of 5)	10099	NM_145981	105653	Mm.192598	NM_145981	ENSMUSG00000003469	Phyhip	AW049870|C630010D02Rik|Lnap1ip|PAHX-AP#1|PAHX-AP1	phytanoyl-CoA hydroxylase interacting protein	protein-coding
mm_60367.1	chr7	44442399	44442425	+	1	NA	promoter-TSS (NM_198250)	promoter-TSS (NM_198250)	-75	NM_198250	272381	Mm.44173	NM_198250	ENSMUSG00000047085	Lrrc4b	A830007M12|Lrig4	leucine rich repeat containing 4B	protein-coding
mm_64888.1	chr7	15922303	15922313	-	1	NA	promoter-TSS (NM_009156)	promoter-TSS (NM_009156)	63	NM_009156	20364	Mm.42829	NM_009156	ENSMUSG00000041571	Selenow	Sepw1|selW	selenoprotein W	protein-coding
mm_129146.1	chr15	76206236	76206243	-	1	NA	promoter-TSS (NM_201389)	promoter-TSS (NM_201389)	82	NM_201389	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
mm_34647.1	chr4	150807790	150807805	+	1	NA	Intergenic	Intergenic	47152	NR_040649	73348	Mm.396218	NR_040649	ENSMUSG00000078492	1700045H11Rik	-	RIKEN cDNA 1700045H11 gene	ncRNA
mm_24121.1	chr3	88200256	88200269	+	1	NA	Intergenic	Intergenic	-14909	NR_037276	100526540		NR_037276	ENSMUSG00000092988	Mir3093	mir-3093|mmu-mir-3093	microRNA 3093	ncRNA
mm_48200.1	chr5	137532774	137532793	-	1	NA	intron (NM_010312, intron 1 of 9)	intron (NM_010312, intron 1 of 9)	446	NM_010312	14693	Mm.30141	NM_010312	ENSMUSG00000029713	Gnb2	Gnb-2	guanine nucleotide binding protein (G protein), beta 2	protein-coding
mm_26396.1	chr3	142594841	142594850	+	1	NA	promoter-TSS (NM_010259)	promoter-TSS (NM_010259)	-2	NM_010259	14468	Mm.457978	NM_010259	ENSMUSG00000040264	Gbp2b	Gbp-1|Gbp1|Mag-1|Mpa-1|Mpa1	guanylate binding protein 2b	protein-coding
mm_127063.1	chr15	97361267	97361284	+	1	NA	5' UTR (NM_172293, exon 4 of 6)	5' UTR (NM_172293, exon 4 of 6)	-113988	NM_001164602	105827	Mm.24005	NM_178114	ENSMUSG00000048218	Amigo2	AI415330|AMIGO-2|AW208913|Ali1	adhesion molecule with Ig like domain 2	protein-coding
mm_96093.1	chr11	60417189	60417195	+	1	NA	promoter-TSS (NM_145427)	promoter-TSS (NM_145427)	47	NM_025757	66771	Mm.29950	NM_025757	ENSMUSG00000018415	Gid4	4933439F18Rik	GID complex subunit 4, VID24 homolog	protein-coding
mm_12609.1	chr2	74683834	74683844	+	1	NA	intron (NM_008273, intron 1 of 1)	intron (NM_008273, intron 1 of 1)	1516	NM_008273	15431	Mm.207763	NM_008273	ENSMUSG00000042499	Hoxd11	E230017H14Rik|Hox-4.6|Hox-5.4|Hox-5.5	homeobox D11	protein-coding
mm_39837.1	chr5	30869624	30869664	+	1	NA	promoter-TSS (NM_144525)	promoter-TSS (NM_144525)	-3	NM_144525	68796	Mm.205169	NM_144525	ENSMUSG00000038828	Tmem214	1110039B18Rik|4921530J21Rik|AI841294|AU018742|C76280	transmembrane protein 214	protein-coding
mm_142346.1	chr17	43612086	43612106	-	1	NA	3' UTR (NM_013737, exon 12 of 12)	3' UTR (NM_013737, exon 12 of 12)	18203	NM_001161366	210510	Mm.329058	NM_198418	ENSMUSG00000040140	Tdrd6	AB097085|Tdr2	tudor domain containing 6	protein-coding
mm_66394.1	chr7	44241247	44241262	-	1	NA	Intergenic	Intergenic	-5132	NR_029436	70004	Mm.158317	NR_029436	ENSMUSG00000038782	1700028J19Rik	-	RIKEN cDNA 1700028J19 gene	ncRNA
mm_120049.1	chr14	56647593	56647605	+	1	NA	exon (NM_001145978, exon 32 of 35)	exon (NM_001145978, exon 32 of 35)	-20649	NM_023773	75339	Mm.152466	NM_023773	ENSMUSG00000079184	Mphosph8	1500035L22Rik|4930548G07Rik|AU040635	M-phase phosphoprotein 8	protein-coding
mm_3847.1	chr1	160195238	160195266	+	1	NA	promoter-TSS (NM_025474)	promoter-TSS (NM_025474)	37	NM_025474	64659	Mm.29599	NM_025474	ENSMUSG00000058267	Mrps14	1810032L21Rik|AL022847|Rpms14	mitochondrial ribosomal protein S14	protein-coding
mm_80157.1	chr9	70956111	70956121	+	1	NA	Intergenic	B4A|SINE|B4	-3895	NM_001324472	15450	Mm.390187	NM_008280	ENSMUSG00000032207	Lipc	AI256194|HL|Hpl	lipase, hepatic	protein-coding
mm_160554.1	chr9	49081260	49081260	+	1	NA	Intergenic	Intergenic	-21519	NM_030709	80893	Mm.72799	NM_030709	ENSMUSG00000032268	Tmprss5	spinesin	transmembrane protease, serine 5 (spinesin)	protein-coding
mm_75396.1	chr8	46152413	46152477	-	1	NA	Intergenic	Intergenic	-17111	NM_025747	66756	Mm.133623	NM_025747	ENSMUSG00000031631	Cfap97	1110068E21Rik|4933411K20Rik|AW049273|Kiaa1430|mKIAA1430	cilia and flagella associated protein 97	protein-coding
mm_9669.1	chr1	178315473	178315482	-	1	NA	Intergenic	Intergenic	-3676	NM_025511	66359	Mm.489720	NM_025511	ENSMUSG00000026500	Cox20	2310005N03Rik|Fam36a	COX20 Cox2 chaperone	protein-coding
mm_102208.1	chr11	54845539	54845544	-	1	NA	intron (NM_029327, intron 4 of 4)	intron (NM_029327, intron 4 of 4)	15050	NM_029327	75530	Mm.83578	NM_029327	ENSMUSG00000020268	Lyrm7	1700024C24Rik|9330147L21Rik	LYR motif containing 7	protein-coding
mm_145008.1	chr18	38457769	38457772	+	1	NA	intron (NM_022996, intron 6 of 7)	ID_B1|SINE|B4	38795	NM_022996	65113	Mm.102496	NM_022996	ENSMUSG00000024425	Ndfip1	0610010M22Rik|N4wbp5	Nedd4 family interacting protein 1	protein-coding
mm_59645.1	chr7	28162724	28162724	+	1	NA	exon (NM_001164655, exon 18 of 20)	exon (NM_001164655, exon 18 of 20)	-7024	NM_007991	14113	Mm.4595	NM_007991	ENSMUSG00000046865	Fbl	AL022665|FIB|FLRN|RNU3IP1	fibrillarin	protein-coding
mm_34955.1	chr4	155993144	155993187	+	1	NA	promoter-TSS (NM_080445)	promoter-TSS (NM_080445)	12	NM_001302469	20318	Mm.293517	NM_011341	ENSMUSG00000029076	Sdf4	Cab45	stromal cell derived factor 4	protein-coding
mm_74409.1	chr8	3623511	3623557	-	1	NA	exon (NM_001129804, exon 4 of 4)	exon (NM_001129804, exon 4 of 4)	1515	NM_001129804	18545	Mm.440882	NM_008790	ENSMUSG00000004630	Pcp2	L7|Pcp-2	Purkinje cell protein 2 (L7)	protein-coding
mm_65148.1	chr7	19592796	19592801	-	1	NA	intron (NM_016680, intron 5 of 20)	PB1|SINE|Alu	11563	NR_125835	53609	Mm.20913	NM_016680	ENSMUSG00000061028	Clasrp	Clasp|Sfrs16|Srsf16|Swap2	CLK4-associating serine/arginine rich protein	protein-coding
mm_120820.1	chr14	75136327	75136346	+	1	NA	promoter-TSS (NM_008879)	promoter-TSS (NM_008879)	-89	NM_008879	18826	Mm.153911	NM_008879	ENSMUSG00000021998	Lcp1	AW536232|D14Ertd310e|LCP-1|Pls2|pp65	lymphocyte cytosolic protein 1	protein-coding
mm_122557.1	chr14	49066658	49066674	-	1	NA	promoter-TSS (NM_207214)	promoter-TSS (NM_207214)	1	NM_207214	105504	Mm.31607	NM_207214	ENSMUSG00000061244	Exoc5	AI447711|AI448003|Gm76|PRO1912|SEC10|Sec10l1	exocyst complex component 5	protein-coding
mm_130687.1	chr15	100681941	100681951	-	1	NA	intron (NM_033612, intron 5 of 7)	B1_Mur2|SINE|Alu	5974	NM_033612	109901	Mm.2131	NM_033612	ENSMUSG00000023031	Cela1	1810009A17Rik|1810062B19Rik|Ela-1|Ela1|PC-TsF	chymotrypsin-like elastase family, member 1	protein-coding
mm_145910.1	chr18	65873479	65873495	+	1	NA	promoter-TSS (NM_175012)	promoter-TSS (NM_175012)	1	NM_175012	225642	Mm.20298	NM_175012	ENSMUSG00000024517	Grp	BLP	gastrin releasing peptide	protein-coding
mm_12305.1	chr2	69111167	69111178	+	1	NA	3' UTR (NM_001347161, exon 11 of 11)	3' UTR (NM_001347161, exon 11 of 11)	-24628	NM_181547	329416	Mm.90047	NM_181547	ENSMUSG00000034738	Nostrin	Daip2|mDaIP2	nitric oxide synthase trafficker	protein-coding
mm_143531.1	chr17	73910202	73910214	-	1	NA	exon (NM_011723, exon 19 of 36)	exon (NM_011723, exon 19 of 36)	39988	NM_011723	22436	Mm.11223	NM_011723	ENSMUSG00000024066	Xdh	XO|Xor|Xox-1|Xox1	xanthine dehydrogenase	protein-coding
mm_171555.1	chr4	147132072	147132072	+	1	NA	Intergenic	Intergenic	-43794	NM_001039209	195531	Mm.270762	NM_001039209	ENSMUSG00000078496	Zfp982	Gm13152|OTTMUSG00000010671	zinc finger protein 982	protein-coding
mm_153618.1	chr19	43986402	43986412	-	1	NA	5' UTR (NM_030703, exon 1 of 9)	5' UTR (NM_030703, exon 1 of 9)	113	NM_030703	93721	Mm.206774	NM_030703	ENSMUSG00000025196	Cpn1	0610011F20Rik|CPN	carboxypeptidase N, polypeptide 1	protein-coding
mm_161597.1	chr16	36221469	36221469	+	1	NA	promoter-TSS (NM_029733)	promoter-TSS (NM_029733)	-93	NM_029733	76770	Mm.327617	NM_029733	ENSMUSG00000095620	2010005H15Rik	-	RIKEN cDNA 2010005H15 gene	protein-coding
mm_168390.1	chr1	126830688	126830689	-	1	NA	promoter-TSS (NM_176957)	promoter-TSS (NM_176957)	-56	NM_176957	210356	Mm.377234	NM_172484	ENSMUSG00000049690	Nckap5	8430408F21|D130011D22Rik|E030049G20Rik|Erih1|Erih2|Gm1548|Nap5	NCK-associated protein 5	protein-coding
mm_49442.1	chr6	29319247	29319251	+	1	NA	exon (NM_001289664, exon 1 of 7)	exon (NM_001289664, exon 1 of 7)	109	NM_001289664	330277	Mm.87624	NM_207258	ENSMUSG00000039742	Fam71f1	GARI-L1|Gm764|NYD-SP18	family with sequence similarity 71, member F1	protein-coding
mm_6488.1	chr1	74124421	74124466	-	1	NA	promoter-TSS (NM_001289895)	promoter-TSS (NM_001289895)	4	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_66753.1	chr7	46712639	46712652	-	1	NA	exon (NM_011315, exon 3 of 4)	exon (NM_011315, exon 3 of 4)	-1994	NM_030233	78935	Mm.289866	NM_030233	ENSMUSG00000006763	Saal1	5031425D22Rik|SPACIA1	serum amyloid A-like 1	protein-coding
mm_15309.1	chr2	155518027	155518088	+	1	NA	promoter-TSS (NM_019811)	promoter-TSS (NM_019811)	14	NM_019811	60525	Mm.255026	NM_019811	ENSMUSG00000027605	Acss2	1110017C11Rik|ACAS|Acas1|Acas2|AceCS1|Acs1	acyl-CoA synthetase short-chain family member 2	protein-coding
mm_45707.1	chr5	84066986	84067014	-	1	NA	intron (NM_007937, intron 15 of 15)	intron (NM_007937, intron 15 of 15)	350382	NM_007937	13839	Mm.137991	NM_007937	ENSMUSG00000029245	Epha5	AI854630|AW125296|Cek7|Ehk1|Els1|Hek7|Rek7|bsk	Eph receptor A5	protein-coding
mm_25964.1	chr3	132724422	132724432	+	1	NA	intron (NM_001163455, intron 10 of 25)	L1MCa|LINE|L1	40283	NM_001163455	271981	Mm.257864	NM_173032	ENSMUSG00000028030	Tbck	1700120J03Rik|9430001M19|A630047E20Rik|C030007I09Rik|Tbckl	TBC1 domain containing kinase	protein-coding
mm_63363.1	chr7	127050520	127050531	+	1	NA	exon (NM_026918, exon 3 of 3)	exon (NM_026918, exon 3 of 3)	1452	NM_026918	69036	Mm.21835	NM_026918	ENSMUSG00000049350	Zg16	1810010M01Rik|AI593689|ZG16p	zymogen granule protein 16	protein-coding
mm_10623.1	chr2	19452469	19452494	+	1	NA	Intergenic	Intergenic	-5807	NR_131924	102637107	Mm.406835	NR_131924	ENSMUSG00000085388	Ptf1aos	Gm13336|OTTMUSG00000011493	pancreas specific transcription factor 1a, opposite strand	ncRNA
mm_138492.1	chr17	35200419	35200430	+	1	NA	exon (NM_013693, exon 4 of 4)	exon (NM_013693, exon 4 of 4)	1583	NM_013693	21926	Mm.1293	NM_013693	ENSMUSG00000024401	Tnf	DIF|TNF-a|TNF-alpha|TNFSF2|TNFalpha|Tnfa|Tnfsf1a|Tnlg1f	tumor necrosis factor	protein-coding
mm_170651.1	chr2	10080474	10080475	-	1	NA	promoter-TSS (NM_001112738)	promoter-TSS (NM_001112738)	36	NM_020615	11949	Mm.12677	NM_020615	ENSMUSG00000025781	Atp5c1	1700094F02Rik	ATP synthase, H+ transporting, mitochondrial F1 complex, gamma polypeptide 1	protein-coding
mm_124706.1	chr15	6547469	6547493	+	1	NA	Intergenic	Intergenic	-32366	NM_001278269	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_91440.1	chr10	33933069	33933088	-	1	NA	intron (NM_028287, intron 6 of 9)	intron (NM_028287, intron 6 of 9)	18134	NM_028287	72580	Mm.248081	NM_028287	ENSMUSG00000039531	Zufsp	2700019D07Rik	zinc finger with UFM1-specific peptidase domain	protein-coding
mm_152555.1	chr19	11484611	11484635	-	1	NA	Intergenic	Intergenic	-7415	NM_001164202	666926	Mm.486382	NM_001164202	ENSMUSG00000058470	Gm8369	EG666926	predicted gene 8369	protein-coding
mm_36101.1	chr4	58553289	58553298	-	1	NA	promoter-TSS (NM_172989)	promoter-TSS (NM_172989)	0	NM_172989	14745	Mm.4772	NM_010336	ENSMUSG00000038668	Lpar1	AI326300|Edg2|Gpcr26|Kdt2|lpA1|vzg-1	lysophosphatidic acid receptor 1	protein-coding
mm_21147.1	chr2	154372703	154372735	-	1	NA	promoter-TSS (NM_025876)	promoter-TSS (NM_025876)	0	NM_025876	66971	Mm.289427	NM_025876	ENSMUSG00000027487	Cdk5rap1	2310066P17Rik	CDK5 regulatory subunit associated protein 1	protein-coding
mm_86869.1	chr10	21994146	21994184	+	1	NA	promoter-TSS (NM_011361)	promoter-TSS (NM_011361)	275	NM_001161850	20393	Mm.28405	NM_011361	ENSMUSG00000019970	Sgk1	Sgk	serum/glucocorticoid regulated kinase 1	protein-coding
mm_16563.1	chr2	3332567	3332650	-	1	NA	promoter-TSS (NM_001013376)	promoter-TSS (NM_001013376)	20	NM_001013376	227522	Mm.293948	NM_001013376	ENSMUSG00000049950	Rpp38	C330006A15Rik	ribonuclease P/MRP 38 subunit	protein-coding
mm_72975.1	chr8	92892636	92892670	+	1	NA	intron (NM_173014, intron 11 of 13)	intron (NM_173014, intron 11 of 13)	-8742	NM_027112	69543	Mm.440514	NM_027112	ENSMUSG00000078144	Capns2	2310005G05Rik|30K-2	calpain, small subunit 2	protein-coding
mm_143280.1	chr17	65772636	65772650	-	1	NA	5' UTR (NM_133685, exon 1 of 7)	5' UTR (NM_133685, exon 1 of 7)	109	NM_133685	106572	Mm.29274	NM_133685	ENSMUSG00000056515	Rab31	1700093E07Rik|AI415285|Rab22B	RAB31, member RAS oncogene family	protein-coding
mm_98448.1	chr11	94944352	94944385	+	1	NA	exon (NM_007742, exon 26 of 51)	exon (NM_007742, exon 26 of 51)	8144	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_19068.1	chr2	77703306	77703325	-	1	NA	promoter-TSS (NM_001113399)	promoter-TSS (NM_001113399)	-43	NM_001113399	241494	Mm.490320	NM_178723	ENSMUSG00000027016	Zfp385b	B830010L13Rik|C130013B13Rik|Zfp533|Znf385b	zinc finger protein 385B	protein-coding
mm_13884.1	chr2	119972750	119972760	+	1	NA	promoter-TSS (NM_011941)	promoter-TSS (NM_011941)	56	NM_011941	26390	Mm.330501	NM_011941	ENSMUSG00000033902	Mapkbp1	2810483F24Rik|AW123212|JNKBP-1|Jnkbp1|mKIAA0596	mitogen-activated protein kinase binding protein 1	protein-coding
mm_39327.1	chr5	8659959	8659960	+	1	NA	promoter-TSS (NM_011076)	promoter-TSS (NM_011076)	-133	NM_011076	18671	Mm.207354	NM_011076	ENSMUSG00000040584	Abcb1a	Abcb4|Evi32|Mdr1a|Mdr3|P-gp|Pgp|Pgy-3|Pgy3|mdr-3	ATP-binding cassette, sub-family B (MDR/TAP), member 1A	protein-coding
mm_11355.1	chr2	30913417	30913432	+	1	NA	Intergenic	Intergenic	-10127	NM_022415	64292	Mm.28768	NM_022415	ENSMUSG00000050737	Ptges	2410099E23Rik|D2Ertd369e|Pges|mPGES|mPGES-1	prostaglandin E synthase	protein-coding
mm_31609.1	chr4	58943576	58943638	+	1	NA	promoter-TSS (NM_001099323)	promoter-TSS (NM_001099323)	-21	NM_001099323	100041581	Mm.463942	NM_001099323	ENSMUSG00000038630	Zkscan16	XM_143800|Zfp483	zinc finger with KRAB and SCAN domains 16	protein-coding
mm_150789.1	chr19	44302997	44303012	+	1	NA	promoter-TSS (NR_039574)	promoter-TSS (NR_039574)	-167	NR_039574	100628619		NR_039574	ENSMUSG00000093315	Mir5114	mmu-mir-5114|mu-mir-5114	microRNA 5114	ncRNA
mm_57634.1	chr6	128355798	128355824	-	1	NA	promoter-TSS (NM_011657)	promoter-TSS (NM_011657)	40	NM_011657	22158	Mm.291783	NM_011657	ENSMUSG00000001521	Tulp3	2310022L06Rik|AI316887	tubby-like protein 3	protein-coding
mm_62276.1	chr7	99588074	99588124	+	1	NA	exon (NM_178220, exon 5 of 15)	exon (NM_178220, exon 5 of 15)	35830	NR_029760	723840		NR_029760	ENSMUSG00000065571	Mir326	Mirn326|mir-326|mmu-mir-326	microRNA 326	ncRNA
mm_1270.1	chr1	63273262	63273275	+	1	NA	promoter-TSS (NM_028673)	promoter-TSS (NM_028673)	-1	NM_028673	73884	Mm.86986	NM_028673	ENSMUSG00000027520	Zdbf2	4930431J08Rik|9330107J05Rik	zinc finger, DBF-type containing 2	protein-coding
mm_74459.1	chr8	4214718	4214730	-	1	NA	exon (NM_207203, exon 6 of 7)	exon (NM_207203, exon 6 of 7)	2588	NM_207203	73072	Mm.477379	NM_207203	ENSMUSG00000064125	Prr36	-	proline rich 36	protein-coding
mm_58933.1	chr7	18009882	18009895	+	1	NA	promoter-TSS (NM_027210)	promoter-TSS (NM_027210)	-1	NM_027210	69785	Mm.46086	NM_027210	ENSMUSG00000057195	Ceacam13	1600012K03Rik|1600025J19Rik	carcinoembryonic antigen-related cell adhesion molecule 13	protein-coding
mm_549.1	chr1	38019116	38019127	+	1	NA	exon (NM_198303, exon 4 of 24)	exon (NM_198303, exon 4 of 24)	21111	NM_198303	226982	Mm.260943	NM_198303	ENSMUSG00000026083	Eif5b	A030003E17Rik|BC018347|IF2	eukaryotic translation initiation factor 5B	protein-coding
mm_115723.1	chr13	16026628	16026673	-	1	NA	exon (NM_008380, exon 5 of 5)	exon (NM_008380, exon 5 of 5)	14799	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_135811.1	chr16	57391670	57391683	-	1	NA	intron (NM_001040397, intron 1 of 4)	RSINE1|SINE|B4	38399	NM_001040397	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding
mm_124404.1	chr14	115471863	115471876	-	1	NA	intron (NM_175500, intron 5 of 7)	intron (NM_175500, intron 5 of 7)	-62317	NR_045761	75088	Mm.444706	NR_045761	ENSMUSG00000093551	4930505G20Rik	-	RIKEN cDNA 4930505G20 gene	ncRNA
mm_47833.1	chr5	134306604	134306616	-	1	NA	intron (NM_001080746, intron 1 of 34)	intron (NM_001080746, intron 1 of 34)	8150	NM_001080746	14886	Mm.261570	NM_010365	ENSMUSG00000060261	Gtf2i	6030441I21Rik|BAP-135|Diws1t|GtfII-I|Spin|TFII-I|WBSCR6	general transcription factor II I	protein-coding
mm_104375.1	chr11	94371741	94371752	-	1	NA	exon (NM_029600, exon 8 of 31)	exon (NM_029600, exon 8 of 31)	21230	NM_029600	76408	Mm.23942	NM_029600	ENSMUSG00000020865	Abcc3	1700019L09Rik|ABC31|MLP2|MOAT-D|MRP3	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	protein-coding
mm_138615.1	chr17	35823328	35823371	+	1	NA	promoter-TSS (NM_008027)	promoter-TSS (NM_008027)	-8	NM_008027	14251	Mm.2931	NM_008027	ENSMUSG00000059714	Flot1	reggie-2	flotillin 1	protein-coding
mm_79605.1	chr9	58582398	58582416	+	1	NA	5' UTR (NM_009145, exon 1 of 8)	5' UTR (NM_009145, exon 1 of 8)	167	NM_009145	20320	Mm.15125	NM_009145	ENSMUSG00000032336	Nptn	AW554172|SDR-1|Sdfr1	neuroplastin	protein-coding
mm_164638.1	chr17	34722383	34722389	-	1	NA	Intergenic	Intergenic	21511	NM_009780	12268	Mm.477109	NM_009780	ENSMUSG00000073418	C4b	C4|Ss	complement component 4B (Chido blood group)	protein-coding
mm_158183.1	chrX	104201100	104201117	-	1	NA	promoter-TSS (NM_001077354)	promoter-TSS (NM_001077354)	9	NM_001077354	245555	Mm.381907	NM_001077354	ENSMUSG00000046449	C77370	A230051P11|C77386|KIDLIA|Kiaa2022|Xpn|mKIAA2022	expressed sequence C77370	protein-coding
mm_6536.1	chr1	74913046	74913049	-	1	NA	intron (NM_001039495, intron 19 of 32)	intron (NM_001039495, intron 19 of 32)	-12326	NR_029876	723900		NR_029876	ENSMUSG00000065616	Mir375	Mirn375|mir-375|mmu-mir-375	microRNA 375	ncRNA
mm_100449.1	chr11	119603581	119603611	+	1	NA	5' UTR (NM_001306081, exon 1 of 33)	5' UTR (NM_001306081, exon 1 of 33)	691	NM_028898	74370	Mm.209933	NM_028898	ENSMUSG00000025583	Rptor	4932417H02Rik|Rap|Raptor|mKIAA1303	regulatory associated protein of MTOR, complex 1	protein-coding
mm_142676.1	chr17	47732428	47732438	-	1	NA	exon (NM_025973, exon 6 of 9)	exon (NM_025973, exon 6 of 9)	-4604	NM_001161722	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_18032.1	chr2	38712196	38712210	-	1	NA	promoter-TSS (NM_001316687)	promoter-TSS (NM_001316687)	31	NM_001316687	26423	Mm.31387	NM_139051	ENSMUSG00000026751	Nr5a1	Ad4BP|ELP|ELP-3|Ftz-F1|Ftzf1|SF-1|SF1|STF-1	nuclear receptor subfamily 5, group A, member 1	protein-coding
mm_136629.1	chr17	5581013	5581016	+	1	NA	intron (NM_146073, intron 1 of 8)	intron (NM_146073, intron 1 of 8)	88414	NM_146073	224454	Mm.487663	NM_146073	ENSMUSG00000034265	Zdhhc14	B530001K09Rik|New1cp	zinc finger, DHHC domain containing 14	protein-coding
mm_76594.1	chr8	89043492	89043517	-	1	NA	intron (NM_021390, intron 1 of 3)	CpG-14342	658	NM_021390	58198	Mm.214361	NM_021390	ENSMUSG00000031665	Sall1	Msal-3	sal-like 1 (Drosophila)	protein-coding
mm_127272.1	chr15	99723981	99723994	+	1	NA	3' UTR (NM_010271, exon 8 of 8)	3' UTR (NM_010271, exon 8 of 8)	-1631	NM_183256	66379	Mm.5265	NM_183256	ENSMUSG00000023020	Cox14	2310016M24Rik|AA959804	cytochrome c oxidase assembly protein 14	protein-coding
mm_67113.1	chr7	70361426	70361437	-	1	NA	promoter-TSS (NM_009697)	promoter-TSS (NM_009697)	-838	NM_009697	11819	Mm.158143	NM_009697	ENSMUSG00000030551	Nr2f2	2700033K02Rik|9430015G03Rik|ARP-1|Aporp1|COUP-TF2|COUP-TFII|COUPTFB|EAR3|SVP40|Tcfcoup2	nuclear receptor subfamily 2, group F, member 2	protein-coding
mm_91535.1	chr10	39133856	39133912	-	1	NA	promoter-TSS (NM_028006)	promoter-TSS (NM_028006)	11	NM_183254	66337	Mm.45187	NM_183254	ENSMUSG00000051736	Fam229b	1700025K23Rik	family with sequence similarity 229, member B	protein-coding
mm_131234.1	chr16	10480121	10480121	+	1	NA	promoter-TSS (NM_001243760)	promoter-TSS (NM_001243760)	49	NM_001302618	12265	Mm.249560	NM_007575	ENSMUSG00000022504	Ciita	C2ta|EG669998|Gm9475|Mhc2ta	class II transactivator	protein-coding
mm_142938.1	chr17	56008355	56008388	-	1	NA	promoter-TSS (NM_026530)	promoter-TSS (NM_026530)	-830	NM_026530	68047	Mm.358710	NM_026530	ENSMUSG00000003199	Mpnd	E130307M08Rik	MPN domain containing	protein-coding
mm_102923.1	chr11	69600585	69600589	-	1	NA	3' UTR (NM_013415, exon 7 of 7)	3' UTR (NM_013415, exon 7 of 7)	5373	NM_013415	11932	Mm.235204	NM_013415	ENSMUSG00000041329	Atp1b2	Amog|Atpb-2	ATPase, Na+/K+ transporting, beta 2 polypeptide	protein-coding
mm_146686.1	chr18	12862455	12862532	-	1	NA	5' UTR (NM_001252492, exon 1 of 14)	5' UTR (NM_001252492, exon 1 of 14)	220	NM_001252493	64291	Mm.259470	NM_020573	ENSMUSG00000044252	Osbpl1a	G430090F17Rik|Gm753|ORP-1|Osbpl1b	oxysterol binding protein-like 1A	protein-coding
mm_120885.1	chr14	75331776	75331793	+	1	NA	exon (NM_026083, exon 15 of 19)	exon (NM_026083, exon 15 of 19)	47411	NM_026083	67302	Mm.74704	NM_026083	ENSMUSG00000022000	Zc3h13	2600010B19Rik|3110050K21Rik|4930570G11Rik|C87618	zinc finger CCCH type containing 13	protein-coding
mm_72466.1	chr8	83348439	83348450	+	1	NA	promoter-TSS (NM_026233)	promoter-TSS (NM_026233)	-28	NM_026233	67555	Mm.84115	NM_026233	ENSMUSG00000035057	Mgat4d	4933434I20Rik|GnT1IP|GnT1IP-L	MGAT4 family, member C	protein-coding
mm_165894.1	chr4	45346554	45346581	-	1	NA	intron (NM_153167, intron 1 of 6)	LSU-rRNA_Hsa|rRNA|rRNA	4466	NM_153167	242418	Mm.317668	NM_153167	ENSMUSG00000035572	Dcaf10	AA959934|Wdr32	DDB1 and CUL4 associated factor 10	protein-coding
mm_81574.1	chr9	110422267	110422278	+	1	NA	exon (NM_008694, exon 4 of 4)	exon (NM_008694, exon 4 of 4)	2464	NM_008694	18054	Mm.236225	NM_008694	ENSMUSG00000032484	Ngp	bectenecin	neutrophilic granule protein	protein-coding
mm_3587.1	chr1	151345502	151345512	+	1	NA	intron (NM_001039511, intron 1 of 7)	intron (NM_001039511, intron 1 of 7)	1009	NM_001039511	117198	Mm.33764	NM_028582	ENSMUSG00000023150	Ivns1abp	1190004M08Rik|1700126I16Rik|AA960440|HSPC068|ND1|NS-1|NS1-BP|Nd1-L|Nd1-S|mKIAA0850	influenza virus NS1A binding protein	protein-coding
mm_29350.1	chr3	108416053	108416066	-	1	NA	promoter-TSS (NM_017392)	promoter-TSS (NM_017392)	-565	NM_001004177	53883	Mm.39728	NM_017392	ENSMUSG00000068740	Celsr2	Adgrc2|EGFL2|Flamingo1|flamingo|mKIAA0279|mfmi1	cadherin, EGF LAG seven-pass G-type receptor 2	protein-coding
mm_82416.1	chr9	14902525	14902559	-	1	NA	intron (NM_022888, intron 1 of 4)	intron (NM_022888, intron 1 of 4)	1409	NM_176807	64931	Mm.86738	NM_022888	ENSMUSG00000031933	Izumo1r	0910001L11Rik|C86255|Folbp3|Folr4|Juno	IZUMO1 receptor, JUNO	protein-coding
mm_129532.1	chr15	79285503	79285516	-	1	NA	promoter-TSS (NM_177580)	promoter-TSS (NM_177580)	0	NM_177580	207495	Mm.309647	NM_177580	ENSMUSG00000018126	Baiap2l2	BC048937	BAI1-associated protein 2-like 2	protein-coding
mm_157776.1	chrX	73781785	73781792	-	1	NA	exon (NM_008323, exon 5 of 13)	exon (NM_008323, exon 5 of 13)	5109	NM_008323	15929	Mm.14825	NM_008323	ENSMUSG00000002010	Idh3g	-	isocitrate dehydrogenase 3 (NAD+), gamma	protein-coding
mm_96554.1	chr11	68901518	68901529	+	1	NA	promoter-TSS (NM_009080)	promoter-TSS (NM_009080)	-43	NM_009080	19941	Mm.3229	NM_009080	ENSMUSG00000060938	Rpl26	SIG-20	ribosomal protein L26	protein-coding
mm_165953.1	chr4	86670250	86670253	+	1	NA	promoter-TSS (NM_007408)	promoter-TSS (NM_007408)	-192	NM_007408	11520	Mm.381	NM_007408	ENSMUSG00000028494	Plin2	AA407157|ADPH|Adfp|Adrp	perilipin 2	protein-coding
mm_104753.1	chr11	98463685	98463769	-	1	NA	TTS (NM_011771)	TTS (NM_011771)	16893	NM_010346	14786	Mm.276702	NM_010346	ENSMUSG00000019312	Grb7	mKIAA4028	growth factor receptor bound protein 7	protein-coding
mm_77899.1	chr9	7348691	7348702	+	1	NA	exon (NM_008605, exon 2 of 10)	exon (NM_008605, exon 2 of 10)	1322	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_160196.1	chr7	79130996	79130996	-	1	NA	promoter-TSS (NM_178255)	promoter-TSS (NM_178255)	22	NM_178255	67666	Mm.178759	NM_178255	ENSMUSG00000030606	Hapln3	4930554N11Rik|Lpr3	hyaluronan and proteoglycan link protein 3	protein-coding
mm_48793.1	chr5	148867884	148867917	-	1	NA	Intergenic	Intergenic	60747	NM_153572	231912	Mm.397405	NM_153572	ENSMUSG00000041298	Katnal1	-	katanin p60 subunit A-like 1	protein-coding
mm_52987.1	chr6	123264623	123264644	+	1	NA	intron (NM_001163161, intron 1 of 5)	Lx2A1|LINE|L1	2526	NM_010819	17474	Mm.441101	NM_010819	ENSMUSG00000030144	Clec4d	Clecsf8|Mpcl|mcl	C-type lectin domain family 4, member d	protein-coding
mm_41583.1	chr5	93205471	93205483	+	1	NA	intron (NM_017367, intron 1 of 6)	intron (NM_017367, intron 1 of 6)	1018	NM_017367	12453	Mm.250419	NM_017367	ENSMUSG00000063015	Ccni	-	cyclin I	protein-coding
mm_165933.1	chr4	68125041	68125051	+	1	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	829351	NM_019967	56710	Mm.248788	NM_019967	ENSMUSG00000028351	Brinp1	BRINP|Dbc1|Dbccr1|Fam5a	bone morphogenic protein/retinoic acid inducible neural specific 1	protein-coding
mm_117163.1	chr13	62760687	62760715	-	1	NA	promoter-TSS (NR_030493)	promoter-TSS (NR_030493)	-38	NR_030493	751548		NR_030493	ENSMUSG00000096098	Mir713	Mirn713|mir-713|mmu-mir-713	microRNA 713	ncRNA
mm_164865.1	chr18	56412140	56412150	+	1	NA	Intergenic	Intergenic	-19987	NM_026240	107022	Mm.24356	NM_026240	ENSMUSG00000001700	Gramd3	9030613F08Rik|9130427A09Rik|AW061306|NS3TP2	GRAM domain containing 3	protein-coding
mm_1055.1	chr1	58846871	58846888	+	1	NA	3' UTR (NM_001277926, exon 10 of 10)	3' UTR (NM_001277926, exon 10 of 10)	44377	NM_001080126	12370	Mm.336851	NM_009812	ENSMUSG00000026029	Casp8	CASP-8|FLICE|MACH|Mch5	caspase 8	protein-coding
mm_101531.1	chr11	33203552	33203561	-	1	NA	promoter-TSS (NM_019916)	promoter-TSS (NM_019916)	32	NM_019916	27140	Mm.25362	NM_019916	ENSMUSG00000040610	Tlx3	Hox11l2|Rnx|Tlx1l2	T cell leukemia, homeobox 3	protein-coding
mm_148769.1	chr19	6085054	6085146	+	1	NA	promoter-TSS (NM_024231)	promoter-TSS (NM_024231)	3	NM_026410	67849	Mm.23526	NM_026410	ENSMUSG00000024791	Cdca5	2610036L13Rik|AL024086|AW536684|C85404	cell division cycle associated 5	protein-coding
mm_164148.1	chr15	60742827	60742828	+	1	NA	Intergenic	Intergenic	-80138	NR_030696	320469	Mm.230853	NM_177166		9930014A18Rik	-	RIKEN cDNA 9930014A18 gene	ncRNA
mm_89128.1	chr10	84917704	84917716	+	1	NA	promoter-TSS (NM_183172)	promoter-TSS (NM_183172)	97	NM_183172	237422	Mm.18936	NM_183172	ENSMUSG00000035620	Ric8b	BC051080|Ric-8|Ric-8b	RIC8 guanine nucleotide exchange factor B	protein-coding
mm_6765.1	chr1	84105708	84105738	-	1	NA	intron (NM_001003948, intron 2 of 2)	ORR1F|LTR|ERVL-MaLR	113238	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_84886.1	chr9	79759756	79759772	-	1	NA	promoter-TSS (NM_009945)	promoter-TSS (NM_009945)	89	NM_009945	12866	Mm.152627	NM_009945	ENSMUSG00000032330	Cox7a2	COX7AL|Cox7a3|CoxVIIa-L	cytochrome c oxidase subunit VIIa 2	protein-coding
mm_68051.1	chr7	101560864	101560866	-	1	NA	promoter-TSS (NR_033804)	promoter-TSS (NR_033804)	0	NR_033804	11871	Mm.439746	NM_007490	ENSMUSG00000092517	Art2a-ps	ARTC2|Art2a|Ly92a|Rt-6|Rt6|Rt6-1	ADP-ribosyltransferase 2a, pseudogene	protein-coding
mm_75705.1	chr8	68892685	68892712	-	1	NA	exon (NM_008509, exon 3 of 10)	exon (NM_008509, exon 3 of 10)	12143	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_50600.1	chr6	49218312	49218327	+	1	NA	Intergenic	CpG	-3365	NM_023670	140488	Mm.281018	NM_023670	ENSMUSG00000029814	Igf2bp3	2610101N11Rik|AA522010|AL022933|AU045931|IMP-3|IMP3|Koc13|Neilsen|mimp3	insulin-like growth factor 2 mRNA binding protein 3	protein-coding
mm_4988.1	chr1	191718396	191718431	+	1	NA	promoter-TSS (NM_001134829)	promoter-TSS (NM_001134829)	18	NM_001134829	226856	Mm.277958	NM_172266	ENSMUSG00000026623	Lpgat1	AI649174|AW112037|BC013667	lysophosphatidylglycerol acyltransferase 1	protein-coding
mm_61629.1	chr7	80246376	80246429	+	1	NA	promoter-TSS (NM_177765)	promoter-TSS (NM_177765)	26	NM_177765	269954	Mm.276780	NM_177765	ENSMUSG00000045467	Ttll13	1700111A04Rik|4921538O11|BC024578	tubulin tyrosine ligase-like family, member 13	protein-coding
mm_88960.1	chr10	81393691	81393701	+	1	NA	intron (NM_001099917, intron 1 of 3)	intron (NM_001099917, intron 1 of 3)	632	NM_001099917	72273	Mm.253147	NM_001099917	ENSMUSG00000078439	Smim24	2210404O07Rik	small integral membrane protein 24	protein-coding
mm_116481.1	chr13	43765248	43765263	-	1	NA	Intergenic	Intergenic	-19857	NM_009856	12522	Mm.57175	NM_009856	ENSMUSG00000015396	Cd83	-	CD83 antigen	protein-coding
mm_54332.1	chr6	30640916	30640951	-	1	NA	exon (NM_025350, exon 4 of 10)	exon (NM_025350, exon 4 of 10)	1715	NM_025350	109697	Mm.25377	NM_025350	ENSMUSG00000054446	Cpa1	0910001L12Rik|Cpa	carboxypeptidase A1, pancreatic	protein-coding
mm_12385.1	chr2	69869917	69869932	+	1	NA	exon (NM_001110145, exon 9 of 12)	exon (NM_001110145, exon 9 of 12)	8362	NM_009278	20823	Mm.10508	NM_009278	ENSMUSG00000068882	Ssb	SS-B	Sjogren syndrome antigen B	protein-coding
mm_69343.1	chr7	130089331	130089339	-	1	NA	Intergenic	Intergenic	127170	NR_046077	100043150	Mm.334264	NR_046077	ENSMUSG00000108504	Gm4265	-	predicted gene 4265	ncRNA
mm_151889.1	chr19	5798735	5798745	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	-2759	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_130890.1	chr15	102350693	102350771	-	1	NA	promoter-TSS (NM_153416)	promoter-TSS (NM_153416)	27	NM_153416	223921	Mm.352946	NM_153416	ENSMUSG00000036678	Aaas	AAA|ADRACALA|D030041N15Rik|GL003	achalasia, adrenocortical insufficiency, alacrimia	protein-coding
mm_9060.1	chr1	167374542	167374573	-	1	NA	intron (NM_025569, intron 4 of 5)	intron (NM_025569, intron 4 of 5)	19240	NM_025569	66447	Mm.218286	NM_025569	ENSMUSG00000026688	Mgst3	2010012L10Rik|2010306B17Rik|2700004G04Rik|AA516734|GST-III	microsomal glutathione S-transferase 3	protein-coding
mm_38922.1	chr4	150003168	150003194	-	1	NA	promoter-TSS (NM_001291004)	promoter-TSS (NM_001291004)	55	NM_001291004	100198	Mm.22183	NM_173371	ENSMUSG00000028980	H6pd	AI785303|G6pd1|Gpd-1|Gpd1	hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase)	protein-coding
mm_81676.1	chr9	111038890	111038901	+	1	NA	exon (NM_008522, exon 15 of 17)	exon (NM_008522, exon 15 of 17)	18349	NM_001302377	54199	Mm.7336	NM_017466	ENSMUSG00000043953	Ccrl2	1810047I05Rik|Ackr5|CCR11|Cmkbr1l2|E01|L-CCR	chemokine (C-C motif) receptor-like 2	protein-coding
mm_89371.1	chr10	88731434	88731450	+	1	NA	promoter-TSS (NM_025859)	promoter-TSS (NM_025859)	28	NM_025859	104303	Mm.291247	NM_025859	ENSMUSG00000060904	Arl1	2310008D22Rik|AU019749	ADP-ribosylation factor-like 1	protein-coding
mm_160093.1	chr7	17074027	17074027	+	1	NA	promoter-TSS (NM_007676)	promoter-TSS (NM_007676)	-13	NM_001310628	26436	Mm.143686	NM_007676	ENSMUSG00000066760	Psg16	Cea11|PSG|bCEA	pregnancy specific glycoprotein 16	protein-coding
mm_41279.1	chr5	90365384	90365419	+	1	NA	intron (NM_198010, intron 1 of 32)	CpG	784	NM_030886	81702	Mm.245522	NM_030886	ENSMUSG00000055204	Ankrd17	4933425K22Rik|A130069E23Rik|A930008M01|AA407558|AA516750|AU040470|Foe|Gtar|Mask|mKIAA0697	ankyrin repeat domain 17	protein-coding
mm_63330.1	chr7	126950499	126950503	+	1	NA	promoter-TSS (NM_001039645)	promoter-TSS (NM_001039645)	-34	NM_144926	233878	Mm.283926	NM_144926	ENSMUSG00000030683	Sez6l2	AI835913|AW121566|BSRP-A|Psk1	seizure related 6 homolog like 2	protein-coding
mm_51527.1	chr6	83186161	83186182	+	1	NA	5' UTR (NM_001347310, exon 1 of 27)	5' UTR (NM_001347310, exon 1 of 27)	225	NM_001347310	13191	Mm.6919	NM_007835	ENSMUSG00000031865	Dctn1	AL022633|DAP-150|DP-150|Glued|p150|p150-glued|p150<glued>	dynactin 1	protein-coding
mm_44577.1	chr5	24842471	24842481	-	1	NA	promoter-TSS (NM_053075)	promoter-TSS (NM_053075)	-115	NM_053075	19744	Mm.319175	NM_053075	ENSMUSG00000028945	Rheb	Rheb1	Ras homolog enriched in brain	protein-coding
mm_3281.1	chr1	136624952	136624995	+	1	NA	promoter-TSS (NM_001160251)	promoter-TSS (NM_001160251)	72	NM_001160251	226442	Mm.62521	NM_177643	ENSMUSG00000041483	Zfp281	Znf281	zinc finger protein 281	protein-coding
mm_53880.1	chr6	3332897	3332900	-	1	NA	Intergenic	L1_Mur3|LINE|L1	44379	NR_036696	667335	Mm.380219	NR_036696	ENSMUSG00000106779	Gm8579	EG667335	spermatogenesis associated glutamate (E)-rich protein 4a pseudogene	pseudo
mm_165031.1	chr19	34165996	34166003	-	1	NA	promoter-TSS (NM_024204)	promoter-TSS (NM_024204)	42	NM_024204	52024	Mm.183030	NM_024204	ENSMUSG00000024774	Ankrd22	5430429D21Rik|D19Ertd675e	ankyrin repeat domain 22	protein-coding
mm_119295.1	chr14	34674207	34674232	+	1	NA	5' UTR (NM_001301330, exon 1 of 19)	5' UTR (NM_001301330, exon 1 of 19)	291	NM_001301330	218914	Mm.27957	NM_001004436	ENSMUSG00000041408	Wapl	A530089A20Rik|BC037674|DIF-2|FOE|Wapal	WAPL cohesin release factor	protein-coding
mm_30031.1	chr3	135691140	135691256	-	1	NA	5' UTR (NM_008689, exon 1 of 25)	5' UTR (NM_008689, exon 1 of 25)	349	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_136887.1	chr17	13010334	13010344	+	1	NA	intron (NM_013671, intron 2 of 4)	intron (NM_013671, intron 2 of 4)	2500	NM_013671	20656	Mm.290876	NM_013671	ENSMUSG00000006818	Sod2	MnSOD|Sod-2	superoxide dismutase 2, mitochondrial	protein-coding
mm_87523.1	chr10	53280276	53280292	+	1	NA	promoter-TSS (NR_038015)	promoter-TSS (NR_038015)	14	NR_038015	100502820	Mm.55827	NR_038015		Gm19395	-	predicted gene, 19395	ncRNA
mm_87835.1	chr10	60374761	60374764	+	1	NA	intron (NR_045556, intron 37 of 68)	intron (NR_045556, intron 37 of 68)	-24964	NM_001164374	100302688	Mm.444135	NM_001164374	ENSMUSG00000090439	Gm17455	-	predicted gene, 17455	protein-coding
mm_114102.1	chr13	54731719	54731728	+	1	NA	intron (NM_001033364, intron 23 of 31)	PB1D10|SINE|Alu	18151	NM_001316710	26913	Mm.41812	NM_012014	ENSMUSG00000069227	Gprin1	GRIN1|Z16	G protein-regulated inducer of neurite outgrowth 1	protein-coding
mm_164974.1	chr19	8722973	8722986	+	1	NA	promoter-TSS (NR_002896)	promoter-TSS (NR_002896)	390	NM_001161413	17254	Mm.4114	NM_008577	ENSMUSG00000010095	Slc3a2	4F2|4F2HC|AI314110|Cd98|Ly-10|Ly-m10|Ly10|Mdu1|Mgp-2hc|NACAE	solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2	protein-coding
mm_96535.1	chr11	68623874	68623876	+	1	NA	Intergenic	Intergenic	36838	NM_177779	276920	Mm.123046	NM_177779	ENSMUSG00000045915	Ccdc42	A530001H01Rik	coiled-coil domain containing 42	protein-coding
mm_85630.1	chr9	107616469	107616492	-	1	NA	exon (NM_008138, exon 6 of 9)	exon (NM_008138, exon 6 of 9)	-7239	NM_001291539	20347	Mm.4083	NM_009153	ENSMUSG00000057969	Sema3b	SemA|Semaa|sema5|semaV	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B	protein-coding
mm_127215.1	chr15	99276281	99276290	+	1	NA	intron (NM_001081254, intron 5 of 7)	intron (NM_001081254, intron 5 of 7)	10895	NM_001081254	545136	Mm.324745	NM_001081254	ENSMUSG00000078907	Fam186b	EG545136	family with sequence similarity 186, member B	protein-coding
mm_115212.1	chr13	109441042	109441097	+	1	NA	intron (NM_011056, intron 3 of 16)	intron (NM_011056, intron 3 of 16)	116325	NR_030644	100124489		NR_030644	ENSMUSG00000076946	Mir582	Mirn582|mir-582|mmu-mir-582	microRNA 582	ncRNA
mm_70756.1	chr8	21084396	21084400	+	1	NA	promoter-TSS (NM_007849)	promoter-TSS (NM_007849)	-44	NM_007849	13236	Mm.376982	NM_007849	ENSMUSG00000094687	Defa25	Defcr-2|Defcr2|Defcr25	defensin, alpha, 25	protein-coding
mm_144127.1	chr18	4920510	4920586	+	1	NA	Intergenic	CpG	108062	NR_045881	100038439	Mm.387569	NR_045881	ENSMUSG00000097043	Gm10556	ENSMUSG00000073646	predicted gene 10556	ncRNA
mm_79032.1	chr9	46050113	46050116	+	1	NA	intron (NM_027498, intron 1 of 24)	RLTR11A2|LTR|ERVK	37294	NM_027498	70661	Mm.219459	NM_027498	ENSMUSG00000034135	Sik3	5730525O22Rik|9030204A07Rik|AI447252|AI846254|AI849445|Qsk|SIK-3|mKIAA0999	SIK family kinase 3	protein-coding
mm_118049.1	chr13	101702129	101702138	-	1	NA	intron (NM_001077495, intron 5 of 15)	intron (NM_001077495, intron 5 of 15)	-9503	NM_001024955	18708	Mm.259333	NM_001024955	ENSMUSG00000041417	Pik3r1	PI3K|p50alpha|p55alpha|p85alpha	phosphatidylinositol 3-kinase, regulatory subunit, polypeptide 1 (p85 alpha)	protein-coding
mm_117116.1	chr13	60624173	60624175	-	1	NA	intron (NM_029653, intron 2 of 25)	RMER19A|LTR|ERVK	21963	NM_134062	69635	Mm.24103	NM_029653	ENSMUSG00000021559	Dapk1	D13Ucla1|DAP-Kinase	death associated protein kinase 1	protein-coding
mm_128562.1	chr15	56172114	56172141	-	1	NA	Intergenic	Intergenic	-265178	NM_016667	20649	Mm.309425	NM_016667	ENSMUSG00000060429	Sntb1	-	syntrophin, basic 1	protein-coding
mm_77619.1	chr8	123931006	123931012	-	1	NA	intron (NM_172288, intron 9 of 25)	intron (NM_172288, intron 9 of 25)	18256	NM_172288	234865	Mm.267812	NM_172288	ENSMUSG00000039509	Nup133	mermaid	nucleoporin 133	protein-coding
mm_27025.1	chr3	26102362	26102362	-	1	NA	intron (NM_138666, intron 3 of 7)	intron (NM_138666, intron 3 of 7)	50945	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_49177.1	chr6	14903485	14903504	+	1	NA	intron (NM_053242, intron 1 of 18)	intron (NM_053242, intron 1 of 18)	2145	NM_053242	114142	Mm.332919	NM_053242	ENSMUSG00000029563	Foxp2	2810043D05Rik|AI449000|CAG-16|D0Kist7	forkhead box P2	protein-coding
mm_76865.1	chr8	105494660	105494675	-	1	NA	intron (NM_175160, intron 1 of 13)	intron (NM_175160, intron 1 of 13)	2203	NM_175160	70796	Mm.100917	NM_175160	ENSMUSG00000039199	Zdhhc1	4432412D04Rik	zinc finger, DHHC domain containing 1	protein-coding
mm_129551.1	chr15	79441803	79441860	-	1	NA	promoter-TSS (NM_001289899)	promoter-TSS (NM_001289899)	-13	NM_001289899	27373	Mm.30199	NM_013767	ENSMUSG00000022433	Csnk1e	AI426939|AI551861|AW457082|CK1epsilon|CKIe|KC1epsilon|tau	casein kinase 1, epsilon	protein-coding
mm_41494.1	chr5	92323768	92323779	+	1	NA	3' UTR (NM_008599, exon 4 of 4)	3' UTR (NM_008599, exon 4 of 4)	4306	NM_008599	17329	Mm.766	NM_008599	ENSMUSG00000029417	Cxcl9	BB139920|CMK|Mig|MuMIG|Scyb9|crg-10	chemokine (C-X-C motif) ligand 9	protein-coding
mm_8018.1	chr1	134955878	134955891	-	1	NA	promoter-TSS (NM_001081307)	promoter-TSS (NM_001081307)	56	NM_001081307	329251	Mm.188709	NM_001081307	ENSMUSG00000073557	Ppp1r12b	1810037O03Rik|9530009M10Rik|AI132431|Mypt2	protein phosphatase 1, regulatory (inhibitor) subunit 12B	protein-coding
mm_171537.1	chr4	146909542	146909542	-	1	NA	Intergenic	Intergenic	-112308	NM_001177767	100043034	Mm.422606	NM_001177767	ENSMUSG00000067919	Rex2	Gm13138|OTTMUSG00000010655	reduced expression 2	protein-coding
mm_29084.1	chr3	104454587	104454590	-	1	NA	3' UTR (NM_001025067, exon 18 of 18)	3' UTR (NM_001025067, exon 18 of 18)	57330	NM_001310698	269473	Mm.34855	NM_001025067	ENSMUSG00000032913	Lrig2	4632419I10Rik|BB096938|LIG-2	leucine-rich repeats and immunoglobulin-like domains 2	protein-coding
mm_115130.1	chr13	104287903	104287923	+	1	NA	promoter-TSS (NM_001081020)	promoter-TSS (NM_001081020)	78	NM_001081020	108154	Mm.208125	NM_175496	ENSMUSG00000046169	Adamts6	A930019D11Rik|ADAM-TS6|b2b1879.1Clo|b2b2029Clo|b2b2182Clo|b2b2187.1Clo|b2b2228Clo	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 6	protein-coding
mm_150593.1	chr19	40679569	40679583	+	1	NA	intron (NM_009848, intron 1 of 9)	intron (NM_009848, intron 1 of 9)	19806	NM_009848	12495	Mm.2824	NM_009848	ENSMUSG00000048120	Entpd1	2610206B08Rik|AA408691|Cd39|NTPDase-1	ectonucleoside triphosphate diphosphohydrolase 1	protein-coding
mm_53805.1	chr6	146861993	146861999	+	1	NA	intron (NM_027059, intron 6 of 9)	intron (NM_027059, intron 6 of 9)	11886	NM_027059	69371	Mm.252733	NM_027059	ENSMUSG00000030292	Smco2	1700023A16Rik	single-pass membrane protein with coiled-coil domains 2	protein-coding
mm_113095.1	chr13	24159914	24159922	+	1	NA	intron (NM_001311122, intron 5 of 37)	intron (NM_001311122, intron 5 of 37)	120872	NM_001311122	68732	Mm.211047	NM_026825	ENSMUSG00000021338	Carmil1	1110037D04Rik|AI425970|CARMIL|CARML1|D130057M20|Lrrc16|Lrrc16a	capping protein regulator and myosin 1 linker 1	protein-coding
mm_5031.1	chr1	193301992	193301996	+	1	NA	promoter-TSS (NM_001277928)	promoter-TSS (NM_001277928)	0	NM_008484	16780	Mm.435441	NM_008484	ENSMUSG00000026639	Lamb3	-	laminin, beta 3	protein-coding
mm_63283.1	chr7	126771099	126771119	+	1	NA	intron (NM_024228, intron 8 of 9)	intron (NM_024228, intron 8 of 9)	4695	NM_024228	68616	Mm.246881	NM_024228	ENSMUSG00000030703	Gdpd3	1110015E22Rik	glycerophosphodiester phosphodiesterase domain containing 3	protein-coding
mm_95776.1	chr11	54909645	54909684	+	1	NA	3' UTR (NM_008161, exon 5 of 5)	3' UTR (NM_008161, exon 5 of 5)	6810	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_49064.1	chr6	5390519	5390546	+	1	NA	intron (NM_023048, intron 1 of 5)	intron (NM_023048, intron 1 of 5)	7146	NM_023048	65255	Mm.51340	NM_023048	ENSMUSG00000042607	Asb4	8430401O13Rik|AV117194|AW060255	ankyrin repeat and SOCS box-containing 4	protein-coding
mm_95196.1	chr11	43155707	43155718	+	1	NA	intron (NM_176999, intron 3 of 22)	intron (NM_176999, intron 3 of 22)	5835	NM_176999	319767	Mm.252339	NM_176999	ENSMUSG00000055415	Atp10b	5930426O13Rik|9030605H24Rik	ATPase, class V, type 10B	protein-coding
mm_18606.1	chr2	68251311	68251332	-	1	NA	intron (NM_016866, intron 16 of 17)	intron (NM_016866, intron 16 of 17)	146649	NM_020283	26877	Mm.226435	NM_020283	ENSMUSG00000034780	B3galt1	beta3Gal-T1	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 1	protein-coding
mm_43950.1	chr5	145140429	145140440	+	1	NA	promoter-TSS (NM_001033313)	promoter-TSS (NM_001033313)	-3	NM_001310770	231889	Mm.277413	NM_001008705	ENSMUSG00000038722	Bud31	C77604|EDG-2|EDG2|G10	BUD31 homolog	protein-coding
mm_18659.1	chr2	70509207	70509219	-	1	NA	exon (NM_025744, exon 1 of 13)	exon (NM_025744, exon 1 of 13)	394	NM_025744	66748	Mm.423014	NM_025744	ENSMUSG00000075302	Erich2	4933404M02Rik	glutamate rich 2	protein-coding
mm_127665.1	chr15	102520847	102520865	+	1	NA	intron (NM_009319, intron 3 of 8)	intron (NM_009319, intron 3 of 8)	2664	NM_009319	21357	Mm.291485	NM_009319	ENSMUSG00000023051	Tarbp2	Prbp|TRBP	TARBP2, RISC loading complex RNA binding subunit	protein-coding
mm_111321.1	chr12	86079020	86079035	-	1	NA	promoter-TSS (NM_009368)	promoter-TSS (NM_009368)	14	NM_009368	21809	Mm.3992	NM_009368	ENSMUSG00000021253	Tgfb3	TGF-beta-3|Tgfb-3	transforming growth factor, beta 3	protein-coding
mm_164313.1	chr15	103897563	103897582	-	1	NA	exon (NM_009267, exon 3 of 4)	exon (NM_009267, exon 3 of 4)	1728	NM_009268	20771	Mm.30276	NM_009268		Mucl1	Spt-2|Spt2	mucin-like 1	protein-coding
mm_40011.1	chr5	33018947	33018965	+	1	NA	5' UTR (NM_011738, exon 1 of 2)	5' UTR (NM_011738, exon 1 of 2)	140	NM_011738	22629	Mm.332314	NM_011738	ENSMUSG00000018965	Ywhah	-	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta polypeptide	protein-coding
mm_30363.1	chr3	151837452	151837528	-	1	NA	promoter-TSS (NM_008966)	promoter-TSS (NM_008966)	38	NM_008966	19220	Mm.331442	NM_008966	ENSMUSG00000028036	Ptgfr	AI957154|PGF|fp	prostaglandin F receptor	protein-coding
mm_110521.1	chr12	54863025	54863070	-	1	NA	promoter-TSS (NM_007688)	promoter-TSS (NM_007688)	-170	NM_007688	12632	Mm.276826	NM_007688	ENSMUSG00000062929	Cfl2	-	cofilin 2, muscle	protein-coding
mm_785.1	chr1	45330552	45330571	+	1	NA	exon (NM_009930, exon 15 of 51)	exon (NM_009930, exon 15 of 51)	19023	NM_009930	12825	Mm.249555	NM_009930	ENSMUSG00000026043	Col3a1	AW550625|Col3a-1|Tsk-2|Tsk2	collagen, type III, alpha 1	protein-coding
mm_140149.1	chr17	80113101	80113111	+	1	NA	Intergenic	Intergenic	-14365	NM_176963	319625	Mm.29098	NM_176963	ENSMUSG00000035473	Galm	A530057M15Rik|AU015645|AU020959	galactose mutarotase	protein-coding
mm_88250.1	chr10	72674222	72674355	+	1	NA	3' UTR (NM_001293683, exon 8 of 8)	3' UTR (NM_001293683, exon 8 of 8)	19442	NM_001293683	52696	Mm.62876	NM_025635	ENSMUSG00000019923	Zwint	2010007E07Rik|2600001N01Rik|D10Ertd749e|Zwint-1	ZW10 interactor	protein-coding
mm_83067.1	chr9	37553392	37553397	-	1	NA	promoter-TSS (NM_022029)	promoter-TSS (NM_022029)	-649	NM_022029	64011	Mm.335065	NM_022029	ENSMUSG00000053310	Nrgn	0710001B06Rik|AI838505|NG|NG/RC3|Pss1|R75334|RC3	neurogranin	protein-coding
mm_131964.1	chr16	24657037	24657060	+	1	NA	intron (NM_001145952, intron 4 of 11)	L2a|LINE|L2	-64807	NM_001145954	210126	Mm.209385	NM_178665	ENSMUSG00000033306	Lpp	9430020K16Rik|AA959454|AU024130|B130055L10Rik|C79715|D630048H16	LIM domain containing preferred translocation partner in lipoma	protein-coding
mm_72220.1	chr8	72688480	72688498	+	1	NA	intron (NM_176940, intron 11 of 18)	B3A|SINE|B2	-34781	NM_001113248	20467	Mm.2137	NM_009188	ENSMUSG00000031622	Sin3b	2810430C10Rik	transcriptional regulator, SIN3B (yeast)	protein-coding
mm_55917.1	chr6	83775768	83775826	-	1	NA	promoter-TSS (NM_009357)	promoter-TSS (NM_009357)	15	NM_009357	21766	Mm.28371	NM_009357	ENSMUSG00000014748	Tex261	3110001O07Rik|AA409339|AI480706|AL033351|TEG-261	testis expressed gene 261	protein-coding
mm_118682.1	chr14	22100937	22100957	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	81235	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_153322.1	chr19	38118383	38118477	-	1	NA	exon (NM_011255, exon 5 of 6)	exon (NM_011255, exon 5 of 6)	6381	NM_011255	19662	Mm.2605	NM_011255	ENSMUSG00000024990	Rbp4	Rbp-4	retinol binding protein 4, plasma	protein-coding
mm_99129.1	chr11	100319862	100319866	+	1	NA	promoter-TSS (NM_011508)	promoter-TSS (NM_011508)	-85	NM_011508	20918	Mm.13886	NM_011508	ENSMUSG00000035530	Eif1	Sui1-rs1	eukaryotic translation initiation factor 1	protein-coding
mm_75506.1	chr8	54393648	54393656	-	1	NA	Intergenic	Intergenic	136346	NM_029701	76687	Mm.86437	NM_029701	ENSMUSG00000054408	Spcs3	1810011E08Rik|SPC22/23	signal peptidase complex subunit 3 homolog (S. cerevisiae)	protein-coding
mm_624.1	chr1	40225052	40225082	+	1	NA	promoter-TSS (NM_008362)	promoter-TSS (NM_008362)	-13	NM_008362	16177	Mm.896	NM_008362	ENSMUSG00000026072	Il1r1	CD121a|CD121b|IL-1R1|IL-iR|Il1r-1	interleukin 1 receptor, type I	protein-coding
mm_165916.1	chr4	57956417	57956424	-	1	NA	promoter-TSS (NM_011660)	promoter-TSS (NM_011660)	-9	NM_011660	22166	Mm.260618	NM_011660	ENSMUSG00000028367	Txn1	ADF|AW550880|Trx1|Txn	thioredoxin 1	protein-coding
mm_16228.1	chr2	173155961	173155970	+	1	NA	exon (NM_011044, exon 6 of 10)	exon (NM_011044, exon 6 of 10)	2892	NM_011044	18534	Mm.266867	NM_011044	ENSMUSG00000027513	Pck1	AI265463|PEPCK|Pck-1	phosphoenolpyruvate carboxykinase 1, cytosolic	protein-coding
mm_34310.1	chr4	141814996	141815033	+	1	NA	TTS (NM_007919)	TTS (NM_007919)	10991	NM_007919	13706	Mm.45316	NM_007919	ENSMUSG00000058579	Cela2a	Ela-2|Ela2|Ela2a	chymotrypsin-like elastase family, member 2A	protein-coding
mm_6168.1	chr1	65071569	65071578	-	1	NA	TTS (NM_007775)	TTS (NM_007775)	1959	NM_007775	12966	Mm.491115	NM_007775	ENSMUSG00000025952	Crygc	Cryg-5	crystallin, gamma C	protein-coding
mm_158520.1	chrX	143827307	143827367	-	1	NA	promoter-TSS (NM_007603)	promoter-TSS (NM_007603)	75	NM_007603	12338	Mm.30290	NM_007603	ENSMUSG00000067276	Capn6	-	calpain 6	protein-coding
mm_57234.1	chr6	123282872	123282890	-	1	NA	3' UTR (NM_019948, exon 6 of 6)	3' UTR (NM_019948, exon 6 of 6)	6990	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_47294.1	chr5	122241383	122241407	-	1	NA	non-coding (NR_104441, exon 13 of 13)	non-coding (NR_104441, exon 13 of 13)	23065	NR_104441	654470	Mm.28804	NM_001039153	ENSMUSG00000038593	Tctn1	G730031O11Rik|Tect1	tectonic family member 1	protein-coding
mm_131376.1	chr16	13927738	13927768	+	1	NA	intron (NM_001289562, intron 1 of 3)	intron (NM_001289562, intron 1 of 3)	-12876	NM_001289563	93734	Mm.76554	NM_033564	ENSMUSG00000022679	Mpv17l	M-LP	Mpv17 transgene, kidney disease mutant-like	protein-coding
mm_126438.1	chr15	80623500	80623549	+	1	NA	promoter-TSS (NM_010815)	promoter-TSS (NM_010815)	41	NM_010815	17444	Mm.12947	NM_010815	ENSMUSG00000042351	Grap2	GRAP-2|GRB2L|GRBLG|GRID|Gads|GrbX|Grf40|GrpL|Mona|P38	GRB2-related adaptor protein 2	protein-coding
mm_105176.1	chr11	101784842	101784856	-	1	NA	intron (NM_008815, intron 1 of 12)	CpG-2651	461	NM_008815	18612	Mm.5025	NM_008815	ENSMUSG00000017724	Etv4	AW414408|Pea-3|Pea3	ets variant 4	protein-coding
mm_157250.1	chrX	19149085	19149103	-	1	NA	Intergenic	L1Md_F2|LINE|L1	-2123	NR_029807	723828		NR_029807	ENSMUSG00000065471	Mir222	Mirn222|mir-222|mmu-mir-222	microRNA 222	ncRNA
mm_47100.1	chr5	118232436	118232465	-	1	NA	exon (NM_001109902, exon 6 of 11)	exon (NM_001109902, exon 6 of 11)	12411	NM_172998	269695	Mm.320042	NM_172998	ENSMUSG00000032850	Rnft2	AW049082|B830028P19Rik|Tmem118	ring finger protein, transmembrane 2	protein-coding
mm_32801.1	chr4	117096797	117096807	+	1	NA	intron (NM_001312903, intron 1 of 21)	intron (NM_001312903, intron 1 of 21)	746	NM_008958	19207	Mm.287037	NM_008958	ENSMUSG00000028681	Ptch2	ptc2	patched 2	protein-coding
mm_151886.1	chr19	5798662	5798675	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	-2687	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_33723.1	chr4	134065867	134065893	+	1	NA	Intergenic	Intergenic	-2572	NM_001162970	230806	Mm.240080	NM_001162970	ENSMUSG00000012123	Aim1l	-	absent in melanoma 1-like	protein-coding
mm_100750.1	chr11	4231656	4231658	-	1	NA	Intergenic	Intergenic	-5128	NM_001013365	18413	Mm.131422	NM_001013365	ENSMUSG00000058755	Osm	OncoM	oncostatin M	protein-coding
mm_105357.1	chr11	103028346	103028364	-	1	NA	promoter-TSS (NM_008707)	promoter-TSS (NM_008707)	-207	NM_008707	18107	Mm.10265	NM_008707	ENSMUSG00000020936	Nmt1	AW536594	N-myristoyltransferase 1	protein-coding
mm_59641.1	chr7	28157989	28157996	+	1	NA	exon (NM_001164655, exon 16 of 20)	exon (NM_001164655, exon 16 of 20)	-11756	NM_007991	14113	Mm.4595	NM_007991	ENSMUSG00000046865	Fbl	AL022665|FIB|FLRN|RNU3IP1	fibrillarin	protein-coding
mm_70759.1	chr8	21473205	21473208	+	1	NA	Intergenic	Intergenic	-16689	NM_001177526	665956	Mm.484981	NM_001177526	ENSMUSG00000079113	Gm7861	EG665956	predicted gene 7861	protein-coding
mm_55110.1	chr6	50382903	50382913	-	1	NA	promoter-TSS (NM_027881)	promoter-TSS (NM_027881)	-71	NM_027881	71720	Mm.44153	NM_027881	ENSMUSG00000029822	Osbpl3	1200014M06Rik|6720421I08Rik|A530055M08|ORP-3|ORP3|OSBP3	oxysterol binding protein-like 3	protein-coding
mm_47894.1	chr5	134723172	134723190	-	1	NA	intron (NM_007925, intron 13 of 36)	(TGGA)n|Simple_repeat|Simple_repeat	24142	NM_007925	13717	Mm.275320	NM_007925	ENSMUSG00000029675	Eln	AI385707|AI480567|E030024M20Rik	elastin	protein-coding
mm_155142.1	chrX	52760426	52760434	+	1	NA	Intergenic	Intergenic	-15837	NR_003188	751866	Mm.381916	NR_003188		Kis2	Kis2-T1|Kis2-T2|Kis2-T3|Kis2-T4|Kis2-T5|Platr24|Xpcl1	Kaplan integration site 2	ncRNA
mm_71266.1	chr8	40918987	40919000	+	1	NA	3' UTR (NM_001044740, exon 12 of 12)	3' UTR (NM_001044740, exon 12 of 12)	-7240	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_76880.1	chr8	105606699	105606710	-	1	NA	intron (NM_001081241, intron 1 of 21)	intron (NM_001081241, intron 1 of 21)	1475	NM_001081241	75687	Mm.41261	NM_001081241	ENSMUSG00000038604	Fam65a	2310066E14Rik|AI837433	family with sequence similarity 65, member A	protein-coding
mm_136836.1	chr17	12746532	12746543	+	1	NA	intron (NR_027773, intron 1 of 2)	intron (NR_027773, intron 1 of 2)	5226	NR_027784	104103	Mm.26553	NR_002853	ENSMUSG00000078247	Airn	2810051F02Rik|2810434M15Rik|AI256653|AI597500|AW049873|Air|B930018I07Rik|D17Ertd663e|IGF2RAS	antisense Igf2r RNA	ncRNA
mm_119251.1	chr14	33923611	33923637	+	1	NA	promoter-TSS (NM_145741)	promoter-TSS (NM_145741)	37	NM_145741	14560	Mm.432071	NM_145741	ENSMUSG00000021943	Gdf10	Bmp3b	growth differentiation factor 10	protein-coding
mm_162919.1	chr10	120625705	120625709	-	1	NA	Intergenic	Intergenic	-140025	NR_038000	70874	Mm.427286	NR_038000	ENSMUSG00000044544	4921513I03Rik	-	RIKEN cDNA 4921513I03 gene	ncRNA
mm_130220.1	chr15	96131823	96131831	-	1	NA	Intergenic	RMER10A|LTR|ERVL	-50973	NR_028311	100043335	Mm.247464	NR_028311		Gm4371	EG667874|Gm8854	eukaryotic translation initiation factor 3, subunit I pseudogene	pseudo
mm_84515.1	chr9	67033975	67034001	-	1	NA	exon (NM_001164251, exon 4 of 10)	exon (NM_001164251, exon 4 of 10)	9883	NM_001164252	22003	Mm.121878	NM_024427	ENSMUSG00000032366	Tpm1	AA986836|AI854628|TM2|Tm3|Tmpa|Tpm-1|alpha-TM	tropomyosin 1, alpha	protein-coding
mm_132417.1	chr16	35093770	35093773	+	1	NA	intron (NM_023587, intron 4 of 6)	B1_Mur1|SINE|Alu	-61865	NM_001012765	224129	Mm.41137	NM_001012765	ENSMUSG00000022840	Adcy5	AW121902|Ac5	adenylate cyclase 5	protein-coding
mm_164369.1	chr16	24090172	24090180	-	1	NA	Intergenic	Intergenic	-101564	NM_009744	12053	Mm.347398	NM_009744	ENSMUSG00000022508	Bcl6	Bcl5	B cell leukemia/lymphoma 6	protein-coding
mm_93390.1	chr10	107272706	107272736	-	1	NA	5' UTR (NM_001284329, exon 1 of 6)	5' UTR (NM_001284329, exon 1 of 6)	327	NM_001284329	108030	Mm.268025	NM_001033223	ENSMUSG00000019906	Lin7a	AI848705|LIN-7A|MALS-1|TIP-33|Veli|Veli1	lin-7 homolog A (C. elegans)	protein-coding
mm_116732.1	chr13	51734645	51734667	-	1	NA	intron (NM_001281880, intron 2 of 16)	intron (NM_001281880, intron 2 of 16)	59091	NM_001281880	20354	Mm.33903	NM_013660	ENSMUSG00000021451	Sema4d	CD100|Semacl2|Semaj|Semcl2|coll-4	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D	protein-coding
mm_146657.1	chr18	11657746	11657756	-	1	NA	intron (NR_045526, intron 1 of 17)	CpG	402	NM_001081223	225182	Mm.154275	NM_175458	ENSMUSG00000041238	Rbbp8	9930104E21Rik|CtIP|RBBP-8|RIM|SAE2	retinoblastoma binding protein 8	protein-coding
mm_155023.1	chrX	42066550	42066561	+	1	NA	Intergenic	Intergenic	-1281	NM_009688	11798	Mm.259879	NM_009688	ENSMUSG00000025860	Xiap	1110015C02Rik|Aipa|Api3|Birc4|IAP3|ILP-1|MIHA	X-linked inhibitor of apoptosis	protein-coding
mm_125414.1	chr15	41788998	41789013	+	1	NA	promoter-TSS (NM_001130163)	promoter-TSS (NM_001130163)	-29	NM_001130165	170719	Mm.254267	NM_130885	ENSMUSG00000022307	Oxr1	2210416C20Rik|C7|C7B	oxidation resistance 1	protein-coding
mm_98361.1	chr11	93886246	93886259	+	1	NA	promoter-TSS (NM_134012)	promoter-TSS (NM_134012)	33	NM_134012	103537	Mm.210334	NM_134012	ENSMUSG00000059474	Mbtd1	AA408199|AI194990|hemp	mbt domain containing 1	protein-coding
mm_74047.1	chr8	122140005	122140022	+	1	NA	Intergenic	Intergenic	-142128	NM_009569	22761	Mm.3105	NM_009569	ENSMUSG00000049577	Zfpm1	FOG|Fog1	zinc finger protein, multitype 1	protein-coding
mm_98238.1	chr11	88142542	88142568	+	1	NA	intron (NM_198013, intron 1 of 10)	intron (NM_198013, intron 1 of 10)	-27010	NM_001172099	103841	Mm.374846	NM_198013	ENSMUSG00000018378	Cuedc1	AI841487|C330016O16Rik	CUE domain containing 1	protein-coding
mm_62854.1	chr7	114482707	114482716	+	1	NA	intron (NM_011055, intron 1 of 15)	intron (NM_011055, intron 1 of 15)	67457	NM_011055	18576	Mm.430730	NM_011055	ENSMUSG00000030671	Pde3b	9830102A01Rik|AI847709	phosphodiesterase 3B, cGMP-inhibited	protein-coding
mm_69812.1	chr7	141263822	141263842	-	1	NA	exon (NM_001252601, exon 8 of 10)	exon (NM_001252601, exon 8 of 10)	2592	NM_001252601	54123	Mm.3233	NM_016850	ENSMUSG00000025498	Irf7	-	interferon regulatory factor 7	protein-coding
mm_105550.1	chr11	106387781	106387797	-	1	NA	Intergenic	Intergenic	-5008	NM_010494	15896	Mm.394	NM_010494	ENSMUSG00000001029	Icam2	CD102|Icam-2|Ly-60	intercellular adhesion molecule 2	protein-coding
mm_77708.1	chr8	126591767	126591784	-	1	NA	exon (NM_001164598, exon 2 of 2)	exon (NM_001164598, exon 2 of 2)	1661	NM_001164598	270110	Mm.334918	NM_001164598	ENSMUSG00000051495	Irf2bp2	E130305N23Rik|IRF-2BP2	interferon regulatory factor 2 binding protein 2	protein-coding
mm_85056.1	chr9	90202686	90202733	-	1	NA	3' UTR (NM_194334, exon 13 of 13)	3' UTR (NM_194334, exon 13 of 13)	39731	NM_001311115	108153	Mm.102141	NM_001003911	ENSMUSG00000032363	Adamts7	ADAM-TS7|ADAMTS7B	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 7	protein-coding
mm_31263.1	chr4	45203916	45203920	+	1	NA	intron (NM_001081172, intron 1 of 15)	intron (NM_001081172, intron 1 of 15)	19012	NM_001081172	666060	Mm.24783	NM_001081172	ENSMUSG00000035615	Frmpd1	BC031840|mKIAA0967	FERM and PDZ domain containing 1	protein-coding
mm_39465.1	chr5	19226903	19226990	+	1	NA	promoter-TSS (NR_102342)	promoter-TSS (NR_102342)	-100	NM_001170746	50791	Mm.332231	NM_015823	ENSMUSG00000040003	Magi2	AIP-1|Acvri1|Acvrinp1|Acvrip1|Magi-2|S-SCAM|mKIAA0705	membrane associated guanylate kinase, WW and PDZ domain containing 2	protein-coding
mm_124878.1	chr15	10223967	10223973	+	1	NA	promoter-TSS (NM_001253781)	promoter-TSS (NM_001253781)	64	NM_001253781	19116	Mm.10516	NM_011169	ENSMUSG00000005268	Prlr	AI987712|Pr-1|Pr-3|Prlr-rs1	prolactin receptor	protein-coding
mm_145921.1	chr18	67072969	67072970	+	1	NA	Intergenic	Intergenic	-15329	NM_177137	14680	Mm.440746	NM_010307	ENSMUSG00000024524	Gnal	2610011C15Rik|9630020G10Rik|Galphaolf|Gna10|Golf	guanine nucleotide binding protein, alpha stimulating, olfactory type	protein-coding
mm_30163.1	chr3	144188913	144188946	-	1	NA	3' UTR (NM_010723, exon 5 of 5)	3' UTR (NM_010723, exon 5 of 5)	13403	NM_001161770	16911	Mm.29187	NM_010723	ENSMUSG00000028266	Lmo4	A730077C12Rik|Crp3|Etohi4	LIM domain only 4	protein-coding
mm_74067.1	chr8	122430557	122430565	+	1	NA	intron (NM_001301284, intron 1 of 4)	intron (NM_001301284, intron 1 of 4)	2379	NM_001301284	13057	Mm.271671	NM_007806	ENSMUSG00000006519	Cyba	b558|nmf333|p22-phox|p22phox	cytochrome b-245, alpha polypeptide	protein-coding
mm_50252.1	chr6	42585218	42585226	+	1	NA	Intergenic	Intergenic	12150	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_158064.1	chrX	101212865	101212884	-	1	NA	3' UTR (NM_001110310, exon 4 of 4)	3' UTR (NM_001110310, exon 4 of 4)	9689	NM_001110311	55988	Mm.206949	NM_018875	ENSMUSG00000046032	Snx12	2610001F05Rik|AW045757|SDP8	sorting nexin 12	protein-coding
mm_2864.1	chr1	131712919	131712929	+	1	NA	3' UTR (NM_145509, exon 6 of 6)	3' UTR (NM_145509, exon 6 of 6)	24229	NM_001311096	226421	Mm.44508	NM_145509	ENSMUSG00000052688	Rab7b	5430435G22Rik	RAB7B, member RAS oncogene family	protein-coding
mm_63875.1	chr7	136268878	136268886	+	1	NA	intron (NR_102277, intron 1 of 3)	MTD|LTR|ERVL-MaLR	558	NR_102277	77383	Mm.227745	NR_102277	ENSMUSG00000110027	C030029H02Rik	-	RIKEN cDNA C030029H02 gene	ncRNA
mm_51053.1	chr6	65631370	65631426	+	1	NA	3' UTR (NM_001001495, exon 8 of 8)	3' UTR (NM_001001495, exon 8 of 8)	-40213	NM_172399	68169	Mm.52392	NM_172399	ENSMUSG00000049001	Ndnf	A930038C07Rik|epidermacan	neuron-derived neurotrophic factor	protein-coding
mm_118826.1	chr14	25588496	25588530	+	1	NA	non-coding (NR_033492, exon 1 of 1)	non-coding (NR_033492, exon 1 of 1)	1709	NR_033492	77592	Mm.444871	NM_175264		4931406H21Rik	-	RIKEN cDNA 4931406H21 gene	ncRNA
mm_140246.1	chr17	84181927	84181963	+	1	NA	Intergenic	Intergenic	6002	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_93147.1	chr10	92375368	92375386	-	1	NA	promoter-TSS (NR_046027)	promoter-TSS (NR_046027)	-4	NR_046027	627800	Mm.391417	NR_046027	ENSMUSG00000098040	Gm20757	-	predicted gene, 20757	ncRNA
mm_56088.1	chr6	87335728	87335756	-	1	NA	promoter-TSS (NM_054041)	promoter-TSS (NM_054041)	33	NM_054041	69538	Mm.232525	NM_054041	ENSMUSG00000033420	Antxr1	2310008J16Rik|2810405N18Rik|Antrx1|Tem8	anthrax toxin receptor 1	protein-coding
mm_53906.1	chr6	3763619	3763624	-	1	NA	promoter-TSS (NM_001042725)	promoter-TSS (NM_001042725)	2	NM_001042725	12311	Mm.4642	NM_007588	ENSMUSG00000023964	Calcr	Clr	calcitonin receptor	protein-coding
mm_90323.1	chr10	127067169	127067181	+	1	NA	TTS (NM_025982)	TTS (NM_025982)	3086	NM_025982	67125	Mm.35650	NM_025982	ENSMUSG00000006736	Tspan31	2700085A14Rik|AW742554|Sas	tetraspanin 31	protein-coding
mm_33099.1	chr4	124700701	124700728	+	1	NA	promoter-TSS (NM_010213)	promoter-TSS (NM_010213)	15	NM_010213	14201	Mm.331856	NM_010213	ENSMUSG00000032643	Fhl3	SLIM2	four and a half LIM domains 3	protein-coding
mm_137639.1	chr17	28505741	28505752	+	1	NA	Intergenic	Intergenic	-19597	NM_010220	14229	Mm.276405	NM_010220	ENSMUSG00000024222	Fkbp5	D17Ertd592e|Dit1|FKBP-5|FKBP51	FK506 binding protein 5	protein-coding
mm_166933.1	chr7	35127912	35127937	-	1	NA	Intergenic	MIR|SINE|MIR	8631	NM_007678	12606	Mm.349667	NM_007678	ENSMUSG00000034957	Cebpa	C/ebpalpha|CBF-A|Cebp	CCAAT/enhancer binding protein (C/EBP), alpha	protein-coding
mm_32957.1	chr4	119733785	119733806	+	1	NA	Intergenic	CpG	-74850	NM_008191	14916	Mm.278	NM_008191	ENSMUSG00000032978	Guca2b	AV066530|Gcap2|Ugn	guanylate cyclase activator 2b (retina)	protein-coding
mm_17690.1	chr2	32332005	32332008	-	1	NA	intron (NM_010065, intron 10 of 20)	B1F|SINE|Alu	13546	NR_029811	387239		NR_029811	ENSMUSG00000092807	Mir199b	Mirn199b|mir-199b	microRNA 199b	ncRNA
mm_109801.1	chr12	3309685	3309702	-	1	NA	5' UTR (NM_016676, exon 1 of 6)	5' UTR (NM_016676, exon 1 of 6)	276	NM_016676	19325	Mm.378993	NM_016676	ENSMUSG00000020671	Rab10	AW107754	RAB10, member RAS oncogene family	protein-coding
mm_21350.1	chr2	157119593	157119597	-	1	NA	intron (NM_018851, intron 6 of 15)	intron (NM_018851, intron 6 of 15)	15627	NM_001139520	56045	Mm.248478	NM_018851	ENSMUSG00000027639	Samhd1	E330031J07Rik|Mg11	SAM domain and HD domain, 1	protein-coding
mm_85433.1	chr9	103761789	103761816	-	1	NA	promoter-TSS (NM_178638)	promoter-TSS (NM_178638)	35	NM_178638	81907	Mm.384704	NM_178638	ENSMUSG00000042757	Tmem108	AI462967|B130017P16Rik|R74726	transmembrane protein 108	protein-coding
mm_170880.1	chr2	20900127	20900127	+	1	NA	intron (NM_001128084, intron 3 of 24)	LSU-rRNA_Hsa|rRNA|rRNA	67594	NM_001081364	71435	Mm.28507	NM_001081364	ENSMUSG00000036591	Arhgap21	5530401C11Rik|AA416458|ARHGAP10	Rho GTPase activating protein 21	protein-coding
mm_170205.1	chr17	6961137	6961139	-	1	NA	promoter-TSS (NM_147155)	promoter-TSS (NM_147155)	18	NM_147155	380608	Mm.371734	NM_147155	ENSMUSG00000052031	Tagap1	2610315E15Rik|AA415005|FKSG15	T cell activation GTPase activating protein 1	protein-coding
mm_139167.1	chr17	47557829	47557839	+	1	NA	intron (NM_001081635, intron 1 of 6)	intron (NM_001081635, intron 1 of 6)	-35633	NM_007632	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_76406.1	chr8	84847004	84847038	-	1	NA	promoter-TSS (NM_007591)	promoter-TSS (NM_007591)	-90	NM_007591	12317	Mm.1971	NM_007591	ENSMUSG00000003814	Calr	CRT|Calregulin	calreticulin	protein-coding
mm_50985.1	chr6	63255878	63255886	+	1	NA	promoter-TSS (NM_008167)	promoter-TSS (NM_008167)	-975	NM_008167	14804	Mm.439651	NM_008167	ENSMUSG00000071424	Grid2	B230104L07Rik|GluD2|GluRdelta2|Lc|Lc<J>|MMS10-AC|Ms10ac|cpr|ho|nmf408|tpr	glutamate receptor, ionotropic, delta 2	protein-coding
mm_143880.1	chr17	84273096	84273102	-	1	NA	intron (NM_183021, intron 29 of 37)	intron (NM_183021, intron 29 of 37)	-85152	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_141860.1	chr17	34804089	34804099	-	1	NA	exon (NM_009995, exon 2 of 10)	exon (NM_009995, exon 2 of 10)	332	NM_009995	13079	Mm.440407	NM_009995	ENSMUSG00000024365	Cyp21a1	21-OH|21OH|21OHA|21OHB|CYP21OH-A|Cyp21|Cyp21-ps1|Cyp21B|Cyp21a2-ps|Cyp21a2ps|Oh21-1|Oh21-2	cytochrome P450, family 21, subfamily a, polypeptide 1	protein-coding
mm_140503.1	chr17	5058489	5058503	-	1	NA	intron (NM_001085355, intron 2 of 19)	intron (NM_001085355, intron 2 of 19)	63422	NM_001085355	239985	Mm.133401	NM_001085355	ENSMUSG00000069729	Arid1b	8030481M12|9330189K18Rik|AI836955|Ardi1b|B230217J03Rik|mKIAA1235	AT rich interactive domain 1B (SWI-like)	protein-coding
mm_11879.1	chr2	49523610	49523613	+	1	NA	intron (NM_172663, intron 4 of 13)	intron (NM_172663, intron 4 of 13)	72125	NM_172663	227867	Mm.29167	NM_172663	ENSMUSG00000069495	Epc2	5830499L14|D2Ertd694e	enhancer of polycomb homolog 2 (Drosophila)	protein-coding
mm_124304.1	chr14	103098897	103098907	-	1	NA	5' UTR (NM_001347601, exon 1 of 5)	5' UTR (NM_001347601, exon 1 of 5)	102	NM_001347601	50789	Mm.214746	NM_015822	ENSMUSG00000022124	Fbxl3	AU041772|AW212966|FBK|Fbl3a|Fbxl3a|Ovtm|Play68	F-box and leucine-rich repeat protein 3	protein-coding
mm_56903.1	chr6	119196545	119196555	-	1	NA	promoter-TSS (NM_009781)	promoter-TSS (NM_009781)	-141	NM_001255999	12288	Mm.41628	NM_009781	ENSMUSG00000051331	Cacna1c	Cav1.2|Cchl1a1|D930026N18Rik|MBC|MELC-CC	calcium channel, voltage-dependent, L type, alpha 1C subunit	protein-coding
mm_27958.1	chr3	79886164	79886173	-	1	NA	5' UTR (NM_133187, exon 1 of 4)	5' UTR (NM_133187, exon 1 of 4)	238	NM_133187	68659	Mm.427274	NM_133187	ENSMUSG00000027955	Fam198b	1110032E23Rik|2210419I08Rik|AV011458|Ened	family with sequence similarity 198, member B	protein-coding
mm_79026.1	chr9	45984926	45984943	+	1	NA	promoter-TSS (NM_008775)	promoter-TSS (NM_008775)	-63	NM_008775	18475	Mm.200859	NM_008775	ENSMUSG00000003131	Pafah1b2	AI747451|AU021353|Pafahb|mus[b]	platelet-activating factor acetylhydrolase, isoform 1b, subunit 2	protein-coding
mm_10382.1	chr2	12301209	12301217	+	1	NA	promoter-TSS (NR_040353)	promoter-TSS (NR_040353)	-33	NR_040353	338535	Mm.483275	NR_040353	ENSMUSG00000086843	E030013I19Rik	-	RIKEN cDNA E030013I19 gene	ncRNA
mm_12082.1	chr2	59812015	59812041	+	1	NA	intron (NM_198294, intron 16 of 26)	intron (NM_198294, intron 16 of 26)	70578	NM_001159636	72137	Mm.288734	NM_028118	ENSMUSG00000026988	Wdsub1	1700048E19Rik|2610014F08Rik	WD repeat, SAM and U-box domain containing 1	protein-coding
mm_5431.1	chr1	34560976	34560982	-	1	NA	promoter-TSS (NM_009356)	promoter-TSS (NM_009356)	-36	NM_009356	21756	Mm.14418	NM_009356	ENSMUSG00000037529	Prss40	Tesp2	protease, serine 40	protein-coding
mm_151671.1	chr19	4190960	4190976	-	1	NA	promoter-TSS (NM_178650)	promoter-TSS (NM_178650)	79	NM_178650	108995	Mm.288312	NM_178650	ENSMUSG00000040247	Tbc1d10c	1810062O14Rik|AI428527	TBC1 domain family, member 10c	protein-coding
mm_127152.1	chr15	98568023	98568036	+	1	NA	promoter-TSS (NM_009833)	promoter-TSS (NM_009833)	-393	NM_009833	12455	Mm.29941	NM_009833	ENSMUSG00000011960	Ccnt1	2810478G24Rik|AI115585|CycT1	cyclin T1	protein-coding
mm_107054.1	chr12	16653570	16653583	+	1	NA	exon (NM_008747, exon 1 of 4)	exon (NM_008747, exon 1 of 4)	106	NM_008747	18217	Mm.281715	NM_008747	ENSMUSG00000020591	Ntsr2	NT2R|NTRL	neurotensin receptor 2	protein-coding
mm_1503.1	chr1	72237417	72237421	+	1	NA	Intergenic	Intergenic	-25112	NM_001005423	381269	Mm.422636	NM_001005423	ENSMUSG00000039395	Mreg	Gm974|Wdt2|dsu	melanoregulin	protein-coding
mm_41678.1	chr5	99978504	99978570	+	1	NA	exon (NM_007516, exon 1 of 8)	exon (NM_007516, exon 1 of 8)	401	NM_001077266	11991	Mm.150231	NM_007516	ENSMUSG00000000568	Hnrnpd	Auf1|Hnrpd	heterogeneous nuclear ribonucleoprotein D	protein-coding
mm_116584.1	chr13	47106177	47106206	-	1	NA	promoter-TSS (NM_025900)	promoter-TSS (NM_025900)	30	NM_025900	110052	Mm.131150	NM_025900	ENSMUSG00000021377	Dek	1810019E15Rik|D13H6S231E	DEK oncogene (DNA binding)	protein-coding
mm_135528.1	chr16	49255789	49255795	-	1	NA	Intergenic	Intergenic	198306	NM_001166210	667772	Mm.301387	NM_001166210	ENSMUSG00000092009	Myh15	EG667772	myosin, heavy chain 15	protein-coding
mm_140304.1	chr17	85624210	85624222	+	1	NA	3' UTR (NM_011381, exon 2 of 2)	3' UTR (NM_011381, exon 2 of 2)	3382	NM_011381	20473	Mm.370208	NM_011381	ENSMUSG00000038805	Six3	E130112M24Rik|Six3a|Six3alpha|Six3b|Six3beta	sine oculis-related homeobox 3	protein-coding
mm_71482.1	chr8	46739754	46739791	+	1	NA	promoter-TSS (NM_008391)	promoter-TSS (NM_008391)	27	NM_008391	16363	Mm.1149	NM_008391	ENSMUSG00000031627	Irf2	9830146E22Rik|AI646973|Irf-2	interferon regulatory factor 2	protein-coding
mm_143642.1	chr17	79354883	79354937	-	1	NA	5' UTR (NM_026514, exon 1 of 2)	5' UTR (NM_026514, exon 1 of 2)	181	NM_026514	260409	Mm.140601	NM_026514	ENSMUSG00000036533	Cdc42ep3	3200001F04Rik|AA986861|Borg2|Cep3|UB1	CDC42 effector protein (Rho GTPase binding) 3	protein-coding
mm_83705.1	chr9	50699001	50699028	-	1	NA	intron (NM_178118, intron 5 of 19)	CpG	28970	NM_178118	330938	Mm.82598	NM_178118	ENSMUSG00000032064	Dixdc1	4930563F16Rik|BC048182|Ccd1|Ccd1Aalpha1L|Ccd1Abeta1L|Ccd1BalphaL|Ccd1BbetaL|Ccd1CL|mKIAA1735	DIX domain containing 1	protein-coding
mm_77786.1	chr9	3025609	3025628	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	13125	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_169032.1	chr13	12702235	12702241	+	1	NA	Intergenic	CpG	-51843	NR_003568	664862	Mm.415635	NR_003568		Gpr137b-ps	2310041G17Rik|ENSMUSG00000075118	G protein-coupled receptor 137B, pseudogene	pseudo
mm_99421.1	chr11	102317005	102317015	+	1	NA	intron (NM_001302955, intron 1 of 19)	CpG	277	NM_001044383	21429	Mm.2845	NM_011551	ENSMUSG00000020923	Ubtf	A930005G04Rik|NOR-90|Tcfubf|UBF|UBF-1|UBF1	upstream binding transcription factor, RNA polymerase I	protein-coding
mm_28079.1	chr3	84480462	84480470	-	1	NA	promoter-TSS (NM_001205355)	promoter-TSS (NM_001205355)	-27	NM_001033301	229474	Mm.331107	NM_001033301	ENSMUSG00000041842	Fhdc1	6330505N24Rik|Gm126	FH2 domain containing 1	protein-coding
mm_36664.1	chr4	95051262	95051312	-	1	NA	5' UTR (NM_010591, exon 1 of 1)	5' UTR (NM_010591, exon 1 of 1)	935	NM_010591	16476	Mm.275071	NM_010591	ENSMUSG00000052684	Jun	AP-1|Junc|c-jun	jun proto-oncogene	protein-coding
mm_10938.1	chr2	25469005	25469014	+	1	NA	exon (NM_008963, exon 2 of 7)	exon (NM_008963, exon 2 of 7)	740	NM_008963	19215	Mm.1008	NM_008963	ENSMUSG00000015090	Ptgds	21kDa|L-PGDS|PGD2|PGDS|PGDS2|Ptgs3	prostaglandin D2 synthase (brain)	protein-coding
mm_157047.1	chrX	8015569	8015581	-	1	NA	intron (NM_027227, intron 1 of 3)	B2_Mm2|SINE|B2	2917	NM_027227	69824	Mm.279756	NM_027227	ENSMUSG00000031163	Glod5	2010001H14Rik|AV061890	glyoxalase domain containing 5	protein-coding
mm_162606.1	chr1	183221514	183221527	-	1	NA	promoter-TSS (NM_001278219)	promoter-TSS (NM_001278219)	9	NM_001278218	68897	Mm.327216	NM_026866	ENSMUSG00000030768	Disp1	1190008H24Rik|DispA	dispatched RND transporter family member 1	protein-coding
mm_49021.1	chr6	4759493	4759504	+	1	NA	3' UTR (NM_130877, exon 2 of 2)	3' UTR (NM_130877, exon 2 of 2)	12192	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_161487.1	chr15	84732877	84732877	+	1	NA	intron (NM_001205334, intron 2 of 12)	intron (NM_001205334, intron 2 of 12)	-12611	NR_040347	328576	Mm.400211	NR_040347		Gm20556	A430075N02	predicted gene, 20556	ncRNA
mm_106679.1	chr11	121956721	121956733	-	1	NA	Intergenic	Intergenic	126509	NM_029049	74675	Mm.61213	NM_029049	ENSMUSG00000039198	Ptchd3	4930451E13Rik|4933440L20Rik|RNDEu-3	patched domain containing 3	protein-coding
mm_159892.1	chr6	29411715	29411715	+	1	NA	exon (NM_001201378, exon 8 of 15)	exon (NM_001201378, exon 8 of 15)	12789	NM_001201378	232664	Mm.251303	NM_145574	ENSMUSG00000029769	Ccdc136	4921511K06Rik|BC006583	coiled-coil domain containing 136	protein-coding
mm_104931.1	chr11	100046543	100046549	-	1	NA	TTS (NM_010659)	TTS (NM_010659)	4005	NM_010659	16660	Mm.439673	NM_010659	ENSMUSG00000048981	Krt31	Ha1|Kha1|Krt1-1|MKHA-1	keratin 31	protein-coding
mm_156610.1	chrX	153360092	153360107	+	1	NA	intron (NM_173780, intron 2 of 6)	intron (NM_173780, intron 2 of 6)	122054	NM_173780	245671	Mm.260751	NM_173780	ENSMUSG00000041649	Klf8	A830097P10Rik|BKLF3|ZNF74	Kruppel-like factor 8	protein-coding
mm_19112.1	chr2	79456751	79456761	-	1	NA	promoter-TSS (NM_010894)	promoter-TSS (NM_010894)	-120	NM_010894	18012	Mm.4636	NM_010894	ENSMUSG00000034701	Neurod1	BETA2|BHF-1|Nd1|Neurod|bHLHa3	neurogenic differentiation 1	protein-coding
mm_79823.1	chr9	64397722	64397726	+	1	NA	intron (NM_172522, intron 1 of 22)	intron (NM_172522, intron 1 of 22)	12098	NM_001134399	214058	Mm.127721	NM_172522	ENSMUSG00000036466	Megf11	2410080H04Rik|D130061K05	multiple EGF-like-domains 11	protein-coding
mm_134277.1	chr16	14159174	14159196	-	1	NA	promoter-TSS (NR_030252)	promoter-TSS (NR_030252)	89	NM_001081154	223989	Mm.85442	NM_001081154	ENSMUSG00000060657	Marf1	4921513D23Rik|BC031575|C87306|E030019O05|Lkap|mKIAA0430	meiosis arrest female 1	protein-coding
mm_38022.1	chr4	133756781	133756794	-	1	NA	Intergenic	CpG	-3176	NM_001080819	93760	Mm.22478	NM_001080819	ENSMUSG00000007880	Arid1a	1110030E03Rik|BAF250a|Osa1|Smarcf1	AT rich interactive domain 1A (SWI-like)	protein-coding
mm_17516.1	chr2	29251428	29251442	-	1	NA	intron (NR_029460, intron 1 of 1)	intron (NR_029460, intron 1 of 1)	1558	NR_029460	76220	Mm.330108	NR_029460	ENSMUSG00000079499	6530402F18Rik	mKIAA1857	RIKEN cDNA 6530402F18 gene	ncRNA
mm_20110.1	chr2	121140372	121140394	-	1	NA	promoter-TSS (NM_001290812)	promoter-TSS (NM_001290812)	-45	NM_001290811	75894	Mm.384805	NM_029475	ENSMUSG00000027259	Adal	4930578F03Rik	adenosine deaminase-like	protein-coding
mm_154516.1	chrM	12685	12750	-	1	NA	NA	Intergenic	NA	NA								
mm_115869.1	chr13	21501449	21501458	-	1	NA	Intergenic	L2c|LINE|L2	5071	NR_026798	100038371	Mm.133328	NR_026798		Zfp389	ENSMUSG00000075041|OTTMUSG00000018077	zinc finger protein 389	pseudo
mm_6268.1	chr1	69548787	69548792	-	1	NA	intron (NM_011770, intron 5 of 7)	intron (NM_011770, intron 5 of 7)	137171	NM_011770	22779	Mm.106343	NM_011770	ENSMUSG00000025997	Ikzf2	A730095J18Rik|Helios|Zfpn1a2|Znfn1a2	IKAROS family zinc finger 2	protein-coding
mm_156167.1	chrX	130051455	130051455	+	1	NA	intron (NM_172493, intron 19 of 26)	intron (NM_172493, intron 19 of 26)	301713	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diaph2	Dia3|Diap2|Drf2|E430022I22Rik	diaphanous related formin 2	protein-coding
mm_171120.1	chr3	141766617	141766620	-	1	NA	intron (NM_001293561, intron 5 of 16)	intron (NM_001293561, intron 5 of 16)	164970	NM_001277218	12167	Mm.39089	NM_007560	ENSMUSG00000052430	Bmpr1b	AI385617|ALK-6|AV355320|Acvrlk6|Alk6|BMPR-1B|BMPR-IB|CFK-43a|SKR6	bone morphogenetic protein receptor, type 1B	protein-coding
mm_75073.1	chr8	33844898	33844911	-	1	NA	intron (NM_001042674, intron 4 of 7)	intron (NM_001042674, intron 4 of 7)	84959	NM_019733	19663	Mm.323997	NM_019733	ENSMUSG00000031586	Rbpms	2010300K22Rik|2700019M19Rik|AU017537|RBP-MS|hermes	RNA binding protein gene with multiple splicing	protein-coding
mm_158899.1	chr1	30863250	30863250	-	1	NA	promoter-TSS (NM_001081080)	promoter-TSS (NM_001081080)	6	NM_001081080	213109	Mm.194486	NM_025871	ENSMUSG00000048874	Phf3	2310061N19Rik|mKIAA0244	PHD finger protein 3	protein-coding
mm_131201.1	chr16	8619491	8619499	+	1	NA	3' UTR (NM_001170978, exon 15 of 15)	3' UTR (NM_001170978, exon 15 of 15)	18206	NM_025708	66690	Mm.10068	NM_025708	ENSMUSG00000043140	Tmem186	2810440M13Rik|4432406C05Rik|AI648175|AW210586	transmembrane protein 186	protein-coding
mm_111409.1	chr12	91330220	91330222	-	1	NA	intron (NM_181815, intron 9 of 25)	intron (NM_181815, intron 9 of 25)	54188	NM_181815	75216	Mm.312204	NM_181815	ENSMUSG00000061533	Cep128	4930534B04Rik|5430424K18Rik|AI449708|AI480494|E230024F20	centrosomal protein 128	protein-coding
mm_51846.1	chr6	90363301	90363317	+	1	NA	3' UTR (NM_144940, exon 20 of 20)	3' UTR (NM_144940, exon 20 of 20)	-6185	NM_173002	80292	Mm.100116	NM_030260	ENSMUSG00000034430	Zxdc	A930012H20|B930086F11Rik|BC003332	ZXD family zinc finger C	protein-coding
mm_52007.1	chr6	93018521	93018524	+	1	NA	intron (NR_015530, intron 1 of 2)	intron (NR_015530, intron 1 of 2)	77940	NR_015530	330385	Mm.483472	NR_015530	ENSMUSG00000097462	9530026P05Rik	B430306B02	RIKEN cDNA 9530026P05 gene	ncRNA
mm_41664.1	chr5	99336729	99336741	+	1	NA	intron (NR_030692, intron 3 of 3)	intron (NR_030692, intron 3 of 3)	-83808	NM_145839	320292	Mm.259074	NM_145839	ENSMUSG00000089809	Rasgef1b	4732452O09Rik|GPIgamma4|Gpig4	RasGEF domain family, member 1B	protein-coding
mm_38622.1	chr4	142048532	142048540	-	1	NA	intron (NM_145402, intron 1 of 2)	MLT1J|LTR|ERVL-MaLR	30638	NR_131014	78917	Mm.139995	NR_131014	ENSMUSG00000085761	4930455G09Rik	-	RIKEN cDNA 4930455G09 gene	ncRNA
mm_2707.1	chr1	128044481	128044487	+	1	NA	intron (NM_027678, intron 3 of 20)	intron (NM_027678, intron 3 of 20)	57987	NM_027678	226409	Mm.425048	NM_027678	ENSMUSG00000036086	Zranb3	4933425L19Rik|AH2|AI316834|C730006D09	zinc finger, RAN-binding domain containing 3	protein-coding
mm_98782.1	chr11	96830191	96830216	+	1	NA	promoter-TSS (NM_008686)	promoter-TSS (NM_008686)	-235	NM_008686	18023	Mm.6743	NM_008686	ENSMUSG00000038615	Nfe2l1	AA408798|AW212678|LCR-F1|Lcrf1|NRF1|TCF-11|TCF11	nuclear factor, erythroid derived 2,-like 1	protein-coding
mm_152340.1	chr19	9982513	9982531	-	1	NA	promoter-TSS (NM_010239)	promoter-TSS (NM_010239)	-124	NM_010239	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
mm_147249.1	chr18	38585008	38585008	-	1	NA	Intergenic	Intergenic	16260	NM_011898	24066	Mm.42038	NM_011898	ENSMUSG00000024427	Spry4	A030006O18Rik|sprouty4	sprouty homolog 4 (Drosophila)	protein-coding
mm_133046.1	chr16	57569703	57569724	+	1	NA	exon (NM_001040397, exon 5 of 5)	exon (NM_001040397, exon 5 of 5)	20471	NM_001177871	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding
mm_68104.1	chr7	102017654	102017671	-	1	NA	5' UTR (NM_010531, exon 2 of 7)	5' UTR (NM_010531, exon 2 of 7)	493	NM_010531	16068	Mm.422756	NM_010531	ENSMUSG00000070427	Il18bp	IL-18BP|Igifbp|MC54L	interleukin 18 binding protein	protein-coding
mm_71505.1	chr8	46818813	46818850	+	1	NA	exon (NM_008391, exon 6 of 9)	exon (NM_008391, exon 6 of 9)	79086	NM_008391	16363	Mm.1149	NM_008391	ENSMUSG00000031627	Irf2	9830146E22Rik|AI646973|Irf-2	interferon regulatory factor 2	protein-coding
mm_55131.1	chr6	50654439	50654448	-	1	NA	promoter-TSS (NM_021892)	promoter-TSS (NM_021892)	-50	NM_021892	60531	Mm.157158	NM_021892	ENSMUSG00000029831	Npvf	Rfrp	neuropeptide VF precursor	protein-coding
mm_136048.1	chr16	78576348	78576397	-	1	NA	5' UTR (NM_001252438, exon 1 of 5)	5' UTR (NM_001252438, exon 1 of 5)	316	NM_001252438	67102	Mm.37332	NM_025967	ENSMUSG00000022864	D16Ertd472e	1700010I10Rik|2310009O17Rik|E330003K22Rik|Eurl	DNA segment, Chr 16, ERATO Doi 472, expressed	protein-coding
mm_54442.1	chr6	34419473	34419483	-	1	NA	exon (NM_009731, exon 6 of 10)	exon (NM_009731, exon 6 of 10)	7116	NM_009731	11997	Mm.482073	NM_009731	ENSMUSG00000052131	Akr1b7	AR|Avdp|MVDP	aldo-keto reductase family 1, member B7	protein-coding
mm_169328.1	chr14	117546575	117546576	+	1	NA	intron (NM_001079844, intron 3 of 9)	L1Md_A|LINE|L1	407272	NR_105747	102465148		NR_105747	ENSMUSG00000098648	Mir6239	Gm28025|mmu-mir-6239	microRNA 6239	ncRNA
mm_17267.1	chr2	26021680	26021779	-	1	NA	promoter-TSS (NM_133835)	promoter-TSS (NM_133835)	31	NM_133835	98766	Mm.247824	NM_133835	ENSMUSG00000036352	Ubac1	1110033G07Rik|AA407978|GBDR1|Gdbr1|Kpc2|Ubadc1	ubiquitin associated domain containing 1	protein-coding
mm_113317.1	chr13	30764788	30764792	+	1	NA	3' UTR (NM_013674, exon 9 of 9)	3' UTR (NM_013674, exon 9 of 9)	15557	NM_013674	16364	Mm.4677	NM_013674	ENSMUSG00000021356	Irf4	AI385587|IRF-4|LSIRF|NF-EM5|Spip	interferon regulatory factor 4	protein-coding
mm_77907.1	chr9	7349201	7349227	+	1	NA	intron (NM_001320077, intron 3 of 10)	B4A|SINE|B4	1840	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_31809.1	chr4	65617673	65617681	+	1	NA	intron (NM_019514, intron 15 of 21)	(T)n|Simple_repeat|Simple_repeat	12691	NM_001161782	69807	Mm.22786	NM_053084	ENSMUSG00000051675	Trim32	1810045E12Rik|3f3|BBS11|Zfp117	tripartite motif-containing 32	protein-coding
mm_91555.1	chr10	39960173	39960187	-	1	NA	promoter-TSS (NM_001173500)	promoter-TSS (NM_001173500)	-27	NM_001173500	100041085	Mm.332530	NM_001173500	ENSMUSG00000071335	Mfsd4b3	G630090E17Rik|Naglt1c	major facilitator superfamily domain containing 4B3	protein-coding
mm_138372.1	chr17	35001381	35001423	+	1	NA	promoter-TSS (NM_033075)	promoter-TSS (NM_033075)	495	NM_011690	22321	Mm.28420	NM_011690	ENSMUSG00000007029	Vars	Bat6|D17H6S56E|G7a|Vars2	valyl-tRNA synthetase	protein-coding
mm_90864.1	chr10	8886034	8886076	-	1	NA	promoter-TSS (NM_175155)	promoter-TSS (NM_175155)	15	NM_175155	70097	Mm.338275	NM_175155	ENSMUSG00000015305	Sash1	1100001C18Rik|2500002E12Rik|A330076K04Rik|mKIAA0790	SAM and SH3 domain containing 1	protein-coding
mm_133819.1	chr16	95719914	95719926	+	1	NA	3' UTR (NM_011809, exon 10 of 10)	3' UTR (NM_011809, exon 10 of 10)	17513	NM_011809	23872	Mm.290207	NM_011809	ENSMUSG00000022895	Ets2	AU022856|Ets-2	E26 avian leukemia oncogene 2, 3' domain	protein-coding
mm_134026.1	chr16	5009159	5009197	-	1	NA	TTS (NM_001253803)	TTS (NM_001253803)	1862	NR_045596	432995	Mm.271618	NM_001253796	ENSMUSG00000096215	Smim22	EG432995|Gm5480	small integral membrane protein 22	protein-coding
mm_101051.1	chr11	8664044	8664064	-	1	NA	intron (NM_001083587, intron 1 of 30)	intron (NM_001083587, intron 1 of 30)	481	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_125599.1	chr15	59653086	59653133	+	1	NA	intron (NM_144549, intron 2 of 2)	intron (NM_144549, intron 2 of 2)	4455	NM_144549	211770	Mm.40298	NM_144549	ENSMUSG00000032501	Trib1	A530090O15Rik|TRB-1|Trb1	tribbles pseudokinase 1	protein-coding
mm_14223.1	chr2	127363225	127363242	+	1	NA	promoter-TSS (NM_009633)	promoter-TSS (NM_009633)	-53	NM_009633	11552	Mm.347390	NM_009633	ENSMUSG00000058620	Adra2b	Adra-2b|[a]2B|a2b-AR|alpha2-C2|alpha2B	adrenergic receptor, alpha 2b	protein-coding
mm_122786.1	chr14	54413916	54413937	-	1	NA	5' UTR (NM_011405, exon 3 of 12)	5' UTR (NM_011405, exon 3 of 12)	3753	NM_001253679	20540	Mm.142455	NM_011405	ENSMUSG00000000958	Slc7a7	AI790233|my+lat1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 7	protein-coding
mm_142734.1	chr17	48387967	48387992	-	1	NA	3' UTR (NM_010913, exon 9 of 9)	3' UTR (NM_010913, exon 9 of 9)	12601	NM_001347402	18044	Mm.4929	NM_010913	ENSMUSG00000023994	Nfya	AA407810|Cbf-b|SEZ-10|SEZ10	nuclear transcription factor-Y alpha	protein-coding
mm_1581.1	chr1	74284489	74284499	+	1	NA	promoter-TSS (NM_025580)	promoter-TSS (NM_025580)	244	NM_146110	227290	Mm.379371	NM_146110	ENSMUSG00000006299	Aamp	AU040907|Aamp-rs	angio-associated migratory protein	protein-coding
mm_68902.1	chr7	126453069	126453098	-	1	NA	exon (NM_007504, exon 11 of 23)	exon (NM_007504, exon 11 of 23)	9990	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_153845.1	chr19	46332871	46332903	-	1	NA	intron (NM_001164291, intron 1 of 8)	intron (NM_001164291, intron 1 of 8)	4703	NM_133694	68431	Mm.19973	NM_133694	ENSMUSG00000025226	Fbxl15	0710008C12Rik|Fbxo37	F-box and leucine-rich repeat protein 15	protein-coding
mm_7644.1	chr1	128128915	128128927	-	1	NA	intron (NM_181750, intron 1 of 26)	intron (NM_181750, intron 1 of 26)	25615	NM_181750	226412	Mm.221041	NM_181750	ENSMUSG00000056211	R3hdm1	R3hdm	R3H domain containing 1	protein-coding
mm_107536.1	chr12	40560266	40560279	+	1	NA	intron (NM_172803, intron 1 of 52)	intron (NM_172803, intron 1 of 52)	114219	NM_172803	238130	Mm.341423	NM_172803	ENSMUSG00000035954	Dock4	5330406C03|6330411N01Rik|AF263288|C030023J22|mKIAA0716	dedicator of cytokinesis 4	protein-coding
mm_13115.1	chr2	91650117	91650133	+	1	NA	promoter-TSS (NM_001145902)	promoter-TSS (NM_001145902)	7	NR_027371	228359	Mm.22413	NM_146124	ENSMUSG00000027247	Arhgap1	B230365D05Rik|C76222|Cdc42GAP|p50rhoGAP	Rho GTPase activating protein 1	protein-coding
mm_5696.1	chr1	43186785	43186792	-	1	NA	intron (NM_001289533, intron 1 of 5)	RMER10A|LTR|ERVL	9973	NM_001289533	14200	Mm.6799	NM_010212	ENSMUSG00000008136	Fhl2	FHL-2|SLIM-3|SLIM3	four and a half LIM domains 2	protein-coding
mm_6974.1	chr1	86351030	86351037	-	1	NA	TTS (NR_106184)	TTS (NR_106184)	252	NR_028478	100303740	Mm.154378	NR_028478	ENSMUSG00000064837	Snora75	MBI-55	small nucleolar RNA, H/ACA box 75	snoRNA
mm_133233.1	chr16	77013778	77013788	+	1	NA	promoter-TSS (NM_013918)	promoter-TSS (NM_013918)	-286	NM_013918	30940	Mm.40986	NM_013918	ENSMUSG00000022867	Usp25	-	ubiquitin specific peptidase 25	protein-coding
mm_120054.1	chr14	56672402	56672413	+	1	NA	exon (NM_023773, exon 2 of 14)	exon (NM_023773, exon 2 of 14)	4159	NM_023773	75339	Mm.152466	NM_023773	ENSMUSG00000079184	Mphosph8	1500035L22Rik|4930548G07Rik|AU040635	M-phase phosphoprotein 8	protein-coding
mm_106043.1	chr11	116079440	116079467	-	1	NA	3' UTR (NM_016852, exon 8 of 8)	3' UTR (NM_016852, exon 8 of 8)	-1492	NM_001009573	70450	Mm.259460	NM_001009573	ENSMUSG00000057948	Unc13d	2610108D09Rik|Jinx|Munc13-4|mFLJ00067	unc-13 homolog D (C. elegans)	protein-coding
mm_5171.1	chr1	10232969	10233000	-	1	NA	promoter-TSS (NM_001102430)	promoter-TSS (NM_001102430)	-314	NM_001102430	211673	Mm.229141	NM_001102430	ENSMUSG00000067851	Arfgef1	ARFGEP1|BIG1|D130059B05Rik|D730028O18Rik|P200	ADP-ribosylation factor guanine nucleotide-exchange factor 1(brefeldin A-inhibited)	protein-coding
mm_131622.1	chr16	19765062	19765066	+	1	NA	intron (NM_001159407, intron 3 of 5)	intron (NM_001159407, intron 3 of 5)	4830	NM_001159407	108105	Mm.33935	NM_054052	ENSMUSG00000022686	B3gnt5	beta3GnT5	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5	protein-coding
mm_130266.1	chr15	96688325	96688343	-	1	NA	3' UTR (NM_175121, exon 16 of 16)	3' UTR (NM_175121, exon 16 of 16)	11364	NM_175121	67760	Mm.46754	NM_175121	ENSMUSG00000022462	Slc38a2	5033402L14Rik|AI316867|ATA2|SAT2|mKIAA1382	solute carrier family 38, member 2	protein-coding
mm_2120.1	chr1	87891910	87891921	+	1	NA	intron (NM_177646, intron 3 of 29)	intron (NM_177646, intron 3 of 29)	-37616	NR_136921	100503175	Mm.426422	NR_136921	ENSMUSG00000101942	Gm19582	-	predicted gene, 19582	ncRNA
mm_50334.1	chr6	48467829	48467838	+	1	NA	intron (NM_173428, intron 42 of 102)	intron (NM_173428, intron 42 of 102)	19604	NM_173428	243369	Mm.25039	NM_173428	ENSMUSG00000029797	Sspo	C79529|Scospondin	SCO-spondin	protein-coding
mm_109483.1	chr12	111429184	111429260	+	1	NA	intron (NM_001289487, intron 12 of 13)	intron (NM_001289487, intron 12 of 13)	11777	NM_001289488	74190	Mm.248640	NM_028807	ENSMUSG00000021280	Exoc3l4	1200009I06Rik|1600013K19Rik	exocyst complex component 3-like 4	protein-coding
mm_45240.1	chr5	53707533	53707590	-	1	NA	5' UTR (NM_009827, exon 1 of 5)	5' UTR (NM_009827, exon 1 of 5)	143	NM_009827	12425	Mm.3521	NM_009827	ENSMUSG00000029193	Cckar	AW106902	cholecystokinin A receptor	protein-coding
mm_132960.1	chr16	50072606	50072610	+	1	NA	intron (NR_045935, intron 1 of 3)	intron (NR_045935, intron 1 of 3)	244	NR_045935	224180	Mm.146439	NM_175010		Gm4827	B130050K08|EG224180	predicted gene 4827	ncRNA
mm_172684.1	chr8	55567297	55567307	-	1	NA	Intergenic	MMVL30-int|LTR|ERV1	339662	NM_175939	244486	Mm.67684	NM_175939	ENSMUSG00000046258	Adam29	-	a disintegrin and metallopeptidase domain 29	protein-coding
mm_97880.1	chr11	83224440	83224491	+	1	NA	non-coding (NR_015519, exon 3 of 4)	non-coding (NR_015519, exon 3 of 4)	889	NR_015519	100043636	Mm.295569	NR_015519	ENSMUSG00000087107	AI662270	AW496474	expressed sequence AI662270	ncRNA
mm_76656.1	chr8	93197772	93197788	-	1	NA	promoter-TSS (NM_053200)	promoter-TSS (NM_053200)	24	NM_053200	104158	Mm.292803	NM_053200	ENSMUSG00000056973	Ces1d	Ces3|TGH	carboxylesterase 1D	protein-coding
mm_70141.1	chr7	143423757	143423760	-	1	NA	intron (NM_008434, intron 15 of 15)	intron (NM_008434, intron 15 of 15)	37292	NM_009876	12577	Mm.168789	NM_009876	ENSMUSG00000037664	Cdkn1c	AL024410|CDKI|Kip2|p57(kip2)|p57Kip2	cyclin-dependent kinase inhibitor 1C (P57)	protein-coding
mm_83092.1	chr9	40321162	40321172	-	1	NA	intron (NM_172768, intron 4 of 19)	intron (NM_172768, intron 4 of 19)	-12305	NR_040728	73558	Mm.398307	NR_040728		1700110K17Rik	-	RIKEN cDNA 1700110K17 gene	ncRNA
mm_31750.1	chr4	63344651	63344657	+	1	NA	promoter-TSS (NM_008768)	promoter-TSS (NM_008768)	98	NM_008768	18405	Mm.4777	NM_008768	ENSMUSG00000039196	Orm1	Agp-1|Agp-2|Orm-1	orosomucoid 1	protein-coding
mm_125258.1	chr15	35371074	35371094	+	1	NA	promoter-TSS (NM_177151)	promoter-TSS (NM_177151)	-462	NM_177151	666173	Mm.309250	NM_177151	ENSMUSG00000037646	Vps13b	1810042B05Rik|2310042E16Rik|4732488H20|C330002D13Rik|C87206|Coh1|D230005K13|mKIAA0532|mKIAA5032	vacuolar protein sorting 13B	protein-coding
mm_61644.1	chr7	80372452	80372455	+	1	NA	Intergenic	MLT1A0|LTR|ERVL-MaLR	-1078	NM_172903	140481	Mm.269245	NM_172903	ENSMUSG00000038886	Man2a2	1700052O22Rik|4931438M07Rik|AI480988|MX|Man IIx	mannosidase 2, alpha 2	protein-coding
mm_138511.1	chr17	35236671	35236679	+	1	NA	promoter-TSS (NM_010909)	promoter-TSS (NM_010909)	79	NM_023179	66237	Mm.396107	NM_023179	ENSMUSG00000024403	Atp6v1g2	1500002D01Rik|Atp6g2|NG38|VAG2	ATPase, H+ transporting, lysosomal V1 subunit G2	protein-coding
mm_31976.1	chr4	88353901	88353913	+	1	NA	intron (NM_001081184, intron 28 of 43)	intron (NM_001081184, intron 28 of 43)	85019	NM_025760	66775	Mm.386788	NM_025760	ENSMUSG00000028497	Hacd4	4933428I03Rik|Hcad4|Ptplad2	3-hydroxyacyl-CoA dehydratase 4	protein-coding
mm_114498.1	chr13	69959885	69959903	+	1	NA	promoter-TSS (NR_138559)	promoter-TSS (NR_138559)	61	NR_138559	67550	Mm.158159	NR_138559		4933416O17Rik	-	RIKEN cDNA 4933416O17 gene	ncRNA
mm_80572.1	chr9	83939125	83939137	+	1	NA	intron (NM_001305935, intron 1 of 10)	RMER6D|LTR|ERVK	-9650	NM_199195	12040	Mm.12819	NM_199195	ENSMUSG00000032263	Bckdhb	BCKDE1B|BCKDH E1-beta	branched chain ketoacid dehydrogenase E1, beta polypeptide	protein-coding
mm_149327.1	chr19	10842844	10842855	+	1	NA	5' UTR (NM_023044, exon 1 of 8)	5' UTR (NM_023044, exon 1 of 8)	305	NM_023044	65221	Mm.27387	NM_023044	ENSMUSG00000024737	Slc15a3	Ci1|cI-1	solute carrier family 15, member 3	protein-coding
mm_113501.1	chr13	37543058	37543073	+	1	NA	Intergenic	Intergenic	197720	NM_010745	17084	Mm.2639	NM_010745	ENSMUSG00000021423	Ly86	MD-1|MD1|ly86_tv2	lymphocyte antigen 86	protein-coding
mm_48456.1	chr5	140760498	140760518	-	1	NA	3' UTR (NM_010302, exon 4 of 4)	3' UTR (NM_010302, exon 4 of 4)	36381	NM_173405	231842	Mm.491298	NM_173405	ENSMUSG00000050022	Amz1	5330426I05|6530401C20Rik	archaelysin family metallopeptidase 1	protein-coding
mm_140821.1	chr17	23586215	23586269	-	1	NA	intron (NM_011747, intron 1 of 5)	intron (NM_011747, intron 1 of 5)	13245	NM_011747	22654	Mm.40326	NM_011747	ENSMUSG00000062012	Zfp13	4933429B21|AI835008|Krox-8|Rhit|Zfp-13	zinc finger protein 13	protein-coding
mm_88063.1	chr10	67647234	67647241	+	1	NA	Intergenic	Intergenic	-98282	NM_001005419	211488	Mm.297250	NM_001005419	ENSMUSG00000057134	Ado	Gm237	2-aminoethanethiol (cysteamine) dioxygenase	protein-coding
mm_20002.1	chr2	119029353	119029355	-	1	NA	promoter-TSS (NM_199310)	promoter-TSS (NM_199310)	39	NM_199310	269336	Mm.292465	NM_199310	ENSMUSG00000039983	Ccdc32	Gm631	coiled-coil domain containing 32	protein-coding
mm_12227.1	chr2	68421207	68421236	+	1	NA	intron (NM_016866, intron 1 of 17)	intron (NM_016866, intron 1 of 17)	50760	NM_016866	53416	Mm.198414	NM_016866	ENSMUSG00000027030	Stk39	AW227544|AW556857|DCHT|RF005|Rnl5|SPAK	serine/threonine kinase 39	protein-coding
mm_87858.1	chr10	61175386	61175399	+	1	NA	exon (NM_001017407, exon 1 of 4)	exon (NM_001017407, exon 1 of 4)	130	NM_023064	65971	Mm.30227	NM_023064	ENSMUSG00000020096	Tbata	1700021K02Rik|AI428928|Spatial|Titest	thymus, brain and testes associated	protein-coding
mm_136460.1	chr16	95290476	95290479	-	1	NA	intron (NR_073406, intron 4 of 5)	intron (NR_073406, intron 4 of 5)	32919	NM_001271690	16516	Mm.272239	NM_019664	ENSMUSG00000062609	Kcnj15	4930414N08Rik|AI182284|AI267127|IRKK|Kir4.2	potassium inwardly-rectifying channel, subfamily J, member 15	protein-coding
mm_147679.1	chr18	60660187	60660201	-	1	NA	Intergenic	Intergenic	-3216	NR_045401	328963	Mm.417203	NR_045401		G630071F17Rik	G630071F17	RIKEN cDNA G630071F17 gene	ncRNA
mm_93334.1	chr10	99467309	99467386	-	1	NA	Intergenic	Intergenic	-141824	NR_038019	100504202	Mm.403801	NR_038019		Gm20110	-	predicted gene, 20110	ncRNA
mm_126061.1	chr15	77015922	77015956	+	1	NA	exon (NM_013593, exon 4 of 4)	exon (NM_013593, exon 4 of 4)	6788	NM_001164048	17189	Mm.404074	NM_013593	ENSMUSG00000018893	Mb	AI325109	myoglobin	protein-coding
mm_172513.1	chr7	76832851	76832852	+	1	NA	intron (NM_001199224, intron 21 of 22)	L1Md_A|LINE|L1	602964	NM_001199224	244071	Mm.322829	NM_172902	ENSMUSG00000025754	Agbl1	Ccp4|D430020F16|EG244071|Nna1-l1	ATP/GTP binding protein-like 1	protein-coding
mm_153283.1	chr19	37263861	37263871	-	1	NA	non-coding (NR_040299, exon 1 of 3)	non-coding (NR_040299, exon 1 of 3)	229	NR_040299	77059	Mm.251476	NR_040298		4931408D14Rik	-	RIKEN cDNA 4931408D14 gene	ncRNA
mm_164371.1	chr16	24193858	24193874	+	1	NA	Intergenic	Intergenic	-199484	NM_178665	210126	Mm.209385	NM_178665	ENSMUSG00000033306	Lpp	9430020K16Rik|AA959454|AU024130|B130055L10Rik|C79715|D630048H16	LIM domain containing preferred translocation partner in lipoma	protein-coding
mm_94378.1	chr11	5136259	5136283	+	1	NA	intron (NM_080595, intron 3 of 14)	intron (NM_080595, intron 3 of 14)	15951	NM_080595	140703	Mm.840	NM_080595	ENSMUSG00000034164	Emid1	AW122071|CO-5|Emu1	EMI domain containing 1	protein-coding
mm_50301.1	chr6	47595162	47595217	+	1	NA	promoter-TSS (NM_001146689)	promoter-TSS (NM_001146689)	-159	NM_001146689	14056	Mm.246688	NM_007971	ENSMUSG00000029687	Ezh2	Enx-1|Enx1h|KMT6|mKIAA4065	enhancer of zeste 2 polycomb repressive complex 2 subunit	protein-coding
mm_108756.1	chr12	89013249	89013295	+	1	NA	intron (NM_172544, intron 2 of 19)	intron (NM_172544, intron 2 of 19)	59882	NM_172544	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding
mm_123875.1	chr14	72604220	72604223	-	1	NA	intron (NM_207636, intron 3 of 25)	(A)n|Simple_repeat|Simple_repeat	105782	NM_207636	319448	Mm.205421	NM_207636	ENSMUSG00000033487	Fndc3a	1700094E19Rik|D14Ertd453e|F730017H24Rik|Fndc3|sys	fibronectin type III domain containing 3A	protein-coding
mm_156547.1	chrX	151359339	151359342	+	1	NA	intron (NM_198105, intron 1 of 15)	intron (NM_198105, intron 1 of 15)	15117	NM_198105	207375	Mm.391339	NM_198105	ENSMUSG00000025262	Fam120c	D930001I21Rik|ORF34	family with sequence similarity 120, member C	protein-coding
mm_77750.1	chr8	128438330	128438333	-	1	NA	intron (NM_008737, intron 6 of 16)	intron (NM_008737, intron 6 of 16)	79090	NR_035436	100316680		NR_035436	ENSMUSG00000084523	Mir1903	Mirn1903|mmu-mir-1903	microRNA 1903	ncRNA
mm_156102.1	chrX	113298232	113298251	+	1	NA	promoter-TSS (NM_001142570)	promoter-TSS (NM_001142570)	-15	NM_033605	93837	Mm.79760	NM_033605	ENSMUSG00000025592	Dach2	9430028N04Rik	dachshund 2 (Drosophila)	protein-coding
mm_42610.1	chr5	117910024	117910029	+	1	NA	intron (NM_008712, intron 10 of 27)	intron (NM_008712, intron 10 of 27)	43187	NM_008712	18125	Mm.44249	NM_008712	ENSMUSG00000029361	Nos1	2310005C01Rik|N-NOS|NC-NOS|NO|NOS|NOS-I|Nos-1|bNOS|nNOS	nitric oxide synthase 1, neuronal	protein-coding
mm_6449.1	chr1	74008522	74008553	-	1	NA	intron (NM_027884, intron 4 of 34)	intron (NM_027884, intron 4 of 34)	115910	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_171272.1	chr3	88775210	88775212	+	1	NA	Intergenic	CpG	-1846	NR_028359	100302730	Mm.482358	NR_028359		5830417I10Rik	3632445O20Rik|AA387005	gon-4-like pseudogene	pseudo
mm_9161.1	chr1	170961086	170961105	-	1	NA	exon (NM_001077189, exon 8 of 8)	exon (NM_001077189, exon 8 of 8)	14976	NM_001077189	14130	Mm.425062	NM_010187	ENSMUSG00000026656	Fcgr2b	AI528646|CD32|F630109E10Rik|Fc[g]RII|FcgRII|Fcgr2|Fcgr2a|Fcr-2|Fcr-3|Ly-17|Ly-m20|LyM-1|Lym-1|fcRII	Fc receptor, IgG, low affinity IIb	protein-coding
mm_41412.1	chr5	90787605	90787633	+	1	NA	3' UTR (NM_203320, exon 4 of 4)	3' UTR (NM_203320, exon 4 of 4)	1518	NM_203320	330122	Mm.244289	NM_203320	ENSMUSG00000029379	Cxcl3	Dcip1|Gm1960	chemokine (C-X-C motif) ligand 3	protein-coding
mm_110534.1	chr12	55015699	55015713	-	1	NA	Intergenic	(A)n|Simple_repeat|Simple_repeat	-29370	NM_013815	217578	Mm.479583	NM_013815	ENSMUSG00000035021	Baz1a	Acf1|B930060C03|BC065123|Gtl5|Wcrf180|cbp146	bromodomain adjacent to zinc finger domain 1A	protein-coding
mm_162717.1	chr10	34673598	34673603	+	1	NA	Intergenic	Lx4A|LINE|L1	190200	NM_010237	14302	Mm.332432	NM_010237	ENSMUSG00000019779	Frk	BSK|BSK/IYK|C85044|GTK|RAK	fyn-related kinase	protein-coding
mm_167965.1	chrX	151521015	151521017	-	1	NA	5' UTR (NM_001113354, exon 1 of 22)	5' UTR (NM_001113354, exon 1 of 22)	344	NM_001113354	320595	Mm.17156	NM_177201	ENSMUSG00000041229	Phf8	9830141C09Rik|mKIAA1111	PHD finger protein 8	protein-coding
mm_108585.1	chr12	85199649	85199650	+	1	NA	Intergenic	Intergenic	-19832	NM_145445	217715	Mm.29041	NM_145445	ENSMUSG00000004788	Eif2b2	EIF-2Bbeta|EIF2B	eukaryotic translation initiation factor 2B, subunit 2 beta	protein-coding
mm_65566.1	chr7	27178815	27178829	-	1	NA	promoter-TSS (NM_029391)	promoter-TSS (NM_029391)	61	NM_029391	19342	Mm.482114	NM_029391	ENSMUSG00000053291	Rab4b	1500031G17Rik	RAB4B, member RAS oncogene family	protein-coding
mm_165601.1	chr3	50175887	50175887	+	1	NA	Intergenic	Intergenic	267726	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_32738.1	chr4	116610979	116611016	+	1	NA	exon (NM_016777, exon 7 of 16)	exon (NM_016777, exon 7 of 16)	-13367	NR_029450	654318	Mm.255685	NR_029450	ENSMUSG00000085408	C530005A16Rik	D930044c15rik	RIKEN cDNA C530005A16 gene	ncRNA
mm_8067.1	chr1	135470704	135470720	-	1	NA	exon (NM_173437, exon 6 of 29)	exon (NM_173437, exon 6 of 29)	-16029	NR_049188	100885827		NR_049188	ENSMUSG00000093515	Mir1231	Gm23720|mir-1231|mmu-mir-1231	microRNA 1231	ncRNA
mm_81196.1	chr9	107554672	107554684	+	1	NA	promoter-TSS (NM_019713)	promoter-TSS (NM_019713)	95	NM_019713	56289	Mm.12091	NM_019713	ENSMUSG00000010067	Rassf1	123F2|AA536941|AU044980|NORE2A|RDA32|REH3P21|Rassf1A|Rassf1B|Rassf1C	Ras association (RalGDS/AF-6) domain family member 1	protein-coding
mm_79929.1	chr9	65631071	65631088	+	1	NA	intron (NM_028030, intron 1 of 7)	CpG	497	NM_028030	71973	Mm.29148	NM_028030	ENSMUSG00000032387	Rbpms2	2400008B06Rik|AI316523	RNA binding protein with multiple splicing 2	protein-coding
mm_156884.1	chrX	166344993	166345031	+	1	NA	5' UTR (NM_001177959, exon 1 of 7)	5' UTR (NM_001177959, exon 1 of 7)	459	NM_001177960	14758	Mm.222320	NM_023122	ENSMUSG00000031342	Gpm6b	AI593561|Gpm6|M6B	glycoprotein m6b	protein-coding
mm_141993.1	chr17	35176049	35176055	-	1	NA	promoter-TSS (NM_019467)	promoter-TSS (NM_019467)	-51	NM_019467	11629	Mm.10747	NM_019467	ENSMUSG00000024397	Aif1	AI607846|AIF-1|D17H6S50E|G1|Iba1	allograft inflammatory factor 1	protein-coding
mm_146148.1	chr18	74787137	74787148	+	1	NA	exon (NM_177470, exon 2 of 10)	exon (NM_177470, exon 2 of 10)	7930	NM_177470	52538	Mm.245724	NM_177470	ENSMUSG00000036880	Acaa2	0610011L04Rik|AI255831|AI265397|D18Ertd240e	acetyl-Coenzyme A acyltransferase 2 (mitochondrial 3-oxoacyl-Coenzyme A thiolase)	protein-coding
mm_143733.1	chr17	81419860	81419863	-	1	NA	intron (NR_104580, intron 7 of 8)	intron (NR_104580, intron 7 of 8)	318526	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_96515.1	chr11	68475432	68475465	+	1	NA	exon (NM_177320, exon 3 of 19)	exon (NM_177320, exon 3 of 19)	-27571	NM_001004435	104709	Mm.234573	NM_001004435	ENSMUSG00000046207	Pik3r6	BB220380|p84|p84 PIKAP|p87(PIKAP)|p87PIKAP	phosphoinositide-3-kinase, regulatory subunit 6	protein-coding
mm_70230.1	chr7	145284396	145284407	-	1	NA	promoter-TSS (NM_146206)	promoter-TSS (NM_146206)	-390	NR_132642	233979	Mm.102235	NM_146206	ENSMUSG00000048677	Tpcn2	D830047E22Rik|Gm35086	two pore segment channel 2	protein-coding
mm_107955.1	chr12	72441983	72441992	+	1	NA	promoter-TSS (NM_001142729)	promoter-TSS (NM_001142729)	121	NM_030070	78257	Mm.266280	NM_030070	ENSMUSG00000021090	Lrrc9	4921529O18Rik|4930432K16Rik	leucine rich repeat containing 9	protein-coding
mm_12635.1	chr2	74705341	74705378	+	1	NA	promoter-TSS (NM_001290730)	promoter-TSS (NM_001290730)	-130	NM_001290730	15437	Mm.280673	NM_008276	ENSMUSG00000027102	Hoxd8	4921540P06Rik|AI047735|Hox-4.3|Hox-5.4	homeobox D8	protein-coding
mm_51355.1	chr6	72558767	72558856	+	1	NA	exon (NM_001042534, exon 8 of 10)	exon (NM_001042534, exon 8 of 10)	9164	NM_001271395	12332	Mm.18626	NM_007599	ENSMUSG00000056737	Capg	gCap39|mbh1	capping protein (actin filament), gelsolin-like	protein-coding
mm_106854.1	chr12	8008595	8008615	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	30928	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_90377.1	chr10	127242708	127242741	+	1	NA	exon (NM_001039000, exon 11 of 29)	exon (NM_001039000, exon 11 of 29)	20639	NM_008447	16572	Mm.30355	NM_008447	ENSMUSG00000074657	Kif5a	D10Bwg0738e|Khc|Kif5|Kns|mKIAA4086	kinesin family member 5A	protein-coding
mm_13101.1	chr2	91265253	91265315	+	1	NA	TTS (NM_028733)	TTS (NM_028733)	169	NM_023854	77038	Mm.43636	NM_023854	ENSMUSG00000027255	Arfgap2	2310032E02Rik|Zfp289	ADP-ribosylation factor GTPase activating protein 2	protein-coding
mm_23132.1	chr3	37761216	37761233	+	1	NA	Intergenic	Intergenic	-36864	NM_198657	381438	Mm.490549	NM_198657	ENSMUSG00000058174	Gm5148	EG381438	predicted gene 5148	protein-coding
mm_70921.1	chr8	25785598	25785603	+	1	NA	promoter-TSS (NM_026032)	promoter-TSS (NM_026032)	9	NM_026032	67207	Mm.30198	NM_026032	ENSMUSG00000037296	Lsm1	2810025O06Rik|CASM	LSM1 homolog, mRNA degradation associated	protein-coding
mm_9376.1	chr1	172210221	172210226	-	1	NA	3' UTR (NM_009813, exon 11 of 11)	3' UTR (NM_009813, exon 11 of 11)	-3419	NM_011063	18611	Mm.544	NM_011063	ENSMUSG00000013698	Pea15a	Mat1|PEA-15|Pea15|Pkcs15	phosphoprotein enriched in astrocytes 15A	protein-coding
mm_92457.1	chr10	77897914	77897931	-	1	NA	3' UTR (NM_145152, exon 2 of 2)	3' UTR (NM_145152, exon 2 of 2)	4502	NR_015547	75188	Mm.348012	NM_029200	ENSMUSG00000096573	1700009J07Rik	4930535B06Rik	RIKEN cDNA 1700009J07 gene	ncRNA
mm_169786.1	chr16	11511641	11511644	-	1	NA	intron (NM_001290148, intron 7 of 13)	LTRIS4B|LTR|ERV1	105994	NM_001290148	74478	Mm.325831	NM_028964	ENSMUSG00000071669	Snx29	4933437K13Rik|ENSMUSG00000079738|Gm11170|Gm1737|Gm930|Rundc2a	sorting nexin 29	protein-coding
mm_42591.1	chr5	117363499	117363512	+	1	NA	intron (NM_021539, intron 1 of 8)	intron (NM_021539, intron 1 of 8)	6200	NM_021539	59043	Mm.28489	NM_021539	ENSMUSG00000029364	Wsb2	AA673511|Swip2|WSB-2	WD repeat and SOCS box-containing 2	protein-coding
mm_126160.1	chr15	78428651	78428671	+	1	NA	promoter-TSS (NM_001289671)	promoter-TSS (NM_001289671)	97	NR_110357	72844	Mm.390816	NM_001081367	ENSMUSG00000033287	Kctd17	2900008M13Rik|AA414907|AW742389|N28155	potassium channel tetramerisation domain containing 17	protein-coding
mm_100414.1	chr11	119428010	119428030	+	1	NA	Intergenic	Intergenic	37548	NR_035453	100316690		NR_035453	ENSMUSG00000088015	Mir1932	mir-1932|mmu-mir-1932	microRNA 1932	ncRNA
mm_53799.1	chr6	146796042	146796072	+	1	NA	Intergenic	CpG	-9473	NM_172309	272322	Mm.333500	NM_172309	ENSMUSG00000040187	Arntl2	4632430A05Rik|BMAL2|CLIF|MOP9|bHLHe6	aryl hydrocarbon receptor nuclear translocator-like 2	protein-coding
mm_59474.1	chr7	27452418	27452469	+	1	NA	promoter-TSS (NM_001290525)	promoter-TSS (NM_001290525)	25	NM_001290525	233016	Mm.24021	NM_144923	ENSMUSG00000040466	Blvrb	-	biliverdin reductase B (flavin reductase (NADPH))	protein-coding
mm_110600.1	chr12	56535950	56535966	-	1	NA	intron (NM_009385, intron 1 of 2)	CpG	950	NM_009385	21869	Mm.89972	NM_009385	ENSMUSG00000001496	Nkx2-1	AV026640|Nkx2.1|T/EBP|Titf1|Ttf-1	NK2 homeobox 1	protein-coding
mm_46027.1	chr5	91402881	91402885	-	1	NA	5' UTR (NM_007568, exon 1 of 6)	5' UTR (NM_007568, exon 1 of 6)	111	NM_007568	12223	Mm.2024	NM_007568	ENSMUSG00000082361	Btc	Bcn	betacellulin, epidermal growth factor family member	protein-coding
mm_40041.1	chr5	33820696	33820835	+	1	NA	Intergenic	CpG	-22347	NM_175231	107823	Mm.19892	NM_175231	ENSMUSG00000057406	Whsc1	5830445G22Rik|9430010A17Rik|AW555663|C130020C13Rik|D030027O06Rik|D930023B08Rik|MMSET|NSD2|Whsc1l|mKIAA1090	Wolf-Hirschhorn syndrome candidate 1 (human)	protein-coding
mm_144396.1	chr18	20673805	20673821	+	1	NA	3' UTR (NM_013697, exon 4 of 4)	3' UTR (NM_013697, exon 4 of 4)	8563	NM_013697	22139	Mm.2108	NM_013697	ENSMUSG00000061808	Ttr	AA408768|AI787086|D17860|prealbumin	transthyretin	protein-coding
mm_169867.1	chr1	63446388	63446404	+	1	NA	exon (NM_011780, exon 1 of 26)	exon (NM_011780, exon 1 of 26)	505	NM_011780	23792	Mm.124892	NM_011780	ENSMUSG00000025964	Adam23	AW046396|MDC3	a disintegrin and metallopeptidase domain 23	protein-coding
mm_165600.1	chr3	49757349	49757355	-	1	NA	promoter-TSS (NM_130448)	promoter-TSS (NM_130448)	-36	NM_130448	73173	Mm.87246	NM_130448	ENSMUSG00000037892	Pcdh18	3110038E07Rik|BB095589|PCDH68L	protocadherin 18	protein-coding
mm_9275.1	chr1	171634158	171634164	-	1	NA	3' UTR (NM_144539, exon 8 of 8)	3' UTR (NM_144539, exon 8 of 8)	7739	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_82949.1	chr9	35558506	35558518	-	1	NA	promoter-TSS (NM_013932)	promoter-TSS (NM_013932)	-42	NM_013932	30959	Mm.291723	NM_013932	ENSMUSG00000032101	Ddx25	AW047046|GRTH	DEAD (Asp-Glu-Ala-Asp) box polypeptide 25	protein-coding
mm_132226.1	chr16	32650772	32650775	+	1	NA	intron (NM_016788, intron 1 of 15)	B1_Mus2|SINE|Alu	6130	NM_016788	51789	Mm.251115	NM_016788	ENSMUSG00000022791	Tnk2	Ack|Ack-1|Ack1|Cdgip|Pyk1	tyrosine kinase, non-receptor, 2	protein-coding
mm_120175.1	chr14	61138446	61138495	+	1	NA	promoter-TSS (NM_172809)	promoter-TSS (NM_172809)	13	NM_172809	50720	Mm.440703	NM_015788	ENSMUSG00000048279	Sacs	A230052M14|DNAJC29|E130115J16Rik|mKIAA0730	sacsin	protein-coding
mm_107066.1	chr12	16812392	16812395	+	1	NA	intron (NM_033270, intron 1 of 6)	intron (NM_033270, intron 1 of 6)	1428	NM_033270	50496	Mm.23296	NM_033270	ENSMUSG00000057469	E2f6	AI462434|E2F6a|E2F6b|EMA	E2F transcription factor 6	protein-coding
mm_155386.1	chrX	71816773	71816813	+	1	NA	promoter-TSS (NM_001081356)	promoter-TSS (NM_001081356)	35	NM_001290780	67048	Mm.41102	NM_001081356	ENSMUSG00000073131	Vma21	2610030H06Rik|AI840175	VMA21 vacuolar H+-ATPase homolog (S. cerevisiae)	protein-coding
mm_76052.1	chr8	77689190	77689198	-	1	NA	exon (NM_010332, exon 3 of 8)	exon (NM_010332, exon 3 of 8)	35258	NM_010332	13617	Mm.283168	NM_010332	ENSMUSG00000031616	Ednra	ET-AR|ETa|Gpcr10	endothelin receptor type A	protein-coding
mm_68577.1	chr7	115846159	115846159	-	1	NA	promoter-TSS (NM_001277326)	promoter-TSS (NM_001277326)	-19	NM_001277326	20679	Mm.323365	NM_011445	ENSMUSG00000051910	Sox6	AI987981|SOX-LZ	SRY (sex determining region Y)-box 6	protein-coding
mm_154280.1	chr19	60790709	60790713	-	1	NA	promoter-TSS (NM_010123)	promoter-TSS (NM_010123)	-18	NM_010123	13669	Mm.2238	NM_010123	ENSMUSG00000024991	Eif3a	A830012B05Rik|Csma|Eif3|Eif3s10|mKIAA0139	eukaryotic translation initiation factor 3, subunit A	protein-coding
mm_21307.1	chr2	157079213	157079276	-	1	NA	promoter-TSS (NM_001164663)	promoter-TSS (NM_001164663)	21	NM_001164663	320706	Mm.79466	NM_001164663	ENSMUSG00000055485	Soga1	9830001H06Rik|AI426038|D430036N24Rik|Soga	suppressor of glucose, autophagy associated 1	protein-coding
mm_101671.1	chr11	37236075	37236084	-	1	NA	Intergenic	Intergenic	-291838	NM_011856	23964	Mm.439889	NM_011856	ENSMUSG00000049336	Tenm2	Odz2|Odz3|Ten-2|Ten-m2	teneurin transmembrane protein 2	protein-coding
mm_27978.1	chr3	80879697	80879715	-	1	NA	exon (NM_010298, exon 3 of 10)	exon (NM_010298, exon 3 of 10)	32412	NM_001345996	14658	Mm.275639	NM_010298	ENSMUSG00000028020	Glrb	AI853901|Glyrb|spa|spastic	glycine receptor, beta subunit	protein-coding
mm_324.1	chr1	24678713	24678758	+	1	NA	promoter-TSS (NM_001310483)	promoter-TSS (NM_001310483)	-183	NM_001310483	68421	Mm.336563	NM_026719	ENSMUSG00000073725	Lmbrd1	0910001K20Rik|AV347960	LMBR1 domain containing 1	protein-coding
mm_164523.1	chr17	3410942	3410944	+	1	NA	intron (NM_011878, intron 1 of 26)	ID_B1|SINE|B4	13736	NM_011878	24001	Mm.137134	NM_011878	ENSMUSG00000023800	Tiam2	3000002F19Rik|STEF|mKIAA2016	T cell lymphoma invasion and metastasis 2	protein-coding
mm_136508.1	chr16	97170529	97170544	-	1	NA	5' UTR (NM_031174, exon 1 of 33)	5' UTR (NM_031174, exon 1 of 33)	199	NM_031174	13508	Mm.102437	NM_031174	ENSMUSG00000050272	Dscam	4932410A21Rik	Down syndrome cell adhesion molecule	protein-coding
mm_108802.1	chr12	91695023	91695042	+	1	NA	intron (NM_175367, intron 4 of 6)	B1_Mur1|SINE|Alu	91404	NM_175367	108800	Mm.23125	NM_175367	ENSMUSG00000020961	Ston2	4933401N24Rik|AI425999|AW544599	stonin 2	protein-coding
mm_151152.1	chr19	53142776	53142778	+	1	NA	promoter-TSS (NM_001164100)	promoter-TSS (NM_001164100)	21	NM_001164100	27360	Mm.426080	NM_013758	ENSMUSG00000025026	Add3	AI463285|R75380	adducin 3 (gamma)	protein-coding
mm_94317.1	chr11	4236443	4236456	+	1	NA	promoter-TSS (NM_001013365)	promoter-TSS (NM_001013365)	-336	NM_001013365	18413	Mm.131422	NM_001013365	ENSMUSG00000058755	Osm	OncoM	oncostatin M	protein-coding
mm_37520.1	chr4	124668188	124668201	-	1	NA	Intergenic	Intergenic	10548	NM_011141	18991	Mm.297371	NM_011141	ENSMUSG00000090125	Pou3f1	Oct-6|Oct6|Otf-6|Otf6|Scip|Test1|Tst-1|Tst1	POU domain, class 3, transcription factor 1	protein-coding
mm_36540.1	chr4	86660165	86660254	-	1	NA	exon (NM_007408, exon 6 of 8)	exon (NM_007408, exon 6 of 8)	9850	NM_007408	11520	Mm.381	NM_007408	ENSMUSG00000028494	Plin2	AA407157|ADPH|Adfp|Adrp	perilipin 2	protein-coding
mm_118374.1	chr13	117014762	117014776	-	1	NA	intron (NM_001081009, intron 3 of 26)	B1F|SINE|Alu	10747	NM_001081009	52552	Mm.274466	NM_027272	ENSMUSG00000021725	Parp8	2810430O08Rik|ARTD16|D13Ertd275e	poly (ADP-ribose) polymerase family, member 8	protein-coding
mm_29703.1	chr3	123236112	123236122	-	1	NA	promoter-TSS (NM_080451)	promoter-TSS (NM_080451)	32	NM_080451	118449	Mm.34359	NM_080451	ENSMUSG00000050315	Synpo2	1110069I04Rik|2310068J10Rik|9530006G20Rik|AI848603|Myo	synaptopodin 2	protein-coding
mm_22176.1	chr2	173213915	173213921	-	1	NA	intron (NM_001139519, intron 3 of 3)	B1_Mur2|SINE|Alu	5004	NM_021394	58203	Mm.116687	NM_021394	ENSMUSG00000027514	Zbp1	2010010H03Rik|Dai|Dlm1|mZaDLM	Z-DNA binding protein 1	protein-coding
mm_19267.1	chr2	84938417	84938428	-	1	NA	intron (NM_021398, intron 3 of 12)	intron (NM_021398, intron 3 of 12)	1776	NM_021398	58207	Mm.290729	NM_021398	ENSMUSG00000027074	Slc43a3	Eeg1|SEEEG-1	solute carrier family 43, member 3	protein-coding
mm_19942.1	chr2	116067356	116067366	-	1	NA	promoter-TSS (NM_001346047)	promoter-TSS (NM_001346047)	83	NM_001346047	17536	Mm.247566	NM_010825	ENSMUSG00000027210	Meis2	A430109D20Rik|Mrg1|Stra10	Meis homeobox 2	protein-coding
mm_62874.1	chr7	114745908	114745931	+	1	NA	5' UTR (NM_173767, exon 1 of 13)	5' UTR (NM_173767, exon 1 of 13)	153	NM_173767	233752	Mm.83037	NM_173767	ENSMUSG00000048782	Insc	3830422K02Rik|C730020D23	inscuteable homolog (Drosophila)	protein-coding
mm_142929.1	chr17	54297186	54297195	-	1	NA	5' UTR (NM_022025, exon 2 of 9)	5' UTR (NM_022025, exon 2 of 9)	1844	NM_022025	63993	Mm.155241	NM_022025	ENSMUSG00000023945	Slc5a7	CHT1	solute carrier family 5 (choline transporter), member 7	protein-coding
mm_135266.1	chr16	38341814	38341859	-	1	NA	promoter-TSS (NM_001081025)	promoter-TSS (NM_001081025)	24	NM_001081025	320214	Mm.294342	NM_177104	ENSMUSG00000022805	Maats1	4932425I24Rik|Aat1|Spata26	MYCBP-associated, testis expressed 1	protein-coding
mm_76619.1	chr8	91656709	91656720	-	1	NA	intron (NM_011936, intron 8 of 8)	intron (NM_011936, intron 8 of 8)	144940	NM_001253822	16373	Mm.238044	NM_008393	ENSMUSG00000031734	Irx3	AI894186	Iroquois related homeobox 3	protein-coding
mm_141774.1	chr17	34287111	34287153	-	1	NA	intron (NM_010378, intron 1 of 4)	PB1D10|SINE|Alu	639	NM_010378	14960	Mm.235338	NM_010378	ENSMUSG00000036594	H2-Aa	Aalpha|H-2Aa|H2Aa|I-Aalpha|IAalpha|Ia-1|Ia1	histocompatibility 2, class II antigen A, alpha	protein-coding
mm_110252.1	chr12	31634418	31634497	-	1	NA	5' UTR (NM_007530, exon 1 of 7)	5' UTR (NM_007530, exon 1 of 7)	140	NM_007530	12033	Mm.242379	NM_007530	ENSMUSG00000020650	Bcap29	AW208404|Bap29	B cell receptor associated protein 29	protein-coding
mm_61272.1	chr7	66689916	66689980	+	1	NA	promoter-TSS (NR_003961)	promoter-TSS (NR_003961)	59	NR_034030	72635	Mm.289796	NM_152815	ENSMUSG00000053091	Lins1	2700083B01Rik|AW547219|Lins|Lins2|Wins2	lines homolog 1	protein-coding
mm_14478.1	chr2	131506602	131506609	+	1	NA	intron (NM_001177836, intron 1 of 7)	intron (NM_001177836, intron 1 of 7)	14743	NM_001177838	228608	Mm.136586	NM_145533	ENSMUSG00000027333	Smox	B130066H01Rik|PAO|PAOh1|SMO	spermine oxidase	protein-coding
mm_4459.1	chr1	172699306	172699316	+	1	NA	3' UTR (NM_007768, exon 2 of 2)	3' UTR (NM_007768, exon 2 of 2)	1255	NM_007768	12944	Mm.28767	NM_007768	ENSMUSG00000037942	Crp	AI255847	C-reactive protein, pentraxin-related	protein-coding
mm_167647.1	chr9	65262810	65262811	+	1	NA	Intergenic	Intergenic	-2370	NM_173385	214425	Mm.138455	NM_173385	ENSMUSG00000042254	Cilp	9830114D16|C130036G17Rik	cartilage intermediate layer protein, nucleotide pyrophosphohydrolase	protein-coding
mm_126363.1	chr15	80091321	80091390	+	1	NA	promoter-TSS (NM_009303)	promoter-TSS (NM_009303)	21	NM_207708	20972	Mm.230301	NM_009303	ENSMUSG00000022415	Syngr1	R75468|Syngr1b|p29	synaptogyrin 1	protein-coding
mm_114792.1	chr13	89540816	89540821	+	1	NA	5' UTR (NM_013500, exon 1 of 5)	5' UTR (NM_013500, exon 1 of 5)	182	NM_013500	12950	Mm.266790	NM_013500	ENSMUSG00000021613	Hapln1	BB099155|CLP|Crtl1|Crtl1l|LP|LP-1	hyaluronan and proteoglycan link protein 1	protein-coding
mm_92688.1	chr10	80656988	80657003	-	1	NA	promoter-TSS (NM_145361)	promoter-TSS (NM_145361)	76	NM_145361	208198	Mm.60720	NM_145361	ENSMUSG00000003344	Btbd2	2610037C03Rik|4930512K17Rik	BTB (POZ) domain containing 2	protein-coding
mm_100668.1	chr11	3334249	3334259	-	1	NA	intron (NM_178149, intron 5 of 5)	intron (NM_178149, intron 5 of 5)	3523	NM_178149	216505	Mm.390323	NM_178149	ENSMUSG00000034614	Pik3ip1	1500004A08Rik|5830455E04Rik|Crkd|Hgfl	phosphoinositide-3-kinase interacting protein 1	protein-coding
mm_56225.1	chr6	90318843	90318848	-	1	NA	intron (NM_027928, intron 1 of 2)	intron (NM_027928, intron 1 of 2)	6340	NM_027928	71797	Mm.49071	NM_027928	ENSMUSG00000056643	Chst13	1110067M19Rik|C4ST-3	carbohydrate (chondroitin 4) sulfotransferase 13	protein-coding
mm_51657.1	chr6	86105189	86105192	+	1	NA	intron (NM_001271857, intron 10 of 15)	intron (NM_001271857, intron 10 of 15)	27142	NM_001271859	11519	Mm.104155	NM_013458	ENSMUSG00000030000	Add2	2900072M03Rik|add97	adducin 2 (beta)	protein-coding
mm_140971.1	chr17	24696066	24696108	-	1	NA	promoter-TSS (NM_027988)	promoter-TSS (NM_027988)	69	NM_023040	11692	Mm.28124	NM_023040	ENSMUSG00000040888	Gfer	Alr|ERV1	growth factor, erv1 (S. cerevisiae)-like (augmenter of liver regeneration)	protein-coding
mm_94881.1	chr11	24855427	24855430	+	1	NA	Intergenic	Intergenic	-124706	NR_033491	100038617	Mm.387376	NR_033491	ENSMUSG00000073103	Gm10466	ENSMUSG00000073103	predicted gene 10466	ncRNA
mm_69965.1	chr7	142376663	142376674	-	1	NA	exon (NM_009983, exon 9 of 9)	exon (NM_009983, exon 9 of 9)	-2922	NM_001347541	320802	Mm.154486	NM_177265	ENSMUSG00000045777	Ifitm10	6330512M04Rik|AI848576|DSPA3	interferon induced transmembrane protein 10	protein-coding
mm_64595.1	chr7	3203885	3203897	-	1	NA	Intergenic	B1_Mus2|SINE|Alu	-14735	NR_029640	100049710		NR_029640	ENSMUSG00000077815	Mir290a	Mir290|Mirn290|mir-290a|mmu-miR-290|mmu-mir-290a	microRNA 290a	ncRNA
mm_153027.1	chr19	31664376	31664443	-	1	NA	promoter-TSS (NM_011160)	promoter-TSS (NM_011160)	-39	NM_011160	19091	Mm.381170	NM_011160	ENSMUSG00000052920	Prkg1	AW125416|CGKI|Gm19690|Prkg1b|Prkgr1b	protein kinase, cGMP-dependent, type I	protein-coding
mm_105723.1	chr11	109011841	109011853	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	91498	NM_015732	12006	Mm.71710	NM_015732	ENSMUSG00000000142	Axin2	Axi1|Axil|Conductin	axin 2	protein-coding
mm_125156.1	chr15	31027775	31027780	+	1	NA	3' UTR (NM_008729, exon 23 of 23)	3' UTR (NM_008729, exon 23 of 23)	-11349	NR_045186	73784	Mm.66947	NR_045186		4930430F21Rik	-	RIKEN cDNA 4930430F21 gene	ncRNA
mm_39563.1	chr5	23314323	23314333	+	1	NA	Intergenic	Intergenic	120025	NR_040469	269630	Mm.425231	NR_040469	ENSMUSG00000073147	5031425E22Rik	-	RIKEN cDNA 5031425E22 gene	ncRNA
mm_782.1	chr1	44795703	44795747	+	1	NA	3' UTR (NM_028450, exon 11 of 11)	3' UTR (NM_028450, exon 11 of 11)	-50776	NR_040602	75066	Mm.416932	NR_040602	ENSMUSG00000101701	4930521E06Rik	-	RIKEN cDNA 4930521E06 gene	ncRNA
mm_95332.1	chr11	46750610	46750617	+	1	NA	promoter-TSS (NM_134248)	promoter-TSS (NM_134248)	102	NM_001166631	171283	Mm.17771	NM_134248	ENSMUSG00000040405	Havcr1	AI503787|KIM-1|TIM-1|Tim1|Timd1	hepatitis A virus cellular receptor 1	protein-coding
mm_110819.1	chr12	72408663	72408673	-	1	NA	5' UTR (NM_001286448, exon 1 of 7)	5' UTR (NM_001286448, exon 1 of 7)	386	NM_001286448	104001	Mm.221275	NM_153457	ENSMUSG00000021087	Rtn1	Nsp	reticulon 1	protein-coding
mm_35248.1	chr4	19877630	19877643	-	1	NA	3' UTR (NM_175406, exon 8 of 8)	3' UTR (NM_175406, exon 8 of 8)	44930	NM_175406	242341	Mm.19298	NM_175406	ENSMUSG00000028238	Atp6v0d2	1620401A02Rik|AI324824|V-ATPase	ATPase, H+ transporting, lysosomal V0 subunit D2	protein-coding
mm_169487.1	chr14	73797310	73797310	-	1	NA	Intergenic	Intergenic	244524	NM_011506	20916	Mm.38951	NM_011506	ENSMUSG00000022110	Sucla2	4930547K18Rik|A-SCS	succinate-Coenzyme A ligase, ADP-forming, beta subunit	protein-coding
mm_117669.1	chr13	93630798	93630802	-	1	NA	intron (NM_016668, intron 2 of 7)	intron (NM_016668, intron 2 of 7)	6958	NM_016668	12116	Mm.329582	NM_016668	ENSMUSG00000074768	Bhmt	-	betaine-homocysteine methyltransferase	protein-coding
mm_54221.1	chr6	26766862	26766875	-	1	NA	Intergenic	Intergenic	835442	NR_040771	626904	Mm.126787	NR_040771	ENSMUSG00000106799	Gm20756	-	predicted gene, 20756	ncRNA
mm_120004.1	chr14	55650163	55650167	+	1	NA	promoter-TSS (NM_001253889)	promoter-TSS (NM_001253889)	-19	NM_001253888	71099	Mm.171300	NM_027673	ENSMUSG00000007591	Tssk4	1700020B19Rik|4933424F08Rik|TSK-4|TSSK-4	testis-specific serine kinase 4	protein-coding
mm_46764.1	chr5	112252514	112252525	-	1	NA	promoter-TSS (NM_021351)	promoter-TSS (NM_021351)	-1	NM_021351	12959	Mm.40324	NM_021351	ENSMUSG00000066975	Cryba4	-	crystallin, beta A4	protein-coding
mm_150492.1	chr19	39011690	39011694	+	1	NA	exon (NM_028089, exon 3 of 9)	exon (NM_028089, exon 3 of 9)	4673	NM_028089	72082	Mm.142581	NM_028089	ENSMUSG00000025002	Cyp2c55	2010318C06Rik	cytochrome P450, family 2, subfamily c, polypeptide 55	protein-coding
mm_2488.1	chr1	105990653	105990718	+	1	NA	5' UTR (NM_001122675, exon 1 of 13)	5' UTR (NM_001122675, exon 1 of 13)	279	NM_001122675	227449	Mm.210188	NM_001122675	ENSMUSG00000038866	Zcchc2	9930114B20Rik|AW212015	zinc finger, CCHC domain containing 2	protein-coding
mm_41006.1	chr5	81019735	81019762	+	1	NA	promoter-TSS (NM_001347367)	promoter-TSS (NM_001347367)	-823	NM_001347367	319387	Mm.273631	NM_198702	ENSMUSG00000037605	Adgrl3	5430402I23Rik|CIRL-3|D130075K09Rik|Gm1379|LEC3|Lphn3|mKIAA0768	adhesion G protein-coupled receptor L3	protein-coding
mm_153227.1	chr19	34879222	34879230	-	1	NA	5' UTR (NM_001114339, exon 1 of 7)	5' UTR (NM_001114339, exon 1 of 7)	229	NM_001114339	75735	Mm.24742	NM_023792	ENSMUSG00000033610	Pank1	Pank|Pank1b	pantothenate kinase 1	protein-coding
mm_12656.1	chr2	75248466	75248482	+	1	NA	Intergenic	Intergenic	195705	NR_040635	77269	Mm.389278	NR_040635		9430019J16Rik	-	RIKEN cDNA 9430019J16 gene	ncRNA
mm_35480.1	chr4	40853893	40853906	-	1	NA	5' UTR (NM_022305, exon 1 of 6)	5' UTR (NM_022305, exon 1 of 6)	638	NM_022305	14595	Mm.15622	NM_022305	ENSMUSG00000028413	B4galt1	B-1,4-GalT|B-1,4-GalT1|GalT|Ggtb|Ggtb2|b4Gal-T1|beta-1,4-GalT|beta-1,4-GalT1|beta4Gal-T1	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1	protein-coding
mm_151673.1	chr19	4191036	4191069	-	1	NA	promoter-TSS (NM_178650)	promoter-TSS (NM_178650)	-5	NM_178650	108995	Mm.288312	NM_178650	ENSMUSG00000040247	Tbc1d10c	1810062O14Rik|AI428527	TBC1 domain family, member 10c	protein-coding
mm_106321.1	chr11	118303553	118303586	-	1	NA	3' UTR (NM_011594, exon 5 of 5)	3' UTR (NM_011594, exon 5 of 5)	-13325	NM_001033528	72344	Mm.232293	NM_001033528	ENSMUSG00000033909	Usp36	2700002L06Rik|mKIAA1453	ubiquitin specific peptidase 36	protein-coding
mm_110111.1	chr12	26443512	26443522	-	1	NA	3' UTR (NM_021384, exon 6 of 6)	3' UTR (NM_021384, exon 6 of 6)	12935	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_124257.1	chr14	102072329	102072344	-	1	NA	Intergenic	RMER10A|LTR|ERVL	231713	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_167136.1	chr7	127218513	127218533	+	1	NA	promoter-TSS (NM_017461)	promoter-TSS (NM_017461)	-78	NM_017461	54204	Mm.18	NM_017461	ENSMUSG00000000486	Sept1	Diff6|Pnutl3	septin 1	protein-coding
mm_73754.1	chr8	114869570	114869572	+	1	NA	intron (NM_019573, intron 8 of 8)	RMER19A|LTR|ERVK	429919	NM_019573	80707	Mm.440420	NM_019573	ENSMUSG00000004637	Wwox	5330426P09Rik|9030416C10Rik|WOX1	WW domain-containing oxidoreductase	protein-coding
mm_119949.1	chr14	55015531	55015571	+	1	NA	promoter-TSS (NM_026890)	promoter-TSS (NM_026890)	97	NM_026890	68966	Mm.21214	NM_026890	ENSMUSG00000022204	Ngdn	1500001L15Rik|Ngd|neuroguidin	neuroguidin, EIF4E binding protein	protein-coding
mm_89366.1	chr10	88605147	88605151	+	1	NA	promoter-TSS (NM_001252372)	promoter-TSS (NM_001252372)	3	NM_001252372	109272	Mm.147208	NM_175418	ENSMUSG00000020061	Mybpc1	8030451F13Rik	myosin binding protein C, slow-type	protein-coding
mm_80489.1	chr9	78395799	78395845	+	1	NA	promoter-TSS (NM_001191044)	promoter-TSS (NM_001191044)	45	NM_001191044	100048658	Mm.158166	NM_001191044	ENSMUSG00000070291	Ddx43	ENSMUSG00000070291|OTTMUSG00000019690	DEAD (Asp-Glu-Ala-Asp) box polypeptide 43	protein-coding
mm_55513.1	chr6	70059232	70059236	-	1	NA	Intergenic	Intergenic	-732060	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_55585.1	chr6	71440417	71440427	-	1	NA	5' UTR (NM_024288, exon 1 of 9)	5' UTR (NM_024288, exon 1 of 9)	215	NM_024288	68477	Mm.28474	NM_024288	ENSMUSG00000002222	Rmnd5a	1110007A06Rik|AJ237586|AW125795|Gid2|MTA.D02.090	required for meiotic nuclear division 5 homolog A	protein-coding
mm_37654.1	chr4	128806437	128806471	-	1	NA	promoter-TSS (NM_001081098)	promoter-TSS (NM_001081098)	-342	NM_001081098	230761	Mm.22616	NM_001081098	ENSMUSG00000028799	Zfp362	-	zinc finger protein 362	protein-coding
mm_68113.1	chr7	102072420	102072428	-	1	NA	intron (NM_001286689, intron 3 of 10)	B1F|SINE|Alu	1205	NM_011644	102443351	Mm.292904	NM_011644	ENSMUSG00000070425	Xntrpc	Xndr-trpc2	Xndc1-transient receptor potential cation channel, subfamily C, member 2 readthrough	protein-coding
mm_35881.1	chr4	49538270	49538302	-	1	NA	exon (NM_144903, exon 8 of 9)	exon (NM_144903, exon 8 of 9)	11260	NM_144903	230163	Mm.482116	NM_144903	ENSMUSG00000028307	Aldob	Aldo-2|Aldo2|BC016435	aldolase B, fructose-bisphosphate	protein-coding
mm_124205.1	chr14	98994325	98994335	-	1	NA	Intergenic	Intergenic	51806	NM_175245	76789	Mm.38912	NM_175245	ENSMUSG00000033186	Mzt1	2410129H14Rik|AI120158|Mozart1	mitotic spindle organizing protein 1	protein-coding
mm_33371.1	chr4	129515136	129515180	+	1	NA	TTS (NM_008228)	TTS (NM_008228)	1577	NM_010807	17357	Mm.424974	NM_010807	ENSMUSG00000047945	Marcksl1	AL022768|AW215397|AW536807|D4Bc1|F52|MacMARCKS|Macs2|Macs3|Mlp|Mrp	MARCKS-like 1	protein-coding
mm_43842.1	chr5	143039004	143039064	+	1	NA	intron (NM_080561, intron 13 of 16)	intron (NM_080561, intron 13 of 16)	73986	NM_207110	108086	Mm.381440	NM_080561	ENSMUSG00000045078	Rnf216	2810055G22Rik|AI647468|AU019462|C86502|F830018F18Rik|TRIAD3|UIP83|Ubce7ip1	ring finger protein 216	protein-coding
mm_133750.1	chr16	94370787	94370807	+	1	NA	promoter-TSS (NM_001159620)	promoter-TSS (NM_001159620)	58	NM_009441	22129	Mm.213408	NM_009441	ENSMUSG00000040785	Ttc3	2610202A04Rik|AA409221|D16Ium21|D16Ium21e|TPRD|mKIAA4119	tetratricopeptide repeat domain 3	protein-coding
mm_14152.1	chr2	126567744	126567754	+	1	NA	exon (NM_011978, exon 4 of 10)	exon (NM_011978, exon 4 of 10)	14725	NM_011978	26458	Mm.290044	NM_011978	ENSMUSG00000027359	Slc27a2	ACSVL1|FATP2|VLCS|Vlac|Vlacs	solute carrier family 27 (fatty acid transporter), member 2	protein-coding
mm_55728.1	chr6	76498096	76498113	-	1	NA	Intergenic	LTRIS3|LTR|ERV1	-744613	NM_028880	74342	Mm.292568	NM_028880	ENSMUSG00000060780	Lrrtm1	4632401D06Rik|AW125451	leucine rich repeat transmembrane neuronal 1	protein-coding
mm_133836.1	chr16	96127544	96127554	+	1	NA	intron (NM_008251, intron 1 of 5)	CpG-5899	176	NM_008251	15312	Mm.2756	NM_008251	ENSMUSG00000040681	Hmgn1	HMG-14|Hmg14	high mobility group nucleosomal binding domain 1	protein-coding
mm_4428.1	chr1	172505880	172505899	+	1	NA	exon (NM_178598, exon 3 of 5)	exon (NM_178598, exon 3 of 5)	5643	NM_178598	21346	Mm.271711	NM_178598	ENSMUSG00000026547	Tagln2	2700094C18Rik|SM22beta|Sm22B|Sm22a	transgelin 2	protein-coding
mm_93776.1	chr10	120476246	120476246	-	1	NA	5' UTR (NM_010441, exon 1 of 5)	5' UTR (NM_010441, exon 1 of 5)	223	NM_001347170	15364	Mm.157190	NM_010441	ENSMUSG00000056758	Hmga2	9430083A20Rik|HMGI-C|Hmgic|pg|pygmy	high mobility group AT-hook 2	protein-coding
mm_24151.1	chr3	88351098	88351112	+	1	NA	exon (NM_178246, exon 12 of 22)	exon (NM_178246, exon 12 of 22)	-13484	NM_198410	68957	Mm.441486	NM_198410	ENSMUSG00000041423	Paqr6	1500001B10Rik	progestin and adipoQ receptor family member VI	protein-coding
mm_62239.1	chr7	98703160	98703170	+	1	NA	promoter-TSS (NM_028410)	promoter-TSS (NM_028410)	-198	NM_028410	72981	Mm.4428	NM_028410	ENSMUSG00000030753	Thap12	2900052B10Rik|Dap4|Prkrir|Rpkrir	THAP domain containing 12	protein-coding
mm_59651.1	chr7	28169745	28169755	+	1	NA	promoter-TSS (NM_007991)	promoter-TSS (NM_007991)	2	NM_007991	14113	Mm.4595	NM_007991	ENSMUSG00000046865	Fbl	AL022665|FIB|FLRN|RNU3IP1	fibrillarin	protein-coding
mm_159264.1	chr2	156007919	156007919	-	1	NA	promoter-TSS (NM_001145352)	promoter-TSS (NM_001145352)	58	NM_001145352	320095	Mm.442175	NM_001145351	ENSMUSG00000074646	6430550D23Rik	-	RIKEN cDNA 6430550D23 gene	protein-coding
mm_140436.1	chr17	88441072	88441091	+	1	NA	intron (NM_180974, intron 1 of 5)	CpG	369	NM_180974	14236	Mm.112824	NM_180974	ENSMUSG00000034998	Foxn2	3230402J05Rik|6030465J18Rik|Fkh19|Foxn1|HTLF	forkhead box N2	protein-coding
mm_73156.1	chr8	94994841	94994852	+	1	NA	intron (NM_018882, intron 1 of 13)	intron (NM_018882, intron 1 of 13)	10447	NM_018882	14766	Mm.290834	NM_018882	ENSMUSG00000031785	Adgrg1	Cyt28|Gpr56|TM7LN4|TM7XN1	adhesion G protein-coupled receptor G1	protein-coding
mm_60923.1	chr7	46846285	46846303	+	1	NA	promoter-TSS (NM_001136069)	promoter-TSS (NM_001136069)	490	NR_102727	16828	Mm.29324	NM_010699	ENSMUSG00000063229	Ldha	Ldh1|Ldhm|l7R2	lactate dehydrogenase A	protein-coding
mm_41060.1	chr5	86816762	86816765	+	1	NA	exon (NM_177680, exon 3 of 17)	exon (NM_177680, exon 3 of 17)	12273	NM_177680	231386	Mm.196325	NM_177680	ENSMUSG00000035851	Ythdc1	A730098D12Rik|C80342|mKIAA1966	YTH domain containing 1	protein-coding
mm_127529.1	chr15	102098444	102098498	+	1	NA	Intergenic	Intergenic	-4517	NM_153533	209039	Mm.29389	NM_153533	ENSMUSG00000037003	Tns2	C1-ten|Tenc1|nep|nph	tensin 2	protein-coding
mm_118840.1	chr14	25644716	25644753	+	1	NA	exon (NM_183208, exon 9 of 24)	exon (NM_183208, exon 9 of 24)	41221	NM_001309430	100188919	Mm.473810	NM_001309430		Israa	-	immune system released activating agent	protein-coding
mm_22631.1	chr3	14767531	14767536	+	1	NA	exon (NM_001083957, exon 6 of 7)	exon (NM_001083957, exon 6 of 7)	10927	NM_001083957	12346	Mm.273195	NM_009799	ENSMUSG00000027556	Car1	AW555628|Ca1|Car-1	carbonic anhydrase 1	protein-coding
mm_128669.1	chr15	60187175	60187183	-	1	NA	Intergenic	Intergenic	-170561	NM_027668	71088	Mm.425950	NM_027668	ENSMUSG00000071749	4933412E24Rik	-	RIKEN cDNA 4933412E24 gene	protein-coding
mm_76332.1	chr8	84706501	84706516	-	1	NA	3' UTR (NM_010906, exon 9 of 9)	3' UTR (NM_010906, exon 9 of 9)	5051	NM_008535	17095	Mm.4925	NM_008535	ENSMUSG00000034041	Lyl1	Lyl-1|bHLHa18	lymphoblastomic leukemia 1	protein-coding
mm_75277.1	chr8	40992825	40992838	-	1	NA	3' UTR (NM_001286413, exon 14 of 14)	3' UTR (NM_001286413, exon 14 of 14)	-24637	NR_015457	78849	Mm.440930	NR_015457	ENSMUSG00000084960	B430010I23Rik	-	RIKEN cDNA B430010I23 gene	ncRNA
mm_168351.1	chr1	113904057	113904058	-	1	NA	Intergenic	L1Md_F3|LINE|L1	-1781080	NM_001077425	636808	Mm.101576	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding
mm_102284.1	chr11	55399259	55399269	-	1	NA	exon (NM_009242, exon 7 of 10)	exon (NM_009242, exon 7 of 10)	20816	NM_009242	20692	Mm.291442	NM_009242	ENSMUSG00000018593	Sparc	BM-40|ON	secreted acidic cysteine rich glycoprotein	protein-coding
mm_53165.1	chr6	125322880	125322892	+	1	NA	intron (NM_011324, intron 1 of 11)	intron (NM_011324, intron 1 of 11)	1546	NM_011324	20276	Mm.144114	NM_011324	ENSMUSG00000030340	Scnn1a	ENaC|SCNEA|Scnn1|mENaC	sodium channel, nonvoltage-gated 1 alpha	protein-coding
mm_29044.1	chr3	103020933	103020953	-	1	NA	intron (NM_144901, intron 1 of 19)	CpG	397	NM_144901	229663	Mm.277713	NM_144901	ENSMUSG00000068823	Csde1	AA960392|BC016898|D3Jfr1|mKIAA0885|unr	cold shock domain containing E1, RNA binding	protein-coding
mm_114510.1	chr13	71487618	71487627	+	1	NA	Intergenic	ORR1A3-int|LTR|ERVL-MaLR	380533	NR_130325	100316804		NR_130325	ENSMUSG00000080580	Mir466f-4	Mirn466f-4|mmu-mir-466f-4	microRNA 466f-4	ncRNA
mm_85794.1	chr9	109848701	109848710	-	1	NA	exon (NM_009921, exon 2 of 4)	exon (NM_009921, exon 2 of 4)	751	NM_009921	12796	Mm.3834	NM_009921	ENSMUSG00000038357	Camp	CAP18|Cnlp|Cramp|FALL39|MCLP	cathelicidin antimicrobial peptide	protein-coding
mm_163131.1	chr11	78649150	78649151	-	1	NA	intron (NM_008702, intron 1 of 10)	intron (NM_008702, intron 1 of 10)	48275	NM_008702	18099	Mm.9001	NM_008702	ENSMUSG00000017376	Nlk	AI194375	nemo like kinase	protein-coding
mm_118301.1	chr13	113093872	113093888	-	1	NA	TTS (NM_010370)	TTS (NM_010370)	7101	NM_010370	14938	Mm.15510	NM_010370	ENSMUSG00000023132	Gzma	AW494114|Ctla-3|Ctla3|Hf|Hf1|SE1|TSP-1|TSP1	granzyme A	protein-coding
mm_48297.1	chr5	138263118	138263133	-	1	NA	promoter-TSS (NR_045821)	promoter-TSS (NR_045821)	-920	NR_045821	69004	Mm.439868	NR_045821	ENSMUSG00000085227	6330418K02Rik	-	RIKEN cDNA 6330418K02 gene	ncRNA
mm_152134.1	chr19	7028980	7028991	-	1	NA	exon (NM_016737, exon 7 of 14)	exon (NM_016737, exon 7 of 14)	-9516	NM_153795	108101	Mm.157591	NM_153795	ENSMUSG00000024965	Fermt3	C79673|Kindlin3	fermitin family member 3	protein-coding
mm_109543.1	chr12	111592650	111592672	+	1	NA	exon (NM_021516, exon 2 of 17)	exon (NM_021516, exon 2 of 17)	18151	NM_022801	17169	Mm.260504	NM_021516	ENSMUSG00000007411	Mark3	1600015G02Rik|A430080F22Rik|C-TAK1|ETK-1|ETK1|Emk2|MPK10	MAP/microtubule affinity regulating kinase 3	protein-coding
mm_113338.1	chr13	31625907	31625919	+	1	NA	promoter-TSS (NM_010225)	promoter-TSS (NM_010225)	97	NM_010225	14238	Mm.125548	NM_010225	ENSMUSG00000038402	Foxf2	FREAC2|Fkh20|LUN	forkhead box F2	protein-coding
mm_19094.1	chr2	79391559	79391561	-	1	NA	intron (NM_001048176, intron 2 of 12)	intron (NM_001048176, intron 2 of 12)	37428	NM_001048176	228094	Mm.440704	NM_001033295	ENSMUSG00000075256	Cerkl	Gm1958|Rp26	ceramide kinase-like	protein-coding
mm_68475.1	chr7	110851619	110851631	-	1	NA	3' UTR (NM_053247, exon 6 of 6)	3' UTR (NM_053247, exon 6 of 6)	-3310	NR_028551	100217456		NR_028551	ENSMUSG00000092887	Snord53	MBII-35	small nucleolar RNA, C/D box 53	snoRNA
mm_152833.1	chr19	23273790	23273796	-	1	NA	exon (NM_001252684, exon 1 of 25)	exon (NM_001252684, exon 1 of 25)	104	NM_153808	226026	Mm.23267	NM_153808	ENSMUSG00000024943	Smc5	MLZ-453|SMC-5|Smc5l1|mKIAA0594|mSMC5	structural maintenance of chromosomes 5	protein-coding
mm_86924.1	chr10	23894848	23894863	+	1	NA	5' UTR (NM_011704, exon 1 of 7)	5' UTR (NM_011704, exon 1 of 7)	167	NM_011704	22361	Mm.27154	NM_011704	ENSMUSG00000037440	Vnn1	V-1	vanin 1	protein-coding
mm_172855.1	chr9	39872032	39872050	-	1	NA	Intergenic	RLTR9D|LTR|ERVK	-1236	NM_146610	258603	Mm.271456	NM_146610	ENSMUSG00000094449	Olfr972	MOR171-17	olfactory receptor 972	protein-coding
mm_166338.1	chr5	114777722	114777741	+	1	NA	intron (NM_026718, intron 1 of 14)	intron (NM_026718, intron 1 of 14)	2591	NM_026718	68420	Mm.275554	NM_026718	ENSMUSG00000041870	Ankrd13a	1100001D10Rik|ANKRD13|AU046136	ankyrin repeat domain 13a	protein-coding
mm_57998.1	chr6	136173095	136173149	-	1	NA	intron (NM_008171, intron 1 of 14)	intron (NM_008171, intron 1 of 14)	389	NM_008171	14812	Mm.436649	NM_008171	ENSMUSG00000030209	Grin2b	AW490526|GluN2B|NR2B|Nmdar2b	glutamate receptor, ionotropic, NMDA2B (epsilon 2)	protein-coding
mm_49508.1	chr6	29854022	29854057	+	1	NA	5' UTR (NM_001347084, exon 2 of 18)	5' UTR (NM_001347084, exon 2 of 18)	298	NM_001347084	74340	Mm.210899	NM_021414	ENSMUSG00000029772	Ahcyl2	4631427C17Rik|AI227036|Adohcyase3|mKIAA0828	S-adenosylhomocysteine hydrolase-like 2	protein-coding
mm_123902.1	chr14	73217162	73217164	-	1	NA	intron (NM_009029, intron 17 of 26)	(GA)n|Simple_repeat|Simple_repeat	-10312	NR_030459	751541		NR_030459	ENSMUSG00000076121	Mir687	Mirn687|mir-687|mmu-mir-687	microRNA 687	ncRNA
mm_144405.1	chr18	20961243	20961249	+	1	NA	intron (NM_026301, intron 1 of 5)	intron (NM_026301, intron 1 of 5)	16621	NM_026301	67664	Mm.45980	NM_026301	ENSMUSG00000033107	Rnf125	4930553F04Rik	ring finger protein 125	protein-coding
mm_147388.1	chr18	44159930	44159938	-	1	NA	promoter-TSS (NM_001281470)	promoter-TSS (NM_001281470)	-49	NM_001281470	100042855	Mm.479515	NM_001165950	ENSMUSG00000069385	Gm10267	ENSMUSG00000069385|Vtlgl1	predicted gene 10267	protein-coding
mm_83158.1	chr9	40465684	40465699	-	1	NA	Intergenic	Intergenic	-9927	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_74564.1	chr8	11008231	11008243	-	1	NA	exon (NM_001081212, exon 1 of 2)	exon (NM_001081212, exon 1 of 2)	193	NM_001081212	384783	Mm.407207	NM_001081212	ENSMUSG00000038894	Irs2	Irs-2	insulin receptor substrate 2	protein-coding
mm_39582.1	chr5	23465219	23465233	+	1	NA	intron (NM_026984, intron 4 of 25)	intron (NM_026984, intron 4 of 25)	30797	NM_026984	69188	Mm.205190	NM_026984	ENSMUSG00000029004	Kmt2e	1810033J14Rik|9530077A04Rik|D230038D11Rik|Mll5|NKp44L	lysine (K)-specific methyltransferase 2E	protein-coding
mm_20057.1	chr2	120328450	120328458	-	1	NA	intron (NR_027618, intron 13 of 25)	intron (NR_027618, intron 13 of 25)	-14289	NM_001024145	271844	Mm.24880	NM_001024145	ENSMUSG00000046971	Pla2g4f	4732472I07Rik|Gm647|Pla2zeta	phospholipase A2, group IVF	protein-coding
mm_128195.1	chr15	35062397	35062407	-	1	NA	intron (NM_019635, intron 6 of 10)	B1_Mus1|SINE|Alu	93404	NM_019635	56274	Mm.262330	NM_019635	ENSMUSG00000022329	Stk3	0610042I06Rik|MST|Mst2|Mst3|Ste20|mess1	serine/threonine kinase 3	protein-coding
mm_145675.1	chr18	61555934	61556000	+	1	NA	intron (NM_146087, intron 1 of 9)	(CACG)n|Simple_repeat|Simple_repeat	385	NM_146087	93687	Mm.26908	NM_146087	ENSMUSG00000024576	Csnk1a1	2610208K14Rik|4632404G05Rik|5430427P18Rik|CK1a|Csnk1a	casein kinase 1, alpha 1	protein-coding
mm_76153.1	chr8	82354334	82354347	-	1	NA	intron (NM_008357, intron 2 of 7)	intron (NM_008357, intron 2 of 7)	48246	NM_001254747	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_159582.1	chr4	119233757	119233757	+	1	NA	promoter-TSS (NM_001042411)	promoter-TSS (NM_001042411)	-72	NM_001042411	56401	Mm.27961	NM_019782	ENSMUSG00000028641	P3h1	2410024C15Rik|Gros1|Lepre1	prolyl 3-hydroxylase 1	protein-coding
mm_55778.1	chr6	81910424	81910429	-	1	NA	intron (NR_046040, intron 1 of 5)	intron (NR_046040, intron 1 of 5)	374	NR_046040	74220	Mm.490521	NR_046040	ENSMUSG00000101404	1700009C05Rik	-	RIKEN cDNA 1700009C05 gene	ncRNA
mm_119125.1	chr14	31135703	31135722	+	1	NA	exon (NM_027289, exon 5 of 13)	exon (NM_027289, exon 5 of 13)	859	NM_027289	70021	Mm.261681	NM_027289	ENSMUSG00000071547	Nt5dc2	2510015F01Rik	5'-nucleotidase domain containing 2	protein-coding
mm_115123.1	chr13	104287119	104287132	+	1	NA	promoter-TSS (NM_001081020)	promoter-TSS (NM_001081020)	-710	NR_136938	108154	Mm.208125	NM_175496	ENSMUSG00000046169	Adamts6	A930019D11Rik|ADAM-TS6|b2b1879.1Clo|b2b2029Clo|b2b2182Clo|b2b2187.1Clo|b2b2228Clo	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 6	protein-coding
mm_85603.1	chr9	107566938	107566984	-	1	NA	TTS (NM_019742)	TTS (NM_019742)	-2202	NM_010489	15587	Mm.4834	NM_010489	ENSMUSG00000010047	Hyal2	AI256841|AU020858|AW555733	hyaluronoglucosaminidase 2	protein-coding
mm_150361.1	chr19	34649182	34649195	+	1	NA	3' UTR (NM_008331, exon 2 of 2)	3' UTR (NM_008331, exon 2 of 2)	8299	NM_008331	15957	Mm.439751	NM_008331	ENSMUSG00000034459	Ifit1	ISG56|Ifi56|P56	interferon-induced protein with tetratricopeptide repeats 1	protein-coding
mm_95615.1	chr11	53519726	53519791	+	1	NA	promoter-TSS (NM_001252332)	promoter-TSS (NM_001252332)	22	NM_001347496	20362	Mm.274399	NM_033144	ENSMUSG00000018398	Sept8	AW046166|Sepl	septin 8	protein-coding
mm_137602.1	chr17	28208304	28208347	+	1	NA	intron (NM_027185, intron 1 of 10)	intron (NM_027185, intron 1 of 10)	547	NM_027185	23853	Mm.204731	NM_027185	ENSMUSG00000002257	Def6	2410003F05Rik|6430538D02Rik|AV094905|Ibp|Slat|Slat2|Slat6	differentially expressed in FDCP 6	protein-coding
mm_65149.1	chr7	19592811	19592829	-	1	NA	intron (NM_016680, intron 5 of 20)	intron (NM_016680, intron 5 of 20)	11541	NR_125835	53609	Mm.20913	NM_016680	ENSMUSG00000061028	Clasrp	Clasp|Sfrs16|Srsf16|Swap2	CLK4-associating serine/arginine rich protein	protein-coding
mm_124499.1	chr14	121879394	121879422	-	1	NA	promoter-TSS (NR_130999)	promoter-TSS (NR_130999)	0	NR_130999	78312	Mm.188743	NR_130999	ENSMUSG00000102112	1810041H14Rik	-	RIKEN cDNA 1810041H14 gene	ncRNA
mm_100848.1	chr11	5803320	5803347	-	1	NA	exon (NM_018870, exon 1 of 3)	exon (NM_018870, exon 1 of 3)	463	NM_018870	56012	Mm.219627	NM_018870	ENSMUSG00000020475	Pgam2	-	phosphoglycerate mutase 2	protein-coding
mm_142161.1	chr17	36129506	36129508	-	1	NA	promoter-TSS (NM_001177467)	promoter-TSS (NM_001177467)	-82	NM_001177467	630294	Mm.484916	NM_001177467	ENSMUSG00000092243	Gm7030	EG630294|H2-t9	predicted gene 7030	protein-coding
mm_23501.1	chr3	60528248	60528256	+	1	NA	intron (NM_001253710, intron 1 of 7)	intron (NM_001253710, intron 1 of 7)	27073	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_139532.1	chr17	56680546	56680552	+	1	NA	intron (NR_045519, intron 1 of 16)	B1_Mus1|SINE|Alu	7324	NM_027933	71810	Mm.29608	NM_027933	ENSMUSG00000002372	Ranbp3	2610024N24Rik|AA408221	RAN binding protein 3	protein-coding
mm_126011.1	chr15	76616647	76616651	+	1	NA	exon (NM_028064, exon 1 of 12)	exon (NM_028064, exon 1 of 12)	203	NM_028064	72027	Mm.276829	NM_028064	ENSMUSG00000063354	Slc39a4	1600025H15Rik|AU041686|AWMS2|ZIP4	solute carrier family 39 (zinc transporter), member 4	protein-coding
mm_133876.1	chr16	96386391	96386400	+	1	NA	intron (NM_001177886, intron 4 of 8)	intron (NM_001177886, intron 4 of 8)	24631	NM_028078	72058	Mm.119714	NM_028078	ENSMUSG00000000159	Igsf5	2010003D20Rik|JCAM|Jam4	immunoglobulin superfamily, member 5	protein-coding
mm_52626.1	chr6	117174193	117174207	+	1	NA	3' UTR (NM_021704, exon 3 of 3)	3' UTR (NM_021704, exon 3 of 3)	5665	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_39534.1	chr5	21375753	21375774	+	1	NA	exon (NM_008013, exon 2 of 2)	exon (NM_008013, exon 2 of 2)	3090	NM_008013	14190	Mm.292100	NM_008013	ENSMUSG00000039899	Fgl2	AI385601|musfiblp	fibrinogen-like protein 2	protein-coding
mm_119861.1	chr14	54467958	54467977	+	1	NA	exon (NM_022993, exon 5 of 7)	exon (NM_022993, exon 5 of 7)	3820	NM_022993	65107	Mm.472719	NM_022993	ENSMUSG00000022175	Lrp10	Lrp9	low-density lipoprotein receptor-related protein 10	protein-coding
mm_162312.1	chr1	37584218	37584220	+	1	NA	Intergenic	Intergenic	-43203	NM_173870	269181	Mm.25861	NM_173870	ENSMUSG00000026110	Mgat4a	9530018I07Rik|GnT-IVa|glcNAc-T-IVa	mannoside acetylglucosaminyltransferase 4, isoenzyme A	protein-coding
mm_48764.1	chr5	148399765	148399782	-	1	NA	5' UTR (NM_007513, exon 1 of 13)	5' UTR (NM_007513, exon 1 of 13)	131	NM_007513	11987	Mm.275489	NM_007513	ENSMUSG00000041313	Slc7a1	4831426K01Rik|AI447493|Atrc-1|Atrc1|Cat1|Rec-1|Rev-1|mCAT-1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 1	protein-coding
mm_109495.1	chr12	111449625	111449651	+	1	NA	intron (NM_009396, intron 7 of 11)	intron (NM_009396, intron 7 of 11)	6977	NM_009396	21928	Mm.255332	NM_009396	ENSMUSG00000021281	Tnfaip2	B94|Exoc3l3|M-sec|Tnfip2|tnfb94	tumor necrosis factor, alpha-induced protein 2	protein-coding
mm_79499.1	chr9	57133759	57133762	+	1	NA	intron (NM_028636, intron 4 of 25)	B1_Mus1|SINE|Alu	-2470	NR_102289	76794	Mm.472839	NR_102289	ENSMUSG00000086728	Man2c1os	2410133F24Rik|AI851351	mannosidase, alpha, class 2C, member 1, opposite strand	ncRNA
mm_31720.1	chr4	62663684	62663709	+	1	NA	intron (NM_134257, intron 10 of 15)	intron (NM_134257, intron 10 of 15)	-10278	NM_001310706	50780	Mm.286753	NM_019492	ENSMUSG00000059810	Rgs3	4930506N09Rik|C2PA-RGS3|C2pa|PDZ-RGS3|RGS3S	regulator of G-protein signaling 3	protein-coding
mm_117658.1	chr13	93192271	93192328	-	1	NA	promoter-TSS (NM_133905)	promoter-TSS (NM_133905)	-16	NM_133905	100715	Mm.242865	NM_133905	ENSMUSG00000042167	Papd4	8030446C20Rik|AI649009|GLD-2|Gld2	PAP associated domain containing 4	protein-coding
mm_106238.1	chr11	117778989	117779029	-	1	NA	exon (NM_181321, exon 3 of 8)	exon (NM_181321, exon 3 of 8)	1612	NM_181321	217353	Mm.286963	NM_145439	ENSMUSG00000025572	Tmc6	D11Ertd204e|EVER1	transmembrane channel-like gene family 6	protein-coding
mm_17220.1	chr2	25500238	25500277	-	1	NA	promoter-TSS (NM_013908)	promoter-TSS (NM_013908)	249	NM_027062	69379	Mm.24596	NM_027062	ENSMUSG00000015083	C8g	-	complement component 8, gamma polypeptide	protein-coding
mm_11016.1	chr2	26591424	26591426	+	1	NA	promoter-TSS (NR_106155)	promoter-TSS (NR_106155)	-5	NR_106155	102465787		NR_106155	ENSMUSG00000105799	Mir126b	mmu-mir-126b	microRNA 126b	ncRNA
mm_96814.1	chr11	69992511	69992541	+	1	NA	intron (NM_019749, intron 2 of 3)	intron (NM_019749, intron 2 of 3)	1156	NM_019749	56486	Mm.272460	NM_019749	ENSMUSG00000018567	Gabarap	-	gamma-aminobutyric acid receptor associated protein	protein-coding
mm_111169.1	chr12	83606454	83606492	-	1	NA	Intergenic	RLTR11B|LTR|ERVK	-9326	NM_183154	217695	Mm.59257	NM_183154	ENSMUSG00000042628	Zfyve1	DFCP1|G630053K23|TAFF1|ZNFN2A1|mKIAA1589	zinc finger, FYVE domain containing 1	protein-coding
mm_168115.1	chr10	15520766	15520785	-	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-271002	NR_131087	77538	Mm.128235	NR_131087		C330004P14Rik	-	RIKEN cDNA C330004P14 gene	ncRNA
mm_73250.1	chr8	104322205	104322237	+	1	NA	promoter-TSS (NM_028524)	promoter-TSS (NM_028524)	-6	NM_028524	75502	Mm.232593	NM_028524	ENSMUSG00000035785	Cmtm2b	1700013O04Rik|Cklfsf22|Cklfsf2b	CKLF-like MARVEL transmembrane domain containing 2B	protein-coding
mm_106758.1	chr12	4234024	4234066	+	1	NA	promoter-TSS (NM_001204912)	promoter-TSS (NM_001204912)	18	NM_001204912	69709	Mm.250552	NM_001204912	ENSMUSG00000096199	Ptrhd1	2410017P09Rik	peptidyl-tRNA hydrolase domain containing 1	protein-coding
mm_38415.1	chr4	139130986	139131021	-	1	NA	promoter-TSS (NR_033745)	promoter-TSS (NR_033745)	34	NR_033745	433771	Mm.305990	NM_001163006	ENSMUSG00000050608	Minos1	2310028O11Rik	mitochondrial inner membrane organizing system 1	protein-coding
mm_123671.1	chr14	69249237	69249248	-	1	NA	intron (NM_026331, intron 2 of 3)	intron (NM_026331, intron 2 of 3)	35861	NM_026331	67712	Mm.293635	NM_026331	ENSMUSG00000034248	Slc25a37	1700020E22Rik|4930513O14Rik|4930526G11Rik|AI848481|C330015G08Rik|Mfrn|Mfrn1|Mscp|frascati|mitoferrin	solute carrier family 25, member 37	protein-coding
mm_65521.1	chr7	25772163	25772186	-	1	NA	intron (NM_001190974, intron 9 of 18)	intron (NM_001190974, intron 9 of 18)	16559	NM_001190974	26362	Mm.4128	NM_009465	ENSMUSG00000002602	Axl	AI323647|Ark|Tyro7|Ufo	AXL receptor tyrosine kinase	protein-coding
mm_147676.1	chr18	60649025	60649037	-	1	NA	Intergenic	Intergenic	-14379	NR_045401	328963	Mm.417203	NR_045401		G630071F17Rik	G630071F17	RIKEN cDNA G630071F17 gene	ncRNA
mm_97258.1	chr11	75758901	75758907	+	1	NA	intron (NM_009536, intron 4 of 5)	intron (NM_009536, intron 4 of 5)	26017	NM_009536	22627	Mm.234700	NM_009536	ENSMUSG00000020849	Ywhae	AU019196	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide	protein-coding
mm_51398.1	chr6	78371831	78371837	+	1	NA	exon (NM_011036, exon 3 of 6)	exon (NM_011036, exon 3 of 6)	949	NM_011036	18489	Mm.2553	NM_011036	ENSMUSG00000071356	Reg3b	HIP|PAP1|Pap|REG-III	regenerating islet-derived 3 beta	protein-coding
mm_136128.1	chr16	85901348	85901362	-	1	NA	promoter-TSS (NM_011782)	promoter-TSS (NM_011782)	-230	NM_011782	23794	Mm.112933	NM_011782	ENSMUSG00000022894	Adamts5	9530092O11Rik|ADAM-TS5|ADAMTS1|ADAMTS11|ADMP-2|AI481094|ASMP-2	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)	protein-coding
mm_136769.1	chr17	8988349	8988395	+	1	NA	promoter-TSS (NM_025851)	promoter-TSS (NM_025851)	39	NM_001347544	66931	Mm.67591	NM_025851	ENSMUSG00000023873	1700010I14Rik	-	RIKEN cDNA 1700010I14 gene	protein-coding
mm_151145.1	chr19	53131254	53131254	+	1	NA	Intergenic	Intergenic	-9189	NM_001164099	27360	Mm.426080	NM_013758	ENSMUSG00000025026	Add3	AI463285|R75380	adducin 3 (gamma)	protein-coding
mm_124331.1	chr14	103843686	103843703	-	1	NA	promoter-TSS (NM_001276296)	promoter-TSS (NM_001276296)	7	NM_007904	13618	Mm.229532	NM_007904	ENSMUSG00000022122	Ednrb	ET-B|ET-BR|ETR-b|ETb|Sox10m1	endothelin receptor type B	protein-coding
mm_129194.1	chr15	76477240	76477259	-	1	NA	promoter-TSS (NM_013481)	promoter-TSS (NM_013481)	20	NM_013481	12181	Mm.4283	NM_013481	ENSMUSG00000022557	Bop1	AU020183|AW146150|D18861|Erb1p|Kiaa0124|mKIAA0124	block of proliferation 1	protein-coding
mm_55068.1	chr6	49051070	49051095	-	1	NA	exon (NM_053110, exon 8 of 11)	exon (NM_053110, exon 8 of 11)	14564	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_127067.1	chr15	97373937	97373948	+	1	NA	intron (NM_172293, intron 4 of 5)	intron (NM_172293, intron 4 of 5)	-126655	NM_001164602	105827	Mm.24005	NM_178114	ENSMUSG00000048218	Amigo2	AI415330|AMIGO-2|AW208913|Ali1	adhesion molecule with Ig like domain 2	protein-coding
mm_100889.1	chr11	6065638	6065663	-	1	NA	promoter-TSS (NM_001174054)	promoter-TSS (NM_001174054)	98	NM_001174054	12323	Mm.439733	NM_007595	ENSMUSG00000057897	Camk2b	CaMKII	calcium/calmodulin-dependent protein kinase II, beta	protein-coding
mm_54456.1	chr6	34755816	34755885	-	1	NA	exon (NM_145575, exon 5 of 12)	exon (NM_145575, exon 5 of 12)	-24582	NM_001289657	76223	Mm.150047	NM_178630	ENSMUSG00000038836	Agbl3	2900053G10Rik|4930431N21Rik|6530406M24Rik|CCP3	ATP/GTP binding protein-like 3	protein-coding
mm_47146.1	chr5	120560405	120560413	-	1	NA	intron (NM_145853, intron 2 of 27)	ORR1B1|LTR|ERVL-MaLR	28204	NM_145853	252972	Mm.114054	NM_145853	ENSMUSG00000032741	Tpcn1	5730403B01Rik|Tpc1|mKIAA1169	two pore channel 1	protein-coding
mm_16451.1	chr2	180461033	180461041	+	1	NA	promoter-TSS (NM_148933)	promoter-TSS (NM_148933)	59	NM_148933	108115	Mm.133687	NM_148933	ENSMUSG00000038963	Slco4a1	OATP-E|Slc21a12	solute carrier organic anion transporter family, member 4a1	protein-coding
mm_57848.1	chr6	129468958	129468972	-	1	NA	exon (NM_020008, exon 3 of 6)	exon (NM_020008, exon 3 of 6)	3814	NM_001309637	56644	Mm.239516	NM_020008	ENSMUSG00000079293	Clec7a	BGR|Clecsf12|beta-GR	C-type lectin domain family 7, member a	protein-coding
mm_87978.1	chr10	63683308	63683310	+	1	NA	intron (NM_177612, intron 5 of 17)	intron (NM_177612, intron 5 of 17)	-137746	NM_001164519	216033	Mm.444692	NM_177612	ENSMUSG00000060843	Ctnna3	4930429L08Rik|4933408A16|Catna3|Vr22	catenin (cadherin associated protein), alpha 3	protein-coding
mm_53920.1	chr6	4086821	4086831	-	1	NA	5' UTR (NM_009748, exon 1 of 4)	5' UTR (NM_009748, exon 1 of 4)	101	NM_009748	12068	Mm.286457	NM_009748	ENSMUSG00000032757	Bet1	AW555236|Bet-1	Bet1 golgi vesicular membrane trafficking protein	protein-coding
mm_121622.1	chr14	8309679	8309725	-	1	NA	promoter-TSS (NM_183187)	promoter-TSS (NM_183187)	74	NM_183187	268709	Mm.256058	NM_183187	ENSMUSG00000021750	Fam107a	DRR1	family with sequence similarity 107, member A	protein-coding
mm_73664.1	chr8	111036903	111036912	+	1	NA	intron (NM_146217, intron 1 of 20)	intron (NM_146217, intron 1 of 20)	3065	NM_146217	234734	Mm.24174	NM_146217	ENSMUSG00000031960	Aars	AI316495|C76919|sti	alanyl-tRNA synthetase	protein-coding
mm_27535.1	chr3	57575845	57575849	-	1	NA	promoter-TSS (NM_133784)	promoter-TSS (NM_133784)	29	NM_133784	97064	Mm.405029	NM_133784	ENSMUSG00000027803	Wwtr1	2310058J06Rik|2610021I22Rik|C78399|Taz	WW domain containing transcription regulator 1	protein-coding
mm_57261.1	chr6	123285492	123285524	-	1	NA	exon (NM_019948, exon 5 of 6)	exon (NM_019948, exon 5 of 6)	4363	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_40306.1	chr5	43818877	43818892	+	1	NA	promoter-TSS (NM_009763)	promoter-TSS (NM_009763)	-9	NM_009763	12182	Mm.246332	NM_009763	ENSMUSG00000029082	Bst1	114/A10|A530073F09|BP-3|Bp3|Bsta1|CD157|Ly65	bone marrow stromal cell antigen 1	protein-coding
mm_73829.1	chr8	117460341	117460349	+	1	NA	3' UTR (NM_001163262, exon 21 of 21)	3' UTR (NM_001163262, exon 21 of 21)	1080	NR_106046	102465653		NR_106046	ENSMUSG00000098483	Mir7078	Gm27386|mmu-mir-7078	microRNA 7078	ncRNA
mm_26641.1	chr3	153723906	153723913	+	1	NA	intron (NM_011372, intron 1 of 4)	intron (NM_011372, intron 1 of 4)	1224	NM_011372	20447	Mm.296453	NM_011372	ENSMUSG00000052544	St6galnac3	Siat7c	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 3	protein-coding
mm_68986.1	chr7	126590254	126590256	-	1	NA	intron (NM_145636, intron 4 of 4)	intron (NM_145636, intron 4 of 4)	-4438	NM_001146311	12752	Mm.268930	NM_009907	ENSMUSG00000030720	Cln3	AI323623	ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease)	protein-coding
mm_26877.1	chr3	17761250	17761267	-	1	NA	Intergenic	Intergenic	-28663	NR_033490	70441	Mm.458192	NR_033490	ENSMUSG00000100252	Mir124-2hg	100040120|2610100L16Rik|6430547I21Rik|A930005K07Rik|AW125202|Gm2612	Mir124-2 host gene (non-protein coding)	ncRNA
mm_159058.1	chr1	195092388	195092388	-	1	NA	promoter-TSS (NM_010778)	promoter-TSS (NM_010778)	-140	NM_010778	17221	Mm.12884	NM_010778	ENSMUSG00000016493	Cd46	Mcp	CD46 antigen, complement regulatory protein	protein-coding
mm_19142.1	chr2	80447387	80447406	-	1	NA	promoter-TSS (NM_011356)	promoter-TSS (NM_011356)	0	NM_011356	20378	Mm.427436	NM_011356	ENSMUSG00000027004	Frzb	Frp|Sfrp3|frezzled|fritz|frzb-1	frizzled-related protein	protein-coding
mm_74601.1	chr8	11678697	11678706	-	1	NA	promoter-TSS (NM_024271)	promoter-TSS (NM_024271)	49	NM_024271	76413	Mm.440041	NM_024271	ENSMUSG00000031509	1700016D06Rik	-	RIKEN cDNA 1700016D06 gene	protein-coding
mm_166495.1	chr5	151406543	151406551	+	1	NA	promoter-TSS (NR_131166)	promoter-TSS (NR_131166)	43	NR_131166	100042166	Mm.443286	NR_131166	ENSMUSG00000097321	Gm3704	-	predicted gene 3704	ncRNA
mm_38574.1	chr4	141816735	141816738	-	1	NA	TTS (NM_015733)	TTS (NM_015733)	9269	NM_007919	13706	Mm.45316	NM_007919	ENSMUSG00000058579	Cela2a	Ela-2|Ela2|Ela2a	chymotrypsin-like elastase family, member 2A	protein-coding
mm_127993.1	chr15	12622404	12622413	-	1	NA	Intergenic	Intergenic	-29852	NM_001081064	68070	Mm.423205	NM_001081064	ENSMUSG00000022197	Pdzd2	4930537L06Rik|A930022H17Rik|Gm21706|Gm82|Pdzk3|mKIAA0300	PDZ domain containing 2	protein-coding
mm_48503.1	chr5	142817399	142817420	-	1	NA	promoter-TSS (NM_001122730)	promoter-TSS (NM_001122730)	-22	NM_001122730	231861	Mm.354649	NM_178242	ENSMUSG00000039477	Tnrc18	BC025631|EG381742|Zfp469	trinucleotide repeat containing 18	protein-coding
mm_47297.1	chr5	122253581	122253584	-	1	NA	intron (NR_104441, intron 5 of 12)	intron (NR_104441, intron 5 of 12)	10878	NR_104441	654470	Mm.28804	NM_001039153	ENSMUSG00000038593	Tctn1	G730031O11Rik|Tect1	tectonic family member 1	protein-coding
mm_44752.1	chr5	31291027	31291143	-	1	NA	promoter-TSS (NM_026298)	promoter-TSS (NM_026298)	29	NM_026298	67661	Mm.293023	NM_026298	ENSMUSG00000038564	Ift172	4930553F24Rik|Slb|avc1|wim	intraflagellar transport 172	protein-coding
mm_131277.1	chr16	11032101	11032139	+	1	NA	Intergenic	RLTR16|LTR|ERVK	23222	NR_040518	100043147	Mm.489001	NR_040518	ENSMUSG00000097056	Gm4262	-	predicted gene 4262	ncRNA
mm_96144.1	chr11	61022333	61022343	+	1	NA	promoter-TSS (NM_001267593)	promoter-TSS (NM_001267593)	-226	NM_001267593	16515	Mm.4970	NM_010603	ENSMUSG00000042529	Kcnj12	IRK-2|IRK2|Kir2.2|MB-IRK2	potassium inwardly-rectifying channel, subfamily J, member 12	protein-coding
mm_135731.1	chr16	55831264	55831287	-	1	NA	intron (NM_030612, intron 2 of 13)	B4|SINE|B4	7366	NM_030612	80859	Mm.247272	NM_030612	ENSMUSG00000035356	Nfkbiz	AA408868|INAP|Mail	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, zeta	protein-coding
mm_151695.1	chr19	4394644	4394647	-	1	NA	intron (NM_001001984, intron 2 of 20)	intron (NM_001001984, intron 2 of 20)	2432	NM_001001984	225876	Mm.31941	NM_001001984	ENSMUSG00000054611	Kdm2a	100043628|5530401A10Rik|AA589516|AW536790|Cxxc8|Fbl11|Fbl7|Fbxl11|Gm4560|Jhdm1|Jhdm1a|lalina	lysine (K)-specific demethylase 2A	protein-coding
mm_34097.1	chr4	138879386	138879399	+	1	NA	intron (NM_012044, intron 1 of 4)	intron (NM_012044, intron 1 of 4)	1450	NM_012044	26970	Mm.296007	NM_012044	ENSMUSG00000028751	Pla2g2e	-	phospholipase A2, group IIE	protein-coding
mm_165674.1	chr3	89437532	89437573	+	1	NA	intron (NM_146131, intron 1 of 10)	intron (NM_146131, intron 1 of 10)	848	NM_146131	229534	Mm.65906	NM_146131	ENSMUSG00000042613	Pbxip1	4732463H20Rik	pre B cell leukemia transcription factor interacting protein 1	protein-coding
mm_161350.1	chr14	55072010	55072010	-	1	NA	exon (NM_001039198, exon 4 of 10)	exon (NM_001039198, exon 4 of 10)	-1081	NR_004444	432855	Mm.490799	NR_004444	ENSMUSG00000093452	Zfhx2os	Zfhx2as	zinc finger homeobox 2, opposite strand	ncRNA
mm_46685.1	chr5	109751659	109751719	-	1	NA	Intergenic	Intergenic	82453	NR_027964	667213	Mm.454429	NR_027964	ENSMUSG00000105044	Gm10416	EG667213|ENSMUSG00000072761	zinc finger protein pseudogene	pseudo
mm_18821.1	chr2	74602131	74602152	-	1	NA	Intergenic	L1MEf|LINE|L1	-23193	NM_027133	69605	Mm.156113	NM_027133	ENSMUSG00000009207	Lnpk	2310011O18Rik|4921514L11Rik|9530051D01Rik|AI666268|Lnp|Lnpk1|Ul|ulnaless	lunapark, ER junction formation factor	protein-coding
mm_158369.1	chrX	135009227	135009236	-	1	NA	promoter-TSS (NM_175446)	promoter-TSS (NM_175446)	-22	NM_175446	215693	Mm.336238	NM_175446	ENSMUSG00000052676	Zmat1	A230096A06|AW990744|B930008K04Rik	zinc finger, matrin type 1	protein-coding
mm_90657.1	chr10	128804756	128804782	+	1	NA	promoter-TSS (NM_178066)	promoter-TSS (NM_178066)	-399	NM_178066	73827	Mm.24630	NM_178066	ENSMUSG00000047090	Tmem198b	1110012D08Rik	transmembrane protein 198b	protein-coding
mm_35276.1	chr4	19922555	19922572	-	1	NA	promoter-TSS (NM_175406)	promoter-TSS (NM_175406)	3	NM_175406	242341	Mm.19298	NM_175406	ENSMUSG00000028238	Atp6v0d2	1620401A02Rik|AI324824|V-ATPase	ATPase, H+ transporting, lysosomal V0 subunit D2	protein-coding
mm_172270.1	chr6	7983418	7983419	-	1	NA	Intergenic	Intergenic	138194	NM_052993	94192	Mm.102752	NM_052993	ENSMUSG00000042460	C1galt1	2210410E06Rik|AV284120|T-synthase	core 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase, 1	protein-coding
mm_169687.1	chr15	73809905	73809924	-	1	NA	intron (NM_001033365, intron 2 of 10)	CpG	29757	NM_001033365	268816	Mm.440635	NM_001033365	ENSMUSG00000072487	Mroh5	Gm628	maestro heat-like repeat family member 5	protein-coding
mm_107701.1	chr12	55465803	55465825	+	1	NA	intron (NR_035430, intron 1 of 3)	intron (NR_035430, intron 1 of 3)	26833	NM_010907	18035	Mm.170515	NM_010907	ENSMUSG00000021025	Nfkbia	AI462015|Nfkbi	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, alpha	protein-coding
mm_11702.1	chr2	36049454	36049507	+	1	NA	promoter-TSS (NM_029309)	promoter-TSS (NM_029309)	7	NM_029309	75495	Mm.276332	NM_029309	ENSMUSG00000026894	Morn5	1700010A17Rik	MORN repeat containing 5	protein-coding
mm_134721.1	chr16	22898177	22898189	-	1	NA	exon (NM_001276450, exon 6 of 7)	exon (NM_001276450, exon 6 of 7)	-3797	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_57928.1	chr6	134566802	134566812	-	1	NA	5' UTR (NM_008514, exon 1 of 23)	5' UTR (NM_008514, exon 1 of 23)	106	NM_008514	16974	Mm.321990	NM_008514	ENSMUSG00000030201	Lrp6	C030016K15Rik|Cd|Gw|ska26|ska<m26Jus>|skax26	low density lipoprotein receptor-related protein 6	protein-coding
mm_35911.1	chr4	49845854	49845863	-	1	NA	promoter-TSS (NM_001276355)	promoter-TSS (NM_001276355)	-89	NM_001276355	242443	Mm.440095	NM_001033351	ENSMUSG00000039579	Grin3a	6430537F04|A830097C19Rik|NMDAR-L|NR3A|mKIAA1973	glutamate receptor ionotropic, NMDA3A	protein-coding
mm_133357.1	chr16	84698921	84698964	+	1	NA	Intergenic	Intergenic	-14081	NR_132106	100653389	Mm.261808	NR_132106	ENSMUSG00000097418	Mir155hg	Bic|Gm26667	Mir155 host gene (non-protein coding)	ncRNA
mm_129033.1	chr15	74983370	74983389	-	1	NA	promoter-TSS (NM_020498)	promoter-TSS (NM_020498)	51	NM_020498	57248	Mm.358339	NM_020498	ENSMUSG00000022586	Ly6i	AI789751|Ly-6I|Ly-6M	lymphocyte antigen 6 complex, locus I	protein-coding
mm_69028.1	chr7	126796659	126796671	-	1	NA	exon (NM_001177307, exon 6 of 10)	exon (NM_001177307, exon 6 of 10)	2513	NM_001177307	11674	Mm.275831	NM_007438	ENSMUSG00000030695	Aldoa	Aldo-1|Aldo1	aldolase A, fructose-bisphosphate	protein-coding
mm_151829.1	chr19	5663636	5663670	-	1	NA	promoter-TSS (NM_001164482)	promoter-TSS (NM_001164482)	54	NM_001164482	20469	Mm.3072	NM_011379	ENSMUSG00000056917	Sipa1	Spa1	signal-induced proliferation associated gene 1	protein-coding
mm_52016.1	chr6	94500388	94500398	+	1	NA	promoter-TSS (NM_026255)	promoter-TSS (NM_026255)	79	NM_026255	67582	Mm.280725	NM_026255	ENSMUSG00000045100	Slc25a26	4930433D19Rik|4933433F13Rik|AW557176|D6Bwg0781e|Slc25a6	solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 26	protein-coding
mm_19453.1	chr2	92024293	92024335	-	1	NA	promoter-TSS (NM_011957)	promoter-TSS (NM_011957)	-144	NM_011957	26427	Mm.10353	NM_011957	ENSMUSG00000027230	Creb3l1	Oasis	cAMP responsive element binding protein 3-like 1	protein-coding
mm_122881.1	chr14	54926785	54926805	-	1	NA	promoter-TSS (NM_010112)	promoter-TSS (NM_010112)	-7	NM_010112	13644	Mm.236438	NM_010112	ENSMUSG00000022203	Efs	-	embryonal Fyn-associated substrate	protein-coding
mm_168326.1	chr11	116308835	116308841	+	1	NA	Intergenic	B2_Mm2|SINE|B2	-2088	NM_001347636	53413	Mm.22530	NM_016857	ENSMUSG00000020792	Exoc7	Exo70|sec70	exocyst complex component 7	protein-coding
mm_101156.1	chr11	16972254	16972274	-	1	NA	3' UTR (NM_019549, exon 10 of 10)	3' UTR (NM_019549, exon 10 of 10)	20854	NM_176982	319701	Mm.120672	NM_176982	ENSMUSG00000044966	Fbxo48	A630050E13Rik	F-box protein 48	protein-coding
mm_2293.1	chr1	91456806	91456812	+	1	NA	intron (NM_011066, intron 1 of 22)	intron (NM_011066, intron 1 of 22)	2519	NM_011066	18627	Mm.482463	NM_011066	ENSMUSG00000055866	Per2	mKIAA0347|mPer2	period circadian clock 2	protein-coding
mm_66026.1	chr7	30612798	30612881	-	1	NA	promoter-TSS (NM_026815)	promoter-TSS (NM_026815)	-105	NM_026815	109637	Mm.25471	NM_026815	ENSMUSG00000006313	Upk1a	1110031P12Rik|AU019298|C87192|Tspan21|Upk1	uroplakin 1A	protein-coding
mm_31949.1	chr4	86748562	86748572	+	1	NA	promoter-TSS (NM_184088)	promoter-TSS (NM_184088)	12	NM_184088	329877	Mm.273718	NM_184088	ENSMUSG00000038024	Dennd4c	1700065A05Rik|AA420392	DENN/MADD domain containing 4C	protein-coding
mm_132926.1	chr16	49840238	49840249	+	1	NA	Intergenic	Intergenic	-15411	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_75690.1	chr8	68206044	68206060	-	1	NA	Intergenic	Intergenic	-70476	NM_028182	72281	Mm.40974	NM_028182	ENSMUSG00000053886	Sh2d4a	2210402M20Rik|SH2A	SH2 domain containing 4A	protein-coding
mm_29901.1	chr3	131470947	131470951	-	1	NA	Intergenic	Intergenic	-93819	NM_001289479	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_112251.1	chr12	113662294	113662309	-	1	NA	Intergenic	Intergenic	118393	NM_174885	238406	Mm.188683	NM_174885	ENSMUSG00000043945	Adam6a	Adam6|tMDCIV	a disintegrin and metallopeptidase domain 6A	protein-coding
mm_51351.1	chr6	72556147	72556158	+	1	NA	exon (NM_001042534, exon 5 of 10)	exon (NM_001042534, exon 5 of 10)	6505	NM_001271395	12332	Mm.18626	NM_007599	ENSMUSG00000056737	Capg	gCap39|mbh1	capping protein (actin filament), gelsolin-like	protein-coding
mm_139789.1	chr17	65817056	65817061	+	1	NA	intron (NR_104465, intron 10 of 18)	intron (NR_104465, intron 10 of 18)	33703	NR_104465	70351	Mm.48686	NM_146081	ENSMUSG00000061950	Ppp4r1	3110001J10Rik|Pp4r1	protein phosphatase 4, regulatory subunit 1	protein-coding
mm_158559.1	chrX	150415078	150415090	-	1	NA	intron (NM_001164686, intron 2 of 2)	intron (NM_001164686, intron 2 of 2)	25821	NM_001164686	382245	Mm.277309	NM_001164683	ENSMUSG00000041353	Tmem29	2700081K05Rik|6330540D07Rik|CXorf44-like	transmembrane protein 29	protein-coding
mm_151906.1	chr19	5799476	5799486	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	3191	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_112717.1	chr13	19190334	19190349	+	1	NA	Intergenic	Intergenic	205472	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_7589.1	chr1	125435475	125435532	-	1	NA	5' UTR (NM_023735, exon 1 of 12)	5' UTR (NM_023735, exon 1 of 12)	224	NM_023735	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding
mm_96845.1	chr11	70031375	70031385	+	1	NA	exon (NM_007864, exon 7 of 20)	exon (NM_007864, exon 7 of 20)	12775	NM_007864	13385	Mm.27256	NM_007864	ENSMUSG00000020886	Dlg4	Dlgh4|PSD-95|PSD95|SAP90|SAP90A	discs, large homolog 4 (Drosophila)	protein-coding
mm_92720.1	chr10	80798856	80798898	-	1	NA	promoter-TSS (NM_023900)	promoter-TSS (NM_023900)	142	NM_013651	20222	Mm.358633	NM_013651	ENSMUSG00000020211	Sf3a2	66kDa|AW047242|PRP11|SFA66|Sap62	splicing factor 3a, subunit 2	protein-coding
mm_75054.1	chr8	33385443	33385453	-	1	NA	promoter-TSS (NM_001122822)	promoter-TSS (NM_001122822)	79	NM_001122822	22427	Mm.228805	NM_011721	ENSMUSG00000031583	Wrn	AI846146	Werner syndrome homolog (human)	protein-coding
mm_120279.1	chr14	63130892	63130922	+	1	NA	intron (NM_007798, intron 1 of 9)	intron (NM_007798, intron 1 of 9)	8445	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_156028.1	chrX	107255705	107255714	+	1	NA	promoter-TSS (NM_001177781)	promoter-TSS (NM_001177781)	-169	NM_001177781	213439	Mm.383562	NM_001033251	ENSMUSG00000073008	Gpr174	Gm376|Lypsr3	G protein-coupled receptor 174	protein-coding
mm_116058.1	chr13	27509622	27509622	-	1	NA	exon (NM_023741, exon 4 of 6)	exon (NM_023741, exon 4 of 6)	3591	NM_023741	74188	Mm.46090	NM_023741	ENSMUSG00000021346	Prl8a8	1600032B14Rik|Ghd14|PLP-Cgamma|Prlpc3	prolactin family 8, subfamily a, member 81	protein-coding
mm_75419.1	chr8	46764996	46765025	-	1	NA	intron (NM_008391, intron 1 of 8)	intron (NM_008391, intron 1 of 8)	25265	NM_008391	16363	Mm.1149	NM_008391	ENSMUSG00000031627	Irf2	9830146E22Rik|AI646973|Irf-2	interferon regulatory factor 2	protein-coding
mm_5490.1	chr1	36939495	36939503	-	1	NA	promoter-TSS (NM_018872)	promoter-TSS (NM_018872)	28	NM_018872	56030	Mm.186943	NM_018872	ENSMUSG00000026116	Tmem131	2610524E03Rik|CC28|D1Bwg0491e|Neg|RW1|YR-23|mKIAA0257	transmembrane protein 131	protein-coding
mm_48535.1	chr5	142904564	142904601	-	1	NA	exon (NM_007393, exon 4 of 6)	exon (NM_007393, exon 4 of 6)	2172	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_125360.1	chr15	39434324	39434334	+	1	NA	intron (NM_001256382, intron 3 of 26)	intron (NM_001256382, intron 3 of 26)	-225182	NM_001256384	116838	Mm.309296	NM_053271	ENSMUSG00000037386	Rims2	2810036I15Rik|AW048769|RIM2|Rab3ip2|Rim2(+40A)|Rim2(+44A)|Rim2(+4A)|Serg2|Syt3-rs|mKIAA0751	regulating synaptic membrane exocytosis 2	protein-coding
mm_136877.1	chr17	13007925	13007954	+	1	NA	promoter-TSS (NM_013671)	promoter-TSS (NM_013671)	100	NM_013671	20656	Mm.290876	NM_013671	ENSMUSG00000006818	Sod2	MnSOD|Sod-2	superoxide dismutase 2, mitochondrial	protein-coding
mm_116129.1	chr13	28953263	28953290	-	1	NA	5' UTR (NM_009238, exon 1 of 1)	5' UTR (NM_009238, exon 1 of 1)	406	NM_009238	20677	Mm.240627	NM_009238	ENSMUSG00000076431	Sox4	AA682046|Sox-4	SRY (sex determining region Y)-box 4	protein-coding
mm_152326.1	chr19	9945893	9945903	-	1	NA	Intergenic	B3|SINE|B2	-34702	NR_073181	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
mm_63533.1	chr7	127971107	127971111	+	1	NA	intron (NM_001347649, intron 3 of 14)	AT_rich|Low_complexity|Low_complexity	3630	NM_139149	233908	Mm.277680	NM_139149	ENSMUSG00000030795	Fus	D430004D17Rik|D930039C12Rik|Fus1|Tls	fused in sarcoma	protein-coding
mm_55403.1	chr6	60828890	60828900	-	1	NA	5' UTR (NM_001042451, exon 1 of 6)	5' UTR (NM_001042451, exon 1 of 6)	109	NM_001042451	20617	Mm.17484	NM_009221	ENSMUSG00000025889	Snca	NACP|alphaSYN	synuclein, alpha	protein-coding
mm_170304.1	chr18	34909931	34909935	-	1	NA	exon (NM_144866, exon 6 of 11)	exon (NM_144866, exon 6 of 11)	22070	NM_144866	225363	Mm.329353	NM_144866	ENSMUSG00000024360	Etf1	AI463371|D6Ertd109e|ERF|ERF1|SUP45L1|TB3-1	eukaryotic translation termination factor 1	protein-coding
mm_39178.1	chr4	155784899	155784933	-	1	NA	intron (NM_001033394, intron 1 of 1)	intron (NM_001033394, intron 1 of 1)	958	NM_001033394	320587	Mm.384382	NM_001033394	ENSMUSG00000073680	Tmem88b	A230069A22Rik	transmembrane protein 88B	protein-coding
mm_136764.1	chr17	8801769	8801788	+	1	NA	promoter-TSS (NM_011866)	promoter-TSS (NM_011866)	33	NM_011866	23984	Mm.87161	NM_011866	ENSMUSG00000023868	Pde10a	-	phosphodiesterase 10A	protein-coding
mm_133434.1	chr16	87698905	87698959	+	1	NA	promoter-TSS (NM_007520)	promoter-TSS (NM_007520)	-22	NM_007520	12013	Mm.26147	NM_007520	ENSMUSG00000025612	Bach1	6230421P05Rik|AI323795	BTB and CNC homology 1, basic leucine zipper transcription factor 1	protein-coding
mm_64260.1	chr7	141745521	141745536	+	1	NA	exon (NM_023566, exon 29 of 46)	exon (NM_023566, exon 29 of 46)	-43483	NM_010844	17833	Mm.334332	NM_010844	ENSMUSG00000037974	Muc5ac	2210005L13Rik|MGM	mucin 5, subtypes A and C, tracheobronchial/gastric	protein-coding
mm_37600.1	chr4	126752078	126752109	-	1	NA	intron (NM_011986, intron 1 of 6)	intron (NM_011986, intron 1 of 6)	1336	NM_011986	26562	Mm.206206	NM_011986	ENSMUSG00000028833	Ncdn	AU042419|MMS10-AE|Ms10ae|mKIAA0607|norbin	neurochondrin	protein-coding
mm_160876.1	chr11	68973840	68973840	-	1	NA	promoter-TSS (NM_021329)	promoter-TSS (NM_021329)	15	NM_021329	57785	Mm.143774	NM_021329	ENSMUSG00000032892	Rangrf	2400006H24Rik|Mog1|Rangnrf	RAN guanine nucleotide release factor	protein-coding
mm_165597.1	chr3	42896712	42896713	+	1	NA	Intergenic	Intergenic	1154094	NM_027271	73852	Mm.29006	NM_027271	ENSMUSG00000025766	D3Ertd751e	2810009O15Rik|4930415G15Rik	DNA segment, Chr 3, ERATO Doi 751, expressed	protein-coding
mm_124341.1	chr14	103844315	103844340	-	1	NA	promoter-TSS (NM_001276296)	promoter-TSS (NM_001276296)	149	NM_001136061	13618	Mm.229532	NM_007904	ENSMUSG00000022122	Ednrb	ET-B|ET-BR|ETR-b|ETb|Sox10m1	endothelin receptor type B	protein-coding
mm_90095.1	chr10	116962463	116962467	+	1	NA	non-coding (NR_038026, exon 3 of 3)	non-coding (NR_038026, exon 3 of 3)	-2275	NR_027847	103175	Mm.27138	NR_027846	ENSMUSG00000031294	D630029K05Rik	AI314111|AI875589	RIKEN cDNA D630029K05 gene	ncRNA
mm_44499.1	chr5	23712854	23712887	-	1	NA	promoter-TSS (NR_038090)	promoter-TSS (NR_038090)	-203	NR_015554	433855	Mm.205125	NR_015554	ENSMUSG00000105987	AI506816	-	expressed sequence AI506816	ncRNA
mm_94579.1	chr11	11690292	11690312	+	1	NA	5' UTR (NM_001301865, exon 1 of 7)	5' UTR (NM_001301865, exon 1 of 7)	125	NM_001301863	22778	Mm.103545	NM_009578	ENSMUSG00000018654	Ikzf1	5832432G11Rik|Ikaros|LyF-1|Zfpn1a1|Znfn1a1|hlk-1|mKIAA4227	IKAROS family zinc finger 1	protein-coding
mm_118649.1	chr14	21657531	21657571	+	1	NA	intron (NM_017479, intron 12 of 16)	intron (NM_017479, intron 12 of 16)	57025	NM_001013826	435391	Mm.295860	NM_001013826	ENSMUSG00000063821	Dupd1	EG435391	dual specificity phosphatase and pro isomerase domain containing 1	protein-coding
mm_59239.1	chr7	24778412	24778421	+	1	NA	exon (NM_007675, exon 2 of 4)	exon (NM_007675, exon 2 of 4)	1212	NM_007675	26366	Mm.30300	NM_007675	ENSMUSG00000054169	Ceacam10	Bgp3|Cea10	carcinoembryonic antigen-related cell adhesion molecule 10	protein-coding
mm_50718.1	chr6	52217634	52217646	+	1	NA	5' UTR (NM_010455, exon 1 of 2)	5' UTR (NM_010455, exon 1 of 2)	933	NM_010455	15404	Mm.294826	NM_010455	ENSMUSG00000038236	Hoxa7	AV118143|Hox-1.1|M6	homeobox A7	protein-coding
mm_46898.1	chr5	114091332	114091346	-	1	NA	promoter-TSS (NM_026805)	promoter-TSS (NM_026805)	41	NM_026805	68666	Mm.63584	NM_026805	ENSMUSG00000042078	Svop	1110030H18Rik|AI415691|msvop	SV2 related protein	protein-coding
mm_139337.1	chr17	49454837	49454848	+	1	NA	3' UTR (NM_020042, exon 11 of 11)	3' UTR (NM_020042, exon 11 of 11)	26478	NM_020042	56738	Mm.22256	NM_020042	ENSMUSG00000064120	Mocs1	3110045D15Rik|AI043170|AW536397	molybdenum cofactor synthesis 1	protein-coding
mm_8618.1	chr1	156037348	156037353	-	1	NA	promoter-TSS (NM_144791)	promoter-TSS (NM_144791)	-870	NM_001160018	208263	Mm.211654	NM_144791	ENSMUSG00000026466	Tor1aip1	LAP1|Lap1B	torsin A interacting protein 1	protein-coding
mm_4354.1	chr1	171917439	171917472	+	1	NA	promoter-TSS (NM_030710)	promoter-TSS (NM_030710)	-7	NM_001347187	30925	Mm.486404	NM_030710	ENSMUSG00000015314	Slamf6	KAL1|KAL1b|Ly108|NTB-A|NTBA|SF2000	SLAM family member 6	protein-coding
mm_41240.1	chr5	88765170	88765191	+	1	NA	5' UTR (NM_007832, exon 1 of 7)	5' UTR (NM_007832, exon 1 of 7)	167	NM_007832	13178	Mm.298892	NM_007832	ENSMUSG00000029366	Dck	-	deoxycytidine kinase	protein-coding
mm_169952.1	chr16	83579406	83579406	+	1	NA	Intergenic	RLTR9D|LTR|ERVK	-791737	NR_040567	75247	Mm.417813	NR_040567		4930553E22Rik	-	RIKEN cDNA 4930553E22 gene	ncRNA
mm_126208.1	chr15	78889821	78889834	+	1	NA	exon (NM_145929, exon 11 of 17)	exon (NM_145929, exon 11 of 17)	-2013	NR_105920	102466210		NR_105920	ENSMUSG00000099267	Mir6955	Gm27769|mmu-mir-6955	microRNA 6955	ncRNA
mm_41321.1	chr5	90472456	90472481	+	1	NA	exon (NM_009654, exon 12 of 15)	exon (NM_009654, exon 12 of 15)	11598	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_144893.1	chr18	36960270	36960298	+	1	NA	promoter-TSS (NM_009959)	promoter-TSS (NM_009959)	-156	NM_009959	12941	Mm.308500	NM_009959	ENSMUSG00000103092	Pcdha5	Cnr6|Crnr6	protocadherin alpha 5	protein-coding
mm_2359.1	chr1	92973114	92973127	+	1	NA	promoter-TSS (NM_001104529)	promoter-TSS (NM_001104529)	1	NM_001104529	64095	Mm.152780	NM_022320	ENSMUSG00000026271	Gpr35	KPG_007	G protein-coupled receptor 35	protein-coding
mm_57082.1	chr6	122582049	122582067	-	1	NA	intron (NM_001134391, intron 5 of 7)	(TG)n|Simple_repeat|Simple_repeat	20386	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_158332.1	chrX	133961773	133961775	-	1	NA	exon (NM_001290718, exon 3 of 14)	exon (NM_001290718, exon 3 of 14)	20038	NM_001290718	27359	Mm.38674	NM_013757	ENSMUSG00000031255	Sytl4	Gph|Slp4	synaptotagmin-like 4	protein-coding
mm_6064.1	chr1	60567078	60567111	-	1	NA	promoter-TSS (NM_001045513)	promoter-TSS (NM_001045513)	-329	NM_001045513	77300	Mm.440325	NM_001045513	ENSMUSG00000026014	Raph1	9430025M21Rik|C730009O10Rik|Lpd	Ras association (RalGDS/AF-6) and pleckstrin homology domains 1	protein-coding
mm_76398.1	chr8	84844664	84844692	-	1	NA	exon (NM_007591, exon 5 of 9)	exon (NM_007591, exon 5 of 9)	2253	NM_007591	12317	Mm.1971	NM_007591	ENSMUSG00000003814	Calr	CRT|Calregulin	calreticulin	protein-coding
mm_71365.1	chr8	45696415	45696418	+	1	NA	intron (NM_001310708, intron 1 of 19)	intron (NM_001310708, intron 1 of 19)	34423	NM_001310708	234214	Mm.211096	NM_172752	ENSMUSG00000031626	Sorbs2	2010203O03Rik|9430041O17Rik|A530071H08|Argbp2|mKIAA0777|nArgBP2	sorbin and SH3 domain containing 2	protein-coding
mm_171301.1	chr3	93676308	93676314	-	1	NA	promoter-TSS (NM_148949)	promoter-TSS (NM_148949)	-28	NM_148949	207213	Mm.425165	NM_148949	ENSMUSG00000094084	Tdpoz1	2cpoz56|Mapp2|Spopl1	TD and POZ domain containing 1	protein-coding
mm_75138.1	chr8	35250706	35250713	-	1	NA	Intergenic	LTR78B|LTR|ERV1	-125032	NM_177741	244416	Mm.247126	NM_177741	ENSMUSG00000046794	Ppp1r3b	6430576E21|AW821953|GL|PTG	protein phosphatase 1, regulatory (inhibitor) subunit 3B	protein-coding
mm_158968.1	chr1	97894456	97894456	-	1	NA	exon (NM_013626, exon 12 of 26)	exon (NM_013626, exon 12 of 26)	124284	NM_026250	252876	Mm.86090	NM_026250	ENSMUSG00000026333	Gin1	4930429M06Rik|8430411H10Rik|Gin-1|Zh2c2	gypsy retrotransposon integrase 1	protein-coding
mm_148418.1	chr19	3936093	3936103	+	1	NA	intron (NM_001161428, intron 2 of 9)	intron (NM_001161428, intron 2 of 9)	912	NM_001161428	54445	Mm.262094	NM_019449	ENSMUSG00000036908	Unc93b1	Unc-93B1|Unc93b	unc-93 homolog B1 (C. elegans)	protein-coding
mm_50704.1	chr6	52103976	52103980	+	1	NA	intron (NR_110440, intron 1 of 2)	intron (NR_110440, intron 1 of 2)	1029	NR_110440	102635415	Mm.333063	NR_110440	ENSMUSG00000085412	Halr1	Gm15055|Haunt|Linchoxa1|OTTMUSG00000018881|linc-Evx1|linc-Hoxa1|linc1547	Hoxa adjacent long noncoding RNA 1	ncRNA
mm_151026.1	chr19	46985519	46985532	+	1	NA	intron (NM_001164363, intron 1 of 17)	B1F|SINE|Alu	-15958	NM_001164365	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_16538.1	chr2	181601348	181601415	+	1	NA	promoter-TSS (NM_133701)	promoter-TSS (NM_133701)	62	NM_133701	68879	Mm.292001	NM_133701	ENSMUSG00000002455	Prpf6	1190003A07Rik|2610031L17Rik|ANT-1|U5-102K	pre-mRNA splicing factor 6	protein-coding
mm_132213.1	chr16	32621572	32621573	+	1	NA	intron (NM_011638, intron 11 of 18)	BC1_Mm|scRNA|scRNA	12676	NM_011638	22042	Mm.28683	NM_011638	ENSMUSG00000022797	Tfrc	2610028K12Rik|CD71|E430033M20Rik|Mtvr1|TFR|TFR1|TR|Trfr|p90	transferrin receptor	protein-coding
mm_48902.1	chr6	3344596	3344622	+	1	NA	Intergenic	Intergenic	54962	NM_010156	209086	Mm.196013	NM_010156	ENSMUSG00000047735	Samd9l	AA175286|ESTM25|mKIAA2005	sterile alpha motif domain containing 9-like	protein-coding
mm_34621.1	chr4	150566456	150566494	+	1	NA	intron (NM_001085492, intron 11 of 22)	L2|LINE|L2	85699	NM_173774	242773	Mm.29280	NM_173774	ENSMUSG00000039838	Slc45a1	C230078B22|Dnb5	solute carrier family 45, member 1	protein-coding
mm_146087.1	chr18	73556924	73556934	+	1	NA	Intergenic	Intergenic	-15776	NM_001039214	240396	Mm.24131	NM_001039214	ENSMUSG00000037253	Mex3c	A130001D14Rik|BC035207|BM-013|Rkhd2	mex3 RNA binding family member C	protein-coding
mm_92920.1	chr10	84440537	84440547	-	1	NA	promoter-TSS (NM_001004363)	promoter-TSS (NM_001004363)	-71	NM_001004363	77976	Mm.25874	NM_001004363	ENSMUSG00000020032	Nuak1	AU014801|AW494241|B230104P22Rik|Omphk1	NUAK family, SNF1-like kinase, 1	protein-coding
mm_101331.1	chr11	23069223	23069228	-	1	NA	Intergenic	RLTR10C|LTR|ERVK	55838	NM_028672	73873	Mm.252406	NM_028672	ENSMUSG00000049811	Fam161a	4930430E16Rik	family with sequence similarity 161, member A	protein-coding
mm_153762.1	chr19	45591781	45591815	-	1	NA	intron (NM_013907, intron 5 of 8)	intron (NM_013907, intron 5 of 8)	31183	NM_172639	226162	Mm.21978	NM_172639	ENSMUSG00000041035	Dpcd	5330431N19Rik|Ndac	deleted in primary ciliary dyskinesia	protein-coding
mm_3752.1	chr1	156035776	156035788	+	1	NA	promoter-TSS (NM_001160182)	promoter-TSS (NM_001160182)	55	NM_001160180	240832	Mm.253335	NM_022329	ENSMUSG00000050565	Tor1aip2	1110020D10Rik|15kDa|A130072J07|AA103493|AW060462|AW610675|C77739|Ifrg15|Lull1	torsin A interacting protein 2	protein-coding
mm_11031.1	chr2	26913380	26913406	+	1	NA	TTS (NM_013677)	TTS (NM_013677)	2586	NM_013721	27176	Mm.328601	NM_013721	ENSMUSG00000062647	Rpl7a	Surf3	ribosomal protein L7A	protein-coding
mm_127487.1	chr15	101293219	101293237	+	1	NA	promoter-TSS (NR_033803)	promoter-TSS (NR_033803)	16	NR_033803	77717	Mm.391998	NR_033803	ENSMUSG00000075408	6030408B16Rik	AI225877	RIKEN cDNA 6030408B16 gene	ncRNA
mm_140404.1	chr17	87640446	87640463	+	1	NA	exon (NM_008532, exon 4 of 10)	exon (NM_008532, exon 4 of 10)	4475	NM_008532	17075	Mm.4259	NM_008532	ENSMUSG00000045394	Epcam	CD326|EGP|EGP-2|Egp314|Ep-CAM|EpCAM1|GA733-2|Ly74|TROP1|Tacsd1|Tacstd1|gp40	epithelial cell adhesion molecule	protein-coding
mm_148604.1	chr19	5308253	5308272	+	1	NA	3' UTR (NM_001024717, exon 3 of 3)	3' UTR (NM_001024717, exon 3 of 3)	9931	NM_001024717	545276	Mm.447174	NM_001024717	ENSMUSG00000047658	Gal3st3	-	galactose-3-O-sulfotransferase 3	protein-coding
mm_74534.1	chr8	9727183	9727186	-	1	NA	intron (NM_001347127, intron 1 of 3)	intron (NM_001347127, intron 1 of 3)	43839	NM_173446	270028	Mm.268163	NM_173446	ENSMUSG00000079157	Fam155a	6430500D16|AW121567|Tmem28	family with sequence similarity 155, member A	protein-coding
mm_63261.1	chr7	126695356	126695431	+	1	NA	promoter-TSS (NM_175103)	promoter-TSS (NM_175103)	390	NM_029420	75764	Mm.280573	NM_029420	ENSMUSG00000059772	Slx1b	1110030E23Rik|2410170E21Rik|4833422P03Rik|AI853643|Giyd1|Giyd2	SLX1 structure-specific endonuclease subunit homolog B (S. cerevisiae)	protein-coding
mm_141215.1	chr17	27167749	27167757	-	1	NA	promoter-TSS (NM_173027)	promoter-TSS (NM_173027)	11	NM_173027	271424	Mm.209679	NM_173027	ENSMUSG00000024210	Ip6k3	D830007E07Rik|Ihpk3	inositol hexaphosphate kinase 3	protein-coding
mm_107540.1	chr12	40575617	40575618	+	1	NA	intron (NM_172803, intron 1 of 52)	intron (NM_172803, intron 1 of 52)	129564	NM_172803	238130	Mm.341423	NM_172803	ENSMUSG00000035954	Dock4	5330406C03|6330411N01Rik|AF263288|C030023J22|mKIAA0716	dedicator of cytokinesis 4	protein-coding
mm_10363.1	chr2	11705438	11705448	+	1	NA	promoter-TSS (NM_001271500)	promoter-TSS (NM_001271500)	150	NM_001271497	16169	Mm.200196	NM_008358	ENSMUSG00000023206	Il15ra	AA690181|IL-15RA	interleukin 15 receptor, alpha chain	protein-coding
mm_107826.1	chr12	69168842	69168854	+	1	NA	promoter-TSS (NM_001081406)	promoter-TSS (NM_001081406)	34	NM_001081406	69706	Mm.28847	NM_027178	ENSMUSG00000034883	Lrr1	2410005L11Rik|AU021780|LRR-1|Ppil5	leucine rich repeat protein 1	protein-coding
mm_148994.1	chr19	8618190	8618200	+	1	NA	5' UTR (NM_008766, exon 1 of 10)	5' UTR (NM_008766, exon 1 of 10)	199	NM_008766	18399	Mm.30090	NM_008766	ENSMUSG00000024650	Slc22a6	NKT|Oat1|Orctl1|mOat1	solute carrier family 22 (organic anion transporter), member 6	protein-coding
mm_51200.1	chr6	71284454	71284465	+	1	NA	exon (NM_145568, exon 4 of 4)	exon (NM_145568, exon 4 of 4)	12440	NM_145568	57896	Mm.250569	NM_145568	ENSMUSG00000053012	Krcc1	AA792894	lysine-rich coiled-coil 1	protein-coding
mm_171285.1	chr3	89998636	89998637	-	1	NA	promoter-TSS (NM_011826)	promoter-TSS (NM_011826)	80	NM_011826	23897	Mm.256035	NM_011826	ENSMUSG00000027944	Hax1	HAX-1|HSP1BP-1|Hs1bp1|SIG-111|Silg111|mHAX-1s	HCLS1 associated X-1	protein-coding
mm_30448.1	chr3	153852391	153852412	-	1	NA	promoter-TSS (NR_040373)	promoter-TSS (NR_040373)	23	NR_040373	72317	Mm.440147	NR_040373	ENSMUSG00000086438	Asb17os	2510003D18Rik	ankyrin repeat and SOCS box-containing 17, opposite strand	ncRNA
mm_86268.1	chr9	121706369	121706388	-	1	NA	Intergenic	Intergenic	-1349	NM_178677	215474	Mm.31421	NM_178677	ENSMUSG00000061536	Sec22c	4932412K21|5930407I15Rik|C530046H07|Sec22l3	SEC22 homolog C, vesicle trafficking protein	protein-coding
mm_43628.1	chr5	138180147	138180150	+	1	NA	intron (NM_009315, intron 12 of 14)	intron (NM_009315, intron 12 of 14)	7038	NM_009315	21343	Mm.248517	NM_009315	ENSMUSG00000036980	Taf6	80kDa|AW549759|TAF(II)80|TAFII70|Taf2e|p80	TATA-box binding protein associated factor 6	protein-coding
mm_31848.1	chr4	74265191	74265193	+	1	NA	intron (NM_001172095, intron 2 of 21)	intron (NM_001172095, intron 2 of 21)	13313	NM_144787	76804	Mm.209059	NM_144787	ENSMUSG00000028397	Kdm4c	2410141F18Rik|AA517467|Gasc1|Jmjd2c	lysine (K)-specific demethylase 4C	protein-coding
mm_173008.1	chrM	236	236	+	1	NA	NA	Intergenic	NA	NA								
mm_65924.1	chr7	30242876	30242882	-	1	NA	intron (NM_146186, intron 26 of 32)	intron (NM_146186, intron 26 of 32)	-6114	NM_001289817	381867	Mm.483986	NM_001289817	ENSMUSG00000100512	Ovol3	Gm1903|movo3	ovo like zinc finger 3	protein-coding
mm_129304.1	chr15	77376911	77376919	-	1	NA	Intergenic	MERV1_I-int|LTR|ERV1	22195	NM_029419	75761	Mm.232636	NM_029419	ENSMUSG00000010601	Apol7a	9130022K13Rik|Apol3	apolipoprotein L 7a	protein-coding
mm_69916.1	chr7	141704390	141704402	-	1	NA	intron (NM_023566, intron 27 of 45)	intron (NM_023566, intron 27 of 45)	14056	NM_023566	17831	Mm.2041	NM_023566		Muc2	2010015E03Rik|MCM|wnn	mucin 2	protein-coding
mm_172427.1	chr7	28338719	28338720	-	1	NA	promoter-TSS (NM_013676)	promoter-TSS (NM_013676)	0	NM_013676	20924	Mm.285906	NM_013676	ENSMUSG00000003435	Supt5	AL033283|AL033321|AU019549|Spt5|Supt5h	suppressor of Ty 5	protein-coding
mm_113967.1	chr13	51645311	51645332	+	1	NA	promoter-TSS (NM_025415)	promoter-TSS (NM_025415)	89	NM_025415	66197	Mm.222228	NM_025415	ENSMUSG00000062248	Cks2	1110038L14Rik|CKSHS2	CDC28 protein kinase regulatory subunit 2	protein-coding
mm_14151.1	chr2	126561663	126561700	+	1	NA	exon (NM_011978, exon 2 of 10)	exon (NM_011978, exon 2 of 10)	8657	NM_011978	26458	Mm.290044	NM_011978	ENSMUSG00000027359	Slc27a2	ACSVL1|FATP2|VLCS|Vlac|Vlacs	solute carrier family 27 (fatty acid transporter), member 2	protein-coding
mm_77185.1	chr8	111743869	111743887	-	1	NA	promoter-TSS (NM_009954)	promoter-TSS (NM_009954)	-29	NM_009954	12927	Mm.3758	NM_009954	ENSMUSG00000031955	Bcar1	AI385681|Cas|Crkas	breast cancer anti-estrogen resistance 1	protein-coding
mm_45126.1	chr5	48331424	48331426	-	1	NA	Intergenic	Intergenic	-40967	NM_025755	66768	Mm.29409	NM_025755	ENSMUSG00000029089	Pacrgl	4933428G09Rik	PARK2 co-regulated-like	protein-coding
mm_141690.1	chr17	33955659	33955686	-	1	NA	promoter-TSS (NM_011296)	promoter-TSS (NM_011296)	-31	NM_011296	20084	Mm.298745	NM_011296	ENSMUSG00000008668	Rps18	H-2Ke3|H2-Ke3|Ke-3|ke3	ribosomal protein S18	protein-coding
mm_141727.1	chr17	34116272	34116287	-	1	NA	exon (NM_001204973, exon 4 of 13)	exon (NM_001204973, exon 4 of 13)	3621	NR_037970	14312	Mm.3444	NM_010238	ENSMUSG00000024335	Brd2	AW228947|D17H6S113E|Frg-1|Fsrg-1|Fsrg1|Nat|Ring3|Rnf3|mKIAA4005	bromodomain containing 2	protein-coding
mm_36022.1	chr4	56990333	56990396	-	1	NA	promoter-TSS (NM_001142965)	promoter-TSS (NM_001142965)	27	NM_001142965	230235	Mm.207654	NM_001142965	ENSMUSG00000045589	Frrs1l	6430704M03Rik	ferric-chelate reductase 1 like	protein-coding
mm_130817.1	chr15	101786516	101786528	-	1	NA	promoter-TSS (NM_213728)	promoter-TSS (NM_213728)	-64	NM_213728	105866	Mm.298210	NM_213728	ENSMUSG00000056605	Krt72	AI507495|K6irs2|Krt2-35|Krt72-ps	keratin 72	protein-coding
mm_37130.1	chr4	116708263	116708269	-	1	NA	promoter-TSS (NM_026714)	promoter-TSS (NM_026714)	119	NM_025962	67096	Mm.252785	NM_025962	ENSMUSG00000028690	Mmachc	1810037K07Rik|CblC	methylmalonic aciduria cblC type, with homocystinuria	protein-coding
mm_130133.1	chr15	90829818	90829818	-	1	NA	Intergenic	RMER19B|LTR|ERVK	68658	NR_033583	20738	Mm.431547	NR_033583		Spn-ps	Cd43-ps	sialophorin, pseudogene	pseudo
mm_59883.1	chr7	30292146	30292169	+	1	NA	5' UTR (NM_001081114, exon 2 of 14)	5' UTR (NM_001081114, exon 2 of 14)	404	NM_001081114	76686	Mm.159258	NM_001081114	ENSMUSG00000013921	Clip3	1500005P14Rik|AI844915|Clipr-59	CAP-GLY domain containing linker protein 3	protein-coding
mm_171940.1	chr5	6741909	6741909	-	1	NA	Intergenic	L1Md_T|LINE|L1	-562255	NM_027603	70920	Mm.158494	NM_027603	ENSMUSG00000040514	4921511H03Rik	-	RIKEN cDNA 4921511H03 gene	protein-coding
mm_132214.1	chr16	32628473	32628492	+	1	NA	exon (NM_011638, exon 18 of 19)	exon (NM_011638, exon 18 of 19)	-16161	NM_001110147	51789	Mm.251115	NM_016788	ENSMUSG00000022791	Tnk2	Ack|Ack-1|Ack1|Cdgip|Pyk1	tyrosine kinase, non-receptor, 2	protein-coding
mm_142845.1	chr17	51796476	51796493	-	1	NA	intron (NM_009122, intron 5 of 10)	(A)n|Simple_repeat|Simple_repeat	15570	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_165180.1	chr2	29194606	29194627	-	1	NA	TTS (NM_133500)	TTS (NM_133500)	53483	NM_001305805	171171	Mm.442448	NM_133500	ENSMUSG00000035513	Ntng2	2610016D08Rik|Lmnt2	netrin G2	protein-coding
mm_153752.1	chr19	45075168	45075200	-	1	NA	promoter-TSS (NM_178929)	promoter-TSS (NM_178929)	-955	NM_178929	107250	Mm.24417	NM_178929	ENSMUSG00000025213	Kazald1	AI842353|Bono1|IGFBP-rP10	Kazal-type serine peptidase inhibitor domain 1	protein-coding
mm_12255.1	chr2	68913566	68913577	+	1	NA	intron (NM_172856, intron 1 of 9)	intron (NM_172856, intron 1 of 9)	52130	NM_001347161	241447	Mm.222222	NM_172856	ENSMUSG00000027035	Cers6	4732462C07Rik|AW544719|Lass6|T1L	ceramide synthase 6	protein-coding
mm_82311.1	chr9	7872918	7872935	-	1	NA	5' UTR (NM_007464, exon 1 of 9)	5' UTR (NM_007464, exon 1 of 9)	244	NM_007464	11796	Mm.2026	NM_007464	ENSMUSG00000032000	Birc3	AW107670|Api1|Api2|Birc2|C-IAP2|HIAP2|IAP1|IAP2|MIAP1|MIAP2|MIHB|MIHC|RNF49|cIAP-1|cIAP-2|cIAP1|cIAP2	baculoviral IAP repeat-containing 3	protein-coding
mm_76315.1	chr8	84663028	84663071	-	1	NA	promoter-TSS (NM_010499)	promoter-TSS (NM_010499)	-197	NM_010499	15936	Mm.399	NM_010499	ENSMUSG00000053560	Ier2	AI317238|Ch1|Pip92	immediate early response 2	protein-coding
mm_89520.1	chr10	94356794	94356804	+	1	NA	Intergenic	Intergenic	-58096	NR_033209	215472	Mm.255656	NM_174999	ENSMUSG00000053420	Gm4792	E130012K09|EG215472	predicted gene 4792	ncRNA
mm_120622.1	chr14	70457429	70457435	+	1	NA	promoter-TSS (NM_145981)	promoter-TSS (NM_145981)	-85	NM_145981	105653	Mm.192598	NM_145981	ENSMUSG00000003469	Phyhip	AW049870|C630010D02Rik|Lnap1ip|PAHX-AP#1|PAHX-AP1	phytanoyl-CoA hydroxylase interacting protein	protein-coding
mm_149239.1	chr19	10186148	10186162	+	1	NA	intron (NM_146094, intron 3 of 11)	intron (NM_146094, intron 3 of 11)	3267	NM_146094	76267	Mm.30158	NM_146094	ENSMUSG00000010663	Fads1	0710001O03Rik|A930006B21Rik|AI317215|DSD	fatty acid desaturase 1	protein-coding
mm_9772.1	chr1	181001940	181001973	-	1	NA	exon (NM_010145, exon 2 of 9)	exon (NM_010145, exon 2 of 9)	15613	NM_010145	13849	Mm.9075	NM_010145	ENSMUSG00000038776	Ephx1	EH|Eph-1|Eph1|Epxh1|mEH	epoxide hydrolase 1, microsomal	protein-coding
mm_45897.1	chr5	88675566	88675592	-	1	NA	promoter-TSS (NM_001098476)	promoter-TSS (NM_001098476)	1	NM_001098476	231413	Mm.332474	NM_178700	ENSMUSG00000044221	Grsf1	BB232551|C80280|D5Wsu31e	G-rich RNA sequence binding factor 1	protein-coding
mm_32358.1	chr4	105157491	105157508	+	1	NA	5' UTR (NM_080555, exon 1 of 6)	5' UTR (NM_080555, exon 1 of 6)	152	NM_080555	67916	Mm.348326	NM_080555	ENSMUSG00000028517	Plpp3	1110003O22Rik|2610002D05Rik|AV025606|D4Bwg0538e|D4Bwg1535e|Lpp3|Ppab2b|Ppap2b	phospholipid phosphatase 3	protein-coding
mm_14763.1	chr2	145167905	145167982	+	1	NA	Intergenic	CpG	-74668	NM_053195	94249	Mm.217171	NM_053195	ENSMUSG00000063873	Slc24a3	NCKX3	solute carrier family 24 (sodium/potassium/calcium exchanger), member 3	protein-coding
mm_105680.1	chr11	107716432	107716447	-	1	NA	promoter-TSS (NM_007582)	promoter-TSS (NM_007582)	37	NM_007582	12299	Mm.57093	NM_007582	ENSMUSG00000020722	Cacng1	-	calcium channel, voltage-dependent, gamma subunit 1	protein-coding
mm_120384.1	chr14	64589862	64589898	+	1	NA	promoter-TSS (NR_029813)	promoter-TSS (NR_029813)	-777	NR_029813	387233		NR_029813	ENSMUSG00000065597	Mir124a-1	Mirn124a|Mirn124a-1	microRNA 124a-1	ncRNA
mm_89898.1	chr10	110934292	110934296	+	1	NA	intron (NM_007792, intron 2 of 5)	intron (NM_007792, intron 2 of 5)	14118	NM_007792	13008	Mm.2020	NM_007792	ENSMUSG00000020186	Csrp2	AW551867|Crp2|SmLim	cysteine and glycine-rich protein 2	protein-coding
mm_148976.1	chr19	7559643	7559665	+	1	NA	intron (NM_139269, intron 2 of 4)	B1_Mur4|SINE|Alu	2195	NM_139269	225845	Mm.274810	NM_139269	ENSMUSG00000060675	Pla2g16	C78643|HRSL3|Hrasls3|Hrev107|MLP-3	phospholipase A2, group XVI	protein-coding
mm_6771.1	chr1	84131290	84131305	-	1	NA	intron (NM_001003948, intron 2 of 2)	intron (NM_001003948, intron 2 of 2)	87664	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_129411.1	chr15	78305718	78305730	-	1	NA	promoter-TSS (NM_007781)	promoter-TSS (NM_007781)	-3	NM_001287389	12984	Mm.1940	NM_007781	ENSMUSG00000071714	Csf2rb2	AIC2A|BetaIl3|Bil3|Csfgmrb|Il3r|Il3rb|Il3rb2	colony stimulating factor 2 receptor, beta 2, low-affinity (granulocyte-macrophage)	protein-coding
mm_167907.1	chrX	83589622	83589627	+	1	NA	intron (NM_007868, intron 7 of 78)	(CAGA)n|Simple_repeat|Simple_repeat	-101700	NM_021898	100502723	Mm.383210	NM_021898	ENSMUSG00000035522	Tsga8	Halap-X|Halapx	testis specific gene A8	protein-coding
mm_76051.1	chr8	77689161	77689172	-	1	NA	exon (NM_010332, exon 3 of 8)	exon (NM_010332, exon 3 of 8)	35286	NM_010332	13617	Mm.283168	NM_010332	ENSMUSG00000031616	Ednra	ET-AR|ETa|Gpcr10	endothelin receptor type A	protein-coding
mm_60654.1	chr7	44896078	44896101	+	1	NA	promoter-TSS (NM_027376)	promoter-TSS (NM_027376)	10	NM_027376	70300	Mm.276298	NM_027376	ENSMUSG00000011658	Fuz	2600013E07Rik|b2b1273Clo	fuzzy planar cell polarity protein	protein-coding
mm_121018.1	chr14	79540194	79540204	+	1	NA	intron (NM_001286411, intron 2 of 8)	intron (NM_001286411, intron 2 of 8)	24525	NM_001286411	13709	Mm.20938	NM_007920	ENSMUSG00000036461	Elf1	Elf-1|Sts1|mElf-1|p70	E74-like factor 1	protein-coding
mm_120553.1	chr14	67812198	67812204	+	1	NA	exon (NM_177780, exon 21 of 52)	exon (NM_177780, exon 21 of 52)	47544	NR_105857	102465310		NR_105857	ENSMUSG00000098866	Mir6539	Gm27464|mir-6539|mmu-mir-6539	microRNA 6539	ncRNA
mm_120595.1	chr14	70077169	70077190	+	1	NA	promoter-TSS (NM_001289927)	promoter-TSS (NM_001289927)	-266	NM_018781	13655	Mm.103737	NM_018781	ENSMUSG00000033730	Egr3	Pilot	early growth response 3	protein-coding
mm_46966.1	chr5	115155176	115155203	-	1	NA	intron (NM_175403, intron 1 of 4)	intron (NM_175403, intron 1 of 4)	2987	NM_175403	109154	Mm.153963	NM_175403	ENSMUSG00000048578	Mlec	2410014A08Rik|AI850530|ESTM19|X83352|mKIAA0152	malectin	protein-coding
mm_162768.1	chr10	66200488	66200492	-	1	NA	Intergenic	Intergenic	55194	NR_131070	77198	Mm.107617	NR_131070		4930407I19Rik	-	RIKEN cDNA 4930407I19 gene	ncRNA
mm_48226.1	chr5	137645725	137645737	-	1	NA	promoter-TSS (NM_010571)	promoter-TSS (NM_010571)	-17	NM_010571	16369	Mm.24486	NM_010571	ENSMUSG00000047182	Irs3	AA408304	insulin receptor substrate 3	protein-coding
mm_23202.1	chr3	41497250	41497259	+	1	NA	Intergenic	Intergenic	-4055	NR_040385	78706	Mm.366094	NR_040385	ENSMUSG00000097639	Platr4	C430002E04Rik	pluripotency associated transcript 4	ncRNA
mm_134438.1	chr16	18245226	18245238	-	1	NA	exon (NM_011239, exon 3 of 6)	exon (NM_011239, exon 3 of 6)	3462	NM_011239	19385	Mm.235287	NM_011239	ENSMUSG00000005732	Ranbp1	Htf9a	RAN binding protein 1	protein-coding
mm_169869.1	chr16	35871399	35871399	-	1	NA	promoter-TSS (NM_001039530)	promoter-TSS (NM_001039530)	-17	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_129937.1	chr15	84856021	84856032	-	1	NA	non-coding (NR_030731, exon 1 of 12)	non-coding (NR_030731, exon 1 of 12)	103	NM_001081166	271305	Mm.101022	NM_001081166	ENSMUSG00000016624	Phf21b	A730032D07Rik	PHD finger protein 21B	protein-coding
mm_149615.1	chr19	16387232	16387267	+	1	NA	3' UTR (NM_008139, exon 7 of 7)	3' UTR (NM_008139, exon 7 of 7)	-48418	NM_008137	14675	Mm.313181	NM_008137	ENSMUSG00000024697	Gna14	AU023208	guanine nucleotide binding protein, alpha 14	protein-coding
mm_136272.1	chr16	91056442	91056460	-	1	NA	intron (NM_001163695, intron 1 of 1)	intron (NM_001163695, intron 1 of 1)	-12072	NM_026110	67367	Mm.347	NM_026110	ENSMUSG00000022974	Paxbp1	1810007M14Rik|C21orf66|Gcfc|Gcfc1|Pax3/7bp	PAX3 and PAX7 binding protein 1	protein-coding
mm_162676.1	chr10	9833636	9833637	+	1	NA	intron (NM_001081344, intron 8 of 25)	ID_B1|SINE|B4	67404	NM_001081344	78808	Mm.331751	NM_030191	ENSMUSG00000019790	Stxbp5	0710001E20Rik|4930565N16Rik|AW742610|LGL3|mKIAA1006	syntaxin binding protein 5 (tomosyn)	protein-coding
mm_111083.1	chr12	80260315	80260325	-	1	NA	promoter-TSS (NM_134156)	promoter-TSS (NM_134156)	51	NM_134156	109711	Mm.253564	NM_134156	ENSMUSG00000015143	Actn1	3110023F10Rik|Actn1a	actinin, alpha 1	protein-coding
mm_48238.1	chr5	137741110	137741185	-	1	NA	promoter-TSS (NM_001347505)	promoter-TSS (NM_001347505)	21	NM_001347505	243300	Mm.74750	NM_175521	ENSMUSG00000045348	Nyap1	6430598A04Rik	neuronal tyrosine-phosphorylated phosphoinositide 3-kinase adaptor 1	protein-coding
mm_151836.1	chr19	5720682	5720690	-	1	NA	exon (NM_001114597, exon 8 of 19)	exon (NM_001114597, exon 8 of 19)	5631	NM_001114595	114601	Mm.210447	NM_053252	ENSMUSG00000024937	Ehbp1l1	G430002G23Rik	EH domain binding protein 1-like 1	protein-coding
mm_148850.1	chr19	6386035	6386056	+	1	NA	exon (NM_011224, exon 4 of 20)	exon (NM_011224, exon 4 of 20)	1637	NM_011224	19309	Mm.27806	NM_011224	ENSMUSG00000032648	Pygm	AI115133|PG	muscle glycogen phosphorylase	protein-coding
mm_141777.1	chr17	34291678	34291716	-	1	NA	Intergenic	Intergenic	-3926	NM_010378	14960	Mm.235338	NM_010378	ENSMUSG00000036594	H2-Aa	Aalpha|H-2Aa|H2Aa|I-Aalpha|IAalpha|Ia-1|Ia1	histocompatibility 2, class II antigen A, alpha	protein-coding
mm_79858.1	chr9	65021189	65021203	+	1	NA	intron (NM_021345, intron 1 of 10)	CpG	521	NM_021345	57874	Mm.308180	NM_021345	ENSMUSG00000033629	Hacd3	4930523M17Rik|AW742319|B-ind1|Hcad3|Hspc121|Ptplad1	3-hydroxyacyl-CoA dehydratase 3	protein-coding
mm_146941.1	chr18	32399984	32399989	-	1	NA	intron (NM_001083334, intron 1 of 14)	intron (NM_001083334, intron 1 of 14)	-21702	NR_045403	402767	Mm.385109	NR_045403	ENSMUSG00000097413	A830052D11Rik	-	RIKEN cDNA A830052D11 gene	ncRNA
mm_81488.1	chr9	110003444	110003448	+	1	NA	3' UTR (NM_001205331, exon 4 of 4)	3' UTR (NM_001205331, exon 4 of 4)	-48575	NM_001311163	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_67499.1	chr7	80778464	80778476	-	1	NA	intron (NM_016721, intron 2 of 37)	intron (NM_016721, intron 2 of 37)	24861	NM_016721	29875	Mm.207619	NM_016721	ENSMUSG00000030536	Iqgap1	AA682088|D7Ertd237e|D7Ertd257e|mKIAA0051	IQ motif containing GTPase activating protein 1	protein-coding
mm_33133.1	chr4	124986458	124986490	+	1	NA	promoter-TSS (NM_138683)	promoter-TSS (NM_138683)	44	NM_138683	192199	Mm.42202	NM_138683	ENSMUSG00000028871	Rspo1	R-spondin|Rspondin	R-spondin 1	protein-coding
mm_20859.1	chr2	148437024	148437070	-	1	NA	3' UTR (NM_010740, exon 2 of 2)	3' UTR (NM_010740, exon 2 of 2)	6488	NM_010740	17064	Mm.681	NM_010740	ENSMUSG00000027435	Cd93	6030404G09Rik|AA145088|AA4.1|AW555904|C1qr1|C1qrp|Ly68	CD93 antigen	protein-coding
mm_106794.1	chr12	4817662	4817672	+	1	NA	promoter-TSS (NM_025323)	promoter-TSS (NM_025323)	59	NM_025323	66055	Mm.102627	NM_025323	ENSMUSG00000037361	Sf3b6	0610009D07Rik|6030419K15Rik|AV001342|Sf3b14	splicing factor 3B, subunit 6	protein-coding
mm_151505.1	chr19	58732019	58732027	+	1	NA	intron (NM_018874, intron 4 of 12)	intron (NM_018874, intron 4 of 12)	3136	NM_018874	18946	Mm.10753	NM_018874	ENSMUSG00000042179	Pnliprp1	Plrp1	pancreatic lipase related protein 1	protein-coding
mm_9423.1	chr1	172376289	172376318	-	1	NA	promoter-TSS (NM_026234)	promoter-TSS (NM_026234)	-228	NM_026234	67556	Mm.26612	NM_026234	ENSMUSG00000050229	Pigm	4933437L05Rik|AI644422|AV302080|C920011G20Rik	phosphatidylinositol glycan anchor biosynthesis, class M	protein-coding
mm_58775.1	chr7	16048381	16048447	+	1	NA	Intergenic	Intergenic	-23431	NM_001347559	666528	Mm.290718	NM_001099277	ENSMUSG00000078796	Zfp541	EG666528|Znf541	zinc finger protein 541	protein-coding
mm_131656.1	chr16	20540628	20540640	+	1	NA	intron (NM_009679, intron 4 of 10)	intron (NM_009679, intron 4 of 10)	5154	NM_009679	11773	Mm.18946	NM_009679	ENSMUSG00000022841	Ap2m1	-	adaptor-related protein complex 2, mu 1 subunit	protein-coding
mm_171214.1	chr3	58987147	58987158	+	1	NA	Intergenic	Intergenic	-19826	NM_177855	329650	Mm.240059	NM_177855	ENSMUSG00000056476	Med12l	A130035F20|A630079M02|AU044581|TRALPUSH	mediator complex subunit 12-like	protein-coding
mm_17725.1	chr2	32424045	32424055	-	1	NA	promoter-TSS (NM_001290558)	promoter-TSS (NM_001290558)	16	NM_001290558	227731	Mm.37395	NM_146118	ENSMUSG00000026819	Slc25a25	1110030N17Rik|MCSC|mKIAA1896	solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 25	protein-coding
mm_136821.1	chr17	12419032	12419046	+	1	NA	TTS (NM_011395)	TTS (NM_011395)	40430	NM_008877	18815	Mm.971	NM_008877	ENSMUSG00000059481	Plg	AI649309|Pg	plasminogen	protein-coding
mm_163077.1	chr11	68854151	68854179	-	1	NA	Intergenic	Intergenic	-1034	NM_023668	83431	Mm.31979	NM_023668	ENSMUSG00000018736	Ndel1	2600006O07Rik|MITAP1|NUDEL|mNudel	nudE neurodevelopment protein 1 like 1	protein-coding
mm_101476.1	chr11	30785664	30785667	-	1	NA	intron (NM_134013, intron 1 of 46)	RMER17B2|LTR|ERVK	13890	NM_134013	103554	Mm.240066	NM_134013	ENSMUSG00000040850	Psme4	AA409398|AU041366|TEMO|mKIAA0077	proteasome (prosome, macropain) activator subunit 4	protein-coding
mm_151606.1	chr19	3686524	3686547	-	1	NA	promoter-TSS (NM_008513)	promoter-TSS (NM_008513)	29	NM_008513	16973	Mm.274581	NM_008513	ENSMUSG00000024913	Lrp5	BMND1|HBM|LR3|LRP7|OPPG|mKIAA4142	low density lipoprotein receptor-related protein 5	protein-coding
mm_5288.1	chr1	20817299	20817325	-	1	NA	exon (NM_008563, exon 3 of 17)	exon (NM_008563, exon 3 of 17)	2901	NM_008563	17215	Mm.4502	NM_008563	ENSMUSG00000041859	Mcm3	AL033361|C80350|Mcmd|P1|p1.m	minichromosome maintenance complex component 3	protein-coding
mm_167178.1	chr7	140218409	140218417	+	1	NA	5' UTR (NM_172909, exon 1 of 14)	5' UTR (NM_172909, exon 1 of 14)	146	NM_172909	244233	Mm.19283	NM_172909	ENSMUSG00000025461	Cd163l1	B430307C05|E430002D04Rik|Scart1	CD163 molecule-like 1	protein-coding
mm_52055.1	chr6	97232562	97232576	+	1	NA	exon (NM_022992, exon 3 of 3)	exon (NM_022992, exon 3 of 3)	20211	NM_001081157	320502	Mm.68163	NM_001081157	ENSMUSG00000044086	Lmod3	5430424A14Rik	leiomodin 3 (fetal)	protein-coding
mm_47707.1	chr5	129887443	129887480	-	1	NA	promoter-TSS (NM_024166)	promoter-TSS (NM_024166)	9	NM_024166	14004	Mm.30133	NM_024166	ENSMUSG00000070493	Chchd2	AL033347|Etohi6	coiled-coil-helix-coiled-coil-helix domain containing 2	protein-coding
mm_132240.1	chr16	32750881	32750900	+	1	NA	exon (NM_080457, exon 2 of 27)	exon (NM_080457, exon 2 of 27)	15004	NM_080457	140474	Mm.214599	NM_080457	ENSMUSG00000079620	Muc4	4933405I11Rik|Asgp	mucin 4	protein-coding
mm_86935.1	chr10	24223540	24223601	+	1	NA	promoter-TSS (NM_021509)	promoter-TSS (NM_021509)	53	NM_021509	59012	Mm.285934	NM_021509	ENSMUSG00000020000	Moxd1	3230402N08Rik|MNCb-5203	monooxygenase, DBH-like 1	protein-coding
mm_72031.1	chr8	70763719	70763739	+	1	NA	exon (NM_023065, exon 6 of 8)	exon (NM_023065, exon 6 of 8)	-2808	NM_183170	234384	Mm.213010	NM_183170	ENSMUSG00000035559	Mpv17l2	Fksg24	MPV17 mitochondrial membrane protein-like 2	protein-coding
mm_40030.1	chr5	33629916	33629930	+	1	NA	promoter-TSS (NM_178390)	promoter-TSS (NM_178390)	-288	NM_178390	74504	Mm.294695	NM_178390	ENSMUSG00000037339	Fam53a	2410018C17Rik|5430419M09Rik|Dntnp	family with sequence similarity 53, member A	protein-coding
mm_61695.1	chr7	81113261	81113272	+	1	NA	Intergenic	Intergenic	-1533	NM_001004184	434203	Mm.389909	NM_001004184	ENSMUSG00000025726	Slc28a1	Cnt1	solute carrier family 28 (sodium-coupled nucleoside transporter), member 1	protein-coding
mm_135019.1	chr16	32487810	32487824	-	1	NA	promoter-TSS (NM_145932)	promoter-TSS (NM_145932)	62	NM_145932	106407	Mm.476915	NM_145932	ENSMUSG00000035699	Slc51a	AV001382|AW261577|D630035O19Rik|OSTalpha|Osta	solute carrier family 51, alpha subunit	protein-coding
mm_66807.1	chr7	47252865	47252873	-	1	NA	promoter-TSS (NM_001288801)	promoter-TSS (NM_001288801)	-21	NM_001288801	668725	Mm.436563	NM_001177566	ENSMUSG00000074111	Mrgpra9	EG668725|MrgA9	MAS-related GPR, member A9	protein-coding
mm_72556.1	chr8	84066903	84066919	+	1	NA	promoter-TSS (NM_009055)	promoter-TSS (NM_009055)	75	NM_009055	19724	Mm.7892	NM_009055	ENSMUSG00000031706	Rfx1	AI047719|AI385641	regulatory factor X, 1 (influences HLA class II expression)	protein-coding
mm_104131.1	chr11	86807625	86807645	-	1	NA	promoter-TSS (NM_026191)	promoter-TSS (NM_026191)	25	NM_026191	67487	Mm.260627	NM_026191	ENSMUSG00000018425	Dhx40	2410016C14Rik|ARG147|DDX40|PAD	DEAH (Asp-Glu-Ala-His) box polypeptide 40	protein-coding
mm_160488.1	chr8	126139179	126139179	+	1	NA	Intergenic	CpG	144077	NM_008430	16525	Mm.10800	NM_008430	ENSMUSG00000033998	Kcnk1	AI788889|TWIK-1	potassium channel, subfamily K, member 1	protein-coding
mm_16328.1	chr2	174327559	174327575	+	1	NA	promoter-TSS (NR_003258)	promoter-TSS (NR_003258)	-201	NM_001310083	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_29946.1	chr3	132950168	132950181	-	1	NA	promoter-TSS (NM_001287103)	promoter-TSS (NM_001287103)	117	NM_001287102	114249	Mm.279310	NM_033525	ENSMUSG00000040998	Npnt	1110009H02Rik|AA682063|AI314031|Nctn|POEM	nephronectin	protein-coding
mm_71398.1	chr8	46163815	46163842	+	1	NA	Intergenic	CpG	-5728	NM_025747	66756	Mm.133623	NM_025747	ENSMUSG00000031631	Cfap97	1110068E21Rik|4933411K20Rik|AW049273|Kiaa1430|mKIAA1430	cilia and flagella associated protein 97	protein-coding
mm_16710.1	chr2	7085639	7085643	-	1	NA	intron (NM_001110231, intron 3 of 15)	(TATG)n|Simple_repeat|Simple_repeat	-4339	NM_001160292	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_80302.1	chr9	73192474	73192485	+	1	NA	Intergenic	Intergenic	79010	NM_198609	225215	Mm.379366	NM_198609	ENSMUSG00000032215	Rsl24d1	2410159K22Rik	ribosomal L24 domain containing 1	protein-coding
mm_19719.1	chr2	104410647	104410658	-	1	NA	promoter-TSS (NM_001033347)	promoter-TSS (NM_001033347)	-318	NM_001033347	241589	Mm.358909	NM_001033347	ENSMUSG00000068373	D430041D05Rik	9630056G07Rik|G2	RIKEN cDNA D430041D05 gene	protein-coding
mm_99247.1	chr11	101082644	101082678	+	1	NA	promoter-TSS (NM_001305982)	promoter-TSS (NM_001305982)	96	NM_001305982	71743	Mm.182271	NM_027896	ENSMUSG00000001755	Coasy	1300003G02Rik|Dpck|Ppat|Ukr1	Coenzyme A synthase	protein-coding
mm_63437.1	chr7	127479192	127479272	+	1	NA	Intergenic	CpG	-5989	NM_010183	14123	Mm.323505	NM_010183	ENSMUSG00000042423	Fbrs	Fbs|Fbs1	fibrosin	protein-coding
mm_35613.1	chr4	43406019	43406053	-	1	NA	promoter-TSS (NM_199057)	promoter-TSS (NM_199057)	-466	NM_199057	100213	Mm.235730	NM_199057	ENSMUSG00000035969	Rusc2	AI840675|mKIAA0375	RUN and SH3 domain containing 2	protein-coding
mm_118776.1	chr14	23149844	23149873	+	1	NA	Intergenic	RMER16-int|LTR|ERVK	-55287	NR_033550	791307	Mm.364384	NR_033550	ENSMUSG00000068680	Gm10248	ENSMUSG00000068680	predicted gene 10248	ncRNA
mm_79462.1	chr9	56418806	56418847	+	1	NA	promoter-TSS (NM_025812)	promoter-TSS (NM_025812)	-20	NM_025812	66867	Mm.150856	NM_025812	ENSMUSG00000032329	Hmg20a	1200004E06Rik|5730490E10Rik|Hmgxb1|Ibraf	high mobility group 20A	protein-coding
mm_106308.1	chr11	118301588	118301613	-	1	NA	3' UTR (NM_011594, exon 5 of 5)	3' UTR (NM_011594, exon 5 of 5)	-11356	NM_001033528	72344	Mm.232293	NM_001033528	ENSMUSG00000033909	Usp36	2700002L06Rik|mKIAA1453	ubiquitin specific peptidase 36	protein-coding
mm_52161.1	chr6	98020044	98020047	+	1	NA	3' UTR (NM_001178049, exon 10 of 10)	3' UTR (NM_001178049, exon 10 of 10)	28262	NM_008601	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_34372.1	chr4	144893417	144893426	+	1	NA	5' UTR (NM_011303, exon 1 of 6)	5' UTR (NM_011303, exon 1 of 6)	284	NM_011303	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding
mm_129669.1	chr15	81360740	81360816	-	1	NA	promoter-TSS (NM_011399)	promoter-TSS (NM_011399)	-13	NM_011399	20524	Mm.222536	NM_011399	ENSMUSG00000022404	Slc25a17	34kDa|47kDa|PMP34|Pmp47	solute carrier family 25 (mitochondrial carrier, peroxisomal membrane protein), member 17	protein-coding
mm_160478.1	chr8	121605052	121605052	-	1	NA	exon (NM_080855, exon 12 of 13)	exon (NM_080855, exon 12 of 13)	14584	NM_026160	67443	Mm.28357	NM_026160	ENSMUSG00000031812	Map1lc3b	1010001C15Rik|Atg8|LC3b|Map1lc3	microtubule-associated protein 1 light chain 3 beta	protein-coding
mm_101877.1	chr11	48902012	48902044	-	1	NA	intron (NM_001024230, intron 1 of 4)	intron (NM_001024230, intron 1 of 4)	124	NM_001024230	432555	Mm.338931	NM_001024230	ENSMUSG00000058163	Gm5431	EG432555|Irgb9b8	predicted gene 5431	protein-coding
mm_62121.1	chr7	96697479	96697491	+	1	NA	intron (NM_001310760, intron 7 of 32)	MER68|LTR|ERVL	104064	NR_045874	791381	Mm.402112	NR_045874	ENSMUSG00000053049	Gm15413	ENSMUSG00000053049|OTTMUSG00000021246	predicted gene 15413	ncRNA
mm_50744.1	chr6	52733185	52733199	+	1	NA	exon (NM_025816, exon 5 of 18)	exon (NM_025816, exon 5 of 18)	19463	NM_025816	52440	Mm.389757	NM_025816	ENSMUSG00000004535	Tax1bp1	1200003J11Rik|1700069J21Rik|AA930106|D6Ertd404e|D6Ertd772e|T6bp|TXBP151	Tax1 (human T cell leukemia virus type I) binding protein 1	protein-coding
mm_90541.1	chr10	128091175	128091186	+	1	NA	TTS (NM_016774)	TTS (NM_016774)	-1603	NM_054078	116848	Mm.252213	NM_054078	ENSMUSG00000040054	Baz2a	AA415431|C030005G16Rik|C78388|Tip5|Walp3|mKIAA0314	bromodomain adjacent to zinc finger domain, 2A	protein-coding
mm_154558.1	chrM	16181	16196	-	1	NA	NA	Intergenic	NA	NA								
mm_129017.1	chr15	74930466	74930484	-	1	NA	Intergenic	Intergenic	-24576	NM_001164039	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_9910.1	chr1	188320831	188320834	-	1	NA	intron (NM_021408, intron 3 of 70)	intron (NM_021408, intron 3 of 70)	57994	NM_021408	22283	Mm.331238	NM_021408	ENSMUSG00000026609	Ush2a	A930011D15Rik|A930037M10Rik|Gm676|Gm983|Mush2a|Usherin|Ushrn	Usher syndrome 2A	protein-coding
mm_19397.1	chr2	91630681	91630694	-	1	NA	exon (NM_010168, exon 7 of 14)	exon (NM_010168, exon 7 of 14)	5770	NM_010168	14061	Mm.89048	NM_010168	ENSMUSG00000027249	F2	Cf-2|Cf2|FII	coagulation factor II	protein-coding
mm_61126.1	chr7	55842207	55842296	+	1	NA	5' UTR (NM_001164662, exon 1 of 31)	5' UTR (NM_001164662, exon 1 of 31)	180	NM_001164661	20430	Mm.37249	NM_011370	ENSMUSG00000030447	Cyfip1	E030028J09Rik|P140SRA-1|P140sra1|Shyc|Sra-1|Sra1|l(7)1Rl|l71Rl|l7Rl1|mKIAA0068|pl-1	cytoplasmic FMR1 interacting protein 1	protein-coding
mm_121116.1	chr14	101840334	101840356	+	1	NA	promoter-TSS (NM_001347628)	promoter-TSS (NM_001347628)	-278	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_12408.1	chr2	70508833	70508839	+	1	NA	promoter-TSS (NM_025744)	promoter-TSS (NM_025744)	17	NM_025744	66748	Mm.423014	NM_025744	ENSMUSG00000075302	Erich2	4933404M02Rik	glutamate rich 2	protein-coding
mm_59939.1	chr7	30424379	30424385	+	1	NA	5' UTR (NM_172142, exon 3 of 11)	5' UTR (NM_172142, exon 3 of 11)	1078	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_47215.1	chr5	121009531	121009577	-	1	NA	promoter-TSS (NM_011286)	promoter-TSS (NM_011286)	-16	NM_011286	19894	Mm.181166	NM_011286	ENSMUSG00000029608	Rph3a	2900002P20Rik|AU022689|AW108370	rabphilin 3A	protein-coding
mm_59843.1	chr7	29768535	29768543	+	1	NA	promoter-TSS (NM_023750)	promoter-TSS (NM_023750)	-13	NM_023750	74352	Mm.251083	NM_023750	ENSMUSG00000046185	Zfp84	2210410P13Rik|4633401C23Rik|AI415447|BB081605|C86188|KRAB18|Zfp69	zinc finger protein 84	protein-coding
mm_170151.1	chr17	45570744	45570747	-	1	NA	exon (NM_008302, exon 5 of 11)	exon (NM_008302, exon 5 of 11)	2516	NM_008302	15516	Mm.2180	NM_008302	ENSMUSG00000023944	Hsp90ab1	90kDa|AL022974|C81438|Hsp84|Hsp84-1|Hsp90|Hspcb	heat shock protein 90 alpha (cytosolic), class B member 1	protein-coding
mm_59491.1	chr7	27507841	27507860	+	1	NA	intron (NM_198048, intron 4 of 6)	CpG	8526	NM_019412	19153	Mm.10119	NM_019412	ENSMUSG00000053198	Prx	L-Periaxin	periaxin	protein-coding
mm_33728.1	chr4	134095155	134095198	+	1	NA	promoter-TSS (NM_013706)	promoter-TSS (NM_013706)	-103	NM_013706	23833	Mm.24130	NM_013706	ENSMUSG00000000682	Cd52	AI463198|B7|B7-Ag|CAMPATH-1|CLS1|MB7	CD52 antigen	protein-coding
mm_36504.1	chr4	83468633	83468652	-	1	NA	exon (NM_001290527, exon 7 of 11)	exon (NM_001290527, exon 7 of 11)	17806	NM_001290527	101739	Mm.105331	NM_133948	ENSMUSG00000028484	Psip1	AA408851|AU015605|Dfs70|Ledgfa|Ledgfb|Psip2	PC4 and SFRS1 interacting protein 1	protein-coding
mm_91696.1	chr10	44003591	44003644	-	1	NA	exon (NM_172393, exon 1 of 20)	exon (NM_172393, exon 1 of 20)	1229	NM_172393	11630	Mm.292082	NM_172393	ENSMUSG00000019866	Aim1	AI462491|AI463325	absent in melanoma 1	protein-coding
mm_62369.1	chr7	100607888	100607899	+	1	NA	non-coding (NR_003559, exon 1 of 8)	non-coding (NR_003559, exon 1 of 8)	103	NR_003559	52443	Mm.473730	NM_198831	ENSMUSG00000030706	Mrpl48	1810030E20Rik|2610028L11Rik|CGI-118|D4Ertd786e	mitochondrial ribosomal protein L48	protein-coding
mm_145052.1	chr18	40257032	40257042	+	1	NA	promoter-TSS (NR_045177)	promoter-TSS (NR_045177)	75	NR_045177	73001	Mm.428647	NR_045177	ENSMUSG00000071860	2900055J20Rik	-	RIKEN cDNA 2900055J20 gene	ncRNA
mm_85640.1	chr9	107655155	107655170	-	1	NA	exon (NM_001199218, exon 14 of 16)	exon (NM_001199218, exon 14 of 16)	12237	NM_023805	76257	Mm.296560	NM_023805	ENSMUSG00000010064	Slc38a3	0610012J02Rik|D9Ucla2|Nat1|Slc38-3|Sn1|Snat3|mNAT	solute carrier family 38, member 3	protein-coding
mm_145657.1	chr18	61130610	61130640	+	1	NA	TTS (NM_178277)	TTS (NM_178277)	13157	NR_105949	102466212		NR_105949	ENSMUSG00000098389	Mir6983	Gm27496|mmu-mir-6983	microRNA 6983	ncRNA
mm_107131.1	chr12	21214875	21214878	+	1	NA	intron (NM_001135192, intron 10 of 28)	intron (NM_001135192, intron 10 of 28)	71361	NM_008403	16413	Mm.273333	NM_008403	ENSMUSG00000062352	Itgb1bp1	AI449260|AU019480|Icap1	integrin beta 1 binding protein 1	protein-coding
mm_84779.1	chr9	75684075	75684083	-	1	NA	promoter-TSS (NM_001164790)	promoter-TSS (NM_001164790)	-23	NM_009130	20255	Mm.2386	NM_009130	ENSMUSG00000032181	Scg3	1B1075|AI385542|Chgd|SgIII	secretogranin III	protein-coding
mm_89135.1	chr10	85386849	85386860	+	1	NA	promoter-TSS (NM_028709)	promoter-TSS (NM_028709)	40	NM_028709	74007	Mm.36544	NM_028709	ENSMUSG00000020042	Btbd11	6330404E16Rik	BTB (POZ) domain containing 11	protein-coding
mm_3734.1	chr1	155104967	155104968	+	1	NA	Intergenic	Intergenic	-5331	NM_010500	15939	Mm.12246	NM_010500	ENSMUSG00000056708	Ier5	-	immediate early response 5	protein-coding
mm_31130.1	chr4	43135815	43135818	+	1	NA	intron (NM_001310758, intron 7 of 38)	RMER1B|Other|Other	76863	NM_001310758	22249	Mm.128892	NM_021468	ENSMUSG00000028456	Unc13b	Munc13-1|Munc13-2|Unc13a|Unc13h1|Unc13h2	unc-13 homolog B (C. elegans)	protein-coding
mm_17285.1	chr2	26140349	26140389	-	1	NA	promoter-TSS (NM_001256522)	promoter-TSS (NM_001256522)	137	NM_001256521	109299	Mm.389259	NM_001256521		C330006A16Rik	AI551216	RIKEN cDNA C330006A16 gene	protein-coding
mm_151427.1	chr19	56874404	56874474	+	1	NA	promoter-TSS (NM_172840)	promoter-TSS (NM_172840)	23	NM_172840	240675	Mm.129534	NM_172840	ENSMUSG00000025082	Vwa2	Amaco	von Willebrand factor A domain containing 2	protein-coding
mm_112567.1	chr13	13559090	13559113	+	1	NA	Intergenic	Intergenic	-31308	NM_010748	17101	Mm.342337	NM_010748	ENSMUSG00000019726	Lyst	D13Sfk13|beige|bg	lysosomal trafficking regulator	protein-coding
mm_64430.1	chr7	142577831	142577841	+	1	NA	promoter-TSS (NR_030416)	promoter-TSS (NR_030416)	310	NR_130974	14955	Mm.14802	NR_001592	ENSMUSG00000000031	H19	AI747191	H19, imprinted maternally expressed transcript	ncRNA
mm_96277.1	chr11	62879450	62879536	+	1	NA	promoter-TSS (NM_026210)	promoter-TSS (NM_026210)	3	NM_026210	67510	Mm.9806	NM_026210	ENSMUSG00000014177	Tvp23b	1810036I24Rik|Fam18b|Fam18b1	trans-golgi network vesicle protein 23B	protein-coding
mm_39902.1	chr5	31242625	31242628	+	1	NA	intron (NM_001347326, intron 1 of 18)	intron (NM_001347326, intron 1 of 18)	1708	NM_147201	192292	Mm.292040	NM_147201	ENSMUSG00000029148	Nrbp1	B230344L17Rik|Nrbp	nuclear receptor binding protein 1	protein-coding
mm_144674.1	chr18	34625010	34625031	+	1	NA	promoter-TSS (NM_009004)	promoter-TSS (NM_009004)	-13	NM_001166406	19348	Mm.258846	NM_009004	ENSMUSG00000003779	Kif20a	AA415432|Rab6kifl	kinesin family member 20A	protein-coding
mm_1350.1	chr1	66321754	66321756	+	1	NA	promoter-TSS (NM_001310634)	promoter-TSS (NM_001310634)	31	NM_001310634	17756	Mm.256966	NM_008632	ENSMUSG00000015222	Map2	G1-397-34|MAP-2|Mtap-2|Mtap2|repro4	microtubule-associated protein 2	protein-coding
mm_63621.1	chr7	128265676	128265690	+	1	NA	promoter-TSS (NM_133254)	promoter-TSS (NM_133254)	-14	NM_133254	246787	Mm.38870	NM_133254	ENSMUSG00000030781	Slc5a2	Sglt2	solute carrier family 5 (sodium/glucose cotransporter), member 2	protein-coding
mm_82487.1	chr9	18469656	18469679	-	1	NA	intron (NM_028935, intron 2 of 7)	MER21B|LTR|ERVL	3892	NM_028935	72230	Mm.289689	NM_028935	ENSMUSG00000074500	Zfp558	1700007A21Rik|4932704I17Rik|Zfp558-ps	zinc finger protein 558	protein-coding
mm_72124.1	chr8	71690383	71690401	+	1	NA	3' UTR (NM_013564, exon 2 of 2)	3' UTR (NM_013564, exon 2 of 2)	1140	NM_013564	16336	Mm.476857	NM_013564	ENSMUSG00000079019	Insl3	Rlf|Rlnl	insulin-like 3	protein-coding
mm_98887.1	chr11	97833288	97833291	+	1	NA	intron (NM_010688, intron 4 of 6)	PB1D9|SINE|Alu	-7491	NM_001080935	68127	Mm.110270	NM_001080935	ENSMUSG00000050538	B230217C12Rik	AI840637	RIKEN cDNA B230217C12 gene	protein-coding
mm_23061.1	chr3	35863803	35863805	+	1	NA	Intergenic	Lx7|LINE|L1	66270	NM_033623	114893	Mm.374810	NM_033623	ENSMUSG00000027708	Dcun1d1	Rp42|SCCRO|Tes3|pTes3	DCN1, defective in cullin neddylation 1, domain containing 1 (S. cerevisiae)	protein-coding
mm_46286.1	chr5	100165575	100165598	-	1	NA	Intergenic	Intergenic	-5778	NM_182841	231503	Mm.99790	NM_182841	ENSMUSG00000050640	Tmem150c	-	transmembrane protein 150C	protein-coding
mm_44611.1	chr5	25485729	25485732	-	1	NA	intron (NM_001081383, intron 1 of 58)	intron (NM_001081383, intron 1 of 58)	13053	NM_001081383	231051	Mm.332268	NM_001081383	ENSMUSG00000038056	Kmt2c	E330008K23Rik|HALR|Mll3|mKIAA1506	lysine (K)-specific methyltransferase 2C	protein-coding
mm_42665.1	chr5	119671012	119671040	+	1	NA	promoter-TSS (NM_011535)	promoter-TSS (NM_011535)	164	NM_198052	21386	Mm.219139	NM_011535	ENSMUSG00000018604	Tbx3	D5Ertd189e	T-box 3	protein-coding
mm_118662.1	chr14	21831843	21831870	+	1	NA	5' UTR (NM_011695, exon 2 of 10)	5' UTR (NM_011695, exon 2 of 10)	295	NM_011695	22334	Mm.262327	NM_011695	ENSMUSG00000021771	Vdac2	Vdac6|mVDAC2|mVDAC6	voltage-dependent anion channel 2	protein-coding
mm_154774.1	chrX	12673276	12673290	+	1	NA	intron (NM_175141, intron 1 of 6)	intron (NM_175141, intron 1 of 6)	356	NM_175141	69155	Mm.15974	NM_175141	ENSMUSG00000044148	1810030O07Rik	-	RIKEN cDNA 1810030O07 gene	protein-coding
mm_56297.1	chr6	91668538	91668545	-	1	NA	Intergenic	Intergenic	-15526	NM_009320	21366	Mm.395650	NM_009320	ENSMUSG00000030096	Slc6a6	AA589629|C80501|Taut	solute carrier family 6 (neurotransmitter transporter, taurine), member 6	protein-coding
mm_48748.1	chr5	147894805	147894830	-	1	NA	promoter-TSS (NM_027872)	promoter-TSS (NM_027872)	-15	NM_027872	71706	Mm.153218	NM_027872	ENSMUSG00000029650	Slc46a3	1200006F02Rik	solute carrier family 46, member 3	protein-coding
mm_159548.1	chr4	96236591	96236591	-	1	NA	Intergenic	Intergenic	-95439	NM_001100182	242546	Mm.302562	NM_001100182	ENSMUSG00000081225	Cyp2j12	BB197342|Cyp2j12-ps|OTTMUSG00000007939	cytochrome P450, family 2, subfamily j, polypeptide 12	protein-coding
mm_111645.1	chr12	102695550	102695582	-	1	NA	intron (NM_172584, intron 1 of 9)	intron (NM_172584, intron 1 of 9)	9303	NM_172584	217837	Mm.482192	NM_172584	ENSMUSG00000057963	Itpk1	BC031182	inositol 1,3,4-triphosphate 5/6 kinase	protein-coding
mm_145813.1	chr18	65430618	65430644	+	1	NA	promoter-TSS (NM_172833)	promoter-TSS (NM_172833)	-366	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_143011.1	chr17	56455694	56455696	-	1	NA	intron (NM_001252455, intron 2 of 27)	intron (NM_001252455, intron 2 of 27)	6526	NM_001252456	19280	Mm.258771	NM_011218	ENSMUSG00000013236	Ptprs	AL022616|PTP|PTP-NU3|PTPNU-3|PTPsigma|Ptpt9|R-PTP-S|RPTPsigma	protein tyrosine phosphatase, receptor type, S	protein-coding
mm_156025.1	chrX	107149465	107149500	+	1	NA	promoter-TSS (NM_175442)	promoter-TSS (NM_175442)	28	NM_001122595	213438	Mm.265244	NM_175442	ENSMUSG00000054293	A630033H20Rik	AI662791|P2ry10	RIKEN cDNA A630033H20 gene	protein-coding
mm_125025.1	chr15	25742315	25742322	+	1	NA	intron (NM_019472, intron 17 of 40)	intron (NM_019472, intron 17 of 40)	-100980	NM_001034851	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_61962.1	chr7	90302401	90302444	+	1	NA	promoter-TSS (NM_001040085)	promoter-TSS (NM_001040085)	67	NR_110348	83671	Mm.26751	NM_031394	ENSMUSG00000030616	Sytl2	AI266830|Slp2|mKIAA1597	synaptotagmin-like 2	protein-coding
mm_117432.1	chr13	74563844	74563861	-	1	NA	Intergenic	Intergenic	-69902	NM_146231	235956	Mm.296909	NM_146231	ENSMUSG00000069208	Zfp825	-	zinc finger protein 825	protein-coding
mm_132863.1	chr16	48594606	48594620	+	1	NA	intron (NM_010816, intron 20 of 26)	intron (NM_010816, intron 20 of 26)	163376	NM_010816	17450	Mm.250060	NM_010816	ENSMUSG00000022652	Morc1	Morc	microrchidia 1	protein-coding
mm_104455.1	chr11	95041336	95041374	-	1	NA	promoter-TSS (NM_133667)	promoter-TSS (NM_133667)	16	NM_133667	18604	Mm.29768	NM_133667	ENSMUSG00000038967	Pdk2	-	pyruvate dehydrogenase kinase, isoenzyme 2	protein-coding
mm_155209.1	chrX	56779677	56779695	+	1	NA	promoter-TSS (NM_001077362)	promoter-TSS (NM_001077362)	3	NM_001077362	14199	Mm.3126	NM_010211	ENSMUSG00000023092	Fhl1	FHL-1|KyoT|RAM14-1|SLIM|SLIM-1	four and a half LIM domains 1	protein-coding
mm_31695.1	chr4	62407838	62407856	+	1	NA	promoter-TSS (NM_027297)	promoter-TSS (NM_027297)	776	NM_139291	66440	Mm.109930	NM_139291	ENSMUSG00000066149	Cdc26	2010012C09Rik	cell division cycle 26	protein-coding
mm_37860.1	chr4	132274278	132274327	-	1	NA	promoter-TSS (NM_025579)	promoter-TSS (NM_025579)	-73	NM_025579	66464	Mm.331926	NM_025579	ENSMUSG00000028899	Taf12	20kDa|2810422D08Rik|AW557038|Taf2J	TATA-box binding protein associated factor 12	protein-coding
mm_51616.1	chr6	85187498	85187510	+	1	NA	promoter-TSS (NM_010131)	promoter-TSS (NM_010131)	-427	NM_010131	13796	Mm.391473	NM_010131	ENSMUSG00000033726	Emx1	-	empty spiracles homeobox 1	protein-coding
mm_147149.1	chr18	36670270	36670317	-	1	NA	promoter-TSS (NM_025291)	promoter-TSS (NM_025291)	18	NM_001164406	24068	Mm.29058	NM_025291	ENSMUSG00000006050	Sra1	AA959952|Sra|Srap|Straa1|Strra1	steroid receptor RNA activator 1	protein-coding
mm_124595.1	chr15	3275032	3275042	+	1	NA	intron (NM_001042613, intron 2 of 4)	intron (NM_001042613, intron 2 of 4)	4060	NM_009155	20363	Mm.392203	NM_009155	ENSMUSG00000064373	Selenop	AU018766|D15Ucla1|Se-P|Sepp1|selp	selenoprotein P	protein-coding
mm_148705.1	chr19	5801852	5801876	+	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	808	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_99321.1	chr11	101442481	101442494	+	1	NA	intron (NM_011289, intron 1 of 4)	intron (NM_011289, intron 1 of 4)	242	NM_011289	19942	Mm.340658	NM_011289	ENSMUSG00000063316	Rpl27	-	ribosomal protein L27	protein-coding
mm_77049.1	chr8	109576763	109576783	-	1	NA	exon (NM_017370, exon 4 of 5)	exon (NM_017370, exon 4 of 5)	2399	NM_017370	15439	Mm.26730	NM_017370	ENSMUSG00000031722	Hp	HP-1|preHP2	haptoglobin	protein-coding
mm_135532.1	chr16	49768752	49768779	-	1	NA	Intergenic	ORR1D1|LTR|ERVL-MaLR	69471	NM_028680	73916	Mm.241276	NM_028680	ENSMUSG00000032965	Ift57	4833420A15Rik|Esrrbl1|Hippi|MHS4R2	intraflagellar transport 57	protein-coding
mm_4792.1	chr1	184694961	184694968	+	1	NA	Intergenic	Intergenic	-17533	NR_040627	74971	Mm.410816	NR_040627	ENSMUSG00000092578	4930488B22Rik	-	RIKEN cDNA 4930488B22 gene	ncRNA
mm_94522.1	chr11	9048576	9048630	+	1	NA	promoter-TSS (NM_001037928)	promoter-TSS (NM_001037928)	11	NM_001037928	626870	Mm.369429	NM_001037928	ENSMUSG00000040978	Gm11992	OTTMUSG00000005148	predicted gene 11992	protein-coding
mm_55311.1	chr6	54992859	54992878	-	1	NA	promoter-TSS (NM_026637)	promoter-TSS (NM_026637)	-1	NM_026637	110175	Mm.294708	NM_026637	ENSMUSG00000002797	Ggct	A030007L17Rik|AA673177|Gctg|Ggc	gamma-glutamyl cyclotransferase	protein-coding
mm_9268.1	chr1	171632870	171632879	-	1	NA	3' UTR (NM_144539, exon 8 of 8)	3' UTR (NM_144539, exon 8 of 8)	9026	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_54563.1	chr6	37442096	37442154	-	1	NA	promoter-TSS (NM_178661)	promoter-TSS (NM_178661)	23	NM_178661	208647	Mm.169929	NM_178661	ENSMUSG00000038648	Creb3l2	BBF2H7|C530025K05Rik|SCIRR69	cAMP responsive element binding protein 3-like 2	protein-coding
mm_39008.1	chr4	152031378	152031393	-	1	NA	exon (NM_031867, exon 4 of 6)	exon (NM_031867, exon 4 of 6)	-3714	NM_133879	100090	Mm.24661	NM_133879	ENSMUSG00000028952	Zbtb48	0610011D15Rik|AI327031|Hkr3	zinc finger and BTB domain containing 48	protein-coding
mm_34986.1	chr4	156026376	156026387	+	1	NA	promoter-TSS (NM_009400)	promoter-TSS (NM_009400)	39	NM_021985	21936	Mm.3180	NM_009400	ENSMUSG00000041954	Tnfrsf18	AITR|Gitr	tumor necrosis factor receptor superfamily, member 18	protein-coding
mm_79714.1	chr9	61373353	61373391	+	1	NA	5' UTR (NM_009389, exon 1 of 20)	5' UTR (NM_009389, exon 1 of 20)	1006	NM_001083927	21887	Mm.24255	NM_009389	ENSMUSG00000032280	Tle3	2610103N05Rik|ESG|Grg3a|Grg3b|mKIAA1547	transducin-like enhancer of split 3	protein-coding
mm_43148.1	chr5	125475865	125475889	+	1	NA	promoter-TSS (NM_030210)	promoter-TSS (NM_030210)	4	NM_030210	78894	Mm.431573	NM_030210	ENSMUSG00000029482	Aacs	2210408B16Rik|SUR5	acetoacetyl-CoA synthetase	protein-coding
mm_44425.1	chr5	20882073	20882075	-	1	NA	promoter-TSS (NM_177601)	promoter-TSS (NM_177601)	50	NM_172992	68770	Mm.86410	NM_172992	ENSMUSG00000039987	Phtf2	1110054G21Rik|9530062N20Rik|AI447096|C77923	putative homeodomain transcription factor 2	protein-coding
mm_28695.1	chr3	95538741	95538768	-	1	NA	exon (NM_021281, exon 3 of 8)	exon (NM_021281, exon 3 of 8)	11968	NM_001267695	13040	Mm.3619	NM_021281	ENSMUSG00000038642	Ctss	Cats	cathepsin S	protein-coding
mm_30683.1	chr4	11321901	11321913	+	1	NA	intron (NM_001081201, intron 1 of 18)	CpG	224	NM_001081201	381510	Mm.331486	NM_001081201	ENSMUSG00000045205	Dpy19l4	Gm1023|Narg3	dpy-19-like 4 (C. elegans)	protein-coding
mm_80022.1	chr9	67996393	67996422	+	1	NA	TTS (NM_177184)	TTS (NM_177184)	29307	NR_045745	434412	Mm.490707	NR_045745	ENSMUSG00000111841	Gm20745	-	predicted gene, 20745	ncRNA
mm_150304.1	chr19	34570331	34570333	+	1	NA	5' UTR (NM_008332, exon 2 of 3)	5' UTR (NM_008332, exon 2 of 3)	-13197	NM_010501	15959	Mm.426079	NM_010501	ENSMUSG00000074896	Ifit3	Ifi49|P49	interferon-induced protein with tetratricopeptide repeats 3	protein-coding
mm_109409.1	chr12	110447244	110447259	+	1	NA	promoter-TSS (NM_001135001)	promoter-TSS (NM_001135001)	72	NM_001135001	26931	Mm.240396	NM_012023	ENSMUSG00000017843	Ppp2r5c	2610043M05Rik|2700063L20Rik|AI060890|AW545884|C85228|D12Bwg0916e|mKIAA0044	protein phosphatase 2, regulatory subunit B', gamma	protein-coding
mm_162702.1	chr10	21907955	21907971	-	1	NA	intron (NM_001161845, intron 1 of 13)	intron (NM_001161845, intron 1 of 13)	25779	NM_001161845	20393	Mm.28405	NM_011361	ENSMUSG00000019970	Sgk1	Sgk	serum/glucocorticoid regulated kinase 1	protein-coding
mm_84805.1	chr9	77261463	77261463	-	1	NA	intron (NM_027150, intron 1 of 7)	intron (NM_027150, intron 1 of 7)	86407	NM_027150	69642	Mm.35008	NM_027150	ENSMUSG00000032355	Mlip	2310046A06Rik|AI931782|CIP	muscular LMNA-interacting protein	protein-coding
mm_30879.1	chr4	32239424	32239443	+	1	NA	Intergenic	CpG	-178002	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_48944.1	chr6	4539577	4539588	+	1	NA	exon (NM_007743, exon 51 of 52)	exon (NM_007743, exon 51 of 52)	33964	NM_007743	12843	Mm.277792	NM_007743	ENSMUSG00000029661	Col1a2	AA960264|AI325291|Col1a-2|Cola-2|Cola2|oim	collagen, type I, alpha 2	protein-coding
mm_99952.1	chr11	112787427	112787430	+	1	NA	3' UTR (NM_011448, exon 3 of 3)	3' UTR (NM_011448, exon 3 of 3)	5218	NM_011448	20682	Mm.286407	NM_011448	ENSMUSG00000000567	Sox9	2010306G03Rik|AV220920|mKIAA4243	SRY (sex determining region Y)-box 9	protein-coding
mm_93270.1	chr10	95773645	95773661	-	1	NA	Intergenic	Intergenic	-167010	NM_001001932	216238	Mm.210035	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding
mm_157980.1	chrX	94123166	94123177	-	1	NA	5' UTR (NM_011768, exon 1 of 8)	5' UTR (NM_011768, exon 1 of 8)	236	NM_011768	22764	Mm.919	NM_011768	ENSMUSG00000079509	Zfx	Zfx5|Zfx5,6|Zfx6	zinc finger protein X-linked	protein-coding
mm_119717.1	chr14	53881558	53881579	+	1	NA	Intergenic	Intergenic	372361	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_132819.1	chr16	45224113	45224123	+	1	NA	promoter-TSS (NM_001037719)	promoter-TSS (NM_001037719)	-219	NM_001037719	208154	Mm.38199	NM_177584	ENSMUSG00000052013	Btla	A630002H24	B and T lymphocyte associated	protein-coding
mm_34396.1	chr4	145026857	145026899	+	1	NA	intron (NM_001276502, intron 64 of 68)	intron (NM_001276502, intron 64 of 68)	133741	NM_011303	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding
mm_133619.1	chr16	91561290	91561301	+	1	NA	intron (NM_008338, intron 5 of 6)	intron (NM_008338, intron 5 of 6)	14201	NM_008338	15980	Mm.249364	NM_008338	ENSMUSG00000022965	Ifngr2	Ifgr2|Ifgt	interferon gamma receptor 2	protein-coding
mm_73130.1	chr8	94923675	94923683	+	1	NA	promoter-TSS (NM_001145972)	promoter-TSS (NM_001145972)	-15	NM_001033468	382045	Mm.334726	NM_001033468	ENSMUSG00000061577	Adgrg5	Gm1109|Gpr114|PGR27	adhesion G protein-coupled receptor G5	protein-coding
mm_69923.1	chr7	141884228	141884252	-	1	NA	3' UTR (NM_023764, exon 6 of 6)	3' UTR (NM_023764, exon 6 of 6)	18166	NM_023764	54473	Mm.103551	NM_023764	ENSMUSG00000025139	Tollip	4930403G24Rik|4931428G15Rik	toll interacting protein	protein-coding
mm_45539.1	chr5	72813024	72813070	-	1	NA	intron (NM_001113461, intron 3 of 17)	intron (NM_001113461, intron 3 of 17)	55401	NM_001113461	21682	Mm.319581	NM_013689	ENSMUSG00000029217	Tec	-	tec protein tyrosine kinase	protein-coding
mm_154212.1	chr19	59171489	59171492	-	1	NA	Intergenic	Intergenic	-1461	NM_009501	22326	Mm.23801	NM_009501	ENSMUSG00000006270	Vax1	-	ventral anterior homeobox 1	protein-coding
mm_118539.1	chr14	16388389	16388401	+	1	NA	exon (NM_009409, exon 6 of 36)	exon (NM_009409, exon 6 of 36)	23189	NM_009409	21974	Mm.130362	NM_009409	ENSMUSG00000017485	Top2b	D230016L12Rik|Top-2	topoisomerase (DNA) II beta	protein-coding
mm_61804.1	chr7	84568312	84568318	+	1	NA	intron (NR_045098, intron 1 of 2)	(TTG)n|Simple_repeat|Simple_repeat	37627	NM_010176	14085	Mm.3798	NM_010176	ENSMUSG00000030630	Fah	-	fumarylacetoacetate hydrolase	protein-coding
mm_38059.1	chr4	134012408	134012430	-	1	NA	intron (NM_145833, intron 2 of 3)	intron (NM_145833, intron 2 of 3)	6397	NM_145833	83557	Mm.302567	NM_145833	ENSMUSG00000050966	Lin28a	AL024421|ENSMUSG00000070700|Gm10299|Lin-28|Lin28|Tex17|lin-28A	lin-28 homolog A (C. elegans)	protein-coding
mm_55009.1	chr6	48840474	48840479	-	1	NA	5' UTR (NM_023056, exon 1 of 7)	5' UTR (NM_023056, exon 1 of 7)	512	NM_023056	65963	Mm.28385	NM_023056	ENSMUSG00000029810	Tmem176b	1810009M01Rik|Clast1|Lr8	transmembrane protein 176B	protein-coding
mm_88690.1	chr10	80116380	80116389	+	1	NA	non-coding (NR_126043, exon 1 of 11)	non-coding (NR_126043, exon 1 of 11)	581	NM_001301854	20869	Mm.44231	NM_011492	ENSMUSG00000003068	Stk11	AA408040|Lkb1|Par-4|R75140	serine/threonine kinase 11	protein-coding
mm_146052.1	chr18	69612636	69612644	+	1	NA	intron (NM_013685, intron 8 of 19)	intron (NM_013685, intron 8 of 19)	266919	NM_001083967	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding
mm_12150.1	chr2	61805041	61805053	+	1	NA	exon (NM_009322, exon 1 of 6)	exon (NM_009322, exon 1 of 6)	594	NM_009322	21375	Mm.308525	NM_009322	ENSMUSG00000035033	Tbr1	-	T-box brain gene 1	protein-coding
mm_61255.1	chr7	65863128	65863130	+	1	NA	intron (NM_011048, intron 1 of 21)	intron (NM_011048, intron 1 of 21)	993	NM_011048	18553	Mm.294007	NM_011048	ENSMUSG00000030513	Pcsk6	C86343|Pace4|SPC4	proprotein convertase subtilisin/kexin type 6	protein-coding
mm_110845.1	chr12	73046703	73046724	-	1	NA	promoter-TSS (NM_009189)	promoter-TSS (NM_009189)	-1	NM_009189	20471	Mm.4645	NM_009189	ENSMUSG00000051367	Six1	BB138287	sine oculis-related homeobox 1	protein-coding
mm_46156.1	chr5	96115603	96115613	-	1	NA	intron (NM_144910, intron 4 of 11)	Lx8|LINE|L1	45939	NM_001285511	231464	Mm.28374	NM_144910	ENSMUSG00000034724	Cnot6l	4932442K20Rik	CCR4-NOT transcription complex, subunit 6-like	protein-coding
mm_137984.1	chr17	33600709	33600752	+	1	NA	intron (NM_053214, intron 21 of 27)	Lx8|LINE|L1	-28362	NR_034153	328801	Mm.181488	NM_026712	ENSMUSG00000073423	Zfp414	0610030H11Rik|Znf414	zinc finger protein 414	protein-coding
mm_162648.1	chr1	195176660	195176682	-	1	NA	promoter-TSS (NM_007758)	promoter-TSS (NM_007758)	44	NM_007758	12902	Mm.235387	NM_007758	ENSMUSG00000026616	Cr2	C3DR|CD21|CD35|Cr-1|Cr-2|Cr1	complement receptor 2	protein-coding
mm_58232.1	chr6	145028619	145028645	-	1	NA	intron (NM_007532, intron 5 of 10)	B1F1|SINE|Alu	20180	NM_001024468	12035	Mm.4606	NM_007532	ENSMUSG00000030268	Bcat1	BCATc|Eca39	branched chain aminotransferase 1, cytosolic	protein-coding
mm_134573.1	chr16	20401096	20401099	-	1	NA	intron (NM_176839, intron 6 of 6)	(A)n|Simple_repeat|Simple_repeat	25297	NM_013790	27416	Mm.20845	NM_013790	ENSMUSG00000022822	Abcc5	2900011L11Rik|AI132311|Abcc5a|Abcc5b|Mrp5	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	protein-coding
mm_157061.1	chrX	8132794	8132857	-	1	NA	promoter-TSS (NM_026137)	promoter-TSS (NM_026137)	33	NM_001290783	73447	Mm.284162	NM_026137	ENSMUSG00000031166	Wdr13	1700060B08Rik|5730411P10Rik|DXHXS7467e|W51679|mMg21	WD repeat domain 13	protein-coding
mm_104480.1	chr11	95569997	95570019	-	1	NA	3' UTR (NM_033217, exon 6 of 6)	3' UTR (NM_033217, exon 6 of 6)	17690	NM_033217	18053	Mm.283893	NM_033217	ENSMUSG00000000120	Ngfr	LNGFR|Tnfrsf16|p75|p75NGFR|p75NTR	nerve growth factor receptor (TNFR superfamily, member 16)	protein-coding
mm_130121.1	chr15	89568234	89568238	-	1	NA	promoter-TSS (NM_013455)	promoter-TSS (NM_013455)	-90	NM_013455	11434	Mm.57	NM_013455	ENSMUSG00000022622	Acr	-	acrosin prepropeptide	protein-coding
mm_55357.1	chr6	56901917	56901919	-	1	NA	promoter-TSS (NM_001252374)	promoter-TSS (NM_001252374)	-32	NM_001252374	107569	Mm.158936	NM_026004	ENSMUSG00000029780	Nt5c3	1600024P05Rik|2610206B05Rik|3110004A18Rik|AI842776|Nt5c3a|Nt5y|PN-1|PN-I|PSN1|UMPH|Umph-1|Umph1|cN-III|lupin|p36	5'-nucleotidase, cytosolic III	protein-coding
mm_39144.1	chr4	155345679	155345689	-	1	NA	5' UTR (NM_001039079, exon 1 of 15)	5' UTR (NM_001039079, exon 1 of 15)	105	NM_001039079	18762	Mm.28561	NM_008860	ENSMUSG00000029053	Prkcz	AI098070|C80388|Pkcz|R74924|aPKCzeta|nPKC-zeta|zetaPKC	protein kinase C, zeta	protein-coding
mm_126653.1	chr15	84167828	84167843	+	1	NA	promoter-TSS (NR_105816)	promoter-TSS (NR_105816)	19	NM_054088	116939	Mm.390817	NM_054088	ENSMUSG00000041653	Pnpla3	Adpn	patatin-like phospholipase domain containing 3	protein-coding
mm_80427.1	chr9	77921477	77921481	+	1	NA	intron (NM_134255, intron 1 of 7)	intron (NM_134255, intron 1 of 7)	4114	NM_134255	68801	Mm.430736	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	ELOVL family member 5, elongation of long chain fatty acids (yeast)	protein-coding
mm_53819.1	chr6	147096551	147096555	+	1	NA	intron (NM_001081237, intron 1 of 2)	intron (NM_001081237, intron 1 of 2)	5478	NM_001081237	232539	Mm.491206	NM_001081237	ENSMUSG00000040102	Klhl42	A330079N23Rik|AI450355|C230080I20Rik|Ctb9|Klhdc5|mKIAA1340	kelch-like 42	protein-coding
mm_3944.1	chr1	163903684	163903688	+	1	NA	intron (NM_001305643, intron 19 of 19)	intron (NM_001305643, intron 19 of 19)	-25414	NM_001286002	240880	Mm.389213	NM_028776	ENSMUSG00000026584	Scyl3	1200016D23Rik|6030457O16|AW214499|Pace1	SCY1-like 3 (S. cerevisiae)	protein-coding
mm_149822.1	chr19	24416004	24416013	+	1	NA	intron (NM_008846, intron 3 of 14)	intron (NM_008846, intron 3 of 14)	61466	NM_026520	68034	Mm.440181	NM_026520	ENSMUSG00000074922	Fam122a	2410124L17Rik|2900009I07Rik|ENSMUSG00000051082|Gm9849	family with sequence similarity 122, member A	protein-coding
mm_139564.1	chr17	56990285	56990330	+	1	NA	promoter-TSS (NM_017393)	promoter-TSS (NM_017393)	43	NM_017393	53895	Mm.287892	NM_017393	ENSMUSG00000002660	Clpp	AU019820|D17Wsu160e	caseinolytic mitochondrial matrix peptidase proteolytic subunit	protein-coding
mm_137971.1	chr17	33556386	33556404	+	1	NA	intron (NM_053214, intron 1 of 27)	ID4_|SINE|ID	688	NM_053214	17916	Mm.42019	NM_053214	ENSMUSG00000024300	Myo1f	C330006B10Rik	myosin IF	protein-coding
mm_87784.1	chr10	60296807	60296817	+	1	NA	intron (NM_011179, intron 8 of 14)	intron (NM_011179, intron 8 of 14)	12351	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_134607.1	chr16	20716160	20716166	-	1	NA	5' UTR (NM_009900, exon 1 of 24)	5' UTR (NM_009900, exon 1 of 24)	473	NM_009900	12724	Mm.177761	NM_009900	ENSMUSG00000022843	Clcn2	AL118368|ClC-2|Clc2|nmf240	chloride channel, voltage-sensitive 2	protein-coding
mm_103013.1	chr11	69734772	69734776	-	1	NA	exon (NM_001291068, exon 29 of 29)	exon (NM_001291068, exon 29 of 29)	23859	NM_001291068	20020	Mm.16533	NM_009089	ENSMUSG00000005198	Polr2a	220kDa|Rpb1|Rpo2-1	polymerase (RNA) II (DNA directed) polypeptide A	protein-coding
mm_40524.1	chr5	57918764	57918775	+	1	NA	intron (NM_001122758, intron 2 of 2)	intron (NM_001122758, intron 2 of 2)	200688	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_8116.1	chr1	135919355	135919359	-	1	NA	promoter-TSS (NM_019645)	promoter-TSS (NM_019645)	-150	NM_019645	18772	Mm.4494	NM_019645	ENSMUSG00000026413	Pkp1	-	plakophilin 1	protein-coding
mm_39546.1	chr5	21645856	21645885	+	1	NA	promoter-TSS (NM_026034)	promoter-TSS (NM_026034)	-114	NM_026034	67211	Mm.260782	NM_026034	ENSMUSG00000038525	Armc10	2810037C14Rik|Svh	armadillo repeat containing 10	protein-coding
mm_155293.1	chrX	61183891	61183909	+	1	NA	3' UTR (NM_001166658, exon 1 of 1)	3' UTR (NM_001166658, exon 1 of 1)	1658	NM_001166658	631990	Mm.401324	NM_001166658	ENSMUSG00000090546	Cdr1	100039759|Cdr|Cdr34|EG631990|Gm2409|Gm7077	cerebellar degeneration related antigen 1	protein-coding
mm_121463.1	chr14	120896840	120896851	+	1	NA	Intergenic	Intergenic	-14349	NM_023579	70572	Mm.221452	NM_023579	ENSMUSG00000030662	Ipo5	1110011C18Rik|5730478E03Rik|AA409333|C76941|IMB3|Kpnb3|Ranbp5	importin 5	protein-coding
mm_21145.1	chr2	154363974	154363989	-	1	NA	intron (NM_025876, intron 5 of 13)	RSINE1|SINE|B4	8738	NM_025876	66971	Mm.289427	NM_025876	ENSMUSG00000027487	Cdk5rap1	2310066P17Rik	CDK5 regulatory subunit associated protein 1	protein-coding
mm_159934.1	chr6	71871206	71871206	+	1	NA	intron (NM_001253681, intron 12 of 14)	MIRb|SINE|MIR	37556	NM_027275	69956	Mm.30256	NM_027275	ENSMUSG00000063884	Ptcd3	2610034F17Rik|2810422B04Rik|AA589622|AU045708|MRP-S39	pentatricopeptide repeat domain 3	protein-coding
mm_35360.1	chr4	32363436	32363446	-	1	NA	Intergenic	Intergenic	-53994	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_78186.1	chr9	21235598	21235615	+	1	NA	intron (NM_001110306, intron 2 of 5)	intron (NM_001110306, intron 2 of 5)	3726	NM_016679	50868	Mm.248266	NM_016679	ENSMUSG00000003308	Keap1	INRF2|mKIAA0132	kelch-like ECH-associated protein 1	protein-coding
mm_93099.1	chr10	89745773	89745778	-	1	NA	intron (NM_029166, intron 1 of 20)	CpG	784	NM_029166	75089	Mm.268922	NM_029166	ENSMUSG00000019951	Uhrf1bp1l	2010319N22Rik|4930506D01Rik|AA589495|C80672|E030041M21Rik|mKIAA0701	UHRF1 (ICBP90) binding protein 1-like	protein-coding
mm_85781.1	chr9	109058675	109058685	-	1	NA	TTS (NM_026381)	TTS (NM_026381)	571	NM_001012236	22040	Mm.439964	NM_011637	ENSMUSG00000049734	Trex1	AU041952	three prime repair exonuclease 1	protein-coding
mm_163280.1	chr11	116532499	116532501	+	1	NA	promoter-TSS (NM_001172472)	promoter-TSS (NM_001172472)	56	NM_001172473	20698	Mm.20944	NM_011451	ENSMUSG00000061878	Sphk1	1110006G24Rik|Sk1|Spk1	sphingosine kinase 1	protein-coding
mm_76849.1	chr8	105326253	105326278	-	1	NA	promoter-TSS (NM_177449)	promoter-TSS (NM_177449)	11	NM_177449	234684	Mm.381717	NM_177449	ENSMUSG00000041679	Lrrc29	A630024J02Rik|FBL9|FBXL9	leucine rich repeat containing 29	protein-coding
mm_145195.1	chr18	49884926	49884934	+	1	NA	intron (NM_001081371, intron 19 of 42)	Lx3B|LINE|L1	51933	NM_001081371	240283	Mm.257790	NM_001081371	ENSMUSG00000037416	Dmxl1	C630007L23Rik|D030030C22	Dmx-like 1	protein-coding
mm_86897.1	chr10	22303024	22303052	+	1	NA	intron (NM_009018, intron 5 of 5)	intron (NM_009018, intron 5 of 5)	-3682	NR_015465	606736	Mm.387042	NR_015465	ENSMUSG00000097352	C920009B18Rik	-	RIKEN cDNA C920009B18 gene	ncRNA
mm_156707.1	chrX	159627266	159627298	+	1	NA	promoter-TSS (NM_001135727)	promoter-TSS (NM_001135727)	10	NM_001135727	58194	Mm.286495	NM_021389	ENSMUSG00000040990	Sh3kbp1	1200007H22Rik|1700125L08Rik|5830464D22Rik|AI447724|Cin85|IN85|Ruk|Seta	SH3-domain kinase binding protein 1	protein-coding
mm_99807.1	chr11	108381167	108381171	+	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	-14128	NM_013475	11818	Mm.2266	NM_013475	ENSMUSG00000000049	Apoh	B2GPI|beta-2-GPI|beta2-GPI	apolipoprotein H	protein-coding
mm_169078.1	chr13	3236643	3236645	+	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	87169	NR_001581	73266	Mm.335891	NR_001581		Speer6-ps1	1700039A02Rik|SPEER-6	spermatogenesis associated glutamate (E)-rich protein 6, pseudogene 1	pseudo
mm_80048.1	chr9	69289903	69289907	+	1	NA	promoter-TSS (NM_001289916)	promoter-TSS (NM_001289916)	64	NM_001289916	19883	Mm.378450	NM_013646	ENSMUSG00000032238	Rora	9530021D13Rik|Nr1f1|ROR1|ROR2|ROR3|nmf267|sg|staggerer|tmgc26	RAR-related orphan receptor alpha	protein-coding
mm_92838.1	chr10	81499623	81499643	-	1	NA	exon (NM_010102, exon 1 of 1)	exon (NM_010102, exon 1 of 1)	504	NM_010102	13611	Mm.33065	NM_010102	ENSMUSG00000044199	S1pr4	Edg6|Lpc1|S1p4	sphingosine-1-phosphate receptor 4	protein-coding
mm_66000.1	chr7	30559601	30559652	-	1	NA	promoter-TSS (NM_001290569)	promoter-TSS (NM_001290569)	20	NM_029377	75660	Mm.379242	NM_029377	ENSMUSG00000036845	Lin37	1810054G18Rik	lin-37 homolog (C. elegans)	protein-coding
mm_50742.1	chr6	52729332	52729370	+	1	NA	exon (NM_025816, exon 4 of 18)	exon (NM_025816, exon 4 of 18)	15622	NM_025816	52440	Mm.389757	NM_025816	ENSMUSG00000004535	Tax1bp1	1200003J11Rik|1700069J21Rik|AA930106|D6Ertd404e|D6Ertd772e|T6bp|TXBP151	Tax1 (human T cell leukemia virus type I) binding protein 1	protein-coding
mm_1231.1	chr1	62769008	62769022	+	1	NA	exon (NM_001077407, exon 11 of 16)	exon (NM_001077407, exon 11 of 16)	25717	NR_040601	74992	Mm.401979	NR_040601		4930487H11Rik	-	RIKEN cDNA 4930487H11 gene	ncRNA
mm_1356.1	chr1	66322022	66322044	+	1	NA	5' UTR (NM_001310634, exon 1 of 15)	5' UTR (NM_001310634, exon 1 of 15)	309	NM_001310634	17756	Mm.256966	NM_008632	ENSMUSG00000015222	Map2	G1-397-34|MAP-2|Mtap-2|Mtap2|repro4	microtubule-associated protein 2	protein-coding
mm_157567.1	chrX	52541995	52541999	-	1	NA	intron (NM_016697, intron 2 of 7)	intron (NM_016697, intron 2 of 7)	-33846	NR_045367	100504594	Mm.447008	NR_045367	ENSMUSG00000055110	A630012P03Rik	-	RIKEN cDNA A630012P03 gene	ncRNA
mm_21638.1	chr2	164327623	164327623	-	1	NA	Intergenic	Lx7|LINE|L1	-5142	NM_009301	20944	Mm.140154	NM_009301	ENSMUSG00000017004	Svs5	BB115186|Semg1|Svp-1|Svp1|Svp5	seminal vesicle secretory protein 5	protein-coding
mm_51368.1	chr6	72699166	72699201	+	1	NA	intron (NM_001079822, intron 3 of 12)	intron (NM_001079822, intron 3 of 12)	69352	NR_040421	100038714	Mm.321330	NR_040421		Gm15401	ENSMUSG00000072999|OTTMUSG00000021199	predicted gene 15401	ncRNA
mm_7330.1	chr1	105157867	105157882	-	1	NA	Intergenic	Intergenic	198836	NM_178779	320311	Mm.389162	NM_178779	ENSMUSG00000047496	Rnf152	A930029B02Rik	ring finger protein 152	protein-coding
mm_208.1	chr1	16656980	16656984	+	1	NA	promoter-TSS (NM_026456)	promoter-TSS (NM_026456)	-117	NM_026456	67923	Mm.289248	NM_026456	ENSMUSG00000079658	Eloc	2610043E24Rik|2610301I15Rik|AA407206|AI987979|AW049146|Tceb1	elongin C	protein-coding
mm_45357.1	chr5	65935658	65935660	-	1	NA	Intergenic	Intergenic	-31465	NM_001081104	231252	Mm.140015	NM_001081104	ENSMUSG00000029205	Chrna9	2410015I05Rik|Acra9|EG666827|Gm8311	cholinergic receptor, nicotinic, alpha polypeptide 9	protein-coding
mm_56694.1	chr6	114464317	114464354	-	1	NA	intron (NM_001317124, intron 1 of 1)	L1MD2|LINE|L1	5813	NM_001317124	15465	Mm.333327	NM_008285	ENSMUSG00000053004	Hrh1	Bphs|H1R|HH1R|Hir	histamine receptor H1	protein-coding
mm_171596.1	chr4	147702602	147702602	-	1	NA	promoter-TSS (NM_001127188)	promoter-TSS (NM_001127188)	29	NM_001127188	100503584	Mm.276881	NM_001127188	ENSMUSG00000062518	Zfp534	Gm13159|OTTMUSG00000010681	zinc finger protein 534	protein-coding
mm_61885.1	chr7	89632952	89632993	+	1	NA	exon (NM_181407, exon 1 of 14)	exon (NM_181407, exon 1 of 14)	154	NM_181407	109264	Mm.334011	NM_181407	ENSMUSG00000030621	Me3	1700020C08Rik|B230207H15Rik	malic enzyme 3, NADP(+)-dependent, mitochondrial	protein-coding
mm_42146.1	chr5	111418652	111418662	+	1	NA	exon (NM_001081235, exon 1 of 2)	exon (NM_001081235, exon 1 of 2)	491	NM_001081235	433938	Mm.332576	NM_001081235	ENSMUSG00000070576	Mn1	AA003644|AA009236	meningioma 1	protein-coding
mm_100732.1	chr11	3931999	3932083	-	1	NA	promoter-TSS (NM_001130458)	promoter-TSS (NM_001130458)	3	NM_015749	21452	Mm.20948	NM_015749	ENSMUSG00000020432	Tcn2	AW208754|Tcn-2	transcobalamin 2	protein-coding
mm_48767.1	chr5	148399864	148399872	-	1	NA	promoter-TSS (NM_007513)	promoter-TSS (NM_007513)	36	NM_007513	11987	Mm.275489	NM_007513	ENSMUSG00000041313	Slc7a1	4831426K01Rik|AI447493|Atrc-1|Atrc1|Cat1|Rec-1|Rev-1|mCAT-1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 1	protein-coding
mm_53804.1	chr6	146861957	146861963	+	1	NA	intron (NM_027059, intron 6 of 9)	intron (NM_027059, intron 6 of 9)	11850	NM_027059	69371	Mm.252733	NM_027059	ENSMUSG00000030292	Smco2	1700023A16Rik	single-pass membrane protein with coiled-coil domains 2	protein-coding
mm_130610.1	chr15	99875383	99875447	-	1	NA	promoter-TSS (NM_001113545)	promoter-TSS (NM_001113545)	41	NM_001113545	65970	Mm.33207	NM_023063	ENSMUSG00000023022	Lima1	Eplin	LIM domain and actin binding 1	protein-coding
mm_69685.1	chr7	139989301	139989313	-	1	NA	exon (NM_001291066, exon 6 of 24)	exon (NM_001291066, exon 6 of 24)	-2433	NR_106029	102465643		NR_106029	ENSMUSG00000099092	Mir7062	Gm27339|mmu-mir-7062	microRNA 7062	ncRNA
mm_65240.1	chr7	19796790	19796829	-	1	NA	promoter-TSS (NM_023224)	promoter-TSS (NM_023224)	0	NM_001161844	80794	Mm.81698	NM_023224	ENSMUSG00000040525	Cblc	2310076I21Rik|2310079L19Rik|Cbl3	Casitas B-lineage lymphoma c	protein-coding
mm_108568.1	chr12	84807026	84807037	+	1	NA	intron (NM_013589, intron 14 of 34)	intron (NM_013589, intron 14 of 34)	33761	NM_028863	74316	Mm.25719	NM_028863	ENSMUSG00000021241	Isca2	0710001C05Rik|5730594E03Rik|Hbld1	iron-sulfur cluster assembly 2	protein-coding
mm_54674.1	chr6	39377615	39377631	-	1	NA	promoter-TSS (NM_028123)	promoter-TSS (NM_028123)	84	NM_028123	72144	Mm.482167	NM_028123	ENSMUSG00000029924	Slc37a3	2610507O21Rik|AU044904	solute carrier family 37 (glycerol-3-phosphate transporter), member 3	protein-coding
mm_21823.1	chr2	165297452	165297485	-	1	NA	intron (NM_001302752, intron 13 of 20)	intron (NM_001302752, intron 13 of 20)	-9630	NR_045544	228875	Mm.21184	NM_144893	ENSMUSG00000017664	Slc35c2	C85957|CGI-15|D2Wsu58e|Ovcov1	solute carrier family 35, member C2	protein-coding
mm_49140.1	chr6	9105074	9105074	+	1	NA	intron (NM_008751, intron 1 of 1)	intron (NM_008751, intron 1 of 1)	155055	NM_008751	18231	Mm.46954	NM_008751	ENSMUSG00000046178	Nxph1	C130005L03Rik	neurexophilin 1	protein-coding
mm_173041.1	chrX	114592557	114592563	-	1	NA	Intergenic	Intergenic	118227	NM_001290477	237010	Mm.132583	NM_172781	ENSMUSG00000025597	Klhl4	B130014A11|C130018J01Rik	kelch-like 4	protein-coding
mm_93419.1	chr10	108699772	108699811	-	1	NA	exon (NM_203660, exon 1 of 1)	exon (NM_203660, exon 1 of 1)	369	NM_203660	368203	Mm.452758	NM_203660		Gm5136	C6.1AL|EG368203	predicted gene 5136	protein-coding
mm_70379.1	chr8	10154097	10154158	+	1	NA	5' UTR (NM_001319151, exon 1 of 35)	5' UTR (NM_001319151, exon 1 of 35)	216	NM_001319151	244281	Mm.422761	NM_001081397	ENSMUSG00000039057	Myo16	BM140241|C230040D10Rik|Gm1105|NYAP3|mKIAA0865	myosin XVI	protein-coding
mm_81984.1	chr9	121382790	121382807	+	1	NA	intron (NM_175114, intron 1 of 15)	intron (NM_175114, intron 1 of 15)	15840	NM_175114	67095	Mm.491112	NM_175114	ENSMUSG00000032536	Trak1	2310001H13Rik|AI413908|AI467545|hyrt|mKIAA1042	trafficking protein, kinesin binding 1	protein-coding
mm_105436.1	chr11	104341279	104341294	-	1	NA	intron (NM_001081045, intron 9 of 13)	MIRb|SINE|MIR	101005	NM_001081045	76719	Mm.136418	NM_001081045	ENSMUSG00000018412	Kansl1	1700081L11Rik|9430041J06Rik|mKIAA1267	KAT8 regulatory NSL complex subunit 1	protein-coding
mm_154745.1	chrX	10485122	10485163	+	1	NA	promoter-TSS (NM_019634)	promoter-TSS (NM_019634)	26	NM_019634	21912	Mm.18590	NM_019634	ENSMUSG00000058254	Tspan7	1200014P11Rik|A15|AI323365|Cd231|Mxs1|PE31|R74651|TALLA|Tm4sf2	tetraspanin 7	protein-coding
mm_5239.1	chr1	16104164	16104204	-	1	NA	intron (NM_011291, intron 1 of 6)	intron (NM_011291, intron 1 of 6)	249	NM_011291	19989	Mm.319659	NM_011291	ENSMUSG00000043716	Rpl7	Rpl7a|Surf-3	ribosomal protein L7	protein-coding
mm_148794.1	chr19	6171958	6171964	+	1	NA	exon (NM_028967, exon 3 of 3)	exon (NM_028967, exon 3 of 3)	7503	NM_028967	74481	Mm.159219	NM_028967	ENSMUSG00000039699	Batf2	4933430F08Rik	basic leucine zipper transcription factor, ATF-like 2	protein-coding
mm_122931.1	chr14	54961763	54961790	-	1	NA	exon (NM_010856, exon 10 of 39)	exon (NM_010856, exon 10 of 39)	4831	NM_001164171	17888	Mm.290003	NM_010856	ENSMUSG00000040752	Myh6	A830009F23Rik|AA517445|Myhc-a|Myhca|alpha-MHC	myosin, heavy polypeptide 6, cardiac muscle, alpha	protein-coding
mm_82542.1	chr9	20879719	20879738	-	1	NA	promoter-TSS (NM_145154)	promoter-TSS (NM_145154)	-18	NM_145154	70726	Mm.34019	NM_145154	ENSMUSG00000038742	Angptl6	6330404E11Rik|AGF|ARP3|Arp5	angiopoietin-like 6	protein-coding
mm_129922.1	chr15	84436296	84436298	-	1	NA	intron (NM_001347543, intron 1 of 5)	intron (NM_001347543, intron 1 of 5)	10313	NM_001347543	72301	Mm.275387	NM_001163145	ENSMUSG00000062760	1810041L15Rik	Kiaa1644	RIKEN cDNA 1810041L15 gene	protein-coding
mm_129327.1	chr15	77771855	77771867	-	1	NA	exon (NM_022410, exon 26 of 41)	exon (NM_022410, exon 26 of 41)	-16632	NM_001081970	239552	Mm.125650	NM_001081970	ENSMUSG00000056656	Apol8	9830006J20Rik|APOL-II|Apol2	apolipoprotein L 8	protein-coding
mm_37334.1	chr4	119656710	119656719	-	1	NA	3' UTR (NM_008191, exon 3 of 3)	3' UTR (NM_008191, exon 3 of 3)	2231	NM_008191	14916	Mm.278	NM_008191	ENSMUSG00000032978	Guca2b	AV066530|Gcap2|Ugn	guanylate cyclase activator 2b (retina)	protein-coding
mm_37273.1	chr4	118620728	118620762	-	1	NA	promoter-TSS (NM_026789)	promoter-TSS (NM_026789)	-54	NM_026932	69072	Mm.29906	NM_026932	ENSMUSG00000028729	Ebna1bp2	1810014B19Rik|AA537058|B830003A16Rik|C81321|Ebp2|Nobp|p40	EBNA1 binding protein 2	protein-coding
mm_32149.1	chr4	99829438	99829462	+	1	NA	promoter-TSS (NM_145549)	promoter-TSS (NM_145549)	-50	NM_145549	230500	Mm.331727	NM_145549	ENSMUSG00000073791	Efcab7	mKIAA1799	EF-hand calcium binding domain 7	protein-coding
mm_114254.1	chr13	56703438	56703445	+	1	NA	promoter-TSS (NM_001164042)	promoter-TSS (NM_001164042)	-227	NM_001164042	17129	Mm.272920	NM_008541	ENSMUSG00000021540	Smad5	1110051M15Rik|AI451355|Dwf-C|Madh5|MusMLP	SMAD family member 5	protein-coding
mm_39055.1	chr4	153957156	153957178	-	1	NA	promoter-TSS (NM_001163019)	promoter-TSS (NM_001163019)	-70	NM_175287	97159	Mm.7066	NM_175287	ENSMUSG00000047613	A430005L14Rik	C79672	RIKEN cDNA A430005L14 gene	protein-coding
mm_34132.1	chr4	139287029	139287066	+	1	NA	exon (NM_001271405, exon 7 of 9)	exon (NM_001271405, exon 7 of 9)	23653	NM_145384	212555	Mm.45131	NM_145384	ENSMUSG00000028744	Pqlc2	BC019216	PQ loop repeat containing 2	protein-coding
mm_166925.1	chr7	31263736	31263744	+	1	NA	promoter-TSS (NM_001310660)	promoter-TSS (NM_001310660)	4	NM_001310660	100043827		NM_001310660		Scgb2b1	Abpbg1|Gm4677	secretoglobin, family 2B, member 1	protein-coding
mm_3190.1	chr1	135800829	135800839	+	1	NA	intron (NM_001112702, intron 2 of 8)	intron (NM_001112702, intron 2 of 8)	1323	NM_001112702	21952	Mm.44379	NM_021467	ENSMUSG00000026418	Tnni1	2700018B22Rik|AI747285|ssTnI	troponin I, skeletal, slow 1	protein-coding
mm_83497.1	chr9	45946968	45946978	-	1	NA	intron (NM_172257, intron 11 of 25)	intron (NM_172257, intron 11 of 25)	-7383	NR_106055	102465659		NR_106055	ENSMUSG00000098327	Mir7087	Gm27273|mmu-mir-7087	microRNA 7087	ncRNA
mm_86256.1	chr9	121495709	121495714	-	1	NA	promoter-TSS (NM_001284508)	promoter-TSS (NM_001284508)	-17	NM_031161	12424	Mm.2619	NM_031161	ENSMUSG00000032532	Cck	-	cholecystokinin	protein-coding
mm_43616.1	chr5	138089284	138089295	+	1	NA	intron (NM_029869, intron 1 of 3)	intron (NM_029869, intron 1 of 3)	4205	NM_029869	74570	Mm.213114	NM_029869	ENSMUSG00000029729	Zkscan1	5930429A01Rik|9130423L19Rik|9230118B16Rik|AI646829|AI788588|C87323|KOX18|PHZ-37|ZNF139	zinc finger with KRAB and SCAN domains 1	protein-coding
mm_91681.1	chr10	43829195	43829197	-	1	NA	intron (NR_131055, intron 1 of 2)	ORR1D1|LTR|ERVL-MaLR	3289	NR_131055	71018	Mm.410796	NR_131055	ENSMUSG00000111342	4933404K13Rik	-	RIKEN cDNA 4933404K13 gene	ncRNA
mm_77167.1	chr8	111689399	111689409	-	1	NA	TTS (NR_106044)	TTS (NR_106044)	270	NR_106044	102466993		NR_106044	ENSMUSG00000099129	Mir7076	Gm27318|mmu-mir-7076	microRNA 7076	ncRNA
mm_18065.1	chr2	42163593	42163600	-	1	NA	intron (NM_053011, intron 2 of 90)	intron (NM_053011, intron 2 of 90)	283972	NR_105754	102465171		NR_105754	ENSMUSG00000098660	Mir6336	Gm27584|mmu-mir-6336	microRNA 6336	ncRNA
mm_170042.1	chr17	24414694	24414700	+	1	NA	promoter-TSS (NM_001080128)	promoter-TSS (NM_001080128)	22	NM_001080128	19826	Mm.1951	NM_009070	ENSMUSG00000034681	Rnps1	-	ribonucleic acid binding protein S1	protein-coding
mm_9863.1	chr1	184827247	184827273	-	1	NA	intron (NM_133684, intron 4 of 7)	intron (NM_133684, intron 4 of 7)	-4772	NR_035502	100316821		NR_035502	ENSMUSG00000088559	Mir1981	mir-1981|mmu-mir-1981	microRNA 1981	ncRNA
mm_89846.1	chr10	106879995	106880006	+	1	NA	intron (NM_001205341, intron 21 of 31)	RLTR20A4|LTR|ERVK	243664	NM_001142804	380660	Mm.336072	NM_198636	ENSMUSG00000035948	Acss3	8430416H19Rik|Gm874	acyl-CoA synthetase short-chain family member 3	protein-coding
mm_74524.1	chr8	9428666	9428672	-	1	NA	intron (NM_001347127, intron 1 of 3)	B1F|SINE|Alu	284000	NR_073360	74688	Mm.159298	NR_073360	ENSMUSG00000109215	4930453L07Rik	-	RIKEN cDNA 4930453L07 gene	ncRNA
mm_14828.1	chr2	147029864	147029878	+	1	NA	exon (NM_011917, exon 13 of 30)	exon (NM_011917, exon 13 of 30)	16811	NM_011917	24128	Mm.3065	NM_011917	ENSMUSG00000027433	Xrn2	-	5'-3' exoribonuclease 2	protein-coding
mm_74953.1	chr8	25994104	25994144	-	1	NA	promoter-TSS (NM_029037)	promoter-TSS (NM_029037)	-3	NM_029037	74653	Mm.17631	NM_029037	ENSMUSG00000037251	Pomk	4930444A02Rik|Sgk196	protein-O-mannose kinase	protein-coding
mm_76470.1	chr8	85386292	85386300	-	1	NA	Intergenic	Intergenic	-5255	NM_001297612	213435	Mm.32804	NM_175441	ENSMUSG00000031698	Mylk3	D830007F02Rik|MLCK	myosin light chain kinase 3	protein-coding
mm_71597.1	chr8	54955214	54955231	+	1	NA	5' UTR (NM_153581, exon 1 of 7)	5' UTR (NM_153581, exon 1 of 7)	494	NM_001253756	234267	Mm.241700	NM_153581	ENSMUSG00000031517	Gpm6a	Gpm6|M6A	glycoprotein m6a	protein-coding
mm_59995.1	chr7	30563801	30563826	+	1	NA	promoter-TSS (NM_025498)	promoter-TSS (NM_025498)	473	NM_170760	233073	Mm.34790	NM_170760	ENSMUSG00000078765	U2af1l4	AA407033|AF419339|AI451269|AW553050|U2af26	U2 small nuclear RNA auxiliary factor 1-like 4	protein-coding
mm_37760.1	chr4	129672783	129672793	-	1	NA	promoter-TSS (NM_008468)	promoter-TSS (NM_008468)	-21	NM_008468	16650	Mm.202358	NM_008468	ENSMUSG00000003731	Kpna6	IPOA7|Kpna5|NPI-2	karyopherin (importin) alpha 6	protein-coding
mm_35396.1	chr4	34551438	34551447	-	1	NA	intron (NM_001007589, intron 1 of 4)	intron (NM_001007589, intron 1 of 4)	827	NM_001007589	433693	Mm.389532	NM_026019	ENSMUSG00000028291	Akirin2	2700059D21Rik|AA114675|AA522011|AU019887|Akirin-2	akirin 2	protein-coding
mm_82323.1	chr9	8004636	8004644	-	1	NA	promoter-TSS (NM_001171147)	promoter-TSS (NM_001171147)	-44	NM_009534	22601	Mm.221992	NM_009534	ENSMUSG00000053110	Yap1	AI325207|Yap|Yap65|Yki|Yorkie	yes-associated protein 1	protein-coding
mm_53998.1	chr6	7677322	7677332	-	1	NA	exon (NM_012055, exon 9 of 12)	exon (NM_012055, exon 9 of 12)	15855	NM_012055	27053	Mm.2942	NM_012055	ENSMUSG00000029752	Asns	-	asparagine synthetase	protein-coding
mm_52190.1	chr6	99692363	99692377	+	1	NA	promoter-TSS (NM_008158)	promoter-TSS (NM_008158)	-309	NM_008158	14761	Mm.35009	NM_008158	ENSMUSG00000072875	Gpr27	-	G protein-coupled receptor 27	protein-coding
mm_38425.1	chr4	139291086	139291091	-	1	NA	exon (NM_001271405, exon 9 of 9)	exon (NM_001271405, exon 9 of 9)	19612	NM_145384	212555	Mm.45131	NM_145384	ENSMUSG00000028744	Pqlc2	BC019216	PQ loop repeat containing 2	protein-coding
mm_111844.1	chr12	107938738	107938749	-	1	NA	intron (NM_001286343, intron 1 of 1)	RLTR20C1_MM|LTR|ERVK	64671	NM_001079883	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_94632.1	chr11	16846325	16846327	+	1	NA	intron (NM_207655, intron 1 of 27)	intron (NM_207655, intron 1 of 27)	94123	NM_007912	13649	Mm.8534	NM_007912	ENSMUSG00000020122	Egfr	9030024J15Rik|AI552599|Erbb|Errb1|Errp|Wa5|wa-2|wa2	epidermal growth factor receptor	protein-coding
mm_15619.1	chr2	160891974	160891999	+	1	NA	intron (NM_001199118, intron 1 of 19)	MIR3|SINE|MIR	3818	NM_001199118	64899	Mm.292111	NM_022883	ENSMUSG00000027412	Lpin3	9130206L11Rik|AA438110|AV236139|mKIAA4023	lipin 3	protein-coding
mm_76615.1	chr8	91135703	91135713	-	1	NA	promoter-TSS (NM_010241)	promoter-TSS (NM_010241)	-214	NM_010241	14339	Mm.324588	NM_010241	ENSMUSG00000031667	Aktip	AL023020|Fif|Ft|Ft1|Fts	thymoma viral proto-oncogene 1 interacting protein	protein-coding
mm_70682.1	chr8	14996157	14996157	+	1	NA	intron (NM_172751, intron 27 of 28)	intron (NM_172751, intron 27 of 28)	-14868	NM_029116	74901	Mm.46675	NM_029116	ENSMUSG00000055675	Kbtbd11	2900016B01Rik|4930465M17Rik|mKIAA0711	kelch repeat and BTB (POZ) domain containing 11	protein-coding
mm_63209.1	chr7	126272429	126272443	+	1	NA	promoter-TSS (NM_145587)	promoter-TSS (NM_145587)	-183	NM_145587	104175	Mm.29660	NM_145587	ENSMUSG00000042978	Sbk1	Sbk	SH3-binding kinase 1	protein-coding
mm_110603.1	chr12	56536072	56536095	-	1	NA	intron (NM_009385, intron 1 of 2)	CpG	825	NM_009385	21869	Mm.89972	NM_009385	ENSMUSG00000001496	Nkx2-1	AV026640|Nkx2.1|T/EBP|Titf1|Ttf-1	NK2 homeobox 1	protein-coding
mm_12583.1	chr2	73322753	73322754	+	1	NA	intron (NM_029022, intron 5 of 7)	B4A|SINE|B4	10101	NM_029022	74616	Mm.247457	NM_029022	ENSMUSG00000008226	Scrn3	4833415E20Rik|AI427019|AV002033|Ses3	secernin 3	protein-coding
mm_112966.1	chr13	21183863	21183874	+	1	NA	exon (NM_009054, exon 3 of 8)	exon (NM_009054, exon 3 of 8)	3937	NM_009054	19720	Mm.314056	NM_009054	ENSMUSG00000021326	Trim27	AW538890|Gm19403|Rfp	tripartite motif-containing 27	protein-coding
mm_53270.1	chr6	128424716	128424729	+	1	NA	exon (NM_133927, exon 1 of 12)	exon (NM_133927, exon 1 of 12)	188	NM_133927	101142	Mm.31345	NM_133927	ENSMUSG00000001518	Itfg2	2700050P07Rik|AI646725	integrin alpha FG-GAP repeat containing 2	protein-coding
mm_110443.1	chr12	50932725	50932728	-	1	NA	Intergenic	MLTR11A|LTR|ERVK	-72430	NR_126468	75494	Mm.416848	NR_126468		1700008C04Rik	-	RIKEN cDNA 1700008C04 gene	ncRNA
mm_169504.1	chr14	78996986	78997001	+	1	NA	intron (NM_173758, intron 16 of 25)	L1Md_Gf|LINE|L1	147815	NM_173758	219189	Mm.159651	NM_027906	ENSMUSG00000058997	Vwa8	1300010F03Rik|4932416F07Rik|AI957255|Kiaa0564|mKIAA0564	von Willebrand factor A domain containing 8	protein-coding
mm_157821.1	chrX	74074899	74074936	-	1	NA	intron (NM_001081979, intron 1 of 2)	intron (NM_001081979, intron 1 of 2)	10773	NM_010788	17257	Mm.131408	NM_010788	ENSMUSG00000031393	Mecp2	1500041B07Rik|D630021H01Rik|Mbd5|WBP10	methyl CpG binding protein 2	protein-coding
mm_56122.1	chr6	87532643	87532649	-	1	NA	intron (NM_001037727, intron 1 of 10)	intron (NM_001037727, intron 1 of 10)	613	NM_001037727	232201	Mm.119564	NM_175476	ENSMUSG00000030047	Arhgap25	A130039I20Rik	Rho GTPase activating protein 25	protein-coding
mm_37798.1	chr4	130520244	130520263	-	1	NA	Intergenic	Intergenic	53783	NM_025998	67149	Mm.423029	NM_025998	ENSMUSG00000078532	Nkain1	2610200G18Rik|2810426C15Rik	Na+/K+ transporting ATPase interacting 1	protein-coding
mm_105202.1	chr11	102097574	102097582	-	1	NA	Intergenic	Intergenic	3722	NM_008918	19064	Mm.1269	NM_008918	ENSMUSG00000017316	Ppy	AV061413|IGSPP|PP	pancreatic polypeptide	protein-coding
mm_141024.1	chr17	25184383	25184402	-	1	NA	promoter-TSS (NM_183150)	promoter-TSS (NM_183150)	-169	NM_183150	214489	Mm.274433	NM_183150	ENSMUSG00000067722	BC003965	Ccsmst1	cDNA sequence BC003965	protein-coding
mm_76916.1	chr8	105933026	105933036	-	1	NA	exon (NM_023182, exon 3 of 7)	exon (NM_023182, exon 3 of 7)	831	NM_023182	109660	Mm.2745	NM_023182	ENSMUSG00000031896	Ctrl	0910001G08Rik|1810004D15Rik|AV005227|Ctra-1|Ctra1|chymopasin|mFLJ00366	chymotrypsin-like	protein-coding
mm_70771.1	chr8	21970591	21970608	+	1	NA	promoter-TSS (NM_026459)	promoter-TSS (NM_026459)	3	NM_026459	67929	Mm.60688	NM_026459	ENSMUSG00000017049	Ccdc70	1700112P19Rik	coiled-coil domain containing 70	protein-coding
mm_10900.1	chr2	25288136	25288150	+	1	NA	promoter-TSS (NM_030055)	promoter-TSS (NM_030055)	-2	NM_030055	78217	Mm.160057	NM_030055	ENSMUSG00000026963	Tmem210	4930571C24Rik	transmembrane protein 210	protein-coding
mm_78740.1	chr9	41591742	41591764	+	1	NA	non-coding (NR_015483, exon 2 of 2)	non-coding (NR_015483, exon 2 of 2)	9827	NR_029822	387236		NR_029822	ENSMUSG00000093354	Mir125b-1	Mirn125b|Mirn125b-1|mir-125b-1	microRNA 125b-1	ncRNA
mm_2275.1	chr1	91250576	91250586	+	1	NA	intron (NM_026454, intron 1 of 9)	CpG	262	NM_026454	67921	Mm.337238	NM_026454	ENSMUSG00000034343	Ube2f	2510010F15Rik|AI851109	ubiquitin-conjugating enzyme E2F (putative)	protein-coding
mm_142149.1	chr17	36015587	36015602	-	1	NA	exon (NM_008207, exon 3 of 6)	exon (NM_008207, exon 3 of 6)	4966	NM_008207	15042	Mm.439654	NM_008207	ENSMUSG00000053835	H2-T24	H-2T24	histocompatibility 2, T region locus 24	protein-coding
mm_129792.1	chr15	82852657	82852672	-	1	NA	exon (NM_013836, exon 2 of 5)	exon (NM_013836, exon 2 of 5)	45797	NR_027799	21378	Mm.417272	NR_027799		Tbrg3	TB-11	transforming growth factor beta regulated gene 3	ncRNA
mm_152272.1	chr19	8819237	8819251	-	1	NA	promoter-TSS (NM_001081196)	promoter-TSS (NM_001081196)	50	NM_027412	70387	Mm.261082	NM_027412	ENSMUSG00000071660	Ttc9c	2210019E14Rik|6330408J23Rik	tetratricopeptide repeat domain 9C	protein-coding
mm_134554.1	chr16	20098081	20098101	-	1	NA	intron (NM_029436, intron 1 of 7)	CpG	537	NM_029436	75785	Mm.392450	NM_029436	ENSMUSG00000062901	Klhl24	1110046J11Rik|4930429H24Rik|6530402O20Rik|C85082	kelch-like 24	protein-coding
mm_142070.1	chr17	35697771	35697781	-	1	NA	intron (NM_007584, intron 1 of 17)	intron (NM_007584, intron 1 of 17)	2814	NM_001198833	12305	Mm.5021	NM_007584	ENSMUSG00000003534	Ddr1	6030432F18|AI323681|CD167a|Cak|Nep|PTK3A	discoidin domain receptor family, member 1	protein-coding
mm_28310.1	chr3	89245006	89245031	-	1	NA	promoter-TSS (NR_121683)	promoter-TSS (NR_121683)	-5	NR_121683	360213	Mm.331156	NM_183037	ENSMUSG00000042766	Trim46	TRIFIC	tripartite motif-containing 46	protein-coding
mm_12054.1	chr2	59239000	59239009	+	1	NA	intron (NM_175464, intron 2 of 20)	intron (NM_175464, intron 2 of 20)	78154	NM_175464	227937	Mm.260938	NM_026361	ENSMUSG00000026991	Pkp4	5031422I09Rik|9430019K17Rik|Armrp|p0071	plakophilin 4	protein-coding
mm_160235.1	chr7	103603763	103603763	+	1	NA	exon (NM_147076, exon 1 of 1)	exon (NM_147076, exon 1 of 1)	174	NM_147076	259080	Mm.377827	NM_147076	ENSMUSG00000073944	Olfr619	MOR31-5	olfactory receptor 619	protein-coding
mm_169099.1	chr1	34116122	34116137	+	1	NA	exon (NM_134448, exon 4 of 98)	exon (NM_134448, exon 4 of 98)	-1230	NR_105861	102466987		NR_105861	ENSMUSG00000105982	Mir6896	mmu-mir-6896	microRNA 6896	ncRNA
mm_71283.1	chr8	40920337	40920371	+	1	NA	3' UTR (NM_001044740, exon 12 of 12)	3' UTR (NM_001044740, exon 12 of 12)	-5879	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_41585.1	chr5	93206004	93206020	+	1	NA	promoter-TSS (NM_029363)	promoter-TSS (NM_029363)	483	NM_017367	12453	Mm.250419	NM_017367	ENSMUSG00000063015	Ccni	-	cyclin I	protein-coding
mm_99068.1	chr11	99168332	99168356	+	1	NA	Intergenic	Intergenic	-13267	NM_007719	12775	Mm.2932	NM_007719	ENSMUSG00000037944	Ccr7	CC-CKR-7|CCR-7|CD197|Cdw197|Cmkbr7|EBI1|Ebi1h	chemokine (C-C motif) receptor 7	protein-coding
mm_18576.1	chr2	66102578	66102590	-	1	NA	exon (NM_015736, exon 3 of 11)	exon (NM_015736, exon 3 of 11)	22209	NM_015736	14425	Mm.439760	NM_015736	ENSMUSG00000026994	Galnt3	-	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 3	protein-coding
mm_92005.1	chr10	62327758	62327768	-	1	NA	intron (NM_010438, intron 4 of 21)	intron (NM_010438, intron 4 of 21)	12658	NM_001146100	15275	Mm.196605	NM_010438	ENSMUSG00000037012	Hk1	BB404130|Hk-1|Hk1-s|dea|mHk1-s	hexokinase 1	protein-coding
mm_18277.1	chr2	52401311	52401328	-	1	NA	3' UTR (NM_182994, exon 6 of 6)	3' UTR (NM_182994, exon 6 of 6)	23555	NM_182994	75423	Mm.314378	NM_182994	ENSMUSG00000036093	Arl5a	2410015N24Rik|2810410P22Rik|AA408731|AW610751|Arl5|T25534	ADP-ribosylation factor-like 5A	protein-coding
mm_64017.1	chr7	140247268	140247314	+	1	NA	promoter-TSS (NM_001128145)	promoter-TSS (NM_001128145)	-10	NM_175533	244234	Mm.85125	NM_175533	ENSMUSG00000054672	5830411N06Rik	Scart2	RIKEN cDNA 5830411N06 gene	protein-coding
mm_143638.1	chr17	79020741	79020803	-	1	NA	promoter-TSS (NM_029239)	promoter-TSS (NM_029239)	44	NM_001171004	75292	Mm.252776	NM_029239	ENSMUSG00000024070	Prkd3	4930557O20Rik|5730497N19Rik|PKD3|Pkcnu|Prkcn	protein kinase D3	protein-coding
mm_11372.1	chr2	31060459	31060473	+	1	NA	intron (NM_001038700, intron 6 of 14)	ORR1B1|LTR|ERVL-MaLR	36034	NM_001177650	14269	Mm.52297	NM_019406	ENSMUSG00000075415	Fnbp1	1110057E06Rik|2210010H06Rik|FBP1|Fbp17	formin binding protein 1	protein-coding
mm_22912.1	chr3	31093893	31093907	+	1	NA	Intergenic	CpG	-1158	NM_011386	20482	Mm.15406	NM_011386	ENSMUSG00000027660	Skil	Skir|SnoN|sno	SKI-like	protein-coding
mm_26060.1	chr3	135826229	135826243	+	1	NA	intron (NM_001135150, intron 1 of 8)	intron (NM_001135150, intron 1 of 8)	446	NM_001135150	67547	Mm.30239	NM_026228	ENSMUSG00000053897	Slc39a8	4933419D20Rik|AA986696|BIGM103|ZIP-8|Zip8	solute carrier family 39 (metal ion transporter), member 8	protein-coding
mm_163921.1	chr14	44500161	44500174	+	1	NA	promoter-TSS (NM_198677)	promoter-TSS (NM_198677)	45	NM_198677	385138	Mm.293026	NM_198677	ENSMUSG00000072145	BC061237	-	cDNA sequence BC061237	protein-coding
mm_52496.1	chr6	114759374	114759402	+	1	NA	intron (NM_001253718, intron 18 of 19)	LTR84b|LTR|ERVL	116291	NM_001253717	74244	Mm.275332	NM_028835	ENSMUSG00000030314	Atg7	1810013K23Rik|Agp7|Apg7l|Atg7l|Gm21553	autophagy related 7	protein-coding
mm_40534.1	chr5	57947941	57947961	+	1	NA	intron (NM_001310608, intron 3 of 3)	intron (NM_001310608, intron 3 of 3)	229870	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_35977.1	chr4	53564682	53564706	-	1	NA	intron (NM_133891, intron 15 of 15)	intron (NM_133891, intron 15 of 15)	-66777	NM_176966	319636	Mm.103464	NM_176966	ENSMUSG00000054752	Fsd1l	A230072O16Rik|Ccdc10|Csdufd1|Fsd1nl|OTTMUSG00000007002	fibronectin type III and SPRY domain containing 1-like	protein-coding
mm_108307.1	chr12	79386145	79386147	+	1	NA	intron (NM_009014, intron 7 of 10)	intron (NM_009014, intron 7 of 10)	88795	NM_001252562	19363	Mm.341756	NM_009014	ENSMUSG00000059060	Rad51b	AI553500|R51H2|Rad51l1|mREC2	RAD51 paralog B	protein-coding
mm_45663.1	chr5	77158893	77158931	-	1	NA	Intergenic	Arthur1|DNA|hAT-Tip100	-43789	NM_175606	74318	Mm.181852	NM_175606	ENSMUSG00000059325	Hopx	1110018K11Rik|1200015P04Rik|2300002F06Rik|AI848177|AW490897|Cameo|Hdop|Hod|Hop|Ob1|Obl|Toto	HOP homeobox	protein-coding
mm_77217.1	chr8	115018967	115018982	-	1	NA	intron (NM_019573, intron 8 of 8)	intron (NM_019573, intron 8 of 8)	579322	NM_019573	80707	Mm.440420	NM_019573	ENSMUSG00000004637	Wwox	5330426P09Rik|9030416C10Rik|WOX1	WW domain-containing oxidoreductase	protein-coding
mm_28252.1	chr3	88531382	88531393	-	1	NA	Intergenic	Intergenic	-1008	NM_001029890	72640	Mm.275154	NM_001029890	ENSMUSG00000074480	Mex3a	2700083E18Rik|Gm411|Rkhd4	mex3 RNA binding family member A	protein-coding
mm_20880.1	chr2	148771452	148771468	-	1	NA	promoter-TSS (NM_030059)	promoter-TSS (NM_030059)	37	NM_030059	78240	Mm.99424	NM_030059	ENSMUSG00000036958	Cst11	9230101F08Rik|BB067629|CRES2|mCSTE1	cystatin 11	protein-coding
mm_133340.1	chr16	81200726	81200739	+	1	NA	promoter-TSS (NM_010954)	promoter-TSS (NM_010954)	35	NM_010954	17968	Mm.433941	NM_010954	ENSMUSG00000022762	Ncam2	Ncam-2|Ocam|RNCAM	neural cell adhesion molecule 2	protein-coding
mm_67640.1	chr7	84410122	84410142	-	1	NA	promoter-TSS (NM_007488)	promoter-TSS (NM_007488)	-94	NM_007488	11864	Mm.38594	NM_007488	ENSMUSG00000015709	Arnt2	Hif-2b|bHLHe1|mKIAA0307	aryl hydrocarbon receptor nuclear translocator 2	protein-coding
mm_32933.1	chr4	119255394	119255426	+	1	NA	promoter-TSS (NM_153105)	promoter-TSS (NM_153105)	-31	NM_153105	242653	Mm.130701	NM_153105	ENSMUSG00000066058	Cldn19	-	claudin 19	protein-coding
mm_171486.1	chr4	146097295	146097295	+	1	NA	promoter-TSS (NM_001037926)	promoter-TSS (NM_001037926)	-17	NM_001037926	626316	Mm.270762	NM_001037926	ENSMUSG00000066009	Zfp987	Gm13051|OTTMUSG00000010104|OTTMUSG00000010173	zinc finger protein 987	protein-coding
mm_131049.1	chr16	4029813	4029821	+	1	NA	Intergenic	Intergenic	-7328	NM_010061	13419	Mm.291048	NM_010061	ENSMUSG00000005980	Dnase1	AI788650|DNaseI|Dnl1	deoxyribonuclease I	protein-coding
mm_107866.1	chr12	69907818	69907826	+	1	NA	5' UTR (NM_178628, exon 2 of 15)	5' UTR (NM_178628, exon 2 of 15)	-14659	NM_201519	399510	Mm.291936	NM_201519	ENSMUSG00000034761	Map4k5	4432415E19Rik|GCKR|KHS|MAPKKKK5	mitogen-activated protein kinase kinase kinase kinase 5	protein-coding
mm_99824.1	chr11	108920372	108920384	+	1	NA	promoter-TSS (NM_015732)	promoter-TSS (NM_015732)	29	NM_015732	12006	Mm.71710	NM_015732	ENSMUSG00000000142	Axin2	Axi1|Axil|Conductin	axin 2	protein-coding
mm_148612.1	chr19	5366765	5366851	+	1	NA	promoter-TSS (NM_027236)	promoter-TSS (NM_027236)	-5	NM_027236	69860	Mm.299167	NM_027236	ENSMUSG00000024841	Eif1ad	2010003J03Rik|AI131644	eukaryotic translation initiation factor 1A domain containing	protein-coding
mm_161269.1	chr14	7105217	7105217	-	1	NA	intron (NM_001024712, intron 1 of 6)	CpG	240	NM_001024712	100042149	Mm.396155	NM_001024712	ENSMUSG00000092167	Gm3696	ENSMUSG00000056940|Gm10014	predicted gene 3696	protein-coding
mm_92701.1	chr10	80713996	80714008	-	1	NA	exon (NM_007460, exon 19 of 31)	exon (NM_007460, exon 19 of 31)	11309	NM_027829	71564	Mm.35802	NM_027829	ENSMUSG00000055862	Izumo4	9030607L17Rik|AI550407	IZUMO family member 4	protein-coding
mm_88307.1	chr10	75406942	75406954	+	1	NA	promoter-TSS (NM_133995)	promoter-TSS (NM_133995)	37	NM_133995	103149	Mm.441195	NM_133995	ENSMUSG00000033427	Upb1	AI195023	ureidopropionase, beta	protein-coding
mm_95188.1	chr11	42421286	42421321	+	1	NA	promoter-TSS (NM_001347314)	promoter-TSS (NM_001347314)	-47	NM_001347314	14401	Mm.338723	NM_008070	ENSMUSG00000007653	Gabrb2	AI834970|C030002O17Rik|C030021G16Rik|Gabrab2|Gabrb-2	gamma-aminobutyric acid (GABA) A receptor, subunit beta 2	protein-coding
mm_108363.1	chr12	80791460	80791466	+	1	NA	intron (NM_001242419, intron 1 of 6)	intron (NM_001242419, intron 1 of 6)	931	NM_001242419	217684	Mm.341776	NM_178682	ENSMUSG00000021133	Susd6	4933426M11Rik|mKIAA0247	sushi domain containing 6	protein-coding
mm_11744.1	chr2	38351206	38351214	+	1	NA	promoter-TSS (NM_010710)	promoter-TSS (NM_010710)	-98	NM_010710	16870	Mm.142856	NM_010710	ENSMUSG00000000247	Lhx2	LH2A|Lh-2|Lim2|ap|apterous	LIM homeobox protein 2	protein-coding
mm_167182.1	chr7	141745553	141745559	+	1	NA	exon (NM_023566, exon 29 of 46)	exon (NM_023566, exon 29 of 46)	-43455	NM_010844	17833	Mm.334332	NM_010844	ENSMUSG00000037974	Muc5ac	2210005L13Rik|MGM	mucin 5, subtypes A and C, tracheobronchial/gastric	protein-coding
mm_143169.1	chr17	57226253	57226263	-	1	NA	exon (NM_009778, exon 3 of 41)	exon (NM_009778, exon 3 of 41)	1878	NM_009778	12266	Mm.19131	NM_009778	ENSMUSG00000024164	C3	AI255234|ASP|HSE-MSF|Plp	complement component 3	protein-coding
mm_40413.1	chr5	53067692	53067702	+	1	NA	exon (NM_011402, exon 10 of 13)	exon (NM_011402, exon 10 of 13)	18344	NM_011402	20531	Mm.284891	NM_011402	ENSMUSG00000029188	Slc34a2	AA536683|D5Ertd227e|NaPi-2b|Npt2b	solute carrier family 34 (sodium phosphate), member 2	protein-coding
mm_4867.1	chr1	187742344	187742345	+	1	NA	intron (NM_001243792, intron 1 of 7)	intron (NM_001243792, intron 1 of 7)	133338	NM_001243792	26381	Mm.89989	NM_011935	ENSMUSG00000026610	Esrrg	ERR3|Errg|NR3B3|mKIAA0832	estrogen-related receptor gamma	protein-coding
mm_8043.1	chr1	135284007	135284066	-	1	NA	promoter-TSS (NM_145417)	promoter-TSS (NM_145417)	48	NM_145417	215615	Mm.291048	NM_145417	ENSMUSG00000041926	Rnpep	-	arginyl aminopeptidase (aminopeptidase B)	protein-coding
mm_103984.1	chr11	84827362	84827374	-	1	NA	intron (NM_177564, intron 1 of 6)	intron (NM_177564, intron 1 of 6)	1635	NM_177564	192970	Mm.192213	NM_177564	ENSMUSG00000034449	Dhrs11	-	dehydrogenase/reductase (SDR family) member 11	protein-coding
mm_46415.1	chr5	104094695	104094712	-	1	NA	exon (NM_010097, exon 3 of 11)	exon (NM_010097, exon 3 of 11)	-17095	NM_001163772	100271704	Mm.366664	NM_001163772	ENSMUSG00000091034	Gm17660	Scpppq1	predicted gene, 17660	protein-coding
mm_12780.1	chr2	79329521	79329529	+	1	NA	3' UTR (NM_010576, exon 28 of 28)	3' UTR (NM_010576, exon 28 of 28)	74099	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D|Itga4B	integrin alpha 4	protein-coding
mm_141782.1	chr17	34296166	34296178	-	1	NA	Intergenic	Intergenic	-8401	NM_010378	14960	Mm.235338	NM_010378	ENSMUSG00000036594	H2-Aa	Aalpha|H-2Aa|H2Aa|I-Aalpha|IAalpha|Ia-1|Ia1	histocompatibility 2, class II antigen A, alpha	protein-coding
mm_64031.1	chr7	140769556	140769584	+	1	NA	exon (NM_021282, exon 4 of 9)	exon (NM_021282, exon 4 of 9)	5738	NM_021282	13106	Mm.21758	NM_021282	ENSMUSG00000025479	Cyp2e1	Cyp2e	cytochrome P450, family 2, subfamily e, polypeptide 1	protein-coding
mm_122661.1	chr14	51912353	51912364	-	1	NA	intron (NM_013864, intron 1 of 15)	A-rich|Low_complexity|Low_complexity	1130	NM_001145959	29811	Mm.26722	NM_013864	ENSMUSG00000004558	Ndrg2	AI182517|AU040374|Ndr2|SYLD	N-myc downstream regulated gene 2	protein-coding
mm_126426.1	chr15	80572577	80572601	+	1	NA	promoter-TSS (NM_001289442)	promoter-TSS (NM_001289442)	-8	NM_001289442	17444	Mm.12947	NM_010815	ENSMUSG00000042351	Grap2	GRAP-2|GRB2L|GRBLG|GRID|Gads|GrbX|Grf40|GrpL|Mona|P38	GRB2-related adaptor protein 2	protein-coding
mm_161462.1	chr15	77508271	77508271	+	1	NA	promoter-TSS (NM_001177533)	promoter-TSS (NM_001177533)	0	NM_001177533	626615	Mm.390820	NM_001177533	ENSMUSG00000091650	Apol11a	EG626615	apolipoprotein L 11a	protein-coding
mm_34875.1	chr4	155563308	155563321	+	1	NA	promoter-TSS (NM_001159637)	promoter-TSS (NM_001159637)	-501	NM_001159637	192185	Mm.28347	NM_138671	ENSMUSG00000029063	Nadk	4432404C02Rik|BC004012	NAD kinase	protein-coding
mm_115920.1	chr13	23543384	23543402	-	1	NA	promoter-TSS (NM_178197)	promoter-TSS (NM_178197)	51	NM_178197	319182	Mm.352273	NM_178197	ENSMUSG00000064168	Hist1h2bh	H2b-221	histone cluster 1, H2bh	protein-coding
mm_15379.1	chr2	156475917	156475934	+	1	NA	5' UTR (NM_001006664, exon 1 of 22)	5' UTR (NM_001006664, exon 1 of 22)	391	NM_001006664	13821	Mm.20852	NM_013510	ENSMUSG00000027624	Epb41l1	4.1N|Epb4.1l1|NBL1|mKIAA0338	erythrocyte membrane protein band 4.1 like 1	protein-coding
mm_157932.1	chrX	81821576	81821591	-	1	NA	Intergenic	Intergenic	-363461	NM_173435	245492	Mm.109633	NM_173435	ENSMUSG00000060673	4930595M18Rik	-	RIKEN cDNA 4930595M18 gene	protein-coding
mm_19318.1	chr2	90563159	90563175	-	1	NA	intron (NM_008982, intron 1 of 23)	intron (NM_008982, intron 1 of 23)	17480	NM_008982	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_70409.1	chr8	11398758	11398768	+	1	NA	exon (NM_009932, exon 5 of 48)	exon (NM_009932, exon 5 of 48)	-79166	NR_126558	102132	Mm.37632	NR_126558	ENSMUSG00000096957	E230013L22Rik	AI645545	RIKEN cDNA E230013L22 gene	ncRNA
mm_35998.1	chr4	56224521	56224544	-	1	NA	Intergenic	Intergenic	516893	NM_025271	11471	Mm.251434	NM_025271	ENSMUSG00000070980	Actl7b	Tact1	actin-like 7b	protein-coding
mm_131523.1	chr16	17619490	17619498	+	1	NA	intron (NM_001164609, intron 1 of 19)	CpG	140	NM_001164609	77626	Mm.34659	NM_029945	ENSMUSG00000005899	Smpd4	4122402O22Rik|mKIAA1418	sphingomyelin phosphodiesterase 4	protein-coding
mm_117051.1	chr13	58391923	58391926	-	1	NA	TTS (NR_029825)	TTS (NR_029825)	962	NR_029825	723902		NR_029825	ENSMUSG00000065434	Mir7-1	Mir7a1|Mirn7-1|miR-7a1|mir-7a-1|mmu-miR-7a1|mmu-mir-7-1	microRNA 7-1	ncRNA
mm_81521.1	chr9	110053307	110053323	+	1	NA	exon (NM_001311164, exon 1 of 10)	exon (NM_001311164, exon 1 of 10)	1294	NM_001311164	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_151458.1	chr19	58231104	58231112	+	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	-65096	NR_040449	791347	Mm.452208	NR_040449		Gm10007	ENSMUSG00000056739	predicted gene 10007	ncRNA
mm_84585.1	chr9	69760925	69760935	-	1	NA	promoter-TSS (NR_040765)	promoter-TSS (NR_040765)	10	NM_022378	64290	Mm.440890	NM_022378	ENSMUSG00000059246	Foxb1	C43|Fkh5|Foxb1a|Foxb1b|Hfh-e5.1|Mf3|Twh	forkhead box B1	protein-coding
mm_53256.1	chr6	127796497	127796500	+	1	NA	Intergenic	Intergenic	-8355	NR_106092	102466996		NR_106092	ENSMUSG00000104804	Mir7233	mmu-mir-7233	microRNA 7233	ncRNA
mm_41945.1	chr5	105731878	105731888	+	1	NA	intron (NM_178701, intron 1 of 2)	intron (NM_178701, intron 1 of 2)	31073	NM_178701	231549	Mm.23837	NM_178701	ENSMUSG00000046079	Lrrc8d	2810473G09Rik|4930525N13Rik|A930019F03|Lrrc5	leucine rich repeat containing 8D	protein-coding
mm_128070.1	chr15	27619268	27619295	-	1	NA	intron (NM_001013792, intron 3 of 6)	intron (NM_001013792, intron 3 of 6)	11412	NM_001013792	432940	Mm.309164	NM_001013792	ENSMUSG00000046034	Otulin	C79097|Fam105b|m3Sapc|m7-1Sapc	OTU deubiquitinase with linear linkage specificity	protein-coding
mm_105117.1	chr11	101119787	101119804	-	1	NA	promoter-TSS (NM_134024)	promoter-TSS (NM_134024)	29	NM_026501	67998	Mm.33881	NM_026501	ENSMUSG00000017802	Fam134c	1300010M03Rik|4933404C01Rik|AI551748	family with sequence similarity 134, member C	protein-coding
mm_61987.1	chr7	91090811	91090847	+	1	NA	promoter-TSS (NM_011807)	promoter-TSS (NM_011807)	43	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_70457.1	chr8	11812382	11812385	+	1	NA	intron (NM_001113517, intron 12 of 18)	intron (NM_001113517, intron 12 of 18)	-28138	NM_029326	75528	Mm.440342	NM_029326	ENSMUSG00000031512	Tex29	1700018L24Rik	testis expressed 29	protein-coding
mm_132983.1	chr16	52147673	52147677	+	1	NA	intron (NM_001033238, intron 9 of 17)	intron (NM_001033238, intron 9 of 17)	116126	NM_001033238	208650	Mm.328206	NM_001033238	ENSMUSG00000022637	Cblb	AI429560|AI851073|Cbl-b	Casitas B-lineage lymphoma b	protein-coding
mm_39300.1	chr5	5890986	5890986	+	1	NA	Intergenic	RMER1C|Other|Other	-141669	NM_027399	70358	Mm.85429	NM_027399	ENSMUSG00000015652	Steap1	2410007B19Rik|Prss24|Steap	six transmembrane epithelial antigen of the prostate 1	protein-coding
mm_15271.1	chr2	155199617	155199618	+	1	NA	intron (NM_008395, intron 14 of 24)	B1_Mur1|SINE|Alu	-36916	NR_111891	67068	Mm.23693	NM_025947	ENSMUSG00000047459	Dynlrb1	2010012N15Rik|2010320M17Rik|9430076K19Rik|AV124457|DNLC2A|Dncl2a|km23-1	dynein light chain roadblock-type 1	protein-coding
mm_141953.1	chr17	35112067	35112075	-	1	NA	TTS (NM_148947)	TTS (NM_148947)	3329	NM_148939	266614	Mm.104680	NM_148939	ENSMUSG00000043807	Ly6g5b	-	lymphocyte antigen 6 complex, locus G5B	protein-coding
mm_163581.1	chr13	34046727	34046735	+	1	NA	intron (NM_026512, intron 2 of 6)	intron (NM_026512, intron 2 of 6)	9090	NM_026512	68021	Mm.140243	NM_026512	ENSMUSG00000038286	Bphl	2010012D11Rik|5730533B08Rik|AI115341	biphenyl hydrolase-like (serine hydrolase, breast epithelial mucin-associated antigen)	protein-coding
mm_130481.1	chr15	98740367	98740414	-	1	NA	exon (NM_007478, exon 5 of 5)	exon (NM_007478, exon 5 of 5)	-12192	NM_024169	66120	Mm.30729	NM_024169	ENSMUSG00000003355	Fkbp11	1110002O23Rik|FKBP-11	FK506 binding protein 11	protein-coding
mm_43852.1	chr5	143370062	143370079	+	1	NA	promoter-TSS (NM_001347529)	promoter-TSS (NM_001347529)	-22	NM_001347529	170935	Mm.197460	NM_133355	ENSMUSG00000010825	Grid2ip	-	glutamate receptor, ionotropic, delta 2 (Grid2) interacting protein 1	protein-coding
mm_17706.1	chr2	32385442	32385463	-	1	NA	exon (NM_008491, exon 5 of 6)	exon (NM_008491, exon 5 of 6)	2287	NM_008491	16819	Mm.9537	NM_008491	ENSMUSG00000026822	Lcn2	24p3|AW212229|NRL|Sip24	lipocalin 2	protein-coding
mm_153884.1	chr19	46946643	46946661	-	1	NA	intron (NM_001164365, intron 2 of 17)	intron (NM_001164365, intron 2 of 17)	15699	NM_029810	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_13949.1	chr2	121300364	121300374	+	1	NA	exon (NM_001173506, exon 4 of 6)	exon (NM_001173506, exon 4 of 6)	4915	NM_001173506	17754	Mm.36501	NM_032393	ENSMUSG00000027254	Map1a	6330416M19Rik|AI853608|Mtap-1|Mtap1|Mtap1a|moth1	microtubule-associated protein 1 A	protein-coding
mm_150333.1	chr19	34575198	34575208	+	1	NA	3' UTR (NM_008332, exon 3 of 3)	3' UTR (NM_008332, exon 3 of 3)	-8326	NM_010501	15959	Mm.426079	NM_010501	ENSMUSG00000074896	Ifit3	Ifi49|P49	interferon-induced protein with tetratricopeptide repeats 3	protein-coding
mm_71473.1	chr8	46535203	46535222	+	1	NA	3' UTR (NM_007981, exon 21 of 21)	3' UTR (NM_007981, exon 21 of 21)	-16857	NM_027973	71876	Mm.22108	NM_027973	ENSMUSG00000031629	Cenpu	1700029A22Rik|Mlf1ip	centromere protein U	protein-coding
mm_150860.1	chr19	45015233	45015248	+	1	NA	promoter-TSS (NM_001130525)	promoter-TSS (NM_001130525)	30	NM_001130525	226154	Mm.28204	NM_145503	ENSMUSG00000035342	Lzts2	BC014695|LAPSER1|mKIAA1813	leucine zipper, putative tumor suppressor 2	protein-coding
mm_104245.1	chr11	88841477	88841491	-	1	NA	intron (NM_001042541, intron 2 of 10)	intron (NM_001042541, intron 2 of 10)	10019	NM_009648	11640	Mm.2969	NM_009648	ENSMUSG00000018428	Akap1	AKAP121|AKAP84|Akap|C76494|C81186|DAKAP1|S-AKAP84	A kinase (PRKA) anchor protein 1	protein-coding
mm_6337.1	chr1	71628471	71628491	-	1	NA	exon (NM_001276413, exon 16 of 44)	exon (NM_001276413, exon 16 of 44)	24753	NM_010233	14268	Mm.193099	NM_010233	ENSMUSG00000026193	Fn1	E330027I09|Fn|Fn-1	fibronectin 1	protein-coding
mm_81905.1	chr9	119983909	119983974	+	1	NA	intron (NM_153287, intron 1 of 4)	CpG	717	NM_153287	215418	Mm.491094	NM_153287	ENSMUSG00000032515	Csrnp1	4931429D10Rik|Axud1|CSRNP-1|URAX1|taip-3	cysteine-serine-rich nuclear protein 1	protein-coding
mm_115868.1	chr13	21468511	21468551	-	1	NA	promoter-TSS (NM_025719)	promoter-TSS (NM_025719)	-30	NM_025719	66707	Mm.116869	NM_025719	ENSMUSG00000059395	Nkapl	4921504I05Rik	NFKB activating protein-like	protein-coding
mm_65662.1	chr7	28140182	28140192	-	1	NA	exon (NM_001164655, exon 5 of 20)	exon (NM_001164655, exon 5 of 20)	10721	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_147932.1	chr18	65970237	65970247	-	1	NA	promoter-TSS (NM_145493)	promoter-TSS (NM_145493)	-64	NM_145493	225644	Mm.192285	NM_145493	ENSMUSG00000024519	Cplx4	A930004D23Rik|CPXIV|Gm957	complexin 4	protein-coding
mm_67507.1	chr7	80782306	80782322	-	1	NA	intron (NM_016721, intron 2 of 37)	intron (NM_016721, intron 2 of 37)	21017	NM_016721	29875	Mm.207619	NM_016721	ENSMUSG00000030536	Iqgap1	AA682088|D7Ertd237e|D7Ertd257e|mKIAA0051	IQ motif containing GTPase activating protein 1	protein-coding
mm_154580.1	chrX	7572613	7572623	+	1	NA	promoter-TSS (NR_029473)	promoter-TSS (NR_029473)	-982	NR_029473	78185	Mm.160055	NR_029473	ENSMUSG00000039545	Ppp1r3fos	4930524L23Rik	protein phosphatase 1, regulatory subunit 3F, opposite strand	ncRNA
mm_152248.1	chr19	8714395	8714414	-	1	NA	promoter-TSS (NM_008577)	promoter-TSS (NM_008577)	-507	NM_008577	17254	Mm.4114	NM_008577	ENSMUSG00000010095	Slc3a2	4F2|4F2HC|AI314110|Cd98|Ly-10|Ly-m10|Ly10|Mdu1|Mgp-2hc|NACAE	solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2	protein-coding
mm_32305.1	chr4	103143053	103143071	+	1	NA	intron (NM_001039081, intron 6 of 12)	intron (NM_001039081, intron 6 of 12)	23672	NM_001039081	71148	Mm.288721	NM_027696	ENSMUSG00000028522	Mier1	4933425I22Rik|5830411K19Rik|er1	MEIR1 treanscription regulator	protein-coding
mm_119076.1	chr14	30880249	30880257	+	1	NA	intron (NM_181390, intron 1 of 2)	intron (NM_181390, intron 1 of 2)	996	NM_181390	66175	Mm.220895	NM_181390	ENSMUSG00000042485	Mustn1	1110028G01Rik|Mustang	musculoskeletal, embryonic nuclear protein 1	protein-coding
mm_51843.1	chr6	90302541	90302561	+	1	NA	intron (NM_177738, intron 2 of 4)	intron (NM_177738, intron 2 of 4)	1281	NM_177738	243535	Mm.233854	NM_177738	ENSMUSG00000049694	BC048671	-	cDNA sequence BC048671	protein-coding
mm_145439.1	chr18	59062489	59062538	+	1	NA	non-coding (NR_033765, exon 1 of 5)	non-coding (NR_033765, exon 1 of 5)	132	NR_033765	225583	Mm.209711	NM_173759	ENSMUSG00000050875	A730017C20Rik	-	RIKEN cDNA A730017C20 gene	protein-coding
mm_78131.1	chr9	20868629	20868706	+	1	NA	promoter-TSS (NM_175687)	promoter-TSS (NM_175687)	25	NM_175687	319278	Mm.249932	NM_175687	ENSMUSG00000038884	A230050P20Rik	RyDEN	RIKEN cDNA A230050P20 gene	protein-coding
mm_46710.1	chr5	110343010	110343039	-	1	NA	promoter-TSS (NM_153400)	promoter-TSS (NM_153400)	11	NM_153400	231602	Mm.55948	NM_153400	ENSMUSG00000029503	P2rx2	P2X2a|P2x2	purinergic receptor P2X, ligand-gated ion channel, 2	protein-coding
mm_123930.1	chr14	73366398	73366409	-	1	NA	exon (NM_008410, exon 3 of 6)	exon (NM_008410, exon 3 of 6)	18868	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_170404.1	chr18	64450006	64450015	-	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	39056	NM_007998	14151	Mm.1070	NM_007998	ENSMUSG00000024588	Fech	AI894116|Fcl|fch	ferrochelatase	protein-coding
mm_165944.1	chr4	81982044	81982085	+	1	NA	Intergenic	MTC-int|LTR|ERVL-MaLR	-83316	NR_040659	545641	Mm.216028	NR_040659	ENSMUSG00000085022	Gm5860	EG545641	predicted gene 5860	ncRNA
mm_104195.1	chr11	87979756	87979773	-	1	NA	3' UTR (NM_001168471, exon 3 of 3)	3' UTR (NM_001168471, exon 3 of 3)	6821	NM_001168472	68097	Mm.246436	NM_026556	ENSMUSG00000020483	Dynll2	1700064A15Rik|6720463E02Rik|C87222|DLC8|DLC8b|Dlc2	dynein light chain LC8-type 2	protein-coding
mm_55426.1	chr6	65144928	65144940	-	1	NA	promoter-TSS (NM_019455)	promoter-TSS (NM_019455)	-204	NM_019455	54486	Mm.410688	NM_019455	ENSMUSG00000029919	Hpgds	H-PGDS|Ptgds2	hematopoietic prostaglandin D synthase	protein-coding
mm_29213.1	chr3	106790176	106790186	-	1	NA	promoter-TSS (NM_007651)	promoter-TSS (NM_007651)	-32	NM_007651	12508	Mm.316861	NM_007651	ENSMUSG00000040747	Cd53	AI323659|Ox-44|Tspan25	CD53 antigen	protein-coding
mm_167910.1	chrX	85188346	85188348	+	1	NA	intron (NM_001314035, intron 14 of 15)	intron (NM_001314035, intron 14 of 15)	-61330	NM_028046	71996	Mm.20201	NM_028046	ENSMUSG00000035491	Fthl17a	1600014K23Rik|AI324104	ferritin, heavy polypeptide-like 17, member A	protein-coding
mm_15144.1	chr2	153974907	153974935	+	1	NA	promoter-TSS (NM_001080811)	promoter-TSS (NM_001080811)	-24	NM_001080811	545477	Mm.379973	NM_001080811	ENSMUSG00000078998	Bpifa6	EG545477|Gm5840|Splunc6	BPI fold containing family A, member 6	protein-coding
mm_121050.1	chr14	84445015	84445032	+	1	NA	5' UTR (NM_001013753, exon 1 of 4)	5' UTR (NM_001013753, exon 1 of 4)	1460	NM_001013753	219228	Mm.153643	NM_001013753	ENSMUSG00000035566	Pcdh17	C030033F14Rik|Gm78	protocadherin 17	protein-coding
mm_130593.1	chr15	99703791	99703809	-	1	NA	exon (NM_031842, exon 4 of 13)	exon (NM_031842, exon 4 of 13)	1513	NM_031842	83797	Mm.273756	NM_031842	ENSMUSG00000023018	Smarcd1	AA407987|Baf60a|D15Kz1	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1	protein-coding
mm_76270.1	chr8	84104745	84104759	-	1	NA	promoter-TSS (NM_172502)	promoter-TSS (NM_172502)	10	NM_172502	212123	Mm.260557	NM_172502	ENSMUSG00000037103	Dcaf15	6720484B16	DDB1 and CUL4 associated factor 15	protein-coding
mm_75111.1	chr8	34155013	34155017	-	1	NA	intron (NM_026432, intron 1 of 5)	intron (NM_026432, intron 1 of 5)	452	NM_026432	67887	Mm.290353	NM_026432	ENSMUSG00000031532	Saraf	1810045K07Rik|Tmem66	store-operated calcium entry-associated regulatory factor	protein-coding
mm_135977.1	chr16	75047792	75047802	-	1	NA	Intergenic	Lx2|LINE|L1	538264	NM_001252513	320355	Mm.99517	NM_177142	ENSMUSG00000032948	Lipi	D930038D03Rik|lpd1	lipase, member I	protein-coding
mm_77157.1	chr8	111687130	111687134	-	1	NA	exon (NM_025583, exon 6 of 7)	exon (NM_025583, exon 6 of 7)	2542	NR_106044	102466993		NR_106044	ENSMUSG00000099129	Mir7076	Gm27318|mmu-mir-7076	microRNA 7076	ncRNA
mm_172616.1	chr8	19784725	19784741	+	1	NA	intron (NM_001270553, intron 6 of 9)	CpG	55157	NM_001039553	626415	Mm.425517	NM_001039553	ENSMUSG00000096265	4930467E23Rik	ENSMUSG00000074453|OTTMUSG00000018948|TSAP	RIKEN cDNA 4930467E23 gene	protein-coding
mm_41451.1	chr5	90905465	90905473	+	1	NA	3' UTR (NM_009140, exon 4 of 4)	3' UTR (NM_009140, exon 4 of 4)	1570	NM_009140	20310	Mm.4979	NM_009140	ENSMUSG00000058427	Cxcl2	CINC-2a|GROb|Gro2|MIP-2|MIP-2a|Mgsa-b|Mip2|Scyb|Scyb2	chemokine (C-X-C motif) ligand 2	protein-coding
mm_68710.1	chr7	119890719	119890734	-	1	NA	intron (NM_001163703, intron 1 of 2)	B1_Mur1|SINE|Alu	4732	NM_173408	233805	Mm.31539	NM_173408	ENSMUSG00000048787	Dcun1d3	1700020A13Rik|BC030335	DCN1, defective in cullin neddylation 1, domain containing 3 (S. cerevisiae)	protein-coding
mm_62011.1	chr7	91267370	91267373	+	1	NA	intron (NM_011807, intron 1 of 22)	intron (NM_011807, intron 1 of 22)	176585	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_30636.1	chr4	8811342	8811342	+	1	NA	intron (NM_001277149, intron 6 of 37)	intron (NM_001277149, intron 6 of 37)	120936	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_17299.1	chr2	26294580	26294588	-	1	NA	promoter-TSS (NM_177841)	promoter-TSS (NM_177841)	-27	NM_177841	329366	Mm.77712	NM_177841	ENSMUSG00000048038	Ccdc187	4932418E24Rik	coiled-coil domain containing 187	protein-coding
mm_63695.1	chr7	130624615	130624622	+	1	NA	exon (NM_001004468, exon 3 of 22)	exon (NM_001004468, exon 3 of 22)	47134	NM_206856	57752	Mm.86322	NM_021314	ENSMUSG00000030852	Tacc2	mKIAA4180	transforming, acidic coiled-coil containing protein 2	protein-coding
mm_165183.1	chr2	29788121	29788140	-	1	NA	promoter-TSS (NM_178693)	promoter-TSS (NM_178693)	-133	NM_178693	227683	Mm.245948	NM_178693	ENSMUSG00000026798	Coq4	A330041N06|D2Ertd97e	coenzyme Q4	protein-coding
mm_119201.1	chr14	32811752	32811759	+	1	NA	intron (NM_001163616, intron 4 of 4)	L1MC4|LINE|L1	-22207	NM_001164485	105511	Mm.32231	NM_001164485	ENSMUSG00000078127	Fam170b	4922501K12Rik|AI449756	family with sequence similarity 170, member B	protein-coding
mm_60997.1	chr7	49290572	49290613	+	1	NA	intron (NM_175272, intron 1 of 37)	intron (NM_175272, intron 1 of 37)	44403	NM_175272	78286	Mm.333881	NM_175272	ENSMUSG00000052512	Nav2	5330421F07Rik|AU067780|BQ960892|HELAD1|POMFIL2|RAINB1|RAINB2|Unc53H2|mKIAA3015	neuron navigator 2	protein-coding
mm_61414.1	chr7	73584259	73584267	+	1	NA	Intergenic	Intergenic	-25868	NR_037569	69170	Mm.34539	NR_037569	ENSMUSG00000101970	1810026B05Rik	-	RIKEN cDNA 1810026B05 gene	ncRNA
mm_132948.1	chr16	49911455	49911476	+	1	NA	3' UTR (NM_010581, exon 10 of 10)	3' UTR (NM_010581, exon 10 of 10)	55811	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_127695.1	chr15	102990534	102990575	+	1	NA	promoter-TSS (NM_010466)	promoter-TSS (NM_010466)	15	NM_010466	15426	Mm.6167	NM_010466	ENSMUSG00000001657	Hoxc8	D130011F21Rik|Hox-3.1	homeobox C8	protein-coding
mm_143604.1	chr17	78417889	78417907	-	1	NA	exon (NM_199448, exon 1 of 8)	exon (NM_199448, exon 1 of 8)	254	NM_001285949	225020	Mm.236835	NM_199448	ENSMUSG00000056121	Fez2	9030616F16|D17Ertd315e	fasciculation and elongation protein zeta 2 (zygin II)	protein-coding
mm_111006.1	chr12	78908376	78908387	-	1	NA	Intergenic	Intergenic	-1443	NM_013738	27260	Mm.103380	NM_013738	ENSMUSG00000021118	Plek2	-	pleckstrin 2	protein-coding
mm_122234.1	chr14	33185490	33185557	-	1	NA	promoter-TSS (NM_001146022)	promoter-TSS (NM_001146022)	-457	NM_001146022	545030	Mm.318345	NM_001146022	ENSMUSG00000051506	Wdfy4	Gm18810	WD repeat and FYVE domain containing 4	protein-coding
mm_50437.1	chr6	48860317	48860338	+	1	NA	Intergenic	Intergenic	18671	NM_001098271	66058	Mm.27061	NM_025326	ENSMUSG00000023367	Tmem176a	0610011I04Rik|AU040201|AU041743|Keg2	transmembrane protein 176A	protein-coding
mm_100571.1	chr11	120762988	120763018	+	1	NA	Intergenic	Intergenic	21201	NM_009053	19719	Mm.871	NM_009053	ENSMUSG00000025158	Rfng	-	RFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	protein-coding
mm_55798.1	chr6	82760140	82760182	-	1	NA	exon (NM_013820, exon 2 of 18)	exon (NM_013820, exon 2 of 18)	14293	NM_013820	15277	Mm.255848	NM_013820	ENSMUSG00000000628	Hk2	AI642394|HKII	hexokinase 2	protein-coding
mm_145877.1	chr18	65476306	65476335	+	1	NA	exon (NM_172833, exon 16 of 16)	exon (NM_172833, exon 16 of 16)	45323	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_2643.1	chr1	125434772	125434785	+	1	NA	intron (NM_001205385, intron 2 of 12)	intron (NM_001205385, intron 2 of 12)	949	NM_023735	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding
mm_128202.1	chr15	35937281	35937292	-	1	NA	intron (NM_053071, intron 1 of 3)	intron (NM_053071, intron 1 of 3)	960	NM_053071	12864	Mm.548	NM_053071	ENSMUSG00000014313	Cox6c	-	cytochrome c oxidase subunit VIc	protein-coding
mm_152704.1	chr19	17339689	17339738	-	1	NA	promoter-TSS (NM_001136484)	promoter-TSS (NM_001136484)	-208	NM_001136484	14537	Mm.244825	NM_010265	ENSMUSG00000038843	Gcnt1	5630400D21Rik|B130048E03|C2 GlcNAcT|C2GNT|IGnT	glucosaminyl (N-acetyl) transferase 1, core 2	protein-coding
mm_149198.1	chr19	9955135	9955146	+	1	NA	Intergenic	Intergenic	-25460	NR_073181	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
mm_141460.1	chr17	30571809	30571855	-	1	NA	intron (NM_172618, intron 1 of 11)	intron (NM_172618, intron 1 of 11)	4455	NM_172618	224671	Mm.41220	NM_027060	ENSMUSG00000062202	Btbd9	1700023F20Rik|4930402L05|AI464421	BTB (POZ) domain containing 9	protein-coding
mm_41972.1	chr5	107403525	107403534	+	1	NA	promoter-TSS (NM_001001804)	promoter-TSS (NM_001001804)	16	NM_001001804	384214	Mm.489863	NM_001001804	ENSMUSG00000033805	Ephx4	Abhd7|Ephxrp|Gm1382	epoxide hydrolase 4	protein-coding
mm_106884.1	chr12	8012051	8012059	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	34378	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_85452.1	chr9	104339133	104339137	-	1	NA	Intergenic	Intergenic	-1413	NM_207668	56318	Mm.19941	NM_019807	ENSMUSG00000032561	Acpp	5'-NT|A030005E02Rik|FRAP|Lap|PAP|Ppal	acid phosphatase, prostate	protein-coding
mm_38094.1	chr4	134245462	134245470	-	1	NA	exon (NM_024215, exon 1 of 3)	exon (NM_024215, exon 1 of 3)	125	NM_024215	68040	Mm.300404	NM_024215	ENSMUSG00000028840	Zfp593	3110024A21Rik|AV062409|E130106C14Rik|ZNF593	zinc finger protein 593	protein-coding
mm_533.1	chr1	37897851	37897853	+	1	NA	intron (NM_027098, intron 5 of 5)	intron (NM_027098, intron 5 of 5)	7299	NM_027098	107734	Mm.26614	NM_027098	ENSMUSG00000026087	Mrpl30	2310001L22Rik|MRP-L28|Rpml28	mitochondrial ribosomal protein L30	protein-coding
mm_72594.1	chr8	84414324	84414334	+	1	NA	Intergenic	CpG	-1035	NM_001252060	12286	Mm.334658	NM_007578	ENSMUSG00000034656	Cacna1a	APCA|BI|Caca1a|Cacnl1a4|Cav2.1|Ccha1a|EA2|FHM|HPCA|MHP|MHP1|SCA6|alpha1A|la|nmf352|rkr|smrl|tg	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	protein-coding
mm_121342.1	chr14	115868765	115868767	+	1	NA	intron (NM_175500, intron 7 of 7)	intron (NM_175500, intron 7 of 7)	-459214	NR_045761	75088	Mm.444706	NR_045761	ENSMUSG00000093551	4930505G20Rik	-	RIKEN cDNA 4930505G20 gene	ncRNA
mm_155560.1	chrX	75416638	75416649	+	1	NA	promoter-TSS (NM_001166459)	promoter-TSS (NM_001166459)	15	NM_001166459	210766	Mm.226957	NM_145956	ENSMUSG00000031201	Brcc3	C6.1A	BRCA1/BRCA2-containing complex, subunit 3	protein-coding
mm_145483.1	chr18	60382598	60382631	+	1	NA	5' UTR (NM_001146275, exon 2 of 3)	5' UTR (NM_001146275, exon 2 of 3)	6585	NM_001146275	60440	Mm.261140	NM_021792	ENSMUSG00000054072	Iigp1	2900074L10Rik|AI046432|AW111922|Ifgga1|Iigp|Irga6	interferon inducible GTPase 1	protein-coding
mm_13883.1	chr2	119972730	119972746	+	1	NA	promoter-TSS (NM_011941)	promoter-TSS (NM_011941)	39	NM_011941	26390	Mm.330501	NM_011941	ENSMUSG00000033902	Mapkbp1	2810483F24Rik|AW123212|JNKBP-1|Jnkbp1|mKIAA0596	mitogen-activated protein kinase binding protein 1	protein-coding
mm_141580.1	chr17	32369413	32369432	-	1	NA	intron (NM_011717, intron 2 of 8)	ERVB7_1-LTR_MM|LTR|ERVK	18395	NM_212438	22404	Mm.274948	NM_011717	ENSMUSG00000024050	Wiz	-	widely-interspaced zinc finger motifs	protein-coding
mm_152391.1	chr19	10482875	10482938	-	1	NA	promoter-TSS (NM_133689)	promoter-TSS (NM_133689)	-9	NM_133689	67752	Mm.25939	NM_133689	ENSMUSG00000035179	Ppp1r32	4930579J09Rik|AU015816|IIIG9|IIIG9L|IIIG9S	protein phosphatase 1, regulatory subunit 32	protein-coding
mm_42404.1	chr5	114989664	114989683	+	1	NA	Intergenic	L1MC4|LINE|L1	-18611	NM_009327	21405	Mm.332607	NM_009327	ENSMUSG00000029556	Hnf1a	AI323641|HNF1|HNF1-alpha|HNF1[a]|Hnf-1|Hnf1alpha|LFB1|Tcf-1|Tcf1	HNF1 homeobox A	protein-coding
mm_17120.1	chr2	24593079	24593096	-	1	NA	Intergenic	Intergenic	-117488	NM_011040	18510	Mm.2533	NM_011040	ENSMUSG00000026976	Pax8	Pax-8	paired box 8	protein-coding
mm_145286.1	chr18	53213906	53213922	+	1	NA	intron (NM_026386, intron 11 of 14)	intron (NM_026386, intron 11 of 14)	-31748	NM_029394	69226	Mm.32414	NM_029394	ENSMUSG00000024535	Snx24	2810011K15Rik|5730433I16Rik|AI451341	sorting nexing 24	protein-coding
mm_118675.1	chr14	22032190	22032229	+	1	NA	intron (NM_028275, intron 2 of 6)	RSINE1|SINE|B4	12497	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_138145.1	chr17	34204508	34204573	+	1	NA	promoter-TSS (NM_011530)	promoter-TSS (NM_011530)	61	NM_011530	21355	Mm.14814	NM_011530	ENSMUSG00000024339	Tap2	ABC18|AI462429|APT2|Abcb3|Ham-2|Ham2|MTP2|PSF2|RING11|Tap-2|Y1|jas	transporter 2, ATP-binding cassette, sub-family B (MDR/TAP)	protein-coding
mm_50870.1	chr6	55452093	55452093	+	1	NA	5' UTR (NM_001025372, exon 1 of 16)	5' UTR (NM_001025372, exon 1 of 16)	115	NM_007407	11517	Mm.44245	NM_007407	ENSMUSG00000029778	Adcyap1r1	2900024I10Rik|AI846590|PAC1|PAC1R|PACAP1-R	adenylate cyclase activating polypeptide 1 receptor 1	protein-coding
mm_147053.1	chr18	34932585	34932608	-	1	NA	promoter-TSS (NM_144866)	promoter-TSS (NM_144866)	-593	NM_144866	225363	Mm.329353	NM_144866	ENSMUSG00000024360	Etf1	AI463371|D6Ertd109e|ERF|ERF1|SUP45L1|TB3-1	eukaryotic translation termination factor 1	protein-coding
mm_136093.1	chr16	85044107	85044110	-	1	NA	intron (NM_001198825, intron 6 of 15)	intron (NM_001198825, intron 6 of 15)	71897	NR_045889	100038614	Mm.441351	NR_045889		Gm10791	ENSMUSG00000074933	predicted gene 10791	ncRNA
mm_107834.1	chr12	69258188	69258194	+	1	NA	intron (NM_178253, intron 7 of 12)	intron (NM_178253, intron 7 of 12)	16359	NM_178253	271005	Mm.180969	NM_178253	ENSMUSG00000051890	Klhdc1	-	kelch domain containing 1	protein-coding
mm_92199.1	chr10	68136628	68136638	-	1	NA	intron (NM_023598, intron 4 of 9)	intron (NM_023598, intron 4 of 9)	142093	NM_023598	71371	Mm.440357	NM_023598	ENSMUSG00000019947	Arid5b	4930580B11|5430435G07Rik|AI467247|Desrt|Mrf2|Mrf2alpha|Mrf2beta	AT rich interactive domain 5B (MRF1-like)	protein-coding
mm_31786.1	chr4	63667588	63667598	+	1	NA	Intergenic	Intergenic	-45164	NM_029324	75524	Mm.38543	NM_029324	ENSMUSG00000058935	1700018C11Rik	bM230C2.3	RIKEN cDNA 1700018C11 gene	protein-coding
mm_121640.1	chr14	8378852	8378870	-	1	NA	promoter-TSS (NM_146050)	promoter-TSS (NM_146050)	-98	NM_146050	18300	Mm.25351	NM_146050	ENSMUSG00000021749	Oit1	2310076N21Rik|AV067083|EF-7|Fam3d	oncoprotein induced transcript 1	protein-coding
mm_92893.1	chr10	82955349	82955373	-	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	-30136	NM_021439	58250	Mm.360747	NM_021439	ENSMUSG00000034612	Chst11	1110020P09Rik|C4ST|C4ST-1|C4ST1|C4s	carbohydrate sulfotransferase 11	protein-coding
mm_167776.1	chr9	113741520	113741524	+	1	NA	promoter-TSS (NM_001114347)	promoter-TSS (NM_001114347)	49	NM_001114347	76499	Mm.222272	NM_029633	ENSMUSG00000033392	Clasp2	1500004F14Rik|8030404L10Rik|C77448|CLASP2beta|mKIAA0627	CLIP associating protein 2	protein-coding
mm_128764.1	chr15	66135458	66135459	-	1	NA	intron (NM_152923, intron 1 of 14)	RMER6A|LTR|ERVK	150766	NM_152923	110862	Mm.255585	NM_152923	ENSMUSG00000056258	Kcnq3	-	potassium voltage-gated channel, subfamily Q, member 3	protein-coding
mm_62503.1	chr7	102041284	102041289	+	1	NA	intron (NM_029211, intron 2 of 8)	intron (NM_029211, intron 2 of 8)	-23131	NM_010531	16068	Mm.422756	NM_010531	ENSMUSG00000070427	Il18bp	IL-18BP|Igifbp|MC54L	interleukin 18 binding protein	protein-coding
mm_66358.1	chr7	43528281	43528302	-	1	NA	3' UTR (NM_001111058, exon 7 of 7)	3' UTR (NM_001111058, exon 7 of 7)	4880	NM_001111058	12489	Mm.140157	NM_021293	ENSMUSG00000004609	Cd33	Siglec-3|gp67	CD33 antigen	protein-coding
mm_90453.1	chr10	127706813	127706839	+	1	NA	exon (NM_001081219, exon 4 of 27)	exon (NM_001081219, exon 4 of 27)	1570	NM_001081219	432516	Mm.90450	NM_001081219	ENSMUSG00000025401	Myo1a	BBM-I|Myhl	myosin IA	protein-coding
mm_78547.1	chr9	35364219	35364261	+	1	NA	Intergenic	Intergenic	83135	NR_040715	71133	Mm.158577	NR_040715	ENSMUSG00000111746	4933422A05Rik	-	RIKEN cDNA 4933422A05 gene	ncRNA
mm_116906.1	chr13	55447617	55447640	-	1	NA	intron (NM_001038018, intron 1 of 15)	intron (NM_001038018, intron 1 of 15)	2297	NM_001112711	26385	Mm.10193	NM_011938	ENSMUSG00000074886	Grk6	Gprk6	G protein-coupled receptor kinase 6	protein-coding
mm_158114.1	chrX	102189340	102189364	-	1	NA	promoter-TSS (NM_009094)	promoter-TSS (NM_009094)	39	NM_009094	20102	Mm.66	NM_009094	ENSMUSG00000031320	Rps4x	Rps4|Rps4-1	ribosomal protein S4, X-linked	protein-coding
mm_67870.1	chr7	99169815	99169836	-	1	NA	exon (NM_026384, exon 2 of 8)	exon (NM_026384, exon 2 of 8)	12888	NM_026384	67800	Mm.180189	NM_026384	ENSMUSG00000030747	Dgat2	0610010B06Rik|ARAT|DGAT-2	diacylglycerol O-acyltransferase 2	protein-coding
mm_133139.1	chr16	68888312	68888346	+	1	NA	Intergenic	L1_Mus1|LINE|L1	912052	NR_130991	78110	Mm.211406	NR_130991	ENSMUSG00000107073	4930428D20Rik	-	RIKEN cDNA 4930428D20 gene	ncRNA
mm_154807.1	chrX	13623386	13623395	+	1	NA	intron (NM_009806, intron 6 of 24)	intron (NM_009806, intron 6 of 24)	-9379	NM_011823	23890	Mm.487326	NM_011823	ENSMUSG00000040229	Gpr34	Lypsr1	G protein-coupled receptor 34	protein-coding
mm_151346.1	chr19	55895571	55895581	+	1	NA	5' UTR (NM_001142924, exon 1 of 12)	5' UTR (NM_001142924, exon 1 of 12)	255	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_98245.1	chr11	88201442	88201456	+	1	NA	intron (NM_001291270, intron 1 of 4)	intron (NM_001291270, intron 1 of 4)	-2939	NM_024174	64656	Mm.168680	NM_024174	ENSMUSG00000023723	Mrps23	D11Bwg1153e|MRP-S23|Rpms23|S23mt	mitochondrial ribosomal protein S23	protein-coding
mm_78055.1	chr9	14858471	14858478	+	1	NA	Intergenic	Intergenic	-1736	NM_001310734	14608	Mm.4672	NM_010287	ENSMUSG00000031932	Gpr83	AW045253|Gir|Gpr72|RP105|RP39|RP82	G protein-coupled receptor 83	protein-coding
mm_91182.1	chr10	20919729	20919734	-	1	NA	Intergenic	RMER19B2|LTR|ERVK	-32816	NM_026203	52906	Mm.253280	NM_026203	ENSMUSG00000019986	Ahi1	1700015F03Rik|Ahi-1|D10Bwg0629e	Abelson helper integration site 1	protein-coding
mm_58399.1	chr7	3217833	3217838	+	1	NA	promoter-TSS (NR_029640)	promoter-TSS (NR_029640)	-791	NR_029640	100049710		NR_029640	ENSMUSG00000077815	Mir290a	Mir290|Mirn290|mir-290a|mmu-miR-290|mmu-mir-290a	microRNA 290a	ncRNA
mm_132589.1	chr16	38444279	38444304	+	1	NA	Intergenic	ORR1C1|LTR|ERVL-MaLR	8398	NM_007414	11544	Mm.20047	NM_007414	ENSMUSG00000002844	Adprh	Arh1	ADP-ribosylarginine hydrolase	protein-coding
mm_107629.1	chr12	51797929	51797943	+	1	NA	exon (NM_144788, exon 10 of 43)	exon (NM_144788, exon 10 of 43)	31600	NM_144788	207304	Mm.249391	NM_144788	ENSMUSG00000035247	Hectd1	A630086P08Rik|AI844876|b2b327Clo|opm	HECT domain containing 1	protein-coding
mm_135383.1	chr16	44140498	44140508	-	1	NA	intron (NM_028108, intron 1 of 4)	intron (NM_028108, intron 1 of 4)	694	NM_028108	72117	Mm.278726	NM_028108	ENSMUSG00000022698	Naa50	2600005K24Rik|2810441M03Rik|AW112078|Mak3|Mak3p|Nat13|Nat5|San	N(alpha)-acetyltransferase 50, NatE catalytic subunit	protein-coding
mm_31891.1	chr4	82537644	82537649	+	1	NA	intron (NR_137202, intron 1 of 1)	intron (NR_137202, intron 1 of 1)	29657	NR_137202	102635783	Mm.41666	NR_137202		Gm11266	OTTMUSG00000000396	predicted gene 11266	ncRNA
mm_150410.1	chr19	36926072	36926177	+	1	NA	promoter-TSS (NM_001080706)	promoter-TSS (NM_001080706)	45	NM_001080706	107182	Mm.295062	NM_001080706	ENSMUSG00000040565	Btaf1	AI414500|AI447930|E430027O22Rik|TAF170	B-TFIID TATA-box binding protein associated factor 1	protein-coding
mm_165591.1	chr3	34408109	34408112	+	1	NA	Intergenic	Intergenic	-152271	NR_015580	320478	Mm.444063	NR_015580	ENSMUSG00000105265	Sox2ot	B230215L15Rik	SOX2 overlapping transcript (non-protein coding)	ncRNA
mm_138071.1	chr17	33947981	33948008	+	1	NA	intron (NM_020603, intron 10 of 14)	PB1D9|SINE|Alu	3494	NM_019420	54218	Mm.11132	NM_019420	ENSMUSG00000067370	B3galt4	Gal-T2|Galt2	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 4	protein-coding
mm_74027.1	chr8	121730392	121730404	+	1	NA	promoter-TSS (NM_020605)	promoter-TSS (NM_020605)	-161	NM_020605	57340	Mm.306870	NM_020605	ENSMUSG00000025318	Jph3	JP-3|Jp3	junctophilin 3	protein-coding
mm_76909.1	chr8	105851982	105852036	-	1	NA	promoter-TSS (NM_177150)	promoter-TSS (NM_177150)	-1	NM_177150	320394	Mm.334775	NM_177150	ENSMUSG00000036672	Cenpt	G630055P03Rik	centromere protein T	protein-coding
mm_51752.1	chr6	87657749	87657759	+	1	NA	intron (NM_024251, intron 5 of 9)	intron (NM_024251, intron 5 of 9)	14414	NM_024251	72103	Mm.31770	NM_024251	ENSMUSG00000030051	Aplf	2010301N04Rik|AI452191	aprataxin and PNKP like factor	protein-coding
mm_16797.1	chr2	10102816	10102822	-	1	NA	exon (NM_010582, exon 15 of 21)	exon (NM_010582, exon 15 of 21)	22207	NM_025280	16588	Mm.35498	NM_025280	ENSMUSG00000037262	Kin	Kin17	Kin17 DNA and RNA binding protein	protein-coding
mm_51863.1	chr6	90540753	90540781	+	1	NA	Intergenic	Intergenic	-10081	NM_027406	107747	Mm.30035	NM_027406	ENSMUSG00000030088	Aldh1l1	1810048F20Rik|FDH|Fthfd|Neut2	aldehyde dehydrogenase 1 family, member L1	protein-coding
mm_35298.1	chr4	22486741	22486768	-	1	NA	3' UTR (NM_008899, exon 1 of 1)	3' UTR (NM_008899, exon 1 of 1)	1612	NM_008899	18992	Mm.129387	NM_008899	ENSMUSG00000095139	Pou3f2	9430075J19Rik|A230098E07Rik|Brn-2|Brn2|OTF-7|Otf7|oct-7	POU domain, class 3, transcription factor 2	protein-coding
mm_152298.1	chr19	9083752	9083776	-	1	NA	exon (NM_011681, exon 3 of 3)	exon (NM_011681, exon 3 of 3)	4192	NM_011681	22287	Mm.2258	NM_011681	ENSMUSG00000024653	Scgb1a1	CC10|CC16|CCSP|PCB-BP|UG|UGB|Utg	secretoglobin, family 1A, member 1 (uteroglobin)	protein-coding
mm_117685.1	chr13	94253041	94253070	-	1	NA	exon (NM_029153, exon 2 of 9)	exon (NM_029153, exon 2 of 9)	32226	NM_029153	107767	Mm.201455	NM_029153	ENSMUSG00000021687	Scamp1	4930505M11Rik|AI415563|AW122395	secretory carrier membrane protein 1	protein-coding
mm_147511.1	chr18	51262802	51262807	-	1	NA	intron (NM_001081224, intron 1 of 1)	intron (NM_001081224, intron 1 of 1)	144906	NM_001081224	71373	Mm.63546	NM_001081224	ENSMUSG00000073565	Prr16	5430406M13Rik|AI607429	proline rich 16	protein-coding
mm_168849.1	chr12	23969137	23969147	-	1	NA	Intergenic	CpG	128127	NM_001256489	66808	Mm.379124	NM_001256489	ENSMUSG00000073158	9030624G23Rik	-	RIKEN cDNA 9030624G23 gene	protein-coding
mm_97074.1	chr11	72999070	72999092	+	1	NA	promoter-TSS (NM_008771)	promoter-TSS (NM_008771)	-64	NM_008771	18436	Mm.25722	NM_008771	ENSMUSG00000020787	P2rx1	AI323649|BB122383|P2x|Pdcd3|RP-2	purinergic receptor P2X, ligand-gated ion channel, 1	protein-coding
mm_172320.1	chr7	106284070	106284074	+	1	NA	Intergenic	L1_Mur3|LINE|L1	40456	NR_030720	668128	Mm.484022	NR_030720		Gm8989	EG668128|Gm21911	very large inducible GTPase 1 pseudogene	pseudo
mm_61935.1	chr7	90168451	90168455	+	1	NA	intron (NM_001252520, intron 4 of 20)	intron (NM_001252520, intron 4 of 20)	38221	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_148106.1	chr18	74207703	74207721	-	1	NA	5' UTR (NM_001164355, exon 1 of 7)	5' UTR (NM_001164355, exon 1 of 7)	106	NM_001164355	66468	Mm.283406	NM_025581	ENSMUSG00000036223	Ska1	2810433K01Rik|AV117428	spindle and kinetochore associated complex subunit 1	protein-coding
mm_96876.1	chr11	70214975	70214982	+	1	NA	exon (NM_153081, exon 3 of 5)	exon (NM_153081, exon 3 of 5)	1068	NM_153081	216867	Mm.289238	NM_153081	ENSMUSG00000040938	Slc16a11	AB041591|MCT 11|MNCb-2717	solute carrier family 16 (monocarboxylic acid transporters), member 11	protein-coding
mm_56336.1	chr6	92706174	92706234	-	1	NA	promoter-TSS (NM_001081146)	promoter-TSS (NM_001081146)	-20	NM_001081146	243548	Mm.248820	NM_001081146	ENSMUSG00000030020	Prickle2	6230400G14Rik|6720451F06Rik|mpk2	prickle planar cell polarity protein 2	protein-coding
mm_111058.1	chr12	80110371	80110395	-	1	NA	exon (NM_007564, exon 2 of 2)	exon (NM_007564, exon 2 of 2)	2630	NM_007564	12192	Mm.235132	NM_007564	ENSMUSG00000021127	Zfp36l1	AW742437|AW743212|Berg36|Brf1|D530020L18Rik|ERF1|TIS11b|cMG1	zinc finger protein 36, C3H type-like 1	protein-coding
mm_28240.1	chr3	88459048	88459074	-	1	NA	promoter-TSS (NM_001163490)	promoter-TSS (NM_001163490)	40	NM_001163490	20351	Mm.439752	NM_013658	ENSMUSG00000028064	Sema4a	AI132332|SemB|Semab	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A	protein-coding
mm_55045.1	chr6	48990236	48990242	-	1	NA	exon (NM_172888, exon 2 of 5)	exon (NM_172888, exon 2 of 5)	3378	NM_172888	243377	Mm.446302	NM_172888	ENSMUSG00000039215	Svs1	9530003A11	seminal vesicle secretory protein 1	protein-coding
mm_58879.1	chr7	16993866	16993926	+	1	NA	promoter-TSS (NM_001101535)	promoter-TSS (NM_001101535)	-692	NM_001101535	434130	Mm.459162	NM_001101535	ENSMUSG00000041117	Ccdc8	ENSMUSG00000041117	coiled-coil domain containing 8	protein-coding
mm_95728.1	chr11	54626341	54626355	+	1	NA	intron (NM_175258, intron 10 of 27)	intron (NM_175258, intron 10 of 27)	30202	NM_001252497	192786	Mm.254404	NM_175258	ENSMUSG00000037533	Rapgef6	A530068K01|AI844632|BB085664|C030018K18Rik|PDZ-GEF2|Pdzgef2|RA-GEF-2|Ragef2|mKIAA4052	Rap guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_40562.1	chr5	61806740	61806750	+	1	NA	Intergenic	Intergenic	-2098	NM_019468	14380	Mm.347430	NM_019468	ENSMUSG00000089992	G6pd2	G6pdx-ps1|Gpd-2|Gpd2	glucose-6-phosphate dehydrogenase 2	protein-coding
mm_106000.1	chr11	115699314	115699324	-	1	NA	5' UTR (NM_008163, exon 2 of 6)	5' UTR (NM_008163, exon 2 of 6)	215	NM_001313937	14784	Mm.439649	NM_008163	ENSMUSG00000059923	Grb2	AA408164|Ash	growth factor receptor bound protein 2	protein-coding
mm_63144.1	chr7	123214777	123214793	+	1	NA	promoter-TSS (NM_146198)	promoter-TSS (NM_146198)	-81	NM_146198	233836	Mm.211838	NM_146198	ENSMUSG00000030769	Slc5a11	2010013B02Rik|Kst1|RKST2|SMIT2|Slc5a10	solute carrier family 5 (sodium/glucose cotransporter), member 11	protein-coding
mm_144641.1	chr18	33007692	33007707	+	1	NA	intron (NM_009793, intron 1 of 10)	intron (NM_009793, intron 1 of 10)	68658	NM_009793	12326	Mm.222329	NM_009793	ENSMUSG00000038128	Camk4	A430110E23Rik|AI666733|CaMKIV|CaMKIV/Gr|D18Bwg0362e	calcium/calmodulin-dependent protein kinase IV	protein-coding
mm_79225.1	chr9	49954894	49954900	+	1	NA	Intergenic	Intergenic	-155504	NM_001311065	17967	Mm.4974	NM_010875	ENSMUSG00000039542	Ncam1	CD56|E-NCAM|NCAM-1|Ncam	neural cell adhesion molecule 1	protein-coding
mm_163260.1	chr11	112784896	112784909	+	1	NA	exon (NM_011448, exon 3 of 3)	exon (NM_011448, exon 3 of 3)	2692	NM_011448	20682	Mm.286407	NM_011448	ENSMUSG00000000567	Sox9	2010306G03Rik|AV220920|mKIAA4243	SRY (sex determining region Y)-box 9	protein-coding
mm_115710.1	chr13	15777611	15777615	-	1	NA	Intergenic	Intergenic	25017	NR_045507	71071	Mm.380845	NR_045507		4933412O06Rik	-	RIKEN cDNA 4933412O06 gene	ncRNA
mm_47078.1	chr5	116633606	116633607	-	1	NA	Intergenic	Intergenic	-41789	NM_026886	68955	Mm.146779	NM_026886	ENSMUSG00000063919	Srrm4	1500001A10Rik|B230202K19Rik|bv|mKIAA1853|nSR100	serine/arginine repetitive matrix 4	protein-coding
mm_33382.1	chr4	129572570	129572587	+	1	NA	intron (NM_001162433, intron 1 of 12)	intron (NM_001162433, intron 1 of 12)	1063	NM_001162433	16818	Mm.293753	NM_010693	ENSMUSG00000000409	Lck	Hck-3|Lsk|Lskt|p56<lck>|p56Lck	lymphocyte protein tyrosine kinase	protein-coding
mm_168038.1	chrY	90742737	90742754	-	1	NA	Intergenic	CpG	12305	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_95514.1	chr11	52098786	52098796	+	1	NA	promoter-TSS (NM_019411)	promoter-TSS (NM_019411)	-33	NM_019411	19052	Mm.260288	NM_019411	ENSMUSG00000020349	Ppp2ca	PP2A|R75353	protein phosphatase 2 (formerly 2A), catalytic subunit, alpha isoform	protein-coding
mm_143743.1	chr17	81512932	81512945	-	1	NA	intron (NR_104580, intron 2 of 8)	intron (NR_104580, intron 2 of 8)	225449	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_156434.1	chrX	141980072	141980080	+	1	NA	Intergenic	Lx7|LINE|L1	216860	NM_001007576	245650	Mm.208511	NM_001007576	ENSMUSG00000042282	Gucy2f	A930002I06|GC-F|GC2	guanylate cyclase 2f	protein-coding
mm_164971.1	chr19	7483060	7483068	-	1	NA	exon (NM_053076, exon 1 of 7)	exon (NM_053076, exon 1 of 7)	227	NM_001271486	20168	Mm.246990	NM_053076	ENSMUSG00000024758	Rtn3	RTN3-A1	reticulon 3	protein-coding
mm_156982.1	chrX	7237690	7237694	-	1	NA	promoter-TSS (NR_030495)	promoter-TSS (NR_030495)	82	NR_030495	723974		NR_030495	ENSMUSG00000070108	Mir500	Mirn500|mir-500|mmu-mir-500	microRNA 500	ncRNA
mm_56251.1	chr6	90757487	90757534	-	1	NA	intron (NM_001134384, intron 1 of 13)	intron (NM_001134384, intron 1 of 13)	-40981	NM_001134383	232227	Mm.196943	NM_182784	ENSMUSG00000034312	Iqsec1	AW561907|BC026481|BRAG2|D6Ertd349e|cI-43	IQ motif and Sec7 domain 1	protein-coding
mm_86148.1	chr9	117252193	117252216	-	1	NA	5' UTR (NM_001172126, exon 1 of 13)	5' UTR (NM_001172126, exon 1 of 13)	279	NM_001172123	207181	Mm.326411	NM_178660	ENSMUSG00000039607	Rbms3	6720477E09Rik|8430436O14Rik	RNA binding motif, single stranded interacting protein	protein-coding
mm_43508.1	chr5	136987658	136987668	+	1	NA	promoter-TSS (NM_001310748)	promoter-TSS (NM_001310748)	296	NM_027318	70103	Mm.273147	NM_027318	ENSMUSG00000059518	Znhit1	2700001K05Rik|ZNFN4A1	zinc finger, HIT domain containing 1	protein-coding
mm_149180.1	chr19	9606815	9606836	+	1	NA	Intergenic	Intergenic	-47577	NR_073559	619371	Mm.316894	NM_001030317		Stxbp3-ps	Munc18c(L)|Stxbp3-1|Stxbp3b	syntaxin-binding protein 3, pseudogene	pseudo
mm_93752.1	chr10	120171314	120171326	-	1	NA	intron (NM_028679, intron 5 of 11)	intron (NM_028679, intron 5 of 11)	30217	NM_028679	73914	Mm.146194	NM_028679	ENSMUSG00000020227	Irak3	4833428C18Rik|AI563835|IRAK-M	interleukin-1 receptor-associated kinase 3	protein-coding
mm_151273.1	chr19	55219710	55219718	+	1	NA	intron (NM_001081076, intron 12 of 20)	intron (NM_001081076, intron 12 of 20)	21522	NM_001081076	73707	Mm.489987	NM_001081076	ENSMUSG00000055523	Gucy2g	2410077I05Rik|GC-G	guanylate cyclase 2g	protein-coding
mm_128165.1	chr15	34081360	34081361	-	1	NA	Intergenic	Intergenic	-1359	NM_026002	67154	Mm.130883	NM_026002	ENSMUSG00000022255	Mtdh	2610103J23Rik|3D3|3D3/Lyric|AEG-1|AV353288|D8Bwg1112e|Lyric	metadherin	protein-coding
mm_173258.1	chrX	94827741	94827761	+	1	NA	Intergenic	IAP1-MM_LTR|LTR|ERVK	-29462	NR_003292	668171	Mm.426134	NR_003292		Zxda	4933406P09Rik|AW413531	zinc finger, X-linked, duplicated A	pseudo
mm_103304.1	chr11	72607758	72607805	-	1	NA	intron (NM_025985, intron 1 of 5)	CpG	520	NM_025985	67128	Mm.458052	NM_025985	ENSMUSG00000020794	Ube2g1	2700059C12Rik|AI256795|AU014992|AW552068|D130023C12Rik	ubiquitin-conjugating enzyme E2G 1	protein-coding
mm_91777.1	chr10	52195027	52195083	-	1	NA	5' UTR (NM_011282, exon 1 of 44)	5' UTR (NM_011282, exon 1 of 44)	189	NM_011282	19886	Mm.236163	NM_011282	ENSMUSG00000019893	Ros1	Ros-1|c-ros	Ros1 proto-oncogene	protein-coding
mm_173253.1	chrX	94542043	94542046	-	1	NA	promoter-TSS (NM_019791)	promoter-TSS (NM_019791)	30	NM_019791	94275	Mm.27578	NM_019791	ENSMUSG00000025151	Maged1	2810433C11Rik|5430405L04Rik|DXBwg1492e|Dlixin|Dlxin-1|Dlxin1|MAGE-D1|NRAGE|mFLJ00163	melanoma antigen, family D, 1	protein-coding
mm_136626.1	chr17	5574915	5574941	+	1	NA	intron (NM_146073, intron 1 of 8)	MLT1H1|LTR|ERVL-MaLR	82328	NM_146073	224454	Mm.487663	NM_146073	ENSMUSG00000034265	Zdhhc14	B530001K09Rik|New1cp	zinc finger, DHHC domain containing 14	protein-coding
mm_12267.1	chr2	68968838	68968842	+	1	NA	intron (NM_172856, intron 3 of 9)	intron (NM_172856, intron 3 of 9)	107399	NM_001347161	241447	Mm.222222	NM_172856	ENSMUSG00000027035	Cers6	4732462C07Rik|AW544719|Lass6|T1L	ceramide synthase 6	protein-coding
mm_153680.1	chr19	44396626	44396638	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	11077	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_27612.1	chr3	59210882	59210883	-	1	NA	promoter-TSS (NM_028808)	promoter-TSS (NM_028808)	0	NM_028808	74191	Mm.90067	NM_028808	ENSMUSG00000036362	P2ry13	2010001L06Rik|GPCR1|GPR94|Gpr86|P2Y13|P2yr13|SP174	purinergic receptor P2Y, G-protein coupled 13	protein-coding
mm_166315.1	chr5	110231141	110231165	+	1	NA	5' UTR (NM_001253814, exon 1 of 13)	5' UTR (NM_001253814, exon 1 of 13)	149	NM_027922	71782	Mm.288442	NM_027922	ENSMUSG00000029501	Ankle2	1110001J12Rik|AI661024|D5Ertd585e	ankyrin repeat and LEM domain containing 2	protein-coding
mm_37487.1	chr4	123607139	123607143	-	1	NA	intron (NM_001199136, intron 1 of 97)	intron (NM_001199136, intron 1 of 97)	-9279	NR_105824	102465214		NR_105824	ENSMUSG00000099005	Mir6398	Gm27657|mmu-mir-6398	microRNA 6398	ncRNA
mm_86651.1	chr10	17724026	17724045	+	1	NA	exon (NM_010828, exon 2 of 2)	exon (NM_010828, exon 2 of 2)	807	NM_010828	17684	Mm.272321	NM_010828	ENSMUSG00000039910	Cited2	AI835299|ER154-like|Mrg1|Msg2|p35srj	Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 2	protein-coding
mm_84769.1	chr9	75611341	75611359	-	1	NA	promoter-TSS (NM_016711)	promoter-TSS (NM_016711)	-25	NM_016711	50876	Mm.291880	NM_016711	ENSMUSG00000032186	Tmod2	N-Tmod|NTMOD	tropomodulin 2	protein-coding
mm_171575.1	chr4	147362007	147362014	+	1	NA	intron (NM_001039209, intron 1 of 2)	intron (NM_001039209, intron 1 of 2)	186144	NM_001039209	195531	Mm.270762	NM_001039209	ENSMUSG00000078496	Zfp982	Gm13152|OTTMUSG00000010671	zinc finger protein 982	protein-coding
mm_172617.1	chr8	20005972	20005977	+	1	NA	intron (NM_001270553, intron 6 of 9)	B3|SINE|B2	276398	NM_001039553	626415	Mm.425517	NM_001039553	ENSMUSG00000096265	4930467E23Rik	ENSMUSG00000074453|OTTMUSG00000018948|TSAP	RIKEN cDNA 4930467E23 gene	protein-coding
mm_75739.1	chr8	69716828	69716843	-	1	NA	promoter-TSS (NM_181274)	promoter-TSS (NM_181274)	67	NM_001039967	66869	Mm.334581	NM_181274	ENSMUSG00000054648	Zfp869	1200003I07Rik	zinc finger protein 869	protein-coding
mm_36968.1	chr4	109441017	109441021	-	1	NA	intron (NM_153392, intron 14 of 17)	intron (NM_153392, intron 14 of 17)	25372	NM_001145948	230603	Mm.33091	NM_153392	ENSMUSG00000028555	Ttc39a	4922503N01Rik	tetratricopeptide repeat domain 39A	protein-coding
mm_152576.1	chr19	11600669	11600689	-	1	NA	intron (NM_026835, intron 3 of 6)	ID4|SINE|ID	4125	NM_026835	68774	Mm.290390	NM_026835	ENSMUSG00000024679	Ms4a6d	1110058E16Rik|AI447446|Ms4a11	membrane-spanning 4-domains, subfamily A, member 6D	protein-coding
mm_135566.1	chr16	50192717	50192734	-	1	NA	3' UTR (NM_027444, exon 17 of 17)	3' UTR (NM_027444, exon 17 of 17)	-119873	NR_045935	224180	Mm.146439	NM_175010		Gm4827	B130050K08|EG224180	predicted gene 4827	ncRNA
mm_119170.1	chr14	32099379	32099399	+	1	NA	exon (NM_145460, exon 6 of 8)	exon (NM_145460, exon 6 of 8)	13661	NM_145460	218885	Mm.202257	NM_145460	ENSMUSG00000021906	Oxnad1	2410002F01Rik|AW492292|BC019806	oxidoreductase NAD-binding domain containing 1	protein-coding
mm_138990.1	chr17	45523417	45523451	+	1	NA	promoter-TSS (NM_013688)	promoter-TSS (NM_013688)	0	NM_013688	21645	Mm.491193	NM_013688	ENSMUSG00000023949	Tcte1	D17Sil1|Tcte-1	t-complex-associated testis expressed 1	protein-coding
mm_38272.1	chr4	136882282	136882296	-	1	NA	exon (NM_009777, exon 2 of 3)	exon (NM_009777, exon 2 of 3)	3888	NM_009777	12260	Mm.2570	NM_009777	ENSMUSG00000036905	C1qb	-	complement component 1, q subcomponent, beta polypeptide	protein-coding
mm_9274.1	chr1	171634128	171634141	-	1	NA	3' UTR (NM_144539, exon 8 of 8)	3' UTR (NM_144539, exon 8 of 8)	7766	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_56706.1	chr6	115039191	115039198	-	1	NA	Intergenic	MTA_Mm-int|LTR|ERVL-MaLR	-1320	NM_026894	68971	Mm.24937	NM_026894	ENSMUSG00000030316	Tamm41	1500001M20Rik|TAM41	TAM41 mitochondrial translocator assembly and maintenance homolog	protein-coding
mm_154772.1	chrX	12652249	12652262	+	1	NA	5' UTR (NM_001101484, exon 1 of 1)	5' UTR (NM_001101484, exon 1 of 1)	372	NM_001101484	245347	Mm.327568	NM_001101484		Gm4984	AI428901|EG245347	predicted pseudogene 4984	protein-coding
mm_41113.1	chr5	87778950	87778961	+	1	NA	intron (NM_007785, intron 5 of 13)	intron (NM_007785, intron 5 of 13)	4505	NM_007785	12993	Mm.4908	NM_007785	ENSMUSG00000061937	Csn1s2a	Csng|PP22	casein alpha s2-like A	protein-coding
mm_100220.1	chr11	117077240	117077245	+	1	NA	promoter-TSS (NR_105853)	promoter-TSS (NR_105853)	-106	NR_105853	102465258		NR_105853	ENSMUSG00000104740	Mir6516	mmu-mir-6516	microRNA 6516	ncRNA
mm_45612.1	chr5	75835618	75835626	-	1	NA	Intergenic	Intergenic	142806	NM_010612	16542	Mm.285	NM_010612	ENSMUSG00000062960	Kdr	6130401C07|Flk-1|Flk1|Krd-1|Ly73|VEGFR-2|VEGFR2|sVEGFR-2	kinase insert domain protein receptor	protein-coding
mm_163870.1	chr14	19419127	19419185	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	183431	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_75585.1	chr8	61550087	61550097	-	1	NA	exon (NM_001293773, exon 10 of 20)	exon (NM_001293773, exon 10 of 20)	41077	NM_001293774	72333	Mm.29933	NM_001081390	ENSMUSG00000058056	Palld	2410003B16Rik|6030492A02	palladin, cytoskeletal associated protein	protein-coding
mm_173160.1	chrX	37194874	37194888	-	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	-3643	NM_019443	54405	Mm.34869	NM_019443	ENSMUSG00000016427	Ndufa1	1810049F12Rik|MWFE	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 1	protein-coding
mm_84467.1	chr9	66593063	66593071	-	1	NA	promoter-TSS (NM_144937)	promoter-TSS (NM_144937)	48	NM_144937	235441	Mm.32465	NM_144937	ENSMUSG00000032376	Usp3	AA409661|BC017156	ubiquitin specific peptidase 3	protein-coding
mm_41827.1	chr5	104046981	104047044	+	1	NA	promoter-TSS (NR_049192)	promoter-TSS (NR_049192)	148	NM_028794	74167	Mm.241484	NM_028794	ENSMUSG00000029310	Nudt9	1190002C07Rik|ADPR-PPase|AI462474	nudix (nucleoside diphosphate linked moiety X)-type motif 9	protein-coding
mm_40642.1	chr5	64924186	64924199	+	1	NA	TTS (NM_030682)	TTS (NM_030682)	8507	NM_030682	21897	Mm.273024	NM_030682	ENSMUSG00000044827	Tlr1	-	toll-like receptor 1	protein-coding
mm_85847.1	chr9	110645329	110645354	-	1	NA	intron (NM_183276, intron 1 of 53)	intron (NM_183276, intron 1 of 53)	8820	NM_183276	235627	Mm.335481	NM_183276	ENSMUSG00000056724	Nbeal2	1110014F23Rik|BC042396|mKIAA0540	neurobeachin-like 2	protein-coding
mm_71853.1	chr8	68906147	68906157	+	1	NA	3' UTR (NM_008509, exon 10 of 10)	3' UTR (NM_008509, exon 10 of 10)	25597	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_137844.1	chr17	31057705	31057713	+	1	NA	promoter-TSS (NM_009593)	promoter-TSS (NM_009593)	15	NM_009593	11307	Mm.15691	NM_009593	ENSMUSG00000024030	Abcg1	AW413978|Abc8|White	ATP-binding cassette, sub-family G (WHITE), member 1	protein-coding
mm_30758.1	chr4	15266188	15266198	+	1	NA	exon (NM_181401, exon 1 of 3)	exon (NM_181401, exon 1 of 3)	373	NM_181401	100201	Mm.394111	NM_181401	ENSMUSG00000043252	Tmem64	9630015D15Rik|AI790744|AV300874	transmembrane protein 64	protein-coding
mm_28656.1	chr3	95232168	95232180	-	1	NA	intron (NM_001038708, intron 2 of 4)	intron (NM_001038708, intron 2 of 4)	3231	NM_001038708	57912	Mm.28189	NM_172395	ENSMUSG00000046722	Cdc42se1	1300002M12Rik|AW558204|Cdcse1|SCIP1|Spec1	CDC42 small effector 1	protein-coding
mm_91723.1	chr10	44470710	44470721	-	1	NA	Intergenic	Intergenic	-11967	NM_007548	12142	Mm.4800	NM_007548	ENSMUSG00000038151	Prdm1	Blimp-1|Blimp1|PRDI-BF1|ZNFPR1A1|b2b1765Clo	PR domain containing 1, with ZNF domain	protein-coding
mm_62525.1	chr7	102231578	102231613	+	1	NA	intron (NR_111937, intron 2 of 5)	intron (NR_111937, intron 2 of 5)	8567	NR_111937	233575	Mm.302013	NM_145583	ENSMUSG00000030990	Pgap2	1810006G21Rik|C76649|Frag1	post-GPI attachment to proteins 2	protein-coding
mm_135725.1	chr16	55822037	55822092	-	1	NA	promoter-TSS (NM_001159394)	promoter-TSS (NM_001159394)	74	NM_001159394	80859	Mm.247272	NM_030612	ENSMUSG00000035356	Nfkbiz	AA408868|INAP|Mail	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, zeta	protein-coding
mm_156622.1	chrX	154350368	154350378	+	1	NA	Intergenic	RLTR48C|LTR|ERV1	-6981	NM_001256259	75071	Mm.159415	NM_001256259	ENSMUSG00000059663	4930524N10Rik	-	RIKEN cDNA 4930524N10 gene	protein-coding
mm_123060.1	chr14	55663452	55663461	-	1	NA	exon (NM_008683, exon 3 of 4)	exon (NM_008683, exon 3 of 4)	-2948	NR_028316	67881	Mm.24601	NM_023397	ENSMUSG00000002329	Mdp1	1810034K20Rik|AI035604	magnesium-dependent phosphatase 1	protein-coding
mm_145124.1	chr18	44381352	44381366	+	1	NA	intron (NM_027490, intron 1 of 10)	intron (NM_027490, intron 1 of 10)	859	NM_027490	70640	Mm.87629	NM_027490	ENSMUSG00000024472	Dcp2	2410015D23Rik|5730537H01Rik|AL118268	decapping mRNA 2	protein-coding
mm_157085.1	chrX	9436249	9436260	-	1	NA	3' UTR (NM_007807, exon 13 of 13)	3' UTR (NM_007807, exon 13 of 13)	33070	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_82685.1	chr9	22240089	22240094	-	1	NA	TTS (NM_001164624)	TTS (NM_001164624)	14379	NM_001164624	235047	Mm.290849	NM_172763	ENSMUSG00000057982	Zfp809	BB114266|C330026E23	zinc finger protein 809	protein-coding
mm_123730.1	chr14	70168022	70168061	-	1	NA	exon (NM_001253736, exon 7 of 10)	exon (NM_001253736, exon 7 of 10)	-8539	NM_001004155	268759	Mm.12148	NM_001004155	ENSMUSG00000044551	9930012K11Rik	-	RIKEN cDNA 9930012K11 gene	protein-coding
mm_40997.1	chr5	77349353	77349402	+	1	NA	TTS (NM_153798)	TTS (NM_153798)	38893	NM_153798	231329	Mm.273217	NM_153798	ENSMUSG00000029250	Polr2b	Pol2rb|Rpb140|Rpb2	polymerase (RNA) II (DNA directed) polypeptide B	protein-coding
mm_124675.1	chr15	6424202	6424212	+	1	NA	exon (NM_001102400, exon 8 of 13)	exon (NM_001102400, exon 8 of 13)	-21126	NM_013485	12279	Mm.29095	NM_013485	ENSMUSG00000022149	C9	-	complement component 9	protein-coding
mm_160996.1	chr11	115026968	115026968	-	1	NA	promoter-TSS (NM_001101656).2	promoter-TSS (NM_001101656).2	-35	NM_001101656	100043123		NM_001101656	ENSMUSG00000069609	Cd300ld4	Gm11710|OTTMUSG00000003605	CD300 molecule like family member D4	protein-coding
mm_48658.1	chr5	145875268	145875293	-	1	NA	intron (NM_007818, intron 3 of 12)	intron (NM_007818, intron 3 of 12)	4574	NM_007818	13112	Mm.332844	NM_007818	ENSMUSG00000056035	Cyp3a11	AI256190|Cyp3a|IIIAm1|Pcn	cytochrome P450, family 3, subfamily a, polypeptide 11	protein-coding
mm_47511.1	chr5	124075738	124075748	-	1	NA	intron (NM_019875, intron 9 of 11)	intron (NM_019875, intron 9 of 11)	20055	NM_019875	56325	Mm.254839	NM_019875	ENSMUSG00000029408	Abcb9	TAPL|mKIAA1520	ATP-binding cassette, sub-family B (MDR/TAP), member 9	protein-coding
mm_113254.1	chr13	28016211	28016215	+	1	NA	promoter-TSS (NM_011165)	promoter-TSS (NM_011165)	-10	NM_011165	19110	Mm.18607	NM_011165	ENSMUSG00000005891	Prl4a1	AA409771|Ghd23|PLP-A|Prlpa	prolactin family 4, subfamily a, member 1	protein-coding
mm_167939.1	chrX	115089791	115089804	+	1	NA	Intergenic	L1_Mus1|LINE|L1	162808	NR_130989	78086		NR_130989	ENSMUSG00000085619	4930555B12Rik	-	RIKEN cDNA 4930555B12 gene	ncRNA
mm_58650.1	chr7	6286574	6286584	+	1	NA	promoter-TSS (NM_001024928)	promoter-TSS (NM_001024928)	-1	NM_001024928	384763	Mm.276279	NM_001024928	ENSMUSG00000054893	Zfp667	A830025F02Rik|Mip1|ZNF667	zinc finger protein 667	protein-coding
mm_38458.1	chr4	140581775	140581795	-	1	NA	intron (NM_001290803, intron 9 of 28)	intron (NM_001290803, intron 9 of 28)	66971	NM_001112723	72754	Mm.29329	NM_172415	ENSMUSG00000040964	Arhgef10l	2810441C07Rik	Rho guanine nucleotide exchange factor (GEF) 10-like	protein-coding
mm_77801.1	chr9	3032348	3032397	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	6371	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_127447.1	chr15	101270652	101270654	+	1	NA	exon (NM_010444, exon 2 of 7)	exon (NM_010444, exon 2 of 7)	3807	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_83455.1	chr9	45245512	45245546	-	1	NA	intron (NM_001198971, intron 4 of 4)	intron (NM_001198971, intron 4 of 4)	21178	NR_106054	102466803		NR_106054	ENSMUSG00000098361	Mir7086	Gm27643|mmu-mir-7086	microRNA 7086	ncRNA
mm_111810.1	chr12	105222762	105222772	-	1	NA	promoter-TSS (NR_110339)	promoter-TSS (NR_110339)	-30	NM_001289468	21432	Mm.18154	NM_009337	ENSMUSG00000041359	Tcl1	Tcl1a	T cell lymphoma breakpoint 1	protein-coding
mm_70204.1	chr7	144738493	144738508	-	1	NA	promoter-TSS (NM_178642)	promoter-TSS (NM_178642)	92	NM_178642	101772	Mm.26700	NM_178642	ENSMUSG00000031075	Ano1	Tmem16a	anoctamin 1, calcium activated chloride channel	protein-coding
mm_30909.1	chr4	32425230	32425239	+	1	NA	intron (NM_001109661, intron 1 of 4)	intron (NM_001109661, intron 1 of 4)	7799	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_104067.1	chr11	86585219	86585255	-	1	NA	3' UTR (NM_029478, exon 12 of 12)	3' UTR (NM_029478, exon 12 of 12)	-1079	NR_029738	387140		NR_029738	ENSMUSG00000065455	Mir21a	Mir21|Mirn21|mmu-mir-21|mmu-mir-21a	microRNA 21a	ncRNA
mm_167849.1	chrX	7899199	7899200	+	1	NA	promoter-TSS (NM_001252528)	promoter-TSS (NM_001252528)	70	NM_001252529	54633	Mm.14616	NM_019478	ENSMUSG00000031157	Pqbp1	PQBP-1|Sfc2|npw38	polyglutamine binding protein 1	protein-coding
mm_118977.1	chr14	28031476	28031479	+	1	NA	intron (NM_001347497, intron 12 of 19)	T-rich|Low_complexity|Low_complexity	409070	NM_177814	238988	Mm.318004	NM_177814	ENSMUSG00000040640	Erc2	6430531D06|CAST|CAST1/ERC2|D14Ertd171e|ELKS2alpha	ELKS/RAB6-interacting/CAST family member 2	protein-coding
mm_56939.1	chr6	119925854	119925875	-	1	NA	3' UTR (NM_001185020, exon 26 of 26)	3' UTR (NM_001185020, exon 26 of 26)	23166	NM_001166381	19365	Mm.149	NM_011236	ENSMUSG00000030166	Rad52	Rad52yh	RAD52 homolog, DNA repair protein	protein-coding
mm_105538.1	chr11	106301529	106301539	-	1	NA	exon (NM_008117, exon 2 of 5)	exon (NM_008117, exon 2 of 5)	362	NM_008117	14599	Mm.343934	NM_008117	ENSMUSG00000020713	Gh	Gh1|Ghb1	growth hormone	protein-coding
mm_13764.1	chr2	118462598	118462600	+	1	NA	intron (NM_001177806, intron 28 of 37)	intron (NM_001177806, intron 28 of 37)	17097	NM_009273	20813	Mm.363404	NM_009273	ENSMUSG00000009549	Srp14	14kDa|AW536328	signal recognition particle 14	protein-coding
mm_28867.1	chr3	97697131	97697144	-	1	NA	exon (NM_001289701, exon 41 of 47)	exon (NM_001289701, exon 41 of 47)	-6575	NR_106084	102466229		NR_106084	ENSMUSG00000098381	Mir7225	Gm27499|mmu-mir-7225	microRNA 7225	ncRNA
mm_120036.1	chr14	56284914	56284918	+	1	NA	Intergenic	PB1D7|SINE|Alu	-22582	NM_013542	14939	Mm.14874	NM_013542	ENSMUSG00000015437	Gzmb	AI553453|CCP-1/C11|CCP1|Ctla-1|Ctla1|GZB	granzyme B	protein-coding
mm_163380.1	chr12	49384333	49384343	+	1	NA	5' UTR (NM_008241, exon 2 of 2)	5' UTR (NM_008241, exon 2 of 2)	1331	NM_008241	15228	Mm.4704	NM_008241	ENSMUSG00000020950	Foxg1	2900064B05Rik|BF-1|Bf1|Hfh9|Hfhbf1	forkhead box G1	protein-coding
mm_171611.1	chr4	150237280	150237281	+	1	NA	promoter-TSS (NM_001025388).2	promoter-TSS (NM_001025388).2	-44	NM_001025388	433182	Mm.70666	NM_001025388	ENSMUSG00000059040	Eno1b	EG433182|Eno1|Gm5506	enolase 1B, retrotransposed	protein-coding
mm_146006.1	chr18	69344504	69344530	+	1	NA	promoter-TSS (NM_013685)	promoter-TSS (NM_013685)	25	NM_013685	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding
mm_155461.1	chrX	73517281	73517304	+	1	NA	intron (NM_001310537, intron 1 of 20)	intron (NM_001310537, intron 1 of 20)	14206	NM_177236	320707	Mm.210095	NM_177236	ENSMUSG00000031376	Atp2b3	6430519O13Rik|Pmca3	ATPase, Ca++ transporting, plasma membrane 3	protein-coding
mm_80188.1	chr9	72394035	72394052	+	1	NA	Intergenic	Intergenic	-44486	NM_008613	17427	Mm.387671	NM_008613	ENSMUSG00000032221	Mns1	AW546487	meiosis-specific nuclear structural protein 1	protein-coding
mm_163026.1	chr11	49712611	49712619	-	1	NA	5' UTR (NM_212484, exon 1 of 12)	5' UTR (NM_212484, exon 1 of 12)	107	NM_212484	104625	Mm.247113	NM_212484	ENSMUSG00000020362	Cnot6	CCR4	CCR4-NOT transcription complex, subunit 6	protein-coding
mm_83798.1	chr9	52679698	52679717	-	1	NA	promoter-TSS (NM_178906)	promoter-TSS (NM_178906)	73	NM_001286641	330941	Mm.335160	NM_177907	ENSMUSG00000078307	AI593442	E130102D23	expressed sequence AI593442	protein-coding
mm_59876.1	chr7	30291660	30291768	+	1	NA	promoter-TSS (NM_001081114)	promoter-TSS (NM_001081114)	-39	NM_001081114	76686	Mm.159258	NM_001081114	ENSMUSG00000013921	Clip3	1500005P14Rik|AI844915|Clipr-59	CAP-GLY domain containing linker protein 3	protein-coding
mm_9149.1	chr1	170913717	170913749	-	1	NA	promoter-TSS (NM_001029984)	promoter-TSS (NM_001029984)	-792	NM_001029984	435653	Mm.337931	NM_001029984	ENSMUSG00000070524	Fcrlb	FREB-2|FREB2|FcRL2|Fcrlm2|Fcry|mFCRL2	Fc receptor-like B	protein-coding
mm_103485.1	chr11	76509232	76509240	-	1	NA	5' UTR (NM_198018, exon 1 of 22)	5' UTR (NM_198018, exon 1 of 22)	183	NM_198018	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_104912.1	chr11	99696452	99696455	-	1	NA	Intergenic	Intergenic	-30493	NM_026834	68768	Mm.416844	NM_026834	ENSMUSG00000075566	Krtap4-6	1110054P19Rik	keratin associated protein 4-6	protein-coding
mm_14040.1	chr2	122234779	122234822	+	1	NA	promoter-TSS (NM_146126)	promoter-TSS (NM_146126)	-39	NM_146126	20322	Mm.371580	NM_146126	ENSMUSG00000027227	Sord	Sdh-1|Sdh1|Sodh-1	sorbitol dehydrogenase	protein-coding
mm_102747.1	chr11	67255436	67255483	-	1	NA	exon (NM_010855, exon 31 of 40)	exon (NM_010855, exon 31 of 40)	17647	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_127524.1	chr15	102073892	102073903	+	1	NA	5' UTR (NM_145625, exon 1 of 15)	5' UTR (NM_145625, exon 1 of 15)	124	NM_145625	75705	Mm.290022	NM_145625	ENSMUSG00000058655	Eif4b	2310046H11Rik|AL024095|C85189|Eif4a2	eukaryotic translation initiation factor 4B	protein-coding
mm_142674.1	chr17	47730661	47730669	-	1	NA	exon (NM_025973, exon 5 of 9)	exon (NM_025973, exon 5 of 9)	3823	NM_025973	109820	Mm.22957	NM_025973	ENSMUSG00000023987	Pgc	2210410L06Rik|Upg-1|Upg1	progastricsin (pepsinogen C)	protein-coding
mm_35695.1	chr4	44143476	44143503	-	1	NA	exon (NM_175201, exon 4 of 11)	exon (NM_175201, exon 4 of 11)	21596	NR_040414	623796	Mm.490409	NR_040414	ENSMUSG00000084274	Gm12504	OTTMUSG00000007209	prothymosin alpha pseudogene	pseudo
mm_122617.1	chr14	51145380	51145426	-	1	NA	3' UTR (NM_011271, exon 2 of 2)	3' UTR (NM_011271, exon 2 of 2)	1364	NM_011271	19752	Mm.235538	NM_011271	ENSMUSG00000035896	Rnase1	AI574248|Rib-1|Rib1	ribonuclease, RNase A family, 1 (pancreatic)	protein-coding
mm_116097.1	chr13	28817614	28817616	-	1	NA	intron (NR_045053, intron 2 of 8)	B4|SINE|B4	67807	NR_045054	72518	Mm.37454	NR_045053		2610307P16Rik	AI666457	RIKEN cDNA 2610307P16 gene	ncRNA
mm_15310.1	chr2	155518097	155518097	+	1	NA	promoter-TSS (NM_019811)	promoter-TSS (NM_019811)	54	NM_019811	60525	Mm.255026	NM_019811	ENSMUSG00000027605	Acss2	1110017C11Rik|ACAS|Acas1|Acas2|AceCS1|Acs1	acyl-CoA synthetase short-chain family member 2	protein-coding
mm_156774.1	chrX	160796159	160796167	+	1	NA	3' UTR (NM_011302, exon 6 of 6)	3' UTR (NM_011302, exon 6 of 6)	28150	NM_011302	20147	Mm.41982	NM_011302	ENSMUSG00000031293	Rs1	Rs1h|Xlrs1|tmgc1	retinoschisis (X-linked, juvenile) 1 (human)	protein-coding
mm_160433.1	chr8	92960120	92960120	+	1	NA	promoter-TSS (NM_009209)	promoter-TSS (NM_009209)	-927	NM_009209	20538	Mm.57040	NM_009209	ENSMUSG00000055368	Slc6a2	NE-T|NET|Slc6a5	solute carrier family 6 (neurotransmitter transporter, noradrenalin), member 2	protein-coding
mm_142588.1	chr17	46729159	46729172	-	1	NA	promoter-TSS (NM_010321)	promoter-TSS (NM_010321)	0	NM_010321	14711	Mm.29395	NM_010321	ENSMUSG00000002769	Gnmt	-	glycine N-methyltransferase	protein-coding
mm_2506.1	chr1	106211497	106211508	+	1	NA	intron (NM_133821, intron 1 of 16)	intron (NM_133821, intron 1 of 16)	39633	NM_133821	98432	Mm.24115	NM_133821	ENSMUSG00000044340	Phlpp1	AI836256|Phlpp|Plekhe1|SCOP|mKIAA0606	PH domain and leucine rich repeat protein phosphatase 1	protein-coding
mm_111818.1	chr12	105685236	105685310	-	1	NA	promoter-TSS (NM_178613)	promoter-TSS (NM_178613)	-32	NM_029654	76559	Mm.114362	NM_029654	ENSMUSG00000041341	Atg2b	2410024A21Rik|AI047755|AI503411|AW558123|C030004M05Rik|C630028L02Rik|mKIAA4067	autophagy related 2B	protein-coding
mm_71519.1	chr8	46846747	46846767	+	1	NA	3' UTR (NM_008391, exon 9 of 9)	3' UTR (NM_008391, exon 9 of 9)	107012	NM_008391	16363	Mm.1149	NM_008391	ENSMUSG00000031627	Irf2	9830146E22Rik|AI646973|Irf-2	interferon regulatory factor 2	protein-coding
mm_49568.1	chr6	30640453	30640463	+	1	NA	intron (NM_025350, intron 2 of 9)	intron (NM_025350, intron 2 of 9)	1240	NM_025350	109697	Mm.25377	NM_025350	ENSMUSG00000054446	Cpa1	0910001L12Rik|Cpa	carboxypeptidase A1, pancreatic	protein-coding
mm_19452.1	chr2	92024144	92024222	-	1	NA	promoter-TSS (NM_011957)	promoter-TSS (NM_011957)	-13	NM_011957	26427	Mm.10353	NM_011957	ENSMUSG00000027230	Creb3l1	Oasis	cAMP responsive element binding protein 3-like 1	protein-coding
mm_25405.1	chr3	107278994	107279012	+	1	NA	exon (NM_026774, exon 1 of 4)	exon (NM_026774, exon 1 of 4)	145	NM_026774	68576	Mm.290035	NM_026774	ENSMUSG00000087260	Lamtor5	1110003H18Rik|Hbxip|XIP	late endosomal/lysosomal adaptor, MAPK and MTOR activator 5	protein-coding
mm_35322.1	chr4	25800287	25800306	-	1	NA	promoter-TSS (NM_010243)	promoter-TSS (NM_010243)	-293	NM_010243	14348	Mm.39101	NM_010243	ENSMUSG00000055373	Fut9	AI746471|AU067636|mFUT9|mFuc-TIX	fucosyltransferase 9	protein-coding
mm_140057.1	chr17	74636121	74636160	+	1	NA	intron (NM_007566, intron 43 of 72)	B1_Mur2|SINE|Alu	-81610	NM_152817	74196	Mm.209503	NM_152817	ENSMUSG00000024078	Ttc27	2610511O17Rik	tetratricopeptide repeat domain 27	protein-coding
mm_142881.1	chr17	51826604	51826635	-	1	NA	promoter-TSS (NM_001163631)	promoter-TSS (NM_001163631)	-31	NM_001163631	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_18578.1	chr2	66124768	66124804	-	1	NA	promoter-TSS (NM_015736)	promoter-TSS (NM_015736)	7	NM_015736	14425	Mm.439760	NM_015736	ENSMUSG00000026994	Galnt3	-	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 3	protein-coding
mm_90013.1	chr10	115315084	115315094	+	1	NA	intron (NM_024454, intron 1 of 6)	intron (NM_024454, intron 1 of 6)	502	NM_024454	216344	Mm.21936	NM_024454	ENSMUSG00000020132	Rab21	9630024B22	RAB21, member RAS oncogene family	protein-coding
mm_54412.1	chr6	32588196	32588213	-	1	NA	promoter-TSS (NM_175750)	promoter-TSS (NM_175750)	-12	NM_175750	243743	Mm.444029	NM_175750	ENSMUSG00000029765	Plxna4	9330117B14|Plxa4|mKIAA1550	plexin A4	protein-coding
mm_31260.1	chr4	45184723	45184760	+	1	NA	promoter-TSS (NM_001081172)	promoter-TSS (NM_001081172)	-165	NM_001081172	666060	Mm.24783	NM_001081172	ENSMUSG00000035615	Frmpd1	BC031840|mKIAA0967	FERM and PDZ domain containing 1	protein-coding
mm_22793.1	chr3	22211320	22211332	+	1	NA	3' UTR (NM_030732, exon 16 of 16)	3' UTR (NM_030732, exon 16 of 16)	-40044	NR_004439	19784		NR_004439		Rprl2	RPRH3|Rmrp3	ribonuclease P RNA-like 2	ncRNA
mm_36359.1	chr4	76104357	76104368	-	1	NA	intron (NM_011211, intron 21 of 39)	intron (NM_011211, intron 21 of 39)	-826076	NM_025849	66928	Mm.24332	NM_025849	ENSMUSG00000028398	Tmem261	1700027K24Rik|3110001D03Rik	transmembrane protein 261	protein-coding
mm_36160.1	chr4	59915036	59915063	-	1	NA	promoter-TSS (NM_021053)	promoter-TSS (NM_021053)	7	NM_021053	30936	Mm.284433	NM_021053	ENSMUSG00000028386	Slc46a2	5430429N04Rik|Ly110|TSO-1C12|Tscot	solute carrier family 46, member 2	protein-coding
mm_1995.1	chr1	87126756	87126765	+	1	NA	exon (NM_007432, exon 8 of 11)	exon (NM_007432, exon 8 of 11)	1752	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_149594.1	chr19	16158733	16158775	+	1	NA	intron (NM_008139, intron 1 of 6)	ID_B1|SINE|B4	-5344	NR_033228	595139	Mm.405662	NR_033228		E030024N20Rik	9030417F11Rik|Ppia-ps8	peptidylprolyl isomerase A pseudogene 8	pseudo
mm_124062.1	chr14	78308032	78308050	-	1	NA	promoter-TSS (NM_011613)	promoter-TSS (NM_011613)	2	NM_011613	21943	Mm.249221	NM_011613	ENSMUSG00000022015	Tnfsf11	Ly109l|ODF|OPGL|RANKL|Trance	tumor necrosis factor (ligand) superfamily, member 11	protein-coding
mm_106513.1	chr11	120530573	120530602	-	1	NA	promoter-TSS (NM_008101)	promoter-TSS (NM_008101)	-140	NM_008101	14527	Mm.22329	NM_008101	ENSMUSG00000025127	Gcgr	GR	glucagon receptor	protein-coding
mm_140636.1	chr17	12652642	12652652	-	1	NA	intron (NM_009202, intron 8 of 10)	intron (NM_009202, intron 8 of 10)	23191	NM_009202	20517	Mm.594	NM_009202	ENSMUSG00000023829	Slc22a1	Lx1|Oct1|Orct|Orct1	solute carrier family 22 (organic cation transporter), member 1	protein-coding
mm_51324.1	chr6	72347383	72347390	+	1	NA	promoter-TSS (NM_026696)	promoter-TSS (NM_026696)	69	NM_026696	68364	Mm.52711	NM_026696	ENSMUSG00000058706	0610030E20Rik	1500031N04Rik|2810411C16Rik|AI461894	RIKEN cDNA 0610030E20 gene	protein-coding
mm_144166.1	chr18	6332588	6332609	+	1	NA	Intergenic	Intergenic	-91074	NM_008448	16573	Mm.223744	NM_008448	ENSMUSG00000006740	Kif5b	AL022807|Khc|Khcs|Kns1|Ukhc	kinesin family member 5B	protein-coding
mm_26798.1	chr3	9853123	9853134	-	1	NA	Intergenic	Intergenic	-19449	NM_001195031	94212	Mm.23897	NM_053182	ENSMUSG00000027508	Pag1	Cbp|F730007C19Rik|Pag	phosphoprotein associated with glycosphingolipid microdomains 1	protein-coding
mm_155015.1	chrX	41673847	41673854	+	1	NA	intron (NM_001281929, intron 15 of 15)	intron (NM_001281929, intron 15 of 15)	238051	NM_001033422	331401	Mm.259498	NM_001033422	ENSMUSG00000037475	Thoc2	6330441O12Rik|D130005M13Rik|Gm1139|Gm1793|Tho2	THO complex 2	protein-coding
mm_134268.1	chr16	13903016	13903035	-	1	NA	promoter-TSS (NM_001289562)	promoter-TSS (NM_001289562)	120	NM_001039533	94184	Mm.171484	NM_053181	ENSMUSG00000022680	Pdxdc1	2210010A19Rik|AA415817|Kiaa0251-hp	pyridoxal-dependent decarboxylase domain containing 1	protein-coding
mm_102077.1	chr11	52274842	52274897	-	1	NA	intron (NM_001313981, intron 3 of 10)	intron (NM_001313981, intron 3 of 10)	7726	NM_009331	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_104210.1	chr11	88340438	88340459	-	1	NA	3' UTR (NM_054043, exon 14 of 14)	3' UTR (NM_054043, exon 14 of 14)	-12325	NR_039545	100628571		NR_039545	ENSMUSG00000092985	Mir378b	mir-378b|mmu-mir-378b	microRNA 378b	ncRNA
mm_103152.1	chr11	70358408	70358414	-	1	NA	Intergenic	Intergenic	-6380	NM_009660	11687	Mm.4584	NM_009660	ENSMUSG00000018924	Alox15	12-LO|12/15-LO|15-LOX|Alox12l|L-12LO	arachidonate 15-lipoxygenase	protein-coding
mm_162445.1	chr1	119211128	119211130	+	1	NA	Intergenic	Intergenic	-157510	NM_001081125	14633	Mm.273292	NM_001081125	ENSMUSG00000048402	Gli2	-	GLI-Kruppel family member GLI2	protein-coding
mm_76389.1	chr8	84842969	84842980	-	1	NA	exon (NM_007591, exon 8 of 9)	exon (NM_007591, exon 8 of 9)	-2309	NM_009010	19358	Mm.255539	NM_009010	ENSMUSG00000003813	Rad23a	2310040P19Rik|AL024030|HR23A|mHR23A	RAD23 homolog A, nucleotide excision repair protein	protein-coding
mm_40080.1	chr5	34369910	34369970	+	1	NA	promoter-TSS (NM_001243123)	promoter-TSS (NM_001243123)	7	NM_001243123	231128	Mm.286885	NM_001030306	ENSMUSG00000037210	Fam193a	-	family with sequence similarity 193, member A	protein-coding
mm_163149.1	chr11	83175155	83175172	+	1	NA	promoter-TSS (NM_011410)	promoter-TSS (NM_011410)	-23	NM_011410	20558	Mm.38192	NM_011410	ENSMUSG00000000204	Slfn4	AI450778	schlafen 4	protein-coding
mm_78004.1	chr9	10446539	10446552	+	1	NA	intron (NM_001033359, intron 2 of 20)	MTB|LTR|ERVL-MaLR	458181	NM_001033359	244682	Mm.187021	NM_001033359	ENSMUSG00000039488	Cntn5	6720426O10Rik|A830025P08Rik|Gm507|NB-2	contactin 5	protein-coding
mm_132777.1	chr16	44779436	44779451	+	1	NA	intron (NM_021325, intron 1 of 6)	B1_Mus1|SINE|Alu	13707	NM_021325	57781	Mm.416152	NM_021325	ENSMUSG00000022667	Cd200r1	CD200R|Mox2r|OX2R	CD200 receptor 1	protein-coding
mm_5626.1	chr1	40393315	40393319	-	1	NA	Intergenic	Intergenic	-36253	NM_001294171	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_120742.1	chr14	73178313	73178321	+	1	NA	intron (NR_033185, intron 14 of 15)	intron (NR_033185, intron 14 of 15)	28534	NR_030459	751541		NR_030459	ENSMUSG00000076121	Mir687	Mirn687|mir-687|mmu-mir-687	microRNA 687	ncRNA
mm_116368.1	chr13	40731045	40731055	-	1	NA	promoter-TSS (NM_001122948)	promoter-TSS (NM_001122948)	-593	NM_001122948	21418	Mm.85544	NM_011547	ENSMUSG00000021359	Tfap2a	AP-2|AP2alpha|Ap-2 (a)|Ap2|Ap2tf|Tcfap2a	transcription factor AP-2, alpha	protein-coding
mm_134037.1	chr16	5049883	5049889	-	1	NA	promoter-TSS (NM_028720)	promoter-TSS (NM_028720)	24	NM_001079814	74022	Mm.21652	NM_028720	ENSMUSG00000022536	Glyr1	2810419J22Rik|3930401K13Rik|AW545332|Npac	glyoxylate reductase 1 homolog (Arabidopsis)	protein-coding
mm_48251.1	chr5	137787618	137787637	-	1	NA	promoter-TSS (NM_001005426)	promoter-TSS (NM_001005426)	-175	NM_001005426	381678	Mm.332765	NM_001005426	ENSMUSG00000037108	Zcwpw1	Gm1053	zinc finger, CW type with PWWP domain 1	protein-coding
mm_48309.1	chr5	138619703	138619747	-	1	NA	promoter-TSS (NM_001163797)	promoter-TSS (NM_001163797)	18	NM_001163797	24135	Mm.27575	NM_013844	ENSMUSG00000058291	Zfp68	KRAB3|KRAZ2|Zfp70|mszf22|mszf49	zinc finger protein 68	protein-coding
mm_36592.1	chr4	88438901	88438933	-	1	NA	promoter-TSS (NM_025760)	promoter-TSS (NM_025760)	9	NM_025760	66775	Mm.386788	NM_025760	ENSMUSG00000028497	Hacd4	4933428I03Rik|Hcad4|Ptplad2	3-hydroxyacyl-CoA dehydratase 4	protein-coding
mm_162132.1	chrX	73149408	73149408	-	1	NA	promoter-TSS (NM_001025384).2	promoter-TSS (NM_001025384).2	42	NM_001025384	574405	Mm.336093	NM_001025384	ENSMUSG00000071745	DXBay18	-	DNA segment, Chr X, Baylor 18	protein-coding
mm_42361.1	chr5	114922108	114922134	+	1	NA	Intergenic	L2|LINE|L2	-1119	NM_145209	231655	Mm.95479	NM_145209	ENSMUSG00000041827	Oasl1	7530414C13Rik|oasl9	2'-5' oligoadenylate synthetase-like 1	protein-coding
mm_107902.1	chr12	70885837	70885839	+	1	NA	intron (NM_028127, intron 7 of 13)	intron (NM_028127, intron 7 of 13)	-52019	NM_019785	56444	Mm.29317	NM_019785	ENSMUSG00000021076	Actr10	Actr11|Arp11	ARP10 actin-related protein 10	protein-coding
mm_151494.1	chr19	58681747	58681757	+	1	NA	TTS (NM_026925)	TTS (NM_026925)	11387	NM_026925	69060	Mm.20407	NM_026925	ENSMUSG00000046008	Pnlip	1810007A24Rik|PL|PTL	pancreatic lipase	protein-coding
mm_130404.1	chr15	97976679	97976696	-	1	NA	exon (NM_001113515, exon 52 of 53)	exon (NM_001113515, exon 52 of 53)	12458	NM_001252153	380967	Mm.196630	NM_201359	ENSMUSG00000052369	Tmem106c	AI046681|BC046621|D15Ertd405e	transmembrane protein 106C	protein-coding
mm_103480.1	chr11	76494951	76495034	-	1	NA	promoter-TSS (NM_001346670)	promoter-TSS (NM_001346670)	-497	NM_001346670	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_168745.1	chr12	115372451	115372451	-	1	NA	Intergenic	Intergenic	323343	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
mm_15986.1	chr2	166906027	166906099	+	1	NA	promoter-TSS (NM_023565)	promoter-TSS (NM_023565)	-33	NM_023565	110750	Mm.22417	NM_023565	ENSMUSG00000002718	Cse1l	2610100P18Rik|AA407533|Capts|Cas|Xpo2	chromosome segregation 1-like (S. cerevisiae)	protein-coding
mm_150212.1	chr19	32820120	32820123	+	1	NA	3' UTR (NM_008960, exon 9 of 9)	3' UTR (NM_008960, exon 9 of 9)	62544	NM_008960	19211	Mm.245395	NM_008960	ENSMUSG00000013663	Pten	2310035O07Rik|A130070J02Rik|AI463227|B430203M17Rik|MMAC1|TEP1	phosphatase and tensin homolog	protein-coding
mm_51565.1	chr6	83575918	83575925	+	1	NA	intron (NR_078345, intron 2 of 7)	intron (NR_078345, intron 2 of 7)	-3417	NM_024239	70527	Mm.32801	NM_024239	ENSMUSG00000006906	Stambp	5330424L14Rik|5730422L11Rik|AW107289|Amsh|mKIAA4198	STAM binding protein	protein-coding
mm_153439.1	chr19	40994156	40994181	-	1	NA	5' UTR (NM_008528, exon 1 of 17)	5' UTR (NM_008528, exon 1 of 17)	367	NM_008528	17060	Mm.9749	NM_008528	ENSMUSG00000061132	Blnk	BASH|Bca|Ly-57|Ly57|Lyw-57|SLP-65	B cell linker	protein-coding
mm_28898.1	chr3	98032355	98032359	-	1	NA	intron (NM_010928, intron 1 of 33)	intron (NM_010928, intron 1 of 33)	18819	NM_010928	18129	Mm.485843	NM_010928	ENSMUSG00000027878	Notch2	AI853703|N2	notch 2	protein-coding
mm_48811.1	chr5	148995177	148995201	-	1	NA	promoter-TSS (NR_102383)	promoter-TSS (NR_102383)	25	NR_102383	319982	Mm.33303	NR_102383	ENSMUSG00000106951	5930430L01Rik	-	RIKEN cDNA 5930430L01 gene	ncRNA
mm_20588.1	chr2	131164049	131164056	-	1	NA	intron (NR_037281, intron 2 of 2)	MLT2F|LTR|ERVL	-3971	NM_001311138	67326	Mm.27711	NM_026091	ENSMUSG00000027327	1700037H04Rik	-	RIKEN cDNA 1700037H04 gene	protein-coding
mm_14443.1	chr2	130933080	130933114	+	1	NA	intron (NM_009730, intron 1 of 28)	RLTR31D_MM|LTR|ERVK	26602	NM_009730	11990	Mm.119936	NM_009730	ENSMUSG00000027312	Atrn	AW558010|Mgca|mg	attractin	protein-coding
mm_20589.1	chr2	131164078	131164087	-	1	NA	intron (NR_037281, intron 2 of 2)	MLT2F|LTR|ERVL	-4001	NM_001311138	67326	Mm.27711	NM_026091	ENSMUSG00000027327	1700037H04Rik	-	RIKEN cDNA 1700037H04 gene	protein-coding
mm_23803.1	chr3	79884577	79884592	+	1	NA	Intergenic	Intergenic	-1346	NM_133187	68659	Mm.427274	NM_133187	ENSMUSG00000027955	Fam198b	1110032E23Rik|2210419I08Rik|AV011458|Ened	family with sequence similarity 198, member B	protein-coding
mm_86134.1	chr9	116612536	116612538	-	1	NA	intron (NM_001172122, intron 11 of 13)	intron (NM_001172122, intron 11 of 13)	-437174	NM_009371	21813	Mm.172346	NM_009371	ENSMUSG00000032440	Tgfbr2	1110020H15Rik|AU042018|DNIIR|RIIDN|TBR-II|TbetaR-II|TbetaRII	transforming growth factor, beta receptor II	protein-coding
mm_25817.1	chr3	127791375	127791390	+	1	NA	intron (NM_145133, intron 1 of 2)	intron (NM_145133, intron 1 of 2)	1469	NM_145133	211550	Mm.31852	NM_145133	ENSMUSG00000046688	Tifa	T2bp	TRAF-interacting protein with forkhead-associated domain	protein-coding
mm_65280.1	chr7	24372472	24372484	-	1	NA	intron (NM_008433, intron 1 of 8)	intron (NM_008433, intron 1 of 8)	2215	NM_008433	16534	Mm.9911	NM_008433	ENSMUSG00000054342	Kcnn4	IK1|IKCA1|KCA4|KCa3.1|SK4|SKCas|mIKCa1	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4	protein-coding
mm_150817.1	chr19	44403255	44403260	+	1	NA	exon (NM_009127, exon 3 of 6)	exon (NM_009127, exon 3 of 6)	4452	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_107541.1	chr12	40602274	40602306	+	1	NA	intron (NM_172803, intron 1 of 52)	Lx7|LINE|L1	156237	NM_172803	238130	Mm.341423	NM_172803	ENSMUSG00000035954	Dock4	5330406C03|6330411N01Rik|AF263288|C030023J22|mKIAA0716	dedicator of cytokinesis 4	protein-coding
mm_93814.1	chr10	121410851	121410867	-	1	NA	3' UTR (NM_138956, exon 5 of 5)	3' UTR (NM_138956, exon 5 of 5)	45769	NM_029364	75612	Mm.207683	NM_029364	ENSMUSG00000034707	Gns	2610016K11Rik|AU042285|C87209|G6S|N28088	glucosamine (N-acetyl)-6-sulfatase	protein-coding
mm_50521.1	chr6	49043384	49043390	+	1	NA	intron (NM_053110, intron 2 of 10)	B3|SINE|B2	6869	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_36703.1	chr4	96786745	96786765	-	1	NA	Intergenic	Intergenic	-1595	NM_001081284	620779	Mm.439625	NM_001081284	ENSMUSG00000078639	Gm12695	OTTMUSG00000008003	predicted gene 12695	protein-coding
mm_114742.1	chr13	83740189	83740201	+	1	NA	Intergenic	Intergenic	1381	NR_029545	723967		NR_029545	ENSMUSG00000065424	Mir9-2	Mirn9-2|mir-9-2|mmu-mir-9-2	microRNA 9-2	ncRNA
mm_65484.1	chr7	25655848	25655851	-	1	NA	intron (NM_007533, intron 1 of 8)	intron (NM_007533, intron 1 of 8)	2912	NM_007533	12039	Mm.25848	NM_007533	ENSMUSG00000060376	Bckdha	-	branched chain ketoacid dehydrogenase E1, alpha polypeptide	protein-coding
mm_8538.1	chr1	155059549	155059557	-	1	NA	Intergenic	Intergenic	40083	NM_010500	15939	Mm.12246	NM_010500	ENSMUSG00000056708	Ier5	-	immediate early response 5	protein-coding
mm_156984.1	chrX	7319187	7319257	-	1	NA	5' UTR (NM_001243762, exon 1 of 14)	5' UTR (NM_001243762, exon 1 of 14)	136	NM_001243762	12728	Mm.486257	NM_016691	ENSMUSG00000004317	Clcn5	5430408K11Rik|ClC-5|Clc4-1|Clc5|Clcn4-1|D930009B12Rik|DXImx42e|Sfc13|T25545	chloride channel, voltage-sensitive 5	protein-coding
mm_56095.1	chr6	87388847	87388862	-	1	NA	promoter-TSS (NM_026860)	promoter-TSS (NM_026860)	81	NM_026860	68888	Mm.46387	NM_026860	ENSMUSG00000030048	Gkn3	1190003M12Rik	gastrokine 3	protein-coding
mm_150552.1	chr19	39324969	39324979	+	1	NA	exon (NM_007815, exon 7 of 9)	exon (NM_007815, exon 7 of 9)	37889	NM_007815	13095	Mm.20764	NM_007815	ENSMUSG00000003053	Cyp2c29	AHOH|AHOHase|AI159681|AI196010|Ah-2|Ahh-1|Cyp2c|P450-2C	cytochrome P450, family 2, subfamily c, polypeptide 29	protein-coding
mm_143830.1	chr17	84050024	84050042	-	1	NA	Intergenic	Intergenic	-28627	NR_045458	74473	Mm.399575	NR_045458		4933433H22Rik	-	RIKEN cDNA 4933433H22 gene	ncRNA
mm_73895.1	chr8	119424462	119424481	+	1	NA	Intergenic	Intergenic	-12691	NM_027950	71839	Mm.272357	NM_027950	ENSMUSG00000074063	Osgin1	1700012B18Rik|Okl38	oxidative stress induced growth inhibitor 1	protein-coding
mm_141568.1	chr17	32284136	32284162	-	1	NA	promoter-TSS (NM_001286630)	promoter-TSS (NM_001286630)	-16	NM_020508	57261	Mm.253518	NM_020508	ENSMUSG00000024002	Brd4	Brd5|HUNK1|MCAP|WI-11513	bromodomain containing 4	protein-coding
mm_105382.1	chr11	103335329	103335334	-	1	NA	intron (NM_133715, intron 8 of 15)	intron (NM_133715, intron 8 of 15)	9371	NM_133715	544817	Mm.259113	NM_133715	ENSMUSG00000034255	Arhgap27	2310069I04Rik|5730442P18Rik|Gm21552|Sh3d20	Rho GTPase activating protein 27	protein-coding
mm_144702.1	chr18	34863057	34863088	+	1	NA	exon (NM_007913, exon 2 of 2)	exon (NM_007913, exon 2 of 2)	1865	NM_007913	13653	Mm.181959	NM_007913	ENSMUSG00000038418	Egr1	A530045N19Rik|ETR103|Egr-1|Krox-1|Krox-24|Krox24|NGF1-A|NGFI-A|NGFIA|TIS8|Zenk|Zfp-6|Zif268|egr	early growth response 1	protein-coding
mm_126399.1	chr15	80234048	80234064	+	1	NA	promoter-TSS (NM_178719)	promoter-TSS (NM_178719)	-24	NM_178719	239555	Mm.307163	NM_178719	ENSMUSG00000022412	Mief1	A230016E22|AI452372|Smcr7l	mitochondrial elongation factor 1	protein-coding
mm_16636.1	chr2	5895326	5895408	-	1	NA	promoter-TSS (NM_021305)	promoter-TSS (NM_021305)	-14	NM_021305	57743	Mm.21435	NM_021305	ENSMUSG00000025816	Sec61a2	-	Sec61, alpha subunit 2 (S. cerevisiae)	protein-coding
mm_92914.1	chr10	83637433	83637472	-	1	NA	intron (NM_145220, intron 2 of 20)	intron (NM_145220, intron 2 of 20)	11212	NM_145220	216190	Mm.282985	NM_145220	ENSMUSG00000020263	Appl2	Dip3b	adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 2	protein-coding
mm_5387.1	chr1	31017596	31017601	-	1	NA	Intergenic	Intergenic	-67843	NM_011200	19243	Mm.491181	NM_011200	ENSMUSG00000026064	Ptp4a1	AA415290|AU019864|C130021B01|Prl-1	protein tyrosine phosphatase 4a1	protein-coding
mm_25420.1	chr3	107853140	107853150	+	1	NA	Intergenic	Intergenic	-24085	NM_133867	99662	Mm.108491	NM_133867	ENSMUSG00000040600	Eps8l3	AI504489|Eps8r3	EPS8-like 3	protein-coding
mm_32658.1	chr4	115089156	115089159	+	1	NA	exon (NM_001164557, exon 1 of 4)	exon (NM_001164557, exon 1 of 4)	449	NM_001164557	67182	Mm.30181	NM_026018	ENSMUSG00000028716	Pdzk1ip1	0610007F13Rik|2700030M23Rik|AU046042|Map17	PDZK1 interacting protein 1	protein-coding
mm_10474.1	chr2	14341888	14341894	+	1	NA	Intergenic	Intergenic	-46507	NM_001012305	277468	Mm.44662	NM_001012305	ENSMUSG00000036949	Slc39a12	AW046938|Gm731	solute carrier family 39 (zinc transporter), member 12	protein-coding
mm_168396.1	chr11	29030830	29030830	-	1	NA	Intergenic	Intergenic	-99921	NM_027869	71701	Mm.211131	NM_027869	ENSMUSG00000020464	Pnpt1	1200003F12Rik|Old35|PNPase|Pnptl1	polyribonucleotide nucleotidyltransferase 1	protein-coding
mm_127848.1	chr15	7398335	7398347	-	1	NA	promoter-TSS (NM_001289498)	promoter-TSS (NM_001289498)	49	NM_001289496	268780	Mm.203208	NM_178748	ENSMUSG00000042961	Egflam	5930412K08|AU040377	EGF-like, fibronectin type III and laminin G domains	protein-coding
mm_115526.1	chr13	5864330	5864351	-	1	NA	intron (NM_011803, intron 1 of 3)	intron (NM_011803, intron 1 of 3)	2851	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_93778.1	chr10	120476312	120476320	-	1	NA	5' UTR (NM_010441, exon 1 of 5)	5' UTR (NM_010441, exon 1 of 5)	153	NM_001347170	15364	Mm.157190	NM_010441	ENSMUSG00000056758	Hmga2	9430083A20Rik|HMGI-C|Hmgic|pg|pygmy	high mobility group AT-hook 2	protein-coding
mm_126291.1	chr15	79347568	79347578	+	1	NA	promoter-TSS (NM_010755)	promoter-TSS (NM_010755)	53	NM_010755	17133	Mm.86646	NM_010755	ENSMUSG00000042622	Maff	-	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein F (avian)	protein-coding
mm_44879.1	chr5	34636991	34637008	-	1	NA	5' UTR (NM_026660, exon 1 of 13)	5' UTR (NM_026660, exon 1 of 13)	115	NM_026660	68294	Mm.34564	NM_026660	ENSMUSG00000001082	Mfsd10	0610009O03Rik|Tetran	major facilitator superfamily domain containing 10	protein-coding
mm_82606.1	chr9	21412242	21412246	-	1	NA	promoter-TSS (NR_045742)	promoter-TSS (NR_045742)	407	NM_021888	60507	Mm.436579	NM_021888	ENSMUSG00000002825	Qtrt1	2610028E17Rik|Tgt	queuine tRNA-ribosyltransferase 1	protein-coding
mm_62477.1	chr7	101871522	101871533	+	1	NA	promoter-TSS (NM_008034)	promoter-TSS (NM_008034)	-739	NM_001252552	14275	Mm.2135	NM_008034	ENSMUSG00000001827	Folr1	FBP1|Folbp-1|Folbp1	folate receptor 1 (adult)	protein-coding
mm_124068.1	chr14	78561915	78561938	-	1	NA	Intergenic	Intergenic	-25066	NM_001164503	219181	Mm.89413	NM_001164503	ENSMUSG00000022016	Akap11	6330501D17Rik|AKAP220|Gm80|PRKA11|mKIAA0629	A kinase (PRKA) anchor protein 11	protein-coding
mm_47193.1	chr5	120771207	120771237	-	1	NA	exon (NM_145226, exon 4 of 16)	exon (NM_145226, exon 4 of 16)	6437	NM_145226	246727	Mm.204887	NM_145226	ENSMUSG00000032661	Oas3	Oasl10	2'-5' oligoadenylate synthetase 3	protein-coding
mm_37179.1	chr4	117252233	117252255	-	1	NA	promoter-TSS (NM_001033774)	promoter-TSS (NM_001033774)	-96	NM_029589	68777	Mm.331805	NM_026837	ENSMUSG00000048772	Tmem53	1110038M16Rik|1500001P22Rik|1700012A05Rik	transmembrane protein 53	protein-coding
mm_91053.1	chr10	18800436	18800440	-	1	NA	TTS (NR_038034)	TTS (NR_038034)	-13645	NM_177706	237300	Mm.444821	NM_177706	ENSMUSG00000044624	Gm4922	4933423E17|EG237300	predicted gene 4922	protein-coding
mm_168719.1	chr12	109014257	109014271	-	1	NA	intron (NM_177602, intron 4 of 6)	4.5SRNA|scRNA|scRNA	53953	NM_001163175	380785	Mm.342085	NM_001163175	ENSMUSG00000040867	Begain	BM948371|Gm897	brain-enriched guanylate kinase-associated	protein-coding
mm_156921.1	chrX	169122319	169122336	+	1	NA	intron (NM_001287530, intron 1 of 12)	B3|SINE|B2	9449	NM_001287530	11856	Mm.441810	NM_009707	ENSMUSG00000031355	Arhgap6	AI504284|RhoGAPX-1	Rho GTPase activating protein 6	protein-coding
mm_52881.1	chr6	122513592	122513600	+	1	NA	promoter-TSS (NM_015776)	promoter-TSS (NM_015776)	12	NM_001347434	50530	Mm.41931	NM_015776	ENSMUSG00000030116	Mfap5	MAGP-2|MFAP-5	microfibrillar associated protein 5	protein-coding
mm_46433.1	chr5	104460330	104460355	-	1	NA	intron (NM_008861, intron 1 of 14)	CpG	885	NM_008861	18764	Mm.6442	NM_008861	ENSMUSG00000034462	Pkd2	C030034P18Rik|PC2|TRPP2	polycystic kidney disease 2	protein-coding
mm_104809.1	chr11	98810080	98810102	-	1	NA	promoter-TSS (NR_033551)	promoter-TSS (NR_033551)	-2	NR_033551	100037262	Mm.442062	NR_033551	ENSMUSG00000075576	Gm12359	OTTMUSG00000006457	predicted gene 12359	ncRNA
mm_88260.1	chr10	73821938	73821951	+	1	NA	promoter-TSS (NM_001142743)	promoter-TSS (NM_001142743)	77	NM_001142735	11994	Mm.338933	NM_023115	ENSMUSG00000052613	Pcdh15	BB078305|ENSMUSG00000046980|Gm9815|Ush1f|av|nmf19|roda	protocadherin 15	protein-coding
mm_15415.1	chr2	156840022	156840032	+	1	NA	promoter-TSS (NM_001291124)	promoter-TSS (NM_001291124)	20	NM_173396	228839	Mm.315625	NM_173396	ENSMUSG00000062175	Tgif2	4921501K24|5730599O09Rik|C80753|C81206	TGFB-induced factor homeobox 2	protein-coding
mm_144624.1	chr18	32938878	32938880	+	1	NA	promoter-TSS (NM_009793)	promoter-TSS (NM_009793)	-162	NM_009793	12326	Mm.222329	NM_009793	ENSMUSG00000038128	Camk4	A430110E23Rik|AI666733|CaMKIV|CaMKIV/Gr|D18Bwg0362e	calcium/calmodulin-dependent protein kinase IV	protein-coding
mm_129677.1	chr15	81399597	81399652	-	1	NA	promoter-TSS (NM_133726)	promoter-TSS (NM_133726)	70	NM_133726	70356	Mm.180337	NM_133726	ENSMUSG00000022403	St13	1110007I03Rik|3110002K08Rik|AW555194|HIP|HOP|HSPABP|HSPABP1|PRO0786|SNC6|p48	suppression of tumorigenicity 13	protein-coding
mm_40161.1	chr5	35588058	35588068	+	1	NA	non-coding (NR_045807, exon 2 of 4)	non-coding (NR_045807, exon 2 of 4)	700	NR_045807	74364	Mm.473123	NM_175208	ENSMUSG00000055061	4931431C16Rik	-	RIKEN cDNA 4931431C16 gene	ncRNA
mm_71859.1	chr8	68906501	68906509	+	1	NA	3' UTR (NM_008509, exon 10 of 10)	3' UTR (NM_008509, exon 10 of 10)	25950	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_95698.1	chr11	54370626	54370632	+	1	NA	promoter-TSS (NM_029105)	promoter-TSS (NM_029105)	-23	NM_029105	74847	Mm.486538	NM_029105	ENSMUSG00000020332	Meikin	4930404A10Rik	meiotic kinetochore factor	protein-coding
mm_158733.1	chrX	164021899	164021942	-	1	NA	intron (NM_181315, intron 1 of 7)	intron (NM_181315, intron 1 of 7)	6090	NM_181315	56078	Mm.180953	NM_181315	ENSMUSG00000031373	Car5b	7330410H16Rik|CAVB|Ca5b|CarVb|D730005F19Rik	carbonic anhydrase 5b, mitochondrial	protein-coding
mm_83557.1	chr9	46242799	46242808	-	1	NA	exon (NM_007468, exon 3 of 3)	exon (NM_007468, exon 3 of 3)	1959	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_28390.1	chr3	90018443	90018480	-	1	NA	exon (NM_001165987, exon 16 of 25)	exon (NM_001165987, exon 16 of 25)	-7251	NR_106129	102465771		NR_106129	ENSMUSG00000098397	Mir7669	Gm27996|mmu-mir-7669	microRNA 7669	ncRNA
mm_25637.1	chr3	120595622	120595636	+	1	NA	intron (NR_130170, intron 12 of 18)	SSU-rRNA_Hsa|rRNA|rRNA	291103	NR_130170	320739	Mm.388474	NR_130170		6530403H02Rik	-	RIKEN cDNA 6530403H02 gene	ncRNA
mm_137031.1	chr17	17889945	17889960	+	1	NA	intron (NM_008039, intron 1 of 1)	intron (NM_008039, intron 1 of 1)	2128	NM_008039	14289	Mm.378918	NM_008039	ENSMUSG00000052270	Fpr2	E330010I07Rik|Fpr-rs2	formyl peptide receptor 2	protein-coding
mm_68756.1	chr7	121074502	121074526	-	1	NA	promoter-TSS (NM_030691)	promoter-TSS (NM_030691)	16	NM_030691	80719	Mm.160384	NM_030691	ENSMUSG00000035004	Igsf6	-	immunoglobulin superfamily, member 6	protein-coding
mm_42205.1	chr5	112343069	112343138	+	1	NA	promoter-TSS (NM_027323)	promoter-TSS (NM_027323)	8	NM_138646	192232	Mm.238043	NM_138646	ENSMUSG00000042328	Hps4	2010205O06Rik|AU040608|BLOC-3|C130020P05Rik|le|mKIAA1667	Hermansky-Pudlak syndrome 4	protein-coding
mm_25586.1	chr3	116885959	116885990	+	1	NA	intron (NM_009146, intron 7 of 16)	intron (NM_009146, intron 7 of 16)	24294	NM_009146	20321	Mm.66293	NM_009146	ENSMUSG00000033386	Frrs1	AI131732|Sdfr2	ferric-chelate reductase 1	protein-coding
mm_50429.1	chr6	48843950	48844015	+	1	NA	exon (NM_025326, exon 5 of 7)	exon (NM_025326, exon 5 of 7)	2326	NM_001098271	66058	Mm.27061	NM_025326	ENSMUSG00000023367	Tmem176a	0610011I04Rik|AU040201|AU041743|Keg2	transmembrane protein 176A	protein-coding
mm_26863.1	chr3	15332286	15332298	-	1	NA	promoter-TSS (NM_001076679)	promoter-TSS (NM_001076679)	10	NM_001076679	751864	Mm.431296	NM_001076679	ENSMUSG00000078783	Gm9733	-	predicted gene 9733	protein-coding
mm_85049.1	chr9	89802743	89802747	-	1	NA	promoter-TSS (NR_029570)	promoter-TSS (NR_029570)	-417	NR_029570	387179		NR_029570	ENSMUSG00000065596	Mir184	Mirn184|mir-184|mmu-mir-184	microRNA 184	ncRNA
mm_125533.1	chr15	57985874	57985894	+	1	NA	promoter-TSS (NM_173862)	promoter-TSS (NM_173862)	-19	NM_173862	239463	Mm.221241	NM_173862	ENSMUSG00000051225	Fam83a	-	family with sequence similarity 83, member A	protein-coding
mm_54207.1	chr6	25689295	25689305	-	1	NA	5' UTR (NM_010338, exon 1 of 2)	5' UTR (NM_010338, exon 1 of 2)	680	NM_010338	14763	Mm.409670	NM_010338	ENSMUSG00000039904	Gpr37	AI848630|Pael-R	G protein-coupled receptor 37	protein-coding
mm_102683.1	chr11	65269948	65269954	-	1	NA	promoter-TSS (NM_145136)	promoter-TSS (NM_145136)	38	NM_145136	214384	Mm.32257	NM_145136	ENSMUSG00000020542	Myocd	BSAC2A|Srfcp	myocardin	protein-coding
mm_85283.1	chr9	99692571	99692582	-	1	NA	3' UTR (NM_001194922, exon 5 of 5)	3' UTR (NM_001194922, exon 5 of 5)	17487	NM_019815	56492	Mm.386784	NM_019815	ENSMUSG00000032473	Cldn18	-	claudin 18	protein-coding
mm_116292.1	chr13	35906325	35906364	-	1	NA	promoter-TSS (NM_145938)	promoter-TSS (NM_145938)	3	NM_145938	208366	Mm.35545	NM_145938	ENSMUSG00000021418	Rpp40	D8Bwg1265e|Rnasep1	ribonuclease P 40 subunit	protein-coding
mm_146819.1	chr18	21116868	21116870	-	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	44525	NM_008586	17288	Mm.2682	NM_008586	ENSMUSG00000024313	Mep1b	Mep-1b	meprin 1 beta	protein-coding
mm_167950.1	chrX	139782496	139782496	-	1	NA	promoter-TSS (NM_001037915)	promoter-TSS (NM_001037915)	-143	NM_001037915	622473	Mm.391312	NM_001037915	ENSMUSG00000072945	Ripply1	-	ripply transcriptional repressor 1	protein-coding
mm_129816.1	chr15	83004965	83004992	-	1	NA	intron (NM_001271414, intron 4 of 5)	B1_Mm|SINE|Alu	18160	NM_028728	74039	Mm.32584	NM_028728	ENSMUSG00000058099	Nfam1	4921501M20Rik|Cnaip	Nfat activating molecule with ITAM motif 1	protein-coding
mm_134580.1	chr16	20405585	20405607	-	1	NA	intron (NM_176839, intron 3 of 6)	intron (NM_176839, intron 3 of 6)	20798	NM_013790	27416	Mm.20845	NM_013790	ENSMUSG00000022822	Abcc5	2900011L11Rik|AI132311|Abcc5a|Abcc5b|Mrp5	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	protein-coding
mm_15132.1	chr2	153925042	153925081	+	1	NA	intron (NM_194357, intron 7 of 15)	intron (NM_194357, intron 7 of 15)	6831	NM_194357	378700	Mm.55392	NM_194357	ENSMUSG00000068008	Bpifb3	Lplunc3|Rya3	BPI fold containing family B, member 3	protein-coding
mm_157309.1	chrX	20931521	20931534	-	1	NA	promoter-TSS (NM_008823)	promoter-TSS (NM_008823)	28	NM_008823	18636	Mm.3064	NM_008823	ENSMUSG00000001128	Cfp	BCFG|Pfc	complement factor properdin	protein-coding
mm_121409.1	chr14	119372937	119372940	+	1	NA	intron (NM_015820, intron 1 of 1)	L2a|LINE|L2	234673	NM_015820	50787	Mm.445777	NM_015820	ENSMUSG00000053465	Hs6st3	6OST3|HS6ST-3	heparan sulfate 6-O-sulfotransferase 3	protein-coding
mm_24660.1	chr3	94484325	94484335	+	1	NA	intron (NR_110353, intron 1 of 11)	intron (NR_110353, intron 1 of 11)	1608	NR_110353	78784	Mm.44292	NM_172434	ENSMUSG00000028137	Celf3	4930415M08Rik|BRUNOL1|CAGH4|ERDA4|Tnrc4	CUGBP, Elav-like family member 3	protein-coding
mm_33821.1	chr4	135434017	135434020	+	1	NA	promoter-TSS (NM_022980)	promoter-TSS (NM_022980)	-213	NM_022980	53902	Mm.331970	NM_022980	ENSMUSG00000059713	Rcan3	AU041093|Csp3|Dscr1l2	regulator of calcineurin 3	protein-coding
mm_116634.1	chr13	48968479	48968489	-	1	NA	promoter-TSS (NM_001033268)	promoter-TSS (NM_001033268)	372	NR_015601	68128	Mm.426304	NR_015601		Fam120aos	C030044B11Rik	family with sequence similarity 120A, opposite strand	ncRNA
mm_154373.1	chrM	10604	10606	+	1	NA	NA	Intergenic	NA	NA								
mm_66463.1	chr7	44901574	44901593	-	1	NA	TTS (NM_027376)	TTS (NM_027376)	5504	NM_027376	70300	Mm.276298	NM_027376	ENSMUSG00000011658	Fuz	2600013E07Rik|b2b1273Clo	fuzzy planar cell polarity protein	protein-coding
mm_77070.1	chr8	110039331	110039350	-	1	NA	promoter-TSS (NM_011998)	promoter-TSS (NM_011998)	-6	NM_011998	26887	Mm.89207	NM_011998	ENSMUSG00000035930	Chst4	GST-3|Gn6st-2|HEC-GlcNAc6ST	carbohydrate (chondroitin 6/keratan) sulfotransferase 4	protein-coding
mm_12681.1	chr2	75832463	75832473	+	1	NA	exon (NM_172666, exon 1 of 20)	exon (NM_172666, exon 1 of 20)	291	NM_172666	228061	Mm.31227	NM_172666	ENSMUSG00000042410	Agps	5832437L22|9930035G10Rik|AW123847|Adaps|Adas|Adhaps|Adps|Aldhpsy|bs2	alkylglycerone phosphate synthase	protein-coding
mm_25465.1	chr3	108591496	108591517	+	1	NA	5' UTR (NM_181400, exon 1 of 15)	5' UTR (NM_181400, exon 1 of 15)	228	NM_181400	99512	Mm.285968	NM_181400	ENSMUSG00000040389	Wdr47	1810073M12Rik|AA552998|mKIAA0893	WD repeat domain 47	protein-coding
mm_119240.1	chr14	33471566	33471582	+	1	NA	Intergenic	Intergenic	-24416	NM_016700	26419	Mm.21495	NM_016700	ENSMUSG00000021936	Mapk8	AI849689|JNK|JNK1|Prkm8|SAPK1	mitogen-activated protein kinase 8	protein-coding
mm_145547.1	chr18	60808931	60808955	+	1	NA	intron (NM_001042605, intron 3 of 8)	intron (NM_001042605, intron 3 of 8)	-3133	NR_039567	100628611		NR_039567	ENSMUSG00000093327	Mir5107	mir-5107|mmu-mir-5107|mu-mir-5107	microRNA 5107	ncRNA
mm_5780.1	chr1	51572796	51572807	-	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	-94402	NM_001310549	109019	Mm.196290	NM_028696	ENSMUSG00000026107	Nabp1	4930434H03Rik|4930442A21Rik|4930488J04Rik|4933440J18Rik|5830411E10Rik|AI852561|Nbp1|Obfc2a|Ssb2	nucleic acid binding protein 1	protein-coding
mm_138136.1	chr17	34197716	34197728	+	1	NA	promoter-TSS (NM_010724)	promoter-TSS (NM_010724)	-473	NM_010724	16913	Mm.180191	NM_010724	ENSMUSG00000024338	Psmb8	Lmp-7|Lmp7	proteasome (prosome, macropain) subunit, beta type 8 (large multifunctional peptidase 7)	protein-coding
mm_127923.1	chr15	10229289	10229295	-	1	NA	intron (NM_001253781, intron 1 of 9)	Lx9|LINE|L1	5386	NM_001253781	19116	Mm.10516	NM_011169	ENSMUSG00000005268	Prlr	AI987712|Pr-1|Pr-3|Prlr-rs1	prolactin receptor	protein-coding
mm_46609.1	chr5	107967797	107967800	-	1	NA	intron (NM_026062, intron 1 of 4)	B1_Mur4|SINE|Alu	19279	NM_026062	67266	Mm.277897	NM_026062	ENSMUSG00000029270	Fam69a	2900024C23Rik|AI315274	family with sequence similarity 69, member A	protein-coding
mm_89256.1	chr10	87859292	87859302	+	1	NA	5' UTR (NM_010512, exon 1 of 5)	5' UTR (NM_010512, exon 1 of 5)	245	NM_010512	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_75716.1	chr8	68906924	68906935	-	1	NA	TTS (NM_008509)	TTS (NM_008509)	26374	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_25665.1	chr3	121734670	121734675	+	1	NA	3' UTR (NM_010171, exon 6 of 6)	3' UTR (NM_010171, exon 6 of 6)	11135	NM_010171	14066	Mm.273188	NM_010171	ENSMUSG00000028128	F3	AA409063|CD142|Cf-3|Cf3|TF	coagulation factor III	protein-coding
mm_159282.1	chr2	167631983	167631983	-	1	NA	promoter-TSS (NM_023230)	promoter-TSS (NM_023230)	22	NM_001311146	66589	Mm.278783	NM_023230	ENSMUSG00000078923	Ube2v1	0610011J09Rik|AI256840|CROC-1|CROC1|D7Bwg1382e|UEV-1	ubiquitin-conjugating enzyme E2 variant 1	protein-coding
mm_136702.1	chr17	7645296	7645303	+	1	NA	Intergenic	Intergenic	159675	NM_001081416	68655	Mm.379161	NM_001081416	ENSMUSG00000071984	Fndc1	1110027O12Rik|1110051A18Rik|mKIAA1866	fibronectin type III domain containing 1	protein-coding
mm_110495.1	chr12	54179513	54179530	-	1	NA	3' UTR (NM_028133, exon 5 of 5)	3' UTR (NM_028133, exon 5 of 5)	24353	NM_028133	112407	Mm.133037	NM_028133	ENSMUSG00000035105	Egln3	2610021G09Rik|AI505553|AI648162|Hif-p4h-3|Phd3|SM-20	egl-9 family hypoxia-inducible factor 3	protein-coding
mm_20013.1	chr2	119229915	119229926	-	1	NA	promoter-TSS (NM_028104)	promoter-TSS (NM_028104)	-55	NM_001290796	72112	Mm.46317	NM_028104	ENSMUSG00000027317	Ppp1r14d	2010107K19Rik|GBPI-1|Ppp1r14	protein phosphatase 1, regulatory (inhibitor) subunit 14D	protein-coding
mm_12687.1	chr2	75927425	75927444	+	1	NA	3' UTR (NM_172666, exon 20 of 20)	3' UTR (NM_172666, exon 20 of 20)	11028	NM_028235	72421	Mm.275109	NM_028235	ENSMUSG00000075273	Ttc30b	2510042P03Rik|Tcc30b	tetratricopeptide repeat domain 30B	protein-coding
mm_20016.1	chr2	119277984	119277992	-	1	NA	Intergenic	Intergenic	-6762	NM_145530	228543	Mm.120274	NM_145530	ENSMUSG00000034226	Rhov	A030005A06Rik|Arhv	ras homolog family member V	protein-coding
mm_97208.1	chr11	75615045	75615047	+	1	NA	intron (NM_008850, intron 7 of 11)	B2_Mm2|SINE|B2	-14815	NR_110477	654359	Mm.439961	NR_110477		Gm12338	OTTMUSG00000006216	cytochrome c oxidase, subunit VIIc pseudogene	pseudo
mm_138923.1	chr17	43667489	43667512	+	1	NA	promoter-TSS (NM_028711)	promoter-TSS (NM_028711)	128	NM_018887	56050	Mm.17991	NM_018887	ENSMUSG00000023963	Cyp39a1	mCYP39A1	cytochrome P450, family 39, subfamily a, polypeptide 1	protein-coding
mm_127332.1	chr15	100443297	100443311	+	1	NA	Intergenic	ERVL-E-int|LTR|ERVL	20111	NR_040351	432982	Mm.234608	NM_001034883	ENSMUSG00000087444	Gm5475	EG432982	predicted gene 5475	ncRNA
mm_80450.1	chr9	77979880	77979892	+	1	NA	exon (NM_134255, exon 6 of 8)	exon (NM_134255, exon 6 of 8)	62521	NM_134255	68801	Mm.430736	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	ELOVL family member 5, elongation of long chain fatty acids (yeast)	protein-coding
mm_161026.1	chr12	3807228	3807228	+	1	NA	promoter-TSS (NM_001271753)	promoter-TSS (NM_001271753)	68	NM_001271753	13435	Mm.5001	NM_007872	ENSMUSG00000020661	Dnmt3a	MmuIIIA	DNA methyltransferase 3A	protein-coding
mm_67407.1	chr7	80066257	80066260	-	1	NA	intron (NR_045695, intron 2 of 2)	intron (NR_045695, intron 2 of 2)	8999	NR_045695	100859962	Mm.392575	NR_045695	ENSMUSG00000108714	Gm21057	-	predicted gene, 21057	ncRNA
mm_65323.1	chr7	24971990	24972004	-	1	NA	intron (NM_010261, intron 2 of 4)	intron (NM_010261, intron 2 of 4)	731	NM_010261	14470	Mm.22473	NM_010261	ENSMUSG00000003380	Rabac1	2310040I06Rik|Gbpap1|PRA1|prenylin	Rab acceptor 1 (prenylated)	protein-coding
mm_98461.1	chr11	94947906	94947942	+	1	NA	exon (NM_007742, exon 40 of 51)	exon (NM_007742, exon 40 of 51)	11700	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_99995.1	chr11	114780490	114780497	+	1	NA	intron (NM_001102615, intron 5 of 19)	intron (NM_001102615, intron 5 of 19)	15104	NM_001102615	286942	Mm.308713	NM_001102615	ENSMUSG00000010021	Kif19a	Kif19	kinesin family member 19A	protein-coding
mm_38087.1	chr4	134156923	134156932	-	1	NA	intron (NM_144527, intron 3 of 13)	intron (NM_144527, intron 3 of 13)	-28174	NM_080559	73723	Mm.22240	NM_080559	ENSMUSG00000028843	Sh3bgrl3	1110004L05Rik|AU022188	SH3 domain binding glutamic acid-rich protein-like 3	protein-coding
mm_6419.1	chr1	73905313	73905315	-	1	NA	Intergenic	Intergenic	-40848	NR_045311	109198	Mm.359721	NR_045311	ENSMUSG00000100301	6030407O03Rik	-	RIKEN cDNA 6030407O03 gene	ncRNA
mm_76170.1	chr8	82391979	82391999	-	1	NA	intron (NM_001254747, intron 1 of 7)	MLT1H|LTR|ERVL-MaLR	10597	NM_001254747	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_28325.1	chr3	89342316	89342365	-	1	NA	exon (NM_001037722, exon 17 of 23)	exon (NM_001037722, exon 17 of 23)	-4312	NM_007910	13639	Mm.16332	NM_007910	ENSMUSG00000028040	Efna4	EFL-4|Epl4|LERK-4	ephrin A4	protein-coding
mm_143293.1	chr17	65884903	65884937	-	1	NA	promoter-TSS (NM_001198949)	promoter-TSS (NM_001198949)	3	NM_001198949	19765	Mm.17009	NM_009067	ENSMUSG00000024096	Ralbp1	RLIP76|Rip1	ralA binding protein 1	protein-coding
mm_143648.1	chr17	79355749	79355786	-	1	NA	promoter-TSS (NM_026514)	promoter-TSS (NM_026514)	-676	NM_026514	260409	Mm.140601	NM_026514	ENSMUSG00000036533	Cdc42ep3	3200001F04Rik|AA986861|Borg2|Cep3|UB1	CDC42 effector protein (Rho GTPase binding) 3	protein-coding
mm_59407.1	chr7	27035550	27035579	+	1	NA	intron (NM_133657, intron 8 of 8)	intron (NM_133657, intron 8 of 8)	6474	NM_133657	13085	Mm.20770	NM_133657	ENSMUSG00000060407	Cyp2a12	-	cytochrome P450, family 2, subfamily a, polypeptide 12	protein-coding
mm_114850.1	chr13	92853103	92853105	+	1	NA	3' UTR (NM_001162945, exon 9 of 9)	3' UTR (NM_001162945, exon 9 of 9)	8317	NM_001162945	382793	Mm.296770	NM_001162945	ENSMUSG00000021704	Mtx3	4930470O13Rik|AA409304|AI853833|AU067765|EG624619|Gm1194|Gm6514	metaxin 3	protein-coding
mm_92152.1	chr10	67285249	67285316	-	1	NA	promoter-TSS (NM_001036293)	promoter-TSS (NM_001036293)	-1	NM_001036293	641340	Mm.136223	NM_001036293	ENSMUSG00000075000	Nrbf2	NRBF-2	nuclear receptor binding factor 2	protein-coding
mm_135650.1	chr16	52390389	52390408	-	1	NA	intron (NM_009655, intron 1 of 15)	intron (NM_009655, intron 1 of 15)	62683	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_965.1	chr1	58115352	58115394	+	1	NA	intron (NM_023617, intron 2 of 34)	B4|SINE|B4	2237	NM_023617	71724	Mm.20108	NM_023617	ENSMUSG00000064294	Aox3	1200011D03Rik|AI326299|Aoh1|Aoh2	aldehyde oxidase 3	protein-coding
mm_70388.1	chr8	10853412	10853420	+	1	NA	Intergenic	Intergenic	29038	NR_040705	320014	Mm.403203	NR_040705	ENSMUSG00000109473	B930025P03Rik	-	RIKEN cDNA B930025P03 gene	ncRNA
mm_123547.1	chr14	66831341	66831354	-	1	NA	intron (NM_009955, intron 4 of 13)	intron (NM_009955, intron 4 of 13)	37253	NM_009955	12934	Mm.352648	NM_009955	ENSMUSG00000022048	Dpysl2	AI851130|Crmp2|DRP2|Musunc33|TOAD-64|Ulip2	dihydropyrimidinase-like 2	protein-coding
mm_23826.1	chr3	81037066	81037076	+	1	NA	5' UTR (NM_019971, exon 1 of 6)	5' UTR (NM_019971, exon 1 of 6)	655	NM_019971	54635	Mm.331089	NM_019971	ENSMUSG00000028019	Pdgfc	1110064L01Rik|AI647969|PDGF-C	platelet-derived growth factor, C polypeptide	protein-coding
mm_115595.1	chr13	11827338	11827350	-	1	NA	intron (NM_023868, intron 15 of 104)	intron (NM_023868, intron 15 of 104)	279601	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding
mm_140006.1	chr17	73111233	73111239	+	1	NA	intron (NM_001081071, intron 1 of 5)	MT2B|LTR|ERVL	3251	NM_001177967	225010	Mm.329194	NM_001081071	ENSMUSG00000054469	Lclat1	AI181996|Agpat8|Alcat1|Gm91|Lycat	lysocardiolipin acyltransferase 1	protein-coding
mm_30100.1	chr3	138489038	138489044	-	1	NA	intron (NM_175224, intron 1 of 10)	CpG	341	NM_175224	75624	Mm.26833	NM_175224	ENSMUSG00000005813	Metap1	1700029C17Rik|AW047992|mKIAA0094	methionyl aminopeptidase 1	protein-coding
mm_123271.1	chr14	61366621	61366642	-	1	NA	3' UTR (NM_008466, exon 17 of 17)	3' UTR (NM_008466, exon 17 of 17)	-6186	NM_026598	68177	Mm.22758	NM_026598	ENSMUSG00000021928	Ebpl	5730442K12Rik|EBRP	emopamil binding protein-like	protein-coding
mm_15859.1	chr2	164822962	164822975	+	1	NA	TTS (NM_178375)	TTS (NM_178375)	282	NM_028028	71971	Mm.161149	NM_028028	ENSMUSG00000017764	Zswim1	2410003H12Rik|AI850991|BB046916	zinc finger SWIM-type containing 1	protein-coding
mm_77775.1	chr9	3016879	3016900	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	21854	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_48504.1	chr5	142817547	142817558	-	1	NA	promoter-TSS (NM_001122730)	promoter-TSS (NM_001122730)	-165	NM_001122730	231861	Mm.354649	NM_178242	ENSMUSG00000039477	Tnrc18	BC025631|EG381742|Zfp469	trinucleotide repeat containing 18	protein-coding
mm_112305.1	chr12	114788854	114788861	-	1	NA	Intergenic	Intergenic	-275163	NR_106063	102465664		NR_106063	ENSMUSG00000098357	Mir7094-2	Gm27508|mmu-mir-7094-2	microRNA 7094-2	ncRNA
mm_76591.1	chr8	89042785	89042798	-	1	NA	intron (NM_021390, intron 1 of 3)	CpG-14342	1371	NM_021390	58198	Mm.214361	NM_021390	ENSMUSG00000031665	Sall1	Msal-3	sal-like 1 (Drosophila)	protein-coding
mm_51370.1	chr6	72854389	72854389	+	1	NA	intron (NM_001347231, intron 3 of 6)	intron (NM_001347231, intron 3 of 6)	44903	NM_001347231	74287	Mm.29194	NM_019715	ENSMUSG00000055239	Kcmf1	1700094M07Rik|Debt91|Pmcf	potassium channel modulatory factor 1	protein-coding
mm_152429.1	chr19	10677247	10677250	-	1	NA	intron (NM_021453, intron 1 of 8)	intron (NM_021453, intron 1 of 8)	823	NM_021453	58803	Mm.34037	NM_021453	ENSMUSG00000024738	Pga5	1110035E17Rik|Pepf	pepsinogen 5, group I	protein-coding
mm_157982.1	chrX	94123435	94123445	-	1	NA	promoter-TSS (NM_011768)	promoter-TSS (NM_011768)	-33	NM_001044386	22764	Mm.919	NM_011768	ENSMUSG00000079509	Zfx	Zfx5|Zfx5,6|Zfx6	zinc finger protein X-linked	protein-coding
mm_64496.1	chr7	143466085	143466106	+	1	NA	Intergenic	Intergenic	-5045	NM_001161624	12577	Mm.168789	NM_009876	ENSMUSG00000037664	Cdkn1c	AL024410|CDKI|Kip2|p57(kip2)|p57Kip2	cyclin-dependent kinase inhibitor 1C (P57)	protein-coding
mm_74750.1	chr8	19026583	19026587	-	1	NA	promoter-TSS (NM_183036)	promoter-TSS (NM_183036)	-56	NM_183036	360212	Mm.271558	NM_183036	ENSMUSG00000053790	Defb38	BD-38	defensin beta 38	protein-coding
mm_14295.1	chr2	128864009	128864021	+	1	NA	promoter-TSS (NM_024237)	promoter-TSS (NM_024237)	83	NM_024237	70370	Mm.5107	NM_024237	ENSMUSG00000027386	Fbln7	1600015H20Rik|AI464334|TM14	fibulin 7	protein-coding
mm_151781.1	chr19	5366254	5366264	-	1	NA	promoter-TSS (NM_027236)	promoter-TSS (NM_027236)	104	NM_001038231	23825	Mm.358649	NM_011793	ENSMUSG00000024844	Banf1	Baf|Bcrp1|L2bp1/Baf	barrier to autointegration factor 1	protein-coding
mm_34806.1	chr4	154869589	154869634	+	1	NA	promoter-TSS (NM_013783)	promoter-TSS (NM_013783)	26	NM_013783	27390	Mm.116944	NM_013783	ENSMUSG00000058183	Mmel1	Mell1|NEP2|NEPII|Nl1|SEP	membrane metallo-endopeptidase-like 1	protein-coding
mm_18997.1	chr2	76868413	76868428	-	1	NA	exon (NM_011652, exon 104 of 313)	exon (NM_011652, exon 104 of 313)	114127	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_27007.1	chr3	25857404	25857407	-	1	NA	intron (NM_001163387, intron 3 of 5)	intron (NM_001163387, intron 3 of 5)	295902	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_106144.1	chr11	116533696	116533709	-	1	NA	intron (NM_025367, intron 1 of 5)	CpG	464	NM_025367	20698	Mm.20944	NM_011451	ENSMUSG00000061878	Sphk1	1110006G24Rik|Sk1|Spk1	sphingosine kinase 1	protein-coding
mm_64318.1	chr7	141924382	141924401	+	1	NA	Intergenic	RLTR27|LTR|ERVK	-21930	NM_001347562	54473	Mm.103551	NM_023764	ENSMUSG00000025139	Tollip	4930403G24Rik|4931428G15Rik	toll interacting protein	protein-coding
mm_49039.1	chr6	4760025	4760050	+	1	NA	3' UTR (NM_130877, exon 2 of 2)	3' UTR (NM_130877, exon 2 of 2)	12731	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_81483.1	chr9	109968972	109968982	+	1	NA	intron (NM_001205330, intron 1 of 18)	intron (NM_001205330, intron 1 of 18)	37203	NM_008633	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_50813.1	chr6	54326985	54326989	+	1	NA	promoter-TSS (NM_030024)	promoter-TSS (NM_030024)	-25	NM_030024	78004	Mm.41984	NM_030024	ENSMUSG00000045725	Prr15	E130201N16Rik|G90	proline rich 15	protein-coding
mm_145604.1	chr18	61065682	61065728	+	1	NA	intron (NM_008809, intron 6 of 22)	intron (NM_008809, intron 6 of 22)	20555	NM_008809	18596	Mm.4146	NM_008809	ENSMUSG00000024620	Pdgfrb	AI528809|CD140b|PDGFR-1|Pdgfr	platelet derived growth factor receptor, beta polypeptide	protein-coding
mm_114138.1	chr13	55253120	55253121	+	1	NA	intron (NM_008739, intron 5 of 22)	intron (NM_008739, intron 5 of 22)	43338	NM_008739	18193	Mm.12964	NM_008739	ENSMUSG00000021488	Nsd1	AI528500|KMT3B	nuclear receptor-binding SET-domain protein 1	protein-coding
mm_2331.1	chr1	92831615	92831640	+	1	NA	promoter-TSS (NM_016696)	promoter-TSS (NM_016696)	-59	NM_016696	14733	Mm.297976	NM_016696	ENSMUSG00000034220	Gpc1	AI462976	glypican 1	protein-coding
mm_86390.1	chr9	123942141	123942153	-	1	NA	Intergenic	Intergenic	26545	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_43750.1	chr5	140419395	140419405	+	1	NA	promoter-TSS (NM_133916)	promoter-TSS (NM_133916)	95	NM_133916	27979	Mm.21671	NM_133916	ENSMUSG00000056076	Eif3b	AL033316|AL033334|AL033369|AW208965|D5Wsu45e|EIF3-ETA|EIF3-P110|EIF3-P116|Eif3s9|PRT1	eukaryotic translation initiation factor 3, subunit B	protein-coding
mm_85315.1	chr9	101199000	101199080	-	1	NA	promoter-TSS (NM_172144)	promoter-TSS (NM_172144)	33	NM_172144	235542	Mm.335386	NM_172144	ENSMUSG00000043154	Ppp2r3a	3222402P14Rik|A730042E07	protein phosphatase 2, regulatory subunit B'', alpha	protein-coding
mm_14777.1	chr2	145822254	145822303	+	1	NA	5' UTR (NM_028724, exon 3 of 13)	5' UTR (NM_028724, exon 3 of 13)	36162	NM_028724	74030	Mm.228799	NM_028724	ENSMUSG00000001768	Rin2	2010003K16Rik|4632403N06Rik|AW821980|RASSF4	Ras and Rab interactor 2	protein-coding
mm_52437.1	chr6	113616064	113616109	+	1	NA	exon (NM_133937, exon 3 of 3)	exon (NM_133937, exon 3 of 3)	-7935	NM_009507	22346	Mm.29407	NM_009507	ENSMUSG00000033933	Vhl	Vhlh	von Hippel-Lindau tumor suppressor	protein-coding
mm_111641.1	chr12	102653327	102653337	-	1	NA	intron (NM_172584, intron 2 of 9)	MIRc|SINE|MIR	31688	NR_035457	100316812		NR_035457	ENSMUSG00000089324	Mir1936	mir-1936|mmu-mir-1936	microRNA 1936	ncRNA
mm_167315.1	chr8	66386261	66386271	+	1	NA	promoter-TSS (NM_001166375)	promoter-TSS (NM_001166375)	-35	NM_001166375	72925	Mm.380457	NM_175188	ENSMUSG00000036469	March1	2900024D24Rik|BB085186	membrane-associated ring finger (C3HC4) 1	protein-coding
mm_72497.1	chr8	83740338	83740356	+	1	NA	intron (NM_001163031, intron 1 of 17)	intron (NM_001163031, intron 1 of 17)	964	NM_001163029	26364	Mm.334648	NM_011925	ENSMUSG00000002885	Adgre5	AA409984|Cd97|TM7LN1	adhesion G protein-coupled receptor E5	protein-coding
mm_24592.1	chr3	93445102	93445114	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	2778	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_13990.1	chr2	121806332	121806341	+	1	NA	intron (NM_172673, intron 1 of 14)	CpG	721	NM_172673	228564	Mm.121514	NM_172673	ENSMUSG00000027238	Frmd5	1500032A09Rik|5830442F04|A930004K21Rik|R75430	FERM domain containing 5	protein-coding
mm_153374.1	chr19	40356660	40356690	-	1	NA	intron (NM_001034963, intron 8 of 22)	intron (NM_001034963, intron 8 of 22)	45635	NM_001034964	20411	Mm.210815	NM_009166	ENSMUSG00000025006	Sorbs1	2310065E01Rik|9530001P15Rik|CAP|SH3P12|Sh3d5|mKIAA1296	sorbin and SH3 domain containing 1	protein-coding
mm_126205.1	chr15	78885284	78885320	+	1	NA	exon (NM_145929, exon 6 of 17)	exon (NM_145929, exon 6 of 17)	-6538	NR_105920	102466210		NR_105920	ENSMUSG00000099267	Mir6955	Gm27769|mmu-mir-6955	microRNA 6955	ncRNA
mm_63504.1	chr7	127841753	127841803	+	1	NA	promoter-TSS (NM_009294)	promoter-TSS (NM_009294)	-30	NM_009294	20909	Mm.24867	NM_009294	ENSMUSG00000030805	Stx4a	Stx4|Syn-4|Syn4	syntaxin 4A (placental)	protein-coding
mm_138589.1	chr17	35506328	35506339	+	1	NA	exon (NM_013633, exon 1 of 5)	exon (NM_013633, exon 1 of 5)	301	NM_013633	18999	Mm.17031	NM_013633	ENSMUSG00000024406	Pou5f1	NF-A3|Oct-3|Oct-3/4|Oct-4|Oct3|Oct3/4|Oct4|Otf-3|Otf-4|Otf3|Otf3-rs7|Otf3g|Otf4	POU domain, class 5, transcription factor 1	protein-coding
mm_27861.1	chr3	79158670	79158680	-	1	NA	Intergenic	L1_Mur3|LINE|L1	-12800	NM_001099624	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_145057.1	chr18	40306236	40306248	+	1	NA	intron (NM_026135, intron 1 of 1)	(CCA)n|Simple_repeat|Simple_repeat	47881	NM_026135	383348	Mm.76366	NM_026135	ENSMUSG00000051401	Kctd16	4930434H12Rik|Gm1267	potassium channel tetramerisation domain containing 16	protein-coding
mm_42373.1	chr5	114928147	114928166	+	1	NA	exon (NM_145209, exon 3 of 7)	exon (NM_145209, exon 3 of 7)	4916	NM_145209	231655	Mm.95479	NM_145209	ENSMUSG00000041827	Oasl1	7530414C13Rik|oasl9	2'-5' oligoadenylate synthetase-like 1	protein-coding
mm_48413.1	chr5	140262597	140262601	-	1	NA	intron (NM_010752, intron 9 of 17)	intron (NM_010752, intron 9 of 17)	58953	NM_010752	17120	Mm.27250	NM_010752	ENSMUSG00000029554	Mad1l1	AI173502|AW550425|Mad1	MAD1 mitotic arrest deficient 1-like 1	protein-coding
mm_160871.1	chr11	67695223	67695223	+	1	NA	promoter-TSS (NM_009038)	promoter-TSS (NM_009038)	-103	NM_009038	19674	Mm.439726	NM_009038	ENSMUSG00000020907	Rcvrn	CAR|S-modulin	recoverin	protein-coding
mm_44012.1	chr5	147188679	147188684	+	1	NA	promoter-TSS (NM_008178)	promoter-TSS (NM_008178)	-15	NM_008178	14842	Mm.4797	NM_008178	ENSMUSG00000053129	Gsx1	Gsh-1|Gsh1	GS homeobox 1	protein-coding
mm_48581.1	chr5	143517196	143517233	-	1	NA	exon (NM_009007, exon 2 of 6)	exon (NM_009007, exon 2 of 6)	10779	NM_009007	19353	Mm.292510	NM_009007	ENSMUSG00000001847	Rac1	AL023026|D5Ertd559e	RAS-related C3 botulinum substrate 1	protein-coding
mm_119602.1	chr14	51090082	51090131	+	1	NA	promoter-TSS (NM_001161731)	promoter-TSS (NM_001161731)	-971	NM_001161731	11727	Mm.202665	NM_007447	ENSMUSG00000072115	Ang	AI385586|Ang1|Rnase5|Rnase5a	angiogenin, ribonuclease, RNase A family, 5	protein-coding
mm_142324.1	chr17	43477758	43477776	-	1	NA	intron (NM_008585, intron 12 of 13)	L1MA6|LINE|L1	25006	NM_008585	17287	Mm.5346	NM_008585	ENSMUSG00000023914	Mep1a	AI098089|AW107200|Mep-1|Mep-1a|Mep1	meprin 1 alpha	protein-coding
mm_45759.1	chr5	86890254	86890261	-	1	NA	3' UTR (NM_153598, exon 6 of 6)	3' UTR (NM_153598, exon 6 of 6)	16680	NM_153598	100727	Mm.281844	NM_153598	ENSMUSG00000029260	Ugt2b34	AI788959	UDP glucuronosyltransferase 2 family, polypeptide B34	protein-coding
mm_85394.1	chr9	103288271	103288281	-	1	NA	promoter-TSS (NM_027918)	promoter-TSS (NM_027918)	21	NM_027918	71775	Mm.18802	NM_027918	ENSMUSG00000033688	1300017J02Rik	Ica|mICA	RIKEN cDNA 1300017J02 gene	protein-coding
mm_109360.1	chr12	109636009	109636020	+	1	NA	promoter-TSS (NR_046302)	promoter-TSS (NR_046302)	2	NR_046302	449562		NR_046302	ENSMUSG00000088294	AF357425	MBII-48	snoRNA AF357425	snoRNA
mm_75386.1	chr8	45410526	45410606	-	1	NA	promoter-TSS (NM_126166)	promoter-TSS (NM_126166)	-27	NM_126166	142980	Mm.33874	NM_126166	ENSMUSG00000031639	Tlr3	AI957183	toll-like receptor 3	protein-coding
mm_51103.1	chr6	67272889	67272913	+	1	NA	exon (NM_025814, exon 5 of 8)	exon (NM_025814, exon 5 of 8)	5922	NM_025814	66870	Mm.240490	NM_025814	ENSMUSG00000036371	Serbp1	1200009K13Rik|9330147J08Rik|AL022786|Pairbp1	serpine1 mRNA binding protein 1	protein-coding
mm_166546.1	chr6	36195416	36195419	-	1	NA	Intergenic	Intergenic	-192667	NM_203491	243764	Mm.448632	NM_203491	ENSMUSG00000045613	Chrm2	AChR-M2|Chrm-2|M2	cholinergic receptor, muscarinic 2, cardiac	protein-coding
mm_58827.1	chr7	16738437	16738476	+	1	NA	promoter-TSS (NM_198613)	promoter-TSS (NM_198613)	12	NM_198613	232910	Mm.333597	NM_198613	ENSMUSG00000008036	Ap2s1	AI043088	adaptor-related protein complex 2, sigma 1 subunit	protein-coding
mm_119020.1	chr14	30009077	30009092	+	1	NA	promoter-TSS (NM_001136240)	promoter-TSS (NM_001136240)	84	NM_001136240	218865	Mm.259916	NM_172264	ENSMUSG00000015970	Chdh	AU041472|D630034H06Rik	choline dehydrogenase	protein-coding
mm_151902.1	chr19	5799304	5799310	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	-3326	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_34163.1	chr4	139592986	139592990	+	1	NA	intron (NM_001205173, intron 1 of 8)	intron (NM_001205173, intron 1 of 8)	18268	NM_001205173	212632	Mm.30464	NM_183148	ENSMUSG00000041025	Iffo2	C79267	intermediate filament family orphan 2	protein-coding
mm_100021.1	chr11	114903400	114903410	+	1	NA	3' UTR (NM_170758, exon 7 of 7)	3' UTR (NM_170758, exon 7 of 7)	13364	NM_170758	217303	Mm.294439	NM_170758	ENSMUSG00000034652	Cd300a	B230315M08Rik|Clm8|LMIR1|MAIR-I|MAIR-Ia|MMAC8|Pigr4|mcpir1	CD300A molecule	protein-coding
mm_94340.1	chr11	4729871	4729888	+	1	NA	intron (NM_026015, intron 3 of 5)	intron (NM_026015, intron 3 of 5)	16899	NM_138948	192650	Mm.207056	NM_138948	ENSMUSG00000009075	Cabp7	-	calcium binding protein 7	protein-coding
mm_168919.1	chr12	58770129	58770131	+	1	NA	Intergenic	L1Md_T|LINE|L1	241887	NM_009147	20334	Mm.491137	NM_009147	ENSMUSG00000020986	Sec23a	Msec23|Sec23r	SEC23 homolog A, COPII coat complex component	protein-coding
mm_169965.1	chr1	70458333	70458347	+	1	NA	intron (NM_029160, intron 14 of 16)	L1_Mm|LINE|L1	-267375	NM_177164	320460	Mm.360649	NM_177164	ENSMUSG00000045648	Vwc2l	A830006F12Rik|Brl	von Willebrand factor C domain-containing protein 2-like	protein-coding
mm_1983.1	chr1	87020505	87020508	+	1	NA	intron (NM_153530, intron 13 of 20)	L2|LINE|L2	69422	NM_007433	11650	Mm.195224	NM_007433	ENSMUSG00000026246	Alppl2	Akp5|C77216|D1Ertd816e|EAP	alkaline phosphatase, placental-like 2	protein-coding
mm_47194.1	chr5	120772972	120772988	-	1	NA	exon (NM_145226, exon 3 of 16)	exon (NM_145226, exon 3 of 16)	4679	NM_145226	246727	Mm.204887	NM_145226	ENSMUSG00000032661	Oas3	Oasl10	2'-5' oligoadenylate synthetase 3	protein-coding
mm_160568.1	chr9	56885299	56885299	+	1	NA	exon (NM_139001, exon 3 of 10)	exon (NM_139001, exon 3 of 10)	20195	NM_139001	121021	Mm.41329	NM_139001	ENSMUSG00000032911	Cspg4	4732461B14Rik|AN2|NG2	chondroitin sulfate proteoglycan 4	protein-coding
mm_95860.1	chr11	58008967	58008987	+	1	NA	promoter-TSS (NM_028451)	promoter-TSS (NM_028451)	-87	NM_028451	73158	Mm.248843	NM_028451	ENSMUSG00000037331	Larp1	1810024J12Rik|3110040D16Rik|Larp|mKIAA0731	La ribonucleoprotein domain family, member 1	protein-coding
mm_53505.1	chr6	135368837	135368869	+	1	NA	intron (NM_001288627, intron 1 of 4)	B4|SINE|B4	1360	NM_001288627	13730	Mm.182785	NM_010128	ENSMUSG00000030208	Emp1	I-8-09|TMP	epithelial membrane protein 1	protein-coding
mm_59740.1	chr7	28814844	28814847	+	1	NA	intron (NM_177301, intron 4 of 12)	intron (NM_177301, intron 4 of 12)	3955	NM_177301	15388	Mm.9043	NM_177301	ENSMUSG00000015165	Hnrnpl	C79783|D830027H13Rik|Hnrpl	heterogeneous nuclear ribonucleoprotein L	protein-coding
mm_98137.1	chr11	87566719	87566732	+	1	NA	Intergenic	Intergenic	-11664	NM_001284398	18952	Mm.2214	NM_011129	ENSMUSG00000020486	Sept4	ARTS|Bh5|OTTMUSG00000001265|Pnutl2	septin 4	protein-coding
mm_99488.1	chr11	102710344	102710345	+	1	NA	Intergenic	Intergenic	-12619	NM_025918	52715	Mm.277638	NM_025918	ENSMUSG00000020925	Ccdc43	2610001E01Rik|D11Ertd707e	coiled-coil domain containing 43	protein-coding
mm_5087.1	chr1	4496450	4496476	-	1	NA	5' UTR (NM_001289467, exon 1 of 3)	5' UTR (NM_001289467, exon 1 of 3)	891	NM_001289464	20671	Mm.279103	NM_011441	ENSMUSG00000025902	Sox17	-	SRY (sex determining region Y)-box 17	protein-coding
mm_99647.1	chr11	105589443	105589476	+	1	NA	promoter-TSS (NM_181071)	promoter-TSS (NM_181071)	-527	NM_181071	77097	Mm.22501	NM_175492	ENSMUSG00000053580	Tanc2	3526402J09Rik|5730590C14Rik	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2	protein-coding
mm_49297.1	chr6	17725343	17725346	+	1	NA	intron (NM_001289624, intron 1 of 15)	intron (NM_001289624, intron 1 of 15)	-18248	NM_001289629	64213	Mm.12051	NM_022332	ENSMUSG00000029534	St7	9430001H04Rik|Fam4a2|HELG|RAY1|SEN4|TSG7	suppression of tumorigenicity 7	protein-coding
mm_31975.1	chr4	88353889	88353899	+	1	NA	intron (NM_001081184, intron 28 of 43)	intron (NM_001081184, intron 28 of 43)	85032	NM_025760	66775	Mm.386788	NM_025760	ENSMUSG00000028497	Hacd4	4933428I03Rik|Hcad4|Ptplad2	3-hydroxyacyl-CoA dehydratase 4	protein-coding
mm_171122.1	chr3	142881632	142881637	-	1	NA	exon (NM_178654, exon 1 of 22)	exon (NM_178654, exon 1 of 22)	370	NM_178654	109333	Mm.244236	NM_178654	ENSMUSG00000004591	Pkn2	6030436C20Rik|AI507382|PRK2|Prkcl2|Stk7	protein kinase N2	protein-coding
mm_127050.1	chr15	96699034	96699044	+	1	NA	intron (NM_175121, intron 1 of 15)	CpG	659	NM_175121	67760	Mm.46754	NM_175121	ENSMUSG00000022462	Slc38a2	5033402L14Rik|AI316867|ATA2|SAT2|mKIAA1382	solute carrier family 38, member 2	protein-coding
mm_160810.1	chr11	20242416	20242416	-	1	NA	intron (NM_172260, intron 1 of 6)	B1_Mus2|SINE|Alu	7008	NM_172260	216543	Mm.260314	NM_172260	ENSMUSG00000044066	Cep68	6030463E10Rik|AI481761|BC027174|Kiaa0582	centrosomal protein 68	protein-coding
mm_13821.1	chr2	119237532	119237552	+	1	NA	intron (NM_016907, intron 1 of 10)	CpG	182	NM_016907	20732	Mm.104955	NM_016907	ENSMUSG00000027315	Spint1	HAI-1	serine protease inhibitor, Kunitz type 1	protein-coding
mm_133223.1	chr16	76373098	76373107	+	1	NA	promoter-TSS (NM_173440)	promoter-TSS (NM_173440)	-53	NM_173440	268903	Mm.74711	NM_173440	ENSMUSG00000048490	Nrip1	6030458L20Rik|8430438I05Rik|9630050P12|AA959574|AW456757|RIP140	nuclear receptor interacting protein 1	protein-coding
mm_61194.1	chr7	63916881	63916916	+	1	NA	promoter-TSS (NM_001256311)	promoter-TSS (NM_001256311)	41	NM_001256311	381994	Mm.425466	NM_001256311	ENSMUSG00000095061	E030018B13Rik	Gm1697	RIKEN cDNA E030018B13 gene	protein-coding
mm_120311.1	chr14	63142358	63142375	+	1	NA	3' UTR (NM_007798, exon 10 of 10)	3' UTR (NM_007798, exon 10 of 10)	19904	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_52982.1	chr6	123263402	123263434	+	1	NA	intron (NM_001163161, intron 1 of 5)	intron (NM_001163161, intron 1 of 5)	1311	NM_010819	17474	Mm.441101	NM_010819	ENSMUSG00000030144	Clec4d	Clecsf8|Mpcl|mcl	C-type lectin domain family 4, member d	protein-coding
mm_110877.1	chr12	74082101	74082115	-	1	NA	intron (NM_172804, intron 1 of 6)	Charlie24|DNA|hAT-Charlie	84347	NM_172804	238266	Mm.311393	NM_172804	ENSMUSG00000044912	Syt16	6430703N11|Strep14|Syt14l|syt14r	synaptotagmin XVI	protein-coding
mm_119505.1	chr14	47380536	47380558	+	1	NA	intron (NM_001145953, intron 3 of 5)	intron (NM_001145953, intron 3 of 5)	6687	NM_001145953	16854	Mm.248615	NM_010705	ENSMUSG00000050335	Lgals3	GBP|L-34|Mac-2|gal3	lectin, galactose binding, soluble 3	protein-coding
mm_14948.1	chr2	151970028	151970029	+	1	NA	exon (NM_146127, exon 2 of 2)	exon (NM_146127, exon 2 of 2)	-2411	NR_035478	100316704		NR_035478	ENSMUSG00000088491	Mir1953	mir-1953|mmu-mir-1953	microRNA 1953	ncRNA
mm_113323.1	chr13	30786397	30786412	+	1	NA	Intergenic	Intergenic	37171	NM_013674	16364	Mm.4677	NM_013674	ENSMUSG00000021356	Irf4	AI385587|IRF-4|LSIRF|NF-EM5|Spip	interferon regulatory factor 4	protein-coding
mm_97312.1	chr11	76845858	76845861	+	1	NA	intron (NM_007754, intron 1 of 20)	MIRb|SINE|MIR	1149	NM_007754	12874	Mm.276736	NM_007754	ENSMUSG00000020841	Cpd	AA960140|AW322530|D830034L15Rik	carboxypeptidase D	protein-coding
mm_168039.1	chrY	90742934	90742954	-	1	NA	Intergenic	CpG	12106	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_147017.1	chr18	34579073	34579130	-	1	NA	promoter-TSS (NM_080637)	promoter-TSS (NM_080637)	5	NM_080637	75533	Mm.275430	NM_080637	ENSMUSG00000035984	Nme5	1700019D05Rik|Nm23-M5	NME/NM23 family member 5	protein-coding
mm_41237.1	chr5	88765005	88765030	+	1	NA	promoter-TSS (NM_007832)	promoter-TSS (NM_007832)	4	NM_007832	13178	Mm.298892	NM_007832	ENSMUSG00000029366	Dck	-	deoxycytidine kinase	protein-coding
mm_50493.1	chr6	48990184	48990200	+	1	NA	exon (NM_172888, exon 2 of 5)	exon (NM_172888, exon 2 of 5)	3331	NM_172888	243377	Mm.446302	NM_172888	ENSMUSG00000039215	Svs1	9530003A11	seminal vesicle secretory protein 1	protein-coding
mm_165708.1	chr3	98221754	98221756	+	1	NA	promoter-TSS (NM_026328)	promoter-TSS (NM_026328)	-401	NM_026328	67709	Mm.46306	NM_026328	ENSMUSG00000027876	Reg4	2010002L15Rik|GISP|RELP	regenerating islet-derived family, member 4	protein-coding
mm_163050.1	chr11	58390308	58390320	-	1	NA	exon (NM_001083884, exon 7 of 7)	exon (NM_001083884, exon 7 of 7)	9668	NM_001330197	70163	Mm.24119	NM_027339	ENSMUSG00000013643	Lypd8	2210415F13Rik	LY6/PLAUR domain containing 8	protein-coding
mm_87198.1	chr10	39533137	39533147	+	1	NA	intron (NM_001122892, intron 9 of 12)	MER5B|DNA|hAT-Charlie	-79792	NM_134000	103213	Mm.436686	NM_134000	ENSMUSG00000019842	Traf3ip2	AI429613|Act1|CIKS	TRAF3 interacting protein 2	protein-coding
mm_19855.1	chr2	113829016	113829068	-	1	NA	promoter-TSS (NM_009162)	promoter-TSS (NM_009162)	49	NM_009162	20394	Mm.4836	NM_009162	ENSMUSG00000023236	Scg5	7B2|AI325031|Sgne-1|Sgne1	secretogranin V	protein-coding
mm_144007.1	chr17	88305333	88305353	-	1	NA	Intergenic	Intergenic	-135369	NM_180974	14236	Mm.112824	NM_180974	ENSMUSG00000034998	Foxn2	3230402J05Rik|6030465J18Rik|Fkh19|Foxn1|HTLF	forkhead box N2	protein-coding
mm_127470.1	chr15	101272818	101272826	+	1	NA	exon (NM_010444, exon 5 of 7)	exon (NM_010444, exon 5 of 7)	5976	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_147336.1	chr18	42899327	42899337	-	1	NA	non-coding (NR_073583, exon 1 of 9)	non-coding (NR_073583, exon 1 of 9)	174	NR_073583	72930	Mm.26134	NM_027531	ENSMUSG00000024500	Ppp2r2b	2900026H06Rik|6330404L05Rik|E130009M08Rik|PP2A-PR55B|PR55-BETA|SCA12	protein phosphatase 2, regulatory subunit B, beta	protein-coding
mm_102509.1	chr11	60777215	60777225	-	1	NA	promoter-TSS (NM_001085440)	promoter-TSS (NM_001085440)	145	NM_009410	21975	Mm.10708	NM_009410	ENSMUSG00000002814	Top3a	-	topoisomerase (DNA) III alpha	protein-coding
mm_10526.1	chr2	16401653	16401663	+	1	NA	intron (NM_026162, intron 1 of 13)	RSINE1|SINE|B4	45354	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding
mm_36371.1	chr4	76487357	76487367	-	1	NA	intron (NM_011211, intron 10 of 39)	Lx7|LINE|L1	-1209076	NM_025849	66928	Mm.24332	NM_025849	ENSMUSG00000028398	Tmem261	1700027K24Rik|3110001D03Rik	transmembrane protein 261	protein-coding
mm_34189.1	chr4	140701609	140701619	+	1	NA	5' UTR (NM_173867, exon 1 of 13)	5' UTR (NM_173867, exon 1 of 13)	141	NM_173867	108911	Mm.253	NM_173867	ENSMUSG00000040945	Rcc2	2610510H01Rik|2610529N02Rik|AA536646|AA675016|Td60|mKIAA1470	regulator of chromosome condensation 2	protein-coding
mm_59160.1	chr7	24378488	24378492	+	1	NA	intron (NM_008433, intron 3 of 8)	intron (NM_008433, intron 3 of 8)	8227	NM_008433	16534	Mm.9911	NM_008433	ENSMUSG00000054342	Kcnn4	IK1|IKCA1|KCA4|KCa3.1|SK4|SKCas|mIKCa1	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4	protein-coding
mm_31612.1	chr4	59003122	59003215	+	1	NA	promoter-TSS (NM_001033165)	promoter-TSS (NM_001033165)	-25	NM_001033165	72429	Mm.317801	NM_001033165	ENSMUSG00000070972	Dnajc25	2010109C08Rik|2010203O07Rik	DnaJ heat shock protein family (Hsp40) member C25	protein-coding
mm_53850.1	chr6	149141536	149141619	+	1	NA	promoter-TSS (NM_001252096)	promoter-TSS (NM_001252096)	64	NM_177101	320204	Mm.274099	NM_177101	ENSMUSG00000039958	Etfbkmt	4833442J19Rik|AI256744|ETFB-KMT|Mettl20	electron transfer flavoprotein beta subunit lysine methyltransferase	protein-coding
mm_160544.1	chr9	44384260	44384260	+	1	NA	exon (NM_021395, exon 9 of 26)	exon (NM_021395, exon 9 of 26)	4770	NM_021395	12282	Mm.116721	NM_021395	ENSMUSG00000032115	Hyou1	AI415631|CBP-140|Cab140|Grp170|Orp150	hypoxia up-regulated 1	protein-coding
mm_53643.1	chr6	140623647	140623715	+	1	NA	5' UTR (NM_009637, exon 1 of 9)	5' UTR (NM_009637, exon 1 of 9)	179	NM_001005605	11569	Mm.86453	NM_009637	ENSMUSG00000030232	Aebp2	AU023766|B230313N05Rik	AE binding protein 2	protein-coding
mm_107334.1	chr12	32378693	32378707	+	1	NA	promoter-TSS (NM_001162903)	promoter-TSS (NM_001162903)	-89	NM_001162903	72123	Mm.341352	NM_028111	ENSMUSG00000090946	Ccdc71l	2010109K11Rik|AV375874	coiled-coil domain containing 71 like	protein-coding
mm_18039.1	chr2	38926360	38926386	-	1	NA	promoter-TSS (NM_010264)	promoter-TSS (NM_010264)	88	NM_010264	14536	Mm.439703	NM_010264	ENSMUSG00000063972	Nr6a1	1700113M01Rik|Gcnf|NCNF|RTR	nuclear receptor subfamily 6, group A, member 1	protein-coding
mm_122475.1	chr14	45610588	45610603	-	1	NA	exon (NM_001042719, exon 8 of 14)	exon (NM_001042719, exon 8 of 14)	47458	NR_039593	100628600		NR_039593	ENSMUSG00000093167	Mir5131	mmu-mir-5131|mu-mir-5131	microRNA 5131	ncRNA
mm_164601.1	chr17	29008099	29008128	-	1	NA	promoter-TSS (NM_134115)	promoter-TSS (NM_134115)	-176	NM_134115	106504	Mm.439986	NM_134115	ENSMUSG00000024006	Stk38	5830476G13Rik|9530097A09Rik|AA617404|Ndr1	serine/threonine kinase 38	protein-coding
mm_76839.1	chr8	105283239	105283276	-	1	NA	exon (NM_028888, exon 6 of 8)	exon (NM_028888, exon 6 of 8)	6271	NM_001166394	74356	Mm.204876	NM_028888	ENSMUSG00000014837	4931428F04Rik	AI426165|Kiaa0895l	RIKEN cDNA 4931428F04 gene	protein-coding
mm_147009.1	chr18	34506789	34506877	-	1	NA	promoter-TSS (NM_146084)	promoter-TSS (NM_146084)	-10	NM_146084	225358	Mm.226899	NM_146084	ENSMUSG00000036501	Fam13b	2610024E20Rik|AW060714|AW546153	family with sequence similarity 13, member B	protein-coding
mm_62896.1	chr7	116334245	116334268	+	1	NA	promoter-TSS (NM_026533)	promoter-TSS (NM_026533)	-66	NM_026533	68052	Mm.14798	NM_026533	ENSMUSG00000090862	Rps13	2700063M04Rik	ribosomal protein S13	protein-coding
mm_74175.1	chr8	123452421	123452431	+	1	NA	intron (NM_001253783, intron 5 of 13)	intron (NM_001253783, intron 5 of 13)	9167	NM_001281803	23854	Mm.275127	NM_054046	ENSMUSG00000001482	Def8	AI449518|D8Ertd713e|DEF-8	differentially expressed in FDCP 8	protein-coding
mm_33443.1	chr4	130366859	130366865	+	1	NA	intron (NM_025645, intron 3 of 9)	intron (NM_025645, intron 3 of 9)	6730	NM_025645	66585	Mm.423019	NM_025645	ENSMUSG00000074088	Snrnp40	0610009C03Rik|Prp8bp|Wdr57	small nuclear ribonucleoprotein 40 (U5)	protein-coding
mm_119491.1	chr14	47377984	47378020	+	1	NA	intron (NM_001145953, intron 1 of 5)	B1F|SINE|Alu	4142	NM_001145953	16854	Mm.248615	NM_010705	ENSMUSG00000050335	Lgals3	GBP|L-34|Mac-2|gal3	lectin, galactose binding, soluble 3	protein-coding
mm_8574.1	chr1	155742126	155742136	-	1	NA	promoter-TSS (NM_010712)	promoter-TSS (NM_010712)	-104	NM_010712	16872	Mm.103624	NM_010712	ENSMUSG00000026468	Lhx4	A330062J17Rik|Gsh-4|Gsh4	LIM homeobox protein 4	protein-coding
mm_143807.1	chr17	83585528	83585528	-	1	NA	TTS (NM_153512)	TTS (NM_153512)	46367	NM_153512	225030	Mm.223506	NM_153512	ENSMUSG00000045053	Kcng3	KV6.3|Kv10.1a|Kv10.1b	potassium voltage-gated channel, subfamily G, member 3	protein-coding
mm_125661.1	chr15	64173271	64173278	+	1	NA	exon (NM_001276467, exon 6 of 30)	exon (NM_001276467, exon 6 of 30)	-112826	NM_144846	223601	Mm.246108	NM_144846	ENSMUSG00000022378	Fam49b	0910001A06Rik|AW122079	family with sequence similarity 49, member B	protein-coding
mm_130991.1	chr15	103420550	103420558	-	1	NA	exon (NM_028797, exon 5 of 9)	exon (NM_028797, exon 5 of 9)	9873	NM_028797	74174	Mm.325325	NM_028797	ENSMUSG00000022487	Gtsf1	1700006H03Rik|Cue110	gametocyte specific factor 1	protein-coding
mm_163642.1	chr13	62621085	62621085	-	1	NA	intron (NM_173381, intron 1 of 2)	intron (NM_173381, intron 1 of 2)	3097	NM_001324406	211378	Mm.247448	NM_173381	ENSMUSG00000072066	6720489N17Rik	9330128I06	RIKEN cDNA 6720489N17 gene	protein-coding
mm_173287.1	chrY	1854010	1854011	-	1	NA	Intergenic	L1Md_F|LINE|L1	316399	NM_009571	22768	Mm.411381	NM_009571	ENSMUSG00000000103	Zfy2	Zfy-2	zinc finger protein 2, Y-linked	protein-coding
mm_118041.1	chr13	101694428	101694431	-	1	NA	intron (NM_001077495, intron 7 of 15)	intron (NM_001077495, intron 7 of 15)	-1799	NM_001024955	18708	Mm.259333	NM_001024955	ENSMUSG00000041417	Pik3r1	PI3K|p50alpha|p55alpha|p85alpha	phosphatidylinositol 3-kinase, regulatory subunit, polypeptide 1 (p85 alpha)	protein-coding
mm_165322.1	chr2	108770968	108770976	+	1	NA	Intergenic	Intergenic	507318	NM_029790	76894	Mm.330451	NM_029790	ENSMUSG00000057234	Mettl15	0610027B03Rik|AI303697|AW049952|Mett5d1	methyltransferase like 15	protein-coding
mm_118099.1	chr13	103911851	103911854	-	1	NA	intron (NM_001005868, intron 1 of 26)	B4A|SINE|B4	8734	NM_001289473	59079	Mm.277354	NM_021563	ENSMUSG00000021709	Erbin	1700028E05Rik|Erbb2ip|mKIAA1225	Erbb2 interacting protein	protein-coding
mm_54084.1	chr6	15758515	15758520	-	1	NA	intron (NM_175088, intron 3 of 4)	B1_Mur1|SINE|Alu	37856	NM_175088	16543	Mm.1314	NM_175088	ENSMUSG00000041390	Mdfic	Kdt1|Mdfid	MyoD family inhibitor domain containing	protein-coding
mm_53949.1	chr6	5254513	5254521	-	1	NA	exon (NM_173006, exon 2 of 9)	exon (NM_173006, exon 2 of 9)	1716	NM_173006	269823	Mm.9122	NM_173006	ENSMUSG00000029759	Pon3	2810004E20|AI786302	paraoxonase 3	protein-coding
mm_139459.1	chr17	55952799	55952814	+	1	NA	5' UTR (NM_015766, exon 1 of 5)	5' UTR (NM_015766, exon 1 of 5)	183	NM_015766	50498	Mm.256798	NM_015766	ENSMUSG00000003206	Ebi3	EBI-3|IL-27	Epstein-Barr virus induced gene 3	protein-coding
mm_159972.1	chr6	100852435	100852435	+	1	NA	intron (NM_182939, intron 2 of 8)	intron (NM_182939, intron 2 of 8)	18797	NM_182939	232314	Mm.27223	NM_182939	ENSMUSG00000052144	Ppp4r2	BE691708|C230060M08Rik	protein phosphatase 4, regulatory subunit 2	protein-coding
mm_64941.1	chr7	16312448	16312470	-	1	NA	intron (NM_133234, intron 2 of 3)	intron (NM_133234, intron 2 of 3)	2876	NM_133234	170770	Mm.7660	NM_133234	ENSMUSG00000002083	Bbc3	PUMA|PUMA/JFY1	BCL2 binding component 3	protein-coding
mm_90650.1	chr10	128747789	128747799	+	1	NA	promoter-TSS (NM_001170869)	promoter-TSS (NM_001170869)	-85	NM_030100	78428	Mm.27358	NM_030100	ENSMUSG00000064030	Pym1	A030010B05Rik|Pym|Wibg	PYM homolog 1, exon junction complex associated factor	protein-coding
mm_80584.1	chr9	84423950	84423957	+	1	NA	Intergenic	Intergenic	-350445	NR_040739	75253	Mm.401984	NR_040739	ENSMUSG00000099724	4930554C24Rik	-	RIKEN cDNA 4930554C24 gene	ncRNA
mm_68752.1	chr7	121065801	121065812	-	1	NA	intron (NM_030691, intron 5 of 5)	ID_B1|SINE|B4	8724	NM_030691	80719	Mm.160384	NM_030691	ENSMUSG00000035004	Igsf6	-	immunoglobulin superfamily, member 6	protein-coding
mm_33831.1	chr4	135626732	135626741	+	1	NA	promoter-TSS (NR_027909)	promoter-TSS (NR_027909)	81	NR_027909	73937	Mm.292326	NM_028688	ENSMUSG00000086788	1700029M20Rik	4930406E24Rik	RIKEN cDNA 1700029M20 gene	ncRNA
mm_104163.1	chr11	87342874	87342881	-	1	NA	intron (NR_106195, intron 6 of 8)	B4A|SINE|B4	16117	NM_177167	320472	Mm.341988	NM_177167	ENSMUSG00000046442	Ppm1e	AW049266|B930008A12Rik|POPX1|PP2CH|mKIAA1072	protein phosphatase 1E (PP2C domain containing)	protein-coding
mm_153006.1	chr19	30175415	30175436	-	1	NA	promoter-TSS (NM_138595)	promoter-TSS (NM_138595)	16	NM_138595	104174	Mm.274852	NM_138595	ENSMUSG00000024827	Gldc	D030049L12Rik|D19Wsu57e	glycine decarboxylase	protein-coding
mm_146157.1	chr18	75018692	75018700	+	1	NA	promoter-TSS (NM_027727)	promoter-TSS (NM_027727)	-76	NM_027727	69190	Mm.173826	NM_027727	ENSMUSG00000035765	Dym	1810041M12Rik|4933427L07Rik|C030019K18Rik	dymeclin	protein-coding
mm_81675.1	chr9	111038743	111038750	+	1	NA	intron (NM_008522, intron 14 of 16)	intron (NM_008522, intron 14 of 16)	18498	NM_001302377	54199	Mm.7336	NM_017466	ENSMUSG00000043953	Ccrl2	1810047I05Rik|Ackr5|CCR11|Cmkbr1l2|E01|L-CCR	chemokine (C-C motif) receptor-like 2	protein-coding
mm_160269.1	chr7	115995131	115995131	-	1	NA	promoter-TSS (NM_011445)	promoter-TSS (NM_011445)	-45	NM_011445	20679	Mm.323365	NM_011445	ENSMUSG00000051910	Sox6	AI987981|SOX-LZ	SRY (sex determining region Y)-box 6	protein-coding
mm_106531.1	chr11	120573236	120573281	-	1	NA	promoter-TSS (NM_011032)	promoter-TSS (NM_011032)	-322	NM_011032	18453	Mm.16660	NM_011032	ENSMUSG00000025130	P4hb	ERp59|PDI|Pdia1|Thbp	prolyl 4-hydroxylase, beta polypeptide	protein-coding
mm_38407.1	chr4	139092752	139092754	-	1	NA	intron (NM_008675, intron 1 of 3)	CpG	217	NM_008675	17965	Mm.9404	NM_008675	ENSMUSG00000041120	Nbl1	D4H1S1733E|DAN|Dana|NO3	neuroblastoma, suppression of tumorigenicity 1	protein-coding
mm_106518.1	chr11	120551127	120551138	-	1	NA	promoter-TSS (NM_026814)	promoter-TSS (NM_026814)	0	NM_026814	68701	Mm.46477	NM_026814	ENSMUSG00000025129	Ppp1r27	1110033I14Rik|Dysfip1|toonin	protein phosphatase 1, regulatory subunit 27	protein-coding
mm_63702.1	chr7	130645878	130645957	+	1	NA	intron (NM_001004468, intron 3 of 21)	intron (NM_001004468, intron 3 of 21)	-46639	NM_001347637	57752	Mm.86322	NM_021314	ENSMUSG00000030852	Tacc2	mKIAA4180	transforming, acidic coiled-coil containing protein 2	protein-coding
mm_114270.1	chr13	58148539	58148548	+	1	NA	intron (NR_126543, intron 1 of 1)	intron (NR_126543, intron 1 of 1)	1594	NR_126543	67339	Mm.121929	NR_126543		1700066J03Rik	-	RIKEN cDNA 1700066J03 gene	ncRNA
mm_23942.1	chr3	84480540	84480568	+	1	NA	promoter-TSS (NM_001033301)	promoter-TSS (NM_001033301)	-115	NM_001033301	229474	Mm.331107	NM_001033301	ENSMUSG00000041842	Fhdc1	6330505N24Rik|Gm126	FH2 domain containing 1	protein-coding
mm_12791.1	chr2	79635301	79635320	+	1	NA	promoter-TSS (NM_080558)	promoter-TSS (NM_080558)	-115	NM_080558	70599	Mm.272881	NM_080558	ENSMUSG00000027007	Ssfa2	5730488C15Rik|CS-1|CS1|KRAP|SPAG13|mKIAA1927	sperm specific antigen 2	protein-coding
mm_150151.1	chr19	31950013	31950024	+	1	NA	TTS (NM_001081074)	TTS (NM_001081074)	81257	NM_001081074	69865	Mm.87538	NM_001081074	ENSMUSG00000052595	A1cf	1810073H04Rik|ACF64|ACF65|ASP|Acf|MCM|MerCreMer|Tg(Myh6-cre/Esr1*)1Jmk|mer	APOBEC1 complementation factor	protein-coding
mm_12191.1	chr2	65620758	65620826	+	1	NA	promoter-TSS (NM_001346679)	promoter-TSS (NM_001346679)	23	NM_001346679	110876	Mm.220329	NM_001099298	ENSMUSG00000075318	Scn2a	6430408L10|A230052E19Rik|Nav1.2|Scn2a1	sodium channel, voltage-gated, type II, alpha	protein-coding
mm_134437.1	chr16	18235075	18235184	-	1	NA	promoter-TSS (NM_172151)	promoter-TSS (NM_172151)	7	NM_172151	27801	Mm.326263	NM_172151	ENSMUSG00000060166	Zdhhc8	D16H22S1738E|DHHC-8|E330009O14Rik|Op53c05|ZDHHCL1	zinc finger, DHHC domain containing 8	protein-coding
mm_129105.1	chr15	76048571	76048580	-	1	NA	exon (NM_134089, exon 33 of 38)	exon (NM_134089, exon 33 of 38)	16313	NR_105917	102466772		NR_105917	ENSMUSG00000098451	Mir6952	Gm27948|mmu-mir-6952	microRNA 6952	ncRNA
mm_67126.1	chr7	70366349	70366416	-	1	NA	5' UTR (NM_183261, exon 1 of 3)	5' UTR (NM_183261, exon 1 of 3)	364	NM_183261	11819	Mm.158143	NM_009697	ENSMUSG00000030551	Nr2f2	2700033K02Rik|9430015G03Rik|ARP-1|Aporp1|COUP-TF2|COUP-TFII|COUPTFB|EAR3|SVP40|Tcfcoup2	nuclear receptor subfamily 2, group F, member 2	protein-coding
mm_15147.1	chr2	153986590	153986595	+	1	NA	intron (NM_001080811, intron 4 of 10)	intron (NM_001080811, intron 4 of 10)	11647	NM_001080811	545477	Mm.379973	NM_001080811	ENSMUSG00000078998	Bpifa6	EG545477|Gm5840|Splunc6	BPI fold containing family A, member 6	protein-coding
mm_29729.1	chr3	126668936	126668983	-	1	NA	intron (NM_001346636, intron 2 of 20)	intron (NM_001346636, intron 2 of 20)	72008	NM_023813	108058	Mm.255822	NM_023813	ENSMUSG00000053819	Camk2d	2810011D23Rik|8030469K03Rik|CaMK II|[d]-CaMKII	calcium/calmodulin-dependent protein kinase II, delta	protein-coding
mm_131112.1	chr16	5146986	5146996	+	1	NA	promoter-TSS (NM_001127725)	promoter-TSS (NM_001127725)	-118	NM_001127725	665119	Mm.102072	NM_001127725	ENSMUSG00000091712	Sec14l5	-	SEC14-like lipid binding 5	protein-coding
mm_150736.1	chr19	43752993	43753064	+	1	NA	promoter-TSS (NM_001113562)	promoter-TSS (NM_001113562)	5	NM_025530	66388	Mm.20257	NM_025530	ENSMUSG00000025193	Cutc	2310039I18Rik|AI326282|CGI-32	cutC copper transporter	protein-coding
mm_65555.1	chr7	27133513	27133538	-	1	NA	3' UTR (NM_007817, exon 10 of 10)	3' UTR (NM_007817, exon 10 of 10)	13570	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_127243.1	chr15	99601194	99601206	+	1	NA	promoter-TSS (NM_175087)	promoter-TSS (NM_175087)	-200	NM_175087	11831	Mm.202309	NM_175087	ENSMUSG00000043144	Aqp6	AI790337	aquaporin 6	protein-coding
mm_90177.1	chr10	119692051	119692069	+	1	NA	intron (NM_133442, intron 1 of 21)	intron (NM_133442, intron 1 of 21)	69639	NR_045359	75321	Mm.402041	NR_045359	ENSMUSG00000084764	Grip1os2	4930564G21Rik	glutamate receptor interacting protein 1, opposite strand 2	ncRNA
mm_78799.1	chr9	44047391	44047422	+	1	NA	exon (NM_009382, exon 4 of 4)	exon (NM_009382, exon 4 of 4)	4022	NM_009382	21838	Mm.3951	NM_009382	ENSMUSG00000032011	Thy1	CD90|T25|Thy-1|Thy-1.2|Thy1.1|Thy1.2	thymus cell antigen 1, theta	protein-coding
mm_57444.1	chr6	124965470	124965483	-	1	NA	promoter-TSS (NM_001164089)	promoter-TSS (NM_001164089)	53	NM_001164089	26894	Mm.244536	NM_012003	ENSMUSG00000030127	Cops7a	D6Ertd35e	COP9 signalosome subunit 7A	protein-coding
mm_162082.1	chrX	26702638	26702638	-	1	NA	promoter-TSS (NM_001162364)	promoter-TSS (NM_001162364)	0	NM_001162364	100039120	Mm.379326	NM_001162364	ENSMUSG00000071788	Gm14525	OTTMUSG00000017011	predicted gene 14525	protein-coding
mm_18885.1	chr2	76704726	76704733	-	1	NA	3' UTR (NM_011652, exon 313 of 313)	3' UTR (NM_011652, exon 313 of 313)	29414	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_137907.1	chr17	32036099	32036113	+	1	NA	promoter-TSS (NM_028244)	promoter-TSS (NM_028244)	-56	NM_028244	72462	Mm.102761	NM_028244	ENSMUSG00000058392	Rrp1b	2600005C20Rik|D030064A17|Kiaa0179|mKIAA0179	ribosomal RNA processing 1 homolog B (S. cerevisiae)	protein-coding
mm_125607.1	chr15	60822980	60822990	+	1	NA	promoter-TSS (NR_030696)	promoter-TSS (NR_030696)	20	NR_030696	320469	Mm.230853	NM_177166		9930014A18Rik	-	RIKEN cDNA 9930014A18 gene	ncRNA
mm_85194.1	chr9	96725972	96725975	-	1	NA	intron (NM_175537, intron 1 of 2)	intron (NM_175537, intron 1 of 2)	5702	NM_175537	245007	Mm.485954	NM_175537	ENSMUSG00000040433	Zbtb38	A930014K01Rik|CIBZ	zinc finger and BTB domain containing 38	protein-coding
mm_167718.1	chr9	99035634	99035642	-	1	NA	promoter-TSS (NM_001080776)	promoter-TSS (NM_001080776)	52	NM_001080776	382097	Mm.293727	NM_001080776	ENSMUSG00000044860	Gm1123	AV052824|CLSP	predicted gene 1123	protein-coding
mm_4141.1	chr1	170868709	170868720	+	1	NA	promoter-TSS (NM_001081304)	promoter-TSS (NM_001081304)	-943	NM_001081304	226641	Mm.377046	NM_001081304	ENSMUSG00000026663	Atf6	9130025P16Rik|9630036G24|AA789574|Atf6alpha|ESTM49	activating transcription factor 6	protein-coding
mm_17190.1	chr2	25461119	25461129	-	1	NA	promoter-TSS (NM_153557)	promoter-TSS (NM_153557)	-30	NM_153557	227622	Mm.261780	NM_153557	ENSMUSG00000047617	BC029214	D930050G13Rik|Paxx	cDNA sequence BC029214	protein-coding
mm_132025.1	chr16	27307633	27307650	+	1	NA	promoter-TSS (NM_198112)	promoter-TSS (NM_198112)	0	NM_198112	239790	Mm.390880	NM_198112	ENSMUSG00000052276	Ostn	Ostc	osteocrin	protein-coding
mm_77065.1	chr8	109868422	109868439	-	1	NA	promoter-TSS (NM_001122594)	promoter-TSS (NM_001122594)	-173	NM_001122594	244650	Mm.23494	NM_001122594	ENSMUSG00000031732	Phlpp2	AI481772|C130044A18Rik|Phlppl	PH domain and leucine rich repeat protein phosphatase 2	protein-coding
mm_82877.1	chr9	32451457	32451466	-	1	NA	intron (NM_008026, intron 5 of 8)	ID4_|SINE|ID	57476	NM_001168354	56379	Mm.390168	NM_019659	ENSMUSG00000041248	Kcnj1	Kir1.1|ROMK|Romk2	potassium inwardly-rectifying channel, subfamily J, member 1	protein-coding
mm_51541.1	chr6	83196026	83196034	+	1	NA	exon (NM_001198867, exon 23 of 28)	exon (NM_001198867, exon 23 of 28)	10084	NM_001347310	13191	Mm.6919	NM_007835	ENSMUSG00000031865	Dctn1	AL022633|DAP-150|DP-150|Glued|p150|p150-glued|p150<glued>	dynactin 1	protein-coding
mm_49809.1	chr6	36388582	36388616	+	1	NA	promoter-TSS (NR_015589)	promoter-TSS (NR_015589)	-365	NR_015589	319472	Mm.226434	NR_015589	ENSMUSG00000073154	9330158H04Rik	-	RIKEN cDNA 9330158H04 gene	ncRNA
mm_2882.1	chr1	131828987	131828992	+	1	NA	intron (NM_173865, intron 1 of 10)	intron (NM_173865, intron 1 of 10)	977	NM_173865	98396	Mm.389181	NM_173865	ENSMUSG00000013275	Slc41a1	AI573938|B230315F01Rik	solute carrier family 41, member 1	protein-coding
mm_76252.1	chr8	83694005	83694044	-	1	NA	promoter-TSS (NM_001199593)	promoter-TSS (NM_001199593)	37	NM_001199593	320795	Mm.213000	NM_177262	ENSMUSG00000057672	Pkn1	DBK|F730027O18Rik|PAK1|PRK1|Pkn|Prkcl1|Stk3	protein kinase N1	protein-coding
mm_21550.1	chr2	164071090	164071118	-	1	NA	promoter-TSS (NM_001291155)	promoter-TSS (NM_001291155)	-2	NM_025996	67145	Mm.23173	NM_025996	ENSMUSG00000018322	Tomm34	2610100K07Rik|TOM34	translocase of outer mitochondrial membrane 34	protein-coding
mm_110110.1	chr12	26443207	26443224	-	1	NA	3' UTR (NM_021384, exon 6 of 6)	3' UTR (NM_021384, exon 6 of 6)	13237	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_170755.1	chr2	156839887	156839895	-	1	NA	promoter-TSS (NM_001291124)	promoter-TSS (NM_001291124)	-116	NM_001291124	228839	Mm.315625	NM_173396	ENSMUSG00000062175	Tgif2	4921501K24|5730599O09Rik|C80753|C81206	TGFB-induced factor homeobox 2	protein-coding
mm_137918.1	chr17	32335555	32335594	+	1	NA	exon (NM_017476, exon 8 of 14)	exon (NM_017476, exon 8 of 14)	-14336	NR_131218	56399	Mm.328945	NM_019774	ENSMUSG00000024045	Akap8	1200016A02Rik|AA673585|AKAP-8|AKAP95|AU015639	A kinase (PRKA) anchor protein 8	protein-coding
mm_94671.1	chr11	17257559	17257637	+	1	NA	promoter-TSS (NM_001330649)	promoter-TSS (NM_001330649)	51	NM_020558	57316	Mm.287982	NM_020558	ENSMUSG00000000581	C1d	1110036E10Rik|AI875855|SUN-CoR	C1D nuclear receptor co-repressor	protein-coding
mm_59891.1	chr7	30307112	30307129	+	1	NA	3' UTR (NM_001081114, exon 14 of 14)	3' UTR (NM_001081114, exon 14 of 14)	-1633	NM_198027	233065	Mm.276277	NM_198027	ENSMUSG00000042831	Alkbh6	AI839550|Abh6|C130099A02	alkB homolog 6	protein-coding
mm_112743.1	chr13	19339971	19339981	+	1	NA	Intergenic	Intergenic	55837	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_99138.1	chr11	100320597	100320623	+	1	NA	intron (NM_011508, intron 1 of 3)	intron (NM_011508, intron 1 of 3)	661	NM_011508	20918	Mm.13886	NM_011508	ENSMUSG00000035530	Eif1	Sui1-rs1	eukaryotic translation initiation factor 1	protein-coding
mm_66033.1	chr7	30626146	30626164	-	1	NA	promoter-TSS (NM_025628)	promoter-TSS (NM_025628)	-4	NM_025628	110323	Mm.400	NM_025628	ENSMUSG00000036751	Cox6b1	2010000G05Rik|Cox6b	cytochrome c oxidase, subunit VIb polypeptide 1	protein-coding
mm_160081.1	chr7	13279264	13279264	+	1	NA	promoter-TSS (NM_001083188)	promoter-TSS (NM_001083188)	-1	NM_001083188	16881	Mm.288179	NM_010715	ENSMUSG00000056394	Lig1	AL033288|LigI	ligase I, DNA, ATP-dependent	protein-coding
mm_23407.1	chr3	58414814	58414829	+	1	NA	5' UTR (NM_001347233, exon 1 of 3)	5' UTR (NM_001347233, exon 1 of 3)	101	NM_001081229	72033	Mm.218409	NM_001081229	ENSMUSG00000027806	Tsc22d2	1810043J12Rik|5530402M19Rik	TSC22 domain family, member 2	protein-coding
mm_133691.1	chr16	92538987	92538987	+	1	NA	intron (NM_172469, intron 5 of 5)	MTEa|LTR|ERVL-MaLR	40840	NM_172469	209195	Mm.44747	NM_172469	ENSMUSG00000022949	Clic6	5730466J16Rik|AL022908|AW045520|CLIC1L	chloride intracellular channel 6	protein-coding
mm_102464.1	chr11	59948108	59948163	-	1	NA	promoter-TSS (NR_045273)	promoter-TSS (NR_045273)	12	NR_045273	100504121	Mm.383770	NR_045273	ENSMUSG00000085260	Med9os	1700013G23Rik	mediator complex subunit 9, opposite strand	ncRNA
mm_1824.1	chr1	82587174	82587192	+	1	NA	promoter-TSS (NM_007735)	promoter-TSS (NM_007735)	262	NM_007734	12828	Mm.389135	NM_007734	ENSMUSG00000079465	Col4a3	[a]3(IV)|alpha3(IV)	collagen, type IV, alpha 3	protein-coding
mm_131404.1	chr16	14389877	14389919	+	1	NA	exon (NM_008576, exon 2 of 31)	exon (NM_008576, exon 2 of 31)	28340	NM_008576	17250	Mm.196634	NM_008576	ENSMUSG00000023088	Abcc1	Abcc1a|Abcc1b|MRP|Mdrap|Mrp1	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	protein-coding
mm_56687.1	chr6	113934680	113934695	-	1	NA	promoter-TSS (NM_001347365)	promoter-TSS (NM_001347365)	-6	NM_001347365	11941	Mm.321755	NM_009723	ENSMUSG00000030302	Atp2b2	D6Abb2e|Gena300|PMCA2|Tmy|dfw|jog|wms|wri	ATPase, Ca++ transporting, plasma membrane 2	protein-coding
mm_29314.1	chr3	108012448	108012462	-	1	NA	3' UTR (NM_010358, exon 8 of 8)	3' UTR (NM_010358, exon 8 of 8)	5518	NM_010358	14862	Mm.37199	NM_010358	ENSMUSG00000058135	Gstm1	Gstb-1|Gstb1	glutathione S-transferase, mu 1	protein-coding
mm_114176.1	chr13	55609774	55609780	+	1	NA	3' UTR (NM_146045, exon 6 of 6)	3' UTR (NM_146045, exon 6 of 6)	9881	NM_001311137	218271	Mm.139825	NM_146045	ENSMUSG00000021504	B4galt7	-	xylosylprotein beta1,4-galactosyltransferase, polypeptide 7 (galactosyltransferase I)	protein-coding
mm_8707.1	chr1	158953491	158953493	-	1	NA	intron (NM_001085376, intron 1 of 21)	intron (NM_001085376, intron 1 of 21)	3946	NM_001085376	23850	Mm.458621	NM_001085376	ENSMUSG00000073530	Pappa2	PAPP-A2|PLAC3|Pappe	pappalysin 2	protein-coding
mm_79621.1	chr9	58822940	58822966	+	1	NA	promoter-TSS (NM_001081192)	promoter-TSS (NM_001081192)	-559	NM_001081192	330953	Mm.151967	NM_001081192	ENSMUSG00000032338	Hcn4	Bcng3|Hcn3	hyperpolarization-activated, cyclic nucleotide-gated K+ 4	protein-coding
mm_25538.1	chr3	115715157	115715172	+	1	NA	promoter-TSS (NM_007901)	promoter-TSS (NM_007901)	-109	NM_007901	13609	Mm.982	NM_007901	ENSMUSG00000045092	S1pr1	AI849002|Edg1|Lpb1|S1p|S1p1	sphingosine-1-phosphate receptor 1	protein-coding
mm_21241.1	chr2	156167709	156167754	-	1	NA	exon (NM_001291114, exon 5 of 17)	exon (NM_001291114, exon 5 of 17)	11849	NM_001291115	170791	Mm.392436	NM_133242	ENSMUSG00000027620	Rbm39	1500012C14Rik|2310040E03Rik|B330012G18Rik|C79248|R75070|Rnpc2|caper	RNA binding motif protein 39	protein-coding
mm_124905.1	chr15	10952349	10952364	+	1	NA	promoter-TSS (NM_030888)	promoter-TSS (NM_030888)	-1	NM_001204134	81799	Mm.280158	NM_030888	ENSMUSG00000058914	C1qtnf3	2310005P21Rik|CORS-26|CORS26|CTRP3|Corcs|Cors	C1q and tumor necrosis factor related protein 3	protein-coding
mm_97084.1	chr11	73111748	73111790	+	1	NA	exon (NM_008399, exon 5 of 31)	exon (NM_008399, exon 5 of 31)	21174	NM_008399	16407	Mm.96	NM_008399	ENSMUSG00000005947	Itgae	A530055J10|CD103|aM290|alpha-E1|alpha-M290	integrin alpha E, epithelial-associated	protein-coding
mm_53279.1	chr6	128674002	128674013	+	1	NA	exon (NM_053165, exon 3 of 5)	exon (NM_053165, exon 3 of 5)	11622	NM_053165	94071	Mm.197689	NM_053165	ENSMUSG00000030364	Clec2h	Clrf|clr-f	C-type lectin domain family 2, member h	protein-coding
mm_143530.1	chr17	73902076	73902107	-	1	NA	intron (NM_011723, intron 24 of 35)	intron (NM_011723, intron 24 of 35)	48105	NM_011723	22436	Mm.11223	NM_011723	ENSMUSG00000024066	Xdh	XO|Xor|Xox-1|Xox1	xanthine dehydrogenase	protein-coding
mm_78702.1	chr9	41327275	41327291	+	1	NA	Intergenic	Intergenic	-49243	NR_040725	73144	Mm.38166	NM_001033153	ENSMUSG00000074415	3110039I08Rik	2610203C20Rik|AI848448|D230004N17Rik|D3Mgi9|Mir100hg	RIKEN cDNA 3110039I08 gene	ncRNA
mm_88743.1	chr10	80283022	80283035	+	1	NA	exon (NM_133188, exon 8 of 12)	exon (NM_133188, exon 8 of 12)	4864	NR_105876	102466207		NR_105876	ENSMUSG00000098672	Mir6911	Gm27822|mmu-mir-6911	microRNA 6911	ncRNA
mm_53633.1	chr6	140591628	140591641	+	1	NA	exon (NM_144920, exon 30 of 31)	exon (NM_144920, exon 30 of 31)	-31029	NM_178803	11569	Mm.86453	NM_009637	ENSMUSG00000030232	Aebp2	AU023766|B230313N05Rik	AE binding protein 2	protein-coding
mm_40186.1	chr5	36374659	36374698	+	1	NA	intron (NM_030889, intron 1 of 26)	L1MB5|LINE|L1	23461	NM_030889	81840	Mm.34113	NM_030889	ENSMUSG00000029093	Sorcs2	N28137|mKIAA1329	sortilin-related VPS10 domain containing receptor 2	protein-coding
mm_13448.1	chr2	105224288	105224308	+	1	NA	promoter-TSS (NM_028747)	promoter-TSS (NM_028747)	-44	NM_028747	74088	Mm.46188	NM_028747	ENSMUSG00000055312	Them7	0610012H03Rik	thioesterase superfamily member 7	protein-coding
mm_40507.1	chr5	57731703	57731709	+	1	NA	intron (NM_001310608, intron 1 of 3)	B1_Mur4|SINE|Alu	13625	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_144493.1	chr18	24205710	24205720	+	1	NA	promoter-TSS (NM_001160404)	promoter-TSS (NM_001160404)	-279	NM_001160404	14423	Mm.30249	NM_013814	ENSMUSG00000000420	Galnt1	-	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 1	protein-coding
mm_140173.1	chr17	80373666	80373701	+	1	NA	promoter-TSS (NR_028385)	promoter-TSS (NR_028385)	-141	NR_028385	791338	Mm.204722	NR_028385		Gm10190	ENSMUSG00000066938	predicted gene 10190	ncRNA
mm_19223.1	chr2	84650761	84650771	-	1	NA	promoter-TSS (NM_001085449)	promoter-TSS (NM_001085449)	-26	NM_001085448	12388	Mm.35738	NM_007615	ENSMUSG00000034101	Ctnnd1	AA409437|AU019353|Catns|Ctnnd|P120|mKIAA0384	catenin (cadherin associated protein), delta 1	protein-coding
mm_24059.1	chr3	87915162	87915183	+	1	NA	3' UTR (NM_008231, exon 6 of 6)	3' UTR (NM_008231, exon 6 of 6)	-4372	NM_026591	67707	Mm.393802	NM_026591	ENSMUSG00000019710	Mrpl24	2010005E08Rik|2810470K06Rik|6720473G22Rik|AA407670	mitochondrial ribosomal protein L24	protein-coding
mm_139313.1	chr17	48351850	48351872	+	1	NA	exon (NM_031254, exon 4 of 5)	exon (NM_031254, exon 4 of 5)	5460	NM_001272078	83433	Mm.261623	NM_031254	ENSMUSG00000023992	Trem2	TREM-2|Trem2a|Trem2b|Trem2c	triggering receptor expressed on myeloid cells 2	protein-coding
mm_102127.1	chr11	53430381	53430389	-	1	NA	intron (NM_001326614, intron 2 of 2)	intron (NM_001326614, intron 2 of 2)	446	NM_025352	22272	Mm.251621	NM_025352	ENSMUSG00000044894	Uqcrq	1100001F06Rik|1500040F11Rik|5830407L17Rik|9.5kDa|AA959903|QP-C|Qpc|Uqcrb|c1502	ubiquinol-cytochrome c reductase, complex III subunit VII	protein-coding
mm_104505.1	chr11	95966453	95966457	-	1	NA	intron (NM_009951, intron 13 of 14)	intron (NM_009951, intron 13 of 14)	-3072	NR_037223	100526468		NR_037223	ENSMUSG00000093358	Mir3063	mmu-mir-3063	microRNA 3063	ncRNA
mm_113604.1	chr13	41249748	41249768	+	1	NA	promoter-TSS (NM_001135577)	promoter-TSS (NM_001135577)	-86	NM_001135577	108934	Mm.38578	NM_001135577	ENSMUSG00000091264	Smim13	2900036K02Rik	small integral membrane protein 13	protein-coding
mm_107193.1	chr12	25254952	25254963	+	1	NA	Intergenic	Intergenic	125783	NR_045844	432641	Mm.112955	NR_045844		Gm17746	-	predicted gene, 17746	ncRNA
mm_128548.1	chr15	55557297	55557332	-	1	NA	promoter-TSS (NM_026759)	promoter-TSS (NM_026759)	-2	NM_026759	68537	Mm.236795	NM_026759	ENSMUSG00000022370	Mrpl13	1110002D09Rik	mitochondrial ribosomal protein L13	protein-coding
mm_67868.1	chr7	99162220	99162223	-	1	NA	intron (NM_026384, intron 4 of 7)	intron (NM_026384, intron 4 of 7)	20492	NM_026384	67800	Mm.180189	NM_026384	ENSMUSG00000030747	Dgat2	0610010B06Rik|ARAT|DGAT-2	diacylglycerol O-acyltransferase 2	protein-coding
mm_20251.1	chr2	126500293	126500294	-	1	NA	Intergenic	Intergenic	-8740	NM_001080944	241633	Mm.222235	NM_001080944	ENSMUSG00000060131	Atp8b4	A530043E15|Im	ATPase, class I, type 8B, member 4	protein-coding
mm_6323.1	chr1	71606858	71606873	-	1	NA	exon (NM_001276413, exon 29 of 44)	exon (NM_001276413, exon 29 of 44)	46369	NM_010233	14268	Mm.193099	NM_010233	ENSMUSG00000026193	Fn1	E330027I09|Fn|Fn-1	fibronectin 1	protein-coding
mm_99524.1	chr11	103170728	103170740	+	1	NA	promoter-TSS (NM_001077698)	promoter-TSS (NM_001077698)	-404	NM_001077698	57778	Mm.138913	NM_019679	ENSMUSG00000055805	Fmnl1	8030453N10Rik|AI553564|Fmnl|Fnrl|Frls	formin-like 1	protein-coding
mm_4684.1	chr1	180587981	180588023	+	1	NA	TTS (NR_105869)	TTS (NR_105869)	801	NR_105869	102466761		NR_105869	ENSMUSG00000098926	Mir6904	Gm27426|mmu-mir-6904	microRNA 6904	ncRNA
mm_143247.1	chr17	64331818	64331957	-	1	NA	promoter-TSS (NM_001025309)	promoter-TSS (NM_001025309)	-4	NM_001025309	224938	Mm.489681	NM_144859	ENSMUSG00000024083	Pja2	AI447901|AL022700|Neurodap1|mKIAA0438	praja 2, RING-H2 motif containing	protein-coding
mm_83066.1	chr9	37552956	37552982	-	1	NA	promoter-TSS (NM_022029)	promoter-TSS (NM_022029)	-224	NM_022029	64011	Mm.335065	NM_022029	ENSMUSG00000053310	Nrgn	0710001B06Rik|AI838505|NG|NG/RC3|Pss1|R75334|RC3	neurogranin	protein-coding
mm_30284.1	chr3	148989103	148989107	-	1	NA	Intergenic	CpG	-34470	NM_001081298	99633	Mm.9776	NM_001081298	ENSMUSG00000028184	Adgrl2	AI450192|CIRL-2|Gm619|Lec1|Lphh1|Lphn2|mKIAA0786	adhesion G protein-coupled receptor L2	protein-coding
mm_75607.1	chr8	61902674	61902713	-	1	NA	promoter-TSS (NM_001293772)	promoter-TSS (NM_001293772)	1	NM_001293772	72333	Mm.29933	NM_001081390	ENSMUSG00000058056	Palld	2410003B16Rik|6030492A02	palladin, cytoskeletal associated protein	protein-coding
mm_67391.1	chr7	79844525	79844539	-	1	NA	Intergenic	Intergenic	-2180	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_20751.1	chr2	140389699	140389729	-	1	NA	promoter-TSS (NM_001033296)	promoter-TSS (NM_001033296)	-4	NM_001033296	228684	Mm.486585	NM_001033296	ENSMUSG00000074764	Sel1l2	Gm118	sel-1 suppressor of lin-12-like 2 (C. elegans)	protein-coding
mm_90718.1	chr10	4432257	4432269	-	1	NA	promoter-TSS (NM_024261)	promoter-TSS (NM_024261)	89	NM_025343	66084	Mm.153111	NM_025343	ENSMUSG00000019763	Rmnd1	0610042C05Rik|AA408137|AI462664|AW536662	required for meiotic nuclear division 1 homolog	protein-coding
mm_12426.1	chr2	70563537	70563547	+	1	NA	promoter-TSS (NR_040496)	promoter-TSS (NR_040496)	-185	NR_040496	68986	Mm.437697	NR_040496	ENSMUSG00000087264	Gad1os	1500002O10Rik	glutamate decarboxylase 1, opposite strand	ncRNA
mm_18350.1	chr2	58160624	58160635	-	1	NA	promoter-TSS (NM_139200)	promoter-TSS (NM_139200)	-507	NM_139200	227929	Mm.273905	NM_139200	ENSMUSG00000026832	Cytip	A130053M09Rik|AI462064|C80816|Cbp|Cybr|Pscdbp	cytohesin 1 interacting protein	protein-coding
mm_20005.1	chr2	119112749	119112769	-	1	NA	promoter-TSS (NM_011234)	promoter-TSS (NM_011234)	-58	NM_011234	19361	Mm.330492	NM_011234	ENSMUSG00000027323	Rad51	AV304093|Rad51a|Reca	RAD51 recombinase	protein-coding
mm_136644.1	chr17	5804656	5804661	+	1	NA	Intergenic	Intergenic	5168	NR_045080	78512	Mm.23696	NR_045079	ENSMUSG00000096965	3300005D01Rik	-	RIKEN cDNA 3300005D01 gene	ncRNA
mm_146772.1	chr18	20059256	20059285	-	1	NA	5' UTR (NM_013505, exon 1 of 17)	5' UTR (NM_013505, exon 1 of 17)	284	NM_013505	13506	Mm.280547	NM_013505	ENSMUSG00000024331	Dsc2	AW228162	desmocollin 2	protein-coding
mm_1708.1	chr1	75236472	75236492	+	1	NA	promoter-TSS (NM_001159883)	promoter-TSS (NM_001159883)	59	NM_001159883	56812	Mm.489660	NM_020266	ENSMUSG00000026203	Dnajb2	2700059H22Rik|Dnajb10|Hsj1|mDj8	DnaJ heat shock protein family (Hsp40) member B2	protein-coding
mm_29696.1	chr3	123114474	123114495	-	1	NA	exon (NM_080451, exon 4 of 5)	exon (NM_080451, exon 4 of 5)	-79497	NM_021503	59006	Mm.141157	NM_021503	ENSMUSG00000028116	Myoz2	1110012I24Rik|Fatz-2|Myozl2	myozenin 2	protein-coding
mm_114339.1	chr13	60751813	60751828	+	1	NA	intron (NM_029653, intron 22 of 25)	intron (NM_029653, intron 22 of 25)	34544	NM_199148	218275	Mm.222427	NM_199148	ENSMUSG00000042243	BC051665	-	cDNA sequence BC051665	protein-coding
mm_100412.1	chr11	119426060	119426070	+	1	NA	Intergenic	Intergenic	35593	NR_035453	100316690		NR_035453	ENSMUSG00000088015	Mir1932	mir-1932|mmu-mir-1932	microRNA 1932	ncRNA
mm_55329.1	chr6	55681331	55681341	-	1	NA	promoter-TSS (NM_009717)	promoter-TSS (NM_009717)	-73	NM_009717	11922	Mm.5106	NM_009717	ENSMUSG00000037984	Neurod6	Atoh2|Math-2|Math2|Nex|Nex1m|bHLHa2	neurogenic differentiation 6	protein-coding
mm_12870.1	chr2	83851070	83851072	+	1	NA	intron (NM_175514, intron 1 of 7)	intron (NM_175514, intron 1 of 7)	38343	NM_175514	241520	Mm.330351	NM_175514	ENSMUSG00000048388	Fam171b	D430039N05Rik	family with sequence similarity 171, member B	protein-coding
mm_60150.1	chr7	38271386	38271418	+	1	NA	promoter-TSS (NM_025390)	promoter-TSS (NM_025390)	-54	NM_025390	66161	Mm.22284	NM_025390	ENSMUSG00000030423	Pop4	1110023P21Rik|Rpp29	processing of precursor 4, ribonuclease P/MRP family, (S. cerevisiae)	protein-coding
mm_125035.1	chr15	25758756	25758776	+	1	NA	intron (NM_019472, intron 19 of 40)	intron (NM_019472, intron 19 of 40)	-84532	NM_001034851	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_80717.1	chr9	92275787	92275795	+	1	NA	5' UTR (NM_001195084, exon 1 of 8)	5' UTR (NM_001195084, exon 1 of 8)	189	NM_001195084	18828	Mm.10306	NM_008880	ENSMUSG00000032372	Plscr2	-	phospholipid scramblase 2	protein-coding
mm_60480.1	chr7	44478376	44478378	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-6140	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_128686.1	chr15	60836318	60836319	-	1	NA	Intergenic	RLTR30D2_MM|LTR|ERV1	-11238	NM_001162926	399603	Mm.411968	NM_207269	ENSMUSG00000072568	Fam84b	BF642811|D330050I23Rik	family with sequence similarity 84, member B	protein-coding
mm_70367.1	chr8	9144601	9144641	+	1	NA	promoter-TSS (NR_073360)	promoter-TSS (NR_073360)	-48	NR_073360	74688	Mm.159298	NR_073360	ENSMUSG00000109215	4930453L07Rik	-	RIKEN cDNA 4930453L07 gene	ncRNA
mm_75546.1	chr8	57511514	57511532	-	1	NA	promoter-TSS (NM_008252)	promoter-TSS (NM_008252)	-320	NM_008252	97165	Mm.276881	NM_008252	ENSMUSG00000054717	Hmgb2	C80539|HMG-2|Hmg2	high mobility group box 2	protein-coding
mm_26959.1	chr3	21958744	21958762	-	1	NA	Intergenic	Intergenic	-117899	NM_030732	81004	Mm.202966	NM_030732	ENSMUSG00000027630	Tbl1xr1	8030499H02Rik|A630076E03Rik|AW539987|C21|C230089I12Rik|DC42|Ira1|TBLR1	transducin (beta)-like 1X-linked receptor 1	protein-coding
mm_42663.1	chr5	119670826	119670836	+	1	NA	promoter-TSS (NM_011535)	promoter-TSS (NM_011535)	-31	NM_198052	21386	Mm.219139	NM_011535	ENSMUSG00000018604	Tbx3	D5Ertd189e	T-box 3	protein-coding
mm_109222.1	chr12	108793018	108793044	+	1	NA	promoter-TSS (NM_009537)	promoter-TSS (NM_009537)	-280	NM_009537	22632	Mm.3868	NM_009537	ENSMUSG00000021264	Yy1	AW488674|NF-E1	YY1 transcription factor	protein-coding
mm_162031.1	chr19	53892278	53892278	+	1	NA	promoter-TSS (NM_011050)	promoter-TSS (NM_011050)	47	NM_011050	18569	Mm.1605	NM_011050	ENSMUSG00000024975	Pdcd4	D19Ucla1|Ma3|Tis	programmed cell death 4	protein-coding
mm_15733.1	chr2	164237175	164237185	+	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	1161	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_135422.1	chr16	45224530	45224534	-	1	NA	intron (NM_177584, intron 1 of 5)	intron (NM_177584, intron 1 of 5)	195	NM_177584	208154	Mm.38199	NM_177584	ENSMUSG00000052013	Btla	A630002H24	B and T lymphocyte associated	protein-coding
mm_108580.1	chr12	85029954	85029956	+	1	NA	exon (NM_178363, exon 5 of 21)	exon (NM_178363, exon 5 of 21)	33634	NM_178363	56531	Mm.153183	NM_178363	ENSMUSG00000021244	Ylpm1	A930013E17Rik|ZAP|Zap3	YLP motif containing 1	protein-coding
mm_124090.1	chr14	79135174	79135177	-	1	NA	intron (NM_027906, intron 37 of 44)	intron (NM_027906, intron 37 of 44)	112192	NM_001033215	105590	Mm.486536	NM_001033215	ENSMUSG00000071262	Zfp957	AU017455	zinc finger protein 957	protein-coding
mm_169717.1	chr15	77775125	77775142	-	1	NA	exon (NM_022410, exon 22 of 41)	exon (NM_022410, exon 22 of 41)	-19904	NM_001081970	239552	Mm.125650	NM_001081970	ENSMUSG00000056656	Apol8	9830006J20Rik|APOL-II|Apol2	apolipoprotein L 8	protein-coding
mm_22675.1	chr3	14970279	14970285	+	1	NA	promoter-TSS (NR_040549)	promoter-TSS (NR_040549)	-919	NR_040549	77127	Mm.195792	NR_040549	ENSMUSG00000098008	A930001A20Rik	-	RIKEN cDNA A930001A20 gene	ncRNA
mm_123799.1	chr14	70520162	70520172	-	1	NA	promoter-TSS (NM_009755)	promoter-TSS (NM_009755)	93	NM_009755	12153	Mm.27757	NM_009755	ENSMUSG00000022098	Bmp1	Pcp|Tld	bone morphogenetic protein 1	protein-coding
mm_162722.1	chr10	37136130	37136136	-	1	NA	exon (NM_008538, exon 2 of 2)	exon (NM_008538, exon 2 of 2)	2793	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_25444.1	chr3	108257161	108257171	+	1	NA	5' UTR (NM_011967, exon 1 of 9)	5' UTR (NM_011967, exon 1 of 9)	240	NM_011967	26442	Mm.208883	NM_011967	ENSMUSG00000068749	Psma5	ZETA	proteasome (prosome, macropain) subunit, alpha type 5	protein-coding
mm_134267.1	chr16	13903000	13903014	-	1	NA	promoter-TSS (NM_001289562)	promoter-TSS (NM_001289562)	138	NM_001039533	94184	Mm.171484	NM_053181	ENSMUSG00000022680	Pdxdc1	2210010A19Rik|AA415817|Kiaa0251-hp	pyridoxal-dependent decarboxylase domain containing 1	protein-coding
mm_69125.1	chr7	127026486	127026496	-	1	NA	promoter-TSS (NM_010772)	promoter-TSS (NM_010772)	-12	NM_010772	17188	Mm.378964	NM_010772	ENSMUSG00000030678	Maz	MAZI|PUR1|Pur-1|SAF-1|SAF-2	MYC-associated zinc finger protein (purine-binding transcription factor)	protein-coding
mm_22778.1	chr3	20308400	20308420	+	1	NA	Intergenic	Intergenic	-32677	NM_029706	76703	Mm.34692	NM_029706	ENSMUSG00000011463	Cpb1	0910001A18Rik|1810063F02Rik|2210008M23Rik|AI504870	carboxypeptidase B1 (tissue)	protein-coding
mm_9379.1	chr1	172210409	172210419	-	1	NA	exon (NM_009813, exon 11 of 11)	exon (NM_009813, exon 11 of 11)	-3610	NM_011063	18611	Mm.544	NM_011063	ENSMUSG00000013698	Pea15a	Mat1|PEA-15|Pea15|Pkcs15	phosphoprotein enriched in astrocytes 15A	protein-coding
mm_18503.1	chr2	62610623	62610640	-	1	NA	exon (NM_027835, exon 7 of 16)	exon (NM_027835, exon 7 of 16)	35624	NM_027835	71586	Mm.136224	NM_027835	ENSMUSG00000026896	Ifih1	9130009C22Rik|Helicard|Hlcd|MDA5|RLR-2	interferon induced with helicase C domain 1	protein-coding
mm_101764.1	chr11	43682657	43682687	-	1	NA	intron (NM_027557, intron 1 of 1)	CpG	674	NM_001164231	70802	Mm.397449	NM_027557	ENSMUSG00000044950	Pwwp2a	4631424J17Rik|AI891583|AU024105|D930040F23Rik	PWWP domain containing 2A	protein-coding
mm_113097.1	chr13	24373512	24373517	+	1	NA	intron (NM_001284519, intron 2 of 17)	RMER17C|LTR|ERVK	-41608	NM_007717	12763	Mm.8396	NM_007717	ENSMUSG00000016756	Cmah	-	cytidine monophospho-N-acetylneuraminic acid hydroxylase	protein-coding
mm_21930.1	chr2	167044192	167044215	-	1	NA	promoter-TSS (NM_001291162)	promoter-TSS (NM_001291162)	-708	NM_001291162	98999	Mm.297074	NM_001033196	ENSMUSG00000039501	Znfx1	AI481105|Astx3	zinc finger, NFX1-type containing 1	protein-coding
mm_3869.1	chr1	160989545	160989561	+	1	NA	exon (NM_080844, exon 3 of 8)	exon (NM_080844, exon 3 of 8)	10947	NM_080844	11905	Mm.260770	NM_080844	ENSMUSG00000026715	Serpinc1	AI114908|ATIII|At-3|At3	serine (or cysteine) peptidase inhibitor, clade C (antithrombin), member 1	protein-coding
mm_166829.1	chr7	18647047	18647049	-	1	NA	3' UTR (NM_027403, exon 5 of 5)	3' UTR (NM_027403, exon 5 of 5)	9677	NM_027403	72242	Mm.326858	NM_027403	ENSMUSG00000070796	Psg21	1600019C01Rik|1600025N01Rik|1600026N13Rik|cea8	pregnancy-specific glycoprotein 21	protein-coding
mm_92226.1	chr10	68358438	68358469	-	1	NA	Intergenic	MTC|LTR|ERVL-MaLR	-37311	NR_045357	75148	Mm.23505	NR_045357		4930545H06Rik	-	RIKEN cDNA 4930545H06 gene	ncRNA
mm_172629.1	chr8	20410451	20410456	-	1	NA	non-coding (NR_028428, exon 2 of 6)	non-coding (NR_028428, exon 2 of 6)	14361	NR_028428	381598	Mm.359054	NM_001024708	ENSMUSG00000071793	2610005L07Rik	2810038F24Rik|6720476A01Rik	cadherin 11 pseudogene	pseudo
mm_51951.1	chr6	91739228	91739231	+	1	NA	intron (NM_009320, intron 6 of 14)	B3|SINE|B2	55162	NM_009320	21366	Mm.395650	NM_009320	ENSMUSG00000030096	Slc6a6	AA589629|C80501|Taut	solute carrier family 6 (neurotransmitter transporter, taurine), member 6	protein-coding
mm_117686.1	chr13	94258687	94258706	-	1	NA	intron (NM_001346609, intron 1 of 8)	L1MA4|LINE|L1	26585	NM_029153	107767	Mm.201455	NM_029153	ENSMUSG00000021687	Scamp1	4930505M11Rik|AI415563|AW122395	secretory carrier membrane protein 1	protein-coding
mm_141647.1	chr17	33649717	33649735	-	1	NA	exon (NM_001109913, exon 15 of 17)	exon (NM_001109913, exon 15 of 17)	11631	NR_028279	378460	Mm.272606	NM_001002842	ENSMUSG00000032739	Pram1	AY665714	PML-RAR alpha-regulated adaptor molecule 1	protein-coding
mm_111910.1	chr12	108792688	108792748	-	1	NA	promoter-TSS (NM_009537)	promoter-TSS (NM_009537)	-593	NM_009537	22632	Mm.3868	NM_009537	ENSMUSG00000021264	Yy1	AW488674|NF-E1	YY1 transcription factor	protein-coding
mm_9346.1	chr1	172066598	172066615	-	1	NA	3' UTR (NM_021607, exon 17 of 17)	3' UTR (NM_021607, exon 17 of 17)	-9010	NM_010916	18071	Mm.2474	NM_010916	ENSMUSG00000051251	Nhlh1	Hen1|Nscl|Tal2|bHLHa35	nescient helix loop helix 1	protein-coding
mm_144816.1	chr18	36288111	36288123	+	1	NA	exon (NM_008989, exon 2 of 2)	exon (NM_008989, exon 2 of 2)	6955	NM_008989	19290	Mm.231802	NM_008989	ENSMUSG00000043991	Pura	CAGER-1|Pur-alpha|ssCRE-BP	purine rich element binding protein A	protein-coding
mm_162294.1	chr1	31149893	31149896	-	1	NA	intron (NR_033445, intron 2 of 2)	intron (NR_033445, intron 2 of 2)	-26541	NM_153601	266744	Mm.389093	NM_153601	ENSMUSG00000050217	Lgsn	Gluld1|Lgs|lengsin	lengsin, lens protein with glutamine synthetase domain	protein-coding
mm_145853.1	chr18	65453994	65454010	+	1	NA	intron (NM_172833, intron 8 of 15)	intron (NM_172833, intron 8 of 15)	23005	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_144987.1	chr18	38250307	38250317	+	1	NA	promoter-TSS (NM_024179)	promoter-TSS (NM_024179)	63	NM_024179	66839	Mm.281086	NM_024179	ENSMUSG00000024442	0610009O20Rik	2700004E22Rik|Dele|Kiaa0141	RIKEN cDNA 0610009O20 gene	protein-coding
mm_107124.1	chr12	19954200	19954203	+	1	NA	Intergenic	CpG	861578	NR_015521	69513	Mm.273972	NR_015521	ENSMUSG00000099759	1700030C10Rik	-	RIKEN cDNA 1700030C10 gene	ncRNA
mm_80689.1	chr9	91378575	91378582	+	1	NA	intron (NM_009576, intron 2 of 4)	CpG	9606	NM_009576	22774	Mm.8062	NM_009576	ENSMUSG00000036972	Zic4	-	zinc finger protein of the cerebellum 4	protein-coding
mm_27651.1	chr3	63964558	63964570	-	1	NA	5' UTR (NM_001272035, exon 1 of 7)	5' UTR (NM_001272035, exon 1 of 7)	169	NM_001331067	11416	Mm.135619	NM_015728	ENSMUSG00000027822	Slc33a1	AI315656|AI788741|Acatn|D630022N01Rik	solute carrier family 33 (acetyl-CoA transporter), member 1	protein-coding
mm_6179.1	chr1	65103008	65103023	-	1	NA	exon (NM_007774, exon 2 of 3)	exon (NM_007774, exon 2 of 3)	348	NM_007774	12964	Mm.26904	NM_007774	ENSMUSG00000044429	Cryga	Cryg-4|DGcry-4	crystallin, gamma A	protein-coding
mm_70644.1	chr8	14095982	14095993	+	1	NA	5' UTR (NM_001145965, exon 1 of 15)	5' UTR (NM_001145965, exon 1 of 15)	112	NM_172910	244310	Mm.404697	NM_172910	ENSMUSG00000047495	Dlgap2	6430596N04Rik|Dap-2|Dap2|Sapap2	discs, large (Drosophila) homolog-associated protein 2	protein-coding
mm_2562.1	chr1	115923978	115923983	+	1	NA	intron (NM_001077425, intron 3 of 23)	intron (NM_001077425, intron 3 of 23)	238843	NM_001077425	636808	Mm.101576	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding
mm_45461.1	chr5	67815853	67815859	-	1	NA	intron (NM_001284345, intron 1 of 36)	intron (NM_001284345, intron 1 of 36)	31575	NM_009727	11980	Mm.153230	NM_009727	ENSMUSG00000037685	Atp8a1	AI481521|AI853962|APLT|AW743152|AW822227|Atp3a2|B230107D19Rik|ClassI	ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1	protein-coding
mm_70724.1	chr8	18500724	18500726	+	1	NA	Intergenic	U2|snRNA|snRNA	-94448	NM_173189	244329	Mm.235296	NM_173189	ENSMUSG00000039842	Mcph1	5430437K10Rik|BRIT1|D030046N04Rik|MCT	microcephaly, primary autosomal recessive 1	protein-coding
mm_154760.1	chrX	12005759	12005788	+	1	NA	Intergenic	Intergenic	74780	NM_175045	71458	Mm.196328	NM_029510	ENSMUSG00000040363	Bcor	2900008C10Rik|5830466J11Rik|8430401K06Rik|BcorR|D930024N20Rik|mKIAA1575	BCL6 interacting corepressor	protein-coding
mm_172217.1	chr6	6351564	6351569	-	1	NA	intron (NR_136905, intron 3 of 3)	(CCA)n|Simple_repeat|Simple_repeat	102907	NR_136905	101056138	Mm.389085	NR_136904	ENSMUSG00000093482	Gm20619	-	predicted gene 20619	ncRNA
mm_44067.1	chr5	148489572	148489584	+	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	63210	NM_011908	24109	Mm.21846	NM_011908	ENSMUSG00000001687	Ubl3	AW108023|HCG	ubiquitin-like 3	protein-coding
mm_38819.1	chr4	148626757	148626775	-	1	NA	non-coding (NR_131120, exon 1 of 8)	non-coding (NR_131120, exon 1 of 8)	230	NR_027864	230908	Mm.22453	NM_145556	ENSMUSG00000041459	Tardbp	1190002A23Rik|C85084|TDP-43|Tdp43	TAR DNA binding protein	protein-coding
mm_151753.1	chr19	5098252	5098275	-	1	NA	TTS (NM_029576)	TTS (NM_029576)	258	NM_001302333	12794	Mm.299737	NM_009920	ENSMUSG00000024873	Cnih2	CNIH-2|Cnil	cornichon family AMPA receptor auxiliary protein 2	protein-coding
mm_114511.1	chr13	72628787	72628795	+	1	NA	promoter-TSS (NR_030701)	promoter-TSS (NR_030701)	-6	NM_010574	16372	Mm.28888	NM_010574	ENSMUSG00000001504	Irx2	-	Iroquois related homeobox 2 (Drosophila)	protein-coding
mm_23972.1	chr3	85608324	85608336	+	1	NA	intron (NM_144896, intron 5 of 12)	intron (NM_144896, intron 5 of 12)	34201	NM_144896	229487	Mm.52275	NM_144896	ENSMUSG00000028085	Gatb	9430026F02Rik|Pet112|Pet112l	glutamyl-tRNA(Gln) amidotransferase, subunit B	protein-coding
mm_8570.1	chr1	155527134	155527155	-	1	NA	promoter-TSS (NR_132128)	promoter-TSS (NR_132128)	-33	NR_132128	433367	Mm.359304	NR_132128	ENSMUSG00000073535	Gm5532	EG433367	predicted gene 5532	ncRNA
mm_70842.1	chr8	23411928	23411941	+	1	NA	exon (NM_013834, exon 1 of 3)	exon (NM_013834, exon 1 of 3)	432	NM_013834	20377	Mm.281691	NM_013834	ENSMUSG00000031548	Sfrp1	2210415K03Rik|AW011917|AW107218|AW742929|sFRP-1	secreted frizzled-related protein 1	protein-coding
mm_104041.1	chr11	86306439	86306443	-	1	NA	intron (NM_001080931, intron 11 of 29)	intron (NM_001080931, intron 11 of 29)	-48873	NM_027421	70422	Mm.171304	NM_027421	ENSMUSG00000018068	Ints2	2810417D08Rik|AA408260|AI987735|mKIAA1287	integrator complex subunit 2	protein-coding
mm_90057.1	chr10	116187686	116187688	+	1	NA	intron (NM_011217, intron 5 of 13)	intron (NM_011217, intron 5 of 13)	10336	NM_001161840	19279	Mm.336316	NM_011217	ENSMUSG00000020151	Ptprr	Gmcp1|PTP-SL|PTPBR7|RPTPRR|mPTP213	protein tyrosine phosphatase, receptor type, R	protein-coding
mm_48623.1	chr5	145128056	145128059	-	1	NA	TTS (NM_001033313)	TTS (NM_001033313)	12032	NM_001033313	231887	Mm.188851	NM_001033313	ENSMUSG00000029623	Pdap1	HASPP28|PAP|PAP1	PDGFA associated protein 1	protein-coding
mm_157615.1	chrX	53778351	53778386	-	1	NA	exon (NM_001291748, exon 8 of 8)	exon (NM_001291748, exon 8 of 8)	-1974	NM_001009549	333473	Mm.327378	NM_001009549	ENSMUSG00000059334	Zfp36l3	AY661338	zinc finger protein 36, C3H type-like 3	protein-coding
mm_49766.1	chr6	34863115	34863120	+	1	NA	promoter-TSS (NM_197986)	promoter-TSS (NM_197986)	-29	NM_197986	68487	Mm.248440	NM_197986	ENSMUSG00000057137	Tmem140	1110007F12Rik	transmembrane protein 140	protein-coding
mm_25961.1	chr3	132629945	132629963	+	1	NA	promoter-TSS (NM_001270430)	promoter-TSS (NM_001270430)	-237	NM_001270430	433653		NM_001270430	ENSMUSG00000091721	Gimd1	EG433653|Gm5549	GIMAP family P-loop NTPase domain containing 1	protein-coding
mm_138527.1	chr17	35242344	35242355	+	1	NA	promoter-TSS (NM_001252457)	promoter-TSS (NM_001252457)	-468	NM_001252457	53817	Mm.439827	NM_019693	ENSMUSG00000019432	Ddx39b	0610030D10Rik|AI428441|Bat-1|Bat1|Bat1a|D17H6S81E|D17H6S81E-1|D6S81Eh	DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B	protein-coding
mm_86828.1	chr10	21161069	21161087	+	1	NA	promoter-TSS (NM_001198914)	promoter-TSS (NM_001198914)	-94	NM_010848	17863	Mm.52109	NM_010848	ENSMUSG00000019982	Myb	AI550390|M16449|c-myb	myeloblastosis oncogene	protein-coding
mm_45375.1	chr5	66052754	66052775	-	1	NA	intron (NM_178446, intron 2 of 6)	intron (NM_178446, intron 2 of 6)	45415	NM_139065	245945	Mm.36863	NM_139065	ENSMUSG00000070780	Rbm47	9530077J19Rik	RNA binding motif protein 47	protein-coding
mm_31556.1	chr4	57346674	57346679	+	1	NA	Intergenic	Intergenic	17616	NR_038179	73349	Mm.393774	NR_038178		1700042G15Rik	-	RIKEN cDNA 1700042G15 gene	ncRNA
mm_121945.1	chr14	24082017	24082024	-	1	NA	Intergenic	Intergenic	-6857	NR_106069	102465697		NR_106069	ENSMUSG00000105723	Mir7210	mir-7210|mmu-mir-7210	microRNA 7210	ncRNA
mm_39039.1	chr4	152319001	152319014	-	1	NA	promoter-TSS (NM_001033489)	promoter-TSS (NM_001033489)	-382	NM_001033489	433809	Mm.156205	NM_001033489	ENSMUSG00000058498	Rnf207	D330010C22Rik|Gm143	ring finger protein 207	protein-coding
mm_85220.1	chr9	97018745	97018761	-	1	NA	promoter-TSS (NM_145134)	promoter-TSS (NM_145134)	-398	NM_145134	211949	Mm.491271	NM_145134	ENSMUSG00000046997	Spsb4	D030068E18Rik|SSB-4|Ssb4	splA/ryanodine receptor domain and SOCS box containing 4	protein-coding
mm_63718.1	chr7	130774187	130774193	+	1	NA	5' UTR (NM_001081038, exon 1 of 16)	5' UTR (NM_001081038, exon 1 of 16)	121	NM_001081038	330660	Mm.271550	NM_001081038	ENSMUSG00000040298	Btbd16	E330040A16Rik	BTB (POZ) domain containing 16	protein-coding
mm_149775.1	chr19	23093897	23093919	+	1	NA	Intergenic	MTC|LTR|ERVL-MaLR	-47318	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_101547.1	chr11	33578860	33578863	-	1	NA	promoter-TSS (NM_146017)	promoter-TSS (NM_146017)	96	NM_146017	216643	Mm.99989	NM_146017	ENSMUSG00000020159	Gabrp	-	gamma-aminobutyric acid (GABA) A receptor, pi	protein-coding
mm_74166.1	chr8	123418146	123418156	+	1	NA	exon (NM_023279, exon 2 of 4)	exon (NM_023279, exon 2 of 4)	6587	NM_023279	22152	Mm.40068	NM_023279	ENSMUSG00000062380	Tubb3	3200002H15Rik|M(beta)3|M(beta)6	tubulin, beta 3 class III	protein-coding
mm_152746.1	chr19	19099774	19099777	-	1	NA	intron (NM_001043354, intron 1 of 9)	intron (NM_001043354, intron 1 of 9)	11421	NM_001043354	225998	Mm.234641	NM_146095	ENSMUSG00000036192	Rorb	Nr1f2|RZR-beta|RZRB|Rorbeta|hstp	RAR-related orphan receptor beta	protein-coding
mm_3221.1	chr1	135847703	135847736	+	1	NA	exon (NM_001130176, exon 6 of 13)	exon (NM_001130176, exon 6 of 13)	6858	NM_001130176	21956	Mm.247470	NM_011619	ENSMUSG00000026414	Tnnt2	Tnt|cTnT	troponin T2, cardiac	protein-coding
mm_121063.1	chr14	90556679	90556708	+	1	NA	Intergenic	(CTAG)n|Simple_repeat|Simple_repeat	429802	NR_045712	74967	Mm.390704	NR_045712		4930474H20Rik	-	RIKEN cDNA 4930474H20 gene	ncRNA
mm_4694.1	chr1	180733167	180733190	+	1	NA	exon (NM_133225, exon 2 of 8)	exon (NM_133225, exon 2 of 8)	7135	NM_133225	170760	Mm.272981	NM_133225	ENSMUSG00000026499	Acbd3	60kDa|8430407O11Rik|D1Ertd10e|GCP60|GOLPH1|Gocap1|Pap7	acyl-Coenzyme A binding domain containing 3	protein-coding
mm_70763.1	chr8	21734491	21734496	+	1	NA	promoter-TSS (NM_007852)	promoter-TSS (NM_007852)	-1	NM_001024225	503491	Mm.443396	NM_001024225	ENSMUSG00000064213	Defa24	Defcr24	defensin, alpha, 24	protein-coding
mm_18445.1	chr2	60905375	60905377	-	1	NA	intron (NM_020296, intron 1 of 13)	intron (NM_020296, intron 1 of 13)	-23938	NM_001141931	56878	Mm.259667	NM_020296	ENSMUSG00000026970	Rbms1	2600014B10Rik|AI255215|MSSP-1|MSSP-2|MSSP-3|YC1	RNA binding motif, single stranded interacting protein 1	protein-coding
mm_52429.1	chr6	113483450	113483473	+	1	NA	promoter-TSS (NM_133930)	promoter-TSS (NM_133930)	-108	NM_133930	171508	Mm.41593	NM_133930	ENSMUSG00000030284	Creld1	AI843811	cysteine-rich with EGF-like domains 1	protein-coding
mm_38294.1	chr4	136892862	136892864	-	1	NA	promoter-TSS (NM_007574)	promoter-TSS (NM_007574)	51	NM_007574	12262	Mm.439732	NM_007574	ENSMUSG00000036896	C1qc	AI385742|C1qg|Ciqc	complement component 1, q subcomponent, C chain	protein-coding
mm_141182.1	chr17	26939084	26939108	-	1	NA	intron (NM_026948, intron 1 of 5)	intron (NM_026948, intron 1 of 5)	362	NR_104458	67675	Mm.439919	NM_026307	ENSMUSG00000024194	Cuta	0610039D01Rik|1810022E02Rik|1810060C03Rik|2700094G22Rik|AI326454	cutA divalent cation tolerance homolog	protein-coding
mm_1153.1	chr1	60811511	60811512	+	1	NA	Intergenic	ORR1B1-int|LTR|ERVL-MaLR	65123	NM_007642	12487	Mm.255003	NM_007642	ENSMUSG00000026012	Cd28	-	CD28 antigen	protein-coding
mm_137498.1	chr17	26971976	26971978	+	1	NA	Intergenic	Intergenic	-1202	NM_001005916	474156	Mm.328890	NM_001005916	ENSMUSG00000079605	Zbtb9	3930402F13Rik	zinc finger and BTB domain containing 9	protein-coding
mm_89346.1	chr10	88135903	88135924	+	1	NA	intron (NM_029249, intron 3 of 10)	intron (NM_029249, intron 3 of 10)	11028	NM_029249	75317	Mm.179378	NM_029249	ENSMUSG00000035365	Parpbp	4930547N16Rik|AI503644|PARI	PARP1 binding protein	protein-coding
mm_69749.1	chr7	140955916	140955926	-	1	NA	promoter-TSS (NM_030694)	promoter-TSS (NM_030694)	40	NM_030694	80876	Mm.379266	NM_030694	ENSMUSG00000060591	Ifitm2	DSPA2c|Ifitm3l|fragilis3|mil-3	interferon induced transmembrane protein 2	protein-coding
mm_161040.1	chr12	32378856	32378856	+	1	NA	promoter-TSS (NM_001162903)	promoter-TSS (NM_001162903)	67	NM_001162903	72123	Mm.341352	NM_028111	ENSMUSG00000090946	Ccdc71l	2010109K11Rik|AV375874	coiled-coil domain containing 71 like	protein-coding
mm_2461.1	chr1	105356718	105356768	+	1	NA	promoter-TSS (NM_001160368)	promoter-TSS (NM_001160368)	-33	NM_001160368	320311	Mm.389162	NM_178779	ENSMUSG00000047496	Rnf152	A930029B02Rik	ring finger protein 152	protein-coding
mm_32165.1	chr4	100145076	100145081	+	1	NA	intron (NM_001312690, intron 1 of 3)	intron (NM_001312690, intron 1 of 3)	49287	NM_001312690	26563	Mm.57252	NM_013845	ENSMUSG00000035305	Ror1	2810404D04Rik|Ntrkr1	receptor tyrosine kinase-like orphan receptor 1	protein-coding
mm_153457.1	chr19	41214355	41214368	-	1	NA	3' UTR (NM_133352, exon 15 of 15)	3' UTR (NM_133352, exon 15 of 15)	-7587	NM_011904	24087	Mm.89983	NM_011904	ENSMUSG00000025013	Tll2	-	tolloid-like 2	protein-coding
mm_48082.1	chr5	136883221	136883232	-	1	NA	promoter-TSS (NM_024474)	promoter-TSS (NM_024474)	-11	NM_001346699	140709	Mm.295020	NM_024474	ENSMUSG00000004415	Col26a1	9430032K24Rik|BC002218|Col26a|Emid2|Emu2	collagen, type XXVI, alpha 1	protein-coding
mm_19835.1	chr2	112367959	112368017	-	1	NA	promoter-TSS (NM_026519)	promoter-TSS (NM_026519)	39	NM_026519	68032	Mm.220942	NM_026519	ENSMUSG00000027131	Emc4	2610318K02Rik|Tmem85	ER membrane protein complex subunit 4	protein-coding
mm_120702.1	chr14	70965544	70965568	+	1	NA	intron (NM_001302094, intron 3 of 7)	intron (NM_001302094, intron 3 of 7)	75449	NM_001302094	14586	Mm.32619	NM_008115	ENSMUSG00000022103	Gfra2	-	glial cell line derived neurotrophic factor family receptor alpha 2	protein-coding
mm_107771.1	chr12	59131474	59131495	+	1	NA	promoter-TSS (NM_001165253)	promoter-TSS (NM_001165253)	31	NM_001165253	338320	Mm.213215	NM_146034	ENSMUSG00000021000	Mia2	Ctage5|D12Bwg0579e|Mea6|Mgea|Mgea6	melanoma inhibitory activity 2	protein-coding
mm_55631.1	chr6	72314769	72314775	-	1	NA	TTS (NM_001282071)	TTS (NM_001282071)	10162	NM_147779	20388	Mm.46033	NM_147779	ENSMUSG00000056370	Sftpb	AI562151|SF-B|SP-B|Sftp-3|Sftp3	surfactant associated protein B	protein-coding
mm_123087.1	chr14	55758309	55758313	-	1	NA	5' UTR (NM_009894, exon 1 of 5)	5' UTR (NM_009894, exon 1 of 5)	113	NM_009894	12684	Mm.466766	NM_009894	ENSMUSG00000022219	Cideb	1110030C18Rik|AI790179|CIDE-B	cell death-inducing DNA fragmentation factor, alpha subunit-like effector B	protein-coding
mm_99093.1	chr11	99865095	99865109	+	1	NA	exon (NM_001177484, exon 1 of 1)	exon (NM_001177484, exon 1 of 1)	626	NM_001177484	100415785	Mm.380213	NM_001177484	ENSMUSG00000090225	Gm11559	OTTMUSG00000002191	predicted gene 11559	protein-coding
mm_64619.1	chr7	3629578	3629616	-	1	NA	promoter-TSS (NM_027328)	promoter-TSS (NM_027328)	332	NM_023524	69714	Mm.358730	NM_023524	ENSMUSG00000006335	Tfpt	2400004F01Rik|AI450389|Amida|FB1	TCF3 (E2A) fusion partner	protein-coding
mm_122168.1	chr14	31436029	31436109	-	1	NA	promoter-TSS (NM_011894)	promoter-TSS (NM_011894)	31	NM_011894	24056	Mm.383198	NM_011894	ENSMUSG00000021892	Sh3bp5	AI606498|SH3BP-5|Sab	SH3-domain binding protein 5 (BTK-associated)	protein-coding
mm_117671.1	chr13	93637586	93637621	-	1	NA	5' UTR (NM_016668, exon 1 of 8)	5' UTR (NM_016668, exon 1 of 8)	155	NM_016668	12116	Mm.329582	NM_016668	ENSMUSG00000074768	Bhmt	-	betaine-homocysteine methyltransferase	protein-coding
mm_28888.1	chr3	97868243	97868261	-	1	NA	intron (NM_001039376, intron 1 of 46)	CpG	20455	NM_001289702	83679	Mm.129840	NM_031401	ENSMUSG00000038170	Pde4dip	4732458A06Rik|9430063L05Rik|C87016|D130016K21Rik|D3Bwg1078e|Usmg4|mKIAA0454	phosphodiesterase 4D interacting protein (myomegalin)	protein-coding
mm_26992.1	chr3	25749075	25749076	-	1	NA	intron (NM_001163387, intron 3 of 5)	intron (NM_001163387, intron 3 of 5)	404232	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_15632.1	chr2	162987520	162987537	+	1	NA	promoter-TSS (NM_013731)	promoter-TSS (NM_013731)	47	NM_013731	27219	Mm.26462	NM_013731	ENSMUSG00000017868	Sgk2	AI098171|AW146006|Sgkl	serum/glucocorticoid regulated kinase 2	protein-coding
mm_167646.1	chr9	65141156	65141158	+	1	NA	promoter-TSS (NM_008988)	promoter-TSS (NM_008988)	-32	NM_008988	19289	Mm.41529	NM_008988	ENSMUSG00000032394	Igdcc3	2810401C09Rik|AI851425|Punc|WI-14920	immunoglobulin superfamily, DCC subclass, member 3	protein-coding
mm_56027.1	chr6	86607649	86607654	-	1	NA	Intergenic	Intergenic	-20523	NM_026414	67855	Mm.183043	NM_026414	ENSMUSG00000033508	Asprv1	2300003P22Rik|AA986851|SASP|SASPase|Taps	aspartic peptidase, retroviral-like 1	protein-coding
mm_39732.1	chr5	29195984	29196032	+	1	NA	promoter-TSS (NM_021470)	promoter-TSS (NM_021470)	15	NR_110371	56874	Mm.87352	NM_021470	ENSMUSG00000029130	Rnf32	1700009J01Rik|2700025B22Rik|4930542N22Rik|Lmbr2	ring finger protein 32	protein-coding
mm_123772.1	chr14	70279873	70279906	-	1	NA	intron (NM_001304991, intron 1 of 14)	intron (NM_001304991, intron 1 of 14)	9608	NM_008915	19057	Mm.439683	NM_008915	ENSMUSG00000022092	Ppp3cc	Calnc|PP2BA gamma	protein phosphatase 3, catalytic subunit, gamma isoform	protein-coding
mm_11806.1	chr2	43900199	43900210	+	1	NA	intron (NM_001301832, intron 7 of 14)	intron (NM_001301832, intron 7 of 14)	151380	NM_001301831	76117	Mm.217350	NM_153820	ENSMUSG00000049744	Arhgap15	5830480G12Rik	Rho GTPase activating protein 15	protein-coding
mm_24648.1	chr3	94387032	94387051	+	1	NA	intron (NR_121656, intron 1 of 9)	intron (NR_121656, intron 1 of 9)	9609	NR_121656	19885	Mm.4372	NM_011281	ENSMUSG00000028150	Rorc	Nr1f3|RORgamma|TOR|Thor	RAR-related orphan receptor gamma	protein-coding
mm_94813.1	chr11	23152084	23152086	+	1	NA	promoter-TSS (NR_131065)	promoter-TSS (NR_131065)	-55	NR_131065	76993	Mm.59224	NR_131065	ENSMUSG00000086366	1700061J23Rik	-	RIKEN cDNA 1700061J23 gene	ncRNA
mm_122560.1	chr14	49525714	49525732	-	1	NA	5' UTR (NM_029238, exon 1 of 8)	5' UTR (NM_029238, exon 1 of 8)	114	NM_029238	75288	Mm.78738	NM_029238	ENSMUSG00000021852	Slc35f4	4930550L21Rik	solute carrier family 35, member F4	protein-coding
mm_34838.1	chr4	155397040	155397051	+	1	NA	intron (NM_008072, intron 1 of 8)	intron (NM_008072, intron 1 of 8)	1024	NM_008072	14403	Mm.388925	NM_008072	ENSMUSG00000029054	Gabrd	AI853201	gamma-aminobutyric acid (GABA) A receptor, subunit delta	protein-coding
mm_148388.1	chr19	3384679	3384682	+	1	NA	3' UTR (NM_013495, exon 19 of 19)	3' UTR (NM_013495, exon 19 of 19)	-4177	NM_001039658	17771	Mm.209941	NM_010841	ENSMUSG00000024905	Mtl5	tesmin	metallothionein-like 5, testis-specific (tesmin)	protein-coding
mm_121220.1	chr14	103055003	103055015	+	1	NA	exon (NM_008392, exon 5 of 5)	exon (NM_008392, exon 5 of 5)	7997	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_26163.1	chr3	138277766	138277777	+	1	NA	intron (NM_007409, intron 1 of 8)	intron (NM_007409, intron 1 of 8)	126	NM_007409	11522	Mm.2409	NM_007409	ENSMUSG00000074207	Adh1	ADH-AA|AI194826|Adh-1|Adh-1-t|Adh-1e|Adh-1t|Adh-3e|Adh1-e|Adh1-t|Adh1tl|Adh3-e	alcohol dehydrogenase 1 (class I)	protein-coding
mm_22842.1	chr3	27961812	27961816	+	1	NA	intron (NM_001164056, intron 2 of 26)	B1_Mus2|SINE|Alu	-22357	NM_008875	18805	Mm.212039	NM_008875	ENSMUSG00000027695	Pld1	AA536939|C85393|Pld1a|Pld1b|mPLD1	phospholipase D1	protein-coding
mm_68309.1	chr7	105750267	105750300	-	1	NA	exon (NM_009906, exon 4 of 13)	exon (NM_009906, exon 4 of 13)	1952	NM_009906	12751	Mm.20837	NM_009906	ENSMUSG00000030894	Tpp1	Cln2|LPIC|TPP-1|TPP-I	tripeptidyl peptidase I	protein-coding
mm_121806.1	chr14	20269254	20269275	-	1	NA	promoter-TSS (NM_029006)	promoter-TSS (NM_029006)	-102	NM_029006	74571	Mm.105571	NM_029006	ENSMUSG00000023387	Kcnk16	4731413G05Rik|TALK-1|TALK1	potassium channel, subfamily K, member 16	protein-coding
mm_152922.1	chr19	28011097	28011132	-	1	NA	promoter-TSS (NM_011265)	promoter-TSS (NM_011265)	52	NM_011265	19726	Mm.313321	NM_011265	ENSMUSG00000040929	Rfx3	C230093O12Rik|MRFX3	regulatory factor X, 3 (influences HLA class II expression)	protein-coding
mm_163778.1	chr13	120044212	120044226	+	1	NA	intron (NM_001302966, intron 4 of 5)	(TC)n|Simple_repeat|Simple_repeat	7985	NM_001302966	100861753	Mm.165042	NM_001302966	ENSMUSG00000095609	Gm21188	-	predicted gene, 21188	protein-coding
mm_113557.1	chr13	38151372	38151393	+	1	NA	promoter-TSS (NM_023842)	promoter-TSS (NM_023842)	88	NM_023842	109620	Mm.355327	NM_023842	ENSMUSG00000054889	Dsp	2300002E22Rik|5730453H04Rik|AA407887|AA407888|AW109828|DP|rul	desmoplakin	protein-coding
mm_83078.1	chr9	39603609	39603632	-	1	NA	promoter-TSS (NM_001199556)	promoter-TSS (NM_001199556)	32	NM_001199556	244810	Mm.208855	NM_178737	ENSMUSG00000038112	AW551984	3222402N16	expressed sequence AW551984	protein-coding
mm_76078.1	chr8	79248840	79248842	-	1	NA	promoter-TSS (NM_026315)	promoter-TSS (NM_026315)	-258	NM_026315	67687	Mm.178707	NM_026315	ENSMUSG00000031682	1700011L22Rik	-	RIKEN cDNA 1700011L22 gene	protein-coding
mm_136444.1	chr16	94902293	94902295	-	1	NA	intron (NM_001025584, intron 2 of 4)	(A)n|Simple_repeat|Simple_repeat	-45604	NM_001025590	16522	Mm.328720	NM_010606	ENSMUSG00000043301	Kcnj6	BIR1|GIRK2|KATP2|KCNJ7|Kir3.2|weaver|wv	potassium inwardly-rectifying channel, subfamily J, member 6	protein-coding
mm_96380.1	chr11	67243224	67243226	+	1	NA	exon (NM_010855, exon 10 of 40)	exon (NM_010855, exon 10 of 40)	5413	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_4411.1	chr1	172492181	172492192	+	1	NA	exon (NM_001145800, exon 9 of 21)	exon (NM_001145800, exon 9 of 21)	-8060	NM_178598	21346	Mm.271711	NM_178598	ENSMUSG00000026547	Tagln2	2700094C18Rik|SM22beta|Sm22B|Sm22a	transgelin 2	protein-coding
mm_63074.1	chr7	122219408	122219416	+	1	NA	promoter-TSS (NM_027363)	promoter-TSS (NM_027363)	-84	NM_027363	70261	Mm.96997	NM_027363	ENSMUSG00000030865	Chp2	2010110P09Rik|Cbhp2	calcineurin-like EF hand protein 2	protein-coding
mm_63035.1	chr7	121074723	121074733	+	1	NA	promoter-TSS (NM_030691)	promoter-TSS (NM_030691)	-198	NM_030691	80719	Mm.160384	NM_030691	ENSMUSG00000035004	Igsf6	-	immunoglobulin superfamily, member 6	protein-coding
mm_86452.1	chr10	4339919	4339921	+	1	NA	intron (NM_031185, intron 2 of 3)	intron (NM_031185, intron 2 of 3)	48188	NM_001033466	381990	Mm.262466	NM_001033466	ENSMUSG00000075327	Zbtb2	Gm1103	zinc finger and BTB domain containing 2	protein-coding
mm_94391.1	chr11	5541873	5541893	+	1	NA	exon (NM_134033, exon 1 of 5)	exon (NM_134033, exon 1 of 5)	334	NM_134033	104479	Mm.210403	NM_134033	ENSMUSG00000020482	Ccdc117	1110004K02Rik|1700026O03Rik|AU018638|AU042822|AV173073|BC018601	coiled-coil domain containing 117	protein-coding
mm_157916.1	chrX	78552819	78552823	-	1	NA	intron (NM_027322, intron 1 of 3)	RLTR14-int|LTR|ERV1	30984	NM_001164275	546336	Mm.211712	NM_027322	ENSMUSG00000047996	Prrg1	2010007L08Rik	proline rich Gla (G-carboxyglutamic acid) 1	protein-coding
mm_62564.1	chr7	104218788	104218826	+	1	NA	promoter-TSS (NM_001013616)	promoter-TSS (NM_001013616)	12	NM_001013616	94088	Mm.274843	NM_001013616	ENSMUSG00000072244	Trim6	C430046K18Rik|D7Ertd684e	tripartite motif-containing 6	protein-coding
mm_149985.1	chr19	29250626	29250638	+	1	NA	Intergenic	Intergenic	-1171	NM_001048177	16452	Mm.275839	NM_008413	ENSMUSG00000024789	Jak2	Fd17	Janus kinase 2	protein-coding
mm_130998.1	chr15	103448456	103448464	-	1	NA	promoter-TSS (NM_177631)	promoter-TSS (NM_177631)	-1	NM_177631	223927	Mm.243718	NM_177631	ENSMUSG00000053508	BC048502	-	cDNA sequence BC048502	protein-coding
mm_107121.1	chr12	19175850	19175854	+	1	NA	Intergenic	CpG	661342	NM_001201330	236366	Mm.352227	NM_001033157	ENSMUSG00000073197	5730507C01Rik	-	RIKEN cDNA 5730507C01 gene	protein-coding
mm_58452.1	chr7	3330376	3330391	+	1	NA	3' UTR (NM_011102, exon 18 of 18)	3' UTR (NM_011102, exon 18 of 18)	-6202	NM_133189	81904	Mm.214994	NM_133189	ENSMUSG00000069806	Cacng7	-	calcium channel, voltage-dependent, gamma subunit 7	protein-coding
mm_22808.1	chr3	27154033	27154060	+	1	NA	promoter-TSS (NM_001177626)	promoter-TSS (NM_001177626)	20	NR_040548	76657	Mm.417839	NR_040548	ENSMUSG00000097584	1700125G22Rik	-	RIKEN cDNA 1700125G22 gene	ncRNA
mm_129683.1	chr15	81408253	81408257	-	1	NA	promoter-TSS (NM_021317)	promoter-TSS (NM_021317)	18	NM_021317	57755	Mm.440590	NM_021317	ENSMUSG00000047108	Dnajb7	4933424H20Rik|Dj5|mDj5	DnaJ heat shock protein family (Hsp40) member B7	protein-coding
mm_87050.1	chr10	28809043	28809053	+	1	NA	intron (NM_001305663, intron 5 of 5)	L1M4|LINE|L1	114459	NR_033601	114676	Mm.390292	NR_033601		4930519F09Rik	-	pyruvate dehydrogenase E1 alpha 1 pseudogene	pseudo
mm_162547.1	chr1	170709795	170709805	+	1	NA	3' UTR (NM_001081304, exon 16 of 16)	3' UTR (NM_001081304, exon 16 of 16)	65268	NM_177068	320078	Mm.287131	NM_177068	ENSMUSG00000038463	Olfml2b	1110018N05Rik|4832415H08Rik|AI467542	olfactomedin-like 2B	protein-coding
mm_69515.1	chr7	134938265	134938313	-	1	NA	5' UTR (NM_001143802, exon 1 of 4)	5' UTR (NM_001143802, exon 1 of 4)	141	NM_001143802	627214	Mm.323610	NM_001143802	ENSMUSG00000073805	Fam196a	B830028B13Rik	family with sequence similarity 196, member A	protein-coding
mm_172354.1	chr7	114706207	114706208	-	1	NA	Intergenic	Intergenic	-12436	NM_054084	116903	Mm.273838	NM_054084	ENSMUSG00000030666	Calcb	CGRP2|Calc2	calcitonin-related polypeptide, beta	protein-coding
mm_168032.1	chrY	90738617	90738629	+	1	NA	Intergenic	IMPB_01|Satellite|Satellite	16427	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_29929.1	chr3	131491387	131491398	-	1	NA	Intergenic	Intergenic	-73376	NM_001289479	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_93016.1	chr10	87493652	87493666	-	1	NA	promoter-TSS (NM_008553)	promoter-TSS (NM_008553)	1	NM_008553	17172	Mm.136217	NM_008553	ENSMUSG00000020052	Ascl1	AI225900|ASH1|Mash1|bHLHa46	achaete-scute family bHLH transcription factor 1	protein-coding
mm_141482.1	chr17	31199009	31199012	-	1	NA	promoter-TSS (NM_001163776)	promoter-TSS (NM_001163776)	-36	NM_001163776	140765	Mm.214638	NM_080727	ENSMUSG00000024034	Tmprss3	-	transmembrane protease, serine 3	protein-coding
mm_20234.1	chr2	126151957	126151961	-	1	NA	promoter-TSS (NM_026981)	promoter-TSS (NM_026981)	45	NM_029455	75823	Mm.444732	NM_029455	ENSMUSG00000027209	Fam227b	4930525F21Rik	family with sequence similarity 227, member B	protein-coding
mm_64326.1	chr7	141997493	141997503	+	1	NA	intron (NM_001009930, intron 16 of 19)	intron (NM_001009930, intron 16 of 19)	5319	NR_037291	100526509		NR_037291	ENSMUSG00000092652	Mir3104	mir-3104|mmu-mir-3104	microRNA 3104	ncRNA
mm_165906.1	chr4	52462965	52462977	+	1	NA	exon (NM_008017, exon 15 of 25)	exon (NM_008017, exon 15 of 25)	23750	NM_001301412	14211	Mm.2999	NM_008017	ENSMUSG00000028312	Smc2	5730502P04Rik|AI255214|AW545314|CAP-E|CAPE|Fin16|SMC-2|Smc2l1	structural maintenance of chromosomes 2	protein-coding
mm_42709.1	chr5	120431910	120431912	+	1	NA	promoter-TSS (NM_008499)	promoter-TSS (NM_008499)	25	NM_008499	16873	Mm.5151	NM_008499	ENSMUSG00000029595	Lhx5	Lim2	LIM homeobox protein 5	protein-coding
mm_53250.1	chr6	127582202	127582212	+	1	NA	intron (NM_001033464, intron 1 of 6)	intron (NM_001033464, intron 1 of 6)	4232	NM_001033464	381812	Mm.296093	NM_001033464	ENSMUSG00000061414	Cracr2a	Efcab4b|Gm1073|Gm462	calcium release activated channel regulator 2A	protein-coding
mm_161459.1	chr15	76659823	76659823	+	1	NA	promoter-TSS (NM_001276335)	promoter-TSS (NM_001276335)	-87	NM_001276335	54151	Mm.247752	NM_019396	ENSMUSG00000053929	Cyhr1	1110031M01Rik|AU042374|Chrp	cysteine and histidine rich 1	protein-coding
mm_104396.1	chr11	94499884	94499959	-	1	NA	promoter-TSS (NM_027984)	promoter-TSS (NM_027984)	53	NM_027984	71889	Mm.248620	NM_027984	ENSMUSG00000010080	Epn3	2310022G12Rik	epsin 3	protein-coding
mm_57417.1	chr6	124911637	124911676	-	1	NA	promoter-TSS (NM_008479)	promoter-TSS (NM_008479)	49	NM_008479	16768	Mm.4528	NM_008479	ENSMUSG00000030124	Lag3	CD223|LAG-3|Ly66	lymphocyte-activation gene 3	protein-coding
mm_5189.1	chr1	13162484	13162516	-	1	NA	intron (NM_001302702, intron 12 of 21)	intron (NM_001302702, intron 12 of 21)	-35337	NM_001081209	383491	Mm.309380	NM_001081209	ENSMUSG00000042414	Prdm14	-	PR domain containing 14	protein-coding
mm_27361.1	chr3	50429977	50429987	-	1	NA	intron (NM_011990, intron 3 of 11)	intron (NM_011990, intron 3 of 11)	13631	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_8919.1	chr1	163313848	163313861	-	1	NA	promoter-TSS (NM_175686)	promoter-TSS (NM_175686)	-204	NM_175686	18933	Mm.288642	NM_011127	ENSMUSG00000026586	Prrx1	A230024N07Rik|AA755424|AI385634|AI843499|K-2|Pmx|Pmx1|Prx1|mHox	paired related homeobox 1	protein-coding
mm_109863.1	chr12	4907394	4907402	-	1	NA	5' UTR (NM_145441, exon 1 of 7)	5' UTR (NM_145441, exon 1 of 7)	122	NM_145441	217379	Mm.259170	NM_145441	ENSMUSG00000020634	Ubxn2a	6330407P03Rik|Ubxd4	UBX domain protein 2A	protein-coding
mm_3834.1	chr1	159931081	159931092	+	1	NA	Intergenic	Intergenic	-113294	NR_028111	67647	Mm.171518	NM_001024470	ENSMUSG00000090394	4930523C07Rik	-	RIKEN cDNA 4930523C07 gene	protein-coding
mm_157739.1	chrX	72918329	72918396	-	1	NA	promoter-TSS (NM_019405)	promoter-TSS (NM_019405)	-18	NM_019405	26370	Mm.24643	NM_019405	ENSMUSG00000031347	Cetn2	1110034A02Rik|AI326150|Calt|caltractin	centrin 2	protein-coding
mm_119985.1	chr14	55578357	55578366	+	1	NA	promoter-TSS (NM_011189)	promoter-TSS (NM_011189)	-133	NM_011189	19186	Mm.830	NM_011189	ENSMUSG00000022216	Psme1	AW413925|PA28a	proteasome (prosome, macropain) activator subunit 1 (PA28 alpha)	protein-coding
mm_64400.1	chr7	142501606	142501628	+	1	NA	intron (NM_001347548, intron 1 of 14)	intron (NM_001347548, intron 1 of 14)	2781	NM_001347551	21957	Mm.389992	NM_011620	ENSMUSG00000061723	Tnnt3	fTnT	troponin T3, skeletal, fast	protein-coding
mm_31913.1	chr4	85205152	85205192	+	1	NA	promoter-TSS (NM_019535)	promoter-TSS (NM_019535)	-284	NM_019535	20404	Mm.143603	NM_019535	ENSMUSG00000028488	Sh3gl2	9530001L19Rik|AI120490|AW555077|B930049H17Rik|EEN-B1|SH3PA|Sh3d2a	SH3-domain GRB2-like 2	protein-coding
mm_2129.1	chr1	88055456	88055466	+	1	NA	promoter-TSS (NM_201641)	promoter-TSS (NM_201641)	50	NM_201641	394430	Mm.300095	NM_201641	ENSMUSG00000090165	Ugt1a10	A13|Ugt1a13	UDP glycosyltransferase 1 family, polypeptide A10	protein-coding
mm_167294.1	chr8	47249300	47249300	-	1	NA	intron (NM_175162, intron 1 of 4)	intron (NM_175162, intron 1 of 4)	40102	NM_001286376	71069	Mm.23973	NM_175162	ENSMUSG00000038143	Stox2	4933409N07Rik|AI449080|AI835114|mKIAA1392	storkhead box 2	protein-coding
mm_142922.1	chr17	53845809	53845824	-	1	NA	5' UTR (NM_026935, exon 1 of 8)	5' UTR (NM_026935, exon 1 of 8)	142	NM_026935	69083	Mm.19320	NM_026935	ENSMUSG00000023122	Sult1c2	1810008N17Rik|ST1C1|ST1C2|Sult1c1	sulfotransferase family, cytosolic, 1C, member 2	protein-coding
mm_118832.1	chr14	25607619	25607656	+	1	NA	intron (NM_001310666, intron 6 of 23)	CpG	4124	NM_001309430	100188919	Mm.473810	NM_001309430		Israa	-	immune system released activating agent	protein-coding
mm_24992.1	chr3	97158853	97158870	+	1	NA	promoter-TSS (NM_019800)	promoter-TSS (NM_019800)	84	NM_019800	66659	Mm.101368	NM_019800	ENSMUSG00000028093	Acp6	5730559A09Rik|ACPL1|AU022842|mPACPL1	acid phosphatase 6, lysophosphatidic	protein-coding
mm_100861.1	chr11	5878252	5878260	-	1	NA	promoter-TSS (NM_008894)	promoter-TSS (NM_008894)	0	NM_008894	18972	Mm.35788	NM_008894	ENSMUSG00000020471	Pold2	50kDa|p50|po1D2	polymerase (DNA directed), delta 2, regulatory subunit	protein-coding
mm_83215.1	chr9	42120327	42120369	-	1	NA	intron (NM_011436, intron 1 of 47)	intron (NM_011436, intron 1 of 47)	3941	NM_011436	20660	Mm.121920	NM_011436	ENSMUSG00000049313	Sorl1	2900010L19Rik|AI596264|AW261561|LR11|SorLA|gp250|mSorLA	sortilin-related receptor, LDLR class A repeats-containing	protein-coding
mm_115622.1	chr13	12082650	12082660	-	1	NA	intron (NM_023868, intron 1 of 104)	intron (NM_023868, intron 1 of 104)	24290	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding
mm_104424.1	chr11	94938031	94938093	-	1	NA	exon (NM_007742, exon 2 of 51)	exon (NM_007742, exon 2 of 51)	1838	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_114966.1	chr13	97128656	97128673	+	1	NA	TTS (NM_021552)	TTS (NM_021552)	9262	NM_021552	59050	Mm.390634	NM_021552	ENSMUSG00000060739	Nsa2	5730427N09Rik|LNR42|Nsa2p|Tinp1|Yr29	NSA2 ribosome biogenesis homolog	protein-coding
mm_31927.1	chr4	85514302	85514342	+	1	NA	Intergenic	CpG	308866	NM_019535	20404	Mm.143603	NM_019535	ENSMUSG00000028488	Sh3gl2	9530001L19Rik|AI120490|AW555077|B930049H17Rik|EEN-B1|SH3PA|Sh3d2a	SH3-domain GRB2-like 2	protein-coding
mm_38196.1	chr4	135428713	135428721	-	1	NA	intron (NM_022980, intron 1 of 4)	L1MC4|LINE|L1	5088	NM_022980	53902	Mm.331970	NM_022980	ENSMUSG00000059713	Rcan3	AU041093|Csp3|Dscr1l2	regulator of calcineurin 3	protein-coding
mm_31117.1	chr4	42950482	42950492	+	1	NA	Intergenic	Intergenic	-2607	NM_019874	56323	Mm.20437	NM_019874	ENSMUSG00000036052	Dnajb5	1110058L06Rik|AI462558|Hsc40|Hsp40-3	DnaJ heat shock protein family (Hsp40) member B5	protein-coding
mm_102191.1	chr11	54267277	54267280	-	1	NA	promoter-TSS (NM_010556)	promoter-TSS (NM_010556)	1	NM_010556	16187	Mm.983	NM_010556	ENSMUSG00000018914	Il3	BPA|Csfmu|HCGF|Il-3|MCGF|PSF	interleukin 3	protein-coding
mm_59213.1	chr7	24547253	24547279	+	1	NA	5' UTR (NM_009532, exon 1 of 17)	5' UTR (NM_009532, exon 1 of 17)	116	NM_009532	22594	Mm.4347	NM_009532	ENSMUSG00000051768	Xrcc1	Xrcc-1	X-ray repair complementing defective repair in Chinese hamster cells 1	protein-coding
mm_39309.1	chr5	8046078	8046078	+	1	NA	promoter-TSS (NM_025618)	promoter-TSS (NM_025618)	0	NM_025618	109552	Mm.96211	NM_025618	ENSMUSG00000003161	Sri	2210417O06Rik|2900070H08Rik|Sor	sorcin	protein-coding
mm_124065.1	chr14	78332082	78332106	-	1	NA	Intergenic	Intergenic	-24051	NM_011613	21943	Mm.249221	NM_011613	ENSMUSG00000022015	Tnfsf11	Ly109l|ODF|OPGL|RANKL|Trance	tumor necrosis factor (ligand) superfamily, member 11	protein-coding
mm_365.1	chr1	33908173	33908184	+	1	NA	promoter-TSS (NM_001310484)	promoter-TSS (NM_001310484)	-47	NM_001276764	13518	Mm.336625	NM_010081	ENSMUSG00000026131	Dst	2310001O04Rik|A830042E19Rik|AW554249|BP230|BPAG1-n|Bpag|Bpag1|Macf2|ah|athetoid|dt|mKIAA0728|nmf203|nmf339	dystonin	protein-coding
mm_114526.1	chr13	73496522	73496524	+	1	NA	intron (NM_145376, intron 5 of 13)	intron (NM_145376, intron 5 of 13)	29140	NM_145376	210992	Mm.284649	NM_145376	ENSMUSG00000021608	Lpcat1	2900035H07Rik|Aytl2|BB137372|BC005662|C87117|LPCAT|rd11	lysophosphatidylcholine acyltransferase 1	protein-coding
mm_26638.1	chr3	153630925	153630929	+	1	NA	intron (NM_011372, intron 1 of 4)	Charlie1|DNA|hAT-Charlie	94206	NM_011372	20447	Mm.296453	NM_011372	ENSMUSG00000052544	St6galnac3	Siat7c	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 3	protein-coding
mm_130759.1	chr15	101274786	101274791	-	1	NA	TTS (NM_010444)	TTS (NM_010444)	7942	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_115508.1	chr13	4279421	4279450	-	1	NA	promoter-TSS (NM_013777)	promoter-TSS (NM_013777)	-36	NM_013777	622402	Mm.27447	NM_013777	ENSMUSG00000021211	Akr1c12	AI266976|Akra	aldo-keto reductase family 1, member C12	protein-coding
mm_55073.1	chr6	49111003	49111012	-	1	NA	intron (NM_023670, intron 6 of 14)	intron (NM_023670, intron 6 of 14)	37212	NM_029353	75593	Mm.439947	NM_029353	ENSMUSG00000029815	Malsu1	2410003K15Rik|Matsu1	mitochondrial assembly of ribosomal large subunit 1	protein-coding
mm_32722.1	chr4	116448679	116448685	+	1	NA	intron (NM_008641, intron 1 of 28)	intron (NM_008641, intron 1 of 28)	15499	NM_001042743	17776	Mm.9287	NM_008641	ENSMUSG00000003810	Mast2	MAST205|Mtssk	microtubule associated serine/threonine kinase 2	protein-coding
mm_139983.1	chr17	72836725	72836750	+	1	NA	promoter-TSS (NM_027166)	promoter-TSS (NM_027166)	33	NM_027166	383295	Mm.277533	NM_027166	ENSMUSG00000039770	Ypel5	2310076K21Rik|CGI-127	yippee-like 5 (Drosophila)	protein-coding
mm_14042.1	chr2	122258585	122258601	+	1	NA	intron (NM_146126, intron 5 of 8)	intron (NM_146126, intron 5 of 8)	23754	NM_146126	20322	Mm.371580	NM_146126	ENSMUSG00000027227	Sord	Sdh-1|Sdh1|Sodh-1	sorbitol dehydrogenase	protein-coding
mm_41524.1	chr5	92571524	92571543	+	1	NA	promoter-TSS (NM_001170571)	promoter-TSS (NM_001170571)	-4	NM_001033478	384198	Mm.76757	NM_001033478	ENSMUSG00000057068	Fam47e	C730043O17|Gm1381	family with sequence similarity 47, member E	protein-coding
mm_140865.1	chr17	23771506	23771537	-	1	NA	promoter-TSS (NM_153791)	promoter-TSS (NM_153791)	70	NM_153791	224613	Mm.328835	NM_153791	ENSMUSG00000040097	Flywch1	E030034P13Rik|mKIAA1552	FLYWCH-type zinc finger 1	protein-coding
mm_42172.1	chr5	112261710	112261721	+	1	NA	intron (NM_023695, intron 3 of 5)	intron (NM_023695, intron 3 of 5)	5895	NM_001312893	12960	Mm.29488	NM_023695	ENSMUSG00000029343	Crybb1	3110006K12Rik|BB1CRY	crystallin, beta B1	protein-coding
mm_5188.1	chr1	13127224	13127249	-	1	NA	promoter-TSS (NM_001081209)	promoter-TSS (NM_001081209)	-73	NM_001081209	383491	Mm.309380	NM_001081209	ENSMUSG00000042414	Prdm14	-	PR domain containing 14	protein-coding
mm_61469.1	chr7	75612187	75612197	+	1	NA	intron (NM_029332, intron 7 of 36)	intron (NM_029332, intron 7 of 36)	156658	NM_029332	75547	Mm.216107	NM_029332	ENSMUSG00000066406	Akap13	1700026G02Rik|5730522G15Rik|5830460E08Rik|AKAP-13|AKAP-Lbc|BRX|Ht31|LBC|PROTO-LB|PROTO-LBC	A kinase (PRKA) anchor protein 13	protein-coding
mm_21671.1	chr2	164425654	164425683	-	1	NA	3' UTR (NM_011521, exon 5 of 5)	3' UTR (NM_011521, exon 5 of 5)	17520	NM_011521	20971	Mm.3815	NM_011521	ENSMUSG00000017009	Sdc4	AA959608|AW108331|S4|Synd4|ryudocan|syndecan-4	syndecan 4	protein-coding
mm_59886.1	chr7	30303470	30303482	+	1	NA	exon (NM_001081114, exon 10 of 14)	exon (NM_001081114, exon 10 of 14)	-5277	NM_198027	233065	Mm.276277	NM_198027	ENSMUSG00000042831	Alkbh6	AI839550|Abh6|C130099A02	alkB homolog 6	protein-coding
mm_31395.1	chr4	48045176	48045190	+	1	NA	promoter-TSS (NM_015743)	promoter-TSS (NM_015743)	-122	NM_015743	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_162066.1	chrX	11311907	11311907	+	1	NA	promoter-TSS (NM_001025260)	promoter-TSS (NM_001025260)	-27	NM_001025260	547160	Mm.350551	NM_001025260	ENSMUSG00000095413	H2al1e	Gm14484|OTTMUSG00000016790	H2A histone family member L1E	protein-coding
mm_40976.1	chr5	77037011	77037043	+	1	NA	intron (NM_027970, intron 1 of 8)	intron (NM_027970, intron 1 of 8)	-18164	NR_077218	68246	Mm.319633	NR_077218	ENSMUSG00000086632	1700112J05Rik	1700110A09Rik	RIKEN cDNA 1700112J05 gene	ncRNA
mm_155943.1	chrX	104483163	104483193	+	1	NA	exon (NM_001081189, exon 1 of 7)	exon (NM_001081189, exon 1 of 7)	396	NM_001081189	331487	Mm.438275	NM_001081189	ENSMUSG00000073016	Uprt	Gm774	uracil phosphoribosyltransferase	protein-coding
mm_142886.1	chr17	51832608	51832633	-	1	NA	promoter-TSS (NM_009122)	promoter-TSS (NM_009122)	27	NM_009122	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_42153.1	chr5	111490922	111490958	+	1	NA	Intergenic	Intergenic	72774	NM_001081235	433938	Mm.332576	NM_001081235	ENSMUSG00000070576	Mn1	AA003644|AA009236	meningioma 1	protein-coding
mm_11816.1	chr2	44118186	44118209	+	1	NA	intron (NM_001301832, intron 10 of 14)	intron (NM_001301832, intron 10 of 14)	-52873	NR_040622	320872	Mm.445023	NR_040622	ENSMUSG00000085089	Arhgap15os	A430092G05Rik	Rho GTPase activating protein 15, opposite strand	ncRNA
mm_50984.1	chr6	62638160	62638186	+	1	NA	Intergenic	RLTR25A|LTR|ERVK	-618684	NM_008167	14804	Mm.439651	NM_008167	ENSMUSG00000071424	Grid2	B230104L07Rik|GluD2|GluRdelta2|Lc|Lc<J>|MMS10-AC|Ms10ac|cpr|ho|nmf408|tpr	glutamate receptor, ionotropic, delta 2	protein-coding
mm_146117.1	chr18	74283155	74283173	+	1	NA	promoter-TSS (NM_028948)	promoter-TSS (NM_028948)	64	NM_028948	74453	Mm.182293	NM_028948	ENSMUSG00000035394	Cfap53	4933415I03Rik|Ccdc11	cilia and flagella associated protein 53	protein-coding
mm_33773.1	chr4	134496866	134496909	+	1	NA	promoter-TSS (NM_001285849)	promoter-TSS (NM_001285849)	126	NM_001285846	71904	Mm.142343	NM_027995	ENSMUSG00000037348	Paqr7	2310021M12Rik|AV001994|BB007237|Mpra|PGLP|mPR	progestin and adipoQ receptor family member VII	protein-coding
mm_106316.1	chr11	118303052	118303073	-	1	NA	3' UTR (NM_011594, exon 5 of 5)	3' UTR (NM_011594, exon 5 of 5)	-12818	NM_001033528	72344	Mm.232293	NM_001033528	ENSMUSG00000033909	Usp36	2700002L06Rik|mKIAA1453	ubiquitin specific peptidase 36	protein-coding
mm_148049.1	chr18	71255246	71255256	-	1	NA	3' UTR (NM_007831, exon 29 of 29)	3' UTR (NM_007831, exon 29 of 29)	686959	NM_010773	17191	Mm.322	NM_010773	ENSMUSG00000024513	Mbd2	MBD2a	methyl-CpG binding domain protein 2	protein-coding
mm_146707.1	chr18	13972512	13972524	-	1	NA	5' UTR (NM_145492, exon 1 of 8)	5' UTR (NM_145492, exon 1 of 8)	215	NM_145492	225207	Mm.40325	NM_145492	ENSMUSG00000024420	Zfp521	B930086A16Rik|Evi3|Znf521	zinc finger protein 521	protein-coding
mm_101337.1	chr11	23519182	23519233	-	1	NA	promoter-TSS (NM_026105)	promoter-TSS (NM_026105)	-12	NM_026105	67358	Mm.87328	NM_026105	ENSMUSG00000020286	1700093K21Rik	-	RIKEN cDNA 1700093K21 gene	protein-coding
mm_102886.1	chr11	69411666	69411678	-	1	NA	intron (NM_001017426, intron 1 of 22)	CpG	2003	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_28722.1	chr3	95681458	95681498	-	1	NA	intron (NM_001301705, intron 8 of 17)	intron (NM_001301705, intron 8 of 17)	6439	NM_144899	229595	Mm.490574	NM_144899	ENSMUSG00000015850	Adamtsl4	ADAMTSL-4|Tsrc1	ADAMTS-like 4	protein-coding
mm_90824.1	chr10	7946821	7946833	-	1	NA	intron (NM_138667, intron 1 of 6)	B1_Mus1|SINE|Alu	9296	NM_138667	68652	Mm.193041	NM_138667	ENSMUSG00000015755	Tab2	1110030N06Rik|A530078N03Rik|Map3k7ip2|mKIAA0733	TGF-beta activated kinase 1/MAP3K7 binding protein 2	protein-coding
mm_73373.1	chr8	105623390	105623405	+	1	NA	Intergenic	Intergenic	7931	NR_035492	100316712		NR_035492	ENSMUSG00000089432	Mir1966	mir-1966|mmu-mir-1966	microRNA 1966	ncRNA
mm_93085.1	chr10	89592927	89592952	-	1	NA	exon (NM_182959, exon 6 of 12)	exon (NM_182959, exon 6 of 12)	6876	NM_001310710	216227	Mm.233921	NM_182959	ENSMUSG00000019935	Slc17a8	BC042593|Vglut3	solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 8	protein-coding
mm_73126.1	chr8	94810447	94810461	+	1	NA	promoter-TSS (NM_011332)	promoter-TSS (NM_011332)	1	NM_011332	20295	Mm.41988	NM_011332	ENSMUSG00000031780	Ccl17	Abcd-2|Scya17|Scya17l|Tarc	chemokine (C-C motif) ligand 17	protein-coding
mm_106753.1	chr12	4133395	4133411	+	1	NA	promoter-TSS (NM_138305)	promoter-TSS (NM_138305)	6	NM_001159536	104111	Mm.489807	NM_138305	ENSMUSG00000020654	Adcy3	AC3|mKIAA0511	adenylate cyclase 3	protein-coding
mm_21456.1	chr2	160859633	160859639	-	1	NA	intron (NM_177263, intron 1 of 3)	intron (NM_177263, intron 1 of 3)	13354	NM_177263	320799	Mm.436734	NM_177263	ENSMUSG00000035877	Zhx3	1810059C13Rik|4932418O04Rik|9530010N21Rik|Tix1|mKIAA0395	zinc fingers and homeoboxes 3	protein-coding
mm_136919.1	chr17	13780000	13780030	+	1	NA	intron (NM_010806, intron 1 of 32)	PB1D10|SINE|Alu	-18621	NM_022311	21646	Mm.486358	NM_022311	ENSMUSG00000038347	Tcte2	AI429268|Tcte-2	t-complex-associated testis expressed 2	protein-coding
mm_38110.1	chr4	134534983	134534993	-	1	NA	intron (NM_029759, intron 1 of 6)	CpG	280	NM_001256112	76824	Mm.30153	NM_029759	ENSMUSG00000046671	Mtfr1l	2410166I05Rik|AI480750|Fam54b	mitochondrial fission regulator 1-like	protein-coding
mm_25123.1	chr3	102012443	102012456	+	1	NA	intron (NM_178777, intron 2 of 2)	CpG	2304	NM_178777	18072	Mm.137286	NM_178777	ENSMUSG00000048540	Nhlh2	6230401I09Rik|Hen2|NSCL2|Nscl-2|bHLHa34	nescient helix loop helix 2	protein-coding
mm_64138.1	chr7	141195132	141195146	+	1	NA	promoter-TSS (NM_153777)	promoter-TSS (NM_153777)	-4	NM_153777	70552	Mm.45104	NM_153777	ENSMUSG00000038637	Lrrc56	5730427C23Rik|BB110509|mFLJ00101	leucine rich repeat containing 56	protein-coding
mm_12618.1	chr2	74695262	74695279	+	1	NA	TTS (NM_013554)	TTS (NM_013554)	-2493	NM_013555	15438	Mm.26544	NM_013555	ENSMUSG00000043342	Hoxd9	Hox-4.4|Hox-5.2	homeobox D9	protein-coding
mm_133595.1	chr16	91464991	91465019	+	1	NA	promoter-TSS (NR_077219)	promoter-TSS (NR_077219)	-99	NR_077219	100503120	Mm.387130	NR_077219	ENSMUSG00000084866	A930006K02Rik	-	RIKEN cDNA A930006K02 gene	ncRNA
mm_18736.1	chr2	72997065	72997073	-	1	NA	Intergenic	Intergenic	-16623	NM_001018042	20687	Mm.124328	NM_011450	ENSMUSG00000027109	Sp3	D130027J01Rik	trans-acting transcription factor 3	protein-coding
mm_99881.1	chr11	109426224	109426255	+	1	NA	promoter-TSS (NM_001252193)	promoter-TSS (NM_001252193)	19	NM_001252193	13929	Mm.211850	NM_025275	ENSMUSG00000020610	Amz2	AA408420|ESTM12|X83328	archaelysin family metallopeptidase 2	protein-coding
mm_170223.1	chr17	80564019	80564028	+	1	NA	promoter-TSS (NM_001033443)	promoter-TSS (NM_001033443)	-189	NM_001033443	381113	Mm.329216	NM_001033443	ENSMUSG00000033966	Cdkl4	AU067824|Gm942	cyclin-dependent kinase-like 4	protein-coding
mm_119477.1	chr14	47319458	47319490	+	1	NA	3' UTR (NM_178684, exon 4 of 4)	3' UTR (NM_178684, exon 4 of 4)	21160	NM_178684	218975	Mm.212297	NM_178684	ENSMUSG00000021840	Mapk1ip1l	9130202B12|C130032J12Rik	mitogen-activated protein kinase 1 interacting protein 1-like	protein-coding
mm_141678.1	chr17	33928201	33928236	-	1	NA	3' UTR (NM_009318, exon 8 of 8)	3' UTR (NM_009318, exon 8 of 8)	-1676	NM_009059	19732	Mm.43777	NM_009059	ENSMUSG00000041354	Rgl2	KE1.5|Rab2l|Rgt2|Rlf	ral guanine nucleotide dissociation stimulator-like 2	protein-coding
mm_65371.1	chr7	25072925	25073024	-	1	NA	promoter-TSS (NM_008168)	promoter-TSS (NM_008168)	-605	NM_008168	14809	Mm.2879	NM_008168	ENSMUSG00000003378	Grik5	GluK5|GluRgamma2|KA2	glutamate receptor, ionotropic, kainate 5 (gamma 2)	protein-coding
mm_23211.1	chr3	41564922	41564933	+	1	NA	promoter-TSS (NM_001130186)	promoter-TSS (NM_001130186)	47	NM_001130186	269424	Mm.286285	NM_172303	ENSMUSG00000025764	Jade1	AU041499|D530048A03Rik|Phf17|mKIAA1807	jade family PHD finger 1	protein-coding
mm_54830.1	chr6	42585903	42585908	-	1	NA	Intergenic	Intergenic	11467	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_117049.1	chr13	58385177	58385188	-	1	NA	promoter-TSS (NM_027335)	promoter-TSS (NM_027335)	43	NM_027335	70153	Mm.296610	NM_027335	ENSMUSG00000021550	2210016F16Rik	-	RIKEN cDNA 2210016F16 gene	protein-coding
mm_54575.1	chr6	38097045	38097076	-	1	NA	intron (NM_080467, intron 1 of 20)	intron (NM_080467, intron 1 of 20)	-12293	NM_029921	77522	Mm.387207	NM_029921	ENSMUSG00000029829	Tmem213	D630002J15Rik	transmembrane protein 213	protein-coding
mm_49762.1	chr6	34780413	34780467	+	1	NA	promoter-TSS (NM_001289656)	promoter-TSS (NM_001289656)	8	NM_001289656	76223	Mm.150047	NM_178630	ENSMUSG00000038836	Agbl3	2900053G10Rik|4930431N21Rik|6530406M24Rik|CCP3	ATP/GTP binding protein-like 3	protein-coding
mm_139441.1	chr17	54420719	54420755	+	1	NA	Intergenic	Intergenic	-50663	NR_045825	69418	Mm.391004	NR_045825	ENSMUSG00000099747	1700025K24Rik	-	RIKEN cDNA 1700025K24 gene	ncRNA
mm_130229.1	chr15	96285886	96285900	-	1	NA	Intergenic	CpG	-1629	NM_175251	77044	Mm.17166	NM_175251	ENSMUSG00000033237	Arid2	1700124K17Rik|4432409D24Rik|zipzap/p200	AT rich interactive domain 2 (ARID, RFX-like)	protein-coding
mm_7079.1	chr1	88277265	88277294	-	1	NA	exon (NM_172505, exon 2 of 5)	exon (NM_172505, exon 2 of 5)	278	NM_172505	212427	Mm.384762	NM_172505		A730008H23Rik	mFleg1	RIKEN cDNA A730008H23 gene	protein-coding
mm_30346.1	chr3	151742366	151742382	-	1	NA	intron (NM_133871, intron 5 of 7)	RMER20B|LTR|ERVK	7585	NM_133871	99899	Mm.30756	NM_133871	ENSMUSG00000028037	Ifi44	A430056A10Rik|AW261460|MTAP44|p44	interferon-induced protein 44	protein-coding
mm_37554.1	chr4	126162620	126162637	-	1	NA	promoter-TSS (NM_025856)	promoter-TSS (NM_025856)	37	NM_025856	66938	Mm.29813	NM_025856	ENSMUSG00000073758	Sh3d21	1700029G01Rik|AU019788	SH3 domain containing 21	protein-coding
mm_50114.1	chr6	41533993	41534015	+	1	NA	Intergenic	Intergenic	12228	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_80860.1	chr9	98490354	98490372	+	1	NA	promoter-TSS (NM_009034)	promoter-TSS (NM_009034)	-174	NM_009034	19660	Mm.12825	NM_009034	ENSMUSG00000032454	Rbp2	Crbp-2|CrbpII|Rbp-2	retinol binding protein 2, cellular	protein-coding
mm_139858.1	chr17	69969332	69969343	+	1	NA	5' UTR (NM_001347412, exon 1 of 14)	5' UTR (NM_001347412, exon 1 of 14)	264	NM_001347411	224997	Mm.311840	NM_027712	ENSMUSG00000003279	Dlgap1	4933422O14Rik|9630002F18|AI845682|AI848168|BB075781|D17Bwg0511e|GKAP/SAPAP|GKPA/SAPAP|Gkap|Sapap1|mKIAA4162	discs, large (Drosophila) homolog-associated protein 1	protein-coding
mm_70032.1	chr7	142576719	142576736	-	1	NA	TTS (NR_030416)	TTS (NR_030416)	420	NR_030416	735280		NR_030416	ENSMUSG00000076275	Mir675	Mirn675|mir-675|mmu-mir-675	microRNA 675	ncRNA
mm_61601.1	chr7	80027115	80027147	+	1	NA	intron (NM_175433, intron 1 of 4)	CpG	903	NM_175433	209225	Mm.290925	NM_175433	ENSMUSG00000048897	Zfp710	5430400N05Rik|9830165K13|AI324798|Znf710	zinc finger protein 710	protein-coding
mm_21143.1	chr2	154303846	154303849	-	1	NA	Intergenic	Intergenic	-3397	NM_001025574	433492	Mm.330682	NM_001025574	ENSMUSG00000067996	Bpifb9b	5430413K10Rik|AI413838|OTTMUSG00000015915	BPI fold containing family B, member 9B	protein-coding
mm_97783.1	chr11	82434832	82434833	+	1	NA	exon (NM_001304439, exon 2 of 9)	exon (NM_001304439, exon 2 of 9)	45932	NM_001304439	270893	Mm.341593	NM_023438	ENSMUSG00000020701	Tmem132e	Gm644	transmembrane protein 132E	protein-coding
mm_80832.1	chr9	97016168	97016194	+	1	NA	intron (NM_145134, intron 1 of 2)	intron (NM_145134, intron 1 of 2)	2174	NM_145134	211949	Mm.491271	NM_145134	ENSMUSG00000046997	Spsb4	D030068E18Rik|SSB-4|Ssb4	splA/ryanodine receptor domain and SOCS box containing 4	protein-coding
mm_154679.1	chrX	7919911	7919920	+	1	NA	promoter-TSS (NM_013892)	promoter-TSS (NM_013892)	93	NM_013892	30052	Mm.4881	NM_013892	ENSMUSG00000039278	Pcsk1n	AI848336|KEP|PEN|PEN19|PEN20|Pan3|SAAS|SAASCT|bLEN|lLEN|proSAAS	proprotein convertase subtilisin/kexin type 1 inhibitor	protein-coding
mm_51602.1	chr6	84008805	84008815	+	1	NA	5' UTR (NM_001077694, exon 1 of 55)	5' UTR (NM_001077694, exon 1 of 55)	212	NM_001077694	26903	Mm.220982	NM_021469	ENSMUSG00000033788	Dysf	2310004N10Rik|AI604795|D6Pas3	dysferlin	protein-coding
mm_47018.1	chr5	115489944	115489953	-	1	NA	Intergenic	CpG	-5464	NM_133760	75387	Mm.332616	NM_133760	ENSMUSG00000029524	Sirt4	4930596O17Rik	sirtuin 4	protein-coding
mm_40015.1	chr5	33104421	33104436	+	1	NA	5' UTR (NM_019810, exon 1 of 15)	5' UTR (NM_019810, exon 1 of 15)	209	NM_019810	20537	Mm.25237	NM_019810	ENSMUSG00000011034	Slc5a1	Sglt1	solute carrier family 5 (sodium/glucose cotransporter), member 1	protein-coding
mm_130561.1	chr15	99287175	99287185	-	1	NA	promoter-TSS (NM_001081254)	promoter-TSS (NM_001081254)	0	NM_001081254	545136	Mm.324745	NM_001081254	ENSMUSG00000078907	Fam186b	EG545136	family with sequence similarity 186, member B	protein-coding
mm_121079.1	chr14	99046435	99046463	+	1	NA	promoter-TSS (NM_175245)	promoter-TSS (NM_175245)	72	NM_175265	77744	Mm.23503	NM_175265	ENSMUSG00000022070	Bora	6720463M24Rik|AI317232	bora, aurora kinase A activator	protein-coding
mm_33785.1	chr4	134922640	134922644	+	1	NA	promoter-TSS (NM_023665)	promoter-TSS (NM_023665)	-983	NM_023665	27981	Mm.331964	NM_023665	ENSMUSG00000037266	Rsrp1	2700043I21Rik|D4Ucla2|D4Wsu53e	arginine/serine rich protein 1	protein-coding
mm_104328.1	chr11	93968298	93968308	-	1	NA	5' UTR (NM_008704, exon 1 of 5)	5' UTR (NM_008704, exon 1 of 5)	218	NM_008704	18102	Mm.439702	NM_008704	ENSMUSG00000037601	Nme1	AL024257|NDPK-A|NM23-M1|NM23A	NME/NM23 nucleoside diphosphate kinase 1	protein-coding
mm_133776.1	chr16	94732126	94732127	+	1	NA	Intergenic	Intergenic	120707	NM_001347731	13548	Mm.310973	NM_007890	ENSMUSG00000022897	Dyrk1a	2310043O08Rik|D16Ertd272e|D16Ertd493e|Dyrk|ENSMUSG00000074897|Gm10783|Mnbh|Mp86|mmb	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1a	protein-coding
mm_87814.1	chr10	60302043	60302055	+	1	NA	TTS (NM_001252635)	TTS (NM_001252635)	17588	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_100497.1	chr11	120479599	120479612	+	1	NA	exon (NM_008244, exon 16 of 22)	exon (NM_008244, exon 16 of 22)	-5064	NM_027204	56282	Mm.133851	NM_027204	ENSMUSG00000039640	Mrpl12	0610034O11Rik|1500031N16Rik|MRP-L12|Rpml12	mitochondrial ribosomal protein L12	protein-coding
mm_47760.1	chr5	131438811	131438822	-	1	NA	3' UTR (NM_177047, exon 19 of 19)	3' UTR (NM_177047, exon 19 of 19)	-131294	NM_145218	212996	Mm.299204	NM_145218	ENSMUSG00000034040	Wbscr17	AA388321|E330012B09Rik	Williams-Beuren syndrome chromosome region 17 homolog (human)	protein-coding
mm_104970.1	chr11	100204282	100204302	-	1	NA	exon (NM_016958, exon 6 of 8)	exon (NM_016958, exon 6 of 8)	1738	NM_001313957	16664	Mm.439898	NM_016958	ENSMUSG00000045545	Krt14	AI626930|CK-14|K14|Krt-1.14|Krt1-14	keratin 14	protein-coding
mm_136944.1	chr17	14399028	14399036	+	1	NA	promoter-TSS (NR_027986)	promoter-TSS (NR_027986)	-90	NR_027986	74917	Mm.32228	NM_183107		4930474M22Rik	-	RIKEN cDNA 4930474M22 gene	ncRNA
mm_52962.1	chr6	123123554	123123564	+	1	NA	5' UTR (NM_001170333, exon 1 of 7)	5' UTR (NM_001170333, exon 1 of 7)	243	NM_001170333	26888	Mm.47384	NM_011999	ENSMUSG00000030148	Clec4a2	Clec4a|Clecsf6|DCIR|Dcir1	C-type lectin domain family 4, member a2	protein-coding
mm_171047.1	chr3	102436372	102436378	-	1	NA	Intergenic	L1Md_T|LINE|L1	-33544	NM_001112698	18049	Mm.1259	NM_013609	ENSMUSG00000027859	Ngf	Ngfb	nerve growth factor	protein-coding
mm_135128.1	chr16	35843957	35843971	-	1	NA	intron (NM_001039530, intron 12 of 16)	RLTR21|LTR|ERVK	27418	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_90663.1	chr10	128819671	128819674	+	1	NA	TTS (NM_028873)	TTS (NM_028873)	1959	NM_024180	66844	Mm.235562	NM_024180	ENSMUSG00000025353	Ormdl2	0610012C09Rik	ORM1-like 2 (S. cerevisiae)	protein-coding
mm_156427.1	chrX	140957240	140957253	+	1	NA	promoter-TSS (NM_001164177)	promoter-TSS (NM_001164177)	-535	NM_001164177	53380	Mm.17640	NM_016883	ENSMUSG00000031429	Psmd10	AW554874	proteasome (prosome, macropain) 26S subunit, non-ATPase, 10	protein-coding
mm_61582.1	chr7	79859213	79859230	+	1	NA	Intergenic	Intergenic	-16869	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_24652.1	chr3	94398536	94398538	+	1	NA	promoter-TSS (NM_177250)	promoter-TSS (NM_177250)	-682	NM_177250	320747	Mm.213001	NM_177250	ENSMUSG00000044505	Lingo4	A530050P17Rik|LERN4|Lrrn6d	leucine rich repeat and Ig domain containing 4	protein-coding
mm_114135.1	chr13	55223138	55223140	+	1	NA	intron (NM_008739, intron 2 of 22)	intron (NM_008739, intron 2 of 22)	13357	NM_008739	18193	Mm.12964	NM_008739	ENSMUSG00000021488	Nsd1	AI528500|KMT3B	nuclear receptor-binding SET-domain protein 1	protein-coding
mm_142794.1	chr17	50190257	50190265	-	1	NA	5' UTR (NM_181397, exon 1 of 10)	5' UTR (NM_181397, exon 1 of 10)	236	NM_181397	76438	Mm.41854	NM_181397	ENSMUSG00000039316	Rftn1	2310015N21Rik|AI853526	raftlin lipid raft linker 1	protein-coding
mm_132414.1	chr16	35068536	35068549	+	1	NA	intron (NM_023587, intron 3 of 6)	intron (NM_023587, intron 3 of 6)	46121	NM_023587	70757	Mm.27286	NM_023587	ENSMUSG00000035376	Hacd2	6330408J20Rik|AI255777|AI481689|Hcad2|Ptplb	3-hydroxyacyl-CoA dehydratase 2	protein-coding
mm_171875.1	chr5	30220959	30220972	+	1	NA	Intergenic	Intergenic	-11616	NM_027652	28042	Mm.168854	NM_027652	ENSMUSG00000075703	Selenoi	4933402G07Rik|AI448296|AI452230|C79563|D5Wsu178e|Ept1|SELI|mKIAA1724	selenoprotein I	protein-coding
mm_173020.1	chrX	101429733	101429734	+	1	NA	promoter-TSS (NM_001252518)	promoter-TSS (NM_001252518)	82	NM_001252518	53610	Mm.280069	NM_023144	ENSMUSG00000031311	Nono	AA407051|AV149256|NRB54|P54NRB|nonA	non-POU-domain-containing, octamer binding protein	protein-coding
mm_39067.1	chr4	154082026	154082030	-	1	NA	intron (NM_011642, intron 3 of 13)	intron (NM_011642, intron 3 of 13)	15145	NM_001126330	22062	Mm.78015	NM_011642	ENSMUSG00000029026	Trp73	TAp73|Tp73|deltaNp73|p73	transformation related protein 73	protein-coding
mm_105186.1	chr11	101973960	101974009	-	1	NA	3' UTR (NM_028207, exon 3 of 3)	3' UTR (NM_028207, exon 3 of 3)	-6969	NM_024449	74499	Mm.265602	NM_024449	ENSMUSG00000001494	Sost	5430411E23Rik	sclerostin	protein-coding
mm_80394.1	chr9	75775695	75775715	+	1	NA	5' UTR (NM_007555, exon 1 of 7)	5' UTR (NM_007555, exon 1 of 7)	340	NM_007555	12160	Mm.428950	NM_007555	ENSMUSG00000032179	Bmp5	AU023399|se	bone morphogenetic protein 5	protein-coding
mm_150403.1	chr19	36833179	36833195	+	1	NA	Intergenic	RMER17C|LTR|ERVK	-1045	NM_001163635	74493	Mm.249310	NM_001163635	ENSMUSG00000024811	Tnks2	5430432P15Rik|AA517131|AI662480|ARTD6|TNKS-2|Tank2	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase 2	protein-coding
mm_65471.1	chr7	25477583	25477594	-	1	NA	promoter-TSS (NM_001039186)	promoter-TSS (NM_001039186)	37	NM_001039185	26365	Mm.322502	NM_011926	ENSMUSG00000074272	Ceacam1	Bgp|Bgp1|C-CAM|CD66a|Cc1|Cea-1|Cea-7|Cea1|Cea7|Hv-2|Hv2|MHVR|MHVR1|Mhv-1|bb-1|mCEA1|mmCGM1|mmCGM1a|mmCGM2	carcinoembryonic antigen-related cell adhesion molecule 1	protein-coding
mm_100254.1	chr11	117331533	117331564	+	1	NA	promoter-TSS (NM_017380)	promoter-TSS (NM_017380)	-167	NM_017380	53860	Mm.38450	NM_017380	ENSMUSG00000059248	Sept9	MSF1|Msf|PNUTL4|Sint1	septin 9	protein-coding
mm_104311.1	chr11	93859731	93859735	-	1	NA	3' UTR (NM_001013375, exon 14 of 14)	3' UTR (NM_001013375, exon 14 of 14)	26033	NM_001013375	217109	Mm.379350	NM_001013375	ENSMUSG00000054079	Utp18	6230425C22Rik|6430513M13|Wdr50	UTP18 small subunit processome component	protein-coding
mm_142598.1	chr17	46763716	46763724	-	1	NA	promoter-TSS (NM_011195)	promoter-TSS (NM_011195)	-8	NM_011195	19208	Mm.215173	NM_011195	ENSMUSG00000036858	Ptcra	gp33|pT-alpha|pT-alpha-TCR|pT[a]|pTa|pTalpha	pre T cell antigen receptor alpha	protein-coding
mm_7033.1	chr1	87099735	87099747	-	1	NA	exon (NM_001081082, exon 8 of 11)	exon (NM_001081082, exon 8 of 11)	1865	NM_001081082	76768	Mm.58068	NM_001081082	ENSMUSG00000079440	Alpi	2010001C14Rik|Akp6|gIAP	alkaline phosphatase, intestinal	protein-coding
mm_140742.1	chr17	15829883	15829902	-	1	NA	Intergenic	Intergenic	-3306	NM_178615	68799	Mm.293466	NM_178615	ENSMUSG00000048027	Rgmb	1110059F19Rik|DRAGON	repulsive guidance molecule family member B	protein-coding
mm_91128.1	chr10	19592745	19592773	-	1	NA	intron (NM_010511, intron 1 of 6)	intron (NM_010511, intron 1 of 6)	810	NM_010511	15979	Mm.549	NM_010511	ENSMUSG00000020009	Ifngr1	CD119|IFN-gammaR|Ifgr|Ifngr|Nktar	interferon gamma receptor 1	protein-coding
mm_171883.1	chr5	33018977	33018979	+	1	NA	5' UTR (NM_011738, exon 1 of 2)	5' UTR (NM_011738, exon 1 of 2)	162	NM_011738	22629	Mm.332314	NM_011738	ENSMUSG00000018965	Ywhah	-	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta polypeptide	protein-coding
mm_1011.1	chr1	58727251	58727261	+	1	NA	intron (NM_001293804, intron 3 of 9)	intron (NM_001293804, intron 3 of 9)	-3296	NM_001293805	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_2614.1	chr1	120485843	120485855	+	1	NA	exon (NM_010766, exon 9 of 17)	exon (NM_010766, exon 9 of 17)	19235	NM_010766	17167	Mm.1856	NM_010766	ENSMUSG00000026390	Marco	AI323439|Ly112|Scara2	macrophage receptor with collagenous structure	protein-coding
mm_36548.1	chr4	86672400	86672404	-	1	NA	Intergenic	B1F|SINE|Alu	-2343	NM_007408	11520	Mm.381	NM_007408	ENSMUSG00000028494	Plin2	AA407157|ADPH|Adfp|Adrp	perilipin 2	protein-coding
mm_78729.1	chr9	41581067	41581100	+	1	NA	promoter-TSS (NR_029822)	promoter-TSS (NR_029822)	-170	NR_015483	73144	Mm.38166	NM_001033153	ENSMUSG00000074415	3110039I08Rik	2610203C20Rik|AI848448|D230004N17Rik|D3Mgi9|Mir100hg	RIKEN cDNA 3110039I08 gene	ncRNA
mm_152071.1	chr19	6543083	6543088	-	1	NA	promoter-TSS (NM_009203)	promoter-TSS (NM_009203)	-15	NM_009203	20521	Mm.391146	NM_009203	ENSMUSG00000061742	Slc22a12	AI987855|OAT4L|Rst|Slc22al2|URAT1	solute carrier family 22 (organic anion/cation transporter), member 12	protein-coding
mm_110717.1	chr12	69541737	69541745	-	1	NA	Intergenic	Intergenic	41287	NM_001033236	207965	Mm.102487	NM_001033236	ENSMUSG00000049882	Vcpkmt	Gm71|Mettl21d|Mettl221d|VCP-KMT	valosin containing protein lysine (K) methyltransferase	protein-coding
mm_61299.1	chr7	67679249	67679261	+	1	NA	intron (NM_001168475, intron 6 of 10)	intron (NM_001168475, intron 6 of 10)	31845	NM_025905	67009	Mm.249356	NM_025905	ENSMUSG00000030555	Ttc23	1600012K10Rik	tetratricopeptide repeat domain 23	protein-coding
mm_73394.1	chr8	105827722	105827751	+	1	NA	promoter-TSS (NM_024445)	promoter-TSS (NM_024445)	-8	NM_024445	72236	Mm.386810	NM_024445	ENSMUSG00000031893	Tsnaxip1	1700016K08Rik|TXI1	translin-associated factor X (Tsnax) interacting protein 1	protein-coding
mm_1880.1	chr1	85650028	85650042	+	1	NA	promoter-TSS (NM_013673)	promoter-TSS (NM_013673)	47	NM_001313714	20684	Mm.290906	NM_013673	ENSMUSG00000026222	Sp100	A430075G10Rik	nuclear antigen Sp100	protein-coding
mm_36097.1	chr4	58545702	58545722	-	1	NA	intron (NM_010336, intron 1 of 3)	intron (NM_010336, intron 1 of 3)	7581	NM_172989	14745	Mm.4772	NM_010336	ENSMUSG00000038668	Lpar1	AI326300|Edg2|Gpcr26|Kdt2|lpA1|vzg-1	lysophosphatidic acid receptor 1	protein-coding
mm_64681.1	chr7	4510020	4510052	-	1	NA	exon (NM_001277904, exon 7 of 13)	exon (NM_001277904, exon 7 of 13)	5939	NM_001277903	21955	Mm.358643	NM_011618	ENSMUSG00000064179	Tnnt1	AW146156|Tnt|sTnT|ssTnT	troponin T1, skeletal, slow	protein-coding
mm_99238.1	chr11	101074032	101074068	+	1	NA	exon (NM_013792, exon 5 of 6)	exon (NM_013792, exon 5 of 6)	3956	NM_013792	27419	Mm.95452	NM_013792	ENSMUSG00000001751	Naglu	-	alpha-N-acetylglucosaminidase (Sanfilippo disease IIIB)	protein-coding
mm_169363.1	chr14	31917624	31917626	-	1	NA	Intergenic	RLTR1B|LTR|ERV1	-87210	NM_001024604	105522	Mm.37660	NM_001024604	ENSMUSG00000014496	Ankrd28	AI465466|AI604979|E430019N21Rik|mKIAA0379	ankyrin repeat domain 28	protein-coding
mm_10450.1	chr2	14276279	14276288	+	1	NA	intron (NM_008625, intron 9 of 29)	intron (NM_008625, intron 9 of 29)	15280	NR_030609	100124488		NR_030609	ENSMUSG00000077897	Mir511	Mirn511|mir-511|mmu-mir-511	microRNA 511	ncRNA
mm_140925.1	chr17	24220709	24220737	-	1	NA	promoter-TSS (NM_028056)	promoter-TSS (NM_028056)	46	NM_028056	72016	Mm.23881	NM_028056	ENSMUSG00000024118	1600002H07Rik	-	RIKEN cDNA 1600002H07 gene	protein-coding
mm_115694.1	chr13	14063246	14063256	-	1	NA	promoter-TSS (NM_194262)	promoter-TSS (NM_194262)	237	NM_001331119	14593	Mm.148039	NM_010282	ENSMUSG00000021302	Ggps1	1810026C22Rik|9530089B04Rik|AI843169|C79210	geranylgeranyl diphosphate synthase 1	protein-coding
mm_68174.1	chr7	103827751	103827762	-	1	NA	intron (NM_001201391, intron 1 of 2)	intron (NM_001201391, intron 1 of 2)	172	NM_001201391	100503605	Mm.288567	NM_001201391	ENSMUSG00000052305	Hbb-bs	Beta-s|Hbbt1|Hbbt2	hemoglobin, beta adult s chain	protein-coding
mm_157472.1	chrX	48034528	48034555	-	1	NA	5' UTR (NM_013912, exon 1 of 3)	5' UTR (NM_013912, exon 1 of 3)	312	NM_013912	30878	Mm.29262	NM_013912	ENSMUSG00000037010	Apln	6030430G11Rik|Apel	apelin	protein-coding
mm_153137.1	chr19	34245085	34245106	-	1	NA	exon (NM_007392, exon 7 of 9)	exon (NM_007392, exon 7 of 9)	10278	NM_007392	11475	Mm.213025	NM_007392	ENSMUSG00000035783	Acta2	0610041G09Rik|Actvs|SMalphaA|a-SMA|alphaSMA	actin, alpha 2, smooth muscle, aorta	protein-coding
mm_140770.1	chr17	17625312	17625361	-	1	NA	promoter-TSS (NM_172827)	promoter-TSS (NM_172827)	-847	NM_172827	240028	Mm.328807	NM_172827	ENSMUSG00000023845	Lnpep	2010309L07Rik|4732490P18Rik|CAP|IRAP|PLAP|gp160|vp165	leucyl/cystinyl aminopeptidase	protein-coding
mm_92458.1	chr10	77902429	77902461	-	1	NA	promoter-TSS (NM_145152)	promoter-TSS (NM_145152)	91	NM_145152	237387	Mm.133301	NM_145152	ENSMUSG00000051652	Lrrc3	1300011L04Rik|C21orf102	leucine rich repeat containing 3	protein-coding
mm_163049.1	chr11	57963658	57963682	-	1	NA	Intergenic	Intergenic	-45394	NM_028451	73158	Mm.248843	NM_028451	ENSMUSG00000037331	Larp1	1810024J12Rik|3110040D16Rik|Larp|mKIAA0731	La ribonucleoprotein domain family, member 1	protein-coding
mm_66668.1	chr7	45725752	45725766	-	1	NA	promoter-TSS (NM_027055)	promoter-TSS (NM_027055)	57	NM_027055	69363	Mm.45607	NM_027055	ENSMUSG00000070563	Spaca4	1700008E09Rik|AV043694|Samp14	sperm acrosome associated 4	protein-coding
mm_53713.1	chr6	143213773	143213777	+	1	NA	Intergenic	Intergenic	-32113	NR_027803	52285	Mm.354898	NM_001033129		D6Ertd474e	1700001I24Rik|AU023129	DNA segment, Chr 6, ERATO Doi 474, expressed	ncRNA
mm_69927.1	chr7	141918482	141918512	-	1	NA	Intergenic	Intergenic	-16036	NM_001347562	54473	Mm.103551	NM_023764	ENSMUSG00000025139	Tollip	4930403G24Rik|4931428G15Rik	toll interacting protein	protein-coding
mm_69508.1	chr7	134413811	134413831	-	1	NA	Intergenic	Intergenic	-36993	NM_001081331	71007	Mm.334285	NM_001081331	ENSMUSG00000030994	D7Ertd443e	4933400E14Rik|FATS|Gm497	DNA segment, Chr 7, ERATO Doi 443, expressed	protein-coding
mm_114669.1	chr13	78235182	78235189	+	1	NA	non-coding (NR_045195, exon 3 of 3)	non-coding (NR_045195, exon 3 of 3)	-36312	NM_010151	13865	Mm.439653	NM_010151	ENSMUSG00000069171	Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR-3|EAR3|Erbal3|SVP44|Tcfcoup1	nuclear receptor subfamily 2, group F, member 1	protein-coding
mm_136231.1	chr16	90284413	90284498	-	1	NA	promoter-TSS (NM_001346799)	promoter-TSS (NM_001346799)	48	NM_178923	224432	Mm.439811	NM_178923	ENSMUSG00000022983	Scaf4	AA517739|Sfrs15|Sra4|Srsf15	SR-related CTD-associated factor 4	protein-coding
mm_121954.1	chr14	24369814	24369819	-	1	NA	Intergenic	Intergenic	76452	NM_001033214	105418	Mm.2077	NM_001033214	ENSMUSG00000038925	E330034G19Rik	AA415275|Zpac	RIKEN cDNA E330034G19 gene	protein-coding
mm_114694.1	chr13	81786858	81786873	+	1	NA	exon (NM_007684, exon 3 of 5)	exon (NM_007684, exon 3 of 5)	3573	NM_007684	12626	Mm.12481	NM_007684	ENSMUSG00000021537	Cetn3	MmCEN3	centrin 3	protein-coding
mm_81265.1	chr9	108049255	108049339	+	1	NA	promoter-TSS (NM_177910)	promoter-TSS (NM_177910)	7	NM_177910	331026	Mm.22554	NM_177910	ENSMUSG00000070284	Gmppb	AI317178|E430010H19	GDP-mannose pyrophosphorylase B	protein-coding
mm_134455.1	chr16	18411783	18411878	-	1	NA	exon (NM_001111062, exon 3 of 6)	exon (NM_001111062, exon 3 of 6)	1664	NM_001111063	12846	Mm.100940	NM_007744	ENSMUSG00000000326	Comt	Comt1|D16Wsu103e|D330014B15Rik	catechol-O-methyltransferase	protein-coding
mm_98425.1	chr11	94644888	94644950	+	1	NA	TTS (NM_177752)	TTS (NM_177752)	8835	NM_177752	268465	Mm.358937	NM_177752	ENSMUSG00000039055	Eme1	6820428D13	essential meiotic structure-specific endonuclease 1	protein-coding
mm_56219.1	chr6	89415912	89415928	-	1	NA	intron (NM_025351, intron 6 of 7)	L2b|LINE|L2	-53307	NM_008881	18844	Mm.3789	NM_008881	ENSMUSG00000030084	Plxna1	2600013D04Rik|NOV|PlexA1|Plxn1|mKIAA4053	plexin A1	protein-coding
mm_111551.1	chr12	101029017	101029042	-	1	NA	promoter-TSS (NM_026681)	promoter-TSS (NM_026681)	-46	NM_026681	68339	Mm.156217	NM_026681	ENSMUSG00000021182	Ccdc88c	0610010D24Rik|AV000935|AW324073|Daple|mKIAA1509	coiled-coil domain containing 88C	protein-coding
mm_139261.1	chr17	47761444	47761457	+	1	NA	intron (NM_001161723, intron 1 of 8)	intron (NM_001161723, intron 1 of 8)	23519	NM_001161723	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_88966.1	chr10	81395087	81395101	+	1	NA	TTS (NM_001099917)	TTS (NM_001099917)	2030	NM_001099917	72273	Mm.253147	NM_001099917	ENSMUSG00000078439	Smim24	2210404O07Rik	small integral membrane protein 24	protein-coding
mm_156680.1	chrX	159364171	159364181	+	1	NA	3' UTR (NM_148945, exon 22 of 22)	3' UTR (NM_148945, exon 22 of 22)	-8019	NM_025437	66235	Mm.294623	NM_025437	ENSMUSG00000067194	Eif1ax	1500010B24Rik|AI426898|Eif1ay	eukaryotic translation initiation factor 1A, X-linked	protein-coding
mm_15680.1	chr2	163570287	163570314	+	1	NA	3' UTR (NM_001312906, exon 11 of 11)	3' UTR (NM_001312906, exon 11 of 11)	23145	NM_008261	15378	Mm.202383	NM_008261	ENSMUSG00000017950	Hnf4a	HNF-4|Hnf4|Hnf4alpha|MODY1|Nr2a1|TCF-14|Tcf14	hepatic nuclear factor 4, alpha	protein-coding
mm_86160.1	chr9	118150202	118150208	-	1	NA	promoter-TSS (NM_026442)	promoter-TSS (NM_026442)	-9	NM_026442	67899	Mm.9953	NM_026442	ENSMUSG00000039163	Cmc1	2010110K16Rik|2010312P05Rik|AI596001	COX assembly mitochondrial protein 1	protein-coding
mm_43520.1	chr5	137151052	137151062	+	1	NA	Intergenic	Intergenic	-34850	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_30383.1	chr3	152244008	152244033	-	1	NA	exon (NM_199465, exon 9 of 13)	exon (NM_199465, exon 9 of 13)	22300	NM_199465	68810	Mm.200188	NM_199465	ENSMUSG00000039103	Nexn	1110046H09Rik|AA553326|NELIN	nexilin	protein-coding
mm_84502.1	chr9	66919647	66919710	-	1	NA	promoter-TSS (NM_173413)	promoter-TSS (NM_173413)	27	NM_173413	235442	Mm.260376	NM_173413	ENSMUSG00000036943	Rab8b	5930437D16|D330025I23Rik	RAB8B, member RAS oncogene family	protein-coding
mm_42723.1	chr5	120589004	120589019	+	1	NA	promoter-TSS (NM_145853)	promoter-TSS (NM_145853)	-12	NM_029408	75732	Mm.425285	NM_029408	ENSMUSG00000029601	Iqcd	4933433C09Rik|AI662646	IQ motif containing D	protein-coding
mm_23509.1	chr3	60529702	60529739	+	1	NA	exon (NM_001253708, exon 2 of 9)	exon (NM_001253708, exon 2 of 9)	28541	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_70845.1	chr8	23446752	23446754	+	1	NA	3' UTR (NM_013834, exon 3 of 3)	3' UTR (NM_013834, exon 3 of 3)	35251	NM_013834	20377	Mm.281691	NM_013834	ENSMUSG00000031548	Sfrp1	2210415K03Rik|AW011917|AW107218|AW742929|sFRP-1	secreted frizzled-related protein 1	protein-coding
mm_79504.1	chr9	57334067	57334077	+	1	NA	Intergenic	Intergenic	-56998	NR_040729	73772	Mm.444684	NR_040729		4930430J02Rik	-	RIKEN cDNA 4930430J02 gene	ncRNA
mm_84400.1	chr9	65552374	65552384	-	1	NA	TTS (NM_153119)	TTS (NM_153119)	27708	NM_153119	102595	Mm.247303	NM_153119	ENSMUSG00000050721	Plekho2	AI840980|Plekhq1	pleckstrin homology domain containing, family O member 2	protein-coding
mm_32113.1	chr4	98923909	98923976	+	1	NA	5' UTR (NM_146144, exon 1 of 9)	5' UTR (NM_146144, exon 1 of 9)	132	NM_146144	230484	Mm.371692	NM_146144	ENSMUSG00000028560	Usp1	-	ubiquitin specific peptidase 1	protein-coding
mm_96633.1	chr11	69324070	69324111	+	1	NA	promoter-TSS (NM_172560)	promoter-TSS (NM_172560)	104	NM_001024206	245828	Mm.28073	NM_001024206	ENSMUSG00000049299	Trappc1	BET5|D11Ertd172e|MUM2	trafficking protein particle complex 1	protein-coding
mm_41551.1	chr5	92939921	92939931	+	1	NA	intron (NM_001077595, intron 3 of 9)	intron (NM_001077595, intron 3 of 9)	41933	NM_001077596	27428	Mm.46014	NM_015756	ENSMUSG00000029381	Shroom3	AL022960|D5Ertd287e|Shrm|Shrm3	shroom family member 3	protein-coding
mm_45730.1	chr5	86197926	86197935	-	1	NA	promoter-TSS (NM_001310651)	promoter-TSS (NM_001310651)	-29	NM_001310651	14715	Mm.26791	NM_010323	ENSMUSG00000029255	Gnrhr	-	gonadotropin releasing hormone receptor	protein-coding
mm_69790.1	chr7	141096833	141096846	-	1	NA	intron (NM_023059, intron 1 of 9)	intron (NM_023059, intron 1 of 9)	3707	NM_023059	24058	Mm.38017	NM_023059	ENSMUSG00000025494	Sigirr	AI256711|TIR8	single immunoglobulin and toll-interleukin 1 receptor (TIR) domain	protein-coding
mm_77844.1	chr9	5299434	5299445	+	1	NA	exon (NM_009807, exon 2 of 10)	exon (NM_009807, exon 2 of 10)	922	NM_009807	12362	Mm.1051	NM_009807	ENSMUSG00000025888	Casp1	ICE|Il1bc	caspase 1	protein-coding
mm_173222.1	chrX	74944042	74944054	+	1	NA	Intergenic	Intergenic	25077	NM_001251890	100503280	Mm.483559	NM_001251890		Gm38425	-	predicted gene, 38425	protein-coding
mm_18362.1	chr2	58743524	58743526	-	1	NA	intron (NM_001289660, intron 1 of 7)	ORR1F|LTR|ERVL-MaLR	-11659	NM_001289659	76654	Mm.200370	NM_029692	ENSMUSG00000026839	Upp2	1700124F02Rik|AI266885|UDRPASE2|UP2|UPASE2	uridine phosphorylase 2	protein-coding
mm_84503.1	chr9	66975388	66975459	-	1	NA	promoter-TSS (NM_030717)	promoter-TSS (NM_030717)	61	NM_030717	80907	Mm.157882	NM_030717	ENSMUSG00000032370	Lactb	LACT-1|Lact1|Mrpl56	lactamase, beta	protein-coding
mm_137203.1	chr17	23941916	23941929	+	1	NA	promoter-TSS (NM_011321)	promoter-TSS (NM_011321)	-74	NM_011321	20234	Mm.390958	NM_011321	ENSMUSG00000024128	Sbp	AV082137|AV082259|p25	spermine binding protein	protein-coding
mm_119284.1	chr14	34376432	34376470	+	1	NA	intron (NM_153127, intron 1 of 6)	intron (NM_153127, intron 1 of 6)	947	NM_153127	105450	Mm.272673	NM_153127	ENSMUSG00000041445	Mmrn2	AA986839|ENDOGLYX1|Emilin3|EndoGlyx-1	multimerin 2	protein-coding
mm_37525.1	chr4	124738777	124738805	-	1	NA	Intergenic	Intergenic	-3059	NM_008385	16330	Mm.296202	NM_008385	ENSMUSG00000028894	Inpp5b	5PTase|AW260155|INPP5P	inositol polyphosphate-5-phosphatase B	protein-coding
mm_159096.1	chr2	35696705	35696705	+	1	NA	promoter-TSS (NM_001290639)	promoter-TSS (NM_001290639)	-27	NM_001290639	69601	Mm.29629	NM_001001602	ENSMUSG00000026883	Dab2ip	2310011D08Rik|AI480459|Aip1|mKIAA1743	disabled 2 interacting protein	protein-coding
mm_122072.1	chr14	30596543	30596546	-	1	NA	intron (NM_011103, intron 17 of 17)	MER58B|DNA|hAT-Charlie	13766	NM_001310682	18753	Mm.2314	NM_011103	ENSMUSG00000021948	Prkcd	AI385711|D14Ertd420e|PKC[d]|PKCdelta|Pkcd	protein kinase C, delta	protein-coding
mm_125878.1	chr15	75634213	75634221	+	1	NA	Intergenic	RLTR14-int|LTR|ERV1	17533	NM_011759	22701	Mm.87210	NM_011759	ENSMUSG00000047003	Zfp41	CTfin92|Zfp-41	zinc finger protein 41	protein-coding
mm_26217.1	chr3	138793341	138793362	+	1	NA	intron (NM_019571, intron 1 of 7)	intron (NM_019571, intron 1 of 7)	51143	NM_019571	56224	Mm.31927	NM_019571	ENSMUSG00000028152	Tspan5	2810455A09Rik|4930505M03Rik|NET-4|Tm4sf9	tetraspanin 5	protein-coding
mm_129930.1	chr15	84557755	84557773	-	1	NA	promoter-TSS (NM_177630)	promoter-TSS (NM_177630)	59	NM_177630	223732	Mm.6471	NM_177630	ENSMUSG00000055745	Ldoc1l	BC058638|Mar6|Mart6	leucine zipper, down-regulated in cancer 1-like	protein-coding
mm_48689.1	chr5	146763088	146763096	-	1	NA	intron (NM_011669, intron 3 of 8)	(A)n|Simple_repeat|Simple_repeat	31864	NM_011669	22217	Mm.167971	NM_011669	ENSMUSG00000029640	Usp12	Ubh1	ubiquitin specific peptidase 12	protein-coding
mm_22710.1	chr3	19188086	19188098	+	1	NA	promoter-TSS (NM_026182)	promoter-TSS (NM_026182)	-129	NM_026182	67472	Mm.45125	NM_026182	ENSMUSG00000027601	Mtfr1	1300002C08Rik|1700080D04Rik|2810026O10Rik|4930579E05Rik|Chppr|Fam54a2	mitochondrial fission regulator 1	protein-coding
mm_140988.1	chr17	24849961	24849979	-	1	NA	promoter-TSS (NM_024284)	promoter-TSS (NM_024284)	332	NM_023480	68636	Mm.347964	NM_023480	ENSMUSG00000045316	Fahd1	1110025H10Rik|AV002085	fumarylacetoacetate hydrolase domain containing 1	protein-coding
mm_68916.1	chr7	126460917	126460927	-	1	NA	intron (NM_007504, intron 3 of 22)	intron (NM_007504, intron 3 of 22)	2151	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_14859.1	chr2	148782051	148782072	+	1	NA	promoter-TSS (NM_030135)	promoter-TSS (NM_030135)	52	NM_030135	78609	Mm.160102	NM_030135	ENSMUSG00000027444	8030411F24Rik	Cst14	RIKEN cDNA 8030411F24 gene	protein-coding
mm_103002.1	chr11	69693652	69693667	-	1	NA	exon (NM_001159503, exon 4 of 13)	exon (NM_001159503, exon 4 of 13)	2439	NM_011614	21944	Mm.8983	NM_011614	ENSMUSG00000097328	Tnfsf12	Apo3l|Dr3l|Dr3lg|Tweak	tumor necrosis factor (ligand) superfamily, member 12	protein-coding
mm_55019.1	chr6	48841047	48841057	-	1	NA	promoter-TSS (NM_001164209)	promoter-TSS (NM_001164209)	-64	NM_023056	65963	Mm.28385	NM_023056	ENSMUSG00000029810	Tmem176b	1810009M01Rik|Clast1|Lr8	transmembrane protein 176B	protein-coding
mm_163055.1	chr11	59541401	59541446	-	1	NA	Intergenic	Intergenic	-1263	NM_145827	216799	Mm.54174	NM_145827	ENSMUSG00000032691	Nlrp3	AGTAVPRL|AII/AVP|Cias1|FCAS|FCU|MWS|Mmig1|NALP3|Pypaf1	NLR family, pyrin domain containing 3	protein-coding
mm_97864.1	chr11	83116975	83116999	+	1	NA	5' UTR (NM_011407, exon 1 of 2)	5' UTR (NM_011407, exon 1 of 2)	142	NM_011407	20555	Mm.10948	NM_011407	ENSMUSG00000078763	Slfn1	AV316259	schlafen 1	protein-coding
mm_78125.1	chr9	20646659	20646680	+	1	NA	3' UTR (NM_001310746, exon 5 of 5)	3' UTR (NM_001310746, exon 5 of 5)	1845	NM_001310746	66177	Mm.390165	NM_025401	ENSMUSG00000084786	Ubl5	1110030M22Rik|beacon	ubiquitin-like 5	protein-coding
mm_139355.1	chr17	50513206	50513209	+	1	NA	intron (NM_013880, intron 1 of 5)	intron (NM_013880, intron 1 of 5)	3660	NM_013880	224860	Mm.217362	NM_013880	ENSMUSG00000038910	Plcl2	PLC-L2|PRIP-2|Plce2|mKIAA1092	phospholipase C-like 2	protein-coding
mm_154696.1	chrX	8132180	8132233	+	1	NA	intron (NM_028542, intron 1 of 8)	intron (NM_028542, intron 1 of 8)	652	NM_001290783	73447	Mm.284162	NM_026137	ENSMUSG00000031166	Wdr13	1700060B08Rik|5730411P10Rik|DXHXS7467e|W51679|mMg21	WD repeat domain 13	protein-coding
mm_69084.1	chr7	127016612	127016622	-	1	NA	TTS (NM_001102563)	TTS (NM_001102563)	735	NM_030240	67278	Mm.345385	NM_030240	ENSMUSG00000030680	Pagr1a	2900092E17Rik|C77040|PA1|PAGR1	PAXIP1 associated glutamate rich protein 1A	protein-coding
mm_42288.1	chr5	114380592	114380612	+	1	NA	promoter-TSS (NM_001159941)	promoter-TSS (NM_001159941)	-18	NM_001331219	117146	Mm.28792	NM_054093	ENSMUSG00000029577	Ube3b	AI449831|AU020130	ubiquitin protein ligase E3B	protein-coding
mm_152823.1	chr19	23136485	23136501	-	1	NA	Intergenic	Intergenic	-4733	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_139565.1	chr17	56990332	56990350	+	1	NA	promoter-TSS (NM_017393)	promoter-TSS (NM_017393)	77	NM_017393	53895	Mm.287892	NM_017393	ENSMUSG00000002660	Clpp	AU019820|D17Wsu160e	caseinolytic mitochondrial matrix peptidase proteolytic subunit	protein-coding
mm_157537.1	chrX	51146415	51146416	-	1	NA	intron (NM_001310515, intron 1 of 6)	intron (NM_001310515, intron 1 of 6)	59575	NM_001310515	171170	Mm.295324	NM_134163	ENSMUSG00000036109	Mbnl3	A530038J18Rik|AI661274|CHCR|E430034C16Rik|MBLX|MBLX39|MBXL	muscleblind-like 3 (Drosophila)	protein-coding
mm_70441.1	chr8	11727946	11727967	+	1	NA	promoter-TSS (NM_001113517)	promoter-TSS (NM_001113517)	-149	NM_001113517	54126	Mm.244068	NM_017402	ENSMUSG00000031511	Arhgef7	Cool|PIX|Pak3bp|betaPix|betaPix-b|betaPix-c|cool-1|mKIAA0142|p85Cool1|p85SPR	Rho guanine nucleotide exchange factor (GEF7)	protein-coding
mm_27540.1	chr3	57576456	57576469	-	1	NA	promoter-TSS (NM_133784)	promoter-TSS (NM_133784)	-552	NM_001168281	97064	Mm.405029	NM_133784	ENSMUSG00000027803	Wwtr1	2310058J06Rik|2610021I22Rik|C78399|Taz	WW domain containing transcription regulator 1	protein-coding
mm_150937.1	chr19	46305973	46305981	+	1	NA	promoter-TSS (NM_001177370)	promoter-TSS (NM_001177370)	47	NM_001177370	18034	Mm.102365	NM_019408	ENSMUSG00000025225	Nfkb2	NF-kappaB2|lyt|p49|p49/p100|p50B|p52	nuclear factor of kappa light polypeptide gene enhancer in B cells 2, p49/p100	protein-coding
mm_158353.1	chrX	134583568	134583581	-	1	NA	promoter-TSS (NM_013482)	promoter-TSS (NM_013482)	-434	NM_013482	12229	Mm.4475	NM_013482	ENSMUSG00000031264	Btk	AI528679|xid	Bruton agammaglobulinemia tyrosine kinase	protein-coding
mm_37518.1	chr4	124451287	124451311	-	1	NA	intron (NR_040774, intron 2 of 3)	intron (NR_040774, intron 2 of 3)	34660	NR_040774	78460	Mm.452060	NR_040774		1700057H15Rik	-	RIKEN cDNA 1700057H15 gene	ncRNA
mm_7115.1	chr1	90014486	90014507	-	1	NA	promoter-TSS (NM_139152)	promoter-TSS (NM_139152)	81	NM_139152	208372	Mm.215164	NM_139152	ENSMUSG00000067081	Asb18	Asb-18	ankyrin repeat and SOCS box-containing 18	protein-coding
mm_113006.1	chr13	21866303	21866310	+	1	NA	Intergenic	Lx3B|LINE|L1	30743	NR_035500	100316716		NR_035500	ENSMUSG00000088148	Mir1983	mmu-mir-1983	microRNA 1983	ncRNA
mm_62775.1	chr7	112374840	112374864	+	1	NA	intron (NM_027587, intron 1 of 9)	intron (NM_027587, intron 1 of 9)	6544	NM_027587	100504195	Mm.291129	NM_027587	ENSMUSG00000030771	Micalcl	4921517J23Rik	MICAL C-terminal like	protein-coding
mm_113251.1	chr13	27637566	27637591	+	1	NA	exon (NM_001164058, exon 5 of 7)	exon (NM_001164058, exon 5 of 7)	4915	NM_001164058	19113	Mm.196424	NM_008930	ENSMUSG00000006488	Prl7a1	AA407021|AA409971|AA410116|PLP-E|PLP-G|Prlpe|Prlpg	prolactin family 7, subfamily a, member 1	protein-coding
mm_1807.1	chr1	81077257	81077265	+	1	NA	promoter-TSS (NM_172849)	promoter-TSS (NM_172849)	-56	NM_172849	241134	Mm.313904	NM_172849	ENSMUSG00000054976	Nyap2	9430031J16Rik|Jr6|Kiaa1486	neuronal tyrosine-phophorylated phosphoinositide 3-kinase adaptor 2	protein-coding
mm_97145.1	chr11	75452721	75452724	+	1	NA	exon (NM_138950, exon 1 of 10)	exon (NM_138950, exon 1 of 10)	1995	NM_138950	192652	Mm.340378	NM_138950	ENSMUSG00000045374	Wdr81	BC054822|Gm883|mFLJ00182|nur5	WD repeat domain 81	protein-coding
mm_165259.1	chr2	72970637	72970644	+	1	NA	exon (NM_001098425, exon 2 of 5)	exon (NM_001098425, exon 2 of 5)	8641	NM_001098425	20687	Mm.124328	NM_011450	ENSMUSG00000027109	Sp3	D130027J01Rik	trans-acting transcription factor 3	protein-coding
mm_32405.1	chr4	106923232	106923276	+	1	NA	intron (NM_023672, intron 4 of 17)	intron (NM_023672, intron 4 of 17)	11784	NM_023672	72475	Mm.195635	NM_023672	ENSMUSG00000061887	Ssbp3	2610021L12Rik|2610200M23Rik|5730488C10Rik|AI854733|AW551939|LAST|SSDP1	single-stranded DNA binding protein 3	protein-coding
mm_10426.1	chr2	13582630	13582678	+	1	NA	3' UTR (NM_011701, exon 9 of 9)	3' UTR (NM_011701, exon 9 of 9)	8343	NM_011701	22352	Mm.268000	NM_011701	ENSMUSG00000026728	Vim	-	vimentin	protein-coding
mm_92689.1	chr10	80657093	80657098	-	1	NA	promoter-TSS (NM_145361)	promoter-TSS (NM_145361)	-24	NM_145361	208198	Mm.60720	NM_145361	ENSMUSG00000003344	Btbd2	2610037C03Rik|4930512K17Rik	BTB (POZ) domain containing 2	protein-coding
mm_85654.1	chr9	107662020	107662030	-	1	NA	intron (NM_001199218, intron 1 of 15)	intron (NM_001199218, intron 1 of 15)	5374	NM_023805	76257	Mm.296560	NM_023805	ENSMUSG00000010064	Slc38a3	0610012J02Rik|D9Ucla2|Nat1|Slc38-3|Sn1|Snat3|mNAT	solute carrier family 38, member 3	protein-coding
mm_171388.1	chr4	121867088	121867094	+	1	NA	Intergenic	RMER16_Mm|LTR|ERVK	-244966	NM_001099309	666927	Mm.465133	NM_001099309	ENSMUSG00000078575	Gm12887	OTTMUSG00000008910	predicted gene 12887	protein-coding
mm_142127.1	chr17	35897372	35897418	-	1	NA	promoter-TSS (NM_001033630)	promoter-TSS (NM_001033630)	-17	NM_001033630	69662	Mm.260159	NM_001033630	ENSMUSG00000050705	2310061I04Rik	-	RIKEN cDNA 2310061I04 gene	protein-coding
mm_110824.1	chr12	72490087	72490091	-	1	NA	intron (NM_030070, intron 23 of 24)	RLTR19|LTR|ERVK	-46268	NM_026327	67708	Mm.11233	NM_026327	ENSMUSG00000034501	Pcnx4	1810048J11Rik|4932413O10|AU017192|Pcnxl4	pecanex homolog 4	protein-coding
mm_89929.1	chr10	111233541	111233556	+	1	NA	intron (NM_175489, intron 3 of 23)	(TTTTC)n|Simple_repeat|Simple_repeat	-65131	NM_027914	71769	Mm.45256	NM_027914	ENSMUSG00000035759	Bbs10	1300007O09Rik|AI452285	Bardet-Biedl syndrome 10 (human)	protein-coding
mm_83260.1	chr9	42457587	42457591	-	1	NA	intron (NM_173038, intron 1 of 7)	intron (NM_173038, intron 1 of 7)	14637	NM_173038	272589	Mm.34483	NM_173038	ENSMUSG00000037287	Tbcel	D330014K23|E130107N23Rik|Lrrc35	tubulin folding cofactor E-like	protein-coding
mm_78155.1	chr9	21025480	21025511	+	1	NA	intron (NM_010493, intron 2 of 6)	intron (NM_010493, intron 2 of 6)	-3878	NM_023892	78369	Mm.30220	NM_023892	ENSMUSG00000001014	Icam4	1810015M19Rik|Cd242|ICAM-4	intercellular adhesion molecule 4, Landsteiner-Wiener blood group	protein-coding
mm_39826.1	chr5	30798267	30798326	+	1	NA	3' UTR (NM_023047, exon 13 of 13)	3' UTR (NM_023047, exon 13 of 13)	-16345	NM_133350	100732	Mm.332295	NM_133350	ENSMUSG00000029166	Mapre3	AI790651|EB2|EB3|EBF3|RP3	microtubule-associated protein, RP/EB family, member 3	protein-coding
mm_133040.1	chr16	57443392	57443395	+	1	NA	intron (NM_001040397, intron 1 of 4)	B1F|SINE|Alu	90116	NM_001040397	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding
mm_57384.1	chr6	124818040	124818054	-	1	NA	intron (NM_001326594, intron 15 of 19)	intron (NM_001326594, intron 15 of 19)	-3751	NM_009415	21991	Mm.4222	NM_009415	ENSMUSG00000023456	Tpi1	AI255506|Tpi|Tpi-1	triosephosphate isomerase 1	protein-coding
mm_172655.1	chr8	36953187	36953188	-	1	NA	promoter-TSS (NM_001194940)	promoter-TSS (NM_001194940)	-745	NM_001194940	50768	Mm.125155	NM_015802	ENSMUSG00000031523	Dlc1	A730069N07Rik|Arhgap7|HP|STARD12|dlc-1	deleted in liver cancer 1	protein-coding
mm_156874.1	chrX	164980661	164980724	+	1	NA	promoter-TSS (NM_175027)	promoter-TSS (NM_175027)	100	NM_175027	237211	Mm.336317	NM_175027	ENSMUSG00000047757	Fancb	BC022692	Fanconi anemia, complementation group B	protein-coding
mm_143308.1	chr17	66042563	66042568	-	1	NA	exon (NM_001025572, exon 4 of 13)	exon (NM_001025572, exon 4 of 13)	34481	NM_001025572	106585	Mm.34706	NM_001025572	ENSMUSG00000034647	Ankrd12	2900001A12Rik|AI447928|ANCO-2|AV347965|GAC-1|mKIAA0874	ankyrin repeat domain 12	protein-coding
mm_44069.1	chr5	148653075	148653094	+	1	NA	Intergenic	Intergenic	-88756	NR_028285	70138	Mm.417834	NR_028285	ENSMUSG00000086494	2210417A02Rik	AV081004	RIKEN cDNA 2210417A02 gene	ncRNA
mm_6864.1	chr1	84278447	84278459	-	1	NA	intron (NM_001003948, intron 1 of 2)	intron (NM_001003948, intron 1 of 2)	6192	NM_001003948	98496	Mm.187470	NM_001003948	ENSMUSG00000045658	Pid1	5033414K04Rik|NYGGF4	phosphotyrosine interaction domain containing 1	protein-coding
mm_9819.1	chr1	182282739	182282807	-	1	NA	promoter-TSS (NM_007853)	promoter-TSS (NM_007853)	-14	NM_007853	13244	Mm.29648	NM_007853	ENSMUSG00000038633	Degs1	AA536663|Degs|Des1|Mdes	delta(4)-desaturase, sphingolipid 1	protein-coding
mm_134069.1	chr16	8660614	8660637	-	1	NA	3' UTR (NM_025821, exon 4 of 4)	3' UTR (NM_025821, exon 4 of 4)	11528	NM_025821	52502	Mm.142095	NM_025821	ENSMUSG00000008393	Carhsp1	1200011K09Rik|Crhsp-24|D16Ertd465e	calcium regulated heat stable protein 1	protein-coding
mm_19011.1	chr2	76905618	76905629	-	1	NA	intron (NM_011652, intron 46 of 312)	intron (NM_011652, intron 46 of 312)	76924	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_22687.1	chr3	17789893	17789955	+	1	NA	promoter-TSS (NR_033490)	promoter-TSS (NR_033490)	3	NR_033490	70441	Mm.458192	NR_033490	ENSMUSG00000100252	Mir124-2hg	100040120|2610100L16Rik|6430547I21Rik|A930005K07Rik|AW125202|Gm2612	Mir124-2 host gene (non-protein coding)	ncRNA
mm_137707.1	chr17	29098758	29098815	+	1	NA	exon (NM_007669, exon 2 of 3)	exon (NM_007669, exon 2 of 3)	5017	NM_007669	12575	Mm.195663	NM_007669	ENSMUSG00000023067	Cdkn1a	CAP20|CDKI|CIP1|Cdkn1|P21|SDI1|Waf1|mda6|p21Cip1|p21WAF	cyclin-dependent kinase inhibitor 1A (P21)	protein-coding
mm_114047.1	chr13	54192107	54192151	+	1	NA	promoter-TSS (NM_008286)	promoter-TSS (NM_008286)	0	NM_001010973	15466	Mm.57243	NM_008286	ENSMUSG00000034987	Hrh2	-	histamine receptor H2	protein-coding
mm_70181.1	chr7	143766917	143766928	-	1	NA	promoter-TSS (NM_203492)	promoter-TSS (NM_203492)	71	NM_203492	381974	Mm.297839	NM_203492	ENSMUSG00000050276	Mrgprg	Gm1098|Mrgg	MAS-related GPR, member G	protein-coding
mm_74089.1	chr8	122564784	122564800	+	1	NA	Intergenic	Intergenic	-3223	NM_026014	67177	Mm.21873	NM_026014	ENSMUSG00000006585	Cdt1	2610318F11Rik|AW545653|C76791|Ris2	chromatin licensing and DNA replication factor 1	protein-coding
mm_131867.1	chr16	23157334	23157349	+	1	NA	exon (NM_009605, exon 3 of 3)	exon (NM_009605, exon 3 of 3)	10805	NM_009605	11450	Mm.3969	NM_009605	ENSMUSG00000022878	Adipoq	30kDa|APN|Acdc|Acrp30|Ad|GBP28|adipo|apM1	adiponectin, C1Q and collagen domain containing	protein-coding
mm_78784.1	chr9	44022363	44022378	+	1	NA	Intergenic	B4A|SINE|B4	-21014	NM_009382	21838	Mm.3951	NM_009382	ENSMUSG00000032011	Thy1	CD90|T25|Thy-1|Thy-1.2|Thy1.1|Thy1.2	thymus cell antigen 1, theta	protein-coding
mm_141947.1	chr17	35066195	35066205	-	1	NA	promoter-TSS (NM_001191012)	promoter-TSS (NM_001191012)	-16	NM_001191012	106722	Mm.390956	NM_001033221	ENSMUSG00000073414	G6b	AU023871|C6orf25|Ng31	immunoreceptor tyrosine-based inhibitory motif (ITIM) containing platelet receptor	protein-coding
mm_28536.1	chr3	92720382	92720387	-	1	NA	promoter-TSS (NM_026394)	promoter-TSS (NM_026394)	-34	NM_026394	67828	Mm.158176	NM_026394	ENSMUSG00000042124	Lce1f	1110055J05Rik	late cornified envelope 1F	protein-coding
mm_92729.1	chr10	80844026	80844067	-	1	NA	promoter-TSS (NM_001013758)	promoter-TSS (NM_001013758)	-7	NM_001013758	237403	Mm.40213	NM_001013758	ENSMUSG00000051067	Lingo3	AI851712|LERN2	leucine rich repeat and Ig domain containing 3	protein-coding
mm_33629.1	chr4	132795068	132795076	+	1	NA	intron (NM_001033308, intron 1 of 5)	intron (NM_001033308, intron 1 of 5)	1292	NM_001033308	230787	Mm.290912	NM_001033308	ENSMUSG00000037731	Themis2	ICB-1	thymocyte selection associated family member 2	protein-coding
mm_37013.1	chr4	112774861	112774871	-	1	NA	promoter-TSS (NM_177668)	promoter-TSS (NM_177668)	-5	NM_177668	230613	Mm.122553	NM_177668	ENSMUSG00000048766	Skint10	A030001H23Rik|Gm570	selection and upkeep of intraepithelial T cells 10	protein-coding
mm_66180.1	chr7	34037471	34037471	-	1	NA	Intergenic	RLTR13F|LTR|ERVK	15904	NM_009596	11354	Mm.8025	NM_009596	ENSMUSG00000066583	Scgb1b27	Abp|Abpa|Abpa27|Sal-1|Tcp	secretoglobin, family 1B, member 27	protein-coding
mm_126954.1	chr15	92161445	92161461	+	1	NA	promoter-TSS (NM_001159647)	promoter-TSS (NM_001159647)	96	NM_001159647	12805	Mm.4911	NM_007727	ENSMUSG00000055022	Cntn1	AW495098|CNTN|F3cam|usl	contactin 1	protein-coding
mm_8212.1	chr1	138136535	138136547	-	1	NA	intron (NM_001111316, intron 1 of 31)	intron (NM_001111316, intron 1 of 31)	38585	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_143426.1	chr17	70849782	70849825	-	1	NA	promoter-TSS (NM_001164076)	promoter-TSS (NM_001164076)	-13	NM_001164076	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_16016.1	chr2	167443764	167443768	+	1	NA	intron (NR_130767, intron 5 of 13)	PB1D9|SINE|Alu	22056	NM_001304542	77031	Mm.278924	NM_148929	ENSMUSG00000039463	Slc9a8	1200006P13Rik|6430709P13Rik|AI182282|NHE-8|NHE8	solute carrier family 9 (sodium/hydrogen exchanger), member 8	protein-coding
mm_152875.1	chr19	24514806	24514812	-	1	NA	intron (NM_008846, intron 1 of 14)	intron (NM_008846, intron 1 of 14)	-37335	NM_026520	68034	Mm.440181	NM_026520	ENSMUSG00000074922	Fam122a	2410124L17Rik|2900009I07Rik|ENSMUSG00000051082|Gm9849	family with sequence similarity 122, member A	protein-coding
mm_133898.1	chr16	97543892	97543901	+	1	NA	intron (NM_013606, intron 2 of 13)	intron (NM_013606, intron 2 of 13)	7813	NM_013606	17858	Mm.14157	NM_013606	ENSMUSG00000023341	Mx2	AI528743|Mx-2	MX dynamin-like GTPase 2	protein-coding
mm_134987.1	chr16	32143167	32143194	-	1	NA	exon (NM_001347181, exon 3 of 3)	exon (NM_001347181, exon 3 of 3)	22296	NM_146069	224109	Mm.33498	NM_146069	ENSMUSG00000052384	Nrros	E430025L02Rik|Lrcc33|Lrrc33	negative regulator of reactive oxygen species	protein-coding
mm_164104.1	chr15	25426027	25426027	+	1	NA	intron (NR_027376, intron 1 of 1)	MER58A|DNA|hAT-Charlie	11835	NR_027376	432939	Mm.146555	NM_001013791		Gm5468	100040583|EG432939	predicted gene 5468	ncRNA
mm_71048.1	chr8	33694603	33694606	+	1	NA	intron (NM_010344, intron 11 of 12)	intron (NM_010344, intron 11 of 12)	-37310	NM_001167921	68153	Mm.286104	NM_026584	ENSMUSG00000031585	Gtf2e2	34kDa|AI462509|C330006J08Rik	general transcription factor II E, polypeptide 2 (beta subunit)	protein-coding
mm_74249.1	chr8	124831756	124831771	+	1	NA	3' UTR (NM_198632, exon 10 of 10)	3' UTR (NM_198632, exon 10 of 10)	31266	NM_025615	66523	Mm.436864	NM_025615	ENSMUSG00000031984	2810004N23Rik	3110004G14Rik|Ayu21-55|Gt(pU21)55Imeg|GtAyu21-55	RIKEN cDNA 2810004N23 gene	protein-coding
mm_152078.1	chr19	6857482	6857504	-	1	NA	exon (NM_001081291, exon 3 of 27)	exon (NM_001081291, exon 3 of 27)	718	NM_001081291	78317	Mm.329596	NM_198008	ENSMUSG00000047810	Ccdc88b	2610041P08Rik|Ccdc88	coiled-coil domain containing 88B	protein-coding
mm_145174.1	chr18	46958843	46958889	+	1	NA	promoter-TSS (NM_178377)	promoter-TSS (NM_178377)	-10	NM_178377	69456	Mm.210734	NM_178377	ENSMUSG00000042705	Commd10	2310003A05Rik|AU019438|DRWMS2	COMM domain containing 10	protein-coding
mm_7859.1	chr1	132529022	132529025	-	1	NA	exon (NM_177129, exon 4 of 23)	exon (NM_177129, exon 4 of 23)	13917	NM_177129	21367	Mm.260861	NM_011531	ENSMUSG00000053024	Cntn2	D130012K04Rik|TAG-1|Tax	contactin 2	protein-coding
mm_58.1	chr1	6544997	6545036	+	1	NA	intron (NM_001244693, intron 2 of 22)	intron (NM_001244693, intron 2 of 22)	57785	NM_001244692	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding
mm_41677.1	chr5	99906255	99906284	+	1	NA	Intergenic	CpG	72669	NM_001077266	11991	Mm.150231	NM_007516	ENSMUSG00000000568	Hnrnpd	Auf1|Hnrpd	heterogeneous nuclear ribonucleoprotein D	protein-coding
mm_146505.1	chr18	3309879	3309916	-	1	NA	non-coding (NR_073193, exon 3 of 8)	non-coding (NR_073193, exon 3 of 8)	-10341	NM_001110853	12916	Mm.5244	NM_013498	ENSMUSG00000063889	Crem	ICER|ICERI	cAMP responsive element modulator	protein-coding
mm_145278.1	chr18	53147879	53147882	+	1	NA	Intergenic	Intergenic	-28485	NM_026386	67804	Mm.252171	NM_026386	ENSMUSG00000034484	Snx2	0610030A03Rik	sorting nexin 2	protein-coding
mm_138769.1	chr17	37082906	37082910	+	1	NA	Intergenic	PB1D7|SINE|Alu	3328	NM_146477	258469	Mm.271392	NM_146477	ENSMUSG00000056600	Olfr90	MOR256-21|bM573K1.2	olfactory receptor 90	protein-coding
mm_23680.1	chr3	68618022	68618034	+	1	NA	intron (NM_001113419, intron 8 of 10)	intron (NM_001113419, intron 8 of 10)	45660	NM_013928	30953	Mm.331064	NM_013928	ENSMUSG00000027777	Schip1	Nf2ip|Schip-1	schwannomin interacting protein 1	protein-coding
mm_170257.1	chr18	14065619	14065632	-	1	NA	Intergenic	4.5SRNA|scRNA|scRNA	-92892	NM_145492	225207	Mm.40325	NM_145492	ENSMUSG00000024420	Zfp521	B930086A16Rik|Evi3|Znf521	zinc finger protein 521	protein-coding
mm_141398.1	chr17	29261969	29261981	-	1	NA	intron (NM_026845, intron 1 of 3)	intron (NM_026845, intron 1 of 3)	1996	NM_026845	68816	Mm.328928	NM_026845	ENSMUSG00000024007	Ppil1	1110060O10Rik|AI327391|Cypl1	peptidylprolyl isomerase (cyclophilin)-like 1	protein-coding
mm_132532.1	chr16	37868185	37868203	+	1	NA	promoter-TSS (NM_177093)	promoter-TSS (NM_177093)	-206	NM_177093	320184	Mm.390882	NM_177093	ENSMUSG00000034158	Lrrc58	1810012N18Rik|C330018J07Rik	leucine rich repeat containing 58	protein-coding
mm_114025.1	chr13	52634280	52634297	+	1	NA	intron (NM_001198977, intron 9 of 13)	L1MC|LINE|L1	37406	NM_011518	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_23391.1	chr3	57433772	57433803	+	1	NA	exon (NM_145539, exon 3 of 5)	exon (NM_145539, exon 3 of 5)	8377	NM_145539	229302	Mm.26618	NM_145539	ENSMUSG00000027801	Tm4sf4	Iltmp	transmembrane 4 superfamily member 4	protein-coding
mm_164050.1	chr14	102811196	102811205	-	1	NA	Intergenic	Intergenic	171432	NR_039592	100628599		NR_039592	ENSMUSG00000092901	Mir5130	mir-5130|mmu-mir-5130|mu-mir-5130	microRNA 5130	ncRNA
mm_89478.1	chr10	93554863	93554866	+	1	NA	intron (NM_175488, intron 4 of 15)	intron (NM_175488, intron 4 of 15)	14232	NM_175488	237465	Mm.477086	NM_175488	ENSMUSG00000036168	Ccdc38	4933417K05Rik	coiled-coil domain containing 38	protein-coding
mm_66757.1	chr7	46714515	46714526	-	1	NA	intron (NM_011315, intron 2 of 3)	MIRb|SINE|MIR	1156	NM_011315	20210	Mm.14277	NM_011315	ENSMUSG00000040026	Saa3	AV098916|Saa-3|l7R3	serum amyloid A 3	protein-coding
mm_166918.1	chr7	30515230	30515236	+	1	NA	intron (NR_036630, intron 1 of 11)	intron (NR_036630, intron 1 of 11)	111	NR_036630	100504207	Mm.297831	NM_001004161	ENSMUSG00000062132	Arhgap33os	Gm1082	Rho GTPase activating protein 33, opposite strand	ncRNA
mm_114331.1	chr13	60646910	60646925	+	1	NA	intron (NM_029653, intron 2 of 25)	Lx8b|LINE|L1	44706	NM_134062	69635	Mm.24103	NM_029653	ENSMUSG00000021559	Dapk1	D13Ucla1|DAP-Kinase	death associated protein kinase 1	protein-coding
mm_48094.1	chr5	137061927	137061930	-	1	NA	3' UTR (NM_008871, exon 9 of 9)	3' UTR (NM_008871, exon 9 of 9)	10344	NM_008871	18787	Mm.250422	NM_008871	ENSMUSG00000037411	Serpine1	PAI-1|PAI1|Planh1	serine (or cysteine) peptidase inhibitor, clade E, member 1	protein-coding
mm_134288.1	chr16	14217991	14218011	-	1	NA	exon (NM_013607, exon 24 of 42)	exon (NM_013607, exon 24 of 42)	54726	NM_001114085	67203	Mm.24105	NM_023317	ENSMUSG00000022678	Nde1	2810027M15Rik|AU042936|AW822251|Nude|mNudE	nudE neurodevelopment protein 1	protein-coding
mm_90353.1	chr10	127165293	127165303	+	1	NA	promoter-TSS (NM_027739)	promoter-TSS (NM_027739)	142	NM_001244617	14421	Mm.386762	NM_008080	ENSMUSG00000006731	B4galnt1	4933429D13Rik|Gal-NAc-T|GalNAc-T|GalNAcT|Galgt1|Ggm-2|Ggm2	beta-1,4-N-acetyl-galactosaminyl transferase 1	protein-coding
mm_157750.1	chrX	73491403	73491436	-	1	NA	exon (NM_007542, exon 3 of 8)	exon (NM_007542, exon 3 of 8)	7818	NM_007542	12111	Mm.2608	NM_007542	ENSMUSG00000031375	Bgn	BG|DSPG1|PG-S1|PGI|SLRR1A	biglycan	protein-coding
mm_38968.1	chr4	150902128	150902147	-	1	NA	intron (NM_020569, intron 5 of 6)	intron (NM_020569, intron 5 of 6)	7784	NM_020569	57320	Mm.277349	NM_020569	ENSMUSG00000028964	Park7	DJ-1|Dj1	Parkinson disease (autosomal recessive, early onset) 7	protein-coding
mm_118154.1	chr13	105249802	105249816	-	1	NA	exon (NM_027934, exon 4 of 8)	exon (NM_027934, exon 4 of 8)	43205	NM_027934	71816	Mm.317015	NM_027934	ENSMUSG00000021720	Rnf180	3110001E11Rik|Rines	ring finger protein 180	protein-coding
mm_67250.1	chr7	75455384	75455398	-	1	NA	promoter-TSS (NM_029332)	promoter-TSS (NM_029332)	-143	NM_029332	75547	Mm.216107	NM_029332	ENSMUSG00000066406	Akap13	1700026G02Rik|5730522G15Rik|5830460E08Rik|AKAP-13|AKAP-Lbc|BRX|Ht31|LBC|PROTO-LB|PROTO-LBC	A kinase (PRKA) anchor protein 13	protein-coding
mm_20610.1	chr2	131847608	131847678	-	1	NA	promoter-TSS (NR_029381)	promoter-TSS (NR_029381)	13	NR_029381	414081	Mm.246905	NR_029381	ENSMUSG00000086822	5330413P13Rik	-	RIKEN cDNA 5330413P13 gene	ncRNA
mm_21018.1	chr2	152397851	152397868	-	1	NA	5' UTR (NM_011438, exon 1 of 1)	5' UTR (NM_011438, exon 1 of 1)	187	NM_011438	20667	Mm.28424	NM_011438	ENSMUSG00000051817	Sox12	2010205A02Rik	SRY (sex determining region Y)-box 12	protein-coding
mm_28405.1	chr3	90243074	90243109	-	1	NA	promoter-TSS (NM_001307935)	promoter-TSS (NM_001307935)	52	NM_001307934	78284	Mm.299952	NM_030080	ENSMUSG00000027938	Creb3l4	1700012K17Rik|5330432F22Rik|AIBZIP|AV040530|AV258827|CREB4|JAL|TISP40|acre1	cAMP responsive element binding protein 3-like 4	protein-coding
mm_75041.1	chr8	32673698	32673707	-	1	NA	Intergenic	L1MB3|LINE|L1	276324	NM_001177589	100042715	Mm.291093	NM_001177589		Gm3985	-	predicted gene 3985	protein-coding
mm_40682.1	chr5	65541952	65541955	+	1	NA	intron (NM_001310618, intron 1 of 4)	B1_Mur4|SINE|Alu	4708	NM_001310619	53323	Mm.319512	NM_016786	ENSMUSG00000029203	Ube2k	AW492011|D5Ertd601e|E2-25k|HIP-2|Hip2|Hypg|Lig	ubiquitin-conjugating enzyme E2K	protein-coding
mm_42083.1	chr5	110176869	110176896	+	1	NA	promoter-TSS (NR_040431)	promoter-TSS (NR_040431)	181	NM_008146	269682	Mm.9392	NM_008146	ENSMUSG00000029502	Golga3	5330413L04|5430416E01Rik|AI449376|AW490576|G1-499-14|Mea-2|Mea2|repro27	golgi autoantigen, golgin subfamily a, 3	protein-coding
mm_154010.1	chr19	53064478	53064482	-	1	NA	Intergenic	Intergenic	-11772	NR_045320	78457	Mm.76932	NR_045320	ENSMUSG00000099988	1700054A03Rik	-	RIKEN cDNA 1700054A03 gene	ncRNA
mm_93815.1	chr10	121426571	121426571	-	1	NA	intron (NM_138956, intron 1 of 4)	L1MDa|LINE|L1	49679	NM_138956	192678	Mm.41265	NM_138956	ENSMUSG00000025795	Rassf3	AW212023|AW322379	Ras association (RalGDS/AF-6) domain family member 3	protein-coding
mm_96954.1	chr11	70607102	70607113	+	1	NA	exon (NM_001045964, exon 14 of 33)	exon (NM_001045964, exon 14 of 33)	-8787	NM_001145537	668433	Mm.425687	NM_001145537	ENSMUSG00000087279	4930544D05Rik	-	RIKEN cDNA 4930544D05 gene	protein-coding
mm_108441.1	chr12	82373149	82373158	+	1	NA	intron (NM_172579, intron 5 of 20)	B1_Mur1|SINE|Alu	61804	NM_172579	217692	Mm.261333	NM_172579	ENSMUSG00000042700	Sipa1l1	4931426N11Rik|AW213287|Spar|mKIAA0440	signal-induced proliferation-associated 1 like 1	protein-coding
mm_48118.1	chr5	137139089	137139100	-	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	-22887	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_166438.1	chr5	137207759	137207784	-	1	NA	Intergenic	Intergenic	-80483	NM_009599	11423	Mm.255464	NM_009599	ENSMUSG00000023328	Ache	-	acetylcholinesterase	protein-coding
mm_41694.1	chr5	100650637	100650644	+	1	NA	Intergenic	Intergenic	23616	NM_027978	71883	Mm.260661	NM_027978	ENSMUSG00000029319	Coq2	2310002F18Rik|PHB:PPT	coenzyme Q2 4-hydroxybenzoate polyprenyltransferase	protein-coding
mm_65794.1	chr7	28898099	28898132	-	1	NA	exon (NM_021895, exon 15 of 21)	exon (NM_021895, exon 15 of 21)	16459	NM_001110807	60594	Mm.476990	NM_021894	ENSMUSG00000054083	Capn12	CANP 12	calpain 12	protein-coding
mm_56429.1	chr6	97312107	97312109	-	1	NA	intron (NM_001346639, intron 11 of 22)	intron (NM_001346639, intron 11 of 22)	-59328	NM_001081157	320502	Mm.68163	NM_001081157	ENSMUSG00000044086	Lmod3	5430424A14Rik	leiomodin 3 (fetal)	protein-coding
mm_79745.1	chr9	62367404	62367441	+	1	NA	intron (NM_009672, intron 1 of 6)	intron (NM_009672, intron 1 of 6)	26079	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	protein-coding
mm_97773.1	chr11	82057915	82057929	+	1	NA	promoter-TSS (NM_011330)	promoter-TSS (NM_011330)	90	NM_011330	20292	Mm.4686	NM_011330	ENSMUSG00000020676	Ccl11	Scya11|eotaxin	chemokine (C-C motif) ligand 11	protein-coding
mm_88614.1	chr10	79826119	79826138	+	1	NA	exon (NM_030218, exon 2 of 5)	exon (NM_030218, exon 2 of 5)	5107	NM_030218	78906	Mm.33087	NM_030218	ENSMUSG00000035852	Misp	9130017N09Rik	mitotic spindle positioning	protein-coding
mm_170153.1	chr17	45571171	45571180	-	1	NA	exon (NM_008302, exon 4 of 11)	exon (NM_008302, exon 4 of 11)	2086	NM_008302	15516	Mm.2180	NM_008302	ENSMUSG00000023944	Hsp90ab1	90kDa|AL022974|C81438|Hsp84|Hsp84-1|Hsp90|Hspcb	heat shock protein 90 alpha (cytosolic), class B member 1	protein-coding
mm_158796.1	chrX	167241508	167241522	-	1	NA	3' UTR (NM_001313760, exon 2 of 2)	3' UTR (NM_001313760, exon 2 of 2)	22814	NM_001313761	170744	Mm.196676	NM_133212	ENSMUSG00000040522	Tlr8	-	toll-like receptor 8	protein-coding
mm_60304.1	chr7	44097446	44097454	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-4842	NM_010642	16616	Mm.443292	NM_010642	ENSMUSG00000066516	Klk1b21	Klk21|mGk-21	kallikrein 1-related peptidase b21	protein-coding
mm_63563.1	chr7	128113204	128113215	+	1	NA	exon (NM_008401, exon 21 of 30)	exon (NM_008401, exon 21 of 30)	-16359	NM_021334	16411	Mm.22378	NM_021334	ENSMUSG00000030789	Itgax	AI449405|Cd11c|Cr4|N418	integrin alpha X	protein-coding
mm_109898.1	chr12	7901607	7901616	-	1	NA	Intergenic	Intergenic	-76066	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_9713.1	chr1	179803073	179803109	-	1	NA	intron (NM_026375, intron 1 of 35)	CpG	924	NM_026375	226747	Mm.128165	NM_026375	ENSMUSG00000026491	Ahctf1	6230412P20Rik|AV011447|Elys	AT hook containing transcription factor 1	protein-coding
mm_96343.1	chr11	66955089	66955102	+	1	NA	Intergenic	Intergenic	-1543	NR_130645	71576	Mm.340077	NR_130315	ENSMUSG00000085683	9130409J20Rik	-	RIKEN cDNA 9130409J20 gene	ncRNA
mm_43315.1	chr5	134946120	134946181	+	1	NA	exon (NM_009903, exon 1 of 1)	exon (NM_009903, exon 1 of 1)	784	NM_009903	12740	Mm.7339	NM_009903	ENSMUSG00000047501	Cldn4	Cep-r|Cpetr|Cpetr1	claudin 4	protein-coding
mm_90625.1	chr10	128459240	128459248	+	1	NA	promoter-TSS (NM_001114096)	promoter-TSS (NM_001114096)	8	NM_001114097	68094	Mm.417338	NM_198160	ENSMUSG00000025369	Smarcc2	5930405J04Rik	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2	protein-coding
mm_49193.1	chr6	15186805	15186844	+	1	NA	intron (NM_212435, intron 1 of 16)	intron (NM_212435, intron 1 of 16)	1318	NM_001286607	114142	Mm.332919	NM_053242	ENSMUSG00000029563	Foxp2	2810043D05Rik|AI449000|CAG-16|D0Kist7	forkhead box P2	protein-coding
mm_53188.1	chr6	125481969	125481979	+	1	NA	intron (NM_007657, intron 1 of 7)	intron (NM_007657, intron 1 of 7)	12781	NM_007657	12527	Mm.210676	NM_007657	ENSMUSG00000030342	Cd9	Tspan29	CD9 antigen	protein-coding
mm_147001.1	chr18	34372502	34372523	-	1	NA	intron (NM_007874, intron 1 of 4)	intron (NM_007874, intron 1 of 4)	903	NM_007874	13476	Mm.280075	NM_007874	ENSMUSG00000005873	Reep5	AI324241|AU022809|AW495741|DP1/TB2|Dp1|R74856|TB2/DP1	receptor accessory protein 5	protein-coding
mm_80872.1	chr9	98864869	98864894	+	1	NA	5' UTR (NM_028033, exon 1 of 1)	5' UTR (NM_028033, exon 1 of 1)	114	NM_028033	71979	Mm.140843	NM_028033	ENSMUSG00000090470	Prr23a3	2410012M07Rik	proline rich 23A, member 3	protein-coding
mm_19663.1	chr2	103281266	103281309	-	1	NA	intron (NM_007914, intron 2 of 8)	intron (NM_007914, intron 2 of 8)	21909	NM_007914	13661	Mm.10724	NM_007914	ENSMUSG00000012350	Ehf	9030625L19Rik|AU019492	ets homologous factor	protein-coding
mm_4122.1	chr1	169693667	169693695	+	1	NA	3' UTR (NM_009063, exon 5 of 5)	3' UTR (NM_009063, exon 5 of 5)	38180	NM_009063	19737	Mm.20954	NM_009063	ENSMUSG00000026678	Rgs5	1110070A02Rik	regulator of G-protein signaling 5	protein-coding
mm_138246.1	chr17	34589800	34589830	+	1	NA	promoter-TSS (NM_134116)	promoter-TSS (NM_134116)	9	NM_134116	106512	Mm.26584	NM_134116	ENSMUSG00000034786	Gpsm3	AA960287|AGS4	G-protein signalling modulator 3 (AGS3-like, C. elegans)	protein-coding
mm_60874.1	chr7	46033718	46033823	+	1	NA	promoter-TSS (NM_153057)	promoter-TSS (NM_153057)	74	NM_153057	211548	Mm.274811	NM_153057	ENSMUSG00000030835	Nomo1	D7Ertd156e|Nomo|pM5	nodal modulator 1	protein-coding
mm_48804.1	chr5	148959560	148959574	-	1	NA	Intergenic	G-rich|Low_complexity|Low_complexity	9317	NR_040686	71473	Mm.90306	NR_040686	ENSMUSG00000079069	8430423G03Rik	-	RIKEN cDNA 8430423G03 gene	ncRNA
mm_17209.1	chr2	25478061	25478072	-	1	NA	Intergenic	Intergenic	-8317	NM_008963	19215	Mm.1008	NM_008963	ENSMUSG00000015090	Ptgds	21kDa|L-PGDS|PGD2|PGDS|PGDS2|Ptgs3	prostaglandin D2 synthase (brain)	protein-coding
mm_9465.1	chr1	173333371	173333383	-	1	NA	TTS (NM_053199)	TTS (NM_053199)	126	NM_010045	13349	Mm.6393	NM_010045	ENSMUSG00000037872	Ackr1	AA162249|CCBP1|CD234|Darc|Dfy|ESTM35|FY|GPD	atypical chemokine receptor 1 (Duffy blood group)	protein-coding
mm_36104.1	chr4	58797598	58797601	-	1	NA	Intergenic	Intergenic	-11879	NM_146920	258922	Mm.223327	NM_146920	ENSMUSG00000043385	Olfr267	MOR262-1	olfactory receptor 267	protein-coding
mm_105834.1	chr11	113514541	113514571	-	1	NA	intron (NM_001166503, intron 4 of 9)	intron (NM_001166503, intron 4 of 9)	51259	NM_001166503	69806	Mm.341021	NM_027216	ENSMUSG00000041654	Slc39a11	1810074D23Rik	solute carrier family 39 (metal ion transporter), member 11	protein-coding
mm_109183.1	chr12	108472880	108472912	+	1	NA	intron (NM_001043335, intron 3 of 21)	intron (NM_001043335, intron 3 of 21)	50080	NM_001043335	68519	Mm.236645	NM_001043335	ENSMUSG00000058070	Eml1	1110008N23Rik|A930030P13Rik|AA171013|AI847476|AI853955|ELP79|EMAP|EMAPL|heco	echinoderm microtubule associated protein like 1	protein-coding
mm_76062.1	chr8	77947838	77947842	-	1	NA	Intergenic	MT2B|LTR|ERVL	-223388	NM_010332	13617	Mm.283168	NM_010332	ENSMUSG00000031616	Ednra	ET-AR|ETa|Gpcr10	endothelin receptor type A	protein-coding
mm_44656.1	chr5	28210415	28210428	-	1	NA	promoter-TSS (NM_001310511)	promoter-TSS (NM_001310511)	-253	NM_001310511	269637	Mm.68286	NM_175651	ENSMUSG00000044681	Cnpy1	1500012D20Rik|9630008K15Rik|AI853839	canopy FGF signaling regulator 1	protein-coding
mm_10125.1	chr2	3749949	3749952	+	1	NA	intron (NM_025626, intron 1 of 3)	intron (NM_025626, intron 1 of 3)	36492	NM_025626	66540	Mm.277864	NM_025626	ENSMUSG00000026655	Fam107b	3110001A13Rik|AA589595|AA959793|AI132312	family with sequence similarity 107, member B	protein-coding
mm_165576.1	chr3	26302246	26302248	+	1	NA	intron (NM_138666, intron 1 of 7)	intron (NM_138666, intron 1 of 7)	29662	NM_138666	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_61415.1	chr7	73586476	73586494	+	1	NA	Intergenic	B4A|SINE|B4	-28090	NR_037569	69170	Mm.34539	NR_037569	ENSMUSG00000101970	1810026B05Rik	-	RIKEN cDNA 1810026B05 gene	ncRNA
mm_131216.1	chr16	8831097	8831110	+	1	NA	intron (NM_001081400, intron 1 of 3)	CpG	1003	NM_001081400	69053	Mm.390868	NM_001081400	ENSMUSG00000022507	1810013L24Rik	1110017P05Rik|3010002C02Rik|AA792997|AW124177|Gm19906|R74903	RIKEN cDNA 1810013L24 gene	protein-coding
mm_168203.1	chr10	69895541	69895544	+	1	NA	intron (NM_146005, intron 18 of 42)	(GA)n|Simple_repeat|Simple_repeat	-29990	NM_170687	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_33146.1	chr4	125150791	125150817	+	1	NA	Intergenic	Intergenic	-22923	NM_153159	230738	Mm.402	NM_153159	ENSMUSG00000042677	Zc3h12a	BC036563|MCPIP|MCPIP-1|Mcpip1|Reg1	zinc finger CCCH type containing 12A	protein-coding
mm_83511.1	chr9	45984817	45984855	-	1	NA	promoter-TSS (NM_008775)	promoter-TSS (NM_008775)	35	NM_008775	18475	Mm.200859	NM_008775	ENSMUSG00000003131	Pafah1b2	AI747451|AU021353|Pafahb|mus[b]	platelet-activating factor acetylhydrolase, isoform 1b, subunit 2	protein-coding
mm_152515.1	chr19	11279647	11279659	-	1	NA	intron (NM_183190, intron 1 of 4)	intron (NM_183190, intron 1 of 4)	4160	NM_183190	269063	Mm.268940	NM_183190	ENSMUSG00000054523	Ms4a5	-	membrane-spanning 4-domains, subfamily A, member 5	protein-coding
mm_39085.1	chr4	154636226	154636238	-	1	NA	non-coding (NR_045643, exon 1 of 1)	non-coding (NR_045643, exon 1 of 1)	135	NR_045643	320939	Mm.436738	NR_045643		5930403L14Rik	-	RIKEN cDNA 5930403L14 gene	ncRNA
mm_30205.1	chr3	144720403	144720416	-	1	NA	promoter-TSS (NM_019464)	promoter-TSS (NM_019464)	-74	NM_001282037	54673	Mm.271775	NM_019464	ENSMUSG00000037062	Sh3glb1	AA409932|AI314629|AU015566|Bif-1|mKIAA0491	SH3-domain GRB2-like B1 (endophilin)	protein-coding
mm_101952.1	chr11	50292303	50292363	-	1	NA	promoter-TSS (NM_175334)	promoter-TSS (NM_175334)	3	NM_175334	103806	Mm.51116	NM_175334	ENSMUSG00000050567	Maml1	AI644666|AW743257|D930008C07Rik|Mam-1|Mam1|mKIAA0200	mastermind like 1 (Drosophila)	protein-coding
mm_81966.1	chr9	120955161	120955173	+	1	NA	promoter-TSS (NR_106058)	promoter-TSS (NR_106058)	81	NR_106058	102465661		NR_106058	ENSMUSG00000106193	Mir7090	mmu-mir-7090	microRNA 7090	ncRNA
mm_120601.1	chr14	70079396	70079407	+	1	NA	exon (NM_001289927, exon 2 of 2)	exon (NM_001289927, exon 2 of 2)	1606	NM_001289927	13655	Mm.103737	NM_018781	ENSMUSG00000033730	Egr3	Pilot	early growth response 3	protein-coding
mm_926.1	chr1	55226612	55226622	+	1	NA	5' UTR (NM_028713, exon 1 of 9)	5' UTR (NM_028713, exon 1 of 9)	165	NM_028713	74013	Mm.292050	NM_028713	ENSMUSG00000025978	Rftn2	2700010E02Rik|3222401M22Rik	raftlin family member 2	protein-coding
mm_78543.1	chr9	35305316	35305335	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	24220	NR_040715	71133	Mm.158577	NR_040715	ENSMUSG00000111746	4933422A05Rik	-	RIKEN cDNA 4933422A05 gene	ncRNA
mm_100543.1	chr11	120673698	120673716	+	1	NA	intron (NM_026877, intron 1 of 15)	intron (NM_026877, intron 1 of 15)	734	NM_026877	68938	Mm.294020	NM_026877	ENSMUSG00000025142	Aspscr1	1190006K01Rik|ASPC|ASPCR1|ASPL|ASPS|RCC17|TUG	alveolar soft part sarcoma chromosome region, candidate 1 (human)	protein-coding
mm_76934.1	chr8	105938431	105938445	-	1	NA	promoter-TSS (NM_013640)	promoter-TSS (NM_013640)	-46	NM_013640	19171	Mm.787	NM_013640	ENSMUSG00000031897	Psmb10	Mecl-1|Mecl1	proteasome (prosome, macropain) subunit, beta type 10	protein-coding
mm_6261.1	chr1	69108536	69108577	-	1	NA	promoter-TSS (NM_010154)	promoter-TSS (NM_010154)	-497	NM_010154	13869	Mm.442420	NM_010154	ENSMUSG00000062209	Erbb4	Her4|c-erbB-4	erb-b2 receptor tyrosine kinase 4	protein-coding
mm_65102.1	chr7	19303559	19303570	-	1	NA	3' UTR (NM_008036, exon 4 of 4)	3' UTR (NM_008036, exon 4 of 4)	6481	NM_008036	14282	Mm.248335	NM_008036	ENSMUSG00000003545	Fosb	-	FBJ osteosarcoma oncogene B	protein-coding
mm_154087.1	chr19	56746759	56746785	-	1	NA	Intergenic	Intergenic	24400	NM_007419	11554	Mm.46797	NM_007419	ENSMUSG00000035283	Adrb1	Adrb-1|beta-AR	adrenergic receptor, beta 1	protein-coding
mm_106819.1	chr12	7983115	7983128	+	1	NA	exon (NM_009693, exon 5 of 29)	exon (NM_009693, exon 5 of 29)	5444	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_49906.1	chr6	38983304	38983317	+	1	NA	intron (NM_011539, intron 4 of 12)	L3|LINE|CR1	64324	NM_011539	21391	Mm.4054	NM_011539	ENSMUSG00000029925	Tbxas1	CYP5|CYP5A1|THAS|TS|TXAS|TXS	thromboxane A synthase 1, platelet	protein-coding
mm_141255.1	chr17	27596814	27596850	-	1	NA	exon (NM_001291046, exon 2 of 5)	exon (NM_001291046, exon 2 of 5)	26132	NM_001291046	56409	Mm.144699	NM_019837	ENSMUSG00000024213	Nudt3	1110011B09Rik|AA960325|Dipp|Dipp1	nudix (nucleotide diphosphate linked moiety X)-type motif 3	protein-coding
mm_115453.1	chr13	118715013	118715027	+	1	NA	5' UTR (NM_008002, exon 1 of 3)	5' UTR (NM_008002, exon 1 of 3)	321	NM_008002	14165	Mm.317323	NM_008002	ENSMUSG00000021732	Fgf10	AEY17|BB213776|Fgf-10|Gsfaey17	fibroblast growth factor 10	protein-coding
mm_145939.1	chr18	67308570	67308598	+	1	NA	intron (NM_053261, intron 3 of 7)	intron (NM_053261, intron 3 of 7)	19361	NM_053261	114663	Mm.34079	NM_053261	ENSMUSG00000024525	Impa2	2210415D20Rik|AI326924|AW259601	inositol (myo)-1(or 4)-monophosphatase 2	protein-coding
mm_92614.1	chr10	80139190	80139204	-	1	NA	non-coding (NR_036582, exon 1 of 11)	non-coding (NR_036582, exon 1 of 11)	170	NR_036582	100503659	Mm.485395	NM_015761	ENSMUSG00000035640	Cbarp	9630008F14|Dos|R29144/1	calcium channel, voltage-dependent, beta subunit associated regulatory protein	protein-coding
mm_92912.1	chr10	83636314	83636322	-	1	NA	intron (NM_145220, intron 2 of 20)	intron (NM_145220, intron 2 of 20)	12346	NM_145220	216190	Mm.282985	NM_145220	ENSMUSG00000020263	Appl2	Dip3b	adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 2	protein-coding
mm_57005.1	chr6	121081590	121081608	-	1	NA	promoter-TSS (NM_153396)	promoter-TSS (NM_153396)	28	NM_153396	194401	Mm.122399	NM_153396	ENSMUSG00000051586	Mical3	C130040D16Rik|Mical-3|mKIAA1364	microtubule associated monooxygenase, calponin and LIM domain containing 3	protein-coding
mm_165300.1	chr2	92375767	92375777	+	1	NA	intron (NM_145122, intron 1 of 10)	intron (NM_145122, intron 1 of 10)	533	NM_145122	18633	Mm.202782	NM_145122	ENSMUSG00000027222	Pex16	-	peroxisomal biogenesis factor 16	protein-coding
mm_170176.1	chr17	57839241	57839243	-	1	NA	intron (NM_001081653, intron 1 of 23)	intron (NM_001081653, intron 1 of 23)	69672	NM_001081653	620292	Mm.391030	NM_001081653	ENSMUSG00000038048	Cntnap5c	Caspr5-3|EG620292|Gm325	contactin associated protein-like 5C	protein-coding
mm_88903.1	chr10	81177810	81177837	+	1	NA	exon (NM_007907, exon 2 of 14)	exon (NM_007907, exon 2 of 14)	-1138	NR_028549	100217454		NR_028549	ENSMUSG00000064441	Snord37	MBII-376	small nucleolar RNA, C/D box 37	snoRNA
mm_60716.1	chr7	45324941	45324943	+	1	NA	promoter-TSS (NR_110499)	promoter-TSS (NR_110499)	-16	NR_110499	100040970	Mm.289810	NR_110499	ENSMUSG00000046721	Rpl14-ps1	ENSMUSG00000046721|Gm9811	ribosomal protein L14, pseudogene 1	pseudo
mm_19391.1	chr2	91430697	91430720	-	1	NA	intron (NM_001311144, intron 1 of 8)	intron (NM_001311144, intron 1 of 8)	13934	NM_175123	228356	Mm.386861	NM_175123	ENSMUSG00000040591	1110051M20Rik	AI586322	RIKEN cDNA 1110051M20 gene	protein-coding
mm_23228.1	chr3	50407023	50407033	+	1	NA	intron (NM_011990, intron 6 of 11)	intron (NM_011990, intron 6 of 11)	36585	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_65075.1	chr7	19118333	19118353	-	1	NA	Intergenic	CpG	-1516	NM_175530	243867	Mm.230830	NM_175530	ENSMUSG00000050428	Fbxo46	20D7-FC4|4932704E22Rik|Fbxo34l	F-box protein 46	protein-coding
mm_76188.1	chr8	82402624	82402635	-	1	NA	promoter-TSS (NM_001254747)	promoter-TSS (NM_001254747)	-43	NM_008357	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_54325.1	chr6	30505960	30505980	-	1	NA	exon (NM_001311093, exon 5 of 15)	exon (NM_001311093, exon 5 of 15)	3803	NM_001347087	72649	Mm.45418	NM_178625	ENSMUSG00000029782	Tmem209	2700094F01Rik|AI428435	transmembrane protein 209	protein-coding
mm_67074.1	chr7	68249584	68249589	-	1	NA	intron (NM_030101, intron 1 of 3)	ORR1B1|LTR|ERVL-MaLR	14647	NM_030101	78444	Mm.425468	NM_030101	ENSMUSG00000030553	Pgpep1l	C330024D12Rik	pyroglutamyl-peptidase I-like	protein-coding
mm_97959.1	chr11	83740646	83740659	+	1	NA	Intergenic	Intergenic	-6288	NM_183249	66107	Mm.902	NM_183249	ENSMUSG00000051748	Wfdc21	1100001G20Rik|Wdnm1-like	WAP four-disulfide core domain 21	protein-coding
mm_87512.1	chr10	52418032	52418042	+	1	NA	exon (NM_030250, exon 1 of 5)	exon (NM_030250, exon 1 of 5)	490	NM_030250	52014	Mm.199964	NM_030250	ENSMUSG00000023068	Nus1	1600027K07Rik|AU019165|AW538011|BC003223|D10Ertd438e	NUS1 dehydrodolichyl diphosphate synthase subunit	protein-coding
mm_28299.1	chr3	89160156	89160202	-	1	NA	promoter-TSS (NM_008227)	promoter-TSS (NM_008227)	-22	NM_008227	15168	Mm.389461	NM_008227	ENSMUSG00000028051	Hcn3	BCNG-4|Bcng4|Hac3|Hcn4	hyperpolarization-activated, cyclic nucleotide-gated K+ 3	protein-coding
mm_140754.1	chr17	17410851	17410858	-	1	NA	intron (NM_025681, intron 1 of 5)	RMER17C2|LTR|ERVK	8168	NM_025681	66643	Mm.268018	NM_025681	ENSMUSG00000047786	Lix1	5730466L18Rik	limb and CNS expressed 1	protein-coding
mm_129512.1	chr15	79062676	79062691	-	1	NA	exon (NM_144849, exon 1 of 8)	exon (NM_144849, exon 1 of 8)	176	NM_144849	223690	Mm.24262	NM_144849	ENSMUSG00000033055	Ankrd54	C730048E16Rik|EST1068184|EST475269|Liar	ankyrin repeat domain 54	protein-coding
mm_3297.1	chr1	136692853	136692859	+	1	NA	Intergenic	ID_B1|SINE|B4	-3355	NR_037986	100503474	Mm.428276	NR_037986		Platr22	Gm16880	pluripotency associated transcript 22	ncRNA
mm_73486.1	chr8	107031296	107031350	+	1	NA	promoter-TSS (NM_126165)	promoter-TSS (NM_126165)	-3	NM_126165	116733	Mm.236004	NM_126165	ENSMUSG00000031913	Vps4a	4930589C15Rik|AI325971|AW553189	vacuolar protein sorting 4A	protein-coding
mm_171863.1	chr5	23347266	23347275	-	1	NA	Intergenic	BGLII_Mus|LTR|ERVK	87083	NR_040469	269630	Mm.425231	NR_040469	ENSMUSG00000073147	5031425E22Rik	-	RIKEN cDNA 5031425E22 gene	ncRNA
mm_170012.1	chr17	17234853	17234871	+	1	NA	Intergenic	Intergenic	-59581	NM_001324550	100862203	Mm.484235	NM_001324550		Gm6712	EG626854	predicted gene 6712	protein-coding
mm_55953.1	chr6	85374543	85374553	-	1	NA	promoter-TSS (NM_177466)	promoter-TSS (NM_177466)	86	NM_177466	52055	Mm.220334	NM_177466	ENSMUSG00000051343	Rab11fip5	9130206P09Rik|C75969|D6Ertd32e|GAF1|RIP11	RAB11 family interacting protein 5 (class I)	protein-coding
mm_87368.1	chr10	44170443	44170467	+	1	NA	promoter-TSS (NR_001582)	promoter-TSS (NR_001582)	8	NR_001582	70365	Mm.87073	NR_001582	ENSMUSG00000091358	Speer5-ps1	1700007C10Rik|SPEER-5|Speer5-ps	spermatogenesis associated glutamate (E)-rich protein 5, pseudogene 1	pseudo
mm_45441.1	chr5	67425161	67425164	-	1	NA	intron (NM_001164806, intron 1 of 4)	intron (NM_001164806, intron 1 of 4)	2637	NM_001164806	666938	Mm.101339	NM_001164806	ENSMUSG00000092060	Bend4	D330027G24Rik|EG666938	BEN domain containing 4	protein-coding
mm_109091.1	chr12	104761627	104761639	+	1	NA	Intergenic	Intergenic	-9681	NM_148948	192119	Mm.21135	NM_148948	ENSMUSG00000041415	Dicer1	1110006F08Rik|D12Ertd7e|mKIAA0928	dicer 1, ribonuclease type III	protein-coding
mm_166001.1	chr4	115847844	115847856	+	1	NA	intron (NM_001285487, intron 2 of 14)	intron (NM_001285487, intron 2 of 14)	8652	NM_001285487	17346	Mm.209327	NM_021461	ENSMUSG00000028708	Mknk1	2410048M24Rik|Mnk1	MAP kinase-interacting serine/threonine kinase 1	protein-coding
mm_71282.1	chr8	40920072	40920082	+	1	NA	3' UTR (NM_001044740, exon 12 of 12)	3' UTR (NM_001044740, exon 12 of 12)	-6156	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_154306.1	chr19	61226338	61226381	-	1	NA	exon (NM_009970, exon 6 of 12)	exon (NM_009970, exon 6 of 12)	2059	NM_009970	12982	Mm.287228	NM_009970	ENSMUSG00000059326	Csf2ra	CD116|Csfgmra|GM-CSF-Ra|GM-CSFR	colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)	protein-coding
mm_128661.1	chr15	60129998	60130003	-	1	NA	Intergenic	L1M2|LINE|L1	-113382	NM_027668	71088	Mm.425950	NM_027668	ENSMUSG00000071749	4933412E24Rik	-	RIKEN cDNA 4933412E24 gene	protein-coding
mm_36747.1	chr4	101162942	101162944	-	1	NA	exon (NM_146145, exon 15 of 25)	exon (NM_146145, exon 15 of 25)	93905	NM_183024	242570	Mm.185636	NM_183024	ENSMUSG00000035275	Raver2	A430091O22Rik	ribonucleoprotein, PTB-binding 2	protein-coding
mm_27533.1	chr3	57555009	57555012	-	1	NA	intron (NM_001168281, intron 2 of 6)	intron (NM_001168281, intron 2 of 6)	20866	NM_133784	97064	Mm.405029	NM_133784	ENSMUSG00000027803	Wwtr1	2310058J06Rik|2610021I22Rik|C78399|Taz	WW domain containing transcription regulator 1	protein-coding
mm_84548.1	chr9	67485187	67485200	-	1	NA	intron (NM_001081242, intron 1 of 57)	intron (NM_001081242, intron 1 of 57)	74510	NM_001081242	70549	Mm.33645	NM_027458	ENSMUSG00000052698	Tln2	5730421P04Rik|AI507121|AI787438|AL118320|mKIAA0320	talin 2	protein-coding
mm_41908.1	chr5	105589793	105589794	+	1	NA	intron (NM_133897, intron 3 of 3)	RLTR11B|LTR|ERVK	70322	NM_133897	100604	Mm.319847	NM_133897	ENSMUSG00000054720	Lrrc8c	AD158|AI326115|E430036I04Rik|fad158	leucine rich repeat containing 8 family, member C	protein-coding
mm_139431.1	chr17	53567315	53567321	+	1	NA	5' UTR (NM_020005, exon 1 of 18)	5' UTR (NM_020005, exon 1 of 18)	347	NM_020005	18519	Mm.255025	NM_020005	ENSMUSG00000000708	Kat2b	A930006P13Rik|AI461839|AW536563|Pcaf|p/CAF	K(lysine) acetyltransferase 2B	protein-coding
mm_112025.1	chr12	111455009	111455017	-	1	NA	TTS (NM_009396)	TTS (NM_009396)	12352	NM_009396	21928	Mm.255332	NM_009396	ENSMUSG00000021281	Tnfaip2	B94|Exoc3l3|M-sec|Tnfip2|tnfb94	tumor necrosis factor, alpha-induced protein 2	protein-coding
mm_164381.1	chr16	31297498	31297506	+	1	NA	exon (NM_007470, exon 6 of 6)	exon (NM_007470, exon 6 of 6)	17306	NM_001301353	11815	Mm.2082	NM_007470	ENSMUSG00000022548	Apod	-	apolipoprotein D	protein-coding
mm_105139.1	chr11	101459700	101459726	-	1	NA	3' UTR (NM_012037, exon 6 of 6)	3' UTR (NM_012037, exon 6 of 6)	6486	NM_012037	26949	Mm.29210	NM_012037	ENSMUSG00000034993	Vat1	VAT-1	vesicle amine transport 1	protein-coding
mm_51514.1	chr6	83137851	83137866	+	1	NA	5' UTR (NM_133641, exon 1 of 12)	5' UTR (NM_133641, exon 1 of 12)	774	NM_009106	20166	Mm.4139	NM_009106	ENSMUSG00000034930	Rtkn	-	rhotekin	protein-coding
mm_93118.1	chr10	91170449	91170487	-	1	NA	promoter-TSS (NM_001283048)	promoter-TSS (NM_001283048)	82	NM_001283048	21917	Mm.159684	NM_011605	ENSMUSG00000019961	Tmpo	5630400D24Rik|AI195756|AI606875|AW214352|AW547477|LAP2|TP	thymopoietin	protein-coding
mm_59617.1	chr7	28147166	28147174	+	1	NA	exon (NM_001164655, exon 8 of 20)	exon (NM_001164655, exon 8 of 20)	17704	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_34165.1	chr4	139623090	139623134	+	1	NA	5' UTR (NM_175438, exon 1 of 15)	5' UTR (NM_175438, exon 1 of 15)	218	NM_175438	212647	Mm.273571	NM_175438	ENSMUSG00000028737	Aldh4a1	A930035F14Rik|Ahd-1|Ahd1|Aldh4|Aldh5a1|E330022C09|P5cd|P5cdh|P5cdhl|P5cdhs|Ssdh1	aldehyde dehydrogenase 4 family, member A1	protein-coding
mm_140217.1	chr17	83846606	83846627	+	1	NA	intron (NM_025325, intron 1 of 9)	intron (NM_025325, intron 1 of 9)	174	NM_025325	107766	Mm.30100	NM_025325	ENSMUSG00000000673	Haao	0610007K21Rik|0610012J07Rik|3-HAO|3-HAOxase|3HAO	3-hydroxyanthranilate 3,4-dioxygenase	protein-coding
mm_85274.1	chr9	99436688	99436733	-	1	NA	promoter-TSS (NM_008624)	promoter-TSS (NM_008624)	2	NM_008624	17532	Mm.2045	NM_008624	ENSMUSG00000032470	Mras	2900078C09Rik|AI326250	muscle and microspikes RAS	protein-coding
mm_60849.1	chr7	45814026	45814036	+	1	NA	intron (NM_011181, intron 1 of 11)	CpG	285	NM_011181	19158	Mm.272130	NM_011181	ENSMUSG00000003269	Cyth2	ARNO|CLM2|Pscd2	cytohesin 2	protein-coding
mm_58899.1	chr7	17150271	17150275	+	1	NA	promoter-TSS (NM_054059)	promoter-TSS (NM_054059)	-127	NM_054059	384557	Mm.486145	NM_054059	ENSMUSG00000053228	Ceacam3	EG384557|Psg24|cea12	carcinoembryonic antigen-related cell adhesion molecule 3	protein-coding
mm_100625.1	chr11	121702454	121702467	+	1	NA	promoter-TSS (NM_144797)	promoter-TSS (NM_144797)	33	NM_144797	210029	Mm.153566	NM_144797	ENSMUSG00000039208	Metrnl	9430048M07Rik|BC019776	meteorin, glial cell differentiation regulator-like	protein-coding
mm_127439.1	chr15	101270346	101270358	+	1	NA	exon (NM_010444, exon 2 of 7)	exon (NM_010444, exon 2 of 7)	3506	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_169074.1	chr13	30377120	30377133	+	1	NA	intron (NM_177322, intron 2 of 2)	IAPLTR1a_Mm|LTR|ERVK	40770	NM_177322	11607	Mm.35062	NM_177322	ENSMUSG00000049115	Agtr1a	1810074K20Rik|AG2S|AI551199|AT1|AT1a|AT2R1|AT2R1A|Agtr-1a|Agtr1|Angtr-1a	angiotensin II receptor, type 1a	protein-coding
mm_152478.1	chr19	11037662	11037667	-	1	NA	Intergenic	L1_Mus3|LINE|L1	12902	NR_102366	107350	Mm.6381	NM_001177351	ENSMUSG00000075010	AW112010	-	expressed sequence AW112010	ncRNA
mm_164000.1	chr14	65683494	65683495	+	1	NA	intron (NM_028903, intron 2 of 8)	intron (NM_028903, intron 2 of 8)	17091	NM_001168318	71145	Mm.83840	NM_028903	ENSMUSG00000022032	Scara5	4932433F15Rik|4933425F03Rik|AV278087|Tesr	scavenger receptor class A, member 5	protein-coding
mm_108483.1	chr12	83664095	83664104	+	1	NA	exon (NM_027349, exon 10 of 19)	exon (NM_027349, exon 10 of 19)	-24464	NM_008943	19164	Mm.998	NM_008943	ENSMUSG00000019969	Psen1	Ad3h|PS-1|PS1|S182	presenilin 1	protein-coding
mm_3467.1	chr1	150104460	150104465	+	1	NA	exon (NM_011198, exon 8 of 10)	exon (NM_011198, exon 8 of 10)	4431	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_4893.1	chr1	189034784	189034795	+	1	NA	Intergenic	Intergenic	-26949	NM_172650	226823	Mm.209880	NM_172650	ENSMUSG00000026608	Kctd3	4930438A20Rik|9330185B06|E330032J19Rik|NY-REN-45	potassium channel tetramerisation domain containing 3	protein-coding
mm_47147.1	chr5	120560417	120560436	-	1	NA	intron (NM_145853, intron 2 of 27)	ORR1B1|LTR|ERVL-MaLR	28187	NM_145853	252972	Mm.114054	NM_145853	ENSMUSG00000032741	Tpcn1	5730403B01Rik|Tpc1|mKIAA1169	two pore channel 1	protein-coding
mm_126551.1	chr15	82063904	82063908	+	1	NA	exon (NM_001166475, exon 2 of 2)	exon (NM_001166475, exon 2 of 2)	4755	NM_001166475	328573	Mm.399189	NM_001166475	ENSMUSG00000075524	4930407I10Rik	Gm747	RIKEN cDNA 4930407I10 gene	protein-coding
mm_157137.1	chrX	9459210	9459223	-	1	NA	intron (NM_007807, intron 3 of 12)	BC1_Mm|scRNA|scRNA	10108	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_82513.1	chr9	20521376	20521427	-	1	NA	promoter-TSS (NM_001135019)	promoter-TSS (NM_001135019)	18	NM_001135019	77519	Mm.431849	NM_001082485	ENSMUSG00000060510	Zfp266	5330440G10Rik|5730601F06Rik|AW552317	zinc finger protein 266	protein-coding
mm_154889.1	chrX	20806503	20806509	+	1	NA	Intergenic	B1_Mur1|SINE|Alu	-42037	NM_009703	11836	Mm.220946	NM_009703	ENSMUSG00000001127	Araf	1200013E08Rik|A-Raf|AW495444|Araf1	Araf proto-oncogene, serine/threonine kinase	protein-coding
mm_28559.1	chr3	93443886	93443890	-	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	1558	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_80179.1	chr9	72275488	72275499	+	1	NA	intron (NM_001311105, intron 1 of 20)	intron (NM_001311105, intron 1 of 20)	605	NM_001311105	235469	Mm.242791	NM_146224	ENSMUSG00000038535	Zfp280d	A930005F02Rik|BC027163|Suhw4|ZNF634|Znf280d	zinc finger protein 280D	protein-coding
mm_74211.1	chr8	123896198	123896220	+	1	NA	TTS (NM_172288)	TTS (NM_172288)	-1434	NM_009606	11459	Mm.214950	NM_009606	ENSMUSG00000031972	Acta1	AA959943|Acta-2|Acts|Actsk-1	actin, alpha 1, skeletal muscle	protein-coding
mm_25384.1	chr3	107215946	107215966	+	1	NA	exon (NM_001111143, exon 5 of 9)	exon (NM_001111143, exon 5 of 9)	5776	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_70754.1	chr8	19689080	19689099	+	1	NA	Intergenic	Intergenic	-40487	NM_001270553	100861668	Mm.491087	NM_001270553	ENSMUSG00000095294	Gm21119	-	predicted gene, 21119	protein-coding
mm_147486.1	chr18	47306463	47306482	-	1	NA	5' UTR (NM_018744, exon 2 of 19)	5' UTR (NM_018744, exon 2 of 19)	62396	NM_018744	20358	Mm.40909	NM_018744	ENSMUSG00000019647	Sema6a	A730020P05Rik|AI851735|Sema6A-1|Semaq|VIa	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A	protein-coding
mm_94865.1	chr11	24078079	24078096	+	1	NA	promoter-TSS (NM_001242934)	promoter-TSS (NM_001242934)	31	NM_001159289	14025	Mm.53687	NM_016707	ENSMUSG00000000861	Bcl11a	2810047E18Rik|BCL-11A|Ctip1|D930021L15Rik|Evi9|Evi9a|Evi9b|Evi9c|mKIAA1809	B cell CLL/lymphoma 11A (zinc finger protein)	protein-coding
mm_45189.1	chr5	52115905	52115917	-	1	NA	Intergenic	CpG	20106	NR_105845	102466648		NR_105845	ENSMUSG00000098726	Mir6417	Gm27334|mmu-mir-6417	microRNA 6417	ncRNA
mm_123354.1	chr14	63142531	63142547	-	1	NA	3' UTR (NM_007798, exon 10 of 10)	3' UTR (NM_007798, exon 10 of 10)	20077	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_112915.1	chr13	20923109	20923119	+	1	NA	intron (NM_012054, intron 11 of 20)	Lx8b|LINE|L1	129001	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_92862.1	chr10	81597331	81597367	-	1	NA	intron (NM_001346695, intron 4 of 13)	intron (NM_001346695, intron 4 of 13)	3551	NM_053254	114606	Mm.206764	NM_053254	ENSMUSG00000034758	Tle6	1810057E06Rik|Grg6	transducin-like enhancer of split 6	protein-coding
mm_78203.1	chr9	21411825	21411853	+	1	NA	promoter-TSS (NR_045742)	promoter-TSS (NR_045742)	2	NM_021888	60507	Mm.436579	NM_021888	ENSMUSG00000002825	Qtrt1	2610028E17Rik|Tgt	queuine tRNA-ribosyltransferase 1	protein-coding
mm_130667.1	chr15	100674472	100674496	-	1	NA	TTS (NM_033612)	TTS (NM_033612)	-4984	NM_001270537	668218	Mm.451225	NM_001270537	ENSMUSG00000098112	Bin2	-	bridging integrator 2	protein-coding
mm_15.1	chr1	4858017	4858048	+	1	NA	promoter-TSS (NM_001159751)	promoter-TSS (NM_001159751)	-296	NM_001159751	21399	Mm.207263	NM_011541	ENSMUSG00000033813	Tcea1	S-II	transcription elongation factor A (SII) 1	protein-coding
mm_137387.1	chr17	25809013	25809032	+	1	NA	promoter-TSS (NM_001164225)	promoter-TSS (NM_001164225)	-63	NM_001164225	214931	Mm.152289	NM_001164225	ENSMUSG00000025738	Fbxl16	BC042620|Scirr1	F-box and leucine-rich repeat protein 16	protein-coding
mm_131844.1	chr16	23050225	23050227	+	1	NA	Intergenic	Intergenic	-8074	NM_023125	16644	Mm.2160	NM_023125	ENSMUSG00000022875	Kng1	Kng	kininogen 1	protein-coding
mm_120395.1	chr14	64652525	64652555	+	1	NA	promoter-TSS (NM_001081177)	promoter-TSS (NM_001081177)	9	NM_001081177	16554	Mm.23611	NM_001081177	ENSMUSG00000060012	Kif13b	5330429L19Rik|6030414C01|AI429803|C130021D12Rik|GAKIN	kinesin family member 13B	protein-coding
mm_26710.1	chr3	157947496	157947510	+	1	NA	promoter-TSS (NM_001013806)	promoter-TSS (NM_001013806)	37	NM_001013806	433667	Mm.265806	NM_001013806	ENSMUSG00000039988	Ankrd13c	AI505652|AU022220	ankyrin repeat domain 13c	protein-coding
mm_93312.1	chr10	98880807	98880818	-	1	NA	Intergenic	L2a|LINE|L2	-34340	NM_026482	67972	Mm.166944	NM_026482	ENSMUSG00000019943	Atp2b1	2810442I22Rik|E130111D10Rik|Pmca1	ATPase, Ca++ transporting, plasma membrane 1	protein-coding
mm_66884.1	chr7	59217667	59217695	-	1	NA	Intergenic	MERVK26-int|LTR|ERVK	-11069	NM_173010	22215	Mm.9002	NM_011668	ENSMUSG00000025326	Ube3a	4732496B02|5830462N02Rik|A130086L21Rik|Hpve6a|mKIAA4216	ubiquitin protein ligase E3A	protein-coding
mm_156513.1	chrX	150552141	150552180	+	1	NA	5' UTR (NM_009653, exon 2 of 11)	5' UTR (NM_009653, exon 2 of 11)	-4715	NR_106147	102465782		NR_106147	ENSMUSG00000099172	Mir3620	Gm27984|mmu-mir-3620	microRNA 3620	ncRNA
mm_87656.1	chr10	58478285	58478303	+	1	NA	exon (NM_011240, exon 20 of 29)	exon (NM_011240, exon 20 of 29)	-19643	NM_001162956	76138	Mm.211744	NM_001162956	ENSMUSG00000038010	Ccdc138	6230424H07Rik|BC042726	coiled-coil domain containing 138	protein-coding
mm_173299.1	chrY	5157381	5157381	+	1	NA	Intergenic	L1Md_T|LINE|L1	1385708	NM_011253	19657	Mm.4711	NM_011253	ENSMUSG00000094658	Rbmy	RBM|Rbm1|Rbm1-rs1|Rbmy1a1|Rbmy1a1-rs1|Rbmy1b	RNA binding motif protein, Y chromosome	protein-coding
mm_156703.1	chrX	159588316	159588352	+	1	NA	intron (NM_001033472, intron 11 of 11)	intron (NM_001033472, intron 11 of 11)	-38938	NM_001135727	58194	Mm.286495	NM_021389	ENSMUSG00000040990	Sh3kbp1	1200007H22Rik|1700125L08Rik|5830464D22Rik|AI447724|Cin85|IN85|Ruk|Seta	SH3-domain kinase binding protein 1	protein-coding
mm_39292.1	chr5	4344709	4344713	+	1	NA	Intergenic	L1MA9|LINE|L1	152344	NM_001042670	208595	Mm.129815	NM_001042670	ENSMUSG00000053178	Mterf1b	ENSMUSG00000053178|Gm9897	mitochondrial transcription termination factor 1b	protein-coding
mm_125722.1	chr15	73091453	73091457	+	1	NA	intron (NM_053068, intron 1 of 2)	intron (NM_053068, intron 1 of 2)	1043	NM_053068	93696	Mm.23095	NM_053068	ENSMUSG00000068391	Chrac1	2410152E03Rik|2810406L04Rik|YCL1	chromatin accessibility complex 1	protein-coding
mm_222.1	chr1	17145358	17145431	+	1	NA	promoter-TSS (NM_010267)	promoter-TSS (NM_010267)	21	NM_010267	14545	Mm.18218	NM_010267	ENSMUSG00000025777	Gdap1	-	ganglioside-induced differentiation-associated-protein 1	protein-coding
mm_93763.1	chr10	120198645	120198665	-	1	NA	intron (NM_028679, intron 1 of 11)	intron (NM_028679, intron 1 of 11)	2882	NM_028679	73914	Mm.146194	NM_028679	ENSMUSG00000020227	Irak3	4833428C18Rik|AI563835|IRAK-M	interleukin-1 receptor-associated kinase 3	protein-coding
mm_106092.1	chr11	116198333	116198347	-	1	NA	promoter-TSS (NM_027107)	promoter-TSS (NM_027107)	-515	NM_027107	69535	Mm.390347	NM_027107	ENSMUSG00000020778	Ten1	2310004N24Rik	TEN1 telomerase capping complex subunit	protein-coding
mm_169649.1	chr15	53574360	53574373	+	1	NA	intron (NM_177225, intron 4 of 4)	L1Md_T|LINE|L1	-228183	NM_010162	14042	Mm.309395	NM_010162	ENSMUSG00000061731	Ext1	AA409028	exostoses (multiple) 1	protein-coding
mm_44685.1	chr5	30120772	30120785	-	1	NA	exon (NM_178878, exon 18 of 20)	exon (NM_178878, exon 18 of 20)	-14692	NM_001256263	433868	Mm.450696	NM_001256263	ENSMUSG00000086815	3110082J24Rik	ENSMUSG00000073106	RIKEN cDNA 3110082J24 gene	protein-coding
mm_9614.1	chr1	176213975	176213977	-	1	NA	promoter-TSS (NM_001195816)	promoter-TSS (NM_001195816)	-34	NM_001195816	319455	Mm.338001	NM_176916	ENSMUSG00000055214	Pld5	B230365F16Rik	phospholipase D family, member 5	protein-coding
mm_94471.1	chr11	6528903	6528915	+	1	NA	promoter-TSS (NR_045893)	promoter-TSS (NR_045893)	-149	NR_045893	100041286	Mm.459507	NR_045893	ENSMUSG00000085156	Snhg15	Gm11974|OTTMUSG00000005115	small nucleolar RNA host gene 15	ncRNA
mm_10335.1	chr2	11642787	11642798	+	1	NA	promoter-TSS (NM_008367)	promoter-TSS (NM_008367)	0	NM_008367	16184	Mm.915	NM_008367	ENSMUSG00000026770	Il2ra	CD25|Il2r|Ly-43	interleukin 2 receptor, alpha chain	protein-coding
mm_138850.1	chr17	40811140	40811174	+	1	NA	promoter-TSS (NM_011269)	promoter-TSS (NM_011269)	8	NM_011269	19743	Mm.12961	NM_011269	ENSMUSG00000023926	Rhag	CD241|Rh50|Rh50A	Rhesus blood group-associated A glycoprotein	protein-coding
mm_97320.1	chr11	76904485	76904503	+	1	NA	promoter-TSS (NM_025655)	promoter-TSS (NM_025655)	-51	NM_025655	66601	Mm.25138	NM_025655	ENSMUSG00000020839	Tmigd1	2010002A20Rik|Tmigd	transmembrane and immunoglobulin domain containing 1	protein-coding
mm_49814.1	chr6	36389432	36389440	+	1	NA	intron (NM_203491, intron 2 of 2)	intron (NM_203491, intron 2 of 2)	-1202	NR_015589	319472	Mm.226434	NR_015589	ENSMUSG00000073154	9330158H04Rik	-	RIKEN cDNA 9330158H04 gene	ncRNA
mm_3978.1	chr1	164249110	164249126	+	1	NA	promoter-TSS (NM_054087)	promoter-TSS (NM_054087)	72	NM_001276455	116914	Mm.35444	NM_054087	ENSMUSG00000040918	Slc19a2	AV276020|AW322295|DDA1|THTR1|TRMA	solute carrier family 19 (thiamine transporter), member 2	protein-coding
mm_80375.1	chr9	75408087	75408099	+	1	NA	intron (NM_015806, intron 1 of 5)	intron (NM_015806, intron 1 of 5)	1266	NM_027418	50772	Mm.480076	NM_015806	ENSMUSG00000042688	Mapk6	2610021I23Rik|D130053K17Rik|Erk3|Mapk4|Mapk63|Prkm4|Prkm6	mitogen-activated protein kinase 6	protein-coding
mm_77543.1	chr8	123158269	123158295	-	1	NA	promoter-TSS (NM_020564)	promoter-TSS (NM_020564)	-2	NM_020564	57429	Mm.6562	NM_020564	ENSMUSG00000000739	Sult5a1	Sult-x1|Sultx1	sulfotransferase family 5A, member 1	protein-coding
mm_57514.1	chr6	125481830	125481837	-	1	NA	intron (NM_007657, intron 1 of 7)	intron (NM_007657, intron 1 of 7)	12922	NM_007657	12527	Mm.210676	NM_007657	ENSMUSG00000030342	Cd9	Tspan29	CD9 antigen	protein-coding
mm_157249.1	chrX	19148999	19149005	-	1	NA	Intergenic	Lx6|LINE|L1	-2031	NR_029807	723828		NR_029807	ENSMUSG00000065471	Mir222	Mirn222|mir-222|mmu-mir-222	microRNA 222	ncRNA
mm_52953.1	chr6	123049981	123049991	+	1	NA	promoter-TSS (NM_027218)	promoter-TSS (NM_027218)	24	NM_001190310	69810	Mm.333374	NM_027218	ENSMUSG00000030147	Clec4b1	1810046I24Rik|Aplra2|Clec4b|DCAR|DCARbeta|Dcar2	C-type lectin domain family 4, member b1	protein-coding
mm_131976.1	chr16	24983003	24983015	+	1	NA	3' UTR (NM_178665, exon 13 of 13)	3' UTR (NM_178665, exon 13 of 13)	-76630	NR_040374	319487	Mm.137341	NR_040374	ENSMUSG00000096960	A230028O05Rik	-	RIKEN cDNA A230028O05 gene	ncRNA
mm_29961.1	chr3	133334097	133334097	-	1	NA	intron (NM_146141, intron 5 of 11)	intron (NM_146141, intron 5 of 11)	23987	NM_146141	74776	Mm.210305	NM_146141	ENSMUSG00000028013	Ppa2	1110013G13Rik|Sid6306	pyrophosphatase (inorganic) 2	protein-coding
mm_163614.1	chr13	52179591	52179592	+	1	NA	Intergenic	Lx8|LINE|L1	82850	NR_045061	74050	Mm.84860	NR_045061		4921525O09Rik	-	RIKEN cDNA 4921525O09 gene	ncRNA
mm_736.1	chr1	43447216	43447219	+	1	NA	intron (NM_010879, intron 1 of 4)	intron (NM_010879, intron 1 of 4)	1466	NM_010879	17974	Mm.389903	NM_010879	ENSMUSG00000066877	Nck2	4833426I10Rik|Grb4|NCKbeta|Nck-2	non-catalytic region of tyrosine kinase adaptor protein 2	protein-coding
mm_139608.1	chr17	57311857	57311870	+	1	NA	exon (NM_001163815, exon 24 of 28)	exon (NM_001163815, exon 24 of 28)	32763	NM_001163815	22324	Mm.248172	NM_011691	ENSMUSG00000034116	Vav1	Vav|vav-T	vav 1 oncogene	protein-coding
mm_93176.1	chr10	93539936	93539948	-	1	NA	promoter-TSS (NM_027908)	promoter-TSS (NM_027908)	91	NM_027908	71761	Mm.244518	NM_027908	ENSMUSG00000015890	Amdhd1	1300019J08Rik	amidohydrolase domain containing 1	protein-coding
mm_35656.1	chr4	43558111	43558122	-	1	NA	intron (NM_011602, intron 1 of 56)	intron (NM_011602, intron 1 of 56)	4467	NM_011602	21894	Mm.208601	NM_011602	ENSMUSG00000028465	Tln1	Tln	talin 1	protein-coding
mm_120957.1	chr14	77519949	77519959	+	1	NA	intron (NM_001253759, intron 7 of 19)	RLTR25A|LTR|ERVK	-13086	NR_033141	629678	Mm.390721	NM_001037935	ENSMUSG00000067973	Gm6994	EG629678	predicted gene 6994	ncRNA
mm_50762.1	chr6	53573656	53573659	+	1	NA	intron (NM_172728, intron 1 of 6)	intron (NM_172728, intron 1 of 6)	283	NM_172728	231991	Mm.227444	NM_172728	ENSMUSG00000053007	Creb5	9430076C15Rik|CRE-BPa|Crebpa|D430026C09Rik	cAMP responsive element binding protein 5	protein-coding
mm_67299.1	chr7	79149043	79149062	-	1	NA	promoter-TSS (NM_008594)	promoter-TSS (NM_008594)	8	NM_001045489	17304	Mm.1451	NM_008594	ENSMUSG00000030605	Mfge8	AA408458|AI325141|MFG-E8|MP47|Mfgm|P47|SED1|lactadherin	milk fat globule-EGF factor 8 protein	protein-coding
mm_20659.1	chr2	132111498	132111508	-	1	NA	intron (NM_018824, intron 1 of 15)	intron (NM_018824, intron 1 of 15)	33605	NM_018824	54338	Mm.103581	NM_018824	ENSMUSG00000027340	Slc23a2	AI844736|NBTL1|SVCT2|Slc23a1|YSPL2|YSPL3|mKIAA0238	solute carrier family 23 (nucleobase transporters), member 2	protein-coding
mm_490.1	chr1	36770422	36770425	+	1	NA	intron (NM_001289765, intron 1 of 12)	intron (NM_001289765, intron 1 of 12)	3489	NM_001289765	22637	Mm.8038	NM_009539	ENSMUSG00000026117	Zap70	Srk|ZAP-70|mrtle|mur	zeta-chain (TCR) associated protein kinase	protein-coding
mm_68941.1	chr7	126503299	126503405	-	1	NA	promoter-TSS (NM_183020)	promoter-TSS (NM_183020)	-50	NM_183020	233871	Mm.231450	NM_183020	ENSMUSG00000032637	Atxn2l	A2D|A2LG|A2RP|A2lp|Atxnl2	ataxin 2-like	protein-coding
mm_48030.1	chr5	136246554	136246558	-	1	NA	Intergenic	Intergenic	-1616	NM_018825	23921	Mm.425294	NM_018825	ENSMUSG00000005057	Sh2b2	Aps	SH2B adaptor protein 2	protein-coding
mm_25462.1	chr3	108554605	108554660	+	1	NA	promoter-TSS (NR_028538)	promoter-TSS (NR_028538)	-230	NR_028538	100217438		NR_028538		Scarna2	MBII-382	small Cajal body-specific RNA 2	ncRNA
mm_89710.1	chr10	97714735	97714751	+	1	NA	promoter-TSS (NR_130993)	promoter-TSS (NR_130993)	-29	NR_130993	78127	Mm.376175	NR_130992		4930525C09Rik	-	RIKEN cDNA 4930525C09 gene	ncRNA
mm_19690.1	chr2	103470382	103470418	-	1	NA	exon (NM_009804, exon 6 of 13)	exon (NM_009804, exon 6 of 13)	14753	NM_009804	12359	Mm.4215	NM_009804	ENSMUSG00000027187	Cat	2210418N07|Cas-1|Cas1|Cs-1	catalase	protein-coding
mm_109772.1	chr12	118847549	118847568	+	1	NA	5' UTR (NM_177082, exon 2 of 3)	5' UTR (NM_177082, exon 2 of 3)	1229	NM_177082	320145	Mm.51682	NM_177082	ENSMUSG00000048562	Sp8	D930049B17Rik|mBtd	trans-acting transcription factor 8	protein-coding
mm_25519.1	chr3	114030585	114030638	+	1	NA	promoter-TSS (NM_007729)	promoter-TSS (NM_007729)	71	NM_007729	12814	Mm.209715	NM_007729	ENSMUSG00000027966	Col11a1	C530001D20Rik|cho	collagen, type XI, alpha 1	protein-coding
mm_165932.1	chr4	65615092	65615103	+	1	NA	exon (NM_053084, exon 2 of 2)	exon (NM_053084, exon 2 of 2)	10111	NM_001161782	69807	Mm.22786	NM_053084	ENSMUSG00000051675	Trim32	1810045E12Rik|3f3|BBS11|Zfp117	tripartite motif-containing 32	protein-coding
mm_95336.1	chr11	46815685	46815709	+	1	NA	exon (NM_178759, exon 2 of 9)	exon (NM_178759, exon 2 of 9)	4898	NM_178759	276891	Mm.69002	NM_178759	ENSMUSG00000055546	Timd4	B430010N18Rik|TIM-4|Tim4	T cell immunoglobulin and mucin domain containing 4	protein-coding
mm_148907.1	chr19	6942624	6942638	+	1	NA	promoter-TSS (NM_001285453)	promoter-TSS (NM_001285453)	69	NM_001285453	12015	Mm.4387	NM_007522	ENSMUSG00000024959	Bad	AI325008|Bbc2	BCL2-associated agonist of cell death	protein-coding
mm_101831.1	chr11	47379375	47379395	-	1	NA	promoter-TSS (NM_011891)	promoter-TSS (NM_011891)	-83	NM_011891	24052	Mm.338890	NM_011891	ENSMUSG00000020354	Sgcd	35kDa|delta-SG	sarcoglycan, delta (dystrophin-associated glycoprotein)	protein-coding
mm_52683.1	chr6	118011314	118011395	+	1	NA	promoter-TSS (NM_001316749)	promoter-TSS (NM_001316749)	-183	NM_001316749	70727	Mm.87660	NM_027526	ENSMUSG00000030134	Rasgef1a	6330404M18Rik|AI835194	RasGEF domain family, member 1A	protein-coding
mm_13004.1	chr2	90904757	90904778	+	1	NA	promoter-TSS (NM_025991)	promoter-TSS (NM_025991)	-19	NM_025991	67136	Mm.330394	NM_025991	ENSMUSG00000005505	Kbtbd4	2510026C23Rik	kelch repeat and BTB (POZ) domain containing 4	protein-coding
mm_137465.1	chr17	26624199	26624199	+	1	NA	intron (NM_026170, intron 3 of 9)	intron (NM_026170, intron 3 of 9)	-52197	NM_025272	11974	Mm.22602	NM_025272	ENSMUSG00000015575	Atp6v0e	Atp6k|Atp6v0e1|M9.2	ATPase, H+ transporting, lysosomal V0 subunit E	protein-coding
mm_41274.1	chr5	89237257	89237269	+	1	NA	3' UTR (NM_001136260, exon 25 of 25)	3' UTR (NM_001136260, exon 25 of 25)	220635	NM_008096	14473	Mm.196595	NM_008096	ENSMUSG00000035540	Gc	DBP|VDB	group specific component	protein-coding
mm_39605.1	chr5	24100579	24100669	+	1	NA	promoter-TSS (NM_026448)	promoter-TSS (NM_026448)	34	NM_001161800	52323	Mm.273768	NM_026448	ENSMUSG00000028986	Klhl7	2700038B03Rik|D5Ertd363e|SBBI26	kelch-like 7	protein-coding
mm_21266.1	chr2	156839739	156839759	-	1	NA	promoter-TSS (NM_001291124)	promoter-TSS (NM_001291124)	-258	NM_001291124	228839	Mm.315625	NM_173396	ENSMUSG00000062175	Tgif2	4921501K24|5730599O09Rik|C80753|C81206	TGFB-induced factor homeobox 2	protein-coding
mm_147861.1	chr18	64277171	64277182	-	1	NA	promoter-TSS (NR_045366)	promoter-TSS (NR_045366)	4	NR_045366	73588	Mm.65475	NR_045366	ENSMUSG00000086128	St8sia3os	1700091E21Rik	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3, opposite strand	ncRNA
mm_94621.1	chr11	16778001	16778033	+	1	NA	intron (NM_207655, intron 1 of 27)	intron (NM_207655, intron 1 of 27)	25814	NM_007912	13649	Mm.8534	NM_007912	ENSMUSG00000020122	Egfr	9030024J15Rik|AI552599|Erbb|Errb1|Errp|Wa5|wa-2|wa2	epidermal growth factor receptor	protein-coding
mm_11701.1	chr2	36049367	36049412	+	1	NA	promoter-TSS (NM_029309)	promoter-TSS (NM_029309)	-84	NM_029309	75495	Mm.276332	NM_029309	ENSMUSG00000026894	Morn5	1700010A17Rik	MORN repeat containing 5	protein-coding
mm_37271.1	chr4	118544916	118544930	-	1	NA	Intergenic	L2b|LINE|L2	-1197	NM_172383	230678	Mm.23639	NM_172383	ENSMUSG00000050854	Tmem125	6330530A05Rik|AV223516	transmembrane protein 125	protein-coding
mm_140080.1	chr17	75178835	75178856	+	1	NA	promoter-TSS (NM_001331237)	promoter-TSS (NM_001331237)	64	NM_001331235	268977	Mm.269747	NM_019919	ENSMUSG00000001870	Ltbp1	9430031G15Rik|9830146M04|Ltbp-1|Ltbp1L|TGF-beta1-BP-1|Tgfb|b2b1000Clo	latent transforming growth factor beta binding protein 1	protein-coding
mm_119785.1	chr14	54185847	54185851	+	1	NA	Intergenic	Intergenic	68080	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_58834.1	chr7	16816274	16816286	+	1	NA	5' UTR (NM_001039878, exon 1 of 18)	5' UTR (NM_001039878, exon 1 of 18)	391	NM_001039878	97387	Mm.21612	NM_133789	ENSMUSG00000030374	Strn4	C80611|ZIN|zinedin	striatin, calmodulin binding protein 4	protein-coding
mm_149672.1	chr19	20373426	20373440	+	1	NA	TTS (NM_010730)	TTS (NM_010730)	17238	NM_010730	16952	Mm.248360	NM_010730	ENSMUSG00000024659	Anxa1	Anx-1|Anx-A1|C430014K04Rik|Lpc-1|Lpc1	annexin A1	protein-coding
mm_34088.1	chr4	138832927	138832935	+	1	NA	non-coding (NR_002926, exon 3 of 5)	non-coding (NR_002926, exon 3 of 5)	1055	NM_001082531	18780	Mm.4675	NM_011108	ENSMUSG00000058908	Pla2g2a	EF|Mom1|Pla2|sPLA2|sPla2-IIA	phospholipase A2, group IIA (platelets, synovial fluid)	protein-coding
mm_126690.1	chr15	85008067	85008067	+	1	NA	Intergenic	Intergenic	-9074	NM_023478	22270	Mm.46214	NM_023478	ENSMUSG00000022435	Upk3a	1110017C07Rik|UP3a|UPIII|Upk3	uroplakin 3A	protein-coding
mm_2462.1	chr1	105356770	105356786	+	1	NA	promoter-TSS (NM_001160368)	promoter-TSS (NM_001160368)	-68	NM_001160368	320311	Mm.389162	NM_178779	ENSMUSG00000047496	Rnf152	A930029B02Rik	ring finger protein 152	protein-coding
mm_45499.1	chr5	72262067	72262079	-	1	NA	intron (NM_153389, intron 11 of 22)	intron (NM_153389, intron 11 of 22)	58730	NM_153389	231287	Mm.32775	NM_153389	ENSMUSG00000046808	Atp10d	9830145H18Rik|ATPVD|D5Buc24e	ATPase, class V, type 10D	protein-coding
mm_126928.1	chr15	91673282	91673293	+	1	NA	promoter-TSS (NM_025730)	promoter-TSS (NM_025730)	63	NM_025730	66725	Mm.37558	NM_025730	ENSMUSG00000036273	Lrrk2	4921513O20Rik|9330188B09Rik|AW561911|D630001M17Rik|Gm927|cI-46	leucine-rich repeat kinase 2	protein-coding
mm_20792.1	chr2	144011203	144011236	-	1	NA	promoter-TSS (NM_133626)	promoter-TSS (NM_133626)	44	NM_133626	81910	Mm.13705	NM_024281	ENSMUSG00000027422	Rrbp1	1700087N07Rik|5730465C04Rik|ES/130|mKIAA1398|mRRp0|mRRp1.8|mRRp10|mRRp15a|mRRp15b|mRRp16.8|mRRp2|mRRp41|mRRp47|mRRp5.4|p180	ribosome binding protein 1	protein-coding
mm_142946.1	chr17	56108658	56108678	-	1	NA	intron (NM_020568, intron 3 of 8)	intron (NM_020568, intron 3 of 8)	1134	NM_020568	57435	Mm.12966	NM_020568	ENSMUSG00000002831	Plin4	S3-12|mKIAA1881	perilipin 4	protein-coding
mm_10875.1	chr2	25241580	25241596	+	1	NA	Intergenic	Intergenic	-1341	NM_176834	68846	Mm.24777	NM_176834	ENSMUSG00000044628	Rnf208	1110061N23Rik	ring finger protein 208	protein-coding
mm_143144.1	chr17	57221353	57221400	-	1	NA	exon (NM_009778, exon 16 of 41)	exon (NM_009778, exon 16 of 41)	-4148	NR_105944	102465591		NR_105944	ENSMUSG00000099066	Mir6978	Gm27858|mmu-mir-6978	microRNA 6978	ncRNA
mm_142979.1	chr17	56218817	56218874	-	1	NA	promoter-TSS (NM_172624)	promoter-TSS (NM_172624)	44	NM_172624	224897	Mm.205535	NM_172624	ENSMUSG00000001229	Dpp9	6430584G11Rik|A330078I11|DPP IX|DPRP2	dipeptidylpeptidase 9	protein-coding
mm_144316.1	chr18	12651814	12651886	+	1	NA	intron (NM_028341, intron 1 of 13)	RSINE1|SINE|B4	8317	NM_028341	72747	Mm.52526	NM_028341	ENSMUSG00000024424	Ttc39c	1700008N02Rik|2810439F02Rik	tetratricopeptide repeat domain 39C	protein-coding
mm_5423.1	chr1	34433250	34433298	-	1	NA	promoter-TSS (NR_039562)	promoter-TSS (NR_039562)	-75	NR_039562	100628580		NR_039562	ENSMUSG00000092852	Mir5103	mir-5103|mmu-mir-5103|mu-mir-5103	microRNA 5103	ncRNA
mm_49953.1	chr6	40628571	40628579	+	1	NA	promoter-TSS (NM_001171003)	promoter-TSS (NM_001171003)	-256	NM_001171003	232714	Mm.33401	NM_001171003	ENSMUSG00000068587	Mgam	6030407P20Rik|MGA	maltase-glucoamylase	protein-coding
mm_86068.1	chr9	114775427	114775437	-	1	NA	intron (NM_001252479, intron 1 of 3)	intron (NM_001252479, intron 1 of 3)	6561	NM_133978	102545	Mm.35600	NM_133978	ENSMUSG00000032436	Cmtm7	AI481279|Cklfsf7|LNV	CKLF-like MARVEL transmembrane domain containing 7	protein-coding
mm_43428.1	chr5	136060038	136060052	+	1	NA	intron (NM_027158, intron 2 of 5)	intron (NM_027158, intron 2 of 5)	2778	NM_027158	69665	Mm.75713	NM_027158	ENSMUSG00000006143	Upk3bl	2310043J07Rik	uroplakin 3B-like	protein-coding
mm_21310.1	chr2	157098459	157098473	-	1	NA	3' UTR (NM_001139520, exon 17 of 17)	3' UTR (NM_001139520, exon 17 of 17)	11411	NM_001177439	383766	Mm.480305	NM_001177439	ENSMUSG00000074628	Tldc2	Gm1332	TBC/LysM associated domain containing 2	protein-coding
mm_8892.1	chr1	162898350	162898368	-	1	NA	intron (NM_018881, intron 1 of 8)	intron (NM_018881, intron 1 of 8)	353	NM_018881	55990	Mm.10929	NM_018881	ENSMUSG00000040170	Fmo2	2310008D08Rik|2310042I22Rik|AW107733	flavin containing monooxygenase 2	protein-coding
mm_50284.1	chr6	47453832	47453868	+	1	NA	promoter-TSS (NM_012042)	promoter-TSS (NM_012042)	-474	NM_012042	26965	Mm.87611	NM_012042	ENSMUSG00000029686	Cul1	-	cullin 1	protein-coding
mm_57294.1	chr6	124436375	124436395	-	1	NA	intron (NM_001346656, intron 16 of 17)	PB1D9|SINE|Alu	-21318	NM_001277805	19305	Mm.22418	NM_008995	ENSMUSG00000005069	Pex5	AW212715|ESTM1|PTS1R|Pxr1|X83306	peroxisomal biogenesis factor 5	protein-coding
mm_94717.1	chr11	20543247	20543268	+	1	NA	promoter-TSS (NM_021372)	promoter-TSS (NM_021372)	4	NM_021372	58172	Mm.339676	NM_021372	ENSMUSG00000049800	Sertad2	AB041541|AU021878|Kiaa0127|MNCb-1504|SEI-2|Sei2|TRIP-Br2|mKIAA0127	SERTA domain containing 2	protein-coding
mm_78540.1	chr9	35279525	35279528	+	1	NA	Intergenic	U4|snRNA|snRNA	-1579	NR_040715	71133	Mm.158577	NR_040715	ENSMUSG00000111746	4933422A05Rik	-	RIKEN cDNA 4933422A05 gene	ncRNA
mm_60714.1	chr7	45277528	45277536	+	1	NA	Intergenic	CpG	-5341	NM_001033176	76713	Mm.425445	NM_001033176	ENSMUSG00000070568	Slc6a21	1700039E15Rik|Gm19188	solute carrier family 6 member 21	protein-coding
mm_138868.1	chr17	43037685	43037696	+	1	NA	exon (NM_178589, exon 2 of 6)	exon (NM_178589, exon 2 of 6)	21135	NM_178589	94185	Mm.200792	NM_178589	ENSMUSG00000023915	Tnfrsf21	AA959878|DR6|R74815|TR7	tumor necrosis factor receptor superfamily, member 21	protein-coding
mm_1393.1	chr1	67129028	67129048	+	1	NA	intron (NM_001080809, intron 1 of 37)	intron (NM_001080809, intron 1 of 37)	6011	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_169416.1	chr14	53007576	53007592	+	1	NA	Intergenic	Intergenic	-511889	NM_001170918	57269	Mm.88822	NM_020512	ENSMUSG00000059887	Olfr1507	MOR244-1|Mor28|Or28	olfactory receptor 1507	protein-coding
mm_88914.1	chr10	81179989	81180018	+	1	NA	TTS (NR_028549)	TTS (NR_028549)	1042	NR_028549	100217454		NR_028549	ENSMUSG00000064441	Snord37	MBII-376	small nucleolar RNA, C/D box 37	snoRNA
mm_45723.1	chr5	86065505	86065525	-	1	NA	promoter-TSS (NM_001345902)	promoter-TSS (NM_001345902)	68	NM_001345902	12617	Mm.4649	NM_007683	ENSMUSG00000029253	Cenpc1	CENP-C|Cenpc	centromere protein C1	protein-coding
mm_116741.1	chr13	51763410	51763427	-	1	NA	intron (NM_013660, intron 1 of 15)	intron (NM_013660, intron 1 of 15)	30329	NM_001281880	20354	Mm.33903	NM_013660	ENSMUSG00000021451	Sema4d	CD100|Semacl2|Semaj|Semcl2|coll-4	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D	protein-coding
mm_86319.1	chr9	122950923	122950953	-	1	NA	promoter-TSS (NM_025419)	promoter-TSS (NM_025419)	62	NM_025419	66202	Mm.268307	NM_025419	ENSMUSG00000032551	1110059G10Rik	-	RIKEN cDNA 1110059G10 gene	protein-coding
mm_159021.1	chr1	172028073	172028073	-	1	NA	promoter-TSS (NM_033509)	promoter-TSS (NM_033509)	-778	NM_033509	93840	Mm.36148	NM_033509	ENSMUSG00000026556	Vangl2	C530001F03Rik|Lootl|Lp|Lpp1|Ltap|Vang1l2|loop-tail|ska17|ska<m17Jus>|stbm|strabismus	vang-like 2 (van gogh, Drosophila)	protein-coding
mm_149354.1	chr19	10937155	10937178	+	1	NA	promoter-TSS (NM_009962)	promoter-TSS (NM_009962)	6	NM_009962	14764	Mm.470721	NM_009962	ENSMUSG00000034117	Ptgdr2	Crth2|Gpr44|Grp45	prostaglandin D2 receptor 2	protein-coding
mm_125746.1	chr15	73724755	73724826	+	1	NA	promoter-TSS (NM_001166388)	promoter-TSS (NM_001166388)	-140	NM_001166388	19245	Mm.390807	NM_008975	ENSMUSG00000059895	Ptp4a3	AV088979|Prl-3|pPtp4a3	protein tyrosine phosphatase 4a3	protein-coding
mm_55878.1	chr6	83523200	83523216	-	1	NA	exon (NM_009610, exon 4 of 9)	exon (NM_009610, exon 4 of 9)	13043	NM_009610	11468	Mm.292865	NM_009610	ENSMUSG00000059430	Actg2	ACTA3|Act-4|Act4|SMGA	actin, gamma 2, smooth muscle, enteric	protein-coding
mm_11716.1	chr2	36239589	36239591	+	1	NA	intron (NM_008969, intron 5 of 10)	B3|SINE|B2	9164	NM_008969	19224	Mm.275434	NM_008969	ENSMUSG00000047250	Ptgs1	COX1|Cox-1|Cox-3|PGHS-1|PHS 1|Pghs1	prostaglandin-endoperoxide synthase 1	protein-coding
mm_165926.1	chr4	63344445	63344448	+	1	NA	promoter-TSS (NM_008768)	promoter-TSS (NM_008768)	-110	NM_008768	18405	Mm.4777	NM_008768	ENSMUSG00000039196	Orm1	Agp-1|Agp-2|Orm-1	orosomucoid 1	protein-coding
mm_154730.1	chrX	9480567	9480570	+	1	NA	Intergenic	RLTR1C|LTR|ERV1	-11244	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_131838.1	chr16	22960942	22960955	+	1	NA	exon (NM_053176, exon 7 of 7)	exon (NM_053176, exon 7 of 7)	9876	NM_053176	94175	Mm.358794	NM_053176	ENSMUSG00000022877	Hrg	AI265597|AW413091|D16jh2|D18020|Hprg|Hrgp	histidine-rich glycoprotein	protein-coding
mm_9584.1	chr1	174028478	174028489	-	1	NA	intron (NM_172648, intron 1 of 6)	intron (NM_172648, intron 1 of 6)	3272	NM_172648	226695	Mm.425061	NM_172648	ENSMUSG00000054203	Ifi205	D3|D3cDNA|Ifi205a	interferon activated gene 205	protein-coding
mm_153352.1	chr19	40073732	40073770	-	1	NA	promoter-TSS (NM_206537)	promoter-TSS (NM_206537)	62	NM_206537	404195	Mm.379575	NM_206537	ENSMUSG00000067225	Cyp2c54	EG404195	cytochrome P450, family 2, subfamily c, polypeptide 54	protein-coding
mm_63483.1	chr7	127746715	127746729	+	1	NA	promoter-TSS (NM_172748)	promoter-TSS (NM_172748)	-53	NM_172748	233902	Mm.259353	NM_172748	ENSMUSG00000030811	Fbxl19	6030430O11|BC059812|Fbl19	F-box and leucine-rich repeat protein 19	protein-coding
mm_29819.1	chr3	129217229	129217259	-	1	NA	intron (NM_011098, intron 4 of 4)	intron (NM_011098, intron 4 of 4)	3312	NM_001287048	18741	Mm.246804	NM_011098	ENSMUSG00000028023	Pitx2	9430085M16Rik|Brx1|Brx1b|Munc30|Otlx2|Ptx2|Rieg	paired-like homeodomain transcription factor 2	protein-coding
mm_116385.1	chr13	41183087	41183093	-	1	NA	3' UTR (NM_019423, exon 8 of 8)	3' UTR (NM_019423, exon 8 of 8)	37072	NM_001311121	54326	Mm.2567	NM_019423	ENSMUSG00000021364	Elovl2	AI317360|Ssc2	elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 2	protein-coding
mm_8284.1	chr1	140183261	140183271	-	1	NA	exon (NM_009888, exon 1 of 22)	exon (NM_009888, exon 1 of 22)	145	NM_009888	12628	Mm.8655	NM_009888	ENSMUSG00000026365	Cfh	Mud-1|NOM|Sas-1|Sas1	complement component factor h	protein-coding
mm_44283.1	chr5	8078494	8078497	-	1	NA	3' UTR (NM_001098225, exon 30 of 30)	3' UTR (NM_001098225, exon 30 of 30)	21953	NM_001080974	109552	Mm.96211	NM_025618	ENSMUSG00000003161	Sri	2210417O06Rik|2900070H08Rik|Sor	sorcin	protein-coding
mm_109367.1	chr12	109645922	109645935	+	1	NA	non-coding (NR_028261, exon 11 of 21)	non-coding (NR_028261, exon 11 of 21)	3090	NR_046303	449561		NR_046303		AF357426	MBII-49	snoRNA AF357426	snoRNA
mm_89857.1	chr10	108131088	108131112	+	1	NA	Intergenic	Intergenic	-31300	NM_027892	17931	Mm.422959	NM_027892	ENSMUSG00000019907	Ppp1r12a	1200015F06Rik|5730577I22Rik|AA792106|AV099298|D10Ertd625e|Mypt1	protein phosphatase 1, regulatory (inhibitor) subunit 12A	protein-coding
mm_36845.1	chr4	106678875	106678916	-	1	NA	promoter-TSS (NM_001172073)	promoter-TSS (NM_001172073)	49	NM_028209	72354	Mm.25806	NM_028209	ENSMUSG00000025413	Ttc4	2810002P21Rik|AF007005|L62	tetratricopeptide repeat domain 4	protein-coding
mm_154605.1	chrX	7644140	7644153	+	1	NA	exon (NM_009305, exon 4 of 7)	exon (NM_009305, exon 4 of 7)	5566	NM_009305	20977	Mm.223674	NM_009305	ENSMUSG00000031144	Syp	A230093K24Rik|AI848995|Syn|p38	synaptophysin	protein-coding
mm_100483.1	chr11	120233929	120233975	+	1	NA	intron (NM_001347621, intron 1 of 27)	CpG	1005	NM_198423	268515	Mm.309498	NM_198423	ENSMUSG00000039741	Bahcc1	B930044J06|BC060615	BAH domain and coiled-coil containing 1	protein-coding
mm_103574.1	chr11	77953691	77953704	-	1	NA	exon (NM_021286, exon 2 of 17)	exon (NM_021286, exon 2 of 17)	22858	NM_021286	20370	Mm.229330	NM_021286	ENSMUSG00000000632	Sez6	BSRP-C|D11Bhm177e|sez-6	seizure related gene 6	protein-coding
mm_82009.1	chr9	121710448	121710456	+	1	NA	promoter-TSS (NM_026794)	promoter-TSS (NM_026794)	63	NM_026794	26901	Mm.24848	NM_026794	ENSMUSG00000032526	Ss18l2	1110020I04Rik|AI463209|Deb1	SS18, nBAF chromatin remodeling complex subunit like 2	protein-coding
mm_172076.1	chr6	141601246	141601249	-	1	NA	Intergenic	RLTR9E|LTR|ERVK	-28271	NM_020495	28253	Mm.272223	NM_020495	ENSMUSG00000030236	Slco1b2	7330442B20Rik|OATP-C|OATP2|Oatp1b2|Oatp4|Slc21a10|Slc21a6|lst-1|mlst-1	solute carrier organic anion transporter family, member 1b2	protein-coding
mm_165934.1	chr4	69157227	69157230	-	1	NA	Intergenic	Intergenic	-202831	NM_019967	56710	Mm.248788	NM_019967	ENSMUSG00000028351	Brinp1	BRINP|Dbc1|Dbccr1|Fam5a	bone morphogenic protein/retinoic acid inducible neural specific 1	protein-coding
mm_167947.1	chrX	137599535	137599537	+	1	NA	intron (NM_030688, intron 1 of 10)	MER124|DNA?|DNA?	28782	NM_030688	60367	Mm.328321	NM_030688	ENSMUSG00000059203	Il1rapl2	-	interleukin 1 receptor accessory protein-like 2	protein-coding
mm_32088.1	chr4	98436965	98436971	+	1	NA	intron (NM_001005784, intron 11 of 19)	intron (NM_001005784, intron 11 of 19)	41142	NM_172696	12695	Mm.90218	NM_007704	ENSMUSG00000061859	Patj	Cipp|Inadl	PATJ, crumbs cell polarity complex component	protein-coding
mm_156240.1	chrX	136224036	136224053	+	1	NA	promoter-TSS (NM_001127169)	promoter-TSS (NM_001127169)	3	NM_001127169	100040972	Mm.18125	NM_001127169	ENSMUSG00000079428	Tceal7	1110018P05Rik	transcription elongation factor A (SII)-like 7	protein-coding
mm_165860.1	chr4	25307774	25307784	+	1	NA	Intergenic	Intergenic	-25958	NM_026194	67490	Mm.226295	NM_026194	ENSMUSG00000040359	Ufl1	1810074P20Rik|AI429228|Kiaa0776|Maxer|Rcad|mKIAA0776	UFM1 specific ligase 1	protein-coding
mm_134712.1	chr16	22894831	22894861	-	1	NA	promoter-TSS (NR_110508)	promoter-TSS (NR_110508)	-460	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_37437.1	chr4	122961174	122961193	-	1	NA	promoter-TSS (NM_029662)	promoter-TSS (NM_029662)	5	NM_029662	76574	Mm.331842	NM_029662	ENSMUSG00000028655	Mfsd2a	1700018O18Rik|Mfsd2|NLS1	major facilitator superfamily domain containing 2A	protein-coding
mm_79923.1	chr9	65630553	65630599	+	1	NA	promoter-TSS (NM_028030)	promoter-TSS (NM_028030)	-6	NM_028030	71973	Mm.29148	NM_028030	ENSMUSG00000032387	Rbpms2	2400008B06Rik|AI316523	RNA binding protein with multiple splicing 2	protein-coding
mm_104761.1	chr11	98477242	98477254	-	1	NA	intron (NM_011771, intron 6 of 7)	intron (NM_011771, intron 6 of 7)	30414	NM_010346	14786	Mm.276702	NM_010346	ENSMUSG00000019312	Grb7	mKIAA4028	growth factor receptor bound protein 7	protein-coding
mm_156664.1	chrX	158149826	158149828	+	1	NA	Intergenic	Intergenic	-106630	NM_177751	245684	Mm.197074	NM_177751	ENSMUSG00000025658	Cnksr2	Cnk2|Ksr2	connector enhancer of kinase suppressor of Ras 2	protein-coding
mm_29641.1	chr3	121815416	121815506	-	1	NA	promoter-TSS (NM_008991)	promoter-TSS (NM_008991)	-246	NM_008991	19299	Mm.399042	NM_008991	ENSMUSG00000028127	Abcd3	AI313901|AU018866|AW146054|PMP68|PMP70|Pxmp1	ATP-binding cassette, sub-family D (ALD), member 3	protein-coding
mm_132251.1	chr16	32751470	32751487	+	1	NA	exon (NM_080457, exon 2 of 27)	exon (NM_080457, exon 2 of 27)	15592	NM_080457	140474	Mm.214599	NM_080457	ENSMUSG00000079620	Muc4	4933405I11Rik|Asgp	mucin 4	protein-coding
mm_127306.1	chr15	100227900	100227904	+	1	NA	promoter-TSS (NM_007497)	promoter-TSS (NM_007497)	43	NM_007497	11908	Mm.676	NM_007497	ENSMUSG00000023027	Atf1	-	activating transcription factor 1	protein-coding
mm_69171.1	chr7	127215330	127215349	-	1	NA	exon (NM_017461, exon 9 of 11)	exon (NM_017461, exon 9 of 11)	3106	NM_017461	54204	Mm.18	NM_017461	ENSMUSG00000000486	Sept1	Diff6|Pnutl3	septin 1	protein-coding
mm_28976.1	chr3	101106352	101106356	-	1	NA	intron (NM_011197, intron 1 of 8)	ID4_|SINE|ID	3812	NM_011197	19221	Mm.24807	NM_011197	ENSMUSG00000027864	Ptgfrn	4833445A08Rik|AU042434|CD9P-1|FPRP|Trim45	prostaglandin F2 receptor negative regulator	protein-coding
mm_140584.1	chr17	10213159	10213176	-	1	NA	3' UTR (NM_001159516, exon 7 of 7)	3' UTR (NM_001159516, exon 7 of 7)	106194	NM_021881	19317	Mm.130694	NM_021881	ENSMUSG00000062078	Qk	1110003F05Rik|1500005P18|QkI|l(17)-1Wis|l17Wis1	quaking	protein-coding
mm_51693.1	chr6	86539709	86539712	+	1	NA	intron (NR_037960, intron 3 of 4)	intron (NR_037960, intron 3 of 4)	12309	NR_037961	72012	Mm.349174	NR_037960	ENSMUSG00000097048	1600020E01Rik	-	RIKEN cDNA 1600020E01 gene	ncRNA
mm_122901.1	chr14	54953050	54953069	-	1	NA	exon (NM_010856, exon 23 of 39)	exon (NM_010856, exon 23 of 39)	-3917	NR_029724	387204		NR_029724	ENSMUSG00000065432	Mir208a	Mirn208|Mirn208a|mir-208|mir-208a|mmu-mir-208	microRNA 208a	ncRNA
mm_105900.1	chr11	114982908	114982918	-	1	NA	3' UTR (NM_145437, exon 4 of 4)	3' UTR (NM_145437, exon 4 of 4)	6973	NM_145437	217305	Mm.275986	NM_145437	ENSMUSG00000034641	Cd300ld	4732429D16Rik|CLM5|Cd300ld1|LMIR4|MAIR-IV|clm-5	CD300 molecule like family member d	protein-coding
mm_59013.1	chr7	19228961	19228971	+	1	NA	intron (NM_207525, intron 1 of 1)	intron (NM_207525, intron 1 of 1)	577	NM_207525	403187	Mm.239583	NM_207525	ENSMUSG00000052214	Opa3	D630048P19Rik|Gm1425|Gm472	optic atrophy 3	protein-coding
mm_25984.1	chr3	133338945	133338971	+	1	NA	intron (NM_146141, intron 5 of 11)	intron (NM_146141, intron 5 of 11)	28848	NM_146141	74776	Mm.210305	NM_146141	ENSMUSG00000028013	Ppa2	1110013G13Rik|Sid6306	pyrophosphatase (inorganic) 2	protein-coding
mm_85080.1	chr9	91364980	91365013	-	1	NA	exon (NM_009573, exon 1 of 3)	exon (NM_009573, exon 1 of 3)	803	NM_009573	22771	Mm.335350	NM_009573	ENSMUSG00000032368	Zic1	ZIC|ZNF201	zinc finger protein of the cerebellum 1	protein-coding
mm_78115.1	chr9	20642947	20642960	+	1	NA	promoter-TSS (NM_013911)	promoter-TSS (NM_013911)	-147	NM_013911	30843	Mm.24608	NM_013911	ENSMUSG00000066892	Fbxl12	3110048D16Rik|Fbl12	F-box and leucine-rich repeat protein 12	protein-coding
mm_27652.1	chr3	63964572	63964604	-	1	NA	5' UTR (NM_001272035, exon 1 of 7)	5' UTR (NM_001272035, exon 1 of 7)	145	NM_001331067	11416	Mm.135619	NM_015728	ENSMUSG00000027822	Slc33a1	AI315656|AI788741|Acatn|D630022N01Rik	solute carrier family 33 (acetyl-CoA transporter), member 1	protein-coding
mm_76669.1	chr8	93427370	93427381	-	1	NA	Intergenic	Intergenic	-90166	NM_021456	12623	Mm.22720	NM_021456	ENSMUSG00000057074	Ces1g	Ces-1|Ces1|Ses-1	carboxylesterase 1G	protein-coding
mm_102411.1	chr11	59191792	59191843	-	1	NA	5' UTR (NM_008193, exon 1 of 8)	5' UTR (NM_008193, exon 1 of 8)	135	NM_008193	14923	Mm.3624	NM_008193	ENSMUSG00000020444	Guk1	AA409738|AL033299|AL033300|AV026611|Gmk|Guk-1	guanylate kinase 1	protein-coding
mm_131048.1	chr16	4003925	4003946	+	1	NA	Intergenic	CpG	-2257	NM_177472	52864	Mm.29935	NM_177472	ENSMUSG00000039738	Slx4	AI256635|AI426760|Btbd12|D16Bwg1016e	SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)	protein-coding
mm_167341.1	chr8	73888376	73888382	+	1	NA	Intergenic	Intergenic	-534839	NM_010687	16795	Mm.324371	NM_010687	ENSMUSG00000004383	Large1	BPFD#36|Gyltl1a|Large|Mbp-1|Mbp1|enr|fg|froggy|myd	LARGE xylosyl- and glucuronyltransferase 1	protein-coding
mm_156799.1	chrX	163908983	163908993	+	1	NA	promoter-TSS (NM_026887)	promoter-TSS (NM_026887)	-29	NM_001290378	108012	Mm.426783	NM_026887	ENSMUSG00000031367	Ap1s2	1500012A13Rik|AI853648|EST1	adaptor-related protein complex 1, sigma 2 subunit	protein-coding
mm_143835.1	chr17	84106404	84106426	-	1	NA	Intergenic	MLT2D|LTR|ERVL	27755	NR_045458	74473	Mm.399575	NR_045458		4933433H22Rik	-	RIKEN cDNA 4933433H22 gene	ncRNA
mm_142582.1	chr17	46705003	46705013	-	1	NA	promoter-TSS (NM_009358)	promoter-TSS (NM_009358)	-6	NM_009358	21770	Mm.295009	NM_009358	ENSMUSG00000059409	Ppp2r5d	B'delta|TEG-271|Tex271	protein phosphatase 2, regulatory subunit B', delta	protein-coding
mm_48706.1	chr5	147076576	147076591	-	1	NA	promoter-TSS (NM_080795)	promoter-TSS (NM_080795)	-11	NM_080795	140887	Mm.272203	NM_080795	ENSMUSG00000016520	Lnx2	9630046H24|AW209022	ligand of numb-protein X 2	protein-coding
mm_130165.1	chr15	92705954	92705970	-	1	NA	intron (NM_001164593, intron 5 of 9)	intron (NM_001164593, intron 5 of 9)	108853	NM_001164594	239618	Mm.309826	NM_001164593	ENSMUSG00000036218	Pdzrn4	1110017D07Rik|LNX4|SAMCAP3L|mKIAA3027	PDZ domain containing RING finger 4	protein-coding
mm_119642.1	chr14	51918453	51918460	+	1	NA	promoter-TSS (NM_001128634)	promoter-TSS (NM_001128634)	-305	NM_001128634	219038	Mm.296425	NM_001128634	ENSMUSG00000008813	Tppp2	Gm1790|Gm77	tubulin polymerization-promoting protein family member 2	protein-coding
mm_54108.1	chr6	16898461	16898471	-	1	NA	promoter-TSS (NM_031198)	promoter-TSS (NM_031198)	-25	NM_031198	21426	Mm.36217	NM_031198	ENSMUSG00000029553	Tfec	BB107417|Tcfec|bHLHe34	transcription factor EC	protein-coding
mm_65267.1	chr7	19940354	19940388	-	1	NA	intron (NM_027308, intron 3 of 4)	intron (NM_027308, intron 3 of 4)	10372	NM_027308	70080	Mm.98583	NM_027308	ENSMUSG00000040498	Igsf23	2210010C17Rik	immunoglobulin superfamily, member 23	protein-coding
mm_71080.1	chr8	34623008	34623051	+	1	NA	intron (NR_040706, intron 1 of 4)	intron (NR_040706, intron 1 of 4)	17287	NR_040706	330734	Mm.149998	NR_040706	ENSMUSG00000109819	B930018H19Rik	B930018H19	RIKEN cDNA B930018H19 gene	ncRNA
mm_154143.1	chr19	58370399	58370401	-	1	NA	intron (NM_001285457, intron 4 of 9)	intron (NM_001285457, intron 4 of 9)	74196	NR_040449	791347	Mm.452208	NR_040449		Gm10007	ENSMUSG00000056739	predicted gene 10007	ncRNA
mm_122766.1	chr14	54253908	54253920	-	1	NA	promoter-TSS (NM_001205181)	promoter-TSS (NM_001205181)	15	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_100893.1	chr11	6065769	6065779	-	1	NA	promoter-TSS (NM_001174054)	promoter-TSS (NM_001174054)	-26	NM_007595	12323	Mm.439733	NM_007595	ENSMUSG00000057897	Camk2b	CaMKII	calcium/calmodulin-dependent protein kinase II, beta	protein-coding
mm_123965.1	chr14	74947842	74947858	-	1	NA	promoter-TSS (NM_001033439)	promoter-TSS (NM_001033439)	27	NM_001252132	380916	Mm.288868	NM_001033439	ENSMUSG00000068015	Lrch1	4832412D13Rik|AI552548|AW215503|Chdc1|mKIAA1016	leucine-rich repeats and calponin homology (CH) domain containing 1	protein-coding
mm_139013.1	chr17	45686336	45686402	+	1	NA	promoter-TSS (NM_026732)	promoter-TSS (NM_026732)	-3	NM_026732	68463	Mm.379158	NM_026732	ENSMUSG00000023939	Mrpl14	1110006I11Rik|AI846816|MRP-L32|Rpml32	mitochondrial ribosomal protein L14	protein-coding
mm_25318.1	chr3	106486010	106486057	+	1	NA	promoter-TSS (NM_028110)	promoter-TSS (NM_028110)	-7	NM_028110	72121	Mm.14816	NM_028110	ENSMUSG00000027901	Dennd2d	2010308M01Rik|AI451421	DENN/MADD domain containing 2D	protein-coding
mm_119043.1	chr14	30595987	30596002	+	1	NA	exon (NM_001310682, exon 17 of 17)	exon (NM_001310682, exon 17 of 17)	14316	NM_001310682	18753	Mm.2314	NM_011103	ENSMUSG00000021948	Prkcd	AI385711|D14Ertd420e|PKC[d]|PKCdelta|Pkcd	protein kinase C, delta	protein-coding
mm_167347.1	chr8	82682360	82682365	+	1	NA	Intergenic	Intergenic	91764	NM_145600	30932	Mm.269248	NM_145600	ENSMUSG00000031711	Zfp330	BC008086|Noa36|Znf330	zinc finger protein 330	protein-coding
mm_91308.1	chr10	24920758	24920776	-	1	NA	exon (NM_007482, exon 3 of 8)	exon (NM_007482, exon 3 of 8)	6703	NM_007482	11846	Mm.154144	NM_007482	ENSMUSG00000019987	Arg1	AI|AI256583|Arg-1|PGIF	arginase, liver	protein-coding
mm_54411.1	chr6	32587347	32587360	-	1	NA	5' UTR (NM_175750, exon 1 of 32)	5' UTR (NM_175750, exon 1 of 32)	839	NM_175750	243743	Mm.444029	NM_175750	ENSMUSG00000029765	Plxna4	9330117B14|Plxa4|mKIAA1550	plexin A4	protein-coding
mm_54144.1	chr6	22307042	22307052	-	1	NA	3' UTR (NM_138587, exon 10 of 10)	3' UTR (NM_138587, exon 10 of 10)	18820	NM_053116	93735	Mm.137403	NM_053116	ENSMUSG00000029671	Wnt16	E130309I19Rik	wingless-type MMTV integration site family, member 16	protein-coding
mm_35990.1	chr4	55532124	55532134	-	1	NA	5' UTR (NM_010637, exon 1 of 5)	5' UTR (NM_010637, exon 1 of 5)	346	NM_010637	16600	Mm.4325	NM_010637	ENSMUSG00000003032	Klf4	EZF|Gklf|Zie	Kruppel-like factor 4 (gut)	protein-coding
mm_119581.1	chr14	50924950	50924965	+	1	NA	promoter-TSS (NM_009687)	promoter-TSS (NM_009687)	8	NM_009687	11792	Mm.203	NM_009687	ENSMUSG00000035960	Apex1	APE|Apex|HAP1|Ref-1	apurinic/apyrimidinic endonuclease 1	protein-coding
mm_79264.1	chr9	50753178	50753198	+	1	NA	promoter-TSS (NM_024441)	promoter-TSS (NM_024441)	217	NM_009964	12955	Mm.178	NM_009964	ENSMUSG00000032060	Cryab	Crya-2|Crya2|HspB5|P23	crystallin, alpha B	protein-coding
mm_51968.1	chr6	91758437	91758460	+	1	NA	3' UTR (NM_009320, exon 15 of 15)	3' UTR (NM_009320, exon 15 of 15)	48945	NM_001159507	243547	Mm.333264	NM_001033353	ENSMUSG00000030098	Grip2	-	glutamate receptor interacting protein 2	protein-coding
mm_58664.1	chr7	6813774	6813775	+	1	NA	intron (NM_021323, intron 2 of 7)	MTE2a|LTR|ERVL-MaLR	10187	NR_037213	100499513		NR_037213	ENSMUSG00000092815	Mir3099	mir-3099|mmu-mir-3099	microRNA 3099	ncRNA
mm_124726.1	chr15	6580279	6580296	+	1	NA	exon (NM_001278269, exon 1 of 17)	exon (NM_001278269, exon 1 of 17)	440	NM_011815	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_30925.1	chr4	32754430	32754442	+	1	NA	exon (NM_001081392, exon 84 of 102)	exon (NM_001081392, exon 84 of 102)	-45823	NM_175364	108755	Mm.1182	NM_175364	ENSMUSG00000045854	Lyrm2	2610208E05Rik	LYR motif containing 2	protein-coding
mm_150727.1	chr19	43689648	43689658	+	1	NA	promoter-TSS (NM_053103)	promoter-TSS (NM_053103)	-36	NM_053103	93685	Mm.248237	NM_053103	ENSMUSG00000025192	Entpd7	1810012B13Rik|1810020C02Rik|2810003F23Rik|LALP1|Lysal2	ectonucleoside triphosphate diphosphohydrolase 7	protein-coding
mm_127617.1	chr15	102460479	102460490	+	1	NA	exon (NM_025385, exon 4 of 5)	exon (NM_025385, exon 4 of 5)	1314	NM_025385	66151	Mm.393955	NM_025385	ENSMUSG00000023048	Prr13	1110020C13Rik|2010324E22Rik	proline rich 13	protein-coding
mm_57166.1	chr6	122801681	122801723	-	1	NA	Intergenic	CpG	-18482	NM_021899	60611	Mm.87142	NM_021899	ENSMUSG00000003154	Foxj2	Fhx	forkhead box J2	protein-coding
mm_123909.1	chr14	73325741	73325751	-	1	NA	promoter-TSS (NM_009029)	promoter-TSS (NM_009029)	45	NM_009029	19645	Mm.273862	NM_009029	ENSMUSG00000022105	Rb1	Rb|Rb-1|pRb	retinoblastoma 1	protein-coding
mm_26991.1	chr3	25743249	25743251	-	1	NA	intron (NM_001163387, intron 3 of 5)	L1M3|LINE|L1	410057	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_40559.1	chr5	61788031	61788033	+	1	NA	Intergenic	Intergenic	-20811	NM_019468	14380	Mm.347430	NM_019468	ENSMUSG00000089992	G6pd2	G6pdx-ps1|Gpd-2|Gpd2	glucose-6-phosphate dehydrogenase 2	protein-coding
mm_22670.1	chr3	14872321	14872339	+	1	NA	TTS (NM_007606)	TTS (NM_007606)	8792	NM_007606	12350	Mm.300	NM_007606	ENSMUSG00000027559	Car3	BB219044|Ca3|Car-3	carbonic anhydrase 3	protein-coding
mm_12455.1	chr2	71214473	71214498	+	1	NA	exon (NM_001198877, exon 2 of 19)	exon (NM_001198877, exon 2 of 19)	2539	NM_010064	13427	Mm.249479	NM_010064	ENSMUSG00000027012	Dync1i2	3110079H08Rik|AW554389|Dncic2	dynein cytoplasmic 1 intermediate chain 2	protein-coding
mm_24665.1	chr3	94487691	94487706	+	1	NA	intron (NR_110353, intron 7 of 11)	intron (NR_110353, intron 7 of 11)	4976	NR_110353	78784	Mm.44292	NM_172434	ENSMUSG00000028137	Celf3	4930415M08Rik|BRUNOL1|CAGH4|ERDA4|Tnrc4	CUGBP, Elav-like family member 3	protein-coding
mm_127808.1	chr15	5010101	5010104	-	1	NA	intron (NM_001243837, intron 12 of 17)	intron (NM_001243837, intron 12 of 17)	53671	NM_001243837	109828	Mm.208034	NM_001243837	ENSMUSG00000079105	C7	A530026G17|Gm1238	complement component 7	protein-coding
mm_49210.1	chr6	15721104	15721197	+	1	NA	intron (NM_175088, intron 1 of 4)	CpG	489	NM_175088	16543	Mm.1314	NM_175088	ENSMUSG00000041390	Mdfic	Kdt1|Mdfid	MyoD family inhibitor domain containing	protein-coding
mm_6658.1	chr1	80177757	80177770	-	1	NA	Intergenic	Intergenic	36181	NM_173425	241128	Mm.145511	NM_173425	ENSMUSG00000043230	Fam124b	A830043J08Rik	family with sequence similarity 124, member B	protein-coding
mm_131242.1	chr16	10489807	10489827	+	1	NA	promoter-TSS (NM_001243761)	promoter-TSS (NM_001243761)	36	NM_001243761	12265	Mm.249560	NM_007575	ENSMUSG00000022504	Ciita	C2ta|EG669998|Gm9475|Mhc2ta	class II transactivator	protein-coding
mm_21794.1	chr2	164857672	164857682	-	1	NA	promoter-TSS (NM_011125)	promoter-TSS (NM_011125)	31	NM_011125	18830	Mm.6105	NM_011125	ENSMUSG00000017754	Pltp	Bpife|OD107	phospholipid transfer protein	protein-coding
mm_144098.1	chr18	3383265	3383267	+	1	NA	promoter-TSS (NM_029402)	promoter-TSS (NM_029402)	41	NM_029402	71745	Mm.291707	NM_029402	ENSMUSG00000024231	Cul2	1300003D18Rik|4932411N15Rik|AI327301|mKIAA4106	cullin 2	protein-coding
mm_145288.1	chr18	53245619	53245634	+	1	NA	promoter-TSS (NM_029394)	promoter-TSS (NM_029394)	-36	NM_029394	69226	Mm.32414	NM_029394	ENSMUSG00000024535	Snx24	2810011K15Rik|5730433I16Rik|AI451341	sorting nexing 24	protein-coding
mm_168819.1	chr12	22156648	22156649	-	1	NA	promoter-TSS (NR_136920)	promoter-TSS (NR_136920)	-2	NR_136920	100043416		NM_001004167	ENSMUSG00000093846	Gm4425	EG432637|Gm5433	KRAB-domain protein pseudogene	pseudo
mm_138940.1	chr17	43985022	43985033	+	1	NA	intron (NM_001286654, intron 2 of 4)	intron (NM_001286654, intron 2 of 4)	31836	NM_030598	53901	Mm.251242	NM_030598	ENSMUSG00000039601	Rcan2	Csp2|Dscr1l1|MCIP2|ZAKI-4	regulator of calcineurin 2	protein-coding
mm_22454.1	chr3	3188017	3188048	+	1	NA	Intergenic	Intergenic	-319998	NM_013920	30942	Mm.330897	NM_013920	ENSMUSG00000017688	Hnf4g	NR2A2	hepatocyte nuclear factor 4, gamma	protein-coding
mm_56397.1	chr6	96116972	96117004	-	1	NA	intron (NM_182808, intron 2 of 4)	intron (NM_182808, intron 2 of 4)	3834	NM_182808	320265	Mm.489890	NM_182808	ENSMUSG00000059187	Fam19a1	C630007B19Rik|FAM19A1 TAFA-1|TAFA1|Tafa-1	family with sequence similarity 19, member A1	protein-coding
mm_22602.1	chr3	14506095	14506102	+	1	NA	TTS (NM_080852)	TTS (NM_080852)	25399	NM_080852	140918	Mm.215250	NM_080852	ENSMUSG00000039710	Slc7a12	Asc-2|XAT1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 12	protein-coding
mm_139073.1	chr17	46650609	46650634	+	1	NA	TTS (NM_001316742)	TTS (NM_001316742)	283	NM_025611	66515	Mm.329078	NM_025611	ENSMUSG00000038545	Cul7	2510004L20Rik|AA409809|C230011P08Rik|p185|p193	cullin 7	protein-coding
mm_158583.1	chrX	150812878	150812930	-	1	NA	intron (NM_030700, intron 1 of 12)	intron (NM_030700, intron 1 of 12)	799	NM_001199246	80884	Mm.22575	NM_030700	ENSMUSG00000025268	Maged2	4833439A22Rik|Mage-d2|ORF1	melanoma antigen, family D, 2	protein-coding
mm_50909.1	chr6	57582655	57582665	+	1	NA	intron (NM_025992, intron 1 of 22)	intron (NM_025992, intron 1 of 22)	1668	NM_025992	67138	Mm.297393	NM_025992	ENSMUSG00000029798	Herc6	1700121D12Rik|2510038N07Rik|4930427L17Rik|AI451296|CEB1|Herc5	hect domain and RLD 6	protein-coding
mm_16851.1	chr2	11620498	11620523	-	1	NA	Intergenic	Intergenic	-17311	NM_152824	76938	Mm.182769	NM_152824	ENSMUSG00000037197	Rbm17	2700027J02Rik	RNA binding motif protein 17	protein-coding
mm_107195.1	chr12	25303754	25303758	+	1	NA	Intergenic	Intergenic	174582	NR_045844	432641	Mm.112955	NR_045844		Gm17746	-	predicted gene, 17746	ncRNA
mm_122586.1	chr14	50870500	50870550	-	1	NA	promoter-TSS (NM_009351)	promoter-TSS (NM_009351)	29	NM_009351	21745	Mm.318736	NM_009351	ENSMUSG00000006281	Tep1	Tp1	telomerase associated protein 1	protein-coding
mm_99934.1	chr11	111026773	111026783	+	1	NA	3' UTR (NM_001252208, exon 2 of 2)	3' UTR (NM_001252208, exon 2 of 2)	2918	NM_001252208	16517	Mm.30176	NM_010604	ENSMUSG00000051497	Kcnj16	6430410F18Rik|AI132396|Kir5.1	potassium inwardly-rectifying channel, subfamily J, member 16	protein-coding
mm_35393.1	chr4	34050056	34050072	-	1	NA	promoter-TSS (NM_026293)	promoter-TSS (NM_026293)	1	NM_001290443	67652	Mm.55848	NM_026293	ENSMUSG00000028264	Spaca1	1700124L11Rik|4930540L03Rik	sperm acrosome associated 1	protein-coding
mm_142604.1	chr17	46801874	46801893	-	1	NA	intron (NM_001100452, intron 10 of 10)	intron (NM_001100452, intron 10 of 10)	-19227	NM_025433	66229	Mm.218533	NM_025433	ENSMUSG00000063888	Rpl7l1	1500016H10Rik	ribosomal protein L7-like 1	protein-coding
mm_4410.1	chr1	172482213	172482231	+	1	NA	promoter-TSS (NM_001145800)	promoter-TSS (NM_001145800)	9	NM_001145800	93842	Mm.214530	NM_033608	ENSMUSG00000037995	Igsf9	644ETD8|Dasm1|Kiaa1355-hp|NRT1|Ncaml|mKIAA1355	immunoglobulin superfamily, member 9	protein-coding
mm_67071.1	chr7	67952950	67952958	-	1	NA	intron (NM_010513, intron 1 of 20)	CpG-13221	697	NM_010513	16001	Mm.275742	NM_010513	ENSMUSG00000005533	Igf1r	A330103N21Rik|CD221|D930020L01|IGF-1R|hyft	insulin-like growth factor I receptor	protein-coding
mm_32105.1	chr4	98728359	98728373	+	1	NA	intron (NM_001081202, intron 2 of 4)	intron (NM_001081202, intron 2 of 4)	1612	NM_001081202	381591	Mm.34340	NM_001081202	ENSMUSG00000087166	L1td1	AA546746|AB211064|D76865|ECAT11	LINE-1 type transposase domain containing 1	protein-coding
mm_93115.1	chr10	91123956	91124044	-	1	NA	promoter-TSS (NM_133668)	promoter-TSS (NM_133668)	-37	NM_133668	18674	Mm.298	NM_133668	ENSMUSG00000061904	Slc25a3	5730556H19Rik|PTP|Phc	solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 3	protein-coding
mm_100680.1	chr11	3452938	3452952	-	1	NA	promoter-TSS (NM_001290473)	promoter-TSS (NM_001290473)	11	NM_001290472	193670	Mm.136973	NM_145355	ENSMUSG00000020448	Rnf185	-	ring finger protein 185	protein-coding
mm_70160.1	chr7	143549056	143549125	-	1	NA	promoter-TSS (NM_008672)	promoter-TSS (NM_008672)	30	NM_001285489	17955	Mm.294625	NM_008672	ENSMUSG00000059119	Nap1l4	2810410H14Rik|AI316776|D7Wsu30e|Nap2	nucleosome assembly protein 1-like 4	protein-coding
mm_19976.1	chr2	118307677	118307684	-	1	NA	intron (NR_045919, intron 2 of 2)	intron (NR_045919, intron 2 of 2)	2766	NR_045919	73358	Mm.437192	NR_045919	ENSMUSG00000085889	1700054M17Rik	-	RIKEN cDNA 1700054M17 gene	ncRNA
mm_64490.1	chr7	143107253	143107286	+	1	NA	promoter-TSS (NM_008434)	promoter-TSS (NM_008434)	15	NM_008434	16535	Mm.439769	NM_008434	ENSMUSG00000009545	Kcnq1	AW559127|KVLQT1|Kcna9	potassium voltage-gated channel, subfamily Q, member 1	protein-coding
mm_163420.1	chr12	80273410	80273420	+	1	NA	Intergenic	MLT1K|LTR|ERVL-MaLR	-13034	NM_001346669	109711	Mm.253564	NM_134156	ENSMUSG00000015143	Actn1	3110023F10Rik|Actn1a	actinin, alpha 1	protein-coding
mm_127830.1	chr15	6565315	6565328	-	1	NA	Intergenic	Intergenic	-14526	NM_001278269	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_97264.1	chr11	75764833	75764847	+	1	NA	3' UTR (NM_009536, exon 6 of 6)	3' UTR (NM_009536, exon 6 of 6)	-30969	NR_136933	102641247	Mm.411386	NR_136932		Gm12339	OTTMUSG00000006218	predicted gene 12339	ncRNA
mm_122397.1	chr14	40994318	40994340	-	1	NA	3' UTR (NM_001316734, exon 6 of 6)	3' UTR (NM_001316734, exon 6 of 6)	12591	NM_001316739	70564	Mm.27227	NM_027464	ENSMUSG00000021792	Fam213a	5730469M10Rik|AU040822|Adrx|Pamm	family with sequence similarity 213, member A	protein-coding
mm_51692.1	chr6	86527313	86527324	+	1	NA	promoter-TSS (NR_037961)	promoter-TSS (NR_037961)	-12	NR_037960	72012	Mm.349174	NR_037960	ENSMUSG00000097048	1600020E01Rik	-	RIKEN cDNA 1600020E01 gene	ncRNA
mm_31413.1	chr4	48049027	48049063	+	1	NA	5' UTR (NM_015743, exon 2 of 8)	5' UTR (NM_015743, exon 2 of 8)	-2201	NM_001307989	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_4577.1	chr1	177983428	177983463	+	1	NA	Intergenic	CpG	-7990	NM_001034899	545391	Mm.442974	NM_001034899	ENSMUSG00000091476	Gm16432	EG545391|EG666250	predicted gene 16432	protein-coding
mm_137252.1	chr17	24548668	24548694	+	1	NA	Intergenic	Intergenic	-1269	NM_013630	18763	Mm.30435	NM_013630	ENSMUSG00000032855	Pkd1	PC1|mFLJ00285	polycystic kidney disease 1 homolog	protein-coding
mm_39131.1	chr4	155086272	155086379	-	1	NA	promoter-TSS (NM_001081100)	promoter-TSS (NM_001081100)	-28	NM_026395	67830	Mm.241604	NM_026395	ENSMUSG00000029048	Rer1	1110060F11Rik|5830454N22Rik|AU043380	retention in endoplasmic reticulum sorting receptor 1	protein-coding
mm_45436.1	chr5	67231684	67231686	-	1	NA	Intergenic	Intergenic	-28880	NM_001285452	67878	Mm.23217	NM_028975	ENSMUSG00000037720	Tmem33	1110006G02Rik|1600019D15Rik|2410089A21Rik|2700052H22Rik|5430406L04Rik|AA388285|AI314185|AI426615|db83	transmembrane protein 33	protein-coding
mm_21433.1	chr2	158361506	158361554	-	1	NA	promoter-TSS (NR_015463)	promoter-TSS (NR_015463)	-8	NR_027887	68108	Mm.119198	NR_015463		Snhg17	9430008C03Rik	small nucleolar RNA host gene 17	ncRNA
mm_88300.1	chr10	75316965	75316988	+	1	NA	promoter-TSS (NM_009630)	promoter-TSS (NM_009630)	99	NM_009630	11540	Mm.333734	NM_009630	ENSMUSG00000020178	Adora2a	A2AAR|A2aR|AA2AR	adenosine A2a receptor	protein-coding
mm_116415.1	chr13	41487351	41487367	-	1	NA	promoter-TSS (NM_001111324)	promoter-TSS (NM_001111324)	1	NM_001111324	18003	Mm.288980	NM_017464	ENSMUSG00000021365	Nedd9	Cas-L|CasL|HEF1|MEF1|Nedd-9|p105	neural precursor cell expressed, developmentally down-regulated gene 9	protein-coding
mm_169978.1	chr17	14979052	14979064	+	1	NA	promoter-TSS (NM_001123368)	promoter-TSS (NM_001123368)	194	NM_001123370	100041574	Mm.393767	NM_001123370	ENSMUSG00000036552	9030025P20Rik	D17Zt9e	RIKEN cDNA 9030025P20 gene	protein-coding
mm_107224.1	chr12	26472620	26472635	+	1	NA	intron (NM_020557, intron 2 of 4)	intron (NM_020557, intron 2 of 4)	3412	NM_020557	22169	Mm.271839	NM_020557	ENSMUSG00000020638	Cmpk2	1200004E04Rik|TDKI|Tyki	cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial	protein-coding
mm_63988.1	chr7	140095028	140095041	+	1	NA	exon (NM_009475, exon 2 of 5)	exon (NM_009475, exon 2 of 5)	1638	NM_009475	22264	Mm.439707	NM_009475	ENSMUSG00000025467	Prap1	Upa	proline-rich acidic protein 1	protein-coding
mm_108395.1	chr12	80948824	80948841	+	1	NA	intron (NM_009159, intron 5 of 7)	intron (NM_009159, intron 5 of 7)	3333	NM_001347415	20384	Mm.43331	NM_009159	ENSMUSG00000021134	Srsf5	Sfrs5	serine/arginine-rich splicing factor 5	protein-coding
mm_10659.1	chr2	20724550	20724560	+	1	NA	intron (NM_029895, intron 6 of 18)	intron (NM_029895, intron 6 of 18)	205042	NM_001177631	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding
mm_93606.1	chr10	117234202	117234249	-	1	NA	3' UTR (NM_029906, exon 4 of 4)	3' UTR (NM_029906, exon 4 of 4)	4456	NM_029906	77397	Mm.118350	NM_029906	ENSMUSG00000020177	9530003J23Rik	Lyzf1	RIKEN cDNA 9530003J23 gene	protein-coding
mm_33835.1	chr4	135686197	135686240	+	1	NA	promoter-TSS (NM_174851)	promoter-TSS (NM_174851)	-239	NM_174851	242700	Mm.259623	NM_174851	ENSMUSG00000062157	Ifnlr1	CRF2-12|Il28ra	interferon lambda receptor 1	protein-coding
mm_82489.1	chr9	18469704	18469712	-	1	NA	intron (NM_028935, intron 2 of 7)	MER21B|LTR|ERVL	3851	NM_028935	72230	Mm.289689	NM_028935	ENSMUSG00000074500	Zfp558	1700007A21Rik|4932704I17Rik|Zfp558-ps	zinc finger protein 558	protein-coding
mm_42820.1	chr5	122093175	122093190	+	1	NA	Intergenic	Intergenic	-7798	NM_010861	17906	Mm.1529	NM_010861	ENSMUSG00000013936	Myl2	MLC-2|MLC-2s/v|MLC-2v|Mlc2v|Mylpc	myosin, light polypeptide 2, regulatory, cardiac, slow	protein-coding
mm_14080.1	chr2	124610593	124610613	+	1	NA	5' UTR (NM_199238, exon 1 of 17)	5' UTR (NM_199238, exon 1 of 17)	307	NM_172537	214968	Mm.330536	NM_172537	ENSMUSG00000027200	Sema6d	1110067B02Rik|AA409156|D330011G23|mKIAA1479	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	protein-coding
mm_156771.1	chrX	160768180	160768183	+	1	NA	5' UTR (NM_011302, exon 1 of 6)	5' UTR (NM_011302, exon 1 of 6)	168	NM_011302	20147	Mm.41982	NM_011302	ENSMUSG00000031293	Rs1	Rs1h|Xlrs1|tmgc1	retinoschisis (X-linked, juvenile) 1 (human)	protein-coding
mm_41179.1	chr5	88196987	88196993	+	1	NA	Intergenic	Intergenic	-71929	NM_001110779	665615	Mm.366701	NM_001110779	ENSMUSG00000090302	Gm7714	EG665615	predicted gene 7714	protein-coding
mm_36189.1	chr4	62285699	62285705	-	1	NA	promoter-TSS (NM_025286)	promoter-TSS (NM_025286)	-727	NM_025286	20530	Mm.292539	NM_025286	ENSMUSG00000066152	Slc31a2	AI604396|CTR2	solute carrier family 31, member 2	protein-coding
mm_78373.1	chr9	27396792	27396823	+	1	NA	promoter-TSS (NM_029299)	promoter-TSS (NM_029299)	0	NM_029299	75469	Mm.45824	NM_029299	ENSMUSG00000031991	Spata19	1700001L23Rik|AV047838|spergen-1	spermatogenesis associated 19	protein-coding
mm_166178.1	chr5	30945476	30945484	-	1	NA	promoter-TSS (NM_026770)	promoter-TSS (NM_026770)	0	NM_026770	68567	Mm.45127	NM_026770	ENSMUSG00000029161	Cgref1	1110004G24Rik|AW045201|Cgr11	cell growth regulator with EF hand domain 1	protein-coding
mm_172901.1	chr9	57481045	57481056	-	1	NA	Intergenic	RLTR1B|LTR|ERV1	-12990	NM_001301635	56807	Mm.102278	NM_020270	ENSMUSG00000040722	Scamp5	Sc5	secretory carrier membrane protein 5	protein-coding
mm_139305.1	chr17	48348481	48348499	+	1	NA	exon (NM_031254, exon 2 of 5)	exon (NM_031254, exon 2 of 5)	2089	NM_001272078	83433	Mm.261623	NM_031254	ENSMUSG00000023992	Trem2	TREM-2|Trem2a|Trem2b|Trem2c	triggering receptor expressed on myeloid cells 2	protein-coding
mm_37966.1	chr4	133432925	133432932	-	1	NA	Intergenic	MTEa|LTR|ERVL-MaLR	-47205	NM_175307	100342	Mm.204656	NM_175307	ENSMUSG00000046694	Fam46b	4732473B16Rik|AU045678|AU046069	family with sequence similarity 46, member B	protein-coding
mm_93706.1	chr10	118633444	118633447	-	1	NA	Intergenic	Intergenic	-76920	NR_104123	103214	Mm.30529	NR_104123		Tmevpg1	AI447422	Theiler's murine encephalomyelitis virus persistence candidate gene 1	ncRNA
mm_58266.1	chr6	145340674	145340687	-	1	NA	Intergenic	Intergenic	-46945	NR_003625	381827	Mm.179075	NM_001001987		1700073E17Rik	-	ribosomal protein L7 pseudogene	pseudo
mm_168445.1	chr1	140649059	140649059	-	1	NA	intron (NR_040604, intron 1 of 3)	intron (NR_040604, intron 1 of 3)	7343	NR_040604	75910	Mm.483845	NR_040604	ENSMUSG00000102368	4930590L20Rik	-	RIKEN cDNA 4930590L20 gene	ncRNA
mm_55885.1	chr6	83527774	83527807	-	1	NA	intron (NM_009610, intron 1 of 8)	RMER4A|LTR|ERVK	8461	NM_009610	11468	Mm.292865	NM_009610	ENSMUSG00000059430	Actg2	ACTA3|Act-4|Act4|SMGA	actin, gamma 2, smooth muscle, enteric	protein-coding
mm_120131.1	chr14	60197300	60197307	+	1	NA	Intergenic	Intergenic	31612	NR_030458	751526		NR_030458	ENSMUSG00000076270	Mir719	Mirn719|mmu-mir-719	microRNA 719	ncRNA
mm_72275.1	chr8	75100121	75100138	+	1	NA	3' UTR (NM_010442, exon 5 of 5)	3' UTR (NM_010442, exon 5 of 5)	6511	NM_010442	15368	Mm.276389	NM_010442	ENSMUSG00000005413	Hmox1	D8Wsu38e|HO-1|HO1|Hemox|Hmox|Hsp32	heme oxygenase 1	protein-coding
mm_125078.1	chr15	25984481	25984491	+	1	NA	5' UTR (NM_144523, exon 1 of 6)	5' UTR (NM_144523, exon 1 of 6)	120	NM_144523	52521	Mm.29145	NM_144523	ENSMUSG00000052253	Zfp622	1110033B05Rik|D15Ertd806e|ZPR9|Znf622	zinc finger protein 622	protein-coding
mm_158045.1	chrX	98890914	98890991	-	1	NA	promoter-TSS (NM_052976)	promoter-TSS (NM_052976)	73	NM_052976	94190	Mm.33536	NM_052976	ENSMUSG00000031214	Ophn1	C130037N19Rik|Wtgr	oligophrenin 1	protein-coding
mm_82903.1	chr9	32901447	32901452	-	1	NA	Intergenic	Intergenic	27517	NR_131058	330917	Mm.488283	NR_131058		Gm27162	A430016B06	predicted gene 27162	ncRNA
mm_104282.1	chr11	89818650	89818660	-	1	NA	Intergenic	Intergenic	-121719	NM_001327810	382543	Mm.60997	NM_172534	ENSMUSG00000047773	Ankfn1	4932411E22Rik|Gm1175|nmf9	ankyrin-repeat and fibronectin type III domain containing 1	protein-coding
mm_62708.1	chr7	110629527	110629531	+	1	NA	3' UTR (NM_009627, exon 4 of 4)	3' UTR (NM_009627, exon 4 of 4)	1860	NM_009627	11535	Mm.1408	NM_009627	ENSMUSG00000030790	Adm	AM	adrenomedullin	protein-coding
mm_18539.1	chr2	64916869	64916904	-	1	NA	exon (NM_016719, exon 12 of 14)	exon (NM_016719, exon 12 of 14)	105880	NM_016719	50915	Mm.214554	NM_016719	ENSMUSG00000026888	Grb14	AI505286	growth factor receptor bound protein 14	protein-coding
mm_57197.1	chr6	122850341	122850361	-	1	NA	exon (NM_009779, exon 2 of 2)	exon (NM_009779, exon 2 of 2)	5806	NM_009779	12267	Mm.2408	NM_009779	ENSMUSG00000040552	C3ar1	AZ3B|C3AR|HNFAG09	complement component 3a receptor 1	protein-coding
mm_126958.1	chr15	92243652	92243654	+	1	NA	intron (NM_007727, intron 7 of 23)	intron (NM_007727, intron 7 of 23)	82296	NM_001159647	12805	Mm.4911	NM_007727	ENSMUSG00000055022	Cntn1	AW495098|CNTN|F3cam|usl	contactin 1	protein-coding
mm_126536.1	chr15	82022741	82022757	+	1	NA	intron (NM_010247, intron 4 of 12)	intron (NM_010247, intron 4 of 12)	6380	NM_010247	14375	Mm.288809	NM_010247	ENSMUSG00000022471	Xrcc6	70kDa|G22p1|Ku70	X-ray repair complementing defective repair in Chinese hamster cells 6	protein-coding
mm_70812.1	chr8	23085469	23085473	+	1	NA	intron (NR_102385, intron 4 of 45)	intron (NR_102385, intron 4 of 45)	27212	NR_102385	11733	Mm.334444	NM_031158	ENSMUSG00000031543	Ank1	Ank-1|nb|pale	ankyrin 1, erythroid	protein-coding
mm_157258.1	chrX	19153995	19154017	-	1	NA	Intergenic	Intergenic	-7035	NR_029807	723828		NR_029807	ENSMUSG00000065471	Mir222	Mirn222|mir-222|mmu-mir-222	microRNA 222	ncRNA
mm_80348.1	chr9	75174080	75174096	+	1	NA	exon (NM_010864, exon 22 of 41)	exon (NM_010864, exon 22 of 41)	-57926	NM_001081322	208943	Mm.41339	NM_001081322	ENSMUSG00000033590	Myo5c	9130003O20Rik|BB085560|C330029I24	myosin VC	protein-coding
mm_144005.1	chr17	88066005	88066087	-	1	NA	promoter-TSS (NM_001081034)	promoter-TSS (NM_001081034)	-761	NM_001081034	225055	Mm.386857	NM_001081034	ENSMUSG00000005371	Fbxo11	C80048|Jf	F-box protein 11	protein-coding
mm_141723.1	chr17	34115449	34115498	-	1	NA	exon (NM_001204973, exon 6 of 13)	exon (NM_001204973, exon 6 of 13)	4427	NR_037970	14312	Mm.3444	NM_010238	ENSMUSG00000024335	Brd2	AW228947|D17H6S113E|Frg-1|Fsrg-1|Fsrg1|Nat|Ring3|Rnf3|mKIAA4005	bromodomain containing 2	protein-coding
mm_16106.1	chr2	169633094	169633103	+	1	NA	promoter-TSS (NM_080455)	promoter-TSS (NM_080455)	-548	NM_080455	228911	Mm.315789	NM_080455	ENSMUSG00000047907	Tshz2	2900073F20Rik|B830045G17|Mtsh2|Sdccag33l|Tsh2|Zfp218|mKIAA4248|teashirt2	teashirt zinc finger family member 2	protein-coding
mm_131369.1	chr16	13829008	13829029	+	1	NA	exon (NM_001346106, exon 5 of 9)	exon (NM_001346106, exon 5 of 9)	9767	NM_001346111	18203	Mm.380410	NM_010946	ENSMUSG00000022681	Ntan1	PNAA|PNAD	N-terminal Asn amidase	protein-coding
mm_54451.1	chr6	34746220	34746246	-	1	NA	intron (NM_001347100, intron 5 of 13)	intron (NM_001347100, intron 5 of 13)	-34199	NM_001289657	76223	Mm.150047	NM_178630	ENSMUSG00000038836	Agbl3	2900053G10Rik|4930431N21Rik|6530406M24Rik|CCP3	ATP/GTP binding protein-like 3	protein-coding
mm_121768.1	chr14	19873388	19873398	-	1	NA	3' UTR (NM_001285911, exon 4 of 4)	3' UTR (NM_001285911, exon 4 of 4)	34468	NR_105025	52512	Mm.483998	NR_105025		D14Ertd670e	-	DNA segment, Chr 14, ERATO Doi 670, expressed	ncRNA
mm_1457.1	chr1	67230860	67230877	+	1	NA	3' UTR (NM_001080809, exon 38 of 38)	3' UTR (NM_001080809, exon 38 of 38)	107841	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_91717.1	chr10	44458669	44458681	-	1	NA	promoter-TSS (NM_007548)	promoter-TSS (NM_007548)	73	NM_007548	12142	Mm.4800	NM_007548	ENSMUSG00000038151	Prdm1	Blimp-1|Blimp1|PRDI-BF1|ZNFPR1A1|b2b1765Clo	PR domain containing 1, with ZNF domain	protein-coding
mm_42733.1	chr5	120630046	120630056	+	1	NA	exon (NM_001195094, exon 5 of 7)	exon (NM_001195094, exon 5 of 7)	4184	NM_001195094	546886	Mm.464847	NM_001195094	ENSMUSG00000094282	Cfap73	Ccdc42b|Gm5988	cilia and flagella associated protein 73	protein-coding
mm_68745.1	chr7	121064465	121064478	-	1	NA	3' UTR (NM_030691, exon 6 of 6)	3' UTR (NM_030691, exon 6 of 6)	10059	NM_030691	80719	Mm.160384	NM_030691	ENSMUSG00000035004	Igsf6	-	immunoglobulin superfamily, member 6	protein-coding
mm_135781.1	chr16	56886017	56886026	-	1	NA	5' UTR (NM_019631, exon 1 of 6)	5' UTR (NM_019631, exon 1 of 6)	142	NM_019631	56277	Mm.262328	NM_019631	ENSMUSG00000022754	Tmem45a	C630002M10Rik|M32486|p19.5	transmembrane protein 45a	protein-coding
mm_74809.1	chr8	22633378	22633408	-	1	NA	TTS (NR_027886)	TTS (NR_027886)	3416	NR_027886	68074	Mm.463136	NR_027886		A930013F10Rik	-	RIKEN cDNA A930013F10 gene	ncRNA
mm_165874.1	chr4	40759976	40759985	-	1	NA	Intergenic	RLTR30|LTR|ERV1	-2095	NM_021535	74255	Mm.289929	NM_021535	ENSMUSG00000028409	Smu1	2600001O03Rik|2610203K23Rik|AB044414|AI845086|AW556129|Bwd	smu-1 suppressor of mec-8 and unc-52 homolog (C. elegans)	protein-coding
mm_143820.1	chr17	83846770	83846810	-	1	NA	promoter-TSS (NM_025325)	promoter-TSS (NM_025325)	0	NM_025325	107766	Mm.30100	NM_025325	ENSMUSG00000000673	Haao	0610007K21Rik|0610012J07Rik|3-HAO|3-HAOxase|3HAO	3-hydroxyanthranilate 3,4-dioxygenase	protein-coding
mm_79239.1	chr9	50504306	50504346	+	1	NA	exon (NM_029639, exon 4 of 4)	exon (NM_029639, exon 4 of 4)	479	NR_040714	69631	Mm.414996	NR_040714	ENSMUSG00000101304	Plet1os	2310014F07Rik	placenta expressed transcript 1, opposite strand	ncRNA
mm_63763.1	chr7	131123268	131123273	+	1	NA	Intergenic	Intergenic	23013	NM_173409	233918	Mm.78341	NM_173409	ENSMUSG00000013668	4933402N03Rik	4930412O05	RIKEN cDNA 4933402N03 gene	protein-coding
mm_119816.1	chr14	54225452	54225460	+	1	NA	Intergenic	Intergenic	28473	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_60763.1	chr7	45540865	45540880	+	1	NA	exon (NM_148927, exon 11 of 20)	exon (NM_148927, exon 11 of 20)	-14056	NM_025330	66065	Mm.285710	NM_025330	ENSMUSG00000030825	Hsd17b14	0610039E24Rik|Dhrs10|retSDR3	hydroxysteroid (17-beta) dehydrogenase 14	protein-coding
mm_8052.1	chr1	135373959	135373964	-	1	NA	intron (NM_175259, intron 2 of 4)	PB1D7|SINE|Alu	1102	NM_175259	77552	Mm.41407	NM_175259	ENSMUSG00000041889	Shisa4	9330132O05Rik|Tmem58|mShisa4	shisa family member 4	protein-coding
mm_5899.1	chr1	54716863	54716868	-	1	NA	intron (NM_001081433, intron 16 of 27)	intron (NM_001081433, intron 16 of 27)	-159181	NM_001163314	241062	Mm.103539	NM_175508	ENSMUSG00000073678	Pgap1	5033403E17Rik|9030223K07Rik|A530084K22|D230012E17Rik|oto	post-GPI attachment to proteins 1	protein-coding
mm_169443.1	chr14	56811686	56811705	-	1	NA	promoter-TSS (NM_001253752)	promoter-TSS (NM_001253752)	21	NM_001253752	219105	Mm.473172	NM_144842	ENSMUSG00000040123	Zmym5	9830124H08Rik	zinc finger, MYM-type 5	protein-coding
mm_56788.1	chr6	116641454	116641482	-	1	NA	exon (NM_178045, exon 8 of 11)	exon (NM_178045, exon 8 of 11)	4579	NR_106010	102466793		NR_106010	ENSMUSG00000098334	Mir7043	Gm27776|mmu-mir-7043	microRNA 7043	ncRNA
mm_131412.1	chr16	14474297	14474336	+	1	NA	3' UTR (NM_008576, exon 31 of 31)	3' UTR (NM_008576, exon 31 of 31)	-88001	NR_033556	545280	Mm.123679	NR_033556	ENSMUSG00000075395	A630010A05Rik	-	RIKEN cDNA A630010A05 gene	ncRNA
mm_66399.1	chr7	44306996	44307004	-	1	NA	promoter-TSS (NM_009131)	promoter-TSS (NM_009131)	-41	NM_009131	20256	Mm.20428	NM_009131	ENSMUSG00000004473	Clec11a	AW457320|Clecsf3|Scgf	C-type lectin domain family 11, member a	protein-coding
mm_54990.1	chr6	48770745	48770762	-	1	NA	promoter-TSS (NM_031247)	promoter-TSS (NM_031247)	98	NM_031247	83408	Mm.333050	NM_031247	ENSMUSG00000039264	Gimap3	2010110D23Rik|Gimap5|Ian4	GTPase, IMAP family member 3	protein-coding
mm_135296.1	chr16	38602657	38602698	-	1	NA	exon (NM_020260, exon 12 of 12)	exon (NM_020260, exon 12 of 12)	39863	NM_026407	67846	Mm.310476	NM_026407	ENSMUSG00000002845	Tmem39a	2610033C09Rik	transmembrane protein 39a	protein-coding
mm_151814.1	chr19	5489047	5489058	-	1	NA	promoter-TSS (NM_027877)	promoter-TSS (NM_027877)	-716	NM_027877	71711	Mm.27697	NM_027877	ENSMUSG00000024906	Mus81	1200008A18Rik|AI182501|AW045863	MUS81 structure-specific endonuclease subunit	protein-coding
mm_5461.1	chr1	36369122	36369159	-	1	NA	promoter-TSS (NM_172652)	promoter-TSS (NM_172652)	41	NM_172652	226976	Mm.24734	NM_172652	ENSMUSG00000010453	Kansl3	4632411B12Rik|4932435K23|AI431067|AI647574|C85723|Kiaa1310|mKIAA1310	KAT8 regulatory NSL complex subunit 3	protein-coding
mm_73791.1	chr8	117256811	117256829	+	1	NA	promoter-TSS (NM_001163262)	promoter-TSS (NM_001163262)	-199	NM_001163262	74440	Mm.233181	NM_028941	ENSMUSG00000034390	Cmip	4933407C03Rik|5830471E12Rik|AI314065|AI464126	c-Maf inducing protein	protein-coding
mm_110316.1	chr12	34528845	34528904	-	1	NA	promoter-TSS (NM_024124)	promoter-TSS (NM_024124)	15	NM_024124	79221	Mm.310551	NM_024124	ENSMUSG00000004698	Hdac9	AV022454|D030072B18Rik|HD7B|HD9|HDRP|Hdac7b|Mitr|mKIAA0744	histone deacetylase 9	protein-coding
mm_151043.1	chr19	47023925	47023934	+	1	NA	3' UTR (NM_146100, exon 3 of 3)	3' UTR (NM_146100, exon 3 of 3)	-8740	NM_001164363	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_90193.1	chr10	120208785	120208801	+	1	NA	promoter-TSS (NM_026617)	promoter-TSS (NM_026617)	-33	NM_026617	68212	Mm.157426	NM_026617	ENSMUSG00000020225	Tmbim4	0610007H07Rik|AU022431	transmembrane BAX inhibitor motif containing 4	protein-coding
mm_28754.1	chr3	95819212	95819247	-	1	NA	promoter-TSS (NM_001081293)	promoter-TSS (NM_001081293)	-276	NM_001081293	75137	Mm.196275	NM_028328	ENSMUSG00000028106	Rprd2	2810036A19Rik|4930535B03Rik|6720469I21Rik|AL022841|AL022940|AU021304|BB077382|mKIAA0460	regulation of nuclear pre-mRNA domain containing 2	protein-coding
mm_173276.1	chrX	99557340	99557344	+	1	NA	Intergenic	Intergenic	-86607	NM_008853	18744	Mm.8211	NM_008853	ENSMUSG00000034403	Pja1	praja-1	praja ring finger 1, E3 ubiquitin protein ligase	protein-coding
mm_53908.1	chr6	3968365	3968381	-	1	NA	promoter-TSS (NM_009364)	promoter-TSS (NM_009364)	2	NM_009364	21789	Mm.25612	NM_009364	ENSMUSG00000029664	Tfpi2	AV000670|PP5/TFPI-2	tissue factor pathway inhibitor 2	protein-coding
mm_56665.1	chr6	113600627	113600643	-	1	NA	promoter-TSS (NM_027633)	promoter-TSS (NM_027633)	80	NM_027633	70979	Mm.72959	NM_027633	ENSMUSG00000033963	Fancd2os	4931417G12Rik	Fancd2 opposite strand	protein-coding
mm_26699.1	chr3	157566855	157566863	+	1	NA	promoter-TSS (NM_011196)	promoter-TSS (NM_011196)	-33	NM_011196	19218	Mm.30424	NM_011196	ENSMUSG00000040016	Ptger3	EP3|Pgerep3|Ptgerep3	prostaglandin E receptor 3 (subtype EP3)	protein-coding
mm_137343.1	chr17	25136707	25136719	+	1	NA	promoter-TSS (NM_001317404)	promoter-TSS (NM_001317404)	82	NM_001317404	26373	Mm.270587	NM_011930	ENSMUSG00000036636	Clcn7	ClC-7|D17Wsu51e	chloride channel, voltage-sensitive 7	protein-coding
mm_101959.1	chr11	50299236	50299269	-	1	NA	exon (NM_001110500, exon 11 of 15)	exon (NM_001110500, exon 11 of 15)	-6916	NM_175334	103806	Mm.51116	NM_175334	ENSMUSG00000050567	Maml1	AI644666|AW743257|D930008C07Rik|Mam-1|Mam1|mKIAA0200	mastermind like 1 (Drosophila)	protein-coding
mm_115848.1	chr13	21287454	21287469	-	1	NA	exon (NM_010343, exon 5 of 5)	exon (NM_010343, exon 5 of 5)	5225	NM_010343	14780	Mm.1332	NM_010343	ENSMUSG00000004344	Gpx5	AV379049|Arep	glutathione peroxidase 5	protein-coding
mm_73190.1	chr8	95369621	95369632	+	1	NA	exon (NM_008609, exon 6 of 10)	exon (NM_008609, exon 6 of 10)	17330	NM_008609	17388	Mm.217116	NM_008609	ENSMUSG00000031790	Mmp15	AI503551|MT-MMP 2|MT2-MMP	matrix metallopeptidase 15	protein-coding
mm_108766.1	chr12	89591488	89591496	+	1	NA	intron (NM_172544, intron 14 of 19)	MIRb|SINE|MIR	-220991	NM_001252074	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding
mm_83516.1	chr9	46112326	46112354	-	1	NA	intron (NM_027498, intron 1 of 24)	intron (NM_027498, intron 1 of 24)	99520	NM_027498	70661	Mm.219459	NM_027498	ENSMUSG00000034135	Sik3	5730525O22Rik|9030204A07Rik|AI447252|AI846254|AI849445|Qsk|SIK-3|mKIAA0999	SIK family kinase 3	protein-coding
mm_134178.1	chr16	10960522	10960544	-	1	NA	3' UTR (NM_019980, exon 4 of 4)	3' UTR (NM_019980, exon 4 of 4)	32588	NM_019980	56722	Mm.294753	NM_019980	ENSMUSG00000022500	Litaf	3222402J11Rik|C85531|N4WBP3|TBX1	LPS-induced TN factor	protein-coding
mm_164998.1	chr19	18888090	18888093	+	1	NA	intron (NM_153417, intron 37 of 38)	intron (NM_153417, intron 37 of 38)	113026	NM_146095	225998	Mm.234641	NM_146095	ENSMUSG00000036192	Rorb	Nr1f2|RZR-beta|RZRB|Rorbeta|hstp	RAR-related orphan receptor beta	protein-coding
mm_82499.1	chr9	20385091	20385146	-	1	NA	promoter-TSS (NM_001004190)	promoter-TSS (NM_001004190)	40	NM_001004190	434377	Mm.379669	NM_001004190	ENSMUSG00000045519	Zfp560	2310030G09Rik|Znf560	zinc finger protein 560	protein-coding
mm_60047.1	chr7	31059853	31059876	+	1	NA	promoter-TSS (NM_144556)	promoter-TSS (NM_144556)	-71	NM_144556	243914	Mm.389870	NM_144556	ENSMUSG00000036560	Lgi4	Lgil3|clp	leucine-rich repeat LGI family, member 4	protein-coding
mm_98305.1	chr11	90033087	90033113	+	1	NA	intron (NM_026433, intron 1 of 2)	intron (NM_026433, intron 1 of 2)	2752	NM_026433	67888	Mm.212428	NM_026433	ENSMUSG00000069763	Tmem100	1810057C19Rik|AV011897	transmembrane protein 100	protein-coding
mm_28753.1	chr3	95819059	95819075	-	1	NA	promoter-TSS (NM_001081293)	promoter-TSS (NM_001081293)	-114	NM_001081293	75137	Mm.196275	NM_028328	ENSMUSG00000028106	Rprd2	2810036A19Rik|4930535B03Rik|6720469I21Rik|AL022841|AL022940|AU021304|BB077382|mKIAA0460	regulation of nuclear pre-mRNA domain containing 2	protein-coding
mm_128304.1	chr15	37734403	37734432	-	1	NA	intron (NM_134094, intron 1 of 6)	intron (NM_134094, intron 1 of 6)	57583	NM_001170866	52589	Mm.283370	NM_134094	ENSMUSG00000051359	Ncald	AI848120|D030020D09Rik|D15Ertd412e	neurocalcin delta	protein-coding
mm_72393.1	chr8	81767752	81767763	+	1	NA	intron (NM_001297593, intron 4 of 23)	intron (NM_001297593, intron 4 of 23)	425195	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_25353.1	chr3	107001638	107001661	+	1	NA	Intergenic	Intergenic	-34513	NM_008418	16491	Mm.30640	NM_008418	ENSMUSG00000047959	Kcna3	Kca1-3|Kv1.3|Mk-3	potassium voltage-gated channel, shaker-related subfamily, member 3	protein-coding
mm_57434.1	chr6	124914940	124914975	-	1	NA	exon (NM_026988, exon 2 of 5)	exon (NM_026988, exon 2 of 5)	2989	NM_026988	69202	Mm.142187	NM_026988	ENSMUSG00000030122	Ptms	2610009E16Rik	parathymosin	protein-coding
mm_4046.1	chr1	165780725	165780754	+	1	NA	Intergenic	Intergenic	-7942	NM_031162	12503	Mm.217308	NM_031162	ENSMUSG00000005763	Cd247	4930549J05Rik|A430104F18Rik|AW552088|Cd3|Cd3-eta|Cd3-zeta|Cd3h|Cd3z|Cd3zeta|T3z|Tcrk|Tcrz	CD247 antigen	protein-coding
mm_1727.1	chr1	75375329	75375339	+	1	NA	promoter-TSS (NM_007463)	promoter-TSS (NM_007463)	37	NM_007463	11790	Mm.275397	NM_007463	ENSMUSG00000026207	Speg	AW125581|Apeg1|BPEG|D1Bwg1450e|SPEGalpha|SPEGbeta|mKIAA1297	SPEG complex locus	protein-coding
mm_15002.1	chr2	152477018	152477020	+	1	NA	promoter-TSS (NM_176950)	promoter-TSS (NM_176950)	-44	NM_176950	319579	Mm.190454	NM_176950	ENSMUSG00000049560	Defb20	9230107O10Rik|BD-20|mBD-20	defensin beta 20	protein-coding
mm_86500.1	chr10	6789045	6789051	+	1	NA	exon (NM_001304950, exon 1 of 5)	exon (NM_001304950, exon 1 of 5)	472	NM_001039652	18390	Mm.438000	NM_011013	ENSMUSG00000000766	Oprm1	M-OR-1|MOP-R|MOR-1|MOR-1O|Oprm|mor|muOR	opioid receptor, mu 1	protein-coding
mm_72649.1	chr8	84723042	84723082	+	1	NA	intron (NM_001297601, intron 6 of 8)	intron (NM_001297601, intron 6 of 8)	21605	NM_008535	17095	Mm.4925	NM_008535	ENSMUSG00000034041	Lyl1	Lyl-1|bHLHa18	lymphoblastomic leukemia 1	protein-coding
mm_38493.1	chr4	140957847	140957858	-	1	NA	promoter-TSS (NR_045911)	promoter-TSS (NR_045911)	50	NR_045911	100126227	Mm.404073	NR_045911	ENSMUSG00000087698	Gm13031	OTTMUSG00000010081	predicted gene 13031	ncRNA
mm_32100.1	chr4	98546920	98546959	+	1	NA	5' UTR (NM_007704, exon 1 of 18)	5' UTR (NM_007704, exon 1 of 18)	305	NM_001005787	12695	Mm.90218	NM_007704	ENSMUSG00000061859	Patj	Cipp|Inadl	PATJ, crumbs cell polarity complex component	protein-coding
mm_170750.1	chr2	156180236	156180237	-	1	NA	promoter-TSS (NM_001291114)	promoter-TSS (NM_001291114)	2	NM_001291114	170791	Mm.392436	NM_133242	ENSMUSG00000027620	Rbm39	1500012C14Rik|2310040E03Rik|B330012G18Rik|C79248|R75070|Rnpc2|caper	RNA binding motif protein 39	protein-coding
mm_71027.1	chr8	33599594	33599606	+	1	NA	promoter-TSS (NM_017374)	promoter-TSS (NM_017374)	-21	NM_017374	19053	Mm.29301	NM_017374	ENSMUSG00000009630	Ppp2cb	AI115466|D8Ertd766e|PP2Ac	protein phosphatase 2 (formerly 2A), catalytic subunit, beta isoform	protein-coding
mm_172024.1	chr6	118404719	118404723	-	1	NA	exon (NM_194339, exon 10 of 23)	exon (NM_194339, exon 10 of 23)	14696	NM_194339	213895	Mm.25269	NM_194339	ENSMUSG00000030138	Bms1	AA408648|AU020092|AU043373|BB007109|BC030906|Bms1l|mKIAA0187	BMS1, ribosome biogenesis factor	protein-coding
mm_50404.1	chr6	48728142	48728157	+	1	NA	Intergenic	Intergenic	9528	NM_146167	231932	Mm.30479	NM_146167	ENSMUSG00000043931	Gimap7	IAN7|Ian3	GTPase, IMAP family member 7	protein-coding
mm_148888.1	chr19	6871208	6871221	+	1	NA	Intergenic	B4|SINE|B4	-13003	NM_001081291	78317	Mm.329596	NM_198008	ENSMUSG00000047810	Ccdc88b	2610041P08Rik|Ccdc88	coiled-coil domain containing 88B	protein-coding
mm_52567.1	chr6	116264274	116264282	+	1	NA	promoter-TSS (NM_001290338)	promoter-TSS (NM_001290338)	59	NM_001290338	67492	Mm.272772	NM_001081317	ENSMUSG00000042213	Zfand4	Anubl1	zinc finger, AN1-type domain 4	protein-coding
mm_135032.1	chr16	32866347	32866361	-	1	NA	intron (NM_172615, intron 1 of 18)	intron (NM_172615, intron 1 of 18)	2012	NM_001200038	100502698	Mm.327319	NM_172615	ENSMUSG00000035629	Rubcn	1700021K19Rik|5330403K09|Kiaa0226|Rubicon|mKIAA0226	RUN domain and cysteine-rich domain containing, Beclin 1-interacting protein	protein-coding
mm_135199.1	chr16	36532187	36532213	-	1	NA	intron (NM_013803, intron 1 of 6)	intron (NM_013803, intron 1 of 6)	29934	NM_013803	12374	Mm.103619	NM_013803	ENSMUSG00000051980	Casr	CaR|Gprc2a	calcium-sensing receptor	protein-coding
mm_102529.1	chr11	60935323	60935339	-	1	NA	intron (NM_008928, intron 1 of 11)	intron (NM_008928, intron 1 of 11)	3274	NM_008928	26397	Mm.18494	NM_008928	ENSMUSG00000018932	Map2k3	AW212142|MEK3|MKK3|Prkmk3|mMKK3b	mitogen-activated protein kinase kinase 3	protein-coding
mm_159995.1	chr6	118011408	118011408	+	1	NA	promoter-TSS (NM_001316749)	promoter-TSS (NM_001316749)	-129	NM_001316749	70727	Mm.87660	NM_027526	ENSMUSG00000030134	Rasgef1a	6330404M18Rik|AI835194	RasGEF domain family, member 1A	protein-coding
mm_38779.1	chr4	148075386	148075405	-	1	NA	Intergenic	Intergenic	12669	NM_009642	11610	Mm.46247	NM_009642	ENSMUSG00000029007	Agtrap	3300002E14Rik|AT1R|Atrap|D4Wsu124e	angiotensin II, type I receptor-associated protein	protein-coding
mm_11033.1	chr2	26916401	26916421	+	1	NA	promoter-TSS (NM_013678)	promoter-TSS (NM_013678)	-10	NM_013678	20931	Mm.389260	NM_013678	ENSMUSG00000014873	Surf2	Surf-2	surfeit gene 2	protein-coding
mm_129906.1	chr15	84055104	84055110	-	1	NA	intron (NM_029946, intron 1 of 31)	MER5A|DNA|hAT-Charlie	10242	NM_029946	77627	Mm.196288	NM_029946	ENSMUSG00000022441	Efcab6	4931407K02Rik|4932408N08Rik|bM150J22.2|mKIAA1672	EF-hand calcium binding domain 6	protein-coding
mm_87257.1	chr10	41519731	41519743	+	1	NA	intron (NM_016898, intron 1 of 5)	CpG	237	NM_016898	53599	Mm.269815	NM_016898	ENSMUSG00000019818	Cd164	A115|A24|AA589639|AW540279|MGC-24|MSSP	CD164 antigen	protein-coding
mm_32756.1	chr4	116687226	116687239	+	1	NA	intron (NM_011034, intron 1 of 5)	intron (NM_011034, intron 1 of 5)	-1210	NR_040442	100502959	Mm.395400	NR_040442		AV051173	-	expressed sequence AV051173	ncRNA
mm_109064.1	chr12	104344205	104344228	+	1	NA	exon (NM_011458, exon 4 of 5)	exon (NM_011458, exon 4 of 5)	5730	NM_011458	20714	Mm.291569	NM_011458	ENSMUSG00000058207	Serpina3k	1300001I07Rik|D12Rp54|MMCM2|MMSpi2|RP54|Spi-2|Spi2|contrapsin	serine (or cysteine) peptidase inhibitor, clade A, member 3K	protein-coding
mm_151485.1	chr19	58677154	58677168	+	1	NA	exon (NM_026925, exon 9 of 13)	exon (NM_026925, exon 9 of 13)	6796	NM_026925	69060	Mm.20407	NM_026925	ENSMUSG00000046008	Pnlip	1810007A24Rik|PL|PTL	pancreatic lipase	protein-coding
mm_99287.1	chr11	101322173	101322189	+	1	NA	3' UTR (NM_011192, exon 11 of 11)	3' UTR (NM_011192, exon 11 of 11)	-2882	NM_178932	237940	Mm.302277	NM_178932	ENSMUSG00000078651	Aoc2	RAO	amine oxidase, copper containing 2 (retina-specific)	protein-coding
mm_57557.1	chr6	126921805	126921827	-	1	NA	promoter-TSS (NM_207210)	promoter-TSS (NM_207210)	23	NM_207210	101320	Mm.44896	NM_207210	ENSMUSG00000030345	Dyrk4	AW049118|Dyrk4a|Dyrk4b	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 4	protein-coding
mm_151280.1	chr19	55253967	55253977	+	1	NA	5' UTR (NM_027976, exon 1 of 22)	5' UTR (NM_027976, exon 1 of 22)	603	NM_027976	433256	Mm.292056	NM_027976	ENSMUSG00000024981	Acsl5	1700030F05Rik|ACS2|ACS5|Facl5	acyl-CoA synthetase long-chain family member 5	protein-coding
mm_72361.1	chr8	80494252	80494255	+	1	NA	intron (NM_010369, intron 1 of 7)	intron (NM_010369, intron 1 of 7)	208	NM_010369	14934	Mm.13123	NM_010369	ENSMUSG00000051839	Gypa	AI853584|CD235a|GPA	glycophorin A	protein-coding
mm_21134.1	chr2	154209898	154209938	-	1	NA	exon (NM_153418, exon 7 of 16)	exon (NM_153418, exon 7 of 16)	9538	NM_153418	228801	Mm.3783	NM_153418	ENSMUSG00000027485	Bpifb1	Lplunc1	BPI fold containing family B, member 1	protein-coding
mm_149517.1	chr19	12436392	12436410	+	1	NA	Intergenic	Lx8|LINE|L1	8496	NM_019540	56093	Mm.285849	NM_019540	ENSMUSG00000040065	Pfpl	Epcs5|Epcs50	pore forming protein-like	protein-coding
mm_83003.1	chr9	36730023	36730025	-	1	NA	Intergenic	Intergenic	-3366	NM_007691	12649	Mm.16753	NM_007691	ENSMUSG00000032113	Chek1	C85740|Chk1|rad27	checkpoint kinase 1	protein-coding
mm_126934.1	chr15	91771370	91771374	+	1	NA	intron (NM_025730, intron 36 of 50)	L1M2|LINE|L1	-66954	NM_207243	239611	Mm.486225	NM_207243		Muc19	MUC-19|sld	mucin 19	protein-coding
mm_62497.1	chr7	101970212	101970223	+	1	NA	intron (NM_133947, intron 1 of 24)	CpG	374	NM_133947	101706	Mm.27259	NM_133947	ENSMUSG00000066306	Numa1	6720401E04Rik|AA764025|AL022610|AU014979|NuMA	nuclear mitotic apparatus protein 1	protein-coding
mm_84751.1	chr9	75541694	75541721	-	1	NA	intron (NM_016963, intron 1 of 9)	intron (NM_016963, intron 1 of 9)	17950	NM_016963	50875	Mm.38445	NM_016963	ENSMUSG00000058587	Tmod3	U-Tmod|UTMOD	tropomodulin 3	protein-coding
mm_59629.1	chr7	28156713	28156729	+	1	NA	exon (NM_001164655, exon 15 of 20)	exon (NM_001164655, exon 15 of 20)	-13027	NM_007991	14113	Mm.4595	NM_007991	ENSMUSG00000046865	Fbl	AL022665|FIB|FLRN|RNU3IP1	fibrillarin	protein-coding
mm_128355.1	chr15	39944525	39944544	-	1	NA	promoter-TSS (NM_172814)	promoter-TSS (NM_172814)	-540	NM_001347036	239393	Mm.39874	NM_172814	ENSMUSG00000022305	Lrp12	AI848829|C820005L12Rik|LRP-12	low density lipoprotein-related protein 12	protein-coding
mm_59513.1	chr7	27581262	27581277	+	1	NA	3' UTR (NM_175107, exon 10 of 10)	3' UTR (NM_175107, exon 10 of 10)	-10283	NM_001110208	11652	Mm.177194	NM_007434	ENSMUSG00000004056	Akt2	2410016A19Rik|AW554154|PKB|PKBbeta	thymoma viral proto-oncogene 2	protein-coding
mm_42121.1	chr5	110879927	110879941	+	1	NA	exon (NM_001267622, exon 1 of 23)	exon (NM_001267622, exon 1 of 23)	131	NM_001267622	209683	Mm.295660	NM_024477	ENSMUSG00000033209	Ttc28	2310015L07Rik|6030435N04|AI428795|AI851761|BC002262|TPRBK	tetratricopeptide repeat domain 28	protein-coding
mm_104873.1	chr11	99418429	99418440	-	1	NA	intron (NM_010661, intron 4 of 7)	intron (NM_010661, intron 4 of 7)	3825	NM_010661	268482	Mm.436651	NM_010661	ENSMUSG00000020912	Krt12	AI835216|K12|Krt-12|Krt1-12	keratin 12	protein-coding
mm_46968.1	chr5	115158136	115158159	-	1	NA	promoter-TSS (NM_175403)	promoter-TSS (NM_175403)	29	NM_175403	109154	Mm.153963	NM_175403	ENSMUSG00000048578	Mlec	2410014A08Rik|AI850530|ESTM19|X83352|mKIAA0152	malectin	protein-coding
mm_112929.1	chr13	20959677	20959684	+	1	NA	intron (NM_012054, intron 12 of 20)	T-rich|Low_complexity|Low_complexity	113619	NM_146535	258528	Mm.377554	NM_146535	ENSMUSG00000042869	Olfr1370	MOR256-14	olfactory receptor 1370	protein-coding
mm_46442.1	chr5	105083764	105083806	-	1	NA	exon (NM_172777, exon 7 of 11)	exon (NM_172777, exon 7 of 11)	26507	NM_172777	236573	Mm.425261	NM_172777	ENSMUSG00000029298	Gbp9	-	guanylate-binding protein 9	protein-coding
mm_128181.1	chr15	34495181	34495276	-	1	NA	promoter-TSS (NM_008287)	promoter-TSS (NM_008287)	18	NM_008287	15473	Mm.491154	NM_008287	ENSMUSG00000022323	Rida	HR12|HRP12|Hrsp12	reactive intermediate imine deaminase A homolog	protein-coding
mm_17779.1	chr2	32929743	32929767	-	1	NA	intron (NM_199302, intron 21 of 24)	intron (NM_199302, intron 21 of 24)	31500	NM_199302	227738	Mm.248037	NM_199302	ENSMUSG00000026792	Lrsam1	-	leucine rich repeat and sterile alpha motif containing 1	protein-coding
mm_137016.1	chr17	17838072	17838088	+	1	NA	intron (NM_001162909, intron 6 of 8)	intron (NM_001162909, intron 6 of 8)	7105	NM_001162909	75202	Mm.227456	NM_029205	ENSMUSG00000080316	Spaca6	4930546H06Rik|9530079D04Rik|B230206P06Rik|Ncrna00085|SPACA6A|let-7e|mir-125a|mir-99b	sperm acrosome associated 6	protein-coding
mm_8324.1	chr1	149831211	149831218	-	1	NA	intron (NM_001305632, intron 16 of 16)	intron (NM_001305632, intron 16 of 16)	91225	NM_001305632	18783	Mm.4186	NM_008869	ENSMUSG00000056220	Pla2g4a	Pla2g4|cPLA2|cPLA2-alpha|cPLA2alpha	phospholipase A2, group IVA (cytosolic, calcium-dependent)	protein-coding
mm_172757.1	chr8	85949286	85949286	+	1	NA	intron (NM_199446, intron 13 of 31)	L1Md_T|LINE|L1	108284	NM_199446	102093	Mm.237296	NM_199446	ENSMUSG00000036879	Phkb	AI463271	phosphorylase kinase beta	protein-coding
mm_54625.1	chr6	38688023	38688032	-	1	NA	Intergenic	Intergenic	24958	NM_001101507	665180	Mm.349066	NM_001101507	ENSMUSG00000079598	Clec2l	AI414054|AW122724|Gm1064	C-type lectin domain family 2, member L	protein-coding
mm_114373.1	chr13	63113269	63113305	+	1	NA	intron (NM_001289926, intron 5 of 15)	intron (NM_001289926, intron 5 of 15)	-126742	NR_110520	72061	Mm.188105	NM_028079	ENSMUSG00000021458	2010111I01Rik	2300006M17Rik|AP-O|AW742919|Aopep|ApO|mir-23b|mir-24-1|mir-27b	RIKEN cDNA 2010111I01 gene	protein-coding
mm_172247.1	chr6	69378493	69378508	-	1	NA	Intergenic	Intergenic	-51326	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_45372.1	chr5	66042642	66042645	-	1	NA	intron (NM_178446, intron 3 of 6)	intron (NM_178446, intron 3 of 6)	-38358	NR_027961	231253	Mm.436542	NM_177679	ENSMUSG00000054598	9130230L23Rik	-	RIKEN cDNA 9130230L23 gene	ncRNA
mm_130803.1	chr15	101709614	101709627	-	1	NA	intron (NM_027011, intron 6 of 8)	(TG)n|Simple_repeat|Simple_repeat	3271	NM_027011	110308	Mm.451847	NM_027011	ENSMUSG00000061527	Krt5	3300001P10Rik|AW146334|CK5|K5|Krt2-5|Tfip8	keratin 5	protein-coding
mm_109606.1	chr12	112721505	112721530	+	1	NA	promoter-TSS (NM_001024602)	promoter-TSS (NM_001024602)	-657	NM_001024602	217882	Mm.23689	NM_001024602	ENSMUSG00000072825	Cep170b	AI466840|AW555464|Kiaa0284|mKIAA0284	centrosomal protein 170B	protein-coding
mm_74929.1	chr8	25602071	25602090	-	1	NA	promoter-TSS (NM_001308482)	promoter-TSS (NM_001308482)	-204	NM_001001735	234135	Mm.217337	NM_001001735	ENSMUSG00000054823	Whsc1l1	6720429E03|A530023P05|AI528490|NSD3|WHISTLE	Wolf-Hirschhorn syndrome candidate 1-like 1 (human)	protein-coding
mm_56045.1	chr6	86737694	86737696	-	1	NA	3' UTR (NM_001331120, exon 13 of 13)	3' UTR (NM_001331120, exon 13 of 13)	-4317	NM_011818	23885	Mm.321452	NM_011818	ENSMUSG00000001157	Gmcl1	2810049L19Rik|Btbd13|DIP|Gcl|Gcl-1|glc-1|mglc-1	germ cell-less, spermatogenesis associated 1	protein-coding
mm_24569.1	chr3	93444435	93444442	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	2108	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_68619.1	chr7	117475165	117475196	-	1	NA	intron (NM_175645, intron 1 of 11)	B4|SINE|B4	94201	NM_175645	233781	Mm.461427	NM_175645	ENSMUSG00000030657	Xylt1	8030490L12	xylosyltransferase 1	protein-coding
mm_125627.1	chr15	61989418	61989435	+	1	NA	exon (NM_001177354, exon 3 of 3)	exon (NM_001177354, exon 3 of 3)	4085	NM_001177352	17869	Mm.2444	NM_010849	ENSMUSG00000022346	Myc	AU016757|Myc2|Niard|Nird|bHLHe39	myelocytomatosis oncogene	protein-coding
mm_107387.1	chr12	33250124	33250154	+	1	NA	3' UTR (NM_028139, exon 4 of 4)	3' UTR (NM_028139, exon 4 of 4)	-52376	NM_001033436	380753	Mm.41540	NM_028139	ENSMUSG00000020564	Atxn7l1	2810423G08Rik|Atxn7l4	ataxin 7-like 1	protein-coding
mm_113802.1	chr13	46430686	46430689	+	1	NA	3' UTR (NM_001081425, exon 4 of 4)	3' UTR (NM_001081425, exon 4 of 4)	12387	NM_001081425	666794	Mm.38269	NM_001081425	ENSMUSG00000038132	Rbm24	6330546B05Rik|AI606861	RNA binding motif protein 24	protein-coding
mm_89084.1	chr10	83565049	83565064	+	1	NA	intron (NM_001033375, intron 14 of 32)	L1M5|LINE|L1	21115	NM_001033375	319277	Mm.491194	NM_001033375	ENSMUSG00000034560	Washc4	A230046K03Rik|AA589518|Kiaa1033|mKIAA1033	WASH complex subunit 4	protein-coding
mm_74439.1	chr8	3803319	3803347	-	1	NA	promoter-TSS (NR_024198)	promoter-TSS (NR_024198)	28	NR_024198	19785		NR_024198		Rprl3	RPRH4|Rmrp4	ribonuclease P RNA-like 3	ncRNA
mm_62332.1	chr7	100493830	100493848	+	1	NA	intron (NM_011671, intron 1 of 7)	intron (NM_011671, intron 1 of 7)	481	NM_011671	22228	Mm.171378	NM_011671	ENSMUSG00000033685	Ucp2	Slc25a8	uncoupling protein 2 (mitochondrial, proton carrier)	protein-coding
mm_15004.1	chr2	152477040	152477045	+	1	NA	promoter-TSS (NM_176950)	promoter-TSS (NM_176950)	-21	NM_176950	319579	Mm.190454	NM_176950	ENSMUSG00000049560	Defb20	9230107O10Rik|BD-20|mBD-20	defensin beta 20	protein-coding
mm_97282.1	chr11	76133966	76133979	+	1	NA	intron (NM_026664, intron 7 of 21)	MLT1G1|LTR|ERVL-MaLR	45658	NM_026664	68299	Mm.46397	NM_026664	ENSMUSG00000017288	Vps53	2010002A08Rik|2310040I21Rik|3100002B05Rik|Hccs1	VPS53 GARP complex subunit	protein-coding
mm_79471.1	chr9	56865080	56865090	+	1	NA	promoter-TSS (NM_139001)	promoter-TSS (NM_139001)	-19	NM_139001	121021	Mm.41329	NM_139001	ENSMUSG00000032911	Cspg4	4732461B14Rik|AN2|NG2	chondroitin sulfate proteoglycan 4	protein-coding
mm_53421.1	chr6	134035692	134035717	+	1	NA	promoter-TSS (NM_007961)	promoter-TSS (NM_007961)	4	NM_007961	14011	Mm.269995	NM_007961	ENSMUSG00000030199	Etv6	AW123102|AW557856|Tel	ets variant 6	protein-coding
mm_153401.1	chr19	40508998	40509014	-	1	NA	intron (NM_009166, intron 1 of 23)	intron (NM_009166, intron 1 of 23)	4730	NM_178362	20411	Mm.210815	NM_009166	ENSMUSG00000025006	Sorbs1	2310065E01Rik|9530001P15Rik|CAP|SH3P12|Sh3d5|mKIAA1296	sorbin and SH3 domain containing 1	protein-coding
mm_118005.1	chr13	100616644	100616655	-	1	NA	TTS (NM_001283011)	TTS (NM_001283011)	295	NM_178410	218518	Mm.25300	NM_178410	ENSMUSG00000021636	Marveld2	BC003296|MARVD2|Mrvldc2|Tric|Trica|Tricb|Tricc	MARVEL (membrane-associating) domain containing 2	protein-coding
mm_147909.1	chr18	65394009	65394021	-	1	NA	promoter-TSS (NM_001037294)	promoter-TSS (NM_001037294)	-127	NM_001037294	225638	Mm.296528	NM_001037294	ENSMUSG00000032845	Alpk2	Gm549|Hak	alpha-kinase 2	protein-coding
mm_142189.1	chr17	36890134	36890161	-	1	NA	promoter-TSS (NM_001172168)	promoter-TSS (NM_001172168)	-22	NM_001172168	195359	Mm.32606	NM_001033235	ENSMUSG00000073399	Trim40	Gm319|Gm35|Gm865	tripartite motif-containing 40	protein-coding
mm_40177.1	chr5	36002047	36002090	+	1	NA	3' UTR (NM_027373, exon 17 of 17)	3' UTR (NM_027373, exon 17 of 17)	108749	NM_027373	70292	Mm.125167	NM_027373	ENSMUSG00000029094	Afap1	2600003E23Rik|9630044L16Rik|AI848729|Afap|mKIAA3018	actin filament associated protein 1	protein-coding
mm_147451.1	chr18	46572946	46572957	-	1	NA	intron (NM_173394, intron 1 of 2)	L2|LINE|L2	1582	NM_173394	225471	Mm.149280	NM_173394	ENSMUSG00000056130	Ticam2	B430113A10|TICAM-2|TRAM|Tirp|Trif	toll-like receptor adaptor molecule 2	protein-coding
mm_84706.1	chr9	72726479	72726505	-	1	NA	exon (NM_010890, exon 14 of 29)	exon (NM_010890, exon 14 of 29)	64145	NM_010890	17999	Mm.279923	NM_010890	ENSMUSG00000032216	Nedd4	AA959633|AL023035|AU019897|E430025J12Rik|Nedd4-1|Nedd4a|mKIAA0093	neural precursor cell expressed, developmentally down-regulated 4	protein-coding
mm_165693.1	chr3	93444004	93444006	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	1675	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_68036.1	chr7	101302021	101302082	-	1	NA	promoter-TSS (NM_001111111)	promoter-TSS (NM_001111111)	37	NM_001111111	73683	Mm.275744	NM_001111111	ENSMUSG00000047767	Atg16l2	2410118P20Rik	autophagy related 16-like 2 (S. cerevisiae)	protein-coding
mm_143272.1	chr17	65654104	65654109	-	1	NA	3' UTR (NM_133685, exon 7 of 7)	3' UTR (NM_133685, exon 7 of 7)	-11902	NM_001146002	213272	Mm.255732	NM_153519	ENSMUSG00000050612	Txndc2	AU021712|Sptrx-1|Sptrx1|Trx4	thioredoxin domain containing 2 (spermatozoa)	protein-coding
mm_24562.1	chr3	93443681	93443730	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	1375	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_119179.1	chr14	32165841	32165856	+	1	NA	promoter-TSS (NM_019744)	promoter-TSS (NM_019744)	59	NM_019744	27057	Mm.371598	NM_019744	ENSMUSG00000056234	Ncoa4	ARA70|Rfg	nuclear receptor coactivator 4	protein-coding
mm_154719.1	chrX	9270251	9270252	+	1	NA	Intergenic	Intergenic	-2533	NM_023500	22439	Mm.56468	NM_023500	ENSMUSG00000015342	Xk	1810038K19Rik|XRG1|Xkh	X-linked Kx blood group	protein-coding
mm_117543.1	chr13	83727170	83727187	-	1	NA	promoter-TSS (NR_015561)	promoter-TSS (NR_015561)	-928	NR_015561	320203	Mm.245636	NM_177100	ENSMUSG00000050334	C130071C03Rik	2810449C10Rik	RIKEN cDNA C130071C03 gene	ncRNA
mm_165161.1	chr2	25079178	25079198	+	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-1135	NM_028093	72090	Mm.33403	NM_028093	ENSMUSG00000036813	Entpd8	-	ectonucleoside triphosphate diphosphohydrolase 8	protein-coding
mm_88323.1	chr10	75566173	75566187	+	1	NA	Intergenic	Intergenic	-2482	NM_001305992	14598	Mm.4559	NM_008116	ENSMUSG00000006345	Ggt1	CD224|GGT|GGT 1|GGT-1|Ggtp|dwg	gamma-glutamyltransferase 1	protein-coding
mm_60241.1	chr7	43713427	43713436	+	1	NA	intron (NM_001039042, intron 1 of 5)	intron (NM_001039042, intron 1 of 5)	864	NM_001039042	626834	Mm.389891	NM_001039042	ENSMUSG00000054046	Klk13	Egfbp-2|mGk-13	kallikrein related-peptidase 13	protein-coding
mm_147749.1	chr18	61196365	61196398	-	1	NA	TTS (NM_007885)	TTS (NM_007885)	15215	NM_007885	13521	Mm.24803	NM_007885	ENSMUSG00000034320	Slc26a2	Dtd|ST-OB	solute carrier family 26 (sulfate transporter), member 2	protein-coding
mm_85916.1	chr9	111062821	111062829	-	1	NA	Intergenic	Intergenic	-5307	NM_001302376	54199	Mm.7336	NM_017466	ENSMUSG00000043953	Ccrl2	1810047I05Rik|Ackr5|CCR11|Cmkbr1l2|E01|L-CCR	chemokine (C-C motif) receptor-like 2	protein-coding
mm_69649.1	chr7	139360892	139360931	-	1	NA	Intergenic	Intergenic	-28198	NM_183144	212111	Mm.28308	NM_183144	ENSMUSG00000025477	Inpp5a	-	inositol polyphosphate-5-phosphatase A	protein-coding
mm_121815.1	chr14	20395065	20395090	-	1	NA	intron (NM_029698, intron 26 of 28)	intron (NM_029698, intron 26 of 28)	-1522	NM_025440	66242	Mm.23747	NM_025440	ENSMUSG00000049960	Mrps16	1500011E11Rik|Mprs16	mitochondrial ribosomal protein S16	protein-coding
mm_46363.1	chr5	103377261	103377294	-	1	NA	Intergenic	Intergenic	-47915	NM_011204	19249	Mm.3414	NM_011204	ENSMUSG00000034573	Ptpn13	AI324989|PTP-BL|PTPL1|Ptpri|RIP	protein tyrosine phosphatase, non-receptor type 13	protein-coding
mm_37621.1	chr4	127252368	127252390	-	1	NA	Intergenic	Intergenic	8595	NM_030252	80284	Mm.139607	NM_030252	ENSMUSG00000042380	Smim12	BC003266	small integral membrane protein 12	protein-coding
mm_103399.1	chr11	75438243	75438281	-	1	NA	intron (NM_008878, intron 2 of 9)	intron (NM_008878, intron 2 of 9)	1239	NM_008878	18816	Mm.279733	NM_008878	ENSMUSG00000038224	Serpinf2	AI747498|Pli|Serpimf2	serine (or cysteine) peptidase inhibitor, clade F, member 2	protein-coding
mm_142107.1	chr17	35835911	35835927	-	1	NA	exon (NM_011655, exon 4 of 4)	exon (NM_011655, exon 4 of 4)	2382	NM_011655	22154	Mm.273538	NM_011655	ENSMUSG00000001525	Tubb5	AA408537|AI596182|B130022C14Rik|M(beta)5	tubulin, beta 5 class I	protein-coding
mm_101215.1	chr11	20089625	20089635	-	1	NA	intron (NM_146243, intron 4 of 8)	intron (NM_146243, intron 4 of 8)	23321	NM_146243	66713	Mm.259045	NM_146243	ENSMUSG00000020152	Actr2	4921510D23Rik|AA409782|Arp2|D6Ertd746e	ARP2 actin-related protein 2	protein-coding
mm_28425.1	chr3	90455090	90455112	-	1	NA	exon (NM_008727, exon 19 of 22)	exon (NM_008727, exon 19 of 22)	10765	NM_008727	18160	Mm.4627	NM_008727	ENSMUSG00000027931	Npr1	AI893888|GC-A|NPR-A|NPRA|Pndr	natriuretic peptide receptor 1	protein-coding
mm_131772.1	chr16	22894413	22894417	+	1	NA	promoter-TSS (NR_110508)	promoter-TSS (NR_110508)	-29	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_161449.1	chr15	74634836	74634836	-	1	NA	5' UTR (NM_001177437, exon 3 of 27)	5' UTR (NM_001177437, exon 3 of 27)	1482	NM_001177437	69439	Mm.263708	NM_001177437	ENSMUSG00000022603	Mroh4	1700016M24Rik	maestro heat-like repeat family member 4	protein-coding
mm_1186.1	chr1	62522636	62522640	+	1	NA	intron (NM_001081050, intron 20 of 22)	intron (NM_001081050, intron 20 of 22)	-180679	NM_001077406	18187	Mm.266341	NM_010939	ENSMUSG00000025969	Nrp2	1110048P06Rik|Np-2|Np2|Npn-2|Npn2	neuropilin 2	protein-coding
mm_57701.1	chr6	128526705	128526720	-	1	NA	promoter-TSS (NM_007376)	promoter-TSS (NM_007376)	8	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_115332.1	chr13	112474812	112474818	+	1	NA	intron (NM_010560, intron 2 of 16)	AT_rich|Low_complexity|Low_complexity	10745	NM_010560	16195	Mm.4364	NM_010560	ENSMUSG00000021756	Il6st	5133400A03Rik|AA389424|BB405851|CD130|D13Ertd699e|gp130	interleukin 6 signal transducer	protein-coding
mm_94536.1	chr11	9120057	9120064	+	1	NA	intron (NM_001159401, intron 2 of 8)	intron (NM_001159401, intron 2 of 8)	1553	NM_001159402	22271	Mm.4610	NM_009477	ENSMUSG00000020407	Upp1	AI325217|UPase|UdRPase|Up|Upp	uridine phosphorylase 1	protein-coding
mm_16449.1	chr2	180456308	180456341	+	1	NA	Intergenic	CpG	-4654	NM_148933	108115	Mm.133687	NM_148933	ENSMUSG00000038963	Slco4a1	OATP-E|Slc21a12	solute carrier organic anion transporter family, member 4a1	protein-coding
mm_20039.1	chr2	120047087	120047088	-	1	NA	Intergenic	Intergenic	13654	NM_145378	211429	Mm.41467	NM_145378	ENSMUSG00000098488	Pla2g4b	A030011C02Rik|Gm1013|cPLA2-beta	phospholipase A2, group IVB (cytosolic)	protein-coding
mm_153609.1	chr19	43968492	43968509	-	1	NA	exon (NM_030703, exon 5 of 9)	exon (NM_030703, exon 5 of 9)	18020	NM_030703	93721	Mm.206774	NM_030703	ENSMUSG00000025196	Cpn1	0610011F20Rik|CPN	carboxypeptidase N, polypeptide 1	protein-coding
mm_154796.1	chrX	13256684	13256712	+	1	NA	Intergenic	Lx5|LINE|L1	-8965	NR_045429	72122	Mm.75434	NR_045429	ENSMUSG00000100714	2010308F09Rik	-	RIKEN cDNA 2010308F09 gene	ncRNA
mm_32902.1	chr4	119106038	119106048	+	1	NA	Intergenic	Intergenic	-2702	NM_011400	20525	Mm.21002	NM_011400	ENSMUSG00000028645	Slc2a1	Glut-1|Glut1	solute carrier family 2 (facilitated glucose transporter), member 1	protein-coding
mm_151070.1	chr19	47511104	47511111	+	1	NA	intron (NM_175360, intron 7 of 9)	intron (NM_175360, intron 7 of 9)	-1875	NR_045322	100503104	Mm.442735	NR_045322	ENSMUSG00000097990	Gm19557	-	predicted gene, 19557	ncRNA
mm_95767.1	chr11	54908536	54908557	+	1	NA	exon (NM_008161, exon 3 of 5)	exon (NM_008161, exon 3 of 5)	5692	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_164696.1	chr17	48518048	48518050	-	1	NA	Intergenic	Intergenic	63148	NM_152823	76589	Mm.311629	NM_152823	ENSMUSG00000043592	Unc5cl	2510009H09Rik|BB155270|Zud	unc-5 family C-terminal like	protein-coding
mm_1075.1	chr1	59482092	59482102	+	1	NA	promoter-TSS (NM_008057)	promoter-TSS (NM_008057)	-50	NM_008057	14369	Mm.297906	NM_008057	ENSMUSG00000041075	Fzd7	Fz7	frizzled class receptor 7	protein-coding
mm_35017.1	chr4	3835596	3835602	-	1	NA	promoter-TSS (NM_026147)	promoter-TSS (NM_026147)	56	NM_026147	67427	Mm.21938	NM_026147	ENSMUSG00000028234	Rps20	4632426K06Rik|Dsk4	ribosomal protein S20	protein-coding
mm_15168.1	chr2	154013675	154013687	+	1	NA	exon (NM_008953, exon 6 of 9)	exon (NM_008953, exon 6 of 9)	5405	NM_008953	19194	Mm.29197	NM_008953	ENSMUSG00000042459	Bpifa2	Bpifa2e|Psp	BPI fold containing family A, member 2	protein-coding
mm_13540.1	chr2	110721588	110721619	+	1	NA	5' UTR (NM_001290786, exon 1 of 4)	5' UTR (NM_001290786, exon 1 of 4)	109	NM_172979	269328	Mm.32566	NM_172979	ENSMUSG00000050808	Muc15	4732460E09|D730046L02Rik|MUC-15	mucin 15	protein-coding
mm_17686.1	chr2	32319396	32319399	-	1	NA	TTS (NR_029811)	TTS (NR_029811)	937	NR_029811	387239		NR_029811	ENSMUSG00000092807	Mir199b	Mirn199b|mir-199b	microRNA 199b	ncRNA
mm_124132.1	chr14	84476381	84476401	-	1	NA	promoter-TSS (NR_015539)	promoter-TSS (NR_015539)	33	NR_015539	319903	Mm.440481	NR_015539		9630013A20Rik	-	RIKEN cDNA 9630013A20 gene	ncRNA
mm_171885.1	chr5	35554130	35554149	+	1	NA	Intergenic	Intergenic	20931	NM_030208	78890	Mm.98522	NM_030208	ENSMUSG00000029097	Trmt44	2310079F23Rik|Mettl19	tRNA methyltransferase 44	protein-coding
mm_14012.1	chr2	122147723	122147728	+	1	NA	promoter-TSS (NM_009735)	promoter-TSS (NM_009735)	38	NM_009735	12010	Mm.163	NM_009735	ENSMUSG00000060802	B2m	Ly-m11|beta2-m|beta2m	beta-2 microglobulin	protein-coding
mm_28282.1	chr3	88950477	88950584	-	1	NA	promoter-TSS (NM_022994)	promoter-TSS (NM_022994)	-248	NM_001164533	65111	Mm.29028	NM_022994	ENSMUSG00000068921	Dap3	4921514D13Rik|DAP-3|MRP-S29|S29mt	death associated protein 3	protein-coding
mm_144568.1	chr18	31777485	31777487	+	1	NA	intron (NM_153515, intron 6 of 7)	PB1D11|SINE|Alu	-11673	NM_027002	69241	Mm.279898	NM_027002	ENSMUSG00000024258	Polr2d	2310002G05Rik|2610028L19Rik|HSRBP4|RBP4	polymerase (RNA) II (DNA directed) polypeptide D	protein-coding
mm_166020.1	chr4	122689398	122689406	+	1	NA	exon (NM_023865, exon 1 of 5)	exon (NM_023865, exon 1 of 5)	143	NM_023865	77432	Mm.491436	NM_023865	ENSMUSG00000023263	9530002B09Rik	Aump|Vpp1|Vppl	RIKEN cDNA 9530002B09 gene	protein-coding
mm_111020.1	chr12	79017361	79017390	-	1	NA	Intergenic	Intergenic	-10098	NM_178745	268567	Mm.341747	NM_178745	ENSMUSG00000046157	Tmem229b	6330442E10Rik|9830138K24|AU019070	transmembrane protein 229B	protein-coding
mm_137916.1	chr17	32284773	32284809	+	1	NA	promoter-TSS (NM_001286630)	promoter-TSS (NM_001286630)	-658	NM_020508	57261	Mm.253518	NM_020508	ENSMUSG00000024002	Brd4	Brd5|HUNK1|MCAP|WI-11513	bromodomain containing 4	protein-coding
mm_73516.1	chr8	107436356	107436421	+	1	NA	promoter-TSS (NM_025830)	promoter-TSS (NM_025830)	-10	NM_025830	66894	Mm.390058	NM_025830	ENSMUSG00000031930	Wwp2	1300010O06Rik|AA690238|AIP2|AW554328	WW domain containing E3 ubiquitin protein ligase 2	protein-coding
mm_171924.1	chr5	5998837	5998837	+	1	NA	Intergenic	RLTR9E|LTR|ERVK	-249520	NM_027399	70358	Mm.85429	NM_027399	ENSMUSG00000015652	Steap1	2410007B19Rik|Prss24|Steap	six transmembrane epithelial antigen of the prostate 1	protein-coding
mm_44511.1	chr5	24329272	24329283	-	1	NA	5' UTR (NM_001294162, exon 1 of 11)	5' UTR (NM_001294162, exon 1 of 11)	314	NM_001294162	16511	Mm.6539	NM_013569	ENSMUSG00000038319	Kcnh2	AI326795|ERG1|LQT|Lqt2|M-erg|Merg1|merg1a|merg1b	potassium voltage-gated channel, subfamily H (eag-related), member 2	protein-coding
mm_127904.1	chr15	9516463	9516493	-	1	NA	exon (NM_008372, exon 3 of 8)	exon (NM_008372, exon 3 of 8)	13398	NM_008372	16197	Mm.389	NM_008372	ENSMUSG00000003882	Il7r	CD127|IL-7Ralpha	interleukin 7 receptor	protein-coding
mm_26486.1	chr3	145027354	145027379	+	1	NA	exon (NM_017474, exon 3 of 14)	exon (NM_017474, exon 3 of 14)	5410	NM_017474	23844	Mm.33483	NM_017474	ENSMUSG00000028255	Clca1	Clca2|Clca3|gob-5|gob5	chloride channel accessory 1	protein-coding
mm_90570.1	chr10	128231756	128231770	+	1	NA	promoter-TSS (NM_001136082)	promoter-TSS (NM_001136082)	-300	NM_001164080	21853	Mm.6458	NM_011589	ENSMUSG00000039994	Timeless	C77407|Debt69|tim	timeless circadian clock 1	protein-coding
mm_83642.1	chr9	49504746	49504757	-	1	NA	3' UTR (NM_001311065, exon 18 of 18)	3' UTR (NM_001311065, exon 18 of 18)	-13537	NR_029465	100036537	Mm.437541	NR_029465	ENSMUSG00000079564	Gm11149	ENSMUSG00000060603|ENSMUSG00000079564	predicted gene 11149	ncRNA
mm_97149.1	chr11	75461625	75461641	+	1	NA	promoter-TSS (NR_030711)	promoter-TSS (NR_030711)	94	NR_030711	100042498	Mm.482242	NR_030711	ENSMUSG00000085148	Mir22hg	2210403K04Rik|mir-22	Mir22 host gene (non-protein coding)	ncRNA
mm_58176.1	chr6	142757241	142757251	-	1	NA	intron (NM_009908, intron 1 of 7)	intron (NM_009908, intron 1 of 7)	560	NM_009908	12764	Mm.3820	NM_009908	ENSMUSG00000030282	Cmas	AW208911|CMPNeu5Ac|D6Bwg0250e	cytidine monophospho-N-acetylneuraminic acid synthetase	protein-coding
mm_153444.1	chr19	40996122	40996136	-	1	NA	Intergenic	Intergenic	-1594	NM_008528	17060	Mm.9749	NM_008528	ENSMUSG00000061132	Blnk	BASH|Bca|Ly-57|Ly57|Lyw-57|SLP-65	B cell linker	protein-coding
mm_150453.1	chr19	38132796	38132810	+	1	NA	promoter-TSS (NM_001170959)	promoter-TSS (NM_001170959)	22	NM_001170959	110855	Mm.450141	NM_033614	ENSMUSG00000024992	Pde6c	cpfl1	phosphodiesterase 6C, cGMP specific, cone, alpha prime	protein-coding
mm_68264.1	chr7	105595105	105595207	-	1	NA	exon (NM_017371, exon 7 of 10)	exon (NM_017371, exon 7 of 10)	4960	NM_017371	15458	Mm.3485	NM_017371	ENSMUSG00000030895	Hpx	Hpxn|hx	hemopexin	protein-coding
mm_142307.1	chr17	42742168	42742189	-	1	NA	promoter-TSS (NM_001033493)	promoter-TSS (NM_001033493)	1	NM_001033493	435529	Mm.136350	NM_001033493	ENSMUSG00000057899	Adgrf2	Gpr111|PGR20	adhesion G protein-coupled receptor F2	protein-coding
mm_140366.1	chr17	86963078	86963094	+	1	NA	promoter-TSS (NM_145491)	promoter-TSS (NM_145491)	-25	NM_145491	104215	Mm.826	NM_145491	ENSMUSG00000024143	Rhoq	Arhq|TC10A|Tc10	ras homolog family member Q	protein-coding
mm_157057.1	chrX	8131725	8131727	-	1	NA	5' UTR (NM_028542, exon 2 of 9)	5' UTR (NM_028542, exon 2 of 9)	1132	NM_001290783	73447	Mm.284162	NM_026137	ENSMUSG00000031166	Wdr13	1700060B08Rik|5730411P10Rik|DXHXS7467e|W51679|mMg21	WD repeat domain 13	protein-coding
mm_124493.1	chr14	121793663	121793668	-	1	NA	intron (NM_134074, intron 1 of 52)	intron (NM_134074, intron 1 of 52)	4069	NM_134074	105445	Mm.378591	NM_134074	ENSMUSG00000025558	Dock9	AA959601|AW538057|B230309H04Rik|D14Wsu89e|Zizimin1|mKIAA1058	dedicator of cytokinesis 9	protein-coding
mm_106478.1	chr11	120142891	120142891	-	1	NA	intron (NM_024249, intron 2 of 16)	intron (NM_024249, intron 2 of 16)	8460	NM_001164799	72055	Mm.253403	NM_024249	ENSMUSG00000061306	Slc38a10	1810073N04Rik	solute carrier family 38, member 10	protein-coding
mm_157617.1	chrX	56212904	56212915	-	1	NA	promoter-TSS (NM_001033423)	promoter-TSS (NM_001033423)	-28	NM_001033423	331416	Mm.387260	NM_001033423	ENSMUSG00000073177	Gm773	-	predicted gene 773	protein-coding
mm_63963.1	chr7	139943969	139943975	+	1	NA	exon (NM_009482, exon 1 of 2)	exon (NM_009482, exon 1 of 2)	116	NM_009482	22286	Mm.10205	NM_009482	ENSMUSG00000047751	Utf1	AI505934	undifferentiated embryonic cell transcription factor 1	protein-coding
mm_132048.1	chr16	29209781	29209791	+	1	NA	promoter-TSS (NM_013751)	promoter-TSS (NM_013751)	91	NM_013751	27281	Mm.103650	NM_013751	ENSMUSG00000022525	Hrasls	2810012B06Rik|A-C1|HRSL1|Hrasrs	HRAS-like suppressor	protein-coding
mm_97120.1	chr11	74831215	74831278	+	1	NA	5' UTR (NM_010813, exon 1 of 6)	5' UTR (NM_010813, exon 1 of 6)	322	NM_010813	17428	Mm.3759	NM_010813	ENSMUSG00000000282	Mnt	Rox|bHLHd3	max binding protein	protein-coding
mm_161630.1	chr16	88751650	88751650	-	1	NA	promoter-TSS (NM_010671)	promoter-TSS (NM_010671)	-22	NM_010671	16699	Mm.353193	NM_010671	ENSMUSG00000050224	Krtap13	4C32	keratin associated protein 13	protein-coding
mm_86775.1	chr10	20148678	20148688	+	1	NA	promoter-TSS (NM_008635)	promoter-TSS (NM_008635)	-237	NM_008635	17761	Mm.20928	NM_008635	ENSMUSG00000019996	Map7	E-MAP-115|MAP-7|Mtap7|R75000|mshi|mste|ste	microtubule-associated protein 7	protein-coding
mm_71180.1	chr8	40861830	40861843	+	1	NA	promoter-TSS (NM_001044740)	promoter-TSS (NM_001044740)	-531	NM_007514	11988	Mm.4676	NM_007514	ENSMUSG00000031596	Slc7a2	20.5|AI158848|Atrc2|CAT-2|Cat2|Tea	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	protein-coding
mm_11559.1	chr2	32775770	32775791	+	1	NA	promoter-TSS (NM_001290563)	promoter-TSS (NM_001290563)	-41	NM_178595	329384	Mm.268037	NM_178595	ENSMUSG00000053746	Ptrh1	2210013M04Rik|AW046744	peptidyl-tRNA hydrolase 1 homolog	protein-coding
mm_68355.1	chr7	106510878	106510889	-	1	NA	Intergenic	Intergenic	-69810	NR_003967	209380	Mm.461779	NM_001001318		Gm4759	EG209380	GTPase, very large interferon inducible 1 pseudogene	pseudo
mm_101705.1	chr11	42000285	42000342	-	1	NA	exon (NM_008073, exon 1 of 10)	exon (NM_008073, exon 1 of 10)	401	NM_177408	14406	Mm.5309	NM_008073	ENSMUSG00000020436	Gabrg2	GABAA-R|Gabrg-2|gamma2	gamma-aminobutyric acid (GABA) A receptor, subunit gamma 2	protein-coding
mm_84058.1	chr9	58198433	58198470	-	1	NA	exon (NM_177193, exon 3 of 3)	exon (NM_177193, exon 3 of 3)	3264	NM_001161535	320563	Mm.186499	NM_177193	ENSMUSG00000051243	Islr2	B930052A04Rik|Linx|Mbu-3|mKIAA1465	immunoglobulin superfamily containing leucine-rich repeat 2	protein-coding
mm_123842.1	chr14	70653082	70653086	-	1	NA	promoter-TSS (NM_181345)	promoter-TSS (NM_181345)	0	NM_181345	328440	Mm.347749	NM_181345	ENSMUSG00000047911	Npm2	-	nucleophosmin/nucleoplasmin 2	protein-coding
mm_83906.1	chr9	56244036	56244047	-	1	NA	intron (NM_172924, intron 4 of 6)	intron (NM_172924, intron 4 of 6)	-82971	NM_019793	56434	Mm.28484	NM_019793	ENSMUSG00000032324	Tspan3	1700055K04Rik|TM4-A|Tm4sf8	tetraspanin 3	protein-coding
mm_125678.1	chr15	66615718	66615734	+	1	NA	exon (NM_001081409, exon 12 of 21)	exon (NM_001081409, exon 12 of 21)	38154	NM_001081409	239510	Mm.267473	NM_178718	ENSMUSG00000072501	Phf20l1	CGI-72|E130113K22Rik	PHD finger protein 20-like 1	protein-coding
mm_54330.1	chr6	30640654	30640700	-	1	NA	exon (NM_025350, exon 3 of 10)	exon (NM_025350, exon 3 of 10)	1459	NM_025350	109697	Mm.25377	NM_025350	ENSMUSG00000054446	Cpa1	0910001L12Rik|Cpa	carboxypeptidase A1, pancreatic	protein-coding
mm_124761.1	chr15	6648091	6648104	+	1	NA	intron (NM_011815, intron 12 of 17)	intron (NM_011815, intron 12 of 17)	-60284	NM_030168	78757	Mm.275811	NM_030168	ENSMUSG00000050310	Rictor	4921505C17Rik|6030405M08Rik|AVO3|AW492497|D530039E11Rik	RPTOR independent companion of MTOR, complex 2	protein-coding
mm_71790.1	chr8	66860216	66860287	+	1	NA	promoter-TSS (NM_001163564)	promoter-TSS (NM_001163564)	34	NM_001163564	234344	Mm.334561	NM_001163564	ENSMUSG00000014907	Naf1	Gm174	nuclear assembly factor 1 ribonucleoprotein	protein-coding
mm_47887.1	chr5	134703517	134703536	-	1	NA	3' UTR (NM_007925, exon 37 of 37)	3' UTR (NM_007925, exon 37 of 37)	-14936	NM_010717	16885	Mm.15409	NM_010717	ENSMUSG00000029674	Limk1	KIZ-1|LIMK-1|Limk	LIM-domain containing, protein kinase	protein-coding
mm_153939.1	chr19	47464407	47464450	-	1	NA	promoter-TSS (NM_008018)	promoter-TSS (NM_008018)	-17	NM_008018	14218	Mm.127560	NM_008018	ENSMUSG00000053617	Sh3pxd2a	2310014D11Rik|AA589508|AI256723|AI413738|C230050L11|EG329070|Fish|Gm5098|Sh3md1|TSK5|Tks5	SH3 and PX domains 2A	protein-coding
mm_87527.1	chr10	53342439	53342443	+	1	NA	intron (NM_001141927, intron 2 of 2)	B1_Mur2|SINE|Alu	4755	NM_001141927	18821	Mm.34145	NM_023129	ENSMUSG00000038583	Pln	Plb	phospholamban	protein-coding
mm_63148.1	chr7	123369746	123369750	+	1	NA	intron (NM_001122641, intron 1 of 18)	C-rich|Low_complexity|Low_complexity	167	NM_001122643	70497	Mm.403318	NM_144529	ENSMUSG00000030766	Arhgap17	5730403H17Rik|Nadrin|Nadrin2|Rich1|Wbp15	Rho GTPase activating protein 17	protein-coding
mm_56857.1	chr6	118197348	118197348	-	1	NA	5' UTR (NM_009050, exon 1 of 20)	5' UTR (NM_009050, exon 1 of 20)	396	NM_009050	19713	Mm.57199	NM_009050	ENSMUSG00000030110	Ret	PTC|RET51|RET9|c-Ret	ret proto-oncogene	protein-coding
mm_135610.1	chr16	52250351	52250376	-	1	NA	3' UTR (NM_001331110, exon 15 of 15)	3' UTR (NM_001331110, exon 15 of 15)	202718	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_145699.1	chr18	62657204	62657212	+	1	NA	intron (NM_177829, intron 5 of 8)	intron (NM_177829, intron 5 of 8)	-60944	NM_001001803	408198	Mm.478742	NM_001001803	ENSMUSG00000060201	Spink7	EG408198|Ecg2	serine peptidase inhibitor, Kazal type 7 (putative)	protein-coding
mm_96195.1	chr11	62005378	62005391	+	1	NA	intron (NM_001310526, intron 1 of 7)	intron (NM_001310526, intron 1 of 7)	48621	NM_001310526	432572	Mm.438022	NM_001029936	ENSMUSG00000042331	Specc1	2810012G08Rik|B230396K10Rik|Cytsb	sperm antigen with calponin homology and coiled-coil domains 1	protein-coding
mm_102699.1	chr11	66061307	66061315	-	1	NA	intron (NM_001099633, intron 26 of 68)	intron (NM_001099633, intron 26 of 68)	107240	NM_001099633	237806	Mm.264210	NM_001099633	ENSMUSG00000056752	Dnah9	9030022M04|A230091C01|C230051G16|D11Ertd686e|Dnahc9|mKIAA0357	dynein, axonemal, heavy chain 9	protein-coding
mm_124296.1	chr14	103055113	103055125	-	1	NA	exon (NM_008392, exon 5 of 5)	exon (NM_008392, exon 5 of 5)	8107	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_161933.1	chr18	84650084	84650084	-	1	NA	promoter-TSS (NM_177450)	promoter-TSS (NM_177450)	11	NM_177450	338403	Mm.23278	NM_177450	ENSMUSG00000056162	Cndp1	AI746433|Cn1	carnosine dipeptidase 1 (metallopeptidase M20 family)	protein-coding
mm_18081.1	chr2	44539373	44539379	-	1	NA	Intergenic	Intergenic	322246	NM_172662	227835	Mm.314312	NM_172662	ENSMUSG00000036890	Gtdc1	E330008O22Rik	glycosyltransferase-like domain containing 1	protein-coding
mm_151045.1	chr19	47024652	47024663	+	1	NA	TTS (NM_146100)	TTS (NM_146100)	-9468	NM_001164363	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_136542.1	chr16	97922555	97922580	-	1	NA	promoter-TSS (NM_174847)	promoter-TSS (NM_174847)	66	NM_174847	207781	Mm.1465	NM_174847	ENSMUSG00000045975	C2cd2	5730563M15|5830404H04Rik|AI314146|AI449533|BF168443|ORF25|mKIAA4045	C2 calcium-dependent domain containing 2	protein-coding
mm_57702.1	chr6	128526910	128526929	-	1	NA	promoter-TSS (NM_007376)	promoter-TSS (NM_007376)	-199	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_157566.1	chrX	52428837	52428851	-	1	NA	exon (NM_016697, exon 3 of 8)	exon (NM_016697, exon 3 of 8)	-6329	NR_030497	751531		NR_030497	ENSMUSG00000076214	Mir717	Mirn717|mir-717|mmu-mir-717	microRNA 717	ncRNA
mm_42538.1	chr5	115908524	115908538	+	1	NA	intron (NM_007708, intron 8 of 46)	intron (NM_007708, intron 8 of 46)	62875	NM_007708	12704	Mm.8321	NM_007708	ENSMUSG00000029516	Cit	C030025P15Rik|CRIK|CRIK-SK|Cit-k	citron	protein-coding
mm_118037.1	chr13	101692499	101692509	-	1	NA	5' UTR (NM_001024955, exon 1 of 10)	5' UTR (NM_001024955, exon 1 of 10)	126	NM_001024955	18708	Mm.259333	NM_001024955	ENSMUSG00000041417	Pik3r1	PI3K|p50alpha|p55alpha|p85alpha	phosphatidylinositol 3-kinase, regulatory subunit, polypeptide 1 (p85 alpha)	protein-coding
mm_14107.1	chr2	125673684	125673694	+	1	NA	3' UTR (NM_025613, exon 1 of 1)	3' UTR (NM_025613, exon 1 of 1)	589	NM_025613	58521	Mm.425101	NM_025613	ENSMUSG00000091337	Eid1	2610002K20Rik|Cri1|EID-1|ORF12|PNAS-22|PTD014	EP300 interacting inhibitor of differentiation 1	protein-coding
mm_132032.1	chr16	27389098	27389111	+	1	NA	exon (NM_026202, exon 1 of 11)	exon (NM_026202, exon 1 of 11)	148	NM_001289436	67501	Mm.258985	NM_026202	ENSMUSG00000038127	Ccdc50	C3orf6	coiled-coil domain containing 50	protein-coding
mm_111947.1	chr12	109068357	109068368	-	1	NA	promoter-TSS (NM_001163175)	promoter-TSS (NM_001163175)	-145	NM_001163175	380785	Mm.342085	NM_001163175	ENSMUSG00000040867	Begain	BM948371|Gm897	brain-enriched guanylate kinase-associated	protein-coding
mm_78021.1	chr9	13749245	13749275	+	1	NA	promoter-TSS (NM_023858)	promoter-TSS (NM_023858)	79	NR_024025	77116	Mm.210405	NM_023858	ENSMUSG00000031918	Mtmr2	6030445P13Rik	myotubularin related protein 2	protein-coding
mm_160886.1	chr11	69834852	69834852	-	1	NA	promoter-TSS (NM_198862)	promoter-TSS (NM_198862)	-3	NM_198862	216856	Mm.151293	NM_198862	ENSMUSG00000051790	Nlgn2	NL2	neuroligin 2	protein-coding
mm_130804.1	chr15	101709649	101709663	-	1	NA	intron (NM_027011, intron 6 of 8)	(TG)n|Simple_repeat|Simple_repeat	3235	NM_027011	110308	Mm.451847	NM_027011	ENSMUSG00000061527	Krt5	3300001P10Rik|AW146334|CK5|K5|Krt2-5|Tfip8	keratin 5	protein-coding
mm_108943.1	chr12	102282862	102282871	+	1	NA	promoter-TSS (NM_001161365)	promoter-TSS (NM_001161365)	-208	NM_177620	217835	Mm.24145	NM_177620	ENSMUSG00000044456	Rin3	6430500K07|C86933	Ras and Rab interactor 3	protein-coding
mm_117901.1	chr13	99427320	99427338	-	1	NA	exon (NM_008634, exon 6 of 7)	exon (NM_008634, exon 6 of 7)	-14503	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_30533.1	chr4	3574856	3574871	+	1	NA	promoter-TSS (NM_028097)	promoter-TSS (NM_028097)	-16	NM_054089	116940	Mm.171323	NM_054089	ENSMUSG00000028233	Tgs1	D4Ertd800e|Ncoa6ip|Pimt	trimethylguanosine synthase 1	protein-coding
mm_122028.1	chr14	29501040	29501041	-	1	NA	intron (NM_009785, intron 3 of 37)	intron (NM_009785, intron 3 of 37)	220824	NM_009785	12294	Mm.386754	NM_009785	ENSMUSG00000021991	Cacna2d3	Cacnad3|alapha2delta3	calcium channel, voltage-dependent, alpha2/delta subunit 3	protein-coding
mm_108219.1	chr12	77064399	77064438	+	1	NA	Intergenic	LTR50|LTR|ERVL	-102170	NM_001146176	17187	Mm.268548	NM_008558	ENSMUSG00000059436	Max	AA960152|AI875693|bHLHd4|bHLHd5|bHLHd6|bHLHd7|bHLHd8	Max protein	protein-coding
mm_5316.1	chr1	22783489	22783503	-	1	NA	intron (NM_001012623, intron 1 of 14).2	(TG)n|Simple_repeat|Simple_repeat	22228	NM_001012625	116837	Mm.60061	NM_053270	ENSMUSG00000041670	Rims1	C030033M19Rik|RIM1|RIM1a|RIM1alpha|Rab3ip1|Rim|Serg1|mKIAA0340	regulating synaptic membrane exocytosis 1	protein-coding
mm_131353.1	chr16	13702567	13702591	+	1	NA	3' UTR (NM_001177552, exon 6 of 6)	3' UTR (NM_001177552, exon 6 of 6)	-27257	NR_040574	76684	Mm.491043	NR_040574		Pla2g10os	1810007I06Rik	phospholipase A2, group X, opposite strand	ncRNA
mm_10772.1	chr2	24276910	24276941	+	1	NA	promoter-TSS (NM_019451)	promoter-TSS (NM_019451)	-29	NM_001146088	54450	Mm.29261	NM_019451	ENSMUSG00000026983	Il1f5	AI413231|Fil1delta|IL-36Ra|IL36RN|Il-1h3|Il1hy1	interleukin 1 family, member 5 (delta)	protein-coding
mm_72290.1	chr8	75213289	75213297	+	1	NA	promoter-TSS (NM_029182)	promoter-TSS (NM_029182)	-651	NM_029182	75141	Mm.179267	NM_029182	ENSMUSG00000034472	Rasd2	4930526B11Rik|AU045414|Rhes|TEM-2|TEM2	RASD family, member 2	protein-coding
mm_167897.1	chrX	73493267	73493277	+	1	NA	exon (NM_007542, exon 7 of 8)	exon (NM_007542, exon 7 of 8)	9671	NM_007542	12111	Mm.2608	NM_007542	ENSMUSG00000031375	Bgn	BG|DSPG1|PG-S1|PGI|SLRR1A	biglycan	protein-coding
mm_78764.1	chr9	43309751	43309761	+	1	NA	Intergenic	Intergenic	-1007	NM_023655	72169	Mm.273277	NM_023655	ENSMUSG00000032013	Trim29	1110047J21Rik|2810431N19Rik|4732461M22Rik|AI119726	tripartite motif-containing 29	protein-coding
mm_53712.1	chr6	143206238	143206273	+	1	NA	3' UTR (NM_029250, exon 8 of 8)	3' UTR (NM_029250, exon 8 of 8)	39025	NM_029250	75320	Mm.272548	NM_029250	ENSMUSG00000030275	Etnk1	1110061E11Rik|4930555L11Rik|AI195356|AI841245|C80956|D6Ertd3e|EKI1	ethanolamine kinase 1	protein-coding
mm_168553.1	chr11	6453071	6453090	+	1	NA	Intergenic	Intergenic	-8637	NM_001347064	77605	Mm.27624	NM_029938	ENSMUSG00000041126	H2afv	C530002L11Rik|H2a.z-2|H2av	H2A histone family, member V	protein-coding
mm_159204.1	chr2	121141897	121141897	+	1	NA	promoter-TSS (NM_029475)	promoter-TSS (NM_029475)	-196	NM_029475	75894	Mm.384805	NM_029475	ENSMUSG00000027259	Adal	4930578F03Rik	adenosine deaminase-like	protein-coding
mm_123603.1	chr14	67933693	67933706	-	1	NA	promoter-TSS (NM_177780)	promoter-TSS (NM_177780)	-127	NM_177780	68813	Mm.258155	NM_177780	ENSMUSG00000044447	Dock5	1110060D06Rik|AI666732|AI956923|BC016533|E130320D18|lr2|rlc	dedicator of cytokinesis 5	protein-coding
mm_167211.1	chr8	3493219	3493237	+	1	NA	promoter-TSS (NM_080461)	promoter-TSS (NM_080461)	90	NM_080461	140482	Mm.299073	NM_080461	ENSMUSG00000047264	Zfp358	Zfend	zinc finger protein 358	protein-coding
mm_57180.1	chr6	122848497	122848526	-	1	NA	3' UTR (NM_009779, exon 2 of 2)	3' UTR (NM_009779, exon 2 of 2)	7646	NM_009779	12267	Mm.2408	NM_009779	ENSMUSG00000040552	C3ar1	AZ3B|C3AR|HNFAG09	complement component 3a receptor 1	protein-coding
mm_81613.1	chr9	110766622	110766638	+	1	NA	exon (NM_010859, exon 3 of 7)	exon (NM_010859, exon 3 of 7)	2949	NM_010859	17897	Mm.7353	NM_010859	ENSMUSG00000059741	Myl3	MLC1s|MLC1v|Mylc|VLC1	myosin, light polypeptide 3	protein-coding
mm_104808.1	chr11	98775372	98775382	-	1	NA	promoter-TSS (NM_145434)	promoter-TSS (NM_145434)	0	NM_145434	217166	Mm.390397	NM_145434	ENSMUSG00000020889	Nr1d1	A530070C09Rik|R75201	nuclear receptor subfamily 1, group D, member 1	protein-coding
mm_100973.1	chr11	6720070	6720074	-	1	NA	promoter-TSS (NR_046025)	promoter-TSS (NR_046025)	-35	NR_046025	626419	Mm.390334	NR_046025	ENSMUSG00000086808	Gm11981	OTTMUSG00000005129	predicted gene 11981	ncRNA
mm_51860.1	chr6	90474298	90474307	+	1	NA	3' UTR (NM_023184, exon 3 of 3)	3' UTR (NM_023184, exon 3 of 3)	11676	NM_023184	66277	Mm.38343	NM_023184	ENSMUSG00000030087	Klf15	1810013I09Rik|AV048136|AW494632|CKLF|KKLF	Kruppel-like factor 15	protein-coding
mm_98845.1	chr11	97657421	97657476	+	1	NA	Intergenic	Intergenic	-5964	NM_139311	246198	Mm.23685	NM_139311	ENSMUSG00000038437	Mllt6	AI315037|Af17	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 6	protein-coding
mm_136290.1	chr16	91406890	91406902	-	1	NA	intron (NM_008349, intron 1 of 6)	intron (NM_008349, intron 1 of 6)	661	NM_008349	16155	Mm.4154	NM_008349	ENSMUSG00000022969	Il10rb	6620401D04Rik|AI528744|CRF2-4|Crfb4|D16H21S58|D21S58h|IL-10R2|Il10r2	interleukin 10 receptor, beta	protein-coding
mm_139594.1	chr17	57226839	57226843	+	1	NA	exon (NM_009778, exon 2 of 41)	exon (NM_009778, exon 2 of 41)	1295	NM_009778	12266	Mm.19131	NM_009778	ENSMUSG00000024164	C3	AI255234|ASP|HSE-MSF|Plp	complement component 3	protein-coding
mm_53431.1	chr6	134045904	134045932	+	1	NA	intron (NM_007961, intron 1 of 7)	intron (NM_007961, intron 1 of 7)	10218	NM_007961	14011	Mm.269995	NM_007961	ENSMUSG00000030199	Etv6	AW123102|AW557856|Tel	ets variant 6	protein-coding
mm_87294.1	chr10	42502198	42502282	+	1	NA	5' UTR (NM_017472, exon 1 of 4)	5' UTR (NM_017472, exon 1 of 4)	186	NM_017472	54198	Mm.277870	NM_017472	ENSMUSG00000019804	Snx3	SDP3	sorting nexin 3	protein-coding
mm_50295.1	chr6	47468130	47468132	+	1	NA	intron (NM_012042, intron 1 of 21)	AT_rich|Low_complexity|Low_complexity	13807	NM_012042	26965	Mm.87611	NM_012042	ENSMUSG00000029686	Cul1	-	cullin 1	protein-coding
mm_14823.1	chr2	147012745	147012794	+	1	NA	promoter-TSS (NM_011917)	promoter-TSS (NM_011917)	-291	NM_011917	24128	Mm.3065	NM_011917	ENSMUSG00000027433	Xrn2	-	5'-3' exoribonuclease 2	protein-coding
mm_141387.1	chr17	29095410	29095416	-	1	NA	intron (NM_007669, intron 1 of 2)	CpG	1644	NM_007669	12575	Mm.195663	NM_007669	ENSMUSG00000023067	Cdkn1a	CAP20|CDKI|CIP1|Cdkn1|P21|SDI1|Waf1|mda6|p21Cip1|p21WAF	cyclin-dependent kinase inhibitor 1A (P21)	protein-coding
mm_34450.1	chr4	148001966	148002007	+	1	NA	TTS (NM_008725)	TTS (NM_008725)	1264	NM_008725	230899	Mm.482123	NM_008725	ENSMUSG00000041616	Nppa	ANP|Anf|Pnd	natriuretic peptide type A	protein-coding
mm_21760.1	chr2	164840143	164840156	-	1	NA	exon (NM_011125, exon 15 of 16)	exon (NM_011125, exon 15 of 16)	6376	NM_008906	19025	Mm.359633	NM_008906	ENSMUSG00000017760	Ctsa	AU019505|PPCA|Ppgb	cathepsin A	protein-coding
mm_116222.1	chr13	32939320	32939330	-	1	NA	Intergenic	Intergenic	-26188	NM_011454	20708	Mm.36526	NM_011454	ENSMUSG00000042842	Serpinb6b	NK13|Spi12|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 6b	protein-coding
mm_105114.1	chr11	101020503	101020526	-	1	NA	exon (NM_001243049, exon 3 of 21)	exon (NM_001243049, exon 3 of 21)	-9826	NR_105893	102466767		NR_105893	ENSMUSG00000098415	Mir6928	Gm27728|mmu-mir-6928	microRNA 6928	ncRNA
mm_125471.1	chr15	54410668	54410678	+	1	NA	promoter-TSS (NM_173422)	promoter-TSS (NM_173422)	-101	NM_173422	239447	Mm.82400	NM_173422	ENSMUSG00000038591	Colec10	CL-L1	collectin sub-family member 10	protein-coding
mm_21015.1	chr2	152397274	152397328	-	1	NA	exon (NM_011438, exon 1 of 1)	exon (NM_011438, exon 1 of 1)	745	NM_011438	20667	Mm.28424	NM_011438	ENSMUSG00000051817	Sox12	2010205A02Rik	SRY (sex determining region Y)-box 12	protein-coding
mm_161292.1	chr14	26258639	26258639	+	1	NA	Intergenic	Intergenic	-3619	NM_001177538	100039227	Mm.428840	NM_001177538	ENSMUSG00000072675	Duxbl2	ENSMUSG00000072675|Gm10394	double homeobox B-like 2	protein-coding
mm_102939.1	chr11	69602453	69602465	-	1	NA	exon (NM_013415, exon 5 of 7)	exon (NM_013415, exon 5 of 7)	3501	NM_013415	11932	Mm.235204	NM_013415	ENSMUSG00000041329	Atp1b2	Amog|Atpb-2	ATPase, Na+/K+ transporting, beta 2 polypeptide	protein-coding
mm_19844.1	chr2	113348011	113348022	-	1	NA	intron (NM_001285458, intron 1 of 16)	intron (NM_001285458, intron 1 of 16)	20280	NM_010230	14260	Mm.4938	NM_010230	ENSMUSG00000044042	Fmn1	Fmn|formin-1|ld	formin 1	protein-coding
mm_54656.1	chr6	39087630	39087643	-	1	NA	exon (NM_172893, exon 12 of 12)	exon (NM_172893, exon 12 of 12)	-20050	NR_040523	69986	Mm.490941	NR_040523	ENSMUSG00000100121	1700025N23Rik	-	RIKEN cDNA 1700025N23 gene	ncRNA
mm_140455.1	chr17	88668644	88668654	+	1	NA	promoter-TSS (NM_023630)	promoter-TSS (NM_023630)	-11	NM_023630	71828	Mm.61330	NM_023630	ENSMUSG00000024154	Gtf2a1l	1700011N16Rik|Alf|Gtf2a1lf	general transcription factor IIA, 1-like	protein-coding
mm_48366.1	chr5	139460605	139460639	-	1	NA	promoter-TSS (NM_028469)	promoter-TSS (NM_028469)	-88	NM_028469	73212	Mm.84294	NM_028469	ENSMUSG00000053553	3110082I17Rik	AW411904	RIKEN cDNA 3110082I17 gene	protein-coding
mm_10409.1	chr2	13578915	13578925	+	1	NA	intron (NM_011701, intron 4 of 8)	intron (NM_011701, intron 4 of 8)	4609	NM_011701	22352	Mm.268000	NM_011701	ENSMUSG00000026728	Vim	-	vimentin	protein-coding
mm_82908.1	chr9	32928929	32928932	-	1	NA	promoter-TSS (NR_131058)	promoter-TSS (NR_131058)	36	NR_131058	330917	Mm.488283	NR_131058		Gm27162	A430016B06	predicted gene 27162	ncRNA
mm_89586.1	chr10	95779981	95779991	+	1	NA	Intergenic	Intergenic	-160677	NM_001001932	216238	Mm.210035	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding
mm_49170.1	chr6	14901288	14901342	+	1	NA	promoter-TSS (NM_053242)	promoter-TSS (NM_053242)	-34	NM_053242	114142	Mm.332919	NM_053242	ENSMUSG00000029563	Foxp2	2810043D05Rik|AI449000|CAG-16|D0Kist7	forkhead box P2	protein-coding
mm_21589.1	chr2	164237455	164237467	-	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	880	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_25034.1	chr3	98222149	98222164	+	1	NA	promoter-TSS (NM_026328)	promoter-TSS (NM_026328)	0	NM_026328	67709	Mm.46306	NM_026328	ENSMUSG00000027876	Reg4	2010002L15Rik|GISP|RELP	regenerating islet-derived family, member 4	protein-coding
mm_87966.1	chr10	63397238	63397264	+	1	NA	exon (NM_013888, exon 3 of 5)	exon (NM_013888, exon 3 of 5)	10688	NM_013888	30045	Mm.32550	NM_013888	ENSMUSG00000036764	Dnajc12	Jdp1|mJDP1	DnaJ heat shock protein family (Hsp40) member C12	protein-coding
mm_30837.1	chr4	22371137	22371144	+	1	NA	intron (NR_104378, intron 1 of 8)	L1_Mm|LINE|L1	13597	NR_104380	269514	Mm.40708	NM_172988	ENSMUSG00000040410	Fbxl4	AI836810|FBL4|FBL5	F-box and leucine-rich repeat protein 4	protein-coding
mm_106247.1	chr11	117813443	117813466	-	1	NA	exon (NM_009304, exon 4 of 4)	exon (NM_009304, exon 4 of 4)	3787	NM_009304	20973	Mm.468228	NM_009304	ENSMUSG00000048277	Syngr2	Clast2|cellugyrin	synaptogyrin 2	protein-coding
mm_72280.1	chr8	75100353	75100376	+	1	NA	3' UTR (NM_010442, exon 5 of 5)	3' UTR (NM_010442, exon 5 of 5)	6746	NM_010442	15368	Mm.276389	NM_010442	ENSMUSG00000005413	Hmox1	D8Wsu38e|HO-1|HO1|Hemox|Hmox|Hsp32	heme oxygenase 1	protein-coding
mm_66635.1	chr7	45525380	45525399	-	1	NA	promoter-TSS (NM_148927)	promoter-TSS (NM_148927)	879	NM_008654	17872	Mm.4048	NM_008654	ENSMUSG00000040435	Ppp1r15a	9630030H21|Gadd34|Myd116	protein phosphatase 1, regulatory (inhibitor) subunit 15A	protein-coding
mm_46076.1	chr5	92323836	92323846	-	1	NA	exon (NM_008599, exon 4 of 4)	exon (NM_008599, exon 4 of 4)	4238	NM_008599	17329	Mm.766	NM_008599	ENSMUSG00000029417	Cxcl9	BB139920|CMK|Mig|MuMIG|Scyb9|crg-10	chemokine (C-X-C motif) ligand 9	protein-coding
mm_115178.1	chr13	108316396	108316407	+	1	NA	promoter-TSS (NM_178683)	promoter-TSS (NM_178683)	64	NM_178683	218581	Mm.32318	NM_178683	ENSMUSG00000021697	Depdc1b	9830132O03|AW260467|XTP1	DEP domain containing 1B	protein-coding
mm_98820.1	chr11	97329541	97329545	+	1	NA	3' UTR (NM_025927, exon 8 of 8)	3' UTR (NM_025927, exon 8 of 8)	13827	NM_025927	67036	Mm.5381	NM_025927	ENSMUSG00000018882	Mrpl45	2600005P05Rik|AU043542|R75241	mitochondrial ribosomal protein L45	protein-coding
mm_143607.1	chr17	78651539	78651541	-	1	NA	Intergenic	Intergenic	85020	NM_011500	268980	Mm.311915	NM_011500	ENSMUSG00000024077	Strn	AU022939|D130055P19	striatin, calmodulin binding protein	protein-coding
mm_70076.1	chr7	142653225	142653235	-	1	NA	3' UTR (NM_010514, exon 4 of 4)	3' UTR (NM_010514, exon 4 of 4)	1766	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_15914.1	chr2	165064137	165064163	+	1	NA	intron (NM_170703, intron 5 of 7)	B4|SINE|B4	8514	NM_011611	21939	Mm.271833	NM_011611	ENSMUSG00000017652	Cd40	AI326936|Bp50|GP39|HIGM1|IGM|IMD3|T-BAM|TRAP|Tnfrsf5|p50	CD40 antigen	protein-coding
mm_99850.1	chr11	109362856	109362868	+	1	NA	promoter-TSS (NM_010303)	promoter-TSS (NM_010303)	68	NM_010303	14674	Mm.193925	NM_010303	ENSMUSG00000020611	Gna13	AU024132|AU043124|Galpha13	guanine nucleotide binding protein, alpha 13	protein-coding
mm_99823.1	chr11	108920343	108920358	+	1	NA	promoter-TSS (NM_015732)	promoter-TSS (NM_015732)	1	NM_015732	12006	Mm.71710	NM_015732	ENSMUSG00000000142	Axin2	Axi1|Axil|Conductin	axin 2	protein-coding
mm_85441.1	chr9	104103002	104103016	-	1	NA	intron (NM_145700, intron 1 of 2)	intron (NM_145700, intron 1 of 2)	23634	NM_145700	252837	Mm.269254	NM_145700	ENSMUSG00000079355	Ackr4	A630091E18Rik|CCBP2|CCR11|CCX-CKR|CCX-CKR1|Ccrl1|Cmkbrl1|PPR1|VSHK1	atypical chemokine receptor 4	protein-coding
mm_58293.1	chr6	145865336	145865359	-	1	NA	promoter-TSS (NM_001271768)	promoter-TSS (NM_001271768)	73	NM_001271768	79362	Mm.154529	NM_024469	ENSMUSG00000030256	Bhlhe41	6430520M22Rik|Bhlhb2l|Bhlhb3|DEC2|Sharp1	basic helix-loop-helix family, member e41	protein-coding
mm_164625.1	chr17	31295807	31295819	+	1	NA	promoter-TSS (NM_001242427)	promoter-TSS (NM_001242427)	330	NM_153062	224674	Mm.311395	NM_153062	ENSMUSG00000024036	Slc37a1	G3PP	solute carrier family 37 (glycerol-3-phosphate transporter), member 1	protein-coding
mm_103197.1	chr11	70649009	70649015	-	1	NA	intron (NM_001316728, intron 3 of 9)	PB1D9|SINE|Alu	1725	NM_027445	70510	Mm.261818	NM_027445	ENSMUSG00000040746	Rnf167	0610010G05Rik|5730408C10Rik|AU019305|AV328608	ring finger protein 167	protein-coding
mm_141177.1	chr17	26841505	26841513	-	1	NA	promoter-TSS (NM_008700)	promoter-TSS (NM_008700)	56	NM_008700	18091	Mm.41974	NM_008700	ENSMUSG00000015579	Nkx2-5	Csx|Nkx-2.5|Nkx2.5|tinman	NK2 homeobox 5	protein-coding
mm_132857.1	chr16	48303915	48303925	+	1	NA	Intergenic	Intergenic	-6354	NM_028615	73703	Mm.27857	NM_028615	ENSMUSG00000072419	Dppa2	2410088E07Rik|C80932|D19Mgi18|ECAT15-2	developmental pluripotency associated 2	protein-coding
mm_93496.1	chr10	112231094	112231102	-	1	NA	Intergenic	Intergenic	-40025	NM_001025581	268345	Mm.336242	NM_001025581	ENSMUSG00000035681	Kcnc2	AW047325|B230117I07|KShIIIA|Kv3.2	potassium voltage gated channel, Shaw-related subfamily, member 2	protein-coding
mm_76218.1	chr8	83571761	83571774	-	1	NA	TTS (NM_027179)	TTS (NM_027179)	5009	NM_025843	66916	Mm.29683	NM_025843	ENSMUSG00000033938	Ndufb7	1110002H15Rik	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 7	protein-coding
mm_59288.1	chr7	24981737	24981752	+	1	NA	exon (NM_001290469, exon 17 of 23)	exon (NM_001290469, exon 17 of 23)	5923	NR_106014	102465634		NR_106014	ENSMUSG00000099258	Mir7047	Gm27270|mmu-mir-7047	microRNA 7047	ncRNA
mm_15073.1	chr2	153114477	153114506	+	1	NA	intron (NM_001172117, intron 1 of 12)	B2_Mm1t|SINE|B2	6023	NM_010407	15162	Mm.715	NM_010407	ENSMUSG00000003283	Hck	AI849071|Bmk	hemopoietic cell kinase	protein-coding
mm_153662.1	chr19	44395739	44395758	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	11961	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_167383.1	chr8	94355193	94355195	+	1	NA	intron (NM_019415, intron 21 of 24)	B1_Mur4|SINE|Alu	25986	NM_001205311	20497	Mm.25804	NM_019415	ENSMUSG00000031766	Slc12a3	AI035291|NCC|NCCT|TSC	solute carrier family 12, member 3	protein-coding
mm_16702.1	chr2	6949436	6949444	-	1	NA	intron (NM_001110229, intron 2 of 14)	intron (NM_001110229, intron 2 of 14)	-20718	NR_027890	68144	Mm.483289	NM_026575		5031426D15Rik	-	RIKEN cDNA 5031426D15 gene	ncRNA
mm_76799.1	chr8	104034321	104034321	-	1	NA	Intergenic	L1M4c|LINE|L1	-67304	NM_009868	12562	Mm.21767	NM_009868	ENSMUSG00000031871	Cdh5	7B4|AA408225|Cd144|VE-Cad|VECD|VEcad|Vec	cadherin 5	protein-coding
mm_166543.1	chr6	34419415	34419417	+	1	NA	exon (NM_009731, exon 6 of 10)	exon (NM_009731, exon 6 of 10)	7054	NM_009731	11997	Mm.482073	NM_009731	ENSMUSG00000052131	Akr1b7	AR|Avdp|MVDP	aldo-keto reductase family 1, member B7	protein-coding
mm_158241.1	chrX	106603621	106603631	-	1	NA	promoter-TSS (NM_001281859)	promoter-TSS (NM_001281859)	53	NM_001281862	58861	Mm.287166	NM_021476	ENSMUSG00000052821	Cysltr1	BB147369|CysLT1R|Cyslt1	cysteinyl leukotriene receptor 1	protein-coding
mm_166718.1	chr6	119902451	119902463	+	1	NA	promoter-TSS (NM_011236)	promoter-TSS (NM_011236)	-241	NM_001166382	19365	Mm.149	NM_011236	ENSMUSG00000030166	Rad52	Rad52yh	RAD52 homolog, DNA repair protein	protein-coding
mm_160017.1	chr6	129660424	129660424	-	1	NA	exon (NM_010653, exon 1 of 6)	exon (NM_010653, exon 1 of 6)	132	NM_010653	16642	Mm.347927	NM_010653	ENSMUSG00000052736	Klrc2	NKG2C	killer cell lectin-like receptor subfamily C, member 2	protein-coding
mm_146133.1	chr18	74708009	74708043	+	1	NA	exon (NM_201600, exon 22 of 39)	exon (NM_201600, exon 22 of 39)	70429	NR_028560	100217466		NR_028560		Scarna17	MBII-119	small Cajal body-specific RNA 17	ncRNA
mm_150659.1	chr19	41981324	41981349	+	1	NA	promoter-TSS (NM_028152)	promoter-TSS (NM_028152)	-200	NM_028152	72199	Mm.218940	NM_028152	ENSMUSG00000025159	Mms19	2410001K24Rik|2610042O15Rik|AI316855|C79368|C86341|Mms19l	MMS19 (MET18 S. cerevisiae)	protein-coding
mm_165175.1	chr2	27487601	27487606	+	1	NA	Intergenic	Intergenic	-11930	NM_001113574	67382	Mm.28721	NM_023336	ENSMUSG00000026918	Brd3	2410084F24Rik|AW060456|Fsrg2|ORFX|RINGL3	bromodomain containing 3	protein-coding
mm_43259.1	chr5	130223914	130223929	+	1	NA	intron (NM_027854, intron 1 of 6)	intron (NM_027854, intron 1 of 6)	1586	NM_027854	71667	Mm.258508	NM_027854	ENSMUSG00000053094	Tmem248	0610007L01Rik|A930023A16Rik|AW557951|G430067H08Rik	transmembrane protein 248	protein-coding
mm_84967.1	chr9	83834544	83834566	-	1	NA	promoter-TSS (NM_001284272)	promoter-TSS (NM_001284272)	-134	NM_009445	22137	Mm.1904	NM_009445	ENSMUSG00000038379	Ttk	AL022661|Esk1|Mps1|PYT|esk	Ttk protein kinase	protein-coding
mm_93811.1	chr10	121311008	121311031	-	1	NA	5' UTR (NM_029057, exon 1 of 12)	5' UTR (NM_029057, exon 1 of 12)	170	NM_029057	74694	Mm.233833	NM_029057	ENSMUSG00000052302	Tbc1d30	4930505D03Rik	TBC1 domain family, member 30	protein-coding
mm_103807.1	chr11	82991106	82991171	-	1	NA	intron (NM_172796, intron 1 of 4)	intron (NM_172796, intron 1 of 4)	692	NM_172796	237886	Mm.270253	NM_172796	ENSMUSG00000069793	Slfn9	9830137M10Rik	schlafen 9	protein-coding
mm_62.1	chr1	6597035	6597040	+	1	NA	intron (NM_001244693, intron 2 of 22)	L1_Mus3|LINE|L1	109806	NM_001244692	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding
mm_159951.1	chr6	85904925	85904925	-	1	NA	promoter-TSS (NM_029331)	promoter-TSS (NM_029331)	13	NM_029331	75541	Mm.24454	NM_029331	ENSMUSG00000068299	Nat8f4	1700019G17Rik	N-acetyltransferase 8 (GCN5-related) family member 4	protein-coding
mm_76595.1	chr8	89044176	89044195	-	1	NA	promoter-TSS (NM_021390)	promoter-TSS (NM_021390)	-23	NM_021390	58198	Mm.214361	NM_021390	ENSMUSG00000031665	Sall1	Msal-3	sal-like 1 (Drosophila)	protein-coding
mm_23104.1	chr3	37366882	37366895	+	1	NA	intron (NM_008006, intron 1 of 2)	intron (NM_008006, intron 1 of 2)	18235	NM_008006	14173	Mm.473689	NM_008006	ENSMUSG00000037225	Fgf2	Fgf-2|Fgfb|bFGF	fibroblast growth factor 2	protein-coding
mm_147627.1	chr18	58209134	58209148	-	1	NA	intron (NM_010181, intron 1 of 64)	intron (NM_010181, intron 1 of 64)	785	NM_010181	14119	Mm.20271	NM_010181	ENSMUSG00000024598	Fbn2	BC063774|Fib-2|mKIAA4226|sne|sy	fibrillin 2	protein-coding
mm_92447.1	chr10	77697288	77697289	-	1	NA	intron (NM_001287074, intron 1 of 11)	intron (NM_001287074, intron 1 of 11)	-6531	NM_001205032	100502831	Mm.486158	NM_001205032	ENSMUSG00000095970	Gm19402	-	predicted gene, 19402	protein-coding
mm_21454.1	chr2	160816670	160816674	-	1	NA	intron (NM_177263, intron 2 of 3)	RMER6C|LTR|ERVK	56318	NM_177263	320799	Mm.436734	NM_177263	ENSMUSG00000035877	Zhx3	1810059C13Rik|4932418O04Rik|9530010N21Rik|Tix1|mKIAA0395	zinc fingers and homeoboxes 3	protein-coding
mm_21218.1	chr2	155819197	155819269	-	1	NA	promoter-TSS (NR_015528)	promoter-TSS (NR_015528)	-30	NR_015528	613262	Mm.330707	NR_015528	ENSMUSG00000074649	BC029722	-	cDNA sequence BC029722	ncRNA
mm_158918.1	chr1	55363522	55363522	-	1	NA	promoter-TSS (NM_029267)	promoter-TSS (NM_029267)	-53	NM_029267	75388	Mm.483408	NM_029267	ENSMUSG00000025977	Boll	4930554P13Rik|4930597B14Rik	bol, boule-like (Drosophila)	protein-coding
mm_98329.1	chr11	90638128	90638207	+	1	NA	promoter-TSS (NM_011505)	promoter-TSS (NM_011505)	-17	NM_199008	69802	Mm.151940	NM_199008	ENSMUSG00000020544	Cox11	2010004I09Rik	cytochrome c oxidase assembly protein 11	protein-coding
mm_31985.1	chr4	89152117	89152120	+	1	NA	intron (NM_024433, intron 3 of 7)	(T)n|Simple_repeat|Simple_repeat	14748	NM_024433	66902	Mm.28500	NM_024433	ENSMUSG00000062937	Mtap	1300019I21Rik|MSAP	methylthioadenosine phosphorylase	protein-coding
mm_145851.1	chr18	65453695	65453714	+	1	NA	exon (NM_172833, exon 8 of 16)	exon (NM_172833, exon 8 of 16)	22707	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_159439.1	chr3	123619250	123619250	-	1	NA	intron (NM_001293682, intron 1 of 11)	intron (NM_001293682, intron 1 of 11)	200	NM_001293682	83398	Mm.443908	NM_031186	ENSMUSG00000027977	Ndst3	4921531K01Rik|4930511P15Rik|N-HSST 3|NDST-3	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 3	protein-coding
mm_102472.1	chr11	60031848	60031869	-	1	NA	intron (NM_001290012, intron 1 of 6)	intron (NM_001290012, intron 1 of 6)	5147	NM_008819	18618	Mm.2731	NM_008819	ENSMUSG00000000301	Pemt	PEAMT|PEMT2|PLMT|Pempt|Pempt2	phosphatidylethanolamine N-methyltransferase	protein-coding
mm_90959.1	chr10	13303971	13303977	-	1	NA	intron (NM_001195065, intron 1 of 12)	intron (NM_001195065, intron 1 of 12)	20186	NM_001195096	215789	Mm.283359	NM_001033257	ENSMUSG00000062866	Phactr2	AV158170|BC012871	phosphatase and actin regulator 2	protein-coding
mm_142239.1	chr17	37482410	37482414	-	1	NA	intron (NM_001347387, intron 3 of 4)	intron (NM_001347387, intron 3 of 4)	1117	NM_008204	14990	Mm.329041	NM_008204	ENSMUSG00000016283	H2-M2	H-2M2|Thy19.4	histocompatibility 2, M region locus 2	protein-coding
mm_121485.1	chr14	121146803	121146807	+	1	NA	intron (NM_134082, intron 2 of 26)	intron (NM_134082, intron 2 of 26)	111231	NM_134082	223254	Mm.223980	NM_134082	ENSMUSG00000025555	Farp1	AW228844|BC030329|Cdep	FERM, RhoGEF (Arhgef) and pleckstrin domain protein 1 (chondrocyte-derived)	protein-coding
mm_114168.1	chr13	55471717	55471757	+	1	NA	intron (NM_001030296, intron 1 of 2)	CpG	6039	NR_105909	102465569		NR_105909	ENSMUSG00000098341	Mir6944	Gm27710|mmu-mir-6944	microRNA 6944	ncRNA
mm_16509.1	chr2	181365385	181365414	+	1	NA	promoter-TSS (NM_001165995)	promoter-TSS (NM_001165995)	5	NM_001165991	76688	Mm.87720	NM_029702	ENSMUSG00000038671	Arfrp1	1500006I01Rik|AI480700	ADP-ribosylation factor related protein 1	protein-coding
mm_6185.1	chr1	65110102	65110108	-	1	NA	intron (NM_175293, intron 5 of 7)	intron (NM_175293, intron 5 of 7)	-6742	NM_007774	12964	Mm.26904	NM_007774	ENSMUSG00000044429	Cryga	Cryg-4|DGcry-4	crystallin, gamma A	protein-coding
mm_65767.1	chr7	28741781	28741843	-	1	NA	promoter-TSS (NM_023637)	promoter-TSS (NM_023637)	-31	NM_011885	24030	Mm.358650	NM_011885	ENSMUSG00000045948	Mrps12	AI327385|Rpms12|rps12	mitochondrial ribosomal protein S12	protein-coding
mm_111482.1	chr12	98737528	98737539	-	1	NA	promoter-TSS (NM_001146199)	promoter-TSS (NM_001146199)	-128	NM_001146199	24000	Mm.4420	NM_011877	ENSMUSG00000021009	Ptpn21	PTPD1|PTPRL10	protein tyrosine phosphatase, non-receptor type 21	protein-coding
mm_159505.1	chr4	46344204	46344204	+	1	NA	promoter-TSS (NM_183298)	promoter-TSS (NM_183298)	10	NM_183298	110805	Mm.354634	NM_183298	ENSMUSG00000070990	Foxe1	Titf2	forkhead box E1	protein-coding
mm_105381.1	chr11	103335309	103335324	-	1	NA	intron (NM_133715, intron 8 of 15)	intron (NM_133715, intron 8 of 15)	9386	NM_133715	544817	Mm.259113	NM_133715	ENSMUSG00000034255	Arhgap27	2310069I04Rik|5730442P18Rik|Gm21552|Sh3d20	Rho GTPase activating protein 27	protein-coding
mm_50824.1	chr6	54595245	54595264	+	1	NA	5' UTR (NM_001164361, exon 1 of 14)	5' UTR (NM_001164361, exon 1 of 14)	143	NM_001164361	231999	Mm.35416	NM_001001335	ENSMUSG00000005225	Plekha8	6330400G01|AA517676|BC052360|Fapp-2|Fapp2	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 8	protein-coding
mm_50536.1	chr6	49045999	49046005	+	1	NA	intron (NM_053110, intron 4 of 10)	intron (NM_053110, intron 4 of 10)	9484	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_86555.1	chr10	10751121	10751130	+	1	NA	promoter-TSS (NR_046010)	promoter-TSS (NR_046010)	79	NR_046010	78056	Mm.271285	NR_046010		4930567K20Rik	1700038H22Rik	RIKEN cDNA 4930567K20 gene	ncRNA
mm_60061.1	chr7	31207833	31207839	+	1	NA	Intergenic	Intergenic	45478	NR_046062	100038516	Mm.387223	NR_046062	ENSMUSG00000100985	Gm10640	EG668322|ENSMUSG00000074193	predicted gene 10640	ncRNA
mm_42679.1	chr5	119796514	119796544	+	1	NA	Intergenic	CpG	-38134	NM_011537	21388	Mm.103636	NM_011537	ENSMUSG00000018263	Tbx5	-	T-box 5	protein-coding
mm_46846.1	chr5	113586079	113586099	-	1	NA	intron (NM_177292, intron 7 of 7)	MMERGLN_LTR|LTR|ERV1	35669	NM_177292	320916	Mm.102783	NM_177292	ENSMUSG00000063430	Wscd2	4933413A10Rik|C530024P05Rik|Gm450	WSC domain containing 2	protein-coding
mm_123617.1	chr14	68120878	68120888	-	1	NA	exon (NM_008691, exon 3 of 3)	exon (NM_008691, exon 3 of 3)	-2869	NR_045897	100043072	Mm.242832	NR_045897		A230070E04Rik	Gm4210	RIKEN cDNA A230070E04 gene	ncRNA
mm_21301.1	chr2	157058720	157058725	-	1	NA	intron (NM_001164663, intron 2 of 14)	intron (NM_001164663, intron 2 of 14)	20543	NM_001164663	320706	Mm.79466	NM_001164663	ENSMUSG00000055485	Soga1	9830001H06Rik|AI426038|D430036N24Rik|Soga	suppressor of glucose, autophagy associated 1	protein-coding
mm_118817.1	chr14	25481259	25481275	+	1	NA	intron (NM_001310666, intron 1 of 23)	intron (NM_001310666, intron 1 of 23)	22082	NM_183208	328365	Mm.227484	NM_183208	ENSMUSG00000007817	Zmiz1	BC065120|E330020C23|ENSMUSG00000072684|Gm10397|I920194n01|Rai17|Zimp10	zinc finger, MIZ-type containing 1	protein-coding
mm_389.1	chr1	34089265	34089279	+	1	NA	intron (NM_001276764, intron 5 of 102)	intron (NM_001276764, intron 5 of 102)	-28087	NR_105861	102466987		NR_105861	ENSMUSG00000105982	Mir6896	mmu-mir-6896	microRNA 6896	ncRNA
mm_130715.1	chr15	101047402	101047404	-	1	NA	Intergenic	CpG	6996	NM_001214911	668225	Mm.385011	NM_001214911	ENSMUSG00000095440	Fignl2	EG668225	fidgetin-like 2	protein-coding
mm_150618.1	chr19	41029380	41029398	+	1	NA	5' UTR (NM_001043228, exon 1 of 11)	5' UTR (NM_001043228, exon 1 of 11)	114	NM_009345	21673	Mm.25620	NM_009345	ENSMUSG00000025014	Dntt	Tdt	deoxynucleotidyltransferase, terminal	protein-coding
mm_55235.1	chr6	52245749	52245763	-	1	NA	promoter-TSS (NM_010450)	promoter-TSS (NM_010450)	54	NM_010450	15396	Mm.26954	NM_010450	ENSMUSG00000038210	Hoxa11	Hox-1.9|Hoxa-11	homeobox A11	protein-coding
mm_147106.1	chr18	35662181	35662195	-	1	NA	promoter-TSS (NM_027733)	promoter-TSS (NM_027733)	-2	NM_027733	71242	Mm.151498	NM_027733	ENSMUSG00000024352	Spata24	2700012K08Rik|4930583E11Rik|5133400G04Rik|AU016220|TIPT|TIPT2	spermatogenesis associated 24	protein-coding
mm_139240.1	chr17	47733062	47733071	+	1	NA	exon (NM_025973, exon 7 of 9)	exon (NM_025973, exon 7 of 9)	-3971	NM_001161722	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_122871.1	chr14	54925609	54925633	-	1	NA	5' UTR (NM_010112, exon 1 of 6)	5' UTR (NM_010112, exon 1 of 6)	1167	NM_010112	13644	Mm.236438	NM_010112	ENSMUSG00000022203	Efs	-	embryonal Fyn-associated substrate	protein-coding
mm_99059.1	chr11	99109564	99109602	+	1	NA	Intergenic	Intergenic	-20277	NM_172564	217169	Mm.262067	NM_172564	ENSMUSG00000017607	Tns4	9930017A07Rik|AA589547|AU016405|Cten	tensin 4	protein-coding
mm_21775.1	chr2	164846767	164846850	-	1	NA	exon (NM_011125, exon 9 of 16)	exon (NM_011125, exon 9 of 16)	10900	NM_011125	18830	Mm.6105	NM_011125	ENSMUSG00000017754	Pltp	Bpife|OD107	phospholipid transfer protein	protein-coding
mm_120787.1	chr14	74732391	74732401	+	1	NA	promoter-TSS (NM_016903)	promoter-TSS (NM_016903)	99	NM_016903	13885	Mm.38055	NM_016903	ENSMUSG00000021996	Esd	Es-10|Es10|FGH|sid478	esterase D/formylglutathione hydrolase	protein-coding
mm_41514.1	chr5	92387674	92387769	+	1	NA	promoter-TSS (NM_181728)	promoter-TSS (NM_181728)	-413	NM_181728	109979	Mm.263514	NM_181728	ENSMUSG00000034842	Art3	4930569O04Rik|ARTC3	ADP-ribosyltransferase 3	protein-coding
mm_122130.1	chr14	31160547	31160557	-	1	NA	exon (NM_138672, exon 12 of 69)	exon (NM_138672, exon 12 of 69)	8089	NM_138672	192187	Mm.220821	NM_138672	ENSMUSG00000042286	Stab1	FEEL-1|FELE-1|MFEEL-1|MS-1|STAB-1|mKIAA0246	stabilin 1	protein-coding
mm_167228.1	chr8	13138662	13138668	+	1	NA	intron (NM_146207, intron 15 of 19)	intron (NM_146207, intron 15 of 19)	2593	NR_106032	102465645		NR_106032	ENSMUSG00000098532	Mir7065	Gm27871|mmu-mir-7065	microRNA 7065	ncRNA
mm_31127.1	chr4	43058940	43058962	+	1	NA	promoter-TSS (NM_021468)	promoter-TSS (NM_021468)	-2	NM_021468	22249	Mm.128892	NM_021468	ENSMUSG00000028456	Unc13b	Munc13-1|Munc13-2|Unc13a|Unc13h1|Unc13h2	unc-13 homolog B (C. elegans)	protein-coding
mm_142658.1	chr17	47687007	47687022	-	1	NA	promoter-TSS (NR_045945)	promoter-TSS (NR_045945)	-596	NR_045945	100415787	Mm.392206	NR_045945	ENSMUSG00000084880	Tomm6os	Gm14872|OTTMUSG00000018355|Prickle4os	translocase of outer mitochondrial membrane 6, opposite strand	ncRNA
mm_59824.1	chr7	29247636	29247670	+	1	NA	TTS (NM_001110201)	TTS (NM_001110201)	814	NM_028179	72275	Mm.441142	NM_028179	ENSMUSG00000030587	2200002D01Rik	2010005J02Rik|H2RSP|IMUP|IMUP-1|IMUP-2	RIKEN cDNA 2200002D01 gene	protein-coding
mm_47168.1	chr5	120743792	120743846	-	1	NA	intron (NM_001347448, intron 3 of 11)	(CAGA)n|Simple_repeat|Simple_repeat	6029	NM_145227	246728	Mm.260926	NM_145227	ENSMUSG00000032690	Oas2	Oasl11	2'-5' oligoadenylate synthetase 2	protein-coding
mm_31805.1	chr4	65339483	65339487	+	1	NA	intron (NM_021362, intron 20 of 21)	intron (NM_021362, intron 20 of 21)	215311	NM_021362	18491	Mm.317854	NM_021362	ENSMUSG00000028370	Pappa	8430414N03Rik|IGFBP-4ase|PAG1|PAPP-A	pregnancy-associated plasma protein A	protein-coding
mm_136346.1	chr16	92644214	92644252	-	1	NA	exon (NM_001111021, exon 6 of 8)	exon (NM_001111021, exon 6 of 8)	53096	NM_001111023	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_31247.1	chr4	44943728	44943791	+	1	NA	Intergenic	Intergenic	-37635	NM_080289	76238	Mm.196574	NM_080289	ENSMUSG00000035637	Grhpr	1110059D05Rik|6430629L09Rik|Glxr	glyoxylate reductase/hydroxypyruvate reductase	protein-coding
mm_1104.1	chr1	59763694	59763702	+	1	NA	promoter-TSS (NM_007561)	promoter-TSS (NM_007561)	-581	NM_007561	12168	Mm.7106	NM_007561	ENSMUSG00000067336	Bmpr2	2610024H22Rik|AL117858|AW546137|BB189135|BMP-2|BMPR-2|BMPR-II|BMPRII|BRK-3|Gm20272	bone morphogenetic protein receptor, type II (serine/threonine kinase)	protein-coding
mm_110725.1	chr12	69682244	69682258	-	1	NA	promoter-TSS (NM_001135559)	promoter-TSS (NM_001135559)	-399	NM_001135559	20663	Mm.3770	NM_001135559	ENSMUSG00000034801	Sos2	SOS-2|mSOS-2	son of sevenless homolog 2 (Drosophila)	protein-coding
mm_5061.1	chr1	194986650	194986683	+	1	NA	Intergenic	Intergenic	-9707	NR_033564	320400	Mm.417608	NR_033564	ENSMUSG00000097325	Gm16897	C030002c11rik	predicted gene, 16897	ncRNA
mm_77340.1	chr8	119566518	119566525	-	1	NA	intron (NM_175185, intron 2 of 4)	intron (NM_175185, intron 2 of 4)	-7760	NM_019709	56453	Mm.206934	NM_019709	ENSMUSG00000031835	Mbtps1	0610038M03Rik|AV003995|S1P|SKI-1|Ski1|mKIAA0091	membrane-bound transcription factor peptidase, site 1	protein-coding
mm_59327.1	chr7	25316974	25316992	+	1	NA	promoter-TSS (NM_001160400)	promoter-TSS (NM_001160400)	-181	NM_001160400	269878	Mm.38527	NM_001160400	ENSMUSG00000045039	Megf8	AW049492|Egfl4|b2b1702.2Clo|b2b1702Clo|b2b288Clo|m687Ddg|mKIAA0817	multiple EGF-like-domains 8	protein-coding
mm_43692.1	chr5	139150212	139150249	+	1	NA	promoter-TSS (NM_001081265)	promoter-TSS (NM_001081265)	7	NM_001081265	433956	Mm.5547	NM_001081265	ENSMUSG00000025857	Dnaaf5	BC053401|C76907|Heatr2	dynein, axonemal assembly factor 5	protein-coding
mm_68771.1	chr7	121981708	121981719	-	1	NA	promoter-TSS (NM_001033318)	promoter-TSS (NM_001033318)	-20	NM_001033318	233824	Mm.442015	NM_001033318	ENSMUSG00000034951	Cog7	5630400E24Rik|Gm167	component of oligomeric golgi complex 7	protein-coding
mm_229.1	chr1	17727382	17727391	+	1	NA	promoter-TSS (NM_031402)	promoter-TSS (NM_031402)	-31	NM_031402	83691	Mm.289625	NM_031402	ENSMUSG00000025776	Crispld1	Cocoacrisp|Lcrisp1	cysteine-rich secretory protein LCCL domain containing 1	protein-coding
mm_164403.1	chr16	35154858	35154869	+	1	NA	promoter-TSS (NM_001012765)	promoter-TSS (NM_001012765)	-773	NM_001012765	224129	Mm.41137	NM_001012765	ENSMUSG00000022840	Adcy5	AW121902|Ac5	adenylate cyclase 5	protein-coding
mm_76488.1	chr8	85840584	85840594	-	1	NA	promoter-TSS (NM_199446)	promoter-TSS (NM_199446)	360	NM_028007	71927	Mm.61018	NM_028007	ENSMUSG00000031703	Itfg1	2310047C21Rik|AI314457|Cda08|D8Wsu49e	integrin alpha FG-GAP repeat containing 1	protein-coding
mm_35723.1	chr4	44704437	44704449	-	1	NA	non-coding (NR_073462, exon 1 of 1)	non-coding (NR_073462, exon 1 of 1)	1643	NR_073462	70602	Mm.491142	NR_073462	ENSMUSG00000103995	5730488B01Rik	-	RIKEN cDNA 5730488B01 gene	ncRNA
mm_148851.1	chr19	6386412	6386427	+	1	NA	exon (NM_011224, exon 5 of 20)	exon (NM_011224, exon 5 of 20)	2011	NM_011224	19309	Mm.27806	NM_011224	ENSMUSG00000032648	Pygm	AI115133|PG	muscle glycogen phosphorylase	protein-coding
mm_162479.1	chr1	133915379	133915383	-	1	NA	exon (NM_054077, exon 2 of 3)	exon (NM_054077, exon 2 of 3)	6020	NM_054077	116847	Mm.214514	NM_054077	ENSMUSG00000041577	Prelp	7330409J17Rik|SLRR2A	proline arginine-rich end leucine-rich repeat	protein-coding
mm_143278.1	chr17	65704782	65704794	-	1	NA	intron (NM_133685, intron 3 of 6)	intron (NM_133685, intron 3 of 6)	-62584	NM_001146002	213272	Mm.255732	NM_153519	ENSMUSG00000050612	Txndc2	AU021712|Sptrx-1|Sptrx1|Trx4	thioredoxin domain containing 2 (spermatozoa)	protein-coding
mm_165862.1	chr4	28815584	28815612	+	1	NA	intron (NM_001290434, intron 1 of 16)	CpG	2453	NM_001122889	13841	Mm.257266	NM_010141	ENSMUSG00000028289	Epha7	Cek11|Ebk|Ehk3|Hek11|Mdk1	Eph receptor A7	protein-coding
mm_102072.1	chr11	52261576	52261600	-	1	NA	exon (NM_009331, exon 3 of 10)	exon (NM_009331, exon 3 of 10)	21007	NM_009331	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_16609.1	chr2	5083864	5083872	-	1	NA	Intergenic	Intergenic	-19930	NM_181848	71648	Mm.116942	NM_181848	ENSMUSG00000026672	Optn	4930441O07Rik|FIP2|HYPL|NRP	optineurin	protein-coding
mm_125147.1	chr15	30646583	30646599	+	1	NA	intron (NM_008729, intron 6 of 22)	CpG	-392535	NR_045186	73784	Mm.66947	NR_045186		4930430F21Rik	-	RIKEN cDNA 4930430F21 gene	ncRNA
mm_142427.1	chr17	45569561	45569582	-	1	NA	exon (NM_008302, exon 7 of 11)	exon (NM_008302, exon 7 of 11)	3690	NM_008302	15516	Mm.2180	NM_008302	ENSMUSG00000023944	Hsp90ab1	90kDa|AL022974|C81438|Hsp84|Hsp84-1|Hsp90|Hspcb	heat shock protein 90 alpha (cytosolic), class B member 1	protein-coding
mm_50565.1	chr6	49047991	49048017	+	1	NA	exon (NM_053110, exon 6 of 11)	exon (NM_053110, exon 6 of 11)	11486	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_23243.1	chr3	51221232	51221245	+	1	NA	Intergenic	Intergenic	-3209	NM_009834	12457	Mm.86541	NM_009834	ENSMUSG00000023087	Noct	AU043840|Ccr4|Ccrn4l	nocturnin	protein-coding
mm_37359.1	chr4	120613871	120613882	-	1	NA	Intergenic	Intergenic	25131	NM_001101603	667063	Mm.90231	NM_001101603	ENSMUSG00000091297	Gm8439	EG667063|Gm1664	predicted gene 8439	protein-coding
mm_9443.1	chr1	172590464	172590475	-	1	NA	promoter-TSS (NM_029084)	promoter-TSS (NM_029084)	99	NM_029084	74748	Mm.179812	NM_029084	ENSMUSG00000053318	Slamf8	5830408F06Rik|Blame|SBBI42	SLAM family member 8	protein-coding
mm_89675.1	chr10	97517452	97517469	+	1	NA	intron (NM_001190451, intron 7 of 7)	intron (NM_001190451, intron 7 of 7)	35129	NM_007833	13179	Mm.56769	NM_007833	ENSMUSG00000019929	Dcn	DC|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding
mm_48697.1	chr5	146897040	146897059	-	1	NA	Intergenic	Intergenic	-51608	NM_025652	66596	Mm.196528	NM_025652	ENSMUSG00000016503	Gtf3a	2010015D03Rik|2610111I01Rik|5330403M05Rik	general transcription factor III A	protein-coding
mm_18829.1	chr2	74705816	74705833	-	1	NA	exon (NM_001290730, exon 1 of 2)	exon (NM_001290730, exon 1 of 2)	335	NM_008276	15437	Mm.280673	NM_008276	ENSMUSG00000027102	Hoxd8	4921540P06Rik|AI047735|Hox-4.3|Hox-5.4	homeobox D8	protein-coding
mm_134829.1	chr16	26095966	26095975	-	1	NA	intron (NM_173379, intron 1 of 14)	intron (NM_173379, intron 1 of 14)	9814	NM_173379	210530	Mm.326869	NM_173379	ENSMUSG00000038168	P3h2	4832416N06|AW553532|Leprel1|Mlat4	prolyl 3-hydroxylase 2	protein-coding
mm_127618.1	chr15	102460501	102460519	+	1	NA	exon (NM_025385, exon 4 of 5)	exon (NM_025385, exon 4 of 5)	1340	NM_025385	66151	Mm.393955	NM_025385	ENSMUSG00000023048	Prr13	1110020C13Rik|2010324E22Rik	proline rich 13	protein-coding
mm_34967.1	chr4	156008697	156008706	+	1	NA	intron (NM_001302468, intron 4 of 6)	intron (NM_001302468, intron 4 of 6)	-4994	NM_011659	22163	Mm.13885	NM_011659	ENSMUSG00000029075	Tnfrsf4	ACT35|CD134|Ly-70|Ox40|TXGP1L|Txgp1	tumor necrosis factor receptor superfamily, member 4	protein-coding
mm_157503.1	chrX	48594570	48594585	-	1	NA	promoter-TSS (NM_001166649)	promoter-TSS (NM_001166649)	-125	NM_001166649	208968	Mm.293819	NM_153532	ENSMUSG00000036916	Zfp280c	BC028839|Suhw3|Zfp633|Znf280c|mKIAA1584	zinc finger protein 280C	protein-coding
mm_77648.1	chr8	124563872	124563905	-	1	NA	exon (NM_007428, exon 2 of 5)	exon (NM_007428, exon 2 of 5)	5819	NM_007428	11606	Mm.301626	NM_007428	ENSMUSG00000031980	Agt	AI265500|AngI|AngII|Aogen|Serpina8	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	protein-coding
mm_127820.1	chr15	5108493	5108565	-	1	NA	promoter-TSS (NM_001163138)	promoter-TSS (NM_001163138)	4	NM_001163138	239319	Mm.31252	NM_001163138	ENSMUSG00000041849	Card6	D730008L15	caspase recruitment domain family, member 6	protein-coding
mm_148386.1	chr19	3376384	3376420	+	1	NA	intron (NM_013495, intron 13 of 18)	intron (NM_013495, intron 13 of 18)	-12455	NM_001039658	17771	Mm.209941	NM_010841	ENSMUSG00000024905	Mtl5	tesmin	metallothionein-like 5, testis-specific (tesmin)	protein-coding
mm_155797.1	chrX	98938201	98938229	+	1	NA	5' UTR (NM_207633, exon 1 of 7)	5' UTR (NM_207633, exon 1 of 7)	434	NM_207633	77929	Mm.212290	NM_207633	ENSMUSG00000047694	Yipf6	A430107J06Rik	Yip1 domain family, member 6	protein-coding
mm_23429.1	chr3	59005909	59005930	+	1	NA	Intergenic	CpG	-1059	NM_177855	329650	Mm.240059	NM_177855	ENSMUSG00000056476	Med12l	A130035F20|A630079M02|AU044581|TRALPUSH	mediator complex subunit 12-like	protein-coding
mm_111785.1	chr12	104561773	104561796	-	1	NA	Intergenic	Intergenic	-88548	NM_010351	14836	Mm.129	NM_010351	ENSMUSG00000021095	Gsc	-	goosecoid homeobox	protein-coding
mm_40058.1	chr5	33996610	33996632	+	1	NA	5' UTR (NM_001001985, exon 1 of 3)	5' UTR (NM_001001985, exon 1 of 3)	637	NM_001001985	269642	Mm.274610	NM_001001985	ENSMUSG00000048142	Nat8l	1110038O08Rik|Shati	N-acetyltransferase 8-like	protein-coding
mm_89826.1	chr10	105841422	105841436	+	1	NA	promoter-TSS (NM_207522)	promoter-TSS (NM_207522)	-49	NM_207522	216292	Mm.250875	NM_207522	ENSMUSG00000036009	Mettl25	-	methyltransferase like 25	protein-coding
mm_37022.1	chr4	114688717	114688732	-	1	NA	Intergenic	Intergenic	-132996	NR_033617	433746	Mm.388908	NR_033617	ENSMUSG00000055198	Gm12830	OTTMUSG00000008584	predicted gene 12830	ncRNA
mm_11961.1	chr2	53128866	53128870	+	1	NA	intron (NM_172409, intron 25 of 26)	intron (NM_172409, intron 25 of 26)	62319	NM_018785	56194	Mm.257474	NM_018785	ENSMUSG00000061136	Prpf40a	2810012K09Rik|FBP-11|FBP11|Fnbp11|Fnbp3	pre-mRNA processing factor 40A	protein-coding
mm_146305.1	chr18	80255345	80255374	+	1	NA	promoter-TSS (NM_001164424)	promoter-TSS (NM_001164424)	114	NM_001164420	66943	Mm.29247	NM_025861	ENSMUSG00000034006	Pqlc1	2310009N05Rik|4933425L21Rik|5730564E11Rik|C78974	PQ loop repeat containing 1	protein-coding
mm_34542.1	chr4	149518217	149518277	+	1	NA	promoter-TSS (NM_023465)	promoter-TSS (NM_023465)	6	NM_023465	67087	Mm.299735	NM_023465	ENSMUSG00000028988	Ctnnbip1	1110008O09Rik|2310001I19Rik|AW457332|Catnbip1|Icat	catenin beta interacting protein 1	protein-coding
mm_147545.1	chr18	54699138	54699176	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	87413	NR_045400	328957	Mm.402781	NR_045400		9330117O12Rik	9330117O12	RIKEN cDNA 9330117O12 gene	ncRNA
mm_63938.1	chr7	139774668	139774676	+	1	NA	Intergenic	ORR1A3|LTR|ERVL-MaLR	-4346	NR_105827	102465215		NR_105827	ENSMUSG00000098619	Mir6401	Gm27442|mmu-mir-6401	microRNA 6401	ncRNA
mm_23198.1	chr3	41408746	41408766	+	1	NA	Intergenic	Intergenic	84443	NR_040385	78706	Mm.366094	NR_040385	ENSMUSG00000097639	Platr4	C430002E04Rik	pluripotency associated transcript 4	ncRNA
mm_115553.1	chr13	8977378	8977390	-	1	NA	exon (NM_027000, exon 14 of 17)	exon (NM_027000, exon 14 of 17)	18628	NM_027000	69237	Mm.41800	NM_027000	ENSMUSG00000021149	Gtpbp4	2610028C09Rik|Crfg|Gtpbp3|NGB|Nog1	GTP binding protein 4	protein-coding
mm_26352.1	chr3	142548833	142548861	+	1	NA	3' UTR (NM_001083312, exon 11 of 11)	3' UTR (NM_001083312, exon 11 of 11)	-11205	NM_018734	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_120661.1	chr14	70545262	70545269	+	1	NA	promoter-TSS (NM_180588)	promoter-TSS (NM_180588)	14	NM_180588	72549	Mm.46742	NM_180588	ENSMUSG00000033589	Reep4	2700029E10Rik	receptor accessory protein 4	protein-coding
mm_133535.1	chr16	91048283	91048285	+	1	NA	Intergenic	Intergenic	-3905	NM_026110	67367	Mm.347	NM_026110	ENSMUSG00000022974	Paxbp1	1810007M14Rik|C21orf66|Gcfc|Gcfc1|Pax3/7bp	PAX3 and PAX7 binding protein 1	protein-coding
mm_126468.1	chr15	81259266	81259271	+	1	NA	Intergenic	RLTR53_Mm|LTR|ERVK	-7406	NR_077230	78102	Mm.296832	NR_077229		8430426J06Rik	-	RIKEN cDNA 8430426J06 gene	ncRNA
mm_109460.1	chr12	111166486	111166520	+	1	NA	5' UTR (NM_011632, exon 1 of 12)	5' UTR (NM_011632, exon 1 of 12)	133	NM_011632	22031	Mm.27431	NM_011632	ENSMUSG00000021277	Traf3	AI528849|CAP-1|CD40bp|CRAF1|LAP1|T-BAM|amn	TNF receptor-associated factor 3	protein-coding
mm_142260.1	chr17	39844132	39844161	-	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	1149	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_68664.1	chr7	118855952	118855960	-	1	NA	promoter-TSS (NM_001168218)	promoter-TSS (NM_001168218)	42	NM_001168218	66356	Mm.482278	NM_023197	ENSMUSG00000030980	Knop1	2310008H09Rik|Tsg118	lysine rich nucleolar protein 1	protein-coding
mm_23729.1	chr3	69026113	69026115	+	1	NA	intron (NM_133786, intron 13 of 23)	intron (NM_133786, intron 13 of 23)	16212	NR_029735	723949		NR_029735	ENSMUSG00000065606	Mir16-2	Mirn16-2|mir-16-2	microRNA 16-2	ncRNA
mm_76103.1	chr8	80395115	80395119	-	1	NA	Intergenic	Intergenic	-98928	NM_010369	14934	Mm.13123	NM_010369	ENSMUSG00000051839	Gypa	AI853584|CD235a|GPA	glycophorin A	protein-coding
mm_142657.1	chr17	47670690	47670701	-	1	NA	intron (NM_198421, intron 2 of 6)	intron (NM_198421, intron 2 of 6)	-16915	NR_045945	100415787	Mm.392206	NR_045945	ENSMUSG00000084880	Tomm6os	Gm14872|OTTMUSG00000018355|Prickle4os	translocase of outer mitochondrial membrane 6, opposite strand	ncRNA
mm_90995.1	chr10	13967477	13967500	-	1	NA	intron (NM_010437, intron 1 of 8)	CpG-904	1109	NM_010437	15273	Mm.42157	NM_010437	ENSMUSG00000015501	Hivep2	Gm20114|MIBP1|Schnurri-2|Shn-2	human immunodeficiency virus type I enhancer binding protein 2	protein-coding
mm_21431.1	chr2	158361462	158361467	-	1	NA	promoter-TSS (NR_015463)	promoter-TSS (NR_015463)	45	NR_015463	68108	Mm.119198	NR_015463		Snhg17	9430008C03Rik	small nucleolar RNA host gene 17	ncRNA
mm_149847.1	chr19	25052537	25052541	+	1	NA	intron (NM_028785, intron 2 of 47)	intron (NM_028785, intron 2 of 47)	53010	NM_028785	76088	Mm.102485	NM_028785	ENSMUSG00000052085	Dock8	1200017A24Rik|5830472H07Rik|A130095G14Rik|AI461977	dedicator of cytokinesis 8	protein-coding
mm_32848.1	chr4	117974983	117975003	+	1	NA	intron (NM_009176, intron 5 of 11)	intron (NM_009176, intron 5 of 11)	-45230	NM_001284192	11876	Mm.56897	NM_009711	ENSMUSG00000028539	Artn	neublastin	artemin	protein-coding
mm_18903.1	chr2	76718409	76718422	-	1	NA	exon (NM_011652, exon 300 of 313)	exon (NM_011652, exon 300 of 313)	43100	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_138392.1	chr17	35050398	35050450	+	1	NA	5' UTR (NM_033444, exon 1 of 6)	5' UTR (NM_033444, exon 1 of 6)	181	NM_033444	114584	Mm.29524	NM_033444	ENSMUSG00000007041	Clic1	Clcp|G6	chloride intracellular channel 1	protein-coding
mm_139690.1	chr17	57421692	57421702	+	1	NA	intron (NM_010130, intron 12 of 21)	Lx5|LINE|L1	63011	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_112167.1	chr12	113414397	113414408	-	1	NA	Intergenic	Intergenic	-75163	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_65516.1	chr7	25755204	25755214	-	1	NA	promoter-TSS (NM_178089)	promoter-TSS (NM_178089)	-489	NM_144922	232989	Mm.254223	NM_144922	ENSMUSG00000040725	Hnrnpul1	E130317O14Rik|E1B-AP5|E1BAP5|Hnrnpul|Hnrpul1	heterogeneous nuclear ribonucleoprotein U-like 1	protein-coding
mm_121057.1	chr14	87416611	87416655	+	1	NA	promoter-TSS (NM_001253755)	promoter-TSS (NM_001253755)	50	NM_001253755	219249	Mm.35168	NM_172605	ENSMUSG00000022019	Tdrd3	4732418C03Rik|6720468N18	tudor domain containing 3	protein-coding
mm_135642.1	chr16	52361887	52361888	-	1	NA	intron (NM_009655, intron 1 of 15)	intron (NM_009655, intron 1 of 15)	91194	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_120173.1	chr14	61046648	61046657	+	1	NA	5' UTR (NM_013869, exon 1 of 10)	5' UTR (NM_013869, exon 1 of 10)	203	NM_013869	29820	Mm.281356	NM_013869	ENSMUSG00000060548	Tnfrsf19	AL023044|AW123854|TAJ|TAJ-ALPHA|TRADE|Troy	tumor necrosis factor receptor superfamily, member 19	protein-coding
mm_3750.1	chr1	156035393	156035431	+	1	NA	promoter-TSS (NM_001160182)	promoter-TSS (NM_001160182)	-252	NM_172843	240832	Mm.253335	NM_022329	ENSMUSG00000050565	Tor1aip2	1110020D10Rik|15kDa|A130072J07|AA103493|AW060462|AW610675|C77739|Ifrg15|Lull1	torsin A interacting protein 2	protein-coding
mm_64012.1	chr7	140218259	140218286	+	1	NA	promoter-TSS (NM_172909)	promoter-TSS (NM_172909)	5	NM_172909	244233	Mm.19283	NM_172909	ENSMUSG00000025461	Cd163l1	B430307C05|E430002D04Rik|Scart1	CD163 molecule-like 1	protein-coding
mm_151785.1	chr19	5366627	5366663	-	1	NA	promoter-TSS (NM_027236)	promoter-TSS (NM_027236)	-168	NM_027236	69860	Mm.299167	NM_027236	ENSMUSG00000024841	Eif1ad	2010003J03Rik|AI131644	eukaryotic translation initiation factor 1A domain containing	protein-coding
mm_40935.1	chr5	76657674	76657722	+	1	NA	Intergenic	CpG	65984	NM_199032	381644	Mm.332452	NM_199032	ENSMUSG00000036403	Cep135	BC062951|Cep4|Gm1044	centrosomal protein 135	protein-coding
mm_44918.1	chr5	35729023	35729039	-	1	NA	5' UTR (NM_194344, exon 1 of 18)	5' UTR (NM_194344, exon 1 of 18)	245	NM_194344	231147	Mm.290429	NM_194344	ENSMUSG00000036553	Sh3tc1	4631428G15|BC024909	SH3 domain and tetratricopeptide repeats 1	protein-coding
mm_29062.1	chr3	103791223	103791318	-	1	NA	promoter-TSS (NM_010432)	promoter-TSS (NM_010432)	5	NM_001301306	15257	Mm.20827	NM_010432	ENSMUSG00000008730	Hipk1	1110062K04Rik|Myak	homeodomain interacting protein kinase 1	protein-coding
mm_90251.1	chr10	121626597	121626652	+	1	NA	promoter-TSS (NM_001081056)	promoter-TSS (NM_001081056)	-308	NM_001081056	73192	Mm.25042	NM_001081056	ENSMUSG00000034667	Xpot	1110004L07Rik|3110065H13Rik|AI452076|C79645|EXPORTIN-T	exportin, tRNA (nuclear export receptor for tRNAs)	protein-coding
mm_154527.1	chrM	13524	13536	-	1	NA	NA	Intergenic	NA	NA								
mm_51954.1	chr6	91755998	91756017	+	1	NA	3' UTR (NM_009320, exon 15 of 15)	3' UTR (NM_009320, exon 15 of 15)	51386	NM_001159507	243547	Mm.333264	NM_001033353	ENSMUSG00000030098	Grip2	-	glutamate receptor interacting protein 2	protein-coding
mm_33229.1	chr4	126764567	126764586	+	1	NA	intron (NM_001035525, intron 2 of 23)	L1M4a1|LINE|L1	10806	NM_001035526	100317	Mm.206206	NM_133886	ENSMUSG00000028830	AU040320	A730047D20Rik|AAVR|Kiaa0319l	expressed sequence AU040320	protein-coding
mm_29189.1	chr3	106547703	106547723	-	1	NA	promoter-TSS (NM_026013)	promoter-TSS (NM_026013)	-85	NM_001286986	67171	Mm.290488	NM_026013	ENSMUSG00000027900	Dram2	2010305N14Rik|2610318G18Rik|AI647667|Tmem77	DNA-damage regulated autophagy modulator 2	protein-coding
mm_16321.1	chr2	174304576	174304576	+	1	NA	intron (NM_001310085, intron 2 of 12)	(CA)n|Simple_repeat|Simple_repeat	6717	NM_001310085	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_53645.1	chr6	140623899	140623911	+	1	NA	exon (NM_009637, exon 1 of 9)	exon (NM_009637, exon 1 of 9)	403	NM_001005605	11569	Mm.86453	NM_009637	ENSMUSG00000030232	Aebp2	AU023766|B230313N05Rik	AE binding protein 2	protein-coding
mm_108267.1	chr12	78748956	78748971	+	1	NA	promoter-TSS (NM_019579)	promoter-TSS (NM_019579)	16	NM_019579	56217	Mm.425777	NM_019579	ENSMUSG00000021112	Mpp5	3830420B02Rik|AI255216|AI644496|Pals1	membrane protein, palmitoylated 5 (MAGUK p55 subfamily member 5)	protein-coding
mm_89470.1	chr10	93489060	93489076	+	1	NA	5' UTR (NM_010401, exon 1 of 20)	5' UTR (NM_010401, exon 1 of 20)	300	NM_010401	15109	Mm.13000	NM_010401	ENSMUSG00000020017	Hal	Hsd|his|histidase	histidine ammonia lyase	protein-coding
mm_14907.1	chr2	150567327	150567351	+	1	NA	Intergenic	Intergenic	-3076	NM_009977	13011	Mm.12965	NM_009977	ENSMUSG00000068129	Cst7	Cmap	cystatin F (leukocystatin)	protein-coding
mm_125336.1	chr15	38999443	38999450	+	1	NA	Intergenic	Intergenic	-6834	NM_001162494	14368	Mm.4769	NM_008056	ENSMUSG00000022297	Fzd6	Fz6	frizzled class receptor 6	protein-coding
mm_115680.1	chr13	13393395	13393423	-	1	NA	exon (NM_031999, exon 1 of 7)	exon (NM_031999, exon 1 of 7)	215	NM_031999	83924	Mm.379269	NM_031999	ENSMUSG00000021306	Gpr137b	AI788917|AU016435|AW546472|C730041E01|C80550|C80741|D13Abb1e|Tm7sf1	G protein-coupled receptor 137B	protein-coding
mm_87363.1	chr10	43901856	43901867	+	1	NA	promoter-TSS (NM_130892)	promoter-TSS (NM_130892)	54	NM_130892	170728	Mm.390253	NM_130892	ENSMUSG00000019864	Rtn4ip1	D10Ertd690e|NIMP	reticulon 4 interacting protein 1	protein-coding
mm_122524.1	chr14	47378069	47378093	-	1	NA	intron (NM_001145953, intron 1 of 5)	B1F|SINE|Alu	4221	NM_001145953	16854	Mm.248615	NM_010705	ENSMUSG00000050335	Lgals3	GBP|L-34|Mac-2|gal3	lectin, galactose binding, soluble 3	protein-coding
mm_49191.1	chr6	15185656	15185665	+	1	NA	5' UTR (NM_001286607, exon 1 of 17)	5' UTR (NM_001286607, exon 1 of 17)	154	NM_001286607	114142	Mm.332919	NM_053242	ENSMUSG00000029563	Foxp2	2810043D05Rik|AI449000|CAG-16|D0Kist7	forkhead box P2	protein-coding
mm_16136.1	chr2	170511419	170511451	+	1	NA	non-coding (NR_040367, exon 1 of 3)	non-coding (NR_040367, exon 1 of 3)	205	NM_001199902	109054	Mm.28808	NM_001013369	ENSMUSG00000052033	Pfdn4	0610025M10Rik|1810063B06Rik|C-1|C1|Pfd4	prefoldin 4	protein-coding
mm_93343.1	chr10	99759664	99759674	-	1	NA	promoter-TSS (NM_027945)	promoter-TSS (NM_027945)	-11	NM_027945	71832	Mm.483162	NM_027945	ENSMUSG00000046934	Csl	1700007H16Rik	citrate synthase like	protein-coding
mm_45332.1	chr5	65619768	65619771	-	1	NA	intron (NM_001081321, intron 29 of 31)	intron (NM_001081321, intron 29 of 31)	78087	NM_001081321	71521	Mm.278974	NM_027818	ENSMUSG00000029202	Pds5a	9030416H16Rik|E230024D05Rik|mKIAA0648	PDS5 cohesin associated factor A	protein-coding
mm_38962.1	chr4	150854931	150854941	-	1	NA	promoter-TSS (NM_133753)	promoter-TSS (NM_133753)	13	NR_040649	73348	Mm.396218	NR_040649	ENSMUSG00000078492	1700045H11Rik	-	RIKEN cDNA 1700045H11 gene	ncRNA
mm_170110.1	chr17	39845051	39845051	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	2054	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_105867.1	chr11	114217602	114217606	-	1	NA	Intergenic	Intergenic	19346	NR_045930	73536	Mm.54275	NR_045930	ENSMUSG00000078600	1700092K14Rik	-	RIKEN cDNA 1700092K14 gene	ncRNA
mm_20280.1	chr2	126890956	126890972	-	1	NA	3' UTR (NM_023220, exon 15 of 15)	3' UTR (NM_023220, exon 15 of 15)	11421	NR_106202	102466258		NR_106202	ENSMUSG00000098896	Mir3473g	Gm27751|mmu-mir-3473g	microRNA 3473g	ncRNA
mm_142290.1	chr17	40319206	40319208	-	1	NA	promoter-TSS (NM_009638)	promoter-TSS (NM_009638)	0	NM_009638	11571	Mm.16781	NM_009638	ENSMUSG00000025431	Crisp1	AW324342|Aeg1|CRISP-1	cysteine-rich secretory protein 1	protein-coding
mm_164622.1	chr17	31186621	31186656	-	1	NA	intron (NM_001163776, intron 9 of 12)	intron (NM_001163776, intron 9 of 12)	11111	NM_080727	140765	Mm.214638	NM_080727	ENSMUSG00000024034	Tmprss3	-	transmembrane protease, serine 3	protein-coding
mm_161616.1	chr16	55283043	55283043	-	1	NA	intron (NM_178720, intron 1 of 11)	(A)n|Simple_repeat|Simple_repeat	194	NM_178720	239852	Mm.245045	NM_178720	ENSMUSG00000064310	Zpld1	9430016A21Rik	zona pellucida like domain containing 1	protein-coding
mm_15050.1	chr2	152869543	152869553	+	1	NA	intron (NM_001141977, intron 3 of 17)	intron (NM_001141977, intron 3 of 17)	4481	NR_049195	100885834		NR_049195	ENSMUSG00000093746	Mir5622	Gm24421|mmu-mir-5622	microRNA 5622	ncRNA
mm_20253.1	chr2	126553263	126553271	-	1	NA	exon (NM_011978, exon 1 of 10)	exon (NM_011978, exon 1 of 10)	243	NM_011978	26458	Mm.290044	NM_011978	ENSMUSG00000027359	Slc27a2	ACSVL1|FATP2|VLCS|Vlac|Vlacs	solute carrier family 27 (fatty acid transporter), member 2	protein-coding
mm_140141.1	chr17	79980629	79980648	+	1	NA	Intergenic	Intergenic	81630	NM_144802	72692	Mm.64579	NM_144802	ENSMUSG00000024095	Hnrnpll	2510028H02Rik|2810036L13Rik|AI256697|AI852082|Hnrpll	heterogeneous nuclear ribonucleoprotein L-like	protein-coding
mm_47690.1	chr5	129670051	129670062	-	1	NA	promoter-TSS (NM_172462)	promoter-TSS (NM_172462)	32	NM_172462	22648	Mm.135067	NM_172462	ENSMUSG00000051034	Zfp11	6720465D24|Krox-6|Zfp-11	zinc finger protein 11	protein-coding
mm_61357.1	chr7	68433070	68433075	+	1	NA	Intergenic	Intergenic	15648	NR_046208	71244	Mm.410787	NR_046208	ENSMUSG00000108924	4933436H12Rik	-	RIKEN cDNA 4933436H12 gene	ncRNA
mm_72545.1	chr8	84001435	84001441	+	1	NA	promoter-TSS (NM_183097)	promoter-TSS (NM_183097)	-268	NM_183097	73453	Mm.75101	NM_183097	ENSMUSG00000046408	1700067K01Rik	-	RIKEN cDNA 1700067K01 gene	protein-coding
mm_43562.1	chr5	137630096	137630110	+	1	NA	intron (NR_033148, intron 1 of 21)	intron (NR_033148, intron 1 of 21)	980	NR_033148	100316903	Mm.200763	NR_033148		Gm20605	Lrch4-sap25	predicted gene 20605	ncRNA
mm_130856.1	chr15	102136178	102136222	-	1	NA	promoter-TSS (NM_001033277)	promoter-TSS (NM_001033277)	15	NM_001033277	223918	Mm.385009	NM_001033277	ENSMUSG00000036966	Spryd3	BC008150	SPRY domain containing 3	protein-coding
mm_72573.1	chr8	84148075	84148086	+	1	NA	promoter-TSS (NM_029045)	promoter-TSS (NM_029045)	42	NM_029045	74666	Mm.33625	NM_029045	ENSMUSG00000008129	4930432K21Rik	-	RIKEN cDNA 4930432K21 gene	protein-coding
mm_150892.1	chr19	45445461	45445542	+	1	NA	intron (NM_001286465, intron 2 of 14)	intron (NM_001286465, intron 2 of 14)	81767	NM_001037758	12234	Mm.119717	NM_009771	ENSMUSG00000025217	Btrc	Beta-Trcp1|E3RS-IkappaB|E3RSIkappaB|FWD1|Fbw1a|HOS|Slimb|b-TrCP|beta-TrCP	beta-transducin repeat containing protein	protein-coding
mm_39980.1	chr5	32459136	32459174	+	1	NA	5' UTR (NM_172707, exon 1 of 8)	5' UTR (NM_172707, exon 1 of 8)	185	NM_172707	19046	Mm.241931	NM_172707	ENSMUSG00000014956	Ppp1cb	1200010B19	protein phosphatase 1, catalytic subunit, beta isoform	protein-coding
mm_110883.1	chr12	75177326	75177359	-	1	NA	promoter-TSS (NM_172805)	promoter-TSS (NM_172805)	-10	NM_172805	238271	Mm.44465	NM_172805	ENSMUSG00000034402	Kcnh5	Eag2	potassium voltage-gated channel, subfamily H (eag-related), member 5	protein-coding
mm_100403.1	chr11	119397936	119397956	+	1	NA	Intergenic	L1Md_F2|LINE|L1	7474	NR_035453	100316690		NR_035453	ENSMUSG00000088015	Mir1932	mir-1932|mmu-mir-1932	microRNA 1932	ncRNA
mm_167240.1	chr8	19979997	19980042	+	1	NA	intron (NM_001270553, intron 6 of 9)	CpG	250443	NM_001039553	626415	Mm.425517	NM_001039553	ENSMUSG00000096265	4930467E23Rik	ENSMUSG00000074453|OTTMUSG00000018948|TSAP	RIKEN cDNA 4930467E23 gene	protein-coding
mm_23169.1	chr3	40745436	40745459	+	1	NA	promoter-TSS (NM_011020)	promoter-TSS (NM_011020)	-166	NM_011020	18415	Mm.39330	NM_011020	ENSMUSG00000025757	Hspa4l	94kDa|AI461691|APG-1|Osp94	heat shock protein 4 like	protein-coding
mm_24170.1	chr3	88568239	88568265	+	1	NA	3' UTR (NM_033526, exon 11 of 11)	3' UTR (NM_033526, exon 11 of 11)	-11419	NM_025448	66256	Mm.7091	NM_025448	ENSMUSG00000041355	Ssr2	1500032E05Rik|AI315033|AU020133|TLAP|TRAPB|TRAPbeta	signal sequence receptor, beta	protein-coding
mm_34860.1	chr4	155546976	155546992	+	1	NA	intron (NM_001160016, intron 7 of 11)	intron (NM_001160016, intron 7 of 11)	-15408	NM_138671	192185	Mm.28347	NM_138671	ENSMUSG00000029063	Nadk	4432404C02Rik|BC004012	NAD kinase	protein-coding
mm_88627.1	chr10	79881046	79881059	+	1	NA	exon (NM_011178, exon 3 of 5)	exon (NM_011178, exon 3 of 5)	1385	NM_011178	19152	Mm.2364	NM_011178	ENSMUSG00000057729	Prtn3	PR3|mPR3	proteinase 3	protein-coding
mm_52586.1	chr6	116651877	116651885	+	1	NA	exon (NM_001166580, exon 2 of 2)	exon (NM_001166580, exon 2 of 2)	1197	NM_001166580	213393	Mm.38231	NM_145980	ENSMUSG00000048489	8430408G22Rik	Depp|Fseg	RIKEN cDNA 8430408G22 gene	protein-coding
mm_98708.1	chr11	96307053	96307055	+	1	NA	promoter-TSS (NR_131758)	promoter-TSS (NR_131758)	-144	NR_131758	75395	Mm.440014	NR_131758	ENSMUSG00000085645	Hoxb5os	0610040B09Rik|AV302770|Hoxb5/6as	homeobox B5 and homeobox B6, opposite strand	ncRNA
mm_131900.1	chr16	23256933	23256953	+	1	NA	intron (NM_001252505, intron 1 of 7)	intron (NM_001252505, intron 1 of 7)	30922	NM_001252505	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_108614.1	chr12	85524654	85524664	+	1	NA	Intergenic	Intergenic	50758	NM_010234	14281	Mm.246513	NM_010234	ENSMUSG00000021250	Fos	D12Rfj1|c-fos|cFos	FBJ osteosarcoma oncogene	protein-coding
mm_110754.1	chr12	70073794	70073798	-	1	NA	intron (NM_001081453, intron 3 of 28)	intron (NM_001081453, intron 3 of 28)	29058	NM_001081453	18080	Mm.244047	NM_008697	ENSMUSG00000021068	Nin	3110068G20Rik|AI385615|AU024711|mKIAA1565	ninein	protein-coding
mm_20962.1	chr2	151959359	151959392	-	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	8242	NR_035478	100316704		NR_035478	ENSMUSG00000088491	Mir1953	mir-1953|mmu-mir-1953	microRNA 1953	ncRNA
mm_114662.1	chr13	78163098	78163106	+	1	NA	intron (NM_001163420, intron 8 of 8)	intron (NM_001163420, intron 8 of 8)	33347	NM_001347538	13865	Mm.439653	NM_010151	ENSMUSG00000069171	Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR-3|EAR3|Erbal3|SVP44|Tcfcoup1	nuclear receptor subfamily 2, group F, member 1	protein-coding
mm_91612.1	chr10	41490370	41490380	-	1	NA	promoter-TSS (NM_009213)	promoter-TSS (NM_009213)	-35	NM_009213	20598	Mm.953	NM_009213	ENSMUSG00000019822	Smpd2	AW108287|nSMase|nSMase1	sphingomyelin phosphodiesterase 2, neutral	protein-coding
mm_164187.1	chr15	77840615	77840646	-	1	NA	intron (NM_022410, intron 1 of 40)	intron (NM_022410, intron 1 of 40)	1545	NM_022410	17886	Mm.29677	NM_022410	ENSMUSG00000022443	Myh9	Fltn|Myhn-1|Myhn1|NMHCIIA|NMMHC-A|NMMHC-IIA|TU72.6	myosin, heavy polypeptide 9, non-muscle	protein-coding
mm_112716.1	chr13	19185096	19185106	+	1	NA	Intergenic	Intergenic	210712	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_4638.1	chr1	179866672	179866674	+	1	NA	Intergenic	Intergenic	-62658	NM_026375	226747	Mm.128165	NM_026375	ENSMUSG00000026491	Ahctf1	6230412P20Rik|AV011447|Elys	AT hook containing transcription factor 1	protein-coding
mm_62159.1	chr7	97162656	97162668	+	1	NA	intron (NM_001162477, intron 1 of 9)	intron (NM_001162477, intron 1 of 9)	80911	NM_010248	14389	Mm.42033	NM_010248	ENSMUSG00000004508	Gab2	AI463667|D130058I17Rik|p97	growth factor receptor bound protein 2-associated protein 2	protein-coding
mm_149550.1	chr19	12599954	12600010	+	1	NA	promoter-TSS (NM_001167907)	promoter-TSS (NM_001167907)	-2	NM_001167907	240549	Mm.302458	NM_001013762	ENSMUSG00000071633	Gm4952	EG240549	predicted gene 4952	protein-coding
mm_84369.1	chr9	64918645	64918684	-	1	NA	3' UTR (NM_001162917, exon 35 of 35)	3' UTR (NM_001162917, exon 35 of 35)	32943	NM_144813	214111	Mm.156124	NM_144813	ENSMUSG00000034452	Slc24a1	-	solute carrier family 24 (sodium/potassium/calcium exchanger), member 1	protein-coding
mm_41729.1	chr5	102481725	102481733	+	1	NA	5' UTR (NM_029270, exon 1 of 10)	5' UTR (NM_029270, exon 1 of 10)	338	NM_029270	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding
mm_53156.1	chr6	125309689	125309724	+	1	NA	intron (NM_010736, intron 6 of 9)	intron (NM_010736, intron 6 of 9)	4164	NM_010736	17000	Mm.3122	NM_010736	ENSMUSG00000030339	Ltbr	AI256028|CD18|LTbetaR|Ltar|TNF-R-III|TNFCR|TNFR-RP|TNFR2-RP|TNFRrp|Tnfbr|Tnfrsf3	lymphotoxin B receptor	protein-coding
mm_60698.1	chr7	45175365	45175382	+	1	NA	TTS (NM_001195255)	TTS (NM_001195255)	2070	NR_106022	102465638		NR_106022	ENSMUSG00000106470	Mir7055	mmu-mir-7055	microRNA 7055	ncRNA
mm_24322.1	chr3	89432900	89432933	+	1	NA	exon (NM_026869, exon 3 of 3)	exon (NM_026869, exon 3 of 3)	1896	NM_001293766	68911	Mm.22521	NM_026869	ENSMUSG00000047824	Pygo2	1190004M21Rik	pygopus 2	protein-coding
mm_131878.1	chr16	23224725	23224804	+	1	NA	promoter-TSS (NM_145933)	promoter-TSS (NM_145933)	24	NM_145933	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_65583.1	chr7	27310229	27310249	-	1	NA	exon (NM_175641, exon 27 of 33)	exon (NM_175641, exon 27 of 33)	23409	NM_001113549	108075	Mm.272251	NM_175641	ENSMUSG00000040488	Ltbp4	2310046A13Rik	latent transforming growth factor beta binding protein 4	protein-coding
mm_126876.1	chr15	89384903	89384910	+	1	NA	Intergenic	Intergenic	-1985	NM_001160178	546648	Mm.478787	NM_001160178	ENSMUSG00000091680	Klhdc7b	EG546648|Gm306	kelch domain containing 7B	protein-coding
mm_111113.1	chr12	80960545	80960559	-	1	NA	exon (NM_001177561, exon 2 of 5)	exon (NM_001177561, exon 2 of 5)	7527	NM_011387	20493	Mm.486361	NM_011387	ENSMUSG00000021135	Slc10a1	Ntcp	solute carrier family 10 (sodium/bile acid cotransporter family), member 1	protein-coding
mm_108319.1	chr12	79722382	79722392	+	1	NA	intron (NM_009014, intron 8 of 10)	intron (NM_009014, intron 8 of 10)	202346	NR_131075	77290	Mm.395042	NR_131073		9430078K24Rik	-	RIKEN cDNA 9430078K24 gene	ncRNA
mm_102040.1	chr11	51874998	51875000	-	1	NA	Intergenic	Intergenic	-17518	NM_199299	76901	Mm.259996	NM_199299	ENSMUSG00000020387	Jade2	1200017K05Rik|AI480685|Phf15|mKIAA0239	jade family PHD finger 2	protein-coding
mm_112803.1	chr13	20477500	20477510	+	1	NA	intron (NM_198093, intron 1 of 6)	intron (NM_198093, intron 1 of 6)	4515	NM_198093	140580	Mm.342392	NM_080288	ENSMUSG00000041112	Elmo1	6330578D22Rik|C230095H21Rik|CED-12	engulfment and cell motility 1	protein-coding
mm_61310.1	chr7	67958327	67958330	+	1	NA	intron (NM_010513, intron 1 of 20)	intron (NM_010513, intron 1 of 20)	6071	NM_010513	16001	Mm.275742	NM_010513	ENSMUSG00000005533	Igf1r	A330103N21Rik|CD221|D930020L01|IGF-1R|hyft	insulin-like growth factor I receptor	protein-coding
mm_89657.1	chr10	97482420	97482455	+	1	NA	5' UTR (NM_007833, exon 1 of 8)	5' UTR (NM_007833, exon 1 of 8)	106	NM_007833	13179	Mm.56769	NM_007833	ENSMUSG00000019929	Dcn	DC|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding
mm_66279.1	chr7	37769727	37769737	-	1	NA	promoter-TSS (NM_172385)	promoter-TSS (NM_172385)	20	NM_172385	243937	Mm.322505	NM_172385	ENSMUSG00000043456	Zfp536	9630010P11Rik|Znf536|mKIAA0390	zinc finger protein 536	protein-coding
mm_54685.1	chr6	39420282	39420329	-	1	NA	promoter-TSS (NM_018810)	promoter-TSS (NM_018810)	64	NM_018810	54484	Mm.270484	NM_018810	ENSMUSG00000029922	Mkrn1	RFP	makorin, ring finger protein, 1	protein-coding
mm_134963.1	chr16	31429720	31429741	-	1	NA	intron (NM_001122683, intron 1 of 6)	CpG	977	NM_001122683	71911	Mm.293470	NM_175177	ENSMUSG00000046598	Bdh1	2310032J20Rik|AI327223|Bdh	3-hydroxybutyrate dehydrogenase, type 1	protein-coding
mm_143429.1	chr17	70851076	70851087	-	1	NA	5' UTR (NM_009372, exon 1 of 3)	5' UTR (NM_009372, exon 1 of 3)	129	NM_009372	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_26001.1	chr3	135212597	135212652	+	1	NA	promoter-TSS (NM_173762)	promoter-TSS (NM_173762)	61	NM_173762	229841	Mm.161470	NM_173762	ENSMUSG00000045328	Cenpe	312kDa|AU019344|BC049989|C530022J18|CENP-E|Kif10	centromere protein E	protein-coding
mm_78850.1	chr9	44335240	44335266	+	1	NA	3' UTR (NM_010436, exon 1 of 1)	3' UTR (NM_010436, exon 1 of 1)	538	NM_010436	15270	Mm.245931	NM_010436	ENSMUSG00000049932	H2afx	AW228881|H2A.X|H2ax|Hist5-2ax|gammaH2ax	H2A histone family, member X	protein-coding
mm_45848.1	chr5	87699448	87699448	-	1	NA	promoter-TSS (NM_001286023)	promoter-TSS (NM_001286023)	-23	NM_001286021	12991	Mm.268737	NM_009972	ENSMUSG00000063157	Csn2	Csnb	casein beta	protein-coding
mm_62150.1	chr7	97131212	97131223	+	1	NA	intron (NM_001162477, intron 1 of 9)	L1_Mur1|LINE|L1	49466	NM_010248	14389	Mm.42033	NM_010248	ENSMUSG00000004508	Gab2	AI463667|D130058I17Rik|p97	growth factor receptor bound protein 2-associated protein 2	protein-coding
mm_43093.1	chr5	124451177	124451194	+	1	NA	intron (NM_001310725, intron 3 of 6)	intron (NM_001310725, intron 3 of 6)	4481	NM_001310727	67956	Mm.137966	NM_030241	ENSMUSG00000049327	Kmt5a	2410195B05Rik|AA617402|AW536475|PR-SET7|PR/SET07|Setd8	lysine methyltransferase 5A	protein-coding
mm_152339.1	chr19	9982485	9982506	-	1	NA	promoter-TSS (NM_010239)	promoter-TSS (NM_010239)	-151	NM_010239	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
mm_144749.1	chr18	35601002	35601005	+	1	NA	intron (NM_026420, intron 1 of 3)	intron (NM_026420, intron 1 of 3)	2336	NM_026420	67869	Mm.126534	NM_026420	ENSMUSG00000037058	Paip2	2310050K10Rik|AU045972	polyadenylate-binding protein-interacting protein 2	protein-coding
mm_42584.1	chr5	117319259	117319284	+	1	NA	promoter-TSS (NM_001033311)	promoter-TSS (NM_001033311)	5	NM_001033311	231668	Mm.298603	NM_001033311	ENSMUSG00000066894	Vsig10	-	V-set and immunoglobulin domain containing 10	protein-coding
mm_147206.1	chr18	37923383	37923386	-	1	NA	intron (NM_001305981, intron 1 of 28)	intron (NM_001305981, intron 1 of 28)	12092	NM_001305980	13367	Mm.195916	NM_007858	ENSMUSG00000024456	Diaph1	D18Wsu154e|Dia1|Diap1|Drf1|p140mDia	diaphanous related formin 1	protein-coding
mm_39392.1	chr5	13399752	13399765	+	1	NA	5' UTR (NM_009152, exon 1 of 17)	5' UTR (NM_009152, exon 1 of 17)	449	NM_009152	20346	Mm.372039	NM_009152	ENSMUSG00000028883	Sema3a	Hsema-I|SEMA1|SemD|Semad|coll-1	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	protein-coding
mm_122200.1	chr14	31781588	31781596	-	1	NA	intron (NM_001024604, intron 1 of 27)	intron (NM_001024604, intron 1 of 27)	48823	NM_001024604	105522	Mm.37660	NM_001024604	ENSMUSG00000014496	Ankrd28	AI465466|AI604979|E430019N21Rik|mKIAA0379	ankyrin repeat domain 28	protein-coding
mm_22840.1	chr3	27938610	27938634	+	1	NA	promoter-TSS (NM_001164056)	promoter-TSS (NM_001164056)	-58	NM_001164056	18805	Mm.212039	NM_008875	ENSMUSG00000027695	Pld1	AA536939|C85393|Pld1a|Pld1b|mPLD1	phospholipase D1	protein-coding
mm_136176.1	chr16	88812233	88812236	-	1	NA	promoter-TSS (NR_045150)	promoter-TSS (NR_045150)	-14	NR_045150	433047	Mm.298027	NR_045150		Gm20741	-	keratin associated protein pseudogene	pseudo
mm_8631.1	chr1	156303573	156303577	-	1	NA	promoter-TSS (NM_001277730)	promoter-TSS (NM_001277730)	31	NM_001277730	214575	Mm.252800	NM_001134741	ENSMUSG00000060985	Tdrd5	Gm103	tudor domain containing 5	protein-coding
mm_143826.1	chr17	84004029	84004041	-	1	NA	intron (NR_130994, intron 1 of 1)	MLT1J-int|LTR|ERVL-MaLR	5483	NR_130994	78148	Mm.243918	NR_130994		8430430B14Rik	-	RIKEN cDNA 8430430B14 gene	ncRNA
mm_30105.1	chr3	138526944	138526963	-	1	NA	promoter-TSS (NM_001313980)	promoter-TSS (NM_001313980)	-315	NM_001313980	13684	Mm.3941	NM_007917	ENSMUSG00000028156	Eif4e	EG668879|Eif4e-ps|If4e|eIF-4E	eukaryotic translation initiation factor 4E	protein-coding
mm_33060.1	chr4	123201451	123201493	+	1	NA	promoter-TSS (NM_001085502)	promoter-TSS (NM_001085502)	-81	NM_001085502	230718	Mm.354635	NM_001085502	ENSMUSG00000054958	Nt5c1a	Cn1a|Gm49	5'-nucleotidase, cytosolic IA	protein-coding
mm_66521.1	chr7	45124356	45124399	-	1	NA	promoter-TSS (NM_013725)	promoter-TSS (NM_013725)	12	NM_013725	27207	Mm.196538	NM_013725	ENSMUSG00000003429	Rps11	-	ribosomal protein S11	protein-coding
mm_133978.1	chr16	4523560	4523573	-	1	NA	promoter-TSS (NM_175347)	promoter-TSS (NM_175347)	-491	NM_001347162	106393	Mm.35811	NM_175347	ENSMUSG00000022519	Srl	9830004M20Rik|AW108387|sar	sarcalumenin	protein-coding
mm_155921.1	chrX	102119458	102119490	+	1	NA	promoter-TSS (NM_027181)	promoter-TSS (NM_027181)	9	NM_027181	69713	Mm.371635	NM_027181	ENSMUSG00000079480	Pin4	2410002I22Rik|EPVH|Par14	protein (peptidyl-prolyl cis/trans isomerase) NIMA-interacting, 4 (parvulin)	protein-coding
mm_163916.1	chr14	36094961	36094969	+	1	NA	promoter-TSS (NM_175008)	promoter-TSS (NM_175008)	0	NM_175008	218921	Mm.212464	NM_175008	ENSMUSG00000096405	4930474N05Rik	-	RIKEN cDNA 4930474N05 gene	protein-coding
mm_124212.1	chr14	99349070	99349086	-	1	NA	Intergenic	Intergenic	50387	NM_009769	12224	Mm.30262	NM_009769	ENSMUSG00000005148	Klf5	4930520J07Rik|Bteb2|CKLF|IKLF	Kruppel-like factor 5	protein-coding
mm_172291.1	chr6	95800637	95800642	-	1	NA	Intergenic	L1Md_T|LINE|L1	-81793	NM_011507	20917	Mm.371585	NM_011507	ENSMUSG00000061838	Suclg2	AF171077|AW556404|D6Wsu120e|G-SCS|GTPSCS|SCS-betaG	succinate-Coenzyme A ligase, GDP-forming, beta subunit	protein-coding
mm_16537.1	chr2	181601329	181601344	+	1	NA	promoter-TSS (NM_133701)	promoter-TSS (NM_133701)	17	NM_133701	68879	Mm.292001	NM_133701	ENSMUSG00000002455	Prpf6	1190003A07Rik|2610031L17Rik|ANT-1|U5-102K	pre-mRNA splicing factor 6	protein-coding
mm_5641.1	chr1	40448368	40448400	-	1	NA	TTS (NM_010743)	TTS (NM_010743)	8755	NM_010743	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_39169.1	chr4	155669172	155669231	-	1	NA	promoter-TSS (NM_001256107)	promoter-TSS (NM_001256107)	53	NM_001256108	76580	Mm.235738	NM_145124	ENSMUSG00000029060	Mib2	2210008I11Rik|Zzank1|skd	mindbomb E3 ubiquitin protein ligase 2	protein-coding
mm_134870.1	chr16	28707329	28707330	-	1	NA	intron (NM_010199, intron 2 of 5)	intron (NM_010199, intron 2 of 5)	45914	NM_010199	14167	Mm.7996	NM_010199	ENSMUSG00000022523	Fgf12	AV114868|B230343J05Rik|FGF-12|FHF-1|Fhf1	fibroblast growth factor 12	protein-coding
mm_118917.1	chr14	26766173	26766202	+	1	NA	Intergenic	Intergenic	-96341	NM_178668	211948	Mm.290758	NM_178668	ENSMUSG00000043702	Pde12	2'-PDE|E430028B21Rik	phosphodiesterase 12	protein-coding
mm_156252.1	chrX	136666388	136666479	+	1	NA	promoter-TSS (NM_001029978)	promoter-TSS (NM_001029978)	58	NM_001029978	594844	Mm.260515	NM_001029978	ENSMUSG00000044550	Tceal3	1100001D19Rik	transcription elongation factor A (SII)-like 3	protein-coding
mm_151566.1	chr19	60756167	60756182	+	1	NA	5' UTR (NM_178421, exon 1 of 1)	5' UTR (NM_178421, exon 1 of 1)	187	NM_178421	332397	Mm.186390	NM_178421	ENSMUSG00000072437	Nanos1	NOS-1	nanos homolog 1 (Drosophila)	protein-coding
mm_10090.1	chr2	3284170	3284182	+	1	NA	promoter-TSS (NM_008708)	promoter-TSS (NM_008708)	-36	NM_008708	18108	Mm.65021	NM_008708	ENSMUSG00000026643	Nmt2	A930001K02Rik|AI605445|AU044698|hNMT-2	N-myristoyltransferase 2	protein-coding
mm_90098.1	chr10	116964780	116964786	+	1	NA	promoter-TSS (NR_027847)	promoter-TSS (NR_027847)	43	NR_027847	103175	Mm.27138	NR_027846	ENSMUSG00000031294	D630029K05Rik	AI314111|AI875589	RIKEN cDNA D630029K05 gene	ncRNA
mm_37825.1	chr4	131937166	131937183	-	1	NA	intron (NM_001128606, intron 13 of 17)	intron (NM_001128606, intron 13 of 17)	15403	NM_001201367	623230	Mm.421179	NM_001201367	ENSMUSG00000070720	Tmem200b	EG623230	transmembrane protein 200B	protein-coding
mm_51207.1	chr6	71329255	71329265	+	1	NA	intron (NM_009858, intron 2 of 5)	ID_B1|SINE|B4	6448	NM_009858	12526	Mm.333148	NM_009858	ENSMUSG00000053044	Cd8b1	Cd8b|Ly-3|Ly-C|Lyt-3	CD8 antigen, beta chain 1	protein-coding
mm_142567.1	chr17	46674299	46674323	-	1	NA	promoter-TSS (NM_144857)	promoter-TSS (NM_144857)	-56	NM_144857	224823	Mm.45101	NM_144857	ENSMUSG00000023971	Rrp36	-	ribosomal RNA processing 36 homolog (S. cerevisiae)	protein-coding
mm_5950.1	chr1	56899091	56899100	-	1	NA	exon (NM_139146, exon 4 of 11)	exon (NM_139146, exon 4 of 11)	72239	NM_139146	212712	Mm.145599	NM_139146	ENSMUSG00000038331	Satb2	mKIAA1034	special AT-rich sequence binding protein 2	protein-coding
mm_133523.1	chr16	90831216	90831224	+	1	NA	non-coding (NR_133572, exon 1 of 6)	non-coding (NR_133572, exon 1 of 6)	361	NM_001316761	70967	Mm.253077	NM_027627	ENSMUSG00000039903	Eva1c	1700092M14Rik|4931408A02Rik|Fam176c	eva-1 homolog C (C. elegans)	protein-coding
mm_104661.1	chr11	97629260	97629280	-	1	NA	exon (NM_175332, exon 1 of 1)	exon (NM_175332, exon 1 of 1)	446	NM_175332	103551	Mm.24506	NM_175332	ENSMUSG00000043439	Epop	AA409164|AI413509|AW539173|E13|E130012A19Rik|esPRC2p48	elongin BC and polycomb repressive complex 2 associated protein	protein-coding
mm_72536.1	chr8	83996341	83996371	+	1	NA	TTS (NM_008854)	TTS (NM_008854)	-1316	NM_001081415	666704	Mm.298091	NM_001081415	ENSMUSG00000079003	Samd1	AA589507	sterile alpha motif domain containing 1	protein-coding
mm_161144.1	chr13	22244238	22244238	+	1	NA	promoter-TSS (NM_001080972)	promoter-TSS (NM_001080972)	23	NM_001080972	626299	Mm.436604	NM_001080972	ENSMUSG00000069297	Vmn1r194	Gm11294|OTTMUSG00000000480	vomeronasal 1 receptor 194	protein-coding
mm_129450.1	chr15	78561404	78561417	-	1	NA	3' UTR (NM_009008, exon 7 of 7)	3' UTR (NM_009008, exon 7 of 7)	11373	NM_009008	19354	Mm.1972	NM_009008	ENSMUSG00000033220	Rac2	AI323801|AI452260	RAS-related C3 botulinum substrate 2	protein-coding
mm_5354.1	chr1	25615532	25615540	-	1	NA	intron (NM_175642, intron 2 of 30)	intron (NM_175642, intron 2 of 30)	214171	NM_175642	210933	Mm.336569	NM_175642	ENSMUSG00000033569	Adgrb3	A830096D10Rik|Bai3	adhesion G protein-coupled receptor B3	protein-coding
mm_18346.1	chr2	58157110	58157121	-	1	NA	intron (NM_139200, intron 1 of 7)	intron (NM_139200, intron 1 of 7)	3007	NM_139200	227929	Mm.273905	NM_139200	ENSMUSG00000026832	Cytip	A130053M09Rik|AI462064|C80816|Cbp|Cybr|Pscdbp	cytohesin 1 interacting protein	protein-coding
mm_86671.1	chr10	18055712	18055790	+	1	NA	promoter-TSS (NM_001111065)	promoter-TSS (NM_001111065)	-189	NM_009048	19707	Mm.4479	NM_009048	ENSMUSG00000019854	Reps1	BB161292	RalBP1 associated Eps domain containing protein	protein-coding
mm_104858.1	chr11	99374896	99374909	-	1	NA	promoter-TSS (NM_027574)	promoter-TSS (NM_027574)	1	NM_027574	70843	Mm.180256	NM_027574	ENSMUSG00000055937	Krt28	4733401L19Rik|Krt25d	keratin 28	protein-coding
mm_173127.1	chrX	170005272	170005284	-	1	NA	Intergenic	PB1D7|SINE|Alu	-26361	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_127223.1	chr15	99393612	99393637	+	1	NA	intron (NM_001171035, intron 1 of 9)	intron (NM_001171035, intron 1 of 9)	405	NM_001171035	110213	Mm.16769	NM_026669	ENSMUSG00000023010	Tmbim6	5031406P05Rik|Bi1|Tegt	transmembrane BAX inhibitor motif containing 6	protein-coding
mm_4650.1	chr1	180333888	180333910	+	1	NA	exon (NM_001081175, exon 2 of 8)	exon (NM_001081175, exon 2 of 8)	-3350	NR_003623	277333	Mm.389223	NM_199472		Gm5069	EG277333	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_70394.1	chr8	11036228	11036239	+	1	NA	intron (NR_046017, intron 1 of 4)	intron (NR_046017, intron 1 of 4)	-27803	NM_001081212	384783	Mm.407207	NM_001081212	ENSMUSG00000038894	Irs2	Irs-2	insulin receptor substrate 2	protein-coding
mm_66368.1	chr7	43553184	43553199	-	1	NA	Intergenic	L1M3|LINE|L1	-9179	NM_001008549	210104	Mm.333821	NM_001008549	ENSMUSG00000056592	Zfp658	-	zinc finger protein 658	protein-coding
mm_142958.1	chr17	56120349	56120366	-	1	NA	exon (NM_029796, exon 2 of 2)	exon (NM_029796, exon 2 of 2)	1589	NM_029796	76905	Mm.348025	NM_029796	ENSMUSG00000037095	Lrg1	1300008B03Rik|2310031E04Rik|Lrg|Lrhg	leucine-rich alpha-2-glycoprotein 1	protein-coding
mm_23985.1	chr3	86104200	86104217	+	1	NA	exon (NM_001082414, exon 5 of 15)	exon (NM_001082414, exon 5 of 15)	19774	NM_001082414	27059	Mm.2454	NM_012059	ENSMUSG00000028082	Sh3d19	AW011754|Kryn	SH3 domain protein D19	protein-coding
mm_119176.1	chr14	32165759	32165767	+	1	NA	promoter-TSS (NM_019744)	promoter-TSS (NM_019744)	-26	NM_019744	27057	Mm.371598	NM_019744	ENSMUSG00000056234	Ncoa4	ARA70|Rfg	nuclear receptor coactivator 4	protein-coding
mm_105740.1	chr11	109362466	109362475	-	1	NA	promoter-TSS (NM_010303)	promoter-TSS (NM_010303)	-324	NM_010303	14674	Mm.193925	NM_010303	ENSMUSG00000020611	Gna13	AU024132|AU043124|Galpha13	guanine nucleotide binding protein, alpha 13	protein-coding
mm_107843.1	chr12	69302343	69302361	+	1	NA	exon (NM_027117, exon 3 of 13)	exon (NM_027117, exon 3 of 13)	5671	NM_027117	69554	Mm.234368	NM_027117	ENSMUSG00000020978	Klhdc2	2310022K15Rik|D12Ertd522e|HCLP-1|LCP	kelch domain containing 2	protein-coding
mm_15113.1	chr2	153649521	153649529	+	1	NA	promoter-TSS (NM_010068)	promoter-TSS (NM_010068)	76	NM_001271747	13436	Mm.89772	NM_010068	ENSMUSG00000027478	Dnmt3b	MmuIIIB	DNA methyltransferase 3B	protein-coding
mm_37719.1	chr4	129555785	129555815	-	1	NA	intron (NM_001162432, intron 8 of 12)	intron (NM_001162432, intron 8 of 12)	2011	NR_106199	102465997		NR_106199	ENSMUSG00000099070	Mir8119	Gm27567|mmu-mir-8119	microRNA 8119	ncRNA
mm_115283.1	chr13	111807838	111807860	+	1	NA	intron (NM_011945, intron 1 of 19)	CpG	1134	NM_011945	26401	Mm.15918	NM_011945	ENSMUSG00000021754	Map3k1	MAPKKK1|MEKK1|Mekk	mitogen-activated protein kinase kinase kinase 1	protein-coding
mm_23153.1	chr3	40531144	40531156	+	1	NA	Intergenic	Intergenic	-8238	NR_040445	100040882	Mm.272869	NR_040445	ENSMUSG00000037884	1700017G19Rik	-	RIKEN cDNA 1700017G19 gene	ncRNA
mm_21312.1	chr2	157098593	157098624	-	1	NA	3' UTR (NM_001139520, exon 17 of 17)	3' UTR (NM_001139520, exon 17 of 17)	11553	NM_001177439	383766	Mm.480305	NM_001177439	ENSMUSG00000074628	Tldc2	Gm1332	TBC/LysM associated domain containing 2	protein-coding
mm_103143.1	chr11	70239708	70239712	-	1	NA	exon (NM_173742, exon 1 of 3)	exon (NM_173742, exon 1 of 3)	142	NM_173742	52898	Mm.29852	NM_173742	ENSMUSG00000040904	Rnasek	2310033H11Rik|AA571397|D11Bwg0434e	ribonuclease, RNase K	protein-coding
mm_58880.1	chr7	16993978	16994039	+	1	NA	promoter-TSS (NM_001101535)	promoter-TSS (NM_001101535)	-580	NM_001101535	434130	Mm.459162	NM_001101535	ENSMUSG00000041117	Ccdc8	ENSMUSG00000041117	coiled-coil domain containing 8	protein-coding
mm_112029.1	chr12	111485977	111486001	-	1	NA	promoter-TSS (NM_001033248)	promoter-TSS (NM_001033248)	-166	NM_001033248	212539	Mm.81916	NM_001033248	ENSMUSG00000010529	Gm266	-	predicted gene 266	protein-coding
mm_75089.1	chr8	33929979	33930009	-	1	NA	promoter-TSS (NM_019733)	promoter-TSS (NM_019733)	-131	NM_001042675	19663	Mm.323997	NM_019733	ENSMUSG00000031586	Rbpms	2010300K22Rik|2700019M19Rik|AU017537|RBP-MS|hermes	RNA binding protein gene with multiple splicing	protein-coding
mm_63634.1	chr7	128523616	128523647	+	1	NA	promoter-TSS (NM_013863)	promoter-TSS (NM_013863)	48	NM_013863	29810	Mm.84073	NM_013863	ENSMUSG00000030847	Bag3	AA407278|Bis|mg638	BCL2-associated athanogene 3	protein-coding
mm_159442.1	chr3	126943471	126943471	-	1	NA	promoter-TSS (NM_001034168)	promoter-TSS (NM_001034168)	-85	NM_001034168	109676	Mm.220242	NM_178655	ENSMUSG00000032826	Ank2	100043364|AI835472|AW491075|Ank-2|Gm4392	ankyrin 2, brain	protein-coding
mm_160931.1	chr11	90548910	90548910	-	1	NA	exon (NM_011505, exon 13 of 18)	exon (NM_011505, exon 13 of 18)	89198	NM_011505	20913	Mm.207203	NM_011505	ENSMUSG00000020546	Stxbp4	6030470M02Rik|Synip	syntaxin binding protein 4	protein-coding
mm_171998.1	chr6	104385374	104385382	-	1	NA	Intergenic	L1Md_T|LINE|L1	-107666	NM_017383	53870	Mm.321671	NM_017383	ENSMUSG00000030092	Cntn6	NB-3	contactin 6	protein-coding
mm_29273.1	chr3	107517912	107517986	-	1	NA	promoter-TSS (NM_001293689)	promoter-TSS (NM_001293689)	69	NM_001293689	229706	Mm.212867	NM_172271	ENSMUSG00000027894	Slc6a17	D130012J15Rik|Ntt4	solute carrier family 6 (neurotransmitter transporter), member 17	protein-coding
mm_41692.1	chr5	100643357	100643368	+	1	NA	Intergenic	Intergenic	30894	NM_027978	71883	Mm.260661	NM_027978	ENSMUSG00000029319	Coq2	2310002F18Rik|PHB:PPT	coenzyme Q2 4-hydroxybenzoate polyprenyltransferase	protein-coding
mm_228.1	chr1	17727035	17727061	+	1	NA	promoter-TSS (NM_031402)	promoter-TSS (NM_031402)	-369	NM_031402	83691	Mm.289625	NM_031402	ENSMUSG00000025776	Crispld1	Cocoacrisp|Lcrisp1	cysteine-rich secretory protein LCCL domain containing 1	protein-coding
mm_84957.1	chr9	83441066	83441110	-	1	NA	promoter-TSS (NM_027448)	promoter-TSS (NM_027448)	11	NM_027448	75782	Mm.199698	NM_027448	ENSMUSG00000032258	Lca5	4930431B11Rik|5730406O13Rik|AV274874|ORF64	Leber congenital amaurosis 5 (human)	protein-coding
mm_50700.1	chr6	52079134	52079168	+	1	NA	Intergenic	Intergenic	-23798	NR_110440	102635415	Mm.333063	NR_110440	ENSMUSG00000085412	Halr1	Gm15055|Haunt|Linchoxa1|OTTMUSG00000018881|linc-Evx1|linc-Hoxa1|linc1547	Hoxa adjacent long noncoding RNA 1	ncRNA
mm_26842.1	chr3	14766491	14766491	-	1	NA	3' UTR (NM_001083957, exon 7 of 7)	3' UTR (NM_001083957, exon 7 of 7)	11969	NM_001083957	12346	Mm.273195	NM_009799	ENSMUSG00000027556	Car1	AW555628|Ca1|Car-1	carbonic anhydrase 1	protein-coding
mm_75827.1	chr8	70488512	70488521	-	1	NA	Intergenic	CpG	-1158	NM_182991	67937	Mm.23002	NM_182991	ENSMUSG00000035964	Tmem59l	5330410G16Rik	transmembrane protein 59-like	protein-coding
mm_67115.1	chr7	70361515	70361523	-	1	NA	promoter-TSS (NM_009697)	promoter-TSS (NM_009697)	-926	NM_009697	11819	Mm.158143	NM_009697	ENSMUSG00000030551	Nr2f2	2700033K02Rik|9430015G03Rik|ARP-1|Aporp1|COUP-TF2|COUP-TFII|COUPTFB|EAR3|SVP40|Tcfcoup2	nuclear receptor subfamily 2, group F, member 2	protein-coding
mm_152288.1	chr19	8984426	8984437	-	1	NA	Intergenic	Intergenic	-4853	NR_104460	66395	Mm.203866	NM_009643	ENSMUSG00000069833	Ahnak	DY6	AHNAK nucleoprotein (desmoyokin)	protein-coding
mm_125551.1	chr15	58648517	58648539	+	1	NA	Intergenic	Intergenic	174899	NM_175212	74868	Mm.293754	NM_175212	ENSMUSG00000062373	Tmem65	2610029O13Rik|4930438D12Rik	transmembrane protein 65	protein-coding
mm_168511.1	chr1	156523997	156524011	+	1	NA	Intergenic	Intergenic	-34783	NM_009595	11352	Mm.329515	NM_009595	ENSMUSG00000026596	Abl2	AA536808|Abll|Arg	v-abl Abelson murine leukemia viral oncogene 2 (arg, Abelson-related gene)	protein-coding
mm_102369.1	chr11	58452920	58452950	-	1	NA	promoter-TSS (NM_207527)	promoter-TSS (NM_207527)	31	NM_207527	403200	Mm.60809	NM_207527	ENSMUSG00000052642	4930504O13Rik	Gm524|Lypd9	RIKEN cDNA 4930504O13 gene	protein-coding
mm_104751.1	chr11	98463620	98463626	-	1	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	16789	NM_010346	14786	Mm.276702	NM_010346	ENSMUSG00000019312	Grb7	mKIAA4028	growth factor receptor bound protein 7	protein-coding
mm_154164.1	chr19	58671833	58671866	-	1	NA	exon (NM_026925, exon 3 of 13)	exon (NM_026925, exon 3 of 13)	1484	NM_026925	69060	Mm.20407	NM_026925	ENSMUSG00000046008	Pnlip	1810007A24Rik|PL|PTL	pancreatic lipase	protein-coding
mm_113174.1	chr13	24813730	24813762	+	1	NA	TTS (NM_024473)	TTS (NM_024473)	12089	NM_024473	79555	Mm.266668	NM_024473	ENSMUSG00000019132	BC005537	8030460C05Rik|C78201	cDNA sequence BC005537	protein-coding
mm_47797.1	chr5	132488527	132488539	-	1	NA	intron (NM_177047, intron 1 of 18)	intron (NM_177047, intron 1 of 18)	53810	NM_177047	319974	Mm.409595	NM_177047	ENSMUSG00000029673	Auts2	2700063G02Rik|A730011F23Rik|D830032G16Rik	autism susceptibility candidate 2	protein-coding
mm_36006.1	chr4	56789211	56789214	-	1	NA	intron (NM_026079, intron 10 of 36)	intron (NM_026079, intron 10 of 36)	-13117	NM_001081420	230234	Mm.268148	NM_001081420	ENSMUSG00000038827	Fam206a	simiate	family with sequence similarity 206, member A	protein-coding
mm_40105.1	chr5	34660362	34660411	+	1	NA	promoter-TSS (NM_019497)	promoter-TSS (NM_019497)	7	NM_019497	14772	Mm.117076	NM_019497	ENSMUSG00000052783	Grk4	A830025H08Rik|GRK|Gprk2l|Gprk4	G protein-coupled receptor kinase 4	protein-coding
mm_23208.1	chr3	41563357	41563392	+	1	NA	promoter-TSS (NM_001130185)	promoter-TSS (NM_001130185)	-9	NM_172303	269424	Mm.286285	NM_172303	ENSMUSG00000025764	Jade1	AU041499|D530048A03Rik|Phf17|mKIAA1807	jade family PHD finger 1	protein-coding
mm_104466.1	chr11	95225536	95225541	-	1	NA	Intergenic	Intergenic	-35991	NM_053093	93670	Mm.40085	NM_053093	ENSMUSG00000020872	Tac4	AW489379|PPT-C	tachykinin 4	protein-coding
mm_76341.1	chr8	84721784	84721823	-	1	NA	exon (NM_010906, exon 7 of 9)	exon (NM_010906, exon 7 of 9)	20346	NM_008535	17095	Mm.4925	NM_008535	ENSMUSG00000034041	Lyl1	Lyl-1|bHLHa18	lymphoblastomic leukemia 1	protein-coding
mm_47290.1	chr5	122234653	122234659	-	1	NA	intron (NM_028752, intron 3 of 6)	B4A|SINE|B4	24369	NM_028752	74096	Mm.28804	NM_028752	ENSMUSG00000064267	Hvcn1	0610039P13Rik|AI450555|BTS|HV1|Vsop.|mVSOP	hydrogen voltage-gated channel 1	protein-coding
mm_99092.1	chr11	99857916	99857918	+	1	NA	promoter-TSS (NM_001205030)	promoter-TSS (NM_001205030)	0	NM_001205030	432600	Mm.60039	NM_001205030	ENSMUSG00000069717	Gm11568	OTTMUSG00000002207	predicted gene 11568	protein-coding
mm_19350.1	chr2	90917840	90917871	-	1	NA	exon (NM_025576, exon 1 of 5)	exon (NM_025576, exon 1 of 5)	195	NM_025576	66461	Mm.23926	NM_025576		Ptpmt1	1110001D10Rik|2810004N20Rik|PLIP	protein tyrosine phosphatase, mitochondrial 1	protein-coding
mm_51913.1	chr6	91233479	91233492	+	1	NA	exon (NM_001081437, exon 2 of 17)	exon (NM_001081437, exon 2 of 17)	20721	NM_007992	14115	Mm.249146	NM_007992	ENSMUSG00000064080	Fbln2	5730577E14Rik|FIBL-2	fibulin 2	protein-coding
mm_77372.1	chr8	119828239	119828276	-	1	NA	intron (NM_028071, intron 2 of 3)	intron (NM_028071, intron 2 of 3)	12322	NM_028071	72042	Mm.393405	NM_028071	ENSMUSG00000031827	Cotl1	1810074P22Rik|2010004C08Rik|Clp	coactosin-like 1 (Dictyostelium)	protein-coding
mm_161284.1	chr14	25651922	25651922	+	1	NA	exon (NM_183208, exon 15 of 24)	exon (NM_183208, exon 15 of 24)	-42248	NM_134084	105675	Mm.41656	NM_134084	ENSMUSG00000021868	Ppif	AW457192|CyP-D|CyP-F|CypD|PPIase	peptidylprolyl isomerase F (cyclophilin F)	protein-coding
mm_6222.1	chr1	66863342	66863350	-	1	NA	promoter-TSS (NM_007381)	promoter-TSS (NM_007381)	-37	NM_007381	11363	Mm.2445	NM_007381	ENSMUSG00000026003	Acadl	AA960361|AU018452|C79855|LCAD	acyl-Coenzyme A dehydrogenase, long-chain	protein-coding
mm_48144.1	chr5	137150553	137150567	-	1	NA	Intergenic	Intergenic	-34353	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_128173.1	chr15	34443177	34443204	-	1	NA	promoter-TSS (NR_028101)	promoter-TSS (NR_028101)	35	NM_009083	19946	Mm.358632	NM_009083	ENSMUSG00000058600	Rpl30	-	ribosomal protein L30	protein-coding
mm_7533.1	chr1	124414598	124414645	-	1	NA	Intergenic	RSINE1|SINE|B4	-369062	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_89059.1	chr10	82887656	82887668	+	1	NA	intron (NM_001042513, intron 13 of 14)	intron (NM_001042513, intron 13 of 14)	21036	NM_025499	66341	Mm.443284	NM_025499	ENSMUSG00000109864	Eid3	1700027M21Rik|NS4EB	EP300 interacting inhibitor of differentiation 3	protein-coding
mm_114058.1	chr13	54371442	54371466	+	1	NA	5' UTR (NM_009946, exon 1 of 4)	5' UTR (NM_009946, exon 1 of 4)	105	NM_009946	12890	Mm.268902	NM_009946	ENSMUSG00000025867	Cplx2	921-L|AI413745|AW492120	complexin 2	protein-coding
mm_165998.1	chr4	115004746	115004749	+	1	NA	intron (NM_001304559, intron 2 of 15)	intron (NM_001304559, intron 2 of 15)	4629	NM_001304555	20460	Mm.3988	NM_009185	ENSMUSG00000028718	Stil	Sil	Scl/Tal1 interrupting locus	protein-coding
mm_46044.1	chr5	92042631	92042701	-	1	NA	promoter-TSS (NM_001276315)	promoter-TSS (NM_001276315)	30	NM_001276315	53886	Mm.44963	NM_016912	ENSMUSG00000029403	Cdkl2	5330436L21Rik|AI505225|KKIAMRE|Kkm	cyclin-dependent kinase-like 2 (CDC2-related kinase)	protein-coding
mm_93860.1	chr10	122857398	122857442	-	1	NA	intron (NM_176919, intron 5 of 8)	intron (NM_176919, intron 5 of 8)	128304	NR_029527	387251		NR_029527	ENSMUSG00000065406	Mirlet7i	Mirnlet7i|let-7i|mmu-let-7i	microRNA let7i	ncRNA
mm_26135.1	chr3	137910671	137910683	+	1	NA	Intergenic	Intergenic	-7878	NM_019920	56692	Mm.331392	NM_019920	ENSMUSG00000091512	Lamtor3	AW556229|Map2k1ip1|Mapbp|Mapksp1|Mp1	late endosomal/lysosomal adaptor, MAPK and MTOR activator 3	protein-coding
mm_7598.1	chr1	125913104	125913118	-	1	NA	promoter-TSS (NM_145100)	promoter-TSS (NM_145100)	-183	NM_001311089	72585	Mm.490405	NM_145100	ENSMUSG00000026344	Lypd1	2700050C12Rik|AI853408|C530008O16Rik|Lynx2|Lypdc1	Ly6/Plaur domain containing 1	protein-coding
mm_144343.1	chr18	15150275	15150289	+	1	NA	intron (NM_134112, intron 1 of 4)	CpG	1164	NM_134112	106931	Mm.329299	NM_134112	ENSMUSG00000036225	Kctd1	4933402K10Rik|AI661543|AW553000	potassium channel tetramerisation domain containing 1	protein-coding
mm_119649.1	chr14	52014929	52014949	+	1	NA	promoter-TSS (NM_001253695)	promoter-TSS (NM_001253695)	-381	NM_001253695	69890	Mm.475652	NM_027248	ENSMUSG00000049295	Zfp219	2010302A17Rik	zinc finger protein 219	protein-coding
mm_131025.1	chr16	3563827	3563831	+	1	NA	Intergenic	Intergenic	-28569	NM_146860	258859	Mm.377723	NM_146860	ENSMUSG00000051003	Olfr161	MOR131-1|OR912-47M6	olfactory receptor 161	protein-coding
mm_125150.1	chr15	30646734	30646775	+	1	NA	intron (NM_008729, intron 6 of 22)	CpG	-392372	NR_045186	73784	Mm.66947	NR_045186		4930430F21Rik	-	RIKEN cDNA 4930430F21 gene	ncRNA
mm_163106.1	chr11	69921401	69921403	-	1	NA	promoter-TSS (NM_001166592)	promoter-TSS (NM_001166592)	-16	NM_181582	276770	Mm.18026	NM_181582	ENSMUSG00000078812	Eif5a	AA410058|D19Wsu54e|Eif4d|Eif5a1|eIF-4D|eIF-5A|eIF-5A-1|eIF-5A1	eukaryotic translation initiation factor 5A	protein-coding
mm_136880.1	chr17	13008190	13008192	+	1	NA	exon (NM_013671, exon 2 of 5)	exon (NM_013671, exon 2 of 5)	352	NM_013671	20656	Mm.290876	NM_013671	ENSMUSG00000006818	Sod2	MnSOD|Sod-2	superoxide dismutase 2, mitochondrial	protein-coding
mm_95924.1	chr11	58286462	58286478	+	1	NA	Intergenic	Intergenic	-20599	NM_182996	103836	Mm.41440	NM_182996	ENSMUSG00000037243	Zfp692	AI746306|AI839920|Zfp692-ps|Znf692	zinc finger protein 692	protein-coding
mm_133070.1	chr16	58670507	58670555	+	1	NA	exon (NM_007757, exon 1 of 7)	exon (NM_007757, exon 1 of 7)	323	NM_007757	12892	Mm.291519	NM_007757	ENSMUSG00000022742	Cpox	CPX|Cpo|HCP|cac|nct	coproporphyrinogen oxidase	protein-coding
mm_54636.1	chr6	38745749	38745758	-	1	NA	intron (NM_001294144, intron 4 of 14)	intron (NM_001294144, intron 4 of 14)	82684	NM_001101507	665180	Mm.349066	NM_001101507	ENSMUSG00000079598	Clec2l	AI414054|AW122724|Gm1064	C-type lectin domain family 2, member L	protein-coding
mm_39249.1	chr5	3497842	3497877	+	1	NA	intron (NM_009873, intron 5 of 7)	intron (NM_009873, intron 5 of 7)	-45974	NM_001042501	68152	Mm.240265	NM_026583	ENSMUSG00000058503	Fam133b	2900022K02Rik|5830415L20Rik	family with sequence similarity 133, member B	protein-coding
mm_31842.1	chr4	74251879	74251891	+	1	NA	promoter-TSS (NM_144787)	promoter-TSS (NM_144787)	6	NM_144787	76804	Mm.209059	NM_144787	ENSMUSG00000028397	Kdm4c	2410141F18Rik|AA517467|Gasc1|Jmjd2c	lysine (K)-specific demethylase 4C	protein-coding
mm_146652.1	chr18	11051480	11051502	-	1	NA	intron (NR_105022, intron 1 of 3)	intron (NR_105022, intron 1 of 3)	-1019	NM_010258	14465	Mm.329287	NM_010258	ENSMUSG00000005836	Gata6	AA410133|GATA-6	GATA binding protein 6	protein-coding
mm_141829.1	chr17	34628006	34628023	-	1	NA	promoter-TSS (NM_019441)	promoter-TSS (NM_019441)	2	NM_001302394	54397	Mm.373627	NM_019441	ENSMUSG00000015474	Ppt2	0610007M19Rik|AA672937	palmitoyl-protein thioesterase 2	protein-coding
mm_131360.1	chr16	13758037	13758039	+	1	NA	Intergenic	Intergenic	-22661	NM_001039521	106298	Mm.288606	NM_001039521	ENSMUSG00000022682	Rrn3	AL023001|E130302O19Rik|R75565|TIF-1A|Tif1a	RRN3 RNA polymerase I transcription factor homolog (yeast)	protein-coding
mm_57392.1	chr6	124840184	124840186	-	1	NA	promoter-TSS (NM_013530)	promoter-TSS (NM_013530)	90	NM_013530	14695	Mm.68889	NM_013530	ENSMUSG00000023439	Gnb3	Gnb-3	guanine nucleotide binding protein (G protein), beta 3	protein-coding
mm_46073.1	chr5	92323692	92323708	-	1	NA	3' UTR (NM_008599, exon 4 of 4)	3' UTR (NM_008599, exon 4 of 4)	4379	NM_008599	17329	Mm.766	NM_008599	ENSMUSG00000029417	Cxcl9	BB139920|CMK|Mig|MuMIG|Scyb9|crg-10	chemokine (C-X-C motif) ligand 9	protein-coding
mm_76745.1	chr8	95332143	95332159	-	1	NA	promoter-TSS (NM_024467)	promoter-TSS (NM_024467)	-133	NM_133954	101985	Mm.29069	NM_133954	ENSMUSG00000031792	Usb1	AA960436	U6 snRNA biogenesis 1	protein-coding
mm_24701.1	chr3	95126219	95126227	+	1	NA	intron (NM_016712, intron 3 of 9)	PB1D10|SINE|Alu	1709	NM_016712	50874	Mm.71935	NM_016712	ENSMUSG00000005628	Tmod4	MTMOD|Sk-Tmod	tropomodulin 4	protein-coding
mm_6236.1	chr1	66945315	66945337	-	1	NA	promoter-TSS (NM_021285)	promoter-TSS (NM_021285)	-270	NM_021285	17901	Mm.1000	NM_021285	ENSMUSG00000061816	Myl1	AI325107|MLC1f|MLC3f|Mylf	myosin, light polypeptide 1	protein-coding
mm_98520.1	chr11	94953120	94953123	+	1	NA	TTS (NM_007742)	TTS (NM_007742)	-14472	NM_018792	54388	Mm.30482	NM_018792	ENSMUSG00000038994	Hils1	H1.9|TISP64	histone H1-like protein in spermatids 1	protein-coding
mm_99291.1	chr11	101330774	101330795	+	1	NA	5' UTR (NM_009675, exon 1 of 4)	5' UTR (NM_009675, exon 1 of 4)	178	NM_009675	11754	Mm.67281	NM_009675	ENSMUSG00000019326	Aoc3	SSAO|VAP1	amine oxidase, copper containing 3	protein-coding
mm_73655.1	chr8	110957728	110957753	+	1	NA	exon (NM_009179, exon 2 of 7)	exon (NM_009179, exon 2 of 7)	37875	NM_009179	20444	Mm.200388	NM_009179	ENSMUSG00000031749	St3gal2	AI429591|AW822065|ST3GalII|Siat5	ST3 beta-galactoside alpha-2,3-sialyltransferase 2	protein-coding
mm_148128.1	chr18	75666186	75666216	-	1	NA	intron (NM_201354, intron 1 of 11)	intron (NM_201354, intron 1 of 11)	31495	NM_201354	269037	Mm.36745	NM_201354	ENSMUSG00000052928	Ctif	Gm672	CBP80/20-dependent translation initiation factor	protein-coding
mm_4470.1	chr1	173419261	173419288	+	1	NA	Intergenic	Intergenic	-1330	NM_001013779	383619	Mm.131453	NM_001013779	ENSMUSG00000037860	Aim2	Gm1313|Ifi210	absent in melanoma 2	protein-coding
mm_135846.1	chr16	58718866	58718891	-	1	NA	promoter-TSS (NM_001162955)	promoter-TSS (NM_001162955)	-154	NM_001162955	71223	Mm.359970	NM_001162955	ENSMUSG00000047293	Gpr15	4933439K08Rik	G protein-coupled receptor 15	protein-coding
mm_98417.1	chr11	94565416	94565443	+	1	NA	exon (NM_007689, exon 1 of 4)	exon (NM_007689, exon 1 of 4)	355	NM_007689	12643	Mm.440523	NM_007689	ENSMUSG00000039084	Chad	SLRR4A	chondroadherin	protein-coding
mm_170968.1	chr2	60050644	60050647	-	1	NA	intron (NM_001001182, intron 2 of 35)	intron (NM_001001182, intron 2 of 35)	75095	NM_001001182	407823	Mm.228071	NM_001001182	ENSMUSG00000026987	Baz2b	5830435C13Rik|BC053917|D2Ertd794e	bromodomain adjacent to zinc finger domain, 2B	protein-coding
mm_7104.1	chr1	89281298	89281302	-	1	NA	Intergenic	Intergenic	124833	NR_040482	77331	Mm.374962	NR_040482	ENSMUSG00000099938	C030007H22Rik	-	RIKEN cDNA C030007H22 gene	ncRNA
mm_43338.1	chr5	135064221	135064254	+	1	NA	promoter-TSS (NM_025362)	promoter-TSS (NM_025362)	31	NM_025362	66114	Mm.178012	NM_025362	ENSMUSG00000061118	Dnajc30	1300007M11Rik|Wbscr18	DnaJ heat shock protein family (Hsp40) member C30	protein-coding
mm_113395.1	chr13	33084062	33084072	+	1	NA	promoter-TSS (NM_173052)	promoter-TSS (NM_173052)	-36	NM_173052	282663	Mm.314490	NM_173052	ENSMUSG00000051029	Serpinb1b	6330533H24Rik|EIB|Serpin1b1|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 1b	protein-coding
mm_145395.1	chr18	57142757	57142765	+	1	NA	intron (NM_001001979, intron 1 of 24)	intron (NM_001001979, intron 1 of 24)	9671	NM_001001979	70417	Mm.297863	NM_001001979	ENSMUSG00000024593	Megf10	3000002B06Rik|Gm331	multiple EGF-like-domains 10	protein-coding
mm_133452.1	chr16	88820048	88820050	+	1	NA	intron (NR_138570, intron 3 of 3)	intron (NR_138570, intron 3 of 3)	6096	NM_013707	23927	Mm.3502	NM_013707	ENSMUSG00000074928	Krtap14	AA589630|Pmg1|mKAP13	keratin associated protein 14	protein-coding
mm_48318.1	chr5	138977096	138977106	-	1	NA	3' UTR (NM_008808, exon 6 of 6)	3' UTR (NM_008808, exon 6 of 6)	17852	NM_008808	18590	Mm.2675	NM_008808	ENSMUSG00000025856	Pdgfa	-	platelet derived growth factor, alpha	protein-coding
mm_90224.1	chr10	121034249	121034265	+	1	NA	5' UTR (NM_011915, exon 1 of 10)	5' UTR (NM_011915, exon 1 of 10)	253	NM_011915	24117	Mm.32831	NM_011915	ENSMUSG00000020218	Wif1	AW107799|WIF-1	Wnt inhibitory factor 1	protein-coding
mm_138932.1	chr17	43801928	43802011	+	1	NA	5' UTR (NM_207649, exon 1 of 5)	5' UTR (NM_207649, exon 1 of 5)	118	NM_207649	53901	Mm.251242	NM_030598	ENSMUSG00000039601	Rcan2	Csp2|Dscr1l1|MCIP2|ZAKI-4	regulator of calcineurin 2	protein-coding
mm_52187.1	chr6	99655666	99655676	+	1	NA	intron (NM_025829, intron 1 of 6)	intron (NM_025829, intron 1 of 6)	11100	NM_025829	66892	Mm.32889	NM_025829	ENSMUSG00000093661	Eif4e3	1300018P11Rik|AI451927|eIF4E-3	eukaryotic translation initiation factor 4E member 3	protein-coding
mm_43845.1	chr5	143181011	143181028	+	1	NA	promoter-TSS (NM_177880)	promoter-TSS (NM_177880)	2	NM_177880	330228	Mm.255752	NM_177880	ENSMUSG00000029586	Spdye4b	4933411G11Rik	speedy/RINGO cell cycle regulator family, member E4B	protein-coding
mm_22053.1	chr2	168513185	168513200	-	1	NA	intron (NM_001291174, intron 6 of 10)	intron (NM_001291174, intron 6 of 10)	77173	NM_001291178	18019	Mm.116802	NM_010899	ENSMUSG00000027544	Nfatc2	AI607462|NF-ATc2|NF-ATp|NFAT1|NFAT1-D|Nfatp	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 2	protein-coding
mm_160577.1	chr9	58582336	58582336	+	1	NA	promoter-TSS (NM_009145)	promoter-TSS (NM_009145)	96	NM_009145	20320	Mm.15125	NM_009145	ENSMUSG00000032336	Nptn	AW554172|SDR-1|Sdfr1	neuroplastin	protein-coding
mm_79175.1	chr9	47853102	47853123	+	1	NA	3' UTR (NM_018770, exon 10 of 10)	3' UTR (NM_018770, exon 10 of 10)	-34904	NR_046048	100038460	Mm.447649	NR_046048		Gm10677	ENSMUSG00000074363	predicted gene 10677	ncRNA
mm_50034.1	chr6	41135132	41135165	+	1	NA	Intergenic	Intergenic	-99639	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_77617.1	chr8	123925892	123925913	-	1	NA	intron (NM_172288, intron 12 of 25)	intron (NM_172288, intron 12 of 25)	23363	NM_172288	234865	Mm.267812	NM_172288	ENSMUSG00000039509	Nup133	mermaid	nucleoporin 133	protein-coding
mm_166184.1	chr5	32138893	32138897	-	1	NA	intron (NM_008037, intron 1 of 3)	intron (NM_008037, intron 1 of 3)	2423	NM_008037	14284	Mm.24684	NM_008037	ENSMUSG00000029135	Fosl2	Fra-2	fos-like antigen 2	protein-coding
mm_167057.1	chr7	90029135	90029150	+	1	NA	promoter-TSS (NR_110365)	promoter-TSS (NR_110365)	-17	NR_110365	319711	Mm.31753	NR_015614	ENSMUSG00000097585	E230029C05Rik	AI452102|B230337J15	RIKEN cDNA E230029C05 gene	ncRNA
mm_170960.1	chr2	56766168	56766173	+	1	NA	Intergenic	L1Md_F3|LINE|L1	-19641	NR_105751	102465169		NR_105751	ENSMUSG00000098437	Mir195b	Gm27491|mmu-mir-195b	microRNA 195b	ncRNA
mm_144507.1	chr18	24653857	24653883	+	1	NA	5' UTR (NM_026779, exon 1 of 15)	5' UTR (NM_026779, exon 1 of 15)	179	NM_026779	68591	Mm.28252	NM_026779	ENSMUSG00000039616	Mocos	1110018O12Rik|HMCS|MCS|MOS	molybdenum cofactor sulfurase	protein-coding
mm_118751.1	chr14	22365135	22365145	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	177658	NR_046307	74896	Mm.444661	NR_046307		4930405A10Rik	4930456G20Rik	RIKEN cDNA 4930405A10 gene	ncRNA
mm_91774.1	chr10	51786941	51786968	-	1	NA	Intergenic	Lx|LINE|L1	-29760	NR_045158	71090	Mm.72588	NM_027670	ENSMUSG00000062224	4933411G06Rik	-	Sumo1 pseudogene	pseudo
mm_4286.1	chr1	171682078	171682092	+	1	NA	promoter-TSS (NM_007649)	promoter-TSS (NM_007649)	30	NM_007649	12506	Mm.1738	NM_007649	ENSMUSG00000015355	Cd48	AI449234|AW610730|BCM1|BLAST|BLAST-1|BLAST1|Bcm-1|MEM-102|SLAMF2|Sgp-60	CD48 antigen	protein-coding
mm_18343.1	chr2	58157007	58157017	-	1	NA	intron (NM_139200, intron 1 of 7)	(GA)n|Simple_repeat|Simple_repeat	3110	NM_139200	227929	Mm.273905	NM_139200	ENSMUSG00000026832	Cytip	A130053M09Rik|AI462064|C80816|Cbp|Cybr|Pscdbp	cytohesin 1 interacting protein	protein-coding
mm_108253.1	chr12	78230499	78230502	+	1	NA	intron (NM_145965, intron 1 of 22)	intron (NM_145965, intron 1 of 22)	3845	NM_145965	268566	Mm.341742	NM_145965	ENSMUSG00000047454	Gphn	5730552E08Rik|AI662856|BC027112|C230040D23|GPH|GPHRYN|geph	gephyrin	protein-coding
mm_24200.1	chr3	88616134	88616151	+	1	NA	promoter-TSS (NM_001198911)	promoter-TSS (NM_001198911)	-65	NM_001198911	16800	Mm.239329	NM_008487	ENSMUSG00000028059	Arhgef2	AA408978|GEF|GEF-H1|GEFH1|LFP40|Lbcl1|Lfc|P40|mKIAA0651	rho/rac guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_103048.1	chr11	69805464	69805467	-	1	NA	non-coding (NR_027913, exon 1 of 1)	non-coding (NR_027913, exon 1 of 1)	159	NM_001033433	380705	Mm.490673	NM_001033433	ENSMUSG00000089876	Tmem102	4632403M07Rik|Cbap|Tmem102-ps	transmembrane protein 102	protein-coding
mm_164269.1	chr15	101248271	101248283	+	1	NA	Intergenic	Intergenic	-18569	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_79426.1	chr9	55430405	55430428	+	1	NA	exon (NM_172923, exon 9 of 11)	exon (NM_172923, exon 9 of 11)	81827	NM_145615	110842	Mm.290853	NM_145615	ENSMUSG00000032314	Etfa	2010200I21Rik|D9Ertd394e	electron transferring flavoprotein, alpha polypeptide	protein-coding
mm_27067.1	chr3	27896348	27896356	-	1	NA	promoter-TSS (NM_001164437)	promoter-TSS (NM_001164437)	16	NM_001164437	208613	Mm.59189	NM_001164437	ENSMUSG00000043164	Tmem212	E030011K20Rik|Gm564	transmembrane protein 212	protein-coding
mm_58981.1	chr7	19076174	19076237	+	1	NA	promoter-TSS (NM_010058)	promoter-TSS (NM_010058)	5	NM_010058	13401	Mm.2852	NM_010058	ENSMUSG00000030410	Dmwd	DMR-N9|Dm9	dystrophia myotonica-containing WD repeat motif	protein-coding
mm_72221.1	chr8	72720580	72720583	+	1	NA	Intergenic	MLT1E1A|LTR|ERVL-MaLR	-2689	NM_001113248	20467	Mm.2137	NM_009188	ENSMUSG00000031622	Sin3b	2810430C10Rik	transcriptional regulator, SIN3B (yeast)	protein-coding
mm_152465.1	chr19	10948503	10948544	-	1	NA	exon (NM_023731, exon 1 of 4)	exon (NM_023731, exon 1 of 4)	743	NM_023731	108673	Mm.294908	NM_023731	ENSMUSG00000024732	Ccdc86	4933411H20Rik|6720480F16Rik|D19Ertd678e	coiled-coil domain containing 86	protein-coding
mm_132128.1	chr16	31754800	31754822	+	1	NA	exon (NM_001252436, exon 1 of 23)	exon (NM_001252436, exon 1 of 23)	461	NM_001252436	13383	Mm.382	NM_007862	ENSMUSG00000022770	Dlg1	B130052P05Rik|Dlgh1|E-dlg/SAP97|SAP-97|SAP97|mKIAA4187	discs, large homolog 1 (Drosophila)	protein-coding
mm_124020.1	chr14	76520851	76520862	-	1	NA	promoter-TSS (NR_045660)	promoter-TSS (NR_045660)	-1	NR_045660	75789	Mm.159571	NR_045660	ENSMUSG00000097172	4930444M15Rik	-	RIKEN cDNA 4930444M15 gene	ncRNA
mm_34435.1	chr4	147361281	147361302	+	1	NA	intron (NM_001039209, intron 1 of 2)	intron (NM_001039209, intron 1 of 2)	185425	NM_001039209	195531	Mm.270762	NM_001039209	ENSMUSG00000078496	Zfp982	Gm13152|OTTMUSG00000010671	zinc finger protein 982	protein-coding
mm_22952.1	chr3	32397027	32397087	+	1	NA	Intergenic	CpG	-31392	NM_009517	22401	Mm.35705	NM_009517	ENSMUSG00000027663	Zmat3	Wig1	zinc finger matrin type 3	protein-coding
mm_131583.1	chr16	18428975	18429008	+	1	NA	intron (NM_013711, intron 1 of 17)	intron (NM_013711, intron 1 of 17)	-2275	NM_001111062	12846	Mm.100940	NM_007744	ENSMUSG00000000326	Comt	Comt1|D16Wsu103e|D330014B15Rik	catechol-O-methyltransferase	protein-coding
mm_92976.1	chr10	86591498	86591519	-	1	NA	Intergenic	Intergenic	-92612	NM_013722	27204	Mm.394931	NM_013722	ENSMUSG00000059602	Syn3	-	synapsin III	protein-coding
mm_75027.1	chr8	31918837	31918877	-	1	NA	promoter-TSS (NM_178591)	promoter-TSS (NM_178591)	-654	NM_178591	211323	Mm.153432	NM_178591	ENSMUSG00000062991	Nrg1	6030402G23Rik|ARIA|D230005F13Rik|GGF|GGFII|HRG|HRGalpha|Hgl|NDF|SMDF	neuregulin 1	protein-coding
mm_142455.1	chr17	45593666	45593690	-	1	NA	promoter-TSS (NM_001199113)	promoter-TSS (NM_001199113)	-38	NM_001199113	63959	Mm.29744	NM_022880	ENSMUSG00000023942	Slc29a1	1200014D21Rik|AA407560|ENT1	solute carrier family 29 (nucleoside transporters), member 1	protein-coding
mm_43838.1	chr5	142972845	142972870	+	1	NA	3' UTR (NM_007984, exon 5 of 5)	3' UTR (NM_007984, exon 5 of 5)	12502	NM_007984	14086	Mm.289707	NM_007984	ENSMUSG00000029581	Fscn1	AI663989|Fan1|fascin-1	fascin actin-bundling protein 1	protein-coding
mm_82841.1	chr9	31167665	31167704	-	1	NA	exon (NM_001102455, exon 7 of 17)	exon (NM_001102455, exon 7 of 17)	-35885	NM_011176	19143	Mm.243926	NM_011176	ENSMUSG00000031995	St14	Epithin|MT-SP1|Prss14|Tmprss14|mCAP3|matriptase	suppression of tumorigenicity 14 (colon carcinoma)	protein-coding
mm_171459.1	chr4	145640951	145640958	+	1	NA	Intergenic	CpG	-29743	NM_001103158	100041379	Mm.276881	NM_001103158	ENSMUSG00000058186	Zfp980	Gm13242|OTTMUSG00000011070	zinc finger protein 980	protein-coding
mm_6947.1	chr1	85736526	85736624	-	1	NA	promoter-TSS (NM_177055)	promoter-TSS (NM_177055)	31	NM_177055	319997	Mm.116691	NM_177055	ENSMUSG00000052760	A630001G21Rik	-	RIKEN cDNA A630001G21 gene	protein-coding
mm_87113.1	chr10	33233898	33233907	+	1	NA	exon (NM_029726, exon 10 of 38)	exon (NM_029726, exon 10 of 38)	22455	NR_040657	442820	Mm.490725	NR_040657		D830005E20Rik	-	RIKEN cDNA D830005E20 gene	ncRNA
mm_136522.1	chr16	97459509	97459531	-	1	NA	intron (NR_003520, intron 2 of 8)	intron (NR_003520, intron 2 of 8)	3385	NM_010846	17857	Mm.33996	NM_010846	ENSMUSG00000000386	Mx1	AI893580|Mx|Mx-1	MX dynamin-like GTPase 1	protein-coding
mm_91785.1	chr10	52419483	52419519	-	1	NA	intron (NM_030250, intron 1 of 4)	intron (NM_030250, intron 1 of 4)	1954	NM_030250	52014	Mm.199964	NM_030250	ENSMUSG00000023068	Nus1	1600027K07Rik|AU019165|AW538011|BC003223|D10Ertd438e	NUS1 dehydrodolichyl diphosphate synthase subunit	protein-coding
mm_94948.1	chr11	29731502	29731507	+	1	NA	intron (NM_024226, intron 1 of 6)	B2_Mm2|SINE|B2	12941	NM_024226	68585	Mm.192580	NM_024226	ENSMUSG00000020458	Rtn4	1110020G17Rik|AA407876|AA409940|AA960376|ASY|C130026I10Rik|NOGO|NSP-CL|NgA|Nogo-A|Nogo-B|Nogo-C|mKIAA0886|mKIAA4153	reticulon 4	protein-coding
mm_105995.1	chr11	115645216	115645239	-	1	NA	3' UTR (NM_008163, exon 6 of 6)	3' UTR (NM_008163, exon 6 of 6)	-16932	NM_001252395	67283	Mm.383426	NM_026071	ENSMUSG00000020744	Slc25a19	2900089E13Rik|DNC|MUP1|TPC	solute carrier family 25 (mitochondrial thiamine pyrophosphate carrier), member 19	protein-coding
mm_69420.1	chr7	132720711	132720712	-	1	NA	intron (NM_001347630, intron 3 of 3)	intron (NM_001347630, intron 3 of 3)	56205	NM_001347630	77938	Mm.225649	NM_175268	ENSMUSG00000030956	Fam53b	A930008G19Rik|mKIAA0140	family with sequence similarity 53, member B	protein-coding
mm_51829.1	chr6	89413908	89413918	+	1	NA	intron (NM_025351, intron 6 of 7)	intron (NM_025351, intron 6 of 7)	-51300	NM_008881	18844	Mm.3789	NM_008881	ENSMUSG00000030084	Plxna1	2600013D04Rik|NOV|PlexA1|Plxn1|mKIAA4053	plexin A1	protein-coding
mm_69213.1	chr7	127512309	127512326	-	1	NA	non-coding (NR_024331, exon 1 of 1)	non-coding (NR_024331, exon 1 of 1)	334	NM_001304266	100043597	Mm.428042	NM_175144	ENSMUSG00000053877	Srcap	B930091H02Rik|D030022P06Rik|F630004O05Rik	Snf2-related CREBBP activator protein	protein-coding
mm_128368.1	chr15	42571195	42571198	-	1	NA	intron (NM_009640, intron 1 of 8)	intron (NM_009640, intron 1 of 8)	105781	NM_001286062	11600	Mm.309336	NM_009640	ENSMUSG00000022309	Angpt1	1110046O21Rik|Ang-1|Ang1	angiopoietin 1	protein-coding
mm_146119.1	chr18	74442353	74442364	+	1	NA	promoter-TSS (NM_201600)	promoter-TSS (NM_201600)	-261	NM_201600	17919	Mm.260098	NM_008661	ENSMUSG00000025885	Myo5b	AI661750|mKIAA1119	myosin VB	protein-coding
mm_138133.1	chr17	34187832	34187867	+	1	NA	promoter-TSS (NM_013585)	promoter-TSS (NM_013585)	293	NM_013683	21354	Mm.482076	NM_013683	ENSMUSG00000037321	Tap1	ABC17|APT1|Abcb2|Ham-1|Ham1|MTP1|PSF1|RING4|TAP|Tap-1|Y3	transporter 1, ATP-binding cassette, sub-family B (MDR/TAP)	protein-coding
mm_68488.1	chr7	111074063	111074104	-	1	NA	exon (NM_013507, exon 20 of 22)	exon (NM_013507, exon 20 of 22)	8947	NM_001040131	13690	Mm.185453	NM_013507	ENSMUSG00000005610	Eif4g2	DAP-5|E130105L11Rik|Nat1|Natm1|p97	eukaryotic translation initiation factor 4, gamma 2	protein-coding
mm_94364.1	chr11	5012583	5012608	+	1	NA	intron (NM_007454, intron 2 of 20)	intron (NM_007454, intron 2 of 20)	25771	NM_007454	11764	Mm.274816	NM_007454	ENSMUSG00000009090	Ap1b1	Adtb1|b2b1660Clo	adaptor protein complex AP-1, beta 1 subunit	protein-coding
mm_144431.1	chr18	21001820	21001829	+	1	NA	promoter-TSS (NM_207623)	promoter-TSS (NM_207623)	-133	NM_001303011	56515	Mm.253542	NM_019706	ENSMUSG00000024317	Rnf138	2410015A17Rik|2810480D20Rik|STRIN|Trif|Trif-d	ring finger protein 138	protein-coding
mm_77654.1	chr8	124568870	124568873	-	1	NA	intron (NM_007428, intron 1 of 4)	PB1D9|SINE|Alu	836	NM_007428	11606	Mm.301626	NM_007428	ENSMUSG00000031980	Agt	AI265500|AngI|AngII|Aogen|Serpina8	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	protein-coding
mm_137363.1	chr17	25370551	25370566	+	1	NA	promoter-TSS (NM_012034)	promoter-TSS (NM_012034)	5	NM_012034	26945	Mm.180108	NM_012034	ENSMUSG00000033200	Tpsg1	Prss31|Tmt	tryptase gamma 1	protein-coding
mm_65687.1	chr7	28372341	28372371	-	1	NA	5' UTR (NM_001083912, exon 1 of 19)	5' UTR (NM_001083912, exon 1 of 19)	306	NM_138752	101497	Mm.235700	NM_138752	ENSMUSG00000037552	Plekhg2	AI194308|Clg|Cslg	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	protein-coding
mm_30472.1	chr3	154597046	154597088	-	1	NA	promoter-TSS (NM_172474)	promoter-TSS (NM_172474)	31	NM_001168358	209584	Mm.347513	NM_172474	ENSMUSG00000047583	Tyw3	5230400J09Rik	tRNA-yW synthesizing protein 3 homolog (S. cerevisiae)	protein-coding
mm_30431.1	chr3	153225754	153225763	-	1	NA	intron (NM_011372, intron 3 of 4)	intron (NM_011372, intron 3 of 4)	72891	NR_126464	75489	Mm.443252	NR_126464	ENSMUSG00000105023	1700012D16Rik	-	RIKEN cDNA 1700012D16 gene	ncRNA
mm_33174.1	chr4	126047027	126047037	+	1	NA	5' UTR (NM_025544, exon 1 of 8)	5' UTR (NM_025544, exon 1 of 8)	104	NM_025544	66407	Mm.195628	NM_025544	ENSMUSG00000028861	Mrps15	1500003E24Rik|2410002B11Rik|Mprs15	mitochondrial ribosomal protein S15	protein-coding
mm_28409.1	chr3	90266394	90266397	-	1	NA	promoter-TSS (NM_201407)	promoter-TSS (NM_201407)	-119	NM_201407	229541	Mm.30571	NM_201407	ENSMUSG00000042404	Dennd4b	-	DENN/MADD domain containing 4B	protein-coding
mm_56556.1	chr6	101199021	101199060	-	1	NA	intron (NM_018884, intron 3 of 9)	intron (NM_018884, intron 3 of 9)	178857	NM_018884	55983	Mm.321654	NM_018884	ENSMUSG00000035357	Pdzrn3	1110020C07Rik|AI429718|AL023082|LNX3|SEMACAP3|Semcap3	PDZ domain containing RING finger 3	protein-coding
mm_81928.1	chr9	120179666	120179677	+	1	NA	Intergenic	L1ME3Cz|LINE|L1	29929	NM_001039364	17433	Mm.486167	NM_008614	ENSMUSG00000032517	Mobp	AI835053|AI839848|MOBP155|MOBP170|MOBP69|MOBP73|MOBP81|R74645	myelin-associated oligodendrocytic basic protein	protein-coding
mm_42680.1	chr5	119796548	119796556	+	1	NA	Intergenic	CpG	-38111	NM_011537	21388	Mm.103636	NM_011537	ENSMUSG00000018263	Tbx5	-	T-box 5	protein-coding
mm_19674.1	chr2	103454401	103454423	-	1	NA	3' UTR (NM_009804, exon 13 of 13)	3' UTR (NM_009804, exon 13 of 13)	30344	NM_010125	13711	Mm.20888	NM_010125	ENSMUSG00000027186	Elf5	ESE-2|ESE-5|ESE-5.	E74-like factor 5	protein-coding
mm_52610.1	chr6	117173727	117173731	+	1	NA	3' UTR (NM_021704, exon 3 of 3)	3' UTR (NM_021704, exon 3 of 3)	5194	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_160558.1	chr9	51105867	51105867	+	1	NA	Intergenic	Intergenic	-2222	NR_029655	723849		NR_029655	ENSMUSG00000065492	Mir34b	Mirn34b|mir-34b|mmu-mir-34b	microRNA 34b	ncRNA
mm_131813.1	chr16	22920245	22920266	+	1	NA	promoter-TSS (NM_021564)	promoter-TSS (NM_021564)	33	NM_001083904	59083	Mm.28461	NM_021564	ENSMUSG00000022871	Fetub	2310011O17Rik|AI255764|D17980|Gugu	fetuin beta	protein-coding
mm_113469.1	chr13	36359794	36359797	+	1	NA	intron (NM_001039189, intron 4 of 5)	intron (NM_001039189, intron 4 of 5)	242152	NM_001039189	69955	Mm.70690	NM_024274	ENSMUSG00000021420	Fars2	Fars1|pheRS	phenylalanine-tRNA synthetase 2 (mitochondrial)	protein-coding
mm_157917.1	chrX	78554268	78554269	-	1	NA	intron (NM_027322, intron 1 of 3)	RLTR14-int|LTR|ERV1	29537	NM_001164275	546336	Mm.211712	NM_027322	ENSMUSG00000047996	Prrg1	2010007L08Rik	proline rich Gla (G-carboxyglutamic acid) 1	protein-coding
mm_124622.1	chr15	3280394	3280398	+	1	NA	TTS (NM_001166063)	TTS (NM_001166063)	9419	NM_009155	20363	Mm.392203	NM_009155	ENSMUSG00000064373	Selenop	AU018766|D15Ucla1|Se-P|Sepp1|selp	selenoprotein P	protein-coding
mm_125408.1	chr15	41751505	41751532	+	1	NA	intron (NM_001130166, intron 3 of 16)	intron (NM_001130166, intron 3 of 16)	-37516	NM_001130165	170719	Mm.254267	NM_130885	ENSMUSG00000022307	Oxr1	2210416C20Rik|C7|C7B	oxidation resistance 1	protein-coding
mm_39517.1	chr5	21256984	21257005	+	1	NA	intron (NM_175437, intron 18 of 30)	A-rich|Low_complexity|Low_complexity	70727	NM_175437	212167	Mm.121705	NM_175437	ENSMUSG00000039934	Gsap	A530088I07Rik|Pion	gamma-secretase activating protein	protein-coding
mm_171159.1	chr3	22731642	22731646	-	1	NA	Intergenic	L1Md_A|LINE|L1	480274	NR_004439	19784		NR_004439		Rprl2	RPRH3|Rmrp3	ribonuclease P RNA-like 2	ncRNA
mm_154471.1	chrM	3798	3811	-	1	NA	NA	tRNA-Gln-CAA_|tRNA|tRNA	NA	NA								
mm_115266.1	chr13	110864952	110864960	+	1	NA	Intergenic	Intergenic	-38543	NR_131193	75139	Mm.490931	NR_131193		Gm38397	-	predicted gene, 38397	ncRNA
mm_115957.1	chr13	23761224	23761236	-	1	NA	promoter-TSS (NM_178192)	promoter-TSS (NM_178192)	19	NM_178192	326619	Mm.228709	NM_178192	ENSMUSG00000060093	Hist1h4a	-	histone cluster 1, H4a	protein-coding
mm_89601.1	chr10	95989559	95989573	+	1	NA	exon (NM_001001932, exon 3 of 29)	exon (NM_001001932, exon 3 of 29)	48903	NM_001001932	216238	Mm.210035	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding
mm_164017.1	chr14	71420992	71420995	+	1	NA	Intergenic	Intergenic	169720	NR_046076	100043132	Mm.399336	NR_046075		Gm4251	-	predicted gene 4251	ncRNA
mm_36561.1	chr4	87226772	87226775	-	1	NA	intron (NM_001110240, intron 1 of 9)	intron (NM_001110240, intron 1 of 9)	1190	NM_001110240	76376	Mm.490487	NM_172426	ENSMUSG00000037996	Slc24a2	2810021B17Rik|6330417K15Rik|AI847460|Nckx2	solute carrier family 24 (sodium/potassium/calcium exchanger), member 2	protein-coding
mm_162934.1	chr10	127288911	127288951	+	1	NA	promoter-TSS (NM_001347171)	promoter-TSS (NM_001347171)	87	NM_001347171	110962	Mm.372826	NM_033072	ENSMUSG00000025409	Mbd6	D10Wsu93e	methyl-CpG binding domain protein 6	protein-coding
mm_77598.1	chr8	123892601	123892616	-	1	NA	exon (NM_009606, exon 5 of 7)	exon (NM_009606, exon 5 of 7)	2167	NM_001272041	11459	Mm.214950	NM_009606	ENSMUSG00000031972	Acta1	AA959943|Acta-2|Acts|Actsk-1	actin, alpha 1, skeletal muscle	protein-coding
mm_74964.1	chr8	26824419	26824430	-	1	NA	promoter-TSS (NR_045904)	promoter-TSS (NR_045904)	-1	NR_045904	72316	Mm.490534	NR_045904	ENSMUSG00000100335	2310008N11Rik	-	RIKEN cDNA 2310008N11 gene	ncRNA
mm_130113.1	chr15	89476387	89476391	-	1	NA	5' UTR (NM_009713, exon 2 of 9)	5' UTR (NM_009713, exon 2 of 9)	137	NR_077233	100532730	Mm.461541	NR_077233		C230037L18Rik	-	RIKEN cDNA C230037L18 gene	ncRNA
mm_104910.1	chr11	99665669	99665685	-	1	NA	exon (NM_026834, exon 1 of 1)	exon (NM_026834, exon 1 of 1)	283	NM_026834	68768	Mm.416844	NM_026834	ENSMUSG00000075566	Krtap4-6	1110054P19Rik	keratin associated protein 4-6	protein-coding
mm_166095.1	chr4	141623139	141623143	-	1	NA	intron (NM_001013780, intron 1 of 4)	intron (NM_001013780, intron 1 of 4)	693	NM_001013780	384071	Mm.295682	NM_001013780	ENSMUSG00000040740	Slc25a34	Gm1369	solute carrier family 25, member 34	protein-coding
mm_9024.1	chr1	166380106	166380131	-	1	NA	intron (NM_030245, intron 1 of 7)	intron (NM_030245, intron 1 of 7)	951	NM_030245	27878	Mm.100665	NM_030245	ENSMUSG00000026563	Tada1	2900026B15Rik|D1Ertd251e|Staf42|Tada1l	transcriptional adaptor 1	protein-coding
mm_90776.1	chr10	5922386	5922407	-	1	NA	promoter-TSS (NM_019958)	promoter-TSS (NM_019958)	4	NM_001161822	56533	Mm.44606	NM_019958	ENSMUSG00000019775	Rgs17	6430507P11Rik|Rgsz2	regulator of G-protein signaling 17	protein-coding
mm_88296.1	chr10	75316726	75316736	+	1	NA	promoter-TSS (NM_009630)	promoter-TSS (NM_009630)	-146	NM_009630	11540	Mm.333734	NM_009630	ENSMUSG00000020178	Adora2a	A2AAR|A2aR|AA2AR	adenosine A2a receptor	protein-coding
mm_137761.1	chr17	29489680	29489692	+	1	NA	Intergenic	Intergenic	-1359	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_86366.1	chr9	123792471	123792471	-	1	NA	3' UTR (NM_001110253, exon 18 of 18)	3' UTR (NM_001110253, exon 18 of 18)	-14006	NM_030712	80901	Mm.124289	NM_030712	ENSMUSG00000048521	Cxcr6	BB217514|BONZO|STRL33	chemokine (C-X-C motif) receptor 6	protein-coding
mm_43726.1	chr5	139547945	139547955	+	1	NA	3' UTR (NM_013702, exon 3 of 3)	3' UTR (NM_013702, exon 3 of 3)	4052	NM_013702	22255	Mm.42190	NM_013702	ENSMUSG00000029546	Uncx	Chx4|Uncx4.1	UNC homeobox	protein-coding
mm_127057.1	chr15	97245678	97245686	+	1	NA	exon (NM_001164602, exon 2 of 2)	exon (NM_001164602, exon 2 of 2)	-1425	NM_172293	239647	Mm.130036	NM_172293	ENSMUSG00000044250	Pced1b	Fam113b	PC-esterase domain containing 1B	protein-coding
mm_157953.1	chrX	87268853	87268855	-	1	NA	intron (NM_001160403, intron 5 of 10)	RLTR13D5|LTR|ERVK	846769	NM_001160403	331461	Mm.121680	NM_001160403	ENSMUSG00000052372	Il1rapl1	6330532G10Rik|C030039N24|IL1R8|IL1RAPL|MRX34|OPHN4|TIGIRR-2	interleukin 1 receptor accessory protein-like 1	protein-coding
mm_86180.1	chr9	119190384	119190410	-	1	NA	promoter-TSS (NM_001037749)	promoter-TSS (NM_001037749)	-4	NM_001037749	382113	Mm.335525	NM_001037749	ENSMUSG00000070280	Slc22a14	Gm1128	solute carrier family 22 (organic cation transporter), member 14	protein-coding
mm_43540.1	chr5	137350372	137350479	+	1	NA	5' UTR (NM_010144, exon 1 of 17)	5' UTR (NM_010144, exon 1 of 17)	316	NM_010144	13846	Mm.34533	NM_010144	ENSMUSG00000029710	Ephb4	AI042935|Htk|MDK2|Myk1|Tyro11	Eph receptor B4	protein-coding
mm_35465.1	chr4	40781845	40781855	-	1	NA	Intergenic	Intergenic	-23965	NM_021535	74255	Mm.289929	NM_021535	ENSMUSG00000028409	Smu1	2600001O03Rik|2610203K23Rik|AB044414|AI845086|AW556129|Bwd	smu-1 suppressor of mec-8 and unc-52 homolog (C. elegans)	protein-coding
mm_87602.1	chr10	57650978	57650985	+	1	NA	promoter-TSS (NM_001190402)	promoter-TSS (NM_001190402)	0	NM_001039050	18768	Mm.262135	NM_008863	ENSMUSG00000019876	Pkib	Pkibeta|Prkacn2	protein kinase inhibitor beta, cAMP dependent, testis specific	protein-coding
mm_123082.1	chr14	55745487	55745502	-	1	NA	promoter-TSS (NM_026403)	promoter-TSS (NM_026403)	190	NM_026819	52585	Mm.21623	NM_026819	ENSMUSG00000002332	Dhrs1	1110029G07Rik|AW112170|D14Ertd484e	dehydrogenase/reductase (SDR family) member 1	protein-coding
mm_37174.1	chr4	117192102	117192120	-	1	NA	Intergenic	Intergenic	-9487	NM_134471	73804	Mm.247651	NM_134471	ENSMUSG00000028678	Kif2c	4930402F02Rik|ESTM5|Knsl6|MCAK|X83316	kinesin family member 2C	protein-coding
mm_120750.1	chr14	73239171	73239190	+	1	NA	exon (NM_175116, exon 1 of 1)	exon (NM_175116, exon 1 of 1)	1289	NM_175116	67168	Mm.390681	NM_175116	ENSMUSG00000033446	Lpar6	2610302I02Rik|P2ry5|P2y5	lysophosphatidic acid receptor 6	protein-coding
mm_102484.1	chr11	60210411	60210428	-	1	NA	intron (NM_001313979, intron 1 of 18)	CpG	-8092	NR_105887	102465556		NR_105887	ENSMUSG00000099259	Mir6922	Gm27269|mmu-mir-6922	microRNA 6922	ncRNA
mm_84922.1	chr9	80344778	80344779	-	1	NA	intron (NM_022016, intron 13 of 16)	intron (NM_022016, intron 13 of 16)	120660	NM_022016	63859	Mm.422780	NM_022016	ENSMUSG00000032343	Impg1	A930015H12Rik|IMP150|SPACR	interphotoreceptor matrix proteoglycan 1	protein-coding
mm_20428.1	chr2	129305889	129305899	-	1	NA	intron (NR_040371, intron 3 of 4)	intron (NR_040371, intron 3 of 4)	4078	NM_010554	16175	Mm.15534	NM_010554	ENSMUSG00000027399	Il1a	Il-1a	interleukin 1 alpha	protein-coding
mm_37398.1	chr4	121109200	121109231	-	1	NA	promoter-TSS (NM_001081312)	promoter-TSS (NM_001081312)	11	NM_001081312	69469	Mm.481120	NM_001081312	ENSMUSG00000078577	Tmco2	1700028F16Rik	transmembrane and coiled-coil domains 2	protein-coding
mm_15212.1	chr2	154215259	154215270	+	1	NA	exon (NM_153418, exon 12 of 16)	exon (NM_153418, exon 12 of 16)	-8478	NM_144890	228802	Mm.167411	NM_144890	ENSMUSG00000038572	Bpifb5	Lplunc5	BPI fold containing family B, member 5	protein-coding
mm_157104.1	chrX	9437703	9437713	-	1	NA	3' UTR (NM_007807, exon 13 of 13)	3' UTR (NM_007807, exon 13 of 13)	31616	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_91913.1	chr10	60294990	60294997	-	1	NA	exon (NM_011179, exon 6 of 15)	exon (NM_011179, exon 6 of 15)	10532	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_18550.1	chr2	65089189	65089190	-	1	NA	3' UTR (NM_177025, exon 14 of 14)	3' UTR (NM_177025, exon 14 of 14)	-66423	NM_016719	50915	Mm.214554	NM_016719	ENSMUSG00000026888	Grb14	AI505286	growth factor receptor bound protein 14	protein-coding
mm_151975.1	chr19	5826830	5826840	-	1	NA	non-coding (NR_131212, exon 1 of 1)	non-coding (NR_131212, exon 1 of 1)	18643	NR_131212	66961	Mm.281895	NR_003513	ENSMUSG00000092274	Neat1	2310043N10Rik|VINC	nuclear paraspeckle assembly transcript 1 (non-protein coding)	ncRNA
mm_115932.1	chr13	23585971	23585981	-	1	NA	promoter-TSS (NM_001290530)	promoter-TSS (NM_001290530)	-6	NM_001290530	319179	Mm.440391	NM_178194	ENSMUSG00000047246	Hist1h2be	-	histone cluster 1, H2be	protein-coding
mm_46053.1	chr5	92137734	92137762	-	1	NA	promoter-TSS (NM_019490)	promoter-TSS (NM_019490)	-190	NM_019490	56041	Mm.15868	NM_019490	ENSMUSG00000029407	Uso1	115kDa|TAP|Vdp	USO1 vesicle docking factor	protein-coding
mm_121733.1	chr14	18271065	18271075	-	1	NA	promoter-TSS (NM_025586)	promoter-TSS (NM_025586)	-66	NM_001316712	69721	Mm.25648	NM_023526	ENSMUSG00000021772	Nkiras1	2400004O09Rik|KBRAS1|kappaB-Ras1	NFKB inhibitor interacting Ras-like protein 1	protein-coding
mm_93338.1	chr10	99759504	99759513	-	1	NA	5' UTR (NM_027945, exon 1 of 1)	5' UTR (NM_027945, exon 1 of 1)	150	NM_027945	71832	Mm.483162	NM_027945	ENSMUSG00000046934	Csl	1700007H16Rik	citrate synthase like	protein-coding
mm_69370.1	chr7	130720763	130720808	-	1	NA	intron (NM_001347637, intron 2 of 14)	intron (NM_001347637, intron 2 of 14)	28229	NM_021314	57752	Mm.86322	NM_021314	ENSMUSG00000030852	Tacc2	mKIAA4180	transforming, acidic coiled-coil containing protein 2	protein-coding
mm_37908.1	chr4	132757105	132757107	-	1	NA	promoter-TSS (NM_133888)	promoter-TSS (NM_133888)	65	NM_133888	100340	Mm.287187	NM_133888	ENSMUSG00000028885	Smpdl3b	1110054A24Rik|AU045240|Asml3b	sphingomyelin phosphodiesterase, acid-like 3B	protein-coding
mm_163354.1	chr12	24890916	24890919	+	1	NA	intron (NM_001083341, intron 3 of 11)	MTC|LTR|ERVL-MaLR	59318	NM_001083341	67216	Mm.167671	NM_026037	ENSMUSG00000020646	Mboat2	2810049G06Rik|AU022889|AW547221|LPCAT4|Moact2|Oact2	membrane bound O-acyltransferase domain containing 2	protein-coding
mm_76996.1	chr8	107096377	107096406	-	1	NA	promoter-TSS (NR_106043)	promoter-TSS (NR_106043)	154	NM_001286200	21750	Mm.6402	NM_009353	ENSMUSG00000031921	Terf2	TRF2	telomeric repeat binding factor 2	protein-coding
mm_160358.1	chr8	21655756	21655756	+	1	NA	promoter-TSS (NM_001167790)	promoter-TSS (NM_001167790)	-11	NM_001167790	23855	Mm.425519	NM_001167790	ENSMUSG00000060208	Defa17	AU014719|Cryp17|Defcr17	defensin, alpha, 17	protein-coding
mm_139188.1	chr17	47597103	47597118	+	1	NA	intron (NM_001081635, intron 4 of 6)	intron (NM_001081635, intron 4 of 6)	3643	NM_007632	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_75798.1	chr8	70120817	70120832	-	1	NA	promoter-TSS (NM_007789)	promoter-TSS (NM_007789)	20	NM_007789	13004	Mm.268079	NM_007789	ENSMUSG00000002341	Ncan	C230035B04|Cspg3|Cspg3-rs|Tgfbit	neurocan	protein-coding
mm_30626.1	chr4	8735947	8735963	+	1	NA	intron (NM_001277149, intron 1 of 37)	intron (NM_001277149, intron 1 of 37)	45549	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_78529.1	chr9	34797803	34797806	+	1	NA	intron (NM_001190912, intron 1 of 15)	intron (NM_001190912, intron 1 of 15)	309073	NM_001190911	67703	Mm.220710	NM_026324	ENSMUSG00000032036	Kirrel3	1500010O20Rik|2900036G11Rik|NEPH2|SST4|mKIAA1867	kin of IRRE like 3 (Drosophila)	protein-coding
mm_169587.1	chr15	25769920	25769935	-	1	NA	intron (NM_019472, intron 19 of 40)	B1F1|SINE|Alu	-73371	NM_001034851	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_48070.1	chr5	136581721	136581743	-	1	NA	Intergenic	Intergenic	-14242	NM_001291238	13047	Mm.320317	NM_009986	ENSMUSG00000029705	Cux1	CDP|Cutl1|Cux|Cux-1	cut-like homeobox 1	protein-coding
mm_64149.1	chr7	141291989	141292033	+	1	NA	promoter-TSS (NM_007878)	promoter-TSS (NM_007878)	5	NM_007878	13491	Mm.41075	NM_007878	ENSMUSG00000025496	Drd4	AW125663|D4R|Drd-4	dopamine receptor D4	protein-coding
mm_13424.1	chr2	104590454	104590533	+	1	NA	promoter-TSS (NM_145529)	promoter-TSS (NM_145529)	9	NM_001037326	228410	Mm.259876	NM_145529	ENSMUSG00000027176	Cstf3	4732468G05Rik|C79532|CstF-77	cleavage stimulation factor, 3' pre-RNA, subunit 3	protein-coding
mm_160775.1	chr10	123127677	123127677	-	1	NA	intron (NM_001301628, intron 13 of 20)	intron (NM_001301628, intron 13 of 20)	-51172	NM_001163025	67074	Mm.169924	NM_153395	ENSMUSG00000034602	Mon2	2610528O22Rik|AW495628|Sf21|mKIAA1040	MON2 homolog, regulator of endosome to Golgi trafficking	protein-coding
mm_27691.1	chr3	66136433	66136449	-	1	NA	intron (NM_145820, intron 9 of 13)	intron (NM_145820, intron 9 of 13)	-83446	NM_008987	19288	Mm.276776	NM_008987	ENSMUSG00000027832	Ptx3	AI607804|TSG-14	pentraxin related gene	protein-coding
mm_138357.1	chr17	34981953	34981986	+	1	NA	promoter-TSS (NM_030597)	promoter-TSS (NM_030597)	115	NM_001204274	27756	Mm.165735	NM_030597	ENSMUSG00000007050	Lsm2	D17H6S56E-2|D17H6S56E2|Dmapl|Dmpkap|G7b|Sm-X5|SmX5|snRNP	LSM2 homolog, U6 small nuclear RNA and mRNA degradation associated	protein-coding
mm_14425.1	chr2	130504281	130504308	+	1	NA	exon (NM_008980, exon 3 of 22)	exon (NM_008980, exon 3 of 22)	54016	NM_001163688	19262	Mm.224246	NM_008980	ENSMUSG00000027303	Ptpra	Ptpa|Ptpalpha|Rptpalpha|Rptra|Rptralpha	protein tyrosine phosphatase, receptor type, A	protein-coding
mm_103896.1	chr11	83575318	83575324	-	1	NA	3' UTR (NM_011338, exon 4 of 4)	3' UTR (NM_011338, exon 4 of 4)	3315	NM_011338	20308	Mm.416125	NM_011338	ENSMUSG00000019122	Ccl9	CCF18|MRP-2|Scya10|Scya9	chemokine (C-C motif) ligand 9	protein-coding
mm_42793.1	chr5	121660529	121660631	+	1	NA	promoter-TSS (NM_001289543)	promoter-TSS (NM_001289543)	17	NM_001289543	72399	Mm.153372	NM_028227	ENSMUSG00000029458	Brap	3010002G07Rik|BRAP2|IMP	BRCA1 associated protein	protein-coding
mm_141672.1	chr17	33909165	33909187	-	1	NA	promoter-TSS (NM_001199733)	promoter-TSS (NM_001199733)	2	NR_045146	407803	Mm.250393	NR_045146	ENSMUSG00000092564	BC051226	-	cDNA sequence BC051226	ncRNA
mm_154145.1	chr19	58443583	58443588	-	1	NA	intron (NR_104342, intron 4 of 11)	intron (NR_104342, intron 4 of 11)	11813	NM_001285457	14585	Mm.88367	NM_010279	ENSMUSG00000025089	Gfra1	AU042498	glial cell line derived neurotrophic factor family receptor alpha 1	protein-coding
mm_35852.1	chr4	49383690	49383716	-	1	NA	intron (NM_145368, intron 2 of 4)	intron (NM_145368, intron 2 of 4)	24448	NM_145368	209186	Mm.35071	NM_145368	ENSMUSG00000060317	Acnat2	C730036D15Rik	acyl-coenzyme A amino acid N-acyltransferase 2	protein-coding
mm_109553.1	chr12	111713314	111713320	+	1	NA	promoter-TSS (NM_026511)	promoter-TSS (NM_026511)	48	NM_026511	68020	Mm.425762	NM_026511	ENSMUSG00000037787	Apopt1	1700081D05Rik|2810002N01Rik|Apop-1|Apop1	apoptogenic, mitochondrial 1	protein-coding
mm_43096.1	chr5	124460672	124460706	+	1	NA	exon (NM_001310723, exon 7 of 7)	exon (NM_001310723, exon 7 of 7)	13985	NM_001310727	67956	Mm.137966	NM_030241	ENSMUSG00000049327	Kmt5a	2410195B05Rik|AA617402|AW536475|PR-SET7|PR/SET07|Setd8	lysine methyltransferase 5A	protein-coding
mm_156431.1	chrX	141150494	141150504	+	1	NA	Intergenic	(CAGAGA)n|Simple_repeat|Simple_repeat	-193788	NM_001164177	53380	Mm.17640	NM_016883	ENSMUSG00000031429	Psmd10	AW554874	proteasome (prosome, macropain) 26S subunit, non-ATPase, 10	protein-coding
mm_142265.1	chr17	39845779	39845787	-	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	2786	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_50273.1	chr6	45285166	45285183	+	1	NA	intron (NM_001004357, intron 1 of 23)	intron (NM_001004357, intron 1 of 23)	225113	NM_001004357	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding
mm_52338.1	chr6	110649099	110649112	+	1	NA	intron (NM_001346640, intron 1 of 10)	(T)n|Simple_repeat|Simple_repeat	3507	NM_177328	108073	Mm.240881	NM_177328	ENSMUSG00000056755	Grm7	6330570A01Rik|BB176677|C030018L03|E130018M02Rik|Gpr1g|Gprc1g|SMN2|Tg(SMN2)89Ahmb|mGluR7	glutamate receptor, metabotropic 7	protein-coding
mm_72797.1	chr8	87175371	87175374	+	1	NA	intron (NR_040697, intron 6 of 6)	intron (NR_040697, intron 6 of 6)	24478	NR_040697	100038706	Mm.334690	NR_040697	ENSMUSG00000099207	Gm10637	ENSMUSG00000074176	predicted gene 10637	ncRNA
mm_27543.1	chr3	57692528	57692549	-	1	NA	promoter-TSS (NM_001033349)	promoter-TSS (NM_001033349)	-1	NM_001033349	242037	Mm.291091	NM_001033349	ENSMUSG00000074591	Ankub1	Gm410	ankrin repeat and ubiquitin domain containing 1	protein-coding
mm_19748.1	chr2	104849496	104849502	-	1	NA	intron (NM_178695, intron 1 of 5)	CpG	351	NM_178695	228413	Mm.259609	NM_178695	ENSMUSG00000027171	Prrg4	9930111I18Rik|TMG4	proline rich Gla (G-carboxyglutamic acid) 4 (transmembrane)	protein-coding
mm_101876.1	chr11	48893416	48893432	-	1	NA	intron (NM_001024230, intron 4 of 4)	L1M2|LINE|L1	8728	NM_001024230	432555	Mm.338931	NM_001024230	ENSMUSG00000058163	Gm5431	EG432555|Irgb9b8	predicted gene 5431	protein-coding
mm_19482.1	chr2	93046141	93046172	-	1	NA	promoter-TSS (NM_001177536)	promoter-TSS (NM_001177536)	-12	NM_001177536	100042784	Mm.102816	NM_001177536	ENSMUSG00000075028	Prdm11	8030443D09Rik|AA163972|Gm707	PR domain containing 11	protein-coding
mm_3595.1	chr1	151499909	151499925	+	1	NA	intron (NM_011277, intron 1 of 6)	intron (NM_011277, intron 1 of 6)	906	NM_011277	19821	Mm.474038	NM_011277	ENSMUSG00000026484	Rnf2	AI326319|AI450156|AU019207|Ring1B|dinG	ring finger protein 2	protein-coding
mm_129340.1	chr15	77838573	77838576	-	1	NA	intron (NM_022410, intron 1 of 40)	intron (NM_022410, intron 1 of 40)	3601	NM_022410	17886	Mm.29677	NM_022410	ENSMUSG00000022443	Myh9	Fltn|Myhn-1|Myhn1|NMHCIIA|NMMHC-A|NMMHC-IIA|TU72.6	myosin, heavy polypeptide 9, non-muscle	protein-coding
mm_45894.1	chr5	88670207	88670256	-	1	NA	exon (NM_178700, exon 5 of 10)	exon (NM_178700, exon 5 of 10)	5349	NM_001098476	231413	Mm.332474	NM_178700	ENSMUSG00000044221	Grsf1	BB232551|C80280|D5Wsu31e	G-rich RNA sequence binding factor 1	protein-coding
mm_77950.1	chr9	7502341	7502345	+	1	NA	promoter-TSS (NM_019471)	promoter-TSS (NM_019471)	1	NM_019471	17384	Mm.14126	NM_019471	ENSMUSG00000047562	Mmp10	AV377895|MMP-10|SL-2	matrix metallopeptidase 10	protein-coding
mm_47412.1	chr5	123135549	123135559	-	1	NA	Intergenic	CpG	-2925	NM_175092	23912	Mm.253876	NM_175092	ENSMUSG00000029449	Rhof	AI845056|AV026554|Arhf|Ifld1|Rif	ras homolog family member F (in filopodia)	protein-coding
mm_103962.1	chr11	84442645	84442668	-	1	NA	intron (NM_019816, intron 11 of 12)	intron (NM_019816, intron 11 of 12)	70845	NM_019816	56321	Mm.257482	NM_019816	ENSMUSG00000018697	Aatf	4933415H02Rik|5830465M17Rik|Che-1|Trb	apoptosis antagonizing transcription factor	protein-coding
mm_168300.1	chr11	106250615	106250620	-	1	NA	exon (NM_025310, exon 16 of 21)	exon (NM_025310, exon 16 of 21)	5185	NM_025310	56095	Mm.29795	NM_025310	ENSMUSG00000020706	Ftsj3	AA537063|AU045295|C79843|D11Ertd400e|Epcs3	FtsJ RNA methyltransferase homolog 3 (E. coli)	protein-coding
mm_108762.1	chr12	89403737	89403742	+	1	NA	intron (NM_172544, intron 8 of 19)	intron (NM_172544, intron 8 of 19)	-408744	NM_001252074	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding
mm_10582.1	chr2	18171752	18171755	+	1	NA	intron (NR_045539, intron 15 of 24)	intron (NR_045539, intron 15 of 24)	107168	NM_001252561	17354	Mm.209175	NM_010804	ENSMUSG00000026743	Mllt10	Af10|B130021D15Rik|D630001B22Rik|mKIAA4140	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 10	protein-coding
mm_152983.1	chr19	29522172	29522191	-	1	NA	promoter-TSS (NM_001081319)	promoter-TSS (NM_001081319)	-101	NM_001081319	226089	Mm.353838	NM_177641	ENSMUSG00000038658	Ric1	C030046E11Rik|C130057E09Rik|Kiaa1432	RAB6A GEF complex partner 1	protein-coding
mm_67023.1	chr7	66337140	66337175	-	1	NA	intron (NM_146191, intron 3 of 33)	intron (NM_146191, intron 3 of 33)	44567	NR_106024	102465640		NR_106024	ENSMUSG00000098353	Mir7057	Gm27550|mmu-mir-7057	microRNA 7057	ncRNA
mm_153643.1	chr19	44215551	44215566	-	1	NA	exon (NM_024450, exon 2 of 6)	exon (NM_024450, exon 2 of 6)	12270	NM_024450	30049	Mm.480594	NM_024450	ENSMUSG00000025202	Scd3	4930513N16Rik	stearoyl-coenzyme A desaturase 3	protein-coding
mm_140848.1	chr17	23676661	23676684	-	1	NA	intron (NM_013749, intron 1 of 3)	CpG	777	NM_001161746	27279	Mm.28518	NM_013749	ENSMUSG00000023905	Tnfrsf12a	AI255180|C87282|Fn14|HPIP|TWEAK-R|TweakR	tumor necrosis factor receptor superfamily, member 12a	protein-coding
mm_84479.1	chr9	66834708	66834710	-	1	NA	promoter-TSS (NM_026674)	promoter-TSS (NM_026674)	-3	NM_026674	68318	Mm.284229	NM_026674	ENSMUSG00000053040	Aph1c	0610008A10Rik|APH-1b|Aph1b	aph1 homolog C, gamma secretase subunit	protein-coding
mm_50094.1	chr6	41532983	41533003	+	1	NA	Intergenic	Intergenic	11217	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_41839.1	chr5	104349135	104349145	+	1	NA	Intergenic	Intergenic	23811	NM_053172	94111	Mm.196672	NM_053172	ENSMUSG00000053863	Mepe	Of45	matrix extracellular phosphoglycoprotein with ASARM motif (bone)	protein-coding
mm_118617.1	chr14	21052578	21052589	+	1	NA	promoter-TSS (NM_134079)	promoter-TSS (NM_134079)	9	NM_134079	11534	Mm.188734	NM_134079	ENSMUSG00000039197	Adk	2310026J05Rik|5033405D03Rik|AI255373|AI987814|Ak	adenosine kinase	protein-coding
mm_138363.1	chr17	34998744	34998756	+	1	NA	exon (NM_033075, exon 2 of 2)	exon (NM_033075, exon 2 of 2)	1996	NM_033075	110956	Mm.22506	NM_033075		D17H6S56E-5	G7e	DNA segment, Chr 17, human D6S56E 5	protein-coding
mm_122299.1	chr14	34600137	34600147	-	1	NA	promoter-TSS (NM_001128599)	promoter-TSS (NM_001128599)	0	NM_001128599	30044	Mm.272060	NM_013887	ENSMUSG00000021799	Opn4	1110007J02Rik|Gm533	opsin 4 (melanopsin)	protein-coding
mm_14733.1	chr2	144271012	144271055	+	1	NA	promoter-TSS (NM_024225)	promoter-TSS (NM_024225)	129	NM_001289630	74528	Mm.386817	NM_028984	ENSMUSG00000027424	Mgme1	8430406I07Rik|AI426476	mitochondrial genome maintainance exonuclease 1	protein-coding
mm_65570.1	chr7	27181152	27181162	-	1	NA	promoter-TSS (NM_019394)	promoter-TSS (NM_019394)	-8	NM_019394	12587	Mm.262447	NM_019394	ENSMUSG00000089661	Mia	CD-RAP|Cdrap|Mia1	melanoma inhibitory activity	protein-coding
mm_17074.1	chr2	22745294	22745327	-	1	NA	Intergenic	Intergenic	-29017	NM_019456	54519	Mm.14255	NM_019456	ENSMUSG00000026786	Apbb1ip	9930118P07Rik|Prp48	amyloid beta (A4) precursor protein-binding, family B, member 1 interacting protein	protein-coding
mm_86453.1	chr10	4341198	4341199	+	1	NA	intron (NM_031185, intron 2 of 3)	intron (NM_031185, intron 2 of 3)	46910	NM_001033466	381990	Mm.262466	NM_001033466	ENSMUSG00000075327	Zbtb2	Gm1103	zinc finger and BTB domain containing 2	protein-coding
mm_87588.1	chr10	57486419	57486454	+	1	NA	promoter-TSS (NM_008297)	promoter-TSS (NM_008297)	51	NM_008297	15500	Mm.261395	NM_008297	ENSMUSG00000019878	Hsf2	AI661205	heat shock factor 2	protein-coding
mm_99516.1	chr11	103116229	103116235	+	1	NA	promoter-TSS (NM_138753)	promoter-TSS (NM_138753)	-93	NM_138753	192231	Mm.8763	NM_138753	ENSMUSG00000048878	Hexim1	7330426E13Rik|CLP-1|Clp1|HIS1	hexamethylene bis-acetamide inducible 1	protein-coding
mm_154992.1	chrX	38329033	38329034	+	1	NA	intron (NM_133690, intron 4 of 7)	URR1B|DNA|hAT-Charlie	12911	NM_133690	67821	Mm.60134	NM_133690	ENSMUSG00000016327	Atp1b4	1110020B02Rik	ATPase, (Na+)/K+ transporting, beta 4 polypeptide	protein-coding
mm_165794.1	chr3	138860518	138860527	+	1	NA	intron (NM_019571, intron 1 of 7)	intron (NM_019571, intron 1 of 7)	118314	NM_019571	56224	Mm.31927	NM_019571	ENSMUSG00000028152	Tspan5	2810455A09Rik|4930505M03Rik|NET-4|Tm4sf9	tetraspanin 5	protein-coding
mm_161230.1	chr13	83625282	83625282	+	1	NA	exon (NM_001170537, exon 5 of 11)	exon (NM_001170537, exon 5 of 11)	51675	NM_001347569	17260	Mm.24001	NM_025282	ENSMUSG00000005583	Mef2c	5430401D19Rik|9930028G15Rik|AV011172|Mef2	myocyte enhancer factor 2C	protein-coding
mm_171583.1	chr4	147553221	147553221	+	1	NA	promoter-TSS (NM_001014397)	promoter-TSS (NM_001014397)	-56	NM_001014397	433804	Mm.332047	NM_001014397	ENSMUSG00000065999	Zfp985	Gm13154|OTTMUSG00000010673	zinc finger protein 985	protein-coding
mm_64903.1	chr7	16018239	16018251	-	1	NA	Intergenic	L2a|LINE|L2	-18750	NM_001081418	243842	Mm.440249	NM_001081418	ENSMUSG00000070808	Gltscr1	-	glioma tumor suppressor candidate region gene 1	protein-coding
mm_38414.1	chr4	139130734	139130861	-	1	NA	non-coding (NR_033745, exon 1 of 4)	non-coding (NR_033745, exon 1 of 4)	240	NR_033745	433771	Mm.305990	NM_001163006	ENSMUSG00000050608	Minos1	2310028O11Rik	mitochondrial inner membrane organizing system 1	protein-coding
mm_10937.1	chr2	25468986	25468993	+	1	NA	exon (NM_008963, exon 2 of 7)	exon (NM_008963, exon 2 of 7)	760	NM_008963	19215	Mm.1008	NM_008963	ENSMUSG00000015090	Ptgds	21kDa|L-PGDS|PGD2|PGDS|PGDS2|Ptgs3	prostaglandin D2 synthase (brain)	protein-coding
mm_109276.1	chr12	109546410	109546493	+	1	NA	non-coding (NR_003633, exon 1 of 5)	non-coding (NR_003633, exon 1 of 5)	1053	NR_003633	17263	Mm.289645	NM_144513	ENSMUSG00000021268	Meg3	2900016C05Rik|3110050O07Rik|6330408G06Rik|AI425946|AW108224|D12Bwg1266e|Gtl2|R74756|R75394	maternally expressed 3	ncRNA
mm_21219.1	chr2	155819405	155819434	-	1	NA	promoter-TSS (NR_015528)	promoter-TSS (NR_015528)	-216	NR_015528	613262	Mm.330707	NR_015528	ENSMUSG00000074649	BC029722	-	cDNA sequence BC029722	ncRNA
mm_17389.1	chr2	27072176	27072186	-	1	NA	promoter-TSS (NM_025376)	promoter-TSS (NM_025376)	-20	NM_025376	66139	Mm.330087	NM_025376	ENSMUSG00000009214	Tmem8c	1110002H13Rik|AI131587	transmembrane protein 8C	protein-coding
mm_31119.1	chr4	42952795	42952805	+	1	NA	promoter-TSS (NM_019874)	promoter-TSS (NM_019874)	-294	NM_019874	56323	Mm.20437	NM_019874	ENSMUSG00000036052	Dnajb5	1110058L06Rik|AI462558|Hsc40|Hsp40-3	DnaJ heat shock protein family (Hsp40) member B5	protein-coding
mm_57940.1	chr6	134792394	134792406	-	1	NA	5' UTR (NM_130447, exon 1 of 7)	5' UTR (NM_130447, exon 1 of 7)	228	NM_130447	70686	Mm.491182	NM_130447	ENSMUSG00000030203	Dusp16	3830417M17Rik|AW558566|D6Ertd213e|MKP-7|MKP7|Mkpm	dual specificity phosphatase 16	protein-coding
mm_206.1	chr1	16618774	16618785	+	1	NA	intron (NM_025773, intron 1 of 5)	CpG	559	NM_025773	66799	Mm.122430	NM_025773	ENSMUSG00000025939	Ube2w	6130401J04Rik	ubiquitin-conjugating enzyme E2W (putative)	protein-coding
mm_49207.1	chr6	15720795	15720803	+	1	NA	5' UTR (NM_175088, exon 1 of 5)	5' UTR (NM_175088, exon 1 of 5)	138	NM_175088	16543	Mm.1314	NM_175088	ENSMUSG00000041390	Mdfic	Kdt1|Mdfid	MyoD family inhibitor domain containing	protein-coding
mm_50683.1	chr6	51575828	51575839	+	1	NA	intron (NM_028035, intron 2 of 6)	intron (NM_028035, intron 2 of 6)	31310	NM_001127348	71982	Mm.294166	NM_028035	ENSMUSG00000038301	Snx10	2410004M09Rik	sorting nexin 10	protein-coding
mm_84668.1	chr9	71997251	71997260	-	1	NA	intron (NM_001253862, intron 5 of 19)	B3|SINE|B2	33814	NR_029879	723889		NR_029879	ENSMUSG00000105200	Mir378a	Mir378|Mirn378|mmu-mir-378|mmu-mir-378a	microRNA 378a	ncRNA
mm_22138.1	chr2	170591651	170591655	-	1	NA	intron (NR_027825, intron 1 of 1)	intron (NR_027825, intron 1 of 1)	10364	NR_027825	67637	Mm.158163	NM_026287	ENSMUSG00000043583	4930470P17Rik	-	RIKEN cDNA 4930470P17 gene	ncRNA
mm_19785.1	chr2	107005915	107005919	-	1	NA	Intergenic	ERVB4_3-LTR_MM|LTR|ERVK	-31520	NM_001025102	212772	Mm.381231	NM_173750	ENSMUSG00000027122	Arl14ep	2700007P21Rik|4930448O08Rik|ARF7EP	ADP-ribosylation factor-like 14 effector protein	protein-coding
mm_153334.1	chr19	38125259	38125306	-	1	NA	promoter-TSS (NM_011255)	promoter-TSS (NM_011255)	39	NM_001159487	19662	Mm.2605	NM_011255	ENSMUSG00000024990	Rbp4	Rbp-4	retinol binding protein 4, plasma	protein-coding
mm_121282.1	chr14	104129059	104129059	+	1	NA	Intergenic	Intergenic	-101917	NR_045953	73877	Mm.399172	NR_045953		4930432J09Rik	-	RIKEN cDNA 4930432J09 gene	ncRNA
mm_121548.1	chr14	122475185	122475191	+	1	NA	promoter-TSS (NR_045046)	promoter-TSS (NR_045046)	11	NR_045046	69248	Mm.235369	NR_045046	ENSMUSG00000085555	2610035F20Rik	-	RIKEN cDNA 2610035F20 gene	ncRNA
mm_152344.1	chr19	9984266	9984326	-	1	NA	TTS (NM_011913)	TTS (NM_011913)	1650	NM_010239	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
mm_60931.1	chr7	46850235	46850253	+	1	NA	exon (NM_001136069, exon 4 of 8)	exon (NM_001136069, exon 4 of 8)	3162	NM_001136069	16828	Mm.29324	NM_010699	ENSMUSG00000063229	Ldha	Ldh1|Ldhm|l7R2	lactate dehydrogenase A	protein-coding
mm_33624.1	chr4	132737626	132737629	+	1	NA	intron (NM_133888, intron 7 of 7)	IAPEY3_LTR|LTR|ERVK	-5081	NM_201368	381560	Mm.44558	NM_201368	ENSMUSG00000037752	Xkr8	4931440N07Rik|AI597014|Gm1031|XRG8|mXkr8	X-linked Kx blood group related 8	protein-coding
mm_3965.1	chr1	164151804	164151814	+	1	NA	promoter-TSS (NM_007976)	promoter-TSS (NM_007976)	-26	NM_007976	14067	Mm.12900	NM_007976	ENSMUSG00000026579	F5	AI173222|Cf-5|Cf5	coagulation factor V	protein-coding
mm_29360.1	chr3	108562329	108562346	-	1	NA	5' UTR (NM_026198, exon 1 of 3)	5' UTR (NM_026198, exon 1 of 3)	129	NM_026198	67495	Mm.32615	NM_026198	ENSMUSG00000068732	Tmem167b	2010200O16Rik	transmembrane protein 167B	protein-coding
mm_82451.1	chr9	15357818	15357829	-	1	NA	promoter-TSS (NM_176976)	promoter-TSS (NM_176976)	-35	NM_176976	319675	Mm.218317	NM_176976	ENSMUSG00000046111	Cep295	5830418K08Rik|5832426L23Rik|Gm1131|Kiaa1731	centrosomal protein 295	protein-coding
mm_47159.1	chr5	120685747	120685767	-	1	NA	intron (NM_008052, intron 3 of 9)	intron (NM_008052, intron 3 of 9)	25912	NM_008052	14357	Mm.1645	NM_008052	ENSMUSG00000029603	Dtx1	Fxit1|mKIAA4160	deltex 1, E3 ubiquitin ligase	protein-coding
mm_57038.1	chr6	122339523	122339579	-	1	NA	intron (NM_001271579, intron 1 of 14)	CpG	106	NM_001042623	13619	Mm.6822	NM_007905	ENSMUSG00000040669	Phc1	AW557034|Edr|Edr1|Mph1|Rae-28|rae28	polyhomeotic-like 1 (Drosophila)	protein-coding
mm_167390.1	chr8	94978898	94978906	+	1	NA	intron (NM_001198894, intron 1 of 13)	intron (NM_001198894, intron 1 of 13)	1793	NM_001198894	14766	Mm.290834	NM_018882	ENSMUSG00000031785	Adgrg1	Cyt28|Gpr56|TM7LN4|TM7XN1	adhesion G protein-coupled receptor G1	protein-coding
mm_77634.1	chr8	124149797	124149800	-	1	NA	Intergenic	Intergenic	-81596	NM_139272	108148	Mm.33808	NM_139272	ENSMUSG00000089704	Galnt2	AI480629	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2	protein-coding
mm_142021.1	chr17	35204647	35204654	-	1	NA	promoter-TSS (NR_105940)	promoter-TSS (NR_105940)	-93	NR_105940	102466990		NR_105940	ENSMUSG00000099006	Mir6974	Gm27658|mmu-mir-6974	microRNA 6974	ncRNA
mm_137367.1	chr17	25471565	25471637	+	1	NA	promoter-TSS (NM_027951)	promoter-TSS (NM_027951)	11	NM_027951	71840	Mm.282330	NM_027951	ENSMUSG00000024175	Tekt4	1700010L19Rik	tektin 4	protein-coding
mm_91618.1	chr10	41685939	41685952	-	1	NA	Intergenic	Intergenic	-79350	NM_001303469	75973	Mm.228517	NM_029493	ENSMUSG00000075225	Ccdc162	5033413D22Rik|Ccdc162p|Gm29096|Gm61|Gm6976	coiled-coil domain containing 162	protein-coding
mm_162260.1	chrY	797375	797375	-	1	NA	promoter-TSS (NM_009570)	promoter-TSS (NM_009570)	34	NM_009570	22767	Mm.4324	NM_009570	ENSMUSG00000053211	Zfy1	Zfy-1|Zfy2	zinc finger protein 1, Y-linked	protein-coding
mm_38420.1	chr4	139192456	139192468	-	1	NA	promoter-TSS (NM_009798)	promoter-TSS (NM_009798)	-437	NM_009798	12345	Mm.2945	NM_009798	ENSMUSG00000028745	Capzb	1700120C01Rik|AI325129|CPB1|CPB2|CPbeat2|CPbeta1|CPbeta2|Cappb1	capping protein (actin filament) muscle Z-line, beta	protein-coding
mm_159740.1	chr5	66676792	66676792	+	1	NA	promoter-TSS (NR_102714)	promoter-TSS (NR_102714)	-295	NR_102714	101202684	Mm.381468	NR_102714	ENSMUSG00000087601	Uchl1os	Gm16832|Uchl1as	ubiquitin carboxy-terminal hydrolase L1, opposite strand	ncRNA
mm_113597.1	chr13	41001301	41001320	+	1	NA	5' UTR (NM_026550, exon 1 of 10)	5' UTR (NM_026550, exon 1 of 10)	300	NM_026550	68083	Mm.24789	NM_026550	ENSMUSG00000038683	Pak1ip1	5830431I15Rik|5930415H02Rik|AA419825|AI314040|AW556169|Gdpd1|PIP1	PAK1 interacting protein 1	protein-coding
mm_98249.1	chr11	88222237	88222245	+	1	NA	Intergenic	Eulor3|DNA?|DNA?	17853	NM_001291271	64656	Mm.168680	NM_024174	ENSMUSG00000023723	Mrps23	D11Bwg1153e|MRP-S23|Rpms23|S23mt	mitochondrial ribosomal protein S23	protein-coding
mm_121691.1	chr14	13961203	13961278	-	1	NA	promoter-TSS (NM_025435)	promoter-TSS (NM_025435)	73	NM_001285780	66231	Mm.295875	NM_025435	ENSMUSG00000053453	Thoc7	Nif3l1bp1	THO complex 7	protein-coding
mm_69333.1	chr7	128744729	128744763	-	1	NA	promoter-TSS (NM_001029982)	promoter-TSS (NM_001029982)	-124	NM_001029982	207352	Mm.297105	NM_001029982	ENSMUSG00000055319	Sec23ip	D7Ertd373e|p125	Sec23 interacting protein	protein-coding
mm_34249.1	chr4	141282786	141282826	+	1	NA	Intergenic	BGLII_B|LTR|ERVK	-18415	NM_010139	13836	Mm.2581	NM_010139	ENSMUSG00000006445	Epha2	AW545284|Eck|Myk2|Sek-2|Sek2	Eph receptor A2	protein-coding
mm_145610.1	chr18	61099477	61099490	+	1	NA	Intergenic	Intergenic	-6089	NM_001037859	12978	Mm.22574	NM_007779	ENSMUSG00000024621	Csf1r	AI323359|CD115|CSF-1R|Csfmr|Fim-2|Fim2|Fms|M-CSF-R|M-CSFR	colony stimulating factor 1 receptor	protein-coding
mm_35509.1	chr4	41093669	41093689	-	1	NA	exon (NM_016689, exon 6 of 6)	exon (NM_016689, exon 6 of 6)	4504	NM_016689	11828	Mm.34043	NM_016689	ENSMUSG00000028435	Aqp3	AQP-2	aquaporin 3	protein-coding
mm_137346.1	chr17	25159655	25159699	+	1	NA	exon (NM_011930, exon 23 of 25)	exon (NM_011930, exon 23 of 25)	-2784	NM_001079929	207209	Mm.207121	NM_001079929	ENSMUSG00000059562	Ccdc154	Ccdc157|Gm317	coiled-coil domain containing 154	protein-coding
mm_11395.1	chr2	31462158	31462181	+	1	NA	Intergenic	Intergenic	-8101	NM_007494	11898	Mm.3217	NM_007494	ENSMUSG00000076441	Ass1	AA408052|ASS|Ass-1|fold	argininosuccinate synthetase 1	protein-coding
mm_168082.1	chr10	121944983	121944986	-	1	NA	intron (NM_001242411, intron 1 of 21)	intron (NM_001242411, intron 1 of 21)	102331	NM_001242411	117600	Mm.288698	NM_001081037	ENSMUSG00000020121	Srgap1	4930572H05Rik|Arhgap13	SLIT-ROBO Rho GTPase activating protein 1	protein-coding
mm_117335.1	chr13	69534113	69534139	-	1	NA	promoter-TSS (NM_198600)	promoter-TSS (NM_198600)	-262	NM_001169131	210106	Mm.315959	NM_198600	ENSMUSG00000034575	Papd7	LAK-1|POLK|Pols|TRF4|TRF4-1	PAP associated domain containing 7	protein-coding
mm_164774.1	chr17	90075120	90075126	+	1	NA	intron (NM_001346959, intron 5 of 6)	intron (NM_001346959, intron 5 of 6)	13245	NM_001346962	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_160273.1	chr7	118764347	118764347	+	1	NA	intron (NM_027815, intron 8 of 30)	RMER19B|LTR|ERVK	24076	NM_027815	71517	Mm.213298	NM_027815	ENSMUSG00000030982	9030624J02Rik	2610029J22Rik	RIKEN cDNA 9030624J02 gene	protein-coding
mm_165955.1	chr4	87230022	87230032	-	1	NA	intron (NM_172426, intron 1 of 10)	intron (NM_172426, intron 1 of 10)	513	NM_172426	76376	Mm.490487	NM_172426	ENSMUSG00000037996	Slc24a2	2810021B17Rik|6330417K15Rik|AI847460|Nckx2	solute carrier family 24 (sodium/potassium/calcium exchanger), member 2	protein-coding
mm_13606.1	chr2	113327712	113327753	+	1	NA	promoter-TSS (NM_010230)	promoter-TSS (NM_010230)	-4	NM_001285458	14260	Mm.4938	NM_010230	ENSMUSG00000044042	Fmn1	Fmn|formin-1|ld	formin 1	protein-coding
mm_105033.1	chr11	100527863	100527878	-	1	NA	5' UTR (NM_134037, exon 1 of 28)	5' UTR (NM_134037, exon 1 of 28)	130	NM_134037	104112	Mm.282039	NM_134037	ENSMUSG00000020917	Acly	A730098H14Rik|AW538652	ATP citrate lyase	protein-coding
mm_39602.1	chr5	23787758	23787774	+	1	NA	promoter-TSS (NM_177323)	promoter-TSS (NM_177323)	55	NM_001310467	72772	Mm.133300	NM_177323	ENSMUSG00000028999	Rint1	1500019C06Rik|2810450M21Rik|Rint-1	RAD50 interactor 1	protein-coding
mm_95998.1	chr11	59209124	59209164	+	1	NA	exon (NM_024210, exon 4 of 7)	exon (NM_024210, exon 4 of 7)	783	NM_024210	67862	Mm.358708	NM_024210	ENSMUSG00000020441	2310033P09Rik	Mmtag2	RIKEN cDNA 2310033P09 gene	protein-coding
mm_76555.1	chr8	88362032	88362034	-	1	NA	5' UTR (NM_012047, exon 1 of 17)	5' UTR (NM_012047, exon 1 of 17)	158	NM_012047	26992	Mm.5400	NM_012047	ENSMUSG00000031660	Brd7	BP75|CELTIX1|Ptpn13ip	bromodomain containing 7	protein-coding
mm_128178.1	chr15	34443726	34443733	-	1	NA	promoter-TSS (NR_028101)	promoter-TSS (NR_028101)	-453	NM_001163485	19946	Mm.358632	NM_009083	ENSMUSG00000058600	Rpl30	-	ribosomal protein L30	protein-coding
mm_127950.1	chr15	10720343	10720343	-	1	NA	intron (NR_045065, intron 3 of 3)	intron (NR_045065, intron 3 of 3)	5443	NR_045065	75259	Mm.33928	NR_045063	ENSMUSG00000097058	4930556M19Rik	1700009D01Rik|C130022M03Rik	RIKEN cDNA 4930556M19 gene	ncRNA
mm_156274.1	chrX	136836118	136836127	+	1	NA	3' UTR (NM_011123, exon 7 of 7)	3' UTR (NM_011123, exon 7 of 7)	13376	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_30883.1	chr4	32248537	32248557	+	1	NA	Intergenic	Intergenic	-168888	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_164272.1	chr15	101485193	101485233	+	1	NA	TTS (NM_001201323)	TTS (NM_001201323)	6090	NM_016879	53622	Mm.347934	NM_016879		Krt85	AA589597|BB007925|Hb5|Krt2-18	keratin 85	protein-coding
mm_119945.1	chr14	54990732	54990748	+	1	NA	intron (NM_080728, intron 10 of 40)	intron (NM_080728, intron 10 of 40)	3809	NM_080728	140781	Mm.457983	NM_080728	ENSMUSG00000053093	Myh7	B-MHC|MyHC-I|Myhc-b|Myhcb|beta-MHC	myosin, heavy polypeptide 7, cardiac muscle, beta	protein-coding
mm_23370.1	chr3	55461868	55461961	+	1	NA	5' UTR (NM_001111052, exon 1 of 14)	5' UTR (NM_001111052, exon 1 of 14)	156	NM_001195540	13175	Mm.393242	NM_019978	ENSMUSG00000027797	Dclk1	1700113D08Rik|2810480F11Rik|AI836758|Click-I|Cpg16|Dcamkl1|Dcl|Dclk|mKIAA0369	doublecortin-like kinase 1	protein-coding
mm_7082.1	chr1	88462567	88462595	-	1	NA	Intergenic	Intergenic	47485	NM_008132	14659	Mm.5187	NM_008132	ENSMUSG00000062310	Glrp1	GRP-1	glutamine repeat protein 1	protein-coding
mm_105800.1	chr11	110154746	110154750	-	1	NA	intron (NM_147220, intron 7 of 38)	ORR1F|LTR|ERVL-MaLR	13405	NM_147220	217262	Mm.291459	NM_147220	ENSMUSG00000041797	Abca9	D630040K07Rik	ATP-binding cassette, sub-family A (ABC1), member 9	protein-coding
mm_47841.1	chr5	134314515	134314548	-	1	NA	5' UTR (NM_010365, exon 1 of 34)	5' UTR (NM_010365, exon 1 of 34)	229	NM_001080746	14886	Mm.261570	NM_010365	ENSMUSG00000060261	Gtf2i	6030441I21Rik|BAP-135|Diws1t|GtfII-I|Spin|TFII-I|WBSCR6	general transcription factor II I	protein-coding
mm_72455.1	chr8	83172890	83172903	+	1	NA	intron (NM_027758, intron 1 of 17)	intron (NM_027758, intron 1 of 17)	7544	NM_027758	71310	Mm.24031	NM_027758	ENSMUSG00000031709	Tbc1d9	4933431N12Rik|AI847101|AW490653|C76116	TBC1 domain family, member 9	protein-coding
mm_18751.1	chr2	73386397	73386479	-	1	NA	promoter-TSS (NM_001276443)	promoter-TSS (NM_001276443)	42	NM_001276443	68526	Mm.451014	NM_001080707	ENSMUSG00000041762	Gpr155	1110017O10Rik|DEPDC3|F730029F15Rik|PGR22	G protein-coupled receptor 155	protein-coding
mm_17748.1	chr2	32714953	32714957	-	1	NA	Intergenic	Intergenic	-1983	NR_039536	100628606		NR_039536	ENSMUSG00000105841	Mir3960	mmu-mir-3960	microRNA 3960	ncRNA
mm_57767.1	chr6	129235817	129235831	-	1	NA	intron (NR_040265, intron 1 of 2)	intron (NR_040265, intron 1 of 2)	2221	NR_040265	76432	Mm.261738	NR_040265	ENSMUSG00000097354	2310001H17Rik	AI646108	RIKEN cDNA 2310001H17 gene	ncRNA
mm_26667.1	chr3	154711126	154711133	+	1	NA	promoter-TSS (NM_175176)	promoter-TSS (NM_175176)	-4	NM_175176	209601	Mm.331454	NM_175176	ENSMUSG00000078161	Erich3	1700013E18Rik|4922501L14Rik|5031409G23Rik|AI596448|Gm133	glutamate rich 3	protein-coding
mm_127329.1	chr15	100364564	100364573	+	1	NA	promoter-TSS (NM_001002900)	promoter-TSS (NM_001002900)	-17	NM_001002900	380975	Mm.268451	NM_001002900	ENSMUSG00000093550	Higd1c	Gm921|HIG1-4|Yghl1-4	HIG1 domain family, member 1C	protein-coding
mm_163989.1	chr14	62654266	62654267	+	1	NA	Intergenic	L1_Mur2|LINE|L1	-9401	NM_001199945	319433	Mm.483827	NM_001199945	ENSMUSG00000091155	Serpine3	E130113E03Rik	serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 3	protein-coding
mm_25347.1	chr3	106785479	106785489	+	1	NA	intron (NM_007651, intron 1 of 7)	intron (NM_007651, intron 1 of 7)	4665	NM_007651	12508	Mm.316861	NM_007651	ENSMUSG00000040747	Cd53	AI323659|Ox-44|Tspan25	CD53 antigen	protein-coding
mm_24311.1	chr3	89418633	89418654	+	1	NA	promoter-TSS (NM_011368)	promoter-TSS (NM_011368)	92	NM_011368	20416	Mm.86595	NM_011368	ENSMUSG00000042626	Shc1	Shc|ShcA|p66|p66shc	src homology 2 domain-containing transforming protein C1	protein-coding
mm_170114.1	chr17	39845539	39845557	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	2551	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_85142.1	chr9	95815344	95815374	-	1	NA	intron (NM_001033210, intron 1 of 15)	intron (NM_001033210, intron 1 of 15)	29920	NM_001033210	102502	Mm.11869	NM_001033210	ENSMUSG00000049493	Pls1	AI427122	plastin 1 (I-isoform)	protein-coding
mm_77395.1	chr8	120332894	120332912	-	1	NA	Intergenic	Intergenic	-104673	NR_110496	434353	Mm.411793	NR_110496	ENSMUSG00000097960	A330074K22Rik	-	RIKEN cDNA A330074K22 gene	ncRNA
mm_70564.1	chr8	13105716	13105764	+	1	NA	promoter-TSS (NM_178708)	promoter-TSS (NM_178708)	19	NM_146207	99375	Mm.212861	NM_146207	ENSMUSG00000031446	Cul4a	2810470J21Rik|AW495282	cullin 4A	protein-coding
mm_32758.1	chr4	116687327	116687329	+	1	NA	intron (NM_011034, intron 1 of 5)	intron (NM_011034, intron 1 of 5)	-1306	NR_040442	100502959	Mm.395400	NR_040442		AV051173	-	expressed sequence AV051173	ncRNA
mm_48780.1	chr5	148552412	148552428	-	1	NA	5' UTR (NM_011908, exon 1 of 5)	5' UTR (NM_011908, exon 1 of 5)	368	NM_011908	24109	Mm.21846	NM_011908	ENSMUSG00000001687	Ubl3	AW108023|HCG	ubiquitin-like 3	protein-coding
mm_48554.1	chr5	143056025	143056028	-	1	NA	intron (NM_080561, intron 13 of 16)	intron (NM_080561, intron 13 of 16)	56994	NM_207110	108086	Mm.381440	NM_080561	ENSMUSG00000045078	Rnf216	2810055G22Rik|AI647468|AU019462|C86502|F830018F18Rik|TRIAD3|UIP83|Ubce7ip1	ring finger protein 216	protein-coding
mm_169387.1	chr14	42133874	42133893	+	1	NA	Intergenic	Intergenic	-38606	NR_073362	73553	Mm.243777	NM_028570	ENSMUSG00000090462	1700091H14Rik	100041930|Gm3578	RIKEN cDNA 1700091H14 gene	ncRNA
mm_125040.1	chr15	25774241	25774254	+	1	NA	intron (NM_019472, intron 19 of 40)	intron (NM_019472, intron 19 of 40)	-69051	NM_001034851	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_46526.1	chr5	105415688	105415704	-	1	NA	promoter-TSS (NM_001033550)	promoter-TSS (NM_001033550)	-79	NM_001033550	433926	Mm.439781	NM_001033550	ENSMUSG00000070639	Lrrc8b	R75581|Ta-lrrp|mKIAA0231	leucine rich repeat containing 8 family, member B	protein-coding
mm_154079.1	chr19	56548215	56548264	-	1	NA	promoter-TSS (NM_018831)	promoter-TSS (NM_018831)	-17	NM_018831	55947	Mm.2805	NM_018831	ENSMUSG00000025077	Dclre1a	2810043H12Rik|AU022226|Pso2|Smn1a|Snm1|mKIAA0086	DNA cross-link repair 1A	protein-coding
mm_2383.1	chr1	93479069	93479073	+	1	NA	promoter-TSS (NM_010891)	promoter-TSS (NM_010891)	10	NM_001159719	18000	Mm.428652	NM_010891	ENSMUSG00000026276	Sept2	AW208991|Nedd-5|Nedd5|mKIAA0158	septin 2	protein-coding
mm_149228.1	chr19	10041661	10041680	+	1	NA	5' UTR (NM_021890, exon 1 of 12)	5' UTR (NM_021890, exon 1 of 12)	122	NM_021890	60527	Mm.253875	NM_021890	ENSMUSG00000024664	Fads3	AI464531	fatty acid desaturase 3	protein-coding
mm_108237.1	chr12	77241348	77241365	+	1	NA	intron (NR_045554, intron 1 of 11)	intron (NR_045554, intron 1 of 11)	2617	NR_045554	53618	Mm.35628	NM_016893	ENSMUSG00000021065	Fut8	-	fucosyltransferase 8	protein-coding
mm_2415.1	chr1	94016909	94016912	+	1	NA	Intergenic	Intergenic	-3583	NM_173772	241159	Mm.214565	NM_173772	ENSMUSG00000034000	Neu4	9330166I04	sialidase 4	protein-coding
mm_34619.1	chr4	150548894	150548898	+	1	NA	intron (NM_001085492, intron 11 of 22)	B2_Mm2|SINE|B2	103278	NM_173774	242773	Mm.29280	NM_173774	ENSMUSG00000039838	Slc45a1	C230078B22|Dnb5	solute carrier family 45, member 1	protein-coding
mm_22091.1	chr2	168767287	168767297	-	1	NA	promoter-TSS (NM_201396)	promoter-TSS (NM_201396)	-91	NM_175303	99377	Mm.434054	NM_175303	ENSMUSG00000027547	Sall4	5730441M18Rik|AA407717|AL022809|AW536104|C330011P20Rik|C78083|C78563|Tex20	sal-like 4 (Drosophila)	protein-coding
mm_8806.1	chr1	161876611	161876647	-	1	NA	promoter-TSS (NM_172645)	promoter-TSS (NM_172645)	32	NM_172645	226551	Mm.170002	NM_172645	ENSMUSG00000040297	Suco	4732491B11|AI848100|AU016931|Opt	SUN domain containing ossification factor	protein-coding
mm_115194.1	chr13	108860073	108860106	+	1	NA	5' UTR (NM_011056, exon 2 of 17)	5' UTR (NM_011056, exon 2 of 17)	205912	NM_011056	238871	Mm.434429	NM_011056	ENSMUSG00000021699	Pde4d	9630011N22Rik|Dpde3	phosphodiesterase 4D, cAMP specific	protein-coding
mm_46215.1	chr5	98484238	98484268	-	1	NA	intron (NM_001024614, intron 2 of 5)	intron (NM_001024614, intron 2 of 5)	-8589	NR_030484	735265		NR_030484	ENSMUSG00000105814	Mir703	Mirn703|mir-703|mmu-mir-703	microRNA 703	ncRNA
mm_169936.1	chr16	61377129	61377145	+	1	NA	Intergenic	Intergenic	-771606	NM_007938	13840	Mm.455790	NM_007938	ENSMUSG00000055540	Epha6	Ehk2|Hek12|m-ehk2	Eph receptor A6	protein-coding
mm_24482.1	chr3	92024482	92024524	+	1	NA	intron (NM_207247, intron 2 of 6)	intron (NM_207247, intron 2 of 6)	9920	NM_207247	242100	Mm.297406	NM_207247	ENSMUSG00000042244	Pglyrp3	Gm420	peptidoglycan recognition protein 3	protein-coding
mm_152044.1	chr19	6141129	6141168	-	1	NA	promoter-TSS (NM_019722)	promoter-TSS (NM_019722)	-11	NM_019722	56327	Mm.21071	NM_019722	ENSMUSG00000024944	Arl2	2610009M23Rik|AI115441|AW553335	ADP-ribosylation factor-like 2	protein-coding
mm_167717.1	chr9	98504946	98504956	+	1	NA	intron (NM_009034, intron 2 of 3)	(CAA)n|Simple_repeat|Simple_repeat	14414	NM_009034	19660	Mm.12825	NM_009034	ENSMUSG00000032454	Rbp2	Crbp-2|CrbpII|Rbp-2	retinol binding protein 2, cellular	protein-coding
mm_75790.1	chr8	70095535	70095550	-	1	NA	3' UTR (NM_007789, exon 15 of 15)	3' UTR (NM_007789, exon 15 of 15)	7044	NR_106033	102465646		NR_106033	ENSMUSG00000099042	Mir7066	Gm27290|mmu-mir-7066	microRNA 7066	ncRNA
mm_96757.1	chr11	69911351	69911360	+	1	NA	intron (NM_001013414, intron 25 of 28)	intron (NM_001013414, intron 25 of 28)	-2837	NM_019726	56310	Mm.477738	NM_019726	ENSMUSG00000023170	Gps2	AI505953	G protein pathway suppressor 2	protein-coding
mm_80902.1	chr9	100450359	100450363	+	1	NA	Intergenic	Intergenic	36112	NM_001033543	213208	Mm.242896	NM_001033543	ENSMUSG00000044244	Il20rb	AV228068|Fndc6|Gm186|Il20R2	interleukin 20 receptor beta	protein-coding
mm_25512.1	chr3	110250144	110250178	+	1	NA	exon (NM_178891, exon 1 of 1)	exon (NM_178891, exon 1 of 1)	838	NM_178891	99890	Mm.36115	NM_178891	ENSMUSG00000049300	Prmt6	AW124876|BB233495|Hrmt1l6	protein arginine N-methyltransferase 6	protein-coding
mm_127774.1	chr15	3279634	3279702	-	1	NA	TTS (NM_001166063)	TTS (NM_001166063)	8691	NM_009155	20363	Mm.392203	NM_009155	ENSMUSG00000064373	Selenop	AU018766|D15Ucla1|Se-P|Sepp1|selp	selenoprotein P	protein-coding
mm_82326.1	chr9	8134429	8134480	-	1	NA	promoter-TSS (NM_001045524)	promoter-TSS (NM_001045524)	-160	NM_001045524	234915	Mm.101341	NM_001045524	ENSMUSG00000040729	Cep126	Kiaa1377|mKIAA1377	centrosomal protein 126	protein-coding
mm_154193.1	chr19	58860976	58860997	-	1	NA	promoter-TSS (NM_175199)	promoter-TSS (NM_175199)	-2	NM_175199	73442	Mm.39739	NM_175199	ENSMUSG00000025092	Hspa12a	1700063D12Rik|AI118035|AI840429|AW048913|AW556406|D5Mgi40|Gm19925|mKIAA0417	heat shock protein 12A	protein-coding
mm_39407.1	chr5	14520898	14520908	+	1	NA	exon (NM_011995, exon 2 of 25)	exon (NM_011995, exon 2 of 25)	5985	NM_001110796	26875	Mm.146275	NM_011995	ENSMUSG00000061601	Pclo	Acz|Pico	piccolo (presynaptic cytomatrix protein)	protein-coding
mm_65526.1	chr7	25787407	25787418	-	1	NA	exon (NM_001190974, exon 2 of 19)	exon (NM_001190974, exon 2 of 19)	1321	NM_001190974	26362	Mm.4128	NM_009465	ENSMUSG00000002602	Axl	AI323647|Ark|Tyro7|Ufo	AXL receptor tyrosine kinase	protein-coding
mm_43985.1	chr5	146385240	146385252	+	1	NA	5' UTR (NM_145155, exon 1 of 10)	5' UTR (NM_145155, exon 1 of 10)	240	NM_145155	245880	Mm.472750	NM_145155	ENSMUSG00000029636	Wasf3	Scar3|Wave3	WAS protein family, member 3	protein-coding
mm_48279.1	chr5	138155695	138155740	-	1	NA	promoter-TSS (NM_019747)	promoter-TSS (NM_019747)	27	NM_019747	56314	Mm.19274	NM_019747	ENSMUSG00000037007	Zfp113	4732456B05Rik|mKIAA4229	zinc finger protein 113	protein-coding
mm_11595.1	chr2	33446765	33446777	+	1	NA	Intergenic	Intergenic	-15447	NM_001276332	241311	Mm.296512	NM_001085507	ENSMUSG00000068966	Zbtb34	Gm349|mKIAA1993	zinc finger and BTB domain containing 34	protein-coding
mm_64732.1	chr7	4723818	4723838	-	1	NA	exon (NM_177887, exon 4 of 5)	exon (NM_177887, exon 4 of 5)	1254	NM_001142792	330460	Mm.361851	NM_177887	ENSMUSG00000046456	Tmem150b	A630041N19|Tmem224	transmembrane protein 150B	protein-coding
mm_29343.1	chr3	108256805	108256841	-	1	NA	promoter-TSS (NM_011967)	promoter-TSS (NM_011967)	-103	NM_011967	26442	Mm.208883	NM_011967	ENSMUSG00000068749	Psma5	ZETA	proteasome (prosome, macropain) subunit, alpha type 5	protein-coding
mm_15530.1	chr2	158382925	158382939	+	1	NA	3' UTR (NM_175692, exon 5 of 5)	3' UTR (NM_175692, exon 5 of 5)	7294	NM_175692	319317	Mm.294494	NM_175692	ENSMUSG00000044349	Snhg11	A930034L06Rik|AI854265|AL022637|AW319638|E130013N09Rik	small nucleolar RNA host gene 11	protein-coding
mm_88239.1	chr10	71482985	71483009	+	1	NA	Intergenic	Intergenic	135234	NM_027184	69718	Mm.245867	NM_027184	ENSMUSG00000060733	Ipmk	2410017C19Rik|AA408208|Impk	inositol polyphosphate multikinase	protein-coding
mm_132443.1	chr16	35957024	35957063	+	1	NA	intron (NM_030253, intron 6 of 10)	intron (NM_030253, intron 6 of 10)	-18016	NM_001013371	209200	Mm.390852	NM_001013371	ENSMUSG00000049502	Dtx3l	AU042200|BC023741	deltex 3-like, E3 ubiquitin ligase	protein-coding
mm_129389.1	chr15	78204149	78204198	-	1	NA	promoter-TSS (NM_001330686)	promoter-TSS (NM_001330686)	64	NM_001330686	19293	Mm.2766	NM_013645	ENSMUSG00000005716	Pvalb	PV|Parv|Pva	parvalbumin	protein-coding
mm_128214.1	chr15	36164857	36164866	-	1	NA	promoter-TSS (NM_001081253)	promoter-TSS (NM_001081253)	23	NM_001081253	78803	Mm.26393	NM_175281	ENSMUSG00000048230	Fbxo43	4930533G20Rik|Emi2	F-box protein 43	protein-coding
mm_169877.1	chr16	37777022	37777022	+	1	NA	promoter-TSS (NM_008047)	promoter-TSS (NM_008047)	-33	NM_008047	14314	Mm.182434	NM_008047	ENSMUSG00000022816	Fstl1	AI316791|AW107808|Fstl|TSC-36	follistatin-like 1	protein-coding
mm_84608.1	chr9	70197471	70197478	-	1	NA	Intergenic	RLTR17|LTR|ERVK	-9876	NM_181072	71602	Mm.249311	NM_181072	ENSMUSG00000032220	Myo1e	2310020N23Rik|9130023P14Rik|AA407778|myosin-1e|myr 3	myosin IE	protein-coding
mm_55656.1	chr6	72381755	72381759	-	1	NA	Intergenic	Intergenic	-1289	NM_001080742	53620	Mm.440321	NM_016872	ENSMUSG00000073002	Vamp5	AF119384|Camp	vesicle-associated membrane protein 5	protein-coding
mm_8418.1	chr1	152287997	152288013	-	1	NA	Intergenic	Intergenic	98677	NM_025677	66637	Mm.379120	NM_025677	ENSMUSG00000014980	Tsen15	5730449L18Rik|AL023077|Sen15	tRNA splicing endonuclease subunit 15	protein-coding
mm_95829.1	chr11	55469678	55469716	+	1	NA	promoter-TSS (NM_013716)	promoter-TSS (NM_013716)	-55	NM_013716	27041	Mm.39631	NM_013716	ENSMUSG00000018583	G3bp1	AI849976|B430204O07|C87777|G3bp|mKIAA4115	GTPase activating protein (SH3 domain) binding protein 1	protein-coding
mm_2549.1	chr1	107590059	107590113	+	1	NA	promoter-TSS (NM_001159748)	promoter-TSS (NM_001159748)	80	NM_001159748	20725	Mm.83909	NM_011459	ENSMUSG00000026315	Serpinb8	CAP-2|CAP2|NK10|Spi8|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 8	protein-coding
mm_26451.1	chr3	142637695	142637756	+	1	NA	3' UTR (NM_010260, exon 11 of 11)	3' UTR (NM_010260, exon 11 of 11)	-13779	NR_105802	102465200		NR_105802	ENSMUSG00000098871	Mir6381	Gm27963|mmu-mir-6381	microRNA 6381	ncRNA
mm_91105.1	chr10	19117102	19117106	-	1	NA	Intergenic	Intergenic	-24645	NR_038021	100504265	Mm.383417	NR_038021		Gm20139	-	predicted gene, 20139	ncRNA
mm_84433.1	chr9	66059939	66059969	-	1	NA	promoter-TSS (NM_011149)	promoter-TSS (NM_011149)	-215	NM_011149	19035	Mm.335249	NM_011149	ENSMUSG00000032383	Ppib	AA408962|AA553318|AI844835|Cphn-2|Cphn2|CyP-20b	peptidylprolyl isomerase B	protein-coding
mm_73235.1	chr8	104133821	104133826	+	1	NA	intron (NM_009868, intron 7 of 11)	intron (NM_009868, intron 7 of 11)	-27950	NR_131138	546096	Mm.252264	NR_131138	ENSMUSG00000110053	Gm29682	-	predicted gene, 29682	ncRNA
mm_40329.1	chr5	43910698	43910711	+	1	NA	3' UTR (NM_007646, exon 8 of 8)	3' UTR (NM_007646, exon 8 of 8)	41895	NM_007646	12494	Mm.249873	NM_007646	ENSMUSG00000029084	Cd38	ADPRC 1|Cd38-rs1|I-19	CD38 antigen	protein-coding
mm_51755.1	chr6	87742327	87742339	+	1	NA	intron (NM_001159697, intron 2 of 7)	MTD|LTR|ERVL-MaLR	11464	NM_001159697	58229	Mm.333229	NM_021418	ENSMUSG00000068263	Efcc1	Ccdc48	EF hand and coiled-coil domain containing 1	protein-coding
mm_79600.1	chr9	58488174	58488176	+	1	NA	promoter-TSS (NM_176921)	promoter-TSS (NM_176921)	-428	NM_176921	319477	Mm.153674	NM_176921	ENSMUSG00000066607	6030419C18Rik	-	RIKEN cDNA 6030419C18 gene	protein-coding
mm_110523.1	chr12	54867200	54867203	-	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	-4324	NM_007688	12632	Mm.276826	NM_007688	ENSMUSG00000062929	Cfl2	-	cofilin 2, muscle	protein-coding
mm_166845.1	chr7	19696477	19696491	+	1	NA	exon (NM_009696, exon 4 of 4)	exon (NM_009696, exon 4 of 4)	1914	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_155405.1	chrX	73342615	73342629	+	1	NA	promoter-TSS (NM_031494)	promoter-TSS (NM_031494)	1	NM_001160229	27081	Mm.26595	NM_031494	ENSMUSG00000031365	Zfp275	5430431L06Rik|AI593314|DXBay20|DXHXS52|DXPas8	zinc finger protein 275	protein-coding
mm_55381.1	chr6	58907102	58907119	-	1	NA	promoter-TSS (NM_021432)	promoter-TSS (NM_021432)	16	NM_021432	58243	Mm.389747	NM_021432	ENSMUSG00000055430	Nap1l5	1110020M21Rik	nucleosome assembly protein 1-like 5	protein-coding
mm_135257.1	chr16	37835742	37835746	-	1	NA	3' UTR (NM_008047, exon 11 of 11)	3' UTR (NM_008047, exon 11 of 11)	-32656	NM_177093	320184	Mm.390882	NM_177093	ENSMUSG00000034158	Lrrc58	1810012N18Rik|C330018J07Rik	leucine rich repeat containing 58	protein-coding
mm_87949.1	chr10	63039102	63039117	+	1	NA	5' UTR (NM_026085, exon 2 of 10)	5' UTR (NM_026085, exon 2 of 10)	14597	NM_026085	67307	Mm.368563	NM_026085	ENSMUSG00000020072	Pbld2	3110049J23Rik|Mawbp	phenazine biosynthesis-like protein domain containing 2	protein-coding
mm_99353.1	chr11	101584438	101584477	+	1	NA	exon (NM_144830, exon 4 of 9)	exon (NM_144830, exon 4 of 9)	2215	NM_144830	217203	Mm.280559	NM_144830	ENSMUSG00000034947	Tmem106a	0610008L10Rik|AI043106|BC022145	transmembrane protein 106A	protein-coding
mm_157570.1	chrX	52569120	52569121	-	1	NA	intron (NM_016697, intron 2 of 7)	intron (NM_016697, intron 2 of 7)	-6723	NR_045367	100504594	Mm.447008	NR_045367	ENSMUSG00000055110	A630012P03Rik	-	RIKEN cDNA A630012P03 gene	ncRNA
mm_85240.1	chr9	98955303	98955313	-	1	NA	promoter-TSS (NR_003248)	promoter-TSS (NR_003248)	2	NR_003248	768252	Mm.129645	NR_003248	ENSMUSG00000097072	Foxl2os	ENSMUSG00000074122	forkhead box L2, opposite strand	ncRNA
mm_167405.1	chr8	104250990	104250998	+	1	NA	non-coding (NR_104433, exon 1 of 5)	non-coding (NR_104433, exon 1 of 5)	133	NM_001286383	75458	Mm.269219	NM_029295	ENSMUSG00000054400	Cklf	1700001C14Rik|1810018M11Rik|A730028G07Rik|C32|CKLF1|CKLF3|CKLF4|CKLF5|Cklf2|Cklf6|HSPC224|UCK-1	chemokine-like factor	protein-coding
mm_17660.1	chr2	32079340	32079350	-	1	NA	intron (NM_175511, intron 1 of 1)	intron (NM_175511, intron 1 of 1)	4360	NM_175511	241303	Mm.250441	NM_175511	ENSMUSG00000050592	Fam78a	A130092J06Rik	family with sequence similarity 78, member A	protein-coding
mm_85356.1	chr9	103214533	103214543	-	1	NA	intron (NM_133977, intron 14 of 16)	intron (NM_133977, intron 14 of 16)	-12473	NM_009275	20818	Mm.273053	NM_009275	ENSMUSG00000032553	Srprb	AA409543	signal recognition particle receptor, B subunit	protein-coding
mm_16774.1	chr2	9881963	9881985	-	1	NA	intron (NR_024257, intron 2 of 4)	intron (NR_024257, intron 2 of 4)	728	NR_024257	381347	Mm.441450	NR_024257		4930412O13Rik	ENSMUSG00000075535|Gm10853	RIKEN cDNA 4930412O13 gene	ncRNA
mm_32248.1	chr4	102570184	102570194	+	1	NA	5' UTR (NM_001177980, exon 1 of 10)	5' UTR (NM_001177980, exon 1 of 10)	129	NM_001177980	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_37010.1	chr4	112434006	112434014	-	1	NA	promoter-TSS (NM_177864)	promoter-TSS (NM_177864)	-25	NM_177864	329918	Mm.246783	NM_177864	ENSMUSG00000049972	Skint9	A030013N09Rik|Skint-9	selection and upkeep of intraepithelial T cells 9	protein-coding
mm_147108.1	chr18	35703085	35703099	-	1	NA	promoter-TSS (NM_029669)	promoter-TSS (NM_029669)	52	NM_029669	76594	Mm.108596	NM_029669	ENSMUSG00000024350	Dnajc18	2700075B01Rik|AU041129	DnaJ heat shock protein family (Hsp40) member C18	protein-coding
mm_94749.1	chr11	21105998	21106020	+	1	NA	intron (NM_023324, intron 1 of 6)	AT_rich|Low_complexity|Low_complexity	14685	NM_023324	67245	Mm.28957	NM_023324	ENSMUSG00000020134	Peli1	2810468L03Rik|A930031K15Rik|AA409794|AI586297|D11Ertd676e	pellino 1	protein-coding
mm_151169.1	chr19	53198034	53198058	+	1	NA	intron (NM_013758, intron 1 of 15)	intron (NM_013758, intron 1 of 15)	54049	NM_013758	27360	Mm.426080	NM_013758	ENSMUSG00000025026	Add3	AI463285|R75380	adducin 3 (gamma)	protein-coding
mm_138406.1	chr17	35066866	35066887	+	1	NA	promoter-TSS (NM_023463)	promoter-TSS (NM_023463)	-449	NM_023463	68468	Mm.215096	NM_023463	ENSMUSG00000092586	Ly6g6c	1110003M04Rik|AU016360|G6c|NG24	lymphocyte antigen 6 complex, locus G6C	protein-coding
mm_17256.1	chr2	25847297	25847307	-	1	NA	promoter-TSS (NM_001001714)	promoter-TSS (NM_001001714)	-54	NM_001001714	227631	Mm.301632	NM_001001714	ENSMUSG00000059625	Sohlh1	Gm110|Nohlh	spermatogenesis and oogenesis specific basic helix-loop-helix 1	protein-coding
mm_104631.1	chr11	97435919	97435951	-	1	NA	Intergenic	Intergenic	-14225	NM_021493	58996	Mm.394118	NM_021493	ENSMUSG00000049807	Arhgap23	A330041B18Rik	Rho GTPase activating protein 23	protein-coding
mm_22497.1	chr3	7289505	7289507	+	1	NA	Intergenic	MTB_Mm-int|LTR|ERVL-MaLR	-77098	NM_008862	18767	Mm.3193	NM_008862	ENSMUSG00000027499	Pkia	AI415001|PKIalpha	protein kinase inhibitor, alpha	protein-coding
mm_133771.1	chr16	94694213	94694251	+	1	NA	3' UTR (NM_001113389, exon 12 of 12)	3' UTR (NM_001113389, exon 12 of 12)	82813	NM_001347731	13548	Mm.310973	NM_007890	ENSMUSG00000022897	Dyrk1a	2310043O08Rik|D16Ertd272e|D16Ertd493e|Dyrk|ENSMUSG00000074897|Gm10783|Mnbh|Mp86|mmb	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1a	protein-coding
mm_34970.1	chr4	156008862	156008884	+	1	NA	exon (NM_011341, exon 5 of 7)	exon (NM_011341, exon 5 of 7)	-4822	NM_011659	22163	Mm.13885	NM_011659	ENSMUSG00000029075	Tnfrsf4	ACT35|CD134|Ly-70|Ox40|TXGP1L|Txgp1	tumor necrosis factor receptor superfamily, member 4	protein-coding
mm_157797.1	chrX	73911284	73911304	-	1	NA	promoter-TSS (NM_001162423)	promoter-TSS (NM_001162423)	4	NM_138630	171207	Mm.482337	NM_138630	ENSMUSG00000031389	Arhgap4	A130009C12Rik|A530015A20Rik|Rgc1|c1|mKIAA0131	Rho GTPase activating protein 4	protein-coding
mm_146214.1	chr18	76949035	76949041	+	1	NA	intron (NM_001039201, intron 1 of 6)	intron (NM_001039201, intron 1 of 6)	4620	NM_001039201	76987	Mm.236127	NM_029826	ENSMUSG00000025421	Hdhd2	0610039H12Rik|3110052N05Rik	haloacid dehalogenase-like hydrolase domain containing 2	protein-coding
mm_116542.1	chr13	45933262	45933265	-	1	NA	intron (NM_001199304, intron 2 of 6)	B1_Mur1|SINE|Alu	31728	NM_001199304	20238	Mm.342683	NM_009124	ENSMUSG00000046876	Atxn1	2900016G23Rik|Atx1|C85907|ENSMUSG00000074917|Gm10786|Sca1	ataxin 1	protein-coding
mm_17871.1	chr2	34944509	34944530	-	1	NA	intron (NM_009421, intron 10 of 10)	B4A|SINE|B4	17253	NM_009421	22029	Mm.239514	NM_009421	ENSMUSG00000026875	Traf1	4732496E14Rik	TNF receptor-associated factor 1	protein-coding
mm_54150.1	chr6	22356013	22356053	-	1	NA	promoter-TSS (NM_138587)	promoter-TSS (NM_138587)	48	NM_138587	27999	Mm.490307	NM_138587	ENSMUSG00000029672	Fam3c	D6Wsu176e|Ilei	family with sequence similarity 3, member C	protein-coding
mm_75530.1	chr8	57320307	57320318	-	1	NA	promoter-TSS (NM_010402)	promoter-TSS (NM_010402)	547	NR_110474	102636514		NR_110474	ENSMUSG00000100510	Uph	-	upperhand	ncRNA
mm_440.1	chr1	34801709	34801776	+	1	NA	promoter-TSS (NM_183019)	promoter-TSS (NM_183019)	20	NM_183019	226970	Mm.41604	NM_183019	ENSMUSG00000037509	Arhgef4	9330140K16Rik|Asef|ENSMUSG00000070955	Rho guanine nucleotide exchange factor (GEF) 4	protein-coding
mm_8608.1	chr1	156035955	156035966	-	1	NA	promoter-TSS (NM_001160182)	promoter-TSS (NM_001160182)	-76	NM_001160182	240832	Mm.253335	NM_022329	ENSMUSG00000050565	Tor1aip2	1110020D10Rik|15kDa|A130072J07|AA103493|AW060462|AW610675|C77739|Ifrg15|Lull1	torsin A interacting protein 2	protein-coding
mm_4344.1	chr1	171856917	171856940	+	1	NA	intron (NM_001289470, intron 3 of 8)	L1_Mur3|LINE|L1	17231	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_27228.1	chr3	36449347	36449363	-	1	NA	exon (NM_009673, exon 13 of 13)	exon (NM_009673, exon 13 of 13)	26169	NR_105976	102466786		NR_105976	ENSMUSG00000098808	Mir7009	Gm27472|mmu-mir-7009	microRNA 7009	ncRNA
mm_37863.1	chr4	132303332	132303350	-	1	NA	promoter-TSS (NM_001081651)	promoter-TSS (NM_001081651)	15	NM_001081651	242681	Mm.331927	NM_001081651	ENSMUSG00000089687	Rab42	9530096D07Rik|Rab42-ps	RAB42, member RAS oncogene family	protein-coding
mm_7832.1	chr1	132131844	132131878	-	1	NA	intron (NM_008795, intron 1 of 15)	intron (NM_008795, intron 1 of 15)	7824	NM_008795	18557	Mm.28130	NM_008795	ENSMUSG00000026437	Cdk18	AA682070|Ctk18|Pctk3	cyclin-dependent kinase 18	protein-coding
mm_112154.1	chr12	113287859	113287877	-	1	NA	Intergenic	Intergenic	101965	NM_153776	69195	Mm.313244	NM_153776	ENSMUSG00000049036	Tmem121	2410008J05Rik|Hole	transmembrane protein 121	protein-coding
mm_66848.1	chr7	49636911	49636923	-	1	NA	promoter-TSS (NM_001005232)	promoter-TSS (NM_001005232)	-82	NM_001005232	13172	Mm.307176	NM_001005232	ENSMUSG00000030507	Dbx1	AI426026|Dbx	developing brain homeobox 1	protein-coding
mm_110330.1	chr12	35527615	35527620	-	1	NA	intron (NM_001314027, intron 1 of 9)	Lx8b|LINE|L1	7372	NM_013464	11622	Mm.341377	NM_013464	ENSMUSG00000019256	Ahr	Ah|Ahh|Ahre|In|bHLHe76	aryl-hydrocarbon receptor	protein-coding
mm_13016.1	chr2	90970475	90970479	+	1	NA	intron (NM_001244891, intron 2 of 14)	ID_B1|SINE|B4	30080	NM_017368	13046	Mm.29495	NM_017368	ENSMUSG00000005506	Celf1	1600010O03Rik|AA407467|Brunol2|CUG-BP|CUG-BP1|CUGBP|Cugbp1|D2Wsu101e|HNAB50|NAB50	CUGBP, Elav-like family member 1	protein-coding
mm_167499.1	chr9	13296738	13296825	+	1	NA	Intergenic	(TC)n|Simple_repeat|Simple_repeat	49825	NM_025534	66396	Mm.290620	NM_025534	ENSMUSG00000079084	Ccdc82	2310043N13Rik	coiled-coil domain containing 82	protein-coding
mm_46831.1	chr5	113221231	113221242	-	1	NA	Intergenic	CpG	-5673	NM_001033428	333048	Mm.332586	NM_001033428	ENSMUSG00000066964	Tmem211	Gm854	transmembrane protein 211	protein-coding
mm_171195.1	chr3	46141550	46141552	+	1	NA	Intergenic	Lx|LINE|L1	306390	NM_001101479	241989	Mm.119234	NM_001101479	ENSMUSG00000090919	Pabpc4l	C330050A14Rik|EG241989	poly(A) binding protein, cytoplasmic 4-like	protein-coding
mm_126395.1	chr15	80193074	80193085	+	1	NA	intron (NM_010795, intron 1 of 1)	intron (NM_010795, intron 1 of 1)	19358	NM_010795	17309	Mm.299693	NM_010795	ENSMUSG00000042428	Mgat3	1110038J12Rik|AI848272|GnT-III	mannoside acetylglucosaminyltransferase 3	protein-coding
mm_17250.1	chr2	25684198	25684204	-	1	NA	intron (NM_178036, intron 3 of 5)	intron (NM_178036, intron 3 of 5)	1475	NM_178036	332578	Mm.246797	NM_178036	ENSMUSG00000047356	Lcn10	9230112J07Rik	lipocalin 10	protein-coding
mm_116792.1	chr13	53472713	53472725	-	1	NA	promoter-TSS (NM_013601)	promoter-TSS (NM_013601)	61	NM_013601	17702	Mm.1763	NM_013601	ENSMUSG00000021469	Msx2	BB122635|Hox-8|Hox8|Hox8.1	msh homeobox 2	protein-coding
mm_28824.1	chr3	96290212	96290224	-	1	NA	intron (NM_010186, intron 3 of 5)	intron (NM_010186, intron 3 of 5)	3751	NM_010186	14129	Mm.150	NM_010186	ENSMUSG00000015947	Fcgr1	AI323638|AV092959|CD64|FcgammaRI|IGGHAFC	Fc receptor, IgG, high affinity I	protein-coding
mm_128936.1	chr15	74672561	74672577	-	1	NA	promoter-TSS (NM_018790)	promoter-TSS (NM_018790)	1	NM_001276684	11838	Mm.491310	NM_018790	ENSMUSG00000022602	Arc	Arc3.1|C86064|arg3.1|mArc	activity regulated cytoskeletal-associated protein	protein-coding
mm_134947.1	chr16	31297454	31297465	-	1	NA	exon (NM_007470, exon 6 of 6)	exon (NM_007470, exon 6 of 6)	17349	NM_001301353	11815	Mm.2082	NM_007470	ENSMUSG00000022548	Apod	-	apolipoprotein D	protein-coding
mm_140197.1	chr17	83666836	83666848	+	1	NA	Intergenic	Intergenic	-34947	NM_153512	225030	Mm.223506	NM_153512	ENSMUSG00000045053	Kcng3	KV6.3|Kv10.1a|Kv10.1b	potassium voltage-gated channel, subfamily G, member 3	protein-coding
mm_113302.1	chr13	30749231	30749247	+	1	NA	promoter-TSS (NM_013674)	promoter-TSS (NM_013674)	6	NM_013674	16364	Mm.4677	NM_013674	ENSMUSG00000021356	Irf4	AI385587|IRF-4|LSIRF|NF-EM5|Spip	interferon regulatory factor 4	protein-coding
mm_104627.1	chr11	97310319	97310335	-	1	NA	Intergenic	Intergenic	-5389	NM_025927	67036	Mm.5381	NM_025927	ENSMUSG00000018882	Mrpl45	2600005P05Rik|AU043542|R75241	mitochondrial ribosomal protein L45	protein-coding
mm_113143.1	chr13	24706075	24706089	+	1	NA	TTS (NM_001080381)	TTS (NM_001080381)	55855	NM_020567	57441	Mm.12239	NM_020567	ENSMUSG00000006715	Gmnn	AW546347|Gem	geminin	protein-coding
mm_66283.1	chr7	37772734	37772774	-	1	NA	Intergenic	CpG	-3002	NM_172385	243937	Mm.322505	NM_172385	ENSMUSG00000043456	Zfp536	9630010P11Rik|Znf536|mKIAA0390	zinc finger protein 536	protein-coding
mm_53467.1	chr6	134920689	134920704	+	1	NA	5' UTR (NM_009875, exon 1 of 3)	5' UTR (NM_009875, exon 1 of 3)	295	NM_009875	12576	Mm.2958	NM_009875	ENSMUSG00000003031	Cdkn1b	AA408329|AI843786|Kip1|p27|p27Kip1	cyclin-dependent kinase inhibitor 1B	protein-coding
mm_132339.1	chr16	33829721	33829768	+	1	NA	promoter-TSS (NM_001145884)	promoter-TSS (NM_001145884)	79	NM_001145884	16419	Mm.6424	NM_010580	ENSMUSG00000022817	Itgb5	AA475909|AI874634|ESTM23|[b]-5|[b]5|[b]5A|[b]5B|beta-5|beta5	integrin beta 5	protein-coding
mm_164129.1	chr15	41504983	41504984	+	1	NA	intron (NM_001130166, intron 1 of 16)	L1MB5|LINE|L1	57501	NM_001130166	170719	Mm.254267	NM_130885	ENSMUSG00000022307	Oxr1	2210416C20Rik|C7|C7B	oxidation resistance 1	protein-coding
mm_170451.1	chr18	84838617	84838633	-	1	NA	Intergenic	Intergenic	-12789	NM_025797	109672	Mm.31018	NM_025797	ENSMUSG00000024646	Cyb5a	0610009N12Rik|Cyb5	cytochrome b5 type A (microsomal)	protein-coding
mm_140043.1	chr17	74489583	74489593	+	1	NA	promoter-TSS (NM_026417)	promoter-TSS (NM_026417)	95	NM_026417	67864	Mm.41891	NM_026417	ENSMUSG00000024072	Yipf4	2310034L04Rik	Yip1 domain family, member 4	protein-coding
mm_105162.1	chr11	101599261	101599271	-	1	NA	Intergenic	Intergenic	-11434	NM_001256318	666331	Mm.303457	NM_001256318		LOC666331	-	uncharacterized LOC666331	protein-coding
mm_138009.1	chr17	33843086	33843129	+	1	NA	promoter-TSS (NM_019421)	promoter-TSS (NM_019421)	16	NM_019421	54219	Mm.11175	NM_019421	ENSMUSG00000002308	Cd320	425O18-1|8D6|D17Ertd716e|NG29|TCblR|VLDL	CD320 antigen	protein-coding
mm_123453.1	chr14	65262392	65262490	-	1	NA	promoter-TSS (NM_021458)	promoter-TSS (NM_021458)	22	NM_021458	14365	Mm.214687	NM_021458	ENSMUSG00000007989	Fzd3	AU020229|D930050A07Rik|Fz3	frizzled class receptor 3	protein-coding
mm_32373.1	chr4	105794174	105794181	+	1	NA	Intergenic	ORR1E-int|LTR|ERVL-MaLR	-522036	NM_183225	329908	Mm.234544	NM_183225	ENSMUSG00000028514	Usp24	2700066K03Rik|2810030C21Rik|AI414051|B130021E18|C79851	ubiquitin specific peptidase 24	protein-coding
mm_110390.1	chr12	41412641	41412650	-	1	NA	intron (NM_053122, intron 4 of 6)	intron (NM_053122, intron 4 of 6)	73412	NM_001271708	16981	Mm.404786	NM_010733	ENSMUSG00000036295	Lrrn3	NLRR-3	leucine rich repeat protein 3, neuronal	protein-coding
mm_157540.1	chrX	51205641	51205671	-	1	NA	intron (NM_134163, intron 1 of 7)	CpG	334	NM_001310515	171170	Mm.295324	NM_134163	ENSMUSG00000036109	Mbnl3	A530038J18Rik|AI661274|CHCR|E430034C16Rik|MBLX|MBLX39|MBXL	muscleblind-like 3 (Drosophila)	protein-coding
mm_67492.1	chr7	80743126	80743149	-	1	NA	exon (NM_016721, exon 18 of 38)	exon (NM_016721, exon 18 of 38)	-54260	NM_173863	70461	Mm.392175	NM_173863	ENSMUSG00000030527	Crtc3	2610312F20Rik|6332415K15Rik|AI429792|BC011210|TORC3	CREB regulated transcription coactivator 3	protein-coding
mm_24215.1	chr3	88644775	88644785	+	1	NA	intron (NM_008487, intron 20 of 21)	B3|SINE|B2	8362	NM_181817	242093	Mm.269130	NM_181817	ENSMUSG00000049741	Rxfp4	GPCR142|Gpr100|Rln3r2|SALPR	relaxin family peptide receptor 4	protein-coding
mm_20852.1	chr2	148395867	148395894	-	1	NA	exon (NM_009219, exon 1 of 1)	exon (NM_009219, exon 1 of 1)	503	NM_009219	20608	Mm.35324	NM_009219	ENSMUSG00000037014	Sstr4	Smstr4|sst4	somatostatin receptor 4	protein-coding
mm_16135.1	chr2	170470848	170470854	+	1	NA	Intergenic	RLTR51B_Mm|LTR|ERVK?	-25577	NM_001013369	109054	Mm.28808	NM_001013369	ENSMUSG00000052033	Pfdn4	0610025M10Rik|1810063B06Rik|C-1|C1|Pfd4	prefoldin 4	protein-coding
mm_141170.1	chr17	26561366	26561386	-	1	NA	promoter-TSS (NM_026170)	promoter-TSS (NM_026170)	-136	NM_026170	67458	Mm.30496	NM_026170	ENSMUSG00000001576	Ergic1	1200007D18Rik|maa-136	endoplasmic reticulum-golgi intermediate compartment (ERGIC) 1	protein-coding
mm_100708.1	chr11	3722161	3722184	-	1	NA	promoter-TSS (NM_001302630)	promoter-TSS (NM_001302630)	55	NM_001302631	74309	Mm.61022	NM_152818	ENSMUSG00000020435	Osbp2	1700095P05Rik|C630001G20Rik|Gm244|ORP-4|OSBPL1	oxysterol binding protein 2	protein-coding
mm_31727.1	chr4	62965561	62965617	+	1	NA	promoter-TSS (NM_028326)	promoter-TSS (NM_028326)	15	NM_028326	72701	Mm.26479	NM_028326	ENSMUSG00000028358	Zfp618	2810031P15Rik|2810040O04Rik|AI415580|AI505139|D430033D05Rik|Nedd10|Znf618|bM257P7.1	zinc finger protein 618	protein-coding
mm_36280.1	chr4	63745191	63745205	-	1	NA	promoter-TSS (NM_177371)	promoter-TSS (NM_177371)	-85	NM_177371	326623	Mm.208152	NM_177371	ENSMUSG00000050395	Tnfsf15	Tl1|Tl1a|Tnlg1b|Vegi	tumor necrosis factor (ligand) superfamily, member 15	protein-coding
mm_7366.1	chr1	106713963	106714049	-	1	NA	5' UTR (NM_177410, exon 1 of 1)	5' UTR (NM_177410, exon 1 of 1)	284	NM_009741	12043	Mm.257460	NM_009741	ENSMUSG00000057329	Bcl2	AW986256|Bcl-2|C430015F12Rik|D630044D05Rik|D830018M01Rik	B cell leukemia/lymphoma 2	protein-coding
mm_130351.1	chr15	97750708	97750737	-	1	NA	intron (NM_144850, intron 19 of 27)	intron (NM_144850, intron 19 of 27)	16944	NM_001177810	223864	Mm.24028	NM_144850	ENSMUSG00000022469	Rapgef3	2310016P22Rik|9330170P05Rik|Epac|Epac1	Rap guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_96557.1	chr11	68956976	68956994	+	1	NA	promoter-TSS (NM_177566)	promoter-TSS (NM_177566)	-127	NM_177566	442801	Mm.376147	NM_177566	ENSMUSG00000052921	Arhgef15	D130071N09|D530030K12Rik|E5	Rho guanine nucleotide exchange factor (GEF) 15	protein-coding
mm_120490.1	chr14	65979799	65979808	+	1	NA	exon (NM_013492, exon 7 of 9)	exon (NM_013492, exon 7 of 9)	11320	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_64721.1	chr7	4658741	4658786	-	1	NA	5' UTR (NM_172894, exon 1 of 24)	5' UTR (NM_172894, exon 1 of 24)	187	NM_172894	243819	Mm.258670	NM_172894	ENSMUSG00000052296	Ppp6r1	2010309P17Rik|AI836219|B430201G11Rik|D030074N20Rik|Pp6r1|Saps1|mKIAA1115	protein phosphatase 6, regulatory subunit 1	protein-coding
mm_115800.1	chr13	19356281	19356305	-	1	NA	Intergenic	Intergenic	39520	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_108805.1	chr12	92005562	92005565	+	1	NA	Intergenic	MIRb|SINE|MIR	-156406	NM_011344	20338	Mm.250605	NM_011344	ENSMUSG00000020964	Sel1l	AW493766|Sel1h|mKIAA4137	sel-1 suppressor of lin-12-like (C. elegans)	protein-coding
mm_68125.1	chr7	102163728	102163749	-	1	NA	exon (NM_001287167, exon 13 of 20)	exon (NM_001287167, exon 13 of 20)	46129	NM_001287167	269966	Mm.439800	NM_022979	ENSMUSG00000063550	Nup98	4732457F17|AI849286|Nup96	nucleoporin 98	protein-coding
mm_35934.1	chr4	53032612	53032624	-	1	NA	3' UTR (NM_013454, exon 50 of 50)	3' UTR (NM_013454, exon 50 of 50)	20738	NM_025623	66536	Mm.38244	NM_025623	ENSMUSG00000015247	Nipsnap3b	2700063N13Rik|Nipsnap3a	nipsnap homolog 3B (C. elegans)	protein-coding
mm_133773.1	chr16	94721956	94721968	+	1	NA	Intergenic	Intergenic	110543	NM_001347731	13548	Mm.310973	NM_007890	ENSMUSG00000022897	Dyrk1a	2310043O08Rik|D16Ertd272e|D16Ertd493e|Dyrk|ENSMUSG00000074897|Gm10783|Mnbh|Mp86|mmb	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1a	protein-coding
mm_156626.1	chrX	155262448	155262458	+	1	NA	promoter-TSS (NM_019736)	promoter-TSS (NM_019736)	10	NM_019736	56360	Mm.268710	NM_019736	ENSMUSG00000025287	Acot9	0610041P13Rik|Acate2|C76421|MT-ACT48|MTE-2|U8|p48	acyl-CoA thioesterase 9	protein-coding
mm_60295.1	chr7	44015287	44015311	+	1	NA	intron (NM_010115, intron 2 of 5)	intron (NM_010115, intron 2 of 5)	2602	NM_010115	13647	Mm.439663	NM_010115		Egfbp2	Egfbp-2|Klk1b26|mGk-13	epidermal growth factor binding protein type B	protein-coding
mm_101185.1	chr11	17052345	17052363	-	1	NA	intron (NM_029861, intron 1 of 2)	intron (NM_029861, intron 1 of 2)	420	NM_029861	380686	Mm.425666	NM_029861	ENSMUSG00000044629	Cnrip1	1500041B16Rik|3110054C06Rik|5330437A18Rik|AI854501|C2orf32	cannabinoid receptor interacting protein 1	protein-coding
mm_53280.1	chr6	128674751	128674761	+	1	NA	exon (NM_053165, exon 4 of 5)	exon (NM_053165, exon 4 of 5)	12371	NM_053165	94071	Mm.197689	NM_053165	ENSMUSG00000030364	Clec2h	Clrf|clr-f	C-type lectin domain family 2, member h	protein-coding
mm_21124.1	chr2	153871077	153871104	-	1	NA	promoter-TSS (NM_001305048)	promoter-TSS (NM_001305048)	-6	NM_029599	76407	Mm.33629	NM_029599	ENSMUSG00000027480	Sun5	1700021O15Rik|SPAG4L-2|SRG4|Spag4l	Sad1 and UNC84 domain containing 5	protein-coding
mm_40601.1	chr5	64264374	64264382	+	1	NA	exon (NM_019636, exon 6 of 20)	exon (NM_019636, exon 6 of 20)	34021	NM_001289514	57915	Mm.286353	NM_019636	ENSMUSG00000029174	Tbc1d1	1110062G02Rik|AI385682|AW555803|Nob1|Nobq1|Tbc1|mKIAA1108	TBC1 domain family, member 1	protein-coding
mm_81728.1	chr9	113279296	113279300	+	1	NA	Intergenic	Intergenic	307854	NR_040760	102688	Mm.394901	NR_040760	ENSMUSG00000109890	AU023762	-	expressed sequence AU023762	ncRNA
mm_22237.1	chr2	174438997	174439029	-	1	NA	promoter-TSS (NM_022325)	promoter-TSS (NM_022325)	26	NM_022325	64138	Mm.156919	NM_022325	ENSMUSG00000016256	Ctsz	AI787083|AU019819|CTSX|D2Wsu143e	cathepsin Z	protein-coding
mm_59983.1	chr7	30493632	30493666	+	1	NA	promoter-TSS (NM_019546)	promoter-TSS (NM_019546)	-9	NM_019546	56189	Mm.270525	NM_019546	ENSMUSG00000036892	Prodh2	2510028N04Rik|2510038B11Rik|MmPOX|MmPOX1|POX1	proline dehydrogenase (oxidase) 2	protein-coding
mm_117635.1	chr13	92354504	92354520	-	1	NA	promoter-TSS (NM_010049)	promoter-TSS (NM_010049)	-271	NM_010049	13361	Mm.23695	NM_010049	ENSMUSG00000021707	Dhfr	8430436I03Rik|AA607882|AI662710|AW555094	dihydrofolate reductase	protein-coding
mm_163717.1	chr13	111808648	111808650	-	1	NA	exon (NM_011945, exon 1 of 20)	exon (NM_011945, exon 1 of 20)	334	NM_011945	26401	Mm.15918	NM_011945	ENSMUSG00000021754	Map3k1	MAPKKK1|MEKK1|Mekk	mitogen-activated protein kinase kinase kinase 1	protein-coding
mm_144076.1	chr17	91092716	91092822	-	1	NA	promoter-TSS (NM_020252)	promoter-TSS (NM_020252)	33	NM_177284	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_71609.1	chr8	56320051	56320060	+	1	NA	intron (NM_008278, intron 6 of 6)	intron (NM_008278, intron 6 of 6)	25503	NM_008278	15446	Mm.18832	NM_008278	ENSMUSG00000031613	Hpgd	15-PGDH|AV026552	hydroxyprostaglandin dehydrogenase 15 (NAD)	protein-coding
mm_166692.1	chr6	113660696	113660706	+	1	NA	intron (NM_001113553, intron 2 of 11)	ORR1D2|LTR|ERVL-MaLR	22234	NM_001113553	108960	Mm.152142	NM_172161	ENSMUSG00000060477	Irak2	6330415L08Rik|AI649099|IRAK-2	interleukin-1 receptor-associated kinase 2	protein-coding
mm_105816.1	chr11	112131782	112131782	-	1	NA	Intergenic	Intergenic	579574	NR_024085	217294	Mm.297761	NM_146031	ENSMUSG00000041674	BC006965	-	cDNA sequence BC006965	ncRNA
mm_103220.1	chr11	70656451	70656463	-	1	NA	promoter-TSS (NM_007933)	promoter-TSS (NM_007933)	-719	NM_001136062	13808	Mm.251322	NM_007933	ENSMUSG00000060600	Eno3	Eno-3|MSE	enolase 3, beta muscle	protein-coding
mm_73658.1	chr8	110997870	110997901	+	1	NA	promoter-TSS (NM_007916)	promoter-TSS (NM_007916)	-62	NM_007916	13680	Mm.287901	NM_007916	ENSMUSG00000015023	Ddx19a	DBP5|Ddx19|Eif4a-rs1	DEAD (Asp-Glu-Ala-Asp) box polypeptide 19a	protein-coding
mm_11155.1	chr2	28540256	28540298	+	1	NA	intron (NM_001145836, intron 1 of 17)	intron (NM_001145836, intron 1 of 17)	6813	NM_001145836	19730	Mm.5236	NM_009058	ENSMUSG00000026821	Ralgds	Gnds|Rgds|mKIAA1308	ral guanine nucleotide dissociation stimulator	protein-coding
mm_79732.1	chr9	62342122	62342145	+	1	NA	intron (NM_009672, intron 1 of 6)	CpG	790	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	protein-coding
mm_143451.1	chr17	70921757	70921765	-	1	NA	Intergenic	MTEb|LTR|ERVL-MaLR	-68229	NM_001164074	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_146667.1	chr18	12213370	12213393	-	1	NA	exon (NM_008720, exon 6 of 25)	exon (NM_008720, exon 6 of 25)	23005	NM_008720	18145	Mm.3484	NM_008720	ENSMUSG00000024413	Npc1	A430089E03Rik|C85354|D18Ertd139e|D18Ertd723e|lcsd|nmf164|spm	Niemann-Pick type C1	protein-coding
mm_155883.1	chrX	101527584	101527620	+	1	NA	Intergenic	MLTR31FA_MM|LTR|ERVK	-5133	NM_001290729	270627	Mm.261750	NM_001081008	ENSMUSG00000031314	Taf1	AU015687|B430306D02Rik|Ccg-1|Ccg1|KAT4|N-TAF1|TAFII250|Taf2a|p250	TATA-box binding protein associated factor 1	protein-coding
mm_116893.1	chr13	55362783	55362804	-	1	NA	promoter-TSS (NM_025828)	promoter-TSS (NM_025828)	-10	NM_025828	66890	Mm.38868	NM_025828	ENSMUSG00000021484	Lman2	1110003H06Rik|1300009F09Rik|AA408240|AL023023|AU040819|GP36B|VIP36	lectin, mannose-binding 2	protein-coding
mm_49682.1	chr6	32968280	32968292	+	1	NA	exon (NM_025336, exon 4 of 8)	exon (NM_025336, exon 4 of 8)	91866	NM_025336	66075	Mm.21501	NM_025336	ENSMUSG00000053768	Chchd3	0610041L09Rik|1700039J09Rik|AW558177	coiled-coil-helix-coiled-coil-helix domain containing 3	protein-coding
mm_107706.1	chr12	55492699	55492727	+	1	NA	promoter-TSS (NM_010907)	promoter-TSS (NM_010907)	-66	NM_010907	18035	Mm.170515	NM_010907	ENSMUSG00000021025	Nfkbia	AI462015|Nfkbi	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, alpha	protein-coding
mm_30028.1	chr3	135687886	135687928	-	1	NA	intron (NM_008689, intron 1 of 24)	intron (NM_008689, intron 1 of 24)	3640	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_154037.1	chr19	53541119	53541125	-	1	NA	exon (NM_001085390, exon 4 of 4)	exon (NM_001085390, exon 4 of 4)	11804	NM_001085390	240672	Mm.482424	NM_001085390	ENSMUSG00000034765	Dusp5	Gm337	dual specificity phosphatase 5	protein-coding
mm_5113.1	chr1	6382544	6382545	-	1	NA	intron (NM_001195732, intron 1 of 4)	intron (NM_001195732, intron 1 of 4)	23213	NM_001195732	620393	Mm.388992	NM_001195732	ENSMUSG00000087247	Fam150a	EG620393	family with sequence similarity 150, member A	protein-coding
mm_25981.1	chr3	133310165	133310169	+	1	NA	promoter-TSS (NM_001293641)	promoter-TSS (NM_001293641)	57	NM_146141	74776	Mm.210305	NM_146141	ENSMUSG00000028013	Ppa2	1110013G13Rik|Sid6306	pyrophosphatase (inorganic) 2	protein-coding
mm_150850.1	chr19	44992128	44992129	+	1	NA	intron (NM_011976, intron 1 of 14)	intron (NM_011976, intron 1 of 14)	2784	NM_011976	26456	Mm.34404	NM_011976	ENSMUSG00000025207	Sema4g	AI507908|AW554132	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4G	protein-coding
mm_17151.1	chr2	25214582	25214608	-	1	NA	promoter-TSS (NM_028961)	promoter-TSS (NM_028961)	35	NM_028961	74472	Mm.176944	NM_028961	ENSMUSG00000036770	Stpg3	4933433C11Rik	sperm tail PG rich repeat containing 3	protein-coding
mm_141163.1	chr17	26509560	26509569	-	1	NA	Intergenic	Intergenic	-1092	NM_013642	19252	Mm.239041	NM_013642	ENSMUSG00000024190	Dusp1	3CH134|MKP1|Ptpn16|U19515|erp|mkp-1	dual specificity phosphatase 1	protein-coding
mm_8291.1	chr1	143093934	143093960	-	1	NA	Intergenic	Intergenic	-546750	NM_020025	26878	Mm.285580	NM_020025	ENSMUSG00000033849	B3galt2	-	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 2	protein-coding
mm_30622.1	chr4	8691304	8691380	+	1	NA	intron (NM_001277149, intron 1 of 37)	CpG	936	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_168132.1	chr10	26107811	26107819	+	1	NA	Intergenic	L1_Mus1|LINE|L1	-28763	NM_029881	77220	Mm.266260	NM_029881	ENSMUSG00000049420	Tmem200a	C030003D03Rik	transmembrane protein 200A	protein-coding
mm_48066.1	chr5	136581572	136581580	-	1	NA	Intergenic	Intergenic	-14086	NM_001291238	13047	Mm.320317	NM_009986	ENSMUSG00000029705	Cux1	CDP|Cutl1|Cux|Cux-1	cut-like homeobox 1	protein-coding
mm_40323.1	chr5	43901918	43901957	+	1	NA	intron (NM_007646, intron 3 of 7)	intron (NM_007646, intron 3 of 7)	33128	NM_007646	12494	Mm.249873	NM_007646	ENSMUSG00000029084	Cd38	ADPRC 1|Cd38-rs1|I-19	CD38 antigen	protein-coding
mm_150711.1	chr19	42745805	42745815	+	1	NA	intron (NM_029011, intron 4 of 15)	intron (NM_029011, intron 4 of 15)	6965	NM_029011	74580	Mm.329858	NM_029011	ENSMUSG00000060224	Pyroxd2	3830409H07Rik|4833409A17Rik	pyridine nucleotide-disulphide oxidoreductase domain 2	protein-coding
mm_23032.1	chr3	34650767	34650780	+	1	NA	exon (NM_011443, exon 1 of 1)	exon (NM_011443, exon 1 of 1)	778	NM_011443	20674	Mm.65396	NM_011443	ENSMUSG00000074637	Sox2	Sox-2|lcc|ysb	SRY (sex determining region Y)-box 2	protein-coding
mm_75500.1	chr8	52197149	52197191	-	1	NA	Intergenic	Intergenic	-1314532	NM_001205054	11593	Mm.334535	NM_001005847	ENSMUSG00000031521	Aga	AW060726	aspartylglucosaminidase	protein-coding
mm_74193.1	chr8	123754333	123754360	+	1	NA	Intergenic	Intergenic	20388	NR_040702	234863	Mm.246601	NR_040702	ENSMUSG00000110599	6030466F02Rik	-	RIKEN cDNA 6030466F02 gene	ncRNA
mm_113974.1	chr13	51651762	51651777	+	1	NA	promoter-TSS (NM_029279)	promoter-TSS (NM_029279)	61	NM_029279	75420	Mm.275981	NM_029279	ENSMUSG00000035139	Secisbp2	2210413N07Rik|2810012K13Rik|SBP2	SECIS binding protein 2	protein-coding
mm_71150.1	chr8	39300837	39300889	+	1	NA	intron (NR_044988, intron 1 of 3)	RMER1A|Other|Other	2883	NR_044988	621335	Mm.208080	NR_044988	ENSMUSG00000109827	Gm6213	EG621335	predicted gene 6213	ncRNA
mm_98718.1	chr11	96318829	96318845	+	1	NA	exon (NM_010459, exon 1 of 2)	exon (NM_010459, exon 1 of 2)	570	NM_010459	15412	Mm.3546	NM_010459	ENSMUSG00000038692	Hoxb4	Hox-2.6	homeobox B4	protein-coding
mm_71933.1	chr8	70302544	70302630	+	1	NA	promoter-TSS (NM_021538)	promoter-TSS (NM_021538)	-135	NM_001024922	234374	Mm.388127	NM_001024922	ENSMUSG00000057788	Ddx49	R27090_2	DEAD (Asp-Glu-Ala-Asp) box polypeptide 49	protein-coding
mm_139314.1	chr17	48352026	48352105	+	1	NA	3' UTR (NM_031254, exon 5 of 5)	3' UTR (NM_031254, exon 5 of 5)	5664	NM_001272078	83433	Mm.261623	NM_031254	ENSMUSG00000023992	Trem2	TREM-2|Trem2a|Trem2b|Trem2c	triggering receptor expressed on myeloid cells 2	protein-coding
mm_26899.1	chr3	19265008	19265023	-	1	NA	promoter-TSS (NM_008802)	promoter-TSS (NM_008802)	-7	NM_008802	18583	Mm.355614	NM_008802	ENSMUSG00000069094	Pde7a	AU015378|AW047537	phosphodiesterase 7A	protein-coding
mm_90517.1	chr10	128052304	128052308	+	1	NA	Intergenic	B2_Mm2|SINE|B2	-6676	NM_019766	56351	Mm.305816	NM_019766	ENSMUSG00000071072	Ptges3	5730442A20Rik|Ptges|Tebp|cPGES|p23|sid3177	prostaglandin E synthase 3 (cytosolic)	protein-coding
mm_31433.1	chr4	48279795	48279852	+	1	NA	promoter-TSS (NM_029572)	promoter-TSS (NM_029572)	63	NM_001281977	16348	Mm.317706	NM_010569	ENSMUSG00000028344	Invs	Nphp2|inv	inversin	protein-coding
mm_146633.1	chr18	10588675	10588678	-	1	NA	intron (NM_001081222, intron 3 of 10)	intron (NM_001081222, intron 3 of 10)	21676	NM_001081222	77805	Mm.210996	NM_144542	ENSMUSG00000024293	Esco1	A930014I12Rik	establishment of sister chromatid cohesion N-acetyltransferase 1	protein-coding
mm_114432.1	chr13	65241475	65241499	+	1	NA	Intergenic	CpG	-35771	NM_175290	97895	Mm.315815	NM_175290	ENSMUSG00000032999	Nlrp4f	C330026N02Rik|C86045|Nalp-kappa|Nalp4f	NLR family, pyrin domain containing 4F	protein-coding
mm_46003.1	chr5	90696092	90696094	-	1	NA	Intergenic	Intergenic	-55566	NM_001310656	73246	Mm.30172	NM_028478	ENSMUSG00000029370	Rassf6	1600016B17Rik	Ras association (RalGDS/AF-6) domain family member 6	protein-coding
mm_5979.1	chr1	58045274	58045276	-	1	NA	intron (NM_009676, intron 3 of 34)	RMER17C|LTR|ERVK	15306	NM_009676	11761	Mm.26787	NM_009676	ENSMUSG00000063558	Aox1	AI196512|AI255253|Ao|Aox-1|Aox-2|Aox2|Moro|Ro	aldehyde oxidase 1	protein-coding
mm_155415.1	chrX	73490798	73490810	+	1	NA	exon (NM_007542, exon 2 of 8)	exon (NM_007542, exon 2 of 8)	7203	NM_007542	12111	Mm.2608	NM_007542	ENSMUSG00000031375	Bgn	BG|DSPG1|PG-S1|PGI|SLRR1A	biglycan	protein-coding
mm_62976.1	chr7	120102448	120102464	+	1	NA	promoter-TSS (NM_145586)	promoter-TSS (NM_145586)	30	NM_145586	233806	Mm.257952	NM_145586	ENSMUSG00000030917	Tmem159	8430420C20Rik	transmembrane protein 159	protein-coding
mm_145556.1	chr18	60811845	60811899	+	1	NA	promoter-TSS (NR_039567)	promoter-TSS (NR_039567)	-204	NR_039567	100628611		NR_039567	ENSMUSG00000093327	Mir5107	mir-5107|mmu-mir-5107|mu-mir-5107	microRNA 5107	ncRNA
mm_124803.1	chr15	8512113	8512140	+	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	-67663	NM_201232	71175	Mm.240329	NM_027707	ENSMUSG00000022141	Nipbl	Idn3	Nipped-B homolog (Drosophila)	protein-coding
mm_93410.1	chr10	108296565	108296578	-	1	NA	Intergenic	ORR1B2|LTR|ERVL-MaLR	-35618	NM_054056	114774	Mm.391419	NM_054056	ENSMUSG00000035873	Pawr	2310001G03Rik|PAR4|Par-4	PRKC, apoptosis, WT1, regulator	protein-coding
mm_69258.1	chr7	127876547	127876610	-	1	NA	5' UTR (NM_146259, exon 1 of 3)	5' UTR (NM_146259, exon 1 of 3)	245	NM_146259	244219	Mm.207872	NM_146259	ENSMUSG00000049728	Zfp668	BC030314|E130018B19Rik|Znf668	zinc finger protein 668	protein-coding
mm_163772.1	chr13	120018186	120018198	+	1	NA	Intergenic	Intergenic	34012	NM_001302966	100861753	Mm.165042	NM_001302966	ENSMUSG00000095609	Gm21188	-	predicted gene, 21188	protein-coding
mm_67117.1	chr7	70361572	70361576	-	1	NA	promoter-TSS (NM_009697)	promoter-TSS (NM_009697)	-981	NM_009697	11819	Mm.158143	NM_009697	ENSMUSG00000030551	Nr2f2	2700033K02Rik|9430015G03Rik|ARP-1|Aporp1|COUP-TF2|COUP-TFII|COUPTFB|EAR3|SVP40|Tcfcoup2	nuclear receptor subfamily 2, group F, member 2	protein-coding
mm_24485.1	chr3	92113187	92113199	+	1	NA	Intergenic	Intergenic	10754	NM_175424	109314	Mm.440617	NM_175424	ENSMUSG00000056270	Prr9	A030004J04Rik	proline rich 9	protein-coding
mm_38853.1	chr4	149385284	149385303	-	1	NA	intron (NM_022022, intron 3 of 26)	intron (NM_022022, intron 3 of 26)	41338	NM_022022	63958	Mm.415260	NM_022022	ENSMUSG00000028960	Ube4b	4930551I19Rik|4933406G05Rik|AU014668|D4Bwg0973e|UFD2|UFD2a|Ufd2p|mKIAA0684	ubiquitination factor E4B	protein-coding
mm_76329.1	chr8	84706199	84706209	-	1	NA	3' UTR (NM_010906, exon 9 of 9)	3' UTR (NM_010906, exon 9 of 9)	4747	NM_008535	17095	Mm.4925	NM_008535	ENSMUSG00000034041	Lyl1	Lyl-1|bHLHa18	lymphoblastomic leukemia 1	protein-coding
mm_153383.1	chr19	40376916	40376935	-	1	NA	exon (NM_178362, exon 7 of 29)	exon (NM_178362, exon 7 of 29)	25385	NM_001034964	20411	Mm.210815	NM_009166	ENSMUSG00000025006	Sorbs1	2310065E01Rik|9530001P15Rik|CAP|SH3P12|Sh3d5|mKIAA1296	sorbin and SH3 domain containing 1	protein-coding
mm_116469.1	chr13	43481082	43481095	-	1	NA	promoter-TSS (NM_019930)	promoter-TSS (NM_019930)	-115	NM_019930	56705	Mm.148781	NM_019930	ENSMUSG00000038546	Ranbp9	IBAP-1|Ibap1|RanBPM	RAN binding protein 9	protein-coding
mm_28651.1	chr3	95228871	95228879	-	1	NA	promoter-TSS (NM_019914)	promoter-TSS (NM_019914)	-68	NM_001038708	57912	Mm.28189	NM_172395	ENSMUSG00000046722	Cdc42se1	1300002M12Rik|AW558204|Cdcse1|SCIP1|Spec1	CDC42 small effector 1	protein-coding
mm_146795.1	chr18	20670045	20670074	-	1	NA	exon (NM_013697, exon 3 of 4)	exon (NM_013697, exon 3 of 4)	4809	NM_013697	22139	Mm.2108	NM_013697	ENSMUSG00000061808	Ttr	AA408768|AI787086|D17860|prealbumin	transthyretin	protein-coding
mm_11904.1	chr2	50335615	50335618	+	1	NA	intron (NR_040362, intron 1 of 2)	RMER15|LTR|ERVL	38806	NR_040362	100502624	Mm.382825	NR_040361	ENSMUSG00000085862	Gm13483	OTTMUSG00000012382	predicted gene 13483	ncRNA
mm_130622.1	chr15	100403383	100403400	-	1	NA	intron (NM_008732, intron 9 of 16)	intron (NM_008732, intron 9 of 16)	19664	NM_001146161	18174	Mm.234608	NM_008732	ENSMUSG00000023030	Slc11a2	DCT1|DMT1|Nramp2|mk|van	solute carrier family 11 (proton-coupled divalent metal ion transporters), member 2	protein-coding
mm_114772.1	chr13	88821607	88821623	+	1	NA	5' UTR (NM_001037987, exon 1 of 11)	5' UTR (NM_001037987, exon 1 of 11)	143	NM_001037987	13612	Mm.125580	NM_010103	ENSMUSG00000034488	Edil3	Del-1|Del1	EGF-like repeats and discoidin I-like domains 3	protein-coding
mm_93567.1	chr10	116549316	116549324	-	1	NA	intron (NM_001037846, intron 1 of 15)	intron (NM_001037846, intron 1 of 15)	32191	NM_001037848	72068	Mm.351553	NM_028082	ENSMUSG00000020166	Cnot2	2600016M12Rik|2810470K03Rik|AA537049|AA959607|AW557563|C79650	CCR4-NOT transcription complex, subunit 2	protein-coding
mm_60410.1	chr7	44476103	44476107	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	5758	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_96193.1	chr11	61982297	61982297	+	1	NA	intron (NM_001310526, intron 1 of 7)	L1MDa|LINE|L1	25534	NM_001310526	432572	Mm.438022	NM_001029936	ENSMUSG00000042331	Specc1	2810012G08Rik|B230396K10Rik|Cytsb	sperm antigen with calponin homology and coiled-coil domains 1	protein-coding
mm_27937.1	chr3	79591282	79591295	-	1	NA	promoter-TSS (NM_026352)	promoter-TSS (NM_026352)	-101	NM_026352	67738	Mm.295252	NM_026352	ENSMUSG00000027804	Ppid	4930564J03Rik|CYP-40|Ppidl|Ppif	peptidylprolyl isomerase D (cyclophilin D)	protein-coding
mm_16156.1	chr2	172370940	172370985	+	1	NA	promoter-TSS (NM_001291185)	promoter-TSS (NM_001291185)	-41	NM_024199	67337	Mm.26944	NM_024199	ENSMUSG00000027498	Cstf1	1700057K18Rik|AI788832	cleavage stimulation factor, 3' pre-RNA, subunit 1	protein-coding
mm_13581.1	chr2	112377218	112377232	+	1	NA	Intergenic	RLTR12D|LTR|ERVK	-1986	NM_024254	72425	Mm.425091	NM_024254	ENSMUSG00000027132	Katnbl1	2410042D21Rik|AA166487|AA473307|AI467442	katanin p80 subunit B like 1	protein-coding
mm_49874.1	chr6	38581982	38581990	+	1	NA	intron (NM_001331223, intron 6 of 12)	intron (NM_001331223, intron 6 of 12)	26263	NM_001331223	192196	Mm.276133	NM_138680	ENSMUSG00000029823	Luc7l2	4930471C18Rik|AA522013|AU015269|CGI59|Cgi74	LUC7-like 2 (S. cerevisiae)	protein-coding
mm_142428.1	chr17	45569591	45569612	-	1	NA	exon (NM_008302, exon 7 of 11)	exon (NM_008302, exon 7 of 11)	3660	NM_008302	15516	Mm.2180	NM_008302	ENSMUSG00000023944	Hsp90ab1	90kDa|AL022974|C81438|Hsp84|Hsp84-1|Hsp90|Hspcb	heat shock protein 90 alpha (cytosolic), class B member 1	protein-coding
mm_107995.1	chr12	73336630	73336640	+	1	NA	intron (NM_001037717, intron 6 of 15)	B1F|SINE|Alu	49787	NM_001037717	625098	Mm.32075	NM_001037717	ENSMUSG00000044712	Slc38a6	AW322671|EG625098	solute carrier family 38, member 6	protein-coding
mm_106614.1	chr11	120817150	120817163	-	1	NA	exon (NM_007988, exon 13 of 43)	exon (NM_007988, exon 13 of 43)	7391	NM_007988	14104	Mm.236443	NM_007988	ENSMUSG00000025153	Fasn	A630082H08Rik|FAS	fatty acid synthase	protein-coding
mm_55191.1	chr6	52191348	52191365	-	1	NA	exon (NM_008265, exon 1 of 2)	exon (NM_008265, exon 1 of 2)	347	NM_008265	15401	Mm.439647	NM_008265	ENSMUSG00000000942	Hoxa4	AV206827|Hox-1.4	homeobox A4	protein-coding
mm_79648.1	chr9	59578295	59578323	+	1	NA	promoter-TSS (NM_175235)	promoter-TSS (NM_175235)	-28	NM_175235	76183	Mm.265415	NM_175235	ENSMUSG00000032297	Celf6	6330569O16Rik|Brunol6	CUGBP, Elav-like family member 6	protein-coding
mm_89169.1	chr10	86311016	86311054	+	1	NA	intron (NM_011595, intron 1 of 4)	B4A|SINE|B4	10623	NM_011595	21859	Mm.4871	NM_011595	ENSMUSG00000020044	Timp3	Timp-3	tissue inhibitor of metalloproteinase 3	protein-coding
mm_112804.1	chr13	20477603	20477662	+	1	NA	intron (NM_198093, intron 1 of 6)	intron (NM_198093, intron 1 of 6)	4642	NM_198093	140580	Mm.342392	NM_080288	ENSMUSG00000041112	Elmo1	6330578D22Rik|C230095H21Rik|CED-12	engulfment and cell motility 1	protein-coding
mm_152574.1	chr19	11592883	11592926	-	1	NA	exon (NM_026835, exon 4 of 7)	exon (NM_026835, exon 4 of 7)	11900	NM_026835	68774	Mm.290390	NM_026835	ENSMUSG00000024679	Ms4a6d	1110058E16Rik|AI447446|Ms4a11	membrane-spanning 4-domains, subfamily A, member 6D	protein-coding
mm_35382.1	chr4	33247545	33247563	-	1	NA	intron (NM_001033225, intron 1 of 1)	CpG	1233	NM_001033225	108767	Mm.27769	NM_001033225	ENSMUSG00000040128	Pnrc1	5730463C12Rik|B4-2|PRR2|Prol2	proline-rich nuclear receptor coactivator 1	protein-coding
mm_110346.1	chr12	36218189	36218205	-	1	NA	promoter-TSS (NM_027699)	promoter-TSS (NM_027699)	5	NM_027699	71156	Mm.250837	NM_027699	ENSMUSG00000020545	Lrrc72	1700108M19Rik|4933421E18Rik	leucine rich repeat containing 72	protein-coding
mm_45517.1	chr5	72504569	72504581	-	1	NA	promoter-TSS (NM_001122756)	promoter-TSS (NM_001122756)	-35	NM_001122756	53419	Mm.332425	NM_016869	ENSMUSG00000005220	Corin	AV273130|Lrp4	corin	protein-coding
mm_115937.1	chr13	23621991	23622003	-	1	NA	promoter-TSS (NM_178194)	promoter-TSS (NM_178194)	561	NM_015787	50709	Mm.170587	NM_015787	ENSMUSG00000051627	Hist1h1e	H1-4|H1.4|H1e|H1f4|H1s-4|H1var2	histone cluster 1, H1e	protein-coding
mm_72699.1	chr8	84977857	84977907	+	1	NA	exon (NM_008416, exon 1 of 1)	exon (NM_008416, exon 1 of 1)	866	NM_008416	16477	Mm.1167	NM_008416	ENSMUSG00000052837	Junb	-	jun B proto-oncogene	protein-coding
mm_64752.1	chr7	4812113	4812147	-	1	NA	intron (NM_133777, intron 1 of 3)	CpG	210	NM_133777	77891	Mm.389787	NM_133777	ENSMUSG00000060860	Ube2s	0910001J09Rik|6720465F12Rik|AA409170|E2-EPF	ubiquitin-conjugating enzyme E2S	protein-coding
mm_145896.1	chr18	65594185	65594186	+	1	NA	intron (NM_207255, intron 2 of 5)	B1F|SINE|Alu	13955	NM_207255	328977	Mm.286232	NM_207255	ENSMUSG00000042439	Zfp532	C530030I18Rik|Znf532|mKIAA1629	zinc finger protein 532	protein-coding
mm_15484.1	chr2	157561938	157561947	+	1	NA	3' UTR (NM_010923, exon 3 of 3)	3' UTR (NM_010923, exon 3 of 3)	1864	NM_180960	18111	Mm.34330	NM_010923	ENSMUSG00000067786	Nnat	5730414I02Rik|AW107673|Peg5	neuronatin	protein-coding
mm_136070.1	chr16	84735927	84735937	-	1	NA	promoter-TSS (NM_017404)	promoter-TSS (NM_017404)	-630	NM_017404	27393	Mm.103655	NM_017404	ENSMUSG00000022889	Mrpl39	C21orf8|MRP-L5|ORF22|Rpml5	mitochondrial ribosomal protein L39	protein-coding
mm_98776.1	chr11	96789150	96789206	+	1	NA	promoter-TSS (NM_007622)	promoter-TSS (NM_007622)	42	NM_007622	12412	Mm.29055	NM_007622	ENSMUSG00000018666	Cbx1	Cbx|Cbx-rs2|E430007M08Rik|HP1B|Hp1beta|M31|MOD1	chromobox 1	protein-coding
mm_152710.1	chr19	17372837	17372850	-	1	NA	promoter-TSS (NM_010265)	promoter-TSS (NM_010265)	1	NM_010265	14537	Mm.244825	NM_010265	ENSMUSG00000038843	Gcnt1	5630400D21Rik|B130048E03|C2 GlcNAcT|C2GNT|IGnT	glucosaminyl (N-acetyl) transferase 1, core 2	protein-coding
mm_16195.1	chr2	172992718	172992719	+	1	NA	intron (NM_001305434, intron 11 of 11)	intron (NM_001305434, intron 11 of 11)	-7399	NM_175112	66679	Mm.4113	NM_175112	ENSMUSG00000027509	Rae1	3230401I12Rik|D2Ertd342e|MNRP|MNRP41	ribonucleic acid export 1	protein-coding
mm_68844.1	chr7	126364895	126364905	-	1	NA	intron (NM_010689, intron 8 of 11)	intron (NM_010689, intron 8 of 11)	3145	NR_106025	102466797		NR_106025	ENSMUSG00000099017	Mir7058	Gm27766|mmu-mir-7058	microRNA 7058	ncRNA
mm_72949.1	chr8	92355964	92356009	+	1	NA	non-coding (NR_033641, exon 1 of 7)	non-coding (NR_033641, exon 1 of 7)	134	NR_110452	71296	Mm.86664	NR_033641	ENSMUSG00000031736	Crnde	4933436C20Rik	colorectal neoplasia differentially expressed (non-protein coding)	ncRNA
mm_49378.1	chr6	24597755	24597778	+	1	NA	promoter-TSS (NM_053098)	promoter-TSS (NM_053098)	-5	NM_053098	93677	Mm.332941	NM_053098	ENSMUSG00000029683	Lmod2	C-Lmod	leiomodin 2 (cardiac)	protein-coding
mm_29800.1	chr3	127780251	127780288	-	1	NA	5' UTR (NM_027808, exon 1 of 14)	5' UTR (NM_027808, exon 1 of 14)	258	NM_027808	71481	Mm.158704	NM_027808	ENSMUSG00000028028	Alpk1	8430410J10Rik|LAK	alpha-kinase 1	protein-coding
mm_130788.1	chr15	101676086	101676103	-	1	NA	TTS (NM_010669)	TTS (NM_010669)	4195	NM_010669	16688	Mm.441891	NM_010669	ENSMUSG00000023041	Krt6b	BB144589|Krt2-6b|mK6[b]	keratin 6B	protein-coding
mm_30114.1	chr3	139075134	139075173	-	1	NA	promoter-TSS (NM_001286759)	promoter-TSS (NM_001286759)	48	NM_145544	229877	Mm.28893	NM_145544	ENSMUSG00000028149	Rap1gds1	BC011279|GDS1	RAP1, GTP-GDP dissociation stimulator 1	protein-coding
mm_57233.1	chr6	123282859	123282865	-	1	NA	3' UTR (NM_019948, exon 6 of 6)	3' UTR (NM_019948, exon 6 of 6)	7009	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_73004.1	chr8	93810833	93810843	+	1	NA	promoter-TSS (NM_010308)	promoter-TSS (NM_010308)	0	NM_010308	14681	Mm.251445	NM_010308	ENSMUSG00000031748	Gnao1	AW050213|Galphao|Gnao|alphaO	guanine nucleotide binding protein, alpha O	protein-coding
mm_38208.1	chr4	135873802	135873853	-	1	NA	promoter-TSS (NM_026383)	promoter-TSS (NM_026383)	19	NM_026383	52830	Mm.29159	NM_026383	ENSMUSG00000028675	Pnrc2	0610011E17Rik|D4Bwg0593e	proline-rich nuclear receptor coactivator 2	protein-coding
mm_128907.1	chr15	73423227	73423239	-	1	NA	promoter-TSS (NM_007982)	promoter-TSS (NM_007982)	-42	NM_001130409	14083	Mm.254494	NM_007982	ENSMUSG00000022607	Ptk2	FAK|FRNK|Fadk|mKIAA4203|p125FAK	PTK2 protein tyrosine kinase 2	protein-coding
mm_4997.1	chr1	191906744	191906767	+	1	NA	promoter-TSS (NM_009579)	promoter-TSS (NM_009579)	-26	NM_009579	22782	Mm.9024	NM_009579	ENSMUSG00000037434	Slc30a1	AI839647|C130040I11Rik|Znt1	solute carrier family 30 (zinc transporter), member 1	protein-coding
mm_29554.1	chr3	116807881	116807889	-	1	NA	intron (NM_001081326, intron 1 of 33)	intron (NM_001081326, intron 1 of 33)	281	NM_001081326	77559	Mm.237099	NM_001081326	ENSMUSG00000033400	Agl	1110061O17Rik|9430004C13Rik|9630046L06Rik|AI850929|C77197	amylo-1,6-glucosidase, 4-alpha-glucanotransferase	protein-coding
mm_46767.1	chr5	112269486	112269517	-	1	NA	TTS (NM_001312894)	TTS (NM_001312894)	-7190	NM_001326590	22022	Mm.250631	NM_009419	ENSMUSG00000029344	Tpst2	AI448750|D5Ucla3|Tango13b|grm|grt	protein-tyrosine sulfotransferase 2	protein-coding
mm_153622.1	chr19	43986553	43986561	-	1	NA	promoter-TSS (NM_030703)	promoter-TSS (NM_030703)	-37	NM_030703	93721	Mm.206774	NM_030703	ENSMUSG00000025196	Cpn1	0610011F20Rik|CPN	carboxypeptidase N, polypeptide 1	protein-coding
mm_38867.1	chr4	149485203	149485223	-	1	NA	promoter-TSS (NM_026963)	promoter-TSS (NM_026963)	-71	NM_133435	66454	Mm.76062	NM_133435	ENSMUSG00000028992	Nmnat1	2610529L11Rik|5730441G13Rik|D4Cole1e|nmnat	nicotinamide nucleotide adenylyltransferase 1	protein-coding
mm_23660.1	chr3	68282264	68282265	+	1	NA	intron (NM_001113420, intron 1 of 6)	intron (NM_001113420, intron 1 of 6)	-185919	NM_001282045	30953	Mm.331064	NM_013928	ENSMUSG00000027777	Schip1	Nf2ip|Schip-1	schwannomin interacting protein 1	protein-coding
mm_164713.1	chr17	55888183	55888183	+	1	NA	Intergenic	RLTR10A|LTR|ERVK	-3910	NM_145490	224893	Mm.294853	NM_145490	ENSMUSG00000003198	Zfp959	-	zinc finger protein 959	protein-coding
mm_136942.1	chr17	14279507	14279513	+	1	NA	promoter-TSS (NM_022315)	promoter-TSS (NM_022315)	4	NM_022315	64074	Mm.30162	NM_022315	ENSMUSG00000023886	Smoc2	1700056C05Rik|5430426J21Rik|Smoc2l	SPARC related modular calcium binding 2	protein-coding
mm_8172.1	chr1	137806798	137806814	-	1	NA	Intergenic	Intergenic	-159649	NR_029795	735252		NR_029795	ENSMUSG00000065565	Mir181a-1	Mirn181a-1|Mirn213|miR-213|mir-181a-1|mmu-mir-213	microRNA 181a-1	ncRNA
mm_46788.1	chr5	112765910	112765947	-	1	NA	intron (NM_028901, intron 34 of 43)	intron (NM_028901, intron 34 of 43)	-27364	NR_040675	67360	Mm.59218	NR_040675	ENSMUSG00000098230	1700095B10Rik	-	RIKEN cDNA 1700095B10 gene	ncRNA
mm_30562.1	chr4	3789992	3790002	+	1	NA	3' UTR (NM_001111096, exon 13 of 13)	3' UTR (NM_001111096, exon 13 of 13)	45658	NM_026147	67427	Mm.21938	NM_026147	ENSMUSG00000028234	Rps20	4632426K06Rik|Dsk4	ribosomal protein S20	protein-coding
mm_74560.1	chr8	10947854	10947862	-	1	NA	Intergenic	Intergenic	-19401	NR_135302	665306	Mm.358758	NR_030715	ENSMUSG00000038917	3930402G23Rik	-	RIKEN cDNA 3930402G23 gene	ncRNA
mm_79595.1	chr9	58455097	58455113	+	1	NA	promoter-TSS (NR_040736)	promoter-TSS (NR_040736)	-68	NR_040736	74879	Mm.416924	NR_040736	ENSMUSG00000097651	4930461G14Rik	-	RIKEN cDNA 4930461G14 gene	ncRNA
mm_156449.1	chrX	142694854	142694856	+	1	NA	intron (NM_001199360, intron 2 of 6)	intron (NM_001199360, intron 2 of 6)	13129	NM_001199360	209497	Mm.249648	NM_177592	ENSMUSG00000047045	Tmem164	AI316850|AI852450|AW547186|F730011B02	transmembrane protein 164	protein-coding
mm_97491.1	chr11	78337812	78337829	+	1	NA	exon (NM_201406, exon 8 of 12)	exon (NM_201406, exon 8 of 12)	-5675	NM_001313985	22248	Mm.284811	NM_011676	ENSMUSG00000002058	Unc119	D11Bhm52|HRG4|MRG4|Rg4|Rtg4|Unc119h	unc-119 lipid binding chaperone	protein-coding
mm_57118.1	chr6	122596653	122596802	-	1	NA	5' UTR (NM_031159, exon 3 of 8)	5' UTR (NM_031159, exon 3 of 8)	5717	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_41301.1	chr5	90465865	90465944	+	1	NA	exon (NM_009654, exon 6 of 15)	exon (NM_009654, exon 6 of 15)	5034	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_96589.1	chr11	69090676	69090678	+	1	NA	3' UTR (NM_009497, exon 5 of 5)	3' UTR (NM_009497, exon 5 of 5)	2149	NM_009497	22318	Mm.28643	NM_009497	ENSMUSG00000020894	Vamp2	Syb-2|Syb2|sybII	vesicle-associated membrane protein 2	protein-coding
mm_63986.1	chr7	140093389	140093402	+	1	NA	promoter-TSS (NM_009475)	promoter-TSS (NM_009475)	-1	NM_009475	22264	Mm.439707	NM_009475	ENSMUSG00000025467	Prap1	Upa	proline-rich acidic protein 1	protein-coding
mm_106304.1	chr11	118290168	118290175	-	1	NA	promoter-TSS (NM_001033528)	promoter-TSS (NM_001033528)	73	NM_001033528	72344	Mm.232293	NM_001033528	ENSMUSG00000033909	Usp36	2700002L06Rik|mKIAA1453	ubiquitin specific peptidase 36	protein-coding
mm_125366.1	chr15	39659513	39659585	+	1	NA	promoter-TSS (NM_001256384)	promoter-TSS (NM_001256384)	38	NM_001256384	116838	Mm.309296	NM_053271	ENSMUSG00000037386	Rims2	2810036I15Rik|AW048769|RIM2|Rab3ip2|Rim2(+40A)|Rim2(+44A)|Rim2(+4A)|Serg2|Syt3-rs|mKIAA0751	regulating synaptic membrane exocytosis 2	protein-coding
mm_158738.1	chrX	164076447	164076462	-	1	NA	promoter-TSS (NM_009173)	promoter-TSS (NM_009173)	39	NM_001308385	20438	Mm.37215	NM_009173	ENSMUSG00000040749	Siah1b	AA960570|Sinh1b|siah-1b	seven in absentia 1B	protein-coding
mm_8500.1	chr1	153900199	153900210	-	1	NA	TTS (NR_106194)	TTS (NR_106194)	275	NM_008131	14645	Mm.210745	NM_008131	ENSMUSG00000026473	Glul	GS|Glns	glutamate-ammonia ligase (glutamine synthetase)	protein-coding
mm_97513.1	chr11	78499491	78499590	+	1	NA	exon (NM_011707, exon 2 of 8)	exon (NM_011707, exon 2 of 8)	420	NM_011707	22370	Mm.3667	NM_011707	ENSMUSG00000017344	Vtn	AI256434|Vn	vitronectin	protein-coding
mm_131616.1	chr16	19760398	19760424	+	1	NA	5' UTR (NM_001159407, exon 1 of 6)	5' UTR (NM_001159407, exon 1 of 6)	177	NM_001159407	108105	Mm.33935	NM_054052	ENSMUSG00000022686	B3gnt5	beta3GnT5	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5	protein-coding
mm_83368.1	chr9	44454731	44454742	-	1	NA	promoter-TSS (NM_009476)	promoter-TSS (NM_009476)	31	NM_009476	22269	Mm.4453	NM_009476	ENSMUSG00000041523	Upk2	AW491716|UPII	uroplakin 2	protein-coding
mm_137533.1	chr17	27555817	27555834	+	1	NA	promoter-TSS (NM_001166545)	promoter-TSS (NM_001166545)	-749	NM_001166536	15361	Mm.4438	NM_016660	ENSMUSG00000046711	Hmga1	AL023995|Hmga1a|Hmga1b|Hmgi|Hmgiy|Hmgy	high mobility group AT-hook 1	protein-coding
mm_17566.1	chr2	30205773	30205791	-	1	NA	promoter-TSS (NM_172404)	promoter-TSS (NM_172404)	-83	NM_172404	70266	Mm.216089	NM_172404	ENSMUSG00000039648	Kyat1	2010009K05Rik|AI182306|Ccbl1|Gtk|Kat1|KatI	kynurenine aminotransferase 1	protein-coding
mm_130009.1	chr15	86574449	86574457	-	1	NA	Intergenic	Intergenic	359994	NM_145476	223754	Mm.28904	NM_145476	ENSMUSG00000051864	Tbc1d22a	BC023106|D15Ertd781e	TBC1 domain family, member 22a	protein-coding
mm_157251.1	chrX	19150652	19150663	-	1	NA	Intergenic	Intergenic	-3686	NR_029807	723828		NR_029807	ENSMUSG00000065471	Mir222	Mirn222|mir-222|mmu-mir-222	microRNA 222	ncRNA
mm_12485.1	chr2	71530730	71530756	+	1	NA	non-coding (NR_002854, exon 2 of 2)	non-coding (NR_002854, exon 2 of 2)	1298	NM_010053	13390	Mm.475101	NM_010053	ENSMUSG00000041911	Dlx1	Dlx|Dlx-1	distal-less homeobox 1	protein-coding
mm_71852.1	chr8	68906090	68906100	+	1	NA	3' UTR (NM_008509, exon 10 of 10)	3' UTR (NM_008509, exon 10 of 10)	25540	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_37550.1	chr4	125346952	125346961	-	1	NA	Intergenic	Intergenic	-143875	NM_001081097	14807	Mm.40896	NM_001081097	ENSMUSG00000001985	Grik3	9630027E11|GluK3|GluR7-3|Glur-7|Glur7	glutamate receptor, ionotropic, kainate 3	protein-coding
mm_96117.1	chr11	60706748	60706756	+	1	NA	exon (NM_001159405, exon 8 of 22)	exon (NM_001159405, exon 8 of 22)	7062	NM_008502	16897	Mm.285453	NM_008502	ENSMUSG00000020536	Llgl1	AI325176|Lgl1|Llglh|Mgl1	lethal giant larvae homolog 1 (Drosophila)	protein-coding
mm_8073.1	chr1	135564553	135564557	-	1	NA	intron (NM_173437, intron 1 of 28)	intron (NM_173437, intron 1 of 28)	20800	NM_173437	215690	Mm.34977	NM_173437	ENSMUSG00000009418	Nav1	9530089B19|9930003A20Rik|C230080M11Rik|Pomfil3|Unc53h1|mKIAA1151|steerin-1	neuron navigator 1	protein-coding
mm_81062.1	chr9	106170919	106170953	+	1	NA	promoter-TSS (NM_029896)	promoter-TSS (NM_029896)	7	NM_029896	77305	Mm.265125	NM_029896	ENSMUSG00000020257	Wdr82	9430077D24Rik|CDW5/WDR82	WD repeat domain containing 82	protein-coding
mm_164099.1	chr15	15236917	15236918	+	1	NA	Intergenic	Intergenic	-1541184	NM_009869	12565	Mm.439758	NM_009869	ENSMUSG00000025370	Cdh9	-	cadherin 9	protein-coding
mm_124614.1	chr15	3279561	3279567	+	1	NA	exon (NM_009155, exon 5 of 5)	exon (NM_009155, exon 5 of 5)	8587	NM_009155	20363	Mm.392203	NM_009155	ENSMUSG00000064373	Selenop	AU018766|D15Ucla1|Se-P|Sepp1|selp	selenoprotein P	protein-coding
mm_163923.1	chr14	45276082	45276086	+	1	NA	intron (NM_027518, intron 3 of 6)	intron (NM_027518, intron 3 of 6)	42488	NM_015774	50527	Mm.387108	NM_015774	ENSMUSG00000021831	Ero1l	ERO1-L|Ero1a	ERO1-like (S. cerevisiae)	protein-coding
mm_95464.1	chr11	50430388	50430426	+	1	NA	intron (NM_172557, intron 1 of 17)	intron (NM_172557, intron 1 of 17)	704	NM_172557	216724	Mm.390400	NM_172557	ENSMUSG00000020375	Rufy1	3000002E04Rik|Rabip4|ZFYVE12	RUN and FYVE domain containing 1	protein-coding
mm_85985.1	chr9	112185930	112185936	-	1	NA	promoter-TSS (NM_001177618)	promoter-TSS (NM_001177618)	16	NM_001177618	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_1815.1	chr1	82316646	82316656	+	1	NA	promoter-TSS (NM_029777)	promoter-TSS (NM_029777)	72	NM_029777	76867	Mm.226994	NM_029777	ENSMUSG00000026142	Rhbdd1	4930418P06Rik|RRP4|mRHBDD1	rhomboid domain containing 1	protein-coding
mm_32557.1	chr4	109440258	109440273	+	1	NA	intron (NM_153392, intron 13 of 17)	intron (NM_153392, intron 13 of 17)	24618	NM_001145948	230603	Mm.33091	NM_153392	ENSMUSG00000028555	Ttc39a	4922503N01Rik	tetratricopeptide repeat domain 39A	protein-coding
mm_128334.1	chr15	38455158	38455171	-	1	NA	Intergenic	MLT1N2|LTR|ERVL-MaLR	35383	NR_105916	102465574		NR_105916	ENSMUSG00000099110	Mir6951	Gm27765|mmu-mir-6951	microRNA 6951	ncRNA
mm_101893.1	chr11	49081485	49081485	-	1	NA	intron (NM_001271677, intron 1 of 2)	intron (NM_001271677, intron 1 of 2)	4898	NM_001271677	15953	Mm.24769	NM_008330	ENSMUSG00000078920	Ifi47	47kDa|IRG-47|Ifggc1|Igrd|Iigp4|Iipg4|Irgd	interferon gamma inducible protein 47	protein-coding
mm_44681.1	chr5	30106076	30106105	-	1	NA	promoter-TSS (NM_001256263)	promoter-TSS (NM_001256263)	-4	NM_001256263	433868	Mm.450696	NM_001256263	ENSMUSG00000086815	3110082J24Rik	ENSMUSG00000073106	RIKEN cDNA 3110082J24 gene	protein-coding
mm_145635.1	chr18	61112693	61112719	+	1	NA	exon (NM_001037859, exon 6 of 22)	exon (NM_001037859, exon 6 of 22)	-4762	NR_105949	102466212		NR_105949	ENSMUSG00000098389	Mir6983	Gm27496|mmu-mir-6983	microRNA 6983	ncRNA
mm_166205.1	chr5	43910387	43910393	+	1	NA	3' UTR (NM_007646, exon 8 of 8)	3' UTR (NM_007646, exon 8 of 8)	41581	NM_007646	12494	Mm.249873	NM_007646	ENSMUSG00000029084	Cd38	ADPRC 1|Cd38-rs1|I-19	CD38 antigen	protein-coding
mm_82893.1	chr9	32542987	32543008	-	1	NA	Intergenic	Intergenic	-1545	NM_008026	14247	Mm.258908	NM_008026	ENSMUSG00000016087	Fli1	EWSR2|Fli-1|SIC-1|Sic1	Friend leukemia integration 1	protein-coding
mm_78116.1	chr9	20643291	20643342	+	1	NA	promoter-TSS (NM_013911)	promoter-TSS (NM_013911)	-2	NM_025401	66177	Mm.390165	NM_025401	ENSMUSG00000084786	Ubl5	1110030M22Rik|beacon	ubiquitin-like 5	protein-coding
mm_69471.1	chr7	133709070	133709099	-	1	NA	promoter-TSS (NM_025392)	promoter-TSS (NM_025392)	211	NM_009479	22276	Mm.3160	NM_009479	ENSMUSG00000030979	Uros	AI415298|UROIIIS|Uros3	uroporphyrinogen III synthase	protein-coding
mm_129945.1	chr15	84949083	84949100	-	1	NA	3' UTR (NM_001033273, exon 10 of 10)	3' UTR (NM_001033273, exon 10 of 10)	2532	NR_037206	100526461		NR_037206	ENSMUSG00000080441	Mir1249	mir-1249|mmu-mir-1249	microRNA 1249	ncRNA
mm_149706.1	chr19	21652851	21652902	+	1	NA	promoter-TSS (NM_025423)	promoter-TSS (NM_025423)	-85	NM_025423	66206	Mm.272430	NM_025423	ENSMUSG00000035171	1110059E24Rik	-	RIKEN cDNA 1110059E24 gene	protein-coding
mm_6887.1	chr1	84695873	84695892	-	1	NA	promoter-TSS (NR_039588)	promoter-TSS (NR_039588)	43	NR_039588	100628595		NR_039588	ENSMUSG00000093254	Mir5126	mir-5126|mmu-mir-5126|mu-mir-5126	microRNA 5126	ncRNA
mm_42094.1	chr5	110330757	110330767	+	1	NA	intron (NM_011132, intron 41 of 48)	intron (NM_011132, intron 41 of 48)	12273	NM_153400	231602	Mm.55948	NM_153400	ENSMUSG00000029503	P2rx2	P2X2a|P2x2	purinergic receptor P2X, ligand-gated ion channel, 2	protein-coding
mm_32064.1	chr4	97777847	97777864	+	1	NA	5' UTR (NM_001122953, exon 1 of 10)	5' UTR (NM_001122953, exon 1 of 10)	229	NM_010905	18027	Mm.31274	NM_010905	ENSMUSG00000028565	Nfia	1110047K16Rik|9430022M17Rik|CTF|NF1-A|NF1A	nuclear factor I/A	protein-coding
mm_24910.1	chr3	96221157	96221167	+	1	NA	promoter-TSS (NM_178214)	promoter-TSS (NM_178214)	90	NM_178214	319190	Mm.439791	NM_178214	ENSMUSG00000068854	Hist2h2be	AV127319|H2b-613|T25626	histone cluster 2, H2be	protein-coding
mm_149665.1	chr19	18749725	18749743	+	1	NA	promoter-TSS (NM_153417)	promoter-TSS (NM_153417)	-249	NM_153417	225997	Mm.215171	NM_153417	ENSMUSG00000024727	Trpm6	CHAK2|TRPM6/CHAK2	transient receptor potential cation channel, subfamily M, member 6	protein-coding
mm_68322.1	chr7	106503047	106503071	-	1	NA	Intergenic	RMER12B|LTR|ERVK	-61986	NR_003967	209380	Mm.461779	NM_001001318		Gm4759	EG209380	GTPase, very large interferon inducible 1 pseudogene	pseudo
mm_22430.1	chr2	181599267	181599280	-	1	NA	promoter-TSS (NM_172676)	promoter-TSS (NM_172676)	-126	NM_172676	229011	Mm.205422	NM_172676	ENSMUSG00000038605	Samd10	D930033N23Rik|E130318E08	sterile alpha motif domain containing 10	protein-coding
mm_21627.1	chr2	164277212	164277224	-	1	NA	exon (NM_009300, exon 2 of 3)	exon (NM_009300, exon 2 of 3)	1089	NM_009300	20941	Mm.1286	NM_009300	ENSMUSG00000016998	Svs4	SVS-IV|Svp-2|Svp-4|Svp2|Svp4	seminal vesicle secretory protein 4	protein-coding
mm_140685.1	chr17	13008356	13008396	-	1	NA	exon (NM_013671, exon 2 of 5)	exon (NM_013671, exon 2 of 5)	537	NM_013671	20656	Mm.290876	NM_013671	ENSMUSG00000006818	Sod2	MnSOD|Sod-2	superoxide dismutase 2, mitochondrial	protein-coding
mm_14065.1	chr2	122704253	122704262	+	1	NA	Intergenic	MLT1F|LTR|ERVL-MaLR	-1594	NM_001290993	22785	Mm.27801	NM_011774	ENSMUSG00000005802	Slc30a4	Znt4|lm|znT-4	solute carrier family 30 (zinc transporter), member 4	protein-coding
mm_171574.1	chr4	147361691	147361707	+	1	NA	intron (NM_001039209, intron 1 of 2)	intron (NM_001039209, intron 1 of 2)	185833	NM_001039209	195531	Mm.270762	NM_001039209	ENSMUSG00000078496	Zfp982	Gm13152|OTTMUSG00000010671	zinc finger protein 982	protein-coding
mm_92128.1	chr10	64090194	64090210	-	1	NA	promoter-TSS (NM_178678)	promoter-TSS (NM_178678)	53	NM_178678	216028	Mm.431318	NM_178678	ENSMUSG00000042846	Lrrtm3	9630044H04Rik	leucine rich repeat transmembrane neuronal 3	protein-coding
mm_97188.1	chr11	75572720	75572735	+	1	NA	3' UTR (NM_001199283, exon 14 of 14)	3' UTR (NM_001199283, exon 14 of 14)	-15352	NM_008850	18738	Mm.3128	NM_008850	ENSMUSG00000017781	Pitpna	Pitpn|vb|vibrator	phosphatidylinositol transfer protein, alpha	protein-coding
mm_47467.1	chr5	123671112	123671130	-	1	NA	intron (NM_001347468, intron 1 of 24)	intron (NM_001347468, intron 1 of 24)	13240	NM_019765	56430	Mm.241109	NM_019765	ENSMUSG00000049550	Clip1	1110007I12Rik|4631429H07Rik|AV017631|C81039|CLIP-170|CLIP170|CYLN1|Clip50|Rsn|mKIAA4046|restin	CAP-GLY domain containing linker protein 1	protein-coding
mm_150149.1	chr19	31949780	31949794	+	1	NA	TTS (NM_001081074)	TTS (NM_001081074)	81026	NM_001081074	69865	Mm.87538	NM_001081074	ENSMUSG00000052595	A1cf	1810073H04Rik|ACF64|ACF65|ASP|Acf|MCM|MerCreMer|Tg(Myh6-cre/Esr1*)1Jmk|mer	APOBEC1 complementation factor	protein-coding
mm_52952.1	chr6	123049968	123049979	+	1	NA	promoter-TSS (NM_027218)	promoter-TSS (NM_027218)	11	NM_001190310	69810	Mm.333374	NM_027218	ENSMUSG00000030147	Clec4b1	1810046I24Rik|Aplra2|Clec4b|DCAR|DCARbeta|Dcar2	C-type lectin domain family 4, member b1	protein-coding
mm_55916.1	chr6	83775747	83775759	-	1	NA	promoter-TSS (NM_009357)	promoter-TSS (NM_009357)	59	NM_009357	21766	Mm.28371	NM_009357	ENSMUSG00000014748	Tex261	3110001O07Rik|AA409339|AI480706|AL033351|TEG-261	testis expressed gene 261	protein-coding
mm_45389.1	chr5	66147563	66147584	-	1	NA	intron (NM_001127382, intron 2 of 7)	intron (NM_001127382, intron 2 of 7)	3405	NM_001291226	245945	Mm.36863	NM_139065	ENSMUSG00000070780	Rbm47	9530077J19Rik	RNA binding motif protein 47	protein-coding
mm_136587.1	chr17	4994698	4994730	+	1	NA	promoter-TSS (NM_001085355)	promoter-TSS (NM_001085355)	-360	NM_001085355	239985	Mm.133401	NM_001085355	ENSMUSG00000069729	Arid1b	8030481M12|9330189K18Rik|AI836955|Ardi1b|B230217J03Rik|mKIAA1235	AT rich interactive domain 1B (SWI-like)	protein-coding
mm_20889.1	chr2	148871993	148872010	-	1	NA	exon (NM_009976, exon 3 of 3)	exon (NM_009976, exon 3 of 3)	3511	NM_009976	13010	Mm.4263	NM_009976	ENSMUSG00000027447	Cst3	CysC	cystatin C	protein-coding
mm_90895.1	chr10	10472394	10472405	-	1	NA	promoter-TSS (NM_001127353)	promoter-TSS (NM_001127353)	-85	NM_001127353	215772	Mm.246573	NM_172547	ENSMUSG00000050994	Adgb	9130014G24Rik	androglobin	protein-coding
mm_28422.1	chr3	90433604	90433619	-	1	NA	promoter-TSS (NM_178876)	promoter-TSS (NM_178876)	25	NM_145540	229543	Mm.268564	NM_145540	ENSMUSG00000027933	Ints3	C77668	integrator complex subunit 3	protein-coding
mm_142457.1	chr17	45595718	45595746	-	1	NA	promoter-TSS (NM_001199116)	promoter-TSS (NM_001199116)	-160	NM_001199116	63959	Mm.29744	NM_022880	ENSMUSG00000023942	Slc29a1	1200014D21Rik|AA407560|ENT1	solute carrier family 29 (nucleoside transporters), member 1	protein-coding
mm_35554.1	chr4	41517327	41517337	-	1	NA	promoter-TSS (NM_001048005)	promoter-TSS (NM_001048005)	1	NM_001048005	73721	Mm.45614	NM_028624	ENSMUSG00000028441	1110017D15Rik	Cbe1|Smrp1	RIKEN cDNA 1110017D15 gene	protein-coding
mm_11972.1	chr2	54854226	54854229	+	1	NA	intron (NM_173030, intron 4 of 12)	intron (NM_173030, intron 4 of 12)	417840	NM_173030	271786	Mm.330227	NM_173030	ENSMUSG00000060988	Galnt13	A230002A12|A230020F20|BB182356	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13	protein-coding
mm_69373.1	chr7	130867364	130867392	-	1	NA	intron (NM_001346515, intron 1 of 12)	intron (NM_001346515, intron 1 of 12)	1468	NM_133942	101476	Mm.323554	NM_133942	ENSMUSG00000040268	Plekha1	AA960558|C920009D07Rik|TAPP1	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 1	protein-coding
mm_65156.1	chr7	19635799	19635820	-	1	NA	exon (NM_019649, exon 10 of 14)	exon (NM_019649, exon 10 of 14)	-6371	NM_009046	19698	Mm.1741	NM_009046	ENSMUSG00000002983	Relb	shep	avian reticuloendotheliosis viral (v-rel) oncogene related B	protein-coding
mm_69589.1	chr7	135705745	135705762	-	1	NA	exon (NM_001081117, exon 7 of 14)	exon (NM_001081117, exon 7 of 14)	10626	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_116839.1	chr13	54688185	54688211	-	1	NA	promoter-TSS (NM_001146025)	promoter-TSS (NM_001146025)	2	NM_001146027	105239	Mm.25366	NM_134064	ENSMUSG00000034928	Rnf44	AI854545|mKIAA1100	ring finger protein 44	protein-coding
mm_117664.1	chr13	93499684	93499702	-	1	NA	5' UTR (NM_021310, exon 1 of 11)	5' UTR (NM_021310, exon 1 of 11)	115	NM_021310	57748	Mm.100273	NM_021310	ENSMUSG00000021690	Jmy	-	junction-mediating and regulatory protein	protein-coding
mm_83675.1	chr9	50124333	50124346	-	1	NA	Intergenic	Intergenic	108843	NR_131161	71873		NR_131161	ENSMUSG00000110916	2310003N18Rik	-	RIKEN cDNA 2310003N18 gene	ncRNA
mm_137599.1	chr17	28177397	28177449	+	1	NA	promoter-TSS (NM_172617)	promoter-TSS (NM_172617)	5	NM_172617	224656	Mm.267359	NM_172617	ENSMUSG00000024220	Zfp523	2810027J07|BC025615|Znf76	zinc finger protein 523	protein-coding
mm_130129.1	chr15	90316444	90316447	-	1	NA	Intergenic	(TAGA)n|Simple_repeat|Simple_repeat	92085	NR_106106	102466838		NR_106106	ENSMUSG00000099319	Mir7648	Gm27736|mmu-mir-7648	microRNA 7648	ncRNA
mm_66775.1	chr7	46855624	46855626	-	1	NA	TTS (NM_001136069)	TTS (NM_001136069)	-5638	NM_013580	16833	Mm.16563	NM_013580	ENSMUSG00000030851	Ldhc	LDH-C4|Ldh-3|Ldh-x|Ldh3|Ldhc4	lactate dehydrogenase C	protein-coding
mm_30430.1	chr3	153152076	153152086	-	1	NA	promoter-TSS (NR_108044)	promoter-TSS (NR_108044)	27	NR_108044	75001		NR_108044		4930482G09Rik	-	RIKEN cDNA 4930482G09 gene	ncRNA
mm_22877.1	chr3	29261000	29261003	+	1	NA	intron (NM_001167748, intron 4 of 12)	intron (NM_001167748, intron 4 of 12)	-155822	NR_030422	791072		NR_030422	ENSMUSG00000076120	Mir551b	Mirn551b|mir-551b	microRNA 551b	ncRNA
mm_164875.1	chr18	57911999	57912018	+	1	NA	exon (NM_009194, exon 12 of 27)	exon (NM_009194, exon 12 of 27)	33330	NM_009194	20496	Mm.399997	NM_009194	ENSMUSG00000024597	Slc12a2	9330166H04Rik|Nkcc1|mBSC2|sy-ns	solute carrier family 12, member 2	protein-coding
mm_130257.1	chr15	96642312	96642347	-	1	NA	promoter-TSS (NM_001166456)	promoter-TSS (NM_001166456)	14	NM_001166456	105727	Mm.103568	NM_134086	ENSMUSG00000023169	Slc38a1	AA408026|AA409865|AL022800|AU015942|NAT2	solute carrier family 38, member 1	protein-coding
mm_102475.1	chr11	60036864	60036914	-	1	NA	5' UTR (NM_008819, exon 1 of 7)	5' UTR (NM_008819, exon 1 of 7)	116	NM_008819	18618	Mm.2731	NM_008819	ENSMUSG00000000301	Pemt	PEAMT|PEMT2|PLMT|Pempt|Pempt2	phosphatidylethanolamine N-methyltransferase	protein-coding
mm_133484.1	chr16	90220570	90220589	+	1	NA	promoter-TSS (NM_011434)	promoter-TSS (NM_011434)	-163	NM_011434	20655	Mm.276325	NM_011434	ENSMUSG00000022982	Sod1	B430204E11Rik|Cu/Zn-SOD|CuZnSOD|Ipo-1|Ipo1|SODC|Sod-1	superoxide dismutase 1, soluble	protein-coding
mm_99164.1	chr11	100626903	100626920	+	1	NA	3' UTR (NM_177790, exon 8 of 8)	3' UTR (NM_177790, exon 8 of 8)	3956	NM_028024	71966	Mm.274734	NM_028024	ENSMUSG00000017837	Nkiras2	2410003M04Rik|4930527H08Rik|D630018G21Rik|KBRAS2	NFKB inhibitor interacting Ras-like protein 2	protein-coding
mm_32709.1	chr4	116150492	116150576	+	1	NA	promoter-TSS (NM_026651)	promoter-TSS (NM_026651)	16	NM_026651	68273	Mm.196045	NM_026651	ENSMUSG00000028700	Pomgnt1	0610016I07Rik|4930467B06Rik	protein O-linked mannose beta 1,2-N-acetylglucosaminyltransferase	protein-coding
mm_111940.1	chr12	108893522	108893546	-	1	NA	promoter-TSS (NM_177602)	promoter-TSS (NM_177602)	-323	NM_011710	22375	Mm.38433	NM_011710	ENSMUSG00000021266	Wars	TrpRS|WRS	tryptophanyl-tRNA synthetase	protein-coding
mm_57431.1	chr6	124914223	124914234	-	1	NA	exon (NM_026988, exon 5 of 5)	exon (NM_026988, exon 5 of 5)	-2523	NM_008479	16768	Mm.4528	NM_008479	ENSMUSG00000030124	Lag3	CD223|LAG-3|Ly66	lymphocyte-activation gene 3	protein-coding
mm_87980.1	chr10	63821044	63821057	+	1	NA	promoter-TSS (NM_001164519)	promoter-TSS (NM_001164519)	-5	NM_001164519	216033	Mm.444692	NM_177612	ENSMUSG00000060843	Ctnna3	4930429L08Rik|4933408A16|Catna3|Vr22	catenin (cadherin associated protein), alpha 3	protein-coding
mm_16643.1	chr2	6130079	6130089	-	1	NA	5' UTR (NM_001159657, exon 1 of 4)	5' UTR (NM_001159657, exon 1 of 4)	101	NM_144883	227545	Mm.133542	NM_144883	ENSMUSG00000045319	Proser2	5430407P10Rik|AU067770	proline and serine rich 2	protein-coding
mm_142808.1	chr17	50993678	50993688	-	1	NA	intron (NM_028162, intron 3 of 21)	RLTR14-int|LTR|ERV1	165695	NM_001285993	72238	Mm.120650	NM_028162	ENSMUSG00000023923	Tbc1d5	1600014N05Rik	TBC1 domain family, member 5	protein-coding
mm_11251.1	chr2	29890862	29890868	+	1	NA	5' UTR (NM_013615, exon 2 of 17)	5' UTR (NM_013615, exon 2 of 17)	802	NM_013615	18286	Mm.330116	NM_013615	ENSMUSG00000026790	Odf2	AI848335|MMTEST29	outer dense fiber of sperm tails 2	protein-coding
mm_136792.1	chr17	12044709	12044719	+	1	NA	intron (NM_016694, intron 10 of 11)	intron (NM_016694, intron 10 of 11)	-74570	NM_026644	68262	Mm.258300	NM_026644	ENSMUSG00000023827	Agpat4	1500003P24Rik	1-acylglycerol-3-phosphate O-acyltransferase 4 (lysophosphatidic acid acyltransferase, delta)	protein-coding
mm_111190.1	chr12	84175640	84175659	-	1	NA	intron (NM_001163501, intron 1 of 12)	intron (NM_001163501, intron 1 of 12)	18366	NM_001163502	238317	Mm.31256	NM_001163501	ENSMUSG00000042507	Elmsan1	9430029N19Rik|C130039O16Rik|Gm260	ELM2 and Myb/SANT-like domain containing 1	protein-coding
mm_9310.1	chr1	171641156	171641168	-	1	NA	TTS (NR_106151)	TTS (NR_106151)	738	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_32647.1	chr4	115059508	115059553	+	1	NA	5' UTR (NM_011527, exon 2 of 5)	5' UTR (NM_011527, exon 2 of 5)	1719	NM_001287388	21349	Mm.239869	NM_011527	ENSMUSG00000028717	Tal1	Hpt|SCL/tal-1|Scl|bHLHa17|tal-1	T cell acute lymphocytic leukemia 1	protein-coding
mm_62719.1	chr7	110772807	110772807	+	1	NA	5' UTR (NM_009667, exon 1 of 15)	5' UTR (NM_009667, exon 1 of 15)	203	NM_009667	11717	Mm.3238	NM_009667	ENSMUSG00000005686	Ampd3	-	adenosine monophosphate deaminase 3	protein-coding
mm_141461.1	chr17	30576164	30576240	-	1	NA	promoter-TSS (NM_027060)	promoter-TSS (NM_027060)	85	NM_172618	224671	Mm.41220	NM_027060	ENSMUSG00000062202	Btbd9	1700023F20Rik|4930402L05|AI464421	BTB (POZ) domain containing 9	protein-coding
mm_70778.1	chr8	22227293	22227320	+	1	NA	promoter-TSS (NM_001293688)	promoter-TSS (NM_001293688)	3	NM_001293688	56229	Mm.32067	NM_019576	ENSMUSG00000031480	Thsd1	4833423O18Rik|Tmtsp	thrombospondin, type I, domain 1	protein-coding
mm_53124.1	chr6	125129864	125129872	+	1	NA	exon (NM_145979, exon 39 of 39)	exon (NM_145979, exon 39 of 39)	-2015	NM_138747	110109	Mm.29203	NM_138747	ENSMUSG00000038279	Nop2	120kDa|A530002O17|Nol1	NOP2 nucleolar protein	protein-coding
mm_82546.1	chr9	20898593	20898631	-	1	NA	promoter-TSS (NM_016876)	promoter-TSS (NM_016876)	-22	NM_016876	53356	Mm.427309	NM_016876	ENSMUSG00000070319	Eif3g	44kDa|D0Jmb4|Eif3s4|TU-189B2|eIF3-p44|p44	eukaryotic translation initiation factor 3, subunit G	protein-coding
mm_93237.1	chr10	95415195	95415220	-	1	NA	promoter-TSS (NM_001168657)	promoter-TSS (NM_001168657)	76	NM_001168657	216233	Mm.474283	NM_007706	ENSMUSG00000020027	Socs2	8030460M17|AI527257|AW108012|CIS2|Cish2|D130043N08Rik|JAB|SOCS-2|SSI-2|hg	suppressor of cytokine signaling 2	protein-coding
mm_171521.1	chr4	146604097	146604115	+	1	NA	Intergenic	CpG	-57233	NR_045468	67524	Mm.444300	NR_045468	ENSMUSG00000086046	1700095A21Rik	-	RIKEN cDNA 1700095A21 gene	ncRNA
mm_106605.1	chr11	120784167	120784176	-	1	NA	promoter-TSS (NM_145370)	promoter-TSS (NM_145370)	33	NM_009053	19719	Mm.871	NM_009053	ENSMUSG00000025158	Rfng	-	RFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	protein-coding
mm_102160.1	chr11	53763682	53763693	-	1	NA	promoter-TSS (NR_106131)	promoter-TSS (NR_106131)	-33	NR_106131	102465772		NR_106131	ENSMUSG00000099153	Mir7671	Gm27802|mmu-mir-7671	microRNA 7671	ncRNA
mm_22897.1	chr3	30793302	30793353	+	1	NA	5' UTR (NM_027016, exon 1 of 8)	5' UTR (NM_027016, exon 1 of 8)	451	NM_027016	69276	Mm.26017	NM_027016	ENSMUSG00000027706	Sec62	3100002M17Rik|AI844545|AW545092|Dtrp1|HTP1|Tloc1	SEC62 homolog (S. cerevisiae)	protein-coding
mm_95449.1	chr11	50298164	50298187	+	1	NA	exon (NM_001110500, exon 12 of 15)	exon (NM_001110500, exon 12 of 15)	-5839	NM_175334	103806	Mm.51116	NM_175334	ENSMUSG00000050567	Maml1	AI644666|AW743257|D930008C07Rik|Mam-1|Mam1|mKIAA0200	mastermind like 1 (Drosophila)	protein-coding
mm_163770.1	chr13	120018147	120018157	+	1	NA	Intergenic	Intergenic	34052	NM_001302966	100861753	Mm.165042	NM_001302966	ENSMUSG00000095609	Gm21188	-	predicted gene, 21188	protein-coding
mm_35503.1	chr4	41064398	41064425	-	1	NA	Intergenic	Intergenic	-16275	NM_007473	11832	Mm.8728	NM_007473	ENSMUSG00000028427	Aqp7	AQP7L|AQPap	aquaporin 7	protein-coding
mm_134046.1	chr16	5203982	5204017	-	1	NA	promoter-TSS (NM_013796)	promoter-TSS (NM_013796)	13	NM_013796	27426	Mm.215641	NM_013796	ENSMUSG00000023143	Nagpa	AI596180|UCE	N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase	protein-coding
mm_23982.1	chr3	86040532	86040571	+	1	NA	Intergenic	Intergenic	-38060	NM_001001650	368202	Mm.253822	NM_001001650	ENSMUSG00000049013	Prss48	Esspl|Gm1019	protease, serine 48	protein-coding
mm_68621.1	chr7	117486546	117486556	-	1	NA	intron (NM_175645, intron 2 of 11)	intron (NM_175645, intron 2 of 11)	105572	NM_175645	233781	Mm.461427	NM_175645	ENSMUSG00000030657	Xylt1	8030490L12	xylosyltransferase 1	protein-coding
mm_123461.1	chr14	65833890	65833905	-	1	NA	promoter-TSS (NM_028039)	promoter-TSS (NM_028039)	72	NM_028039	71988	Mm.249280	NM_028039	ENSMUSG00000022034	Esco2	2410004I17Rik|D030072L07Rik	establishment of sister chromatid cohesion N-acetyltransferase 2	protein-coding
mm_63769.1	chr7	131303690	131303719	+	1	NA	Intergenic	Intergenic	18588	NM_008411	16433	Mm.142717	NM_008411	ENSMUSG00000040205	Cuzd1	Erg-1|Itmap1|Uo-44|Usg|Utczp	CUB and zona pellucida-like domains 1	protein-coding
mm_47575.1	chr5	124531195	124531232	-	1	NA	5' UTR (NM_021430, exon 1 of 7)	5' UTR (NM_021430, exon 1 of 7)	178	NM_021430	75695	Mm.41180	NM_021430	ENSMUSG00000029392	Rilpl1	2900002H16Rik|6330559I19Rik|GOSPEL	Rab interacting lysosomal protein-like 1	protein-coding
mm_145153.1	chr18	46474072	46474072	+	1	NA	Intergenic	MLT1L|LTR|ERVL-MaLR	-8256	NR_045438	72076	Mm.82766	NM_028086		Mospd4	2010013H21Rik	motile sperm domain containing 4	pseudo
mm_70043.1	chr7	142577909	142577920	-	1	NA	promoter-TSS (NR_030416)	promoter-TSS (NR_030416)	232	NR_130974	14955	Mm.14802	NR_001592	ENSMUSG00000000031	H19	AI747191	H19, imprinted maternally expressed transcript	ncRNA
mm_80215.1	chr9	72531934	72531950	+	1	NA	promoter-TSS (NM_001033536)	promoter-TSS (NM_001033536)	-84	NR_045735	75115	Mm.280755	NR_045735	ENSMUSG00000096986	4930509E16Rik	-	RIKEN cDNA 4930509E16 gene	ncRNA
mm_161711.1	chr17	25136635	25136635	+	1	NA	promoter-TSS (NM_001317404)	promoter-TSS (NM_001317404)	4	NM_001317404	26373	Mm.270587	NM_011930	ENSMUSG00000036636	Clcn7	ClC-7|D17Wsu51e	chloride channel, voltage-sensitive 7	protein-coding
mm_118681.1	chr14	22100753	22100763	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	81046	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_139866.1	chr17	70522084	70522144	+	1	NA	promoter-TSS (NM_001128180)	promoter-TSS (NM_001128180)	4	NM_001128180	224997	Mm.311840	NM_027712	ENSMUSG00000003279	Dlgap1	4933422O14Rik|9630002F18|AI845682|AI848168|BB075781|D17Bwg0511e|GKAP/SAPAP|GKPA/SAPAP|Gkap|Sapap1|mKIAA4162	discs, large (Drosophila) homolog-associated protein 1	protein-coding
mm_102752.1	chr11	67279032	67279048	-	1	NA	exon (NM_177369, exon 3 of 40)	exon (NM_177369, exon 3 of 40)	1916	NM_177369	17885	Mm.340163	NM_177369	ENSMUSG00000055775	Myh8	4832426G23Rik|AI327267|MHCp|MyHC-pn|Myhs-p|Myhsp	myosin, heavy polypeptide 8, skeletal muscle, perinatal	protein-coding
mm_114028.1	chr13	52641149	52641156	+	1	NA	intron (NM_001198977, intron 11 of 13)	intron (NM_001198977, intron 11 of 13)	44270	NM_011518	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_16832.1	chr2	11493940	11493969	-	1	NA	exon (NM_001177754, exon 2 of 16)	exon (NM_001177754, exon 2 of 16)	8136	NM_001177754	170768	Mm.19669	NM_133232	ENSMUSG00000026773	Pfkfb3	E330010H22Rik|iPFK-2|uPFK-2	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	protein-coding
mm_58843.1	chr7	16842957	16842963	+	1	NA	promoter-TSS (NM_178900)	promoter-TSS (NM_178900)	58	NM_001252458	101540	Mm.1881	NM_178900	ENSMUSG00000041187	Prkd2	AI325941|PKD2	protein kinase D2	protein-coding
mm_17620.1	chr2	30967860	30967924	-	1	NA	promoter-TSS (NM_144884)	promoter-TSS (NM_144884)	26	NM_144884	30931	Mm.154994	NM_144884	ENSMUSG00000026849	Tor1a	DQ2|Dyt1|torsinA	torsin family 1, member A (torsin A)	protein-coding
mm_151794.1	chr19	5406602	5406606	-	1	NA	promoter-TSS (NR_015545)	promoter-TSS (NR_015545)	-211	NR_015545	74931	Mm.388511	NR_015545	ENSMUSG00000086938	4930481A15Rik	-	RIKEN cDNA 4930481A15 gene	ncRNA
mm_113411.1	chr13	33979691	33979694	+	1	NA	intron (NM_020282, intron 5 of 7)	intron (NM_020282, intron 5 of 7)	12539	NM_001163242	18105	Mm.264036	NM_020282	ENSMUSG00000046949	Nqo2	NMO2|Nmor2|Ox2	NAD(P)H dehydrogenase, quinone 2	protein-coding
mm_96671.1	chr11	69410945	69410975	+	1	NA	intron (NM_001017426, intron 1 of 22)	CpG	2715	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_50209.1	chr6	42261958	42262007	+	1	NA	promoter-TSS (NM_175408)	promoter-TSS (NM_175408)	12	NM_175408	109218	Mm.480678	NM_175408	ENSMUSG00000071506	Tmem139	A930027H06Rik	transmembrane protein 139	protein-coding
mm_43232.1	chr5	129941903	129941940	+	1	NA	promoter-TSS (NM_001286382)	promoter-TSS (NM_001286382)	-188	NM_001001327	69568	Mm.288718	NM_027121	ENSMUSG00000066735	Vkorc1l1	2310024K08Rik	vitamin K epoxide reductase complex, subunit 1-like 1	protein-coding
mm_78147.1	chr9	21002916	21002926	+	1	NA	5' UTR (NM_023167, exon 1 of 9)	5' UTR (NM_023167, exon 1 of 9)	184	NM_023167	66163	Mm.427576	NM_023167	ENSMUSG00000003299	Mrpl4	1110017G11Rik	mitochondrial ribosomal protein L4	protein-coding
mm_108562.1	chr12	84760715	84760797	+	1	NA	exon (NM_023409, exon 3 of 4)	exon (NM_023409, exon 3 of 4)	12356	NM_023409	67963	Mm.282556	NM_023409	ENSMUSG00000021242	Npc2	2700012J19Rik|AA408070|AU045843|HE1	Niemann-Pick type C2	protein-coding
mm_147326.1	chr18	42275122	42275135	-	1	NA	promoter-TSS (NM_172626)	promoter-TSS (NM_172626)	69	NR_033452	100042757	Mm.100172	NR_033452		Gm4013	-	predicted gene 4013	ncRNA
mm_71889.1	chr8	69832486	69832535	+	1	NA	promoter-TSS (NM_001024954)	promoter-TSS (NM_001024954)	-194	NM_001024954	80720	Mm.210823	NM_030555	ENSMUSG00000031860	Pbx4	2410015M21Rik|AI429113|AW045266	pre B cell leukemia homeobox 4	protein-coding
mm_152494.1	chr19	11081035	11081045	-	1	NA	promoter-TSS (NM_022430)	promoter-TSS (NM_022430)	63	NM_022430	64381	Mm.34460	NM_022430	ENSMUSG00000024730	Ms4a8a	2010004L09Rik|AI481240|CD20L5|Ms4a8	membrane-spanning 4-domains, subfamily A, member 8A	protein-coding
mm_159258.1	chr2	154307227	154307227	+	1	NA	promoter-TSS (NM_001025574)	promoter-TSS (NM_001025574)	-17	NM_001025574	433492	Mm.330682	NM_001025574	ENSMUSG00000067996	Bpifb9b	5430413K10Rik|AI413838|OTTMUSG00000015915	BPI fold containing family B, member 9B	protein-coding
mm_85942.1	chr9	112099458	112099468	-	1	NA	intron (NM_001177618, intron 17 of 18)	intron (NM_001177618, intron 17 of 18)	19248	NR_029823	723815		NR_029823	ENSMUSG00000065441	Mir128-2	Mirn128-2|Mirn128b|mir-128-2|mir-128b	microRNA 128-2	ncRNA
mm_9247.1	chr1	171360727	171360765	-	1	NA	promoter-TSS (NM_001033039)	promoter-TSS (NM_001033039)	52	NM_001033039	68874	Mm.10756	NM_001033039	ENSMUSG00000045259	Klhdc9	1190002J23Rik|AA087357|ESTM31	kelch domain containing 9	protein-coding
mm_139043.1	chr17	46227870	46227870	+	1	NA	exon (NM_028198, exon 18 of 32)	exon (NM_028198, exon 18 of 32)	-3661	NR_030466	751553		NR_030466	ENSMUSG00000076141	Mir693	Mirn693|mir-693|mmu-mir-693	microRNA 693	ncRNA
mm_92499.1	chr10	78352065	78352067	-	1	NA	promoter-TSS (NM_053014)	promoter-TSS (NM_053014)	-366	NM_053014	28169	Mm.141230	NM_053014	ENSMUSG00000001211	Agpat3	AW061257|AW493985|D10Jhu12e|lpaat3	1-acylglycerol-3-phosphate O-acyltransferase 3	protein-coding
mm_96945.1	chr11	70540854	70540888	+	1	NA	exon (NM_001302476, exon 2 of 10)	exon (NM_001302476, exon 2 of 10)	599	NM_001302476	18806	Mm.260177	NM_008876	ENSMUSG00000020828	Pld2	PLD1C	phospholipase D2	protein-coding
mm_31602.1	chr4	57956623	57956626	+	1	NA	promoter-TSS (NM_011660)	promoter-TSS (NM_011660)	-213	NM_011660	22166	Mm.260618	NM_011660	ENSMUSG00000028367	Txn1	ADF|AW550880|Trx1|Txn	thioredoxin 1	protein-coding
mm_127760.1	chr15	103515109	103515133	+	1	NA	5' UTR (NM_001285890, exon 1 of 15)	5' UTR (NM_001285890, exon 1 of 15)	144	NM_001285890	18574	Mm.390792	NM_008800	ENSMUSG00000022489	Pde1b	Pde1b1	phosphodiesterase 1B, Ca2+-calmodulin dependent	protein-coding
mm_171658.1	chr4	43000434	43000438	-	1	NA	promoter-TSS (NM_009503)	promoter-TSS (NM_009503)	71	NM_009503	269523	Mm.245976	NM_009503	ENSMUSG00000028452	Vcp	3110001E05|CDC48|p97|p97/VCP	valosin containing protein	protein-coding
mm_30809.1	chr4	20042116	20042120	+	1	NA	promoter-TSS (NM_010281)	promoter-TSS (NM_010281)	66	NM_010281	14590	Mm.20461	NM_010281	ENSMUSG00000073987	Ggh	gamma-GH	gamma-glutamyl hydrolase	protein-coding
mm_14731.1	chr2	144270623	144270672	+	1	NA	promoter-TSS (NM_024225)	promoter-TSS (NM_024225)	-75	NM_024225	69178	Mm.273379	NM_024225	ENSMUSG00000027423	Snx5	0910001N05Rik|1810032P22Rik|AU019504|D2Ertd52e	sorting nexin 5	protein-coding
mm_92572.1	chr10	79910332	79910348	-	1	NA	3' UTR (NM_177994, exon 8 of 8)	3' UTR (NM_177994, exon 8 of 8)	-1402	NM_198107	216154	Mm.260089	NM_198107	ENSMUSG00000013833	Med16	95kDa|A630083L04|Thrap5|Trap95	mediator complex subunit 16	protein-coding
mm_70703.1	chr8	15057150	15057160	+	1	NA	promoter-TSS (NM_008664)	promoter-TSS (NM_008664)	-498	NM_008664	17930	Mm.272115	NM_008664	ENSMUSG00000031461	Myom2	AW146149	myomesin 2	protein-coding
mm_131459.1	chr16	16983418	16983428	+	1	NA	promoter-TSS (NM_001038663)	promoter-TSS (NM_001038663)	41	NM_001038663	26413	Mm.196581	NM_011949	ENSMUSG00000063358	Mapk1	9030612K14Rik|AA407128|AU018647|C78273|ERK|Erk2|MAPK2|PRKM2|Prkm1|p41mapk|p42mapk	mitogen-activated protein kinase 1	protein-coding
mm_134743.1	chr16	23029404	23029416	-	1	NA	promoter-TSS (NM_201375)	promoter-TSS (NM_201375)	-309	NM_001102410	385643	Mm.440414	NM_201375	ENSMUSG00000060459	Kng2	-	kininogen 2	protein-coding
mm_63420.1	chr7	127471356	127471368	+	1	NA	promoter-TSS (NM_145589)	promoter-TSS (NM_145589)	-252	NM_145589	233895	Mm.44183	NM_145589	ENSMUSG00000030822	Prr14	BC006909	proline rich 14	protein-coding
mm_74828.1	chr8	23191048	23191058	-	1	NA	5' UTR (NM_018743, exon 2 of 13)	5' UTR (NM_018743, exon 2 of 13)	17400	NM_018743	102247	Mm.200898	NM_018743	ENSMUSG00000031545	Gpat4	AU041707|AW545732|Agpat6|Tsarg7	glycerol-3-phosphate acyltransferase 4	protein-coding
mm_24321.1	chr3	89432471	89432495	+	1	NA	exon (NM_026869, exon 3 of 3)	exon (NM_026869, exon 3 of 3)	1463	NM_001293766	68911	Mm.22521	NM_026869	ENSMUSG00000047824	Pygo2	1190004M21Rik	pygopus 2	protein-coding
mm_137198.1	chr17	23867890	23867906	+	1	NA	promoter-TSS (NM_020487)	promoter-TSS (NM_020487)	-174	NM_020487	57256	Mm.386785	NM_020487	ENSMUSG00000024116	Prss21	1700023E12Rik|TESP5|mT4|testisin	protease, serine 21	protein-coding
mm_75570.1	chr8	60941401	60941417	-	1	NA	exon (NM_173873, exon 3 of 13)	exon (NM_173873, exon 3 of 13)	13390	NM_173876	12725	Mm.25263	NM_007711	ENSMUSG00000004319	Clcn3	Clc3	chloride channel, voltage-sensitive 3	protein-coding
mm_115614.1	chr13	12051218	12051229	-	1	NA	intron (NM_023868, intron 1 of 104)	B1_Mus1|SINE|Alu	55722	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding
mm_162939.1	chr10	127878316	127878343	-	1	NA	Intergenic	Lx8|LINE|L1	10370	NM_017473	54150	Mm.6696	NM_017473	ENSMUSG00000040134	Rdh7	AI194929|CRAD2	retinol dehydrogenase 7	protein-coding
mm_23802.1	chr3	79884497	79884571	+	1	NA	Intergenic	Intergenic	-1396	NM_133187	68659	Mm.427274	NM_133187	ENSMUSG00000027955	Fam198b	1110032E23Rik|2210419I08Rik|AV011458|Ened	family with sequence similarity 198, member B	protein-coding
mm_3075.1	chr1	134289969	134289977	+	1	NA	promoter-TSS (NM_031189)	promoter-TSS (NM_031189)	-31	NM_031189	17928	Mm.16528	NM_031189	ENSMUSG00000026459	Myog	MYF4|bHLHc3|myo	myogenin	protein-coding
mm_103112.1	chr11	69981282	69981293	-	1	NA	promoter-TSS (NM_001253700)	promoter-TSS (NM_001253700)	-52	NM_018740	54351	Mm.13430	NM_018740	ENSMUSG00000018565	Elp5	Derp6|Rai12	elongator acetyltransferase complex subunit 5	protein-coding
mm_73978.1	chr8	120537364	120537393	+	1	NA	promoter-TSS (NM_001145896)	promoter-TSS (NM_001145896)	-31	NM_001145896	382034	Mm.334856	NM_198671	ENSMUSG00000031822	Gse1	2210013I18Rik|mKIAA0182	genetic suppressor element 1, coiled-coil protein	protein-coding
mm_117522.1	chr13	81570654	81570671	-	1	NA	intron (NM_054053, intron 11 of 89)	intron (NM_054053, intron 11 of 89)	62482	NM_054053	110789	Mm.288694	NM_054053	ENSMUSG00000069170	Adgrv1	Frings|Gpr98|Mass1|Mgr1|VLGR1	adhesion G protein-coupled receptor V1	protein-coding
mm_10831.1	chr2	24386605	24386628	+	1	NA	intron (NM_177611, intron 1 of 16)	intron (NM_177611, intron 1 of 16)	1219	NM_177611	215632	Mm.490434	NM_177611	ENSMUSG00000026979	Psd4	BC046518|EFA6B	pleckstrin and Sec7 domain containing 4	protein-coding
mm_45051.1	chr5	41764494	41764494	-	1	NA	promoter-TSS (NM_007524)	promoter-TSS (NM_007524)	-274	NM_007524	12020	Mm.2530	NM_007524	ENSMUSG00000049691	Nkx3-2	Bapx1|NKX3.2|Nkx-3.2	NK3 homeobox 2	protein-coding
mm_104892.1	chr11	99581010	99581024	-	1	NA	promoter-TSS (NM_027157)	promoter-TSS (NM_027157)	-1	NM_027157	69664	Mm.38303	NM_027157	ENSMUSG00000047253	Krtap1-5	2310043L02Rik|AI592983	keratin associated protein 1-5	protein-coding
mm_48049.1	chr5	136471915	136471927	-	1	NA	intron (NM_001291239, intron 2 of 22)	intron (NM_001291239, intron 2 of 22)	94060	NM_001291239	13047	Mm.320317	NM_009986	ENSMUSG00000029705	Cux1	CDP|Cutl1|Cux|Cux-1	cut-like homeobox 1	protein-coding
mm_28205.1	chr3	88296926	88296939	-	1	NA	promoter-TSS (NM_009836)	promoter-TSS (NM_009836)	-94	NM_029801	76927	Mm.273330	NM_029801	ENSMUSG00000010538	Tsacc	1700021C14Rik|SIP	TSSK6 activating co-chaperone	protein-coding
mm_171838.1	chr5	149053017	149053017	-	1	NA	promoter-TSS (NM_010439)	promoter-TSS (NM_010439)	40	NM_010439	15289	Mm.207047	NM_010439	ENSMUSG00000066551	Hmgb1	HMG-1|Hmg1|SBP-1|p30	high mobility group box 1	protein-coding
mm_39978.1	chr5	32353625	32353654	+	1	NA	promoter-TSS (NM_172147)	promoter-TSS (NM_172147)	59	NM_172147	665270	Mm.160067	NM_030072	ENSMUSG00000029134	Plb1	4632413E21Rik|4930433E17Rik|4930539A06Rik|BC033606	phospholipase B1	protein-coding
mm_162207.1	chrX	135840616	135840616	+	1	NA	intron (NM_001163015, intron 3 of 6)	intron (NM_001163015, intron 3 of 6)	1582	NM_001163017	245607	Mm.489763	NM_001163015	ENSMUSG00000072966	Gprasp2	5330440H13Rik|GASP-2|GASP2|Prpl5	G protein-coupled receptor associated sorting protein 2	protein-coding
mm_157373.1	chrX	37878522	37878533	-	1	NA	exon (NM_001004193, exon 2 of 4)	exon (NM_001004193, exon 2 of 4)	417	NM_001004193	434768	Mm.336025	NM_001004193	ENSMUSG00000064137	Rhox8	Tox	reproductive homeobox 8	protein-coding
mm_84732.1	chr9	75071124	75071142	-	1	NA	promoter-TSS (NM_010864)	promoter-TSS (NM_010864)	-73	NM_010864	17918	Mm.3645	NM_010864	ENSMUSG00000034593	Myo5a	9630007J19Rik|AI413174|AI661011|Dbv|MVa|Myo5|MyoVA|Sev-1|d|d-120J|flail|flr	myosin VA	protein-coding
mm_167711.1	chr9	96899816	96899850	-	1	NA	Intergenic	Intergenic	-10359	NM_001289645	235534	Mm.233031	NM_153420	ENSMUSG00000043587	Pxylp1	9430094M07Rik|Acpl2|BB177120|C130099A20Rik	2-phosphoxylose phosphatase 1	protein-coding
mm_14053.1	chr2	122426433	122426461	+	1	NA	promoter-TSS (NM_172980)	promoter-TSS (NM_172980)	-30	NM_172980	269346	Mm.29510	NM_172980	ENSMUSG00000027219	Slc28a2	2010208B10Rik|B430217P18|BB152493|Cnt2	solute carrier family 28 (sodium-coupled nucleoside transporter), member 2	protein-coding
mm_115807.1	chr13	19358568	19358572	-	1	NA	intron (NM_024270, intron 8 of 8)	intron (NM_024270, intron 8 of 8)	37243	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_77112.1	chr8	111081856	111081871	-	1	NA	promoter-TSS (NM_181549)	promoter-TSS (NM_181549)	-155	NM_181549	353287	Mm.135495	NM_181549	ENSMUSG00000033633	Clec18a	Mrcl	C-type lectin domain family 18, member A	protein-coding
mm_61301.1	chr7	67950227	67950230	+	1	NA	Intergenic	Intergenic	-2029	NM_010513	16001	Mm.275742	NM_010513	ENSMUSG00000005533	Igf1r	A330103N21Rik|CD221|D930020L01|IGF-1R|hyft	insulin-like growth factor I receptor	protein-coding
mm_18263.1	chr2	52307713	52307723	-	1	NA	exon (NM_010889, exon 17 of 157)	exon (NM_010889, exon 17 of 157)	16716	NR_040620	78049	Mm.243883	NR_040620		4930573O16Rik	-	RIKEN cDNA 4930573O16 gene	ncRNA
mm_136466.1	chr16	95459283	95459384	-	1	NA	promoter-TSS (NM_001302154)	promoter-TSS (NM_001302154)	15	NM_001302154	13876	Mm.164531	NM_133659	ENSMUSG00000040732	Erg	D030036I24Rik	avian erythroblastosis virus E-26 (v-ets) oncogene related	protein-coding
mm_125568.1	chr15	59302627	59302635	+	1	NA	Intergenic	ORR1B2|LTR|ERVL-MaLR	-4317	NR_045613	100416830	Mm.490788	NR_045613	ENSMUSG00000098528	Zfp572	4930472F24Rik	zinc finger protein 572	pseudo
mm_111358.1	chr12	86990523	86990533	-	1	NA	Intergenic	CpG	-1852	NM_001080943	238331	Mm.185890	NM_001080943	ENSMUSG00000048483	Zdhhc22	Gm262	zinc finger, DHHC-type containing 22	protein-coding
mm_11271.1	chr2	30061862	30061864	+	1	NA	promoter-TSS (NM_023871)	promoter-TSS (NM_023871)	-133	NM_023871	56086	Mm.326055	NM_023871	ENSMUSG00000054766	Set	2610030F17Rik|5730420M11Rik|AA407739|I-2PP2A|StF-IT-1|TAF-I	SET nuclear oncogene	protein-coding
mm_134070.1	chr16	8666488	8666496	-	1	NA	intron (NM_025821, intron 1 of 3)	intron (NM_025821, intron 1 of 3)	5661	NM_025821	52502	Mm.142095	NM_025821	ENSMUSG00000008393	Carhsp1	1200011K09Rik|Crhsp-24|D16Ertd465e	calcium regulated heat stable protein 1	protein-coding
mm_124746.1	chr15	6619597	6619631	+	1	NA	exon (NM_001278269, exon 2 of 17)	exon (NM_001278269, exon 2 of 17)	39767	NM_011815	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_172452.1	chr7	33099747	33099756	-	1	NA	Intergenic	L1Md_A|LINE|L1	-43199	NM_001281523	624439	Mm.326965	NM_001281523	ENSMUSG00000097972	Scgb2b15	Abpb15|EG624439|Gm6504	secretoglobin, family 2B, member 15	protein-coding
mm_152358.1	chr19	10065691	10065731	-	1	NA	intron (NM_019699, intron 9 of 11)	intron (NM_019699, intron 9 of 11)	24163	NM_021890	60527	Mm.253875	NM_021890	ENSMUSG00000024664	Fads3	AI464531	fatty acid desaturase 3	protein-coding
mm_90785.1	chr10	7054893	7054897	-	1	NA	Intergenic	Intergenic	-31710	NM_001033391	320495	Mm.331674	NM_001033391	ENSMUSG00000064065	Ipcef1	A130090K04Rik	interaction protein for cytohesin exchange factors 1	protein-coding
mm_105049.1	chr11	100619675	100619685	-	1	NA	5' UTR (NM_019795, exon 1 of 14)	5' UTR (NM_019795, exon 1 of 14)	488	NM_019795	56354	Mm.402409	NM_019795	ENSMUSG00000014195	Dnajc7	2010003F24Rik|2010004G07Rik|CCRP|Ttc2|mDj11|mTpr2	DnaJ heat shock protein family (Hsp40) member C7	protein-coding
mm_65558.1	chr7	27166428	27166467	-	1	NA	intron (NM_053208, intron 1 of 5)	CpG	355	NM_053208	112406	Mm.29978	NM_053208	ENSMUSG00000058709	Egln2	0610011A13Rik|C85656|Hif-p4h-1|Ier4|Phd1|SM-20	egl-9 family hypoxia-inducible factor 2	protein-coding
mm_116908.1	chr13	55476190	55476212	-	1	NA	exon (NM_019813, exon 11 of 14)	exon (NM_019813, exon 11 of 14)	1575	NR_105909	102465569		NR_105909	ENSMUSG00000098341	Mir6944	Gm27710|mmu-mir-6944	microRNA 6944	ncRNA
mm_46288.1	chr5	100237489	100237517	-	1	NA	Intergenic	RLTR44D|LTR|ERVK	26811	NR_040679	69571	Mm.396412	NR_040679	ENSMUSG00000100157	2310034O05Rik	-	RIKEN cDNA 2310034O05 gene	ncRNA
mm_45511.1	chr5	72504250	72504276	-	1	NA	promoter-TSS (NM_016869)	promoter-TSS (NM_016869)	-55	NM_016869	53419	Mm.332425	NM_016869	ENSMUSG00000005220	Corin	AV273130|Lrp4	corin	protein-coding
mm_155680.1	chrX	93286500	93286522	+	1	NA	promoter-TSS (NM_007492)	promoter-TSS (NM_007492)	4	NM_001305940	11878	Mm.275547	NM_007492	ENSMUSG00000035277	Arx	-	aristaless related homeobox	protein-coding
mm_33976.1	chr4	137664708	137664787	+	1	NA	promoter-TSS (NM_029563)	promoter-TSS (NM_029563)	21	NR_138591	110351	Mm.180763	NM_029563	ENSMUSG00000041351	Rap1gap	1300019I11Rik|2310004O14Rik|AI427470|ARPP-90|Gap|Rap1GAP1|Rap1ga1	Rap1 GTPase-activating protein	protein-coding
mm_137427.1	chr17	26270261	26270292	+	1	NA	intron (NR_037906, intron 5 of 8)	intron (NR_037906, intron 5 of 8)	17366	NR_037905	66978	Mm.440216	NM_025881	ENSMUSG00000024188	Luc7l	1810045C04Rik|2410018D03Rik	Luc7-like	protein-coding
mm_31685.1	chr4	62298165	62298209	+	1	NA	3' UTR (NM_025286, exon 4 of 4)	3' UTR (NM_025286, exon 4 of 4)	6640	NM_001290518	20530	Mm.292539	NM_025286	ENSMUSG00000066152	Slc31a2	AI604396|CTR2	solute carrier family 31, member 2	protein-coding
mm_137244.1	chr17	24488405	24488450	+	1	NA	promoter-TSS (NM_027937)	promoter-TSS (NM_027937)	-356	NM_027937	268932	Mm.70989	NM_027937	ENSMUSG00000033597	Caskin1	3300002N10Rik|C130061I24|C630036E02Rik|mKIAA1306	CASK interacting protein 1	protein-coding
mm_171279.1	chr3	88835225	88835227	+	1	NA	promoter-TSS (NM_027389)	promoter-TSS (NM_027389)	-5	NM_027389	76022	Mm.126870	NM_027389	ENSMUSG00000054199	Gon4l	1500041I23Rik|2610100B20Rik|3632445O20Rik|5430404N14Rik|AA387005	gon-4-like (C.elegans)	protein-coding
mm_109421.1	chr12	110499416	110499468	+	1	NA	intron (NM_012023, intron 1 of 13)	intron (NM_012023, intron 1 of 13)	13703	NM_012023	26931	Mm.240396	NM_012023	ENSMUSG00000017843	Ppp2r5c	2610043M05Rik|2700063L20Rik|AI060890|AW545884|C85228|D12Bwg0916e|mKIAA0044	protein phosphatase 2, regulatory subunit B', gamma	protein-coding
mm_6859.1	chr1	84262791	84262823	-	1	NA	intron (NM_001003948, intron 1 of 2)	L1MA10|LINE|L1	21838	NM_001003948	98496	Mm.187470	NM_001003948	ENSMUSG00000045658	Pid1	5033414K04Rik|NYGGF4	phosphotyrosine interaction domain containing 1	protein-coding
mm_127749.1	chr15	103473535	103473548	+	1	NA	exon (NM_153505, exon 14 of 31)	exon (NM_153505, exon 14 of 31)	19716	NM_153505	105855	Mm.30805	NM_153505	ENSMUSG00000022488	Nckap1l	4930568P13Rik|AI463083|Hem1|Hemp1	NCK associated protein 1 like	protein-coding
mm_163793.1	chr14	14703090	14703092	+	1	NA	promoter-TSS (NM_001033270)	promoter-TSS (NM_001033270)	66	NM_001033270	218756	Mm.258893	NM_001033270	ENSMUSG00000021733	Slc4a7	E430014N10Rik|NBC3|NBCn1|NBCn1-G	solute carrier family 4, sodium bicarbonate cotransporter, member 7	protein-coding
mm_114203.1	chr13	56067542	56067548	+	1	NA	Intergenic	Intergenic	68005	NM_012015	26914	Mm.283802	NM_012015	ENSMUSG00000015937	H2afy	H2AF12M|mH2a1|macroH2A1	H2A histone family, member Y	protein-coding
mm_69669.1	chr7	139983864	139983878	-	1	NA	exon (NM_001291066, exon 20 of 24)	exon (NM_001291066, exon 20 of 24)	3003	NR_106029	102465643		NR_106029	ENSMUSG00000099092	Mir7062	Gm27339|mmu-mir-7062	microRNA 7062	ncRNA
mm_73295.1	chr8	104972698	104972703	+	1	NA	Intergenic	RMER19B|LTR|ERVK	10982	NM_197999	72361	Mm.26580	NM_197999	ENSMUSG00000031877	Ces2g	2210023G05Rik|Ces2l	carboxylesterase 2G	protein-coding
mm_65481.1	chr7	25615836	25615859	-	1	NA	promoter-TSS (NM_001039243)	promoter-TSS (NM_001039243)	45	NM_001039243	632778	Mm.423112	NM_001039243	ENSMUSG00000074261	Erich4	EG632778|Gm7092|Kseg1	glutamate rich 4	protein-coding
mm_27598.1	chr3	59142702	59142706	-	1	NA	intron (NM_001287119, intron 1 of 2)	intron (NM_001287119, intron 1 of 2)	-10242	NM_001287120	140795	Mm.439021	NM_133200	ENSMUSG00000036381	P2ry14	A330108O13Rik|Gpr105|P2Y14	purinergic receptor P2Y, G-protein coupled, 14	protein-coding
mm_94037.1	chr10	128043814	128043826	-	1	NA	exon (NM_001113199, exon 3 of 9)	exon (NM_001113199, exon 3 of 9)	8474	NM_001113199	17938	Mm.3746	NM_013608	ENSMUSG00000061315	Naca	AL022831|AL024382|Gm1878|mKIAA0363|skNAC	nascent polypeptide-associated complex alpha polypeptide	protein-coding
mm_170070.1	chr17	32403522	32403522	-	1	NA	promoter-TSS (NM_178785)	promoter-TSS (NM_178785)	59	NM_178785	320484	Mm.122284	NM_178785	ENSMUSG00000052142	Rasal3	A430107D22Rik	RAS protein activator like 3	protein-coding
mm_135772.1	chr16	56831831	56831835	-	1	NA	intron (NM_019631, intron 1 of 5)	intron (NM_019631, intron 1 of 5)	-35975	NM_172825	239853	Mm.258979	NM_172825	ENSMUSG00000022755	Adgrg7	9130020O16Rik|Gpr128	adhesion G protein-coupled receptor G7	protein-coding
mm_135398.1	chr16	44558826	44558851	-	1	NA	promoter-TSS (NR_037242)	promoter-TSS (NR_037242)	32	NM_172506	117606	Mm.41561	NM_172506	ENSMUSG00000022687	Boc	4732455C11|mFLJ00376	biregional cell adhesion molecule-related/down-regulated by oncogenes (Cdon) binding protein	protein-coding
mm_127790.1	chr15	3582162	3582181	-	1	NA	promoter-TSS (NM_001286370)	promoter-TSS (NM_001286370)	-329	NM_001286370	14600	Mm.3986	NM_010284	ENSMUSG00000055737	Ghr	GHBP|GHR/BP	growth hormone receptor	protein-coding
mm_117557.1	chr13	85127088	85127104	-	1	NA	Intergenic	Intergenic	-62289	NM_001347587	66671	Mm.18474	NM_023243	ENSMUSG00000021548	Ccnh	6330408H09Rik|AI661354|AV102684|AW538719	cyclin H	protein-coding
mm_47513.1	chr5	124077282	124077325	-	1	NA	exon (NM_019875, exon 8 of 12)	exon (NM_019875, exon 8 of 12)	18495	NM_019875	56325	Mm.254839	NM_019875	ENSMUSG00000029408	Abcb9	TAPL|mKIAA1520	ATP-binding cassette, sub-family B (MDR/TAP), member 9	protein-coding
mm_149457.1	chr19	11517229	11517241	+	1	NA	Intergenic	MLTR18C_MM|LTR|ERVK	-1324	NM_027209	69774	Mm.436639	NM_027209	ENSMUSG00000024677	Ms4a6b	1810027D10Rik	membrane-spanning 4-domains, subfamily A, member 6B	protein-coding
mm_30178.1	chr3	144205508	144205530	-	1	NA	promoter-TSS (NM_010723)	promoter-TSS (NM_010723)	-264	NM_010723	16911	Mm.29187	NM_010723	ENSMUSG00000028266	Lmo4	A730077C12Rik|Crp3|Etohi4	LIM domain only 4	protein-coding
mm_141923.1	chr17	35001943	35001960	-	1	NA	intron (NM_011690, intron 2 of 29)	intron (NM_011690, intron 2 of 29)	1044	NM_011690	22321	Mm.28420	NM_011690	ENSMUSG00000007029	Vars	Bat6|D17H6S56E|G7a|Vars2	valyl-tRNA synthetase	protein-coding
mm_165596.1	chr3	42361408	42361415	+	1	NA	Intergenic	Intergenic	618793	NM_027271	73852	Mm.29006	NM_027271	ENSMUSG00000025766	D3Ertd751e	2810009O15Rik|4930415G15Rik	DNA segment, Chr 3, ERATO Doi 751, expressed	protein-coding
mm_129973.1	chr15	85811618	85811628	-	1	NA	promoter-TSS (NM_001164626)	promoter-TSS (NM_001164626)	74	NM_001164626	72355	Mm.33706	NM_197998	ENSMUSG00000064284	Cdpf1	2210021J22Rik	cysteine rich, DPF motif domain containing 1	protein-coding
mm_67080.1	chr7	68265478	68265507	-	1	NA	TTS (NR_040341)	TTS (NR_040341)	-1259	NM_030101	78444	Mm.425468	NM_030101	ENSMUSG00000030553	Pgpep1l	C330024D12Rik	pyroglutamyl-peptidase I-like	protein-coding
mm_160092.1	chr7	16994363	16994363	+	1	NA	promoter-TSS (NM_001101535)	promoter-TSS (NM_001101535)	-225	NM_001101535	434130	Mm.459162	NM_001101535	ENSMUSG00000041117	Ccdc8	ENSMUSG00000041117	coiled-coil domain containing 8	protein-coding
mm_8719.1	chr1	160025742	160025765	-	1	NA	Intergenic	Intergenic	-18627	NR_028111	67647	Mm.171518	NM_001024470	ENSMUSG00000090394	4930523C07Rik	-	RIKEN cDNA 4930523C07 gene	protein-coding
mm_69401.1	chr7	132317139	132317159	-	1	NA	promoter-TSS (NM_029935)	promoter-TSS (NM_029935)	6	NM_029935	77590	Mm.213582	NM_029935	ENSMUSG00000030930	Chst15	4631426J05Rik|BRAG|GalNAcS-6ST|MAd5|mKIAA0598	carbohydrate (N-acetylgalactosamine 4-sulfate 6-O) sulfotransferase 15	protein-coding
mm_140494.1	chr17	3557719	3557733	-	1	NA	promoter-TSS (NR_045303)	promoter-TSS (NR_045303)	-13	NM_146074	224481	Mm.226554	NM_146074	ENSMUSG00000036983	Tfb1m	AI429207	transcription factor B1, mitochondrial	protein-coding
mm_162248.1	chrX	160390541	160390541	+	1	NA	promoter-TSS (NM_178712)	promoter-TSS (NM_178712)	-149	NM_001079847	237175	Mm.213016	NM_178712	ENSMUSG00000031298	Adgrg2	AW212196|B830041D06Rik|Gpr64|Me6	adhesion G protein-coupled receptor G2	protein-coding
mm_173201.1	chrX	67835486	67835496	-	1	NA	Intergenic	IAPLTR4|LTR|ERVK	85959	NM_025763	66780	Mm.79193	NM_025763	ENSMUSG00000025288	4933436I01Rik	-	RIKEN cDNA 4933436I01 gene	protein-coding
mm_83182.1	chr9	40984480	40984487	-	1	NA	intron (NM_001281954, intron 5 of 9)	intron (NM_001281954, intron 5 of 9)	20145	NM_001281954	54698	Mm.42791	NM_019465	ENSMUSG00000032021	Crtam	-	cytotoxic and regulatory T cell molecule	protein-coding
mm_111679.1	chr12	103382551	103382551	-	1	NA	intron (NR_033587, intron 1 of 5)	ORR1A2|LTR|ERVL-MaLR	5657	NR_033587	68149	Mm.127378	NM_026580	ENSMUSG00000021203	Otub2	2010015L18Rik|4930586I02Rik|AI413508|AW557219|OTB2|OTU2	OTU domain, ubiquitin aldehyde binding 2	protein-coding
mm_5310.1	chr1	22509351	22509372	-	1	NA	intron (NM_001012623, intron 8 of 14).2	intron (NM_001012623, intron 8 of 14).2	-76518	NM_183018	116837	Mm.60061	NM_053270	ENSMUSG00000041670	Rims1	C030033M19Rik|RIM1|RIM1a|RIM1alpha|Rab3ip1|Rim|Serg1|mKIAA0340	regulating synaptic membrane exocytosis 1	protein-coding
mm_1724.1	chr1	75367128	75367166	+	1	NA	3' UTR (NM_010043, exon 9 of 9)	3' UTR (NM_010043, exon 9 of 9)	6855	NM_010043	13346	Mm.6712	NM_010043	ENSMUSG00000026208	Des	-	desmin	protein-coding
mm_79184.1	chr9	48403925	48403938	+	1	NA	Intergenic	Intergenic	41890	NM_172921	244853	Mm.325522	NM_172921	ENSMUSG00000044229	Nxpe4	C130036J11|D930028F11Rik|Fam55d	neurexophilin and PC-esterase domain family, member 4	protein-coding
mm_155039.1	chrX	42149289	42149306	+	1	NA	promoter-TSS (NM_001077712)	promoter-TSS (NM_001077712)	-115	NM_001077712	20843	Mm.290422	NM_021465	ENSMUSG00000025862	Stag2	9230105L23Rik|B230112I07Rik|SA-2|SAP2	stromal antigen 2	protein-coding
mm_69554.1	chr7	135698765	135698784	-	1	NA	exon (NM_001081117, exon 12 of 14)	exon (NM_001081117, exon 12 of 14)	17605	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_118918.1	chr14	26766325	26766332	+	1	NA	Intergenic	Intergenic	-96482	NM_178668	211948	Mm.290758	NM_178668	ENSMUSG00000043702	Pde12	2'-PDE|E430028B21Rik	phosphodiesterase 12	protein-coding
mm_30095.1	chr3	138239671	138239685	-	1	NA	promoter-TSS (NR_045760)	promoter-TSS (NR_045760)	-15	NR_045760	68369	Mm.441136	NR_045760	ENSMUSG00000099146	0610031O16Rik	-	RIKEN cDNA 0610031O16 gene	ncRNA
mm_80104.1	chr9	70342043	70342055	+	1	NA	exon (NM_181072, exon 14 of 28)	exon (NM_181072, exon 14 of 28)	63704	NR_049200	100885839		NR_049200	ENSMUSG00000093763	Mir5626	Gm25590|mir-5626|mmu-mir-5626	microRNA 5626	ncRNA
mm_74577.1	chr8	11219190	11219201	-	1	NA	exon (NM_009931, exon 34 of 52)	exon (NM_009931, exon 34 of 52)	-93610	NM_009932	12827	Mm.181021	NM_009932	ENSMUSG00000031503	Col4a2	Col4a-2	collagen, type IV, alpha 2	protein-coding
mm_123247.1	chr14	60444257	60444297	-	1	NA	Intergenic	Intergenic	65991	NM_001164705	72125	Mm.275499	NM_028113	ENSMUSG00000021986	Amer2	2600011E07Rik|Fam123a	APC membrane recruitment 2	protein-coding
mm_73987.1	chr8	120668266	120668268	+	1	NA	promoter-TSS (NM_009941)	promoter-TSS (NM_009941)	42	NM_009941	12857	Mm.386758	NM_009941	ENSMUSG00000031818	Cox4i1	AL024441|COX|COX IV-1|COXIV|Cox4|Cox4a|IV-1	cytochrome c oxidase subunit IV isoform 1	protein-coding
mm_51793.1	chr6	88272375	88272379	+	1	NA	intron (NM_023060, intron 6 of 6)	intron (NM_023060, intron 6 of 6)	50109	NM_019964	56691	Mm.272871	NM_019964	ENSMUSG00000048206	Dnajb8	1700016F14Rik|1700031F10Rik|AI326313|mDj6	DnaJ heat shock protein family (Hsp40) member B8	protein-coding
mm_153625.1	chr19	44005566	44005613	-	1	NA	exon (NM_001001446, exon 9 of 9)	exon (NM_001001446, exon 9 of 9)	-19069	NM_030703	93721	Mm.206774	NM_030703	ENSMUSG00000025196	Cpn1	0610011F20Rik|CPN	carboxypeptidase N, polypeptide 1	protein-coding
mm_164108.1	chr15	27571361	27571368	+	1	NA	promoter-TSS (NR_106065)	promoter-TSS (NR_106065)	-130	NR_106065	102466808		NR_106065	ENSMUSG00000098416	Mir7117	Gm27729|mmu-mir-7117	microRNA 7117	ncRNA
mm_161786.1	chr17	45465763	45465763	+	1	NA	intron (NM_027649, intron 1 of 7)	intron (NM_027649, intron 1 of 7)	9175	NM_027649	71020	Mm.44257	NM_027649	ENSMUSG00000023935	Spats1	1700011H05Rik|4933400B06Rik|Daip2|Ddip|Srsp1	spermatogenesis associated, serine-rich 1	protein-coding
mm_162334.1	chr1	43742562	43742564	-	1	NA	TTS (NM_024283)	TTS (NM_024283)	11961	NM_024283	78896	Mm.50109	NM_024283	ENSMUSG00000026051	1500015O10Rik	Ecrg4	RIKEN cDNA 1500015O10 gene	protein-coding
mm_48663.1	chr5	145981229	145981239	-	1	NA	intron (NR_030782, intron 11 of 11)	ORR1D1|LTR|ERVL-MaLR	28383	NM_019792	56388	Mm.301900	NM_019792	ENSMUSG00000029630	Cyp3a25	AI327008	cytochrome P450, family 3, subfamily a, polypeptide 25	protein-coding
mm_75090.1	chr8	34048949	34048955	-	1	NA	Intergenic	B3A|SINE|B2	58862	NM_001293758	22428	Mm.150373	NM_011722	ENSMUSG00000031516	Dctn6	AU044699|WS-3|p27	dynactin 6	protein-coding
mm_152590.1	chr19	11604809	11604817	-	1	NA	promoter-TSS (NM_026835)	promoter-TSS (NM_026835)	-9	NM_026835	68774	Mm.290390	NM_026835	ENSMUSG00000024679	Ms4a6d	1110058E16Rik|AI447446|Ms4a11	membrane-spanning 4-domains, subfamily A, member 6D	protein-coding
mm_5894.1	chr1	54483167	54483171	-	1	NA	intron (NM_001163314, intron 25 of 26)	intron (NM_001163314, intron 25 of 26)	-44143	NM_001033194	98488	Mm.25856	NM_001033194	ENSMUSG00000041303	Gtf3c3	TF3C-gamma|TFIIIC102	general transcription factor IIIC, polypeptide 3	protein-coding
mm_29124.1	chr3	105054877	105054884	-	1	NA	Intergenic	Intergenic	-1734	NM_030249	80281	Mm.200327	NM_030249	ENSMUSG00000062127	Cttnbp2nl	AA552995|AA589392|AU018624|BC003236|mKIAA1433	CTTNBP2 N-terminal like	protein-coding
mm_99315.1	chr11	101442290	101442294	+	1	NA	promoter-TSS (NM_011289)	promoter-TSS (NM_011289)	47	NM_011289	19942	Mm.340658	NM_011289	ENSMUSG00000063316	Rpl27	-	ribosomal protein L27	protein-coding
mm_140062.1	chr17	74682423	74682425	+	1	NA	intron (NM_007566, intron 65 of 72)	B3|SINE|B2	-35326	NM_152817	74196	Mm.209503	NM_152817	ENSMUSG00000024078	Ttc27	2610511O17Rik	tetratricopeptide repeat domain 27	protein-coding
mm_137679.1	chr17	28817704	28817721	+	1	NA	exon (NM_001081315, exon 6 of 13)	exon (NM_001081315, exon 6 of 13)	16586	NM_001081315	268936	Mm.291877	NM_199061	ENSMUSG00000063952	Brpf3	AI413466|AW493400|mKIAA1286	bromodomain and PHD finger containing, 3	protein-coding
mm_11154.1	chr2	28540228	28540238	+	1	NA	intron (NM_001145836, intron 1 of 17)	intron (NM_001145836, intron 1 of 17)	6769	NM_001145836	19730	Mm.5236	NM_009058	ENSMUSG00000026821	Ralgds	Gnds|Rgds|mKIAA1308	ral guanine nucleotide dissociation stimulator	protein-coding
mm_97546.1	chr11	78926094	78926105	+	1	NA	intron (NM_001313922, intron 1 of 25)	intron (NM_001313922, intron 1 of 25)	808	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_157947.1	chrX	86401055	86401064	-	1	NA	Intergenic	Intergenic	-46065	NR_036689	245502	Mm.490821	NR_036689		Gm41	-	melanoma antigen, family B, 4 pseudogene	pseudo
mm_158146.1	chrX	103467455	103467554	-	1	NA	non-coding (NR_001570, exon 7 of 8)	non-coding (NR_001570, exon 7 of 8)	15729	NR_001570	213742	Mm.274770	NR_001463	ENSMUSG00000086503	Xist	A430022B11|AI314753	inactive X specific transcripts	ncRNA
mm_12558.1	chr2	72476174	72476212	+	1	NA	promoter-TSS (NM_025866)	promoter-TSS (NM_025866)	-26	NM_025866	66953	Mm.270676	NM_025866	ENSMUSG00000055612	Cdca7	2310021G01Rik|AU044109|JPO1	cell division cycle associated 7	protein-coding
mm_144925.1	chr18	37689813	37689875	+	1	NA	promoter-TSS (NM_033575)	promoter-TSS (NM_033575)	-15	NM_033575	93700	Mm.247203	NM_033575	ENSMUSG00000102748	Pcdhgb2	-	protocadherin gamma subfamily B, 2	protein-coding
mm_85474.1	chr9	105827997	105828049	-	1	NA	promoter-TSS (NM_001102607)	promoter-TSS (NM_001102607)	62	NM_001102607	245026	Mm.482507	NM_172927	ENSMUSG00000043719	Col6a6	E330019B14|E330026B02Rik	collagen, type VI, alpha 6	protein-coding
mm_170606.1	chr19	5845179	5845181	-	1	NA	non-coding (NR_003513, exon 1 of 1)	non-coding (NR_003513, exon 1 of 1)	298	NR_131212	66961	Mm.281895	NR_003513	ENSMUSG00000092274	Neat1	2310043N10Rik|VINC	nuclear paraspeckle assembly transcript 1 (non-protein coding)	ncRNA
mm_63524.1	chr7	127904825	127904839	+	1	NA	5' UTR (NM_009739, exon 2 of 12)	5' UTR (NM_009739, exon 2 of 12)	759	NM_009739	12041	Mm.425495	NM_009739	ENSMUSG00000030802	Bckdk	AI327402	branched chain ketoacid dehydrogenase kinase	protein-coding
mm_28222.1	chr3	88447180	88447184	-	1	NA	intron (NM_001163491, intron 10 of 14)	BC1_Mm|scRNA|scRNA	-6231	NR_105978	102465611		NR_105978	ENSMUSG00000098655	Mir7011	Gm27677|mmu-mir-7011	microRNA 7011	ncRNA
mm_38661.1	chr4	144408398	144408440	-	1	NA	promoter-TSS (NM_029948)	promoter-TSS (NM_029948)	45	NM_029948	77632	Mm.31283	NM_029948	ENSMUSG00000028591	Pramef12	4930569K13Rik|AU023001|C86578	PRAME family member 12	protein-coding
mm_72844.1	chr8	88301169	88301170	+	1	NA	intron (NM_001037723, intron 3 of 27)	B4A|SINE|B4	6965	NM_001037724	11513	Mm.288206	NM_007406	ENSMUSG00000031659	Adcy7	AA407758	adenylate cyclase 7	protein-coding
mm_1422.1	chr1	67174350	67174358	+	1	NA	exon (NM_001080809, exon 19 of 38)	exon (NM_001080809, exon 19 of 38)	51327	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_15036.1	chr2	152756997	152757005	+	1	NA	intron (NM_053091, intron 2 of 4)	intron (NM_053091, intron 2 of 4)	2828	NM_053091	84682	Mm.196668	NM_053091	ENSMUSG00000009876	Cox4i2	Cox4b|CoxIV-2	cytochrome c oxidase subunit IV isoform 2	protein-coding
mm_149629.1	chr19	17205532	17205542	+	1	NA	intron (NM_181348, intron 15 of 19)	RMER4B|LTR|ERVK	133968	NM_001136484	14537	Mm.244825	NM_010265	ENSMUSG00000038843	Gcnt1	5630400D21Rik|B130048E03|C2 GlcNAcT|C2GNT|IGnT	glucosaminyl (N-acetyl) transferase 1, core 2	protein-coding
mm_45303.1	chr5	65419134	65419162	-	1	NA	intron (NM_009466, intron 7 of 11)	intron (NM_009466, intron 7 of 11)	16694	NM_009466	22235	Mm.344831	NM_009466	ENSMUSG00000029201	Ugdh	Udpgdh	UDP-glucose dehydrogenase	protein-coding
mm_95869.1	chr11	58043105	58043109	+	1	NA	intron (NM_028451, intron 7 of 18)	intron (NM_028451, intron 7 of 18)	34043	NM_028451	73158	Mm.248843	NM_028451	ENSMUSG00000037331	Larp1	1810024J12Rik|3110040D16Rik|Larp|mKIAA0731	La ribonucleoprotein domain family, member 1	protein-coding
mm_137997.1	chr17	33677371	33677410	+	1	NA	exon (NM_001109913, exon 2 of 17)	exon (NM_001109913, exon 2 of 17)	8068	NM_001109913	76936	Mm.311439	NM_029804	ENSMUSG00000059208	Hnrnpm	2610023M21Rik|AA409009|Hnrpm|mKIAA4193	heterogeneous nuclear ribonucleoprotein M	protein-coding
mm_112877.1	chr13	20854055	20854063	+	1	NA	intron (NM_012054, intron 4 of 20)	Tigger5b|DNA|TcMar-Tigger	59946	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_167624.1	chr9	59707595	59707612	+	1	NA	promoter-TSS (NM_001033498)	promoter-TSS (NM_001033498)	-161	NM_001033498	546134	Mm.297580	NM_001033498	ENSMUSG00000074259	Gramd2	BC064463	GRAM domain containing 2	protein-coding
mm_136181.1	chr16	88885111	88885114	-	1	NA	promoter-TSS (NM_130873)	promoter-TSS (NM_130873)	-23	NM_130873	170654	Mm.196689	NM_130873	ENSMUSG00000043982	Krtap19-4	Krtap16-4	keratin associated protein 19-4	protein-coding
mm_32389.1	chr4	106588969	106588977	+	1	NA	3' UTR (NM_053272, exon 9 of 9)	3' UTR (NM_053272, exon 9 of 9)	27935	NM_053272	74754	Mm.133370	NM_053272	ENSMUSG00000034926	Dhcr24	2310076D10Rik|5830417J06Rik|mKIAA0018	24-dehydrocholesterol reductase	protein-coding
mm_164175.1	chr15	76198426	76198436	-	1	NA	promoter-TSS (NM_201393)	promoter-TSS (NM_201393)	-222	NM_201393	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
mm_44178.1	chr5	150992214	150992218	+	1	NA	3' UTR (NM_013823, exon 5 of 5)	3' UTR (NM_013823, exon 5 of 5)	39609	NM_013823	16591	Mm.6500	NM_013823	ENSMUSG00000058488	Kl	alpha-kl	klotho	protein-coding
mm_78449.1	chr9	32224325	32224330	+	1	NA	promoter-TSS (NM_177379)	promoter-TSS (NM_177379)	78	NM_177379	330914	Mm.46683	NM_177379	ENSMUSG00000041444	Arhgap32	3426406O18Rik|Gc-gap|Grit|Px-rics|Rics|mKIAA0712|p200Rhogap|p250Gap	Rho GTPase activating protein 32	protein-coding
mm_39850.1	chr5	30913505	30913515	+	1	NA	promoter-TSS (NM_133918)	promoter-TSS (NM_133918)	-276	NM_133918	100952	Mm.286375	NM_133918	ENSMUSG00000029163	Emilin1	5830419M17Rik|AW229038|BB105748|EMILIN-1|gp115	elastin microfibril interfacer 1	protein-coding
mm_29285.1	chr3	107696346	107696348	-	1	NA	5' UTR (NM_145542, exon 1 of 17)	5' UTR (NM_145542, exon 1 of 17)	201	NM_145542	229709	Mm.220328	NM_145542	ENSMUSG00000027893	Ahcyl1	1110034F20Rik|AA409031|AA414901|Ahcy-rs3|DCAL|Irbit	S-adenosylhomocysteine hydrolase-like 1	protein-coding
mm_144134.1	chr18	4980588	4980598	+	1	NA	Intergenic	Intergenic	-65996	NM_153153	225115	Mm.136791	NM_153153	ENSMUSG00000024236	Svil	AU024053|B430302E16Rik	supervillin	protein-coding
mm_170054.1	chr17	29492169	29492177	+	1	NA	intron (NM_008842, intron 4 of 5)	CpG-6203	1128	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_62424.1	chr7	101330354	101330368	+	1	NA	intron (NM_019990, intron 2 of 6)	intron (NM_019990, intron 2 of 6)	9042	NM_019990	56018	Mm.28896	NM_019990	ENSMUSG00000030688	Stard10	AV048538|CGI-52|NY-C0-28|PC-TP2|PCTP2|Pctpl|Sdccag28|SdccagG28|TISP-81	START domain containing 10	protein-coding
mm_136482.1	chr16	96064447	96064450	-	1	NA	intron (NM_001103179, intron 8 of 40)	Lx3A|LINE|L1	17980	NM_001103179	93871	Mm.240871	NM_145125	ENSMUSG00000022914	Brwd1	5330419I02Rik|D530019K20Rik|G1-403-16|Wdr9|repro5	bromodomain and WD repeat domain containing 1	protein-coding
mm_154096.1	chr19	56964862	56964864	-	1	NA	intron (NM_146102, intron 1 of 20)	intron (NM_146102, intron 1 of 20)	43712	NM_146102	226250	Mm.226284	NM_146102	ENSMUSG00000025083	Afap1l2	AU041783|C86904|mKIAA1914	actin filament associated protein 1-like 2	protein-coding
mm_95699.1	chr11	54400953	54400976	+	1	NA	intron (NM_029105, intron 9 of 13)	intron (NM_029105, intron 9 of 13)	30312	NM_029105	74847	Mm.486538	NM_029105	ENSMUSG00000020332	Meikin	4930404A10Rik	meiotic kinetochore factor	protein-coding
mm_44632.1	chr5	27791341	27791420	-	1	NA	5' UTR (NM_018878, exon 1 of 21)	5' UTR (NM_018878, exon 1 of 21)	170	NM_018878	55982	Mm.277190	NM_018878	ENSMUSG00000002221	Paxip1	D5Ertd149e|PTIP	PAX interacting (with transcription-activation domain) protein 1	protein-coding
mm_9331.1	chr1	171919316	171919326	-	1	NA	intron (NM_001347187, intron 1 of 7)	intron (NM_001347187, intron 1 of 7)	1784	NM_030710	30925	Mm.486404	NM_030710	ENSMUSG00000015314	Slamf6	KAL1|KAL1b|Ly108|NTB-A|NTBA|SF2000	SLAM family member 6	protein-coding
mm_123413.1	chr14	64104230	64104238	-	1	NA	promoter-TSS (NM_028525)	promoter-TSS (NM_028525)	1	NR_046192	78176	Mm.108055	NR_046192	ENSMUSG00000091686	4930471C04Rik	-	RIKEN cDNA 4930471C04 gene	ncRNA
mm_60207.1	chr7	43437587	43437596	+	1	NA	exon (NM_024253, exon 2 of 4)	exon (NM_024253, exon 2 of 4)	453	NM_024253	72310	Mm.34613	NM_024253	ENSMUSG00000004612	Nkg7	2500004F03Rik	natural killer cell group 7 sequence	protein-coding
mm_47265.1	chr5	121836853	121836880	-	1	NA	promoter-TSS (NM_001306128)	promoter-TSS (NM_001306128)	-7	NM_008507	16923	Mm.65493	NM_008507	ENSMUSG00000042594	Sh2b3	AI429800|Lnk	SH2B adaptor protein 3	protein-coding
mm_11172.1	chr2	28641228	28641262	+	1	NA	promoter-TSS (NM_001289576)	promoter-TSS (NM_001289576)	12	NM_022887	64930	Mm.224354	NM_022887	ENSMUSG00000026812	Tsc1	-	tuberous sclerosis 1	protein-coding
mm_117348.1	chr13	69611451	69611477	-	1	NA	promoter-TSS (NM_175283)	promoter-TSS (NM_175283)	-1	NM_175283	78925	Mm.451912	NM_175283	ENSMUSG00000021594	Srd5a1	0610031P22Rik|4930435F02Rik|S5AR 1|Srd5a-1	steroid 5 alpha-reductase 1	protein-coding
mm_93126.1	chr10	91181659	91181715	-	1	NA	Intergenic	CpG	-10068	NM_001080130	21917	Mm.159684	NM_011605	ENSMUSG00000019961	Tmpo	5630400D24Rik|AI195756|AI606875|AW214352|AW547477|LAP2|TP	thymopoietin	protein-coding
mm_117487.1	chr13	78183123	78183134	-	1	NA	Intergenic	Intergenic	13321	NM_001347538	13865	Mm.439653	NM_010151	ENSMUSG00000069171	Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR-3|EAR3|Erbal3|SVP44|Tcfcoup1	nuclear receptor subfamily 2, group F, member 1	protein-coding
mm_21061.1	chr2	152765360	152765374	-	1	NA	TTS (NM_053091)	TTS (NM_053091)	11194	NM_053091	84682	Mm.196668	NM_053091	ENSMUSG00000009876	Cox4i2	Cox4b|CoxIV-2	cytochrome c oxidase subunit IV isoform 2	protein-coding
mm_144022.1	chr17	90036280	90036290	-	1	NA	3' UTR (NM_001347419, exon 3 of 3)	3' UTR (NM_001347419, exon 3 of 3)	52083	NM_001346962	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_150990.1	chr19	46573423	46573436	+	1	NA	promoter-TSS (NM_053196)	promoter-TSS (NM_053196)	64	NM_053196	94279	Mm.296837	NM_053196	ENSMUSG00000025036	Sfxn2	C79732|F630107H02Rik	sideroflexin 2	protein-coding
mm_42334.1	chr5	114902856	114902874	+	1	NA	intron (NM_011854, intron 3 of 5)	B4|SINE|B4	5931	NM_011854	23962	Mm.228363	NM_011854	ENSMUSG00000029561	Oasl2	M1204|Mmu-OASL|Oasl	2'-5' oligoadenylate synthetase-like 2	protein-coding
mm_77911.1	chr9	7350007	7350027	+	1	NA	exon (NM_008605, exon 4 of 10)	exon (NM_008605, exon 4 of 10)	2643	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_116300.1	chr13	36726479	36726491	-	1	NA	3' UTR (NM_153529, exon 3 of 3)	3' UTR (NM_153529, exon 3 of 3)	7992	NM_153529	68404	Mm.232930	NM_153529	ENSMUSG00000039114	Nrn1	0710008J23Rik|Cpg15|Nrn	neuritin 1	protein-coding
mm_35938.1	chr4	53033750	53033767	-	1	NA	3' UTR (NM_013454, exon 50 of 50)	3' UTR (NM_013454, exon 50 of 50)	21878	NM_025623	66536	Mm.38244	NM_025623	ENSMUSG00000015247	Nipsnap3b	2700063N13Rik|Nipsnap3a	nipsnap homolog 3B (C. elegans)	protein-coding
mm_130829.1	chr15	101846392	101846410	-	1	NA	exon (NM_008473, exon 8 of 9)	exon (NM_008473, exon 8 of 9)	4385	NM_008473	16678	Mm.183137	NM_008473	ENSMUSG00000046834	Krt1	Krt-2.1|Krt2-1|Krt86	keratin 1	protein-coding
mm_7831.1	chr1	132116967	132116984	-	1	NA	exon (NM_008795, exon 11 of 16)	exon (NM_008795, exon 11 of 16)	22710	NM_008795	18557	Mm.28130	NM_008795	ENSMUSG00000026437	Cdk18	AA682070|Ctk18|Pctk3	cyclin-dependent kinase 18	protein-coding
mm_60060.1	chr7	31162098	31162105	+	1	NA	promoter-TSS (NR_046062)	promoter-TSS (NR_046062)	-257	NR_046062	100038516	Mm.387223	NR_046062	ENSMUSG00000100985	Gm10640	EG668322|ENSMUSG00000074193	predicted gene 10640	ncRNA
mm_68647.1	chr7	118491467	118491516	-	1	NA	5' UTR (NM_001033380, exon 1 of 1)	5' UTR (NM_001033380, exon 1 of 1)	484	NM_001033380	319622	Mm.323386	NM_001033380	ENSMUSG00000095115	Itpripl2	C130081G24|E030018N11Rik	inositol 1,4,5-triphosphate receptor interacting protein-like 2	protein-coding
mm_78902.1	chr9	44733969	44733983	+	1	NA	intron (NM_153537, intron 1 of 21)	CpG	1222	NM_153537	102693	Mm.28639	NM_153537	ENSMUSG00000048537	Phldb1	AU041016|D330037A14Rik|Ll5a	pleckstrin homology like domain, family B, member 1	protein-coding
mm_68921.1	chr7	126463298	126463307	-	1	NA	promoter-TSS (NM_007504)	promoter-TSS (NM_007504)	-229	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_25410.1	chr3	107291286	107291301	+	1	NA	promoter-TSS (NM_146136)	promoter-TSS (NM_146136)	1	NM_146136	229699	Mm.38384	NM_146136	ENSMUSG00000027896	Slc16a4	AW146050|MCT 5	solute carrier family 16 (monocarboxylic acid transporters), member 4	protein-coding
mm_59732.1	chr7	28809231	28809251	+	1	NA	Intergenic	Intergenic	-1649	NM_177301	15388	Mm.9043	NM_177301	ENSMUSG00000015165	Hnrnpl	C79783|D830027H13Rik|Hnrpl	heterogeneous nuclear ribonucleoprotein L	protein-coding
mm_2789.1	chr1	130849573	130849583	+	1	NA	exon (NM_011082, exon 9 of 11)	exon (NM_011082, exon 9 of 11)	-16199	NM_026976	69169	Mm.46042	NM_026976	ENSMUSG00000042474	Fcmr	1810037B05Rik|Faim3|FcmuR|Toso	Fc fragment of IgM receptor	protein-coding
mm_102997.1	chr11	69687030	69687045	-	1	NA	exon (NM_001159503, exon 7 of 13)	exon (NM_001159503, exon 7 of 13)	-1483	NM_023517	69583	Mm.8983	NM_023517	ENSMUSG00000089669	Tnfsf13	2310026N09Rik|April|Tall2|Tnlg7b|Trdl1	tumor necrosis factor (ligand) superfamily, member 13	protein-coding
mm_151910.1	chr19	5799607	5799615	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	3061	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_126190.1	chr15	78670631	78670650	+	1	NA	3' UTR (NM_183141, exon 2 of 2)	3' UTR (NM_183141, exon 2 of 2)	47473	NM_183141	207393	Mm.323188	NM_183141	ENSMUSG00000043460	Elfn2	6330514E13|AW048948|BC094219|Lrrc62|Ppp1r29	leucine rich repeat and fibronectin type III, extracellular 2	protein-coding
mm_52377.1	chr6	113086825	113086828	+	1	NA	intron (NM_028385, intron 1 of 21)	intron (NM_028385, intron 1 of 21)	9187	NM_028385	72895	Mm.367159	NM_028385	ENSMUSG00000034269	Setd5	2900045N06Rik|C330007C20|C85544|mKIAA1757	SET domain containing 5	protein-coding
mm_97184.1	chr11	75566860	75566875	+	1	NA	intron (NM_173388, intron 9 of 13)	intron (NM_173388, intron 9 of 13)	15438	NR_039553	100628624		NR_039553	ENSMUSG00000093100	Mir3971	mmu-mir-3971|mu-mir-3971	microRNA 3971	ncRNA
mm_39401.1	chr5	14032734	14032734	+	1	NA	intron (NM_011348, intron 1 of 16)	intron (NM_011348, intron 1 of 16)	7458	NM_011348	20349	Mm.134093	NM_011348	ENSMUSG00000063531	Sema3e	6430702L12|AA408817|Semah|mKIAA0331	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	protein-coding
mm_56204.1	chr6	88902749	88902768	-	1	NA	intron (NM_011906, intron 1 of 11)	CpG	507	NM_011906	24100	Mm.284480	NM_011906	ENSMUSG00000002871	Tpra1	40kDa|Gpr175|Tpra40	transmembrane protein, adipocyte asscociated 1	protein-coding
mm_95738.1	chr11	54691461	54691487	+	1	NA	exon (NM_001252494, exon 27 of 29)	exon (NM_001252494, exon 27 of 29)	95328	NM_001252497	192786	Mm.254404	NM_175258	ENSMUSG00000037533	Rapgef6	A530068K01|AI844632|BB085664|C030018K18Rik|PDZ-GEF2|Pdzgef2|RA-GEF-2|Ragef2|mKIAA4052	Rap guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_97102.1	chr11	73389822	73389831	+	1	NA	Intergenic	Intergenic	9669	NM_146921	258923	Mm.246523	NM_146921	ENSMUSG00000069823	Olfr1	I54|MOR135-13	olfactory receptor 1	protein-coding
mm_40812.1	chr5	71699978	71699997	+	1	NA	promoter-TSS (NM_008069)	promoter-TSS (NM_008069)	-29	NM_008069	14400	Mm.38567	NM_008069	ENSMUSG00000029212	Gabrb1	AW061132|B230208N19Rik|Gabrb-1	gamma-aminobutyric acid (GABA) A receptor, subunit beta 1	protein-coding
mm_109379.1	chr12	109706798	109706812	+	1	NA	Intergenic	Intergenic	-2255	NR_029880	723858		NR_029880	ENSMUSG00000065498	Mir379	Mirn379|mir-379|mmu-mir-379	microRNA 379	ncRNA
mm_145743.1	chr18	64340021	64340042	+	1	NA	promoter-TSS (NM_194268)	promoter-TSS (NM_194268)	-333	NM_194268	225631	Mm.234723	NM_194268	ENSMUSG00000045991	Onecut2	C730009D12|OC-2|Oc2	one cut domain, family member 2	protein-coding
mm_122275.1	chr14	34379183	34379230	-	1	NA	intron (NM_153127, intron 1 of 6)	intron (NM_153127, intron 1 of 6)	3702	NM_153127	105450	Mm.272673	NM_153127	ENSMUSG00000041445	Mmrn2	AA986839|ENDOGLYX1|Emilin3|EndoGlyx-1	multimerin 2	protein-coding
mm_97096.1	chr11	73199446	73199500	+	1	NA	promoter-TSS (NM_031251)	promoter-TSS (NM_031251)	-9	NM_029031	74637	Mm.200905	NM_029031	ENSMUSG00000005951	Shpk	4930431K22Rik|AI194947|AW260459|Carkl	sedoheptulokinase	protein-coding
mm_160252.1	chr7	107209683	107209683	+	1	NA	exon (NM_029660, exon 1 of 1)	exon (NM_029660, exon 1 of 1)	238	NM_029660	76572	Mm.128134	NM_029660	ENSMUSG00000073894	Rbmxl2	1700012H05Rik|Hnrnpg-t	RNA binding motif protein, X-linked-like 2	protein-coding
mm_134367.1	chr16	17121709	17121711	-	1	NA	intron (NM_183287, intron 2 of 7)	intron (NM_183287, intron 2 of 7)	2432	NR_029659	723816		NR_029659	ENSMUSG00000065572	Mir130b	Mirn130b|mir-130b	microRNA 130b	ncRNA
mm_37099.1	chr4	116618915	116618945	-	1	NA	exon (NM_016777, exon 4 of 16)	exon (NM_016777, exon 4 of 16)	8567	NM_001081475	50927	Mm.257181	NM_016777	ENSMUSG00000028693	Nasp	5033430J04Rik|AI131596|AI317140|D4Ertd767e|Epcs32|Nasp-T	nuclear autoantigenic sperm protein (histone-binding)	protein-coding
mm_53735.1	chr6	145121856	145121861	+	1	NA	5' UTR (NM_008511, exon 1 of 19)	5' UTR (NM_008511, exon 1 of 19)	119	NM_008511	16970	Mm.843	NM_008511	ENSMUSG00000030263	Lrmp	D6Int3|D6Int4|D6Int5|D6Int7|D6Int8|Jaw1	lymphoid-restricted membrane protein	protein-coding
mm_164400.1	chr16	34262936	34262942	-	1	NA	intron (NM_001164268, intron 10 of 33)	intron (NM_001164268, intron 10 of 33)	251088	NM_001164268	545156	Mm.82274	NM_177357	ENSMUSG00000061751	Kalrn	2210407G14Rik|AV235988|DUET|E530005C20Rik|Gm539|Hapip|TRAD	kalirin, RhoGEF kinase	protein-coding
mm_55209.1	chr6	52217515	52217550	-	1	NA	5' UTR (NM_010455, exon 1 of 2)	5' UTR (NM_010455, exon 1 of 2)	1041	NM_010455	15404	Mm.294826	NM_010455	ENSMUSG00000038236	Hoxa7	AV118143|Hox-1.1|M6	homeobox A7	protein-coding
mm_139244.1	chr17	47733814	47733830	+	1	NA	exon (NM_025973, exon 8 of 9)	exon (NM_025973, exon 8 of 9)	-3215	NM_001161722	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_54404.1	chr6	31563841	31563854	-	1	NA	promoter-TSS (NM_013723)	promoter-TSS (NM_013723)	90	NM_013723	27205	Mm.89918	NM_013723	ENSMUSG00000025608	Podxl	AW121214|Ly102|PC|PCLP-1|Pclp1	podocalyxin-like	protein-coding
mm_43785.1	chr5	142464019	142464072	+	1	NA	5' UTR (NM_172725, exon 1 of 17)	5' UTR (NM_172725, exon 1 of 17)	114	NM_172725	231855	Mm.78250	NM_172725	ENSMUSG00000039623	Ap5z1	C330006K01Rik	adaptor-related protein complex 5, zeta 1 subunit	protein-coding
mm_3723.1	chr1	154204907	154204919	+	1	NA	exon (NM_001204908, exon 2 of 2)	exon (NM_001204908, exon 2 of 2)	3726	NM_001204908	100503355	Mm.484410	NM_001204908	ENSMUSG00000066797	Zfp648	ENSMUSG00000066797|Gm10178|Gm203	zinc finger protein 648	protein-coding
mm_29071.1	chr3	103809279	103809409	-	1	NA	promoter-TSS (NM_001163552)	promoter-TSS (NM_001163552)	43	NM_133865	140917	Mm.374850	NM_133865	ENSMUSG00000027845	Dclre1b	AI452214|Apollo|SNMIB|mSNM1B	DNA cross-link repair 1B	protein-coding
mm_42117.1	chr5	110840232	110840283	+	1	NA	promoter-TSS (NM_153571)	promoter-TSS (NM_153571)	240	NM_016681	50883	Mm.279308	NM_016681	ENSMUSG00000029521	Chek2	CHK2|Cds1|HUCDS1|Rad53	checkpoint kinase 2	protein-coding
mm_92798.1	chr10	81357377	81357393	-	1	NA	promoter-TSS (NM_028657)	promoter-TSS (NM_028657)	-185	NM_028657	73822	Mm.182281	NM_028657	ENSMUSG00000034854	Mfsd12	C19orf28|F630110N24Rik|Wdt1	major facilitator superfamily domain containing 12	protein-coding
mm_30134.1	chr3	142169197	142169261	-	1	NA	promoter-TSS (NM_001277217)	promoter-TSS (NM_001277217)	-1	NM_001277216	12167	Mm.39089	NM_007560	ENSMUSG00000052430	Bmpr1b	AI385617|ALK-6|AV355320|Acvrlk6|Alk6|BMPR-1B|BMPR-IB|CFK-43a|SKR6	bone morphogenetic protein receptor, type 1B	protein-coding
mm_15376.1	chr2	156475712	156475738	+	1	NA	5' UTR (NM_001006664, exon 1 of 22)	5' UTR (NM_001006664, exon 1 of 22)	191	NM_001006664	13821	Mm.20852	NM_013510	ENSMUSG00000027624	Epb41l1	4.1N|Epb4.1l1|NBL1|mKIAA0338	erythrocyte membrane protein band 4.1 like 1	protein-coding
mm_8668.1	chr1	156667478	156667490	-	1	NA	intron (NM_023141, intron 3 of 5)	intron (NM_023141, intron 3 of 5)	6855	NM_023141	30935	Mm.206737	NM_023141	ENSMUSG00000060519	Tor3a	Adir	torsin family 3, member A	protein-coding
mm_160033.1	chr6	132595792	132595792	+	1	NA	promoter-TSS (NM_031499)	promoter-TSS (NM_031499)	-154	NM_031499	83380	Mm.333439	NM_031499	ENSMUSG00000058295	Prp2	MP14	proline rich protein 2	protein-coding
mm_112503.1	chr13	8292967	8292979	+	1	NA	intron (NR_110345, intron 1 of 10)	B4A|SINE|B4	90107	NM_052977	94191	Mm.425794	NM_052977	ENSMUSG00000052551	Adarb2	Adar3|RED2	adenosine deaminase, RNA-specific, B2	protein-coding
mm_87887.1	chr10	61733140	61733157	+	1	NA	intron (NM_001284300, intron 6 of 9)	intron (NM_001284300, intron 6 of 9)	12499	NM_153779	71361	Mm.286309	NM_153779	ENSMUSG00000020085	Aifm2	5430437E11Rik|Amid|D730001I10Rik|PRG3	apoptosis-inducing factor, mitochondrion-associated 2	protein-coding
mm_171035.1	chr2	91457480	91457480	+	1	NA	promoter-TSS (NM_001145857)	promoter-TSS (NM_001145857)	-51	NM_172668	228357	Mm.275149	NM_172668	ENSMUSG00000027253	Lrp4	6430526J12Rik|D230026E03|Megf7|mdig	low density lipoprotein receptor-related protein 4	protein-coding
mm_102102.1	chr11	52403369	52403390	-	1	NA	exon (NM_153117, exon 2 of 3)	exon (NM_153117, exon 2 of 3)	6951	NM_153117	213673	Mm.291979	NM_153117	ENSMUSG00000036275	9530068E07Rik	C85061|Kct2	RIKEN cDNA 9530068E07 gene	protein-coding
mm_40348.1	chr5	45669908	45669945	+	1	NA	promoter-TSS (NM_019438)	promoter-TSS (NM_019438)	1	NM_019438	54392	Mm.32012	NM_019438	ENSMUSG00000015880	Ncapg	5730507H05Rik|Hcapg|MFT.M05.13	non-SMC condensin I complex, subunit G	protein-coding
mm_107907.1	chr12	70974657	70974686	+	1	NA	promoter-TSS (NM_011184)	promoter-TSS (NM_011184)	48	NM_011184	19167	Mm.296338	NM_011184	ENSMUSG00000060073	Psma3	Lmpc8	proteasome (prosome, macropain) subunit, alpha type 3	protein-coding
mm_40572.1	chr5	63812448	63812538	+	1	NA	promoter-TSS (NM_029554)	promoter-TSS (NM_029554)	-2	NM_029554	76261	Mm.38143	NM_029554	ENSMUSG00000060512	0610040J01Rik	AI662686	RIKEN cDNA 0610040J01 gene	protein-coding
mm_118021.1	chr13	100833219	100833248	-	1	NA	5' UTR (NM_022885, exon 1 of 16)	5' UTR (NM_022885, exon 1 of 16)	194	NM_022885	69048	Mm.402215	NM_022885	ENSMUSG00000021629	Slc30a5	1810010K08Rik|AF233321|ZNT5|ZTL1|ZnT-5|Zntl1	solute carrier family 30 (zinc transporter), member 5	protein-coding
mm_63858.1	chr7	135672049	135672052	+	1	NA	intron (NM_001316681, intron 12 of 17)	intron (NM_001316681, intron 12 of 17)	-19736	NR_015548	67765	Mm.445272	NR_015548	ENSMUSG00000097471	5830432E09Rik	-	RIKEN cDNA 5830432E09 gene	ncRNA
mm_110746.1	chr12	69893163	69893176	-	1	NA	promoter-TSS (NM_201519)	promoter-TSS (NM_201519)	-6	NM_201519	399510	Mm.291936	NM_201519	ENSMUSG00000034761	Map4k5	4432415E19Rik|GCKR|KHS|MAPKKKK5	mitogen-activated protein kinase kinase kinase kinase 5	protein-coding
mm_168562.1	chr11	6895073	6895075	-	1	NA	Intergenic	Intergenic	-168415	NM_009622	432530	Mm.259733	NM_009622	ENSMUSG00000020431	Adcy1	AC1|D11Bwg1392e|I-AC|brl|mKIAA4070	adenylate cyclase 1	protein-coding
mm_34495.1	chr4	148593886	148593911	+	1	NA	exon (NM_009272, exon 5 of 7)	exon (NM_009272, exon 5 of 7)	2385	NM_009272	20810	Mm.10	NM_009272	ENSMUSG00000006442	Srm	AA407669|SpdST|SpdSy	spermidine synthase	protein-coding
mm_145065.1	chr18	40541398	40541408	+	1	NA	Intergenic	Intergenic	283042	NM_026135	383348	Mm.76366	NM_026135	ENSMUSG00000051401	Kctd16	4930434H12Rik|Gm1267	potassium channel tetramerisation domain containing 16	protein-coding
mm_109654.1	chr12	112866703	112866717	+	1	NA	Intergenic	Intergenic	-5794	NM_019925	56696	Mm.20455	NM_019925	ENSMUSG00000021298	Gpr132	G2a	G protein-coupled receptor 132	protein-coding
mm_47097.1	chr5	118067848	118067856	-	1	NA	3' UTR (NM_172721, exon 11 of 11)	3' UTR (NM_172721, exon 11 of 11)	40028	NM_021344	57816	Mm.273285	NM_021344	ENSMUSG00000029359	Tesc	1010001A17Rik|2410011K10Rik|TE-1	tescalcin	protein-coding
mm_94277.1	chr11	3925020	3925062	+	1	NA	exon (NM_001130458, exon 5 of 10)	exon (NM_001130458, exon 5 of 10)	6920	NM_001130459	21452	Mm.20948	NM_015749	ENSMUSG00000020432	Tcn2	AW208754|Tcn-2	transcobalamin 2	protein-coding
mm_67302.1	chr7	79300961	79300982	-	1	NA	intron (NM_018811, intron 3 of 10)	intron (NM_018811, intron 3 of 10)	27705	NM_018811	54608	Mm.365490	NM_018811	ENSMUSG00000039202	Abhd2	2210009N18Rik|LABH2|Labh-2	abhydrolase domain containing 2	protein-coding
mm_88240.1	chr10	71527294	71527325	+	1	NA	Intergenic	Intergenic	179546	NM_027184	69718	Mm.245867	NM_027184	ENSMUSG00000060733	Ipmk	2410017C19Rik|AA408208|Impk	inositol polyphosphate multikinase	protein-coding
mm_77645.1	chr8	124559309	124559317	-	1	NA	exon (NM_007428, exon 3 of 5)	exon (NM_007428, exon 3 of 5)	10394	NM_007428	11606	Mm.301626	NM_007428	ENSMUSG00000031980	Agt	AI265500|AngI|AngII|Aogen|Serpina8	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	protein-coding
mm_126516.1	chr15	81850309	81850325	+	1	NA	3' UTR (NM_020507, exon 2 of 2)	3' UTR (NM_020507, exon 2 of 2)	8009	NM_020507	57259	Mm.323595	NM_020507	ENSMUSG00000048546	Tob2	2900090N22Rik|4930545K18Rik|AV071822|mKIAA1663	transducer of ERBB2, 2	protein-coding
mm_82421.1	chr9	14903852	14903854	-	1	NA	promoter-TSS (NM_176807)	promoter-TSS (NM_176807)	98	NM_176807	64931	Mm.86738	NM_022888	ENSMUSG00000031933	Izumo1r	0910001L11Rik|C86255|Folbp3|Folr4|Juno	IZUMO1 receptor, JUNO	protein-coding
mm_42119.1	chr5	110879789	110879842	+	1	NA	promoter-TSS (NM_001267622)	promoter-TSS (NM_001267622)	12	NM_001267622	209683	Mm.295660	NM_024477	ENSMUSG00000033209	Ttc28	2310015L07Rik|6030435N04|AI428795|AI851761|BC002262|TPRBK	tetratricopeptide repeat domain 28	protein-coding
mm_97016.1	chr11	71019869	71019888	+	1	NA	promoter-TSS (NM_001291148)	promoter-TSS (NM_001291148)	-37	NM_001291146	116891	Mm.28131	NM_033562	ENSMUSG00000018442	Derl2	CGI-101|Derlin-2|F-lana|Flana	Der1-like domain family, member 2	protein-coding
mm_69379.1	chr7	131320105	131320115	-	1	NA	exon (NM_008411, exon 2 of 9)	exon (NM_008411, exon 2 of 9)	2182	NM_008411	16433	Mm.142717	NM_008411	ENSMUSG00000040205	Cuzd1	Erg-1|Itmap1|Uo-44|Usg|Utczp	CUB and zona pellucida-like domains 1	protein-coding
mm_7740.1	chr1	130911545	130911548	-	1	NA	promoter-TSS (NM_021380)	promoter-TSS (NM_021380)	-250	NM_021380	58181	Mm.103794	NM_021380	ENSMUSG00000026416	Il20	Zcyto10	interleukin 20	protein-coding
mm_23587.1	chr3	63984215	63984238	+	1	NA	intron (NM_001033300, intron 3 of 15)	intron (NM_001033300, intron 3 of 15)	8083	NM_001033300	229363	Mm.331051	NM_001033300	ENSMUSG00000027823	Gmps	670032|AA591640|AI047208|Gm9479	guanine monophosphate synthetase	protein-coding
mm_137102.1	chr17	21707683	21707741	+	1	NA	promoter-TSS (NM_001008501)	promoter-TSS (NM_001008501)	-29	NM_001008501	240034	Mm.34723	NM_001008501	ENSMUSG00000067928	Zfp760	9430018I06|BC029103	zinc finger protein 760	protein-coding
mm_61666.1	chr7	80779710	80779727	+	1	NA	intron (NM_016721, intron 2 of 37)	intron (NM_016721, intron 2 of 37)	23613	NM_016721	29875	Mm.207619	NM_016721	ENSMUSG00000030536	Iqgap1	AA682088|D7Ertd237e|D7Ertd257e|mKIAA0051	IQ motif containing GTPase activating protein 1	protein-coding
mm_96209.1	chr11	62281441	62281456	+	1	NA	promoter-TSS (NM_028360)	promoter-TSS (NM_028360)	-25	NM_028360	72795	Mm.489722	NM_028360	ENSMUSG00000042298	Ttc19	2010204O13Rik|2810460C24Rik|AI505442	tetratricopeptide repeat domain 19	protein-coding
mm_11902.1	chr2	50297034	50297036	+	1	NA	promoter-TSS (NM_133839)	promoter-TSS (NM_133839)	225	NR_040362	100502624	Mm.382825	NR_040361	ENSMUSG00000085862	Gm13483	OTTMUSG00000012382	predicted gene 13483	ncRNA
mm_151447.1	chr19	57611021	57611079	+	1	NA	promoter-TSS (NM_181415)	promoter-TSS (NM_181415)	16	NM_181415	226255	Mm.245340	NM_181415	ENSMUSG00000054843	Atrnl1	AI504415|AW555641|Alp|Atrnl|Atrnlp	attractin like 1	protein-coding
mm_51559.1	chr6	83353219	83353249	+	1	NA	intron (NM_175277, intron 3 of 3)	intron (NM_175277, intron 3 of 3)	3750	NM_175277	78653	Mm.391470	NM_175277	ENSMUSG00000045160	Bola3	1810056O20Rik	bolA-like 3 (E. coli)	protein-coding
mm_32302.1	chr4	103123588	103123590	+	1	NA	intron (NM_001039081, intron 1 of 12)	intron (NM_001039081, intron 1 of 12)	4199	NM_001039081	71148	Mm.288721	NM_027696	ENSMUSG00000028522	Mier1	4933425I22Rik|5830411K19Rik|er1	MEIR1 treanscription regulator	protein-coding
mm_110029.1	chr12	16800961	16800971	-	1	NA	promoter-TSS (NM_015764)	promoter-TSS (NM_015764)	-80	NM_015764	268527	Mm.428062	NM_015764	ENSMUSG00000036523	Greb1	5730583K22Rik|9130004E13|AF180470|AU023194|mKIAA0575	gene regulated by estrogen in breast cancer protein	protein-coding
mm_128685.1	chr15	60824943	60824966	-	1	NA	5' UTR (NM_001162926, exon 1 of 2)	5' UTR (NM_001162926, exon 1 of 2)	126	NM_001162926	399603	Mm.411968	NM_207269	ENSMUSG00000072568	Fam84b	BF642811|D330050I23Rik	family with sequence similarity 84, member B	protein-coding
mm_128155.1	chr15	32244633	32244670	-	1	NA	promoter-TSS (NM_009154)	promoter-TSS (NM_009154)	11	NR_038186	100616095	Mm.391938	NR_038186	ENSMUSG00000096956	Snhg18	0610007N19Rik|Snord123	small nucleolar RNA host gene 18	ncRNA
mm_111593.1	chr12	101975980	101975984	-	1	NA	promoter-TSS (NM_016856)	promoter-TSS (NM_016856)	8	NM_016856	51786	Mm.716	NM_016856	ENSMUSG00000041781	Cpsf2	100kDa|2610024B04Rik|AI662483|Cpsf|MCPSF|mKIAA1367	cleavage and polyadenylation specific factor 2	protein-coding
mm_165967.1	chr4	95934127	95934133	-	1	NA	Intergenic	Intergenic	32905	NR_045777	319247	Mm.473527	NM_175680	ENSMUSG00000044125	9530080O11Rik	-	RIKEN cDNA 9530080O11 gene	ncRNA
mm_89939.1	chr10	111273122	111273139	+	1	NA	exon (NM_001003717, exon 11 of 23)	exon (NM_001003717, exon 11 of 23)	-25549	NM_027914	71769	Mm.45256	NM_027914	ENSMUSG00000035759	Bbs10	1300007O09Rik|AI452285	Bardet-Biedl syndrome 10 (human)	protein-coding
mm_25411.1	chr3	107333790	107333802	+	1	NA	promoter-TSS (NM_001045807)	promoter-TSS (NM_001045807)	-507	NM_001045807	229700	Mm.27966	NM_001045807	ENSMUSG00000048109	Rbm15	C230088J01Rik|mKIAA1438	RNA binding motif protein 15	protein-coding
mm_137188.1	chr17	23821027	23821047	+	1	NA	exon (NM_175229, exon 10 of 14)	exon (NM_175229, exon 10 of 14)	8072	NM_026305	67673	Mm.153758	NM_026305	ENSMUSG00000055839	Elob	0610040H15Rik|Tceb2	elongin B	protein-coding
mm_133095.1	chr16	64851972	64851982	+	1	NA	promoter-TSS (NM_178647)	promoter-TSS (NM_178647)	-108	NM_178647	106143	Mm.10160	NM_178647	ENSMUSG00000054604	Cggbp1	AA960172|AL023996|AW045841	CGG triplet repeat binding protein 1	protein-coding
mm_2906.1	chr1	131974294	131974341	+	1	NA	intron (NM_145977, intron 1 of 4)	intron (NM_145977, intron 1 of 4)	3708	NM_145977	212980	Mm.200307	NM_145977	ENSMUSG00000026435	Slc45a3	2210413P12Rik|AU023994|AU043764|IPCA-6|PRST|Pcanap6	solute carrier family 45, member 3	protein-coding
mm_148831.1	chr19	6342535	6342542	+	1	NA	intron (NM_009006, intron 5 of 31)	intron (NM_009006, intron 5 of 31)	1378	NR_117093	26412	Mm.25860	NM_009006	ENSMUSG00000024948	Map4k2	AI385662|BL44|GCK|Rab8ip	mitogen-activated protein kinase kinase kinase kinase 2	protein-coding
mm_138341.1	chr17	34911202	34911227	+	1	NA	intron (NM_147151, intron 22 of 26)	intron (NM_147151, intron 22 of 26)	-3252	NM_023557	70129	Mm.183126	NM_023557	ENSMUSG00000007034	Slc44a4	2210409B01Rik|NG22	solute carrier family 44, member 4	protein-coding
mm_68541.1	chr7	113816982	113816992	-	1	NA	intron (NM_145584, intron 2 of 15)	MER5A|DNA|hAT-Charlie	50989	NM_145584	233744	Mm.334160	NM_145584	ENSMUSG00000038156	Spon1	AI666765|AW455831|BC020531|D330035F22Rik|FSP	spondin 1, (f-spondin) extracellular matrix protein	protein-coding
mm_34680.1	chr4	151376430	151376482	+	1	NA	intron (NM_001081557, intron 5 of 23)	intron (NM_001081557, intron 5 of 23)	286886	NM_001308446	105704528	Mm.415128	NM_001308446	ENSMUSG00000078491	Gm13090	OTTMUSG00000010356	predicted gene 13090	protein-coding
mm_126268.1	chr15	79109188	79109209	+	1	NA	5' UTR (NM_177461, exon 1 of 16)	5' UTR (NM_177461, exon 1 of 16)	215	NM_177461	27008	Mm.196480	NM_177461	ENSMUSG00000033039	Micall1	AI448246|D15Mit260|D15N2e|EST573322|EST820961|MIRab13|mKIAA1668	microtubule associated monooxygenase, calponin and LIM domain containing -like 1	protein-coding
mm_141985.1	chr17	35165129	35165137	-	1	NA	promoter-TSS (NM_020027)	promoter-TSS (NM_020027)	-256	NM_020027	53761	Mm.272462	NM_020027	ENSMUSG00000024393	Prrc2a	3110039B05Rik|Bat-2|Bat2|D17H6S51E|G2|Wbp12|mKIAA4178	proline-rich coiled-coil 2A	protein-coding
mm_67626.1	chr7	84151869	84151938	-	1	NA	promoter-TSS (NM_133722)	promoter-TSS (NM_133722)	-10	NM_133722	70178	Mm.23914	NM_133722	ENSMUSG00000038459	Abhd17c	2210412D01Rik|AL023007|Fam108c|Fam108c1	abhydrolase domain containing 17C	protein-coding
mm_109696.1	chr12	113152638	113152651	+	1	NA	intron (NM_007763, intron 1 of 4)	intron (NM_007763, intron 1 of 4)	632	NM_007763	12925	Mm.272368	NM_007763	ENSMUSG00000006360	Crip1	CRHP|CRP1|Crip	cysteine-rich protein 1 (intestinal)	protein-coding
mm_55264.1	chr6	53820477	53820506	-	1	NA	5' UTR (NM_025817, exon 1 of 1)	5' UTR (NM_025817, exon 1 of 1)	334	NM_025817	66873	Mm.422727	NM_025817	ENSMUSG00000043496	Tril	1200009O22Rik|AI316813|mKIAA0644	TLR4 interactor with leucine-rich repeats	protein-coding
mm_152539.1	chr19	11327988	11328013	-	1	NA	exon (NM_001276398, exon 3 of 7)	exon (NM_001276398, exon 3 of 7)	6695	NM_001276398	109225	Mm.491251	NM_027836	ENSMUSG00000024672	Ms4a7	9130422I10Rik|A430103C15Rik|CD20l4|CFFMA	membrane-spanning 4-domains, subfamily A, member 7	protein-coding
mm_144056.1	chr17	90607114	90607118	-	1	NA	intron (NM_001346957, intron 9 of 18)	intron (NM_001346957, intron 9 of 18)	-151236	NM_001346959	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_123776.1	chr14	70318854	70318869	-	1	NA	exon (NM_144808, exon 3 of 10)	exon (NM_144808, exon 3 of 10)	-29364	NM_001304992	19057	Mm.439683	NM_008915	ENSMUSG00000022092	Ppp3cc	Calnc|PP2BA gamma	protein phosphatase 3, catalytic subunit, gamma isoform	protein-coding
mm_85083.1	chr9	91365411	91365421	-	1	NA	5' UTR (NM_009573, exon 1 of 3)	5' UTR (NM_009573, exon 1 of 3)	383	NM_009573	22771	Mm.335350	NM_009573	ENSMUSG00000032368	Zic1	ZIC|ZNF201	zinc finger protein of the cerebellum 1	protein-coding
mm_67241.1	chr7	75308978	75308980	-	1	NA	promoter-TSS (NM_001109753)	promoter-TSS (NM_001109753)	277	NR_045814	68954	Mm.46960	NR_045812	ENSMUSG00000097247	1500012K07Rik	-	RIKEN cDNA 1500012K07 gene	ncRNA
mm_20601.1	chr2	131352858	131352889	-	1	NA	promoter-TSS (NM_178607)	promoter-TSS (NM_178607)	19	NM_178607	51902	Mm.477523	NM_178607	ENSMUSG00000048911	Rnf24	2810473M14Rik|4930505A13Rik|AI317164|C86507|D2Ertd504e	ring finger protein 24	protein-coding
mm_139258.1	chr17	47738146	47738189	+	1	NA	5' UTR (NM_001161723, exon 1 of 9)	5' UTR (NM_001161723, exon 1 of 9)	236	NM_001161723	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_101535.1	chr11	33513627	33513666	-	1	NA	promoter-TSS (NR_110973)	promoter-TSS (NR_110973)	100	NR_110973	66011	Mm.383775	NM_023146	ENSMUSG00000040594	Ranbp17	-	RAN binding protein 17	protein-coding
mm_161444.1	chr15	73624744	73624744	-	1	NA	promoter-TSS (NM_001033219)	promoter-TSS (NM_001033219)	0	NM_001033219	106068	Mm.212813	NM_001033219	ENSMUSG00000079020	Slc45a4	9330175B01Rik|AW552276	solute carrier family 45, member 4	protein-coding
mm_144236.1	chr18	10617859	10617873	+	1	NA	promoter-TSS (NM_009226)	promoter-TSS (NM_009226)	70	NM_009226	20641	Mm.603	NM_009226	ENSMUSG00000002477	Snrpd1	AA407109|AL023031|SMD1	small nuclear ribonucleoprotein D1	protein-coding
mm_107507.1	chr12	40038110	40038118	+	1	NA	promoter-TSS (NM_007487)	promoter-TSS (NM_007487)	-127	NM_001039515	11861	Mm.12723	NM_007487	ENSMUSG00000047446	Arl4a	AI467555|Arl4	ADP-ribosylation factor-like 4A	protein-coding
mm_70753.1	chr8	19682631	19682665	+	1	NA	Intergenic	Intergenic	-46928	NM_001270553	100861668	Mm.491087	NM_001270553	ENSMUSG00000095294	Gm21119	-	predicted gene, 21119	protein-coding
mm_11960.1	chr2	53123873	53123886	+	1	NA	intron (NM_172409, intron 23 of 26)	intron (NM_172409, intron 23 of 26)	67308	NM_018785	56194	Mm.257474	NM_018785	ENSMUSG00000061136	Prpf40a	2810012K09Rik|FBP-11|FBP11|Fnbp11|Fnbp3	pre-mRNA processing factor 40A	protein-coding
mm_169925.1	chr16	57391428	57391429	-	1	NA	intron (NM_001040397, intron 1 of 4)	LSU-rRNA_Hsa|rRNA|rRNA	38151	NM_001040397	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding
mm_129072.1	chr15	75678733	75678805	-	1	NA	promoter-TSS (NM_028404)	promoter-TSS (NM_028404)	21	NM_028404	72960	Mm.182401	NM_028404	ENSMUSG00000000934	Top1mt	2900052H09Rik	DNA topoisomerase 1, mitochondrial	protein-coding
mm_102107.1	chr11	53257717	53257741	-	1	NA	Intergenic	Intergenic	42750	NM_008300	15525	Mm.239865	NM_008300	ENSMUSG00000020361	Hspa4	70kDa|AI317151|APG-2|Hsp110|Hsp70RY|mKIAA4025	heat shock protein 4	protein-coding
mm_125694.1	chr15	66891379	66891389	+	1	NA	promoter-TSS (NM_018865)	promoter-TSS (NM_018865)	-9	NM_018865	22402	Mm.10222	NM_018865	ENSMUSG00000005124	Wisp1	AW146261|CCN4|Elm1	WNT1 inducible signaling pathway protein 1	protein-coding
mm_77681.1	chr8	125669738	125669754	-	1	NA	promoter-TSS (NM_028908)	promoter-TSS (NM_028908)	-72	NM_028908	74393	Mm.41709	NM_028908	ENSMUSG00000050930	Map10	4933403G14Rik|AI835009|mKIAA1383	microtubule-associated protein 10	protein-coding
mm_140294.1	chr17	85620817	85620843	+	1	NA	promoter-TSS (NM_011381)	promoter-TSS (NM_011381)	-4	NM_011381	20473	Mm.370208	NM_011381	ENSMUSG00000038805	Six3	E130112M24Rik|Six3a|Six3alpha|Six3b|Six3beta	sine oculis-related homeobox 3	protein-coding
mm_28047.1	chr3	84040152	84040171	-	1	NA	promoter-TSS (NM_172681)	promoter-TSS (NM_172681)	0	NM_172681	229473	Mm.28838	NM_172681	ENSMUSG00000033767	D930015E06Rik	Kiaa0922|mKIAA0922	RIKEN cDNA D930015E06 gene	protein-coding
mm_27233.1	chr3	36468921	36468948	-	1	NA	intron (NM_009673, intron 2 of 12)	intron (NM_009673, intron 2 of 12)	6590	NR_105976	102466786		NR_105976	ENSMUSG00000098808	Mir7009	Gm27472|mmu-mir-7009	microRNA 7009	ncRNA
mm_136565.1	chr17	3326553	3326585	+	1	NA	promoter-TSS (NM_001122998)	promoter-TSS (NM_001122998)	-4	NM_001122998	24001	Mm.137134	NM_011878	ENSMUSG00000023800	Tiam2	3000002F19Rik|STEF|mKIAA2016	T cell lymphoma invasion and metastasis 2	protein-coding
mm_172545.1	chr7	99249276	99249288	-	1	NA	Intergenic	Intergenic	-10671	NM_177448	233549	Mm.208030	NM_177448	ENSMUSG00000052396	Mogat2	DGAT2L5|MGAT2|Mgat1l	monoacylglycerol O-acyltransferase 2	protein-coding
mm_164731.1	chr17	65642146	65642152	-	1	NA	promoter-TSS (NM_001146002)	promoter-TSS (NM_001146002)	55	NM_001146002	213272	Mm.255732	NM_153519	ENSMUSG00000050612	Txndc2	AU021712|Sptrx-1|Sptrx1|Trx4	thioredoxin domain containing 2 (spermatozoa)	protein-coding
mm_108544.1	chr12	84361637	84361643	+	1	NA	promoter-TSS (NM_172582)	promoter-TSS (NM_172582)	181	NM_172581	217705	Mm.259468	NM_172581	ENSMUSG00000021234	Fam161b	9330169D17|9830169C18Rik	family with sequence similarity 161, member B	protein-coding
mm_72171.1	chr8	72268704	72268712	+	1	NA	Intergenic	Intergenic	28690	NM_007456	11767	Mm.290086	NM_007456	ENSMUSG00000003033	Ap1m1	AA408894|AP47|Adtm1A|Cltnm|mu1A	adaptor-related protein complex AP-1, mu subunit 1	protein-coding
mm_44474.1	chr5	23433278	23433293	-	1	NA	non-coding (NR_040469, exon 1 of 1)	non-coding (NR_040469, exon 1 of 1)	1068	NR_040469	269630	Mm.425231	NR_040469	ENSMUSG00000073147	5031425E22Rik	-	RIKEN cDNA 5031425E22 gene	ncRNA
mm_13626.1	chr2	113525392	113525409	+	1	NA	exon (NM_001285459, exon 4 of 17)	exon (NM_001285459, exon 4 of 17)	84336	NM_001285459	14260	Mm.4938	NM_010230	ENSMUSG00000044042	Fmn1	Fmn|formin-1|ld	formin 1	protein-coding
mm_78534.1	chr9	35211178	35211224	+	1	NA	promoter-TSS (NM_172291)	promoter-TSS (NM_172291)	-2	NM_026130	67398	Mm.284688	NM_026130	ENSMUSG00000032042	Srpr	1300011P19Rik|D11Mgi27|Srpra	signal recognition particle receptor ('docking protein')	protein-coding
mm_9936.1	chr1	190144496	190144520	-	1	NA	intron (NM_008937, intron 4 of 4)	MIRc|SINE|MIR	26172	NM_008937	19130	Mm.132579	NM_008937	ENSMUSG00000010175	Prox1	A230003G05Rik	prospero homeobox 1	protein-coding
mm_104300.1	chr11	90549428	90549436	-	1	NA	intron (NM_011505, intron 12 of 17)	intron (NM_011505, intron 12 of 17)	88676	NM_011505	20913	Mm.207203	NM_011505	ENSMUSG00000020546	Stxbp4	6030470M02Rik|Synip	syntaxin binding protein 4	protein-coding
mm_127206.1	chr15	99215143	99215187	+	1	NA	Intergenic	B3A|SINE|B2	-9811	NM_010601	16512	Mm.374793	NM_010601	ENSMUSG00000037579	Kcnh3	AU019351|C030044P22Rik|Elk2|Kv12.2|Melk2	potassium voltage-gated channel, subfamily H (eag-related), member 3	protein-coding
mm_53957.1	chr6	5484157	5484173	-	1	NA	3' UTR (NM_013743, exon 11 of 11)	3' UTR (NM_013743, exon 11 of 11)	12113	NM_013743	27273	Mm.235547	NM_013743	ENSMUSG00000019577	Pdk4	AV005916	pyruvate dehydrogenase kinase, isoenzyme 4	protein-coding
mm_91449.1	chr10	33947809	33947813	-	1	NA	intron (NM_028287, intron 3 of 9)	L1MC|LINE|L1	3401	NM_028287	72580	Mm.248081	NM_028287	ENSMUSG00000039531	Zufsp	2700019D07Rik	zinc finger with UFM1-specific peptidase domain	protein-coding
mm_146979.1	chr18	33832785	33832800	-	1	NA	intron (NM_013512, intron 13 of 23)	B4|SINE|B4	37900	NR_038151	69749	Mm.248787	NR_038151	ENSMUSG00000087590	Epb41l4aos	2410004N09Rik|Epb4.1l4aos	erythrocyte membrane protein band 4.1 like 4a, opposite strand	ncRNA
mm_171446.1	chr4	143978477	143978485	-	1	NA	Intergenic	MMVL30-int|LTR|ERV1	15888	NM_001085540	626943		NM_001085540	ENSMUSG00000078509	Pramef17	Gm13107|OTTMUSG00000010438	PRAME family member 17	protein-coding
mm_15247.1	chr2	154689600	154689622	+	1	NA	exon (NM_029362, exon 2 of 5)	exon (NM_029362, exon 2 of 5)	32585	NM_029362	75608	Mm.262480	NM_029362	ENSMUSG00000038467	Chmp4b	2010012F05Rik|C76846|Snf7-2	charged multivesicular body protein 4B	protein-coding
mm_120588.1	chr14	69840394	69840465	+	1	NA	promoter-TSS (NM_028526)	promoter-TSS (NM_028526)	22	NM_028526	73523	Mm.23509	NM_028526	ENSMUSG00000022085	Pebp4	PEBP-4	phosphatidylethanolamine binding protein 4	protein-coding
mm_19083.1	chr2	77946377	77946392	-	1	NA	promoter-TSS (NM_001290740)	promoter-TSS (NM_001290740)	-28	NM_030560	80744	Mm.288151	NM_030560	ENSMUSG00000027014	Cwc22	AA684037|AI173004|AL022752|B230213M24|mKIAA1604	CWC22 spliceosome-associated protein	protein-coding
mm_36826.1	chr4	105110597	105110603	-	1	NA	promoter-TSS (NM_178143)	promoter-TSS (NM_178143)	-702	NM_178143	108079	Mm.48638	NM_178143	ENSMUSG00000028518	Prkaa2	2310008I11Rik|A830082D05|AMPKalpha2	protein kinase, AMP-activated, alpha 2 catalytic subunit	protein-coding
mm_21465.1	chr2	160912350	160912355	-	1	NA	promoter-TSS (NM_001291145)	promoter-TSS (NM_001291145)	-13	NM_182840	280635	Mm.330747	NM_182840	ENSMUSG00000050700	Emilin3	1110013O17Rik|EMILIN-3|EMILIN-5|EMILIN-T|Emilin5	elastin microfibril interfacer 3	protein-coding
mm_48095.1	chr5	137062050	137062065	-	1	NA	3' UTR (NM_008871, exon 9 of 9)	3' UTR (NM_008871, exon 9 of 9)	10215	NM_008871	18787	Mm.250422	NM_008871	ENSMUSG00000037411	Serpine1	PAI-1|PAI1|Planh1	serine (or cysteine) peptidase inhibitor, clade E, member 1	protein-coding
mm_160153.1	chr7	43690185	43690185	+	1	NA	promoter-TSS (NM_174866)	promoter-TSS (NM_174866)	-233	NM_174866	317653	Mm.247377	NM_174866	ENSMUSG00000044737	Klk14	GK14	kallikrein related-peptidase 14	protein-coding
mm_118058.1	chr13	102682607	102682642	-	1	NA	Intergenic	Intergenic	-10934	NM_008533	17079	Mm.373974	NM_008533	ENSMUSG00000021624	Cd180	F630107B15|Ly78|RP105	CD180 antigen	protein-coding
mm_161098.1	chr12	99449862	99449862	-	1	NA	intron (NM_183186, intron 1 of 5)	B2_Mm2|SINE|B2	212	NM_183186	71375	Mm.341972	NM_183186	ENSMUSG00000033713	Foxn3	5430426H20Rik|AA589593|AW556347|Ches1|Ches1l|HTLFL1	forkhead box N3	protein-coding
mm_167071.1	chr7	99601678	99601715	+	1	NA	3' UTR (NM_178220, exon 15 of 15)	3' UTR (NM_178220, exon 15 of 15)	25407	NM_001195529	100503386	Mm.180719	NM_001195529	ENSMUSG00000096606	Tpbgl	EG245190|Gm4980	trophoblast glycoprotein-like	protein-coding
mm_22314.1	chr2	180439554	180439560	-	1	NA	Intergenic	B4|SINE|B4	-21421	NM_148933	108115	Mm.133687	NM_148933	ENSMUSG00000038963	Slco4a1	OATP-E|Slc21a12	solute carrier organic anion transporter family, member 4a1	protein-coding
mm_88181.1	chr10	69925856	69925870	+	1	NA	5' UTR (NM_009670, exon 1 of 20)	5' UTR (NM_009670, exon 1 of 20)	331	NM_009670	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_94628.1	chr11	16810905	16810915	+	1	NA	intron (NM_207655, intron 1 of 27)	intron (NM_207655, intron 1 of 27)	58707	NM_007912	13649	Mm.8534	NM_007912	ENSMUSG00000020122	Egfr	9030024J15Rik|AI552599|Erbb|Errb1|Errp|Wa5|wa-2|wa2	epidermal growth factor receptor	protein-coding
mm_172947.1	chr9	81678084	81678094	+	1	NA	Intergenic	Intergenic	-45537	NM_010482	15551	Mm.445308	NM_010482	ENSMUSG00000049511	Htr1b	-	5-hydroxytryptamine (serotonin) receptor 1B	protein-coding
mm_134157.1	chr16	10790942	10790950	-	1	NA	promoter-TSS (NM_013638)	promoter-TSS (NM_013638)	-32	NM_013638	19120	Mm.291887	NM_013638	ENSMUSG00000050058	Prm3	BC061127|PX|Pxg	protamine 3	protein-coding
mm_17157.1	chr2	25228421	25228459	-	1	NA	TTS (NM_080854)	TTS (NM_080854)	-3738	NM_146116	227613	Mm.227260	NM_146116	ENSMUSG00000036752	Tubb4b	4930542G03Rik|Tubb2c|Tubb2c1	tubulin, beta 4B class IVB	protein-coding
mm_46588.1	chr5	107724075	107724109	-	1	NA	5' UTR (NM_010278, exon 1 of 6)	5' UTR (NM_010278, exon 1 of 6)	251	NM_010278	14581	Mm.2078	NM_010278	ENSMUSG00000029275	Gfi1	AW495828|Gfi-1|Pal-1|Pal1	growth factor independent 1	protein-coding
mm_154182.1	chr19	58793269	58793276	-	1	NA	intron (NM_026208, intron 1 of 5)	intron (NM_026208, intron 1 of 5)	1142	NM_026208	67507	Mm.27027	NM_026208	ENSMUSG00000026931	1700019N19Rik	-	RIKEN cDNA 1700019N19 gene	protein-coding
mm_7532.1	chr1	124375770	124375772	-	1	NA	Intergenic	Intergenic	-330212	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_78831.1	chr9	44134654	44134670	+	1	NA	promoter-TSS (NM_023061)	promoter-TSS (NM_023061)	4	NM_023061	84004	Mm.275003	NM_023061	ENSMUSG00000032135	Mcam	1-gicerin|AV025631|CD146|CD149|Muc18|s-endo|s-gicerin	melanoma cell adhesion molecule	protein-coding
mm_78017.1	chr9	13662585	13662630	+	1	NA	5' UTR (NM_173776, exon 1 of 4)	5' UTR (NM_173776, exon 1 of 4)	147	NM_173776	270118	Mm.116898	NM_173776	ENSMUSG00000031925	Maml2	5930431H10|BC032967	mastermind like 2 (Drosophila)	protein-coding
mm_62944.1	chr7	119526221	119526264	+	1	NA	promoter-TSS (NM_178758)	promoter-TSS (NM_178758)	-23	NM_178758	272428	Mm.185183	NM_178758	ENSMUSG00000030972	Acsm5	C730019D22|C730027J19Rik	acyl-CoA synthetase medium-chain family member 5	protein-coding
mm_95044.1	chr11	32277908	32277928	+	1	NA	exon (NM_010405, exon 3 of 3)	exon (NM_010405, exon 3 of 3)	1318	NM_010405	15126	Mm.141758	NM_010405	ENSMUSG00000055609	Hba-x	AI450015|Hbz	hemoglobin X, alpha-like embryonic chain in Hba complex	protein-coding
mm_80953.1	chr9	103007931	103007952	+	1	NA	promoter-TSS (NM_033314)	promoter-TSS (NM_033314)	-548	NM_033314	24059	Mm.207106	NM_033314	ENSMUSG00000032548	Slco2a1	2310021C19Rik|Pgt|Slc21a2|mPgt	solute carrier organic anion transporter family, member 2a1	protein-coding
mm_29994.1	chr3	135550460	135550470	-	1	NA	intron (NM_027288, intron 11 of 16)	RMER17D|LTR|ERVK	64854	NM_027288	110173	Mm.280536	NM_027288	ENSMUSG00000028164	Manba	2410030O07Rik|B930014J03Rik|Bmn	mannosidase, beta A, lysosomal	protein-coding
mm_130392.1	chr15	97910603	97910617	-	1	NA	Intergenic	Intergenic	-2314	NM_009504	22337	Mm.245084	NM_009504	ENSMUSG00000022479	Vdr	Nr1i1	vitamin D receptor	protein-coding
mm_35500.1	chr4	41048087	41048119	-	1	NA	promoter-TSS (NM_007473)	promoter-TSS (NM_007473)	33	NM_007473	11832	Mm.8728	NM_007473	ENSMUSG00000028427	Aqp7	AQP7L|AQPap	aquaporin 7	protein-coding
mm_61941.1	chr7	90182819	90182831	+	1	NA	intron (NM_001252520, intron 13 of 20)	intron (NM_001252520, intron 13 of 20)	52593	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_69849.1	chr7	141427369	141427390	-	1	NA	3' UTR (NM_021316, exon 2 of 2)	3' UTR (NM_021316, exon 2 of 2)	2041	NM_021316	57754	Mm.87027	NM_021316	ENSMUSG00000060240	Cend1	1500001H12Rik|AI415214|BM88	cell cycle exit and neuronal differentiation 1	protein-coding
mm_122891.1	chr14	54949430	54949466	-	1	NA	promoter-TSS (NR_029724)	promoter-TSS (NR_029724)	-306	NR_029724	387204		NR_029724	ENSMUSG00000065432	Mir208a	Mirn208|Mirn208a|mir-208|mir-208a|mmu-mir-208	microRNA 208a	ncRNA
mm_164584.1	chr17	25901806	25901822	+	1	NA	TTS (NR_028042)	TTS (NR_028042)	413	NR_028042	100043160	Mm.482893	NR_028042		Gm10012	ENSMUSG00000056875	cytochrome c oxidase, subunit VIIc pseudogene	pseudo
mm_24585.1	chr3	93444888	93444896	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	2562	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_129641.1	chr15	80264277	80264322	-	1	NA	promoter-TSS (NM_175109)	promoter-TSS (NM_175109)	7	NM_175109	66538	Mm.39485	NM_175109	ENSMUSG00000051518	Rps19bp1	2510038A11Rik|AI604923|S19BP	ribosomal protein S19 binding protein 1	protein-coding
mm_104481.1	chr11	95570387	95570396	-	1	NA	3' UTR (NM_033217, exon 6 of 6)	3' UTR (NM_033217, exon 6 of 6)	17307	NM_033217	18053	Mm.283893	NM_033217	ENSMUSG00000000120	Ngfr	LNGFR|Tnfrsf16|p75|p75NGFR|p75NTR	nerve growth factor receptor (TNFR superfamily, member 16)	protein-coding
mm_29441.1	chr3	110143514	110143525	-	1	NA	promoter-TSS (NM_001163350)	promoter-TSS (NM_001163350)	-47	NM_030699	80883	Mm.39262	NM_030699	ENSMUSG00000059857	Ntng1	A930010C08Rik|AI853992|Lmnt1	netrin G1	protein-coding
mm_20166.1	chr2	122215356	122215376	-	1	NA	Intergenic	Intergenic	-19473	NM_146126	20322	Mm.371580	NM_146126	ENSMUSG00000027227	Sord	Sdh-1|Sdh1|Sodh-1	sorbitol dehydrogenase	protein-coding
mm_41503.1	chr5	92331829	92331847	+	1	NA	promoter-TSS (NM_001310664)	promoter-TSS (NM_001310664)	11	NM_001310664	109979	Mm.263514	NM_181728	ENSMUSG00000034842	Art3	4930569O04Rik|ARTC3	ADP-ribosyltransferase 3	protein-coding
mm_115794.1	chr13	19341703	19341709	-	1	NA	Intergenic	Intergenic	54107	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_151418.1	chr19	56745518	56745525	+	1	NA	Intergenic	(T)n|Simple_repeat|Simple_repeat	23149	NM_007419	11554	Mm.46797	NM_007419	ENSMUSG00000035283	Adrb1	Adrb-1|beta-AR	adrenergic receptor, beta 1	protein-coding
mm_160089.1	chr7	16425849	16425849	+	1	NA	intron (NM_198631, intron 10 of 13)	intron (NM_198631, intron 10 of 13)	24653	NM_198631	330474	Mm.333594	NM_198631	ENSMUSG00000059273	Zc3h4	Bwq1|Gm768|Kiaa1064-hp|mKIAA1064	zinc finger CCCH-type containing 4	protein-coding
mm_137089.1	chr17	21489201	21489222	+	1	NA	5' UTR (NM_013843, exon 1 of 5)	5' UTR (NM_013843, exon 1 of 5)	223	NM_013843	24132	Mm.42140	NM_013843	ENSMUSG00000057409	Zfp53	D030067O06Rik|KRAZ1|Zfp-53|Zfp118|zfas8	zinc finger protein 53	protein-coding
mm_56241.1	chr6	90716412	90716420	-	1	NA	5' UTR (NM_001134383, exon 1 of 14)	5' UTR (NM_001134383, exon 1 of 14)	113	NM_001134383	232227	Mm.196943	NM_182784	ENSMUSG00000034312	Iqsec1	AW561907|BC026481|BRAG2|D6Ertd349e|cI-43	IQ motif and Sec7 domain 1	protein-coding
mm_25019.1	chr3	98013593	98013609	+	1	NA	promoter-TSS (NM_010928)	promoter-TSS (NM_010928)	63	NM_010928	18129	Mm.485843	NM_010928	ENSMUSG00000027878	Notch2	AI853703|N2	notch 2	protein-coding
mm_128232.1	chr15	36605516	36605554	-	1	NA	exon (NM_008774, exon 3 of 15)	exon (NM_008774, exon 3 of 15)	3438	NM_008774	18458	Mm.371570	NM_008774	ENSMUSG00000022283	Pabpc1	PABP|Pabp1|PabpI|Pabpl1|ePAB	poly(A) binding protein, cytoplasmic 1	protein-coding
mm_63471.1	chr7	127598666	127598668	+	1	NA	intron (NM_172281, intron 17 of 19)	B4|SINE|B4	5778	NR_027915	68232	Mm.347960	NM_026628	ENSMUSG00000099579	1700120K04Rik	-	RIKEN cDNA 1700120K04 gene	ncRNA
mm_57546.1	chr6	126712688	126712696	-	1	NA	intron (NM_013568, intron 1 of 1)	L2a|LINE|L2	27982	NM_013568	16494	Mm.62535	NM_013568	ENSMUSG00000038077	Kcna6	Kv1.6|MK1.6	potassium voltage-gated channel, shaker-related, subfamily, member 6	protein-coding
mm_159527.1	chr4	62291553	62291553	+	1	NA	promoter-TSS (NM_001290518)	promoter-TSS (NM_001290518)	6	NM_001290518	20530	Mm.292539	NM_025286	ENSMUSG00000066152	Slc31a2	AI604396|CTR2	solute carrier family 31, member 2	protein-coding
mm_35753.1	chr4	45811173	45811200	-	1	NA	3' UTR (NM_018741, exon 5 of 5)	3' UTR (NM_018741, exon 5 of 5)	12164	NM_028270	72535	Mm.331583	NM_028270	ENSMUSG00000035561	Aldh1b1	2700007F14Rik	aldehyde dehydrogenase 1 family, member B1	protein-coding
mm_170733.1	chr2	152226931	152226938	+	1	NA	promoter-TSS (NM_007788)	promoter-TSS (NM_007788)	94	NM_007788	12995	Mm.23692	NM_007788	ENSMUSG00000074698	Csnk2a1	Csnk2a1-rs4	casein kinase 2, alpha 1 polypeptide	protein-coding
mm_121546.1	chr14	122474819	122474825	+	1	NA	promoter-TSS (NM_009574)	promoter-TSS (NM_009574)	377	NR_045046	69248	Mm.235369	NR_045046	ENSMUSG00000085555	2610035F20Rik	-	RIKEN cDNA 2610035F20 gene	ncRNA
mm_143423.1	chr17	70846251	70846287	-	1	NA	exon (NM_001164077, exon 1 of 2)	exon (NM_001164077, exon 1 of 2)	508	NM_001164077	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_67814.1	chr7	98162319	98162367	-	1	NA	promoter-TSS (NM_001301250)	promoter-TSS (NM_001301250)	-1	NM_001301250	12337	Mm.326847	NM_007602	ENSMUSG00000035547	Capn5	nCL-3	calpain 5	protein-coding
mm_155133.1	chrX	49493117	49493139	+	1	NA	intron (NM_001081123, intron 1 of 12)	intron (NM_001081123, intron 1 of 12)	22678	NM_001081123	75404	Mm.44305	NM_001081123	ENSMUSG00000036198	Arhgap36	1100001E04Rik|rho-gap	Rho GTPase activating protein 36	protein-coding
mm_88428.1	chr10	77416260	77416265	+	1	NA	intron (NM_001024837, intron 1 of 10)	intron (NM_001024837, intron 1 of 10)	2011	NM_130895	110532	Mm.276815	NM_130895	ENSMUSG00000020262	Adarb1	1700057H01Rik|AW124433|AW558573|Adar2|BB220382|D10Bwg0447e|Red1	adenosine deaminase, RNA-specific, B1	protein-coding
mm_14738.1	chr2	144337814	144337832	+	1	NA	Intergenic	B4A|SINE|B4	-5743	NM_026924	107586	Mm.252750	NM_026924	ENSMUSG00000037279	Ovol2	1700108N11Rik|1810007D21Rik|M-OVO|M-OVO-A|M-OVO-B|MOVO|Ovo2|Zfp339|movo2	ovo like zinc finger 2	protein-coding
mm_17562.1	chr2	30194152	30194167	-	1	NA	intron (NM_172404, intron 2 of 13)	intron (NM_172404, intron 2 of 13)	11540	NM_172404	70266	Mm.216089	NM_172404	ENSMUSG00000039648	Kyat1	2010009K05Rik|AI182306|Ccbl1|Gtk|Kat1|KatI	kynurenine aminotransferase 1	protein-coding
mm_21083.1	chr2	152951548	152951608	-	1	NA	promoter-TSS (NM_001159376)	promoter-TSS (NM_001159376)	4	NM_001159376	252864	Mm.330671	NM_145744	ENSMUSG00000042662	Dusp15	AI851682|LMW-DSP10|T-DSP10	dual specificity phosphatase-like 15	protein-coding
mm_144741.1	chr18	35571985	35571999	+	1	NA	5' UTR (NM_010771, exon 2 of 15)	5' UTR (NM_010771, exon 2 of 15)	9834	NM_010771	17184	Mm.215034	NM_010771	ENSMUSG00000037236	Matr3	1110061A14Rik|2810017I02Rik|AI841759|AW555618|D030046F20Rik|mKIAA0723	matrin 3	protein-coding
mm_108283.1	chr12	79130801	79130816	+	1	NA	promoter-TSS (NM_009705)	promoter-TSS (NM_009705)	20	NM_009705	11847	Mm.3506	NM_009705	ENSMUSG00000021125	Arg2	AII|AU022422	arginase type II	protein-coding
mm_29700.1	chr3	123117196	123117198	-	1	NA	exon (NM_080451, exon 3 of 5)	exon (NM_080451, exon 3 of 5)	-82210	NM_021503	59006	Mm.141157	NM_021503	ENSMUSG00000028116	Myoz2	1110012I24Rik|Fatz-2|Myozl2	myozenin 2	protein-coding
mm_146673.1	chr18	12648455	12648472	-	1	NA	intron (NM_028341, intron 1 of 13)	intron (NM_028341, intron 1 of 13)	4930	NM_028341	72747	Mm.52526	NM_028341	ENSMUSG00000024424	Ttc39c	1700008N02Rik|2810439F02Rik	tetratricopeptide repeat domain 39C	protein-coding
mm_76716.1	chr8	94696224	94696287	-	1	NA	promoter-TSS (NM_026385)	promoter-TSS (NM_026385)	-13	NM_026385	67801	Mm.279977	NM_026385	ENSMUSG00000031775	Pllp	0610010I06Rik|AV001002|Plapi|Tm4sf11	plasma membrane proteolipid	protein-coding
mm_61081.1	chr7	51622128	51622142	+	1	NA	5' UTR (NM_080853, exon 1 of 12)	5' UTR (NM_080853, exon 1 of 12)	305	NM_080853	140919	Mm.256618	NM_080853	ENSMUSG00000030500	Slc17a6	2900073D12Rik|DNPI|VGLUT2	solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 6	protein-coding
mm_112752.1	chr13	19342059	19342069	+	1	NA	Intergenic	Intergenic	53749	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_158264.1	chrX	109013474	109013484	-	1	NA	promoter-TSS (NM_016710)	promoter-TSS (NM_016710)	-99	NM_016710	50887	Mm.298443	NM_016710	ENSMUSG00000031245	Hmgn5	GARP45|NBP-45|Nsbp1	high-mobility group nucleosome binding domain 5	protein-coding
mm_108093.1	chr12	74298324	74298334	+	1	NA	5' UTR (NM_198866, exon 1 of 1)	5' UTR (NM_198866, exon 1 of 1)	855	NM_198866	386753	Mm.341686	NM_198866	ENSMUSG00000029878	Dbpht2	Spot2	DNA binding protein with his-thr domain	protein-coding
mm_107450.1	chr12	36677369	36677369	+	1	NA	intron (NM_178629, intron 9 of 9)	RMER1A|Other|Other	-138836	NR_039558	100628578		NR_039558	ENSMUSG00000092998	Mir5099	mmu-mir-5099|mu-mir-5099	microRNA 5099	ncRNA
mm_155382.1	chrX	71812811	71812821	+	1	NA	Intergenic	Intergenic	-3264	NM_001290781	67048	Mm.41102	NM_001081356	ENSMUSG00000073131	Vma21	2610030H06Rik|AI840175	VMA21 vacuolar H+-ATPase homolog (S. cerevisiae)	protein-coding
mm_109173.1	chr12	108371222	108371244	+	1	NA	promoter-TSS (NM_001286346)	promoter-TSS (NM_001286346)	80	NM_001286346	68519	Mm.236645	NM_001043335	ENSMUSG00000058070	Eml1	1110008N23Rik|A930030P13Rik|AA171013|AI847476|AI853955|ELP79|EMAP|EMAPL|heco	echinoderm microtubule associated protein like 1	protein-coding
mm_18479.1	chr2	62483638	62483653	-	1	NA	promoter-TSS (NM_008100)	promoter-TSS (NM_008100)	8	NM_008100	14526	Mm.45494	NM_008100	ENSMUSG00000000394	Gcg	GLP-1|Glu|PPG	glucagon	protein-coding
mm_21420.1	chr2	158137627	158137632	-	1	NA	intron (NM_009373, intron 3 of 12)	intron (NM_009373, intron 3 of 12)	8763	NM_009373	21817	Mm.330731	NM_009373	ENSMUSG00000037820	Tgm2	G[a]h|TG2|TGase2|tTG|tTGas	transglutaminase 2, C polypeptide	protein-coding
mm_135048.1	chr16	33251308	33251319	-	1	NA	promoter-TSS (NM_080557)	promoter-TSS (NM_080557)	-143	NM_080557	69150	Mm.28196	NM_080557	ENSMUSG00000022808	Snx4	1810036H14Rik|AI037066	sorting nexin 4	protein-coding
mm_2069.1	chr1	87625512	87625531	+	1	NA	intron (NM_010566, intron 1 of 26)	L1MB7|LINE|L1	5209	NM_001110193	16331	Mm.15105	NM_010566	ENSMUSG00000026288	Inpp5d	SHIP|SHIP-1|SHIP1|SIP-145|p150Ship|s-SHIP	inositol polyphosphate-5-phosphatase D	protein-coding
mm_9923.1	chr1	189688045	189688059	-	1	NA	promoter-TSS (NM_001081363)	promoter-TSS (NM_001081363)	34	NM_001081363	108000	Mm.129746	NM_001081363	ENSMUSG00000026605	Cenpf	6530404A22Rik|AI325968|CENF|Lek1|PRO1779|mitosin	centromere protein F	protein-coding
mm_92313.1	chr10	75317564	75317574	-	1	NA	promoter-TSS (NM_001331095)	promoter-TSS (NM_001331095)	-31	NM_001331095	11540	Mm.333734	NM_009630	ENSMUSG00000020178	Adora2a	A2AAR|A2aR|AA2AR	adenosine A2a receptor	protein-coding
mm_120021.1	chr14	55764688	55764728	+	1	NA	Intergenic	Intergenic	-1254	NM_008519	16995	Mm.20853	NM_008519	ENSMUSG00000046908	Ltb4r1	BLT1|BLTR|Ltb4r|mBLTR	leukotriene B4 receptor 1	protein-coding
mm_57037.1	chr6	122339447	122339517	-	1	NA	intron (NM_001271579, intron 1 of 14)	CpG	175	NM_001042623	13619	Mm.6822	NM_007905	ENSMUSG00000040669	Phc1	AW557034|Edr|Edr1|Mph1|Rae-28|rae28	polyhomeotic-like 1 (Drosophila)	protein-coding
mm_168166.1	chr10	52115260	52115270	-	1	NA	intron (NM_011282, intron 27 of 43)	L1Md_T|LINE|L1	79979	NM_011282	19886	Mm.236163	NM_011282	ENSMUSG00000019893	Ros1	Ros-1|c-ros	Ros1 proto-oncogene	protein-coding
mm_115571.1	chr13	10360943	10360970	-	1	NA	promoter-TSS (NM_033269)	promoter-TSS (NM_033269)	-153	NM_033269	12671	Mm.342315	NM_033269	ENSMUSG00000046159	Chrm3	Chrm-3|M3|M3R	cholinergic receptor, muscarinic 3, cardiac	protein-coding
mm_2919.1	chr1	132023881	132023885	+	1	NA	3' UTR (NM_007923, exon 5 of 5)	3' UTR (NM_007923, exon 5 of 5)	16278	NM_007923	13714	Mm.254233	NM_007923	ENSMUSG00000026436	Elk4	2310011G17Rik|A130026I01Rik|BB162516|SAP-1|Sap1	ELK4, member of ETS oncogene family	protein-coding
mm_22896.1	chr3	30793129	30793147	+	1	NA	5' UTR (NM_027016, exon 1 of 8)	5' UTR (NM_027016, exon 1 of 8)	262	NM_027016	69276	Mm.26017	NM_027016	ENSMUSG00000027706	Sec62	3100002M17Rik|AI844545|AW545092|Dtrp1|HTP1|Tloc1	SEC62 homolog (S. cerevisiae)	protein-coding
mm_12648.1	chr2	74745677	74745681	+	1	NA	intron (NM_010468, intron 2 of 2)	intron (NM_010468, intron 2 of 2)	-7005	NR_110447	102634401	Mm.235021	NR_110447	ENSMUSG00000085015	LOC102634401	-	uncharacterized LOC102634401	ncRNA
mm_154434.1	chrM	762	788	-	1	NA	NA	Intergenic	NA	NA								
mm_123895.1	chr14	73049080	73049091	-	1	NA	promoter-TSS (NM_001162412)	promoter-TSS (NM_001162412)	29	NM_133720	70086	Mm.158324	NM_133720	ENSMUSG00000033470	Cysltr2	2300001H05Rik|CYSLT2R|Cltr2|Cyslt2	cysteinyl leukotriene receptor 2	protein-coding
mm_146771.1	chr18	20002373	20002383	-	1	NA	promoter-TSS (NM_001291809)	promoter-TSS (NM_001291809)	-281	NM_001291809	13507	Mm.89935	NM_007882	ENSMUSG00000059898	Dsc3	5430426I24Rik	desmocollin 3	protein-coding
mm_58011.1	chr6	136519059	136519077	-	1	NA	intron (NM_019426, intron 1 of 14)	CpG	217	NM_019426	54343	Mm.173271	NM_019426	ENSMUSG00000030213	Atf7ip	2610204M12Rik|AM|Mcaf1	activating transcription factor 7 interacting protein	protein-coding
mm_53314.1	chr6	129182999	129183009	+	1	NA	intron (NM_053109, intron 1 of 4)	intron (NM_053109, intron 1 of 4)	2389	NM_053109	93694	Mm.197536	NM_053109	ENSMUSG00000030157	Clec2d	Clr-b|Clrb|Ocil	C-type lectin domain family 2, member d	protein-coding
mm_12953.1	chr2	89916967	89916969	+	1	NA	Intergenic	ERVB4_3-I_MM-int|LTR|ERVK	-12843	NM_146978	258980	Mm.223370	NM_146978	ENSMUSG00000049149	Olfr1258	MOR232-3	olfactory receptor 1258	protein-coding
mm_147270.1	chr18	38929174	38929199	-	1	NA	intron (NM_001033789, intron 3 of 4)	intron (NM_001033789, intron 3 of 4)	-10487	NM_010197	14164	Mm.241282	NM_010197	ENSMUSG00000036585	Fgf1	Dffrx|Fam|Fgf-1|Fgfa	fibroblast growth factor 1	protein-coding
mm_39027.1	chr4	152132398	152132415	-	1	NA	intron (NM_207688, intron 3 of 10)	intron (NM_207688, intron 3 of 10)	-3481	NM_019585	56226	Mm.264215	NM_019585	ENSMUSG00000028943	Espn	je	espin	protein-coding
mm_99908.1	chr11	109764267	109764267	+	1	NA	Intergenic	Intergenic	-42011	NM_153782	208659	Mm.208662	NM_153782	ENSMUSG00000020614	Fam20a	AI606893	family with sequence similarity 20, member A	protein-coding
mm_82366.1	chr9	14574604	14574606	-	1	NA	intron (NM_001081395, intron 4 of 12)	intron (NM_001081395, intron 4 of 12)	40395	NM_001081395	75723	Mm.159552	NM_001081395	ENSMUSG00000013076	Amotl1	2310010G08Rik|2310067L22Rik|4932416D09Rik|JEAP|mFLJ00155	angiomotin-like 1	protein-coding
mm_15164.1	chr2	154011351	154011376	+	1	NA	exon (NM_008953, exon 5 of 9)	exon (NM_008953, exon 5 of 9)	3087	NM_008953	19194	Mm.29197	NM_008953	ENSMUSG00000042459	Bpifa2	Bpifa2e|Psp	BPI fold containing family A, member 2	protein-coding
mm_137660.1	chr17	28691420	28691445	+	1	NA	promoter-TSS (NM_011951)	promoter-TSS (NM_011951)	90	NM_001168514	26416	Mm.311337	NM_011951	ENSMUSG00000053436	Mapk14	CSBP2|Crk1|Csbp1|Mxi2|PRKM14|PRKM15|p38|p38-alpha|p38MAPK|p38a|p38alpha	mitogen-activated protein kinase 14	protein-coding
mm_63454.1	chr7	127520086	127520090	+	1	NA	intron (NM_001304266, intron 4 of 33)	intron (NM_001304266, intron 4 of 33)	-7219	NR_024331	629159	Mm.256720	NR_024331	ENSMUSG00000101225	1700008J07Rik	AW048743	RIKEN cDNA 1700008J07 gene	ncRNA
mm_54710.1	chr6	39725294	39725357	-	1	NA	5' UTR (NM_139294, exon 1 of 22)	5' UTR (NM_139294, exon 1 of 22)	138	NM_139294	109880	Mm.245513	NM_139294	ENSMUSG00000002413	Braf	9930012E13Rik|AA120551|AA387315|AA473386|B-raf|Braf-2|Braf2|C230098H17|C87398|D6Ertd631e	Braf transforming gene	protein-coding
mm_153367.1	chr19	40271814	40271822	-	1	NA	promoter-TSS (NM_016861)	promoter-TSS (NM_016861)	-202	NM_016861	54132	Mm.5567	NM_016861	ENSMUSG00000055044	Pdlim1	CLP36|Clim1|mClim1	PDZ and LIM domain 1 (elfin)	protein-coding
mm_26915.1	chr3	20150601	20150617	-	1	NA	exon (NM_013755, exon 4 of 7)	exon (NM_013755, exon 4 of 7)	4507	NM_013755	27357	Mm.6375	NM_013755	ENSMUSG00000019528	Gyg	AU017667|Gyg1	glycogenin	protein-coding
mm_63526.1	chr7	127912678	127912717	+	1	NA	exon (NM_026370, exon 1 of 11)	exon (NM_026370, exon 1 of 11)	180	NM_026370	67773	Mm.425492	NM_026370	ENSMUSG00000030801	Kat8	2010203C02Rik|5830450F21Rik|D7Ertd629e|MOF|Myst1	K(lysine) acetyltransferase 8	protein-coding
mm_46070.1	chr5	92322733	92322742	-	1	NA	3' UTR (NM_008599, exon 4 of 4)	3' UTR (NM_008599, exon 4 of 4)	5342	NM_008599	17329	Mm.766	NM_008599	ENSMUSG00000029417	Cxcl9	BB139920|CMK|Mig|MuMIG|Scyb9|crg-10	chemokine (C-X-C motif) ligand 9	protein-coding
mm_21641.1	chr2	164333405	164333411	-	1	NA	exon (NM_009301, exon 2 of 3)	exon (NM_009301, exon 2 of 3)	643	NM_009301	20944	Mm.140154	NM_009301	ENSMUSG00000017004	Svs5	BB115186|Semg1|Svp-1|Svp1|Svp5	seminal vesicle secretory protein 5	protein-coding
mm_67695.1	chr7	89518129	89518149	-	1	NA	promoter-TSS (NM_029614)	promoter-TSS (NM_029614)	-553	NM_029614	76453	Mm.250438	NM_029614	ENSMUSG00000039405	Prss23	2310046G15Rik|4930479H08Rik|AI790574|Spuve	protease, serine 23	protein-coding
mm_50741.1	chr6	52727193	52727230	+	1	NA	exon (NM_025816, exon 3 of 18)	exon (NM_025816, exon 3 of 18)	13482	NM_025816	52440	Mm.389757	NM_025816	ENSMUSG00000004535	Tax1bp1	1200003J11Rik|1700069J21Rik|AA930106|D6Ertd404e|D6Ertd772e|T6bp|TXBP151	Tax1 (human T cell leukemia virus type I) binding protein 1	protein-coding
mm_170385.1	chr18	60376023	60376035	+	1	NA	promoter-TSS (NM_001146275)	promoter-TSS (NM_001146275)	0	NM_021792	60440	Mm.261140	NM_021792	ENSMUSG00000054072	Iigp1	2900074L10Rik|AI046432|AW111922|Ifgga1|Iigp|Irga6	interferon inducible GTPase 1	protein-coding
mm_154582.1	chrX	7572667	7572671	+	1	NA	promoter-TSS (NR_029473)	promoter-TSS (NR_029473)	-931	NR_029473	78185	Mm.160055	NR_029473	ENSMUSG00000039545	Ppp1r3fos	4930524L23Rik	protein phosphatase 1, regulatory subunit 3F, opposite strand	ncRNA
mm_51259.1	chr6	72097375	72097386	+	1	NA	promoter-TSS (NM_011375)	promoter-TSS (NM_011375)	-228	NM_001035228	20454	Mm.38248	NM_011375	ENSMUSG00000056091	St3gal5	3S-T|Siat9|[a]2	ST3 beta-galactoside alpha-2,3-sialyltransferase 5	protein-coding
mm_41352.1	chr5	90504354	90504396	+	1	NA	exon (NM_007423, exon 10 of 15)	exon (NM_007423, exon 10 of 15)	13661	NM_007423	11576	Mm.358570	NM_007423	ENSMUSG00000054932	Afp	-	alpha fetoprotein	protein-coding
mm_141585.1	chr17	32403527	32403535	-	1	NA	promoter-TSS (NM_178785)	promoter-TSS (NM_178785)	50	NM_178785	320484	Mm.122284	NM_178785	ENSMUSG00000052142	Rasal3	A430107D22Rik	RAS protein activator like 3	protein-coding
mm_82506.1	chr9	20480906	20480919	-	1	NA	intron (NM_146221, intron 1 of 6)	intron (NM_146221, intron 1 of 6)	11834	NM_146221	235028	Mm.297660	NM_146221	ENSMUSG00000059475	Zfp426	2900057C04Rik|KRAB1|Zfo61|Zfp68-rs1|Znf426|mKIAA4237	zinc finger protein 426	protein-coding
mm_27362.1	chr3	50431203	50431218	-	1	NA	intron (NM_011990, intron 3 of 11)	intron (NM_011990, intron 3 of 11)	12403	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_18716.1	chr2	72442928	72442945	-	1	NA	TTS (NM_023057)	TTS (NM_023057)	-33283	NM_025866	66953	Mm.270676	NM_025866	ENSMUSG00000055612	Cdca7	2310021G01Rik|AU044109|JPO1	cell division cycle associated 7	protein-coding
mm_105695.1	chr11	107915007	107915039	-	1	NA	promoter-TSS (NM_001199301)	promoter-TSS (NM_001199301)	32	NM_001199301	140723	Mm.87663	NM_080644	ENSMUSG00000040373	Cacng5	-	calcium channel, voltage-dependent, gamma subunit 5	protein-coding
mm_80728.1	chr9	92608164	92608176	+	1	NA	3' UTR (NM_011961, exon 19 of 19)	3' UTR (NM_011961, exon 19 of 19)	-65301	NR_029474	78575	Mm.407669	NR_029474	ENSMUSG00000103622	B430319G15Rik	D530025C14Rik	RIKEN cDNA B430319G15 gene	ncRNA
mm_53559.1	chr6	136954522	136954529	+	1	NA	promoter-TSS (NM_023898)	promoter-TSS (NM_023898)	2	NM_023898	78600	Mm.290622	NM_023898	ENSMUSG00000064330	Pde6h	A930033D18Rik|PDEgamma	phosphodiesterase 6H, cGMP-specific, cone, gamma	protein-coding
mm_52657.1	chr6	117879964	117879982	+	1	NA	Intergenic	Intergenic	16896	NM_001001792	22685	Mm.249661	NM_008616	ENSMUSG00000042097	Zfp239	Mok-2|Mok2|Znf239	zinc finger protein 239	protein-coding
mm_31065.1	chr4	41316840	41316848	+	1	NA	Intergenic	Intergenic	-1943	NM_026893	68970	Mm.28891	NM_026893	ENSMUSG00000028436	Dcaf12	1500001L20Rik|5830424K06Rik|AA420338|AI851081|Wdr40a	DDB1 and CUL4 associated factor 12	protein-coding
mm_56107.1	chr6	87496280	87496332	-	1	NA	promoter-TSS (NM_175476)	promoter-TSS (NM_175476)	21	NR_104483	232201	Mm.119564	NM_175476	ENSMUSG00000030047	Arhgap25	A130039I20Rik	Rho GTPase activating protein 25	protein-coding
mm_49319.1	chr6	18848698	18848709	+	1	NA	promoter-TSS (NM_133939)	promoter-TSS (NM_133939)	68	NM_133939	76522	Mm.275158	NM_133939	ENSMUSG00000044155	Lsm8	2010003I05Rik|AW214405|Naa38	LSM8 homolog, U6 small nuclear RNA associated	protein-coding
mm_66648.1	chr7	45694186	45694194	-	1	NA	exon (NM_001289693, exon 7 of 7)	exon (NM_001289693, exon 7 of 7)	212	NM_001271578	56546	Mm.56914	NM_019934	ENSMUSG00000040364	Sec1	Fut10|Fut3	secretory blood group 1	protein-coding
mm_52024.1	chr6	94699215	94699224	+	1	NA	intron (NM_008377, intron 1 of 18)	intron (NM_008377, intron 1 of 18)	926	NM_008377	16206	Mm.245210	NM_008377	ENSMUSG00000030029	Lrig1	D6Bwg0781e|Img|LIG-1	leucine-rich repeats and immunoglobulin-like domains 1	protein-coding
mm_29272.1	chr3	107517770	107517792	-	1	NA	5' UTR (NM_001293689, exon 1 of 12)	5' UTR (NM_001293689, exon 1 of 12)	237	NM_001293689	229706	Mm.212867	NM_172271	ENSMUSG00000027894	Slc6a17	D130012J15Rik|Ntt4	solute carrier family 6 (neurotransmitter transporter), member 17	protein-coding
mm_36865.1	chr4	107058865	107058876	-	1	NA	intron (NM_025500, intron 5 of 6)	intron (NM_025500, intron 5 of 6)	7996	NM_025500	56280	Mm.29517	NM_025500	ENSMUSG00000028622	Mrpl37	2300004O14Rik|AI132596|MRP-L2|Rpml2	mitochondrial ribosomal protein L37	protein-coding
mm_127563.1	chr15	102204016	102204075	+	1	NA	promoter-TSS (NM_001289690)	promoter-TSS (NM_001289690)	400	NM_001289691	68744	Mm.352945	NM_153194	ENSMUSG00000046897	Zfp740	1110034O07Rik|AW548228|Znf740	zinc finger protein 740	protein-coding
mm_111494.1	chr12	99172420	99172421	-	1	NA	Intergenic	B3|SINE|B2	-9612	NR_038130	67639	Mm.87374	NR_038130		4930474N09Rik	-	RIKEN cDNA 4930474N09 gene	ncRNA
mm_39578.1	chr5	23434536	23434554	+	1	NA	promoter-TSS (NR_040469)	promoter-TSS (NR_040469)	116	NM_026984	69188	Mm.205190	NM_026984	ENSMUSG00000029004	Kmt2e	1810033J14Rik|9530077A04Rik|D230038D11Rik|Mll5|NKp44L	lysine (K)-specific methyltransferase 2E	protein-coding
mm_62676.1	chr7	109519140	109519242	+	1	NA	promoter-TSS (NR_028079)	promoter-TSS (NR_028079)	-4	NM_011975	26451	Mm.305750	NM_011975	ENSMUSG00000046364	Rpl27a	L27'|L27A|L29	ribosomal protein L27A	protein-coding
mm_30036.1	chr3	135691412	135691417	-	1	NA	5' UTR (NM_008689, exon 1 of 25)	5' UTR (NM_008689, exon 1 of 25)	133	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_150709.1	chr19	42550937	42550940	+	1	NA	intron (NM_177464, intron 1 of 6)	intron (NM_177464, intron 1 of 6)	32133	NM_177464	52013	Mm.254169	NM_177464	ENSMUSG00000025184	R3hcc1l	1700036B12Rik|AI450607|C10orf28|D19Ertd386e|GIDRP86|Gidrp88	R3H domain and coiled-coil containing 1 like	protein-coding
mm_156929.1	chrX	169320610	169320634	+	1	NA	promoter-TSS (NM_001331050)	promoter-TSS (NM_001331050)	-250	NM_001331049	15159	Mm.284033	NM_008222	ENSMUSG00000031352	Hccs	-	holocytochrome c synthetase	protein-coding
mm_58063.1	chr6	136872732	136872749	-	1	NA	exon (NM_008597, exon 4 of 4)	exon (NM_008597, exon 4 of 4)	3083	NM_008597	17313	Mm.243085	NM_008597	ENSMUSG00000030218	Mgp	Mglap	matrix Gla protein	protein-coding
mm_39804.1	chr5	30623284	30623309	+	1	NA	3' UTR (NM_010608, exon 2 of 2)	3' UTR (NM_010608, exon 2 of 2)	-24640	NR_049199	100885838		NR_049199	ENSMUSG00000093710	Mir5625	Gm23930|mmu-mir-5625	microRNA 5625	ncRNA
mm_14785.1	chr2	145860162	145860175	+	1	NA	exon (NM_028724, exon 9 of 13)	exon (NM_028724, exon 9 of 13)	-43073	NM_026425	67877	Mm.151168	NM_026425	ENSMUSG00000002728	Naa20	1500004D14Rik|2900026I01Rik|AU041458|D2Ertd186e|Nat5	N(alpha)-acetyltransferase 20, NatB catalytic subunit	protein-coding
mm_4793.1	chr1	184728951	184728960	+	1	NA	intron (NM_008250, intron 3 of 3)	intron (NM_008250, intron 3 of 3)	3538	NM_008250	15284	Mm.1347	NM_008250	ENSMUSG00000039377	Hlx	Hlx1	H2.0-like homeobox	protein-coding
mm_169533.1	chr14	92603271	92603290	-	1	NA	Intergenic	Intergenic	1285608	NM_001271800	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding
mm_94998.1	chr11	31872226	31872264	+	1	NA	5' UTR (NM_026252, exon 1 of 10)	5' UTR (NM_026252, exon 1 of 10)	1305	NM_026252	67579	Mm.339792	NM_026252	ENSMUSG00000020300	Cpeb4	Cpe-bp4|Cpeb-4|mCPEB-4	cytoplasmic polyadenylation element binding protein 4	protein-coding
mm_84175.1	chr9	59949327	59949338	-	1	NA	intron (NM_013708, intron 1 of 7)	intron (NM_013708, intron 1 of 7)	747	NM_013708	23958	Mm.103641	NM_013708	ENSMUSG00000032292	Nr2e3	A930035N01Rik|PNR|RNR|rd7	nuclear receptor subfamily 2, group E, member 3	protein-coding
mm_65120.1	chr7	19404083	19404130	-	1	NA	promoter-TSS (NM_001286039)	promoter-TSS (NM_001286039)	-2	NM_001286039	232943	Mm.213403	NM_146182	ENSMUSG00000040714	Klc3	BC017147|Klct	kinesin light chain 3	protein-coding
mm_45188.1	chr5	52115806	52115848	-	1	NA	Intergenic	CpG	20190	NR_105845	102466648		NR_105845	ENSMUSG00000098726	Mir6417	Gm27334|mmu-mir-6417	microRNA 6417	ncRNA
mm_56653.1	chr6	113434500	113434514	-	1	NA	5' UTR (NM_178373, exon 2 of 6)	5' UTR (NM_178373, exon 2 of 6)	1248	NM_178373	14311	Mm.10026	NM_178373	ENSMUSG00000030278	Cidec	CIDE-3|Fsp27	cell death-inducing DFFA-like effector c	protein-coding
mm_155435.1	chrX	73494632	73494642	+	1	NA	exon (NM_007542, exon 8 of 8)	exon (NM_007542, exon 8 of 8)	-8449	NM_001310537	320707	Mm.210095	NM_177236	ENSMUSG00000031376	Atp2b3	6430519O13Rik|Pmca3	ATPase, Ca++ transporting, plasma membrane 3	protein-coding
mm_16787.1	chr2	10028958	10028974	-	1	NA	intron (NM_027748, intron 2 of 6)	intron (NM_027748, intron 2 of 6)	19643	NM_027748	209361	Mm.86343	NM_027748	ENSMUSG00000025782	Taf3	140kDa|4933439M23Rik|AW539625|TAF140|TAFII-140|TAFII140|mTAFII140	TATA-box binding protein associated factor 3	protein-coding
mm_102765.1	chr11	67965607	67965630	-	1	NA	promoter-TSS (NM_018768)	promoter-TSS (NM_018768)	24	NM_027963	71860	Mm.441823	NM_027963	ENSMUSG00000020904	Cfap52	1700019F09Rik|4933417B11Rik|WDRPUH|Wdr16	cilia and flagella associated protein 52	protein-coding
mm_28386.1	chr3	90009289	90009306	-	1	NA	exon (NM_001165987, exon 23 of 25)	exon (NM_001165987, exon 23 of 25)	1913	NR_106129	102465771		NR_106129	ENSMUSG00000098397	Mir7669	Gm27996|mmu-mir-7669	microRNA 7669	ncRNA
mm_128016.1	chr15	22714891	22714891	-	1	NA	promoter-TSS (NM_001165971)	promoter-TSS (NM_001165971)	93	NM_001165971	545091	Mm.475598	NM_001165971		Gm5803	EG545091	predicted gene 5803	protein-coding
mm_68947.1	chr7	126562640	126562660	-	1	NA	exon (NM_146200, exon 8 of 21)	exon (NM_146200, exon 8 of 21)	3716	NM_146200	56347	Mm.22776	NM_146200	ENSMUSG00000030738	Eif3c	110kDa|3230401O13Rik|Eif3s8|NIPIL(A3)|NipilA3|Xs|Xsl	eukaryotic translation initiation factor 3, subunit C	protein-coding
mm_125398.1	chr15	41447420	41447431	+	1	NA	promoter-TSS (NM_001130166)	promoter-TSS (NM_001130166)	-57	NM_001130166	170719	Mm.254267	NM_130885	ENSMUSG00000022307	Oxr1	2210416C20Rik|C7|C7B	oxidation resistance 1	protein-coding
mm_105815.1	chr11	111800871	111800880	-	1	NA	Intergenic	Intergenic	734711	NM_008425	16518	Mm.4951	NM_008425	ENSMUSG00000041695	Kcnj2	IRK1|Kcnf1|Kir2.1	potassium inwardly-rectifying channel, subfamily J, member 2	protein-coding
mm_53969.1	chr6	6104779	6104783	-	1	NA	intron (NM_015829, intron 11 of 17)	intron (NM_015829, intron 11 of 17)	112392	NM_015829	50799	Mm.24513	NM_015829	ENSMUSG00000015112	Slc25a13	AI785475|Ctrn	solute carrier family 25 (mitochondrial carrier, adenine nucleotide translocator), member 13	protein-coding
mm_81592.1	chr9	110477081	110477097	+	1	NA	promoter-TSS (NM_001163569)	promoter-TSS (NM_001163569)	95	NM_001163569	16578	Mm.42170	NM_010628	ENSMUSG00000032489	Kif9	-	kinesin family member 9	protein-coding
mm_30476.1	chr3	154711322	154711329	-	1	NA	exon (NM_175176, exon 1 of 7)	exon (NM_175176, exon 1 of 7)	192	NM_175176	209601	Mm.331454	NM_175176	ENSMUSG00000078161	Erich3	1700013E18Rik|4922501L14Rik|5031409G23Rik|AI596448|Gm133	glutamate rich 3	protein-coding
mm_92991.1	chr10	86702231	86702241	-	1	NA	intron (NM_011631, intron 4 of 17)	intron (NM_011631, intron 4 of 17)	3208	NM_011631	22027	Mm.87773	NM_011631	ENSMUSG00000020048	Hsp90b1	ERp99|GRP94|TA-3|Targ2|Tra-1|Tra1|endoplasmin|gp96	heat shock protein 90, beta (Grp94), member 1	protein-coding
mm_108736.1	chr12	88360632	88360657	+	1	NA	promoter-TSS (NM_028105)	promoter-TSS (NM_028105)	130	NM_001277297	72113	Mm.181387	NM_028105	ENSMUSG00000021044	Adck1	2610005A10Rik	aarF domain containing kinase 1	protein-coding
mm_124518.1	chr14	121965129	121965139	-	1	NA	promoter-TSS (NM_183031)	promoter-TSS (NM_183031)	59	NM_183031	321019	Mm.265618	NM_183031	ENSMUSG00000051212	Gpr183	Ebi2	G protein-coupled receptor 183	protein-coding
mm_81689.1	chr9	111146696	111146724	+	1	NA	intron (NM_027742, intron 3 of 13)	intron (NM_027742, intron 3 of 13)	28599	NM_001164838	71268	Mm.302287	NM_027742	ENSMUSG00000032497	Lrrfip2	5133400F20Rik|AI850587	leucine rich repeat (in FLII) interacting protein 2	protein-coding
mm_12141.1	chr2	61776664	61776691	+	1	NA	exon (NM_021526, exon 8 of 12)	exon (NM_021526, exon 8 of 12)	-27776	NM_009322	21375	Mm.308525	NM_009322	ENSMUSG00000035033	Tbr1	-	T-box brain gene 1	protein-coding
mm_61286.1	chr7	67495064	67495067	+	1	NA	Intergenic	Intergenic	-122207	NM_001291195	17258	Mm.132788	NM_001033713	ENSMUSG00000030557	Mef2a	A430079H05Rik	myocyte enhancer factor 2A	protein-coding
mm_118757.1	chr14	22371948	22371953	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	170848	NR_046307	74896	Mm.444661	NR_046307		4930405A10Rik	4930456G20Rik	RIKEN cDNA 4930405A10 gene	ncRNA
mm_90954.1	chr10	13193097	13193155	-	1	NA	promoter-TSS (NM_181470)	promoter-TSS (NM_181470)	11	NM_181470	353258	Mm.117581	NM_181470	ENSMUSG00000019814	Ltv1	2610020N02Rik	LTV1 ribosome biogenesis factor	protein-coding
mm_121625.1	chr14	8317597	8317604	-	1	NA	Intergenic	Intergenic	-7824	NM_183187	268709	Mm.256058	NM_183187	ENSMUSG00000021750	Fam107a	DRR1	family with sequence similarity 107, member A	protein-coding
mm_59389.1	chr7	26386903	26386915	+	1	NA	intron (NM_001042612, intron 1 of 8)	RLTR9D|LTR|ERVK	7334	NM_001042612	330490	Mm.212174	NM_194062	ENSMUSG00000040614	Nlrp9c	AA636537|BB062542|Nalp-zeta|Nalp9c	NLR family, pyrin domain containing 9C	protein-coding
mm_102563.1	chr11	61488116	61488130	-	1	NA	TTS (NM_001291037)	TTS (NM_001291037)	2679	NM_029568	76293	Mm.272278	NM_029568	ENSMUSG00000042436	Mfap4	1110007F23Rik	microfibrillar-associated protein 4	protein-coding
mm_105676.1	chr11	107470760	107470777	-	1	NA	promoter-TSS (NM_145823)	promoter-TSS (NM_145823)	-48	NM_145823	71795	Mm.397413	NM_145823	ENSMUSG00000040430	Pitpnc1	1110020B03Rik|5830436L09Rik|AI662802|AI851387|C330017I21Rik|Dnr411|RDGBB|RDGBB1|rdgB-beta	phosphatidylinositol transfer protein, cytoplasmic 1	protein-coding
mm_111812.1	chr12	105523474	105523487	-	1	NA	Intergenic	Intergenic	10047	NR_102381	104932	Mm.274150	NR_102381		AU015791	-	expressed sequence AU015791	ncRNA
mm_11583.1	chr2	33130890	33130899	+	1	NA	Intergenic	Intergenic	-43690	NM_178888	99326	Mm.41290	NM_178888	ENSMUSG00000038860	Garnl3	AW120551	GTPase activating RANGAP domain-like 3	protein-coding
mm_85883.1	chr9	111031096	111031104	-	1	NA	exon (NM_008522, exon 13 of 17)	exon (NM_008522, exon 13 of 17)	11808	NM_008522	17002	Mm.282359	NM_008522	ENSMUSG00000032496	Ltf	Csp82|Lf|MMS10R|Ms10r	lactotransferrin	protein-coding
mm_7822.1	chr1	132010606	132010608	-	1	NA	intron (NM_007923, intron 1 of 4)	intron (NM_007923, intron 1 of 4)	3002	NM_007923	13714	Mm.254233	NM_007923	ENSMUSG00000026436	Elk4	2310011G17Rik|A130026I01Rik|BB162516|SAP-1|Sap1	ELK4, member of ETS oncogene family	protein-coding
mm_167800.1	chr9	123927878	123927887	-	1	NA	Intergenic	Intergenic	40810	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_96889.1	chr11	70436312	70436348	+	1	NA	intron (NM_001271359, intron 3 of 15)	intron (NM_001271359, intron 3 of 15)	-1925	NR_106064	102465670		NR_106064	ENSMUSG00000099109	Mir7115	Gm27902|mmu-mir-7115	microRNA 7115	ncRNA
mm_156670.1	chrX	159210508	159210517	+	1	NA	Intergenic	Intergenic	-45270	NM_148945	110651	Mm.328476	NM_148945	ENSMUSG00000031309	Rps6ka3	MAPKAPK-1b|MPK-9|Rsk2|S6K-alpha3|p90RSK3|pp90RSK2	ribosomal protein S6 kinase polypeptide 3	protein-coding
mm_125490.1	chr15	54752983	54753017	+	1	NA	3' UTR (NM_010930, exon 5 of 5)	3' UTR (NM_010930, exon 5 of 5)	7072	NM_010930	18133	Mm.5167	NM_010930	ENSMUSG00000037362	Nov	C130088N23Rik|CCN3	nephroblastoma overexpressed gene	protein-coding
mm_70421.1	chr8	11464603	11464631	+	1	NA	intron (NM_011227, intron 1 of 1)	intron (NM_011227, intron 1 of 1)	-13312	NR_126558	102132	Mm.37632	NR_126558	ENSMUSG00000096957	E230013L22Rik	AI645545	RIKEN cDNA E230013L22 gene	ncRNA
mm_49264.1	chr6	17464133	17464149	+	1	NA	5' UTR (NM_008591, exon 1 of 22)	5' UTR (NM_008591, exon 1 of 22)	184	NM_008591	17295	Mm.86844	NM_008591	ENSMUSG00000009376	Met	AI838057|HGF|HGFR|Par4|c-Met	met proto-oncogene	protein-coding
mm_20038.1	chr2	119898340	119898375	-	1	NA	intron (NM_001164274, intron 1 of 22)	intron (NM_001164274, intron 1 of 22)	1129	NM_013720	29808	Mm.87532	NM_013720	ENSMUSG00000033943	Mga	AV312082|C130042M01Rik|C80739|D030062C11Rik|Mad5	MAX gene associated	protein-coding
mm_96645.1	chr11	69339988	69339989	+	1	NA	promoter-TSS (NR_027827)	promoter-TSS (NR_027827)	-781	NR_027827	80515	Mm.5324	NM_020591	ENSMUSG00000043419	Chd3os	2310043C11Rik|A030009H04Rik|AA589459|AB041807|MNCb-2875|RNF21	chromodomain helicase DNA binding protein 3, opposite strand	ncRNA
mm_173357.1	chrY	90819323	90819330	+	1	NA	Intergenic	(CAGAGA)n|Simple_repeat|Simple_repeat	20080	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_623.1	chr1	40224986	40225043	+	1	NA	promoter-TSS (NM_008362)	promoter-TSS (NM_008362)	-66	NM_008362	16177	Mm.896	NM_008362	ENSMUSG00000026072	Il1r1	CD121a|CD121b|IL-1R1|IL-iR|Il1r-1	interleukin 1 receptor, type I	protein-coding
mm_63557.1	chr7	128081634	128081646	+	1	NA	exon (NM_008401, exon 8 of 30)	exon (NM_008401, exon 8 of 30)	19000	NM_008401	16409	Mm.262106	NM_008401	ENSMUSG00000030786	Itgam	CD11b/CD18|CR3|CR3A|Cd11b|F730045J24Rik|Ly-40|MAC1|Mac-1|Mac-1a	integrin alpha M	protein-coding
mm_11523.1	chr2	32621530	32621553	+	1	NA	promoter-TSS (NM_001198790)	promoter-TSS (NM_001198790)	-217	NM_001198790	11636	Mm.29189	NM_021515	ENSMUSG00000026817	Ak1	Ak-1|B430205N08Rik	adenylate kinase 1	protein-coding
mm_10403.1	chr2	13578404	13578464	+	1	NA	exon (NM_011701, exon 3 of 9)	exon (NM_011701, exon 3 of 9)	4123	NM_011701	22352	Mm.268000	NM_011701	ENSMUSG00000026728	Vim	-	vimentin	protein-coding
mm_64137.1	chr7	141195048	141195083	+	1	NA	promoter-TSS (NM_153777)	promoter-TSS (NM_153777)	-78	NM_153777	70552	Mm.45104	NM_153777	ENSMUSG00000038637	Lrrc56	5730427C23Rik|BB110509|mFLJ00101	leucine rich repeat containing 56	protein-coding
mm_54069.1	chr6	14754717	14754729	-	1	NA	exon (NM_080464, exon 1 of 4)	exon (NM_080464, exon 1 of 4)	551	NM_080464	140491	Mm.209429	NM_080464	ENSMUSG00000042717	Ppp1r3a	GM|RG1|RGL	protein phosphatase 1, regulatory (inhibitor) subunit 3A	protein-coding
mm_76858.1	chr8	105413474	105413526	-	1	NA	promoter-TSS (NM_177791)	promoter-TSS (NM_177791)	2	NM_177791	279499	Mm.67628	NM_177791	ENSMUSG00000051648	Kctd19	4922504H04Rik	potassium channel tetramerisation domain containing 19	protein-coding
mm_63421.1	chr7	127471460	127471483	+	1	NA	promoter-TSS (NM_145589)	promoter-TSS (NM_145589)	-143	NM_145589	233895	Mm.44183	NM_145589	ENSMUSG00000030822	Prr14	BC006909	proline rich 14	protein-coding
mm_20363.1	chr2	128318880	128318889	-	1	NA	intron (NR_028590, intron 2 of 2)	ID_B1|SINE|B4	110467	NR_028591	100043424	Mm.297222	NR_028589		Gm14005	OTTMUSG00000015351	predicted gene 14005	ncRNA
mm_82156.1	chr9	123781187	123781198	+	1	NA	3' UTR (NM_001166625, exon 4 of 4)	3' UTR (NM_001166625, exon 4 of 4)	13981	NM_001166625	12769	Mm.440604	NM_009913	ENSMUSG00000029530	Ccr9	A130091K22Rik|Cmkbr10|GPR-9-6	chemokine (C-C motif) receptor 9	protein-coding
mm_127106.1	chr15	97843675	97843698	+	1	NA	intron (NM_001204275, intron 1 of 24)	intron (NM_001204275, intron 1 of 24)	816	NM_001204279	56233	Mm.384027	NM_019572	ENSMUSG00000022475	Hdac7	5830434K02Rik|HD7|HD7a|Hdac7a|mFLJ00062	histone deacetylase 7	protein-coding
mm_139833.1	chr17	69156507	69156514	+	1	NA	promoter-TSS (NM_013813)	promoter-TSS (NM_013813)	-300	NM_013813	13823	Mm.131135	NM_013813	ENSMUSG00000024044	Epb41l3	4.1B|DAL1P|Dal1|Epb4.1l3|NBL3	erythrocyte membrane protein band 4.1 like 3	protein-coding
mm_90324.1	chr10	127070375	127070421	+	1	NA	promoter-TSS (NR_040660)	promoter-TSS (NR_040660)	-83	NR_040660	100504703	Mm.387029	NR_040660		A730063M14Rik	-	RIKEN cDNA A730063M14 gene	ncRNA
mm_49342.1	chr6	21949635	21949683	+	1	NA	promoter-TSS (NM_023626)	promoter-TSS (NM_023626)	44	NM_023626	71777	Mm.39999	NM_023626	ENSMUSG00000029670	Ing3	1300013A07Rik|P47ING3	inhibitor of growth family, member 3	protein-coding
mm_35896.1	chr4	49549524	49549538	-	1	NA	promoter-TSS (NM_144903)	promoter-TSS (NM_144903)	15	NM_144903	230163	Mm.482116	NM_144903	ENSMUSG00000028307	Aldob	Aldo-2|Aldo2|BC016435	aldolase B, fructose-bisphosphate	protein-coding
mm_83313.1	chr9	44113471	44113528	-	1	NA	promoter-TSS (NM_153762)	promoter-TSS (NM_153762)	-448	NM_153762	213211	Mm.392032	NM_153762	ENSMUSG00000053128	Rnf26	8030450I18Rik	ring finger protein 26	protein-coding
mm_70826.1	chr8	23140102	23140127	+	1	NA	exon (NM_001282148, exon 5 of 6)	exon (NM_001282148, exon 5 of 6)	1084	NM_001310437	11733	Mm.334444	NM_031158	ENSMUSG00000031543	Ank1	Ank-1|nb|pale	ankyrin 1, erythroid	protein-coding
mm_7030.1	chr1	87099446	87099454	-	1	NA	exon (NM_001081082, exon 9 of 11)	exon (NM_001081082, exon 9 of 11)	2156	NM_001081082	76768	Mm.58068	NM_001081082	ENSMUSG00000079440	Alpi	2010001C14Rik|Akp6|gIAP	alkaline phosphatase, intestinal	protein-coding
mm_115785.1	chr13	19337036	19337044	-	1	NA	Intergenic	Intergenic	58773	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_94847.1	chr11	23769811	23769821	+	1	NA	intron (NM_009044, intron 1 of 9)	intron (NM_009044, intron 1 of 9)	1154	NM_009044	19696	Mm.4869	NM_009044	ENSMUSG00000020275	Rel	c-Rel	reticuloendotheliosis oncogene	protein-coding
mm_8432.1	chr1	152615162	152615167	-	1	NA	intron (NM_001346119, intron 2 of 17)	LTR90A|LTR|LTR	10053	NM_016846	19731	Mm.245270	NM_016846	ENSMUSG00000026482	Rgl1	Rgl|mKIAA0959	ral guanine nucleotide dissociation stimulator,-like 1	protein-coding
mm_166545.1	chr6	35882530	35882536	+	1	NA	Intergenic	MRLTR33|LTR|ERVK	-342645	NM_008098	14489	Mm.182746	NM_008098	ENSMUSG00000029840	Mtpn	5033418D15Rik|Gcdp|V1	myotrophin	protein-coding
mm_1984.1	chr1	87068002	87068018	+	1	NA	Intergenic	Intergenic	21918	NM_007433	11650	Mm.195224	NM_007433	ENSMUSG00000026246	Alppl2	Akp5|C77216|D1Ertd816e|EAP	alkaline phosphatase, placental-like 2	protein-coding
mm_102192.1	chr11	54310138	54310143	-	1	NA	intron (NM_001033597, intron 1 of 20)	intron (NM_001033597, intron 1 of 20)	-4763	NM_001033599	216739	Mm.267478	NM_144823	ENSMUSG00000020333	Acsl6	A330035H04Rik|AW050338|Facl6|LACS|Lacsl|mKIAA0837	acyl-CoA synthetase long-chain family member 6	protein-coding
mm_166601.1	chr6	67533306	67533338	-	1	NA	TTS (NM_020047)	TTS (NM_020047)	2500	NM_020047	56753	Mm.439913	NM_020047	ENSMUSG00000051397	Tacstd2	C80403|EGP-1|GA733-1|Ly97|TROP2	tumor-associated calcium signal transducer 2	protein-coding
mm_128363.1	chr15	41830764	41830770	-	1	NA	promoter-TSS (NM_001130164)	promoter-TSS (NM_001130164)	-191	NM_001130164	170719	Mm.254267	NM_130885	ENSMUSG00000022307	Oxr1	2210416C20Rik|C7|C7B	oxidation resistance 1	protein-coding
mm_62493.1	chr7	101969637	101969674	+	1	NA	promoter-TSS (NM_133947)	promoter-TSS (NM_133947)	-188	NM_133947	101706	Mm.27259	NM_133947	ENSMUSG00000066306	Numa1	6720401E04Rik|AA764025|AL022610|AU014979|NuMA	nuclear mitotic apparatus protein 1	protein-coding
mm_144317.1	chr18	12651961	12651990	+	1	NA	intron (NM_028341, intron 1 of 13)	AT_rich|Low_complexity|Low_complexity	8442	NM_028341	72747	Mm.52526	NM_028341	ENSMUSG00000024424	Ttc39c	1700008N02Rik|2810439F02Rik	tetratricopeptide repeat domain 39C	protein-coding
mm_439.1	chr1	34750585	34750652	+	1	NA	Intergenic	CpG	-51104	NM_183019	226970	Mm.41604	NM_183019	ENSMUSG00000037509	Arhgef4	9330140K16Rik|Asef|ENSMUSG00000070955	Rho guanine nucleotide exchange factor (GEF) 4	protein-coding
mm_45881.1	chr5	88328455	88328475	-	1	NA	exon (NM_008644, exon 3 of 3)	exon (NM_008644, exon 3 of 3)	11153	NM_008644	17830	Mm.200411	NM_008644	ENSMUSG00000064156	Prol1	Muc10	proline rich, lacrimal 1	protein-coding
mm_132905.1	chr16	48872679	48872688	+	1	NA	promoter-TSS (NM_181596)	promoter-TSS (NM_181596)	75	NM_181596	245195	Mm.231288	NM_181596	ENSMUSG00000022651	Retnlg	Fizz3|Relmg|Xcp1	resistin like gamma	protein-coding
mm_171255.1	chr3	81689555	81689559	+	1	NA	Intergenic	Intergenic	-112468	NR_138586	320566	Mm.208417	NR_138586	ENSMUSG00000103695	A830029E22Rik	-	RIKEN cDNA A830029E22 gene	ncRNA
mm_19316.1	chr2	90556274	90556317	-	1	NA	intron (NM_008982, intron 1 of 23)	intron (NM_008982, intron 1 of 23)	24352	NM_008982	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_108180.1	chr12	76417599	76417641	+	1	NA	promoter-TSS (NM_001163103)	promoter-TSS (NM_001163103)	21	NM_001163103	210762	Mm.292354	NM_001163103	ENSMUSG00000052221	Ppp1r36	Gm70	protein phosphatase 1, regulatory subunit 36	protein-coding
mm_143548.1	chr17	74017356	74017361	-	1	NA	TTS (NM_053188)	TTS (NM_053188)	30558	NM_053188	94224	Mm.38933	NM_053188	ENSMUSG00000038541	Srd5a2	5ART2|S5AR 2	steroid 5 alpha-reductase 2	protein-coding
mm_134160.1	chr16	10791634	10791640	-	1	NA	promoter-TSS (NM_013638)	promoter-TSS (NM_013638)	468	NM_008933	19119	Mm.325769	NM_008933	ENSMUSG00000038015	Prm2	AI528784|Prm-2	protamine 2	protein-coding
mm_96788.1	chr11	69965655	69965695	+	1	NA	5' UTR (NM_016887, exon 1 of 4)	5' UTR (NM_016887, exon 1 of 4)	254	NM_016887	53624	Mm.281896	NM_016887	ENSMUSG00000018569	Cldn7	-	claudin 7	protein-coding
mm_35897.1	chr4	49593876	49593915	-	1	NA	intron (NM_025944, intron 1 of 1)	MER2|DNA|TcMar-Tigger	3975	NM_025944	67063	Mm.490285	NM_025944	ENSMUSG00000039611	Tmem246	2810432L12Rik|9330170P15Rik|AI835809	transmembrane protein 246	protein-coding
mm_23544.1	chr3	61364556	61364633	+	1	NA	promoter-TSS (NM_028712)	promoter-TSS (NM_028712)	87	NM_028712	74012	Mm.422674	NM_028712	ENSMUSG00000036894	Rap2b	4021402C18Rik|AA408554	RAP2B, member of RAS oncogene family	protein-coding
mm_89902.1	chr10	111164756	111164778	+	1	NA	promoter-TSS (NM_001003717)	promoter-TSS (NM_001003717)	-35	NM_001003717	237542	Mm.220204	NM_175489	ENSMUSG00000020189	Osbpl8	AA536976|AA536995|C730029P18Rik|D330025H14Rik|ORP-8	oxysterol binding protein-like 8	protein-coding
mm_156177.1	chrX	130339115	130339137	+	1	NA	intron (NM_172493, intron 26 of 26)	intron (NM_172493, intron 26 of 26)	589384	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diaph2	Dia3|Diap2|Drf2|E430022I22Rik	diaphanous related formin 2	protein-coding
mm_90950.1	chr10	13177990	13178004	-	1	NA	promoter-TSS (NM_029172)	promoter-TSS (NM_029172)	26	NM_029172	75122	Mm.159433	NM_029172	ENSMUSG00000019815	Zc2hc1b	4930519B02Rik|Fam164b	zinc finger, C2HC-type containing 1B	protein-coding
mm_117676.1	chr13	93674277	93674297	-	1	NA	promoter-TSS (NM_022884)	promoter-TSS (NM_022884)	15	NM_022884	64918	Mm.29981	NM_022884	ENSMUSG00000042118	Bhmt2	C81077|D13Ucla2	betaine-homocysteine methyltransferase 2	protein-coding
mm_1816.1	chr1	82316664	82316674	+	1	NA	promoter-TSS (NM_029777)	promoter-TSS (NM_029777)	90	NM_029777	76867	Mm.226994	NM_029777	ENSMUSG00000026142	Rhbdd1	4930418P06Rik|RRP4|mRHBDD1	rhomboid domain containing 1	protein-coding
mm_126977.1	chr15	93435918	93435935	+	1	NA	intron (NM_175363, intron 3 of 8)	intron (NM_175363, intron 3 of 8)	37462	NM_001285863	223828	Mm.74208	NM_146062	ENSMUSG00000036167	Pphln1	CR|HSPC206|HSPC232	periphilin 1	protein-coding
mm_105231.1	chr11	102316661	102316678	-	1	NA	intron (NM_001302955, intron 1 of 19)	CpG	618	NM_001044383	21429	Mm.2845	NM_011551	ENSMUSG00000020923	Ubtf	A930005G04Rik|NOR-90|Tcfubf|UBF|UBF-1|UBF1	upstream binding transcription factor, RNA polymerase I	protein-coding
mm_2795.1	chr1	130851534	130851544	+	1	NA	3' UTR (NM_011082, exon 11 of 11)	3' UTR (NM_011082, exon 11 of 11)	-14238	NM_026976	69169	Mm.46042	NM_026976	ENSMUSG00000042474	Fcmr	1810037B05Rik|Faim3|FcmuR|Toso	Fc fragment of IgM receptor	protein-coding
mm_40098.1	chr5	34573745	34573792	+	1	NA	promoter-TSS (NR_106111)	promoter-TSS (NR_106111)	104	NM_001331086	11518	Mm.289106	NM_013457	ENSMUSG00000029106	Add1	AI256389	adducin 1 (alpha)	protein-coding
mm_130810.1	chr15	101734404	101734412	-	1	NA	3' UTR (NM_019956, exon 9 of 9)	3' UTR (NM_019956, exon 9 of 9)	8689	NM_019956	56735	Mm.358677	NM_019956	ENSMUSG00000051879	Krt71	AA589543|Ca|Cal4|Cu|Krt2-6g|mK6irs|mK6irs1	keratin 71	protein-coding
mm_172478.1	chr7	48742142	48742152	-	1	NA	Intergenic	MMVL30-int|LTR|ERV1	-46856	NM_028031	243983	Mm.279116	NM_028031	ENSMUSG00000030471	Zdhhc13	2410004E01Rik|C530010M18|HIP3RP|Hip14l|kojak|skc4	zinc finger, DHHC domain containing 13	protein-coding
mm_47074.1	chr5	116591783	116591793	-	1	NA	promoter-TSS (NM_026886)	promoter-TSS (NM_026886)	29	NM_026886	68955	Mm.146779	NM_026886	ENSMUSG00000063919	Srrm4	1500001A10Rik|B230202K19Rik|bv|mKIAA1853|nSR100	serine/arginine repetitive matrix 4	protein-coding
mm_140391.1	chr17	87446146	87446150	+	1	NA	intron (NM_007589, intron 1 of 5)	CpG	787	NM_007589	12314	Mm.329243	NM_007589	ENSMUSG00000036438	Calm2	1500001E21Rik|AL024017	calmodulin 2	protein-coding
mm_76724.1	chr8	94876270	94876321	-	1	NA	promoter-TSS (NM_053246)	promoter-TSS (NM_053246)	17	NM_053246	114255	Mm.203949	NM_053246	ENSMUSG00000040631	Dok4	-	docking protein 4	protein-coding
mm_902.1	chr1	53784480	53784490	+	1	NA	intron (NM_133810, intron 1 of 7)	intron (NM_133810, intron 1 of 7)	730	NM_133810	98267	Mm.25559	NM_133810	ENSMUSG00000026094	Stk17b	3110009A03Rik|AI120141|Drak2	serine/threonine kinase 17b (apoptosis-inducing)	protein-coding
mm_146020.1	chr18	69519594	69519610	+	1	NA	intron (NM_013685, intron 5 of 19)	intron (NM_013685, intron 5 of 19)	173881	NM_001083967	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding
mm_130016.1	chr15	88687986	88687989	-	1	NA	3' UTR (NM_001033274, exon 13 of 13)	3' UTR (NM_001033274, exon 13 of 13)	46232	NM_001033274	223770	Mm.254438	NM_001033274	ENSMUSG00000022387	Brd1	1110059H06Rik|AI316859|mKIAA4191	bromodomain containing 1	protein-coding
mm_83000.1	chr9	36726141	36726155	-	1	NA	intron (NM_007691, intron 1 of 12)	intron (NM_007691, intron 1 of 12)	510	NM_007691	12649	Mm.16753	NM_007691	ENSMUSG00000032113	Chek1	C85740|Chk1|rad27	checkpoint kinase 1	protein-coding
mm_77066.1	chr8	109961912	109961933	-	1	NA	exon (NM_028584, exon 1 of 3)	exon (NM_028584, exon 1 of 3)	283	NM_212447	73608	Mm.86833	NM_028584	ENSMUSG00000001672	Marveld3	1810006A16Rik|AI642133|Marvd3|Mrvldc3	MARVEL (membrane-associating) domain containing 3	protein-coding
mm_2149.1	chr1	88138365	88138371	+	1	NA	intron (NM_145079, intron 1 of 5)	intron (NM_145079, intron 1 of 5)	3559	NM_145079	94284	Mm.300095	NM_145079	ENSMUSG00000054545	Ugt1a6a	UDPGT|UDPGT 1-6|UGT1-06|UGT1.6|Ugt1a6|Ugt1a7	UDP glucuronosyltransferase 1 family, polypeptide A6A	protein-coding
mm_63124.1	chr7	122969912	122969966	+	1	NA	promoter-TSS (NM_175023)	promoter-TSS (NM_175023)	520	NR_045614	73951	Mm.389936	NR_045614		4930413G21Rik	-	RIKEN cDNA 4930413G21 gene	ncRNA
mm_48359.1	chr5	139382921	139382949	-	1	NA	intron (NM_030258, intron 1 of 1)	intron (NM_030258, intron 1 of 1)	2268	NM_030258	80290	Mm.270003	NM_030258	ENSMUSG00000044197	Gpr146	BC003323|PGR8	G protein-coupled receptor 146	protein-coding
mm_33689.1	chr4	133417204	133417229	+	1	NA	intron (NM_016981, intron 4 of 11)	intron (NM_016981, intron 4 of 11)	47440	NR_039582	100628620		NR_039582	ENSMUSG00000092745	Mir5122	mmu-mir-5122|mu-mir-5122	microRNA 5122	ncRNA
mm_115650.1	chr13	12332060	12332104	-	1	NA	intron (NM_033268, intron 1 of 20)	intron (NM_033268, intron 1 of 20)	8650	NM_033268	11472	Mm.37638	NM_033268	ENSMUSG00000052374	Actn2	1110008F24Rik	actinin alpha 2	protein-coding
mm_58568.1	chr7	4793090	4793094	+	1	NA	intron (NM_009081, intron 1 of 4)	CpG	127	NM_009081	19943	Mm.379002	NM_009081	ENSMUSG00000030432	Rpl28	D7Wsu21e	ribosomal protein L28	protein-coding
mm_171550.1	chr4	147125169	147125177	+	1	NA	Intergenic	CpG	-50693	NM_001039209	195531	Mm.270762	NM_001039209	ENSMUSG00000078496	Zfp982	Gm13152|OTTMUSG00000010671	zinc finger protein 982	protein-coding
mm_144738.1	chr18	35562735	35562751	+	1	NA	intron (NM_010771, intron 1 of 14)	CpG	585	NM_010771	17184	Mm.215034	NM_010771	ENSMUSG00000037236	Matr3	1110061A14Rik|2810017I02Rik|AI841759|AW555618|D030046F20Rik|mKIAA0723	matrin 3	protein-coding
mm_118847.1	chr14	25664375	25664399	+	1	NA	3' UTR (NM_183208, exon 24 of 24)	3' UTR (NM_183208, exon 24 of 24)	-29783	NM_134084	105675	Mm.41656	NM_134084	ENSMUSG00000021868	Ppif	AW457192|CyP-D|CyP-F|CypD|PPIase	peptidylprolyl isomerase F (cyclophilin F)	protein-coding
mm_35680.1	chr4	43668801	43668831	-	1	NA	promoter-TSS (NM_175517)	promoter-TSS (NM_175517)	43	NM_175517	242408	Mm.440423	NM_175517	ENSMUSG00000043633	Fam221b	4930412F15Rik	family with sequence similarity 221, member B	protein-coding
mm_120073.1	chr14	57250114	57250122	+	1	NA	Intergenic	Intergenic	-116507	NM_001010937	14623	Mm.25652	NM_008128	ENSMUSG00000040055	Gjb6	AA958971|Cx30|D14Bwg0506e	gap junction protein, beta 6	protein-coding
mm_154053.1	chr19	55103093	55103099	-	1	NA	Intergenic	Intergenic	-3649	NM_008149	14732	Mm.210196	NM_008149	ENSMUSG00000024978	Gpam	GPAT|GPAT1	glycerol-3-phosphate acyltransferase, mitochondrial	protein-coding
mm_42987.1	chr5	123302414	123302426	+	1	NA	Intergenic	Intergenic	-42028	NM_029850	77045	Mm.151960	NM_029850	ENSMUSG00000029438	Bcl7a	4432415N06Rik|AI448316	B cell CLL/lymphoma 7A	protein-coding
mm_83451.1	chr9	45064460	45064495	-	1	NA	intron (NM_001093749, intron 2 of 5)	L2b|LINE|L2	9296	NM_001093749	319742	Mm.49611	NM_176993	ENSMUSG00000070305	Mpzl3	5430427F17Rik|A530065I17Rik|rc	myelin protein zero-like 3	protein-coding
mm_145499.1	chr18	60390829	60390844	+	1	NA	exon (NM_001146275, exon 3 of 3)	exon (NM_001146275, exon 3 of 3)	14807	NM_001146275	60440	Mm.261140	NM_021792	ENSMUSG00000054072	Iigp1	2900074L10Rik|AI046432|AW111922|Ifgga1|Iigp|Irga6	interferon inducible GTPase 1	protein-coding
mm_65885.1	chr7	29853612	29853683	-	1	NA	promoter-TSS (NM_173738)	promoter-TSS (NM_173738)	1	NM_173738	233057	Mm.296864	NM_173738	ENSMUSG00000050855	Zfp940	-	zinc finger protein 940	protein-coding
mm_12262.1	chr2	68959819	68959834	+	1	NA	intron (NM_172856, intron 3 of 9)	intron (NM_172856, intron 3 of 9)	98385	NM_001347161	241447	Mm.222222	NM_172856	ENSMUSG00000027035	Cers6	4732462C07Rik|AW544719|Lass6|T1L	ceramide synthase 6	protein-coding
mm_71616.1	chr8	57321002	57321013	+	1	NA	promoter-TSS (NM_010402)	promoter-TSS (NM_010402)	24	NM_010402	15111	Mm.430844	NM_010402	ENSMUSG00000038193	Hand2	AI225906|AI661148|Ehand2|Hed|Th2|Thing2|bHLHa26|dHAND	heart and neural crest derivatives expressed transcript 2	protein-coding
mm_52564.1	chr6	116226967	116226980	+	1	NA	intron (NM_026585, intron 14 of 30)	intron (NM_026585, intron 14 of 30)	18940	NM_026585	28006	Mm.28524	NM_026585	ENSMUSG00000024104	Washc2	A130095H06|C530005J20Rik|D6Wsu116e|Fam21	WASH complex subunit 2	protein-coding
mm_98705.1	chr11	96304081	96304092	+	1	NA	exon (NM_008268, exon 1 of 2)	exon (NM_008268, exon 1 of 2)	574	NM_008268	15413	Mm.207	NM_008268	ENSMUSG00000038700	Hoxb5	AI385717|Hox-2.1	homeobox B5	protein-coding
mm_47356.1	chr5	122779279	122779434	-	1	NA	promoter-TSS (NM_001199676)	promoter-TSS (NM_001199676)	54	NM_001199676	207565	Mm.289237	NM_145358	ENSMUSG00000029471	Camkk2	6330570N16Rik|AW061083|mKIAA0787	calcium/calmodulin-dependent protein kinase kinase 2, beta	protein-coding
mm_78097.1	chr9	18478383	18478401	+	1	NA	promoter-TSS (NM_028557)	promoter-TSS (NM_028557)	-3	NM_028557	73503	Mm.160088	NM_028557	ENSMUSG00000038691	Mbd3l1	1700070G05Rik|1700095H13Rik|Mbd3l	methyl-CpG binding domain protein 3-like 1	protein-coding
mm_31846.1	chr4	74258802	74258810	+	1	NA	intron (NM_144787, intron 1 of 21)	intron (NM_144787, intron 1 of 21)	6927	NM_144787	76804	Mm.209059	NM_144787	ENSMUSG00000028397	Kdm4c	2410141F18Rik|AA517467|Gasc1|Jmjd2c	lysine (K)-specific demethylase 4C	protein-coding
mm_37310.1	chr4	119294521	119294538	-	1	NA	promoter-TSS (NM_011732)	promoter-TSS (NM_011732)	-16	NM_011732	22608	Mm.258204	NM_011732	ENSMUSG00000028639	Ybx1	1700102N10Rik|C79409|EF1A|MSY1|Nsep1|YB-1|dbpB|mYB-1a	Y box protein 1	protein-coding
mm_68117.1	chr7	102100228	102100258	-	1	NA	promoter-TSS (NM_007491)	promoter-TSS (NM_007491)	-14	NM_007491	11875	Mm.2816	NM_007491	ENSMUSG00000070424	Art5	ARTC5|Yac-2	ADP-ribosyltransferase 5	protein-coding
mm_136677.1	chr17	6256891	6256938	+	1	NA	Intergenic	CpG	-13556	NM_001033178	77106	Mm.381893	NM_001033178	ENSMUSG00000038141	Tmem181a	5930418K15Rik|C76977|Gpr178|Tmem181|mKIAA1423	transmembrane protein 181A	protein-coding
mm_140277.1	chr17	84957994	84958018	+	1	NA	promoter-TSS (NM_011151)	promoter-TSS (NM_011151)	5	NM_001159496	19043	Mm.249695	NM_011151	ENSMUSG00000061130	Ppm1b	PP2CB	protein phosphatase 1B, magnesium dependent, beta isoform	protein-coding
mm_152295.1	chr19	9083715	9083723	-	1	NA	TTS (NM_011681)	TTS (NM_011681)	4237	NM_011681	22287	Mm.2258	NM_011681	ENSMUSG00000024653	Scgb1a1	CC10|CC16|CCSP|PCB-BP|UG|UGB|Utg	secretoglobin, family 1A, member 1 (uteroglobin)	protein-coding
mm_141265.1	chr17	27623789	27623815	-	1	NA	promoter-TSS (NM_001291046)	promoter-TSS (NM_001291046)	-350	NM_019837	56409	Mm.144699	NM_019837	ENSMUSG00000024213	Nudt3	1110011B09Rik|AA960325|Dipp|Dipp1	nudix (nucleotide diphosphate linked moiety X)-type motif 3	protein-coding
mm_33399.1	chr4	129821238	129821262	+	1	NA	intron (NM_001164745, intron 1 of 5)	intron (NM_001164745, intron 1 of 5)	542	NM_001164745	19244	Mm.193688	NM_008974	ENSMUSG00000028788	Ptp4a2	Prl-2	protein tyrosine phosphatase 4a2	protein-coding
mm_93741.1	chr10	120142803	120142813	-	1	NA	exon (NM_028679, exon 12 of 12)	exon (NM_028679, exon 12 of 12)	-29843	NM_080446	117599	Mm.214703	NM_080446	ENSMUSG00000020228	Helb	AI447783|D10Ertd664e	helicase (DNA) B	protein-coding
mm_7562.1	chr1	124723376	124723382	-	1	NA	Intergenic	Intergenic	-677820	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_38871.1	chr4	149664893	149664893	-	1	NA	intron (NM_001164051, intron 2 of 23)	ID_B1|SINE|B4	-1577	NM_001164052	18707	Mm.229108	NM_008840	ENSMUSG00000039936	Pik3cd	2410099E07Rik|2610208K16Rik|AW545373|p110delta	phosphatidylinositol 3-kinase catalytic delta polypeptide	protein-coding
mm_92538.1	chr10	79637843	79637908	-	1	NA	promoter-TSS (NM_001024539)	promoter-TSS (NM_001024539)	43	NM_001024539	216148	Mm.39424	NM_001024539	ENSMUSG00000020312	Shc2	6720466E06|SCK|ShcB|Sli	SHC (Src homology 2 domain containing) transforming protein 2	protein-coding
mm_26340.1	chr3	142547210	142547224	+	1	NA	3' UTR (NM_001083312, exon 11 of 11)	3' UTR (NM_001083312, exon 11 of 11)	-12835	NM_018734	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_130773.1	chr15	101438789	101438804	-	1	NA	promoter-TSS (NM_001003668)	promoter-TSS (NM_001003668)	8	NM_001003668	406219	Mm.347934	NM_001003668	ENSMUSG00000047641	Krt87	K83|K87|Krt2-25|Krt83	keratin 87	protein-coding
mm_118834.1	chr14	25607798	25607810	+	1	NA	intron (NM_001310666, intron 6 of 23)	CpG	4291	NM_001309430	100188919	Mm.473810	NM_001309430		Israa	-	immune system released activating agent	protein-coding
mm_106530.1	chr11	120573221	120573230	-	1	NA	promoter-TSS (NM_011032)	promoter-TSS (NM_011032)	-289	NM_011032	18453	Mm.16660	NM_011032	ENSMUSG00000025130	P4hb	ERp59|PDI|Pdia1|Thbp	prolyl 4-hydroxylase, beta polypeptide	protein-coding
mm_62817.1	chr7	113295488	113295511	+	1	NA	exon (NM_007489, exon 12 of 20)	exon (NM_007489, exon 12 of 20)	73840	NM_133700	68815	Mm.238034	NM_133700	ENSMUSG00000038187	Btbd10	1110056N09Rik|Gmrp1	BTB (POZ) domain containing 10	protein-coding
mm_44295.1	chr5	8622769	8622854	-	1	NA	5' UTR (NM_198620, exon 1 of 10)	5' UTR (NM_198620, exon 1 of 10)	141	NM_001347311	242819	Mm.332192	NM_198620	ENSMUSG00000040570	Rundc3b	Gm440	RUN domain containing 3B	protein-coding
mm_114725.1	chr13	83715330	83715345	+	1	NA	Intergenic	Intergenic	-12769	NR_015561	320203	Mm.245636	NM_177100	ENSMUSG00000050334	C130071C03Rik	2810449C10Rik	RIKEN cDNA C130071C03 gene	ncRNA
mm_2935.1	chr1	132298664	132298674	+	1	NA	promoter-TSS (NM_144810)	promoter-TSS (NM_144810)	43	NM_144810	213417	Mm.39723	NM_144810	ENSMUSG00000042115	Klhdc8a	A630065K24Rik	kelch domain containing 8A	protein-coding
mm_70080.1	chr7	142653898	142653909	-	1	NA	exon (NM_010514, exon 4 of 4)	exon (NM_010514, exon 4 of 4)	1093	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_105302.1	chr11	102579072	102579083	-	1	NA	promoter-TSS (NR_040286)	promoter-TSS (NR_040286)	42	NR_040286	100040792	Mm.277966	NR_040286	ENSMUSG00000078640	Gm11627	OTTMUSG00000002879	predicted gene 11627	ncRNA
mm_14177.1	chr2	126738009	126738047	+	1	NA	exon (NM_001252580, exon 10 of 19)	exon (NM_001252580, exon 10 of 19)	30700	NM_019729	84092	Mm.272629	NM_019729	ENSMUSG00000027363	Usp8	AI574262|AW557536|Ubpy|mKIAA0055	ubiquitin specific peptidase 8	protein-coding
mm_156145.1	chrX	129774217	129774220	+	1	NA	intron (NM_172493, intron 1 of 26)	T-rich|Low_complexity|Low_complexity	24476	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diaph2	Dia3|Diap2|Drf2|E430022I22Rik	diaphanous related formin 2	protein-coding
mm_153220.1	chr19	34811987	34811999	-	1	NA	3' UTR (NM_023792, exon 7 of 7)	3' UTR (NM_023792, exon 7 of 7)	8780	NR_029783	723826		NR_029783	ENSMUSG00000065594	Mir107	Mirn107|mir-107|mmu-mir-107	microRNA 107	ncRNA
mm_28597.1	chr3	94484216	94484228	-	1	NA	intron (NR_110353, intron 1 of 11)	intron (NR_110353, intron 1 of 11)	1500	NR_110353	78784	Mm.44292	NM_172434	ENSMUSG00000028137	Celf3	4930415M08Rik|BRUNOL1|CAGH4|ERDA4|Tnrc4	CUGBP, Elav-like family member 3	protein-coding
mm_29503.1	chr3	116129376	116129387	-	1	NA	5' UTR (NM_011693, exon 1 of 9)	5' UTR (NM_011693, exon 1 of 9)	307	NM_011693	22329	Mm.76649	NM_011693	ENSMUSG00000027962	Vcam1	CD106|Vcam-1	vascular cell adhesion molecule 1	protein-coding
mm_10593.1	chr2	18676828	18676885	+	1	NA	promoter-TSS (NM_007552)	promoter-TSS (NM_007552)	-162	NM_007552	12151	Mm.289584	NM_007552	ENSMUSG00000026739	Bmi1	AW546694|Bmi-1|Pcgf4	Bmi1 polycomb ring finger oncogene	protein-coding
mm_79886.1	chr9	65294180	65294204	+	1	NA	promoter-TSS (NM_011802)	promoter-TSS (NM_011802)	-68	NM_001044389	270166	Mm.30088	NM_011802	ENSMUSG00000015357	Clpx	AU014732|E330029I21	caseinolytic mitochondrial matrix peptidase chaperone subunit	protein-coding
mm_167345.1	chr8	79248574	79248580	-	1	NA	promoter-TSS (NM_026315)	promoter-TSS (NM_026315)	6	NM_026315	67687	Mm.178707	NM_026315	ENSMUSG00000031682	1700011L22Rik	-	RIKEN cDNA 1700011L22 gene	protein-coding
mm_64804.1	chr7	6691309	6691319	-	1	NA	intron (NM_011769, intron 2 of 7)	B4A|SINE|B4	5118	NM_011769	22776	Mm.89976	NM_011769	ENSMUSG00000002266	Zim1	-	zinc finger, imprinted 1	protein-coding
mm_10085.1	chr2	3114221	3114225	+	1	NA	promoter-TSS (NM_001310434)	promoter-TSS (NM_001310434)	-1	NM_001310434	269233	Mm.23044	NM_001081161	ENSMUSG00000050530	Fam171a1	9630050M13Rik|AA409679	family with sequence similarity 171, member A1	protein-coding
mm_30243.1	chr3	146499808	146499818	-	1	NA	promoter-TSS (NM_001316756)	promoter-TSS (NM_001316756)	-23	NM_010318	14707	Mm.140804	NM_010318	ENSMUSG00000068523	Gng5	G(y)5	guanine nucleotide binding protein (G protein), gamma 5	protein-coding
mm_42452.1	chr5	115435095	115435105	+	1	NA	intron (NM_008629, intron 5 of 14)	intron (NM_008629, intron 5 of 14)	5415	NM_008629	17690	Mm.5077	NM_008629	ENSMUSG00000054256	Msi1	Msi1h|Musahi1|m-Msi-1	musashi RNA-binding protein 1	protein-coding
mm_21976.1	chr2	167349344	167349371	-	1	NA	promoter-TSS (NM_019835)	promoter-TSS (NM_019835)	-179	NM_019835	56336	Mm.200886	NM_019835	ENSMUSG00000017929	B4galt5	9430078I07Rik|AW049941|AW539721	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 5	protein-coding
mm_49915.1	chr6	39044385	39044397	+	1	NA	intron (NM_011539, intron 9 of 12)	B3A|SINE|B2	23195	NR_040523	69986	Mm.490941	NR_040523	ENSMUSG00000100121	1700025N23Rik	-	RIKEN cDNA 1700025N23 gene	ncRNA
mm_30733.1	chr4	13804138	13804158	+	1	NA	intron (NM_009822, intron 1 of 10)	intron (NM_009822, intron 1 of 10)	19366	NM_009822	12395	Mm.4909	NM_009822	ENSMUSG00000006586	Runx1t1	Cbfa2t1h|ETO|MTG8	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	protein-coding
mm_27472.1	chr3	52856456	52856463	-	1	NA	Intergenic	Intergenic	71207	NR_040555	622124	Mm.389434	NR_040555	ENSMUSG00000104401	Gm20750	-	predicted gene, 20750	ncRNA
mm_12023.1	chr2	58157539	58157556	+	1	NA	intron (NM_139200, intron 1 of 7)	intron (NM_139200, intron 1 of 7)	2575	NM_139200	227929	Mm.273905	NM_139200	ENSMUSG00000026832	Cytip	A130053M09Rik|AI462064|C80816|Cbp|Cybr|Pscdbp	cytohesin 1 interacting protein	protein-coding
mm_170885.1	chr2	22165318	22165321	-	1	NA	Intergenic	L1Md_T|LINE|L1	-62184	NM_148413	667663	Mm.330033	NM_148413	ENSMUSG00000025716	Myo3a	9030416P08Rik	myosin IIIA	protein-coding
mm_111765.1	chr12	104009001	104009035	-	1	NA	intron (NM_027997, intron 1 of 4)	MIRc|SINE|MIR	4634	NM_027997	71907	Mm.326723	NM_027997	ENSMUSG00000058260	Serpina9	2310014L03Rik|AW049635|Centerin	serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9	protein-coding
mm_29354.1	chr3	108475017	108475034	-	1	NA	exon (NM_001033304, exon 7 of 21)	exon (NM_001033304, exon 7 of 21)	-29766	NM_001204979	20226	Mm.28688	NM_011319	ENSMUSG00000068739	Sars	Sars1|Strs|serRS	seryl-aminoacyl-tRNA synthetase	protein-coding
mm_37078.1	chr4	116329866	116329869	-	1	NA	intron (NM_008641, intron 7 of 28)	intron (NM_008641, intron 7 of 28)	107953	NM_181585	18710	Mm.253819	NM_181585	ENSMUSG00000028698	Pik3r3	AA414954|p55pik	phosphatidylinositol 3 kinase, regulatory subunit, polypeptide 3 (p55)	protein-coding
mm_28324.1	chr3	89340436	89340477	-	1	NA	exon (NM_001037722, exon 21 of 23)	exon (NM_001037722, exon 21 of 23)	-2428	NM_007910	13639	Mm.16332	NM_007910	ENSMUSG00000028040	Efna4	EFL-4|Epl4|LERK-4	ephrin A4	protein-coding
mm_52665.1	chr6	117906756	117906801	+	1	NA	promoter-TSS (NM_001166431)	promoter-TSS (NM_001166431)	-4	NM_001166431	98758	Mm.422979	NM_133834	ENSMUSG00000042079	Hnrnpf	4833420I20Rik|AA407306|Hnrpf	heterogeneous nuclear ribonucleoprotein F	protein-coding
mm_78994.1	chr9	45403228	45403241	+	1	NA	promoter-TSS (NM_052823)	promoter-TSS (NM_052823)	96	NM_052823	11936	Mm.22742	NM_007503	ENSMUSG00000059412	Fxyd2	Atp1g1	FXYD domain-containing ion transport regulator 2	protein-coding
mm_81994.1	chr9	121489961	121489966	+	1	NA	3' UTR (NM_001284508, exon 4 of 4)	3' UTR (NM_001284508, exon 4 of 4)	5731	NM_001284508	12424	Mm.2619	NM_031161	ENSMUSG00000032532	Cck	-	cholecystokinin	protein-coding
mm_53057.1	chr6	124829517	124829539	+	1	NA	promoter-TSS (NM_013538)	promoter-TSS (NM_013538)	-44	NM_013700	22225	Mm.3571	NM_013700	ENSMUSG00000038429	Usp5	AA407472|ISOT|ISOT-1|Ucht	ubiquitin specific peptidase 5 (isopeptidase T)	protein-coding
mm_136678.1	chr17	6270457	6270508	+	1	NA	promoter-TSS (NM_001033178)	promoter-TSS (NM_001033178)	12	NM_001033178	77106	Mm.381893	NM_001033178	ENSMUSG00000038141	Tmem181a	5930418K15Rik|C76977|Gpr178|Tmem181|mKIAA1423	transmembrane protein 181A	protein-coding
mm_5544.1	chr1	38603923	38603925	-	1	NA	intron (NM_001290814, intron 1 of 21)	intron (NM_001290814, intron 1 of 21)	23320	NM_001290814	16764	Mm.336679	NM_010678	ENSMUSG00000037138	Aff3	3222402O04Rik|A730046J16|LAF-4|Laf4	AF4/FMR2 family, member 3	protein-coding
mm_61655.1	chr7	80501178	80501185	+	1	NA	intron (NM_001042527, intron 7 of 21)	intron (NM_001042527, intron 7 of 21)	33817	NM_007550	12144	Mm.12932	NM_007550	ENSMUSG00000030528	Blm	-	Bloom syndrome, RecQ helicase-like	protein-coding
mm_46103.1	chr5	92347722	92347737	-	1	NA	intron (NM_021274, intron 3 of 3)	intron (NM_021274, intron 3 of 3)	1160	NM_021274	15945	Mm.877	NM_021274	ENSMUSG00000034855	Cxcl10	C7|CRG-2|INP10|IP-10|IP10|Ifi10|Scyb10|gIP-10|mob-1	chemokine (C-X-C motif) ligand 10	protein-coding
mm_122321.1	chr14	36935588	36935590	-	1	NA	promoter-TSS (NM_028407)	promoter-TSS (NM_028407)	-21	NM_028407	72972	Mm.27621	NM_027045	ENSMUSG00000058690	Ccser2	1700012P13Rik|2900054P12Rik|AI035535|AW108503|Fam190b|Gcap14	coiled-coil serine rich 2	protein-coding
mm_97492.1	chr11	78341838	78341886	+	1	NA	exon (NM_201406, exon 12 of 12)	exon (NM_201406, exon 12 of 12)	-1633	NM_001313985	22248	Mm.284811	NM_011676	ENSMUSG00000002058	Unc119	D11Bhm52|HRG4|MRG4|Rg4|Rtg4|Unc119h	unc-119 lipid binding chaperone	protein-coding
mm_140801.1	chr17	21921296	21921296	-	1	NA	Intergenic	L1_Mus3|LINE|L1	-11370	NM_001256493	70081	Mm.245648	NM_001256493	ENSMUSG00000078546	Zfp995	2210404O09Rik	zinc finger protein 995	protein-coding
mm_3581.1	chr1	151133001	151133011	+	1	NA	Intergenic	Intergenic	-5028	NR_038011	402734	Mm.337666	NR_038011		C730036E19Rik	lncLSTR	RIKEN cDNA C730036E19 gene	ncRNA
mm_58136.1	chr6	141601147	141601182	-	1	NA	Intergenic	RLTR9E|LTR|ERVK	-28354	NM_020495	28253	Mm.272223	NM_020495	ENSMUSG00000030236	Slco1b2	7330442B20Rik|OATP-C|OATP2|Oatp1b2|Oatp4|Slc21a10|Slc21a6|lst-1|mlst-1	solute carrier organic anion transporter family, member 1b2	protein-coding
mm_21879.1	chr2	166154797	166154859	-	1	NA	intron (NM_028072, intron 1 of 20)	CpG	457	NM_001252578	72043	Mm.1011	NM_028072	ENSMUSG00000006800	Sulf2	2010004N24Rik|AU020235|MSulf-2|mKIAA1247	sulfatase 2	protein-coding
mm_71732.1	chr8	61988461	61988509	+	1	NA	intron (NM_001293783, intron 24 of 37)	intron (NM_001293783, intron 24 of 37)	60398	NM_001293783	234311	Mm.275233	NM_144928	ENSMUSG00000037921	Ddx60	9830118M07	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	protein-coding
mm_148989.1	chr19	8617992	8618000	+	1	NA	promoter-TSS (NM_008766)	promoter-TSS (NM_008766)	0	NM_008766	18399	Mm.30090	NM_008766	ENSMUSG00000024650	Slc22a6	NKT|Oat1|Orctl1|mOat1	solute carrier family 22 (organic anion transporter), member 6	protein-coding
mm_143390.1	chr17	69384172	69384215	-	1	NA	5' UTR (NM_009547, exon 1 of 3)	5' UTR (NM_009547, exon 1 of 3)	215	NM_009547	22666	Mm.29434	NM_009547	ENSMUSG00000049672	Zbtb14	ZF5|Zfp161|b2b1982Clo	zinc finger and BTB domain containing 14	protein-coding
mm_118841.1	chr14	25649721	25649763	+	1	NA	exon (NM_183208, exon 12 of 24)	exon (NM_183208, exon 12 of 24)	-44428	NM_134084	105675	Mm.41656	NM_134084	ENSMUSG00000021868	Ppif	AW457192|CyP-D|CyP-F|CypD|PPIase	peptidylprolyl isomerase F (cyclophilin F)	protein-coding
mm_89305.1	chr10	87915288	87915313	+	1	NA	exon (NM_010512, exon 4 of 5)	exon (NM_010512, exon 4 of 5)	-51371	NR_000040	22172	Mm.391420	NR_000040		Tyms-ps	-	thymidylate synthase, pseudogene	pseudo
mm_8841.1	chr1	162692405	162692437	-	1	NA	exon (NM_001081290, exon 22 of 35)	exon (NM_001081290, exon 22 of 35)	-34202	NM_001177581	100038657	Mm.416999	NM_001177581	ENSMUSG00000091060	7420461P10Rik	ENSMUSG00000073516	RIKEN cDNA 7420461P10 gene	protein-coding
mm_107925.1	chr12	71097637	71097650	+	1	NA	3' UTR (NM_001081195, exon 24 of 24)	3' UTR (NM_001081195, exon 24 of 24)	-13785	NM_029227	75266	Mm.402075	NM_029227	ENSMUSG00000021078	Tomm20l	4930553D19Rik	translocase of outer mitochondrial membrane 20 homolog (yeast)-like	protein-coding
mm_79733.1	chr9	62342450	62342473	+	1	NA	intron (NM_009672, intron 1 of 6)	CpG	1118	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	protein-coding
mm_49160.1	chr6	13413366	13413369	+	1	NA	promoter-TSS (NR_038149)	promoter-TSS (NR_038149)	30	NR_038149	69413	Mm.177847	NR_038149	ENSMUSG00000101894	1700016P04Rik	-	RIKEN cDNA 1700016P04 gene	ncRNA
mm_124009.1	chr14	76109035	76109064	-	1	NA	intron (NM_026177, intron 1 of 7)	B3A|SINE|B2	1766	NM_026177	67467	Mm.260767	NM_026177	ENSMUSG00000022008	Gpalpp1	1200011I18Rik|Kiaa1704	GPALPP motifs containing 1	protein-coding
mm_77876.1	chr9	6193591	6193595	+	1	NA	intron (NM_027924, intron 1 of 6)	intron (NM_027924, intron 1 of 6)	24981	NM_027924	71785	Mm.390122	NM_027924	ENSMUSG00000032006	Pdgfd	1110003I09Rik	platelet-derived growth factor, D polypeptide	protein-coding
mm_156045.1	chrX	108484436	108484440	+	1	NA	Intergenic	Intergenic	349917	NM_001081477	382236	Mm.100112	NM_001081477	ENSMUSG00000063663	Brwd3	Brodl|D030064D06Rik|Gm596	bromodomain and WD repeat domain containing 3	protein-coding
mm_152707.1	chr19	17356609	17356624	-	1	NA	promoter-TSS (NM_173442)	promoter-TSS (NM_173442)	51	NM_173442	14537	Mm.244825	NM_010265	ENSMUSG00000038843	Gcnt1	5630400D21Rik|B130048E03|C2 GlcNAcT|C2GNT|IGnT	glucosaminyl (N-acetyl) transferase 1, core 2	protein-coding
mm_109796.1	chr12	3288821	3288832	-	1	NA	intron (NM_016676, intron 1 of 5)	intron (NM_016676, intron 1 of 5)	21143	NM_016676	19325	Mm.378993	NM_016676	ENSMUSG00000020671	Rab10	AW107754	RAB10, member RAS oncogene family	protein-coding
mm_138818.1	chr17	39847444	39847448	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	4449	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_22169.1	chr2	173119403	173119415	-	1	NA	5' UTR (NM_001081387, exon 1 of 11)	5' UTR (NM_001081387, exon 1 of 11)	116	NM_001081387	664799	Mm.389396	NM_001081387	ENSMUSG00000070495	Ctcfl	Boris|OTTMUSG00000016680	CCCTC-binding factor (zinc finger protein)-like	protein-coding
mm_11080.1	chr2	27710297	27710308	+	1	NA	promoter-TSS (NM_001290482)	promoter-TSS (NM_001290482)	-281	NM_001290482	20181	Mm.24624	NM_011305	ENSMUSG00000015846	Rxra	9530071D11Rik|Nr2b1|RXRalpha1	retinoid X receptor alpha	protein-coding
mm_43220.1	chr5	129757632	129757635	+	1	NA	3' UTR (NM_008095, exon 10 of 10)	3' UTR (NM_008095, exon 10 of 10)	29620	NM_133900	100678	Mm.271784	NM_133900	ENSMUSG00000029446	Psph	AI480570|PSP|PSPase	phosphoserine phosphatase	protein-coding
mm_150504.1	chr19	39022767	39022773	+	1	NA	intron (NM_028089, intron 4 of 8)	intron (NM_028089, intron 4 of 8)	15751	NM_028089	72082	Mm.142581	NM_028089	ENSMUSG00000025002	Cyp2c55	2010318C06Rik	cytochrome P450, family 2, subfamily c, polypeptide 55	protein-coding
mm_28741.1	chr3	95737875	95737891	-	1	NA	exon (NM_007899, exon 4 of 11)	exon (NM_007899, exon 4 of 11)	1686	NM_007899	13601	Mm.3433	NM_007899	ENSMUSG00000028108	Ecm1	AI663821|p85	extracellular matrix protein 1	protein-coding
mm_118140.1	chr13	105054247	105054258	-	1	NA	5' UTR (NM_029879, exon 1 of 6)	5' UTR (NM_029879, exon 1 of 6)	678	NM_029879	52882	Mm.100348	NM_029879	ENSMUSG00000021719	Rgs7bp	A930030I01Rik|AI842293|D13Bwg1146e|R7bp	regulator of G-protein signalling 7 binding protein	protein-coding
mm_9746.1	chr1	180483411	180483485	-	1	NA	promoter-TSS (NM_001081227)	promoter-TSS (NM_001081227)	56	NM_001081227	381310	Mm.44791	NM_001081227	ENSMUSG00000053963	Stum	6330403A02Rik|ENSMUSG00000056615|Gm10001|R75555	mechanosensory transduction mediator	protein-coding
mm_117983.1	chr13	100152812	100152822	-	1	NA	intron (NM_010872, intron 12 of 15)	intron (NM_010872, intron 12 of 15)	27962	NM_011420	20595	Mm.2025	NM_011420	ENSMUSG00000021645	Smn1	AI849087|Gemin1|Smn	survival motor neuron 1	protein-coding
mm_103913.1	chr11	83588609	83588611	-	1	NA	3' UTR (NM_009139, exon 4 of 4)	3' UTR (NM_009139, exon 4 of 4)	4477	NM_009139	20305	Mm.137	NM_009139	ENSMUSG00000018927	Ccl6	MRP-1|Scya6|c10	chemokine (C-C motif) ligand 6	protein-coding
mm_109816.1	chr12	3427740	3427802	-	1	NA	intron (NM_001270988, intron 1 of 11)	intron (NM_001270988, intron 1 of 11)	914	NM_172421	75302	Mm.120475	NM_172421	ENSMUSG00000037486	Asxl2	4930556B16Rik|mKIAA1685	additional sex combs like 2 (Drosophila)	protein-coding
mm_58824.1	chr7	16721955	16721959	+	1	NA	promoter-TSS (NM_011927)	promoter-TSS (NM_011927)	28	NM_011927	26368	Mm.27096	NM_011927	ENSMUSG00000007209	Ceacam9	AA410097|AW545709|Cea-5|Cea5|mmCGM8	carcinoembryonic antigen-related cell adhesion molecule 9	protein-coding
mm_97210.1	chr11	75620661	75620682	+	1	NA	intron (NM_008850, intron 10 of 11)	intron (NM_008850, intron 10 of 11)	-10349	NM_008916	19062	Mm.1458	NM_008916	ENSMUSG00000006127	Inpp5k	C62|Pps|SKIP	inositol polyphosphate 5-phosphatase K	protein-coding
mm_32251.1	chr4	102570455	102570473	+	1	NA	5' UTR (NM_001177980, exon 1 of 10)	5' UTR (NM_001177980, exon 1 of 10)	404	NM_001177980	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_60921.1	chr7	46845833	46845848	+	1	NA	promoter-TSS (NM_010699)	promoter-TSS (NM_010699)	36	NR_102727	16828	Mm.29324	NM_010699	ENSMUSG00000063229	Ldha	Ldh1|Ldhm|l7R2	lactate dehydrogenase A	protein-coding
mm_60259.1	chr7	43798024	43798096	+	1	NA	5' UTR (NM_008940, exon 1 of 5)	5' UTR (NM_008940, exon 1 of 5)	483	NM_008940	259277	Mm.458023	NM_008940	ENSMUSG00000064023	Klk8	BSP1|NP|Nrpn|Prss19	kallikrein related-peptidase 8	protein-coding
mm_76026.1	chr8	75100587	75100593	-	1	NA	TTS (NM_010442)	TTS (NM_010442)	6972	NM_010442	15368	Mm.276389	NM_010442	ENSMUSG00000005413	Hmox1	D8Wsu38e|HO-1|HO1|Hemox|Hmox|Hsp32	heme oxygenase 1	protein-coding
mm_94080.1	chr10	128492956	128492967	-	1	NA	promoter-TSS (NM_001317220)	promoter-TSS (NM_001317220)	48	NM_001317220	17904	Mm.337074	NM_010860	ENSMUSG00000090841	Myl6	ESMLC|LC17|LC17-GI|MLC-3|MLC1SM|Myln	myosin, light polypeptide 6, alkali, smooth muscle and non-muscle	protein-coding
mm_49035.1	chr6	4759889	4759897	+	1	NA	3' UTR (NM_130877, exon 2 of 2)	3' UTR (NM_130877, exon 2 of 2)	12587	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_22993.1	chr3	34019918	34019926	+	1	NA	promoter-TSS (NM_001113188)	promoter-TSS (NM_001113188)	-157	NM_001113189	14359	Mm.259021	NM_008053	ENSMUSG00000027680	Fxr1	1110050J02Rik|9530073J07Rik|AI851072|Fxr1h|Fxr1p	fragile X mental retardation gene 1, autosomal homolog	protein-coding
mm_98057.1	chr11	85821962	85821968	+	1	NA	intron (NR_077059, intron 1 of 4)	intron (NR_077059, intron 1 of 4)	10423	NR_077059	69909	Mm.440214	NR_077059	ENSMUSG00000087013	2610027K06Rik	-	RIKEN cDNA 2610027K06 gene	ncRNA
mm_104019.1	chr11	85719738	85719750	-	1	NA	promoter-TSS (NR_045875)	promoter-TSS (NR_045875)	0	NR_045875	71489	Mm.442482	NR_045875	ENSMUSG00000086199	Bcas3os1	8430403D17Rik	breast carcinoma amplified sequence 3, opposite strand 1	ncRNA
mm_128398.1	chr15	43869972	43869976	-	1	NA	promoter-TSS (NM_175502)	promoter-TSS (NM_175502)	55	NM_175502	239408	Mm.41219	NM_175502	ENSMUSG00000054409	Tmem74	AA549547|B230382K22Rik	transmembrane protein 74	protein-coding
mm_80935.1	chr9	102690734	102690755	+	1	NA	Intergenic	Intergenic	-27060	NM_019764	56332	Mm.21145	NM_019764	ENSMUSG00000032531	Amotl2	AW549739|C79691|Lccp|MASCOT|mKIAA0989	angiomotin-like 2	protein-coding
mm_28978.1	chr3	101110282	101110294	-	1	NA	promoter-TSS (NM_011197)	promoter-TSS (NM_011197)	-122	NM_011197	19221	Mm.24807	NM_011197	ENSMUSG00000027864	Ptgfrn	4833445A08Rik|AU042434|CD9P-1|FPRP|Trim45	prostaglandin F2 receptor negative regulator	protein-coding
mm_23694.1	chr3	68692074	68692087	+	1	NA	exon (NM_008351, exon 2 of 7)	exon (NM_008351, exon 2 of 7)	656	NM_008351	16159	Mm.103783	NM_008351	ENSMUSG00000027776	Il12a	IL-12p35|Il-12a|Ll12a|p35	interleukin 12a	protein-coding
mm_139292.1	chr17	48300500	48300524	+	1	NA	5' UTR (NM_001033405, exon 1 of 5)	5' UTR (NM_001033405, exon 1 of 5)	474	NM_001033405	328833	Mm.329104	NM_001033405	ENSMUSG00000071068	Treml2	AW049306|Gm750|Tlt2	triggering receptor expressed on myeloid cells-like 2	protein-coding
mm_136354.1	chr16	92727215	92727218	-	1	NA	intron (NM_001111022, intron 2 of 6)	intron (NM_001111022, intron 2 of 6)	-29887	NM_009821	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_1376.1	chr1	66700853	66700859	+	1	NA	promoter-TSS (NM_001310644)	promoter-TSS (NM_001310644)	25	NM_001310644	66646	Mm.240912	NM_025683	ENSMUSG00000026005	Rpe	2810429B02Rik|5730518J08Rik	ribulose-5-phosphate-3-epimerase	protein-coding
mm_131231.1	chr16	10452814	10452838	+	1	NA	Intergenic	Intergenic	-5476	NM_001013778	383103	Mm.325732	NM_001013778	ENSMUSG00000050908	Tvp23a	Fam18a	trans-golgi network vesicle protein 23A	protein-coding
mm_160154.1	chr7	43950649	43950649	+	1	NA	promoter-TSS (NM_008457)	promoter-TSS (NM_008457)	-17	NM_008457	16624	Mm.435488	NM_008457	ENSMUSG00000063089	Klk1b8	Klk8|Nrpn|TADG14|kallikrein|mGK-8	kallikrein 1-related peptidase b8	protein-coding
mm_41394.1	chr5	90772061	90772071	+	1	NA	promoter-TSS (NM_019932)	promoter-TSS (NM_019932)	-369	NM_019932	56744	Mm.332490	NM_019932	ENSMUSG00000029373	Pf4	Cxcl4|Scyb4	platelet factor 4	protein-coding
mm_139159.1	chr17	47542531	47542534	+	1	NA	intron (NM_001081635, intron 1 of 6)	intron (NM_001081635, intron 1 of 6)	37481	NM_001081635	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_167901.1	chrX	74085555	74085563	-	1	NA	exon (NM_001081979, exon 1 of 3)	exon (NM_001081979, exon 1 of 3)	131	NM_010788	17257	Mm.131408	NM_010788	ENSMUSG00000031393	Mecp2	1500041B07Rik|D630021H01Rik|Mbd5|WBP10	methyl CpG binding protein 2	protein-coding
mm_15664.1	chr2	163323348	163323360	+	1	NA	TTS (NM_001098799)	TTS (NM_001098799)	74619	NM_021566	59091	Mm.34459	NM_021566	ENSMUSG00000017817	Jph2	1110002E14Rik|JP-2|Jp2	junctophilin 2	protein-coding
mm_113128.1	chr13	24614206	24614214	+	1	NA	promoter-TSS (NM_001286101)	promoter-TSS (NM_001286101)	-396	NM_001286101	193385	Mm.217319	NM_029679	ENSMUSG00000036006	Fam65b	-	family with sequence similarity 65, member B	protein-coding
mm_14110.1	chr2	125791726	125791782	+	1	NA	Intergenic	Intergenic	-8884	NM_177608	70354	Mm.138091	NM_133725	ENSMUSG00000035093	Secisbp2l	3110001I20Rik|AI504340|C630011I23	SECIS binding protein 2-like	protein-coding
mm_121272.1	chr14	103513305	103513324	+	1	NA	promoter-TSS (NM_022886)	promoter-TSS (NM_022886)	-27	NM_022886	64929	Mm.244003	NM_022886	ENSMUSG00000022123	Scel	9230114I02Rik	sciellin	protein-coding
mm_71709.1	chr8	61936073	61936085	+	1	NA	intron (NM_001293783, intron 1 of 37)	intron (NM_001293783, intron 1 of 37)	7992	NM_001293783	234311	Mm.275233	NM_144928	ENSMUSG00000037921	Ddx60	9830118M07	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	protein-coding
mm_125952.1	chr15	76249019	76249042	+	1	NA	TTS (NR_105918)	TTS (NR_105918)	839	NR_105918	102465575		NR_105918	ENSMUSG00000098625	Mir6953	Gm27738|mmu-mir-6953	microRNA 6953	ncRNA
mm_99126.1	chr11	100243255	100243267	+	1	NA	Intergenic	Intergenic	5641	NM_001313958	16666	Mm.422799	NM_008470	ENSMUSG00000053797	Krt16	AI324768|CK-16|K16|Krt1-16	keratin 16	protein-coding
mm_147692.1	chr18	60747004	60747019	-	1	NA	Intergenic	Intergenic	-27585	NM_020600	20044	Mm.43778	NM_020600	ENSMUSG00000024608	Rps14	2600014J02Rik|AL023078	ribosomal protein S14	protein-coding
mm_155602.1	chrX	82948993	82949023	+	1	NA	5' UTR (NM_007868, exon 1 of 79)	5' UTR (NM_007868, exon 1 of 79)	138	NM_007868	13405	Mm.275608	NM_007868	ENSMUSG00000045103	Dmd	DXSmh7|DXSmh9|Dp427|Dp71|dys|mdx|pke	dystrophin, muscular dystrophy	protein-coding
mm_102572.1	chr11	61579623	61579629	-	1	NA	promoter-TSS (NM_010148)	promoter-TSS (NM_010148)	61	NM_010148	13855	Mm.139695	NM_010148	ENSMUSG00000001036	Epn2	9530051D10Rik|AA536924|Ibp2	epsin 2	protein-coding
mm_89215.1	chr10	86779001	86779009	+	1	NA	promoter-TSS (NM_175331)	promoter-TSS (NM_175331)	0	NM_175331	103466	Mm.200446	NM_175331	ENSMUSG00000054027	Nt5dc3	AU040402|AW540062|C630002B14Rik|TU12B1-TY	5'-nucleotidase domain containing 3	protein-coding
mm_141854.1	chr17	34803033	34803054	-	1	NA	exon (NM_009995, exon 6 of 10)	exon (NM_009995, exon 6 of 10)	1383	NM_009995	13079	Mm.440407	NM_009995	ENSMUSG00000024365	Cyp21a1	21-OH|21OH|21OHA|21OHB|CYP21OH-A|Cyp21|Cyp21-ps1|Cyp21B|Cyp21a2-ps|Cyp21a2ps|Oh21-1|Oh21-2	cytochrome P450, family 21, subfamily a, polypeptide 1	protein-coding
mm_142885.1	chr17	51831885	51831895	-	1	NA	intron (NM_001163632, intron 1 of 10)	CpG	757	NM_009122	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_86835.1	chr10	21377291	21377327	+	1	NA	promoter-TSS (NM_178713)	promoter-TSS (NM_178713)	9	NM_178713	237320	Mm.90181	NM_178713	ENSMUSG00000037542	Aldh8a1	Raldh4	aldehyde dehydrogenase 8 family, member A1	protein-coding
mm_151768.1	chr19	5273069	5273079	-	1	NA	promoter-TSS (NM_153129)	promoter-TSS (NM_153129)	45	NM_153129	107975	Mm.234923	NM_153129	ENSMUSG00000024855	Pacs1	AI325977	phosphofurin acidic cluster sorting protein 1	protein-coding
mm_106968.1	chr12	8937429	8937449	+	1	NA	intron (NM_008640, intron 6 of 6)	intron (NM_008640, intron 6 of 6)	-10490	NM_010770	17182	Mm.42226	NM_010770	ENSMUSG00000020583	Matn3	AV009181	matrilin 3	protein-coding
mm_56518.1	chr6	99500205	99500207	-	1	NA	intron (NM_001347345, intron 1 of 19)	intron (NM_001347345, intron 1 of 19)	20787	NM_001347345	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_27804.1	chr3	75956596	75956609	-	1	NA	5' UTR (NM_175193, exon 1 of 15)	5' UTR (NM_175193, exon 1 of 15)	347	NM_175193	73124	Mm.249232	NM_175193	ENSMUSG00000034109	Golim4	3110027H23Rik|GIMPC|GPP130|Golph4|P138	golgi integral membrane protein 4	protein-coding
mm_127386.1	chr15	101040908	101040922	+	1	NA	3' UTR (NM_011323, exon 26 of 26)	3' UTR (NM_011323, exon 26 of 26)	13484	NM_001214911	668225	Mm.385011	NM_001214911	ENSMUSG00000095440	Fignl2	EG668225	fidgetin-like 2	protein-coding
mm_140472.1	chr17	94608148	94608148	+	1	NA	Intergenic	Intergenic	141744	NM_176917	76781	Mm.139146	NM_176917	ENSMUSG00000055660	Mettl4	2410198H06Rik|A730091E08Rik|AV296509|HsT661	methyltransferase like 4	protein-coding
mm_126081.1	chr15	77805944	77805954	+	1	NA	intron (NM_022410, intron 3 of 40)	intron (NM_022410, intron 3 of 40)	36226	NM_022410	17886	Mm.29677	NM_022410	ENSMUSG00000022443	Myh9	Fltn|Myhn-1|Myhn1|NMHCIIA|NMMHC-A|NMMHC-IIA|TU72.6	myosin, heavy polypeptide 9, non-muscle	protein-coding
mm_92430.1	chr10	77113677	77113692	-	1	NA	promoter-TSS (NM_001109991)	promoter-TSS (NM_001109991)	21	NM_001109991	12822	Mm.4352	NM_009929	ENSMUSG00000001435	Col18a1	-	collagen, type XVIII, alpha 1	protein-coding
mm_13367.1	chr2	103456902	103456924	+	1	NA	exon (NM_009804, exon 11 of 13)	exon (NM_009804, exon 11 of 13)	28240	NM_009804	12359	Mm.4215	NM_009804	ENSMUSG00000027187	Cat	2210418N07|Cas-1|Cas1|Cs-1	catalase	protein-coding
mm_120104.1	chr14	59201032	59201053	+	1	NA	promoter-TSS (NM_027764)	promoter-TSS (NM_027764)	-186	NM_027764	71330	Mm.234195	NM_027764	ENSMUSG00000035469	Rcbtb1	5430409I18Rik|AW111883|CLLD7|CLLL7	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 1	protein-coding
mm_62459.1	chr7	101537793	101537803	+	1	NA	Intergenic	Intergenic	18004	NM_007490	11871	Mm.439746	NM_007490	ENSMUSG00000092517	Art2a-ps	ARTC2|Art2a|Ly92a|Rt-6|Rt6|Rt6-1	ADP-ribosyltransferase 2a, pseudogene	protein-coding
mm_54961.1	chr6	48708207	48708252	-	1	NA	promoter-TSS (NM_153175)	promoter-TSS (NM_153175)	15	NM_153175	231931	Mm.321047	NM_153175	ENSMUSG00000047867	Gimap6	4833419H03Rik|Ian6|mFLJ00102	GTPase, IMAP family member 6	protein-coding
mm_48181.1	chr5	137333517	137333557	-	1	NA	promoter-TSS (NM_031406)	promoter-TSS (NM_031406)	45	NM_031406	83704	Mm.235625	NM_031406	ENSMUSG00000037344	Slc12a9	CIP1	solute carrier family 12 (potassium/chloride transporters), member 9	protein-coding
mm_150818.1	chr19	44406603	44406632	+	1	NA	exon (NM_009127, exon 2 of 6)	exon (NM_009127, exon 2 of 6)	1092	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_91814.1	chr10	54061823	54061839	-	1	NA	intron (NM_008548, intron 2 of 12)	RLTR20D|LTR|ERVK	13965	NM_008548	17155	Mm.117294	NM_008548	ENSMUSG00000003746	Man1a	Man1a1|PCR1	mannosidase 1, alpha	protein-coding
mm_70205.1	chr7	144738521	144738597	-	1	NA	promoter-TSS (NM_178642)	promoter-TSS (NM_178642)	33	NM_178642	101772	Mm.26700	NM_178642	ENSMUSG00000031075	Ano1	Tmem16a	anoctamin 1, calcium activated chloride channel	protein-coding
mm_47680.1	chr5	128904253	128904266	-	1	NA	intron (NM_001310733, intron 1 of 20)	intron (NM_001310733, intron 1 of 20)	49227	NM_001081388	231760	Mm.233996	NM_001081388	ENSMUSG00000029420	Rimbp2	A930033C01Rik|mKIAA0318	RIMS binding protein 2	protein-coding
mm_101641.1	chr11	36433040	36433050	-	1	NA	intron (NM_011856, intron 2 of 28)	intron (NM_011856, intron 2 of 28)	-452956	NM_170779	211652	Mm.31267	NM_170779	ENSMUSG00000018849	Wwc1	AA408228|AU017197|BC037006|Kibra|mKIAA0869	WW, C2 and coiled-coil domain containing 1	protein-coding
mm_76337.1	chr8	84714257	84714288	-	1	NA	intron (NM_001297601, intron 7 of 8)	intron (NM_001297601, intron 7 of 8)	12815	NM_008535	17095	Mm.4925	NM_008535	ENSMUSG00000034041	Lyl1	Lyl-1|bHLHa18	lymphoblastomic leukemia 1	protein-coding
mm_169304.1	chr14	104072094	104072100	-	1	NA	Intergenic	Intergenic	-44955	NR_045953	73877	Mm.399172	NR_045953		4930432J09Rik	-	RIKEN cDNA 4930432J09 gene	ncRNA
mm_122136.1	chr14	31163436	31163450	-	1	NA	exon (NM_138672, exon 3 of 69)	exon (NM_138672, exon 3 of 69)	5198	NM_138672	192187	Mm.220821	NM_138672	ENSMUSG00000042286	Stab1	FEEL-1|FELE-1|MFEEL-1|MS-1|STAB-1|mKIAA0246	stabilin 1	protein-coding
mm_78840.1	chr9	44326989	44326999	+	1	NA	5' UTR (NM_007875, exon 1 of 9)	5' UTR (NM_007875, exon 1 of 9)	149	NM_007875	13478	Mm.18353	NM_007875	ENSMUSG00000032123	Dpagt1	AU021132|Dpagt2|GPT|Gnpta	dolichyl-phosphate (UDP-N-acetylglucosamine) acetylglucosaminephosphotransferase 1 (GlcNAc-1-P transferase)	protein-coding
mm_160643.1	chr9	109745895	109745895	-	1	NA	intron (NM_198674, intron 1 of 9)	intron (NM_198674, intron 1 of 9)	194	NM_198674	382109	Mm.246849	NM_198674	ENSMUSG00000059547	Fbxw26	EG382109|Gm5163	F-box and WD-40 domain protein 26	protein-coding
mm_33348.1	chr4	129335963	129335987	+	1	NA	promoter-TSS (NM_009030)	promoter-TSS (NM_009030)	-51	NM_025970	67106	Mm.36575	NM_025970	ENSMUSG00000057572	Zbtb8os	2010001H09Rik|2310028N13Rik|AI851226|Arch|Archm	zinc finger and BTB domain containing 8 opposite strand	protein-coding
mm_84715.1	chr9	73133015	73133042	-	1	NA	Intergenic	Intergenic	19559	NM_198609	225215	Mm.379366	NM_198609	ENSMUSG00000032215	Rsl24d1	2410159K22Rik	ribosomal L24 domain containing 1	protein-coding
mm_35473.1	chr4	40823724	40823736	-	1	NA	intron (NM_022305, intron 1 of 5)	intron (NM_022305, intron 1 of 5)	26408	NR_039584	100628614		NR_039584	ENSMUSG00000096377	Mir5123	mmu-mir-5123|mu-mir-5123	microRNA 5123	ncRNA
mm_137650.1	chr17	28558287	28558326	+	1	NA	TTS (NR_105935)	TTS (NR_105935)	195	NR_105935	102465585		NR_105935	ENSMUSG00000099152	Mir6969	Gm27305|mmu-mir-6969	microRNA 6969	ncRNA
mm_38752.1	chr4	147698489	147698503	-	1	NA	intron (NM_001127188, intron 1 of 3)	intron (NM_001127188, intron 1 of 3)	4135	NM_001127188	100503584	Mm.276881	NM_001127188	ENSMUSG00000062518	Zfp534	Gm13159|OTTMUSG00000010681	zinc finger protein 534	protein-coding
mm_1081.1	chr1	59482941	59482952	+	1	NA	5' UTR (NM_008057, exon 1 of 1)	5' UTR (NM_008057, exon 1 of 1)	799	NM_008057	14369	Mm.297906	NM_008057	ENSMUSG00000041075	Fzd7	Fz7	frizzled class receptor 7	protein-coding
mm_30298.1	chr3	149077115	149077128	-	1	NA	Intergenic	Intergenic	-122486	NM_001081298	99633	Mm.9776	NM_001081298	ENSMUSG00000028184	Adgrl2	AI450192|CIRL-2|Gm619|Lec1|Lphh1|Lphn2|mKIAA0786	adhesion G protein-coupled receptor L2	protein-coding
mm_40222.1	chr5	37242323	37242342	+	1	NA	exon (NM_001136058, exon 1 of 14)	exon (NM_001136058, exon 1 of 14)	274	NM_001136058	12933	Mm.290995	NM_007765	ENSMUSG00000029121	Crmp1	CRMP-1|DRP-1|Dpysl1|ULIP-3|Ulip3	collapsin response mediator protein 1	protein-coding
mm_29223.1	chr3	107212819	107212827	-	1	NA	exon (NM_001111143, exon 8 of 9)	exon (NM_001111143, exon 8 of 9)	8909	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_19672.1	chr2	103454324	103454330	-	1	NA	3' UTR (NM_009804, exon 13 of 13)	3' UTR (NM_009804, exon 13 of 13)	30259	NM_010125	13711	Mm.20888	NM_010125	ENSMUSG00000027186	Elf5	ESE-2|ESE-5|ESE-5.	E74-like factor 5	protein-coding
mm_163449.1	chr12	87892803	87892806	+	1	NA	promoter-TSS (NM_001177574)	promoter-TSS (NM_001177574)	-30	NM_001177574	100039052	Mm.431321	NM_001177574		Gm2022	-	predicted pseudogene 2022	protein-coding
mm_115591.1	chr13	11827127	11827133	-	1	NA	intron (NM_023868, intron 15 of 104)	intron (NM_023868, intron 15 of 104)	279815	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding
mm_110164.1	chr12	27160478	27160492	-	1	NA	promoter-TSS (NR_045869)	promoter-TSS (NR_045869)	31	NR_045868	636791	Mm.423496	NM_001039248	ENSMUSG00000094002	Gm9866	EG636791|ENSMUSG00000052076	predicted gene 9866	ncRNA
mm_47709.1	chr5	129993588	129993601	-	1	NA	exon (NM_010368, exon 10 of 12)	exon (NM_010368, exon 10 of 12)	9234	NM_010368	110006	Mm.3317	NM_010368	ENSMUSG00000025534	Gusb	AI747421|Gur|Gus|Gus-r|Gus-s|Gus-t|Gus-u|Gut|asd|g	glucuronidase, beta	protein-coding
mm_128758.1	chr15	65786983	65786993	-	1	NA	promoter-TSS (NM_133766)	promoter-TSS (NM_133766)	-53	NM_133766	76740	Mm.260647	NM_133766	ENSMUSG00000015002	Efr3a	A130089M23Rik|BB071175|C76891|C920006C10Rik|D030063F01Rik|mKIAA0143	EFR3 homolog A	protein-coding
mm_144796.1	chr18	36013318	36013327	+	1	NA	non-coding (NR_110349, exon 15 of 15)	non-coding (NR_110349, exon 15 of 15)	48492	NR_110349	74002	Mm.196944	NM_028707	ENSMUSG00000024347	Psd2	6330404E20Rik|AW125584|EFA6C	pleckstrin and Sec7 domain containing 2	protein-coding
mm_81599.1	chr9	110532608	110532640	+	1	NA	promoter-TSS (NM_001081340)	promoter-TSS (NM_001081340)	27	NM_001081340	235626	Mm.288949	NM_001081340	ENSMUSG00000044791	Setd2	4921524K10Rik|BC031601|KMT3A	SET domain containing 2	protein-coding
mm_142488.1	chr17	45756961	45756974	-	1	NA	Intergenic	Intergenic	-23123	NM_028164	72240	Mm.482897	NM_028164	ENSMUSG00000094690	1600014C23Rik	-	RIKEN cDNA 1600014C23 gene	protein-coding
mm_3662.1	chr1	153406482	153406501	+	1	NA	non-coding (NR_033736, exon 4 of 4)	non-coding (NR_033736, exon 4 of 4)	7742	NR_033736	626058	Mm.31556	NM_001177359		E330020D12Rik	EG626058|F430003O07Rik|Gm6648	Riken cDNA E330020D12 gene	ncRNA
mm_2916.1	chr1	132008901	132008910	+	1	NA	intron (NM_007923, intron 1 of 4)	intron (NM_007923, intron 1 of 4)	1300	NM_007923	13714	Mm.254233	NM_007923	ENSMUSG00000026436	Elk4	2310011G17Rik|A130026I01Rik|BB162516|SAP-1|Sap1	ELK4, member of ETS oncogene family	protein-coding
mm_107912.1	chr12	70995070	70995070	+	1	NA	3' UTR (NM_011184, exon 11 of 11)	3' UTR (NM_011184, exon 11 of 11)	20447	NM_011184	19167	Mm.296338	NM_011184	ENSMUSG00000060073	Psma3	Lmpc8	proteasome (prosome, macropain) subunit, alpha type 3	protein-coding
mm_11855.1	chr2	46519978	46519980	+	1	NA	Intergenic	Lx8|LINE|L1	823374	NR_040497	69405	Mm.396184	NR_040497	ENSMUSG00000086202	1700019E08Rik	-	RIKEN cDNA 1700019E08 gene	ncRNA
mm_159274.1	chr2	164613679	164613679	-	1	NA	promoter-TSS (NM_001080550)	promoter-TSS (NM_001080550)	-21	NM_001012725	433502	Mm.376157	NM_001012725	ENSMUSG00000070531	Wfdc6b	WAP6b|Wfdc6	WAP four-disulfide core domain 6B	protein-coding
mm_92560.1	chr10	79849888	79849893	-	1	NA	intron (NR_038088, intron 3 of 4)	intron (NR_038088, intron 3 of 4)	-4542	NM_001077363	19205	Mm.265610	NM_008956	ENSMUSG00000006498	Ptbp1	AA407203|AL033359|HNRPI|PTB-1|PTB2|PTB3|PTB4|Ptb|pPTB	polypyrimidine tract binding protein 1	protein-coding
mm_50905.1	chr6	57581703	57581728	+	1	NA	intron (NM_025992, intron 1 of 22)	B3|SINE|B2	723	NM_025992	67138	Mm.297393	NM_025992	ENSMUSG00000029798	Herc6	1700121D12Rik|2510038N07Rik|4930427L17Rik|AI451296|CEB1|Herc5	hect domain and RLD 6	protein-coding
mm_47477.1	chr5	123721091	123721112	-	1	NA	promoter-TSS (NM_027494)	promoter-TSS (NM_027494)	-57	NM_027494	70650	Mm.279427	NM_027494	ENSMUSG00000029427	Zcchc8	5730565F05Rik	zinc finger, CCHC domain containing 8	protein-coding
mm_69952.1	chr7	142372322	142372336	-	1	NA	promoter-TSS (NM_177265)	promoter-TSS (NM_177265)	-2	NM_001347542	320802	Mm.154486	NM_177265	ENSMUSG00000045777	Ifitm10	6330512M04Rik|AI848576|DSPA3	interferon induced transmembrane protein 10	protein-coding
mm_147869.1	chr18	64479384	64479392	-	1	NA	intron (NM_007998, intron 2 of 10)	intron (NM_007998, intron 2 of 10)	9678	NM_007998	14151	Mm.1070	NM_007998	ENSMUSG00000024588	Fech	AI894116|Fcl|fch	ferrochelatase	protein-coding
mm_35464.1	chr4	40780998	40781001	-	1	NA	Intergenic	Intergenic	-23114	NM_021535	74255	Mm.289929	NM_021535	ENSMUSG00000028409	Smu1	2600001O03Rik|2610203K23Rik|AB044414|AI845086|AW556129|Bwd	smu-1 suppressor of mec-8 and unc-52 homolog (C. elegans)	protein-coding
mm_122075.1	chr14	30599487	30599500	-	1	NA	exon (NM_001310682, exon 15 of 17)	exon (NM_001310682, exon 15 of 17)	10817	NM_001310682	18753	Mm.2314	NM_011103	ENSMUSG00000021948	Prkcd	AI385711|D14Ertd420e|PKC[d]|PKCdelta|Pkcd	protein kinase C, delta	protein-coding
mm_72273.1	chr8	75100037	75100049	+	1	NA	3' UTR (NM_010442, exon 5 of 5)	3' UTR (NM_010442, exon 5 of 5)	6425	NM_010442	15368	Mm.276389	NM_010442	ENSMUSG00000005413	Hmox1	D8Wsu38e|HO-1|HO1|Hemox|Hmox|Hsp32	heme oxygenase 1	protein-coding
mm_41199.1	chr5	88328224	88328257	+	1	NA	exon (NM_008644, exon 3 of 3)	exon (NM_008644, exon 3 of 3)	10928	NM_008644	17830	Mm.200411	NM_008644	ENSMUSG00000064156	Prol1	Muc10	proline rich, lacrimal 1	protein-coding
mm_134163.1	chr16	10793134	10793165	-	1	NA	Intergenic	ORR1A4-int|LTR|ERVL-MaLR	-1044	NM_008933	19119	Mm.325769	NM_008933	ENSMUSG00000038015	Prm2	AI528784|Prm-2	protamine 2	protein-coding
mm_141628.1	chr17	32917194	32917197	-	1	NA	promoter-TSS (NM_022434)	promoter-TSS (NM_022434)	-108	NM_022434	64385	Mm.486449	NM_022434	ENSMUSG00000024292	Cyp4f14	1300014O15Rik|cyp4f-14	cytochrome P450, family 4, subfamily f, polypeptide 14	protein-coding
mm_52825.1	chr6	121356924	121356926	+	1	NA	exon (NM_133661, exon 7 of 15)	exon (NM_133661, exon 7 of 15)	10228	NM_133661	14411	Mm.274506	NM_133661	ENSMUSG00000030109	Slc6a12	BGT1|GAT-2|GAT2|Gabt2	solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12	protein-coding
mm_40220.1	chr5	37242087	37242091	+	1	NA	promoter-TSS (NM_001136058)	promoter-TSS (NM_001136058)	31	NM_001136058	12933	Mm.290995	NM_007765	ENSMUSG00000029121	Crmp1	CRMP-1|DRP-1|Dpysl1|ULIP-3|Ulip3	collapsin response mediator protein 1	protein-coding
mm_38865.1	chr4	149454972	149454986	-	1	NA	promoter-TSS (NM_022020)	promoter-TSS (NM_022020)	-11	NM_022020	63954	Mm.46023	NM_022020	ENSMUSG00000028996	Rbp7	1110002J23Rik|CRBP-III	retinol binding protein 7, cellular	protein-coding
mm_111692.1	chr12	103646990	103647001	-	1	NA	exon (NM_007618, exon 5 of 5)	exon (NM_007618, exon 5 of 5)	10223	NM_007618	12401	Mm.290079	NM_007618	ENSMUSG00000060807	Serpina6	Cbg	serine (or cysteine) peptidase inhibitor, clade A, member 6	protein-coding
mm_107389.1	chr12	33313990	33314019	+	1	NA	intron (NM_001033436, intron 1 of 7)	intron (NM_001033436, intron 1 of 7)	11489	NM_001033436	380753	Mm.41540	NM_028139	ENSMUSG00000020564	Atxn7l1	2810423G08Rik|Atxn7l4	ataxin 7-like 1	protein-coding
mm_42718.1	chr5	120511214	120511246	+	1	NA	promoter-TSS (NM_133221)	promoter-TSS (NM_133221)	38	NM_001177594	170756	Mm.291070	NM_133221	ENSMUSG00000032754	Slc8b1	AF261233|NCKX6|NCLX|Slc24a6	solute carrier family 8 (sodium/lithium/calcium exchanger), member B1	protein-coding
mm_43267.1	chr5	130369482	130369495	+	1	NA	promoter-TSS (NM_181045)	promoter-TSS (NM_181045)	30	NM_181045	140904	Mm.40875	NM_021371	ENSMUSG00000060371	Caln1	9630012C17Rik|Cabp8|MNCb-0849	calneuron 1	protein-coding
mm_136901.1	chr17	13015205	13015224	+	1	NA	3' UTR (NM_013671, exon 5 of 5)	3' UTR (NM_013671, exon 5 of 5)	7375	NM_013671	20656	Mm.290876	NM_013671	ENSMUSG00000006818	Sod2	MnSOD|Sod-2	superoxide dismutase 2, mitochondrial	protein-coding
mm_73686.1	chr8	111556549	111556559	+	1	NA	intron (NM_001168623, intron 1 of 4)	RMER21B|LTR|ERV1	18211	NM_001168623	170737	Mm.271578	NM_133206	ENSMUSG00000033545	Znrf1	B830022L21Rik|Rnf42|Zrfp1|nin283	zinc and ring finger 1	protein-coding
mm_47997.1	chr5	136136127	136136134	-	1	NA	promoter-TSS (NM_027891)	promoter-TSS (NM_027891)	-15	NM_001347492	72041	Mm.486605	NM_028070	ENSMUSG00000039754	Alkbh4	2010004B12Rik|Abj4	alkB homolog 4, lysine demethylase	protein-coding
mm_148840.1	chr19	6363990	6364042	+	1	NA	non-coding (NR_122118, exon 1 of 12)	non-coding (NR_122118, exon 1 of 12)	326	NR_122118	22668	Mm.256422	NM_011750	ENSMUSG00000024949	Sf1	BBP|MZFM|WBP4|Zfp162	splicing factor 1	protein-coding
mm_166346.1	chr5	118952323	118952335	+	1	NA	promoter-TSS (NR_040694)	promoter-TSS (NR_040694)	-10	NR_040694	74627	Mm.410828	NR_040694	ENSMUSG00000107144	4930413E15Rik	-	RIKEN cDNA 4930413E15 gene	ncRNA
mm_62206.1	chr7	97842906	97842912	+	1	NA	promoter-TSS (NM_011035)	promoter-TSS (NM_011035)	-30	NM_011035	18479	Mm.260227	NM_011035	ENSMUSG00000030774	Pak1	AW045634|PAK-1|Paka	p21 protein (Cdc42/Rac)-activated kinase 1	protein-coding
mm_33199.1	chr4	126286780	126286790	+	1	NA	promoter-TSS (NM_199473)	promoter-TSS (NM_199473)	-9	NM_199473	329941	Mm.296327	NM_199473	ENSMUSG00000056174	Col8a2	AI429819	collagen, type VIII, alpha 2	protein-coding
mm_52557.1	chr6	116137418	116137457	+	1	NA	intron (NM_177412, intron 2 of 5)	intron (NM_177412, intron 2 of 5)	55937	NM_177412	330401	Mm.425352	NM_177412	ENSMUSG00000030126	Tmcc1	3632431M01Rik|mKIAA0779	transmembrane and coiled coil domains 1	protein-coding
mm_1584.1	chr1	74295635	74295647	+	1	NA	intron (NM_027154, intron 1 of 11)	intron (NM_027154, intron 1 of 11)	8695	NM_027154	69660	Mm.261182	NM_027154	ENSMUSG00000006301	Tmbim1	2310061B02Rik|AA960455|AU024746|C78899|RECS1|Tmbib1|mKIAA4161	transmembrane BAX inhibitor motif containing 1	protein-coding
mm_46403.1	chr5	104093036	104093055	-	1	NA	exon (NM_010097, exon 4 of 11)	exon (NM_010097, exon 4 of 11)	-15437	NM_001163772	100271704	Mm.366664	NM_001163772	ENSMUSG00000091034	Gm17660	Scpppq1	predicted gene, 17660	protein-coding
mm_127084.1	chr15	97718736	97718747	+	1	NA	intron (NM_001168693, intron 6 of 9)	intron (NM_001168693, intron 6 of 9)	2409	NM_008902	19011	Mm.1001	NM_008902	ENSMUSG00000022468	Endou	Pp11r|Tcl-30	endonuclease, polyU-specific	protein-coding
mm_78629.1	chr9	38731191	38731248	+	1	NA	intron (NM_172767, intron 11 of 19)	intron (NM_172767, intron 11 of 19)	12951	NM_172767	67776	Mm.290950	NM_172767	ENSMUSG00000023186	Vwa5a	5830475I06Rik|AW552491|BCSC-1|E130119J22|Loh11cr2a	von Willebrand factor A domain containing 5A	protein-coding
mm_21374.1	chr2	157337425	157337427	-	1	NA	promoter-TSS (NM_001329683)	promoter-TSS (NM_001329683)	0	NM_001329683	14601	Mm.389327	NM_010285	ENSMUSG00000027643	Ghrh	GRF|Ghrf	growth hormone releasing hormone	protein-coding
mm_161646.1	chr17	3532610	3532610	+	1	NA	promoter-TSS (NM_001101560)	promoter-TSS (NM_001101560)	56	NM_001101560	621628	Mm.469914	NM_001101560	ENSMUSG00000091530	Cldn20	EG621628	claudin 20	protein-coding
mm_125973.1	chr15	76294789	76294821	+	1	NA	exon (NM_001195537, exon 1 of 7)	exon (NM_001195537, exon 1 of 7)	371	NM_001195537	100503915	Mm.393455	NM_001195537	ENSMUSG00000071724	Smpd5	ENSMUSG00000071724|Gm10345|MA-nSMase	sphingomyelin phosphodiesterase 5	protein-coding
mm_151171.1	chr19	53310421	53310447	+	1	NA	promoter-TSS (NM_001008542)	promoter-TSS (NM_001008542)	-72	NM_001008542	17859	Mm.2154	NM_010847	ENSMUSG00000025025	Mxi1	ENSMUSG00000067085|Gm10197|Mad2|bHLHc11	MAX interactor 1, dimerization protein	protein-coding
mm_92542.1	chr10	79671472	79671489	-	1	NA	intron (NM_148934, intron 1 of 1)	RMER17D|LTR|ERVK	2070	NM_148934	110012	Mm.22623	NM_148934	ENSMUSG00000020308	Tpgs1	AV005629|Gm16517|Gtrgeo22|PGs1	tubulin polyglutamylase complex subunit 1	protein-coding
mm_127442.1	chr15	101270446	101270465	+	1	NA	exon (NM_010444, exon 2 of 7)	exon (NM_010444, exon 2 of 7)	3609	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_100263.1	chr11	117332411	117332454	+	1	NA	5' UTR (NM_001113488, exon 1 of 10)	5' UTR (NM_001113488, exon 1 of 10)	119	NM_001113488	53860	Mm.38450	NM_017380	ENSMUSG00000059248	Sept9	MSF1|Msf|PNUTL4|Sint1	septin 9	protein-coding
mm_172310.1	chr7	104950485	104950485	-	1	NA	Intergenic	L1Md_F2|LINE|L1	10245	NM_207146	384703	Mm.377901	NM_207146	ENSMUSG00000044705	Olfr670	GA_x5J8B7W6B6J-141796-141659|MOR32-8	olfactory receptor 670	protein-coding
mm_112241.1	chr12	113482474	113482483	-	1	NA	Intergenic	Intergenic	-7087	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_130673.1	chr15	100674719	100674720	-	1	NA	intron (NM_033612, intron 7 of 7)	intron (NM_033612, intron 7 of 7)	-5219	NM_001270537	668218	Mm.451225	NM_001270537	ENSMUSG00000098112	Bin2	-	bridging integrator 2	protein-coding
mm_120442.1	chr14	65903029	65903039	+	1	NA	Intergenic	Intergenic	50710	NM_172604	219151	Mm.344095	NM_172604	ENSMUSG00000034463	Scara3	APC7|C130058N24Rik|CSR|CSR1|MSLR1|MSRL1	scavenger receptor class A, member 3	protein-coding
mm_15773.1	chr2	164332809	164332812	+	1	NA	promoter-TSS (NM_009301)	promoter-TSS (NM_009301)	45	NM_009301	20944	Mm.140154	NM_009301	ENSMUSG00000017004	Svs5	BB115186|Semg1|Svp-1|Svp1|Svp5	seminal vesicle secretory protein 5	protein-coding
mm_70187.1	chr7	143780236	143780257	-	1	NA	3' UTR (NM_175534, exon 2 of 2)	3' UTR (NM_175534, exon 2 of 2)	4254	NM_175534	244238	Mm.183561	NM_175534	ENSMUSG00000048965	Mrgpre	C130069N09Rik|Ebrt3|Mgrf|MrgE	MAS-related GPR, member E	protein-coding
mm_132362.1	chr16	34690749	34690774	+	1	NA	exon (NM_172824, exon 1 of 13)	exon (NM_172824, exon 1 of 13)	145	NM_172824	239839	Mm.272045	NM_172824	ENSMUSG00000022833	Ccdc14	G630039H03Rik	coiled-coil domain containing 14	protein-coding
mm_166664.1	chr6	90325178	90325203	-	1	NA	promoter-TSS (NM_027928)	promoter-TSS (NM_027928)	-5	NM_027928	71797	Mm.49071	NM_027928	ENSMUSG00000056643	Chst13	1110067M19Rik|C4ST-3	carbohydrate (chondroitin 4) sulfotransferase 13	protein-coding
mm_63462.1	chr7	127573377	127573437	+	1	NA	promoter-TSS (NM_026888)	promoter-TSS (NM_026888)	59	NM_026888	68961	Mm.274473	NM_026888	ENSMUSG00000030815	Phkg2	1500017I02Rik	phosphorylase kinase, gamma 2 (testis)	protein-coding
mm_58885.1	chr7	17088033	17088049	+	1	NA	intron (NM_001310628, intron 1 of 5)	intron (NM_001310628, intron 1 of 5)	14001	NM_007676	26436	Mm.143686	NM_007676	ENSMUSG00000066760	Psg16	Cea11|PSG|bCEA	pregnancy specific glycoprotein 16	protein-coding
mm_91340.1	chr10	26078988	26079028	-	1	NA	promoter-TSS (NM_029881)	promoter-TSS (NM_029881)	44	NM_029881	77220	Mm.266260	NM_029881	ENSMUSG00000049420	Tmem200a	C030003D03Rik	transmembrane protein 200A	protein-coding
mm_91537.1	chr10	39227765	39227765	-	1	NA	Intergenic	Intergenic	-63971	NM_001127376	327743	Mm.208111	NM_001127376	ENSMUSG00000062074	Wisp3	CCN6|ENSMUSG00000062074|Gm735|WISP-3	WNT1 inducible signaling pathway protein 3	protein-coding
mm_54216.1	chr6	25689920	25689966	-	1	NA	promoter-TSS (NM_010338)	promoter-TSS (NM_010338)	37	NM_010338	14763	Mm.409670	NM_010338	ENSMUSG00000039904	Gpr37	AI848630|Pael-R	G protein-coupled receptor 37	protein-coding
mm_118952.1	chr14	27379531	27379593	+	1	NA	intron (NM_001289686, intron 5 of 12)	intron (NM_001289686, intron 5 of 12)	18173	NM_001289688	71704	Mm.248606	NM_027871	ENSMUSG00000021895	Arhgef3	1200004I24Rik|9830169H03Rik|C76747|Xpln	Rho guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_32640.1	chr4	115057011	115057039	+	1	NA	promoter-TSS (NM_001287388)	promoter-TSS (NM_001287388)	599	NM_011527	21349	Mm.239869	NM_011527	ENSMUSG00000028717	Tal1	Hpt|SCL/tal-1|Scl|bHLHa17|tal-1	T cell acute lymphocytic leukemia 1	protein-coding
mm_153526.1	chr19	41794995	41795032	-	1	NA	intron (NM_027667, intron 1 of 11)	intron (NM_027667, intron 1 of 11)	7071	NM_001163495	71085	Mm.21646	NM_027667	ENSMUSG00000025154	Arhgap19	4933411B03Rik|AI120128|AW546831|mFLJ00368	Rho GTPase activating protein 19	protein-coding
mm_169136.1	chr13	59478086	59478099	-	1	NA	intron (NM_023328, intron 18 of 25)	intron (NM_023328, intron 18 of 25)	66359	NM_001284221	67269	Mm.153008	NM_023328	ENSMUSG00000021557	Agtpbp1	1700020N17Rik|2310001G17Rik|2900054O13Rik|4930445M19Rik|5730402G09Rik|CCP1|Nna1|nmf243|pcd	ATP/GTP binding protein 1	protein-coding
mm_169106.1	chr13	44869644	44869644	-	1	NA	intron (NM_001205044, intron 4 of 18)	LSU-rRNA_Hsa|rRNA|rRNA	132452	NM_025772	94245	Mm.352311	NM_025772	ENSMUSG00000057531	Dtnbp1	5430437B18Rik|AW048963|Bloc1s8|dysbindin|sdy	dystrobrevin binding protein 1	protein-coding
mm_71389.1	chr8	46151857	46151865	+	1	NA	Intergenic	CpG	-17695	NM_025747	66756	Mm.133623	NM_025747	ENSMUSG00000031631	Cfap97	1110068E21Rik|4933411K20Rik|AW049273|Kiaa1430|mKIAA1430	cilia and flagella associated protein 97	protein-coding
mm_3816.1	chr1	159232242	159232252	+	1	NA	promoter-TSS (NM_011931)	promoter-TSS (NM_011931)	-79	NM_011931	26374	Mm.328135	NM_011931	ENSMUSG00000040782	Rfwd2	AI316802|C80879|Cop1	ring finger and WD repeat domain 2	protein-coding
mm_68060.1	chr7	101845268	101845276	-	1	NA	promoter-TSS (NM_008035)	promoter-TSS (NM_008035)	59	NM_001303231	14276	Mm.439666	NM_008035	ENSMUSG00000032725	Folr2	FBP2|FR-P3|FR-beta|Folbp-2|Folbp2	folate receptor 2 (fetal)	protein-coding
mm_32365.1	chr4	105257100	105257107	+	1	NA	Intergenic	Intergenic	99756	NM_080555	67916	Mm.348326	NM_080555	ENSMUSG00000028517	Plpp3	1110003O22Rik|2610002D05Rik|AV025606|D4Bwg0538e|D4Bwg1535e|Lpp3|Ppab2b|Ppap2b	phospholipid phosphatase 3	protein-coding
mm_170502.1	chr19	24290240	24290244	-	1	NA	Intergenic	Intergenic	-9656	NM_008044	14297	Mm.7319	NM_008044	ENSMUSG00000059363	Fxn	FA|FARR|Frda|X25	frataxin	protein-coding
mm_69680.1	chr7	139985904	139985915	-	1	NA	TTS (NR_106029)	TTS (NR_106029)	965	NR_106029	102465643		NR_106029	ENSMUSG00000099092	Mir7062	Gm27339|mmu-mir-7062	microRNA 7062	ncRNA
mm_78771.1	chr9	43743690	43743712	+	1	NA	promoter-TSS (NM_021424)	promoter-TSS (NM_021424)	-875	NM_021424	58235	Mm.335096	NM_021424	ENSMUSG00000032012	Nectin1	AI835281|AW549174|Cd111|HIgR|HveC|PRR|PRR1|Pvrl1|nectin-1	nectin cell adhesion molecule 1	protein-coding
mm_18996.1	chr2	76868376	76868393	-	1	NA	exon (NM_011652, exon 104 of 313)	exon (NM_011652, exon 104 of 313)	114163	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_98818.1	chr11	97310255	97310278	+	1	NA	Intergenic	Intergenic	-5450	NM_025927	67036	Mm.5381	NM_025927	ENSMUSG00000018882	Mrpl45	2600005P05Rik|AU043542|R75241	mitochondrial ribosomal protein L45	protein-coding
mm_142695.1	chr17	47834435	47834447	-	1	NA	5' UTR (NM_001109973, exon 1 of 5)	5' UTR (NM_001109973, exon 1 of 5)	250	NM_001109973	17240	Mm.329100	NM_010783	ENSMUSG00000032717	Mdfi	I-mf|I-mfa	MyoD family inhibitor	protein-coding
mm_104371.1	chr11	94358869	94358877	-	1	NA	exon (NM_029600, exon 23 of 31)	exon (NM_029600, exon 23 of 31)	30872	NM_146024	71452	Mm.141054	NM_027799	ENSMUSG00000020864	Ankrd40	1110011C06Rik|5530600A18Rik|Gcap15	ankyrin repeat domain 40	protein-coding
mm_137415.1	chr17	26123505	26123513	+	1	NA	promoter-TSS (NM_024227)	promoter-TSS (NM_024227)	6	NM_024227	68611	Mm.273102	NM_024227	ENSMUSG00000024181	Mrpl28	1110015G04Rik|L28mt|MAAT1|MRP-L28|p15	mitochondrial ribosomal protein L28	protein-coding
mm_149422.1	chr19	11443597	11443609	+	1	NA	promoter-TSS (NM_021718)	promoter-TSS (NM_021718)	45	NM_021718	60361	Mm.33957	NM_021718	ENSMUSG00000056290	Ms4a4b	AI463180|Chandra|Ly116	membrane-spanning 4-domains, subfamily A, member 4B	protein-coding
mm_30532.1	chr4	3369988	3369988	+	1	NA	Intergenic	Intergenic	-167102	NR_037306	100499523		NR_037306	ENSMUSG00000094253	Mir3471-2	mmu-mir-3471-2	microRNA 3471-2	ncRNA
mm_139700.1	chr17	57451356	57451380	+	1	NA	intron (NM_010130, intron 17 of 21)	intron (NM_010130, intron 17 of 21)	92682	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_77151.1	chr8	111644298	111644325	-	1	NA	intron (NM_001037665, intron 1 of 3)	MLTR25C|LTR|ERVK	868	NM_011742	22640	Mm.4184	NM_011742	ENSMUSG00000055835	Zfp1	Fnp-1|Zfp-1|mkr-1	zinc finger protein 1	protein-coding
mm_98569.1	chr11	95413787	95413815	+	1	NA	promoter-TSS (NM_025287)	promoter-TSS (NM_025287)	-282	NM_025287	20747	Mm.285454	NM_025287	ENSMUSG00000057522	Spop	AI315626|Pcif1|TEF2	speckle-type POZ protein	protein-coding
mm_87548.1	chr10	53635462	53635476	+	1	NA	intron (NM_001081428, intron 16 of 17)	intron (NM_001081428, intron 16 of 17)	-5030	NM_027830	71567	Mm.278221	NM_027830	ENSMUSG00000058298	Mcm9	9030408O17Rik|Gm235|Mcmdc1	minichromosome maintenance 9 homologous recombination repair factor	protein-coding
mm_76702.1	chr8	94434260	94434297	-	1	NA	non-coding (NR_015514, exon 2 of 3)	non-coding (NR_015514, exon 2 of 3)	825	NR_015514	320377	Mm.486022	NR_015514		9330175E14Rik	A630085K21	RIKEN cDNA 9330175E14 gene	ncRNA
mm_136510.1	chr16	97170796	97170814	-	1	NA	promoter-TSS (NM_031174)	promoter-TSS (NM_031174)	-70	NM_031174	13508	Mm.102437	NM_031174	ENSMUSG00000050272	Dscam	4932410A21Rik	Down syndrome cell adhesion molecule	protein-coding
mm_155659.1	chrX	86191732	86191739	+	1	NA	promoter-TSS (NM_007430)	promoter-TSS (NM_007430)	-40	NM_007430	11614	Mm.5180	NM_007430	ENSMUSG00000025056	Nr0b1	AHX|Ahc|Ahch|DAX-1|Dax1	nuclear receptor subfamily 0, group B, member 1	protein-coding
mm_145629.1	chr18	61109803	61109813	+	1	NA	exon (NM_001037859, exon 3 of 22)	exon (NM_001037859, exon 3 of 22)	4236	NM_001037859	12978	Mm.22574	NM_007779	ENSMUSG00000024621	Csf1r	AI323359|CD115|CSF-1R|Csfmr|Fim-2|Fim2|Fms|M-CSF-R|M-CSFR	colony stimulating factor 1 receptor	protein-coding
mm_134083.1	chr16	8738885	8738895	-	1	NA	promoter-TSS (NM_001003918)	promoter-TSS (NM_001003918)	-548	NM_001003918	252870	Mm.295330	NM_001003918	ENSMUSG00000022710	Usp7	2210010O09Rik|AA409944|AA617399|AU019296|AW548146|C80752|Hausp	ubiquitin specific peptidase 7	protein-coding
mm_23005.1	chr3	34104449	34104475	+	1	NA	Intergenic	Intergenic	-23108	NM_026332	67713	Mm.274266	NM_026332	ENSMUSG00000027679	Dnajc19	1810055D05Rik|AA959924|Tim14	DnaJ heat shock protein family (Hsp40) member C19	protein-coding
mm_48016.1	chr5	136170635	136170661	-	1	NA	promoter-TSS (NM_178751)	promoter-TSS (NM_178751)	8	NM_178751	269717	Mm.308396	NM_178751	ENSMUSG00000039747	Orai2	A730041O15Rik|Tmem142b	ORAI calcium release-activated calcium modulator 2	protein-coding
mm_39197.1	chr4	156015926	156015950	-	1	NA	exon (NM_011659, exon 5 of 7)	exon (NM_011659, exon 5 of 7)	2243	NM_011659	22163	Mm.13885	NM_011659	ENSMUSG00000029075	Tnfrsf4	ACT35|CD134|Ly-70|Ox40|TXGP1L|Txgp1	tumor necrosis factor receptor superfamily, member 4	protein-coding
mm_16965.1	chr2	17689880	17689890	-	1	NA	intron (NM_028757, intron 2 of 6)	IMPB_01|Satellite|Satellite	41183	NM_028757	74103	Mm.120298	NM_028757	ENSMUSG00000053702	Nebl	1200007O21Rik|A630080F05Rik|BB140644|D830029A09Rik|Lnebl	nebulette	protein-coding
mm_169637.1	chr15	47540063	47540065	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	916759	NR_045811	75281	Mm.159487	NR_045811	ENSMUSG00000051198	4930548G14Rik	-	RIKEN cDNA 4930548G14 gene	ncRNA
mm_117004.1	chr13	57798729	57798734	-	1	NA	intron (NM_001166464, intron 2 of 10)	intron (NM_001166464, intron 2 of 10)	109601	NM_009262	20745	Mm.379020	NM_009262	ENSMUSG00000056222	Spock1	Spock|Ticn1|testican	sparc/osteonectin, cwcv and kazal-like domains proteoglycan 1	protein-coding
mm_78469.1	chr9	32636211	32636221	+	1	NA	Intergenic	Intergenic	-59826	NM_011808	23871	Mm.292415	NM_011808	ENSMUSG00000032035	Ets1	AI196000|AI448617|D230050P06|Ets-1|Tpl1|vs	E26 avian leukemia oncogene 1, 5' domain	protein-coding
mm_61637.1	chr7	80291247	80291271	+	1	NA	3' UTR (NM_178070, exon 23 of 23)	3' UTR (NM_178070, exon 23 of 23)	-3192	NM_145150	233406	Mm.227274	NM_145150	ENSMUSG00000038943	Prc1	D7Ertd348e	protein regulator of cytokinesis 1	protein-coding
mm_143947.1	chr17	86753467	86753480	-	1	NA	promoter-TSS (NM_010137)	promoter-TSS (NM_010137)	-391	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_138998.1	chr17	45555879	45555900	+	1	NA	5' UTR (NM_008690, exon 1 of 6)	5' UTR (NM_008690, exon 1 of 6)	189	NM_001304956	18037	Mm.57043	NM_008690	ENSMUSG00000023947	Nfkbie	I-kappa-B-epsilon|IKBE|IkB-E|NF-kappa-BIE|ikB-epsilon	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, epsilon	protein-coding
mm_43599.1	chr5	137787854	137787871	+	1	NA	promoter-TSS (NM_001005426)	promoter-TSS (NM_001005426)	60	NM_001005426	381678	Mm.332765	NM_001005426	ENSMUSG00000037108	Zcwpw1	Gm1053	zinc finger, CW type with PWWP domain 1	protein-coding
mm_10950.1	chr2	25617793	25617800	+	1	NA	promoter-TSS (NM_029859)	promoter-TSS (NM_029859)	-118	NM_029859	77058	Mm.478493	NM_029859	ENSMUSG00000026940	Ccdc183	4921530D09Rik|Cccd183|Kiaa1984	coiled-coil domain containing 183	protein-coding
mm_92747.1	chr10	81001259	81001288	-	1	NA	promoter-TSS (NM_001038655)	promoter-TSS (NM_001038655)	92	NM_001038655	14708	Mm.222496	NM_010319	ENSMUSG00000048240	Gng7	AI840417	guanine nucleotide binding protein (G protein), gamma 7	protein-coding
mm_166696.1	chr6	114004755	114004766	+	1	NA	intron (NM_009723, intron 1 of 21)	MTE2a|LTR|ERVL-MaLR	37320	NM_009723	11941	Mm.321755	NM_009723	ENSMUSG00000030302	Atp2b2	D6Abb2e|Gena300|PMCA2|Tmy|dfw|jog|wms|wri	ATPase, Ca++ transporting, plasma membrane 2	protein-coding
mm_122037.1	chr14	30008818	30008835	-	1	NA	promoter-TSS (NM_001136240)	promoter-TSS (NM_001136240)	70	NM_019583	50905	Mm.269363	NM_019583	ENSMUSG00000015966	Il17rb	Evi27|IL-17ER|IL-17Rh1|IL17RH1|Il17br	interleukin 17 receptor B	protein-coding
mm_65373.1	chr7	25073131	25073164	-	1	NA	promoter-TSS (NM_008168)	promoter-TSS (NM_008168)	-778	NM_008168	14809	Mm.2879	NM_008168	ENSMUSG00000003378	Grik5	GluK5|GluRgamma2|KA2	glutamate receptor, ionotropic, kainate 5 (gamma 2)	protein-coding
mm_90713.1	chr10	4387973	4388002	-	1	NA	5' UTR (NM_001033466, exon 1 of 3)	5' UTR (NM_001033466, exon 1 of 3)	121	NM_001033466	381990	Mm.262466	NM_001033466	ENSMUSG00000075327	Zbtb2	Gm1103	zinc finger and BTB domain containing 2	protein-coding
mm_55901.1	chr6	83627203	83627249	-	1	NA	Intergenic	Intergenic	28890	NM_016751	51811	Mm.3115	NM_016751	ENSMUSG00000014542	Clec4f	Clecsf13|D18063|KUCR_MOUSE|Kclr	C-type lectin domain family 4, member f	protein-coding
mm_32047.1	chr4	97581689	97581696	+	1	NA	promoter-TSS (NM_001122952)	promoter-TSS (NM_001122952)	-251	NM_001122952	18027	Mm.31274	NM_010905	ENSMUSG00000028565	Nfia	1110047K16Rik|9430022M17Rik|CTF|NF1-A|NF1A	nuclear factor I/A	protein-coding
mm_22074.1	chr2	168749429	168749455	-	1	NA	3' UTR (NM_201396, exon 3 of 3)	3' UTR (NM_201396, exon 3 of 3)	-7306	NM_001289446	11981	Mm.330819	NM_015731	ENSMUSG00000027546	Atp9a	IIa	ATPase, class II, type 9A	protein-coding
mm_117403.1	chr13	73763530	73763545	-	1	NA	promoter-TSS (NM_011390)	promoter-TSS (NM_011390)	-160	NM_011390	20499	Mm.275800	NM_011390	ENSMUSG00000017756	Slc12a7	AA408796|D13Ertd261e|Kcc4	solute carrier family 12, member 7	protein-coding
mm_25640.1	chr3	121291726	121291817	+	1	NA	promoter-TSS (NM_024178)	promoter-TSS (NM_024178)	-46	NM_024178	66789	Mm.269881	NM_024178	ENSMUSG00000039887	Alg14	5430428G01Rik|AI854024	asparagine-linked glycosylation 14	protein-coding
mm_138436.1	chr17	35110696	35110704	+	1	NA	exon (NM_148947, exon 2 of 3)	exon (NM_148947, exon 2 of 3)	2400	NM_148947	114652	Mm.222643	NM_148947	ENSMUSG00000034482	Ly6g5c	G5c|NG33	lymphocyte antigen 6 complex, locus G5C	protein-coding
mm_129160.1	chr15	76243110	76243130	-	1	NA	exon (NM_001163575, exon 2 of 11)	exon (NM_001163575, exon 2 of 11)	320	NM_001163576	671535	Mm.373750	NM_001163575	ENSMUSG00000063268	Parp10	-	poly (ADP-ribose) polymerase family, member 10	protein-coding
mm_107804.1	chr12	64969302	64969308	+	1	NA	intron (NM_177805, intron 1 of 19)	intron (NM_177805, intron 1 of 19)	3563	NM_177805	328108	Mm.138465	NM_177805	ENSMUSG00000035614	Fam179b	A430041B07Rik|BC062107|C130034K06|mKIAA0423	family with sequence similarity 179, member B	protein-coding
mm_125446.1	chr15	47520694	47520701	+	1	NA	Intergenic	Intergenic	897392	NR_045811	75281	Mm.159487	NR_045811	ENSMUSG00000051198	4930548G14Rik	-	RIKEN cDNA 4930548G14 gene	ncRNA
mm_746.1	chr1	43537284	43537297	+	1	NA	intron (NM_010879, intron 3 of 4)	intron (NM_010879, intron 3 of 4)	91539	NM_010879	17974	Mm.389903	NM_010879	ENSMUSG00000066877	Nck2	4833426I10Rik|Grb4|NCKbeta|Nck-2	non-catalytic region of tyrosine kinase adaptor protein 2	protein-coding
mm_105082.1	chr11	100845898	100845911	-	1	NA	intron (NM_001113563, intron 1 of 18)	intron (NM_001113563, intron 1 of 18)	4681	NM_001113563	20851	Mm.34064	NM_011489	ENSMUSG00000020919	Stat5b	-	signal transducer and activator of transcription 5B	protein-coding
mm_85818.1	chr9	110408209	110408217	-	1	NA	promoter-TSS (NM_001081043)	promoter-TSS (NM_001081043)	-3	NM_001081043	104831	Mm.335477	NM_001081043	ENSMUSG00000036057	Ptpn23	AI462446|PTP-TD14	protein tyrosine phosphatase, non-receptor type 23	protein-coding
mm_75763.1	chr8	69974119	69974160	-	1	NA	5' UTR (NM_001113346, exon 1 of 13)	5' UTR (NM_001113346, exon 1 of 13)	244	NM_001113346	234366	Mm.270044	NM_145596	ENSMUSG00000036180	Gatad2a	1110066C11Rik|BC031407|C80248	GATA zinc finger domain containing 2A	protein-coding
mm_877.1	chr1	52155284	52155312	+	1	NA	intron (NM_001205313, intron 23 of 24)	intron (NM_001205313, intron 23 of 24)	35676	NM_001205313	20846	Mm.277406	NM_009283	ENSMUSG00000026104	Stat1	2010005J02Rik|AA408197	signal transducer and activator of transcription 1	protein-coding
mm_166719.1	chr6	120294695	120294717	-	1	NA	promoter-TSS (NM_198884)	promoter-TSS (NM_198884)	-147	NM_198884	330406	Mm.321840	NM_198884	ENSMUSG00000041372	B4galnt3	AB114826|B4GalNAcT3|C330047A21	beta-1,4-N-acetyl-galactosaminyl transferase 3	protein-coding
mm_43246.1	chr5	130145066	130145083	+	1	NA	5' UTR (NM_172509, exon 1 of 4)	5' UTR (NM_172509, exon 1 of 4)	186	NM_172509	212919	Mm.55812	NM_172509	ENSMUSG00000034110	Kctd7	4932409E18|9430010P06Rik	potassium channel tetramerisation domain containing 7	protein-coding
mm_150538.1	chr19	39307695	39307709	+	1	NA	exon (NM_007815, exon 4 of 9)	exon (NM_007815, exon 4 of 9)	20617	NM_007815	13095	Mm.20764	NM_007815	ENSMUSG00000003053	Cyp2c29	AHOH|AHOHase|AI159681|AI196010|Ah-2|Ahh-1|Cyp2c|P450-2C	cytochrome P450, family 2, subfamily c, polypeptide 29	protein-coding
mm_121477.1	chr14	121035485	121035500	+	1	NA	promoter-TSS (NM_134082)	promoter-TSS (NM_134082)	-82	NM_134082	223254	Mm.223980	NM_134082	ENSMUSG00000025555	Farp1	AW228844|BC030329|Cdep	FERM, RhoGEF (Arhgef) and pleckstrin domain protein 1 (chondrocyte-derived)	protein-coding
mm_150396.1	chr19	36409968	36409978	+	1	NA	intron (NM_029508, intron 1 of 8)	CpG	30906	NM_029508	76073	Mm.259180	NM_029508	ENSMUSG00000024805	Pcgf5	0610009F02Rik|1110054A01Rik|5830406C17Rik|5830443C21Rik|9530023M17Rik|AI324127	polycomb group ring finger 5	protein-coding
mm_137093.1	chr17	21535548	21535571	+	1	NA	promoter-TSS (NM_144515)	promoter-TSS (NM_144515)	20	NM_144515	22710	Mm.296100	NM_144515	ENSMUSG00000051341	Zfp52	KRAB11|Zfp-52|Zfp76|mszf23-2|mszf24|mszf34|mszf75|zfec29	zinc finger protein 52	protein-coding
mm_83535.1	chr9	46233171	46233203	-	1	NA	3' UTR (NM_001289755, exon 4 of 4)	3' UTR (NM_001289755, exon 4 of 4)	2112	NM_001289833	11814	Mm.390161	NM_023114	ENSMUSG00000032081	Apoc3	apo-CIII|apoC-III	apolipoprotein C-III	protein-coding
mm_130574.1	chr15	99497889	99497917	-	1	NA	3' UTR (NM_028224, exon 12 of 12)	3' UTR (NM_028224, exon 12 of 12)	-23173	NM_029236	75284	Mm.32826	NM_029236	ENSMUSG00000037525	Bcdin3d	4930556P03Rik|AV138748	BCDIN3 domain containing	protein-coding
mm_122813.1	chr14	54603356	54603371	-	1	NA	intron (NM_028890, intron 1 of 6)	CpG	2545	NM_028890	74359	Mm.79815	NM_028890	ENSMUSG00000022179	4931414P19Rik	-	RIKEN cDNA 4931414P19 gene	protein-coding
mm_40656.1	chr5	65131185	65131214	+	1	NA	promoter-TSS (NM_175174)	promoter-TSS (NM_175174)	-32	NM_175174	71778	Mm.10281	NM_175174	ENSMUSG00000054920	Klhl5	1300013C10Rik	kelch-like 5	protein-coding
mm_153909.1	chr19	47138215	47138237	-	1	NA	promoter-TSS (NM_133746)	promoter-TSS (NM_133746)	68	NM_133746	72691	Mm.31663	NM_133746	ENSMUSG00000033033	Calhm2	2810048G17Rik|Fam26b	calcium homeostasis modulator 2	protein-coding
mm_141650.1	chr17	33665534	33665554	-	1	NA	exon (NM_001109913, exon 8 of 17)	exon (NM_001109913, exon 8 of 17)	19914	NM_001109913	76936	Mm.311439	NM_029804	ENSMUSG00000059208	Hnrnpm	2610023M21Rik|AA409009|Hnrpm|mKIAA4193	heterogeneous nuclear ribonucleoprotein M	protein-coding
mm_118695.1	chr14	22140258	22140285	+	1	NA	intron (NM_028275, intron 2 of 6)	ORR1C1|LTR|ERVL-MaLR	120559	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_54286.1	chr6	29232005	29232014	-	1	NA	Intergenic	Intergenic	-15645	NM_001302934	23917	Mm.260707	NM_011829	ENSMUSG00000003500	Impdh1	B930086D20Rik|IMPDH-I	inosine 5'-phosphate dehydrogenase 1	protein-coding
mm_5190.1	chr1	13217095	13217099	-	1	NA	intron (NM_001302702, intron 4 of 21)	intron (NM_001302702, intron 4 of 21)	-89934	NM_001081209	383491	Mm.309380	NM_001081209	ENSMUSG00000042414	Prdm14	-	PR domain containing 14	protein-coding
mm_62491.1	chr7	101933954	101934026	+	1	NA	promoter-TSS (NM_027053)	promoter-TSS (NM_027053)	-133	NM_001162973	69358	Mm.214841	NM_027053	ENSMUSG00000064307	Lrrc51	1700008D07Rik|Lrtomt	leucine rich repeat containing 51	protein-coding
mm_677.1	chr1	40466181	40466210	+	1	NA	TTS (NM_001025602)	TTS (NM_001025602)	189	NM_008365	16182	Mm.253664	NM_008365	ENSMUSG00000026070	Il18r1	Il18ralpha|Il1rrp	interleukin 18 receptor 1	protein-coding
mm_150488.1	chr19	39007052	39007093	+	1	NA	promoter-TSS (NM_028089)	promoter-TSS (NM_028089)	53	NM_028089	72082	Mm.142581	NM_028089	ENSMUSG00000025002	Cyp2c55	2010318C06Rik	cytochrome P450, family 2, subfamily c, polypeptide 55	protein-coding
mm_24396.1	chr3	90293296	90293311	+	1	NA	Intergenic	(CCCCCG)n|Simple_repeat|Simple_repeat	23154	NR_105979	102465612		NR_105979	ENSMUSG00000099199	Mir7012	Gm27370|mmu-mir-7012	microRNA 7012	ncRNA
mm_35895.1	chr4	49549486	49549514	-	1	NA	promoter-TSS (NM_144903)	promoter-TSS (NM_144903)	46	NM_144903	230163	Mm.482116	NM_144903	ENSMUSG00000028307	Aldob	Aldo-2|Aldo2|BC016435	aldolase B, fructose-bisphosphate	protein-coding
mm_60707.1	chr7	45220484	45220510	+	1	NA	exon (NM_001285498, exon 5 of 12)	exon (NM_001285498, exon 5 of 12)	4744	NM_001285498	21677	Mm.3019	NM_011565	ENSMUSG00000030796	Tead2	ETF|Etdf|TEAD-2|TEF-4|TEF4	TEA domain family member 2	protein-coding
mm_137681.1	chr17	28823573	28823602	+	1	NA	intron (NM_001081315, intron 8 of 12)	intron (NM_001081315, intron 8 of 12)	22461	NM_001081315	268936	Mm.291877	NM_199061	ENSMUSG00000063952	Brpf3	AI413466|AW493400|mKIAA1286	bromodomain and PHD finger containing, 3	protein-coding
mm_109270.1	chr12	109545575	109545606	+	1	NA	TTS (NR_035440).2	TTS (NR_035440).2	192	NR_003633	17263	Mm.289645	NM_144513	ENSMUSG00000021268	Meg3	2900016C05Rik|3110050O07Rik|6330408G06Rik|AI425946|AW108224|D12Bwg1266e|Gtl2|R74756|R75394	maternally expressed 3	ncRNA
mm_109219.1	chr12	108792337	108792355	+	1	NA	promoter-TSS (NM_009537)	promoter-TSS (NM_009537)	-965	NM_009537	22632	Mm.3868	NM_009537	ENSMUSG00000021264	Yy1	AW488674|NF-E1	YY1 transcription factor	protein-coding
mm_107326.1	chr12	31654849	31654891	+	1	NA	promoter-TSS (NM_001163126)	promoter-TSS (NM_001163126)	1	NM_001163126	238123	Mm.173068	NM_001163126	ENSMUSG00000035933	Cog5	5430405C01Rik|C87247|D18362|GOLTC1|GTC90	component of oligomeric golgi complex 5	protein-coding
mm_121334.1	chr14	115042276	115042287	+	1	NA	Intergenic	CpG	-1390	NR_029785	723905		NR_029785	ENSMUSG00000065508	Mir17	Mirn17|mir-17|mmu-mir-17	microRNA 17	ncRNA
mm_162573.1	chr1	175105056	175105056	+	1	NA	intron (NM_001347195, intron 9 of 17)	intron (NM_001347195, intron 9 of 17)	-183237	NM_011825	23893	Mm.25760	NM_011825	ENSMUSG00000050069	Grem2	Gremlin2|Prdc	gremlin 2, DAN family BMP antagonist	protein-coding
mm_61886.1	chr7	89633006	89633022	+	1	NA	exon (NM_181407, exon 1 of 14)	exon (NM_181407, exon 1 of 14)	196	NM_181407	109264	Mm.334011	NM_181407	ENSMUSG00000030621	Me3	1700020C08Rik|B230207H15Rik	malic enzyme 3, NADP(+)-dependent, mitochondrial	protein-coding
mm_22789.1	chr3	22087417	22087420	+	1	NA	intron (NM_030732, intron 1 of 15)	intron (NM_030732, intron 1 of 15)	10766	NM_030732	81004	Mm.202966	NM_030732	ENSMUSG00000027630	Tbl1xr1	8030499H02Rik|A630076E03Rik|AW539987|C21|C230089I12Rik|DC42|Ira1|TBLR1	transducin (beta)-like 1X-linked receptor 1	protein-coding
mm_105487.1	chr11	105975080	105975091	-	1	NA	promoter-TSS (NM_009598)	promoter-TSS (NM_009598)	-123	NM_009598	11421	Mm.754	NM_009598	ENSMUSG00000020681	Ace	AW208573|CD143	angiotensin I converting enzyme (peptidyl-dipeptidase A) 1	protein-coding
mm_50846.1	chr6	54848906	54848921	+	1	NA	intron (NM_199143, intron 1 of 4)	intron (NM_199143, intron 1 of 4)	31997	NM_199143	387524	Mm.286149	NM_199143	ENSMUSG00000058446	Znrf2	1190002C14Rik|AU044205|D6Ertd365e	zinc and ring finger 2	protein-coding
mm_26466.1	chr3	144188712	144188733	+	1	NA	3' UTR (NM_010723, exon 5 of 5)	3' UTR (NM_010723, exon 5 of 5)	13610	NM_001161770	16911	Mm.29187	NM_010723	ENSMUSG00000028266	Lmo4	A730077C12Rik|Crp3|Etohi4	LIM domain only 4	protein-coding
mm_113718.1	chr13	43616028	43616044	+	1	NA	5' UTR (NM_183204, exon 1 of 2)	5' UTR (NM_183204, exon 1 of 2)	239	NM_183204	328234	Mm.40588	NM_183204	ENSMUSG00000044164	Rnf182	C630023L15Rik	ring finger protein 182	protein-coding
mm_98577.1	chr11	95712960	95712980	+	1	NA	promoter-TSS (NR_045780)	promoter-TSS (NR_045780)	-216	NR_045780	432396	Mm.426849	NR_045780	ENSMUSG00000086191	Zfp652os	1110035M17Rik	zinc finger protein 652, opposite strand	ncRNA
mm_44736.1	chr5	31174018	31174030	-	1	NA	exon (NM_027901, exon 3 of 19)	exon (NM_027901, exon 3 of 19)	6120	NM_027901	71752	Mm.271923	NM_027901	ENSMUSG00000101678	Gtf3c2	1300004C11Rik|2610510G03Rik|AI225816|AU041069|TFIIIC110|mKIAA0011	general transcription factor IIIC, polypeptide 2, beta	protein-coding
mm_168092.1	chr10	128083282	128083283	+	1	NA	promoter-TSS (NM_016774)	promoter-TSS (NM_016774)	-25	NM_016774	11947	Mm.238973	NM_016774	ENSMUSG00000025393	Atp5b	-	ATP synthase, H+ transporting mitochondrial F1 complex, beta subunit	protein-coding
mm_164847.1	chr18	44315648	44315656	+	1	NA	Intergenic	Intergenic	-18422	NM_001033621	58916	Mm.143804	NM_001033621	ENSMUSG00000024471	Myot	5530402I04Rik|Ttid	myotilin	protein-coding
mm_19449.1	chr2	91986282	91986289	-	1	NA	exon (NM_011957, exon 10 of 12)	exon (NM_011957, exon 10 of 12)	-22722	NM_138306	104418	Mm.314923	NM_138306	ENSMUSG00000040479	Dgkz	E130307B02Rik|ENSMUSG00000075035|F730209L11Rik|mDGK[z]	diacylglycerol kinase zeta	protein-coding
mm_20194.1	chr2	122704093	122704129	-	1	NA	Intergenic	MLT1F|LTR|ERVL-MaLR	-1448	NM_001290993	22785	Mm.27801	NM_011774	ENSMUSG00000005802	Slc30a4	Znt4|lm|znT-4	solute carrier family 30 (zinc transporter), member 4	protein-coding
mm_69228.1	chr7	127649371	127649371	-	1	NA	Intergenic	Intergenic	-34938	NM_177226	320683	Mm.156718	NM_177226	ENSMUSG00000045639	Zfp629	9330199A09Rik|Znf629	zinc finger protein 629	protein-coding
mm_172671.1	chr8	44935247	44935248	+	1	NA	Intergenic	CpG	-14961	NM_001081286	14107	Mm.27365	NM_001081286	ENSMUSG00000070047	Fat1	2310038E12Rik|AU023433|Fath|mFat1	FAT atypical cadherin 1	protein-coding
mm_44976.1	chr5	36826117	36826132	-	1	NA	exon (NM_008550, exon 4 of 19)	exon (NM_008550, exon 4 of 19)	4525	NM_008550	17160	Mm.761	NM_008550	ENSMUSG00000029119	Man2b2	mKIAA0935	mannosidase 2, alpha B2	protein-coding
mm_108015.1	chr12	73594523	73594542	+	1	NA	intron (NM_001313977, intron 2 of 14)	intron (NM_001313977, intron 2 of 14)	9736	NM_008856	18755	Mm.341677	NM_008856	ENSMUSG00000021108	Prkch	Pkch	protein kinase C, eta	protein-coding
mm_31787.1	chr4	63667606	63667632	+	1	NA	Intergenic	Intergenic	-45190	NM_029324	75524	Mm.38543	NM_029324	ENSMUSG00000058935	1700018C11Rik	bM230C2.3	RIKEN cDNA 1700018C11 gene	protein-coding
mm_39153.1	chr4	155414767	155414778	-	1	NA	non-coding (NR_102287, exon 2 of 4)	non-coding (NR_102287, exon 2 of 4)	5582	NM_001166029	544678	Mm.472798	NM_177674	ENSMUSG00000078490	Cfap74	2010015L04Rik|A530045M11	cilia and flagella associated protein 74	protein-coding
mm_125475.1	chr15	54435012	54435016	+	1	NA	exon (NM_173422, exon 2 of 6)	exon (NM_173422, exon 2 of 6)	24240	NM_173422	239447	Mm.82400	NM_173422	ENSMUSG00000038591	Colec10	CL-L1	collectin sub-family member 10	protein-coding
mm_97536.1	chr11	78550922	78550960	+	1	NA	promoter-TSS (NM_133706)	promoter-TSS (NM_133706)	-206	NM_133706	69071	Mm.29431	NM_133706	ENSMUSG00000037278	Tmem97	1810014L12Rik|AI115531|AL022956|D11Bhm182e	transmembrane protein 97	protein-coding
mm_101521.1	chr11	32614701	32614710	-	1	NA	exon (NM_009288, exon 16 of 19)	exon (NM_009288, exon 16 of 19)	-27850	NM_001271348	103583	Mm.28017	NM_134015	ENSMUSG00000020271	Fbxw11	2310065A07Rik|AA536858|BTRC2|BTRCP2|Fbxw1b|HOS	F-box and WD-40 domain protein 11	protein-coding
mm_37011.1	chr4	112774817	112774832	-	1	NA	promoter-TSS (NM_177668)	promoter-TSS (NM_177668)	37	NM_177668	230613	Mm.122553	NM_177668	ENSMUSG00000048766	Skint10	A030001H23Rik|Gm570	selection and upkeep of intraepithelial T cells 10	protein-coding
mm_161106.1	chr12	102899375	102899375	+	1	NA	promoter-TSS (NM_001039049)	promoter-TSS (NM_001039049)	69	NM_001039049	75483	Mm.660	NM_001039049	ENSMUSG00000043319	Cox8c	1700007F21Rik|COX8-3|COXVIII-3	cytochrome c oxidase subunit VIIIc	protein-coding
mm_155326.1	chrX	64497004	64497010	+	1	NA	Intergenic	AT_rich|Low_complexity|Low_complexity	-220011	NM_178740	245446	Mm.101707	NM_178740	ENSMUSG00000046699	Slitrk4	6430513G13|D930039I09Rik	SLIT and NTRK-like family, member 4	protein-coding
mm_135124.1	chr16	35843767	35843793	-	1	NA	intron (NM_001039530, intron 12 of 16)	RLTR17B_Mm|LTR|ERVK	27602	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_50098.1	chr6	41533087	41533097	+	1	NA	Intergenic	Intergenic	11316	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_11817.1	chr2	44160235	44160237	+	1	NA	intron (NM_001301832, intron 11 of 14)	intron (NM_001301832, intron 11 of 14)	-94912	NR_040622	320872	Mm.445023	NR_040622	ENSMUSG00000085089	Arhgap15os	A430092G05Rik	Rho GTPase activating protein 15, opposite strand	ncRNA
mm_160629.1	chr9	106429534	106429534	+	1	NA	5' UTR (NM_001324533, exon 1 of 4)	5' UTR (NM_001324533, exon 1 of 4)	123	NM_009082	19944	Mm.288696	NM_009082	ENSMUSG00000048758	Rpl29	Rpl43	ribosomal protein L29	protein-coding
mm_106963.1	chr12	8928149	8928166	+	1	NA	intron (NM_008640, intron 1 of 6)	B2_Mm2|SINE|B2	6850	NM_008640	17775	Mm.30071	NM_008640	ENSMUSG00000020585	Laptm4a	AA286466|LAPTM4|MTP|Mtrp|mKIAA0108	lysosomal-associated protein transmembrane 4A	protein-coding
mm_6648.1	chr1	79672085	79672088	-	1	NA	promoter-TSS (NM_183027)	promoter-TSS (NM_183027)	-114	NM_183027	252903	Mm.32409	NM_183027	ENSMUSG00000054702	Ap1s3	1190009B22|Jr2|[s]3A	adaptor-related protein complex AP-1, sigma 3	protein-coding
mm_3449.1	chr1	150103005	150103014	+	1	NA	intron (NM_011198, intron 5 of 9)	intron (NM_011198, intron 5 of 9)	2978	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_149858.1	chr19	25097236	25097246	+	1	NA	intron (NM_028785, intron 11 of 47)	intron (NM_028785, intron 11 of 47)	97712	NM_028785	76088	Mm.102485	NM_028785	ENSMUSG00000052085	Dock8	1200017A24Rik|5830472H07Rik|A130095G14Rik|AI461977	dedicator of cytokinesis 8	protein-coding
mm_22046.1	chr2	168230576	168230604	-	1	NA	promoter-TSS (NM_010072)	promoter-TSS (NM_010072)	-32	NM_001160330	69372	Mm.482182	NM_001160330	ENSMUSG00000074576	Mocs3	1700020H17Rik|Uba4	molybdenum cofactor synthesis 3	protein-coding
mm_165065.1	chr19	44294004	44294041	+	1	NA	5' UTR (NM_009128, exon 1 of 6)	5' UTR (NM_009128, exon 1 of 6)	346	NM_009128	20250	Mm.487021	NM_009128	ENSMUSG00000025203	Scd2	Mir5114|Scd-2|mir-5114|swty	stearoyl-Coenzyme A desaturase 2	protein-coding
mm_92107.1	chr10	63023861	63023871	-	1	NA	promoter-TSS (NM_001079824)	promoter-TSS (NM_001079824)	-17	NM_001079824	432467	Mm.274784	NM_001079824	ENSMUSG00000020069	Hnrnph3	AA693301|AI666703|Hnrph3	heterogeneous nuclear ribonucleoprotein H3	protein-coding
mm_73425.1	chr8	106135402	106135431	+	1	NA	promoter-TSS (NR_040346)	promoter-TSS (NR_040346)	16	NR_040346	69771	Mm.393274	NR_040344		1810019D21Rik	-	RIKEN cDNA 1810019D21 gene	ncRNA
mm_108098.1	chr12	74804221	74804222	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	373111	NM_172805	238271	Mm.44465	NM_172805	ENSMUSG00000034402	Kcnh5	Eag2	potassium voltage-gated channel, subfamily H (eag-related), member 5	protein-coding
mm_106448.1	chr11	119937447	119937466	-	1	NA	Intergenic	Intergenic	-5636	NM_001037754	108100	Mm.197534	NM_130862	ENSMUSG00000025372	Baiap2	IRSp53|R75030	brain-specific angiogenesis inhibitor 1-associated protein 2	protein-coding
mm_33875.1	chr4	136147222	136147248	+	1	NA	Intergenic	Intergenic	3413	NM_008321	15903	Mm.110	NM_008321	ENSMUSG00000007872	Id3	Hlh462|Idb3|bHLHb25	inhibitor of DNA binding 3	protein-coding
mm_144121.1	chr18	4634978	4634990	+	1	NA	promoter-TSS (NM_001081963)	promoter-TSS (NM_001081963)	55	NM_001081963	240185	Mm.33179	NM_001081963	ENSMUSG00000033960	9430020K01Rik	1110056P05Rik|Gm328|Jcad|mKIAA1462	RIKEN cDNA 9430020K01 gene	protein-coding
mm_45096.1	chr5	44226802	44226837	-	1	NA	promoter-TSS (NM_173764)	promoter-TSS (NM_173764)	-213	NM_173764	231225	Mm.30688	NM_173764	ENSMUSG00000046985	Tapt1	4932414K18Rik	transmembrane anterior posterior transformation 1	protein-coding
mm_26614.1	chr3	152350005	152350012	+	1	NA	intron (NM_001076676, intron 1 of 23)	(T)n|Simple_repeat|Simple_repeat	3530	NM_001076676	170822	Mm.258320	NM_133247	ENSMUSG00000025437	Usp33	9830169D19Rik|AA409780|Vdu1	ubiquitin specific peptidase 33	protein-coding
mm_88387.1	chr10	76468867	76468993	+	1	NA	promoter-TSS (NM_019434)	promoter-TSS (NM_019434)	-41	NM_019434	54387	Mm.30098	NM_019434	ENSMUSG00000001150	Mcm3ap	GANP|mKIAA0572	minichromosome maintenance complex component 3 associated protein	protein-coding
mm_160560.1	chr9	52168352	52168352	-	1	NA	promoter-TSS (NM_001162921)	promoter-TSS (NM_001162921)	-241	NM_001162921	244871	Mm.295686	NM_001162921	ENSMUSG00000035164	Zc3h12c	A230108E06|C230027N18Rik|mKIAA1726	zinc finger CCCH type containing 12C	protein-coding
mm_126485.1	chr15	81608084	81608088	+	1	NA	intron (NM_177821, intron 2 of 30)	intron (NM_177821, intron 2 of 30)	21872	NM_177821	328572	Mm.258397	NM_177821	ENSMUSG00000055024	Ep300	A430090G16|A730011L11|KAT3B|p300|p300 HAT	E1A binding protein p300	protein-coding
mm_162910.1	chr10	118107308	118107310	+	1	NA	Intergenic	Intergenic	-34478	NM_001162904	17245	Mm.101191	NM_010785	ENSMUSG00000020212	Mdm1	Arrd2|Mdm-1	transformed mouse 3T3 cell double minute 1	protein-coding
mm_146112.1	chr18	74268213	74268227	+	1	NA	promoter-TSS (NM_013594)	promoter-TSS (NM_013594)	-68	NM_013594	17190	Mm.22522	NM_013594	ENSMUSG00000024561	Mbd1	Cxxc3|PCM1	methyl-CpG binding domain protein 1	protein-coding
mm_134094.1	chr16	9895030	9895043	-	1	NA	intron (NM_008170, intron 1 of 11)	intron (NM_008170, intron 1 of 11)	97497	NM_008170	14811	Mm.2953	NM_008170	ENSMUSG00000059003	Grin2a	GluN2A|NMDAR2A|NR2A	glutamate receptor, ionotropic, NMDA2A (epsilon 1)	protein-coding
mm_86934.1	chr10	24223410	24223430	+	1	NA	promoter-TSS (NM_021509)	promoter-TSS (NM_021509)	-97	NM_021509	59012	Mm.285934	NM_021509	ENSMUSG00000020000	Moxd1	3230402N08Rik|MNCb-5203	monooxygenase, DBH-like 1	protein-coding
mm_73210.1	chr8	95714608	95714622	+	1	NA	3' UTR (NM_145602, exon 14 of 14)	3' UTR (NM_145602, exon 14 of 14)	-1298	NM_001035123	66083	Mm.261321	NM_001035123	ENSMUSG00000031671	Setd6	0610039J04Rik|3110004G14Rik|AI413388|C76402	SET domain containing 6	protein-coding
mm_83179.1	chr9	40963044	40963046	-	1	NA	intron (NM_001081121, intron 1 of 8)	intron (NM_001081121, intron 1 of 8)	1067	NM_001081121	70989	Mm.335087	NM_001081121	ENSMUSG00000032023	Jhy	4931429I11Rik|BB239335	juvenile hydrocephalus	protein-coding
mm_132990.1	chr16	52746470	52746473	+	1	NA	Intergenic	Intergenic	69273	NR_040495	73820	Mm.60493	NR_040495		4930404A05Rik	-	RIKEN cDNA 4930404A05 gene	ncRNA
mm_83863.1	chr9	54802961	54802971	-	1	NA	Intergenic	Intergenic	38218	NM_013496	12903	Mm.34797	NM_013496	ENSMUSG00000032291	Crabp1	AI326249|CRABP-I|Crabp-1|CrabpI|Rbp-5	cellular retinoic acid binding protein I	protein-coding
mm_86691.1	chr10	18431293	18431304	+	1	NA	intron (NM_173390, intron 1 of 6)	intron (NM_173390, intron 1 of 6)	23623	NM_173390	215819	Mm.297971	NM_173390	ENSMUSG00000039835	Nhsl1	5730409E15Rik|A630035H13Rik|A730096F01|BC013565|D10Bwg0940e|mKIAA1357	NHS-like 1	protein-coding
mm_123650.1	chr14	69171828	69171837	-	1	NA	promoter-TSS (NM_010920)	promoter-TSS (NM_010920)	11	NR_045931	73554	Mm.320005	NR_045931	ENSMUSG00000092499	1700092C10Rik	-	RIKEN cDNA 1700092C10 gene	ncRNA
mm_45861.1	chr5	87843435	87843459	-	1	NA	exon (NM_001163551, exon 5 of 6)	exon (NM_001163551, exon 5 of 6)	-6912	NR_003652	654494	Mm.475331	NM_001039193	ENSMUSG00000067156	Gm7337	EG654494	DAZ interacting protein 1 pseudogene	pseudo
mm_76335.1	chr8	84713813	84713828	-	1	NA	exon (NM_010906, exon 8 of 9)	exon (NM_010906, exon 8 of 9)	12363	NM_008535	17095	Mm.4925	NM_008535	ENSMUSG00000034041	Lyl1	Lyl-1|bHLHa18	lymphoblastomic leukemia 1	protein-coding
mm_7612.1	chr1	126604673	126604732	-	1	NA	intron (NM_001081756, intron 2 of 16)	intron (NM_001081756, intron 2 of 16)	-111775	NM_172484	210356	Mm.377234	NM_172484	ENSMUSG00000049690	Nckap5	8430408F21|D130011D22Rik|E030049G20Rik|Erih1|Erih2|Gm1548|Nap5	NCK-associated protein 5	protein-coding
mm_13851.1	chr2	119618722	119618737	+	1	NA	promoter-TSS (NM_001042653)	promoter-TSS (NM_001042653)	-224	NM_001042653	70645	Mm.246412	NM_001042653	ENSMUSG00000072980	Oip5	5730547N13Rik|Lint-25|Ms18b	Opa interacting protein 5	protein-coding
mm_72551.1	chr8	84026060	84026086	+	1	NA	intron (NM_028877, intron 2 of 6)	CpG	4599	NM_028877	74337	Mm.250943	NM_028877	ENSMUSG00000047986	Palm3	4432412L15Rik|AL024300	paralemmin 3	protein-coding
mm_139944.1	chr17	71183705	71183715	+	1	NA	promoter-TSS (NM_022882)	promoter-TSS (NM_022882)	-268	NM_022882	64898	Mm.227924	NM_022882	ENSMUSG00000024052	Lpin2	2610511G02Rik|AI481352|AW742896	lipin 2	protein-coding
mm_93895.1	chr10	125389313	125389325	-	1	NA	Intergenic	CpG	-60784	NM_011391	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|Mct2	solute carrier family 16 (monocarboxylic acid transporters), member 7	protein-coding
mm_91264.1	chr10	23785817	23785821	-	1	NA	promoter-TSS (NR_037681)	promoter-TSS (NR_037681)	2	NR_037681	100529075		NR_037681	ENSMUSG00000080486	Snord100	MBII-429|Z51	small nucleolar RNA, C/D box 100	snoRNA
mm_33900.1	chr4	136284638	136284652	+	1	NA	Intergenic	Intergenic	-1424	NM_009557	22704	Mm.1504	NM_009557	ENSMUSG00000051351	Zfp46	AI426962|Mlz-4|Zfp-46|Znf436	zinc finger protein 46	protein-coding
mm_54061.1	chr6	13871460	13871471	-	1	NA	promoter-TSS (NR_024619)	promoter-TSS (NR_024619)	18	NR_024619	66520	Mm.29615	NM_183258		2610001J05Rik	C79299	RIKEN cDNA 2610001J05 gene	ncRNA
mm_95669.1	chr11	53856960	53856985	+	1	NA	intron (NR_033332, intron 1 of 3)	MT2A|LTR|ERVL	2284	NR_033332	622459	Mm.479656	NR_033332	ENSMUSG00000081769	Gm12216	602-19-115|OTTMUSG00000005650	predicted gene 12216	ncRNA
mm_33655.1	chr4	133096857	133096863	+	1	NA	Intergenic	RLTR4_MM-int|LTR|ERV1	-33773	NM_153423	242687	Mm.23566	NM_153423	ENSMUSG00000028868	Wasf2	AW742646|D4Ertd13e|WAVE2	WAS protein family, member 2	protein-coding
mm_129001.1	chr15	74842619	74842628	-	1	NA	promoter-TSS (NM_001033229)	promoter-TSS (NM_001033229)	-980	NM_001033229	110115	Mm.322606	NM_001033229	ENSMUSG00000075604	Cyp11b1	AA389061|CPN1|Cyp11b|Cyp11b-1|FHI	cytochrome P450, family 11, subfamily b, polypeptide 1	protein-coding
mm_77499.1	chr8	122611420	122611438	-	1	NA	promoter-TSS (NM_016722)	promoter-TSS (NM_016722)	58	NM_001193645	50917	Mm.1786	NM_016722	ENSMUSG00000015027	Galns	mFLJ00319	galactosamine (N-acetyl)-6-sulfate sulfatase	protein-coding
mm_140225.1	chr17	83980574	83980623	+	1	NA	Intergenic	Intergenic	-17954	NR_130994	78148	Mm.243918	NR_130994		8430430B14Rik	-	RIKEN cDNA 8430430B14 gene	ncRNA
mm_133055.1	chr16	58408482	58408523	+	1	NA	promoter-TSS (NM_028523)	promoter-TSS (NM_028523)	-33	NM_028523	73379	Mm.373589	NM_028523	ENSMUSG00000035107	Dcbld2	1700055P21Rik|AW146002|CLCP1|Esdn	discoidin, CUB and LCCL domain containing 2	protein-coding
mm_98478.1	chr11	94950704	94950744	+	1	NA	exon (NM_007742, exon 49 of 51)	exon (NM_007742, exon 49 of 51)	14500	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_58143.1	chr6	141946961	141946964	-	1	NA	promoter-TSS (NM_013797)	promoter-TSS (NM_013797)	0	NM_013797	28248	Mm.103665	NM_013797	ENSMUSG00000041698	Slco1a1	A530084B21|OATP-1|Oatp1|Oatp1a1|Slc21a1	solute carrier organic anion transporter family, member 1a1	protein-coding
mm_39046.1	chr4	152448809	152448848	-	1	NA	promoter-TSS (NM_001252656)	promoter-TSS (NM_001252656)	27	NM_001252655	16498	Mm.388924	NM_010598	ENSMUSG00000028931	Kcnab2	F5|I2rf5|Kcnb3|kv-beta-2	potassium voltage-gated channel, shaker-related subfamily, beta member 2	protein-coding
mm_149026.1	chr19	8766715	8766727	+	1	NA	3' UTR (NM_001276704, exon 10 of 20)	3' UTR (NM_001276704, exon 10 of 20)	-4275	NM_025791	66836	Mm.440071	NM_025791	ENSMUSG00000010097	Tmem223	0610006I08Rik	transmembrane protein 223	protein-coding
mm_94190.1	chr10	128960966	128960982	-	1	NA	promoter-TSS (NM_027853)	promoter-TSS (NM_027853)	14	NM_027853	71664	Mm.337232	NM_027853	ENSMUSG00000025347	Mettl7b	0610006F02Rik|AI266817	methyltransferase like 7B	protein-coding
mm_142659.1	chr17	47688029	47688101	-	1	NA	TTS (NM_001290337)	TTS (NM_001290337)	321	NM_025365	66119	Mm.89912	NM_025365	ENSMUSG00000033475	Tomm6	1110002E23Rik|AI663970	translocase of outer mitochondrial membrane 6 homolog (yeast)	protein-coding
mm_33995.1	chr4	137905246	137905254	+	1	NA	intron (NM_199307, intron 2 of 19)	hAT-N1_Mam|DNA|hAT?	43013	NM_199307	230857	Mm.401062	NM_199307	ENSMUSG00000057530	Ece1	AW322500|ECE-1|ECE-1a|ECE-1b|ECE-1d	endothelin converting enzyme 1	protein-coding
mm_153661.1	chr19	44395617	44395639	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	12081	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_154945.1	chrX	36328400	36328418	+	1	NA	promoter-TSS (NM_028894)	promoter-TSS (NM_028894)	0	NM_028894	74365	Mm.327654	NM_028894	ENSMUSG00000016239	Lonrf3	4932412G04Rik|5730439E01Rik|A830039N02Rik|AU023707|Rnf127	LON peptidase N-terminal domain and ring finger 3	protein-coding
mm_138174.1	chr17	34264881	34264891	+	1	NA	exon (NM_207105, exon 2 of 6)	exon (NM_207105, exon 2 of 6)	1659	NM_207105	14961	Mm.254067	NM_207105	ENSMUSG00000073421	H2-Ab1	AI845868|Abeta|H-2Ab|H2-Ab|I-Abeta|IAb|Ia-2|Ia2|Rmcs1	histocompatibility 2, class II antigen A, beta 1	protein-coding
mm_140159.1	chr17	80207522	80207543	+	1	NA	promoter-TSS (NM_001195487)	promoter-TSS (NM_001195487)	-227	NM_001195485	225027	Mm.292016	NM_146083	ENSMUSG00000024097	Srsf7	35kDa|9430065L19Rik|9G8|NX-96|Sfrs7	serine/arginine-rich splicing factor 7	protein-coding
mm_128372.1	chr15	42676270	42676303	-	1	NA	exon (NM_001286062, exon 1 of 9)	exon (NM_001286062, exon 1 of 9)	691	NM_001286062	11600	Mm.309336	NM_009640	ENSMUSG00000022309	Angpt1	1110046O21Rik|Ang-1|Ang1	angiopoietin 1	protein-coding
mm_113697.1	chr13	43125881	43125891	+	1	NA	intron (NM_001005740, intron 9 of 12)	intron (NM_001005740, intron 9 of 12)	3047	NM_001005748	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding
mm_165266.1	chr2	74716003	74716007	-	1	NA	non-coding (NR_027899, exon 1 of 3)	non-coding (NR_027899, exon 1 of 3)	125	NR_027899	73429	Mm.443313	NR_027899		Hoxd3os1	1700064D17Rik|1700109F18Rik	homeobox D3, opposite strand 1	ncRNA
mm_111594.1	chr12	101976024	101976035	-	1	NA	promoter-TSS (NM_016856)	promoter-TSS (NM_016856)	55	NM_016856	51786	Mm.716	NM_016856	ENSMUSG00000041781	Cpsf2	100kDa|2610024B04Rik|AI662483|Cpsf|MCPSF|mKIAA1367	cleavage and polyadenylation specific factor 2	protein-coding
mm_144232.1	chr18	10346150	10346152	+	1	NA	intron (NM_001083628, intron 1 of 32)	intron (NM_001083628, intron 1 of 32)	20972	NM_001083628	381157	Mm.261535	NM_001083628	ENSMUSG00000042942	Greb1l	mKIAA4095	growth regulation by estrogen in breast cancer-like	protein-coding
mm_25909.1	chr3	131112786	131112803	+	1	NA	promoter-TSS (NM_001276403)	promoter-TSS (NM_001276403)	3	NM_001276403	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_159524.1	chr4	61673528	61673528	-	1	NA	exon (NM_001199333, exon 2 of 7)	exon (NM_001199333, exon 2 of 7)	562	NM_001134644	100048885	Mm.422695	NM_001134644		Gm2083	-	major urinary protein LOC100048885	protein-coding
mm_67421.1	chr7	80339991	80340010	-	1	NA	intron (NM_133952, intron 1 of 19)	CpG	219	NM_133952	101869	Mm.243024	NM_133952	ENSMUSG00000030533	Unc45a	AW538196	unc-45 myosin chaperone A	protein-coding
mm_37385.1	chr4	120985289	120985303	-	1	NA	exon (NM_133716, exon 2 of 10)	exon (NM_133716, exon 2 of 10)	-11974	NR_105982	102465614		NR_105982	ENSMUSG00000106436	Mir7015	mmu-mir-7015	microRNA 7015	ncRNA
mm_55044.1	chr6	48988483	48988532	-	1	NA	exon (NM_172888, exon 1 of 5)	exon (NM_172888, exon 1 of 5)	1646	NM_172888	243377	Mm.446302	NM_172888	ENSMUSG00000039215	Svs1	9530003A11	seminal vesicle secretory protein 1	protein-coding
mm_106772.1	chr12	4600241	4600246	+	1	NA	intron (NM_011365, intron 1 of 38)	B4A|SINE|B4	7235	NM_001198968	20403	Mm.341204	NM_011365	ENSMUSG00000020640	Itsn2	AI327390|Ese2|Sh3d1B|Sh3p18|mKIAA1256	intersectin 2	protein-coding
mm_158794.1	chrX	167241109	167241140	-	1	NA	TTS (NM_001313760)	TTS (NM_001313760)	23205	NM_001313761	170744	Mm.196676	NM_133212	ENSMUSG00000040522	Tlr8	-	toll-like receptor 8	protein-coding
mm_934.1	chr1	55456721	55456737	+	1	NA	intron (NM_001114663, intron 1 of 5)	B1_Mus1|SINE|Alu	50783	NM_001114663	227120	Mm.194183	NM_001114663	ENSMUSG00000038349	Plcl1	C230017K02Rik|PLC-L|PLC-L1|PLCE|PLCL|PLDL1|PRIP|PRIP-1	phospholipase C-like 1	protein-coding
mm_40048.1	chr5	33983538	33983548	+	1	NA	exon (NM_001033458, exon 1 of 4)	exon (NM_001033458, exon 1 of 4)	110	NM_001310546	381633	Mm.4923	NM_001033458	ENSMUSG00000070858	Gm1673	-	predicted gene 1673	protein-coding
mm_7489.1	chr1	121328028	121328044	-	1	NA	promoter-TSS (NM_001271531)	promoter-TSS (NM_001271531)	-12	NM_133748	72999	Mm.27136	NM_133748	ENSMUSG00000003721	Insig2	2900053I11Rik|C730043J18Rik|Insig-2	insulin induced gene 2	protein-coding
mm_121910.1	chr14	21988415	21988436	-	1	NA	intron (NM_145459, intron 1 of 2)	CpG-4314	1176	NM_145459	218820	Mm.292401	NM_145459	ENSMUSG00000039081	Zfp503	AI181838|B830002A16Rik|Nolz-1|Nolz1|Znf503	zinc finger protein 503	protein-coding
mm_135592.1	chr16	50722792	50722802	-	1	NA	Intergenic	MLT1A1|LTR|ERVL-MaLR	-4335	NR_105782	102466634		NR_105782	ENSMUSG00000098482	Mir6363	Gm28026|mmu-mir-6363	microRNA 6363	ncRNA
mm_105195.1	chr11	102088440	102088470	-	1	NA	promoter-TSS (NM_016695)	promoter-TSS (NM_016695)	60	NM_016695	50997	Mm.36242	NM_016695	ENSMUSG00000017314	Mpp2	D11Bwg0652e|Dlg2|Dlgh2|Pals4	membrane protein, palmitoylated 2 (MAGUK p55 subfamily member 2)	protein-coding
mm_16209.1	chr2	173065303	173065307	+	1	NA	Intergenic	MTC|LTR|ERVL-MaLR	43403	NM_019547	56190	Mm.485782	NM_019547	ENSMUSG00000027510	Rbm38	Rnpc1|Seb4|Seb4l	RNA binding motif protein 38	protein-coding
mm_96036.1	chr11	59556338	59556347	+	1	NA	intron (NM_145827, intron 6 of 9)	intron (NM_145827, intron 6 of 9)	13656	NM_145827	216799	Mm.54174	NM_145827	ENSMUSG00000032691	Nlrp3	AGTAVPRL|AII/AVP|Cias1|FCAS|FCU|MWS|Mmig1|NALP3|Pypaf1	NLR family, pyrin domain containing 3	protein-coding
mm_171818.1	chr5	138504794	138504795	+	1	NA	Intergenic	Intergenic	59900	NM_029693	76658	Mm.73235	NM_029693	ENSMUSG00000029526	1700123K08Rik	-	RIKEN cDNA 1700123K08 gene	protein-coding
mm_151972.1	chr19	5825982	5826007	-	1	NA	non-coding (NR_131212, exon 1 of 1)	non-coding (NR_131212, exon 1 of 1)	19484	NR_131212	66961	Mm.281895	NR_003513	ENSMUSG00000092274	Neat1	2310043N10Rik|VINC	nuclear paraspeckle assembly transcript 1 (non-protein coding)	ncRNA
mm_161035.1	chr12	21316257	21316257	+	1	NA	promoter-TSS (NM_026347)	promoter-TSS (NM_026347)	-135	NM_026347	67732	Mm.335830	NM_026347	ENSMUSG00000062054	Iah1	1500019E20Rik|4833421E05Rik	isoamyl acetate-hydrolyzing esterase 1 homolog	protein-coding
mm_55103.1	chr6	50223115	50223158	-	1	NA	intron (NM_018769, intron 5 of 9)	ORR1E|LTR|ERVL-MaLR	38633	NM_018769	54722	Mm.248361	NM_018769	ENSMUSG00000029821	Dfna5	2310037D07Rik|4932441K13Rik|Dfna5h|EG14210|Fin15	deafness, autosomal dominant 5 (human)	protein-coding
mm_95047.1	chr11	32286992	32287007	+	1	NA	promoter-TSS (NM_001033981)	promoter-TSS (NM_001033981)	35	NM_001033981	544763	Mm.450958	NM_001033981	ENSMUSG00000073063	Hbq1b	F830116E18Rik|Hbqt1	hemoglobin, theta 1B	protein-coding
mm_108033.1	chr12	73756012	73756042	+	1	NA	intron (NM_001313977, intron 11 of 14)	intron (NM_001313977, intron 11 of 14)	-145297	NM_001313920	15251	Mm.3879	NM_010431	ENSMUSG00000021109	Hif1a	AA959795|HIF-1-alpha|HIF1-alpha|HIF1alpha|MOP1|bHLHe78	hypoxia inducible factor 1, alpha subunit	protein-coding
mm_121578.1	chr14	122913193	122913218	+	1	NA	promoter-TSS (NM_145466)	promoter-TSS (NM_145466)	-40	NM_145466	223267	Mm.379358	NM_145466	ENSMUSG00000041625	Ggact	A2ld1	gamma-glutamylamine cyclotransferase	protein-coding
mm_96679.1	chr11	69423336	69423338	+	1	NA	intron (NM_001081330, intron 79 of 85)	intron (NM_001081330, intron 79 of 85)	-9662	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_32213.1	chr4	101550412	101550432	+	1	NA	promoter-TSS (NM_001164583)	promoter-TSS (NM_001164583)	-172	NM_001164583	72685	Mm.76494	NM_198412	ENSMUSG00000028528	Dnajc6	2810027M23Rik|mKIAA0473	DnaJ heat shock protein family (Hsp40) member C6	protein-coding
mm_128118.1	chr15	28229878	28229891	-	1	NA	intron (NM_133365, intron 4 of 78)	intron (NM_133365, intron 4 of 78)	26118	NM_133365	110082	Mm.248464	NM_133365	ENSMUSG00000022262	Dnah5	AU022615|Dnahc5|Mdnah5|b2b1134Clo|b2b1154Clo|b2b1537Clo|b2b1565Clo|b2b601Clo|mKIAA1603	dynein, axonemal, heavy chain 5	protein-coding
mm_165162.1	chr2	25289952	25289961	+	1	NA	promoter-TSS (NM_146117)	promoter-TSS (NM_146117)	45	NM_146117	227618	Mm.275228	NM_146117	ENSMUSG00000026961	Lrrc26	-	leucine rich repeat containing 26	protein-coding
mm_121365.1	chr14	117368210	117368212	+	1	NA	intron (NM_001079844, intron 2 of 9)	intron (NM_001079844, intron 2 of 9)	442914	NM_011821	23888	Mm.440025	NM_011821	ENSMUSG00000058571	Gpc6	-	glypican 6	protein-coding
mm_108141.1	chr12	76255245	76255257	+	1	NA	promoter-TSS (NM_138745)	promoter-TSS (NM_138745)	19	NM_138745	108156	Mm.29584	NM_138745	ENSMUSG00000021048	Mthfd1	Dcs|E430024A07Rik|Mthfd	methylenetetrahydrofolate dehydrogenase (NADP+ dependent), methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthase	protein-coding
mm_83419.1	chr9	44925656	44925669	-	1	NA	3' UTR (NM_145400, exon 20 of 20)	3' UTR (NM_145400, exon 20 of 20)	-4920	NM_013795	27425	Mm.14663	NM_013795	ENSMUSG00000038717	Atp5l	4933437C06Rik	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit G	protein-coding
mm_114451.1	chr13	66933385	66933424	+	1	NA	promoter-TSS (NM_025547)	promoter-TSS (NM_025547)	-332	NM_025547	66410	Mm.347939	NM_025547	ENSMUSG00000021519	Mterf3	2410017I18Rik|Mterfd1	mitochondrial transcription termination factor 3	protein-coding
mm_35350.1	chr4	32255457	32255462	-	1	NA	Intergenic	Intergenic	-161976	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_41313.1	chr5	90469572	90469580	+	1	NA	exon (NM_009654, exon 9 of 15)	exon (NM_009654, exon 9 of 15)	8706	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_15751.1	chr2	164237767	164237774	+	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	571	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_107107.1	chr12	17791353	17791364	+	1	NA	3' UTR (NM_016677, exon 4 of 4)	3' UTR (NM_016677, exon 4 of 4)	100544	NM_016677	53602	Mm.313619	NM_016677	ENSMUSG00000071379	Hpcal1	NVP-3|Nvp3|VILIP3|Vnsl3|Vsnl3	hippocalcin-like 1	protein-coding
mm_37036.1	chr4	115487245	115487276	-	1	NA	exon (NM_007822, exon 12 of 12)	exon (NM_007822, exon 12 of 12)	8881	NM_007822	13119	Mm.250901	NM_007822	ENSMUSG00000028715	Cyp4a14	AI314743	cytochrome P450, family 4, subfamily a, polypeptide 14	protein-coding
mm_131607.1	chr16	19232604	19232608	+	1	NA	Intergenic	Intergenic	54135	NM_146451	258443	Mm.377506	NM_146451	ENSMUSG00000050742	Olfr164	MOR279-2	olfactory receptor 164	protein-coding
mm_62358.1	chr7	100499332	100499358	+	1	NA	exon (NM_011671, exon 8 of 8)	exon (NM_011671, exon 8 of 8)	5987	NM_011671	22228	Mm.171378	NM_011671	ENSMUSG00000033685	Ucp2	Slc25a8	uncoupling protein 2 (mitochondrial, proton carrier)	protein-coding
mm_359.1	chr1	33813377	33813404	+	1	NA	intron (NM_001290699, intron 2 of 12)	intron (NM_001290699, intron 2 of 12)	1205	NM_133817	98403	Mm.289103	NM_133817	ENSMUSG00000042197	Zfp451	4930515K21Rik|4933435G09Rik|AI596398|COASTER|Kiaa0576-hp|Znf451|mKIAA1702	zinc finger protein 451	protein-coding
mm_81820.1	chr9	118043883	118043920	+	1	NA	intron (NM_001286507, intron 1 of 6)	intron (NM_001286507, intron 1 of 6)	3379	NM_013727	27215	Mm.92705	NM_013727	ENSMUSG00000039285	Azi2	AA410145|AZ2	5-azacytidine induced gene 2	protein-coding
mm_31619.1	chr4	59189241	59189254	+	1	NA	promoter-TSS (NM_011673)	promoter-TSS (NM_011673)	-303	NM_011673	22234	Mm.198803	NM_011673	ENSMUSG00000028381	Ugcg	AU043821|C80537|Epcs21|GlcT-1|Ugcgl	UDP-glucose ceramide glucosyltransferase	protein-coding
mm_153783.1	chr19	45784041	45784051	-	1	NA	promoter-TSS (NM_023799)	promoter-TSS (NM_023799)	-755	NM_023799	76055	Mm.122725	NM_023799	ENSMUSG00000025220	Mgea5	2810009A20Rik|4833427O07Rik|5830447M11Rik|AA408215|Hy5|Ncoat|OGA|mKIAA0679	meningioma expressed antigen 5 (hyaluronidase)	protein-coding
mm_6604.1	chr1	75362183	75362223	-	1	NA	exon (NM_010043, exon 2 of 9)	exon (NM_010043, exon 2 of 9)	1911	NM_010043	13346	Mm.6712	NM_010043	ENSMUSG00000026208	Des	-	desmin	protein-coding
mm_74124.1	chr8	123186164	123186174	+	1	NA	promoter-TSS (NM_007876)	promoter-TSS (NM_007876)	-66	NM_007876	13479	Mm.20388	NM_007876	ENSMUSG00000019278	Dpep1	AI327012|MBD	dipeptidase 1 (renal)	protein-coding
mm_3430.1	chr1	150100965	150101057	+	1	NA	exon (NM_011198, exon 2 of 10)	exon (NM_011198, exon 2 of 10)	980	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_22362.1	chr2	181039233	181039282	-	1	NA	promoter-TSS (NM_015730)	promoter-TSS (NM_015730)	-80	NM_015730	11438	Mm.252369	NM_015730	ENSMUSG00000027577	Chrna4	Acra-4|Acra4|EBN1|ENFL1	cholinergic receptor, nicotinic, alpha polypeptide 4	protein-coding
mm_149269.1	chr19	10582222	10582252	+	1	NA	intron (NM_001282067, intron 4 of 8)	intron (NM_001282067, intron 4 of 8)	-4851	NR_126092	72982	Mm.391194	NM_028411	ENSMUSG00000024666	Tmem138	1700113I01Rik|2900055D14Rik	transmembrane protein 138	protein-coding
mm_96304.1	chr11	63158415	63158434	+	1	NA	3' UTR (NM_008885, exon 5 of 5)	3' UTR (NM_008885, exon 5 of 5)	25621	NM_001302260	18858	Mm.1237	NM_008885	ENSMUSG00000018217	Pmp22	22kDa|Gas-3|HNPP|Tr|trembler	peripheral myelin protein 22	protein-coding
mm_108074.1	chr12	73945661	73945674	+	1	NA	exon (NM_010431, exon 15 of 15)	exon (NM_010431, exon 15 of 15)	-18863	NM_178392	75627	Mm.25937	NM_178392	ENSMUSG00000021113	Snapc1	2700033G17Rik|AU015787	small nuclear RNA activating complex, polypeptide 1	protein-coding
mm_18552.1	chr2	65171665	65171685	-	1	NA	intron (NM_027225, intron 1 of 12)	intron (NM_027225, intron 1 of 12)	66951	NM_177025	319876	Mm.34159	NM_027225	ENSMUSG00000034903	Cobll1	1810047P18Rik|Coblr1|D430044D16Rik	Cobl-like 1	protein-coding
mm_89131.1	chr10	85102759	85102833	+	1	NA	promoter-TSS (NM_010214)	promoter-TSS (NM_010214)	169	NM_001013028	103266	Mm.335025	NM_001013028	ENSMUSG00000060935	Tmem263	AI597468	transmembrane protein 263	protein-coding
mm_68227.1	chr7	104439293	104439307	-	1	NA	intron (NM_009099, intron 1 of 7)	Lx4A|LINE|L1	25893	NM_009099	20128	Mm.295578	NM_009099	ENSMUSG00000030921	Trim30a	Rpt-1|Rpt1|Trim30	tripartite motif-containing 30A	protein-coding
mm_55136.1	chr6	51320888	51320896	-	1	NA	Intergenic	Intergenic	-50982	NR_029719	387166		NR_029719	ENSMUSG00000065505	Mir148a	Mirn148|Mirn148a|mir-148a	microRNA 148a	ncRNA
mm_117546.1	chr13	83729670	83729680	-	1	NA	intron (NR_015561, intron 1 of 3)	intron (NR_015561, intron 1 of 3)	1569	NR_015561	320203	Mm.245636	NM_177100	ENSMUSG00000050334	C130071C03Rik	2810449C10Rik	RIKEN cDNA C130071C03 gene	ncRNA
mm_157095.1	chrX	9437285	9437285	-	1	NA	3' UTR (NM_007807, exon 13 of 13)	3' UTR (NM_007807, exon 13 of 13)	32039	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_2338.1	chr1	92848626	92848672	+	1	NA	intron (NM_016696, intron 1 of 8)	CpG	-1729	NR_029559	387167		NR_029559	ENSMUSG00000065470	Mir149	Mirn149|mir-149|mmu-mir-149	microRNA 149	ncRNA
mm_74505.1	chr8	8484737	8484750	-	1	NA	Intergenic	Intergenic	176030	NM_010111	13642	Mm.209813	NM_010111	ENSMUSG00000001300	Efnb2	ELF-2|Epl5|Eplg5|Htk-L|LERK-5|Lerk5|NLERK-1	ephrin B2	protein-coding
mm_60728.1	chr7	45413658	45413705	+	1	NA	promoter-TSS (NM_198190)	promoter-TSS (NM_198190)	-14	NM_198190	78405	Mm.20344	NM_198190	ENSMUSG00000074121	Ntf5	2900040K06Rik|AI462899|NT-4|NT-5|NT4|NT4/5|Ntf-5|Ntf4	neurotrophin 5	protein-coding
mm_161073.1	chr12	80475877	80475877	+	1	NA	exon (NM_133798, exon 2 of 9)	exon (NM_133798, exon 2 of 9)	12782	NM_133798	97827	Mm.206631	NM_133798	ENSMUSG00000032705	Exd2	4930539P14Rik|C85658|Exdl2	exonuclease 3'-5' domain containing 2	protein-coding
mm_162927.1	chr10	122270980	122270981	+	1	NA	Intergenic	Intergenic	151283	NR_027637	100043513	Mm.429141	NR_027637		Gm4489	Gm241	predicted gene 4489	ncRNA
mm_59378.1	chr7	25897652	25897672	+	1	NA	promoter-TSS (NM_009999)	promoter-TSS (NM_009999)	4	NM_009999	13088	Mm.218749	NM_009999	ENSMUSG00000030483	Cyp2b10	Cyp2b|Cyp2b20|p16	cytochrome P450, family 2, subfamily b, polypeptide 10	protein-coding
mm_27855.1	chr3	79157258	79157264	-	1	NA	Intergenic	L1_Mur3|LINE|L1	-11386	NM_001099624	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_5787.1	chr1	51858084	51858089	-	1	NA	intron (NM_001290982, intron 3 of 28)	intron (NM_001290982, intron 3 of 28)	57892	NM_001290982	17912	Mm.3390	NM_010863	ENSMUSG00000018417	Myo1b	AA406997|MIH-L|MMIa	myosin IB	protein-coding
mm_97667.1	chr11	79660675	79660690	+	1	NA	intron (NM_175543, intron 3 of 14)	CpG	14404	NR_045898	72218	Mm.443271	NR_045898	ENSMUSG00000086569	Rab11fip4os2	1700020F10Rik|4930542H20Rik|Rab11fib4os2	RAB11 family interacting protein 4 (class II), opposite strand 2	ncRNA
mm_48160.1	chr5	137152726	137152795	-	1	NA	Intergenic	Intergenic	-36553	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_92817.1	chr10	81431548	81431562	-	1	NA	Intergenic	Intergenic	-4382	NM_026756	18029	Mm.426936	NM_008688	ENSMUSG00000055053	Nfic	1110019L22Rik|1500041O16Rik|AA589446|AI746521|NF1-C	nuclear factor I/C	protein-coding
mm_81220.1	chr9	107590947	107590976	+	1	NA	exon (NM_025903, exon 7 of 12)	exon (NM_025903, exon 7 of 12)	3243	NM_025903	15983	Mm.215335	NM_025903	ENSMUSG00000010048	Ifrd2	1810034A24Rik|AA470234|AI838527|SKMc15	interferon-related developmental regulator 2	protein-coding
mm_73492.1	chr8	107057192	107057211	+	1	NA	promoter-TSS (NM_139229)	promoter-TSS (NM_139229)	324	NR_028367	66164	Mm.334789	NM_025391	ENSMUSG00000031917	Nip7	1110017C15Rik|6330509M23Rik|AA408773|AA410017|PEachy	NIP7, nucleolar pre-rRNA processing protein	protein-coding
mm_31701.1	chr4	62559804	62559808	+	1	NA	promoter-TSS (NM_019492)	promoter-TSS (NM_019492)	-41	NM_019492	50780	Mm.286753	NM_019492	ENSMUSG00000059810	Rgs3	4930506N09Rik|C2PA-RGS3|C2pa|PDZ-RGS3|RGS3S	regulator of G-protein signaling 3	protein-coding
mm_118531.1	chr14	15437582	15437592	+	1	NA	intron (NM_146052, intron 1 of 1)	intron (NM_146052, intron 1 of 1)	1400	NM_146052	218763	Mm.138039	NM_146052	ENSMUSG00000045201	Lrrc3b	BC019794|LRP15	leucine rich repeat containing 3B	protein-coding
mm_84480.1	chr9	66834717	66834724	-	1	NA	promoter-TSS (NM_026674)	promoter-TSS (NM_026674)	-14	NM_026674	68318	Mm.284229	NM_026674	ENSMUSG00000053040	Aph1c	0610008A10Rik|APH-1b|Aph1b	aph1 homolog C, gamma secretase subunit	protein-coding
mm_41840.1	chr5	104384770	104384791	+	1	NA	Intergenic	Intergenic	-50331	NM_001204201	20750	Mm.288474	NM_009263	ENSMUSG00000029304	Spp1	2AR|Apl-1|BNSP|BSPI|Bsp|ETA-1|Eta|OP|Opn|Opnl|Ric|Spp-1	secreted phosphoprotein 1	protein-coding
mm_16960.1	chr2	17460584	17460594	-	1	NA	intron (NM_028757, intron 4 of 6)	intron (NM_028757, intron 4 of 6)	-102925	NR_105847	102465964		NR_105847	ENSMUSG00000099161	Mir6419	Gm27713|mmu-mir-6419	microRNA 6419	ncRNA
mm_162542.1	chr1	170016245	170016246	+	1	NA	intron (NM_022563, intron 2 of 16)	RLTR1F_Mm|LTR|ERVK	46836	NR_040438	67303	Mm.396611	NR_040438	ENSMUSG00000097503	3110045C21Rik	AI838577	RIKEN cDNA 3110045C21 gene	ncRNA
mm_161606.1	chr16	43978838	43978838	-	1	NA	intron (NM_001007460, intron 1 of 3)	intron (NM_001007460, intron 1 of 3)	212	NM_001007460	332175	Mm.327852	NM_001007460	ENSMUSG00000036304	Zdhhc23	Gm1751|Gm779|nidd	zinc finger, DHHC domain containing 23	protein-coding
mm_61454.1	chr7	75586364	75586376	+	1	NA	intron (NM_029332, intron 5 of 36)	intron (NM_029332, intron 5 of 36)	130836	NM_029332	75547	Mm.216107	NM_029332	ENSMUSG00000066406	Akap13	1700026G02Rik|5730522G15Rik|5830460E08Rik|AKAP-13|AKAP-Lbc|BRX|Ht31|LBC|PROTO-LB|PROTO-LBC	A kinase (PRKA) anchor protein 13	protein-coding
mm_12512.1	chr2	72054586	72054597	+	1	NA	promoter-TSS (NM_001204166)	promoter-TSS (NM_001204166)	-26	NM_001204166	56508	Mm.196153	NM_019688	ENSMUSG00000049044	Rapgef4	1300003D15Rik|5730402K07Rik|6330581N18Rik|EPAC 2|Epac-2|Epac2|mKIAA4040	Rap guanine nucleotide exchange factor (GEF) 4	protein-coding
mm_3896.1	chr1	161494650	161494656	+	1	NA	promoter-TSS (NM_183391)	promoter-TSS (NM_183391)	-4	NM_183391	240873	Mm.276823	NM_183391	ENSMUSG00000066755	Tnfsf18	Gitrl|Tnlg2a	tumor necrosis factor (ligand) superfamily, member 18	protein-coding
mm_153440.1	chr19	40994190	40994200	-	1	NA	5' UTR (NM_008528, exon 1 of 17)	5' UTR (NM_008528, exon 1 of 17)	340	NM_008528	17060	Mm.9749	NM_008528	ENSMUSG00000061132	Blnk	BASH|Bca|Ly-57|Ly57|Lyw-57|SLP-65	B cell linker	protein-coding
mm_150170.1	chr19	32491302	32491312	+	1	NA	intron (NM_010799, intron 1 of 4)	intron (NM_010799, intron 1 of 4)	5538	NM_010799	17330	Mm.255116	NM_010799	ENSMUSG00000024896	Minpp1	AA408516	multiple inositol polyphosphate histidine phosphatase 1	protein-coding
mm_164967.1	chr19	6531607	6531617	+	1	NA	exon (NM_001205234, exon 23 of 23)	exon (NM_001205234, exon 23 of 23)	11458	NM_009203	20521	Mm.391146	NM_009203	ENSMUSG00000061742	Slc22a12	AI987855|OAT4L|Rst|Slc22al2|URAT1	solute carrier family 22 (organic anion/cation transporter), member 12	protein-coding
mm_88273.1	chr10	75015309	75015332	+	1	NA	3' UTR (NM_010311, exon 4 of 4)	3' UTR (NM_010311, exon 4 of 4)	17233	NM_001163535	71236	Mm.414817	NM_027730	ENSMUSG00000009070	Rsph14	4933431K05Rik|Rtdr1	radial spoke head homolog 14 (Chlamydomonas)	protein-coding
mm_17873.1	chr2	34958079	34958088	-	1	NA	5' UTR (NM_001326601, exon 4 of 10)	5' UTR (NM_001326601, exon 4 of 10)	3689	NM_009421	22029	Mm.239514	NM_009421	ENSMUSG00000026875	Traf1	4732496E14Rik	TNF receptor-associated factor 1	protein-coding
mm_74160.1	chr8	123397893	123397915	+	1	NA	intron (NM_001286362, intron 12 of 16)	intron (NM_001286362, intron 12 of 16)	-9178	NM_008559	17199	Mm.324942	NM_008559	ENSMUSG00000074037	Mc1r	Mcr1|Mshra|Tob|e	melanocortin 1 receptor	protein-coding
mm_158002.1	chrX	95026672	95026701	-	1	NA	promoter-TSS (NM_178753)	promoter-TSS (NM_178753)	-4	NM_178753	270624	Mm.115205	NM_178753	ENSMUSG00000071722	Spin4	9630042H07Rik	spindlin family, member 4	protein-coding
mm_171664.1	chr4	4556636	4556636	-	1	NA	Intergenic	ERVB7_3-LTR_MM|LTR|ERVK	-27178	NM_001277919	622019	Mm.246123	NM_001277919		Gm11780	OTTMUSG00000004194	predicted gene 11780	protein-coding
mm_100324.1	chr11	118146049	118146063	+	1	NA	Intergenic	Intergenic	-16837	NM_001167746	69926	Mm.473893	NM_001167746	ENSMUSG00000033987	Dnah17	2810003K23Rik|Dnahc17|Dnahcl1|Gm1178|mKIAA3028	dynein, axonemal, heavy chain 17	protein-coding
mm_173360.1	chrY	90819512	90819518	+	1	NA	Intergenic	IMPB_01|Satellite|Satellite	19891	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_113203.1	chr13	25055279	25055297	+	1	NA	promoter-TSS (NM_177577)	promoter-TSS (NM_177577)	-716	NM_001195617	195208	Mm.284719	NM_177577	ENSMUSG00000035910	Dcdc2a	AW492955|Dcdc2|RU2	doublecortin domain containing 2a	protein-coding
mm_136064.1	chr16	84725161	84725173	-	1	NA	exon (NM_017404, exon 7 of 10)	exon (NM_017404, exon 7 of 10)	10135	NM_017404	27393	Mm.103655	NM_017404	ENSMUSG00000022889	Mrpl39	C21orf8|MRP-L5|ORF22|Rpml5	mitochondrial ribosomal protein L39	protein-coding
mm_129508.1	chr15	79025915	79025926	-	1	NA	Intergenic	Intergenic	-2292	NM_008197	14958	Mm.24350	NM_008197	ENSMUSG00000096210	H1f0	D130017D06Rik|H1(0)|H1fv	H1 histone family, member 0	protein-coding
mm_103407.1	chr11	75449885	75449898	-	1	NA	exon (NM_138950, exon 2 of 10)	exon (NM_138950, exon 2 of 10)	4826	NM_138950	192652	Mm.340378	NM_138950	ENSMUSG00000045374	Wdr81	BC054822|Gm883|mFLJ00182|nur5	WD repeat domain 81	protein-coding
mm_479.1	chr1	36702409	36702409	+	1	NA	intron (NM_146107, intron 4 of 10)	intron (NM_146107, intron 4 of 10)	7516	NM_146107	226977	Mm.28521	NM_146107	ENSMUSG00000037351	Actr1b	2310066K23Rik|AA960180|AI851923|Arp1b	ARP1 actin-related protein 1B, centractin beta	protein-coding
mm_25929.1	chr3	131222792	131222793	+	1	NA	intron (NM_001276403, intron 11 of 11)	intron (NM_001276403, intron 11 of 11)	49309	NM_008212	15107	Mm.260164	NM_008212	ENSMUSG00000027984	Hadh	AA409008|AU019341|AW742602|HCDH|Hadhsc|Schad	hydroxyacyl-Coenzyme A dehydrogenase	protein-coding
mm_94108.1	chr10	128589651	128589673	-	1	NA	promoter-TSS (NM_010153)	promoter-TSS (NM_010153)	-161	NM_010153	13867	Mm.373043	NM_010153	ENSMUSG00000018166	Erbb3	C76256|Erbb-3|Erbb3r|Her3	erb-b2 receptor tyrosine kinase 3	protein-coding
mm_8555.1	chr1	155232610	155232637	-	1	NA	Intergenic	Intergenic	73920	NM_021433	58244	Mm.66264	NM_021433	ENSMUSG00000026470	Stx6	2310039E05Rik|2410005I16Rik|AA437559|AI415714|AI845861	syntaxin 6	protein-coding
mm_78386.1	chr9	28403481	28403496	+	1	NA	intron (NM_177906, intron 1 of 7)	CpG	612219	NM_177906	330908	Mm.379474	NM_177906	ENSMUSG00000062257	Opcml	2900075O15Rik|3732419F12|AI844366|B930023M13Rik|C230027C17|Gm181|Obcam	opioid binding protein/cell adhesion molecule-like	protein-coding
mm_41961.1	chr5	106351529	106351552	+	1	NA	Intergenic	Intergenic	30200	NR_136913	102635633	Mm.383511	NR_136913	ENSMUSG00000105508	Gm32921	-	predicted gene, 32921	ncRNA
mm_27976.1	chr3	80802746	80802770	-	1	NA	promoter-TSS (NM_013540)	promoter-TSS (NM_013540)	33	NM_013540	14800	Mm.220224	NM_013540	ENSMUSG00000033981	Gria2	GluA2|GluR-B|Glur-2|Glur2	glutamate receptor, ionotropic, AMPA2 (alpha 2)	protein-coding
mm_159924.1	chr6	56362811	56362811	-	1	NA	promoter-TSS (NM_001159953)	promoter-TSS (NM_001159953)	-1	NM_001159960	18575	Mm.5145	NM_011054	ENSMUSG00000004347	Pde1c	-	phosphodiesterase 1C	protein-coding
mm_97045.1	chr11	72435235	72435302	+	1	NA	promoter-TSS (NM_027819)	promoter-TSS (NM_027819)	-258	NM_027819	71522	Mm.23336	NM_027819	ENSMUSG00000040471	Ggt6	9030405D14Rik|AI427679|AW490214	gamma-glutamyltransferase 6	protein-coding
mm_20320.1	chr2	127319161	127319183	-	1	NA	Intergenic	MER90a|LTR|ERV1	-16987	NM_010090	13537	Mm.4729	NM_010090	ENSMUSG00000027368	Dusp2	PAC1	dual specificity phosphatase 2	protein-coding
mm_30627.1	chr4	8735970	8736085	+	1	NA	intron (NM_001277149, intron 1 of 37)	intron (NM_001277149, intron 1 of 37)	45621	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_35133.1	chr4	11322110	11322146	-	1	NA	promoter-TSS (NM_001081201)	promoter-TSS (NM_001081201)	3	NM_001081201	381510	Mm.331486	NM_001081201	ENSMUSG00000045205	Dpy19l4	Gm1023|Narg3	dpy-19-like 4 (C. elegans)	protein-coding
mm_28088.1	chr3	85778123	85778126	-	1	NA	Intergenic	Intergenic	-31915	NM_172682	229488	Mm.119926	NM_172682	ENSMUSG00000051000	Fam160a1	9930021J17Rik	family with sequence similarity 160, member A1	protein-coding
mm_128700.1	chr15	63479544	63479554	-	1	NA	promoter-TSS (NR_045279)	promoter-TSS (NR_045279)	59	NR_045279	432958	Mm.255105	NR_045279		Gm20740	-	predicted gene, 20740	ncRNA
mm_168298.1	chr11	106033372	106033384	-	1	NA	intron (NM_001037712, intron 12 of 12)	IAPLTR1_Mm|LTR|ERVK	-3494	NM_027946	71833	Mm.307455	NM_027946	ENSMUSG00000049354	Dcaf7	1700012F10Rik|2610037L01Rik|C86529|HAN11|Wdr68	DDB1 and CUL4 associated factor 7	protein-coding
mm_21827.1	chr2	165387037	165387048	-	1	NA	intron (NM_178411, intron 1 of 4)	intron (NM_178411, intron 1 of 4)	1217	NM_178411	228876	Mm.26316	NM_178411	ENSMUSG00000017667	Zfp334	D2Ertd535e	zinc finger protein 334	protein-coding
mm_20032.1	chr2	119666151	119666153	-	1	NA	Intergenic	Intergenic	-3354	NM_027175	69702	Mm.5390	NM_027175	ENSMUSG00000027305	Ndufaf1	2410001M24Rik|CGI-65|CIA30	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, assembly factor 1	protein-coding
mm_83587.1	chr9	48388377	48388381	-	1	NA	intron (NM_172921, intron 2 of 8)	intron (NM_172921, intron 2 of 8)	26338	NM_172921	244853	Mm.325522	NM_172921	ENSMUSG00000044229	Nxpe4	C130036J11|D930028F11Rik|Fam55d	neurexophilin and PC-esterase domain family, member 4	protein-coding
mm_124113.1	chr14	79480996	79481020	-	1	NA	promoter-TSS (NM_007920)	promoter-TSS (NM_007920)	-186	NM_007920	13709	Mm.20938	NM_007920	ENSMUSG00000036461	Elf1	Elf-1|Sts1|mElf-1|p70	E74-like factor 1	protein-coding
mm_114853.1	chr13	93299630	93299646	+	1	NA	Intergenic	Intergenic	-4119	NM_147176	26556	Mm.37533	NM_011982	ENSMUSG00000007617	Homer1	PSD-Zip45|SYN47|Ves-1|homer-1|vesl-1	homer scaffolding protein 1	protein-coding
mm_75497.1	chr8	52196867	52196898	-	1	NA	Intergenic	Intergenic	-1314820	NM_001205054	11593	Mm.334535	NM_001005847	ENSMUSG00000031521	Aga	AW060726	aspartylglucosaminidase	protein-coding
mm_142028.1	chr17	35234997	35235034	-	1	NA	promoter-TSS (NM_001347351)	promoter-TSS (NM_001347351)	5	NM_001347351	66237	Mm.396107	NM_023179	ENSMUSG00000024403	Atp6v1g2	1500002D01Rik|Atp6g2|NG38|VAG2	ATPase, H+ transporting, lysosomal V1 subunit G2	protein-coding
mm_19543.1	chr2	98662780	98662825	-	1	NA	Intergenic	SYNREP_MM|Satellite|Satellite	1195145	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_151212.1	chr19	53623046	53623058	+	1	NA	exon (NM_007790, exon 11 of 29)	exon (NM_007790, exon 11 of 29)	22656	NM_007790	13006	Mm.14910	NM_007790	ENSMUSG00000024974	Smc3	Bamacan|Cspg6|HCAP|Mmip1|SMC-3|SmcD	structural maintenance of chromosomes 3	protein-coding
mm_48761.1	chr5	148371526	148371532	-	1	NA	intron (NM_007513, intron 1 of 12)	intron (NM_007513, intron 1 of 12)	21286	NM_001301424	11987	Mm.275489	NM_007513	ENSMUSG00000041313	Slc7a1	4831426K01Rik|AI447493|Atrc-1|Atrc1|Cat1|Rec-1|Rev-1|mCAT-1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 1	protein-coding
mm_106081.1	chr11	116174855	116174867	-	1	NA	intron (NM_001271898, intron 11 of 13)	PB1D10|SINE|Alu	-6683	NM_172571	217335	Mm.35241	NM_172571	ENSMUSG00000020776	Fbf1	1110033G01Rik|5930413D20|mKIAA1863	Fas (TNFRSF6) binding factor 1	protein-coding
mm_59611.1	chr7	28142484	28142510	+	1	NA	exon (NM_001164655, exon 6 of 20)	exon (NM_001164655, exon 6 of 20)	13031	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_156096.1	chrX	112495267	112495281	+	1	NA	promoter-TSS (NM_026333)	promoter-TSS (NM_026333)	0	NM_026333	67715	Mm.45323	NM_026333	ENSMUSG00000025528	2010106E10Rik	-	RIKEN cDNA 2010106E10 gene	protein-coding
mm_89427.1	chr10	90970240	90970279	+	1	NA	3' UTR (NM_001128086, exon 25 of 25)	3' UTR (NM_001128086, exon 25 of 25)	112484	NM_001042558	11783	Mm.220289	NM_009684	ENSMUSG00000019979	Apaf1	6230400I06Rik|Apaf-1|Apaf1l|fog|mKIAA0413	apoptotic peptidase activating factor 1	protein-coding
mm_16435.1	chr2	180394423	180394448	+	1	NA	intron (NR_045331, intron 3 of 3)	intron (NR_045331, intron 3 of 3)	-3944	NR_029901	723954		NR_029901	ENSMUSG00000065460	Mir133a-2	Mirn133a-2|mir-133a-2	microRNA 133a-2	ncRNA
mm_59483.1	chr7	27462608	27462622	+	1	NA	exon (NM_144923, exon 4 of 5)	exon (NM_144923, exon 4 of 5)	10197	NM_001290525	233016	Mm.24021	NM_144923	ENSMUSG00000040466	Blvrb	-	biliverdin reductase B (flavin reductase (NADPH))	protein-coding
mm_109566.1	chr12	111971546	111971598	+	1	NA	promoter-TSS (NM_029056)	promoter-TSS (NM_029056)	13	NM_029056	74691	Mm.60648	NM_029056	ENSMUSG00000054003	Tdrd9	4930441E05Rik	tudor domain containing 9	protein-coding
mm_73336.1	chr8	105304569	105304597	+	1	NA	exon (NM_148952, exon 10 of 10)	exon (NM_148952, exon 10 of 10)	-1018	NM_172760	234683	Mm.237966	NM_172760	ENSMUSG00000014791	Elmo3	9930107J06|BC058752|CED-12|Ced12	engulfment and cell motility 3	protein-coding
mm_100393.1	chr11	119390464	119390490	+	1	NA	promoter-TSS (NR_035453)	promoter-TSS (NR_035453)	5	NR_035453	100316690		NR_035453	ENSMUSG00000088015	Mir1932	mir-1932|mmu-mir-1932	microRNA 1932	ncRNA
mm_93170.1	chr10	93310964	93310989	-	1	NA	5' UTR (NM_001322268, exon 1 of 6)	5' UTR (NM_001322268, exon 1 of 6)	183	NM_001322268	13713	Mm.4454	NM_013508	ENSMUSG00000008398	Elk3	D430049E23Rik|Erp|Etrp|Net|Sap-2	ELK3, member of ETS oncogene family	protein-coding
mm_44374.1	chr5	17814254	17814268	-	1	NA	exon (NM_001159558, exon 7 of 16)	exon (NM_001159558, exon 7 of 16)	21635	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_120344.1	chr14	63748319	63748323	+	1	NA	intron (NM_173393, intron 1 of 2)	intron (NM_173393, intron 1 of 2)	21132	NR_030611	100124452		NR_030611	ENSMUSG00000076049	Mir598	Mirn598|mir-598|mmu-mir-598	microRNA 598	ncRNA
mm_140622.1	chr17	12108054	12108061	-	1	NA	Intergenic	Intergenic	-11227	NM_026644	68262	Mm.258300	NM_026644	ENSMUSG00000023827	Agpat4	1500003P24Rik	1-acylglycerol-3-phosphate O-acyltransferase 4 (lysophosphatidic acid acyltransferase, delta)	protein-coding
mm_134211.1	chr16	11176252	11176260	-	1	NA	non-coding (NR_027502, exon 1 of 23)	non-coding (NR_027502, exon 1 of 23)	137	NR_027502	106205	Mm.226860	NM_145931	ENSMUSG00000037965	Zc3h7a	A430104C18Rik|AI447294|AW556219|HSPC055|Zc3h7|Zc3hdc7	zinc finger CCCH type containing 7 A	protein-coding
mm_113152.1	chr13	24801138	24801158	+	1	NA	promoter-TSS (NM_024473)	promoter-TSS (NM_024473)	-509	NM_024473	79555	Mm.266668	NM_024473	ENSMUSG00000019132	BC005537	8030460C05Rik|C78201	cDNA sequence BC005537	protein-coding
mm_107976.1	chr12	72939939	72939941	+	1	NA	promoter-TSS (NM_011384)	promoter-TSS (NM_011384)	58	NM_011384	20476	Mm.57138	NM_011384	ENSMUSG00000021099	Six6	Optx2|Six9	sine oculis-related homeobox 6	protein-coding
mm_63515.1	chr7	127876171	127876254	+	1	NA	5' UTR (NM_146259, exon 1 of 3)	5' UTR (NM_146259, exon 1 of 3)	611	NM_146259	244219	Mm.207872	NM_146259	ENSMUSG00000049728	Zfp668	BC030314|E130018B19Rik|Znf668	zinc finger protein 668	protein-coding
mm_113600.1	chr13	41236023	41236066	+	1	NA	Intergenic	Intergenic	-13800	NM_001135577	108934	Mm.38578	NM_001135577	ENSMUSG00000091264	Smim13	2900036K02Rik	small integral membrane protein 13	protein-coding
mm_57138.1	chr6	122609924	122609935	-	1	NA	exon (NM_008108, exon 1 of 2)	exon (NM_008108, exon 1 of 2)	158	NM_008108	14562	Mm.299742	NM_008108	ENSMUSG00000030117	Gdf3	C78318|Gdf-3|Vgr-2|Vgr2|ecat9	growth differentiation factor 3	protein-coding
mm_25280.1	chr3	105491535	105491544	+	1	NA	intron (NM_001039347, intron 2 of 6)	intron (NM_001039347, intron 2 of 6)	32723	NM_019931	56543	Mm.44530	NM_019931	ENSMUSG00000040896	Kcnd3	AW045978|Kncd3|Kv4.3	potassium voltage-gated channel, Shal-related family, member 3	protein-coding
mm_30555.1	chr4	3697349	3697366	+	1	NA	intron (NM_010747, intron 1 of 12)	ID4_|SINE|ID	-17607	NR_028126	70720	Mm.445696	NR_028126		6330407A03Rik	-	RIKEN cDNA 6330407A03 gene	ncRNA
mm_142094.1	chr17	35834590	35834615	-	1	NA	3' UTR (NM_011655, exon 4 of 4)	3' UTR (NM_011655, exon 4 of 4)	3699	NM_011655	22154	Mm.273538	NM_011655	ENSMUSG00000001525	Tubb5	AA408537|AI596182|B130022C14Rik|M(beta)5	tubulin, beta 5 class I	protein-coding
mm_72291.1	chr8	75213326	75213334	+	1	NA	promoter-TSS (NM_029182)	promoter-TSS (NM_029182)	-614	NM_029182	75141	Mm.179267	NM_029182	ENSMUSG00000034472	Rasd2	4930526B11Rik|AU045414|Rhes|TEM-2|TEM2	RASD family, member 2	protein-coding
mm_99819.1	chr11	108637405	108637415	+	1	NA	intron (NM_029606, intron 21 of 27)	intron (NM_029606, intron 21 of 27)	-45199	NM_145688	76380	Mm.344071	NM_029586	ENSMUSG00000020728	Cep112	1700001M19Rik|1700029K01Rik|8430407H02Rik|AV043680|AV207351|Ccdc46|Macoco	centrosomal protein 112	protein-coding
mm_11633.1	chr2	34775788	34775822	+	1	NA	exon (NM_001163434, exon 9 of 9)	exon (NM_001163434, exon 9 of 9)	3715	NM_022310	14828	Mm.330160	NM_022310	ENSMUSG00000026864	Hspa5	AL022860|AU019543|Bip|D2Wsu141e|D2Wsu17e|Grp78|Hsce70|SEZ-7|Sez7|baffled|mBiP	heat shock protein 5	protein-coding
mm_65491.1	chr7	25689101	25689109	-	1	NA	intron (NM_011577, intron 1 of 6)	intron (NM_011577, intron 1 of 6)	2103	NM_011577	21803	Mm.248380	NM_011577	ENSMUSG00000002603	Tgfb1	TGF-beta1|TGFbeta1|Tgfb|Tgfb-1	transforming growth factor, beta 1	protein-coding
mm_101662.1	chr11	36677951	36677966	-	1	NA	intron (NM_011856, intron 2 of 28)	intron (NM_011856, intron 2 of 28)	266283	NM_001290702	23964	Mm.439889	NM_011856	ENSMUSG00000049336	Tenm2	Odz2|Odz3|Ten-2|Ten-m2	teneurin transmembrane protein 2	protein-coding
mm_88399.1	chr10	76583876	76583882	+	1	NA	intron (NM_080845, intron 8 of 13)	intron (NM_080845, intron 8 of 13)	8231	NM_080845	14317	Mm.36278	NM_080845	ENSMUSG00000001155	Ftcd	-	formiminotransferase cyclodeaminase	protein-coding
mm_125514.1	chr15	56695484	56695485	+	1	NA	promoter-TSS (NM_008216)	promoter-TSS (NM_008216)	-938	NM_008216	15117	Mm.5148	NM_008216	ENSMUSG00000022367	Has2	-	hyaluronan synthase 2	protein-coding
mm_128421.1	chr15	45114927	45114938	-	1	NA	promoter-TSS (NM_026200)	promoter-TSS (NM_026200)	2	NM_026200	67498	Mm.300079	NM_026200	ENSMUSG00000022342	Kcnv1	2700023A03Rik|vibe	potassium channel, subfamily V, member 1	protein-coding
mm_148871.1	chr19	6497725	6497744	+	1	NA	intron (NM_001205234, intron 17 of 22)	CpG	45336	NM_009203	20521	Mm.391146	NM_009203	ENSMUSG00000061742	Slc22a12	AI987855|OAT4L|Rst|Slc22al2|URAT1	solute carrier family 22 (organic anion/cation transporter), member 12	protein-coding
mm_152544.1	chr19	11336108	11336124	-	1	NA	promoter-TSS (NM_027836)	promoter-TSS (NM_027836)	30	NM_001025610	109225	Mm.491251	NM_027836	ENSMUSG00000024672	Ms4a7	9130422I10Rik|A430103C15Rik|CD20l4|CFFMA	membrane-spanning 4-domains, subfamily A, member 7	protein-coding
mm_94964.1	chr11	30812479	30812493	+	1	NA	intron (NM_134013, intron 11 of 46)	PB1D10|SINE|Alu	40711	NM_134013	103554	Mm.240066	NM_134013	ENSMUSG00000040850	Psme4	AA409398|AU041366|TEMO|mKIAA0077	proteasome (prosome, macropain) activator subunit 4	protein-coding
mm_30850.1	chr4	24972509	24972521	+	1	NA	promoter-TSS (NM_030733)	promoter-TSS (NM_030733)	-904	NM_030733	81006	Mm.160412	NM_030733	ENSMUSG00000040372	Gpr63	PSP24beta|Psp24-2	G protein-coupled receptor 63	protein-coding
mm_52232.1	chr6	103697735	103697791	+	1	NA	intron (NM_007697, intron 14 of 26)	intron (NM_007697, intron 14 of 26)	186887	NM_007697	12661	Mm.251288	NM_007697	ENSMUSG00000030077	Chl1	A530023M13Rik|AI465420|CALL|LICAM2	cell adhesion molecule L1-like	protein-coding
mm_167184.1	chr7	141997446	141997447	+	1	NA	intron (NM_001009930, intron 16 of 19)	intron (NM_001009930, intron 16 of 19)	5267	NR_037291	100526509		NR_037291	ENSMUSG00000092652	Mir3104	mir-3104|mmu-mir-3104	microRNA 3104	ncRNA
mm_70178.1	chr7	143735864	143735866	-	1	NA	intron (NM_024289, intron 1 of 21)	intron (NM_024289, intron 1 of 21)	4495	NM_001199227	79196	Mm.21199	NM_024289	ENSMUSG00000037606	Osbpl5	1110006M06Rik|AI462538|ORP5|Obph1|Osbp2	oxysterol binding protein-like 5	protein-coding
mm_66338.1	chr7	43399515	43399523	-	1	NA	Intergenic	Intergenic	-8761	NM_172900	243958	Mm.24444	NM_172900	ENSMUSG00000030468	Siglecg	9830164H23|A630096C01Rik|Siglec-G|Siglec10|mSiglec-G	sialic acid binding Ig-like lectin G	protein-coding
mm_115883.1	chr13	21787242	21787256	-	1	NA	promoter-TSS (NM_001290466)	promoter-TSS (NM_001290466)	-31	NM_178184	319170		NM_178184	ENSMUSG00000069309	Hist1h2an	-	histone cluster 1, H2an	protein-coding
mm_13031.1	chr2	91054145	91054175	+	1	NA	5' UTR (NM_008948, exon 1 of 12)	5' UTR (NM_008948, exon 1 of 12)	144	NM_008948	19182	Mm.289832	NM_008948	ENSMUSG00000002102	Psmc3	TBP-1	proteasome (prosome, macropain) 26S subunit, ATPase 3	protein-coding
mm_153960.1	chr19	47705625	47705633	-	1	NA	Intergenic	Intergenic	-13587	NM_001290825	12821	Mm.1225	NM_007732	ENSMUSG00000025064	Col17a1	BP180|Bpag|Bpag2	collagen, type XVII, alpha 1	protein-coding
mm_125349.1	chr15	39198245	39198267	+	1	NA	promoter-TSS (NM_053271)	promoter-TSS (NM_053271)	-30	NM_001256382	116838	Mm.309296	NM_053271	ENSMUSG00000037386	Rims2	2810036I15Rik|AW048769|RIM2|Rab3ip2|Rim2(+40A)|Rim2(+44A)|Rim2(+4A)|Serg2|Syt3-rs|mKIAA0751	regulating synaptic membrane exocytosis 2	protein-coding
mm_3416.1	chr1	144952891	144952908	+	1	NA	Intergenic	Intergenic	-177478	NM_022881	64214	Mm.253927	NM_022881	ENSMUSG00000026357	Rgs18	-	regulator of G-protein signaling 18	protein-coding
mm_70371.1	chr8	9977767	9977788	+	1	NA	promoter-TSS (NM_026868)	promoter-TSS (NM_026868)	60	NM_026868	68904	Mm.142570	NM_026868	ENSMUSG00000040396	Abhd13	1110065L07Rik|AI463703|AI788994	abhydrolase domain containing 13	protein-coding
mm_158038.1	chrX	98853389	98853394	-	1	NA	intron (NM_001313755, intron 2 of 23)	L1_Rod|LINE|L1	37634	NM_052976	94190	Mm.33536	NM_052976	ENSMUSG00000031214	Ophn1	C130037N19Rik|Wtgr	oligophrenin 1	protein-coding
mm_41776.1	chr5	103715205	103715222	+	1	NA	Intergenic	Lx8|LINE|L1	-38949	NM_133919	17355	Mm.6949	NM_133919	ENSMUSG00000029313	Aff1	9630032B01Rik|AW319193|Af4|Mllt2h|Rob	AF4/FMR2 family, member 1	protein-coding
mm_101657.1	chr11	36677732	36677742	-	1	NA	intron (NM_011856, intron 2 of 28)	intron (NM_011856, intron 2 of 28)	266504	NM_001290702	23964	Mm.439889	NM_011856	ENSMUSG00000049336	Tenm2	Odz2|Odz3|Ten-2|Ten-m2	teneurin transmembrane protein 2	protein-coding
mm_19175.1	chr2	84359708	84359714	-	1	NA	intron (NM_018782, intron 9 of 15)	intron (NM_018782, intron 9 of 15)	65555	NM_018782	54598	Mm.75467	NM_018782	ENSMUSG00000059588	Calcrl	AV071593|CRLR	calcitonin receptor-like	protein-coding
mm_54126.1	chr6	18514742	18514770	-	1	NA	promoter-TSS (NM_080285)	promoter-TSS (NM_080285)	69	NM_080285	30785	Mm.224189	NM_080285	ENSMUSG00000000416	Cttnbp2	3010022N24Rik|4732477G22Rik|6430526E05|9130022E09Rik|AU040881|Cortbp2|ORF4|mKIAA1758	cortactin binding protein 2	protein-coding
mm_48898.1	chr6	3201108	3201148	+	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	-87391	NR_036696	667335	Mm.380219	NR_036696	ENSMUSG00000106779	Gm8579	EG667335	spermatogenesis associated glutamate (E)-rich protein 4a pseudogene	pseudo
mm_15335.1	chr2	155956538	155956607	+	1	NA	promoter-TSS (NM_008383)	promoter-TSS (NM_008383)	14	NM_177217	16328	Mm.288729	NM_008383	ENSMUSG00000038241	Cep250	AW490617|B230210E21Rik|Cep2|Inmp	centrosomal protein 250	protein-coding
mm_72814.1	chr8	87563877	87563914	+	1	NA	promoter-TSS (NM_177901)	promoter-TSS (NM_177901)	-12	NM_177901	330820	Mm.212913	NM_177901	ENSMUSG00000069971	4933402J07Rik	-	RIKEN cDNA 4933402J07 gene	protein-coding
mm_61508.1	chr7	78719423	78719449	+	1	NA	Intergenic	Tigger15a|DNA|TcMar-Tigger	-1216	NR_015542	414121	Mm.482537	NR_015542	ENSMUSG00000059146	E430016F16Rik	-	RIKEN cDNA E430016F16 gene	ncRNA
mm_115460.1	chr13	119428450	119428485	+	1	NA	promoter-TSS (NM_001079849)	promoter-TSS (NM_001079849)	-133	NM_001079849	218693	Mm.490243	NM_145457	ENSMUSG00000025451	Paip1	PAIP-1	polyadenylate binding protein-interacting protein 1	protein-coding
mm_170319.1	chr18	39491088	39491094	-	1	NA	Intergenic	Intergenic	-3846	NM_008173	14815	Mm.129481	NM_008173	ENSMUSG00000024431	Nr3c1	GR|Grl-1|Grl1	nuclear receptor subfamily 3, group C, member 1	protein-coding
mm_171604.1	chr4	148655147	148655155	-	1	NA	intron (NM_001085505, intron 3 of 10)	intron (NM_001085505, intron 3 of 10)	11834	NM_001085505	230909	Mm.332067	NM_001085505	ENSMUSG00000070577	Gm572	b2b1167Clo	predicted gene 572	protein-coding
mm_14282.1	chr2	128801812	128801822	+	1	NA	3' UTR (NM_008587, exon 19 of 19)	3' UTR (NM_008587, exon 19 of 19)	-16486	NM_028248	72477	Mm.259688	NM_028248	ENSMUSG00000014353	Tmem87b	2610301K12Rik|2810431I02Rik|AU014804	transmembrane protein 87B	protein-coding
mm_145492.1	chr18	60390121	60390134	+	1	NA	exon (NM_001146275, exon 3 of 3)	exon (NM_001146275, exon 3 of 3)	14098	NM_001146275	60440	Mm.261140	NM_021792	ENSMUSG00000054072	Iigp1	2900074L10Rik|AI046432|AW111922|Ifgga1|Iigp|Irga6	interferon inducible GTPase 1	protein-coding
mm_18992.1	chr2	76867219	76867233	-	1	NA	exon (NM_011652, exon 108 of 313)	exon (NM_011652, exon 108 of 313)	115321	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_132707.1	chr16	43399209	43399220	+	1	NA	intron (NM_181058, intron 2 of 6)	intron (NM_181058, intron 2 of 6)	20982	NR_046026	626693	Mm.447083	NR_046026	ENSMUSG00000085499	Gm15713	OTTMUSG00000025617	predicted gene 15713	ncRNA
mm_114678.1	chr13	80886161	80886201	+	1	NA	intron (NM_001042591, intron 1 of 7)	CpG	2759	NM_001042591	105171	Mm.423137	NM_001042591	ENSMUSG00000074794	Arrdc3	AI450344|mKIAA1376	arrestin domain containing 3	protein-coding
mm_108207.1	chr12	76909502	76909511	+	1	NA	intron (NM_145927, intron 8 of 11)	intron (NM_145927, intron 8 of 11)	52742	NM_008558	17187	Mm.268548	NM_008558	ENSMUSG00000059436	Max	AA960152|AI875693|bHLHd4|bHLHd5|bHLHd6|bHLHd7|bHLHd8	Max protein	protein-coding
mm_154713.1	chrX	8893022	8893077	+	1	NA	non-coding (NR_045448, exon 1 of 1)	non-coding (NR_045448, exon 1 of 1)	696	NR_045448	102941	Mm.41588	NM_175327	ENSMUSG00000052364	B630019K06Rik	AI843180	novel protein similar to F-box and leucine-rich repeat protein 17 (Fbxl17)	pseudo
mm_158271.1	chrX	110812815	110812823	-	1	NA	Intergenic	Intergenic	-1560	NM_008901	18994	Mm.56946	NM_008901	ENSMUSG00000056854	Pou3f4	Brn-4|Brn4|OTF-9|Otf9|Slf|oct-9	POU domain, class 3, transcription factor 4	protein-coding
mm_141790.1	chr17	34315907	34315921	-	1	NA	3' UTR (NM_010382, exon 6 of 6)	3' UTR (NM_010382, exon 6 of 6)	-9761	NM_001033978	381091	Mm.139204	NM_001033978	ENSMUSG00000067341	H2-Eb2	A130038H09Rik|H-2Eb2|Ia-5|Ia5|Iebeta2	histocompatibility 2, class II antigen E beta2	protein-coding
mm_125584.1	chr15	59599109	59599136	+	1	NA	intron (NM_026746, intron 6 of 6)	intron (NM_026746, intron 6 of 6)	-49532	NM_144549	211770	Mm.40298	NM_144549	ENSMUSG00000032501	Trib1	A530090O15Rik|TRB-1|Trb1	tribbles pseudokinase 1	protein-coding
mm_122680.1	chr14	52010869	52010905	-	1	NA	intron (NM_027248, intron 1 of 4)	intron (NM_027248, intron 1 of 4)	3671	NM_001253695	69890	Mm.475652	NM_027248	ENSMUSG00000049295	Zfp219	2010302A17Rik	zinc finger protein 219	protein-coding
mm_168972.1	chr12	86470128	86470128	+	1	NA	intron (NM_011934, intron 1 of 6)	CpG	48484	NM_011934	26380	Mm.235550	NM_011934	ENSMUSG00000021255	Esrrb	Err2|Errb|Estrrb|Nr3b2	estrogen related receptor, beta	protein-coding
mm_79146.1	chr9	47703561	47703596	+	1	NA	intron (NM_001025600, intron 1 of 8)	intron (NM_001025600, intron 1 of 8)	114630	NR_046048	100038460	Mm.447649	NR_046048		Gm10677	ENSMUSG00000074363	predicted gene 10677	ncRNA
mm_154138.1	chr19	57360669	57360793	-	1	NA	promoter-TSS (NM_145505)	promoter-TSS (NM_145505)	168	NR_040316	320879	Mm.375089	NR_040316	ENSMUSG00000097785	B230217O12Rik	-	RIKEN cDNA B230217O12 gene	ncRNA
mm_68503.1	chr7	111081597	111081637	-	1	NA	5' UTR (NM_013507, exon 2 of 22)	5' UTR (NM_013507, exon 2 of 22)	1413	NM_001040131	13690	Mm.185453	NM_013507	ENSMUSG00000005610	Eif4g2	DAP-5|E130105L11Rik|Nat1|Natm1|p97	eukaryotic translation initiation factor 4, gamma 2	protein-coding
mm_73735.1	chr8	113643207	113643231	+	1	NA	promoter-TSS (NM_001048145)	promoter-TSS (NM_001048145)	6	NM_001048145	668110	Mm.390078	NM_029139	ENSMUSG00000033409	Syce1l	4930481F22Rik|MMRP|PSESS|mmrp2	synaptonemal complex central element protein 1 like	protein-coding
mm_6002.1	chr1	58973287	58973300	-	1	NA	promoter-TSS (NM_172656)	promoter-TSS (NM_172656)	189	NM_172406	70827	Mm.222887	NM_172406	ENSMUSG00000026028	Trak2	2900022D04Rik|4733401O11Rik|AI480836|AW046271|Als2cr3|CALS-C|GRIF-1|GRIF1|OIP98|mKIAA0549	trafficking protein, kinesin binding 2	protein-coding
mm_5993.1	chr1	58695945	58695964	-	1	NA	promoter-TSS (NM_175370)	promoter-TSS (NM_175370)	35	NM_175370	108812	Mm.442063	NM_175370	ENSMUSG00000047528	Als2cr12	4933405P16Rik|4933425F06Rik	amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 12 (human)	protein-coding
mm_138737.1	chr17	36973586	36973634	+	1	NA	Intergenic	B1_Mur2|SINE|Alu	7627	NM_029747	76797	Mm.159787	NM_029747	ENSMUSG00000064308	2410137M14Rik	-	RIKEN cDNA 2410137M14 gene	protein-coding
mm_76881.1	chr8	105617737	105617752	-	1	NA	exon (NM_001081241, exon 13 of 22)	exon (NM_001081241, exon 13 of 22)	2278	NR_035492	100316712		NR_035492	ENSMUSG00000089432	Mir1966	mir-1966|mmu-mir-1966	microRNA 1966	ncRNA
mm_83180.1	chr9	40963506	40963513	-	1	NA	intron (NM_001081121, intron 1 of 8)	(A)n|Simple_repeat|Simple_repeat	603	NM_001081121	70989	Mm.335087	NM_001081121	ENSMUSG00000032023	Jhy	4931429I11Rik|BB239335	juvenile hydrocephalus	protein-coding
mm_69876.1	chr7	141613713	141613727	-	1	NA	promoter-TSS (NR_040337)	promoter-TSS (NR_040337)	27	NR_040337	100036523	Mm.398994	NR_040337	ENSMUSG00000097170	Gm16982	-	predicted gene, 16982	ncRNA
mm_121124.1	chr14	101840708	101840736	+	1	NA	promoter-TSS (NM_001347628)	promoter-TSS (NM_001347628)	99	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_79466.1	chr9	56437423	56437431	+	1	NA	intron (NM_025812, intron 1 of 9)	intron (NM_025812, intron 1 of 9)	18581	NM_025812	66867	Mm.150856	NM_025812	ENSMUSG00000032329	Hmg20a	1200004E06Rik|5730490E10Rik|Hmgxb1|Ibraf	high mobility group 20A	protein-coding
mm_31097.1	chr4	41755590	41755608	+	1	NA	promoter-TSS (NM_001302511)	promoter-TSS (NM_001302511)	371	NM_016658	14430	Mm.439669	NM_016658	ENSMUSG00000036073	Galt	AW553376	galactose-1-phosphate uridyl transferase	protein-coding
mm_68362.1	chr7	106519177	106519189	-	1	NA	Intergenic	Lx9|LINE|L1	-78110	NR_003967	209380	Mm.461779	NM_001001318		Gm4759	EG209380	GTPase, very large interferon inducible 1 pseudogene	pseudo
mm_122744.1	chr14	54149262	54149280	-	1	NA	Intergenic	Intergenic	104658	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_162325.1	chr1	40079375	40079376	+	1	NA	intron (NR_037980, intron 3 of 3)	intron (NR_037980, intron 3 of 3)	-5393	NM_010555	16178	Mm.1349	NM_010555	ENSMUSG00000026073	Il1r2	CD121b|Il1r-2	interleukin 1 receptor, type II	protein-coding
mm_126014.1	chr15	76659850	76659903	+	1	NA	promoter-TSS (NM_001276335)	promoter-TSS (NM_001276335)	-140	NM_001276335	54151	Mm.247752	NM_019396	ENSMUSG00000053929	Cyhr1	1110031M01Rik|AU042374|Chrp	cysteine and histidine rich 1	protein-coding
mm_39859.1	chr5	30950136	30950147	+	1	NA	promoter-TSS (NR_003522)	promoter-TSS (NR_003522)	35	NM_021304	57742	Mm.389615	NM_021304	ENSMUSG00000006638	Abhd1	LABH-1|LABH1	abhydrolase domain containing 1	protein-coding
mm_171440.1	chr4	141210364	141210366	-	1	NA	Intergenic	IAPLTR2_Mm|LTR|ERVK	-3591	NM_001081174	76166	Mm.271064	NM_001081174	ENSMUSG00000073733	Rsg1	6330545A04Rik|Gm723	REM2 and RAB-like small GTPase 1	protein-coding
mm_15244.1	chr2	154657215	154657237	+	1	NA	exon (NM_029362, exon 1 of 5)	exon (NM_029362, exon 1 of 5)	200	NM_029362	75608	Mm.262480	NM_029362	ENSMUSG00000038467	Chmp4b	2010012F05Rik|C76846|Snf7-2	charged multivesicular body protein 4B	protein-coding
mm_163616.1	chr13	54731820	54731828	+	1	NA	intron (NM_001033364, intron 23 of 31)	(CA)n|Simple_repeat|Simple_repeat	18050	NM_001316710	26913	Mm.41812	NM_012014	ENSMUSG00000069227	Gprin1	GRIN1|Z16	G protein-regulated inducer of neurite outgrowth 1	protein-coding
mm_25715.1	chr3	122728945	122728995	+	1	NA	promoter-TSS (NM_153422)	promoter-TSS (NM_153422)	-188	NM_153422	242202	Mm.134911	NM_153422	ENSMUSG00000053965	Pde5a	Cgbpde|Cn5n|PDE5a2|Pde5|Pde5a1	phosphodiesterase 5A, cGMP-specific	protein-coding
mm_129889.1	chr15	83510838	83510859	-	1	NA	promoter-TSS (NM_178869)	promoter-TSS (NM_178869)	59	NM_178869	319953	Mm.235007	NM_178869	ENSMUSG00000022442	Ttll1	6330444E16Rik|AV014541	tubulin tyrosine ligase-like 1	protein-coding
mm_142941.1	chr17	56036547	56036647	-	1	NA	promoter-TSS (NM_013664)	promoter-TSS (NM_013664)	40	NM_013664	20405	Mm.1773	NM_013664	ENSMUSG00000003200	Sh3gl1	C77078|EEN|SH3P8|Sh3d2b	SH3-domain GRB2-like 1	protein-coding
mm_108720.1	chr12	87163772	87163797	+	1	NA	exon (NM_001252556, exon 8 of 8)	exon (NM_001252556, exon 8 of 8)	-8299	NR_136901	625237	Mm.390529	NR_136901		Gm6566	EG625237	predicted gene 6566	ncRNA
mm_13175.1	chr2	92946071	92946107	+	1	NA	exon (NM_030725, exon 4 of 6)	exon (NM_030725, exon 4 of 6)	30988	NM_030725	80976	Mm.33490	NM_030725	ENSMUSG00000027220	Syt13	5730409J20Rik|AI549909|mKIAA1427	synaptotagmin XIII	protein-coding
mm_134334.1	chr16	16490537	16490548	-	1	NA	exon (NM_001301817, exon 3 of 17)	exon (NM_001301817, exon 3 of 17)	36869	NM_001301818	224014	Mm.256131	NM_139232	ENSMUSG00000022788	Fgd4	9030023J02Rik|9330209B17Rik|Frabp|ZFYVE6	FYVE, RhoGEF and PH domain containing 4	protein-coding
mm_137794.1	chr17	29662247	29662250	+	1	NA	intron (NM_028791, intron 1 of 23)	intron (NM_028791, intron 1 of 23)	1653	NM_028791	74157	Mm.390979	NM_028791	ENSMUSG00000024019	Cmtr1	1300018I05Rik|AI451264|Ftsjd2|MTr1	cap methyltransferase 1	protein-coding
mm_23532.1	chr3	60626965	60626993	+	1	NA	3' UTR (NM_001253711, exon 8 of 8)	3' UTR (NM_001253711, exon 8 of 8)	125800	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_11409.1	chr2	31572648	31572658	+	1	NA	promoter-TSS (NM_001290548)	promoter-TSS (NM_001290548)	2	NM_001290548	320267	Mm.207261	NM_001033389	ENSMUSG00000026843	Fubp3	A330051M14Rik|AV006371|FBP3|Marta2	far upstream element (FUSE) binding protein 3	protein-coding
mm_20988.1	chr2	152109234	152109305	-	1	NA	3' UTR (NM_029688, exon 2 of 2)	3' UTR (NM_029688, exon 2 of 2)	3745	NM_029688	76650	Mm.218639	NM_029688	ENSMUSG00000032802	Srxn1	1700127B04Rik|AI854065|AW488194|Npn3|Srx|Srx1|TX01	sulfiredoxin 1 homolog (S. cerevisiae)	protein-coding
mm_129490.1	chr15	78773503	78773509	-	1	NA	promoter-TSS (NM_008595)	promoter-TSS (NM_008595)	-61	NM_008595	17305	Mm.149235	NM_008595	ENSMUSG00000018169	Mfng	AW546563	MFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	protein-coding
mm_3452.1	chr1	150103107	150103120	+	1	NA	intron (NM_011198, intron 5 of 9)	intron (NM_011198, intron 5 of 9)	3082	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_137211.1	chr17	24162305	24162323	+	1	NA	intron (NM_172935, intron 3 of 10)	intron (NM_172935, intron 3 of 10)	1419	NM_172935	245847	Mm.87319	NM_172935	ENSMUSG00000036820	Amdhd2	5730457F11Rik	amidohydrolase domain containing 2	protein-coding
mm_79773.1	chr9	62838768	62838816	+	1	NA	promoter-TSS (NM_001033175)	promoter-TSS (NM_001033175)	5	NM_001033175	76524	Mm.283636	NM_001033175	ENSMUSG00000032245	Cln6	1810065L06Rik|AW743417|D9Bwg1455e|nclf	ceroid-lipofuscinosis, neuronal 6	protein-coding
mm_165219.1	chr2	45060998	45061038	+	1	NA	intron (NM_001289521, intron 1 of 8)	intron (NM_001289521, intron 1 of 8)	-37841	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_39285.1	chr5	3981383	3981386	+	1	NA	intron (NM_194462, intron 14 of 47)	intron (NM_194462, intron 14 of 47)	53198	NM_194462	100986	Mm.46044	NM_194462	ENSMUSG00000040407	Akap9	5730481H23Rik|AKAP-9|AKAP450|AW545847|C79026|G1-448-15|PRKA9|mKIAA0803|mei2-5|repro12	A kinase (PRKA) anchor protein (yotiao) 9	protein-coding
mm_65257.1	chr7	19887909	19887945	-	1	NA	promoter-TSS (NM_177036)	promoter-TSS (NM_177036)	38	NM_177036	319930	Mm.215839	NM_177036	ENSMUSG00000049848	Ceacam19	C130022P09Rik|CEAL1	carcinoembryonic antigen-related cell adhesion molecule 19	protein-coding
mm_58188.1	chr6	142989692	142989721	-	1	NA	Intergenic	Intergenic	-25254	NM_011374	20449	Mm.260838	NM_011374	ENSMUSG00000030283	St8sia1	9330109E03Rik|GD3S|Sia-T|Siat8|Siat8a	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 1	protein-coding
mm_93503.1	chr10	112928950	112928973	-	1	NA	promoter-TSS (NM_001033474)	promoter-TSS (NM_001033474)	65	NM_001033474	382423	Mm.431239	NM_001033474	ENSMUSG00000074748	Atxn7l3b	4921506J03Rik|6230409E21Rik|AI315132|ENSMUSG00000074747	ataxin 7-like 3B	protein-coding
mm_1626.1	chr1	74409383	74409399	+	1	NA	promoter-TSS (NM_009509)	promoter-TSS (NM_009509)	7	NM_009509	22349	Mm.471601	NM_009509	ENSMUSG00000026175	Vil1	Vil	villin 1	protein-coding
mm_6983.1	chr1	86357032	86357072	-	1	NA	promoter-TSS (NR_002851)	promoter-TSS (NR_002851)	-725	NR_002851	80828		NR_002851	ENSMUSG00000064823	Snord82	Rnu82|U82|Z25	small nucleolar RNA, C/D box 82	snoRNA
mm_159275.1	chr2	164715319	164715319	+	1	NA	promoter-TSS (NM_001040055)	promoter-TSS (NM_001040055)	14	NM_001040055	641368	Mm.422380	NM_001040055	ENSMUSG00000074593	Spint5	Gm14316|OTTMUSG00000016293	serine protease inhibitor, Kunitz type 5	protein-coding
mm_115449.1	chr13	118714379	118714388	+	1	NA	promoter-TSS (NM_008002)	promoter-TSS (NM_008002)	-316	NM_008002	14165	Mm.317323	NM_008002	ENSMUSG00000021732	Fgf10	AEY17|BB213776|Fgf-10|Gsfaey17	fibroblast growth factor 10	protein-coding
mm_70605.1	chr8	13386644	13386652	+	1	NA	exon (NM_009724, exon 7 of 7)	exon (NM_009724, exon 7 of 7)	10130	NM_009724	11945	Mm.154039	NM_009724	ENSMUSG00000031449	Atp4b	AV080843	ATPase, H+/K+ exchanging, beta polypeptide	protein-coding
mm_16375.1	chr2	178141894	178141916	+	1	NA	promoter-TSS (NM_028806)	promoter-TSS (NM_028806)	-28	NM_028806	74189	Mm.44413	NM_028806	ENSMUSG00000027525	Phactr3	1500003N10Rik|4930415A02Rik|H17739|Scapin1|Scapinin|mKIAA4224	phosphatase and actin regulator 3	protein-coding
mm_34535.1	chr4	149485261	149485307	+	1	NA	promoter-TSS (NM_026963)	promoter-TSS (NM_026963)	-49	NM_026963	69151	Mm.464434	NM_026963	ENSMUSG00000028990	Lzic	1810030J04Rik|AW047580	leucine zipper and CTNNBIP1 domain containing	protein-coding
mm_141048.1	chr17	25433743	25433767	-	1	NA	promoter-TSS (NM_021415)	promoter-TSS (NM_021415)	28	NM_021415	58226	Mm.268378	NM_021415	ENSMUSG00000024112	Cacna1h	Cav3.2|MNCb-1209|alpha13.2	calcium channel, voltage-dependent, T type, alpha 1H subunit	protein-coding
mm_56715.1	chr6	115362224	115362230	-	1	NA	promoter-TSS (NM_001308354)	promoter-TSS (NM_001308354)	-122	NM_001308354	19016	Mm.3020	NM_011146	ENSMUSG00000000440	Pparg	Nr1c3|PPAR-gamma|PPAR-gamma2|PPARgamma|PPARgamma2	peroxisome proliferator activated receptor gamma	protein-coding
mm_66948.1	chr7	61998901	61998917	-	1	NA	Intergenic	Intergenic	-16550	NR_037287	100526507		NR_037287	ENSMUSG00000092850	Mir344g	mir-344g|mmu-mir-344g	microRNA 344g	ncRNA
mm_93492.1	chr10	112002724	112002760	-	1	NA	Intergenic	Intergenic	-5478	NM_028608	73690	Mm.173790	NM_028608	ENSMUSG00000056888	Glipr1	2410114O14Rik|RTVP-1|RTVP1|mRTVP-1	GLI pathogenesis-related 1 (glioma)	protein-coding
mm_43100.1	chr5	124479039	124479054	+	1	NA	promoter-TSS (NM_030259)	promoter-TSS (NM_030259)	-811	NM_030259	80291	Mm.425280	NM_030259	ENSMUSG00000029401	Rilpl2	-	Rab interacting lysosomal protein-like 2	protein-coding
mm_106169.1	chr11	116679186	116679191	-	1	NA	intron (NM_009180, intron 7 of 8)	intron (NM_009180, intron 7 of 8)	4591	NR_028570	100216538		NR_028570	ENSMUSG00000065094	Snord1a	snR38	small nucleolar RNA, C/D box 1A	snoRNA
mm_98877.1	chr11	97806303	97806341	+	1	NA	intron (NM_010688, intron 1 of 6)	intron (NM_010688, intron 1 of 6)	6650	NM_010688	16796	Mm.271967	NM_010688	ENSMUSG00000038366	Lasp1	AA408629|Def-4|SH3P6|Tg(Col1a1-lacZ)1Ngma	LIM and SH3 protein 1	protein-coding
mm_97535.1	chr11	78536531	78536541	+	1	NA	promoter-TSS (NM_018854)	promoter-TSS (NM_018854)	100	NM_018854	55978	Mm.358671	NM_018854	ENSMUSG00000001105	Ift20	0610009H04Rik|AU015496	intraflagellar transport 20	protein-coding
mm_105792.1	chr11	109995642	109995653	-	1	NA	5' UTR (NM_013851, exon 1 of 39)	5' UTR (NM_013851, exon 1 of 39)	169	NM_013851	27404	Mm.341004	NM_013851	ENSMUSG00000020620	Abca8b	Abca8	ATP-binding cassette, sub-family A (ABC1), member 8b	protein-coding
mm_108296.1	chr12	79208929	79208939	+	1	NA	promoter-TSS (NM_030017)	promoter-TSS (NM_030017)	21	NM_030017	77974	Mm.274373	NM_030017	ENSMUSG00000021123	Rdh12	-	retinol dehydrogenase 12	protein-coding
mm_96344.1	chr11	66956481	66956489	+	1	NA	promoter-TSS (NR_130315)	promoter-TSS (NR_130315)	-153	NR_130645	71576	Mm.340077	NR_130315	ENSMUSG00000085683	9130409J20Rik	-	RIKEN cDNA 9130409J20 gene	ncRNA
mm_119704.1	chr14	53800706	53800713	+	1	NA	Intergenic	Intergenic	453220	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_155072.1	chrX	43590962	43590972	+	1	NA	promoter-TSS (NM_001195271)	promoter-TSS (NM_001195271)	-22	NM_001195271	637093	Mm.368463	NM_001195271	ENSMUSG00000078320	Tex13c1	Gm362|Tex13c	TEX13 family member C1	protein-coding
mm_39477.1	chr5	20416775	20416777	+	1	NA	intron (NM_001170746, intron 9 of 22)	Lx9|LINE|L1	465348	NM_172992	68770	Mm.86410	NM_172992	ENSMUSG00000039987	Phtf2	1110054G21Rik|9530062N20Rik|AI447096|C77923	putative homeodomain transcription factor 2	protein-coding
mm_12991.1	chr2	90885528	90885561	+	1	NA	promoter-TSS (NM_026161)	promoter-TSS (NM_026161)	-242	NM_026161	67445	Mm.258993	NM_026161	ENSMUSG00000040794	C1qtnf4	0710001E10Rik|9430004J15Rik|CTRP4	C1q and tumor necrosis factor related protein 4	protein-coding
mm_2533.1	chr1	106980980	106980985	+	1	NA	promoter-TSS (NM_172852)	promoter-TSS (NM_172852)	-2	NM_172852	241196	Mm.110886	NM_172852	ENSMUSG00000048775	Serpinb13	5430417G24|HUR7|HURPIN|PI13|headpin	serine (or cysteine) peptidase inhibitor, clade B (ovalbumin), member 13	protein-coding
mm_62658.1	chr7	107708979	107708986	+	1	NA	intron (NM_001163557, intron 7 of 25)	intron (NM_001163557, intron 7 of 25)	49050	NM_001205227	320635	Mm.132828	NM_177216	ENSMUSG00000048065	Cyb5r2	D630003K02Rik|b5R.2	cytochrome b5 reductase 2	protein-coding
mm_114123.1	chr13	55209777	55209788	+	1	NA	promoter-TSS (NM_008739)	promoter-TSS (NM_008739)	0	NM_008739	18193	Mm.12964	NM_008739	ENSMUSG00000021488	Nsd1	AI528500|KMT3B	nuclear receptor-binding SET-domain protein 1	protein-coding
mm_97352.1	chr11	77493312	77493335	+	1	NA	promoter-TSS (NM_001004144)	promoter-TSS (NM_001004144)	-89	NM_001004144	216963	Mm.290182	NM_001004144	ENSMUSG00000011877	Git1	Cat-1|p95Cat	G protein-coupled receptor kinase-interactor 1	protein-coding
mm_76353.1	chr8	84771971	84771983	-	1	NA	exon (NM_010906, exon 2 of 9)	exon (NM_010906, exon 2 of 9)	2392	NM_001081981	18032	Mm.9394	NM_010906	ENSMUSG00000001911	Nfix	CTF|NF-I/X|NF1-X|NFI-X	nuclear factor I/X	protein-coding
mm_120118.1	chr14	59557446	59557470	+	1	NA	Intergenic	ORR1C1|LTR|ERVL-MaLR	40501	NM_001168537	71891	Mm.439850	NM_027986	ENSMUSG00000021982	Cdadc1	2310010M10Rik|AI449174|AI463398|BB130816|NYD-SP15	cytidine and dCMP deaminase domain containing 1	protein-coding
mm_156264.1	chrX	136831218	136831226	+	1	NA	exon (NM_011123, exon 2 of 7)	exon (NM_011123, exon 2 of 7)	8476	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_58202.1	chr6	143221442	143221454	-	1	NA	Intergenic	Intergenic	-24440	NR_027803	52285	Mm.354898	NM_001033129		D6Ertd474e	1700001I24Rik|AU023129	DNA segment, Chr 6, ERATO Doi 474, expressed	ncRNA
mm_62954.1	chr7	119617794	119617802	+	1	NA	promoter-TSS (NM_054094)	promoter-TSS (NM_054094)	-30	NM_054094	117147	Mm.427560	NM_054094	ENSMUSG00000033533	Acsm1	Acas3|Bucs1|Macs	acyl-CoA synthetase medium-chain family member 1	protein-coding
mm_24474.1	chr3	90692632	90692638	+	1	NA	TTS (NM_001281852)	TTS (NM_001281852)	3086	NM_001281852	20202	Mm.2128	NM_009114	ENSMUSG00000056071	S100a9	60B8Ag|AW546964|BEE22|Cagb|GAGB|L1Ag|MRP14|p14	S100 calcium binding protein A9 (calgranulin B)	protein-coding
mm_113585.1	chr13	40887094	40887116	+	1	NA	5' UTR (NM_008105, exon 1 of 3)	5' UTR (NM_008105, exon 1 of 3)	347	NM_008105	14538	Mm.314757	NM_008105	ENSMUSG00000021360	Gcnt2	5330430K10Rik|IGnT|IGnTA|IGnTB|IGnTC	glucosaminyl (N-acetyl) transferase 2, I-branching enzyme	protein-coding
mm_52736.1	chr6	120434991	120435001	+	1	NA	intron (NM_145997, intron 27 of 27)	B2_Mm2|SINE|B2	-28201	NM_008359	16172	Mm.4481	NM_008359	ENSMUSG00000002897	Il17ra	AW538159|Cdw217|Il17r|VDw217	interleukin 17 receptor A	protein-coding
mm_51620.1	chr6	85332565	85332566	+	1	NA	intron (NM_178639, intron 1 of 13)	CpG	857	NM_178639	94282	Mm.121485	NM_178639	ENSMUSG00000033720	Sfxn5	C230001H08Rik	sideroflexin 5	protein-coding
mm_137372.1	chr17	25570875	25570931	+	1	NA	promoter-TSS (NR_045176)	promoter-TSS (NR_045176)	92	NR_045176	72834	Mm.33042	NR_045176	ENSMUSG00000091475	2810468N07Rik	-	RIKEN cDNA 2810468N07 gene	ncRNA
mm_169584.1	chr15	25046416	25046416	+	1	NA	Intergenic	B1_Mus1|SINE|Alu	367348	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	brain abundant, membrane attached signal protein 1	protein-coding
mm_109916.1	chr12	8482135	8482139	-	1	NA	Intergenic	Intergenic	17848	NM_007483	11852	Mm.687	NM_007483	ENSMUSG00000054364	Rhob	AA017882|Arh6|Arhb	ras homolog family member B	protein-coding
mm_22671.1	chr3	14872462	14872478	+	1	NA	TTS (NM_007606)	TTS (NM_007606)	8932	NM_007606	12350	Mm.300	NM_007606	ENSMUSG00000027559	Car3	BB219044|Ca3|Car-3	carbonic anhydrase 3	protein-coding
mm_73271.1	chr8	104540823	104540835	+	1	NA	promoter-TSS (NM_053070)	promoter-TSS (NM_053070)	22	NM_053070	12354	Mm.129265	NM_053070	ENSMUSG00000031883	Car7	AV343731|Ca7	carbonic anhydrase 7	protein-coding
mm_66886.1	chr7	59242577	59242602	-	1	NA	intron (NM_011668, intron 2 of 12)	intron (NM_011668, intron 2 of 12)	13837	NM_011668	22215	Mm.9002	NM_011668	ENSMUSG00000025326	Ube3a	4732496B02|5830462N02Rik|A130086L21Rik|Hpve6a|mKIAA4216	ubiquitin protein ligase E3A	protein-coding
mm_26996.1	chr3	25824372	25824374	-	1	NA	intron (NM_001163387, intron 3 of 5)	intron (NM_001163387, intron 3 of 5)	328934	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_142083.1	chr17	35704575	35704632	-	1	NA	promoter-TSS (NM_172962)	promoter-TSS (NM_172962)	-464	NM_172962	12305	Mm.5021	NM_007584	ENSMUSG00000003534	Ddr1	6030432F18|AI323681|CD167a|Cak|Nep|PTK3A	discoidin domain receptor family, member 1	protein-coding
mm_77298.1	chr8	117068160	117068207	-	1	NA	exon (NM_029686, exon 6 of 43)	exon (NM_029686, exon 6 of 43)	14266	NM_029686	76645	Mm.159753	NM_029686	ENSMUSG00000034416	Pkd1l2	1700126L06Rik	polycystic kidney disease 1 like 2	protein-coding
mm_155230.1	chrX	57196589	57196596	+	1	NA	Intergenic	Intergenic	-4045	NR_038463	100502842	Mm.164733	NR_038463	ENSMUSG00000085808	Gm14718	OTTMUSG00000017790	predicted gene 14718	ncRNA
mm_92869.1	chr10	81643737	81643767	-	1	NA	exon (NM_027480, exon 17 of 20)	exon (NM_027480, exon 17 of 20)	-5317	NM_001142963	100233208	Mm.327168	NM_001142963	ENSMUSG00000096856	Gm10778	ENSMUSG00000074860	predicted gene 10778	protein-coding
mm_169233.1	chr13	68236146	68236157	-	1	NA	Intergenic	MMVL30-int|LTR|ERV1	345953	NM_001308475	210009	Mm.205514	NM_172480	ENSMUSG00000034617	Mtrr	4732420G08|MSR	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	protein-coding
mm_74781.1	chr8	22039583	22039585	-	1	NA	intron (NM_007511, intron 1 of 20)	intron (NM_007511, intron 1 of 20)	20490	NM_007511	11979	Mm.87854	NM_007511	ENSMUSG00000006567	Atp7b	Atp7a|WND|tx	ATPase, Cu++ transporting, beta polypeptide	protein-coding
mm_43327.1	chr5	135009439	135009453	+	1	NA	promoter-TSS (NR_033794)	promoter-TSS (NR_033794)	-10	NR_033794	68758	Mm.389700	NM_145215	ENSMUSG00000040532	Abhd11	1110054D16Rik|A630008N09Rik|Wbscr21	abhydrolase domain containing 11	protein-coding
mm_117151.1	chr13	61203429	61203430	-	1	NA	promoter-TSS (NM_021445)	promoter-TSS (NM_021445)	-37	NM_021445	58518	Mm.143794	NM_021445	ENSMUSG00000021441	Cts6	1600022N02Rik	cathepsin 6	protein-coding
mm_112383.1	chr12	119238099	119238122	-	1	NA	5' UTR (NM_177290, exon 1 of 14)	5' UTR (NM_177290, exon 1 of 14)	166	NM_177290	320910	Mm.217000	NM_177290	ENSMUSG00000025321	Itgb8	4832412O06Rik	integrin beta 8	protein-coding
mm_170290.1	chr18	3000164	3000166	+	1	NA	Intergenic	Intergenic	123247	NM_001167539	100312476	Mm.480293	NM_001167539	ENSMUSG00000091539	Vmn1r238	-	vomeronasal 1 receptor, 238	protein-coding
mm_96292.1	chr11	63131554	63131570	+	1	NA	5' UTR (NM_008885, exon 1 of 5)	5' UTR (NM_008885, exon 1 of 5)	105	NM_001302255	18858	Mm.1237	NM_008885	ENSMUSG00000018217	Pmp22	22kDa|Gas-3|HNPP|Tr|trembler	peripheral myelin protein 22	protein-coding
mm_159813.1	chr5	120795531	120795531	-	1	NA	promoter-TSS (NM_145210)	promoter-TSS (NM_145210)	-1	NM_145210	231699	Mm.379383	NM_145210	ENSMUSG00000066867	Oas1e	C87484|oasl7	2'-5' oligoadenylate synthetase 1E	protein-coding
mm_46001.1	chr5	90654425	90654437	-	1	NA	Intergenic	L1_Mur3|LINE|L1	-13904	NM_001310656	73246	Mm.30172	NM_028478	ENSMUSG00000029370	Rassf6	1600016B17Rik	Ras association (RalGDS/AF-6) domain family member 6	protein-coding
mm_70957.1	chr8	26978612	26978618	+	1	NA	exon (NM_001101502, exon 2 of 2)	exon (NM_001101502, exon 2 of 2)	1279	NM_001110508	353310	Mm.212469	NM_001101502	ENSMUSG00000085795	Zfp703	1110032O19Rik|AI430822|AL022941|Csmn1|End2|Zeppo1|Znf703|Zpo1	zinc finger protein 703	protein-coding
mm_12705.1	chr2	76539967	76539979	+	1	NA	intron (NM_001290733, intron 4 of 26)	intron (NM_001290733, intron 4 of 26)	40967	NM_001290735	99031	Mm.240435	NM_145525	ENSMUSG00000042359	Osbpl6	1110062M20Rik|AI596402|ORP-6|mKIAA4128	oxysterol binding protein-like 6	protein-coding
mm_127752.1	chr15	103479181	103479185	+	1	NA	intron (NM_153505, intron 20 of 30)	intron (NM_153505, intron 20 of 30)	-23851	NM_008800	18574	Mm.390792	NM_008800	ENSMUSG00000022489	Pde1b	Pde1b1	phosphodiesterase 1B, Ca2+-calmodulin dependent	protein-coding
mm_111555.1	chr12	101058729	101058739	-	1	NA	exon (NM_001160214, exon 4 of 15)	exon (NM_001160214, exon 4 of 15)	-23717	NR_038048	319760	Mm.440198	NM_176997	ENSMUSG00000097121	D130020L05Rik	9430007L23Rik	RIKEN cDNA D130020L05 gene	ncRNA
mm_110427.1	chr12	46819021	46819026	-	1	NA	promoter-TSS (NM_021361)	promoter-TSS (NM_021361)	-248	NM_021361	664883	Mm.247195	NM_021361	ENSMUSG00000021047	Nova1	9430099M15Rik|G630039L02|Nova-1	neuro-oncological ventral antigen 1	protein-coding
mm_93358.1	chr10	103029061	103029080	-	1	NA	promoter-TSS (NM_172553)	promoter-TSS (NM_172553)	-293	NM_172553	216285	Mm.19287	NM_172553	ENSMUSG00000036602	Alx1	AI314867|C130005I02|Cart1	ALX homeobox 1	protein-coding
mm_130476.1	chr15	98728107	98728117	-	1	NA	promoter-TSS (NM_024169)	promoter-TSS (NM_024169)	86	NM_024169	66120	Mm.30729	NM_024169	ENSMUSG00000003355	Fkbp11	1110002O23Rik|FKBP-11	FK506 binding protein 11	protein-coding
mm_133646.1	chr16	91793597	91793614	+	1	NA	intron (NM_001110275, intron 4 of 28)	intron (NM_001110275, intron 4 of 28)	64234	NM_010587	16443	Mm.40546	NM_010587	ENSMUSG00000022957	Itsn1	AA517634|AA545208|AI316805|AI839402|AI848451|Ehsh1|Ese1|Itsn|Sh3p17	intersectin 1 (SH3 domain protein 1A)	protein-coding
mm_50583.1	chr6	49056590	49056598	+	1	NA	3' UTR (NM_053110, exon 11 of 11)	3' UTR (NM_053110, exon 11 of 11)	-17201	NM_029353	75593	Mm.439947	NM_029353	ENSMUSG00000029815	Malsu1	2410003K15Rik|Matsu1	mitochondrial assembly of ribosomal large subunit 1	protein-coding
mm_128893.1	chr15	73185303	73185317	-	1	NA	promoter-TSS (NM_153178)	promoter-TSS (NM_153178)	-363	NM_153178	239528	Mm.23095	NM_153178	ENSMUSG00000036698	Ago2	1110029L17Rik|2310051F07Rik|AI225898|AL022874|AW546247|ENSMUSG00000072493|Eif2c2|Gerp95|Gm10365|mKIAA4215	argonaute RISC catalytic subunit 2	protein-coding
mm_157945.1	chrX	85886762	85886775	-	1	NA	intron (NM_001163539, intron 1 of 1)	intron (NM_001163539, intron 1 of 1)	16495	NM_001163539	71398	Mm.185296	NM_001163539	ENSMUSG00000025058	5430427O19Rik	-	RIKEN cDNA 5430427O19 gene	protein-coding
mm_9150.1	chr1	170913755	170913759	-	1	NA	promoter-TSS (NM_001029984)	promoter-TSS (NM_001029984)	-816	NM_001029984	435653	Mm.337931	NM_001029984	ENSMUSG00000070524	Fcrlb	FREB-2|FREB2|FcRL2|Fcrlm2|Fcry|mFCRL2	Fc receptor-like B	protein-coding
mm_145974.1	chr18	67934078	67934097	+	1	NA	intron (NM_172631, intron 1 of 5)	CpG	830	NM_172631	52662	Mm.440183	NM_172631	ENSMUSG00000024544	Ldlrad4	8230401C20Rik|A430083H02|A430108L08Rik|C18orf1|D18Ertd653e|D330030L18Rik	low density lipoprotein receptor class A domain containing 4	protein-coding
mm_108635.1	chr12	85746541	85746551	+	1	NA	promoter-TSS (NM_145447)	promoter-TSS (NM_145447)	7	NM_145447	217721	Mm.301076	NM_145447	ENSMUSG00000034258	Mfsd7c	CCT|Flvcr2	major facilitator superfamily domain containing 7C	protein-coding
mm_30323.1	chr3	151731857	151731874	-	1	NA	3' UTR (NM_133871, exon 8 of 8)	3' UTR (NM_133871, exon 8 of 8)	18094	NM_133871	99899	Mm.30756	NM_133871	ENSMUSG00000028037	Ifi44	A430056A10Rik|AW261460|MTAP44|p44	interferon-induced protein 44	protein-coding
mm_48810.1	chr5	148995162	148995173	-	1	NA	promoter-TSS (NR_102383)	promoter-TSS (NR_102383)	47	NR_102383	319982	Mm.33303	NR_102383	ENSMUSG00000106951	5930430L01Rik	-	RIKEN cDNA 5930430L01 gene	ncRNA
mm_130207.1	chr15	95528430	95528445	-	1	NA	promoter-TSS (NM_001289653)	promoter-TSS (NM_001289653)	-185	NM_001289653	54003	Mm.3959	NM_016743	ENSMUSG00000022454	Nell2	A330108N19Rik|R75516|mel91	NEL-like 2	protein-coding
mm_144391.1	chr18	20670071	20670098	+	1	NA	exon (NM_013697, exon 3 of 4)	exon (NM_013697, exon 3 of 4)	4834	NM_013697	22139	Mm.2108	NM_013697	ENSMUSG00000061808	Ttr	AA408768|AI787086|D17860|prealbumin	transthyretin	protein-coding
mm_76672.1	chr8	93535805	93535859	-	1	NA	promoter-TSS (NM_001003951)	promoter-TSS (NM_001003951)	-125	NM_001003951	67935	Mm.65457	NM_001003951	ENSMUSG00000058019	Ces5a	1700081L16Rik|1700122C07Rik|BB081581|Ces7|Gm503|cauxin	carboxylesterase 5A	protein-coding
mm_152115.1	chr19	6979875	6979896	-	1	NA	intron (NM_008020, intron 1 of 5)	CpG	555	NM_008020	14227	Mm.4234	NM_008020	ENSMUSG00000056629	Fkbp2	13kDa|FKBP-2|mFKBP13|mFKBP2	FK506 binding protein 2	protein-coding
mm_52893.1	chr6	122607942	122607982	+	1	NA	intron (NM_008108, intron 1 of 1)	intron (NM_008108, intron 1 of 1)	2125	NM_008108	14562	Mm.299742	NM_008108	ENSMUSG00000030117	Gdf3	C78318|Gdf-3|Vgr-2|Vgr2|ecat9	growth differentiation factor 3	protein-coding
mm_26442.1	chr3	142633455	142633485	+	1	NA	exon (NM_010260, exon 8 of 11)	exon (NM_010260, exon 8 of 11)	-9524	NR_105802	102465200		NR_105802	ENSMUSG00000098871	Mir6381	Gm27963|mmu-mir-6381	microRNA 6381	ncRNA
mm_121032.1	chr14	79769918	79769922	+	1	NA	exon (NM_021543, exon 1 of 3)	exon (NM_021543, exon 1 of 3)	1392	NM_001042726	18530	Mm.390715	NM_021543	ENSMUSG00000036422	Pcdh8	1700080P15Rik|Papc	protocadherin 8	protein-coding
mm_646.1	chr1	40424116	40424157	+	1	NA	Intergenic	Intergenic	-5434	NM_001294171	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_66174.1	chr7	33945075	33945102	-	1	NA	promoter-TSS (NM_178308)	promoter-TSS (NM_178308)	-103	NM_178308	110187	Mm.155750	NM_178308	ENSMUSG00000066586	Scgb2b26	Abpbg26|Abpbg4|Abpg|C2d|Scgb2b4	secretoglobin, family 2B, member 26	protein-coding
mm_139176.1	chr17	47590708	47590711	+	1	NA	intron (NM_001081635, intron 2 of 6)	RLTR51A_Mm|LTR|ERVK?	-2758	NM_007632	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_140136.1	chr17	79650301	79650304	+	1	NA	exon (NM_201361, exon 3 of 11)	exon (NM_201361, exon 3 of 11)	35402	NM_201361	381110	Mm.209801	NM_201361	ENSMUSG00000036368	Rmdn2	AW061290|Fam82a1|RMD-2|mRMD-2	regulator of microtubule dynamics 2	protein-coding
mm_82599.1	chr9	21312337	21312345	-	1	NA	promoter-TSS (NM_009678)	promoter-TSS (NM_009678)	-8	NM_001110300	11768	Mm.22239	NM_009678	ENSMUSG00000003309	Ap1m2	D9Ertd818e|[m]1B|mu1B	adaptor protein complex AP-1, mu 2 subunit	protein-coding
mm_60184.1	chr7	43214020	43214053	+	1	NA	promoter-TSS (NM_001177525)	promoter-TSS (NM_001177525)	-3	NM_001177525	100170401		NM_001177525		EU599041	TU7	expressed sequence EU599041	protein-coding
mm_59090.1	chr7	19696430	19696441	+	1	NA	exon (NM_009696, exon 4 of 4)	exon (NM_009696, exon 4 of 4)	1963	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_97125.1	chr11	74925879	74925909	+	1	NA	promoter-TSS (NM_001163311)	promoter-TSS (NM_001163311)	22	NM_001002764	103677	Mm.288460	NM_001002764	ENSMUSG00000038290	Smg6	AI317223|AU041178	Smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans)	protein-coding
mm_64856.1	chr7	13035473	13035535	-	1	NA	promoter-TSS (NM_026885)	promoter-TSS (NM_026885)	-727	NM_026885	68953	Mm.295670	NM_026885	ENSMUSG00000033916	Chmp2a	1500016L11Rik	charged multivesicular body protein 2A	protein-coding
mm_85920.1	chr9	111271523	111271562	-	1	NA	promoter-TSS (NM_026810)	promoter-TSS (NM_026810)	66	NM_026810	17350	Mm.486383	NM_026810	ENSMUSG00000032498	Mlh1	1110035C23Rik|AI317206|AI325952|AI561766	mutL homolog 1	protein-coding
mm_36616.1	chr4	89294555	89294588	-	1	NA	promoter-TSS (NR_132431)	promoter-TSS (NR_132431)	48	NM_009877	12578	Mm.4733	NM_009877	ENSMUSG00000044303	Cdkn2a	ARF-INK4a|Arf|INK4a-ARF|Ink4a/Arf|MTS1|Pctr1|p16|p16(INK4a)|p16INK4a|p19<ARF>|p19ARF	cyclin-dependent kinase inhibitor 2A	protein-coding
mm_142336.1	chr17	43568505	43568529	-	1	NA	promoter-TSS (NM_013737)	promoter-TSS (NM_013737)	66	NM_013737	27226	Mm.9277	NM_013737	ENSMUSG00000023913	Pla2g7	PAF-AH|R75400	phospholipase A2, group VII (platelet-activating factor acetylhydrolase, plasma)	protein-coding
mm_94121.1	chr10	128645785	128645816	-	1	NA	exon (NM_011772, exon 1 of 8)	exon (NM_011772, exon 1 of 8)	193	NM_011772	22781	Mm.358648	NM_011772	ENSMUSG00000002578	Ikzf4	A630026H08Rik|Eos|Zfpn1a4|Znfn1a4	IKAROS family zinc finger 4	protein-coding
mm_147662.1	chr18	60610059	60610068	-	1	NA	promoter-TSS (NM_001109975)	promoter-TSS (NM_001109975)	41	NM_001109975	104027	Mm.252321	NM_177340	ENSMUSG00000043079	Synpo	9030217H17Rik|9130229N11|9330140I15Rik|AW046661	synaptopodin	protein-coding
mm_101099.1	chr11	11898093	11898150	-	1	NA	promoter-TSS (NM_001190448)	promoter-TSS (NM_001190448)	23	NM_001190448	13195	Mm.12906	NM_016672	ENSMUSG00000020182	Ddc	Aadc	dopa decarboxylase	protein-coding
mm_126637.1	chr15	83565428	83565460	+	1	NA	intron (NM_009775, intron 1 of 3)	intron (NM_009775, intron 1 of 3)	1871	NM_009775	12257	Mm.1508	NM_009775	ENSMUSG00000041736	Tspo	Bzrp|IBP|PBR|Tspo1	translocator protein	protein-coding
mm_86852.1	chr10	21593192	21593197	+	1	NA	promoter-TSS (NR_027968)	promoter-TSS (NR_027968)	49	NR_027968	67692	Mm.54306	NM_183266	ENSMUSG00000050844	1700020N01Rik	-	RIKEN cDNA 1700020N01 gene	ncRNA
mm_36429.1	chr4	82293884	82293897	-	1	NA	3' UTR (NM_001113209, exon 12 of 12)	3' UTR (NM_001113209, exon 12 of 12)	211889	NM_001286127	18028	Mm.317947	NM_008687	ENSMUSG00000008575	Nfib	6720429L07Rik|CTF|E030026I10Rik|NF-I/B|NF1-B|NFI-B	nuclear factor I/B	protein-coding
mm_160821.1	chr11	30219689	30219689	-	1	NA	promoter-TSS (NM_175836)	promoter-TSS (NM_175836)	83	NM_175836	20742	Mm.123110	NM_009260	ENSMUSG00000020315	Sptbn1	9930031C03Rik|AL033301|SPTB2|Spnb-2|Spnb2|elf1|elf3|mKIAA4049	spectrin beta, non-erythrocytic 1	protein-coding
mm_111722.1	chr12	103740216	103740220	-	1	NA	Intergenic	Intergenic	-2029	NM_009244	20701	Mm.439692	NM_009244	ENSMUSG00000071178	Serpina1b	D12Ucla2|Dom2|PI2|Spi1-2	serine (or cysteine) preptidase inhibitor, clade A, member 1B	protein-coding
mm_22337.1	chr2	180709986	180710017	-	1	NA	promoter-TSS (NM_001291432)	promoter-TSS (NM_001291432)	-2	NM_001291432	23856	Mm.253836	NM_011805	ENSMUSG00000038914	Dido1	6720461J16Rik|D130048F08Rik|DATF-1|DIO-1|Datf1|dido	death inducer-obliterator 1	protein-coding
mm_172327.1	chr7	107243007	107243018	+	1	NA	Intergenic	ORR1A0|LTR|ERVL-MaLR	33567	NM_029660	76572	Mm.128134	NM_029660	ENSMUSG00000073894	Rbmxl2	1700012H05Rik|Hnrnpg-t	RNA binding motif protein, X-linked-like 2	protein-coding
mm_144180.1	chr18	6765227	6765254	+	1	NA	promoter-TSS (NM_181070)	promoter-TSS (NM_181070)	73	NM_001278447	19330	Mm.132802	NM_181070	ENSMUSG00000073639	Rab18	AA959686	RAB18, member RAS oncogene family	protein-coding
mm_119365.1	chr14	41121388	41121414	+	1	NA	exon (NM_133653, exon 8 of 10)	exon (NM_133653, exon 8 of 10)	-10387	NM_023134	20387	Mm.46062	NM_023134	ENSMUSG00000021789	Sftpa1	SP-A|Sftp-1|Sftp1	surfactant associated protein A1	protein-coding
mm_72685.1	chr8	84966754	84966766	+	1	NA	promoter-TSS (NM_027187)	promoter-TSS (NM_027187)	-749	NM_027187	69724	Mm.182470	NM_027187	ENSMUSG00000052926	Rnaseh2a	2400006P09Rik|RNASEHI|RNHIA|RNHL	ribonuclease H2, large subunit	protein-coding
mm_84800.1	chr9	77251830	77251838	-	1	NA	intron (NM_027150, intron 1 of 7)	intron (NM_027150, intron 1 of 7)	96036	NM_027150	69642	Mm.35008	NM_027150	ENSMUSG00000032355	Mlip	2310046A06Rik|AI931782|CIP	muscular LMNA-interacting protein	protein-coding
mm_153558.1	chr19	42142151	42142156	-	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-5236	NM_183195	277010	Mm.206250	NM_183195	ENSMUSG00000044345	Marveld1	AI504298|Mrvldc1	MARVEL (membrane-associating) domain containing 1	protein-coding
mm_161750.1	chr17	34670354	34670354	+	1	NA	promoter-TSS (NM_031176)	promoter-TSS (NM_031176)	-181	NM_031176	81877	Mm.290527	NM_031176	ENSMUSG00000033327	Tnxb	Tn-mhc|Tnx	tenascin XB	protein-coding
mm_86140.1	chr9	116979140	116979151	-	1	NA	intron (NM_001172122, intron 3 of 13)	B4A|SINE|B4	273338	NM_001172123	207181	Mm.326411	NM_178660	ENSMUSG00000039607	Rbms3	6720477E09Rik|8430436O14Rik	RNA binding motif, single stranded interacting protein	protein-coding
mm_43500.1	chr5	136973912	136973929	+	1	NA	intron (NM_021719, intron 2 of 4)	intron (NM_021719, intron 2 of 4)	6051	NM_021719	60363	Mm.87202	NM_021719	ENSMUSG00000001739	Cldn15	2210009B08Rik|BB107105	claudin 15	protein-coding
mm_61525.1	chr7	78914315	78914334	+	1	NA	promoter-TSS (NM_001113527)	promoter-TSS (NM_001113527)	89	NM_001113527	57444	Mm.322843	NM_020583	ENSMUSG00000039236	Isg20	1600023I01Rik|2010107M23Rik|20kDa|DnaQL|HEM45	interferon-stimulated protein	protein-coding
mm_22311.1	chr2	180439485	180439485	-	1	NA	Intergenic	B4|SINE|B4	-21493	NM_148933	108115	Mm.133687	NM_148933	ENSMUSG00000038963	Slco4a1	OATP-E|Slc21a12	solute carrier organic anion transporter family, member 4a1	protein-coding
mm_77679.1	chr8	125538432	125538440	-	1	NA	Intergenic	Intergenic	-45726	NM_001081337	244668	Mm.271668	NM_001081337	ENSMUSG00000001995	Sipa1l2	BC058408|mKIAA1389	signal-induced proliferation-associated 1 like 2	protein-coding
mm_121751.1	chr14	18896721	18896725	-	1	NA	Intergenic	RLTR10C|LTR|ERVK	-3096	NM_144839	218793	Mm.23551	NM_144839	ENSMUSG00000058317	Ube2e2	BC016265	ubiquitin-conjugating enzyme E2E 2	protein-coding
mm_74385.1	chr8	128720439	128720453	+	1	NA	exon (NM_010578, exon 11 of 16)	exon (NM_010578, exon 11 of 16)	34792	NM_010578	16412	Mm.263396	NM_010578	ENSMUSG00000025809	Itgb1	4633401G24Rik|AA409975|AA960159|CD29|ENSMUSG00000051907|Fnrb|Gm9863|gpIIa	integrin beta 1 (fibronectin receptor beta)	protein-coding
mm_68670.1	chr7	118973713	118973716	-	1	NA	3' UTR (NM_022420, exon 4 of 4)	3' UTR (NM_022420, exon 4 of 4)	21497	NM_022420	64297	Mm.103439	NM_022420	ENSMUSG00000008734	Gprc5b	AW125761|Raig2	G protein-coupled receptor, family C, group 5, member B	protein-coding
mm_1364.1	chr1	66386969	66386999	+	1	NA	intron (NM_001310634, intron 4 of 14)	intron (NM_001310634, intron 4 of 14)	65260	NM_001310634	17756	Mm.256966	NM_008632	ENSMUSG00000015222	Map2	G1-397-34|MAP-2|Mtap-2|Mtap2|repro4	microtubule-associated protein 2	protein-coding
mm_33577.1	chr4	132351769	132351777	+	1	NA	TTS (NR_003270)	TTS (NR_003270)	1913	NR_003270	399101	Mm.486919	NR_002904	ENSMUSG00000085241	Snhg3	Rnu17d|U17HG	small nucleolar RNA host gene 3	ncRNA
mm_141270.1	chr17	27753827	27753876	-	1	NA	exon (NM_001271511, exon 4 of 4)	exon (NM_001271511, exon 4 of 4)	-24900	NM_013891	30051	Mm.26768	NM_013891	ENSMUSG00000024215	Spdef	PDEF|Pse	SAM pointed domain containing ets transcription factor	protein-coding
mm_11331.1	chr2	30442064	30442078	+	1	NA	intron (NM_138748, intron 8 of 9)	intron (NM_138748, intron 8 of 9)	26021	NM_138748	110854	Mm.275393	NM_138748	ENSMUSG00000039515	Ptpa	2610042B21Rik|C77440|N28142|PR53|Ppp2r4	protein phosphatase 2 protein activator	protein-coding
mm_104065.1	chr11	86585084	86585097	-	1	NA	promoter-TSS (NR_029738)	promoter-TSS (NR_029738)	-932	NR_029738	387140		NR_029738	ENSMUSG00000065455	Mir21a	Mir21|Mirn21|mmu-mir-21|mmu-mir-21a	microRNA 21a	ncRNA
mm_135511.1	chr16	48589347	48589348	-	1	NA	intron (NM_010816, intron 19 of 26)	4.5SRNA|scRNA|scRNA	158110	NM_010816	17450	Mm.250060	NM_010816	ENSMUSG00000022652	Morc1	Morc	microrchidia 1	protein-coding
mm_122993.1	chr14	54990369	54990382	-	1	NA	exon (NM_080728, exon 11 of 41)	exon (NM_080728, exon 11 of 41)	4174	NM_080728	140781	Mm.457983	NM_080728	ENSMUSG00000053093	Myh7	B-MHC|MyHC-I|Myhc-b|Myhcb|beta-MHC	myosin, heavy polypeptide 7, cardiac muscle, beta	protein-coding
mm_85407.1	chr9	103365745	103365756	-	1	NA	promoter-TSS (NM_001134427)	promoter-TSS (NM_001134427)	30	NM_175833	321022	Mm.261025	NM_175565	ENSMUSG00000032803	Cdv3	2510010F10Rik|C230084J24Rik|C79446|TPP36	carnitine deficiency-associated gene expressed in ventricle 3	protein-coding
mm_130767.1	chr15	101374995	101375009	-	1	NA	Intergenic	Intergenic	-4877	NM_028770	74127	Mm.440055	NM_028770	ENSMUSG00000037185	Krt80	1200016G03Rik|2310041I20Rik|Kb20	keratin 80	protein-coding
mm_53258.1	chr6	127887709	127887757	+	1	NA	5' UTR (NM_026743, exon 1 of 8)	5' UTR (NM_026743, exon 1 of 8)	111	NM_026743	68498	Mm.174368	NM_026743	ENSMUSG00000030351	Tspan11	1110014F12Rik|AU067806	tetraspanin 11	protein-coding
mm_48288.1	chr5	138184712	138184722	-	1	NA	intron (NM_009315, intron 1 of 14)	PB1D9|SINE|Alu	2469	NM_009315	21343	Mm.248517	NM_009315	ENSMUSG00000036980	Taf6	80kDa|AW549759|TAF(II)80|TAFII70|Taf2e|p80	TATA-box binding protein associated factor 6	protein-coding
mm_16516.1	chr2	181381308	181381365	+	1	NA	TTS (NM_144894)	TTS (NM_144894)	101	NM_023684	72699	Mm.440138	NM_023684	ENSMUSG00000090077	Lime1	2810038K19Rik|LIME	Lck interacting transmembrane adaptor 1	protein-coding
mm_136609.1	chr17	5324961	5324965	+	1	NA	intron (NM_001085355, intron 13 of 19)	(T)n|Simple_repeat|Simple_repeat	93804	NM_175349	106557	Mm.432764	NM_175349	ENSMUSG00000101959	Ldhal6b	4933402O15Rik|AI326310|LDHL|Ldhal	lactate dehydrogenase A-like 6B	protein-coding
mm_127187.1	chr15	99029916	99029924	+	1	NA	promoter-TSS (NM_009448)	promoter-TSS (NM_009448)	29	NM_009448	22146	Mm.88212	NM_009448	ENSMUSG00000043091	Tuba1c	M[a]6|Tuba6	tubulin, alpha 1C	protein-coding
mm_25788.1	chr3	126803314	126803316	+	1	NA	intron (NM_001025438, intron 13 of 18)	intron (NM_001025438, intron 13 of 18)	140071	NM_001034168	109676	Mm.220242	NM_178655	ENSMUSG00000032826	Ank2	100043364|AI835472|AW491075|Ank-2|Gm4392	ankyrin 2, brain	protein-coding
mm_160324.1	chr8	3258807	3258807	-	1	NA	exon (NM_001330056, exon 2 of 22)	exon (NM_001330056, exon 2 of 22)	20810	NM_010568	16337	Mm.268003	NM_010568	ENSMUSG00000005534	Insr	4932439J01Rik|CD220|D630014A15Rik|IR|IR-A|IR-B	insulin receptor	protein-coding
mm_82889.1	chr9	32541425	32541431	-	1	NA	promoter-TSS (NM_008026)	promoter-TSS (NM_008026)	24	NM_008026	14247	Mm.258908	NM_008026	ENSMUSG00000016087	Fli1	EWSR2|Fli-1|SIC-1|Sic1	Friend leukemia integration 1	protein-coding
mm_45586.1	chr5	74068362	74068438	-	1	NA	promoter-TSS (NM_177561)	promoter-TSS (NM_177561)	11	NM_177561	69727	Mm.48795	NM_177561	ENSMUSG00000054814	Usp46	1190009E20Rik|2410018I08Rik|AI451644	ubiquitin specific peptidase 46	protein-coding
mm_40023.1	chr5	33337057	33337060	+	1	NA	intron (NM_021500, intron 1 of 8)	intron (NM_021500, intron 1 of 8)	1486	NM_021500	59003	Mm.138617	NM_021500	ENSMUSG00000079562	Maea	1110030D19Rik|EMP|Gid9	macrophage erythroblast attacher	protein-coding
mm_10596.1	chr2	18677056	18677066	+	1	NA	promoter-TSS (NM_007552)	promoter-TSS (NM_007552)	43	NM_007552	12151	Mm.289584	NM_007552	ENSMUSG00000026739	Bmi1	AW546694|Bmi-1|Pcgf4	Bmi1 polycomb ring finger oncogene	protein-coding
mm_137786.1	chr17	29549784	29549798	+	1	NA	promoter-TSS (NM_001162901)	promoter-TSS (NM_001162901)	-11	NM_198647	381085	Mm.328934	NM_198647	ENSMUSG00000042203	Tbc1d22b	BC045600	TBC1 domain family, member 22B	protein-coding
mm_3000.1	chr1	133246093	133246099	+	1	NA	promoter-TSS (NM_001160268)	promoter-TSS (NM_001160268)	-1	NM_001160268	240753	Mm.253559	NM_182930	ENSMUSG00000041757	Plekha6	9530028L01Rik|AU042621|Pepp3	pleckstrin homology domain containing, family A member 6	protein-coding
mm_98999.1	chr11	98795822	98795840	+	1	NA	promoter-TSS (NM_028722)	promoter-TSS (NM_028722)	62	NM_028722	74026	Mm.258352	NM_028722	ENSMUSG00000052915	Msl1	2810017F12Rik|4121402D02Rik|4930463F05Rik|AA682082|Msl-1	male-specific lethal 1 homolog (Drosophila)	protein-coding
mm_50929.1	chr6	57663001	57663025	+	1	NA	3' UTR (NM_025992, exon 23 of 23)	3' UTR (NM_025992, exon 23 of 23)	29065	NM_025574	66459	Mm.44201	NM_025574	ENSMUSG00000043162	Pyurf	2610022G08Rik|AI847956|Prey	Pigy upstream reading frame	protein-coding
mm_149857.1	chr19	25095426	25095434	+	1	NA	intron (NM_028785, intron 10 of 47)	intron (NM_028785, intron 10 of 47)	95901	NM_028785	76088	Mm.102485	NM_028785	ENSMUSG00000052085	Dock8	1200017A24Rik|5830472H07Rik|A130095G14Rik|AI461977	dedicator of cytokinesis 8	protein-coding
mm_172065.1	chr6	135363050	135363051	+	1	NA	5' UTR (NM_001288628, exon 1 of 6)	5' UTR (NM_001288628, exon 1 of 6)	119	NM_001288628	13730	Mm.182785	NM_010128	ENSMUSG00000030208	Emp1	I-8-09|TMP	epithelial membrane protein 1	protein-coding
mm_81560.1	chr9	110380942	110380949	+	1	NA	intron (NM_001103162, intron 16 of 22)	CpG-15428	27265	NM_001081043	104831	Mm.335477	NM_001081043	ENSMUSG00000036057	Ptpn23	AI462446|PTP-TD14	protein tyrosine phosphatase, non-receptor type 23	protein-coding
mm_97883.1	chr11	83291672	83291682	+	1	NA	promoter-TSS (NR_028363)	promoter-TSS (NR_028363)	-22	NR_028363	613254	Mm.383758	NR_028363	ENSMUSG00000093483	AA465934	-	expressed sequence AA465934	ncRNA
mm_87622.1	chr10	57800995	57801006	+	1	NA	exon (NM_020561, exon 2 of 8)	exon (NM_020561, exon 2 of 8)	6456	NM_020561	57319	Mm.2379	NM_020561	ENSMUSG00000019872	Smpdl3a	0610010C24Rik|AI529588|ASM3A|ASML3|ASML3A	sphingomyelin phosphodiesterase, acid-like 3A	protein-coding
mm_71118.1	chr8	36094885	36094895	+	1	NA	promoter-TSS (NM_172911)	promoter-TSS (NM_172911)	62	NM_172911	244418	Mm.244971	NM_172911	ENSMUSG00000050271	Prag1	9830148H23|D8Ertd82e|NACK|Sgk223|mFLJ00269	PEAK1 related kinase activating pseudokinase 1	protein-coding
mm_29207.1	chr3	106790004	106790028	-	1	NA	5' UTR (NM_007651, exon 1 of 8)	5' UTR (NM_007651, exon 1 of 8)	133	NM_007651	12508	Mm.316861	NM_007651	ENSMUSG00000040747	Cd53	AI323659|Ox-44|Tspan25	CD53 antigen	protein-coding
mm_23773.1	chr3	75562915	75562918	+	1	NA	intron (NM_009250, intron 1 of 8)	intron (NM_009250, intron 1 of 8)	5383	NM_009250	20713	Mm.41560	NM_009250	ENSMUSG00000027834	Serpini1	AI837402|Ns|PI-12|PI12|Spi17	serine (or cysteine) peptidase inhibitor, clade I, member 1	protein-coding
mm_140390.1	chr17	87283203	87283220	+	1	NA	promoter-TSS (NR_015506)	promoter-TSS (NR_015506)	325	NM_028639	225049	Mm.77396	NM_028639	ENSMUSG00000036918	Ttc7	1110035E02Rik|1700007L07Rik|Ttc7a|fsn|hea	tetratricopeptide repeat domain 7	protein-coding
mm_44755.1	chr5	31489107	31489154	-	1	NA	TTS (NM_026296)	TTS (NM_026296)	3271	NM_026296	67656	Mm.23355	NM_026296	ENSMUSG00000029138	4930548H24Rik	AI427865	RIKEN cDNA 4930548H24 gene	protein-coding
mm_32998.1	chr4	120517495	120517500	+	1	NA	intron (NM_001159630, intron 13 of 17)	intron (NM_001159630, intron 13 of 17)	-14734	NM_177570	194219	Mm.29788	NM_177570	ENSMUSG00000047518	Slfnl1	4933406A14Rik	schlafen like 1	protein-coding
mm_275.1	chr1	21240598	21240628	+	1	NA	promoter-TSS (NM_010356)	promoter-TSS (NM_010356)	28	NM_010356	14859	Mm.394593	NM_010356	ENSMUSG00000025934	Gsta3	Gst2-3	glutathione S-transferase, alpha 3	protein-coding
mm_140427.1	chr17	88042697	88042741	+	1	NA	intron (NM_001081034, intron 1 of 22)	intron (NM_001081034, intron 1 of 22)	22566	NM_001081034	225055	Mm.386857	NM_001081034	ENSMUSG00000005371	Fbxo11	C80048|Jf	F-box protein 11	protein-coding
mm_135319.1	chr16	38781170	38781180	-	1	NA	intron (NM_178924, intron 5 of 7)	intron (NM_178924, intron 5 of 7)	19028	NM_178924	22268	Mm.130793	NM_178924	ENSMUSG00000049436	Upk1b	AI413235|Tspan20|UPIb|Upk1	uroplakin 1B	protein-coding
mm_20127.1	chr2	121300668	121300737	-	1	NA	exon (NM_001173506, exon 4 of 6)	exon (NM_001173506, exon 4 of 6)	5248	NM_001173506	17754	Mm.36501	NM_032393	ENSMUSG00000027254	Map1a	6330416M19Rik|AI853608|Mtap-1|Mtap1|Mtap1a|moth1	microtubule-associated protein 1 A	protein-coding
mm_57957.1	chr6	135197919	135197963	-	1	NA	promoter-TSS (NM_028982)	promoter-TSS (NM_028982)	-46	NM_028982	74525	Mm.34182	NM_028982	ENSMUSG00000030207	Fam234b	8430419L09Rik|Kiaa1467|mKIAA1467	family with sequence similarity 234, member B	protein-coding
mm_8621.1	chr1	156204999	156205032	-	1	NA	promoter-TSS (NM_177838)	promoter-TSS (NM_177838)	11	NM_177838	329274	Mm.150857	NM_177838	ENSMUSG00000015484	Fam163a	A230106N23Rik	family with sequence similarity 163, member A	protein-coding
mm_136348.1	chr16	92677469	92677472	-	1	NA	intron (NM_001111023, intron 2 of 5)	B4A|SINE|B4	19859	NM_001111023	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_116131.1	chr13	28953384	28953402	-	1	NA	5' UTR (NM_009238, exon 1 of 1)	5' UTR (NM_009238, exon 1 of 1)	289	NM_009238	20677	Mm.240627	NM_009238	ENSMUSG00000076431	Sox4	AA682046|Sox-4	SRY (sex determining region Y)-box 4	protein-coding
mm_122779.1	chr14	54410124	54410141	-	1	NA	promoter-TSS (NM_001253680)	promoter-TSS (NM_001253680)	-660	NM_001253680	20540	Mm.142455	NM_011405	ENSMUSG00000000958	Slc7a7	AI790233|my+lat1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 7	protein-coding
mm_27864.1	chr3	79159049	79159093	-	1	NA	Intergenic	L1_Mur3|LINE|L1	-13196	NM_001099624	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_79690.1	chr9	60482729	60482738	+	1	NA	intron (NM_001040426, intron 2 of 17)	intron (NM_001040426, intron 2 of 17)	28302	NM_001040426	207596	Mm.28791	NM_172444	ENSMUSG00000032289	Thsd4	ADAMTSL-6|ADAMTSL6|AI585901|Adamtsl4|B230114P05Rik	thrombospondin, type I, domain containing 4	protein-coding
mm_82689.1	chr9	22321474	22321475	-	1	NA	intron (NR_030448, intron 1 of 4)	intron (NR_030448, intron 1 of 4)	9216	NR_033622	625603	Mm.37987	NR_033622		Gm6607	EG625603	40S ribosomal protein S20 pseudogene	pseudo
mm_165749.1	chr3	107852852	107852860	-	1	NA	Intergenic	Intergenic	-24374	NM_133867	99662	Mm.108491	NM_133867	ENSMUSG00000040600	Eps8l3	AI504489|Eps8r3	EPS8-like 3	protein-coding
mm_55754.1	chr6	78378852	78378862	-	1	NA	promoter-TSS (NM_001161741)	promoter-TSS (NM_001161741)	8	NM_001161741	30053	Mm.33691	NM_013893	ENSMUSG00000068341	Reg3d	INGAP|Ingaprp	regenerating islet-derived 3 delta	protein-coding
mm_59726.1	chr7	28788253	28788266	+	1	NA	promoter-TSS (NM_177158)	promoter-TSS (NM_177158)	-710	NM_177158	320435	Mm.74632	NM_177158	ENSMUSG00000051735	Rinl	5830482F20Rik|9930116N10Rik	Ras and Rab interactor-like	protein-coding
mm_13683.1	chr2	116972406	116972420	+	1	NA	Intergenic	Intergenic	72261	NR_040335	320975	Mm.132509	NR_040335	ENSMUSG00000085316	D330050G23Rik	-	RIKEN cDNA D330050G23 gene	ncRNA
mm_19091.1	chr2	79369071	79369090	-	1	NA	intron (NM_001048176, intron 2 of 12)	intron (NM_001048176, intron 2 of 12)	59908	NM_001048176	228094	Mm.440704	NM_001033295	ENSMUSG00000075256	Cerkl	Gm1958|Rp26	ceramide kinase-like	protein-coding
mm_125246.1	chr15	34495365	34495385	+	1	NA	promoter-TSS (NM_008287)	promoter-TSS (NM_008287)	64	NM_152894	67724	Mm.248779	NM_026340	ENSMUSG00000022325	Pop1	4932434G09Rik	processing of precursor 1, ribonuclease P/MRP family, (S. cerevisiae)	protein-coding
mm_46826.1	chr5	113213373	113213405	-	1	NA	Intergenic	RLTR20A4|LTR|ERVK	-13520	NM_001033428	333048	Mm.332586	NM_001033428	ENSMUSG00000066964	Tmem211	Gm854	transmembrane protein 211	protein-coding
mm_106154.1	chr11	116623786	116623817	-	1	NA	intron (NM_172572, intron 1 of 18)	CpG	451	NM_001167680	217344	Mm.89695	NM_172572	ENSMUSG00000020806	Rhbdf2	4732465I17Rik|Rhbdl6|cub	rhomboid 5 homolog 2	protein-coding
mm_156739.1	chrX	159942981	159942994	+	1	NA	5' UTR (NM_001290664, exon 1 of 6)	5' UTR (NM_001290664, exon 1 of 6)	294	NM_001290664	58194	Mm.286495	NM_021389	ENSMUSG00000040990	Sh3kbp1	1200007H22Rik|1700125L08Rik|5830464D22Rik|AI447724|Cin85|IN85|Ruk|Seta	SH3-domain kinase binding protein 1	protein-coding
mm_33802.1	chr4	134930900	134930910	+	1	NA	promoter-TSS (NM_026780)	promoter-TSS (NM_026780)	-75	NM_026780	68592	Mm.29989	NM_026780	ENSMUSG00000028821	Syf2	1110018L13Rik|Cbpin|D4Bwg1551e|Gcipip|Ntc31|mp29|p29	SYF2 homolog, RNA splicing factor (S. cerevisiae)	protein-coding
mm_132938.1	chr16	49856219	49856250	+	1	NA	intron (NM_010581, intron 1 of 9)	intron (NM_010581, intron 1 of 9)	580	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_129452.1	chr15	78561947	78562000	-	1	NA	exon (NM_009008, exon 6 of 7)	exon (NM_009008, exon 6 of 7)	10810	NM_009008	19354	Mm.1972	NM_009008	ENSMUSG00000033220	Rac2	AI323801|AI452260	RAS-related C3 botulinum substrate 2	protein-coding
mm_65294.1	chr7	24507436	24507457	-	1	NA	intron (NR_110958, intron 1 of 2)	CpG	359	NR_110958	232969	Mm.181332	NM_146183	ENSMUSG00000064264	Zfp428	2410005H09Rik|AV271806|AW047854|Znf428	zinc finger protein 428	protein-coding
mm_159808.1	chr5	117866805	117866805	+	1	NA	promoter-TSS (NM_008712)	promoter-TSS (NM_008712)	-34	NM_008712	18125	Mm.44249	NM_008712	ENSMUSG00000029361	Nos1	2310005C01Rik|N-NOS|NC-NOS|NO|NOS|NOS-I|Nos-1|bNOS|nNOS	nitric oxide synthase 1, neuronal	protein-coding
mm_129986.1	chr15	86058576	86058591	-	1	NA	promoter-TSS (NM_001205353)	promoter-TSS (NM_001205353)	-144	NM_001205353	223752	Mm.24442	NM_172611	ENSMUSG00000035900	Gramd4	9930016O13	GRAM domain containing 4	protein-coding
mm_170409.1	chr18	65798485	65798489	-	1	NA	Intergenic	ORR1A0|LTR|ERVL-MaLR	-2091	NM_025468	66286	Mm.27800	NM_025468	ENSMUSG00000024516	Sec11c	1810029G24Rik|Sec11l3	SEC11 homolog C, signal peptidase complex subunit	protein-coding
mm_66671.1	chr7	45731578	45731593	-	1	NA	intron (NM_017465, intron 5 of 6)	intron (NM_017465, intron 5 of 6)	-5769	NM_027055	69363	Mm.45607	NM_027055	ENSMUSG00000070563	Spaca4	1700008E09Rik|AV043694|Samp14	sperm acrosome associated 4	protein-coding
mm_142864.1	chr17	51814230	51814236	-	1	NA	intron (NM_001163632, intron 1 of 10)	intron (NM_001163632, intron 1 of 10)	-2179	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_154383.1	chrM	11372	11423	+	1	NA	NA	Intergenic	NA	NA								
mm_135316.1	chr16	38713392	38713407	-	1	NA	promoter-TSS (NM_020260)	promoter-TSS (NM_020260)	-364	NM_020260	12549	Mm.370848	NM_020260	ENSMUSG00000022799	Arhgap31	5830477L08Rik|AU041750|Cdgap|D330026I07Rik	Rho GTPase activating protein 31	protein-coding
mm_97978.1	chr11	83875529	83875555	+	1	NA	intron (NM_001291269, intron 4 of 8)	intron (NM_001291269, intron 4 of 8)	22582	NM_001291269	21410	Mm.7226	NM_009330	ENSMUSG00000020679	Hnf1b	HNF-1-beta|HNF-1B|HNF-1Beta|Hnf1beta|LFB3|Tcf-2|Tcf2|vHNF1	HNF1 homeobox B	protein-coding
mm_144224.1	chr18	9957948	9957987	+	1	NA	promoter-TSS (NM_153552)	promoter-TSS (NM_153552)	-213	NM_153552	225160	Mm.219648	NM_153552	ENSMUSG00000024287	Thoc1	3110002N20Rik|AW107452|NMP-84	THO complex 1	protein-coding
mm_137088.1	chr17	21489092	21489117	+	1	NA	5' UTR (NM_013843, exon 1 of 5)	5' UTR (NM_013843, exon 1 of 5)	116	NM_013843	24132	Mm.42140	NM_013843	ENSMUSG00000057409	Zfp53	D030067O06Rik|KRAZ1|Zfp-53|Zfp118|zfas8	zinc finger protein 53	protein-coding
mm_162148.1	chrX	74837055	74837055	+	1	NA	promoter-TSS (NM_001081670)	promoter-TSS (NM_001081670)	-141	NM_001081670	546325	Mm.436644	NM_001081670	ENSMUSG00000079531	Gm5936	EG546325	predicted gene 5936	protein-coding
mm_87234.1	chr10	40673070	40673110	+	1	NA	intron (NR_133568, intron 3 of 4)	intron (NR_133568, intron 3 of 4)	-10192	NM_177793	327747	Mm.80407	NM_177793	ENSMUSG00000045555	Mettl24	9030224M15Rik	methyltransferase like 24	protein-coding
mm_37623.1	chr4	127326220	127326246	-	1	NA	exon (NM_001160012, exon 2 of 2)	exon (NM_001160012, exon 2 of 2)	2892	NM_008126	14620	Mm.90003	NM_008126	ENSMUSG00000042367	Gjb3	Cnx31|Cx31|D4Wsu144e|Gjb-3	gap junction protein, beta 3	protein-coding
mm_127357.1	chr15	100641211	100641245	+	1	NA	3' UTR (NM_001270537, exon 11 of 11)	3' UTR (NM_001270537, exon 11 of 11)	-4288	NM_001033872	207818	Mm.26282	NM_174992	ENSMUSG00000053559	Smagp	-	small cell adhesion glycoprotein	protein-coding
mm_138048.1	chr17	33925993	33926029	+	1	NA	exon (NM_009318, exon 5 of 8)	exon (NM_009318, exon 5 of 8)	-3883	NM_009059	19732	Mm.43777	NM_009059	ENSMUSG00000041354	Rgl2	KE1.5|Rab2l|Rgt2|Rlf	ral guanine nucleotide dissociation stimulator-like 2	protein-coding
mm_108460.1	chr12	83424636	83424673	+	1	NA	intron (NM_058212, intron 1 of 8)	intron (NM_058212, intron 1 of 8)	63082	NM_001267626	70127	Mm.151308	NM_058212	ENSMUSG00000021221	Dpf3	2810403B03Rik|6530402L11Rik|BAF45C|C78788|CERD4|cer-d4	D4, zinc and double PHD fingers, family 3	protein-coding
mm_146858.1	chr18	24433508	24433510	-	1	NA	Intergenic	B4|SINE|B4	-4339	NR_029573	387182		NR_029573	ENSMUSG00000065532	Mir187	Mirn187|mir-187|mmu-mir-187	microRNA 187	ncRNA
mm_129966.1	chr15	85581928	85581949	-	1	NA	promoter-TSS (NM_009528)	promoter-TSS (NM_009528)	-117	NM_009528	22422	Mm.306946	NM_009528	ENSMUSG00000022382	Wnt7b	Wnt-7b	wingless-type MMTV integration site family, member 7B	protein-coding
mm_112979.1	chr13	21312199	21312220	+	1	NA	promoter-TSS (NM_145451)	promoter-TSS (NM_145451)	6	NM_145451	75512	Mm.46195	NM_145451	ENSMUSG00000004341	Gpx6	1700020G18Rik|Ry2d1|olfactory	glutathione peroxidase 6	protein-coding
mm_149089.1	chr19	8922125	8922136	+	1	NA	intron (NM_024256, intron 2 of 4)	intron (NM_024256, intron 2 of 4)	1737	NM_024256	72727	Mm.259	NM_024256	ENSMUSG00000071649	B3gat3	2810405M13Rik	beta-1,3-glucuronyltransferase 3 (glucuronosyltransferase I)	protein-coding
mm_70658.1	chr8	14651710	14651733	+	1	NA	intron (NM_172910, intron 4 of 15)	intron (NM_172910, intron 4 of 15)	-236815	NM_012000	26889	Mm.254027	NM_012000	ENSMUSG00000026317	Cln8	mnd	ceroid-lipofuscinosis, neuronal 8	protein-coding
mm_30827.1	chr4	21874423	21874442	+	1	NA	exon (NM_025669, exon 11 of 12)	exon (NM_025669, exon 11 of 12)	-5243	NM_172687	230027	Mm.5662	NM_172687	ENSMUSG00000028247	Coq3	4732433J24|C77934	coenzyme Q3 methyltransferase	protein-coding
mm_1338.1	chr1	66175168	66175180	+	1	NA	promoter-TSS (NM_008632)	promoter-TSS (NM_008632)	-155	NM_008632	17756	Mm.256966	NM_008632	ENSMUSG00000015222	Map2	G1-397-34|MAP-2|Mtap-2|Mtap2|repro4	microtubule-associated protein 2	protein-coding
mm_60489.1	chr7	44478610	44478620	+	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	-5902	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_24264.1	chr3	89187871	89187896	+	1	NA	intron (NM_001014995, intron 9 of 11)	intron (NM_001014995, intron 9 of 11)	4658	NM_001014995	68521	Mm.274708	NM_001014995	ENSMUSG00000032657	Fam189b	1110013L07Rik	family with sequence similarity 189, member B	protein-coding
mm_18416.1	chr2	60705567	60705590	-	1	NA	intron (NM_001159564, intron 1 of 17)	intron (NM_001159564, intron 1 of 17)	17025	NM_001159564	16420	Mm.98193	NM_021359	ENSMUSG00000026971	Itgb6	2210409C20Rik|4831415H04Rik	integrin beta 6	protein-coding
mm_93879.1	chr10	125308793	125308801	-	1	NA	intron (NM_011391, intron 1 of 6)	intron (NM_011391, intron 1 of 6)	19738	NM_011391	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|Mct2	solute carrier family 16 (monocarboxylic acid transporters), member 7	protein-coding
mm_96027.1	chr11	59548949	59548967	+	1	NA	exon (NM_145827, exon 4 of 10)	exon (NM_145827, exon 4 of 10)	6272	NM_145827	216799	Mm.54174	NM_145827	ENSMUSG00000032691	Nlrp3	AGTAVPRL|AII/AVP|Cias1|FCAS|FCU|MWS|Mmig1|NALP3|Pypaf1	NLR family, pyrin domain containing 3	protein-coding
mm_100113.1	chr11	115824030	115824097	+	1	NA	promoter-TSS (NM_001252532)	promoter-TSS (NM_001252532)	5	NM_001252532	217325	Mm.290450	NM_145438	ENSMUSG00000020782	Llgl2	9130006H11Rik|Llglh2	lethal giant larvae homolog 2 (Drosophila)	protein-coding
mm_6525.1	chr1	74588118	74588145	-	1	NA	promoter-TSS (NM_025784)	promoter-TSS (NM_025784)	-103	NM_029888	77264	Mm.207298	NM_029888	ENSMUSG00000026135	Zfp142	9330177B18Rik|BB154236|mKIAA0236	zinc finger protein 142	protein-coding
mm_168420.1	chr11	33160859	33160862	-	1	NA	exon (NM_001252261, exon 4 of 10)	exon (NM_001252261, exon 4 of 10)	2346	NM_001252261	18148	Mm.485384	NM_008722	ENSMUSG00000057113	Npm1	B23|NO38|Npm	nucleophosmin 1	protein-coding
mm_13329.1	chr2	102784778	102784785	+	1	NA	3' UTR (NM_001077514, exon 11 of 11)	3' UTR (NM_001077514, exon 11 of 11)	78343	NM_001077515	20511	Mm.267547	NM_011393	ENSMUSG00000005089	Slc1a2	1700091C19Rik|2900019G14Rik|AI159670|Eaat2|GLT-1|GLT1|MGLT1	solute carrier family 1 (glial high affinity glutamate transporter), member 2	protein-coding
mm_149387.1	chr19	11386477	11386487	+	1	NA	intron (NM_001310331, intron 4 of 6)	intron (NM_001310331, intron 4 of 6)	10994	NM_001310331	666907		NM_001310331	ENSMUSG00000101389	Ms4a4a	EG666907	membrane-spanning 4-domains, subfamily A, member 4A	protein-coding
mm_93771.1	chr10	120363733	120363745	-	1	NA	3' UTR (NM_010441, exon 5 of 5)	3' UTR (NM_010441, exon 5 of 5)	-25784	NR_040626	320626	Mm.446091	NR_040626	ENSMUSG00000090191	9230105E05Rik	-	RIKEN cDNA 9230105E05 gene	ncRNA
mm_63869.1	chr7	135715907	135715949	+	1	NA	intron (NM_001081117, intron 1 of 13)	CpG	451	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_17641.1	chr2	31163527	31163542	-	1	NA	intron (NM_178760, intron 1 of 17)	intron (NM_178760, intron 1 of 17)	11218	NM_178760	277463	Mm.236074	NM_178760	ENSMUSG00000000194	Gpr107	9930033D15Rik|AI790205|C530034M11|mKIAA1624	G protein-coupled receptor 107	protein-coding
mm_7249.1	chr1	93654199	93654212	-	1	NA	Intergenic	MT2B1|LTR|ERVL	-18478	NM_021537	59041	Mm.28761	NM_021537	ENSMUSG00000026277	Stk25	1500019J11Rik|AU018434|C86992|Ste20-like|Ysk1	serine/threonine kinase 25 (yeast)	protein-coding
mm_83487.1	chr9	45945048	45945057	-	1	NA	intron (NM_172257, intron 15 of 25)	MIRb|SINE|MIR	-5462	NR_106055	102465659		NR_106055	ENSMUSG00000098327	Mir7087	Gm27273|mmu-mir-7087	microRNA 7087	ncRNA
mm_63126.1	chr7	122999838	122999858	+	1	NA	exon (NM_011247, exon 17 of 18)	exon (NM_011247, exon 17 of 18)	29284	NM_175023	19647	Mm.4480	NM_011247	ENSMUSG00000030779	Rbbp6	4933422O15Rik|AI316869|BB233631|C030034J04Rik|C77662|P2P-R|PACT	retinoblastoma binding protein 6	protein-coding
mm_138016.1	chr17	33909578	33909600	+	1	NA	promoter-TSS (NM_001199733)	promoter-TSS (NM_001199733)	-12	NM_001199733	13163	Mm.271809	NM_007829	ENSMUSG00000002307	Daxx	-	Fas death domain-associated protein	protein-coding
mm_44258.1	chr5	5479121	5479136	-	1	NA	promoter-TSS (NM_001200025)	promoter-TSS (NM_001200025)	15	NM_001200025	381716	Mm.276086	NM_001200025	ENSMUSG00000079666	1700015F17Rik	Gm1686	RIKEN cDNA 1700015F17 gene	protein-coding
mm_38543.1	chr4	141598231	141598245	-	1	NA	intron (NM_133754, intron 1 of 8)	intron (NM_133754, intron 1 of 8)	1686	NM_001163256	74202	Mm.490327	NM_133754	ENSMUSG00000006219	Fblim1	2410043F08Rik|Cal|Fblp1|Gt10|migfilin|migfilin(s)	filamin binding LIM protein 1	protein-coding
mm_115080.1	chr13	102410819	102410821	+	1	NA	Intergenic	Intergenic	-282738	NM_008533	17079	Mm.373974	NM_008533	ENSMUSG00000021624	Cd180	F630107B15|Ly78|RP105	CD180 antigen	protein-coding
mm_80307.1	chr9	74110343	74110366	+	1	NA	promoter-TSS (NM_001033500)	promoter-TSS (NM_001033500)	20	NM_001033500	546144	Mm.335289	NM_177908	ENSMUSG00000044976	Wdr72	AW558070|D230040E23	WD repeat domain 72	protein-coding
mm_7558.1	chr1	124709029	124709054	-	1	NA	Intergenic	B3A|SINE|B2	-663482	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_160959.1	chr11	98551085	98551085	+	1	NA	promoter-TSS (NM_001166494)	promoter-TSS (NM_001166494)	-12	NM_199419	69376	Mm.55996	NM_027061	ENSMUSG00000017195	Zpbp2	1700017D11Rik|2610022C02Rik|ZPBPL	zona pellucida binding protein 2	protein-coding
mm_66450.1	chr7	44869572	44869574	-	1	NA	5' UTR (NM_133949, exon 1 of 12)	5' UTR (NM_133949, exon 1 of 12)	215	NM_133949	84113	Mm.42855	NM_133949	ENSMUSG00000038502	Ptov1	1110030G05Rik|AU041779|Gcap3	prostate tumor over expressed gene 1	protein-coding
mm_111544.1	chr12	100899437	100899448	-	1	NA	promoter-TSS (NM_001177674)	promoter-TSS (NM_001177674)	82	NM_001177674	238377	Mm.32160	NM_175493	ENSMUSG00000047415	Gpr68	BB131428|Ogr1	G protein-coupled receptor 68	protein-coding
mm_111395.1	chr12	90728199	90728223	-	1	NA	3' UTR (NM_010050, exon 2 of 2)	3' UTR (NM_010050, exon 2 of 2)	10826	NM_010050	13371	Mm.21389	NM_010050	ENSMUSG00000007682	Dio2	5DII|AI324267|DIOII	deiodinase, iodothyronine, type II	protein-coding
mm_106777.1	chr12	4633478	4633495	+	1	NA	exon (NM_001198969, exon 11 of 17)	exon (NM_001198969, exon 11 of 17)	40478	NM_001198968	20403	Mm.341204	NM_011365	ENSMUSG00000020640	Itsn2	AI327390|Ese2|Sh3d1B|Sh3p18|mKIAA1256	intersectin 2	protein-coding
mm_89920.1	chr10	111204837	111204846	+	1	NA	intron (NM_001003717, intron 2 of 22)	intron (NM_001003717, intron 2 of 22)	40039	NM_175489	237542	Mm.220204	NM_175489	ENSMUSG00000020189	Osbpl8	AA536976|AA536995|C730029P18Rik|D330025H14Rik|ORP-8	oxysterol binding protein-like 8	protein-coding
mm_127899.1	chr15	9506751	9506762	-	1	NA	3' UTR (NM_008372, exon 8 of 8)	3' UTR (NM_008372, exon 8 of 8)	23120	NM_008372	16197	Mm.389	NM_008372	ENSMUSG00000003882	Il7r	CD127|IL-7Ralpha	interleukin 7 receptor	protein-coding
mm_155590.1	chrX	81070647	81070740	+	1	NA	promoter-TSS (NM_138751)	promoter-TSS (NM_138751)	49	NM_138751	192216	Mm.490421	NM_138751	ENSMUSG00000025666	Tmem47	3010015F07Rik|AI115536|BCMP1|Tm4sf10	transmembrane protein 47	protein-coding
mm_15367.1	chr2	156421084	156421114	+	1	NA	5' UTR (NM_001291121, exon 1 of 22)	5' UTR (NM_001291121, exon 1 of 22)	190	NM_001291123	13821	Mm.20852	NM_013510	ENSMUSG00000027624	Epb41l1	4.1N|Epb4.1l1|NBL1|mKIAA0338	erythrocyte membrane protein band 4.1 like 1	protein-coding
mm_124241.1	chr14	101478947	101478958	-	1	NA	intron (NM_001081278, intron 9 of 18)	intron (NM_001081278, intron 9 of 18)	130239	NM_001081278	210789	Mm.320639	NM_173380	ENSMUSG00000033083	Tbc1d4	5930406J04Rik|A930035N22|AV295684|As160	TBC1 domain family, member 4	protein-coding
mm_6642.1	chr1	79440016	79440035	-	1	NA	promoter-TSS (NM_009129)	promoter-TSS (NM_009129)	65	NM_009129	20254	Mm.5038	NM_009129	ENSMUSG00000050711	Scg2	Chgc|SgII	secretogranin II	protein-coding
mm_162539.1	chr1	168582819	168582840	-	1	NA	Intergenic	Intergenic	92186	NR_105766	102465178		NR_105766	ENSMUSG00000098407	Mir6348	Gm27412|mmu-mir-6348	microRNA 6348	ncRNA
mm_163786.1	chr13	120312160	120312162	-	1	NA	Intergenic	MT2B|LTR|ERVL	-4701	NM_153523	236219	Mm.302175	NM_153523	ENSMUSG00000095821	Tcstv3	-	2-cell-stage, variable group, member 3	protein-coding
mm_101450.1	chr11	30198206	30198226	-	1	NA	promoter-TSS (NM_009260)	promoter-TSS (NM_009260)	41	NM_009260	20742	Mm.123110	NM_009260	ENSMUSG00000020315	Sptbn1	9930031C03Rik|AL033301|SPTB2|Spnb-2|Spnb2|elf1|elf3|mKIAA4049	spectrin beta, non-erythrocytic 1	protein-coding
mm_9170.1	chr1	170976113	170976120	-	1	NA	promoter-TSS (NM_001077189)	promoter-TSS (NM_001077189)	-45	NM_010187	14130	Mm.425062	NM_010187	ENSMUSG00000026656	Fcgr2b	AI528646|CD32|F630109E10Rik|Fc[g]RII|FcgRII|Fcgr2|Fcgr2a|Fcr-2|Fcr-3|Ly-17|Ly-m20|LyM-1|Lym-1|fcRII	Fc receptor, IgG, low affinity IIb	protein-coding
mm_91333.1	chr10	25299208	25299224	-	1	NA	promoter-TSS (NM_018747)	promoter-TSS (NM_018747)	-53	NM_018747	432442	Mm.485937	NM_018747	ENSMUSG00000039166	Akap7	6430401D08|AI662165|AKAP15|Akap18|BB170514	A kinase (PRKA) anchor protein 7	protein-coding
mm_5083.1	chr1	4493599	4493614	-	1	NA	intron (NM_001289464, intron 2 of 3)	CpG-4	3748	NM_001289464	20671	Mm.279103	NM_011441	ENSMUSG00000025902	Sox17	-	SRY (sex determining region Y)-box 17	protein-coding
mm_16536.1	chr2	181579563	181579567	+	1	NA	promoter-TSS (NR_027290)	promoter-TSS (NR_027290)	33	NR_027290	100271841	Mm.438007	NR_027289	ENSMUSG00000010492	Uckl1os	Gm16119|OTTMUSG00000030649	uridine-cytidine kinase 1-like 1, opposite strand	ncRNA
mm_31336.1	chr4	46468680	46468702	+	1	NA	exon (NM_130889, exon 4 of 7)	exon (NM_130889, exon 4 of 7)	17765	NM_130889	67628	Mm.263913	NM_130889	ENSMUSG00000028333	Anp32b	2410015B15Rik|PAL31|PHAPI2a|Ssp29	acidic (leucine-rich) nuclear phosphoprotein 32 family, member B	protein-coding
mm_110482.1	chr12	51866427	51866445	-	1	NA	Intergenic	Intergenic	-36900	NM_144788	207304	Mm.249391	NM_144788	ENSMUSG00000035247	Hectd1	A630086P08Rik|AI844876|b2b327Clo|opm	HECT domain containing 1	protein-coding
mm_12949.1	chr2	87566222	87566224	+	1	NA	Intergenic	Lx4A|LINE|L1	-8863	NM_001011836	258111	Mm.376122	NM_001011836	ENSMUSG00000062272	Olfr1129	MOR264-23|MOR264-9P	olfactory receptor 1129	protein-coding
mm_91258.1	chr10	23185561	23185571	-	1	NA	intron (NM_010167, intron 3 of 18)	intron (NM_010167, intron 3 of 18)	164324	NM_001347372	14051	Mm.332128	NM_010167	ENSMUSG00000010461	Eya4	B130023L16Rik	EYA transcriptional coactivator and phosphatase 4	protein-coding
mm_119282.1	chr14	34375489	34375499	+	1	NA	promoter-TSS (NM_011430)	promoter-TSS (NM_011430)	-10	NM_153127	105450	Mm.272673	NM_153127	ENSMUSG00000041445	Mmrn2	AA986839|ENDOGLYX1|Emilin3|EndoGlyx-1	multimerin 2	protein-coding
mm_66010.1	chr7	30588721	30588749	-	1	NA	promoter-TSS (NR_106134)	promoter-TSS (NR_106134)	-9	NM_029274	75410	Mm.168688	NM_029274	ENSMUSG00000006307	Kmt2b	2610014H22Rik|Mll2|Wbp7|mKIAA0304	lysine (K)-specific methyltransferase 2B	protein-coding
mm_70852.1	chr8	23535194	23535202	+	1	NA	Intergenic	Intergenic	123696	NM_013834	20377	Mm.281691	NM_013834	ENSMUSG00000031548	Sfrp1	2210415K03Rik|AW011917|AW107218|AW742929|sFRP-1	secreted frizzled-related protein 1	protein-coding
mm_71057.1	chr8	33732197	33732236	+	1	NA	promoter-TSS (NM_001167922)	promoter-TSS (NM_001167922)	-123	NM_001167922	68153	Mm.286104	NM_026584	ENSMUSG00000031585	Gtf2e2	34kDa|AI462509|C330006J08Rik	general transcription factor II E, polypeptide 2 (beta subunit)	protein-coding
mm_121976.1	chr14	25769034	25769083	-	1	NA	promoter-TSS (NM_001101433)	promoter-TSS (NM_001101433)	-202	NM_001101433	71918	Mm.41904	NM_001101433	ENSMUSG00000055538	Zcchc24	2310047A01Rik	zinc finger, CCHC domain containing 24	protein-coding
mm_162283.1	chr1	20869972	20869977	-	1	NA	Intergenic	Intergenic	20499	NR_040492	77741	Mm.159984	NR_040492	ENSMUSG00000097934	6720483E21Rik	-	RIKEN cDNA 6720483E21 gene	ncRNA
mm_97338.1	chr11	77348260	77348269	+	1	NA	promoter-TSS (NM_001291190)	promoter-TSS (NM_001291190)	-16	NM_001291190	237860	Mm.440381	NM_177710	ENSMUSG00000037926	Ssh2	SSH-2|SSH-2L|mSSH-2L	slingshot homolog 2 (Drosophila)	protein-coding
mm_144222.1	chr18	9848702	9848740	+	1	NA	exon (NM_130449, exon 5 of 10)	exon (NM_130449, exon 5 of 10)	-109459	NM_153552	225160	Mm.219648	NM_153552	ENSMUSG00000024287	Thoc1	3110002N20Rik|AW107452|NMP-84	THO complex 1	protein-coding
mm_135648.1	chr16	52388857	52388867	-	1	NA	intron (NM_009655, intron 1 of 15)	intron (NM_009655, intron 1 of 15)	64219	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_15197.1	chr2	154206431	154206433	+	1	NA	exon (NM_153418, exon 5 of 16)	exon (NM_153418, exon 5 of 16)	6052	NM_153418	228801	Mm.3783	NM_153418	ENSMUSG00000027485	Bpifb1	Lplunc1	BPI fold containing family B, member 1	protein-coding
mm_82322.1	chr9	8004586	8004623	-	1	NA	promoter-TSS (NM_001171147)	promoter-TSS (NM_001171147)	-8	NM_009534	22601	Mm.221992	NM_009534	ENSMUSG00000053110	Yap1	AI325207|Yap|Yap65|Yki|Yorkie	yes-associated protein 1	protein-coding
mm_111921.1	chr12	108875626	108875630	-	1	NA	intron (NM_011710, intron 5 of 10)	intron (NM_011710, intron 5 of 10)	17570	NM_001164488	22375	Mm.38433	NM_011710	ENSMUSG00000021266	Wars	TrpRS|WRS	tryptophanyl-tRNA synthetase	protein-coding
mm_85547.1	chr9	106685368	106685385	-	1	NA	5' UTR (NM_011573, exon 1 of 6)	5' UTR (NM_011573, exon 1 of 6)	440	NM_011573	21767	Mm.22266	NM_011573	ENSMUSG00000040813	Tex264	TEG-264	testis expressed gene 264	protein-coding
mm_68412.1	chr7	109637607	109637620	-	1	NA	Intergenic	Intergenic	-20466	NM_029811	76954	Mm.252009	NM_029811	ENSMUSG00000031024	St5	2010004M01Rik|2610305K15Rik	suppression of tumorigenicity 5	protein-coding
mm_148069.1	chr18	72341709	72341712	-	1	NA	intron (NM_007831, intron 1 of 28)	intron (NM_007831, intron 1 of 28)	9359	NM_007831	13176	Mm.167882	NM_007831	ENSMUSG00000060534	Dcc	C030036D22Rik|Igdcc1	deleted in colorectal carcinoma	protein-coding
mm_66136.1	chr7	31111006	31111016	-	1	NA	promoter-TSS (NM_001276269)	promoter-TSS (NM_001276269)	-14	NM_001276269	15451	Mm.19182	NM_008281	ENSMUSG00000001249	Hpn	Hlb320	hepsin	protein-coding
mm_86382.1	chr9	123862014	123862020	-	1	NA	promoter-TSS (NM_011798)	promoter-TSS (NM_011798)	12	NM_011798	23832	Mm.390241	NM_011798	ENSMUSG00000060509	Xcr1	Ccxcr1|Gpr5|mXcr1	chemokine (C motif) receptor 1	protein-coding
mm_43742.1	chr5	140062462	140062468	+	1	NA	intron (NM_010752, intron 17 of 17)	intron (NM_010752, intron 17 of 17)	154522	NM_175522	243312	Mm.237102	NM_175522	ENSMUSG00000048988	Elfn1	A930017N06Rik|AI197272|Ppp1r28	leucine rich repeat and fibronectin type III, extracellular 1	protein-coding
mm_121762.1	chr14	19751125	19751146	-	1	NA	promoter-TSS (NM_008695)	promoter-TSS (NM_008695)	-122	NM_008695	18074	Mm.20348	NM_008695	ENSMUSG00000021806	Nid2	AW547149|Ly111|NID-2|entactin-2|nidogen-2	nidogen 2	protein-coding
mm_150.1	chr1	11299453	11299482	+	1	NA	3' UTR (NM_029525, exon 40 of 40)	3' UTR (NM_029525, exon 40 of 40)	35504	NM_001033636	109294	Mm.123247	NM_029525	ENSMUSG00000048960	Prex2	6230420N16Rik|AI316880|AI553603|C030045D06Rik|D430013K02|Depdc2|P-Rex2	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	protein-coding
mm_105086.1	chr11	100848405	100848413	-	1	NA	intron (NM_001113563, intron 1 of 18)	intron (NM_001113563, intron 1 of 18)	2176	NM_001113563	20851	Mm.34064	NM_011489	ENSMUSG00000020919	Stat5b	-	signal transducer and activator of transcription 5B	protein-coding
mm_7556.1	chr1	124700571	124700574	-	1	NA	Intergenic	Intergenic	-655013	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_99880.1	chr11	109426155	109426222	+	1	NA	promoter-TSS (NM_001252193)	promoter-TSS (NM_001252193)	-32	NM_001252193	13929	Mm.211850	NM_025275	ENSMUSG00000020610	Amz2	AA408420|ESTM12|X83328	archaelysin family metallopeptidase 2	protein-coding
mm_169362.1	chr14	31917623	31917623	-	1	NA	Intergenic	RLTR1B|LTR|ERV1	-87208	NM_001024604	105522	Mm.37660	NM_001024604	ENSMUSG00000014496	Ankrd28	AI465466|AI604979|E430019N21Rik|mKIAA0379	ankyrin repeat domain 28	protein-coding
mm_4048.1	chr1	165788660	165788662	+	1	NA	promoter-TSS (NM_031162)	promoter-TSS (NM_031162)	-20	NM_031162	12503	Mm.217308	NM_031162	ENSMUSG00000005763	Cd247	4930549J05Rik|A430104F18Rik|AW552088|Cd3|Cd3-eta|Cd3-zeta|Cd3h|Cd3z|Cd3zeta|T3z|Tcrk|Tcrz	CD247 antigen	protein-coding
mm_48408.1	chr5	140261572	140261587	-	1	NA	exon (NM_010752, exon 10 of 18)	exon (NM_010752, exon 10 of 18)	59973	NM_010752	17120	Mm.27250	NM_010752	ENSMUSG00000029554	Mad1l1	AI173502|AW550425|Mad1	MAD1 mitotic arrest deficient 1-like 1	protein-coding
mm_131378.1	chr16	13940738	13940746	+	1	NA	promoter-TSS (NM_033564)	promoter-TSS (NM_033564)	77	NM_033564	93734	Mm.76554	NM_033564	ENSMUSG00000022679	Mpv17l	M-LP	Mpv17 transgene, kidney disease mutant-like	protein-coding
mm_75911.1	chr8	71395795	71395821	-	1	NA	promoter-TSS (NM_181418)	promoter-TSS (NM_181418)	-7	NM_181418	234395	Mm.34874	NM_181418	ENSMUSG00000034911	Ushbp1	2210404N08Rik|9430064H24|AIEBP|MCC2	Usher syndrome 1C binding protein 1	protein-coding
mm_169580.1	chr1	52312979	52312981	+	1	NA	Intergenic	MMERGLN_LTR|LTR|ERV1	-79748	NM_001113383	14660	Mm.398608	NM_001081081	ENSMUSG00000026103	Gls	6330442B14|AI314027|B230365M23Rik	glutaminase	protein-coding
mm_101033.1	chr11	8589439	8589441	-	1	NA	intron (NM_001083587, intron 3 of 30)	intron (NM_001083587, intron 3 of 30)	75095	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_31052.1	chr4	41152976	41152984	+	1	NA	intron (NM_026275, intron 1 of 4)	RSINE1|SINE|B4	16959	NM_026275	67615	Mm.389540	NM_026275	ENSMUSG00000036241	Ube2r2	1200003M11Rik|Cdc34b|Ubc3b	ubiquitin-conjugating enzyme E2R 2	protein-coding
mm_93547.1	chr10	116113890	116113933	-	1	NA	promoter-TSS (NM_001161855)	promoter-TSS (NM_001161855)	6	NM_001161855	619332	Mm.391427	NM_001033821	ENSMUSG00000074734	4933416C03Rik	-	RIKEN cDNA 4933416C03 gene	protein-coding
mm_17589.1	chr2	30474213	30474222	-	1	NA	promoter-TSS (NM_030244)	promoter-TSS (NM_030244)	-18	NM_030244	72500	Mm.295464	NM_030244	ENSMUSG00000089762	Ier5l	2610524G09Rik	immediate early response 5-like	protein-coding
mm_15128.1	chr2	153874979	153874987	+	1	NA	promoter-TSS (NM_025631)	promoter-TSS (NM_025631)	-62	NM_025631	66557	Mm.46448	NM_025631	ENSMUSG00000027481	Bpifb2	2310034L21Rik|2310069A01Rik|AV089125|Bpil1|LPLUNC2|RYSR	BPI fold containing family B, member 2	protein-coding
mm_9479.1	chr1	173367667	173367692	-	1	NA	promoter-TSS (NM_053199)	promoter-TSS (NM_053199)	16	NM_053199	94332	Mm.330524	NM_053199	ENSMUSG00000005338	Cadm3	BIgR|Igsf4b|Necl-1|Necl1|SynCAM3|Tsll1	cell adhesion molecule 3	protein-coding
mm_38987.1	chr4	151057934	151057969	-	1	NA	promoter-TSS (NM_009498)	promoter-TSS (NM_009498)	2	NM_009498	22319	Mm.273930	NM_009498	ENSMUSG00000028955	Vamp3	D130027G05Rik|VAMP-3|ceb	vesicle-associated membrane protein 3	protein-coding
mm_141913.1	chr17	34982478	34982491	-	1	NA	intron (NM_001204273, intron 1 of 5)	CpG	354	NM_030597	27756	Mm.165735	NM_030597	ENSMUSG00000007050	Lsm2	D17H6S56E-2|D17H6S56E2|Dmapl|Dmpkap|G7b|Sm-X5|SmX5|snRNP	LSM2 homolog, U6 small nuclear RNA and mRNA degradation associated	protein-coding
mm_107456.1	chr12	37108633	37108643	+	1	NA	promoter-TSS (NM_008584)	promoter-TSS (NM_008584)	92	NM_008584	17286	Mm.341398	NM_008584	ENSMUSG00000036144	Meox2	AI528662|Gax|Mox-2|Mox2	mesenchyme homeobox 2	protein-coding
mm_130573.1	chr15	99474697	99474735	-	1	NA	promoter-TSS (NM_029236)	promoter-TSS (NM_029236)	14	NM_029236	75284	Mm.32826	NM_029236	ENSMUSG00000037525	Bcdin3d	4930556P03Rik|AV138748	BCDIN3 domain containing	protein-coding
mm_109715.1	chr12	115258087	115258126	+	1	NA	Intergenic	Intergenic	437688	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
mm_46051.1	chr5	92112249	92112276	-	1	NA	Intergenic	Intergenic	-25676	NM_019490	56041	Mm.15868	NM_019490	ENSMUSG00000029407	Uso1	115kDa|TAP|Vdp	USO1 vesicle docking factor	protein-coding
mm_10198.1	chr2	4928659	4928667	+	1	NA	intron (NM_010726, intron 4 of 8)	intron (NM_010726, intron 4 of 8)	9667	NM_010726	16922	Mm.391704	NM_010726	ENSMUSG00000026664	Phyh	AI256161|AI265699|Lnap1|PAHX	phytanoyl-CoA hydroxylase	protein-coding
mm_86991.1	chr10	25536366	25536396	+	1	NA	promoter-TSS (NM_001195596)	promoter-TSS (NM_001195596)	-5	NR_136909	102640597	Mm.412041	NR_136909	ENSMUSG00000101537	Gm29571	-	predicted gene 29571	ncRNA
mm_125888.1	chr15	75863244	75863267	+	1	NA	intron (NM_026960, intron 1 of 10)	intron (NM_026960, intron 1 of 10)	916	NM_026960	69146	Mm.27385	NM_026960	ENSMUSG00000022575	Gsdmd	1810036L03Rik|AW558049|DF5L|Dfna5l|Gsdmdc1|M2-4	gasdermin D	protein-coding
mm_168503.1	chr1	153407567	153407568	-	1	NA	intron (NR_033736, intron 3 of 3)	intron (NR_033736, intron 3 of 3)	6666	NR_033736	626058	Mm.31556	NM_001177359		E330020D12Rik	EG626058|F430003O07Rik|Gm6648	Riken cDNA E330020D12 gene	ncRNA
mm_8918.1	chr1	163313694	163313696	-	1	NA	promoter-TSS (NM_175686)	promoter-TSS (NM_175686)	-45	NM_175686	18933	Mm.288642	NM_011127	ENSMUSG00000026586	Prrx1	A230024N07Rik|AA755424|AI385634|AI843499|K-2|Pmx|Pmx1|Prx1|mHox	paired related homeobox 1	protein-coding
mm_27905.1	chr3	79511175	79511199	-	1	NA	intron (NM_001162999, intron 5 of 16)	intron (NM_001162999, intron 5 of 16)	56492	NM_001162999	329679	Mm.244005	NM_001162999	ENSMUSG00000061175	Fnip2	D630023B12Rik|mKIAA1450	folliculin interacting protein 2	protein-coding
mm_36943.1	chr4	108780812	108780848	-	1	NA	intron (NM_001347163, intron 1 of 18)	intron (NM_001347163, intron 1 of 18)	258	NM_001347163	230597	Mm.196776	NM_183300	ENSMUSG00000034557	Zfyve9	Madhip|NSP|SARA|SMADIP	zinc finger, FYVE domain containing 9	protein-coding
mm_16357.1	chr2	174439075	174439126	+	1	NA	promoter-TSS (NM_022325)	promoter-TSS (NM_022325)	-61	NM_022325	64138	Mm.156919	NM_022325	ENSMUSG00000016256	Ctsz	AI787083|AU019819|CTSX|D2Wsu143e	cathepsin Z	protein-coding
mm_57983.1	chr6	135733608	135733616	-	1	NA	exon (NM_008171, exon 15 of 15)	exon (NM_008171, exon 15 of 15)	74699	NR_126088	75024	Mm.399147	NR_126088	ENSMUSG00000107396	4930425L21Rik	4930473P14Rik	RIKEN cDNA 4930425L21 gene	ncRNA
mm_32190.1	chr4	101217784	101217818	+	1	NA	intron (NM_146145, intron 1 of 24)	HAL1|LINE|L1	47481	NM_146145	16451	Mm.289657	NM_146145	ENSMUSG00000028530	Jak1	AA960307|BAP004|C130039L05Rik	Janus kinase 1	protein-coding
mm_118520.1	chr14	14704058	14704061	+	1	NA	intron (NM_001033270, intron 1 of 24)	intron (NM_001033270, intron 1 of 24)	1034	NM_001033270	218756	Mm.258893	NM_001033270	ENSMUSG00000021733	Slc4a7	E430014N10Rik|NBC3|NBCn1|NBCn1-G	solute carrier family 4, sodium bicarbonate cotransporter, member 7	protein-coding
mm_26146.1	chr3	138066626	138066648	+	1	NA	intron (NR_037975, intron 1 of 3)	intron (NR_037975, intron 1 of 3)	751	NR_037975	329763	Mm.169710	NM_177860	ENSMUSG00000049349	Gm5105	D830013H12|EG329763	predicted gene 5105	ncRNA
mm_130115.1	chr15	89476486	89476525	-	1	NA	5' UTR (NM_009713, exon 2 of 9)	5' UTR (NM_009713, exon 2 of 9)	253	NR_077233	100532730	Mm.461541	NR_077233		C230037L18Rik	-	RIKEN cDNA C230037L18 gene	ncRNA
mm_132663.1	chr16	41988452	41988469	+	1	NA	intron (NM_001347236, intron 3 of 6)	MERVL_2A-int|LTR|ERVL	315009	NR_105858	102466172		NR_105858	ENSMUSG00000098300	Mir6540	Gm27780|mir-6540|mmu-mir-6540	microRNA 6540	ncRNA
mm_123837.1	chr14	70635854	70635879	-	1	NA	TTS (NM_008004)	TTS (NM_008004)	182	NM_001252664	13829	Mm.210863	NM_013514	ENSMUSG00000022099	Dmtn	AI325486|Epb4.9|Epb49|dematin	dematin actin binding protein	protein-coding
mm_136388.1	chr16	93142060	93142072	-	1	NA	Intergenic	(CTG)n|Simple_repeat|Simple_repeat	211123	NR_040486	69857	Mm.81192	NR_040486	ENSMUSG00000100277	1810053B23Rik	1810008L18Rik|1810056K14Rik	RIKEN cDNA 1810053B23 gene	ncRNA
mm_136449.1	chr16	94995127	94995140	-	1	NA	intron (NM_001025584, intron 1 of 4)	intron (NM_001025584, intron 1 of 4)	2563	NM_001025584	16522	Mm.328720	NM_010606	ENSMUSG00000043301	Kcnj6	BIR1|GIRK2|KATP2|KCNJ7|Kir3.2|weaver|wv	potassium inwardly-rectifying channel, subfamily J, member 6	protein-coding
mm_140558.1	chr17	7927988	7927998	-	1	NA	intron (NM_145968, intron 4 of 9)	intron (NM_145968, intron 4 of 9)	1993	NM_145968	72536	Mm.119680	NM_145968	ENSMUSG00000033450	Tagap	2610315E15Rik	T cell activation Rho GTPase activating protein	protein-coding
mm_50286.1	chr6	47453914	47453929	+	1	NA	promoter-TSS (NM_012042)	promoter-TSS (NM_012042)	-403	NM_012042	26965	Mm.87611	NM_012042	ENSMUSG00000029686	Cul1	-	cullin 1	protein-coding
mm_16055.1	chr2	167775530	167775553	+	1	NA	Intergenic	Intergenic	84364	NR_015500	329562	Mm.123101	NM_177851	ENSMUSG00000006462	A530013C23Rik	-	RIKEN cDNA A530013C23 gene	ncRNA
mm_154288.1	chr19	60874527	60874550	-	1	NA	promoter-TSS (NM_007452)	promoter-TSS (NM_007452)	0	NM_007452	11757	Mm.29821	NM_007452	ENSMUSG00000024997	Prdx3	AW822249|Aop1|D0Tohi1|Ef2l|Mer5|Prx3|SP22|TDXM	peroxiredoxin 3	protein-coding
mm_2183.1	chr1	88754925	88754935	+	1	NA	promoter-TSS (NR_040493)	promoter-TSS (NR_040493)	40	NR_040493	78650	Mm.243767	NR_040493	ENSMUSG00000097398	Platr5	2410088K16Rik	pluripotency associated transcript 5	ncRNA
mm_155041.1	chrX	42149535	42149547	+	1	NA	5' UTR (NM_001077712, exon 1 of 33)	5' UTR (NM_001077712, exon 1 of 33)	129	NM_001077712	20843	Mm.290422	NM_021465	ENSMUSG00000025862	Stag2	9230105L23Rik|B230112I07Rik|SA-2|SAP2	stromal antigen 2	protein-coding
mm_84575.1	chr9	69034455	69034468	-	1	NA	intron (NM_013646, intron 1 of 10)	intron (NM_013646, intron 1 of 10)	-255380	NM_001289916	19883	Mm.378450	NM_013646	ENSMUSG00000032238	Rora	9530021D13Rik|Nr1f1|ROR1|ROR2|ROR3|nmf267|sg|staggerer|tmgc26	RAR-related orphan receptor alpha	protein-coding
mm_41935.1	chr5	105700903	105700914	+	1	NA	promoter-TSS (NM_178701)	promoter-TSS (NM_178701)	98	NM_178701	231549	Mm.23837	NM_178701	ENSMUSG00000046079	Lrrc8d	2810473G09Rik|4930525N13Rik|A930019F03|Lrrc5	leucine rich repeat containing 8D	protein-coding
mm_163722.1	chr13	113614151	113614171	+	1	NA	intron (NM_130796, intron 1 of 1)	intron (NM_130796, intron 1 of 1)	4403	NM_130796	170625	Mm.33721	NM_130796	ENSMUSG00000042364	Snx18	Snag1	sorting nexin 18	protein-coding
mm_38468.1	chr4	140648737	140648781	-	1	NA	promoter-TSS (NM_172415)	promoter-TSS (NM_172415)	-3	NM_172415	72754	Mm.29329	NM_172415	ENSMUSG00000040964	Arhgef10l	2810441C07Rik	Rho guanine nucleotide exchange factor (GEF) 10-like	protein-coding
mm_5313.1	chr1	22512517	22512559	-	1	NA	intron (NM_001012623, intron 8 of 14).2	intron (NM_001012623, intron 8 of 14).2	-79695	NM_183018	116837	Mm.60061	NM_053270	ENSMUSG00000041670	Rims1	C030033M19Rik|RIM1|RIM1a|RIM1alpha|Rab3ip1|Rim|Serg1|mKIAA0340	regulating synaptic membrane exocytosis 1	protein-coding
mm_127484.1	chr15	101284281	101284308	+	1	NA	promoter-TSS (NM_026566)	promoter-TSS (NM_026566)	-7	NM_026566	68118	Mm.482360	NM_026566	ENSMUSG00000037204	Atg101	9430023L20Rik|AA407441|AU022967	autophagy related 101	protein-coding
mm_123672.1	chr14	69249339	69249350	-	1	NA	intron (NM_026331, intron 2 of 3)	intron (NM_026331, intron 2 of 3)	35759	NM_026331	67712	Mm.293635	NM_026331	ENSMUSG00000034248	Slc25a37	1700020E22Rik|4930513O14Rik|4930526G11Rik|AI848481|C330015G08Rik|Mfrn|Mfrn1|Mscp|frascati|mitoferrin	solute carrier family 25, member 37	protein-coding
mm_66493.1	chr7	45054192	45054223	-	1	NA	intron (NM_022999, intron 6 of 6)	intron (NM_022999, intron 6 of 6)	-1326	NM_175022	233210	Mm.219137	NM_175022	ENSMUSG00000046574	Prr12	6720469B10|BC058674	proline rich 12	protein-coding
mm_31290.1	chr4	45965328	45965342	+	1	NA	promoter-TSS (NM_001290475)	promoter-TSS (NM_001290475)	0	NM_001290475	100121	Mm.275413	NM_146142	ENSMUSG00000035517	Tdrd7	5730495N10Rik|AI447470|PCTAIRE2BP	tudor domain containing 7	protein-coding
mm_127949.1	chr15	10720304	10720324	-	1	NA	intron (NR_045065, intron 3 of 3)	intron (NR_045065, intron 3 of 3)	5414	NR_045065	75259	Mm.33928	NR_045063	ENSMUSG00000097058	4930556M19Rik	1700009D01Rik|C130022M03Rik	RIKEN cDNA 4930556M19 gene	ncRNA
mm_25163.1	chr3	103058354	103058365	+	1	NA	promoter-TSS (NM_010937)	promoter-TSS (NM_010937)	74	NM_010937	18176	Mm.400954	NM_010937	ENSMUSG00000027852	Nras	AV095280|N-ras	neuroblastoma ras oncogene	protein-coding
mm_27982.1	chr3	81965138	81965159	-	1	NA	intron (NM_019911, intron 7 of 11)	intron (NM_019911, intron 7 of 11)	10580	NM_019911	56720	Mm.258622	NM_019911	ENSMUSG00000028011	Tdo2	AA407491|TDO|TO|chky	tryptophan 2,3-dioxygenase	protein-coding
mm_131706.1	chr16	20732898	20732941	+	1	NA	promoter-TSS (NM_009893)	promoter-TSS (NM_009893)	-208	NM_001278041	12667	Mm.20457	NM_009893	ENSMUSG00000006958	Chrd	Chd	chordin	protein-coding
mm_23512.1	chr3	60531235	60531252	+	1	NA	intron (NM_001310514, intron 2 of 8)	intron (NM_001310514, intron 2 of 8)	30064	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_69625.1	chr7	137314369	137314379	-	1	NA	promoter-TSS (NM_001113414)	promoter-TSS (NM_001113414)	71	NM_001113415	13593	Mm.258708	NM_010096	ENSMUSG00000010476	Ebf3	3110018A08Rik|O/E-2|mKIAA4201	early B cell factor 3	protein-coding
mm_50572.1	chr6	49051367	49051377	+	1	NA	intron (NM_053110, intron 8 of 10)	intron (NM_053110, intron 8 of 10)	14854	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_111937.1	chr12	108893401	108893411	-	1	NA	promoter-TSS (NM_177602)	promoter-TSS (NM_177602)	-195	NM_011710	22375	Mm.38433	NM_011710	ENSMUSG00000021266	Wars	TrpRS|WRS	tryptophanyl-tRNA synthetase	protein-coding
mm_137115.1	chr17	22429259	22429263	+	1	NA	intron (NM_198003, intron 2 of 6)	intron (NM_198003, intron 2 of 6)	5059	NM_001331198	74149	Mm.30767	NM_198003	ENSMUSG00000071266	Zfp946	1300003B13Rik	zinc finger protein 946	protein-coding
mm_92672.1	chr10	80539108	80539129	-	1	NA	promoter-TSS (NM_026094)	promoter-TSS (NM_026094)	6	NM_026094	67331	Mm.52511	NM_026094	ENSMUSG00000003341	Atp8b3	1700042F02Rik|1700056N23Rik|ATPIK|SAPLT	ATPase, class I, type 8B, member 3	protein-coding
mm_28985.1	chr3	101283963	101283969	-	1	NA	intron (NM_013486, intron 2 of 4)	intron (NM_013486, intron 2 of 4)	3973	NM_013486	12481	Mm.22842	NM_013486	ENSMUSG00000027863	Cd2	LFA-2|Ly-37|Ly37	CD2 antigen	protein-coding
mm_22639.1	chr3	14863487	14863494	+	1	NA	promoter-TSS (NM_007606)	promoter-TSS (NM_007606)	-48	NM_007606	12350	Mm.300	NM_007606	ENSMUSG00000027559	Car3	BB219044|Ca3|Car-3	carbonic anhydrase 3	protein-coding
mm_50048.1	chr6	41151740	41151760	+	1	NA	Intergenic	Intergenic	-116241	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_75720.1	chr8	69077222	69077243	-	1	NA	5' UTR (NM_153054, exon 2 of 17)	5' UTR (NM_153054, exon 2 of 17)	-11504	NM_007509	11966	Mm.249096	NM_007509	ENSMUSG00000006273	Atp6v1b2	AI194269|AI790362|Atp6b2|HO57|R74844	ATPase, H+ transporting, lysosomal V1 subunit B2	protein-coding
mm_62036.1	chr7	92180611	92180621	+	1	NA	intron (NM_011807, intron 13 of 22)	intron (NM_011807, intron 13 of 22)	-54354	NM_001243047	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_94808.1	chr11	23010977	23011001	+	1	NA	Intergenic	RLTR53_Mm|LTR|ERVK	-2398	NM_028672	73873	Mm.252406	NM_028672	ENSMUSG00000049811	Fam161a	4930430E16Rik	family with sequence similarity 161, member A	protein-coding
mm_100446.1	chr11	119491619	119491660	+	1	NA	promoter-TSS (NM_177394)	promoter-TSS (NM_177394)	19	NM_177394	338371	Mm.271946	NM_177394	ENSMUSG00000039850	Endov	A730011L01Rik	endonuclease V	protein-coding
mm_6570.1	chr1	75191935	75191997	-	1	NA	promoter-TSS (NM_001288613)	promoter-TSS (NM_001288613)	44	NM_001003917	245860	Mm.238266	NM_001003917	ENSMUSG00000033124	Atg9a	AU019532|Apg9l1|Atg9|Atg9l1	autophagy related 9A	protein-coding
mm_137683.1	chr17	28823667	28823707	+	1	NA	intron (NM_001081315, intron 8 of 12)	intron (NM_001081315, intron 8 of 12)	22561	NM_001081315	268936	Mm.291877	NM_199061	ENSMUSG00000063952	Brpf3	AI413466|AW493400|mKIAA1286	bromodomain and PHD finger containing, 3	protein-coding
mm_127045.1	chr15	96642510	96642525	+	1	NA	promoter-TSS (NM_001166456)	promoter-TSS (NM_001166456)	-174	NM_001166456	105727	Mm.103568	NM_134086	ENSMUSG00000023169	Slc38a1	AA408026|AA409865|AL022800|AU015942|NAT2	solute carrier family 38, member 1	protein-coding
mm_9242.1	chr1	171330297	171330302	-	1	NA	intron (NM_011615, intron 1 of 4)	intron (NM_011615, intron 1 of 4)	1154	NM_011615	21945	Mm.270139	NM_011615	ENSMUSG00000013973	Dedd	CASP8IP1|DEFT|Dedpro1|FLDED1|KE05	death effector domain-containing	protein-coding
mm_60345.1	chr7	44357971	44357984	+	1	NA	3' UTR (NM_001034115, exon 25 of 25)	3' UTR (NM_001034115, exon 25 of 25)	17053	NM_027049	69349	Mm.358922	NM_027049	ENSMUSG00000008028	1700008O03Rik	-	RIKEN cDNA 1700008O03 gene	protein-coding
mm_30803.1	chr4	20009368	20009406	+	1	NA	intron (NM_015767, intron 1 of 4)	intron (NM_015767, intron 1 of 4)	1058	NM_015767	50500	Mm.24375	NM_015767	ENSMUSG00000073988	Ttpa	alpha-TTP	tocopherol (alpha) transfer protein	protein-coding
mm_63218.1	chr7	126292474	126292488	+	1	NA	exon (NM_145587, exon 4 of 4)	exon (NM_145587, exon 4 of 4)	19862	NM_145587	104175	Mm.29660	NM_145587	ENSMUSG00000042978	Sbk1	Sbk	SH3-binding kinase 1	protein-coding
mm_22688.1	chr3	17789957	17789972	+	1	NA	promoter-TSS (NR_033490)	promoter-TSS (NR_033490)	43	NR_033490	70441	Mm.458192	NR_033490	ENSMUSG00000100252	Mir124-2hg	100040120|2610100L16Rik|6430547I21Rik|A930005K07Rik|AW125202|Gm2612	Mir124-2 host gene (non-protein coding)	ncRNA
mm_38985.1	chr4	151044565	151044691	-	1	NA	promoter-TSS (NM_001289878)	promoter-TSS (NM_001289878)	37	NM_011067	18628	Mm.121361	NM_011067	ENSMUSG00000028957	Per3	2810049O06Rik|mPer3	period circadian clock 3	protein-coding
mm_18110.1	chr2	44991180	44991196	-	1	NA	intron (NM_001289521, intron 8 of 8)	intron (NM_001289521, intron 8 of 8)	31989	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_67849.1	chr7	98656793	98656813	-	1	NA	promoter-TSS (NM_172280)	promoter-TSS (NM_172280)	-234	NM_172280	233545	Mm.387819	NM_172280	ENSMUSG00000035401	Emsy	2210018M11Rik|2310016L09Rik|AU019521|AU019557	EMSY, BRCA2-interacting transcriptional repressor	protein-coding
mm_46039.1	chr5	91962840	91962887	-	1	NA	promoter-TSS (NR_028429)	promoter-TSS (NR_028429)	-19	NR_028429	381650	Mm.159453	NR_028429	ENSMUSG00000102644	Thap6	4930534K21Rik|AI448650	THAP domain containing 6	pseudo
mm_170922.1	chr2	37261987	37261989	-	1	NA	Intergenic	RLTR9D|LTR|ERVK	-4963	NM_001081010	545417	Mm.379955	NM_001081010		Olfr367-ps	EG545417|MOR128-1|ORL1283|OTTMUSG00000012147|Olfr367	olfactory receptor 367, pseudogene	protein-coding
mm_121769.1	chr14	19874350	19874351	-	1	NA	3' UTR (NM_001285911, exon 4 of 4)	3' UTR (NM_001285911, exon 4 of 4)	35425	NR_105025	52512	Mm.483998	NR_105025		D14Ertd670e	-	DNA segment, Chr 14, ERATO Doi 670, expressed	ncRNA
mm_166057.1	chr4	133035624	133035627	+	1	NA	intron (NM_146155, intron 2 of 6)	intron (NM_146155, intron 2 of 6)	24119	NM_146155	230793	Mm.31816	NM_146155	ENSMUSG00000037692	Ahdc1	D030015G18Rik	AT hook, DNA binding motif, containing 1	protein-coding
mm_20050.1	chr2	120245124	120245143	-	1	NA	5' UTR (NM_177845, exon 1 of 20)	5' UTR (NM_177845, exon 1 of 20)	202	NM_177845	329502	Mm.330505	NM_177845	ENSMUSG00000050211	Pla2g4e	2310026J01Rik|C230096D22|Pla2epsilon	phospholipase A2, group IVE	protein-coding
mm_152411.1	chr19	10605411	10605466	-	1	NA	promoter-TSS (NM_015735)	promoter-TSS (NM_015735)	-187	NM_015735	13194	Mm.289915	NM_015735	ENSMUSG00000024740	Ddb1	127kDa|AA408517|p127-Ddb1	damage specific DNA binding protein 1	protein-coding
mm_168050.1	chrY	90811972	90811982	+	1	NA	intron (NM_133362, intron 2 of 3)	IMPB_01|Satellite|Satellite	26535	NM_133362	170942	Mm.76062	NM_133362	ENSMUSG00000096768	Erdr1	edr	erythroid differentiation regulator 1	protein-coding
mm_840.1	chr1	51593994	51593998	+	1	NA	Intergenic	L1MA10|LINE|L1	-115597	NM_001310549	109019	Mm.196290	NM_028696	ENSMUSG00000026107	Nabp1	4930434H03Rik|4930442A21Rik|4930488J04Rik|4933440J18Rik|5830411E10Rik|AI852561|Nbp1|Obfc2a|Ssb2	nucleic acid binding protein 1	protein-coding
mm_60800.1	chr7	45621828	45621841	+	1	NA	promoter-TSS (NM_001018013)	promoter-TSS (NM_001018013)	23	NM_001018013	73456	Mm.380445	NM_001018013	ENSMUSG00000064158	Izumo1	1700058F15Rik|Izumo	izumo sperm-egg fusion 1	protein-coding
mm_144581.1	chr18	31931306	31931348	+	1	NA	promoter-TSS (NM_144862)	promoter-TSS (NM_144862)	-180	NM_144862	225341	Mm.24551	NM_144862	ENSMUSG00000024395	Lims2	PINCH2	LIM and senescent cell antigen like domains 2	protein-coding
mm_120441.1	chr14	65856495	65856504	+	1	NA	exon (NM_145944, exon 6 of 9)	exon (NM_145944, exon 6 of 9)	19197	NM_145944	67179	Mm.214576	NM_145944	ENSMUSG00000022035	Ccdc25	2610528H13Rik|NSrp70	coiled-coil domain containing 25	protein-coding
mm_153955.1	chr19	47691947	47691979	-	1	NA	promoter-TSS (NM_007732)	promoter-TSS (NM_007732)	79	NM_007732	12821	Mm.1225	NM_007732	ENSMUSG00000025064	Col17a1	BP180|Bpag|Bpag2	collagen, type XVII, alpha 1	protein-coding
mm_170394.1	chr1	86358109	86358111	-	1	NA	exon (NM_010880, exon 2 of 14)	exon (NM_010880, exon 2 of 14)	1345	NM_010880	17975	Mm.154378	NM_010880	ENSMUSG00000026234	Ncl	B530004O11Rik|C23|D0Nds28|D1Nds28|Nucl	nucleolin	protein-coding
mm_173236.1	chrX	80876051	80876068	-	1	NA	Intergenic	RLTR13D6|LTR|ERVK	-194585	NM_138751	192216	Mm.490421	NM_138751	ENSMUSG00000025666	Tmem47	3010015F07Rik|AI115536|BCMP1|Tm4sf10	transmembrane protein 47	protein-coding
mm_146015.1	chr18	69382242	69382251	+	1	NA	intron (NM_013685, intron 3 of 19)	intron (NM_013685, intron 3 of 19)	36525	NM_001083967	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding
mm_101775.1	chr11	44574796	44574799	-	1	NA	Intergenic	RLTR26_Mus|LTR|ERVK	-11520	NR_126460	75389	Mm.261421	NR_126460	ENSMUSG00000086501	4930597A21Rik	-	RIKEN cDNA 4930597A21 gene	ncRNA
mm_144293.1	chr18	12163436	12163439	+	1	NA	Intergenic	Intergenic	-5293	NM_029623	76482	Mm.196596	NM_029623	ENSMUSG00000024410	3110002H16Rik	2400010D15Rik|Mic-1|Mic1	RIKEN cDNA 3110002H16 gene	protein-coding
mm_14579.1	chr2	135659626	135659650	+	1	NA	Intergenic	CpG	-76418	NR_015544	320684	Mm.421433	NR_015544	ENSMUSG00000085631	9630028H03Rik	-	RIKEN cDNA 9630028H03 gene	ncRNA
mm_30000.1	chr3	135594362	135594400	-	1	NA	intron (NM_008689, intron 18 of 24)	intron (NM_008689, intron 18 of 24)	97166	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_19521.1	chr2	94066799	94066816	-	1	NA	intron (NM_019657, intron 4 of 10)	MIR3|SINE|MIR	-56077	NM_026944	69113	Mm.272498	NM_026944	ENSMUSG00000040174	Alkbh3	1700108H04Rik|1810020C19Rik|Abh3|mABH3	alkB homolog 3, alpha-ketoglutarate-dependent dioxygenase	protein-coding
mm_79036.1	chr9	46173195	46173236	+	1	NA	intron (NM_027498, intron 4 of 24)	intron (NM_027498, intron 4 of 24)	-55415	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2|apo-AI|apoA-I	apolipoprotein A-I	protein-coding
mm_168706.1	chr11	98203357	98203373	+	1	NA	promoter-TSS (NM_026952)	promoter-TSS (NM_026952)	60	NM_001109626	69131	Mm.260516	NM_026952	ENSMUSG00000003119	Cdk12	1810022J16Rik|AI646528|Crk7|Crkrs|D11Ertd752e|Pksc	cyclin-dependent kinase 12	protein-coding
mm_26880.1	chr3	17785569	17785584	-	1	NA	Intergenic	Intergenic	-4345	NR_033490	70441	Mm.458192	NR_033490	ENSMUSG00000100252	Mir124-2hg	100040120|2610100L16Rik|6430547I21Rik|A930005K07Rik|AW125202|Gm2612	Mir124-2 host gene (non-protein coding)	ncRNA
mm_145881.1	chr18	65477100	65477106	+	1	NA	3' UTR (NM_172833, exon 16 of 16)	3' UTR (NM_172833, exon 16 of 16)	46106	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_774.1	chr1	44551484	44551499	+	1	NA	promoter-TSS (NM_028450)	promoter-TSS (NM_028450)	-180	NM_028450	70676	Mm.133132	NM_027506	ENSMUSG00000056870	Gulp1	3110030A04Rik|5730529O06Rik|CED-6|Ced6|GULP|Gulp-2	GULP, engulfment adaptor PTB domain containing 1	protein-coding
mm_123151.1	chr14	57100227	57100254	-	1	NA	exon (NM_008125, exon 2 of 2)	exon (NM_008125, exon 2 of 2)	4462	NM_008125	14619	Mm.390683	NM_008125	ENSMUSG00000046352	Gjb2	AI325222|Cnx26|Cx26|Gjb-2	gap junction protein, beta 2	protein-coding
mm_38271.1	chr4	136882202	136882238	-	1	NA	exon (NM_009777, exon 2 of 3)	exon (NM_009777, exon 2 of 3)	3957	NM_009777	12260	Mm.2570	NM_009777	ENSMUSG00000036905	C1qb	-	complement component 1, q subcomponent, beta polypeptide	protein-coding
mm_143772.1	chr17	81671659	81671672	-	1	NA	intron (NR_104580, intron 1 of 8)	MER5B|DNA|hAT-Charlie	66722	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_102697.1	chr11	65806542	65806585	-	1	NA	promoter-TSS (NM_026107)	promoter-TSS (NM_026107)	-612	NM_001302374	52712	Mm.340052	NM_026107	ENSMUSG00000018347	Zkscan6	1700128E15Rik|D11Ertd714e|KOX11|Zfp535|Znf18	zinc finger with KRAB and SCAN domains 6	protein-coding
mm_34719.1	chr4	152129042	152129052	+	1	NA	promoter-TSS (NM_019585)	promoter-TSS (NM_019585)	-122	NM_019585	56226	Mm.264215	NM_019585	ENSMUSG00000028943	Espn	je	espin	protein-coding
mm_12820.1	chr2	80316880	80316880	+	1	NA	intron (NM_024181, intron 1 of 22)	RLTR31D_MM|LTR|ERVK	1414	NM_024181	66861	Mm.21762	NM_024181	ENSMUSG00000027006	Dnajc10	1200006L06Rik|D2Ertd706e|ERdj5|JPDI	DnaJ heat shock protein family (Hsp40) member C10	protein-coding
mm_122777.1	chr14	54410012	54410026	-	1	NA	promoter-TSS (NM_001253680)	promoter-TSS (NM_001253680)	-547	NM_001253680	20540	Mm.142455	NM_011405	ENSMUSG00000000958	Slc7a7	AI790233|my+lat1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 7	protein-coding
mm_173180.1	chrX	56516171	56516171	-	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	33435	NM_001033372	270599	Mm.424438	NM_001033372	ENSMUSG00000064016	Gm648	-	predicted gene 648	protein-coding
mm_37775.1	chr4	129823328	129823348	-	1	NA	intron (NM_001164745, intron 1 of 5)	intron (NM_001164745, intron 1 of 5)	2630	NM_001164745	19244	Mm.193688	NM_008974	ENSMUSG00000028788	Ptp4a2	Prl-2	protein tyrosine phosphatase 4a2	protein-coding
mm_105308.1	chr11	102818410	102818412	-	1	NA	intron (NM_001159383, intron 1 of 2)	AT_rich|Low_complexity|Low_complexity	748	NM_001159382	14615	Mm.390369	NM_008122	ENSMUSG00000034520	Gjc1	C130009G16Rik|Cnx45|Cx45|Gja-7|Gja7	gap junction protein, gamma 1	protein-coding
mm_14061.1	chr2	122637868	122637923	+	1	NA	promoter-TSS (NM_001004174)	promoter-TSS (NM_001004174)	8	NM_001004174	433470	Mm.36783	NM_001004174	ENSMUSG00000033213	AA467197	Nmes1|mir-147	expressed sequence AA467197	protein-coding
mm_33079.1	chr4	123904990	123905051	+	1	NA	promoter-TSS (NM_019660)	promoter-TSS (NM_019660)	7	NM_019660	56309	Mm.446553	NM_019660	ENSMUSG00000028647	Mycbp	5730488M09Rik|AW552132|AW742590|Amy-1	MYC binding protein	protein-coding
mm_170150.1	chr17	45570728	45570731	-	1	NA	exon (NM_008302, exon 5 of 11)	exon (NM_008302, exon 5 of 11)	2532	NM_008302	15516	Mm.2180	NM_008302	ENSMUSG00000023944	Hsp90ab1	90kDa|AL022974|C81438|Hsp84|Hsp84-1|Hsp90|Hspcb	heat shock protein 90 alpha (cytosolic), class B member 1	protein-coding
mm_105482.1	chr11	105939988	105939997	-	1	NA	intron (NM_007805, intron 1 of 5)	intron (NM_007805, intron 1 of 5)	4155	NM_007805	13056	Mm.149403	NM_007805	ENSMUSG00000019590	Cyb561	-	cytochrome b-561	protein-coding
mm_23564.1	chr3	63295425	63295438	+	1	NA	promoter-TSS (NM_008604)	promoter-TSS (NM_008604)	-4	NM_001289462	17380	Mm.296022	NM_008604	ENSMUSG00000027820	Mme	6030454K05Rik|C85356|CALLA|CD10|NEP|SFE	membrane metallo endopeptidase	protein-coding
mm_154925.1	chrX	24008461	24008505	+	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	115720	NM_001034864	236749	Mm.296422	NM_001034864	ENSMUSG00000068113	Gm4907	EG236749	predicted gene 4907	protein-coding
mm_31385.1	chr4	48039927	48039946	+	1	NA	Intergenic	Intergenic	-5369	NM_015743	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_133029.1	chr16	57239698	57239702	+	1	NA	Intergenic	Intergenic	-8234	NM_026254	67581	Mm.257819	NM_026254	ENSMUSG00000022749	Tbc1d23	4930451A13Rik|AU015720|AU043671|AU043778|D030022P07Rik|W51689	TBC1 domain family, member 23	protein-coding
mm_113555.1	chr13	38151325	38151339	+	1	NA	promoter-TSS (NM_023842)	promoter-TSS (NM_023842)	38	NM_023842	109620	Mm.355327	NM_023842	ENSMUSG00000054889	Dsp	2300002E22Rik|5730453H04Rik|AA407887|AA407888|AW109828|DP|rul	desmoplakin	protein-coding
mm_45313.1	chr5	65435718	65435734	-	1	NA	5' UTR (NM_009466, exon 1 of 12)	5' UTR (NM_009466, exon 1 of 12)	116	NM_009466	22235	Mm.344831	NM_009466	ENSMUSG00000029201	Ugdh	Udpgdh	UDP-glucose dehydrogenase	protein-coding
mm_97847.1	chr11	83066532	83066536	+	1	NA	intron (NM_011408, intron 1 of 1)	intron (NM_011408, intron 1 of 1)	1422	NM_011408	20556	Mm.278689	NM_011408	ENSMUSG00000072620	Slfn2	Shlf2	schlafen 2	protein-coding
mm_85917.1	chr9	111095818	111095828	-	1	NA	Intergenic	B4|SINE|B4	-22288	NM_027742	71268	Mm.302287	NM_027742	ENSMUSG00000032497	Lrrfip2	5133400F20Rik|AI850587	leucine rich repeat (in FLII) interacting protein 2	protein-coding
mm_15965.1	chr2	166059187	166059220	+	1	NA	exon (NM_008679, exon 15 of 23)	exon (NM_008679, exon 15 of 23)	66566	NM_008679	17979	Mm.469663	NM_008679	ENSMUSG00000027678	Ncoa3	2010305B15Rik|AW321064|Actr|Aib1|KAT13B|Rac3|Src3|Tram-1|Tram1|bHLHe42|p/Cip|pCip	nuclear receptor coactivator 3	protein-coding
mm_156606.1	chrX	153140112	153140122	+	1	NA	5' UTR (NM_001004154, exon 1 of 11)	5' UTR (NM_001004154, exon 1 of 11)	159	NM_001004154	245670	Mm.190922	NM_001004154	ENSMUSG00000041658	Rragb	-	Ras-related GTP binding B	protein-coding
mm_66329.1	chr7	42711486	42711491	-	1	NA	Intergenic	A-rich|Low_complexity|Low_complexity	-18770	NM_001008427	434179	Mm.284947	NM_001008427	ENSMUSG00000069727	Zfp975	EG434179|Gm5595|mszf88	zinc finger protein 975	protein-coding
mm_111525.1	chr12	100205662	100205701	-	1	NA	exon (NM_009790, exon 4 of 6)	exon (NM_009790, exon 4 of 6)	5537	NM_001313934	12313	Mm.285993	NM_009790	ENSMUSG00000001175	Calm1	AI256814|AI327027|AI461935|AL024000|CaM|Calm	calmodulin 1	protein-coding
mm_45721.1	chr5	86037104	86037111	-	1	NA	intron (NM_007683, intron 8 of 18)	intron (NM_007683, intron 8 of 18)	28476	NM_001345902	12617	Mm.4649	NM_007683	ENSMUSG00000029253	Cenpc1	CENP-C|Cenpc	centromere protein C1	protein-coding
mm_128197.1	chr15	35155652	35155732	-	1	NA	5' UTR (NM_019635, exon 1 of 11)	5' UTR (NM_019635, exon 1 of 11)	114	NM_019635	56274	Mm.262330	NM_019635	ENSMUSG00000022329	Stk3	0610042I06Rik|MST|Mst2|Mst3|Ste20|mess1	serine/threonine kinase 3	protein-coding
mm_22478.1	chr3	5219040	5219053	+	1	NA	intron (NM_030708, intron 1 of 10)	C-rich|Low_complexity|Low_complexity	492	NM_030708	80892	Mm.41522	NM_030708	ENSMUSG00000025255	Zfhx4	A930021B15|C130041O22Rik|Zfh-4|Zfh4	zinc finger homeodomain 4	protein-coding
mm_110741.1	chr12	69791326	69791338	-	1	NA	promoter-TSS (NM_183294)	promoter-TSS (NM_183294)	-625	NM_183294	71091	Mm.132325	NM_183294	ENSMUSG00000020990	Cdkl1	4933411O17Rik	cyclin-dependent kinase-like 1 (CDC2-related kinase)	protein-coding
mm_2797.1	chr1	130851585	130851600	+	1	NA	3' UTR (NM_011082, exon 11 of 11)	3' UTR (NM_011082, exon 11 of 11)	-14185	NM_026976	69169	Mm.46042	NM_026976	ENSMUSG00000042474	Fcmr	1810037B05Rik|Faim3|FcmuR|Toso	Fc fragment of IgM receptor	protein-coding
mm_82233.1	chr9	3036348	3036373	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	2383	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_104850.1	chr11	99318587	99318608	-	1	NA	intron (NM_133730, intron 3 of 7)	intron (NM_133730, intron 3 of 7)	4344	NM_133730	70810	Mm.268173	NM_133730	ENSMUSG00000035831	Krt25	4631426H08Rik|Ka38|Krt25a|mIRSa1	keratin 25	protein-coding
mm_118594.1	chr14	20674497	20674559	+	1	NA	intron (NM_001168273, intron 1 of 23)	CpG	207	NM_001168273	218811	Mm.173119	NM_172596	ENSMUSG00000039367	Sec24c	2610204K03Rik|mKIAA0079	Sec24 related gene family, member C (S. cerevisiae)	protein-coding
mm_31628.1	chr4	59262991	59263002	+	1	NA	non-coding (NR_105031, exon 3 of 4)	non-coding (NR_105031, exon 3 of 4)	2945	NR_105031	101055769	Mm.421401	NR_105031		Gm12596	OTTMUSG00000007649	predicted gene 12596	ncRNA
mm_4440.1	chr1	172506986	172506997	+	1	NA	3' UTR (NM_178598, exon 5 of 5)	3' UTR (NM_178598, exon 5 of 5)	6745	NM_178598	21346	Mm.271711	NM_178598	ENSMUSG00000026547	Tagln2	2700094C18Rik|SM22beta|Sm22B|Sm22a	transgelin 2	protein-coding
mm_136498.1	chr16	96372421	96372427	-	1	NA	intron (NM_001177886, intron 2 of 8)	intron (NM_001177886, intron 2 of 8)	10660	NM_028078	72058	Mm.119714	NM_028078	ENSMUSG00000000159	Igsf5	2010003D20Rik|JCAM|Jam4	immunoglobulin superfamily, member 5	protein-coding
mm_22145.1	chr2	172345671	172345683	-	1	NA	promoter-TSS (NM_025912)	promoter-TSS (NM_025912)	100	NM_025912	67017	Mm.30013	NM_025912	ENSMUSG00000027495	Fam210b	2010011I20Rik|AI430961|AV108736	family with sequence similarity 210, member B	protein-coding
mm_16206.1	chr2	173061746	173061756	+	1	NA	Intergenic	Intergenic	39849	NM_019547	56190	Mm.485782	NM_019547	ENSMUSG00000027510	Rbm38	Rnpc1|Seb4|Seb4l	RNA binding motif protein 38	protein-coding
mm_149496.1	chr19	11912291	11912306	+	1	NA	promoter-TSS (NM_172635)	promoter-TSS (NM_172635)	-101	NM_172635	225929	Mm.42711	NM_172635	ENSMUSG00000046139	Patl1	AV312086|Pat1b	protein associated with topoisomerase II homolog 1 (yeast)	protein-coding
mm_43776.1	chr5	141856693	141856711	+	1	NA	intron (NM_177879, intron 5 of 44)	intron (NM_177879, intron 5 of 44)	-544795	NM_199068	17425	Mm.24214	NM_010812	ENSMUSG00000056493	Foxk1	A630048H08Rik|AI463295|ENSMUSG00000075577|Gm10868|Mnf	forkhead box K1	protein-coding
mm_43382.1	chr5	135725714	135725740	+	1	NA	intron (NM_008898, intron 2 of 15)	intron (NM_008898, intron 2 of 15)	10162	NR_106001	102466791		NR_106001	ENSMUSG00000099197	Mir7034	Gm27372|mmu-mir-7034	microRNA 7034	ncRNA
mm_140322.1	chr17	86656694	86656698	+	1	NA	3' UTR (NM_011104, exon 15 of 15)	3' UTR (NM_011104, exon 15 of 15)	-97168	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_155507.1	chrX	73853780	73853800	+	1	NA	TTS (NM_008478)	TTS (NM_008478)	27044	NM_008478	16728	Mm.260568	NM_008478	ENSMUSG00000031391	L1cam	CD171|L1|N-CAM-L1|NCAM-L1	L1 cell adhesion molecule	protein-coding
mm_151044.1	chr19	47024049	47024059	+	1	NA	3' UTR (NM_146100, exon 3 of 3)	3' UTR (NM_146100, exon 3 of 3)	-8865	NM_001164363	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_143640.1	chr17	79354861	79354864	-	1	NA	5' UTR (NM_026514, exon 1 of 2)	5' UTR (NM_026514, exon 1 of 2)	229	NM_026514	260409	Mm.140601	NM_026514	ENSMUSG00000036533	Cdc42ep3	3200001F04Rik|AA986861|Borg2|Cep3|UB1	CDC42 effector protein (Rho GTPase binding) 3	protein-coding
mm_149888.1	chr19	25395314	25395332	+	1	NA	intron (NM_181404, intron 4 of 13)	intron (NM_181404, intron 4 of 13)	-110383	NM_015826	50796	Mm.391208	NM_015826	ENSMUSG00000024837	Dmrt1	-	doublesex and mab-3 related transcription factor 1	protein-coding
mm_9582.1	chr1	174028416	174028428	-	1	NA	exon (NM_172648, exon 2 of 7)	exon (NM_172648, exon 2 of 7)	3333	NM_172648	226695	Mm.425061	NM_172648	ENSMUSG00000054203	Ifi205	D3|D3cDNA|Ifi205a	interferon activated gene 205	protein-coding
mm_114194.1	chr13	55895814	55895827	+	1	NA	Intergenic	MTEa|LTR|ERVL-MaLR	-64395	NM_011097	18740	Mm.135195	NM_011097	ENSMUSG00000021506	Pitx1	Bft|P-OTX|Potx|Ptx1	paired-like homeodomain transcription factor 1	protein-coding
mm_109323.1	chr12	109561996	109562013	+	1	NA	non-coding (NR_003633, exon 5 of 5)	non-coding (NR_003633, exon 5 of 5)	-1688	NR_030427	791079		NR_030427	ENSMUSG00000076451	Mir770	Mirn770|mir-770|mmu-mir-770	microRNA 770	ncRNA
mm_52956.1	chr6	123122657	123122732	+	1	NA	promoter-TSS (NM_001170333)	promoter-TSS (NM_001170333)	4	NM_001170332	26888	Mm.47384	NM_011999	ENSMUSG00000030148	Clec4a2	Clec4a|Clecsf6|DCIR|Dcir1	C-type lectin domain family 4, member a2	protein-coding
mm_47565.1	chr5	124445378	124445391	-	1	NA	promoter-TSS (NM_001310723)	promoter-TSS (NM_001310723)	-115	NM_001310723	67956	Mm.137966	NM_030241	ENSMUSG00000049327	Kmt5a	2410195B05Rik|AA617402|AW536475|PR-SET7|PR/SET07|Setd8	lysine methyltransferase 5A	protein-coding
mm_143968.1	chr17	87282772	87282786	-	1	NA	promoter-TSS (NM_028639)	promoter-TSS (NM_028639)	35	NR_015506	74597	Mm.63783	NR_015506	ENSMUSG00000085287	4833418N02Rik	-	RIKEN cDNA 4833418N02 gene	ncRNA
mm_101389.1	chr11	24172776	24172786	-	1	NA	exon (NM_001159290, exon 5 of 5)	exon (NM_001159290, exon 5 of 5)	92086	NM_001159290	14025	Mm.53687	NM_016707	ENSMUSG00000000861	Bcl11a	2810047E18Rik|BCL-11A|Ctip1|D930021L15Rik|Evi9|Evi9a|Evi9b|Evi9c|mKIAA1809	B cell CLL/lymphoma 11A (zinc finger protein)	protein-coding
mm_21603.1	chr2	164238293	164238296	-	1	NA	promoter-TSS (NM_017390)	promoter-TSS (NM_017390)	47	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_148787.1	chr19	6115571	6115587	+	1	NA	TTS (NM_133678)	TTS (NM_133678)	3007	NM_133678	66406	Mm.303924	NM_133678	ENSMUSG00000024790	Sac3d1	2410004C24Rik|AU015683|shd1	SAC3 domain containing 1	protein-coding
mm_51023.1	chr6	65106804	65106808	+	1	NA	intron (NM_001253392, intron 17 of 21)	intron (NM_001253392, intron 17 of 21)	37924	NM_019455	54486	Mm.410688	NM_019455	ENSMUSG00000029919	Hpgds	H-PGDS|Ptgds2	hematopoietic prostaglandin D synthase	protein-coding
mm_43381.1	chr5	135715979	135715999	+	1	NA	exon (NM_008898, exon 2 of 16)	exon (NM_008898, exon 2 of 16)	19900	NR_106001	102466791		NR_106001	ENSMUSG00000099197	Mir7034	Gm27372|mmu-mir-7034	microRNA 7034	ncRNA
mm_45239.1	chr5	53707509	53707519	-	1	NA	5' UTR (NM_009827, exon 1 of 5)	5' UTR (NM_009827, exon 1 of 5)	190	NM_009827	12425	Mm.3521	NM_009827	ENSMUSG00000029193	Cckar	AW106902	cholecystokinin A receptor	protein-coding
mm_153872.1	chr19	46761249	46761263	-	1	NA	promoter-TSS (NM_001102471)	promoter-TSS (NM_001102471)	-353	NM_033569	94219	Mm.306903	NM_033569	ENSMUSG00000064105	Cnnm2	AU015877|AW048635|Acdp2|Clp2	cyclin M2	protein-coding
mm_167841.1	chrM	12454	12465	+	1	NA	NA	Intergenic	NA	NA								
mm_22234.1	chr2	174438898	174438938	-	1	NA	5' UTR (NM_022325, exon 1 of 6)	5' UTR (NM_022325, exon 1 of 6)	121	NM_022325	64138	Mm.156919	NM_022325	ENSMUSG00000016256	Ctsz	AI787083|AU019819|CTSX|D2Wsu143e	cathepsin Z	protein-coding
mm_102217.1	chr11	54909658	54909687	-	1	NA	3' UTR (NM_008161, exon 5 of 5)	3' UTR (NM_008161, exon 5 of 5)	6818	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_124977.1	chr15	20491471	20491474	+	1	NA	Intergenic	Lx10|LINE|L1	175278	NM_022816	64833	Mm.352763	NM_022816	ENSMUSG00000047565	Acot10	Acate3|MT-ACT48|p48	acyl-CoA thioesterase 10	protein-coding
mm_302.1	chr1	23761788	23761807	+	1	NA	promoter-TSS (NM_172124)	promoter-TSS (NM_172124)	-129	NM_172124	280645	Mm.471661	NM_172124	ENSMUSG00000026156	B3gat2	GlcAT-S|Glcats	beta-1,3-glucuronyltransferase 2 (glucuronosyltransferase S)	protein-coding
mm_133510.1	chr16	90738345	90738430	+	1	NA	promoter-TSS (NM_029844)	promoter-TSS (NM_029844)	63	NM_029844	77037	Mm.22455	NM_029844	ENSMUSG00000039956	Mrap	1110025G12Rik|Falp|ORF61	melanocortin 2 receptor accessory protein	protein-coding
mm_108357.1	chr12	80692644	80692717	+	1	NA	promoter-TSS (NR_037995)	promoter-TSS (NR_037995)	79	NM_001177503	217682	Mm.154541	NM_001177503	ENSMUSG00000066438	Plekhd1	3830431G21Rik	pleckstrin homology domain containing, family D (with coiled-coil domains) member 1	protein-coding
mm_52093.1	chr6	97836502	97836541	+	1	NA	intron (NM_001113198, intron 1 of 9)	intron (NM_001113198, intron 1 of 9)	29463	NM_001113198	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_164259.1	chr15	100270089	100270103	+	1	NA	Intergenic	RLTR9E|LTR|ERVK	-10741	NM_183109	75002	Mm.261400	NM_183109	ENSMUSG00000045631	Tmprss12	4930478A21Rik	transmembrane (C-terminal) protease, serine 12	protein-coding
mm_71131.1	chr8	36549420	36549428	+	1	NA	Intergenic	Intergenic	60233	NM_176952	319582	Mm.180924	NM_176952	ENSMUSG00000039620	6430573F11Rik	Kiaa1456|TRM9L	RIKEN cDNA 6430573F11 gene	protein-coding
mm_100286.1	chr11	117813293	117813303	+	1	NA	exon (NM_009304, exon 4 of 4)	exon (NM_009304, exon 4 of 4)	3631	NM_009304	20973	Mm.468228	NM_009304	ENSMUSG00000048277	Syngr2	Clast2|cellugyrin	synaptogyrin 2	protein-coding
mm_154177.1	chr19	58737040	58737062	-	1	NA	exon (NM_018874, exon 9 of 13)	exon (NM_018874, exon 9 of 13)	8164	NM_018874	18946	Mm.10753	NM_018874	ENSMUSG00000042179	Pnliprp1	Plrp1	pancreatic lipase related protein 1	protein-coding
mm_101223.1	chr11	20200908	20200923	-	1	NA	promoter-TSS (NM_008996)	promoter-TSS (NM_008996)	-687	NM_008996	19324	Mm.271944	NM_008996	ENSMUSG00000020149	Rab1a	Gtbp|Rab-1|Rab1|Ypt1|mKIAA3012	RAB1A, member RAS oncogene family	protein-coding
mm_91438.1	chr10	33924663	33924677	-	1	NA	Intergenic	L1_Mus3|LINE|L1	19559	NM_001162957	212892	Mm.131949	NM_001162957	ENSMUSG00000039552	Rsph4a	A230081C05|Rshl3	radial spoke head 4 homolog A (Chlamydomonas)	protein-coding
mm_41309.1	chr5	90468636	90468650	+	1	NA	exon (NM_009654, exon 8 of 15)	exon (NM_009654, exon 8 of 15)	7773	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_30198.1	chr3	144714088	144714106	-	1	NA	intron (NM_001282042, intron 1 of 9)	intron (NM_001282042, intron 1 of 9)	6238	NM_001282042	54673	Mm.271775	NM_019464	ENSMUSG00000037062	Sh3glb1	AA409932|AI314629|AU015566|Bif-1|mKIAA0491	SH3-domain GRB2-like B1 (endophilin)	protein-coding
mm_150416.1	chr19	37207698	37207727	+	1	NA	promoter-TSS (NM_198300)	promoter-TSS (NM_198300)	167	NM_001164336	69104	Mm.175989	NM_027314	ENSMUSG00000023307	March5	1810015H18Rik|2310008I22Rik|2700055A20Rik|5730499H23Rik|E130202O05Rik|MARCH-V|MITOL|Marchv|Rnf153	membrane-associated ring finger (C3HC4) 5	protein-coding
mm_81715.1	chr9	111351910	111351922	+	1	NA	intron (NM_001164659, intron 7 of 21)	intron (NM_001164659, intron 7 of 21)	40177	NM_001164659	320429	Mm.270754	NM_001164659	ENSMUSG00000062296	Trank1	A230061D21Rik|C030048J01Rik|Gm187|Lba1	tetratricopeptide repeat and ankyrin repeat containing 1	protein-coding
mm_1163.1	chr1	60909224	60909266	+	1	NA	exon (NM_009843, exon 1 of 4)	exon (NM_009843, exon 1 of 4)	220	NM_001281976	12477	Mm.390	NM_009843	ENSMUSG00000026011	Ctla4	Cd152|Ctla-4|Ly-56	cytotoxic T-lymphocyte-associated protein 4	protein-coding
mm_156333.1	chrX	139007667	139007677	+	1	NA	3' UTR (NM_013724, exon 28 of 28)	3' UTR (NM_013724, exon 28 of 28)	77564	NM_177920	331535	Mm.211704	NM_177920	ENSMUSG00000031271	Serpina7	C730040N12Rik|Tbg	serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 7	protein-coding
mm_47475.1	chr5	123721008	123721062	-	1	NA	promoter-TSS (NM_027494)	promoter-TSS (NM_027494)	9	NM_027494	70650	Mm.279427	NM_027494	ENSMUSG00000029427	Zcchc8	5730565F05Rik	zinc finger, CCHC domain containing 8	protein-coding
mm_1998.1	chr1	87126962	87126971	+	1	NA	exon (NM_007432, exon 9 of 11)	exon (NM_007432, exon 9 of 11)	1958	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_87471.1	chr10	51491898	51491950	+	1	NA	exon (NM_013532, exon 4 of 9)	exon (NM_013532, exon 4 of 9)	1026	NM_013532	14728	Mm.34408	NM_013532	ENSMUSG00000062593	Lilrb4a	CD85K|Gp49b|HM18|ILT3|LIR-5|Lilrb4|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4A	protein-coding
mm_24287.1	chr3	89243750	89243798	+	1	NA	exon (NM_183037, exon 3 of 10)	exon (NM_183037, exon 3 of 10)	1239	NR_121683	360213	Mm.331156	NM_183037	ENSMUSG00000042766	Trim46	TRIFIC	tripartite motif-containing 46	protein-coding
mm_149654.1	chr19	18670909	18670928	+	1	NA	5' UTR (NM_026120, exon 1 of 8)	5' UTR (NM_026120, exon 1 of 8)	138	NM_026120	67383	Mm.306602	NM_026120	ENSMUSG00000024726	Carnmt1	2410127L17Rik	carnosine N-methyltransferase 1	protein-coding
mm_134018.1	chr16	4880161	4880178	-	1	NA	promoter-TSS (NM_145359)	promoter-TSS (NM_145359)	-318	NM_145359	207740	Mm.268895	NM_145359	ENSMUSG00000039568	Ubald1	1500031H01Rik|BC013706|Fam100a	UBA-like domain containing 1	protein-coding
mm_25060.1	chr3	98881250	98881253	+	1	NA	intron (NM_019545, intron 5 of 8)	intron (NM_019545, intron 5 of 8)	11979	NM_019545	56185	Mm.281874	NM_019545	ENSMUSG00000027870	Hao2	AI325478|Hao-2|Hao3|Haox3	hydroxyacid oxidase 2	protein-coding
mm_7854.1	chr1	132391768	132391805	-	1	NA	promoter-TSS (NM_178874)	promoter-TSS (NM_178874)	-400	NM_178874	68875	Mm.273785	NM_178874	ENSMUSG00000042066	Tmcc2	1110063G11Rik	transmembrane and coiled-coil domains 2	protein-coding
mm_80323.1	chr9	74953562	74953575	+	1	NA	intron (NM_001113283, intron 1 of 12)	intron (NM_001113283, intron 1 of 12)	515	NM_001113283	235493	Mm.208955	NM_153584	ENSMUSG00000034858	Fam214a	6330415I01Rik|AI553555|C130047D21Rik|Kiaa1370|mKIAA1370	family with sequence similarity 214, member A	protein-coding
mm_133930.1	chr16	3723329	3723335	-	1	NA	Intergenic	Intergenic	-5208	NM_001161791	54483	Mm.143718	NM_019453	ENSMUSG00000022534	Mefv	FMF|TRIM20|pyrin	Mediterranean fever	protein-coding
mm_2174.1	chr1	88406957	88406965	+	1	NA	promoter-TSS (NM_029269)	promoter-TSS (NM_029269)	-49	NM_029269	75396	Mm.173058	NM_029269	ENSMUSG00000026295	Spp2	0610038O04Rik|pp-24|spp24	secreted phosphoprotein 2	protein-coding
mm_165269.1	chr2	75704399	75704402	-	1	NA	exon (NM_010902, exon 1 of 5)	exon (NM_010902, exon 1 of 5)	263	NR_132727	18024	Mm.1025	NM_010902	ENSMUSG00000015839	Nfe2l2	Nrf2	nuclear factor, erythroid derived 2, like 2	protein-coding
mm_85236.1	chr9	98563581	98563620	-	1	NA	promoter-TSS (NM_015827)	promoter-TSS (NM_015827)	11	NR_029444	75881	Mm.483402	NM_175227	ENSMUSG00000051074	4930579K19Rik	-	RIKEN cDNA 4930579K19 gene	ncRNA
mm_49171.1	chr6	14901345	14901364	+	1	NA	promoter-TSS (NM_053242)	promoter-TSS (NM_053242)	5	NM_053242	114142	Mm.332919	NM_053242	ENSMUSG00000029563	Foxp2	2810043D05Rik|AI449000|CAG-16|D0Kist7	forkhead box P2	protein-coding
mm_8832.1	chr1	162571434	162571442	-	1	NA	intron (NM_001347125, intron 1 of 7)	CpG	610	NM_001347125	53330	Mm.10699	NM_016796	ENSMUSG00000026696	Vamp4	D1Ertd147e	vesicle-associated membrane protein 4	protein-coding
mm_96797.1	chr11	69981040	69981086	+	1	NA	promoter-TSS (NM_026017)	promoter-TSS (NM_026017)	-105	NM_026017	67181	Mm.41678	NM_026017	ENSMUSG00000018559	Ctdnep1	2610507E10Rik|Dullard	CTD nuclear envelope phosphatase 1	protein-coding
mm_65288.1	chr7	24445589	24445610	-	1	NA	promoter-TSS (NM_199013)	promoter-TSS (NM_199013)	83	NM_199013	210145	Mm.33811	NM_199013	ENSMUSG00000062028	Irgc1	F630044M05Rik|Gm1102|Gm474|Ifgge|Iigp5|Irgc	immunity-related GTPase family, cinema 1	protein-coding
mm_168475.1	chr11	48951421	48951436	+	1	NA	intron (NM_001114679, intron 3 of 3)	L1Md_F3|LINE|L1	-5018	NM_001281472	621823	Mm.440151	NM_001281472	ENSMUSG00000078153	Psme2b	PA28b-p|PA28b2|Psme2-like|Psme2b-ps	protease (prosome, macropain) activator subunit 2B	protein-coding
mm_55683.1	chr6	72611397	72611408	-	1	NA	3' UTR (NM_009444, exon 4 of 4)	3' UTR (NM_009444, exon 4 of 4)	5346	NM_009444	22135	Mm.246563	NM_009444		Tgoln2	TGN38B|TGN41|TGN46|Ttgn2	trans-golgi network protein 2	protein-coding
mm_54329.1	chr6	30610935	30610941	-	1	NA	promoter-TSS (NM_144537)	promoter-TSS (NM_144537)	-72	NM_144537	74649	Mm.159276	NM_144537	ENSMUSG00000029788	Cpa5	4930430M09Rik	carboxypeptidase A5	protein-coding
mm_22152.1	chr2	172440517	172440529	-	1	NA	promoter-TSS (NM_025542)	promoter-TSS (NM_025542)	-55	NM_025542	66404	Mm.25157	NM_025542	ENSMUSG00000027502	Rtfdc1	1700067C04Rik|2410001C21Rik|5730427M17Rik|AA589417	replication termination factor 2 domain containing 1	protein-coding
mm_84453.1	chr9	66518599	66518602	-	1	NA	intron (NM_001302122, intron 12 of 12)	intron (NM_001302122, intron 12 of 12)	-4007	NM_175206	74165	Mm.297998	NM_175206	ENSMUSG00000050503	Fbxl22	1110004B15Rik	F-box and leucine-rich repeat protein 22	protein-coding
mm_41813.1	chr5	103784151	103784162	+	1	NA	exon (NM_133919, exon 3 of 20)	exon (NM_133919, exon 3 of 20)	29583	NM_001080798	17355	Mm.6949	NM_133919	ENSMUSG00000029313	Aff1	9630032B01Rik|AW319193|Af4|Mllt2h|Rob	AF4/FMR2 family, member 1	protein-coding
mm_37408.1	chr4	122793767	122793784	-	1	NA	Intergenic	Intergenic	-42452	NM_008917	19063	Mm.277719	NM_008917	ENSMUSG00000028657	Ppt1	9530043G02Rik|AA960502|C77813|CLN1|D4Ertd184e|INCL|PPT	palmitoyl-protein thioesterase 1	protein-coding
mm_101920.1	chr11	50200740	50200790	-	1	NA	TTS (NM_026543)	TTS (NM_026543)	10055	NM_001290769	18412	Mm.40828	NM_011018	ENSMUSG00000015837	Sqstm1	A170|OSF-6|Osi|STAP|STONE14|p62	sequestosome 1	protein-coding
mm_85513.1	chr9	106269426	106269461	-	1	NA	Intergenic	Intergenic	-11618	NM_027354	70235	Mm.23054	NM_027354	ENSMUSG00000023345	Poc1a	2510040D07Rik|Wdr51a|cha	POC1 centriolar protein A	protein-coding
mm_89013.1	chr10	81649008	81649040	+	1	NA	promoter-TSS (NM_001142963)	promoter-TSS (NM_001142963)	-45	NM_001142963	100233208	Mm.327168	NM_001142963	ENSMUSG00000096856	Gm10778	ENSMUSG00000074860	predicted gene 10778	protein-coding
mm_63815.1	chr7	133747641	133747656	+	1	NA	intron (NM_133941, intron 3 of 11)	intron (NM_133941, intron 3 of 11)	12621	NM_001286030	101437	Mm.199223	NM_133941	ENSMUSG00000030986	Dhx32	3110079L04Rik|4732469F02Rik|AA408140|Ddx32	DEAH (Asp-Glu-Ala-His) box polypeptide 32	protein-coding
mm_18515.1	chr2	62645545	62645598	-	1	NA	exon (NM_027835, exon 1 of 16)	exon (NM_027835, exon 1 of 16)	684	NM_027835	71586	Mm.136224	NM_027835	ENSMUSG00000026896	Ifih1	9130009C22Rik|Helicard|Hlcd|MDA5|RLR-2	interferon induced with helicase C domain 1	protein-coding
mm_148083.1	chr18	73572277	73572314	-	1	NA	promoter-TSS (NM_001039214)	promoter-TSS (NM_001039214)	-410	NM_001039214	240396	Mm.24131	NM_001039214	ENSMUSG00000037253	Mex3c	A130001D14Rik|BC035207|BM-013|Rkhd2	mex3 RNA binding family member C	protein-coding
mm_166283.1	chr5	96747694	96747698	+	1	NA	intron (NM_175473, intron 58 of 73)	intron (NM_175473, intron 58 of 73)	-45689	NM_013470	11745	Mm.7214	NM_013470	ENSMUSG00000029484	Anxa3	Anx3	annexin A3	protein-coding
mm_136207.1	chr16	89833196	89833207	-	1	NA	exon (NM_001145886, exon 15 of 28)	exon (NM_001145886, exon 15 of 28)	-14849	NM_001145887	21844	Mm.310902	NM_009384	ENSMUSG00000002489	Tiam1	AI847750|D16Ium10|D16Ium10e	T cell lymphoma invasion and metastasis 1	protein-coding
mm_115520.1	chr13	5857519	5857561	-	1	NA	intron (NR_045891, intron 1 of 2)	intron (NR_045891, intron 1 of 2)	552	NR_045891	71867	Mm.179181	NR_045891	ENSMUSG00000100625	1700016G22Rik	-	RIKEN cDNA 1700016G22 gene	ncRNA
mm_32419.1	chr4	107066986	107067007	+	1	NA	promoter-TSS (NM_025500)	promoter-TSS (NM_025500)	8	NM_175471	230582	Mm.44608	NM_175471	ENSMUSG00000028621	Cyb5rl	2810410C14Rik	cytochrome b5 reductase-like	protein-coding
mm_23426.1	chr3	58987129	58987138	+	1	NA	Intergenic	Intergenic	-19845	NM_177855	329650	Mm.240059	NM_177855	ENSMUSG00000056476	Med12l	A130035F20|A630079M02|AU044581|TRALPUSH	mediator complex subunit 12-like	protein-coding
mm_97132.1	chr11	75038550	75038568	+	1	NA	intron (NM_001002764, intron 10 of 18)	intron (NM_001002764, intron 10 of 18)	27432	NR_030454	735274		NR_030454	ENSMUSG00000106252	Mir684-1	Mirn684-1	microRNA 684-1	ncRNA
mm_15052.1	chr2	152876595	152876608	+	1	NA	exon (NM_001141978, exon 7 of 18)	exon (NM_001141978, exon 7 of 18)	11534	NR_049195	100885834		NR_049195	ENSMUSG00000093746	Mir5622	Gm24421|mmu-mir-5622	microRNA 5622	ncRNA
mm_56599.1	chr6	108688507	108688510	-	1	NA	Intergenic	Intergenic	-27574	NR_104577	75394	Mm.395061	NR_040757	ENSMUSG00000087341	0610040F04Rik	-	RIKEN cDNA 0610040F04 gene	ncRNA
mm_126261.1	chr15	79108869	79108885	+	1	NA	promoter-TSS (NM_177461)	promoter-TSS (NM_177461)	-106	NM_177461	27008	Mm.196480	NM_177461	ENSMUSG00000033039	Micall1	AI448246|D15Mit260|D15N2e|EST573322|EST820961|MIRab13|mKIAA1668	microtubule associated monooxygenase, calponin and LIM domain containing -like 1	protein-coding
mm_104727.1	chr11	98326187	98326198	-	1	NA	3' UTR (NM_010895, exon 2 of 2)	3' UTR (NM_010895, exon 2 of 2)	3453	NM_010895	18013	Mm.4814	NM_010895	ENSMUSG00000038255	Neurod2	Ndrf|bHLHa1	neurogenic differentiation 2	protein-coding
mm_166819.1	chr7	18057988	18057988	+	1	NA	Intergenic	ERVB5_1-LTR_MM|LTR|ERVK	-7941	NM_001162524	67315	Mm.46089	NM_026087	ENSMUSG00000030366	Ceacam12	1600031J20Rik|Ceacam12-C1|Ceacam12-C3|Ceacam12C1|Ceacam12C3	carcinoembryonic antigen-related cell adhesion molecule 12	protein-coding
mm_41371.1	chr5	90561065	90561078	+	1	NA	promoter-TSS (NM_001252661)	promoter-TSS (NM_001252661)	-138	NM_001252661	622307	Mm.389654	NM_001252661	ENSMUSG00000070690	5830473C10Rik	Arg|Gm17754	RIKEN cDNA 5830473C10 gene	protein-coding
mm_152619.1	chr19	12461711	12461773	-	1	NA	exon (NM_010821, exon 2 of 2)	exon (NM_010821, exon 2 of 2)	963	NM_010821	17476	Mm.3999	NM_010821	ENSMUSG00000046805	Mpeg1	MPS1|Mpg-1	macrophage expressed gene 1	protein-coding
mm_173219.1	chrX	74305223	74305223	+	1	NA	TTS (NM_018794)	TTS (NM_018794)	211	NM_010273	14567	Mm.205830	NM_010273	ENSMUSG00000015291	Gdi1	GDIA|GDIalpha	guanosine diphosphate (GDP) dissociation inhibitor 1	protein-coding
mm_35226.1	chr4	19693880	19693891	-	1	NA	intron (NR_074089, intron 1 of 23)	intron (NR_074089, intron 1 of 23)	15119	NM_177327	107568	Mm.78312	NM_177327	ENSMUSG00000041058	Wwp1	8030445B08Rik|AIP5|SDRP1|Tiul1	WW domain containing E3 ubiquitin protein ligase 1	protein-coding
mm_133939.1	chr16	3907696	3907707	-	1	NA	intron (NM_028484, intron 1 of 2)	intron (NM_028484, intron 1 of 2)	988	NM_028484	73261	Mm.486226	NM_028484	ENSMUSG00000005983	1700037C18Rik	2810022L20Rik	RIKEN cDNA 1700037C18 gene	protein-coding
mm_7759.1	chr1	131138127	131138131	-	1	NA	exon (NM_145508, exon 1 of 3)	exon (NM_145508, exon 1 of 3)	105	NM_145508	226419	Mm.39299	NM_145508	ENSMUSG00000016526	Dyrk3	BC006704	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 3	protein-coding
mm_73636.1	chr8	110730056	110730076	+	1	NA	exon (NM_198625, exon 9 of 14)	exon (NM_198625, exon 9 of 14)	4340	NM_001310591	244654	Mm.490385	NM_198625	ENSMUSG00000033763	Mtss1l	ABBA	metastasis suppressor 1-like	protein-coding
mm_145261.1	chr18	52615909	52615996	+	1	NA	promoter-TSS (NM_025749)	promoter-TSS (NM_025749)	37	NM_025749	66758	Mm.251599	NM_025749	ENSMUSG00000046886	Zfp474	4933409D10Rik|Znf474	zinc finger protein 474	protein-coding
mm_100313.1	chr11	117986839	117986899	+	1	NA	promoter-TSS (NM_133757)	promoter-TSS (NM_133757)	12	NM_133757	74451	Mm.28864	NM_133757	ENSMUSG00000017715	Pgs1	2610019F11Rik|4933424M23Rik|SAF	phosphatidylglycerophosphate synthase 1	protein-coding
mm_73637.1	chr8	110732122	110732134	+	1	NA	exon (NM_198625, exon 10 of 14)	exon (NM_198625, exon 10 of 14)	6402	NM_001310591	244654	Mm.490385	NM_198625	ENSMUSG00000033763	Mtss1l	ABBA	metastasis suppressor 1-like	protein-coding
mm_48777.1	chr5	148552103	148552123	-	1	NA	5' UTR (NM_011908, exon 1 of 5)	5' UTR (NM_011908, exon 1 of 5)	675	NM_011908	24109	Mm.21846	NM_011908	ENSMUSG00000001687	Ubl3	AW108023|HCG	ubiquitin-like 3	protein-coding
mm_58308.1	chr6	146212943	146212969	-	1	NA	intron (NM_010586, intron 44 of 55)	intron (NM_010586, intron 44 of 55)	278809	NM_010656	16651	Mm.49689	NM_010656	ENSMUSG00000030255	Sspn	Krag	sarcospan	protein-coding
mm_11742.1	chr2	38341069	38341080	+	1	NA	intron (NM_001290646, intron 1 of 4)	intron (NM_001290646, intron 1 of 4)	1793	NM_001290646	16870	Mm.142856	NM_010710	ENSMUSG00000000247	Lhx2	LH2A|Lh-2|Lim2|ap|apterous	LIM homeobox protein 2	protein-coding
mm_68524.1	chr7	112140391	112140401	-	1	NA	intron (NM_015814, intron 4 of 7)	intron (NM_015814, intron 4 of 7)	18661	NM_015814	50781	Mm.55143	NM_015814	ENSMUSG00000030772	Dkk3	AW061014|C87148	dickkopf WNT signaling pathway inhibitor 3	protein-coding
mm_13686.1	chr2	117120729	117120754	+	1	NA	promoter-TSS (NM_001277256)	promoter-TSS (NM_001277256)	-330	NM_001277256	114715	Mm.245890	NM_033524	ENSMUSG00000027351	Spred1	5730461F13Rik|AL024345|AW047647	sprouty protein with EVH-1 domain 1, related sequence	protein-coding
mm_5426.1	chr1	34473159	34473181	-	1	NA	intron (NM_011206, intron 13 of 14)	intron (NM_011206, intron 13 of 14)	13424	NM_011206	19253	Mm.361	NM_011206	ENSMUSG00000026126	Ptpn18	FLP1|HSCF|PTP-HSCF|PTP-K1|Ptpk1	protein tyrosine phosphatase, non-receptor type 18	protein-coding
mm_60900.1	chr7	46440817	46440824	+	1	NA	Intergenic	Intergenic	44352	NM_001112739	16502	Mm.249386	NM_008421	ENSMUSG00000058975	Kcnc1	C230009H10Rik|KShIIIB|KV4|Kcr2-1|Kv3.1|NGK2|Shaw	potassium voltage gated channel, Shaw-related subfamily, member 1	protein-coding
mm_158435.1	chrX	140062296	140062340	-	1	NA	promoter-TSS (NM_177921)	promoter-TSS (NM_177921)	250	NM_001081668	279706	Mm.102590	NM_001081668	ENSMUSG00000072944	Nup62cl	Gm719	nucleoporin 62 C-terminal like	protein-coding
mm_116510.1	chr13	45650834	45650843	-	1	NA	intron (NM_001199304, intron 5 of 6)	intron (NM_001199304, intron 5 of 6)	143394	NM_025508	66355	Mm.290802	NM_025508	ENSMUSG00000000253	Gmpr	2310004P21Rik|AV028449|GMPR 1	guanosine monophosphate reductase	protein-coding
mm_79048.1	chr9	46228929	46228946	+	1	NA	intron (NM_009692, intron 1 of 3)	intron (NM_009692, intron 1 of 3)	307	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2|apo-AI|apoA-I	apolipoprotein A-I	protein-coding
mm_3429.1	chr1	150100947	150100949	+	1	NA	intron (NM_011198, intron 1 of 9)	intron (NM_011198, intron 1 of 9)	917	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_172190.1	chr6	51047506	51047508	+	1	NA	Intergenic	(CCCTAA)n|Simple_repeat|Simple_repeat	222403	NR_029719	387166		NR_029719	ENSMUSG00000065505	Mir148a	Mirn148|Mirn148a|mir-148a	microRNA 148a	ncRNA
mm_84051.1	chr9	58156333	58156363	-	1	NA	TTS (NM_012043)	TTS (NM_012043)	2206	NM_001195431	26968	Mm.367887	NM_012043	ENSMUSG00000037206	Islr	AW553146|Meflin	immunoglobulin superfamily containing leucine-rich repeat	protein-coding
mm_7621.1	chr1	127206062	127206082	-	1	NA	intron (NM_145128, intron 1 of 17)	intron (NM_145128, intron 1 of 17)	1086	NM_145128	107895	Mm.214682	NM_145128	ENSMUSG00000036155	Mgat5	4930471A21Rik|5330407H02Rik|AI480971|GlcNAc-TV	mannoside acetylglucosaminyltransferase 5	protein-coding
mm_6444.1	chr1	74001506	74001516	-	1	NA	intron (NM_027884, intron 6 of 34)	intron (NM_027884, intron 6 of 34)	122936	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_82184.1	chr9	123936901	123936908	+	1	NA	Intergenic	Intergenic	31788	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_150389.1	chr19	36404883	36404887	+	1	NA	intron (NM_029508, intron 1 of 8)	intron (NM_029508, intron 1 of 8)	25818	NM_029508	76073	Mm.259180	NM_029508	ENSMUSG00000024805	Pcgf5	0610009F02Rik|1110054A01Rik|5830406C17Rik|5830443C21Rik|9530023M17Rik|AI324127	polycomb group ring finger 5	protein-coding
mm_98565.1	chr11	95384663	95384682	+	1	NA	promoter-TSS (NM_016752)	promoter-TSS (NM_016752)	-250	NM_016752	110172	Mm.4593	NM_016752	ENSMUSG00000020873	Slc35b1	Ugalt2	solute carrier family 35, member B1	protein-coding
mm_172420.1	chr7	26387149	26387149	+	1	NA	intron (NM_001042612, intron 1 of 8)	RLTR9D|LTR|ERVK	7094	NM_001042612	330490	Mm.212174	NM_194062	ENSMUSG00000040614	Nlrp9c	AA636537|BB062542|Nalp-zeta|Nalp9c	NLR family, pyrin domain containing 9C	protein-coding
mm_150186.1	chr19	32665476	32665515	+	1	NA	exon (NM_011864, exon 13 of 13)	exon (NM_011864, exon 13 of 13)	45490	NM_011864	23972	Mm.203916	NM_011864	ENSMUSG00000024899	Papss2	1810018P12Rik|AI159688|AtpsU2|Atpsk2|Sk2|bm	3'-phosphoadenosine 5'-phosphosulfate synthase 2	protein-coding
mm_113186.1	chr13	24937179	24937204	+	1	NA	promoter-TSS (NR_102323)	promoter-TSS (NR_102323)	-210	NR_102323	493800	Mm.458692	NR_102323		9330162012Rik	-	cDNA RIKEN 9330162012 gene	ncRNA
mm_77957.1	chr9	7593688	7593693	+	1	NA	Intergenic	Intergenic	22294	NM_001310717	234911	Mm.334940	NM_001030289	ENSMUSG00000070323	Mmp27	Gm180	matrix metallopeptidase 27	protein-coding
mm_51605.1	chr6	84019365	84019383	+	1	NA	promoter-TSS (NM_021469)	promoter-TSS (NM_021469)	-12	NM_001310152	26903	Mm.220982	NM_021469	ENSMUSG00000033788	Dysf	2310004N10Rik|AI604795|D6Pas3	dysferlin	protein-coding
mm_36490.1	chr4	83233166	83233177	-	1	NA	intron (NM_027238, intron 17 of 19)	intron (NM_027238, intron 17 of 19)	91018	NM_027238	69863	Mm.5540	NM_025782	ENSMUSG00000038172	Ttc39b	1810054D07Rik|9130422G05Rik|AI450603|AV103077|AW215585	tetratricopeptide repeat domain 39B	protein-coding
mm_57857.1	chr6	129494409	129494422	-	1	NA	intron (NM_138648, intron 4 of 7)	MIR|SINE|MIR	12750	NM_001301094	108078	Mm.293626	NM_138648	ENSMUSG00000030162	Olr1	LOX-1|SR-EI|Scare1	oxidized low density lipoprotein (lectin-like) receptor 1	protein-coding
mm_92045.1	chr10	62495024	62495027	-	1	NA	exon (NM_011157, exon 3 of 3)	exon (NM_011157, exon 3 of 3)	-8220	NM_133672	30930	Mm.260703	NM_133672	ENSMUSG00000020078	Vps26a	AA407240|HB58|Vps26	VPS26 retromer complex component A	protein-coding
mm_112996.1	chr13	21754032	21754045	+	1	NA	promoter-TSS (NM_178201)	promoter-TSS (NM_178201)	-85	NM_178201	319187		NM_178201	ENSMUSG00000095217	Hist1h2bn	-	histone cluster 1, H2bn	protein-coding
mm_14741.1	chr2	144368962	144368994	+	1	NA	promoter-TSS (NM_001166640)	promoter-TSS (NM_001166640)	-5	NM_001164813	100048644	Mm.227925	NM_001164813	ENSMUSG00000098387	Pet117	Gm20571	PET117 homolog	protein-coding
mm_84217.1	chr9	61914539	61914574	-	1	NA	promoter-TSS (NM_018853)	promoter-TSS (NM_018853)	-46	NM_018853	56040	Mm.3158	NM_018853	ENSMUSG00000007892	Rplp1	2410042H16Rik|Arpp1|C430017H15Rik	ribosomal protein, large, P1	protein-coding
mm_131265.1	chr16	10835047	10835084	+	1	NA	promoter-TSS (NM_001162932)	promoter-TSS (NM_001162932)	6	NM_001162932	223970	Mm.325777	NM_001033278	ENSMUSG00000037991	Rmi2	A630055G03Rik|Gm537|Gm929	RecQ mediated genome instability 2	protein-coding
mm_41415.1	chr5	90801649	90801664	+	1	NA	3' UTR (NM_011339, exon 4 of 4)	3' UTR (NM_011339, exon 4 of 4)	7122	NM_011339	20309	Mm.64326	NM_011339	ENSMUSG00000029375	Cxcl15	Il8|Scyb15|lungkine|weche	chemokine (C-X-C motif) ligand 15	protein-coding
mm_21672.1	chr2	164425769	164425779	-	1	NA	3' UTR (NM_011521, exon 5 of 5)	3' UTR (NM_011521, exon 5 of 5)	17414	NM_011521	20971	Mm.3815	NM_011521	ENSMUSG00000017009	Sdc4	AA959608|AW108331|S4|Synd4|ryudocan|syndecan-4	syndecan 4	protein-coding
mm_16853.1	chr2	11635094	11635097	-	1	NA	Intergenic	ID4|SINE|ID	-7697	NM_008367	16184	Mm.915	NM_008367	ENSMUSG00000026770	Il2ra	CD25|Il2r|Ly-43	interleukin 2 receptor, alpha chain	protein-coding
mm_170494.1	chr19	23120656	23120656	+	1	NA	Intergenic	B1_Mus1|SINE|Alu	-20570	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_54565.1	chr6	37604184	37604186	-	1	NA	Intergenic	RLTR9A|LTR|ERVK	74012	NM_145364	208665	Mm.262635	NM_145364	ENSMUSG00000038641	Akr1d1	-	aldo-keto reductase family 1, member D1	protein-coding
mm_52479.1	chr6	114310185	114310194	+	1	NA	exon (NM_178703, exon 11 of 16)	exon (NM_178703, exon 11 of 16)	27554	NM_178703	232333	Mm.5260	NM_178703	ENSMUSG00000030310	Slc6a1	A730043E01|GABATHG|GABATR|GAT-1|Gabt|Gabt1|Gat1|XT-1|Xtrp1	solute carrier family 6 (neurotransmitter transporter, GABA), member 1	protein-coding
mm_56137.1	chr6	87731439	87731472	-	1	NA	exon (NM_001159697, exon 1 of 8)	exon (NM_001159697, exon 1 of 8)	586	NM_001159697	58229	Mm.333229	NM_021418	ENSMUSG00000068263	Efcc1	Ccdc48	EF hand and coiled-coil domain containing 1	protein-coding
mm_9953.1	chr1	190979281	190979302	-	1	NA	promoter-TSS (NM_144879)	promoter-TSS (NM_144879)	5	NR_027352	226841	Mm.22856	NM_144879	ENSMUSG00000037568	Vash2	B130052G07Rik	vasohibin 2	protein-coding
mm_73733.1	chr8	113642497	113642511	+	1	NA	promoter-TSS (NM_001048145)	promoter-TSS (NM_001048145)	-709	NM_029139	668110	Mm.390078	NM_029139	ENSMUSG00000033409	Syce1l	4930481F22Rik|MMRP|PSESS|mmrp2	synaptonemal complex central element protein 1 like	protein-coding
mm_59514.1	chr7	27591514	27591562	+	1	NA	promoter-TSS (NM_001110208)	promoter-TSS (NM_001110208)	-14	NM_001110208	11652	Mm.177194	NM_007434	ENSMUSG00000004056	Akt2	2410016A19Rik|AW554154|PKB|PKBbeta	thymoma viral proto-oncogene 2	protein-coding
mm_172118.1	chr6	3201081	3201081	+	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	-87438	NR_036696	667335	Mm.380219	NR_036696	ENSMUSG00000106779	Gm8579	EG667335	spermatogenesis associated glutamate (E)-rich protein 4a pseudogene	pseudo
mm_164801.1	chr18	23891177	23891214	+	1	NA	3' UTR (NM_001162942, exon 8 of 8)	3' UTR (NM_001162942, exon 8 of 8)	-63493	NM_027007	69256	Mm.218343	NM_027007	ENSMUSG00000024276	Zfp397	2810411K16Rik|6720480F11Rik|AI461664	zinc finger protein 397	protein-coding
mm_127171.1	chr15	98830854	98830865	+	1	NA	TTS (NM_001033276)	TTS (NM_001033276)	649	NM_016781	19082	Mm.6670	NM_016781	ENSMUSG00000067713	Prkag1	AA571379|BB036179|Prkaac	protein kinase, AMP-activated, gamma 1 non-catalytic subunit	protein-coding
mm_122118.1	chr14	31014228	31014231	-	1	NA	TTS (NR_028531)	TTS (NR_028531)	122	NR_028531	100217431		NR_028531		Snord69	MBII-210	small nucleolar RNA, C/D box 69	snoRNA
mm_146818.1	chr18	21001529	21001546	-	1	NA	promoter-TSS (NM_207623)	promoter-TSS (NM_207623)	237	NM_001303005	56515	Mm.253542	NM_019706	ENSMUSG00000024317	Rnf138	2410015A17Rik|2810480D20Rik|STRIN|Trif|Trif-d	ring finger protein 138	protein-coding
mm_127004.1	chr15	95790972	95791008	+	1	NA	exon (NM_001253813, exon 1 of 21)	exon (NM_001253813, exon 1 of 21)	147	NM_001253813	105722	Mm.38087	NM_175344	ENSMUSG00000064210	Ano6	2900059G15Rik|AA407480|AW554778|F730003B03Rik|Tmem16f	anoctamin 6	protein-coding
mm_144428.1	chr18	21001767	21001777	+	1	NA	promoter-TSS (NM_207623)	promoter-TSS (NM_207623)	-185	NM_001303011	56515	Mm.253542	NM_019706	ENSMUSG00000024317	Rnf138	2410015A17Rik|2810480D20Rik|STRIN|Trif|Trif-d	ring finger protein 138	protein-coding
mm_39416.1	chr5	15934557	15934624	+	1	NA	promoter-TSS (NM_001110843)	promoter-TSS (NM_001110843)	-101	NM_001110843	12293	Mm.159842	NM_009784	ENSMUSG00000040118	Cacna2d1	Ca(v)alpha2delta1|Cacna2|Cchl2a	calcium channel, voltage-dependent, alpha2/delta subunit 1	protein-coding
mm_2447.1	chr1	99790201	99790203	+	1	NA	intron (NM_172851, intron 1 of 23)	intron (NM_172851, intron 1 of 23)	17437	NM_172851	241175	Mm.251301	NM_172851	ENSMUSG00000067028	Cntnap5b	C230078M14Rik|Caspr5-2	contactin associated protein-like 5B	protein-coding
mm_160232.1	chr7	102702388	102702388	+	1	NA	promoter-TSS (NM_147093)	promoter-TSS (NM_147093)	65	NM_147093	259097	Mm.121813	NM_147093	ENSMUSG00000070423	Olfr558	MOR18-1|POGR	olfactory receptor 558	protein-coding
mm_92009.1	chr10	62340135	62340154	-	1	NA	promoter-TSS (NR_038038)	promoter-TSS (NR_038038)	277	NM_001146100	15275	Mm.196605	NM_010438	ENSMUSG00000037012	Hk1	BB404130|Hk-1|Hk1-s|dea|mHk1-s	hexokinase 1	protein-coding
mm_134407.1	chr16	17663444	17663475	-	1	NA	exon (NM_001285884, exon 9 of 18)	exon (NM_001285884, exon 9 of 18)	16989	NM_001166164	72315	Mm.297777	NM_001166164	ENSMUSG00000041617	Ccdc74a	2310015A05Rik	coiled-coil domain containing 74A	protein-coding
mm_94996.1	chr11	31871811	31871822	+	1	NA	5' UTR (NM_026252, exon 1 of 10)	5' UTR (NM_026252, exon 1 of 10)	876	NM_026252	67579	Mm.339792	NM_026252	ENSMUSG00000020300	Cpeb4	Cpe-bp4|Cpeb-4|mCPEB-4	cytoplasmic polyadenylation element binding protein 4	protein-coding
mm_76250.1	chr8	83683353	83683362	-	1	NA	intron (NM_177262, intron 7 of 21)	intron (NM_177262, intron 7 of 21)	10704	NM_001199593	320795	Mm.213000	NM_177262	ENSMUSG00000057672	Pkn1	DBK|F730027O18Rik|PAK1|PRK1|Pkn|Prkcl1|Stk3	protein kinase N1	protein-coding
mm_89070.1	chr10	82985346	82985381	+	1	NA	promoter-TSS (NM_021439)	promoter-TSS (NM_021439)	-134	NM_021439	58250	Mm.360747	NM_021439	ENSMUSG00000034612	Chst11	1110020P09Rik|C4ST|C4ST-1|C4ST1|C4s	carbohydrate sulfotransferase 11	protein-coding
mm_21080.1	chr2	152933166	152933189	-	1	NA	promoter-TSS (NM_010226)	promoter-TSS (NM_010226)	31	NM_010226	14239	Mm.205798	NM_010226	ENSMUSG00000074676	Foxs1	FREAC10|Fkh3|Fkhl18	forkhead box S1	protein-coding
mm_143114.1	chr17	57206229	57206241	-	1	NA	exon (NM_009778, exon 36 of 41)	exon (NM_009778, exon 36 of 41)	10993	NR_105944	102465591		NR_105944	ENSMUSG00000099066	Mir6978	Gm27858|mmu-mir-6978	microRNA 6978	ncRNA
mm_135027.1	chr16	32794676	32794688	-	1	NA	exon (NM_146071, exon 2 of 4)	exon (NM_146071, exon 2 of 4)	2753	NM_146071	224116	Mm.153301	NM_146071	ENSMUSG00000035638	Muc20	BC026367	mucin 20	protein-coding
mm_89252.1	chr10	87859200	87859216	+	1	NA	5' UTR (NM_010512, exon 1 of 5)	5' UTR (NM_010512, exon 1 of 5)	156	NM_010512	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_96308.1	chr11	63158563	63158596	+	1	NA	3' UTR (NM_008885, exon 5 of 5)	3' UTR (NM_008885, exon 5 of 5)	25776	NM_001302260	18858	Mm.1237	NM_008885	ENSMUSG00000018217	Pmp22	22kDa|Gas-3|HNPP|Tr|trembler	peripheral myelin protein 22	protein-coding
mm_45052.1	chr5	41764550	41764561	-	1	NA	promoter-TSS (NM_007524)	promoter-TSS (NM_007524)	-335	NM_007524	12020	Mm.2530	NM_007524	ENSMUSG00000049691	Nkx3-2	Bapx1|NKX3.2|Nkx-3.2	NK3 homeobox 2	protein-coding
mm_138386.1	chr17	35050126	35050127	+	1	NA	promoter-TSS (NM_033444)	promoter-TSS (NM_033444)	-117	NM_033444	114584	Mm.29524	NM_033444	ENSMUSG00000007041	Clic1	Clcp|G6	chloride intracellular channel 1	protein-coding
mm_84287.1	chr9	62987916	62987941	-	1	NA	Intergenic	Intergenic	-7049	NM_019663	56469	Mm.431253	NM_019663	ENSMUSG00000032405	Pias1	2900068C24Rik|Ddxbp1|GBP	protein inhibitor of activated STAT 1	protein-coding
mm_78499.1	chr9	32732186	32732193	+	1	NA	intron (NM_011808, intron 3 of 7)	intron (NM_011808, intron 3 of 7)	36147	NM_001038642	23871	Mm.292415	NM_011808	ENSMUSG00000032035	Ets1	AI196000|AI448617|D230050P06|Ets-1|Tpl1|vs	E26 avian leukemia oncogene 1, 5' domain	protein-coding
mm_41647.1	chr5	98186601	98186624	+	1	NA	exon (NM_029947, exon 4 of 4)	exon (NM_029947, exon 4 of 4)	5743	NM_029947	77630	Mm.332511	NM_029947	ENSMUSG00000035456	Prdm8	4930565F05Rik|PFM5	PR domain containing 8	protein-coding
mm_33299.1	chr4	128993293	128993334	+	1	NA	promoter-TSS (NM_016895)	promoter-TSS (NM_016895)	89	NM_001033966	11637	Mm.29460	NM_016895	ENSMUSG00000028792	Ak2	Ak-2|D4Ertd220e	adenylate kinase 2	protein-coding
mm_164969.1	chr19	7297585	7297591	-	1	NA	intron (NM_007928, intron 1 of 17)	intron (NM_007928, intron 1 of 17)	-2141	NM_001080390	13728	Mm.258986	NM_007928	ENSMUSG00000024969	Mark2	EMK-1|Emk|Par-1|Par-1b	MAP/microtubule affinity regulating kinase 2	protein-coding
mm_33016.1	chr4	120969255	120969280	+	1	NA	3' UTR (NM_133716, exon 10 of 10)	3' UTR (NM_133716, exon 10 of 10)	4055	NR_105982	102465614		NR_105982	ENSMUSG00000106436	Mir7015	mmu-mir-7015	microRNA 7015	ncRNA
mm_2082.1	chr1	87676195	87676209	+	1	NA	intron (NM_010566, intron 5 of 26)	intron (NM_010566, intron 5 of 26)	55890	NM_001110193	16331	Mm.15105	NM_010566	ENSMUSG00000026288	Inpp5d	SHIP|SHIP-1|SHIP1|SIP-145|p150Ship|s-SHIP	inositol polyphosphate-5-phosphatase D	protein-coding
mm_6746.1	chr1	83278797	83278828	-	1	NA	exon (NM_172430, exon 7 of 11)	exon (NM_172430, exon 7 of 11)	119050	NM_027725	71227	Mm.256482	NM_027725	ENSMUSG00000053161	Daw1	4930563E19Rik|4933429D11Rik|Wdr69|b2b1116Clo|b2b1584Clo	dynein assembly factor with WDR repeat domains 1	protein-coding
mm_156941.1	chrX	169927550	169927589	+	1	NA	exon (NM_001290504, exon 2 of 10)	exon (NM_001290504, exon 2 of 10)	47950	NM_001290505	17318	Mm.34441	NM_010797	ENSMUSG00000035299	Mid1	61B3-R|DXHXS1141|Fxy|Trim18	midline 1	protein-coding
mm_137268.1	chr17	24698221	24698252	+	1	NA	5' UTR (NM_027988, exon 2 of 9)	5' UTR (NM_027988, exon 2 of 9)	2002	NM_027988	71893	Mm.390971	NM_027988	ENSMUSG00000019320	Noxo1	2310034C04Rik|P41NOX|P41NOXA|P41NOXB|P41NOXC|Snx28|hslt	NADPH oxidase organizer 1	protein-coding
mm_65501.1	chr7	25722926	25722956	-	1	NA	exon (NM_144922, exon 14 of 15)	exon (NM_144922, exon 14 of 15)	-3888	NM_028771	52132	Mm.278798	NM_028771	ENSMUSG00000002608	Ccdc97	1200014H14Rik|2810446P04Rik|AA545218|D7Ertd462e	coiled-coil domain containing 97	protein-coding
mm_156354.1	chrX	139334250	139334256	+	1	NA	exon (NM_011635, exon 1 of 3)	exon (NM_011635, exon 1 of 3)	570	NM_011635	22037	Mm.1297	NM_011635	ENSMUSG00000051257	Trap1a	Tra-P1A	tumor rejection antigen P1A	protein-coding
mm_92349.1	chr10	75860300	75860310	-	1	NA	promoter-TSS (NM_010798)	promoter-TSS (NM_010798)	-55	NM_010798	17319	Mm.2326	NM_010798	ENSMUSG00000033307	Mif	GIF|Glif	macrophage migration inhibitory factor	protein-coding
mm_93113.1	chr10	91122857	91122872	-	1	NA	intron (NM_133668, intron 2 of 7)	intron (NM_133668, intron 2 of 7)	1099	NM_133668	18674	Mm.298	NM_133668	ENSMUSG00000061904	Slc25a3	5730556H19Rik|PTP|Phc	solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 3	protein-coding
mm_73219.1	chr8	98882544	98882553	+	1	NA	Intergenic	Intergenic	-129339	NR_110579	100873092	Mm.414599	NR_110579	ENSMUSG00000089819	Gm15679	OTTMUSG00000025218	predicted gene 15679	ncRNA
mm_168188.1	chr10	62507782	62507782	-	1	NA	promoter-TSS (NM_011157)	promoter-TSS (NM_011157)	-27	NM_011157	19073	Mm.338790	NM_011157	ENSMUSG00000020077	Srgn	Prg|Prg1|Sgc	serglycin	protein-coding
mm_66609.1	chr7	45466379	45466428	-	1	NA	intron (NM_007527, intron 1 of 5)	intron (NM_007527, intron 1 of 5)	495	NM_007527	12028	Mm.19904	NM_007527	ENSMUSG00000003873	Bax	-	BCL2-associated X protein	protein-coding
mm_43162.1	chr5	127030807	127030821	+	1	NA	promoter-TSS (NR_040685)	promoter-TSS (NR_040685)	25	NR_040685	71247	Mm.399586	NR_040685	ENSMUSG00000105490	4933438B17Rik	-	RIKEN cDNA 4933438B17 gene	ncRNA
mm_44864.1	chr5	34336171	34336224	-	1	NA	promoter-TSS (NM_011278)	promoter-TSS (NM_011278)	-53	NM_011278	19822	Mm.21281	NM_011278	ENSMUSG00000029110	Rnf4	AU018689|Gtrgeo8|SNURF	ring finger protein 4	protein-coding
mm_140422.1	chr17	87975045	87975085	+	1	NA	promoter-TSS (NM_010830)	promoter-TSS (NM_010830)	15	NM_010830	17688	Mm.18210	NM_010830	ENSMUSG00000005370	Msh6	AU044881|AW550279|GTBP|Gtmbp	mutS homolog 6	protein-coding
mm_70120.1	chr7	142969259	142969269	-	1	NA	promoter-TSS (NM_008554)	promoter-TSS (NM_008554)	0	NM_008554	17173	Mm.196417	NM_008554	ENSMUSG00000009248	Ascl2	2410083I15Rik|Mash2|bHLHa45	achaete-scute family bHLH transcription factor 2	protein-coding
mm_29411.1	chr3	108955645	108955655	-	1	NA	intron (NM_025723, intron 5 of 7)	intron (NM_025723, intron 5 of 7)	15093	NM_001078646	66715	Mm.158124	NM_025723	ENSMUSG00000045662	Henmt1	4921515J06Rik|Hen1|mHEN1	HEN1 methyltransferase homolog 1 (Arabidopsis)	protein-coding
mm_148605.1	chr19	5308303	5308313	+	1	NA	3' UTR (NM_001024717, exon 3 of 3)	3' UTR (NM_001024717, exon 3 of 3)	9977	NM_001024717	545276	Mm.447174	NM_001024717	ENSMUSG00000047658	Gal3st3	-	galactose-3-O-sulfotransferase 3	protein-coding
mm_146863.1	chr18	24530204	24530245	-	1	NA	promoter-TSS (NM_144861)	promoter-TSS (NM_144861)	-20	NM_144861	225283	Mm.28427	NM_144861	ENSMUSG00000040446	Rprd1a	C77387|mKIAA4077	regulation of nuclear pre-mRNA domain containing 1A	protein-coding
mm_129726.1	chr15	82016135	82016170	-	1	NA	promoter-TSS (NM_010247)	promoter-TSS (NM_010247)	-12	NM_134095	28075	Mm.474453	NM_134095	ENSMUSG00000022472	Desi1	AI427858|AI850401|D15Wsu75e|DeSI-1|Fam152b|Pppde2	desumoylating isopeptidase 1	protein-coding
mm_145226.1	chr18	50083906	50083909	+	1	NA	intron (NM_134131, intron 1 of 1)	intron (NM_134131, intron 1 of 1)	30625	NM_134131	106869	Mm.27740	NM_134131	ENSMUSG00000062210	Tnfaip8	AA987150|E130304C20Rik|ENSMUSG00000073567|Gg2-1|Gm10539|Nded|Ssc-2|Tipe	tumor necrosis factor, alpha-induced protein 8	protein-coding
mm_119998.1	chr14	55617998	55618011	+	1	NA	promoter-TSS (NM_020002)	promoter-TSS (NM_020002)	-162	NM_020002	56739	Mm.23149	NM_020002	ENSMUSG00000002324	Rec8	Rec8L1|mrec	REC8 meiotic recombination protein	protein-coding
mm_47529.1	chr5	124187151	124187225	-	1	NA	promoter-TSS (NM_001289472)	promoter-TSS (NM_001289472)	-6	NM_001289472	19679	Mm.44261	NM_011256	ENSMUSG00000029406	Pitpnm2	NIR3|RDGBA2|Rdgb2|mKIAA1457	phosphatidylinositol transfer protein, membrane-associated 2	protein-coding
mm_98596.1	chr11	95824579	95824593	+	1	NA	promoter-TSS (NM_153104)	promoter-TSS (NM_153104)	86	NM_153104	237928	Mm.133075	NM_153104	ENSMUSG00000050860	Phospho1	D11Moh36|Phospo1	phosphatase, orphan 1	protein-coding
mm_76550.1	chr8	88334179	88334191	-	1	NA	exon (NM_012047, exon 14 of 17)	exon (NM_012047, exon 14 of 17)	28006	NM_012047	26992	Mm.5400	NM_012047	ENSMUSG00000031660	Brd7	BP75|CELTIX1|Ptpn13ip	bromodomain containing 7	protein-coding
mm_5789.1	chr1	51896023	51896031	-	1	NA	intron (NM_001290982, intron 1 of 28)	intron (NM_001290982, intron 1 of 28)	19951	NM_001290982	17912	Mm.3390	NM_010863	ENSMUSG00000018417	Myo1b	AA406997|MIH-L|MMIa	myosin IB	protein-coding
mm_130897.1	chr15	102398695	102398711	-	1	NA	Intergenic	Intergenic	-7613	NM_013672	20683	Mm.4618	NM_013672	ENSMUSG00000001280	Sp1	1110003E12Rik|AA450830|AI845540|Sp1-1	trans-acting transcription factor 1	protein-coding
mm_115586.1	chr13	11826698	11826713	-	1	NA	intron (NM_023868, intron 15 of 104)	IMPB_01|Satellite|Satellite	280240	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding
mm_141324.1	chr17	28441690	28441706	-	1	NA	intron (NM_010220, intron 1 of 10)	intron (NM_010220, intron 1 of 10)	44451	NM_010220	14229	Mm.276405	NM_010220	ENSMUSG00000024222	Fkbp5	D17Ertd592e|Dit1|FKBP-5|FKBP51	FK506 binding protein 5	protein-coding
mm_140777.1	chr17	17877019	17877031	-	1	NA	exon (NM_013521, exon 2 of 2)	exon (NM_013521, exon 2 of 2)	6914	NM_013521	14293	Mm.56951	NM_013521	ENSMUSG00000045551	Fpr1	FPR|LXA4R|fMLF-R	formyl peptide receptor 1	protein-coding
mm_121502.1	chr14	121929679	121929684	+	1	NA	intron (NM_026861, intron 4 of 8)	intron (NM_026861, intron 4 of 8)	-13907	NM_182806	110168	Mm.37405	NM_182806	ENSMUSG00000050350	Gpr18	-	G protein-coupled receptor 18	protein-coding
mm_132817.1	chr16	45223940	45223951	+	1	NA	promoter-TSS (NM_001037719)	promoter-TSS (NM_001037719)	-392	NM_001037719	208154	Mm.38199	NM_177584	ENSMUSG00000052013	Btla	A630002H24	B and T lymphocyte associated	protein-coding
mm_105127.1	chr11	101278928	101278969	-	1	NA	promoter-TSS (NM_026618)	promoter-TSS (NM_026618)	0	NM_026618	52469	Mm.52	NM_026618	ENSMUSG00000017188	Coa3	1810033A19Rik|Ccdc56|D11Ertd99e|HSPC009	cytochrome C oxidase assembly factor 3	protein-coding
mm_106566.1	chr11	120633670	120633676	-	1	NA	promoter-TSS (NM_010756)	promoter-TSS (NM_010756)	-126	NM_010756	17134	Mm.268010	NM_010756	ENSMUSG00000051510	Mafg	AA545192|C630022N07Rik	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein G (avian)	protein-coding
mm_49760.1	chr6	34774035	34774040	+	1	NA	3' UTR (NM_145575, exon 12 of 12)	3' UTR (NM_145575, exon 12 of 12)	-6395	NM_001289657	76223	Mm.150047	NM_178630	ENSMUSG00000038836	Agbl3	2900053G10Rik|4930431N21Rik|6530406M24Rik|CCP3	ATP/GTP binding protein-like 3	protein-coding
mm_45228.1	chr5	53510574	53510604	-	1	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	-45190	NM_001080928	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_115254.1	chr13	110397970	110397992	+	1	NA	exon (NM_152804, exon 8 of 14)	exon (NM_152804, exon 8 of 14)	2937	NM_152804	20620	Mm.380	NM_152804	ENSMUSG00000021701	Plk2	Snk	polo-like kinase 2	protein-coding
mm_165853.1	chr4	11386614	11386629	-	1	NA	5' UTR (NM_001290383, exon 1 of 16)	5' UTR (NM_001290383, exon 1 of 16)	157	NM_001347052	207920	Mm.387719	NM_194055	ENSMUSG00000040728	Esrp1	2210008M09Rik|A630065D16|BC031468|Rbm35a	epithelial splicing regulatory protein 1	protein-coding
mm_30945.1	chr4	33077373	33077379	+	1	NA	intron (NM_008076, intron 2 of 8)	intron (NM_008076, intron 2 of 8)	14264	NM_008076	14409	Mm.6227	NM_008076	ENSMUSG00000023267	Gabrr2	-	gamma-aminobutyric acid (GABA) C receptor, subunit rho 2	protein-coding
mm_142498.1	chr17	46030952	46031016	-	1	NA	intron (NM_001317041, intron 1 of 6)	CpG	1393	NM_001287058	22339	Mm.282184	NM_009505	ENSMUSG00000023951	Vegfa	Vegf|Vpf	vascular endothelial growth factor A	protein-coding
mm_153288.1	chr19	37315143	37315145	-	1	NA	intron (NM_031156, intron 5 of 23)	intron (NM_031156, intron 5 of 23)	15469	NM_031156	15925	Mm.28366	NM_031156	ENSMUSG00000056999	Ide	1300012G03Rik|4833415K22Rik|AA675336|AI507533	insulin degrading enzyme	protein-coding
mm_75785.1	chr8	70093581	70093602	-	1	NA	3' UTR (NM_007789, exon 15 of 15)	3' UTR (NM_007789, exon 15 of 15)	8995	NR_106033	102465646		NR_106033	ENSMUSG00000099042	Mir7066	Gm27290|mmu-mir-7066	microRNA 7066	ncRNA
mm_11122.1	chr2	28222428	28222461	+	1	NA	intron (NM_019498, intron 4 of 5)	intron (NM_019498, intron 4 of 5)	16755	NM_019498	56177	Mm.43278	NM_019498	ENSMUSG00000026833	Olfm1	AMY|AW742568|Noe1|OlfA|Pancortin|Pancortin3	olfactomedin 1	protein-coding
mm_16959.1	chr2	17411157	17411161	-	1	NA	intron (NM_028757, intron 4 of 6)	intron (NM_028757, intron 4 of 6)	-152355	NR_105847	102465964		NR_105847	ENSMUSG00000099161	Mir6419	Gm27713|mmu-mir-6419	microRNA 6419	ncRNA
mm_109128.1	chr12	105784696	105784743	+	1	NA	promoter-TSS (NM_001347440)	promoter-TSS (NM_001347440)	22	NM_001347440	18789	Mm.255877	NM_011112	ENSMUSG00000021111	Papola	Pap|PapIII|Plap	poly (A) polymerase alpha	protein-coding
mm_56790.1	chr6	116645156	116645181	-	1	NA	TTS (NR_106010)	TTS (NR_106010)	879	NR_106010	102466793		NR_106010	ENSMUSG00000098334	Mir7043	Gm27776|mmu-mir-7043	microRNA 7043	ncRNA
mm_162021.1	chr19	46035500	46035500	-	1	NA	exon (NM_010697, exon 6 of 11)	exon (NM_010697, exon 6 of 11)	4121	NM_010697	16825	Mm.327442	NM_010697	ENSMUSG00000025223	Ldb1	CLIM2|NLI	LIM domain binding 1	protein-coding
mm_9489.1	chr1	173729355	173729365	-	1	NA	exon (NM_001204910, exon 5 of 8)	exon (NM_001204910, exon 5 of 8)	12449	NM_001204910	226691	Mm.440876	NM_001204910	ENSMUSG00000073490	Ifi207	AI607873|Pyhin-A	interferon activated gene 207	protein-coding
mm_144557.1	chr18	31635075	31635138	+	1	NA	intron (NM_172965, intron 1 of 20)	CpG	723	NM_172965	269003	Mm.194538	NM_172965	ENSMUSG00000024260	Sap130	2610304F09Rik|6720406D06	Sin3A associated protein	protein-coding
mm_143636.1	chr17	78985429	78985468	-	1	NA	intron (NM_001171004, intron 2 of 18)	intron (NM_001171004, intron 2 of 18)	23057	NM_001171005	75292	Mm.252776	NM_029239	ENSMUSG00000024070	Prkd3	4930557O20Rik|5730497N19Rik|PKD3|Pkcnu|Prkcn	protein kinase D3	protein-coding
mm_147763.1	chr18	61375171	61375186	-	1	NA	intron (NM_133249, intron 1 of 11)	(TG)n|Simple_repeat|Simple_repeat	25253	NM_133249	170826	Mm.415302	NM_133249	ENSMUSG00000033871	Ppargc1b	4631412G21Rik|Perc	peroxisome proliferative activated receptor, gamma, coactivator 1 beta	protein-coding
mm_22731.1	chr3	19689812	19689823	+	1	NA	intron (NM_001081281, intron 9 of 9)	intron (NM_001081281, intron 9 of 9)	5579	NM_205769	12918	Mm.290689	NM_205769	ENSMUSG00000049796	Crh	CRF|Gm1347	corticotropin releasing hormone	protein-coding
mm_16414.1	chr2	180099839	180099847	+	1	NA	non-coding (NR_102309, exon 3 of 3)	non-coding (NR_102309, exon 3 of 3)	4564	NR_102309	99296	Mm.285360	NM_133849	ENSMUSG00000039059	Hrh3	AW049250|H3R|HH3R	histamine receptor H3	protein-coding
mm_38449.1	chr4	140106254	140106286	-	1	NA	intron (NM_198610, intron 3 of 9)	intron (NM_198610, intron 3 of 9)	-138244	NM_173427	242721	Mm.60400	NM_173427	ENSMUSG00000078234	Klhdc7a	B230308G19Rik	kelch domain containing 7A	protein-coding
mm_171111.1	chr3	136443776	136443778	-	1	NA	non-coding (NR_040592, exon 3 of 5)	non-coding (NR_040592, exon 3 of 5)	5572	NR_040592	70055	Mm.261063	NR_040592	ENSMUSG00000099508	1700030L20Rik	-	RIKEN cDNA 1700030L20 gene	ncRNA
mm_125822.1	chr15	74957151	74957160	+	1	NA	intron (NM_001164039, intron 2 of 4)	intron (NM_001164039, intron 2 of 4)	2049	NM_001164040	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_106537.1	chr11	120578733	120578757	-	1	NA	3' UTR (NM_133796, exon 6 of 6)	3' UTR (NM_133796, exon 6 of 6)	2875	NM_133796	192662	Mm.30016	NM_133796	ENSMUSG00000025132	Arhgdia	5330430M07Rik|Gdi-1|Rho-GDI|RhoDGI|RhoGDI-1	Rho GDP dissociation inhibitor (GDI) alpha	protein-coding
mm_29329.1	chr3	108085347	108085412	-	1	NA	promoter-TSS (NM_001289720)	promoter-TSS (NM_001289720)	23	NM_001346665	109674	Mm.274335	NM_028779	ENSMUSG00000027889	Ampd2	1200014F01Rik|AI552571|Ampd-2|m4521Dajl	adenosine monophosphate deaminase 2	protein-coding
mm_22517.1	chr3	7624622	7624642	+	1	NA	Intergenic	L2a|LINE|L2	-10872	NM_001313888	16196	Mm.3825	NM_008371	ENSMUSG00000040329	Il7	A630026I06Rik|Il-7|hlb368	interleukin 7	protein-coding
mm_45773.1	chr5	87092008	87092022	-	1	NA	exon (NM_001029867, exon 1 of 6)	exon (NM_001029867, exon 1 of 6)	540	NM_001029867	231396	Mm.439851	NM_001029867	ENSMUSG00000070704	Ugt2b36	-	UDP glucuronosyltransferase 2 family, polypeptide B36	protein-coding
mm_128801.1	chr15	66935116	66935123	-	1	NA	intron (NM_008681, intron 14 of 15)	intron (NM_008681, intron 14 of 15)	34522	NM_008681	17988	Mm.30837	NM_008681	ENSMUSG00000005125	Ndrg1	CAP43|CMT4D|DRG1|HMSNL|NMSL|Ndr1|Ndrl|PROXY1|RTP|TDD5	N-myc downstream regulated gene 1	protein-coding
mm_95795.1	chr11	55098105	55098129	+	1	NA	5' UTR (NM_010299, exon 1 of 4)	5' UTR (NM_010299, exon 1 of 4)	132	NM_010299	14667	Mm.287807	NM_010299	ENSMUSG00000000594	Gm2a	AA408702|AW215435|GM2-AP|SAP-3	GM2 ganglioside activator protein	protein-coding
mm_108768.1	chr12	89642382	89642394	+	1	NA	intron (NM_172544, intron 14 of 19)	(T)n|Simple_repeat|Simple_repeat	-170095	NM_001252074	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding
mm_37154.1	chr4	117121287	117121318	-	1	NA	non-coding (NR_024078, exon 6 of 7)	non-coding (NR_024078, exon 6 of 7)	4423	NR_024078	78611	Mm.446227	NM_001033187		Btbd19	9530048O09Rik|BB115071	BTB (POZ) domain containing 19	ncRNA
mm_20318.1	chr2	127315300	127315304	-	1	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	-20857	NM_010090	13537	Mm.4729	NM_010090	ENSMUSG00000027368	Dusp2	PAC1	dual specificity phosphatase 2	protein-coding
mm_40571.1	chr5	63784846	63784847	+	1	NA	intron (NM_177006, intron 3 of 6)	intron (NM_177006, intron 3 of 6)	-27649	NM_029554	76261	Mm.38143	NM_029554	ENSMUSG00000060512	0610040J01Rik	AI662686	RIKEN cDNA 0610040J01 gene	protein-coding
mm_154594.1	chrX	7584449	7584451	+	1	NA	intron (NM_001199348, intron 1 of 12)	intron (NM_001199348, intron 1 of 12)	3967	NM_001199348	20371	Mm.182291	NM_054039	ENSMUSG00000039521	Foxp3	JM2|scurfin|sf	forkhead box P3	protein-coding
mm_70992.1	chr8	27447665	27447681	+	1	NA	promoter-TSS (NM_027618)	promoter-TSS (NM_027618)	3	NM_027618	70952	Mm.158160	NM_026256	ENSMUSG00000063932	Poteg	4921537P18Rik|4930456F22Rik|Gsarp1|Gsarp2	POTE ankyrin domain family, member G	protein-coding
mm_106944.1	chr12	8771041	8771062	+	1	NA	promoter-TSS (NM_011519)	promoter-TSS (NM_011519)	-345	NM_011519	20969	Mm.2580	NM_011519	ENSMUSG00000020592	Sdc1	AA408134|AA409076|CD138|Sstn|Synd|Synd1|syn-1	syndecan 1	protein-coding
mm_26391.1	chr3	142572657	142572671	+	1	NA	exon (NM_018734, exon 11 of 11)	exon (NM_018734, exon 11 of 11)	12168	NM_001289493	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_116950.1	chr13	56135657	56135668	-	1	NA	promoter-TSS (NM_001159515)	promoter-TSS (NM_001159515)	-112	NM_001159513	26914	Mm.283802	NM_012015	ENSMUSG00000015937	H2afy	H2AF12M|mH2a1|macroH2A1	H2A histone family, member Y	protein-coding
mm_66786.1	chr7	47008819	47008822	-	1	NA	promoter-TSS (NM_175318)	promoter-TSS (NM_175318)	-406	NM_175318	101685	Mm.155687	NM_175318	ENSMUSG00000049516	Spty2d1	5830435K17Rik|AI852426|P16H6	SPT2, Suppressor of Ty, domain containing 1 (S. cerevisiae)	protein-coding
mm_109053.1	chr12	104339364	104339381	+	1	NA	intron (NM_011458, intron 1 of 4)	CT-rich|Low_complexity|Low_complexity	886	NM_011458	20714	Mm.291569	NM_011458	ENSMUSG00000058207	Serpina3k	1300001I07Rik|D12Rp54|MMCM2|MMSpi2|RP54|Spi-2|Spi2|contrapsin	serine (or cysteine) peptidase inhibitor, clade A, member 3K	protein-coding
mm_97180.1	chr11	75533404	75533414	+	1	NA	intron (NM_173388, intron 2 of 13)	intron (NM_173388, intron 2 of 13)	1297	NM_001199283	215113	Mm.11186	NM_173388	ENSMUSG00000038178	Slc43a2	7630402D21Rik|BC042513|Lat4	solute carrier family 43, member 2	protein-coding
mm_25081.1	chr3	100426434	100426457	+	1	NA	promoter-TSS (NR_040543)	promoter-TSS (NR_040543)	40	NR_040543	73806	Mm.396549	NR_040543	ENSMUSG00000086923	4930406D18Rik	-	RIKEN cDNA 4930406D18 gene	ncRNA
mm_8010.1	chr1	134803743	134803753	-	1	NA	promoter-TSS (NR_015606)	promoter-TSS (NR_015606)	-27	NR_015606	329251	Mm.188709	NM_001081307	ENSMUSG00000073557	Ppp1r12b	1810037O03Rik|9530009M10Rik|AI132431|Mypt2	protein phosphatase 1, regulatory (inhibitor) subunit 12B	protein-coding
mm_19840.1	chr2	112561699	112561704	-	1	NA	intron (NM_001165935, intron 1 of 4)	RMER19C|LTR|ERVK	2019	NM_001165935	74268	Mm.315125	NM_028844	ENSMUSG00000003604	Aven	1700013A01Rik|1700056A21Rik|mAven-L|mAven-S	apoptosis, caspase activation inhibitor	protein-coding
mm_75967.1	chr8	71757586	71757597	-	1	NA	Intergenic	Intergenic	-31910	NM_028715	74015	Mm.22025	NM_028715	ENSMUSG00000070000	Fcho1	3322402E17Rik|N28152	FCH domain only 1	protein-coding
mm_33273.1	chr4	128318975	128319011	+	1	NA	intron (NM_001281955, intron 10 of 70)	B4|SINE|B4	57949	NR_130980	75242	Mm.488254	NR_130980		Hmgb4os	4930546G22Rik	high-mobility group box 4, opposite strand	ncRNA
mm_155199.1	chrX	56609844	56609864	+	1	NA	promoter-TSS (NM_172780)	promoter-TSS (NM_172780)	19	NM_172780	236794	Mm.17815	NM_172780	ENSMUSG00000060681	Slc9a6	3732426M05|6430520C02Rik|NHE6|mKIAA0267	solute carrier family 9 (sodium/hydrogen exchanger), member 6	protein-coding
mm_2093.1	chr1	87701244	87701252	+	1	NA	exon (NM_001110192, exon 16 of 27)	exon (NM_001110192, exon 16 of 27)	-54763	NM_029846	77040	Mm.272972	NM_029846	ENSMUSG00000026289	Atg16l1	1500009K01Rik|Apg16l|Atg16l|WDR30	autophagy related 16-like 1 (S. cerevisiae)	protein-coding
mm_6757.1	chr1	84054564	84054584	-	1	NA	intron (NM_001003948, intron 2 of 2)	intron (NM_001003948, intron 2 of 2)	164387	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_33212.1	chr4	126557040	126557048	+	1	NA	promoter-TSS (NM_175554)	promoter-TSS (NM_175554)	64	NM_175554	269582	Mm.243962	NM_175554	ENSMUSG00000042489	Clspn	B130025E01|C85083|E130314M08Rik	claspin	protein-coding
mm_1046.1	chr1	58795932	58795945	+	1	NA	intron (NM_009812, intron 1 of 8)	intron (NM_009812, intron 1 of 8)	564	NM_009812	12370	Mm.336851	NM_009812	ENSMUSG00000026029	Casp8	CASP-8|FLICE|MACH|Mch5	caspase 8	protein-coding
mm_76350.1	chr8	84746270	84746286	-	1	NA	intron (NM_001297601, intron 2 of 8)	intron (NM_001297601, intron 2 of 8)	28091	NM_001081981	18032	Mm.9394	NM_010906	ENSMUSG00000001911	Nfix	CTF|NF-I/X|NF1-X|NFI-X	nuclear factor I/X	protein-coding
mm_125440.1	chr15	44619552	44619630	+	1	NA	promoter-TSS (NM_019480)	promoter-TSS (NM_019480)	-50	NM_019480	55960	Mm.287896	NM_019480	ENSMUSG00000022339	Ebag9	AI835379|Rcas1	estrogen receptor-binding fragment-associated gene 9	protein-coding
mm_111398.1	chr12	90738956	90738975	-	1	NA	promoter-TSS (NM_010050)	promoter-TSS (NM_010050)	72	NM_010050	13371	Mm.21389	NM_010050	ENSMUSG00000007682	Dio2	5DII|AI324267|DIOII	deiodinase, iodothyronine, type II	protein-coding
mm_11205.1	chr2	29191632	29191644	+	1	NA	Intergenic	Intergenic	56461	NM_001305805	171171	Mm.442448	NM_133500	ENSMUSG00000035513	Ntng2	2610016D08Rik|Lmnt2	netrin G2	protein-coding
mm_43790.1	chr5	142692458	142692481	+	1	NA	Intergenic	Intergenic	-9632	NM_146257	243328	Mm.125942	NM_146257	ENSMUSG00000050822	Slc29a4	ENT4|mPMAT	solute carrier family 29 (nucleoside transporters), member 4	protein-coding
mm_127092.1	chr15	97784468	97784475	+	1	NA	5' UTR (NM_026353, exon 1 of 3)	5' UTR (NM_026353, exon 1 of 3)	106	NM_026353	67739	Mm.28955	NM_026353	ENSMUSG00000081534	Slc48a1	4930570C03Rik	solute carrier family 48 (heme transporter), member 1	protein-coding
mm_145146.1	chr18	45559930	45559943	+	1	NA	promoter-TSS (NM_080465)	promoter-TSS (NM_080465)	-218	NM_080465	140492	Mm.411614	NM_080465	ENSMUSG00000054477	Kcnn2	KCa2.2|SK2|SKCA2|bc|fri	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2	protein-coding
mm_62284.1	chr7	99859124	99859140	+	1	NA	promoter-TSS (NM_001164258)	promoter-TSS (NM_001164258)	-86	NM_001164258	446101	Mm.440757	NM_001164258	ENSMUSG00000035211	Xrra1	AI449753	X-ray radiation resistance associated 1	protein-coding
mm_16756.1	chr2	9868874	9868885	-	1	NA	exon (NM_008091, exon 4 of 6)	exon (NM_008091, exon 4 of 6)	9721	NM_008091	14462	Mm.313866	NM_008091	ENSMUSG00000015619	Gata3	Gata-3|jal	GATA binding protein 3	protein-coding
mm_26888.1	chr3	18228616	18228624	-	1	NA	intron (NM_007825, intron 1 of 5)	intron (NM_007825, intron 1 of 5)	14718	NM_007825	13123	Mm.316000	NM_007825	ENSMUSG00000039519	Cyp7b1	AW261589|D3Ertd552e|hct-1	cytochrome P450, family 7, subfamily b, polypeptide 1	protein-coding
mm_26140.1	chr3	137918865	137918867	+	1	NA	intron (NM_019920, intron 1 of 6)	intron (NM_019920, intron 1 of 6)	311	NM_019920	56692	Mm.331392	NM_019920	ENSMUSG00000091512	Lamtor3	AW556229|Map2k1ip1|Mapbp|Mapksp1|Mp1	late endosomal/lysosomal adaptor, MAPK and MTOR activator 3	protein-coding
mm_3729.1	chr1	155062302	155062319	+	1	NA	Intergenic	Intergenic	37326	NM_010500	15939	Mm.12246	NM_010500	ENSMUSG00000056708	Ier5	-	immediate early response 5	protein-coding
mm_85052.1	chr9	90114359	90114383	-	1	NA	intron (NM_001039147, intron 1 of 12)	CpG	449	NM_001039147	21761	Mm.426209	NM_024431	ENSMUSG00000062270	Morf4l1	MORFRG15|MRG15|TEG-189|Tex189|mKIAA4002	mortality factor 4 like 1	protein-coding
mm_61835.1	chr7	88281380	88281505	+	1	NA	exon (NM_009982, exon 2 of 7)	exon (NM_009982, exon 2 of 7)	3357	NM_001311790	13032	Mm.89295	NM_009982	ENSMUSG00000030560	Ctsc	AI047818|CatC|DPP1|DPPI	cathepsin C	protein-coding
mm_13159.1	chr2	92577454	92577457	+	1	NA	Intergenic	Intergenic	-14751	NR_106080	102466819		NR_106080	ENSMUSG00000099223	Mir7221	Gm27378|mmu-mir-7221	microRNA 7221	ncRNA
mm_52166.1	chr6	98276505	98276525	+	1	NA	intron (NM_001128092, intron 2 of 3)	intron (NM_001128092, intron 2 of 3)	66239	NM_001128092	330390	Mm.484161	NM_001128092	ENSMUSG00000090667	Gm765	-	predicted gene 765	protein-coding
mm_61139.1	chr7	56239785	56239828	+	1	NA	promoter-TSS (NM_021879)	promoter-TSS (NM_021879)	35	NM_021879	18431	Mm.137052	NM_021879	ENSMUSG00000030450	Oca2	D7H15S12|D7Icr28RN|D7Nic1|p|p<cas>	oculocutaneous albinism II	protein-coding
mm_88190.1	chr10	70026291	70026295	+	1	NA	3' UTR (NM_170688, exon 43 of 43)	3' UTR (NM_170688, exon 43 of 43)	-70828	NM_001111121	76551	Mm.281741	NM_001111121	ENSMUSG00000048701	Ccdc6	2810012H18Rik|AA536681|AA960498|AW061011	coiled-coil domain containing 6	protein-coding
mm_117637.1	chr13	92451257	92451276	-	1	NA	intron (NM_001163627, intron 5 of 5)	intron (NM_001163627, intron 5 of 5)	25297	NM_175455	218440	Mm.213623	NM_175455	ENSMUSG00000045034	Ankrd34b	6430502M16Rik|DP58	ankyrin repeat domain 34B	protein-coding
mm_158584.1	chrX	150812933	150812973	-	1	NA	intron (NM_030700, intron 1 of 12)	CpG	750	NM_001199246	80884	Mm.22575	NM_030700	ENSMUSG00000025268	Maged2	4833439A22Rik|Mage-d2|ORF1	melanoma antigen, family D, 2	protein-coding
mm_135289.1	chr16	38522588	38522652	-	1	NA	promoter-TSS (NM_024273)	promoter-TSS (NM_024273)	43	NM_024273	76916	Mm.132231	NM_024273	ENSMUSG00000002846	Timmdc1	2810021C21Rik|4930455C21Rik|AV135763	translocase of inner mitochondrial membrane domain containing 1	protein-coding
mm_167242.1	chr8	20550211	20550227	+	1	NA	Intergenic	CpG	-64708	NM_001270553	100861668	Mm.491087	NM_001270553	ENSMUSG00000095294	Gm21119	-	predicted gene, 21119	protein-coding
mm_24039.1	chr3	87846726	87846772	+	1	NA	promoter-TSS (NM_021309)	promoter-TSS (NM_021309)	-6	NM_001025571	27371	Mm.86361	NM_021309	ENSMUSG00000028071	Sh2d2a	Lad|Ribp|Tsad	SH2 domain containing 2A	protein-coding
mm_111313.1	chr12	85824497	85824505	-	1	NA	promoter-TSS (NM_001081423)	promoter-TSS (NM_001081423)	44	NM_021446	58520	Mm.143795	NM_021446	ENSMUSG00000021252	0610007P14Rik	1190004E09Rik|AU019315|C77855|ORF11	RIKEN cDNA 0610007P14 gene	protein-coding
mm_19745.1	chr2	104816942	104816955	-	1	NA	promoter-TSS (NM_001123327)	promoter-TSS (NM_001123327)	-252	NM_001123327	99003	Mm.274314	NM_001123327	ENSMUSG00000074994	Qser1	4732486I23Rik|AI502974	glutamine and serine rich 1	protein-coding
mm_20063.1	chr2	120353095	120353143	-	1	NA	promoter-TSS (NM_178851)	promoter-TSS (NM_178851)	14	NM_178851	269338	Mm.246131	NM_147153	ENSMUSG00000027291	Vps39	A230065P22Rik|AW743070|Vam6|Vam6P|mVam6	VPS39 HOPS complex subunit	protein-coding
mm_48480.1	chr5	141000657	141000679	-	1	NA	promoter-TSS (NM_175362)	promoter-TSS (NM_175362)	-72	NM_175362	108723	Mm.46187	NM_175362	ENSMUSG00000036526	Card11	0610008L17Rik|2410011D02Rik|BIMP3|CARMA1	caspase recruitment domain family, member 11	protein-coding
mm_49079.1	chr6	6299462	6299475	+	1	NA	intron (NR_136905, intron 1 of 3)	intron (NR_136905, intron 1 of 3)	50809	NR_136905	101056138	Mm.389085	NR_136904	ENSMUSG00000093482	Gm20619	-	predicted gene 20619	ncRNA
mm_136939.1	chr17	14249834	14249856	+	1	NA	Intergenic	Intergenic	-29661	NM_022315	64074	Mm.30162	NM_022315	ENSMUSG00000023886	Smoc2	1700056C05Rik|5430426J21Rik|Smoc2l	SPARC related modular calcium binding 2	protein-coding
mm_111689.1	chr12	103457279	103457282	-	1	NA	promoter-TSS (NM_145449)	promoter-TSS (NM_145449)	-57	NM_145449	217845	Mm.298416	NM_145449	ENSMUSG00000021208	Ifi27l2b	1810023F06Rik|ISG12(b2)	interferon, alpha-inducible protein 27 like 2B	protein-coding
mm_107238.1	chr12	26478471	26478481	+	1	NA	3' UTR (NM_020557, exon 5 of 5)	3' UTR (NM_020557, exon 5 of 5)	9261	NM_020557	22169	Mm.271839	NM_020557	ENSMUSG00000020638	Cmpk2	1200004E04Rik|TDKI|Tyki	cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial	protein-coding
mm_64195.1	chr7	141465100	141465133	+	1	NA	intron (NM_001025103, intron 6 of 9)	intron (NM_001025103, intron 6 of 9)	-2246	NM_009842	12476	Mm.30246	NM_009842	ENSMUSG00000025510	Cd151	PETA-3|SFA-1|Tspan24	CD151 antigen	protein-coding
mm_171304.1	chr3	93943541	93943547	-	1	NA	promoter-TSS (NM_001163730)	promoter-TSS (NM_001163730)	-1	NM_001163730	668359	Mm.80593	NM_001163730	ENSMUSG00000094328	Gm9125	EG668359	predicted gene 9125	protein-coding
mm_41986.1	chr5	107688159	107688179	+	1	NA	Intergenic	CpG	15311	NR_045871	654809	Mm.399159	NR_045871	ENSMUSG00000106333	4930428O21Rik	-	RIKEN cDNA 4930428O21 gene	ncRNA
mm_140840.1	chr17	23670944	23670944	-	1	NA	intron (NM_001008425, intron 1 of 12)	intron (NM_001008425, intron 1 of 12)	-2664	NM_181821	353502	Mm.359030	NM_181821	ENSMUSG00000023904	Hcfc1r1	HPIP	host cell factor C1 regulator 1 (XPO1-dependent)	protein-coding
mm_130014.1	chr15	88315628	88315637	-	1	NA	intron (NR_045281, intron 1 of 2)	intron (NR_045281, intron 1 of 2)	758	NR_045281	328579	Mm.146839	NR_045281		B230214G05Rik	B230214G05	RIKEN cDNA B230214G05 gene	ncRNA
mm_3287.1	chr1	136674691	136674699	+	1	NA	Intergenic	MER5B|DNA|hAT-Charlie	-8701	NR_045324	100503460	Mm.30630	NR_045324	ENSMUSG00000097113	Gm19705	-	predicted gene, 19705	ncRNA
mm_118039.1	chr13	101692606	101692621	-	1	NA	promoter-TSS (NM_001024955)	promoter-TSS (NM_001024955)	17	NM_001024955	18708	Mm.259333	NM_001024955	ENSMUSG00000041417	Pik3r1	PI3K|p50alpha|p55alpha|p85alpha	phosphatidylinositol 3-kinase, regulatory subunit, polypeptide 1 (p85 alpha)	protein-coding
mm_72342.1	chr8	79546287	79546332	+	1	NA	Intergenic	RLTR9D|LTR|ERVK	-93367	NM_001256033	73945	Mm.34348	NM_001081164	ENSMUSG00000036990	Otud4	4930431L18Rik|AI449692|D8Ertd69e|mKIAA1046	OTU domain containing 4	protein-coding
mm_47666.1	chr5	126727276	126727300	-	1	NA	Intergenic	MTEa|LTR|ERVL-MaLR	-303501	NR_040685	71247	Mm.399586	NR_040685	ENSMUSG00000105490	4933438B17Rik	-	RIKEN cDNA 4933438B17 gene	ncRNA
mm_98765.1	chr11	96618504	96618506	+	1	NA	intron (NM_001033186, intron 4 of 12)	(TTTTG)n|Simple_repeat|Simple_repeat	153914	NM_001177898	78473	Mm.395840	NM_001033186	ENSMUSG00000057058	Skap1	1700091G21Rik|Scap1|Skap-55	src family associated phosphoprotein 1	protein-coding
mm_64095.1	chr7	140998134	140998139	+	1	NA	Intergenic	Intergenic	12608	NM_025378	66141	Mm.141021	NM_025378	ENSMUSG00000025492	Ifitm3	1110004C05Rik|Cd225|Cdw217|DSPA2b|Fgls|IP15|mil-1	interferon induced transmembrane protein 3	protein-coding
mm_112346.1	chr12	117151240	117151250	-	1	NA	promoter-TSS (NR_033538)	promoter-TSS (NR_033538)	24	NR_033538	100038689	Mm.445351	NR_033538	ENSMUSG00000099907	Gm10421	ENSMUSG00000072792	predicted gene 10421	ncRNA
mm_57295.1	chr6	124450160	124450174	-	1	NA	intron (NM_001346656, intron 10 of 17)	ID4|SINE|ID	12577	NM_001346656	232370	Mm.193701	NM_153508	ENSMUSG00000008153	Clstn3	CSTN3|Cs3|Cst-3|alc-beta	calsyntenin 3	protein-coding
mm_123925.1	chr14	73365697	73365708	-	1	NA	intron (NM_008410, intron 4 of 5)	intron (NM_008410, intron 4 of 5)	19569	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_19857.1	chr2	113829589	113829604	-	1	NA	promoter-TSS (NM_009162)	promoter-TSS (NM_009162)	-505	NM_009162	20394	Mm.4836	NM_009162	ENSMUSG00000023236	Scg5	7B2|AI325031|Sgne-1|Sgne1	secretogranin V	protein-coding
mm_2899.1	chr1	131932119	131932134	+	1	NA	3' UTR (NM_001145804, exon 7 of 7)	3' UTR (NM_001145804, exon 7 of 7)	21668	NM_001145804	98415	Mm.246869	NM_175294	ENSMUSG00000026434	Nucks1	2700010L10Rik|8430423A01Rik|AI647518|C78391|Nucks	nuclear casein kinase and cyclin-dependent kinase substrate 1	protein-coding
mm_80615.1	chr9	88327633	88327663	+	1	NA	promoter-TSS (NM_011851)	promoter-TSS (NM_011851)	39	NM_011851	23959	Mm.244235	NM_011851	ENSMUSG00000032420	Nt5e	2210401F01Rik|5'-NT|AI447961|CD73|NT|Nt5|eNT	5' nucleotidase, ecto	protein-coding
mm_61019.1	chr7	49398972	49398993	+	1	NA	intron (NM_175272, intron 4 of 37)	intron (NM_175272, intron 4 of 37)	152793	NM_175272	78286	Mm.333881	NM_175272	ENSMUSG00000052512	Nav2	5330421F07Rik|AU067780|BQ960892|HELAD1|POMFIL2|RAINB1|RAINB2|Unc53H2|mKIAA3015	neuron navigator 2	protein-coding
mm_164975.1	chr19	8724384	8724412	+	1	NA	intron (NR_002896, intron 2 of 9)	intron (NR_002896, intron 2 of 9)	911	NR_002896	83673	Mm.292489	NR_002896	ENSMUSG00000108414	Snhg1	-	small nucleolar RNA host gene 1	ncRNA
mm_154001.1	chr19	52953099	52953127	-	1	NA	Intergenic	Intergenic	29932	NR_030678	100043450	Mm.145594	NR_030678		AA387883	-	expressed sequence AA387883	ncRNA
mm_96576.1	chr11	69059751	69059809	+	1	NA	promoter-TSS (NM_028005)	promoter-TSS (NM_028005)	5	NM_028005	71923	Mm.340257	NM_028005	ENSMUSG00000045176	Borcs6	2310047M10Rik	BLOC-1 related complex subunit 6	protein-coding
mm_65388.1	chr7	25091777	25091800	-	1	NA	3' UTR (NM_001163556, exon 14 of 14)	3' UTR (NM_001163556, exon 14 of 14)	5387	NR_105855	102465968		NR_105855	ENSMUSG00000098441	Mir6537	Gm27808|mmu-mir-6537	microRNA 6537	ncRNA
mm_96846.1	chr11	70034965	70034972	+	1	NA	intron (NM_001109752, intron 8 of 19)	B1_Mur1|SINE|Alu	16363	NM_007864	13385	Mm.27256	NM_007864	ENSMUSG00000020886	Dlg4	Dlgh4|PSD-95|PSD95|SAP90|SAP90A	discs, large homolog 4 (Drosophila)	protein-coding
mm_81875.1	chr9	119133588	119133615	+	1	NA	intron (NM_177117, intron 19 of 36)	MTD|LTR|ERVL-MaLR	23492	NM_146230	235674	Mm.379402	NM_146230	ENSMUSG00000010651	Acaa1b	-	acetyl-Coenzyme A acyltransferase 1B	protein-coding
mm_122463.1	chr14	45477873	45477883	-	1	NA	intron (NM_146054, intron 4 of 14)	intron (NM_146054, intron 4 of 14)	52187	NM_146054	218952	Mm.210018	NM_146054	ENSMUSG00000037712	Fermt2	AA960555|Kindlin-2|Mig2|Plekhc1	fermitin family member 2	protein-coding
mm_74451.1	chr8	4214086	4214096	-	1	NA	exon (NM_207203, exon 6 of 7)	exon (NM_207203, exon 6 of 7)	3221	NM_207203	73072	Mm.477379	NM_207203	ENSMUSG00000064125	Prr36	-	proline rich 36	protein-coding
mm_62666.1	chr7	108938470	108938488	+	1	NA	exon (NM_025344, exon 4 of 8)	exon (NM_025344, exon 4 of 8)	4064	NM_025344	66085	Mm.182962	NM_025344	ENSMUSG00000031029	Eif3f	0610037M02Rik|AA409853|Eif3s5	eukaryotic translation initiation factor 3, subunit F	protein-coding
mm_26265.1	chr3	142501385	142501396	+	1	NA	intron (NM_153564, intron 3 of 10)	intron (NM_153564, intron 3 of 10)	4456	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_21657.1	chr2	164404607	164404621	-	1	NA	5' UTR (NM_013592, exon 1 of 11)	intron (NM_009036, intron 2 of 11)	204	NM_013592	17183	Mm.29428	NM_013592	ENSMUSG00000016995	Matn4	matrilin-4	matrilin 4	protein-coding
mm_14118.1	chr2	125893346	125893368	+	1	NA	exon (NM_001291002, exon 4 of 10)	exon (NM_001291002, exon 4 of 10)	27134	NM_001291002	69976	Mm.20216	NM_175154	ENSMUSG00000027207	Galk2	2810017M24Rik|AI327030|Gk2	galactokinase 2	protein-coding
mm_159346.1	chr3	63300115	63300115	+	1	NA	intron (NM_001289463, intron 1 of 22)	RLTR17B_Mm|LTR|ERVK	4020	NM_001289463	17380	Mm.296022	NM_008604	ENSMUSG00000027820	Mme	6030454K05Rik|C85356|CALLA|CD10|NEP|SFE	membrane metallo endopeptidase	protein-coding
mm_30441.1	chr3	153650236	153650252	-	1	NA	intron (NM_011372, intron 1 of 4)	Lx9|LINE|L1	74889	NM_011372	20447	Mm.296453	NM_011372	ENSMUSG00000052544	St6galnac3	Siat7c	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 3	protein-coding
mm_22818.1	chr3	27194366	27194373	+	1	NA	intron (NM_178772, intron 1 of 4)	intron (NM_178772, intron 1 of 4)	11365	NM_178772	320024	Mm.24576	NM_178772	ENSMUSG00000027698	Nceh1	Aadacl1|B230106I24Rik|CPO-BP|Nceh	neutral cholesterol ester hydrolase 1	protein-coding
mm_75669.1	chr8	67818219	67818269	-	1	NA	promoter-TSS (NM_027626)	promoter-TSS (NM_027626)	51	NM_027626	234353	Mm.32525	NM_027626	ENSMUSG00000030465	Psd3	4931420C21Rik|AI661273|BC003498|D430018P08|EFA6D	pleckstrin and Sec7 domain containing 3	protein-coding
mm_62600.1	chr7	105736703	105736735	+	1	NA	promoter-TSS (NM_025897)	promoter-TSS (NM_025897)	-6	NM_010562	16202	Mm.274846	NM_010562	ENSMUSG00000030890	Ilk	AA511515|ESTM24	integrin linked kinase	protein-coding
mm_116417.1	chr13	41605531	41605545	-	1	NA	promoter-TSS (NM_001163572)	promoter-TSS (NM_001163572)	-678	NM_001163572	621976	Mm.259830	NM_001163572	ENSMUSG00000087370	Tmem170b	EG621976	transmembrane protein 170B	protein-coding
mm_131457.1	chr16	16896557	16896598	+	1	NA	5' UTR (NM_176833, exon 1 of 8)	5' UTR (NM_176833, exon 1 of 8)	108	NM_176833	68606	Mm.230296	NM_176833	ENSMUSG00000026181	Ppm1f	1110021B16Rik|4933427B07Rik|CaMKPase|Popx2|mKIAA0015	protein phosphatase 1F (PP2C domain containing)	protein-coding
mm_122653.1	chr14	51911120	51911124	-	1	NA	exon (NM_013864, exon 3 of 16)	exon (NM_013864, exon 3 of 16)	2366	NM_001145959	29811	Mm.26722	NM_013864	ENSMUSG00000004558	Ndrg2	AI182517|AU040374|Ndr2|SYLD	N-myc downstream regulated gene 2	protein-coding
mm_100376.1	chr11	119267958	119267968	+	1	NA	promoter-TSS (NM_008064)	promoter-TSS (NM_008064)	0	NM_001159324	14387	Mm.4793	NM_008064	ENSMUSG00000025579	Gaa	E430018M07Rik	glucosidase, alpha, acid	protein-coding
mm_96346.1	chr11	66956535	66956557	+	1	NA	promoter-TSS (NR_130315)	promoter-TSS (NR_130315)	-92	NR_130645	71576	Mm.340077	NR_130315	ENSMUSG00000085683	9130409J20Rik	-	RIKEN cDNA 9130409J20 gene	ncRNA
mm_141268.1	chr17	27728938	27728956	-	1	NA	promoter-TSS (NM_013891)	promoter-TSS (NM_013891)	4	NM_013891	30051	Mm.26768	NM_013891	ENSMUSG00000024215	Spdef	PDEF|Pse	SAM pointed domain containing ets transcription factor	protein-coding
mm_1812.1	chr1	81187503	81187505	+	1	NA	intron (NM_172849, intron 2 of 4)	intron (NM_172849, intron 2 of 4)	110187	NM_172849	241134	Mm.313904	NM_172849	ENSMUSG00000054976	Nyap2	9430031J16Rik|Jr6|Kiaa1486	neuronal tyrosine-phophorylated phosphoinositide 3-kinase adaptor 2	protein-coding
mm_20866.1	chr2	148440894	148440914	-	1	NA	3' UTR (NM_010740, exon 2 of 2)	3' UTR (NM_010740, exon 2 of 2)	2631	NM_010740	17064	Mm.681	NM_010740	ENSMUSG00000027435	Cd93	6030404G09Rik|AA145088|AA4.1|AW555904|C1qr1|C1qrp|Ly68	CD93 antigen	protein-coding
mm_8475.1	chr1	153415132	153415161	-	1	NA	promoter-TSS (NR_033736)	promoter-TSS (NR_033736)	-913	NR_033736	626058	Mm.31556	NM_001177359		E330020D12Rik	EG626058|F430003O07Rik|Gm6648	Riken cDNA E330020D12 gene	ncRNA
mm_133546.1	chr16	91269728	91269733	+	1	NA	promoter-TSS (NM_016968)	promoter-TSS (NM_016968)	-39	NM_016968	50914	Mm.39300	NM_016968	ENSMUSG00000046160	Olig1	AI836478|AW494459|Bhlhb6|Olg-1|Oligo1|bHLHe21	oligodendrocyte transcription factor 1	protein-coding
mm_121338.1	chr14	115092245	115092278	+	1	NA	promoter-TSS (NM_175500)	promoter-TSS (NM_175500)	46	NM_175500	103978	Mm.320791	NM_175500	ENSMUSG00000022112	Gpc5	A230034F01Rik	glypican 5	protein-coding
mm_106647.1	chr11	121055057	121055067	-	1	NA	exon (NM_026907, exon 5 of 5)	exon (NM_026907, exon 5 of 5)	8507	NM_026907	58210	Mm.116986	NM_026907	ENSMUSG00000039364	Sectm1b	1810003C24Rik|K12|Sectm1	secreted and transmembrane 1B	protein-coding
mm_79549.1	chr9	57922568	57922581	+	1	NA	exon (NM_027086, exon 9 of 11)	exon (NM_027086, exon 9 of 11)	11588	NM_001122873	69459	Mm.41735	NM_027086	ENSMUSG00000055720	Ubl7	2300004C15Rik	ubiquitin-like 7 (bone marrow stromal cell-derived)	protein-coding
mm_63039.1	chr7	121083404	121083404	+	1	NA	promoter-TSS (NM_139310)	promoter-TSS (NM_139310)	-34	NM_139310	246190	Mm.221073	NM_139310	ENSMUSG00000034990	Otoa	-	otoancorin	protein-coding
mm_68485.1	chr7	110982473	110982483	-	1	NA	promoter-TSS (NM_194464)	promoter-TSS (NM_194464)	-17	NM_194464	17540	Mm.250023	NM_010826	ENSMUSG00000005611	Mrvi1	BB115629|Irag|Ris1	MRV integration site 1	protein-coding
mm_121249.1	chr14	103057382	103057404	+	1	NA	TTS (NM_008392)	TTS (NM_008392)	10381	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_45529.1	chr5	72675286	72675286	-	1	NA	Intergenic	Intergenic	27490	NM_001081205	70701	Mm.38884	NM_001081205	ENSMUSG00000067219	Nipal1	3830408G10Rik|Npal1	NIPA-like domain containing 1	protein-coding
mm_37017.1	chr4	113999488	113999497	-	1	NA	promoter-TSS (NM_001167878)	promoter-TSS (NM_001167878)	11	NM_001167878	242627	Mm.484115	NM_001167876	ENSMUSG00000078598	Skint5	OTTMUSG00000008560|Skint-5	selection and upkeep of intraepithelial T cells 5	protein-coding
mm_155997.1	chrX	106157100	106157111	+	1	NA	exon (NM_205820, exon 3 of 3)	exon (NM_205820, exon 3 of 3)	13830	NM_205820	279572	Mm.336203	NM_205820	ENSMUSG00000033777	Tlr13	AI666735|Gm713	toll-like receptor 13	protein-coding
mm_12785.1	chr2	79332034	79332037	+	1	NA	TTS (NM_001048176)	TTS (NM_001048176)	76609	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D|Itga4B	integrin alpha 4	protein-coding
mm_126768.1	chr15	86036504	86036511	+	1	NA	Intergenic	ID4|SINE|ID	-2730	NM_009886	12614	Mm.22680	NM_009886	ENSMUSG00000016028	Celsr1	Adgrc1|Crsh|Scy|crash	cadherin, EGF LAG seven-pass G-type receptor 1	protein-coding
mm_145831.1	chr18	65439541	65439562	+	1	NA	intron (NM_172833, intron 2 of 15)	B3|SINE|B2	8554	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_123101.1	chr14	55882068	55882081	-	1	NA	3' UTR (NM_019820, exon 3 of 3)	3' UTR (NM_019820, exon 3 of 3)	2182	NM_019820	56410	Mm.97163	NM_019820	ENSMUSG00000040380	Cbln3	-	cerebellin 3 precursor protein	protein-coding
mm_38701.1	chr4	145215047	145215062	-	1	NA	3' UTR (NM_011610, exon 10 of 10)	3' UTR (NM_011610, exon 10 of 10)	-20049	NM_001276465	230895	Mm.240310	NM_001033190	ENSMUSG00000020220	Vps13d	-	vacuolar protein sorting 13D	protein-coding
mm_36252.1	chr4	63409994	63410004	-	1	NA	Intergenic	Intergenic	-6554	NM_001045514	100182	Mm.387725	NM_001045514	ENSMUSG00000039158	Akna	AI597013	AT-hook transcription factor	protein-coding
mm_22813.1	chr3	27188377	27188409	+	1	NA	intron (NM_178772, intron 1 of 4)	intron (NM_178772, intron 1 of 4)	5389	NM_178772	320024	Mm.24576	NM_178772	ENSMUSG00000027698	Nceh1	Aadacl1|B230106I24Rik|CPO-BP|Nceh	neutral cholesterol ester hydrolase 1	protein-coding
mm_68179.1	chr7	103851866	103851876	-	1	NA	3' UTR (NM_008221, exon 3 of 3)	3' UTR (NM_008221, exon 3 of 3)	1336	NM_008221	15135	Mm.440164	NM_008221	ENSMUSG00000052187	Hbb-y	Ey|Hby	hemoglobin Y, beta-like embryonic chain	protein-coding
mm_98836.1	chr11	97438186	97438188	+	1	NA	Intergenic	Intergenic	-11973	NM_021493	58996	Mm.394118	NM_021493	ENSMUSG00000049807	Arhgap23	A330041B18Rik	Rho GTPase activating protein 23	protein-coding
mm_102519.1	chr11	60819317	60819317	-	1	NA	Intergenic	Intergenic	-8052	NM_009171	20425	Mm.364956	NM_009171	ENSMUSG00000020534	Shmt1	AI324848|AI385541|C81125|Shmt|mshmt|mshmt1|mshmt2	serine hydroxymethyltransferase 1 (soluble)	protein-coding
mm_79650.1	chr9	59589331	59589353	+	1	NA	promoter-TSS (NM_001311092)	promoter-TSS (NM_001311092)	28	NM_001311092	76183	Mm.265415	NM_175235	ENSMUSG00000032297	Celf6	6330569O16Rik|Brunol6	CUGBP, Elav-like family member 6	protein-coding
mm_144414.1	chr18	20961746	20961754	+	1	NA	intron (NM_026301, intron 1 of 5)	CpG	17125	NM_026301	67664	Mm.45980	NM_026301	ENSMUSG00000033107	Rnf125	4930553F04Rik	ring finger protein 125	protein-coding
mm_90358.1	chr10	127165414	127165424	+	1	NA	promoter-TSS (NM_027739)	promoter-TSS (NM_027739)	263	NM_001244617	14421	Mm.386762	NM_008080	ENSMUSG00000006731	B4galnt1	4933429D13Rik|Gal-NAc-T|GalNAc-T|GalNAcT|Galgt1|Ggm-2|Ggm2	beta-1,4-N-acetyl-galactosaminyl transferase 1	protein-coding
mm_88402.1	chr10	76615037	76615070	+	1	NA	exon (NM_146007, exon 2 of 28)	exon (NM_146007, exon 2 of 28)	8351	NM_146007	12834	Mm.1949	NM_146007	ENSMUSG00000020241	Col6a2	Col6a-2	collagen, type VI, alpha 2	protein-coding
mm_6593.1	chr1	75264677	75264693	-	1	NA	promoter-TSS (NM_008985)	promoter-TSS (NM_008985)	-477	NM_008985	19275	Mm.2902	NM_008985	ENSMUSG00000026204	Ptprn	IA-2|mIA-A|mKIAA4064	protein tyrosine phosphatase, receptor type, N	protein-coding
mm_155226.1	chrX	57066302	57066314	+	1	NA	exon (NM_029371, exon 9 of 9)	exon (NM_029371, exon 9 of 9)	12474	NM_029371	72459	Mm.2152	NM_028242	ENSMUSG00000067873	Htatsf1	1600023H17Rik|2600017A12Rik|2700077B20Rik|TAT-SF1	HIV TAT specific factor 1	protein-coding
mm_49467.1	chr6	29467734	29467764	+	1	NA	promoter-TSS (NM_025381)	promoter-TSS (NM_025381)	-34	NM_025381	66144	Mm.371614	NM_025381	ENSMUSG00000004285	Atp6v1f	1110004G16Rik	ATPase, H+ transporting, lysosomal V1 subunit F	protein-coding
mm_166769.1	chr6	135197982	135197992	+	1	NA	promoter-TSS (NM_028982)	promoter-TSS (NM_028982)	0	NM_028982	74525	Mm.34182	NM_028982	ENSMUSG00000030207	Fam234b	8430419L09Rik|Kiaa1467|mKIAA1467	family with sequence similarity 234, member B	protein-coding
mm_128510.1	chr15	53303403	53303405	-	1	NA	intron (NM_010162, intron 1 of 10)	intron (NM_010162, intron 1 of 10)	42779	NM_010162	14042	Mm.309395	NM_010162	ENSMUSG00000061731	Ext1	AA409028	exostoses (multiple) 1	protein-coding
mm_36554.1	chr4	86857293	86857303	-	1	NA	promoter-TSS (NM_009096)	promoter-TSS (NM_009096)	69	NM_009096	20104	Mm.379007	NM_009096	ENSMUSG00000028495	Rps6	S6R	ribosomal protein S6	protein-coding
mm_25232.1	chr3	103863198	103863200	+	1	NA	intron (NR_104070, intron 3 of 22)	intron (NR_104070, intron 3 of 22)	2922	NM_008979	19260	Mm.395	NM_008979	ENSMUSG00000027843	Ptpn22	70zpep|PEP|Ptpn8	protein tyrosine phosphatase, non-receptor type 22 (lymphoid)	protein-coding
mm_116910.1	chr13	55483674	55483684	-	1	NA	intron (NM_001177371, intron 1 of 14)	intron (NM_001177371, intron 1 of 14)	4397	NM_001177371	56320	Mm.19016	NM_019813	ENSMUSG00000034675	Dbn1	-	drebrin 1	protein-coding
mm_132447.1	chr16	35983308	35983395	+	1	NA	promoter-TSS (NM_008465)	promoter-TSS (NM_008465)	-12	NM_008465	16646	Mm.3991	NM_008465	ENSMUSG00000022905	Kpna1	AW494490|IPOA5|NPI1|Rch2|mSRP1	karyopherin (importin) alpha 1	protein-coding
mm_160894.1	chr11	72314467	72314467	+	1	NA	promoter-TSS (NM_001099688)	promoter-TSS (NM_001099688)	23	NM_001099688	628100	Mm.390365	NM_001099688	ENSMUSG00000070388	Fbxo39	1700010H23Rik	F-box protein 39	protein-coding
mm_69836.1	chr7	141322030	141322043	-	1	NA	exon (NM_001282073, exon 6 of 12)	exon (NM_001282073, exon 6 of 12)	5689	NM_016874	54006	Mm.28392	NM_016874	ENSMUSG00000058886	Deaf1	AU042387|C230009B13Rik|NUDR	deformed epidermal autoregulatory factor 1 (Drosophila)	protein-coding
mm_19154.1	chr2	80581273	80581293	-	1	NA	promoter-TSS (NM_001290745)	promoter-TSS (NM_001290745)	-101	NM_016965	50884	Mm.25203	NM_016965	ENSMUSG00000027002	Nckap1	C79304|H19|Hem-2|Hem2|Nap1|mKIAA0587|mh19|p125Nap1	NCK-associated protein 1	protein-coding
mm_93067.1	chr10	89257646	89257657	-	1	NA	non-coding (NR_102339, exon 1 of 27)	non-coding (NR_102339, exon 1 of 27)	139	NM_001277188	320091	Mm.236464	NM_178773	ENSMUSG00000035189	Ano4	A330096O15Rik|Gm65|Tmem16d	anoctamin 4	protein-coding
mm_21949.1	chr2	167062865	167062873	-	1	NA	promoter-TSS (NR_138563)	promoter-TSS (NR_138563)	-65	NR_138563	68949	Mm.391959	NM_001081005		Zfas1	1500012F01Rik|Zfos1	zinc finger, NFX1-type containing 1, antisense RNA 1	ncRNA
mm_168283.1	chr1	109834005	109834012	+	1	NA	Intergenic	Intergenic	-148892	NM_001316743	241201	Mm.213407	NM_172853	ENSMUSG00000026312	Cdh7	9330156F07Rik|CDH7L1	cadherin 7, type 2	protein-coding
mm_108859.1	chr12	98771019	98771041	+	1	NA	promoter-TSS (NM_001160108)	promoter-TSS (NM_001160108)	8	NM_001160108	75553	Mm.25549	NM_029334	ENSMUSG00000021012	Zc3h14	1010001P15Rik|1700016A15Rik|2700069A02Rik|AU014748	zinc finger CCCH type containing 14	protein-coding
mm_27008.1	chr3	25868707	25868754	-	1	NA	intron (NM_001163387, intron 3 of 5)	intron (NM_001163387, intron 3 of 5)	284577	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_155216.1	chrX	56792076	56792107	+	1	NA	3' UTR (NM_010211, exon 7 of 7)	3' UTR (NM_010211, exon 7 of 7)	5564	NM_001287800	14199	Mm.3126	NM_010211	ENSMUSG00000023092	Fhl1	FHL-1|KyoT|RAM14-1|SLIM|SLIM-1	four and a half LIM domains 1	protein-coding
mm_36109.1	chr4	58844956	58844972	-	1	NA	intron (NM_172381, intron 15 of 48)	intron (NM_172381, intron 15 of 48)	-59244	NM_146920	258922	Mm.223327	NM_146920	ENSMUSG00000043385	Olfr267	MOR262-1	olfactory receptor 267	protein-coding
mm_118764.1	chr14	22438697	22438711	+	1	NA	intron (NM_028275, intron 2 of 6)	ID_B1|SINE|B4	104094	NR_046307	74896	Mm.444661	NR_046307		4930405A10Rik	4930456G20Rik	RIKEN cDNA 4930405A10 gene	ncRNA
mm_91245.1	chr10	22704284	22704284	-	1	NA	TTS (NM_178934)	TTS (NM_178934)	25148	NR_106123	102465768		NR_106123	ENSMUSG00000098714	Mir7663	Gm28034|mmu-mir-7663	microRNA 7663	ncRNA
mm_59763.1	chr7	28831376	28831389	+	1	NA	intron (NM_016772, intron 7 of 9)	intron (NM_016772, intron 7 of 9)	-2412	NM_010706	16855	Mm.210336	NM_010706	ENSMUSG00000053964	Lgals4	gal-4	lectin, galactose binding, soluble 4	protein-coding
mm_4486.1	chr1	173631006	173631018	+	1	NA	5' UTR (NM_175026, exon 1 of 7)	5' UTR (NM_175026, exon 1 of 7)	153	NM_175026	236312	Mm.447	NM_175026	ENSMUSG00000043263	Ifi209	4930422C14|AI447904|Ifix|Pyhin-1|Pyhin1	interferon activated gene 209	protein-coding
mm_93282.1	chr10	96163419	96163428	-	1	NA	Intergenic	Intergenic	-62784	NR_110448	74881	Mm.410819	NR_110448		4930459C07Rik	-	RIKEN cDNA 4930459C07 gene	ncRNA
mm_115716.1	chr13	15908790	15908801	-	1	NA	Intergenic	Lx9|LINE|L1	101552	NR_046131	328190	Mm.446957	NR_046131		A530046M15Rik	A530046M15	RIKEN cDNA A530046M15 gene	ncRNA
mm_106413.1	chr11	119086267	119086284	-	1	NA	promoter-TSS (NM_007625)	promoter-TSS (NM_007625)	-38	NM_007625	12418	Mm.268070	NM_007625	ENSMUSG00000039989	Cbx4	MPc2|PC2	chromobox 4	protein-coding
mm_32590.1	chr4	111719976	111720047	+	1	NA	promoter-TSS (NM_026470)	promoter-TSS (NM_026470)	1	NM_026470	67946	Mm.275526	NM_026470	ENSMUSG00000034401	Spata6	1700062C23Rik|AI790763|Hash|KRP|Mash	spermatogenesis associated 6	protein-coding
mm_48111.1	chr5	137112352	137112360	-	1	NA	3' UTR (NM_201373, exon 3 of 3)	3' UTR (NM_201373, exon 3 of 3)	3851	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_9887.1	chr1	186634022	186634034	-	1	NA	intron (NM_001329107, intron 3 of 7)	intron (NM_001329107, intron 3 of 7)	71961	NM_009367	21808	Mm.18213	NM_009367	ENSMUSG00000039239	Tgfb2	BB105277|Tgf-beta2|Tgfb-2	transforming growth factor, beta 2	protein-coding
mm_42837.1	chr5	122103148	122103167	+	1	NA	intron (NM_010861, intron 3 of 6)	intron (NM_010861, intron 3 of 6)	2177	NM_010861	17906	Mm.1529	NM_010861	ENSMUSG00000013936	Myl2	MLC-2|MLC-2s/v|MLC-2v|Mlc2v|Mylpc	myosin, light polypeptide 2, regulatory, cardiac, slow	protein-coding
mm_91142.1	chr10	19851599	19851611	-	1	NA	promoter-TSS (NM_029529)	promoter-TSS (NM_029529)	-146	NM_029529	76157	Mm.74324	NM_029529	ENSMUSG00000050473	Slc35d3	6230421J19Rik|Frcl1	solute carrier family 35, member D3	protein-coding
mm_78800.1	chr9	44047485	44047496	+	1	NA	3' UTR (NM_009382, exon 4 of 4)	3' UTR (NM_009382, exon 4 of 4)	4106	NM_009382	21838	Mm.3951	NM_009382	ENSMUSG00000032011	Thy1	CD90|T25|Thy-1|Thy-1.2|Thy1.1|Thy1.2	thymus cell antigen 1, theta	protein-coding
mm_77688.1	chr8	126584582	126584585	-	1	NA	Intergenic	Intergenic	8853	NM_001164598	270110	Mm.334918	NM_001164598	ENSMUSG00000051495	Irf2bp2	E130305N23Rik|IRF-2BP2	interferon regulatory factor 2 binding protein 2	protein-coding
mm_150970.1	chr19	46500989	46501000	+	1	NA	promoter-TSS (NM_053100)	promoter-TSS (NM_053100)	-654	NM_053100	93679	Mm.392177	NM_053100	ENSMUSG00000025034	Trim8	AA408830|BB006755|GERP|Rnf27	tripartite motif-containing 8	protein-coding
mm_124388.1	chr14	108914238	108914257	-	1	NA	promoter-TSS (NM_199065)	promoter-TSS (NM_199065)	-8	NM_199065	76965	Mm.257268	NM_199065	ENSMUSG00000075478	Slitrk1	3200001I04Rik	SLIT and NTRK-like family, member 1	protein-coding
mm_169420.1	chr1	45311710	45311710	+	1	NA	5' UTR (NM_009930, exon 1 of 51)	5' UTR (NM_009930, exon 1 of 51)	172	NM_009930	12825	Mm.249555	NM_009930	ENSMUSG00000026043	Col3a1	AW550625|Col3a-1|Tsk-2|Tsk2	collagen, type III, alpha 1	protein-coding
mm_33018.1	chr4	121039557	121039680	+	1	NA	promoter-TSS (NM_007741)	promoter-TSS (NM_007741)	52	NM_007741	12840	Mm.269384	NM_007741	ENSMUSG00000028626	Col9a2	AI427499|Col9a-2	collagen, type IX, alpha 2	protein-coding
mm_99333.1	chr11	101465479	101465499	+	1	NA	intron (NM_012037, intron 1 of 5)	intron (NM_012037, intron 1 of 5)	710	NM_012037	26949	Mm.29210	NM_012037	ENSMUSG00000034993	Vat1	VAT-1	vesicle amine transport 1	protein-coding
mm_77490.1	chr8	122575018	122575033	-	1	NA	exon (NM_009698, exon 5 of 5)	exon (NM_009698, exon 5 of 5)	1882	NM_009698	11821	Mm.1786	NM_009698	ENSMUSG00000006589	Aprt	C85684	adenine phosphoribosyl transferase	protein-coding
mm_16325.1	chr2	174308314	174308335	+	1	NA	intron (NM_001310085, intron 2 of 12)	intron (NM_001310085, intron 2 of 12)	10465	NM_001310085	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_156169.1	chrX	130166979	130166982	+	1	NA	intron (NM_172493, intron 22 of 26)	intron (NM_172493, intron 22 of 26)	417238	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diaph2	Dia3|Diap2|Drf2|E430022I22Rik	diaphanous related formin 2	protein-coding
mm_158620.1	chrX	152657763	152657783	-	1	NA	intron (NM_001290684, intron 4 of 9)	intron (NM_001290684, intron 4 of 9)	-13225	NM_001290685	110380	Mm.40796	NM_172441	ENSMUSG00000045180	Shroom2	4832440C16|Apxl|C630003H05Rik|Shrm2	shroom family member 2	protein-coding
mm_144559.1	chr18	31759818	31759851	+	1	NA	promoter-TSS (NM_001242430)	promoter-TSS (NM_001242430)	10	NM_153515	225339	Mm.290804	NM_153515	ENSMUSG00000041915	Ammecr1l	5430429D03Rik|AU022236|AU040755|AW111353|E230022H04Rik	AMME chromosomal region gene 1-like	protein-coding
mm_62418.1	chr7	101321080	101321134	+	1	NA	promoter-TSS (NM_019990)	promoter-TSS (NM_019990)	-212	NM_019990	56018	Mm.28896	NM_019990	ENSMUSG00000030688	Stard10	AV048538|CGI-52|NY-C0-28|PC-TP2|PCTP2|Pctpl|Sdccag28|SdccagG28|TISP-81	START domain containing 10	protein-coding
mm_28483.1	chr3	92457242	92457252	-	1	NA	exon (NM_011478, exon 2 of 2)	exon (NM_011478, exon 2 of 2)	1473	NM_001204427	20766	Mm.57092	NM_011478	ENSMUSG00000045539	Sprr3	SPR3	small proline-rich protein 3	protein-coding
mm_101012.1	chr11	8514465	8514467	-	1	NA	intron (NM_001083587, intron 16 of 30)	intron (NM_001083587, intron 16 of 30)	150069	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_89269.1	chr10	87860222	87860240	+	1	NA	promoter-TSS (NM_001111276)	promoter-TSS (NM_001111276)	-880	NM_001111274	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_141587.1	chr17	32403595	32403605	-	1	NA	promoter-TSS (NM_178785)	promoter-TSS (NM_178785)	-18	NM_001347343	320484	Mm.122284	NM_178785	ENSMUSG00000052142	Rasal3	A430107D22Rik	RAS protein activator like 3	protein-coding
mm_132409.1	chr16	35023460	35023461	+	1	NA	intron (NM_023587, intron 1 of 6)	B1F1|SINE|Alu	1039	NM_023587	70757	Mm.27286	NM_023587	ENSMUSG00000035376	Hacd2	6330408J20Rik|AI255777|AI481689|Hcad2|Ptplb	3-hydroxyacyl-CoA dehydratase 2	protein-coding
mm_46555.1	chr5	106691143	106691158	-	1	NA	intron (NM_026856, intron 1 of 6)	intron (NM_026856, intron 1 of 6)	5680	NM_026856	52397	Mm.249474	NM_026856	ENSMUSG00000049606	Zfp644	1110068L01Rik|AA408882|BM-005|D5Ertd689e|Zep-2	zinc finger protein 644	protein-coding
mm_99764.1	chr11	106788714	106788731	+	1	NA	promoter-TSS (NM_177088)	promoter-TSS (NM_177088)	-228	NM_007840	13207	Mm.491096	NM_007840	ENSMUSG00000020719	Ddx5	2600009A06Rik|G17P1|HUMP68|Hlr1|p68	DEAD (Asp-Glu-Ala-Asp) box polypeptide 5	protein-coding
mm_145580.1	chr18	60963859	60963863	+	1	NA	exon (NM_001286809, exon 1 of 6)	exon (NM_001286809, exon 1 of 6)	307	NM_001286809	12322	Mm.131530	NM_009792	ENSMUSG00000024617	Camk2a	CaMKII|R74975|mKIAA0968	calcium/calmodulin-dependent protein kinase II alpha	protein-coding
mm_148283.1	chr18	82527741	82527750	-	1	NA	intron (NM_001025245, intron 3 of 3)	intron (NM_001025245, intron 3 of 3)	-26718	NM_001025256	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_121782.1	chr14	19929331	19929333	-	1	NA	intron (NM_001285909, intron 3 of 5)	intron (NM_001285909, intron 3 of 5)	47361	NM_001285911	14702	Mm.41737	NM_010315	ENSMUSG00000043004	Gng2	-	guanine nucleotide binding protein (G protein), gamma 2	protein-coding
mm_72040.1	chr8	70897626	70897670	+	1	NA	promoter-TSS (NM_029751)	promoter-TSS (NM_029751)	-205	NM_029751	76808	Mm.379251	NM_029751	ENSMUSG00000045128	Rpl18a	2510019J09Rik	ribosomal protein L18A	protein-coding
mm_152352.1	chr19	10001562	10001582	-	1	NA	promoter-TSS (NM_011913)	promoter-TSS (NM_011913)	61	NM_011913	24115	Mm.31577	NM_011913	ENSMUSG00000037418	Best1	Bmd|Vmd2|mBest1	bestrophin 1	protein-coding
mm_129354.1	chr15	77928698	77928717	-	1	NA	intron (NM_019913, intron 1 of 3)	intron (NM_019913, intron 1 of 3)	287	NM_019913	56551	Mm.291917	NM_019913	ENSMUSG00000005354	Txn2	2510006J11Rik|AI788873|Trx2	thioredoxin 2	protein-coding
mm_2230.1	chr1	90998723	90998796	+	1	NA	promoter-TSS (NM_001111312)	promoter-TSS (NM_001111312)	32	NM_001111312	16978	Mm.45039	NM_008515	ENSMUSG00000026305	Lrrfip1	AU024550|Fliiap1	leucine rich repeat (in FLII) interacting protein 1	protein-coding
mm_165701.1	chr3	95283061	95283084	-	1	NA	promoter-TSS (NM_173347)	promoter-TSS (NM_173347)	137	NM_199475	75007	Mm.279287	NM_133858	ENSMUSG00000038712	Fam63a	1810005H09Rik|4930504E06Rik|AA562754|AA960384|AW561904|cI-40|mKIAA1390|ni	family with sequence similarity 63, member A	protein-coding
mm_167597.1	chr9	49798948	49798958	-	1	NA	5' UTR (NM_001311065, exon 1 of 18)	5' UTR (NM_001311065, exon 1 of 18)	116	NM_001081445	17967	Mm.4974	NM_010875	ENSMUSG00000039542	Ncam1	CD56|E-NCAM|NCAM-1|Ncam	neural cell adhesion molecule 1	protein-coding
mm_136505.1	chr16	96762805	96762808	-	1	NA	intron (NM_031174, intron 11 of 32)	intron (NM_031174, intron 11 of 32)	295200	NM_008791	18546	Mm.5023	NM_008791	ENSMUSG00000090223	Pcp4	P16Rimb19|Pcp-4|Pep19	Purkinje cell protein 4	protein-coding
mm_90975.1	chr10	13500909	13500947	-	1	NA	promoter-TSS (NM_001330198)	promoter-TSS (NM_001330198)	-100	NM_001330198	66848	Mm.26625	NM_025799	ENSMUSG00000019810	Fuca2	0610025O11Rik|5530401P20Rik	fucosidase, alpha-L- 2, plasma	protein-coding
mm_40026.1	chr5	33378530	33378584	+	1	NA	promoter-TSS (NM_001081101)	promoter-TSS (NM_001081101)	-139	NM_001081101	71101	Mm.132178	NM_001081101	ENSMUSG00000037355	Uvssa	4933407H18Rik|D330017J19Rik|Kiaa1530|mKIAA1530	UV stimulated scaffold protein A	protein-coding
mm_71258.1	chr8	40917636	40917647	+	1	NA	3' UTR (NM_001044740, exon 12 of 12)	3' UTR (NM_001044740, exon 12 of 12)	-8592	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_76024.1	chr8	75096896	75096932	-	1	NA	exon (NM_010442, exon 3 of 5)	exon (NM_010442, exon 3 of 5)	3296	NM_010442	15368	Mm.276389	NM_010442	ENSMUSG00000005413	Hmox1	D8Wsu38e|HO-1|HO1|Hemox|Hmox|Hsp32	heme oxygenase 1	protein-coding
mm_165672.1	chr3	89402589	89402589	-	1	NA	promoter-TSS (NM_020517)	promoter-TSS (NM_020517)	61	NM_020517	57275	Mm.482283	NM_020517	ENSMUSG00000078173	Lenep	AU018355|Lep503	lens epithelial protein	protein-coding
mm_39774.1	chr5	30019547	30019556	+	1	NA	3' UTR (NM_031168, exon 5 of 5)	3' UTR (NM_031168, exon 5 of 5)	6437	NM_031168	16193	Mm.1019	NM_031168	ENSMUSG00000025746	Il6	Il-6	interleukin 6	protein-coding
mm_34882.1	chr4	155582736	155582744	+	1	NA	intron (NM_138671, intron 3 of 11)	intron (NM_138671, intron 3 of 11)	-18676	NM_177186	320541	Mm.306018	NM_177186	ENSMUSG00000042202	Slc35e2	A530082C11Rik|AI957035	solute carrier family 35, member E2	protein-coding
mm_21511.1	chr2	163625414	163625458	-	1	NA	3' UTR (NM_012032, exon 10 of 10)	3' UTR (NM_012032, exon 10 of 10)	18224	NM_001305803	76080	Mm.89828	NM_029512	ENSMUSG00000017679	Ttpal	3110080A02Rik|5830472M02Rik	tocopherol (alpha) transfer protein-like	protein-coding
mm_146584.1	chr18	7703656	7703659	-	1	NA	Intergenic	Intergenic	-76794	NM_001161620	75739	Mm.133293	NM_001081287	ENSMUSG00000057440	Mpp7	1110068J02Rik|2810038M04Rik|5430426E14Rik|AI415104|Gm955	membrane protein, palmitoylated 7 (MAGUK p55 subfamily member 7)	protein-coding
mm_4902.1	chr1	189844664	189844669	+	1	NA	intron (NM_008976, intron 11 of 18)	MTD|LTR|ERVL-MaLR	77622	NM_026796	226830	Mm.156895	NM_026796	ENSMUSG00000026603	Smyd2	1110020E07Rik|4930402C15|KMT3C|Zmynd14	SET and MYND domain containing 2	protein-coding
mm_269.1	chr1	20951726	20951734	+	1	NA	5' UTR (NM_027974, exon 1 of 11)	5' UTR (NM_027974, exon 1 of 11)	104	NM_027974	71877	Mm.29178	NM_027974	ENSMUSG00000041809	Efhc1	1700029F22Rik|mRib72-1|myoclonin1	EF-hand domain (C-terminal) containing 1	protein-coding
mm_13770.1	chr2	118598272	118598300	+	1	NA	promoter-TSS (NM_009773)	promoter-TSS (NM_009773)	75	NM_009773	12236	Mm.29133	NM_009773	ENSMUSG00000040084	Bub1b	AU045529|BUBR1	BUB1B, mitotic checkpoint serine/threonine kinase	protein-coding
mm_47689.1	chr5	129128564	129128575	-	1	NA	intron (NM_001347486, intron 5 of 24)	intron (NM_001347486, intron 5 of 24)	31819	NM_001347486	243277	Mm.440501	NM_177734	ENSMUSG00000044017	Adgrd1	E230012M21Rik|Gpr133	adhesion G protein-coupled receptor D1	protein-coding
mm_23133.1	chr3	38223564	38223575	+	1	NA	Intergenic	Intergenic	-15450	NR_040541	71342	Mm.410782	NR_040541	ENSMUSG00000106002	5430434I15Rik	-	RIKEN cDNA 5430434I15 gene	ncRNA
mm_14734.1	chr2	144271629	144271633	+	1	NA	promoter-TSS (NM_001199188)	promoter-TSS (NM_001199188)	727	NM_001289630	74528	Mm.386817	NM_028984	ENSMUSG00000027424	Mgme1	8430406I07Rik|AI426476	mitochondrial genome maintainance exonuclease 1	protein-coding
mm_101607.1	chr11	34839117	34839125	-	1	NA	Intergenic	MTC|LTR|ERVL-MaLR	-5480	NM_027411	70385	Mm.194368	NM_027411	ENSMUSG00000069910	Spdl1	1700018I02Rik|2600001J17Rik|2810049B11Rik|AA409762|Ccdc99	spindle apparatus coiled-coil protein 1	protein-coding
mm_139491.1	chr17	56092506	56092507	+	1	NA	intron (NM_001331053, intron 3 of 15)	intron (NM_001331053, intron 3 of 15)	12875	NM_001304785	15193	Mm.12966	NM_008233	ENSMUSG00000002833	Hdgfrp2	HRP-2	hepatoma-derived growth factor, related protein 2	protein-coding
mm_130072.1	chr15	89355530	89355632	-	1	NA	promoter-TSS (NM_001271601)	promoter-TSS (NM_001271601)	78	NM_178919	105847	Mm.34511	NM_178919	ENSMUSG00000022614	Lmf2	AI451006|Tmem112b|Tmem153	lipase maturation factor 2	protein-coding
mm_60307.1	chr7	44112658	44112666	+	1	NA	promoter-TSS (NM_010114)	promoter-TSS (NM_010114)	-11	NM_010114	13646	Mm.5193	NM_010114	ENSMUSG00000060177	Klk1b22	EGF-BP A|Egfbp-1|Egfbp1|Klk22|mGk-22	kallikrein 1-related peptidase b22	protein-coding
mm_147705.1	chr18	60811317	60811359	-	1	NA	promoter-TSS (NR_039567)	promoter-TSS (NR_039567)	-738	NR_039567	100628611		NR_039567	ENSMUSG00000093327	Mir5107	mir-5107|mmu-mir-5107|mu-mir-5107	microRNA 5107	ncRNA
mm_133057.1	chr16	58415599	58415607	+	1	NA	intron (NM_028523, intron 1 of 15)	intron (NM_028523, intron 1 of 15)	7068	NM_028523	73379	Mm.373589	NM_028523	ENSMUSG00000035107	Dcbld2	1700055P21Rik|AW146002|CLCP1|Esdn	discoidin, CUB and LCCL domain containing 2	protein-coding
mm_65720.1	chr7	28379226	28379235	-	1	NA	promoter-TSS (NM_011756)	promoter-TSS (NM_011756)	-2	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_9972.1	chr1	191189929	191189942	-	1	NA	Intergenic	Intergenic	-6602	NM_007498	11910	Mm.2706	NM_007498	ENSMUSG00000026628	Atf3	LRG-21	activating transcription factor 3	protein-coding
mm_62326.1	chr7	100472961	100472975	+	1	NA	promoter-TSS (NM_009464)	promoter-TSS (NM_009464)	-23	NM_009464	22229	Mm.6254	NM_009464	ENSMUSG00000032942	Ucp3	AI645527|Slc25a9|UCP-3	uncoupling protein 3 (mitochondrial, proton carrier)	protein-coding
mm_127326.1	chr15	100304783	100304848	+	1	NA	promoter-TSS (NM_027334)	promoter-TSS (NM_027334)	-2	NM_027334	70152	Mm.488086	NM_027334	ENSMUSG00000054619	Mettl7a1	2210414H16Rik|3300001H21Rik|Aam-B|Mettl7a|UbiE1	methyltransferase like 7A1	protein-coding
mm_120077.1	chr14	57525053	57525105	+	1	NA	intron (NM_145837, intron 1 of 2)	CpG	250	NM_145837	239114	Mm.390726	NM_145837	ENSMUSG00000050222	Il17d	AI462269|IL-17D	interleukin 17D	protein-coding
mm_11538.1	chr2	32633721	32633746	+	1	NA	3' UTR (NM_001198792, exon 6 of 6)	3' UTR (NM_001198792, exon 6 of 6)	4233	NM_021515	11636	Mm.29189	NM_021515	ENSMUSG00000026817	Ak1	Ak-1|B430205N08Rik	adenylate kinase 1	protein-coding
mm_114238.1	chr13	56609647	56609648	+	1	NA	promoter-TSS (NM_009369)	promoter-TSS (NM_009369)	44	NM_009369	21810	Mm.14455	NM_009369	ENSMUSG00000035493	Tgfbi	68kDa|AI181842|AI747162|Beta-ig|big-h3	transforming growth factor, beta induced	protein-coding
mm_107093.1	chr12	17544959	17544971	+	1	NA	promoter-TSS (NM_013614)	promoter-TSS (NM_013614)	92	NM_013614	18263	Mm.34102	NM_013614	ENSMUSG00000011179	Odc1	ODC	ornithine decarboxylase, structural 1	protein-coding
mm_1690.1	chr1	75141634	75141705	+	1	NA	intron (NM_026977, intron 1 of 8)	CpG	699	NM_026977	69171	Mm.28193	NM_026977	ENSMUSG00000033159	Cnppd1	1810031K17Rik|AU043960	cyclin Pas1/PHO80 domain containing 1	protein-coding
mm_103536.1	chr11	77489803	77489809	-	1	NA	promoter-TSS (NM_172945)	promoter-TSS (NM_172945)	-128	NM_172945	268445	Mm.39296	NM_172945	ENSMUSG00000037907	Ankrd13b	AW124583|B930093C12Rik	ankyrin repeat domain 13b	protein-coding
mm_145468.1	chr18	60293373	60293387	+	1	NA	promoter-TSS (NM_001101475)	promoter-TSS (NM_001101475)	0	NM_001101475	240328	Mm.329461	NM_001101475	ENSMUSG00000090942	F830016B08Rik	Ifgga4	RIKEN cDNA F830016B08 gene	protein-coding
mm_33280.1	chr4	128743434	128743452	+	1	NA	exon (NM_018774, exon 10 of 15)	exon (NM_018774, exon 10 of 15)	-15815	NM_001009819	215493	Mm.300900	NM_001009819	ENSMUSG00000028794	A3galt2	Gm433|iGb3|iGb3S	alpha 1,3-galactosyltransferase 2 (isoglobotriaosylceramide synthase)	protein-coding
mm_132036.1	chr16	27417219	27417233	+	1	NA	intron (NM_001025615, intron 4 of 9)	intron (NM_001025615, intron 4 of 9)	28270	NM_001289436	67501	Mm.258985	NM_026202	ENSMUSG00000038127	Ccdc50	C3orf6	coiled-coil domain containing 50	protein-coding
mm_113682.1	chr13	42856762	42856786	+	1	NA	intron (NM_001005740, intron 1 of 12)	B3A|SINE|B2	-9473	NM_001302636	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding
mm_61199.1	chr7	63939221	63939275	+	1	NA	promoter-TSS (NM_021366)	promoter-TSS (NM_021366)	-333	NM_021366	50794	Mm.240473	NM_021366	ENSMUSG00000052040	Klf13	0610043C13Rik|9430029L20Rik|Bteb3|FKLF-2|FKLF2|NSLP1|RFLAT-1|RFLAT1	Kruppel-like factor 13	protein-coding
mm_125805.1	chr15	74922478	74922491	+	1	NA	Intergenic	Intergenic	-32567	NM_001164039	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_85635.1	chr9	107651700	107651709	-	1	NA	3' UTR (NM_001199218, exon 16 of 16)	3' UTR (NM_001199218, exon 16 of 16)	15695	NM_023805	76257	Mm.296560	NM_023805	ENSMUSG00000010064	Slc38a3	0610012J02Rik|D9Ucla2|Nat1|Slc38-3|Sn1|Snat3|mNAT	solute carrier family 38, member 3	protein-coding
mm_91420.1	chr10	32578338	32578342	-	1	NA	intron (NM_001013411, intron 1 of 6)	intron (NM_001013411, intron 1 of 6)	311575	NM_001013411	432450	Mm.49665	NM_001013411	ENSMUSG00000069670	Nkain2	6330571D19Rik|AW455467|Tcba1	Na+/K+ transporting ATPase interacting 2	protein-coding
mm_169859.1	chr16	3350406	3350425	+	1	NA	Intergenic	Intergenic	-241983	NM_146860	258859	Mm.377723	NM_146860	ENSMUSG00000051003	Olfr161	MOR131-1|OR912-47M6	olfactory receptor 161	protein-coding
mm_84138.1	chr9	59284179	59284189	-	1	NA	Intergenic	Intergenic	-7388	NM_028121	72141	Mm.22456	NM_028121	ENSMUSG00000025236	Adpgk	2610017G09Rik|Adp-gk|C77577	ADP-dependent glucokinase	protein-coding
mm_120385.1	chr14	64589901	64589910	+	1	NA	promoter-TSS (NR_029813)	promoter-TSS (NR_029813)	-752	NR_029813	387233		NR_029813	ENSMUSG00000065597	Mir124a-1	Mirn124a|Mirn124a-1	microRNA 124a-1	ncRNA
mm_73364.1	chr8	105602825	105602826	+	1	NA	Intergenic	Intergenic	-2404	NM_001081241	75687	Mm.41261	NM_001081241	ENSMUSG00000038604	Fam65a	2310066E14Rik|AI837433	family with sequence similarity 65, member A	protein-coding
mm_114991.1	chr13	97559942	97559978	+	1	NA	promoter-TSS (NR_046157)	promoter-TSS (NR_046157)	-40	NR_046157	328314	Mm.138047	NR_046157	ENSMUSG00000110235	Gm5086	B230311A21|EG328314	predicted gene 5086	ncRNA
mm_146030.1	chr18	69521367	69521378	+	1	NA	intron (NM_013685, intron 6 of 19)	intron (NM_013685, intron 6 of 19)	175651	NM_001083967	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding
mm_120472.1	chr14	65973422	65973435	+	1	NA	exon (NM_013492, exon 3 of 9)	exon (NM_013492, exon 3 of 9)	4945	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_89945.1	chr10	111282136	111282146	+	1	NA	exon (NM_001003717, exon 16 of 23)	exon (NM_001003717, exon 16 of 23)	-16538	NM_027914	71769	Mm.45256	NM_027914	ENSMUSG00000035759	Bbs10	1300007O09Rik|AI452285	Bardet-Biedl syndrome 10 (human)	protein-coding
mm_12695.1	chr2	76406530	76406580	+	1	NA	promoter-TSS (NM_145525)	promoter-TSS (NM_145525)	47	NM_001290733	99031	Mm.240435	NM_145525	ENSMUSG00000042359	Osbpl6	1110062M20Rik|AI596402|ORP-6|mKIAA4128	oxysterol binding protein-like 6	protein-coding
mm_27867.1	chr3	79159519	79159529	-	1	NA	Intergenic	B3|SINE|B2	-13649	NM_001099624	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_58141.1	chr6	141946792	141946821	-	1	NA	5' UTR (NM_013797, exon 1 of 14)	5' UTR (NM_013797, exon 1 of 14)	156	NM_013797	28248	Mm.103665	NM_013797	ENSMUSG00000041698	Slco1a1	A530084B21|OATP-1|Oatp1|Oatp1a1|Slc21a1	solute carrier organic anion transporter family, member 1a1	protein-coding
mm_138827.1	chr17	39847996	39848009	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	5005	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_109138.1	chr12	106408423	106408461	+	1	NA	Intergenic	Intergenic	39224	NR_036593	76639	Mm.375609	NR_036593	ENSMUSG00000092066	1700121N20Rik	-	RIKEN cDNA 1700121N20 gene	ncRNA
mm_100981.1	chr11	7210183	7210194	-	1	NA	exon (NM_008343, exon 2 of 5)	exon (NM_008343, exon 2 of 5)	3735	NM_008343	16009	Mm.29254	NM_008343	ENSMUSG00000020427	Igfbp3	AI649005|IGFBP-3|IGgfbp3	insulin-like growth factor binding protein 3	protein-coding
mm_38589.1	chr4	141821791	141821840	-	1	NA	exon (NM_007919, exon 4 of 8)	exon (NM_007919, exon 4 of 8)	4190	NM_007919	13706	Mm.45316	NM_007919	ENSMUSG00000058579	Cela2a	Ela-2|Ela2|Ela2a	chymotrypsin-like elastase family, member 2A	protein-coding
mm_11582.1	chr2	32966998	32967009	+	1	NA	Intergenic	CpG	3702	NR_002898	104367	Mm.250030	NR_002898	ENSMUSG00000065124	Snora65	MBII-351|Rnu65	small nucleolar RNA, H/ACA box 65	snoRNA
mm_144712.1	chr18	35034175	35034191	+	1	NA	Intergenic	Intergenic	-79832	NM_010481	15526	Mm.209419	NM_010481	ENSMUSG00000024359	Hspa9	74kDa|Csa|Grp75|Hsc74|Hsp74|Hsp74a|Hspa9a|Mortalin|Mot-2|Mot2|Mthsp70|Pbp74	heat shock protein 9	protein-coding
mm_160029.1	chr6	131314020	131314020	-	1	NA	promoter-TSS (NM_172891)	promoter-TSS (NM_172891)	-193	NM_172891	243659	Mm.20114	NM_172891	ENSMUSG00000032899	Styk1	9130025L13|AI326477|Nok	serine/threonine/tyrosine kinase 1	protein-coding
mm_52874.1	chr6	122342710	122342717	+	1	NA	Intergenic	Intergenic	-2486	NM_001271579	13619	Mm.6822	NM_007905	ENSMUSG00000040669	Phc1	AW557034|Edr|Edr1|Mph1|Rae-28|rae28	polyhomeotic-like 1 (Drosophila)	protein-coding
mm_37869.1	chr4	132351638	132351646	-	1	NA	TTS (NR_003270)	TTS (NR_003270)	2044	NR_003270	399101	Mm.486919	NR_002904	ENSMUSG00000085241	Snhg3	Rnu17d|U17HG	small nucleolar RNA host gene 3	ncRNA
mm_101092.1	chr11	11881138	11881147	-	1	NA	intron (NM_001190448, intron 1 of 14)	intron (NM_001190448, intron 1 of 14)	9266	NM_016672	13195	Mm.12906	NM_016672	ENSMUSG00000020182	Ddc	Aadc	dopa decarboxylase	protein-coding
mm_135263.1	chr16	38088672	38088705	-	1	NA	promoter-TSS (NM_019827)	promoter-TSS (NM_019827)	-313	NM_001347232	56637	Mm.394930	NM_019827	ENSMUSG00000022812	Gsk3b	7330414F15Rik|8430431H08Rik|C86142|GSK-3|GSK-3beta|GSK3	glycogen synthase kinase 3 beta	protein-coding
mm_133777.1	chr16	94780156	94780167	+	1	NA	intron (NM_001025584, intron 3 of 4)	intron (NM_001025584, intron 3 of 4)	76529	NM_001025590	16522	Mm.328720	NM_010606	ENSMUSG00000043301	Kcnj6	BIR1|GIRK2|KATP2|KCNJ7|Kir3.2|weaver|wv	potassium inwardly-rectifying channel, subfamily J, member 6	protein-coding
mm_120495.1	chr14	65981355	65981371	+	1	NA	3' UTR (NM_013492, exon 9 of 9)	3' UTR (NM_013492, exon 9 of 9)	12880	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_160742.1	chr10	80671980	80671980	-	1	NA	exon (NM_021462, exon 3 of 14)	exon (NM_021462, exon 3 of 14)	4313	NM_021462	17347	Mm.42126	NM_021462	ENSMUSG00000020190	Mknk2	2010016G11Rik|Gprk7|Mnk2	MAP kinase-interacting serine/threonine kinase 2	protein-coding
mm_5181.1	chr1	12991110	12991152	-	1	NA	promoter-TSS (NM_172841)	promoter-TSS (NM_172841)	4	NM_172841	240726	Mm.24481	NM_172841	ENSMUSG00000025938	Slco5a1	4732454B15|A630033C23Rik|AA407151	solute carrier organic anion transporter family, member 5A1	protein-coding
mm_171155.1	chr3	20455006	20455006	-	1	NA	Intergenic	RLTR9F|LTR|ERVK	-87829	NM_175086	11608	Mm.134863	NM_175086	ENSMUSG00000054988	Agtr1b	AT1B|AT2R1B|Agtr-1b|Angtr-1b	angiotensin II receptor, type 1b	protein-coding
mm_79454.1	chr9	56123290	56123305	+	1	NA	exon (NM_011193, exon 7 of 15)	exon (NM_011193, exon 7 of 15)	33321	NM_011193	19200	Mm.2534	NM_011193	ENSMUSG00000032322	Pstpip1	CD2BP1|def-2	proline-serine-threonine phosphatase-interacting protein 1	protein-coding
mm_23788.1	chr3	79529958	79529970	+	1	NA	intron (NM_001162999, intron 1 of 16)	intron (NM_001162999, intron 1 of 16)	37715	NM_001162999	329679	Mm.244005	NM_001162999	ENSMUSG00000061175	Fnip2	D630023B12Rik|mKIAA1450	folliculin interacting protein 2	protein-coding
mm_1841.1	chr1	82840156	82840171	+	1	NA	intron (NM_001347077, intron 1 of 12)	CpG	703	NM_001347077	15463	Mm.392569	NM_010472	ENSMUSG00000026159	Agfg1	AU045498|C130049H11Rik|C85612|D730048C23Rik|Hrb|RAB|Rip	ArfGAP with FG repeats 1	protein-coding
mm_33148.1	chr4	125176522	125176541	+	1	NA	Intergenic	Intergenic	-48650	NM_153159	230738	Mm.402	NM_153159	ENSMUSG00000042677	Zc3h12a	BC036563|MCPIP|MCPIP-1|Mcpip1|Reg1	zinc finger CCCH type containing 12A	protein-coding
mm_59387.1	chr7	26224223	26224231	+	1	NA	Intergenic	RMER17B|LTR|ERVK	-42604	NM_001167540	100312477	Mm.480246	NM_001167540	ENSMUSG00000046130	Vmn1r184	-	vomeronasal 1 receptor, 184	protein-coding
mm_170969.1	chr2	60050670	60050673	-	1	NA	intron (NM_001001182, intron 2 of 35)	intron (NM_001001182, intron 2 of 35)	75069	NM_001001182	407823	Mm.228071	NM_001001182	ENSMUSG00000026987	Baz2b	5830435C13Rik|BC053917|D2Ertd794e	bromodomain adjacent to zinc finger domain, 2B	protein-coding
mm_159784.1	chr5	106925750	106925750	-	1	NA	intron (NM_001252516, intron 1 of 9)	CpG	140	NM_177873	330149	Mm.121664	NM_177873	ENSMUSG00000043410	Hfm1	A330009G12Rik|Gm1046|Mer3|Sec63d1	HFM1, ATP-dependent DNA helicase homolog	protein-coding
mm_54653.1	chr6	39067581	39067591	-	1	NA	promoter-TSS (NR_040523)	promoter-TSS (NR_040523)	0	NR_040523	69986	Mm.490941	NR_040523	ENSMUSG00000100121	1700025N23Rik	-	RIKEN cDNA 1700025N23 gene	ncRNA
mm_9549.1	chr1	173922039	173922064	-	1	NA	3' UTR (NM_001302650, exon 9 of 9)	3' UTR (NM_001302650, exon 9 of 9)	-9005	NM_001033450	381308	Mm.490248	NM_001033450	ENSMUSG00000026536	Ifi211	A730048F03|Ifi205b|Mnda|ifi-205-B	interferon activated gene 211	protein-coding
mm_57388.1	chr6	124829468	124829478	-	1	NA	promoter-TSS (NM_013538)	promoter-TSS (NM_013538)	11	NM_001326594	22225	Mm.3571	NM_013700	ENSMUSG00000038429	Usp5	AA407472|ISOT|ISOT-1|Ucht	ubiquitin specific peptidase 5 (isopeptidase T)	protein-coding
mm_32397.1	chr4	106840208	106840246	+	1	NA	Intergenic	CpG	-35220	NM_001347159	329910	Mm.222956	NM_025590	ENSMUSG00000034853	Acot11	1110020M10Rik|2010309H15Rik|AW060409|BFIT|BFIT1|Thea|Them1|mKIAA0707	acyl-CoA thioesterase 11	protein-coding
mm_35175.1	chr4	15148962	15148972	-	1	NA	5' UTR (NM_178617, exon 1 of 13)	5' UTR (NM_178617, exon 1 of 13)	164	NM_178617	69352	Mm.389031	NM_178617	ENSMUSG00000040536	Necab1	1700003H21Rik|Efcbp1|STIP-1	N-terminal EF-hand calcium binding protein 1	protein-coding
mm_46658.1	chr5	108674810	108674815	-	1	NA	promoter-TSS (NM_001310692)	promoter-TSS (NM_001310692)	-16	NM_001310691	231583	Mm.440571	NM_174870	ENSMUSG00000046959	Slc26a1	Sat1	solute carrier family 26 (sulfate transporter), member 1	protein-coding
mm_72626.1	chr8	84657949	84657951	+	1	NA	Intergenic	RMER17C|LTR|ERVK	4902	NM_010499	15936	Mm.399	NM_010499	ENSMUSG00000053560	Ier2	AI317238|Ch1|Pip92	immediate early response 2	protein-coding
mm_103477.1	chr11	76494644	76494683	-	1	NA	promoter-TSS (NM_001346670)	promoter-TSS (NM_001346670)	-168	NM_001346670	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_141088.1	chr17	25952054	25952082	-	1	NA	Intergenic	CpG	-7137	NM_001039038	621239	Mm.381070	NM_001039038	ENSMUSG00000090113	Nhlrc4	F430201B04Rik	NHL repeat containing 4	protein-coding
mm_73073.1	chr8	94449668	94449672	+	1	NA	Intergenic	B1_Mur4|SINE|Alu	-14567	NR_015514	320377	Mm.486022	NR_015514		9330175E14Rik	A630085K21	RIKEN cDNA 9330175E14 gene	ncRNA
mm_14130.1	chr2	126034766	126034794	+	1	NA	5' UTR (NM_008008, exon 1 of 4)	5' UTR (NM_008008, exon 1 of 4)	122	NM_008008	14178	Mm.330557	NM_008008	ENSMUSG00000027208	Fgf7	Kgf	fibroblast growth factor 7	protein-coding
mm_156246.1	chrX	136270303	136270352	+	1	NA	promoter-TSS (NM_009750)	promoter-TSS (NM_009750)	74	NM_001110234	12070	Mm.90787	NM_009750	ENSMUSG00000046432	Bex3	AL033356|DXWsu67e|Gcap27|Nade|Ngfrap1	brain expressed X-linked 3	protein-coding
mm_167382.1	chr8	94355160	94355168	+	1	NA	intron (NM_019415, intron 21 of 24)	B1_Mur4|SINE|Alu	25956	NM_001205311	20497	Mm.25804	NM_019415	ENSMUSG00000031766	Slc12a3	AI035291|NCC|NCCT|TSC	solute carrier family 12, member 3	protein-coding
mm_120931.1	chr14	76488538	76488541	+	1	NA	5' UTR (NM_001177751, exon 1 of 3)	5' UTR (NM_001177751, exon 1 of 3)	103	NM_001177751	21807	Mm.153272	NM_009366	ENSMUSG00000022010	Tsc22d1	AA589566|AW105905|Egr5|TSC-22|Tgfb1i4|Tsc|Tsc22	TSC22 domain family, member 1	protein-coding
mm_113394.1	chr13	33084050	33084058	+	1	NA	promoter-TSS (NM_173052)	promoter-TSS (NM_173052)	-49	NM_173052	282663	Mm.314490	NM_173052	ENSMUSG00000051029	Serpinb1b	6330533H24Rik|EIB|Serpin1b1|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 1b	protein-coding
mm_109197.1	chr12	108635847	108635858	+	1	NA	promoter-TSS (NM_001163396)	promoter-TSS (NM_001163396)	99	NM_001163396	14026	Mm.238841	NM_007965	ENSMUSG00000021262	Evl	AI528774	Ena-vasodilator stimulated phosphoprotein	protein-coding
mm_140144.1	chr17	80061425	80061484	+	1	NA	intron (NM_144802, intron 1 of 12)	CpG	814	NM_144802	72692	Mm.64579	NM_144802	ENSMUSG00000024095	Hnrnpll	2510028H02Rik|2810036L13Rik|AI256697|AI852082|Hnrpll	heterogeneous nuclear ribonucleoprotein L-like	protein-coding
mm_55815.1	chr6	83033413	83033419	-	1	NA	promoter-TSS (NM_013586)	promoter-TSS (NM_013586)	55	NM_010070	13448	Mm.156	NM_010070	ENSMUSG00000068335	Dok1	AW557123|p62DOK	docking protein 1	protein-coding
mm_70785.1	chr8	22476874	22476909	+	1	NA	promoter-TSS (NM_001146117)	promoter-TSS (NM_001146117)	-12	NM_001146117	102032	Mm.378231	NM_001012667	ENSMUSG00000031534	Smim19	AI316807|BG694986|EST-c39	small integral membrane protein 19	protein-coding
mm_71007.1	chr8	31115039	31115063	+	1	NA	intron (NM_175136, intron 1 of 5)	intron (NM_175136, intron 1 of 5)	3205	NM_175136	68867	Mm.29532	NM_175136	ENSMUSG00000039328	Rnf122	1110063C11Rik	ring finger protein 122	protein-coding
mm_94044.1	chr10	128176592	128176611	-	1	NA	promoter-TSS (NM_019711)	promoter-TSS (NM_019711)	-33	NM_019711	56516	Mm.42247	NM_019711	ENSMUSG00000040043	Rbms2	2610315E04Rik|Scr3	RNA binding motif, single stranded interacting protein 2	protein-coding
mm_107722.1	chr12	56691512	56691528	+	1	NA	Intergenic	CpG	-3951	NM_011041	18511	Mm.5035	NM_011041	ENSMUSG00000001497	Pax9	Pax-9	paired box 9	protein-coding
mm_97122.1	chr11	74898082	74898106	+	1	NA	promoter-TSS (NM_177325)	promoter-TSS (NM_177325)	14	NM_177325	104662	Mm.220843	NM_177325	ENSMUSG00000038335	Tsr1	AU040765|AW550801|mKIAA1401	TSR1 20S rRNA accumulation	protein-coding
mm_134389.1	chr16	17346957	17346987	-	1	NA	intron (NM_001001983, intron 19 of 54)	Lx5b|LINE|L1	15601	NM_001331047	15160	Mm.6609	NM_008223	ENSMUSG00000022766	Serpind1	AA985900|AI303446|HC-II|HCII|Hcf2	serine (or cysteine) peptidase inhibitor, clade D, member 1	protein-coding
mm_143211.1	chr17	62881393	62881458	-	1	NA	promoter-TSS (NM_207654)	promoter-TSS (NM_207654)	-108	NM_010109	13640	Mm.7978	NM_010109	ENSMUSG00000048915	Efna5	AL-1|AV158822|EFL-5|Ephrin-A5|Epl7|LERK-7|RAGS	ephrin A5	protein-coding
mm_158710.1	chrX	162531117	162531121	-	1	NA	intron (NM_178256, intron 5 of 17)	B1F|SINE|Alu	112539	NM_001290633	194590	Mm.442441	NM_178256	ENSMUSG00000040855	Reps2	POB1	RALBP1 associated Eps domain containing protein 2	protein-coding
mm_36013.1	chr4	56865136	56865208	-	1	NA	promoter-TSS (NM_018761)	promoter-TSS (NM_018761)	39	NM_018761	54366	Mm.218891	NM_018761	ENSMUSG00000038816	Ctnnal1	ACRP|AI616177|AW545119|C86009|Catnal1	catenin (cadherin associated protein), alpha-like 1	protein-coding
mm_53564.1	chr6	137252339	137252354	+	1	NA	promoter-TSS (NM_011216)	promoter-TSS (NM_011216)	47	NM_011216	19277	Mm.186361	NM_011216	ENSMUSG00000030223	Ptpro	D28|GLEPP1|PTPBK|PTPROt|PTPU2|PTPoc|PTPphi|Ptpn15|R-PTP-O	protein tyrosine phosphatase, receptor type, O	protein-coding
mm_59601.1	chr7	28140078	28140083	+	1	NA	exon (NM_001164655, exon 5 of 20)	exon (NM_001164655, exon 5 of 20)	10614	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_19229.1	chr2	84670728	84670742	-	1	NA	promoter-TSS (NM_001033166)	promoter-TSS (NM_001033166)	-27	NM_001037279	72657	Mm.259293	NM_001033166	ENSMUSG00000076437	Selenoh	2700094K13Rik|Selh	selenoprotein H	protein-coding
mm_165885.1	chr4	42880377	42880405	+	1	NA	Intergenic	Intergenic	-6188	NM_177785	277773	Mm.212727	NM_177785	ENSMUSG00000050141	Fam205c	4931430D02|FAM205CP	family with sequence similarity 205, member C	protein-coding
mm_146121.1	chr18	74442425	74442436	+	1	NA	promoter-TSS (NM_201600)	promoter-TSS (NM_201600)	-189	NM_201600	17919	Mm.260098	NM_008661	ENSMUSG00000025885	Myo5b	AI661750|mKIAA1119	myosin VB	protein-coding
mm_20976.1	chr2	151973459	151973472	-	1	NA	promoter-TSS (NM_001289151)	promoter-TSS (NM_001289151)	-71	NM_001289151	73847	Mm.272444	NM_028666	ENSMUSG00000027459	Fam110a	1700008J10Rik|5430432M24Rik|AI747080	family with sequence similarity 110, member A	protein-coding
mm_5233.1	chr1	14310220	14310242	-	1	NA	promoter-TSS (NM_001252192)	promoter-TSS (NM_001252192)	-32	NM_010164	14048	Mm.250185	NM_010164	ENSMUSG00000025932	Eya1	bor	EYA transcriptional coactivator and phosphatase 1	protein-coding
mm_89415.1	chr10	90829983	90829986	+	1	NA	5' UTR (NM_001347053, exon 1 of 9)	5' UTR (NM_001347053, exon 1 of 9)	141	NM_001347053	77531	Mm.440605	NM_181398	ENSMUSG00000058589	Anks1b	AIDA-1b|C030032C09Rik|E530015N03Rik|ENSMUSG00000078431|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding
mm_89871.1	chr10	108260831	108260845	+	1	NA	exon (NM_027892, exon 16 of 26)	exon (NM_027892, exon 16 of 26)	-71351	NM_054056	114774	Mm.391419	NM_054056	ENSMUSG00000035873	Pawr	2310001G03Rik|PAR4|Par-4	PRKC, apoptosis, WT1, regulator	protein-coding
mm_124787.1	chr15	8103018	8103018	+	1	NA	Intergenic	ORR1A3|LTR|ERVL-MaLR	-3809	NM_001081402	545085	Mm.321312	NM_198413	ENSMUSG00000039828	Wdr70	4833422F06Rik	WD repeat domain 70	protein-coding
mm_47207.1	chr5	120941976	120941984	-	1	NA	3' UTR (NM_011286, exon 22 of 22)	3' UTR (NM_011286, exon 22 of 22)	27162	NM_133893	100535	Mm.247620	NM_133893	ENSMUSG00000032623	Oas1d	AA536864|C85127|oasl8	2'-5' oligoadenylate synthetase 1D	protein-coding
mm_153046.1	chr19	32068804	32068812	-	1	NA	intron (NM_018830, intron 2 of 23)	intron (NM_018830, intron 2 of 23)	34332	NM_018830	54447	Mm.491229	NM_018830	ENSMUSG00000024887	Asah2	AI585898	N-acylsphingosine amidohydrolase 2	protein-coding
mm_152223.1	chr19	8663290	8663314	-	1	NA	promoter-TSS (NM_007698)	promoter-TSS (NM_007698)	33	NR_045314	402757	Mm.150255	NR_045314		9830166K06Rik	-	RIKEN cDNA 9830166K06 gene	ncRNA
mm_103294.1	chr11	72454440	72454474	-	1	NA	intron (NM_153060, intron 9 of 12)	intron (NM_153060, intron 9 of 12)	13079	NM_016776	18432	Mm.147946	NM_016776	ENSMUSG00000040463	Mybbp1a	AL024407|AU019902|P160|p160MBP|p67MBP	MYB binding protein (P160) 1a	protein-coding
mm_116310.1	chr13	37049183	37049191	-	1	NA	promoter-TSS (NM_028784)	promoter-TSS (NM_028784)	26	NM_028784	74145	Mm.235105	NM_028784	ENSMUSG00000039109	F13a1	1200014I03Rik|AI462306|F13a	coagulation factor XIII, A1 subunit	protein-coding
mm_93941.1	chr10	127193134	127193160	-	1	NA	exon (NM_030714, exon 4 of 6)	exon (NM_030714, exon 4 of 6)	-2102	NR_045715	100038591	Mm.441071	NR_045715	ENSMUSG00000097331	F420014N23Rik	ENSMUSG00000074658	RIKEN cDNA F420014N23 gene	ncRNA
mm_173265.1	chrX	94917726	94917743	+	1	NA	Intergenic	Intergenic	108948	NM_178753	270624	Mm.115205	NM_178753	ENSMUSG00000071722	Spin4	9630042H07Rik	spindlin family, member 4	protein-coding
mm_128667.1	chr15	60187028	60187031	-	1	NA	Intergenic	Intergenic	-170411	NM_027668	71088	Mm.425950	NM_027668	ENSMUSG00000071749	4933412E24Rik	-	RIKEN cDNA 4933412E24 gene	protein-coding
mm_101183.1	chr11	17008648	17008687	-	1	NA	promoter-TSS (NM_019549)	promoter-TSS (NM_019549)	51	NM_019549	56193	Mm.98232	NM_019549	ENSMUSG00000020120	Plek	2010300B13Rik	pleckstrin	protein-coding
mm_95625.1	chr11	53583963	53583973	+	1	NA	exon (NM_008443, exon 7 of 18)	exon (NM_008443, exon 7 of 18)	16599	NM_001290806	16568	Mm.88694	NM_008443	ENSMUSG00000018395	Kif3a	Kif3|Kifl|Kns3	kinesin family member 3A	protein-coding
mm_108397.1	chr12	81036181	81036184	+	1	NA	intron (NM_022316, intron 1 of 12)	intron (NM_022316, intron 1 of 12)	9374	NM_022316	64075	Mm.273295	NM_022316	ENSMUSG00000021136	Smoc1	2600002F22Rik|AI848508|SRG	SPARC related modular calcium binding 1	protein-coding
mm_172831.1	chr9	22203809	22203828	-	1	NA	intron (NR_030448, intron 1 of 4)	ORR1A1|LTR|ERVL-MaLR	10042	NR_027981	69862	Mm.488068	NM_001033151	ENSMUSG00000090925	1810064F22Rik	-	RIKEN cDNA 1810064F22 gene	ncRNA
mm_159438.1	chr3	123279165	123279165	+	1	NA	exon (NM_027135, exon 3 of 23)	exon (NM_027135, exon 3 of 23)	11669	NM_027135	69608	Mm.29293	NM_027135	ENSMUSG00000039234	Sec24d	2310020L09Rik|Gm1349	Sec24 related gene family, member D (S. cerevisiae)	protein-coding
mm_39667.1	chr5	25247345	25247356	+	1	NA	intron (NM_144908, intron 1 of 11)	intron (NM_144908, intron 1 of 11)	24457	NM_144908	231050	Mm.21814	NM_144908	ENSMUSG00000038072	Galnt11	A430075I06Rik|AI648252|E430002F06Rik	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 11	protein-coding
mm_168178.1	chr10	56497510	56497523	+	1	NA	Intergenic	Intergenic	120216	NM_010288	14609	Mm.378921	NM_010288	ENSMUSG00000050953	Gja1	AU042049|AW546267|Cnx43|Cx43|Cx43alpha1|Gja-1|Npm1|connexin43	gap junction protein, alpha 1	protein-coding
mm_75223.1	chr8	39610465	39610479	-	1	NA	intron (NM_001113326, intron 7 of 9)	L1MC2|LINE|L1	32206	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_27899.1	chr3	79458498	79458524	-	1	NA	3' UTR (NM_001162999, exon 17 of 17)	3' UTR (NM_001162999, exon 17 of 17)	109168	NM_001162999	329679	Mm.244005	NM_001162999	ENSMUSG00000061175	Fnip2	D630023B12Rik|mKIAA1450	folliculin interacting protein 2	protein-coding
mm_152913.1	chr19	27399085	27399094	-	1	NA	exon (NM_177474, exon 15 of 18)	exon (NM_177474, exon 15 of 18)	30819	NM_177474	52874	Mm.261027	NM_177474	ENSMUSG00000041360	Pum3	1110069H02Rik|AA675048|D19Bwg1357e|Kiaa0020	pumilio RNA-binding family member 3	protein-coding
mm_98623.1	chr11	95858906	95858932	+	1	NA	non-coding (NR_045187, exon 1 of 2)	non-coding (NR_045187, exon 1 of 2)	102	NR_045187	73906	Mm.399894	NR_045187	ENSMUSG00000086015	4833417C18Rik	-	RIKEN cDNA 4833417C18 gene	ncRNA
mm_108003.1	chr12	73548477	73548481	+	1	NA	promoter-TSS (NR_044985)	promoter-TSS (NR_044985)	-4	NR_044985	73644	Mm.369885	NR_044985		2210039B01Rik	-	RIKEN cDNA 2210039B01 gene	ncRNA
mm_8147.1	chr1	136415509	136415530	-	1	NA	promoter-TSS (NR_024328)	promoter-TSS (NR_024328)	0	NR_024328	320054	Mm.208000	NR_024328	ENSMUSG00000097403	9230116N13Rik	-	RIKEN cDNA 9230116N13 gene	ncRNA
mm_3121.1	chr1	134646702	134646711	+	1	NA	promoter-TSS (NM_009307)	promoter-TSS (NM_009307)	25	NM_009307	20980	Mm.5102	NM_009307	ENSMUSG00000026452	Syt2	IP4BP|R74640|mKIAA4194	synaptotagmin II	protein-coding
mm_130305.1	chr15	97020080	97020086	-	1	NA	intron (NM_027052, intron 1 of 15)	intron (NM_027052, intron 1 of 15)	35873	NM_027052	69354	Mm.250980	NM_027052	ENSMUSG00000022464	Slc38a4	1110012E16Rik|1700012A18Rik|Ata3|mATA3|mNAT3	solute carrier family 38, member 4	protein-coding
mm_94014.1	chr10	127643661	127643672	-	1	NA	intron (NM_009284, intron 1 of 21)	intron (NM_009284, intron 1 of 21)	680	NM_009284	20852	Mm.121721	NM_009284	ENSMUSG00000002147	Stat6	-	signal transducer and activator of transcription 6	protein-coding
mm_63785.1	chr7	132129782	132129783	+	1	NA	intron (NM_018867, intron 2 of 13)	intron (NM_018867, intron 2 of 13)	24959	NM_018867	55987	Mm.471654	NM_018867	ENSMUSG00000030862	Cpxm2	4632435C11Rik|CPX-2|Cpx2	carboxypeptidase X 2 (M14 family)	protein-coding
mm_44958.1	chr5	36696698	36696731	-	1	NA	promoter-TSS (NM_001081232)	promoter-TSS (NM_001081232)	-693	NM_001081232	320661	Mm.26480	NM_177221	ENSMUSG00000029190	D5Ertd579e	9030221A05Rik|A930018H20Rik|Kiaa0232	DNA segment, Chr 5, ERATO Doi 579, expressed	protein-coding
mm_110015.1	chr12	16646958	16646975	-	1	NA	Intergenic	Intergenic	-6504	NM_008747	18217	Mm.281715	NM_008747	ENSMUSG00000020591	Ntsr2	NT2R|NTRL	neurotensin receptor 2	protein-coding
mm_86145.1	chr9	117252066	117252082	-	1	NA	5' UTR (NM_001172126, exon 1 of 13)	5' UTR (NM_001172126, exon 1 of 13)	409	NM_001172123	207181	Mm.326411	NM_178660	ENSMUSG00000039607	Rbms3	6720477E09Rik|8430436O14Rik	RNA binding motif, single stranded interacting protein	protein-coding
mm_172747.1	chr8	81770759	81770760	+	1	NA	intron (NM_001024617, intron 6 of 24)	intron (NM_001024617, intron 6 of 24)	428197	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_43505.1	chr5	136987444	136987459	+	1	NA	promoter-TSS (NM_001310748)	promoter-TSS (NM_001310748)	432	NM_011962	26433	Mm.251003	NM_011962	ENSMUSG00000004846	Plod3	AI414586|LH3	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3	protein-coding
mm_81015.1	chr9	104076404	104076438	+	1	NA	exon (NM_175324, exon 4 of 20)	exon (NM_175324, exon 4 of 20)	12718	NM_175324	102632	Mm.41274	NM_175324	ENSMUSG00000090150	Acad11	5730439E10Rik|AI987948	acyl-Coenzyme A dehydrogenase family, member 11	protein-coding
mm_31406.1	chr4	48047385	48047389	+	1	NA	intron (NM_015743, intron 1 of 7)	CpG	2082	NM_015743	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_154652.1	chrX	7841761	7841774	+	1	NA	promoter-TSS (NM_001290536)	promoter-TSS (NM_001290536)	-64	NM_001290536	54644	Mm.142827	NM_138604	ENSMUSG00000031154	Otud5	AA407879|AI553596|BB114028|DUBA|DXImx46e|Sfc7	OTU domain containing 5	protein-coding
mm_169720.1	chr15	77895318	77895318	-	1	NA	Intergenic	IAPLTR1_Mm|LTR|ERVK	33676	NM_019913	56551	Mm.291917	NM_019913	ENSMUSG00000005354	Txn2	2510006J11Rik|AI788873|Trx2	thioredoxin 2	protein-coding
mm_75040.1	chr8	32668430	32668435	-	1	NA	Intergenic	Intergenic	281594	NM_001177589	100042715	Mm.291093	NM_001177589		Gm3985	-	predicted gene 3985	protein-coding
mm_124951.1	chr15	12824842	12824883	+	1	NA	promoter-TSS (NM_029998)	promoter-TSS (NM_029998)	47	NM_001130149	14000	Mm.293142	NM_026799	ENSMUSG00000022191	Drosha	1110013A17Rik|AI874853|Etohi2|Rn3|Rnasen	drosha, ribonuclease type III	protein-coding
mm_155960.1	chrX	106012127	106012130	+	1	NA	promoter-TSS (NM_001190409)	promoter-TSS (NM_001190409)	-229	NM_025952	67075	Mm.275943	NM_025952	ENSMUSG00000031232	Magt1	2410001C15Rik|2610529C04Rik|2810482I07Rik|IAG2|IAP	magnesium transporter 1	protein-coding
mm_34522.1	chr4	149104131	149104189	+	1	NA	promoter-TSS (NM_001025296)	promoter-TSS (NM_001025296)	18	NM_001025296	13347	Mm.41433	NM_010044	ENSMUSG00000028974	Dffa	A330085O09Rik|DFF35|Dff45|ICAD|ICAD-L|ICAD-S	DNA fragmentation factor, alpha subunit	protein-coding
mm_107103.1	chr12	17748281	17748285	+	1	NA	intron (NM_016677, intron 1 of 3)	intron (NM_016677, intron 1 of 3)	57469	NM_016677	53602	Mm.313619	NM_016677	ENSMUSG00000071379	Hpcal1	NVP-3|Nvp3|VILIP3|Vnsl3|Vsnl3	hippocalcin-like 1	protein-coding
mm_94489.1	chr11	6672695	6672696	+	1	NA	intron (NM_019511, intron 1 of 2)	intron (NM_019511, intron 1 of 2)	-12459	NR_028586	100041311	Mm.388018	NR_028586	ENSMUSG00000086373	Gm11978	OTTMUSG00000005125|OTTMUSG00000005127	predicted gene 11978	pseudo
mm_23923.1	chr3	83686676	83686681	+	1	NA	Intergenic	Intergenic	-79643	NM_009144	20319	Mm.19155	NM_009144	ENSMUSG00000027996	Sfrp2	AI851596|Sdf5	secreted frizzled-related protein 2	protein-coding
mm_89739.1	chr10	99023438	99023457	+	1	NA	3' UTR (NM_026482, exon 21 of 21)	3' UTR (NM_026482, exon 21 of 21)	-83724	NM_027740	382406	Mm.440656	NM_027740	ENSMUSG00000019952	Poc1b	4933430F16Rik|Wdr51b	POC1 centriolar protein B	protein-coding
mm_120178.1	chr14	61173087	61173100	+	1	NA	intron (NM_172809, intron 2 of 9)	CpG	34636	NM_172809	50720	Mm.440703	NM_015788	ENSMUSG00000048279	Sacs	A230052M14|DNAJC29|E130115J16Rik|mKIAA0730	sacsin	protein-coding
mm_112405.1	chr13	3541811	3541814	+	1	NA	intron (NM_008112, intron 1 of 10)	intron (NM_008112, intron 1 of 10)	3737	NM_008112	14569	Mm.153226	NM_008112	ENSMUSG00000021218	Gdi2	GDI-B|GDIB|Gdi3	guanosine diphosphate (GDP) dissociation inhibitor 2	protein-coding
mm_56950.1	chr6	119981460	119981478	-	1	NA	intron (NM_001185021, intron 4 of 25)	intron (NM_001185021, intron 4 of 25)	52842	NR_030487	735290		NR_030487	ENSMUSG00000076217	Mir706	Mirn706|mir-706|mmu-mir-706	microRNA 706	ncRNA
mm_60702.1	chr7	45215774	45215816	+	1	NA	promoter-TSS (NM_001285498)	promoter-TSS (NM_001285498)	42	NM_001285498	21677	Mm.3019	NM_011565	ENSMUSG00000030796	Tead2	ETF|Etdf|TEAD-2|TEF-4|TEF4	TEA domain family member 2	protein-coding
mm_27258.1	chr3	37419574	37419605	-	1	NA	promoter-TSS (NM_001291044)	promoter-TSS (NM_001291044)	7	NM_001291044	229228	Mm.436967	NM_153561	ENSMUSG00000050174	Nudt6	Asfgf2b	nudix (nucleoside diphosphate linked moiety X)-type motif 6	protein-coding
mm_118249.1	chr13	112001188	112001195	-	1	NA	Intergenic	Intergenic	133255	NR_130345	102636620	Mm.402328	NR_130345	ENSMUSG00000086111	Gm15326	OTTMUSG00000020187	predicted gene 15326	ncRNA
mm_90876.1	chr10	9649718	9649733	-	1	NA	intron (NM_177271, intron 1 of 1)	intron (NM_177271, intron 1 of 1)	25483	NM_177271	320825	Mm.101115	NM_177271	ENSMUSG00000060487	Samd5	E130306M17Rik	sterile alpha motif domain containing 5	protein-coding
mm_28031.1	chr3	83049115	83049129	-	1	NA	intron (NM_181849, intron 1 of 7)	PB1D7|SINE|Alu	741	NM_181849	110135	Mm.30063	NM_181849	ENSMUSG00000033831	Fgb	2510049G14Rik	fibrinogen beta chain	protein-coding
mm_49426.1	chr6	29271331	29271380	+	1	NA	Intergenic	Intergenic	-1133	NM_001190461	69573	Mm.45161	NM_023516	ENSMUSG00000043421	Hilpda	2310016C08Rik|AW049004|Hig2	hypoxia inducible lipid droplet associated	protein-coding
mm_77184.1	chr8	111743800	111743857	-	1	NA	promoter-TSS (NM_009954)	promoter-TSS (NM_009954)	21	NM_009954	12927	Mm.3758	NM_009954	ENSMUSG00000031955	Bcar1	AI385681|Cas|Crkas	breast cancer anti-estrogen resistance 1	protein-coding
mm_64307.1	chr7	141862974	141862987	+	1	NA	exon (NM_028801, exon 31 of 49)	exon (NM_028801, exon 31 of 49)	23908	NM_028801	74180	Mm.200752	NM_028801	ENSMUSG00000066108	Muc5b	2300002I04Rik|A130042M24|AV085033|MUC5|MUC9|mucin 5b	mucin 5, subtype B, tracheobronchial	protein-coding
mm_46090.1	chr5	92347035	92347055	-	1	NA	3' UTR (NM_021274, exon 4 of 4)	3' UTR (NM_021274, exon 4 of 4)	1844	NM_021274	15945	Mm.877	NM_021274	ENSMUSG00000034855	Cxcl10	C7|CRG-2|INP10|IP-10|IP10|Ifi10|Scyb10|gIP-10|mob-1	chemokine (C-X-C motif) ligand 10	protein-coding
mm_154275.1	chr19	60787834	60787837	-	1	NA	intron (NM_010123, intron 1 of 21)	PB1D10|SINE|Alu	2858	NM_010123	13669	Mm.2238	NM_010123	ENSMUSG00000024991	Eif3a	A830012B05Rik|Csma|Eif3|Eif3s10|mKIAA0139	eukaryotic translation initiation factor 3, subunit A	protein-coding
mm_100877.1	chr11	5972447	5972472	-	1	NA	intron (NM_007595, intron 19 of 20)	intron (NM_007595, intron 19 of 20)	16701	NM_019661	56418	Mm.294821	NM_019661	ENSMUSG00000002741	Ykt6	0610042I15Rik|1810013M05Rik|AW105923	YKT6 v-SNARE homolog (S. cerevisiae)	protein-coding
mm_161665.1	chr17	12855039	12855039	-	1	NA	5' UTR (NM_008552, exon 4 of 9)	5' UTR (NM_008552, exon 4 of 9)	13104	NM_008552	17171	Mm.425994	NM_008552	ENSMUSG00000068037	Mas1	Mas-1|Mgra	MAS1 oncogene	protein-coding
mm_99527.1	chr11	103170964	103170978	+	1	NA	promoter-TSS (NM_001077698)	promoter-TSS (NM_001077698)	-167	NM_001077698	57778	Mm.138913	NM_019679	ENSMUSG00000055805	Fmnl1	8030453N10Rik|AI553564|Fmnl|Fnrl|Frls	formin-like 1	protein-coding
mm_53855.1	chr6	149193902	149193905	+	1	NA	Intergenic	RLTR30B_MM|LTR|ERV1	-5191	NM_001113424	232566	Mm.209147	NM_001113424	ENSMUSG00000068250	Amn1	5830467E07Rik|A230083D09|C730024G19Rik	antagonist of mitotic exit network 1	protein-coding
mm_87791.1	chr10	60299093	60299198	+	1	NA	exon (NM_011179, exon 9 of 15)	exon (NM_011179, exon 9 of 15)	14684	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_171986.1	chr5	93382048	93382052	-	1	NA	Intergenic	L1Md_T|LINE|L1	114477	NM_007635	12452	Mm.3527	NM_007635	ENSMUSG00000029385	Ccng2	-	cyclin G2	protein-coding
mm_38967.1	chr4	150902101	150902119	-	1	NA	intron (NM_020569, intron 5 of 6)	intron (NM_020569, intron 5 of 6)	7811	NM_020569	57320	Mm.277349	NM_020569	ENSMUSG00000028964	Park7	DJ-1|Dj1	Parkinson disease (autosomal recessive, early onset) 7	protein-coding
mm_100853.1	chr11	5837728	5837736	-	1	NA	exon (NM_017401, exon 1 of 11)	exon (NM_017401, exon 1 of 11)	284	NM_017401	54125	Mm.260194	NM_017401	ENSMUSG00000020474	Polm	AI462166|B230309I03Rik|Tdt-N	polymerase (DNA directed), mu	protein-coding
mm_88262.1	chr10	73822178	73822193	+	1	NA	5' UTR (NM_001142743, exon 1 of 35)	5' UTR (NM_001142743, exon 1 of 35)	318	NM_001142735	11994	Mm.338933	NM_023115	ENSMUSG00000052613	Pcdh15	BB078305|ENSMUSG00000046980|Gm9815|Ush1f|av|nmf19|roda	protocadherin 15	protein-coding
mm_134549.1	chr16	19918289	19918293	-	1	NA	Intergenic	Intergenic	-34017	NR_015488	68162	Mm.35159	NR_015488		A930003A15Rik	AI853191	RIKEN cDNA A930003A15 gene	ncRNA
mm_106533.1	chr11	120573660	120573661	-	1	NA	promoter-TSS (NM_011032)	promoter-TSS (NM_011032)	-724	NM_011032	18453	Mm.16660	NM_011032	ENSMUSG00000025130	P4hb	ERp59|PDI|Pdia1|Thbp	prolyl 4-hydroxylase, beta polypeptide	protein-coding
mm_12376.1	chr2	69822798	69822870	+	1	NA	intron (NM_177784, intron 1 of 3)	CpG	464	NM_177784	277396	Mm.138073	NM_177784	ENSMUSG00000042155	Klhl23	C130068N17Rik	kelch-like 23	protein-coding
mm_144397.1	chr18	20673832	20673867	+	1	NA	3' UTR (NM_013697, exon 4 of 4)	3' UTR (NM_013697, exon 4 of 4)	8599	NM_013697	22139	Mm.2108	NM_013697	ENSMUSG00000061808	Ttr	AA408768|AI787086|D17860|prealbumin	transthyretin	protein-coding
mm_75058.1	chr8	33660606	33660618	-	1	NA	intron (NM_010344, intron 1 of 12)	intron (NM_010344, intron 1 of 12)	7374	NM_010344	14782	Mm.283573	NM_010344	ENSMUSG00000031584	Gsr	AI325518|D8Ertd238e|Gr-1|Gr1	glutathione reductase	protein-coding
mm_70135.1	chr7	143242713	143242720	-	1	NA	non-coding (NR_001461, exon 1 of 1)	non-coding (NR_001461, exon 1 of 1)	53831	NR_001461	63830	Mm.356096	NR_001461	ENSMUSG00000101609	Kcnq1ot1	Kvlqt1-as|Lit1|Tssc8	KCNQ1 overlapping transcript 1	ncRNA
mm_86072.1	chr9	114778788	114778808	-	1	NA	intron (NM_001252479, intron 1 of 3)	intron (NM_001252479, intron 1 of 3)	3195	NM_133978	102545	Mm.35600	NM_133978	ENSMUSG00000032436	Cmtm7	AI481279|Cklfsf7|LNV	CKLF-like MARVEL transmembrane domain containing 7	protein-coding
mm_43432.1	chr5	136083943	136084010	+	1	NA	promoter-TSS (NM_133914)	promoter-TSS (NM_133914)	60	NM_001039103	54153	Mm.290655	NM_133914	ENSMUSG00000004952	Rasa4	AA793972|AW112107|BB079060|CAPRI|GAPL	RAS p21 protein activator 4	protein-coding
mm_36702.1	chr4	96786735	96786737	-	1	NA	Intergenic	Intergenic	-1576	NM_001081284	620779	Mm.439625	NM_001081284	ENSMUSG00000078639	Gm12695	OTTMUSG00000008003	predicted gene 12695	protein-coding
mm_60239.1	chr7	43713211	43713214	+	1	NA	intron (NM_001039042, intron 1 of 5)	intron (NM_001039042, intron 1 of 5)	645	NM_001039042	626834	Mm.389891	NM_001039042	ENSMUSG00000054046	Klk13	Egfbp-2|mGk-13	kallikrein related-peptidase 13	protein-coding
mm_51983.1	chr6	91983368	91983370	+	1	NA	intron (NM_172731, intron 1 of 20)	intron (NM_172731, intron 1 of 20)	4404	NM_172731	232237	Mm.295740	NM_172731	ENSMUSG00000034037	Fgd5	C330025N11Rik|ZFYVE23|mFLJ00274	FYVE, RhoGEF and PH domain containing 5	protein-coding
mm_62212.1	chr7	97911107	97911132	+	1	NA	exon (NM_011035, exon 15 of 15)	exon (NM_011035, exon 15 of 15)	-8839	NM_177696	233537	Mm.375772	NM_177696	ENSMUSG00000035582	Gdpd4	4921513O04	glycerophosphodiester phosphodiesterase domain containing 4	protein-coding
mm_137847.1	chr17	31057769	31057778	+	1	NA	promoter-TSS (NM_009593)	promoter-TSS (NM_009593)	79	NM_009593	11307	Mm.15691	NM_009593	ENSMUSG00000024030	Abcg1	AW413978|Abc8|White	ATP-binding cassette, sub-family G (WHITE), member 1	protein-coding
mm_13805.1	chr2	119047117	119047121	+	1	NA	promoter-TSS (NM_029617)	promoter-TSS (NM_029617)	0	NM_029617	76464	Mm.202518	NM_029617	ENSMUSG00000027326	Knl1	2310043D08Rik|5730505K17Rik|Casc5	kinetochore scaffold 1	protein-coding
mm_109423.1	chr12	110516209	110516213	+	1	NA	intron (NM_012023, intron 1 of 13)	intron (NM_012023, intron 1 of 13)	30472	NM_012023	26931	Mm.240396	NM_012023	ENSMUSG00000017843	Ppp2r5c	2610043M05Rik|2700063L20Rik|AI060890|AW545884|C85228|D12Bwg0916e|mKIAA0044	protein phosphatase 2, regulatory subunit B', gamma	protein-coding
mm_5224.1	chr1	14304617	14304683	-	1	NA	intron (NM_001310459, intron 1 of 17)	intron (NM_001310459, intron 1 of 17)	5549	NM_001310459	14048	Mm.250185	NM_010164	ENSMUSG00000025932	Eya1	bor	EYA transcriptional coactivator and phosphatase 1	protein-coding
mm_103682.1	chr11	79287573	79287584	-	1	NA	Intergenic	Intergenic	-32883	NM_019653	78889	Mm.307022	NM_019653	ENSMUSG00000017677	Wsb1	1110056B13Rik|2700038M07Rik	WD repeat and SOCS box-containing 1	protein-coding
mm_6791.1	chr1	84144512	84144520	-	1	NA	intron (NM_001003948, intron 2 of 2)	MER2|DNA|TcMar-Tigger	74445	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_96089.1	chr11	60353325	60353408	+	1	NA	promoter-TSS (NM_001039093)	promoter-TSS (NM_001039093)	-14	NM_029044	74665	Mm.133570	NM_029044	ENSMUSG00000056598	Lrrc48	4930449E07Rik|Drc3	leucine rich repeat containing 48	protein-coding
mm_152233.1	chr19	8709257	8709267	-	1	NA	exon (NM_008577, exon 6 of 9)	exon (NM_008577, exon 6 of 9)	4635	NM_008577	17254	Mm.4114	NM_008577	ENSMUSG00000010095	Slc3a2	4F2|4F2HC|AI314110|Cd98|Ly-10|Ly-m10|Ly10|Mdu1|Mgp-2hc|NACAE	solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2	protein-coding
mm_88563.1	chr10	79664554	79664564	+	1	NA	promoter-TSS (NM_013591)	promoter-TSS (NM_013591)	-15	NM_013591	17123	Mm.391556	NM_013591	ENSMUSG00000020310	Madcam1	AV211525	mucosal vascular addressin cell adhesion molecule 1	protein-coding
mm_88947.1	chr10	81340848	81340870	+	1	NA	intron (NM_148951, intron 3 of 5)	intron (NM_148951, intron 3 of 5)	2407	NM_148951	209047	Mm.218755	NM_148951	ENSMUSG00000034872	Gipc3	Ahl5|Rgs19ip3	GIPC PDZ domain containing family, member 3	protein-coding
mm_161258.1	chr13	115090873	115090873	-	1	NA	promoter-TSS (NM_134058)	promoter-TSS (NM_134058)	-715	NM_134058	105083	Mm.486295	NM_134058	ENSMUSG00000042275	Pelo	AA409897|AI852218	pelota homolog (Drosophila)	protein-coding
mm_154969.1	chrX	37131000	37131033	+	1	NA	exon (NM_025937, exon 2 of 9)	exon (NM_025937, exon 2 of 9)	4253	NM_025937	67050	Mm.55422	NM_025937	ENSMUSG00000016409	Nkap	2610020O08Rik|AA987160|AI849147|AL024236	NFKB activating protein	protein-coding
mm_42234.1	chr5	113550999	113551017	+	1	NA	exon (NM_177292, exon 1 of 8)	exon (NM_177292, exon 1 of 8)	588	NM_177292	320916	Mm.102783	NM_177292	ENSMUSG00000063430	Wscd2	4933413A10Rik|C530024P05Rik|Gm450	WSC domain containing 2	protein-coding
mm_149596.1	chr19	16226955	16226964	+	1	NA	intron (NM_008139, intron 2 of 6)	Lx3A|LINE|L1	62861	NR_033228	595139	Mm.405662	NR_033228		E030024N20Rik	9030417F11Rik|Ppia-ps8	peptidylprolyl isomerase A pseudogene 8	pseudo
mm_156397.1	chrX	139808272	139808290	+	1	NA	intron (NM_016675, intron 1 of 1)	intron (NM_016675, intron 1 of 1)	7473	NM_016675	12738	Mm.117068	NM_016675	ENSMUSG00000047230	Cldn2	AL022813	claudin 2	protein-coding
mm_53137.1	chr6	125215573	125215591	+	1	NA	promoter-TSS (NM_001080557)	promoter-TSS (NM_001080557)	1	NM_001080557	22317	Mm.32321	NM_009496	ENSMUSG00000030337	Vamp1	Syb-1|Syb1|VAMP-1|lew	vesicle-associated membrane protein 1	protein-coding
mm_104219.1	chr11	88366973	88366983	-	1	NA	intron (NM_054043, intron 10 of 13)	intron (NM_054043, intron 10 of 13)	14205	NR_039545	100628571		NR_039545	ENSMUSG00000092985	Mir378b	mir-378b|mmu-mir-378b	microRNA 378b	ncRNA
mm_83755.1	chr9	51328899	51328923	-	1	NA	promoter-TSS (NM_027217)	promoter-TSS (NM_027217)	6	NM_027217	69809	Mm.75315	NM_027217	ENSMUSG00000036027	1810046K07Rik	-	RIKEN cDNA 1810046K07 gene	protein-coding
mm_115866.1	chr13	21468464	21468473	-	1	NA	promoter-TSS (NM_025719)	promoter-TSS (NM_025719)	33	NM_025719	66707	Mm.116869	NM_025719	ENSMUSG00000059395	Nkapl	4921504I05Rik	NFKB activating protein-like	protein-coding
mm_131448.1	chr16	16303537	16303564	+	1	NA	exon (NM_198246, exon 1 of 5)	exon (NM_198246, exon 1 of 5)	585	NM_198246	70120	Mm.37486	NM_198246	ENSMUSG00000022792	Yars2	2210023C10Rik|tyrRS	tyrosyl-tRNA synthetase 2 (mitochondrial)	protein-coding
mm_89193.1	chr10	86347539	86347549	+	1	NA	3' UTR (NM_011595, exon 5 of 5)	3' UTR (NM_011595, exon 5 of 5)	47132	NM_011595	21859	Mm.4871	NM_011595	ENSMUSG00000020044	Timp3	Timp-3	tissue inhibitor of metalloproteinase 3	protein-coding
mm_17403.1	chr2	27225194	27225209	-	1	NA	intron (NM_138665, intron 12 of 20)	ORR1E|LTR|ERVL-MaLR	22102	NM_138665	192166	Mm.278467	NM_138665	ENSMUSG00000009614	Sardh	-	sarcosine dehydrogenase	protein-coding
mm_145510.1	chr18	60392092	60392110	+	1	NA	3' UTR (NM_001146275, exon 3 of 3)	3' UTR (NM_001146275, exon 3 of 3)	16072	NM_001146275	60440	Mm.261140	NM_021792	ENSMUSG00000054072	Iigp1	2900074L10Rik|AI046432|AW111922|Ifgga1|Iigp|Irga6	interferon inducible GTPase 1	protein-coding
mm_89841.1	chr10	106879389	106879395	+	1	NA	intron (NM_001205341, intron 21 of 31)	(CA)n|Simple_repeat|Simple_repeat	244272	NM_001142804	380660	Mm.336072	NM_198636	ENSMUSG00000035948	Acss3	8430416H19Rik|Gm874	acyl-CoA synthetase short-chain family member 3	protein-coding
mm_81939.1	chr9	120384851	120384857	+	1	NA	intron (NM_144557, intron 2 of 16)	intron (NM_144557, intron 2 of 16)	80781	NM_144557	245049	Mm.100936	NM_144557	ENSMUSG00000041794	Myrip	A230081N12Rik|Slac2-c|Slac2c	myosin VIIA and Rab interacting protein	protein-coding
mm_115386.1	chr13	113209758	113209772	+	1	NA	5' UTR (NM_023612, exon 1 of 3)	5' UTR (NM_023612, exon 1 of 3)	106	NM_023612	71690	Mm.38929	NM_023612	ENSMUSG00000042379	Esm1	0610042H23Rik|AV004503|ESM-1	endothelial cell-specific molecule 1	protein-coding
mm_25714.1	chr3	122724998	122725039	+	1	NA	Intergenic	L1_Rod|LINE|L1	-4140	NM_153422	242202	Mm.134911	NM_153422	ENSMUSG00000053965	Pde5a	Cgbpde|Cn5n|PDE5a2|Pde5|Pde5a1	phosphodiesterase 5A, cGMP-specific	protein-coding
mm_164211.1	chr15	82338865	82338875	-	1	NA	promoter-TSS (NM_008669)	promoter-TSS (NM_008669)	-44	NM_008669	17939	Mm.20325	NM_008669	ENSMUSG00000022453	Naga	-	N-acetyl galactosaminidase, alpha	protein-coding
mm_94111.1	chr10	128626422	128626443	-	1	NA	promoter-TSS (NM_013765)	promoter-TSS (NM_013765)	74	NM_013765	27370	Mm.32118	NM_013765	ENSMUSG00000025362	Rps26	-	ribosomal protein S26	protein-coding
mm_57279.1	chr6	124321633	124321654	-	1	NA	intron (NM_053094, intron 11 of 16)	RLTR19-int|LTR|ERVK	16992	NM_053094	93671	Mm.37426	NM_053094	ENSMUSG00000008845	Cd163	CD163v2|CD163v3	CD163 antigen	protein-coding
mm_36227.1	chr4	62525037	62525080	-	1	NA	promoter-TSS (NM_021498)	promoter-TSS (NM_021498)	-44	NM_021498	59001	Mm.27444	NM_021498	ENSMUSG00000028394	Pole3	1810034K18Rik|YBL1	polymerase (DNA directed), epsilon 3 (p17 subunit)	protein-coding
mm_87477.1	chr10	51492842	51492859	+	1	NA	intron (NM_001291894, intron 4 of 8)	intron (NM_001291894, intron 4 of 8)	1952	NM_013532	14728	Mm.34408	NM_013532	ENSMUSG00000062593	Lilrb4a	CD85K|Gp49b|HM18|ILT3|LIR-5|Lilrb4|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4A	protein-coding
mm_162911.1	chr10	118156598	118156599	+	1	NA	intron (NM_148922, intron 7 of 13)	intron (NM_148922, intron 7 of 13)	14811	NM_010785	17245	Mm.101191	NM_010785	ENSMUSG00000020212	Mdm1	Arrd2|Mdm-1	transformed mouse 3T3 cell double minute 1	protein-coding
mm_172795.1	chr9	110946119	110946121	-	1	NA	promoter-TSS (NM_011562)	promoter-TSS (NM_011562)	38	NM_011562	21667	Mm.5090	NM_011562	ENSMUSG00000032494	Tdgf1	CR1|cripto	teratocarcinoma-derived growth factor 1	protein-coding
mm_110094.1	chr12	25189096	25189101	-	1	NA	Intergenic	Intergenic	59924	NR_045844	432641	Mm.112955	NR_045844		Gm17746	-	predicted gene, 17746	ncRNA
mm_12932.1	chr2	85050440	85050500	+	1	NA	promoter-TSS (NM_001081260)	promoter-TSS (NM_001081260)	10	NM_001081260	228140	Mm.23606	NM_001081260	ENSMUSG00000033955	Tnks1bp1	Tab182|mKIAA1741	tankyrase 1 binding protein 1	protein-coding
mm_83518.1	chr9	46175476	46175492	-	1	NA	intron (NM_027498, intron 4 of 24)	ORR1B2|LTR|ERVL-MaLR	-53146	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2|apo-AI|apoA-I	apolipoprotein A-I	protein-coding
mm_40839.1	chr5	73256957	73256968	+	1	NA	promoter-TSS (NM_028194)	promoter-TSS (NM_028194)	-344	NM_028194	72313	Mm.260594	NM_028194	ENSMUSG00000070733	Fryl	2010313D22Rik|2310004H21Rik|2510002A14Rik|9030227G01Rik|mKIAA0826	FRY like transcription coactivator	protein-coding
mm_40421.1	chr5	53421050	53421096	+	1	NA	Intergenic	Intergenic	-134706	NM_001080928	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_151024.1	chr19	46961809	46961820	+	1	NA	intron (NM_001164363, intron 1 of 17)	CpG	537	NM_029810	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_34187.1	chr4	140701511	140701521	+	1	NA	promoter-TSS (NM_173867)	promoter-TSS (NM_173867)	43	NM_173867	108911	Mm.253	NM_173867	ENSMUSG00000040945	Rcc2	2610510H01Rik|2610529N02Rik|AA536646|AA675016|Td60|mKIAA1470	regulator of chromosome condensation 2	protein-coding
mm_140157.1	chr17	80184018	80184026	+	1	NA	exon (NM_176963, exon 7 of 7)	exon (NM_176963, exon 7 of 7)	23283	NM_001195486	225027	Mm.292016	NM_146083	ENSMUSG00000024097	Srsf7	35kDa|9430065L19Rik|9G8|NX-96|Sfrs7	serine/arginine-rich splicing factor 7	protein-coding
mm_30884.1	chr4	32249274	32249310	+	1	NA	Intergenic	Intergenic	-168143	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_30705.1	chr4	11965896	11965909	+	1	NA	promoter-TSS (NM_001290387)	promoter-TSS (NM_001290387)	79	NM_001290387	381511	Mm.331489	NM_001033453	ENSMUSG00000049225	Pdp1	Gm1024|Ppm2c	pyruvate dehyrogenase phosphatase catalytic subunit 1	protein-coding
mm_36920.1	chr4	108118529	108118553	-	1	NA	promoter-TSS (NM_011327)	promoter-TSS (NM_011327)	6	NM_011327	20280	Mm.379011	NM_011327	ENSMUSG00000028603	Scp2	AA409774|AA409893|C76618|C79031|NSL-TP|SCP-2|SCP-X|SCPX|ns-LTP	sterol carrier protein 2, liver	protein-coding
mm_147279.1	chr18	39487000	39487011	-	1	NA	exon (NM_008173, exon 1 of 8)	exon (NM_008173, exon 1 of 8)	240	NM_008173	14815	Mm.129481	NM_008173	ENSMUSG00000024431	Nr3c1	GR|Grl-1|Grl1	nuclear receptor subfamily 3, group C, member 1	protein-coding
mm_153098.1	chr19	32712338	32712340	-	1	NA	promoter-TSS (NM_026487)	promoter-TSS (NM_026487)	-41	NM_026487	67979	Mm.27123	NM_026487	ENSMUSG00000013662	Atad1	4921525H23Rik|AW107648|Thorase	ATPase family, AAA domain containing 1	protein-coding
mm_125983.1	chr15	76337573	76337597	+	1	NA	Intergenic	Intergenic	-5938	NM_025567	66445	Mm.29196	NM_025567	ENSMUSG00000022551	Cyc1	2610002H19Rik|AA408921|Cyct1	cytochrome c-1	protein-coding
mm_158037.1	chrX	98757515	98757525	-	1	NA	intron (NM_001313755, intron 4 of 23)	intron (NM_001313755, intron 4 of 23)	133505	NM_052976	94190	Mm.33536	NM_052976	ENSMUSG00000031214	Ophn1	C130037N19Rik|Wtgr	oligophrenin 1	protein-coding
mm_29997.1	chr3	135589973	135590014	-	1	NA	intron (NM_008689, intron 23 of 24)	intron (NM_008689, intron 23 of 24)	101554	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_75942.1	chr8	71566634	71566640	-	1	NA	promoter-TSS (NM_145598)	promoter-TSS (NM_145598)	12	NM_145598	234404	Mm.213208	NM_145598	ENSMUSG00000034829	Nxnl1	A930031O08Rik|RdCVF|Txnl6	nucleoredoxin-like 1	protein-coding
mm_15846.1	chr2	164771302	164771324	+	1	NA	exon (NM_026785, exon 3 of 6)	exon (NM_026785, exon 3 of 6)	1384	NM_026785	68612	Mm.89830	NM_026785	ENSMUSG00000001403	Ube2c	1110015A16Rik|D2Ertd695e	ubiquitin-conjugating enzyme E2C	protein-coding
mm_108758.1	chr12	89063917	89063958	+	1	NA	intron (NM_172544, intron 2 of 19)	intron (NM_172544, intron 2 of 19)	110547	NM_172544	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding
mm_4543.1	chr1	176996953	176996969	+	1	NA	intron (NM_029756, intron 16 of 17)	intron (NM_029756, intron 16 of 17)	-160828	NR_037996	15365	Mm.441435	NR_037996		Hmga2-ps1	EG666235|Gm7996|Hmgic-ps1|[y]i-c	high mobility group AT-hook 2, pseudogene 1	pseudo
mm_118302.1	chr13	113096305	113096317	-	1	NA	exon (NM_010370, exon 3 of 5)	exon (NM_010370, exon 3 of 5)	4670	NM_010370	14938	Mm.15510	NM_010370	ENSMUSG00000023132	Gzma	AW494114|Ctla-3|Ctla3|Hf|Hf1|SE1|TSP-1|TSP1	granzyme A	protein-coding
mm_101972.1	chr11	50313618	50313630	-	1	NA	intron (NM_001110500, intron 1 of 14)	intron (NM_001110500, intron 1 of 14)	12049	NM_001110499	12330	Mm.248827	NM_007597	ENSMUSG00000020368	Canx	1110069N15Rik|AI988026|Cnx|D11Ertd153e	calnexin	protein-coding
mm_26565.1	chr3	146549200	146549204	+	1	NA	Intergenic	Intergenic	-27779	NM_027371	70285	Mm.28128	NM_027332	ENSMUSG00000028187	Rpf1	2210420E24Rik|2310066N05Rik|Bxdc5	ribosome production factor 1 homolog	protein-coding
mm_102984.1	chr11	69681960	69681981	-	1	NA	promoter-TSS (NM_030702)	promoter-TSS (NM_030702)	0	NM_030702	80886	Mm.284592	NM_030702	ENSMUSG00000005204	Senp3	AA408656|Smt3ip|Smt3ip1	SUMO/sentrin specific peptidase 3	protein-coding
mm_20662.1	chr2	132118518	132118525	-	1	NA	intron (NM_018824, intron 1 of 15)	URR1A|DNA|hAT-Charlie	26587	NM_018824	54338	Mm.103581	NM_018824	ENSMUSG00000027340	Slc23a2	AI844736|NBTL1|SVCT2|Slc23a1|YSPL2|YSPL3|mKIAA0238	solute carrier family 23 (nucleobase transporters), member 2	protein-coding
mm_17685.1	chr2	32315032	32315049	-	1	NA	non-coding (NR_125959, exon 18 of 22)	non-coding (NR_125959, exon 18 of 22)	-3225	NR_128563	104795665		NR_128563	ENSMUSG00000092765	Gm23363	Mir3154|mir-3154|mmu-mir-3154	predicted gene, 23363	ncRNA
mm_43953.1	chr5	145208556	145208562	+	1	NA	intron (NM_001167944, intron 2 of 3)	RLTRETN_Mm|LTR|ERVK	4000	NM_001167944	22757	Mm.332842	NM_016683	ENSMUSG00000055991	Zkscan5	AI132486|AI326970|Zfp95|hKraba1	zinc finger with KRAB and SCAN domains 5	protein-coding
mm_100642.1	chr11	121830232	121830250	+	1	NA	promoter-TSS (NM_029049)	promoter-TSS (NM_029049)	23	NM_029049	74675	Mm.61213	NM_029049	ENSMUSG00000039198	Ptchd3	4930451E13Rik|4933440L20Rik|RNDEu-3	patched domain containing 3	protein-coding
mm_79273.1	chr9	50754312	50754328	+	1	NA	intron (NM_009964, intron 1 of 2)	intron (NM_009964, intron 1 of 2)	1349	NM_009964	12955	Mm.178	NM_009964	ENSMUSG00000032060	Cryab	Crya-2|Crya2|HspB5|P23	crystallin, alpha B	protein-coding
mm_53305.1	chr6	129180952	129180968	+	1	NA	intron (NM_053109, intron 1 of 4)	intron (NM_053109, intron 1 of 4)	345	NM_053109	93694	Mm.197536	NM_053109	ENSMUSG00000030157	Clec2d	Clr-b|Clrb|Ocil	C-type lectin domain family 2, member d	protein-coding
mm_171636.1	chr4	22699803	22699814	+	1	NA	Intergenic	RLTR10D2|LTR|ERVK	209260	NR_131335	105500046		NR_131335	ENSMUSG00000107859	Gm30731	Pnky|lnc-pou3f2	predicted gene, 30731	ncRNA
mm_14251.1	chr2	128128112	128128124	+	1	NA	intron (NM_001284410, intron 1 of 3)	CpG-8520	543	NM_001284410	12125	Mm.141083	NM_009754	ENSMUSG00000027381	Bcl2l11	1500006F24Rik|Bim|Bod|bcl2-L-11	BCL2-like 11 (apoptosis facilitator)	protein-coding
mm_127251.1	chr15	99692219	99692229	+	1	NA	5' UTR (NM_001289791, exon 1 of 10)	5' UTR (NM_001289791, exon 1 of 10)	469	NM_001289791	11419	Mm.440107	NM_009597	ENSMUSG00000023017	Asic1	AI843610|ASIC|ASIC1a|Accn2|B530003N02Rik|BNaC2	acid-sensing (proton-gated) ion channel 1	protein-coding
mm_105647.1	chr11	107132115	107132166	-	1	NA	promoter-TSS (NM_176850)	promoter-TSS (NM_176850)	-218	NM_176850	207165	Mm.343986	NM_176850	ENSMUSG00000040481	Bptf	9430093H17Rik|Falz	bromodomain PHD finger transcription factor	protein-coding
mm_120228.1	chr14	62858579	62858602	+	1	NA	intron (NM_175546, intron 1 of 11)	intron (NM_175546, intron 1 of 11)	-6952	NR_105860	102465311		NR_105860	ENSMUSG00000098858	Mir6541	Gm27311|mmu-mir-6541	microRNA 6541	ncRNA
mm_8839.1	chr1	162675878	162675881	-	1	NA	intron (NM_001081290, intron 33 of 34)	intron (NM_001081290, intron 33 of 34)	-17660	NM_001177581	100038657	Mm.416999	NM_001177581	ENSMUSG00000091060	7420461P10Rik	ENSMUSG00000073516	RIKEN cDNA 7420461P10 gene	protein-coding
mm_156741.1	chrX	159943047	159943057	+	1	NA	5' UTR (NM_001290664, exon 1 of 6)	5' UTR (NM_001290664, exon 1 of 6)	359	NM_001290664	58194	Mm.286495	NM_021389	ENSMUSG00000040990	Sh3kbp1	1200007H22Rik|1700125L08Rik|5830464D22Rik|AI447724|Cin85|IN85|Ruk|Seta	SH3-domain kinase binding protein 1	protein-coding
mm_29154.1	chr3	106014599	106014607	-	1	NA	promoter-TSS (NM_001200028)	promoter-TSS (NM_001200028)	43	NM_001200028	100503311	Mm.386825	NM_029604	ENSMUSG00000010136	Pifo	1700027A23Rik	primary cilia formation	protein-coding
mm_43981.1	chr5	146261300	146261327	+	1	NA	intron (NM_153599, intron 2 of 12)	LSU-rRNA_Hsa|rRNA|rRNA	29638	NM_153599	264064	Mm.260576	NM_153599	ENSMUSG00000029635	Cdk8	-	cyclin-dependent kinase 8	protein-coding
mm_117944.1	chr13	99434956	99434969	-	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-22136	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_103369.1	chr11	75190459	75190488	-	1	NA	promoter-TSS (NM_144491)	promoter-TSS (NM_144491)	10	NM_144491	116905	Mm.41496	NM_144491	ENSMUSG00000078789	Dph1	2310011M22Rik|4930488F09Rik|AW551873|Dph2l1|Ovca1	diphthamide biosynthesis 1	protein-coding
mm_41078.1	chr5	87674191	87674220	+	1	NA	exon (NM_007784, exon 12 of 34)	exon (NM_007784, exon 12 of 34)	7997	NM_001286016	12990	Mm.427467	NM_007784	ENSMUSG00000070702	Csn1s1	AA959832|AW212882|Csna	casein alpha s1	protein-coding
mm_39987.1	chr5	32487640	32487655	+	1	NA	exon (NM_172707, exon 7 of 8)	exon (NM_172707, exon 7 of 8)	28677	NM_172707	19046	Mm.241931	NM_172707	ENSMUSG00000014956	Ppp1cb	1200010B19	protein phosphatase 1, catalytic subunit, beta isoform	protein-coding
mm_31045.1	chr4	41135655	41135659	+	1	NA	promoter-TSS (NM_026275)	promoter-TSS (NM_026275)	-364	NM_026275	67615	Mm.389540	NM_026275	ENSMUSG00000036241	Ube2r2	1200003M11Rik|Cdc34b|Ubc3b	ubiquitin-conjugating enzyme E2R 2	protein-coding
mm_22490.1	chr3	5860629	5860652	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-284392	NM_001163305	19302	Mm.132336	NM_008994	ENSMUSG00000040374	Pex2	D3Ertd138e|PAF-1|PMP35|Pxmp3	peroxisomal biogenesis factor 2	protein-coding
mm_36667.1	chr4	95215162	95215196	-	1	NA	Intergenic	Intergenic	-162957	NM_010591	16476	Mm.275071	NM_010591	ENSMUSG00000052684	Jun	AP-1|Junc|c-jun	jun proto-oncogene	protein-coding
mm_12549.1	chr2	72405339	72405347	+	1	NA	3' UTR (NM_001164791, exon 12 of 12)	3' UTR (NM_001164791, exon 12 of 12)	-70876	NM_025866	66953	Mm.270676	NM_025866	ENSMUSG00000055612	Cdca7	2310021G01Rik|AU044109|JPO1	cell division cycle associated 7	protein-coding
mm_90786.1	chr10	7054918	7054927	-	1	NA	Intergenic	Intergenic	-31737	NM_001033391	320495	Mm.331674	NM_001033391	ENSMUSG00000064065	Ipcef1	A130090K04Rik	interaction protein for cytohesin exchange factors 1	protein-coding
mm_111382.1	chr12	87388318	87388336	-	1	NA	promoter-TSS (NM_011479)	promoter-TSS (NM_011479)	28	NM_011479	20773	Mm.565	NM_011479	ENSMUSG00000021036	Sptlc2	LCB2|LCB2a|Spt2	serine palmitoyltransferase, long chain base subunit 2	protein-coding
mm_71529.1	chr8	46887564	46887579	+	1	NA	Intergenic	Intergenic	-99316	NM_177304	320981	Mm.211429	NM_177304	ENSMUSG00000038173	Enpp6	4833421B01Rik|B830047L21Rik|D8Ertd514e|E-NPP 6|GPC-Cpde|Npp6	ectonucleotide pyrophosphatase/phosphodiesterase 6	protein-coding
mm_30385.1	chr3	152247109	152247152	-	1	NA	exon (NM_199465, exon 8 of 13)	exon (NM_199465, exon 8 of 13)	19190	NM_199465	68810	Mm.200188	NM_199465	ENSMUSG00000039103	Nexn	1110046H09Rik|AA553326|NELIN	nexilin	protein-coding
mm_78221.1	chr9	21546843	21546936	+	1	NA	promoter-TSS (NM_021531)	promoter-TSS (NM_021531)	-5	NM_021531	59035	Mm.178115	NM_021531	ENSMUSG00000032185	Carm1	Prmt4	coactivator-associated arginine methyltransferase 1	protein-coding
mm_113229.1	chr13	27241022	27241038	+	1	NA	Intergenic	RLTR9E|LTR|ERVK	-1400	NM_008865	18776	Mm.37203	NM_008865	ENSMUSG00000038891	Prl3b1	Csh2|Ghd8|PL|Pl-2|Pl2|mPL-II|mplII	prolactin family 3, subfamily b, member 1	protein-coding
mm_69182.1	chr7	127232891	127232968	-	1	NA	promoter-TSS (NM_146201)	promoter-TSS (NM_146201)	201	NR_030674	100043580	Mm.482209	NR_030674	ENSMUSG00000000486	Gm4532	-	predicted gene 4532	ncRNA
mm_6577.1	chr1	75216950	75216971	-	1	NA	exon (NM_009447, exon 3 of 4)	exon (NM_009447, exon 3 of 4)	2334	NM_001313723	22145	Mm.1155	NM_009447	ENSMUSG00000026202	Tuba4a	M[a]4|Tuba4	tubulin, alpha 4A	protein-coding
mm_105121.1	chr11	101170328	101170334	-	1	NA	intron (NM_001346769, intron 1 of 12)	intron (NM_001346769, intron 1 of 12)	971	NM_146030	217198	Mm.273254	NM_146030	ENSMUSG00000035172	Plekhh3	BC020025	pleckstrin homology domain containing, family H (with MyTH4 domain) member 3	protein-coding
mm_40624.1	chr5	64812337	64812350	+	1	NA	intron (NM_008453, intron 1 of 5)	intron (NM_008453, intron 1 of 5)	8820	NM_008453	16599	Mm.392759	NM_008453	ENSMUSG00000029178	Klf3	9930027G08Rik|AL024007|Bklf|Tef-2	Kruppel-like factor 3 (basic)	protein-coding
mm_57161.1	chr6	122765262	122765273	-	1	NA	Intergenic	Intergenic	-22522	NM_011401	20527	Mm.395108	NM_011401	ENSMUSG00000003153	Slc2a3	AA408729|AL023014|AL024341|AU040424|C78366|Glut-3|Glut3	solute carrier family 2 (facilitated glucose transporter), member 3	protein-coding
mm_122769.1	chr14	54397676	54397679	-	1	NA	intron (NM_001253679, intron 3 of 10)	intron (NM_001253679, intron 3 of 10)	11795	NM_001253680	20540	Mm.142455	NM_011405	ENSMUSG00000000958	Slc7a7	AI790233|my+lat1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 7	protein-coding
mm_101728.1	chr11	42321018	42321039	-	1	NA	promoter-TSS (NM_008068)	promoter-TSS (NM_008068)	44	NM_008068	14399	Mm.4915	NM_008068	ENSMUSG00000020428	Gabra6	GABA-ARalpha6|Gabra-6|alpha6	gamma-aminobutyric acid (GABA) A receptor, subunit alpha 6	protein-coding
mm_73514.1	chr8	107374319	107374354	+	1	NA	3' UTR (NM_018823, exon 15 of 15)	3' UTR (NM_018823, exon 15 of 15)	28869	NM_008706	18104	Mm.252	NM_008706	ENSMUSG00000003849	Nqo1	AV001255|Dia4|Dtd|Nmo-1|Nmo1|Nmor1|Ox-1|Ox1|Qr1	NAD(P)H dehydrogenase, quinone 1	protein-coding
mm_165518.1	chr2	173719448	173719456	+	1	NA	promoter-TSS (NM_029308)	promoter-TSS (NM_029308)	37	NM_029308	75485	Mm.308031	NM_029308	ENSMUSG00000057047	1700010B08Rik	-	RIKEN cDNA 1700010B08 gene	protein-coding
mm_35898.1	chr4	49597232	49597268	-	1	NA	intron (NM_025944, intron 1 of 1)	CpG	620	NM_025944	67063	Mm.490285	NM_025944	ENSMUSG00000039611	Tmem246	2810432L12Rik|9330170P15Rik|AI835809	transmembrane protein 246	protein-coding
mm_146572.1	chr18	6595475	6595479	-	1	NA	Intergenic	RMER17B|LTR|ERVK	-8156	NM_027598	70901	Mm.158484	NM_027598	ENSMUSG00000039540	4921524L21Rik	-	RIKEN cDNA 4921524L21 gene	protein-coding
mm_159002.1	chr1	153891488	153891488	+	1	NA	promoter-TSS (NM_178244)	promoter-TSS (NM_178244)	-158	NM_178244	240819	Mm.453236	NM_178244	ENSMUSG00000047053	Teddm1a	Epdd1|Teddm1|e9-1	transmembrane epididymal protein 1A	protein-coding
mm_171452.1	chr4	145510720	145510720	+	1	NA	promoter-TSS (NM_001324553)	promoter-TSS (NM_001324553)	-39	NM_001324553	101056073	Mm.276881	NM_001324553	ENSMUSG00000078503	LOC101056073	-	zinc finger protein 501-like	protein-coding
mm_56083.1	chr6	87335475	87335483	-	1	NA	5' UTR (NM_054041, exon 1 of 18)	5' UTR (NM_054041, exon 1 of 18)	296	NM_054041	69538	Mm.232525	NM_054041	ENSMUSG00000033420	Antxr1	2310008J16Rik|2810405N18Rik|Antrx1|Tem8	anthrax toxin receptor 1	protein-coding
mm_171172.1	chr3	32483295	32483295	+	1	NA	intron (NM_001195074, intron 1 of 3)	B4A|SINE|B4	8674	NM_001195074	100502876	Mm.383358	NM_001195074	ENSMUSG00000091091	Kcnmb3	EG435726|Gm5707	potassium large conductance calcium-activated channel, subfamily M, beta member 3	protein-coding
mm_17433.1	chr2	27507657	27507662	-	1	NA	Intergenic	Intergenic	-7488	NM_080848	140858	Mm.28265	NM_080848	ENSMUSG00000026917	Wdr5	2410008O07Rik|AA408785|AA960360|Big|Big-3	WD repeat domain 5	protein-coding
mm_2554.1	chr1	109983278	109983303	+	1	NA	promoter-TSS (NM_172853)	promoter-TSS (NM_172853)	-12	NM_001316744	241201	Mm.213407	NM_172853	ENSMUSG00000026312	Cdh7	9330156F07Rik|CDH7L1	cadherin 7, type 2	protein-coding
mm_57493.1	chr6	125313055	125313083	-	1	NA	exon (NM_010736, exon 3 of 10)	exon (NM_010736, exon 3 of 10)	801	NM_010736	17000	Mm.3122	NM_010736	ENSMUSG00000030339	Ltbr	AI256028|CD18|LTbetaR|Ltar|TNF-R-III|TNFCR|TNFR-RP|TNFR2-RP|TNFRrp|Tnfbr|Tnfrsf3	lymphotoxin B receptor	protein-coding
mm_53385.1	chr6	129533184	129533205	+	1	NA	promoter-TSS (NR_045270)	promoter-TSS (NR_045270)	2	NM_020590	57436	Mm.14638	NM_020590	ENSMUSG00000030161	Gabarapl1	3110025G09Rik|9130422N19Rik|AI196471|Apg8l|Atg8l|GECI|MNCb-0091	gamma-aminobutyric acid (GABA) A receptor-associated protein-like 1	protein-coding
mm_28478.1	chr3	92142739	92142766	-	1	NA	promoter-TSS (NM_027042)	promoter-TSS (NM_027042)	2	NM_027042	69332	Mm.120271	NM_027042	ENSMUSG00000027927	Lelp1	1700012F11Rik	late cornified envelope-like proline-rich 1	protein-coding
mm_129375.1	chr15	78120164	78120184	-	1	NA	promoter-TSS (NM_007583)	promoter-TSS (NM_007583)	-894	NM_007583	12300	Mm.277338	NM_007583	ENSMUSG00000019146	Cacng2	AW060990|B230105C07Rik|B930041E13Rik|stargazer|stargazin|stg|wag|waggler	calcium channel, voltage-dependent, gamma subunit 2	protein-coding
mm_139997.1	chr17	72939622	72939635	+	1	NA	3' UTR (NM_029999, exon 3 of 3)	3' UTR (NM_029999, exon 3 of 3)	21323	NM_029999	77889	Mm.154109	NM_029999	ENSMUSG00000024063	Lbh	1810009F10Rik|6720416L16Rik	limb-bud and heart	protein-coding
mm_126723.1	chr15	85418121	85418125	+	1	NA	intron (NM_016843, intron 9 of 11)	intron (NM_016843, intron 9 of 11)	81742	NM_016843	54138	Mm.248906	NM_016843	ENSMUSG00000016541	Atxn10	AI325283|C77170|E46|Sca10|TEG-169|Tex169	ataxin 10	protein-coding
mm_158404.1	chrX	136837648	136837684	-	1	NA	3' UTR (NM_011123, exon 7 of 7)	3' UTR (NM_011123, exon 7 of 7)	14920	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_27761.1	chr3	69599249	69599281	-	1	NA	promoter-TSS (NM_020026)	promoter-TSS (NM_020026)	-305	NM_020026	26879	Mm.153710	NM_020026	ENSMUSG00000043300	B3galnt1	B3galt3|b3GT3	UDP-GalNAc:betaGlcNAc beta 1,3-galactosaminyltransferase, polypeptide 1	protein-coding
mm_14798.1	chr2	145878872	145878878	+	1	NA	exon (NM_028724, exon 11 of 13)	exon (NM_028724, exon 11 of 13)	-24366	NM_026425	67877	Mm.151168	NM_026425	ENSMUSG00000002728	Naa20	1500004D14Rik|2900026I01Rik|AU041458|D2Ertd186e|Nat5	N(alpha)-acetyltransferase 20, NatB catalytic subunit	protein-coding
mm_65226.1	chr7	19713718	19713733	-	1	NA	exon (NM_001109748, exon 3 of 9)	exon (NM_001109748, exon 3 of 9)	1704	NM_001109748	53333	Mm.61682	NM_016871	ENSMUSG00000002984	Tomm40	AW539759|Mom35|Tom40	translocase of outer mitochondrial membrane 40 homolog (yeast)	protein-coding
mm_127995.1	chr15	12674207	12674217	-	1	NA	Intergenic	Intergenic	-81656	NM_001081064	68070	Mm.423205	NM_001081064	ENSMUSG00000022197	Pdzd2	4930537L06Rik|A930022H17Rik|Gm21706|Gm82|Pdzk3|mKIAA0300	PDZ domain containing 2	protein-coding
mm_13672.1	chr2	115599186	115599200	+	1	NA	intron (NM_001145898, intron 1 of 10)	intron (NM_001145898, intron 1 of 10)	17477	NM_001145898	399568	Mm.134929	NM_207264	ENSMUSG00000040282	BC052040	-	cDNA sequence BC052040	protein-coding
mm_19639.1	chr2	102829462	102829471	-	1	NA	intron (NM_001039151, intron 5 of 8)	LSU-rRNA_Hsa|rRNA|rRNA	72199	NM_001177785	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_54643.1	chr6	38875874	38875880	-	1	NA	5' UTR (NM_010433, exon 1 of 15)	5' UTR (NM_010433, exon 1 of 15)	313	NM_010433	15258	Mm.23790	NM_010433	ENSMUSG00000061436	Hipk2	1110014O20Rik|B230339E18Rik|Stank	homeodomain interacting protein kinase 2	protein-coding
mm_1664.1	chr1	74771726	74771751	+	1	NA	promoter-TSS (NM_009526)	promoter-TSS (NM_009526)	-154	NM_009526	22420	Mm.268282	NM_009526	ENSMUSG00000033227	Wnt6	AA409270|Wnt-6	wingless-type MMTV integration site family, member 6	protein-coding
mm_171049.1	chr3	102832662	102832670	+	1	NA	intron (NM_011516, intron 30 of 32)	intron (NM_011516, intron 30 of 32)	-49952	NM_001165940	22094	Mm.110730	NM_009432	ENSMUSG00000027857	Tshb	-	thyroid stimulating hormone, beta subunit	protein-coding
mm_157968.1	chrX	91782984	91783007	-	1	NA	promoter-TSS (NM_028847)	promoter-TSS (NM_028847)	-19	NM_028847	74271	Mm.141337	NM_028847	ENSMUSG00000061392	Mageb5	1700056A17Rik|mMage-b5	melanoma antigen, family B, 5	protein-coding
mm_2826.1	chr1	131149730	131149737	+	1	NA	Intergenic	RMER17C|LTR|ERVK	-3474	NM_001136070	16865	Mm.276294	NM_010709	ENSMUSG00000026427	Eif2d	D1Ertd5e|Lgtn	eukaryotic translation initiation factor 2D	protein-coding
mm_167619.1	chr9	57708617	57708626	+	1	NA	promoter-TSS (NM_153799)	promoter-TSS (NM_153799)	52	NM_153799	353190	Mm.268104	NM_153799	ENSMUSG00000038957	Edc3	AA517853|Lsm16|Yjdc	enhancer of mRNA decapping 3	protein-coding
mm_159938.1	chr6	80019495	80019495	+	1	NA	promoter-TSS (NM_178731)	promoter-TSS (NM_178731)	-148	NM_001347261	243499	Mm.483425	NM_178731	ENSMUSG00000052581	Lrrtm4	7530419J18Rik|A230052N11	leucine rich repeat transmembrane neuronal 4	protein-coding
mm_129373.1	chr15	78119955	78120005	-	1	NA	promoter-TSS (NM_007583)	promoter-TSS (NM_007583)	-700	NM_007583	12300	Mm.277338	NM_007583	ENSMUSG00000019146	Cacng2	AW060990|B230105C07Rik|B930041E13Rik|stargazer|stargazin|stg|wag|waggler	calcium channel, voltage-dependent, gamma subunit 2	protein-coding
mm_82522.1	chr9	20642625	20642637	-	1	NA	promoter-TSS (NM_025401)	promoter-TSS (NM_025401)	175	NM_013911	30843	Mm.24608	NM_013911	ENSMUSG00000066892	Fbxl12	3110048D16Rik|Fbl12	F-box and leucine-rich repeat protein 12	protein-coding
mm_116712.1	chr13	51568053	51568094	-	1	NA	promoter-TSS (NM_009167)	promoter-TSS (NM_009167)	-989	NM_009167	20418	Mm.131870	NM_009167	ENSMUSG00000021448	Shc3	N-Shc|Rai|ShcC	src homology 2 domain-containing transforming protein C3	protein-coding
mm_102581.1	chr11	61762041	61762082	-	1	NA	promoter-TSS (NM_144806)	promoter-TSS (NM_144806)	27	NM_144806	212627	Mm.27703	NM_144806	ENSMUSG00000020528	Prpsap2	A230054F23Rik	phosphoribosyl pyrophosphate synthetase-associated protein 2	protein-coding
mm_127925.1	chr15	10272104	10272108	-	1	NA	intron (NM_001253781, intron 1 of 9)	ORR1C1|LTR|ERVL-MaLR	-21545	NM_001253782	19116	Mm.10516	NM_011169	ENSMUSG00000005268	Prlr	AI987712|Pr-1|Pr-3|Prlr-rs1	prolactin receptor	protein-coding
mm_105282.1	chr11	102435266	102435280	-	1	NA	exon (NM_008175, exon 10 of 13)	exon (NM_008175, exon 10 of 13)	4951	NM_008175	14824	Mm.1568	NM_008175	ENSMUSG00000034708	Grn	Pgrn|epithelin	granulin	protein-coding
mm_8338.1	chr1	150164819	150164826	-	1	NA	non-coding (NR_110420, exon 1 of 2)	non-coding (NR_110420, exon 1 of 2)	126	NR_110420	102639566	Mm.417208	NR_110420	ENSMUSG00000097754	Ptgs2os2	Gm26687|Linc-cox2|Lincrna-cox2	prostaglandin-endoperoxide synthase 2, opposite strand 2	ncRNA
mm_172725.1	chr8	73319691	73319706	-	1	NA	intron (NM_010687, intron 1 of 14)	intron (NM_010687, intron 1 of 14)	33842	NM_001317391	16795	Mm.324371	NM_010687	ENSMUSG00000004383	Large1	BPFD#36|Gyltl1a|Large|Mbp-1|Mbp1|enr|fg|froggy|myd	LARGE xylosyl- and glucuronyltransferase 1	protein-coding
mm_19211.1	chr2	84601458	84601491	-	1	NA	3' UTR (NM_001085449, exon 17 of 17)	3' UTR (NM_001085449, exon 17 of 17)	49036	NM_001085453	12388	Mm.35738	NM_007615	ENSMUSG00000034101	Ctnnd1	AA409437|AU019353|Catns|Ctnnd|P120|mKIAA0384	catenin (cadherin associated protein), delta 1	protein-coding
mm_79014.1	chr9	45838573	45838592	+	1	NA	promoter-TSS (NM_001145947)	promoter-TSS (NM_001145947)	37	NM_011792	23821	Mm.24044	NM_011792	ENSMUSG00000032086	Bace1	ASP2|Bace|C76936	beta-site APP cleaving enzyme 1	protein-coding
mm_42990.1	chr5	123310534	123310544	+	1	NA	Intergenic	Intergenic	-33909	NM_029850	77045	Mm.151960	NM_029850	ENSMUSG00000029438	Bcl7a	4432415N06Rik|AI448316	B cell CLL/lymphoma 7A	protein-coding
mm_78290.1	chr9	22225734	22225760	+	1	NA	promoter-TSS (NM_001164624)	promoter-TSS (NM_001164624)	35	NM_001164624	235047	Mm.290849	NM_172763	ENSMUSG00000057982	Zfp809	BB114266|C330026E23	zinc finger protein 809	protein-coding
mm_54673.1	chr6	39347422	39347440	-	1	NA	intron (NM_028123, intron 9 of 14)	intron (NM_028123, intron 9 of 14)	30276	NM_028123	72144	Mm.482167	NM_028123	ENSMUSG00000029924	Slc37a3	2610507O21Rik|AU044904	solute carrier family 37 (glycerol-3-phosphate transporter), member 3	protein-coding
mm_13136.1	chr2	91963855	91963894	+	1	NA	promoter-TSS (NM_138306)	promoter-TSS (NM_138306)	-311	NM_138306	104418	Mm.314923	NM_138306	ENSMUSG00000040479	Dgkz	E130307B02Rik|ENSMUSG00000075035|F730209L11Rik|mDGK[z]	diacylglycerol kinase zeta	protein-coding
mm_161089.1	chr12	87816579	87816579	+	1	NA	promoter-TSS (NM_001177573).2	promoter-TSS (NM_001177573).2	2	NM_001177573	544881	Mm.327146	NM_001033788	ENSMUSG00000079031	BB287469	-	expressed sequence BB287469	protein-coding
mm_89741.1	chr10	99025412	99025421	+	1	NA	3' UTR (NM_026482, exon 21 of 21)	3' UTR (NM_026482, exon 21 of 21)	-81755	NM_027740	382406	Mm.440656	NM_027740	ENSMUSG00000019952	Poc1b	4933430F16Rik|Wdr51b	POC1 centriolar protein B	protein-coding
mm_39462.1	chr5	17828933	17828939	+	1	NA	5' UTR (NM_001159558, exon 4 of 16)	5' UTR (NM_001159558, exon 4 of 16)	6960	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_71248.1	chr8	40915054	40915072	+	1	NA	intron (NM_007514, intron 11 of 11)	intron (NM_007514, intron 11 of 11)	-11170	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_168350.1	chr11	12904860	12904860	+	1	NA	Intergenic	L1Md_T|LINE|L1	-439900	NM_001282993	12808	Mm.22847	NM_172496	ENSMUSG00000020173	Cobl	-	cordon-bleu WH2 repeat	protein-coding
mm_56072.1	chr6	86795693	86795733	-	1	NA	Intergenic	RMER10A|LTR|ERVL	-2129	NM_013471	11746	Mm.259702	NM_013471	ENSMUSG00000029994	Anxa4	AI265406|AIV|AW106930|Anx4|Xanx-4	annexin A4	protein-coding
mm_9426.1	chr1	172482061	172482068	-	1	NA	promoter-TSS (NM_001145800)	promoter-TSS (NM_001145800)	-149	NM_001145800	93842	Mm.214530	NM_033608	ENSMUSG00000037995	Igsf9	644ETD8|Dasm1|Kiaa1355-hp|NRT1|Ncaml|mKIAA1355	immunoglobulin superfamily, member 9	protein-coding
mm_60771.1	chr7	45557538	45557548	+	1	NA	intron (NM_025330, intron 3 of 8)	intron (NM_025330, intron 3 of 8)	2615	NM_025330	66065	Mm.285710	NM_025330	ENSMUSG00000030825	Hsd17b14	0610039E24Rik|Dhrs10|retSDR3	hydroxysteroid (17-beta) dehydrogenase 14	protein-coding
mm_15913.1	chr2	165063558	165063569	+	1	NA	intron (NM_170703, intron 5 of 7)	intron (NM_170703, intron 5 of 7)	7927	NM_011611	21939	Mm.271833	NM_011611	ENSMUSG00000017652	Cd40	AI326936|Bp50|GP39|HIGM1|IGM|IMD3|T-BAM|TRAP|Tnfrsf5|p50	CD40 antigen	protein-coding
mm_110173.1	chr12	27336829	27336837	-	1	NA	3' UTR (NM_009234, exon 1 of 1)	3' UTR (NM_009234, exon 1 of 1)	5885	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding
mm_129809.1	chr15	82993963	82993965	-	1	NA	Intergenic	Intergenic	29174	NM_028728	74039	Mm.32584	NM_028728	ENSMUSG00000058099	Nfam1	4921501M20Rik|Cnaip	Nfat activating molecule with ITAM motif 1	protein-coding
mm_141958.1	chr17	35118487	35118512	-	1	NA	exon (NM_009975, exon 4 of 7)	exon (NM_009975, exon 4 of 7)	2793	NM_001303476	13001	Mm.378901	NM_009975	ENSMUSG00000024387	Csnk2b	CK II beta	casein kinase 2, beta polypeptide	protein-coding
mm_67001.1	chr7	64925583	64925611	-	1	NA	intron (NM_183087, intron 2 of 9)	L1MC3|LINE|L1	-52557	NM_023239	66647	Mm.19944	NM_023239	ENSMUSG00000070520	Ndnl2	5730494G16Rik|AI642138|BB044375|HCA4|Mageg1|Nsmce3|mage-g1	necdin-like 2	protein-coding
mm_132723.1	chr16	43610725	43610743	+	1	NA	exon (NM_019778, exon 8 of 9)	exon (NM_019778, exon 8 of 9)	-29921	NR_030576	100124467		NR_030576	ENSMUSG00000076372	Mir568	Mirn568|mmu-mir-568	microRNA 568	ncRNA
mm_67832.1	chr7	98361276	98361295	-	1	NA	promoter-TSS (NM_001168539)	promoter-TSS (NM_001168539)	3	NM_001168540	244152	Mm.25317	NM_001024619	ENSMUSG00000049580	Tsku	9530051K01Rik|E2ig4|Lrrc54|Tsk	tsukushi, small leucine rich proteoglycan	protein-coding
mm_10004.1	chr1	191565904	191565913	-	1	NA	intron (NM_001305233, intron 5 of 15)	intron (NM_001305233, intron 5 of 15)	9636	NM_001305233	76843	Mm.189102	NM_029766	ENSMUSG00000037474	Dtl	2810047L02Rik|5730564G15Rik|L2dtl|Ramp	denticleless E3 ubiquitin protein ligase	protein-coding
mm_151435.1	chr19	57360689	57360704	+	1	NA	promoter-TSS (NM_145505)	promoter-TSS (NM_145505)	203	NR_040316	320879	Mm.375089	NR_040316	ENSMUSG00000097785	B230217O12Rik	-	RIKEN cDNA B230217O12 gene	ncRNA
mm_2649.1	chr1	125561102	125561122	+	1	NA	promoter-TSS (NM_028787)	promoter-TSS (NM_028787)	96	NM_028787	74150	Mm.28654	NM_028787	ENSMUSG00000026342	Slc35f5	1300003P13Rik|AI646727	solute carrier family 35, member F5	protein-coding
mm_59551.1	chr7	28071231	28071242	+	1	NA	promoter-TSS (NM_001122603)	promoter-TSS (NM_001122603)	0	NM_001122603	215384	Mm.292276	NM_175444	ENSMUSG00000047730	Fcgbp	A430096B05Rik	Fc fragment of IgG binding protein	protein-coding
mm_97800.1	chr11	82952096	82952125	+	1	NA	promoter-TSS (NM_183201)	promoter-TSS (NM_183201)	8	NM_183201	327978	Mm.42147	NM_183201	ENSMUSG00000054404	Slfn5	AI956840	schlafen 5	protein-coding
mm_112100.1	chr12	112785282	112785312	-	1	NA	Intergenic	Intergenic	-23678	NM_145450	217887	Mm.186678	NM_145450	ENSMUSG00000037594	BC022687	AW050009|C130001I08Rik|Flj20080	cDNA sequence BC022687	protein-coding
mm_77024.1	chr8	108584723	108584732	-	1	NA	promoter-TSS (NR_077224)	promoter-TSS (NR_077224)	-50	NR_077224	109215	Mm.65282	NR_077224	ENSMUSG00000110613	Lncbate1	3010033K07Rik|Lnc-BATE1	brown adipose tissue enriched long non-coding RNA 1	ncRNA
mm_162631.1	chr1	187942908	187942910	+	1	NA	intron (NM_001243792, intron 2 of 7)	intron (NM_001243792, intron 2 of 7)	-54918	NM_011935	26381	Mm.89989	NM_011935	ENSMUSG00000026610	Esrrg	ERR3|Errg|NR3B3|mKIAA0832	estrogen-related receptor gamma	protein-coding
mm_164728.1	chr17	59040825	59040825	-	1	NA	Intergenic	Intergenic	-27503	NM_026497	67993	Mm.36507	NM_026497	ENSMUSG00000024228	Nudt12	0610016O18Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 12	protein-coding
mm_98009.1	chr11	84180310	84180360	+	1	NA	Intergenic	CpG	-12859	NM_001037932	628813	Mm.390389	NM_001037932	ENSMUSG00000051452	Gm11437	AI463690|OTTMUSG00000000997	predicted gene 11437	protein-coding
mm_150127.1	chr19	30030440	30030528	+	1	NA	promoter-TSS (NM_144873)	promoter-TSS (NM_144873)	-29	NM_144873	109113	Mm.313364	NM_144873	ENSMUSG00000024817	Uhrf2	2310065A22Rik|AI426270|AW214556|D130071B19Rik|Nirf	ubiquitin-like, containing PHD and RING finger domains 2	protein-coding
mm_29988.1	chr3	135437985	135438006	-	1	NA	promoter-TSS (NM_025356)	promoter-TSS (NM_025356)	670	NR_030689	319587	Mm.358971	NR_030689	ENSMUSG00000097032	4930539J05Rik	8030475D13Rik	RIKEN cDNA 4930539J05 gene	ncRNA
mm_166609.1	chr6	69632196	69632232	-	1	NA	Intergenic	Intergenic	-305040	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_46033.1	chr5	91949614	91949624	-	1	NA	non-coding (NR_073442, exon 10 of 10)	non-coding (NR_073442, exon 10 of 10)	12937	NR_073442	68098	Mm.159453	NM_026557	ENSMUSG00000029397	Rchy1	ARNIP|CHIMP|Pirh2|Zfp363|Znf363	ring finger and CHY zinc finger domain containing 1	protein-coding
mm_10219.1	chr2	5951481	5951536	+	1	NA	promoter-TSS (NM_001081132)	promoter-TSS (NM_001081132)	39	NM_001081132	326622	Mm.31102	NM_001081132	ENSMUSG00000043241	Upf2	-	UPF2 regulator of nonsense transcripts homolog (yeast)	protein-coding
mm_114582.1	chr13	75707514	75707544	+	1	NA	promoter-TSS (NM_138953)	promoter-TSS (NM_138953)	45	NM_138953	192657	Mm.21288	NM_138953	ENSMUSG00000001542	Ell2	-	elongation factor RNA polymerase II 2	protein-coding
mm_144492.1	chr18	24205696	24205704	+	1	NA	promoter-TSS (NM_001160404)	promoter-TSS (NM_001160404)	-294	NM_001160404	14423	Mm.30249	NM_013814	ENSMUSG00000000420	Galnt1	-	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 1	protein-coding
mm_78795.1	chr9	44046789	44046818	+	1	NA	exon (NM_009382, exon 3 of 4)	exon (NM_009382, exon 3 of 4)	3419	NM_009382	21838	Mm.3951	NM_009382	ENSMUSG00000032011	Thy1	CD90|T25|Thy-1|Thy-1.2|Thy1.1|Thy1.2	thymus cell antigen 1, theta	protein-coding
mm_167040.1	chr7	79825794	79825853	-	1	NA	exon (NM_008486, exon 18 of 20)	exon (NM_008486, exon 18 of 20)	15096	NM_008589	17293	Mm.31472	NM_008589	ENSMUSG00000030543	Mesp2	bHLHc6	mesoderm posterior 2	protein-coding
mm_153448.1	chr19	41031123	41031136	-	1	NA	intron (NM_009345, intron 1 of 11)	intron (NM_009345, intron 1 of 11)	1854	NM_009345	21673	Mm.25620	NM_009345	ENSMUSG00000025014	Dntt	Tdt	deoxynucleotidyltransferase, terminal	protein-coding
mm_27885.1	chr3	79173349	79173360	-	1	NA	Intergenic	Intergenic	-27479	NM_001099624	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_7167.1	chr1	92049005	92049040	-	1	NA	intron (NM_207225, intron 3 of 26)	MIRc|SINE|MIR	131319	NM_207225	208727	Mm.318567	NM_207225	ENSMUSG00000026313	Hdac4	4932408F19Rik|HD4	histone deacetylase 4	protein-coding
mm_124382.1	chr14	108882596	108882604	-	1	NA	Intergenic	Intergenic	31639	NM_199065	76965	Mm.257268	NM_199065	ENSMUSG00000075478	Slitrk1	3200001I04Rik	SLIT and NTRK-like family, member 1	protein-coding
mm_8931.1	chr1	164152937	164152962	-	1	NA	promoter-TSS (NR_037987)	promoter-TSS (NR_037987)	-732	NR_037987	100503816	Mm.398579	NR_037987	ENSMUSG00000086593	Gm16548	-	predicted gene 16548	ncRNA
mm_85386.1	chr9	103228052	103228072	-	1	NA	exon (NM_133977, exon 2 of 17)	exon (NM_133977, exon 2 of 17)	2224	NM_133977	22041	Mm.37214	NM_133977	ENSMUSG00000032554	Trf	AI266983|Cd176|HP|Tf|Tfn|hpx	transferrin	protein-coding
mm_113861.1	chr13	48261082	48261091	+	1	NA	promoter-TSS (NM_031166)	promoter-TSS (NM_031166)	-341	NM_031166	15904	Mm.458006	NM_031166	ENSMUSG00000021379	Id4	Idb4|bHLHb27	inhibitor of DNA binding 4	protein-coding
mm_70973.1	chr8	27141459	27141469	+	1	NA	3' UTR (NM_001080813, exon 6 of 6)	3' UTR (NM_001080813, exon 6 of 6)	-1446	NR_045840	71082	Mm.395259	NR_045840		4933416M07Rik	-	RIKEN cDNA 4933416M07 gene	ncRNA
mm_61856.1	chr7	88308110	88308127	+	1	NA	exon (NM_009982, exon 6 of 7)	exon (NM_009982, exon 6 of 7)	30033	NM_001311790	13032	Mm.89295	NM_009982	ENSMUSG00000030560	Ctsc	AI047818|CatC|DPP1|DPPI	cathepsin C	protein-coding
mm_43226.1	chr5	129845846	129845863	+	1	NA	3' UTR (NM_009838, exon 13 of 13)	3' UTR (NM_009838, exon 13 of 13)	-1136	NM_026445	67902	Mm.103546	NM_026445	ENSMUSG00000025538	Sumf2	2610040F05Rik	sulfatase modifying factor 2	protein-coding
mm_95955.1	chr11	58640395	58640430	+	1	NA	promoter-TSS (NM_001039047)	promoter-TSS (NM_001039047)	-53	NM_001039047	216781	Mm.339507	NM_001039047	ENSMUSG00000037124	Trim58	Gm16|Gm1783	tripartite motif-containing 58	protein-coding
mm_40525.1	chr5	57919565	57919568	+	1	NA	intron (NM_001122758, intron 2 of 2)	B1_Mus1|SINE|Alu	201485	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_17286.1	chr2	26140469	26140530	-	1	NA	promoter-TSS (NM_001256522)	promoter-TSS (NM_001256522)	7	NM_001256521	109299	Mm.389259	NM_001256521		C330006A16Rik	AI551216	RIKEN cDNA C330006A16 gene	protein-coding
mm_147342.1	chr18	43059618	43059642	-	1	NA	promoter-TSS (NM_028392)	promoter-TSS (NM_028392)	-159	NM_028392	72930	Mm.26134	NM_027531	ENSMUSG00000024500	Ppp2r2b	2900026H06Rik|6330404L05Rik|E130009M08Rik|PP2A-PR55B|PR55-BETA|SCA12	protein phosphatase 2, regulatory subunit B, beta	protein-coding
mm_146917.1	chr18	31605554	31605561	-	1	NA	intron (NM_026165, intron 3 of 7)	Charlie1a|DNA|hAT-Charlie	4345	NM_026165	67453	Mm.23896	NM_026165	ENSMUSG00000024259	Slc25a46	1200007B05Rik|AI325987	solute carrier family 25, member 46	protein-coding
mm_79989.1	chr9	67013082	67013092	+	1	NA	Intergenic	Intergenic	30784	NM_001164252	22003	Mm.121878	NM_024427	ENSMUSG00000032366	Tpm1	AA986836|AI854628|TM2|Tm3|Tmpa|Tpm-1|alpha-TM	tropomyosin 1, alpha	protein-coding
mm_42879.1	chr5	122309152	122309173	+	1	NA	intron (NM_177242, intron 2 of 5)	intron (NM_177242, intron 2 of 5)	24764	NM_177242	320717	Mm.489670	NM_177242	ENSMUSG00000038582	Pptc7	9130017A15Rik|AA672638|AI848390|TA-PP2C	PTC7 protein phosphatase homolog	protein-coding
mm_38504.1	chr4	141115341	141115393	-	1	NA	non-coding (NR_102344, exon 3 of 3)	non-coding (NR_102344, exon 3 of 3)	24429	NR_102344	213491	Mm.332006	NM_174996	ENSMUSG00000040842	Szrd1	1110022I03|D4Ertd22e	SUZ RNA binding domain containing 1	protein-coding
mm_129856.1	chr15	83237963	83237984	-	1	NA	intron (NM_001004150, intron 1 of 2)	intron (NM_001004150, intron 1 of 2)	13758	NM_001170954	239559	Mm.323805	NM_001004150	ENSMUSG00000047878	A4galt	-	alpha 1,4-galactosyltransferase	protein-coding
mm_41541.1	chr5	92876364	92876368	+	1	NA	intron (NM_001077595, intron 1 of 9)	intron (NM_001077595, intron 1 of 9)	-21627	NM_001077596	27428	Mm.46014	NM_015756	ENSMUSG00000029381	Shroom3	AL022960|D5Ertd287e|Shrm|Shrm3	shroom family member 3	protein-coding
mm_150846.1	chr19	44989074	44989100	+	1	NA	promoter-TSS (NM_011976)	promoter-TSS (NM_011976)	-257	NM_011976	26456	Mm.34404	NM_011976	ENSMUSG00000025207	Sema4g	AI507908|AW554132	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4G	protein-coding
mm_130862.1	chr15	102189033	102189050	-	1	NA	promoter-TSS (NM_144942)	promoter-TSS (NM_144942)	2	NM_144942	246277	Mm.296382	NM_144942	ENSMUSG00000023044	Csad	Csd	cysteine sulfinic acid decarboxylase	protein-coding
mm_56275.1	chr6	91116472	91116480	-	1	NA	intron (NM_018815, intron 1 of 39)	CpG	350	NM_018815	54563	Mm.28162	NM_018815	ENSMUSG00000030091	Nup210	9830001L10|AI836801|Pom210|gp190|gp210	nucleoporin 210	protein-coding
mm_39386.1	chr5	13398681	13398696	+	1	NA	promoter-TSS (NM_009152)	promoter-TSS (NM_009152)	-309	NM_001243073	20346	Mm.372039	NM_009152	ENSMUSG00000028883	Sema3a	Hsema-I|SEMA1|SemD|Semad|coll-1	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	protein-coding
mm_86524.1	chr10	7792898	7792936	+	1	NA	promoter-TSS (NM_026141)	promoter-TSS (NM_026141)	23	NM_026141	67418	Mm.38927	NM_026141	ENSMUSG00000015757	Ppil4	3732410E19Rik|3830425H19Rik|AI788954|AW146233|PPIase	peptidylprolyl isomerase (cyclophilin)-like 4	protein-coding
mm_72426.1	chr8	82863283	82863297	+	1	NA	promoter-TSS (NM_177378)	promoter-TSS (NM_177378)	-66	NM_177378	330812	Mm.491438	NM_177378	ENSMUSG00000047747	Rnf150	A630007N06Rik|C030044C12Rik|Greul5|mKIAA1214	ring finger protein 150	protein-coding
mm_43841.1	chr5	143027816	143027820	+	1	NA	intron (NM_080561, intron 14 of 16)	intron (NM_080561, intron 14 of 16)	67463	NM_007984	14086	Mm.289707	NM_007984	ENSMUSG00000029581	Fscn1	AI663989|Fan1|fascin-1	fascin actin-bundling protein 1	protein-coding
mm_73391.1	chr8	105708252	105708261	+	1	NA	promoter-TSS (NM_198299)	promoter-TSS (NM_198299)	-47	NM_027655	71046	Mm.280888	NM_027655	ENSMUSG00000013158	4933405L10Rik	-	RIKEN cDNA 4933405L10 gene	protein-coding
mm_15035.1	chr2	152756762	152756790	+	1	NA	intron (NM_053091, intron 2 of 4)	intron (NM_053091, intron 2 of 4)	2603	NM_053091	84682	Mm.196668	NM_053091	ENSMUSG00000009876	Cox4i2	Cox4b|CoxIV-2	cytochrome c oxidase subunit IV isoform 2	protein-coding
mm_5909.1	chr1	55003479	55003497	-	1	NA	exon (NM_031179, exon 10 of 25)	exon (NM_031179, exon 10 of 25)	23990	NM_031179	81898	Mm.279736	NM_031179	ENSMUSG00000025982	Sf3b1	155kDa|2810001M05Rik|AA409119|Prp10|SAP155|SF3b155|TA-8|Targ4	splicing factor 3b, subunit 1	protein-coding
mm_83273.1	chr9	43064034	43064038	-	1	NA	intron (NM_027144, intron 1 of 40)	intron (NM_027144, intron 1 of 40)	41682	NM_027144	69632	Mm.275266	NM_027144	ENSMUSG00000059495	Arhgef12	2310014B11Rik|AU019857|Larg|mKIAA0382	Rho guanine nucleotide exchange factor (GEF) 12	protein-coding
mm_18342.1	chr2	58156966	58156986	-	1	NA	intron (NM_139200, intron 1 of 7)	intron (NM_139200, intron 1 of 7)	3146	NM_139200	227929	Mm.273905	NM_139200	ENSMUSG00000026832	Cytip	A130053M09Rik|AI462064|C80816|Cbp|Cybr|Pscdbp	cytohesin 1 interacting protein	protein-coding
mm_99996.1	chr11	114789624	114789651	+	1	NA	intron (NM_001102615, intron 18 of 19)	intron (NM_001102615, intron 18 of 19)	6255	NM_028055	72014	Mm.38347	NM_028055	ENSMUSG00000000202	Btbd17	1500005I02Rik|Tango10a	BTB (POZ) domain containing 17	protein-coding
mm_101395.1	chr11	26570148	26570151	-	1	NA	intron (NM_001252447, intron 2 of 11)	intron (NM_001252447, intron 2 of 11)	23771	NM_027260	69922	Mm.285351	NM_027260	ENSMUSG00000064090	Vrk2	2810003O05Rik|AI447698	vaccinia related kinase 2	protein-coding
mm_31330.1	chr4	46451119	46451126	+	1	NA	5' UTR (NM_130889, exon 1 of 7)	5' UTR (NM_130889, exon 1 of 7)	196	NM_130889	67628	Mm.263913	NM_130889	ENSMUSG00000028333	Anp32b	2410015B15Rik|PAL31|PHAPI2a|Ssp29	acidic (leucine-rich) nuclear phosphoprotein 32 family, member B	protein-coding
mm_115139.1	chr13	104684908	104684920	+	1	NA	intron (NM_026072, intron 11 of 13)	intron (NM_026072, intron 11 of 13)	132039	NM_026072	67285	Mm.235398	NM_026072	ENSMUSG00000021715	Cwc27	3110009E13Rik|NY-CO-10|Sdccag10	CWC27 spliceosome-associated protein	protein-coding
mm_155892.1	chrX	101652476	101652487	+	1	NA	intron (NM_139144, intron 4 of 21)	intron (NM_139144, intron 4 of 21)	12263	NM_001290535	108155	Mm.487332	NM_139144	ENSMUSG00000034160	Ogt	1110038P24Rik|4831420N21Rik|AI115525|Ogtl	O-linked N-acetylglucosamine (GlcNAc) transferase (UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase)	protein-coding
mm_123385.1	chr14	63321545	63321551	-	1	NA	Intergenic	B1F1|SINE|Alu	-76277	NM_001310610	14463	Mm.247669	NM_008092	ENSMUSG00000021944	Gata4	Gata-4	GATA binding protein 4	protein-coding
mm_33612.1	chr4	132608544	132608561	+	1	NA	Intergenic	MLT1A1|LTR|ERVL-MaLR	-30494	NM_210071	14050	Mm.227733	NM_010166	ENSMUSG00000028886	Eya3	AI844637	EYA transcriptional coactivator and phosphatase 3	protein-coding
mm_19190.1	chr2	84422499	84422518	-	1	NA	intron (NM_018782, intron 1 of 15)	intron (NM_018782, intron 1 of 15)	2758	NM_018782	54598	Mm.75467	NM_018782	ENSMUSG00000059588	Calcrl	AV071593|CRLR	calcitonin receptor-like	protein-coding
mm_73267.1	chr8	104430725	104430727	+	1	NA	intron (NM_001013380, intron 4 of 12)	intron (NM_001013380, intron 4 of 12)	12321	NM_001013380	234663	Mm.289583	NM_001013380	ENSMUSG00000035770	Dync1li2	AA409702|C920003I06|Dncli2|Dnclic2|LIC2	dynein, cytoplasmic 1 light intermediate chain 2	protein-coding
mm_124273.1	chr14	103017128	103017163	-	1	NA	intron (NR_045657, intron 2 of 2)	intron (NR_045657, intron 2 of 2)	16658	NR_045657	71264	Mm.399572	NR_045657		4933432I03Rik	-	RIKEN cDNA 4933432I03 gene	ncRNA
mm_52530.1	chr6	115762255	115762298	+	1	NA	5' UTR (NM_001168257, exon 1 of 11)	5' UTR (NM_001168257, exon 1 of 11)	190	NM_001168256	94346	Mm.29739	NM_144805	ENSMUSG00000059900	Tmem40	9030407H20Rik|AV091463|W64236	transmembrane protein 40	protein-coding
mm_171765.1	chr5	107900598	107900599	+	1	NA	promoter-TSS (NM_016980)	promoter-TSS (NM_016980)	70	NM_016980	100503670	Mm.277897	NM_016980	ENSMUSG00000058558	Rpl5	U21RNA	ribosomal protein L5	protein-coding
mm_71825.1	chr8	68896589	68896606	+	1	NA	intron (NM_008509, intron 5 of 9)	intron (NM_008509, intron 5 of 9)	16042	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_171610.1	chr4	150153057	150153061	-	1	NA	intron (NM_001085529, intron 3 of 11)	intron (NM_001085529, intron 3 of 11)	4087	NM_001085529	435818	Mm.359648	NM_001085529	ENSMUSG00000062064	Slc2a7	OTTMUSG00000010396	solute carrier family 2 (facilitated glucose transporter), member 7	protein-coding
mm_1367.1	chr1	66421717	66421761	+	1	NA	exon (NM_008632, exon 10 of 14)	exon (NM_008632, exon 10 of 14)	-46708	NM_175510	329178	Mm.44798	NM_175510	ENSMUSG00000055567	Unc80	C030018G13Rik|C230061B10Rik|UNC-80	unc-80, NALCN activator	protein-coding
mm_149081.1	chr19	8898096	8898122	+	1	NA	promoter-TSS (NM_008060)	promoter-TSS (NM_008060)	52	NM_008060	14376	Mm.3196	NM_008060	ENSMUSG00000071650	Ganab	AU042638|G2an|GluII|mKIAA0088	alpha glucosidase 2 alpha neutral subunit	protein-coding
mm_6946.1	chr1	85734480	85734483	-	1	NA	intron (NM_177055, intron 1 of 5)	B1_Mus2|SINE|Alu	2125	NM_177055	319997	Mm.116691	NM_177055	ENSMUSG00000052760	A630001G21Rik	-	RIKEN cDNA A630001G21 gene	protein-coding
mm_109241.1	chr12	109452751	109452760	+	1	NA	promoter-TSS (NM_010052)	promoter-TSS (NM_010052)	-68	NR_033813	13386	Mm.157069	NM_010052	ENSMUSG00000040856	Dlk1	AW742678|DLK-1|DlkI|FA1|Ly107|Peg9|SCP1|ZOG|pG2|pref-1	delta-like 1 homolog (Drosophila)	protein-coding
mm_44790.1	chr5	32299674	32299676	-	1	NA	intron (NM_001081407, intron 19 of 58)	intron (NM_001081407, intron 19 of 58)	-53905	NM_172147	665270	Mm.160067	NM_030072	ENSMUSG00000029134	Plb1	4632413E21Rik|4930433E17Rik|4930539A06Rik|BC033606	phospholipase B1	protein-coding
mm_142775.1	chr17	50091611	50091624	-	1	NA	intron (NM_181397, intron 3 of 9)	L2|LINE|L2	98880	NM_181397	76438	Mm.41854	NM_181397	ENSMUSG00000039316	Rftn1	2310015N21Rik|AI853526	raftlin lipid raft linker 1	protein-coding
mm_58474.1	chr7	3391020	3391040	+	1	NA	Intergenic	Intergenic	-3012	NM_133190	81905	Mm.357990	NM_133190	ENSMUSG00000053395	Cacng8	-	calcium channel, voltage-dependent, gamma subunit 8	protein-coding
mm_20775.1	chr2	143862934	143862950	-	1	NA	5' UTR (NM_001291061, exon 1 of 8)	5' UTR (NM_001291061, exon 1 of 8)	231	NM_009751	12075	Mm.275937	NM_009751	ENSMUSG00000027420	Bfsp1	CP95	beaded filament structural protein 1, in lens-CP94	protein-coding
mm_158922.1	chr1	59163306	59163306	-	1	NA	promoter-TSS (NM_001164682)	promoter-TSS (NM_001164682)	83	NM_001164682	227157	Mm.474049	NM_145143	ENSMUSG00000079550	Mpp4	Dlg6	membrane protein, palmitoylated 4 (MAGUK p55 subfamily member 4)	protein-coding
mm_70039.1	chr7	142577565	142577569	-	1	NA	promoter-TSS (NR_030416)	promoter-TSS (NR_030416)	-420	NR_030416	735280		NR_030416	ENSMUSG00000076275	Mir675	Mirn675|mir-675|mmu-mir-675	microRNA 675	ncRNA
mm_127897.1	chr15	9357074	9357077	-	1	NA	intron (NM_144845, intron 3 of 6)	RLTRETN_Mm|LTR|ERVK	21477	NM_144845	223337	Mm.422853	NM_144845	ENSMUSG00000049152	Ugt3a2	AI313915	UDP glycosyltransferases 3 family, polypeptide A2	protein-coding
mm_157460.1	chrX	44368330	44368352	-	1	NA	promoter-TSS (NM_175539)	promoter-TSS (NM_175539)	-4	NM_175539	245403	Mm.55270	NM_175539	ENSMUSG00000050926	Dcaf12l2	A130007F10Rik|Wdr40c	DDB1 and CUL4 associated factor 12-like 2	protein-coding
mm_81849.1	chr9	118570516	118570522	+	1	NA	intron (NM_018748, intron 21 of 23)	intron (NM_018748, intron 21 of 23)	-36190	NM_133721	104099	Mm.335520	NM_133721	ENSMUSG00000039115	Itga9	(alpha)9|2610002H11Rik|6720458D17Rik|AI461869|D130073C02|D9Ertd428e	integrin alpha 9	protein-coding
mm_82818.1	chr9	31029931	31029947	-	1	NA	promoter-TSS (NM_001115130)	promoter-TSS (NM_001115130)	-705	NM_001115130	235132	Mm.239355	NM_172765	ENSMUSG00000047412	Zbtb44	6030404E16Rik|Btbd15|E230011F09	zinc finger and BTB domain containing 44	protein-coding
mm_113083.1	chr13	23839578	23839587	+	1	NA	5' UTR (NM_001164743, exon 1 of 12)	5' UTR (NM_001164743, exon 1 of 12)	148	NM_134069	105355	Mm.27038	NM_134069	ENSMUSG00000036083	Slc17a3	AW261723|Npt4	solute carrier family 17 (sodium phosphate), member 3	protein-coding
mm_71228.1	chr8	40904446	40904536	+	1	NA	exon (NM_001044740, exon 5 of 12)	exon (NM_001044740, exon 5 of 12)	-21742	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_59508.1	chr7	27566391	27566414	+	1	NA	intron (NM_175107, intron 6 of 9)	B2_Mm2|SINE|B2	5926	NM_001122767	66367	Mm.29831	NM_175107	ENSMUSG00000049643	2310022A10Rik	-	RIKEN cDNA 2310022A10 gene	protein-coding
mm_166569.1	chr6	48988536	48988536	+	1	NA	exon (NM_172888, exon 1 of 5)	exon (NM_172888, exon 1 of 5)	1675	NM_172888	243377	Mm.446302	NM_172888	ENSMUSG00000039215	Svs1	9530003A11	seminal vesicle secretory protein 1	protein-coding
mm_13700.1	chr2	117126206	117126223	+	1	NA	intron (NM_033524, intron 1 of 6)	intron (NM_033524, intron 1 of 6)	5143	NM_033524	114715	Mm.245890	NM_033524	ENSMUSG00000027351	Spred1	5730461F13Rik|AL024345|AW047647	sprouty protein with EVH-1 domain 1, related sequence	protein-coding
mm_125445.1	chr15	46623359	46623367	+	1	NA	promoter-TSS (NR_045811)	promoter-TSS (NR_045811)	58	NR_045811	75281	Mm.159487	NR_045811	ENSMUSG00000051198	4930548G14Rik	-	RIKEN cDNA 4930548G14 gene	ncRNA
mm_26264.1	chr3	142501299	142501340	+	1	NA	exon (NM_153564, exon 3 of 11)	exon (NM_153564, exon 3 of 11)	4385	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_137871.1	chr17	31433055	31433063	+	1	NA	intron (NM_008804, intron 4 of 18)	intron (NM_008804, intron 4 of 18)	46825	NM_001163748	18585	Mm.10812	NM_008804	ENSMUSG00000041119	Pde9a	PDE9A1	phosphodiesterase 9A	protein-coding
mm_11749.1	chr2	38369097	38369107	+	1	NA	exon (NM_010710, exon 5 of 5)	exon (NM_010710, exon 5 of 5)	17794	NM_010710	16870	Mm.142856	NM_010710	ENSMUSG00000000247	Lhx2	LH2A|Lh-2|Lim2|ap|apterous	LIM homeobox protein 2	protein-coding
mm_171026.1	chr2	87716785	87716785	+	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	-4881	NM_001011833	258101	Mm.377350	NM_001011833	ENSMUSG00000075150	Olfr1137	MOR177-20|MOR40-9P	olfactory receptor 1137	protein-coding
mm_8375.1	chr1	151155169	151155179	-	1	NA	Intergenic	Intergenic	17140	NR_038011	402734	Mm.337666	NR_038011		C730036E19Rik	lncLSTR	RIKEN cDNA C730036E19 gene	ncRNA
mm_165973.1	chr4	101728523	101728526	+	1	NA	intron (NM_146146, intron 2 of 18)	intron (NM_146146, intron 2 of 18)	11117	NM_010704	16847	Mm.259282	NM_010704	ENSMUSG00000057722	Lepr	LEPROT|Leprb|Modb1|OB-RGRP|Obr|db|diabetes|obese-like|obl	leptin receptor	protein-coding
mm_11273.1	chr2	30061906	30061912	+	1	NA	promoter-TSS (NM_023871)	promoter-TSS (NM_023871)	-87	NM_023871	56086	Mm.326055	NM_023871	ENSMUSG00000054766	Set	2610030F17Rik|5730420M11Rik|AA407739|I-2PP2A|StF-IT-1|TAF-I	SET nuclear oncogene	protein-coding
mm_112626.1	chr13	15850947	15850950	+	1	NA	Intergenic	Intergenic	43705	NR_046131	328190	Mm.446957	NR_046131		A530046M15Rik	A530046M15	RIKEN cDNA A530046M15 gene	ncRNA
mm_146778.1	chr18	20059619	20059641	-	1	NA	promoter-TSS (NM_013505)	promoter-TSS (NM_013505)	-76	NM_001317365	13506	Mm.280547	NM_013505	ENSMUSG00000024331	Dsc2	AW228162	desmocollin 2	protein-coding
mm_46775.1	chr5	112343470	112343505	-	1	NA	promoter-TSS (NM_027323)	promoter-TSS (NM_027323)	392	NM_138646	192232	Mm.238043	NM_138646	ENSMUSG00000042328	Hps4	2010205O06Rik|AU040608|BLOC-3|C130020P05Rik|le|mKIAA1667	Hermansky-Pudlak syndrome 4	protein-coding
mm_22804.1	chr3	26637647	26637660	+	1	NA	promoter-TSS (NM_029150)	promoter-TSS (NM_029150)	22	NM_027583	70862	Mm.330943	NM_027583	ENSMUSG00000039335	Spata16	4921511F01Rik|4930503K02Rik|Nyd-sp12	spermatogenesis associated 16	protein-coding
mm_42451.1	chr5	115435077	115435089	+	1	NA	intron (NM_008629, intron 5 of 14)	intron (NM_008629, intron 5 of 14)	5398	NM_008629	17690	Mm.5077	NM_008629	ENSMUSG00000054256	Msi1	Msi1h|Musahi1|m-Msi-1	musashi RNA-binding protein 1	protein-coding
mm_11793.1	chr2	43195677	43195719	+	1	NA	Intergenic	Intergenic	-359627	NM_001289593	70789	Mm.105278	NM_027552	ENSMUSG00000026866	Kynu	4432411A05Rik	kynureninase (L-kynurenine hydrolase)	protein-coding
mm_95810.1	chr11	55110338	55110356	+	1	NA	3' UTR (NM_010299, exon 4 of 4)	3' UTR (NM_010299, exon 4 of 4)	12362	NM_010299	14667	Mm.287807	NM_010299	ENSMUSG00000000594	Gm2a	AA408702|AW215435|GM2-AP|SAP-3	GM2 ganglioside activator protein	protein-coding
mm_60645.1	chr7	44850365	44850392	+	1	NA	TTS (NR_030488)	TTS (NR_030488)	371	NM_001253920	67605	Mm.148007	NM_026270	ENSMUSG00000011096	Akt1s1	1110012J22Rik|AI227026|Lobe|Lobel|PRAS40	AKT1 substrate 1 (proline-rich)	protein-coding
mm_8286.1	chr1	140183405	140183415	-	1	NA	promoter-TSS (NM_009888)	promoter-TSS (NM_009888)	1	NM_009888	12628	Mm.8655	NM_009888	ENSMUSG00000026365	Cfh	Mud-1|NOM|Sas-1|Sas1	complement component factor h	protein-coding
mm_79828.1	chr9	64789650	64789657	+	1	NA	Intergenic	Intergenic	-21358	NM_001162917	102442	Mm.222473	NM_176935	ENSMUSG00000053641	Dennd4a	AI115600|AI851943|F730015K02Rik	DENN/MADD domain containing 4A	protein-coding
mm_172640.1	chr8	25454241	25454260	+	1	NA	Intergenic	Intergenic	-64509	NM_001079909	14182	Mm.265716	NM_010206	ENSMUSG00000031565	Fgfr1	AW208770|Eask|FGFR-I|FLG|Fgfr-1|Flt-2|Hspy|MFR|bFGF-R-1|c-fgr	fibroblast growth factor receptor 1	protein-coding
mm_153192.1	chr19	34515086	34515098	-	1	NA	intron (NM_001111100, intron 3 of 9)	intron (NM_001111100, intron 3 of 9)	12382	NM_001111100	16889	Mm.157545	NM_021460	ENSMUSG00000024781	Lipa	AA960673|Lal|Lip-1|Lip1	lysosomal acid lipase A	protein-coding
mm_90679.1	chr10	128909431	128909443	+	1	NA	promoter-TSS (NM_007653)	promoter-TSS (NM_007653)	92	NM_001282966	12512	Mm.371552	NM_007653	ENSMUSG00000025351	Cd63	C75951|ME491|Tspan30	CD63 antigen	protein-coding
mm_11788.1	chr2	43128686	43128692	+	1	NA	Intergenic	RMER1B|Other|Other	-426636	NM_001289593	70789	Mm.105278	NM_027552	ENSMUSG00000026866	Kynu	4432411A05Rik	kynureninase (L-kynurenine hydrolase)	protein-coding
mm_6343.1	chr1	71638506	71638527	-	1	NA	exon (NM_001276413, exon 11 of 44)	exon (NM_001276413, exon 11 of 44)	14718	NM_010233	14268	Mm.193099	NM_010233	ENSMUSG00000026193	Fn1	E330027I09|Fn|Fn-1	fibronectin 1	protein-coding
mm_93224.1	chr10	95264952	95264961	-	1	NA	intron (NM_009950, intron 2 of 2)	intron (NM_009950, intron 2 of 2)	58753	NM_001330138	12905	Mm.473739	NM_009950	ENSMUSG00000045867	Cradd	RAIDD	CASP2 and RIPK1 domain containing adaptor with death domain	protein-coding
mm_116537.1	chr13	45885785	45885788	-	1	NA	intron (NM_001199304, intron 2 of 6)	intron (NM_001199304, intron 2 of 6)	79205	NM_001199304	20238	Mm.342683	NM_009124	ENSMUSG00000046876	Atxn1	2900016G23Rik|Atx1|C85907|ENSMUSG00000074917|Gm10786|Sca1	ataxin 1	protein-coding
mm_86777.1	chr10	20148979	20149014	+	1	NA	promoter-TSS (NM_008635)	promoter-TSS (NM_008635)	76	NM_001198635	17761	Mm.20928	NM_008635	ENSMUSG00000019996	Map7	E-MAP-115|MAP-7|Mtap7|R75000|mshi|mste|ste	microtubule-associated protein 7	protein-coding
mm_2460.1	chr1	105304906	105304906	+	1	NA	intron (NM_001160368, intron 1 of 1)	intron (NM_001160368, intron 1 of 1)	51804	NM_178779	320311	Mm.389162	NM_178779	ENSMUSG00000047496	Rnf152	A930029B02Rik	ring finger protein 152	protein-coding
mm_157822.1	chrX	74085341	74085357	-	1	NA	intron (NM_010788, intron 1 of 3)	CpG	341	NM_010788	17257	Mm.131408	NM_010788	ENSMUSG00000031393	Mecp2	1500041B07Rik|D630021H01Rik|Mbd5|WBP10	methyl CpG binding protein 2	protein-coding
mm_21992.1	chr2	167643765	167643802	-	1	NA	3' UTR (NM_145538, exon 6 of 6)	3' UTR (NM_145538, exon 6 of 6)	-11778	NM_023230	66589	Mm.278783	NM_023230	ENSMUSG00000078923	Ube2v1	0610011J09Rik|AI256840|CROC-1|CROC1|D7Bwg1382e|UEV-1	ubiquitin-conjugating enzyme E2 variant 1	protein-coding
mm_2841.1	chr1	131638271	131638296	+	1	NA	promoter-TSS (NM_007799)	promoter-TSS (NM_007799)	-31	NM_007799	13034	Mm.230249	NM_007799	ENSMUSG00000004552	Ctse	A430072O03Rik|C920004C08Rik|CE|CatE	cathepsin E	protein-coding
mm_173335.1	chrY	90811201	90811201	+	1	NA	intron (NM_133362, intron 2 of 3)	RLTR40|LTR|ERVK	25759	NM_133362	170942	Mm.76062	NM_133362	ENSMUSG00000096768	Erdr1	edr	erythroid differentiation regulator 1	protein-coding
mm_98697.1	chr11	96303574	96303580	+	1	NA	promoter-TSS (NM_008268)	promoter-TSS (NM_008268)	65	NM_008268	15413	Mm.207	NM_008268	ENSMUSG00000038700	Hoxb5	AI385717|Hox-2.1	homeobox B5	protein-coding
mm_106347.1	chr11	118393425	118393437	-	1	NA	exon (NM_011150, exon 6 of 6)	exon (NM_011150, exon 6 of 6)	8500	NM_011150	19039	Mm.3152	NM_011150	ENSMUSG00000033880	Lgals3bp	90K|CyCAP|MAC-2BP|Ppicap|Tango10b	lectin, galactoside-binding, soluble, 3 binding protein	protein-coding
mm_140661.1	chr17	12895573	12895579	-	1	NA	exon (NM_001034866, exon 11 of 19)	exon (NM_001034866, exon 11 of 19)	14424	NM_001034866	240023	Mm.242315	NM_001034866	ENSMUSG00000073460	Pnldc1	Gm313	poly(A)-specific ribonuclease (PARN)-like domain containing 1	protein-coding
mm_52038.1	chr6	96258620	96258634	+	1	NA	intron (NM_182808, intron 2 of 4)	(T)n|Simple_repeat|Simple_repeat	-92422	NR_003643	78482	Mm.391486	NM_030107	ENSMUSG00000072878	1700123L14Rik	-	nucleoporin 50 pseudogene	pseudo
mm_140392.1	chr17	87446678	87446680	+	1	NA	intron (NM_007589, intron 1 of 5)	CpG	256	NM_007589	12314	Mm.329243	NM_007589	ENSMUSG00000036438	Calm2	1500001E21Rik|AL024017	calmodulin 2	protein-coding
mm_80859.1	chr9	98486111	98486125	+	1	NA	Intergenic	Intergenic	-4419	NM_009034	19660	Mm.12825	NM_009034	ENSMUSG00000032454	Rbp2	Crbp-2|CrbpII|Rbp-2	retinol binding protein 2, cellular	protein-coding
mm_41966.1	chr5	107331138	107331146	+	1	NA	promoter-TSS (NM_054054)	promoter-TSS (NM_054054)	-52	NM_001079873	114642	Mm.182836	NM_054054	ENSMUSG00000029279	Brdt	7420412D09Rik|Brd6|Fsrg3	bromodomain, testis-specific	protein-coding
mm_21217.1	chr2	155819182	155819190	-	1	NA	promoter-TSS (NR_015528)	promoter-TSS (NR_015528)	17	NR_015528	613262	Mm.330707	NR_015528	ENSMUSG00000074649	BC029722	-	cDNA sequence BC029722	ncRNA
mm_120478.1	chr14	65975626	65975636	+	1	NA	exon (NM_013492, exon 5 of 9)	exon (NM_013492, exon 5 of 9)	7148	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_106430.1	chr11	119355485	119355526	-	1	NA	promoter-TSS (NM_018822)	promoter-TSS (NM_018822)	5	NM_018822	27029	Mm.103788	NM_018822	ENSMUSG00000005043	Sgsh	4632406A19Rik	N-sulfoglucosamine sulfohydrolase (sulfamidase)	protein-coding
mm_37290.1	chr4	119176716	119176765	-	1	NA	3' UTR (NM_013848, exon 13 of 13)	3' UTR (NM_013848, exon 13 of 13)	-2545	NM_001145936	195522	Mm.169620	NM_183140	ENSMUSG00000045268	Zfp691	6430544H17Rik|Znf691	zinc finger protein 691	protein-coding
mm_91255.1	chr10	23177016	23177020	-	1	NA	intron (NM_010167, intron 3 of 18)	intron (NM_010167, intron 3 of 18)	172872	NM_001347372	14051	Mm.332128	NM_010167	ENSMUSG00000010461	Eya4	B130023L16Rik	EYA transcriptional coactivator and phosphatase 4	protein-coding
mm_148997.1	chr19	8664307	8664337	+	1	NA	promoter-TSS (NR_045314)	promoter-TSS (NR_045314)	317	NM_001112697	12669	Mm.240607	NM_007698	ENSMUSG00000032773	Chrm1	Chrm-1|M1|M1R	cholinergic receptor, muscarinic 1, CNS	protein-coding
mm_150133.1	chr19	30056998	30057011	+	1	NA	intron (NM_144873, intron 3 of 15)	intron (NM_144873, intron 3 of 15)	26491	NM_144873	109113	Mm.313364	NM_144873	ENSMUSG00000024817	Uhrf2	2310065A22Rik|AI426270|AW214556|D130071B19Rik|Nirf	ubiquitin-like, containing PHD and RING finger domains 2	protein-coding
mm_49145.1	chr6	11907825	11907902	+	1	NA	promoter-TSS (NM_010886)	promoter-TSS (NM_010886)	-417	NM_010886	17992	Mm.415865	NM_010886	ENSMUSG00000029632	Ndufa4	MLRQ	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 4	protein-coding
mm_114266.1	chr13	58073260	58073294	+	1	NA	intron (NM_001195075, intron 5 of 16)	intron (NM_001195075, intron 5 of 16)	29151	NM_001195075	100503085	Mm.379256	NM_001195075	ENSMUSG00000014164	Klhl3	7530408C15Rik|AI430941|EG627648	kelch-like 3	protein-coding
mm_171781.1	chr5	110097449	110097478	-	1	NA	Intergenic	Intergenic	-2506	NM_207279	403178	Mm.297057	NM_207279	ENSMUSG00000064247	Plcxd1	A330045H12Rik|Gm576	phosphatidylinositol-specific phospholipase C, X domain containing 1	protein-coding
mm_71738.1	chr8	62951196	62951215	+	1	NA	promoter-TSS (NM_001252621)	promoter-TSS (NM_001252621)	-27	NM_001252620	72902	Mm.334552	NM_023689	ENSMUSG00000054162	Spock3	2900045C01Rik|AI428471|mKIAA4039	sparc/osteonectin, cwcv and kazal-like domains proteoglycan 3	protein-coding
mm_117315.1	chr13	67609668	67609695	-	1	NA	promoter-TSS (NM_001163246)	promoter-TSS (NM_001163246)	26	NM_001163246	100416706	Mm.478045	NM_001163246	ENSMUSG00000058093	Zfp729b	AA987127	zinc finger protein 729b	protein-coding
mm_109001.1	chr12	103311011	103311030	+	1	NA	Intergenic	MER117|DNA|hAT-Charlie	3749	NR_136894	102632488	Mm.109435	NR_136894	ENSMUSG00000100789	Gm29508	-	predicted gene 29508	ncRNA
mm_97394.1	chr11	77802425	77802435	+	1	NA	intron (NM_001291214, intron 1 of 38)	intron (NM_001291214, intron 1 of 38)	1132	NM_001291215	360013	Mm.341248	NM_011586	ENSMUSG00000000631	Myo18a	MAJN|MyoPDZ|MysPDZ|SP-R210	myosin XVIIIA	protein-coding
mm_154519.1	chrM	13011	13058	-	1	NA	NA	Intergenic	NA	NA								
mm_73559.1	chr8	109247311	109247314	+	1	NA	intron (NR_126329, intron 8 of 9)	intron (NR_126329, intron 8 of 9)	93596	NR_002928	384864	Mm.390083	NR_002928		Gm1943	-	WD repeat domain 70 pseudogene	pseudo
mm_160010.1	chr6	124998346	124998346	+	1	NA	promoter-TSS (NM_001145926)	promoter-TSS (NM_001145926)	-91	NM_001145927	319352	Mm.295327	NM_175696	ENSMUSG00000030329	Pianp	AI255183|AU067746|C530028O21Rik|Panp	PILR alpha associated neural protein	protein-coding
mm_24761.1	chr3	95499218	95499220	+	1	NA	promoter-TSS (NM_007802)	promoter-TSS (NM_007802)	9	NM_007802	13038	Mm.272085	NM_007802	ENSMUSG00000028111	Ctsk	AI323530|MMS10-Q|Ms10q|catK	cathepsin K	protein-coding
mm_93679.1	chr10	117779223	117779260	-	1	NA	intron (NM_134010, intron 8 of 27)	B3|SINE|B2	13464	NM_134010	103468	Mm.12568	NM_134010	ENSMUSG00000052798	Nup107	AW541137|C76801	nucleoporin 107	protein-coding
mm_150835.1	chr19	44825235	44825238	+	1	NA	intron (NM_011037, intron 7 of 9)	intron (NM_011037, intron 7 of 9)	10702	NR_045315	73322	Mm.250457	NR_045315	ENSMUSG00000092369	1700039E22Rik	-	RIKEN cDNA 1700039E22 gene	ncRNA
mm_7790.1	chr1	131490269	131490272	-	1	NA	intron (NM_001081011, intron 2 of 22)	intron (NM_001081011, intron 2 of 22)	37091	NM_001081011	14270	Mm.276259	NM_019520	ENSMUSG00000026425	Srgap2	9930124L22Rik|AI448945|FBP2|Fnbp2|srGAP3	SLIT-ROBO Rho GTPase activating protein 2	protein-coding
mm_59580.1	chr7	28129379	28129388	+	1	NA	promoter-TSS (NM_001164655)	promoter-TSS (NM_001164655)	-83	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_2943.1	chr1	132329964	132329986	+	1	NA	exon (NM_028778, exon 5 of 7)	exon (NM_028778, exon 5 of 7)	13850	NM_001195025	74137	Mm.100666	NM_028778	ENSMUSG00000009772	Nuak2	1200013B22Rik|Omphk2|Snark|mKIAA0537	NUAK family, SNF1-like kinase, 2	protein-coding
mm_144481.1	chr18	23954849	23954873	+	1	NA	5' UTR (NM_027007, exon 1 of 4)	5' UTR (NM_027007, exon 1 of 4)	173	NM_027007	69256	Mm.218343	NM_027007	ENSMUSG00000024276	Zfp397	2810411K16Rik|6720480F11Rik|AI461664	zinc finger protein 397	protein-coding
mm_66072.1	chr7	30880264	30880290	-	1	NA	promoter-TSS (NM_001043317)	promoter-TSS (NM_001043317)	65	NR_102723	12483	Mm.260994	NM_009845	ENSMUSG00000030577	Cd22	A530093D23|Lyb-8|Lyb8	CD22 antigen	protein-coding
mm_30127.1	chr3	141931567	141931576	-	1	NA	promoter-TSS (NM_001277220)	promoter-TSS (NM_001277220)	17	NM_001277218	12167	Mm.39089	NM_007560	ENSMUSG00000052430	Bmpr1b	AI385617|ALK-6|AV355320|Acvrlk6|Alk6|BMPR-1B|BMPR-IB|CFK-43a|SKR6	bone morphogenetic protein receptor, type 1B	protein-coding
mm_80864.1	chr9	98504755	98504766	+	1	NA	intron (NM_009034, intron 2 of 3)	intron (NM_009034, intron 2 of 3)	14223	NM_009034	19660	Mm.12825	NM_009034	ENSMUSG00000032454	Rbp2	Crbp-2|CrbpII|Rbp-2	retinol binding protein 2, cellular	protein-coding
mm_152087.1	chr19	6907667	6907698	-	1	NA	intron (NM_012021, intron 2 of 5)	intron (NM_012021, intron 2 of 5)	1963	NM_012021	54683	Mm.279782	NM_012021	ENSMUSG00000024953	Prdx5	AOEB166|AOPP|Pmp20|Prdx6|PrxV	peroxiredoxin 5	protein-coding
mm_103388.1	chr11	75416280	75416290	-	1	NA	exon (NM_011340, exon 3 of 8)	exon (NM_011340, exon 3 of 8)	6338	NM_011340	20317	Mm.2044	NM_011340	ENSMUSG00000000753	Serpinf1	AI195227|EPC-1|Pedf|Pedfl|Sdf3	serine (or cysteine) peptidase inhibitor, clade F, member 1	protein-coding
mm_26777.1	chr3	9004423	9004428	-	1	NA	promoter-TSS (NM_009412)	promoter-TSS (NM_009412)	90	NM_009412	21985	Mm.371590	NM_009412	ENSMUSG00000027506	Tpd52	AI043038|mD52	tumor protein D52	protein-coding
mm_121598.1	chr14	7994538	7994554	-	1	NA	promoter-TSS (NM_007870)	promoter-TSS (NM_007870)	-364	NM_007870	13421	Mm.272258	NM_007870	ENSMUSG00000025279	Dnase1l3	DNasegamma|Dhp2|Lsd	deoxyribonuclease 1-like 3	protein-coding
mm_157462.1	chrX	44790147	44790169	-	1	NA	promoter-TSS (NM_178739)	promoter-TSS (NM_178739)	3	NM_001190718	245404	Mm.55685	NM_178739	ENSMUSG00000045284	Dcaf12l1	9330180J20|A230038L21Rik|Decaf12l1|Wdr40b	DDB1 and CUL4 associated factor 12-like 1	protein-coding
mm_7301.1	chr1	97977062	97977113	-	1	NA	5' UTR (NM_013626, exon 2 of 26)	5' UTR (NM_013626, exon 2 of 26)	70706	NR_037993	78603	Mm.442597	NR_037993	ENSMUSG00000089706	B230216N24Rik	-	RIKEN cDNA B230216N24 gene	ncRNA
mm_21132.1	chr2	154206476	154206485	-	1	NA	exon (NM_153418, exon 5 of 16)	exon (NM_153418, exon 5 of 16)	6100	NM_153418	228801	Mm.3783	NM_153418	ENSMUSG00000027485	Bpifb1	Lplunc1	BPI fold containing family B, member 1	protein-coding
mm_52405.1	chr6	113378159	113378191	+	1	NA	promoter-TSS (NM_026552)	promoter-TSS (NM_026552)	62	NM_001170485	68089	Mm.289306	NM_026552	ENSMUSG00000079426	Arpc4	20kDa|5330419I20Rik|AI327076|p20-Arc	actin related protein 2/3 complex, subunit 4	protein-coding
mm_105359.1	chr11	103101610	103101662	-	1	NA	promoter-TSS (NM_025988)	promoter-TSS (NM_025988)	22	NM_152813	72469	Mm.264743	NM_152813	ENSMUSG00000020937	Plcd3	2610205J15Rik|mKIAA1964	phospholipase C, delta 3	protein-coding
mm_171153.1	chr3	18009156	18009174	+	1	NA	Intergenic	Intergenic	-45160	NM_021560	59058	Mm.149938	NM_021560	ENSMUSG00000025128	Bhlhe22	Beta3|Beta3a|Bhlhb5	basic helix-loop-helix family, member e22	protein-coding
mm_56678.1	chr6	113740676	113740708	-	1	NA	promoter-TSS (NM_024206)	promoter-TSS (NM_024206)	-11	NM_024206	110379	Mm.29296	NM_024206	ENSMUSG00000030298	Sec13	1110003H02Rik|Sec13l1|Sec13r	SEC13 homolog, nuclear pore and COPII coat complex component	protein-coding
mm_87164.1	chr10	36975073	36975120	+	1	NA	intron (NM_008229, intron 1 of 13)	CpG	552	NM_008229	15182	Mm.19806	NM_008229	ENSMUSG00000019777	Hdac2	D10Wsu179e|YAF1|Yy1bp|mRPD3	histone deacetylase 2	protein-coding
mm_24955.1	chr3	96643810	96643811	+	1	NA	non-coding (NR_027845, exon 4 of 4)	non-coding (NR_027845, exon 4 of 4)	-1774	NM_001302471	213119	Mm.32741	NM_001081053	ENSMUSG00000090210	Itga10	A630048L14	integrin, alpha 10	protein-coding
mm_55314.1	chr6	54992926	54992936	-	1	NA	promoter-TSS (NM_026637)	promoter-TSS (NM_026637)	-64	NM_026637	110175	Mm.294708	NM_026637	ENSMUSG00000002797	Ggct	A030007L17Rik|AA673177|Gctg|Ggc	gamma-glutamyl cyclotransferase	protein-coding
mm_166288.1	chr5	98954098	98954098	-	1	NA	intron (NM_008926, intron 14 of 18)	L1MC1|LINE|L1	82981	NM_008926	19092	Mm.263002	NM_008926	ENSMUSG00000029334	Prkg2	AW212535|CGKII|Prkgr2|cGK-II	protein kinase, cGMP-dependent, type II	protein-coding
mm_72179.1	chr8	72319621	72319634	+	1	NA	exon (NM_008452, exon 2 of 3)	exon (NM_008452, exon 2 of 3)	565	NM_008452	16598	Mm.26938	NM_008452	ENSMUSG00000055148	Klf2	Lklf	Kruppel-like factor 2 (lung)	protein-coding
mm_81656.1	chr9	110960890	110960896	+	1	NA	exon (NM_028838, exon 3 of 9)	exon (NM_028838, exon 3 of 9)	9348	NM_028838	74249	Mm.307615	NM_028838	ENSMUSG00000032495	Lrrc2	2400002D05Rik|4933431K03Rik	leucine rich repeat containing 2	protein-coding
mm_44593.1	chr5	24995801	24995811	-	1	NA	promoter-TSS (NM_001310480)	promoter-TSS (NM_001310480)	-53	NM_001310480	108099	Mm.33649	NM_145401	ENSMUSG00000028944	Prkag2	2410051C13Rik|AAKG|AAKG2|AI854673|H91620p|WPWS	protein kinase, AMP-activated, gamma 2 non-catalytic subunit	protein-coding
mm_151375.1	chr19	55933173	55933183	+	1	NA	non-coding (NR_138565, exon 16 of 16)	non-coding (NR_138565, exon 16 of 16)	37857	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_82130.1	chr9	123520591	123520611	+	1	NA	3' UTR (NM_013860, exon 8 of 8)	3' UTR (NM_013860, exon 8 of 8)	-9281	NM_030692	83493	Mm.273671	NM_030692	ENSMUSG00000025240	Sacm1l	SAC1|Sac1p|mKIAA0851	SAC1 suppressor of actin mutations 1-like (yeast)	protein-coding
mm_66910.1	chr7	60003139	60003156	-	1	NA	intron (NM_001082962, intron 2 of 10)	intron (NM_001082962, intron 2 of 10)	2009	NM_013670	20646	Mm.274995	NM_013670	ENSMUSG00000102252	Snrpn	2410045I01Rik|HCERN3|Peg4|Pwcr1|SMN	small nuclear ribonucleoprotein N	protein-coding
mm_44193.1	chr5	3502575	3502588	-	1	NA	intron (NM_009873, intron 5 of 7)	intron (NM_009873, intron 5 of 7)	-41252	NM_001042501	68152	Mm.240265	NM_026583	ENSMUSG00000058503	Fam133b	2900022K02Rik|5830415L20Rik	family with sequence similarity 133, member B	protein-coding
mm_145852.1	chr18	65453912	65453945	+	1	NA	intron (NM_172833, intron 8 of 15)	intron (NM_172833, intron 8 of 15)	22931	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_125848.1	chr15	74959104	74959114	+	1	NA	3' UTR (NM_001164036, exon 4 of 4)	3' UTR (NM_001164036, exon 4 of 4)	4003	NM_001164040	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_1853.1	chr1	84276892	84276894	+	1	NA	intron (NM_001003948, intron 1 of 2)	intron (NM_001003948, intron 1 of 2)	7752	NM_001003948	98496	Mm.187470	NM_001003948	ENSMUSG00000045658	Pid1	5033414K04Rik|NYGGF4	phosphotyrosine interaction domain containing 1	protein-coding
mm_75595.1	chr8	61698032	61698034	-	1	NA	intron (NM_001081390, intron 8 of 19)	intron (NM_001081390, intron 8 of 19)	62065	NM_001293773	72333	Mm.29933	NM_001081390	ENSMUSG00000058056	Palld	2410003B16Rik|6030492A02	palladin, cytoskeletal associated protein	protein-coding
mm_64052.1	chr7	140835549	140835613	+	1	NA	promoter-TSS (NM_029821)	promoter-TSS (NM_029821)	85	NM_029821	76974	Mm.272359	NM_029821	ENSMUSG00000025481	Urah	1190003J15Rik|2810420C16Rik	urate (5-hydroxyiso-) hydrolase	protein-coding
mm_55960.1	chr6	85451864	85451892	-	1	NA	promoter-TSS (NM_001163427)	promoter-TSS (NM_001163427)	92	NR_028081	73327	Mm.379221	NM_028505	ENSMUSG00000030008	Pradc1	1700040I03Rik|Pap21	protease-associated domain containing 1	protein-coding
mm_46409.1	chr5	104093245	104093266	-	1	NA	exon (NM_010097, exon 4 of 11)	exon (NM_010097, exon 4 of 11)	-15647	NM_001163772	100271704	Mm.366664	NM_001163772	ENSMUSG00000091034	Gm17660	Scpppq1	predicted gene, 17660	protein-coding
mm_151017.1	chr19	46761828	46761849	+	1	NA	exon (NM_001102471, exon 1 of 7)	exon (NM_001102471, exon 1 of 7)	229	NM_001102471	94219	Mm.306903	NM_033569	ENSMUSG00000064105	Cnnm2	AU015877|AW048635|Acdp2|Clp2	cyclin M2	protein-coding
mm_141380.1	chr17	29078983	29078994	-	1	NA	non-coding (NR_036469, exon 1 of 2)	non-coding (NR_036469, exon 1 of 2)	138	NR_036469	100504267	Mm.438550	NR_036469	ENSMUSG00000085912	Trp53cor1	Gm16197|OTTMUSG00000031656|linc-p21|lincRNA-p21	tumor protein p53 pathway corepressor 1	ncRNA
mm_27712.1	chr3	67515705	67515737	-	1	NA	promoter-TSS (NM_001164763)	promoter-TSS (NM_001164763)	-198	NM_001164763	109222	Mm.38002	NM_001164763	ENSMUSG00000049404	Rarres1	5430417P09Rik|AI662122	retinoic acid receptor responder (tazarotene induced) 1	protein-coding
mm_124024.1	chr14	76556908	76556918	-	1	NA	promoter-TSS (NR_027699)	promoter-TSS (NR_027699)	-24	NR_027699	72661	Mm.320384	NM_001160326	ENSMUSG00000052584	Serp2	2810032E02Rik	stress-associated endoplasmic reticulum protein family member 2	protein-coding
mm_84278.1	chr9	62811664	62811668	-	1	NA	promoter-TSS (NM_010193)	promoter-TSS (NM_010193)	-18	NM_010193	14155	Mm.24069	NM_010193	ENSMUSG00000032244	Fem1b	mKIAA0396	feminization 1 homolog b (C. elegans)	protein-coding
mm_83618.1	chr9	48799665	48799669	-	1	NA	intron (NM_001033324, intron 2 of 6)	B1F1|SINE|Alu	36278	NM_001033324	235320	Mm.457803	NM_001033324	ENSMUSG00000066687	Zbtb16	AI467657|PLZF|Zfp145|lu	zinc finger and BTB domain containing 16	protein-coding
mm_41638.1	chr5	97962008	97962012	+	1	NA	intron (NM_133738, intron 11 of 16)	intron (NM_133738, intron 11 of 16)	68952	NM_133738	71914	Mm.24842	NM_133738	ENSMUSG00000029338	Antxr2	2310046B19Rik|AW561899|CMG-2|CMG2|cI-35	anthrax toxin receptor 2	protein-coding
mm_64381.1	chr7	142471839	142471910	+	1	NA	promoter-TSS (NM_019391)	promoter-TSS (NM_019391)	31	NM_019391	16985	Mm.234003	NM_019391	ENSMUSG00000018819	Lsp1	Lsp-1|WP34|p50|pp52	lymphocyte specific 1	protein-coding
mm_13430.1	chr2	104821347	104821393	+	1	NA	Intergenic	Intergenic	-4674	NM_001123327	99003	Mm.274314	NM_001123327	ENSMUSG00000074994	Qser1	4732486I23Rik|AI502974	glutamine and serine rich 1	protein-coding
mm_112925.1	chr13	20936573	20936588	+	1	NA	intron (NM_012054, intron 11 of 20)	BGLII_Mus|LTR|ERVK	136719	NM_146535	258528	Mm.377554	NM_146535	ENSMUSG00000042869	Olfr1370	MOR256-14	olfactory receptor 1370	protein-coding
mm_2998.1	chr1	133241218	133241260	+	1	NA	Intergenic	Intergenic	-4858	NM_001160268	240753	Mm.253559	NM_182930	ENSMUSG00000041757	Plekha6	9530028L01Rik|AU042621|Pepp3	pleckstrin homology domain containing, family A member 6	protein-coding
mm_33628.1	chr4	132795052	132795063	+	1	NA	intron (NM_001033308, intron 1 of 5)	intron (NM_001033308, intron 1 of 5)	1307	NM_001033308	230787	Mm.290912	NM_001033308	ENSMUSG00000037731	Themis2	ICB-1	thymocyte selection associated family member 2	protein-coding
mm_102272.1	chr11	55395136	55395188	-	1	NA	3' UTR (NM_009242, exon 10 of 10)	3' UTR (NM_009242, exon 10 of 10)	24918	NM_009242	20692	Mm.291442	NM_009242	ENSMUSG00000018593	Sparc	BM-40|ON	secreted acidic cysteine rich glycoprotein	protein-coding
mm_37137.1	chr4	116821473	116821487	-	1	NA	promoter-TSS (NM_146256)	promoter-TSS (NM_146256)	28	NM_146256	242642	Mm.279897	NM_146256	ENSMUSG00000043155	Hpdl	A830048M07Rik|BC034099|Gloxd1	4-hydroxyphenylpyruvate dioxygenase-like	protein-coding
mm_53361.1	chr6	129361884	129361890	+	1	NA	intron (NM_177686, intron 5 of 5)	(TG)n|Simple_repeat|Simple_repeat	11643	NM_177686	232413	Mm.90241	NM_177686	ENSMUSG00000053063	Clec12a	CLL-1|D230024O04|KLRL1|Micl	C-type lectin domain family 12, member a	protein-coding
mm_22026.1	chr2	168050077	168050081	-	1	NA	Intergenic	Intergenic	-30925	NM_021409	58220	Mm.292834	NM_021409	ENSMUSG00000044641	Pard6b	AV025615|Par6b	par-6 family cell polarity regulator beta	protein-coding
mm_164366.1	chr16	23192204	23192216	+	1	NA	Intergenic	Lx8|LINE|L1	-32530	NM_145933	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_52273.1	chr6	108658611	108658621	+	1	NA	intron (NR_104577, intron 1 of 6)	intron (NR_104577, intron 1 of 6)	-2013	NM_011498	20893	Mm.2436	NM_011498	ENSMUSG00000030103	Bhlhe40	Bhlhb2|C130042M06Rik|CR8|Clast5|Dec1|Sharp2|Stra13|Stra14	basic helix-loop-helix family, member e40	protein-coding
mm_37138.1	chr4	116821489	116821499	-	1	NA	promoter-TSS (NM_146256)	promoter-TSS (NM_146256)	14	NM_146256	242642	Mm.279897	NM_146256	ENSMUSG00000043155	Hpdl	A830048M07Rik|BC034099|Gloxd1	4-hydroxyphenylpyruvate dioxygenase-like	protein-coding
mm_61811.1	chr7	87253359	87253376	+	1	NA	intron (NM_001285833, intron 2 of 19)	intron (NM_001285833, intron 2 of 19)	6718	NM_001285833	50490	Mm.31748	NM_015760	ENSMUSG00000030562	Nox4	AI648021	NADPH oxidase 4	protein-coding
mm_102422.1	chr11	59290747	59290758	-	1	NA	promoter-TSS (NM_009522)	promoter-TSS (NM_009522)	-1	NM_009522	22416	Mm.1367	NM_009522	ENSMUSG00000009900	Wnt3a	Wnt-3a|vt	wingless-type MMTV integration site family, member 3A	protein-coding
mm_63475.1	chr7	127691925	127691984	+	1	NA	intron (NM_001347652, intron 5 of 5)	intron (NM_001347652, intron 5 of 5)	-16533	NR_030428	791073		NR_030428	ENSMUSG00000076454	Mir762	Mirn762|mir-762|mmu-mir-762	microRNA 762	ncRNA
mm_105394.1	chr11	103395123	103395135	-	1	NA	exon (NM_183034, exon 4 of 12)	exon (NM_183034, exon 4 of 12)	17535	NM_183034	353047	Mm.18556	NM_183034	ENSMUSG00000034247	Plekhm1	AP162|B2|BC038943|D330036J23Rik	pleckstrin homology domain containing, family M (with RUN domain) member 1	protein-coding
mm_22078.1	chr2	168764805	168764808	-	1	NA	intron (NM_201395, intron 1 of 3)	intron (NM_201395, intron 1 of 3)	2395	NM_201395	99377	Mm.434054	NM_175303	ENSMUSG00000027547	Sall4	5730441M18Rik|AA407717|AL022809|AW536104|C330011P20Rik|C78083|C78563|Tex20	sal-like 4 (Drosophila)	protein-coding
mm_128662.1	chr15	60141620	60141653	-	1	NA	Intergenic	B1F2|SINE|Alu	-125018	NM_027668	71088	Mm.425950	NM_027668	ENSMUSG00000071749	4933412E24Rik	-	RIKEN cDNA 4933412E24 gene	protein-coding
mm_14717.1	chr2	143915542	143915568	+	1	NA	5' UTR (NM_019771, exon 1 of 4)	5' UTR (NM_019771, exon 1 of 4)	224	NM_019771	56431	Mm.28919	NM_019771	ENSMUSG00000015932	Dstn	2610043P17Rik|ADF|AU042046|Dsn|corn1|sid23p	destrin	protein-coding
mm_64718.1	chr7	4657695	4657699	-	1	NA	intron (NM_172894, intron 1 of 23)	L2c|LINE|L2	1253	NM_172894	243819	Mm.258670	NM_172894	ENSMUSG00000052296	Ppp6r1	2010309P17Rik|AI836219|B430201G11Rik|D030074N20Rik|Pp6r1|Saps1|mKIAA1115	protein phosphatase 6, regulatory subunit 1	protein-coding
mm_95433.1	chr11	50210306	50210383	+	1	NA	intron (NM_001290769, intron 1 of 7)	CpG	476	NM_001290769	18412	Mm.40828	NM_011018	ENSMUSG00000015837	Sqstm1	A170|OSF-6|Osi|STAP|STONE14|p62	sequestosome 1	protein-coding
mm_133772.1	chr16	94721881	94721900	+	1	NA	Intergenic	Intergenic	110471	NM_001347731	13548	Mm.310973	NM_007890	ENSMUSG00000022897	Dyrk1a	2310043O08Rik|D16Ertd272e|D16Ertd493e|Dyrk|ENSMUSG00000074897|Gm10783|Mnbh|Mp86|mmb	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1a	protein-coding
mm_136345.1	chr16	92620761	92620773	-	1	NA	intron (NM_001111022, intron 5 of 6)	intron (NM_001111022, intron 5 of 6)	76562	NM_001111023	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_161164.1	chr13	33249608	33249608	+	1	NA	promoter-TSS (NM_011456)	promoter-TSS (NM_011456)	-2	NM_011456	20710	Mm.379809	NM_011456	ENSMUSG00000062342	Serpinb9e	AW540195|NK26|Spi14|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 9e	protein-coding
mm_74008.1	chr8	121116191	121116201	+	1	NA	promoter-TSS (NM_013519)	promoter-TSS (NM_013519)	25	NM_013519	14234	Mm.14092	NM_013519	ENSMUSG00000046714	Foxc2	Fkh14|Hfhbf3|MFH-1|Mfh1	forkhead box C2	protein-coding
mm_142639.1	chr17	47422580	47422588	-	1	NA	promoter-TSS (NM_001347584)	promoter-TSS (NM_001347584)	-704	NM_001347584	75462	Mm.46129	NM_029296	ENSMUSG00000047150	1700001C19Rik	-	RIKEN cDNA 1700001C19 gene	protein-coding
mm_90497.1	chr10	128035340	128035355	+	1	NA	promoter-TSS (NM_013608)	promoter-TSS (NM_013608)	1	NM_001113199	17938	Mm.3746	NM_013608	ENSMUSG00000061315	Naca	AL022831|AL024382|Gm1878|mKIAA0363|skNAC	nascent polypeptide-associated complex alpha polypeptide	protein-coding
mm_107465.1	chr12	37241906	37241921	+	1	NA	5' UTR (NM_178767, exon 1 of 13)	5' UTR (NM_178767, exon 1 of 13)	274	NM_178767	319660	Mm.485540	NM_178767	ENSMUSG00000050103	Agmo	A530016O06Rik|AI790538|Tmem195	alkylglycerol monooxygenase	protein-coding
mm_17158.1	chr2	25234178	25234192	-	1	NA	promoter-TSS (NM_080854)	promoter-TSS (NM_080854)	49	NM_080854	142681	Mm.346652	NM_080854	ENSMUSG00000006469	Slc34a3	AI649385|Npt2c|Npt2c-v1|NptIIc|naPi-2c	solute carrier family 34 (sodium phosphate), member 3	protein-coding
mm_34713.1	chr4	152124587	152124613	+	1	NA	intron (NM_207688, intron 8 of 10)	intron (NM_207688, intron 8 of 10)	4325	NM_019585	56226	Mm.264215	NM_019585	ENSMUSG00000028943	Espn	je	espin	protein-coding
mm_159532.1	chr4	72145419	72145419	-	1	NA	exon (NM_011599, exon 9 of 20)	exon (NM_011599, exon 9 of 20)	55474	NM_011599	21885	Mm.278444	NM_011599	ENSMUSG00000008305	Tle1	C230057C06Rik|Estm14|Grg-1|Grg1|Tle4l	transducin-like enhancer of split 1	protein-coding
mm_167084.1	chr7	101845346	101845348	-	1	NA	promoter-TSS (NM_008035)	promoter-TSS (NM_008035)	-16	NM_008035	14276	Mm.439666	NM_008035	ENSMUSG00000032725	Folr2	FBP2|FR-P3|FR-beta|Folbp-2|Folbp2	folate receptor 2 (fetal)	protein-coding
mm_59140.1	chr7	24175033	24175061	+	1	NA	promoter-TSS (NM_001029933)	promoter-TSS (NM_001029933)	2	NM_001029933	232966	Mm.435485	NM_001029933	ENSMUSG00000068962	Zfp114	Gm1957|Zfp110	zinc finger protein 114	protein-coding
mm_70508.1	chr8	12926205	12926218	+	1	NA	intron (NM_178076, intron 1 of 30)	intron (NM_178076, intron 1 of 30)	10318	NM_178076	17207	Mm.334413	NM_178076	ENSMUSG00000031442	Mcf2l	C130040G20Rik|Dbs|Ost|mKIAA0362	mcf.2 transforming sequence-like	protein-coding
mm_72575.1	chr8	84189978	84189980	+	1	NA	Intergenic	B1F|SINE|Alu	-11018	NR_029821	723819		NR_029821	ENSMUSG00000065483	Mir181c	Mirn181c|mir-181c	microRNA 181c	ncRNA
mm_151319.1	chr19	55892674	55892684	+	1	NA	intron (NR_138565, intron 4 of 15)	intron (NR_138565, intron 4 of 15)	-2642	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_93794.1	chr10	120782701	120782703	-	1	NA	3' UTR (NM_177092, exon 7 of 7)	3' UTR (NM_177092, exon 7 of 7)	16970	NR_038003	70874	Mm.427286	NR_038000	ENSMUSG00000044544	4921513I03Rik	-	RIKEN cDNA 4921513I03 gene	ncRNA
mm_96909.1	chr11	70459612	70459633	+	1	NA	promoter-TSS (NM_001029929)	promoter-TSS (NM_001029929)	0	NM_001029929	574428	Mm.472771	NM_001029929	ENSMUSG00000040829	Zmynd15	-	zinc finger, MYND-type containing 15	protein-coding
mm_164339.1	chr16	14211322	14211342	+	1	NA	exon (NM_013607, exon 27 of 42)	exon (NM_013607, exon 27 of 42)	48057	NM_001114085	67203	Mm.24105	NM_023317	ENSMUSG00000022678	Nde1	2810027M15Rik|AU042936|AW822251|Nude|mNudE	nudE neurodevelopment protein 1	protein-coding
mm_125945.1	chr15	76248497	76248498	+	1	NA	TTS (NR_105918)	TTS (NR_105918)	306	NR_105918	102465575		NR_105918	ENSMUSG00000098625	Mir6953	Gm27738|mmu-mir-6953	microRNA 6953	ncRNA
mm_83928.1	chr9	56635625	56635691	-	1	NA	promoter-TSS (NM_001311076)	promoter-TSS (NM_001311076)	-10	NM_001311076	235402	Mm.246605	NM_181074	ENSMUSG00000049556	Lingo1	4930471K13Rik|AV148400|LERN1|LINGO-1|Lrrn6a|UNQ201	leucine rich repeat and Ig domain containing 1	protein-coding
mm_162612.1	chr1	183298330	183298332	-	1	NA	intron (NM_181732, intron 1 of 9)	intron (NM_181732, intron 1 of 9)	1271	NM_181732	108909	Mm.290502	NM_145626	ENSMUSG00000042901	Aida	2610208M17Rik|BC004835	axin interactor, dorsalization associated	protein-coding
mm_124117.1	chr14	79482382	79482396	-	1	NA	intron (NM_007920, intron 1 of 8)	intron (NM_007920, intron 1 of 8)	-1121	NM_018765	22380	Mm.476813	NM_018765	ENSMUSG00000022023	Wbp4	AW545037|BB101031|FBP21	WW domain binding protein 4	protein-coding
mm_39770.1	chr5	30013911	30013915	+	1	NA	intron (NM_001314054, intron 2 of 4)	intron (NM_001314054, intron 2 of 4)	799	NM_031168	16193	Mm.1019	NM_031168	ENSMUSG00000025746	Il6	Il-6	interleukin 6	protein-coding
mm_11484.1	chr2	32395668	32395679	+	1	NA	promoter-TSS (NM_133783)	promoter-TSS (NM_133783)	-217	NM_133783	96979	Mm.28048	NM_133783	ENSMUSG00000026820	Ptges2	0610038H10Rik|C79137|Gbf1|Mpges2|Pges2	prostaglandin E synthase 2	protein-coding
mm_37593.1	chr4	126533442	126533479	-	1	NA	promoter-TSS (NM_153177)	promoter-TSS (NM_153177)	-2	NM_153177	76850	Mm.86705	NM_153177	ENSMUSG00000042500	Ago4	5730550L01Rik|AI481660|Eif2c4	argonaute RISC catalytic subunit 4	protein-coding
mm_71655.1	chr8	60516015	60516041	+	1	NA	exon (NM_011834, exon 3 of 13)	exon (NM_011834, exon 3 of 13)	9904	NM_011834	23923	Mm.35020	NM_011834	ENSMUSG00000057228	Aadat	AI875679|Aadt|KATII|Kat2|Kyat2|mKat-2	aminoadipate aminotransferase	protein-coding
mm_33126.1	chr4	124804552	124804561	+	1	NA	intron (NM_008636, intron 1 of 10)	B1_Mur1|SINE|Alu	2007	NM_008636	17764	Mm.272397	NM_008636	ENSMUSG00000028890	Mtf1	MTF-1|Thyls	metal response element binding transcription factor 1	protein-coding
mm_40941.1	chr5	76809874	76809889	+	1	NA	Intergenic	Intergenic	-30718	NM_001163793	320827	Mm.101504	NM_001163793	ENSMUSG00000036377	C530008M17Rik	2810489J07Rik|4930529A19Rik|4931405B09Rik|Kiaa1211|mKIAA1211	RIKEN cDNA C530008M17 gene	protein-coding
mm_153461.1	chr19	41262524	41262527	-	1	NA	intron (NM_133352, intron 1 of 14)	intron (NM_133352, intron 1 of 14)	1479	NM_133352	107358	Mm.246440	NM_133352	ENSMUSG00000025016	Tm9sf3	1810073M23Rik|2810031D16Rik|AI115521|AI413748|AW146116|AW549777|Smbp|mKIAA4036	transmembrane 9 superfamily member 3	protein-coding
mm_25046.1	chr3	98299207	98299226	+	1	NA	exon (NM_008256, exon 6 of 10)	exon (NM_008256, exon 6 of 10)	18785	NM_008256	15360	Mm.289131	NM_008256	ENSMUSG00000027875	Hmgcs2	1300002P16|mHS	3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2	protein-coding
mm_18209.1	chr2	48935259	48935269	-	1	NA	intron (NR_033442, intron 4 of 13)	intron (NR_033442, intron 4 of 13)	14003	NM_001177313	26428	Mm.291059	NM_011958	ENSMUSG00000026761	Orc4	Orc4P|Orc4l|mMmORC4	origin recognition complex, subunit 4	protein-coding
mm_89502.1	chr10	94036947	94036981	+	1	NA	intron (NM_053072, intron 1 of 20)	intron (NM_053072, intron 1 of 20)	963	NM_053072	13998	Mm.269596	NM_053072	ENSMUSG00000020021	Fgd6	AA123052|Etohd4|ZFYVE24	FYVE, RhoGEF and PH domain containing 6	protein-coding
mm_79803.1	chr9	64174913	64174972	+	1	NA	promoter-TSS (NR_028548)	promoter-TSS (NR_028548)	-490	NR_028548	100217453		NR_028548	ENSMUSG00000094411	Snord16a	MBII-98	small nucleolar RNA, C/D box 16A	snoRNA
mm_96887.1	chr11	70436150	70436170	+	1	NA	intron (NM_001271359, intron 2 of 15)	intron (NM_001271359, intron 2 of 15)	-2095	NR_106064	102465670		NR_106064	ENSMUSG00000099109	Mir7115	Gm27902|mmu-mir-7115	microRNA 7115	ncRNA
mm_79789.1	chr9	63719257	63719292	+	1	NA	intron (NM_016769, intron 1 of 8)	intron (NM_016769, intron 1 of 8)	38720	NM_016769	17127	Mm.7320	NM_016769	ENSMUSG00000032402	Smad3	AU022421|Madh3	SMAD family member 3	protein-coding
mm_105193.1	chr11	102051685	102051706	-	1	NA	intron (NM_001160711, intron 6 of 7)	intron (NM_001160711, intron 6 of 7)	10184	NM_001160713	52685	Mm.266885	NM_027987	ENSMUSG00000017309	Cd300lg	2310016B05Rik|Clm9|D11Ertd736e	CD300 molecule like family member G	protein-coding
mm_32310.1	chr4	103313807	103313820	+	1	NA	promoter-TSS (NM_025909)	promoter-TSS (NM_025909)	-33	NM_025909	67013	Mm.30021	NM_025909	ENSMUSG00000035069	Oma1	2010001O09Rik|MPRP-1|ZMPOMA1	OMA1 zinc metallopeptidase	protein-coding
mm_2467.1	chr1	105663856	105663866	+	1	NA	promoter-TSS (NM_013784)	promoter-TSS (NM_013784)	0	NM_029349	227446	Mm.337339	NM_029349	ENSMUSG00000026319	2310035C23Rik	6430401N10|Kiaa1468|mKIAA1468	RIKEN cDNA 2310035C23 gene	protein-coding
mm_35334.1	chr4	30702743	30702747	-	1	NA	intron (NR_040655, intron 2 of 6)	intron (NR_040655, intron 2 of 6)	38149	NR_040655	75332	Mm.108636	NR_040655		4930556G01Rik	-	RIKEN cDNA 4930556G01 gene	ncRNA
mm_103346.1	chr11	74724688	74724702	-	1	NA	promoter-TSS (NR_037610)	promoter-TSS (NR_037610)	-311	NM_013625	18472	Mm.397111	NM_013625	ENSMUSG00000020745	Pafah1b1	LIS-1|Lis1|MMS10-U|Mdsh|Ms10u|Pafaha	platelet-activating factor acetylhydrolase, isoform 1b, subunit 1	protein-coding
mm_83354.1	chr9	44375215	44375238	-	1	NA	Intergenic	Intergenic	-4264	NM_021395	12282	Mm.116721	NM_021395	ENSMUSG00000032115	Hyou1	AI415631|CBP-140|Cab140|Grp170|Orp150	hypoxia up-regulated 1	protein-coding
mm_169253.1	chr13	78261702	78261702	+	1	NA	Intergenic	L1Md_T|LINE|L1	-62829	NM_010151	13865	Mm.439653	NM_010151	ENSMUSG00000069171	Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR-3|EAR3|Erbal3|SVP44|Tcfcoup1	nuclear receptor subfamily 2, group F, member 1	protein-coding
mm_92361.1	chr10	75939965	75940002	-	1	NA	exon (NM_001277132, exon 3 of 7)	exon (NM_001277132, exon 3 of 7)	689	NM_001277132	333670	Mm.291320	NM_001037714	ENSMUSG00000050157	Gm867	Gm736	predicted gene 867	protein-coding
mm_80015.1	chr9	67858847	67858865	+	1	NA	exon (NM_177184, exon 4 of 85)	exon (NM_177184, exon 4 of 85)	18460	NM_177184	320528	Mm.241454	NM_177184	ENSMUSG00000035284	Vps13c	AI552542|AV026040|C230055H22Rik|W51662|chorein	vacuolar protein sorting 13C	protein-coding
mm_123541.1	chr14	66824418	66824436	-	1	NA	exon (NM_009955, exon 8 of 14)	exon (NM_009955, exon 8 of 14)	44173	NM_009955	12934	Mm.352648	NM_009955	ENSMUSG00000022048	Dpysl2	AI851130|Crmp2|DRP2|Musunc33|TOAD-64|Ulip2	dihydropyrimidinase-like 2	protein-coding
mm_100095.1	chr11	115604170	115604180	+	1	NA	promoter-TSS (NM_173048)	promoter-TSS (NM_173048)	24	NM_025305	50529	Mm.193040	NM_025305	ENSMUSG00000046756	Mrps7	MRP-S7|Rpms7	mitchondrial ribosomal protein S7	protein-coding
mm_153386.1	chr19	40377750	40377761	-	1	NA	intron (NM_178362, intron 6 of 28)	intron (NM_178362, intron 6 of 28)	24555	NM_001034964	20411	Mm.210815	NM_009166	ENSMUSG00000025006	Sorbs1	2310065E01Rik|9530001P15Rik|CAP|SH3P12|Sh3d5|mKIAA1296	sorbin and SH3 domain containing 1	protein-coding
mm_140984.1	chr17	24719960	24719970	-	1	NA	promoter-TSS (NR_028515)	promoter-TSS (NR_028515)	0	NR_027900	73474	Mm.443320	NR_027900	ENSMUSG00000090101	Snhg9	1700072N11Rik	small nucleolar RNA host gene 9	ncRNA
mm_71958.1	chr8	70527738	70527766	+	1	NA	promoter-TSS (NM_001199631)	promoter-TSS (NM_001199631)	9	NM_010223	14232	Mm.141864	NM_010223	ENSMUSG00000019428	Fkbp8	38kDa|FKBP-38|FKBP-8|Fkbp38	FK506 binding protein 8	protein-coding
mm_125241.1	chr15	34306768	34306784	+	1	NA	promoter-TSS (NM_016762)	promoter-TSS (NM_016762)	95	NM_016762	17181	Mm.396856	NM_016762	ENSMUSG00000022324	Matn2	Crtm2|matrilin-2	matrilin 2	protein-coding
mm_172528.1	chr7	86089742	86089760	+	1	NA	Intergenic	RLTR9D|LTR|ERVK	81973	NM_001102578	546981	Mm.469835	NM_001102578	ENSMUSG00000090436	Vmn2r75	EG546981	vomeronasal 2, receptor 75	protein-coding
mm_61975.1	chr7	90540265	90540271	+	1	NA	Intergenic	MTE2b|LTR|ERVL-MaLR	-64273	NM_026734	68472	Mm.289791	NM_026734	ENSMUSG00000030614	Tmem126b	1110001A23Rik	transmembrane protein 126B	protein-coding
mm_109548.1	chr12	111698642	111698649	+	1	NA	Intergenic	Intergenic	14308	NM_001324481	70369	Mm.44239	NM_027404	ENSMUSG00000049792	Bag5	1600025G07Rik|4930405J06Rik|Bag-5	BCL2-associated athanogene 5	protein-coding
mm_167265.1	chr8	28084789	28084812	+	1	NA	promoter-TSS (NR_033590)	promoter-TSS (NR_033590)	53	NR_033590	666422	Mm.484413	NR_033590	ENSMUSG00000110372	Gm8096	EG666422	3-phosphoglycerate dehydrogenase pseudogene	pseudo
mm_143905.1	chr17	84958488	84958498	-	1	NA	promoter-TSS (NR_027930)	promoter-TSS (NR_027930)	492	NM_001159496	19043	Mm.249695	NM_011151	ENSMUSG00000061130	Ppm1b	PP2CB	protein phosphatase 1B, magnesium dependent, beta isoform	protein-coding
mm_130468.1	chr15	98645246	98645249	-	1	NA	TTS (NM_001044741)	TTS (NM_001044741)	10480	NM_001286226	12297	Mm.3544	NM_007581	ENSMUSG00000003352	Cacnb3	Beta3|CAB3|Ca(v)beta3|Cchb3	calcium channel, voltage-dependent, beta 3 subunit	protein-coding
mm_84194.1	chr9	60522076	60522082	-	1	NA	Intergenic	CpG	-11044	NM_001040426	207596	Mm.28791	NM_172444	ENSMUSG00000032289	Thsd4	ADAMTSL-6|ADAMTSL6|AI585901|Adamtsl4|B230114P05Rik	thrombospondin, type I, domain containing 4	protein-coding
mm_44180.1	chr5	151252505	151252511	+	1	NA	Intergenic	Intergenic	-62315	NM_146258	243362	Mm.209272	NM_146258	ENSMUSG00000016128	Stard13	DLC2|GT650	StAR-related lipid transfer (START) domain containing 13	protein-coding
mm_46207.1	chr5	98031452	98031463	-	1	NA	promoter-TSS (NM_133738)	promoter-TSS (NM_133738)	-495	NM_133738	71914	Mm.24842	NM_133738	ENSMUSG00000029338	Antxr2	2310046B19Rik|AW561899|CMG-2|CMG2|cI-35	anthrax toxin receptor 2	protein-coding
mm_17377.1	chr2	27019932	27019953	-	1	NA	intron (NM_029862, intron 5 of 5)	intron (NM_029862, intron 5 of 5)	8056	NM_172659	227659	Mm.41203	NM_172659	ENSMUSG00000036067	Slc2a6	A330096C23|F630103L12Rik|Glut6|Glut9	solute carrier family 2 (facilitated glucose transporter), member 6	protein-coding
mm_107923.1	chr12	71069990	71069994	+	1	NA	exon (NM_001081195, exon 17 of 24)	exon (NM_001081195, exon 17 of 24)	-41436	NM_029227	75266	Mm.402075	NM_029227	ENSMUSG00000021078	Tomm20l	4930553D19Rik	translocase of outer mitochondrial membrane 20 homolog (yeast)-like	protein-coding
mm_168625.1	chr11	79976297	79976315	-	1	NA	Intergenic	BGLII|LTR|ERVK	-13919	NM_144826	216987	Mm.274961	NM_144826	ENSMUSG00000035575	Utp6	4732497O03Rik|HCA66	UTP6 small subunit processome component	protein-coding
mm_143504.1	chr17	71598725	71598781	-	1	NA	promoter-TSS (NR_015549)	promoter-TSS (NR_015549)	8	NR_015549	68789	Mm.75202	NR_015549	ENSMUSG00000085492	Trmt61b	1110039F03Rik|623451|Gm6431	tRNA methyltransferase 61B	ncRNA
mm_124549.1	chr14	122891104	122891107	-	1	NA	3' UTR (NM_145466, exon 3 of 3)	3' UTR (NM_145466, exon 3 of 3)	22060	NM_145466	223267	Mm.379358	NM_145466	ENSMUSG00000041625	Ggact	A2ld1	gamma-glutamylamine cyclotransferase	protein-coding
mm_134036.1	chr16	5049840	5049879	-	1	NA	promoter-TSS (NM_028720)	promoter-TSS (NM_028720)	51	NM_001079814	74022	Mm.21652	NM_028720	ENSMUSG00000022536	Glyr1	2810419J22Rik|3930401K13Rik|AW545332|Npac	glyoxylate reductase 1 homolog (Arabidopsis)	protein-coding
mm_72863.1	chr8	88582781	88582782	+	1	NA	intron (NM_001163660, intron 2 of 7)	intron (NM_001163660, intron 2 of 7)	53347	NM_027840	71607	Mm.270607	NM_027840	ENSMUSG00000031662	Snx20	9130017C17Rik	sorting nexin 20	protein-coding
mm_17857.1	chr2	34799712	34799726	-	1	NA	intron (NM_145522, intron 1 of 7)	intron (NM_145522, intron 1 of 7)	193	NM_145522	227746	Mm.158705	NM_145522	ENSMUSG00000070953	Rabepk	8430412M01Rik|9530020D24Rik|AV073337|C87311|Rab9p40	Rab9 effector protein with kelch motifs	protein-coding
mm_102376.1	chr11	58801945	58801968	-	1	NA	promoter-TSS (NM_001162878)	promoter-TSS (NM_001162878)	4	NM_001162878	75429	Mm.296819	NM_029283	ENSMUSG00000049154	Fam183b	3100002J23Rik|Theg6	family with sequence similarity 183, member B	protein-coding
mm_66117.1	chr7	31042358	31042389	-	1	NA	promoter-TSS (NM_001111073)	promoter-TSS (NM_001111073)	-42	NM_001287217	18301	Mm.1870	NM_008761	ENSMUSG00000009687	Fxyd5	EF-8|Oit2|RIC	FXYD domain-containing ion transport regulator 5	protein-coding
mm_94997.1	chr11	31872101	31872104	+	1	NA	5' UTR (NM_026252, exon 1 of 10)	5' UTR (NM_026252, exon 1 of 10)	1162	NM_026252	67579	Mm.339792	NM_026252	ENSMUSG00000020300	Cpeb4	Cpe-bp4|Cpeb-4|mCPEB-4	cytoplasmic polyadenylation element binding protein 4	protein-coding
mm_154568.1	chrX	6577260	6577294	+	1	NA	promoter-TSS (NM_001313765)	promoter-TSS (NM_001313765)	-9	NM_001313765	208431	Mm.23208	NM_001040459	ENSMUSG00000068270	Shroom4	D430043L16Rik|Gm724|Shrm4	shroom family member 4	protein-coding
mm_64763.1	chr7	4964334	4964365	-	1	NA	promoter-TSS (NM_001146329)	promoter-TSS (NM_001146329)	-1	NM_001146329	381836	Mm.297829	NM_001146329	ENSMUSG00000030433	Sbk2	Gm1079|Sgk069	SH3-binding domain kinase family, member 2	protein-coding
mm_81684.1	chr9	111118207	111118217	+	1	NA	5' UTR (NM_001164838, exon 1 of 15)	5' UTR (NM_001164838, exon 1 of 15)	101	NM_001164838	71268	Mm.302287	NM_027742	ENSMUSG00000032497	Lrrfip2	5133400F20Rik|AI850587	leucine rich repeat (in FLII) interacting protein 2	protein-coding
mm_37392.1	chr4	121098023	121098089	-	1	NA	5' UTR (NM_172700, exon 1 of 10)	5' UTR (NM_172700, exon 1 of 10)	187	NM_172700	230709	Mm.34399	NM_172700	ENSMUSG00000043207	Zmpste24	A530043O15Rik|D030046F19|FACE1|Face-1|MADB|STE24|Ste24p	zinc metallopeptidase, STE24	protein-coding
mm_7663.1	chr1	128417317	128417350	-	1	NA	promoter-TSS (NM_145507)	promoter-TSS (NM_145507)	83	NM_177445	226414	Mm.28693	NM_145507	ENSMUSG00000026356	Dars	5730439G15Rik	aspartyl-tRNA synthetase	protein-coding
mm_38519.1	chr4	141416029	141416037	-	1	NA	promoter-TSS (NM_019701)	promoter-TSS (NM_019701)	-45	NM_019701	56365	Mm.24882	NM_019701	ENSMUSG00000006216	Clcnkb	CLCKB|Clc-Ka|Clck2|Clcnk1l	chloride channel, voltage-sensitive Kb	protein-coding
mm_167249.1	chr8	24399223	24399226	+	1	NA	Intergenic	Intergenic	39722	NM_026931	69068	Mm.25775	NM_026931	ENSMUSG00000056313	1810011O10Rik	1110065B09Rik|AW121743|AW321058	RIKEN cDNA 1810011O10 gene	protein-coding
mm_157696.1	chrX	60446676	60446685	-	1	NA	intron (NM_001039240, intron 2 of 3)	intron (NM_001039240, intron 2 of 3)	9515	NM_001039240	631784	Mm.424878	NM_001039240	ENSMUSG00000079583	Gm7073	-	predicted gene 7073	protein-coding
mm_50554.1	chr6	49047426	49047436	+	1	NA	exon (NM_053110, exon 5 of 11)	exon (NM_053110, exon 5 of 11)	10913	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_34723.1	chr4	152177958	152178013	+	1	NA	promoter-TSS (NM_133348)	promoter-TSS (NM_133348)	-115	NM_133348	70025	Mm.296191	NM_133348	ENSMUSG00000028937	Acot7	2410041A17Rik|Ach1|Act|Bach|CTE-IIa|Cte-II|Lach1	acyl-CoA thioesterase 7	protein-coding
mm_87889.1	chr10	61783248	61783277	+	1	NA	intron (NM_207000, intron 1 of 8)	CpG	602	NM_207000	404634	Mm.272870	NM_207000	ENSMUSG00000020086	H2afy2	macroH2A2	H2A histone family, member Y2	protein-coding
mm_47395.1	chr5	123018971	123018977	-	1	NA	intron (NM_175423, intron 1 of 1)	MIR|SINE|MIR	3900	NM_175423	109305	Mm.218582	NM_175423	ENSMUSG00000049686	Orai1	D730049H07Rik|Tmem142a|orai-1	ORAI calcium release-activated calcium modulator 1	protein-coding
mm_110848.1	chr12	73053890	73053912	-	1	NA	Intergenic	CpG	-7189	NM_009189	20471	Mm.4645	NM_009189	ENSMUSG00000051367	Six1	BB138287	sine oculis-related homeobox 1	protein-coding
mm_85129.1	chr9	95577698	95577730	-	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	17897	NM_198414	75552	Mm.151485	NM_198414	ENSMUSG00000064225	Paqr9	1700020G04Rik	progestin and adipoQ receptor family member IX	protein-coding
mm_10860.1	chr2	25062720	25062728	+	1	NA	3' UTR (NM_020276, exon 14 of 14)	3' UTR (NM_020276, exon 14 of 14)	2913	NR_106124	102465989		NR_106124	ENSMUSG00000099320	Mir7664	Gm28015|mmu-mir-7664	microRNA 7664	ncRNA
mm_93187.1	chr10	93889759	93889826	-	1	NA	5' UTR (NM_019648, exon 2 of 12)	5' UTR (NM_019648, exon 2 of 12)	1410	NM_019648	56307	Mm.289329	NM_019648	ENSMUSG00000036112	Metap2	4930584B20Rik|A930035J23Rik|AI047573|AL024412|AU014659|Amp2|Mnpep|p67|p67eIF2	methionine aminopeptidase 2	protein-coding
mm_71687.1	chr8	61225845	61225857	+	1	NA	5' UTR (NM_021506, exon 2 of 12)	5' UTR (NM_021506, exon 2 of 12)	1680	NM_021506	59009	Mm.27949	NM_021506	ENSMUSG00000031642	Sh3rf1	2200003J05Rik|Posh|R75531|Sh3md2	SH3 domain containing ring finger 1	protein-coding
mm_42897.1	chr5	122406075	122406115	+	1	NA	TTS (NM_019824)	TTS (NM_019824)	14217	NM_019824	56378	Mm.275942	NM_019824	ENSMUSG00000029465	Arpc3	1110006A04Rik|p21-ARC|p21-Ar|p21Arc	actin related protein 2/3 complex, subunit 3	protein-coding
mm_34941.1	chr4	155847394	155847467	+	1	NA	5' UTR (NM_010091, exon 1 of 15)	5' UTR (NM_010091, exon 1 of 15)	113	NM_010091	13542	Mm.3400	NM_010091	ENSMUSG00000029071	Dvl1	Dvl|mKIAA4029	dishevelled segment polarity protein 1	protein-coding
mm_36947.1	chr4	108848357	108848405	-	1	NA	exon (NM_029571, exon 1 of 1)	exon (NM_029571, exon 1 of 1)	524	NM_029571	100087	Mm.440007	NM_029571	ENSMUSG00000073775	Kti12	1110001A12Rik|AI326810|AU014758	KTI12 homolog, chromatin associated	protein-coding
mm_60265.1	chr7	43825405	43825417	+	1	NA	promoter-TSS (NM_011177)	promoter-TSS (NM_011177)	-39	NM_011177	19144	Mm.3944	NM_011177	ENSMUSG00000050063	Klk6	AI849898|BSP|Bssp|Klk29|MSP|Prss18|Prss9|neurosin	kallikrein related-peptidase 6	protein-coding
mm_91759.1	chr10	51480435	51480443	-	1	NA	promoter-TSS (NM_008147)	promoter-TSS (NM_008147)	-173	NM_008147	14727	Mm.439661	NM_008147	ENSMUSG00000062593	Lilr4b	Gp49a|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4B	protein-coding
mm_49340.1	chr6	21468594	21468604	+	1	NA	intron (NM_019697, intron 1 of 5)	intron (NM_019697, intron 1 of 5)	252490	NM_019697	16508	Mm.425316	NM_019697	ENSMUSG00000060882	Kcnd2	AI839615|AW555701|Kv4.2|R75121|mKIAA1044	potassium voltage-gated channel, Shal-related family, member 2	protein-coding
mm_43240.1	chr5	130079392	130079403	+	1	NA	promoter-TSS (NM_001130476)	promoter-TSS (NM_001130476)	27	NM_001130476	22021	Mm.332720	NM_013837	ENSMUSG00000034118	Tpst1	R75054|Tango13a	protein-tyrosine sulfotransferase 1	protein-coding
mm_17872.1	chr2	34953478	34953507	-	1	NA	intron (NM_009421, intron 6 of 10)	B4A|SINE|B4	8280	NM_009421	22029	Mm.239514	NM_009421	ENSMUSG00000026875	Traf1	4732496E14Rik	TNF receptor-associated factor 1	protein-coding
mm_125343.1	chr15	39112924	39112935	+	1	NA	promoter-TSS (NM_198606)	promoter-TSS (NM_198606)	55	NM_198606	223499	Mm.321937	NM_198606	ENSMUSG00000022300	Dcaf13	Gm83|Wdsof1	DDB1 and CUL4 associated factor 13	protein-coding
mm_6961.1	chr1	86110827	86110849	-	1	NA	exon (NM_008311, exon 2 of 4)	exon (NM_008311, exon 2 of 4)	1132	NM_008311	15559	Mm.439747	NM_008311	ENSMUSG00000026228	Htr2b	5-HT2B|AJ012488|AV377389	5-hydroxytryptamine (serotonin) receptor 2B	protein-coding
mm_2110.1	chr1	87853265	87853306	+	1	NA	promoter-TSS (NM_177646)	promoter-TSS (NM_177646)	-2	NM_177646	227333	Mm.277217	NM_177646	ENSMUSG00000070738	Dgkd	AI841987|D330025K09|DGKdelta|dgkd-2	diacylglycerol kinase, delta	protein-coding
mm_55193.1	chr6	52191619	52191645	-	1	NA	promoter-TSS (NM_008265)	promoter-TSS (NM_008265)	71	NM_008265	15401	Mm.439647	NM_008265	ENSMUSG00000000942	Hoxa4	AV206827|Hox-1.4	homeobox A4	protein-coding
mm_64972.1	chr7	16675618	16675623	-	1	NA	promoter-TSS (NM_175315)	promoter-TSS (NM_175315)	85	NM_175315	101434	Mm.102767	NM_175315	ENSMUSG00000078795	Ceacam15	AA407838|C430002N04Rik	carcinoembryonic antigen-related cell adhesion molecule 15	protein-coding
mm_142911.1	chr17	53463316	53463340	-	1	NA	promoter-TSS (NM_172497)	promoter-TSS (NM_172497)	-7	NM_172497	211482	Mm.60887	NM_172497	ENSMUSG00000023931	Efhb	4921525D22Rik	EF hand domain family, member B	protein-coding
mm_144902.1	chr18	37320375	37320401	+	1	NA	promoter-TSS (NM_053130)	promoter-TSS (NM_053130)	7	NM_053130	93876	Mm.196698	NM_053130	ENSMUSG00000063687	Pcdhb5	Pcdhb4A|PcdhbE	protocadherin beta 5	protein-coding
mm_120966.1	chr14	77904475	77904503	+	1	NA	exon (NM_029495, exon 1 of 12)	exon (NM_029495, exon 1 of 12)	250	NM_029495	108670	Mm.68134	NM_029495	ENSMUSG00000022014	Epsti1	2310046K10Rik|5033415K03Rik|BRESI1	epithelial stromal interaction 1 (breast)	protein-coding
mm_52412.1	chr6	113389273	113389281	+	1	NA	promoter-TSS (NM_001142732)	promoter-TSS (NM_001142732)	17	NM_001142732	101100	Mm.388573	NM_133923	ENSMUSG00000030276	Ttll3	4833441J24Rik|AI450050	tubulin tyrosine ligase-like family, member 3	protein-coding
mm_39079.1	chr4	154334784	154334795	-	1	NA	intron (NM_001177995, intron 11 of 15)	intron (NM_001177995, intron 11 of 15)	-34894	NM_001112744	230972	Mm.38481	NM_001112744	ENSMUSG00000029032	Arhgef16	-	Rho guanine nucleotide exchange factor (GEF) 16	protein-coding
mm_81024.1	chr9	104547268	104547295	+	1	NA	Intergenic	Intergenic	-22507	NM_028719	74020	Mm.326240	NM_028719	ENSMUSG00000032564	Cpne4	3632411M23Rik|4933406O10Rik	copine IV	protein-coding
mm_15150.1	chr2	154000223	154000229	+	1	NA	3' UTR (NM_001080811, exon 11 of 11)	3' UTR (NM_001080811, exon 11 of 11)	-8050	NM_008953	19194	Mm.29197	NM_008953	ENSMUSG00000042459	Bpifa2	Bpifa2e|Psp	BPI fold containing family A, member 2	protein-coding
mm_153160.1	chr19	34492864	34492892	-	1	NA	3' UTR (NM_021460, exon 10 of 10)	3' UTR (NM_021460, exon 10 of 10)	-17743	NM_009890	12642	Mm.30824	NM_009890	ENSMUSG00000050370	Ch25h	AI462618|m25OH	cholesterol 25-hydroxylase	protein-coding
mm_38220.1	chr4	135973494	135973516	-	1	NA	promoter-TSS (NM_011942)	promoter-TSS (NM_011942)	-911	NM_011942	26394	Mm.34302	NM_011942	ENSMUSG00000028670	Lypla2	LysoII	lysophospholipase 2	protein-coding
mm_150590.1	chr19	40667233	40667243	+	1	NA	intron (NM_009848, intron 1 of 9)	intron (NM_009848, intron 1 of 9)	7468	NM_009848	12495	Mm.2824	NM_009848	ENSMUSG00000048120	Entpd1	2610206B08Rik|AA408691|Cd39|NTPDase-1	ectonucleoside triphosphate diphosphohydrolase 1	protein-coding
mm_55942.1	chr6	85069450	85069523	-	1	NA	promoter-TSS (NM_177077)	promoter-TSS (NM_177077)	27	NM_177077	75914	Mm.159621	NM_177077	ENSMUSG00000033769	Exoc6b	4930569O18Rik|G430127E12Rik|Sec15b|Sec15l2|mKIAA0919	exocyst complex component 6B	protein-coding
mm_84283.1	chr9	62819578	62819612	-	1	NA	Intergenic	Intergenic	-7947	NM_010193	14155	Mm.24069	NM_010193	ENSMUSG00000032244	Fem1b	mKIAA0396	feminization 1 homolog b (C. elegans)	protein-coding
mm_41643.1	chr5	98031300	98031310	+	1	NA	promoter-TSS (NM_133738)	promoter-TSS (NM_133738)	-343	NM_133738	71914	Mm.24842	NM_133738	ENSMUSG00000029338	Antxr2	2310046B19Rik|AW561899|CMG-2|CMG2|cI-35	anthrax toxin receptor 2	protein-coding
mm_40717.1	chr5	65955638	65955646	+	1	NA	Intergenic	Intergenic	-11482	NM_001081104	231252	Mm.140015	NM_001081104	ENSMUSG00000029205	Chrna9	2410015I05Rik|Acra9|EG666827|Gm8311	cholinergic receptor, nicotinic, alpha polypeptide 9	protein-coding
mm_112657.1	chr13	16026839	16026849	+	1	NA	exon (NM_008380, exon 5 of 5)	exon (NM_008380, exon 5 of 5)	14993	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_29754.1	chr3	127140449	127140452	-	1	NA	intron (NM_001327938, intron 1 of 47)	intron (NM_001327938, intron 1 of 47)	-20855	NR_105030	100862268	Mm.444603	NR_105029	ENSMUSG00000097456	LOC100862268	-	uncharacterized LOC100862268	ncRNA
mm_144948.1	chr18	37807039	37807091	+	1	NA	exon (NM_033581, exon 1 of 4)	exon (NM_033581, exon 1 of 4)	655	NM_033581	93706	Mm.247203	NM_033581	ENSMUSG00000102918	Pcdhgc3	PC43|Pcdh2	protocadherin gamma subfamily C, 3	protein-coding
mm_14585.1	chr2	135929504	135929512	+	1	NA	intron (NM_013829, intron 6 of 36)	intron (NM_013829, intron 6 of 36)	-128419	NM_029530	76161	Mm.41638	NM_029530	ENSMUSG00000027270	Lamp5	3110035N03Rik|6330527O06Rik|BAD-LAMP|LAMP-5	lysosomal-associated membrane protein family, member 5	protein-coding
mm_153619.1	chr19	43986480	43986491	-	1	NA	promoter-TSS (NM_030703)	promoter-TSS (NM_030703)	35	NM_030703	93721	Mm.206774	NM_030703	ENSMUSG00000025196	Cpn1	0610011F20Rik|CPN	carboxypeptidase N, polypeptide 1	protein-coding
mm_57426.1	chr6	124914062	124914065	-	1	NA	3' UTR (NM_026988, exon 5 of 5)	3' UTR (NM_026988, exon 5 of 5)	-2358	NM_008479	16768	Mm.4528	NM_008479	ENSMUSG00000030124	Lag3	CD223|LAG-3|Ly66	lymphocyte-activation gene 3	protein-coding
mm_55183.1	chr6	52164539	52164549	-	1	NA	exon (NM_010451, exon 1 of 2)	exon (NM_010451, exon 1 of 2)	287	NM_010451	15399	Mm.131	NM_010451	ENSMUSG00000014704	Hoxa2	AI324701|HOX1.11|Hox-1.11	homeobox A2	protein-coding
mm_47668.1	chr5	127281621	127281627	-	1	NA	promoter-TSS (NR_038129)	promoter-TSS (NR_038129)	-1	NR_038128	67351	Mm.320172	NR_038127	ENSMUSG00000087104	Tmem132cos	1700085B03Rik	transmembrane protein 132C, opposite strand	ncRNA
mm_92548.1	chr10	79759177	79759227	-	1	NA	exon (NM_144528, exon 9 of 9)	exon (NM_144528, exon 9 of 9)	4083	NM_023304	67112	Mm.154211	NM_023304	ENSMUSG00000020327	Fgf22	2210414E06Rik|FGF-22	fibroblast growth factor 22	protein-coding
mm_74685.1	chr8	14872118	14872119	-	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	-16418	NM_012000	26889	Mm.254027	NM_012000	ENSMUSG00000026317	Cln8	mnd	ceroid-lipofuscinosis, neuronal 8	protein-coding
mm_51732.1	chr6	87042839	87042918	+	1	NA	promoter-TSS (NM_013528)	promoter-TSS (NM_013528)	32	NM_013528	14583	Mm.19893	NM_013528	ENSMUSG00000029992	Gfpt1	2810423A18Rik|AI324119|AI449986|GFA|GFAT|GFAT1|GFAT1m|Gfpt	glutamine fructose-6-phosphate transaminase 1	protein-coding
mm_94415.1	chr11	5861977	5861989	+	1	NA	5' UTR (NM_009636, exon 1 of 21)	5' UTR (NM_009636, exon 1 of 21)	117	NM_001291857	11568	Mm.3317	NM_009636	ENSMUSG00000020473	Aebp1	ACLP	AE binding protein 1	protein-coding
mm_67848.1	chr7	98656531	98656600	-	1	NA	promoter-TSS (NM_172280)	promoter-TSS (NM_172280)	4	NM_172280	233545	Mm.387819	NM_172280	ENSMUSG00000035401	Emsy	2210018M11Rik|2310016L09Rik|AU019521|AU019557	EMSY, BRCA2-interacting transcriptional repressor	protein-coding
mm_106565.1	chr11	120633623	120633650	-	1	NA	promoter-TSS (NM_010756)	promoter-TSS (NM_010756)	-89	NM_010756	17134	Mm.268010	NM_010756	ENSMUSG00000051510	Mafg	AA545192|C630022N07Rik	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein G (avian)	protein-coding
mm_4539.1	chr1	176814912	176814922	+	1	NA	5' UTR (NM_029756, exon 1 of 18)	5' UTR (NM_029756, exon 1 of 18)	257	NM_029756	76816	Mm.171399	NM_029756	ENSMUSG00000026504	Sdccag8	2700048G21Rik|5730470G24Rik|Cccap	serologically defined colon cancer antigen 8	protein-coding
mm_160060.1	chr7	4837072	4837072	-	1	NA	intron (NM_001290291, intron 1 of 4)	G-rich|Low_complexity|Low_complexity	7624	NM_001290291	232813	Mm.44666	NM_172737	ENSMUSG00000053550	Shisa7	ckamp59	shisa family member 7	protein-coding
mm_3038.1	chr1	134040229	134040239	+	1	NA	exon (NM_021355, exon 2 of 3)	exon (NM_021355, exon 2 of 3)	2719	NM_021355	14264	Mm.287146	NM_021355	ENSMUSG00000041559	Fmod	AI131919|AU041740|SLRR2E	fibromodulin	protein-coding
mm_38653.1	chr4	143299276	143299290	-	1	NA	5' UTR (NM_010329, exon 1 of 6)	5' UTR (NM_010329, exon 1 of 6)	281	NM_010329	14726	Mm.2976	NM_010329	ENSMUSG00000028583	Pdpn	Gp38|OTS-8|RANDAM-2|T1-alpha|T1a|T1alpha	podoplanin	protein-coding
mm_43675.1	chr5	138793224	138793236	+	1	NA	exon (NM_030565, exon 4 of 10)	exon (NM_030565, exon 4 of 10)	-26850	NM_001195128	384244	Mm.485002	NM_001195128	ENSMUSG00000094504	Gm5294	EG384244	predicted gene 5294	protein-coding
mm_104826.1	chr11	99073929	99073966	-	1	NA	exon (NM_172564, exon 7 of 13)	exon (NM_172564, exon 7 of 13)	15359	NM_172564	217169	Mm.262067	NM_172564	ENSMUSG00000017607	Tns4	9930017A07Rik|AA589547|AU016405|Cten	tensin 4	protein-coding
mm_42737.1	chr5	120649214	120649259	+	1	NA	promoter-TSS (NM_001281999)	promoter-TSS (NM_001281999)	48	NM_001281999	19415	Mm.41209	NM_013832	ENSMUSG00000029602	Rasal1	MRASAL	RAS protein activator like 1 (GAP1 like)	protein-coding
mm_59575.1	chr7	28117384	28117392	+	1	NA	exon (NM_001122603, exon 18 of 20)	exon (NM_001122603, exon 18 of 20)	-12078	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_149243.1	chr19	10204181	10204191	+	1	NA	promoter-TSS (NM_001271614)	promoter-TSS (NM_001271614)	-16	NM_026919	69038	Mm.375100	NM_026919	ENSMUSG00000036372	Tmem258	1810006K21Rik	transmembrane protein 258	protein-coding
mm_109522.1	chr12	111535653	111535660	+	1	NA	Intergenic	Intergenic	-2445	NM_178041	217869	Mm.271222	NM_173363	ENSMUSG00000021282	Eif5	2810011H21Rik|D12Ertd549e	eukaryotic translation initiation factor 5	protein-coding
mm_22862.1	chr3	28727967	28728016	+	1	NA	3' UTR (NM_031197, exon 11 of 11)	3' UTR (NM_031197, exon 11 of 11)	30088	NM_031197	20526	Mm.18443	NM_031197	ENSMUSG00000027690	Slc2a2	AI266973|Glut-2|Glut2	solute carrier family 2 (facilitated glucose transporter), member 2	protein-coding
mm_149685.1	chr19	20493008	20493021	+	1	NA	intron (NR_015502, intron 1 of 3)	intron (NR_015502, intron 1 of 3)	299	NR_015502	320092	Mm.482524	NR_015502		E030003E18Rik	1700127G21Rik	RIKEN cDNA E030003E18 gene	ncRNA
mm_65587.1	chr7	27310696	27310706	-	1	NA	TTS (NM_001310678)	TTS (NM_001310678)	22947	NM_001113549	108075	Mm.272251	NM_175641	ENSMUSG00000040488	Ltbp4	2310046A13Rik	latent transforming growth factor beta binding protein 4	protein-coding
mm_21351.1	chr2	157120511	157120528	-	1	NA	exon (NM_001139520, exon 6 of 17)	exon (NM_001139520, exon 6 of 17)	14703	NM_001139520	56045	Mm.248478	NM_018851	ENSMUSG00000027639	Samhd1	E330031J07Rik|Mg11	SAM domain and HD domain, 1	protein-coding
mm_72640.1	chr8	84701763	84701769	+	1	NA	5' UTR (NM_008535, exon 1 of 4)	5' UTR (NM_008535, exon 1 of 4)	309	NM_008535	17095	Mm.4925	NM_008535	ENSMUSG00000034041	Lyl1	Lyl-1|bHLHa18	lymphoblastomic leukemia 1	protein-coding
mm_74360.1	chr8	128359066	128359085	+	1	NA	promoter-TSS (NM_008737)	promoter-TSS (NM_008737)	2	NM_008737	18186	Mm.271745	NM_008737	ENSMUSG00000025810	Nrp1	C530029I03|NP-1|NPN-1|Npn1|Nrp	neuropilin 1	protein-coding
mm_169874.1	chr16	37654368	37654381	-	1	NA	promoter-TSS (NM_026610)	promoter-TSS (NM_026610)	-6	NM_026610	68194	Mm.379154	NM_026610	ENSMUSG00000022820	Ndufb4	0610006N12Rik|1300010H20Rik	NADH dehydrogenase (ubiquinone) 1 beta subcomplex 4	protein-coding
mm_89326.1	chr10	87931575	87931585	+	1	NA	3' UTR (NM_010512, exon 5 of 5)	3' UTR (NM_010512, exon 5 of 5)	-35091	NR_000040	22172	Mm.391420	NR_000040		Tyms-ps	-	thymidylate synthase, pseudogene	pseudo
mm_13217.1	chr2	96318074	96318084	+	1	NA	promoter-TSS (NM_001289742)	promoter-TSS (NM_001289742)	-90	NM_001289742	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_53449.1	chr6	134451140	134451146	+	1	NA	intron (NM_008514, intron 22 of 22)	intron (NM_008514, intron 22 of 22)	54814	NM_025778	66813	Mm.474472	NM_025778	ENSMUSG00000030200	Bcl2l14	4930452K23Rik|4933405K19Rik|9030625M01Rik|AI429211|Bclg	BCL2-like 14 (apoptosis facilitator)	protein-coding
mm_135821.1	chr16	58499334	58499347	-	1	NA	intron (NM_018784, intron 2 of 10)	intron (NM_018784, intron 2 of 10)	23972	NM_018784	54613	Mm.212742	NM_018784	ENSMUSG00000022747	St3gal6	1700023B24Rik|AI930218|AW552396|Siat10|St3galVI	ST3 beta-galactoside alpha-2,3-sialyltransferase 6	protein-coding
mm_110288.1	chr12	32123726	32123742	-	1	NA	Intergenic	Intergenic	-62455	NM_011158	19088	Mm.25594	NM_011158	ENSMUSG00000002997	Prkar2b	AI451071|AW061005|PKARIIbeta|Pkarb2|RII(beta)	protein kinase, cAMP dependent regulatory, type II beta	protein-coding
mm_76364.1	chr8	84773808	84773812	-	1	NA	5' UTR (NM_001081981, exon 1 of 11)	5' UTR (NM_001081981, exon 1 of 11)	559	NM_001081981	18032	Mm.9394	NM_010906	ENSMUSG00000001911	Nfix	CTF|NF-I/X|NF1-X|NFI-X	nuclear factor I/X	protein-coding
mm_21820.1	chr2	165286914	165286933	-	1	NA	intron (NM_144893, intron 1 of 9)	intron (NM_144893, intron 1 of 9)	864	NM_001252574	228875	Mm.21184	NM_144893	ENSMUSG00000017664	Slc35c2	C85957|CGI-15|D2Wsu58e|Ovcov1	solute carrier family 35, member C2	protein-coding
mm_27465.1	chr3	52390872	52390921	-	1	NA	Intergenic	ORR1C2|LTR|ERVL-MaLR	122559	NM_019739	56458	Mm.29891	NM_019739	ENSMUSG00000044167	Foxo1	AI876417|Afxh|FKHR|Fkhr1|Foxo1a	forkhead box O1	protein-coding
mm_53634.1	chr6	140591645	140591662	+	1	NA	exon (NM_144920, exon 30 of 31)	exon (NM_144920, exon 30 of 31)	-31010	NM_178803	11569	Mm.86453	NM_009637	ENSMUSG00000030232	Aebp2	AU023766|B230313N05Rik	AE binding protein 2	protein-coding
mm_138012.1	chr17	33905103	33905116	+	1	NA	promoter-TSS (NR_040470)	promoter-TSS (NR_040470)	-26	NR_040470	474160	Mm.206186	NR_040470	ENSMUSG00000092349	Platr17	-	pluripotency associated transcript 17	ncRNA
mm_13852.1	chr2	119650413	119650416	+	1	NA	TTS (NM_001042652)	TTS (NM_001042652)	12384	NM_027175	69702	Mm.5390	NM_027175	ENSMUSG00000027305	Ndufaf1	2410001M24Rik|CGI-65|CIA30	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, assembly factor 1	protein-coding
mm_65434.1	chr7	25369049	25369115	-	1	NA	5' UTR (NM_028219, exon 2 of 5)	5' UTR (NM_028219, exon 2 of 5)	642	NM_001081375	72383	Mm.34382	NM_028219	ENSMUSG00000063651	Cnfn	2210418J09Rik	cornifelin	protein-coding
mm_52189.1	chr6	99692281	99692323	+	1	NA	promoter-TSS (NM_008158)	promoter-TSS (NM_008158)	-377	NM_008158	14761	Mm.35009	NM_008158	ENSMUSG00000072875	Gpr27	-	G protein-coupled receptor 27	protein-coding
mm_15848.1	chr2	164771863	164771879	+	1	NA	exon (NM_026785, exon 4 of 6)	exon (NM_026785, exon 4 of 6)	1942	NM_026785	68612	Mm.89830	NM_026785	ENSMUSG00000001403	Ube2c	1110015A16Rik|D2Ertd695e	ubiquitin-conjugating enzyme E2C	protein-coding
mm_44561.1	chr5	24622647	24622653	-	1	NA	Intergenic	Intergenic	-20648	NM_025891	66993	Mm.436539	NM_025891	ENSMUSG00000028949	Smarcd3	1500001J14Rik|2210409C08Rik|BAF60C	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3	protein-coding
mm_67274.1	chr7	76237576	76237587	-	1	NA	intron (NM_001199224, intron 1 of 22)	RMER19B2|LTR|ERVK	7694	NM_001199224	244071	Mm.322829	NM_172902	ENSMUSG00000025754	Agbl1	Ccp4|D430020F16|EG244071|Nna1-l1	ATP/GTP binding protein-like 1	protein-coding
mm_20634.1	chr2	132007457	132007478	-	1	NA	exon (NM_175445, exon 4 of 11)	exon (NM_175445, exon 4 of 11)	22521	NM_175445	215653	Mm.204737	NM_175445	ENSMUSG00000027339	Rassf2	3830431H01Rik|9030412M04Rik|AI852669|AW495050	Ras association (RalGDS/AF-6) domain family member 2	protein-coding
mm_202.1	chr1	16105857	16105870	+	1	NA	promoter-TSS (NM_133832)	promoter-TSS (NM_133832)	-19	NM_133832	98711	Mm.274376	NM_133832	ENSMUSG00000025921	Rdh10	3110069K09Rik|4921506A21Rik|AI875664|AW549993|D1Ertd762e|m366Asp	retinol dehydrogenase 10 (all-trans)	protein-coding
mm_27545.1	chr3	57842637	57842652	-	1	NA	3' UTR (NM_019410, exon 3 of 3)	3' UTR (NM_019410, exon 3 of 3)	5113	NM_019410	18645	Mm.271744	NM_019410	ENSMUSG00000027805	Pfn2	Pfn	profilin 2	protein-coding
mm_10200.1	chr2	4935137	4935138	+	1	NA	intron (NM_010726, intron 6 of 8)	intron (NM_010726, intron 6 of 8)	16141	NM_010726	16922	Mm.391704	NM_010726	ENSMUSG00000026664	Phyh	AI256161|AI265699|Lnap1|PAHX	phytanoyl-CoA hydroxylase	protein-coding
mm_95168.1	chr11	40733640	40733703	+	1	NA	promoter-TSS (NM_013552)	promoter-TSS (NM_013552)	10	NM_001290697	52653	Mm.276504	NM_026023	ENSMUSG00000020328	Nudcd2	-	NudC domain containing 2	protein-coding
mm_123515.1	chr14	66274745	66274752	-	1	NA	intron (NM_001162365, intron 1 of 30)	intron (NM_001162365, intron 1 of 30)	6304	NM_172498	19229	Mm.21613	NM_172498	ENSMUSG00000059456	Ptk2b	CADTK|CAKB|CAKbeta|E430023O05Rik|FADK2|FAK2|PYK2|Raftk	PTK2 protein tyrosine kinase 2 beta	protein-coding
mm_40233.1	chr5	37291363	37291385	+	1	NA	3' UTR (NM_001136058, exon 14 of 14)	3' UTR (NM_001136058, exon 14 of 14)	45507	NM_021292	59056	Mm.479678	NM_021292	ENSMUSG00000029122	Evc	-	Ellis van Creveld gene syndrome	protein-coding
mm_18551.1	chr2	65090439	65090441	-	1	NA	intron (NM_027225, intron 12 of 12)	L1_Rod|LINE|L1	-67674	NM_016719	50915	Mm.214554	NM_016719	ENSMUSG00000026888	Grb14	AI505286	growth factor receptor bound protein 14	protein-coding
mm_35551.1	chr4	41508964	41508969	-	1	NA	intron (NM_001253788, intron 2 of 5)	intron (NM_001253788, intron 2 of 5)	-1202	NM_001253778	73721	Mm.45614	NM_028624	ENSMUSG00000028441	1110017D15Rik	Cbe1|Smrp1	RIKEN cDNA 1110017D15 gene	protein-coding
mm_90439.1	chr10	127643115	127643121	+	1	NA	5' UTR (NM_009284, exon 1 of 22)	5' UTR (NM_009284, exon 1 of 22)	132	NM_009284	20852	Mm.121721	NM_009284	ENSMUSG00000002147	Stat6	-	signal transducer and activator of transcription 6	protein-coding
mm_77226.1	chr8	115703751	115703764	-	1	NA	3' UTR (NM_001025577, exon 1 of 1)	3' UTR (NM_001025577, exon 1 of 1)	3137	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_172397.1	chr7	141447669	141447671	+	1	NA	promoter-TSS (NM_026020)	promoter-TSS (NM_026020)	20	NM_026020	67186	Mm.380435	NM_026020	ENSMUSG00000025508	Rplp2	2700049I22Rik	ribosomal protein, large P2	protein-coding
mm_46553.1	chr5	106624411	106624417	-	1	NA	intron (NM_026856, intron 5 of 6)	MLT1A0-int|LTR|ERVL-MaLR	72416	NM_026856	52397	Mm.249474	NM_026856	ENSMUSG00000049606	Zfp644	1110068L01Rik|AA408882|BM-005|D5Ertd689e|Zep-2	zinc finger protein 644	protein-coding
mm_7246.1	chr1	93635693	93635711	-	1	NA	promoter-TSS (NM_021537)	promoter-TSS (NM_021537)	25	NM_021537	59041	Mm.28761	NM_021537	ENSMUSG00000026277	Stk25	1500019J11Rik|AU018434|C86992|Ste20-like|Ysk1	serine/threonine kinase 25 (yeast)	protein-coding
mm_83171.1	chr9	40531363	40531390	-	1	NA	Intergenic	CpG	-75612	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_71823.1	chr8	68895798	68895843	+	1	NA	exon (NM_008509, exon 5 of 10)	exon (NM_008509, exon 5 of 10)	15265	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_19816.1	chr2	110363136	110363151	-	1	NA	promoter-TSS (NM_026271)	promoter-TSS (NM_026271)	-150	NM_026271	67606	Mm.291809	NM_026271	ENSMUSG00000074971	Fibin	1110018M03Rik	fin bud initiation factor homolog (zebrafish)	protein-coding
mm_80500.1	chr9	78520723	78520735	+	1	NA	Intergenic	RLTR51A_Mm|LTR|ERVK?	-39005	NM_010106	13627	Mm.138471	NM_010106	ENSMUSG00000037742	Eef1a1	-	eukaryotic translation elongation factor 1 alpha 1	protein-coding
mm_156419.1	chrX	140907555	140907557	+	1	NA	promoter-TSS (NM_030181)	promoter-TSS (NM_030181)	-52	NM_030181	78789	Mm.244932	NM_026103	ENSMUSG00000031430	Vsig1	1700062D20Rik|4930405J24Rik	V-set and immunoglobulin domain containing 1	protein-coding
mm_144636.1	chr18	32961300	32961328	+	1	NA	intron (NM_009793, intron 1 of 10)	intron (NM_009793, intron 1 of 10)	22273	NM_009793	12326	Mm.222329	NM_009793	ENSMUSG00000038128	Camk4	A430110E23Rik|AI666733|CaMKIV|CaMKIV/Gr|D18Bwg0362e	calcium/calmodulin-dependent protein kinase IV	protein-coding
mm_90520.1	chr10	128059036	128059052	+	1	NA	promoter-TSS (NM_019766)	promoter-TSS (NM_019766)	62	NM_019766	56351	Mm.305816	NM_019766	ENSMUSG00000071072	Ptges3	5730442A20Rik|Ptges|Tebp|cPGES|p23|sid3177	prostaglandin E synthase 3 (cytosolic)	protein-coding
mm_137978.1	chr17	33584291	33584302	+	1	NA	intron (NM_053214, intron 12 of 27)	ID_B1|SINE|B4	28589	NM_053214	17916	Mm.42019	NM_053214	ENSMUSG00000024300	Myo1f	C330006B10Rik	myosin IF	protein-coding
mm_170090.1	chr17	35969660	35969671	-	1	NA	promoter-TSS (NM_013854)	promoter-TSS (NM_013854)	85	NM_013854	224742	Mm.329022	NM_013854	ENSMUSG00000038762	Abcf1	AU041969|Abc50|D17Wsu166e|GCN20	ATP-binding cassette, sub-family F (GCN20), member 1	protein-coding
mm_3766.1	chr1	156303474	156303501	+	1	NA	promoter-TSS (NM_001134741)	promoter-TSS (NM_001134741)	119	NM_001277730	214575	Mm.252800	NM_001134741	ENSMUSG00000060985	Tdrd5	Gm103	tudor domain containing 5	protein-coding
mm_39545.1	chr5	21543618	21543638	+	1	NA	5' UTR (NM_028977, exon 1 of 4)	5' UTR (NM_028977, exon 1 of 4)	101	NM_028977	74511	Mm.439963	NM_028977	ENSMUSG00000039883	Lrrc17	37kDa|4833425M04Rik|6130400C22Rik|P37nb	leucine rich repeat containing 17	protein-coding
mm_125455.1	chr15	52040148	52040161	+	1	NA	promoter-TSS (NM_175503)	promoter-TSS (NM_175503)	47	NM_175503	239435	Mm.24204	NM_175503	ENSMUSG00000068522	Aard	A5D3|AV328152	alanine and arginine rich domain containing protein	protein-coding
mm_73221.1	chr8	99663920	99663963	+	1	NA	intron (NR_132435, intron 1 of 4)	intron (NR_132435, intron 1 of 4)	247267	NR_132435	234624	Mm.124595	NM_175479	ENSMUSG00000052479	A330008L17Rik	-	RIKEN cDNA A330008L17 gene	ncRNA
mm_80567.1	chr9	83866562	83866570	+	1	NA	intron (NM_009445, intron 18 of 21)	intron (NM_009445, intron 18 of 21)	31877	NM_001284272	22137	Mm.1904	NM_009445	ENSMUSG00000038379	Ttk	AL022661|Esk1|Mps1|PYT|esk	Ttk protein kinase	protein-coding
mm_78881.1	chr9	44522136	44522166	+	1	NA	intron (NM_007551, intron 1 of 1)	intron (NM_007551, intron 1 of 1)	4270	NM_007551	12145	Mm.6246	NM_007551	ENSMUSG00000047880	Cxcr5	Blr1|CXC-R5|CXCR-5|Gpcr6|MDR15	chemokine (C-X-C motif) receptor 5	protein-coding
mm_43661.1	chr5	138754418	138754428	+	1	NA	promoter-TSS (NM_030565)	promoter-TSS (NM_030565)	-658	NM_030565	80752	Mm.320355	NM_030565	ENSMUSG00000025854	Fam20c	C76981|DMP-4|DMP4|GEF-CK|mKIAA4081	family with sequence similarity 20, member C	protein-coding
mm_99537.1	chr11	103193132	103193142	+	1	NA	exon (NM_001077698, exon 14 of 26)	exon (NM_001077698, exon 14 of 26)	15411	NM_001254724	69441	Mm.380648	NM_027082	ENSMUSG00000020940	1700023F06Rik	-	RIKEN cDNA 1700023F06 gene	protein-coding
mm_112273.1	chr12	114254098	114254104	-	1	NA	Intergenic	Intergenic	215365	NR_106062	102465663		NR_106062	ENSMUSG00000105438	Mir7094-1	mmu-mir-7094-1	microRNA 7094-1	ncRNA
mm_35630.1	chr4	43493052	43493065	-	1	NA	promoter-TSS (NR_001460)	promoter-TSS (NR_001460)	1	NR_001460	19782		NR_001460	ENSMUSG00000088088	Rmrp	1110032O22Rik|Rmrpr	RNA component of mitochondrial RNAase P	ncRNA
mm_87013.1	chr10	26892068	26892088	+	1	NA	intron (NM_176837, intron 12 of 14)	B4A|SINE|B4	119566	NM_176837	73910	Mm.356496	NM_176837	ENSMUSG00000039031	Arhgap18	4833419J07Rik|AI314906|AI843501	Rho GTPase activating protein 18	protein-coding
mm_160536.1	chr9	39873476	39873476	+	1	NA	exon (NM_146610, exon 1 of 1)	exon (NM_146610, exon 1 of 1)	199	NM_146610	258603	Mm.271456	NM_146610	ENSMUSG00000094449	Olfr972	MOR171-17	olfactory receptor 972	protein-coding
mm_76463.1	chr8	85365342	85365353	-	1	NA	promoter-TSS (NM_175441)	promoter-TSS (NM_175441)	-23	NM_175441	213435	Mm.32804	NM_175441	ENSMUSG00000031698	Mylk3	D830007F02Rik|MLCK	myosin light chain kinase 3	protein-coding
mm_19165.1	chr2	84331509	84331519	-	1	NA	3' UTR (NM_018782, exon 16 of 16)	3' UTR (NM_018782, exon 16 of 16)	93752	NM_018782	54598	Mm.75467	NM_018782	ENSMUSG00000059588	Calcrl	AV071593|CRLR	calcitonin receptor-like	protein-coding
mm_125579.1	chr15	59469390	59469392	+	1	NA	intron (NM_026746, intron 4 of 6)	intron (NM_026746, intron 4 of 6)	95193	NM_001164604	68501	Mm.27762	NM_026746	ENSMUSG00000059586	Nsmce2	1110014D18Rik|AI661537	NSE2/MMS21 homolog, SMC5-SMC6 complex SUMO ligase	protein-coding
mm_7344.1	chr1	105990065	105990089	-	1	NA	promoter-TSS (NM_001122675)	promoter-TSS (NM_001122675)	-329	NM_001122676	227449	Mm.210188	NM_001122675	ENSMUSG00000038866	Zcchc2	9930114B20Rik|AW212015	zinc finger, CCHC domain containing 2	protein-coding
mm_30856.1	chr4	28813154	28813173	+	1	NA	promoter-TSS (NM_010141)	promoter-TSS (NM_010141)	18	NM_001122889	13841	Mm.257266	NM_010141	ENSMUSG00000028289	Epha7	Cek11|Ebk|Ehk3|Hek11|Mdk1	Eph receptor A7	protein-coding
mm_145319.1	chr18	54611789	54611799	+	1	NA	promoter-TSS (NR_045400)	promoter-TSS (NR_045400)	50	NR_045400	328957	Mm.402781	NR_045400		9330117O12Rik	9330117O12	RIKEN cDNA 9330117O12 gene	ncRNA
mm_17612.1	chr2	30928049	30928061	-	1	NA	Intergenic	B3A|SINE|B2	-24758	NM_022415	64292	Mm.28768	NM_022415	ENSMUSG00000050737	Ptges	2410099E23Rik|D2Ertd369e|Pges|mPGES|mPGES-1	prostaglandin E synthase	protein-coding
mm_135623.1	chr16	52273960	52273977	-	1	NA	exon (NM_001331110, exon 11 of 15)	exon (NM_001331110, exon 11 of 15)	179113	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_30935.1	chr4	32983418	32983428	+	1	NA	5' UTR (NM_027491, exon 1 of 7)	5' UTR (NM_027491, exon 1 of 7)	425	NM_027491	52187	Mm.300814	NM_027491	ENSMUSG00000028278	Rragd	5730543C08Rik|AI467523|C030003H22Rik|D4Ertd174e	Ras-related GTP binding D	protein-coding
mm_15748.1	chr2	164237597	164237603	+	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	741	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_31460.1	chr4	49059257	49059330	+	1	NA	promoter-TSS (NM_178756)	promoter-TSS (NM_178756)	-169	NM_178756	272031	Mm.299460	NM_178756	ENSMUSG00000063446	Plppr1	E130309F12Rik|Lppr1|PRG-3|mKIAA4247	phospholipid phosphatase related 1	protein-coding
mm_36893.1	chr4	107680851	107680871	-	1	NA	intron (NM_019872, intron 1 of 3)	intron (NM_019872, intron 1 of 3)	3301	NM_019872	56296	Mm.141324	NM_019872	ENSMUSG00000028610	Dmrtb1	Dmrt6|Prp13	DMRT-like family B with proline-rich C-terminal, 1	protein-coding
mm_158629.1	chrX	153037490	153037547	-	1	NA	promoter-TSS (NM_023788)	promoter-TSS (NM_023788)	45	NM_023788	75625	Mm.6890	NM_023788	ENSMUSG00000047238	Mageh1	2010107K23Rik|APR-1|APR1	melanoma antigen, family H, 1	protein-coding
mm_62280.1	chr7	99603896	99603903	+	1	NA	3' UTR (NM_178220, exon 15 of 15)	3' UTR (NM_178220, exon 15 of 15)	23204	NM_001195529	100503386	Mm.180719	NM_001195529	ENSMUSG00000096606	Tpbgl	EG245190|Gm4980	trophoblast glycoprotein-like	protein-coding
mm_51229.1	chr6	71373598	71373611	+	1	NA	exon (NM_009857, exon 1 of 4)	exon (NM_009857, exon 1 of 4)	177	NM_001081110	12525	Mm.1858	NM_009857	ENSMUSG00000053977	Cd8a	BB154331|Ly-2|Ly-35|Ly-B|Lyt-2	CD8 antigen, alpha chain	protein-coding
mm_54919.1	chr6	47803836	47803862	-	1	NA	promoter-TSS (NR_030485)	promoter-TSS (NR_030485)	-197	NR_030485	735289		NR_030485	ENSMUSG00000076060	Mir704	Mirn704|mir-704|mmu-mir-704	microRNA 704	ncRNA
mm_148721.1	chr19	5846773	5846784	+	1	NA	Intergenic	Intergenic	-1298	NR_003513	66961	Mm.281895	NR_003513	ENSMUSG00000092274	Neat1	2310043N10Rik|VINC	nuclear paraspeckle assembly transcript 1 (non-protein coding)	ncRNA
mm_69453.1	chr7	133122186	133122214	-	1	NA	intron (NM_009980, intron 1 of 10)	CpG	1283	NM_009980	13017	Mm.246240	NM_009980	ENSMUSG00000030970	Ctbp2	AA407280|D7Ertd45e|Gtrgeo6|Ribeye	C-terminal binding protein 2	protein-coding
mm_23175.1	chr3	40784116	40784169	+	1	NA	intron (NM_011020, intron 14 of 18)	L1MB4|LINE|L1	-15809	NM_173169	20873	Mm.3794	NM_011495	ENSMUSG00000025758	Plk4	1700028H20|AI385771|Sak|Stk18	polo-like kinase 4	protein-coding
mm_1643.1	chr1	74588310	74588328	+	1	NA	promoter-TSS (NM_025784)	promoter-TSS (NM_025784)	30	NM_025784	66821	Mm.358700	NM_025784	ENSMUSG00000026172	Bcs1l	9130022O19Rik	BCS1-like (yeast)	protein-coding
mm_93837.1	chr10	121603354	121603358	-	1	NA	intron (NM_001081056, intron 17 of 24)	intron (NM_001081056, intron 17 of 24)	-16562	NM_019786	56480	Mm.34580	NM_019786	ENSMUSG00000020115	Tbk1	1200008B05Rik|AI462036|AW048562	TANK-binding kinase 1	protein-coding
mm_71354.1	chr8	45658325	45658338	+	1	NA	intron (NM_001310707, intron 1 of 23)	intron (NM_001310707, intron 1 of 23)	-3662	NM_001310708	234214	Mm.211096	NM_172752	ENSMUSG00000031626	Sorbs2	2010203O03Rik|9430041O17Rik|A530071H08|Argbp2|mKIAA0777|nArgBP2	sorbin and SH3 domain containing 2	protein-coding
mm_29119.1	chr3	105052561	105052574	-	1	NA	intron (NM_030249, intron 1 of 5)	intron (NM_030249, intron 1 of 5)	386	NM_001163333	80281	Mm.200327	NM_030249	ENSMUSG00000062127	Cttnbp2nl	AA552995|AA589392|AU018624|BC003236|mKIAA1433	CTTNBP2 N-terminal like	protein-coding
mm_130763.1	chr15	101364573	101364585	-	1	NA	intron (NM_028770, intron 1 of 8)	intron (NM_028770, intron 1 of 8)	-4773	NR_035462	100316694		NR_035462	ENSMUSG00000088459	Mir1941	mmu-mir-1941	microRNA 1941	ncRNA
mm_3524.1	chr1	150108805	150108823	+	1	NA	TTS (NM_011198)	TTS (NM_011198)	8783	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_9320.1	chr1	171649003	171649012	-	1	NA	promoter-TSS (NM_001347184)	promoter-TSS (NM_001347184)	-8	NM_001347184	75345	Mm.164642	NM_144539	ENSMUSG00000038179	Slamf7	19A|19A24|4930560D03Rik|CRACC|CS1	SLAM family member 7	protein-coding
mm_10362.1	chr2	11705391	11705401	+	1	NA	promoter-TSS (NM_001271500)	promoter-TSS (NM_001271500)	103	NM_001271497	16169	Mm.200196	NM_008358	ENSMUSG00000023206	Il15ra	AA690181|IL-15RA	interleukin 15 receptor, alpha chain	protein-coding
mm_131513.1	chr16	17508948	17509007	+	1	NA	promoter-TSS (NM_001331226)	promoter-TSS (NM_001331226)	-235	NM_001331226	66863	Mm.161726	NM_025808	ENSMUSG00000022761	Lztr1	1200003E21Rik|AI591627|AW550890	leucine-zipper-like transcriptional regulator, 1	protein-coding
mm_130298.1	chr15	97019471	97019482	-	1	NA	intron (NM_027052, intron 2 of 15)	intron (NM_027052, intron 2 of 15)	36480	NM_027052	69354	Mm.250980	NM_027052	ENSMUSG00000022464	Slc38a4	1110012E16Rik|1700012A18Rik|Ata3|mATA3|mNAT3	solute carrier family 38, member 4	protein-coding
mm_67961.1	chr7	100539317	100539326	-	1	NA	exon (NM_183270, exon 2 of 2)	exon (NM_183270, exon 2 of 2)	2221	NM_183270	68185	Mm.228995	NM_183270	ENSMUSG00000044881	Coa4	5330414O08Rik|AI115477|AW047259|Chchd8|E2ig2	cytochrome c oxidase assembly factor 4	protein-coding
mm_42791.1	chr5	121567704	121567726	+	1	NA	3' UTR (NM_009656, exon 13 of 13)	3' UTR (NM_009656, exon 13 of 13)	-21823	NM_010765	17165	Mm.272206	NM_010765	ENSMUSG00000029454	Mapkapk5	MK5|PRAK	MAP kinase-activated protein kinase 5	protein-coding
mm_168777.1	chr12	17548555	17548557	+	1	NA	exon (NM_013614, exon 7 of 12)	exon (NM_013614, exon 7 of 12)	3683	NM_013614	18263	Mm.34102	NM_013614	ENSMUSG00000011179	Odc1	ODC	ornithine decarboxylase, structural 1	protein-coding
mm_85725.1	chr9	108339877	108339893	-	1	NA	exon (NM_008160, exon 2 of 2)	exon (NM_008160, exon 2 of 2)	805	NM_001329528	14775	Mm.1090	NM_008160	ENSMUSG00000063856	Gpx1	AI195024|AL033363|CGPx|GPx-1|GSHPx-1|Gpx	glutathione peroxidase 1	protein-coding
mm_21178.1	chr2	154892888	154892894	-	1	NA	promoter-TSS (NM_026030)	promoter-TSS (NM_026030)	15	NM_026030	67204	Mm.377134	NM_026030	ENSMUSG00000074656	Eif2s2	2810026E11Rik|38kDa|AA408636|AA571381|AA986487|AW822225|D2Ertd303e|EIF2|EIF2B	eukaryotic translation initiation factor 2, subunit 2 (beta)	protein-coding
mm_165159.1	chr2	24819204	24819230	-	1	NA	intron (NM_001012518, intron 16 of 26)	intron (NM_001012518, intron 16 of 26)	-56065	NM_007579	12287	Mm.4424	NM_007579	ENSMUSG00000004113	Cacna1b	AW050276|AW060892|AW822256|BIII|Cav2.2|Cchn1a|alpha(1B)	calcium channel, voltage-dependent, N type, alpha 1B subunit	protein-coding
mm_28355.1	chr3	89732316	89732326	-	1	NA	intron (NM_019655, intron 1 of 14)	intron (NM_019655, intron 1 of 14)	1603	NM_019655	56417	Mm.316628	NM_019655	ENSMUSG00000027951	Adar	AV242451|Adar1|Adar1p110|Adar1p150|mZaADAR	adenosine deaminase, RNA-specific	protein-coding
mm_27017.1	chr3	26027361	26027369	-	1	NA	intron (NM_138666, intron 3 of 7)	intron (NM_138666, intron 3 of 7)	125942	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_44803.1	chr5	33218161	33218222	-	1	NA	promoter-TSS (NM_133903)	promoter-TSS (NM_133903)	47	NM_133903	100689	Mm.34694	NM_133903	ENSMUSG00000037379	Spon2	2310045I24Rik|AI504350|M-spondin|Mindin|Mspondin	spondin 2, extracellular matrix protein	protein-coding
mm_16703.1	chr2	7012651	7012654	-	1	NA	intron (NM_001110231, intron 3 of 15)	intron (NM_001110231, intron 3 of 15)	68650	NM_001110230	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_148645.1	chr19	5490513	5490525	+	1	NA	promoter-TSS (NM_007687)	promoter-TSS (NM_007687)	64	NM_007687	12631	Mm.329655	NM_007687	ENSMUSG00000056201	Cfl1	AA959946|Cof	cofilin 1, non-muscle	protein-coding
mm_137120.1	chr17	22674309	22674328	+	1	NA	Intergenic	Intergenic	73170	NM_001104575	628185	Mm.390947	NM_001104575	ENSMUSG00000094921	Vmn2r112	EG628185|V2rp1	vomeronasal 2, receptor 112	protein-coding
mm_127237.1	chr15	99457944	99457972	+	1	NA	promoter-TSS (NM_001001884)	promoter-TSS (NM_001001884)	-210	NM_001001884	380969	Mm.22915	NM_001001884	ENSMUSG00000023009	Nckap5l	C230021P08Rik|Cep169	NCK-associated protein 5-like	protein-coding
mm_85928.1	chr9	112077913	112077952	-	1	NA	intron (NM_001177618, intron 17 of 18)	(TG)n|Simple_repeat|Simple_repeat	40779	NR_029823	723815		NR_029823	ENSMUSG00000065441	Mir128-2	Mirn128-2|Mirn128b|mir-128-2|mir-128b	microRNA 128-2	ncRNA
mm_172647.1	chr8	26587286	26587286	-	1	NA	Intergenic	L1Md_T|LINE|L1	237137	NR_045904	72316	Mm.490534	NR_045904	ENSMUSG00000100335	2310008N11Rik	-	RIKEN cDNA 2310008N11 gene	ncRNA
mm_162833.1	chr10	82178326	82178345	+	1	NA	Intergenic	CpG	50322	NM_001163064	216177	Mm.482395	NM_001163064	ENSMUSG00000078435	AU041133	-	expressed sequence AU041133	protein-coding
mm_170292.1	chr18	3005439	3005440	+	1	NA	Intergenic	Intergenic	117973	NM_001167539	100312476	Mm.480293	NM_001167539	ENSMUSG00000091539	Vmn1r238	-	vomeronasal 1 receptor, 238	protein-coding
mm_51328.1	chr6	72355746	72355765	+	1	NA	intron (NM_144916, intron 1 of 7)	CpG	272	NM_144916	232086	Mm.491165	NM_144916	ENSMUSG00000055912	Tmem150a	BC014685|Tmem150	transmembrane protein 150A	protein-coding
mm_165912.1	chr4	57845269	57845273	+	1	NA	promoter-TSS (NM_001035532)	promoter-TSS (NM_001035532)	23	NM_001035532	11641	Mm.467752	NM_009649	ENSMUSG00000038729	Akap2	AA959716|AI649048|Akap-2|Akap-kl|B230340M18Rik|Prka2	A kinase (PRKA) anchor protein 2	protein-coding
mm_30632.1	chr4	8803428	8803441	+	1	NA	intron (NM_001277149, intron 4 of 37)	intron (NM_001277149, intron 4 of 37)	113028	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_103628.1	chr11	78935404	78935432	-	1	NA	exon (NM_010927, exon 6 of 27)	exon (NM_010927, exon 6 of 27)	10127	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_13648.1	chr2	114054345	114054353	+	1	NA	promoter-TSS (NR_028422)	promoter-TSS (NR_028422)	-47	NR_028422	100303644	Mm.330469	NR_028422	ENSMUSG00000092397	C130080G10Rik	-	RIKEN cDNA C130080G10 gene	ncRNA
mm_101273.1	chr11	21370667	21370673	-	1	NA	promoter-TSS (NM_139297)	promoter-TSS (NM_139297)	-41	NM_139297	216558	Mm.28877	NM_139297	ENSMUSG00000001891	Ugp2	UDPGP|UGPase	UDP-glucose pyrophosphorylase 2	protein-coding
mm_70676.1	chr8	14961881	14961899	+	1	NA	intron (NM_172751, intron 16 of 28)	intron (NM_172751, intron 16 of 28)	-49135	NM_029116	74901	Mm.46675	NM_029116	ENSMUSG00000055675	Kbtbd11	2900016B01Rik|4930465M17Rik|mKIAA0711	kelch repeat and BTB (POZ) domain containing 11	protein-coding
mm_36770.1	chr4	102569109	102569136	-	1	NA	promoter-TSS (NM_001177980)	promoter-TSS (NM_001177980)	-938	NM_001177980	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_42714.1	chr5	120440589	120440607	+	1	NA	3' UTR (NM_008499, exon 5 of 5)	3' UTR (NM_008499, exon 5 of 5)	8712	NM_008499	16873	Mm.5151	NM_008499	ENSMUSG00000029595	Lhx5	Lim2	LIM homeobox protein 5	protein-coding
mm_93333.1	chr10	99461753	99461763	-	1	NA	Intergenic	Intergenic	-147413	NR_038019	100504202	Mm.403801	NR_038019		Gm20110	-	predicted gene, 20110	ncRNA
mm_28149.1	chr3	87512638	87512649	-	1	NA	Intergenic	Intergenic	-12935	NM_001083318	27049	Mm.219460	NM_012051	ENSMUSG00000003382	Etv3	AI414410|METS|Pe1	ets variant 3	protein-coding
mm_92087.1	chr10	62808359	62808382	-	1	NA	3' UTR (NM_001253857, exon 12 of 12)	3' UTR (NM_001253857, exon 12 of 12)	-16002	NM_026201	67500	Mm.196371	NM_026201	ENSMUSG00000020074	Ccar1	2610511G16Rik|9430036H15Rik|Carp1	cell division cycle and apoptosis regulator 1	protein-coding
mm_154561.1	chrX	5984670	5984710	+	1	NA	Intergenic	Intergenic	-62817	NM_021431	58242	Mm.41198	NM_021431	ENSMUSG00000073295	Nudt11	DIPP3|DIPP3b	nudix (nucleoside diphosphate linked moiety X)-type motif 11	protein-coding
mm_147385.1	chr18	43737558	43737565	-	1	NA	promoter-TSS (NM_009258)	promoter-TSS (NM_009258)	-324	NM_009258	20730	Mm.272	NM_009258	ENSMUSG00000024503	Spink1	Spink3|p12	serine peptidase inhibitor, Kazal type 1	protein-coding
mm_139963.1	chr17	71657516	71657556	+	1	NA	exon (NM_175639, exon 18 of 18)	exon (NM_175639, exon 18 of 18)	-15725	NM_177087	320159	Mm.187372	NM_177087	ENSMUSG00000045761	Fam179a	4632412N22Rik	family with sequence similarity 179, member A	protein-coding
mm_112344.1	chr12	116485602	116485614	-	1	NA	promoter-TSS (NM_011215)	promoter-TSS (NM_011215)	-112	NM_011215	19276	Mm.206054	NM_011215	ENSMUSG00000056553	Ptprn2	4930425H11Rik|IA2beta|PTP-NP|Phol|mKIAA0387|phogrin	protein tyrosine phosphatase, receptor type, N polypeptide 2	protein-coding
mm_127183.1	chr15	98990001	98990017	+	1	NA	TTS (NR_045991)	TTS (NR_045991)	4044	NR_045991	75951	Mm.441657	NR_045991	ENSMUSG00000097587	4930578M01Rik	3010001K12Rik	RIKEN cDNA 4930578M01 gene	ncRNA
mm_52532.1	chr6	115853000	115853035	+	1	NA	promoter-TSS (NM_031177)	promoter-TSS (NM_031177)	324	NM_010774	17193	Mm.259308	NM_010774	ENSMUSG00000030322	Mbd4	Med1	methyl-CpG binding domain protein 4	protein-coding
mm_31725.1	chr4	62699670	62699689	+	1	NA	intron (NM_001310706, intron 3 of 6)	intron (NM_001310706, intron 3 of 6)	25705	NM_001310706	50780	Mm.286753	NM_019492	ENSMUSG00000059810	Rgs3	4930506N09Rik|C2PA-RGS3|C2pa|PDZ-RGS3|RGS3S	regulator of G-protein signaling 3	protein-coding
mm_153527.1	chr19	41802029	41802060	-	1	NA	promoter-TSS (NM_001163495)	promoter-TSS (NM_001163495)	40	NM_001163495	71085	Mm.21646	NM_027667	ENSMUSG00000025154	Arhgap19	4933411B03Rik|AI120128|AW546831|mFLJ00368	Rho GTPase activating protein 19	protein-coding
mm_153808.1	chr19	46045308	46045318	-	1	NA	promoter-TSS (NM_001113408)	promoter-TSS (NM_001113408)	-102	NM_001113408	16825	Mm.327442	NM_010697	ENSMUSG00000025223	Ldb1	CLIM2|NLI	LIM domain binding 1	protein-coding
mm_65350.1	chr7	24997238	24997251	-	1	NA	exon (NM_001290469, exon 8 of 23)	exon (NM_001290469, exon 8 of 23)	8693	NM_001290469	232975	Mm.44101	NM_144921	ENSMUSG00000040907	Atp1a3	Atpa-2	ATPase, Na+/K+ transporting, alpha 3 polypeptide	protein-coding
mm_44560.1	chr5	24606342	24606378	-	1	NA	Intergenic	Intergenic	-4358	NM_025891	66993	Mm.436539	NM_025891	ENSMUSG00000028949	Smarcd3	1500001J14Rik|2210409C08Rik|BAF60C	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3	protein-coding
mm_45938.1	chr5	90228980	90228998	-	1	NA	3' UTR (NM_030886, exon 34 of 34)	3' UTR (NM_030886, exon 34 of 34)	-4993	NM_001163456	231430	Mm.319697	NM_001033310	ENSMUSG00000035505	Cox18	BC038311	cytochrome c oxidase assembly protein 18	protein-coding
mm_142177.1	chr17	36271090	36271102	-	1	NA	intron (NM_024468, intron 1 of 6)	CpG	337	NM_178281	79263	Mm.40624	NM_024468	ENSMUSG00000045409	Trim39	1100001D15Rik|E130103K13Rik|RBCC-B30.2|Rnf23|mKIAA4179|tfp	tripartite motif-containing 39	protein-coding
mm_115500.1	chr13	3910493	3910496	-	1	NA	intron (NM_019671, intron 2 of 11)	RMER17A|LTR|ERVK	7726	NM_019671	56349	Mm.22261	NM_019671	ENSMUSG00000021215	Net1	Net1a|mNET1	neuroepithelial cell transforming gene 1	protein-coding
mm_122789.1	chr14	54417627	54417648	-	1	NA	promoter-TSS (NM_011405)	promoter-TSS (NM_011405)	42	NM_001253679	20540	Mm.142455	NM_011405	ENSMUSG00000000958	Slc7a7	AI790233|my+lat1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 7	protein-coding
mm_56345.1	chr6	92918068	92918085	-	1	NA	Intergenic	Intergenic	-16635	NM_175314	101401	Mm.158235	NM_175314	ENSMUSG00000030022	Adamts9	1810011L16Rik|8430403M15Rik|AW743315|E030027K14Rik	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 9	protein-coding
mm_86513.1	chr10	7667507	7667558	+	1	NA	promoter-TSS (NM_145706)	promoter-TSS (NM_145706)	28	NM_145706	69912	Mm.299887	NM_145706	ENSMUSG00000040034	Nup43	2610016K01Rik|2610529I12Rik|AA409950|p42	nucleoporin 43	protein-coding
mm_119876.1	chr14	54814145	54814156	+	1	NA	Intergenic	CpG	-32264	NM_016972	50934	Mm.276831	NM_016972	ENSMUSG00000022180	Slc7a8	AA408822|LAT2	solute carrier family 7 (cationic amino acid transporter, y+ system), member 8	protein-coding
mm_125063.1	chr15	25940981	25940997	+	1	NA	5' UTR (NM_001277315, exon 1 of 7)	5' UTR (NM_001277315, exon 1 of 7)	163	NM_025459	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_100741.1	chr11	4116712	4116744	-	1	NA	exon (NM_144520, exon 2 of 12)	exon (NM_144520, exon 2 of 12)	2001	NM_144520	67815	Mm.253922	NM_144520	ENSMUSG00000003585	Sec14l2	1300013M05Rik|Spf|TAP	SEC14-like lipid binding 2	protein-coding
mm_103919.1	chr11	83590628	83590643	-	1	NA	intron (NM_009139, intron 1 of 3)	L1MB3|LINE|L1	2452	NM_009139	20305	Mm.137	NM_009139	ENSMUSG00000018927	Ccl6	MRP-1|Scya6|c10	chemokine (C-C motif) ligand 6	protein-coding
mm_101016.1	chr11	8558975	8558985	-	1	NA	intron (NM_001083587, intron 4 of 30)	intron (NM_001083587, intron 4 of 30)	105555	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_27047.1	chr3	27194070	27194084	-	1	NA	intron (NM_178772, intron 1 of 4)	intron (NM_178772, intron 1 of 4)	11073	NM_178772	320024	Mm.24576	NM_178772	ENSMUSG00000027698	Nceh1	Aadacl1|B230106I24Rik|CPO-BP|Nceh	neutral cholesterol ester hydrolase 1	protein-coding
mm_13478.1	chr2	106003328	106003340	+	1	NA	non-coding (NR_033993, exon 1 of 4)	non-coding (NR_033993, exon 1 of 4)	215	NM_026992	99349	Mm.25661	NM_026992	ENSMUSG00000027166	Dnajc24	1700030A21Rik|2610027M02Rik|AV066965|AW240712|Dph4|MmDjC7|Zcsl3	DnaJ heat shock protein family (Hsp40) member C24	protein-coding
mm_142213.1	chr17	37023331	37023341	-	1	NA	promoter-TSS (NM_010814)	promoter-TSS (NM_010814)	62	NM_010814	17441	Mm.210857	NM_010814	ENSMUSG00000076439	Mog	B230317G11Rik	myelin oligodendrocyte glycoprotein	protein-coding
mm_119840.1	chr14	54431598	54431673	+	1	NA	promoter-TSS (NM_008608)	promoter-TSS (NM_008608)	37	NM_008608	17387	Mm.280175	NM_008608	ENSMUSG00000000957	Mmp14	AI325305|MMP-X1|MT-MMP-1|MT1-MMP|sabe	matrix metallopeptidase 14 (membrane-inserted)	protein-coding
mm_171081.1	chr3	121426543	121426544	+	1	NA	promoter-TSS (NM_028044)	promoter-TSS (NM_028044)	2	NM_028044	71994	Mm.275555	NM_028044	ENSMUSG00000053931	Cnn3	1600014M03Rik|C85854|Calpo3	calponin 3, acidic	protein-coding
mm_160777.1	chr10	126995605	126995605	+	1	NA	promoter-TSS (NM_146012)	promoter-TSS (NM_146012)	-8	NM_146012	52468	Mm.29490	NM_146012	ENSMUSG00000078429	Ctdsp2	AI586070|D10Ertd73e|OS-4|OS4|SCP2	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 2	protein-coding
mm_104930.1	chr11	100041548	100041561	-	1	NA	promoter-TSS (NM_027563)	promoter-TSS (NM_027563)	0	NM_027563	16672	Mm.289644	NM_027563	ENSMUSG00000043485	Krt34	4733401E01Rik|Ha2|K34|Krt1-4	keratin 34	protein-coding
mm_80798.1	chr9	96258792	96258802	+	1	NA	promoter-TSS (NM_001184710)	promoter-TSS (NM_001184710)	92	NM_001184709	211586	Mm.17977	NM_178667	ENSMUSG00000032411	Tfdp2	1110029I05Rik|A330080J22Rik|DP-3|DP3	transcription factor Dp 2	protein-coding
mm_99264.1	chr11	101246346	101246350	+	1	NA	promoter-TSS (NM_019444)	promoter-TSS (NM_019444)	14	NM_019444	54409	Mm.260698	NM_019444	ENSMUSG00000001240	Ramp2	-	receptor (calcitonin) activity modifying protein 2	protein-coding
mm_71387.1	chr8	46010597	46010635	+	1	NA	promoter-TSS (NM_026278)	promoter-TSS (NM_026278)	14	NM_026278	67620	Mm.383914	NM_026278	ENSMUSG00000031637	Lrp2bp	1700113N17Rik|2310006J04Rik|4930479L12Rik|MegBP	Lrp2 binding protein	protein-coding
mm_149608.1	chr19	16384856	16384871	+	1	NA	3' UTR (NM_008139, exon 7 of 7)	3' UTR (NM_008139, exon 7 of 7)	-50804	NM_008137	14675	Mm.313181	NM_008137	ENSMUSG00000024697	Gna14	AU023208	guanine nucleotide binding protein, alpha 14	protein-coding
mm_141451.1	chr17	30229162	30229170	-	1	NA	intron (NM_172618, intron 9 of 11)	intron (NM_172618, intron 9 of 11)	27369	NR_105839	102465223		NR_105839	ENSMUSG00000098522	Mir6412	Gm27364|mmu-mir-6412	microRNA 6412	ncRNA
mm_27635.1	chr3	61415992	61416005	-	1	NA	Intergenic	Intergenic	51491	NM_028712	74012	Mm.422674	NM_028712	ENSMUSG00000036894	Rap2b	4021402C18Rik|AA408554	RAP2B, member of RAS oncogene family	protein-coding
mm_154362.1	chrM	7006	7022	+	1	NA	NA	Intergenic	NA	NA								
mm_88788.1	chr10	80614950	80614979	+	1	NA	3' UTR (NM_019575, exon 7 of 7)	3' UTR (NM_019575, exon 7 of 7)	5704	NR_105877	102465550		NR_105877	ENSMUSG00000099283	Mir6912	Gm27990|mmu-mir-6912	microRNA 6912	ncRNA
mm_86387.1	chr9	123938076	123938078	-	1	NA	Intergenic	Intergenic	30615	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_43747.1	chr5	140388251	140388259	+	1	NA	intron (NM_172277, intron 1 of 10)	B3A|SINE|B2	1053	NM_172277	231834	Mm.27098	NM_172277	ENSMUSG00000029560	Snx8	B130023O14Rik	sorting nexin 8	protein-coding
mm_30983.1	chr4	34893762	34893766	+	1	NA	promoter-TSS (NM_009889)	promoter-TSS (NM_009889)	-15	NM_009889	12640	Mm.1361	NM_009889	ENSMUSG00000028298	Cga	CG-alpha|FSHA|GPHA1|GPHalpha|HCG|LHA|Tsha|aGSU|alpha-GSU|alphaGSU|alphaSU	glycoprotein hormones, alpha subunit	protein-coding
mm_108373.1	chr12	80833870	80833877	+	1	NA	intron (NM_178682, intron 2 of 5)	intron (NM_178682, intron 2 of 5)	43341	NM_001242419	217684	Mm.341776	NM_178682	ENSMUSG00000021133	Susd6	4933426M11Rik|mKIAA0247	sushi domain containing 6	protein-coding
mm_62898.1	chr7	116504364	116504397	+	1	NA	promoter-TSS (NM_001130479)	promoter-TSS (NM_001130479)	11	NM_001130479	53322	Mm.9901	NM_016773	ENSMUSG00000030659	Nucb2	AI607786|Calnuc|Nefa|Nesfatin-1	nucleobindin 2	protein-coding
mm_50026.1	chr6	41121550	41121566	+	1	NA	Intergenic	Intergenic	-86049	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_14746.1	chr2	144527516	144527527	+	1	NA	promoter-TSS (NM_029763)	promoter-TSS (NM_029763)	-123	NM_172859	241688	Mm.442156	NM_172859	ENSMUSG00000037259	Dzank1	2810039F03Rik|6330439K17Rik|6430408C01|AI851115|Ankrd64	double zinc ribbon and ankyrin repeat domains 1	protein-coding
mm_134568.1	chr16	20362223	20362232	-	1	NA	exon (NM_013790, exon 24 of 30)	exon (NM_013790, exon 24 of 30)	-36823	NM_183158	224044	Mm.276400	NM_183158	ENSMUSG00000022818	Cyp2ab1	EG224044|F730023N20	cytochrome P450, family 2, subfamily ab, polypeptide 1	protein-coding
mm_18916.1	chr2	76737248	76737258	-	1	NA	exon (NM_011652, exon 275 of 313)	exon (NM_011652, exon 275 of 313)	61938	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_21926.1	chr2	166996207	166996220	-	1	NA	promoter-TSS (NM_011490)	promoter-TSS (NM_011490)	86	NM_011490	20853	Mm.73276	NM_011490	ENSMUSG00000039536	Stau1	5830401L18Rik|AW549911|C85792|Stau	staufen (RNA binding protein) homolog 1 (Drosophila)	protein-coding
mm_92122.1	chr10	63382745	63382794	-	1	NA	intron (NM_001253685, intron 1 of 4)	intron (NM_001253685, intron 1 of 4)	326	NM_001253685	30045	Mm.32550	NM_013888	ENSMUSG00000036764	Dnajc12	Jdp1|mJDP1	DnaJ heat shock protein family (Hsp40) member C12	protein-coding
mm_73595.1	chr8	109998351	109998361	+	1	NA	exon (NM_146214, exon 11 of 12)	exon (NM_146214, exon 11 of 12)	7920	NM_146214	234724	Mm.28110	NM_146214	ENSMUSG00000001670	Tat	-	tyrosine aminotransferase	protein-coding
mm_120689.1	chr14	70774413	70774423	+	1	NA	promoter-TSS (NM_010071)	promoter-TSS (NM_010071)	37	NM_010071	13449	Mm.243323	NM_010071	ENSMUSG00000022102	Dok2	DokR|Frip	docking protein 2	protein-coding
mm_29375.1	chr3	108722264	108722274	-	1	NA	promoter-TSS (NM_029522)	promoter-TSS (NM_029522)	30	NM_029522	76123	Mm.226941	NM_029522	ENSMUSG00000027883	Gpsm2	6230410J09Rik|LGN|Pins	G-protein signalling modulator 2 (AGS3-like, C. elegans)	protein-coding
mm_78727.1	chr9	41580945	41580967	+	1	NA	promoter-TSS (NR_029822)	promoter-TSS (NR_029822)	-297	NR_015483	73144	Mm.38166	NM_001033153	ENSMUSG00000074415	3110039I08Rik	2610203C20Rik|AI848448|D230004N17Rik|D3Mgi9|Mir100hg	RIKEN cDNA 3110039I08 gene	ncRNA
mm_169181.1	chr13	65817694	65817697	-	1	NA	Intergenic	Intergenic	-295758	NM_001177832	628709	Mm.390595	NM_001177832	ENSMUSG00000095909	Gm10324	ENSMUSG00000071302	predicted gene 10324	protein-coding
mm_160778.1	chr10	127060311	127060311	-	1	NA	promoter-TSS (NM_001033262)	promoter-TSS (NM_001033262)	-127	NM_001033262	216438	Mm.37892	NM_001033262	ENSMUSG00000040502	March9	AI608492|BC019560	membrane-associated ring finger (C3HC4) 9	protein-coding
mm_114809.1	chr13	91484540	91484556	+	1	NA	intron (NM_024272, intron 1 of 16)	intron (NM_024272, intron 1 of 16)	23451	NM_024186	66970	Mm.343095	NM_024186	ENSMUSG00000003992	Ssbp2	1500004K09Rik|2310079I02Rik|9330163K02Rik|A830008M03Rik|AU067692|AW558684|Hspc116|SSDP2	single-stranded DNA binding protein 2	protein-coding
mm_80801.1	chr9	96259247	96259261	+	1	NA	promoter-TSS (NM_001184710)	promoter-TSS (NM_001184710)	6	NM_001184710	211586	Mm.17977	NM_178667	ENSMUSG00000032411	Tfdp2	1110029I05Rik|A330080J22Rik|DP-3|DP3	transcription factor Dp 2	protein-coding
mm_30479.1	chr3	154847348	154847358	-	1	NA	intron (NM_177066, intron 21 of 24)	intron (NM_177066, intron 21 of 24)	136220	NM_175176	209601	Mm.331454	NM_175176	ENSMUSG00000078161	Erich3	1700013E18Rik|4922501L14Rik|5031409G23Rik|AI596448|Gm133	glutamate rich 3	protein-coding
mm_62466.1	chr7	101663728	101663734	+	1	NA	promoter-TSS (NM_009191)	promoter-TSS (NM_009191)	-37	NM_009191	20480	Mm.3990	NM_009191	ENSMUSG00000001829	Clpb	AL118244|Skd3	ClpB caseinolytic peptidase B	protein-coding
mm_134300.1	chr16	15594474	15594503	-	1	NA	promoter-TSS (NM_001159351)	promoter-TSS (NM_001159351)	30	NM_001159351	70620	Mm.235407	NM_023585	ENSMUSG00000022674	Ube2v2	1110021H13Rik|4632410D19Rik|5730524P06Rik|6820402M05|AI848315|C81524|MMS2	ubiquitin-conjugating enzyme E2 variant 2	protein-coding
mm_124797.1	chr15	8443606	8443636	+	1	NA	intron (NM_201232, intron 1 of 45)	intron (NM_201232, intron 1 of 45)	842	NM_027707	71175	Mm.240329	NM_027707	ENSMUSG00000022141	Nipbl	Idn3	Nipped-B homolog (Drosophila)	protein-coding
mm_157074.1	chrX	8252335	8252400	-	1	NA	promoter-TSS (NM_001290430)	promoter-TSS (NM_001290430)	39	NM_133991	54632	Mm.327529	NM_133991	ENSMUSG00000031171	Ftsj1	AI931847|Ftsj|Ftsjl|Sfc12	FtsJ RNA methyltransferase homolog 1 (E. coli)	protein-coding
mm_53812.1	chr6	147032529	147032547	+	1	NA	promoter-TSS (NM_025620)	promoter-TSS (NM_025620)	1	NM_025620	66532	Mm.45888	NM_025620	ENSMUSG00000040121	Rep15	2210417D09Rik	RAB15 effector protein	protein-coding
mm_5656.1	chr1	42498533	42498533	-	1	NA	Intergenic	Helitron3Na_Mam|RC|Helitron	196292	NR_027826	66297	Mm.45203	NM_183252	ENSMUSG00000060424	Pantr1	2610017I09Rik|Pou3f3os|linc-Brn1a	POU domain, class 3, transcription factor 3 adjacent noncoding transcript 1	ncRNA
mm_34883.1	chr4	155582762	155582772	+	1	NA	intron (NM_138671, intron 3 of 11)	intron (NM_138671, intron 3 of 11)	-18649	NM_177186	320541	Mm.306018	NM_177186	ENSMUSG00000042202	Slc35e2	A530082C11Rik|AI957035	solute carrier family 35, member E2	protein-coding
mm_129290.1	chr15	77203287	77203304	-	1	NA	intron (NM_053104, intron 2 of 13)	intron (NM_053104, intron 2 of 13)	-49483	NM_001286418	93686	Mm.202774	NM_053104	ENSMUSG00000033565	Rbfox2	Fbm2|Fxh|Hrnbp2|Rbm9	RNA binding protein, fox-1 homolog (C. elegans) 2	protein-coding
mm_11862.1	chr2	48815344	48815352	+	1	NA	intron (NM_007396, intron 1 of 10)	intron (NM_007396, intron 1 of 10)	1239	NM_007396	11480	Mm.314338	NM_007396	ENSMUSG00000052155	Acvr2a	ActrIIa|Acvr2|TactrII	activin receptor IIA	protein-coding
mm_124940.1	chr15	12321426	12321460	+	1	NA	promoter-TSS (NM_025673)	promoter-TSS (NM_025673)	-53	NM_025673	66629	Mm.157655	NM_025673	ENSMUSG00000022200	Golph3	4733401N08Rik|5730410D03Rik|AW413496	golgi phosphoprotein 3	protein-coding
mm_122486.1	chr14	46388363	46388396	-	1	NA	intron (NM_007554, intron 1 of 3)	CpG	2290	NM_001316360	12159	Mm.6813	NM_007554	ENSMUSG00000021835	Bmp4	Bmp-4|Bmp2b|Bmp2b-1|Bmp2b1	bone morphogenetic protein 4	protein-coding
mm_73303.1	chr8	105131877	105131879	+	1	NA	promoter-TSS (NM_146213)	promoter-TSS (NM_146213)	78	NM_146213	234677	Mm.120297	NM_146213	ENSMUSG00000060560	Ces4a	Ces8	carboxylesterase 4A	protein-coding
mm_36416.1	chr4	78211759	78211790	-	1	NA	5' UTR (NM_011211, exon 1 of 40)	5' UTR (NM_011211, exon 1 of 40)	121	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding
mm_240.1	chr1	19209039	19209053	+	1	NA	5' UTR (NM_009334, exon 1 of 7)	5' UTR (NM_009334, exon 1 of 7)	132	NM_001286340	21419	Mm.137021	NM_009334	ENSMUSG00000025927	Tfap2b	AI606113|AP-2(beta)|E130018K07Rik|Tcfap2b	transcription factor AP-2 beta	protein-coding
mm_150486.1	chr19	39006915	39006923	+	1	NA	promoter-TSS (NM_028089)	promoter-TSS (NM_028089)	-100	NM_028089	72082	Mm.142581	NM_028089	ENSMUSG00000025002	Cyp2c55	2010318C06Rik	cytochrome P450, family 2, subfamily c, polypeptide 55	protein-coding
mm_110263.1	chr12	31928798	31928801	-	1	NA	TTS (NM_177993)	TTS (NM_177993)	21736	NM_177993	73389	Mm.390461	NM_153198	ENSMUSG00000002996	Hbp1	1700058O05Rik|BE629963|C330012F01Rik|C86454	high mobility group box transcription factor 1	protein-coding
mm_47821.1	chr5	134232256	134232264	-	1	NA	Intergenic	Intergenic	-2635	NR_104383	17969	Mm.425296	NM_010876	ENSMUSG00000015950	Ncf1	NCF-47K|NOXO2|Ncf-1|p47-phox|p47<phox>|p47phox	neutrophil cytosolic factor 1	protein-coding
mm_32545.1	chr4	109343092	109343100	+	1	NA	promoter-TSS (NM_001159964)	promoter-TSS (NM_001159964)	40	NM_001159964	13858	Mm.318250	NM_007943	ENSMUSG00000028552	Eps15	2410112D09Rik	epidermal growth factor receptor pathway substrate 15	protein-coding
mm_22165.1	chr2	173023360	173023381	-	1	NA	exon (NM_019547, exon 3 of 4)	exon (NM_019547, exon 3 of 4)	1468	NM_019547	56190	Mm.485782	NM_019547	ENSMUSG00000027510	Rbm38	Rnpc1|Seb4|Seb4l	RNA binding motif protein 38	protein-coding
mm_132090.1	chr16	31067021	31067037	+	1	NA	intron (NM_198626, intron 1 of 3)	intron (NM_198626, intron 1 of 3)	14403	NM_198626	268880	Mm.286693	NM_198626	ENSMUSG00000047434	Xxylt1	AI480653	xyloside xylosyltransferase 1	protein-coding
mm_11390.1	chr2	31449892	31449899	+	1	NA	Intergenic	Intergenic	-20375	NM_007494	11898	Mm.3217	NM_007494	ENSMUSG00000076441	Ass1	AA408052|ASS|Ass-1|fold	argininosuccinate synthetase 1	protein-coding
mm_118150.1	chr13	105242653	105242666	-	1	NA	intron (NM_027934, intron 5 of 7)	Lx9|LINE|L1	50355	NM_027934	71816	Mm.317015	NM_027934	ENSMUSG00000021720	Rnf180	3110001E11Rik|Rines	ring finger protein 180	protein-coding
mm_67719.1	chr7	90046364	90046401	-	1	NA	intron (NR_110364, intron 5 of 5)	RMER15|LTR|ERVL	17223	NR_110364	319711	Mm.31753	NR_015614	ENSMUSG00000097585	E230029C05Rik	AI452102|B230337J15	RIKEN cDNA E230029C05 gene	ncRNA
mm_67721.1	chr7	90047034	90047042	-	1	NA	intron (NR_110364, intron 5 of 5)	intron (NR_110364, intron 5 of 5)	17879	NR_110364	319711	Mm.31753	NR_015614	ENSMUSG00000097585	E230029C05Rik	AI452102|B230337J15	RIKEN cDNA E230029C05 gene	ncRNA
mm_64692.1	chr7	4522800	4522812	-	1	NA	promoter-TSS (NM_009406)	promoter-TSS (NM_009406)	-363	NM_009406	21954	Mm.27674	NM_009406	ENSMUSG00000035458	Tnni3	Tn1|cTnI	troponin I, cardiac 3	protein-coding
mm_117795.1	chr13	97198288	97198337	-	1	NA	promoter-TSS (NM_010422)	promoter-TSS (NM_010422)	45	NM_010422	15212	Mm.27816	NM_010422	ENSMUSG00000021665	Hexb	-	hexosaminidase B	protein-coding
mm_59425.1	chr7	27124898	27124906	+	1	NA	exon (NM_007817, exon 4 of 10)	exon (NM_007817, exon 4 of 10)	4947	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_88355.1	chr10	75935857	75935872	+	1	NA	5' UTR (NM_175329, exon 1 of 4)	5' UTR (NM_175329, exon 1 of 4)	291	NM_175329	103172	Mm.333849	NM_175329	ENSMUSG00000049422	Chchd10	1620401E04Rik|AI267078|Ndg2	coiled-coil-helix-coiled-coil-helix domain containing 10	protein-coding
mm_19026.1	chr2	76968458	76968470	-	1	NA	exon (NM_011652, exon 9 of 313)	exon (NM_011652, exon 9 of 313)	14083	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_74342.1	chr8	127234052	127234062	+	1	NA	intron (NM_001309391, intron 2 of 24)	intron (NM_001309391, intron 2 of 24)	-65555	NM_001013581	93742	Mm.299254	NM_033620	ENSMUSG00000025812	Pard3	AA960621|AI256638|Asip|D8Ertd580e|Par-3|Par3|Pard-3|Pard3a|Phip	par-3 family cell polarity regulator	protein-coding
mm_164477.1	chr16	72957462	72957466	+	1	NA	intron (NM_019413, intron 6 of 28)	intron (NM_019413, intron 6 of 28)	294315	NM_019413	19876	Mm.310772	NM_019413	ENSMUSG00000022883	Robo1	AW494633|AW742721|DUTT1|Gm310	roundabout guidance receptor 1	protein-coding
mm_29812.1	chr3	127894605	127894608	-	1	NA	intron (NM_027482, intron 1 of 1)	intron (NM_027482, intron 1 of 1)	1717	NM_027482	70617	Mm.317049	NM_027482	ENSMUSG00000050549	5730508B09Rik	2700063A17Rik|C80506	RIKEN cDNA 5730508B09 gene	protein-coding
mm_141750.1	chr17	34239705	34239718	-	1	NA	intron (NM_010389, intron 1 of 5)	intron (NM_010389, intron 1 of 5)	806	NM_010389	15002	Mm.327358	NM_010389	ENSMUSG00000041538	H2-Ob	A-beta-2|A-beta2|H-2Ab|H-2I|H-2Ob|H2-Ab|H2-Ab2|H2-IAb2|Ob	histocompatibility 2, O region beta locus	protein-coding
mm_90997.1	chr10	14059701	14059708	-	1	NA	intron (NM_010437, intron 1 of 8)	CT-rich|Low_complexity|Low_complexity	93325	NM_010437	15273	Mm.42157	NM_010437	ENSMUSG00000015501	Hivep2	Gm20114|MIBP1|Schnurri-2|Shn-2	human immunodeficiency virus type I enhancer binding protein 2	protein-coding
mm_53073.1	chr6	124931500	124931539	+	1	NA	5' UTR (NM_001170341, exon 1 of 9)	5' UTR (NM_001170341, exon 1 of 9)	131	NM_001170341	30853	Mm.29737	NM_145385	ENSMUSG00000030120	Mlf2	AI256856|AU018944|C77284	myeloid leukemia factor 2	protein-coding
mm_148029.1	chr18	70053269	70053292	-	1	NA	5' UTR (NM_030554, exon 1 of 6)	5' UTR (NM_030554, exon 1 of 6)	308	NM_001302798	80718	Mm.246753	NM_030554	ENSMUSG00000024511	Rab27b	2310021G14Rik|B130064M09Rik	RAB27B, member RAS oncogene family	protein-coding
mm_146114.1	chr18	74268252	74268337	+	1	NA	promoter-TSS (NM_013594)	promoter-TSS (NM_013594)	6	NM_013594	17190	Mm.22522	NM_013594	ENSMUSG00000024561	Mbd1	Cxxc3|PCM1	methyl-CpG binding domain protein 1	protein-coding
mm_164275.1	chr15	101743128	101743145	-	1	NA	promoter-TSS (NM_019956)	promoter-TSS (NM_019956)	-39	NM_019956	56735	Mm.358677	NM_019956	ENSMUSG00000051879	Krt71	AA589543|Ca|Cal4|Cu|Krt2-6g|mK6irs|mK6irs1	keratin 71	protein-coding
mm_120402.1	chr14	64950265	64950307	+	1	NA	promoter-TSS (NM_001347626)	promoter-TSS (NM_001347626)	241	NM_001253731	210925	Mm.71332	NM_153414	ENSMUSG00000021975	Ints9	BC028953|D14Ertd231e	integrator complex subunit 9	protein-coding
mm_97057.1	chr11	72671206	72671208	+	1	NA	intron (NM_025985, intron 2 of 5)	intron (NM_025985, intron 2 of 5)	-18795	NM_009671	11736	Mm.10313	NM_009671	ENSMUSG00000020790	Ankfy1	Ankhzn|ZFYVE14|mKIAA1255	ankyrin repeat and FYVE domain containing 1	protein-coding
mm_108520.1	chr12	84052176	84052184	+	1	NA	promoter-TSS (NM_134246)	promoter-TSS (NM_134246)	29	NM_134246	171281	Mm.202331	NM_134246	ENSMUSG00000021228	Acot3	AW108394|PTE-Ia|Pte2a	acyl-CoA thioesterase 3	protein-coding
mm_28423.1	chr3	90451387	90451395	-	1	NA	exon (NM_008727, exon 21 of 22)	exon (NM_008727, exon 21 of 22)	14475	NM_008727	18160	Mm.4627	NM_008727	ENSMUSG00000027931	Npr1	AI893888|GC-A|NPR-A|NPRA|Pndr	natriuretic peptide receptor 1	protein-coding
mm_7833.1	chr1	132139639	132139645	-	1	NA	promoter-TSS (NM_008795)	promoter-TSS (NM_008795)	43	NM_008795	18557	Mm.28130	NM_008795	ENSMUSG00000026437	Cdk18	AA682070|Ctk18|Pctk3	cyclin-dependent kinase 18	protein-coding
mm_119024.1	chr14	30010086	30010099	+	1	NA	intron (NM_001136240, intron 1 of 7)	intron (NM_001136240, intron 1 of 7)	1092	NM_001136240	218865	Mm.259916	NM_172264	ENSMUSG00000015970	Chdh	AU041472|D630034H06Rik	choline dehydrogenase	protein-coding
mm_7765.1	chr1	131199933	131199952	-	1	NA	exon (NM_001311094, exon 1 of 5)	exon (NM_001311094, exon 1 of 5)	243	NM_001311094	54354	Mm.248291	NM_018750	ENSMUSG00000026430	Rassf5	1300019G20Rik|Maxp1|Nore1|Nore1A|Nore1B|Rapl	Ras association (RalGDS/AF-6) domain family member 5	protein-coding
mm_2404.1	chr1	93755149	93755168	+	1	NA	promoter-TSS (NM_025920)	promoter-TSS (NM_025920)	125	NM_174874	66615	Mm.29087	NM_174874	ENSMUSG00000026280	Atg4b	2510009N07Rik|AW048066|Apg4b|Atg4bl|Autl1	autophagy related 4B, cysteine peptidase	protein-coding
mm_128611.1	chr15	58823472	58823482	-	1	NA	promoter-TSS (NM_175212)	promoter-TSS (NM_175212)	-50	NM_175212	74868	Mm.293754	NM_175212	ENSMUSG00000062373	Tmem65	2610029O13Rik|4930438D12Rik	transmembrane protein 65	protein-coding
mm_8307.1	chr1	144076778	144076788	-	1	NA	Intergenic	Intergenic	-72634	NM_009061	19735	Mm.28262	NM_009061	ENSMUSG00000026360	Rgs2	GOS8	regulator of G-protein signaling 2	protein-coding
mm_135836.1	chr16	58523717	58523730	-	1	NA	promoter-TSS (NM_018784)	promoter-TSS (NM_018784)	-411	NM_018784	54613	Mm.212742	NM_018784	ENSMUSG00000022747	St3gal6	1700023B24Rik|AI930218|AW552396|Siat10|St3galVI	ST3 beta-galactoside alpha-2,3-sialyltransferase 6	protein-coding
mm_49501.1	chr6	29768474	29768542	+	1	NA	promoter-TSS (NM_021414)	promoter-TSS (NM_021414)	65	NM_001171000	74340	Mm.210899	NM_021414	ENSMUSG00000029772	Ahcyl2	4631427C17Rik|AI227036|Adohcyase3|mKIAA0828	S-adenosylhomocysteine hydrolase-like 2	protein-coding
mm_38852.1	chr4	149351709	149351721	-	1	NA	intron (NM_022022, intron 17 of 26)	intron (NM_022022, intron 17 of 26)	17076	NR_131918	74310	Mm.440455	NR_131918	ENSMUSG00000085286	Ube4bos3	1700121F15Rik	ubiquitination factor E4B, opposite strand 3	ncRNA
mm_66595.1	chr7	45434591	45434646	-	1	NA	promoter-TSS (NM_030678)	promoter-TSS (NM_030678)	-154	NM_011304	20174	Mm.34410	NM_011304	ENSMUSG00000003868	Ruvbl2	mp47|p47	RuvB-like protein 2	protein-coding
mm_171351.1	chr4	109374921	109374940	-	1	NA	intron (NM_001159964, intron 9 of 12)	intron (NM_001159964, intron 9 of 12)	31327	NR_131195	102635290	Mm.427859	NR_131195		Ttc39aos1	Gm12750|OTTMUSG00000008290|lincRNA-EPS	Ttc39a opposite strand RNA 1	ncRNA
mm_130895.1	chr15	102395227	102395239	-	1	NA	Intergenic	Intergenic	-11083	NM_013672	20683	Mm.4618	NM_013672	ENSMUSG00000001280	Sp1	1110003E12Rik|AA450830|AI845540|Sp1-1	trans-acting transcription factor 1	protein-coding
mm_141847.1	chr17	34801420	34801455	-	1	NA	TTS (NM_009995)	TTS (NM_009995)	2989	NM_009995	13079	Mm.440407	NM_009995	ENSMUSG00000024365	Cyp21a1	21-OH|21OH|21OHA|21OHB|CYP21OH-A|Cyp21|Cyp21-ps1|Cyp21B|Cyp21a2-ps|Cyp21a2ps|Oh21-1|Oh21-2	cytochrome P450, family 21, subfamily a, polypeptide 1	protein-coding
mm_81221.1	chr9	107606779	107606811	+	1	NA	5' UTR (NM_001291538, exon 2 of 20)	5' UTR (NM_001291538, exon 2 of 20)	297	NM_001291538	20347	Mm.4083	NM_009153	ENSMUSG00000057969	Sema3b	SemA|Semaa|sema5|semaV	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B	protein-coding
mm_74744.1	chr8	18978212	18978227	-	1	NA	promoter-TSS (NM_183039)	promoter-TSS (NM_183039)	-103	NM_183039	360217	Mm.271560	NM_183039	ENSMUSG00000053678	Defb40	BD-40	defensin beta 40	protein-coding
mm_149559.1	chr19	12695784	12695809	+	1	NA	promoter-TSS (NM_029550)	promoter-TSS (NM_029550)	6	NM_029550	64697	Mm.218561	NM_029550	ENSMUSG00000024694	Keg1	0610008P16Rik|AI316519|GS4059	kidney expressed gene 1	protein-coding
mm_144464.1	chr18	23752362	23752401	+	1	NA	promoter-TSS (NM_001162942)	promoter-TSS (NM_001162942)	48	NM_001162942	212307	Mm.132237	NM_153058	ENSMUSG00000024277	Mapre2	AI314113|C820009F03Rik|D18Abb1e|EB1|EB2|RP1	microtubule-associated protein, RP/EB family, member 2	protein-coding
mm_109581.1	chr12	112589226	112589266	+	1	NA	intron (NM_198411, intron 1 of 22)	intron (NM_198411, intron 1 of 22)	462	NM_198411	70435	Mm.250193	NM_198411	ENSMUSG00000037679	Inf2	2610204M08Rik|AA589465|AW125550|EG629699	inverted formin, FH2 and WH2 domain containing	protein-coding
mm_158702.1	chrX	162085385	162085388	-	1	NA	intron (NM_001081052, intron 1 of 7)	intron (NM_001081052, intron 1 of 7)	74055	NM_001081052	195727	Mm.336313	NM_001081052	ENSMUSG00000059493	Nhs	Gm389|Gm48|Nhs1|Xcat	Nance-Horan syndrome (human)	protein-coding
mm_36536.1	chr4	86655521	86655531	-	1	NA	Intergenic	B1_Mus1|SINE|Alu	14533	NM_007408	11520	Mm.381	NM_007408	ENSMUSG00000028494	Plin2	AA407157|ADPH|Adfp|Adrp	perilipin 2	protein-coding
mm_150323.1	chr19	34574131	34574159	+	1	NA	exon (NM_008332, exon 3 of 3)	exon (NM_008332, exon 3 of 3)	-9384	NM_010501	15959	Mm.426079	NM_010501	ENSMUSG00000074896	Ifit3	Ifi49|P49	interferon-induced protein with tetratricopeptide repeats 3	protein-coding
mm_63926.1	chr7	139400506	139400528	+	1	NA	intron (NM_183144, intron 1 of 15)	intron (NM_183144, intron 1 of 15)	11408	NM_001127363	212111	Mm.28308	NM_183144	ENSMUSG00000025477	Inpp5a	-	inositol polyphosphate-5-phosphatase A	protein-coding
mm_38312.1	chr4	137048778	137048807	-	1	NA	promoter-TSS (NM_198248)	promoter-TSS (NM_198248)	-97	NM_198248	230848	Mm.31068	NM_198248	ENSMUSG00000060862	Zbtb40	BC059177|C230087D24|Gm571|mKIAA0478	zinc finger and BTB domain containing 40	protein-coding
mm_159286.1	chr2	169884847	169884847	+	1	NA	exon (NM_080455, exon 2 of 2)	exon (NM_080455, exon 2 of 2)	78340	NR_131974	446211	Mm.266854	NR_131974	ENSMUSG00000103935	AY702102	STDP1	cDNA sequence AY702102	ncRNA
mm_127652.1	chr15	102493209	102493212	+	1	NA	intron (NM_001103165, intron 14 of 14)	intron (NM_001103165, intron 14 of 14)	22578	NM_001174073	18521	Mm.236513	NM_011042	ENSMUSG00000056851	Pcbp2	AW412548|Hnrpx|alphaCP-2	poly(rC) binding protein 2	protein-coding
mm_40392.1	chr5	52784266	52784267	+	1	NA	intron (NM_001308144, intron 2 of 12)	B1_Mur4|SINE|Alu	1211	NM_030185	78796	Mm.266886	NM_030185	ENSMUSG00000029179	Zcchc4	4930449I23Rik	zinc finger, CCHC domain containing 4	protein-coding
mm_40009.1	chr5	33018868	33018885	+	1	NA	promoter-TSS (NM_011738)	promoter-TSS (NM_011738)	60	NM_011738	22629	Mm.332314	NM_011738	ENSMUSG00000018965	Ywhah	-	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta polypeptide	protein-coding
mm_37249.1	chr4	118231780	118231794	-	1	NA	exon (NM_011213, exon 12 of 33)	exon (NM_011213, exon 12 of 33)	-21223	NR_106085	102466820		NR_106085	ENSMUSG00000098596	Mir7226	Gm27630|mmu-mir-7226	microRNA 7226	ncRNA
mm_146678.1	chr18	12819813	12819829	-	1	NA	promoter-TSS (NR_045524)	promoter-TSS (NR_045524)	86	NR_045524	64291	Mm.259470	NM_020573	ENSMUSG00000044252	Osbpl1a	G430090F17Rik|Gm753|ORP-1|Osbpl1b	oxysterol binding protein-like 1A	protein-coding
mm_5266.1	chr1	17097799	17097806	-	1	NA	promoter-TSS (NM_020604)	promoter-TSS (NM_020604)	87	NM_020604	57339	Mm.143761	NM_020604	ENSMUSG00000042686	Jph1	ENSMUSG00000054314|JP-1|Jp1	junctophilin 1	protein-coding
mm_80946.1	chr9	102834865	102834947	+	1	NA	promoter-TSS (NM_013649)	promoter-TSS (NM_013649)	-14	NM_013649	20187	Mm.335391	NM_013649	ENSMUSG00000032547	Ryk	AW536699|ERK-3|Vik	receptor-like tyrosine kinase	protein-coding
mm_134775.1	chr16	23974939	23974953	-	1	NA	exon (NM_009744, exon 4 of 10)	exon (NM_009744, exon 4 of 10)	13666	NM_009744	12053	Mm.347398	NM_009744	ENSMUSG00000022508	Bcl6	Bcl5	B cell leukemia/lymphoma 6	protein-coding
mm_61732.1	chr7	81862675	81862692	+	1	NA	promoter-TSS (NM_001291282)	promoter-TSS (NM_001291282)	-4	NM_001291282	107769	Mm.221412	NM_145375	ENSMUSG00000038623	Tm6sf1	AI428514|BC023123|C630016D09Rik	transmembrane 6 superfamily member 1	protein-coding
mm_21881.1	chr2	166155070	166155080	-	1	NA	5' UTR (NM_001252578, exon 1 of 21)	5' UTR (NM_001252578, exon 1 of 21)	210	NM_001252578	72043	Mm.1011	NM_028072	ENSMUSG00000006800	Sulf2	2010004N24Rik|AU020235|MSulf-2|mKIAA1247	sulfatase 2	protein-coding
mm_129254.1	chr15	76697962	76697992	-	1	NA	exon (NM_182805, exon 5 of 11)	exon (NM_182805, exon 5 of 11)	1251	NM_182805	76282	Mm.30130	NM_182805	ENSMUSG00000022546	Gpt	1300007J06Rik|2310022B03Rik|ALT|ALT1|Gpt-1|Gpt1	glutamic pyruvic transaminase, soluble	protein-coding
mm_92095.1	chr10	62877059	62877065	-	1	NA	intron (NM_027384, intron 1 of 10)	B2_Mm2|SINE|B2	2952	NM_027384	52463	Mm.17774	NM_027384	ENSMUSG00000047146	Tet1	2510010B09Rik|AA517754|BB001228|Cxxc6|D10Ertd17e|LCX|mKIAA1676	tet methylcytosine dioxygenase 1	protein-coding
mm_51218.1	chr6	71360976	71360988	+	1	NA	Intergenic	Intergenic	-12445	NM_009857	12525	Mm.1858	NM_009857	ENSMUSG00000053977	Cd8a	BB154331|Ly-2|Ly-35|Ly-B|Lyt-2	CD8 antigen, alpha chain	protein-coding
mm_99183.1	chr11	100860350	100860350	+	1	NA	promoter-TSS (NM_001164062)	promoter-TSS (NM_001164062)	-134	NM_001164062	20850	Mm.277403	NM_011488	ENSMUSG00000004043	Stat5a	AA959963|STAT5	signal transducer and activator of transcription 5A	protein-coding
mm_31457.1	chr4	48663547	48663563	+	1	NA	promoter-TSS (NM_026509)	promoter-TSS (NM_026509)	41	NM_026509	68016	Mm.133444	NM_026509	ENSMUSG00000028348	Murc	2310039E09Rik	muscle-related coiled-coil protein	protein-coding
mm_87285.1	chr10	42276893	42276900	+	1	NA	promoter-TSS (NM_019740)	promoter-TSS (NM_019740)	-154	NM_019740	56484	Mm.338613	NM_019740	ENSMUSG00000048756	Foxo3	1110048B16Rik|2010203A17Rik|C76856|FKHRL1|Fkhr2|Foxo3a	forkhead box O3	protein-coding
mm_138474.1	chr17	35194503	35194521	+	1	NA	promoter-TSS (NM_008518)	promoter-TSS (NM_008518)	5	NM_008518	16994	Mm.1715	NM_008518	ENSMUSG00000024399	Ltb	AI662801|LTbeta|Tnfc|Tnfsf3|Tnlg1c|p33	lymphotoxin B	protein-coding
mm_28087.1	chr3	85533263	85533283	-	1	NA	Intergenic	ORR1C2|LTR|ERVL-MaLR	-40856	NM_144896	229487	Mm.52275	NM_144896	ENSMUSG00000028085	Gatb	9430026F02Rik|Pet112|Pet112l	glutamyl-tRNA(Gln) amidotransferase, subunit B	protein-coding
mm_113134.1	chr13	24633465	24633477	+	1	NA	intron (NM_178658, intron 1 of 13)	intron (NM_178658, intron 1 of 13)	-5177	NM_001080381	193385	Mm.217319	NM_029679	ENSMUSG00000036006	Fam65b	-	family with sequence similarity 65, member B	protein-coding
mm_159003.1	chr1	154726120	154726120	-	1	NA	promoter-TSS (NM_009782)	promoter-TSS (NM_009782)	-200	NM_009782	12290	Mm.267517	NM_009782	ENSMUSG00000004110	Cacna1e	A430040I15|BII|Cach6|Cacnl1a6|Cav2.3|Cchra1|alpha1E	calcium channel, voltage-dependent, R type, alpha 1E subunit	protein-coding
mm_154364.1	chrM	7760	7794	+	1	NA	NA	Intergenic	NA	NA								
mm_148311.1	chr18	83754183	83754206	-	1	NA	Intergenic	RMER30|DNA|hAT-Charlie	332368	NM_001081300	110796	Mm.102136	NM_001081300	ENSMUSG00000046982	Tshz1	5730407I04Rik|D18Bwg1409e|Mtsh1|NY-CO-33|Sdccag33|Tsh1|mKIAA4206|teashirt1	teashirt zinc finger family member 1	protein-coding
mm_59063.1	chr7	19420158	19420171	+	1	NA	exon (NM_007710, exon 7 of 8)	exon (NM_007710, exon 7 of 8)	1253	NR_073014	100503495	Mm.410762	NR_073014	ENSMUSG00000040705	A930016O22Rik	-	RIKEN cDNA A930016O22 gene	ncRNA
mm_74727.1	chr8	17535252	17535390	-	1	NA	promoter-TSS (NM_053171)	promoter-TSS (NM_053171)	64	NM_053171	94109	Mm.436988	NM_053171	ENSMUSG00000060924	Csmd1	B930082H09|mKIAA1890	CUB and Sushi multiple domains 1	protein-coding
mm_28856.1	chr3	96925920	96925941	-	1	NA	5' UTR (NM_008123, exon 1 of 2)	5' UTR (NM_008123, exon 1 of 2)	121	NM_008123	14616	Mm.258183	NM_008123	ENSMUSG00000049908	Gja8	Aey5|Cnx50|Cx50|Lop10	gap junction protein, alpha 8	protein-coding
mm_129923.1	chr15	84444289	84444315	-	1	NA	intron (NM_001347543, intron 1 of 5)	intron (NM_001347543, intron 1 of 5)	2308	NM_001347543	72301	Mm.275387	NM_001163145	ENSMUSG00000062760	1810041L15Rik	Kiaa1644	RIKEN cDNA 1810041L15 gene	protein-coding
mm_69093.1	chr7	127018567	127018577	-	1	NA	3' UTR (NM_001102563, exon 4 of 4)	3' UTR (NM_001102563, exon 4 of 4)	-1220	NM_030240	67278	Mm.345385	NM_030240	ENSMUSG00000030680	Pagr1a	2900092E17Rik|C77040|PA1|PAGR1	PAXIP1 associated glutamate rich protein 1A	protein-coding
mm_62158.1	chr7	97162556	97162565	+	1	NA	intron (NM_001162477, intron 1 of 9)	ORR1B1|LTR|ERVL-MaLR	80809	NM_010248	14389	Mm.42033	NM_010248	ENSMUSG00000004508	Gab2	AI463667|D130058I17Rik|p97	growth factor receptor bound protein 2-associated protein 2	protein-coding
mm_148837.1	chr19	6363727	6363737	+	1	NA	promoter-TSS (NR_122118)	promoter-TSS (NR_122118)	42	NR_122118	22668	Mm.256422	NM_011750	ENSMUSG00000024949	Sf1	BBP|MZFM|WBP4|Zfp162	splicing factor 1	protein-coding
mm_33370.1	chr4	129514965	129514981	+	1	NA	exon (NM_010807, exon 2 of 2)	exon (NM_010807, exon 2 of 2)	1392	NM_010807	17357	Mm.424974	NM_010807	ENSMUSG00000047945	Marcksl1	AL022768|AW215397|AW536807|D4Bc1|F52|MacMARCKS|Macs2|Macs3|Mlp|Mrp	MARCKS-like 1	protein-coding
mm_8805.1	chr1	161876589	161876607	-	1	NA	promoter-TSS (NM_172645)	promoter-TSS (NM_172645)	63	NM_172645	226551	Mm.170002	NM_172645	ENSMUSG00000040297	Suco	4732491B11|AI848100|AU016931|Opt	SUN domain containing ossification factor	protein-coding
mm_45628.1	chr5	76304519	76304551	-	1	NA	promoter-TSS (NM_007715)	promoter-TSS (NM_007715)	13	NM_007715	12753	Mm.3552	NM_007715	ENSMUSG00000029238	Clock	5330400M04Rik|KAT13D	circadian locomotor output cycles kaput	protein-coding
mm_26329.1	chr3	142544038	142544069	+	1	NA	exon (NM_001083312, exon 8 of 11)	exon (NM_001083312, exon 8 of 11)	13717	NM_145545	229900	Mm.45740	NM_145545	ENSMUSG00000040253	Gbp7	9830147J24Rik	guanylate binding protein 7	protein-coding
mm_128575.1	chr15	57772832	57772842	-	1	NA	intron (NM_199449, intron 2 of 3)	Tigger9b|DNA|TcMar-Tigger	78170	NM_199449	387609	Mm.36557	NM_199449	ENSMUSG00000071757	Zhx2	Afr-1|Afr1|Raf|mKIAA0854	zinc fingers and homeoboxes 2	protein-coding
mm_17751.1	chr2	32716690	32716704	-	1	NA	Intergenic	RMER19B|LTR|ERVK	-3725	NR_039536	100628606		NR_039536	ENSMUSG00000105841	Mir3960	mmu-mir-3960	microRNA 3960	ncRNA
mm_77189.1	chr8	111876662	111876725	-	1	NA	promoter-TSS (NM_025781)	promoter-TSS (NM_025781)	-18	NM_025781	66817	Mm.345350	NM_025781	ENSMUSG00000031953	Tmem170	9030409E16Rik|AA403674|D8Bwg1414e|Tmem170a	transmembrane protein 170	protein-coding
mm_150965.1	chr19	46500202	46500230	+	1	NA	Intergenic	CpG	-1432	NM_053100	93679	Mm.392177	NM_053100	ENSMUSG00000025034	Trim8	AA408830|BB006755|GERP|Rnf27	tripartite motif-containing 8	protein-coding
mm_44465.1	chr5	23386476	23386499	-	1	NA	Intergenic	Intergenic	47866	NR_040469	269630	Mm.425231	NR_040469	ENSMUSG00000073147	5031425E22Rik	-	RIKEN cDNA 5031425E22 gene	ncRNA
mm_1965.1	chr1	86487772	86487831	+	1	NA	Intergenic	CpG	-38935	NM_008972	19231	Mm.19187	NM_008972	ENSMUSG00000026238	Ptma	Thym	prothymosin alpha	protein-coding
mm_49427.1	chr6	29272410	29272431	+	1	NA	promoter-TSS (NM_001190461)	promoter-TSS (NM_001190461)	-68	NM_001190461	69573	Mm.45161	NM_023516	ENSMUSG00000043421	Hilpda	2310016C08Rik|AW049004|Hig2	hypoxia inducible lipid droplet associated	protein-coding
mm_49461.1	chr6	29419200	29419206	+	1	NA	exon (NM_145574, exon 15 of 16)	exon (NM_145574, exon 15 of 16)	-13950	NM_001081185	68794	Mm.39046	NM_026839	ENSMUSG00000068699	Flnc	1110055E19Rik|ABP-280|ABPL|Fln2	filamin C, gamma	protein-coding
mm_147426.1	chr18	46237860	46237879	-	1	NA	Intergenic	Intergenic	-25262	NM_178872	28105	Mm.277382	NM_178872	ENSMUSG00000033949	Trim36	D18Wsu100e|haprin	tripartite motif-containing 36	protein-coding
mm_11607.1	chr2	34406846	34406880	+	1	NA	promoter-TSS (NM_177345)	promoter-TSS (NM_177345)	12	NM_001290626	227743	Mm.270866	NM_177345	ENSMUSG00000038696	Mapkap1	AI591529|D230039K05Rik|Sin1	mitogen-activated protein kinase associated protein 1	protein-coding
mm_47923.1	chr5	135012747	135012761	-	1	NA	TTS (NM_001190437)	TTS (NM_001190437)	403	NR_026688	69812	Mm.18422	NR_026688	ENSMUSG00000085042	Abhd11os	2010001M06Rik|AI462243|Wbscr26|Wnscr26	abhydrolase domain containing 11, opposite strand	ncRNA
mm_147931.1	chr18	65970204	65970222	-	1	NA	promoter-TSS (NM_145493)	promoter-TSS (NM_145493)	-35	NM_145493	225644	Mm.192285	NM_145493	ENSMUSG00000024519	Cplx4	A930004D23Rik|CPXIV|Gm957	complexin 4	protein-coding
mm_11492.1	chr2	32456091	32456103	+	1	NA	TTS (NM_194335)	TTS (NM_194335)	-4627	NM_146118	227731	Mm.37395	NM_146118	ENSMUSG00000026819	Slc25a25	1110030N17Rik|MCSC|mKIAA1896	solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 25	protein-coding
mm_60000.1	chr7	30606917	30606948	+	1	NA	exon (NM_026815, exon 5 of 8)	exon (NM_026815, exon 5 of 8)	5802	NM_026815	109637	Mm.25471	NM_026815	ENSMUSG00000006313	Upk1a	1110031P12Rik|AU019298|C87192|Tspan21|Upk1	uroplakin 1A	protein-coding
mm_127843.1	chr15	6874743	6874787	-	1	NA	promoter-TSS (NM_011019)	promoter-TSS (NM_011019)	-452	NM_001310469	18414	Mm.10760	NM_011019	ENSMUSG00000022146	Osmr	OSMRB	oncostatin M receptor	protein-coding
mm_161775.1	chr17	37660565	37660565	-	1	NA	promoter-TSS (NM_207155)	promoter-TSS (NM_207155)	-234	NM_207155	258263	Mm.377399	NM_207155	ENSMUSG00000095286	Olfr117	MOR256-33	olfactory receptor 117	protein-coding
mm_100687.1	chr11	3504994	3505003	-	1	NA	promoter-TSS (NM_172439)	promoter-TSS (NM_172439)	-177	NM_172439	170835	Mm.24313	NM_172439	ENSMUSG00000034570	Inpp5j	Pib5pa|Pipp	inositol polyphosphate 5-phosphatase J	protein-coding
mm_17656.1	chr2	32065090	32065119	-	1	NA	Intergenic	Intergenic	14158	NR_106135	102466844		NR_106135	ENSMUSG00000099075	Mir7674	Gm27563|mmu-mir-7674	microRNA 7674	ncRNA
mm_43271.1	chr5	130384719	130384760	+	1	NA	promoter-TSS (NM_198665)	promoter-TSS (NM_198665)	-108	NM_198665	381673	Mm.192133	NM_198665	ENSMUSG00000052014	A330070K13Rik	Gm1051	RIKEN cDNA A330070K13 gene	protein-coding
mm_164345.1	chr16	16852298	16852312	+	1	NA	Intergenic	Intergenic	11680	NM_001190325	16136	Mm.184441	NM_001190325	ENSMUSG00000075370	Igll1	BB139905|Igl-5|Igll|Lambda5	immunoglobulin lambda-like polypeptide 1	protein-coding
mm_49606.1	chr6	30744879	30744890	+	1	NA	exon (NM_001252293, exon 8 of 12)	exon (NM_001252293, exon 8 of 12)	3585	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_129548.1	chr15	79414682	79414683	-	1	NA	Intergenic	Intergenic	-11379	NM_172608	223693	Mm.323358	NM_172608	ENSMUSG00000009035	Tmem184b	2610507A11|4732495E13Rik	transmembrane protein 184b	protein-coding
mm_95541.1	chr11	52282689	52282705	+	1	NA	promoter-TSS (NM_009331)	promoter-TSS (NM_009331)	-102	NM_009331	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_59833.1	chr7	29303988	29304003	+	1	NA	promoter-TSS (NM_013874)	promoter-TSS (NM_013874)	-10	NM_013874	29861	Mm.101885	NM_013874	ENSMUSG00000030584	Dpf1	Neud4	D4, zinc and double PHD fingers family 1	protein-coding
mm_47024.1	chr5	115500463	115500495	-	1	NA	Intergenic	Intergenic	-6197	NM_011223	19303	Mm.18714	NM_011223	ENSMUSG00000029528	Pxn	AW108311|AW123232|Pax	paxillin	protein-coding
mm_151042.1	chr19	47023838	47023848	+	1	NA	3' UTR (NM_146100, exon 3 of 3)	3' UTR (NM_146100, exon 3 of 3)	-8654	NM_001164363	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_87018.1	chr10	27936329	27936333	+	1	NA	Intergenic	Intergenic	-138489	NM_008983	19272	Mm.332303	NM_008983	ENSMUSG00000019889	Ptprk	AI853699|PTPk|RPTPkappa	protein tyrosine phosphatase, receptor type, K	protein-coding
mm_27708.1	chr3	67515469	67515484	-	1	NA	promoter-TSS (NM_001164763)	promoter-TSS (NM_001164763)	47	NM_001164763	109222	Mm.38002	NM_001164763	ENSMUSG00000049404	Rarres1	5430417P09Rik|AI662122	retinoic acid receptor responder (tazarotene induced) 1	protein-coding
mm_94330.1	chr11	4266668	4266673	+	1	NA	promoter-TSS (NM_001039537)	promoter-TSS (NM_001039537)	-126	NM_001039537	16878	Mm.4964	NM_008501	ENSMUSG00000034394	Lif	-	leukemia inhibitory factor	protein-coding
mm_102998.1	chr11	69687062	69687081	-	1	NA	exon (NM_001159503, exon 7 of 13)	exon (NM_001159503, exon 7 of 13)	-1517	NM_023517	69583	Mm.8983	NM_023517	ENSMUSG00000089669	Tnfsf13	2310026N09Rik|April|Tall2|Tnlg7b|Trdl1	tumor necrosis factor (ligand) superfamily, member 13	protein-coding
mm_145289.1	chr18	53245639	53245659	+	1	NA	promoter-TSS (NM_029394)	promoter-TSS (NM_029394)	-13	NM_029394	69226	Mm.32414	NM_029394	ENSMUSG00000024535	Snx24	2810011K15Rik|5730433I16Rik|AI451341	sorting nexing 24	protein-coding
mm_167775.1	chr9	112308225	112308249	+	1	NA	intron (NR_033433, intron 2 of 3)	intron (NR_033433, intron 2 of 3)	51663	NR_033433	620760	Mm.259863	NR_015468	ENSMUSG00000087038	2900079G21Rik	C130083B14|Gm6179	RIKEN cDNA 2900079G21 gene	ncRNA
mm_2138.1	chr1	88087803	88087848	+	1	NA	intron (NM_201644, intron 1 of 4)	intron (NM_201644, intron 1 of 4)	-7176	NM_201642	394432	Mm.300095	NM_201642	ENSMUSG00000090124	Ugt1a7c	A10'|A13|Ugt1a10	UDP glucuronosyltransferase 1 family, polypeptide A7C	protein-coding
mm_62972.1	chr7	119900100	119900102	+	1	NA	promoter-TSS (NR_126475)	promoter-TSS (NR_126475)	-10	NR_126475	73919	Mm.46381	NM_029610	ENSMUSG00000030922	Lyrm1	1110065L10Rik|2310004B22Rik|4930404J24Rik	LYR motif containing 1	protein-coding
mm_172618.1	chr8	20122286	20122298	+	1	NA	Intergenic	CpG	175140	NR_030708	547150	Mm.359054	NR_030708	ENSMUSG00000071796	6820431F20Rik	-	cadherin 11 pseudogene	pseudo
mm_147058.1	chr18	34947972	34948020	-	1	NA	exon (NM_010481, exon 7 of 17)	exon (NM_010481, exon 7 of 17)	6355	NM_010481	15526	Mm.209419	NM_010481	ENSMUSG00000024359	Hspa9	74kDa|Csa|Grp75|Hsc74|Hsp74|Hsp74a|Hspa9a|Mortalin|Mot-2|Mot2|Mthsp70|Pbp74	heat shock protein 9	protein-coding
mm_120333.1	chr14	63416976	63416982	+	1	NA	5' UTR (NM_007549, exon 1 of 13)	5' UTR (NM_007549, exon 1 of 13)	208	NM_007549	12143	Mm.3962	NM_007549	ENSMUSG00000014453	Blk	-	B lymphoid kinase	protein-coding
mm_18298.1	chr2	52742403	52742441	-	1	NA	promoter-TSS (NM_019667)	promoter-TSS (NM_019667)	-273	NM_019667	56324	Mm.263639	NM_019667	ENSMUSG00000055371	Stam2	1200004O12Rik|5730456G07Rik|BB145015|Hbp	signal transducing adaptor molecule (SH3 domain and ITAM motif) 2	protein-coding
mm_2012.1	chr1	87127709	87127711	+	1	NA	exon (NM_007432, exon 11 of 11)	exon (NM_007432, exon 11 of 11)	2702	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_34827.1	chr4	155095890	155095898	+	1	NA	intron (NM_001081100, intron 6 of 13)	AT_rich|Low_complexity|Low_complexity	9317	NM_001081100	76866	Mm.200590	NM_001081100	ENSMUSG00000029049	Morn1	2900057D20Rik|4930417P05Rik|AU042805	MORN repeat containing 1	protein-coding
mm_57396.1	chr6	124863051	124863061	-	1	NA	intron (NM_013533, intron 1 of 4)	intron (NM_013533, intron 1 of 4)	861	NM_013533	14788	Mm.2514	NM_013533	ENSMUSG00000038390	Gpr162	A-2|BC031437|Grca	G protein-coupled receptor 162	protein-coding
mm_50415.1	chr6	48746224	48746234	+	1	NA	promoter-TSS (NM_175035)	promoter-TSS (NM_175035)	32	NM_175035	317757	Mm.455917	NM_175035	ENSMUSG00000043505	Gimap5	D630024P16|E230026N22Rik	GTPase, IMAP family member 5	protein-coding
mm_41774.1	chr5	103692373	103692431	+	1	NA	Intergenic	CpG	-36670	NM_001163550	74218	Mm.159141	NM_028824	ENSMUSG00000029320	1700016H13Rik	-	RIKEN cDNA 1700016H13 gene	protein-coding
mm_118582.1	chr14	19830676	19830685	+	1	NA	Intergenic	Intergenic	-6857	NM_026528	68045	Mm.21932	NM_026528	ENSMUSG00000021807	2700060E02Rik	-	RIKEN cDNA 2700060E02 gene	protein-coding
mm_125667.1	chr15	65810180	65810186	+	1	NA	intron (NM_133766, intron 1 of 22)	intron (NM_133766, intron 1 of 22)	23142	NM_133766	76740	Mm.260647	NM_133766	ENSMUSG00000015002	Efr3a	A130089M23Rik|BB071175|C76891|C920006C10Rik|D030063F01Rik|mKIAA0143	EFR3 homolog A	protein-coding
mm_8884.1	chr1	162866503	162866616	-	1	NA	promoter-TSS (NM_010231)	promoter-TSS (NM_010231)	51	NM_010231	14261	Mm.976	NM_010231	ENSMUSG00000040181	Fmo1	-	flavin containing monooxygenase 1	protein-coding
mm_109430.1	chr12	110615468	110615469	+	1	NA	intron (NM_030238, intron 5 of 76)	L1_Mus3|LINE|L1	14073	NM_030238	13424	Mm.181430	NM_030238	ENSMUSG00000018707	Dync1h1	9930018I23Rik|AI894280|DHC1|DHC1a|DNCL|Dnchc1|Dnec1|Dnecl|Loa|MAP1C|P22|Swl|mKIAA0325	dynein cytoplasmic 1 heavy chain 1	protein-coding
mm_94565.1	chr11	11685910	11685947	+	1	NA	promoter-TSS (NM_009578)	promoter-TSS (NM_009578)	3	NM_001025597	22778	Mm.103545	NM_009578	ENSMUSG00000018654	Ikzf1	5832432G11Rik|Ikaros|LyF-1|Zfpn1a1|Znfn1a1|hlk-1|mKIAA4227	IKAROS family zinc finger 1	protein-coding
mm_103517.1	chr11	76779225	76779243	-	1	NA	3' UTR (NM_007754, exon 21 of 21)	3' UTR (NM_007754, exon 21 of 21)	-15679	NM_016810	53334	Mm.20931	NM_016810	ENSMUSG00000010392	Gosr1	AI414660|AI426320|BB145494|GOS-28|GOSRI|GS28	golgi SNAP receptor complex member 1	protein-coding
mm_39041.1	chr4	152361018	152361025	-	1	NA	exon (NM_001081376, exon 9 of 42)	exon (NM_001081376, exon 9 of 42)	22370	NM_001081376	269610	Mm.40192	NM_029216	ENSMUSG00000005045	Chd5	4930532L22Rik|AW060752|B230399N07Rik|CHD-5	chromodomain helicase DNA binding protein 5	protein-coding
mm_58341.1	chr6	147042684	147042720	-	1	NA	promoter-TSS (NM_145573)	promoter-TSS (NM_145573)	-68	NM_145573	232536	Mm.46656	NM_145573	ENSMUSG00000040112	Mrps35	MDSO23|MRP-S28|MRPS28	mitochondrial ribosomal protein S35	protein-coding
mm_23635.1	chr3	66985648	66985678	+	1	NA	promoter-TSS (NM_025822)	promoter-TSS (NM_025822)	-9	NM_025822	66880	Mm.316418	NM_025822	ENSMUSG00000034544	Rsrc1	1200013F24Rik|SRrp53	arginine/serine-rich coiled-coil 1	protein-coding
mm_161672.1	chr17	14956761	14956761	-	1	NA	exon (NM_024250, exon 3 of 12)	exon (NM_024250, exon 3 of 12)	4499	NM_024250	72057	Mm.440085	NM_024250	ENSMUSG00000023883	Phf10	1810055P05Rik|AV024533	PHD finger protein 10	protein-coding
mm_72969.1	chr8	92864882	92864883	+	1	NA	intron (NM_173014, intron 1 of 13)	intron (NM_173014, intron 1 of 13)	9532	NM_173014	270084	Mm.21463	NM_173014	ENSMUSG00000033192	Lpcat2	A330042H22|Aytl1|Aytl1a|lpafat1	lysophosphatidylcholine acyltransferase 2	protein-coding
mm_28148.1	chr3	87512587	87512601	-	1	NA	Intergenic	Intergenic	-12984	NM_001083318	27049	Mm.219460	NM_012051	ENSMUSG00000003382	Etv3	AI414410|METS|Pe1	ets variant 3	protein-coding
mm_128967.1	chr15	74832156	74832170	-	1	NA	Intergenic	B3|SINE|B2	9480	NM_001033229	110115	Mm.322606	NM_001033229	ENSMUSG00000075604	Cyp11b1	AA389061|CPN1|Cyp11b|Cyp11b-1|FHI	cytochrome P450, family 11, subfamily b, polypeptide 1	protein-coding
mm_85934.1	chr9	112097822	112097836	-	1	NA	intron (NM_001177618, intron 17 of 18)	B4A|SINE|B4	20882	NR_029823	723815		NR_029823	ENSMUSG00000065441	Mir128-2	Mirn128-2|Mirn128b|mir-128-2|mir-128b	microRNA 128-2	ncRNA
mm_112290.1	chr12	114513786	114513798	-	1	NA	promoter-TSS (NR_106063)	promoter-TSS (NR_106063)	-98	NR_106063	102465664		NR_106063	ENSMUSG00000098357	Mir7094-2	Gm27508|mmu-mir-7094-2	microRNA 7094-2	ncRNA
mm_28157.1	chr3	87753258	87753259	-	1	NA	intron (NM_001032413, intron 16 of 23)	intron (NM_001032413, intron 16 of 23)	-4635	NM_028971	74485	Mm.474494	NM_028971	ENSMUSG00000023084	Lrrc71	4933430H15Rik	leucine rich repeat containing 71	protein-coding
mm_29530.1	chr3	116662093	116662104	-	1	NA	intron (NM_008246, intron 1 of 11)	CpG	579	NM_008246	15247	Mm.280077	NM_008246	ENSMUSG00000089911	Mfsd14a	Hiat1	major facilitator superfamily domain containing 14A	protein-coding
mm_148375.1	chr19	3205579	3205593	+	1	NA	Intergenic	Intergenic	-7883	NR_045304	70011	Mm.393871	NR_045304	ENSMUSG00000100969	1700030N03Rik	1700087C08Rik	RIKEN cDNA 1700030N03 gene	ncRNA
mm_10297.1	chr2	10439876	10439879	+	1	NA	TTS (NM_001198809)	TTS (NM_001198809)	-26786	NR_130333	100526481		NR_130333	ENSMUSG00000092793	Mir466m	mmu-mir-466m	microRNA 466m	ncRNA
mm_22221.1	chr2	174427817	174427834	-	1	NA	TTS (NM_020580)	TTS (NM_020580)	11214	NM_022325	64138	Mm.156919	NM_022325	ENSMUSG00000016256	Ctsz	AI787083|AU019819|CTSX|D2Wsu143e	cathepsin Z	protein-coding
mm_168922.1	chr12	59999872	59999875	-	1	NA	Intergenic	RLTR9D|LTR|ERVK	-780390	NM_001033156	70611	Mm.311026	NM_001033156	ENSMUSG00000035329	Fbxo33	5730501N20Rik|AI642135	F-box protein 33	protein-coding
mm_10969.1	chr2	25706744	25706794	+	1	NA	promoter-TSS (NM_023326)	promoter-TSS (NM_023326)	-110	NM_023326	107771	Mm.330057	NM_023326	ENSMUSG00000049086	Bmyc	2900002K07Rik|AW060705|Mycb	brain expressed myelocytomatosis oncogene	protein-coding
mm_133779.1	chr16	94969259	94969281	+	1	NA	intron (NM_001025584, intron 1 of 4)	intron (NM_001025584, intron 1 of 4)	28426	NM_001025584	16522	Mm.328720	NM_010606	ENSMUSG00000043301	Kcnj6	BIR1|GIRK2|KATP2|KCNJ7|Kir3.2|weaver|wv	potassium inwardly-rectifying channel, subfamily J, member 6	protein-coding
mm_133274.1	chr16	77389923	77389938	+	1	NA	intron (NR_015543, intron 2 of 4)	intron (NR_015543, intron 2 of 4)	60602	NR_015543	77994	Mm.394688	NR_015543	ENSMUSG00000090386	Mir99ahg	2810055G20Rik|D730043B02Rik	Mir99a and Mirlet7c-1 host gene (non-protein coding)	ncRNA
mm_149987.1	chr19	29251749	29251854	+	1	NA	promoter-TSS (NM_008413)	promoter-TSS (NM_008413)	-2	NM_001048177	16452	Mm.275839	NM_008413	ENSMUSG00000024789	Jak2	Fd17	Janus kinase 2	protein-coding
mm_117019.1	chr13	58127972	58127996	-	1	NA	exon (NM_029872, exon 1 of 1)	exon (NM_029872, exon 1 of 1)	572	NM_029872	77134	Mm.490274	NM_029872	ENSMUSG00000007836	Hnrnpa0	1110055B05Rik|3010025E17Rik|Hnrpa0|hnRNP A0	heterogeneous nuclear ribonucleoprotein A0	protein-coding
mm_78064.1	chr9	15208435	15208440	+	1	NA	Intergenic	Intergenic	-30608	NM_026955	69137	Mm.41396	NM_026955	ENSMUSG00000031937	Vstm5	2200002K05Rik	V-set and transmembrane domain containing 5	protein-coding
mm_27366.1	chr3	50438031	50438035	-	1	NA	intron (NM_011990, intron 2 of 11)	intron (NM_011990, intron 2 of 11)	5580	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_19243.1	chr2	84727237	84727299	-	1	NA	promoter-TSS (NM_133840)	promoter-TSS (NM_133840)	0	NM_133840	98985	Mm.21583	NM_133840	ENSMUSG00000027079	Clp1	AI462438|Heab	CLP1, cleavage and polyadenylation factor I subunit	protein-coding
mm_13675.1	chr2	116073884	116073885	+	1	NA	TTS (NR_033447)	TTS (NR_033447)	2212	NR_033447	69974	Mm.440293	NR_033447		2810405F15Rik	-	RIKEN cDNA 2810405F15 gene	ncRNA
mm_118098.1	chr13	103909840	103909841	-	1	NA	intron (NM_001005868, intron 1 of 26)	ID4_|SINE|ID	10746	NM_001289473	59079	Mm.277354	NM_021563	ENSMUSG00000021709	Erbin	1700028E05Rik|Erbb2ip|mKIAA1225	Erbb2 interacting protein	protein-coding
mm_166540.1	chr6	31955243	31955255	+	1	NA	Intergenic	Intergenic	-95039	NM_029587	76382	Mm.23510	NM_029587	ENSMUSG00000029766	1700012A03Rik	AI429084	RIKEN cDNA 1700012A03 gene	protein-coding
mm_67957.1	chr7	100514764	100514785	-	1	NA	promoter-TSS (NM_153527)	promoter-TSS (NM_153527)	41	NM_153527	69387	Mm.278554	NM_153527	ENSMUSG00000030708	Dnajb13	1700014P03Rik|Tsarg	DnaJ heat shock protein family (Hsp40) member B13	protein-coding
mm_23738.1	chr3	69156797	69156838	+	1	NA	non-coding (NR_126533, exon 3 of 3)	non-coding (NR_126533, exon 3 of 3)	25584	NR_126533	381452	Mm.331067	NM_001243000	ENSMUSG00000094763	Gm1647	-	predicted gene 1647	ncRNA
mm_18124.1	chr2	44997391	44997411	-	1	NA	exon (NM_015753, exon 8 of 10)	exon (NM_015753, exon 8 of 10)	25776	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_121672.1	chr14	12467060	12467081	-	1	NA	exon (NM_001042617, exon 21 of 31)	exon (NM_001042617, exon 21 of 31)	-121205	NM_080433	54713	Mm.34644	NM_080433	ENSMUSG00000021743	Fezf2	AI451466|AI852056|Fez|Fezl|Zfp312	Fez family zinc finger 2	protein-coding
mm_162420.1	chr1	91456406	91456409	-	1	NA	intron (NM_011066, intron 1 of 22)	intron (NM_011066, intron 1 of 22)	2921	NM_011066	18627	Mm.482463	NM_011066	ENSMUSG00000055866	Per2	mKIAA0347|mPer2	period circadian clock 2	protein-coding
mm_115102.1	chr13	102760241	102760272	+	1	NA	promoter-TSS (NR_130171)	promoter-TSS (NR_130171)	1	NR_130171	76624	Mm.426384	NR_130171	ENSMUSG00000091906	1700099I09Rik	-	RIKEN cDNA 1700099I09 gene	ncRNA
mm_35250.1	chr4	19877747	19877757	-	1	NA	3' UTR (NM_175406, exon 8 of 8)	3' UTR (NM_175406, exon 8 of 8)	44814	NM_175406	242341	Mm.19298	NM_175406	ENSMUSG00000028238	Atp6v0d2	1620401A02Rik|AI324824|V-ATPase	ATPase, H+ transporting, lysosomal V0 subunit D2	protein-coding
mm_66895.1	chr7	59651673	59651679	-	1	NA	intron (NR_015351, intron 5 of 5)	RMER10A|LTR|ERVL	24403	NR_002895	64243	Mm.423722	NR_002895	ENSMUSG00000096019	Snord116	MBII-85|Pwcr1	small nucleolar RNA, C/D box 116	snoRNA
mm_16012.1	chr2	167395999	167396003	+	1	NA	Intergenic	RMER17C|LTR|ERVK	-25709	NM_148929	77031	Mm.278924	NM_148929	ENSMUSG00000039463	Slc9a8	1200006P13Rik|6430709P13Rik|AI182282|NHE-8|NHE8	solute carrier family 9 (sodium/hydrogen exchanger), member 8	protein-coding
mm_92224.1	chr10	68279164	68279178	-	1	NA	promoter-TSS (NM_023598)	promoter-TSS (NM_023598)	-445	NM_023598	71371	Mm.440357	NM_023598	ENSMUSG00000019947	Arid5b	4930580B11|5430435G07Rik|AI467247|Desrt|Mrf2|Mrf2alpha|Mrf2beta	AT rich interactive domain 5B (MRF1-like)	protein-coding
mm_4685.1	chr1	180598241	180598254	+	1	NA	exon (NM_007415, exon 19 of 23)	exon (NM_007415, exon 19 of 23)	11046	NR_105869	102466761		NR_105869	ENSMUSG00000098926	Mir6904	Gm27426|mmu-mir-6904	microRNA 6904	ncRNA
mm_59953.1	chr7	30427099	30427110	+	1	NA	exon (NM_172142, exon 9 of 11)	exon (NM_172142, exon 9 of 11)	3800	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_152862.1	chr19	24224893	24224909	-	1	NA	5' UTR (NM_011597, exon 1 of 23)	5' UTR (NM_011597, exon 1 of 23)	125	NM_011597	21873	Mm.104744	NM_011597	ENSMUSG00000024812	Tjp2	ZO-2	tight junction protein 2	protein-coding
mm_163453.1	chr12	89852342	89852343	+	1	NA	intron (NM_001252074, intron 1 of 6)	intron (NM_001252074, intron 1 of 6)	39859	NM_001252074	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding
mm_161590.1	chr16	33596564	33596564	+	1	NA	intron (NM_001083902, intron 5 of 11)	intron (NM_001083902, intron 5 of 11)	77969	NM_001083902	171286	Mm.35253	NM_134251	ENSMUSG00000035506	Slc12a8	CCC9|E330020C02Rik	solute carrier family 12 (potassium/chloride transporters), member 8	protein-coding
mm_58554.1	chr7	4740584	4740594	+	1	NA	intron (NM_146177, intron 1 of 8)	intron (NM_146177, intron 1 of 8)	462	NM_001115018	232811	Mm.247844	NM_146177	ENSMUSG00000059851	Kmt5c	BC024816|Suv4-20h2|Suv420h2	lysine methyltransferase 5C	protein-coding
mm_145228.1	chr18	50128201	50128205	+	1	NA	promoter-TSS (NM_008292)	promoter-TSS (NM_008292)	2	NM_008292	15488	Mm.277857	NM_008292	ENSMUSG00000024507	Hsd17b4	17-beta-HSD|17[b]-HSD|DBP|MFE-2|MFP2|MPF-2|Mfp-2|perMFE-2	hydroxysteroid (17-beta) dehydrogenase 4	protein-coding
mm_169398.1	chr14	46882937	46882937	+	1	NA	promoter-TSS (NM_028966)	promoter-TSS (NM_028966)	-28	NM_028966	74480	Mm.214454	NM_028966	ENSMUSG00000021838	Samd4	1700024G08Rik|1700111L17Rik|4933436G17Rik|Samd4a|Smaug|Smaug1|sunk	sterile alpha motif domain containing 4	protein-coding
mm_56806.1	chr6	116657489	116657514	-	1	NA	intron (NM_178045, intron 3 of 10)	intron (NM_178045, intron 3 of 10)	6817	NM_001166580	213393	Mm.38231	NM_145980	ENSMUSG00000048489	8430408G22Rik	Depp|Fseg	RIKEN cDNA 8430408G22 gene	protein-coding
mm_150398.1	chr19	36554662	36554688	+	1	NA	promoter-TSS (NM_001163471)	promoter-TSS (NM_001163471)	36	NM_172637	226098	Mm.61107	NM_172637	ENSMUSG00000041180	Hectd2	4921524L07|A630025O09Rik|AW212605	HECT domain containing 2	protein-coding
mm_125059.1	chr15	25933547	25933580	+	1	NA	promoter-TSS (NM_001277318)	promoter-TSS (NM_001277318)	11	NM_001277318	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_140704.1	chr17	14680007	14680015	-	1	NA	exon (NM_011581, exon 11 of 22)	exon (NM_011581, exon 11 of 22)	14251	NM_011581	21826	Mm.26688	NM_011581	ENSMUSG00000023885	Thbs2	TSP2|Thbs-2	thrombospondin 2	protein-coding
mm_70086.1	chr7	142654391	142654407	-	1	NA	TTS (NR_030251)	TTS (NR_030251)	597	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_122328.1	chr14	37098349	37098363	-	1	NA	promoter-TSS (NM_130878)	promoter-TSS (NM_130878)	-45	NM_130878	170677	Mm.156506	NM_130878	ENSMUSG00000021803	Cdhr1	Pcdh21|Prcad|mKIAA1775	cadherin-related family member 1	protein-coding
mm_40340.1	chr5	44226781	44226818	+	1	NA	promoter-TSS (NM_173764)	promoter-TSS (NM_173764)	-193	NM_173764	231225	Mm.30688	NM_173764	ENSMUSG00000046985	Tapt1	4932414K18Rik	transmembrane anterior posterior transformation 1	protein-coding
mm_7860.1	chr1	132542858	132542878	-	1	NA	promoter-TSS (NM_177129)	promoter-TSS (NM_177129)	72	NM_177129	21367	Mm.260861	NM_011531	ENSMUSG00000053024	Cntn2	D130012K04Rik|TAG-1|Tax	contactin 2	protein-coding
mm_37006.1	chr4	111880644	111880677	-	1	NA	intron (NM_145551, intron 13 of 14)	intron (NM_145551, intron 13 of 14)	22136	NM_145551	230612	Mm.26630	NM_145551	ENSMUSG00000028544	Slc5a9	AI159731|SGLT4	solute carrier family 5 (sodium/glucose cotransporter), member 9	protein-coding
mm_26621.1	chr3	152415778	152415781	+	1	NA	intron (NM_001287139, intron 1 of 13)	intron (NM_001287139, intron 1 of 13)	19095	NM_001287139	108946	Mm.379292	NM_198416	ENSMUSG00000039068	Zzz3	3110065C23Rik|6430567E01Rik|AA408566|AI481057|AW556059|R75514	zinc finger, ZZ domain containing 3	protein-coding
mm_45857.1	chr5	87786656	87786689	-	1	NA	exon (NM_001304768, exon 11 of 13)	exon (NM_001304768, exon 11 of 13)	12222	NM_007785	12993	Mm.4908	NM_007785	ENSMUSG00000061937	Csn1s2a	Csng|PP22	casein alpha s2-like A	protein-coding
mm_100255.1	chr11	117331697	117331712	+	1	NA	promoter-TSS (NM_017380)	promoter-TSS (NM_017380)	-11	NM_017380	53860	Mm.38450	NM_017380	ENSMUSG00000059248	Sept9	MSF1|Msf|PNUTL4|Sint1	septin 9	protein-coding
mm_105542.1	chr11	106314495	106314577	-	1	NA	promoter-TSS (NM_008339)	promoter-TSS (NM_008339)	26	NM_008339	15985	Mm.2987	NM_008339	ENSMUSG00000040592	Cd79b	B29|Ig-beta|Igb|Igbeta	CD79B antigen	protein-coding
mm_29446.1	chr3	110143938	110143948	-	1	NA	promoter-TSS (NM_001163350)	promoter-TSS (NM_001163350)	-471	NM_030699	80883	Mm.39262	NM_030699	ENSMUSG00000059857	Ntng1	A930010C08Rik|AI853992|Lmnt1	netrin G1	protein-coding
mm_16030.1	chr2	167590739	167590750	+	1	NA	Intergenic	Intergenic	41261	NM_001311146	66589	Mm.278783	NM_023230	ENSMUSG00000078923	Ube2v1	0610011J09Rik|AI256840|CROC-1|CROC1|D7Bwg1382e|UEV-1	ubiquitin-conjugating enzyme E2 variant 1	protein-coding
mm_137439.1	chr17	26508698	26508731	+	1	NA	promoter-TSS (NM_013642)	promoter-TSS (NM_013642)	-242	NM_013642	19252	Mm.239041	NM_013642	ENSMUSG00000024190	Dusp1	3CH134|MKP1|Ptpn16|U19515|erp|mkp-1	dual specificity phosphatase 1	protein-coding
mm_72718.1	chr8	85026852	85026899	+	1	NA	promoter-TSS (NM_026760)	promoter-TSS (NM_026760)	42	NM_026760	68544	Mm.196005	NM_026760	ENSMUSG00000041203	2310036O22Rik	1110002H14Rik|AI854688	RIKEN cDNA 2310036O22 gene	protein-coding
mm_41402.1	chr5	90786391	90786410	+	1	NA	exon (NM_203320, exon 2 of 4)	exon (NM_203320, exon 2 of 4)	299	NM_203320	330122	Mm.244289	NM_203320	ENSMUSG00000029379	Cxcl3	Dcip1|Gm1960	chemokine (C-X-C motif) ligand 3	protein-coding
mm_130850.1	chr15	101940428	101940434	-	1	NA	promoter-TSS (NM_146063)	promoter-TSS (NM_146063)	-107	NM_146063	223917	Mm.162744	NM_146063	ENSMUSG00000061397	Krt79	BC031593	keratin 79	protein-coding
mm_156987.1	chrX	7412735	7412741	-	1	NA	intron (NR_027924, intron 1 of 1)	intron (NR_027924, intron 1 of 1)	8309	NR_027925	68355	Mm.45111	NR_027924		2010204K13Rik	0610010M13Rik|Cip7	RIKEN cDNA 2010204K13 gene	ncRNA
mm_64502.1	chr7	143476111	143476122	+	1	NA	5' UTR (NM_008767, exon 2 of 11)	5' UTR (NM_008767, exon 2 of 11)	1000	NM_001042760	18400	Mm.271740	NM_008767	ENSMUSG00000000154	Slc22a18	AW260131|BWR1A|BWSCR1A|HET|ITM|Impt1|Orctl2|Slc22a1l|TSSC5|p45-BWR1A	solute carrier family 22 (organic cation transporter), member 18	protein-coding
mm_43245.1	chr5	130144873	130144937	+	1	NA	promoter-TSS (NM_172509)	promoter-TSS (NM_172509)	17	NM_172509	212919	Mm.55812	NM_172509	ENSMUSG00000034110	Kctd7	4932409E18|9430010P06Rik	potassium channel tetramerisation domain containing 7	protein-coding
mm_18213.1	chr2	49330485	49330487	-	1	NA	Intergenic	RMER17D|LTR|ERVK	84586	NM_001290656	109241	Mm.440436	NM_029924	ENSMUSG00000036792	Mbd5	9430004D19Rik|AA536666|AI426407|C030040A15Rik|Gm1630|OTTMUSG00000012483	methyl-CpG binding domain protein 5	protein-coding
mm_140090.1	chr17	75465573	75465590	+	1	NA	promoter-TSS (NM_207246)	promoter-TSS (NM_207246)	43	NM_207246	240168	Mm.329203	NM_207246	ENSMUSG00000071042	Rasgrp3	BC066069|Gm327	RAS, guanyl releasing protein 3	protein-coding
mm_165525.1	chr2	174774821	174774829	+	1	NA	intron (NM_007903, intron 2 of 4)	intron (NM_007903, intron 2 of 4)	14206	NM_007903	13616	Mm.9478	NM_007903	ENSMUSG00000027524	Edn3	ET-3|PPET3|ls|tmgc48	endothelin 3	protein-coding
mm_140900.1	chr17	24098090	24098094	-	1	NA	intron (NM_001080773, intron 7 of 13)	intron (NM_001080773, intron 7 of 13)	-24607	NM_027008	69259	Mm.28171	NM_027008	ENSMUSG00000016946	Kctd5	2610030N08Rik|mKIAA0176	potassium channel tetramerisation domain containing 5	protein-coding
mm_62579.1	chr7	105226186	105226203	+	1	NA	Intergenic	Intergenic	-21853	NM_147069	259072	Mm.377823	NM_147069	ENSMUSG00000048425	Olfr686	MOR35-1	olfactory receptor 686	protein-coding
mm_146507.1	chr18	3337310	3337328	-	1	NA	intron (NR_033457, intron 1 of 1)	CpG	270	NM_001110851	12916	Mm.5244	NM_013498	ENSMUSG00000063889	Crem	ICER|ICERI	cAMP responsive element modulator	protein-coding
mm_33992.1	chr4	137901898	137901902	+	1	NA	intron (NM_199307, intron 1 of 19)	L1ME2|LINE|L1	39663	NM_199307	230857	Mm.401062	NM_199307	ENSMUSG00000057530	Ece1	AW322500|ECE-1|ECE-1a|ECE-1b|ECE-1d	endothelin converting enzyme 1	protein-coding
mm_169405.1	chr14	50856233	50856252	+	1	NA	intron (NM_009351, intron 9 of 54)	RLTR9D|LTR|ERVK	14312	NM_009351	21745	Mm.318736	NM_009351	ENSMUSG00000006281	Tep1	Tp1	telomerase associated protein 1	protein-coding
mm_39021.1	chr4	152131690	152131709	-	1	NA	intron (NM_207688, intron 3 of 10)	CpG-10714	-2774	NM_019585	56226	Mm.264215	NM_019585	ENSMUSG00000028943	Espn	je	espin	protein-coding
mm_75880.1	chr8	70776651	70776716	-	1	NA	promoter-TSS (NR_029440)	promoter-TSS (NR_029440)	29	NM_008841	18709	Mm.12945	NM_008841	ENSMUSG00000031834	Pik3r2	p85beta	phosphatidylinositol 3-kinase, regulatory subunit, polypeptide 2 (p85 beta)	protein-coding
mm_122758.1	chr14	54225286	54225299	-	1	NA	Intergenic	Intergenic	28637	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_39103.1	chr4	154921560	154921601	-	1	NA	TTS (NM_178931)	TTS (NM_178931)	6497	NM_178931	230979	Mm.215147	NM_178931	ENSMUSG00000042333	Tnfrsf14	Atar|HveA|Hvem|Tnfrs14	tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)	protein-coding
mm_18759.1	chr2	73452667	73452712	-	1	NA	intron (NM_153138, intron 1 of 7)	intron (NM_153138, intron 1 of 7)	1200	NM_001289722	215280	Mm.223504	NM_153138	ENSMUSG00000075284	Wipf1	AI115543|D2Ertd120e|WIP|Waspip	WAS/WASL interacting protein family, member 1	protein-coding
mm_6976.1	chr1	86352085	86352088	-	1	NA	promoter-TSS (NR_106184)	promoter-TSS (NR_106184)	41	NR_106184	102465895		NR_106184	ENSMUSG00000104627	Gm24148	Mir3535|mir-3535|mmu-mir-3535	predicted gene, 24148	ncRNA
mm_88699.1	chr10	80142522	80142526	+	1	NA	exon (NM_025313, exon 1 of 4)	exon (NM_025313, exon 1 of 4)	209	NM_025313	66043	Mm.278560	NM_025313	ENSMUSG00000003072	Atp5d	0610008F14Rik|1500000I11Rik|AA960090|AI876556|AU020773|C85518	ATP synthase, H+ transporting, mitochondrial F1 complex, delta subunit	protein-coding
mm_110918.1	chr12	76255073	76255110	-	1	NA	promoter-TSS (NM_138745)	promoter-TSS (NM_138745)	-141	NM_138745	108156	Mm.29584	NM_138745	ENSMUSG00000021048	Mthfd1	Dcs|E430024A07Rik|Mthfd	methylenetetrahydrofolate dehydrogenase (NADP+ dependent), methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthase	protein-coding
mm_171300.1	chr3	93555104	93555106	+	1	NA	promoter-TSS (NM_009112)	promoter-TSS (NM_009112)	-12	NM_009112	20194	Mm.1	NM_009112	ENSMUSG00000041959	S100a10	42C|AA409961|AL024248|CAL12|CLP11|Cal1l|p10|p11	S100 calcium binding protein A10 (calpactin)	protein-coding
mm_28813.1	chr3	96259775	96259789	-	1	NA	Intergenic	Intergenic	3535	NM_033596	97122	Mm.227295	NM_033596	ENSMUSG00000091405	Hist2h4	H4|X04652	histone cluster 2, H4	protein-coding
mm_136653.1	chr17	5975706	5975732	+	1	NA	5' UTR (NM_001113351, exon 1 of 25)	5' UTR (NM_001113351, exon 1 of 25)	133	NM_011523	20975	Mm.236068	NM_011523	ENSMUSG00000023805	Synj2	AI481647|SJ2|mKIAA0348	synaptojanin 2	protein-coding
mm_25542.1	chr3	115801810	115801823	+	1	NA	Intergenic	ID4_|SINE|ID	86243	NR_027894	68161	Mm.392043	NR_015487	ENSMUSG00000054426	A930005H10Rik	-	RIKEN cDNA A930005H10 gene	ncRNA
mm_163415.1	chr12	79130750	79130789	+	1	NA	promoter-TSS (NM_009705)	promoter-TSS (NM_009705)	-19	NM_009705	11847	Mm.3506	NM_009705	ENSMUSG00000021125	Arg2	AII|AU022422	arginase type II	protein-coding
mm_85819.1	chr9	110408224	110408234	-	1	NA	promoter-TSS (NM_001081043)	promoter-TSS (NM_001081043)	-19	NM_001081043	104831	Mm.335477	NM_001081043	ENSMUSG00000036057	Ptpn23	AI462446|PTP-TD14	protein tyrosine phosphatase, non-receptor type 23	protein-coding
mm_20025.1	chr2	119456425	119456437	-	1	NA	exon (NM_026574, exon 4 of 36)	exon (NM_026574, exon 4 of 36)	21198	NM_026574	68142	Mm.330496	NM_026574	ENSMUSG00000034154	Ino80	2310079N15Rik|4632409L19Rik|Inoc1	INO80 complex subunit	protein-coding
mm_138865.1	chr17	43016537	43016591	+	1	NA	promoter-TSS (NM_178589)	promoter-TSS (NM_178589)	9	NM_178589	94185	Mm.200792	NM_178589	ENSMUSG00000023915	Tnfrsf21	AA959878|DR6|R74815|TR7	tumor necrosis factor receptor superfamily, member 21	protein-coding
mm_96326.1	chr11	64438527	64438531	+	1	NA	intron (NM_178870, intron 1 of 1)	intron (NM_178870, intron 1 of 1)	-1855	NR_028445	654805	Mm.436132	NR_028445		F930015N05Rik	-	RIKEN cDNA F930015N05 gene	ncRNA
mm_31171.1	chr4	43454163	43454192	+	1	NA	intron (NM_007654, intron 2 of 8)	intron (NM_007654, intron 2 of 8)	449	NM_001110320	12517	Mm.188157	NM_007654	ENSMUSG00000028459	Cd72	CD72c|Ly-19|Ly-32|Ly-m19|Lyb-2	CD72 antigen	protein-coding
mm_136667.1	chr17	6106609	6106617	+	1	NA	promoter-TSS (NM_001103181)	promoter-TSS (NM_001103181)	-217	NM_001103181	68842	Mm.449307	NM_054040	ENSMUSG00000034377	Tulp4	1110057P05Rik|2210038L17Rik|Tusp	tubby like protein 4	protein-coding
mm_54997.1	chr6	48833966	48833995	-	1	NA	non-coding (NR_104575, exon 7 of 7)	non-coding (NR_104575, exon 7 of 7)	7008	NM_023056	65963	Mm.28385	NM_023056	ENSMUSG00000029810	Tmem176b	1810009M01Rik|Clast1|Lr8	transmembrane protein 176B	protein-coding
mm_155720.1	chrX	96115426	96115444	+	1	NA	intron (NM_010833, intron 1 of 12)	ORR1B2|LTR|ERVL-MaLR	19390	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_43108.1	chr5	124530688	124530741	+	1	NA	exon (NM_021430, exon 1 of 7)	exon (NM_021430, exon 1 of 7)	677	NM_021430	75695	Mm.41180	NM_021430	ENSMUSG00000029392	Rilpl1	2900002H16Rik|6330559I19Rik|GOSPEL	Rab interacting lysosomal protein-like 1	protein-coding
mm_18030.1	chr2	38643906	38643927	-	1	NA	promoter-TSS (NM_011187)	promoter-TSS (NM_011187)	-10	NM_011187	19177	Mm.389251	NM_011187	ENSMUSG00000026750	Psmb7	AU020723|MC14	proteasome (prosome, macropain) subunit, beta type 7	protein-coding
mm_17721.1	chr2	32388223	32388254	-	1	NA	promoter-TSS (NM_008491)	promoter-TSS (NM_008491)	-499	NM_008491	16819	Mm.9537	NM_008491	ENSMUSG00000026822	Lcn2	24p3|AW212229|NRL|Sip24	lipocalin 2	protein-coding
mm_130496.1	chr15	98807963	98807976	-	1	NA	promoter-TSS (NM_001013741)	promoter-TSS (NM_001013741)	-44	NM_001013741	13199	Mm.390810	NM_001013741	ENSMUSG00000059213	Ddn	Gm748	dendrin	protein-coding
mm_19737.1	chr2	104676645	104676653	-	1	NA	Intergenic	B1_Mur4|SINE|Alu	35513	NM_177190	320554	Mm.249065	NM_177190	ENSMUSG00000027175	Tcp11l1	C130096D04Rik	t-complex 11 like 1	protein-coding
mm_128479.1	chr15	50889958	50889968	-	1	NA	promoter-TSS (NR_035444)	promoter-TSS (NR_035444)	78	NM_032000	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_131126.1	chr16	5884922	5884962	+	1	NA	5' UTR (NM_021477, exon 1 of 17)	5' UTR (NM_021477, exon 1 of 17)	149	NM_021477	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_34703.1	chr4	152096737	152096782	+	1	NA	promoter-TSS (NM_001285999)	promoter-TSS (NM_001285999)	40	NM_001285999	269608	Mm.332102	NM_001004156	ENSMUSG00000039713	Plekhg5	BC023181|Syx	pleckstrin homology domain containing, family G (with RhoGef domain) member 5	protein-coding
mm_36771.1	chr4	102569152	102569158	-	1	NA	promoter-TSS (NM_001177980)	promoter-TSS (NM_001177980)	-905	NM_001177980	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_13382.1	chr2	103945156	103945193	+	1	NA	Intergenic	Intergenic	-12821	NM_001142337	16909	Mm.29266	NM_008505	ENSMUSG00000032698	Lmo2	Rbtn-2|Rbtn2|Rhom-2|Ttg2	LIM domain only 2	protein-coding
mm_153865.1	chr19	46670712	46670721	-	1	NA	exon (NM_007809, exon 3 of 8)	exon (NM_007809, exon 3 of 8)	2284	NM_007809	13074	Mm.1262	NM_007809	ENSMUSG00000003555	Cyp17a1	Cyp17|p450c17	cytochrome P450, family 17, subfamily a, polypeptide 1	protein-coding
mm_87250.1	chr10	41450364	41450421	+	1	NA	promoter-TSS (NM_001277230)	promoter-TSS (NM_001277230)	34	NR_102360	268294	Mm.258475	NM_153398	ENSMUSG00000019826	Zbtb24	BC055367|Bif1|Bsg1|ZNF450	zinc finger and BTB domain containing 24	protein-coding
mm_65729.1	chr7	28381293	28381297	-	1	NA	Intergenic	Intergenic	-2067	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_130344.1	chr15	97731533	97731546	-	1	NA	promoter-TSS (NM_001168693)	promoter-TSS (NM_001168693)	-134	NM_001168693	19011	Mm.1001	NM_008902	ENSMUSG00000022468	Endou	Pp11r|Tcl-30	endonuclease, polyU-specific	protein-coding
mm_172797.1	chr9	113758695	113758704	+	1	NA	intron (NM_001286599, intron 1 of 10)	RMER13A1|LTR|ERVK	17226	NM_001114347	76499	Mm.222272	NM_029633	ENSMUSG00000033392	Clasp2	1500004F14Rik|8030404L10Rik|C77448|CLASP2beta|mKIAA0627	CLIP associating protein 2	protein-coding
mm_42728.1	chr5	120621312	120621318	+	1	NA	intron (NM_028041, intron 10 of 19)	intron (NM_028041, intron 10 of 19)	8185	NM_028041	71990	Mm.24495	NM_028041	ENSMUSG00000029599	Ddx54	2410015A15Rik|AI414901|DP97	DEAD (Asp-Glu-Ala-Asp) box polypeptide 54	protein-coding
mm_73519.1	chr8	107457797	107457805	+	1	NA	intron (NM_025830, intron 3 of 23)	intron (NM_025830, intron 3 of 23)	21403	NM_025830	66894	Mm.390058	NM_025830	ENSMUSG00000031930	Wwp2	1300010O06Rik|AA690238|AIP2|AW554328	WW domain containing E3 ubiquitin protein ligase 2	protein-coding
mm_173252.1	chrX	94541964	94541964	-	1	NA	5' UTR (NM_019791, exon 1 of 13)	5' UTR (NM_019791, exon 1 of 13)	110	NM_019791	94275	Mm.27578	NM_019791	ENSMUSG00000025151	Maged1	2810433C11Rik|5430405L04Rik|DXBwg1492e|Dlixin|Dlxin-1|Dlxin1|MAGE-D1|NRAGE|mFLJ00163	melanoma antigen, family D, 1	protein-coding
mm_13471.1	chr2	105682684	105682687	+	1	NA	intron (NM_001310146, intron 1 of 9)	intron (NM_001310146, intron 1 of 9)	222	NM_001310145	18508	Mm.3608	NM_013627	ENSMUSG00000027168	Pax6	1500038E17Rik|AEY11|Dey|Gsfaey11|Pax-6|Sey	paired box 6	protein-coding
mm_153372.1	chr19	40305433	40305434	-	1	NA	intron (NM_001034963, intron 20 of 22)	intron (NM_001034963, intron 20 of 22)	-33817	NM_016861	54132	Mm.5567	NM_016861	ENSMUSG00000055044	Pdlim1	CLP36|Clim1|mClim1	PDZ and LIM domain 1 (elfin)	protein-coding
mm_5071.1	chr1	3319505	3319507	-	1	NA	intron (NM_001011874, intron 2 of 2)	intron (NM_001011874, intron 2 of 2)	351992	NM_001011874	497097	Mm.454496	NM_001011874	ENSMUSG00000051951	Xkr4	AY534250|Gm210|XRG4|mKIAA1889	X-linked Kx blood group related 4	protein-coding
mm_37824.1	chr4	131929759	131929784	-	1	NA	exon (NM_001128607, exon 15 of 18)	exon (NM_001128607, exon 15 of 18)	8000	NM_001201367	623230	Mm.421179	NM_001201367	ENSMUSG00000070720	Tmem200b	EG623230	transmembrane protein 200B	protein-coding
mm_104367.1	chr11	94351347	94351350	-	1	NA	intron (NM_029600, intron 28 of 30)	intron (NM_029600, intron 28 of 30)	23347	NM_146024	71452	Mm.141054	NM_027799	ENSMUSG00000020864	Ankrd40	1110011C06Rik|5530600A18Rik|Gcap15	ankyrin repeat domain 40	protein-coding
mm_133698.1	chr16	92824632	92824639	+	1	NA	intron (NM_001111022, intron 2 of 6)	intron (NM_001111022, intron 2 of 6)	1439	NM_001111021	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_47429.1	chr5	123174398	123174413	-	1	NA	exon (NM_008277, exon 12 of 14)	exon (NM_008277, exon 12 of 14)	8281	NM_008277	15445	Mm.439709	NM_008277	ENSMUSG00000029445	Hpd	Fla|Flp|Hppd|Laf	4-hydroxyphenylpyruvic acid dioxygenase	protein-coding
mm_3364.1	chr1	138273771	138273781	+	1	NA	promoter-TSS (NM_177397)	promoter-TSS (NM_177397)	38	NM_177397	338375	Mm.114424	NM_177397	ENSMUSG00000026394	Atp6v1g3	-	ATPase, H+ transporting, lysosomal V1 subunit G3	protein-coding
mm_131446.1	chr16	16302956	16302987	+	1	NA	promoter-TSS (NM_198246)	promoter-TSS (NM_198246)	6	NM_198246	70120	Mm.37486	NM_198246	ENSMUSG00000022792	Yars2	2210023C10Rik|tyrRS	tyrosyl-tRNA synthetase 2 (mitochondrial)	protein-coding
mm_140922.1	chr17	24209378	24209416	-	1	NA	promoter-TSS (NM_010947)	promoter-TSS (NM_010947)	-10	NM_010947	18209	Mm.259542	NM_010947	ENSMUSG00000036473	Ntn3	Ntn2l	netrin 3	protein-coding
mm_78043.1	chr9	14500626	14500651	+	1	NA	promoter-TSS (NM_023153)	promoter-TSS (NM_023153)	19	NM_023153	66070	Mm.245938	NM_023153	ENSMUSG00000004096	Cwc15	0610040D20Rik|2900052N06Rik|Ed1|c11orf5|mED1	CWC15 spliceosome-associated protein	protein-coding
mm_159944.1	chr6	83794962	83794962	+	1	NA	promoter-TSS (NM_001164187)	promoter-TSS (NM_001164187)	-38	NM_001347315	56174	Mm.190650	NM_019542	ENSMUSG00000034744	Nagk	Gnk	N-acetylglucosamine kinase	protein-coding
mm_134176.1	chr16	10954776	10954782	-	1	NA	Intergenic	Intergenic	38342	NM_019980	56722	Mm.294753	NM_019980	ENSMUSG00000022500	Litaf	3222402J11Rik|C85531|N4WBP3|TBX1	LPS-induced TN factor	protein-coding
mm_139465.1	chr17	55959126	55959140	+	1	NA	promoter-TSS (NM_028381)	promoter-TSS (NM_028381)	-54	NM_028381	72886	Mm.22796	NM_028381	ENSMUSG00000003208	Ccdc94	2900016D05Rik|AI413813	coiled-coil domain containing 94	protein-coding
mm_109131.1	chr12	105837991	105838007	+	1	NA	3' UTR (NM_001347440, exon 21 of 21)	3' UTR (NM_001347440, exon 21 of 21)	53302	NM_001347440	18789	Mm.255877	NM_011112	ENSMUSG00000021111	Papola	Pap|PapIII|Plap	poly (A) polymerase alpha	protein-coding
mm_81211.1	chr9	107580737	107580744	+	1	NA	promoter-TSS (NM_178020)	promoter-TSS (NM_178020)	71	NM_019750	56441	Mm.10305	NM_019750	ENSMUSG00000079334	Nat6	AI225910|Fus2	N-acetyltransferase 6	protein-coding
mm_123296.1	chr14	61614874	61614877	-	1	NA	intron (NR_028264, intron 5 of 6)	AT_rich|Low_complexity|Low_complexity	7418	NM_001039105	328424	Mm.224464	NM_206974	ENSMUSG00000046168	Kcnrg	Clld4|E030012H22Rik|Gm745	potassium channel regulator	protein-coding
mm_298.1	chr1	23288778	23288780	+	1	NA	Intergenic	Intergenic	-2922	NR_029717	723964		NR_029717	ENSMUSG00000065567	Mir30c-2	Mirn30c-2|mir-30c-2	microRNA 30c-2	ncRNA
mm_6552.1	chr1	75133894	75133913	-	1	NA	promoter-TSS (NM_194333)	promoter-TSS (NM_194333)	-13	NM_194333	22626	Mm.68157	NM_194333	ENSMUSG00000026205	Slc23a3	SVCT3|Yspl1	solute carrier family 23 (nucleobase transporters), member 3	protein-coding
mm_160514.1	chr9	21835546	21835546	+	1	NA	promoter-TSS (NM_001080940)	promoter-TSS (NM_001080940)	36	NM_001080940	624219	Mm.440264	NM_001080940	ENSMUSG00000047822	Angptl8	EG624219|Gm6484|Rifl	angiopoietin-like 8	protein-coding
mm_43951.1	chr5	145167208	145167259	+	1	NA	promoter-TSS (NM_178576)	promoter-TSS (NM_178576)	20	NM_001291248	54188	Mm.196884	NM_178576	ENSMUSG00000029625	Cpsf4	30kDa|C79664	cleavage and polyadenylation specific factor 4	protein-coding
mm_119800.1	chr14	54211392	54211404	+	1	NA	Intergenic	Intergenic	42531	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_171942.1	chr5	70210212	70210215	-	1	NA	Intergenic	L1Md_T|LINE|L1	-617909	NM_001347363	67980	Mm.33830	NM_027681	ENSMUSG00000029209	Gnpda2	4921523I18Rik|4933412A11Rik|BB189630|GNPDA|Gnp2|Sb52|mKIAA4008	glucosamine-6-phosphate deaminase 2	protein-coding
mm_58443.1	chr7	3298876	3298880	+	1	NA	3' UTR (NM_016969, exon 3 of 3)	3' UTR (NM_016969, exon 3 of 3)	-4654	NM_001291434	18752	Mm.7980	NM_011102	ENSMUSG00000078816	Prkcg	PKCgamma|Pkcc|Prkcc	protein kinase C, gamma	protein-coding
mm_21492.1	chr2	163397843	163397856	-	1	NA	5' UTR (NM_021566, exon 1 of 6)	5' UTR (NM_021566, exon 1 of 6)	124	NM_021566	59091	Mm.34459	NM_021566	ENSMUSG00000017817	Jph2	1110002E14Rik|JP-2|Jp2	junctophilin 2	protein-coding
mm_109634.1	chr12	112767877	112767892	+	1	NA	exon (NM_178911, exon 9 of 11)	exon (NM_178911, exon 9 of 11)	7229	NM_178911	104759	Mm.203915	NM_178911	ENSMUSG00000052160	Pld4	AI132321|thss	phospholipase D family, member 4	protein-coding
mm_123319.1	chr14	62531074	62531086	-	1	NA	Intergenic	Intergenic	-24657	NM_001243857	629059	Mm.291864	NM_001243857	ENSMUSG00000035184	Fam124a	EG629059	family with sequence similarity 124, member A	protein-coding
mm_76020.1	chr8	75034368	75034417	-	1	NA	intron (NM_001136259, intron 1 of 15)	MIR|SINE|MIR	706	NM_011622	21968	Mm.1967	NM_011622	ENSMUSG00000042870	Tom1	-	target of myb1 trafficking protein	protein-coding
mm_10185.1	chr2	4881799	4881836	+	1	NA	5' UTR (NM_175400, exon 1 of 9)	5' UTR (NM_175400, exon 1 of 9)	253	NM_175400	109079	Mm.34329	NM_175400	ENSMUSG00000026662	Sephs1	1110046B24Rik|AA589574|AI505014|AW111620|SELD|SPS|SPS1	selenophosphate synthetase 1	protein-coding
mm_56528.1	chr6	99522571	99522592	-	1	NA	Intergenic	CpG-12329	-1588	NM_001347345	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_133943.1	chr16	3908597	3908611	-	1	NA	promoter-TSS (NM_029738)	promoter-TSS (NM_029738)	85	NM_028484	73261	Mm.486226	NM_028484	ENSMUSG00000005983	1700037C18Rik	2810022L20Rik	RIKEN cDNA 1700037C18 gene	protein-coding
mm_48204.1	chr5	137597306	137597318	-	1	NA	exon (NM_030037, exon 5 of 6)	exon (NM_030037, exon 5 of 6)	3396	NM_001254762	68929	Mm.41355	NM_030037	ENSMUSG00000037221	Mospd3	1190005J19Rik|5133401H10Rik|Gtig2|R124	motile sperm domain containing 3	protein-coding
mm_140280.1	chr17	85018918	85018919	+	1	NA	intron (NM_001159497, intron 5 of 5)	intron (NM_001159497, intron 5 of 5)	-9429	NM_009205	20532	Mm.227176	NM_009205	ENSMUSG00000024131	Slc3a1	D2H|NBAT|NTAA|RBAT	solute carrier family 3, member 1	protein-coding
mm_58249.1	chr6	145048750	145048805	-	1	NA	promoter-TSS (NM_001024468)	promoter-TSS (NM_001024468)	35	NM_001024468	12035	Mm.4606	NM_007532	ENSMUSG00000030268	Bcat1	BCATc|Eca39	branched chain aminotransferase 1, cytosolic	protein-coding
mm_11208.1	chr2	29362922	29362924	+	1	NA	intron (NM_029615, intron 2 of 4)	Tigger7|DNA|TcMar-Tigger	-15591	NM_001290489	68975	Mm.330109	NM_026896	ENSMUSG00000026799	Med27	1500015J03Rik|2310042P07Rik|AA682045|Crsp8|D2Ertd434e	mediator complex subunit 27	protein-coding
mm_82929.1	chr9	35175972	35176021	-	1	NA	promoter-TSS (NM_027030)	promoter-TSS (NM_027030)	-9	NM_027030	69305	Mm.229110	NM_027030	ENSMUSG00000032040	Dcps	1700001E16Rik|AA408441	decapping enzyme, scavenger	protein-coding
mm_153066.1	chr19	32210970	32211002	-	1	NA	promoter-TSS (NM_001168526)	promoter-TSS (NM_001168526)	27	NM_001168526	208449	Mm.329810	NM_144792	ENSMUSG00000040451	Sgms1	9530058O11Rik|AI841905|C80702|Mob|Sms1|Sor1|Tmem23	sphingomyelin synthase 1	protein-coding
mm_60866.1	chr7	45918028	45918053	+	1	NA	TTS (NM_144801)	TTS (NM_144801)	2809	NM_001146346	13732	Mm.20829	NM_010129	ENSMUSG00000040212	Emp3	H-4|H4|HNMP-1|MI-35|Ymp	epithelial membrane protein 3	protein-coding
mm_167060.1	chr7	93986333	93986333	+	1	NA	Intergenic	Intergenic	906454	NM_021427	58238	Mm.113787	NM_021427	ENSMUSG00000051515	Fam181b	A830059I20Rik|AB041569	family with sequence similarity 181, member B	protein-coding
mm_38536.1	chr4	141571518	141571544	-	1	NA	Intergenic	Intergenic	25369	NR_030695	320456	Mm.32859	NM_177163		B330016D10Rik	-	RIKEN cDNA B330016D10 gene	ncRNA
mm_140447.1	chr17	88597620	88597628	+	1	NA	Intergenic	Intergenic	-28931	NM_029858	77057	Mm.482203	NM_029858	ENSMUSG00000033855	Ston1	4921524J06Rik|C86231|Salf|Sblf	stonin 1	protein-coding
mm_21837.1	chr2	165792862	165792875	-	1	NA	exon (NM_001281926, exon 20 of 23)	exon (NM_001281926, exon 20 of 23)	65305	NM_001252585	228880	Mm.227598	NM_027230	ENSMUSG00000039671	Zmynd8	1110013E22Rik|2010005I16Rik|3632413B07Rik|AI316811|AL024039|Prkcbp1|RACK7	zinc finger, MYND-type containing 8	protein-coding
mm_56314.1	chr6	92242462	92242472	-	1	NA	3' UTR (NM_009426, exon 3 of 3)	3' UTR (NM_009426, exon 3 of 3)	2183	NM_009426	22044	Mm.1363	NM_009426	ENSMUSG00000005892	Trh	Pro-TRH|Trf	thyrotropin releasing hormone	protein-coding
mm_133206.1	chr16	74620032	74620039	+	1	NA	Intergenic	Intergenic	-209123	NM_175549	268902	Mm.171736	NM_175549	ENSMUSG00000052516	Robo2	2600013A04Rik|9430089E08Rik|BB097918|D230004I22Rik|mKIAA1568	roundabout guidance receptor 2	protein-coding
mm_156732.1	chrX	159941694	159941712	+	1	NA	promoter-TSS (NM_001290664)	promoter-TSS (NM_001290664)	-990	NM_001290661	58194	Mm.286495	NM_021389	ENSMUSG00000040990	Sh3kbp1	1200007H22Rik|1700125L08Rik|5830464D22Rik|AI447724|Cin85|IN85|Ruk|Seta	SH3-domain kinase binding protein 1	protein-coding
mm_22963.1	chr3	32529533	32529543	+	1	NA	promoter-TSS (NM_024200)	promoter-TSS (NM_024200)	56	NM_024200	67414	Mm.290414	NM_024200	ENSMUSG00000027668	Mfn1	2310002F04Rik|6330416C07Rik|D3Ertd265e|HR2|mKIAA4032	mitofusin 1	protein-coding
mm_33669.1	chr4	133185663	133185725	+	1	NA	exon (NM_153423, exon 4 of 9)	exon (NM_153423, exon 4 of 9)	-9961	NR_105984	102466215		NR_105984	ENSMUSG00000099202	Mir7017	Gm27945|mmu-mir-7017	microRNA 7017	ncRNA
mm_63321.1	chr7	126941969	126941974	+	1	NA	intron (NM_172747, intron 4 of 5)	MIR|SINE|MIR	7610	NM_001347657	233879	Mm.444143	NM_001039645	ENSMUSG00000046378	Asphd1	A830007L07Rik|Gm168	aspartate beta-hydroxylase domain containing 1	protein-coding
mm_68649.1	chr7	118491810	118491868	-	1	NA	5' UTR (NM_001033380, exon 1 of 1)	5' UTR (NM_001033380, exon 1 of 1)	136	NM_001033380	319622	Mm.323386	NM_001033380	ENSMUSG00000095115	Itpripl2	C130081G24|E030018N11Rik	inositol 1,4,5-triphosphate receptor interacting protein-like 2	protein-coding
mm_145281.1	chr18	53181873	53181876	+	1	NA	intron (NM_026386, intron 1 of 14)	L1M2|LINE|L1	5509	NM_026386	67804	Mm.252171	NM_026386	ENSMUSG00000034484	Snx2	0610030A03Rik	sorting nexin 2	protein-coding
mm_143428.1	chr17	70851058	70851068	-	1	NA	5' UTR (NM_009372, exon 1 of 3)	5' UTR (NM_009372, exon 1 of 3)	147	NM_009372	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_109316.1	chr12	109561222	109561235	+	1	NA	non-coding (NR_003633, exon 5 of 5)	non-coding (NR_003633, exon 5 of 5)	-2464	NR_030427	791079		NR_030427	ENSMUSG00000076451	Mir770	Mirn770|mir-770|mmu-mir-770	microRNA 770	ncRNA
mm_148347.1	chr18	84675298	84675317	-	1	NA	intron (NM_023149, intron 5 of 11)	intron (NM_023149, intron 5 of 11)	6752	NM_001289531	66054	Mm.29646	NM_023149	ENSMUSG00000024644	Cndp2	0610010E05Rik|C76600|Cn2|Dip-2|Pep-1|Pep1	CNDP dipeptidase 2 (metallopeptidase M20 family)	protein-coding
mm_36399.1	chr4	77822918	77822919	-	1	NA	intron (NM_011211, intron 2 of 39)	intron (NM_011211, intron 2 of 39)	388977	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding
mm_128171.1	chr15	34442936	34442970	-	1	NA	intron (NM_001163485, intron 2 of 4)	CpG	272	NM_009083	19946	Mm.358632	NM_009083	ENSMUSG00000058600	Rpl30	-	ribosomal protein L30	protein-coding
mm_101255.1	chr11	20831205	20831219	-	1	NA	promoter-TSS (NM_173752)	promoter-TSS (NM_173752)	-104	NM_173752	216551	Mm.76694	NM_173752	ENSMUSG00000042363	Lgalsl	1110067D22Rik|A530071M23|Grpa|Hspc159|Lgalsla	lectin, galactoside binding-like	protein-coding
mm_5769.1	chr1	51466108	51466115	-	1	NA	Intergenic	Intergenic	12288	NM_028696	109019	Mm.196290	NM_028696	ENSMUSG00000026107	Nabp1	4930434H03Rik|4930442A21Rik|4930488J04Rik|4933440J18Rik|5830411E10Rik|AI852561|Nbp1|Obfc2a|Ssb2	nucleic acid binding protein 1	protein-coding
mm_147411.1	chr18	44828898	44828933	-	1	NA	exon (NM_001163013, exon 1 of 30)	exon (NM_001163013, exon 1 of 30)	250	NM_001163013	240255	Mm.244482	NM_001163013	ENSMUSG00000034653	Ythdc2	3010002F02Rik|BC037178	YTH domain containing 2	protein-coding
mm_30652.1	chr4	8842712	8842714	+	1	NA	intron (NM_001277149, intron 19 of 37)	intron (NM_001277149, intron 19 of 37)	152307	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_13789.1	chr2	118830023	118830027	+	1	NA	intron (NM_026412, intron 7 of 8)	AT_rich|Low_complexity|Low_complexity	16022	NM_026412	51944	Mm.252695	NM_026412	ENSMUSG00000027331	Knstrn	1700025D04Rik|C15orf23|D2Ertd750e|SKAP|Traf4af1	kinetochore-localized astrin/SPAG5 binding	protein-coding
mm_126604.1	chr15	82456337	82456348	+	1	NA	exon (NM_010006, exon 8 of 9)	exon (NM_010006, exon 8 of 9)	3965	NM_010006	13105	Mm.226708	NM_010006	ENSMUSG00000068086	Cyp2d9	Cyp2d|P450-2D	cytochrome P450, family 2, subfamily d, polypeptide 9	protein-coding
mm_65936.1	chr7	30360418	30360424	-	1	NA	exon (NM_175478, exon 2 of 3)	exon (NM_175478, exon 2 of 3)	2351	NM_175478	233067	Mm.23157	NM_175478	ENSMUSG00000036957	Lrfn3	A530045B06Rik|SALM4	leucine rich repeat and fibronectin type III domain containing 3	protein-coding
mm_114014.1	chr13	52610898	52610916	+	1	NA	exon (NM_011518, exon 2 of 14)	exon (NM_011518, exon 2 of 14)	14025	NM_011518	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_131433.1	chr16	15887449	15887461	+	1	NA	exon (NM_007679, exon 1 of 1)	exon (NM_007679, exon 1 of 1)	169	NM_007679	12609	Mm.347407	NM_007679	ENSMUSG00000071637	Cebpd	c/EBPdelta	CCAAT/enhancer binding protein (C/EBP), delta	protein-coding
mm_35154.1	chr4	12147773	12147786	-	1	NA	Intergenic	MTB-int|LTR|ERVL-MaLR	7662	NM_028226	72397	Mm.430709	NM_028226	ENSMUSG00000046667	Rbm12b1	3000004N20Rik|Rbm12b|Rbm12ba	RNA binding motif protein 12 B1	protein-coding
mm_10898.1	chr2	25272476	25272486	+	1	NA	promoter-TSS (NM_175300)	promoter-TSS (NM_175300)	15	NM_175300	99152	Mm.291624	NM_175300	ENSMUSG00000026965	Anapc2	9230107K09Rik|AL024279|Apc2|Emi4|Imi4|mKIAA1406	anaphase promoting complex subunit 2	protein-coding
mm_122419.1	chr14	41185189	41185199	-	1	NA	promoter-TSS (NM_009160)	promoter-TSS (NM_009160)	4	NM_009160	20390	Mm.1321	NM_009160	ENSMUSG00000021795	Sftpd	AI573415|SP-D|Sfpd|Sftp4	surfactant associated protein D	protein-coding
mm_75721.1	chr8	69077253	69077269	-	1	NA	5' UTR (NM_153054, exon 2 of 17)	5' UTR (NM_153054, exon 2 of 17)	-11475	NM_007509	11966	Mm.249096	NM_007509	ENSMUSG00000006273	Atp6v1b2	AI194269|AI790362|Atp6b2|HO57|R74844	ATPase, H+ transporting, lysosomal V1 subunit B2	protein-coding
mm_70978.1	chr8	27174812	27174830	+	1	NA	promoter-TSS (NM_001080813)	promoter-TSS (NM_001080813)	-175	NM_001080813	75767	Mm.205335	NM_029423	ENSMUSG00000031488	Rab11fip1	2010200K21Rik|4833414G05Rik|Rcp	RAB11 family interacting protein 1 (class I)	protein-coding
mm_41374.1	chr5	90703211	90703228	+	1	NA	Intergenic	Intergenic	-56079	NM_009141	20311	Mm.4660	NM_009141	ENSMUSG00000029371	Cxcl5	AMCF-II|Cxcl6|ENA-78|GCP-2|LIX|Scyb5|Scyb6	chemokine (C-X-C motif) ligand 5	protein-coding
mm_97580.1	chr11	78944733	78944776	+	1	NA	exon (NM_010927, exon 12 of 27)	exon (NM_010927, exon 12 of 27)	19463	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_12728.1	chr2	78868796	78868808	+	1	NA	promoter-TSS (NM_009454)	promoter-TSS (NM_009454)	-245	NM_009454	22193	Mm.1485	NM_009454	ENSMUSG00000027011	Ube2e3	Ubce4|ubcM2	ubiquitin-conjugating enzyme E2E 3	protein-coding
mm_8734.1	chr1	160206191	160206200	-	1	NA	exon (NM_009786, exon 4 of 6)	exon (NM_009786, exon 4 of 6)	6697	NM_009786	12301	Mm.10702	NM_009786	ENSMUSG00000014226	Cacybp	SIP	calcyclin binding protein	protein-coding
mm_160907.1	chr11	78115626	78115626	+	1	NA	intron (NM_001346762, intron 1 of 2)	intron (NM_001346762, intron 1 of 2)	20953	NM_145430	216971	Mm.119387	NM_145430	ENSMUSG00000037750	Fam222b	9630020I17Rik	family with sequence similarity 222, member B	protein-coding
mm_87240.1	chr10	40883621	40883634	+	1	NA	promoter-TSS (NM_027879)	promoter-TSS (NM_027879)	93	NM_031877	83767	Mm.41353	NM_031877	ENSMUSG00000019831	Wasf1	AI195380|AI838537|Scar|WAVE|WAVE-1	WAS protein family, member 1	protein-coding
mm_89546.1	chr10	94576218	94576220	+	1	NA	promoter-TSS (NM_177026)	promoter-TSS (NM_177026)	-44	NM_177026	319880	Mm.23047	NM_172051	ENSMUSG00000020023	Tmcc3	AW488095|C630016B22Rik|C88213|Tmcc1	transmembrane and coiled coil domains 3	protein-coding
mm_108218.1	chr12	77060312	77060319	+	1	NA	Intergenic	Intergenic	-98067	NM_001146176	17187	Mm.268548	NM_008558	ENSMUSG00000059436	Max	AA960152|AI875693|bHLHd4|bHLHd5|bHLHd6|bHLHd7|bHLHd8	Max protein	protein-coding
mm_89754.1	chr10	99269974	99269977	+	1	NA	Intergenic	Intergenic	6744	NM_026268	67603	Mm.1791	NM_026268	ENSMUSG00000019960	Dusp6	1300019I03Rik|MKP-3|MKP3|PYST1	dual specificity phosphatase 6	protein-coding
mm_28538.1	chr3	92765061	92765066	-	1	NA	promoter-TSS (NM_026335)	promoter-TSS (NM_026335)	2	NM_026335	67718	Mm.23784	NM_026335	ENSMUSG00000049593	Lce1h	2310066F03Rik|AI426284|Sprrl9	late cornified envelope 1H	protein-coding
mm_41483.1	chr5	91987472	91987479	+	1	NA	promoter-TSS (NM_001177577)	promoter-TSS (NM_001177577)	2	NM_001177577	381651	Mm.332494	NM_001177577	ENSMUSG00000096035	Gm1045	Gm1045-a|Gm1045-b	predicted gene 1045	protein-coding
mm_40479.1	chr5	54050216	54050223	+	1	NA	intron (NM_001081103, intron 1 of 11)	intron (NM_001081103, intron 1 of 11)	51696	NM_001081103	116873	Mm.265985	NM_054083	ENSMUSG00000039156	Stim2	-	stromal interaction molecule 2	protein-coding
mm_148959.1	chr19	7417587	7417650	+	1	NA	promoter-TSS (NM_175381)	promoter-TSS (NM_175381)	-7	NM_175381	108899	Mm.386838	NM_175381	ENSMUSG00000053080	2700081O15Rik	AI255177|AI848741|AW742297	RIKEN cDNA 2700081O15 gene	protein-coding
mm_169774.1	chr1	60704235	60704235	+	1	NA	Intergenic	Intergenic	-42153	NM_007642	12487	Mm.255003	NM_007642	ENSMUSG00000026012	Cd28	-	CD28 antigen	protein-coding
mm_35582.1	chr4	41741279	41741300	-	1	NA	promoter-TSS (NM_001286551)	promoter-TSS (NM_001286551)	70	NM_001286540	18391	Mm.425181	NM_011014	ENSMUSG00000036078	Sigmar1	Oprs1|Sig1R|sigma1R	sigma non-opioid intracellular receptor 1	protein-coding
mm_97802.1	chr11	82956594	82956604	+	1	NA	exon (NM_183201, exon 3 of 6)	exon (NM_183201, exon 3 of 6)	4082	NR_045932	76392	Mm.295205	NR_045932	ENSMUSG00000086327	Slfn5os	1700003F17Rik	schlafen 5, opposite strand	ncRNA
mm_76401.1	chr8	84845925	84845947	-	1	NA	exon (NM_007591, exon 3 of 9)	exon (NM_007591, exon 3 of 9)	995	NM_007591	12317	Mm.1971	NM_007591	ENSMUSG00000003814	Calr	CRT|Calregulin	calreticulin	protein-coding
mm_171691.1	chr4	65823555	65823555	+	1	NA	intron (NM_019514, intron 9 of 21)	L1Md_T|LINE|L1	218569	NM_001161782	69807	Mm.22786	NM_053084	ENSMUSG00000051675	Trim32	1810045E12Rik|3f3|BBS11|Zfp117	tripartite motif-containing 32	protein-coding
mm_67254.1	chr7	75587889	75587912	-	1	NA	intron (NM_029332, intron 5 of 36)	intron (NM_029332, intron 5 of 36)	132366	NM_029332	75547	Mm.216107	NM_029332	ENSMUSG00000066406	Akap13	1700026G02Rik|5730522G15Rik|5830460E08Rik|AKAP-13|AKAP-Lbc|BRX|Ht31|LBC|PROTO-LB|PROTO-LBC	A kinase (PRKA) anchor protein 13	protein-coding
mm_20614.1	chr2	131855135	131855155	-	1	NA	3' UTR (NM_001166206, exon 2 of 2)	3' UTR (NM_001166206, exon 2 of 2)	4602	NM_001166206	71995	Mm.22	NM_028045	ENSMUSG00000037482	Erv3	1600014E20Rik|AA389086|AI426069|AI448024|D19349	endogenous retroviral sequence 3	protein-coding
mm_111966.1	chr12	109615589	109615599	-	1	NA	intron (NR_028261, intron 2 of 20)	intron (NR_028261, intron 2 of 20)	-2664	NR_029918	723854		NR_029918	ENSMUSG00000065433	Mir370	Mirn370|mir-370|mmu-mir-370	microRNA 370	ncRNA
mm_2573.1	chr1	118481463	118481477	+	1	NA	intron (NM_001293300, intron 8 of 40)	intron (NM_001293300, intron 8 of 40)	-22205	NR_027901	68204	Mm.443536	NR_027901	ENSMUSG00000107722	2900060B14Rik	-	RIKEN cDNA 2900060B14 gene	ncRNA
mm_150810.1	chr19	44386158	44386165	+	1	NA	Intergenic	Intergenic	21548	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_65061.1	chr7	18821599	18821612	-	1	NA	promoter-TSS (NM_007677)	promoter-TSS (NM_007677)	-14	NM_007677	26437	Mm.302844	NM_007677	ENSMUSG00000004540	Psg17	Cea-2|Cea2|mmCGM5	pregnancy specific glycoprotein 17	protein-coding
mm_16154.1	chr2	172370646	172370656	+	1	NA	promoter-TSS (NM_001291185)	promoter-TSS (NM_001291185)	-81	NM_011497	20878	Mm.249363	NM_011497	ENSMUSG00000027496	Aurka	AIRK1|ARK-1|AU019385|AW539821|Ark1|Aurora-A|Ayk1|IAK|IAK1|Stk6	aurora kinase A	protein-coding
mm_70213.1	chr7	144931364	144931379	-	1	NA	TTS (NR_039539)	TTS (NR_039539)	764	NR_039539	100628615		NR_039539	ENSMUSG00000092633	Mir3962	mmu-mir-3962|mu-mir-3962	microRNA 3962	ncRNA
mm_145453.1	chr18	60223331	60223336	+	1	NA	intron (NM_001033767, intron 2 of 2)	B3|SINE|B2	11256	NM_001033767	240327	Mm.357104	NM_001033767	ENSMUSG00000073555	Gm4951	EG240327|Ifgga2	predicted gene 4951	protein-coding
mm_128546.1	chr15	55084097	55084111	-	1	NA	exon (NM_183089, exon 5 of 9)	exon (NM_183089, exon 5 of 9)	6374	NM_183089	72107	Mm.486550	NM_183089	ENSMUSG00000022422	Dscc1	2010006I05Rik|2600005O03Rik|Dcc1	DNA replication and sister chromatid cohesion 1	protein-coding
mm_30027.1	chr3	135674593	135674634	-	1	NA	intron (NM_008689, intron 1 of 24)	intron (NM_008689, intron 1 of 24)	16934	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_70.1	chr1	6666015	6666026	+	1	NA	intron (NM_001244693, intron 2 of 22)	Lx8|LINE|L1	-64031	NR_045189	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding
mm_89151.1	chr10	86022209	86022253	+	1	NA	promoter-TSS (NM_001310745)	promoter-TSS (NM_001310745)	77	NM_001347151	69754	Mm.44236	NM_153195	ENSMUSG00000001786	Fbxo7	2410015K21Rik|A230052G17Rik|AI117679|AW260462|C85118	F-box protein 7	protein-coding
mm_46566.1	chr5	107168535	107168538	-	1	NA	intron (NM_011578, intron 4 of 16)	intron (NM_011578, intron 4 of 16)	121059	NM_011578	21814	Mm.200775	NM_011578	ENSMUSG00000029287	Tgfbr3	1110036H20Rik|AU015626|AW215636|TBRIII	transforming growth factor, beta receptor III	protein-coding
mm_82615.1	chr9	21769860	21769887	-	1	NA	intron (NM_145611, intron 10 of 11)	intron (NM_145611, intron 10 of 11)	-9587	NM_026282	67629	Mm.295642	NM_026282	ENSMUSG00000074476	Spc24	2410030K01Rik|AV109292|Spbc24	SPC24, NDC80 kinetochore complex component, homolog (S. cerevisiae)	protein-coding
mm_77150.1	chr8	111643878	111643897	-	1	NA	intron (NM_001037665, intron 1 of 3)	CpG	444	NM_011742	22640	Mm.4184	NM_011742	ENSMUSG00000055835	Zfp1	Fnp-1|Zfp-1|mkr-1	zinc finger protein 1	protein-coding
mm_80551.1	chr9	82976172	82976175	+	1	NA	promoter-TSS (NM_001081216)	promoter-TSS (NM_001081216)	-684	NM_001081216	83946	Mm.221688	NM_031879	ENSMUSG00000032253	Phip	2810004D21Rik|4632404O06Rik|Ndrp|Wdr11	pleckstrin homology domain interacting protein	protein-coding
mm_161695.1	chr17	23745885	23745885	-	1	NA	promoter-TSS (NM_028416)	promoter-TSS (NM_028416)	-56	NM_028416	73016	Mm.221319	NM_028416	ENSMUSG00000040680	Kremen2	2900054E04Rik|Krm2	kringle containing transmembrane protein 2	protein-coding
mm_9470.1	chr1	173334023	173334033	-	1	NA	promoter-TSS (NM_010045)	promoter-TSS (NM_010045)	-525	NM_010045	13349	Mm.6393	NM_010045	ENSMUSG00000037872	Ackr1	AA162249|CCBP1|CD234|Darc|Dfy|ESTM35|FY|GPD	atypical chemokine receptor 1 (Duffy blood group)	protein-coding
mm_36697.1	chr4	96664054	96664064	-	1	NA	promoter-TSS (NM_010007)	promoter-TSS (NM_010007)	60	NM_010007	13109	Mm.12838	NM_010007	ENSMUSG00000052520	Cyp2j5	-	cytochrome P450, family 2, subfamily j, polypeptide 5	protein-coding
mm_131856.1	chr16	23074719	23074752	+	1	NA	exon (NM_001102411, exon 7 of 10)	exon (NM_001102411, exon 7 of 10)	16435	NM_001102412	16644	Mm.2160	NM_023125	ENSMUSG00000022875	Kng1	Kng	kininogen 1	protein-coding
mm_112417.1	chr13	4048973	4048983	+	1	NA	Intergenic	Intergenic	-10613	NM_134072	105387	Mm.26838	NM_134072	ENSMUSG00000033715	Akr1c14	9030611N15Rik|AW557061	aldo-keto reductase family 1, member C14	protein-coding
mm_1388.1	chr1	67111857	67111905	+	1	NA	Intergenic	Intergenic	-11146	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_98459.1	chr11	94947706	94947737	+	1	NA	exon (NM_007742, exon 39 of 51)	exon (NM_007742, exon 39 of 51)	11497	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_137555.1	chr17	27655534	27655544	+	1	NA	promoter-TSS (NM_001286743)	promoter-TSS (NM_001286743)	-52	NM_011861	23969	Mm.4926	NM_011861	ENSMUSG00000040276	Pacsin1	A830061D09Rik|H74|mKIAA1379|syndapin	protein kinase C and casein kinase substrate in neurons 1	protein-coding
mm_81241.1	chr9	107935877	107935938	+	1	NA	promoter-TSS (NM_145621)	promoter-TSS (NM_145621)	-13	NM_145621	235604	Mm.274540	NM_145621	ENSMUSG00000032936	Camkv	1G5|BB074618|BC017634	CaM kinase-like vesicle-associated	protein-coding
mm_103398.1	chr11	75437447	75437471	-	1	NA	exon (NM_008878, exon 5 of 10)	exon (NM_008878, exon 5 of 10)	2042	NM_008878	18816	Mm.279733	NM_008878	ENSMUSG00000038224	Serpinf2	AI747498|Pli|Serpimf2	serine (or cysteine) peptidase inhibitor, clade F, member 2	protein-coding
mm_135991.1	chr16	75130117	75130119	-	1	NA	Intergenic	Intergenic	455943	NM_001252513	320355	Mm.99517	NM_177142	ENSMUSG00000032948	Lipi	D930038D03Rik|lpd1	lipase, member I	protein-coding
mm_90586.1	chr10	128269327	128269341	+	1	NA	exon (NM_133997, exon 2 of 2)	exon (NM_133997, exon 2 of 2)	-1242	NM_019963	20847	Mm.293120	NM_019963	ENSMUSG00000040033	Stat2	1600010G07Rik|AW496480	signal transducer and activator of transcription 2	protein-coding
mm_31455.1	chr4	48662383	48662408	+	1	NA	3' UTR (NM_021436, exon 10 of 10)	3' UTR (NM_021436, exon 10 of 10)	-1119	NM_026509	68016	Mm.133444	NM_026509	ENSMUSG00000028348	Murc	2310039E09Rik	muscle-related coiled-coil protein	protein-coding
mm_19414.1	chr2	91710527	91710582	-	1	NA	promoter-TSS (NM_178724)	promoter-TSS (NM_178724)	38	NM_145528	51897	Mm.28492	NM_145528	ENSMUSG00000027244	Atg13	1110053A20Rik|D2Ertd391e|Harbi1	autophagy related 13	protein-coding
mm_44462.1	chr5	22589653	22589670	-	1	NA	Intergenic	LTR16A|LTR|ERVL	39248	NR_102315	320719	Mm.459265	NR_102315	ENSMUSG00000097207	6030443J06Rik	1700030G06Rik	RIKEN cDNA 6030443J06 gene	ncRNA
mm_116786.1	chr13	53370258	53370266	-	1	NA	intron (NM_009269, intron 3 of 14)	intron (NM_009269, intron 3 of 14)	7099	NM_009269	268656	Mm.240336	NM_009269	ENSMUSG00000021468	Sptlc1	AW552086|C77762|E030036H05|Lcb1	serine palmitoyltransferase, long chain base subunit 1	protein-coding
mm_84858.1	chr9	78537680	78537690	-	1	NA	3' UTR (NM_172773, exon 11 of 11)	3' UTR (NM_172773, exon 11 of 11)	50360	NM_172773	235504	Mm.46932	NM_172773	ENSMUSG00000049624	Slc17a5	4631416G20Rik|4732491M05|AST|ISSD|NSD|SD|SIALIN|SIASD|SLD	solute carrier family 17 (anion/sugar transporter), member 5	protein-coding
mm_93699.1	chr10	118011951	118011954	-	1	NA	Intergenic	Intergenic	86493	NR_045342	71067	Mm.410793	NR_045342		4933411E08Rik	-	RIKEN cDNA 4933411E08 gene	ncRNA
mm_94495.1	chr11	7063424	7063496	+	1	NA	promoter-TSS (NM_009622)	promoter-TSS (NM_009622)	-29	NM_009622	432530	Mm.259733	NM_009622	ENSMUSG00000020431	Adcy1	AC1|D11Bwg1392e|I-AC|brl|mKIAA4070	adenylate cyclase 1	protein-coding
mm_166737.1	chr6	123260226	123260234	-	1	NA	Intergenic	Intergenic	-1877	NM_001163161	17474	Mm.441101	NM_010819	ENSMUSG00000030144	Clec4d	Clecsf8|Mpcl|mcl	C-type lectin domain family 4, member d	protein-coding
mm_156798.1	chrX	162901763	162901773	+	1	NA	promoter-TSS (NR_033143)	promoter-TSS (NR_033143)	173	NM_018737	55936	Mm.2065	NM_018737	ENSMUSG00000031360	Ctps2	A830031M15Rik|AI326475|Ctpsh	cytidine 5'-triphosphate synthase 2	protein-coding
mm_76067.1	chr8	78437322	78437344	-	1	NA	promoter-TSS (NM_138944)	promoter-TSS (NM_138944)	-681	NM_138944	18997	Mm.234261	NM_138944	ENSMUSG00000031688	Pou4f2	Brn-3.2|Brn-3b|Brn3b|Pou4f-rs1|mBrn3-3R	POU domain, class 4, transcription factor 2	protein-coding
mm_32815.1	chr4	117251978	117252004	+	1	NA	promoter-TSS (NM_001033774)	promoter-TSS (NM_001033774)	40	NM_001285815	68777	Mm.331805	NM_026837	ENSMUSG00000048772	Tmem53	1110038M16Rik|1500001P22Rik|1700012A05Rik	transmembrane protein 53	protein-coding
mm_114486.1	chr13	69617427	69617445	+	1	NA	exon (NM_145354, exon 5 of 19)	exon (NM_145354, exon 5 of 19)	5420	NM_145354	28114	Mm.260009	NM_145354	ENSMUSG00000021595	Nsun2	D13Wsu123e|Misu	NOL1/NOP2/Sun domain family member 2	protein-coding
mm_36313.1	chr4	69925898	69925923	-	1	NA	Intergenic	Intergenic	484525	NM_001313762	214444	Mm.370777	NM_145990	ENSMUSG00000039298	Cdk5rap2	2900018K03Rik|an|mKIAA1633	CDK5 regulatory subunit associated protein 2	protein-coding
mm_77477.1	chr8	122443433	122443439	-	1	NA	promoter-TSS (NM_138656)	promoter-TSS (NM_138656)	-14	NR_028354	192156	Mm.28146	NM_138656	ENSMUSG00000006517	Mvd	C78718|Mpd	mevalonate (diphospho) decarboxylase	protein-coding
mm_22758.1	chr3	19989135	19989149	+	1	NA	exon (NM_007752, exon 18 of 19)	exon (NM_007752, exon 18 of 19)	32088	NM_007752	12870	Mm.13787	NM_007752	ENSMUSG00000003617	Cp	D3Ertd555e	ceruloplasmin	protein-coding
mm_150667.1	chr19	42041630	42041643	+	1	NA	intron (NM_020033, intron 4 of 8)	intron (NM_020033, intron 4 of 8)	-4215	NM_026152	67432	Mm.24196	NM_026152	ENSMUSG00000025176	Hoga1	0610010D20Rik|Dhdpsl|Npl2	4-hydroxy-2-oxoglutarate aldolase 1	protein-coding
mm_109026.1	chr12	103947127	103947132	+	1	NA	exon (NM_009247, exon 5 of 5)	exon (NM_009247, exon 5 of 5)	9768	NM_009247	20704	Mm.312593	NM_009247	ENSMUSG00000072849	Serpina1e	Dom5|PI5|Spi1-5	serine (or cysteine) peptidase inhibitor, clade A, member 1E	protein-coding
mm_99514.1	chr11	103104772	103104791	+	1	NA	intron (NM_025988, intron 6 of 9)	intron (NM_025988, intron 6 of 9)	3093	NM_025988	67131	Mm.390367	NM_025988	ENSMUSG00000056938	Acbd4	2010009P05Rik|2010015A21Rik|AI849317	acyl-Coenzyme A binding domain containing 4	protein-coding
mm_156825.1	chrX	164162168	164162194	+	1	NA	intron (NM_001130513, intron 6 of 18)	intron (NM_001130513, intron 6 of 18)	21701	NM_027286	70008	Mm.13451	NM_027286	ENSMUSG00000015405	Ace2	2010305L05Rik	angiotensin I converting enzyme (peptidyl-dipeptidase A) 2	protein-coding
mm_34943.1	chr4	155869541	155869623	+	1	NA	promoter-TSS (NM_024472)	promoter-TSS (NM_024472)	15	NM_028020	71957	Mm.475640	NM_028020	ENSMUSG00000029034	Cpsf3l	2410006F12Rik|AU044035	cleavage and polyadenylation specific factor 3-like	protein-coding
mm_168818.1	chr12	22030877	22030877	-	1	NA	Intergenic	CpG	125769	NR_136920	100043416		NM_001004167	ENSMUSG00000093846	Gm4425	EG432637|Gm5433	KRAB-domain protein pseudogene	pseudo
mm_36880.1	chr4	107178361	107178373	-	1	NA	promoter-TSS (NM_029565)	promoter-TSS (NM_029565)	-1	NM_025617	66526	Mm.246956	NM_025617	ENSMUSG00000028619	Tceanc2	2210010B22Rik|2210012G02Rik|6330404A07Rik|AU015593|Tdeanc2	transcription elongation factor A (SII) N-terminal and central domain containing 2	protein-coding
mm_170029.1	chr17	21920809	21920822	-	1	NA	Intergenic	Intergenic	-10889	NM_001256493	70081	Mm.245648	NM_001256493	ENSMUSG00000078546	Zfp995	2210404O09Rik	zinc finger protein 995	protein-coding
mm_139956.1	chr17	71315441	71315459	+	1	NA	Intergenic	Lx8|LINE|L1	-4485	NM_145158	246707	Mm.23462	NM_145158	ENSMUSG00000024053	Emilin2	FOAP-10	elastin microfibril interfacer 2	protein-coding
mm_24601.1	chr3	93445404	93445412	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	3078	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_159588.1	chr4	123233386	123233386	+	1	NA	promoter-TSS (NM_013905)	promoter-TSS (NM_013905)	-170	NM_013905	56198	Mm.103615	NM_013905	ENSMUSG00000032744	Heyl	Hey3|Hrt3|bHLHb33|hesr3	hairy/enhancer-of-split related with YRPW motif-like	protein-coding
mm_84150.1	chr9	59486324	59486415	-	1	NA	promoter-TSS (NM_019927)	promoter-TSS (NM_019927)	5	NM_019927	23806	Mm.305925	NM_019927	ENSMUSG00000025234	Arih1	AU021774|Ari|Ari1|Hari|Hhari|Ubch7bp|Uip77	ariadne RBR E3 ubiquitin protein ligase 1	protein-coding
mm_86893.1	chr10	22301941	22301971	+	1	NA	intron (NM_009018, intron 5 of 5)	intron (NM_009018, intron 5 of 5)	-4764	NR_015465	606736	Mm.387042	NR_015465	ENSMUSG00000097352	C920009B18Rik	-	RIKEN cDNA C920009B18 gene	ncRNA
mm_102556.1	chr11	61378307	61378347	-	1	NA	promoter-TSS (NM_026183)	promoter-TSS (NM_026183)	-252	NM_026183	67473	Mm.100741	NM_026183	ENSMUSG00000010122	Slc47a1	1300013J15Rik|AI036982|MATE1|mMATE1	solute carrier family 47, member 1	protein-coding
mm_152979.1	chr19	29488530	29488568	-	1	NA	Intergenic	Intergenic	33438	NR_015567	77779	Mm.458738	NR_015567	ENSMUSG00000097855	A930007I19Rik	-	RIKEN cDNA A930007I19 gene	ncRNA
mm_63361.1	chr7	127021439	127021447	+	1	NA	promoter-TSS (NM_001102563)	promoter-TSS (NM_001102563)	-232	NM_001102563	69017	Mm.392047	NM_001102563	ENSMUSG00000045114	Prrt2	1500031I19Rik|AI195361|DSPB3	proline-rich transmembrane protein 2	protein-coding
mm_44200.1	chr5	3648014	3648038	-	1	NA	promoter-TSS (NM_026033)	promoter-TSS (NM_026033)	-90	NM_026033	67210	Mm.178424	NM_026033	ENSMUSG00000007415	Gatad1	2310031E19Rik|2810047M21Rik|8430439A17Rik|9130430G15Rik|B330017N08Rik|ENSMUSG00000073241|Odag	GATA zinc finger domain containing 1	protein-coding
mm_51771.1	chr6	88060924	88060930	+	1	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	-15657	NM_009005	19349	Mm.333233	NM_009005	ENSMUSG00000079477	Rab7	Rab7a	RAB7, member RAS oncogene family	protein-coding
mm_69877.1	chr7	141625296	141625311	-	1	NA	intron (NM_007459, intron 15 of 21)	intron (NM_007459, intron 15 of 21)	4602	NR_106030	102466798		NR_106030	ENSMUSG00000098759	Mir7063	Gm27654|mmu-mir-7063	microRNA 7063	ncRNA
mm_47701.1	chr5	129879009	129879019	-	1	NA	promoter-TSS (NM_011079)	promoter-TSS (NM_011079)	69	NM_011079	18682	Mm.3159	NM_011079	ENSMUSG00000025537	Phkg1	Phkg	phosphorylase kinase gamma 1	protein-coding
mm_171339.1	chr4	102875782	102875788	-	1	NA	intron (NM_001285862, intron 6 of 19)	IAPLTR1_Mm|LTR|ERVK	-110594	NM_001163767	67344	Mm.111346	NM_026100	ENSMUSG00000028523	Tctex1d1	1700055O19Rik	Tctex1 domain containing 1	protein-coding
mm_7951.1	chr1	133915306	133915323	-	1	NA	exon (NM_054077, exon 2 of 3)	exon (NM_054077, exon 2 of 3)	6087	NM_054077	116847	Mm.214514	NM_054077	ENSMUSG00000041577	Prelp	7330409J17Rik|SLRR2A	proline arginine-rich end leucine-rich repeat	protein-coding
mm_151226.1	chr19	53717892	53717904	+	1	NA	intron (NM_001170847, intron 1 of 13)	intron (NM_001170847, intron 1 of 13)	40592	NM_001170847	73713	Mm.313695	NM_001170847	ENSMUSG00000043639	Rbm20	1110018J23Rik|2010003H22Rik|AI646761	RNA binding motif protein 20	protein-coding
mm_86862.1	chr10	21992217	21992234	+	1	NA	promoter-TSS (NM_001161849)	promoter-TSS (NM_001161849)	2	NM_001161849	20393	Mm.28405	NM_011361	ENSMUSG00000019970	Sgk1	Sgk	serum/glucocorticoid regulated kinase 1	protein-coding
mm_466.1	chr1	36332703	36332709	+	1	NA	Intergenic	L1MDa|LINE|L1	16052	NR_105863	102465541		NR_105863	ENSMUSG00000098680	Mir6898	Gm27816|mmu-mir-6898	microRNA 6898	ncRNA
mm_108930.1	chr12	101083713	101083743	+	1	NA	promoter-TSS (NM_001160214)	promoter-TSS (NM_001160214)	-26	NM_001160214	68734	Mm.87077	NM_211355	ENSMUSG00000041846	Smek1	1110034C04Rik|BC064465|Ppp4r3a|mKIAA2010	SMEK homolog 1, suppressor of mek1 (Dictyostelium)	protein-coding
mm_6519.1	chr1	74415144	74415154	-	1	NA	exon (NM_009509, exon 2 of 20)	exon (NM_009509, exon 2 of 20)	5765	NM_009509	22349	Mm.471601	NM_009509	ENSMUSG00000026175	Vil1	Vil	villin 1	protein-coding
mm_32138.1	chr4	99240525	99240547	+	1	NA	intron (NM_175029, intron 10 of 10)	(TTTTTG)n|Simple_repeat|Simple_repeat	46389	NM_001145967	242557	Mm.241663	NM_175029	ENSMUSG00000028550	Atg4c	Apg4-C|Apg4c|Atg4cl|Autl1	autophagy related 4C, cysteine peptidase	protein-coding
mm_155478.1	chrX	73673157	73673174	+	1	NA	promoter-TSS (NM_001142809)	promoter-TSS (NM_001142809)	32	NM_001142809	102857	Mm.274553	NM_133987	ENSMUSG00000019558	Slc6a8	AA589632|CRT|CRTR|CT1|CTR5|Creat	solute carrier family 6 (neurotransmitter transporter, creatine), member 8	protein-coding
mm_120547.1	chr14	67398827	67398865	+	1	NA	intron (NM_010095, intron 11 of 16)	intron (NM_010095, intron 11 of 16)	-1104	NR_045961	73977	Mm.414915	NR_045961	ENSMUSG00000093472	4930438E09Rik	-	RIKEN cDNA 4930438E09 gene	ncRNA
mm_3268.1	chr1	136415290	136415337	+	1	NA	promoter-TSS (NM_026500)	promoter-TSS (NM_026500)	42	NM_026500	67997	Mm.385462	NM_026500	ENSMUSG00000026404	Ddx59	1210002B07Rik|4833411G06Rik	DEAD (Asp-Glu-Ala-Asp) box polypeptide 59	protein-coding
mm_162844.1	chr10	86300675	86300683	+	1	NA	5' UTR (NM_011595, exon 1 of 5)	5' UTR (NM_011595, exon 1 of 5)	267	NM_011595	21859	Mm.4871	NM_011595	ENSMUSG00000020044	Timp3	Timp-3	tissue inhibitor of metalloproteinase 3	protein-coding
mm_89949.1	chr10	111286109	111286142	+	1	NA	exon (NM_001003717, exon 18 of 23)	exon (NM_001003717, exon 18 of 23)	-12554	NM_027914	71769	Mm.45256	NM_027914	ENSMUSG00000035759	Bbs10	1300007O09Rik|AI452285	Bardet-Biedl syndrome 10 (human)	protein-coding
mm_160331.1	chr8	9770789	9770789	-	1	NA	exon (NM_173446, exon 1 of 3)	exon (NM_173446, exon 1 of 3)	234	NM_173446	270028	Mm.268163	NM_173446	ENSMUSG00000079157	Fam155a	6430500D16|AW121567|Tmem28	family with sequence similarity 155, member A	protein-coding
mm_22676.1	chr3	15000911	15000951	+	1	NA	intron (NR_040550, intron 3 of 3)	RLTR41A2|LTR|ERV1	29730	NR_040550	77127	Mm.195792	NR_040549	ENSMUSG00000098008	A930001A20Rik	-	RIKEN cDNA A930001A20 gene	ncRNA
mm_141131.1	chr17	26201449	26201492	-	1	NA	promoter-TSS (NM_008113)	promoter-TSS (NM_008113)	-120	NM_008113	14570	Mm.1383	NM_008113	ENSMUSG00000073433	Arhgdig	Gdi5|RIP2|Rho-GDI-3|Rho-GDI2	Rho GDP dissociation inhibitor (GDI) gamma	protein-coding
mm_160203.1	chr7	81692906	81692906	-	1	NA	promoter-TSS (NM_001164087)	promoter-TSS (NM_001164087)	59	NM_001164087	26557	Mm.228	NM_011983	ENSMUSG00000025813	Homer2	9330120H11Rik|AW539445|CPD|Vesl-2	homer scaffolding protein 2	protein-coding
mm_41047.1	chr5	86093264	86093279	+	1	NA	intron (NM_001310639, intron 5 of 7)	intron (NM_001310639, intron 5 of 7)	21525	NM_001310639	56792	Mm.131237	NM_019992	ENSMUSG00000029254	Stap1	AI586015|Brdg1|STAP-1	signal transducing adaptor family member 1	protein-coding
mm_4517.1	chr1	174751647	174751651	+	1	NA	intron (NM_019445, intron 15 of 17)	intron (NM_019445, intron 15 of 17)	170170	NM_011825	23893	Mm.25760	NM_011825	ENSMUSG00000050069	Grem2	Gremlin2|Prdc	gremlin 2, DAN family BMP antagonist	protein-coding
mm_79154.1	chr9	47745911	47745930	+	1	NA	intron (NM_001025600, intron 1 of 8)	intron (NM_001025600, intron 1 of 8)	72288	NR_046048	100038460	Mm.447649	NR_046048		Gm10677	ENSMUSG00000074363	predicted gene 10677	ncRNA
mm_68624.1	chr7	118119210	118119250	-	1	NA	3' UTR (NM_019419, exon 6 of 6)	3' UTR (NM_019419, exon 6 of 6)	-3083	NM_170669	267019	Mm.288212	NM_170669	ENSMUSG00000008683	Rps15a	A630031B11Rik	ribosomal protein S15A	protein-coding
mm_122869.1	chr14	54919835	54919865	-	1	NA	exon (NM_010112, exon 4 of 6)	exon (NM_010112, exon 4 of 6)	-6718	NM_021551	59049	Mm.27435	NM_021551	ENSMUSG00000022199	Slc22a17	1700094C23Rik|24p3R|AU041908|AW555662|BOIT|Boct	solute carrier family 22 (organic cation transporter), member 17	protein-coding
mm_120186.1	chr14	61492714	61492721	+	1	NA	promoter-TSS (NR_045714)	promoter-TSS (NR_045714)	29	NR_045714	75349	Mm.233613	NR_045714		4930556J02Rik	-	RIKEN cDNA 4930556J02 gene	ncRNA
mm_62234.1	chr7	98655818	98655853	+	1	NA	intron (NM_172280, intron 1 of 19)	CpG	734	NM_172280	233545	Mm.387819	NM_172280	ENSMUSG00000035401	Emsy	2210018M11Rik|2310016L09Rik|AU019521|AU019557	EMSY, BRCA2-interacting transcriptional repressor	protein-coding
mm_134640.1	chr16	21762896	21762905	-	1	NA	exon (NM_023737, exon 7 of 7)	exon (NM_023737, exon 7 of 7)	24934	NM_023737	74147	Mm.28100	NM_023737	ENSMUSG00000022853	Ehhadh	1300002P22Rik|HD|L-PBE|LBFP|LBP|MFP|MFP1|PBFE	enoyl-Coenzyme A, hydratase/3-hydroxyacyl Coenzyme A dehydrogenase	protein-coding
mm_102973.1	chr11	69671215	69671238	-	1	NA	intron (NM_001159375, intron 1 of 10)	intron (NM_001159375, intron 1 of 10)	1197	NM_144958	13681	Mm.26680	NM_144958	ENSMUSG00000059796	Eif4a1	BM-010|Ddx2a|Eif4	eukaryotic translation initiation factor 4A1	protein-coding
mm_144519.1	chr18	24746643	24746654	+	1	NA	intron (NM_175276, intron 1 of 26)	B3|SINE|B2	38025	NM_001289655	225288	Mm.329322	NM_175276	ENSMUSG00000034295	Fhod3	A930009H06Rik|FHOS2|mKIAA1695	formin homology 2 domain containing 3	protein-coding
mm_147380.1	chr18	43737168	43737180	-	1	NA	promoter-TSS (NM_009258)	promoter-TSS (NM_009258)	63	NM_009258	20730	Mm.272	NM_009258	ENSMUSG00000024503	Spink1	Spink3|p12	serine peptidase inhibitor, Kazal type 1	protein-coding
mm_128658.1	chr15	59994957	59994961	-	1	NA	Intergenic	Intergenic	21659	NM_027668	71088	Mm.425950	NM_027668	ENSMUSG00000071749	4933412E24Rik	-	RIKEN cDNA 4933412E24 gene	protein-coding
mm_96004.1	chr11	59505637	59505683	+	1	NA	promoter-TSS (NR_135273)	promoter-TSS (NR_135273)	7	NR_015585	74476	Mm.440257	NR_015585	ENSMUSG00000072893	4933439C10Rik	2610028M21Rik	RIKEN cDNA 4933439C10 gene	ncRNA
mm_173023.1	chrX	103076073	103076076	+	1	NA	Intergenic	Intergenic	110590	NM_008671	17954	Mm.388694	NM_008671	ENSMUSG00000082229	Nap1l2	Bpx	nucleosome assembly protein 1-like 2	protein-coding
mm_133719.1	chr16	93683185	93683223	+	1	NA	promoter-TSS (NM_173047)	promoter-TSS (NM_173047)	-15	NM_173047	109857	Mm.4512	NM_173047	ENSMUSG00000022947	Cbr3	1110001J05Rik|C81353	carbonyl reductase 3	protein-coding
mm_108489.1	chr12	83672729	83672744	+	1	NA	exon (NM_027349, exon 14 of 19)	exon (NM_027349, exon 14 of 19)	-15827	NM_008943	19164	Mm.998	NM_008943	ENSMUSG00000019969	Psen1	Ad3h|PS-1|PS1|S182	presenilin 1	protein-coding
mm_107886.1	chr12	70453097	70453107	+	1	NA	promoter-TSS (NM_028339)	promoter-TSS (NM_028339)	-52	NM_028339	72736	Mm.204670	NM_028339	ENSMUSG00000021072	Tmx1	2810425A04Rik|AI465319|Txndc1	thioredoxin-related transmembrane protein 1	protein-coding
mm_59419.1	chr7	27121918	27121932	+	1	NA	exon (NM_007817, exon 3 of 10)	exon (NM_007817, exon 3 of 10)	1970	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_148260.1	chr18	80869686	80869689	-	1	NA	intron (NM_001201569, intron 7 of 29)	AT_rich|Low_complexity|Low_complexity	64371	NM_001201569	50771	Mm.247138	NM_015805	ENSMUSG00000024566	Atp9b	AA934181|Atpc2b|IIb|MMR	ATPase, class II, type 9B	protein-coding
mm_53684.1	chr6	142387216	142387269	+	1	NA	promoter-TSS (NM_001204907)	promoter-TSS (NM_001204907)	-1	NM_025872	66964	Mm.3676	NM_025872	ENSMUSG00000030245	Golt1b	2310061A22Rik|AA407874|AU024291|CGI-141	golgi transport 1B	protein-coding
mm_111658.1	chr12	103236017	103236041	-	1	NA	intron (NM_133364, intron 2 of 4)	intron (NM_133364, intron 2 of 4)	6117	NM_133364	170952	Mm.217019	NM_133364	ENSMUSG00000041669	Prima1	B230212M13Rik|BB120497|PRiMA	proline rich membrane anchor 1	protein-coding
mm_70267.1	chr8	3587641	3587687	+	1	NA	5' UTR (NM_027171, exon 1 of 17)	5' UTR (NM_027171, exon 1 of 17)	214	NM_001347111	69697	Mm.390010	NM_027171	ENSMUSG00000044433	Camsap3	2310057J16Rik|Kiaa1543|Nezha	calmodulin regulated spectrin-associated protein family, member 3	protein-coding
mm_3265.1	chr1	136364990	136365021	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-18901	NM_001347110	67886	Mm.144143	NM_001081360	ENSMUSG00000041570	Camsap2	1600013L13Rik|4930541M15Rik|Camsap1l1|mKIAA1078	calmodulin regulated spectrin-associated protein family, member 2	protein-coding
mm_94185.1	chr10	128958946	128958954	-	1	NA	TTS (NM_008398)	TTS (NM_008398)	2038	NM_027853	71664	Mm.337232	NM_027853	ENSMUSG00000025347	Mettl7b	0610006F02Rik|AI266817	methyltransferase like 7B	protein-coding
mm_100054.1	chr11	115180956	115180959	+	1	NA	3' UTR (NM_012030, exon 6 of 6)	3' UTR (NM_012030, exon 6 of 6)	6359	NM_025400	66176	Mm.86823	NM_025400	ENSMUSG00000015542	Nat9	1110028N05Rik	N-acetyltransferase 9 (GCN5-related, putative)	protein-coding
mm_133184.1	chr16	72663049	72663065	+	1	NA	promoter-TSS (NM_019413)	promoter-TSS (NM_019413)	-92	NM_019413	19876	Mm.310772	NM_019413	ENSMUSG00000022883	Robo1	AW494633|AW742721|DUTT1|Gm310	roundabout guidance receptor 1	protein-coding
mm_102927.1	chr11	69600673	69600680	-	1	NA	3' UTR (NM_013415, exon 7 of 7)	3' UTR (NM_013415, exon 7 of 7)	5284	NM_013415	11932	Mm.235204	NM_013415	ENSMUSG00000041329	Atp1b2	Amog|Atpb-2	ATPase, Na+/K+ transporting, beta 2 polypeptide	protein-coding
mm_136688.1	chr17	6828096	6828139	+	1	NA	Intergenic	CpG	-45337	NM_009510	22350	Mm.277812	NM_009510	ENSMUSG00000052397	Ezr	AW146364|R75297|Vil2|p81	ezrin	protein-coding
mm_13692.1	chr2	117120994	117120998	+	1	NA	promoter-TSS (NM_001277256)	promoter-TSS (NM_001277256)	-75	NM_001277256	114715	Mm.245890	NM_033524	ENSMUSG00000027351	Spred1	5730461F13Rik|AL024345|AW047647	sprouty protein with EVH-1 domain 1, related sequence	protein-coding
mm_21735.1	chr2	164769643	164769655	-	1	NA	promoter-TSS (NM_026785)	promoter-TSS (NM_026785)	-280	NM_026785	68612	Mm.89830	NM_026785	ENSMUSG00000001403	Ube2c	1110015A16Rik|D2Ertd695e	ubiquitin-conjugating enzyme E2C	protein-coding
mm_106012.1	chr11	115871326	115871326	-	1	NA	Intergenic	Intergenic	-28813	NM_183259	66528	Mm.275740	NM_183259	ENSMUSG00000048442	Smim5	2210020M01Rik	small integral membrane protein 5	protein-coding
mm_65401.1	chr7	25205953	25205962	-	1	NA	intron (NM_207677, intron 4 of 4)	MIRb|SINE|MIR	11768	NR_106015	102466794		NR_106015	ENSMUSG00000098325	Mir7048	Gm27274|mmu-mir-7048	microRNA 7048	ncRNA
mm_119225.1	chr14	33250415	33250435	+	1	NA	intron (NM_153800, intron 2 of 10)	intron (NM_153800, intron 2 of 10)	33602	NM_153800	239027	Mm.318350	NM_153800	ENSMUSG00000063506	Arhgap22	B230341L19Rik|RHOGAP2|p68RacGAP	Rho GTPase activating protein 22	protein-coding
mm_106271.1	chr11	117987186	117987196	-	1	NA	intron (NM_133757, intron 1 of 9)	CpG	334	NM_133757	74451	Mm.28864	NM_133757	ENSMUSG00000017715	Pgs1	2610019F11Rik|4933424M23Rik|SAF	phosphatidylglycerophosphate synthase 1	protein-coding
mm_51531.1	chr6	83188896	83188903	+	1	NA	intron (NM_001347310, intron 2 of 26)	intron (NM_001347310, intron 2 of 26)	2953	NM_001347310	13191	Mm.6919	NM_007835	ENSMUSG00000031865	Dctn1	AL022633|DAP-150|DP-150|Glued|p150|p150-glued|p150<glued>	dynactin 1	protein-coding
mm_105080.1	chr11	100822509	100822517	-	1	NA	promoter-TSS (NM_011489)	promoter-TSS (NM_011489)	57	NM_011489	20851	Mm.34064	NM_011489	ENSMUSG00000020919	Stat5b	-	signal transducer and activator of transcription 5B	protein-coding
mm_85642.1	chr9	107655351	107655385	-	1	NA	exon (NM_001199218, exon 13 of 16)	exon (NM_001199218, exon 13 of 16)	12031	NM_023805	76257	Mm.296560	NM_023805	ENSMUSG00000010064	Slc38a3	0610012J02Rik|D9Ucla2|Nat1|Slc38-3|Sn1|Snat3|mNAT	solute carrier family 38, member 3	protein-coding
mm_105629.1	chr11	106920609	106920643	-	1	NA	promoter-TSS (NM_025481)	promoter-TSS (NM_025481)	89	NM_025481	66313	Mm.340955	NM_025481	ENSMUSG00000018363	Smurf2	2810411E22Rik|AI558114|AI649275	SMAD specific E3 ubiquitin protein ligase 2	protein-coding
mm_149171.1	chr19	9083715	9083721	+	1	NA	TTS (NM_011681)	TTS (NM_011681)	4238	NM_011681	22287	Mm.2258	NM_011681	ENSMUSG00000024653	Scgb1a1	CC10|CC16|CCSP|PCB-BP|UG|UGB|Utg	secretoglobin, family 1A, member 1 (uteroglobin)	protein-coding
mm_123055.1	chr14	55643721	55643764	-	1	NA	promoter-TSS (NM_028780)	promoter-TSS (NM_028780)	64	NM_028780	74140	Mm.132857	NM_028780	ENSMUSG00000002320	Tm9sf1	1200014D02Rik|AI893436|MP70	transmembrane 9 superfamily member 1	protein-coding
mm_116136.1	chr13	28953691	28953705	-	1	NA	promoter-TSS (NM_009238)	promoter-TSS (NM_009238)	-16	NM_009238	20677	Mm.240627	NM_009238	ENSMUSG00000076431	Sox4	AA682046|Sox-4	SRY (sex determining region Y)-box 4	protein-coding
mm_124384.1	chr14	108913877	108913891	-	1	NA	5' UTR (NM_199065, exon 1 of 1)	5' UTR (NM_199065, exon 1 of 1)	355	NM_199065	76965	Mm.257268	NM_199065	ENSMUSG00000075478	Slitrk1	3200001I04Rik	SLIT and NTRK-like family, member 1	protein-coding
mm_136782.1	chr17	10496372	10496396	+	1	NA	intron (NM_027032, intron 4 of 4)	intron (NM_027032, intron 4 of 4)	40168	NR_077238	319750	Mm.383485	NR_077237	ENSMUSG00000089633	A230009B12Rik	-	RIKEN cDNA A230009B12 gene	ncRNA
mm_150781.1	chr19	44294998	44295018	+	1	NA	exon (NM_009128, exon 2 of 6)	exon (NM_009128, exon 2 of 6)	1332	NM_009128	20250	Mm.487021	NM_009128	ENSMUSG00000025203	Scd2	Mir5114|Scd-2|mir-5114|swty	stearoyl-Coenzyme A desaturase 2	protein-coding
mm_8900.1	chr1	163085644	163085674	-	1	NA	promoter-TSS (NM_030071)	promoter-TSS (NM_030071)	11	NM_030071	78258	Mm.78368	NM_030071	ENSMUSG00000071890	Mroh9	4921528O07Rik|Armc11	maestro heat-like repeat family member 9	protein-coding
mm_58089.1	chr6	137169749	137169762	-	1	NA	promoter-TSS (NM_001164214)	promoter-TSS (NM_001164214)	-37	NM_001164212	232441	Mm.46233	NM_181988	ENSMUSG00000030222	Rerg	-	RAS-like, estrogen-regulated, growth-inhibitor	protein-coding
mm_26654.1	chr3	154597144	154597156	+	1	NA	promoter-TSS (NM_172474)	promoter-TSS (NM_172474)	-52	NM_172474	209584	Mm.347513	NM_172474	ENSMUSG00000047583	Tyw3	5230400J09Rik	tRNA-yW synthesizing protein 3 homolog (S. cerevisiae)	protein-coding
mm_151344.1	chr19	55895509	55895511	+	1	NA	5' UTR (NM_001142924, exon 1 of 12)	5' UTR (NM_001142924, exon 1 of 12)	189	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_100360.1	chr11	118476825	118476830	+	1	NA	promoter-TSS (NM_172573)	promoter-TSS (NM_172573)	-133	NM_172573	217364	Mm.473963	NM_172573	ENSMUSG00000033857	Engase	C130099A03|D230014K01Rik	endo-beta-N-acetylglucosaminidase	protein-coding
mm_62080.1	chr7	92933031	92933042	+	1	NA	exon (NM_028243, exon 9 of 9)	exon (NM_028243, exon 9 of 9)	57783	NM_028243	72461	Mm.389969	NM_028243	ENSMUSG00000061119	Prcp	2510048K03Rik|2610104A14Rik|AI451719|HUMPCP|PCP	prolylcarboxypeptidase (angiotensinase C)	protein-coding
mm_107554.1	chr12	41253694	41253704	+	1	NA	intron (NM_053122, intron 4 of 6)	B1_Mus1|SINE|Alu	229609	NM_053122	93757	Mm.363813	NM_053122	ENSMUSG00000056899	Immp2l	AI853880|IMP2	IMP2 inner mitochondrial membrane peptidase-like (S. cerevisiae)	protein-coding
mm_59557.1	chr7	28075334	28075350	+	1	NA	exon (NM_001122603, exon 3 of 20)	exon (NM_001122603, exon 3 of 20)	4106	NM_001122603	215384	Mm.292276	NM_175444	ENSMUSG00000047730	Fcgbp	A430096B05Rik	Fc fragment of IgG binding protein	protein-coding
mm_120140.1	chr14	60377681	60377703	+	1	NA	promoter-TSS (NM_001164705)	promoter-TSS (NM_001164705)	-594	NM_028113	72125	Mm.275499	NM_028113	ENSMUSG00000021986	Amer2	2600011E07Rik|Fam123a	APC membrane recruitment 2	protein-coding
mm_102254.1	chr11	55151704	55151712	-	1	NA	promoter-TSS (NM_172258)	promoter-TSS (NM_172258)	-2	NM_172258	215332	Mm.87054	NM_172258	ENSMUSG00000049491	Slc36a3	PAT3|TRAMD2|tramdorin2	solute carrier family 36 (proton/amino acid symporter), member 3	protein-coding
mm_40934.1	chr5	76657650	76657669	+	1	NA	Intergenic	CpG	65945	NM_199032	381644	Mm.332452	NM_199032	ENSMUSG00000036403	Cep135	BC062951|Cep4|Gm1044	centrosomal protein 135	protein-coding
mm_86063.1	chr9	114640176	114640218	-	1	NA	promoter-TSS (NM_153585)	promoter-TSS (NM_153585)	3	NM_153585	78893	Mm.283708	NM_153585	ENSMUSG00000056167	Cnot10	2600001P13Rik	CCR4-NOT transcription complex, subunit 10	protein-coding
mm_43423.1	chr5	136057124	136057131	+	1	NA	promoter-TSS (NM_027158)	promoter-TSS (NM_027158)	-140	NM_027158	69665	Mm.75713	NM_027158	ENSMUSG00000006143	Upk3bl	2310043J07Rik	uroplakin 3B-like	protein-coding
mm_102448.1	chr11	59787270	59787283	-	1	NA	promoter-TSS (NR_110894)	promoter-TSS (NR_110894)	-54	NR_110894	194908	Mm.344651	NM_183139	ENSMUSG00000043648	Pld6	4933433K01Rik|Gm10|Zuc|mZuc|mitoPLD	phospholipase D family, member 6	protein-coding
mm_68098.1	chr7	102007757	102007760	-	1	NA	intron (NM_133947, intron 15 of 24)	AT_rich|Low_complexity|Low_complexity	10397	NM_010531	16068	Mm.422756	NM_010531	ENSMUSG00000070427	Il18bp	IL-18BP|Igifbp|MC54L	interleukin 18 binding protein	protein-coding
mm_149274.1	chr19	10605540	10605554	+	1	NA	promoter-TSS (NM_015735)	promoter-TSS (NM_015735)	-78	NM_015735	13194	Mm.289915	NM_015735	ENSMUSG00000024740	Ddb1	127kDa|AA408517|p127-Ddb1	damage specific DNA binding protein 1	protein-coding
mm_164908.1	chr18	70472555	70472557	+	1	NA	promoter-TSS (NM_001289649)	promoter-TSS (NM_001289649)	-16	NM_001289648	170461	Mm.83623	NM_029019	ENSMUSG00000079608	Stard6	1700011K09Rik|4833424I06Rik|4933429L05Rik|AI644424	StAR-related lipid transfer (START) domain containing 6	protein-coding
mm_55337.1	chr6	56362357	56362386	-	1	NA	promoter-TSS (NM_001159953)	promoter-TSS (NM_001159953)	21	NM_001159952	18575	Mm.5145	NM_011054	ENSMUSG00000004347	Pde1c	-	phosphodiesterase 1C	protein-coding
mm_121483.1	chr14	121057634	121057637	+	1	NA	intron (NM_134082, intron 1 of 26)	B1_Mus2|SINE|Alu	22061	NM_134082	223254	Mm.223980	NM_134082	ENSMUSG00000025555	Farp1	AW228844|BC030329|Cdep	FERM, RhoGEF (Arhgef) and pleckstrin domain protein 1 (chondrocyte-derived)	protein-coding
mm_143309.1	chr17	66051635	66051640	-	1	NA	intron (NM_001025572, intron 2 of 12)	intron (NM_001025572, intron 2 of 12)	25409	NM_001025572	106585	Mm.34706	NM_001025572	ENSMUSG00000034647	Ankrd12	2900001A12Rik|AI447928|ANCO-2|AV347965|GAC-1|mKIAA0874	ankyrin repeat domain 12	protein-coding
mm_92206.1	chr10	68137362	68137374	-	1	NA	intron (NM_023598, intron 4 of 9)	intron (NM_023598, intron 4 of 9)	141358	NM_023598	71371	Mm.440357	NM_023598	ENSMUSG00000019947	Arid5b	4930580B11|5430435G07Rik|AI467247|Desrt|Mrf2|Mrf2alpha|Mrf2beta	AT rich interactive domain 5B (MRF1-like)	protein-coding
mm_111764.1	chr12	104008737	104008753	-	1	NA	exon (NM_027997, exon 2 of 5)	exon (NM_027997, exon 2 of 5)	4907	NM_027997	71907	Mm.326723	NM_027997	ENSMUSG00000058260	Serpina9	2310014L03Rik|AW049635|Centerin	serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9	protein-coding
mm_155768.1	chrX	96240490	96240491	+	1	NA	non-coding (NR_030718, exon 2 of 3)	non-coding (NR_030718, exon 2 of 3)	564	NR_030718	100038363	Mm.30815	NR_030718	ENSMUSG00000078122	F630028O10Rik	ENSMUSG00000065522|Gm14924|OTTMUSG00000018496|mir-223	RIKEN cDNA F630028O10 gene	ncRNA
mm_98619.1	chr11	95843837	95843856	+	1	NA	5' UTR (NM_001284397, exon 2 of 4)	5' UTR (NM_001284397, exon 2 of 4)	601	NM_001284397	14710	Mm.46299	NM_023121	ENSMUSG00000038811	Gngt2	AV096488	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 2	protein-coding
mm_165668.1	chr3	88616424	88616438	+	1	NA	5' UTR (NM_001198911, exon 1 of 23)	5' UTR (NM_001198911, exon 1 of 23)	224	NM_001198911	16800	Mm.239329	NM_008487	ENSMUSG00000028059	Arhgef2	AA408978|GEF|GEF-H1|GEFH1|LFP40|Lbcl1|Lfc|P40|mKIAA0651	rho/rac guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_161344.1	chr14	52350211	52350211	-	1	NA	promoter-TSS (NM_001012269)	promoter-TSS (NM_001012269)	-167	NM_001012269	258008	Mm.377327	NM_001012269	ENSMUSG00000095030	Olfr1513	MOR223-10|MOR223-7P	olfactory receptor 1513	protein-coding
mm_65890.1	chr7	29954050	29954089	-	1	NA	Intergenic	Intergenic	-2176	NM_178384	72723	Mm.371648	NM_178384	ENSMUSG00000059975	Zfp74	2810054M15Rik|KRAB8|Zfp66|Znf569|mszf21|mszf77	zinc finger protein 74	protein-coding
mm_143044.1	chr17	56831059	56831128	-	1	NA	promoter-TSS (NM_009056)	promoter-TSS (NM_009056)	-85	NM_027787	19725	Mm.102	NM_009056	ENSMUSG00000024206	Rfx2	5430432H19Rik	regulatory factor X, 2 (influences HLA class II expression)	protein-coding
mm_137640.1	chr17	28522723	28522761	+	1	NA	Intergenic	Intergenic	-8119	NM_026290	67645	Mm.46170	NM_026290	ENSMUSG00000024223	Armc12	4930511I11Rik|AV041658	armadillo repeat containing 12	protein-coding
mm_158409.1	chrX	136958001	136958028	-	1	NA	promoter-TSS (NM_001080967)	promoter-TSS (NM_001080967)	-35	NM_001080967	100034363	Mm.381904	NM_001080967	ENSMUSG00000089996	Tmsb15b2	Tb15c	thymosin beta 15b2	protein-coding
mm_69152.1	chr7	127137808	127137827	-	1	NA	promoter-TSS (NM_001037810)	promoter-TSS (NM_001037810)	6	NR_110337	20737	Mm.283714	NM_009259	ENSMUSG00000051457	Spn	A630014B01Rik|Cd43|Galgp|Ly-48|Ly48	sialophorin	protein-coding
mm_55650.1	chr6	72366968	72366975	-	1	NA	promoter-TSS (NM_001331167)	promoter-TSS (NM_001331167)	1	NM_001331167	66510	Mm.170023	NM_025607	ENSMUSG00000055850	Rnf181	1700047F16Rik|2500002L14Rik|6230415N01Rik|C77350	ring finger protein 181	protein-coding
mm_100673.1	chr11	3371308	3371409	-	1	NA	promoter-TSS (NM_173053)	promoter-TSS (NM_173053)	34	NM_173053	16886	Mm.124176	NM_010718	ENSMUSG00000020451	Limk2	Limk-2|whe	LIM motif-containing protein kinase 2	protein-coding
mm_84048.1	chr9	58102273	58102305	-	1	NA	promoter-TSS (NM_029212)	promoter-TSS (NM_029212)	8	NM_001311085	382077	Mm.335193	NM_029212	ENSMUSG00000037716	Ccdc33	4930535E21Rik|Gm1117|Tzip1	coiled-coil domain containing 33	protein-coding
mm_162323.1	chr1	39608597	39608621	-	1	NA	Intergenic	Intergenic	-31262	NM_001033135	67702	Mm.28614	NM_001033135	ENSMUSG00000048234	Rnf149	1600023E10Rik|AV037261|C76763|Gm15832|Greul4|OTTMUSG00000026591	ring finger protein 149	protein-coding
mm_129451.1	chr15	78561466	78561490	-	1	NA	3' UTR (NM_009008, exon 7 of 7)	3' UTR (NM_009008, exon 7 of 7)	11305	NM_009008	19354	Mm.1972	NM_009008	ENSMUSG00000033220	Rac2	AI323801|AI452260	RAS-related C3 botulinum substrate 2	protein-coding
mm_123503.1	chr14	66232283	66232322	-	1	NA	intron (NM_001162365, intron 1 of 30)	intron (NM_001162365, intron 1 of 30)	-18750	NM_001162366	19229	Mm.21613	NM_172498	ENSMUSG00000059456	Ptk2b	CADTK|CAKB|CAKbeta|E430023O05Rik|FADK2|FAK2|PYK2|Raftk	PTK2 protein tyrosine kinase 2 beta	protein-coding
mm_158083.1	chrX	101266255	101266275	-	1	NA	exon (NM_013563, exon 5 of 8)	exon (NM_013563, exon 5 of 8)	1990	NM_001308535	16186	Mm.2923	NM_013563	ENSMUSG00000031304	Il2rg	CD132|[g]c|gamma(c)|gc|p64	interleukin 2 receptor, gamma chain	protein-coding
mm_150282.1	chr19	34290671	34290716	+	1	NA	promoter-TSS (NM_001146708)	promoter-TSS (NM_001146708)	34	NM_001146708	14102	Mm.1626	NM_007987	ENSMUSG00000024778	Fas	AI196731|APO1|APT1|CD95|TNFR6|Tnfrsf6|lpr	Fas (TNF receptor superfamily member 6)	protein-coding
mm_25196.1	chr3	103771927	103771938	+	1	NA	intron (NM_001301304, intron 2 of 15)	intron (NM_001301304, intron 2 of 15)	19343	NM_001301306	15257	Mm.20827	NM_010432	ENSMUSG00000008730	Hipk1	1110062K04Rik|Myak	homeodomain interacting protein kinase 1	protein-coding
mm_28025.1	chr3	83046687	83046714	-	1	NA	exon (NM_181849, exon 2 of 8)	exon (NM_181849, exon 2 of 8)	3163	NM_181849	110135	Mm.30063	NM_181849	ENSMUSG00000033831	Fgb	2510049G14Rik	fibrinogen beta chain	protein-coding
mm_9905.1	chr1	187199697	187199715	-	1	NA	intron (NM_028848, intron 1 of 9)	(GTGTG)n|Simple_repeat|Simple_repeat	15740	NM_029067	74717	Mm.250430	NM_028848	ENSMUSG00000026611	Spata17	1700065F16Rik|4930504I07Rik|4930513F16Rik|MSRG-11	spermatogenesis associated 17	protein-coding
mm_114841.1	chr13	92611169	92611179	+	1	NA	promoter-TSS (NM_172588)	promoter-TSS (NM_172588)	36	NM_172588	218442	Mm.297970	NM_172588	ENSMUSG00000021703	Serinc5	A130038L21Rik|AIGP3|C86123|TPO1	serine incorporator 5	protein-coding
mm_36486.1	chr4	83052148	83052185	-	1	NA	promoter-TSS (NM_001198811)	promoter-TSS (NM_001198811)	1	NM_001198811	329872	Mm.242337	NM_177863	ENSMUSG00000059049	Frem1	BC037594|D430009N09|D630008K06|crf11|eye<m02Jus>|eyes2|heb|qbrick	Fras1 related extracellular matrix protein 1	protein-coding
mm_53409.1	chr6	132569805	132569809	+	1	NA	promoter-TSS (NM_011174)	promoter-TSS (NM_011174)	-35	NM_011174	19131	Mm.425348	NM_011174	ENSMUSG00000059934	Prh1	MP2|Prp	proline rich protein HaeIII subfamily 1	protein-coding
mm_59429.1	chr7	27129756	27129762	+	1	NA	exon (NM_007817, exon 6 of 10)	exon (NM_007817, exon 6 of 10)	9804	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_96749.1	chr11	69884282	69884290	+	1	NA	intron (NM_153788, intron 17 of 21)	intron (NM_153788, intron 17 of 21)	-2192	NR_105889	102466208		NR_105889	ENSMUSG00000104996	Mir6924	mmu-mir-6924	microRNA 6924	ncRNA
mm_80723.1	chr9	92309392	92309401	+	1	NA	promoter-TSS (NM_001033184)	promoter-TSS (NM_001033184)	19	NM_001033184	78459	Mm.179195	NM_001033184	ENSMUSG00000074139	1700057G04Rik	-	RIKEN cDNA 1700057G04 gene	protein-coding
mm_76381.1	chr8	84840628	84840681	-	1	NA	promoter-TSS (NM_001297607)	promoter-TSS (NM_001297607)	11	NM_001297607	19358	Mm.255539	NM_009010	ENSMUSG00000003813	Rad23a	2310040P19Rik|AL024030|HR23A|mHR23A	RAD23 homolog A, nucleotide excision repair protein	protein-coding
mm_44126.1	chr5	149636818	149636841	+	1	NA	promoter-TSS (NM_013559)	promoter-TSS (NM_013559)	-493	NM_001347534	15505	Mm.270681	NM_013559	ENSMUSG00000029657	Hsph1	105kDa|AI790491|Hsp105|Hsp110|hsp-E7I|hsp110/105	heat shock 105kDa/110kDa protein 1	protein-coding
mm_43782.1	chr5	142401485	142401532	+	1	NA	promoter-TSS (NM_199068)	promoter-TSS (NM_199068)	11	NM_199068	17425	Mm.24214	NM_010812	ENSMUSG00000056493	Foxk1	A630048H08Rik|AI463295|ENSMUSG00000075577|Gm10868|Mnf	forkhead box K1	protein-coding
mm_985.1	chr1	58445532	58445618	+	1	NA	promoter-TSS (NM_027351)	promoter-TSS (NM_027351)	-89	NM_001285827	70225	Mm.340195	NM_027351	ENSMUSG00000026035	Ppil3	2310076N22Rik|2510026K04Rik|Cyp10l	peptidylprolyl isomerase (cyclophilin)-like 3	protein-coding
mm_50036.1	chr6	41137633	41137679	+	1	NA	Intergenic	Lx3_Mus|LINE|L1	-102147	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_10961.1	chr2	25700040	25700042	+	1	NA	promoter-TSS (NM_153558)	promoter-TSS (NM_153558)	-33	NM_153558	227627	Mm.44630	NM_153558	ENSMUSG00000062061	Obp2a	BC027556|Lcn13	odorant binding protein 2A	protein-coding
mm_18166.1	chr2	45102190	45102252	-	1	NA	intron (NM_001289521, intron 1 of 8)	intron (NM_001289521, intron 1 of 8)	8056	NM_001289521	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_86320.1	chr9	122950961	122951006	-	1	NA	promoter-TSS (NM_025419)	promoter-TSS (NM_025419)	17	NM_025419	66202	Mm.268307	NM_025419	ENSMUSG00000032551	1110059G10Rik	-	RIKEN cDNA 1110059G10 gene	protein-coding
mm_166514.1	chr6	14755328	14755332	-	1	NA	promoter-TSS (NM_080464)	promoter-TSS (NM_080464)	-56	NM_080464	140491	Mm.209429	NM_080464	ENSMUSG00000042717	Ppp1r3a	GM|RG1|RGL	protein phosphatase 1, regulatory (inhibitor) subunit 3A	protein-coding
mm_72247.1	chr8	75058344	75058357	+	1	NA	intron (NM_001136259, intron 8 of 15)	intron (NM_001136259, intron 8 of 15)	24664	NM_011622	21968	Mm.1967	NM_011622	ENSMUSG00000042870	Tom1	-	target of myb1 trafficking protein	protein-coding
mm_172334.1	chr7	109519616	109519621	+	1	NA	promoter-TSS (NR_028079)	promoter-TSS (NR_028079)	423	NM_011975	26451	Mm.305750	NM_011975	ENSMUSG00000046364	Rpl27a	L27'|L27A|L29	ribosomal protein L27A	protein-coding
mm_161503.1	chr15	96420637	96420637	-	1	NA	exon (NM_028148, exon 11 of 15)	exon (NM_028148, exon 11 of 15)	40206	NM_028148	72193	Mm.324474	NM_028148	ENSMUSG00000033228	Scaf11	1110061H03Rik|2610510E10Rik|AI462454|CASP11|SIP1|SRRP129|Sfrs2ip|Srsf2ip|mKIAA3013	SR-related CTD-associated factor 11	protein-coding
mm_2525.1	chr1	106860995	106861005	+	1	NA	promoter-TSS (NM_009257)	promoter-TSS (NM_009257)	-180	NM_009257	20724	Mm.268618	NM_009257	ENSMUSG00000067006	Serpinb5	1110036M19Rik|AI462524|AI646751|Maspin|PI-5|Spi7|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 5	protein-coding
mm_54382.1	chr6	31213793	31213797	-	1	NA	intron (NR_110469, intron 1 of 3)	intron (NR_110469, intron 1 of 3)	4679	NR_110470	232685	Mm.443019	NM_144555	ENSMUSG00000044471	Lncpint	Lincpint|MNCb-1768|Pint|linc-Pint	long non-protein coding RNA, Trp53 induced transcript	ncRNA
mm_159106.1	chr2	38712113	38712113	-	1	NA	5' UTR (NM_001316687, exon 1 of 7)	5' UTR (NM_001316687, exon 1 of 7)	121	NM_001316687	26423	Mm.31387	NM_139051	ENSMUSG00000026751	Nr5a1	Ad4BP|ELP|ELP-3|Ftz-F1|Ftzf1|SF-1|SF1|STF-1	nuclear receptor subfamily 5, group A, member 1	protein-coding
mm_125845.1	chr15	74958908	74958919	+	1	NA	3' UTR (NM_001164036, exon 4 of 4)	3' UTR (NM_001164036, exon 4 of 4)	3807	NM_001164040	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_128849.1	chr15	71728225	71728244	-	1	NA	promoter-TSS (NM_177819)	promoter-TSS (NM_177819)	-396	NM_177819	70363	Mm.126450	NM_177819	ENSMUSG00000036800	Fam135b	1700010C24Rik|A830008O07Rik	family with sequence similarity 135, member B	protein-coding
mm_149973.1	chr19	29067272	29067297	+	1	NA	promoter-TSS (NR_045687)	promoter-TSS (NR_045687)	-17	NR_045687	100503337	Mm.103412	NR_045687		Gm9895	ENSMUSG00000052976	predicted gene 9895	ncRNA
mm_55439.1	chr6	67035528	67035544	-	1	NA	3' UTR (NM_007836, exon 4 of 4)	3' UTR (NM_007836, exon 4 of 4)	-1063	NR_040278	320172	Mm.449039	NR_040278	ENSMUSG00000087231	E230016M11Rik	-	RIKEN cDNA E230016M11 gene	ncRNA
mm_20790.1	chr2	144010811	144010883	-	1	NA	intron (NM_024281, intron 1 of 23)	CpG	416	NM_133626	81910	Mm.13705	NM_024281	ENSMUSG00000027422	Rrbp1	1700087N07Rik|5730465C04Rik|ES/130|mKIAA1398|mRRp0|mRRp1.8|mRRp10|mRRp15a|mRRp15b|mRRp16.8|mRRp2|mRRp41|mRRp47|mRRp5.4|p180	ribosome binding protein 1	protein-coding
mm_134714.1	chr16	22895258	22895266	-	1	NA	promoter-TSS (NR_110508)	promoter-TSS (NR_110508)	-876	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_65507.1	chr7	25748424	25748458	-	1	NA	exon (NM_178089, exon 3 of 8)	exon (NM_178089, exon 3 of 8)	6260	NM_178089	232989	Mm.254223	NM_144922	ENSMUSG00000040725	Hnrnpul1	E130317O14Rik|E1B-AP5|E1BAP5|Hnrnpul|Hnrpul1	heterogeneous nuclear ribonucleoprotein U-like 1	protein-coding
mm_7950.1	chr1	133915291	133915295	-	1	NA	exon (NM_054077, exon 2 of 3)	exon (NM_054077, exon 2 of 3)	6108	NM_054077	116847	Mm.214514	NM_054077	ENSMUSG00000041577	Prelp	7330409J17Rik|SLRR2A	proline arginine-rich end leucine-rich repeat	protein-coding
mm_10819.1	chr2	24350989	24351029	+	1	NA	3' UTR (NM_031167, exon 5 of 5)	3' UTR (NM_031167, exon 5 of 5)	5638	NM_001039701	16181	Mm.882	NM_031167	ENSMUSG00000026981	Il1rn	F630041P17Rik|IL-1ra	interleukin 1 receptor antagonist	protein-coding
mm_170227.1	chr17	8147779	8147794	-	1	NA	promoter-TSS (NM_001083938)	promoter-TSS (NM_001083938)	2	NM_001083938	100037283	Mm.426736	NM_001083938	ENSMUSG00000095687	Rnaset2a	0610007O07Rik|4833423A10Rik|4930532K22Rik|C79750|RNASE6PL|Rnaset2	ribonuclease T2A	protein-coding
mm_159513.1	chr4	58943756	58943756	+	1	NA	intron (NM_001099323, intron 1 of 5)	CpG	128	NM_001099323	100041581	Mm.463942	NM_001099323	ENSMUSG00000038630	Zkscan16	XM_143800|Zfp483	zinc finger with KRAB and SCAN domains 16	protein-coding
mm_131989.1	chr16	25042344	25042346	+	1	NA	Intergenic	Intergenic	-17294	NR_040374	319487	Mm.137341	NR_040374	ENSMUSG00000096960	A230028O05Rik	-	RIKEN cDNA A230028O05 gene	ncRNA
mm_11851.1	chr2	45277031	45277090	+	1	NA	Intergenic	Intergenic	-163781	NM_015753	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_72790.1	chr8	86894024	86894027	+	1	NA	Intergenic	Intergenic	-8767	NM_030563	80750	Mm.25117	NM_030563	ENSMUSG00000031652	N4bp1	AI481586|C81621	NEDD4 binding protein 1	protein-coding
mm_162259.1	chrX	169927006	169927006	+	1	NA	5' UTR (NM_001290504, exon 2 of 10)	5' UTR (NM_001290504, exon 2 of 10)	47387	NM_001290505	17318	Mm.34441	NM_010797	ENSMUSG00000035299	Mid1	61B3-R|DXHXS1141|Fxy|Trim18	midline 1	protein-coding
mm_20592.1	chr2	131164155	131164170	-	1	NA	intron (NR_037281, intron 2 of 2)	MLT2F|LTR|ERVL	-4081	NM_001311138	67326	Mm.27711	NM_026091	ENSMUSG00000027327	1700037H04Rik	-	RIKEN cDNA 1700037H04 gene	protein-coding
mm_170130.1	chr17	39847226	39847238	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	4235	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_162128.1	chrX	73097019	73097019	-	1	NA	promoter-TSS (NM_001110784)	promoter-TSS (NM_001110784)	76	NM_001110784	22445	Mm.475098	NM_011726	ENSMUSG00000057836	Xlr3a	Xlr3	X-linked lymphocyte-regulated 3A	protein-coding
mm_151919.1	chr19	5799846	5799856	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	2821	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_68086.1	chr7	101870802	101870807	-	1	NA	promoter-TSS (NM_008034)	promoter-TSS (NM_008034)	-16	NM_001252552	14275	Mm.2135	NM_008034	ENSMUSG00000001827	Folr1	FBP1|Folbp-1|Folbp1	folate receptor 1 (adult)	protein-coding
mm_135834.1	chr16	58523542	58523592	-	1	NA	promoter-TSS (NM_018784)	promoter-TSS (NM_018784)	-255	NM_018784	54613	Mm.212742	NM_018784	ENSMUSG00000022747	St3gal6	1700023B24Rik|AI930218|AW552396|Siat10|St3galVI	ST3 beta-galactoside alpha-2,3-sialyltransferase 6	protein-coding
mm_48177.1	chr5	137307634	137307728	-	1	NA	promoter-TSS (NM_031405)	promoter-TSS (NM_031405)	-7	NM_001109909	83701	Mm.387734	NM_031405	ENSMUSG00000037364	Srrt	2810019G02Rik|ASR2A|ASR2B|ASR2C|ASR2D|Ars2|Asr2	serrate RNA effector molecule homolog (Arabidopsis)	protein-coding
mm_60405.1	chr7	44475969	44475973	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	5624	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_171711.1	chr4	79327696	79327696	+	1	NA	Intergenic	Intergenic	733649	NR_131142	623726		NR_131142		A430085M09Rik	EG623726	RIKEN cDNA A430085M09 gene	ncRNA
mm_8203.1	chr1	138123533	138123543	-	1	NA	intron (NM_001111316, intron 2 of 31)	intron (NM_001111316, intron 2 of 31)	51588	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_92074.1	chr10	62651171	62651192	-	1	NA	promoter-TSS (NM_053183)	promoter-TSS (NM_053183)	17	NM_053183	94213	Mm.114116	NM_053183	ENSMUSG00000020076	Ddx50	4933429B04Rik|8430408E17Rik|GU2|RH-II	DEAD (Asp-Glu-Ala-Asp) box polypeptide 50	protein-coding
mm_138669.1	chr17	35879826	35879845	+	1	NA	promoter-TSS (NM_026987)	promoter-TSS (NM_026987)	57	NM_026987	69192	Mm.390986	NM_026987	ENSMUSG00000024422	Dhx16	2410006N22Rik|DBP2|Ddx16|mKIAA0577	DEAH (Asp-Glu-Ala-His) box polypeptide 16	protein-coding
mm_42222.1	chr5	113364936	113364952	+	1	NA	Intergenic	Intergenic	7650	NM_001012726	503692	Mm.348794	NM_001012726	ENSMUSG00000053873	Aym1	-	activator of yeast meiotic promoters 1	protein-coding
mm_30357.1	chr3	151764185	151764202	-	1	NA	Intergenic	Intergenic	-1302	NM_031367	15061	Mm.219544	NM_031367	ENSMUSG00000039146	Ifi44l	H-28|H28|H28-1|NS1178	interferon-induced protein 44 like	protein-coding
mm_142935.1	chr17	56005559	56005565	-	1	NA	promoter-TSS (NR_102313)	promoter-TSS (NR_102313)	44	NM_145934	106766	Mm.204991	NM_145934	ENSMUSG00000038781	Stap2	AW049765|STAP-2	signal transducing adaptor family member 2	protein-coding
mm_133848.1	chr16	96205861	96205865	+	1	NA	intron (NM_015825, intron 1 of 7)	intron (NM_015825, intron 1 of 7)	5393	NM_015825	50795	Mm.28638	NM_015825	ENSMUSG00000040666	Sh3bgr	5430437A18Rik	SH3-binding domain glutamic acid-rich protein	protein-coding
mm_54068.1	chr6	14754591	14754600	-	1	NA	exon (NM_080464, exon 1 of 4)	exon (NM_080464, exon 1 of 4)	679	NM_080464	140491	Mm.209429	NM_080464	ENSMUSG00000042717	Ppp1r3a	GM|RG1|RGL	protein phosphatase 1, regulatory (inhibitor) subunit 3A	protein-coding
mm_42975.1	chr5	123148257	123148269	+	1	NA	exon (NM_001040398, exon 6 of 17)	exon (NM_001040398, exon 6 of 17)	6070	NM_001040398	208043	Mm.250391	NM_177581	ENSMUSG00000038384	Setd1b	AA516740|BC035291|KMT2G|mKIAA1076	SET domain containing 1B	protein-coding
mm_73521.1	chr8	107503183	107503202	+	1	NA	intron (NM_025830, intron 6 of 23)	intron (NM_025830, intron 6 of 23)	-48052	NR_029553	387158		NR_029553	ENSMUSG00000065439	Mir140	Mirn140|mir-140|mmu-mir-140	microRNA 140	ncRNA
mm_33726.1	chr4	134093537	134093542	+	1	NA	TTS (NM_013706)	TTS (NM_013706)	1534	NM_013706	23833	Mm.24130	NM_013706	ENSMUSG00000000682	Cd52	AI463198|B7|B7-Ag|CAMPATH-1|CLS1|MB7	CD52 antigen	protein-coding
mm_45285.1	chr5	64960033	64960069	-	1	NA	promoter-TSS (NM_011604)	promoter-TSS (NM_011604)	-17	NM_011604	21899	Mm.42146	NM_011604	ENSMUSG00000051498	Tlr6	-	toll-like receptor 6	protein-coding
mm_153243.1	chr19	36119358	36119367	-	1	NA	exon (NM_013468, exon 2 of 9)	exon (NM_013468, exon 2 of 9)	482	NM_013468	107765	Mm.10279	NM_013468	ENSMUSG00000024803	Ankrd1	Alrp|CARP|Crap|MARP1	ankyrin repeat domain 1 (cardiac muscle)	protein-coding
mm_138452.1	chr17	35135858	35135870	+	1	NA	intron (NM_001252469, intron 1 of 23)	intron (NM_001252469, intron 1 of 23)	150	NM_001252469	224727	Mm.203962	NM_057171	ENSMUSG00000024392	Bag6	2410045D21Rik|AA408914|BAG-6|Bat3|D17H6S52E|G3|Scythe	BCL2-associated athanogene 6	protein-coding
mm_118308.1	chr13	113101228	113101236	-	1	NA	promoter-TSS (NM_010370)	promoter-TSS (NM_010370)	-251	NM_010370	14938	Mm.15510	NM_010370	ENSMUSG00000023132	Gzma	AW494114|Ctla-3|Ctla3|Hf|Hf1|SE1|TSP-1|TSP1	granzyme A	protein-coding
mm_156560.1	chrX	151803314	151803376	+	1	NA	promoter-TSS (NM_021523)	promoter-TSS (NM_021523)	63	NM_021523	59026	Mm.27372	NM_021523	ENSMUSG00000025261	Huwe1	5430439H10Rik|AU041296|Arf-bp1|C430014N20Rik|C80292|Gm1718|Ib772|LASU1|Mule|Ureb1	HECT, UBA and WWE domain containing 1	protein-coding
mm_74645.1	chr8	13351008	13351011	-	1	NA	intron (NM_001291766, intron 2 of 10)	intron (NM_001291766, intron 2 of 10)	12205	NM_009361	21781	Mm.925	NM_009361	ENSMUSG00000038482	Tfdp1	Dp1|Drtf1	transcription factor Dp 1	protein-coding
mm_55645.1	chr6	72361037	72361039	-	1	NA	intron (NM_001331171, intron 3 of 4)	intron (NM_001331171, intron 3 of 4)	1394	NR_138581	66510	Mm.170023	NM_025607	ENSMUSG00000055850	Rnf181	1700047F16Rik|2500002L14Rik|6230415N01Rik|C77350	ring finger protein 181	protein-coding
mm_37900.1	chr4	132727628	132727640	-	1	NA	3' UTR (NM_201368, exon 3 of 3)	3' UTR (NM_201368, exon 3 of 3)	4912	NM_201368	381560	Mm.44558	NM_201368	ENSMUSG00000037752	Xkr8	4931440N07Rik|AI597014|Gm1031|XRG8|mXkr8	X-linked Kx blood group related 8	protein-coding
mm_150699.1	chr19	42255705	42255761	+	1	NA	promoter-TSS (NM_027694)	promoter-TSS (NM_027694)	-6	NM_027694	71146	Mm.329851	NM_027694	ENSMUSG00000042532	Golga7b	4933417O08Rik|AI839934	golgi autoantigen, golgin subfamily a, 7B	protein-coding
mm_2974.1	chr1	133092286	133092298	+	1	NA	exon (NM_001099276, exon 21 of 33)	exon (NM_001099276, exon 21 of 33)	-38874	NM_133819	108954	Mm.293628	NM_133819	ENSMUSG00000046062	Ppp1r15b	1810033K10Rik|AI606441|C530022L24Rik|CReP	protein phosphatase 1, regulatory (inhibitor) subunit 15b	protein-coding
mm_17085.1	chr2	22987549	22987589	-	1	NA	intron (NM_001331043, intron 2 of 10)	intron (NM_001331043, intron 2 of 10)	52672	NM_001077192	11308	Mm.205647	NM_007380	ENSMUSG00000058835	Abi1	E3B1|NAP1|Ssh3bp1|abi-1	abl-interactor 1	protein-coding
mm_123957.1	chr14	74806523	74806523	-	1	NA	intron (NM_001252132, intron 10 of 18)	intron (NM_001252132, intron 10 of 18)	74226	NM_016903	13885	Mm.38055	NM_016903	ENSMUSG00000021996	Esd	Es-10|Es10|FGH|sid478	esterase D/formylglutathione hydrolase	protein-coding
mm_98980.1	chr11	98740659	98740672	+	1	NA	Intergenic	Intergenic	-1120	NM_178060	21833	Mm.265917	NM_178060	ENSMUSG00000058756	Thra	6430529J03Rik|AW259572|Erba|Nr1a1|Rvr|T3R[a]|T3Ralpha|Thra1|Thra2|c-erbA-1|c-erbA-alpha|c-erbAalpha	thyroid hormone receptor alpha	protein-coding
mm_87270.1	chr10	41809949	41809963	+	1	NA	promoter-TSS (NM_001162908)	promoter-TSS (NM_001162908)	-88	NM_026643	103268	Mm.338605	NM_026643	ENSMUSG00000019813	Cep57l1	2410017P07Rik|4930484D11Rik|AI607327|cep57R	centrosomal protein 57-like 1	protein-coding
mm_195.1	chr1	15805624	15805632	+	1	NA	promoter-TSS (NM_001286628)	promoter-TSS (NM_001286628)	-18	NM_009352	21749	Mm.4306	NM_009352	ENSMUSG00000025925	Terf1	Pin2|Trbf1|Trf1	telomeric repeat binding factor 1	protein-coding
mm_22905.1	chr3	30864270	30864310	+	1	NA	intron (NM_001286994, intron 1 of 3)	MTD|LTR|ERVL-MaLR	8340	NM_001286994	71862	Mm.272019	NM_027965	ENSMUSG00000037661	Gpr160	1700025D19Rik|GPCR150	G protein-coupled receptor 160	protein-coding
mm_12360.1	chr2	69749918	69749930	+	1	NA	exon (NM_001081086, exon 14 of 14)	exon (NM_001081086, exon 14 of 14)	26836	NM_001081086	228005	Mm.11815	NM_001081086	ENSMUSG00000042133	Ppig	AU019516|AU022200|B230312B02Rik|CYP|SRCyp	peptidyl-prolyl isomerase G (cyclophilin G)	protein-coding
mm_65079.1	chr7	19165134	19165154	-	1	NA	intron (NM_001080815, intron 1 of 13)	intron (NM_001080815, intron 1 of 13)	983	NM_001080815	381853	Mm.333633	NM_001080815	ENSMUSG00000030406	Gipr	GIP-R|Gm1081|Gm160	gastric inhibitory polypeptide receptor	protein-coding
mm_57165.1	chr6	122801662	122801677	-	1	NA	Intergenic	CpG	-18515	NM_021899	60611	Mm.87142	NM_021899	ENSMUSG00000003154	Foxj2	Fhx	forkhead box J2	protein-coding
mm_48048.1	chr5	136466065	136466070	-	1	NA	intron (NM_001291239, intron 2 of 22)	(A)n|Simple_repeat|Simple_repeat	-90264	NR_030500	723975		NR_030500	ENSMUSG00000106479	Mir721	Mirn721|miRY|mir-721|mmu-mir-721	microRNA 721	ncRNA
mm_115198.1	chr13	109111047	109111054	+	1	NA	intron (NM_011056, intron 3 of 16)	intron (NM_011056, intron 3 of 16)	-213694	NR_030644	100124489		NR_030644	ENSMUSG00000076946	Mir582	Mirn582|mir-582|mmu-mir-582	microRNA 582	ncRNA
mm_127421.1	chr15	101267101	101267112	+	1	NA	intron (NM_010444, intron 1 of 6)	intron (NM_010444, intron 1 of 6)	260	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_66824.1	chr7	48691777	48691781	-	1	NA	Intergenic	Intergenic	-47978	NM_207537	404238	Mm.377926	NM_207537	ENSMUSG00000070546	Mrgprb3	MrgB3	MAS-related GPR, member B3	protein-coding
mm_81658.1	chr9	110965257	110965278	+	1	NA	intron (NM_028838, intron 4 of 8)	ORR1E|LTR|ERVL-MaLR	13722	NM_028838	74249	Mm.307615	NM_028838	ENSMUSG00000032495	Lrrc2	2400002D05Rik|4933431K03Rik	leucine rich repeat containing 2	protein-coding
mm_34734.1	chr4	152190049	152190080	+	1	NA	intron (NM_001146057, intron 1 of 8)	intron (NM_001146057, intron 1 of 8)	3930	NM_001146057	70025	Mm.296191	NM_133348	ENSMUSG00000028937	Acot7	2410041A17Rik|Ach1|Act|Bach|CTE-IIa|Cte-II|Lach1	acyl-CoA thioesterase 7	protein-coding
mm_15617.1	chr2	160888102	160888113	+	1	NA	promoter-TSS (NM_001199118)	promoter-TSS (NM_001199118)	-61	NM_001199118	64899	Mm.292111	NM_022883	ENSMUSG00000027412	Lpin3	9130206L11Rik|AA438110|AV236139|mKIAA4023	lipin 3	protein-coding
mm_145467.1	chr18	60291334	60291345	+	1	NA	Intergenic	Lx7|LINE|L1	-2041	NM_001101475	240328	Mm.329461	NM_001101475	ENSMUSG00000090942	F830016B08Rik	Ifgga4	RIKEN cDNA F830016B08 gene	protein-coding
mm_72309.1	chr8	77549446	77549464	+	1	NA	promoter-TSS (NM_001081240)	promoter-TSS (NM_001081240)	58	NM_001081240	102182	Mm.197630	NM_178903	ENSMUSG00000037134	Prmt9	AI931714|Prmt10	protein arginine methyltransferase 9	protein-coding
mm_138226.1	chr17	34354788	34354836	+	1	NA	promoter-TSS (NM_079835)	promoter-TSS (NM_079835)	-10	NM_079835	547431	Mm.441007	NM_079835	ENSMUSG00000024340	Btnl2	BTL-II|BTLN2|Btl2|Gm315|NG9	butyrophilin-like 2	protein-coding
mm_141307.1	chr17	28232540	28232562	-	1	NA	promoter-TSS (NM_011145)	promoter-TSS (NM_011145)	-203	NM_011145	19015	Mm.328914	NM_011145	ENSMUSG00000002250	Ppard	NUC-1|NUC1|Nr1c2|PPAR-beta|PPAR-delta|PPAR[b]|PPARdelta|Pparb|Pparb/d	peroxisome proliferator activator receptor delta	protein-coding
mm_156983.1	chrX	7319158	7319178	-	1	NA	5' UTR (NM_001243762, exon 1 of 14)	5' UTR (NM_001243762, exon 1 of 14)	190	NM_001243762	12728	Mm.486257	NM_016691	ENSMUSG00000004317	Clcn5	5430408K11Rik|ClC-5|Clc4-1|Clc5|Clcn4-1|D930009B12Rik|DXImx42e|Sfc13|T25545	chloride channel, voltage-sensitive 5	protein-coding
mm_1889.1	chr1	85682389	85682402	+	1	NA	3' UTR (NM_001313714, exon 12 of 12)	3' UTR (NM_001313714, exon 12 of 12)	32407	NM_001313714	20684	Mm.290906	NM_013673	ENSMUSG00000026222	Sp100	A430075G10Rik	nuclear antigen Sp100	protein-coding
mm_27784.1	chr3	74126429	74126438	-	1	NA	Intergenic	RMER17B|LTR|ERVK	-109156	NR_040450	100504692	Mm.394454	NR_040450	ENSMUSG00000104096	Gm20356	-	predicted gene, 20356	ncRNA
mm_114272.1	chr13	58157628	58157634	+	1	NA	promoter-TSS (NM_001048060)	promoter-TSS (NM_001048060)	-18	NM_001048060	75731	Mm.293919	NM_198004	ENSMUSG00000050002	Idnk	5133401N09Rik	idnK gluconokinase homolog (E. coli)	protein-coding
mm_102906.1	chr11	69555779	69555789	-	1	NA	3' UTR (NM_007911, exon 5 of 5)	3' UTR (NM_007911, exon 5 of 5)	4453	NM_007911	13643	Mm.249637	NM_007911	ENSMUSG00000003934	Efnb3	EFL-6|ELF-3|Elk-L3|Epl8|LERK-8|NLERK-2	ephrin B3	protein-coding
mm_24836.1	chr3	95659261	95659280	+	1	NA	exon (NM_008562, exon 1 of 3)	exon (NM_008562, exon 1 of 3)	549	NM_008562	17210	Mm.1639	NM_008562	ENSMUSG00000038612	Mcl1	AW556805|Mcl-1	myeloid cell leukemia sequence 1	protein-coding
mm_96568.1	chr11	69027341	69027359	+	1	NA	exon (NM_001281465, exon 8 of 23)	exon (NM_001281465, exon 8 of 23)	11439	NM_001013256	68964	Mm.285785	NM_001013256	ENSMUSG00000020898	Ctc1	1500010J02Rik|AAF-132|AAF132	CTS telomere maintenance complex component 1	protein-coding
mm_66683.1	chr7	45814303	45814321	-	1	NA	promoter-TSS (NM_001112701)	promoter-TSS (NM_001112701)	4	NM_011181	19158	Mm.272130	NM_011181	ENSMUSG00000003269	Cyth2	ARNO|CLM2|Pscd2	cytohesin 2	protein-coding
mm_24627.1	chr3	93555156	93555171	+	1	NA	promoter-TSS (NM_009112)	promoter-TSS (NM_009112)	46	NM_009112	20194	Mm.1	NM_009112	ENSMUSG00000041959	S100a10	42C|AA409961|AL024248|CAL12|CLP11|Cal1l|p10|p11	S100 calcium binding protein A10 (calpactin)	protein-coding
mm_137550.1	chr17	27561307	27561315	+	1	NA	intron (NM_001166546, intron 3 of 4)	intron (NM_001166546, intron 3 of 4)	4416	NM_001002895	106672	Mm.61488	NM_001002895	ENSMUSG00000062753	AI413582	AI854251	expressed sequence AI413582	protein-coding
mm_50343.1	chr6	48554777	48554845	+	1	NA	promoter-TSS (NM_177736)	promoter-TSS (NM_177736)	12	NM_177736	243371	Mm.290764	NM_177736	ENSMUSG00000073096	Lrrc61	BC027309	leucine rich repeat containing 61	protein-coding
mm_96478.1	chr11	67682156	67682165	+	1	NA	intron (NM_001109657, intron 12 of 13)	intron (NM_001109657, intron 12 of 13)	-13166	NM_009038	19674	Mm.439726	NM_009038	ENSMUSG00000020907	Rcvrn	CAR|S-modulin	recoverin	protein-coding
mm_127845.1	chr15	7244967	7244987	-	1	NA	intron (NM_001289496, intron 12 of 22)	(TG)n|Simple_repeat|Simple_repeat	104435	NM_013584	16880	Mm.149720	NM_013584	ENSMUSG00000054263	Lifr	A230075M04Rik|AW061234|LIF	leukemia inhibitory factor receptor	protein-coding
mm_131179.1	chr16	7144696	7144708	+	1	NA	intron (NM_183188, intron 1 of 12)	intron (NM_183188, intron 1 of 12)	74867	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_72860.1	chr8	88521249	88521280	+	1	NA	promoter-TSS (NM_027280)	promoter-TSS (NM_027280)	-80	NM_027280	93960	Mm.30219	NM_027280	ENSMUSG00000031661	Nkd1	2810434J10Rik|9030215G15Rik|Nkd	naked cuticle 1 homolog (Drosophila)	protein-coding
mm_39071.1	chr4	154158157	154158194	-	1	NA	3' UTR (NM_026388, exon 4 of 4)	3' UTR (NM_026388, exon 4 of 4)	2509	NM_026388	67808	Mm.288737	NM_026388	ENSMUSG00000029030	Tprgl	1200015A19Rik|Svap30|Tprg1l|mover	transformation related protein 63 regulated like	protein-coding
mm_144350.1	chr18	15195374	15195384	+	1	NA	Intergenic	Intergenic	-43933	NM_134112	106931	Mm.329299	NM_134112	ENSMUSG00000036225	Kctd1	4933402K10Rik|AI661543|AW553000	potassium channel tetramerisation domain containing 1	protein-coding
mm_116964.1	chr13	56176011	56176035	-	1	NA	3' UTR (NM_001168615, exon 3 of 3)	3' UTR (NM_001168615, exon 3 of 3)	2862	NM_145976	212937	Mm.116697	NM_145976	ENSMUSG00000049625	Tifab	-	TRAF-interacting protein with forkhead-associated domain, family member B	protein-coding
mm_149030.1	chr19	8774485	8774496	+	1	NA	promoter-TSS (NR_015538)	promoter-TSS (NR_015538)	5	NR_015538	100039957	Mm.220886	NR_015538		Gm2518	D630022E15Rik	interferon induced transmembrane protein 2 pseudogene	pseudo
mm_46687.1	chr5	109845003	109845009	-	1	NA	Intergenic	Intergenic	-10864	NR_027964	667213	Mm.454429	NR_027964	ENSMUSG00000105044	Gm10416	EG667213|ENSMUSG00000072761	zinc finger protein pseudogene	pseudo
mm_143259.1	chr17	65594932	65594991	-	1	NA	exon (NM_013933, exon 2 of 6)	exon (NM_013933, exon 2 of 6)	18594	NM_013933	30960	Mm.266767	NM_013933	ENSMUSG00000024091	Vapa	33kDa|VAP33	vesicle-associated membrane protein, associated protein A	protein-coding
mm_59439.1	chr7	27132455	27132516	+	1	NA	exon (NM_007817, exon 9 of 10)	exon (NM_007817, exon 9 of 10)	12530	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_93.1	chr1	7119820	7119825	+	1	NA	intron (NM_183028, intron 1 of 5)	intron (NM_183028, intron 1 of 5)	30902	NM_183028	319263	Mm.21539	NM_183028	ENSMUSG00000051285	Pcmtd1	8430411F12Rik|A030012M09Rik	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding
mm_72584.1	chr8	84208894	84208902	+	1	NA	promoter-TSS (NR_037294)	promoter-TSS (NR_037294)	9	NR_037294	100526528		NR_037294	ENSMUSG00000105458	Mir3074-2	mir-3074-2|mmu-mir-3074-2	microRNA 3074-2	ncRNA
mm_30539.1	chr4	3649252	3649259	+	1	NA	Intergenic	Intergenic	-7251	NR_040643	70143	Mm.417835	NR_040643	ENSMUSG00000085394	2210414B05Rik	-	RIKEN cDNA 2210414B05 gene	ncRNA
mm_20446.1	chr2	129364706	129364728	-	1	NA	3' UTR (NM_008361, exon 7 of 7)	3' UTR (NM_008361, exon 7 of 7)	-5185	NR_015474	329514	Mm.207315	NM_177848	ENSMUSG00000074805	Il1bos	9430083I22|Gm14047|OTTMUSG00000015529	interleukin 1 beta, opposite strand	ncRNA
mm_101475.1	chr11	30771661	30771679	-	1	NA	promoter-TSS (NM_134013)	promoter-TSS (NM_134013)	-105	NM_134013	103554	Mm.240066	NM_134013	ENSMUSG00000040850	Psme4	AA409398|AU041366|TEMO|mKIAA0077	proteasome (prosome, macropain) activator subunit 4	protein-coding
mm_114962.1	chr13	97071628	97071637	+	1	NA	promoter-TSS (NM_001100458)	promoter-TSS (NM_001100458)	-11	NM_001100458	320557	Mm.458280	NM_001100458	ENSMUSG00000041817	Fam169a	B230112C05Rik|SLAP75	family with sequence similarity 169, member A	protein-coding
mm_122343.1	chr14	37135311	37135321	-	1	NA	promoter-TSS (NM_001199122)	promoter-TSS (NM_001199122)	6	NM_078478	66092	Mm.182912	NM_078478	ENSMUSG00000041028	Ghitm	1010001P14Rik|C77840|MICS1|PTD010|Tmbim5	growth hormone inducible transmembrane protein	protein-coding
mm_17135.1	chr2	24975085	24975095	-	1	NA	promoter-TSS (NM_001031808)	promoter-TSS (NM_001031808)	8	NM_001031808	107733	Mm.23010	NM_001031808	ENSMUSG00000036850	Mrpl41	MRP-L27|Rpml27	mitochondrial ribosomal protein L41	protein-coding
mm_132912.1	chr16	48873624	48873638	+	1	NA	exon (NM_181596, exon 3 of 4)	exon (NM_181596, exon 3 of 4)	1023	NM_181596	245195	Mm.231288	NM_181596	ENSMUSG00000022651	Retnlg	Fizz3|Relmg|Xcp1	resistin like gamma	protein-coding
mm_86945.1	chr10	24640758	24640761	+	1	NA	3' UTR (NM_008813, exon 25 of 25)	3' UTR (NM_008813, exon 25 of 25)	45317	NM_010217	14219	Mm.390287	NM_010217	ENSMUSG00000019997	Ctgf	Ccn2|Fisp12|Hcs24|fisp-12	connective tissue growth factor	protein-coding
mm_19476.1	chr2	92540968	92540987	-	1	NA	Intergenic	Intergenic	-51229	NR_106080	102466819		NR_106080	ENSMUSG00000099223	Mir7221	Gm27378|mmu-mir-7221	microRNA 7221	ncRNA
mm_74952.1	chr8	25990093	25990115	-	1	NA	intron (NM_029037, intron 1 of 4)	intron (NM_029037, intron 1 of 4)	4017	NM_029037	74653	Mm.17631	NM_029037	ENSMUSG00000037251	Pomk	4930444A02Rik|Sgk196	protein-O-mannose kinase	protein-coding
mm_58652.1	chr7	6363288	6363300	+	1	NA	promoter-TSS (NM_001025163)	promoter-TSS (NM_001025163)	-14	NM_001025163	330463	Mm.136456	NM_177888	ENSMUSG00000055150	Zfp78	A330079D15|KRAB12|Zfp77	zinc finger protein 78	protein-coding
mm_49741.1	chr6	34745859	34745867	+	1	NA	exon (NM_145575, exon 3 of 12)	exon (NM_145575, exon 3 of 12)	-34569	NM_001289657	76223	Mm.150047	NM_178630	ENSMUSG00000038836	Agbl3	2900053G10Rik|4930431N21Rik|6530406M24Rik|CCP3	ATP/GTP binding protein-like 3	protein-coding
mm_105896.1	chr11	114982610	114982616	-	1	NA	3' UTR (NM_145437, exon 4 of 4)	3' UTR (NM_145437, exon 4 of 4)	7273	NM_145437	217305	Mm.275986	NM_145437	ENSMUSG00000034641	Cd300ld	4732429D16Rik|CLM5|Cd300ld1|LMIR4|MAIR-IV|clm-5	CD300 molecule like family member d	protein-coding
mm_77320.1	chr8	118465745	118465751	-	1	NA	intron (NM_019707, intron 1 of 13)	intron (NM_019707, intron 1 of 13)	182137	NM_019707	12554	Mm.334841	NM_019707	ENSMUSG00000031841	Cdh13	4932416G01Rik|Cdht|Tcad	cadherin 13	protein-coding
mm_142424.1	chr17	45569099	45569109	-	1	NA	exon (NM_008302, exon 9 of 11)	exon (NM_008302, exon 9 of 11)	4157	NM_008302	15516	Mm.2180	NM_008302	ENSMUSG00000023944	Hsp90ab1	90kDa|AL022974|C81438|Hsp84|Hsp84-1|Hsp90|Hspcb	heat shock protein 90 alpha (cytosolic), class B member 1	protein-coding
mm_61103.1	chr7	51887898	51887941	+	1	NA	5' UTR (NM_001330607, exon 2 of 8)	5' UTR (NM_001330607, exon 2 of 8)	8952	NM_001330607	14453	Mm.207360	NM_008087	ENSMUSG00000030498	Gas2	Gas-2	growth arrest specific 2	protein-coding
mm_64468.1	chr7	143005650	143005673	+	1	NA	promoter-TSS (NM_001128082)	promoter-TSS (NM_001128082)	2	NM_001128081	27027	Mm.28172	NM_020286	ENSMUSG00000000244	Tspan32	AW208513|Art-1|BB235973|D7Wsu37e|Phemx|Tssc6	tetraspanin 32	protein-coding
mm_142330.1	chr17	43504268	43504277	-	1	NA	Intergenic	Intergenic	-1499	NM_008585	17287	Mm.5346	NM_008585	ENSMUSG00000023914	Mep1a	AI098089|AW107200|Mep-1|Mep-1a|Mep1	meprin 1 alpha	protein-coding
mm_100015.1	chr11	114883500	114883525	+	1	NA	Intergenic	Intergenic	-6529	NM_001347654	217303	Mm.294439	NM_170758	ENSMUSG00000034652	Cd300a	B230315M08Rik|Clm8|LMIR1|MAIR-I|MAIR-Ia|MMAC8|Pigr4|mcpir1	CD300A molecule	protein-coding
mm_51521.1	chr6	83161793	83161804	+	1	NA	exon (NM_027948, exon 4 of 4)	exon (NM_027948, exon 4 of 4)	-4126	NM_001198866	13191	Mm.6919	NM_007835	ENSMUSG00000031865	Dctn1	AL022633|DAP-150|DP-150|Glued|p150|p150-glued|p150<glued>	dynactin 1	protein-coding
mm_149403.1	chr19	11392687	11392692	+	1	NA	exon (NM_001310331, exon 7 of 7)	exon (NM_001310331, exon 7 of 7)	-14972	NM_029499	64380	Mm.440715	NM_029499	ENSMUSG00000024675	Ms4a4c	5830413L19Rik|AI449185|Ms4a9	membrane-spanning 4-domains, subfamily A, member 4C	protein-coding
mm_22544.1	chr3	8923898	8923912	+	1	NA	promoter-TSS (NM_025434)	promoter-TSS (NM_025434)	-48	NM_025434	66230	Mm.38460	NM_025434	ENSMUSG00000040269	Mrps28	1500012D08Rik|AW061224	mitochondrial ribosomal protein S28	protein-coding
mm_150184.1	chr19	32649136	32649139	+	1	NA	intron (NM_011864, intron 8 of 12)	intron (NM_011864, intron 8 of 12)	29132	NM_011864	23972	Mm.203916	NM_011864	ENSMUSG00000024899	Papss2	1810018P12Rik|AI159688|AtpsU2|Atpsk2|Sk2|bm	3'-phosphoadenosine 5'-phosphosulfate synthase 2	protein-coding
mm_145901.1	chr18	65697985	65698004	+	1	NA	promoter-TSS (NM_177028)	promoter-TSS (NM_177028)	-274	NM_177028	319888	Mm.183576	NM_177028	ENSMUSG00000046610	Oacyl	5330437I02Rik|Acyl3	O-acyltransferase like	protein-coding
mm_103312.1	chr11	73137298	73137341	-	1	NA	exon (NM_010353, exon 1 of 1)	exon (NM_010353, exon 1 of 1)	975	NM_010353	14841	Mm.42045	NM_010353	ENSMUSG00000050107	Gsg2	Haspin	germ cell associated 2, haspin	protein-coding
mm_124344.1	chr14	103844421	103844432	-	1	NA	promoter-TSS (NM_001136061)	promoter-TSS (NM_001136061)	50	NM_001136061	13618	Mm.229532	NM_007904	ENSMUSG00000022122	Ednrb	ET-B|ET-BR|ETR-b|ETb|Sox10m1	endothelin receptor type B	protein-coding
mm_9241.1	chr1	171329510	171329537	-	1	NA	5' UTR (NM_001128609, exon 1 of 6)	5' UTR (NM_001128609, exon 1 of 6)	378	NM_011615	21945	Mm.270139	NM_011615	ENSMUSG00000013973	Dedd	CASP8IP1|DEFT|Dedpro1|FLDED1|KE05	death effector domain-containing	protein-coding
mm_143477.1	chr17	71256864	71256878	-	1	NA	intron (NM_145158, intron 4 of 7)	intron (NM_145158, intron 4 of 7)	52217	NM_001164885	64898	Mm.227924	NM_022882	ENSMUSG00000024052	Lpin2	2610511G02Rik|AI481352|AW742896	lipin 2	protein-coding
mm_46570.1	chr5	107192359	107192371	-	1	NA	intron (NM_011578, intron 3 of 16)	intron (NM_011578, intron 3 of 16)	97230	NM_011578	21814	Mm.200775	NM_011578	ENSMUSG00000029287	Tgfbr3	1110036H20Rik|AU015626|AW215636|TBRIII	transforming growth factor, beta receptor III	protein-coding
mm_121020.1	chr14	79587655	79587668	+	1	NA	promoter-TSS (NM_026474)	promoter-TSS (NM_026474)	-30	NM_026474	67955	Mm.18972	NM_026474	ENSMUSG00000022024	Sugt1	2410174K12Rik|SGT1	SGT1, suppressor of G2 allele of SKP1 (S. cerevisiae)	protein-coding
mm_22164.1	chr2	172978342	172978381	-	1	NA	Intergenic	L2c|LINE|L2	-1481	NM_012046	26972	Mm.23495	NM_012046	ENSMUSG00000005883	Spo11	AI449549|Spo11a|Spo11b	SPO11 meiotic protein covalently bound to DSB	protein-coding
mm_79083.1	chr9	46242472	46242492	+	1	NA	exon (NM_007468, exon 3 of 3)	exon (NM_007468, exon 3 of 3)	1638	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_46251.1	chr5	99250236	99250273	-	1	NA	intron (NM_145839, intron 1 of 13)	intron (NM_145839, intron 1 of 13)	2673	NM_181318	320292	Mm.259074	NM_145839	ENSMUSG00000089809	Rasgef1b	4732452O09Rik|GPIgamma4|Gpig4	RasGEF domain family, member 1B	protein-coding
mm_91866.1	chr10	59447987	59447989	-	1	NA	3' UTR (NM_001033259, exon 8 of 8)	3' UTR (NM_001033259, exon 8 of 8)	-6209	NM_010959	18302	Mm.123013	NM_010959	ENSMUSG00000009654	Oit3	EF-9|LZP	oncoprotein induced transcript 3	protein-coding
mm_80712.1	chr9	92275676	92275687	+	1	NA	promoter-TSS (NM_001195084)	promoter-TSS (NM_001195084)	79	NM_001195084	18828	Mm.10306	NM_008880	ENSMUSG00000032372	Plscr2	-	phospholipid scramblase 2	protein-coding
mm_19614.1	chr2	102811832	102811844	-	1	NA	3' UTR (NM_009851, exon 19 of 19)	3' UTR (NM_009851, exon 19 of 19)	89827	NM_001177785	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_24405.1	chr3	90363090	90363094	+	1	NA	Intergenic	Intergenic	21438	NM_139304	229542	Mm.270999	NM_139304	ENSMUSG00000042390	Gatad2b	AL118180|C430014D17Rik|P66beta|mKIAA1150	GATA zinc finger domain containing 2B	protein-coding
mm_48060.1	chr5	136566469	136566502	-	1	NA	promoter-TSS (NM_001291240)	promoter-TSS (NM_001291240)	-504	NM_001291233	13047	Mm.320317	NM_009986	ENSMUSG00000029705	Cux1	CDP|Cutl1|Cux|Cux-1	cut-like homeobox 1	protein-coding
mm_100404.1	chr11	119403664	119403671	+	1	NA	Intergenic	B3|SINE|B2	13195	NR_035453	100316690		NR_035453	ENSMUSG00000088015	Mir1932	mir-1932|mmu-mir-1932	microRNA 1932	ncRNA
mm_46950.1	chr5	114935947	114935993	-	1	NA	exon (NM_145209, exon 6 of 7)	exon (NM_145209, exon 6 of 7)	-6232	NM_028211	72357	Mm.292672	NM_028211	ENSMUSG00000029559	2210016L21Rik	-	RIKEN cDNA 2210016L21 gene	protein-coding
mm_34119.1	chr4	139233377	139233403	+	1	NA	intron (NM_001271405, intron 1 of 8)	intron (NM_001271405, intron 1 of 8)	39279	NM_001271405	12345	Mm.2945	NM_009798	ENSMUSG00000028745	Capzb	1700120C01Rik|AI325129|CPB1|CPB2|CPbeat2|CPbeta1|CPbeta2|Cappb1	capping protein (actin filament) muscle Z-line, beta	protein-coding
mm_150209.1	chr19	32805446	32805449	+	1	NA	intron (NM_008960, intron 5 of 8)	intron (NM_008960, intron 5 of 8)	47870	NM_008960	19211	Mm.245395	NM_008960	ENSMUSG00000013663	Pten	2310035O07Rik|A130070J02Rik|AI463227|B430203M17Rik|MMAC1|TEP1	phosphatase and tensin homolog	protein-coding
mm_134474.1	chr16	18588199	18588208	-	1	NA	intron (NM_001285472, intron 1 of 8)	CpG	-1234	NM_001285476	21380	Mm.295194	NM_011532	ENSMUSG00000009097	Tbx1	-	T-box 1	protein-coding
mm_15728.1	chr2	164129875	164129879	+	1	NA	intron (NM_021420, intron 10 of 10)	intron (NM_021420, intron 10 of 10)	41236	NM_008435	16538	Mm.6217	NM_008435	ENSMUSG00000040164	Kcns1	Kv9.1	K+ voltage-gated channel, subfamily S, 1	protein-coding
mm_44546.1	chr5	24577371	24577429	-	1	NA	promoter-TSS (NM_001190443)	promoter-TSS (NM_001190443)	67	NM_013853	27407	Mm.21629	NM_013853	ENSMUSG00000028953	Abcf2	0710005O05Rik|Drr3|E430001O06	ATP-binding cassette, sub-family F (GCN20), member 2	protein-coding
mm_24143.1	chr3	88297197	88297218	+	1	NA	promoter-TSS (NM_009836)	promoter-TSS (NM_009836)	72	NM_009836	12462	Mm.256034	NM_009836	ENSMUSG00000001416	Cct3	AL024092|Cctg|Tcp1-rs3|TriC-P5	chaperonin containing Tcp1, subunit 3 (gamma)	protein-coding
mm_12744.1	chr2	79122765	79122788	+	1	NA	Intergenic	Intergenic	-132650	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D|Itga4B	integrin alpha 4	protein-coding
mm_17575.1	chr2	30414105	30414118	-	1	NA	intron (NM_007760, intron 1 of 13)	intron (NM_007760, intron 1 of 13)	1637	NM_007760	12908	Mm.20396	NM_007760	ENSMUSG00000026853	Crat	AW107812|CARAT	carnitine acetyltransferase	protein-coding
mm_100685.1	chr11	3504748	3504762	-	1	NA	promoter-TSS (NM_172439)	promoter-TSS (NM_172439)	66	NM_172439	170835	Mm.24313	NM_172439	ENSMUSG00000034570	Inpp5j	Pib5pa|Pipp	inositol polyphosphate 5-phosphatase J	protein-coding
mm_33067.1	chr4	123282779	123282795	+	1	NA	promoter-TSS (NM_130881)	promoter-TSS (NM_130881)	-124	NM_130881	230721	Mm.277091	NM_130881	ENSMUSG00000011257	Pabpc4	-	poly(A) binding protein, cytoplasmic 4	protein-coding
mm_90682.1	chr10	128909896	128909930	+	1	NA	promoter-TSS (NM_007653)	promoter-TSS (NM_007653)	47	NM_007653	12512	Mm.371552	NM_007653	ENSMUSG00000025351	Cd63	C75951|ME491|Tspan30	CD63 antigen	protein-coding
mm_79934.1	chr9	65890292	65890343	+	1	NA	promoter-TSS (NM_026515)	promoter-TSS (NM_026515)	-6	NM_026515	68026	Mm.351273	NM_026515	ENSMUSG00000040204	Pclaf	2810417H13Rik|AA409629|Ns5apt9|Ns5atp9|PAF15|Paf|mKIAA0101|p15(PAF)	PCNA clamp associated factor	protein-coding
mm_48604.1	chr5	144255651	144255669	-	1	NA	intron (NM_018772, intron 1 of 2)	CpG	435	NM_018772	55950	Mm.38011	NM_018772	ENSMUSG00000047843	Bri3	I3	brain protein I3	protein-coding
mm_149573.1	chr19	12806201	12806231	+	1	NA	intron (NM_134152, intron 2 of 8)	intron (NM_134152, intron 2 of 8)	7607	NM_134152	107321	Mm.313136	NM_134152	ENSMUSG00000024696	Lpxn	4933402K05Rik|A530083L21Rik|AV278559|LDPL	leupaxin	protein-coding
mm_122606.1	chr14	51057262	51057288	-	1	NA	promoter-TSS (NM_001011875)	promoter-TSS (NM_001011875)	-33	NM_001011875	497106	Mm.379740	NM_001011875	ENSMUSG00000068407	Rnase12	Rai1	ribonuclease, RNase A family, 12 (non-active)	protein-coding
mm_8720.1	chr1	160044290	160044319	-	1	NA	promoter-TSS (NR_028111)	promoter-TSS (NR_028111)	-76	NR_028111	67647	Mm.171518	NM_001024470	ENSMUSG00000090394	4930523C07Rik	-	RIKEN cDNA 4930523C07 gene	protein-coding
mm_52529.1	chr6	115731963	115731976	+	1	NA	intron (NM_144805, intron 8 of 11)	IAPLTR2_Mm|LTR|ERVK	27030	NM_144805	94346	Mm.29739	NM_144805	ENSMUSG00000059900	Tmem40	9030407H20Rik|AV091463|W64236	transmembrane protein 40	protein-coding
mm_21298.1	chr2	157027750	157027758	-	1	NA	intron (NM_001164663, intron 10 of 14)	intron (NM_001164663, intron 10 of 14)	-20679	NM_025853	66934	Mm.25410	NM_025853	ENSMUSG00000027635	Dsn1	1700022L09Rik|AW552447	DSN1 homolog, MIS12 kinetochore complex component	protein-coding
mm_112.1	chr1	9601492	9601504	+	1	NA	5' UTR (NM_178399, exon 1 of 6)	5' UTR (NM_178399, exon 1 of 6)	231	NM_178399	76982	Mm.491098	NM_178399	ENSMUSG00000067879	3110035E14Rik	AI415019|AV164974|R75066	RIKEN cDNA 3110035E14 gene	protein-coding
mm_30461.1	chr3	153964621	153964624	-	1	NA	Intergenic	RLTR20C2_MM|LTR|ERVK	-8814	NM_001081263	242259	Mm.239962	NM_001081263	ENSMUSG00000028360	Slc44a5	AA117069|Gm422	solute carrier family 44, member 5	protein-coding
mm_68302.1	chr7	105746474	105746496	-	1	NA	3' UTR (NM_009906, exon 13 of 13)	3' UTR (NM_009906, exon 13 of 13)	-2147	NM_020024	24075	Mm.274846	NM_020024	ENSMUSG00000043866	Taf10	30kDa|AU041226|TAFII30|Taf2h	TATA-box binding protein associated factor 10	protein-coding
mm_17166.1	chr2	25288054	25288073	-	1	NA	promoter-TSS (NM_030055)	promoter-TSS (NM_030055)	-82	NM_030055	78217	Mm.160057	NM_030055	ENSMUSG00000026963	Tmem210	4930571C24Rik	transmembrane protein 210	protein-coding
mm_30068.1	chr3	137954740	137954758	-	1	NA	intron (NM_011932, intron 3 of 8)	intron (NM_011932, intron 3 of 8)	26800	NM_011932	26377	Mm.254835	NM_011932	ENSMUSG00000028159	Dapp1	Bam32	dual adaptor for phosphotyrosine and 3-phosphoinositides 1	protein-coding
mm_87633.1	chr10	58328706	58328709	+	1	NA	intron (NM_026148, intron 1 of 9)	ID_B1|SINE|B4	5241	NM_026148	110829	Mm.57734	NM_026148	ENSMUSG00000019920	Lims1	2310016J22Rik|4921524A02Rik|AI507642|AU021743|AW551584|C430041B13Rik|Lims1l|PINCH|PINCH1	LIM and senescent cell antigen-like domains 1	protein-coding
mm_2517.1	chr1	106318639	106318650	+	1	NA	intron (NM_133821, intron 3 of 16)	intron (NM_133821, intron 3 of 16)	146775	NM_133821	98432	Mm.24115	NM_133821	ENSMUSG00000044340	Phlpp1	AI836256|Phlpp|Plekhe1|SCOP|mKIAA0606	PH domain and leucine rich repeat protein phosphatase 1	protein-coding
mm_70704.1	chr8	15057335	15057344	+	1	NA	promoter-TSS (NM_008664)	promoter-TSS (NM_008664)	-314	NM_008664	17930	Mm.272115	NM_008664	ENSMUSG00000031461	Myom2	AW146149	myomesin 2	protein-coding
mm_103116.1	chr11	69997294	69997328	-	1	NA	promoter-TSS (NM_001291127)	promoter-TSS (NM_001291127)	-151	NM_001291127	78246	Mm.20805	NM_030064	ENSMUSG00000018572	Phf23	JUNE-1	PHD finger protein 23	protein-coding
mm_107032.1	chr12	13412770	13412785	+	1	NA	intron (NM_027706, intron 32 of 51)	intron (NM_027706, intron 32 of 51)	143650	NM_027706	71169	Mm.177520	NM_027706	ENSMUSG00000020576	Nbas	4933425L03Rik|Nag	neuroblastoma amplified sequence	protein-coding
mm_160989.1	chr11	105975247	105975247	+	1	NA	promoter-TSS (NM_009598)	promoter-TSS (NM_009598)	39	NM_009598	11421	Mm.754	NM_009598	ENSMUSG00000020681	Ace	AW208573|CD143	angiotensin I converting enzyme (peptidyl-dipeptidase A) 1	protein-coding
mm_91857.1	chr10	59431000	59431038	-	1	NA	intron (NM_010959, intron 4 of 8)	intron (NM_010959, intron 4 of 8)	10760	NM_010959	18302	Mm.123013	NM_010959	ENSMUSG00000009654	Oit3	EF-9|LZP	oncoprotein induced transcript 3	protein-coding
mm_21244.1	chr2	156173728	156173731	-	1	NA	intron (NM_133242, intron 3 of 16)	intron (NM_133242, intron 3 of 16)	5851	NM_001291115	170791	Mm.392436	NM_133242	ENSMUSG00000027620	Rbm39	1500012C14Rik|2310040E03Rik|B330012G18Rik|C79248|R75070|Rnpc2|caper	RNA binding motif protein 39	protein-coding
mm_62733.1	chr7	110808826	110808854	+	1	NA	intron (NM_001276301, intron 13 of 14)	PB1D7|SINE|Alu	35541	NM_025999	67150	Mm.96867	NM_025999	ENSMUSG00000030788	Rnf141	2610110L04Rik|AA792898|AU022812|ZFP36|ZNF230	ring finger protein 141	protein-coding
mm_44013.1	chr5	147270092	147270102	+	1	NA	promoter-TSS (NM_008814)	promoter-TSS (NM_008814)	-34	NM_008814	18609	Mm.389714	NM_008814	ENSMUSG00000029644	Pdx1	IDX-1|IPF-1|Ipf1|Mody4|STF-1|pdx-1	pancreatic and duodenal homeobox 1	protein-coding
mm_94774.1	chr11	21255932	21255936	+	1	NA	intron (NM_139061, intron 1 of 22)	intron (NM_139061, intron 1 of 22)	16902	NM_001290628	245944	Mm.170103	NM_139061	ENSMUSG00000020128	Vps54	Hcc8|Vps54l|mSLP8|wr	VPS54 GARP complex subunit	protein-coding
mm_81884.1	chr9	119357544	119357564	+	1	NA	5' UTR (NM_001199568, exon 1 of 20)	5' UTR (NM_001199568, exon 1 of 20)	173	NM_001199568	102448	Mm.219497	NM_001033209	ENSMUSG00000035769	Xylb	AI132223|AI327421	xylulokinase homolog (H. influenzae)	protein-coding
mm_128906.1	chr15	73423181	73423218	-	1	NA	promoter-TSS (NM_007982)	promoter-TSS (NM_007982)	-8	NM_001130409	14083	Mm.254494	NM_007982	ENSMUSG00000022607	Ptk2	FAK|FRNK|Fadk|mKIAA4203|p125FAK	PTK2 protein tyrosine kinase 2	protein-coding
mm_126404.1	chr15	80250384	80250387	+	1	NA	3' UTR (NM_178719, exon 6 of 6)	3' UTR (NM_178719, exon 6 of 6)	-4799	NM_001287180	11911	Mm.641	NM_009716	ENSMUSG00000042406	Atf4	Atf-4|C/ATF|CREB2|TAXREB67	activating transcription factor 4	protein-coding
mm_44049.1	chr5	147869459	147869478	+	1	NA	exon (NM_025624, exon 4 of 6)	exon (NM_025624, exon 4 of 6)	8840	NM_025624	66537	Mm.332855	NM_025624	ENSMUSG00000029649	Pomp	2510048O06Rik|Ump1	proteasome maturation protein	protein-coding
mm_144476.1	chr18	23913366	23913371	+	1	NA	Intergenic	B4|SINE|B4	-41320	NM_027007	69256	Mm.218343	NM_027007	ENSMUSG00000024276	Zfp397	2810411K16Rik|6720480F11Rik|AI461664	zinc finger protein 397	protein-coding
mm_78846.1	chr9	44327607	44327621	+	1	NA	exon (NM_007875, exon 2 of 9)	exon (NM_007875, exon 2 of 9)	769	NM_007875	13478	Mm.18353	NM_007875	ENSMUSG00000032123	Dpagt1	AU021132|Dpagt2|GPT|Gnpta	dolichyl-phosphate (UDP-N-acetylglucosamine) acetylglucosaminephosphotransferase 1 (GlcNAc-1-P transferase)	protein-coding
mm_11592.1	chr2	33228356	33228366	+	1	NA	exon (NM_011923, exon 2 of 5)	exon (NM_011923, exon 2 of 5)	12400	NM_011923	26360	Mm.208919	NM_011923	ENSMUSG00000004105	Angptl2	AI593246|AW260363|Arp2	angiopoietin-like 2	protein-coding
mm_150960.1	chr19	46397010	46397033	+	1	NA	5' UTR (NM_015752, exon 1 of 12)	5' UTR (NM_015752, exon 1 of 12)	125	NM_015752	24069	Mm.41210	NM_015752	ENSMUSG00000025231	Sufu	Su(fu)	suppressor of fused homolog (Drosophila)	protein-coding
mm_166062.1	chr4	134012433	134012435	-	1	NA	intron (NM_145833, intron 2 of 3)	intron (NM_145833, intron 2 of 3)	6382	NM_145833	83557	Mm.302567	NM_145833	ENSMUSG00000050966	Lin28a	AL024421|ENSMUSG00000070700|Gm10299|Lin-28|Lin28|Tex17|lin-28A	lin-28 homolog A (C. elegans)	protein-coding
mm_85006.1	chr9	86880699	86880712	-	1	NA	promoter-TSS (NM_001277986)	promoter-TSS (NM_001277986)	-256	NM_001277983	20616	Mm.281651	NM_013669	ENSMUSG00000033419	Snap91	91kDa|AP180|F1-20|mKIAA0656	synaptosomal-associated protein 91	protein-coding
mm_30305.1	chr3	149329707	149329711	-	1	NA	Intergenic	RMER5|LTR|ERV1	54972	NR_040591	381482	Mm.393866	NR_040591		Gm1653	-	predicted gene 1653	ncRNA
mm_51918.1	chr6	91234217	91234237	+	1	NA	exon (NM_001081437, exon 2 of 17)	exon (NM_001081437, exon 2 of 17)	21463	NM_007992	14115	Mm.249146	NM_007992	ENSMUSG00000064080	Fbln2	5730577E14Rik|FIBL-2	fibulin 2	protein-coding
mm_142544.1	chr17	46556130	46556148	-	1	NA	promoter-TSS (NM_020493)	promoter-TSS (NM_020493)	23	NM_020493	20807	Mm.45044	NM_020493	ENSMUSG00000015605	Srf	AW049942|AW240594	serum response factor	protein-coding
mm_89903.1	chr10	111164795	111164811	+	1	NA	promoter-TSS (NM_001003717)	promoter-TSS (NM_001003717)	1	NM_175489	237542	Mm.220204	NM_175489	ENSMUSG00000020189	Osbpl8	AA536976|AA536995|C730029P18Rik|D330025H14Rik|ORP-8	oxysterol binding protein-like 8	protein-coding
mm_55586.1	chr6	71440438	71440455	-	1	NA	5' UTR (NM_024288, exon 1 of 9)	5' UTR (NM_024288, exon 1 of 9)	191	NM_024288	68477	Mm.28474	NM_024288	ENSMUSG00000002222	Rmnd5a	1110007A06Rik|AJ237586|AW125795|Gid2|MTA.D02.090	required for meiotic nuclear division 5 homolog A	protein-coding
mm_169531.1	chr14	91832416	91832416	-	1	NA	Intergenic	Lx7|LINE|L1	1705525	NR_045712	74967	Mm.390704	NR_045712		4930474H20Rik	-	RIKEN cDNA 4930474H20 gene	ncRNA
mm_113096.1	chr13	24327416	24327461	+	1	NA	promoter-TSS (NM_001111110)	promoter-TSS (NM_001111110)	34	NM_001111110	12763	Mm.8396	NM_007717	ENSMUSG00000016756	Cmah	-	cytidine monophospho-N-acetylneuraminic acid hydroxylase	protein-coding
mm_60149.1	chr7	38212907	38212911	+	1	NA	Intergenic	Intergenic	15085	NM_024413	72287	Mm.333798	NM_024413	ENSMUSG00000074170	Plekhf1	1810013P09Rik|APPD|LAPF|PHAFIN1|ZFYVE15	pleckstrin homology domain containing, family F (with FYVE domain) member 1	protein-coding
mm_50673.1	chr6	51544622	51544630	+	1	NA	5' UTR (NM_001127348, exon 1 of 7)	5' UTR (NM_001127348, exon 1 of 7)	103	NM_001127348	71982	Mm.294166	NM_028035	ENSMUSG00000038301	Snx10	2410004M09Rik	sorting nexin 10	protein-coding
mm_143611.1	chr17	78736535	78736586	-	1	NA	promoter-TSS (NM_011500)	promoter-TSS (NM_011500)	0	NM_011500	268980	Mm.311915	NM_011500	ENSMUSG00000024077	Strn	AU022939|D130055P19	striatin, calmodulin binding protein	protein-coding
mm_113249.1	chr13	27559296	27559303	+	1	NA	exon (NM_023332, exon 5 of 6)	exon (NM_023332, exon 5 of 6)	5307	NM_001316721	67310	Mm.46091	NM_023332	ENSMUSG00000006490	Prl8a9	1600019F10Rik|Ghd15|PLP-C2|PLP-Cbeta|Prlpc2	prolactin family8, subfamily a, member 9	protein-coding
mm_22849.1	chr3	28263206	28263214	+	1	NA	promoter-TSS (NM_001163009)	promoter-TSS (NM_001163009)	-4	NM_001163007	665113	Mm.126193	NM_026910	ENSMUSG00000027692	Tnik	1500031A17Rik|4831440I19Rik|AI451411|C530008O15Rik|C630040K21Rik	TRAF2 and NCK interacting kinase	protein-coding
mm_8007.1	chr1	134802714	134802718	-	1	NA	intron (NM_001081307, intron 18 of 23)	intron (NM_001081307, intron 18 of 23)	1005	NR_015606	329251	Mm.188709	NM_001081307	ENSMUSG00000073557	Ppp1r12b	1810037O03Rik|9530009M10Rik|AI132431|Mypt2	protein phosphatase 1, regulatory (inhibitor) subunit 12B	protein-coding
mm_55292.1	chr6	54566485	54566491	-	1	NA	promoter-TSS (NM_027268)	promoter-TSS (NM_027268)	-106	NM_027268	69938	Mm.41557	NM_027268	ENSMUSG00000019124	Scrn1	2810019K23Rik|6330535A03Rik|AI852905|SES1|mKIAA0193	secernin 1	protein-coding
mm_40044.1	chr5	33854867	33854870	+	1	NA	intron (NM_001177884, intron 3 of 8)	PB1D9|SINE|Alu	11756	NM_001177884	107823	Mm.19892	NM_175231	ENSMUSG00000057406	Whsc1	5830445G22Rik|9430010A17Rik|AW555663|C130020C13Rik|D030027O06Rik|D930023B08Rik|MMSET|NSD2|Whsc1l|mKIAA1090	Wolf-Hirschhorn syndrome candidate 1 (human)	protein-coding
mm_10264.1	chr2	9681808	9681818	+	1	NA	Intergenic	Intergenic	196787	NM_008091	14462	Mm.313866	NM_008091	ENSMUSG00000015619	Gata3	Gata-3|jal	GATA binding protein 3	protein-coding
mm_79728.1	chr9	62341442	62341452	+	1	NA	5' UTR (NM_009672, exon 1 of 7)	5' UTR (NM_009672, exon 1 of 7)	104	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	protein-coding
mm_6243.1	chr1	67038787	67038815	-	1	NA	promoter-TSS (NM_001190985)	promoter-TSS (NM_001190985)	33	NM_001190984	14768	Mm.20522	NM_021295	ENSMUSG00000026000	Lancl1	AW124738|Gpr69|Gpr69a|p40	LanC (bacterial lantibiotic synthetase component C)-like 1	protein-coding
mm_58574.1	chr7	4866357	4866410	+	1	NA	promoter-TSS (NM_026158)	promoter-TSS (NM_026158)	-204	NM_026158	67441	Mm.41385	NM_026158	ENSMUSG00000052605	Isoc2b	0610042E07Rik|AI553388|Isoc2	isochorismatase domain containing 2b	protein-coding
mm_139217.1	chr17	47729264	47729274	+	1	NA	exon (NM_025973, exon 3 of 9)	exon (NM_025973, exon 3 of 9)	2427	NM_025973	109820	Mm.22957	NM_025973	ENSMUSG00000023987	Pgc	2210410L06Rik|Upg-1|Upg1	progastricsin (pepsinogen C)	protein-coding
mm_97437.1	chr11	78177230	78177235	+	1	NA	promoter-TSS (NM_001291235)	promoter-TSS (NM_001291235)	-566	NM_080849	140859	Mm.23788	NM_080849	ENSMUSG00000017405	Nek8	4632401F23Rik|b2b1449Clo|jck	NIMA (never in mitosis gene a)-related expressed kinase 8	protein-coding
mm_130171.1	chr15	93334990	93335004	-	1	NA	intron (NR_028315, intron 2 of 4)	(A)n|Simple_repeat|Simple_repeat	1938	NR_028315	67057	Mm.4714	NM_024189	ENSMUSG00000022634	Yaf2	2810021M11Rik	YY1 associated factor 2	protein-coding
mm_38151.1	chr4	134915011	134915019	-	1	NA	promoter-TSS (NM_027935)	promoter-TSS (NM_027935)	-99	NM_027935	71817	Mm.88349	NM_027935	ENSMUSG00000028822	Tmem50a	3200001F09Rik|CAM|Smp1	transmembrane protein 50A	protein-coding
mm_41041.1	chr5	86089366	86089368	+	1	NA	intron (NM_001310639, intron 4 of 7)	intron (NM_001310639, intron 4 of 7)	17621	NM_001310639	56792	Mm.131237	NM_019992	ENSMUSG00000029254	Stap1	AI586015|Brdg1|STAP-1	signal transducing adaptor family member 1	protein-coding
mm_33386.1	chr4	129650241	129650243	+	1	NA	intron (NM_008468, intron 12 of 13)	B1_Mus2|SINE|Alu	-9177	NM_001199695	109658	Mm.268863	NM_001005506	ENSMUSG00000053841	Txlna	2600010N21Rik|AI425952|AW209241|Il14|Txln	taxilin alpha	protein-coding
mm_6190.1	chr1	65123109	65123193	-	1	NA	promoter-TSS (NM_001285881)	promoter-TSS (NM_001285881)	63	NM_175293	98303	Mm.348057	NM_175293	ENSMUSG00000044816	D630023F18Rik	AI314969	RIKEN cDNA D630023F18 gene	protein-coding
mm_83154.1	chr9	40456388	40456396	-	1	NA	promoter-TSS (NM_172768)	promoter-TSS (NM_172768)	-628	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_119310.1	chr14	35580839	35580874	+	1	NA	3' UTR (NM_008166, exon 16 of 16)	3' UTR (NM_008166, exon 16 of 16)	231122	NM_001033766	239036	Mm.239970	NM_001033766	ENSMUSG00000041068	4930596D02Rik	-	RIKEN cDNA 4930596D02 gene	protein-coding
mm_127290.1	chr15	100067502	100067513	+	1	NA	intron (NM_001159361, intron 1 of 37)	intron (NM_001159361, intron 1 of 37)	28843	NM_001159361	239667	Mm.243658	NM_172819	ENSMUSG00000023026	Dip2b	4932422C22|AI317237|AI854602|mKIAA1463	disco interacting protein 2 homolog B	protein-coding
mm_106022.1	chr11	116024490	116024511	-	1	NA	promoter-TSS (NM_008211)	promoter-TSS (NM_008211)	4	NM_008211	15081	Mm.18516	NM_008211	ENSMUSG00000016559	H3f3b	9430068D06Rik|H3.3B	H3 histone, family 3B	protein-coding
mm_58907.1	chr7	17203470	17203485	+	1	NA	promoter-TSS (NM_054064)	promoter-TSS (NM_054064)	0	NM_054064	114872	Mm.322280	NM_054064	ENSMUSG00000023159	Psg29	AA102956|AA409969|cea17	pregnancy-specific glycoprotein 29	protein-coding
mm_147648.1	chr18	60501516	60501620	-	1	NA	5' UTR (NM_134133, exon 1 of 2)	5' UTR (NM_134133, exon 1 of 2)	415	NM_134133	106878	Mm.273197	NM_134133	ENSMUSG00000038059	Smim3	2010002N04Rik|AI195350|AW561905|Nid67|cI-41	small integral membrane protein 3	protein-coding
mm_142167.1	chr17	36167688	36167704	-	1	NA	exon (NM_001081032, exon 3 of 8)	exon (NM_001081032, exon 3 of 8)	841	NM_001081032	667977	Mm.441651	NM_001081032	ENSMUSG00000073402	Gm8909	EG667977|H2-Tw5l|H2-gs17	predicted gene 8909	protein-coding
mm_105726.1	chr11	109011904	109011940	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	91573	NM_015732	12006	Mm.71710	NM_015732	ENSMUSG00000000142	Axin2	Axi1|Axil|Conductin	axin 2	protein-coding
mm_165441.1	chr2	154309491	154309493	+	1	NA	exon (NM_001025574, exon 2 of 15)	exon (NM_001025574, exon 2 of 15)	2248	NM_001025574	433492	Mm.330682	NM_001025574	ENSMUSG00000067996	Bpifb9b	5430413K10Rik|AI413838|OTTMUSG00000015915	BPI fold containing family B, member 9B	protein-coding
mm_32265.1	chr4	102603521	102603549	+	1	NA	intron (NM_001177982, intron 9 of 9)	intron (NM_001177982, intron 9 of 9)	13692	NM_001177981	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_68744.1	chr7	121064386	121064394	-	1	NA	3' UTR (NM_030691, exon 6 of 6)	3' UTR (NM_030691, exon 6 of 6)	10140	NM_030691	80719	Mm.160384	NM_030691	ENSMUSG00000035004	Igsf6	-	immunoglobulin superfamily, member 6	protein-coding
mm_41339.1	chr5	90497249	90497267	+	1	NA	exon (NM_007423, exon 5 of 15)	exon (NM_007423, exon 5 of 15)	6544	NM_007423	11576	Mm.358570	NM_007423	ENSMUSG00000054932	Afp	-	alpha fetoprotein	protein-coding
mm_22860.1	chr3	28697947	28697980	+	1	NA	promoter-TSS (NM_031197)	promoter-TSS (NM_031197)	60	NM_031197	20526	Mm.18443	NM_031197	ENSMUSG00000027690	Slc2a2	AI266973|Glut-2|Glut2	solute carrier family 2 (facilitated glucose transporter), member 2	protein-coding
mm_80009.1	chr9	67840381	67840383	+	1	NA	promoter-TSS (NM_177184)	promoter-TSS (NM_177184)	-14	NM_177184	320528	Mm.241454	NM_177184	ENSMUSG00000035284	Vps13c	AI552542|AV026040|C230055H22Rik|W51662|chorein	vacuolar protein sorting 13C	protein-coding
mm_130293.1	chr15	97010190	97010201	-	1	NA	exon (NM_027052, exon 8 of 16)	exon (NM_027052, exon 8 of 16)	45761	NM_027052	69354	Mm.250980	NM_027052	ENSMUSG00000022464	Slc38a4	1110012E16Rik|1700012A18Rik|Ata3|mATA3|mNAT3	solute carrier family 38, member 4	protein-coding
mm_56847.1	chr6	117907696	117907733	-	1	NA	promoter-TSS (NM_001166429)	intron (NM_133834, intron 1 of 3)	-90	NM_001166428	98758	Mm.422979	NM_133834	ENSMUSG00000042079	Hnrnpf	4833420I20Rik|AA407306|Hnrpf	heterogeneous nuclear ribonucleoprotein F	protein-coding
mm_161655.1	chr17	6673420	6673420	+	1	NA	promoter-TSS (NM_031395)	promoter-TSS (NM_031395)	-190	NM_031395	83672	Mm.442201	NM_031395	ENSMUSG00000041831	Sytl3	A430092N21|Slp3|Slp3-a|Slp3-b|mFLJ00307	synaptotagmin-like 3	protein-coding
mm_97954.1	chr11	83709094	83709096	+	1	NA	promoter-TSS (NM_007969)	promoter-TSS (NM_007969)	91	NM_007969	14038	Mm.1650	NM_007969	ENSMUSG00000000983	Wfdc18	Expi|Kal1|WDNM1	WAP four-disulfide core domain 18	protein-coding
mm_96946.1	chr11	70540892	70540907	+	1	NA	exon (NM_001302476, exon 2 of 10)	exon (NM_001302476, exon 2 of 10)	627	NM_001302476	18806	Mm.260177	NM_008876	ENSMUSG00000020828	Pld2	PLD1C	phospholipase D2	protein-coding
mm_78787.1	chr9	44032245	44032249	+	1	NA	Intergenic	Intergenic	-11137	NM_009382	21838	Mm.3951	NM_009382	ENSMUSG00000032011	Thy1	CD90|T25|Thy-1|Thy-1.2|Thy1.1|Thy1.2	thymus cell antigen 1, theta	protein-coding
mm_99674.1	chr11	105975182	105975195	+	1	NA	promoter-TSS (NM_009598)	promoter-TSS (NM_009598)	-20	NM_009598	11421	Mm.754	NM_009598	ENSMUSG00000020681	Ace	AW208573|CD143	angiotensin I converting enzyme (peptidyl-dipeptidase A) 1	protein-coding
mm_38183.1	chr4	135272799	135272819	-	1	NA	promoter-TSS (NM_013885)	promoter-TSS (NM_013885)	-49	NM_013885	29876	Mm.257765	NM_013885	ENSMUSG00000037242	Clic4	D0Jmb3|TU-74|mc3s5|mtCLIC	chloride intracellular channel 4 (mitochondrial)	protein-coding
mm_52054.1	chr6	97225038	97225052	+	1	NA	intron (NM_022992, intron 1 of 2)	PB1D11|SINE|Alu	14253	NM_022992	65106	Mm.291014	NM_022992	ENSMUSG00000035199	Arl6ip5	5930404D22Rik|AV001879|Aip-5|Gtrap3-18|addiscin	ADP-ribosylation factor-like 6 interacting protein 5	protein-coding
mm_135035.1	chr16	32868287	32868318	-	1	NA	promoter-TSS (NM_001200038)	promoter-TSS (NM_001200038)	64	NM_001200038	100502698	Mm.327319	NM_172615	ENSMUSG00000035629	Rubcn	1700021K19Rik|5330403K09|Kiaa0226|Rubicon|mKIAA0226	RUN domain and cysteine-rich domain containing, Beclin 1-interacting protein	protein-coding
mm_134022.1	chr16	4939580	4939603	-	1	NA	promoter-TSS (NR_037666)	promoter-TSS (NR_037666)	-6	NR_037666	100503704	Mm.480572	NR_037666	ENSMUSG00000097397	Gm16861	-	predicted gene, 16861	ncRNA
mm_22634.1	chr3	14862806	14862833	+	1	NA	promoter-TSS (NM_007606)	promoter-TSS (NM_007606)	-719	NM_007606	12350	Mm.300	NM_007606	ENSMUSG00000027559	Car3	BB219044|Ca3|Car-3	carbonic anhydrase 3	protein-coding
mm_15538.1	chr2	158383819	158383829	+	1	NA	3' UTR (NM_175692, exon 5 of 5)	3' UTR (NM_175692, exon 5 of 5)	8186	NM_175692	319317	Mm.294494	NM_175692	ENSMUSG00000044349	Snhg11	A930034L06Rik|AI854265|AL022637|AW319638|E130013N09Rik	small nucleolar RNA host gene 11	protein-coding
mm_66042.1	chr7	30664987	30664999	-	1	NA	promoter-TSS (NM_027999)	promoter-TSS (NM_027999)	1	NM_027999	71909	Mm.290410	NM_027999	ENSMUSG00000078762	Haus5	2310022K01Rik	HAUS augmin-like complex, subunit 5	protein-coding
mm_103969.1	chr11	84513486	84513553	-	1	NA	promoter-TSS (NM_019816)	promoter-TSS (NM_019816)	-18	NM_019816	56321	Mm.257482	NM_019816	ENSMUSG00000018697	Aatf	4933415H02Rik|5830465M17Rik|Che-1|Trb	apoptosis antagonizing transcription factor	protein-coding
mm_42290.1	chr5	114406771	114406787	+	1	NA	exon (NM_054093, exon 17 of 28)	exon (NM_054093, exon 17 of 28)	2311	NR_105994	102465621		NR_105994	ENSMUSG00000098731	Mir7027	Gm27831|mmu-mir-7027	microRNA 7027	ncRNA
mm_135674.1	chr16	52418440	52418478	-	1	NA	intron (NM_009655, intron 1 of 15)	intron (NM_009655, intron 1 of 15)	34622	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_126227.1	chr15	78934920	78934992	+	1	NA	promoter-TSS (NM_133800)	promoter-TSS (NM_133800)	23	NM_133800	97961	Mm.157216	NM_133800	ENSMUSG00000033099	Nol12	C78541|Nop25	nucleolar protein 12	protein-coding
mm_103242.1	chr11	70688098	70688132	-	1	NA	promoter-TSS (NM_001190378)	promoter-TSS (NM_001190378)	-10	NM_001190379	216874	Mm.473726	NM_178116	ENSMUSG00000040712	Camta2	Kiaa0909-hp|mKIAA0909	calmodulin binding transcription activator 2	protein-coding
mm_83616.1	chr9	48740702	48740704	-	1	NA	intron (NM_001033324, intron 3 of 6)	intron (NM_001033324, intron 3 of 6)	95242	NM_001033324	235320	Mm.457803	NM_001033324	ENSMUSG00000066687	Zbtb16	AI467657|PLZF|Zfp145|lu	zinc finger and BTB domain containing 16	protein-coding
mm_131348.1	chr16	13671945	13671978	+	1	NA	5' UTR (NM_001177552, exon 1 of 6)	5' UTR (NM_001177552, exon 1 of 6)	103	NM_025653	67118	Mm.223689	NM_025653	ENSMUSG00000022684	Bfar	3010001A07Rik|3110001I22Rik|AI666707|AW107665|Bar|Rnf47	bifunctional apoptosis regulator	protein-coding
mm_111015.1	chr12	78983477	78983493	-	1	NA	promoter-TSS (NM_001170401)	promoter-TSS (NM_001170401)	-7	NM_001170401	268567	Mm.341747	NM_178745	ENSMUSG00000046157	Tmem229b	6330442E10Rik|9830138K24|AU019070	transmembrane protein 229B	protein-coding
mm_58267.1	chr6	145340701	145340719	-	1	NA	Intergenic	CpG	-46915	NR_003625	381827	Mm.179075	NM_001001987		1700073E17Rik	-	ribosomal protein L7 pseudogene	pseudo
mm_76360.1	chr8	84772365	84772415	-	1	NA	intron (NM_001081982, intron 1 of 9)	G-rich|Low_complexity|Low_complexity	1979	NM_001081981	18032	Mm.9394	NM_010906	ENSMUSG00000001911	Nfix	CTF|NF-I/X|NF1-X|NFI-X	nuclear factor I/X	protein-coding
mm_54055.1	chr6	13839487	13839510	-	1	NA	intron (NM_145066, intron 1 of 3)	intron (NM_145066, intron 1 of 3)	444	NM_001330666	64450	Mm.167625	NM_145066	ENSMUSG00000048216	Gpr85	2900026B03Rik	G protein-coupled receptor 85	protein-coding
mm_44786.1	chr5	32146865	32146902	-	1	NA	exon (NM_008037, exon 2 of 4)	exon (NM_008037, exon 2 of 4)	10411	NM_008037	14284	Mm.24684	NM_008037	ENSMUSG00000029135	Fosl2	Fra-2	fos-like antigen 2	protein-coding
mm_51661.1	chr6	86195311	86195329	+	1	NA	promoter-TSS (NM_031199)	promoter-TSS (NM_031199)	93	NM_031199	21802	Mm.137222	NM_031199	ENSMUSG00000029999	Tgfa	wa-1|wa1	transforming growth factor alpha	protein-coding
mm_94839.1	chr11	23666123	23666202	+	1	NA	promoter-TSS (NM_023651)	promoter-TSS (NM_023651)	186	NM_028304	74467	Mm.29536	NM_028304	ENSMUSG00000020280	Pus10	2810013G11Rik|4933435A13Rik|AU014648|C77560|Ccdc139	pseudouridylate synthase 10	protein-coding
mm_40963.1	chr5	76974693	76974727	+	1	NA	promoter-TSS (NM_025691)	promoter-TSS (NM_025691)	9	NM_025691	66661	Mm.296976	NM_025691	ENSMUSG00000036323	Srp72	5730576P14Rik|72kDa|AI132477|BC019196|C77589	signal recognition particle 72	protein-coding
mm_8423.1	chr1	152386690	152386694	-	1	NA	promoter-TSS (NM_025677)	promoter-TSS (NM_025677)	-10	NM_025677	66637	Mm.379120	NM_025677	ENSMUSG00000014980	Tsen15	5730449L18Rik|AL023077|Sen15	tRNA splicing endonuclease subunit 15	protein-coding
mm_132071.1	chr16	30065334	30065351	+	1	NA	promoter-TSS (NM_008235)	promoter-TSS (NM_008235)	-15	NM_008235	15205	Mm.390859	NM_008235	ENSMUSG00000022528	Hes1	Hry|bHLHb39	hairy and enhancer of split 1 (Drosophila)	protein-coding
mm_53484.1	chr6	135018160	135018170	+	1	NA	exon (NM_026360, exon 8 of 12)	exon (NM_026360, exon 8 of 12)	6553	NM_026360	67755	Mm.166524	NM_026360	ENSMUSG00000030204	Ddx47	4930588A18Rik|C77285	DEAD (Asp-Glu-Ala-Asp) box polypeptide 47	protein-coding
mm_80623.1	chr9	88735678	88735688	+	1	NA	Intergenic	RMER10A|LTR|ERVL	-3833	NM_007536	12047	Mm.378888	NM_007536	ENSMUSG00000099974	Bcl2a1d	A1-d	B cell leukemia/lymphoma 2 related protein A1d	protein-coding
mm_64090.1	chr7	140968113	140968153	+	1	NA	promoter-TSS (NM_001112715)	promoter-TSS (NM_001112715)	57	NM_001112715	68713	Mm.175661	NM_026820	ENSMUSG00000025491	Ifitm1	1110036C17Rik|DSPA2a|Mil-2|Mil2	interferon induced transmembrane protein 1	protein-coding
mm_25049.1	chr3	98309089	98309099	+	1	NA	3' UTR (NM_008256, exon 10 of 10)	3' UTR (NM_008256, exon 10 of 10)	28663	NM_008256	15360	Mm.289131	NM_008256	ENSMUSG00000027875	Hmgcs2	1300002P16|mHS	3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2	protein-coding
mm_86724.1	chr10	19062693	19062702	+	1	NA	Intergenic	Intergenic	-47287	NM_009397	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_65976.1	chr7	30442863	30442873	-	1	NA	exon (NM_007467, exon 4 of 17)	exon (NM_007467, exon 4 of 17)	2714	NM_007467	11803	Mm.2381	NM_007467	ENSMUSG00000006651	Aplp1	-	amyloid beta (A4) precursor-like protein 1	protein-coding
mm_46327.1	chr5	100820930	100820975	-	1	NA	promoter-TSS (NM_172405)	promoter-TSS (NM_172405)	-17	NM_172405	70681	Mm.486560	NM_172405	ENSMUSG00000035234	Fam175a	3830405G04Rik|5630400M01Rik|AI506069|AL024423|AV118690|Ccdc98	family with sequence similarity 175, member A	protein-coding
mm_149873.1	chr19	25158646	25158658	+	1	NA	intron (NM_028785, intron 29 of 47)	intron (NM_028785, intron 29 of 47)	-78550	NM_181404	107351	Mm.260722	NM_181404	ENSMUSG00000032702	Kank1	A930031B09Rik|AU015049|AW121052|Ankrd15|D330024H06Rik|mKIAA0172	KN motif and ankyrin repeat domains 1	protein-coding
mm_104309.1	chr11	92047407	92047414	-	1	NA	Intergenic	RMER17B|LTR|ERVK	-469855	NM_028547	73470	Mm.67677	NM_028547	ENSMUSG00000046755	Kif2b	1700063D03Rik	kinesin family member 2B	protein-coding
mm_143634.1	chr17	78985394	78985400	-	1	NA	intron (NM_001171004, intron 2 of 18)	intron (NM_001171004, intron 2 of 18)	23108	NM_001171005	75292	Mm.252776	NM_029239	ENSMUSG00000024070	Prkd3	4930557O20Rik|5730497N19Rik|PKD3|Pkcnu|Prkcn	protein kinase D3	protein-coding
mm_143616.1	chr17	78769059	78769076	-	1	NA	intron (NM_001081179, intron 27 of 35)	intron (NM_001081179, intron 27 of 35)	-32507	NM_011500	268980	Mm.311915	NM_011500	ENSMUSG00000024077	Strn	AU022939|D130055P19	striatin, calmodulin binding protein	protein-coding
mm_154348.1	chrM	5757	5799	+	1	NA	NA	Intergenic	NA	NA								
mm_46752.1	chr5	112228634	112228680	-	1	NA	non-coding (NR_033657, exon 1 of 7)	non-coding (NR_033657, exon 1 of 7)	291	NR_033657	330166	Mm.44854	NR_003718	ENSMUSG00000097767	Miat	3632434I06|A230057G18Rik|Rncr2|gomafu	myocardial infarction associated transcript (non-protein coding)	ncRNA
mm_153971.1	chr19	47859462	47859485	-	1	NA	exon (NM_010362, exon 4 of 6)	exon (NM_010362, exon 4 of 6)	4500	NM_010362	14873	Mm.378931	NM_010362	ENSMUSG00000025068	Gsto1	AA407097|AI194287|AU018802|Gsto-1|Gstx|Spg-r|p28	glutathione S-transferase omega 1	protein-coding
mm_105971.1	chr11	115498239	115498278	-	1	NA	exon (NM_008258, exon 5 of 5)	exon (NM_008258, exon 5 of 5)	-6444	NM_015807	50773	Mm.390379	NM_015807	ENSMUSG00000020736	Nt5c	Dnt|Dnt1|Umph-2|Umph2	5',3'-nucleotidase, cytosolic	protein-coding
mm_152448.1	chr19	10829898	10829902	-	1	NA	5' UTR (NM_009852, exon 1 of 13)	5' UTR (NM_009852, exon 1 of 13)	158	NM_001037801	12511	Mm.290897	NM_009852	ENSMUSG00000024670	Cd6	-	CD6 antigen	protein-coding
mm_13844.1	chr2	119547702	119547762	+	1	NA	promoter-TSS (NM_172857)	promoter-TSS (NM_172857)	25	NM_019769	56398	Mm.214765	NM_019769	ENSMUSG00000014077	Chp1	1500003O03Rik|AA960066|AI046351|Cahp|Chp|Sid470p|p24|vac	calcineurin-like EF hand protein 1	protein-coding
mm_29549.1	chr3	116807728	116807730	-	1	NA	intron (NM_001081326, intron 1 of 33)	intron (NM_001081326, intron 1 of 33)	437	NM_001081326	77559	Mm.237099	NM_001081326	ENSMUSG00000033400	Agl	1110061O17Rik|9430004C13Rik|9630046L06Rik|AI850929|C77197	amylo-1,6-glucosidase, 4-alpha-glucanotransferase	protein-coding
mm_116439.1	chr13	43008565	43008572	-	1	NA	intron (NM_001005740, intron 2 of 12)	intron (NM_001005740, intron 2 of 12)	-114271	NM_001005748	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding
mm_14426.1	chr2	130539411	130539424	+	1	NA	intron (NM_001163688, intron 10 of 20)	intron (NM_001163688, intron 10 of 20)	24332	NR_040348	321014	Mm.442588	NR_040348	ENSMUSG00000060029	4930473A02Rik	-	RIKEN cDNA 4930473A02 gene	ncRNA
mm_95118.1	chr11	34078156	34078162	+	1	NA	intron (NM_010696, intron 10 of 20)	intron (NM_010696, intron 10 of 20)	30958	NM_010696	16822	Mm.265350	NM_010696	ENSMUSG00000002699	Lcp2	AI323664|BB161688|SLP-76|SLP76|m1Khoe|twm	lymphocyte cytosolic protein 2	protein-coding
mm_64301.1	chr7	141861766	141861768	+	1	NA	exon (NM_028801, exon 31 of 49)	exon (NM_028801, exon 31 of 49)	22695	NM_028801	74180	Mm.200752	NM_028801	ENSMUSG00000066108	Muc5b	2300002I04Rik|A130042M24|AV085033|MUC5|MUC9|mucin 5b	mucin 5, subtype B, tracheobronchial	protein-coding
mm_23148.1	chr3	39979778	39979785	+	1	NA	Intergenic	Intergenic	543131	NR_040445	100040882	Mm.272869	NR_040445	ENSMUSG00000037884	1700017G19Rik	-	RIKEN cDNA 1700017G19 gene	ncRNA
mm_169446.1	chr14	57890331	57890331	-	1	NA	promoter-TSS (NM_029492)	promoter-TSS (NM_029492)	-69	NM_029492	75965	Mm.29044	NM_029492	ENSMUSG00000021969	Zdhhc20	4930542A17Rik|5033406L14Rik|AI448102|B230110O18Rik|ENSMUSG00000055956|HK11	zinc finger, DHHC domain containing 20	protein-coding
mm_96972.1	chr11	70650638	70650650	+	1	NA	intron (NM_027445, intron 7 of 8)	intron (NM_027445, intron 7 of 8)	3357	NM_027445	70510	Mm.261818	NM_027445	ENSMUSG00000040746	Rnf167	0610010G05Rik|5730408C10Rik|AU019305|AV328608	ring finger protein 167	protein-coding
mm_102353.1	chr11	58214718	58214721	-	1	NA	promoter-TSS (NM_019440)	promoter-TSS (NM_019440)	-258	NM_019440	54396	Mm.458517	NM_019440	ENSMUSG00000069874	Irgm2	AI481100|GTPI|Ifggd2|Iigp2	immunity-related GTPase family M member 2	protein-coding
mm_34169.1	chr4	139942667	139942691	+	1	NA	intron (NR_045159, intron 1 of 2)	RMER17B|LTR|ERVK	840	NR_045159	71235	Mm.61253	NR_045159	ENSMUSG00000085928	4933427I22Rik	-	RIKEN cDNA 4933427I22 gene	ncRNA
mm_94273.1	chr11	3839983	3840007	+	1	NA	intron (NM_152818, intron 1 of 13)	RSINE1|SINE|B4	23908	NM_152818	74309	Mm.61022	NM_152818	ENSMUSG00000020435	Osbp2	1700095P05Rik|C630001G20Rik|Gm244|ORP-4|OSBPL1	oxysterol binding protein 2	protein-coding
mm_158029.1	chrX	96935245	96935250	-	1	NA	Intergenic	Intergenic	-137349	NM_001033361	245526	Mm.336164	NM_001033361	ENSMUSG00000031212	Pgr15l	-	G protein-coupled receptor 15-like	protein-coding
mm_173341.1	chrY	90812169	90812173	+	1	NA	intron (NM_133362, intron 2 of 3)	(CAGAGA)n|Simple_repeat|Simple_repeat	26729	NM_133362	170942	Mm.76062	NM_133362	ENSMUSG00000096768	Erdr1	edr	erythroid differentiation regulator 1	protein-coding
mm_44691.1	chr5	30198399	30198425	-	1	NA	exon (NM_001014394, exon 9 of 14)	exon (NM_001014394, exon 9 of 14)	7310	NM_001014394	381628	Mm.291148	NM_001014394	ENSMUSG00000067642	Adgrf3	Gm1041|Gpr113|Pgr23	adhesion G protein-coupled receptor F3	protein-coding
mm_163736.1	chr13	119690421	119690431	+	1	NA	promoter-TSS (NM_001291439)	promoter-TSS (NM_001291439)	75	NM_001291439	208715	Mm.61526	NM_145942	ENSMUSG00000093930	Hmgcs1	B130032C06Rik	3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1	protein-coding
mm_65235.1	chr7	19756785	19756804	-	1	NA	exon (NM_020486, exon 14 of 15)	exon (NM_020486, exon 14 of 15)	-7221	NM_001159724	19294	Mm.4341	NM_008990	ENSMUSG00000062300	Nectin2	AI325026|AI987993|Cd112|MPH|Pvr|Pvrl2|Pvs|nectin-2	nectin cell adhesion molecule 2	protein-coding
mm_112157.1	chr12	113307913	113307923	-	1	NA	Intergenic	Intergenic	122015	NM_153776	69195	Mm.313244	NM_153776	ENSMUSG00000049036	Tmem121	2410008J05Rik|Hole	transmembrane protein 121	protein-coding
mm_118433.1	chr14	8016535	8016549	+	1	NA	intron (NM_001331064, intron 1 of 8)	intron (NM_001331064, intron 1 of 8)	13576	NM_001331064	66082	Mm.181473	NM_025341	ENSMUSG00000025277	Abhd6	0610041D24Rik|AA673485|AV065425	abhydrolase domain containing 6	protein-coding
mm_165821.1	chr3	146899458	146899512	+	1	NA	intron (NM_001302957, intron 5 of 21)	intron (NM_001302957, intron 5 of 21)	47118	NM_001302958	70892	Mm.187793	NM_027594	ENSMUSG00000036745	Ttll7	1110049N09Rik|4921517B04Rik|C630030B20|mTTLL7	tubulin tyrosine ligase-like family, member 7	protein-coding
mm_29801.1	chr3	127780310	127780338	-	1	NA	5' UTR (NM_027808, exon 1 of 14)	5' UTR (NM_027808, exon 1 of 14)	203	NM_027808	71481	Mm.158704	NM_027808	ENSMUSG00000028028	Alpk1	8430410J10Rik|LAK	alpha-kinase 1	protein-coding
mm_135640.1	chr16	52356071	52356114	-	1	NA	intron (NM_009655, intron 1 of 15)	B4|SINE|B4	96989	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_158536.1	chrX	143932998	143933008	-	1	NA	5' UTR (NM_001110222, exon 1 of 7)	5' UTR (NM_001110222, exon 1 of 7)	121	NM_001110222	13193	Mm.12871	NM_010025	ENSMUSG00000031285	Dcx	Dbct	doublecortin	protein-coding
mm_40638.1	chr5	64909286	64909332	+	1	NA	Intergenic	Intergenic	23390	NM_030682	21897	Mm.273024	NM_030682	ENSMUSG00000044827	Tlr1	-	toll-like receptor 1	protein-coding
mm_97165.1	chr11	75490455	75490475	+	1	NA	exon (NM_138659, exon 5 of 42)	exon (NM_138659, exon 5 of 42)	3688	NM_138659	192159	Mm.3757	NM_138659	ENSMUSG00000020850	Prpf8	AU019467|D11Bwg0410e|DBF3/PRP8|Prp8|Sfprp8l	pre-mRNA processing factor 8	protein-coding
mm_139818.1	chr17	67629613	67629622	+	1	NA	Intergenic	Intergenic	3106	NM_001033340	240131	Mm.295736	NM_001033340	ENSMUSG00000073375	Lrrc30	Gm326	leucine rich repeat containing 30	protein-coding
mm_148278.1	chr18	81927709	81927709	-	1	NA	Intergenic	Intergenic	64371	NR_039589	100628596		NR_039589	ENSMUSG00000093036	Mir5127	mmu-mir-5127|mu-mir-5127	microRNA 5127	ncRNA
mm_114022.1	chr13	52630038	52630054	+	1	NA	intron (NM_001198977, intron 7 of 13)	intron (NM_001198977, intron 7 of 13)	33164	NM_011518	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_35485.1	chr4	40876830	40876857	-	1	NA	Intergenic	Intergenic	-22306	NM_022305	14595	Mm.15622	NM_022305	ENSMUSG00000028413	B4galt1	B-1,4-GalT|B-1,4-GalT1|GalT|Ggtb|Ggtb2|b4Gal-T1|beta-1,4-GalT|beta-1,4-GalT1|beta4Gal-T1	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1	protein-coding
mm_111869.1	chr12	108001992	108001994	-	1	NA	intron (NM_001079883, intron 1 of 3)	intron (NM_001079883, intron 1 of 3)	1421	NM_001079883	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_7631.1	chr1	127732526	127732556	-	1	NA	intron (NM_001033041, intron 1 of 9)	RCHARR1|DNA|hAT-Charlie	3128	NM_001033041	266645	Mm.25735	NM_001033041	ENSMUSG00000026348	Acmsd	-	amino carboxymuconate semialdehyde decarboxylase	protein-coding
mm_76195.1	chr8	82403204	82403227	-	1	NA	promoter-TSS (NM_001254747)	promoter-TSS (NM_001254747)	-629	NM_008357	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_129482.1	chr15	78770902	78770925	-	1	NA	intron (NM_008595, intron 1 of 7)	intron (NM_008595, intron 1 of 7)	2532	NM_008595	17305	Mm.149235	NM_008595	ENSMUSG00000018169	Mfng	AW546563	MFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	protein-coding
mm_70884.1	chr8	25426669	25426671	+	1	NA	Intergenic	Intergenic	-92089	NM_001079909	14182	Mm.265716	NM_010206	ENSMUSG00000031565	Fgfr1	AW208770|Eask|FGFR-I|FLG|Fgfr-1|Flt-2|Hspy|MFR|bFGF-R-1|c-fgr	fibroblast growth factor receptor 1	protein-coding
mm_82373.1	chr9	14615390	14615401	-	1	NA	promoter-TSS (NM_001081395)	promoter-TSS (NM_001081395)	-395	NM_001081395	75723	Mm.159552	NM_001081395	ENSMUSG00000013076	Amotl1	2310010G08Rik|2310067L22Rik|4932416D09Rik|JEAP|mFLJ00155	angiomotin-like 1	protein-coding
mm_15796.1	chr2	164443408	164443418	+	1	NA	promoter-TSS (NM_011521)	promoter-TSS (NM_011521)	-225	NM_011521	20971	Mm.3815	NM_011521	ENSMUSG00000017009	Sdc4	AA959608|AW108331|S4|Synd4|ryudocan|syndecan-4	syndecan 4	protein-coding
mm_13192.1	chr2	93199808	93199839	+	1	NA	exon (NM_001025246, exon 8 of 8)	exon (NM_001025246, exon 8 of 8)	12239	NM_001025246	277414	Mm.41033	NM_001025246	ENSMUSG00000068735	Trp53i11	Tp53i11	transformation related protein 53 inducible protein 11	protein-coding
mm_38843.1	chr4	149177600	149177616	-	1	NA	3' UTR (NM_001290995, exon 49 of 49)	3' UTR (NM_001290995, exon 49 of 49)	-10901	NM_001081274	110208	Mm.252080	NM_025801	ENSMUSG00000028961	Pgd	0610042A05Rik|AU019875|C78335	phosphogluconate dehydrogenase	protein-coding
mm_18469.1	chr2	62411807	62411822	-	1	NA	5' UTR (NM_010074, exon 1 of 26)	5' UTR (NM_010074, exon 1 of 26)	417	NM_010074	13482	Mm.1151	NM_010074	ENSMUSG00000035000	Dpp4	Cd26|Dpp-4|THAM	dipeptidylpeptidase 4	protein-coding
mm_75294.1	chr8	41054772	41054802	-	1	NA	promoter-TSS (NM_001005864)	promoter-TSS (NM_001005864)	9	NM_001005864	102103	Mm.149438	NM_001005863	ENSMUSG00000045636	Mtus1	AI481402|ATBP135|Atip1|B430010I23Rik|B430305I03Rik|C85752|Cctsg1-440|MD44|MTSG1|mKIAA1288	mitochondrial tumor suppressor 1	protein-coding
mm_104239.1	chr11	88718137	88718161	-	1	NA	promoter-TSS (NM_054043)	promoter-TSS (NM_054043)	80	NM_054043	76626	Mm.400451	NM_054043	ENSMUSG00000069769	Msi2	1700105C15Rik|AI451722|AI563628|AW489193|Msi2h	musashi RNA-binding protein 2	protein-coding
mm_20138.1	chr2	121413773	121413777	-	1	NA	promoter-TSS (NM_007952)	promoter-TSS (NM_007952)	17	NM_153075	212670	Mm.384318	NM_153075	ENSMUSG00000033486	Catsper2	-	cation channel, sperm associated 2	protein-coding
mm_162224.1	chrX	145487040	145487040	-	1	NA	exon (NM_153319, exon 1 of 11)	exon (NM_153319, exon 1 of 11)	599	NM_001290274	27494	Mm.100068	NM_153319	ENSMUSG00000041688	Amot	CAG-2|D0Kist1|Sii6	angiomotin	protein-coding
mm_65979.1	chr7	30445463	30445494	-	1	NA	5' UTR (NM_007467, exon 1 of 17)	5' UTR (NM_007467, exon 1 of 17)	104	NM_007467	11803	Mm.2381	NM_007467	ENSMUSG00000006651	Aplp1	-	amyloid beta (A4) precursor-like protein 1	protein-coding
mm_27179.1	chr3	34351686	34351703	-	1	NA	Intergenic	Intergenic	-208687	NR_015580	320478	Mm.444063	NR_015580	ENSMUSG00000105265	Sox2ot	B230215L15Rik	SOX2 overlapping transcript (non-protein coding)	ncRNA
mm_3797.1	chr1	157458555	157458597	+	1	NA	promoter-TSS (NM_001033284)	promoter-TSS (NM_001033284)	-6	NM_001033284	226527	Mm.215960	NM_001033284	ENSMUSG00000033488	BC026585	-	cDNA sequence BC026585	protein-coding
mm_107873.1	chr12	69946143	69946159	+	1	NA	intron (NM_178628, intron 7 of 14)	intron (NM_178628, intron 7 of 14)	-17258	NR_036607	100040999	Mm.394588	NR_036607	ENSMUSG00000079076	Gm3086	-	RuvB-like protein 1 pseudogene	pseudo
mm_52370.1	chr6	113046478	113046488	+	1	NA	intron (NM_008188, intron 1 of 9)	CpG	156	NM_008188	14911	Mm.781	NM_008188	ENSMUSG00000030264	Thumpd3	AW556087|Gt(ROSA)26asSor|Gtrosa26as	THUMP domain containing 3	protein-coding
mm_52018.1	chr6	94661670	94661706	+	1	NA	intron (NM_008377, intron 2 of 18)	intron (NM_008377, intron 2 of 18)	38457	NM_008377	16206	Mm.245210	NM_008377	ENSMUSG00000030029	Lrig1	D6Bwg0781e|Img|LIG-1	leucine-rich repeats and immunoglobulin-like domains 1	protein-coding
mm_49632.1	chr6	30804901	30804914	+	1	NA	intron (NM_017478, intron 20 of 23)	intron (NM_017478, intron 20 of 23)	63608	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_164252.1	chr15	97995625	97995635	-	1	NA	intron (NM_031163, intron 11 of 53)	intron (NM_031163, intron 11 of 53)	9094	NM_031163	12824	Mm.2423	NM_031163	ENSMUSG00000022483	Col2a1	Col2|Col2a|Col2a-1|Del1|Dmm|Lpk|Rgsc856	collagen, type II, alpha 1	protein-coding
mm_85913.1	chr9	111057457	111057485	-	1	NA	promoter-TSS (NM_017466)	promoter-TSS (NM_017466)	47	NM_001302376	54199	Mm.7336	NM_017466	ENSMUSG00000043953	Ccrl2	1810047I05Rik|Ackr5|CCR11|Cmkbr1l2|E01|L-CCR	chemokine (C-C motif) receptor-like 2	protein-coding
mm_57711.1	chr6	128622874	128622895	-	1	NA	promoter-TSS (NM_001159902)	promoter-TSS (NM_001159902)	50	NM_001159902	17057	Mm.16729	NM_010737	ENSMUSG00000030361	Klrb1a	Ly55a|NKR-P1.7|NKR-P1A|NKRP12|Nkrp1-a|Nkrp1a|ly-55A	killer cell lectin-like receptor subfamily B member 1A	protein-coding
mm_128065.1	chr15	26816528	26816541	-	1	NA	intron (NM_176959, intron 1 of 3)	intron (NM_176959, intron 1 of 3)	79030	NM_176959	448987	Mm.253378	NM_176959	ENSMUSG00000043556	Fbxl7	AL023057|D230018M15Rik|FBL7|Fbl6	F-box and leucine-rich repeat protein 7	protein-coding
mm_81808.1	chr9	117317524	117317546	+	1	NA	intron (NM_001172121, intron 2 of 14)	intron (NM_001172121, intron 2 of 14)	-65052	NM_001172126	207181	Mm.326411	NM_178660	ENSMUSG00000039607	Rbms3	6720477E09Rik|8430436O14Rik	RNA binding motif, single stranded interacting protein	protein-coding
mm_134188.1	chr16	10966499	10966566	-	1	NA	exon (NM_019980, exon 2 of 4)	exon (NM_019980, exon 2 of 4)	26589	NM_019980	56722	Mm.294753	NM_019980	ENSMUSG00000022500	Litaf	3222402J11Rik|C85531|N4WBP3|TBX1	LPS-induced TN factor	protein-coding
mm_92495.1	chr10	78312016	78312030	-	1	NA	intron (NM_053014, intron 2 of 9)	intron (NM_053014, intron 2 of 9)	28184	NR_106119	102465765		NR_106119	ENSMUSG00000098885	Mir7659	Gm27433|mmu-mir-7659	microRNA 7659	ncRNA
mm_29406.1	chr3	108908054	108908066	-	1	NA	exon (NM_025845, exon 3 of 6)	exon (NM_025845, exon 3 of 6)	3644	NM_025845	66921	Mm.51049	NM_025845	ENSMUSG00000027881	Prpf38b	1110021E09Rik|AU018955	PRP38 pre-mRNA processing factor 38 (yeast) domain containing B	protein-coding
mm_69286.1	chr7	128205923	128205937	-	1	NA	TTS (NM_001029872)	TTS (NM_001029872)	436	NM_009943	12862	Mm.43824	NM_009943	ENSMUSG00000030785	Cox6a2	CoxVIaH|VIaH	cytochrome c oxidase subunit VIa polypeptide 2	protein-coding
mm_93165.1	chr10	93276535	93276546	-	1	NA	intron (NM_013508, intron 2 of 4)	intron (NM_013508, intron 2 of 4)	34619	NM_001322268	13713	Mm.4454	NM_013508	ENSMUSG00000008398	Elk3	D430049E23Rik|Erp|Etrp|Net|Sap-2	ELK3, member of ETS oncogene family	protein-coding
mm_131864.1	chr16	23127784	23127824	+	1	NA	promoter-TSS (NM_145480)	promoter-TSS (NM_145480)	-74	NM_145480	106344	Mm.386835	NM_145480	ENSMUSG00000022881	Rfc4	A1|AI894123|AU040575|RFC37	replication factor C (activator 1) 4	protein-coding
mm_50126.1	chr6	41539200	41539211	+	1	NA	Intergenic	Intergenic	17429	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_107428.1	chr12	35579355	35579379	+	1	NA	Intergenic	Intergenic	-44378	NM_001314027	11622	Mm.341377	NM_013464	ENSMUSG00000019256	Ahr	Ah|Ahh|Ahre|In|bHLHe76	aryl-hydrocarbon receptor	protein-coding
mm_78610.1	chr9	37545106	37545122	+	1	NA	TTS (NM_020518)	TTS (NM_020518)	5859	NM_020518	57276	Mm.27478	NM_020518	ENSMUSG00000001943	Vsig2	1190004B15Rik|2210413P10Rik|AU040484|CTX|Ctm	V-set and immunoglobulin domain containing 2	protein-coding
mm_137463.1	chr17	26621513	26621521	+	1	NA	intron (NM_026170, intron 3 of 9)	intron (NM_026170, intron 3 of 9)	-54879	NM_025272	11974	Mm.22602	NM_025272	ENSMUSG00000015575	Atp6v0e	Atp6k|Atp6v0e1|M9.2	ATPase, H+ transporting, lysosomal V0 subunit E	protein-coding
mm_158095.1	chrX	101421141	101421158	-	1	NA	promoter-TSS (NM_019831)	promoter-TSS (NM_019831)	-464	NM_001177987	56364	Mm.23458	NM_019831	ENSMUSG00000031310	Zmym3	9030216B10Rik|AW122925|DXS6673El|Zfp261	zinc finger, MYM-type 3	protein-coding
mm_47990.1	chr5	135957532	135957571	-	1	NA	Intergenic	Intergenic	16925	NM_001160366	109267	Mm.332750	NM_001160366	ENSMUSG00000029699	Ssc4d	C330016E03Rik|S4D-SRCRB|SRCRB-S4D|Srcrb4d	scavenger receptor cysteine rich family, 4 domains	protein-coding
mm_13900.1	chr2	120476851	120476851	+	1	NA	promoter-TSS (NM_001109761)	promoter-TSS (NM_001109761)	-58	NM_001109761	12335	Mm.458021	NM_007601	ENSMUSG00000079110	Capn3	AI323605|Capa-3|Capa3|Lp82|p94	calpain 3	protein-coding
mm_151594.1	chr19	3414465	3414481	-	1	NA	promoter-TSS (NM_001329667)	promoter-TSS (NM_001329667)	71	NM_001329667	14419	Mm.4655	NM_010253	ENSMUSG00000024907	Gal	Galn	galanin	protein-coding
mm_137407.1	chr17	26087273	26087287	+	1	NA	intron (NM_011933, intron 4 of 8)	intron (NM_011933, intron 4 of 8)	2884	NM_011933	26378	Mm.292869	NM_011933	ENSMUSG00000036775	Decr2	-	2-4-dienoyl-Coenzyme A reductase 2, peroxisomal	protein-coding
mm_13225.1	chr2	97467576	97467586	+	1	NA	promoter-TSS (NM_178725)	promoter-TSS (NM_178725)	-76	NM_001289744	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_129579.1	chr15	79741282	79741297	-	1	NA	intron (NM_001205346, intron 1 of 17)	intron (NM_001205346, intron 1 of 17)	1247	NM_194342	223697	Mm.202715	NM_194342	ENSMUSG00000042524	Sun2	B230369L08Rik|C030011B15|Unc84b	Sad1 and UNC84 domain containing 2	protein-coding
mm_110706.1	chr12	69322257	69322268	-	1	NA	exon (NM_025441, exon 23 of 33)	exon (NM_025441, exon 23 of 33)	25581	NM_027117	69554	Mm.234368	NM_027117	ENSMUSG00000020978	Klhdc2	2310022K15Rik|D12Ertd522e|HCLP-1|LCP	kelch domain containing 2	protein-coding
mm_46058.1	chr5	92256309	92256330	-	1	NA	Intergenic	Intergenic	-3160	NM_011148	19023	Mm.87155	NM_011148	ENSMUSG00000029410	Ppef2	-	protein phosphatase, EF hand calcium-binding domain 2	protein-coding
mm_126310.1	chr15	79659197	79659267	+	1	NA	promoter-TSS (NM_028634)	promoter-TSS (NM_028634)	5	NM_028634	73739	Mm.294441	NM_028634	ENSMUSG00000022428	Cby1	1110014P06Rik|CBY|PGEA14|Pgea1|arb1	chibby family member 1, beta catenin antagonist	protein-coding
mm_103099.1	chr11	69936173	69936211	-	1	NA	promoter-TSS (NM_001347634)	promoter-TSS (NM_001347634)	-136	NM_001347634	53422	Mm.29286	NM_016875	ENSMUSG00000018554	Ybx2	Msy2	Y box protein 2	protein-coding
mm_141412.1	chr17	29411178	29411226	-	1	NA	Intergenic	ID_B1|SINE|B4	50288	NM_001159538	26382	Mm.279187	NM_013710	ENSMUSG00000024013	Fgd2	Tcd-2|Tcd2|ZFYVE4|tcs-2|tcs2	FYVE, RhoGEF and PH domain containing 2	protein-coding
mm_143690.1	chr17	80260464	80260466	-	1	NA	intron (NM_198942, intron 10 of 22)	intron (NM_198942, intron 10 of 22)	-29747	NM_194269	378462	Mm.45208	NM_194269	ENSMUSG00000045257	Morn2	Mopt	MORN repeat containing 2	protein-coding
mm_62849.1	chr7	114317665	114317675	+	1	NA	intron (NR_029437, intron 3 of 3)	intron (NR_029437, intron 3 of 3)	-41554	NM_011965	26440	Mm.121265	NM_011965	ENSMUSG00000030751	Psma1	C2|HC2|Pros-30|alpha-type	proteasome (prosome, macropain) subunit, alpha type 1	protein-coding
mm_115273.1	chr13	111686128	111686128	+	1	NA	promoter-TSS (NM_172593)	promoter-TSS (NM_172593)	-50	NM_172593	218613	Mm.31012	NM_172593	ENSMUSG00000032727	Mier3	5730509D14|AU015422|D130064H19Rik	MIER family member 3	protein-coding
mm_98964.1	chr11	98664361	98664373	+	1	NA	promoter-TSS (NM_021347)	promoter-TSS (NM_021347)	16	NM_021347	57911	Mm.458085	NM_021347	ENSMUSG00000017204	Gsdma	BB149167|Gsdm|Gsdm1|Gsdma1|H312E	gasdermin A	protein-coding
mm_99767.1	chr11	106999691	106999728	+	1	NA	promoter-TSS (NM_010655)	promoter-TSS (NM_010655)	-184	NM_010655	16647	Mm.12508	NM_010655	ENSMUSG00000018362	Kpna2	2410044B12Rik|IPOA1|PTAC58|Rch1	karyopherin (importin) alpha 2	protein-coding
mm_169764.1	chr15	99703172	99703176	+	1	NA	exon (NM_031842, exon 2 of 13)	exon (NM_031842, exon 2 of 13)	887	NM_031842	83797	Mm.273756	NM_031842	ENSMUSG00000023018	Smarcd1	AA407987|Baf60a|D15Kz1	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1	protein-coding
mm_143372.1	chr17	67632641	67632664	-	1	NA	promoter-TSS (NM_001033340)	promoter-TSS (NM_001033340)	71	NM_001033340	240131	Mm.295736	NM_001033340	ENSMUSG00000073375	Lrrc30	Gm326	leucine rich repeat containing 30	protein-coding
mm_27102.1	chr3	30509682	30509746	-	1	NA	promoter-TSS (NM_021442)	promoter-TSS (NM_021442)	-227	NM_021442	14013	Mm.56965	NM_007963	ENSMUSG00000027684	Mecom	D630039M04Rik|Evi-1|Evi1|Jbo|Mds|Mds1|Mds1-Evi1|Prdm3|Znfpr1b1	MDS1 and EVI1 complex locus	protein-coding
mm_157924.1	chrX	79631175	79631199	-	1	NA	intron (NM_028025, intron 2 of 3)	intron (NM_028025, intron 2 of 3)	4395	NM_001113734	71967	Mm.379207	NM_028025	ENSMUSG00000046942	Mageb16	2410003J06Rik	melanoma antigen family B, 16	protein-coding
mm_130821.1	chr15	101845470	101845487	-	1	NA	TTS (NM_008473)	TTS (NM_008473)	5308	NM_008473	16678	Mm.183137	NM_008473	ENSMUSG00000046834	Krt1	Krt-2.1|Krt2-1|Krt86	keratin 1	protein-coding
mm_5801.1	chr1	52164839	52164859	-	1	NA	3' UTR (NM_001081081, exon 18 of 18)	3' UTR (NM_001081081, exon 18 of 18)	45227	NM_001205313	20846	Mm.277406	NM_009283	ENSMUSG00000026104	Stat1	2010005J02Rik|AA408197	signal transducer and activator of transcription 1	protein-coding
mm_103714.1	chr11	79523761	79523761	-	1	NA	promoter-TSS (NM_001077496)	promoter-TSS (NM_001077496)	1	NM_001077496	216984	Mm.439665	NM_001077496	ENSMUSG00000093938	Evi2b	Evi-2|Evi2	ecotropic viral integration site 2b	protein-coding
mm_101393.1	chr11	26210554	26210585	-	1	NA	promoter-TSS (NR_027973)	promoter-TSS (NR_027973)	7	NR_027973	70626	Mm.379180	NM_027486		5730522E02Rik	-	RIKEN cDNA 5730522E02 gene	ncRNA
mm_56182.1	chr6	88373916	88373919	-	1	NA	intron (NM_023060, intron 2 of 6)	intron (NM_023060, intron 2 of 6)	72622	NM_023060	65967	Mm.333237	NM_023060	ENSMUSG00000033216	Eefsec	Selb|sec	eukaryotic elongation factor, selenocysteine-tRNA-specific	protein-coding
mm_125327.1	chr15	38544144	38544156	+	1	NA	Intergenic	Intergenic	-24884	NM_018745	54375	Mm.250214	NM_018745	ENSMUSG00000037458	Azin1	1700085L02Rik|AZI|Oazi|Oazin	antizyme inhibitor 1	protein-coding
mm_17098.1	chr2	23155865	23155925	-	1	NA	promoter-TSS (NM_013771)	promoter-TSS (NM_013771)	129	NM_025979	67121	Mm.253721	NM_025979	ENSMUSG00000026779	Mastl	2700091H24Rik|C88295|GW|GWL|MAST-L|THC2	microtubule associated serine/threonine kinase-like	protein-coding
mm_54.1	chr1	6528254	6528274	+	1	NA	intron (NM_001244693, intron 2 of 22)	intron (NM_001244693, intron 2 of 22)	41033	NM_001244692	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding
mm_110302.1	chr12	32816020	32816021	-	1	NA	Intergenic	MTE-int|LTR|ERVL-MaLR	-4315	NM_021524	59027	Mm.202727	NM_021524	ENSMUSG00000020572	Nampt	1110035O14Rik|AI314458|AI480535|NAmPRTase|Pbef|Pbef1|Visfatin	nicotinamide phosphoribosyltransferase	protein-coding
mm_77978.1	chr9	7870749	7870758	+	1	NA	intron (NM_007464, intron 1 of 8)	ORR1C2|LTR|ERVL-MaLR	2417	NM_007464	11796	Mm.2026	NM_007464	ENSMUSG00000032000	Birc3	AW107670|Api1|Api2|Birc2|C-IAP2|HIAP2|IAP1|IAP2|MIAP1|MIAP2|MIHB|MIHC|RNF49|cIAP-1|cIAP-2|cIAP1|cIAP2	baculoviral IAP repeat-containing 3	protein-coding
mm_128005.1	chr15	12824665	12824675	-	1	NA	promoter-TSS (NM_029998)	promoter-TSS (NM_029998)	-13	NM_001166360	77877	Mm.207311	NM_029998	ENSMUSG00000022195	6030458C11Rik	-	RIKEN cDNA 6030458C11 gene	protein-coding
mm_58758.1	chr7	13450873	13450883	+	1	NA	promoter-TSS (NM_001301682)	promoter-TSS (NM_001301682)	37	NM_001301682	330470	Mm.291102	NM_001033418	ENSMUSG00000074378	Bsph1	Gm767	binder of sperm protein homolog 1	protein-coding
mm_41663.1	chr5	99274652	99274664	+	1	NA	Intergenic	Intergenic	-21731	NM_145839	320292	Mm.259074	NM_145839	ENSMUSG00000089809	Rasgef1b	4732452O09Rik|GPIgamma4|Gpig4	RasGEF domain family, member 1B	protein-coding
mm_117709.1	chr13	95222322	95222322	-	1	NA	intron (NM_001170669, intron 1 of 18)	intron (NM_001170669, intron 1 of 18)	728	NM_001170669	218461	Mm.100167	NM_172263	ENSMUSG00000021684	Pde8b	B230331L10Rik|C030047E14Rik	phosphodiesterase 8B	protein-coding
mm_166146.1	chr5	3803210	3803220	+	1	NA	promoter-TSS (NM_001003909)	promoter-TSS (NM_001003909)	34	NR_033173	79264	Mm.32368	NM_030675	ENSMUSG00000000600	Krit1	2010007K12Rik|A630036P20Rik|AA432855|AI450393|AI643869|BB155247|BB235701|Ccm1	KRIT1, ankyrin repeat containing	protein-coding
mm_5191.1	chr1	13225929	13225947	-	1	NA	intron (NM_001302702, intron 2 of 21)	intron (NM_001302702, intron 2 of 21)	-98775	NM_001081209	383491	Mm.309380	NM_001081209	ENSMUSG00000042414	Prdm14	-	PR domain containing 14	protein-coding
mm_124268.1	chr14	102982631	102982645	-	1	NA	promoter-TSS (NR_039592)	promoter-TSS (NR_039592)	-1	NM_177715	239217	Mm.246466	NM_177715	ENSMUSG00000098557	Kctd12	AU046135|AW538430|Pfet1|Pfetin	potassium channel tetramerisation domain containing 12	protein-coding
mm_169337.1	chr14	122118680	122118694	+	1	NA	intron (NM_080556, intron 1 of 16)	(TGG)n|Simple_repeat|Simple_repeat	11605	NM_080556	68059	Mm.275191	NM_080556	ENSMUSG00000025544	Tm9sf2	1500001N15Rik|AA536814|D14Ertd64e|P76	transmembrane 9 superfamily member 2	protein-coding
mm_89918.1	chr10	111190316	111190324	+	1	NA	intron (NM_175489, intron 1 of 23)	intron (NM_175489, intron 1 of 23)	25518	NM_175489	237542	Mm.220204	NM_175489	ENSMUSG00000020189	Osbpl8	AA536976|AA536995|C730029P18Rik|D330025H14Rik|ORP-8	oxysterol binding protein-like 8	protein-coding
mm_68366.1	chr7	106985399	106985410	-	1	NA	Intergenic	Lx5b|LINE|L1	-9953	NM_147035	259037	Mm.223420	NM_147035	ENSMUSG00000045013	Olfr711	MOR103-4	olfactory receptor 711	protein-coding
mm_102234.1	chr11	54956034	54956040	-	1	NA	5' UTR (NM_001199275, exon 2 of 19)	5' UTR (NM_001199275, exon 2 of 19)	6903	NM_021327	57783	Mm.259671	NM_021327	ENSMUSG00000020400	Tnip1	ABIN|ABIN-1|ABIN1|AU018810|Naf1|Nef|VAN	TNFAIP3 interacting protein 1	protein-coding
mm_146352.1	chr18	82561770	82561817	+	1	NA	exon (NM_001025251, exon 2 of 7)	exon (NM_001025251, exon 2 of 7)	7285	NM_001025254	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_90801.1	chr10	7663554	7663565	-	1	NA	promoter-TSS (NM_008786)	promoter-TSS (NM_008786)	25	NM_008786	18537	Mm.258431	NM_008786	ENSMUSG00000019795	Pcmt1	C79501|PIMT	protein-L-isoaspartate (D-aspartate) O-methyltransferase 1	protein-coding
mm_85556.1	chr9	106789131	106789208	-	1	NA	promoter-TSS (NM_030730)	promoter-TSS (NM_030730)	44	NM_030730	81000	Mm.246689	NM_030730	ENSMUSG00000040661	Rad54l2	Arip4|D130058C05|G630026H09Rik|Srisnf2l	RAD54 like 2 (S. cerevisiae)	protein-coding
mm_7100.1	chr1	88702341	88702356	-	1	NA	promoter-TSS (NM_177305)	promoter-TSS (NM_177305)	-157	NM_177305	320982	Mm.27968	NM_177305	ENSMUSG00000049866	Arl4c	A630084M22Rik|Arl7|LAK	ADP-ribosylation factor-like 4C	protein-coding
mm_140224.1	chr17	83980542	83980572	+	1	NA	Intergenic	Intergenic	-17995	NR_130994	78148	Mm.243918	NR_130994		8430430B14Rik	-	RIKEN cDNA 8430430B14 gene	ncRNA
mm_3937.1	chr1	163779560	163779570	+	1	NA	promoter-TSS (NM_010629)	promoter-TSS (NM_010629)	-18	NM_001305643	16579	Mm.4651	NM_010629	ENSMUSG00000026585	Kifap3	KAP-3|KAP3|SMAP	kinesin-associated protein 3	protein-coding
mm_123857.1	chr14	70994598	70994607	-	1	NA	Intergenic	Intergenic	104495	NM_001302094	14586	Mm.32619	NM_008115	ENSMUSG00000022103	Gfra2	-	glial cell line derived neurotrophic factor family receptor alpha 2	protein-coding
mm_119811.1	chr14	54222809	54222819	+	1	NA	Intergenic	Intergenic	31115	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_676.1	chr1	40466089	40466111	+	1	NA	promoter-TSS (NM_008365)	promoter-TSS (NM_008365)	94	NM_008365	16182	Mm.253664	NM_008365	ENSMUSG00000026070	Il18r1	Il18ralpha|Il1rrp	interleukin 18 receptor 1	protein-coding
mm_146145.1	chr18	74779204	74779224	+	1	NA	promoter-TSS (NR_028560)	promoter-TSS (NR_028560)	2	NM_177470	52538	Mm.245724	NM_177470	ENSMUSG00000036880	Acaa2	0610011L04Rik|AI255831|AI265397|D18Ertd240e	acetyl-Coenzyme A acyltransferase 2 (mitochondrial 3-oxoacyl-Coenzyme A thiolase)	protein-coding
mm_97212.1	chr11	75626292	75626329	+	1	NA	3' UTR (NM_008850, exon 12 of 12)	3' UTR (NM_008850, exon 12 of 12)	-4710	NM_008916	19062	Mm.1458	NM_008916	ENSMUSG00000006127	Inpp5k	C62|Pps|SKIP	inositol polyphosphate 5-phosphatase K	protein-coding
mm_43104.1	chr5	124483510	124483520	+	1	NA	intron (NM_029532, intron 1 of 1)	CpG	360	NM_029532	76167	Mm.156035	NM_029532	ENSMUSG00000029402	Snrnp35	6330548G22Rik	small nuclear ribonucleoprotein 35 (U11/U12)	protein-coding
mm_60689.1	chr7	45163916	45163926	+	1	NA	promoter-TSS (NM_182993)	promoter-TSS (NM_182993)	0	NM_182993	72961	Mm.255631	NM_182993	ENSMUSG00000070570	Slc17a7	2900052E22Rik|AI851913|Vglut1	solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 7	protein-coding
mm_8923.1	chr1	163403628	163403679	-	1	NA	promoter-TSS (NM_178883)	promoter-TSS (NM_178883)	16	NM_001313738	98376	Mm.32901	NM_178883	ENSMUSG00000040124	Gorab	NTKL-BP1|SCYL1-BP1|Scyl1bp1	golgin, RAB6-interacting	protein-coding
mm_23273.1	chr3	51660354	51660364	+	1	NA	promoter-TSS (NM_174995)	promoter-TSS (NM_174995)	-820	NM_174995	211666	Mm.24679	NM_174995	ENSMUSG00000074604	Mgst2	GST2|MGST-II	microsomal glutathione S-transferase 2	protein-coding
mm_139334.1	chr17	49439454	49439487	+	1	NA	exon (NM_020042, exon 4 of 11)	exon (NM_020042, exon 4 of 11)	11106	NM_020042	56738	Mm.22256	NM_020042	ENSMUSG00000064120	Mocs1	3110045D15Rik|AI043170|AW536397	molybdenum cofactor synthesis 1	protein-coding
mm_79517.1	chr9	57537519	57537577	+	1	NA	promoter-TSS (NM_001166364)	promoter-TSS (NM_001166364)	20	NM_001166364	78323	Mm.25814	NM_175273	ENSMUSG00000032305	Fam219b	2310046O06Rik|AI594866	family with sequence similarity 219, member B	protein-coding
mm_73315.1	chr8	105216737	105216753	+	1	NA	3' UTR (NM_001161458, exon 6 of 6)	3' UTR (NM_001161458, exon 6 of 6)	-8443	NM_145604	234678	Mm.27186	NM_145604	ENSMUSG00000031889	D230025D16Rik	BC006874|Lin10	RIKEN cDNA D230025D16 gene	protein-coding
mm_44082.1	chr5	149157381	149157391	+	1	NA	intron (NR_015478, intron 1 of 2)	intron (NR_015478, intron 1 of 2)	-1194	NR_028061	667410	Mm.441522	NR_028061		Gm8615	EG667410	glucosamine-6-phosphate deaminase 1 pseudogene	pseudo
mm_81756.1	chr9	113969210	113969216	+	1	NA	intron (NM_013699, intron 11 of 15)	intron (NM_013699, intron 11 of 15)	24587	NR_039590	100628597		NR_039590	ENSMUSG00000092958	Mir5128	mir-5128|mmu-mir-5128|mu-mir-5128	microRNA 5128	ncRNA
mm_84370.1	chr9	64949277	64949297	-	1	NA	exon (NM_144813, exon 2 of 10)	exon (NM_144813, exon 2 of 10)	2320	NM_144813	214111	Mm.156124	NM_144813	ENSMUSG00000034452	Slc24a1	-	solute carrier family 24 (sodium/potassium/calcium exchanger), member 1	protein-coding
mm_41730.1	chr5	102481763	102481769	+	1	NA	5' UTR (NM_029270, exon 1 of 10)	5' UTR (NM_029270, exon 1 of 10)	375	NM_029270	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding
mm_23097.1	chr3	37063705	37063715	+	1	NA	promoter-TSS (NM_009350)	promoter-TSS (NM_009350)	54	NM_009350	21744	Mm.8122	NM_009350	ENSMUSG00000027719	Adad1	Tenr	adenosine deaminase domain containing 1 (testis specific)	protein-coding
mm_27124.1	chr3	31330938	31330940	-	1	NA	Intergenic	Intergenic	-20620	NM_172861	241919	Mm.285366	NM_172861	ENSMUSG00000069072	Slc7a14	A930013N06|BC061928	solute carrier family 7 (cationic amino acid transporter, y+ system), member 14	protein-coding
mm_114062.1	chr13	54378580	54378590	+	1	NA	5' UTR (NM_009946, exon 2 of 4)	5' UTR (NM_009946, exon 2 of 4)	7236	NM_009946	12890	Mm.268902	NM_009946	ENSMUSG00000025867	Cplx2	921-L|AI413745|AW492120	complexin 2	protein-coding
mm_51587.1	chr6	83795206	83795238	+	1	NA	promoter-TSS (NM_001164187)	promoter-TSS (NM_001164187)	64	NM_001164187	56174	Mm.190650	NM_019542	ENSMUSG00000034744	Nagk	Gnk	N-acetylglucosamine kinase	protein-coding
mm_102979.1	chr11	69680642	69680665	-	1	NA	exon (NM_001163571, exon 2 of 11)	exon (NM_001163571, exon 2 of 11)	1317	NM_030702	80886	Mm.284592	NM_030702	ENSMUSG00000005204	Senp3	AA408656|Smt3ip|Smt3ip1	SUMO/sentrin specific peptidase 3	protein-coding
mm_71918.1	chr8	70141621	70141629	+	1	NA	intron (NM_001309841, intron 1 of 5)	AT_rich|Low_complexity|Low_complexity	1348	NM_001309841	72368	Mm.644	NM_001145552	ENSMUSG00000002345	Borcs8	2310045N01Rik|Mef2bnb	BLOC-1 related complex subunit 8	protein-coding
mm_44526.1	chr5	24423493	24423501	-	1	NA	promoter-TSS (NM_007668)	promoter-TSS (NM_007668)	33	NM_007668	12568	Mm.298798	NM_007668	ENSMUSG00000028969	Cdk5	AW048668|Crk6	cyclin-dependent kinase 5	protein-coding
mm_34695.1	chr4	152027803	152027825	+	1	NA	promoter-TSS (NM_133879)	promoter-TSS (NM_133879)	-143	NM_133879	100090	Mm.24661	NM_133879	ENSMUSG00000028952	Zbtb48	0610011D15Rik|AI327031|Hkr3	zinc finger and BTB domain containing 48	protein-coding
mm_9421.1	chr1	172335934	172335946	-	1	NA	Intergenic	Intergenic	-5270	NM_001039484	16513	Mm.254563	NM_020269	ENSMUSG00000044708	Kcnj10	BIR10|BIRK-1|Kir1.2|Kir4.1	potassium inwardly-rectifying channel, subfamily J, member 10	protein-coding
mm_7218.1	chr1	93160908	93160955	-	1	NA	promoter-TSS (NM_001159940)	promoter-TSS (NM_001159940)	17	NM_172411	71874	Mm.158766	NM_172411	ENSMUSG00000034159	2310007B03Rik	-	RIKEN cDNA 2310007B03 gene	protein-coding
mm_38416.1	chr4	139131030	139131056	-	1	NA	promoter-TSS (NR_033745)	promoter-TSS (NR_033745)	-6	NR_033745	433771	Mm.305990	NM_001163006	ENSMUSG00000050608	Minos1	2310028O11Rik	mitochondrial inner membrane organizing system 1	protein-coding
mm_96685.1	chr11	69580393	69580419	+	1	NA	promoter-TSS (NM_011640)	promoter-TSS (NM_011640)	47	NM_001127233	22059	Mm.222	NM_011640	ENSMUSG00000059552	Trp53	Tp53|bbl|bfy|bhy|p44|p53	transformation related protein 53	protein-coding
mm_14990.1	chr2	152274081	152274086	+	1	NA	intron (NM_007788, intron 9 of 12)	intron (NM_007788, intron 9 of 12)	-19789	NM_024196	67231	Mm.288733	NM_024196	ENSMUSG00000027465	Tbc1d20	1110028I04Rik|2810442O16Rik|AI414693|bs	TBC1 domain family, member 20	protein-coding
mm_106960.1	chr12	8922018	8922028	+	1	NA	exon (NM_008640, exon 1 of 7)	exon (NM_008640, exon 1 of 7)	716	NM_008640	17775	Mm.30071	NM_008640	ENSMUSG00000020585	Laptm4a	AA286466|LAPTM4|MTP|Mtrp|mKIAA0108	lysosomal-associated protein transmembrane 4A	protein-coding
mm_52628.1	chr6	117174238	117174244	+	1	NA	3' UTR (NM_021704, exon 3 of 3)	3' UTR (NM_021704, exon 3 of 3)	5706	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_164126.1	chr15	38710691	38710730	+	1	NA	Intergenic	Intergenic	17806	NR_131206	105463124	Mm.432448	NR_131206		Borg	-	BMP/OP-responsive gene	ncRNA
mm_20478.1	chr2	129595663	129595725	-	1	NA	intron (NM_001291022, intron 1 of 4)	intron (NM_001291022, intron 1 of 4)	2525	NM_001291022	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_162544.1	chr1	170644345	170644351	-	1	NA	promoter-TSS (NM_177068)	promoter-TSS (NM_177068)	-184	NM_177068	320078	Mm.287131	NM_177068	ENSMUSG00000038463	Olfml2b	1110018N05Rik|4832415H08Rik|AI467542	olfactomedin-like 2B	protein-coding
mm_5982.1	chr1	58419996	58420006	-	1	NA	non-coding (NR_027854, exon 3 of 11)	non-coding (NR_027854, exon 3 of 11)	4087	NR_027853	12747	Mm.1761	NM_009905	ENSMUSG00000026034	Clk1	STY	CDC-like kinase 1	protein-coding
mm_35821.1	chr4	47010798	47010807	-	1	NA	Intergenic	Intergenic	-19088	NM_001081141	242425	Mm.101909	NM_001081141	ENSMUSG00000039809	Gabbr2	GABABR2|Gb2|Gm425|Gpr51	gamma-aminobutyric acid (GABA) B receptor, 2	protein-coding
mm_4489.1	chr1	173631108	173631126	+	1	NA	5' UTR (NM_175026, exon 1 of 7)	5' UTR (NM_175026, exon 1 of 7)	258	NM_175026	236312	Mm.447	NM_175026	ENSMUSG00000043263	Ifi209	4930422C14|AI447904|Ifix|Pyhin-1|Pyhin1	interferon activated gene 209	protein-coding
mm_44819.1	chr5	33652529	33652587	-	1	NA	promoter-TSS (NM_001289725)	promoter-TSS (NM_001289725)	16	NM_001289725	20492	Mm.4172	NM_009193	ENSMUSG00000004642	Slbp	-	stem-loop binding protein	protein-coding
mm_59143.1	chr7	24280553	24280597	+	1	NA	Intergenic	Intergenic	10157	NM_009567	22755	Mm.383535	NM_009567	ENSMUSG00000055305	Zfp93	Znf235	zinc finger protein 93	protein-coding
mm_136395.1	chr16	93154059	93154071	-	1	NA	Intergenic	Intergenic	199124	NR_040486	69857	Mm.81192	NR_040486	ENSMUSG00000100277	1810053B23Rik	1810008L18Rik|1810056K14Rik	RIKEN cDNA 1810053B23 gene	ncRNA
mm_98748.1	chr11	96542432	96542434	+	1	NA	intron (NM_001033186, intron 4 of 12)	intron (NM_001033186, intron 4 of 12)	77842	NM_001177898	78473	Mm.395840	NM_001033186	ENSMUSG00000057058	Skap1	1700091G21Rik|Scap1|Skap-55	src family associated phosphoprotein 1	protein-coding
mm_85631.1	chr9	107619733	107619815	-	1	NA	exon (NM_008138, exon 4 of 9)	exon (NM_008138, exon 4 of 9)	-10533	NM_001291539	20347	Mm.4083	NM_009153	ENSMUSG00000057969	Sema3b	SemA|Semaa|sema5|semaV	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B	protein-coding
mm_44149.1	chr5	150260131	150260141	+	1	NA	5' UTR (NM_172887, exon 1 of 61)	5' UTR (NM_172887, exon 1 of 61)	206	NM_172887	320365	Mm.216590	NM_172887	ENSMUSG00000056602	Fry	13CDNA73|9330186A19Rik|AF346502|AI462658|C87180|D930046M03|cg003|mKIAA4143	FRY microtubule binding protein	protein-coding
mm_23112.1	chr3	37481560	37481570	+	1	NA	intron (NM_001310473, intron 14 of 16)	LSU-rRNA_Hsa|rRNA|rRNA	61615	NM_021343	57815	Mm.172679	NM_021343	ENSMUSG00000027722	Spata5	2510048F20Rik|C78064|Spaf	spermatogenesis associated 5	protein-coding
mm_102816.1	chr11	68973333	68973353	-	1	NA	TTS (NM_028048)	TTS (NM_028048)	512	NM_021329	57785	Mm.143774	NM_021329	ENSMUSG00000032892	Rangrf	2400006H24Rik|Mog1|Rangnrf	RAN guanine nucleotide release factor	protein-coding
mm_167519.1	chr9	16442381	16442384	+	1	NA	Intergenic	Intergenic	-64151	NM_001080814	270120	Mm.195010	NM_001080814	ENSMUSG00000074505	Fat3	9430076A06Rik|D430038H04Rik|Gm1132|Gm510|MFAT3F	FAT atypical cadherin 3	protein-coding
mm_68770.1	chr7	121981670	121981706	-	1	NA	promoter-TSS (NM_001033318)	promoter-TSS (NM_001033318)	5	NM_001033318	233824	Mm.442015	NM_001033318	ENSMUSG00000034951	Cog7	5630400E24Rik|Gm167	component of oligomeric golgi complex 7	protein-coding
mm_84100.1	chr9	58278989	58278993	-	1	NA	Intergenic	MLTR25A|LTR|ERVK	25827	NM_026942	69106	Mm.216502	NM_026942	ENSMUSG00000032333	Stoml1	1810015E19Rik|AI847431|SLP1|STORP|UNC24|WPB72	stomatin-like 1	protein-coding
mm_158681.1	chrX	160138350	160138371	-	1	NA	promoter-TSS (NM_008810)	promoter-TSS (NM_008810)	70	NM_008810	18597	Mm.34775	NM_008810	ENSMUSG00000031299	Pdha1	Pdha-1	pyruvate dehydrogenase E1 alpha 1	protein-coding
mm_76292.1	chr8	84201984	84201992	-	1	NA	Intergenic	B1F|SINE|Alu	-6530	NR_029740	387216		NR_029740	ENSMUSG00000065611	Mir23a	Mirn23a|mir-23a|mmu-mir-23a	microRNA 23a	ncRNA
mm_162731.1	chr10	44058862	44058883	-	1	NA	Intergenic	Intergenic	-54026	NM_172393	11630	Mm.292082	NM_172393	ENSMUSG00000019866	Aim1	AI462491|AI463325	absent in melanoma 1	protein-coding
mm_73164.1	chr8	95017708	95017726	+	1	NA	promoter-TSS (NM_173036)	promoter-TSS (NM_173036)	25	NM_173036	54672	Mm.27995	NM_173036	ENSMUSG00000060470	Adgrg3	A030001G24Rik|AW214383|Gpr97|Pb1|Pb99	adhesion G protein-coupled receptor G3	protein-coding
mm_93881.1	chr10	125308810	125308825	-	1	NA	intron (NM_011391, intron 1 of 6)	intron (NM_011391, intron 1 of 6)	19718	NM_011391	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|Mct2	solute carrier family 16 (monocarboxylic acid transporters), member 7	protein-coding
mm_48950.1	chr6	4540575	4540585	+	1	NA	exon (NM_007743, exon 52 of 52)	exon (NM_007743, exon 52 of 52)	34962	NM_007743	12843	Mm.277792	NM_007743	ENSMUSG00000029661	Col1a2	AA960264|AI325291|Col1a-2|Cola-2|Cola2|oim	collagen, type I, alpha 2	protein-coding
mm_48794.1	chr5	148928586	148928618	-	1	NA	promoter-TSS (NM_153572)	promoter-TSS (NM_153572)	45	NM_153572	231912	Mm.397405	NM_153572	ENSMUSG00000041298	Katnal1	-	katanin p60 subunit A-like 1	protein-coding
mm_21299.1	chr2	157027794	157027804	-	1	NA	intron (NM_001164663, intron 10 of 14)	intron (NM_001164663, intron 10 of 14)	-20724	NM_025853	66934	Mm.25410	NM_025853	ENSMUSG00000027635	Dsn1	1700022L09Rik|AW552447	DSN1 homolog, MIS12 kinetochore complex component	protein-coding
mm_56310.1	chr6	92177453	92177456	-	1	NA	intron (NM_025578, intron 2 of 3)	BC1_Mm|scRNA|scRNA	6569	NM_025578	64658	Mm.87062	NM_025578	ENSMUSG00000014551	Mrps25	2810429N01Rik|Rpms25	mitochondrial ribosomal protein S25	protein-coding
mm_9051.1	chr1	167285139	167285149	-	1	NA	promoter-TSS (NM_030724)	promoter-TSS (NM_030724)	-17	NM_030724	80914	Mm.280895	NM_030724	ENSMUSG00000026558	Uck2	AA407809|AI481316|AU018180|AU020720|TSA903|UK|UMK|Umpk	uridine-cytidine kinase 2	protein-coding
mm_110137.1	chr12	26447517	26447527	-	1	NA	intron (NM_021384, intron 4 of 5)	intron (NM_021384, intron 4 of 5)	8930	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_14156.1	chr2	126587814	126587823	+	1	NA	exon (NM_011978, exon 10 of 10)	exon (NM_011978, exon 10 of 10)	30860	NM_008230	15186	Mm.18603	NM_008230	ENSMUSG00000027360	Hdc	AW108189|Hdc-a|Hdc-c|Hdc-e|Hdc-s	histidine decarboxylase	protein-coding
mm_109931.1	chr12	8921845	8921873	-	1	NA	5' UTR (NM_008640, exon 1 of 7)	5' UTR (NM_008640, exon 1 of 7)	552	NM_008640	17775	Mm.30071	NM_008640	ENSMUSG00000020585	Laptm4a	AA286466|LAPTM4|MTP|Mtrp|mKIAA0108	lysosomal-associated protein transmembrane 4A	protein-coding
mm_162195.1	chrX	114907761	114907761	+	1	NA	5' UTR (NM_001081661, exon 1 of 2)	5' UTR (NM_001081661, exon 1 of 2)	179	NM_001081661	75097	Mm.50414	NM_001081661	ENSMUSG00000047079	Ube2dnl2	4930524E20Rik	ubiquitin-conjugating enzyme E2D N-terminal like 2	protein-coding
mm_70075.1	chr7	142653204	142653222	-	1	NA	3' UTR (NM_010514, exon 4 of 4)	3' UTR (NM_010514, exon 4 of 4)	1783	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_46865.1	chr5	113823074	113823077	-	1	NA	intron (NM_009151, intron 1 of 1)	intron (NM_009151, intron 1 of 1)	7426	NM_009151	20345	Mm.332590	NM_009151	ENSMUSG00000048163	Selplg	CD162|Psgl-1|Psgl1|Selp1|Selpl	selectin, platelet (p-selectin) ligand	protein-coding
mm_23927.1	chr3	83766617	83766621	+	1	NA	exon (NM_009144, exon 1 of 3)	exon (NM_009144, exon 1 of 3)	298	NM_009144	20319	Mm.19155	NM_009144	ENSMUSG00000027996	Sfrp2	AI851596|Sdf5	secreted frizzled-related protein 2	protein-coding
mm_134458.1	chr16	18411948	18411964	-	1	NA	exon (NM_001111062, exon 3 of 6)	exon (NM_001111062, exon 3 of 6)	1538	NM_001111063	12846	Mm.100940	NM_007744	ENSMUSG00000000326	Comt	Comt1|D16Wsu103e|D330014B15Rik	catechol-O-methyltransferase	protein-coding
mm_98659.1	chr11	96271454	96271482	+	1	NA	5' UTR (NM_008270, exon 1 of 2)	5' UTR (NM_008270, exon 1 of 2)	138	NM_008270	15417	Mm.258271	NM_008270	ENSMUSG00000020875	Hoxb9	Hox-2.5	homeobox B9	protein-coding
mm_163417.1	chr12	79390375	79390378	+	1	NA	intron (NM_009014, intron 7 of 10)	intron (NM_009014, intron 7 of 10)	93025	NM_001252562	19363	Mm.341756	NM_009014	ENSMUSG00000059060	Rad51b	AI553500|R51H2|Rad51l1|mREC2	RAD51 paralog B	protein-coding
mm_63501.1	chr7	127800845	127800849	+	1	NA	TTS (NM_178029)	TTS (NM_178029)	238	NM_001040684	101502	Mm.157103	NM_133943	ENSMUSG00000042289	Hsd3b7	AI195443|BB098564	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 7	protein-coding
mm_163284.1	chr11	117334164	117334185	-	1	NA	intron (NM_001113488, intron 1 of 9)	intron (NM_001113488, intron 1 of 9)	1861	NM_001113488	53860	Mm.38450	NM_017380	ENSMUSG00000059248	Sept9	MSF1|Msf|PNUTL4|Sint1	septin 9	protein-coding
mm_86172.1	chr9	119157056	119157075	-	1	NA	promoter-TSS (NM_146230)	promoter-TSS (NM_146230)	28	NM_146230	235674	Mm.379402	NM_146230	ENSMUSG00000010651	Acaa1b	-	acetyl-Coenzyme A acyltransferase 1B	protein-coding
mm_43532.1	chr5	137294605	137294640	+	1	NA	promoter-TSS (NM_027356)	promoter-TSS (NM_027356)	-47	NM_027356	70240	Mm.124666	NM_027356	ENSMUSG00000051502	Ufsp1	2700038N03Rik|D5Ertd655e	UFM1-specific peptidase 1	protein-coding
mm_139832.1	chr17	69127451	69127462	+	1	NA	Intergenic	Intergenic	-29354	NM_013813	13823	Mm.131135	NM_013813	ENSMUSG00000024044	Epb41l3	4.1B|DAL1P|Dal1|Epb4.1l3|NBL3	erythrocyte membrane protein band 4.1 like 3	protein-coding
mm_14360.1	chr2	129616286	129616309	+	1	NA	exon (NM_007547, exon 4 of 8)	exon (NM_007547, exon 4 of 8)	23128	NM_001291022	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_43329.1	chr5	135009701	135009726	+	1	NA	exon (NM_145215, exon 1 of 6)	exon (NM_145215, exon 1 of 6)	257	NR_033794	68758	Mm.389700	NM_145215	ENSMUSG00000040532	Abhd11	1110054D16Rik|A630008N09Rik|Wbscr21	abhydrolase domain containing 11	protein-coding
mm_35892.1	chr4	49547932	49547947	-	1	NA	intron (NM_144903, intron 1 of 8)	intron (NM_144903, intron 1 of 8)	1607	NM_144903	230163	Mm.482116	NM_144903	ENSMUSG00000028307	Aldob	Aldo-2|Aldo2|BC016435	aldolase B, fructose-bisphosphate	protein-coding
mm_2911.1	chr1	132008094	132008154	+	1	NA	intron (NM_007923, intron 1 of 4)	CpG	519	NM_007923	13714	Mm.254233	NM_007923	ENSMUSG00000026436	Elk4	2310011G17Rik|A130026I01Rik|BB162516|SAP-1|Sap1	ELK4, member of ETS oncogene family	protein-coding
mm_160337.1	chr8	13837893	13837893	-	1	NA	exon (NM_153093, exon 1 of 1)	exon (NM_153093, exon 1 of 1)	196	NM_153093	231201	Mm.423959	NM_153093	ENSMUSG00000057116	AF366264	Susp4	cDNA sequence AF366264	protein-coding
mm_126601.1	chr15	82452373	82452385	+	1	NA	promoter-TSS (NM_010006)	promoter-TSS (NM_010006)	2	NM_010006	13105	Mm.226708	NM_010006	ENSMUSG00000068086	Cyp2d9	Cyp2d|P450-2D	cytochrome P450, family 2, subfamily d, polypeptide 9	protein-coding
mm_55822.1	chr6	83054416	83054485	-	1	NA	promoter-TSS (NR_125891)	promoter-TSS (NR_125891)	-71	NR_125891	11993	Mm.386752	NM_007517	ENSMUSG00000068328	Aup1	AA589454	ancient ubiquitous protein 1	protein-coding
mm_145380.1	chr18	56927080	56927088	+	1	NA	Intergenic	Intergenic	-1536	NM_177115	320253	Mm.312623	NM_177115	ENSMUSG00000032656	March3	6330411I15Rik|A530081L18Rik|AI843639|MARCH-III	membrane-associated ring finger (C3HC4) 3	protein-coding
mm_73823.1	chr8	117459325	117459336	+	1	NA	promoter-TSS (NR_106046)	promoter-TSS (NR_106046)	65	NR_106046	102465653		NR_106046	ENSMUSG00000098483	Mir7078	Gm27386|mmu-mir-7078	microRNA 7078	ncRNA
mm_13262.1	chr2	98666453	98666463	+	1	NA	Intergenic	SYNREP_MM|Satellite|Satellite	1198801	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_162961.1	chr11	5976231	5976238	-	1	NA	intron (NM_007595, intron 17 of 20)	intron (NM_007595, intron 17 of 20)	20476	NM_019661	56418	Mm.294821	NM_019661	ENSMUSG00000002741	Ykt6	0610042I15Rik|1810013M05Rik|AW105923	YKT6 v-SNARE homolog (S. cerevisiae)	protein-coding
mm_11136.1	chr2	28469781	28469791	+	1	NA	exon (NM_001166031, exon 4 of 4)	exon (NM_001166031, exon 4 of 4)	1720	NM_001166031	118451	Mm.294951	NM_080452	ENSMUSG00000035772	Mrps2	1500019M10Rik	mitochondrial ribosomal protein S2	protein-coding
mm_126865.1	chr15	89336017	89336025	+	1	NA	exon (NM_019977, exon 6 of 10)	exon (NM_019977, exon 6 of 10)	1548	NM_019977	56727	Mm.158200	NM_019977	ENSMUSG00000022613	Miox	0610009I10Rik|AI314022|Aldrl6|C85427|RSOR	myo-inositol oxygenase	protein-coding
mm_127667.1	chr15	102634979	102634987	+	1	NA	Intergenic	Intergenic	-9519	NM_001310066	223922	Mm.208714	NM_146065	ENSMUSG00000052414	Atf7	1110012F10Rik|9430065F09Rik|AI549878|C130020M04Rik	activating transcription factor 7	protein-coding
mm_118451.1	chr14	8367371	8367390	+	1	NA	intron (NM_146050, intron 1 of 9)	RMER17C|LTR|ERVK	11383	NM_146050	18300	Mm.25351	NM_146050	ENSMUSG00000021749	Oit1	2310076N21Rik|AV067083|EF-7|Fam3d	oncoprotein induced transcript 1	protein-coding
mm_89660.1	chr10	97483389	97483396	+	1	NA	exon (NM_007833, exon 2 of 8)	exon (NM_007833, exon 2 of 8)	1061	NM_007833	13179	Mm.56769	NM_007833	ENSMUSG00000019929	Dcn	DC|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding
mm_39609.1	chr5	24128147	24128151	+	1	NA	intron (NM_001161800, intron 4 of 9)	intron (NM_001161800, intron 4 of 9)	1819	NR_037304	100499521		NR_037304	ENSMUSG00000092880	Mir3471-1	mmu-mir-3471-1	microRNA 3471-1	ncRNA
mm_22236.1	chr2	174438962	174438995	-	1	NA	promoter-TSS (NM_022325)	promoter-TSS (NM_022325)	61	NM_022325	64138	Mm.156919	NM_022325	ENSMUSG00000016256	Ctsz	AI787083|AU019819|CTSX|D2Wsu143e	cathepsin Z	protein-coding
mm_3698.1	chr1	153761224	153761256	+	1	NA	intron (NM_011882, intron 8 of 8)	intron (NM_011882, intron 8 of 8)	11814	NM_011882	24014	Mm.259254	NM_011882	ENSMUSG00000066800	Rnasel	E230029I04Rik	ribonuclease L (2', 5'-oligoisoadenylate synthetase-dependent)	protein-coding
mm_139321.1	chr17	48410270	48410288	+	1	NA	promoter-TSS (NM_010913)	promoter-TSS (NM_010913)	279	NM_207219	106821	Mm.203943	NM_207219	ENSMUSG00000040771	Oard1	AI314976|AW558560	O-acyl-ADP-ribose deacylase 1	protein-coding
mm_96135.1	chr11	60930940	60930960	+	1	NA	intron (NR_027800, intron 1 of 1)	intron (NR_027800, intron 1 of 1)	917	NR_027800	24082	Mm.46270	NM_025293	ENSMUSG00000042549	Map2k3os	F3-1|Gm16516|Gtlf3a	mitogen-activated protein kinase kinase 3, opposite strand	ncRNA
mm_40532.1	chr5	57928313	57928357	+	1	NA	intron (NM_001122758, intron 2 of 2)	intron (NM_001122758, intron 2 of 2)	210254	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_25740.1	chr3	122899444	122899459	+	1	NA	TTS (NM_007980)	TTS (NM_007980)	4379	NM_007980	14079	Mm.28398	NM_007980	ENSMUSG00000023057	Fabp2	Fabpi|I-FABP	fatty acid binding protein 2, intestinal	protein-coding
mm_22988.1	chr3	33800145	33800153	+	1	NA	promoter-TSS (NM_025978)	promoter-TSS (NM_025978)	-34	NM_027619	67120	Mm.275710	NM_025978	ENSMUSG00000027677	Ttc14	2700016E08Rik|4930434D01Rik|4931403I22Rik|4933402I15Rik|AI662468|AU014779|AW561908|cI-44|mKIAA1980	tetratricopeptide repeat domain 14	protein-coding
mm_146631.1	chr18	10182163	10182179	-	1	NA	promoter-TSS (NM_009071)	promoter-TSS (NM_009071)	-379	NM_009071	19877	Mm.6710	NM_009071	ENSMUSG00000024290	Rock1	1110055K06Rik|Rock-I	Rho-associated coiled-coil containing protein kinase 1	protein-coding
mm_46193.1	chr5	98018223	98018240	-	1	NA	intron (NM_133738, intron 3 of 16)	intron (NM_133738, intron 3 of 16)	12731	NM_133738	71914	Mm.24842	NM_133738	ENSMUSG00000029338	Antxr2	2310046B19Rik|AW561899|CMG-2|CMG2|cI-35	anthrax toxin receptor 2	protein-coding
mm_96544.1	chr11	68767990	68768018	+	1	NA	intron (NM_175260, intron 12 of 40)	RSINE1|SINE|B4	76089	NM_175260	77579	Mm.218233	NM_175260	ENSMUSG00000020900	Myh10	5730504C04Rik|9330167F11Rik|Fltn|Myhn-2|Myhn2|NMHC II-B|NMHC-B|NMHCII-B|NMMHC II-b|NMMHC-B|NMMHC-IIB|SMemb|mKIAA3005	myosin, heavy polypeptide 10, non-muscle	protein-coding
mm_102980.1	chr11	69681794	69681804	-	1	NA	TTS (NM_001159503)	TTS (NM_001159503)	171	NM_030702	80886	Mm.284592	NM_030702	ENSMUSG00000005204	Senp3	AA408656|Smt3ip|Smt3ip1	SUMO/sentrin specific peptidase 3	protein-coding
mm_94928.1	chr11	29548366	29548403	+	1	NA	promoter-TSS (NM_024277)	promoter-TSS (NM_024277)	-344	NM_001033865	78294	Mm.180003	NM_024277	ENSMUSG00000020460	Rps27a	0610006J14Rik|Uba52|Ubb|Ubc	ribosomal protein S27A	protein-coding
mm_14868.1	chr2	148799529	148799534	+	1	NA	intron (NM_009978, intron 1 of 3)	intron (NM_009978, intron 1 of 3)	692	NM_009978	13012	Mm.20435	NM_009978	ENSMUSG00000027442	Cst8	Cres|Cst-rs1	cystatin 8 (cystatin-related epididymal spermatogenic)	protein-coding
mm_167335.1	chr8	71381618	71381692	-	1	NA	5' UTR (NM_010150, exon 1 of 4)	5' UTR (NM_010150, exon 1 of 4)	297	NM_010150	13864	Mm.28989	NM_010150	ENSMUSG00000002393	Nr2f6	AV090102|COUP-TF3|EAR2|Erbal2	nuclear receptor subfamily 2, group F, member 6	protein-coding
mm_148489.1	chr19	4153363	4153402	+	1	NA	exon (NM_011778, exon 10 of 11)	exon (NM_011778, exon 10 of 11)	-1264	NM_016933	19265	Mm.271937	NM_016933	ENSMUSG00000045826	Ptprcap	AI605264|CD-45-AP|LPAP|LSM-1	protein tyrosine phosphatase, receptor type, C polypeptide-associated protein	protein-coding
mm_135670.1	chr16	52411679	52411690	-	1	NA	intron (NM_009655, intron 1 of 15)	L1MA7|LINE|L1	41397	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_144923.1	chr18	37680255	37680307	+	1	NA	promoter-TSS (NM_033574)	promoter-TSS (NM_033574)	-177	NM_033574	93699	Mm.247203	NM_033574	ENSMUSG00000103037	Pcdhgb1	-	protocadherin gamma subfamily B, 1	protein-coding
mm_118229.1	chr13	111489770	111489772	-	1	NA	5' UTR (NM_028487, exon 1 of 13)	5' UTR (NM_028487, exon 1 of 13)	270	NM_028487	73274	Mm.57286	NM_028487	ENSMUSG00000032745	Gpbp1	1700034P14Rik|AU019836|D230035M11Rik|Gpbp|mGPBP	GC-rich promoter binding protein 1	protein-coding
mm_78052.1	chr9	14784661	14784702	+	1	NA	promoter-TSS (NM_018736)	promoter-TSS (NM_018736)	27	NM_018736	17535	Mm.149071	NM_018736	ENSMUSG00000031928	Mre11a	Mre11|Mre11b	MRE11A homolog A, double strand break repair nuclease	protein-coding
mm_72158.1	chr8	72183987	72183990	+	1	NA	Intergenic	Intergenic	-5680	NM_197944	209488	Mm.157431	NM_197944	ENSMUSG00000062007	Hsh2d	ALX|Hsh2	hematopoietic SH2 domain containing	protein-coding
mm_112662.1	chr13	16027065	16027076	+	1	NA	exon (NM_008380, exon 5 of 5)	exon (NM_008380, exon 5 of 5)	15219	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_104339.1	chr11	94172369	94172372	-	1	NA	Intergenic	Intergenic	-39084	NM_009427	22057	Mm.259673	NM_009427	ENSMUSG00000037573	Tob1	Tob|Trob	transducer of ErbB-2.1	protein-coding
mm_27146.1	chr3	32864610	32864611	-	1	NA	intron (NM_001013024, intron 5 of 20)	MTD|LTR|ERVL-MaLR	46984	NM_001013024	72607	Mm.316153	NM_001013024	ENSMUSG00000056900	Usp13	2700071E21Rik|AI848077|ISOT3|IsoT-3	ubiquitin specific peptidase 13 (isopeptidase T-3)	protein-coding
mm_1480.1	chr1	71557169	71557240	+	1	NA	promoter-TSS (NM_026195)	promoter-TSS (NM_026195)	48	NM_026195	108147	Mm.38010	NM_026195	ENSMUSG00000026192	Atic	2610509C24Rik|AA536954|AW212393	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	protein-coding
mm_57306.1	chr6	124712132	124712171	-	1	NA	promoter-TSS (NM_013536)	promoter-TSS (NM_013536)	27	NM_013536	14791	Mm.6390	NM_013536	ENSMUSG00000004268	Emg1	C2f|Grcc2f	EMG1 N1-specific pseudouridine methyltransferase	protein-coding
mm_34465.1	chr4	148140784	148140790	+	1	NA	5' UTR (NM_027985, exon 1 of 8)	5' UTR (NM_027985, exon 1 of 8)	297	NM_027985	71890	Mm.9648	NM_027985	ENSMUSG00000029003	Mad2l2	2310033C13Rik|G1-453-4|MAD2B|REV7|repro22	MAD2 mitotic arrest deficient-like 2	protein-coding
mm_149756.1	chr19	22734960	22734980	+	1	NA	intron (NM_001035243, intron 6 of 23)	intron (NM_001035243, intron 6 of 23)	-15635	NR_029591	387200		NR_029591	ENSMUSG00000065507	Mir204	Mirn204|mir-204|mmu-mir-204	microRNA 204	ncRNA
mm_94239.1	chr11	3293110	3293128	+	1	NA	intron (NM_019574, intron 1 of 3)	intron (NM_019574, intron 1 of 3)	2662	NM_019574	56218	Mm.275563	NM_019574	ENSMUSG00000020453	Patz1	8430401L15Rik|AI447519|Mazr|Patz|Zfp278	POZ (BTB) and AT hook containing zinc finger 1	protein-coding
mm_60470.1	chr7	44478065	44478087	+	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	-6441	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_134745.1	chr16	23099699	23099715	-	1	NA	Intergenic	Intergenic	-7690	NM_001347179	13682	Mm.260084	NM_013506	ENSMUSG00000022884	Eif4a2	4833432N07Rik|BM-010|Ddx2b|Eif4|eIF-4A-II|eIF4A-II	eukaryotic translation initiation factor 4A2	protein-coding
mm_29185.1	chr3	106543196	106543199	-	1	NA	intron (NM_133869, intron 1 of 8)	intron (NM_133869, intron 1 of 8)	-4601	NM_001286986	67171	Mm.290488	NM_026013	ENSMUSG00000027900	Dram2	2010305N14Rik|2610318G18Rik|AI647667|Tmem77	DNA-damage regulated autophagy modulator 2	protein-coding
mm_107632.1	chr12	51866123	51866130	+	1	NA	Intergenic	Intergenic	-36590	NM_144788	207304	Mm.249391	NM_144788	ENSMUSG00000035247	Hectd1	A630086P08Rik|AI844876|b2b327Clo|opm	HECT domain containing 1	protein-coding
mm_105183.1	chr11	101894397	101894401	-	1	NA	promoter-TSS (NM_010791)	promoter-TSS (NM_010791)	-45	NM_010791	17285	Mm.3404	NM_010791	ENSMUSG00000001493	Meox1	AI385561|D330041M02Rik|Mox-1|Mox1	mesenchyme homeobox 1	protein-coding
mm_80863.1	chr9	98498708	98498735	+	1	NA	exon (NM_009034, exon 2 of 4)	exon (NM_009034, exon 2 of 4)	8184	NM_009034	19660	Mm.12825	NM_009034	ENSMUSG00000032454	Rbp2	Crbp-2|CrbpII|Rbp-2	retinol binding protein 2, cellular	protein-coding
mm_32794.1	chr4	116995349	116995370	+	1	NA	promoter-TSS (NM_009478)	promoter-TSS (NM_009478)	11	NM_175244	76608	Mm.251420	NM_175244	ENSMUSG00000046861	Hectd3	1700064K09Rik|AI467540|AW743312	HECT domain containing 3	protein-coding
mm_102315.1	chr11	56459360	56459373	-	1	NA	Intergenic	CpG	-418379	NM_153079	216749	Mm.213205	NM_153079	ENSMUSG00000037393	Nmur2	Nmu2r	neuromedin U receptor 2	protein-coding
mm_150847.1	chr19	44989243	44989318	+	1	NA	promoter-TSS (NM_011976)	promoter-TSS (NM_011976)	-64	NM_011976	26456	Mm.34404	NM_011976	ENSMUSG00000025207	Sema4g	AI507908|AW554132	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4G	protein-coding
mm_78573.1	chr9	36693226	36693232	+	1	NA	promoter-TSS (NM_007391)	promoter-TSS (NM_007391)	9	NM_007391	11451	Mm.4776	NM_007391	ENSMUSG00000032110	Acrv1	Msa63|SP-10	acrosomal vesicle protein 1	protein-coding
mm_14977.1	chr2	152108014	152108022	+	1	NA	intron (NM_029688, intron 1 of 1)	MLT1D|LTR|ERVL-MaLR	2494	NM_029688	76650	Mm.218639	NM_029688	ENSMUSG00000032802	Srxn1	1700127B04Rik|AI854065|AW488194|Npn3|Srx|Srx1|TX01	sulfiredoxin 1 homolog (S. cerevisiae)	protein-coding
mm_7585.1	chr1	125422162	125422176	-	1	NA	intron (NM_001205385, intron 2 of 12)	intron (NM_001205385, intron 2 of 12)	13558	NM_023735	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding
mm_46406.1	chr5	104093142	104093180	-	1	NA	exon (NM_010097, exon 4 of 11)	exon (NM_010097, exon 4 of 11)	-15553	NM_001163772	100271704	Mm.366664	NM_001163772	ENSMUSG00000091034	Gm17660	Scpppq1	predicted gene, 17660	protein-coding
mm_164442.1	chr16	49855261	49855266	+	1	NA	promoter-TSS (NM_010581)	promoter-TSS (NM_010581)	-391	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_37755.1	chr4	129641061	129641080	-	1	NA	promoter-TSS (NM_001199695)	promoter-TSS (NM_001199695)	-5	NM_001199695	109658	Mm.268863	NM_001005506	ENSMUSG00000053841	Txlna	2600010N21Rik|AI425952|AW209241|Il14|Txln	taxilin alpha	protein-coding
mm_24131.1	chr3	88212740	88212771	+	1	NA	Intergenic	Intergenic	-2416	NR_037276	100526540		NR_037276	ENSMUSG00000092988	Mir3093	mir-3093|mmu-mir-3093	microRNA 3093	ncRNA
mm_126245.1	chr15	79005239	79005318	+	1	NA	3' UTR (NM_138579, exon 24 of 24)	3' UTR (NM_138579, exon 24 of 24)	3055	NR_105921	102465577		NR_105921	ENSMUSG00000099180	Mir6956	Gm27880|mmu-mir-6956	microRNA 6956	ncRNA
mm_119592.1	chr14	50951623	50951641	+	1	NA	3' UTR (NM_013632, exon 6 of 6)	3' UTR (NM_013632, exon 6 of 6)	-4509	NM_001123371	667034	Mm.482171	NM_001123371	ENSMUSG00000068417	Pnp2	-	purine-nucleoside phosphorylase 2	protein-coding
mm_63333.1	chr7	126950599	126950609	+	1	NA	promoter-TSS (NM_001252566)	promoter-TSS (NM_001252566)	69	NM_001252566	233878	Mm.283926	NM_144926	ENSMUSG00000030683	Sez6l2	AI835913|AW121566|BSRP-A|Psk1	seizure related 6 homolog like 2	protein-coding
mm_106830.1	chr12	8001834	8001853	+	1	NA	exon (NM_009693, exon 22 of 29)	exon (NM_009693, exon 22 of 29)	24166	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_145803.1	chr18	65382050	65382073	+	1	NA	intron (NM_001037294, intron 1 of 12)	intron (NM_001037294, intron 1 of 12)	11827	NM_001037294	225638	Mm.296528	NM_001037294	ENSMUSG00000032845	Alpk2	Gm549|Hak	alpha-kinase 2	protein-coding
mm_76430.1	chr8	84978525	84978540	-	1	NA	5' UTR (NM_008416, exon 1 of 1)	5' UTR (NM_008416, exon 1 of 1)	216	NM_008416	16477	Mm.1167	NM_008416	ENSMUSG00000052837	Junb	-	jun B proto-oncogene	protein-coding
mm_151552.1	chr19	59458717	59458727	+	1	NA	promoter-TSS (NM_010132)	promoter-TSS (NM_010132)	32	NM_010132	13797	Mm.245394	NM_010132	ENSMUSG00000043969	Emx2	Pdo	empty spiracles homeobox 2	protein-coding
mm_54917.1	chr6	47799240	47799269	-	1	NA	exon (NM_009787, exon 8 of 10)	exon (NM_009787, exon 8 of 10)	4398	NR_030485	735289		NR_030485	ENSMUSG00000076060	Mir704	Mirn704|mir-704|mmu-mir-704	microRNA 704	ncRNA
mm_168057.1	chrY	90825307	90825308	-	1	NA	Intergenic	CpG	14099	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_134760.1	chr16	23233570	23233601	-	1	NA	intron (NM_001252505, intron 1 of 7)	intron (NM_001252505, intron 1 of 7)	7564	NM_001252505	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_10408.1	chr2	13578838	13578850	+	1	NA	intron (NM_011701, intron 4 of 8)	intron (NM_011701, intron 4 of 8)	4533	NM_011701	22352	Mm.268000	NM_011701	ENSMUSG00000026728	Vim	-	vimentin	protein-coding
mm_151247.1	chr19	53903809	53903827	+	1	NA	intron (NM_001168491, intron 1 of 11)	CpG	467	NM_001168491	18569	Mm.1605	NM_011050	ENSMUSG00000024975	Pdcd4	D19Ucla1|Ma3|Tis	programmed cell death 4	protein-coding
mm_128050.1	chr15	25765078	25765115	-	1	NA	intron (NM_019472, intron 19 of 40)	intron (NM_019472, intron 19 of 40)	-78202	NM_001034851	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_25871.1	chr3	130060768	130060791	+	1	NA	5' UTR (NM_207209, exon 1 of 24)	5' UTR (NM_207209, exon 1 of 24)	128	NM_207209	99683	Mm.192303	NM_207209	ENSMUSG00000001052	Sec24b	AI605202|SEC24	Sec24 related gene family, member B (S. cerevisiae)	protein-coding
mm_105627.1	chr11	106900032	106900035	-	1	NA	intron (NM_025481, intron 1 of 18)	intron (NM_025481, intron 1 of 18)	20682	NM_025481	66313	Mm.340955	NM_025481	ENSMUSG00000018363	Smurf2	2810411E22Rik|AI558114|AI649275	SMAD specific E3 ubiquitin protein ligase 2	protein-coding
mm_115047.1	chr13	100108015	100108143	+	1	NA	promoter-TSS (NM_011353)	promoter-TSS (NM_011353)	60	NM_011353	20365	Mm.286177	NM_011353	ENSMUSG00000021643	Serf1	4F5|Msmac1|m4F5	small EDRK-rich factor 1	protein-coding
mm_953.1	chr1	57774749	57774762	+	1	NA	promoter-TSS (NM_144882)	promoter-TSS (NM_144882)	-106	NM_144882	67198	Mm.159989	NM_144882	ENSMUSG00000038305	Spats2l	2810022L02Rik|A230104H11Rik|AA987173|AI480531|AI842453|AW413586	spermatogenesis associated, serine-rich 2-like	protein-coding
mm_116393.1	chr13	41216952	41216955	-	1	NA	intron (NM_019423, intron 1 of 7)	intron (NM_019423, intron 1 of 7)	3209	NM_001311121	54326	Mm.2567	NM_019423	ENSMUSG00000021364	Elovl2	AI317360|Ssc2	elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 2	protein-coding
mm_166509.1	chr6	8532086	8532089	+	1	NA	intron (NM_001286728, intron 1 of 7)	Lx8|LINE|L1	12029	NM_001286729	170772	Mm.210787	NM_133236	ENSMUSG00000029638	Glcci1	2310047L21Rik|A130036A18Rik|Fam117c|Gig18|Tssn1	glucocorticoid induced transcript 1	protein-coding
mm_116123.1	chr13	28951440	28951452	-	1	NA	3' UTR (NM_009238, exon 1 of 1)	3' UTR (NM_009238, exon 1 of 1)	2236	NM_009238	20677	Mm.240627	NM_009238	ENSMUSG00000076431	Sox4	AA682046|Sox-4	SRY (sex determining region Y)-box 4	protein-coding
mm_126333.1	chr15	79895018	79895036	+	1	NA	promoter-TSS (NM_001347041)	promoter-TSS (NM_001347041)	4	NM_001347041	80287	Mm.284059	NM_030255	ENSMUSG00000009585	Apobec3	Apobec|Arp3|BC003314|Cem15|Rfv3	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 3	protein-coding
mm_112477.1	chr13	5868816	5868827	+	1	NA	3' UTR (NM_011803, exon 4 of 4)	3' UTR (NM_011803, exon 4 of 4)	7332	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_163434.1	chr12	85397466	85397492	-	1	NA	Intergenic	Intergenic	-22762	NM_026775	68581	Mm.379159	NM_026775	ENSMUSG00000021248	Tmed10	1110014C03Rik|Tmp21|p23|p24delta1	transmembrane p24 trafficking protein 10	protein-coding
mm_41685.1	chr5	100429707	100429748	+	1	NA	promoter-TSS (NR_034038)	promoter-TSS (NR_034038)	-192	NR_034038	100503199	Mm.392282	NR_034038	ENSMUSG00000097772	5430416N02Rik	100041797|Adapt33|Gm3514	RIKEN cDNA 5430416N02 gene	ncRNA
mm_98093.1	chr11	86604014	86604040	+	1	NA	intron (NM_029478, intron 9 of 11)	intron (NM_029478, intron 9 of 11)	-19869	NR_029738	387140		NR_029738	ENSMUSG00000065455	Mir21a	Mir21|Mirn21|mmu-mir-21|mmu-mir-21a	microRNA 21a	ncRNA
mm_149784.1	chr19	23140108	23140111	+	1	NA	Intergenic	Intergenic	-1117	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_116426.1	chr13	41847483	41847490	-	1	NA	promoter-TSS (NM_175417)	promoter-TSS (NM_175417)	2	NM_175417	109254	Mm.25195	NM_175417	ENSMUSG00000058022	Adtrp	9530008L14Rik	androgen dependent TFPI regulating protein	protein-coding
mm_113037.1	chr13	23551831	23551863	+	1	NA	promoter-TSS (NM_175655)	promoter-TSS (NM_175655)	-204	NM_175655	319157	Mm.442307	NM_175655	ENSMUSG00000069274	Hist1h4f	-	histone cluster 1, H4f	protein-coding
mm_70353.1	chr8	5210768	5210770	+	1	NA	Intergenic	L1_Mur1|LINE|L1	-105482	NM_011388	20494	Mm.3500	NM_011388	ENSMUSG00000023073	Slc10a2	9130221J18Rik|AI605518|ASBT|IBAT|ISBT	solute carrier family 10, member 2	protein-coding
mm_124435.1	chr14	118511390	118511392	-	1	NA	intron (NM_001033336, intron 26 of 30)	intron (NM_001033336, intron 26 of 30)	81081	NR_105815	102465208		NR_105815	ENSMUSG00000098433	Mir6391	Gm27914|mmu-mir-6391	microRNA 6391	ncRNA
mm_21186.1	chr2	155250039	155250070	-	1	NA	non-coding (NR_111891, exon 4 of 4)	non-coding (NR_111891, exon 4 of 4)	13446	NM_001291108	67068	Mm.23693	NM_025947	ENSMUSG00000047459	Dynlrb1	2010012N15Rik|2010320M17Rik|9430076K19Rik|AV124457|DNLC2A|Dncl2a|km23-1	dynein light chain roadblock-type 1	protein-coding
mm_162584.1	chr1	180312864	180312879	-	1	NA	Intergenic	Intergenic	-17605	NM_001081175	320404	Mm.132535	NM_001081175	ENSMUSG00000038855	Itpkb	1110033J02Rik|E130307H12Rik	inositol 1,4,5-trisphosphate 3-kinase B	protein-coding
mm_99191.1	chr11	100940119	100940146	+	1	NA	promoter-TSS (NM_011486)	promoter-TSS (NM_011486)	-592	NM_011486	20848	Mm.249934	NM_011486	ENSMUSG00000004040	Stat3	1110034C02Rik|AW109958|Aprf	signal transducer and activator of transcription 3	protein-coding
mm_120176.1	chr14	61172967	61173018	+	1	NA	intron (NM_172809, intron 2 of 9)	CpG	34535	NM_172809	50720	Mm.440703	NM_015788	ENSMUSG00000048279	Sacs	A230052M14|DNAJC29|E130115J16Rik|mKIAA0730	sacsin	protein-coding
mm_52440.1	chr6	113624049	113624062	+	1	NA	promoter-TSS (NM_009507)	promoter-TSS (NM_009507)	34	NM_009507	22346	Mm.29407	NM_009507	ENSMUSG00000033933	Vhl	Vhlh	von Hippel-Lindau tumor suppressor	protein-coding
mm_16272.1	chr2	173719427	173719437	+	1	NA	promoter-TSS (NM_029308)	promoter-TSS (NM_029308)	17	NM_029308	75485	Mm.308031	NM_029308	ENSMUSG00000057047	1700010B08Rik	-	RIKEN cDNA 1700010B08 gene	protein-coding
mm_36959.1	chr4	109156805	109156827	-	1	NA	intron (NM_001346502, intron 2 of 23)	intron (NM_001346502, intron 2 of 23)	-38780	NM_001134791	100273	Mm.366315	NM_133885	ENSMUSG00000028559	Osbpl9	2600011I06Rik|AU015843|Orp-9	oxysterol binding protein-like 9	protein-coding
mm_169083.1	chr13	34394544	34394554	-	1	NA	Intergenic	Intergenic	-49367	NM_001033167	73102	Mm.23932	NM_001033167	ENSMUSG00000038267	Slc22a23	3110004L20Rik	solute carrier family 22, member 23	protein-coding
mm_3686.1	chr1	153749450	153749491	+	1	NA	promoter-TSS (NM_011882)	promoter-TSS (NM_011882)	44	NM_011882	24014	Mm.259254	NM_011882	ENSMUSG00000066800	Rnasel	E230029I04Rik	ribonuclease L (2', 5'-oligoisoadenylate synthetase-dependent)	protein-coding
mm_133832.1	chr16	95900544	95900544	+	1	NA	intron (NR_040484, intron 1 of 3)	L1MC5|LINE|L1	-1831	NR_040485	69776	Mm.120470	NR_040484	ENSMUSG00000086899	1600002D24Rik	-	RIKEN cDNA 1600002D24 gene	ncRNA
mm_7038.1	chr1	87100599	87100612	-	1	NA	exon (NM_001081082, exon 5 of 11)	exon (NM_001081082, exon 5 of 11)	1001	NM_001081082	76768	Mm.58068	NM_001081082	ENSMUSG00000079440	Alpi	2010001C14Rik|Akp6|gIAP	alkaline phosphatase, intestinal	protein-coding
mm_34636.1	chr4	150614575	150614597	+	1	NA	exon (NM_001085492, exon 18 of 23)	exon (NM_001085492, exon 18 of 23)	37588	NM_173774	242773	Mm.29280	NM_173774	ENSMUSG00000039838	Slc45a1	C230078B22|Dnb5	solute carrier family 45, member 1	protein-coding
mm_41086.1	chr5	87680845	87680869	+	1	NA	exon (NM_007784, exon 32 of 34)	exon (NM_007784, exon 32 of 34)	14649	NM_001286016	12990	Mm.427467	NM_007784	ENSMUSG00000070702	Csn1s1	AA959832|AW212882|Csna	casein alpha s1	protein-coding
mm_125880.1	chr15	75641877	75641897	+	1	NA	Intergenic	Intergenic	25203	NM_011759	22701	Mm.87210	NM_011759	ENSMUSG00000047003	Zfp41	CTfin92|Zfp-41	zinc finger protein 41	protein-coding
mm_167301.1	chr8	56288422	56288423	+	1	NA	Intergenic	Lx8|LINE|L1	-6130	NM_008278	15446	Mm.18832	NM_008278	ENSMUSG00000031613	Hpgd	15-PGDH|AV026552	hydroxyprostaglandin dehydrogenase 15 (NAD)	protein-coding
mm_48647.1	chr5	145855065	145855076	-	1	NA	exon (NM_007818, exon 13 of 13)	exon (NM_007818, exon 13 of 13)	24784	NM_007818	13112	Mm.332844	NM_007818	ENSMUSG00000056035	Cyp3a11	AI256190|Cyp3a|IIIAm1|Pcn	cytochrome P450, family 3, subfamily a, polypeptide 11	protein-coding
mm_154951.1	chrX	36602159	36602170	+	1	NA	exon (NM_016783, exon 2 of 3)	exon (NM_016783, exon 2 of 3)	3971	NM_016783	53328	Mm.9052	NM_016783	ENSMUSG00000006373	Pgrmc1	AA415812|HPR6.6|PPMR|Vema	progesterone receptor membrane component 1	protein-coding
mm_53497.1	chr6	135362304	135362320	+	1	NA	promoter-TSS (NM_001288628)	promoter-TSS (NM_001288628)	-619	NM_010128	13730	Mm.182785	NM_010128	ENSMUSG00000030208	Emp1	I-8-09|TMP	epithelial membrane protein 1	protein-coding
mm_46753.1	chr5	112228770	112228810	-	1	NA	non-coding (NR_033657, exon 1 of 7)	non-coding (NR_033657, exon 1 of 7)	158	NR_033657	330166	Mm.44854	NR_003718	ENSMUSG00000097767	Miat	3632434I06|A230057G18Rik|Rncr2|gomafu	myocardial infarction associated transcript (non-protein coding)	ncRNA
mm_106952.1	chr12	8791787	8791831	+	1	NA	3' UTR (NM_011519, exon 5 of 5)	3' UTR (NM_011519, exon 5 of 5)	20413	NM_011519	20969	Mm.2580	NM_011519	ENSMUSG00000020592	Sdc1	AA408134|AA409076|CD138|Sstn|Synd|Synd1|syn-1	syndecan 1	protein-coding
mm_114198.1	chr13	55926015	55926041	+	1	NA	Intergenic	Intergenic	-94603	NM_011097	18740	Mm.135195	NM_011097	ENSMUSG00000021506	Pitx1	Bft|P-OTX|Potx|Ptx1	paired-like homeodomain transcription factor 1	protein-coding
mm_64486.1	chr7	143067402	143067476	+	1	NA	3' UTR (NM_133655, exon 8 of 8)	3' UTR (NM_133655, exon 8 of 8)	-1929	NM_020285	56844	Mm.139675	NM_020285	ENSMUSG00000045752	Tssc4	AA241958|ESTM671070	tumor-suppressing subchromosomal transferable fragment 4	protein-coding
mm_19716.1	chr2	104410554	104410568	-	1	NA	promoter-TSS (NM_001033347)	promoter-TSS (NM_001033347)	-227	NM_001033347	241589	Mm.358909	NM_001033347	ENSMUSG00000068373	D430041D05Rik	9630056G07Rik|G2	RIKEN cDNA D430041D05 gene	protein-coding
mm_35608.1	chr4	43046197	43046216	-	1	NA	promoter-TSS (NM_172691)	promoter-TSS (NM_172691)	14	NR_045567	230088	Mm.260162	NM_172691	ENSMUSG00000036002	Fam214b	B230312A22Rik	family with sequence similarity 214, member B	protein-coding
mm_39220.1	chr4	156197514	156197520	-	1	NA	promoter-TSS (NM_021604)	promoter-TSS (NM_021604)	-29	NM_021604	11603	Mm.273098	NM_021604	ENSMUSG00000041936	Agrn	Agrin|nmf380	agrin	protein-coding
mm_24728.1	chr3	95282950	95282958	+	1	NA	promoter-TSS (NM_133858)	promoter-TSS (NM_133858)	19	NM_199475	75007	Mm.279287	NM_133858	ENSMUSG00000038712	Fam63a	1810005H09Rik|4930504E06Rik|AA562754|AA960384|AW561904|cI-40|mKIAA1390|ni	family with sequence similarity 63, member A	protein-coding
mm_111328.1	chr12	86490213	86490224	-	1	NA	intron (NM_001159500, intron 3 of 6)	MTC|LTR|ERVL-MaLR	68574	NM_011934	26380	Mm.235550	NM_011934	ENSMUSG00000021255	Esrrb	Err2|Errb|Estrrb|Nr3b2	estrogen related receptor, beta	protein-coding
mm_157999.1	chrX	94542038	94542042	-	1	NA	promoter-TSS (NM_019791)	promoter-TSS (NM_019791)	34	NM_019791	94275	Mm.27578	NM_019791	ENSMUSG00000025151	Maged1	2810433C11Rik|5430405L04Rik|DXBwg1492e|Dlixin|Dlxin-1|Dlxin1|MAGE-D1|NRAGE|mFLJ00163	melanoma antigen, family D, 1	protein-coding
mm_116470.1	chr13	43481102	43481108	-	1	NA	promoter-TSS (NM_019930)	promoter-TSS (NM_019930)	-132	NM_019930	56705	Mm.148781	NM_019930	ENSMUSG00000038546	Ranbp9	IBAP-1|Ibap1|RanBPM	RAN binding protein 9	protein-coding
mm_99916.1	chr11	110180184	110180211	+	1	NA	intron (NM_147218, intron 36 of 38)	intron (NM_147218, intron 36 of 38)	-12044	NM_147220	217262	Mm.291459	NM_147220	ENSMUSG00000041797	Abca9	D630040K07Rik	ATP-binding cassette, sub-family A (ABC1), member 9	protein-coding
mm_46611.1	chr5	107976221	107976223	-	1	NA	intron (NM_026062, intron 1 of 4)	intron (NM_026062, intron 1 of 4)	10855	NM_026062	67266	Mm.277897	NM_026062	ENSMUSG00000029270	Fam69a	2900024C23Rik|AI315274	family with sequence similarity 69, member A	protein-coding
mm_62066.1	chr7	92561543	92561553	+	1	NA	exon (NM_025515, exon 1 of 9)	exon (NM_025515, exon 1 of 9)	399	NM_001162918	66365	Mm.21173	NM_025515	ENSMUSG00000030613	Ccdc90b	2310015N07Rik|C86558	coiled-coil domain containing 90B	protein-coding
mm_113347.1	chr13	31806769	31806784	+	1	NA	5' UTR (NM_008592, exon 1 of 1)	5' UTR (NM_008592, exon 1 of 1)	130	NM_008592	17300	Mm.12949	NM_008592	ENSMUSG00000050295	Foxc1	FREAC3|Fkh1|Mf1|Mf4|ch|fkh-1|frkhda	forkhead box C1	protein-coding
mm_163859.1	chr14	19418647	19418674	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	183927	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_46204.1	chr5	98031376	98031388	-	1	NA	promoter-TSS (NM_133738)	promoter-TSS (NM_133738)	-420	NM_133738	71914	Mm.24842	NM_133738	ENSMUSG00000029338	Antxr2	2310046B19Rik|AW561899|CMG-2|CMG2|cI-35	anthrax toxin receptor 2	protein-coding
mm_9640.1	chr1	177131068	177131078	-	1	NA	exon (NM_011785, exon 2 of 13)	exon (NM_011785, exon 2 of 13)	117694	NM_011785	23797	Mm.235194	NM_011785	ENSMUSG00000019699	Akt3	AI851531|D930002M15Rik|Nmf350	thymoma viral proto-oncogene 3	protein-coding
mm_88415.1	chr10	77033305	77033315	+	1	NA	promoter-TSS (NM_031196)	promoter-TSS (NM_031196)	98	NM_031196	20509	Mm.265060	NM_031196	ENSMUSG00000001436	Slc19a1	AI323572|RFC|RFC-1|RFC1	solute carrier family 19 (folate transporter), member 1	protein-coding
mm_28947.1	chr3	100141714	100141725	-	1	NA	intron (NM_175552, intron 23 of 26)	intron (NM_175552, intron 23 of 26)	20684	NM_175552	269470	Mm.24591	NM_175552	ENSMUSG00000033285	Wdr3	AW546279|D030020G18Rik	WD repeat domain 3	protein-coding
mm_51669.1	chr6	86404192	86404198	+	1	NA	promoter-TSS (NM_011585)	promoter-TSS (NM_011585)	-24	NM_001164079	21841	Mm.333219	NM_011585	ENSMUSG00000071337	Tia1	2310050N03Rik|AI256674|TIA-1|mTIA-1	cytotoxic granule-associated RNA binding protein 1	protein-coding
mm_131857.1	chr16	23079002	23079012	+	1	NA	exon (NM_001102411, exon 10 of 10)	exon (NM_001102411, exon 10 of 10)	20707	NM_001102412	16644	Mm.2160	NM_023125	ENSMUSG00000022875	Kng1	Kng	kininogen 1	protein-coding
mm_116856.1	chr13	54762949	54762971	-	1	NA	exon (NM_033610, exon 3 of 6)	exon (NM_033610, exon 3 of 6)	3480	NM_033610	104069	Mm.200843	NM_033610	ENSMUSG00000034891	Sncb	AI838531|betaSYN	synuclein, beta	protein-coding
mm_56785.1	chr6	116637820	116637850	-	1	NA	3' UTR (NM_178045, exon 11 of 11)	3' UTR (NM_178045, exon 11 of 11)	8212	NR_106010	102466793		NR_106010	ENSMUSG00000098334	Mir7043	Gm27776|mmu-mir-7043	microRNA 7043	ncRNA
mm_143175.1	chr17	57244327	57244349	-	1	NA	exon (NM_030084, exon 5 of 17)	exon (NM_030084, exon 5 of 17)	3132	NM_001308074	78308	Mm.28468	NM_030084	ENSMUSG00000005823	Gpr108	1810015L19Rik|AA589464|C79132|Lustr2	G protein-coupled receptor 108	protein-coding
mm_103.1	chr1	9545922	9545988	+	1	NA	exon (NM_021511, exon 1 of 1)	exon (NM_021511, exon 1 of 1)	547	NM_021511	59014	Mm.29061	NM_021511	ENSMUSG00000061024	Rrs1	5730466A07Rik|AA415037|D1Ertd701e|Rrr	ribosome biogenesis regulator 1	protein-coding
mm_148185.1	chr18	78596896	78596907	-	1	NA	promoter-TSS (NM_207651)	promoter-TSS (NM_207651)	49	NM_207651	27411	Mm.44158	NM_030683	ENSMUSG00000024552	Slc14a2	UT-A1|UT-A3	solute carrier family 14 (urea transporter), member 2	protein-coding
mm_115257.1	chr13	110399968	110399971	+	1	NA	intron (NM_152804, intron 13 of 13)	intron (NM_152804, intron 13 of 13)	4925	NM_152804	20620	Mm.380	NM_152804	ENSMUSG00000021701	Plk2	Snk	polo-like kinase 2	protein-coding
mm_24956.1	chr3	96645580	96645608	+	1	NA	promoter-TSS (NM_001302471)	promoter-TSS (NM_001302471)	10	NM_001302471	213119	Mm.32741	NM_001081053	ENSMUSG00000090210	Itga10	A630048L14	integrin, alpha 10	protein-coding
mm_86270.1	chr9	121718928	121719013	-	1	NA	promoter-TSS (NM_010918)	promoter-TSS (NM_010918)	-211	NM_010918	18087	Mm.32842	NM_010918	ENSMUSG00000032525	Nktr	5330401F18Rik|D9Wsu172e	natural killer tumor recognition sequence	protein-coding
mm_43630.1	chr5	138187500	138187521	+	1	NA	promoter-TSS (NM_178612)	promoter-TSS (NM_178612)	-25	NM_178612	66455	Mm.24592	NM_178612	ENSMUSG00000036968	Cnpy4	2610019P18Rik	canopy FGF signaling regulator 4	protein-coding
mm_24101.1	chr3	88138790	88138805	+	1	NA	Intergenic	Intergenic	-3575	NM_001310587	17261	Mm.28184	NM_133665	ENSMUSG00000001419	Mef2d	C80750	myocyte enhancer factor 2D	protein-coding
mm_26657.1	chr3	154597205	154597215	+	1	NA	promoter-TSS (NM_172474)	promoter-TSS (NM_172474)	-112	NM_172474	209584	Mm.347513	NM_172474	ENSMUSG00000047583	Tyw3	5230400J09Rik	tRNA-yW synthesizing protein 3 homolog (S. cerevisiae)	protein-coding
mm_170057.1	chr17	30612599	30612611	-	1	NA	promoter-TSS (NM_001113560)	promoter-TSS (NM_001113560)	54	NM_025374	109801	Mm.261984	NM_025374	ENSMUSG00000024026	Glo1	0610009E22Rik|1110008E19Rik|2510049H23Rik|AW550643|GLY1|Glo-1|Glo-1r|Glo-1s|Glo1-r|Glo1-s|Qglo	glyoxalase 1	protein-coding
mm_56172.1	chr6	88012210	88012217	-	1	NA	intron (NM_001293652, intron 5 of 7)	intron (NM_001293652, intron 5 of 7)	7582	NM_001293654	19349	Mm.333233	NM_009005	ENSMUSG00000079477	Rab7	Rab7a	RAB7, member RAS oncogene family	protein-coding
mm_143476.1	chr17	71256852	71256862	-	1	NA	intron (NM_145158, intron 4 of 7)	intron (NM_145158, intron 4 of 7)	52203	NM_001164885	64898	Mm.227924	NM_022882	ENSMUSG00000024052	Lpin2	2610511G02Rik|AI481352|AW742896	lipin 2	protein-coding
mm_698.1	chr1	40580522	40580531	+	1	NA	exon (NM_177084, exon 1 of 12)	exon (NM_177084, exon 1 of 12)	299	NM_177084	110895	Mm.108602	NM_177084	ENSMUSG00000026065	Slc9a4	AW990558|D730009J23Rik|NHE4	solute carrier family 9 (sodium/hydrogen exchanger), member 4	protein-coding
mm_45775.1	chr5	87092075	87092087	-	1	NA	exon (NM_001029867, exon 1 of 6)	exon (NM_001029867, exon 1 of 6)	474	NM_001029867	231396	Mm.439851	NM_001029867	ENSMUSG00000070704	Ugt2b36	-	UDP glucuronosyltransferase 2 family, polypeptide B36	protein-coding
mm_8402.1	chr1	151500954	151500960	-	1	NA	promoter-TSS (NM_011277)	promoter-TSS (NM_011277)	-134	NM_011277	19821	Mm.474038	NM_011277	ENSMUSG00000026484	Rnf2	AI326319|AI450156|AU019207|Ring1B|dinG	ring finger protein 2	protein-coding
mm_128139.1	chr15	31503540	31503542	-	1	NA	intron (NM_172606, intron 3 of 25)	intron (NM_172606, intron 3 of 25)	27496	NM_172606	223455	Mm.272185	NM_172606	ENSMUSG00000039100	March6	3830408G03|F830029L24Rik|mKIAA0597	membrane-associated ring finger (C3HC4) 6	protein-coding
mm_147281.1	chr18	39487064	39487094	-	1	NA	exon (NM_008173, exon 1 of 8)	exon (NM_008173, exon 1 of 8)	166	NM_008173	14815	Mm.129481	NM_008173	ENSMUSG00000024431	Nr3c1	GR|Grl-1|Grl1	nuclear receptor subfamily 3, group C, member 1	protein-coding
mm_129010.1	chr15	74914125	74914131	-	1	NA	Intergenic	Intergenic	-32424	NM_025929	67038	Mm.154566	NM_025929	ENSMUSG00000063522	2010109I03Rik	Ly6m	RIKEN cDNA 2010109I03 gene	protein-coding
mm_99925.1	chr11	110968057	110968070	+	1	NA	promoter-TSS (NM_001252207)	promoter-TSS (NM_001252207)	30	NM_001252207	16517	Mm.30176	NM_010604	ENSMUSG00000051497	Kcnj16	6430410F18Rik|AI132396|Kir5.1	potassium inwardly-rectifying channel, subfamily J, member 16	protein-coding
mm_117438.1	chr13	74727335	74727338	-	1	NA	exon (NM_009817, exon 19 of 31)	exon (NM_009817, exon 19 of 31)	6925	NM_001301158	12380	Mm.29163	NM_009817	ENSMUSG00000021585	Cast	-	calpastatin	protein-coding
mm_115566.1	chr13	9765138	9765184	-	1	NA	promoter-TSS (NM_001347480)	promoter-TSS (NM_001347480)	160	NM_001347474	66505	Mm.397307	NM_144516	ENSMUSG00000021156	Zmynd11	2210402G22Rik|BS69	zinc finger, MYND domain containing 11	protein-coding
mm_155666.1	chrX	88607233	88607236	+	1	NA	Intergenic	Lx7|LINE|L1	152319	NR_035440	100316809		NR_035440	ENSMUSG00000084535	Mir1906-1	Mir1906|Mirn1906|mmu-mir-1906|mmu-mir-1906-1	microRNA 1906-1	ncRNA
mm_66199.1	chr7	34230285	34230308	-	1	NA	promoter-TSS (NM_008155)	promoter-TSS (NM_008155)	40	NM_008155	14751	Mm.589	NM_008155	ENSMUSG00000036427	Gpi1	Amf|Gpi|Gpi-1|Gpi-1r|Gpi-1s|Gpi-1t|Gpi1-r|Gpi1-s|Gpi1-t|Gpi1s|MF|NK|NK/GPI|Nlk|Org|Pgi|Phi	glucose phosphate isomerase 1	protein-coding
mm_103799.1	chr11	82890542	82890626	-	1	NA	promoter-TSS (NM_001277939)	promoter-TSS (NM_001277939)	40	NR_102719	19364	Mm.9286	NM_011235	ENSMUSG00000018841	Rad51d	R51H3|Rad51l3|TRAD|Trad-d5	RAD51 paralog D	protein-coding
mm_52169.1	chr6	99094732	99094737	+	1	NA	intron (NM_001347345, intron 5 of 19)	intron (NM_001347345, intron 5 of 19)	-66436	NM_001197322	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_117577.1	chr13	86050353	86050396	-	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	-3579	NM_007749	12867	Mm.378898	NM_007749	ENSMUSG00000017778	Cox7c	COXVIIc|Cox7c1	cytochrome c oxidase subunit VIIc	protein-coding
mm_110696.1	chr12	69197608	69197615	-	1	NA	non-coding (NR_033222, exon 1 of 2)	non-coding (NR_033222, exon 1 of 2)	400	NR_033222	414085	Mm.256223	NR_033222	ENSMUSG00000097061	9330151L19Rik	-	RIKEN cDNA 9330151L19 gene	ncRNA
mm_155170.1	chrX	53434945	53434949	+	1	NA	promoter-TSS (NR_034074)	promoter-TSS (NR_034074)	29	NR_034074	69501	Mm.63828	NM_175147	ENSMUSG00000060967	Etd	1700030K02Rik	embryonic testis differentiation	ncRNA
mm_114826.1	chr13	91930630	91930637	+	1	NA	intron (NM_009027, intron 5 of 14)	intron (NM_009027, intron 5 of 14)	-53748	NM_198415	76722	Mm.316438	NM_198415	ENSMUSG00000021622	Ckmt2	2300008A19Rik|ScCKmit	creatine kinase, mitochondrial 2	protein-coding
mm_24253.1	chr3	89183132	89183207	+	1	NA	promoter-TSS (NM_001014995)	promoter-TSS (NM_001014995)	-56	NM_001014995	68521	Mm.274708	NM_001014995	ENSMUSG00000032657	Fam189b	1110013L07Rik	family with sequence similarity 189, member B	protein-coding
mm_5602.1	chr1	39571001	39571027	-	1	NA	intron (NM_001033135, intron 1 of 6)	B3|SINE|B2	6333	NM_001033135	67702	Mm.28614	NM_001033135	ENSMUSG00000048234	Rnf149	1600023E10Rik|AV037261|C76763|Gm15832|Greul4|OTTMUSG00000026591	ring finger protein 149	protein-coding
mm_92861.1	chr10	81596488	81596491	-	1	NA	intron (NM_001346695, intron 4 of 13)	ID_B1|SINE|B4	4411	NM_053254	114606	Mm.206764	NM_053254	ENSMUSG00000034758	Tle6	1810057E06Rik|Grg6	transducin-like enhancer of split 6	protein-coding
mm_105050.1	chr11	100620166	100620209	-	1	NA	promoter-TSS (NM_019795)	promoter-TSS (NM_019795)	-19	NM_019795	56354	Mm.402409	NM_019795	ENSMUSG00000014195	Dnajc7	2010003F24Rik|2010004G07Rik|CCRP|Ttc2|mDj11|mTpr2	DnaJ heat shock protein family (Hsp40) member C7	protein-coding
mm_52449.1	chr6	113668059	113668097	+	1	NA	intron (NM_172161, intron 3 of 12)	B1_Mus1|SINE|Alu	-28972	NM_001347356	381801	Mm.333322	NM_001033463	ENSMUSG00000056952	Tatdn2	AI646012|mKIAA0218	TatD DNase domain containing 2	protein-coding
mm_68819.1	chr7	126082407	126082428	-	1	NA	promoter-TSS (NM_001101488)	promoter-TSS (NM_001101488)	-6	NM_001101488	269994	Mm.39599	NM_001101488	ENSMUSG00000046182	Gsg1l	AI852434|C230098I05Rik|G630023A01Rik|Gm637|g1l	GSG1-like	protein-coding
mm_8272.1	chr1	139631951	139631960	-	1	NA	Intergenic	L1VL2|LINE|L1	-71733	NM_015780	50702	Mm.220362	NM_015780	ENSMUSG00000057037	Cfhr1	AI194696|CFHRB|Cfhl1	complement factor H-related 1	protein-coding
mm_44390.1	chr5	17829206	17829220	-	1	NA	intron (NM_007643, intron 2 of 14)	intron (NM_007643, intron 2 of 14)	6683	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_111613.1	chr12	102401622	102401633	-	1	NA	intron (NM_011175, intron 8 of 13)	B3A|SINE|B2	38186	NM_011175	19141	Mm.17185	NM_011175	ENSMUSG00000021190	Lgmn	AEP|AI746452|AU022324|Prsc1	legumain	protein-coding
mm_56346.1	chr6	92943371	92943382	-	1	NA	intron (NR_015530, intron 1 of 2)	CpG	2794	NR_015530	330385	Mm.483472	NR_015530	ENSMUSG00000097462	9530026P05Rik	B430306B02	RIKEN cDNA 9530026P05 gene	ncRNA
mm_48817.1	chr5	149015853	149015867	-	1	NA	Intergenic	Intergenic	8898	NR_040429	100503307	Mm.188008	NR_040429	ENSMUSG00000086610	Gm15408	OTTMUSG00000021225	predicted gene 15408	ncRNA
mm_132039.1	chr16	27423060	27423099	+	1	NA	intron (NM_001025615, intron 5 of 9)	intron (NM_001025615, intron 5 of 9)	34123	NM_001289436	67501	Mm.258985	NM_026202	ENSMUSG00000038127	Ccdc50	C3orf6	coiled-coil domain containing 50	protein-coding
mm_50575.1	chr6	49051956	49051996	+	1	NA	exon (NM_053110, exon 9 of 11)	exon (NM_053110, exon 9 of 11)	15458	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_5915.1	chr1	55027474	55027484	-	1	NA	promoter-TSS (NM_031179)	promoter-TSS (NM_031179)	-1	NM_031179	81898	Mm.279736	NM_031179	ENSMUSG00000025982	Sf3b1	155kDa|2810001M05Rik|AA409119|Prp10|SAP155|SF3b155|TA-8|Targ4	splicing factor 3b, subunit 1	protein-coding
mm_159904.1	chr6	40613107	40613107	-	1	NA	exon (NM_001001451, exon 1 of 1)	exon (NM_001001451, exon 1 of 1)	203	NM_001001451	387513	Mm.377920	NM_001001451	ENSMUSG00000058250	Tas2r138	T2R138|Tas2r38|mt2r31	taste receptor, type 2, member 138	protein-coding
mm_143096.1	chr17	57080819	57080830	-	1	NA	exon (NM_009451, exon 4 of 4)	exon (NM_009451, exon 4 of 4)	-2314	NM_153551	70785	Mm.284447	NM_153551	ENSMUSG00000002668	Dennd1c	4432409M07Rik	DENN/MADD domain containing 1C	protein-coding
mm_163556.1	chr13	24024424	24024428	+	1	NA	exon (NM_026825, exon 36 of 38)	exon (NM_026825, exon 36 of 38)	-33212	NM_145399	214189	Mm.255667	NM_145399	ENSMUSG00000021337	Scgn	-	secretagogin, EF-hand calcium binding protein	protein-coding
mm_102567.1	chr11	61493970	61494046	-	1	NA	5' UTR (NM_001291037, exon 1 of 6)	5' UTR (NM_001291037, exon 1 of 6)	258	NM_001291037	23939	Mm.38172	NM_011841	ENSMUSG00000001034	Mapk7	BMK-1|BMK1|ERK-5|ERK5|Erk5-T|PRKM7	mitogen-activated protein kinase 7	protein-coding
mm_24778.1	chr3	95538748	95538816	+	1	NA	exon (NM_021281, exon 3 of 8)	exon (NM_021281, exon 3 of 8)	11996	NM_001267695	13040	Mm.3619	NM_021281	ENSMUSG00000038642	Ctss	Cats	cathepsin S	protein-coding
mm_107498.1	chr12	38829754	38829757	+	1	NA	intron (NM_001347379, intron 5 of 11)	intron (NM_001347379, intron 5 of 11)	46044	NM_001163154	14009	Mm.4866	NM_007960	ENSMUSG00000004151	Etv1	ER81|Etsrp81	ets variant 1	protein-coding
mm_64300.1	chr7	141861712	141861718	+	1	NA	exon (NM_028801, exon 31 of 49)	exon (NM_028801, exon 31 of 49)	22643	NM_028801	74180	Mm.200752	NM_028801	ENSMUSG00000066108	Muc5b	2300002I04Rik|A130042M24|AV085033|MUC5|MUC9|mucin 5b	mucin 5, subtype B, tracheobronchial	protein-coding
mm_122386.1	chr14	40899390	40899398	-	1	NA	Intergenic	MLT1J2|LTR|ERVL-MaLR	-6429	NM_177816	328381	Mm.235694	NM_177816	ENSMUSG00000037833	Sh2d4b	A430109M18Rik|D030001E08	SH2 domain containing 4B	protein-coding
mm_70467.1	chr8	11952655	11952679	+	1	NA	Intergenic	B3|SINE|B2	112146	NM_029326	75528	Mm.440342	NM_029326	ENSMUSG00000031512	Tex29	1700018L24Rik	testis expressed 29	protein-coding
mm_29117.1	chr3	104961735	104961745	-	1	NA	promoter-TSS (NM_009520)	promoter-TSS (NM_009520)	-31	NM_009520	22414	Mm.10740	NM_009520	ENSMUSG00000027840	Wnt2b	Wnt13	wingless-type MMTV integration site family, member 2B	protein-coding
mm_23126.1	chr3	37654766	37654778	+	1	NA	Intergenic	Intergenic	14825	NM_001305442	24063	Mm.330986	NM_011896	ENSMUSG00000037211	Spry1	sprouty1|spry-1	sprouty homolog 1 (Drosophila)	protein-coding
mm_137333.1	chr17	25089390	25089441	+	1	NA	exon (NM_134126, exon 23 of 30)	exon (NM_134126, exon 23 of 30)	-8301	NM_001001183	407831	Mm.34379	NM_001001183	ENSMUSG00000024168	Tmem204	-	transmembrane protein 204	protein-coding
mm_7110.1	chr1	89931182	89931198	-	1	NA	promoter-TSS (NM_010262)	promoter-TSS (NM_010262)	-14	NM_010262	14472	Mm.204730	NM_010262	ENSMUSG00000034486	Gbx2	D130058E05Rik|Gbx-2|MMoxA|Stra7	gastrulation brain homeobox 2	protein-coding
mm_30572.1	chr4	3809106	3809111	+	1	NA	Intergenic	RMER19C|LTR|ERVK	26547	NM_026147	67427	Mm.21938	NM_026147	ENSMUSG00000028234	Rps20	4632426K06Rik|Dsk4	ribosomal protein S20	protein-coding
mm_64019.1	chr7	140261481	140261497	+	1	NA	exon (NM_001128146, exon 4 of 16)	exon (NM_001128146, exon 4 of 16)	14108	NM_001128145	244234	Mm.85125	NM_175533	ENSMUSG00000054672	5830411N06Rik	Scart2	RIKEN cDNA 5830411N06 gene	protein-coding
mm_97811.1	chr11	82962321	82962338	+	1	NA	3' UTR (NM_183201, exon 6 of 6)	3' UTR (NM_183201, exon 6 of 6)	-1648	NR_045932	76392	Mm.295205	NR_045932	ENSMUSG00000086327	Slfn5os	1700003F17Rik	schlafen 5, opposite strand	ncRNA
mm_137956.1	chr17	32993124	32993160	+	1	NA	promoter-TSS (NM_001045559)	promoter-TSS (NM_001045559)	3	NM_001045559	240067	Mm.246667	NM_199020	ENSMUSG00000053390	Zfp952	BC057593|C920016K16Rik	zinc finger protein 952	protein-coding
mm_19005.1	chr2	76886372	76886376	-	1	NA	exon (NM_011652, exon 79 of 313)	exon (NM_011652, exon 79 of 313)	96173	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_154661.1	chrX	7864753	7864765	+	1	NA	intron (NM_138604, intron 2 of 8)	intron (NM_138604, intron 2 of 8)	-13547	NM_138606	18715	Mm.347478	NM_138606	ENSMUSG00000031155	Pim2	DXCch3|Pim-2	proviral integration site 2	protein-coding
mm_172998.1	chrM	1554	1555	+	1	NA	NA	Intergenic	NA	NA								
mm_54503.1	chr6	35510595	35510615	-	1	NA	3' UTR (NM_008098, exon 4 of 4)	3' UTR (NM_008098, exon 4 of 4)	29283	NM_008098	14489	Mm.182746	NM_008098	ENSMUSG00000029840	Mtpn	5033418D15Rik|Gcdp|V1	myotrophin	protein-coding
mm_44921.1	chr5	35729261	35729286	-	1	NA	promoter-TSS (NM_194344)	promoter-TSS (NM_194344)	3	NM_194344	231147	Mm.290429	NM_194344	ENSMUSG00000036553	Sh3tc1	4631428G15|BC024909	SH3 domain and tetratricopeptide repeats 1	protein-coding
mm_72957.1	chr8	92815405	92815413	+	1	NA	Intergenic	Intergenic	-11888	NM_008610	17390	Mm.29564	NM_008610	ENSMUSG00000031740	Mmp2	Clg4a|GelA|MMP-2	matrix metallopeptidase 2	protein-coding
mm_76376.1	chr8	84835324	84835347	-	1	NA	3' UTR (NM_183358, exon 2 of 2)	3' UTR (NM_183358, exon 2 of 2)	3053	NM_183358	102060	Mm.489649	NM_183358	ENSMUSG00000033751	Gadd45gip1	2310040G17Rik|AI425883|Crif1|MRP-L59|Plinp1	growth arrest and DNA-damage-inducible, gamma interacting protein 1	protein-coding
mm_55810.1	chr6	83004933	83004972	-	1	NA	intron (NM_033079, intron 5 of 9)	intron (NM_033079, intron 5 of 9)	28519	NM_010070	13448	Mm.156	NM_010070	ENSMUSG00000068335	Dok1	AW557123|p62DOK	docking protein 1	protein-coding
mm_42336.1	chr5	114903451	114903474	+	1	NA	intron (NM_011854, intron 3 of 5)	L1M5|LINE|L1	6528	NM_011854	23962	Mm.228363	NM_011854	ENSMUSG00000029561	Oasl2	M1204|Mmu-OASL|Oasl	2'-5' oligoadenylate synthetase-like 2	protein-coding
mm_110751.1	chr12	69987040	69987100	-	1	NA	promoter-TSS (NM_022028)	promoter-TSS (NM_022028)	-68	NM_022028	64010	Mm.390480	NM_022028	ENSMUSG00000021067	Sav1	1700040G09Rik|Salv|Sav|WW45|Wwp3|Wwp4	salvador family WW domain containing 1	protein-coding
mm_31791.1	chr4	63734432	63734435	+	1	NA	intron (NM_177371, intron 1 of 3)	intron (NM_177371, intron 1 of 3)	10680	NM_177371	326623	Mm.208152	NM_177371	ENSMUSG00000050395	Tnfsf15	Tl1|Tl1a|Tnlg1b|Vegi	tumor necrosis factor (ligand) superfamily, member 15	protein-coding
mm_142286.1	chr17	40232609	40232617	-	1	NA	exon (NM_009639, exon 5 of 8)	exon (NM_009639, exon 5 of 8)	9645	NM_009639	11572	Mm.14138	NM_009639	ENSMUSG00000025433	Crisp3	Aeg2|CRISP-3|CRS3|SGP28	cysteine-rich secretory protein 3	protein-coding
mm_21003.1	chr2	152343983	152344007	-	1	NA	promoter-TSS (NM_175093)	promoter-TSS (NM_175093)	65	NM_175093	228775	Mm.276018	NM_144554	ENSMUSG00000032715	Trib3	Ifld2|Nipk|SINK|SKIP3|TRB-3|Trb3	tribbles pseudokinase 3	protein-coding
mm_147147.1	chr18	36560206	36560230	-	1	NA	promoter-TSS (NM_175375)	promoter-TSS (NM_175375)	-385	NM_175375	108857	Mm.482287	NM_175375	ENSMUSG00000024483	Ankhd1	1110004O12Rik|4933432B13Rik|9130019P20Rik|A530027J04Rik|A630021B20Rik|AA571404|Mask|mFLJ00246|mKIAA1085	ankyrin repeat and KH domain containing 1	protein-coding
mm_81809.1	chr9	117856911	117856913	+	1	NA	Intergenic	Intergenic	-183610	NM_001286508	27215	Mm.92705	NM_013727	ENSMUSG00000039285	Azi2	AA410145|AZ2	5-azacytidine induced gene 2	protein-coding
mm_160422.1	chr8	85014410	85014410	-	1	NA	promoter-TSS (NM_001130194)	promoter-TSS (NM_001130194)	-2	NM_001130194	212989	Mm.215154	NM_001130194	ENSMUSG00000052819	Best2	Vmd2l1	bestrophin 2	protein-coding
mm_87468.1	chr10	51491427	51491440	+	1	NA	intron (NM_001291894, intron 2 of 8)	intron (NM_001291894, intron 2 of 8)	535	NM_013532	14728	Mm.34408	NM_013532	ENSMUSG00000062593	Lilrb4a	CD85K|Gp49b|HM18|ILT3|LIR-5|Lilrb4|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4A	protein-coding
mm_34053.1	chr4	138304707	138304715	+	1	NA	promoter-TSS (NM_007838)	promoter-TSS (NM_007838)	-27	NM_007838	13200	Mm.7236	NM_007838	ENSMUSG00000028757	Ddost	-	dolichyl-di-phosphooligosaccharide-protein glycotransferase	protein-coding
mm_136094.1	chr16	85056410	85056426	-	1	NA	exon (NM_001198823, exon 6 of 18)	exon (NM_001198823, exon 6 of 18)	84207	NR_045889	100038614	Mm.441351	NR_045889		Gm10791	ENSMUSG00000074933	predicted gene 10791	ncRNA
mm_15838.1	chr2	164715270	164715284	+	1	NA	promoter-TSS (NM_001040055)	promoter-TSS (NM_001040055)	-28	NM_001040055	641368	Mm.422380	NM_001040055	ENSMUSG00000074593	Spint5	Gm14316|OTTMUSG00000016293	serine protease inhibitor, Kunitz type 5	protein-coding
mm_100823.1	chr11	5261711	5261721	-	1	NA	promoter-TSS (NM_032396)	promoter-TSS (NM_032396)	-106	NM_032396	84035	Mm.209989	NM_032396	ENSMUSG00000020393	Kremen1	AV002070|Kremen|Krm1	kringle containing transmembrane protein 1	protein-coding
mm_64958.1	chr7	16604501	16604506	-	1	NA	intron (NM_172739, intron 1 of 6)	intron (NM_172739, intron 1 of 6)	-9321	NR_136928	102634559	Mm.421602	NR_136928	ENSMUSG00000100583	Gm29443	-	predicted gene 29443	ncRNA
mm_35941.1	chr4	53094911	53094917	-	1	NA	intron (NM_013454, intron 8 of 49)	intron (NM_013454, intron 8 of 49)	64981	NM_013454	11303	Mm.277376	NM_013454	ENSMUSG00000015243	Abca1	ABC-1|Abc1	ATP-binding cassette, sub-family A (ABC1), member 1	protein-coding
mm_30554.1	chr4	3697332	3697343	+	1	NA	intron (NM_010747, intron 1 of 12)	ID4_|SINE|ID	-17627	NR_028126	70720	Mm.445696	NR_028126		6330407A03Rik	-	RIKEN cDNA 6330407A03 gene	ncRNA
mm_97583.1	chr11	78945229	78945264	+	1	NA	exon (NM_010927, exon 13 of 27)	exon (NM_010927, exon 13 of 27)	19955	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_164980.1	chr19	8839329	8839334	-	1	NA	promoter-TSS (NM_008144)	promoter-TSS (NM_008144)	3	NM_008144	14705	Mm.345134	NM_008144	ENSMUSG00000071657	Bscl2	2900097C17Rik|AI046355|Gng3lg	Berardinelli-Seip congenital lipodystrophy 2 (seipin)	protein-coding
mm_11939.1	chr2	52857845	52857851	+	1	NA	promoter-TSS (NM_172409)	promoter-TSS (NM_172409)	-20	NM_172409	71409	Mm.394427	NM_172409	ENSMUSG00000036053	Fmnl2	5430425K04Rik|Man	formin-like 2	protein-coding
mm_83306.1	chr9	44041139	44041167	-	1	NA	Intergenic	Intergenic	-2231	NM_009382	21838	Mm.3951	NM_009382	ENSMUSG00000032011	Thy1	CD90|T25|Thy-1|Thy-1.2|Thy1.1|Thy1.2	thymus cell antigen 1, theta	protein-coding
mm_162670.1	chr10	7325697	7325699	+	1	NA	Intergenic	PB1D10|SINE|Alu	-113461	NM_172546	215748	Mm.37984	NM_172546	ENSMUSG00000015202	Cnksr3	6820402C05|BC024086|Magi1	Cnksr family member 3	protein-coding
mm_70850.1	chr8	23446974	23446993	+	1	NA	3' UTR (NM_013834, exon 3 of 3)	3' UTR (NM_013834, exon 3 of 3)	35481	NM_013834	20377	Mm.281691	NM_013834	ENSMUSG00000031548	Sfrp1	2210415K03Rik|AW011917|AW107218|AW742929|sFRP-1	secreted frizzled-related protein 1	protein-coding
mm_152666.1	chr19	14597149	14597173	-	1	NA	promoter-TSS (NM_001302951)	promoter-TSS (NM_001302951)	52	NM_001302951	21888	Mm.103638	NM_011600	ENSMUSG00000024642	Tle4	5730411M05Rik|AA792082|Bce-1|Bce1|ESTM13|ESTM14|Grg4|X83332|X83333|grg-4	transducin-like enhancer of split 4	protein-coding
mm_29106.1	chr3	104818481	104818504	-	1	NA	promoter-TSS (NM_008619)	promoter-TSS (NM_008619)	71	NM_001163440	17454	Mm.1597	NM_008619	ENSMUSG00000002227	Mov10	C77703|Mov-10	Moloney leukemia virus 10	protein-coding
mm_132821.1	chr16	45224145	45224169	+	1	NA	promoter-TSS (NM_001037719)	promoter-TSS (NM_001037719)	-180	NM_001037719	208154	Mm.38199	NM_177584	ENSMUSG00000052013	Btla	A630002H24	B and T lymphocyte associated	protein-coding
mm_81099.1	chr9	106429400	106429457	+	1	NA	promoter-TSS (NM_001324533)	promoter-TSS (NM_001324533)	17	NM_009082	19944	Mm.288696	NM_009082	ENSMUSG00000048758	Rpl29	Rpl43	ribosomal protein L29	protein-coding
mm_545.1	chr1	38018980	38019023	+	1	NA	exon (NM_198303, exon 4 of 24)	exon (NM_198303, exon 4 of 24)	20991	NM_198303	226982	Mm.260943	NM_198303	ENSMUSG00000026083	Eif5b	A030003E17Rik|BC018347|IF2	eukaryotic translation initiation factor 5B	protein-coding
mm_148417.1	chr19	3936067	3936091	+	1	NA	intron (NM_001161428, intron 2 of 9)	intron (NM_001161428, intron 2 of 9)	893	NM_001161428	54445	Mm.262094	NM_019449	ENSMUSG00000036908	Unc93b1	Unc-93B1|Unc93b	unc-93 homolog B1 (C. elegans)	protein-coding
mm_139642.1	chr17	57377610	57377620	+	1	NA	intron (NM_010130, intron 2 of 21)	Lx5b|LINE|L1	18929	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_119599.1	chr14	51007951	51007975	+	1	NA	promoter-TSS (NM_029145)	promoter-TSS (NM_029145)	34	NM_029145	75019	Mm.318775	NM_029145	ENSMUSG00000021872	Rnase10	4930474F22Rik|Rah1	ribonuclease, RNase A family, 10 (non-active)	protein-coding
mm_19360.1	chr2	91084573	91084585	-	1	NA	Intergenic	Intergenic	-12099	NM_011355	20375	Mm.1302	NM_011355	ENSMUSG00000002111	Spi1	Dis-1|Dis1|PU.1|Sfpi-1|Sfpi1|Spi-1|Tcfpu1|Tfpu.1	spleen focus forming virus (SFFV) proviral integration oncogene	protein-coding
mm_103120.1	chr11	70185222	70185242	-	1	NA	Intergenic	B3A|SINE|B2	18609	NM_010796	17312	Mm.252405	NM_010796	ENSMUSG00000000318	Clec10a	CD301a|M-ASGP-BP-1|Mgl|Mgl1	C-type lectin domain family 10, member A	protein-coding
mm_124283.1	chr14	103048701	103048707	-	1	NA	intron (NM_008392, intron 1 of 4)	intron (NM_008392, intron 1 of 4)	1692	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_128503.1	chr15	52786223	52786232	-	1	NA	Intergenic	Intergenic	73782	NM_027212	69790	Mm.195562	NM_027212	ENSMUSG00000038622	Med30	1810038N03Rik|2510044J04Rik|TRAP25|Thrap6	mediator complex subunit 30	protein-coding
mm_119126.1	chr14	31138062	31138086	+	1	NA	TTS (NM_138672)	TTS (NM_138672)	3221	NM_027289	70021	Mm.261681	NM_027289	ENSMUSG00000071547	Nt5dc2	2510015F01Rik	5'-nucleotidase domain containing 2	protein-coding
mm_143213.1	chr17	62882102	62882173	-	1	NA	promoter-TSS (NM_207654)	promoter-TSS (NM_207654)	-820	NM_010109	13640	Mm.7978	NM_010109	ENSMUSG00000048915	Efna5	AL-1|AV158822|EFL-5|Ephrin-A5|Epl7|LERK-7|RAGS	ephrin A5	protein-coding
mm_51891.1	chr6	90609465	90609488	+	1	NA	intron (NM_027868, intron 1 of 10)	intron (NM_027868, intron 1 of 10)	4596	NM_027868	71699	Mm.272633	NM_027868	ENSMUSG00000030089	Slc41a3	1010001P06Rik|AI480742|SLC41A1-L2	solute carrier family 41, member 3	protein-coding
mm_82168.1	chr9	123840642	123840661	+	1	NA	intron (NM_148925, intron 3 of 18)	intron (NM_148925, intron 3 of 18)	11010	NM_148925	17281	Mm.252941	NM_148925	ENSMUSG00000025241	Fyco1	2810409M01Rik|Mem2|RUFY3|ZFYVE7	FYVE and coiled-coil domain containing 1	protein-coding
mm_79343.1	chr9	53403250	53403260	+	1	NA	Intergenic	Intergenic	-2031	NM_029247	75311	Mm.26078	NM_029247	ENSMUSG00000005131	4930550C14Rik	AU017961	RIKEN cDNA 4930550C14 gene	protein-coding
mm_151463.1	chr19	58606378	58606382	+	1	NA	promoter-TSS (NR_038136)	promoter-TSS (NR_038136)	51	NR_038136	69055	Mm.396318	NR_038136	ENSMUSG00000100001	1810007D17Rik	-	RIKEN cDNA 1810007D17 gene	ncRNA
mm_101498.1	chr11	31824542	31824552	-	1	NA	promoter-TSS (NR_102314)	promoter-TSS (NR_102314)	0	NR_102310	414116	Mm.150222	NR_102310	ENSMUSG00000085772	D630024D03Rik	-	RIKEN cDNA D630024D03 gene	ncRNA
mm_166960.1	chr7	44480079	44480083	+	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	-4436	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_54811.1	chr6	42324555	42324599	-	1	NA	promoter-TSS (NM_001113327)	promoter-TSS (NM_001113327)	63	NM_001286584	76156	Mm.234314	NM_029528	ENSMUSG00000029861	Fam131b	6330503C03Rik|6530406I18Rik|AV277466	family with sequence similarity 131, member B	protein-coding
mm_118621.1	chr14	21077022	21077025	+	1	NA	intron (NM_001243041, intron 1 of 10)	intron (NM_001243041, intron 1 of 10)	871	NM_001243041	11534	Mm.188734	NM_134079	ENSMUSG00000039197	Adk	2310026J05Rik|5033405D03Rik|AI255373|AI987814|Ak	adenosine kinase	protein-coding
mm_46817.1	chr5	113138450	113138514	-	1	NA	5' UTR (NM_001347397, exon 1 of 8)	5' UTR (NM_001347397, exon 1 of 8)	103	NM_001347397	243219	Mm.160131	NM_172884	ENSMUSG00000051339	2900026A02Rik	8430408O14Rik|A530094D01|AW539426|Gm449|Kiaa1671|mKIAA1671	RIKEN cDNA 2900026A02 gene	protein-coding
mm_493.1	chr1	36780114	36780124	+	1	NA	intron (NM_009539, intron 9 of 12)	IMPB_01|Satellite|Satellite	1135	NM_001289612	22637	Mm.8038	NM_009539	ENSMUSG00000026117	Zap70	Srk|ZAP-70|mrtle|mur	zeta-chain (TCR) associated protein kinase	protein-coding
mm_5430.1	chr1	34560934	34560966	-	1	NA	promoter-TSS (NM_009356)	promoter-TSS (NM_009356)	-7	NM_009356	21756	Mm.14418	NM_009356	ENSMUSG00000037529	Prss40	Tesp2	protease, serine 40	protein-coding
mm_4990.1	chr1	191743116	191743140	+	1	NA	intron (NM_172266, intron 2 of 7)	intron (NM_172266, intron 2 of 7)	24733	NM_001134829	226856	Mm.277958	NM_172266	ENSMUSG00000026623	Lpgat1	AI649174|AW112037|BC013667	lysophosphatidylglycerol acyltransferase 1	protein-coding
mm_53672.1	chr6	141685759	141685769	+	1	NA	3' UTR (NM_020495, exon 16 of 16)	3' UTR (NM_020495, exon 16 of 16)	56246	NM_020495	28253	Mm.272223	NM_020495	ENSMUSG00000030236	Slco1b2	7330442B20Rik|OATP-C|OATP2|Oatp1b2|Oatp4|Slc21a10|Slc21a6|lst-1|mlst-1	solute carrier organic anion transporter family, member 1b2	protein-coding
mm_98083.1	chr11	86577435	86577460	+	1	NA	Intergenic	Intergenic	6711	NR_029738	387140		NR_029738	ENSMUSG00000065455	Mir21a	Mir21|Mirn21|mmu-mir-21|mmu-mir-21a	microRNA 21a	ncRNA
mm_123472.1	chr14	65974897	65974927	-	1	NA	exon (NM_013492, exon 4 of 9)	exon (NM_013492, exon 4 of 9)	6429	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_51101.1	chr6	67271958	67271982	+	1	NA	exon (NM_025814, exon 3 of 8)	exon (NM_025814, exon 3 of 8)	4991	NM_025814	66870	Mm.240490	NM_025814	ENSMUSG00000036371	Serbp1	1200009K13Rik|9330147J08Rik|AL022786|Pairbp1	serpine1 mRNA binding protein 1	protein-coding
mm_50214.1	chr6	42286661	42286671	+	1	NA	promoter-TSS (NM_013491)	promoter-TSS (NM_013491)	-19	NM_013491	12723	Mm.386757	NM_013491	ENSMUSG00000029862	Clcn1	Clc-1|Clc1|SMCC1|adr|mto|myotonia|nmf355	chloride channel, voltage-sensitive 1	protein-coding
mm_12112.1	chr2	61593126	61593175	+	1	NA	promoter-TSS (NM_001164072)	promoter-TSS (NM_001164072)	53	NM_001164071	21353	Mm.244393	NM_011529	ENSMUSG00000064289	Tank	C86182|E430026L09Rik|I-TRAF	TRAF family member-associated Nf-kappa B activator	protein-coding
mm_105853.1	chr11	113750784	113750847	-	1	NA	5' UTR (NM_020006, exon 1 of 2)	5' UTR (NM_020006, exon 1 of 2)	345	NM_020006	56699	Mm.293378	NM_020006	ENSMUSG00000041598	Cdc42ep4	1500041M20Rik|Borg4|CEP4	CDC42 effector protein (Rho GTPase binding) 4	protein-coding
mm_98917.1	chr11	98253074	98253078	+	1	NA	3' UTR (NM_001109626, exon 14 of 14)	3' UTR (NM_001109626, exon 14 of 14)	-9530	NR_039579	100628613		NR_039579	ENSMUSG00000093176	Mir5119	mmu-mir-5119|mu-mir-5119	microRNA 5119	ncRNA
mm_111721.1	chr12	103737903	103737930	-	1	NA	intron (NM_009244, intron 1 of 4)	intron (NM_009244, intron 1 of 4)	273	NM_009244	20701	Mm.439692	NM_009244	ENSMUSG00000071178	Serpina1b	D12Ucla2|Dom2|PI2|Spi1-2	serine (or cysteine) preptidase inhibitor, clade A, member 1B	protein-coding
mm_26053.1	chr3	135824054	135824056	+	1	NA	Intergenic	Lx2|LINE|L1	-1224	NM_026228	67547	Mm.30239	NM_026228	ENSMUSG00000053897	Slc39a8	4933419D20Rik|AA986696|BIGM103|ZIP-8|Zip8	solute carrier family 39 (metal ion transporter), member 8	protein-coding
mm_109785.1	chr12	3248068	3248081	-	1	NA	3' UTR (NM_016676, exon 6 of 6)	3' UTR (NM_016676, exon 6 of 6)	12283	NR_015551	74173	Mm.309774	NM_028796	ENSMUSG00000079179	Rab10os	1700012B15Rik|1810036A22Rik	RAB10, member RAS oncogene family, opposite strand	ncRNA
mm_39615.1	chr5	24383497	24383521	+	1	NA	TTS (NM_001002897)	TTS (NM_001002897)	8634	NM_001002897	213948	Mm.332252	NM_001002897	ENSMUSG00000038295	Atg9b	Apg912|Apg9l2|Apgdc2|Gm574|Nos3as|eONE|sONE	autophagy related 9B	protein-coding
mm_63235.1	chr7	126502626	126502655	+	1	NA	promoter-TSS (NM_001347658)	promoter-TSS (NM_001347658)	-215	NM_001347658	233871	Mm.231450	NM_183020	ENSMUSG00000032637	Atxn2l	A2D|A2LG|A2RP|A2lp|Atxnl2	ataxin 2-like	protein-coding
mm_55966.1	chr6	85820937	85820962	-	1	NA	promoter-TSS (NM_023493)	promoter-TSS (NM_023493)	23	NM_023493	69049	Mm.441449	NM_023493	ENSMUSG00000079494	Nat8f5	1810018F03Rik|Cml5	N-acetyltransferase 8 (GCN5-related) family member 5	protein-coding
mm_17839.1	chr2	34371111	34371155	-	1	NA	intron (NM_016768, intron 1 of 8)	CpG	912	NM_001290576	18516	Mm.239941	NM_016768	ENSMUSG00000038718	Pbx3	-	pre B cell leukemia homeobox 3	protein-coding
mm_31970.1	chr4	88124433	88124441	+	1	NA	intron (NM_001081184, intron 2 of 43)	MIR|SINE|MIR	2397	NR_030478	735282		NR_030478	ENSMUSG00000070077	Mir491	Mirn491|mir-491|mmu-mir-491	microRNA 491	ncRNA
mm_85225.1	chr9	97090826	97090828	-	1	NA	intron (NM_138756, intron 4 of 6)	intron (NM_138756, intron 4 of 6)	20214	NM_138756	192287	Mm.228067	NM_138756	ENSMUSG00000032449	Slc25a36	C330005L02Rik	solute carrier family 25, member 36	protein-coding
mm_105528.1	chr11	106300816	106300820	-	1	NA	exon (NM_008117, exon 4 of 5)	exon (NM_008117, exon 4 of 5)	1078	NM_008117	14599	Mm.343934	NM_008117	ENSMUSG00000020713	Gh	Gh1|Ghb1	growth hormone	protein-coding
mm_124881.1	chr15	10225244	10225246	+	1	NA	intron (NM_001253781, intron 1 of 9)	B4A|SINE|B4	1339	NM_001253781	19116	Mm.10516	NM_011169	ENSMUSG00000005268	Prlr	AI987712|Pr-1|Pr-3|Prlr-rs1	prolactin receptor	protein-coding
mm_73415.1	chr8	106058788	106058834	+	1	NA	promoter-TSS (NM_010901)	promoter-TSS (NM_010901)	-792	NM_010901	18021	Mm.383185	NM_010901	ENSMUSG00000031902	Nfatc3	C80703|D8Ertd281e|NFAT4|NFATx	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 3	protein-coding
mm_117431.1	chr13	74563808	74563827	-	1	NA	Intergenic	Intergenic	-69867	NM_146231	235956	Mm.296909	NM_146231	ENSMUSG00000069208	Zfp825	-	zinc finger protein 825	protein-coding
mm_109265.1	chr12	109544933	109544940	+	1	NA	promoter-TSS (NR_003633)	promoter-TSS (NR_003633)	395	NR_037313	100499530		NR_037313	ENSMUSG00000084559	Mir1906-2	mmu-mir-1906-2	microRNA 1906-2	ncRNA
mm_113957.1	chr13	51137682	51137685	+	1	NA	intron (NM_011462, intron 1 of 3)	intron (NM_011462, intron 1 of 3)	3365	NM_011462	20729	Mm.188432	NM_011462	ENSMUSG00000021395	Spin1	Spin	spindlin 1	protein-coding
mm_41431.1	chr5	90903810	90903811	+	1	NA	promoter-TSS (NM_009140)	promoter-TSS (NM_009140)	-89	NM_009140	20310	Mm.4979	NM_009140	ENSMUSG00000058427	Cxcl2	CINC-2a|GROb|Gro2|MIP-2|MIP-2a|Mgsa-b|Mip2|Scyb|Scyb2	chemokine (C-X-C motif) ligand 2	protein-coding
mm_114789.1	chr13	89540663	89540678	+	1	NA	promoter-TSS (NM_013500)	promoter-TSS (NM_013500)	34	NM_013500	12950	Mm.266790	NM_013500	ENSMUSG00000021613	Hapln1	BB099155|CLP|Crtl1|Crtl1l|LP|LP-1	hyaluronan and proteoglycan link protein 1	protein-coding
mm_8013.1	chr1	134866556	134866566	-	1	NA	intron (NM_001081307, intron 12 of 23)	intron (NM_001081307, intron 12 of 23)	-62840	NR_015606	329251	Mm.188709	NM_001081307	ENSMUSG00000073557	Ppp1r12b	1810037O03Rik|9530009M10Rik|AI132431|Mypt2	protein phosphatase 1, regulatory (inhibitor) subunit 12B	protein-coding
mm_144756.1	chr18	35740674	35740712	+	1	NA	promoter-TSS (NM_001289592)	promoter-TSS (NM_001289592)	-139	NM_001289591	72512	Mm.45995	NM_028261	ENSMUSG00000024349	Tmem173	2610307O08Rik|ERIS|MPYS|Mita|STING	transmembrane protein 173	protein-coding
mm_9655.1	chr1	177763692	177763702	-	1	NA	3' UTR (NM_007422, exon 13 of 13)	3' UTR (NM_007422, exon 13 of 13)	32812	NM_007422	11566	Mm.338021	NM_007422	ENSMUSG00000015961	Adss	AI314886|AS|Adss2	adenylosuccinate synthetase, non muscle	protein-coding
mm_101422.1	chr11	29547821	29547870	-	1	NA	promoter-TSS (NM_028504)	promoter-TSS (NM_028504)	-105	NM_028504	73324	Mm.69388	NM_028504	ENSMUSG00000020461	Clhc1	1700034F02Rik	clathrin heavy chain linker domain containing 1	protein-coding
mm_124914.1	chr15	11076331	11076333	+	1	NA	intron (NM_175501, intron 2 of 23)	L1MD1|LINE|L1	11559	NM_175501	239337	Mm.224825	NM_175501	ENSMUSG00000047497	Adamts12	ADAMTS-12|AI605170	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 12	protein-coding
mm_155125.1	chrX	48884947	48884958	+	1	NA	Intergenic	Intergenic	-7239	NM_001085499	209005	Mm.336054	NM_001085499	ENSMUSG00000079606	Gm595	-	predicted gene 595	protein-coding
mm_113620.1	chr13	41605905	41605929	+	1	NA	promoter-TSS (NM_001163572)	promoter-TSS (NM_001163572)	-299	NM_001163572	621976	Mm.259830	NM_001163572	ENSMUSG00000087370	Tmem170b	EG621976	transmembrane protein 170B	protein-coding
mm_58306.1	chr6	146212832	146212842	-	1	NA	intron (NM_010586, intron 44 of 55)	(TG)n|Simple_repeat|Simple_repeat	278690	NM_010656	16651	Mm.49689	NM_010656	ENSMUSG00000030255	Sspn	Krag	sarcospan	protein-coding
mm_103688.1	chr11	79484028	79484057	-	1	NA	promoter-TSS (NR_045305)	promoter-TSS (NR_045305)	-11	NR_045305	104522	Mm.436987	NR_045305	ENSMUSG00000091523	AU040972	AU040954	expressed sequence AU040972	ncRNA
mm_155381.1	chrX	71812801	71812807	+	1	NA	Intergenic	Intergenic	-3276	NM_001290781	67048	Mm.41102	NM_001081356	ENSMUSG00000073131	Vma21	2610030H06Rik|AI840175	VMA21 vacuolar H+-ATPase homolog (S. cerevisiae)	protein-coding
mm_6907.1	chr1	84838659	84838740	-	1	NA	intron (NM_133975, intron 1 of 40)	CpG	605	NM_133975	14897	Mm.209265	NM_133975	ENSMUSG00000026219	Trip12	1110036I07Rik|6720416K24Rik|AA410158|Gtl6|TRIP-12	thyroid hormone receptor interactor 12	protein-coding
mm_39458.1	chr5	17577039	17577046	+	1	NA	intron (NM_013657, intron 2 of 17)	(T)n|Simple_repeat|Simple_repeat	2226	NM_013657	20348	Mm.5071	NM_013657	ENSMUSG00000028780	Sema3c	1110036B02Rik|SemE|Semae	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	protein-coding
mm_128435.1	chr15	50682635	50682653	-	1	NA	intron (NM_001310481, intron 4 of 5)	intron (NM_001310481, intron 4 of 5)	206405	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_152783.1	chr19	21440853	21440872	-	1	NA	intron (NM_010266, intron 1 of 13)	L1MC4|LINE|L1	31799	NM_010266	14544	Mm.45054	NM_010266	ENSMUSG00000058624	Gda	AU015411|AW047581|GAH	guanine deaminase	protein-coding
mm_82799.1	chr9	29412515	29412533	-	1	NA	intron (NM_172290, intron 1 of 7)	CpG	550605	NM_172290	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding
mm_51314.1	chr6	72314425	72314447	+	1	NA	TTS (NM_001282071)	TTS (NM_001282071)	9826	NM_147779	20388	Mm.46033	NM_147779	ENSMUSG00000056370	Sftpb	AI562151|SF-B|SP-B|Sftp-3|Sftp3	surfactant associated protein B	protein-coding
mm_92935.1	chr10	84533902	84533913	-	1	NA	promoter-TSS (NM_175451)	promoter-TSS (NM_175451)	-19	NM_175451	216197	Mm.334999	NM_175451	ENSMUSG00000046841	Ckap4	5630400A09Rik|CLIMP-63|P63	cytoskeleton-associated protein 4	protein-coding
mm_48259.1	chr5	137836211	137836233	-	1	NA	promoter-TSS (NM_153510)	promoter-TSS (NM_153510)	56	NM_153510	231805	Mm.379385	NM_153510	ENSMUSG00000046245	Pilra	AV021745|FDF03	paired immunoglobin-like type 2 receptor alpha	protein-coding
mm_45642.1	chr5	76951161	76951174	-	1	NA	promoter-TSS (NM_025939)	promoter-TSS (NM_025939)	-244	NM_025939	67054	Mm.182931	NM_025939	ENSMUSG00000029247	Paics	2610511I09Rik|ADE2H1|AIRC|PAIS	phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoribosylaminoimidazole, succinocarboxamide synthetase	protein-coding
mm_89475.1	chr10	93540606	93540614	+	1	NA	promoter-TSS (NM_027908)	promoter-TSS (NM_027908)	-22	NM_175488	237465	Mm.477086	NM_175488	ENSMUSG00000036168	Ccdc38	4933417K05Rik	coiled-coil domain containing 38	protein-coding
mm_47621.1	chr5	125245818	125245828	-	1	NA	Intergenic	CpG	-66609	NM_001253904	20602	Mm.278646	NM_011424	ENSMUSG00000029478	Ncor2	N-CoR|SMRT|SMRTe	nuclear receptor co-repressor 2	protein-coding
mm_126740.1	chr15	85671826	85671837	+	1	NA	Intergenic	CpG	-31942	NR_110483	102800312	Mm.33117	NR_110483		Lncppara	Lincppara|Mirlet7bhg|linc-Ppara	long noncoding RNA near Ppara	ncRNA
mm_110272.1	chr12	31996958	31996965	-	1	NA	intron (NM_011158, intron 2 of 10)	MamRep605|LTR?|LTR?	-46426	NM_153198	73389	Mm.390461	NM_153198	ENSMUSG00000002996	Hbp1	1700058O05Rik|BE629963|C330012F01Rik|C86454	high mobility group box transcription factor 1	protein-coding
mm_42061.1	chr5	108762560	108762564	+	1	NA	Intergenic	Intergenic	-1280	NR_040691	73295	Mm.416858	NR_040691	ENSMUSG00000101762	1700047L14Rik	-	RIKEN cDNA 1700047L14 gene	ncRNA
mm_71508.1	chr8	46837730	46837740	+	1	NA	exon (NM_008391, exon 7 of 9)	exon (NM_008391, exon 7 of 9)	97990	NM_008391	16363	Mm.1149	NM_008391	ENSMUSG00000031627	Irf2	9830146E22Rik|AI646973|Irf-2	interferon regulatory factor 2	protein-coding
mm_69587.1	chr7	135705646	135705661	-	1	NA	exon (NM_001081117, exon 7 of 14)	exon (NM_001081117, exon 7 of 14)	10726	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_77411.1	chr8	120589082	120589090	-	1	NA	promoter-TSS (NM_178856)	promoter-TSS (NM_178856)	-11	NM_178856	272551	Mm.275910	NM_178856	ENSMUSG00000031821	Gins2	2210013I18Rik|4833427B12Rik|AI323585|Pfs2	GINS complex subunit 2 (Psf2 homolog)	protein-coding
mm_63966.1	chr7	139944580	139944586	+	1	NA	exon (NM_009482, exon 2 of 2)	exon (NM_009482, exon 2 of 2)	727	NM_009482	22286	Mm.10205	NM_009482	ENSMUSG00000047751	Utf1	AI505934	undifferentiated embryonic cell transcription factor 1	protein-coding
mm_63779.1	chr7	131560649	131560672	+	1	NA	intron (NM_001317350, intron 1 of 7)	CpG	166	NM_001317350	12237	Mm.927	NM_009774	ENSMUSG00000066979	Bub3	AU019800|AU021329|AU043350|AW146323|C78067	BUB3 mitotic checkpoint protein	protein-coding
mm_65992.1	chr7	30535083	30535093	-	1	NA	promoter-TSS (NM_001289670)	promoter-TSS (NM_001289670)	-28	NM_001289682	233071	Mm.190704	NM_178252	ENSMUSG00000036882	Arhgap33	AW324378|NOMA-GAP|Snx26|TCGAP	Rho GTPase activating protein 33	protein-coding
mm_155929.1	chrX	103447786	103447796	+	1	NA	non-coding (NR_002844, exon 2 of 4)	non-coding (NR_002844, exon 2 of 4)	16274	NR_002844	22097	Mm.472939	NR_002844	ENSMUSG00000085715	Tsix	-	X (inactive)-specific transcript, opposite strand	ncRNA
mm_165599.1	chr3	49757317	49757323	-	1	NA	promoter-TSS (NM_130448)	promoter-TSS (NM_130448)	-4	NM_130448	73173	Mm.87246	NM_130448	ENSMUSG00000037892	Pcdh18	3110038E07Rik|BB095589|PCDH68L	protocadherin 18	protein-coding
mm_24031.1	chr3	87539334	87539344	+	1	NA	3' UTR (NM_012051, exon 5 of 5)	3' UTR (NM_012051, exon 5 of 5)	13761	NM_012051	27049	Mm.219460	NM_012051	ENSMUSG00000003382	Etv3	AI414410|METS|Pe1	ets variant 3	protein-coding
mm_127190.1	chr15	99030313	99030328	+	1	NA	5' UTR (NM_009448, exon 1 of 4)	5' UTR (NM_009448, exon 1 of 4)	429	NM_009448	22146	Mm.88212	NM_009448	ENSMUSG00000043091	Tuba1c	M[a]6|Tuba6	tubulin, alpha 1C	protein-coding
mm_11056.1	chr2	27487896	27487906	+	1	NA	Intergenic	T-rich|Low_complexity|Low_complexity	-12228	NM_001113574	67382	Mm.28721	NM_023336	ENSMUSG00000026918	Brd3	2410084F24Rik|AW060456|Fsrg2|ORFX|RINGL3	bromodomain containing 3	protein-coding
mm_163472.1	chr12	103899239	103899277	-	1	NA	exon (NM_009245, exon 2 of 5)	exon (NM_009245, exon 2 of 5)	5692	NM_009245	20702	Mm.439692	NM_009245	ENSMUSG00000079015	Serpina1c	Pi3|Pi6|Skalp|Spi1-3|Spi1-6|Wap3	serine (or cysteine) peptidase inhibitor, clade A, member 1C	protein-coding
mm_21012.1	chr2	152396563	152396584	-	1	NA	3' UTR (NM_011438, exon 1 of 1)	3' UTR (NM_011438, exon 1 of 1)	1473	NM_011438	20667	Mm.28424	NM_011438	ENSMUSG00000051817	Sox12	2010205A02Rik	SRY (sex determining region Y)-box 12	protein-coding
mm_144888.1	chr18	36936297	36936319	+	1	NA	intron (NM_054072, intron 1 of 3)	B1_Mus2|SINE|Alu	-2897	NM_198117	353234	Mm.308500	NM_198117	ENSMUSG00000104148	Pcdha2	-	protocadherin alpha 2	protein-coding
mm_30493.1	chr3	156606138	156606139	-	1	NA	intron (NM_177274, intron 1 of 6)	intron (NM_177274, intron 1 of 6)	44344	NM_001039094	320840	Mm.317293	NM_177274	ENSMUSG00000040037	Negr1	5330422G01Rik|KILON|Ntra	neuronal growth regulator 1	protein-coding
mm_144388.1	chr18	20668927	20668928	+	1	NA	intron (NM_013697, intron 2 of 3)	intron (NM_013697, intron 2 of 3)	3677	NM_013697	22139	Mm.2108	NM_013697	ENSMUSG00000061808	Ttr	AA408768|AI787086|D17860|prealbumin	transthyretin	protein-coding
mm_4383.1	chr1	172198608	172198625	+	1	NA	3' UTR (NM_001329871, exon 4 of 4)	3' UTR (NM_001329871, exon 4 of 4)	8188	NM_001329871	18611	Mm.544	NM_011063	ENSMUSG00000013698	Pea15a	Mat1|PEA-15|Pea15|Pkcs15	phosphoprotein enriched in astrocytes 15A	protein-coding
mm_35469.1	chr4	40806011	40806025	-	1	NA	3' UTR (NM_022305, exon 6 of 6)	3' UTR (NM_022305, exon 6 of 6)	44120	NR_039584	100628614		NR_039584	ENSMUSG00000096377	Mir5123	mmu-mir-5123|mu-mir-5123	microRNA 5123	ncRNA
mm_12439.1	chr2	70690409	70690419	+	1	NA	intron (NR_027343, intron 10 of 10)	intron (NR_027343, intron 10 of 10)	28905	NM_027352	70231	Mm.271950	NM_027352	ENSMUSG00000014959	Gorasp2	0610011A07Rik|2410043M02Rik|5730520M13Rik|9430094F20Rik|AW552058|ENSMUSG00000075299|GOLPH2|GRASP55|GRS2|p59	golgi reassembly stacking protein 2	protein-coding
mm_131366.1	chr16	13813944	13813954	+	1	NA	3' UTR (NM_001039521, exon 18 of 18)	3' UTR (NM_001039521, exon 18 of 18)	-5302	NM_010946	18203	Mm.380410	NM_010946	ENSMUSG00000022681	Ntan1	PNAA|PNAD	N-terminal Asn amidase	protein-coding
mm_27089.1	chr3	30014388	30014390	-	1	NA	Intergenic	Intergenic	-1185	NM_007963	14013	Mm.56965	NM_007963	ENSMUSG00000027684	Mecom	D630039M04Rik|Evi-1|Evi1|Jbo|Mds|Mds1|Mds1-Evi1|Prdm3|Znfpr1b1	MDS1 and EVI1 complex locus	protein-coding
mm_64365.1	chr7	142434796	142434817	+	1	NA	promoter-TSS (NM_001285857)	promoter-TSS (NM_001285857)	-171	NM_001285857	55925	Mm.213002	NM_018802	ENSMUSG00000031098	Syt8	-	synaptotagmin VIII	protein-coding
mm_160142.1	chr7	34652767	34652767	-	1	NA	promoter-TSS (NM_146188)	promoter-TSS (NM_146188)	74	NM_146188	233107	Mm.486198	NM_146188	ENSMUSG00000030499	Kctd15	BC031749	potassium channel tetramerisation domain containing 15	protein-coding
mm_134560.1	chr16	20301812	20301820	-	1	NA	intron (NM_001005767, intron 1 of 9)	intron (NM_001005767, intron 1 of 9)	546	NM_001005767	381038	Mm.371737	NM_001005767	ENSMUSG00000033918	Parl	D16Ertd607e|PRO2207|PSARL1|PSENIP2|Psarl	presenilin associated, rhomboid-like	protein-coding
mm_39174.1	chr4	155761043	155761109	-	1	NA	promoter-TSS (NM_179203)	promoter-TSS (NM_179203)	22	NM_179203	108888	Mm.241152	NM_179203	ENSMUSG00000029036	Atad3a	2400004H09Rik|Atad3|Tob3|mKIAA1273	ATPase family, AAA domain containing 3A	protein-coding
mm_136734.1	chr17	8311102	8311168	+	1	NA	promoter-TSS (NM_134114)	promoter-TSS (NM_134114)	-17	NR_073374	75060	Mm.426530	NR_073374	ENSMUSG00000087478	4930506C21Rik	-	RIKEN cDNA 4930506C21 gene	ncRNA
mm_58198.1	chr6	143100120	143100163	-	1	NA	promoter-TSS (NM_029897)	promoter-TSS (NM_029897)	11	NM_001286578	74741	Mm.130260	NM_029081	ENSMUSG00000030279	C2cd5	5730419I09Rik|C030008B15Rik|CDP138	C2 calcium-dependent domain containing 5	protein-coding
mm_164466.1	chr16	59559217	59559222	+	1	NA	Intergenic	Intergenic	-3467	NM_174848	224273	Mm.246424	NM_174848	ENSMUSG00000022723	Crybg3	5031404N19|AU022790|Gm9581	beta-gamma crystallin domain containing 3	protein-coding
mm_44811.1	chr5	33524172	33524182	-	1	NA	Intergenic	Intergenic	-90087	NM_011320	672284		NM_011320	ENSMUSG00000029112	Nkx1-1	Nkx-1.1|Sax2	NK1 transcription factor related, locus 1 (Drosophila)	protein-coding
mm_114034.1	chr13	52981222	52981244	+	1	NA	promoter-TSS (NM_017373)	promoter-TSS (NM_017373)	-194	NM_017373	18030	Mm.136604	NM_017373	ENSMUSG00000056749	Nfil3	AV225605|E4BP4	nuclear factor, interleukin 3, regulated	protein-coding
mm_116862.1	chr13	54766554	54766572	-	1	NA	promoter-TSS (NM_033610)	promoter-TSS (NM_033610)	-123	NM_033610	104069	Mm.200843	NM_033610	ENSMUSG00000034891	Sncb	AI838531|betaSYN	synuclein, beta	protein-coding
mm_138898.1	chr17	43568559	43568592	+	1	NA	5' UTR (NM_013737, exon 1 of 12)	5' UTR (NM_013737, exon 1 of 12)	124	NM_013737	27226	Mm.9277	NM_013737	ENSMUSG00000023913	Pla2g7	PAF-AH|R75400	phospholipase A2, group VII (platelet-activating factor acetylhydrolase, plasma)	protein-coding
mm_135913.1	chr16	67594782	67594808	-	1	NA	intron (NM_178721, intron 1 of 9)	B1_Mur4|SINE|Alu	26113	NM_001347247	239857	Mm.394300	NM_178721	ENSMUSG00000064115	Cadm2	2900078E11Rik|9330131D06|A830029E02Rik|Igdf4d|Igsf4d|NECL3|SynCAM 2|SynCAM2	cell adhesion molecule 2	protein-coding
mm_72432.1	chr8	82863997	82864020	+	1	NA	5' UTR (NM_177378, exon 1 of 7)	5' UTR (NM_177378, exon 1 of 7)	652	NM_177378	330812	Mm.491438	NM_177378	ENSMUSG00000047747	Rnf150	A630007N06Rik|C030044C12Rik|Greul5|mKIAA1214	ring finger protein 150	protein-coding
mm_71920.1	chr8	70152755	70152769	+	1	NA	promoter-TSS (NM_001045484)	promoter-TSS (NM_001045484)	1	NM_001045484	17259	Mm.432505	NM_008578	ENSMUSG00000079033	Mef2b	AI451606	myocyte enhancer factor 2B	protein-coding
mm_9744.1	chr1	180393033	180393072	-	1	NA	intron (NM_001081175, intron 2 of 7)	intron (NM_001081175, intron 2 of 7)	-62503	NR_003623	277333	Mm.389223	NM_199472		Gm5069	EG277333	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_133799.1	chr16	95296923	95296941	+	1	NA	non-coding (NR_073406, exon 6 of 6)	non-coding (NR_073406, exon 6 of 6)	39374	NM_001271690	16516	Mm.272239	NM_019664	ENSMUSG00000062609	Kcnj15	4930414N08Rik|AI182284|AI267127|IRKK|Kir4.2	potassium inwardly-rectifying channel, subfamily J, member 15	protein-coding
mm_63941.1	chr7	139834190	139834201	+	1	NA	promoter-TSS (NM_177469)	promoter-TSS (NM_177469)	21	NM_177469	52389	Mm.39863	NM_177469	ENSMUSG00000025475	Adgra1	2900059M17Rik|D7Ertd680e|Gpr123	adhesion G protein-coupled receptor A1	protein-coding
mm_79542.1	chr9	57911026	57911036	+	1	NA	promoter-TSS (NM_027086)	promoter-TSS (NM_027086)	45	NM_001122873	69459	Mm.41735	NM_027086	ENSMUSG00000055720	Ubl7	2300004C15Rik	ubiquitin-like 7 (bone marrow stromal cell-derived)	protein-coding
mm_146089.1	chr18	73572756	73572836	+	1	NA	promoter-TSS (NM_001039214)	promoter-TSS (NM_001039214)	91	NM_001039214	240396	Mm.24131	NM_001039214	ENSMUSG00000037253	Mex3c	A130001D14Rik|BC035207|BM-013|Rkhd2	mex3 RNA binding family member C	protein-coding
mm_55273.1	chr6	53821225	53821259	-	1	NA	promoter-TSS (NM_025817)	promoter-TSS (NM_025817)	-417	NM_025817	66873	Mm.422727	NM_025817	ENSMUSG00000043496	Tril	1200009O22Rik|AI316813|mKIAA0644	TLR4 interactor with leucine-rich repeats	protein-coding
mm_159570.1	chr4	115133983	115133983	-	1	NA	promoter-TSS (NM_001003947)	promoter-TSS (NM_001003947)	-6	NM_001003947	81906	Mm.215544	NM_001003947	ENSMUSG00000047155	Cyp4x1	A230025G20|CYPIVX1|CYP_a|Cyp4a28-ps	cytochrome P450, family 4, subfamily x, polypeptide 1	protein-coding
mm_1935.1	chr1	86128193	86128211	+	1	NA	exon (NM_027357, exon 20 of 25)	exon (NM_027357, exon 20 of 25)	-16232	NM_008311	15559	Mm.439747	NM_008311	ENSMUSG00000026228	Htr2b	5-HT2B|AJ012488|AV377389	5-hydroxytryptamine (serotonin) receptor 2B	protein-coding
mm_13893.1	chr2	120404788	120404831	+	1	NA	promoter-TSS (NM_173734)	promoter-TSS (NM_173734)	-693	NM_001110496	211499	Mm.260712	NM_173734	ENSMUSG00000033808	Tmem87a	A930025J12Rik	transmembrane protein 87A	protein-coding
mm_144558.1	chr18	31698651	31698659	+	1	NA	exon (NM_172965, exon 16 of 21)	exon (NM_172965, exon 16 of 21)	-61169	NM_153515	225339	Mm.290804	NM_153515	ENSMUSG00000041915	Ammecr1l	5430429D03Rik|AU022236|AU040755|AW111353|E230022H04Rik	AMME chromosomal region gene 1-like	protein-coding
mm_25600.1	chr3	116903720	116903752	+	1	NA	TTS (NM_001113478)	TTS (NM_001113478)	42056	NM_009146	20321	Mm.66293	NM_009146	ENSMUSG00000033386	Frrs1	AI131732|Sdfr2	ferric-chelate reductase 1	protein-coding
mm_152648.1	chr19	12540786	12540794	-	1	NA	Intergenic	Intergenic	-32720	NM_001346545	107373	Mm.1643	NM_026640	ENSMUSG00000024691	Fam111a	4632417K18Rik|AW413625	family with sequence similarity 111, member A	protein-coding
mm_103653.1	chr11	78973097	78973119	-	1	NA	exon (NM_010708, exon 3 of 11)	exon (NM_010708, exon 3 of 11)	11816	NM_001159301	16859	Mm.341434	NM_010708	ENSMUSG00000001123	Lgals9	AA407335|AI194909|AI265545|LGALS35|Lgals5|gal-9|galectin-9	lectin, galactose binding, soluble 9	protein-coding
mm_97576.1	chr11	78940347	78940355	+	1	NA	intron (NM_001313921, intron 10 of 25)	intron (NM_001313921, intron 10 of 25)	15060	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_131796.1	chr16	22899085	22899116	+	1	NA	non-coding (NR_075099, exon 6 of 6)	non-coding (NR_075099, exon 6 of 6)	-4714	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_26121.1	chr3	137865060	137865121	+	1	NA	intron (NM_001316995, intron 1 of 4)	CpG	603	NM_016750	51788	Mm.117541	NM_016750	ENSMUSG00000037894	H2afz	H2A.Z|H2a.z-1	H2A histone family, member Z	protein-coding
mm_56631.1	chr6	112947247	112947277	-	1	NA	promoter-TSS (NM_080448)	promoter-TSS (NM_080448)	4	NM_080448	259302	Mm.236401	NM_080448	ENSMUSG00000030257	Srgap3	AI452337|Arhgap14|D130026O08Rik|Gbi|MEGAP|WRP|mKIAA0411	SLIT-ROBO Rho GTPase activating protein 3	protein-coding
mm_95096.1	chr11	34023080	34023085	+	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-24119	NM_010696	16822	Mm.265350	NM_010696	ENSMUSG00000002699	Lcp2	AI323664|BB161688|SLP-76|SLP76|m1Khoe|twm	lymphocyte cytosolic protein 2	protein-coding
mm_32258.1	chr4	102572365	102572377	+	1	NA	intron (NM_019840, intron 6 of 14)	intron (NM_019840, intron 6 of 14)	2311	NM_001177980	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_126094.1	chr15	77956796	77956808	+	1	NA	promoter-TSS (NM_001017983)	promoter-TSS (NM_001017983)	-80	NM_001017983	239554	Mm.295605	NM_001017983	ENSMUSG00000016552	Foxred2	A430097D04Rik|D15Bwg0759e|Gm304	FAD-dependent oxidoreductase domain containing 2	protein-coding
mm_130675.1	chr15	100675376	100675402	-	1	NA	exon (NM_033612, exon 7 of 8)	exon (NM_033612, exon 7 of 8)	-5889	NM_001270537	668218	Mm.451225	NM_001270537	ENSMUSG00000098112	Bin2	-	bridging integrator 2	protein-coding
mm_2523.1	chr1	106541939	106541976	+	1	NA	3' UTR (NM_009741, exon 2 of 2)	3' UTR (NM_009741, exon 2 of 2)	4674	NR_106164	102466254		NR_106164	ENSMUSG00000098344	Mir3473f	Gm27846|mmu-mir-3473f	microRNA 3473f	ncRNA
mm_140859.1	chr17	23740302	23740359	-	1	NA	promoter-TSS (NM_023824)	promoter-TSS (NM_023824)	0	NM_023824	76498	Mm.491253	NM_023824	ENSMUSG00000023909	Paqr4	1500004C10Rik	progestin and adipoQ receptor family member IV	protein-coding
mm_80247.1	chr9	72748961	72748980	+	1	NA	3' UTR (NM_010890, exon 29 of 29)	3' UTR (NM_010890, exon 29 of 29)	-58304	NM_175485	235472	Mm.31696	NM_175485	ENSMUSG00000036030	Prtg	A230098A12Rik|Igdcc5	protogenin	protein-coding
mm_59113.1	chr7	19822898	19822916	+	1	NA	promoter-TSS (NM_033601)	promoter-TSS (NM_033601)	-152	NM_033601	12051	Mm.439658	NM_033601	ENSMUSG00000053175	Bcl3	AI528691|Bcl-3	B cell leukemia/lymphoma 3	protein-coding
mm_15595.1	chr2	160645972	160645993	+	1	NA	promoter-TSS (NM_009408)	promoter-TSS (NM_009408)	85	NM_009408	21969	Mm.217233	NM_009408	ENSMUSG00000070544	Top1	AI467334|D130064I21Rik|Top-1	topoisomerase (DNA) I	protein-coding
mm_98592.1	chr11	95778158	95778179	+	1	NA	Intergenic	MLT1F1|LTR|ERVL-MaLR	29101	NM_201609	268469	Mm.389038	NM_201609	ENSMUSG00000075595	Zfp652	9530033F24Rik|ZNF652	zinc finger protein 652	protein-coding
mm_32991.1	chr4	120405260	120405287	+	1	NA	promoter-TSS (NM_013883)	promoter-TSS (NM_013883)	-8	NM_001159630	29871	Mm.427014	NM_013883	ENSMUSG00000000085	Scmh1	AI315320|AI851618|Scml1|Scml3	sex comb on midleg homolog 1	protein-coding
mm_132.1	chr1	10039825	10039845	+	1	NA	intron (NM_026493, intron 1 of 29)	CpG	1617	NM_026493	211660	Mm.244046	NM_026493	ENSMUSG00000056763	Cspp1	2310020J12Rik|4930413O22Rik|AA387550|BC055915|Cspp2|Cspp3	centrosome and spindle pole associated protein 1	protein-coding
mm_96905.1	chr11	70456029	70456039	+	1	NA	exon (NM_023158, exon 4 of 5)	exon (NM_023158, exon 4 of 5)	-3588	NM_001029929	574428	Mm.472771	NM_001029929	ENSMUSG00000040829	Zmynd15	-	zinc finger, MYND-type containing 15	protein-coding
mm_13282.1	chr2	101624735	101624756	+	1	NA	promoter-TSS (NM_009020)	promoter-TSS (NM_009020)	-3	NM_009020	19374	Mm.4988	NM_009020	ENSMUSG00000032864	Rag2	Rag-2	recombination activating gene 2	protein-coding
mm_145944.1	chr18	67390515	67390527	+	1	NA	promoter-TSS (NM_026473)	promoter-TSS (NM_026473)	-210	NM_026473	67951	Mm.181860	NM_026473	ENSMUSG00000001473	Tubb6	2310057H16Rik|BB220206	tubulin, beta 6 class V	protein-coding
mm_96337.1	chr11	66168007	66168022	+	1	NA	intron (NM_001099633, intron 1 of 68)	intron (NM_001099633, intron 1 of 68)	537	NM_001099633	237806	Mm.264210	NM_001099633	ENSMUSG00000056752	Dnah9	9030022M04|A230091C01|C230051G16|D11Ertd686e|Dnahc9|mKIAA0357	dynein, axonemal, heavy chain 9	protein-coding
mm_63639.1	chr7	128540111	128540132	+	1	NA	exon (NM_013863, exon 2 of 4)	exon (NM_013863, exon 2 of 4)	16538	NM_013863	29810	Mm.84073	NM_013863	ENSMUSG00000030847	Bag3	AA407278|Bis|mg638	BCL2-associated athanogene 3	protein-coding
mm_142140.1	chr17	35969725	35969785	-	1	NA	promoter-TSS (NM_013854)	promoter-TSS (NM_013854)	-5	NM_013854	224742	Mm.329022	NM_013854	ENSMUSG00000038762	Abcf1	AU041969|Abc50|D17Wsu166e|GCN20	ATP-binding cassette, sub-family F (GCN20), member 1	protein-coding
mm_28891.1	chr3	97888629	97888647	-	1	NA	promoter-TSS (NM_001289701)	promoter-TSS (NM_001289701)	69	NM_001289702	83679	Mm.129840	NM_031401	ENSMUSG00000038170	Pde4dip	4732458A06Rik|9430063L05Rik|C87016|D130016K21Rik|D3Bwg1078e|Usmg4|mKIAA0454	phosphodiesterase 4D interacting protein (myomegalin)	protein-coding
mm_55561.1	chr6	71341307	71341317	-	1	NA	Intergenic	Intergenic	18500	NM_009858	12526	Mm.333148	NM_009858	ENSMUSG00000053044	Cd8b1	Cd8b|Ly-3|Ly-C|Lyt-3	CD8 antigen, beta chain 1	protein-coding
mm_124907.1	chr15	10981781	10981805	+	1	NA	promoter-TSS (NM_008537)	promoter-TSS (NM_008537)	37	NM_008537	17117	Mm.2787	NM_008537	ENSMUSG00000022244	Amacr	Macr1	alpha-methylacyl-CoA racemase	protein-coding
mm_27304.1	chr3	49757174	49757203	-	1	NA	5' UTR (NM_130448, exon 1 of 4)	5' UTR (NM_130448, exon 1 of 4)	128	NM_130448	73173	Mm.87246	NM_130448	ENSMUSG00000037892	Pcdh18	3110038E07Rik|BB095589|PCDH68L	protocadherin 18	protein-coding
mm_85295.1	chr9	100480015	100480044	-	1	NA	intron (NM_001033543, intron 1 of 6)	ID4_|SINE|ID	6444	NM_001033543	213208	Mm.242896	NM_001033543	ENSMUSG00000044244	Il20rb	AV228068|Fndc6|Gm186|Il20R2	interleukin 20 receptor beta	protein-coding
mm_96334.1	chr11	65667763	65667764	+	1	NA	Intergenic	Intergenic	67069	NR_030417	791070		NR_030417	ENSMUSG00000076460	Mir744	Mirn744|mir-744|mmu-mir-744	microRNA 744	ncRNA
mm_16267.1	chr2	173659626	173659654	+	1	NA	promoter-TSS (NM_024436)	promoter-TSS (NM_024436)	-101	NR_027957	100043911	Mm.260590	NM_001033179	ENSMUSG00000055897	Ppp4r1l-ps	1700007P14Rik|5830403E09Rik|C030010B13Rik|Ppp4r1l	protein phosphatase 4, regulatory subunit 1-like, pseudogene	pseudo
mm_46401.1	chr5	104093001	104093010	-	1	NA	exon (NM_010097, exon 4 of 11)	exon (NM_010097, exon 4 of 11)	-15397	NM_001163772	100271704	Mm.366664	NM_001163772	ENSMUSG00000091034	Gm17660	Scpppq1	predicted gene, 17660	protein-coding
mm_128617.1	chr15	58933310	58933344	-	1	NA	promoter-TSS (NM_023172)	promoter-TSS (NM_023172)	403	NM_175151	69694	Mm.383230	NM_175151	ENSMUSG00000050891	Tatdn1	2310079P03Rik|CDA11	TatD DNase domain containing 1	protein-coding
mm_50623.1	chr6	50144688	50144698	+	1	NA	intron (NM_019939, intron 2 of 12)	ORR1F|LTR|ERVL-MaLR	34452	NM_001164733	56524	Mm.41288	NM_008016	ENSMUSG00000038388	Mpp6	P55t|Pals2	membrane protein, palmitoylated 6 (MAGUK p55 subfamily member 6)	protein-coding
mm_8681.1	chr1	156938783	156938809	-	1	NA	intron (NR_027640, intron 1 of 19)	intron (NR_027640, intron 1 of 19)	591	NM_001159966	78255	Mm.28376	NM_023884	ENSMUSG00000026594	Ralgps2	1810020P17Rik|2210408F11Rik|4921528G01Rik|9130014M22Rik|AU043409|AW046161	Ral GEF with PH domain and SH3 binding motif 2	protein-coding
mm_8962.1	chr1	165160673	165160685	-	1	NA	promoter-TSS (NM_032005)	promoter-TSS (NM_032005)	94	NM_032005	83993	Mm.190649	NM_032005	ENSMUSG00000026572	Tbx19	AU019250|D1Ertd754e|Tpit	T-box 19	protein-coding
mm_60425.1	chr7	44476607	44476617	+	1	NA	Intergenic	L1MEd|LINE|L1	6265	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_145883.1	chr18	65482057	65482060	+	1	NA	intron (NR_105742, intron 3 of 6)	L1_Mur3|LINE|L1	51061	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_110752.1	chr12	69987102	69987112	-	1	NA	promoter-TSS (NM_022028)	promoter-TSS (NM_022028)	-105	NM_022028	64010	Mm.390480	NM_022028	ENSMUSG00000021067	Sav1	1700040G09Rik|Salv|Sav|WW45|Wwp3|Wwp4	salvador family WW domain containing 1	protein-coding
mm_150142.1	chr19	31113927	31113943	+	1	NA	intron (NM_011160, intron 3 of 17)	RLTR17|LTR|ERVK	31094	NM_031249	83410	Mm.22031	NM_031249	ENSMUSG00000053536	Cstf2t	64kDa|C77975|tCstF-64|tauCstF-64	cleavage stimulation factor, 3' pre-RNA subunit 2, tau	protein-coding
mm_73702.1	chr8	111686645	111686661	+	1	NA	exon (NM_025583, exon 7 of 7)	exon (NM_025583, exon 7 of 7)	3021	NR_106044	102466993		NR_106044	ENSMUSG00000099129	Mir7076	Gm27318|mmu-mir-7076	microRNA 7076	ncRNA
mm_64348.1	chr7	142380930	142380960	+	1	NA	exon (NM_009983, exon 5 of 9)	exon (NM_009983, exon 5 of 9)	6925	NM_009983	13033	Mm.231395	NM_009983	ENSMUSG00000007891	Ctsd	CD|CatD	cathepsin D	protein-coding
mm_9373.1	chr1	172207702	172207706	-	1	NA	promoter-TSS (NM_001329871)	promoter-TSS (NM_001329871)	-900	NM_011063	18611	Mm.544	NM_011063	ENSMUSG00000013698	Pea15a	Mat1|PEA-15|Pea15|Pkcs15	phosphoprotein enriched in astrocytes 15A	protein-coding
mm_1914.1	chr1	86018069	86018084	+	1	NA	Intergenic	Intergenic	-3866	NM_001122732	70060	Mm.196313	NM_027029	ENSMUSG00000026226	Spata3	1700011N12Rik|1700029H01Rik|4930424D10Rik|Mtsarg1|Tsarg1	spermatogenesis associated 3	protein-coding
mm_88596.1	chr10	79780973	79780984	+	1	NA	TTS (NM_001042710)	TTS (NM_001042710)	3704	NM_031380	83554	Mm.251710	NM_031380	ENSMUSG00000020325	Fstl3	E030038F23Rik|Flrg	follistatin-like 3	protein-coding
mm_146711.1	chr18	14683282	14683309	-	1	NA	promoter-TSS (NM_001161371)	promoter-TSS (NM_001161371)	-381	NM_001161370	268996	Mm.31761	NM_009280	ENSMUSG00000037013	Ss18	D130059H17|Ssxt|Syt	SS18, nBAF chromatin remodeling complex subunit	protein-coding
mm_155285.1	chrX	61183289	61183315	+	1	NA	TTS (NM_001166658)	TTS (NM_001166658)	2256	NM_001166658	631990	Mm.401324	NM_001166658	ENSMUSG00000090546	Cdr1	100039759|Cdr|Cdr34|EG631990|Gm2409|Gm7077	cerebellar degeneration related antigen 1	protein-coding
mm_35402.1	chr4	34687383	34687452	-	1	NA	promoter-TSS (NM_011895)	promoter-TSS (NM_011895)	21	NM_011895	24060	Mm.281885	NM_011895	ENSMUSG00000028293	Slc35a1	AA408150|AI314851	solute carrier family 35 (CMP-sialic acid transporter), member 1	protein-coding
mm_39998.1	chr5	32613490	32613494	+	1	NA	intron (NM_009535, intron 1 of 11)	intron (NM_009535, intron 1 of 11)	2321	NM_009535	22612	Mm.4558	NM_009535	ENSMUSG00000014932	Yes1	Yes|p61-Yes	YES proto-oncogene 1, Src family tyrosine kinase	protein-coding
mm_165864.1	chr4	33260564	33260569	+	1	NA	Intergenic	MTB_Mm|LTR|ERVL-MaLR	-11779	NM_001033225	108767	Mm.27769	NM_001033225	ENSMUSG00000040128	Pnrc1	5730463C12Rik|B4-2|PRR2|Prol2	proline-rich nuclear receptor coactivator 1	protein-coding
mm_29187.1	chr3	106547565	106547578	-	1	NA	promoter-TSS (NM_026013)	promoter-TSS (NM_026013)	-227	NM_001286986	67171	Mm.290488	NM_026013	ENSMUSG00000027900	Dram2	2010305N14Rik|2610318G18Rik|AI647667|Tmem77	DNA-damage regulated autophagy modulator 2	protein-coding
mm_103950.1	chr11	84068376	84068386	-	1	NA	promoter-TSS (NM_019819)	promoter-TSS (NM_019819)	-24	NM_019819	56405	Mm.240885	NM_019819	ENSMUSG00000018648	Dusp14	1110014C10Rik|2310042C07Rik|D11Ertd395e|MKP-L|Mkp6	dual specificity phosphatase 14	protein-coding
mm_169373.1	chr14	34620424	34620424	-	1	NA	Intergenic	B1_Mus1|SINE|Alu	-20282	NM_013887	30044	Mm.272060	NM_013887	ENSMUSG00000021799	Opn4	1110007J02Rik|Gm533	opsin 4 (melanopsin)	protein-coding
mm_50084.1	chr6	41523761	41523771	+	1	NA	intron (NM_009430, intron 2 of 4)	intron (NM_009430, intron 2 of 4)	1990	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_45908.1	chr5	89416340	89416342	-	1	NA	Intergenic	Intergenic	41557	NM_008096	14473	Mm.196595	NM_008096	ENSMUSG00000035540	Gc	DBP|VDB	group specific component	protein-coding
mm_127413.1	chr15	101257236	101257252	+	1	NA	Intergenic	Intergenic	-9602	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_4533.1	chr1	175767011	175767055	+	1	NA	exon (NM_029453, exon 12 of 28)	exon (NM_029453, exon 12 of 28)	68440	NM_029453	75820	Mm.50361	NM_029453	ENSMUSG00000026523	Wdr64	4930415O10Rik|4930511H01Rik	WD repeat domain 64	protein-coding
mm_36752.1	chr4	101253607	101253610	-	1	NA	intron (NM_146145, intron 1 of 24)	intron (NM_146145, intron 1 of 24)	11674	NM_146145	16451	Mm.289657	NM_146145	ENSMUSG00000028530	Jak1	AA960307|BAP004|C130039L05Rik	Janus kinase 1	protein-coding
mm_136333.1	chr16	92434518	92434527	-	1	NA	intron (NM_001081549, intron 1 of 3)	intron (NM_001081549, intron 1 of 3)	31647	NM_001081549	54720	Mm.265744	NM_019466	ENSMUSG00000022951	Rcan1	Adapt78|CALP1L|CSP1|DSC1|Dscr1|MCIP1|RCN1	regulator of calcineurin 1	protein-coding
mm_37690.1	chr4	129239166	129239194	-	1	NA	promoter-TSS (NM_001285865)	promoter-TSS (NM_001285865)	38	NM_001285865	97130	Mm.331907	NM_001033189	ENSMUSG00000050390	C77080	Kiaa1522|mKIAA1522	expressed sequence C77080	protein-coding
mm_62138.1	chr7	97090754	97090783	+	1	NA	intron (NM_001162477, intron 1 of 9)	intron (NM_001162477, intron 1 of 9)	9017	NM_010248	14389	Mm.42033	NM_010248	ENSMUSG00000004508	Gab2	AI463667|D130058I17Rik|p97	growth factor receptor bound protein 2-associated protein 2	protein-coding
mm_27605.1	chr3	59153630	59153634	-	1	NA	promoter-TSS (NR_045641)	promoter-TSS (NR_045641)	-4	NR_045641	320463	Mm.484506	NR_045641	ENSMUSG00000036381	F630111L10Rik	-	RIKEN cDNA F630111L10 gene	ncRNA
mm_172045.1	chr6	128466465	128466468	+	1	NA	intron (NR_028593, intron 2 of 4)	RLTR12H|LTR|ERVK	27709	NR_028592	791299	Mm.297516	NR_028592	ENSMUSG00000059659	Gm10069	ENSMUSG00000059659	predicted gene 10069	ncRNA
mm_157625.1	chrX	56597868	56597879	-	1	NA	promoter-TSS (NM_146234)	promoter-TSS (NM_146234)	46	NM_146234	236792	Mm.291824	NM_146234	ENSMUSG00000061273	Mmgt1	9630048L06Rik|BC032271|Emc5|Mir5116|Tmem32|mir-5116	membrane magnesium transporter 1	protein-coding
mm_834.1	chr1	51478625	51478652	+	1	NA	promoter-TSS (NM_001310549)	promoter-TSS (NM_001310549)	-239	NM_001310549	109019	Mm.196290	NM_028696	ENSMUSG00000026107	Nabp1	4930434H03Rik|4930442A21Rik|4930488J04Rik|4933440J18Rik|5830411E10Rik|AI852561|Nbp1|Obfc2a|Ssb2	nucleic acid binding protein 1	protein-coding
mm_74605.1	chr8	11948315	11948318	-	1	NA	Intergenic	Intergenic	107795	NM_029326	75528	Mm.440342	NM_029326	ENSMUSG00000031512	Tex29	1700018L24Rik	testis expressed 29	protein-coding
mm_81222.1	chr9	107614427	107614444	+	1	NA	3' UTR (NM_008138, exon 9 of 9)	3' UTR (NM_008138, exon 9 of 9)	-5194	NM_001291539	20347	Mm.4083	NM_009153	ENSMUSG00000057969	Sema3b	SemA|Semaa|sema5|semaV	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B	protein-coding
mm_48714.1	chr5	147307217	147307230	-	1	NA	promoter-TSS (NM_007673)	promoter-TSS (NM_007673)	26	NM_007673	12591	Mm.20358	NM_007673	ENSMUSG00000029646	Cdx2	Cdx-2	caudal type homeobox 2	protein-coding
mm_22600.1	chr3	14481264	14481306	+	1	NA	exon (NM_080852, exon 1 of 4)	exon (NM_080852, exon 1 of 4)	586	NM_080852	140918	Mm.215250	NM_080852	ENSMUSG00000039710	Slc7a12	Asc-2|XAT1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 12	protein-coding
mm_9877.1	chr1	185441716	185441735	-	1	NA	promoter-TSS (NR_038006)	promoter-TSS (NR_038006)	94	NR_038006	319562	Mm.184335	NM_176943	ENSMUSG00000051295	9630028B13Rik	-	RIKEN cDNA 9630028B13 gene	ncRNA
mm_142965.1	chr17	56121898	56121920	-	1	NA	promoter-TSS (NM_029796)	promoter-TSS (NM_029796)	37	NM_029796	76905	Mm.348025	NM_029796	ENSMUSG00000037095	Lrg1	1300008B03Rik|2310031E04Rik|Lrg|Lrhg	leucine-rich alpha-2-glycoprotein 1	protein-coding
mm_44045.1	chr5	147860452	147860469	+	1	NA	promoter-TSS (NM_025624)	promoter-TSS (NM_025624)	-168	NM_025624	66537	Mm.332855	NM_025624	ENSMUSG00000029649	Pomp	2510048O06Rik|Ump1	proteasome maturation protein	protein-coding
mm_122498.1	chr14	46788268	46788329	-	1	NA	promoter-TSS (NM_009919)	promoter-TSS (NM_009919)	59	NM_009919	12793	Mm.3261	NM_009919	ENSMUSG00000015759	Cnih1	0610007J15|CNIH-1|Cnih	cornichon family AMPA receptor auxiliary protein 1	protein-coding
mm_67605.1	chr7	83746062	83746106	-	1	NA	Intergenic	Intergenic	-10594	NM_010551	16170	Mm.10137	NM_010551	ENSMUSG00000001741	Il16	mKIAA4048	interleukin 16	protein-coding
mm_104243.1	chr11	88827273	88827314	-	1	NA	Intergenic	Intergenic	24210	NM_009648	11640	Mm.2969	NM_009648	ENSMUSG00000018428	Akap1	AKAP121|AKAP84|Akap|C76494|C81186|DAKAP1|S-AKAP84	A kinase (PRKA) anchor protein 1	protein-coding
mm_158319.1	chrX	133688979	133689005	-	1	NA	promoter-TSS (NM_001105246)	promoter-TSS (NM_001105246)	1	NM_001105245	279653	Mm.39738	NM_001105245	ENSMUSG00000051323	Pcdh19	B530002L05Rik|Gm717|mKIAA1313	protocadherin 19	protein-coding
mm_154895.1	chrX	20870237	20870273	+	1	NA	promoter-TSS (NM_011593)	promoter-TSS (NM_011593)	89	NM_001294280	21857	Mm.8245	NM_011593	ENSMUSG00000001131	Timp1	Clgi|EPA|TIMP-1|TPA-S1|Timp	tissue inhibitor of metalloproteinase 1	protein-coding
mm_12643.1	chr2	74716989	74716995	+	1	NA	promoter-TSS (NR_027899)	promoter-TSS (NR_027899)	-862	NR_027899	73429	Mm.443313	NR_027899		Hoxd3os1	1700064D17Rik|1700109F18Rik	homeobox D3, opposite strand 1	ncRNA
mm_133633.1	chr16	91654622	91654675	+	1	NA	exon (NM_019973, exon 3 of 5)	exon (NM_019973, exon 3 of 5)	6824	NM_178880	20658	Mm.46401	NM_019973	ENSMUSG00000022961	Son	2900011L12Rik|AA409051|AU067731|C81487|mKIAA1019|nrebp	Son DNA binding protein	protein-coding
mm_107675.1	chr12	54239239	54239245	+	1	NA	intron (NR_108033, intron 1 of 2)	U1|snRNA|snRNA	5627	NR_108033	73592	Mm.416874	NR_108033		1700104L18Rik	-	RIKEN cDNA 1700104L18 gene	ncRNA
mm_108877.1	chr12	99687167	99687168	+	1	NA	Intergenic	Intergenic	-59193	NR_045288	73457	Mm.383439	NR_045288	ENSMUSG00000100211	1700064M15Rik	-	RIKEN cDNA 1700064M15 gene	ncRNA
mm_737.1	chr1	43447347	43447355	+	1	NA	intron (NM_010879, intron 1 of 4)	intron (NM_010879, intron 1 of 4)	1600	NM_010879	17974	Mm.389903	NM_010879	ENSMUSG00000066877	Nck2	4833426I10Rik|Grb4|NCKbeta|Nck-2	non-catalytic region of tyrosine kinase adaptor protein 2	protein-coding
mm_11001.1	chr2	26446022	26446033	+	1	NA	promoter-TSS (NM_153125)	promoter-TSS (NM_153125)	-811	NM_153125	227648	Mm.206371	NM_153125	ENSMUSG00000026924	Sec16a	AU024582|C230052J16Rik	SEC16 homolog A, endoplasmic reticulum export factor	protein-coding
mm_147070.1	chr18	35215009	35215033	-	1	NA	promoter-TSS (NM_178005)	promoter-TSS (NM_178005)	3	NM_178005	107065	Mm.39900	NM_178005	ENSMUSG00000071862	Lrrtm2	AI851755|BB129880|C630011A14Rik|mKIAA0416	leucine rich repeat transmembrane neuronal 2	protein-coding
mm_170812.1	chr2	176153463	176153479	-	1	NA	Intergenic	Intergenic	-73094	NM_001305137	100504263	Mm.379980	NM_001305136	ENSMUSG00000078894	2210418O10Rik	Gm6182	predicted gene 2210418O10Rik	protein-coding
mm_92745.1	chr10	80998147	80998163	-	1	NA	intron (NM_010319, intron 1 of 3)	intron (NM_010319, intron 1 of 3)	3210	NM_001038655	14708	Mm.222496	NM_010319	ENSMUSG00000048240	Gng7	AI840417	guanine nucleotide binding protein (G protein), gamma 7	protein-coding
mm_125999.1	chr15	76477405	76477461	+	1	NA	promoter-TSS (NM_013481)	promoter-TSS (NM_013481)	71	NR_138589	15499	Mm.347444	NM_008296	ENSMUSG00000022556	Hsf1	AA960185|HSTF|HSTF 1|Hsf1alpha|Hsf1beta	heat shock factor 1	protein-coding
mm_95056.1	chr11	32400381	32400393	+	1	NA	intron (NM_177364, intron 6 of 12)	intron (NM_177364, intron 6 of 12)	52576	NM_177364	268396	Mm.227616	NM_177364	ENSMUSG00000040711	Sh3pxd2b	G431001E03Rik|TSK4|fad49	SH3 and PX domains 2B	protein-coding
mm_82426.1	chr9	14903963	14903971	-	1	NA	promoter-TSS (NM_176807)	promoter-TSS (NM_176807)	-16	NM_022888	64931	Mm.86738	NM_022888	ENSMUSG00000031933	Izumo1r	0910001L11Rik|C86255|Folbp3|Folr4|Juno	IZUMO1 receptor, JUNO	protein-coding
mm_101803.1	chr11	46291536	46291578	-	1	NA	exon (NM_001252459, exon 2 of 31)	exon (NM_001252459, exon 2 of 31)	20801	NM_001252460	76884	Mm.154358	NM_133769	ENSMUSG00000020340	Cyfip2	1500004I01Rik|6430511D02Rik|AA930218|AU022376|Pir121|mKIAA1168	cytoplasmic FMR1 interacting protein 2	protein-coding
mm_234.1	chr1	19104174	19104188	+	1	NA	intron (NM_153154, intron 1 of 7)	intron (NM_153154, intron 1 of 7)	1159	NM_153154	226896	Mm.244858	NM_153154	ENSMUSG00000042596	Tfap2d	Tcfap2d	transcription factor AP-2, delta	protein-coding
mm_97832.1	chr11	83064491	83064498	+	1	NA	promoter-TSS (NM_011408)	promoter-TSS (NM_011408)	-618	NM_011408	20556	Mm.278689	NM_011408	ENSMUSG00000072620	Slfn2	Shlf2	schlafen 2	protein-coding
mm_54088.1	chr6	15846026	15846041	-	1	NA	Intergenic	LTR33A_|LTR|ERVL	125372	NM_175088	16543	Mm.1314	NM_175088	ENSMUSG00000041390	Mdfic	Kdt1|Mdfid	MyoD family inhibitor domain containing	protein-coding
mm_150890.1	chr19	45364079	45364111	+	1	NA	intron (NM_009771, intron 1 of 13)	intron (NM_009771, intron 1 of 13)	361	NM_001037758	12234	Mm.119717	NM_009771	ENSMUSG00000025217	Btrc	Beta-Trcp1|E3RS-IkappaB|E3RSIkappaB|FWD1|Fbw1a|HOS|Slimb|b-TrCP|beta-TrCP	beta-transducin repeat containing protein	protein-coding
mm_92305.1	chr10	75131728	75131752	-	1	NA	intron (NM_001081412, intron 4 of 22)	intron (NM_001081412, intron 4 of 22)	70844	NM_001081412	110279	Mm.333722	NM_001081412	ENSMUSG00000009681	Bcr	5133400C09Rik|AI561783|AI853148|mKIAA3017	breakpoint cluster region	protein-coding
mm_40699.1	chr5	65858177	65858183	+	1	NA	Intergenic	Intergenic	-5389	NM_001081105	74734	Mm.20323	NM_001081105	ENSMUSG00000029204	Rhoh	5830400A04Rik|AU019774|Arhh	ras homolog family member H	protein-coding
mm_145897.1	chr18	65624034	65624071	+	1	NA	exon (NM_207255, exon 3 of 6)	exon (NM_207255, exon 3 of 6)	-4437	NR_105742	100526497		NR_105742	ENSMUSG00000077113	Mir466p	mmu-mir-466p	microRNA 466p	ncRNA
mm_111034.1	chr12	79190956	79190976	-	1	NA	intron (NM_021557, intron 1 of 6)	intron (NM_021557, intron 1 of 6)	853	NM_021557	17252	Mm.291799	NM_021557	ENSMUSG00000066441	Rdh11	2610319N22Rik|AI428145|AU045252|Arsdr1|C85936|CGI-82|HCBP12|M42C60|Mdt1|Psdr1|SCALD|UBE-1c1|Ube-1c	retinol dehydrogenase 11	protein-coding
mm_165522.1	chr2	174284269	174284293	+	1	NA	promoter-TSS (NM_022000)	promoter-TSS (NM_022000)	-39	NM_019690	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_125242.1	chr15	34434178	34434204	+	1	NA	intron (NM_016762, intron 18 of 18)	(T)n|Simple_repeat|Simple_repeat	9034	NM_009083	19946	Mm.358632	NM_009083	ENSMUSG00000058600	Rpl30	-	ribosomal protein L30	protein-coding
mm_145864.1	chr18	65461017	65461030	+	1	NA	intron (NM_172833, intron 9 of 15)	MIR|SINE|MIR	30026	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_106067.1	chr11	116138790	116138848	-	1	NA	promoter-TSS (NM_024177)	promoter-TSS (NM_024177)	49	NM_024177	60441	Mm.29974	NM_024177	ENSMUSG00000020775	Mrpl38	1110036N21Rik|4733401F03Rik|MRP-L3|R75240|Rpml3	mitochondrial ribosomal protein L38	protein-coding
mm_76177.1	chr8	82398604	82398718	-	1	NA	intron (NM_001254747, intron 1 of 7)	intron (NM_001254747, intron 1 of 7)	3925	NM_001254747	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_143780.1	chr17	81730886	81730892	-	1	NA	intron (NR_104580, intron 1 of 8)	B4|SINE|B4	7498	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_162350.1	chr1	54583872	54583880	+	1	NA	Intergenic	RMER17C|LTR|ERVK	-26192	NM_001163314	241062	Mm.103539	NM_175508	ENSMUSG00000073678	Pgap1	5033403E17Rik|9030223K07Rik|A530084K22|D230012E17Rik|oto	post-GPI attachment to proteins 1	protein-coding
mm_58731.1	chr7	13029857	13029868	+	1	NA	exon (NM_011588, exon 13 of 17)	exon (NM_011588, exon 13 of 17)	4915	NM_026885	68953	Mm.295670	NM_026885	ENSMUSG00000033916	Chmp2a	1500016L11Rik	charged multivesicular body protein 2A	protein-coding
mm_49537.1	chr6	30175358	30175379	+	1	NA	Intergenic	Intergenic	-1243	NR_126541	101447999		NR_126540		Mirc35hg	-	microRNA cluster 35, host gene	ncRNA
mm_47432.1	chr5	123176185	123176204	-	1	NA	exon (NM_008277, exon 10 of 14)	exon (NM_008277, exon 10 of 14)	6492	NM_008277	15445	Mm.439709	NM_008277	ENSMUSG00000029445	Hpd	Fla|Flp|Hppd|Laf	4-hydroxyphenylpyruvic acid dioxygenase	protein-coding
mm_146311.1	chr18	80279439	80279443	+	1	NA	intron (NM_025861, intron 4 of 5)	intron (NM_025861, intron 4 of 5)	23135	NM_001164423	66943	Mm.29247	NM_025861	ENSMUSG00000034006	Pqlc1	2310009N05Rik|4933425L21Rik|5730564E11Rik|C78974	PQ loop repeat containing 1	protein-coding
mm_48634.1	chr5	145140258	145140281	-	1	NA	promoter-TSS (NM_001033313)	promoter-TSS (NM_001033313)	-107	NM_001310771	231889	Mm.277413	NM_001008705	ENSMUSG00000038722	Bud31	C77604|EDG-2|EDG2|G10	BUD31 homolog	protein-coding
mm_107499.1	chr12	38861018	38861026	+	1	NA	intron (NM_001347379, intron 10 of 11)	intron (NM_001347379, intron 10 of 11)	77311	NM_001163154	14009	Mm.4866	NM_007960	ENSMUSG00000004151	Etv1	ER81|Etsrp81	ets variant 1	protein-coding
mm_72705.1	chr8	84980188	84980197	+	1	NA	Intergenic	Intergenic	-1444	NM_008416	16477	Mm.1167	NM_008416	ENSMUSG00000052837	Junb	-	jun B proto-oncogene	protein-coding
mm_57666.1	chr6	128487965	128487982	-	1	NA	exon (NM_007376, exon 30 of 36)	exon (NM_007376, exon 30 of 36)	38747	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_71410.1	chr8	46471888	46471901	+	1	NA	intron (NM_007981, intron 1 of 20)	intron (NM_007981, intron 1 of 20)	857	NM_007981	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_64315.1	chr7	141864977	141864984	+	1	NA	exon (NM_028801, exon 31 of 49)	exon (NM_028801, exon 31 of 49)	25908	NM_028801	74180	Mm.200752	NM_028801	ENSMUSG00000066108	Muc5b	2300002I04Rik|A130042M24|AV085033|MUC5|MUC9|mucin 5b	mucin 5, subtype B, tracheobronchial	protein-coding
mm_110646.1	chr12	58976355	58976358	-	1	NA	intron (NM_009147, intron 14 of 19)	Charlie6|DNA|hAT-Charlie	35661	NM_009147	20334	Mm.491137	NM_009147	ENSMUSG00000020986	Sec23a	Msec23|Sec23r	SEC23 homolog A, COPII coat complex component	protein-coding
mm_126714.1	chr15	85336238	85336278	+	1	NA	promoter-TSS (NM_016843)	promoter-TSS (NM_016843)	-123	NM_016843	54138	Mm.248906	NM_016843	ENSMUSG00000016541	Atxn10	AI325283|C77170|E46|Sca10|TEG-169|Tex169	ataxin 10	protein-coding
mm_26748.1	chr3	7613643	7613656	-	1	NA	promoter-TSS (NM_001313890)	promoter-TSS (NM_001313890)	111	NM_008371	16196	Mm.3825	NM_008371	ENSMUSG00000040329	Il7	A630026I06Rik|Il-7|hlb368	interleukin 7	protein-coding
mm_19862.1	chr2	113848602	113848613	-	1	NA	promoter-TSS (NM_181416)	promoter-TSS (NM_181416)	54	NM_181416	228482	Mm.45753	NM_181416	ENSMUSG00000041219	Arhgap11a	6530401L14Rik|mKIAA0013	Rho GTPase activating protein 11A	protein-coding
mm_9286.1	chr1	171634740	171634764	-	1	NA	3' UTR (NM_144539, exon 8 of 8)	3' UTR (NM_144539, exon 8 of 8)	7148	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_149056.1	chr19	8839353	8839375	+	1	NA	promoter-TSS (NM_008144)	promoter-TSS (NM_008144)	36	NM_008144	14705	Mm.345134	NM_008144	ENSMUSG00000071657	Bscl2	2900097C17Rik|AI046355|Gng3lg	Berardinelli-Seip congenital lipodystrophy 2 (seipin)	protein-coding
mm_15893.1	chr2	164940743	164940765	+	1	NA	Intergenic	MamTip1|DNA|hAT-Tip100	-7465	NM_013599	17395	Mm.4406	NM_013599	ENSMUSG00000017737	Mmp9	AW743869|B/MMP9|Clg4b|Gel B|MMP-9|pro-MMP-9	matrix metallopeptidase 9	protein-coding
mm_138789.1	chr17	37271126	37271153	+	1	NA	exon (NM_013819, exon 3 of 8)	exon (NM_013819, exon 3 of 8)	905	NM_013819	14991	Mm.14437	NM_013819	ENSMUSG00000016206	H2-M3	H-2M3|Hmt|M3a|MuprM3|MuprM301|MuprM302|R4B2	histocompatibility 2, M region locus 3	protein-coding
mm_164106.1	chr15	25940801	25940809	+	1	NA	promoter-TSS (NM_001277316)	promoter-TSS (NM_001277316)	-21	NM_001277316	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_131528.1	chr16	17646465	17646507	+	1	NA	promoter-TSS (NM_001166164)	promoter-TSS (NM_001166164)	16	NM_001166164	72315	Mm.297777	NM_001166164	ENSMUSG00000041617	Ccdc74a	2310015A05Rik	coiled-coil domain containing 74A	protein-coding
mm_65675.1	chr7	28312028	28312061	-	1	NA	promoter-TSS (NM_025616)	promoter-TSS (NM_025616)	2	NM_025616	66525	Mm.167913	NM_025616	ENSMUSG00000003438	Timm50	2810403L02Rik|AU015082|TIM50L	translocase of inner mitochondrial membrane 50	protein-coding
mm_22473.1	chr3	5218564	5218587	+	1	NA	promoter-TSS (NM_030708)	promoter-TSS (NM_030708)	21	NM_030708	80892	Mm.41522	NM_030708	ENSMUSG00000025255	Zfhx4	A930021B15|C130041O22Rik|Zfh-4|Zfh4	zinc finger homeodomain 4	protein-coding
mm_18323.1	chr2	57114971	57114975	-	1	NA	promoter-TSS (NM_013613)	promoter-TSS (NM_013613)	65	NM_013613	18227	Mm.3507	NM_013613	ENSMUSG00000026826	Nr4a2	HZF-3|NOT|Nurr1|RNR-1|TINOR|TINUR	nuclear receptor subfamily 4, group A, member 2	protein-coding
mm_13346.1	chr2	102944250	102944260	+	1	NA	Intergenic	Intergenic	-42590	NM_001039150	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_167846.1	chrX	6346292	6346292	+	1	NA	Intergenic	Intergenic	-25568	NM_009757	12155	Mm.42160	NM_009757	ENSMUSG00000023279	Bmp15	AU015375|AU018861|AU021453|Bmp-15|C86824|C87336|GDF-9B	bone morphogenetic protein 15	protein-coding
mm_64943.1	chr7	16314035	16314049	-	1	NA	intron (NM_133234, intron 3 of 3)	CpG	4459	NM_133234	170770	Mm.7660	NM_133234	ENSMUSG00000002083	Bbc3	PUMA|PUMA/JFY1	BCL2 binding component 3	protein-coding
mm_171918.1	chr5	5782541	5782547	-	1	NA	Intergenic	Intergenic	-33227	NM_027399	70358	Mm.85429	NM_027399	ENSMUSG00000015652	Steap1	2410007B19Rik|Prss24|Steap	six transmembrane epithelial antigen of the prostate 1	protein-coding
mm_121491.1	chr14	121253143	121253153	+	1	NA	intron (NM_134082, intron 13 of 26)	intron (NM_134082, intron 13 of 26)	126082	NM_145465	223255	Mm.390756	NM_145465	ENSMUSG00000063410	Stk24	1810013H02Rik|C76483|MST-3|Mst3|STE20	serine/threonine kinase 24	protein-coding
mm_103576.1	chr11	78080361	78080387	-	1	NA	promoter-TSS (NM_022313)	promoter-TSS (NM_022313)	9	NM_022313	57837	Mm.21096	NM_022313	ENSMUSG00000020832	Eral1	2610524P08Rik|9130407C09Rik|AU019798|Era|M-ERA|MERA-S|MERA-W	Era (G-protein)-like 1 (E. coli)	protein-coding
mm_132422.1	chr16	35451041	35451043	+	1	NA	intron (NM_028295, intron 6 of 16)	intron (NM_028295, intron 6 of 16)	39831	NM_028295	72599	Mm.71015	NM_028295	ENSMUSG00000022844	Pdia5	2700053F16Rik|AU015525|Pdir	protein disulfide isomerase associated 5	protein-coding
mm_87438.1	chr10	51480237	51480255	+	1	NA	promoter-TSS (NM_008147)	promoter-TSS (NM_008147)	-366	NM_008147	14727	Mm.439661	NM_008147	ENSMUSG00000062593	Lilr4b	Gp49a|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4B	protein-coding
mm_84334.1	chr9	64022112	64022129	-	1	NA	promoter-TSS (NM_008542)	promoter-TSS (NM_008542)	-61	NM_008542	17130	Mm.325757	NM_008542	ENSMUSG00000036867	Smad6	Madh6|b2b390Clo	SMAD family member 6	protein-coding
mm_110133.1	chr12	26445192	26445201	-	1	NA	3' UTR (NM_021384, exon 6 of 6)	3' UTR (NM_021384, exon 6 of 6)	11256	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_162362.1	chr1	64532672	64532720	-	1	NA	promoter-TSS (NM_009952)	promoter-TSS (NM_009952)	-108	NM_133828	12912	Mm.422634	NM_009952	ENSMUSG00000025958	Creb1	2310001E10Rik|3526402H21Rik|AV083133|Creb|Creb-1	cAMP responsive element binding protein 1	protein-coding
mm_56357.1	chr6	93792467	93792482	-	1	NA	exon (NM_010367, exon 4 of 22)	exon (NM_010367, exon 4 of 22)	120489	NR_104594	14924	Mm.217216	NM_010367	ENSMUSG00000045095	Magi1	AIP3|BAP1|Baiap1|Gukmi1|MAGI1c|Magi-1|TNRC19|WWP3|mKIAA4129	membrane associated guanylate kinase, WW and PDZ domain containing 1	protein-coding
mm_112997.1	chr13	21754054	21754061	+	1	NA	promoter-TSS (NM_178201)	promoter-TSS (NM_178201)	-66	NM_178201	319187		NM_178201	ENSMUSG00000095217	Hist1h2bn	-	histone cluster 1, H2bn	protein-coding
mm_53202.1	chr6	125590861	125590868	+	1	NA	intron (NM_011708, intron 8 of 51)	intron (NM_011708, intron 8 of 51)	37916	NM_011708	22371	Mm.22339	NM_011708	ENSMUSG00000001930	Vwf	6820430P06Rik|AI551257|B130011O06Rik|C630030D09|F8VWF|VWD	Von Willebrand factor	protein-coding
mm_68364.1	chr7	106644630	106644663	-	1	NA	promoter-TSS (NM_001277183)	promoter-TSS (NM_001277183)	-1	NM_001277182	434223	Mm.276443	NM_001277179		Gm1966	-	predicted gene 1966	protein-coding
mm_126018.1	chr15	76667690	76667700	+	1	NA	TTS (NM_007989)	TTS (NM_007989)	2253	NM_007989	14106	Mm.42011	NM_007989	ENSMUSG00000033837	Foxh1	Fast1|Fast2|fast-1|fast-2	forkhead box H1	protein-coding
mm_157851.1	chrX	74425293	74425319	-	1	NA	intron (NM_001136067, intron 1 of 10)	intron (NM_001136067, intron 1 of 10)	694	NM_001136067	16151	Mm.12967	NM_010547	ENSMUSG00000004221	Ikbkg	1110037D23Rik|AI848108|AI851264|AW124339|IKK[g]|NEMO	inhibitor of kappaB kinase gamma	protein-coding
mm_155289.1	chrX	61183553	61183563	+	1	NA	3' UTR (NM_001166658, exon 1 of 1)	3' UTR (NM_001166658, exon 1 of 1)	2000	NM_001166658	631990	Mm.401324	NM_001166658	ENSMUSG00000090546	Cdr1	100039759|Cdr|Cdr34|EG631990|Gm2409|Gm7077	cerebellar degeneration related antigen 1	protein-coding
mm_112302.1	chr12	114740890	114740892	-	1	NA	Intergenic	Intergenic	-227197	NR_106063	102465664		NR_106063	ENSMUSG00000098357	Mir7094-2	Gm27508|mmu-mir-7094-2	microRNA 7094-2	ncRNA
mm_80265.1	chr9	72925491	72925514	+	1	NA	promoter-TSS (NM_028116)	promoter-TSS (NM_028116)	-148	NM_028116	72135	Mm.273605	NM_028116	ENSMUSG00000034910	Pygo1	2600014C22Rik	pygopus 1	protein-coding
mm_154393.1	chrM	13131	13141	+	1	NA	NA	Intergenic	NA	NA								
mm_160076.1	chr7	7209906	7209906	-	1	NA	promoter-TSS (NM_145577)	promoter-TSS (NM_145577)	92	NM_145577	232855	Mm.360403	NM_145577	ENSMUSG00000066838	Zfp772	-	zinc finger protein 772	protein-coding
mm_88753.1	chr10	80300998	80301050	+	1	NA	promoter-TSS (NM_011789)	promoter-TSS (NM_011789)	-796	NM_011789	23805	Mm.57247	NM_011789	ENSMUSG00000020135	Apc2	AI852447|APCL|R75424	adenomatosis polyposis coli 2	protein-coding
mm_31075.1	chr4	41379541	41379559	+	1	NA	exon (NM_001290454, exon 4 of 6)	exon (NM_001290454, exon 4 of 6)	30554	NM_023305	67123	Mm.289795	NM_023305	ENSMUSG00000028437	Ubap1	2700092A01Rik|NAG20|UBAP-1|Ubap	ubiquitin-associated protein 1	protein-coding
mm_102012.1	chr11	51606841	51606857	-	1	NA	promoter-TSS (NM_010448)	promoter-TSS (NM_010448)	32	NM_001048061	15384	Mm.256875	NM_010448	ENSMUSG00000020358	Hnrnpab	3010025C11Rik|CBF-A|Cgbfa|Hnrpab	heterogeneous nuclear ribonucleoprotein A/B	protein-coding
mm_48762.1	chr5	148379569	148379572	-	1	NA	intron (NM_007513, intron 1 of 12)	intron (NM_007513, intron 1 of 12)	13245	NM_001301424	11987	Mm.275489	NM_007513	ENSMUSG00000041313	Slc7a1	4831426K01Rik|AI447493|Atrc-1|Atrc1|Cat1|Rec-1|Rev-1|mCAT-1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 1	protein-coding
mm_59041.1	chr7	19345085	19345127	+	1	NA	promoter-TSS (NM_007948)	promoter-TSS (NM_007948)	35	NM_007948	13870	Mm.280913	NM_007948	ENSMUSG00000003549	Ercc1	Ercc-1	excision repair cross-complementing rodent repair deficiency, complementation group 1	protein-coding
mm_9847.1	chr1	184732160	184732187	-	1	NA	5' UTR (NM_008250, exon 1 of 4)	5' UTR (NM_008250, exon 1 of 4)	320	NM_008250	15284	Mm.1347	NM_008250	ENSMUSG00000039377	Hlx	Hlx1	H2.0-like homeobox	protein-coding
mm_58001.1	chr6	136173531	136173550	-	1	NA	promoter-TSS (NM_008171)	promoter-TSS (NM_008171)	-29	NM_008171	14812	Mm.436649	NM_008171	ENSMUSG00000030209	Grin2b	AW490526|GluN2B|NR2B|Nmdar2b	glutamate receptor, ionotropic, NMDA2B (epsilon 2)	protein-coding
mm_41979.1	chr5	107497763	107497802	+	1	NA	promoter-TSS (NM_001007574)	promoter-TSS (NM_001007574)	3	NM_001168557	231570	Mm.261891	NM_001007574	ENSMUSG00000044060	A830010M20Rik	AI849226|Kiaa1107|mKIAA1107	RIKEN cDNA A830010M20 gene	protein-coding
mm_4655.1	chr1	180345985	180346003	+	1	NA	intron (NM_001081175, intron 2 of 7)	intron (NM_001081175, intron 2 of 7)	-15445	NR_003623	277333	Mm.389223	NM_199472		Gm5069	EG277333	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_23919.1	chr3	83055517	83055565	+	1	NA	promoter-TSS (NM_016784)	promoter-TSS (NM_016784)	3	NM_016784	53317	Mm.286349	NM_016784	ENSMUSG00000027998	Plrg1	AA958940|C80566|Tango4	pleiotropic regulator 1	protein-coding
mm_45987.1	chr5	90492757	90492765	-	1	NA	exon (NM_007423, exon 3 of 15)	exon (NM_007423, exon 3 of 15)	2047	NM_007423	11576	Mm.358570	NM_007423	ENSMUSG00000054932	Afp	-	alpha fetoprotein	protein-coding
mm_51279.1	chr6	72153672	72153691	+	1	NA	3' UTR (NM_011375, exon 7 of 7)	3' UTR (NM_011375, exon 7 of 7)	-30484	NR_045165	71265	Mm.442035	NR_045163	ENSMUSG00000108709	4933431G14Rik	4930565C19Rik	RIKEN cDNA 4933431G14 gene	ncRNA
mm_15956.1	chr2	165992679	165992687	+	1	NA	promoter-TSS (NM_008679)	promoter-TSS (NM_008679)	46	NM_008679	17979	Mm.469663	NM_008679	ENSMUSG00000027678	Ncoa3	2010305B15Rik|AW321064|Actr|Aib1|KAT13B|Rac3|Src3|Tram-1|Tram1|bHLHe42|p/Cip|pCip	nuclear receptor coactivator 3	protein-coding
mm_31285.1	chr4	45849022	45849037	+	1	NA	promoter-TSS (NM_028788)	promoter-TSS (NM_028788)	82	NM_028788	74152	Mm.63645	NM_028788	ENSMUSG00000028327	Stra6l	1300002K09Rik|Rbpr2	STRA6-like	protein-coding
mm_39382.1	chr5	13125514	13125537	+	1	NA	Intergenic	Intergenic	-271259	NM_001243072	20346	Mm.372039	NM_009152	ENSMUSG00000028883	Sema3a	Hsema-I|SEMA1|SemD|Semad|coll-1	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	protein-coding
mm_90496.1	chr10	128035331	128035338	+	1	NA	promoter-TSS (NM_013608)	promoter-TSS (NM_013608)	-12	NM_013608	17938	Mm.3746	NM_013608	ENSMUSG00000061315	Naca	AL022831|AL024382|Gm1878|mKIAA0363|skNAC	nascent polypeptide-associated complex alpha polypeptide	protein-coding
mm_95700.1	chr11	54401014	54401036	+	1	NA	intron (NM_029105, intron 9 of 13)	intron (NM_029105, intron 9 of 13)	30373	NM_029105	74847	Mm.486538	NM_029105	ENSMUSG00000020332	Meikin	4930404A10Rik	meiotic kinetochore factor	protein-coding
mm_140656.1	chr17	12764014	12764016	-	1	NA	intron (NM_010515, intron 1 of 47)	intron (NM_010515, intron 1 of 47)	5691	NM_010515	16004	Mm.26553	NM_010515	ENSMUSG00000023830	Igf2r	AI661837|CD222|CI-MPR|M6P/IGF2R|Mpr300	insulin-like growth factor 2 receptor	protein-coding
mm_91951.1	chr10	61099032	61099043	-	1	NA	3' UTR (NM_001316673, exon 15 of 15)	3' UTR (NM_001316673, exon 15 of 15)	9706	NM_025273	13180	Mm.39473	NM_025273	ENSMUSG00000020098	Pcbd1	Dcoh|Pcbd|Pcd|Phs	pterin 4 alpha carbinolamine dehydratase/dimerization cofactor of hepatocyte nuclear factor 1 alpha (TCF1) 1	protein-coding
mm_10673.1	chr2	21306895	21306896	+	1	NA	Intergenic	Intergenic	-60672	NM_001004761	241263	Mm.166647	NM_175706	ENSMUSG00000045967	Gpr158	5330427M13Rik|mKIAA1136	G protein-coupled receptor 158	protein-coding
mm_148048.1	chr18	71255215	71255223	-	1	NA	3' UTR (NM_007831, exon 29 of 29)	3' UTR (NM_007831, exon 29 of 29)	686927	NM_010773	17191	Mm.322	NM_010773	ENSMUSG00000024513	Mbd2	MBD2a	methyl-CpG binding domain protein 2	protein-coding
mm_140995.1	chr17	24885873	24885893	-	1	NA	promoter-TSS (NM_001163750)	promoter-TSS (NM_001163750)	467	NM_011956	26426	Mm.36718	NM_011956	ENSMUSG00000039183	Nubp2	D17Wsu11e	nucleotide binding protein 2	protein-coding
mm_89214.1	chr10	86731754	86731756	+	1	NA	TTS (NM_153595)	TTS (NM_153595)	18990	NM_153595	103220	Mm.440762	NM_153595	ENSMUSG00000044937	Ttc41	AI449705|AU041509|Gnn	tetratricopeptide repeat domain 41	protein-coding
mm_110426.1	chr12	46818983	46819004	-	1	NA	promoter-TSS (NM_021361)	promoter-TSS (NM_021361)	-218	NM_021361	664883	Mm.247195	NM_021361	ENSMUSG00000021047	Nova1	9430099M15Rik|G630039L02|Nova-1	neuro-oncological ventral antigen 1	protein-coding
mm_104790.1	chr11	98707758	98707777	-	1	NA	exon (NM_011869, exon 20 of 26)	exon (NM_011869, exon 20 of 26)	6454	NM_009971	12985	Mm.1238	NM_009971	ENSMUSG00000038067	Csf3	Csfg|G-CSF|MGI-IG	colony stimulating factor 3 (granulocyte)	protein-coding
mm_154619.1	chrX	7722215	7722257	+	1	NA	promoter-TSS (NM_172372)	promoter-TSS (NM_172372)	16	NM_001290792	54636	Mm.305725	NM_172372	ENSMUSG00000039382	Wdr45	C79260|DXImx38e|JM5|Sfc19|WIPI-4|Wdrx1	WD repeat domain 45	protein-coding
mm_61197.1	chr7	63936686	63936695	+	1	NA	intron (NM_021366, intron 1 of 1)	intron (NM_021366, intron 1 of 1)	2225	NM_021366	50794	Mm.240473	NM_021366	ENSMUSG00000052040	Klf13	0610043C13Rik|9430029L20Rik|Bteb3|FKLF-2|FKLF2|NSLP1|RFLAT-1|RFLAT1	Kruppel-like factor 13	protein-coding
mm_6982.1	chr1	86356639	86356651	-	1	NA	promoter-TSS (NR_002851)	promoter-TSS (NR_002851)	-318	NR_002851	80828		NR_002851	ENSMUSG00000064823	Snord82	Rnu82|U82|Z25	small nucleolar RNA, C/D box 82	snoRNA
mm_89282.1	chr10	87864872	87864902	+	1	NA	exon (NM_010512, exon 2 of 5)	exon (NM_010512, exon 2 of 5)	3776	NM_001111276	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_57328.1	chr6	124738851	124738877	-	1	NA	promoter-TSS (NM_001077705)	promoter-TSS (NM_001077705)	-155	NM_001077705	15170	Mm.271799	NM_013545	ENSMUSG00000004266	Ptpn6	70Z-SHP|Hcph|PTPTY-42|Ptp1C|SH-PTP1|SHP-1|hcp|me	protein tyrosine phosphatase, non-receptor type 6	protein-coding
mm_33534.1	chr4	130932419	130932436	+	1	NA	intron (NM_010686, intron 7 of 7)	intron (NM_010686, intron 7 of 7)	-11958	NM_010769	17180	Mm.271796	NM_010769	ENSMUSG00000040533	Matn1	CMP|Crtm|Mat1|matrilin-1	matrilin 1, cartilage matrix protein	protein-coding
mm_60335.1	chr7	44335676	44335687	+	1	NA	intron (NM_001034115, intron 15 of 24)	C-rich|Low_complexity|Low_complexity	25417	NM_001034115	243961	Mm.360368	NM_001034115	ENSMUSG00000038738	Shank1	-	SH3/ankyrin domain gene 1	protein-coding
mm_95933.1	chr11	58380562	58380619	+	1	NA	promoter-TSS (NM_001330197)	promoter-TSS (NM_001330197)	-56	NM_001330197	70163	Mm.24119	NM_027339	ENSMUSG00000013643	Lypd8	2210415F13Rik	LY6/PLAUR domain containing 8	protein-coding
mm_96184.1	chr11	61669029	61669033	+	1	NA	intron (NM_027817, intron 3 of 4)	intron (NM_027817, intron 3 of 4)	-15379	NM_178618	69640	Mm.458559	NM_178618	ENSMUSG00000042377	Fam83g	2310040C09Rik|AI506990|wly	family with sequence similarity 83, member G	protein-coding
mm_137349.1	chr17	25184611	25184618	+	1	NA	promoter-TSS (NM_183150)	promoter-TSS (NM_183150)	53	NM_183150	214489	Mm.274433	NM_183150	ENSMUSG00000067722	BC003965	Ccsmst1	cDNA sequence BC003965	protein-coding
mm_134219.1	chr16	11254146	11254158	-	1	NA	TTS (NR_035466)	TTS (NR_035466)	173	NM_001130008	14852	Mm.325827	NM_146066	ENSMUSG00000062203	Gspt1	AI314175|AI326449|AV307676|C79774|G1st|Gst-1	G1 to S phase transition 1	protein-coding
mm_129993.1	chr15	86169830	86169842	-	1	NA	intron (NM_145475, intron 1 of 12)	intron (NM_145475, intron 1 of 12)	16305	NM_145475	223753	Mm.222685	NM_145475	ENSMUSG00000035891	Cerk	AI848610|D330016D08Rik|mKIAA1646	ceramide kinase	protein-coding
mm_58756.1	chr7	13398151	13398168	+	1	NA	promoter-TSS (NM_013877)	promoter-TSS (NM_013877)	4	NM_013877	29865	Mm.103669	NM_013877	ENSMUSG00000005649	Cabp5	-	calcium binding protein 5	protein-coding
mm_71770.1	chr8	66443322	66443325	+	1	NA	intron (NM_175188, intron 6 of 7)	MER2|DNA|TcMar-Tigger	43184	NM_025465	66282	Mm.294985	NM_025465	ENSMUSG00000025591	Tma16	1810029B16Rik	translation machinery associated 16	protein-coding
mm_152733.1	chr19	18936598	18936606	-	1	NA	3' UTR (NM_001289921, exon 11 of 11)	3' UTR (NM_001289921, exon 11 of 11)	64515	NM_146095	225998	Mm.234641	NM_146095	ENSMUSG00000036192	Rorb	Nr1f2|RZR-beta|RZRB|Rorbeta|hstp	RAR-related orphan receptor beta	protein-coding
mm_33239.1	chr4	127023440	127023460	+	1	NA	exon (NM_023603, exon 3 of 10)	exon (NM_023603, exon 3 of 10)	2149	NM_023603	71514	Mm.257276	NM_023603	ENSMUSG00000028820	Sfpq	1110004P21Rik|2810416M14Rik|5730453G22Rik|9030402K04Rik|AU021830|D4Ertd314e|Gm12940|OTTMUSG00000009329|PSF|REP1	splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)	protein-coding
mm_112047.1	chr12	111712880	111712904	-	1	NA	promoter-TSS (NM_026511)	promoter-TSS (NM_026511)	61	NM_001324481	70369	Mm.44239	NM_027404	ENSMUSG00000049792	Bag5	1600025G07Rik|4930405J06Rik|Bag-5	BCL2-associated athanogene 5	protein-coding
mm_145681.1	chr18	61589216	61589228	+	1	NA	TTS (NM_146087)	TTS (NM_146087)	33640	NM_146087	93687	Mm.26908	NM_146087	ENSMUSG00000024576	Csnk1a1	2610208K14Rik|4632404G05Rik|5430427P18Rik|CK1a|Csnk1a	casein kinase 1, alpha 1	protein-coding
mm_106642.1	chr11	121038307	121038311	-	1	NA	exon (NM_009854, exon 2 of 4)	exon (NM_009854, exon 2 of 4)	1169	NM_009854	12516	Mm.4100	NM_009854	ENSMUSG00000025163	Cd7	-	CD7 antigen	protein-coding
mm_32334.1	chr4	104367640	104367642	+	1	NA	non-coding (NR_104385, exon 1 of 16)	non-coding (NR_104385, exon 1 of 16)	103	NM_177259	13131	Mm.289682	NM_010014	ENSMUSG00000028519	Dab1	AI956902|C630028C02Rik|scm|scr|scrambler|yot	disabled 1	protein-coding
mm_151032.1	chr19	47015220	47015289	+	1	NA	promoter-TSS (NM_001164363)	promoter-TSS (NM_001164363)	-65	NM_001164363	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_138241.1	chr17	34564301	34564319	+	1	NA	promoter-TSS (NM_010929)	promoter-TSS (NM_010929)	15	NM_010929	18132	Mm.173813	NM_010929	ENSMUSG00000015468	Notch4	Int-3|Int3|N4	notch 4	protein-coding
mm_114065.1	chr13	54380287	54380303	+	1	NA	3' UTR (NM_009946, exon 4 of 4)	3' UTR (NM_009946, exon 4 of 4)	8946	NM_009946	12890	Mm.268902	NM_009946	ENSMUSG00000025867	Cplx2	921-L|AI413745|AW492120	complexin 2	protein-coding
mm_161532.1	chr15	102366920	102366920	-	1	NA	promoter-TSS (NM_130458)	promoter-TSS (NM_130458)	-649	NM_130458	170574	Mm.263284	NM_130458	ENSMUSG00000060284	Sp7	6430578P22Rik|C22|Osx	Sp7 transcription factor 7	protein-coding
mm_104984.1	chr11	100265077	100265085	-	1	NA	intron (NM_212483, intron 4 of 7)	intron (NM_212483, intron 4 of 7)	-4052	NM_010663	16667	Mm.14046	NM_010663	ENSMUSG00000035557	Krt17	K17|Krt1-17	keratin 17	protein-coding
mm_85759.1	chr9	108649601	108649609	-	1	NA	promoter-TSS (NM_011790)	promoter-TSS (NM_011790)	-225	NM_011790	23807	Mm.290447	NM_011790	ENSMUSG00000064145	Arih2	AI843547|ARI2|TRIAD1|UIP48	ariadne RBR E3 ubiquitin protein ligase 2	protein-coding
mm_123591.1	chr14	67336161	67336198	-	1	NA	intron (NR_045961, intron 5 of 5)	intron (NR_045961, intron 5 of 5)	-21468	NM_001037931	628416	Mm.390723	NM_001037931		Gm6878	EG628416	predicted gene 6878	protein-coding
mm_90073.1	chr10	116377632	116377632	+	1	NA	intron (NM_029928, intron 30 of 31)	intron (NM_029928, intron 30 of 31)	-40489	NR_028107	67342	Mm.245800	NM_026098	ENSMUSG00000020164	Kcnmb4os1	1700058G18Rik	potassium large conductance calcium-activated channel, subfamily M, beta member 4, opposite strand 1	ncRNA
mm_50620.1	chr6	50110895	50110926	+	1	NA	intron (NM_019939, intron 1 of 12)	intron (NM_019939, intron 1 of 12)	669	NM_001164733	56524	Mm.41288	NM_008016	ENSMUSG00000038388	Mpp6	P55t|Pals2	membrane protein, palmitoylated 6 (MAGUK p55 subfamily member 6)	protein-coding
mm_134628.1	chr16	21650202	21650213	-	1	NA	3' UTR (NM_001001881, exon 2 of 2)	3' UTR (NM_001001881, exon 2 of 2)	44458	NM_001001881	72190	Mm.131606	NM_001001881	ENSMUSG00000043391	2510009E07Rik	AI194952	RIKEN cDNA 2510009E07 gene	protein-coding
mm_117287.1	chr13	66244102	66244113	-	1	NA	Intergenic	Intergenic	130654	NM_001177832	628709	Mm.390595	NM_001177832	ENSMUSG00000095909	Gm10324	ENSMUSG00000071302	predicted gene 10324	protein-coding
mm_86459.1	chr10	4355436	4355470	+	1	NA	exon (NM_031185, exon 3 of 4)	exon (NM_031185, exon 3 of 4)	32655	NM_001033466	381990	Mm.262466	NM_001033466	ENSMUSG00000075327	Zbtb2	Gm1103	zinc finger and BTB domain containing 2	protein-coding
mm_61786.1	chr7	83799457	83799458	+	1	NA	Intergenic	Intergenic	-4618	NM_029335	75556	Mm.17649	NM_029335	ENSMUSG00000011154	Cfap161	1700026D08Rik|AW047638|AW551802	cilia and flagella associated protein 161	protein-coding
mm_93400.1	chr10	107719908	107719957	-	1	NA	promoter-TSS (NM_001081432)	promoter-TSS (NM_001081432)	95	NM_001081432	237523	Mm.391418	NM_001081432	ENSMUSG00000035916	Ptprq	-	protein tyrosine phosphatase, receptor type, Q	protein-coding
mm_14593.1	chr2	136058139	136058149	+	1	NA	5' UTR (NM_029530, exon 1 of 6)	5' UTR (NM_029530, exon 1 of 6)	217	NM_029530	76161	Mm.41638	NM_029530	ENSMUSG00000027270	Lamp5	3110035N03Rik|6330527O06Rik|BAD-LAMP|LAMP-5	lysosomal-associated membrane protein family, member 5	protein-coding
mm_69946.1	chr7	142241136	142241140	-	1	NA	Intergenic	Intergenic	-11167	NM_001037822	114666	Mm.444495	NM_001037822	ENSMUSG00000073785	Krtap5-5	A030001H12Rik|AI586182|BB149782	keratin associated protein 5-5	protein-coding
mm_8591.1	chr1	156005875	156005888	-	1	NA	3' UTR (NM_144791, exon 7 of 7)	3' UTR (NM_144791, exon 7 of 7)	28936	NM_001160019	208263	Mm.211654	NM_144791	ENSMUSG00000026466	Tor1aip1	LAP1|Lap1B	torsin A interacting protein 1	protein-coding
mm_34176.1	chr4	140699867	140699882	+	1	NA	Intergenic	Intergenic	-1599	NM_173867	108911	Mm.253	NM_173867	ENSMUSG00000040945	Rcc2	2610510H01Rik|2610529N02Rik|AA536646|AA675016|Td60|mKIAA1470	regulator of chromosome condensation 2	protein-coding
mm_25392.1	chr3	107218681	107218689	+	1	NA	exon (NM_001111143, exon 3 of 9)	exon (NM_001111143, exon 3 of 9)	3047	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_82947.1	chr9	35558398	35558451	-	1	NA	promoter-TSS (NM_013932)	promoter-TSS (NM_013932)	46	NM_013932	30959	Mm.291723	NM_013932	ENSMUSG00000032101	Ddx25	AW047046|GRTH	DEAD (Asp-Glu-Ala-Asp) box polypeptide 25	protein-coding
mm_171283.1	chr3	89715714	89715715	+	1	NA	intron (NM_001038587, intron 1 of 14)	intron (NM_001038587, intron 1 of 14)	692	NM_001038587	56417	Mm.316628	NM_019655	ENSMUSG00000027951	Adar	AV242451|Adar1|Adar1p110|Adar1p150|mZaADAR	adenosine deaminase, RNA-specific	protein-coding
mm_71374.1	chr8	45791511	45791513	+	1	NA	intron (NM_172752, intron 13 of 22)	intron (NM_172752, intron 13 of 22)	27785	NR_045739	319940	Mm.441720	NR_045739	ENSMUSG00000085440	Sorbs2os	D330022K07Rik	sorbin and SH3 domain containing 2, opposite strand	ncRNA
mm_38406.1	chr4	139085568	139085600	-	1	NA	exon (NM_008675, exon 2 of 4)	exon (NM_008675, exon 2 of 4)	7386	NM_008675	17965	Mm.9404	NM_008675	ENSMUSG00000041120	Nbl1	D4H1S1733E|DAN|Dana|NO3	neuroblastoma, suppression of tumorigenicity 1	protein-coding
mm_10000.1	chr1	191465324	191465343	-	1	NA	Intergenic	Intergenic	-68292	NM_144880	226849	Mm.205569	NM_144880	ENSMUSG00000026626	Ppp2r5a	PR61alpha	protein phosphatase 2, regulatory subunit B', alpha	protein-coding
mm_48905.1	chr6	3526669	3526679	+	1	NA	intron (NM_001167750, intron 9 of 27)	intron (NM_001167750, intron 9 of 27)	28281	NM_001167750	73288	Mm.45539	NM_024260	ENSMUSG00000001376	Vps50	1700034M03Rik|8430415E05Rik|BLM|C87205|Ccdc132|mKIAA1861	VPS50 EARP/GARPII complex subunit	protein-coding
mm_138069.1	chr17	33940716	33940729	+	1	NA	promoter-TSS (NM_010385)	promoter-TSS (NM_010385)	-1	NM_020603	57315	Mm.2437	NM_020603	ENSMUSG00000024312	Wdr46	2310007I04Rik|Bing4|C78447|C78559	WD repeat domain 46	protein-coding
mm_109139.1	chr12	106459135	106459157	+	1	NA	Intergenic	Intergenic	-11480	NR_036593	76639	Mm.375609	NR_036593	ENSMUSG00000092066	1700121N20Rik	-	RIKEN cDNA 1700121N20 gene	ncRNA
mm_68006.1	chr7	100938829	100938890	-	1	NA	exon (NM_183168, exon 3 of 3)	exon (NM_183168, exon 3 of 3)	-6698	NM_001081116	207212	Mm.29954	NM_001081116	ENSMUSG00000032875	Arhgef17	8030463K16|AI428794|AW558066|BC035332|mKIAA0337	Rho guanine nucleotide exchange factor (GEF) 17	protein-coding
mm_32066.1	chr4	97777873	97777881	+	1	NA	5' UTR (NM_001122953, exon 1 of 10)	5' UTR (NM_001122953, exon 1 of 10)	251	NM_010905	18027	Mm.31274	NM_010905	ENSMUSG00000028565	Nfia	1110047K16Rik|9430022M17Rik|CTF|NF1-A|NF1A	nuclear factor I/A	protein-coding
mm_22711.1	chr3	19188100	19188108	+	1	NA	promoter-TSS (NM_026182)	promoter-TSS (NM_026182)	-117	NM_026182	67472	Mm.45125	NM_026182	ENSMUSG00000027601	Mtfr1	1300002C08Rik|1700080D04Rik|2810026O10Rik|4930579E05Rik|Chppr|Fam54a2	mitochondrial fission regulator 1	protein-coding
mm_22560.1	chr3	9886978	9886988	+	1	NA	Intergenic	MER20|DNA|hAT-Charlie	-53304	NM_001195031	94212	Mm.23897	NM_053182	ENSMUSG00000027508	Pag1	Cbp|F730007C19Rik|Pag	phosphoprotein associated with glycosphingolipid microdomains 1	protein-coding
mm_49686.1	chr6	33374630	33374645	+	1	NA	intron (NM_001347089, intron 7 of 9)	intron (NM_001347089, intron 7 of 9)	125487	NM_009148	20336	Mm.265512	NM_009148	ENSMUSG00000029763	Exoc4	C78892|Sec8|Sec8l1	exocyst complex component 4	protein-coding
mm_163401.1	chr12	73202012	73202053	+	1	NA	intron (NM_008612, intron 6 of 7)	intron (NM_008612, intron 6 of 7)	78315	NM_008612	17420	Mm.246750	NM_008612	ENSMUSG00000021103	Mnat1	E130115E11Rik|MAT1|P36	menage a trois 1	protein-coding
mm_65059.1	chr7	18798505	18798516	-	1	NA	promoter-TSS (NM_011964)	promoter-TSS (NM_011964)	0	NM_011964	26439	Mm.36878	NM_011964	ENSMUSG00000004542	Psg19	CGM7|Cea-4|Cea4	pregnancy specific glycoprotein 19	protein-coding
mm_164528.1	chr17	6006477	6006487	+	1	NA	intron (NM_001113352, intron 7 of 25)	intron (NM_001113352, intron 7 of 25)	-1098	NM_001290698	20975	Mm.236068	NM_011523	ENSMUSG00000023805	Synj2	AI481647|SJ2|mKIAA0348	synaptojanin 2	protein-coding
mm_135248.1	chr16	37539738	37539751	-	1	NA	promoter-TSS (NM_001042499)	promoter-TSS (NM_001042499)	25	NM_028812	74197	Mm.287795	NM_028812	ENSMUSG00000022828	Gtf2e1	2610024P03Rik|56kDa|AI303800|FE|TFIIE-A	general transcription factor II E, polypeptide 1 (alpha subunit)	protein-coding
mm_42090.1	chr5	110261475	110261479	+	1	NA	intron (NM_028273, intron 5 of 5)	ID_B1|SINE|B4	8422	NM_028273	72542	Mm.61682	NM_028273	ENSMUSG00000029500	Pgam5	2610528A17Rik	phosphoglycerate mutase family member 5	protein-coding
mm_1283.1	chr1	64053712	64053716	+	1	NA	intron (NM_033563, intron 2 of 3)	intron (NM_033563, intron 2 of 3)	-11213	NR_105864	102466760		NR_105864	ENSMUSG00000098487	Mir6899	Gm27384|mmu-mir-6899	microRNA 6899	ncRNA
mm_16889.1	chr2	13011757	13011778	-	1	NA	promoter-TSS (NM_153155)	promoter-TSS (NM_153155)	-903	NM_153155	227580	Mm.229322	NM_153155	ENSMUSG00000049630	C1ql3	1110065A22Rik|AI661623|C1ql|C1qtnf13|CTRP13|K100	C1q-like 3	protein-coding
mm_149366.1	chr19	11356091	11356103	+	1	NA	Intergenic	Intergenic	-19391	NM_001310331	666907		NM_001310331	ENSMUSG00000101389	Ms4a4a	EG666907	membrane-spanning 4-domains, subfamily A, member 4A	protein-coding
mm_27229.1	chr3	36450662	36450705	-	1	NA	exon (NM_009673, exon 11 of 13)	exon (NM_009673, exon 11 of 13)	24841	NR_105976	102466786		NR_105976	ENSMUSG00000098808	Mir7009	Gm27472|mmu-mir-7009	microRNA 7009	ncRNA
mm_95173.1	chr11	40734172	40734191	+	1	NA	promoter-TSS (NM_013552)	promoter-TSS (NM_013552)	520	NM_001290697	52653	Mm.276504	NM_026023	ENSMUSG00000020328	Nudcd2	-	NudC domain containing 2	protein-coding
mm_143683.1	chr17	80062200	80062247	-	1	NA	promoter-TSS (NM_144802)	promoter-TSS (NM_144802)	45	NM_144802	72692	Mm.64579	NM_144802	ENSMUSG00000024095	Hnrnpll	2510028H02Rik|2810036L13Rik|AI256697|AI852082|Hnrpll	heterogeneous nuclear ribonucleoprotein L-like	protein-coding
mm_148547.1	chr19	4711359	4711361	+	1	NA	5' UTR (NM_021287, exon 1 of 37)	5' UTR (NM_021287, exon 1 of 37)	137	NM_021287	20743	Mm.329668	NM_021287	ENSMUSG00000067889	Sptbn2	Spnb3|mKIAA0302	spectrin beta, non-erythrocytic 2	protein-coding
mm_53445.1	chr6	134414437	134414458	+	1	NA	intron (NM_025778, intron 2 of 6)	intron (NM_025778, intron 2 of 6)	18118	NM_025778	66813	Mm.474472	NM_025778	ENSMUSG00000030200	Bcl2l14	4930452K23Rik|4933405K19Rik|9030625M01Rik|AI429211|Bclg	BCL2-like 14 (apoptosis facilitator)	protein-coding
mm_124639.1	chr15	4375627	4375656	+	1	NA	5' UTR (NM_177355, exon 1 of 3)	5' UTR (NM_177355, exon 1 of 3)	150	NM_177355	239318	Mm.308996	NM_177355	ENSMUSG00000049148	Plcxd3	B130016O10Rik	phosphatidylinositol-specific phospholipase C, X domain containing 3	protein-coding
mm_29060.1	chr3	103778258	103778277	-	1	NA	non-coding (NR_125731, exon 2 of 16)	non-coding (NR_125731, exon 2 of 16)	13008	NM_001301306	15257	Mm.20827	NM_010432	ENSMUSG00000008730	Hipk1	1110062K04Rik|Myak	homeodomain interacting protein kinase 1	protein-coding
mm_21701.1	chr2	164564179	164564215	-	1	NA	exon (NM_026323, exon 3 of 5)	exon (NM_026323, exon 3 of 5)	1481	NM_026323	67701	Mm.27289	NM_026323	ENSMUSG00000017723	Wfdc2	1600023A02Rik|HE4|WAP5	WAP four-disulfide core domain 2	protein-coding
mm_111892.1	chr12	108275410	108275417	-	1	NA	promoter-TSS (NM_001159910)	promoter-TSS (NM_001159910)	4	NM_001159910	668158	Mm.482792	NM_001159910	ENSMUSG00000084883	Ccdc85c	EG668158|Gm265|Gm9010	coiled-coil domain containing 85C	protein-coding
mm_65653.1	chr7	28131752	28131768	-	1	NA	exon (NM_001164655, exon 3 of 20)	exon (NM_001164655, exon 3 of 20)	2294	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_113632.1	chr13	42051285	42051322	+	1	NA	promoter-TSS (NM_007772)	promoter-TSS (NM_007772)	-718	NM_007772	110521	Mm.4808	NM_007772	ENSMUSG00000021366	Hivep1	Cryabp1	human immunodeficiency virus type I enhancer binding protein 1	protein-coding
mm_69526.1	chr7	135652094	135652113	-	1	NA	exon (NM_011212, exon 5 of 21)	exon (NM_011212, exon 5 of 21)	204	NM_001316681	19267	Mm.945	NM_011212	ENSMUSG00000041836	Ptpre	PTPe|PTPepsilon|RPTPepsilon	protein tyrosine phosphatase, receptor type, E	protein-coding
mm_18738.1	chr2	72997194	72997207	-	1	NA	Intergenic	Intergenic	-16754	NM_001018042	20687	Mm.124328	NM_011450	ENSMUSG00000027109	Sp3	D130027J01Rik	trans-acting transcription factor 3	protein-coding
mm_101063.1	chr11	9048515	9048521	-	1	NA	promoter-TSS (NM_001037928)	promoter-TSS (NM_001037928)	-74	NM_001037928	626870	Mm.369429	NM_001037928	ENSMUSG00000040978	Gm11992	OTTMUSG00000005148	predicted gene 11992	protein-coding
mm_103127.1	chr11	70220970	70221027	-	1	NA	promoter-TSS (NM_172371)	promoter-TSS (NM_172371)	-4	NM_172371	69309	Mm.93266	NM_172371	ENSMUSG00000044367	Slc16a13	1700007D07Rik	solute carrier family 16 (monocarboxylic acid transporters), member 13	protein-coding
mm_145421.1	chr18	58556091	58556100	+	1	NA	promoter-TSS (NM_001081072)	promoter-TSS (NM_001081072)	-145	NM_001081072	225579	Mm.258517	NM_001081072	ENSMUSG00000024600	Slc27a6	4732438L20Rik|FACVL2|FATP6|VLCS-H1	solute carrier family 27 (fatty acid transporter), member 6	protein-coding
mm_19860.1	chr2	113829678	113829685	-	1	NA	promoter-TSS (NM_009162)	promoter-TSS (NM_009162)	-590	NM_009162	20394	Mm.4836	NM_009162	ENSMUSG00000023236	Scg5	7B2|AI325031|Sgne-1|Sgne1	secretogranin V	protein-coding
mm_139495.1	chr17	56225192	56225204	+	1	NA	Intergenic	Intergenic	-6309	NM_172624	224897	Mm.205535	NM_172624	ENSMUSG00000001229	Dpp9	6430584G11Rik|A330078I11|DPP IX|DPRP2	dipeptidylpeptidase 9	protein-coding
mm_3140.1	chr1	135133854	135133885	+	1	NA	exon (NM_177081, exon 2 of 10)	exon (NM_177081, exon 2 of 10)	1144	NM_177081	320139	Mm.258388	NM_177081	ENSMUSG00000031506	Ptpn7	BPTP-4|C920001D21Rik|HEPTP|LC-PTP|LPTP	protein tyrosine phosphatase, non-receptor type 7	protein-coding
mm_24512.1	chr3	92598677	92598698	+	1	NA	Intergenic	Lx7|LINE|L1	-9663	NM_008574	17235	Mm.331192	NM_008574		Smcp	Mcs|Mcsp	sperm mitochondria-associated cysteine-rich protein	protein-coding
mm_77858.1	chr9	5312870	5312880	+	1	NA	intron (NM_007609, intron 1 of 8)	L1M2|LINE|L1	4026	NM_007609	12363	Mm.1569	NM_007609	ENSMUSG00000033538	Casp4	CASP-11|CASP-4|Casp11|Caspl|ich-3	caspase 4, apoptosis-related cysteine peptidase	protein-coding
mm_1208.1	chr1	62726479	62726494	+	1	NA	intron (NM_001077405, intron 2 of 15)	MIRb|SINE|MIR	23169	NM_001077405	18187	Mm.266341	NM_010939	ENSMUSG00000025969	Nrp2	1110048P06Rik|Np-2|Np2|Npn-2|Npn2	neuropilin 2	protein-coding
mm_6349.1	chr1	71643077	71643126	-	1	NA	exon (NM_001276413, exon 7 of 44)	exon (NM_001276413, exon 7 of 44)	10133	NM_010233	14268	Mm.193099	NM_010233	ENSMUSG00000026193	Fn1	E330027I09|Fn|Fn-1	fibronectin 1	protein-coding
mm_100439.1	chr11	119486295	119486335	+	1	NA	Intergenic	Intergenic	-5032	NM_001164636	338371	Mm.271946	NM_177394	ENSMUSG00000039850	Endov	A730011L01Rik	endonuclease V	protein-coding
mm_78001.1	chr9	8901700	8901784	+	1	NA	exon (NM_008829, exon 1 of 8)	exon (NM_008829, exon 1 of 8)	1909	NM_008829	18667	Mm.12798	NM_008829	ENSMUSG00000031870	Pgr	9930019P03Rik|BB114106|ENSMUSG00000074510|NR3C3|PR|PR-A|PR-B	progesterone receptor	protein-coding
mm_165580.1	chr3	28463680	28463682	+	1	NA	intron (NM_026910, intron 2 of 32)	intron (NM_026910, intron 2 of 32)	43738	NR_130342	100628591		NR_130342	ENSMUSG00000092990	Mir466q	Mir446q|mmu-mir-466q|mu-mir-446q	microRNA 466q	ncRNA
mm_51830.1	chr6	89422242	89422254	+	1	NA	intron (NM_001167736, intron 4 of 6)	intron (NM_001167736, intron 4 of 6)	-59635	NM_008881	18844	Mm.3789	NM_008881	ENSMUSG00000030084	Plxna1	2600013D04Rik|NOV|PlexA1|Plxn1|mKIAA4053	plexin A1	protein-coding
mm_61829.1	chr7	88278127	88278141	+	1	NA	promoter-TSS (NM_009982)	promoter-TSS (NM_009982)	49	NM_001311790	13032	Mm.89295	NM_009982	ENSMUSG00000030560	Ctsc	AI047818|CatC|DPP1|DPPI	cathepsin C	protein-coding
mm_126314.1	chr15	79671137	79671148	+	1	NA	intron (NM_172609, intron 1 of 3)	CpG	274	NM_172609	223696	Mm.246435	NM_172609	ENSMUSG00000022427	Tomm22	2310047D01|Tom22	translocase of outer mitochondrial membrane 22 homolog (yeast)	protein-coding
mm_115822.1	chr13	20091521	20091527	-	1	NA	intron (NM_080288, intron 1 of 21)	CpG	1017	NM_080288	140580	Mm.342392	NM_080288	ENSMUSG00000041112	Elmo1	6330578D22Rik|C230095H21Rik|CED-12	engulfment and cell motility 1	protein-coding
mm_4441.1	chr1	172513246	172513257	+	1	NA	Intergenic	Intergenic	-7879	NM_027972	71870	Mm.78373	NM_027972	ENSMUSG00000026546	Cfap45	1700028D05Rik|Ccdc19|Nesg1	cilia and flagella associated protein 45	protein-coding
mm_17532.1	chr2	29624805	29624810	-	1	NA	intron (NM_001039087, intron 1 of 25)	intron (NM_001039087, intron 1 of 25)	5087	NM_001039086	107746	Mm.298274	NM_054050	ENSMUSG00000039844	Rapgef1	4932418O06Rik|C3G|Grf2	Rap guanine nucleotide exchange factor (GEF) 1	protein-coding
mm_70579.1	chr8	13167201	13167249	+	1	NA	exon (NM_010684, exon 3 of 9)	exon (NM_010684, exon 3 of 9)	8064	NM_010684	16783	Mm.16716	NM_010684	ENSMUSG00000031447	Lamp1	CD107a|LGP-120|LGP-A|Lamp-1|P2B	lysosomal-associated membrane protein 1	protein-coding
mm_16770.1	chr2	9879564	9879586	-	1	NA	promoter-TSS (NM_008091)	promoter-TSS (NM_008091)	-975	NM_008091	14462	Mm.313866	NM_008091	ENSMUSG00000015619	Gata3	Gata-3|jal	GATA binding protein 3	protein-coding
mm_72868.1	chr8	88658076	88658098	+	1	NA	intron (NM_145857, intron 2 of 12)	RMER12C|LTR|ERVK	10740	NM_145857	257632	Mm.222633	NM_145857	ENSMUSG00000055994	Nod2	ACUG|BLAU|CD|Card15|F830032C23Rik|IBD1|Nlrc2	nucleotide-binding oligomerization domain containing 2	protein-coding
mm_158718.1	chrX	162829339	162829373	-	1	NA	promoter-TSS (NM_001290778)	promoter-TSS (NM_001290778)	98	NM_001290776	353170	Mm.270186	NM_178935	ENSMUSG00000038344	Txlng	4932441K18Rik|Fiat|Lrp	taxilin gamma	protein-coding
mm_76299.1	chr8	84237047	84237061	-	1	NA	promoter-TSS (NM_172503)	promoter-TSS (NM_172503)	-12	NM_172503	212168	Mm.117094	NM_172503	ENSMUSG00000035671	Zswim4	D330002I24|E130119J17Rik	zinc finger SWIM-type containing 4	protein-coding
mm_45387.1	chr5	66145746	66145746	-	1	NA	intron (NM_001127382, intron 2 of 7)	intron (NM_001127382, intron 2 of 7)	5232	NM_001291226	245945	Mm.36863	NM_139065	ENSMUSG00000070780	Rbm47	9530077J19Rik	RNA binding motif protein 47	protein-coding
mm_66707.1	chr7	45923189	45923197	-	1	NA	Intergenic	Intergenic	-1767	NM_010129	13732	Mm.20829	NM_010129	ENSMUSG00000040212	Emp3	H-4|H4|HNMP-1|MI-35|Ymp	epithelial membrane protein 3	protein-coding
mm_144321.1	chr18	12741340	12741355	+	1	NA	promoter-TSS (NM_001042420)	promoter-TSS (NM_001042420)	-8	NM_001042419	71132	Mm.179740	NM_027687	ENSMUSG00000024430	Cabyr	1700016C01Rik|4933421A18Rik|CBP86|FSP-2	calcium-binding tyrosine-(Y)-phosphorylation regulated (fibrousheathin 2)	protein-coding
mm_107344.1	chr12	32724723	32724734	+	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-95607	NM_021524	59027	Mm.202727	NM_021524	ENSMUSG00000020572	Nampt	1110035O14Rik|AI314458|AI480535|NAmPRTase|Pbef|Pbef1|Visfatin	nicotinamide phosphoribosyltransferase	protein-coding
mm_128290.1	chr15	37233096	37233109	-	1	NA	promoter-TSS (NM_026496)	promoter-TSS (NM_026496)	66	NM_026496	252973	Mm.244612	NM_026496	ENSMUSG00000022286	Grhl2	0610015A08Rik|BOM|Tcfcp2l3|clft3	grainyhead-like 2 (Drosophila)	protein-coding
mm_114136.1	chr13	55242925	55242927	+	1	NA	intron (NM_008739, intron 4 of 22)	MTB_Mm|LTR|ERVL-MaLR	33144	NM_008739	18193	Mm.12964	NM_008739	ENSMUSG00000021488	Nsd1	AI528500|KMT3B	nuclear receptor-binding SET-domain protein 1	protein-coding
mm_66386.1	chr7	44016106	44016130	-	1	NA	exon (NM_010644, exon 3 of 5)	exon (NM_010644, exon 3 of 5)	3421	NM_010115	13647	Mm.439663	NM_010115		Egfbp2	Egfbp-2|Klk1b26|mGk-13	epidermal growth factor binding protein type B	protein-coding
mm_151864.1	chr19	5797463	5797527	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	-1514	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_173333.1	chrY	90785074	90785074	+	1	NA	promoter-TSS (NR_137282)	promoter-TSS (NR_137282)	-368	NR_137282	170942	Mm.76062	NM_133362	ENSMUSG00000096768	Erdr1	edr	erythroid differentiation regulator 1	protein-coding
mm_159293.1	chr2	174643648	174643648	+	1	NA	exon (NM_001099328, exon 1 of 5)	exon (NM_001099328, exon 1 of 5)	114	NM_001099328	100043757	Mm.48711	NM_001099328	ENSMUSG00000050600	Zfp831	ENSMUSG00000050600|OTTMUSG00000017459	zinc finger protein 831	protein-coding
mm_73264.1	chr8	104345274	104345293	+	1	NA	exon (NM_024217, exon 4 of 5)	exon (NM_024217, exon 4 of 5)	4689	NM_024217	68119	Mm.390108	NM_024217	ENSMUSG00000031875	Cmtm3	9430096L06Rik|AI413895|BNAS2|Cklfsf3	CKLF-like MARVEL transmembrane domain containing 3	protein-coding
mm_82329.1	chr9	9142424	9142427	-	1	NA	intron (NM_027823, intron 3 of 22)	intron (NM_027823, intron 3 of 22)	-93863	NR_045754	100579151	Mm.412450	NR_045754	ENSMUSG00000085253	Gm16833	-	predicted gene, 16833	ncRNA
mm_117244.1	chr13	64363749	64363759	-	1	NA	3' UTR (NM_009984, exon 8 of 8)	3' UTR (NM_009984, exon 8 of 8)	6766	NM_009984	13039	Mm.930	NM_009984	ENSMUSG00000021477	Ctsl	1190035F06Rik|CatL|Ctsl1|MEP|fs|nkt	cathepsin L	protein-coding
mm_108016.1	chr12	73595502	73595528	+	1	NA	intron (NM_001313977, intron 2 of 14)	intron (NM_001313977, intron 2 of 14)	10719	NM_008856	18755	Mm.341677	NM_008856	ENSMUSG00000021108	Prkch	Pkch	protein kinase C, eta	protein-coding
mm_134819.1	chr16	25960031	25960053	-	1	NA	TTS (NM_173379)	TTS (NM_173379)	145742	NM_173379	210530	Mm.326869	NM_173379	ENSMUSG00000038168	P3h2	4832416N06|AW553532|Leprel1|Mlat4	prolyl 3-hydroxylase 2	protein-coding
mm_120843.1	chr14	75197922	75197942	+	1	NA	intron (NM_008879, intron 2 of 16)	intron (NM_008879, intron 2 of 16)	-44355	NM_019775	56373	Mm.24242	NM_019775	ENSMUSG00000021999	Cpb2	1110032P04Rik|4930405E17Rik|AI255929|CPR|Cpu|TAFI	carboxypeptidase B2 (plasma)	protein-coding
mm_102951.1	chr11	69631334	69631343	-	1	NA	Intergenic	Intergenic	-1633	NM_011814	23879	Mm.41930	NM_011814	ENSMUSG00000018765	Fxr2	Fxr2h	fragile X mental retardation, autosomal homolog 2	protein-coding
mm_60297.1	chr7	44016076	44016090	+	1	NA	exon (NM_010644, exon 3 of 5)	exon (NM_010644, exon 3 of 5)	3386	NM_010115	13647	Mm.439663	NM_010115		Egfbp2	Egfbp-2|Klk1b26|mGk-13	epidermal growth factor binding protein type B	protein-coding
mm_92066.1	chr10	62527414	62527435	-	1	NA	Intergenic	Intergenic	-19669	NM_011157	19073	Mm.338790	NM_011157	ENSMUSG00000020077	Srgn	Prg|Prg1|Sgc	serglycin	protein-coding
mm_58171.1	chr6	142702260	142702290	-	1	NA	promoter-TSS (NM_011511)	promoter-TSS (NM_011511)	-1	NM_001310143	20928	Mm.35670	NM_011511	ENSMUSG00000030249	Abcc9	AI414027|AI449286|SUR2A|SUR2B|Sur2	ATP-binding cassette, sub-family C (CFTR/MRP), member 9	protein-coding
mm_40235.1	chr5	37338600	37338619	+	1	NA	exon (NM_145920, exon 1 of 20)	exon (NM_145920, exon 1 of 20)	131	NM_145920	68525	Mm.25506	NM_145920	ENSMUSG00000050248	Evc2	1110017L09Rik|Lbn|limbin	Ellis van Creveld syndrome 2	protein-coding
mm_1439.1	chr1	67215524	67215533	+	1	NA	exon (NM_001080809, exon 32 of 38)	exon (NM_001080809, exon 32 of 38)	92501	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_63102.1	chr7	122628441	122628448	+	1	NA	3' UTR (NM_008855, exon 17 of 17)	3' UTR (NM_008855, exon 17 of 17)	-43300	NM_019430	54376	Mm.444212	NM_019430	ENSMUSG00000066189	Cacng3	-	calcium channel, voltage-dependent, gamma subunit 3	protein-coding
mm_112128.1	chr12	112929795	112929824	-	1	NA	promoter-TSS (NM_010588)	promoter-TSS (NM_010588)	-314	NM_010588	16450	Mm.186146	NM_010588	ENSMUSG00000002799	Jag2	D12Ggc2e|Serh|mJagged2-1|sm	jagged 2	protein-coding
mm_106066.1	chr11	116138776	116138788	-	1	NA	promoter-TSS (NM_024177)	promoter-TSS (NM_024177)	86	NM_024177	60441	Mm.29974	NM_024177	ENSMUSG00000020775	Mrpl38	1110036N21Rik|4733401F03Rik|MRP-L3|R75240|Rpml3	mitochondrial ribosomal protein L38	protein-coding
mm_125248.1	chr15	34674998	34675007	+	1	NA	promoter-TSS (NR_045883)	promoter-TSS (NR_045883)	-71	NR_045883	71637	Mm.410827	NR_045883		4930413F20Rik	-	RIKEN cDNA 4930413F20 gene	ncRNA
mm_70893.1	chr8	25597695	25597705	+	1	NA	promoter-TSS (NM_173012)	promoter-TSS (NM_173012)	-213	NM_173012	270035	Mm.268349	NM_173012	ENSMUSG00000037363	Letm2	6030453H13|D030041N04Rik	leucine zipper-EF-hand containing transmembrane protein 2	protein-coding
mm_65896.1	chr7	30169702	30169766	-	1	NA	promoter-TSS (NM_001033540)	promoter-TSS (NM_001033540)	-7	NM_011980	26465	Mm.446516	NM_011980	ENSMUSG00000037029	Zfp146	OZF|Znf146	zinc finger protein 146	protein-coding
mm_166682.1	chr6	99173378	99173388	-	1	NA	intron (NM_001347345, intron 4 of 19)	intron (NM_001347345, intron 4 of 19)	93132	NM_001197321	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_1828.1	chr1	82676385	82676390	+	1	NA	intron (NM_007734, intron 27 of 51)	intron (NM_007734, intron 27 of 51)	-48503	NM_001310697	75734	Mm.396863	NM_029409	ENSMUSG00000026150	Mff	5230400G24Rik|AI314724	mitochondrial fission factor	protein-coding
mm_28512.1	chr3	92584166	92584176	-	1	NA	exon (NM_008574, exon 2 of 2)	exon (NM_008574, exon 2 of 2)	4853	NM_008574	17235	Mm.331192	NM_008574		Smcp	Mcs|Mcsp	sperm mitochondria-associated cysteine-rich protein	protein-coding
mm_169731.1	chr15	81811414	81811414	+	1	NA	promoter-TSS (NM_017376)	promoter-TSS (NM_017376)	0	NM_017376	21685	Mm.270278	NM_017376	ENSMUSG00000022389	Tef	2310028D20Rik	thyrotroph embryonic factor	protein-coding
mm_106363.1	chr11	118393957	118393970	-	1	NA	exon (NM_011150, exon 6 of 6)	exon (NM_011150, exon 6 of 6)	7968	NM_011150	19039	Mm.3152	NM_011150	ENSMUSG00000033880	Lgals3bp	90K|CyCAP|MAC-2BP|Ppicap|Tango10b	lectin, galactoside-binding, soluble, 3 binding protein	protein-coding
mm_53698.1	chr6	142756824	142756852	+	1	NA	exon (NM_009908, exon 1 of 8)	exon (NM_009908, exon 1 of 8)	152	NM_009908	12764	Mm.3820	NM_009908	ENSMUSG00000030282	Cmas	AW208911|CMPNeu5Ac|D6Bwg0250e	cytidine monophospho-N-acetylneuraminic acid synthetase	protein-coding
mm_136325.1	chr16	92321426	92321446	-	1	NA	promoter-TSS (NM_029252)	promoter-TSS (NM_029252)	5	NM_029252	75328	Mm.72970	NM_029252	ENSMUSG00000051728	4930563D23Rik	-	RIKEN cDNA 4930563D23 gene	protein-coding
mm_163379.1	chr12	48529625	48529632	-	1	NA	Intergenic	Intergenic	-228166	NR_039586	100628593		NR_039586	ENSMUSG00000092981	Mir5125	mmu-mir-5125|mu-mir-5125	microRNA 5125	ncRNA
mm_13965.1	chr2	121424553	121424580	+	1	NA	exon (NM_007952, exon 3 of 13)	exon (NM_007952, exon 3 of 13)	10664	NM_007952	14827	Mm.263177	NM_007952	ENSMUSG00000027248	Pdia3	58kDa|ERp57|ERp60|ERp61|Erp|Grp58|PDI|PDI-Q2|PI-PLC|PLC[a]|Plca	protein disulfide isomerase associated 3	protein-coding
mm_133882.1	chr16	96525391	96525401	+	1	NA	exon (NM_008791, exon 3 of 3)	exon (NM_008791, exon 3 of 3)	57790	NM_008791	18546	Mm.5023	NM_008791	ENSMUSG00000090223	Pcp4	P16Rimb19|Pcp-4|Pep19	Purkinje cell protein 4	protein-coding
mm_42216.1	chr5	113068711	113068724	+	1	NA	exon (NM_007773, exon 3 of 7)	exon (NM_007773, exon 3 of 7)	1400	NM_007773	12961	Mm.1215	NM_007773	ENSMUSG00000042240	Crybb2	Cryb-2	crystallin, beta B2	protein-coding
mm_76575.1	chr8	89006641	89006654	-	1	NA	Intergenic	CpG	-18088	NR_106190	102465899		NR_106190	ENSMUSG00000099078	Mir8110	Gm27571|mmu-mir-8110	microRNA 8110	ncRNA
mm_171667.1	chr4	46575897	46575911	+	1	NA	intron (NM_001164804, intron 1 of 11)	RLTR3_Mm|LTR|ERVK	-9464	NM_178893	107684	Mm.416311	NM_178893	ENSMUSG00000028337	Coro2a	9030208C03Rik|AI563590|IR10	coronin, actin binding protein 2A	protein-coding
mm_88954.1	chr10	81384419	81384452	+	1	NA	promoter-TSS (NM_133964)	promoter-TSS (NM_133964)	7	NM_133964	102115	Mm.294975	NM_133964	ENSMUSG00000078440	Dohh	1110033C18Rik|AI585913|AL022869|Hlrc1	deoxyhypusine hydroxylase/monooxygenase	protein-coding
mm_85264.1	chr9	99420323	99420334	-	1	NA	intron (NM_008624, intron 1 of 5)	intron (NM_008624, intron 1 of 5)	16384	NM_008624	17532	Mm.2045	NM_008624	ENSMUSG00000032470	Mras	2900078C09Rik|AI326250	muscle and microspikes RAS	protein-coding
mm_110012.1	chr12	16589744	16589826	-	1	NA	promoter-TSS (NM_015763)	promoter-TSS (NM_015763)	-15	NM_172950	14245	Mm.153625	NM_015763	ENSMUSG00000020593	Lpin1	4631420P06|Kiaa0188|Lipin1|fld|mKIAA0188	lipin 1	protein-coding
mm_13447.1	chr2	105163121	105163123	+	1	NA	intron (NM_144783, intron 5 of 9)	intron (NM_144783, intron 5 of 9)	36593	NM_144783	22431	Mm.389339	NM_144783	ENSMUSG00000016458	Wt1	D630046I19Rik|Wt-1	Wilms tumor 1 homolog	protein-coding
mm_30681.1	chr4	11191777	11191789	+	1	NA	promoter-TSS (NM_009830)	promoter-TSS (NM_009830)	74	NM_001282943	12448	Mm.35867	NM_009830	ENSMUSG00000028212	Ccne2	-	cyclin E2	protein-coding
mm_95692.1	chr11	54314961	54314999	+	1	NA	promoter-TSS (NM_001033599)	promoter-TSS (NM_001033599)	77	NM_001033599	216739	Mm.267478	NM_144823	ENSMUSG00000020333	Acsl6	A330035H04Rik|AW050338|Facl6|LACS|Lacsl|mKIAA0837	acyl-CoA synthetase long-chain family member 6	protein-coding
mm_25227.1	chr3	103860266	103860293	+	1	NA	promoter-TSS (NM_008979)	promoter-TSS (NM_008979)	2	NM_008979	19260	Mm.395	NM_008979	ENSMUSG00000027843	Ptpn22	70zpep|PEP|Ptpn8	protein tyrosine phosphatase, non-receptor type 22 (lymphoid)	protein-coding
mm_28461.1	chr3	90695050	90695067	-	1	NA	intron (NM_009114, intron 2 of 2)	intron (NM_009114, intron 2 of 2)	663	NM_001281852	20202	Mm.2128	NM_009114	ENSMUSG00000056071	S100a9	60B8Ag|AW546964|BEE22|Cagb|GAGB|L1Ag|MRP14|p14	S100 calcium binding protein A9 (calgranulin B)	protein-coding
mm_152238.1	chr19	8712036	8712040	-	1	NA	intron (NM_001161413, intron 3 of 9)	intron (NM_001161413, intron 3 of 9)	1859	NM_008577	17254	Mm.4114	NM_008577	ENSMUSG00000010095	Slc3a2	4F2|4F2HC|AI314110|Cd98|Ly-10|Ly-m10|Ly10|Mdu1|Mgp-2hc|NACAE	solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2	protein-coding
mm_171128.1	chr3	146499911	146499913	+	1	NA	promoter-TSS (NM_001316756)	promoter-TSS (NM_001316756)	76	NM_010318	14707	Mm.140804	NM_010318	ENSMUSG00000068523	Gng5	G(y)5	guanine nucleotide binding protein (G protein), gamma 5	protein-coding
mm_42207.1	chr5	112449406	112449414	+	1	NA	promoter-TSS (NM_001177504)	promoter-TSS (NM_001177504)	-16	NM_001177504	625464	Mm.389676	NM_001177504	ENSMUSG00000072722	Gm6588	EG625464	predicted gene 6588	protein-coding
mm_39561.1	chr5	23102378	23102387	+	1	NA	intron (NM_001081231, intron 1 of 3)	intron (NM_001081231, intron 1 of 3)	331971	NR_040469	269630	Mm.425231	NR_040469	ENSMUSG00000073147	5031425E22Rik	-	RIKEN cDNA 5031425E22 gene	ncRNA
mm_111270.1	chr12	85288420	85288427	-	1	NA	promoter-TSS (NM_172414)	promoter-TSS (NM_172414)	-168	NM_172414	72350	Mm.158810	NM_172414	ENSMUSG00000045064	Zc2hc1c	2810002I04Rik|AV046379|Fam164c	zinc finger, C2HC-type containing 1C	protein-coding
mm_21650.1	chr2	164333634	164333636	-	1	NA	3' UTR (NM_009301, exon 2 of 3)	3' UTR (NM_009301, exon 2 of 3)	870	NM_009301	20944	Mm.140154	NM_009301	ENSMUSG00000017004	Svs5	BB115186|Semg1|Svp-1|Svp1|Svp5	seminal vesicle secretory protein 5	protein-coding
mm_127512.1	chr15	101740233	101740238	+	1	NA	intron (NM_019956, intron 2 of 8)	intron (NM_019956, intron 2 of 8)	2862	NM_019956	56735	Mm.358677	NM_019956	ENSMUSG00000051879	Krt71	AA589543|Ca|Cal4|Cu|Krt2-6g|mK6irs|mK6irs1	keratin 71	protein-coding
mm_46102.1	chr5	92347621	92347631	-	1	NA	intron (NM_021274, intron 3 of 3)	intron (NM_021274, intron 3 of 3)	1263	NM_021274	15945	Mm.877	NM_021274	ENSMUSG00000034855	Cxcl10	C7|CRG-2|INP10|IP-10|IP10|Ifi10|Scyb10|gIP-10|mob-1	chemokine (C-X-C motif) ligand 10	protein-coding
mm_171100.1	chr3	132828774	132828775	+	1	NA	intron (NM_001163455, intron 25 of 25)	L1Md_T|LINE|L1	49822	NR_102297	101243624	Mm.306256	NR_102297	ENSMUSG00000106230	Gm29811	-	predicted gene, 29811	ncRNA
mm_96862.1	chr11	70106273	70106274	+	1	NA	TTS (NM_007493)	TTS (NM_007493)	13629	NM_001313927	11890	Mm.1357	NM_007493	ENSMUSG00000040963	Asgr2	ASGPR2|Asgr|Asgr-2|HL-2	asialoglycoprotein receptor 2	protein-coding
mm_6501.1	chr1	74295282	74295302	-	1	NA	exon (NM_027154, exon 2 of 12)	exon (NM_027154, exon 2 of 12)	9044	NM_027154	69660	Mm.261182	NM_027154	ENSMUSG00000006301	Tmbim1	2310061B02Rik|AA960455|AU024746|C78899|RECS1|Tmbib1|mKIAA4161	transmembrane BAX inhibitor motif containing 1	protein-coding
mm_47301.1	chr5	122371976	122371980	-	1	NA	promoter-TSS (NM_026883)	promoter-TSS (NM_026883)	-15	NM_026883	68948	Mm.474469	NM_026883	ENSMUSG00000029463	Fam216a	1500011H22Rik	family with sequence similarity 216, member A	protein-coding
mm_65261.1	chr7	19906543	19906545	-	1	NA	intron (NM_027514, intron 6 of 7)	ID_B1|SINE|B4	14599	NM_027514	52118	Mm.227506	NM_027514	ENSMUSG00000040511	Pvr	3830421F03Rik|CD155|D7Ertd458e|HVED|PVS|Taa1|Tage4|mE4|necl-5	poliovirus receptor	protein-coding
mm_70429.1	chr8	11555785	11555794	+	1	NA	promoter-TSS (NM_001302457)	promoter-TSS (NM_001302457)	27	NM_001302458	26356	Mm.25709	NM_011919	ENSMUSG00000045969	Ing1	2610028J21Rik|AA407184|AI875420|mING1h|p33Ing1|p37Ing1b	inhibitor of growth family, member 1	protein-coding
mm_65572.1	chr7	27195647	27195674	-	1	NA	promoter-TSS (NM_001046637)	promoter-TSS (NM_001046637)	100	NM_001046637	53607	Mm.386890	NM_015782	ENSMUSG00000061479	Snrpa	C430021M15Rik|Rnu1a-1|Rnu1a1|U1-A|U1A	small nuclear ribonucleoprotein polypeptide A	protein-coding
mm_63632.1	chr7	128523262	128523270	+	1	NA	promoter-TSS (NM_013863)	promoter-TSS (NM_013863)	-317	NM_013863	29810	Mm.84073	NM_013863	ENSMUSG00000030847	Bag3	AA407278|Bis|mg638	BCL2-associated athanogene 3	protein-coding
mm_72279.1	chr8	75100301	75100322	+	1	NA	3' UTR (NM_010442, exon 5 of 5)	3' UTR (NM_010442, exon 5 of 5)	6693	NM_010442	15368	Mm.276389	NM_010442	ENSMUSG00000005413	Hmox1	D8Wsu38e|HO-1|HO1|Hemox|Hmox|Hsp32	heme oxygenase 1	protein-coding
mm_106915.1	chr12	8216637	8216666	+	1	NA	intron (NM_001167767, intron 1 of 5)	intron (NM_001167767, intron 1 of 5)	8524	NM_001167767	68832	Mm.25608	NM_172401	ENSMUSG00000037669	Ldah	1110057K04Rik|mLDAH	lipid droplet associated hydrolase	protein-coding
mm_22562.1	chr3	9942943	9942961	+	1	NA	Intergenic	L2|LINE|L2	-69633	NM_001272097	16592	Mm.741	NM_010634	ENSMUSG00000027533	Fabp5	E-FABP|Fabpe|Klbp|PA-FABP|mal1	fatty acid binding protein 5, epidermal	protein-coding
mm_30768.1	chr4	16164087	16164118	+	1	NA	promoter-TSS (NR_045765)	promoter-TSS (NR_045765)	-8	NR_045765	100415915	Mm.387180	NR_045765	ENSMUSG00000085112	A530072M11Rik	-	RIKEN cDNA gene A530072M11	ncRNA
mm_170604.1	chr19	5844189	5844192	-	1	NA	non-coding (NR_003513, exon 1 of 1)	non-coding (NR_003513, exon 1 of 1)	1288	NR_131212	66961	Mm.281895	NR_003513	ENSMUSG00000092274	Neat1	2310043N10Rik|VINC	nuclear paraspeckle assembly transcript 1 (non-protein coding)	ncRNA
mm_130612.1	chr15	99931646	99931673	-	1	NA	promoter-TSS (NM_028180)	promoter-TSS (NM_028180)	-1	NM_028180	72277	Mm.272766	NM_028180	ENSMUSG00000045350	1700030F18Rik	FAM186A	RIKEN cDNA 1700030F18 gene	protein-coding
mm_99687.1	chr11	106036961	106036972	+	1	NA	promoter-TSS (NM_027946)	promoter-TSS (NM_027946)	94	NM_027946	71833	Mm.307455	NM_027946	ENSMUSG00000049354	Dcaf7	1700012F10Rik|2610037L01Rik|C86529|HAN11|Wdr68	DDB1 and CUL4 associated factor 7	protein-coding
mm_64822.1	chr7	7299493	7299540	-	1	NA	promoter-TSS (NM_001302387)	promoter-TSS (NM_001302387)	41	NR_126156	12727	Mm.297883	NM_011334	ENSMUSG00000000605	Clcn4	Clc4-2|Clcn4-2	chloride channel, voltage-sensitive 4	protein-coding
mm_69825.1	chr7	141266019	141266030	-	1	NA	5' UTR (NM_001252601, exon 2 of 10)	5' UTR (NM_001252601, exon 2 of 10)	400	NM_001252601	54123	Mm.3233	NM_016850	ENSMUSG00000025498	Irf7	-	interferon regulatory factor 7	protein-coding
mm_51930.1	chr6	91476773	91476802	+	1	NA	intron (NM_028766, intron 1 of 11)	intron (NM_028766, intron 1 of 11)	3036	NM_028766	74122	Mm.38801	NM_028766	ENSMUSG00000030095	Tmem43	1200015A22Rik|LUMA	transmembrane protein 43	protein-coding
mm_102639.1	chr11	62617135	62617138	-	1	NA	intron (NM_198861, intron 2 of 3)	intron (NM_198861, intron 2 of 3)	12606	NR_028541	100217444		NR_028541		Snord65	MBII-135|snoRNA135	small nucleolar RNA, C/D box 65	snoRNA
mm_35957.1	chr4	53130964	53130974	-	1	NA	intron (NM_013454, intron 3 of 49)	intron (NM_013454, intron 3 of 49)	28926	NM_013454	11303	Mm.277376	NM_013454	ENSMUSG00000015243	Abca1	ABC-1|Abc1	ATP-binding cassette, sub-family A (ABC1), member 1	protein-coding
mm_17021.1	chr2	18998214	18998303	-	1	NA	promoter-TSS (NR_024323)	promoter-TSS (NR_024323)	-61	NR_024323	74629	Mm.117687	NR_024323	ENSMUSG00000026736	4930426L09Rik	-	RIKEN cDNA 4930426L09 gene	ncRNA
mm_57656.1	chr6	128486149	128486167	-	1	NA	exon (NM_007376, exon 33 of 36)	exon (NM_007376, exon 33 of 36)	40562	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_26170.1	chr3	138285275	138285309	+	1	NA	intron (NM_007409, intron 5 of 8)	intron (NM_007409, intron 5 of 8)	7647	NM_007409	11522	Mm.2409	NM_007409	ENSMUSG00000074207	Adh1	ADH-AA|AI194826|Adh-1|Adh-1-t|Adh-1e|Adh-1t|Adh-3e|Adh1-e|Adh1-t|Adh1tl|Adh3-e	alcohol dehydrogenase 1 (class I)	protein-coding
mm_117594.1	chr13	89742491	89742515	-	1	NA	promoter-TSS (NM_001134474)	promoter-TSS (NM_001134474)	9	NM_001081249	13003	Mm.158700	NM_019389	ENSMUSG00000021614	Vcan	5430420N07Rik|9430051N09|Cspg2|DPEAAE|NG2|PG-M|PG-M(V0)|PG-M(V1)|hdf	versican	protein-coding
mm_79993.1	chr9	67033899	67033904	+	1	NA	exon (NM_001164251, exon 4 of 10)	exon (NM_001164251, exon 4 of 10)	9970	NM_001164252	22003	Mm.121878	NM_024427	ENSMUSG00000032366	Tpm1	AA986836|AI854628|TM2|Tm3|Tmpa|Tpm-1|alpha-TM	tropomyosin 1, alpha	protein-coding
mm_169348.1	chr14	20348018	20348019	-	1	NA	promoter-TSS (NM_172379)	promoter-TSS (NM_172379)	103	NM_027475	70601	Mm.35105	NM_027475	ENSMUSG00000021810	Ecd	5730461K03Rik|Hsgt1	ecdysoneless homolog (Drosophila)	protein-coding
mm_86167.1	chr9	118925375	118925442	-	1	NA	Intergenic	CpG	-1128	NM_133710	69274	Mm.439928	NM_133710	ENSMUSG00000047409	Ctdspl	2810418J22Rik|AI426263|HYA22|SCP3	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase-like	protein-coding
mm_43527.1	chr5	137288043	137288120	+	1	NA	promoter-TSS (NM_009599)	promoter-TSS (NM_009599)	-173	NM_009599	11423	Mm.255464	NM_009599	ENSMUSG00000023328	Ache	-	acetylcholinesterase	protein-coding
mm_94921.1	chr11	29505561	29505571	+	1	NA	intron (NM_176841, intron 30 of 31)	intron (NM_176841, intron 30 of 31)	9467	NM_026465	67939	Mm.251087	NM_026465	ENSMUSG00000032673	Prorsd1	2010316F05Rik|Ncrna00117|Prdxdd1	prolyl-tRNA synthetase domain containing 1	protein-coding
mm_103695.1	chr11	79516272	79516272	-	1	NA	exon (NM_001077496, exon 2 of 2)	exon (NM_001077496, exon 2 of 2)	7490	NM_001077496	216984	Mm.439665	NM_001077496	ENSMUSG00000093938	Evi2b	Evi-2|Evi2	ecotropic viral integration site 2b	protein-coding
mm_167742.1	chr9	108339743	108339750	+	1	NA	intron (NM_001329527, intron 1 of 1)	intron (NM_001329527, intron 1 of 1)	666	NM_001329528	14775	Mm.1090	NM_008160	ENSMUSG00000063856	Gpx1	AI195024|AL033363|CGPx|GPx-1|GSHPx-1|Gpx	glutathione peroxidase 1	protein-coding
mm_66922.1	chr7	61055405	61055418	-	1	NA	Intergenic	Intergenic	559916	NR_045727	319752	Mm.294476	NR_045727		B230209E15Rik	-	RIKEN cDNA B230209E15 gene	ncRNA
mm_86718.1	chr10	19012084	19012104	+	1	NA	promoter-TSS (NM_001166402)	promoter-TSS (NM_001166402)	-131	NM_001166402	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_91003.1	chr10	14545358	14545368	-	1	NA	promoter-TSS (NM_001002268)	promoter-TSS (NM_001002268)	-327	NM_001002268	215798	Mm.440142	NM_001002268	ENSMUSG00000039116	Adgrg6	1190004A11Rik|AI449247|AW045736|DREG|Gm222|Gpr126	adhesion G protein-coupled receptor G6	protein-coding
mm_36169.1	chr4	61835186	61835190	-	1	NA	promoter-TSS (NM_008649)	promoter-TSS (NM_008649)	-8	NM_008649	17844	Mm.445286	NM_008649	ENSMUSG00000058523	Mup5	Mup18	major urinary protein 5	protein-coding
mm_47882.1	chr5	134703237	134703248	-	1	NA	3' UTR (NM_007925, exon 37 of 37)	3' UTR (NM_007925, exon 37 of 37)	-14652	NM_010717	16885	Mm.15409	NM_010717	ENSMUSG00000029674	Limk1	KIZ-1|LIMK-1|Limk	LIM-domain containing, protein kinase	protein-coding
mm_25326.1	chr3	106567865	106567876	+	1	NA	intron (NM_001025582, intron 5 of 6)	intron (NM_001025582, intron 5 of 6)	-20068	NM_133869	99712	Mm.429443	NM_133869	ENSMUSG00000040774	Cept1	9930118K05Rik|mCEPT1	choline/ethanolaminephosphotransferase 1	protein-coding
mm_5312.1	chr1	22512492	22512513	-	1	NA	intron (NM_001012623, intron 8 of 14).2	intron (NM_001012623, intron 8 of 14).2	-79659	NM_183018	116837	Mm.60061	NM_053270	ENSMUSG00000041670	Rims1	C030033M19Rik|RIM1|RIM1a|RIM1alpha|Rab3ip1|Rim|Serg1|mKIAA0340	regulating synaptic membrane exocytosis 1	protein-coding
mm_76318.1	chr8	84687547	84687571	-	1	NA	intron (NM_025788, intron 1 of 5)	CpG	303	NM_025788	66830	Mm.289698	NM_025788	ENSMUSG00000001910	Nacc1	2010001H03Rik|4930511N13Rik|Btbd14b|Nac1	nucleus accumbens associated 1, BEN and BTB (POZ) domain containing	protein-coding
mm_167214.1	chr8	4419356	4419357	+	1	NA	Intergenic	L1Md_F2|LINE|L1	69768	NM_009138	20300	Mm.7275	NM_009138	ENSMUSG00000023235	Ccl25	A130072A22Rik|AI852536|CKb15|Scya25|TECK	chemokine (C-C motif) ligand 25	protein-coding
mm_144059.1	chr17	90658046	90658052	-	1	NA	intron (NM_001346957, intron 6 of 18)	AT_rich|Low_complexity|Low_complexity	135427	NR_136930	102634634		NR_136930		Gm20491	-	enolase 1, alpha non-neuron pseudogene	pseudo
mm_168702.1	chr11	97859980	97859987	+	1	NA	intron (NM_001081435, intron 7 of 10)	ORR1A1|LTR|ERVL-MaLR	19203	NM_001080935	68127	Mm.110270	NM_001080935	ENSMUSG00000050538	B230217C12Rik	AI840637	RIKEN cDNA B230217C12 gene	protein-coding
mm_20761.1	chr2	140790433	140790449	-	1	NA	intron (NM_001013802, intron 3 of 18)	intron (NM_001013802, intron 3 of 18)	-118965	NM_178382	71436	Mm.426781	NM_178382	ENSMUSG00000051379	Flrt3	5530600M07Rik|C430047I10Rik|mKIAA1469	fibronectin leucine rich transmembrane protein 3	protein-coding
mm_103337.1	chr11	74674371	74674381	-	1	NA	non-coding (NR_037610, exon 11 of 11)	non-coding (NR_037610, exon 11 of 11)	24881	NM_001081158	74148	Mm.214574	NM_001081158	ENSMUSG00000020741	Cluh	1300001I01Rik|Kiaa0664|mKIAA0664	clustered mitochondria (cluA/CLU1) homolog	protein-coding
mm_75166.1	chr8	36613891	36613921	-	1	NA	promoter-TSS (NM_015802)	promoter-TSS (NM_015802)	37	NM_015802	50768	Mm.125155	NM_015802	ENSMUSG00000031523	Dlc1	A730069N07Rik|Arhgap7|HP|STARD12|dlc-1	deleted in liver cancer 1	protein-coding
mm_22800.1	chr3	24356782	24356789	+	1	NA	intron (NM_001326288, intron 4 of 13)	B2_Mm2|SINE|B2	427221	NM_001326288	635702	Mm.448351	NM_001326288	ENSMUSG00000102758	Naaladl2	2810043G22Rik|EG635702|Gm1021	N-acetylated alpha-linked acidic dipeptidase-like 2	protein-coding
mm_83982.1	chr9	57299837	57299859	-	1	NA	Intergenic	MER54A|LTR|ERVL	-37249	NM_028820	74211	Mm.428905	NM_028820	ENSMUSG00000032300	1700017B05Rik	AA682102|D9Ertd278e	RIKEN cDNA 1700017B05 gene	protein-coding
mm_90775.1	chr10	5922342	5922384	-	1	NA	promoter-TSS (NM_019958)	promoter-TSS (NM_019958)	37	NM_001161822	56533	Mm.44606	NM_019958	ENSMUSG00000019775	Rgs17	6430507P11Rik|Rgsz2	regulator of G-protein signaling 17	protein-coding
mm_114448.1	chr13	66932803	66932843	+	1	NA	promoter-TSS (NM_008959)	promoter-TSS (NM_008959)	-7	NM_008959	19210	Mm.281464	NM_008959	ENSMUSG00000021518	Ptdss1	AU044268|AW539008|PSS-1|mKIAA0024	phosphatidylserine synthase 1	protein-coding
mm_54902.1	chr6	47556099	47556114	-	1	NA	exon (NM_001146689, exon 5 of 20)	exon (NM_001146689, exon 5 of 20)	38924	NM_007971	14056	Mm.246688	NM_007971	ENSMUSG00000029687	Ezh2	Enx-1|Enx1h|KMT6|mKIAA4065	enhancer of zeste 2 polycomb repressive complex 2 subunit	protein-coding
mm_150511.1	chr19	39025989	39025997	+	1	NA	intron (NM_028089, intron 4 of 8)	intron (NM_028089, intron 4 of 8)	18974	NM_028089	72082	Mm.142581	NM_028089	ENSMUSG00000025002	Cyp2c55	2010318C06Rik	cytochrome P450, family 2, subfamily c, polypeptide 55	protein-coding
mm_67414.1	chr7	80130409	80130422	-	1	NA	Intergenic	Intergenic	-15065	NM_173011	269951	Mm.246432	NM_173011	ENSMUSG00000030541	Idh2	E430004F23|IDPm|Idh-2	isocitrate dehydrogenase 2 (NADP+), mitochondrial	protein-coding
mm_163405.1	chr12	75521511	75521513	+	1	NA	intron (NM_012024, intron 2 of 13)	B3|SINE|B2	74688	NM_012024	26932	Mm.259626	NM_012024	ENSMUSG00000021051	Ppp2r5e	4633401M22Rik|AI449017|B56beta	protein phosphatase 2, regulatory subunit B', epsilon	protein-coding
mm_172803.1	chr9	120127812	120127815	+	1	NA	promoter-TSS (NM_011029)	promoter-TSS (NM_011029)	47	NM_011029	16785	Mm.4071	NM_011029	ENSMUSG00000032518	Rpsa	67kDa|67lr|AL022858|Lamr|Lamr1|Lamrl1|MLR|P40|P40-3|P40-8	ribosomal protein SA	protein-coding
mm_81741.1	chr9	113793348	113793358	+	1	NA	promoter-TSS (NM_001286603)	promoter-TSS (NM_001286603)	23	NM_001286603	76499	Mm.222272	NM_029633	ENSMUSG00000033392	Clasp2	1500004F14Rik|8030404L10Rik|C77448|CLASP2beta|mKIAA0627	CLIP associating protein 2	protein-coding
mm_34775.1	chr4	153975140	153975153	+	1	NA	promoter-TSS (NM_177673)	promoter-TSS (NM_177673)	-65	NM_007859	13368	Mm.388918	NM_007859	ENSMUSG00000029027	Dffb	40kDa|5730477D02Rik|CAD|CPAN|DFF40|Didff	DNA fragmentation factor, beta subunit	protein-coding
mm_16202.1	chr2	173023045	173023060	+	1	NA	intron (NM_019547, intron 2 of 3)	intron (NM_019547, intron 2 of 3)	1150	NM_019547	56190	Mm.485782	NM_019547	ENSMUSG00000027510	Rbm38	Rnpc1|Seb4|Seb4l	RNA binding motif protein 38	protein-coding
mm_107588.1	chr12	47812986	47813024	+	1	NA	Intergenic	Intergenic	488457	NR_039586	100628593		NR_039586	ENSMUSG00000092981	Mir5125	mmu-mir-5125|mu-mir-5125	microRNA 5125	ncRNA
mm_59010.1	chr7	19228328	19228351	+	1	NA	promoter-TSS (NM_207525)	promoter-TSS (NM_207525)	-50	NM_207525	403187	Mm.239583	NM_207525	ENSMUSG00000052214	Opa3	D630048P19Rik|Gm1425|Gm472	optic atrophy 3	protein-coding
mm_94343.1	chr11	4736241	4736263	+	1	NA	intron (NM_026015, intron 5 of 5)	intron (NM_026015, intron 5 of 5)	10526	NM_138948	192650	Mm.207056	NM_138948	ENSMUSG00000009075	Cabp7	-	calcium binding protein 7	protein-coding
mm_80624.1	chr9	88956980	88957003	+	1	NA	promoter-TSS (NM_009742)	promoter-TSS (NM_009742)	71	NM_009742	12044	Mm.425593	NM_009742	ENSMUSG00000102037	Bcl2a1a	A1|BB218357|Bcl2a1|Bfl-1|Hbpa1	B cell leukemia/lymphoma 2 related protein A1a	protein-coding
mm_51378.1	chr6	73248578	73248588	+	1	NA	promoter-TSS (NM_019879)	promoter-TSS (NM_019879)	78	NM_019879	56451	Mm.29845	NM_019879	ENSMUSG00000052738	Suclg1	1500000I01Rik|Sucla1	succinate-CoA ligase, GDP-forming, alpha subunit	protein-coding
mm_20164.1	chr2	122152863	122152875	-	1	NA	3' UTR (NM_009735, exon 4 of 4)	3' UTR (NM_009735, exon 4 of 4)	5182	NM_009735	12010	Mm.163	NM_009735	ENSMUSG00000060802	B2m	Ly-m11|beta2-m|beta2m	beta-2 microglobulin	protein-coding
mm_108053.1	chr12	73913498	73913531	+	1	NA	intron (NM_010431, intron 1 of 14)	intron (NM_010431, intron 1 of 14)	5647	NM_001313919	15251	Mm.3879	NM_010431	ENSMUSG00000021109	Hif1a	AA959795|HIF-1-alpha|HIF1-alpha|HIF1alpha|MOP1|bHLHe78	hypoxia inducible factor 1, alpha subunit	protein-coding
mm_98061.1	chr11	85831792	85831805	+	1	NA	promoter-TSS (NM_009324)	promoter-TSS (NM_009324)	590	NR_077059	69909	Mm.440214	NR_077059	ENSMUSG00000087013	2610027K06Rik	-	RIKEN cDNA 2610027K06 gene	ncRNA
mm_57799.1	chr6	129326707	129326725	-	1	NA	exon (NM_199034, exon 3 of 5)	exon (NM_199034, exon 3 of 5)	5065	NM_199034	381816	Mm.46114	NM_199034	ENSMUSG00000047720	4922502D21Rik	Clec2m|Gm1074|SPATA78	RIKEN cDNA 4922502D21 gene	protein-coding
mm_67530.1	chr7	81213676	81213680	-	1	NA	promoter-TSS (NM_008803)	promoter-TSS (NM_008803)	-126	NM_008803	18584	Mm.371577	NM_008803	ENSMUSG00000025584	Pde8a	AI551852|Pde8	phosphodiesterase 8A	protein-coding
mm_82782.1	chr9	28994787	28994797	-	1	NA	Intergenic	Intergenic	968337	NM_172290	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding
mm_135138.1	chr16	35852764	35852777	-	1	NA	exon (NM_001039530, exon 8 of 17)	exon (NM_001039530, exon 8 of 17)	18612	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_20678.1	chr2	132385436	132385448	-	1	NA	promoter-TSS (NM_144944)	promoter-TSS (NM_144944)	5	NM_144944	246313	Mm.283777	NM_144944	ENSMUSG00000050558	Prokr2	B830005M06Rik|EG-VEGRF2|Gpcr73l1|Gpr73l1|PKR2	prokineticin receptor 2	protein-coding
mm_155379.1	chrX	71803612	71803615	+	1	NA	Intergenic	Intergenic	-12467	NM_001290781	67048	Mm.41102	NM_001081356	ENSMUSG00000073131	Vma21	2610030H06Rik|AI840175	VMA21 vacuolar H+-ATPase homolog (S. cerevisiae)	protein-coding
mm_138407.1	chr17	35066902	35066910	+	1	NA	promoter-TSS (NM_023463)	promoter-TSS (NM_023463)	-419	NM_023463	68468	Mm.215096	NM_023463	ENSMUSG00000092586	Ly6g6c	1110003M04Rik|AU016360|G6c|NG24	lymphocyte antigen 6 complex, locus G6C	protein-coding
mm_140868.1	chr17	23777246	23777256	-	1	NA	intron (NM_029798, intron 2 of 2)	intron (NM_029798, intron 2 of 2)	-5660	NM_153791	224613	Mm.328835	NM_153791	ENSMUSG00000040097	Flywch1	E030034P13Rik|mKIAA1552	FLYWCH-type zinc finger 1	protein-coding
mm_160801.1	chr11	5129843	5129843	-	1	NA	intron (NM_080595, intron 8 of 14)	intron (NM_080595, intron 8 of 14)	22379	NM_080595	140703	Mm.840	NM_080595	ENSMUSG00000034164	Emid1	AW122071|CO-5|Emu1	EMI domain containing 1	protein-coding
mm_57551.1	chr6	126840842	126840845	-	1	NA	intron (NM_025358, intron 4 of 10)	intron (NM_025358, intron 4 of 10)	8301	NM_025358	66108	Mm.29939	NM_025358	ENSMUSG00000000399	Ndufa9	1010001N11Rik	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 9	protein-coding
mm_12862.1	chr2	83775344	83775373	+	1	NA	intron (NM_008402, intron 12 of 29)	B1_Mur4|SINE|Alu	-37370	NM_175514	241520	Mm.330351	NM_175514	ENSMUSG00000048388	Fam171b	D430039N05Rik	family with sequence similarity 171, member B	protein-coding
mm_87305.1	chr10	42614236	42614258	+	1	NA	Intergenic	CpG	-30659	NM_152229	21907	Mm.287100	NM_152229	ENSMUSG00000019803	Nr2e1	Mtl1|Mtll|TLL|Tlx|XTLL|fierce|frc|tailless	nuclear receptor subfamily 2, group E, member 1	protein-coding
mm_5646.1	chr1	40516458	40516474	-	1	NA	5' UTR (NM_010553, exon 3 of 13)	5' UTR (NM_010553, exon 3 of 13)	1104	NM_010553	16174	Mm.20466	NM_010553	ENSMUSG00000026068	Il18rap	AcPL|IL-18R-beta|IL-18RAcP|IL-18Rbeta|IL-1RAcPL	interleukin 18 receptor accessory protein	protein-coding
mm_94532.1	chr11	9118572	9118593	+	1	NA	promoter-TSS (NM_001159402)	promoter-TSS (NM_001159402)	75	NM_001159402	22271	Mm.4610	NM_009477	ENSMUSG00000020407	Upp1	AI325217|UPase|UdRPase|Up|Upp	uridine phosphorylase 1	protein-coding
mm_150944.1	chr19	46307352	46307373	+	1	NA	intron (NM_001177369, intron 6 of 22)	intron (NM_001177369, intron 6 of 22)	1432	NM_001177370	18034	Mm.102365	NM_019408	ENSMUSG00000025225	Nfkb2	NF-kappaB2|lyt|p49|p49/p100|p50B|p52	nuclear factor of kappa light polypeptide gene enhancer in B cells 2, p49/p100	protein-coding
mm_78039.1	chr9	14276493	14276501	+	1	NA	5' UTR (NM_030261, exon 1 of 10)	5' UTR (NM_030261, exon 1 of 10)	196	NM_030261	75747	Mm.325126	NM_030261	ENSMUSG00000032009	Sesn3	5630400E15Rik|BC003348|SEST3	sestrin 3	protein-coding
mm_14619.1	chr2	136765390	136765402	+	1	NA	intron (NM_011428, intron 4 of 7)	LTR16B|LTR|ERVL	51946	NM_001291056	20614	Mm.45953	NM_011428	ENSMUSG00000027273	Snap25	Bdr|GENA70|SNAP-25|SUP|sp	synaptosomal-associated protein 25	protein-coding
mm_87231.1	chr10	40570610	40570618	+	1	NA	intron (NM_027572, intron 1 of 7)	intron (NM_027572, intron 1 of 7)	252	NM_027572	70840	Mm.332570	NM_027572	ENSMUSG00000019834	Slc22a16	4921504E14Rik|CT2|FLIPT2|OCT6|OKB1	solute carrier family 22 (organic cation transporter), member 16	protein-coding
mm_155280.1	chrX	61127967	61127979	+	1	NA	intron (NR_030706, intron 5 of 7)	intron (NR_030706, intron 5 of 7)	11595	NR_030706	331424	Mm.127263	NM_177916	ENSMUSG00000071753	C230004F18Rik	-	RIKEN cDNA C230004F18 gene	ncRNA
mm_80162.1	chr9	71157407	71157416	+	1	NA	intron (NR_073483, intron 1 of 6)	intron (NR_073483, intron 1 of 6)	5222	NM_001271843	64008	Mm.449427	NM_022026	ENSMUSG00000032204	Aqp9	1700020I22Rik|AI266899|AQP-9	aquaporin 9	protein-coding
mm_61522.1	chr7	78913952	78913991	+	1	NA	promoter-TSS (NM_001113527)	promoter-TSS (NM_001113527)	206	NM_020583	57444	Mm.322843	NM_020583	ENSMUSG00000039236	Isg20	1600023I01Rik|2010107M23Rik|20kDa|DnaQL|HEM45	interferon-stimulated protein	protein-coding
mm_73625.1	chr8	110618674	110618693	+	1	NA	promoter-TSS (NM_146216)	promoter-TSS (NM_146216)	45	NM_146216	234729	Mm.274894	NM_146216	ENSMUSG00000010936	Vac14	AA959718|BC032215|D8Wsu151e|Tax1bp2|Trx|ingls	Vac14 homolog (S. cerevisiae)	protein-coding
mm_170293.1	chr18	3005706	3005708	+	1	NA	Intergenic	Intergenic	117705	NM_001167539	100312476	Mm.480293	NM_001167539	ENSMUSG00000091539	Vmn1r238	-	vomeronasal 1 receptor, 238	protein-coding
mm_106237.1	chr11	117775039	117775049	-	1	NA	TTS (NM_181321)	TTS (NM_181321)	5577	NM_181321	217353	Mm.286963	NM_145439	ENSMUSG00000025572	Tmc6	D11Ertd204e|EVER1	transmembrane channel-like gene family 6	protein-coding
mm_472.1	chr1	36461997	36462007	+	1	NA	Intergenic	Intergenic	-9595	NM_033570	94220	Mm.422638	NM_033570	ENSMUSG00000037408	Cnnm4	5430430O18Rik|Acdp4	cyclin M4	protein-coding
mm_88775.1	chr10	80398967	80399035	+	1	NA	intron (NM_001306143, intron 1 of 6)	CpG	530	NM_013595	17192	Mm.7142	NM_013595	ENSMUSG00000035478	Mbd3	AI181826|AU019209	methyl-CpG binding domain protein 3	protein-coding
mm_59118.1	chr7	19851995	19852022	+	1	NA	promoter-TSS (NM_001270489)	promoter-TSS (NM_001270489)	5	NM_001270489	100502736	Mm.445354	NM_001270489	ENSMUSG00000092216	Gm19345	-	predicted gene, 19345	protein-coding
mm_88124.1	chr10	69236378	69236379	+	1	NA	intron (NM_001252637, intron 2 of 10)	intron (NM_001252637, intron 2 of 10)	23184	NM_001252638	69288	Mm.26659	NM_001081347	ENSMUSG00000019944	Rhobtb1	1700008H16Rik|3110048G13Rik|AI173445|AI573858|AV350930	Rho-related BTB domain containing 1	protein-coding
mm_6699.1	chr1	80758537	80758558	-	1	NA	promoter-TSS (NM_175291)	promoter-TSS (NM_175291)	6	NM_175291	210293	Mm.133473	NM_175291	ENSMUSG00000038608	Dock10	9330153B10Rik|A630054M16Rik|Jr4|Jr5|R75174|ZIZ3|Zizimin3|mKIAA0694	dedicator of cytokinesis 10	protein-coding
mm_46576.1	chr5	107289562	107289637	-	1	NA	promoter-TSS (NM_011578)	promoter-TSS (NM_011578)	-4	NM_011578	21814	Mm.200775	NM_011578	ENSMUSG00000029287	Tgfbr3	1110036H20Rik|AU015626|AW215636|TBRIII	transforming growth factor, beta receptor III	protein-coding
mm_126266.1	chr15	79109121	79109134	+	1	NA	5' UTR (NM_177461, exon 1 of 16)	5' UTR (NM_177461, exon 1 of 16)	144	NM_177461	27008	Mm.196480	NM_177461	ENSMUSG00000033039	Micall1	AI448246|D15Mit260|D15N2e|EST573322|EST820961|MIRab13|mKIAA1668	microtubule associated monooxygenase, calponin and LIM domain containing -like 1	protein-coding
mm_5276.1	chr1	19337538	19337541	-	1	NA	Intergenic	Intergenic	125485	NM_001025305	21419	Mm.137021	NM_009334	ENSMUSG00000025927	Tfap2b	AI606113|AP-2(beta)|E130018K07Rik|Tcfap2b	transcription factor AP-2 beta	protein-coding
mm_115501.1	chr13	3918145	3918151	-	1	NA	promoter-TSS (NM_019671)	promoter-TSS (NM_019671)	72	NM_019671	56349	Mm.22261	NM_019671	ENSMUSG00000021215	Net1	Net1a|mNET1	neuroepithelial cell transforming gene 1	protein-coding
mm_61593.1	chr7	80025907	80025921	+	1	NA	promoter-TSS (NM_175433)	promoter-TSS (NM_175433)	-314	NM_175433	209225	Mm.290925	NM_175433	ENSMUSG00000048897	Zfp710	5430400N05Rik|9830165K13|AI324798|Znf710	zinc finger protein 710	protein-coding
mm_60232.1	chr7	43672042	43672057	+	1	NA	promoter-TSS (NM_145582)	promoter-TSS (NM_145582)	18	NM_145582	233189	Mm.26514	NM_145582	ENSMUSG00000038888	Ctu1	Atpbd3|BC005752	cytosolic thiouridylase subunit 1	protein-coding
mm_157772.1	chrX	73717851	73717864	-	1	NA	promoter-TSS (NM_001313698)	promoter-TSS (NM_001313698)	-42	NM_001313698	27061	Mm.17	NM_012060	ENSMUSG00000002015	Bcap31	Bap31	B cell receptor associated protein 31	protein-coding
mm_58763.1	chr7	15881622	15881630	+	1	NA	promoter-TSS (NR_038092)	promoter-TSS (NR_038092)	-991	NR_038092	546024	Mm.259041	NM_001033638	ENSMUSG00000074365	Crxos	AA606869|AY590891|Crxos1|Egam1	cone-rod homeobox, opposite strand	protein-coding
mm_30563.1	chr4	3790018	3790020	+	1	NA	3' UTR (NM_001111096, exon 13 of 13)	3' UTR (NM_001111096, exon 13 of 13)	45636	NM_026147	67427	Mm.21938	NM_026147	ENSMUSG00000028234	Rps20	4632426K06Rik|Dsk4	ribosomal protein S20	protein-coding
mm_128928.1	chr15	74636269	74636273	-	1	NA	promoter-TSS (NM_001177437)	promoter-TSS (NM_001177437)	47	NM_001177437	69439	Mm.263708	NM_001177437	ENSMUSG00000022603	Mroh4	1700016M24Rik	maestro heat-like repeat family member 4	protein-coding
mm_87002.1	chr10	26799187	26799219	+	1	NA	intron (NM_176837, intron 1 of 14)	intron (NM_176837, intron 1 of 14)	26691	NM_176837	73910	Mm.356496	NM_176837	ENSMUSG00000039031	Arhgap18	4833419J07Rik|AI314906|AI843501	Rho GTPase activating protein 18	protein-coding
mm_137708.1	chr17	29099349	29099351	+	1	NA	exon (NM_007669, exon 3 of 3)	exon (NM_007669, exon 3 of 3)	5581	NM_007669	12575	Mm.195663	NM_007669	ENSMUSG00000023067	Cdkn1a	CAP20|CDKI|CIP1|Cdkn1|P21|SDI1|Waf1|mda6|p21Cip1|p21WAF	cyclin-dependent kinase inhibitor 1A (P21)	protein-coding
mm_124375.1	chr14	106261251	106261254	-	1	NA	Intergenic	U4|snRNA|snRNA	155054	NR_073203	212085	Mm.78128	NM_198601	ENSMUSG00000022113	Trim52	4921513B05Rik	tripartite motif-containing 52	protein-coding
mm_140878.1	chr17	23828822	23828830	-	1	NA	intron (NM_026305, intron 2 of 3)	CpG	283	NM_026305	67673	Mm.153758	NM_026305	ENSMUSG00000055839	Elob	0610040H15Rik|Tceb2	elongin B	protein-coding
mm_7590.1	chr1	125435536	125435557	-	1	NA	5' UTR (NM_023735, exon 1 of 12)	5' UTR (NM_023735, exon 1 of 12)	181	NM_023735	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding
mm_70896.1	chr8	25601506	25601516	+	1	NA	promoter-TSS (NM_001308482)	promoter-TSS (NM_001308482)	-90	NM_001308481	234135	Mm.217337	NM_001001735	ENSMUSG00000054823	Whsc1l1	6720429E03|A530023P05|AI528490|NSD3|WHISTLE	Wolf-Hirschhorn syndrome candidate 1-like 1 (human)	protein-coding
mm_113331.1	chr13	31558158	31558176	+	1	NA	promoter-TSS (NM_008239)	promoter-TSS (NM_008239)	-3	NM_008239	15220	Mm.44235	NM_008239	ENSMUSG00000038415	Foxq1	HFH-1|Hfh1|Hfh1l|sa	forkhead box Q1	protein-coding
mm_154672.1	chrX	7884023	7884055	+	1	NA	promoter-TSS (NM_001083937)	promoter-TSS (NM_001083937)	-205	NM_001083937	22232	Mm.214976	NM_078484	ENSMUSG00000031156	Slc35a2	AI327289|Had-1|Had1|Sfc8|UGT|Ugalt	solute carrier family 35 (UDP-galactose transporter), member A2	protein-coding
mm_63773.1	chr7	131410634	131410726	+	1	NA	promoter-TSS (NM_025826)	promoter-TSS (NM_025826)	79	NM_025826	66885	Mm.334274	NM_025826	ENSMUSG00000030861	Acadsb	1300003O09Rik|2-MEBCAD|BB066609|SBCAD	acyl-Coenzyme A dehydrogenase, short/branched chain	protein-coding
mm_29435.1	chr3	109362001	109362010	-	1	NA	intron (NM_020505, intron 1 of 26)	intron (NM_020505, intron 1 of 26)	21322	NM_020505	57257	Mm.282257	NM_020505	ENSMUSG00000033721	Vav3	A530094I06Rik|AA986410|Idd18.1	vav 3 oncogene	protein-coding
mm_23976.1	chr3	85971071	85971175	+	1	NA	Intergenic	CpG	31368	NM_001001650	368202	Mm.253822	NM_001001650	ENSMUSG00000049013	Prss48	Esspl|Gm1019	protease, serine 48	protein-coding
mm_144916.1	chr18	37504267	37504296	+	1	NA	promoter-TSS (NM_053145)	promoter-TSS (NM_053145)	17	NM_053145	93891	Mm.172449	NM_053145	ENSMUSG00000046191	Pcdhb20	Pcdhb14|PcdhbT	protocadherin beta 20	protein-coding
mm_8363.1	chr1	150465564	150465604	-	1	NA	5' UTR (NM_021400, exon 2 of 13)	5' UTR (NM_021400, exon 2 of 13)	581	NM_021400	96875	Mm.174256	NM_021400	ENSMUSG00000006014	Prg4	CACP|DOL54|JCAP|MSF|SZP|lubricin	proteoglycan 4 (megakaryocyte stimulating factor, articular superficial zone protein)	protein-coding
mm_101646.1	chr11	36538814	36538829	-	1	NA	intron (NM_011856, intron 2 of 28)	intron (NM_011856, intron 2 of 28)	405420	NM_001290702	23964	Mm.439889	NM_011856	ENSMUSG00000049336	Tenm2	Odz2|Odz3|Ten-2|Ten-m2	teneurin transmembrane protein 2	protein-coding
mm_9490.1	chr1	173729457	173729467	-	1	NA	exon (NM_001204910, exon 5 of 8)	exon (NM_001204910, exon 5 of 8)	12347	NM_001204910	226691	Mm.440876	NM_001204910	ENSMUSG00000073490	Ifi207	AI607873|Pyhin-A	interferon activated gene 207	protein-coding
mm_95772.1	chr11	54909103	54909113	+	1	NA	exon (NM_008161, exon 4 of 5)	exon (NM_008161, exon 4 of 5)	6254	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_115699.1	chr13	14064701	14064710	-	1	NA	intron (NM_198122, intron 1 of 22)	CpG	921	NM_198122	94246	Mm.439784	NM_194262	ENSMUSG00000039219	Arid4b	BCAA|BRCAA1|RBBP1L1|Rbp1l1|SAP180	AT rich interactive domain 4B (RBP1-like)	protein-coding
mm_167895.1	chrX	70630503	70630505	+	1	NA	Intergenic	Intergenic	84946	NM_001081476	628053	Mm.439630	NM_001081476		Gm14725	OTTMUSG00000017827	predicted gene 14725	protein-coding
mm_136222.1	chr16	90143765	90143775	-	1	NA	non-coding (NR_033476, exon 1 of 1)	non-coding (NR_033476, exon 1 of 1)	1533	NR_033476	100038709	Mm.484070	NR_033476		Gm10789	ENSMUSG00000074924	predicted gene 10789	ncRNA
mm_64764.1	chr7	4964369	4964386	-	1	NA	promoter-TSS (NM_001146329)	promoter-TSS (NM_001146329)	-29	NM_001146329	381836	Mm.297829	NM_001146329	ENSMUSG00000030433	Sbk2	Gm1079|Sgk069	SH3-binding domain kinase family, member 2	protein-coding
mm_102620.1	chr11	62463356	62463368	-	1	NA	intron (NM_001039536, intron 1 of 6)	intron (NM_001039536, intron 1 of 6)	4902	NM_001039536	327942	Mm.390358	NM_199026	ENSMUSG00000014245	Pigl	Gm737	phosphatidylinositol glycan anchor biosynthesis, class L	protein-coding
mm_30474.1	chr3	154711035	154711043	-	1	NA	promoter-TSS (NM_175176)	promoter-TSS (NM_175176)	-94	NM_175176	209601	Mm.331454	NM_175176	ENSMUSG00000078161	Erich3	1700013E18Rik|4922501L14Rik|5031409G23Rik|AI596448|Gm133	glutamate rich 3	protein-coding
mm_141983.1	chr17	35164892	35164901	-	1	NA	promoter-TSS (NM_020027)	promoter-TSS (NM_020027)	-19	NM_020027	53761	Mm.272462	NM_020027	ENSMUSG00000024393	Prrc2a	3110039B05Rik|Bat-2|Bat2|D17H6S51E|G2|Wbp12|mKIAA4178	proline-rich coiled-coil 2A	protein-coding
mm_157188.1	chrX	11126592	11126614	-	1	NA	Intergenic	(CTG)n|Simple_repeat|Simple_repeat	-172654	NM_001111037	100042922	Mm.374311	NM_001111037	ENSMUSG00000100626	H2al1a	Gm14483|OTTMUSG00000016789	H2A histone family member L1A	protein-coding
mm_36866.1	chr4	107058914	107058922	-	1	NA	intron (NM_025500, intron 5 of 6)	intron (NM_025500, intron 5 of 6)	7948	NM_025500	56280	Mm.29517	NM_025500	ENSMUSG00000028622	Mrpl37	2300004O14Rik|AI132596|MRP-L2|Rpml2	mitochondrial ribosomal protein L37	protein-coding
mm_27981.1	chr3	81965102	81965105	-	1	NA	intron (NM_019911, intron 7 of 11)	L2|LINE|L2	10625	NM_019911	56720	Mm.258622	NM_019911	ENSMUSG00000028011	Tdo2	AA407491|TDO|TO|chky	tryptophan 2,3-dioxygenase	protein-coding
mm_776.1	chr1	44551651	44551704	+	1	NA	promoter-TSS (NM_028450)	promoter-TSS (NM_028450)	6	NM_028450	70676	Mm.133132	NM_027506	ENSMUSG00000056870	Gulp1	3110030A04Rik|5730529O06Rik|CED-6|Ced6|GULP|Gulp-2	GULP, engulfment adaptor PTB domain containing 1	protein-coding
mm_12479.1	chr2	71529549	71529564	+	1	NA	5' UTR (NM_010053, exon 1 of 3)	5' UTR (NM_010053, exon 1 of 3)	111	NM_010053	13390	Mm.475101	NM_010053	ENSMUSG00000041911	Dlx1	Dlx|Dlx-1	distal-less homeobox 1	protein-coding
mm_100349.1	chr11	118428246	118428256	+	1	NA	promoter-TSS (NM_001204129)	promoter-TSS (NM_001204129)	-206	NM_001204129	56745	Mm.23845	NM_019959	ENSMUSG00000017446	C1qtnf1	1600017K21Rik|CTRP1|Zsig37	C1q and tumor necrosis factor related protein 1	protein-coding
mm_170998.1	chr2	75662034	75662034	+	1	NA	exon (NM_198090, exon 4 of 11)	exon (NM_198090, exon 4 of 11)	2744	NR_033513	627828	Mm.459502	NR_033513	ENSMUSG00000092086	Gm6793	EG627828	heterogeneous nuclear ribonucleoprotein A3 pseudogene	pseudo
mm_172907.1	chr9	59661967	59661973	+	1	NA	intron (NM_001253883, intron 1 of 10)	intron (NM_001253883, intron 1 of 10)	5602	NM_001253883	18746	Mm.326167	NM_011099	ENSMUSG00000032294	Pkm	AA414905|AL024370|AL024424|Pk-2|Pk-3|Pk3|Pkm2	pyruvate kinase, muscle	protein-coding
mm_6711.1	chr1	82287443	82287462	-	1	NA	exon (NM_010570, exon 1 of 2)	exon (NM_010570, exon 1 of 2)	3987	NM_010570	16367	Mm.4952	NM_010570	ENSMUSG00000055980	Irs1	G972R|IRS-1	insulin receptor substrate 1	protein-coding
mm_34424.1	chr4	145283715	145283759	+	1	NA	intron (NM_009401, intron 10 of 12)	intron (NM_009401, intron 10 of 12)	31410	NM_009401	21941	Mm.12810	NM_009401	ENSMUSG00000028602	Tnfrsf8	Cd30|D1S166E|Ki|Ki-1	tumor necrosis factor receptor superfamily, member 8	protein-coding
mm_156638.1	chrX	157598165	157598188	+	1	NA	intron (NM_172307, intron 1 of 10)	CpG	539	NM_172307	270669	Mm.37577	NM_172307	ENSMUSG00000046873	Mbtps2	9630032G22Rik|AI662535	membrane-bound transcription factor peptidase, site 2	protein-coding
mm_5761.1	chr1	46893050	46893066	-	1	NA	Intergenic	Intergenic	-39549	NM_172653	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|mKIAA1265	solute carrier family 39 (zinc transporter), member 10	protein-coding
mm_55335.1	chr6	56362242	56362255	-	1	NA	5' UTR (NM_001159953, exon 1 of 19)	5' UTR (NM_001159953, exon 1 of 19)	144	NM_001159952	18575	Mm.5145	NM_011054	ENSMUSG00000004347	Pde1c	-	phosphodiesterase 1C	protein-coding
mm_45134.1	chr5	48866123	48866129	-	1	NA	intron (NM_001199244, intron 1 of 7)	(A)n|Simple_repeat|Simple_repeat	23431	NM_030265	80334	Mm.160172	NM_030265	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding
mm_106367.1	chr11	118396759	118396769	-	1	NA	exon (NM_011150, exon 5 of 6)	exon (NM_011150, exon 5 of 6)	5167	NM_011150	19039	Mm.3152	NM_011150	ENSMUSG00000033880	Lgals3bp	90K|CyCAP|MAC-2BP|Ppicap|Tango10b	lectin, galactoside-binding, soluble, 3 binding protein	protein-coding
mm_39352.1	chr5	9073721	9073729	+	1	NA	Intergenic	Intergenic	-27012	NM_001081029	652925	Mm.439954	NM_001081029	ENSMUSG00000079659	Tmem243	4930420K17Rik|E030031F02Rik	transmembrane protein 243, mitochondrial	protein-coding
mm_31338.1	chr4	46469913	46469944	+	1	NA	exon (NM_130889, exon 5 of 7)	exon (NM_130889, exon 5 of 7)	19002	NM_130889	67628	Mm.263913	NM_130889	ENSMUSG00000028333	Anp32b	2410015B15Rik|PAL31|PHAPI2a|Ssp29	acidic (leucine-rich) nuclear phosphoprotein 32 family, member B	protein-coding
mm_145220.1	chr18	50053467	50053523	+	1	NA	5' UTR (NM_134131, exon 1 of 2)	5' UTR (NM_134131, exon 1 of 2)	213	NM_134131	106869	Mm.27740	NM_134131	ENSMUSG00000062210	Tnfaip8	AA987150|E130304C20Rik|ENSMUSG00000073567|Gg2-1|Gm10539|Nded|Ssc-2|Tipe	tumor necrosis factor, alpha-induced protein 8	protein-coding
mm_45030.1	chr5	38936873	38936879	-	1	NA	Intergenic	Intergenic	-60183	NM_013748	27278	Mm.440845	NM_013748	ENSMUSG00000039315	Clnk	MIST	cytokine-dependent hematopoietic cell linker	protein-coding
mm_94844.1	chr11	23728823	23728828	+	1	NA	intron (NM_028304, intron 16 of 17)	intron (NM_028304, intron 16 of 17)	42145	NM_009044	19696	Mm.4869	NM_009044	ENSMUSG00000020275	Rel	c-Rel	reticuloendotheliosis oncogene	protein-coding
mm_30559.1	chr4	3779212	3779257	+	1	NA	intron (NM_010747, intron 10 of 12)	intron (NM_010747, intron 10 of 12)	56421	NM_026147	67427	Mm.21938	NM_026147	ENSMUSG00000028234	Rps20	4632426K06Rik|Dsk4	ribosomal protein S20	protein-coding
mm_139129.1	chr17	47505159	47505164	+	1	NA	5' UTR (NM_001081636, exon 1 of 7)	5' UTR (NM_001081636, exon 1 of 7)	110	NM_001081635	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_123179.1	chr14	57664955	57664995	-	1	NA	promoter-TSS (NM_020506)	promoter-TSS (NM_020506)	-19	NM_020506	57258	Mm.202747	NM_020506	ENSMUSG00000021952	Xpo4	B430309A01Rik|mKIAA1721	exportin 4	protein-coding
mm_84767.1	chr9	75611279	75611295	-	1	NA	promoter-TSS (NM_016711)	promoter-TSS (NM_016711)	38	NM_016711	50876	Mm.291880	NM_016711	ENSMUSG00000032186	Tmod2	N-Tmod|NTMOD	tropomodulin 2	protein-coding
mm_122751.1	chr14	54192479	54192482	-	1	NA	Intergenic	Intergenic	61449	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_118731.1	chr14	22247016	22247022	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	227307	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_2038.1	chr1	87214377	87214389	+	1	NA	5' UTR (NM_001039169, exon 1 of 7)	5' UTR (NM_001039169, exon 1 of 7)	444	NM_001039169	26987	Mm.227183	NM_023314	ENSMUSG00000026254	Eif4e2	2700069E09Rik|AI036339|AV129531|D0H0S6743E|Eif4el3	eukaryotic translation initiation factor 4E member 2	protein-coding
mm_71481.1	chr8	46638474	46638491	+	1	NA	3' UTR (NM_009810, exon 7 of 7)	3' UTR (NM_009810, exon 7 of 7)	21191	NM_009810	12367	Mm.34405	NM_009810	ENSMUSG00000031628	Casp3	A830040C14Rik|AC-3|CASP-3|CC3|CPP-32|CPP32|Caspase-3|Lice|SCA-1|Yama|mldy	caspase 3	protein-coding
mm_36029.1	chr4	57120043	57120065	-	1	NA	intron (NM_019427, intron 1 of 15)	intron (NM_019427, intron 1 of 15)	23102	NM_019427	54357	Mm.28217	NM_019427	ENSMUSG00000028434	Epb41l4b	6430543G08Rik|AA589614|AU021054|BB007528|D4Ertd346e|Ehm2|Epb4.1l4b|Lulu2	erythrocyte membrane protein band 4.1 like 4b	protein-coding
mm_60573.1	chr7	44481593	44481604	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-2919	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_144610.1	chr18	32435257	32435281	+	1	NA	3' UTR (NM_009668, exon 19 of 19)	3' UTR (NM_009668, exon 19 of 19)	-56985	NR_045403	402767	Mm.385109	NR_045403	ENSMUSG00000097413	A830052D11Rik	-	RIKEN cDNA A830052D11 gene	ncRNA
mm_137500.1	chr17	26972373	26972381	+	1	NA	promoter-TSS (NM_001005916)	promoter-TSS (NM_001005916)	-802	NM_001005916	474156	Mm.328890	NM_001005916	ENSMUSG00000079605	Zbtb9	3930402F13Rik	zinc finger and BTB domain containing 9	protein-coding
mm_50023.1	chr6	41118819	41118851	+	1	NA	Intergenic	Intergenic	-83326	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_139943.1	chr17	71183602	71183610	+	1	NA	promoter-TSS (NM_022882)	promoter-TSS (NM_022882)	-372	NM_022882	64898	Mm.227924	NM_022882	ENSMUSG00000024052	Lpin2	2610511G02Rik|AI481352|AW742896	lipin 2	protein-coding
mm_141858.1	chr17	34803942	34803955	-	1	NA	intron (NM_009995, intron 2 of 9)	intron (NM_009995, intron 2 of 9)	478	NM_009995	13079	Mm.440407	NM_009995	ENSMUSG00000024365	Cyp21a1	21-OH|21OH|21OHA|21OHB|CYP21OH-A|Cyp21|Cyp21-ps1|Cyp21B|Cyp21a2-ps|Cyp21a2ps|Oh21-1|Oh21-2	cytochrome P450, family 21, subfamily a, polypeptide 1	protein-coding
mm_45740.1	chr5	86518563	86518577	-	1	NA	promoter-TSS (NM_177162)	promoter-TSS (NM_177162)	30	NM_177162	320454	Mm.184522	NM_177162	ENSMUSG00000079451	Tmprss11g	9930032O22Rik|Desc4	transmembrane protease, serine 11g	protein-coding
mm_45573.1	chr5	73339889	73339894	-	1	NA	promoter-TSS (NM_001310636)	promoter-TSS (NM_001310636)	-944	NM_001310636	433904	Mm.274892	NM_026950	ENSMUSG00000029153	Ociad2	1810027I20Rik	OCIA domain containing 2	protein-coding
mm_164636.1	chr17	34211963	34211969	+	1	NA	exon (NM_011530, exon 6 of 12)	exon (NM_011530, exon 6 of 12)	7487	NM_011530	21355	Mm.14814	NM_011530	ENSMUSG00000024339	Tap2	ABC18|AI462429|APT2|Abcb3|Ham-2|Ham2|MTP2|PSF2|RING11|Tap-2|Y1|jas	transporter 2, ATP-binding cassette, sub-family B (MDR/TAP)	protein-coding
mm_127629.1	chr15	102463631	102463644	+	1	NA	TTS (NM_025385)	TTS (NM_025385)	4467	NM_025385	66151	Mm.393955	NM_025385	ENSMUSG00000023048	Prr13	1110020C13Rik|2010324E22Rik	proline rich 13	protein-coding
mm_108398.1	chr12	81054753	81054757	+	1	NA	intron (NM_022316, intron 1 of 12)	intron (NM_022316, intron 1 of 12)	27947	NM_022316	64075	Mm.273295	NM_022316	ENSMUSG00000021136	Smoc1	2600002F22Rik|AI848508|SRG	SPARC related modular calcium binding 1	protein-coding
mm_92102.1	chr10	63019905	63019911	-	1	NA	intron (NM_001079824, intron 1 of 9)	intron (NM_001079824, intron 1 of 9)	392	NM_001347457	432467	Mm.274784	NM_001079824	ENSMUSG00000020069	Hnrnph3	AA693301|AI666703|Hnrph3	heterogeneous nuclear ribonucleoprotein H3	protein-coding
mm_100174.1	chr11	116533258	116533275	+	1	NA	promoter-TSS (NM_025367)	promoter-TSS (NM_025367)	28	NM_025367	20698	Mm.20944	NM_011451	ENSMUSG00000061878	Sphk1	1110006G24Rik|Sk1|Spk1	sphingosine kinase 1	protein-coding
mm_12638.1	chr2	74711859	74711873	+	1	NA	promoter-TSS (NM_010468)	promoter-TSS (NM_010468)	-127	NM_010468	15434	Mm.430708	NM_010468	ENSMUSG00000079277	Hoxd3	Hox-4.1|Hox-5.5	homeobox D3	protein-coding
mm_110786.1	chr12	71384186	71384235	-	1	NA	promoter-TSS (NR_136902)	promoter-TSS (NR_136902)	-2	NR_136902	67348	Mm.54261	NR_136902	ENSMUSG00000100668	1700083H02Rik	100041190|Gm3190	RIKEN cDNA 1700083H02 gene	ncRNA
mm_120965.1	chr14	77904449	77904453	+	1	NA	5' UTR (NM_029495, exon 1 of 12)	5' UTR (NM_029495, exon 1 of 12)	212	NM_029495	108670	Mm.68134	NM_029495	ENSMUSG00000022014	Epsti1	2310046K10Rik|5033415K03Rik|BRESI1	epithelial stromal interaction 1 (breast)	protein-coding
mm_143336.1	chr17	66484041	66484052	-	1	NA	Intergenic	RLTR9A3|LTR|ERVK	-34296	NM_001114098	68617	Mm.33421	NM_172963	ENSMUSG00000052105	Mtcl1	1110012J17Rik|Ccdc165|D130071O13|Kiaa0802|Soga2|mKIAA0802|t8219b25	microtubule crosslinking factor 1	protein-coding
mm_80593.1	chr9	85843373	85843386	+	1	NA	intron (NM_001164792, intron 1 of 1)	CpG	527	NM_001164792	21983	Mm.20864	NM_011627	ENSMUSG00000035274	Tpbg	5T4|AW495680|WAIF1	trophoblast glycoprotein	protein-coding
mm_40725.1	chr5	65975883	65975893	+	1	NA	intron (NM_001081104, intron 4 of 4)	intron (NM_001081104, intron 4 of 4)	8764	NM_001081104	231252	Mm.140015	NM_001081104	ENSMUSG00000029205	Chrna9	2410015I05Rik|Acra9|EG666827|Gm8311	cholinergic receptor, nicotinic, alpha polypeptide 9	protein-coding
mm_48088.1	chr5	136987758	136987768	-	1	NA	promoter-TSS (NM_001310748)	promoter-TSS (NM_001310748)	196	NM_027318	70103	Mm.273147	NM_027318	ENSMUSG00000059518	Znhit1	2700001K05Rik|ZNFN4A1	zinc finger, HIT domain containing 1	protein-coding
mm_19916.1	chr2	115780541	115780548	-	1	NA	Intergenic	Intergenic	141819	NR_035476	100316703		NR_035476	ENSMUSG00000088606	Mir1951	mir-1951|mmu-mir-1951	microRNA 1951	ncRNA
mm_168083.1	chr10	123131429	123131431	-	1	NA	intron (NM_001301628, intron 8 of 20)	intron (NM_001301628, intron 8 of 20)	-54925	NM_001163025	67074	Mm.169924	NM_153395	ENSMUSG00000034602	Mon2	2610528O22Rik|AW495628|Sf21|mKIAA1040	MON2 homolog, regulator of endosome to Golgi trafficking	protein-coding
mm_67689.1	chr7	89510034	89510043	-	1	NA	exon (NM_029614, exon 2 of 2)	exon (NM_029614, exon 2 of 2)	7548	NM_029614	76453	Mm.250438	NM_029614	ENSMUSG00000039405	Prss23	2310046G15Rik|4930479H08Rik|AI790574|Spuve	protease, serine 23	protein-coding
mm_53126.1	chr6	125131870	125131953	+	1	NA	promoter-TSS (NM_138747)	promoter-TSS (NM_138747)	28	NM_138747	110109	Mm.29203	NM_138747	ENSMUSG00000038279	Nop2	120kDa|A530002O17|Nol1	NOP2 nucleolar protein	protein-coding
mm_108612.1	chr12	85486230	85486249	+	1	NA	Intergenic	CpG	12338	NM_010234	14281	Mm.246513	NM_010234	ENSMUSG00000021250	Fos	D12Rfj1|c-fos|cFos	FBJ osteosarcoma oncogene	protein-coding
mm_132512.1	chr16	37037876	37037889	+	1	NA	intron (NM_029977, intron 9 of 29)	Lx5c|LINE|L1	26096	NM_001159369	77782	Mm.259114	NM_029977	ENSMUSG00000034206	Polq	A430110D14Rik	polymerase (DNA directed), theta	protein-coding
mm_14017.1	chr2	122150876	122150886	+	1	NA	exon (NM_009735, exon 2 of 4)	exon (NM_009735, exon 2 of 4)	3194	NM_009735	12010	Mm.163	NM_009735	ENSMUSG00000060802	B2m	Ly-m11|beta2-m|beta2m	beta-2 microglobulin	protein-coding
mm_11139.1	chr2	28479373	28479397	+	1	NA	Intergenic	RMER17B|LTR|ERVK	11319	NM_001166031	118451	Mm.294951	NM_080452	ENSMUSG00000035772	Mrps2	1500019M10Rik	mitochondrial ribosomal protein S2	protein-coding
mm_1671.1	chr1	74791807	74791818	+	1	NA	promoter-TSS (NM_009518)	promoter-TSS (NM_009518)	-207	NM_009518	22409	Mm.5130	NM_009518	ENSMUSG00000026167	Wnt10a	-	wingless-type MMTV integration site family, member 10A	protein-coding
mm_28564.1	chr3	93444803	93444843	-	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	2493	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_153369.1	chr19	40271875	40271888	-	1	NA	promoter-TSS (NM_016861)	promoter-TSS (NM_016861)	-265	NM_016861	54132	Mm.5567	NM_016861	ENSMUSG00000055044	Pdlim1	CLP36|Clim1|mClim1	PDZ and LIM domain 1 (elfin)	protein-coding
mm_90594.1	chr10	128292492	128292499	+	1	NA	3' UTR (NM_019963, exon 24 of 24)	3' UTR (NM_019963, exon 24 of 24)	5589	NM_031252	83430	Mm.125482	NM_031252	ENSMUSG00000025383	Il23a	IL-23|p19	interleukin 23, alpha subunit p19	protein-coding
mm_33429.1	chr4	130055091	130055101	+	1	NA	intron (NM_028266, intron 8 of 69)	intron (NM_028266, intron 8 of 69)	7256	NM_028266	107581	Mm.41860	NM_028266	ENSMUSG00000040690	Col16a1	2700007F12Rik|A530052M23Rik|AI838662|CA1F	collagen, type XVI, alpha 1	protein-coding
mm_108021.1	chr12	73605133	73605166	+	1	NA	intron (NM_001313977, intron 2 of 14)	intron (NM_001313977, intron 2 of 14)	20353	NM_008856	18755	Mm.341677	NM_008856	ENSMUSG00000021108	Prkch	Pkch	protein kinase C, eta	protein-coding
mm_97737.1	chr11	80431467	80431476	+	1	NA	intron (NM_178616, intron 1 of 13)	intron (NM_178616, intron 1 of 13)	2856	NM_178616	69077	Mm.260539	NM_178616	ENSMUSG00000017428	Psmd11	1700089D09Rik|1810019E17Rik|2610024G20Rik|2810055C24Rik|C78232|P44.5|S9	proteasome (prosome, macropain) 26S subunit, non-ATPase, 11	protein-coding
mm_80200.1	chr9	72401743	72401745	+	1	NA	Intergenic	Intergenic	-36785	NM_008613	17427	Mm.387671	NM_008613	ENSMUSG00000032221	Mns1	AW546487	meiosis-specific nuclear structural protein 1	protein-coding
mm_152706.1	chr19	17342059	17342073	-	1	NA	intron (NM_010265, intron 1 of 2)	intron (NM_010265, intron 1 of 2)	-2561	NM_001136484	14537	Mm.244825	NM_010265	ENSMUSG00000038843	Gcnt1	5630400D21Rik|B130048E03|C2 GlcNAcT|C2GNT|IGnT	glucosaminyl (N-acetyl) transferase 1, core 2	protein-coding
mm_21938.1	chr2	167060103	167060127	-	1	NA	5' UTR (NM_001033196, exon 2 of 14)	5' UTR (NM_001033196, exon 2 of 14)	-2819	NR_138563	68949	Mm.391959	NM_001081005		Zfas1	1500012F01Rik|Zfos1	zinc finger, NFX1-type containing 1, antisense RNA 1	ncRNA
mm_10304.1	chr2	11171882	11171915	+	1	NA	promoter-TSS (NM_008859)	promoter-TSS (NM_008859)	-484	NM_008859	18761	Mm.329993	NM_008859	ENSMUSG00000026778	Prkcq	A130035A12Rik|AW494342|PKC-0|PKC-theta|PKCtheta|Pkcq	protein kinase C, theta	protein-coding
mm_90333.1	chr10	127079041	127079069	+	1	NA	5' UTR (NM_001301014, exon 1 of 18)	5' UTR (NM_001301014, exon 1 of 18)	148	NM_001033263	216439	Mm.336761	NM_001033263	ENSMUSG00000025422	Agap2	AGAP-2|Centg1|PIKE|cnt-g1|mKIAA0167	ArfGAP with GTPase domain, ankyrin repeat and PH domain 2	protein-coding
mm_18481.1	chr2	62573906	62573979	-	1	NA	promoter-TSS (NM_007986)	promoter-TSS (NM_007986)	79	NM_007986	14089	Mm.41816	NM_007986	ENSMUSG00000000392	Fap	SIMP	fibroblast activation protein	protein-coding
mm_75045.1	chr8	32820157	32820184	-	1	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	129856	NM_001177589	100042715	Mm.291093	NM_001177589		Gm3985	-	predicted gene 3985	protein-coding
mm_77007.1	chr8	107505712	107505725	-	1	NA	intron (NM_025830, intron 6 of 23)	intron (NM_025830, intron 6 of 23)	-45526	NR_029553	387158		NR_029553	ENSMUSG00000065439	Mir140	Mirn140|mir-140|mmu-mir-140	microRNA 140	ncRNA
mm_122697.1	chr14	52088823	52088827	-	1	NA	intron (NM_001170982, intron 1 of 7)	intron (NM_001170982, intron 1 of 7)	15203	NM_001170982	15381	Mm.427321	NM_016884	ENSMUSG00000060373	Hnrnpc	AL022939|D14Wsu171e|Hnrpc|Hnrpc1|Hnrpc2|hnRNPC1|hnRNPC2|hnrnp-C	heterogeneous nuclear ribonucleoprotein C	protein-coding
mm_31517.1	chr4	54297858	54297881	+	1	NA	Intergenic	Intergenic	471824	NM_028053	52076	Mm.27184	NM_028053	ENSMUSG00000028420	Tmem38b	1600017F22Rik|AA437809|AV051057|D4Ertd89e|TRIC-B|mg33b	transmembrane protein 38B	protein-coding
mm_85703.1	chr9	108110817	108110868	-	1	NA	exon (NM_007567, exon 5 of 12)	exon (NM_007567, exon 5 of 12)	-16362	NM_146226	235606	Mm.219639	NM_146226	ENSMUSG00000032590	Apeh	-	acylpeptide hydrolase	protein-coding
mm_96780.1	chr11	69940587	69940599	+	1	NA	exon (NM_016875, exon 7 of 9)	exon (NM_016875, exon 7 of 9)	4265	NM_001347634	53422	Mm.29286	NM_016875	ENSMUSG00000018554	Ybx2	Msy2	Y box protein 2	protein-coding
mm_58865.1	chr7	16922050	16922064	+	1	NA	intron (NM_007590, intron 1 of 5)	intron (NM_007590, intron 1 of 5)	1975	NM_007590	12315	Mm.288630	NM_007590	ENSMUSG00000019370	Calm3	CaMA|R75142	calmodulin 3	protein-coding
mm_128877.1	chr15	73052238	73052245	-	1	NA	exon (NM_001164643, exon 3 of 9)	exon (NM_001164643, exon 3 of 9)	3571	NM_029640	76510	Mm.158902	NM_029640	ENSMUSG00000047921	Trappc9	1810044A24Rik|2900005P22Rik|4632408O18Rik|Ibp|Nibp|TRS130|mKIAA1882	trafficking protein particle complex 9	protein-coding
mm_1600.1	chr1	74375584	74375605	+	1	NA	intron (NM_013612, intron 1 of 14)	intron (NM_013612, intron 1 of 14)	391	NM_013612	18173	Mm.2913	NM_013612	ENSMUSG00000026177	Slc11a1	Bcg|Ity|Ity1|Lsh|Nramp|Nramp1|ity	solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1	protein-coding
mm_57939.1	chr6	134792371	134792386	-	1	NA	5' UTR (NM_130447, exon 1 of 7)	5' UTR (NM_130447, exon 1 of 7)	250	NM_130447	70686	Mm.491182	NM_130447	ENSMUSG00000030203	Dusp16	3830417M17Rik|AW558566|D6Ertd213e|MKP-7|MKP7|Mkpm	dual specificity phosphatase 16	protein-coding
mm_124634.1	chr15	4069312	4069318	+	1	NA	intron (NM_024188, intron 7 of 16)	intron (NM_024188, intron 7 of 16)	-41909	NR_028266	414066	Mm.394461	NR_028266		BC037032	-	cDNA Sequence BC037032	ncRNA
mm_68285.1	chr7	105633434	105633442	-	1	NA	TTS (NM_029802)	TTS (NM_029802)	133	NM_018880	55992	Mm.29290	NM_018880	ENSMUSG00000036989	Trim3	BERP1|HAC1|Rnf22	tripartite motif-containing 3	protein-coding
mm_139932.1	chr17	71070655	71070656	+	1	NA	intron (NM_010867, intron 13 of 37)	intron (NM_010867, intron 13 of 37)	51098	NM_001083934	17929	Mm.4103	NM_010867	ENSMUSG00000024049	Myom1	D430047A17Rik	myomesin 1	protein-coding
mm_171579.1	chr4	147461123	147461137	+	1	NA	intron (NM_001039209, intron 1 of 2)	intron (NM_001039209, intron 1 of 2)	-92147	NM_001014397	433804	Mm.332047	NM_001014397	ENSMUSG00000065999	Zfp985	Gm13154|OTTMUSG00000010673	zinc finger protein 985	protein-coding
mm_25479.1	chr3	108940109	108940125	+	1	NA	promoter-TSS (NM_001078646)	promoter-TSS (NM_001078646)	33	NM_025723	66715	Mm.158124	NM_025723	ENSMUSG00000045662	Henmt1	4921515J06Rik|Hen1|mHEN1	HEN1 methyltransferase homolog 1 (Arabidopsis)	protein-coding
mm_14577.1	chr2	135659541	135659591	+	1	NA	Intergenic	CpG	-76346	NR_015544	320684	Mm.421433	NR_015544	ENSMUSG00000085631	9630028H03Rik	-	RIKEN cDNA 9630028H03 gene	ncRNA
mm_4405.1	chr1	172475388	172475412	+	1	NA	promoter-TSS (NM_029612)	promoter-TSS (NM_029612)	40	NM_029612	98365	Mm.150050	NM_029612	ENSMUSG00000026548	Slamf9	2310026I04Rik|AI462096|CD2F-10|CD84-H1|Cd2f10|SF2001	SLAM family member 9	protein-coding
mm_168403.1	chr11	30137303	30137306	-	1	NA	exon (NM_009260, exon 15 of 31)	exon (NM_009260, exon 15 of 31)	60953	NM_009260	20742	Mm.123110	NM_009260	ENSMUSG00000020315	Sptbn1	9930031C03Rik|AL033301|SPTB2|Spnb-2|Spnb2|elf1|elf3|mKIAA4049	spectrin beta, non-erythrocytic 1	protein-coding
mm_21888.1	chr2	166155327	166155338	-	1	NA	promoter-TSS (NM_001252578)	promoter-TSS (NM_001252578)	-47	NM_001252578	72043	Mm.1011	NM_028072	ENSMUSG00000006800	Sulf2	2010004N24Rik|AU020235|MSulf-2|mKIAA1247	sulfatase 2	protein-coding
mm_166701.1	chr6	115522105	115522106	+	1	NA	Intergenic	Intergenic	-22599	NM_199033	381802	Mm.291208	NM_199033	ENSMUSG00000042389	Tsen2	AU067695	tRNA splicing endonuclease subunit 2	protein-coding
mm_144150.1	chr18	5591392	5591408	+	1	NA	promoter-TSS (NM_011546)	promoter-TSS (NM_011546)	-460	NM_011546	21417	Mm.3929	NM_011546	ENSMUSG00000024238	Zeb1	3110032K11Rik|AREB6|BZP|MEB1|Nil2|TCF-8|Tcf18|Tcf8|Tw|ZEB|Zfhep|Zfhx1a|Zfx1a|Zfx1ha|[delta]EF1	zinc finger E-box binding homeobox 1	protein-coding
mm_156970.1	chrX	169997492	169997506	+	1	NA	Intergenic	CpG	-18582	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_1391.1	chr1	67123640	67123659	+	1	NA	intron (NM_001080809, intron 1 of 37)	intron (NM_001080809, intron 1 of 37)	622	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_60488.1	chr7	44478596	44478606	+	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	-5916	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_138929.1	chr17	43801871	43801882	+	1	NA	promoter-TSS (NM_207649)	promoter-TSS (NM_207649)	25	NM_207649	53901	Mm.251242	NM_030598	ENSMUSG00000039601	Rcan2	Csp2|Dscr1l1|MCIP2|ZAKI-4	regulator of calcineurin 2	protein-coding
mm_158737.1	chrX	164076101	164076129	-	1	NA	promoter-TSS (NM_009173)	promoter-TSS (NM_009173)	20	NM_001308386	20438	Mm.37215	NM_009173	ENSMUSG00000040749	Siah1b	AA960570|Sinh1b|siah-1b	seven in absentia 1B	protein-coding
mm_156578.1	chrX	152023035	152023059	+	1	NA	exon (NM_019710, exon 3 of 25)	exon (NM_019710, exon 3 of 25)	6619	NM_019710	24061	Mm.482095	NM_019710	ENSMUSG00000041133	Smc1a	5830426I24Rik|SMC-1A|Sb1.8|Smc1|Smc1alpha|Smc1l1|Smcb|mKIAA0178	structural maintenance of chromosomes 1A	protein-coding
mm_40996.1	chr5	77349239	77349276	+	1	NA	TTS (NM_008048)	TTS (NM_008048)	38773	NM_153798	231329	Mm.273217	NM_153798	ENSMUSG00000029250	Polr2b	Pol2rb|Rpb140|Rpb2	polymerase (RNA) II (DNA directed) polypeptide B	protein-coding
mm_141447.1	chr17	29981728	29981748	-	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	-23349	NM_148926	21769	Mm.220972	NM_148926	ENSMUSG00000044477	Zfand3	AW539211|TEG-27|Tex27	zinc finger, AN1-type domain 3	protein-coding
mm_135394.1	chr16	44484987	44485018	-	1	NA	TTS (NM_172506)	TTS (NM_172506)	73127	NR_037242	100526478		NR_037242	ENSMUSG00000093046	Mir3081	mir-3081|mmu-mir-3081	microRNA 3081	ncRNA
mm_167588.1	chr9	46240836	46240850	+	1	NA	promoter-TSS (NM_007468)	promoter-TSS (NM_007468)	-1	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_83239.1	chr9	42399710	42399722	-	1	NA	5' UTR (NM_001324548, exon 1 of 24)	5' UTR (NM_001324548, exon 1 of 24)	213	NM_009347	21683	Mm.42209	NM_009347	ENSMUSG00000037705	Tecta	Tctna	tectorin alpha	protein-coding
mm_116511.1	chr13	45654675	45654694	-	1	NA	intron (NM_001199304, intron 5 of 6)	intron (NM_001199304, intron 5 of 6)	147240	NM_025508	66355	Mm.290802	NM_025508	ENSMUSG00000000253	Gmpr	2310004P21Rik|AV028449|GMPR 1	guanosine monophosphate reductase	protein-coding
mm_106466.1	chr11	120070589	120070595	-	1	NA	exon (NM_009734, exon 15 of 26)	exon (NM_009734, exon 15 of 26)	16235	NM_009734	12009	Mm.2556	NM_009734	ENSMUSG00000039781	Cep131	AZ1|Azi|Azi1	centrosomal protein 131	protein-coding
mm_42587.1	chr5	117356631	117356641	+	1	NA	promoter-TSS (NM_021539)	promoter-TSS (NM_021539)	-669	NM_021539	59043	Mm.28489	NM_021539	ENSMUSG00000029364	Wsb2	AA673511|Swip2|WSB-2	WD repeat and SOCS box-containing 2	protein-coding
mm_146473.1	chr18	88994608	88994608	+	1	NA	intron (NM_175542, intron 10 of 48)	intron (NM_175542, intron 10 of 48)	22578	NR_105777	102466633		NR_105777	ENSMUSG00000098676	Mir6359	Gm27328|mmu-mir-6359	microRNA 6359	ncRNA
mm_7120.1	chr1	90775732	90775744	-	1	NA	exon (NM_001243009, exon 37 of 41)	exon (NM_001243009, exon 37 of 41)	68233	NM_001243009	12835	Mm.7562	NM_009935	ENSMUSG00000048126	Col6a3	AI507288|Col6a-3	collagen, type VI, alpha 3	protein-coding
mm_33497.1	chr4	130823796	130823798	+	1	NA	3' UTR (NM_011520, exon 5 of 5)	3' UTR (NM_011520, exon 5 of 5)	31260	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_31471.1	chr4	49632135	49632139	+	1	NA	promoter-TSS (NM_001163263)	promoter-TSS (NM_001163263)	77	NM_182999	109331	Mm.24765	NM_182999	ENSMUSG00000028309	Rnf20	4833430L21Rik|AW540162|C79397|mKIAA4116	ring finger protein 20	protein-coding
mm_49547.1	chr6	30509828	30509848	+	1	NA	promoter-TSS (NM_027073)	promoter-TSS (NM_027073)	-11	NM_027073	75647	Mm.46117	NM_027073	ENSMUSG00000029784	Ssmem1	1700016K02Rik|1700025E21Rik	serine-rich single-pass membrane protein 1	protein-coding
mm_164926.1	chr18	78123370	78123372	-	1	NA	promoter-TSS (NM_028122)	promoter-TSS (NM_028122)	55	NM_001171010	108052	Mm.33832	NM_028122	ENSMUSG00000059336	Slc14a1	2610507K20Rik|3021401A05Rik|UT-B|Utb1	solute carrier family 14 (urea transporter), member 1	protein-coding
mm_116387.1	chr13	41184293	41184302	-	1	NA	3' UTR (NM_019423, exon 8 of 8)	3' UTR (NM_019423, exon 8 of 8)	35865	NM_001311121	54326	Mm.2567	NM_019423	ENSMUSG00000021364	Elovl2	AI317360|Ssc2	elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 2	protein-coding
mm_22261.1	chr2	178364874	178364898	-	1	NA	exon (NM_177191, exon 26 of 44)	exon (NM_177191, exon 26 of 44)	42772	NM_177191	320558	Mm.70781	NM_177191	ENSMUSG00000060445	Sycp2	3830402K23Rik|4930518F03Rik	synaptonemal complex protein 2	protein-coding
mm_15292.1	chr2	155381809	155381884	+	1	NA	promoter-TSS (NM_178111)	promoter-TSS (NM_178111)	-10	NM_178111	68728	Mm.293605	NM_178111	ENSMUSG00000038375	Trp53inp2	1110029F20Rik|Tp53inp2	transformation related protein 53 inducible nuclear protein 2	protein-coding
mm_91742.1	chr10	49218975	49218978	-	1	NA	intron (NM_001111268, intron 14 of 16)	intron (NM_001111268, intron 14 of 16)	-123133	NR_046212	100418235	Mm.185993	NR_046212		C130030K03Rik	-	proteasome (prosome, macropain) subunit, alpha type 6 pseudogene	pseudo
mm_172066.1	chr6	136531064	136531068	+	1	NA	intron (NM_019426, intron 1 of 14)	intron (NM_019426, intron 1 of 14)	12215	NM_019426	54343	Mm.173271	NM_019426	ENSMUSG00000030213	Atf7ip	2610204M12Rik|AM|Mcaf1	activating transcription factor 7 interacting protein	protein-coding
mm_36495.1	chr4	83285142	83285169	-	1	NA	intron (NM_027238, intron 2 of 19)	intron (NM_027238, intron 2 of 19)	39034	NM_027238	69863	Mm.5540	NM_025782	ENSMUSG00000038172	Ttc39b	1810054D07Rik|9130422G05Rik|AI450603|AV103077|AW215585	tetratricopeptide repeat domain 39B	protein-coding
mm_102994.1	chr11	69686888	69686898	-	1	NA	exon (NM_011614, exon 7 of 7)	exon (NM_011614, exon 7 of 7)	-1339	NM_023517	69583	Mm.8983	NM_023517	ENSMUSG00000089669	Tnfsf13	2310026N09Rik|April|Tall2|Tnlg7b|Trdl1	tumor necrosis factor (ligand) superfamily, member 13	protein-coding
mm_139757.1	chr17	64332407	64332417	+	1	NA	promoter-TSS (NM_001025309)	promoter-TSS (NM_001025309)	-529	NM_001025309	224938	Mm.489681	NM_144859	ENSMUSG00000024083	Pja2	AI447901|AL022700|Neurodap1|mKIAA0438	praja 2, RING-H2 motif containing	protein-coding
mm_87551.1	chr10	54074510	54074524	+	1	NA	exon (NM_008548, exon 2 of 13)	exon (NM_008548, exon 2 of 13)	1279	NM_008548	17155	Mm.117294	NM_008548	ENSMUSG00000003746	Man1a	Man1a1|PCR1	mannosidase 1, alpha	protein-coding
mm_2712.1	chr1	128141918	128141933	+	1	NA	intron (NM_181750, intron 1 of 26)	intron (NM_181750, intron 1 of 26)	38619	NM_181750	226412	Mm.221041	NM_181750	ENSMUSG00000056211	R3hdm1	R3hdm	R3H domain containing 1	protein-coding
mm_65297.1	chr7	24545995	24546012	-	1	NA	promoter-TSS (NM_001037143)	promoter-TSS (NM_001037143)	2	NM_001037143	641361	Mm.333661	NM_001037143	ENSMUSG00000011632	Pinlyp	2310033E01Rik	phospholipase A2 inhibitor and LY6/PLAUR domain containing	protein-coding
mm_59698.1	chr7	28597190	28597196	+	1	NA	intron (NM_027470, intron 1 of 9)	MIR|SINE|MIR	991	NM_027470	70584	Mm.21876	NM_027470	ENSMUSG00000030602	Pak4	5730488L07Rik|AW555722|mKIAA1142	p21 protein (Cdc42/Rac)-activated kinase 4	protein-coding
mm_152522.1	chr19	11304477	11304481	-	1	NA	Intergenic	Intergenic	-20666	NM_183190	269063	Mm.268940	NM_183190	ENSMUSG00000054523	Ms4a5	-	membrane-spanning 4-domains, subfamily A, member 5	protein-coding
mm_137239.1	chr17	24470173	24470186	+	1	NA	promoter-TSS (NM_025954)	promoter-TSS (NM_025954)	-294	NM_025954	67078	Mm.28541	NM_025954	ENSMUSG00000043445	Pgp	1700012G19Rik|AI481330|AUM|G3PP	phosphoglycolate phosphatase	protein-coding
mm_53218.1	chr6	126854373	126854383	+	1	NA	intron (NM_009650, intron 1 of 5)	B4A|SINE|B4	1280	NM_009650	11642	Mm.87748	NM_009650	ENSMUSG00000030344	Akap3	Prka3	A kinase (PRKA) anchor protein 3	protein-coding
mm_48356.1	chr5	139372214	139372242	-	1	NA	intron (NM_028469, intron 2 of 4)	CpG	-2483	NR_029768	723898		NR_029768	ENSMUSG00000065593	Mir339	Mirn339|mir-339|mmu-mir-339	microRNA 339	ncRNA
mm_65262.1	chr7	19921105	19921121	-	1	NA	promoter-TSS (NM_027514)	promoter-TSS (NM_027514)	30	NM_027514	52118	Mm.227506	NM_027514	ENSMUSG00000040511	Pvr	3830421F03Rik|CD155|D7Ertd458e|HVED|PVS|Taa1|Tage4|mE4|necl-5	poliovirus receptor	protein-coding
mm_9664.1	chr1	177796664	177796673	-	1	NA	promoter-TSS (NM_007422)	promoter-TSS (NM_007422)	-159	NM_007422	11566	Mm.338021	NM_007422	ENSMUSG00000015961	Adss	AI314886|AS|Adss2	adenylosuccinate synthetase, non muscle	protein-coding
mm_79500.1	chr9	57158378	57158416	+	1	NA	promoter-TSS (NM_025417)	promoter-TSS (NM_025417)	-98	NM_025417	66199	Mm.41687	NM_025417	ENSMUSG00000032299	Commd4	1110039H05Rik	COMM domain containing 4	protein-coding
mm_33543.1	chr4	130934582	130934593	+	1	NA	3' UTR (NM_010686, exon 8 of 8)	3' UTR (NM_010686, exon 8 of 8)	-9798	NM_010769	17180	Mm.271796	NM_010769	ENSMUSG00000040533	Matn1	CMP|Crtm|Mat1|matrilin-1	matrilin 1, cartilage matrix protein	protein-coding
mm_139229.1	chr17	47730748	47730766	+	1	NA	exon (NM_025973, exon 5 of 9)	exon (NM_025973, exon 5 of 9)	3915	NM_025973	109820	Mm.22957	NM_025973	ENSMUSG00000023987	Pgc	2210410L06Rik|Upg-1|Upg1	progastricsin (pepsinogen C)	protein-coding
mm_10690.1	chr2	22622348	22622366	+	1	NA	promoter-TSS (NM_008078)	promoter-TSS (NM_008078)	30	NM_008078	14417	Mm.4784	NM_008078	ENSMUSG00000026787	Gad2	6330404F12Rik|GAD(65)|GAD65|Gad-2	glutamic acid decarboxylase 2	protein-coding
mm_61314.1	chr7	68102300	68102303	+	1	NA	intron (NM_010513, intron 2 of 20)	intron (NM_010513, intron 2 of 20)	150044	NM_010513	16001	Mm.275742	NM_010513	ENSMUSG00000005533	Igf1r	A330103N21Rik|CD221|D930020L01|IGF-1R|hyft	insulin-like growth factor I receptor	protein-coding
mm_83917.1	chr9	56418929	56418963	-	1	NA	promoter-TSS (NM_025812)	promoter-TSS (NM_025812)	100	NM_025812	66867	Mm.150856	NM_025812	ENSMUSG00000032329	Hmg20a	1200004E06Rik|5730490E10Rik|Hmgxb1|Ibraf	high mobility group 20A	protein-coding
mm_51190.1	chr6	71199872	71199888	+	1	NA	promoter-TSS (NM_017399)	promoter-TSS (NM_017399)	-8	NM_017399	14080	Mm.22126	NM_017399	ENSMUSG00000054422	Fabp1	Fabpl|L-FABP	fatty acid binding protein 1, liver	protein-coding
mm_91569.1	chr10	40072993	40072996	-	1	NA	intron (NM_001114332, intron 3 of 5)	intron (NM_001114332, intron 3 of 5)	-47726	NM_144821	215929	Mm.55513	NM_144821	ENSMUSG00000038522	Mfsd4b1	AI317395|AI482555|Naglt1a	major facilitator superfamily domain containing 4B1	protein-coding
mm_89219.1	chr10	86779098	86779104	+	1	NA	promoter-TSS (NM_175331)	promoter-TSS (NM_175331)	96	NM_175331	103466	Mm.200446	NM_175331	ENSMUSG00000054027	Nt5dc3	AU040402|AW540062|C630002B14Rik|TU12B1-TY	5'-nucleotidase domain containing 3	protein-coding
mm_55805.1	chr6	82883859	82883864	-	1	NA	Intergenic	MIRc|SINE|MIR	-2008	NR_040520	69652	Mm.96357	NR_040520	ENSMUSG00000100291	2310069B03Rik	-	RIKEN cDNA 2310069B03 gene	ncRNA
mm_153370.1	chr19	40293410	40293430	-	1	NA	3' UTR (NM_001034964, exon 22 of 22)	3' UTR (NM_001034964, exon 22 of 22)	-21804	NM_016861	54132	Mm.5567	NM_016861	ENSMUSG00000055044	Pdlim1	CLP36|Clim1|mClim1	PDZ and LIM domain 1 (elfin)	protein-coding
mm_113958.1	chr13	51157179	51157182	+	1	NA	Intergenic	PB1D10|SINE|Alu	-13845	NM_029173	75124	Mm.179243	NM_029173	ENSMUSG00000021396	Nxnl2	4930519N16Rik|Rdcvf2	nucleoredoxin-like 2	protein-coding
mm_133097.1	chr16	64851999	64852074	+	1	NA	promoter-TSS (NM_178647)	promoter-TSS (NM_178647)	-49	NM_178647	106143	Mm.10160	NM_178647	ENSMUSG00000054604	Cggbp1	AA960172|AL023996|AW045841	CGG triplet repeat binding protein 1	protein-coding
mm_64864.1	chr7	13038312	13038322	-	1	NA	promoter-TSS (NM_145578)	promoter-TSS (NM_145578)	-42	NM_001168469	22192	Mm.196580	NM_145578	ENSMUSG00000005575	Ube2m	2510040H03Rik|UBC12|Ubc-rs2	ubiquitin-conjugating enzyme E2M	protein-coding
mm_28396.1	chr3	90052464	90052521	-	1	NA	promoter-TSS (NM_001165987)	promoter-TSS (NM_001165987)	-17	NM_001165987	74383	Mm.25610	NM_028475	ENSMUSG00000042520	Ubap2l	3110083O19Rik|4932431F02Rik|A430103N23Rik|C77168|Nice-4|mKIAA0144	ubiquitin-associated protein 2-like	protein-coding
mm_21503.1	chr2	163517616	163517622	-	1	NA	intron (NM_001312907, intron 1 of 10)	intron (NM_001312907, intron 1 of 10)	10762	NM_001312907	15378	Mm.202383	NM_008261	ENSMUSG00000017950	Hnf4a	HNF-4|Hnf4|Hnf4alpha|MODY1|Nr2a1|TCF-14|Tcf14	hepatic nuclear factor 4, alpha	protein-coding
mm_18049.1	chr2	39185552	39185554	-	1	NA	intron (NM_178778, intron 2 of 17)	ID_B1|SINE|B4	5177	NM_178778	320271	Mm.204836	NM_178778	ENSMUSG00000035236	Scai	9330112M16|A930041I02Rik|AI662729	suppressor of cancer cell invasion	protein-coding
mm_104685.1	chr11	97718438	97718451	-	1	NA	3' UTR (NM_054051, exon 10 of 10)	3' UTR (NM_054051, exon 10 of 10)	15010	NM_011971	26446	Mm.21874	NM_011971	ENSMUSG00000069744	Psmb3	AL033320|C10-II	proteasome (prosome, macropain) subunit, beta type 3	protein-coding
mm_133165.1	chr16	70499390	70499400	+	1	NA	intron (NM_028803, intron 12 of 15)	intron (NM_028803, intron 12 of 15)	-117030	NR_040474	52645	Mm.188475	NR_040474		D16Ertd519e	-	DNA segment, Chr 16, ERATO Doi 519, expressed	ncRNA
mm_34370.1	chr4	144893212	144893224	+	1	NA	promoter-TSS (NM_011303)	promoter-TSS (NM_011303)	81	NM_011303	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding
mm_21980.1	chr2	167421452	167421467	-	1	NA	promoter-TSS (NM_001304542)	promoter-TSS (NM_001304542)	-251	NM_148929	77031	Mm.278924	NM_148929	ENSMUSG00000039463	Slc9a8	1200006P13Rik|6430709P13Rik|AI182282|NHE-8|NHE8	solute carrier family 9 (sodium/hydrogen exchanger), member 8	protein-coding
mm_145470.1	chr18	60300966	60300983	+	1	NA	exon (NM_001101475, exon 2 of 2)	exon (NM_001101475, exon 2 of 2)	7594	NM_001101475	240328	Mm.329461	NM_001101475	ENSMUSG00000090942	F830016B08Rik	Ifgga4	RIKEN cDNA F830016B08 gene	protein-coding
mm_163010.1	chr11	40673890	40673898	-	1	NA	Intergenic	Intergenic	18788	NM_134017	108645	Mm.293771	NM_134017	ENSMUSG00000042032	Mat2b	1110064C04Rik|2410018D16Rik|AI182287|AU022853|MAT-II|MATIIbeta|TGR	methionine adenosyltransferase II, beta	protein-coding
mm_120537.1	chr14	67234589	67234617	+	1	NA	intron (NM_010095, intron 1 of 16)	CpG	1311	NM_001276387	13592	Mm.319947	NM_010095	ENSMUSG00000022053	Ebf2	D14Ggc1e|EBF-2|Mmot1|O/E-3|OE-3	early B cell factor 2	protein-coding
mm_140781.1	chr17	17883964	17883974	-	1	NA	promoter-TSS (NM_013521)	promoter-TSS (NM_013521)	-30	NM_013521	14293	Mm.56951	NM_013521	ENSMUSG00000045551	Fpr1	FPR|LXA4R|fMLF-R	formyl peptide receptor 1	protein-coding
mm_34804.1	chr4	154864503	154864507	+	1	NA	intron (NM_172878, intron 6 of 6)	intron (NM_172878, intron 6 of 6)	-5080	NM_013783	27390	Mm.116944	NM_013783	ENSMUSG00000058183	Mmel1	Mell1|NEP2|NEPII|Nl1|SEP	membrane metallo-endopeptidase-like 1	protein-coding
mm_119437.1	chr14	46387488	46387525	+	1	NA	intron (NM_007554, intron 1 of 3)	CpG	3163	NM_001316360	12159	Mm.6813	NM_007554	ENSMUSG00000021835	Bmp4	Bmp-4|Bmp2b|Bmp2b-1|Bmp2b1	bone morphogenetic protein 4	protein-coding
mm_18582.1	chr2	66210181	66210184	-	1	NA	intron (NM_001047604, intron 19 of 28)	intron (NM_001047604, intron 19 of 28)	46435	NM_001047604	73668	Mm.250868	NM_001047604	ENSMUSG00000034848	Ttc21b	2410066K11Rik|Thm1|aln|mKIAA1992	tetratricopeptide repeat domain 21B	protein-coding
mm_31227.1	chr4	44167448	44167466	+	1	NA	promoter-TSS (NM_175201)	promoter-TSS (NM_175201)	81	NM_175201	73469	Mm.262859	NM_175201	ENSMUSG00000035696	Rnf38	1700065B19Rik|2610202O07Rik|AA673263|Oip1	ring finger protein 38	protein-coding
mm_96842.1	chr11	70029814	70029837	+	1	NA	intron (NM_001109752, intron 2 of 19)	intron (NM_001109752, intron 2 of 19)	11220	NM_007864	13385	Mm.27256	NM_007864	ENSMUSG00000020886	Dlg4	Dlgh4|PSD-95|PSD95|SAP90|SAP90A	discs, large homolog 4 (Drosophila)	protein-coding
mm_132192.1	chr16	32431291	32431308	+	1	NA	promoter-TSS (NM_001163160)	promoter-TSS (NM_001163160)	69	NM_001163160	13026	Mm.98775	NM_009981	ENSMUSG00000005615	Pcyt1a	CTalpha|Cctalpha|Ctpct|Cttalpha	phosphate cytidylyltransferase 1, choline, alpha isoform	protein-coding
mm_170303.1	chr18	34631219	34631224	+	1	NA	TTS (NM_178347)	TTS (NM_178347)	6188	NM_001166406	19348	Mm.258846	NM_009004	ENSMUSG00000003779	Kif20a	AA415432|Rab6kifl	kinesin family member 20A	protein-coding
mm_163592.1	chr13	41381438	41381443	-	1	NA	intron (NM_001111324, intron 2 of 7)	intron (NM_001111324, intron 2 of 7)	-22439	NM_017464	18003	Mm.288980	NM_017464	ENSMUSG00000021365	Nedd9	Cas-L|CasL|HEF1|MEF1|Nedd-9|p105	neural precursor cell expressed, developmentally down-regulated gene 9	protein-coding
mm_74501.1	chr8	8021159	8021161	-	1	NA	Intergenic	Lx5b|LINE|L1	639613	NM_010111	13642	Mm.209813	NM_010111	ENSMUSG00000001300	Efnb2	ELF-2|Epl5|Eplg5|Htk-L|LERK-5|Lerk5|NLERK-1	ephrin B2	protein-coding
mm_81517.1	chr9	110045433	110045437	+	1	NA	intron (NM_001205330, intron 8 of 18)	intron (NM_001205330, intron 8 of 18)	-6586	NM_001311163	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_54742.1	chr6	41030941	41030962	-	1	NA	3' UTR (NM_023333, exon 5 of 5)	3' UTR (NM_023333, exon 5 of 5)	4558	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_54797.1	chr6	41680835	41680844	-	1	NA	promoter-TSS (NM_001007572)	promoter-TSS (NM_001007572)	-116	NM_001007572	194352	Mm.135734	NM_001007572	ENSMUSG00000036899	Trpv5	CAT2|D630033B11|ECAC1	transient receptor potential cation channel, subfamily V, member 5	protein-coding
mm_11260.1	chr2	29965316	29965328	+	1	NA	promoter-TSS (NM_001177668)	promoter-TSS (NM_001177668)	-238	NM_001177668	20740	Mm.204969	NM_001076554	ENSMUSG00000057738	Sptan1	2610027H02Rik|Spna-2|Spna2	spectrin alpha, non-erythrocytic 1	protein-coding
mm_140893.1	chr17	24025234	24025239	-	1	NA	Intergenic	MTC-int|LTR|ERVL-MaLR	-13007	NM_175440	213171	Mm.133083	NM_175440	ENSMUSG00000050762	Prss27	CAPH2|Mpn|marapsin	protease, serine 27	protein-coding
mm_130774.1	chr15	101463759	101463770	-	1	NA	promoter-TSS (NM_001166157)	promoter-TSS (NM_001166157)	1	NM_001166157	64818	Mm.347934	NM_001166157	ENSMUSG00000067615	Krt81	AA589625|Krt2-19	keratin 81	protein-coding
mm_70767.1	chr8	21946751	21946762	+	1	NA	promoter-TSS (NM_139223)	promoter-TSS (NM_139223)	-6	NM_139223	246083	Mm.219548	NM_139223	ENSMUSG00000044222	Defb13	BD-13	defensin beta 13	protein-coding
mm_39522.1	chr5	21258127	21258174	+	1	NA	intron (NM_175437, intron 19 of 30)	intron (NM_175437, intron 19 of 30)	71883	NM_175437	212167	Mm.121705	NM_175437	ENSMUSG00000039934	Gsap	A530088I07Rik|Pion	gamma-secretase activating protein	protein-coding
mm_19365.1	chr2	91168625	91168627	-	1	NA	intron (NM_001177720, intron 9 of 34)	PB1D7|SINE|Alu	10695	NM_001177720	228355	Mm.36410	NM_145527	ENSMUSG00000040687	Madd	9630059K23Rik|IG20	MAP-kinase activating death domain	protein-coding
mm_171970.1	chr5	88167831	88167853	-	1	NA	Intergenic	ERVB7_1-LTR_MM|LTR|ERVK	81286	NM_001252680	20600	Mm.1397	NM_021289	ENSMUSG00000029281	Smr2	MSG2|Vcs2	submaxillary gland androgen regulated protein 2	protein-coding
mm_4417.1	chr1	172500003	172500013	+	1	NA	promoter-TSS (NM_178598)	promoter-TSS (NM_178598)	-238	NM_178598	21346	Mm.271711	NM_178598	ENSMUSG00000026547	Tagln2	2700094C18Rik|SM22beta|Sm22B|Sm22a	transgelin 2	protein-coding
mm_77191.1	chr8	111933762	111933816	-	1	NA	promoter-TSS (NM_001033321)	promoter-TSS (NM_001033321)	2	NM_001033321	234740	Mm.87513	NM_001033321	ENSMUSG00000031951	Tmem231	4932417I16Rik|Gm178	transmembrane protein 231	protein-coding
mm_77343.1	chr8	119572081	119572091	-	1	NA	intron (NM_175185, intron 1 of 4)	intron (NM_175185, intron 1 of 4)	3114	NM_175185	72552	Mm.36756	NM_175185	ENSMUSG00000034189	Hsdl1	2700067E09Rik	hydroxysteroid dehydrogenase like 1	protein-coding
mm_160219.1	chr7	100293915	100293915	+	1	NA	exon (NM_177161, exon 3 of 13)	exon (NM_177161, exon 3 of 13)	8395	NM_177161	320452	Mm.150294	NM_177161	ENSMUSG00000051048	P4ha3	D930031A02Rik	procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide III	protein-coding
mm_75973.1	chr8	72135732	72135766	-	1	NA	intron (NM_001001491, intron 1 of 7)	CpG	457	NM_001001491	326618	Mm.295124	NM_001001491	ENSMUSG00000031799	Tpm4	2610528G24Rik|Tpm4.2|Tpm4.2cy	tropomyosin 4	protein-coding
mm_107076.1	chr12	16965036	16965065	+	1	NA	exon (NM_009072, exon 19 of 33)	exon (NM_009072, exon 19 of 33)	35068	NM_172574	217430	Mm.379451	NM_172574	ENSMUSG00000045679	Pqlc3	C78076|E030024M05Rik	PQ loop repeat containing	protein-coding
mm_138648.1	chr17	35866933	35866946	+	1	NA	5' UTR (NM_175242, exon 1 of 3)	5' UTR (NM_175242, exon 1 of 3)	324	NM_175242	76448	Mm.359982	NM_175242	ENSMUSG00000034595	Ppp1r18	2310014H01Rik|AA407849|AI450394	protein phosphatase 1, regulatory subunit 18	protein-coding
mm_96742.1	chr11	69846375	69846387	+	1	NA	promoter-TSS (NM_001168497)	promoter-TSS (NM_001168497)	9	NM_001168497	70310	Mm.28874	NM_023564	ENSMUSG00000019461	Plscr3	2210403O21Rik|2610037N06Rik|ESTM3|X83310	phospholipid scramblase 3	protein-coding
mm_89139.1	chr10	85829371	85829413	+	1	NA	Intergenic	CpG	-42439	NM_133993	103136	Mm.18834	NM_133993	ENSMUSG00000001785	Pwp1	2310058A11Rik|2610205J09Rik|AI098170|AL022879|AV083409|AW550690	PWP1 homolog, endonuclein	protein-coding
mm_103687.1	chr11	79483897	79483901	-	1	NA	intron (NR_045305, intron 1 of 3)	intron (NR_045305, intron 1 of 3)	132	NR_045305	104522	Mm.436987	NR_045305	ENSMUSG00000091523	AU040972	AU040954	expressed sequence AU040972	ncRNA
mm_20167.1	chr2	122298719	122298737	-	1	NA	promoter-TSS (NM_177610)	promoter-TSS (NM_177610)	-172	NM_025777	66811	Mm.171333	NM_025777	ENSMUSG00000027225	Duoxa2	9030623N16Rik|Nip2	dual oxidase maturation factor 2	protein-coding
mm_4204.1	chr1	171231167	171231195	+	1	NA	exon (NM_010185, exon 2 of 5)	exon (NM_010185, exon 2 of 5)	3168	NM_010185	14127	Mm.22673	NM_010185	ENSMUSG00000058715	Fcer1g	AI573376|CD23|FcR-gamma|FcR[g]|FcRgamma|Fce1g|FcepsilonRI|Ly-50	Fc receptor, IgE, high affinity I, gamma polypeptide	protein-coding
mm_94175.1	chr10	128891675	128891715	-	1	NA	promoter-TSS (NM_010272)	promoter-TSS (NM_010272)	23	NM_010272	14561	Mm.299218	NM_010272	ENSMUSG00000025352	Gdf11	BMP-11|Bmp11	growth differentiation factor 11	protein-coding
mm_10341.1	chr2	11653589	11653598	+	1	NA	intron (NM_008367, intron 1 of 7)	intron (NM_008367, intron 1 of 7)	10801	NM_008367	16184	Mm.915	NM_008367	ENSMUSG00000026770	Il2ra	CD25|Il2r|Ly-43	interleukin 2 receptor, alpha chain	protein-coding
mm_23613.1	chr3	65528458	65528471	+	1	NA	promoter-TSS (NM_178892)	promoter-TSS (NM_178892)	17	NM_178892	99929	Mm.246398	NM_178892	ENSMUSG00000034640	Tiparp	ARTD14|AW558171|PARP7	TCDD-inducible poly(ADP-ribose) polymerase	protein-coding
mm_63885.1	chr7	137437583	137437589	+	1	NA	promoter-TSS (NM_023140)	promoter-TSS (NM_023140)	-62	NM_023140	30926	Mm.267692	NM_023140	ENSMUSG00000031068	Glrx3	PICOT|Txnl2	glutaredoxin 3	protein-coding
mm_133672.1	chr16	92083714	92083720	+	1	NA	3' UTR (NM_017391, exon 2 of 2)	3' UTR (NM_017391, exon 2 of 2)	25381	NM_080456	121022	Mm.217354	NM_080456	ENSMUSG00000039680	Mrps6	AW046321	mitochondrial ribosomal protein S6	protein-coding
mm_1297.1	chr1	64532821	64532859	+	1	NA	promoter-TSS (NM_009952)	promoter-TSS (NM_009952)	36	NM_001037726	12912	Mm.422634	NM_009952	ENSMUSG00000025958	Creb1	2310001E10Rik|3526402H21Rik|AV083133|Creb|Creb-1	cAMP responsive element binding protein 1	protein-coding
mm_45686.1	chr5	77355645	77355675	-	1	NA	exon (NM_008048, exon 2 of 5)	exon (NM_008048, exon 2 of 5)	45176	NM_153798	231329	Mm.273217	NM_153798	ENSMUSG00000029250	Polr2b	Pol2rb|Rpb140|Rpb2	polymerase (RNA) II (DNA directed) polypeptide B	protein-coding
mm_24630.1	chr3	94046722	94046722	+	1	NA	Intergenic	MTA_Mm|LTR|ERVL-MaLR	8163	NM_001163730	668359	Mm.80593	NM_001163730	ENSMUSG00000094328	Gm9125	EG668359	predicted gene 9125	protein-coding
mm_15641.1	chr2	163059168	163059193	+	1	NA	intron (NM_008652, intron 1 of 13)	B1_Mur3|SINE|Alu	4545	NM_008652	17865	Mm.4594	NM_008652	ENSMUSG00000017861	Mybl2	B-Myb|Bmyb	myeloblastosis oncogene-like 2	protein-coding
mm_134980.1	chr16	32079228	32079241	-	1	NA	5' UTR (NM_177326, exon 1 of 15)	5' UTR (NM_177326, exon 1 of 15)	108	NM_177326	224105	Mm.234204	NM_177326	ENSMUSG00000022781	Pak2	5330420P17Rik|A130002K10Rik|AI836325|D16Ertd269e|PAK-2|mKIAA4182	p21 protein (Cdc42/Rac)-activated kinase 2	protein-coding
mm_92182.1	chr10	67912621	67912685	-	1	NA	promoter-TSS (NM_178679)	promoter-TSS (NM_178679)	9	NM_178679	216049	Mm.268346	NM_178679	ENSMUSG00000037855	Zfp365	AI839779|AV340892|DBZ|Su48|Znf365|talanin	zinc finger protein 365	protein-coding
mm_130653.1	chr15	100636993	100637002	-	1	NA	promoter-TSS (NM_174992)	promoter-TSS (NM_174992)	-57	NM_001033872	207818	Mm.26282	NM_174992	ENSMUSG00000053559	Smagp	-	small cell adhesion glycoprotein	protein-coding
mm_167436.1	chr8	119666331	119666345	+	1	NA	promoter-TSS (NM_023395)	promoter-TSS (NM_023395)	-27	NM_023395	67866	Mm.87599	NM_023395	ENSMUSG00000023336	Wfdc1	2310058A03Rik|ps20	WAP four-disulfide core domain 1	protein-coding
mm_139802.1	chr17	66123541	66123582	+	1	NA	promoter-TSS (NM_001003919)	promoter-TSS (NM_001003919)	41	NM_001003919	320209	Mm.259605	NM_001003919	ENSMUSG00000035842	Ddx11	4732462I11Rik|CHL1|CHLR1|KRG2|essa15a	DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11	protein-coding
mm_137206.1	chr17	24035326	24035333	+	1	NA	Intergenic	RLTR30D2_MM|LTR|ERV1	-2914	NM_175440	213171	Mm.133083	NM_175440	ENSMUSG00000050762	Prss27	CAPH2|Mpn|marapsin	protease, serine 27	protein-coding
mm_136157.1	chr16	88225433	88225446	-	1	NA	intron (NM_146072, intron 1 of 16)	intron (NM_146072, intron 1 of 16)	64819	NM_146072	14805	Mm.5134	NM_010348	ENSMUSG00000022935	Grik1	A830007B11Rik|D16Ium24|D16Ium24e|GluK1|GluK5|Glur-5|Glur5|Glurbeta1	glutamate receptor, ionotropic, kainate 1	protein-coding
mm_26015.1	chr3	135438115	135438126	+	1	NA	promoter-TSS (NM_025356)	promoter-TSS (NM_025356)	545	NR_030689	319587	Mm.358971	NR_030689	ENSMUSG00000097032	4930539J05Rik	8030475D13Rik	RIKEN cDNA 4930539J05 gene	ncRNA
mm_140018.1	chr17	73804884	73804901	+	1	NA	promoter-TSS (NM_020578)	promoter-TSS (NM_020578)	51	NM_020578	57440	Mm.18526	NM_020578	ENSMUSG00000024065	Ehd3	Ehd2	EH-domain containing 3	protein-coding
mm_83617.1	chr9	48793966	48793969	-	1	NA	intron (NM_001033324, intron 2 of 6)	intron (NM_001033324, intron 2 of 6)	41978	NM_001033324	235320	Mm.457803	NM_001033324	ENSMUSG00000066687	Zbtb16	AI467657|PLZF|Zfp145|lu	zinc finger and BTB domain containing 16	protein-coding
mm_151207.1	chr19	53600378	53600435	+	1	NA	promoter-TSS (NM_007790)	promoter-TSS (NM_007790)	10	NM_007790	13006	Mm.14910	NM_007790	ENSMUSG00000024974	Smc3	Bamacan|Cspg6|HCAP|Mmip1|SMC-3|SmcD	structural maintenance of chromosomes 3	protein-coding
mm_171802.1	chr5	124540794	124540796	+	1	NA	promoter-TSS (NM_019770)	promoter-TSS (NM_019770)	4	NM_019770	56334	Mm.325307	NM_019770	ENSMUSG00000029390	Tmed2	1110032D12Rik|1810020N21Rik|Rnp24|Sid394|p24beta1	transmembrane p24 trafficking protein 2	protein-coding
mm_6274.1	chr1	69681086	69681122	-	1	NA	intron (NM_011770, intron 3 of 7)	intron (NM_011770, intron 3 of 7)	4856	NM_011770	22779	Mm.106343	NM_011770	ENSMUSG00000025997	Ikzf2	A730095J18Rik|Helios|Zfpn1a2|Znfn1a2	IKAROS family zinc finger 2	protein-coding
mm_41517.1	chr5	92387917	92387927	+	1	NA	promoter-TSS (NM_181728)	promoter-TSS (NM_181728)	-212	NM_181728	109979	Mm.263514	NM_181728	ENSMUSG00000034842	Art3	4930569O04Rik|ARTC3	ADP-ribosyltransferase 3	protein-coding
mm_71056.1	chr8	33732188	33732188	+	1	NA	promoter-TSS (NM_001167922)	promoter-TSS (NM_001167922)	121	NM_026584	68153	Mm.286104	NM_026584	ENSMUSG00000031585	Gtf2e2	34kDa|AI462509|C330006J08Rik	general transcription factor II E, polypeptide 2 (beta subunit)	protein-coding
mm_49138.1	chr6	8949813	8949830	+	1	NA	promoter-TSS (NM_008751)	promoter-TSS (NM_008751)	-198	NM_008751	18231	Mm.46954	NM_008751	ENSMUSG00000046178	Nxph1	C130005L03Rik	neurexophilin 1	protein-coding
mm_54446.1	chr6	34713163	34713174	-	1	NA	intron (NM_145575, intron 1 of 11)	(TG)n|Simple_repeat|Simple_repeat	3724	NM_145575	109624	Mm.308134	NM_145575	ENSMUSG00000029761	Cald1	4833423D12Rik|AI195384|AV071549|AW536160|C920027I18Rik	caldesmon 1	protein-coding
mm_46287.1	chr5	100217942	100217946	-	1	NA	non-coding (NR_040679, exon 4 of 4)	non-coding (NR_040679, exon 4 of 4)	7252	NR_040679	69571	Mm.396412	NR_040679	ENSMUSG00000100157	2310034O05Rik	-	RIKEN cDNA 2310034O05 gene	ncRNA
mm_135822.1	chr16	58499350	58499362	-	1	NA	intron (NM_018784, intron 2 of 10)	intron (NM_018784, intron 2 of 10)	23956	NM_018784	54613	Mm.212742	NM_018784	ENSMUSG00000022747	St3gal6	1700023B24Rik|AI930218|AW552396|Siat10|St3galVI	ST3 beta-galactoside alpha-2,3-sialyltransferase 6	protein-coding
mm_132366.1	chr16	34784897	34784909	+	1	NA	promoter-TSS (NM_139300)	promoter-TSS (NM_139300)	-47	NM_139300	107589	Mm.33360	NM_139300	ENSMUSG00000022836	Mylk	9530072E15Rik|A930019C19Rik|AW489456|KRP|MLCK108|MLCK210|Mlck|nmMlck|smMLCK	myosin, light polypeptide kinase	protein-coding
mm_110712.1	chr12	69372444	69372540	-	1	NA	5' UTR (NM_007481, exon 2 of 2)	5' UTR (NM_007481, exon 2 of 2)	342	NM_007481	11845	Mm.27308	NM_007481	ENSMUSG00000044147	Arf6	AI788669|AW496366	ADP-ribosylation factor 6	protein-coding
mm_99935.1	chr11	111026878	111026888	+	1	NA	3' UTR (NM_001252208, exon 2 of 2)	3' UTR (NM_001252208, exon 2 of 2)	3023	NM_001252208	16517	Mm.30176	NM_010604	ENSMUSG00000051497	Kcnj16	6430410F18Rik|AI132396|Kir5.1	potassium inwardly-rectifying channel, subfamily J, member 16	protein-coding
mm_75507.1	chr8	54412292	54412327	-	1	NA	Intergenic	Intergenic	117689	NM_029701	76687	Mm.86437	NM_029701	ENSMUSG00000054408	Spcs3	1810011E08Rik|SPC22/23	signal peptidase complex subunit 3 homolog (S. cerevisiae)	protein-coding
mm_56201.1	chr6	88875036	88875053	-	1	NA	promoter-TSS (NM_176973)	promoter-TSS (NM_176973)	0	NM_001347327	319655	Mm.302613	NM_176973	ENSMUSG00000033152	Podxl2	D130074J02Rik|PODLX2	podocalyxin-like 2	protein-coding
mm_51308.1	chr6	72313700	72313710	+	1	NA	intron (NM_001282071, intron 10 of 10)	intron (NM_001282071, intron 10 of 10)	9095	NM_147779	20388	Mm.46033	NM_147779	ENSMUSG00000056370	Sftpb	AI562151|SF-B|SP-B|Sftp-3|Sftp3	surfactant associated protein B	protein-coding
mm_46019.1	chr5	90904234	90904244	-	1	NA	exon (NM_009140, exon 2 of 4)	exon (NM_009140, exon 2 of 4)	340	NM_009140	20310	Mm.4979	NM_009140	ENSMUSG00000058427	Cxcl2	CINC-2a|GROb|Gro2|MIP-2|MIP-2a|Mgsa-b|Mip2|Scyb|Scyb2	chemokine (C-X-C motif) ligand 2	protein-coding
mm_145594.1	chr18	60986120	60986134	+	1	NA	3' UTR (NM_001286809, exon 6 of 6)	3' UTR (NM_001286809, exon 6 of 6)	22573	NM_001286809	12322	Mm.131530	NM_009792	ENSMUSG00000024617	Camk2a	CaMKII|R74975|mKIAA0968	calcium/calmodulin-dependent protein kinase II alpha	protein-coding
mm_163385.1	chr12	54141929	54141944	-	1	NA	Intergenic	Intergenic	61938	NM_028133	112407	Mm.133037	NM_028133	ENSMUSG00000035105	Egln3	2610021G09Rik|AI505553|AI648162|Hif-p4h-3|Phd3|SM-20	egl-9 family hypoxia-inducible factor 3	protein-coding
mm_158664.1	chrX	157492178	157492246	-	1	NA	promoter-TSS (NM_009214)	promoter-TSS (NM_009214)	-166	NM_009214	20603	Mm.18652	NM_009214	ENSMUSG00000071708	Sms	AI427066|Gy|SPMSY|SpmST|gyro	spermine synthase	protein-coding
mm_157779.1	chrX	73786889	73786899	-	1	NA	promoter-TSS (NM_008323)	promoter-TSS (NM_008323)	3	NM_008323	15929	Mm.14825	NM_008323	ENSMUSG00000002010	Idh3g	-	isocitrate dehydrogenase 3 (NAD+), gamma	protein-coding
mm_63995.1	chr7	140115813	140115826	+	1	NA	intron (NM_053119, intron 1 of 7)	intron (NM_053119, intron 1 of 7)	604	NM_053119	93747	Mm.24452	NM_053119	ENSMUSG00000025465	Echs1	C80529	enoyl Coenzyme A hydratase, short chain, 1, mitochondrial	protein-coding
mm_59811.1	chr7	29170321	29170327	+	1	NA	promoter-TSS (NM_182696)	promoter-TSS (NM_182696)	-66	NM_182696	243897	Mm.389886	NM_182694	ENSMUSG00000031493	Ggn	AI593290	gametogenetin	protein-coding
mm_58682.1	chr7	12512523	12512540	+	1	NA	promoter-TSS (NM_028434)	promoter-TSS (NM_028434)	-20	NM_028434	73090	Mm.84622	NM_028434	ENSMUSG00000030385	2900092C05Rik	-	RIKEN cDNA 2900092C05 gene	protein-coding
mm_3211.1	chr1	135836381	135836396	+	1	NA	promoter-TSS (NM_001130178)	promoter-TSS (NM_001130178)	54	NM_001130179	21956	Mm.247470	NM_011619	ENSMUSG00000026414	Tnnt2	Tnt|cTnT	troponin T2, cardiac	protein-coding
mm_72382.1	chr8	81558969	81558972	+	1	NA	intron (NM_001297591, intron 2 of 24)	RMER19A|LTR|ERVK	216408	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_60630.1	chr7	44748989	44748997	+	1	NA	promoter-TSS (NM_178734)	promoter-TSS (NM_178734)	364	NM_133945	101568	Mm.28816	NM_133945	ENSMUSG00000002205	Vrk3	AI428238	vaccinia related kinase 3	protein-coding
mm_11190.1	chr2	29122627	29122668	+	1	NA	Intergenic	Lx8|LINE|L1	-2345	NM_198033	269254	Mm.41867	NM_198033	ENSMUSG00000043535	Setx	A130090N03|A930037J23Rik|AOA2|AW060766|Als4|SCAR1|Sen1|mKIAA0625	senataxin	protein-coding
mm_89557.1	chr10	95218018	95218028	+	1	NA	intron (NM_009950, intron 2 of 2)	intron (NM_009950, intron 2 of 2)	-72198	NR_131146	628062		NR_131146		Gm29684	-	predicted gene, 29684	ncRNA
mm_106490.1	chr11	120237310	120237335	-	1	NA	intron (NM_001347621, intron 2 of 27)	CpG-2934	4375	NM_198423	268515	Mm.309498	NM_198423	ENSMUSG00000039741	Bahcc1	B930044J06|BC060615	BAH domain and coiled-coil containing 1	protein-coding
mm_70250.1	chr8	3482489	3482496	+	1	NA	intron (NM_029598, intron 4 of 8)	intron (NM_029598, intron 4 of 8)	-10646	NM_080461	140482	Mm.299073	NM_080461	ENSMUSG00000047264	Zfp358	Zfend	zinc finger protein 358	protein-coding
mm_12045.1	chr2	59160793	59160825	+	1	NA	promoter-TSS (NM_026361)	promoter-TSS (NM_026361)	-41	NM_026361	227937	Mm.260938	NM_026361	ENSMUSG00000026991	Pkp4	5031422I09Rik|9430019K17Rik|Armrp|p0071	plakophilin 4	protein-coding
mm_153590.1	chr19	43524463	43524580	-	1	NA	promoter-TSS (NM_010324)	promoter-TSS (NM_010324)	84	NM_010324	14718	Mm.19039	NM_010324	ENSMUSG00000025190	Got1	AI789014|Got-1|cAspAT|cCAT	glutamic-oxaloacetic transaminase 1, soluble	protein-coding
mm_27715.1	chr3	68692205	68692213	-	1	NA	intron (NM_001159424, intron 3 of 7)	intron (NM_001159424, intron 3 of 7)	785	NM_008351	16159	Mm.103783	NM_008351	ENSMUSG00000027776	Il12a	IL-12p35|Il-12a|Ll12a|p35	interleukin 12a	protein-coding
mm_81391.1	chr9	108985164	108985181	+	1	NA	promoter-TSS (NM_145077)	promoter-TSS (NM_145077)	-991	NM_145077	171530	Mm.388865	NM_145077	ENSMUSG00000049699	Ucn2	Ucn II|Ucn-2|ucn-II	urocortin 2	protein-coding
mm_74991.1	chr8	27174624	27174651	-	1	NA	promoter-TSS (NM_001080813)	promoter-TSS (NM_001080813)	9	NM_029423	75767	Mm.205335	NM_029423	ENSMUSG00000031488	Rab11fip1	2010200K21Rik|4833414G05Rik|Rcp	RAB11 family interacting protein 1 (class I)	protein-coding
mm_130469.1	chr15	98662872	98662911	-	1	NA	promoter-TSS (NM_001080981)	promoter-TSS (NM_001080981)	-2	NM_001080981	74351	Mm.45725	NM_001080981	ENSMUSG00000003360	Ddx23	3110082M05Rik|4921506D17Rik	DEAD (Asp-Glu-Ala-Asp) box polypeptide 23	protein-coding
mm_34685.1	chr4	151862245	151862255	+	1	NA	promoter-TSS (NM_001195565)	promoter-TSS (NM_001195565)	-482	NM_001195565	100072	Mm.318846	NM_001081557	ENSMUSG00000014592	Camta1	1810059M14Rik|2310058O09Rik|AI316882|AW987475|mKIAA0833	calmodulin binding transcription activator 1	protein-coding
mm_674.1	chr1	40465977	40466006	+	1	NA	promoter-TSS (NM_008365)	promoter-TSS (NM_008365)	-15	NM_008365	16182	Mm.253664	NM_008365	ENSMUSG00000026070	Il18r1	Il18ralpha|Il1rrp	interleukin 18 receptor 1	protein-coding
mm_14598.1	chr2	136058271	136058293	+	1	NA	5' UTR (NM_029530, exon 1 of 6)	5' UTR (NM_029530, exon 1 of 6)	355	NM_029530	76161	Mm.41638	NM_029530	ENSMUSG00000027270	Lamp5	3110035N03Rik|6330527O06Rik|BAD-LAMP|LAMP-5	lysosomal-associated membrane protein family, member 5	protein-coding
mm_115166.1	chr13	107955577	107955583	+	1	NA	Intergenic	Intergenic	-65516	NM_145456	67263	Mm.490418	NM_145456	ENSMUSG00000032846	Zswim6	2900036G02Rik|mKIAA1577	zinc finger SWIM-type containing 6	protein-coding
mm_56959.1	chr6	120037966	120037976	-	1	NA	5' UTR (NM_001185020, exon 1 of 26)	5' UTR (NM_001185020, exon 1 of 26)	684	NM_001199083	232341	Mm.333349	NM_198703	ENSMUSG00000045962	Wnk1	6430573H23Rik|EG406236|Hsn2|Prkwnk1|mKIAA0344	WNK lysine deficient protein kinase 1	protein-coding
mm_113310.1	chr13	30753479	30753499	+	1	NA	exon (NM_013674, exon 5 of 9)	exon (NM_013674, exon 5 of 9)	4256	NM_013674	16364	Mm.4677	NM_013674	ENSMUSG00000021356	Irf4	AI385587|IRF-4|LSIRF|NF-EM5|Spip	interferon regulatory factor 4	protein-coding
mm_10020.1	chr1	192074467	192074491	-	1	NA	intron (NM_011633, intron 1 of 9)	intron (NM_011633, intron 1 of 9)	18120	NM_011633	22033	Mm.380491	NM_011633		Traf5	-	TNF receptor-associated factor 5	protein-coding
mm_55857.1	chr6	83455455	83455472	-	1	NA	5' UTR (NM_001347313, exon 2 of 12)	5' UTR (NM_001347313, exon 2 of 12)	929	NM_001347313	194388	Mm.211030	NM_183138	ENSMUSG00000034832	Tet3	B430006D22Rik|BC037432|D230004J03Rik	tet methylcytosine dioxygenase 3	protein-coding
mm_97392.1	chr11	77802371	77802397	+	1	NA	intron (NM_001291214, intron 1 of 38)	intron (NM_001291214, intron 1 of 38)	1086	NM_001291215	360013	Mm.341248	NM_011586	ENSMUSG00000000631	Myo18a	MAJN|MyoPDZ|MysPDZ|SP-R210	myosin XVIIIA	protein-coding
mm_147533.1	chr18	53249677	53249693	-	1	NA	intron (NM_029394, intron 1 of 6)	intron (NM_029394, intron 1 of 6)	4023	NM_029394	69226	Mm.32414	NM_029394	ENSMUSG00000024535	Snx24	2810011K15Rik|5730433I16Rik|AI451341	sorting nexing 24	protein-coding
mm_87844.1	chr10	60749233	60749238	+	1	NA	intron (NM_023596, intron 2 of 5)	intron (NM_023596, intron 2 of 5)	3547	NM_023596	71279	Mm.284462	NM_023596	ENSMUSG00000020100	Slc29a3	4933435C21Rik|AW987637|Ent3	solute carrier family 29 (nucleoside transporters), member 3	protein-coding
mm_326.1	chr1	24685859	24685883	+	1	NA	intron (NM_001310483, intron 2 of 15)	B4A|SINE|B4	6953	NM_001310483	68421	Mm.336563	NM_026719	ENSMUSG00000073725	Lmbrd1	0910001K20Rik|AV347960	LMBR1 domain containing 1	protein-coding
mm_80371.1	chr9	75347756	75347763	+	1	NA	promoter-TSS (NM_013479)	promoter-TSS (NM_013479)	1	NM_013479	12049	Mm.25988	NM_013479	ENSMUSG00000032191	Bcl2l10	AA420380|AU023065|Boo|C85687|Diva	Bcl2-like 10	protein-coding
mm_22121.1	chr2	170193454	170193464	-	1	NA	Intergenic	Intergenic	-50784	NM_001159683	228913	Mm.22858	NM_001033299	ENSMUSG00000052056	Zfp217	4933431C08Rik|AW987152|Gm562|ZABC1|Znf217	zinc finger protein 217	protein-coding
mm_99295.1	chr11	101330880	101330886	+	1	NA	5' UTR (NM_009675, exon 1 of 4)	5' UTR (NM_009675, exon 1 of 4)	277	NM_009675	11754	Mm.67281	NM_009675	ENSMUSG00000019326	Aoc3	SSAO|VAP1	amine oxidase, copper containing 3	protein-coding
mm_135220.1	chr16	36770096	36770098	-	1	NA	intron (NM_021301, intron 7 of 21)	IAPLTR1_Mm|LTR|ERVK	14865	NM_001145899	57738	Mm.281804	NM_021301	ENSMUSG00000022899	Slc15a2	8430408C16Rik|C78862|Pept2	solute carrier family 15 (H+/peptide transporter), member 2	protein-coding
mm_46688.1	chr5	109845019	109845058	-	1	NA	Intergenic	Intergenic	-10896	NR_027964	667213	Mm.454429	NR_027964	ENSMUSG00000105044	Gm10416	EG667213|ENSMUSG00000072761	zinc finger protein pseudogene	pseudo
mm_158845.1	chrX	169779631	169779639	-	1	NA	promoter-TSS (NR_003635)	promoter-TSS (NR_003635)	0	NR_003635	66747	Mm.34441	NM_025743	ENSMUSG00000055357	4933400A11Rik	-	capping protein (actin filament) muscle Z-line, alpha 1 pseudogene	pseudo
mm_4222.1	chr1	171331341	171331358	+	1	NA	intron (NM_001128609, intron 2 of 5)	intron (NM_001128609, intron 2 of 5)	2204	NM_011615	21945	Mm.270139	NM_011615	ENSMUSG00000013973	Dedd	CASP8IP1|DEFT|Dedpro1|FLDED1|KE05	death effector domain-containing	protein-coding
mm_134262.1	chr16	13750832	13750842	-	1	NA	Intergenic	RCHARR1|DNA|hAT-Charlie	-20353	NM_011987	26565	Mm.4214	NM_011987	ENSMUSG00000022683	Pla2g10	GX sPLA2|PLA2GX|sPLA2-X	phospholipase A2, group X	protein-coding
mm_69304.1	chr7	128376273	128376282	-	1	NA	intron (NM_026418, intron 4 of 4)	intron (NM_026418, intron 4 of 4)	41895	NM_026418	67865	Mm.18635	NM_026418	ENSMUSG00000030844	Rgs10	2310010N19Rik	regulator of G-protein signalling 10	protein-coding
mm_61966.1	chr7	90426509	90426544	+	1	NA	5' UTR (NM_027298, exon 1 of 1)	5' UTR (NM_027298, exon 1 of 1)	214	NM_027298	70054	Mm.307198	NM_027298	ENSMUSG00000044362	Ccdc89	1700019B01Rik|AU022100|BOIP	coiled-coil domain containing 89	protein-coding
mm_132151.1	chr16	32108861	32108879	+	1	NA	TTS (NM_025892)	TTS (NM_025892)	9068	NM_025892	66994	Mm.22990	NM_025892	ENSMUSG00000035790	Cep19	1500031L02Rik|AI428934|AL022620	centrosomal protein 19	protein-coding
mm_24041.1	chr3	87846841	87846854	+	1	NA	promoter-TSS (NM_021309)	promoter-TSS (NM_021309)	92	NM_021309	27371	Mm.86361	NM_021309	ENSMUSG00000028071	Sh2d2a	Lad|Ribp|Tsad	SH2 domain containing 2A	protein-coding
mm_40256.1	chr5	38228100	38228108	+	1	NA	exon (NM_025281, exon 5 of 9)	exon (NM_025281, exon 5 of 9)	7622	NM_025281	17089	Mm.28560	NM_025281	ENSMUSG00000067367	Lyar	MLZ-264	Ly1 antibody reactive clone	protein-coding
mm_111776.1	chr12	104153059	104153066	-	1	NA	intron (NM_008458, intron 1 of 4)	GA-rich|Low_complexity|Low_complexity	810	NM_008458	16625	Mm.422814	NM_008458	ENSMUSG00000066361	Serpina3c	1A1|Kalbp|Klkbp|spi2	serine (or cysteine) peptidase inhibitor, clade A, member 3C	protein-coding
mm_125511.1	chr15	55591753	55591762	+	1	NA	intron (NM_134092, intron 13 of 21)	intron (NM_134092, intron 13 of 21)	34349	NM_001168250	105837	Mm.390829	NM_134092	ENSMUSG00000022369	Mtbp	AI429604|MDM2BP	Mdm2, transformed 3T3 cell double minute p53 binding protein	protein-coding
mm_25702.1	chr3	122419794	122419806	+	1	NA	promoter-TSS (NM_013867)	promoter-TSS (NM_013867)	20	NM_013867	29815	Mm.45815	NM_013867	ENSMUSG00000028121	Bcar3	AI131758|AND-34	breast cancer anti-estrogen resistance 3	protein-coding
mm_52233.1	chr6	104345812	104345820	+	1	NA	Intergenic	RLTR51A_Mm|LTR|ERVK?	-147228	NM_017383	53870	Mm.321671	NM_017383	ENSMUSG00000030092	Cntn6	NB-3	contactin 6	protein-coding
mm_117003.1	chr13	57695803	57695806	-	1	NA	intron (NM_001166464, intron 4 of 10)	intron (NM_001166464, intron 4 of 10)	212528	NM_009262	20745	Mm.379020	NM_009262	ENSMUSG00000056222	Spock1	Spock|Ticn1|testican	sparc/osteonectin, cwcv and kazal-like domains proteoglycan 1	protein-coding
mm_161593.1	chr16	35938494	35938494	+	1	NA	promoter-TSS (NM_030253)	promoter-TSS (NM_030253)	24	NM_030253	80285	Mm.49074	NM_030253	ENSMUSG00000022906	Parp9	ARTD9|AW214463|BC003281|Bagl|Bal|PARP-9	poly (ADP-ribose) polymerase family, member 9	protein-coding
mm_5895.1	chr1	54484819	54484842	-	1	NA	intron (NM_001163314, intron 25 of 26)	intron (NM_001163314, intron 25 of 26)	-45804	NM_001033194	98488	Mm.25856	NM_001033194	ENSMUSG00000041303	Gtf3c3	TF3C-gamma|TFIIIC102	general transcription factor IIIC, polypeptide 3	protein-coding
mm_168762.1	chr1	21201467	21201467	-	1	NA	Intergenic	L1Md_T|LINE|L1	-17108	NM_001290679	75712	Mm.304763	NM_029398	ENSMUSG00000025933	Tmem14a	5730496E24Rik|C85783|PTD011	transmembrane protein 14A	protein-coding
mm_71396.1	chr8	46163766	46163778	+	1	NA	Intergenic	CpG	-5784	NM_025747	66756	Mm.133623	NM_025747	ENSMUSG00000031631	Cfap97	1110068E21Rik|4933411K20Rik|AW049273|Kiaa1430|mKIAA1430	cilia and flagella associated protein 97	protein-coding
mm_38382.1	chr4	138757579	138757606	-	1	NA	promoter-TSS (NM_012045)	promoter-TSS (NM_012045)	6	NM_012045	26971	Mm.331989	NM_012045	ENSMUSG00000028749	Pla2g2f	-	phospholipase A2, group IIF	protein-coding
mm_166943.1	chr7	43462323	43462328	+	1	NA	promoter-TSS (NM_001290316)	promoter-TSS (NM_001290316)	-908	NM_001290316	75690	Mm.30200	NM_001290316	ENSMUSG00000070604	Vsig10l	-	V-set and immunoglobulin domain containing 10 like	protein-coding
mm_11107.1	chr2	28193008	28193028	+	1	NA	promoter-TSS (NM_001038613)	promoter-TSS (NM_001038613)	-75	NM_001038613	56177	Mm.43278	NM_019498	ENSMUSG00000026833	Olfm1	AMY|AW742568|Noe1|OlfA|Pancortin|Pancortin3	olfactomedin 1	protein-coding
mm_19458.1	chr2	92389013	92389019	-	1	NA	exon (NM_011162, exon 3 of 12)	exon (NM_011162, exon 3 of 12)	-1570	NR_105966	102466783		NR_105966	ENSMUSG00000099093	Mir7000	Gm27338|mmu-mir-7000	microRNA 7000	ncRNA
mm_172082.1	chr6	145932963	145932964	-	1	NA	intron (NM_001310837, intron 1 of 2)	LSU-rRNA_Hsa|rRNA|rRNA	1090	NM_001310837	16651	Mm.49689	NM_010656	ENSMUSG00000030255	Sspn	Krag	sarcospan	protein-coding
mm_49133.1	chr6	8948609	8948619	+	1	NA	Intergenic	CpG	-1405	NM_008751	18231	Mm.46954	NM_008751	ENSMUSG00000046178	Nxph1	C130005L03Rik	neurexophilin 1	protein-coding
mm_88822.1	chr10	80803646	80803660	+	1	NA	exon (NM_013651, exon 7 of 9)	exon (NM_013651, exon 7 of 9)	-1595	NM_007445	11705	Mm.376094	NM_007445	ENSMUSG00000035262	Amh	MIS	anti-Mullerian hormone	protein-coding
mm_51859.1	chr6	90466312	90466330	+	1	NA	intron (NM_023184, intron 1 of 2)	intron (NM_023184, intron 1 of 2)	3695	NM_023184	66277	Mm.38343	NM_023184	ENSMUSG00000030087	Klf15	1810013I09Rik|AV048136|AW494632|CKLF|KKLF	Kruppel-like factor 15	protein-coding
mm_19721.1	chr2	104430777	104430789	-	1	NA	exon (NM_001145824, exon 15 of 16)	exon (NM_001145824, exon 15 of 16)	-1843	NR_035432	100316678		NR_035432	ENSMUSG00000084516	Mir1902	Mirn1902|mmu-mir-1902	microRNA 1902	ncRNA
mm_149747.1	chr19	22514488	22514497	+	1	NA	intron (NM_177341, intron 1 of 26)	intron (NM_177341, intron 1 of 26)	66284	NM_177341	226025	Mm.131943	NM_177341	ENSMUSG00000052387	Trpm3	6330504P12Rik|9330180E14|AU018608|B930001P07Rik|LTRPC3|MLSN2	transient receptor potential cation channel, subfamily M, member 3	protein-coding
mm_49608.1	chr6	30747126	30747162	+	1	NA	TTS (NM_017478)	TTS (NM_017478)	5845	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_164626.1	chr17	31558008	31558014	-	1	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	-6762	NR_027493	18771	Mm.259295	NM_016670	ENSMUSG00000006705	Pknox1	D17Wsu76e|PREP1	Pbx/knotted 1 homeobox	protein-coding
mm_92330.1	chr10	75781412	75781434	-	1	NA	promoter-TSS (NM_133994)	promoter-TSS (NM_133994)	-1	NM_001346523	103140	Mm.5731	NM_133994	ENSMUSG00000001665	Gstt3	AI118089	glutathione S-transferase, theta 3	protein-coding
mm_66006.1	chr7	30562997	30563024	-	1	NA	promoter-TSS (NM_170760)	promoter-TSS (NM_170760)	174	NM_025498	66340	Mm.86557	NM_025498	ENSMUSG00000036835	Psenen	1700023M09Rik|Pen-2	presenilin enhancer gamma secretase subunit	protein-coding
mm_150872.1	chr19	45055360	45055373	+	1	NA	3' UTR (NM_053197, exon 11 of 11)	3' UTR (NM_053197, exon 11 of 11)	7790	NM_001178013	94280	Mm.36169	NM_053197	ENSMUSG00000025212	Sfxn3	-	sideroflexin 3	protein-coding
mm_128538.1	chr15	54920011	54920037	-	1	NA	5' UTR (NM_001285995, exon 1 of 26)	5' UTR (NM_001285995, exon 1 of 26)	122	NM_015744	18606	Mm.250256	NM_015744	ENSMUSG00000022425	Enpp2	ATX|E-NPP 2|Npps2|PD-Ialpha|Pdnp2|lysoPLD	ectonucleotide pyrophosphatase/phosphodiesterase 2	protein-coding
mm_68395.1	chr7	109534858	109534868	-	1	NA	intron (NM_001001326, intron 12 of 19)	intron (NM_001001326, intron 12 of 19)	14731	NR_028079	100302499	Mm.482651	NR_028079	ENSMUSG00000065016	Snora3	MBI-28	small nucleolar RNA, H/ACA box 3	snoRNA
mm_9586.1	chr1	174031780	174031789	-	1	NA	promoter-TSS (NM_172648)	promoter-TSS (NM_172648)	-29	NM_172648	226695	Mm.425061	NM_172648	ENSMUSG00000054203	Ifi205	D3|D3cDNA|Ifi205a	interferon activated gene 205	protein-coding
mm_8833.1	chr1	162571474	162571487	-	1	NA	intron (NM_001347125, intron 1 of 7)	CpG	652	NM_001347125	53330	Mm.10699	NM_016796	ENSMUSG00000026696	Vamp4	D1Ertd147e	vesicle-associated membrane protein 4	protein-coding
mm_152400.1	chr19	10556199	10556275	-	1	NA	promoter-TSS (NM_026798)	promoter-TSS (NM_026798)	1	NM_026798	68642	Mm.31236	NM_026798	ENSMUSG00000024667	Tmem216	1110017C22Rik|2810441K11Rik|4921533J23Rik|A930021F15Rik|AI482550	transmembrane protein 216	protein-coding
mm_33090.1	chr4	124695843	124695861	+	1	NA	Intergenic	Intergenic	-2298	NM_026031	67205	Mm.259121	NM_026031	ENSMUSG00000028907	Utp11l	2700082D03Rik|CGI-94|Cgi94|Utp11	UTP11-like, U3 small nucleolar ribonucleoprotein, (yeast)	protein-coding
mm_21846.1	chr2	165852555	165852562	-	1	NA	intron (NM_001252584, intron 2 of 22)	ORR1E|LTR|ERVL-MaLR	5615	NM_001252585	228880	Mm.227598	NM_027230	ENSMUSG00000039671	Zmynd8	1110013E22Rik|2010005I16Rik|3632413B07Rik|AI316811|AL024039|Prkcbp1|RACK7	zinc finger, MYND-type containing 8	protein-coding
mm_106045.1	chr11	116079767	116079785	-	1	NA	exon (NM_016852, exon 7 of 8)	exon (NM_016852, exon 7 of 8)	-1815	NM_001009573	70450	Mm.259460	NM_001009573	ENSMUSG00000057948	Unc13d	2610108D09Rik|Jinx|Munc13-4|mFLJ00067	unc-13 homolog D (C. elegans)	protein-coding
mm_67705.1	chr7	89941043	89941053	-	1	NA	non-coding (NR_111916, exon 1 of 1)	non-coding (NR_111916, exon 1 of 1)	156	NM_001291289	67669	Mm.28679	NM_026304	ENSMUSG00000062797	Hikeshi	0610007P06Rik|1110002N09Rik|l(7)6Rn|l7Rn6	heat shock protein nuclear import factor	protein-coding
mm_159369.1	chr3	88629415	88629415	+	1	NA	intron (NM_001198912, intron 1 of 21)	intron (NM_001198912, intron 1 of 21)	8021	NM_001198912	16800	Mm.239329	NM_008487	ENSMUSG00000028059	Arhgef2	AA408978|GEF|GEF-H1|GEFH1|LFP40|Lbcl1|Lfc|P40|mKIAA0651	rho/rac guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_50173.1	chr6	41558530	41558544	+	1	NA	Intergenic	Intergenic	36761	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_95435.1	chr11	50213293	50213304	+	1	NA	Intergenic	Intergenic	-2478	NM_011018	18412	Mm.40828	NM_011018	ENSMUSG00000015837	Sqstm1	A170|OSF-6|Osi|STAP|STONE14|p62	sequestosome 1	protein-coding
mm_37606.1	chr4	126753373	126753440	-	1	NA	promoter-TSS (NM_001035526)	promoter-TSS (NM_001035526)	23	NM_011986	26562	Mm.206206	NM_011986	ENSMUSG00000028833	Ncdn	AU042419|MMS10-AE|Ms10ae|mKIAA0607|norbin	neurochondrin	protein-coding
mm_36043.1	chr4	57262581	57262608	-	1	NA	intron (NM_011207, intron 4 of 25)	intron (NM_011207, intron 4 of 25)	39243	NM_011207	545622	Mm.246552	NM_011207	ENSMUSG00000038764	Ptpn3	9530011I20Rik|PTP-H1|PTPCL	protein tyrosine phosphatase, non-receptor type 3	protein-coding
mm_166291.1	chr5	101703579	101703615	+	1	NA	Intergenic	Intergenic	-38886	NM_144955	18096	Mm.193072	NM_144955	ENSMUSG00000035187	Nkx6-1	NKX6A|Nkx6.1	NK6 homeobox 1	protein-coding
mm_120731.1	chr14	73143565	73143599	+	1	NA	intron (NR_033185, intron 1 of 15)	CpG	797	NR_033185	105670	Mm.280068	NM_134083	ENSMUSG00000022106	Rcbtb2	2610028E02Rik|2810420M18Rik|AI448345|AW240694|Chc1l|RC/BTB2	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 2	protein-coding
mm_115295.1	chr13	111983027	111983059	+	1	NA	Intergenic	Intergenic	115107	NR_130345	102636620	Mm.402328	NR_130345	ENSMUSG00000086111	Gm15326	OTTMUSG00000020187	predicted gene 15326	ncRNA
mm_74149.1	chr8	123332677	123332740	+	1	NA	promoter-TSS (NM_172287)	promoter-TSS (NM_172287)	-5	NM_172287	234857	Mm.150200	NM_172287	ENSMUSG00000010154	Spire2	BC026502|Spir-2|Spir2	spire homolog 2 (Drosophila)	protein-coding
mm_166157.1	chr5	15577289	15577317	+	1	NA	5' UTR (NM_001310450, exon 1 of 5)	5' UTR (NM_001310450, exon 1 of 5)	356	NM_001310450	105242399		NM_001310450	ENSMUSG00000096878	LOC105242399	-	spermatogenesis associated glutamate (E)-rich protein-like	protein-coding
mm_98091.1	chr11	86598768	86598798	+	1	NA	intron (NM_029478, intron 10 of 11)	intron (NM_029478, intron 10 of 11)	-14625	NR_029738	387140		NR_029738	ENSMUSG00000065455	Mir21a	Mir21|Mirn21|mmu-mir-21|mmu-mir-21a	microRNA 21a	ncRNA
mm_59699.1	chr7	28629922	28629929	+	1	NA	intron (NM_175319, intron 1 of 12)	MIR|SINE|MIR	1090	NM_175319	101744	Mm.26022	NM_175319	ENSMUSG00000037469	Acp7	AU017076|C330005M16Rik|Papl	acid phosphatase 7, tartrate resistant	protein-coding
mm_137694.1	chr17	28952426	28952532	+	1	NA	promoter-TSS (NM_025888)	promoter-TSS (NM_025888)	-737	NM_025888	66989	Mm.435	NM_025888	ENSMUSG00000005936	Kctd20	2410004N11Rik|AI451943|AW541186|D17Ertd562e	potassium channel tetramerisation domain containing 20	protein-coding
mm_139233.1	chr17	47732392	47732412	+	1	NA	exon (NM_025973, exon 6 of 9)	exon (NM_025973, exon 6 of 9)	-4635	NM_001161722	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_131247.1	chr16	10536857	10536860	+	1	NA	intron (NM_021428, intron 1 of 1)	intron (NM_021428, intron 1 of 1)	6196	NM_021428	58239	Mm.353006	NM_021428	ENSMUSG00000038055	Dexi	1810029J14Rik|AI836170|AW413143|D16Bwg0586e|Myle	dexamethasone-induced transcript	protein-coding
mm_15657.1	chr2	163204484	163204522	+	1	NA	Intergenic	CpG	-20951	NM_001098799	269389	Mm.207709	NM_001098799	ENSMUSG00000074607	Tox2	AI851523|AV026525|BI987407|Gcx1|RxHMG1	TOX high mobility group box family member 2	protein-coding
mm_160851.1	chr11	54249895	54249895	-	1	NA	promoter-TSS (NM_009969)	promoter-TSS (NM_009969)	4	NM_009969	12981	Mm.4922	NM_009969	ENSMUSG00000018916	Csf2	Csfgm|GMCSF|Gm-CSf|MGI-IGM	colony stimulating factor 2 (granulocyte-macrophage)	protein-coding
mm_108344.1	chr12	80435172	80435235	+	1	NA	intron (NM_177267, intron 1 of 8)	CpG	1398	NM_177267	320808	Mm.220310	NM_177267	ENSMUSG00000049106	Dcaf5	9430020B07Rik|AI325023|AI430035|AI848110|AW124614|BCRG2|BCRP2|Wdr22	DDB1 and CUL4 associated factor 5	protein-coding
mm_93331.1	chr10	99460223	99460239	-	1	NA	Intergenic	Intergenic	-148940	NR_038019	100504202	Mm.403801	NR_038019		Gm20110	-	predicted gene, 20110	ncRNA
mm_170547.1	chr19	4037907	4037907	-	1	NA	promoter-TSS (NM_013541)	promoter-TSS (NM_013541)	5	NM_013541	14870	Mm.299292	NM_013541	ENSMUSG00000060803	Gstp1	GstpiB	glutathione S-transferase, pi 1	protein-coding
mm_74339.1	chr8	127111517	127111518	+	1	NA	intron (NM_001309391, intron 1 of 24)	intron (NM_001309391, intron 1 of 24)	47461	NM_001309391	93742	Mm.299254	NM_033620	ENSMUSG00000025812	Pard3	AA960621|AI256638|Asip|D8Ertd580e|Par-3|Par3|Pard-3|Pard3a|Phip	par-3 family cell polarity regulator	protein-coding
mm_102373.1	chr11	58612557	58612582	-	1	NA	exon (NM_144544, exon 3 of 6)	exon (NM_144544, exon 3 of 6)	923	NM_144544	78354	Mm.58038	NM_144544	ENSMUSG00000037145	2210407C18Rik	Ep1	RIKEN cDNA 2210407C18 gene	protein-coding
mm_19628.1	chr2	102813714	102813724	-	1	NA	3' UTR (NM_009851, exon 19 of 19)	3' UTR (NM_009851, exon 19 of 19)	87946	NM_001177785	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_93484.1	chr10	111996633	111996643	-	1	NA	intron (NM_028608, intron 1 of 5)	intron (NM_028608, intron 1 of 5)	626	NM_028608	73690	Mm.173790	NM_028608	ENSMUSG00000056888	Glipr1	2410114O14Rik|RTVP-1|RTVP1|mRTVP-1	GLI pathogenesis-related 1 (glioma)	protein-coding
mm_90474.1	chr10	127866413	127866417	+	1	NA	promoter-TSS (NM_145424)	promoter-TSS (NM_145424)	-61	NM_145424	216454	Mm.214923	NM_145424	ENSMUSG00000074639	BC089597	CRAD-L	cDNA sequence BC089597	protein-coding
mm_171063.1	chr3	110683181	110683184	-	1	NA	Intergenic	L1_Mur3|LINE|L1	-432183	NR_024139	99890	Mm.36115	NM_178891	ENSMUSG00000049300	Prmt6	AW124876|BB233495|Hrmt1l6	protein arginine N-methyltransferase 6	protein-coding
mm_161447.1	chr15	74540889	74540889	+	1	NA	exon (NM_174991, exon 7 of 31)	exon (NM_174991, exon 7 of 31)	24693	NM_174991	107831	Mm.43133	NM_174991	ENSMUSG00000034730	Adgrb1	B830018M07Rik|Bai1|R75078|mKIAA4089	adhesion G protein-coupled receptor B1	protein-coding
mm_36254.1	chr4	63410189	63410212	-	1	NA	Intergenic	Intergenic	-6755	NM_001045514	100182	Mm.387725	NM_001045514	ENSMUSG00000039158	Akna	AI597013	AT-hook transcription factor	protein-coding
mm_3879.1	chr1	161035163	161035169	+	1	NA	promoter-TSS (NM_173424)	promoter-TSS (NM_173424)	0	NR_002840	14455	Mm.270065	NR_002840	ENSMUSG00000053332	Gas5	Gas-5|Mir5117|Snhg2	growth arrest specific 5	ncRNA
mm_144926.1	chr18	37694361	37694388	+	1	NA	promoter-TSS (NM_033588)	promoter-TSS (NM_033588)	-127	NM_033588	93713	Mm.247203	NM_033588	ENSMUSG00000103567	Pcdhga5	-	protocadherin gamma subfamily A, 5	protein-coding
mm_85749.1	chr9	108578702	108578721	-	1	NA	promoter-TSS (NM_031392)	promoter-TSS (NM_031392)	-41	NM_031392	83669	Mm.335454	NM_031392	ENSMUSG00000066357	Wdr6	mWDR6	WD repeat domain 6	protein-coding
mm_59940.1	chr7	30424420	30424424	+	1	NA	5' UTR (NM_172142, exon 3 of 11)	5' UTR (NM_172142, exon 3 of 11)	1118	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_136535.1	chr16	97659527	97659540	-	1	NA	Intergenic	Intergenic	-48338	NM_015775	50528	Mm.276145	NM_015775	ENSMUSG00000000385	Tmprss2	D16Ertd61e	transmembrane protease, serine 2	protein-coding
mm_155458.1	chrX	73503075	73503116	+	1	NA	promoter-TSS (NM_177236)	promoter-TSS (NM_177236)	9	NM_177236	320707	Mm.210095	NM_177236	ENSMUSG00000031376	Atp2b3	6430519O13Rik|Pmca3	ATPase, Ca++ transporting, plasma membrane 3	protein-coding
mm_63407.1	chr7	127333571	127333581	+	1	NA	exon (NM_001253873, exon 31 of 31)	exon (NM_001253873, exon 31 of 31)	11738	NM_146202	233890	Mm.23031	NM_146202	ENSMUSG00000047371	Zfp768	BC026432|Znf768	zinc finger protein 768	protein-coding
mm_141414.1	chr17	29428962	29428975	-	1	NA	Intergenic	Intergenic	-62077	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_86394.1	chr9	123968543	123968557	-	1	NA	5' UTR (NM_009912, exon 1 of 2)	5' UTR (NM_009912, exon 1 of 2)	142	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_43754.1	chr5	140437314	140437326	+	1	NA	exon (NM_133916, exon 12 of 19)	exon (NM_133916, exon 12 of 19)	9981	NR_106005	102466792		NR_106005	ENSMUSG00000098319	Mir7038	Gm27955|mmu-mir-7038	microRNA 7038	ncRNA
mm_91791.1	chr10	53361004	53361006	-	1	NA	intron (NM_001204983, intron 1 of 12)	intron (NM_001204983, intron 1 of 12)	18846	NM_001204983	100038725	Mm.441403	NM_001204983	ENSMUSG00000038594	Cep85l	ENSMUSG00000038594|Gm9766	centrosomal protein 85-like	protein-coding
mm_90114.1	chr10	117277641	117277676	+	1	NA	3' UTR (NM_017372, exon 4 of 4)	3' UTR (NM_017372, exon 4 of 4)	4614	NM_017372	17105	Mm.45436	NM_017372	ENSMUSG00000069516	Lyz2	AI326280|Lys|Lysm|Lyzf2|Lyzs|Lzm|Lzm-s1|Lzp	lysozyme 2	protein-coding
mm_71666.1	chr8	60655546	60655562	+	1	NA	promoter-TSS (NM_001177882)	promoter-TSS (NM_001177882)	-3	NM_001177882	71306	Mm.23242	NM_027756	ENSMUSG00000031647	Mfap3l	4933428A15Rik|5430405D20Rik|AI461995|AW125052|NYD-sp9|mKIAA0626	microfibrillar-associated protein 3-like	protein-coding
mm_68145.1	chr7	102249363	102249374	-	1	NA	intron (NM_019566, intron 1 of 1)	intron (NM_019566, intron 1 of 1)	750	NM_019566	56212	Mm.259795	NM_019566	ENSMUSG00000073982	Rhog	2810426G09Rik|Arhg|Sid10750	ras homolog family member G	protein-coding
mm_82357.1	chr9	14381491	14381525	-	1	NA	promoter-TSS (NM_028013)	promoter-TSS (NM_028013)	-266	NM_028013	71946	Mm.41423	NM_028013	ENSMUSG00000037419	Endod1	2210414F18Rik|2310067E08Rik|C85344	endonuclease domain containing 1	protein-coding
mm_36848.1	chr4	106730959	106730975	-	1	NA	Intergenic	Intergenic	-2948	NM_146149	230579	Mm.222956	NM_146149	ENSMUSG00000034871	Fam151a	2010309H15Rik	family with sequence simliarity 151, member A	protein-coding
mm_89060.1	chr10	82887698	82887713	+	1	NA	intron (NM_001042513, intron 13 of 14)	intron (NM_001042513, intron 13 of 14)	21079	NM_025499	66341	Mm.443284	NM_025499	ENSMUSG00000109864	Eid3	1700027M21Rik|NS4EB	EP300 interacting inhibitor of differentiation 3	protein-coding
mm_168878.1	chr12	40884680	40884693	-	1	NA	Intergenic	RMER1A|Other|Other	-139404	NM_053122	93757	Mm.363813	NM_053122	ENSMUSG00000056899	Immp2l	AI853880|IMP2	IMP2 inner mitochondrial membrane peptidase-like (S. cerevisiae)	protein-coding
mm_42932.1	chr5	122850200	122850214	+	1	NA	promoter-TSS (NM_030564)	promoter-TSS (NM_030564)	19	NM_030564	80751	Mm.388529	NM_030564	ENSMUSG00000029474	Rnf34	AW061037|AW536122|BC004042|C88279|RIFF	ring finger protein 34	protein-coding
mm_150577.1	chr19	40612393	40612407	+	1	NA	promoter-TSS (NM_026260)	promoter-TSS (NM_026260)	34	NM_001304721	12495	Mm.2824	NM_009848	ENSMUSG00000048120	Entpd1	2610206B08Rik|AA408691|Cd39|NTPDase-1	ectonucleoside triphosphate diphosphohydrolase 1	protein-coding
mm_43111.1	chr5	124552846	124552903	+	1	NA	promoter-TSS (NM_001190795)	promoter-TSS (NM_001190795)	10	NM_026409	67848	Mm.281601	NM_026409	ENSMUSG00000029389	Ddx55	2810021H22Rik|mKIAA1595	DEAD (Asp-Glu-Ala-Asp) box polypeptide 55	protein-coding
mm_128512.1	chr15	53327371	53327384	-	1	NA	intron (NM_010162, intron 1 of 10)	intron (NM_010162, intron 1 of 10)	18806	NM_010162	14042	Mm.309395	NM_010162	ENSMUSG00000061731	Ext1	AA409028	exostoses (multiple) 1	protein-coding
mm_74351.1	chr8	128148760	128148775	+	1	NA	Intergenic	ORR1D1|LTR|ERVL-MaLR	129458	NR_105822	102465212		NR_105822	ENSMUSG00000099326	Mir21c	Gm28013|mmu-mir-21c	microRNA 21c	ncRNA
mm_6889.1	chr1	84696007	84696015	-	1	NA	TTS (NR_039588)	TTS (NR_039588)	172	NR_039588	100628595		NR_039588	ENSMUSG00000093254	Mir5126	mir-5126|mmu-mir-5126|mu-mir-5126	microRNA 5126	ncRNA
mm_84198.1	chr9	60649687	60649740	-	1	NA	intron (NM_001311095, intron 7 of 15)	intron (NM_001311095, intron 7 of 15)	37821	NM_001311095	102747	Mm.269413	NM_145616	ENSMUSG00000047766	Lrrc49	AI430817|AW050057|D430025H09Rik|PGs4|p79	leucine rich repeat containing 49	protein-coding
mm_153298.1	chr19	37930977	37930990	-	1	NA	intron (NM_001302140, intron 38 of 53)	intron (NM_001302140, intron 38 of 53)	112594	NM_001099634	226101	Mm.34674	NM_177035	ENSMUSG00000048612	Myof	2310004N10Rik|2310051D19Rik|E030042N20Rik|Fer1l3	myoferlin	protein-coding
mm_127541.1	chr15	102104589	102104601	+	1	NA	exon (NM_153533, exon 2 of 29)	exon (NM_153533, exon 2 of 29)	1607	NM_153533	209039	Mm.29389	NM_153533	ENSMUSG00000037003	Tns2	C1-ten|Tenc1|nep|nph	tensin 2	protein-coding
mm_117221.1	chr13	64133930	64133933	-	1	NA	3' UTR (NM_175494, exon 5 of 5)	3' UTR (NM_175494, exon 5 of 5)	-4601	NM_001001321	70484	Mm.133731	NM_001001321	ENSMUSG00000033114	Slc35d2	5730408I21Rik|SQV7L|UGTrel8|hfrc|mUGTrel8	solute carrier family 35, member D2	protein-coding
mm_102601.1	chr11	62391014	62391042	-	1	NA	exon (NM_001252313, exon 12 of 45)	exon (NM_001252313, exon 12 of 45)	47487	NM_001252313	20185	Mm.271814	NM_011308	ENSMUSG00000018501	Ncor1	5730405M06Rik|A230020K14Rik|N-CoR|RIP13|Rxrip13|mKIAA1047	nuclear receptor co-repressor 1	protein-coding
mm_160020.1	chr6	130026994	130026994	-	1	NA	promoter-TSS (NM_053154)	promoter-TSS (NM_053154)	-34	NM_053154	93971	Mm.14112	NM_053154		Klra19	Ly49s	killer cell lectin-like receptor, subfamily A, member 19	protein-coding
mm_144705.1	chr18	34863495	34863505	+	1	NA	exon (NM_007913, exon 2 of 2)	exon (NM_007913, exon 2 of 2)	2293	NM_007913	13653	Mm.181959	NM_007913	ENSMUSG00000038418	Egr1	A530045N19Rik|ETR103|Egr-1|Krox-1|Krox-24|Krox24|NGF1-A|NGFI-A|NGFIA|TIS8|Zenk|Zfp-6|Zif268|egr	early growth response 1	protein-coding
mm_60758.1	chr7	45518240	45518263	+	1	NA	intron (NM_001290996, intron 4 of 10)	ZP3AR|Satellite|Satellite	3649	NM_001290998	56734	Mm.439742	NM_008807	ENSMUSG00000023467	Tulp2	Pdet	tubby-like protein 2	protein-coding
mm_60387.1	chr7	44474012	44474019	+	1	NA	Intergenic	Intergenic	3668	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_118471.1	chr14	11570019	11570031	+	1	NA	intron (NM_008981, intron 1 of 29)	intron (NM_008981, intron 1 of 29)	16472	NM_008981	19270	Mm.431266	NM_008981	ENSMUSG00000021745	Ptprg	5430405N12Rik|AW046354|AW549872|RPTPgamma	protein tyrosine phosphatase, receptor type, G	protein-coding
mm_117472.1	chr13	76256539	76256573	-	1	NA	Intergenic	Intergenic	-128405	NM_030174	78771	Mm.316249	NM_030174	ENSMUSG00000021596	Mctp1	2810465F10Rik	multiple C2 domains, transmembrane 1	protein-coding
mm_78324.1	chr9	25147423	25147433	+	1	NA	intron (NM_020586, intron 1 of 7)	intron (NM_020586, intron 1 of 7)	4353	NM_020586	80517	Mm.142843	NM_020586	ENSMUSG00000008429	Herpud2	5031400M07Rik|AB041580	HERPUD family member 2	protein-coding
mm_70553.1	chr8	13060592	13060620	+	1	NA	promoter-TSS (NM_025834)	promoter-TSS (NM_025834)	-302	NM_025834	66901	Mm.441140	NM_025834	ENSMUSG00000031445	Proz	1300015B06Rik	protein Z, vitamin K-dependent plasma glycoprotein	protein-coding
mm_78738.1	chr9	41587432	41587437	+	1	NA	intron (NR_015483, intron 1 of 1)	intron (NR_015483, intron 1 of 1)	5508	NR_029822	387236		NR_029822	ENSMUSG00000093354	Mir125b-1	Mirn125b|Mirn125b-1|mir-125b-1	microRNA 125b-1	ncRNA
mm_7267.1	chr1	95667521	95667540	-	1	NA	promoter-TSS (NM_001159745)	promoter-TSS (NM_001159745)	64	NM_009183	20452	Mm.306228	NM_009183	ENSMUSG00000040710	St8sia4	PST|PST-1|SIAT8-D|ST8SiaIV|Siat8d	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4	protein-coding
mm_168659.1	chr11	88896406	88896413	-	1	NA	Intergenic	RLTR4_Mm|LTR|ERV1	-9519	NR_045955	73921	Mm.439148	NR_045955	ENSMUSG00000087338	Scpep1os	4930405P13Rik	serine carboxypeptidase 1, opposite strand	ncRNA
mm_113840.1	chr13	47193916	47193926	+	1	NA	promoter-TSS (NM_001170643)	promoter-TSS (NM_001170643)	-82	NM_001170643	218215	Mm.287609	NM_146042	ENSMUSG00000038068	Rnf144b	BC025007|E130105P19Rik|Ibrdc2|Pir2	ring finger protein 144B	protein-coding
mm_39419.1	chr5	15934732	15934746	+	1	NA	promoter-TSS (NM_001110843)	promoter-TSS (NM_001110843)	48	NM_001110844	12293	Mm.159842	NM_009784	ENSMUSG00000040118	Cacna2d1	Ca(v)alpha2delta1|Cacna2|Cchl2a	calcium channel, voltage-dependent, alpha2/delta subunit 1	protein-coding
mm_130662.1	chr15	100645025	100645035	-	1	NA	exon (NM_001270537, exon 10 of 11)	exon (NM_001270537, exon 10 of 11)	4199	NR_105926	102465580		NR_105926	ENSMUSG00000098527	Mir6961	Gm27367|mmu-mir-6961	microRNA 6961	ncRNA
mm_63753.1	chr7	131106261	131106270	+	1	NA	exon (NM_007769, exon 39 of 47)	exon (NM_007769, exon 39 of 47)	40018	NM_173409	233918	Mm.78341	NM_173409	ENSMUSG00000013668	4933402N03Rik	4930412O05	RIKEN cDNA 4933402N03 gene	protein-coding
mm_61607.1	chr7	80030745	80030753	+	1	NA	intron (NM_175433, intron 1 of 4)	MT2B|LTR|ERVL	4521	NM_175433	209225	Mm.290925	NM_175433	ENSMUSG00000048897	Zfp710	5430400N05Rik|9830165K13|AI324798|Znf710	zinc finger protein 710	protein-coding
mm_66428.1	chr7	44626928	44626951	-	1	NA	intron (NM_001271538, intron 26 of 40)	intron (NM_001271538, intron 26 of 40)	36053	NM_001290682	16504	Mm.40312	NM_008422	ENSMUSG00000062785	Kcnc3	KShIIID|Kcr2-3|Kv3.3	potassium voltage gated channel, Shaw-related subfamily, member 3	protein-coding
mm_65170.1	chr7	19681374	19681374	-	1	NA	promoter-TSS (NM_007385)	promoter-TSS (NM_007385)	86	NM_007385	11425	Mm.477720	NM_007385	ENSMUSG00000074336	Apoc4	Acl|apo-CIV|apoC-IV	apolipoprotein C-IV	protein-coding
mm_112363.1	chr12	119160357	119160359	-	1	NA	Intergenic	Intergenic	77918	NM_177290	320910	Mm.217000	NM_177290	ENSMUSG00000025321	Itgb8	4832412O06Rik	integrin beta 8	protein-coding
mm_1912.1	chr1	85928880	85928903	+	1	NA	non-coding (NR_037692, exon 1 of 3)	non-coding (NR_037692, exon 1 of 3)	408	NR_037692	71141	Mm.314965	NR_037692	ENSMUSG00000026224	4933407L21Rik	-	RIKEN cDNA 4933407L21 gene	ncRNA
mm_154640.1	chrX	7764324	7764351	+	1	NA	intron (NM_001271491, intron 1 of 8)	intron (NM_001271491, intron 1 of 8)	296	NM_001271491	209446	Mm.249142	NM_172472	ENSMUSG00000000134	Tfe3	F830016E06Rik|Tcfe3|Tfe-3|bHLHe33	transcription factor E3	protein-coding
mm_6814.1	chr1	84158639	84158669	-	1	NA	intron (NM_001003948, intron 2 of 2)	intron (NM_001003948, intron 2 of 2)	60307	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_28264.1	chr3	88623132	88623147	-	1	NA	intron (NM_001198912, intron 1 of 21)	intron (NM_001198912, intron 1 of 21)	1745	NM_001198912	16800	Mm.239329	NM_008487	ENSMUSG00000028059	Arhgef2	AA408978|GEF|GEF-H1|GEFH1|LFP40|Lbcl1|Lfc|P40|mKIAA0651	rho/rac guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_119655.1	chr14	52110940	52110953	+	1	NA	promoter-TSS (NM_001168515)	promoter-TSS (NM_001168515)	43	NM_023879	77945	Mm.21662	NM_023879	ENSMUSG00000057132	Rpgrip1	0610005A07Rik|4930401L23Rik|4930505G06Rik|A930002K18Rik|AA415034|nmf247	retinitis pigmentosa GTPase regulator interacting protein 1	protein-coding
mm_156659.1	chrX	157711389	157711399	+	1	NA	intron (NR_045569, intron 3 of 6)	tRNA-Gly-GGA|tRNA|tRNA	12421	NR_103722	66106	Mm.140340	NM_025357	ENSMUSG00000041476	Smpx	1010001C09Rik|Csl	small muscle protein, X-linked	protein-coding
mm_103511.1	chr11	76623313	76623354	-	1	NA	Intergenic	CpG	-45594	NM_198894	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_52584.1	chr6	116650726	116650729	+	1	NA	promoter-TSS (NM_001166580)	promoter-TSS (NM_001166580)	43	NM_001166580	213393	Mm.38231	NM_145980	ENSMUSG00000048489	8430408G22Rik	Depp|Fseg	RIKEN cDNA 8430408G22 gene	protein-coding
mm_40314.1	chr5	43868654	43868666	+	1	NA	promoter-TSS (NM_007646)	promoter-TSS (NM_007646)	-149	NM_007646	12494	Mm.249873	NM_007646	ENSMUSG00000029084	Cd38	ADPRC 1|Cd38-rs1|I-19	CD38 antigen	protein-coding
mm_152360.1	chr19	10088965	10088999	-	1	NA	exon (NM_019699, exon 3 of 12)	exon (NM_019699, exon 3 of 12)	12521	NM_019699	56473	Mm.38901	NM_019699	ENSMUSG00000024665	Fads2	2900042M13Rik|Fadsd2	fatty acid desaturase 2	protein-coding
mm_46799.1	chr5	113015474	113015567	-	1	NA	promoter-TSS (NM_001285806)	promoter-TSS (NM_001285806)	18	NM_001285806	320129	Mm.285619	NM_177078	ENSMUSG00000042249	Grk3	4833444A01Rik|AI851927|AW551196|Adrbk-2|Adrbk2|Bark-2	G protein-coupled receptor kinase 3	protein-coding
mm_171433.1	chr4	139338305	139338307	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	14270	NM_001290810	69902	Mm.27871	NM_023536	ENSMUSG00000028741	Mrto4	2610012O22Rik|Mg684|Mrt4	mRNA turnover 4, ribosome maturation factor	protein-coding
mm_68160.1	chr7	102759466	102759478	-	1	NA	promoter-TSS (NM_001168503)	promoter-TSS (NM_001168503)	-1	NM_001168503	170639	Mm.184372	NM_130866	ENSMUSG00000043366	Olfr78	4633402A21Rik|MOL2.3|MOR18-2|Or51e2|PSGR|RA1c	olfactory receptor 78	protein-coding
mm_17374.1	chr2	26933356	26933396	-	1	NA	promoter-TSS (NM_198628)	promoter-TSS (NM_198628)	135	NM_011512	20932	Mm.300594	NM_011512	ENSMUSG00000014867	Surf4	AL033340|AL033373|Surf-4	surfeit gene 4	protein-coding
mm_134652.1	chr16	21995479	21995517	-	1	NA	promoter-TSS (NM_153404)	promoter-TSS (NM_153404)	44	NM_001289582	239759	Mm.33192	NM_153404	ENSMUSG00000044626	Liph	C130037N08Rik|D16Wsu119e|H06|Lpdlr|P3|PLA1B|lpd1|lpd2|mPA-PLA1	lipase, member H	protein-coding
mm_25037.1	chr3	98280428	98280444	+	1	NA	promoter-TSS (NM_008256)	promoter-TSS (NM_008256)	5	NM_008256	15360	Mm.289131	NM_008256	ENSMUSG00000027875	Hmgcs2	1300002P16|mHS	3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2	protein-coding
mm_6956.1	chr1	85991459	85991468	-	1	NA	Intergenic	L1MCb|LINE|L1	-30408	NM_001033290	227326	Mm.244158	NM_001033290	ENSMUSG00000049608	Gpr55	CTFL|Gm218|Lpir1	G protein-coupled receptor 55	protein-coding
mm_78352.1	chr9	25481591	25481612	+	1	NA	promoter-TSS (NM_026189)	promoter-TSS (NM_026189)	4	NM_026189	67484	Mm.112977	NM_026189	ENSMUSG00000036611	Eepd1	2310005P05Rik|AI481005	endonuclease/exonuclease/phosphatase family domain containing 1	protein-coding
mm_15660.1	chr2	163225501	163225511	+	1	NA	promoter-TSS (NM_001098799)	promoter-TSS (NM_001098799)	52	NM_001098799	269389	Mm.207709	NM_001098799	ENSMUSG00000074607	Tox2	AI851523|AV026525|BI987407|Gcx1|RxHMG1	TOX high mobility group box family member 2	protein-coding
mm_165176.1	chr2	27535375	27535378	+	1	NA	3' UTR (NM_080848, exon 14 of 14)	3' UTR (NM_080848, exon 14 of 14)	20229	NM_080848	140858	Mm.28265	NM_080848	ENSMUSG00000026917	Wdr5	2410008O07Rik|AA408785|AA960360|Big|Big-3	WD repeat domain 5	protein-coding
mm_101082.1	chr11	11769847	11769857	-	1	NA	3' UTR (NM_009578, exon 7 of 7)	3' UTR (NM_009578, exon 7 of 7)	39110	NM_021891	60530	Mm.236114	NM_021891	ENSMUSG00000035455	Fignl1	-	fidgetin-like 1	protein-coding
mm_19081.1	chr2	77946315	77946327	-	1	NA	promoter-TSS (NM_001290740)	promoter-TSS (NM_001290740)	35	NM_001290740	80744	Mm.288151	NM_030560	ENSMUSG00000027014	Cwc22	AA684037|AI173004|AL022752|B230213M24|mKIAA1604	CWC22 spliceosome-associated protein	protein-coding
mm_17467.1	chr2	28558086	28558123	-	1	NA	exon (NM_009885, exon 8 of 11)	exon (NM_009885, exon 8 of 11)	5299	NM_009885	12613	Mm.236017	NM_009885	ENSMUSG00000026818	Cel	1810036E18Rik|BAL	carboxyl ester lipase	protein-coding
mm_80770.1	chr9	95560037	95560045	+	1	NA	exon (NM_198414, exon 1 of 1)	exon (NM_198414, exon 1 of 1)	224	NM_198414	75552	Mm.151485	NM_198414	ENSMUSG00000064225	Paqr9	1700020G04Rik	progestin and adipoQ receptor family member IX	protein-coding
mm_39516.1	chr5	21256954	21256980	+	1	NA	intron (NM_175437, intron 18 of 30)	intron (NM_175437, intron 18 of 30)	70700	NM_175437	212167	Mm.121705	NM_175437	ENSMUSG00000039934	Gsap	A530088I07Rik|Pion	gamma-secretase activating protein	protein-coding
mm_114419.1	chr13	64368127	64368208	+	1	NA	exon (NM_009984, exon 3 of 8)	exon (NM_009984, exon 3 of 8)	2353	NM_009984	13039	Mm.930	NM_009984	ENSMUSG00000021477	Ctsl	1190035F06Rik|CatL|Ctsl1|MEP|fs|nkt	cathepsin L	protein-coding
mm_16014.1	chr2	167421707	167421732	+	1	NA	promoter-TSS (NM_001304542)	promoter-TSS (NM_001304542)	9	NM_001304542	77031	Mm.278924	NM_148929	ENSMUSG00000039463	Slc9a8	1200006P13Rik|6430709P13Rik|AI182282|NHE-8|NHE8	solute carrier family 9 (sodium/hydrogen exchanger), member 8	protein-coding
mm_49998.1	chr6	41048253	41048261	+	1	NA	Intergenic	Intergenic	-12748	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_8971.1	chr1	165236893	165236956	-	1	NA	promoter-TSS (NM_145513)	promoter-TSS (NM_145513)	34	NM_145513	226591	Mm.21520	NM_145513	ENSMUSG00000040843	Tiprl	1810011K17Rik	TIP41, TOR signalling pathway regulator-like (S. cerevisiae)	protein-coding
mm_18403.1	chr2	60284293	60284301	-	1	NA	5' UTR (NM_025422, exon 1 of 5)	5' UTR (NM_025422, exon 1 of 5)	187	NM_025422	66205	Mm.227281	NM_025422	ENSMUSG00000060703	Cd302	1110055L24Rik|AI159627	CD302 antigen	protein-coding
mm_57689.1	chr6	128519428	128519457	-	1	NA	exon (NM_007376, exon 8 of 36)	exon (NM_007376, exon 8 of 36)	7278	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_138682.1	chr17	35916931	35916939	+	1	NA	promoter-TSS (NM_025878)	promoter-TSS (NM_025878)	-261	NM_001163818	52040	Mm.29385	NM_175934	ENSMUSG00000039220	Ppp1r10	2610025H06Rik|Cat53|D17Ertd808e|Fb19|Pnuts	protein phosphatase 1, regulatory subunit 10	protein-coding
mm_114223.1	chr13	56438916	56438917	+	1	NA	intron (NM_177809, intron 1 of 7)	intron (NM_177809, intron 1 of 7)	561	NM_177809	328258	Mm.482177	NM_177809	ENSMUSG00000021509	Slc25a48	AU042651|E230025K15	solute carrier family 25, member 48	protein-coding
mm_18556.1	chr2	65211984	65211988	-	1	NA	intron (NM_027225, intron 1 of 12)	B1_Mur4|SINE|Alu	26640	NM_177025	319876	Mm.34159	NM_027225	ENSMUSG00000034903	Cobll1	1810047P18Rik|Coblr1|D430044D16Rik	Cobl-like 1	protein-coding
mm_145544.1	chr18	60808053	60808057	+	1	NA	exon (NM_010545, exon 2 of 8)	exon (NM_010545, exon 2 of 8)	-4021	NR_039567	100628611		NR_039567	ENSMUSG00000093327	Mir5107	mir-5107|mmu-mir-5107|mu-mir-5107	microRNA 5107	ncRNA
mm_156453.1	chrX	142736602	142736627	+	1	NA	intron (NM_001199360, intron 2 of 6)	ID_B1|SINE|B4	-2386	NR_030523	723976		NR_030523	ENSMUSG00000076011	Mir652	Mirn652|miRX|mmu-mir-652	microRNA 652	ncRNA
mm_83418.1	chr9	44920699	44920725	-	1	NA	promoter-TSS (NM_013795)	promoter-TSS (NM_013795)	30	NM_013795	27425	Mm.14663	NM_013795	ENSMUSG00000038717	Atp5l	4933437C06Rik	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit G	protein-coding
mm_60348.1	chr7	44358575	44358583	+	1	NA	TTS (NM_001034115)	TTS (NM_001034115)	16451	NM_027049	69349	Mm.358922	NM_027049	ENSMUSG00000008028	1700008O03Rik	-	RIKEN cDNA 1700008O03 gene	protein-coding
mm_29531.1	chr3	116662271	116662339	-	1	NA	intron (NM_008246, intron 1 of 11)	CpG	372	NM_008246	15247	Mm.280077	NM_008246	ENSMUSG00000089911	Mfsd14a	Hiat1	major facilitator superfamily domain containing 14A	protein-coding
mm_73545.1	chr8	108749510	108749525	+	1	NA	intron (NM_007496, intron 1 of 9)	intron (NM_007496, intron 1 of 9)	34873	NM_007496	11906	Mm.416972	NM_007496	ENSMUSG00000038872	Zfhx3	A230102L03Rik|Atbf1|Sci|WBP9|mKIAA4228	zinc finger homeobox 3	protein-coding
mm_115062.1	chr13	100744205	100744240	+	1	NA	intron (NM_001190264, intron 1 of 3)	CpG	437	NM_001190264	66128	Mm.306173	NM_025369	ENSMUSG00000061474	Mrps36	1110018B13Rik|S36mt	mitochondrial ribosomal protein S36	protein-coding
mm_159629.1	chr4	137545285	137545285	+	1	NA	exon (NM_008305, exon 60 of 97)	exon (NM_008305, exon 60 of 97)	6999	NR_105985	102465616		NR_105985	ENSMUSG00000099134	Mir7018	Gm27606|mmu-mir-7018	microRNA 7018	ncRNA
mm_143239.1	chr17	63500532	63500598	-	1	NA	promoter-TSS (NM_015794)	promoter-TSS (NM_015794)	15	NM_015794	50758	Mm.136366	NM_015794	ENSMUSG00000023965	Fbxl17	6330576B01Rik|AI452053|BB073797|C130023C01Rik|Fbx13|Fbxo13	F-box and leucine-rich repeat protein 17	protein-coding
mm_161244.1	chr13	98032536	98032536	-	1	NA	intron (NM_012026, intron 7 of 35)	intron (NM_012026, intron 7 of 35)	173629	NM_012026	110596	Mm.252718	NM_012026	ENSMUSG00000021662	Arhgef28	9230110L08Rik|AI323540|D13Bwg1089e|RIP2|Rgnef|RhoGEF|Rhoip2|p190RhoGEF	Rho guanine nucleotide exchange factor (GEF) 28	protein-coding
mm_97560.1	chr11	78935363	78935366	+	1	NA	exon (NM_010927, exon 6 of 27)	exon (NM_010927, exon 6 of 27)	10073	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_18711.1	chr2	72232296	72232307	-	1	NA	intron (NM_001204165, intron 23 of 30)	intron (NM_001204165, intron 23 of 30)	-53336	NM_023057	65964	Mm.304143	NM_023057	ENSMUSG00000004085	Map3k20	AV006891|B230120H23Rik|MLTK|MLTKalpha|MLTKbeta|Zak	mitogen-activated protein kinase kinase kinase 20	protein-coding
mm_17782.1	chr2	32961636	32961646	-	1	NA	promoter-TSS (NM_009076)	promoter-TSS (NM_009076)	-71	NM_009076	269261	Mm.250030	NM_009076	ENSMUSG00000038900	Rpl12	E430018F03	ribosomal protein L12	protein-coding
mm_104362.1	chr11	94321444	94321494	-	1	NA	intron (NM_026313, intron 1 of 10)	CpG	442	NM_026313	67684	Mm.30927	NM_026313	ENSMUSG00000020863	Luc7l3	3300001P08Rik|Luc7a	LUC7-like 3 (S. cerevisiae)	protein-coding
mm_130923.1	chr15	102722121	102722137	-	1	NA	promoter-TSS (NM_026192)	promoter-TSS (NM_026192)	49	NM_026192	67488	Mm.71682	NM_026192	ENSMUSG00000023055	Calcoco1	1810009B06Rik|Cocoa|Gcap11|mKIAA1536	calcium binding and coiled coil domain 1	protein-coding
mm_85252.1	chr9	99237223	99237245	-	1	NA	promoter-TSS (NM_001244762)	promoter-TSS (NM_001244762)	5	NM_001244762	623459	Mm.260891	NM_001244762	ENSMUSG00000096316	Faiml	EG623459|Gm6432	Fas apoptotic inhibitory molecule like	protein-coding
mm_158243.1	chrX	106603710	106603718	-	1	NA	promoter-TSS (NM_001281859)	promoter-TSS (NM_001281859)	-35	NM_001281859	58861	Mm.287166	NM_021476	ENSMUSG00000052821	Cysltr1	BB147369|CysLT1R|Cyslt1	cysteinyl leukotriene receptor 1	protein-coding
mm_39845.1	chr5	30889414	30889425	+	1	NA	promoter-TSS (NM_001294262)	promoter-TSS (NM_001294262)	85	NM_001294262	231093	Mm.440364	NM_174849	ENSMUSG00000029165	Agbl5	9430057O19Rik|CCP5	ATP/GTP binding protein-like 5	protein-coding
mm_26332.1	chr3	142545962	142545988	+	1	NA	exon (NM_001083312, exon 10 of 11)	exon (NM_001083312, exon 10 of 11)	-14077	NM_018734	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_108463.1	chr12	83520505	83520517	+	1	NA	promoter-TSS (NM_030246)	promoter-TSS (NM_030246)	45	NM_030246	73828	Mm.38238	NM_030246	ENSMUSG00000021222	Dcaf4	1110018E21Rik|Wdr21	DDB1 and CUL4 associated factor 4	protein-coding
mm_14296.1	chr2	128924905	128924905	+	1	NA	Intergenic	Intergenic	19115	NM_020594	57432	Mm.11675	NM_020594	ENSMUSG00000027387	Zc3h8	AU020882|E130108N08Rik|Fliz1|Zc3hdc8	zinc finger CCCH type containing 8	protein-coding
mm_45670.1	chr5	77211406	77211458	-	1	NA	promoter-TSS (NM_001289764)	promoter-TSS (NM_001289764)	39	NM_183284	69982	Mm.46106	NM_183284	ENSMUSG00000053030	Spink2	1700007F22Rik|AV038945|HUSI-II	serine peptidase inhibitor, Kazal type 2	protein-coding
mm_151536.1	chr19	58943433	58943441	+	1	NA	promoter-TSS (NM_178689)	promoter-TSS (NM_178689)	12	NM_178689	226265	Mm.103154	NM_178689	ENSMUSG00000048029	Eno4	6430537H07Rik	enolase 4	protein-coding
mm_127335.1	chr15	100469057	100469075	+	1	NA	promoter-TSS (NM_134093)	promoter-TSS (NM_134093)	32	NM_134093	68614	Mm.275272	NM_134093	ENSMUSG00000037353	Letmd1	1110019O13Rik|AI593524|BB130465|BB235638|HCCR-2|HCCR1|MCC-32|Mccr	LETM1 domain containing 1	protein-coding
mm_52900.1	chr6	122706595	122706605	+	1	NA	promoter-TSS (NM_001289831)	promoter-TSS (NM_001289831)	-889	NM_001289831	71950	Mm.6047	NM_028016	ENSMUSG00000012396	Nanog	2410002E02Rik|ENK|ecat4	Nanog homeobox	protein-coding
mm_29229.1	chr3	107213453	107213459	-	1	NA	exon (NM_001111143, exon 7 of 9)	exon (NM_001111143, exon 7 of 9)	8276	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_80993.1	chr9	103423045	103423047	+	1	NA	promoter-TSS (NR_040466)	promoter-TSS (NR_040466)	-532	NR_040466	100529079	Mm.437003	NR_040466	ENSMUSG00000086236	5830418P13Rik	-	RIKEN cDNA 5830418P13 gene	ncRNA
mm_42981.1	chr5	123228239	123228301	+	1	NA	promoter-TSS (NM_026000)	promoter-TSS (NM_026000)	80	NM_026000	67151	Mm.278997	NM_026000	ENSMUSG00000029440	Psmd9	1500011J20Rik|2610202L11Rik|Bridge-1|P27	proteasome (prosome, macropain) 26S subunit, non-ATPase, 9	protein-coding
mm_138735.1	chr17	36970726	36970739	+	1	NA	Intergenic	Intergenic	10505	NM_029747	76797	Mm.159787	NM_029747	ENSMUSG00000064308	2410137M14Rik	-	RIKEN cDNA 2410137M14 gene	protein-coding
mm_172930.1	chr9	76314167	76314171	+	1	NA	intron (NM_198962, intron 1 of 7)	ORR1A2|LTR|ERVL-MaLR	9409	NM_198962	387285	Mm.335300	NM_198962	ENSMUSG00000032360	Hcrtr2	OX2R|mOX2aR|mOX2bR|mOXR2	hypocretin (orexin) receptor 2	protein-coding
mm_70143.1	chr7	143458580	143458620	-	1	NA	3' UTR (NM_001161624, exon 4 of 4)	3' UTR (NM_001161624, exon 4 of 4)	2450	NM_009876	12577	Mm.168789	NM_009876	ENSMUSG00000037664	Cdkn1c	AL024410|CDKI|Kip2|p57(kip2)|p57Kip2	cyclin-dependent kinase inhibitor 1C (P57)	protein-coding
mm_50434.1	chr6	48845963	48845985	+	1	NA	TTS (NM_025326)	TTS (NM_025326)	4318	NM_001098271	66058	Mm.27061	NM_025326	ENSMUSG00000023367	Tmem176a	0610011I04Rik|AU040201|AU041743|Keg2	transmembrane protein 176A	protein-coding
mm_152594.1	chr19	11640714	11640726	-	1	NA	5' UTR (NM_133246, exon 1 of 7)	5' UTR (NM_133246, exon 1 of 7)	131	NM_133246	170813	Mm.240438	NM_133246	ENSMUSG00000024681	Ms4a3	HTm4	membrane-spanning 4-domains, subfamily A, member 3	protein-coding
mm_30843.1	chr4	24556693	24556701	+	1	NA	intron (NM_199467, intron 13 of 23)	intron (NM_199467, intron 13 of 23)	60235	NM_199467	212377	Mm.120919	NM_199467	ENSMUSG00000045751	Mms22l	F730047E07Rik|Gm134	MMS22-like, DNA repair protein	protein-coding
mm_78826.1	chr9	44107269	44107279	+	1	NA	promoter-TSS (NM_001040631)	promoter-TSS (NM_001040631)	3	NM_001040632	235312	Mm.227110	NM_145613	ENSMUSG00000079592	C1qtnf5	Ctrp5	C1q and tumor necrosis factor related protein 5	protein-coding
mm_31700.1	chr4	62543313	62543342	+	1	NA	intron (NM_177607, intron 10 of 14)	intron (NM_177607, intron 10 of 14)	-16520	NM_019492	50780	Mm.286753	NM_019492	ENSMUSG00000059810	Rgs3	4930506N09Rik|C2PA-RGS3|C2pa|PDZ-RGS3|RGS3S	regulator of G-protein signaling 3	protein-coding
mm_48751.1	chr5	147902159	147902168	-	1	NA	Intergenic	Intergenic	-7361	NM_027872	71706	Mm.153218	NM_027872	ENSMUSG00000029650	Slc46a3	1200006F02Rik	solute carrier family 46, member 3	protein-coding
mm_11462.1	chr2	32236632	32236701	+	1	NA	promoter-TSS (NM_145145)	promoter-TSS (NM_145145)	-17	NM_145145	99011	Mm.31192	NM_145145	ENSMUSG00000039254	Pomt1	AI505244	protein-O-mannosyltransferase 1	protein-coding
mm_46173.1	chr5	96921183	96921198	-	1	NA	promoter-TSS (NR_131152)	promoter-TSS (NR_131152)	-82	NR_131152	666266	Mm.32442	NR_131152	ENSMUSG00000106357	Gm8013	EG666266	predicted gene 8013	ncRNA
mm_44409.1	chr5	17849705	17849735	-	1	NA	promoter-TSS (NM_001159557)	promoter-TSS (NM_001159557)	72	NM_001159557	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_22456.1	chr3	3188079	3188087	+	1	NA	Intergenic	Intergenic	-319947	NM_013920	30942	Mm.330897	NM_013920	ENSMUSG00000017688	Hnf4g	NR2A2	hepatocyte nuclear factor 4, gamma	protein-coding
mm_142931.1	chr17	55712572	55712630	-	1	NA	promoter-TSS (NM_028370)	promoter-TSS (NM_028370)	27	NM_028370	72836	Mm.177073	NM_028370	ENSMUSG00000024174	Pot1b	2810458H16Rik	protection of telomeres 1B	protein-coding
mm_85636.1	chr9	107652224	107652234	-	1	NA	exon (NM_001199218, exon 15 of 16)	exon (NM_001199218, exon 15 of 16)	15170	NM_023805	76257	Mm.296560	NM_023805	ENSMUSG00000010064	Slc38a3	0610012J02Rik|D9Ucla2|Nat1|Slc38-3|Sn1|Snat3|mNAT	solute carrier family 38, member 3	protein-coding
mm_46948.1	chr5	114922159	114922175	-	1	NA	Intergenic	L2|LINE|L2	-1073	NM_145209	231655	Mm.95479	NM_145209	ENSMUSG00000041827	Oasl1	7530414C13Rik|oasl9	2'-5' oligoadenylate synthetase-like 1	protein-coding
mm_154799.1	chrX	13284919	13284922	+	1	NA	exon (NM_010028, exon 3 of 17)	exon (NM_010028, exon 3 of 17)	3898	NM_010028	13205	Mm.289662	NM_010028	ENSMUSG00000000787	Ddx3x	D1Pas1-rs2|Ddx3|Fin14	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 3, X-linked	protein-coding
mm_30508.1	chr3	158029240	158029244	-	1	NA	intron (NM_001093752, intron 2 of 12)	intron (NM_001093752, intron 2 of 12)	2512	NM_001093753	69207	Mm.223946	NM_026989	ENSMUSG00000055436	Srsf11	0610009J05Rik|2610019N13Rik|BF642805|Sfrs11	serine/arginine-rich splicing factor 11	protein-coding
mm_60556.1	chr7	44481177	44481179	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-3339	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_59864.1	chr7	30169862	30169912	+	1	NA	promoter-TSS (NM_001033540)	promoter-TSS (NM_001033540)	-35	NM_001033540	330503	Mm.434058	NM_001033540	ENSMUSG00000066647	Gm5113	B430201F14|EG330503	predicted gene 5113	protein-coding
mm_165378.1	chr2	128429481	128429490	+	1	NA	promoter-TSS (NR_028591)	promoter-TSS (NR_028591)	-134	NR_028590	100043424	Mm.297222	NR_028589		Gm14005	OTTMUSG00000015351	predicted gene 14005	ncRNA
mm_78647.1	chr9	40323415	40323458	+	1	NA	intron (NM_172768, intron 4 of 19)	intron (NM_172768, intron 4 of 19)	-10036	NR_040728	73558	Mm.398307	NR_040728		1700110K17Rik	-	RIKEN cDNA 1700110K17 gene	ncRNA
mm_81456.1	chr9	109833136	109833157	+	1	NA	intron (NM_018757, intron 1 of 6)	intron (NM_018757, intron 1 of 6)	352	NM_018757	54369	Mm.12951	NM_018757	ENSMUSG00000032478	Nme6	nm23-M6	NME/NM23 nucleoside diphosphate kinase 6	protein-coding
mm_168170.1	chr10	54619335	54619339	-	1	NA	Intergenic	L1Md_T|LINE|L1	543415	NR_038016	100502920	Mm.403982	NR_038016	ENSMUSG00000097069	Gm16998	-	predicted gene, 16998	ncRNA
mm_4580.1	chr1	178187722	178187725	+	1	NA	5' UTR (NM_024282, exon 1 of 5)	5' UTR (NM_024282, exon 1 of 5)	306	NM_024282	78825	Mm.440132	NM_024282	ENSMUSG00000026502	Desi2	5830417C01Rik|DeSI-2|Fam152a|Pppde1	desumoylating isopeptidase 2	protein-coding
mm_48988.1	chr6	4755948	4755948	+	1	NA	exon (NM_130877, exon 2 of 2)	exon (NM_130877, exon 2 of 2)	8642	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_158810.1	chrX	167307347	167307354	-	1	NA	exon (NM_001290758, exon 4 of 4)	exon (NM_001290758, exon 4 of 4)	23221	NM_001290757	170743	Mm.23979	NM_133211	ENSMUSG00000044583	Tlr7	-	toll-like receptor 7	protein-coding
mm_100562.1	chr11	120730418	120730453	+	1	NA	exon (NM_007621, exon 5 of 8)	exon (NM_007621, exon 5 of 8)	1586	NM_007621	12409	Mm.21454	NM_007621	ENSMUSG00000025150	Cbr2	MLCR	carbonyl reductase 2	protein-coding
mm_83839.1	chr9	54415833	54415852	-	1	NA	exon (NM_172771, exon 18 of 44)	exon (NM_172771, exon 18 of 44)	85784	NM_172771	235380	Mm.93636	NM_172771	ENSMUSG00000041268	Dmxl2	6330586A12|6430411K14Rik|E130119P06Rik|mKIAA0856	Dmx-like 2	protein-coding
mm_134491.1	chr16	18733152	18733193	-	1	NA	Intergenic	Intergenic	-43675	NM_013805	12741	Mm.22768	NM_013805	ENSMUSG00000041378	Cldn5	AI854493|MBEC1|Tmvcf	claudin 5	protein-coding
mm_123578.1	chr14	67006435	67006438	-	1	NA	intron (NM_009761, intron 1 of 5)	intron (NM_009761, intron 1 of 5)	2441	NM_009761	12177	Mm.29820	NM_009761	ENSMUSG00000022051	Bnip3l	C86132|D14Ertd719e|Nip3L|Nix	BCL2/adenovirus E1B interacting protein 3-like	protein-coding
mm_130798.1	chr15	101693847	101693880	-	1	NA	exon (NM_008476, exon 1 of 9)	exon (NM_008476, exon 1 of 9)	442	NM_008476	16687	Mm.302399	NM_008476	ENSMUSG00000058354	Krt6a	2310016L08Rik|Krt2-6a|Krt2-6c|MK6a|mK6[a]	keratin 6A	protein-coding
mm_45801.1	chr5	87568940	87568951	-	1	NA	promoter-TSS (NM_016771)	promoter-TSS (NM_016771)	61	NM_016771	53315	Mm.6824	NM_016771	ENSMUSG00000029273	Sult1d1	5033411P13Rik|AI987815|ST1d1|SULT-N|Sultn	sulfotransferase family 1D, member 1	protein-coding
mm_10626.1	chr2	19657814	19657824	+	1	NA	promoter-TSS (NR_033642)	promoter-TSS (NR_033642)	78	NR_033642	100041244	Mm.407223	NR_033642		Gm3230	-	predicted gene 3230	ncRNA
mm_65782.1	chr7	28767125	28767154	-	1	NA	promoter-TSS (NM_010908)	promoter-TSS (NM_010908)	387	NM_001122766	64383	Mm.272443	NM_022432	ENSMUSG00000015149	Sirt2	5730427M03Rik|SIR2L2|Sir2l	sirtuin 2	protein-coding
mm_45147.1	chr5	49204274	49204281	-	1	NA	intron (NM_001199244, intron 1 of 7)	intron (NM_001199244, intron 1 of 7)	81382	NM_001199244	80334	Mm.160172	NM_030265	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding
mm_13140.1	chr2	92184179	92184218	+	1	NA	promoter-TSS (NM_138755)	promoter-TSS (NM_138755)	16	NM_001346704	192285	Mm.330408	NM_138755	ENSMUSG00000058318	Phf21a	80kDa|Bhc|Bhc80|D030065N23Rik|PFTF1	PHD finger protein 21A	protein-coding
mm_92837.1	chr10	81499597	81499608	-	1	NA	exon (NM_010102, exon 1 of 1)	exon (NM_010102, exon 1 of 1)	535	NM_010102	13611	Mm.33065	NM_010102	ENSMUSG00000044199	S1pr4	Edg6|Lpc1|S1p4	sphingosine-1-phosphate receptor 4	protein-coding
mm_71558.1	chr8	49370929	49370955	+	1	NA	Intergenic	Intergenic	-696252	NM_011857	23965	Mm.42191	NM_011857	ENSMUSG00000031561	Tenm3	2610100B16Rik|Odz1|Odz3|Ten-m3|mKIAA1455	teneurin transmembrane protein 3	protein-coding
mm_114988.1	chr13	97495251	97495259	+	1	NA	non-coding (NR_110432, exon 2 of 2)	non-coding (NR_110432, exon 2 of 2)	12554	NR_110431	100039691	Mm.219358	NR_110430	ENSMUSG00000078952	Lncenc1	ENSMUSG00000078952|Gm11019|Gm2373|Lincenc1|Platr18|linc-Enc1	long non-coding RNA, embryonic stem cells expressed 1	ncRNA
mm_10296.1	chr2	10380552	10380556	+	1	NA	intron (NM_001198808, intron 2 of 22)	PB1D7|SINE|Alu	8118	NM_177386	353282	Mm.329991	NM_177386	ENSMUSG00000061186	Sfmbt2	D2Wsu23e|D330030P06Rik	Scm-like with four mbt domains 2	protein-coding
mm_130638.1	chr15	100495056	100495057	-	1	NA	5' UTR (NM_153407, exon 1 of 5)	5' UTR (NM_153407, exon 1 of 5)	183	NM_153407	207785	Mm.294969	NM_153407	ENSMUSG00000044636	Csrnp2	CSRNP-2|Csnrp2|taip-12	cysteine-serine-rich nuclear protein 2	protein-coding
mm_79629.1	chr9	59311782	59311791	+	1	NA	intron (NM_028121, intron 4 of 6)	intron (NM_028121, intron 4 of 6)	20214	NM_028121	72141	Mm.22456	NM_028121	ENSMUSG00000025236	Adpgk	2610017G09Rik|Adp-gk|C77577	ADP-dependent glucokinase	protein-coding
mm_28771.1	chr3	95925196	95925200	-	1	NA	Intergenic	MRLTR33|LTR|ERVK	-4059	NM_001253758	66471	Mm.218657	NM_023210	ENSMUSG00000015749	Anp32e	2810018A15Rik|AI047746|AI326868|CPD1|LANP-L|LANPL|mLANP-L	acidic (leucine-rich) nuclear phosphoprotein 32 family, member E	protein-coding
mm_78856.1	chr9	44379537	44379624	+	1	NA	promoter-TSS (NM_021395)	promoter-TSS (NM_021395)	90	NM_021395	12282	Mm.116721	NM_021395	ENSMUSG00000032115	Hyou1	AI415631|CBP-140|Cab140|Grp170|Orp150	hypoxia up-regulated 1	protein-coding
mm_16122.1	chr2	170132380	170132386	+	1	NA	intron (NM_001159683, intron 1 of 6)	intron (NM_001159683, intron 1 of 6)	-1163	NM_001033299	228913	Mm.22858	NM_001033299	ENSMUSG00000052056	Zfp217	4933431C08Rik|AW987152|Gm562|ZABC1|Znf217	zinc finger protein 217	protein-coding
mm_42881.1	chr5	122354362	122354368	+	1	NA	promoter-TSS (NM_019780)	promoter-TSS (NM_019780)	-4	NM_001347453	56433	Mm.216528	NM_019780	ENSMUSG00000029462	Vps29	2010015D08Rik|AW049835|PEP11	VPS29 retromer complex component	protein-coding
mm_171778.1	chr5	109907403	109907417	-	1	NA	Intergenic	RLTR4_Mm|LTR|ERV1	-26153	NR_040366	100642166		NR_040366	ENSMUSG00000090015	Gm15446	OTTMUSG00000022004	predicted gene 15446	ncRNA
mm_32520.1	chr4	108834648	108834705	+	1	NA	promoter-TSS (NM_025334)	promoter-TSS (NM_025334)	-2	NM_025334	66073	Mm.159965	NM_025334	ENSMUSG00000028567	Txndc12	0610040B21Rik|ERp16|ERp19	thioredoxin domain containing 12 (endoplasmic reticulum)	protein-coding
mm_36183.1	chr4	62208700	62208717	-	1	NA	promoter-TSS (NM_009554)	promoter-TSS (NM_009554)	-162	NM_001290350	22696	Mm.5011	NM_009554	ENSMUSG00000028389	Zfp37	Tzn|Zfp-37	zinc finger protein 37	protein-coding
mm_141456.1	chr17	30424373	30424375	-	1	NA	intron (NM_172618, intron 6 of 11)	intron (NM_172618, intron 6 of 11)	-28194	NR_030688	623169	Mm.440508	NR_030688		Gm6402	EG623169	ribosomal protein S17 pseudogene	pseudo
mm_41544.1	chr5	92897957	92897974	+	1	NA	promoter-TSS (NM_001077596)	promoter-TSS (NM_001077596)	-28	NM_001077596	27428	Mm.46014	NM_015756	ENSMUSG00000029381	Shroom3	AL022960|D5Ertd287e|Shrm|Shrm3	shroom family member 3	protein-coding
mm_148922.1	chr19	6976501	6976524	+	1	NA	intron (NM_008889, intron 1 of 3)	intron (NM_008889, intron 1 of 3)	1464	NM_008889	18938	Mm.140	NM_008889	ENSMUSG00000056612	Ppp1r14b	AOM172|PHI-1|PLCB3N|Png	protein phosphatase 1, regulatory (inhibitor) subunit 14B	protein-coding
mm_133885.1	chr16	96525599	96525609	+	1	NA	3' UTR (NM_008791, exon 3 of 3)	3' UTR (NM_008791, exon 3 of 3)	57998	NM_008791	18546	Mm.5023	NM_008791	ENSMUSG00000090223	Pcp4	P16Rimb19|Pcp-4|Pep19	Purkinje cell protein 4	protein-coding
mm_162197.1	chrX	118480737	118480737	-	1	NA	promoter-TSS (NM_001142750)	promoter-TSS (NM_001142750)	0	NM_001142750	100039551	Mm.272850	NM_001142750	ENSMUSG00000100194	Tgif2lx2	-	TGFB-induced factor homeobox 2-like, X-linked 2	protein-coding
mm_60312.1	chr7	44188206	44188222	+	1	NA	promoter-TSS (NM_010643)	promoter-TSS (NM_010643)	-22	NM_010643	16617	Mm.483098	NM_010643	ENSMUSG00000063713	Klk1b24	Klk24|mGk-24	kallikrein 1-related peptidase b24	protein-coding
mm_115809.1	chr13	19395729	19395789	-	1	NA	promoter-TSS (NM_024270)	promoter-TSS (NM_024270)	54	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_90034.1	chr10	115452584	115452588	+	1	NA	exon (NM_010195, exon 18 of 18)	exon (NM_010195, exon 18 of 18)	67627	NM_001033261	216345	Mm.207621	NM_001033261	ENSMUSG00000034163	Zfc3h1	BC033596|Ccdc131|Psrc2	zinc finger, C3H1-type containing	protein-coding
mm_53927.1	chr6	4717170	4717184	-	1	NA	intron (NM_011360, intron 3 of 10)	intron (NM_011360, intron 3 of 10)	30027	NM_001130188	20392	Mm.8739	NM_011360	ENSMUSG00000004631	Sgce	e-SG	sarcoglycan, epsilon	protein-coding
mm_45850.1	chr5	87780023	87780025	-	1	NA	exon (NM_001304768, exon 7 of 13)	exon (NM_001304768, exon 7 of 13)	5574	NM_007785	12993	Mm.4908	NM_007785	ENSMUSG00000061937	Csn1s2a	Csng|PP22	casein alpha s2-like A	protein-coding
mm_106188.1	chr11	116807651	116807661	-	1	NA	3' UTR (NM_001347633, exon 5 of 5)	3' UTR (NM_001347633, exon 5 of 5)	20390	NM_026280	67622	Mm.64962	NM_026280	ENSMUSG00000020814	Mxra7	1810057P16Rik|E130302J09Rik	matrix-remodelling associated 7	protein-coding
mm_86580.1	chr10	12976230	12976251	+	1	NA	Intergenic	Intergenic	-11981	NM_001163591	74732	Mm.248648	NM_029075	ENSMUSG00000039232	Stx11	5830405C08Rik	syntaxin 11	protein-coding
mm_92833.1	chr10	81482656	81482725	-	1	NA	promoter-TSS (NM_176954)	promoter-TSS (NM_176954)	19	NM_176954	319586	Mm.152689	NM_176954	ENSMUSG00000034818	Celf5	4930565A21Rik|Brunol5	CUGBP, Elav-like family member 5	protein-coding
mm_58324.1	chr6	146502112	146502133	-	1	NA	5' UTR (NM_019923, exon 1 of 57)	5' UTR (NM_019923, exon 1 of 57)	101	NM_010586	16439	Mm.7800	NM_010586	ENSMUSG00000030287	Itpr2	AI649341|InsP3R-2|InsP3R-5|Ip3r2|Itpr5|insP3R2	inositol 1,4,5-triphosphate receptor 2	protein-coding
mm_9500.1	chr1	173730141	173730160	-	1	NA	exon (NM_001204910, exon 5 of 8)	exon (NM_001204910, exon 5 of 8)	11659	NM_001204910	226691	Mm.440876	NM_001204910	ENSMUSG00000073490	Ifi207	AI607873|Pyhin-A	interferon activated gene 207	protein-coding
mm_36361.1	chr4	76222560	76222566	-	1	NA	intron (NM_011211, intron 13 of 39)	intron (NM_011211, intron 13 of 39)	-944277	NM_025849	66928	Mm.24332	NM_025849	ENSMUSG00000028398	Tmem261	1700027K24Rik|3110001D03Rik	transmembrane protein 261	protein-coding
mm_135676.1	chr16	52419952	52419963	-	1	NA	intron (NM_009655, intron 1 of 15)	intron (NM_009655, intron 1 of 15)	33124	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_116702.1	chr13	50443911	50443914	-	1	NA	Intergenic	Intergenic	-23395	NM_001033400	328250	Mm.315205	NM_001033400	ENSMUSG00000071909	Nutm2	Fam22|Gm806	NUT family member 2	protein-coding
mm_166741.1	chr6	124722150	124722160	-	1	NA	intron (NM_001077705, intron 11 of 15)	intron (NM_001077705, intron 11 of 15)	-3765	NR_029792	723944		NR_029792	ENSMUSG00000065462	Mir200c	Mirn200c|mir-200c	microRNA 200c	ncRNA
mm_48729.1	chr5	147426578	147426589	-	1	NA	Intergenic	Intergenic	-3997	NM_028291	72587	Mm.320469	NM_028291	ENSMUSG00000029647	Pan3	2700050F09Rik|A430027N15Rik|AU014670	PAN3 poly(A) specific ribonuclease subunit	protein-coding
mm_32462.1	chr4	107434571	107434599	+	1	NA	promoter-TSS (NM_147221)	promoter-TSS (NM_147221)	-134	NM_147221	230587	Mm.331757	NM_147221	ENSMUSG00000034762	Glis1	Gli5|Gli6|GliH1	GLIS family zinc finger 1	protein-coding
mm_65041.1	chr7	18567288	18567298	-	1	NA	promoter-TSS (NM_001037168)	promoter-TSS (NM_001037168)	12	NM_001037168	545925	Mm.440302	NM_001037168	ENSMUSG00000070797	Psg27	EG545925|cea15	pregnancy-specific glycoprotein 27	protein-coding
mm_166300.1	chr5	104114070	104114099	-	1	NA	promoter-TSS (NM_010097)	promoter-TSS (NM_010097)	4	NM_010097	13602	Mm.29027	NM_010097	ENSMUSG00000029309	Sparcl1	Ecm2|Sc1|hevin|mast9	SPARC-like 1	protein-coding
mm_81740.1	chr9	113793317	113793340	+	1	NA	promoter-TSS (NM_001286603)	promoter-TSS (NM_001286603)	-2	NM_001286603	76499	Mm.222272	NM_029633	ENSMUSG00000033392	Clasp2	1500004F14Rik|8030404L10Rik|C77448|CLASP2beta|mKIAA0627	CLIP associating protein 2	protein-coding
mm_95273.1	chr11	45851934	45851946	+	1	NA	promoter-TSS (NM_001045520)	promoter-TSS (NM_001045520)	-24	NM_001346760	216705	Mm.169673	NM_001045520	ENSMUSG00000006169	Clint1	AI642036|AW537616|C530049I24Rik|Enth|Epn4|F630206G17Rik|mKIAA0171	clathrin interactor 1	protein-coding
mm_8492.1	chr1	153850745	153850755	-	1	NA	exon (NM_178243, exon 1 of 1)	exon (NM_178243, exon 1 of 1)	445	NM_178243	240817	Mm.439405	NM_178243	ENSMUSG00000045968	Teddm2	5830403L16Rik|AJ554213|Me9|e92	transmembrane epididymal family member 2	protein-coding
mm_24054.1	chr3	87906892	87906909	+	1	NA	promoter-TSS (NM_001331051)	promoter-TSS (NM_001331051)	50	NM_001331052	15191	Mm.292208	NM_008231	ENSMUSG00000004897	Hdgf	AI118077|D3Ertd299e	hepatoma-derived growth factor	protein-coding
mm_27929.1	chr3	79567359	79567375	-	1	NA	intron (NM_001162999, intron 1 of 16)	intron (NM_001162999, intron 1 of 16)	312	NM_001162999	329679	Mm.244005	NM_001162999	ENSMUSG00000061175	Fnip2	D630023B12Rik|mKIAA1450	folliculin interacting protein 2	protein-coding
mm_164141.1	chr15	58134992	58134998	-	1	NA	promoter-TSS (NM_027435)	promoter-TSS (NM_027435)	87	NM_027435	70472	Mm.221758	NM_027435	ENSMUSG00000022360	Atad2	2610509G12Rik	ATPase family, AAA domain containing 2	protein-coding
mm_9047.1	chr1	167284704	167284716	-	1	NA	intron (NM_030724, intron 1 of 6)	CpG	417	NM_030724	80914	Mm.280895	NM_030724	ENSMUSG00000026558	Uck2	AA407809|AI481316|AU018180|AU020720|TSA903|UK|UMK|Umpk	uridine-cytidine kinase 2	protein-coding
mm_46160.1	chr5	96162458	96162471	-	1	NA	promoter-TSS (NM_178854)	promoter-TSS (NM_178854)	-474	NM_144910	231464	Mm.28374	NM_144910	ENSMUSG00000034724	Cnot6l	4932442K20Rik	CCR4-NOT transcription complex, subunit 6-like	protein-coding
mm_39206.1	chr4	156050466	156050473	-	1	NA	intron (NM_029264, intron 1 of 14)	intron (NM_029264, intron 1 of 14)	348	NM_029264	330010	Mm.440232	NM_029264	ENSMUSG00000029074	Ttll10	4833412E22Rik|4930595O22Rik|AU022799|BC042775|Ttll5	tubulin tyrosine ligase-like family, member 10	protein-coding
mm_8523.1	chr1	154884186	154884197	-	1	NA	Intergenic	Intergenic	-158271	NM_009782	12290	Mm.267517	NM_009782	ENSMUSG00000004110	Cacna1e	A430040I15|BII|Cach6|Cacnl1a6|Cav2.3|Cchra1|alpha1E	calcium channel, voltage-dependent, R type, alpha 1E subunit	protein-coding
mm_33112.1	chr4	124737743	124737759	+	1	NA	Intergenic	Intergenic	-4099	NM_008385	16330	Mm.296202	NM_008385	ENSMUSG00000028894	Inpp5b	5PTase|AW260155|INPP5P	inositol polyphosphate-5-phosphatase B	protein-coding
mm_3327.1	chr1	137928101	137928135	+	1	NA	Intergenic	Intergenic	-38337	NR_029795	735252		NR_029795	ENSMUSG00000065565	Mir181a-1	Mirn181a-1|Mirn213|miR-213|mir-181a-1|mmu-mir-213	microRNA 181a-1	ncRNA
mm_80771.1	chr9	95560398	95560430	+	1	NA	exon (NM_198414, exon 1 of 1)	exon (NM_198414, exon 1 of 1)	597	NM_198414	75552	Mm.151485	NM_198414	ENSMUSG00000064225	Paqr9	1700020G04Rik	progestin and adipoQ receptor family member IX	protein-coding
mm_88808.1	chr10	80755391	80755399	+	1	NA	5' UTR (NM_199322, exon 1 of 28)	5' UTR (NM_199322, exon 1 of 28)	189	NM_199322	208266	Mm.152371	NM_199322	ENSMUSG00000061589	Dot1l	A630076O07|AW907654|Dot1|KMT4|mDot1	DOT1-like, histone H3 methyltransferase (S. cerevisiae)	protein-coding
mm_64783.1	chr7	5125938	5125958	-	1	NA	promoter-TSS (NM_009028)	promoter-TSS (NM_009028)	2	NM_009028	19428	Mm.322186	NM_009028	ENSMUSG00000083649	Rasl2-9	M2|Ran|Ran/M2|Rasl2-9-ps	RAS-like, family 2, locus 9	protein-coding
mm_31085.1	chr4	41630595	41630607	+	1	NA	exon (NM_175138, exon 16 of 20)	exon (NM_175138, exon 16 of 20)	9701	NM_027147	69638	Mm.372459	NM_027147	ENSMUSG00000028445	Enho	1110065P19Rik|2310040A07Rik	energy homeostasis associated	protein-coding
mm_71454.1	chr8	46521760	46521767	+	1	NA	intron (NM_001302163, intron 11 of 20)	Lx7|LINE|L1	-30306	NM_027973	71876	Mm.22108	NM_027973	ENSMUSG00000031629	Cenpu	1700029A22Rik|Mlf1ip	centromere protein U	protein-coding
mm_43573.1	chr5	137745954	137745964	+	1	NA	promoter-TSS (NM_023910)	promoter-TSS (NM_023910)	-10	NM_023910	78829	Mm.286399	NM_023910	ENSMUSG00000029723	Tsc22d4	0610009M14Rik|1700023B23Rik|AI415410|Thg-1pit|Tilz2	TSC22 domain family, member 4	protein-coding
mm_46827.1	chr5	113219517	113219527	-	1	NA	Intergenic	Intergenic	-7387	NM_001033428	333048	Mm.332586	NM_001033428	ENSMUSG00000066964	Tmem211	Gm854	transmembrane protein 211	protein-coding
mm_11476.1	chr2	32384707	32384720	+	1	NA	TTS (NM_008491)	TTS (NM_008491)	-2798	NM_198001	73737	Mm.27608	NM_198001	ENSMUSG00000039195	1110008P14Rik	C79326	RIKEN cDNA 1110008P14 gene	protein-coding
mm_36241.1	chr4	63172087	63172102	-	1	NA	promoter-TSS (NM_010616)	promoter-TSS (NM_010616)	37	NM_010616	16552	Mm.216057	NM_010616	ENSMUSG00000028357	Kif12	-	kinesin family member 12	protein-coding
mm_125883.1	chr15	75704301	75704317	+	1	NA	promoter-TSS (NM_001163465)	promoter-TSS (NM_001163465)	21	NM_008164	14787	Mm.57052	NM_008164	ENSMUSG00000022580	Rhpn1	BB023497|Grbp|Rhophilin|mKIAA1929	rhophilin, Rho GTPase binding protein 1	protein-coding
mm_149227.1	chr19	10041552	10041581	+	1	NA	promoter-TSS (NM_021890)	promoter-TSS (NM_021890)	18	NM_021890	60527	Mm.253875	NM_021890	ENSMUSG00000024664	Fads3	AI464531	fatty acid desaturase 3	protein-coding
mm_139008.1	chr17	45570402	45570461	+	1	NA	exon (NM_008302, exon 6 of 11)	exon (NM_008302, exon 6 of 11)	2830	NM_008302	15516	Mm.2180	NM_008302	ENSMUSG00000023944	Hsp90ab1	90kDa|AL022974|C81438|Hsp84|Hsp84-1|Hsp90|Hspcb	heat shock protein 90 alpha (cytosolic), class B member 1	protein-coding
mm_47694.1	chr5	129704965	129704989	-	1	NA	5' UTR (NM_028826, exon 2 of 11)	5' UTR (NM_028826, exon 2 of 11)	3534	NM_028826	74222	Mm.159143	NM_028826	ENSMUSG00000034219	Sept14	1700016K13Rik	septin 14	protein-coding
mm_153980.1	chr19	47864953	47864958	-	1	NA	promoter-TSS (NM_026619)	promoter-TSS (NM_026619)	-590	NM_030051	68214	Mm.63791	NM_026619	ENSMUSG00000025069	Gsto2	1700020F09Rik|4930425C18Rik|GSTO 2-2	glutathione S-transferase omega 2	protein-coding
mm_116216.1	chr13	32806961	32806978	-	1	NA	exon (NM_030215, exon 3 of 7)	exon (NM_030215, exon 3 of 7)	4939	NM_030215	78903	Mm.286680	NM_030215	ENSMUSG00000021400	Wrnip1	4833444L21Rik|WHIP|Wrnip	Werner helicase interacting protein 1	protein-coding
mm_8706.1	chr1	158887783	158887784	-	1	NA	intron (NM_001085376, intron 2 of 21)	Lx8|LINE|L1	69655	NM_001085376	23850	Mm.458621	NM_001085376	ENSMUSG00000073530	Pappa2	PAPP-A2|PLAC3|Pappe	pappalysin 2	protein-coding
mm_160246.1	chr7	105181336	105181336	-	1	NA	promoter-TSS (NM_001011857)	promoter-TSS (NM_001011857)	-25	NM_001011857	258160	Mm.377366	NM_001011857	ENSMUSG00000047794	Olfr685	MOR37-1	olfactory receptor 685	protein-coding
mm_44614.1	chr5	25498749	25498772	-	1	NA	promoter-TSS (NM_001081383)	promoter-TSS (NM_001081383)	23	NM_001081383	231051	Mm.332268	NM_001081383	ENSMUSG00000038056	Kmt2c	E330008K23Rik|HALR|Mll3|mKIAA1506	lysine (K)-specific methyltransferase 2C	protein-coding
mm_101369.1	chr11	23762092	23762095	-	1	NA	intron (NM_009044, intron 1 of 9)	B1_Mur1|SINE|Alu	8877	NM_009044	19696	Mm.4869	NM_009044	ENSMUSG00000020275	Rel	c-Rel	reticuloendotheliosis oncogene	protein-coding
mm_151037.1	chr19	47023445	47023460	+	1	NA	exon (NM_146100, exon 3 of 3)	exon (NM_146100, exon 3 of 3)	-8263	NM_001164363	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_59796.1	chr7	29001535	29001552	+	1	NA	intron (NM_008279, intron 27 of 31)	intron (NM_008279, intron 27 of 31)	18689	NM_008279	26411	Mm.148278	NM_008279	ENSMUSG00000037337	Map4k1	Hpk1|mHPK1	mitogen-activated protein kinase kinase kinase kinase 1	protein-coding
mm_118137.1	chr13	104863914	104863921	-	1	NA	promoter-TSS (NM_029984)	promoter-TSS (NM_029984)	-24	NM_029984	77803	Mm.159995	NM_029984	ENSMUSG00000042655	Fam159b	A930021C24Rik	family with sequence similarity 159, member B	protein-coding
mm_62847.1	chr7	114316713	114316724	+	1	NA	intron (NR_029437, intron 3 of 3)	intron (NR_029437, intron 3 of 3)	-40602	NM_011965	26440	Mm.121265	NM_011965	ENSMUSG00000030751	Psma1	C2|HC2|Pros-30|alpha-type	proteasome (prosome, macropain) subunit, alpha type 1	protein-coding
mm_54668.1	chr6	39207151	39207161	-	1	NA	promoter-TSS (NM_001033430)	promoter-TSS (NM_001033430)	-383	NM_001033430	338523	Mm.293175	NM_001033430	ENSMUSG00000042599	Kdm7a	A630082K20Rik|BB041802|ENSMUSG00000073143|Jhdm1d|mKIAA1718	lysine (K)-specific demethylase 7A	protein-coding
mm_17229.1	chr2	25574576	25574632	-	1	NA	TTS (NM_001005424)	TTS (NM_001005424)	267	NM_029293	75454	Mm.458079	NM_029293	ENSMUSG00000036504	Phpt1	1700008C22Rik|PHP|Php14	phosphohistidine phosphatase 1	protein-coding
mm_81039.1	chr9	105053261	105053303	+	1	NA	promoter-TSS (NM_053159)	promoter-TSS (NM_053159)	14	NM_053159	94062	Mm.29746	NM_053159	ENSMUSG00000032563	Mrpl3	2010320L16Rik|5930422H18Rik|AA407889	mitochondrial ribosomal protein L3	protein-coding
mm_172611.1	chr8	18627214	18627223	+	1	NA	exon (NM_173189, exon 6 of 14)	exon (NM_173189, exon 6 of 14)	32045	NM_173189	244329	Mm.235296	NM_173189	ENSMUSG00000039842	Mcph1	5430437K10Rik|BRIT1|D030046N04Rik|MCT	microcephaly, primary autosomal recessive 1	protein-coding
mm_148173.1	chr18	78101477	78101487	-	1	NA	3' UTR (NM_028122, exon 9 of 9)	3' UTR (NM_028122, exon 9 of 9)	21944	NM_001171010	108052	Mm.33832	NM_028122	ENSMUSG00000059336	Slc14a1	2610507K20Rik|3021401A05Rik|UT-B|Utb1	solute carrier family 14 (urea transporter), member 1	protein-coding
mm_46201.1	chr5	98031138	98031254	-	1	NA	promoter-TSS (NM_133738)	promoter-TSS (NM_133738)	-234	NM_133738	71914	Mm.24842	NM_133738	ENSMUSG00000029338	Antxr2	2310046B19Rik|AW561899|CMG-2|CMG2|cI-35	anthrax toxin receptor 2	protein-coding
mm_102850.1	chr11	69370151	69370182	-	1	NA	promoter-TSS (NM_146019)	promoter-TSS (NM_146019)	-740	NM_146019	216848	Mm.178246	NM_146019	ENSMUSG00000018474	Chd3	2600010P09Rik|AF020312|Chd7|Prp7|Prp9-1	chromodomain helicase DNA binding protein 3	protein-coding
mm_140250.1	chr17	84185747	84185761	+	1	NA	exon (NM_001001806, exon 2 of 2)	exon (NM_001001806, exon 2 of 2)	2193	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_55622.1	chr6	72235239	72235278	-	1	NA	5' UTR (NM_153778, exon 1 of 3)	5' UTR (NM_153778, exon 1 of 3)	319	NM_153778	71093	Mm.87449	NM_153778	ENSMUSG00000037621	Atoh8	4933425C05Rik|Hath6|Math6|bHLHa21|okadin	atonal bHLH transcription factor 8	protein-coding
mm_95134.1	chr11	34783958	34783990	+	1	NA	promoter-TSS (NM_033374)	promoter-TSS (NM_033374)	-69	NM_033374	94176	Mm.380679	NM_033374	ENSMUSG00000020143	Dock2	AI662014|AW122239|CED-5|Hch|MBC	dedicator of cyto-kinesis 2	protein-coding
mm_9444.1	chr1	172590478	172590489	-	1	NA	promoter-TSS (NM_029084)	promoter-TSS (NM_029084)	85	NM_029084	74748	Mm.179812	NM_029084	ENSMUSG00000053318	Slamf8	5830408F06Rik|Blame|SBBI42	SLAM family member 8	protein-coding
mm_103955.1	chr11	84083621	84083624	-	1	NA	intron (NM_172562, intron 14 of 15)	intron (NM_172562, intron 14 of 15)	-15265	NM_019819	56405	Mm.240885	NM_019819	ENSMUSG00000018648	Dusp14	1110014C10Rik|2310042C07Rik|D11Ertd395e|MKP-L|Mkp6	dual specificity phosphatase 14	protein-coding
mm_39927.1	chr5	31602611	31602655	+	1	NA	Intergenic	Intergenic	-11318	NM_025796	66845	Mm.120763	NM_025796	ENSMUSG00000106918	Mrpl33	0610009M10Rik|L33mt|MRP-L33	mitochondrial ribosomal protein L33	protein-coding
mm_82781.1	chr9	27375954	27375954	-	1	NA	Intergenic	RLTR23|LTR|ERV1	-20853	NM_029299	75469	Mm.45824	NM_029299	ENSMUSG00000031991	Spata19	1700001L23Rik|AV047838|spergen-1	spermatogenesis associated 19	protein-coding
mm_57950.1	chr6	134928446	134928463	-	1	NA	promoter-TSS (NR_037955)	promoter-TSS (NR_037955)	-638	NR_037956	381822	Mm.5935	NR_037955	ENSMUSG00000098318	Lockd	1190002F15Rik|AI120476|Droc	lncRNA downstream of Cdkn1b	ncRNA
mm_95639.1	chr11	53719961	53719974	+	1	NA	promoter-TSS (NM_010558)	promoter-TSS (NM_010558)	-827	NM_010558	16191	Mm.4461	NM_010558	ENSMUSG00000036117	Il5	Il-5	interleukin 5	protein-coding
mm_138980.1	chr17	45456957	45456981	+	1	NA	intron (NM_027649, intron 4 of 7)	intron (NM_027649, intron 4 of 7)	17969	NM_027649	71020	Mm.44257	NM_027649	ENSMUSG00000023935	Spats1	1700011H05Rik|4933400B06Rik|Daip2|Ddip|Srsp1	spermatogenesis associated, serine-rich 1	protein-coding
mm_156909.1	chrX	169052860	169052887	+	1	NA	intron (NR_109847, intron 1 of 14)	B1_Mur4|SINE|Alu	16262	NR_109847	11856	Mm.441810	NM_009707	ENSMUSG00000031355	Arhgap6	AI504284|RhoGAPX-1	Rho GTPase activating protein 6	protein-coding
mm_131203.1	chr16	8619598	8619623	+	1	NA	3' UTR (NM_001170978, exon 15 of 15)	3' UTR (NM_001170978, exon 15 of 15)	18091	NM_025708	66690	Mm.10068	NM_025708	ENSMUSG00000043140	Tmem186	2810440M13Rik|4432406C05Rik|AI648175|AW210586	transmembrane protein 186	protein-coding
mm_144910.1	chr18	37435603	37435636	+	1	NA	promoter-TSS (NM_053137)	promoter-TSS (NM_053137)	-2	NM_053137	93883	Mm.196701	NM_053137	ENSMUSG00000043458	Pcdhb12	Pcdh3|Pcdhb5F|PcdhbL	protocadherin beta 12	protein-coding
mm_122601.1	chr14	51041862	51041879	-	1	NA	promoter-TSS (NM_183032)	promoter-TSS (NM_183032)	-3	NM_183032	328401	Mm.99528	NM_183032	ENSMUSG00000052382	Rnase9	ESRL|Rak1	ribonuclease, RNase A family, 9 (non-active)	protein-coding
mm_111221.1	chr12	84553036	84553084	-	1	NA	Intergenic	Intergenic	-16768	NM_007701	12677	Mm.4405	NM_007701	ENSMUSG00000021239	Vsx2	Chx10|Hox-10|Hox10|or	visual system homeobox 2	protein-coding
mm_97598.1	chr11	78949084	78949117	+	1	NA	exon (NM_010927, exon 18 of 27)	exon (NM_010927, exon 18 of 27)	23809	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_20309.1	chr2	127247686	127247702	-	1	NA	promoter-TSS (NM_175145)	promoter-TSS (NM_175145)	122	NM_025296	26371	Mm.45179	NM_025296	ENSMUSG00000003662	Ciao1	AW210570|Wdr39	cytosolic iron-sulfur protein assembly 1	protein-coding
mm_87896.1	chr10	62071452	62071460	+	1	NA	Intergenic	Intergenic	39557	NM_027251	69894	Mm.294126	NM_027251	ENSMUSG00000020083	2010107G23Rik	AA545165	RIKEN cDNA 2010107G23 gene	protein-coding
mm_61562.1	chr7	79536142	79536166	+	1	NA	Intergenic	CpG	20719	NR_040312	101694	Mm.41661	NR_040311	ENSMUSG00000097023	Mir9-3hg	AI854517	Mir9-3 host gene	ncRNA
mm_57333.1	chr6	124741279	124741289	-	1	NA	promoter-TSS (NM_013535)	promoter-TSS (NM_013535)	-205	NM_013535	14790	Mm.439877	NM_013535	ENSMUSG00000072772	Grcc10	2310033H05Rik|C10	gene rich cluster, C10 gene	protein-coding
mm_60065.1	chr7	31213344	31213350	+	1	NA	Intergenic	Intergenic	-50389	NM_001310660	100043827		NM_001310660		Scgb2b1	Abpbg1|Gm4677	secretoglobin, family 2B, member 1	protein-coding
mm_94916.1	chr11	29463713	29463733	+	1	NA	exon (NM_176841, exon 15 of 32)	exon (NM_176841, exon 15 of 32)	51310	NM_026465	67939	Mm.251087	NM_026465	ENSMUSG00000032673	Prorsd1	2010316F05Rik|Ncrna00117|Prdxdd1	prolyl-tRNA synthetase domain containing 1	protein-coding
mm_69629.1	chr7	137410699	137410705	-	1	NA	promoter-TSS (NM_029886)	promoter-TSS (NM_029886)	54	NM_029886	77252	Mm.29184	NM_029886	ENSMUSG00000040139	9430038I01Rik	-	RIKEN cDNA 9430038I01 gene	protein-coding
mm_61744.1	chr7	82612697	82612698	+	1	NA	3' UTR (NM_001190374, exon 30 of 30)	3' UTR (NM_001190374, exon 30 of 30)	35831	NM_177894	330577	Mm.222812	NM_177894	ENSMUSG00000038570	Saxo2	1700129I04Rik|D030069K18|Fam154b	stabilizer of axonemal microtubules 2	protein-coding
mm_58161.1	chr6	142472990	142472997	-	1	NA	5' UTR (NM_145572, exon 1 of 17)	5' UTR (NM_145572, exon 1 of 17)	116	NM_145572	232493	Mm.275975	NM_145572	ENSMUSG00000030244	Gys2	BC021322|LGS	glycogen synthase 2	protein-coding
mm_119381.1	chr14	41134637	41134652	+	1	NA	3' UTR (NM_023134, exon 6 of 6)	3' UTR (NM_023134, exon 6 of 6)	2856	NM_023134	20387	Mm.46062	NM_023134	ENSMUSG00000021789	Sftpa1	SP-A|Sftp-1|Sftp1	surfactant associated protein A1	protein-coding
mm_54385.1	chr6	31218374	31218387	-	1	NA	promoter-TSS (NR_110471)	promoter-TSS (NR_110471)	94	NR_110470	232685	Mm.443019	NM_144555	ENSMUSG00000044471	Lncpint	Lincpint|MNCb-1768|Pint|linc-Pint	long non-protein coding RNA, Trp53 induced transcript	ncRNA
mm_82258.1	chr9	5311427	5311447	-	1	NA	intron (NM_007609, intron 1 of 8)	RLTR17|LTR|ERVK	2588	NM_007609	12363	Mm.1569	NM_007609	ENSMUSG00000033538	Casp4	CASP-11|CASP-4|Casp11|Caspl|ich-3	caspase 4, apoptosis-related cysteine peptidase	protein-coding
mm_97253.1	chr11	75756862	75756936	+	1	NA	exon (NM_009536, exon 4 of 6)	exon (NM_009536, exon 4 of 6)	24012	NM_009536	22627	Mm.234700	NM_009536	ENSMUSG00000020849	Ywhae	AU019196	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide	protein-coding
mm_23216.1	chr3	45432848	45432874	+	1	NA	3' UTR (NM_001098170, exon 5 of 5)	3' UTR (NM_001098170, exon 5 of 5)	6448	NR_040594	72274	Mm.396202	NR_040594	ENSMUSG00000100799	1700027H10Rik	-	RIKEN cDNA 1700027H10 gene	ncRNA
mm_25219.1	chr3	103851290	103851304	+	1	NA	intron (NM_001142960, intron 3 of 3)	intron (NM_001142960, intron 3 of 3)	-8498	NR_104070	19260	Mm.395	NM_008979	ENSMUSG00000027843	Ptpn22	70zpep|PEP|Ptpn8	protein tyrosine phosphatase, non-receptor type 22 (lymphoid)	protein-coding
mm_20306.1	chr2	127188789	127188792	-	1	NA	intron (NM_198630, intron 1 of 1)	intron (NM_198630, intron 1 of 1)	19490	NM_198630	329509	Mm.120738	NM_198630	ENSMUSG00000044145	1810024B03Rik	-	RIKEN cDNA 1810024B03 gene	protein-coding
mm_27521.1	chr3	57295086	57295109	-	1	NA	intron (NM_008536, intron 2 of 6)	intron (NM_008536, intron 2 of 6)	6822	NM_008536	17112	Mm.856	NM_008536	ENSMUSG00000027800	Tm4sf1	L6|M3s1	transmembrane 4 superfamily member 1	protein-coding
mm_55483.1	chr6	69017129	69017135	-	1	NA	Intergenic	Intergenic	310042	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_48760.1	chr5	148342109	148342156	-	1	NA	exon (NM_007513, exon 7 of 13)	exon (NM_007513, exon 7 of 13)	50683	NM_001301424	11987	Mm.275489	NM_007513	ENSMUSG00000041313	Slc7a1	4831426K01Rik|AI447493|Atrc-1|Atrc1|Cat1|Rec-1|Rev-1|mCAT-1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 1	protein-coding
mm_35353.1	chr4	32268070	32268107	-	1	NA	Intergenic	Intergenic	-149347	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_113580.1	chr13	40860125	40860139	+	1	NA	5' UTR (NM_023887, exon 1 of 3)	5' UTR (NM_023887, exon 1 of 3)	364	NM_023887	14538	Mm.314757	NM_008105	ENSMUSG00000021360	Gcnt2	5330430K10Rik|IGnT|IGnTA|IGnTB|IGnTC	glucosaminyl (N-acetyl) transferase 2, I-branching enzyme	protein-coding
mm_121999.1	chr14	26591669	26591677	-	1	NA	intron (NM_001134465, intron 1 of 19)	intron (NM_001134465, intron 1 of 19)	12123	NM_145969	211922	Mm.260512	NM_145969	ENSMUSG00000040818	Dennd6a	Fam116a	DENN/MADD domain containing 6A	protein-coding
mm_125154.1	chr15	30730206	30730211	+	1	NA	intron (NM_008729, intron 9 of 22)	intron (NM_008729, intron 9 of 22)	-308918	NR_045186	73784	Mm.66947	NR_045186		4930430F21Rik	-	RIKEN cDNA 4930430F21 gene	ncRNA
mm_121215.1	chr14	103054625	103054635	+	1	NA	exon (NM_008392, exon 5 of 5)	exon (NM_008392, exon 5 of 5)	7618	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_61723.1	chr7	81858994	81859010	+	1	NA	promoter-TSS (NM_145375)	promoter-TSS (NM_145375)	1	NM_145375	107769	Mm.221412	NM_145375	ENSMUSG00000038623	Tm6sf1	AI428514|BC023123|C630016D09Rik	transmembrane 6 superfamily member 1	protein-coding
mm_95835.1	chr11	57011708	57011718	+	1	NA	promoter-TSS (NM_001113325)	promoter-TSS (NM_001113325)	95	NM_008165	14799	Mm.4920	NM_008165	ENSMUSG00000020524	Gria1	2900051M01Rik|Glr-1|Glr1|GluA1|GluR-A|GluRA|Glur-1|Glur1|HIPA1|gluR-K1	glutamate receptor, ionotropic, AMPA1 (alpha 1)	protein-coding
mm_55530.1	chr6	70726753	70726815	-	1	NA	Intergenic	Intergenic	65391	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_123323.1	chr14	62838496	62838540	-	1	NA	TTS (NR_106174)	TTS (NR_106174)	797	NR_106174	102465889		NR_106174	ENSMUSG00000099245	Mir8098	Gm27462|mmu-mir-8098	microRNA 8098	ncRNA
mm_47677.1	chr5	128736012	128736018	-	1	NA	promoter-TSS (NM_021311)	promoter-TSS (NM_021311)	-231	NM_021311	57749	Mm.272720	NM_021311	ENSMUSG00000029423	Piwil1	MIWI	piwi-like RNA-mediated gene silencing 1	protein-coding
mm_67242.1	chr7	75309018	75309018	-	1	NA	promoter-TSS (NM_001109753)	promoter-TSS (NM_001109753)	244	NM_153579	64176	Mm.273082	NM_153579	ENSMUSG00000053025	Sv2b	A830038F04Rik|AI850768|mKIAA0735	synaptic vesicle glycoprotein 2 b	protein-coding
mm_20602.1	chr2	131434372	131434381	-	1	NA	intron (NR_037281, intron 1 of 2)	intron (NR_037281, intron 1 of 2)	-57486	NM_001177834	228608	Mm.136586	NM_145533	ENSMUSG00000027333	Smox	B130066H01Rik|PAO|PAOh1|SMO	spermine oxidase	protein-coding
mm_68223.1	chr7	104428486	104428497	-	1	NA	intron (NM_009099, intron 4 of 7)	intron (NM_009099, intron 4 of 7)	36702	NM_009099	20128	Mm.295578	NM_009099	ENSMUSG00000030921	Trim30a	Rpt-1|Rpt1|Trim30	tripartite motif-containing 30A	protein-coding
mm_130291.1	chr15	97008987	97009007	-	1	NA	exon (NM_027052, exon 10 of 16)	exon (NM_027052, exon 10 of 16)	46959	NM_027052	69354	Mm.250980	NM_027052	ENSMUSG00000022464	Slc38a4	1110012E16Rik|1700012A18Rik|Ata3|mATA3|mNAT3	solute carrier family 38, member 4	protein-coding
mm_128523.1	chr15	54278651	54278679	-	1	NA	promoter-TSS (NM_008764)	promoter-TSS (NM_008764)	-181	NM_008764	18383	Mm.15383	NM_008764	ENSMUSG00000063727	Tnfrsf11b	OCIF|Opg|TR1	tumor necrosis factor receptor superfamily, member 11b (osteoprotegerin)	protein-coding
mm_45917.1	chr5	89441264	89441303	-	1	NA	exon (NM_008096, exon 6 of 13)	exon (NM_008096, exon 6 of 13)	16615	NM_008096	14473	Mm.196595	NM_008096	ENSMUSG00000035540	Gc	DBP|VDB	group specific component	protein-coding
mm_105103.1	chr11	100956967	100957001	-	1	NA	3' UTR (NM_008986, exon 2 of 2)	3' UTR (NM_008986, exon 2 of 2)	13633	NM_008986	19285	Mm.21864	NM_008986	ENSMUSG00000004044	Ptrf	2310075E07Rik|AW546441|Cav-p60|Cavin	polymerase I and transcript release factor	protein-coding
mm_92561.1	chr10	79852458	79852471	-	1	NA	non-coding (NR_029447, exon 1 of 1)	non-coding (NR_029447, exon 1 of 1)	-1968	NM_001077363	19205	Mm.265610	NM_008956	ENSMUSG00000006498	Ptbp1	AA407203|AL033359|HNRPI|PTB-1|PTB2|PTB3|PTB4|Ptb|pPTB	polypyrimidine tract binding protein 1	protein-coding
mm_62300.1	chr7	100159318	100159330	+	1	NA	promoter-TSS (NM_026010)	promoter-TSS (NM_026010)	47	NM_026010	67164	Mm.46777	NM_026010	ENSMUSG00000030725	Lipt2	2610209A20Rik	lipoyl(octanoyl) transferase 2 (putative)	protein-coding
mm_30728.1	chr4	13751577	13751592	+	1	NA	5' UTR (NM_001111027, exon 1 of 12)	5' UTR (NM_001111027, exon 1 of 12)	287	NM_001111027	12395	Mm.4909	NM_009822	ENSMUSG00000006586	Runx1t1	Cbfa2t1h|ETO|MTG8	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	protein-coding
mm_113116.1	chr13	24487832	24487838	+	1	NA	Intergenic	RMER15|LTR|ERVL	72713	NM_001284520	12763	Mm.8396	NM_007717	ENSMUSG00000016756	Cmah	-	cytidine monophospho-N-acetylneuraminic acid hydroxylase	protein-coding
mm_142930.1	chr17	54298719	54298732	-	1	NA	5' UTR (NM_022025, exon 1 of 9)	5' UTR (NM_022025, exon 1 of 9)	309	NM_022025	63993	Mm.155241	NM_022025	ENSMUSG00000023945	Slc5a7	CHT1	solute carrier family 5 (choline transporter), member 7	protein-coding
mm_116643.1	chr13	49147667	49147684	-	1	NA	intron (NM_029361, intron 1 of 27)	CpG-3837	653	NM_029361	75607	Mm.342723	NM_029361	ENSMUSG00000037989	Wnk2	1810073P09Rik|AW122246|ESTM15|X83337|mKIAA1760	WNK lysine deficient protein kinase 2	protein-coding
mm_164003.1	chr14	66361259	66361266	+	1	NA	3' UTR (NM_019675, exon 6 of 6)	3' UTR (NM_019675, exon 6 of 6)	16966	NM_019675	56471	Mm.35474	NM_019675	ENSMUSG00000022044	Stmn4	Lagl|R75359|RB3	stathmin-like 4	protein-coding
mm_112243.1	chr12	113482557	113482571	-	1	NA	Intergenic	Intergenic	-7001	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_78394.1	chr9	28920401	28920411	+	1	NA	3' UTR (NM_177906, exon 8 of 8)	3' UTR (NM_177906, exon 8 of 8)	1042723	NM_172290	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding
mm_30138.1	chr3	142249681	142249689	-	1	NA	intron (NM_001190852, intron 12 of 15)	intron (NM_001190852, intron 12 of 15)	-80457	NM_001277216	12167	Mm.39089	NM_007560	ENSMUSG00000052430	Bmpr1b	AI385617|ALK-6|AV355320|Acvrlk6|Alk6|BMPR-1B|BMPR-IB|CFK-43a|SKR6	bone morphogenetic protein receptor, type 1B	protein-coding
mm_94699.1	chr11	20140563	20140584	+	1	NA	Intergenic	RLTR17|LTR|ERVK	-27622	NM_146243	66713	Mm.259045	NM_146243	ENSMUSG00000020152	Actr2	4921510D23Rik|AA409782|Arp2|D6Ertd746e	ARP2 actin-related protein 2	protein-coding
mm_11900.1	chr2	50235920	50235920	+	1	NA	Intergenic	Intergenic	60757	NM_133839	109129	Mm.29214	NM_133839	ENSMUSG00000026766	Mmadhc	2010311D03Rik|AI314967|CblD	methylmalonic aciduria (cobalamin deficiency) cblD type, with homocystinuria	protein-coding
mm_163934.1	chr14	48670190	48670202	+	1	NA	intron (NR_029384, intron 1 of 4)	intron (NR_029384, intron 1 of 4)	908	NR_029384	606497	Mm.165199	NR_029384	ENSMUSG00000098682	Otx2os1	-	orthodenticle homeobox 2 opposite strand 1	ncRNA
mm_86833.1	chr10	21289144	21289148	+	1	NA	Intergenic	Intergenic	-6833	NM_001042593	56422	Mm.25527	NM_019702	ENSMUSG00000019977	Hbs1l	2810035F15Rik|AI326327|eRFS	Hbs1-like (S. cerevisiae)	protein-coding
mm_19552.1	chr2	98666505	98666528	-	1	NA	Intergenic	SYNREP_MM|Satellite|Satellite	1198859	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_23510.1	chr3	60530077	60530079	+	1	NA	intron (NM_001310514, intron 2 of 8)	intron (NM_001310514, intron 2 of 8)	28899	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_126875.1	chr15	89384889	89384899	+	1	NA	Intergenic	Intergenic	-1997	NM_001160178	546648	Mm.478787	NM_001160178	ENSMUSG00000091680	Klhdc7b	EG546648|Gm306	kelch domain containing 7B	protein-coding
mm_104706.1	chr11	98013002	98013022	-	1	NA	intron (NM_001282977, intron 3 of 13)	intron (NM_001282977, intron 3 of 13)	5360	NM_001159320	12295	Mm.41252	NM_031173	ENSMUSG00000020882	Cacnb1	CAB1|Cchb1|Cchlb1	calcium channel, voltage-dependent, beta 1 subunit	protein-coding
mm_135299.1	chr16	38636921	38636954	-	1	NA	exon (NM_020260, exon 3 of 12)	exon (NM_020260, exon 3 of 12)	74123	NM_026407	67846	Mm.310476	NM_026407	ENSMUSG00000002845	Tmem39a	2610033C09Rik	transmembrane protein 39a	protein-coding
mm_112559.1	chr13	13182713	13182717	+	1	NA	promoter-TSS (NM_181852)	promoter-TSS (NM_181852)	-1	NM_181852	107849	Mm.392548	NM_181852	ENSMUSG00000055360	Prl2c5	Ghd3|MRP-4|Mrpplf4|PLF-4	prolactin family 2, subfamily c, member 5	protein-coding
mm_21077.1	chr2	152830709	152830728	-	1	NA	promoter-TSS (NM_001289716)	promoter-TSS (NM_001289716)	-1	NM_001289739	12048	Mm.238213	NM_009743	ENSMUSG00000007659	Bcl2l1	Bcl(X)L|Bcl-XL|Bcl2l|BclX|bcl-x|bcl2-L-1	BCL2-like 1	protein-coding
mm_75912.1	chr8	71395832	71395840	-	1	NA	promoter-TSS (NM_181418)	promoter-TSS (NM_181418)	-35	NM_181418	234395	Mm.34874	NM_181418	ENSMUSG00000034911	Ushbp1	2210404N08Rik|9430064H24|AIEBP|MCC2	Usher syndrome 1C binding protein 1	protein-coding
mm_59007.1	chr7	19202373	19202384	+	1	NA	intron (NM_001347582, intron 18 of 21)	intron (NM_001347582, intron 18 of 21)	-10160	NM_175668	319197	Mm.135984	NM_175668	ENSMUSG00000044317	Gpr4	-	G protein-coupled receptor 4	protein-coding
mm_3690.1	chr1	153751882	153751907	+	1	NA	5' UTR (NM_011882, exon 2 of 9)	5' UTR (NM_011882, exon 2 of 9)	2468	NM_011882	24014	Mm.259254	NM_011882	ENSMUSG00000066800	Rnasel	E230029I04Rik	ribonuclease L (2', 5'-oligoisoadenylate synthetase-dependent)	protein-coding
mm_159959.1	chr6	88013677	88013677	-	1	NA	exon (NM_009005, exon 2 of 6)	exon (NM_009005, exon 2 of 6)	6118	NM_001293654	19349	Mm.333233	NM_009005	ENSMUSG00000079477	Rab7	Rab7a	RAB7, member RAS oncogene family	protein-coding
mm_124876.1	chr15	10223837	10223845	+	1	NA	promoter-TSS (NM_001253781)	promoter-TSS (NM_001253781)	-65	NM_001253781	19116	Mm.10516	NM_011169	ENSMUSG00000005268	Prlr	AI987712|Pr-1|Pr-3|Prlr-rs1	prolactin receptor	protein-coding
mm_132390.1	chr16	34995004	34995018	+	1	NA	intron (NM_139300, intron 29 of 31)	intron (NM_139300, intron 29 of 31)	-27410	NM_023587	70757	Mm.27286	NM_023587	ENSMUSG00000035376	Hacd2	6330408J20Rik|AI255777|AI481689|Hcad2|Ptplb	3-hydroxyacyl-CoA dehydratase 2	protein-coding
mm_108977.1	chr12	102743700	102743711	+	1	NA	promoter-TSS (NM_177140)	promoter-TSS (NM_177140)	-7	NM_001324515	320351	Mm.86546	NM_177140	ENSMUSG00000046675	Tmem251	D230037D09Rik	transmembrane protein 251	protein-coding
mm_168090.1	chr10	128035572	128035572	+	1	NA	5' UTR (NM_013608, exon 1 of 8)	5' UTR (NM_013608, exon 1 of 8)	226	NM_001113199	17938	Mm.3746	NM_013608	ENSMUSG00000061315	Naca	AL022831|AL024382|Gm1878|mKIAA0363|skNAC	nascent polypeptide-associated complex alpha polypeptide	protein-coding
mm_131320.1	chr16	11984362	11984382	+	1	NA	5' UTR (NM_028277, exon 1 of 5)	5' UTR (NM_028277, exon 1 of 5)	259	NM_001174086	72555	Mm.310139	NM_028277	ENSMUSG00000022494	Shisa9	2700045P11Rik|Ckamp44	shisa family member 9	protein-coding
mm_32441.1	chr4	107253920	107253939	+	1	NA	promoter-TSS (NM_029985)	promoter-TSS (NM_029985)	-5	NM_028394	72938	Mm.21787	NM_028394	ENSMUSG00000063172	Hspb11	2900042B11Rik|IFT25	heat shock protein family B (small), member 11	protein-coding
mm_118083.1	chr13	103335962	103335968	-	1	NA	Intergenic	Intergenic	-1473	NM_175171	328329	Mm.202606	NM_175171	ENSMUSG00000034751	Mast4	4930420O11Rik|AI642422|mKIAA0303	microtubule associated serine/threonine kinase family member 4	protein-coding
mm_14379.1	chr2	129630688	129630716	+	1	NA	3' UTR (NM_001291022, exon 5 of 5)	3' UTR (NM_001291022, exon 5 of 5)	37533	NM_001291022	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_107939.1	chr12	71889452	71889466	+	1	NA	promoter-TSS (NM_001286452)	promoter-TSS (NM_001286452)	-84	NM_001286452	208846	Mm.87417	NM_026102	ENSMUSG00000034574	Daam1	-	dishevelled associated activator of morphogenesis 1	protein-coding
mm_58387.1	chr6	149332238	149332238	-	1	NA	intron (NM_026054, intron 4 of 4)	PB1D10|SINE|Alu	22824	NM_001289662	67246	Mm.333515	NM_026054	ENSMUSG00000032712	2810474O19Rik	6720435I21Rik|AA536804|AU020969|GET|Kiaa1551	RIKEN cDNA 2810474O19 gene	protein-coding
mm_27622.1	chr3	59344153	59344165	-	1	NA	promoter-TSS (NM_001162884)	promoter-TSS (NM_001162884)	97	NM_001162884	242050	Mm.228086	NM_001162884	ENSMUSG00000036334	Igsf10	6530405F15Rik|9030224D03|AA409708|AA536958|AI414626|Adlican2|CMF608	immunoglobulin superfamily, member 10	protein-coding
mm_109659.1	chr12	113014516	113014539	+	1	NA	promoter-TSS (NM_001291445)	promoter-TSS (NM_001291445)	19	NM_001291444	217893	Mm.35754	NM_198165	ENSMUSG00000021143	Pacs2	6720425G15Rik|AW208651|AW489976|E230011J22|Pacs1l|mKIAA0602	phosphofurin acidic cluster sorting protein 2	protein-coding
mm_1551.1	chr1	72940328	72940333	+	1	NA	Intergenic	Intergenic	-65465	NM_010518	16011	Mm.405761	NM_010518	ENSMUSG00000026185	Igfbp5	AI256729|AW208790|IGFBP-5|IGFBP-5P	insulin-like growth factor binding protein 5	protein-coding
mm_75457.1	chr8	47714136	47714156	-	1	NA	promoter-TSS (NM_172407)	promoter-TSS (NM_172407)	-215	NM_172407	70925	Mm.393807	NM_172407	ENSMUSG00000038069	Cdkn2aip	4921511I16Rik|AW208986|CARF	CDKN2A interacting protein	protein-coding
mm_14697.1	chr2	142217604	142217608	+	1	NA	exon (NM_001013802, exon 11 of 19)	exon (NM_001013802, exon 11 of 19)	683858	NM_001081133	16558	Mm.251934	NM_001081133	ENSMUSG00000038844	Kif16b	8430434E15Rik|AA623607|AI789011|C80253|C80902|mKIAA1590	kinesin family member 16B	protein-coding
mm_168476.1	chr11	48951617	48951632	+	1	NA	intron (NM_001114679, intron 3 of 3)	L1Md_F3|LINE|L1	-5214	NM_001281472	621823	Mm.440151	NM_001281472	ENSMUSG00000078153	Psme2b	PA28b-p|PA28b2|Psme2-like|Psme2b-ps	protease (prosome, macropain) activator subunit 2B	protein-coding
mm_583.1	chr1	39367901	39367931	+	1	NA	promoter-TSS (NM_053257)	promoter-TSS (NM_053257)	65	NM_001252218	114641	Mm.379302	NM_053257	ENSMUSG00000073702	Rpl31	Dts	ribosomal protein L31	protein-coding
mm_136119.1	chr16	85899335	85899356	-	1	NA	exon (NM_011782, exon 1 of 8)	exon (NM_011782, exon 1 of 8)	1780	NM_011782	23794	Mm.112933	NM_011782	ENSMUSG00000022894	Adamts5	9530092O11Rik|ADAM-TS5|ADAMTS1|ADAMTS11|ADMP-2|AI481094|ASMP-2	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)	protein-coding
mm_169614.1	chr15	37943787	37943801	-	1	NA	intron (NM_199476, intron 5 of 8)	intron (NM_199476, intron 5 of 8)	17261	NM_199476	382985	Mm.24738	NM_199476	ENSMUSG00000022292	Rrm2b	p53R2	ribonucleotide reductase M2 B (TP53 inducible)	protein-coding
mm_7502.1	chr1	121567636	121567656	-	1	NA	intron (NM_025860, intron 1 of 12)	CpG	334	NM_025860	66942	Mm.44219	NM_025860	ENSMUSG00000001674	Ddx18	2310005B10Rik	DEAD (Asp-Glu-Ala-Asp) box polypeptide 18	protein-coding
mm_36821.1	chr4	104876442	104876463	-	1	NA	promoter-TSS (NM_146148)	promoter-TSS (NM_146148)	-54	NM_001316667	230558	Mm.197638	NM_146148	ENSMUSG00000035031	C8a	-	complement component 8, alpha polypeptide	protein-coding
mm_122137.1	chr14	31163851	31163861	-	1	NA	exon (NM_138672, exon 2 of 69)	exon (NM_138672, exon 2 of 69)	4785	NM_138672	192187	Mm.220821	NM_138672	ENSMUSG00000042286	Stab1	FEEL-1|FELE-1|MFEEL-1|MS-1|STAB-1|mKIAA0246	stabilin 1	protein-coding
mm_64827.1	chr7	12780608	12780679	-	1	NA	Intergenic	CpG	-4985	NM_001017955	232875	Mm.333573	NM_001017955	ENSMUSG00000070822	Zscan18	EG232875	zinc finger and SCAN domain containing 18	protein-coding
mm_23846.1	chr3	83008144	83008172	+	1	NA	exon (NM_133862, exon 2 of 10)	exon (NM_133862, exon 2 of 10)	434	NM_001317105	99571	Mm.16422	NM_133862	ENSMUSG00000033860	Fgg	3010002H13Rik|AI256424	fibrinogen gamma chain	protein-coding
mm_111558.1	chr12	101083450	101083487	-	1	NA	non-coding (NR_038049, exon 1 of 2)	non-coding (NR_038049, exon 1 of 2)	234	NM_211355	68734	Mm.87077	NM_211355	ENSMUSG00000041846	Smek1	1110034C04Rik|BC064465|Ppp4r3a|mKIAA2010	SMEK homolog 1, suppressor of mek1 (Dictyostelium)	protein-coding
mm_11305.1	chr2	30262799	30262802	+	1	NA	3' UTR (NM_177725, exon 4 of 4)	3' UTR (NM_177725, exon 4 of 4)	-3403	NM_001252568	227696	Mm.297949	NM_172267	ENSMUSG00000079484	Phyhd1	-	phytanoyl-CoA dioxygenase domain containing 1	protein-coding
mm_54390.1	chr6	31219035	31219045	-	1	NA	promoter-TSS (NR_110471)	promoter-TSS (NR_110471)	-566	NR_110469	232685	Mm.443019	NM_144555	ENSMUSG00000044471	Lncpint	Lincpint|MNCb-1768|Pint|linc-Pint	long non-protein coding RNA, Trp53 induced transcript	ncRNA
mm_129328.1	chr15	77773396	77773418	-	1	NA	exon (NM_022410, exon 25 of 41)	exon (NM_022410, exon 25 of 41)	-18178	NM_001081970	239552	Mm.125650	NM_001081970	ENSMUSG00000056656	Apol8	9830006J20Rik|APOL-II|Apol2	apolipoprotein L 8	protein-coding
mm_95140.1	chr11	35121066	35121118	+	1	NA	promoter-TSS (NM_011412)	promoter-TSS (NM_011412)	-364	NM_011412	20564	Mm.478604	NM_011412	ENSMUSG00000056427	Slit3	Slil2|Slit1|b2b2362.1Clo	slit homolog 3 (Drosophila)	protein-coding
mm_38835.1	chr4	149154214	149154231	-	1	NA	exon (NM_001081274, exon 9 of 13)	exon (NM_001081274, exon 9 of 13)	12485	NM_001081274	110208	Mm.252080	NM_025801	ENSMUSG00000028961	Pgd	0610042A05Rik|AU019875|C78335	phosphogluconate dehydrogenase	protein-coding
mm_147468.1	chr18	46715733	46715750	-	1	NA	exon (NM_033037, exon 4 of 5)	exon (NM_033037, exon 4 of 5)	12601	NM_033037	12583	Mm.241056	NM_033037	ENSMUSG00000033022	Cdo1	1300002L19Rik|Cdo|D18Ucla3	cysteine dioxygenase 1, cytosolic	protein-coding
mm_75395.1	chr8	46097785	46097788	-	1	NA	intron (NM_207213, intron 4 of 17)	L1_Mur2|LINE|L1	26360	NM_207213	102141	Mm.267258	NM_207213	ENSMUSG00000038291	Snx25	AI661919|Gm1699|Gm173|Sbbi31	sorting nexin 25	protein-coding
mm_17579.1	chr2	30415419	30415429	-	1	NA	promoter-TSS (NM_138748)	promoter-TSS (NM_138748)	324	NM_007760	12908	Mm.20396	NM_007760	ENSMUSG00000026853	Crat	AW107812|CARAT	carnitine acetyltransferase	protein-coding
mm_150459.1	chr19	38264656	38264703	+	1	NA	promoter-TSS (NM_020278)	promoter-TSS (NM_020278)	-103	NM_020278	56839	Mm.298251	NM_020278	ENSMUSG00000067242	Lgi1	BB130740	leucine-rich repeat LGI family, member 1	protein-coding
mm_12732.1	chr2	78869202	78869262	+	1	NA	5' UTR (NM_009454, exon 1 of 6)	5' UTR (NM_009454, exon 1 of 6)	185	NM_009454	22193	Mm.1485	NM_009454	ENSMUSG00000027011	Ube2e3	Ubce4|ubcM2	ubiquitin-conjugating enzyme E2E 3	protein-coding
mm_164918.1	chr18	75791514	75791515	+	1	NA	Intergenic	Intergenic	-28664	NM_145356	207259	Mm.159332	NM_145356	ENSMUSG00000044646	Zbtb7c	B230208J24Rik|Kr-pok|Zbtb36	zinc finger and BTB domain containing 7C	protein-coding
mm_78143.1	chr9	20975913	20975927	+	1	NA	intron (NM_010333, intron 1 of 1)	CpG	873	NM_010333	14739	Mm.46493	NM_010333	ENSMUSG00000043895	S1pr2	1100001A16Rik|Edg5|Gpcr13|H218|LPb2|S1P2	sphingosine-1-phosphate receptor 2	protein-coding
mm_133764.1	chr16	94569652	94569713	+	1	NA	promoter-TSS (NM_007890)	promoter-TSS (NM_007890)	-524	NM_007890	13548	Mm.310973	NM_007890	ENSMUSG00000022897	Dyrk1a	2310043O08Rik|D16Ertd272e|D16Ertd493e|Dyrk|ENSMUSG00000074897|Gm10783|Mnbh|Mp86|mmb	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1a	protein-coding
mm_125401.1	chr15	41447521	41447539	+	1	NA	promoter-TSS (NM_001130166)	promoter-TSS (NM_001130166)	48	NM_001130166	170719	Mm.254267	NM_130885	ENSMUSG00000022307	Oxr1	2210416C20Rik|C7|C7B	oxidation resistance 1	protein-coding
mm_89172.1	chr10	86323888	86323892	+	1	NA	intron (NM_011595, intron 1 of 4)	intron (NM_011595, intron 1 of 4)	23478	NM_011595	21859	Mm.4871	NM_011595	ENSMUSG00000020044	Timp3	Timp-3	tissue inhibitor of metalloproteinase 3	protein-coding
mm_40773.1	chr5	67260698	67260711	+	1	NA	5' UTR (NM_030108, exon 1 of 9)	5' UTR (NM_030108, exon 1 of 9)	139	NM_030108	67878	Mm.23217	NM_028975	ENSMUSG00000037720	Tmem33	1110006G02Rik|1600019D15Rik|2410089A21Rik|2700052H22Rik|5430406L04Rik|AA388285|AI314185|AI426615|db83	transmembrane protein 33	protein-coding
mm_36246.1	chr4	63401671	63401701	-	1	NA	intron (NM_001045514, intron 1 of 21)	intron (NM_001045514, intron 1 of 21)	1759	NM_001045514	100182	Mm.387725	NM_001045514	ENSMUSG00000039158	Akna	AI597013	AT-hook transcription factor	protein-coding
mm_7370.1	chr1	106759652	106759658	-	1	NA	promoter-TSS (NM_027534)	promoter-TSS (NM_027534)	87	NM_027534	70750	Mm.458911	NM_027534	ENSMUSG00000009905	Kdsr	6330410P18Rik|9430079B08Rik|Fvt1	3-ketodihydrosphingosine reductase	protein-coding
mm_116001.1	chr13	24599534	24599541	-	1	NA	intron (NR_024599, intron 1 of 1)	intron (NR_024599, intron 1 of 1)	5230	NR_024599	76024	Mm.440710	NR_024599		Gm11346	5830431A10Rik|AI447617|Gm11347|OTTMUSG00000000601|OTTMUSG00000000602	X-linked lymphocyte-regulated 5 pseudogene	pseudo
mm_163960.1	chr14	54894275	54894323	+	1	NA	exon (NM_019402, exon 1 of 7)	exon (NM_019402, exon 1 of 7)	156	NM_019402	54196	Mm.7723	NM_019402	ENSMUSG00000022194	Pabpn1	PAB2|Pabp3|mPABII	poly(A) binding protein, nuclear 1	protein-coding
mm_110921.1	chr12	76306965	76307007	-	1	NA	intron (NM_138745, intron 21 of 27)	intron (NM_138745, intron 21 of 27)	-17905	NM_001101471	238276	Mm.311452	NM_001101471	ENSMUSG00000021057	Akap5	3526401B18Rik|AKAP 150|AKAP-5|AKAP150|BB098886|Gm258|P150	A kinase (PRKA) anchor protein 5	protein-coding
mm_158994.1	chr1	136467841	136467841	+	1	NA	promoter-TSS (NM_001287179)	promoter-TSS (NM_001287179)	-7	NM_001287179	381293	Mm.458468	NM_001081258	ENSMUSG00000041498	Kif14	D1Ertd367e|E130203M01	kinesin family member 14	protein-coding
mm_149143.1	chr19	9004136	9004150	+	1	NA	exon (NM_009643, exon 5 of 5)	exon (NM_009643, exon 5 of 5)	-13761	NR_105786	102465190		NR_105786	ENSMUSG00000099308	Mir6367	Gm27467|mmu-mir-6367	microRNA 6367	ncRNA
mm_379.1	chr1	34022712	34022723	+	1	NA	intron (NM_133833, intron 1 of 92)	PB1D10|SINE|Alu	10892	NM_134448	13518	Mm.336625	NM_010081	ENSMUSG00000026131	Dst	2310001O04Rik|A830042E19Rik|AW554249|BP230|BPAG1-n|Bpag|Bpag1|Macf2|ah|athetoid|dt|mKIAA0728|nmf203|nmf339	dystonin	protein-coding
mm_139909.1	chr17	70900971	70900979	+	1	NA	Intergenic	RLTR9A|LTR|ERVK	-47443	NM_001164074	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_117651.1	chr13	93092482	93092484	-	1	NA	exon (NM_023821, exon 2 of 13)	exon (NM_023821, exon 2 of 13)	-2350	NR_046182	408254	Mm.474857	NR_046182		A630019I02Rik	-	RIKEN cDNA A630019I02 gene	ncRNA
mm_97400.1	chr11	77838128	77838148	+	1	NA	intron (NM_001291214, intron 19 of 38)	intron (NM_001291214, intron 19 of 38)	36840	NM_001291215	360013	Mm.341248	NM_011586	ENSMUSG00000000631	Myo18a	MAJN|MyoPDZ|MysPDZ|SP-R210	myosin XVIIIA	protein-coding
mm_9404.1	chr1	172274124	172274147	-	1	NA	3' UTR (NM_178405, exon 23 of 23)	3' UTR (NM_178405, exon 23 of 23)	-15711	NM_013734	27222	Mm.482392	NM_013734	ENSMUSG00000007107	Atp1a4	-	ATPase, Na+/K+ transporting, alpha 4 polypeptide	protein-coding
mm_112568.1	chr13	13559134	13559138	+	1	NA	Intergenic	Intergenic	-31273	NM_010748	17101	Mm.342337	NM_010748	ENSMUSG00000019726	Lyst	D13Sfk13|beige|bg	lysosomal trafficking regulator	protein-coding
mm_1273.1	chr1	63442495	63442499	+	1	NA	Intergenic	MLTR25A|LTR|ERVK	-3394	NM_011780	23792	Mm.124892	NM_011780	ENSMUSG00000025964	Adam23	AW046396|MDC3	a disintegrin and metallopeptidase domain 23	protein-coding
mm_24606.1	chr3	93446077	93446084	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	3750	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_7596.1	chr1	125561439	125561458	-	1	NA	intron (NM_028787, intron 1 of 15)	intron (NM_028787, intron 1 of 15)	432	NM_028787	74150	Mm.28654	NM_028787	ENSMUSG00000026342	Slc35f5	1300003P13Rik|AI646727	solute carrier family 35, member F5	protein-coding
mm_94178.1	chr10	128919191	128919227	-	1	NA	promoter-TSS (NM_134006)	promoter-TSS (NM_134006)	88	NM_134006	19682	Mm.439856	NM_134006	ENSMUSG00000025350	Rdh5	9-cis|AI987873|RDH4|cRDH	retinol dehydrogenase 5	protein-coding
mm_37802.1	chr4	130574125	130574144	-	1	NA	promoter-TSS (NM_025998)	promoter-TSS (NM_025998)	-98	NM_025998	67149	Mm.423029	NM_025998	ENSMUSG00000078532	Nkain1	2610200G18Rik|2810426C15Rik	Na+/K+ transporting ATPase interacting 1	protein-coding
mm_82178.1	chr9	123852143	123852208	+	1	NA	promoter-TSS (NM_001110253)	promoter-TSS (NM_001110253)	-276	NM_001110253	17281	Mm.252941	NM_148925	ENSMUSG00000025241	Fyco1	2810409M01Rik|Mem2|RUFY3|ZFYVE7	FYVE and coiled-coil domain containing 1	protein-coding
mm_83807.1	chr9	53536696	53536711	-	1	NA	promoter-TSS (NM_001081152)	promoter-TSS (NM_001081152)	-32	NM_007499	11920	Mm.5088	NM_007499	ENSMUSG00000034218	Atm	AI256621|C030026E19Rik	ataxia telangiectasia mutated	protein-coding
mm_145554.1	chr18	60811399	60811410	+	1	NA	promoter-TSS (NR_039567)	promoter-TSS (NR_039567)	-672	NR_039567	100628611		NR_039567	ENSMUSG00000093327	Mir5107	mir-5107|mmu-mir-5107|mu-mir-5107	microRNA 5107	ncRNA
mm_43854.1	chr5	143403788	143403815	+	1	NA	promoter-TSS (NM_025841)	promoter-TSS (NM_025841)	-19	NM_025841	66913	Mm.181880	NM_025841	ENSMUSG00000079111	Kdelr2	1110007A14Rik	KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 2	protein-coding
mm_111622.1	chr12	102421399	102421420	-	1	NA	intron (NM_011175, intron 2 of 13)	B4|SINE|B4	18404	NM_011175	19141	Mm.17185	NM_011175	ENSMUSG00000021190	Lgmn	AEP|AI746452|AU022324|Prsc1	legumain	protein-coding
mm_113195.1	chr13	24943486	24943509	+	1	NA	5' UTR (NM_008156, exon 2 of 26)	5' UTR (NM_008156, exon 2 of 26)	345	NM_008156	14756	Mm.291831	NM_008156	ENSMUSG00000021340	Gpld1	6330541J12Rik|AW546131	glycosylphosphatidylinositol specific phospholipase D1	protein-coding
mm_163147.1	chr11	82962985	82962985	+	1	NA	3' UTR (NM_183201, exon 6 of 6)	3' UTR (NM_183201, exon 6 of 6)	-2304	NR_045932	76392	Mm.295205	NR_045932	ENSMUSG00000086327	Slfn5os	1700003F17Rik	schlafen 5, opposite strand	ncRNA
mm_92915.1	chr10	83648603	83648629	-	1	NA	promoter-TSS (NM_145220)	promoter-TSS (NM_145220)	48	NM_145220	216190	Mm.282985	NM_145220	ENSMUSG00000020263	Appl2	Dip3b	adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 2	protein-coding
mm_115129.1	chr13	104287856	104287882	+	1	NA	promoter-TSS (NM_001081020)	promoter-TSS (NM_001081020)	34	NM_001081020	108154	Mm.208125	NM_175496	ENSMUSG00000046169	Adamts6	A930019D11Rik|ADAM-TS6|b2b1879.1Clo|b2b2029Clo|b2b2182Clo|b2b2187.1Clo|b2b2228Clo	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 6	protein-coding
mm_27218.1	chr3	36000565	36000608	-	1	NA	promoter-TSS (NM_023644)	promoter-TSS (NM_023644)	92	NM_023644	72039	Mm.249016	NM_023644	ENSMUSG00000027709	Mccc1	1810045E08Rik|2310058B18Rik|MCCalpha|Mcca|R75106	methylcrotonoyl-Coenzyme A carboxylase 1 (alpha)	protein-coding
mm_153784.1	chr19	45812294	45812307	-	1	NA	promoter-TSS (NM_001276358)	promoter-TSS (NM_001276358)	-9	NM_001276358	80906	Mm.213204	NM_030716	ENSMUSG00000025221	Kcnip2	KChIP2	Kv channel-interacting protein 2	protein-coding
mm_58225.1	chr6	144209748	144209762	-	1	NA	promoter-TSS (NM_011444)	promoter-TSS (NM_011444)	-187	NM_001243163	20678	Mm.1752	NM_011444	ENSMUSG00000041540	Sox5	A730017D01Rik|AI528773	SRY (sex determining region Y)-box 5	protein-coding
mm_96732.1	chr11	69692650	69692662	+	1	NA	intron (NM_001034097, intron 5 of 12)	L2|LINE|L2	3442	NM_011614	21944	Mm.8983	NM_011614	ENSMUSG00000097328	Tnfsf12	Apo3l|Dr3l|Dr3lg|Tweak	tumor necrosis factor (ligand) superfamily, member 12	protein-coding
mm_85520.1	chr9	106447585	106447689	-	1	NA	promoter-TSS (NM_145919)	promoter-TSS (NM_145919)	41	NM_145919	68644	Mm.268925	NM_145919	ENSMUSG00000042210	Abhd14a	1110013B16Rik|AW558221|Dorz1	abhydrolase domain containing 14A	protein-coding
mm_43247.1	chr5	130145103	130145125	+	1	NA	exon (NM_172509, exon 1 of 4)	exon (NM_172509, exon 1 of 4)	226	NM_172509	212919	Mm.55812	NM_172509	ENSMUSG00000034110	Kctd7	4932409E18|9430010P06Rik	potassium channel tetramerisation domain containing 7	protein-coding
mm_52882.1	chr6	122513619	122513641	+	1	NA	promoter-TSS (NM_015776)	promoter-TSS (NM_015776)	46	NM_001347434	50530	Mm.41931	NM_015776	ENSMUSG00000030116	Mfap5	MAGP-2|MFAP-5	microfibrillar associated protein 5	protein-coding
mm_49538.1	chr6	30175381	30175399	+	1	NA	Intergenic	Intergenic	-1233	NR_038124	100463519	Mm.361139	NR_038124		BB283400	BF465573|Rncr4	expressed sequence BB283400	ncRNA
mm_141499.1	chr17	31565682	31565691	-	1	NA	intron (NM_016670, intron 1 of 10)	intron (NM_016670, intron 1 of 10)	913	NM_016670	18771	Mm.259295	NM_016670	ENSMUSG00000006705	Pknox1	D17Wsu76e|PREP1	Pbx/knotted 1 homeobox	protein-coding
mm_31767.1	chr4	63544800	63544853	+	1	NA	promoter-TSS (NM_024173)	promoter-TSS (NM_024173)	61	NM_024173	66290	Mm.371615	NM_024173	ENSMUSG00000039105	Atp6v1g1	1810024D14Rik|AA960677|ATP6J|Atp6g1|VAG1|Vma10	ATPase, H+ transporting, lysosomal V1 subunit G1	protein-coding
mm_13814.1	chr2	119208976	119209029	+	1	NA	promoter-TSS (NM_139139)	promoter-TSS (NM_139139)	-207	NM_139139	69408	Mm.222241	NM_139139	ENSMUSG00000034278	Dnajc17	1700025B16Rik|C87112|D9Bwg1371e	DnaJ heat shock protein family (Hsp40) member C17	protein-coding
mm_170567.1	chr19	47092828	47092833	+	1	NA	exon (NM_011053, exon 2 of 36)	exon (NM_011053, exon 2 of 36)	2064	NM_011053	18572	Mm.41166	NM_011053	ENSMUSG00000025047	Pdcd11	1110021I22Rik|ALG-4|Pdcd7|mKIAA0185	programmed cell death 11	protein-coding
mm_1595.1	chr1	74375209	74375229	+	1	NA	promoter-TSS (NM_013612)	promoter-TSS (NM_013612)	16	NM_013612	18173	Mm.2913	NM_013612	ENSMUSG00000026177	Slc11a1	Bcg|Ity|Ity1|Lsh|Nramp|Nramp1|ity	solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1	protein-coding
mm_72077.1	chr8	71568958	71568983	+	1	NA	promoter-TSS (NM_011977)	promoter-TSS (NM_011977)	43	NM_011977	26457	Mm.38165	NM_011977	ENSMUSG00000031808	Slc27a1	FATP1|Fatp	solute carrier family 27 (fatty acid transporter), member 1	protein-coding
mm_67464.1	chr7	80405426	80405433	-	1	NA	promoter-TSS (NM_001081454)	promoter-TSS (NM_001081454)	7	NM_001081454	18550	Mm.5241	NM_011046	ENSMUSG00000030530	Furin	9130404I01Rik|Fur|PACE|Pcsk3|SPC1	furin (paired basic amino acid cleaving enzyme)	protein-coding
mm_20824.1	chr2	146198026	146198036	-	1	NA	Intergenic	Lx8|LINE|L1	-23966	NM_016889	53626	Mm.379070	NM_016889	ENSMUSG00000068154	Insm1	IA-1	insulinoma-associated 1	protein-coding
mm_70654.1	chr8	14381944	14382003	+	1	NA	intron (NM_172910, intron 3 of 15)	intron (NM_172910, intron 3 of 15)	286098	NM_172910	244310	Mm.404697	NM_172910	ENSMUSG00000047495	Dlgap2	6430596N04Rik|Dap-2|Dap2|Sapap2	discs, large (Drosophila) homolog-associated protein 2	protein-coding
mm_154886.1	chrX	20797780	20797784	+	1	NA	Intergenic	Lx2|LINE|L1	-50761	NM_009703	11836	Mm.220946	NM_009703	ENSMUSG00000001127	Araf	1200013E08Rik|A-Raf|AW495444|Araf1	Araf proto-oncogene, serine/threonine kinase	protein-coding
mm_80094.1	chr9	70240368	70240385	+	1	NA	intron (NM_181072, intron 1 of 27)	intron (NM_181072, intron 1 of 27)	33026	NM_181072	71602	Mm.249311	NM_181072	ENSMUSG00000032220	Myo1e	2310020N23Rik|9130023P14Rik|AA407778|myosin-1e|myr 3	myosin IE	protein-coding
mm_43249.1	chr5	130187159	130187166	+	1	NA	promoter-TSS (NM_019983)	promoter-TSS (NM_019983)	-18	NM_019983	56715	Mm.288639	NM_019983	ENSMUSG00000025340	Rabgef1	Rab5ef|Rabex5|Rin2	RAB guanine nucleotide exchange factor (GEF) 1	protein-coding
mm_28752.1	chr3	95818942	95818990	-	1	NA	promoter-TSS (NM_001081293)	promoter-TSS (NM_001081293)	-13	NM_001081293	75137	Mm.196275	NM_028328	ENSMUSG00000028106	Rprd2	2810036A19Rik|4930535B03Rik|6720469I21Rik|AL022841|AL022940|AU021304|BB077382|mKIAA0460	regulation of nuclear pre-mRNA domain containing 2	protein-coding
mm_95148.1	chr11	35707704	35707722	+	1	NA	intron (NM_011412, intron 35 of 35)	intron (NM_011412, intron 35 of 35)	-61782	NM_145962	211347	Mm.255044	NM_145962	ENSMUSG00000018846	Pank3	-	pantothenate kinase 3	protein-coding
mm_47056.1	chr5	116381621	116381638	-	1	NA	Intergenic	MLT1B|LTR|ERVL-MaLR	41235	NM_030704	80888	Mm.21549	NM_030704	ENSMUSG00000041548	Hspb8	AU018630|AW413033|Cryac|D5Ucla4|E2IG1|H11|H11K|HSP20-like|HSP22	heat shock protein 8	protein-coding
mm_153168.1	chr19	34493439	34493456	-	1	NA	3' UTR (NM_021460, exon 10 of 10)	3' UTR (NM_021460, exon 10 of 10)	-18312	NM_009890	12642	Mm.30824	NM_009890	ENSMUSG00000050370	Ch25h	AI462618|m25OH	cholesterol 25-hydroxylase	protein-coding
mm_92082.1	chr10	62777830	62777834	-	1	NA	intron (NM_026201, intron 6 of 24)	(A)n|Simple_repeat|Simple_repeat	-12226	NR_028557	100217463		NR_028557		Snord98	MBII-419	small nucleolar RNA, C/D box 98	snoRNA
mm_61878.1	chr7	89632406	89632414	+	1	NA	promoter-TSS (NM_181407)	promoter-TSS (NM_181407)	-408	NM_181407	109264	Mm.334011	NM_181407	ENSMUSG00000030621	Me3	1700020C08Rik|B230207H15Rik	malic enzyme 3, NADP(+)-dependent, mitochondrial	protein-coding
mm_164152.1	chr15	63878549	63878549	-	1	NA	promoter-TSS (NM_183194)	promoter-TSS (NM_183194)	9	NM_183194	270328	Mm.483471	NM_183194	ENSMUSG00000055827	Gsdmc3	9930109F21Rik	gasdermin C3	protein-coding
mm_11318.1	chr2	30392406	30392440	+	1	NA	non-coding (NR_110963, exon 1 of 5)	non-coding (NR_110963, exon 1 of 5)	169	NM_001290508	57170	Mm.285167	NM_020329	ENSMUSG00000026856	Dolpp1	0610011H20Rik|AB030189|LSFR2	dolichyl pyrophosphate phosphatase 1	protein-coding
mm_146591.1	chr18	9376804	9376807	-	1	NA	intron (NM_026484, intron 3 of 9)	intron (NM_026484, intron 3 of 9)	73345	NM_026484	67974	Mm.86523	NM_026484	ENSMUSG00000024286	Ccny	1700025H17Rik|3110050L10Rik|4631402G10Rik|5730405I09Rik	cyclin Y	protein-coding
mm_26660.1	chr3	154620885	154620890	+	1	NA	intron (NM_009968, intron 6 of 8)	intron (NM_009968, intron 6 of 8)	-23789	NM_172474	209584	Mm.347513	NM_172474	ENSMUSG00000047583	Tyw3	5230400J09Rik	tRNA-yW synthesizing protein 3 homolog (S. cerevisiae)	protein-coding
mm_8854.1	chr1	162710752	162710801	-	1	NA	exon (NM_001081290, exon 12 of 35)	exon (NM_001081290, exon 12 of 35)	29780	NM_001081290	226562	Mm.245446	NM_001081290	ENSMUSG00000040225	Prrc2c	1810043M20Rik|9630039I18Rik|A630006J20|Bat2d|Bat2d1|Bat2l2|E130112L15Rik|Prrc3|mKIAA1096	proline-rich coiled-coil 2C	protein-coding
mm_163573.1	chr13	30814322	30814328	-	1	NA	3' UTR (NM_025588, exon 28 of 28)	3' UTR (NM_025588, exon 28 of 28)	65092	NM_013674	16364	Mm.4677	NM_013674	ENSMUSG00000021356	Irf4	AI385587|IRF-4|LSIRF|NF-EM5|Spip	interferon regulatory factor 4	protein-coding
mm_85260.1	chr9	99411195	99411240	-	1	NA	intron (NM_008624, intron 2 of 5)	intron (NM_008624, intron 2 of 5)	25495	NM_008624	17532	Mm.2045	NM_008624	ENSMUSG00000032470	Mras	2900078C09Rik|AI326250	muscle and microspikes RAS	protein-coding
mm_39356.1	chr5	9101203	9101232	+	1	NA	5' UTR (NM_001081029, exon 2 of 5)	5' UTR (NM_001081029, exon 2 of 5)	480	NM_001081029	652925	Mm.439954	NM_001081029	ENSMUSG00000079659	Tmem243	4930420K17Rik|E030031F02Rik	transmembrane protein 243, mitochondrial	protein-coding
mm_39351.1	chr5	8971912	8971920	+	1	NA	intron (NM_023733, intron 13 of 17)	intron (NM_023733, intron 13 of 17)	25230	NM_023733	74114	Mm.28197	NM_023733	ENSMUSG00000003623	Crot	1200003H03Rik	carnitine O-octanoyltransferase	protein-coding
mm_133121.1	chr16	65815278	65815286	+	1	NA	promoter-TSS (NM_028572)	promoter-TSS (NM_028572)	-351	NM_028572	73569	Mm.25670	NM_028572	ENSMUSG00000091243	Vgll3	1700110N18Rik|4832416J22|C80713|Vgl-3|Vito-2	vestigial like family member 3	protein-coding
mm_167707.1	chr9	96259221	96259234	+	1	NA	promoter-TSS (NM_001184710)	promoter-TSS (NM_001184710)	-21	NM_001184711	211586	Mm.17977	NM_178667	ENSMUSG00000032411	Tfdp2	1110029I05Rik|A330080J22Rik|DP-3|DP3	transcription factor Dp 2	protein-coding
mm_35927.1	chr4	53032269	53032280	-	1	NA	3' UTR (NM_013454, exon 50 of 50)	3' UTR (NM_013454, exon 50 of 50)	20394	NM_025623	66536	Mm.38244	NM_025623	ENSMUSG00000015247	Nipsnap3b	2700063N13Rik|Nipsnap3a	nipsnap homolog 3B (C. elegans)	protein-coding
mm_8200.1	chr1	138121808	138121832	-	1	NA	intron (NM_001111316, intron 3 of 31)	intron (NM_001111316, intron 3 of 31)	53306	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_147835.1	chr18	62548881	62548894	-	1	NA	promoter-TSS (NM_177829)	promoter-TSS (NM_177829)	-24	NM_177829	328971	Mm.312675	NM_177829	ENSMUSG00000044176	Spink10	A230091H23Rik	serine peptidase inhibitor, Kazal type 10	protein-coding
mm_136201.1	chr16	89818316	89818327	-	1	NA	promoter-TSS (NM_001145887)	promoter-TSS (NM_001145887)	31	NM_001145887	21844	Mm.310902	NM_009384	ENSMUSG00000002489	Tiam1	AI847750|D16Ium10|D16Ium10e	T cell lymphoma invasion and metastasis 1	protein-coding
mm_8845.1	chr1	162702253	162702266	-	1	NA	exon (NM_001081290, exon 17 of 35)	exon (NM_001081290, exon 17 of 35)	38297	NM_001081290	226562	Mm.245446	NM_001081290	ENSMUSG00000040225	Prrc2c	1810043M20Rik|9630039I18Rik|A630006J20|Bat2d|Bat2d1|Bat2l2|E130112L15Rik|Prrc3|mKIAA1096	proline-rich coiled-coil 2C	protein-coding
mm_35292.1	chr4	21848417	21848455	-	1	NA	promoter-TSS (NR_028384)	promoter-TSS (NR_028384)	12	NR_028384	67735	Mm.391650	NR_028384		4930528A17Rik	-	RIKEN cDNA 4930528A17 gene	ncRNA
mm_39925.1	chr5	31596866	31596939	+	1	NA	Intergenic	Intergenic	-17049	NM_025796	66845	Mm.120763	NM_025796	ENSMUSG00000106918	Mrpl33	0610009M10Rik|L33mt|MRP-L33	mitochondrial ribosomal protein L33	protein-coding
mm_19339.1	chr2	90580579	90580612	-	1	NA	promoter-TSS (NM_008982)	promoter-TSS (NM_008982)	52	NM_008982	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_37024.1	chr4	114908920	114908946	-	1	NA	promoter-TSS (NM_008593)	promoter-TSS (NM_008593)	-35	NM_008593	17301	Mm.7997	NM_008593	ENSMUSG00000055210	Foxd2	AI426778|Mf2	forkhead box D2	protein-coding
mm_100586.1	chr11	120948715	120948746	+	1	NA	promoter-TSS (NM_001038654)	promoter-TSS (NM_001038654)	246	NM_030696	80879	Mm.28632	NM_030696	ENSMUSG00000025161	Slc16a3	Mct3|Mct4	solute carrier family 16 (monocarboxylic acid transporters), member 3	protein-coding
mm_101268.1	chr11	21239695	21239716	-	1	NA	intron (NM_139061, intron 1 of 22)	intron (NM_139061, intron 1 of 22)	673	NM_001290628	245944	Mm.170103	NM_139061	ENSMUSG00000020128	Vps54	Hcc8|Vps54l|mSLP8|wr	VPS54 GARP complex subunit	protein-coding
mm_52713.1	chr6	119481461	119481488	+	1	NA	3' UTR (NM_133940, exon 1 of 1)	3' UTR (NM_133940, exon 1 of 1)	1806	NM_133940	101358	Mm.125477	NM_133940	ENSMUSG00000030019	Fbxl14	AW322056|Fbx14l	F-box and leucine-rich repeat protein 14	protein-coding
mm_87606.1	chr10	57784860	57784903	+	1	NA	promoter-TSS (NM_021272)	promoter-TSS (NM_021272)	-42	NM_021272	12140	Mm.3644	NM_021272	ENSMUSG00000019874	Fabp7	B-FABP|BFABP|Blbp|MRG	fatty acid binding protein 7, brain	protein-coding
mm_44776.1	chr5	32122477	32122487	-	1	NA	Intergenic	Intergenic	-13990	NM_008037	14284	Mm.24684	NM_008037	ENSMUSG00000029135	Fosl2	Fra-2	fos-like antigen 2	protein-coding
mm_26969.1	chr3	24760325	24760328	-	1	NA	intron (NM_001326288, intron 1 of 13)	Lx4A|LINE|L1	23680	NM_001326288	635702	Mm.448351	NM_001326288	ENSMUSG00000102758	Naaladl2	2810043G22Rik|EG635702|Gm1021	N-acetylated alpha-linked acidic dipeptidase-like 2	protein-coding
mm_152635.1	chr19	12501837	12501847	-	1	NA	5' UTR (NM_172442, exon 1 of 9)	5' UTR (NM_172442, exon 1 of 9)	154	NM_172442	207521	Mm.247695	NM_172442	ENSMUSG00000039982	Dtx4	AI449438|BC044798|D930042H13|RNF155	deltex 4, E3 ubiquitin ligase	protein-coding
mm_126179.1	chr15	78602713	78602733	+	1	NA	exon (NM_028195, exon 2 of 13)	exon (NM_028195, exon 2 of 13)	5676	NM_028195	72318	Mm.32911	NM_028195	ENSMUSG00000018008	Cyth4	2510004M07Rik|5830469K17Rik|AI467541|Pscd4|mFLJ00017	cytohesin 4	protein-coding
mm_107213.1	chr12	26445019	26445035	+	1	NA	3' UTR (NM_021384, exon 6 of 6)	3' UTR (NM_021384, exon 6 of 6)	11425	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_108640.1	chr12	85814549	85814552	+	1	NA	TTS (NM_021446)	TTS (NM_021446)	9995	NM_021446	58520	Mm.143795	NM_021446	ENSMUSG00000021252	0610007P14Rik	1190004E09Rik|AU019315|C77855|ORF11	RIKEN cDNA 0610007P14 gene	protein-coding
mm_102950.1	chr11	69618070	69618085	-	1	NA	promoter-TSS (NM_011367)	promoter-TSS (NM_011367)	-172	NM_011367	20415	Mm.1431	NM_011367	ENSMUSG00000005202	Shbg	ABP	sex hormone binding globulin	protein-coding
mm_76251.1	chr8	83690108	83690112	-	1	NA	intron (NM_177262, intron 3 of 21)	MurERV4-int|LTR|ERVK	3951	NM_001199593	320795	Mm.213000	NM_177262	ENSMUSG00000057672	Pkn1	DBK|F730027O18Rik|PAK1|PRK1|Pkn|Prkcl1|Stk3	protein kinase N1	protein-coding
mm_80652.1	chr9	90054247	90054259	+	1	NA	promoter-TSS (NM_007801)	promoter-TSS (NM_007801)	-14	NM_007801	13036	Mm.2277	NM_007801	ENSMUSG00000032359	Ctsh	AL022844	cathepsin H	protein-coding
mm_85090.1	chr9	91961170	91961179	-	1	NA	Intergenic	Intergenic	-231762	NM_001195693	100504689	Mm.464262	NM_001195693	ENSMUSG00000095654	Plscr5	331000	phospholipid scramblase family, member 5	protein-coding
mm_169994.1	chr17	15746951	15746960	+	1	NA	intron (NM_007690, intron 17 of 35)	MER5A|DNA|hAT-Charlie	41988	NM_007690	12648	Mm.8137	NM_007690	ENSMUSG00000023852	Chd1	4930525N21Rik|AI851787|AW555109	chromodomain helicase DNA binding protein 1	protein-coding
mm_106791.1	chr12	4782061	4782068	+	1	NA	Intergenic	Intergenic	12769	NM_028376	382562	Mm.251575	NM_028376	ENSMUSG00000020639	Pfn4	2900024P18Rik	profilin family, member 4	protein-coding
mm_67373.1	chr7	79841935	79841939	-	1	NA	exon (NM_008486, exon 1 of 20)	exon (NM_008486, exon 1 of 20)	415	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_20733.1	chr2	137093451	137093461	-	1	NA	intron (NM_013822, intron 8 of 25)	intron (NM_013822, intron 8 of 25)	23064	NM_013822	16449	Mm.22398	NM_013822	ENSMUSG00000027276	Jag1	ABE2|Gsfabe2|Htu|Ozz|Ser-1	jagged 1	protein-coding
mm_129967.1	chr15	85653879	85653912	-	1	NA	Intergenic	Intergenic	-49878	NR_110483	102800312	Mm.33117	NR_110483		Lncppara	Lincppara|Mirlet7bhg|linc-Ppara	long noncoding RNA near Ppara	ncRNA
mm_98749.1	chr11	96544720	96544723	+	1	NA	intron (NM_001033186, intron 4 of 12)	B3A|SINE|B2	80130	NM_001177898	78473	Mm.395840	NM_001033186	ENSMUSG00000057058	Skap1	1700091G21Rik|Scap1|Skap-55	src family associated phosphoprotein 1	protein-coding
mm_68936.1	chr7	126502095	126502109	-	1	NA	intron (NM_183020, intron 1 of 22)	CpG	323	NM_001347658	233871	Mm.231450	NM_183020	ENSMUSG00000032637	Atxn2l	A2D|A2LG|A2RP|A2lp|Atxnl2	ataxin 2-like	protein-coding
mm_44009.1	chr5	147076705	147076729	+	1	NA	promoter-TSS (NM_080795)	promoter-TSS (NM_080795)	-145	NM_080795	140887	Mm.272203	NM_080795	ENSMUSG00000016520	Lnx2	9630046H24|AW209022	ligand of numb-protein X 2	protein-coding
mm_4084.1	chr1	167000973	167001017	+	1	NA	promoter-TSS (NM_175461)	promoter-TSS (NM_175461)	-422	NM_175461	226610	Mm.389217	NM_175461	ENSMUSG00000060568	Fam78b	C030014K22Rik|C030020L09Rik	family with sequence similarity 78, member B	protein-coding
mm_156002.1	chrX	106583185	106583187	+	1	NA	promoter-TSS (NM_001033541)	promoter-TSS (NM_001033541)	0	NM_001033541	331493	Mm.249319	NM_001033541	ENSMUSG00000073010	Gm5127	B130007I08|EG331493	predicted gene 5127	protein-coding
mm_63088.1	chr7	122295785	122295789	+	1	NA	intron (NM_001316672, intron 2 of 16)	intron (NM_001316672, intron 2 of 16)	6662	NM_008855	18751	Mm.207496	NM_008855	ENSMUSG00000052889	Prkcb	PKC-B|PKC-Beta|Pkcb|Prkcb1|Prkcb2	protein kinase C, beta	protein-coding
mm_120380.1	chr14	64588337	64588361	+	1	NA	intron (NR_040709, intron 1 of 3)	intron (NR_040709, intron 1 of 3)	234	NR_040709	268755	Mm.194050	NR_040709	ENSMUSG00000097545	Mir124a-1hg	A930011O12Rik|Rncr3|mir-124-1|mir-3078	Mir124-1 host gene (non-protein coding)	ncRNA
mm_161473.1	chr15	79532759	79532759	-	1	NA	5' UTR (NM_152806, exon 1 of 2)	5' UTR (NM_152806, exon 1 of 2)	158	NM_152806	67040	Mm.29644	NM_152806	ENSMUSG00000055065	Ddx17	2610007K22Rik|A430025E01Rik|AI047725|C80929|Gm926|p72	DEAD (Asp-Glu-Ala-Asp) box polypeptide 17	protein-coding
mm_68976.1	chr7	126587560	126587571	-	1	NA	exon (NM_138310, exon 2 of 4)	exon (NM_138310, exon 2 of 4)	-1748	NM_001146311	12752	Mm.268930	NM_009907	ENSMUSG00000030720	Cln3	AI323623	ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease)	protein-coding
mm_139557.1	chr17	56875524	56875535	+	1	NA	promoter-TSS (NM_030141)	promoter-TSS (NM_030141)	-104	NM_030141	78625	Mm.160106	NM_030141	ENSMUSG00000024209	1700061G19Rik	1700026H02|AI507598	RIKEN cDNA 1700061G19 gene	protein-coding
mm_150274.1	chr19	34244941	34244973	+	1	NA	exon (NM_007392, exon 7 of 9)	exon (NM_007392, exon 7 of 9)	10416	NM_007392	11475	Mm.213025	NM_007392	ENSMUSG00000035783	Acta2	0610041G09Rik|Actvs|SMalphaA|a-SMA|alphaSMA	actin, alpha 2, smooth muscle, aorta	protein-coding
mm_166990.1	chr7	45924110	45924120	-	1	NA	Intergenic	Intergenic	-2689	NM_010129	13732	Mm.20829	NM_010129	ENSMUSG00000040212	Emp3	H-4|H4|HNMP-1|MI-35|Ymp	epithelial membrane protein 3	protein-coding
mm_150279.1	chr19	34251743	34251802	+	1	NA	exon (NM_007392, exon 3 of 9)	exon (NM_007392, exon 3 of 9)	3601	NM_007392	11475	Mm.213025	NM_007392	ENSMUSG00000035783	Acta2	0610041G09Rik|Actvs|SMalphaA|a-SMA|alphaSMA	actin, alpha 2, smooth muscle, aorta	protein-coding
mm_169709.1	chr15	75909274	75909274	-	1	NA	promoter-TSS (NM_001285430)	promoter-TSS (NM_001285430)	70	NM_001285433	66656	Mm.258927	NM_023240	ENSMUSG00000055762	Eef1d	EF-1-delta	eukaryotic translation elongation factor 1 delta (guanine nucleotide exchange protein)	protein-coding
mm_69702.1	chr7	140082200	140082201	-	1	NA	5' UTR (NM_001190386, exon 1 of 7)	5' UTR (NM_001190386, exon 1 of 7)	101	NM_001190386	68566	Mm.44241	NM_026769	ENSMUSG00000025468	Caly	0710001P07Rik|1110004A22Rik|Calcyon|Drd1ip	calcyon neuron-specific vesicular protein	protein-coding
mm_106726.1	chr12	3873104	3873120	+	1	NA	intron (NM_007872, intron 5 of 22)	intron (NM_007872, intron 5 of 22)	-10868	NR_045884	100038522	Mm.417270	NR_045884	ENSMUSG00000073242	Dnmt3aos	ENSMUSG00000073242|Gm10485	DNA methyltransferase 3A, opposite strand	ncRNA
mm_74583.1	chr8	11282082	11282090	-	1	NA	intron (NR_133670, intron 1 of 52)	intron (NR_133670, intron 1 of 52)	-30719	NM_009932	12827	Mm.181021	NM_009932	ENSMUSG00000031503	Col4a2	Col4a-2	collagen, type IV, alpha 2	protein-coding
mm_26769.1	chr3	8923797	8923822	-	1	NA	promoter-TSS (NM_025434)	promoter-TSS (NM_025434)	48	NM_025434	66230	Mm.38460	NM_025434	ENSMUSG00000040269	Mrps28	1500012D08Rik|AW061224	mitochondrial ribosomal protein S28	protein-coding
mm_31631.1	chr4	59287429	59287451	+	1	NA	Intergenic	Intergenic	27389	NR_105031	101055769	Mm.421401	NR_105031		Gm12596	OTTMUSG00000007649	predicted gene 12596	ncRNA
mm_76569.1	chr8	88662362	88662364	-	1	NA	intron (NM_145857, intron 3 of 12)	intron (NM_145857, intron 3 of 12)	15016	NM_145857	257632	Mm.222633	NM_145857	ENSMUSG00000055994	Nod2	ACUG|BLAU|CD|Card15|F830032C23Rik|IBD1|Nlrc2	nucleotide-binding oligomerization domain containing 2	protein-coding
mm_172648.1	chr8	27260378	27260382	+	1	NA	promoter-TSS (NM_007918)	promoter-TSS (NM_007918)	53	NM_007918	13685	Mm.6700	NM_007918	ENSMUSG00000031490	Eif4ebp1	4e-bp1|AA959816|PHAS-I	eukaryotic translation initiation factor 4E binding protein 1	protein-coding
mm_145372.1	chr18	56733755	56733759	+	1	NA	intron (NM_010721, intron 5 of 10)	L1M4c|LINE|L1	25944	NM_010721	16906	Mm.4105	NM_010721	ENSMUSG00000024590	Lmnb1	-	lamin B1	protein-coding
mm_72801.1	chr8	87472772	87472782	+	1	NA	promoter-TSS (NM_019626)	promoter-TSS (NM_019626)	-35	NR_033430	100040294	Mm.213632	NR_033430	ENSMUSG00000097248	Gm2694	C230036H16Rik|linc1582	predicted gene 2694	ncRNA
mm_23417.1	chr3	58539552	58539566	+	1	NA	exon (NM_001005509, exon 4 of 14)	exon (NM_001005509, exon 4 of 14)	-13675	NM_030685	28146	Mm.29702	NM_030685	ENSMUSG00000027808	Serp1	D3Ucla1|Ramp4	stress-associated endoplasmic reticulum protein 1	protein-coding
mm_12715.1	chr2	77291024	77291028	+	1	NA	Intergenic	Intergenic	-10434	NM_175465	228071	Mm.27120	NM_175465	ENSMUSG00000042272	Sestd1	1500031J16Rik|A930010O20|Solo/Trio8	SEC14 and spectrin domains 1	protein-coding
mm_30463.1	chr3	154094070	154094080	-	1	NA	intron (NM_001081263, intron 1 of 21)	intron (NM_001081263, intron 1 of 21)	120639	NM_001081263	242259	Mm.239962	NM_001081263	ENSMUSG00000028360	Slc44a5	AA117069|Gm422	solute carrier family 44, member 5	protein-coding
mm_169620.1	chr15	39244518	39244521	-	1	NA	intron (NM_001256382, intron 1 of 26)	RLTR1B-int|LTR|ERV1	46233	NM_053271	116838	Mm.309296	NM_053271	ENSMUSG00000037386	Rims2	2810036I15Rik|AW048769|RIM2|Rab3ip2|Rim2(+40A)|Rim2(+44A)|Rim2(+4A)|Serg2|Syt3-rs|mKIAA0751	regulating synaptic membrane exocytosis 2	protein-coding
mm_109490.1	chr12	111445072	111445099	+	1	NA	exon (NM_009396, exon 2 of 12)	exon (NM_009396, exon 2 of 12)	2424	NM_009396	21928	Mm.255332	NM_009396	ENSMUSG00000021281	Tnfaip2	B94|Exoc3l3|M-sec|Tnfip2|tnfb94	tumor necrosis factor, alpha-induced protein 2	protein-coding
mm_86454.1	chr10	4346790	4346802	+	1	NA	intron (NM_031185, intron 2 of 3)	CpG	41312	NM_001033466	381990	Mm.262466	NM_001033466	ENSMUSG00000075327	Zbtb2	Gm1103	zinc finger and BTB domain containing 2	protein-coding
mm_99349.1	chr11	101583485	101583494	+	1	NA	intron (NM_144830, intron 2 of 8)	intron (NM_144830, intron 2 of 8)	1247	NM_144830	217203	Mm.280559	NM_144830	ENSMUSG00000034947	Tmem106a	0610008L10Rik|AI043106|BC022145	transmembrane protein 106A	protein-coding
mm_148788.1	chr19	6115718	6115726	+	1	NA	TTS (NM_133678)	TTS (NM_133678)	2864	NM_133678	66406	Mm.303924	NM_133678	ENSMUSG00000024790	Sac3d1	2410004C24Rik|AU015683|shd1	SAC3 domain containing 1	protein-coding
mm_146887.1	chr18	25753612	25753632	-	1	NA	exon (NM_001146295, exon 1 of 2)	exon (NM_001146295, exon 1 of 2)	361	NM_133195	108013	Mm.266435	NM_133195	ENSMUSG00000024268	Celf4	A230070D14Rik|BRUNOL-4|Brul4|Brunol4|C130060B05Rik	CUGBP, Elav-like family member 4	protein-coding
mm_88749.1	chr10	80295931	80296003	+	1	NA	intron (NR_038088, intron 1 of 4)	intron (NR_038088, intron 1 of 4)	3458	NM_001310726	20054	Mm.643	NM_009091	ENSMUSG00000063457	Rps15	rig	ribosomal protein S15	protein-coding
mm_89322.1	chr10	87931302	87931331	+	1	NA	3' UTR (NM_010512, exon 5 of 5)	3' UTR (NM_010512, exon 5 of 5)	-35355	NR_000040	22172	Mm.391420	NR_000040		Tyms-ps	-	thymidylate synthase, pseudogene	pseudo
mm_114435.1	chr13	65278811	65278838	+	1	NA	promoter-TSS (NM_178364)	promoter-TSS (NM_178364)	-30	NM_178364	170936	Mm.151546	NM_178364	ENSMUSG00000021514	Zfp369	B930030B22Rik|D230020H11Rik|NRIF2	zinc finger protein 369	protein-coding
mm_113211.1	chr13	25097576	25097579	+	1	NA	intron (NM_001195617, intron 2 of 7)	intron (NM_001195617, intron 2 of 7)	41573	NM_177577	195208	Mm.284719	NM_177577	ENSMUSG00000035910	Dcdc2a	AW492955|Dcdc2|RU2	doublecortin domain containing 2a	protein-coding
mm_53254.1	chr6	127796456	127796476	+	1	NA	Intergenic	Intergenic	-8323	NR_106092	102466996		NR_106092	ENSMUSG00000104804	Mir7233	mmu-mir-7233	microRNA 7233	ncRNA
mm_13842.1	chr2	119478863	119478871	+	1	NA	Intergenic	Intergenic	-1238	NM_026574	68142	Mm.330496	NM_026574	ENSMUSG00000034154	Ino80	2310079N15Rik|4632409L19Rik|Inoc1	INO80 complex subunit	protein-coding
mm_50857.1	chr6	55203461	55203496	+	1	NA	promoter-TSS (NM_001142781)	promoter-TSS (NM_001142781)	95	NM_001142781	330323	Mm.268997	NM_177883	ENSMUSG00000038022	Fam188b	C330043M08Rik|Gm1406	family with sequence similarity 188, member B	protein-coding
mm_49549.1	chr6	30512284	30512288	+	1	NA	promoter-TSS (NM_029373)	promoter-TSS (NM_029373)	0	NM_029373	75647	Mm.46117	NM_027073	ENSMUSG00000029784	Ssmem1	1700016K02Rik|1700025E21Rik	serine-rich single-pass membrane protein 1	protein-coding
mm_120923.1	chr14	76438413	76438417	+	1	NA	intron (NM_001310646, intron 3 of 4)	intron (NM_001310646, intron 3 of 4)	22594	NM_207652	21807	Mm.153272	NM_009366	ENSMUSG00000022010	Tsc22d1	AA589566|AW105905|Egr5|TSC-22|Tgfb1i4|Tsc|Tsc22	TSC22 domain family, member 1	protein-coding
mm_120134.1	chr14	60265217	60265336	+	1	NA	promoter-TSS (NM_144843)	promoter-TSS (NM_144843)	71	NM_144843	219135	Mm.247007	NM_144843	ENSMUSG00000021987	Mtmr6	4022440C11Rik|AI428804|AU041072	myotubularin related protein 6	protein-coding
mm_126792.1	chr15	86333833	86333844	+	1	NA	intron (NM_145476, intron 8 of 12)	intron (NM_145476, intron 8 of 12)	119379	NM_145476	223754	Mm.28904	NM_145476	ENSMUSG00000051864	Tbc1d22a	BC023106|D15Ertd781e	TBC1 domain family, member 22a	protein-coding
mm_113398.1	chr13	33192953	33192964	+	1	NA	promoter-TSS (NM_011460)	promoter-TSS (NM_011460)	-1	NM_011460	20726	Mm.234774	NM_011460	ENSMUSG00000054266	Serpinb9d	AT2|Spi9|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 9d	protein-coding
mm_62207.1	chr7	97842918	97842980	+	1	NA	promoter-TSS (NM_011035)	promoter-TSS (NM_011035)	10	NM_011035	18479	Mm.260227	NM_011035	ENSMUSG00000030774	Pak1	AW045634|PAK-1|Paka	p21 protein (Cdc42/Rac)-activated kinase 1	protein-coding
mm_133485.1	chr16	90220595	90220610	+	1	NA	promoter-TSS (NM_011434)	promoter-TSS (NM_011434)	-140	NM_011434	20655	Mm.276325	NM_011434	ENSMUSG00000022982	Sod1	B430204E11Rik|Cu/Zn-SOD|CuZnSOD|Ipo-1|Ipo1|SODC|Sod-1	superoxide dismutase 1, soluble	protein-coding
mm_43803.1	chr5	142895287	142895349	+	1	NA	promoter-TSS (NM_001033312)	promoter-TSS (NM_001033312)	-80	NM_001033312	231863	Mm.89753	NM_001033312	ENSMUSG00000066640	Fbxl18	AI427077|B130019G13Rik|C330021B20Rik	F-box and leucine-rich repeat protein 18	protein-coding
mm_48639.1	chr5	145191567	145191572	-	1	NA	promoter-TSS (NM_020582)	promoter-TSS (NM_020582)	23	NM_020582	57423	Mm.133551	NM_020582	ENSMUSG00000038690	Atp5j2	1110019H14Rik	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit F2	protein-coding
mm_123210.1	chr14	59397175	59397216	-	1	NA	intron (NM_001320725, intron 14 of 23)	intron (NM_001320725, intron 14 of 23)	-3683	NM_001164289	628705	Mm.479244	NM_001164289	ENSMUSG00000091144	Phf11c	EG628705|Gm6907|Phf11	PHD finger protein 11C	protein-coding
mm_76588.1	chr8	89042592	89042620	-	1	NA	intron (NM_021390, intron 1 of 3)	CpG-14342	1556	NM_021390	58198	Mm.214361	NM_021390	ENSMUSG00000031665	Sall1	Msal-3	sal-like 1 (Drosophila)	protein-coding
mm_124052.1	chr14	77874846	77874856	-	1	NA	promoter-TSS (NM_025384)	promoter-TSS (NM_025384)	66	NM_025384	66148	Mm.248046	NM_025384	ENSMUSG00000022013	Dnajc15	1110003P16Rik|Dnajd1	DnaJ heat shock protein family (Hsp40) member C15	protein-coding
mm_4184.1	chr1	171160309	171160335	+	1	NA	3' UTR (NM_008623, exon 8 of 8)	3' UTR (NM_008623, exon 8 of 8)	4804	NM_001315500	17528	Mm.9986	NM_008623	ENSMUSG00000056569	Mpz	Mpp|P-zero|P0	myelin protein zero	protein-coding
mm_8448.1	chr1	152902629	152902669	-	1	NA	promoter-TSS (NM_001160256)	promoter-TSS (NM_001160256)	-3	NM_001005507	226517	Mm.270775	NM_001005507	ENSMUSG00000042772	Smg7	9430023P16Rik|mKIAA0250	Smg-7 homolog, nonsense mediated mRNA decay factor (C. elegans)	protein-coding
mm_26530.1	chr3	146117469	146117521	+	1	NA	Intergenic	Intergenic	-4296	NM_134160	171166	Mm.114683	NM_134160	ENSMUSG00000036853	Mcoln3	6720490O21Rik|TRPML3|Va	mucolipin 3	protein-coding
mm_114391.1	chr13	63272794	63272808	+	1	NA	intron (NR_110520, intron 2 of 5)	intron (NR_110520, intron 2 of 5)	24346	NR_045794	100504114	Mm.437070	NR_045794	ENSMUSG00000097242	Gm16907	-	predicted gene, 16907	ncRNA
mm_36814.1	chr4	103290854	103290870	-	1	NA	promoter-TSS (NM_001163494)	promoter-TSS (NM_001163494)	1	NM_027612	70941	Mm.158501	NM_027612	ENSMUSG00000028520	4921539E11Rik	-	RIKEN cDNA 4921539E11 gene	protein-coding
mm_65603.1	chr7	27361344	27361360	-	1	NA	intron (NM_001199235, intron 15 of 17)	intron (NM_001199235, intron 15 of 17)	-5344	NM_138676	192192	Mm.21297	NM_138676	ENSMUSG00000089832	Shkbp1	B930062H15Rik|Sb1	Sh3kbp1 binding protein 1	protein-coding
mm_101213.1	chr11	20080602	20080605	-	1	NA	intron (NM_146243, intron 5 of 8)	B2_Mm2|SINE|B2	32348	NM_146243	66713	Mm.259045	NM_146243	ENSMUSG00000020152	Actr2	4921510D23Rik|AA409782|Arp2|D6Ertd746e	ARP2 actin-related protein 2	protein-coding
mm_56029.1	chr6	86607695	86607721	-	1	NA	Intergenic	Intergenic	-20466	NM_026414	67855	Mm.183043	NM_026414	ENSMUSG00000033508	Asprv1	2300003P22Rik|AA986851|SASP|SASPase|Taps	aspartic peptidase, retroviral-like 1	protein-coding
mm_55926.1	chr6	84587036	84587084	-	1	NA	intron (NM_001177713, intron 2 of 6)	intron (NM_001177713, intron 2 of 6)	6750	NM_175475	232174	Mm.255246	NM_175475	ENSMUSG00000063415	Cyp26b1	CP26|P450RAI-2	cytochrome P450, family 26, subfamily b, polypeptide 1	protein-coding
mm_40437.1	chr5	53590657	53590668	+	1	NA	5' UTR (NM_001080927, exon 1 of 11)	5' UTR (NM_001080927, exon 1 of 11)	176	NM_001080927	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_16074.1	chr2	168159080	168159088	+	1	NA	Intergenic	Intergenic	-4571	NR_040327	77017	Mm.407822	NR_040327	ENSMUSG00000087648	E130018N17Rik	-	RIKEN cDNA E130018N17 gene	ncRNA
mm_5694.1	chr1	43186301	43186311	-	1	NA	intron (NM_001289533, intron 1 of 5)	B4|SINE|B4	10455	NM_001289533	14200	Mm.6799	NM_010212	ENSMUSG00000008136	Fhl2	FHL-2|SLIM-3|SLIM3	four and a half LIM domains 2	protein-coding
mm_79927.1	chr9	65630755	65630761	+	1	NA	5' UTR (NM_028030, exon 1 of 8)	5' UTR (NM_028030, exon 1 of 8)	176	NM_028030	71973	Mm.29148	NM_028030	ENSMUSG00000032387	Rbpms2	2400008B06Rik|AI316523	RNA binding protein with multiple splicing 2	protein-coding
mm_57735.1	chr6	128970475	128970480	-	1	NA	promoter-TSS (NM_001316752)	promoter-TSS (NM_001316752)	-683	NM_001168224	70809	Mm.439891	NM_027562	ENSMUSG00000000248	Clec2g	4632413B12Rik|Clr-c|Clr-d|Clrc|Clrd|Clrx|Ddv10|Ocilrp1	C-type lectin domain family 2, member g	protein-coding
mm_154688.1	chrX	7922943	7922975	+	1	NA	exon (NM_013892, exon 3 of 3)	exon (NM_013892, exon 3 of 3)	3137	NM_013892	30052	Mm.4881	NM_013892	ENSMUSG00000039278	Pcsk1n	AI848336|KEP|PEN|PEN19|PEN20|Pan3|SAAS|SAASCT|bLEN|lLEN|proSAAS	proprotein convertase subtilisin/kexin type 1 inhibitor	protein-coding
mm_36818.1	chr4	104858732	104858754	-	1	NA	intron (NM_001290645, intron 3 of 9)	intron (NM_001290645, intron 3 of 9)	17655	NM_001290645	230558	Mm.197638	NM_146148	ENSMUSG00000035031	C8a	-	complement component 8, alpha polypeptide	protein-coding
mm_142620.1	chr17	47010514	47010568	-	1	NA	promoter-TSS (NM_001177374)	promoter-TSS (NM_001177374)	-9	NM_001177374	224826	Mm.28234	NM_146078	ENSMUSG00000023977	Ubr2	9930021A08Rik|AI462103|AW540746|E130209G04Rik|ENSMUSG00000043296|mKIAA0349	ubiquitin protein ligase E3 component n-recognin 2	protein-coding
mm_169601.1	chr15	35371788	35371792	+	1	NA	intron (NM_177151, intron 1 of 61)	CpG	244	NM_177151	666173	Mm.309250	NM_177151	ENSMUSG00000037646	Vps13b	1810042B05Rik|2310042E16Rik|4732488H20|C330002D13Rik|C87206|Coh1|D230005K13|mKIAA0532|mKIAA5032	vacuolar protein sorting 13B	protein-coding
mm_115623.1	chr13	12104485	12104488	-	1	NA	intron (NM_023868, intron 1 of 104)	intron (NM_023868, intron 1 of 104)	2459	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding
mm_146329.1	chr18	80715372	80715382	+	1	NA	Intergenic	Intergenic	-2306	NM_001164109	18018	Mm.329560	NM_016791	ENSMUSG00000033016	Nfatc1	2210017P03Rik|AI449492|AV076380|NF-ATc|NFAT2|NFATc|Nfatcb	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 1	protein-coding
mm_80439.1	chr9	77941254	77941270	+	1	NA	intron (NM_134255, intron 1 of 7)	intron (NM_134255, intron 1 of 7)	23897	NM_134255	68801	Mm.430736	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	ELOVL family member 5, elongation of long chain fatty acids (yeast)	protein-coding
mm_61708.1	chr7	81214046	81214066	+	1	NA	exon (NM_008803, exon 1 of 22)	exon (NM_008803, exon 1 of 22)	252	NM_008803	18584	Mm.371577	NM_008803	ENSMUSG00000025584	Pde8a	AI551852|Pde8	phosphodiesterase 8A	protein-coding
mm_28305.1	chr3	89227386	89227388	-	1	NA	promoter-TSS (NR_030579)	promoter-TSS (NR_030579)	-189	NR_030579	100124470		NR_030579	ENSMUSG00000076255	Mir92b	Mirn92b|mir-92b|mmu-mir-92b	microRNA 92b	ncRNA
mm_145475.1	chr18	60376054	60376079	+	1	NA	promoter-TSS (NM_001146275)	promoter-TSS (NM_001146275)	37	NM_001146275	60440	Mm.261140	NM_021792	ENSMUSG00000054072	Iigp1	2900074L10Rik|AI046432|AW111922|Ifgga1|Iigp|Irga6	interferon inducible GTPase 1	protein-coding
mm_119596.1	chr14	50964921	50964931	+	1	NA	TTS (NM_001123371)	TTS (NM_001123371)	8785	NM_001123371	667034	Mm.482171	NM_001123371	ENSMUSG00000068417	Pnp2	-	purine-nucleoside phosphorylase 2	protein-coding
mm_173002.1	chrM	1824	1842	+	1	NA	NA	Intergenic	NA	NA								
mm_21068.1	chr2	152814971	152814975	-	1	NA	intron (NM_001289717, intron 2 of 2)	B1_Mus2|SINE|Alu	15744	NM_001289716	12048	Mm.238213	NM_009743	ENSMUSG00000007659	Bcl2l1	Bcl(X)L|Bcl-XL|Bcl2l|BclX|bcl-x|bcl2-L-1	BCL2-like 1	protein-coding
mm_145462.1	chr18	60246598	60246629	+	1	NA	exon (NM_001033767, exon 3 of 3)	exon (NM_001033767, exon 3 of 3)	26654	NM_001034859	225594	Mm.329460	NM_001034859	ENSMUSG00000068606	Gm4841	EG225594|Ifgga3	predicted gene 4841	protein-coding
mm_124501.1	chr14	121879532	121879538	-	1	NA	promoter-TSS (NR_130999)	promoter-TSS (NR_130999)	-127	NR_130999	78312	Mm.188743	NR_130999	ENSMUSG00000102112	1810041H14Rik	-	RIKEN cDNA 1810041H14 gene	ncRNA
mm_38633.1	chr4	142422176	142422177	-	1	NA	Intergenic	Intergenic	-182775	NM_001109685	71529	Mm.255986	NM_144531	ENSMUSG00000040606	Kazn	2310007B04Rik|9030409G11Rik|AI256607|AI666764|AW061099|Kaz|Kazrin	kazrin, periplakin interacting protein	protein-coding
mm_21474.1	chr2	161109037	161109091	-	1	NA	promoter-TSS (NM_173368)	promoter-TSS (NM_173368)	22	NM_173368	71389	Mm.122738	NM_173368	ENSMUSG00000057133	Chd6	5430439G14Rik|6330406J24Rik|CHD-6	chromodomain helicase DNA binding protein 6	protein-coding
mm_50364.1	chr6	48651773	48651775	+	1	NA	intron (NM_001286629, intron 3 of 4)	RMER19B2|LTR|ERVK	4413	NM_212486	243374	Mm.86514	NM_212486	ENSMUSG00000064262	Gimap8	Gm457|IAN9|IMAP8	GTPase, IMAP family member 8	protein-coding
mm_162080.1	chrX	26310013	26310013	-	1	NA	promoter-TSS (NM_001100445)	promoter-TSS (NM_001100445)	31	NM_001100445	100039065	Mm.411645	NM_001100445	ENSMUSG00000083628	Gm2030	-	predicted gene 2030	protein-coding
mm_54602.1	chr6	38307253	38307311	-	1	NA	exon (NM_001347122, exon 13 of 13)	exon (NM_001347122, exon 13 of 13)	-8023	NM_172467	209032	Mm.101389	NM_172467	ENSMUSG00000047749	Zc3hav1l	B130055L09Rik|E430016P22Rik	zinc finger CCCH-type, antiviral 1-like	protein-coding
mm_68102.1	chr7	102016146	102016157	-	1	NA	exon (NM_010531, exon 6 of 7)	exon (NM_010531, exon 6 of 7)	2004	NM_010531	16068	Mm.422756	NM_010531	ENSMUSG00000070427	Il18bp	IL-18BP|Igifbp|MC54L	interleukin 18 binding protein	protein-coding
mm_95635.1	chr11	53706818	53706829	+	1	NA	intron (NM_009012, intron 1 of 24)	CpG	496	NM_009012	19360	Mm.4888	NM_009012	ENSMUSG00000020380	Rad50	Mrell|Rad50l	RAD50 double strand break repair protein	protein-coding
mm_73751.1	chr8	114752741	114752741	+	1	NA	intron (NM_019573, intron 8 of 8)	intron (NM_019573, intron 8 of 8)	313089	NM_019573	80707	Mm.440420	NM_019573	ENSMUSG00000004637	Wwox	5330426P09Rik|9030416C10Rik|WOX1	WW domain-containing oxidoreductase	protein-coding
mm_22847.1	chr3	28052643	28052643	+	1	NA	intron (NM_008875, intron 11 of 25)	intron (NM_008875, intron 11 of 25)	68472	NM_008875	18805	Mm.212039	NM_008875	ENSMUSG00000027695	Pld1	AA536939|C85393|Pld1a|Pld1b|mPLD1	phospholipase D1	protein-coding
mm_112741.1	chr13	19339847	19339863	+	1	NA	Intergenic	Intergenic	55958	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_93351.1	chr10	100590428	100590432	-	1	NA	Intergenic	Intergenic	-1171	NM_175128	68281	Mm.268474	NM_175128	ENSMUSG00000046567	4930430F08Rik	4930571E09Rik|A730088G13Rik|AW551239|C430008C19Rik	RIKEN cDNA 4930430F08 gene	protein-coding
mm_147471.1	chr18	46728348	46728363	-	1	NA	promoter-TSS (NM_033037)	promoter-TSS (NM_033037)	-13	NM_033037	12583	Mm.241056	NM_033037	ENSMUSG00000033022	Cdo1	1300002L19Rik|Cdo|D18Ucla3	cysteine dioxygenase 1, cytosolic	protein-coding
mm_167282.1	chr8	39605468	39605474	-	1	NA	3' UTR (NM_031195, exon 9 of 9)	3' UTR (NM_031195, exon 9 of 9)	37207	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_142543.1	chr17	46556105	46556115	-	1	NA	promoter-TSS (NM_020493)	promoter-TSS (NM_020493)	52	NM_020493	20807	Mm.45044	NM_020493	ENSMUSG00000015605	Srf	AW049942|AW240594	serum response factor	protein-coding
mm_111424.1	chr12	91590033	91590056	-	1	NA	promoter-TSS (NM_031391)	promoter-TSS (NM_031391)	-395	NM_031391	83602	Mm.275728	NM_031391	ENSMUSG00000020962	Gtf2a1	6330549H03Rik|AA536742|AA959775|AW060250|TfIIAa/b|Tfiia1	general transcription factor II A, 1	protein-coding
mm_88929.1	chr10	81257317	81257333	+	1	NA	promoter-TSS (NM_001285854)	promoter-TSS (NM_001285854)	26	NM_001285853	17179	Mm.2918	NM_010768	ENSMUSG00000004933	Matk	CHK|HYL|Ntk|p56ntk	megakaryocyte-associated tyrosine kinase	protein-coding
mm_130920.1	chr15	102707072	102707084	-	1	NA	3' UTR (NM_026192, exon 15 of 15)	3' UTR (NM_026192, exon 15 of 15)	15100	NM_026192	67488	Mm.71682	NM_026192	ENSMUSG00000023055	Calcoco1	1810009B06Rik|Cocoa|Gcap11|mKIAA1536	calcium binding and coiled coil domain 1	protein-coding
mm_138249.1	chr17	34589955	34589965	+	1	NA	5' UTR (NM_134116, exon 1 of 4)	5' UTR (NM_134116, exon 1 of 4)	154	NM_134116	106512	Mm.26584	NM_134116	ENSMUSG00000034786	Gpsm3	AA960287|AGS4	G-protein signalling modulator 3 (AGS3-like, C. elegans)	protein-coding
mm_79953.1	chr9	66126656	66126722	+	1	NA	promoter-TSS (NM_026635)	promoter-TSS (NM_026635)	78	NM_026635	68250	Mm.27107	NM_026635	ENSMUSG00000032381	Fam96a	5730536A07Rik	family with sequence similarity 96, member A	protein-coding
mm_53485.1	chr6	135065667	135065682	+	1	NA	promoter-TSS (NM_181444)	promoter-TSS (NM_181444)	12	NM_181444	232431	Mm.23575	NM_181444	ENSMUSG00000046733	Gprc5a	Rai3|Raig1	G protein-coupled receptor, family C, group 5, member A	protein-coding
mm_21531.1	chr2	163645126	163645136	-	1	NA	promoter-TSS (NM_012032)	promoter-TSS (NM_012032)	12	NM_012032	26943	Mm.218473	NM_012032	ENSMUSG00000017707	Serinc3	AA959945|AA960047|AIGP1|DIFF33|TMS-1|Tde1	serine incorporator 3	protein-coding
mm_82669.1	chr9	22130204	22130213	-	1	NA	intron (NM_001102405, intron 1 of 4)	intron (NM_001102405, intron 1 of 4)	390	NM_007388	11433	Mm.46354	NM_007388	ENSMUSG00000001348	Acp5	TRACP|TRAP	acid phosphatase 5, tartrate resistant	protein-coding
mm_29298.1	chr3	107895807	107895817	-	1	NA	promoter-TSS (NM_010360)	promoter-TSS (NM_010360)	-42	NM_010360	14866	Mm.282351	NM_010360	ENSMUSG00000004032	Gstm5	-	glutathione S-transferase, mu 5	protein-coding
mm_161290.1	chr14	26206980	26206980	-	1	NA	promoter-TSS (NM_001270496)	promoter-TSS (NM_001270496)	45	NM_001270495	100039257	Mm.33344	NM_001270495	ENSMUSG00000021867	Tmem254b	ENSMUSG00000021867|Gm9746	transmembrane protein 254b	protein-coding
mm_19799.1	chr2	110210267	110210267	-	1	NA	Intergenic	Intergenic	95458	NM_130452	170442	Mm.27335	NM_130452	ENSMUSG00000041660	Bbox1	AI874739	butyrobetaine (gamma), 2-oxoglutarate dioxygenase 1 (gamma-butyrobetaine hydroxylase)	protein-coding
mm_150121.1	chr19	29951809	29951819	+	1	NA	intron (NM_133775, intron 2 of 7)	MTEa|LTR|ERVL-MaLR	6024	NM_001164724	77125	Mm.182359	NM_133775	ENSMUSG00000024810	Il33	9230117N10Rik|Il-33|Il1f11|NF-HEV	interleukin 33	protein-coding
mm_38687.1	chr4	145194954	145194964	-	1	NA	promoter-TSS (NM_001276465)	promoter-TSS (NM_001276465)	46	NM_001276465	230895	Mm.240310	NM_001033190	ENSMUSG00000020220	Vps13d	-	vacuolar protein sorting 13D	protein-coding
mm_31371.1	chr4	47353284	47353304	+	1	NA	promoter-TSS (NM_009370)	promoter-TSS (NM_009370)	72	NM_009370	21812	Mm.197552	NM_009370	ENSMUSG00000007613	Tgfbr1	ALK5|AU017191|Alk-5|ESK2|TGFR-1|TbetaR-I|TbetaRI	transforming growth factor, beta receptor I	protein-coding
mm_23333.1	chr3	54361104	54361116	+	1	NA	promoter-TSS (NM_015784)	promoter-TSS (NM_015784)	3	NM_015784	50706	Mm.236067	NM_015784	ENSMUSG00000027750	Postn	A630052E07Rik|AI747096|OSF-2|Osf2|PLF|PN	periostin, osteoblast specific factor	protein-coding
mm_82515.1	chr9	20581294	20581306	-	1	NA	promoter-TSS (NM_172919)	promoter-TSS (NM_172919)	-28	NM_172919	244721	Mm.86627	NM_172919	ENSMUSG00000058192	Zfp846	2210010B09Rik|9130221F13|Znf846	zinc finger protein 846	protein-coding
mm_61405.1	chr7	73418287	73418289	+	1	NA	3' UTR (NM_177740, exon 4 of 4)	3' UTR (NM_177740, exon 4 of 4)	-42514	NR_040324	319783	Mm.349813	NR_040324	ENSMUSG00000097756	A730056A06Rik	C76391	RIKEN cDNA A730056A06 gene	ncRNA
mm_76791.1	chr8	102739284	102739297	-	1	NA	intron (NM_009866, intron 1 of 12)	intron (NM_009866, intron 1 of 12)	45821	NM_009866	12552	Mm.1571	NM_009866	ENSMUSG00000031673	Cdh11	Cad11|OSF-4	cadherin 11	protein-coding
mm_36386.1	chr4	77154742	77154750	-	1	NA	intron (NM_011211, intron 7 of 39)	RSINE1|SINE|B4	1057149	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding
mm_77587.1	chr8	123859926	123859955	-	1	NA	5' UTR (NM_028536, exon 1 of 4)	5' UTR (NM_028536, exon 1 of 4)	269	NM_028536	73420	Mm.157746	NM_028536	ENSMUSG00000031971	Ccsap	1700054N08Rik|AI853424	centriole, cilia and spindle associated protein	protein-coding
mm_71974.1	chr8	70594177	70594210	+	1	NA	promoter-TSS (NM_023627)	promoter-TSS (NM_023627)	-288	NM_023627	71780	Mm.29357	NM_023627	ENSMUSG00000019139	Isyna1	1300017C10Rik|AU018670	myo-inositol 1-phosphate synthase A1	protein-coding
mm_8910.1	chr1	163313006	163313006	-	1	NA	5' UTR (NM_175686, exon 1 of 5)	5' UTR (NM_175686, exon 1 of 5)	644	NM_011127	18933	Mm.288642	NM_011127	ENSMUSG00000026586	Prrx1	A230024N07Rik|AA755424|AI385634|AI843499|K-2|Pmx|Pmx1|Prx1|mHox	paired related homeobox 1	protein-coding
mm_125359.1	chr15	39434298	39434306	+	1	NA	intron (NM_001256382, intron 3 of 26)	intron (NM_001256382, intron 3 of 26)	-225209	NM_001256384	116838	Mm.309296	NM_053271	ENSMUSG00000037386	Rims2	2810036I15Rik|AW048769|RIM2|Rab3ip2|Rim2(+40A)|Rim2(+44A)|Rim2(+4A)|Serg2|Syt3-rs|mKIAA0751	regulating synaptic membrane exocytosis 2	protein-coding
mm_138412.1	chr17	35068823	35068831	+	1	NA	intron (NM_023463, intron 1 of 2)	intron (NM_023463, intron 1 of 2)	1502	NM_023463	68468	Mm.215096	NM_023463	ENSMUSG00000092586	Ly6g6c	1110003M04Rik|AU016360|G6c|NG24	lymphocyte antigen 6 complex, locus G6C	protein-coding
mm_101786.1	chr11	45955427	45955437	-	1	NA	promoter-TSS (NM_001290737)	promoter-TSS (NM_001290737)	71	NM_001080969	66628	Mm.269083	NM_001080969	ENSMUSG00000011254	Thg1l	-	tRNA-histidine guanylyltransferase 1-like (S. cerevisiae)	protein-coding
mm_16128.1	chr2	170284961	170284980	+	1	NA	Intergenic	Intergenic	-71391	NR_040610	73303	Mm.443297	NR_040610	ENSMUSG00000086999	Bcas1os2	1700040N02Rik	breast carcinoma amplified sequence 1, opposite strand 2	ncRNA
mm_101479.1	chr11	30986247	30986257	-	1	NA	5' UTR (NM_026527, exon 1 of 3)	5' UTR (NM_026527, exon 1 of 3)	113	NM_026527	68044	Mm.32656	NM_026527	ENSMUSG00000020309	Chac2	-	ChaC, cation transport regulator 2	protein-coding
mm_166647.1	chr6	85475657	85475659	-	1	NA	intron (NM_001001160, intron 10 of 13)	intron (NM_001001160, intron 10 of 13)	-23688	NR_028081	73327	Mm.379221	NM_028505	ENSMUSG00000030008	Pradc1	1700040I03Rik|Pap21	protease-associated domain containing 1	protein-coding
mm_95760.1	chr11	54906784	54906793	+	1	NA	intron (NM_001329860, intron 1 of 5)	intron (NM_001329860, intron 1 of 5)	3934	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_66725.1	chr7	46122910	46122926	-	1	NA	exon (NM_011510, exon 20 of 39)	exon (NM_011510, exon 20 of 39)	-22154	NM_001204411	16514	Mm.333863	NM_010602	ENSMUSG00000096146	Kcnj11	Kir6.2|mBIR	potassium inwardly rectifying channel, subfamily J, member 11	protein-coding
mm_35020.1	chr4	3899012	3899015	-	1	NA	Intergenic	Intergenic	-26908	NM_020021	17451	Mm.459300	NM_020021	ENSMUSG00000078365	Mos	c-mos	Moloney sarcoma oncogene	protein-coding
mm_127519.1	chr15	102028201	102028211	+	1	NA	promoter-TSS (NM_010664)	promoter-TSS (NM_010664)	-10	NM_010664	16668	Mm.22479	NM_010664	ENSMUSG00000023043	Krt18	CK18|K18|Krt1-18	keratin 18	protein-coding
mm_30917.1	chr4	32626873	32626891	+	1	NA	intron (NM_001122978, intron 2 of 10)	intron (NM_001122978, intron 2 of 10)	11412	NM_011997	26885	Mm.22279	NM_011997	ENSMUSG00000028282	Casp8ap2	D4Ertd659e|FLASH	caspase 8 associated protein 2	protein-coding
mm_74252.1	chr8	124862630	124862636	+	1	NA	promoter-TSS (NM_010322)	promoter-TSS (NM_010322)	396	NM_025615	66523	Mm.436864	NM_025615	ENSMUSG00000031984	2810004N23Rik	3110004G14Rik|Ayu21-55|Gt(pU21)55Imeg|GtAyu21-55	RIKEN cDNA 2810004N23 gene	protein-coding
mm_53313.1	chr6	129182933	129182950	+	1	NA	intron (NM_053109, intron 1 of 4)	intron (NM_053109, intron 1 of 4)	2326	NM_053109	93694	Mm.197536	NM_053109	ENSMUSG00000030157	Clec2d	Clr-b|Clrb|Ocil	C-type lectin domain family 2, member d	protein-coding
mm_131110.1	chr16	5146942	5146959	+	1	NA	promoter-TSS (NM_001127725)	promoter-TSS (NM_001127725)	-159	NM_001127725	665119	Mm.102072	NM_001127725	ENSMUSG00000091712	Sec14l5	-	SEC14-like lipid binding 5	protein-coding
mm_162574.1	chr1	176837533	176837538	+	1	NA	intron (NM_029756, intron 5 of 17)	AT_rich|Low_complexity|Low_complexity	-1402	NR_037996	15365	Mm.441435	NR_037996		Hmga2-ps1	EG666235|Gm7996|Hmgic-ps1|[y]i-c	high mobility group AT-hook 2, pseudogene 1	pseudo
mm_92627.1	chr10	80320556	80320560	-	1	NA	promoter-TSS (NM_025521)	promoter-TSS (NM_025521)	-10	NM_025521	66374	Mm.383824	NM_025521	ENSMUSG00000020133	2310011J03Rik	AI452186|AW545358	RIKEN cDNA 2310011J03 gene	protein-coding
mm_120939.1	chr14	76599751	76599760	+	1	NA	Intergenic	Intergenic	-42866	NR_027699	72661	Mm.320384	NM_001160326	ENSMUSG00000052584	Serp2	2810032E02Rik	stress-associated endoplasmic reticulum protein family member 2	protein-coding
mm_136249.1	chr16	90937353	90937364	-	1	NA	3' UTR (NM_001045515, exon 33 of 33)	3' UTR (NM_001045515, exon 33 of 33)	-2509	NM_026502	68001	Mm.45374	NM_026502	ENSMUSG00000022972	1110004E09Rik	-	RIKEN cDNA 1110004E09 gene	protein-coding
mm_67069.1	chr7	67759765	67759779	-	1	NA	promoter-TSS (NM_207663)	promoter-TSS (NM_207663)	-30	NM_207663	233335	Mm.60526	NM_183312	ENSMUSG00000030554	Synm	4930412K21Rik|AI852401|Dmn|E130104F11|Syn|Synemin	synemin, intermediate filament protein	protein-coding
mm_148495.1	chr19	4156587	4156607	+	1	NA	TTS (NM_021485)	TTS (NM_021485)	1951	NM_016933	19265	Mm.271937	NM_016933	ENSMUSG00000045826	Ptprcap	AI605264|CD-45-AP|LPAP|LSM-1	protein tyrosine phosphatase, receptor type, C polypeptide-associated protein	protein-coding
mm_127775.1	chr15	3303522	3303569	-	1	NA	promoter-TSS (NM_001166063)	promoter-TSS (NM_001166063)	-19	NM_001166063	100039139	Mm.455610	NM_001166063	ENSMUSG00000091119	Ccdc152	ENSMUSG00000071814	coiled-coil domain containing 152	protein-coding
mm_161585.1	chr16	32400267	32400267	+	1	NA	promoter-TSS (NM_001160402)	promoter-TSS (NM_001160402)	-239	NM_001160402	277203	Mm.484240	NM_001160402	ENSMUSG00000079625	Tm4sf19	EG277203	transmembrane 4 L six family member 19	protein-coding
mm_126975.1	chr15	93432918	93432931	+	1	NA	intron (NM_175363, intron 3 of 8)	intron (NM_175363, intron 3 of 8)	34460	NM_001285863	223828	Mm.74208	NM_146062	ENSMUSG00000036167	Pphln1	CR|HSPC206|HSPC232	periphilin 1	protein-coding
mm_16817.1	chr2	11398496	11398517	-	1	NA	promoter-TSS (NR_040615)	promoter-TSS (NR_040615)	-6	NR_040615	77543	Mm.490670	NR_040615	ENSMUSG00000102674	8030442B05Rik	-	RIKEN cDNA 8030442B05 gene	ncRNA
mm_161030.1	chr12	8921283	8921283	+	1	NA	promoter-TSS (NM_008640)	promoter-TSS (NM_008640)	-24	NM_008640	17775	Mm.30071	NM_008640	ENSMUSG00000020585	Laptm4a	AA286466|LAPTM4|MTP|Mtrp|mKIAA0108	lysosomal-associated protein transmembrane 4A	protein-coding
mm_172553.1	chr8	103943918	103943929	-	1	NA	Intergenic	IAP1-MM_LTR|LTR|ERVK	-157702	NM_009868	12562	Mm.21767	NM_009868	ENSMUSG00000031871	Cdh5	7B4|AA408225|Cd144|VE-Cad|VECD|VEcad|Vec	cadherin 5	protein-coding
mm_113594.1	chr13	41001003	41001052	+	1	NA	promoter-TSS (NM_026550)	promoter-TSS (NM_026550)	17	NM_026550	68083	Mm.24789	NM_026550	ENSMUSG00000038683	Pak1ip1	5830431I15Rik|5930415H02Rik|AA419825|AI314040|AW556169|Gdpd1|PIP1	PAK1 interacting protein 1	protein-coding
mm_61578.1	chr7	79842018	79842090	+	1	NA	exon (NM_008486, exon 1 of 20)	exon (NM_008486, exon 1 of 20)	298	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_12390.1	chr2	69897221	69897247	+	1	NA	promoter-TSS (NM_177783)	promoter-TSS (NM_177783)	-12	NM_001303033	68795	Mm.314576	NM_177783	ENSMUSG00000044308	Ubr3	1110059H15Rik|4833421P10Rik|A130030D10Rik|AA409735|AA414972|AA422631|AI646861|AU016126|Zfp650|Znf650	ubiquitin protein ligase E3 component n-recognin 3	protein-coding
mm_150294.1	chr19	34493477	34493499	+	1	NA	3' UTR (NM_021460, exon 10 of 10)	3' UTR (NM_021460, exon 10 of 10)	-18353	NM_009890	12642	Mm.30824	NM_009890	ENSMUSG00000050370	Ch25h	AI462618|m25OH	cholesterol 25-hydroxylase	protein-coding
mm_149208.1	chr19	9980859	9980867	+	1	NA	non-coding (NR_073181, exon 1 of 5)	non-coding (NR_073181, exon 1 of 5)	263	NR_073181	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
mm_146924.1	chr18	31949572	31949588	-	1	NA	promoter-TSS (NM_001025381)	promoter-TSS (NM_001025381)	56	NM_001025381	574402	Mm.391108	NM_001025381	ENSMUSG00000052229	Gpr17	AI853548	G protein-coupled receptor 17	protein-coding
mm_6100.1	chr1	63730347	63730354	-	1	NA	promoter-TSS (NM_172422)	promoter-TSS (NM_172422)	-32	NM_029696	76668	Mm.30494	NM_029696	ENSMUSG00000025963	Mdh1b	1700124B08Rik|AV255588	malate dehydrogenase 1B, NAD (soluble)	protein-coding
mm_24539.1	chr3	93279707	93279718	+	1	NA	Intergenic	Intergenic	-40037	NM_133698	68723	Mm.208047	NM_133698	ENSMUSG00000041991	Hrnr	1110033K19Rik|A530063N20Rik|S100a18	hornerin	protein-coding
mm_106512.1	chr11	120493494	120493501	-	1	NA	intron (NM_013770, intron 1 of 10)	intron (NM_013770, intron 1 of 10)	1660	NM_013770	27376	Mm.3991	NM_013770	ENSMUSG00000025792	Slc25a10	Dic	solute carrier family 25 (mitochondrial carrier, dicarboxylate transporter), member 10	protein-coding
mm_55061.1	chr6	49047960	49047980	-	1	NA	exon (NM_053110, exon 6 of 11)	exon (NM_053110, exon 6 of 11)	11452	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_139769.1	chr17	64677998	64677999	+	1	NA	intron (NM_008549, intron 10 of 21)	intron (NM_008549, intron 10 of 21)	76349	NM_008549	17158	Mm.2433	NM_008549	ENSMUSG00000024085	Man2a1	Mana-2|Mana2|Map-2	mannosidase 2, alpha 1	protein-coding
mm_117802.1	chr13	97435062	97435070	-	1	NA	promoter-TSS (NR_110432)	promoter-TSS (NR_110432)	96	NR_110432	100039691	Mm.219358	NR_110430	ENSMUSG00000078952	Lncenc1	ENSMUSG00000078952|Gm11019|Gm2373|Lincenc1|Platr18|linc-Enc1	long non-coding RNA, embryonic stem cells expressed 1	ncRNA
mm_137432.1	chr17	26360367	26360416	+	1	NA	Intergenic	Intergenic	-54574	NM_001081656	240055	Mm.133211	NM_001081656	ENSMUSG00000034413	Neurl1b	C230078M08Rik|EG240055	neuralized E3 ubiquitin protein ligase 1B	protein-coding
mm_173242.1	chrX	89199837	89199839	+	1	NA	Intergenic	Intergenic	209851	NM_008821	18630	Mm.3086	NM_008821	ENSMUSG00000035395	Pet2	PC231|PC326|Pex3	plasmacytoma expressed transcript 2	protein-coding
mm_26801.1	chr3	9886699	9886712	-	1	NA	Intergenic	Intergenic	-53026	NM_001195031	94212	Mm.23897	NM_053182	ENSMUSG00000027508	Pag1	Cbp|F730007C19Rik|Pag	phosphoprotein associated with glycosphingolipid microdomains 1	protein-coding
mm_151479.1	chr19	58676199	58676228	+	1	NA	exon (NM_026925, exon 7 of 13)	exon (NM_026925, exon 7 of 13)	5848	NM_026925	69060	Mm.20407	NM_026925	ENSMUSG00000046008	Pnlip	1810007A24Rik|PL|PTL	pancreatic lipase	protein-coding
mm_73830.1	chr8	117460418	117460419	+	1	NA	3' UTR (NM_001163262, exon 21 of 21)	3' UTR (NM_001163262, exon 21 of 21)	1153	NR_106046	102465653		NR_106046	ENSMUSG00000098483	Mir7078	Gm27386|mmu-mir-7078	microRNA 7078	ncRNA
mm_28018.1	chr3	83044997	83045001	-	1	NA	exon (NM_181849, exon 4 of 8)	exon (NM_181849, exon 4 of 8)	4864	NM_181849	110135	Mm.30063	NM_181849	ENSMUSG00000033831	Fgb	2510049G14Rik	fibrinogen beta chain	protein-coding
mm_125611.1	chr15	61985378	61985397	+	1	NA	promoter-TSS (NM_001177354)	promoter-TSS (NM_001177354)	46	NM_001177352	17869	Mm.2444	NM_010849	ENSMUSG00000022346	Myc	AU016757|Myc2|Niard|Nird|bHLHe39	myelocytomatosis oncogene	protein-coding
mm_130704.1	chr15	100720156	100720173	-	1	NA	5' UTR (NM_172451, exon 2 of 12)	5' UTR (NM_172451, exon 2 of 12)	313	NM_001161768	207839	Mm.22969	NM_172451	ENSMUSG00000037280	Galnt6	4632410F13|AW047994|GalNAc-T6	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 6	protein-coding
mm_62509.1	chr7	102107147	102107149	+	1	NA	exon (NM_009710, exon 3 of 5)	exon (NM_009710, exon 3 of 5)	5405	NM_009710	11870	Mm.261071	NM_009710	ENSMUSG00000030996	Art1	ADPRT|ARTC1|Yac-1	ADP-ribosyltransferase 1	protein-coding
mm_44989.1	chr5	37717195	37717205	-	1	NA	promoter-TSS (NM_022416)	promoter-TSS (NM_022416)	-47	NM_022416	64293	Mm.103714	NM_022416	ENSMUSG00000029123	Stk32b	2510009F08Rik|STKG6|Stk32|YANK2	serine/threonine kinase 32B	protein-coding
mm_134229.1	chr16	11365774	11365778	-	1	NA	intron (NM_028964, intron 3 of 20)	intron (NM_028964, intron 3 of 20)	-39872	NM_001290148	74478	Mm.325831	NM_028964	ENSMUSG00000071669	Snx29	4933437K13Rik|ENSMUSG00000079738|Gm11170|Gm1737|Gm930|Rundc2a	sorting nexin 29	protein-coding
mm_16908.1	chr2	13491961	13491974	-	1	NA	promoter-TSS (NM_001081084)	promoter-TSS (NM_001081084)	-91	NM_001081084	65969	Mm.313915	NM_001081084	ENSMUSG00000026726	Cubn	AA408369|AL022750|D2Wsu88e	cubilin (intrinsic factor-cobalamin receptor)	protein-coding
mm_36354.1	chr4	74251775	74251788	-	1	NA	promoter-TSS (NM_144787)	promoter-TSS (NM_144787)	-98	NM_144787	76804	Mm.209059	NM_144787	ENSMUSG00000028397	Kdm4c	2410141F18Rik|AA517467|Gasc1|Jmjd2c	lysine (K)-specific demethylase 4C	protein-coding
mm_84104.1	chr9	58312351	58312439	-	1	NA	exon (NM_010729, exon 1 of 7)	exon (NM_010729, exon 1 of 7)	817	NM_010729	16949	Mm.250492	NM_010729	ENSMUSG00000032334	Loxl1	Loxl	lysyl oxidase-like 1	protein-coding
mm_116294.1	chr13	36117270	36117270	-	1	NA	promoter-TSS (NM_024274)	promoter-TSS (NM_024274)	87	NM_201358	380840	Mm.390576	NM_201358	ENSMUSG00000046573	Lyrm4	BC034664|Gm903	LYR motif containing 4	protein-coding
mm_113018.1	chr13	21981518	21981522	+	1	NA	5' UTR (NM_001162929, exon 1 of 2)	5' UTR (NM_001162929, exon 1 of 2)	326	NM_001162929	195236	Mm.204664	NM_001162928	ENSMUSG00000016982	Pom121l2	Gm24	POM121 membrane glycoprotein-like 2 (rat)	protein-coding
mm_148178.1	chr18	78142168	78142176	-	1	NA	promoter-TSS (NM_001171011)	promoter-TSS (NM_001171011)	-53	NM_001171011	108052	Mm.33832	NM_028122	ENSMUSG00000059336	Slc14a1	2610507K20Rik|3021401A05Rik|UT-B|Utb1	solute carrier family 14 (urea transporter), member 1	protein-coding
mm_7374.1	chr1	106768980	106768984	-	1	NA	Intergenic	Intergenic	-9240	NM_001316750	70750	Mm.458911	NM_027534	ENSMUSG00000009905	Kdsr	6330410P18Rik|9430079B08Rik|Fvt1	3-ketodihydrosphingosine reductase	protein-coding
mm_54896.1	chr6	47302667	47302667	-	1	NA	Intergenic	ID_B1|SINE|B4	58271	NM_025771	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding
mm_163855.1	chr14	19418468	19418535	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	184086	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_68398.1	chr7	109600783	109600784	-	1	NA	intron (NM_001001326, intron 1 of 19)	B1F|SINE|Alu	15785	NR_037617	76954	Mm.252009	NM_029811	ENSMUSG00000031024	St5	2010004M01Rik|2610305K15Rik	suppression of tumorigenicity 5	protein-coding
mm_108971.1	chr12	102554967	102554984	+	1	NA	promoter-TSS (NM_007693)	promoter-TSS (NM_007693)	34	NM_007693	12652	Mm.4137	NM_007693	ENSMUSG00000021194	Chga	ChrA|cgA	chromogranin A	protein-coding
mm_93642.1	chr10	117339748	117339750	-	1	NA	Intergenic	Intergenic	37224	NM_001013391	432508	Mm.478881	NM_001013391	ENSMUSG00000055531	Cpsf6	4733401N12Rik|AI256641|CFIM|CFIM68|HPBRII-4|HPBRII-7	cleavage and polyadenylation specific factor 6	protein-coding
mm_112582.1	chr13	13710220	13710238	+	1	NA	intron (NM_010748, intron 36 of 52)	B2_Mm2|SINE|B2	-73830	NM_001302997	14706	Mm.215394	NM_010317	ENSMUSG00000021303	Gng4	-	guanine nucleotide binding protein (G protein), gamma 4	protein-coding
mm_169241.1	chr13	74522488	74522499	-	1	NA	Intergenic	Intergenic	-28543	NM_146231	235956	Mm.296909	NM_146231	ENSMUSG00000069208	Zfp825	-	zinc finger protein 825	protein-coding
mm_90442.1	chr10	127658222	127658229	+	1	NA	exon (NM_009284, exon 17 of 22)	exon (NM_009284, exon 17 of 22)	8478	NM_001122895	17937	Mm.336898	NM_008668	ENSMUSG00000025402	Nab2	AI451907	Ngfi-A binding protein 2	protein-coding
mm_3336.1	chr1	137961471	137961477	+	1	NA	Intergenic	(GGGA)n|Simple_repeat|Simple_repeat	-4981	NR_029795	735252		NR_029795	ENSMUSG00000065565	Mir181a-1	Mirn181a-1|Mirn213|miR-213|mir-181a-1|mmu-mir-213	microRNA 181a-1	ncRNA
mm_91008.1	chr10	14705460	14705515	-	1	NA	promoter-TSS (NM_025418)	promoter-TSS (NM_025418)	2	NM_025418	66201	Mm.227983	NM_025418	ENSMUSG00000019868	Vta1	1110001D18Rik|1110059P08Rik|AU040813|C85340|LIP5|SBP1	vesicle (multivesicular body) trafficking 1	protein-coding
mm_112697.1	chr13	17695410	17695436	+	1	NA	promoter-TSS (NM_138654)	promoter-TSS (NM_138654)	10	NM_025479	66308	Mm.291109	NM_025479	ENSMUSG00000012429	Mplkip	2810021B07Rik|C330007M08Rik|Ttdn1	M-phase specific PLK1 intereacting protein	protein-coding
mm_131518.1	chr16	17561993	17562042	+	1	NA	promoter-TSS (NM_001145435)	promoter-TSS (NM_001145435)	132	NM_001159561	18440	Mm.8032	NM_011028	ENSMUSG00000022758	P2rx6	P2rxl1|P2x6|P2xm	purinergic receptor P2X, ligand-gated ion channel, 6	protein-coding
mm_78877.1	chr9	44486589	44486624	+	1	NA	Intergenic	Intergenic	-12530	NM_030256	80288	Mm.370270	NM_030256	ENSMUSG00000063382	Bcl9l	B9L|BC003321|BCL9-2|DLNB11	B cell CLL/lymphoma 9-like	protein-coding
mm_67724.1	chr7	90068061	90068064	-	1	NA	Intergenic	Intergenic	38903	NR_110364	319711	Mm.31753	NR_015614	ENSMUSG00000097585	E230029C05Rik	AI452102|B230337J15	RIKEN cDNA E230029C05 gene	ncRNA
mm_39422.1	chr5	15934954	15934962	+	1	NA	5' UTR (NM_001110843, exon 1 of 39)	5' UTR (NM_001110843, exon 1 of 39)	267	NM_001110844	12293	Mm.159842	NM_009784	ENSMUSG00000040118	Cacna2d1	Ca(v)alpha2delta1|Cacna2|Cchl2a	calcium channel, voltage-dependent, alpha2/delta subunit 1	protein-coding
mm_40070.1	chr5	34288645	34288670	+	1	NA	promoter-TSS (NM_001015039)	promoter-TSS (NM_001015039)	-333	NM_001015039	231125	Mm.113388	NM_001015039	ENSMUSG00000037224	Zfyve28	9630058O20Rik|Gm146|mKIAA1643	zinc finger, FYVE domain containing 28	protein-coding
mm_100077.1	chr11	115463745	115463753	+	1	NA	intron (NM_001080934, intron 1 of 3)	intron (NM_001080934, intron 1 of 3)	1276	NM_001080934	217316	Mm.25773	NM_001080934	ENSMUSG00000045775	Slc16a5	A130015N09Rik|MCT 5|MCT 6|MCT5	solute carrier family 16 (monocarboxylic acid transporters), member 5	protein-coding
mm_64160.1	chr7	141360209	141360230	+	1	NA	non-coding (NR_033532, exon 2 of 2)	non-coding (NR_033532, exon 2 of 2)	4891	NR_033532	320871	Mm.475463	NM_177280	ENSMUSG00000086844	B230206H07Rik	-	RIKEN cDNA B230206H07 gene	ncRNA
mm_138298.1	chr17	34630943	34630954	+	1	NA	exon (NM_030890, exon 2 of 4)	exon (NM_030890, exon 2 of 4)	1262	NM_030890	260297	Mm.390965	NM_030890	ENSMUSG00000015476	Prrt1	Bat-4|Bat4|D17H6S54E|DSPD1|G5b|NG5|ORF31	proline-rich transmembrane protein 1	protein-coding
mm_6607.1	chr1	75375003	75375031	-	1	NA	promoter-TSS (NM_007463)	promoter-TSS (NM_007463)	-2	NR_037976	100503248	Mm.403916	NR_037976	ENSMUSG00000085653	Gm15179	OTTMUSG00000019417	predicted gene 15179	ncRNA
mm_59944.1	chr7	30425328	30425334	+	1	NA	exon (NM_172142, exon 4 of 11)	exon (NM_172142, exon 4 of 11)	2027	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_112550.1	chr13	12408521	12408555	+	1	NA	intron (NM_144835, intron 12 of 44)	intron (NM_144835, intron 12 of 44)	13163	NM_144835	217995	Mm.171186	NM_144835	ENSMUSG00000050244	Heatr1	AA517551|B130016L12Rik|BC019693	HEAT repeat containing 1	protein-coding
mm_61065.1	chr7	50599181	50599201	+	1	NA	promoter-TSS (NM_172901)	promoter-TSS (NM_172901)	1	NM_172901	243996	Mm.443270	NM_172901	ENSMUSG00000084234	4933405O20Rik	-	RIKEN cDNA 4933405O20 gene	protein-coding
mm_169777.1	chr16	10801303	10801319	+	1	NA	Intergenic	Intergenic	-4488	NM_013637	19118	Mm.42733	NM_013637	ENSMUSG00000022501	Prm1	Prm-1	protamine 1	protein-coding
mm_109930.1	chr12	8916453	8916463	-	1	NA	Intergenic	Intergenic	-4849	NM_008640	17775	Mm.30071	NM_008640	ENSMUSG00000020585	Laptm4a	AA286466|LAPTM4|MTP|Mtrp|mKIAA0108	lysosomal-associated protein transmembrane 4A	protein-coding
mm_102313.1	chr11	56040986	56041023	-	1	NA	promoter-TSS (NM_153079)	promoter-TSS (NM_153079)	-17	NM_153079	216749	Mm.213205	NM_153079	ENSMUSG00000037393	Nmur2	Nmu2r	neuromedin U receptor 2	protein-coding
mm_64990.1	chr7	16916919	16916938	-	1	NA	3' UTR (NM_007590, exon 6 of 6)	3' UTR (NM_007590, exon 6 of 6)	7104	NM_007590	12315	Mm.288630	NM_007590	ENSMUSG00000019370	Calm3	CaMA|R75142	calmodulin 3	protein-coding
mm_112725.1	chr13	19192520	19192529	+	1	NA	Intergenic	Intergenic	203289	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_140430.1	chr17	88112092	88112113	+	1	NA	Intergenic	Intergenic	-13410	NM_001190356	225058	Mm.312053	NM_001190356		Gm4832	EG225058	predicted gene 4832	protein-coding
mm_149900.1	chr19	25505834	25505845	+	1	NA	5' UTR (NM_015826, exon 1 of 5)	5' UTR (NM_015826, exon 1 of 5)	133	NM_015826	50796	Mm.391208	NM_015826	ENSMUSG00000024837	Dmrt1	-	doublesex and mab-3 related transcription factor 1	protein-coding
mm_88686.1	chr10	80115780	80115824	+	1	NA	promoter-TSS (NM_011492)	promoter-TSS (NM_011492)	-1	NM_001301853	20869	Mm.44231	NM_011492	ENSMUSG00000003068	Stk11	AA408040|Lkb1|Par-4|R75140	serine/threonine kinase 11	protein-coding
mm_133980.1	chr16	4541795	4541839	-	1	NA	Intergenic	CpG	17903	NM_031182	83383	Mm.273210	NM_031182	ENSMUSG00000005718	Tfap4	AI642933|AP-4|D930048N17Rik|Tcfap4|bHLHc41	transcription factor AP4	protein-coding
mm_2526.1	chr1	106861145	106861197	+	1	NA	promoter-TSS (NM_009257)	promoter-TSS (NM_009257)	-9	NM_009257	20724	Mm.268618	NM_009257	ENSMUSG00000067006	Serpinb5	1110036M19Rik|AI462524|AI646751|Maspin|PI-5|Spi7|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 5	protein-coding
mm_55315.1	chr6	54992947	54992957	-	1	NA	promoter-TSS (NM_026637)	promoter-TSS (NM_026637)	-85	NM_026637	110175	Mm.294708	NM_026637	ENSMUSG00000002797	Ggct	A030007L17Rik|AA673177|Gctg|Ggc	gamma-glutamyl cyclotransferase	protein-coding
mm_61007.1	chr7	49350317	49350317	+	1	NA	intron (NM_175272, intron 1 of 37)	intron (NM_175272, intron 1 of 37)	104128	NM_175272	78286	Mm.333881	NM_175272	ENSMUSG00000052512	Nav2	5330421F07Rik|AU067780|BQ960892|HELAD1|POMFIL2|RAINB1|RAINB2|Unc53H2|mKIAA3015	neuron navigator 2	protein-coding
mm_162604.1	chr1	183221447	183221457	-	1	NA	promoter-TSS (NM_001278219)	promoter-TSS (NM_001278219)	77	NM_001278218	68897	Mm.327216	NM_026866	ENSMUSG00000030768	Disp1	1190008H24Rik|DispA	dispatched RND transporter family member 1	protein-coding
mm_87712.1	chr10	60042086	60042117	+	1	NA	intron (NM_026937, intron 5 of 10)	intron (NM_026937, intron 5 of 10)	38774	NM_001199187	69090	Mm.155839	NM_026937	ENSMUSG00000044475	Ascc1	1810015P09Rik|AI550520|ASC1p50|CGI-18	activating signal cointegrator 1 complex subunit 1	protein-coding
mm_110334.1	chr12	35642355	35642370	-	1	NA	Intergenic	RLTR13D6|LTR|ERVK	43942	NR_045051	71581	Mm.100110	NR_045050		9130015A21Rik	100043575|Gm4527	RIKEN cDNA 9130015A21 gene	ncRNA
mm_71937.1	chr8	70315837	70315846	+	1	NA	promoter-TSS (NM_001163282)	promoter-TSS (NM_001163282)	66	NM_001163282	14559	Mm.258280	NM_008107	ENSMUSG00000087408	Gdf1	AI385651|Gdf-1	growth differentiation factor 1	protein-coding
mm_64176.1	chr7	141457999	141458009	+	1	NA	intron (NM_001163689, intron 3 of 8)	intron (NM_001163689, intron 3 of 8)	2816	NM_001163689	66853	Mm.29998	NM_025802	ENSMUSG00000025509	Pnpla2	0610039C21Rik|1110001C14Rik|Atgl|TTS-2.2	patatin-like phospholipase domain containing 2	protein-coding
mm_18293.1	chr2	52676572	52676588	-	1	NA	promoter-TSS (NM_001037099)	promoter-TSS (NM_001037099)	29	NM_001037099	12298	Mm.330223	NM_146123	ENSMUSG00000017412	Cacnb4	3110038O15Rik|Cchb4|lh	calcium channel, voltage-dependent, beta 4 subunit	protein-coding
mm_33248.1	chr4	127109809	127109813	+	1	NA	intron (NR_104366, intron 12 of 15)	intron (NR_104366, intron 12 of 15)	-16232	NM_001099319	100039968	Mm.392655	NM_001099319	ENSMUSG00000070737	Tmem35b	Gm12942|OTTMUSG00000009332|Zmym6nb	transmembrane protein 35B	protein-coding
mm_18712.1	chr2	72351428	72351433	-	1	NA	intron (NM_023057, intron 2 of 19)	intron (NM_023057, intron 2 of 19)	65729	NM_178084	65964	Mm.304143	NM_023057	ENSMUSG00000004085	Map3k20	AV006891|B230120H23Rik|MLTK|MLTKalpha|MLTKbeta|Zak	mitogen-activated protein kinase kinase kinase 20	protein-coding
mm_111212.1	chr12	84400912	84400925	-	1	NA	promoter-TSS (NM_001286049)	promoter-TSS (NM_001286049)	16	NM_001286058	12499	Mm.10211	NM_007647	ENSMUSG00000021236	Entpd5	AI196558|AI987697|Cd39l4|ER-UDPase|NTPDase-5|NTPDase5|Pcph|mNTPase	ectonucleoside triphosphate diphosphohydrolase 5	protein-coding
mm_166270.1	chr5	90472113	90472120	+	1	NA	exon (NM_009654, exon 11 of 15)	exon (NM_009654, exon 11 of 15)	11246	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_5663.1	chr1	42693118	42693137	-	1	NA	intron (NR_027826, intron 1 of 3)	intron (NR_027826, intron 1 of 3)	1698	NR_027826	66297	Mm.45203	NM_183252	ENSMUSG00000060424	Pantr1	2610017I09Rik|Pou3f3os|linc-Brn1a	POU domain, class 3, transcription factor 3 adjacent noncoding transcript 1	ncRNA
mm_165999.1	chr4	115090997	115091006	+	1	NA	intron (NM_026018, intron 2 of 4)	intron (NM_026018, intron 2 of 4)	2293	NM_001164557	67182	Mm.30181	NM_026018	ENSMUSG00000028716	Pdzk1ip1	0610007F13Rik|2700030M23Rik|AU046042|Map17	PDZK1 interacting protein 1	protein-coding
mm_158180.1	chrX	103981169	103981181	-	1	NA	5' UTR (NM_011276, exon 1 of 5)	5' UTR (NM_011276, exon 1 of 5)	109	NM_011276	19820	Mm.427762	NM_011276	ENSMUSG00000056537	Rlim	AL022832|AW743871|Ha1r|Rlim1|Rnf12	ring finger protein, LIM domain interacting	protein-coding
mm_171603.1	chr4	148152078	148152080	-	1	NA	promoter-TSS (NM_001163707)	promoter-TSS (NM_001163707)	-50	NM_001163706	50762	Mm.27445	NM_015797	ENSMUSG00000055401	Fbxo6	AA408845|FBG2|Fbs2|Fbx6b|Fbxo6b	F-box protein 6	protein-coding
mm_82572.1	chr9	21091975	21092007	-	1	NA	promoter-TSS (NM_027911)	promoter-TSS (NM_027911)	-3	NM_027911	71766	Mm.196137	NM_027911	ENSMUSG00000010205	Raver1	1300006N24Rik|AA050359|mKIAA1978	ribonucleoprotein, PTB-binding 1	protein-coding
mm_14754.1	chr2	144698242	144698256	+	1	NA	intron (NM_025314, intron 4 of 5)	intron (NM_025314, intron 4 of 5)	98296	NM_025314	66044	Mm.28109	NM_025314	ENSMUSG00000027430	Dtd1	0610006H08Rik|DUE-B|Hars2	D-tyrosyl-tRNA deacylase 1	protein-coding
mm_140632.1	chr17	12507356	12507360	-	1	NA	5' UTR (NM_011395, exon 1 of 11)	5' UTR (NM_011395, exon 1 of 11)	346	NM_011395	20519	Mm.99252	NM_011395	ENSMUSG00000023828	Slc22a3	EMT|Oct3|Orct3|Slca22a3	solute carrier family 22 (organic cation transporter), member 3	protein-coding
mm_1308.1	chr1	64927727	64927743	+	1	NA	intron (NM_001039493, intron 2 of 7)	PB1D10|SINE|Alu	29089	NM_001039493	241075	Mm.239534	NM_175509	ENSMUSG00000051344	Plekhm3	9430067K14Rik|A230102O09Rik|AI449570|DAPR|Plekhm1l	pleckstrin homology domain containing, family M, member 3	protein-coding
mm_12145.1	chr2	61804687	61804701	+	1	NA	5' UTR (NM_009322, exon 1 of 6)	5' UTR (NM_009322, exon 1 of 6)	241	NM_009322	21375	Mm.308525	NM_009322	ENSMUSG00000035033	Tbr1	-	T-box brain gene 1	protein-coding
mm_131249.1	chr16	10545359	10545388	+	1	NA	promoter-TSS (NM_177562)	promoter-TSS (NM_177562)	34	NM_001204229	74374	Mm.159176	NM_177562	ENSMUSG00000068663	Clec16a	4932416N17Rik|curt|mKIAA0350	C-type lectin domain family 16, member A	protein-coding
mm_144560.1	chr18	31759855	31759868	+	1	NA	promoter-TSS (NM_001242430)	promoter-TSS (NM_001242430)	37	NM_153515	225339	Mm.290804	NM_153515	ENSMUSG00000041915	Ammecr1l	5430429D03Rik|AU022236|AU040755|AW111353|E230022H04Rik	AMME chromosomal region gene 1-like	protein-coding
mm_55899.1	chr6	83575823	83575832	-	1	NA	intron (NR_078345, intron 2 of 7)	intron (NR_078345, intron 2 of 7)	-3323	NM_024239	70527	Mm.32801	NM_024239	ENSMUSG00000006906	Stambp	5330424L14Rik|5730422L11Rik|AW107289|Amsh|mKIAA4198	STAM binding protein	protein-coding
mm_83016.1	chr9	36784818	36784824	-	1	NA	intron (NM_007915, intron 7 of 10)	intron (NM_007915, intron 7 of 10)	12247	NM_007915	13663	Mm.4337	NM_007915	ENSMUSG00000062762	Ei24	AA536736|AI115355|PIG8	etoposide induced 2.4 mRNA	protein-coding
mm_65790.1	chr7	28893981	28893992	-	1	NA	TTS (NM_001110807)	TTS (NM_001110807)	12330	NM_001110807	60594	Mm.476990	NM_021894	ENSMUSG00000054083	Capn12	CANP 12	calpain 12	protein-coding
mm_54882.1	chr6	42710037	42710120	-	1	NA	Intergenic	Intergenic	-17019	NM_029930	77574	Mm.24652	NM_029930	ENSMUSG00000036667	Tcaf1	2810407D09Rik|3321401G04Rik|A230020K05Rik|AI848529|Fam115a	TRPM8 channel-associated factor 1	protein-coding
mm_14941.1	chr2	151572607	151572627	+	1	NA	promoter-TSS (NM_145535)	promoter-TSS (NM_145535)	-6	NM_145535	228765	Mm.32068	NM_145535	ENSMUSG00000027456	Sdcbp2	-	syndecan binding protein (syntenin) 2	protein-coding
mm_125451.1	chr15	51877440	51877506	+	1	NA	promoter-TSS (NM_030132)	promoter-TSS (NM_030132)	32	NM_030132	78581	Mm.176347	NM_030132	ENSMUSG00000022313	Utp23	1700010I21Rik|AI662478|BB238373|D530033C11Rik	UTP23 small subunit processome component	protein-coding
mm_157611.1	chrX	53776322	53776332	-	1	NA	promoter-TSS (NM_001009549)	promoter-TSS (NM_001009549)	67	NM_001009549	333473	Mm.327378	NM_001009549	ENSMUSG00000059334	Zfp36l3	AY661338	zinc finger protein 36, C3H type-like 3	protein-coding
mm_72557.1	chr8	84073859	84073874	+	1	NA	exon (NM_009055, exon 2 of 21)	exon (NM_009055, exon 2 of 21)	7030	NM_009055	19724	Mm.7892	NM_009055	ENSMUSG00000031706	Rfx1	AI047719|AI385641	regulatory factor X, 1 (influences HLA class II expression)	protein-coding
mm_25023.1	chr3	98109200	98109218	+	1	NA	intron (NM_010928, intron 12 of 33)	B4|SINE|B4	-51425	NM_027665	71078	Mm.50711	NM_027665	ENSMUSG00000043468	Adam30	4933424D07Rik|svph4	a disintegrin and metallopeptidase domain 30	protein-coding
mm_171223.1	chr3	60494900	60494908	-	1	NA	intron (NM_001253713, intron 2 of 9)	IAPLTR1_Mm|LTR|ERVK	-6275	NM_001253711	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_60503.1	chr7	44479409	44479430	+	1	NA	Intergenic	L1MC4|LINE|L1	-5098	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_57736.1	chr6	128974899	128974919	-	1	NA	promoter-TSS (NR_106107).2	promoter-TSS (NR_106107).2	-14	NR_106107	102465757		NR_106107	ENSMUSG00000098359	Mir7649	mmu-mir-7649	microRNA 7649	ncRNA
mm_141845.1	chr17	34743850	34743890	-	1	NA	promoter-TSS (NM_009780)	promoter-TSS (NM_009780)	27	NM_009780	12268	Mm.477109	NM_009780	ENSMUSG00000073418	C4b	C4|Ss	complement component 4B (Chido blood group)	protein-coding
mm_49489.1	chr6	29694183	29694194	+	1	NA	promoter-TSS (NM_001301407)	promoter-TSS (NM_001301407)	-26	NM_001301407	232670	Mm.225289	NM_146173	ENSMUSG00000001763	Tspan33	1300010A20Rik|Pen	tetraspanin 33	protein-coding
mm_6875.1	chr1	84341078	84341097	-	1	NA	Intergenic	L1_Mus1|LINE|L1	-56442	NM_001003948	98496	Mm.187470	NM_001003948	ENSMUSG00000045658	Pid1	5033414K04Rik|NYGGF4	phosphotyrosine interaction domain containing 1	protein-coding
mm_84675.1	chr9	72077488	72077501	-	1	NA	intron (NM_001253862, intron 3 of 19)	intron (NM_001253862, intron 3 of 19)	33707	NM_001253862	21406	Mm.171615	NM_011544	ENSMUSG00000032228	Tcf12	A130037E08Rik|ALF1|HEB|HEBAlt|HTF-4|HTF4|ME1|REB|bHLHb20	transcription factor 12	protein-coding
mm_157310.1	chrX	20950546	20950593	-	1	NA	promoter-TSS (NM_007922)	promoter-TSS (NM_007922)	39	NM_007922	13712	Mm.405823	NM_007922	ENSMUSG00000009406	Elk1	Elk-1	ELK1, member of ETS oncogene family	protein-coding
mm_71956.1	chr8	70511555	70511562	+	1	NA	Intergenic	Lx7|LINE|L1	-1191	NM_019883	22186	Mm.297372	NM_019883	ENSMUSG00000090137	Uba52	D8Ertd21e|Gm1863|Rps27a|Ubb|Ubc	ubiquitin A-52 residue ribosomal protein fusion product 1	protein-coding
mm_131971.1	chr16	24879375	24879403	+	1	NA	intron (NM_001145954, intron 4 of 7)	intron (NM_001145954, intron 4 of 7)	157534	NM_001145954	210126	Mm.209385	NM_178665	ENSMUSG00000033306	Lpp	9430020K16Rik|AA959454|AU024130|B130055L10Rik|C79715|D630048H16	LIM domain containing preferred translocation partner in lipoma	protein-coding
mm_86861.1	chr10	21992207	21992213	+	1	NA	promoter-TSS (NM_001161849)	promoter-TSS (NM_001161849)	-13	NM_001161849	20393	Mm.28405	NM_011361	ENSMUSG00000019970	Sgk1	Sgk	serum/glucocorticoid regulated kinase 1	protein-coding
mm_131933.1	chr16	23612871	23612895	+	1	NA	exon (NM_023386, exon 2 of 2)	exon (NM_023386, exon 2 of 2)	2964	NM_023386	67775	Mm.475107	NM_023386	ENSMUSG00000033355	Rtp4	5830458K16Rik|Ifrg28	receptor transporter protein 4	protein-coding
mm_140982.1	chr17	24719890	24719916	-	1	NA	promoter-TSS (NR_028515)	promoter-TSS (NR_028515)	62	NR_027900	73474	Mm.443320	NR_027900	ENSMUSG00000090101	Snhg9	1700072N11Rik	small nucleolar RNA host gene 9	ncRNA
mm_5976.1	chr1	57970033	57970065	-	1	NA	promoter-TSS (NM_001159864)	promoter-TSS (NM_001159864)	35	NM_001159864	51960	Mm.339711	NM_030211	ENSMUSG00000054770	Kctd18	4932411A20Rik|6530404F10Rik	potassium channel tetramerisation domain containing 18	protein-coding
mm_167660.1	chr9	71215368	71215380	+	1	NA	promoter-TSS (NM_009022)	promoter-TSS (NM_009022)	12	NR_110518	100041660	Mm.487231	NR_110518		Gm3458	-	predicted gene 3458	ncRNA
mm_56582.1	chr6	106794212	106794246	-	1	NA	exon (NM_021449, exon 4 of 11)	exon (NM_021449, exon 4 of 11)	5858	NM_021449	58799	Mm.290085	NM_021449	ENSMUSG00000005362	Crbn	2610203G15Rik|2900045O07Rik|AF229032|AW108261|piL	cereblon	protein-coding
mm_47530.1	chr5	124189689	124189697	-	1	NA	intron (NM_011256, intron 2 of 24)	intron (NM_011256, intron 2 of 24)	-2511	NM_001289472	19679	Mm.44261	NM_011256	ENSMUSG00000029406	Pitpnm2	NIR3|RDGBA2|Rdgb2|mKIAA1457	phosphatidylinositol transfer protein, membrane-associated 2	protein-coding
mm_159371.1	chr3	88775152	88775152	-	1	NA	Intergenic	CpG	-1905	NR_028359	100302730	Mm.482358	NR_028359		5830417I10Rik	3632445O20Rik|AA387005	gon-4-like pseudogene	pseudo
mm_140842.1	chr17	23673826	23673887	-	1	NA	promoter-TSS (NM_001008425)	promoter-TSS (NM_001008425)	-86	NM_001008425	386612	Mm.328831	NM_001008425	ENSMUSG00000041319	Thoc6	F830014G06Rik|Wdr58	THO complex 6	protein-coding
mm_36832.1	chr4	106316243	106316260	-	1	NA	promoter-TSS (NM_183225)	promoter-TSS (NM_183225)	38	NM_183225	329908	Mm.234544	NM_183225	ENSMUSG00000028514	Usp24	2700066K03Rik|2810030C21Rik|AI414051|B130021E18|C79851	ubiquitin specific peptidase 24	protein-coding
mm_56938.1	chr6	119921612	119921615	-	1	NA	TTS (NM_001166383)	TTS (NM_001166383)	18915	NM_001166381	19365	Mm.149	NM_011236	ENSMUSG00000030166	Rad52	Rad52yh	RAD52 homolog, DNA repair protein	protein-coding
mm_95898.1	chr11	58201351	58201371	+	1	NA	intron (NM_018738, intron 1 of 2)	intron (NM_018738, intron 1 of 2)	1805	NM_018738	16145	Mm.33902	NM_018738	ENSMUSG00000078853	Igtp	AW558444|Irgm3	interferon gamma induced GTPase	protein-coding
mm_1288.1	chr1	64235710	64235712	+	1	NA	Intergenic	MER53|DNA|hAT	-114322	NM_033563	93691	Mm.29466	NM_033563	ENSMUSG00000025959	Klf7	9830124P08Rik	Kruppel-like factor 7 (ubiquitous)	protein-coding
mm_157891.1	chrX	76129030	76129071	-	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	-135256	NM_001013760	238829	Mm.292319	NM_001013760	ENSMUSG00000071738	Cldn34b3	EG238829|Gm4937	claudin 34B3	protein-coding
mm_163666.1	chr13	79022616	79022616	+	1	NA	Intergenic	Intergenic	-823743	NM_010151	13865	Mm.439653	NM_010151	ENSMUSG00000069171	Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR-3|EAR3|Erbal3|SVP44|Tcfcoup1	nuclear receptor subfamily 2, group F, member 1	protein-coding
mm_162385.1	chr1	74385288	74385294	+	1	NA	exon (NM_013612, exon 14 of 15)	exon (NM_013612, exon 14 of 15)	-6318	NM_153088	227292	Mm.165042	NM_153088	ENSMUSG00000026176	Ctdsp1	GIP|NLIIF|Nif3|SCP1	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 1	protein-coding
mm_155533.1	chrX	74303817	74303833	+	1	NA	exon (NM_018794, exon 10 of 10)	exon (NM_018794, exon 10 of 10)	-1187	NM_010273	14567	Mm.205830	NM_010273	ENSMUSG00000015291	Gdi1	GDIA|GDIalpha	guanosine diphosphate (GDP) dissociation inhibitor 1	protein-coding
mm_76066.1	chr8	78436641	78436649	-	1	NA	promoter-TSS (NM_138944)	promoter-TSS (NM_138944)	7	NM_138944	18997	Mm.234261	NM_138944	ENSMUSG00000031688	Pou4f2	Brn-3.2|Brn-3b|Brn3b|Pou4f-rs1|mBrn3-3R	POU domain, class 4, transcription factor 2	protein-coding
mm_24475.1	chr3	90692718	90692749	+	1	NA	3' UTR (NM_001281852, exon 3 of 3)	3' UTR (NM_001281852, exon 3 of 3)	2988	NM_001281852	20202	Mm.2128	NM_009114	ENSMUSG00000056071	S100a9	60B8Ag|AW546964|BEE22|Cagb|GAGB|L1Ag|MRP14|p14	S100 calcium binding protein A9 (calgranulin B)	protein-coding
mm_51775.1	chr6	88093922	88093946	+	1	NA	exon (NM_133933, exon 4 of 10)	exon (NM_133933, exon 4 of 10)	9461	NM_133933	103963	Mm.188544	NM_133933	ENSMUSG00000030062	Rpn1	AU018702|D6Wsu137e|Rpn-1	ribophorin I	protein-coding
mm_79686.1	chr9	59951291	59951302	+	1	NA	promoter-TSS (NM_001101600)	promoter-TSS (NM_001101600)	2	NM_001101600	665389	Mm.335214	NM_001101600		Gm7616	EG665389	predicted gene 7616	protein-coding
mm_10836.1	chr2	24919753	24919783	+	1	NA	promoter-TSS (NM_001109687)	promoter-TSS (NM_001109687)	-159	NM_001109686	77683	Mm.24176	NM_172545	ENSMUSG00000036893	Ehmt1	9230102N17Rik|D330003E03|Eu-HMTase1|GLP|GLP1|KMT1D|mKIAA1876	euchromatic histone methyltransferase 1	protein-coding
mm_42766.1	chr5	121220386	121220390	+	1	NA	5' UTR (NM_181421, exon 1 of 76)	5' UTR (NM_181421, exon 1 of 76)	169	NM_181421	269700	Mm.184589	NM_181421	ENSMUSG00000042744	Gm15800	A130010L24|AU042671|BC019639|EG545802|OTTMUSG00000026283|mKIAA0614	predicted gene 15800	protein-coding
mm_23248.1	chr3	51224546	51224560	+	1	NA	5' UTR (NM_009834, exon 1 of 3)	5' UTR (NM_009834, exon 1 of 3)	106	NM_009834	12457	Mm.86541	NM_009834	ENSMUSG00000023087	Noct	AU043840|Ccr4|Ccrn4l	nocturnin	protein-coding
mm_102544.1	chr11	61267424	61267474	-	1	NA	promoter-TSS (NM_001331115)	promoter-TSS (NM_001331115)	79	NM_001331115	11671	Mm.398221	NM_007437	ENSMUSG00000010025	Aldh3a2	AI194803|Ahd-3|Ahd-3r|Ahd3|Ahd3-r|Aldh4|Aldh4-r|FALDH	aldehyde dehydrogenase family 3, subfamily A2	protein-coding
mm_18617.1	chr2	68471926	68471944	-	1	NA	promoter-TSS (NM_016866)	promoter-TSS (NM_016866)	46	NM_016866	53416	Mm.198414	NM_016866	ENSMUSG00000027030	Stk39	AW227544|AW556857|DCHT|RF005|Rnl5|SPAK	serine/threonine kinase 39	protein-coding
mm_138189.1	chr17	34269119	34269127	+	1	NA	3' UTR (NM_207105, exon 6 of 6)	3' UTR (NM_207105, exon 6 of 6)	5896	NM_207105	14961	Mm.254067	NM_207105	ENSMUSG00000073421	H2-Ab1	AI845868|Abeta|H-2Ab|H2-Ab|I-Abeta|IAb|Ia-2|Ia2|Rmcs1	histocompatibility 2, class II antigen A, beta 1	protein-coding
mm_138161.1	chr17	34257935	34257965	+	1	NA	Intergenic	Intergenic	-5277	NM_207105	14961	Mm.254067	NM_207105	ENSMUSG00000073421	H2-Ab1	AI845868|Abeta|H-2Ab|H2-Ab|I-Abeta|IAb|Ia-2|Ia2|Rmcs1	histocompatibility 2, class II antigen A, beta 1	protein-coding
mm_7519.1	chr1	124045524	124045571	-	1	NA	promoter-TSS (NM_199021)	promoter-TSS (NM_199021)	12	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_114791.1	chr13	89540706	89540712	+	1	NA	promoter-TSS (NM_013500)	promoter-TSS (NM_013500)	73	NM_013500	12950	Mm.266790	NM_013500	ENSMUSG00000021613	Hapln1	BB099155|CLP|Crtl1|Crtl1l|LP|LP-1	hyaluronan and proteoglycan link protein 1	protein-coding
mm_130748.1	chr15	101261550	101261562	-	1	NA	Intergenic	Intergenic	-5290	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_95891.1	chr11	58183796	58183817	+	1	NA	promoter-TSS (NM_001135115)	promoter-TSS (NM_001135115)	-37	NM_001135115	631323	Mm.394103	NM_001135115		Gm12250	Irgb10|OTTMUSG00000005723	predicted gene 12250	protein-coding
mm_77158.1	chr8	111687136	111687144	-	1	NA	exon (NM_025583, exon 6 of 7)	exon (NM_025583, exon 6 of 7)	2534	NR_106044	102466993		NR_106044	ENSMUSG00000099129	Mir7076	Gm27318|mmu-mir-7076	microRNA 7076	ncRNA
mm_97124.1	chr11	74925838	74925867	+	1	NA	promoter-TSS (NM_001163311)	promoter-TSS (NM_001163311)	-20	NM_001002764	103677	Mm.288460	NM_001002764	ENSMUSG00000038290	Smg6	AI317223|AU041178	Smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans)	protein-coding
mm_39905.1	chr5	31251912	31251922	+	1	NA	TTS (NM_147201)	TTS (NM_147201)	211	NM_027221	69815	Mm.389609	NM_027221	ENSMUSG00000029149	Krtcap3	2010001C09Rik|AW321088|Kcp3	keratinocyte associated protein 3	protein-coding
mm_78118.1	chr9	20643388	20643396	+	1	NA	promoter-TSS (NM_013911)	promoter-TSS (NM_013911)	74	NM_025401	66177	Mm.390165	NM_025401	ENSMUSG00000084786	Ubl5	1110030M22Rik|beacon	ubiquitin-like 5	protein-coding
mm_73937.1	chr8	120042963	120042972	+	1	NA	intron (NM_030209, intron 14 of 14)	intron (NM_030209, intron 14 of 14)	50529	NM_001310635	78892	Mm.264680	NM_030209	ENSMUSG00000031825	Crispld2	1810049K24Rik|Lcrisp2|Lgl1|coffeecrisp	cysteine-rich secretory protein LCCL domain containing 2	protein-coding
mm_20235.1	chr2	126151969	126152009	-	1	NA	promoter-TSS (NM_026981)	promoter-TSS (NM_026981)	15	NM_029455	75823	Mm.444732	NM_029455	ENSMUSG00000027209	Fam227b	4930525F21Rik	family with sequence similarity 227, member B	protein-coding
mm_56774.1	chr6	116628956	116629004	-	1	NA	promoter-TSS (NM_026057)	promoter-TSS (NM_026057)	19	NM_026057	67255	Mm.18810	NM_026057	ENSMUSG00000059878	Zfp422	2900028O21Rik|AU041373|KOX15|Krox-25-2|Krox-26|Krox25|Krox26|Znf22	zinc finger protein 422	protein-coding
mm_22031.1	chr2	168068255	168068303	-	1	NA	Intergenic	Intergenic	-12725	NM_021409	58220	Mm.292834	NM_021409	ENSMUSG00000044641	Pard6b	AV025615|Par6b	par-6 family cell polarity regulator beta	protein-coding
mm_38509.1	chr4	141139800	141139808	-	1	NA	promoter-TSS (NR_102344)	promoter-TSS (NR_102344)	-8	NR_102343	213491	Mm.332006	NM_174996	ENSMUSG00000040842	Szrd1	1110022I03|D4Ertd22e	SUZ RNA binding domain containing 1	protein-coding
mm_49533.1	chr6	30172861	30172870	+	1	NA	intron (NR_126541, intron 1 of 1)	intron (NR_126541, intron 1 of 1)	1260	NR_126540	101447999		NR_126540		Mirc35hg	-	microRNA cluster 35, host gene	ncRNA
mm_25973.1	chr3	132949417	132949417	+	1	NA	intron (NM_033525, intron 1 of 12)	intron (NM_033525, intron 1 of 12)	397	NM_001287103	114249	Mm.279310	NM_033525	ENSMUSG00000040998	Npnt	1110009H02Rik|AA682063|AI314031|Nctn|POEM	nephronectin	protein-coding
mm_155760.1	chrX	96167904	96167920	+	1	NA	3' UTR (NM_010833, exon 13 of 13)	3' UTR (NM_010833, exon 13 of 13)	71867	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_76191.1	chr8	82402881	82402901	-	1	NA	promoter-TSS (NM_001254747)	promoter-TSS (NM_001254747)	-305	NM_008357	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_12151.1	chr2	61812507	61812517	+	1	NA	3' UTR (NM_009322, exon 6 of 6)	3' UTR (NM_009322, exon 6 of 6)	8059	NM_009322	21375	Mm.308525	NM_009322	ENSMUSG00000035033	Tbr1	-	T-box brain gene 1	protein-coding
mm_57531.1	chr6	126535387	126535413	-	1	NA	5' UTR (NM_145983, exon 1 of 1)	5' UTR (NM_145983, exon 1 of 1)	155	NM_145983	16493	Mm.222831	NM_145983	ENSMUSG00000045534	Kcna5	Kv1.5	potassium voltage-gated channel, shaker-related subfamily, member 5	protein-coding
mm_167700.1	chr9	90054473	90054483	+	1	NA	5' UTR (NM_007801, exon 1 of 12)	5' UTR (NM_007801, exon 1 of 12)	211	NM_001312649	13036	Mm.2277	NM_007801	ENSMUSG00000032359	Ctsh	AL022844	cathepsin H	protein-coding
mm_120471.1	chr14	65973378	65973396	+	1	NA	exon (NM_013492, exon 3 of 9)	exon (NM_013492, exon 3 of 9)	4904	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_171020.1	chr2	83983941	83983958	+	1	NA	Intergenic	CpG	-42723	NM_027964	71861	Mm.116957	NM_027964	ENSMUSG00000034552	Zswim2	1700025P14Rik|4933437F18Rik|MEX	zinc finger SWIM-type containing 2	protein-coding
mm_49355.1	chr6	22006422	22006422	+	1	NA	intron (NM_001081351, intron 1 of 21)	intron (NM_001081351, intron 1 of 21)	20512	NM_001081351	214642	Mm.221404	NM_001081351	ENSMUSG00000062980	Cped1	6720481P07|A430107O13Rik|AI552584	cadherin-like and PC-esterase domain containing 1	protein-coding
mm_158835.1	chrX	168672483	168672507	-	1	NA	intron (NM_010832, intron 1 of 11)	intron (NM_010832, intron 1 of 11)	1407	NM_010832	17692	Mm.24248	NM_010832	ENSMUSG00000031358	Msl3	AU018931|Msl31|Msl3l1	male-specific lethal 3 homolog (Drosophila)	protein-coding
mm_69576.1	chr7	135700999	135701009	-	1	NA	exon (NM_001081117, exon 12 of 14)	exon (NM_001081117, exon 12 of 14)	15375	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_33907.1	chr4	136310953	136310984	+	1	NA	promoter-TSS (NM_001277123)	promoter-TSS (NM_001277123)	26	NM_001277123	74326	Mm.31051	NM_028871	ENSMUSG00000066037	Hnrnpr	2610003J05Rik|2610528B01Rik|Hnrpr	heterogeneous nuclear ribonucleoprotein R	protein-coding
mm_129123.1	chr15	76124650	76124664	-	1	NA	exon (NM_001142968, exon 7 of 16)	exon (NM_001142968, exon 7 of 16)	1899	NM_001142968	271278	Mm.205253	NM_198172	ENSMUSG00000044361	BC024139	6230424I18Rik	cDNA sequence BC024139	protein-coding
mm_38551.1	chr4	141606012	141606058	-	1	NA	promoter-TSS (NM_133754)	promoter-TSS (NM_133754)	17	NM_133754	74202	Mm.490327	NM_133754	ENSMUSG00000006219	Fblim1	2410043F08Rik|Cal|Fblp1|Gt10|migfilin|migfilin(s)	filamin binding LIM protein 1	protein-coding
mm_42796.1	chr5	121686629	121686630	+	1	NA	3' UTR (NM_001289543, exon 11 of 11)	3' UTR (NM_001289543, exon 11 of 11)	-24980	NM_009125	20239	Mm.260900	NM_009125	ENSMUSG00000042605	Atxn2	9630045M23Rik|ATX2|AW544490|Sca2	ataxin 2	protein-coding
mm_84853.1	chr9	78481658	78481714	-	1	NA	promoter-TSS (NM_010106)	promoter-TSS (NM_010106)	38	NM_010106	13627	Mm.138471	NM_010106	ENSMUSG00000037742	Eef1a1	-	eukaryotic translation elongation factor 1 alpha 1	protein-coding
mm_160953.1	chr11	97776054	97776054	-	1	NA	promoter-TSS (NM_028156)	promoter-TSS (NM_028156)	-136	NM_028156	72215	Mm.269049	NM_028156	ENSMUSG00000018543	1700001P01Rik	-	RIKEN cDNA 1700001P01 gene	protein-coding
mm_41874.1	chr5	104571666	104571694	+	1	NA	promoter-TSS (NM_001346671)	promoter-TSS (NM_001346671)	8	NM_001346671	69623	Mm.69919	NM_027142		Zfp33b	2310012P17Rik	zinc finger protein 33B	protein-coding
mm_89006.1	chr10	81627692	81627742	+	1	NA	promoter-TSS (NM_027480)	promoter-TSS (NM_027480)	-109	NM_181586	50721	Mm.25643	NM_181586	ENSMUSG00000034748	Sirt6	2810449N18Rik|AI043036|Sir2l6	sirtuin 6	protein-coding
mm_91948.1	chr10	60938124	60938142	-	1	NA	promoter-TSS (NR_033616)	promoter-TSS (NR_033616)	-1	NR_033616	73616	Mm.159038	NR_033616	ENSMUSG00000037247	Pldi	1700125F08Rik|Poldi	polymorphic derived intron containing	ncRNA
mm_100901.1	chr11	6173065	6173066	-	1	NA	non-coding (NR_029471, exon 1 of 1)	non-coding (NR_029471, exon 1 of 1)	266	NR_029471	100042173	Mm.441799	NR_029471		Rps15a-ps6	Gm11968|OTTMUSG00000005107	ribosomal protein S15A, pseudogene 6	pseudo
mm_26615.1	chr3	152385073	152385080	+	1	NA	intron (NM_001076676, intron 21 of 23)	intron (NM_001076676, intron 21 of 23)	-10397	NM_001346655	108946	Mm.379292	NM_198416	ENSMUSG00000039068	Zzz3	3110065C23Rik|6430567E01Rik|AA408566|AI481057|AW556059|R75514	zinc finger, ZZ domain containing 3	protein-coding
mm_119791.1	chr14	54193966	54193974	+	1	NA	Intergenic	L3b|LINE|CR1	59959	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_69338.1	chr7	129648983	129648990	-	1	NA	Intergenic	Intergenic	57123	NM_172255	207425	Mm.229323	NM_172255	ENSMUSG00000042055	Wdr11	2900055P10Rik|AW489876|Brwd2|mKIAA1351	WD repeat domain 11	protein-coding
mm_42115.1	chr5	110810308	110810327	+	1	NA	promoter-TSS (NM_009469)	promoter-TSS (NM_009469)	-236	NM_001347394	22241	Mm.271898	NM_009469	ENSMUSG00000029512	Ulk1	AU041434|Unc51.1|mKIAA0722	unc-51 like kinase 1	protein-coding
mm_107627.1	chr12	51691201	51691232	+	1	NA	5' UTR (NM_001329699, exon 1 of 6)	5' UTR (NM_001329699, exon 1 of 6)	250	NM_001329698	11782	Mm.386749	NM_021710	ENSMUSG00000020955	Ap4s1	AI314282	adaptor-related protein complex AP-4, sigma 1	protein-coding
mm_135339.1	chr16	42340585	42340591	-	1	NA	promoter-TSS (NM_008083)	promoter-TSS (NM_008083)	63	NM_008083	14432	Mm.1222	NM_008083	ENSMUSG00000047261	Gap43	B-50|Basp2|GAP-43	growth associated protein 43	protein-coding
mm_105333.1	chr11	102946702	102946725	-	1	NA	promoter-TSS (NM_011795)	promoter-TSS (NM_011795)	-252	NM_011795	23829	Mm.57154	NM_011795	ENSMUSG00000045532	C1ql1	C1qrf|CRF|CTRP14|gliacolin	complement component 1, q subcomponent-like 1	protein-coding
mm_39505.1	chr5	21202731	21202740	+	1	NA	intron (NM_175437, intron 3 of 30)	L1MDa|LINE|L1	16468	NM_175437	212167	Mm.121705	NM_175437	ENSMUSG00000039934	Gsap	A530088I07Rik|Pion	gamma-secretase activating protein	protein-coding
mm_24795.1	chr3	95545522	95545541	+	1	NA	exon (NM_021281, exon 5 of 8)	exon (NM_021281, exon 5 of 8)	-14146	NM_026489	67981	Mm.179050	NM_026489	ENSMUSG00000028109	Hormad1	4921522K05Rik|Nohma	HORMA domain containing 1	protein-coding
mm_108204.1	chr12	76902208	76902231	+	1	NA	intron (NM_145927, intron 7 of 11)	HAL1|LINE|L1	60029	NM_008558	17187	Mm.268548	NM_008558	ENSMUSG00000059436	Max	AA960152|AI875693|bHLHd4|bHLHd5|bHLHd6|bHLHd7|bHLHd8	Max protein	protein-coding
mm_73770.1	chr8	116126917	116126927	+	1	NA	Intergenic	Intergenic	-378093	NM_029297	75465	Mm.23114	NM_029297	ENSMUSG00000034467	Dynlrb2	1700009A04Rik|DNLC2B|Dncl2b	dynein light chain roadblock-type 2	protein-coding
mm_130537.1	chr15	98937356	98937386	-	1	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	-2981	NM_011654	22143	Mm.392113	NM_011654	ENSMUSG00000023004	Tuba1b	Tuba2	tubulin, alpha 1B	protein-coding
mm_157769.1	chrX	73716199	73716209	-	1	NA	promoter-TSS (NM_012060)	promoter-TSS (NM_012060)	0	NM_012060	27061	Mm.17	NM_012060	ENSMUSG00000002015	Bcap31	Bap31	B cell receptor associated protein 31	protein-coding
mm_123686.1	chr14	69624270	69624277	-	1	NA	intron (NM_033325, intron 1 of 13)	MTA_Mm|LTR|ERVL-MaLR	14797	NM_033325	94352	Mm.116714	NM_033325	ENSMUSG00000034205	Loxl2	1110004B06Rik|4930526G11Rik|9430067E15Rik	lysyl oxidase-like 2	protein-coding
mm_99613.1	chr11	104584296	104584310	+	1	NA	intron (NM_010858, intron 5 of 8)	intron (NM_010858, intron 5 of 8)	-22105	NR_130177	100415912	Mm.446786	NR_130177		Gm11665	Gm11664|OTTMUSG00000003182|OTTMUSG00000003183	predicted gene 11665	ncRNA
mm_70085.1	chr7	142654341	142654376	-	1	NA	TTS (NR_030251)	TTS (NR_030251)	638	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_103577.1	chr11	78100849	78100861	-	1	NA	intron (NM_001346762, intron 1 of 2)	intron (NM_001346762, intron 1 of 2)	6182	NM_145430	216971	Mm.119387	NM_145430	ENSMUSG00000037750	Fam222b	9630020I17Rik	family with sequence similarity 222, member B	protein-coding
mm_161879.1	chr18	37442389	37442389	+	1	NA	promoter-TSS (NM_053138)	promoter-TSS (NM_053138)	-128	NM_053138	93884	Mm.196700	NM_053138	ENSMUSG00000047307	Pcdhb13	Pcdbh6|PcdhbM	protocadherin beta 13	protein-coding
mm_95500.1	chr11	51884074	51884121	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-26616	NM_199299	76901	Mm.259996	NM_199299	ENSMUSG00000020387	Jade2	1200017K05Rik|AI480685|Phf15|mKIAA0239	jade family PHD finger 2	protein-coding
mm_111754.1	chr12	103951387	103951412	-	1	NA	exon (NM_009247, exon 2 of 5)	exon (NM_009247, exon 2 of 5)	5498	NM_009247	20704	Mm.312593	NM_009247	ENSMUSG00000072849	Serpina1e	Dom5|PI5|Spi1-5	serine (or cysteine) peptidase inhibitor, clade A, member 1E	protein-coding
mm_108121.1	chr12	75818377	75818385	+	1	NA	promoter-TSS (NM_001005510)	promoter-TSS (NM_001005510)	63	NM_001005510	319565	Mm.26652	NM_001005510	ENSMUSG00000063450	Syne2	6820443O06Rik|AW546258|Cpfl8|D12Ertd777e|NUA|Nesp2g|dice|mKIAA1011	spectrin repeat containing, nuclear envelope 2	protein-coding
mm_103265.1	chr11	71202852	71202885	-	1	NA	intron (NM_001040696, intron 3 of 14)	intron (NM_001040696, intron 3 of 14)	-1412	NM_001162414	637515	Mm.390402	NM_001039680	ENSMUSG00000070390	Nlrp1b	ENSMUSG00000070390|Nalp1b|OTTMUSG00000006087|OTTMUSG00000006089	NLR family, pyrin domain containing 1B	protein-coding
mm_51431.1	chr6	78466773	78466779	+	1	NA	exon (NM_011260, exon 5 of 6)	exon (NM_011260, exon 5 of 6)	2098	NM_011260	19695	Mm.252385	NM_011260	ENSMUSG00000030017	Reg3g	AI449515|REG-3-gamma|reg III-gamma	regenerating islet-derived 3 gamma	protein-coding
mm_165571.1	chr3	19985612	19985623	+	1	NA	exon (NM_007752, exon 15 of 19)	exon (NM_007752, exon 15 of 19)	28563	NM_007752	12870	Mm.13787	NM_007752	ENSMUSG00000003617	Cp	D3Ertd555e	ceruloplasmin	protein-coding
mm_152623.1	chr19	12465274	12465277	-	1	NA	TTS (NM_010821)	TTS (NM_010821)	4496	NM_010821	17476	Mm.3999	NM_010821	ENSMUSG00000046805	Mpeg1	MPS1|Mpg-1	macrophage expressed gene 1	protein-coding
mm_100009.1	chr11	114852184	114852191	+	1	NA	5' UTR (NM_147217, exon 1 of 4)	5' UTR (NM_147217, exon 1 of 4)	157	NM_147217	70355	Mm.242413	NM_147217	ENSMUSG00000051043	Gprc5c	1110028I06Rik|3200002M13Rik|Raig3	G protein-coupled receptor, family C, group 5, member C	protein-coding
mm_14157.1	chr2	126588096	126588109	+	1	NA	3' UTR (NM_011978, exon 10 of 10)	3' UTR (NM_011978, exon 10 of 10)	30576	NM_008230	15186	Mm.18603	NM_008230	ENSMUSG00000027360	Hdc	AW108189|Hdc-a|Hdc-c|Hdc-e|Hdc-s	histidine decarboxylase	protein-coding
mm_23995.1	chr3	86539845	86539855	+	1	NA	intron (NM_001077687, intron 38 of 50)	intron (NM_001077687, intron 38 of 50)	8433	NM_011839	23937	Mm.389466	NM_011839	ENSMUSG00000057777	Mab21l2	-	mab-21-like 2 (C. elegans)	protein-coding
mm_150393.1	chr19	36409763	36409771	+	1	NA	intron (NM_029508, intron 1 of 8)	CpG	30700	NM_029508	76073	Mm.259180	NM_029508	ENSMUSG00000024805	Pcgf5	0610009F02Rik|1110054A01Rik|5830406C17Rik|5830443C21Rik|9530023M17Rik|AI324127	polycomb group ring finger 5	protein-coding
mm_101251.1	chr11	20770754	20770757	-	1	NA	Intergenic	RMER2|LTR|ERV1	-29199	NM_181411	216549	Mm.356580	NM_181411	ENSMUSG00000049659	Aftph	-	aftiphilin	protein-coding
mm_127590.1	chr15	102376955	102376974	+	1	NA	Intergenic	Intergenic	-10693	NM_130458	170574	Mm.263284	NM_130458	ENSMUSG00000060284	Sp7	6430578P22Rik|C22|Osx	Sp7 transcription factor 7	protein-coding
mm_77290.1	chr8	116944101	116944129	-	1	NA	intron (NM_177700, intron 1 of 3)	intron (NM_177700, intron 1 of 3)	722	NM_177700	234776	Mm.259736	NM_177700	ENSMUSG00000047388	Atmin	Asciz|gpg6|mKIAA0431	ATM interactor	protein-coding
mm_45831.1	chr5	87694674	87694682	-	1	NA	exon (NM_001286023, exon 5 of 7)	exon (NM_001286023, exon 5 of 7)	4747	NM_001286020	12991	Mm.268737	NM_009972	ENSMUSG00000063157	Csn2	Csnb	casein beta	protein-coding
mm_150940.1	chr19	46306118	46306154	+	1	NA	intron (NM_001177369, intron 2 of 22)	intron (NM_001177369, intron 2 of 22)	206	NM_001177370	18034	Mm.102365	NM_019408	ENSMUSG00000025225	Nfkb2	NF-kappaB2|lyt|p49|p49/p100|p50B|p52	nuclear factor of kappa light polypeptide gene enhancer in B cells 2, p49/p100	protein-coding
mm_95610.1	chr11	53457210	53457265	+	1	NA	promoter-TSS (NM_027917)	promoter-TSS (NM_027917)	32	NM_027917	71774	Mm.274370	NM_027917	ENSMUSG00000018387	Shroom1	Apx|Shrm1	shroom family member 1	protein-coding
mm_164939.1	chr18	90419011	90419025	+	1	NA	Intergenic	L1_Mur1|LINE|L1	-91136	NM_198295	67988	Mm.268041	NM_198295	ENSMUSG00000024614	Tmx3	6430411B10Rik|A730024F05Rik|AV259382|Txndc10|mKIAA1830	thioredoxin-related transmembrane protein 3	protein-coding
mm_9951.1	chr1	190979196	190979232	-	1	NA	promoter-TSS (NM_144879)	promoter-TSS (NM_144879)	82	NR_027352	226841	Mm.22856	NM_144879	ENSMUSG00000037568	Vash2	B130052G07Rik	vasohibin 2	protein-coding
mm_30754.1	chr4	15022531	15022556	+	1	NA	intron (NM_178617, intron 5 of 12)	intron (NM_178617, intron 5 of 12)	91902	NM_001243100	100038514	Mm.331495	NM_001243100		Gm11837	OTTMUSG00000004551	predicted gene 11837	protein-coding
mm_54431.1	chr6	34172039	34172043	-	1	NA	intron (NM_021435, intron 1 of 9)	intron (NM_021435, intron 1 of 9)	5013	NM_021435	58246	Mm.245527	NM_021435	ENSMUSG00000018999	Slc35b4	4930474D06Rik|AB041549|AW494345	solute carrier family 35, member B4	protein-coding
mm_148064.1	chr18	72258773	72258784	-	1	NA	intron (NM_007831, intron 1 of 28)	MER20|DNA|hAT-Charlie	92291	NM_007831	13176	Mm.167882	NM_007831	ENSMUSG00000060534	Dcc	C030036D22Rik|Igdcc1	deleted in colorectal carcinoma	protein-coding
mm_6866.1	chr1	84278920	84278932	-	1	NA	intron (NM_001003948, intron 1 of 2)	intron (NM_001003948, intron 1 of 2)	5719	NM_001003948	98496	Mm.187470	NM_001003948	ENSMUSG00000045658	Pid1	5033414K04Rik|NYGGF4	phosphotyrosine interaction domain containing 1	protein-coding
mm_919.1	chr1	55088307	55088352	+	1	NA	promoter-TSS (NM_010477)	promoter-TSS (NM_010477)	181	NM_008303	15528	Mm.215667	NM_008303	ENSMUSG00000073676	Hspe1	10kDa|Hsp10|mt-cpn10	heat shock protein 1 (chaperonin 10)	protein-coding
mm_73789.1	chr8	117256734	117256755	+	1	NA	promoter-TSS (NM_001163262)	promoter-TSS (NM_001163262)	-275	NM_001163262	74440	Mm.233181	NM_028941	ENSMUSG00000034390	Cmip	4933407C03Rik|5830471E12Rik|AI314065|AI464126	c-Maf inducing protein	protein-coding
mm_166607.1	chr6	69284335	69284350	-	1	NA	Intergenic	Intergenic	42832	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_86434.1	chr10	3863881	3863889	+	1	NA	intron (NM_001159942, intron 2 of 16)	intron (NM_001159942, intron 2 of 16)	-8782	NM_001033253	213783	Mm.150831	NM_001033253	ENSMUSG00000040624	Plekhg1	D10Ertd733e|Gm521|mKIAA1209	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	protein-coding
mm_169213.1	chr13	66589048	66589066	-	1	NA	Intergenic	Intergenic	-147939	NM_001290196	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
mm_169114.1	chr13	49544436	49544441	+	1	NA	promoter-TSS (NM_025711)	promoter-TSS (NM_025711)	-5	NM_001172481	66695	Mm.383216	NM_025711	ENSMUSG00000021388	Aspn	4631401G09Rik|AA986886|Plap1|Slrr1c	asporin	protein-coding
mm_32349.1	chr4	104913555	104913579	+	1	NA	exon (NM_001162980, exon 1 of 20)	exon (NM_001162980, exon 1 of 20)	111	NM_001285952	242594	Mm.65181	NM_001162980	ENSMUSG00000078612	1700024P16Rik	C1orf168|Gm620	RIKEN cDNA 1700024P16 gene	protein-coding
mm_91845.1	chr10	58447378	58447431	-	1	NA	intron (NM_011240, intron 1 of 28)	CpG	552	NM_011240	19386	Mm.431695	NM_011240	ENSMUSG00000003226	Ranbp2	A430087B05Rik|AI256741|NUP358	RAN binding protein 2	protein-coding
mm_129117.1	chr15	76091493	76091530	-	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	-1498	NM_144847	223649	Mm.101946	NM_144847	ENSMUSG00000075590	Nrbp2	BC011468	nuclear receptor binding protein 2	protein-coding
mm_139504.1	chr17	56303428	56303467	+	1	NA	promoter-TSS (NM_001111080)	promoter-TSS (NM_001111080)	110	NM_001111079	18140	Mm.42196	NM_010931	ENSMUSG00000001228	Uhrf1	AL022808|ICBP90|Np95|RNF106	ubiquitin-like, containing PHD and RING finger domains, 1	protein-coding
mm_161033.1	chr12	17177085	17177085	-	1	NA	promoter-TSS (NM_201531)	promoter-TSS (NM_201531)	-197	NM_201531	382571	Mm.40173	NM_201531	ENSMUSG00000051726	Kcnf1	Gm1182|Kv5.1	potassium voltage-gated channel, subfamily F, member 1	protein-coding
mm_135045.1	chr16	33124050	33124064	-	1	NA	3' UTR (NM_172823, exon 17 of 17)	3' UTR (NM_172823, exon 17 of 17)	18696	NR_035469	100316698		NR_035469	ENSMUSG00000088860	Mir1947	mir-1947|mmu-mir-1947	microRNA 1947	ncRNA
mm_80454.1	chr9	77982689	77982698	+	1	NA	exon (NM_134255, exon 8 of 8)	exon (NM_134255, exon 8 of 8)	65328	NM_134255	68801	Mm.430736	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	ELOVL family member 5, elongation of long chain fatty acids (yeast)	protein-coding
mm_57108.1	chr6	122593049	122593060	-	1	NA	intron (NM_031159, intron 3 of 7)	B3A|SINE|B2	9390	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_118961.1	chr14	27429972	27429975	+	1	NA	intron (NM_028945, intron 1 of 23)	intron (NM_028945, intron 1 of 23)	1126	NM_001114879	218850	Mm.247767	NM_028945	ENSMUSG00000040651	Fam208a	4732418E12|4933409E02Rik|D14Abb1e|MommeD6	family with sequence similarity 208, member A	protein-coding
mm_110931.1	chr12	76369821	76369829	-	1	NA	promoter-TSS (NM_001172104)	promoter-TSS (NM_001172104)	-265	NM_028356	109929	Mm.41880	NM_028356	ENSMUSG00000056459	Zbtb25	2810462M08Rik|2900064P18Rik|AI842128|Kup|Zfp-50|Zfp50	zinc finger and BTB domain containing 25	protein-coding
mm_61248.1	chr7	65804017	65804023	+	1	NA	promoter-TSS (NR_045301)	promoter-TSS (NR_045301)	-32	NR_045301	100503969	Mm.383527	NR_045301		1810008I18Rik	-	RIKEN cDNA 1810008I18 gene	ncRNA
mm_61090.1	chr7	51628672	51628681	+	1	NA	intron (NM_080853, intron 3 of 11)	intron (NM_080853, intron 3 of 11)	6846	NM_080853	140919	Mm.256618	NM_080853	ENSMUSG00000030500	Slc17a6	2900073D12Rik|DNPI|VGLUT2	solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 6	protein-coding
mm_155732.1	chrX	96165963	96165974	+	1	NA	exon (NM_010833, exon 12 of 13)	exon (NM_010833, exon 12 of 13)	69923	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_55059.1	chr6	49047908	49047918	-	1	NA	exon (NM_053110, exon 6 of 11)	exon (NM_053110, exon 6 of 11)	11395	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_44008.1	chr5	147076189	147076199	+	1	NA	intron (NM_080795, intron 1 of 9)	intron (NM_080795, intron 1 of 9)	378	NM_080795	140887	Mm.272203	NM_080795	ENSMUSG00000016520	Lnx2	9630046H24|AW209022	ligand of numb-protein X 2	protein-coding
mm_50227.1	chr6	42350779	42350790	+	1	NA	intron (NM_001289619, intron 2 of 8)	intron (NM_001289619, intron 2 of 8)	956	NM_001289619	22793	Mm.282303	NM_011777	ENSMUSG00000029860	Zyx	9530098H06Rik|R75157	zyxin	protein-coding
mm_152122.1	chr19	6987622	6987764	-	1	NA	promoter-TSS (NM_011697)	promoter-TSS (NM_011697)	-42	NM_011697	22340	Mm.15607	NM_011697	ENSMUSG00000024962	Vegfb	VEGF-B|Vrf	vascular endothelial growth factor B	protein-coding
mm_109795.1	chr12	3264710	3264757	-	1	NA	exon (NM_016676, exon 2 of 6)	exon (NM_016676, exon 2 of 6)	28942	NR_015551	74173	Mm.309774	NM_028796	ENSMUSG00000079179	Rab10os	1700012B15Rik|1810036A22Rik	RAB10, member RAS oncogene family, opposite strand	ncRNA
mm_111822.1	chr12	106716297	106716306	-	1	NA	promoter-TSS (NR_015512)	promoter-TSS (NR_015512)	23	NR_015512	71033	Mm.159404	NR_015512	ENSMUSG00000085820	4933406K04Rik	4930426M03Rik|4930485I22Rik|4933427G14Rik	RIKEN cDNA 4933406K04 gene	ncRNA
mm_148373.1	chr18	89769480	89769558	-	1	NA	promoter-TSS (NM_001039173)	promoter-TSS (NM_001039173)	-383	NM_001039173	623279	Mm.447164	NM_001039173	ENSMUSG00000073514	Dok6	Dok-6	docking protein 6	protein-coding
mm_6040.1	chr1	59670813	59670830	-	1	NA	promoter-TSS (NM_009460)	promoter-TSS (NM_009460)	13	NM_009460	22218	Mm.362118	NM_009460	ENSMUSG00000026021	Sumo1	GMP1|PIC1|SENTRIN|SMT3|SMT3H3|SMTP3|SUMO-1|Smt3C|Ubl1	small ubiquitin-like modifier 1	protein-coding
mm_33731.1	chr4	134098856	134098867	+	1	NA	Intergenic	Intergenic	-3722	NR_045571	67586	Mm.282029	NM_026257	ENSMUSG00000012126	Ubxn11	4930506L07Rik|D4Bwg1540e|Soc|Soci|Ubxd5	UBX domain protein 11	protein-coding
mm_96913.1	chr11	70459961	70459985	+	1	NA	promoter-TSS (NM_023158)	promoter-TSS (NM_023158)	11	NM_023158	66102	Mm.425692	NM_023158	ENSMUSG00000018920	Cxcl16	0910001K24Rik|AV290116|BB024863|CXCL16v1|CXCL16v2|SR-PSOX|Zmynd15|b2b498Clo	chemokine (C-X-C motif) ligand 16	protein-coding
mm_132424.1	chr16	35580836	35580839	+	1	NA	intron (NM_013661, intron 1 of 21)	intron (NM_013661, intron 1 of 21)	39475	NM_013661	20357	Mm.42015	NM_013661	ENSMUSG00000052133	Sema5b	AI893641|SemG|Semag|mKIAA1445	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B	protein-coding
mm_128281.1	chr15	37004135	37004139	-	1	NA	intron (NM_026521, intron 1 of 3)	intron (NM_026521, intron 1 of 3)	3265	NM_026521	68036	Mm.371631	NM_026521	ENSMUSG00000062397	Zfp706	3110006P09Rik|AA793007|AW536850|C77232|Znf706	zinc finger protein 706	protein-coding
mm_36740.1	chr4	99829123	99829179	-	1	NA	promoter-TSS (NM_145549)	promoter-TSS (NM_145549)	-33	NM_026348	67733	Mm.257094	NM_026348	ENSMUSG00000028549	Itgb3bp	4930471O16Rik|AU022583	integrin beta 3 binding protein (beta3-endonexin)	protein-coding
mm_124437.1	chr14	118693789	118693796	-	1	NA	intron (NM_001033336, intron 1 of 30)	intron (NM_001033336, intron 1 of 30)	12427	NM_001163676	239273	Mm.40537	NM_001033336	ENSMUSG00000032849	Abcc4	ABCC4-N1|D630049P08Rik|MOATB|MRP4	ATP-binding cassette, sub-family C (CFTR/MRP), member 4	protein-coding
mm_159565.1	chr4	109235734	109235734	+	1	NA	exon (NM_001033226, exon 1 of 8)	exon (NM_001033226, exon 1 of 8)	102	NM_001033226	108802	Mm.318248	NM_001033226	ENSMUSG00000028558	Calr4	4933403L16Rik|AU017583	calreticulin 4	protein-coding
mm_16462.1	chr2	180601040	180601041	+	1	NA	intron (NM_009936, intron 4 of 31)	intron (NM_009936, intron 4 of 31)	2818	NM_009936	12841	Mm.141312	NM_009936	ENSMUSG00000027570	Col9a3	AV006866	collagen, type IX, alpha 3	protein-coding
mm_97343.1	chr11	77462427	77462438	+	1	NA	Intergenic	CpG	-1481	NM_139129	216961	Mm.33477	NM_139128	ENSMUSG00000020836	Coro6	-	coronin 6	protein-coding
mm_170621.1	chr19	6673791	6673803	+	1	NA	Intergenic	RLTR1B|LTR|ERV1	-130727	NM_009203	20521	Mm.391146	NM_009203	ENSMUSG00000061742	Slc22a12	AI987855|OAT4L|Rst|Slc22al2|URAT1	solute carrier family 22 (organic anion/cation transporter), member 12	protein-coding
mm_134513.1	chr16	19200231	19200250	-	1	NA	Intergenic	Intergenic	86501	NM_146451	258443	Mm.377506	NM_146451	ENSMUSG00000050742	Olfr164	MOR279-2	olfactory receptor 164	protein-coding
mm_89092.1	chr10	84308825	84308843	+	1	NA	Intergenic	Intergenic	131637	NM_001004363	77976	Mm.25874	NM_001004363	ENSMUSG00000020032	Nuak1	AU014801|AW494241|B230104P22Rik|Omphk1	NUAK family, SNF1-like kinase, 1	protein-coding
mm_142224.1	chr17	37480707	37480718	-	1	NA	TTS (NM_008204)	TTS (NM_008204)	2817	NM_008204	14990	Mm.329041	NM_008204	ENSMUSG00000016283	H2-M2	H-2M2|Thy19.4	histocompatibility 2, M region locus 2	protein-coding
mm_110290.1	chr12	32185200	32185208	-	1	NA	intron (NM_001146200, intron 10 of 10)	intron (NM_001146200, intron 10 of 10)	23134	NM_001146201	30955	Mm.101369	NM_020272	ENSMUSG00000020573	Pik3cg	5830428L06Rik|PI3Kgamma|p110gamma	phosphoinositide-3-kinase, catalytic, gamma polypeptide	protein-coding
mm_153295.1	chr19	37697613	37697630	-	1	NA	promoter-TSS (NM_007811)	promoter-TSS (NM_007811)	-187	NM_007811	13082	Mm.42230	NM_007811	ENSMUSG00000024987	Cyp26a1	Cyp26|P450RA|P450RAI|RAH	cytochrome P450, family 26, subfamily a, polypeptide 1	protein-coding
mm_14604.1	chr2	136501979	136501997	+	1	NA	Intergenic	Intergenic	-30333	NM_175667	319196	Mm.477841	NM_175667	ENSMUSG00000074771	Ankef1	AV276460|Ankrd5	ankyrin repeat and EF-hand domain containing 1	protein-coding
mm_10929.1	chr2	25457633	25457670	+	1	NA	intron (NM_027085, intron 1 of 5)	intron (NM_027085, intron 1 of 5)	808	NM_027085	69454	Mm.44194	NM_027085	ENSMUSG00000015093	Clic3	2300003G24Rik	chloride intracellular channel 3	protein-coding
mm_133175.1	chr16	72027708	72027720	+	1	NA	Intergenic	Intergenic	206613	NR_131116	319533	Mm.373754	NR_131115		8030451O07Rik	-	RIKEN cDNA 8030451O07 gene	ncRNA
mm_90491.1	chr10	128033267	128033270	+	1	NA	Intergenic	RMER10A|LTR|ERVL	-2078	NM_013608	17938	Mm.3746	NM_013608	ENSMUSG00000061315	Naca	AL022831|AL024382|Gm1878|mKIAA0363|skNAC	nascent polypeptide-associated complex alpha polypeptide	protein-coding
mm_73856.1	chr8	118283608	118283618	+	1	NA	promoter-TSS (NM_019707)	promoter-TSS (NM_019707)	2	NM_019707	12554	Mm.334841	NM_019707	ENSMUSG00000031841	Cdh13	4932416G01Rik|Cdht|Tcad	cadherin 13	protein-coding
mm_29234.1	chr3	107214247	107214277	-	1	NA	exon (NM_001111143, exon 6 of 9)	exon (NM_001111143, exon 6 of 9)	7470	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_18703.1	chr2	71750307	71750321	-	1	NA	intron (NR_039557, intron 2 of 3).2	intron (NR_039557, intron 2 of 3).2	30897	NR_037979	381371	Mm.330284	NM_201366	ENSMUSG00000064263	Platr26	Gm1631	pluripotency associated transcript 26	ncRNA
mm_2890.1	chr1	131867614	131867632	+	1	NA	5' UTR (NM_144875, exon 2 of 6)	5' UTR (NM_144875, exon 2 of 6)	346	NM_144875	226422	Mm.34027	NM_144875	ENSMUSG00000026433	Rab29	Rab7l1	RAB29, member RAS oncogene family	protein-coding
mm_78592.1	chr9	37385943	37385957	+	1	NA	3' UTR (NM_175189, exon 7 of 7)	3' UTR (NM_175189, exon 7 of 7)	-15947	NM_028783	74144	Mm.485070	NM_028783	ENSMUSG00000032125	Robo4	1200012D01Rik|AI593217	roundabout guidance receptor 4	protein-coding
mm_20379.1	chr2	128687358	128687396	-	1	NA	promoter-TSS (NM_008569)	promoter-TSS (NM_008569)	18	NM_008569	17222	Mm.277408	NM_008569	ENSMUSG00000014355	Anapc1	2610021O03Rik|AI047775|AI853536|AW547281|Apc1|Mcpr|tsg24	anaphase promoting complex subunit 1	protein-coding
mm_36640.1	chr4	93481356	93481390	-	1	NA	Intergenic	Intergenic	-145862	NM_026954	69136	Mm.171558	NM_026954	ENSMUSG00000054000	Tusc1	2200001D17Rik|TSG-9	tumor suppressor candidate 1	protein-coding
mm_57502.1	chr6	125380504	125380526	-	1	NA	promoter-TSS (NM_198604)	promoter-TSS (NM_198604)	-11	NM_198604	213522	Mm.333396	NM_198604	ENSMUSG00000038167	Plekhg6	BC026778|Gm155	pleckstrin homology domain containing, family G (with RhoGef domain) member 6	protein-coding
mm_171191.1	chr3	44668122	44668125	+	1	NA	Intergenic	L1Md_T|LINE|L1	710137	NR_045172	72511	Mm.140700	NR_045172	ENSMUSG00000097040	2610316D01Rik	-	RIKEN cDNA 2610316D01 gene	ncRNA
mm_94976.1	chr11	31545894	31545898	+	1	NA	Intergenic	RLTR10D2|LTR|ERVK	125966	NM_001024919	69556	Mm.34183	NM_001024919	ENSMUSG00000044502	Bod1	2310022M17Rik|BOD2.1|Fam44b	biorientation of chromosomes in cell division 1	protein-coding
mm_170521.1	chr19	32466560	32466578	-	1	NA	Intergenic	Intergenic	-19200	NM_010799	17330	Mm.255116	NM_010799	ENSMUSG00000024896	Minpp1	AA408516	multiple inositol polyphosphate histidine phosphatase 1	protein-coding
mm_129682.1	chr15	81400054	81400093	-	1	NA	promoter-TSS (NM_133726)	promoter-TSS (NM_133726)	-65	NM_001347075	321003	Mm.390833	NM_177310	ENSMUSG00000022401	Xpnpep3	APP3|E430012M05Rik	X-prolyl aminopeptidase 3, mitochondrial	protein-coding
mm_65623.1	chr7	27541706	27541728	-	1	NA	exon (NM_011116, exon 6 of 14)	exon (NM_011116, exon 6 of 14)	11501	NM_011116	18807	Mm.6483	NM_011116	ENSMUSG00000003363	Pld3	Sam-9	phospholipase D family, member 3	protein-coding
mm_77283.1	chr8	116733062	116733076	-	1	NA	promoter-TSS (NM_029441)	promoter-TSS (NM_029441)	-78	NM_029441	75796	Mm.159575	NM_029441	ENSMUSG00000031758	Cdyl2	1700029M19Rik|4930453I21Rik|Gm20194	chromodomain protein, Y chromosome-like 2	protein-coding
mm_144457.1	chr18	23415163	23415215	+	1	NA	promoter-TSS (NM_207650)	promoter-TSS (NM_207650)	-220	NM_010087	13527	Mm.94371	NM_010087	ENSMUSG00000024302	Dtna	2210407P21Rik|DTN-A|Dtn|Gm19389|a-DB-1|adbn	dystrobrevin alpha	protein-coding
mm_95008.1	chr11	31928117	31928137	+	1	NA	intron (NM_001290676, intron 7 of 8)	intron (NM_001290676, intron 7 of 8)	-37506	NM_026262	67592	Mm.78654	NM_026262	ENSMUSG00000020299	4930524B15Rik	-	RIKEN cDNA 4930524B15 gene	protein-coding
mm_22935.1	chr3	31163877	31163890	+	1	NA	3' UTR (NM_008770, exon 3 of 3)	3' UTR (NM_008770, exon 3 of 3)	13963	NM_008770	18417	Mm.4425	NM_008770	ENSMUSG00000037625	Cldn11	Claudin-11|Claudin11|Osp|Otm	claudin 11	protein-coding
mm_134891.1	chr16	29544853	29544869	-	1	NA	promoter-TSS (NM_001164613)	promoter-TSS (NM_001164613)	3	NM_001164613	224079	Mm.54954	NM_172613	ENSMUSG00000038094	Atp13a4	4631413J11Rik|4832416L12|9330174J19Rik	ATPase type 13A4	protein-coding
mm_69657.1	chr7	139978671	139978681	-	1	NA	promoter-TSS (NM_001033465)	promoter-TSS (NM_001033465)	79	NM_001347614	381933	Mm.440431	NM_001033465	ENSMUSG00000073795	6430531B16Rik	Gm1093	RIKEN cDNA 6430531B16 gene	protein-coding
mm_39338.1	chr5	8808096	8808106	+	1	NA	intron (NM_011075, intron 4 of 27)	PB1D9|SINE|Alu	9954	NM_011075	18669	Mm.146649	NM_011075	ENSMUSG00000028970	Abcb1b	Abcb1|Mdr1|Mdr1b|Pgy-1|Pgy1|mdr	ATP-binding cassette, sub-family B (MDR/TAP), member 1B	protein-coding
mm_17901.1	chr2	35182295	35182325	-	1	NA	exon (NM_026697, exon 8 of 8)	exon (NM_026697, exon 8 of 8)	18810	NM_026697	68365	Mm.198264	NM_026697	ENSMUSG00000026878	Rab14	0610030G24Rik|2810475J17Rik|A830021G03Rik|AI314285|AI649155|D030017L14Rik	RAB14, member RAS oncogene family	protein-coding
mm_96387.1	chr11	67248562	67248567	+	1	NA	exon (NM_010855, exon 16 of 40)	exon (NM_010855, exon 16 of 40)	10752	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_45445.1	chr5	67427700	67427776	-	1	NA	promoter-TSS (NM_001164806)	promoter-TSS (NM_001164806)	61	NM_001164806	666938	Mm.101339	NM_001164806	ENSMUSG00000092060	Bend4	D330027G24Rik|EG666938	BEN domain containing 4	protein-coding
mm_78732.1	chr9	41581332	41581351	+	1	NA	promoter-TSS (NR_029822)	promoter-TSS (NR_029822)	88	NR_015483	73144	Mm.38166	NM_001033153	ENSMUSG00000074415	3110039I08Rik	2610203C20Rik|AI848448|D230004N17Rik|D3Mgi9|Mir100hg	RIKEN cDNA 3110039I08 gene	ncRNA
mm_70576.1	chr8	13165911	13165929	+	1	NA	exon (NM_010684, exon 2 of 9)	exon (NM_010684, exon 2 of 9)	6759	NM_010684	16783	Mm.16716	NM_010684	ENSMUSG00000031447	Lamp1	CD107a|LGP-120|LGP-A|Lamp-1|P2B	lysosomal-associated membrane protein 1	protein-coding
mm_80259.1	chr9	72807336	72807351	+	1	NA	promoter-TSS (NM_175485)	promoter-TSS (NM_175485)	69	NM_175485	235472	Mm.31696	NM_175485	ENSMUSG00000036030	Prtg	A230098A12Rik|Igdcc5	protogenin	protein-coding
mm_10368.1	chr2	11713231	11713242	+	1	NA	intron (NM_001271499, intron 1 of 6)	intron (NM_001271499, intron 1 of 6)	7524	NM_001271500	16169	Mm.200196	NM_008358	ENSMUSG00000023206	Il15ra	AA690181|IL-15RA	interleukin 15 receptor, alpha chain	protein-coding
mm_6038.1	chr1	59670381	59670394	-	1	NA	intron (NM_009460, intron 1 of 4)	intron (NM_009460, intron 1 of 4)	447	NM_009460	22218	Mm.362118	NM_009460	ENSMUSG00000026021	Sumo1	GMP1|PIC1|SENTRIN|SMT3|SMT3H3|SMTP3|SUMO-1|Smt3C|Ubl1	small ubiquitin-like modifier 1	protein-coding
mm_104577.1	chr11	96955920	96955957	-	1	NA	exon (NM_030220, exon 6 of 7)	exon (NM_030220, exon 6 of 7)	11792	NR_003293	319371	Mm.436865	NR_003293	ENSMUSG00000078700	D030028A08Rik	-	RIKEN cDNA D030028A08 gene	ncRNA
mm_141394.1	chr17	29237777	29237827	-	1	NA	promoter-TSS (NM_153166)	promoter-TSS (NM_153166)	-12	NM_153166	240058	Mm.39905	NM_153166	ENSMUSG00000024008	Cpne5	A830083G22Rik	copine V	protein-coding
mm_127034.1	chr15	96460209	96460225	+	1	NA	intron (NM_028148, intron 1 of 14)	CpG	626	NM_028148	72193	Mm.324474	NM_028148	ENSMUSG00000033228	Scaf11	1110061H03Rik|2610510E10Rik|AI462454|CASP11|SIP1|SRRP129|Sfrs2ip|Srsf2ip|mKIAA3013	SR-related CTD-associated factor 11	protein-coding
mm_131235.1	chr16	10480132	10480134	+	1	NA	promoter-TSS (NM_001243760)	promoter-TSS (NM_001243760)	61	NM_001302618	12265	Mm.249560	NM_007575	ENSMUSG00000022504	Ciita	C2ta|EG669998|Gm9475|Mhc2ta	class II transactivator	protein-coding
mm_92617.1	chr10	80141363	80141382	-	1	NA	promoter-TSS (NM_025313)	promoter-TSS (NM_025313)	-903	NM_001347092	66043	Mm.278560	NM_025313	ENSMUSG00000003072	Atp5d	0610008F14Rik|1500000I11Rik|AA960090|AI876556|AU020773|C85518	ATP synthase, H+ transporting, mitochondrial F1 complex, delta subunit	protein-coding
mm_156290.1	chrX	136837470	136837488	+	1	NA	3' UTR (NM_011123, exon 7 of 7)	3' UTR (NM_011123, exon 7 of 7)	14733	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_151376.1	chr19	55938487	55938500	+	1	NA	Intergenic	Intergenic	43172	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_139622.1	chr17	57362695	57362707	+	1	NA	intron (NM_010130, intron 2 of 21)	RLTR22_Mur|LTR|ERVK	4015	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_155498.1	chrX	73774398	73774412	+	1	NA	promoter-TSS (NM_019684)	promoter-TSS (NM_019684)	0	NM_019684	56504	Mm.111904	NM_019684	ENSMUSG00000002007	Srpk3	Mssk1|Stk23	serine/arginine-rich protein specific kinase 3	protein-coding
mm_92845.1	chr10	81509097	81509105	-	1	NA	intron (NM_010304, intron 5 of 6)	intron (NM_010304, intron 5 of 6)	-8964	NM_010102	13611	Mm.33065	NM_010102	ENSMUSG00000044199	S1pr4	Edg6|Lpc1|S1p4	sphingosine-1-phosphate receptor 4	protein-coding
mm_43901.1	chr5	144244419	144244427	+	1	NA	promoter-TSS (NM_001163709)	promoter-TSS (NM_001163709)	-14	NM_001163709	55950	Mm.38011	NM_018772	ENSMUSG00000047843	Bri3	I3	brain protein I3	protein-coding
mm_98041.1	chr11	85492721	85492732	+	1	NA	intron (NM_138681, intron 14 of 25)	intron (NM_138681, intron 14 of 25)	139562	NM_001166643	192197	Mm.209989	NM_138681	ENSMUSG00000059439	Bcas3	1500019F07Rik|2610028P08Rik|AU021018|BC028339|K20D4|rudhira	breast carcinoma amplified sequence 3	protein-coding
mm_64421.1	chr7	142576949	142576976	+	1	NA	TTS (NR_030416)	TTS (NR_030416)	185	NR_030416	735280		NR_030416	ENSMUSG00000076275	Mir675	Mirn675|mir-675|mmu-mir-675	microRNA 675	ncRNA
mm_27562.1	chr3	58577273	58577285	-	1	NA	intron (NM_001040396, intron 1 of 5)	CpG	621	NM_001040396	69227	Mm.270950	NM_001040396	ENSMUSG00000075700	Selenot	2810407C02Rik|5730408P04Rik|Selt	selenoprotein T	protein-coding
mm_13795.1	chr2	118901429	118901488	+	1	NA	promoter-TSS (NM_001045523)	promoter-TSS (NM_001045523)	-157	NM_001045523	228536	Mm.330487	NM_001045523	ENSMUSG00000040007	Bahd1	AL022997|AW541238|Gm117|mKIAA0945	bromo adjacent homology domain containing 1	protein-coding
mm_17418.1	chr2	27404726	27404727	-	1	NA	intron (NM_009500, intron 1 of 27)	intron (NM_009500, intron 1 of 27)	22882	NR_133905	22325	Mm.179011	NM_009500	ENSMUSG00000009621	Vav2	2810040F13Rik|AI847175|Vav-2	vav 2 oncogene	protein-coding
mm_19107.1	chr2	79454987	79454992	-	1	NA	exon (NM_010894, exon 2 of 2)	exon (NM_010894, exon 2 of 2)	1647	NM_010894	18012	Mm.4636	NM_010894	ENSMUSG00000034701	Neurod1	BETA2|BHF-1|Nd1|Neurod|bHLHa3	neurogenic differentiation 1	protein-coding
mm_150405.1	chr19	36834216	36834297	+	1	NA	promoter-TSS (NM_001163635)	promoter-TSS (NM_001163635)	24	NM_001163635	74493	Mm.249310	NM_001163635	ENSMUSG00000024811	Tnks2	5430432P15Rik|AA517131|AI662480|ARTD6|TNKS-2|Tank2	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase 2	protein-coding
mm_79195.1	chr9	48495073	48495115	+	1	NA	promoter-TSS (NM_001004191)	promoter-TSS (NM_001004191)	236	NM_001326355	67010	Mm.76911	NM_144948	ENSMUSG00000042396	Rbm7	1200007M24Rik|1500011D06Rik|AU041934|AW554393	RNA binding motif protein 7	protein-coding
mm_159573.1	chr4	115518302	115518302	+	1	NA	promoter-TSS (NM_010011)	promoter-TSS (NM_010011)	15	NM_010011	13117	Mm.10742	NM_010011	ENSMUSG00000066072	Cyp4a10	AI647584|Cyp4a|D4Rp1|Msp-3|RP1	cytochrome P450, family 4, subfamily a, polypeptide 10	protein-coding
mm_130982.1	chr15	103344775	103344789	-	1	NA	3' UTR (NM_010577, exon 30 of 30)	3' UTR (NM_010577, exon 30 of 30)	-4696	NM_013866	29813	Mm.14099	NM_013866	ENSMUSG00000000552	Zfp385a	Hzf|Zfp385|Znf385a	zinc finger protein 385A	protein-coding
mm_109007.1	chr12	103336889	103336899	+	1	NA	intron (NM_023049, intron 3 of 9)	intron (NM_023049, intron 3 of 9)	19107	NM_023049	65256	Mm.27159	NM_023049	ENSMUSG00000021200	Asb2	1110008E15Rik	ankyrin repeat and SOCS box-containing 2	protein-coding
mm_159246.1	chr2	151476153	151476153	-	1	NA	promoter-TSS (NM_198655)	promoter-TSS (NM_198655)	-2	NM_198655	381393	Mm.280614	NM_198655	ENSMUSG00000061525	4921509C19Rik	Gm1005	RIKEN cDNA 4921509C19 gene	protein-coding
mm_99614.1	chr11	104586283	104586296	+	1	NA	intron (NM_010858, intron 8 of 8)	MTD|LTR|ERVL-MaLR	-21711	NM_016780	16416	Mm.87150	NM_016780	ENSMUSG00000020689	Itgb3	CD61|GP3A|INGRB3	integrin beta 3	protein-coding
mm_43806.1	chr5	142903765	142903787	+	1	NA	3' UTR (NM_007393, exon 6 of 6)	3' UTR (NM_007393, exon 6 of 6)	2978	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_155418.1	chrX	73490905	73490941	+	1	NA	exon (NM_007542, exon 2 of 8)	exon (NM_007542, exon 2 of 8)	7322	NM_007542	12111	Mm.2608	NM_007542	ENSMUSG00000031375	Bgn	BG|DSPG1|PG-S1|PGI|SLRR1A	biglycan	protein-coding
mm_9112.1	chr1	170174782	170174796	-	1	NA	5' UTR (NM_133806, exon 1 of 11)	5' UTR (NM_133806, exon 1 of 11)	175	NM_001305046	107652	Mm.27969	NM_133806	ENSMUSG00000026670	Uap1	AA420407|AA437972|AGX-1|AGX-2|AGX1|AgX|ESTM38|SPAG2	UDP-N-acetylglucosamine pyrophosphorylase 1	protein-coding
mm_115187.1	chr13	108471867	108471868	+	1	NA	Intergenic	Tigger17a|DNA|TcMar-Tigger	155530	NM_178683	218581	Mm.32318	NM_178683	ENSMUSG00000021697	Depdc1b	9830132O03|AW260467|XTP1	DEP domain containing 1B	protein-coding
mm_99193.1	chr11	101009466	101009528	+	1	NA	promoter-TSS (NM_001243049)	promoter-TSS (NM_001243049)	45	NM_001243051	11975	Mm.340818	NM_016920	ENSMUSG00000019302	Atp6v0a1	AA959968|ATP6a1|Atp6n1|Atp6n1a|Atpv0a1|Vpp-1|Vpp1	ATPase, H+ transporting, lysosomal V0 subunit A1	protein-coding
mm_9908.1	chr1	187215455	187215478	-	1	NA	promoter-TSS (NM_029067)	promoter-TSS (NM_029067)	-20	NM_028848	74717	Mm.250430	NM_028848	ENSMUSG00000026611	Spata17	1700065F16Rik|4930504I07Rik|4930513F16Rik|MSRG-11	spermatogenesis associated 17	protein-coding
mm_111549.1	chr12	101016123	101016148	-	1	NA	intron (NM_026681, intron 3 of 29)	intron (NM_026681, intron 3 of 29)	5633	NR_035421	100316805		NR_035421	ENSMUSG00000080575	Mir1190	Mirn1190|mmu-mir-1190	microRNA 1190	ncRNA
mm_48896.1	chr5	151651217	151651237	-	1	NA	promoter-TSS (NM_027009)	promoter-TSS (NM_027009)	-19	NM_027009	69263	Mm.12553	NM_027009	ENSMUSG00000033970	Rfc3	2810416I22Rik|38kDa|AU022547|Recc3	replication factor C (activator 1) 3	protein-coding
mm_145034.1	chr18	39353561	39353564	+	1	NA	intron (NM_175164, intron 20 of 22)	L1ME4a|LINE|L1	133683	NM_008173	14815	Mm.129481	NM_008173	ENSMUSG00000024431	Nr3c1	GR|Grl-1|Grl1	nuclear receptor subfamily 3, group C, member 1	protein-coding
mm_161148.1	chr13	22852472	22852472	-	1	NA	promoter-TSS (NM_134243)	promoter-TSS (NM_134243)	23	NM_134243	171277	Mm.377228	NM_134243	ENSMUSG00000063998	Vmn1r211	V1rh20	vomeronasal 1 receptor 211	protein-coding
mm_87383.1	chr10	44731008	44731016	+	1	NA	Intergenic	Intergenic	-272264	NM_007548	12142	Mm.4800	NM_007548	ENSMUSG00000038151	Prdm1	Blimp-1|Blimp1|PRDI-BF1|ZNFPR1A1|b2b1765Clo	PR domain containing 1, with ZNF domain	protein-coding
mm_158815.1	chrX	167308297	167308309	-	1	NA	exon (NM_001290758, exon 4 of 4)	exon (NM_001290758, exon 4 of 4)	22268	NM_001290757	170743	Mm.23979	NM_133211	ENSMUSG00000044583	Tlr7	-	toll-like receptor 7	protein-coding
mm_173207.1	chrX	69938523	69938526	-	1	NA	intron (NR_033213, intron 8 of 8)	intron (NR_033213, intron 8 of 8)	-6757	NM_029316	75509	Mm.233475	NM_029316	ENSMUSG00000059690	1700020N15Rik	-	RIKEN cDNA 1700020N15 gene	protein-coding
mm_86069.1	chr9	114775444	114775458	-	1	NA	intron (NM_001252479, intron 1 of 3)	intron (NM_001252479, intron 1 of 3)	6542	NM_133978	102545	Mm.35600	NM_133978	ENSMUSG00000032436	Cmtm7	AI481279|Cklfsf7|LNV	CKLF-like MARVEL transmembrane domain containing 7	protein-coding
mm_43429.1	chr5	136060056	136060086	+	1	NA	exon (NM_027158, exon 3 of 6)	exon (NM_027158, exon 3 of 6)	2804	NM_027158	69665	Mm.75713	NM_027158	ENSMUSG00000006143	Upk3bl	2310043J07Rik	uroplakin 3B-like	protein-coding
mm_73127.1	chr8	94838389	94838425	+	1	NA	promoter-TSS (NM_026452)	promoter-TSS (NM_026452)	-10	NM_026452	67914	Mm.169234	NM_026452	ENSMUSG00000031782	Coq9	2310005O14Rik|C78387	coenzyme Q9	protein-coding
mm_127567.1	chr15	102243485	102243501	+	1	NA	intron (NM_011244, intron 3 of 9)	intron (NM_011244, intron 3 of 9)	3007	NM_001042727	19411	Mm.1273	NM_011244	ENSMUSG00000001288	Rarg	Nr1b3|RAR-gamma|RARD|RARgamma2	retinoic acid receptor, gamma	protein-coding
mm_123311.1	chr14	62347028	62347030	-	1	NA	intron (NM_026001, intron 2 of 10)	intron (NM_026001, intron 2 of 10)	14924	NM_026001	67153	Mm.26040	NM_026001	ENSMUSG00000021932	Rnaseh2b	1110019N06Rik|2610207P08Rik|Dleu8	ribonuclease H2, subunit B	protein-coding
mm_86749.1	chr10	19506247	19506257	+	1	NA	Intergenic	Intergenic	-85697	NM_010511	15979	Mm.549	NM_010511	ENSMUSG00000020009	Ifngr1	CD119|IFN-gammaR|Ifgr|Ifngr|Nktar	interferon gamma receptor 1	protein-coding
mm_46091.1	chr5	92347061	92347092	-	1	NA	3' UTR (NM_021274, exon 4 of 4)	3' UTR (NM_021274, exon 4 of 4)	1813	NM_021274	15945	Mm.877	NM_021274	ENSMUSG00000034855	Cxcl10	C7|CRG-2|INP10|IP-10|IP10|Ifi10|Scyb10|gIP-10|mob-1	chemokine (C-X-C motif) ligand 10	protein-coding
mm_112514.1	chr13	9093886	9093892	+	1	NA	promoter-TSS (NM_172585)	promoter-TSS (NM_172585)	8	NM_172585	217980	Mm.234944	NM_172585	ENSMUSG00000033499	Larp4b	A630096F19|AI256361|D13Wsu64e|Larp5	La ribonucleoprotein domain family, member 4B	protein-coding
mm_6582.1	chr1	75219912	75219922	-	1	NA	promoter-TSS (NM_001313724)	promoter-TSS (NM_001313724)	-623	NM_001313724	22145	Mm.1155	NM_009447	ENSMUSG00000026202	Tuba4a	M[a]4|Tuba4	tubulin, alpha 4A	protein-coding
mm_134591.1	chr16	20426376	20426386	-	1	NA	promoter-TSS (NM_013790)	promoter-TSS (NM_013790)	13	NM_013790	27416	Mm.20845	NM_013790	ENSMUSG00000022822	Abcc5	2900011L11Rik|AI132311|Abcc5a|Abcc5b|Mrp5	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	protein-coding
mm_49983.1	chr6	41033046	41033057	+	1	NA	exon (NM_023333, exon 3 of 5)	exon (NM_023333, exon 3 of 5)	2458	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_124807.1	chr15	8838068	8838082	+	1	NA	Intergenic	(T)n|Simple_repeat|Simple_repeat	-127268	NM_148938	20512	Mm.204834	NM_148938	ENSMUSG00000005360	Slc1a3	AI504299|B430115D02Rik|Eaat1|GLAST|GLAST-1|GLU-T|GluT-1|Gmt1|MGluT1	solute carrier family 1 (glial high affinity glutamate transporter), member 3	protein-coding
mm_138171.1	chr17	34264803	34264813	+	1	NA	exon (NM_207105, exon 2 of 6)	exon (NM_207105, exon 2 of 6)	1581	NM_207105	14961	Mm.254067	NM_207105	ENSMUSG00000073421	H2-Ab1	AI845868|Abeta|H-2Ab|H2-Ab|I-Abeta|IAb|Ia-2|Ia2|Rmcs1	histocompatibility 2, class II antigen A, beta 1	protein-coding
mm_6370.1	chr1	72284225	72284228	-	1	NA	promoter-TSS (NM_175564)	promoter-TSS (NM_175564)	88	NM_023523	111175	Mm.281738	NM_023523	ENSMUSG00000026189	Pecr	2400003B18Rik|TERP	peroxisomal trans-2-enoyl-CoA reductase	protein-coding
mm_22723.1	chr3	19560251	19560260	+	1	NA	intron (NM_025489, intron 2 of 4)	U1|snRNA|snRNA	29008	NM_001163537	66326	Mm.45615	NM_025489	ENSMUSG00000027606	Dnajc5b	1700008A05Rik	DnaJ heat shock protein family (Hsp40) member C5 beta	protein-coding
mm_167415.1	chr8	107846843	107846850	+	1	NA	Intergenic	Intergenic	-258364	NM_010817	17463	Mm.18347	NM_010817	ENSMUSG00000039067	Psmd7	AW107203|Mov-34|Mov34	proteasome (prosome, macropain) 26S subunit, non-ATPase, 7	protein-coding
mm_51506.1	chr6	83135829	83135874	+	1	NA	promoter-TSS (NM_001136227)	promoter-TSS (NM_001136227)	43	NM_001136227	20166	Mm.4139	NM_009106	ENSMUSG00000034930	Rtkn	-	rhotekin	protein-coding
mm_93525.1	chr10	115314910	115314930	-	1	NA	intron (NM_024454, intron 1 of 6)	intron (NM_024454, intron 1 of 6)	671	NM_024454	216344	Mm.21936	NM_024454	ENSMUSG00000020132	Rab21	9630024B22	RAB21, member RAS oncogene family	protein-coding
mm_16927.1	chr2	13793729	13793753	-	1	NA	promoter-TSS (NM_145838)	promoter-TSS (NM_145838)	-221	NM_145838	241230	Mm.330004	NM_145838	ENSMUSG00000003418	St8sia6	1700007J08Rik|AI314453|AI875066|ST8SiaVI|Siat8f	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 6	protein-coding
mm_144857.1	chr18	36679576	36679592	+	1	NA	promoter-TSS (NM_146085)	promoter-TSS (NM_146085)	-218	NM_146085	225372	Mm.89673	NM_146085	ENSMUSG00000006050	Apbb3	Fe65l2|Rirl2|TR2S	amyloid beta (A4) precursor protein-binding, family B, member 3	protein-coding
mm_111559.1	chr12	101083576	101083611	-	1	NA	non-coding (NR_038049, exon 1 of 2)	non-coding (NR_038049, exon 1 of 2)	109	NM_211355	68734	Mm.87077	NM_211355	ENSMUSG00000041846	Smek1	1110034C04Rik|BC064465|Ppp4r3a|mKIAA2010	SMEK homolog 1, suppressor of mek1 (Dictyostelium)	protein-coding
mm_163729.1	chr13	119613859	119613878	-	1	NA	Intergenic	PB1D7|SINE|Alu	-9951	NM_020279	56838	Mm.143745	NM_020279	ENSMUSG00000074715	Ccl28	CCK1|MEC|Scya28	chemokine (C-C motif) ligand 28	protein-coding
mm_76163.1	chr8	82379055	82379065	-	1	NA	intron (NM_008357, intron 2 of 7)	intron (NM_008357, intron 2 of 7)	23526	NM_001254747	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_141455.1	chr17	30415845	30415848	-	1	NA	intron (NM_172618, intron 6 of 11)	intron (NM_172618, intron 6 of 11)	-19666	NR_030688	623169	Mm.440508	NR_030688		Gm6402	EG623169	ribosomal protein S17 pseudogene	pseudo
mm_101278.1	chr11	21565889	21565907	-	1	NA	exon (NM_001316675, exon 3 of 9)	exon (NM_001316675, exon 3 of 9)	6036	NM_008618	17449	Mm.212703	NM_008618	ENSMUSG00000020321	Mdh1	B230377B03Rik|D17921|MDH-s|MDHA|Mor-2|Mor2	malate dehydrogenase 1, NAD (soluble)	protein-coding
mm_46706.1	chr5	110286044	110286052	-	1	NA	promoter-TSS (NM_011132)	promoter-TSS (NM_011132)	120	NM_008993	19301	Mm.21853	NM_008993	ENSMUSG00000029499	Pxmp2	22kDa|PMP22	peroxisomal membrane protein 2	protein-coding
mm_10337.1	chr2	11642843	11642863	+	1	NA	promoter-TSS (NM_008367)	promoter-TSS (NM_008367)	61	NM_008367	16184	Mm.915	NM_008367	ENSMUSG00000026770	Il2ra	CD25|Il2r|Ly-43	interleukin 2 receptor, alpha chain	protein-coding
mm_119074.1	chr14	30879534	30879549	+	1	NA	5' UTR (NM_181390, exon 1 of 3)	5' UTR (NM_181390, exon 1 of 3)	284	NM_181390	66175	Mm.220895	NM_181390	ENSMUSG00000042485	Mustn1	1110028G01Rik|Mustang	musculoskeletal, embryonic nuclear protein 1	protein-coding
mm_107862.1	chr12	69893222	69893276	+	1	NA	promoter-TSS (NM_201519)	promoter-TSS (NM_201519)	-86	NM_201519	399510	Mm.291936	NM_201519	ENSMUSG00000034761	Map4k5	4432415E19Rik|GCKR|KHS|MAPKKKK5	mitogen-activated protein kinase kinase kinase kinase 5	protein-coding
mm_154835.1	chrX	19112458	19112468	+	1	NA	Intergenic	Intergenic	33925	NR_029806	723827		NR_029806	ENSMUSG00000065422	Mir221	Mirn221|mir-221|mmu-mir-221	microRNA 221	ncRNA
mm_19323.1	chr2	90571972	90571992	-	1	NA	intron (NM_008982, intron 1 of 23)	intron (NM_008982, intron 1 of 23)	8665	NM_008982	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_172814.1	chr9	123689615	123689619	-	1	NA	Intergenic	Intergenic	-10785	NM_139142	102680	Mm.440867	NM_139142	ENSMUSG00000036814	Slc6a20a	A730081N20Rik|AU022428|Xt3s1|Xtrp3s1	solute carrier family 6 (neurotransmitter transporter), member 20A	protein-coding
mm_53047.1	chr6	124714007	124714031	+	1	NA	exon (NM_007531, exon 4 of 9)	exon (NM_007531, exon 4 of 9)	1730	NM_007531	12034	Mm.36241	NM_007531	ENSMUSG00000004264	Phb2	AU044498|BAP|Bap37|Bcap37|REA	prohibitin 2	protein-coding
mm_129819.1	chr15	83033230	83033240	-	1	NA	5' UTR (NM_001271412, exon 1 of 6)	5' UTR (NM_001271412, exon 1 of 6)	162	NM_001271412	74039	Mm.32584	NM_028728	ENSMUSG00000058099	Nfam1	4921501M20Rik|Cnaip	Nfat activating molecule with ITAM motif 1	protein-coding
mm_101675.1	chr11	39360135	39360140	-	1	NA	intron (NR_126439, intron 2 of 2)	intron (NR_126439, intron 2 of 2)	30088	NR_126439	75315	Mm.461295	NR_126439		4930553C11Rik	-	RIKEN cDNA 4930553C11 gene	ncRNA
mm_103839.1	chr11	83040417	83040432	-	1	NA	promoter-TSS (NR_073523)	promoter-TSS (NR_073523)	109	NR_073524	237887	Mm.341645	NM_181542	ENSMUSG00000072621	Slfn10-ps	Slfn10|mFLJ00257	schlafen 10, pseudogene	pseudo
mm_104766.1	chr11	98508813	98508833	-	1	NA	intron (NM_011771, intron 3 of 7)	intron (NM_011771, intron 3 of 7)	37208	NM_011771	22780	Mm.133367	NM_011771	ENSMUSG00000018168	Ikzf3	5830411O07Rik|Aiolos|Zfpn1a3|Znfn1a3	IKAROS family zinc finger 3	protein-coding
mm_155286.1	chrX	61183323	61183334	+	1	NA	TTS (NM_001166658)	TTS (NM_001166658)	2230	NM_001166658	631990	Mm.401324	NM_001166658	ENSMUSG00000090546	Cdr1	100039759|Cdr|Cdr34|EG631990|Gm2409|Gm7077	cerebellar degeneration related antigen 1	protein-coding
mm_60182.1	chr7	43091597	43091601	+	1	NA	Intergenic	Intergenic	72801	NM_001105061	668612	Mm.469896	NM_001105061	ENSMUSG00000091528	Gm9268	EG668612|Vmn2r64	predicted gene 9268	protein-coding
mm_54886.1	chr6	43666135	43666145	-	1	NA	5' UTR (NM_013861, exon 1 of 9)	5' UTR (NM_013861, exon 1 of 9)	138	NM_001311111	29807	Mm.320979	NM_013861	ENSMUSG00000029735	Tpk1	-	thiamine pyrophosphokinase	protein-coding
mm_135847.1	chr16	59171306	59171341	-	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-3182	NM_146779	258775	Mm.438896	NM_146779	ENSMUSG00000096695	Olfr196	MOR183-1	olfactory receptor 196	protein-coding
mm_38613.1	chr4	141932907	141932932	-	1	NA	intron (NM_177868, intron 15 of 31)	intron (NM_177868, intron 15 of 31)	-50073	NR_040672	545691	Mm.332015	NR_040672	ENSMUSG00000085424	Fhad1os1	Gm13037|OTTMUSG00000010113	forkhead-associated (FHA) phosphopeptide binding domain 1, opposite strand 1	ncRNA
mm_86623.1	chr10	13966240	13966244	+	1	NA	promoter-TSS (NM_010437)	promoter-TSS (NM_010437)	-137	NM_010437	15273	Mm.42157	NM_010437	ENSMUSG00000015501	Hivep2	Gm20114|MIBP1|Schnurri-2|Shn-2	human immunodeficiency virus type I enhancer binding protein 2	protein-coding
mm_20470.1	chr2	129371132	129371146	-	1	NA	promoter-TSS (NM_008361)	promoter-TSS (NM_008361)	0	NM_008361	16176	Mm.222830	NM_008361	ENSMUSG00000027398	Il1b	IL-1beta|Il-1b	interleukin 1 beta	protein-coding
mm_61715.1	chr7	81571247	81571318	+	1	NA	promoter-TSS (NM_001004185)	promoter-TSS (NM_001004185)	-10	NM_001004185	434204	Mm.181641	NM_001004185	ENSMUSG00000045795	Whamm	BB081391|Whdc1|mKIAA1971	WAS protein homolog associated with actin, golgi membranes and microtubules	protein-coding
mm_77915.1	chr9	7350107	7350117	+	1	NA	exon (NM_008605, exon 4 of 10)	exon (NM_008605, exon 4 of 10)	2738	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_39368.1	chr5	9295402	9295409	+	1	NA	intron (NM_172706, intron 1 of 21)	intron (NM_172706, intron 1 of 21)	29212	NM_172706	231014	Mm.130063	NM_172706	ENSMUSG00000056004	9330182L06Rik	Eig121l	RIKEN cDNA 9330182L06 gene	protein-coding
mm_139311.1	chr17	48351742	48351785	+	1	NA	exon (NM_031254, exon 4 of 5)	exon (NM_031254, exon 4 of 5)	5362	NM_001272078	83433	Mm.261623	NM_031254	ENSMUSG00000023992	Trem2	TREM-2|Trem2a|Trem2b|Trem2c	triggering receptor expressed on myeloid cells 2	protein-coding
mm_143188.1	chr17	58991344	58991354	-	1	NA	promoter-TSS (NM_027001)	promoter-TSS (NM_027001)	26	NM_027001	69239	Mm.246732	NM_027001	ENSMUSG00000024227	Pdzph1	2610034M16Rik|AV114557	PDZ and pleckstrin homology domains 1	protein-coding
mm_23978.1	chr3	85998868	85998871	+	1	NA	intron (NM_001001650, intron 3 of 5)	MTD|LTR|ERVL-MaLR	3622	NM_001001650	368202	Mm.253822	NM_001001650	ENSMUSG00000049013	Prss48	Esspl|Gm1019	protease, serine 48	protein-coding
mm_151628.1	chr19	3912712	3912722	-	1	NA	promoter-TSS (NM_001271444)	promoter-TSS (NM_001271444)	57	NM_144870	225887	Mm.44227	NM_144870	ENSMUSG00000059734	Ndufs8	BC021616|CI-23kD|TYKY	NADH dehydrogenase (ubiquinone) Fe-S protein 8	protein-coding
mm_148643.1	chr19	5489319	5489361	+	1	NA	Intergenic	Intergenic	-1004	NM_027877	71711	Mm.27697	NM_027877	ENSMUSG00000024906	Mus81	1200008A18Rik|AI182501|AW045863	MUS81 structure-specific endonuclease subunit	protein-coding
mm_22085.1	chr2	168767063	168767065	-	1	NA	5' UTR (NM_201396, exon 1 of 3)	5' UTR (NM_201396, exon 1 of 3)	137	NM_201395	99377	Mm.434054	NM_175303	ENSMUSG00000027547	Sall4	5730441M18Rik|AA407717|AL022809|AW536104|C330011P20Rik|C78083|C78563|Tex20	sal-like 4 (Drosophila)	protein-coding
mm_94836.1	chr11	23497840	23497850	+	1	NA	exon (NM_172391, exon 1 of 9)	exon (NM_172391, exon 1 of 9)	194	NM_001290655	268390	Mm.13148	NM_172391	ENSMUSG00000020288	Ahsa2	-	AHA1, activator of heat shock protein ATPase 2	protein-coding
mm_154653.1	chrX	7841801	7841866	+	1	NA	promoter-TSS (NM_001290536)	promoter-TSS (NM_001290536)	2	NM_138604	54644	Mm.142827	NM_138604	ENSMUSG00000031154	Otud5	AA407879|AI553596|BB114028|DUBA|DXImx46e|Sfc7	OTU domain containing 5	protein-coding
mm_133861.1	chr16	96313726	96313727	+	1	NA	5' UTR (NM_001122993, exon 3 of 4)	5' UTR (NM_001122993, exon 3 of 4)	32694	NM_033149	93961	Mm.154783	NM_033149	ENSMUSG00000074892	B3galt5	1190002B21Rik|AU045265|b3Galt-V	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 5	protein-coding
mm_62568.1	chr7	104244450	104244460	+	1	NA	promoter-TSS (NM_030684)	promoter-TSS (NM_030684)	-2	NM_030684	94094	Mm.326945	NM_030684	ENSMUSG00000056144	Trim34a	Trim34|Trim34-1	tripartite motif-containing 34A	protein-coding
mm_14172.1	chr2	126707184	126707235	+	1	NA	promoter-TSS (NM_001252580)	promoter-TSS (NM_001252580)	-119	NM_001252580	84092	Mm.272629	NM_019729	ENSMUSG00000027363	Usp8	AI574262|AW557536|Ubpy|mKIAA0055	ubiquitin specific peptidase 8	protein-coding
mm_123193.1	chr14	57999216	57999226	-	1	NA	promoter-TSS (NM_028643)	promoter-TSS (NM_028643)	41	NM_028643	68514	Mm.26834	NM_028643	ENSMUSG00000021973	Micu2	1110008L20Rik|4833427E09Rik|AU041871|Efha1|Smhs2	mitochondrial calcium uptake 2	protein-coding
mm_98969.1	chr11	98682789	98682818	+	1	NA	exon (NM_009439, exon 1 of 12)	exon (NM_009439, exon 1 of 12)	249	NM_009439	22123	Mm.12194	NM_009439	ENSMUSG00000017221	Psmd3	AI255837|AntP91a|D11Bwg1349e|Psd3|Tstap91a	proteasome (prosome, macropain) 26S subunit, non-ATPase, 3	protein-coding
mm_60955.1	chr7	47053024	47053030	+	1	NA	exon (NM_026436, exon 2 of 3)	exon (NM_026436, exon 2 of 3)	2387	NM_026436	67893	Mm.27338	NM_026436	ENSMUSG00000010307	Tmem86a	1810054O13Rik|AI414959|AW742698	transmembrane protein 86A	protein-coding
mm_169548.1	chr15	103242288	103242292	+	1	NA	exon (NM_010447, exon 5 of 10)	exon (NM_010447, exon 5 of 10)	1836	NR_002883	434858	Mm.391346	NR_002883		Gm5643	EG434858	heterogeneous nuclear ribonucleoprotein A1 pseudogene	pseudo
mm_3120.1	chr1	134646603	134646686	+	1	NA	promoter-TSS (NM_009307)	promoter-TSS (NM_009307)	-37	NM_009307	20980	Mm.5102	NM_009307	ENSMUSG00000026452	Syt2	IP4BP|R74640|mKIAA4194	synaptotagmin II	protein-coding
mm_67648.1	chr7	84669898	84669901	-	1	NA	intron (NM_022985, intron 1 of 7)	intron (NM_022985, intron 1 of 7)	9452	NM_022985	65098	Mm.209349	NM_022985	ENSMUSG00000030629	Zfand6	3110005P07Rik|Awp1|Za20d3	zinc finger, AN1-type domain 6	protein-coding
mm_28464.1	chr3	90695246	90695325	-	1	NA	exon (NM_001281852, exon 2 of 3)	exon (NM_001281852, exon 2 of 3)	436	NM_001281852	20202	Mm.2128	NM_009114	ENSMUSG00000056071	S100a9	60B8Ag|AW546964|BEE22|Cagb|GAGB|L1Ag|MRP14|p14	S100 calcium binding protein A9 (calgranulin B)	protein-coding
mm_71165.1	chr8	40546304	40546332	+	1	NA	3' UTR (NM_033560, exon 12 of 12)	3' UTR (NM_033560, exon 12 of 12)	-30471	NM_001271542	18983	Mm.272551	NM_011135	ENSMUSG00000031601	Cnot7	AU022737|CAF-1|Caf1|Pop2	CCR4-NOT transcription complex, subunit 7	protein-coding
mm_150738.1	chr19	43753113	43753131	+	1	NA	promoter-TSS (NM_001113562)	promoter-TSS (NM_001113562)	99	NM_025530	66388	Mm.20257	NM_025530	ENSMUSG00000025193	Cutc	2310039I18Rik|AI326282|CGI-32	cutC copper transporter	protein-coding
mm_148262.1	chr18	80933974	80934045	-	1	NA	promoter-TSS (NM_015805)	promoter-TSS (NM_015805)	49	NM_001201569	50771	Mm.247138	NM_015805	ENSMUSG00000024566	Atp9b	AA934181|Atpc2b|IIb|MMR	ATPase, class II, type 9B	protein-coding
mm_71791.1	chr8	66860295	66860314	+	1	NA	promoter-TSS (NM_001163564)	promoter-TSS (NM_001163564)	87	NM_001163564	234344	Mm.334561	NM_001163564	ENSMUSG00000014907	Naf1	Gm174	nuclear assembly factor 1 ribonucleoprotein	protein-coding
mm_20434.1	chr2	129306562	129306584	-	1	NA	exon (NM_010554, exon 4 of 7)	exon (NM_010554, exon 4 of 7)	3399	NM_010554	16175	Mm.15534	NM_010554	ENSMUSG00000027399	Il1a	Il-1a	interleukin 1 alpha	protein-coding
mm_77860.1	chr9	5312913	5312924	+	1	NA	intron (NM_007609, intron 1 of 8)	L1M2|LINE|L1	4069	NM_007609	12363	Mm.1569	NM_007609	ENSMUSG00000033538	Casp4	CASP-11|CASP-4|Casp11|Caspl|ich-3	caspase 4, apoptosis-related cysteine peptidase	protein-coding
mm_23452.1	chr3	60031815	60031823	+	1	NA	promoter-TSS (NM_023383)	promoter-TSS (NM_023383)	31	NM_023383	67758	Mm.24547	NM_023383	ENSMUSG00000027761	Aadac	5033417E09Rik|AI265437|Aada	arylacetamide deacetylase (esterase)	protein-coding
mm_170587.1	chr19	5799834	5799839	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	2836	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_147376.1	chr18	43687556	43687582	-	1	NA	5' UTR (NM_001163637, exon 1 of 22)	5' UTR (NM_001163637, exon 1 of 22)	204	NM_001163637	76217	Mm.134602	NM_001163637	ENSMUSG00000024502	Jakmip2	6430702L21Rik|AI850334|D930046L20Rik	janus kinase and microtubule interacting protein 2	protein-coding
mm_88105.1	chr10	69096118	69096143	+	1	NA	Intergenic	Intergenic	-112422	NM_001252636	69288	Mm.26659	NM_001081347	ENSMUSG00000019944	Rhobtb1	1700008H16Rik|3110048G13Rik|AI173445|AI573858|AV350930	Rho-related BTB domain containing 1	protein-coding
mm_45650.1	chr5	77018858	77018867	-	1	NA	promoter-TSS (NR_077218)	promoter-TSS (NR_077218)	1	NR_077218	68246	Mm.319633	NR_077218	ENSMUSG00000086632	1700112J05Rik	1700110A09Rik	RIKEN cDNA 1700112J05 gene	ncRNA
mm_78665.1	chr9	40687843	40687853	+	1	NA	intron (NM_133733, intron 1 of 6)	intron (NM_133733, intron 1 of 6)	1884	NM_133733	71566	Mm.280560	NM_133733	ENSMUSG00000032024	Clmp	9030425E11Rik|ACAM|ASP5|AW557819	CXADR-like membrane protein	protein-coding
mm_20325.1	chr2	127458211	127458232	-	1	NA	non-coding (NR_110989, exon 9 of 9)	non-coding (NR_110989, exon 9 of 9)	-13656	NM_029629	68126	Mm.288676	NM_029629	ENSMUSG00000027371	Fahd2a	1500003K14Rik|B430104H02Rik|Cgi-105|Fahd2	fumarylacetoacetate hydrolase domain containing 2A	protein-coding
mm_129457.1	chr15	78572669	78572675	-	1	NA	5' UTR (NM_009008, exon 1 of 7)	5' UTR (NM_009008, exon 1 of 7)	111	NM_009008	19354	Mm.1972	NM_009008	ENSMUSG00000033220	Rac2	AI323801|AI452260	RAS-related C3 botulinum substrate 2	protein-coding
mm_141800.1	chr17	34420175	34420187	-	1	NA	intron (NM_001001177, intron 5 of 19)	intron (NM_001001177, intron 5 of 19)	21361	NM_001163855	407788	Mm.73205	NM_001001177	ENSMUSG00000057246	BC051142	NG8|TSBP|Tesb|Tesbp	cDNA sequence BC051142	protein-coding
mm_95345.1	chr11	48800358	48800369	+	1	NA	promoter-TSS (NM_008143)	promoter-TSS (NM_008143)	3	NM_008143	14694	Mm.5305	NM_008143	ENSMUSG00000020372	Rack1	AL033335|GB-like|Gnb2-rs1|Gnb2l1|p205	receptor for activated C kinase 1	protein-coding
mm_42972.1	chr5	123142111	123142121	+	1	NA	promoter-TSS (NM_001040398)	promoter-TSS (NM_001040398)	-77	NM_001040398	208043	Mm.250391	NM_177581	ENSMUSG00000038384	Setd1b	AA516740|BC035291|KMT2G|mKIAA1076	SET domain containing 1B	protein-coding
mm_60247.1	chr7	43774609	43774622	+	1	NA	promoter-TSS (NM_001177373)	promoter-TSS (NM_001177373)	-2	NM_001177373	56538	Mm.154276	NM_019974	ENSMUSG00000067616	Klk11	2310015I08Rik|Prss20|TLSP	kallikrein related-peptidase 11	protein-coding
mm_53154.1	chr6	125266241	125266252	+	1	NA	intron (NR_015527, intron 1 of 3)	intron (NR_015527, intron 1 of 3)	721	NR_015527	73870	Mm.440681	NR_015527	ENSMUSG00000108129	4930417O13Rik	-	RIKEN cDNA 4930417O13 gene	ncRNA
mm_162501.1	chr1	140245916	140245922	+	1	NA	promoter-TSS (NM_001081027)	promoter-TSS (NM_001081027)	-338	NM_001081027	240776	Mm.483845	NM_001081027	ENSMUSG00000052726	Kcnt2	E330038N15Rik|Slick	potassium channel, subfamily T, member 2	protein-coding
mm_82436.1	chr9	15278790	15278793	-	1	NA	intron (NM_144933, intron 1 of 11)	AT_rich|Low_complexity|Low_complexity	1076	NM_144933	234959	Mm.44151	NM_144933	ENSMUSG00000031935	Med17	77kDa|C330002H14Rik|Crsp6|Trap80	mediator complex subunit 17	protein-coding
mm_26936.1	chr3	20263708	20263730	-	1	NA	exon (NM_029706, exon 7 of 11)	exon (NM_029706, exon 7 of 11)	12014	NM_029706	76703	Mm.34692	NM_029706	ENSMUSG00000011463	Cpb1	0910001A18Rik|1810063F02Rik|2210008M23Rik|AI504870	carboxypeptidase B1 (tissue)	protein-coding
mm_154593.1	chrX	7580501	7580509	+	1	NA	promoter-TSS (NM_001199348)	promoter-TSS (NM_001199348)	22	NM_001199348	20371	Mm.182291	NM_054039	ENSMUSG00000039521	Foxp3	JM2|scurfin|sf	forkhead box P3	protein-coding
mm_170080.1	chr17	34543721	34543738	+	1	NA	Intergenic	IAP1-MM_LTR|LTR|ERVK	-20566	NM_010929	18132	Mm.173813	NM_010929	ENSMUSG00000015468	Notch4	Int-3|Int3|N4	notch 4	protein-coding
mm_72413.1	chr8	81856055	81856066	+	1	NA	intron (NM_001297591, intron 7 of 24)	intron (NM_001297591, intron 7 of 24)	513498	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_25362.1	chr3	107100929	107100989	+	1	NA	promoter-TSS (NM_008417)	promoter-TSS (NM_008417)	-608	NM_008417	16490	Mm.39285	NM_008417	ENSMUSG00000040724	Kcna2	Akr6a4|ENSMUSG00000074335|Gm10672|Kca1-2|Kv1.2|Mk-2	potassium voltage-gated channel, shaker-related subfamily, member 2	protein-coding
mm_11571.1	chr2	32911383	32911405	+	1	NA	exon (NM_146119, exon 4 of 14)	exon (NM_146119, exon 4 of 14)	35260	NM_146119	227737	Mm.301646	NM_146119	ENSMUSG00000026796	Fam129b	9130404D14Rik	family with sequence similarity 129, member B	protein-coding
mm_11243.1	chr2	29889803	29889836	+	1	NA	promoter-TSS (NM_001113213)	promoter-TSS (NM_001113213)	99	NM_001177659	18286	Mm.330116	NM_013615	ENSMUSG00000026790	Odf2	AI848335|MMTEST29	outer dense fiber of sperm tails 2	protein-coding
mm_107570.1	chr12	44328850	44328863	+	1	NA	promoter-TSS (NM_176930)	promoter-TSS (NM_176930)	-29	NM_176930	319504	Mm.208439	NM_176930	ENSMUSG00000020598	Nrcam	Bravo|C030017F07Rik|C130076O07Rik|mKIAA0343	neuronal cell adhesion molecule	protein-coding
mm_48968.1	chr6	4623956	4623973	+	1	NA	intron (NM_145398, intron 8 of 17)	intron (NM_145398, intron 8 of 17)	22898	NM_145398	213819	Mm.270703	NM_145398	ENSMUSG00000015189	Casd1	Cas1|Cast1	CAS1 domain containing 1	protein-coding
mm_171180.1	chr3	35932810	35932811	-	1	NA	promoter-TSS (NM_001205362)	promoter-TSS (NM_001205362)	156	NM_001205361	114893	Mm.374810	NM_033623	ENSMUSG00000027708	Dcun1d1	Rp42|SCCRO|Tes3|pTes3	DCN1, defective in cullin neddylation 1, domain containing 1 (S. cerevisiae)	protein-coding
mm_94771.1	chr11	21239974	21239977	+	1	NA	intron (NM_139061, intron 1 of 22)	AT_rich|Low_complexity|Low_complexity	943	NM_001290628	245944	Mm.170103	NM_139061	ENSMUSG00000020128	Vps54	Hcc8|Vps54l|mSLP8|wr	VPS54 GARP complex subunit	protein-coding
mm_79178.1	chr9	48162009	48162045	+	1	NA	Intergenic	LTR67B|LTR|ERVL	178871	NM_030069	78252	Mm.31626	NM_030069	ENSMUSG00000032028	Nxpe2	4432416J03Rik|AI323362|Fam55b	neurexophilin and PC-esterase domain family, member 2	protein-coding
mm_110231.1	chr12	29291011	29291042	-	1	NA	Intergenic	Intergenic	-237358	NM_001093775	17933	Mm.253067	NM_008666	ENSMUSG00000061911	Myt1l	2900046C06Rik|2900093J19Rik|C630034G21Rik|Nztf1|Pmng1|Png-1|mKIAA1106	myelin transcription factor 1-like	protein-coding
mm_106129.1	chr11	116448395	116448406	-	1	NA	exon (NM_001033267, exon 3 of 14)	exon (NM_001033267, exon 3 of 14)	5947	NM_001033267	217341	Mm.387352	NM_001033267	ENSMUSG00000070331	Qrich2	Gm66	glutamine rich 2	protein-coding
mm_76076.1	chr8	78821137	78821143	-	1	NA	promoter-TSS (NM_030145)	promoter-TSS (NM_030145)	12	NM_001191004	78651	Mm.28694	NM_030145	ENSMUSG00000031683	Lsm6	1500031N17Rik|2410088K19Rik|AI747288	LSM6 homolog, U6 small nuclear RNA and mRNA degradation associated	protein-coding
mm_52638.1	chr6	117174696	117174715	+	1	NA	3' UTR (NM_021704, exon 3 of 3)	3' UTR (NM_021704, exon 3 of 3)	6170	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_38642.1	chr4	143212668	143212678	-	1	NA	promoter-TSS (NM_001081355)	promoter-TSS (NM_001081355)	36	NM_001081355	110593	Mm.332020	NM_001081355	ENSMUSG00000057637	Prdm2	4833427P12Rik|E330024L24Rik|Gm1033|Gm19732|KMT8|Riz|Riz1|Znfpr1c1	PR domain containing 2, with ZNF domain	protein-coding
mm_152266.1	chr19	8798496	8798565	-	1	NA	promoter-TSS (NM_026329)	promoter-TSS (NM_026329)	27	NM_026329	67710	Mm.22117	NM_026329	ENSMUSG00000071662	Polr2g	2410046K11Rik|A230108L04Rik|C76415|RBP7|Rpo2-7l	polymerase (RNA) II (DNA directed) polypeptide G	protein-coding
mm_59498.1	chr7	27537603	27537645	+	1	NA	exon (NM_011116, exon 10 of 14)	exon (NM_011116, exon 10 of 14)	14363	NM_001033315	233020	Mm.429716	NM_001033315	ENSMUSG00000040424	Hipk4	Gm162	homeodomain interacting protein kinase 4	protein-coding
mm_112687.1	chr13	16030958	16030973	+	1	NA	3' UTR (NM_008380, exon 5 of 5)	3' UTR (NM_008380, exon 5 of 5)	19114	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_19298.1	chr2	90463108	90463130	-	1	NA	exon (NM_008982, exon 7 of 24)	exon (NM_008982, exon 7 of 24)	16055	NM_001135657	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_88305.1	chr10	75324969	75324979	+	1	NA	5' UTR (NM_001331096, exon 1 of 3)	5' UTR (NM_001331096, exon 1 of 3)	116	NM_001331096	11540	Mm.333734	NM_009630	ENSMUSG00000020178	Adora2a	A2AAR|A2aR|AA2AR	adenosine A2a receptor	protein-coding
mm_94776.1	chr11	21272146	21272180	+	1	NA	intron (NM_139061, intron 5 of 22)	intron (NM_139061, intron 5 of 22)	33131	NM_001290628	245944	Mm.170103	NM_139061	ENSMUSG00000020128	Vps54	Hcc8|Vps54l|mSLP8|wr	VPS54 GARP complex subunit	protein-coding
mm_23123.1	chr3	37644820	37644823	+	1	NA	TTS (NM_011896)	TTS (NM_011896)	4874	NM_001305442	24063	Mm.330986	NM_011896	ENSMUSG00000037211	Spry1	sprouty1|spry-1	sprouty homolog 1 (Drosophila)	protein-coding
mm_84464.1	chr9	66592973	66592985	-	1	NA	5' UTR (NM_144937, exon 1 of 15)	5' UTR (NM_144937, exon 1 of 15)	136	NM_144937	235441	Mm.32465	NM_144937	ENSMUSG00000032376	Usp3	AA409661|BC017156	ubiquitin specific peptidase 3	protein-coding
mm_41824.1	chr5	104046882	104046899	+	1	NA	promoter-TSS (NM_028794)	promoter-TSS (NM_028794)	26	NM_028794	74167	Mm.241484	NM_028794	ENSMUSG00000029310	Nudt9	1190002C07Rik|ADPR-PPase|AI462474	nudix (nucleoside diphosphate linked moiety X)-type motif 9	protein-coding
mm_16071.1	chr2	168081282	168081301	+	1	NA	5' UTR (NM_021409, exon 1 of 3)	5' UTR (NM_021409, exon 1 of 3)	287	NM_021409	58220	Mm.292834	NM_021409	ENSMUSG00000044641	Pard6b	AV025615|Par6b	par-6 family cell polarity regulator beta	protein-coding
mm_84711.1	chr9	73039645	73039674	-	1	NA	promoter-TSS (NM_018889)	promoter-TSS (NM_018889)	40	NM_018889	55981	Mm.139905	NM_018889	ENSMUSG00000079469	Pigb	Pig-b	phosphatidylinositol glycan anchor biosynthesis, class B	protein-coding
mm_10922.1	chr2	25428567	25428576	+	1	NA	promoter-TSS (NM_007379)	promoter-TSS (NM_007379)	-103	NM_007379	11305	Mm.2210	NM_007379	ENSMUSG00000026944	Abca2	AI413825|Abc2|D2H0S1474E|mKIAA1062	ATP-binding cassette, sub-family A (ABC1), member 2	protein-coding
mm_109264.1	chr12	109544808	109544838	+	1	NA	promoter-TSS (NR_003633)	promoter-TSS (NR_003633)	282	NR_037313	100499530		NR_037313	ENSMUSG00000084559	Mir1906-2	mmu-mir-1906-2	microRNA 1906-2	ncRNA
mm_101694.1	chr11	40750694	40750707	-	1	NA	3' UTR (NM_009831, exon 6 of 6)	3' UTR (NM_009831, exon 6 of 6)	4586	NM_009831	12450	Mm.2103	NM_009831	ENSMUSG00000020326	Ccng1	AI314029	cyclin G1	protein-coding
mm_92272.1	chr10	71159810	71159829	-	1	NA	promoter-TSS (NM_001347189)	promoter-TSS (NM_001347189)	-129	NM_001347189	83675	Mm.286834	NM_031397	ENSMUSG00000014329	Bicc1	Bic-C|bpk|jcpk	BicC family RNA binding protein 1	protein-coding
mm_65939.1	chr7	30394431	30394441	-	1	NA	Intergenic	Intergenic	-19352	NM_011662	22177	Mm.46301	NM_011662	ENSMUSG00000030579	Tyrobp	DAP12|KARAP|Ly83	TYRO protein tyrosine kinase binding protein	protein-coding
mm_103397.1	chr11	75437422	75437431	-	1	NA	exon (NM_008878, exon 5 of 10)	exon (NM_008878, exon 5 of 10)	2075	NM_008878	18816	Mm.279733	NM_008878	ENSMUSG00000038224	Serpinf2	AI747498|Pli|Serpimf2	serine (or cysteine) peptidase inhibitor, clade F, member 2	protein-coding
mm_83134.1	chr9	40435234	40435242	-	1	NA	intron (NM_172768, intron 1 of 19)	intron (NM_172768, intron 1 of 19)	20526	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_84492.1	chr9	66847626	66847643	-	1	NA	3' UTR (NM_173413, exon 8 of 8)	3' UTR (NM_173413, exon 8 of 8)	-12928	NM_026674	68318	Mm.284229	NM_026674	ENSMUSG00000053040	Aph1c	0610008A10Rik|APH-1b|Aph1b	aph1 homolog C, gamma secretase subunit	protein-coding
mm_41852.1	chr5	104439396	104439494	+	1	NA	exon (NM_001204203, exon 6 of 7)	exon (NM_001204203, exon 6 of 7)	3253	NM_001204233	20750	Mm.288474	NM_009263	ENSMUSG00000029304	Spp1	2AR|Apl-1|BNSP|BSPI|Bsp|ETA-1|Eta|OP|Opn|Opnl|Ric|Spp-1	secreted phosphoprotein 1	protein-coding
mm_79770.1	chr9	62838580	62838603	+	1	NA	promoter-TSS (NM_001033175)	promoter-TSS (NM_001033175)	-196	NM_001033175	76524	Mm.283636	NM_001033175	ENSMUSG00000032245	Cln6	1810065L06Rik|AW743417|D9Bwg1455e|nclf	ceroid-lipofuscinosis, neuronal 6	protein-coding
mm_116552.1	chr13	46727055	46727057	-	1	NA	intron (NM_175749, intron 1 of 21)	CpG	793	NM_175749	218210	Mm.255398	NM_175749	ENSMUSG00000021374	Nup153	B130015D15Rik|C88147	nucleoporin 153	protein-coding
mm_14240.1	chr2	127702414	127702421	+	1	NA	Intergenic	Intergenic	27480	NM_145532	228576	Mm.133036	NM_145532	ENSMUSG00000027377	Mall	BC012256|BENE	mal, T cell differentiation protein-like	protein-coding
mm_43801.1	chr5	142821864	142821895	+	1	NA	Intergenic	Intergenic	-4492	NM_001122730	231861	Mm.354649	NM_178242	ENSMUSG00000039477	Tnrc18	BC025631|EG381742|Zfp469	trinucleotide repeat containing 18	protein-coding
mm_26507.1	chr3	145810448	145810465	+	1	NA	intron (NM_026993, intron 1 of 5)	intron (NM_026993, intron 1 of 5)	51764	NM_026993	69219	Mm.234247	NM_026993	ENSMUSG00000028194	Ddah1	2410006N07Rik|2510015N06Rik|AI987801|AW050362	dimethylarginine dimethylaminohydrolase 1	protein-coding
mm_21009.1	chr2	152377060	152377080	-	1	NA	promoter-TSS (NM_001009948)	promoter-TSS (NM_001009948)	-504	NM_001009948	228777	Mm.330667	NM_001009948	ENSMUSG00000059361	Nrsn2	Gm123|Neurensin-2	neurensin 2	protein-coding
mm_64165.1	chr7	141395590	141395602	+	1	NA	intron (NM_011528, intron 1 of 7)	intron (NM_011528, intron 1 of 7)	3436	NM_011528	21351	Mm.29182	NM_011528	ENSMUSG00000025503	Taldo1	-	transaldolase 1	protein-coding
mm_13533.1	chr2	110600538	110600548	+	1	NA	intron (NM_001177624, intron 1 of 14)	intron (NM_001177624, intron 1 of 14)	3244	NM_001177624	241612	Mm.277148	NM_001003915	ENSMUSG00000041644	Slc5a12	AI315119|D630015G19|SMCT2	solute carrier family 5 (sodium/glucose cotransporter), member 12	protein-coding
mm_108934.1	chr12	101222063	101222082	+	1	NA	Intergenic	Intergenic	76463	NR_033653	74947	Mm.488905	NR_033653	ENSMUSG00000092054	Kif4-ps	4930463M05Rik|Kif4b	kinesin family member 4, pseudogene	pseudo
mm_22268.1	chr2	178416605	178416607	-	1	NA	intron (NM_001081289, intron 1 of 3)	intron (NM_001081289, intron 1 of 3)	2072	NM_001081289	71532	Mm.40216	NM_001081289	ENSMUSG00000070476	Fam217b	9030418K01Rik|AI851938	family with sequence similarity 217, member B	protein-coding
mm_49293.1	chr6	17693966	17693989	+	1	NA	promoter-TSS (NM_001289625)	promoter-TSS (NM_001289625)	-17	NM_001289624	64213	Mm.12051	NM_022332	ENSMUSG00000029534	St7	9430001H04Rik|Fam4a2|HELG|RAY1|SEN4|TSG7	suppression of tumorigenicity 7	protein-coding
mm_127133.1	chr15	98167893	98167910	+	1	NA	promoter-TSS (NM_177716)	promoter-TSS (NM_177716)	95	NM_177716	239650	Mm.54140	NM_177716	ENSMUSG00000029875	Ccdc184	5630400A08|AI836003	coiled-coil domain containing 184	protein-coding
mm_153387.1	chr19	40377768	40377838	-	1	NA	intron (NM_178362, intron 6 of 28)	intron (NM_178362, intron 6 of 28)	24507	NM_001034964	20411	Mm.210815	NM_009166	ENSMUSG00000025006	Sorbs1	2310065E01Rik|9530001P15Rik|CAP|SH3P12|Sh3d5|mKIAA1296	sorbin and SH3 domain containing 1	protein-coding
mm_143037.1	chr17	56716789	56716858	-	1	NA	promoter-TSS (NM_027244)	promoter-TSS (NM_027244)	98	NM_178926	106639	Mm.37290	NM_178926	ENSMUSG00000054723	Vmac	AI662250	vimentin-type intermediate filament associated coiled-coil protein	protein-coding
mm_53720.1	chr6	143947178	143947184	+	1	NA	promoter-TSS (NM_001347506)	promoter-TSS (NM_001347506)	-75	NM_001347506	20678	Mm.1752	NM_011444	ENSMUSG00000041540	Sox5	A730017D01Rik|AI528773	SRY (sex determining region Y)-box 5	protein-coding
mm_140196.1	chr17	83666807	83666827	+	1	NA	Intergenic	Intergenic	-34922	NM_153512	225030	Mm.223506	NM_153512	ENSMUSG00000045053	Kcng3	KV6.3|Kv10.1a|Kv10.1b	potassium voltage-gated channel, subfamily G, member 3	protein-coding
mm_83929.1	chr9	56635698	56635717	-	1	NA	promoter-TSS (NM_001311076)	promoter-TSS (NM_001311076)	-59	NM_001311076	235402	Mm.246605	NM_181074	ENSMUSG00000049556	Lingo1	4930471K13Rik|AV148400|LERN1|LINGO-1|Lrrn6a|UNQ201	leucine rich repeat and Ig domain containing 1	protein-coding
mm_4263.1	chr1	171458106	171458119	+	1	NA	intron (NM_172647, intron 1 of 9)	B1_Mus1|SINE|Alu	20551	NM_172647	16456	Mm.294882	NM_172647	ENSMUSG00000038235	F11r	9130004G24|AA638916|ESTM33|JAM|JAM-1|JAM-A|Jcam|Jcam1|Ly106	F11 receptor	protein-coding
mm_45840.1	chr5	87696176	87696179	-	1	NA	exon (NM_001286023, exon 3 of 7)	exon (NM_001286023, exon 3 of 7)	3248	NM_001286020	12991	Mm.268737	NM_009972	ENSMUSG00000063157	Csn2	Csnb	casein beta	protein-coding
mm_1676.1	chr1	74817001	74817039	+	1	NA	Intergenic	CpG	25001	NM_009518	22409	Mm.5130	NM_009518	ENSMUSG00000026167	Wnt10a	-	wingless-type MMTV integration site family, member 10A	protein-coding
mm_79544.1	chr9	57911095	57911095	+	1	NA	intron (NM_001122873, intron 1 of 10)	intron (NM_001122873, intron 1 of 10)	109	NM_001122873	69459	Mm.41735	NM_027086	ENSMUSG00000055720	Ubl7	2300004C15Rik	ubiquitin-like 7 (bone marrow stromal cell-derived)	protein-coding
mm_50471.1	chr6	48987859	48987872	+	1	NA	exon (NM_172888, exon 1 of 5)	exon (NM_172888, exon 1 of 5)	1004	NM_172888	243377	Mm.446302	NM_172888	ENSMUSG00000039215	Svs1	9530003A11	seminal vesicle secretory protein 1	protein-coding
mm_133514.1	chr16	90738532	90738564	+	1	NA	5' UTR (NM_029844, exon 1 of 3)	5' UTR (NM_029844, exon 1 of 3)	224	NM_029844	77037	Mm.22455	NM_029844	ENSMUSG00000039956	Mrap	1110025G12Rik|Falp|ORF61	melanocortin 2 receptor accessory protein	protein-coding
mm_140021.1	chr17	73830374	73830401	+	1	NA	exon (NM_020578, exon 6 of 6)	exon (NM_020578, exon 6 of 6)	25546	NM_020578	57440	Mm.18526	NM_020578	ENSMUSG00000024065	Ehd3	Ehd2	EH-domain containing 3	protein-coding
mm_110450.1	chr12	51620648	51620657	-	1	NA	intron (NM_052973, intron 15 of 17)	AT_rich|Low_complexity|Low_complexity	27311	NM_001198835	12810	Mm.21325	NM_007728	ENSMUSG00000020953	Coch	AW122937|Coch-5B2|D12H14S564E	cochlin	protein-coding
mm_66866.1	chr7	57240291	57240294	-	1	NA	intron (NM_008074, intron 3 of 9)	MTD|LTR|ERVL-MaLR	146579	NM_008074	14407	Mm.434343	NM_008074	ENSMUSG00000055026	Gabrg3	B230362M20Rik|Gabrg-3	gamma-aminobutyric acid (GABA) A receptor, subunit gamma 3	protein-coding
mm_110073.1	chr12	21417527	21417587	-	1	NA	promoter-TSS (NM_011739)	promoter-TSS (NM_011739)	-121	NM_011739	22630	Mm.289630	NM_011739	ENSMUSG00000076432	Ywhaq	2700028P07Rik|AA409740|AU021156|R74690	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide	protein-coding
mm_116424.1	chr13	41828469	41828475	-	1	NA	intron (NM_001145875, intron 1 of 6)	intron (NM_001145875, intron 1 of 6)	19016	NM_175417	109254	Mm.25195	NM_175417	ENSMUSG00000058022	Adtrp	9530008L14Rik	androgen dependent TFPI regulating protein	protein-coding
mm_45031.1	chr5	39338860	39338880	-	1	NA	Intergenic	Intergenic	264704	NR_045416	75095	Mm.332354	NR_045416	ENSMUSG00000106741	4930513D17Rik	-	RIKEN cDNA 4930513D17 gene	ncRNA
mm_148513.1	chr19	4231962	4231977	+	1	NA	promoter-TSS (NM_027196)	promoter-TSS (NM_027196)	76	NM_027196	69745	Mm.32518	NM_027196	ENSMUSG00000024854	Pold4	2410012M21Rik|AI463381|AW060307|Polds|p12	polymerase (DNA-directed), delta 4	protein-coding
mm_7496.1	chr1	121346223	121346227	-	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-13636	NM_178082	72999	Mm.27136	NM_133748	ENSMUSG00000003721	Insig2	2900053I11Rik|C730043J18Rik|Insig-2	insulin induced gene 2	protein-coding
mm_55824.1	chr6	83078216	83078235	-	1	NA	promoter-TSS (NM_197992)	promoter-TSS (NM_197992)	-165	NM_197992	69837	Mm.12261	NM_197992	ENSMUSG00000069678	Pcgf1	2010002K04Rik|AU024121|Nspc1	polycomb group ring finger 1	protein-coding
mm_10897.1	chr2	25272463	25272473	+	1	NA	promoter-TSS (NM_175300)	promoter-TSS (NM_175300)	2	NM_175300	99152	Mm.291624	NM_175300	ENSMUSG00000026965	Anapc2	9230107K09Rik|AL024279|Apc2|Emi4|Imi4|mKIAA1406	anaphase promoting complex subunit 2	protein-coding
mm_85174.1	chr9	96525246	96525257	-	1	NA	Intergenic	Intergenic	-46576	NM_001311135	19823	Mm.28235	NM_011279	ENSMUSG00000051234	Rnf7	Rbx2|SAG	ring finger protein 7	protein-coding
mm_159325.1	chr3	27371321	27371321	+	1	NA	promoter-TSS (NM_177330)	promoter-TSS (NM_177330)	-30	NM_177330	208188	Mm.194721	NM_177330	ENSMUSG00000051136	Ghsr	C530020I22Rik|Ghsr1a	growth hormone secretagogue receptor	protein-coding
mm_2893.1	chr1	131910559	131910572	+	1	NA	5' UTR (NM_001145804, exon 1 of 7)	5' UTR (NM_001145804, exon 1 of 7)	107	NM_001145804	98415	Mm.246869	NM_175294	ENSMUSG00000026434	Nucks1	2700010L10Rik|8430423A01Rik|AI647518|C78391|Nucks	nuclear casein kinase and cyclin-dependent kinase substrate 1	protein-coding
mm_134179.1	chr16	10960581	10960591	-	1	NA	3' UTR (NM_019980, exon 4 of 4)	3' UTR (NM_019980, exon 4 of 4)	32535	NM_019980	56722	Mm.294753	NM_019980	ENSMUSG00000022500	Litaf	3222402J11Rik|C85531|N4WBP3|TBX1	LPS-induced TN factor	protein-coding
mm_33822.1	chr4	135439431	135439440	+	1	NA	Intergenic	Intergenic	-5630	NM_022980	53902	Mm.331970	NM_022980	ENSMUSG00000059713	Rcan3	AU041093|Csp3|Dscr1l2	regulator of calcineurin 3	protein-coding
mm_73419.1	chr8	106059784	106059793	+	1	NA	5' UTR (NM_010901, exon 1 of 10)	5' UTR (NM_010901, exon 1 of 10)	185	NM_010901	18021	Mm.383185	NM_010901	ENSMUSG00000031902	Nfatc3	C80703|D8Ertd281e|NFAT4|NFATx	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 3	protein-coding
mm_131605.1	chr16	19218573	19218603	+	1	NA	Intergenic	L1_Rod|LINE|L1	68153	NM_146451	258443	Mm.377506	NM_146451	ENSMUSG00000050742	Olfr164	MOR279-2	olfactory receptor 164	protein-coding
mm_58781.1	chr7	16062740	16062743	+	1	NA	Intergenic	Intergenic	-9104	NM_001347559	666528	Mm.290718	NM_001099277	ENSMUSG00000078796	Zfp541	EG666528|Znf541	zinc finger protein 541	protein-coding
mm_33247.1	chr4	127077375	127077461	+	1	NA	promoter-TSS (NM_177462)	promoter-TSS (NM_177462)	35	NM_001285887	100177	Mm.276096	NM_177462	ENSMUSG00000042408	Zmym6	9330177P20Rik|AI593204|AI661340|D4Wsu24e|Zfp258	zinc finger, MYM-type 6	protein-coding
mm_41235.1	chr5	88764929	88764946	+	1	NA	promoter-TSS (NM_007832)	promoter-TSS (NM_007832)	-76	NM_007832	13178	Mm.298892	NM_007832	ENSMUSG00000029366	Dck	-	deoxycytidine kinase	protein-coding
mm_56993.1	chr6	120916814	120916867	-	1	NA	promoter-TSS (NM_007544)	promoter-TSS (NM_007544)	-20	NM_007544	12122	Mm.235081	NM_007544	ENSMUSG00000004446	Bid	2700049M22Rik|AI875481|AU022477	BH3 interacting domain death agonist	protein-coding
mm_30418.1	chr3	152265884	152265901	-	1	NA	intron (NM_199465, intron 1 of 12)	CpG	428	NM_199465	68810	Mm.200188	NM_199465	ENSMUSG00000039103	Nexn	1110046H09Rik|AA553326|NELIN	nexilin	protein-coding
mm_56613.1	chr6	112490832	112490844	-	1	NA	Intergenic	Intergenic	-1030	NM_001081147	18430	Mm.333310	NM_001081147	ENSMUSG00000049112	Oxtr	OTR	oxytocin receptor	protein-coding
mm_132998.1	chr16	55820386	55820414	+	1	NA	intron (NM_001159395, intron 2 of 12)	intron (NM_001159395, intron 2 of 12)	1738	NM_001159394	80859	Mm.247272	NM_030612	ENSMUSG00000035356	Nfkbiz	AA408868|INAP|Mail	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, zeta	protein-coding
mm_147476.1	chr18	47070890	47070891	-	1	NA	intron (NM_178377, intron 5 of 6)	MIR|SINE|MIR	112014	NM_178377	69456	Mm.210734	NM_178377	ENSMUSG00000042705	Commd10	2310003A05Rik|AU019438|DRWMS2	COMM domain containing 10	protein-coding
mm_8106.1	chr1	135850816	135850825	-	1	NA	exon (NM_001130176, exon 10 of 13)	exon (NM_001130176, exon 10 of 13)	9959	NM_001130176	21956	Mm.247470	NM_011619	ENSMUSG00000026414	Tnnt2	Tnt|cTnT	troponin T2, cardiac	protein-coding
mm_75918.1	chr8	71485929	71485943	-	1	NA	5' UTR (NM_001164679, exon 1 of 17)	5' UTR (NM_001164679, exon 1 of 17)	131	NM_001164679	382014	Mm.260360	NM_001164679	ENSMUSG00000034863	Ano8	BC053460|Tmem16h	anoctamin 8	protein-coding
mm_45876.1	chr5	88328081	88328134	-	1	NA	exon (NM_008644, exon 3 of 3)	exon (NM_008644, exon 3 of 3)	10795	NM_008644	17830	Mm.200411	NM_008644	ENSMUSG00000064156	Prol1	Muc10	proline rich, lacrimal 1	protein-coding
mm_33095.1	chr4	124696834	124696868	+	1	NA	Intergenic	B1_Mm|SINE|Alu	-3297	NM_026031	67205	Mm.259121	NM_026031	ENSMUSG00000028907	Utp11l	2700082D03Rik|CGI-94|Cgi94|Utp11	UTP11-like, U3 small nucleolar ribonucleoprotein, (yeast)	protein-coding
mm_114728.1	chr13	83721291	83721309	+	1	NA	Intergenic	Intergenic	-6806	NR_015561	320203	Mm.245636	NM_177100	ENSMUSG00000050334	C130071C03Rik	2810449C10Rik	RIKEN cDNA C130071C03 gene	ncRNA
mm_73893.1	chr8	119419014	119419018	+	1	NA	Intergenic	Intergenic	-18146	NM_027950	71839	Mm.272357	NM_027950	ENSMUSG00000074063	Osgin1	1700012B18Rik|Okl38	oxidative stress induced growth inhibitor 1	protein-coding
mm_37149.1	chr4	117120298	117120306	-	1	NA	non-coding (NR_024078, exon 7 of 7)	non-coding (NR_024078, exon 7 of 7)	5423	NR_024078	78611	Mm.446227	NM_001033187		Btbd19	9530048O09Rik|BB115071	BTB (POZ) domain containing 19	ncRNA
mm_45953.1	chr5	90450155	90450158	-	1	NA	Intergenic	Intergenic	-10714	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_144620.1	chr18	32866170	32866173	+	1	NA	3' UTR (NM_001110015, exon 23 of 23)	3' UTR (NM_001110015, exon 23 of 23)	14502	NR_105779	102465186		NR_105779	ENSMUSG00000098252	Mir6361	Gm27612|mmu-mir-6361	microRNA 6361	ncRNA
mm_169237.1	chr13	72391812	72391812	-	1	NA	Intergenic	L1Md_T|LINE|L1	236752	NR_030701	328287	Mm.235072	NR_030701		Gm20554	D430050G20	predicted gene, 20554	ncRNA
mm_62727.1	chr7	110777555	110777574	+	1	NA	intron (NM_009667, intron 1 of 14)	intron (NM_009667, intron 1 of 14)	4960	NM_009667	11717	Mm.3238	NM_009667	ENSMUSG00000005686	Ampd3	-	adenosine monophosphate deaminase 3	protein-coding
mm_123974.1	chr14	75174806	75174807	-	1	NA	intron (NM_008879, intron 1 of 16)	intron (NM_008879, intron 1 of 16)	38381	NM_008879	18826	Mm.153911	NM_008879	ENSMUSG00000021998	Lcp1	AW536232|D14Ertd310e|LCP-1|Pls2|pp65	lymphocyte cytosolic protein 1	protein-coding
mm_105204.1	chr11	102097881	102097910	-	1	NA	Intergenic	RSINE1|SINE|B4	3405	NM_008918	19064	Mm.1269	NM_008918	ENSMUSG00000017316	Ppy	AV061413|IGSPP|PP	pancreatic polypeptide	protein-coding
mm_120146.1	chr14	60485158	60485168	+	1	NA	Intergenic	Intergenic	106877	NM_001164705	72125	Mm.275499	NM_028113	ENSMUSG00000021986	Amer2	2600011E07Rik|Fam123a	APC membrane recruitment 2	protein-coding
mm_128784.1	chr15	66803845	66803857	-	1	NA	intron (NM_001029841, intron 1 of 7)	intron (NM_001029841, intron 1 of 7)	27978	NM_001029841	20491	Mm.7601	NM_009192	ENSMUSG00000022372	Sla	Slap|Slap-1	src-like adaptor	protein-coding
mm_86457.1	chr10	4347812	4347822	+	1	NA	intron (NM_031185, intron 2 of 3)	intron (NM_031185, intron 2 of 3)	40291	NM_001033466	381990	Mm.262466	NM_001033466	ENSMUSG00000075327	Zbtb2	Gm1103	zinc finger and BTB domain containing 2	protein-coding
mm_54025.1	chr6	8778515	8778531	-	1	NA	promoter-TSS (NM_010492)	promoter-TSS (NM_010492)	-39	NM_010492	15893	Mm.275683	NM_010492	ENSMUSG00000062995	Ica1	69kDa|ICA69	islet cell autoantigen 1	protein-coding
mm_165350.1	chr2	120186764	120186765	+	1	NA	intron (NM_177845, intron 6 of 19)	intron (NM_177845, intron 6 of 19)	-32189	NM_133838	98878	Mm.132226	NM_133838	ENSMUSG00000027293	Ehd4	2210022F10Rik|AI197390|AI846352|AV006278|Past2	EH-domain containing 4	protein-coding
mm_94402.1	chr11	5762122	5762182	+	1	NA	promoter-TSS (NR_015577)	promoter-TSS (NR_015577)	2	NR_015577	76508	Mm.260203	NR_015577	ENSMUSG00000083844	Ube2d-ps	1600028I17Rik|2210015D19Rik|AI596465	ubiquitin-conjugating enzyme E2D, pseudogene	ncRNA
mm_41358.1	chr5	90506550	90506563	+	1	NA	exon (NM_007423, exon 12 of 15)	exon (NM_007423, exon 12 of 15)	-12393	NM_145146	280662	Mm.348786	NM_145146	ENSMUSG00000029369	Afm	Alf|alpha-Alb	afamin	protein-coding
mm_43894.1	chr5	144174942	144174976	+	1	NA	exon (NM_001081109, exon 11 of 14)	exon (NM_001081109, exon 11 of 14)	-15327	NM_010800	17341	Mm.386767	NM_010800	ENSMUSG00000052271	Bhlha15	1810009C13Rik|Bhlhb8|MIST-1|Mist1	basic helix-loop-helix family, member a15	protein-coding
mm_36327.1	chr4	70410423	70410463	-	1	NA	promoter-TSS (NM_001313762)	promoter-TSS (NM_001313762)	-8	NM_145990	214444	Mm.370777	NM_145990	ENSMUSG00000039298	Cdk5rap2	2900018K03Rik|an|mKIAA1633	CDK5 regulatory subunit associated protein 2	protein-coding
mm_61916.1	chr7	90149032	90149035	+	1	NA	intron (NM_001252520, intron 1 of 20)	intron (NM_001252520, intron 1 of 20)	18801	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_6900.1	chr1	84766031	84766055	-	1	NA	exon (NM_133975, exon 10 of 41)	exon (NM_133975, exon 10 of 41)	-69822	NM_152915	227325	Mm.292560	NM_152915	ENSMUSG00000036766	Dner	A930026D19Rik|BET|Bret	delta/notch-like EGF repeat containing	protein-coding
mm_117451.1	chr13	74808545	74808558	-	1	NA	promoter-TSS (NM_009817)	promoter-TSS (NM_009817)	209	NM_001301153	12380	Mm.29163	NM_009817	ENSMUSG00000021585	Cast	-	calpastatin	protein-coding
mm_3286.1	chr1	136662147	136662159	+	1	NA	Intergenic	Intergenic	-21243	NR_045324	100503460	Mm.30630	NR_045324	ENSMUSG00000097113	Gm19705	-	predicted gene, 19705	ncRNA
mm_96549.1	chr11	68872033	68872043	+	1	NA	Intergenic	Intergenic	-16515	NM_177060	320040	Mm.305696	NM_177060	ENSMUSG00000046490	Rnf222	9930039A11Rik	ring finger protein 222	protein-coding
mm_158518.1	chrX	143483063	143483122	-	1	NA	Intergenic	L1Md_F2|LINE|L1	-35499	NM_001195048	18481	Mm.40035	NM_008778	ENSMUSG00000031284	Pak3	PAK-3|Pak65alpha|Pak65beta|Stk4	p21 protein (Cdc42/Rac)-activated kinase 3	protein-coding
mm_4641.1	chr1	179960775	179960779	+	1	NA	promoter-TSS (NM_001033285)	promoter-TSS (NM_001033285)	17	NM_001346805	226751	Mm.259655	NM_001033285	ENSMUSG00000026490	Cdc42bpa	A930014J19Rik|DMPK-like	CDC42 binding protein kinase alpha	protein-coding
mm_28448.1	chr3	90514251	90514334	-	1	NA	promoter-TSS (NM_009113)	promoter-TSS (NM_009113)	38	NM_011309	20193	Mm.24662	NM_011309	ENSMUSG00000044080	S100a1	AI266795|S100|S100a	S100 calcium binding protein A1	protein-coding
mm_123684.1	chr14	69555284	69555336	-	1	NA	promoter-TSS (NM_026174)	promoter-TSS (NM_026174)	77	NR_045091	100504477	Mm.396396	NR_045091		Gm16677	-	predicted gene, 16677	ncRNA
mm_13493.1	chr2	106693578	106693602	+	1	NA	5' UTR (NM_001143683, exon 1 of 7)	5' UTR (NM_001143683, exon 1 of 7)	131	NM_001143683	77015	Mm.45628	NM_029837	ENSMUSG00000016386	Mpped2	239Fb|2700082O15Rik|AV354767|AW060960	metallophosphoesterase domain containing 2	protein-coding
mm_146713.1	chr18	14729334	14729336	-	1	NA	intron (NM_001163609, intron 3 of 6)	intron (NM_001163609, intron 3 of 6)	23184	NM_001163609	73677	Mm.87277	NM_001163609	ENSMUSG00000036743	Psma8	2410072D24Rik	proteasome (prosome, macropain) subunit, alpha type, 8	protein-coding
mm_118556.1	chr14	17945213	17945220	+	1	NA	intron (NM_001113417, intron 3 of 9)	L1_Mus2|LINE|L1	-36428	NM_009380	21834	Mm.32563	NM_009380	ENSMUSG00000021779	Thrb	Nr1a2|T3R[b]|T3Rbeta|Thrb1|Thrb2|c-erbAbeta	thyroid hormone receptor beta	protein-coding
mm_49447.1	chr6	29348137	29348142	+	1	NA	promoter-TSS (NM_184053)	promoter-TSS (NM_184053)	33	NM_184053	12321	Mm.392075	NM_007594	ENSMUSG00000029767	Calu	9530075H20Rik	calumenin	protein-coding
mm_26828.1	chr3	10439961	10439977	-	1	NA	5' UTR (NM_001127191, exon 1 of 7)	5' UTR (NM_001127191, exon 1 of 7)	161	NM_029068	74718	Mm.440548	NM_029068	ENSMUSG00000027534	Snx16	4930522N22Rik|AI117577|AI747675	sorting nexin 16	protein-coding
mm_146045.1	chr18	69593362	69593450	+	1	NA	intron (NM_013685, intron 8 of 19)	intron (NM_013685, intron 8 of 19)	247685	NM_001083967	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding
mm_132752.1	chr16	44160343	44160368	+	1	NA	3' UTR (NM_028108, exon 5 of 5)	3' UTR (NM_028108, exon 5 of 5)	-13042	NM_001029889	207806	Mm.310566	NM_001029889	ENSMUSG00000068284	Usf3	5530400K22Rik|Gm1779|Gm608|mKIAA2018	upstream transcription factor family member 3	protein-coding
mm_158881.1	chr1	5917411	5917411	-	1	NA	promoter-TSS (NM_010342)	promoter-TSS (NM_010342)	-13	NM_010342	226304	Mm.291110	NM_010342	ENSMUSG00000033774	Npbwr1	Gpr7|Nbpwr1	neuropeptides B/W receptor 1	protein-coding
mm_168631.1	chr1	182201592	182201593	+	1	NA	Intergenic	RLTR13B2|LTR|ERVK	-43494	NM_001166728	625823	Mm.479992	NM_001166728	ENSMUSG00000091013	Vmn1r1	EG625823|Gm6628	vomeronasal 1 receptor 1	protein-coding
mm_18439.1	chr2	60881335	60881354	-	1	NA	promoter-TSS (NM_001141932)	promoter-TSS (NM_001141932)	94	NM_001141932	56878	Mm.259667	NM_020296	ENSMUSG00000026970	Rbms1	2600014B10Rik|AI255215|MSSP-1|MSSP-2|MSSP-3|YC1	RNA binding motif, single stranded interacting protein 1	protein-coding
mm_163618.1	chr13	55322085	55322092	+	1	NA	promoter-TSS (NM_025596)	promoter-TSS (NM_025596)	33	NM_025596	66494	Mm.439805	NM_025596	ENSMUSG00000021486	Prelid1	2610524G07Rik|Preli	PRELI domain containing 1	protein-coding
mm_172799.1	chr9	114671478	114671495	-	1	NA	Intergenic	4.5SRNA|scRNA|scRNA	-17345	NM_146229	235661	Mm.128627	NM_146229	ENSMUSG00000032435	Dync1li1	1110053F02Rik|Dnclic1|LIC-1	dynein cytoplasmic 1 light intermediate chain 1	protein-coding
mm_41435.1	chr5	90904140	90904158	+	1	NA	exon (NM_009140, exon 2 of 4)	exon (NM_009140, exon 2 of 4)	250	NM_009140	20310	Mm.4979	NM_009140	ENSMUSG00000058427	Cxcl2	CINC-2a|GROb|Gro2|MIP-2|MIP-2a|Mgsa-b|Mip2|Scyb|Scyb2	chemokine (C-X-C motif) ligand 2	protein-coding
mm_171958.1	chr5	81205131	81205133	+	1	NA	intron (NM_001347371, intron 2 of 23)	L1Md_T|LINE|L1	183539	NM_198702	319387	Mm.273631	NM_198702	ENSMUSG00000037605	Adgrl3	5430402I23Rik|CIRL-3|D130075K09Rik|Gm1379|LEC3|Lphn3|mKIAA0768	adhesion G protein-coupled receptor L3	protein-coding
mm_162210.1	chrX	136068132	136068132	-	1	NA	5' UTR (NM_009749, exon 1 of 3)	5' UTR (NM_009749, exon 1 of 3)	104	NM_009749	12069	Mm.94160	NM_009749	ENSMUSG00000042750	Bex2	AL024066|Bex1	brain expressed X-linked 2	protein-coding
mm_135932.1	chr16	73958386	73958406	-	1	NA	exon (NM_175549, exon 15 of 28)	exon (NM_175549, exon 15 of 28)	383671	NR_030464	751561		NR_030464	ENSMUSG00000104758	Mir691	Mirn691|mir-691|mmu-mir-691	microRNA 691	ncRNA
mm_40434.1	chr5	53590354	53590377	+	1	NA	promoter-TSS (NM_001277116)	promoter-TSS (NM_001277116)	19	NM_001277116	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_65067.1	chr7	18910392	18910411	-	1	NA	promoter-TSS (NM_001033314)	promoter-TSS (NM_001033314)	3	NM_001033314	232933	Mm.333624	NM_001033314	ENSMUSG00000074358	Ccdc61	C530028I08Rik|Gm159	coiled-coil domain containing 61	protein-coding
mm_49729.1	chr6	34709474	34709497	+	1	NA	promoter-TSS (NM_145575)	promoter-TSS (NM_145575)	41	NM_145575	109624	Mm.308134	NM_145575	ENSMUSG00000029761	Cald1	4833423D12Rik|AI195384|AV071549|AW536160|C920027I18Rik	caldesmon 1	protein-coding
mm_100865.1	chr11	5898011	5898043	-	1	NA	intron (NM_022879, intron 3 of 6)	intron (NM_022879, intron 3 of 6)	755	NM_022879	17898	Mm.46514	NM_022879	ENSMUSG00000020469	Myl7	MLC-2alpha|MLC2a|MYL2A|Mylc2a|RLC-A	myosin, light polypeptide 7, regulatory	protein-coding
mm_39244.1	chr5	3343908	3343945	+	1	NA	promoter-TSS (NM_009873)	promoter-TSS (NM_009873)	33	NM_009873	12571	Mm.31672	NM_009873	ENSMUSG00000040274	Cdk6	AI504062|Crk2	cyclin-dependent kinase 6	protein-coding
mm_43254.1	chr5	130219707	130219720	+	1	NA	promoter-TSS (NM_001081394)	promoter-TSS (NM_001081394)	-31	NM_001081394	71667	Mm.258508	NM_027854	ENSMUSG00000053094	Tmem248	0610007L01Rik|A930023A16Rik|AW557951|G430067H08Rik	transmembrane protein 248	protein-coding
mm_101017.1	chr11	8573447	8573452	-	1	NA	intron (NM_001083587, intron 4 of 30)	intron (NM_001083587, intron 4 of 30)	91086	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_83283.1	chr9	43106042	43106096	-	1	NA	promoter-TSS (NM_027144)	promoter-TSS (NM_027144)	-351	NM_027144	69632	Mm.275266	NM_027144	ENSMUSG00000059495	Arhgef12	2310014B11Rik|AU019857|Larg|mKIAA0382	Rho guanine nucleotide exchange factor (GEF) 12	protein-coding
mm_85895.1	chr9	111055654	111055665	-	1	NA	exon (NM_017466, exon 2 of 2)	exon (NM_017466, exon 2 of 2)	1585	NM_001302377	54199	Mm.7336	NM_017466	ENSMUSG00000043953	Ccrl2	1810047I05Rik|Ackr5|CCR11|Cmkbr1l2|E01|L-CCR	chemokine (C-C motif) receptor-like 2	protein-coding
mm_145672.1	chr18	61555259	61555290	+	1	NA	promoter-TSS (NM_146087)	promoter-TSS (NM_146087)	-308	NM_146087	93687	Mm.26908	NM_146087	ENSMUSG00000024576	Csnk1a1	2610208K14Rik|4632404G05Rik|5430427P18Rik|CK1a|Csnk1a	casein kinase 1, alpha 1	protein-coding
mm_19499.1	chr2	93461945	93461956	-	1	NA	promoter-TSS (NM_001271461)	promoter-TSS (NM_001271461)	-99	NM_001271461	12521	Mm.4261	NM_007656	ENSMUSG00000027215	Cd82	AA682076|AL023070|C33|IA4|Kai1|Tspan27	CD82 antigen	protein-coding
mm_5684.1	chr1	43164078	43164099	-	1	NA	promoter-TSS (NM_010212)	promoter-TSS (NM_010212)	-127	NM_010212	14200	Mm.6799	NM_010212	ENSMUSG00000008136	Fhl2	FHL-2|SLIM-3|SLIM3	four and a half LIM domains 2	protein-coding
mm_40195.1	chr5	36867647	36867659	+	1	NA	promoter-TSS (NM_172994)	promoter-TSS (NM_172994)	-917	NM_172994	269643	Mm.41694	NM_172994	ENSMUSG00000029120	Ppp2r2c	6330548O06Rik|IMYPNO|IMYPNO1|PR52	protein phosphatase 2, regulatory subunit B, gamma	protein-coding
mm_139078.1	chr17	46680425	46680478	+	1	NA	promoter-TSS (NM_010787)	promoter-TSS (NM_010787)	-2	NM_001277310	17256	Mm.329083	NM_010787	ENSMUSG00000002768	Mea1	Mea-1	male enhanced antigen 1	protein-coding
mm_172092.1	chr6	21986779	21986792	+	1	NA	5' UTR (NM_001081351, exon 1 of 22)	5' UTR (NM_001081351, exon 1 of 22)	875	NM_001081351	214642	Mm.221404	NM_001081351	ENSMUSG00000062980	Cped1	6720481P07|A430107O13Rik|AI552584	cadherin-like and PC-esterase domain containing 1	protein-coding
mm_170400.1	chr1	86359399	86359400	-	1	NA	promoter-TSS (NM_010880)	promoter-TSS (NM_010880)	56	NM_010880	17975	Mm.154378	NM_010880	ENSMUSG00000026234	Ncl	B530004O11Rik|C23|D0Nds28|D1Nds28|Nucl	nucleolin	protein-coding
mm_53502.1	chr6	135362824	135362845	+	1	NA	promoter-TSS (NM_001288628)	promoter-TSS (NM_001288628)	-97	NM_010128	13730	Mm.182785	NM_010128	ENSMUSG00000030208	Emp1	I-8-09|TMP	epithelial membrane protein 1	protein-coding
mm_104578.1	chr11	96955965	96955975	-	1	NA	intron (NM_001080964, intron 5 of 6)	intron (NM_001080964, intron 5 of 6)	11824	NR_003293	319371	Mm.436865	NR_003293	ENSMUSG00000078700	D030028A08Rik	-	RIKEN cDNA D030028A08 gene	ncRNA
mm_128084.1	chr15	27697734	27697746	-	1	NA	Intergenic	Intergenic	-16198	NM_001242423	223433	Mm.266485	NM_198301	ENSMUSG00000056069	Fam105a	9830126M18	family with sequence similarity 105, member A	protein-coding
mm_4219.1	chr1	171329449	171329501	+	1	NA	5' UTR (NM_001128609, exon 1 of 6)	5' UTR (NM_001128609, exon 1 of 6)	330	NM_011615	21945	Mm.270139	NM_011615	ENSMUSG00000013973	Dedd	CASP8IP1|DEFT|Dedpro1|FLDED1|KE05	death effector domain-containing	protein-coding
mm_53164.1	chr6	125321859	125321869	+	1	NA	5' UTR (NM_011324, exon 1 of 12)	5' UTR (NM_011324, exon 1 of 12)	524	NM_011324	20276	Mm.144114	NM_011324	ENSMUSG00000030340	Scnn1a	ENaC|SCNEA|Scnn1|mENaC	sodium channel, nonvoltage-gated 1 alpha	protein-coding
mm_36234.1	chr4	63152691	63152706	-	1	NA	exon (NM_007443, exon 2 of 10)	exon (NM_007443, exon 2 of 10)	1474	NM_007443	11699	Mm.2197	NM_007443	ENSMUSG00000028356	Ambp	AI194774|ASPI|HI-30|Intin4|Itil|UTI	alpha 1 microglobulin/bikunin	protein-coding
mm_15124.1	chr2	153779269	153779279	+	1	NA	Intergenic	Intergenic	-1605	NR_036629	100504221	Mm.246778	NM_177849	ENSMUSG00000044083	Efcab8	A630008I04|EG329541	EF-hand calcium binding domain 8	ncRNA
mm_163031.1	chr11	51755657	51755666	-	1	NA	intron (NM_001290785, intron 1 of 22)	intron (NM_001290785, intron 1 of 22)	1173	NM_001290785	77371	Mm.33878	NM_175255	ENSMUSG00000036391	Sec24a	-	Sec24 related gene family, member A (S. cerevisiae)	protein-coding
mm_19827.1	chr2	111139660	111139664	-	1	NA	Intergenic	Intergenic	89938	NM_026248	67575	Mm.84331	NM_026248	ENSMUSG00000027157	4930430A15Rik	-	RIKEN cDNA 4930430A15 gene	protein-coding
mm_146047.1	chr18	69593492	69593505	+	1	NA	intron (NM_013685, intron 8 of 19)	intron (NM_013685, intron 8 of 19)	247777	NM_001083967	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding
mm_156197.1	chrX	134295383	134295404	+	1	NA	5' UTR (NM_026239, exon 1 of 2)	5' UTR (NM_026239, exon 1 of 2)	168	NM_026239	67564	Mm.41489	NM_026239	ENSMUSG00000033578	Tmem35a	9030603L14Rik|AI841526|PMP52|Tmem35	transmembrane protein 35A	protein-coding
mm_135308.1	chr16	38712925	38712937	-	1	NA	5' UTR (NM_020260, exon 1 of 12)	5' UTR (NM_020260, exon 1 of 12)	104	NM_020260	12549	Mm.370848	NM_020260	ENSMUSG00000022799	Arhgap31	5830477L08Rik|AU041750|Cdgap|D330026I07Rik	Rho GTPase activating protein 31	protein-coding
mm_70848.1	chr8	23446913	23446932	+	1	NA	3' UTR (NM_013834, exon 3 of 3)	3' UTR (NM_013834, exon 3 of 3)	35420	NM_013834	20377	Mm.281691	NM_013834	ENSMUSG00000031548	Sfrp1	2210415K03Rik|AW011917|AW107218|AW742929|sFRP-1	secreted frizzled-related protein 1	protein-coding
mm_50948.1	chr6	58640599	58640610	+	1	NA	intron (NM_011920, intron 1 of 15)	CpG	43932	NM_011920	26357	Mm.333096	NM_011920	ENSMUSG00000029802	Abcg2	ABC15|ABCP|AI428558|BCRP|Bcrp1|MXR|MXR1	ATP-binding cassette, sub-family G (WHITE), member 2	protein-coding
mm_70019.1	chr7	142575555	142575577	-	1	NA	TTS (NR_130974)	TTS (NR_130974)	1581	NR_030416	735280		NR_030416	ENSMUSG00000076275	Mir675	Mirn675|mir-675|mmu-mir-675	microRNA 675	ncRNA
mm_121734.1	chr14	18271192	18271205	-	1	NA	promoter-TSS (NM_025586)	promoter-TSS (NM_025586)	62	NM_023526	69721	Mm.25648	NM_023526	ENSMUSG00000021772	Nkiras1	2400004O09Rik|KBRAS1|kappaB-Ras1	NFKB inhibitor interacting Ras-like protein 1	protein-coding
mm_73297.1	chr8	105048593	105048608	+	1	NA	promoter-TSS (NM_001164681)	promoter-TSS (NM_001164681)	1	NM_198672	382053	Mm.295534	NM_198672	ENSMUSG00000069922	Ces3a	Ces3|Ces31|Es31	carboxylesterase 3A	protein-coding
mm_75708.1	chr8	68901256	68901292	-	1	NA	exon (NM_008509, exon 8 of 10)	exon (NM_008509, exon 8 of 10)	20719	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_7889.1	chr1	133256323	133256345	-	1	NA	non-coding (NR_037984, exon 3 of 4)	non-coding (NR_037984, exon 3 of 4)	10237	NM_182930	240753	Mm.253559	NM_182930	ENSMUSG00000041757	Plekha6	9530028L01Rik|AU042621|Pepp3	pleckstrin homology domain containing, family A member 6	protein-coding
mm_18021.1	chr2	38613696	38613706	-	1	NA	intron (NM_011187, intron 5 of 7)	intron (NM_011187, intron 5 of 7)	30205	NM_011187	19177	Mm.389251	NM_011187	ENSMUSG00000026750	Psmb7	AU020723|MC14	proteasome (prosome, macropain) subunit, beta type 7	protein-coding
mm_1369.1	chr1	66440169	66440188	+	1	NA	3' UTR (NM_008632, exon 14 of 14)	3' UTR (NM_008632, exon 14 of 14)	-28269	NM_175510	329178	Mm.44798	NM_175510	ENSMUSG00000055567	Unc80	C030018G13Rik|C230061B10Rik|UNC-80	unc-80, NALCN activator	protein-coding
mm_115811.1	chr13	19619759	19619811	-	1	NA	promoter-TSS (NM_134065)	promoter-TSS (NM_134065)	45	NM_134065	105298	Mm.275054	NM_134065	ENSMUSG00000002808	Epdr1	AU040950|AV006210|Epdm2|Epdr2|MERP-1|MERP-2|MERP2|Ucc1	ependymin related protein 1 (zebrafish)	protein-coding
mm_63750.1	chr7	131042974	131042985	+	1	NA	intron (NM_001347632, intron 4 of 47)	intron (NM_001347632, intron 4 of 47)	10903	NM_007769	12945	Mm.4138	NM_007769	ENSMUSG00000047517	Dmbt1	CRP|CRP-[a]|CRP-[b]|Crpd|DBMT1|gp300|p80	deleted in malignant brain tumors 1	protein-coding
mm_52801.1	chr6	121336862	121336872	+	1	NA	exon (NM_144512, exon 14 of 15)	exon (NM_144512, exon 14 of 15)	-6209	NM_001347433	14411	Mm.274506	NM_133661	ENSMUSG00000030109	Slc6a12	BGT1|GAT-2|GAT2|Gabt2	solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12	protein-coding
mm_44761.1	chr5	31573438	31573444	-	1	NA	Intergenic	Intergenic	-2044	NR_102275	100740	Mm.23370	NR_102275		AI839979	-	expressed sequence AI839979	ncRNA
mm_97200.1	chr11	75596125	75596146	+	1	NA	intron (NM_008850, intron 2 of 11)	intron (NM_008850, intron 2 of 11)	4096	NR_110477	654359	Mm.439961	NR_110477		Gm12338	OTTMUSG00000006216	cytochrome c oxidase, subunit VIIc pseudogene	pseudo
mm_57580.1	chr6	127150664	127150676	-	1	NA	exon (NM_009829, exon 1 of 5)	exon (NM_009829, exon 1 of 5)	378	NM_009829	12444	Mm.333406	NM_009829	ENSMUSG00000000184	Ccnd2	2600016F06Rik|AI256817|BF642806|C86853|Vin-1|Vin1|cD2	cyclin D2	protein-coding
mm_125885.1	chr15	75842085	75842133	+	1	NA	promoter-TSS (NM_172121)	promoter-TSS (NM_172121)	-201	NM_172121	223642	Mm.209800	NM_172121	ENSMUSG00000075600	Zc3h3	BC049953|Kiaa0150|Smicl|Zc3hdc3	zinc finger CCCH type containing 3	protein-coding
mm_151968.1	chr19	5803506	5803521	-	1	NA	promoter-TSS (NR_002847)	promoter-TSS (NR_002847)	-841	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_115582.1	chr13	11676394	11676397	-	1	NA	intron (NM_023868, intron 62 of 104)	intron (NM_023868, intron 62 of 104)	154343	NR_027813	664793	Mm.410565	NR_027813		Zp4-ps	EG664793|Zp4|Zpb	zona pellucida glycoprotein 4, pseudogene	pseudo
mm_36463.1	chr4	82505834	82505838	-	1	NA	promoter-TSS (NM_001113209)	promoter-TSS (NM_001113209)	-57	NM_008687	18028	Mm.317947	NM_008687	ENSMUSG00000008575	Nfib	6720429L07Rik|CTF|E030026I10Rik|NF-I/B|NF1-B|NFI-B	nuclear factor I/B	protein-coding
mm_89302.1	chr10	87914377	87914387	+	1	NA	intron (NM_001314010, intron 4 of 4)	intron (NM_001314010, intron 4 of 4)	-52289	NR_000040	22172	Mm.391420	NR_000040		Tyms-ps	-	thymidylate synthase, pseudogene	pseudo
mm_170617.1	chr19	61223878	61223897	+	1	NA	TTS (NM_009970)	TTS (NM_009970)	4531	NM_009970	12982	Mm.287228	NM_009970	ENSMUSG00000059326	Csf2ra	CD116|Csfgmra|GM-CSF-Ra|GM-CSFR	colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)	protein-coding
mm_57487.1	chr6	125266106	125266147	-	1	NA	intron (NR_015527, intron 1 of 3)	intron (NR_015527, intron 1 of 3)	601	NR_015527	73870	Mm.440681	NR_015527	ENSMUSG00000108129	4930417O13Rik	-	RIKEN cDNA 4930417O13 gene	ncRNA
mm_138423.1	chr17	35069617	35069627	+	1	NA	3' UTR (NM_023463, exon 3 of 3)	3' UTR (NM_023463, exon 3 of 3)	2297	NM_023463	68468	Mm.215096	NM_023463	ENSMUSG00000092586	Ly6g6c	1110003M04Rik|AU016360|G6c|NG24	lymphocyte antigen 6 complex, locus G6C	protein-coding
mm_132767.1	chr16	44765733	44765751	+	1	NA	promoter-TSS (NM_021325)	promoter-TSS (NM_021325)	6	NM_021325	57781	Mm.416152	NM_021325	ENSMUSG00000022667	Cd200r1	CD200R|Mox2r|OX2R	CD200 receptor 1	protein-coding
mm_9480.1	chr1	173367856	173367886	-	1	NA	promoter-TSS (NM_053199)	promoter-TSS (NM_053199)	-176	NM_053199	94332	Mm.330524	NM_053199	ENSMUSG00000005338	Cadm3	BIgR|Igsf4b|Necl-1|Necl1|SynCAM3|Tsll1	cell adhesion molecule 3	protein-coding
mm_74804.1	chr8	22593736	22593776	-	1	NA	promoter-TSS (NM_001198998)	promoter-TSS (NM_001198998)	57	NM_001198998	22335	Mm.227704	NM_011696	ENSMUSG00000008892	Vdac3	-	voltage-dependent anion channel 3	protein-coding
mm_97060.1	chr11	72699158	72699159	+	1	NA	intron (NM_009671, intron 1 of 24)	intron (NM_009671, intron 1 of 24)	9156	NM_009671	11736	Mm.10313	NM_009671	ENSMUSG00000020790	Ankfy1	Ankhzn|ZFYVE14|mKIAA1255	ankyrin repeat and FYVE domain containing 1	protein-coding
mm_34613.1	chr4	150371858	150371927	+	1	NA	intron (NM_001085492, intron 1 of 22)	CpG	89976	NM_001085492	68703	Mm.291274	NM_001085492	ENSMUSG00000039852	Rere	1110033A15Rik|AI414665|ARG|ARP|ATN1L|AW742570|Atr2|DNB1|eye<m03Jus>|eyes3|mKIAA0458	arginine glutamic acid dipeptide (RE) repeats	protein-coding
mm_144779.1	chr18	35830092	35830111	+	1	NA	intron (NM_133687, intron 1 of 2)	CpG	283	NM_133687	67393	Mm.94560	NM_133687	ENSMUSG00000046668	Cxxc5	4930415K17Rik	CXXC finger 5	protein-coding
mm_172366.1	chr7	122441998	122442018	+	1	NA	intron (NM_001316672, intron 3 of 16)	intron (NM_001316672, intron 3 of 16)	152883	NM_008855	18751	Mm.207496	NM_008855	ENSMUSG00000052889	Prkcb	PKC-B|PKC-Beta|Pkcb|Prkcb1|Prkcb2	protein kinase C, beta	protein-coding
mm_27703.1	chr3	67463617	67463627	-	1	NA	exon (NM_016753, exon 1 of 6)	exon (NM_016753, exon 1 of 6)	285	NM_016753	17035	Mm.2632	NM_016753	ENSMUSG00000047557	Lxn	-	latexin	protein-coding
mm_16508.1	chr2	181319807	181319815	+	1	NA	promoter-TSS (NM_001166665)	promoter-TSS (NM_001166665)	87	NM_001001882	269400	Mm.11333	NM_001001882	ENSMUSG00000038685	Rtel1	AI451565|AW540478|Rtel	regulator of telomere elongation helicase 1	protein-coding
mm_122068.1	chr14	30491489	30491506	-	1	NA	promoter-TSS (NM_028981)	promoter-TSS (NM_028981)	-341	NM_028981	12289	Mm.9772	NM_028981	ENSMUSG00000015968	Cacna1d	8430418G19Rik|C79217|Cach3|Cacn4|Cacnl1a2|Cav1.3|Cchl1a|Cchl1a2|D-LTCC	calcium channel, voltage-dependent, L type, alpha 1D subunit	protein-coding
mm_108367.1	chr12	80816678	80816684	+	1	NA	intron (NM_001242419, intron 1 of 6)	intron (NM_001242419, intron 1 of 6)	26149	NM_001242419	217684	Mm.341776	NM_178682	ENSMUSG00000021133	Susd6	4933426M11Rik|mKIAA0247	sushi domain containing 6	protein-coding
mm_92715.1	chr10	80797970	80797990	-	1	NA	promoter-TSS (NM_013651)	promoter-TSS (NM_013651)	646	NM_023900	78670	Mm.41479	NM_023900	ENSMUSG00000035278	Plekhj1	9530063M10Rik	pleckstrin homology domain containing, family J member 1	protein-coding
mm_155200.1	chrX	56731367	56731416	+	1	NA	promoter-TSS (NM_010211)	promoter-TSS (NM_010211)	-370	NM_010211	14199	Mm.3126	NM_010211	ENSMUSG00000023092	Fhl1	FHL-1|KyoT|RAM14-1|SLIM|SLIM-1	four and a half LIM domains 1	protein-coding
mm_86220.1	chr9	120091983	120092014	-	1	NA	promoter-TSS (NM_007720)	promoter-TSS (NM_007720)	-135	NM_007720	12776	Mm.442098	NM_007720	ENSMUSG00000042262	Ccr8	C-C|C-C CKR-8|CC-CKR-8|CCR-8|CKR-8|Cmkbr8|mCCR8	chemokine (C-C motif) receptor 8	protein-coding
mm_77627.1	chr8	123983121	123983152	-	1	NA	promoter-TSS (NM_019552)	promoter-TSS (NM_019552)	-14	NM_019552	56199	Mm.274243	NM_019552	ENSMUSG00000031974	Abcb10	Abc-me|Abcb12	ATP-binding cassette, sub-family B (MDR/TAP), member 10	protein-coding
mm_123583.1	chr14	67062560	67062564	-	1	NA	intron (NM_001205188, intron 2 of 9)	intron (NM_001205188, intron 2 of 9)	9909	NM_028032	71978	Mm.273997	NM_028032	ENSMUSG00000022052	Ppp2r2a	2410004D02Rik|mKIAA1541	protein phosphatase 2, regulatory subunit B, alpha	protein-coding
mm_86025.1	chr9	112235941	112235946	-	1	NA	TTS (NR_015468)	TTS (NR_015468)	-1102	NM_001177619	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_74380.1	chr8	128685850	128685856	+	1	NA	5' UTR (NM_010578, exon 1 of 16)	5' UTR (NM_010578, exon 1 of 16)	199	NM_010578	16412	Mm.263396	NM_010578	ENSMUSG00000025809	Itgb1	4633401G24Rik|AA409975|AA960159|CD29|ENSMUSG00000051907|Fnrb|Gm9863|gpIIa	integrin beta 1 (fibronectin receptor beta)	protein-coding
mm_132813.1	chr16	45169860	45169903	+	1	NA	exon (NM_026402, exon 4 of 12)	exon (NM_026402, exon 4 of 12)	11052	NM_026402	67841	Mm.41775	NM_026402	ENSMUSG00000022663	Atg3	2610016C12Rik|APG3|Apg3l|Atg3l|PC3-96	autophagy related 3	protein-coding
mm_21271.1	chr2	156862918	156862964	-	1	NA	promoter-TSS (NM_026124)	promoter-TSS (NM_026124)	4	NR_015591	74487	Mm.490465	NR_015591	ENSMUSG00000085741	5430405H02Rik	2610307N17Rik	RIKEN cDNA 5430405H02 gene	ncRNA
mm_56210.1	chr6	89316750	89316766	-	1	NA	3' UTR (NM_008881, exon 32 of 32)	3' UTR (NM_008881, exon 32 of 32)	-31033	NR_131021	75131	Mm.391482	NR_131021	ENSMUSG00000107622	4930512J16Rik	-	RIKEN cDNA 4930512J16 gene	ncRNA
mm_145820.1	chr18	65431145	65431155	+	1	NA	5' UTR (NM_172833, exon 1 of 16)	5' UTR (NM_172833, exon 1 of 16)	153	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_71875.1	chr8	69716581	69716589	+	1	NA	promoter-TSS (NM_181274)	promoter-TSS (NM_181274)	-99	NM_181274	66869	Mm.334581	NM_181274	ENSMUSG00000054648	Zfp869	1200003I07Rik	zinc finger protein 869	protein-coding
mm_41781.1	chr5	103716826	103716835	+	1	NA	Intergenic	Intergenic	-37332	NM_133919	17355	Mm.6949	NM_133919	ENSMUSG00000029313	Aff1	9630032B01Rik|AW319193|Af4|Mllt2h|Rob	AF4/FMR2 family, member 1	protein-coding
mm_1467.1	chr1	69826866	69826915	+	1	NA	promoter-TSS (NM_029160)	promoter-TSS (NM_029160)	-80	NM_029160	66722	Mm.440554	NM_025728	ENSMUSG00000053153	Spag16	4921511D23Rik|4930524F24Rik|4930585K05Rik|AV261009|Pf20|Wdr29	sperm associated antigen 16	protein-coding
mm_45599.1	chr5	75004345	75004354	-	1	NA	TTS (NM_028850)	TTS (NM_028850)	40292	NM_028850	74277	Mm.239814	NM_028850	ENSMUSG00000029229	Chic2	1700081B18Rik|4930502K01Rik|BTL	cysteine-rich hydrophobic domain 2	protein-coding
mm_47826.1	chr5	134266078	134266078	-	1	NA	intron (NM_001080746, intron 13 of 34)	intron (NM_001080746, intron 13 of 34)	-36453	NR_104383	17969	Mm.425296	NM_010876	ENSMUSG00000015950	Ncf1	NCF-47K|NOXO2|Ncf-1|p47-phox|p47<phox>|p47phox	neutrophil cytosolic factor 1	protein-coding
mm_8597.1	chr1	156033789	156033804	-	1	NA	exon (NM_144791, exon 2 of 7)	exon (NM_144791, exon 2 of 7)	1021	NM_001160019	208263	Mm.211654	NM_144791	ENSMUSG00000026466	Tor1aip1	LAP1|Lap1B	torsin A interacting protein 1	protein-coding
mm_99089.1	chr11	99620973	99620976	+	1	NA	promoter-TSS (NM_001177537)	promoter-TSS (NM_001177537)	-570	NM_001177537	100502803	Mm.351892	NM_001177537	ENSMUSG00000062278	Gm11562	OTTMUSG00000002199	predicted gene 11562	protein-coding
mm_6910.1	chr1	84839311	84839321	-	1	NA	promoter-TSS (NM_025386)	promoter-TSS (NM_025386)	-12	NM_133975	14897	Mm.209265	NM_133975	ENSMUSG00000026219	Trip12	1110036I07Rik|6720416K24Rik|AA410158|Gtl6|TRIP-12	thyroid hormone receptor interactor 12	protein-coding
mm_86625.1	chr10	13966978	13967008	+	1	NA	intron (NM_010437, intron 1 of 8)	CpG-904	614	NM_010437	15273	Mm.42157	NM_010437	ENSMUSG00000015501	Hivep2	Gm20114|MIBP1|Schnurri-2|Shn-2	human immunodeficiency virus type I enhancer binding protein 2	protein-coding
mm_55603.1	chr6	71823806	71823814	-	1	NA	promoter-TSS (NM_025430)	promoter-TSS (NM_025430)	-26	NM_025430	66223	Mm.28579	NM_025430	ENSMUSG00000052962	Mrpl35	1110066C01Rik	mitochondrial ribosomal protein L35	protein-coding
mm_122947.1	chr14	54965957	54965967	-	1	NA	intron (NM_001164171, intron 1 of 38)	intron (NM_001164171, intron 1 of 38)	645	NM_001164171	17888	Mm.290003	NM_010856	ENSMUSG00000040752	Myh6	A830009F23Rik|AA517445|Myhc-a|Myhca|alpha-MHC	myosin, heavy polypeptide 6, cardiac muscle, alpha	protein-coding
mm_141686.1	chr17	33951439	33951493	-	1	NA	promoter-TSS (NM_019420)	promoter-TSS (NM_019420)	22	NM_019420	54218	Mm.11132	NM_019420	ENSMUSG00000067370	B3galt4	Gal-T2|Galt2	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 4	protein-coding
mm_157542.1	chrX	51205853	51205874	-	1	NA	5' UTR (NM_134163, exon 1 of 8)	5' UTR (NM_134163, exon 1 of 8)	127	NM_001310515	171170	Mm.295324	NM_134163	ENSMUSG00000036109	Mbnl3	A530038J18Rik|AI661274|CHCR|E430034C16Rik|MBLX|MBLX39|MBXL	muscleblind-like 3 (Drosophila)	protein-coding
mm_101140.1	chr11	14179041	14179081	-	1	NA	promoter-TSS (NR_131011)	promoter-TSS (NR_131011)	-20	NR_131011	75280	Mm.108492	NR_131011	ENSMUSG00000085452	4930554G24Rik	-	RIKEN cDNA 4930554G24 gene	ncRNA
mm_21594.1	chr2	164237722	164237724	-	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	618	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_148.1	chr1	11089769	11089774	+	1	NA	exon (NM_029525, exon 6 of 40)	exon (NM_029525, exon 6 of 40)	96306	NM_029525	109294	Mm.123247	NM_029525	ENSMUSG00000048960	Prex2	6230420N16Rik|AI316880|AI553603|C030045D06Rik|D430013K02|Depdc2|P-Rex2	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	protein-coding
mm_39679.1	chr5	25753581	25753595	+	1	NA	Intergenic	Intergenic	-6385	NM_001310504	242894	Mm.150319	NM_001004365	ENSMUSG00000056367	Actr3b	9630005C02|ARP11|AW047569|Arp3b|Arp3beta	ARP3 actin-related protein 3B	protein-coding
mm_63309.1	chr7	126862432	126862447	+	1	NA	promoter-TSS (NM_153580)	promoter-TSS (NM_153580)	467	NM_172746	233876	Mm.363427	NM_172746	ENSMUSG00000042606	Hirip3	B130036O03|C86302	HIRA interacting protein 3	protein-coding
mm_115754.1	chr13	19192704	19192708	-	1	NA	Intergenic	Intergenic	203107	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_54907.1	chr6	47636871	47636883	-	1	NA	Intergenic	Intergenic	18217	NR_002841	19799		NR_002841		Rn4.5s	-	4.5S RNA	rRNA
mm_114680.1	chr13	80886289	80886312	+	1	NA	intron (NM_001042591, intron 1 of 7)	CpG	2878	NM_001042591	105171	Mm.423137	NM_001042591	ENSMUSG00000074794	Arrdc3	AI450344|mKIAA1376	arrestin domain containing 3	protein-coding
mm_86925.1	chr10	23902147	23902156	+	1	NA	intron (NM_011704, intron 5 of 6)	intron (NM_011704, intron 5 of 6)	7463	NM_011704	22361	Mm.27154	NM_011704	ENSMUSG00000037440	Vnn1	V-1	vanin 1	protein-coding
mm_40936.1	chr5	76657728	76657732	+	1	NA	Intergenic	CpG	66016	NM_199032	381644	Mm.332452	NM_199032	ENSMUSG00000036403	Cep135	BC062951|Cep4|Gm1044	centrosomal protein 135	protein-coding
mm_76671.1	chr8	93535789	93535799	-	1	NA	promoter-TSS (NM_001003951)	promoter-TSS (NM_001003951)	-87	NM_001003951	67935	Mm.65457	NM_001003951	ENSMUSG00000058019	Ces5a	1700081L16Rik|1700122C07Rik|BB081581|Ces7|Gm503|cauxin	carboxylesterase 5A	protein-coding
mm_106667.1	chr11	121519327	121519341	-	1	NA	promoter-TSS (NM_178763)	promoter-TSS (NM_178763)	8	NM_178763	319530	Mm.11395	NM_178763	ENSMUSG00000039238	Zfp750	A030007D23Rik|Znf750	zinc finger protein 750	protein-coding
mm_133758.1	chr16	94454473	94454484	+	1	NA	exon (NM_009441, exon 38 of 46)	exon (NM_009441, exon 38 of 46)	72151	NM_007834	13185	Mm.7472	NM_007834	ENSMUSG00000022898	Dscr3	AW538125|Dcra	Down syndrome critical region gene 3	protein-coding
mm_95836.1	chr11	57011725	57011735	+	1	NA	5' UTR (NM_001113325, exon 1 of 16)	5' UTR (NM_001113325, exon 1 of 16)	112	NM_008165	14799	Mm.4920	NM_008165	ENSMUSG00000020524	Gria1	2900051M01Rik|Glr-1|Glr1|GluA1|GluR-A|GluRA|Glur-1|Glur1|HIPA1|gluR-K1	glutamate receptor, ionotropic, AMPA1 (alpha 1)	protein-coding
mm_38097.1	chr4	134245539	134245577	-	1	NA	promoter-TSS (NM_024215)	promoter-TSS (NM_024215)	33	NM_024215	68040	Mm.300404	NM_024215	ENSMUSG00000028840	Zfp593	3110024A21Rik|AV062409|E130106C14Rik|ZNF593	zinc finger protein 593	protein-coding
mm_135341.1	chr16	42340697	42340723	-	1	NA	promoter-TSS (NM_008083)	promoter-TSS (NM_008083)	-59	NM_008083	14432	Mm.1222	NM_008083	ENSMUSG00000047261	Gap43	B-50|Basp2|GAP-43	growth associated protein 43	protein-coding
mm_34497.1	chr4	148594524	148594528	+	1	NA	TTS (NM_009272)	TTS (NM_009272)	3013	NM_009272	20810	Mm.10	NM_009272	ENSMUSG00000006442	Srm	AA407669|SpdST|SpdSy	spermidine synthase	protein-coding
mm_79094.1	chr9	46242901	46242907	+	1	NA	exon (NM_007468, exon 3 of 3)	exon (NM_007468, exon 3 of 3)	2060	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_82283.1	chr9	7593402	7593411	-	1	NA	Intergenic	Intergenic	22010	NM_001310717	234911	Mm.334940	NM_001030289	ENSMUSG00000070323	Mmp27	Gm180	matrix metallopeptidase 27	protein-coding
mm_24879.1	chr3	95994097	95994122	+	1	NA	intron (NM_023320, intron 2 of 5)	intron (NM_023320, intron 2 of 5)	1730	NM_023320	67220	Mm.458147	NM_023320	ENSMUSG00000015745	Plekho1	2810052M02Rik|CKIP-1|Ckip1|JZA-20|Jza2	pleckstrin homology domain containing, family O member 1	protein-coding
mm_130342.1	chr15	97731458	97731475	-	1	NA	promoter-TSS (NM_001168693)	promoter-TSS (NM_001168693)	-61	NM_001168693	19011	Mm.1001	NM_008902	ENSMUSG00000022468	Endou	Pp11r|Tcl-30	endonuclease, polyU-specific	protein-coding
mm_98419.1	chr11	94638844	94638865	+	1	NA	intron (NM_133807, intron 5 of 6)	PB1D10|SINE|Alu	9030	NM_133807	98238	Mm.172720	NM_133807	ENSMUSG00000020869	Lrrc59	AA959742|C78668	leucine rich repeat containing 59	protein-coding
mm_133035.1	chr16	57353103	57353117	+	1	NA	promoter-TSS (NM_001040397)	promoter-TSS (NM_001040397)	-167	NM_001040397	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding
mm_54791.1	chr6	41636338	41636365	-	1	NA	promoter-TSS (NM_022413)	promoter-TSS (NM_022413)	54	NM_022413	64177	Mm.296889	NM_022413	ENSMUSG00000029868	Trpv6	CAT|CaT1|Cac|Ecac2|Otrpc3	transient receptor potential cation channel, subfamily V, member 6	protein-coding
mm_29694.1	chr3	123114239	123114255	-	1	NA	exon (NM_080451, exon 4 of 5)	exon (NM_080451, exon 4 of 5)	-79260	NM_021503	59006	Mm.141157	NM_021503	ENSMUSG00000028116	Myoz2	1110012I24Rik|Fatz-2|Myozl2	myozenin 2	protein-coding
mm_41570.1	chr5	93167611	93167623	+	1	NA	exon (NM_001310669, exon 9 of 11)	exon (NM_001310669, exon 9 of 11)	38878	NM_017367	12453	Mm.250419	NM_017367	ENSMUSG00000063015	Ccni	-	cyclin I	protein-coding
mm_154887.1	chrX	20797790	20797824	+	1	NA	Intergenic	Lx2|LINE|L1	-50736	NM_009703	11836	Mm.220946	NM_009703	ENSMUSG00000001127	Araf	1200013E08Rik|A-Raf|AW495444|Araf1	Araf proto-oncogene, serine/threonine kinase	protein-coding
mm_131799.1	chr16	22899219	22899224	+	1	NA	non-coding (NR_075099, exon 6 of 6)	non-coding (NR_075099, exon 6 of 6)	-4835	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_7128.1	chr1	90969608	90969631	-	1	NA	promoter-TSS (NM_008998)	promoter-TSS (NM_008998)	1	NM_008998	19329	Mm.279780	NM_008998	ENSMUSG00000026304	Rab17	AW413472	RAB17, member RAS oncogene family	protein-coding
mm_24082.1	chr3	87953047	87953056	+	1	NA	3' UTR (NM_007759, exon 4 of 4)	3' UTR (NM_007759, exon 4 of 4)	4358	NM_007759	12904	Mm.4757	NM_007759	ENSMUSG00000004885	Crabp2	AI893628|Crabp-2|CrabpII	cellular retinoic acid binding protein II	protein-coding
mm_125043.1	chr15	25780000	25780033	+	1	NA	intron (NM_019472, intron 23 of 40)	B4A|SINE|B4	-63282	NM_001034851	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_118117.1	chr13	104036562	104036603	-	1	NA	intron (NM_029447, intron 11 of 12)	intron (NM_029447, intron 11 of 12)	73032	NM_029447	75805	Mm.127692	NM_029447	ENSMUSG00000021710	Nln	4930472G13Rik|C79345	neurolysin (metallopeptidase M3 family)	protein-coding
mm_17501.1	chr2	28840275	28840358	-	1	NA	promoter-TSS (NM_001166033)	promoter-TSS (NM_001166033)	44	NM_172977	269252	Mm.26043	NM_172977	ENSMUSG00000035666	Gtf3c4	5330400C03|AI426938|AU014771|AU017413|KAT12|TFIIIC90	general transcription factor IIIC, polypeptide 4	protein-coding
mm_71913.1	chr8	70131323	70131326	+	1	NA	promoter-TSS (NM_001025587)	promoter-TSS (NM_001025587)	-3	NR_104434	75692	Mm.161167	NM_001025586	ENSMUSG00000071078	Nr2c2ap	2310073E15Rik	nuclear receptor 2C2-associated protein	protein-coding
mm_46298.1	chr5	100429504	100429523	-	1	NA	promoter-TSS (NR_034038)	promoter-TSS (NR_034038)	22	NR_034038	100503199	Mm.392282	NR_034038	ENSMUSG00000097772	5430416N02Rik	100041797|Adapt33|Gm3514	RIKEN cDNA 5430416N02 gene	ncRNA
mm_146896.1	chr18	29496562	29496576	-	1	NA	promoter-TSS (NR_045391)	promoter-TSS (NR_045391)	-153	NR_045391	78058	Mm.416952	NR_045391		4930578E11Rik	-	RIKEN cDNA 4930578E11 gene	ncRNA
mm_29499.1	chr3	116006448	116006451	-	1	NA	promoter-TSS (NM_021388)	promoter-TSS (NM_021388)	957	NM_023214	66500	Mm.34550	NM_023214	ENSMUSG00000054414	Slc30a7	1810059J10Rik|2610034N15Rik|4833428C12Rik|AI467242|ZnT-7|ZnT7|Zntl2	solute carrier family 30 (zinc transporter), member 7	protein-coding
mm_81646.1	chr9	110953154	110953176	+	1	NA	intron (NM_028838, intron 1 of 8)	ID_B1|SINE|B4	1620	NM_028838	74249	Mm.307615	NM_028838	ENSMUSG00000032495	Lrrc2	2400002D05Rik|4933431K03Rik	leucine rich repeat containing 2	protein-coding
mm_51978.1	chr6	91904213	91904273	+	1	NA	promoter-TSS (NM_198668)	promoter-TSS (NM_198668)	10	NM_198668	381798	Mm.444785	NM_198668	ENSMUSG00000034063	4930590J08Rik	Gm1071	RIKEN cDNA 4930590J08 gene	protein-coding
mm_17584.1	chr2	30415615	30415624	-	1	NA	promoter-TSS (NM_138748)	promoter-TSS (NM_138748)	129	NM_007760	12908	Mm.20396	NM_007760	ENSMUSG00000026853	Crat	AW107812|CARAT	carnitine acetyltransferase	protein-coding
mm_13511.1	chr2	109899300	109899303	+	1	NA	3' UTR (NM_011699, exon 5 of 5)	3' UTR (NM_011699, exon 5 of 5)	8423	NM_011699	22343	Mm.235300	NM_011699	ENSMUSG00000027162	Lin7c	9130007B12Rik|AI303698|AU019331|AW125731|D2Ertd520e|LIN-7-C|LIN-7C|MALS-3|Veli3	lin-7 homolog C (C. elegans)	protein-coding
mm_169302.1	chr14	103228649	103228654	+	1	NA	intron (NM_207215, intron 28 of 84)	(GGGA)n|Simple_repeat|Simple_repeat	118149	NM_207215	105689	Mm.6478	NM_207215	ENSMUSG00000033004	Mycbp2	AU023734|AW107953|AW546647|C130061D10Rik|Pam|Phr1|R75243	MYC binding protein 2	protein-coding
mm_103271.1	chr11	72037504	72037512	-	1	NA	promoter-TSS (NM_053245)	promoter-TSS (NM_053245)	1	NM_053245	114230	Mm.95707	NM_053245	ENSMUSG00000040554	Aipl1	A930007I01Rik	aryl hydrocarbon receptor-interacting protein-like 1	protein-coding
mm_27591.1	chr3	59130647	59130660	-	1	NA	5' UTR (NM_001287124, exon 1 of 2)	5' UTR (NM_001287124, exon 1 of 2)	109	NM_001008497	140795	Mm.439021	NM_133200	ENSMUSG00000036381	P2ry14	A330108O13Rik|Gpr105|P2Y14	purinergic receptor P2Y, G-protein coupled, 14	protein-coding
mm_26592.1	chr3	151437922	151437956	+	1	NA	promoter-TSS (NM_133222)	promoter-TSS (NM_133222)	57	NM_133222	170757	Mm.317261	NM_133222	ENSMUSG00000039167	Adgrl4	1110033N21Rik|ETL1|Eltd1|Etl	adhesion G protein-coupled receptor L4	protein-coding
mm_145551.1	chr18	60810312	60810376	+	1	NA	exon (NM_010545, exon 6 of 8)	exon (NM_010545, exon 6 of 8)	-1732	NR_039567	100628611		NR_039567	ENSMUSG00000093327	Mir5107	mir-5107|mmu-mir-5107|mu-mir-5107	microRNA 5107	ncRNA
mm_78437.1	chr9	32040420	32040420	+	1	NA	Intergenic	Intergenic	-75716	NM_001195632	330914	Mm.46683	NM_177379	ENSMUSG00000041444	Arhgap32	3426406O18Rik|Gc-gap|Grit|Px-rics|Rics|mKIAA0712|p200Rhogap|p250Gap	Rho GTPase activating protein 32	protein-coding
mm_103672.1	chr11	79146414	79146422	-	1	NA	promoter-TSS (NM_013571)	promoter-TSS (NM_013571)	-64	NM_013571	16706	Mm.4745	NM_013571	ENSMUSG00000018334	Ksr1	AW492498|B-KSR1|D11Bhm183e|D11Bhm184e|Ksr|RSU2|hb	kinase suppressor of ras 1	protein-coding
mm_164282.1	chr15	102471807	102471809	+	1	NA	intron (NM_001174073, intron 1 of 12)	intron (NM_001174073, intron 1 of 12)	1176	NM_001174073	18521	Mm.236513	NM_011042	ENSMUSG00000056851	Pcbp2	AW412548|Hnrpx|alphaCP-2	poly(rC) binding protein 2	protein-coding
mm_49735.1	chr6	34745692	34745728	+	1	NA	exon (NM_145575, exon 3 of 12)	exon (NM_145575, exon 3 of 12)	-34722	NM_001289657	76223	Mm.150047	NM_178630	ENSMUSG00000038836	Agbl3	2900053G10Rik|4930431N21Rik|6530406M24Rik|CCP3	ATP/GTP binding protein-like 3	protein-coding
mm_22118.1	chr2	170151687	170151700	-	1	NA	Intergenic	Intergenic	-9018	NM_001159683	228913	Mm.22858	NM_001033299	ENSMUSG00000052056	Zfp217	4933431C08Rik|AW987152|Gm562|ZABC1|Znf217	zinc finger protein 217	protein-coding
mm_2881.1	chr1	131828344	131828363	+	1	NA	5' UTR (NM_173865, exon 1 of 11)	5' UTR (NM_173865, exon 1 of 11)	341	NM_173865	98396	Mm.389181	NM_173865	ENSMUSG00000013275	Slc41a1	AI573938|B230315F01Rik	solute carrier family 41, member 1	protein-coding
mm_172669.1	chr8	43603789	43603803	-	1	NA	Intergenic	L1Md_F3|LINE|L1	23389	NM_001025240	384813	Mm.383319	NM_001025240	ENSMUSG00000050190	Gm5346	EG384813	predicted gene 5346	protein-coding
mm_78808.1	chr9	44067073	44067134	+	1	NA	promoter-TSS (NM_198092)	promoter-TSS (NM_198092)	82	NM_198092	53376	Mm.272770	NM_016808	ENSMUSG00000032010	Usp2	B930035K21Rik|Ubp41	ubiquitin specific peptidase 2	protein-coding
mm_68606.1	chr7	116264275	116264280	-	1	NA	intron (NM_001305185, intron 3 of 26)	intron (NM_001305185, intron 3 of 26)	-26501	NM_001305186	233765	Mm.3741	NM_172743	ENSMUSG00000045659	Plekha7	A430081P20Rik|AI414265	pleckstrin homology domain containing, family A member 7	protein-coding
mm_46946.1	chr5	114921946	114921967	-	1	NA	Intergenic	Intergenic	-1284	NM_145209	231655	Mm.95479	NM_145209	ENSMUSG00000041827	Oasl1	7530414C13Rik|oasl9	2'-5' oligoadenylate synthetase-like 1	protein-coding
mm_91666.1	chr10	43108855	43108858	-	1	NA	intron (NM_175407, intron 4 of 6)	intron (NM_175407, intron 4 of 6)	65674	NM_175407	109205	Mm.153750	NM_175407	ENSMUSG00000038248	Sobp	2900009C16Rik|5330439J01Rik|JXC1|jc	sine oculis-binding protein homolog (Drosophila)	protein-coding
mm_65734.1	chr7	28382977	28382991	-	1	NA	Intergenic	Intergenic	-3756	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_90898.1	chr10	10558097	10558125	-	1	NA	promoter-TSS (NM_026405)	promoter-TSS (NM_026405)	96	NM_026405	67844	Mm.31486	NM_026405	ENSMUSG00000019832	Rab32	2810011A17Rik|AU022057	RAB32, member RAS oncogene family	protein-coding
mm_21221.1	chr2	155826466	155826481	-	1	NA	5' UTR (NM_010579, exon 1 of 6)	5' UTR (NM_010579, exon 1 of 6)	452	NM_010579	16418	Mm.271674	NM_010579	ENSMUSG00000027613	Eif6	1110004P11|AA408895|CAB|Itgb4bp|eIF-6|imc-415|p27(BBP)|p27BBP	eukaryotic translation initiation factor 6	protein-coding
mm_20432.1	chr2	129306502	129306531	-	1	NA	exon (NM_010554, exon 4 of 7)	exon (NM_010554, exon 4 of 7)	3456	NM_010554	16175	Mm.15534	NM_010554	ENSMUSG00000027399	Il1a	Il-1a	interleukin 1 alpha	protein-coding
mm_106666.1	chr11	121519298	121519311	-	1	NA	promoter-TSS (NM_178763)	promoter-TSS (NM_178763)	38	NM_178763	319530	Mm.11395	NM_178763	ENSMUSG00000039238	Zfp750	A030007D23Rik|Znf750	zinc finger protein 750	protein-coding
mm_66634.1	chr7	45524812	45524873	-	1	NA	exon (NM_008654, exon 2 of 3)	exon (NM_008654, exon 2 of 3)	1426	NM_008654	17872	Mm.4048	NM_008654	ENSMUSG00000040435	Ppp1r15a	9630030H21|Gadd34|Myd116	protein phosphatase 1, regulatory (inhibitor) subunit 15A	protein-coding
mm_114330.1	chr13	60641016	60641019	+	1	NA	intron (NM_029653, intron 2 of 25)	intron (NM_029653, intron 2 of 25)	38806	NM_134062	69635	Mm.24103	NM_029653	ENSMUSG00000021559	Dapk1	D13Ucla1|DAP-Kinase	death associated protein kinase 1	protein-coding
mm_138699.1	chr17	35994494	35994539	+	1	NA	promoter-TSS (NR_015618)	promoter-TSS (NR_015618)	12	NR_015618	77810	Mm.483143	NR_015618		A930015D03Rik	-	RIKEN cDNA A930015D03 gene	ncRNA
mm_164764.1	chr17	85621072	85621089	-	1	NA	5' UTR (NM_011381, exon 1 of 2)	5' UTR (NM_011381, exon 1 of 2)	246	NM_011381	20473	Mm.370208	NM_011381	ENSMUSG00000038805	Six3	E130112M24Rik|Six3a|Six3alpha|Six3b|Six3beta	sine oculis-related homeobox 3	protein-coding
mm_171968.1	chr5	87737202	87737207	-	1	NA	Intergenic	L1_Mus3|LINE|L1	-37246	NM_001304768	12993	Mm.4908	NM_007785	ENSMUSG00000061937	Csn1s2a	Csng|PP22	casein alpha s2-like A	protein-coding
mm_99888.1	chr11	109485632	109485713	+	1	NA	intron (NM_028710, intron 2 of 13)	intron (NM_028710, intron 2 of 13)	-12076	NM_001029842	104681	Mm.265874	NM_134038	ENSMUSG00000041920	Slc16a6	AW743111|ESTM12|MCT 6|MCT 7|MCT6	solute carrier family 16 (monocarboxylic acid transporters), member 6	protein-coding
mm_84428.1	chr9	65885025	65885069	-	1	NA	5' UTR (NM_019797, exon 4 of 16)	5' UTR (NM_019797, exon 4 of 16)	126	NM_001170907	56404	Mm.208379	NM_019797	ENSMUSG00000032386	Trip4	4930558E03Rik|ASC-1|Asc1|BB191711	thyroid hormone receptor interactor 4	protein-coding
mm_44931.1	chr5	36277757	36277769	-	1	NA	intron (NM_030889, intron 1 of 26)	MTD|LTR|ERVL-MaLR	-23807	NR_106162	102465792		NR_106162	ENSMUSG00000098884	Mir7689	Gm27434|mmu-mir-7689	microRNA 7689	ncRNA
mm_4194.1	chr1	171225663	171225710	+	1	NA	exon (NM_013474, exon 3 of 4)	exon (NM_013474, exon 3 of 4)	632	NM_013474	11807	Mm.389209	NM_013474	ENSMUSG00000005681	Apoa2	Alp-2|Apo-AII|ApoA-II|ApoAII|Apoa-2|Hdl-1	apolipoprotein A-II	protein-coding
mm_8458.1	chr1	153186103	153186122	-	1	NA	intron (NM_008485, intron 1 of 23)	CpG	335	NM_008485	16782	Mm.329272	NM_008485	ENSMUSG00000026479	Lamc2	AA589349	laminin, gamma 2	protein-coding
mm_116475.1	chr13	43547850	43547852	-	1	NA	intron (NM_001081059, intron 6 of 8)	intron (NM_001081059, intron 6 of 8)	12340	NM_001081059	76137	Mm.426290	NM_001081059	ENSMUSG00000021371	Mcur1	6230416A05Rik|AU015498|AV136929|AW554392|C88263|Ccdc90a	mitochondrial calcium uniporter regulator 1	protein-coding
mm_112963.1	chr13	21180951	21180953	+	1	NA	intron (NM_009054, intron 1 of 7)	CpG	1021	NM_009054	19720	Mm.314056	NM_009054	ENSMUSG00000021326	Trim27	AW538890|Gm19403|Rfp	tripartite motif-containing 27	protein-coding
mm_157040.1	chrX	7967818	7967875	-	1	NA	promoter-TSS (NM_008089)	promoter-TSS (NM_008089)	64	NM_008089	14460	Mm.335973	NM_008089	ENSMUSG00000031162	Gata1	Gata-1|Gf-1|eryf1	GATA binding protein 1	protein-coding
mm_131080.1	chr16	4738723	4738723	+	1	NA	intron (NM_001136066, intron 1 of 5)	B1_Mus1|SINE|Alu	-2890	NM_010443	15369	Mm.272866	NM_010443	ENSMUSG00000004070	Hmox2	HO-2|HO2	heme oxygenase 2	protein-coding
mm_117126.1	chr13	60904840	60904851	-	1	NA	promoter-TSS (NM_026429)	promoter-TSS (NM_026429)	2	NM_026429	116913	Mm.443229	NM_026429	ENSMUSG00000062705	Tpbpb	1600012N09Rik	trophoblast specific protein beta	protein-coding
mm_165510.1	chr2	172398208	172398229	+	1	NA	intron (NM_001080820, intron 1 of 6)	intron (NM_001080820, intron 1 of 6)	4424	NM_001276423	320664	Mm.210195	NM_001033538	ENSMUSG00000074570	Cass4	F730031O20Rik	Cas scaffolding protein family member 4	protein-coding
mm_127159.1	chr15	98632394	98632411	+	1	NA	promoter-TSS (NM_001044741)	promoter-TSS (NM_001044741)	74	NM_001044741	12297	Mm.3544	NM_007581	ENSMUSG00000003352	Cacnb3	Beta3|CAB3|Ca(v)beta3|Cchb3	calcium channel, voltage-dependent, beta 3 subunit	protein-coding
mm_105972.1	chr11	115514103	115514122	-	1	NA	intron (NM_008258, intron 1 of 4)	CpG	258	NM_008258	15374	Mm.1775	NM_008258	ENSMUSG00000020737	Hn1	-	hematological and neurological expressed sequence 1	protein-coding
mm_114204.1	chr13	56073623	56073625	+	1	NA	TTS (NM_001159515)	TTS (NM_001159515)	61926	NM_012015	26914	Mm.283802	NM_012015	ENSMUSG00000015937	H2afy	H2AF12M|mH2a1|macroH2A1	H2A histone family, member Y	protein-coding
mm_147758.1	chr18	61259988	61259988	-	1	NA	intron (NM_146086, intron 13 of 21)	intron (NM_146086, intron 13 of 21)	39489	NM_146086	225600	Mm.391106	NM_146086	ENSMUSG00000024575	Pde6a	Pdea|nmf282	phosphodiesterase 6A, cGMP-specific, rod, alpha	protein-coding
mm_125485.1	chr15	54601037	54601040	+	1	NA	3' UTR (NM_178920, exon 4 of 4)	3' UTR (NM_178920, exon 4 of 4)	29672	NM_178920	105853	Mm.410994	NM_178920	ENSMUSG00000024479	Mal2	AI461653	mal, T cell differentiation protein 2	protein-coding
mm_134731.1	chr16	22899094	22899098	-	1	NA	non-coding (NR_075099, exon 6 of 6)	non-coding (NR_075099, exon 6 of 6)	-4710	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_128038.1	chr15	25364801	25364814	-	1	NA	exon (NM_027395, exon 2 of 2)	exon (NM_027395, exon 2 of 2)	48957	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	brain abundant, membrane attached signal protein 1	protein-coding
mm_89553.1	chr10	94750341	94750374	+	1	NA	exon (NM_029852, exon 9 of 16)	exon (NM_029852, exon 9 of 16)	61567	NM_029852	77048	Mm.296971	NM_029852	ENSMUSG00000020024	Cep83	2600001G24Rik|4921537D05Rik|5730513H21Rik|Ccdc41	centrosomal protein 83	protein-coding
mm_100223.1	chr11	117109952	117109962	+	1	NA	Intergenic	Intergenic	-5215	NR_029459	74136	Mm.272312	NM_028777	ENSMUSG00000020823	Sec14l1	1200017E04Rik|2810012L19Rik|Naa-35	SEC14-like lipid binding 1	protein-coding
mm_163421.1	chr12	80367482	80367482	+	1	NA	intron (NM_177267, intron 6 of 8)	intron (NM_177267, intron 6 of 8)	24195	NR_037207	100526530		NR_037207	ENSMUSG00000105972	Mir1843a	Mir1843|mir-1843a|mmu-mir-1843|mmu-mir-1843a	microRNA 1843a	ncRNA
mm_162400.1	chr1	84839909	84839916	+	1	NA	promoter-TSS (NM_025386)	promoter-TSS (NM_025386)	71	NM_025386	66153	Mm.381192	NM_025386	ENSMUSG00000073633	Fbxo36	0610008D19Rik|1110020F21Rik|2410002G19Rik|D1Ertd757e	F-box protein 36	protein-coding
mm_55791.1	chr6	82705353	82705386	-	1	NA	Intergenic	Intergenic	-52504	NM_025882	66979	Mm.195753	NM_025882	ENSMUSG00000030042	Pole4	2400007P05Rik|5830430F06Rik	polymerase (DNA-directed), epsilon 4 (p12 subunit)	protein-coding
mm_10224.1	chr2	6209864	6209866	+	1	NA	intron (NM_024208, intron 1 of 4)	intron (NM_024208, intron 1 of 4)	3129	NM_024208	67856	Mm.38342	NM_024208	ENSMUSG00000039063	Echdc3	2310005D12Rik|AI662097	enoyl Coenzyme A hydratase domain containing 3	protein-coding
mm_164413.1	chr16	38396387	38396428	+	1	NA	3' UTR (NM_134102, exon 11 of 11)	3' UTR (NM_134102, exon 11 of 11)	34217	NM_022318	64082	Mm.390856	NM_022318	ENSMUSG00000022803	Popdc2	AV006127|Pop2	popeye domain containing 2	protein-coding
mm_67715.1	chr7	89980936	89981009	-	1	NA	promoter-TSS (NM_021876)	promoter-TSS (NM_021876)	4	NM_021876	13626	Mm.380914	NM_021876	ENSMUSG00000030619	Eed	ENSMUSG00000039373|l(7)5Rn|l7Rn5|lusk	embryonic ectoderm development	protein-coding
mm_87795.1	chr10	60299850	60299875	+	1	NA	exon (NM_011179, exon 11 of 15)	exon (NM_011179, exon 11 of 15)	15401	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_13955.1	chr2	121305986	121305991	+	1	NA	exon (NM_001173506, exon 4 of 6)	exon (NM_001173506, exon 4 of 6)	10534	NM_001173506	17754	Mm.36501	NM_032393	ENSMUSG00000027254	Map1a	6330416M19Rik|AI853608|Mtap-1|Mtap1|Mtap1a|moth1	microtubule-associated protein 1 A	protein-coding
mm_57511.1	chr6	125481769	125481773	-	1	NA	intron (NM_007657, intron 1 of 7)	intron (NM_007657, intron 1 of 7)	12984	NM_007657	12527	Mm.210676	NM_007657	ENSMUSG00000030342	Cd9	Tspan29	CD9 antigen	protein-coding
mm_50943.1	chr6	57824646	57824649	+	1	NA	intron (NM_146168, intron 1 of 4)	CpG	478	NM_146168	232023	Mm.24642	NM_146168	ENSMUSG00000037788	Vopp1	AW146242|Ecop	vesicular, overexpressed in cancer, prosurvival protein 1	protein-coding
mm_54859.1	chr6	42597302	42597315	-	1	NA	promoter-TSS (NM_203396)	promoter-TSS (NM_203396)	64	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_36425.1	chr4	82065890	82065893	-	1	NA	non-coding (NR_040659, exon 1 of 3)	non-coding (NR_040659, exon 1 of 3)	511	NR_040659	545641	Mm.216028	NR_040659	ENSMUSG00000085022	Gm5860	EG545641	predicted gene 5860	ncRNA
mm_87575.1	chr10	56388355	56388363	+	1	NA	exon (NM_010288, exon 2 of 2)	exon (NM_010288, exon 2 of 2)	11059	NM_010288	14609	Mm.378921	NM_010288	ENSMUSG00000050953	Gja1	AU042049|AW546267|Cnx43|Cx43|Cx43alpha1|Gja-1|Npm1|connexin43	gap junction protein, alpha 1	protein-coding
mm_35537.1	chr4	41314878	41314889	-	1	NA	promoter-TSS (NM_026893)	promoter-TSS (NM_026893)	18	NM_026893	68970	Mm.28891	NM_026893	ENSMUSG00000028436	Dcaf12	1500001L20Rik|5830424K06Rik|AA420338|AI851081|Wdr40a	DDB1 and CUL4 associated factor 12	protein-coding
mm_92553.1	chr10	79766812	79766825	-	1	NA	exon (NM_144528, exon 1 of 9)	exon (NM_144528, exon 1 of 9)	134	NM_144528	70294	Mm.466670	NM_144528	ENSMUSG00000035890	Rnf126	2610010O19Rik	ring finger protein 126	protein-coding
mm_127763.1	chr15	103538099	103538111	+	1	NA	promoter-TSS (NM_021391)	promoter-TSS (NM_021391)	-113	NM_021391	58200	Mm.143788	NM_021391	ENSMUSG00000022490	Ppp1r1a	0610038N18Rik|I-1	protein phosphatase 1, regulatory (inhibitor) subunit 1A	protein-coding
mm_6389.1	chr1	72849308	72849311	-	1	NA	exon (NM_008342, exon 2 of 4)	exon (NM_008342, exon 2 of 4)	23922	NM_001310659	16008	Mm.141936	NM_008342	ENSMUSG00000039323	Igfbp2	AI255832|IBP-2|Igfbp-2|mIGFBP-2	insulin-like growth factor binding protein 2	protein-coding
mm_134814.1	chr16	25057978	25057993	-	1	NA	Intergenic	Intergenic	-1654	NR_040374	319487	Mm.137341	NR_040374	ENSMUSG00000096960	A230028O05Rik	-	RIKEN cDNA A230028O05 gene	ncRNA
mm_120566.1	chr14	68661416	68661454	+	1	NA	Intergenic	Intergenic	-5593	NM_183366	13522	Mm.117450	NM_010082	ENSMUSG00000014725	Adam28	C130072N01Rik|D430033C21Rik|Dtgn1|MDC-L|MDCL|TECADAM|eMDCII	a disintegrin and metallopeptidase domain 28	protein-coding
mm_1057.1	chr1	58973522	58973582	+	1	NA	promoter-TSS (NM_172406)	promoter-TSS (NM_172406)	-19	NM_172656	227154	Mm.286006	NM_172656	ENSMUSG00000026027	Stradb	AA792893|Als2cr2|B830008M19|D1Ucla2|ILPIP|ILPIPA|PRO1038|Papk|Syradb	STE20-related kinase adaptor beta	protein-coding
mm_166649.1	chr6	86600008	86600022	-	1	NA	Intergenic	Intergenic	-28159	NM_026414	67855	Mm.183043	NM_026414	ENSMUSG00000033508	Asprv1	2300003P22Rik|AA986851|SASP|SASPase|Taps	aspartic peptidase, retroviral-like 1	protein-coding
mm_129987.1	chr15	86067459	86067484	-	1	NA	intron (NM_001205353, intron 1 of 18)	Tigger15a|DNA|TcMar-Tigger	8744	NM_001205353	223752	Mm.24442	NM_172611	ENSMUSG00000035900	Gramd4	9930016O13	GRAM domain containing 4	protein-coding
mm_108322.1	chr12	79766859	79766877	+	1	NA	intron (NM_009014, intron 8 of 10)	intron (NM_009014, intron 8 of 10)	157865	NR_131075	77290	Mm.395042	NR_131073		9430078K24Rik	-	RIKEN cDNA 9430078K24 gene	ncRNA
mm_24359.1	chr3	90069068	90069073	+	1	NA	promoter-TSS (NR_030543)	promoter-TSS (NR_030543)	-950	NR_030543	100124481		NR_030543	ENSMUSG00000077996	Mir190b	Mirn190b|mir-190b	microRNA 190b	ncRNA
mm_23690.1	chr3	68691628	68691650	+	1	NA	intron (NM_001159424, intron 2 of 7)	intron (NM_001159424, intron 2 of 7)	215	NM_008351	16159	Mm.103783	NM_008351	ENSMUSG00000027776	Il12a	IL-12p35|Il-12a|Ll12a|p35	interleukin 12a	protein-coding
mm_46323.1	chr5	100798533	100798549	-	1	NA	promoter-TSS (NM_026826)	promoter-TSS (NM_026826)	59	NM_001081107	191578	Mm.21469	NM_180984	ENSMUSG00000035266	Helq	AU021725|D430018E21Rik|Hel308	helicase, POLQ-like	protein-coding
mm_618.1	chr1	40084765	40084770	+	1	NA	promoter-TSS (NM_010555)	promoter-TSS (NM_010555)	-1	NM_010555	16178	Mm.1349	NM_010555	ENSMUSG00000026073	Il1r2	CD121b|Il1r-2	interleukin 1 receptor, type II	protein-coding
mm_104112.1	chr11	86722236	86722261	-	1	NA	exon (NM_001003908, exon 9 of 32)	exon (NM_001003908, exon 9 of 32)	35244	NM_001003908	67300	Mm.254588	NM_001003908	ENSMUSG00000047126	Cltc	3110065L21Rik|CHC|R74732	clathrin, heavy polypeptide (Hc)	protein-coding
mm_164612.1	chr17	31161395	31161398	+	1	NA	TTS (NM_009362)	TTS (NM_009362)	3657	NM_009362	21784	Mm.2854	NM_009362	ENSMUSG00000024032	Tff1	Bcei|PS2	trefoil factor 1	protein-coding
mm_93718.1	chr10	119076160	119076173	-	1	NA	Intergenic	Intergenic	-16739	NR_045348	73400	Mm.416864	NR_045348	ENSMUSG00000100681	1700064J06Rik	-	RIKEN cDNA 1700064J06 gene	ncRNA
mm_86989.1	chr10	25489697	25489724	+	1	NA	intron (NM_001199265, intron 12 of 19)	intron (NM_001199265, intron 12 of 19)	46562	NM_001195596	100504474	Mm.46323	NM_001195596	ENSMUSG00000096546	Smlr1	2010003K15Rik	small leucine-rich protein 1	protein-coding
mm_4725.1	chr1	181251270	181251282	+	1	NA	Intergenic	RLTR17|LTR|ERVK	-39298	NM_145514	226757	Mm.289082	NM_145514	ENSMUSG00000038733	Wdr26	1600024A01Rik|AA693241|AI447817|AU044014|C77982|Gid7	WD repeat domain 26	protein-coding
mm_23087.1	chr3	36863180	36863190	+	1	NA	promoter-TSS (NM_172679)	promoter-TSS (NM_172679)	79	NM_172679	229227	Mm.207907	NM_172679	ENSMUSG00000037270	4932438A13Rik	4732443H21|B830039D19Rik|D630029K19Rik|FSA|Kiaa1109|Tweek	RIKEN cDNA 4932438A13 gene	protein-coding
mm_127634.1	chr15	102471170	102471184	+	1	NA	intron (NM_001174073, intron 1 of 12)	CpG	545	NM_001174073	18521	Mm.236513	NM_011042	ENSMUSG00000056851	Pcbp2	AW412548|Hnrpx|alphaCP-2	poly(rC) binding protein 2	protein-coding
mm_35241.1	chr4	19877327	19877345	-	1	NA	3' UTR (NM_175406, exon 8 of 8)	3' UTR (NM_175406, exon 8 of 8)	45230	NM_175406	242341	Mm.19298	NM_175406	ENSMUSG00000028238	Atp6v0d2	1620401A02Rik|AI324824|V-ATPase	ATPase, H+ transporting, lysosomal V0 subunit D2	protein-coding
mm_104806.1	chr11	98775262	98775293	-	1	NA	promoter-TSS (NM_145434)	promoter-TSS (NM_145434)	100	NM_145434	217166	Mm.390397	NM_145434	ENSMUSG00000020889	Nr1d1	A530070C09Rik|R75201	nuclear receptor subfamily 1, group D, member 1	protein-coding
mm_75963.1	chr8	71723288	71723298	-	1	NA	intron (NR_131256, intron 1 of 25)	intron (NR_131256, intron 1 of 25)	2388	NR_131256	74015	Mm.22025	NM_028715	ENSMUSG00000070000	Fcho1	3322402E17Rik|N28152	FCH domain only 1	protein-coding
mm_42177.1	chr5	112261883	112261893	+	1	NA	intron (NM_023695, intron 3 of 5)	(TCCA)n|Simple_repeat|Simple_repeat	6068	NM_001312893	12960	Mm.29488	NM_023695	ENSMUSG00000029343	Crybb1	3110006K12Rik|BB1CRY	crystallin, beta B1	protein-coding
mm_157165.1	chrX	9467105	9467192	-	1	NA	exon (NM_007807, exon 2 of 13)	exon (NM_007807, exon 2 of 13)	2176	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_5804.1	chr1	52232402	52232432	-	1	NA	intron (NM_001081081, intron 1 of 17)	CpG	815	NM_001081081	14660	Mm.398608	NM_001081081	ENSMUSG00000026103	Gls	6330442B14|AI314027|B230365M23Rik	glutaminase	protein-coding
mm_115711.1	chr13	15802628	15802638	-	1	NA	promoter-TSS (NR_045507)	promoter-TSS (NR_045507)	-3	NR_045507	71071	Mm.380845	NR_045507		4933412O06Rik	-	RIKEN cDNA 4933412O06 gene	ncRNA
mm_114704.1	chr13	83524594	83524618	+	1	NA	promoter-TSS (NM_001347567)	promoter-TSS (NM_001347567)	-137	NM_001347567	17260	Mm.24001	NM_025282	ENSMUSG00000005583	Mef2c	5430401D19Rik|9930028G15Rik|AV011172|Mef2	myocyte enhancer factor 2C	protein-coding
mm_92913.1	chr10	83636348	83636357	-	1	NA	intron (NM_145220, intron 2 of 20)	intron (NM_145220, intron 2 of 20)	12312	NM_145220	216190	Mm.282985	NM_145220	ENSMUSG00000020263	Appl2	Dip3b	adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 2	protein-coding
mm_143393.1	chr17	70393557	70393560	-	1	NA	intron (NM_001347411, intron 3 of 14)	intron (NM_001347411, intron 3 of 14)	-31234	NM_177639	224997	Mm.311840	NM_027712	ENSMUSG00000003279	Dlgap1	4933422O14Rik|9630002F18|AI845682|AI848168|BB075781|D17Bwg0511e|GKAP/SAPAP|GKPA/SAPAP|Gkap|Sapap1|mKIAA4162	discs, large (Drosophila) homolog-associated protein 1	protein-coding
mm_80565.1	chr9	83834685	83834736	+	1	NA	promoter-TSS (NM_001284272)	promoter-TSS (NM_001284272)	21	NM_001284272	22137	Mm.1904	NM_009445	ENSMUSG00000038379	Ttk	AL022661|Esk1|Mps1|PYT|esk	Ttk protein kinase	protein-coding
mm_135085.1	chr16	34514176	34514184	-	1	NA	promoter-TSS (NM_177357)	promoter-TSS (NM_177357)	-153	NM_177357	545156	Mm.82274	NM_177357	ENSMUSG00000061751	Kalrn	2210407G14Rik|AV235988|DUET|E530005C20Rik|Gm539|Hapip|TRAD	kalirin, RhoGEF kinase	protein-coding
mm_24928.1	chr3	96559115	96559144	+	1	NA	exon (NM_023719, exon 3 of 8)	exon (NM_023719, exon 3 of 8)	1172	NM_023719	56338	Mm.410189	NM_023719	ENSMUSG00000038393	Txnip	1200008J08Rik|AA682105|Hyplip1|THIF|Tbp-2|VDUP1	thioredoxin interacting protein	protein-coding
mm_135330.1	chr16	38800344	38800358	-	1	NA	promoter-TSS (NM_178924)	promoter-TSS (NM_178924)	-148	NM_178924	22268	Mm.130793	NM_178924	ENSMUSG00000049436	Upk1b	AI413235|Tspan20|UPIb|Upk1	uroplakin 1B	protein-coding
mm_77854.1	chr9	5310307	5310313	+	1	NA	intron (NM_007609, intron 1 of 8)	intron (NM_007609, intron 1 of 8)	1461	NM_007609	12363	Mm.1569	NM_007609	ENSMUSG00000033538	Casp4	CASP-11|CASP-4|Casp11|Caspl|ich-3	caspase 4, apoptosis-related cysteine peptidase	protein-coding
mm_43239.1	chr5	130029386	130029396	+	1	NA	promoter-TSS (NM_007761)	promoter-TSS (NM_007761)	85	NM_007761	12909	Mm.18072	NM_007761	ENSMUSG00000025532	Crcp	AL022669	calcitonin gene-related peptide-receptor component protein	protein-coding
mm_30659.1	chr4	9269286	9269335	+	1	NA	promoter-TSS (NM_028940)	promoter-TSS (NM_028940)	-7	NM_028940	74438	Mm.473368	NM_028940	ENSMUSG00000041216	Clvs1	4933402J24Rik|Clvl1|Rlbp1l1	clavesin 1	protein-coding
mm_81918.1	chr9	120114994	120115008	+	1	NA	intron (NM_144793, intron 1 of 6)	intron (NM_144793, intron 1 of 6)	4602	NM_144793	208638	Mm.236656	NM_144793	ENSMUSG00000032519	Slc25a38	AV019094|BC010801|appoptosin	solute carrier family 25, member 38	protein-coding
mm_40154.1	chr5	35413350	35413376	+	1	NA	Intergenic	Intergenic	24246	NM_010445	15371	Mm.358606	NM_010445	ENSMUSG00000067438	Hmx1	Nkx5-3	H6 homeobox 1	protein-coding
mm_126214.1	chr15	78905791	78905801	+	1	NA	exon (NM_009164, exon 11 of 18)	exon (NM_009164, exon 11 of 18)	6028	NM_009164	20401	Mm.4462	NM_009164	ENSMUSG00000022436	Sh3bp1	3BP-1	SH3-domain binding protein 1	protein-coding
mm_144062.1	chr17	90798123	90798126	-	1	NA	intron (NM_001346957, intron 3 of 18)	intron (NM_001346957, intron 3 of 18)	-4648	NR_136930	102634634		NR_136930		Gm20491	-	enolase 1, alpha non-neuron pseudogene	pseudo
mm_133415.1	chr16	85546998	85547007	+	1	NA	intron (NM_144853, intron 1 of 3)	intron (NM_144853, intron 1 of 3)	3371	NM_144853	224405	Mm.213203	NM_144853	ENSMUSG00000041134	Cyyr1	-	cysteine and tyrosine-rich protein 1	protein-coding
mm_121925.1	chr14	23589831	23589834	-	1	NA	intron (NM_001253366, intron 5 of 29)	intron (NM_001253366, intron 5 of 29)	414373	NM_001253375	16531	Mm.343607	NM_010610	ENSMUSG00000063142	Kcnma1	5730414M22Rik|BKCa|MaxiK|Slo|Slo1|mSlo|mSlo1	potassium large conductance calcium-activated channel, subfamily M, alpha member 1	protein-coding
mm_169868.1	chr16	3535837	3535845	+	1	NA	Intergenic	ORR1A1|LTR|ERVL-MaLR	-56557	NM_146860	258859	Mm.377723	NM_146860	ENSMUSG00000051003	Olfr161	MOR131-1|OR912-47M6	olfactory receptor 161	protein-coding
mm_42161.1	chr5	112257464	112257474	+	1	NA	exon (NM_001312894, exon 2 of 6)	exon (NM_001312894, exon 2 of 6)	1649	NM_001312893	12960	Mm.29488	NM_023695	ENSMUSG00000029343	Crybb1	3110006K12Rik|BB1CRY	crystallin, beta B1	protein-coding
mm_126837.1	chr15	89020341	89020355	+	1	NA	exon (NM_031260, exon 17 of 27)	exon (NM_031260, exon 17 of 27)	37354	NM_031260	83456	Mm.358791	NM_031260	ENSMUSG00000015365	Mov10l1	CHAMP|Csm	Moloney leukemia virus 10-like 1	protein-coding
mm_10332.1	chr2	11535711	11535721	+	1	NA	intron (NM_001177758, intron 1 of 14)	CpG	18213	NM_001177758	170768	Mm.19669	NM_133232	ENSMUSG00000026773	Pfkfb3	E330010H22Rik|iPFK-2|uPFK-2	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	protein-coding
mm_165637.1	chr3	73643794	73643799	+	1	NA	intron (NM_009738, intron 3 of 3)	intron (NM_009738, intron 3 of 3)	64619	NM_009738	12038	Mm.250719	NM_009738	ENSMUSG00000027792	Bche	C730038G20Rik	butyrylcholinesterase	protein-coding
mm_152313.1	chr19	9899428	9899439	-	1	NA	promoter-TSS (NM_016692)	promoter-TSS (NM_016692)	100	NM_016692	16319	Mm.29755	NM_016692	ENSMUSG00000024660	Incenp	2700067E22Rik|AU019509|C130081E20|C77457	inner centromere protein	protein-coding
mm_138382.1	chr17	35045122	35045137	+	1	NA	non-coding (NR_130641, exon 4 of 24)	non-coding (NR_130641, exon 4 of 24)	1493	NM_013600	17687	Mm.24192	NM_013600	ENSMUSG00000007035	Msh5	Mut5	mutS homolog 5	protein-coding
mm_48765.1	chr5	148399798	148399850	-	1	NA	promoter-TSS (NM_007513)	promoter-TSS (NM_007513)	80	NM_007513	11987	Mm.275489	NM_007513	ENSMUSG00000041313	Slc7a1	4831426K01Rik|AI447493|Atrc-1|Atrc1|Cat1|Rec-1|Rev-1|mCAT-1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 1	protein-coding
mm_163150.1	chr11	83175264	83175278	+	1	NA	promoter-TSS (NM_011410)	promoter-TSS (NM_011410)	85	NM_001302559	20558	Mm.38192	NM_011410	ENSMUSG00000000204	Slfn4	AI450778	schlafen 4	protein-coding
mm_168495.1	chr11	51455809	51455824	-	1	NA	intron (NM_153393, intron 2 of 28)	(CCCTAA)n|Simple_repeat|Simple_repeat	-128941	NM_028398	72947	Mm.256875	NM_028398	ENSMUSG00000020359	Phykpl	2900006B13Rik|Agxt2l2	5-phosphohydroxy-L-lysine phospholyase	protein-coding
mm_86175.1	chr9	119190255	119190258	-	1	NA	intron (NM_001037749, intron 1 of 11)	intron (NM_001037749, intron 1 of 11)	137	NM_001037749	382113	Mm.335525	NM_001037749	ENSMUSG00000070280	Slc22a14	Gm1128	solute carrier family 22 (organic cation transporter), member 14	protein-coding
mm_43535.1	chr5	137333641	137333659	+	1	NA	promoter-TSS (NM_031406)	promoter-TSS (NM_031406)	-68	NM_031406	83704	Mm.235625	NM_031406	ENSMUSG00000037344	Slc12a9	CIP1	solute carrier family 12 (potassium/chloride transporters), member 9	protein-coding
mm_52546.1	chr6	115935035	115935045	+	1	NA	intron (NM_145383, intron 2 of 4)	intron (NM_145383, intron 2 of 4)	3113	NM_145383	212541	Mm.2965	NM_145383	ENSMUSG00000030324	Rho	Noerg1|Opn2|Ops|RP4	rhodopsin	protein-coding
mm_45354.1	chr5	65918200	65918204	-	1	NA	Intergenic	HAL1_SS|LINE|L1	-48922	NM_001081104	231252	Mm.140015	NM_001081104	ENSMUSG00000029205	Chrna9	2410015I05Rik|Acra9|EG666827|Gm8311	cholinergic receptor, nicotinic, alpha polypeptide 9	protein-coding
mm_57330.1	chr6	124741102	124741118	-	1	NA	promoter-TSS (NM_013535)	promoter-TSS (NM_013535)	-31	NM_013535	14790	Mm.439877	NM_013535	ENSMUSG00000072772	Grcc10	2310033H05Rik|C10	gene rich cluster, C10 gene	protein-coding
mm_138837.1	chr17	39848527	39848607	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	5570	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_124528.1	chr14	122233600	122233613	-	1	NA	promoter-TSS (NR_015532)	promoter-TSS (NR_015532)	32	NR_015532	68245	Mm.443285	NR_015532	ENSMUSG00000100585	1700108J01Rik	-	RIKEN cDNA 1700108J01 gene	ncRNA
mm_93019.1	chr10	87830765	87830789	-	1	NA	Intergenic	LTR16A|LTR|ERVL	-27488	NM_001314010	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_77111.1	chr8	111081833	111081843	-	1	NA	promoter-TSS (NM_181549)	promoter-TSS (NM_181549)	-130	NM_181549	353287	Mm.135495	NM_181549	ENSMUSG00000033633	Clec18a	Mrcl	C-type lectin domain family 18, member A	protein-coding
mm_65509.1	chr7	25754630	25754640	-	1	NA	promoter-TSS (NM_178089)	promoter-TSS (NM_178089)	66	NM_178089	232989	Mm.254223	NM_144922	ENSMUSG00000040725	Hnrnpul1	E130317O14Rik|E1B-AP5|E1BAP5|Hnrnpul|Hnrpul1	heterogeneous nuclear ribonucleoprotein U-like 1	protein-coding
mm_65735.1	chr7	28383125	28383150	-	1	NA	Intergenic	Intergenic	-3909	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_73207.1	chr8	95703048	95703063	+	1	NA	promoter-TSS (NM_145602)	promoter-TSS (NM_145602)	18	NM_145602	234593	Mm.29846	NM_145602	ENSMUSG00000036564	Ndrg4	D8Bwg1337e|Ndr1-rs|Ndr4|R74996|SMAP-8	N-myc downstream regulated gene 4	protein-coding
mm_93825.1	chr10	121494030	121494055	-	1	NA	Intergenic	Intergenic	-17792	NM_138956	192678	Mm.41265	NM_138956	ENSMUSG00000025795	Rassf3	AW212023|AW322379	Ras association (RalGDS/AF-6) domain family member 3	protein-coding
mm_52700.1	chr6	119236580	119236598	+	1	NA	promoter-TSS (NM_001033382)	promoter-TSS (NM_001033382)	63	NM_001347427	319734	Mm.440773	NM_001033382	ENSMUSG00000041460	Cacna2d4	5730412N02Rik|BE686333	calcium channel, voltage-dependent, alpha 2/delta subunit 4	protein-coding
mm_141964.1	chr17	35121214	35121275	-	1	NA	promoter-TSS (NM_009975)	promoter-TSS (NM_009975)	48	NM_001303476	13001	Mm.378901	NM_009975	ENSMUSG00000024387	Csnk2b	CK II beta	casein kinase 2, beta polypeptide	protein-coding
mm_38092.1	chr4	134238327	134238369	-	1	NA	promoter-TSS (NM_001081047)	promoter-TSS (NM_001081047)	51	NM_001081047	194231	Mm.331958	NM_001081047	ENSMUSG00000028841	Cnksr1	BC037758	connector enhancer of kinase suppressor of Ras 1	protein-coding
mm_83086.1	chr9	40295075	40295109	-	1	NA	Intergenic	Intergenic	25876	NM_178227	235281	Mm.290083	NM_153522	ENSMUSG00000049281	Scn3b	1110001K16Rik|4833414B02Rik|Scnb3	sodium channel, voltage-gated, type III, beta	protein-coding
mm_172682.1	chr8	52308662	52308680	+	1	NA	Intergenic	L1Md_T|LINE|L1	-1203031	NM_001205054	11593	Mm.334535	NM_001005847	ENSMUSG00000031521	Aga	AW060726	aspartylglucosaminidase	protein-coding
mm_106279.1	chr11	118143878	118143880	-	1	NA	Intergenic	RLTR14|LTR|ERV1	-14660	NM_001167746	69926	Mm.473893	NM_001167746	ENSMUSG00000033987	Dnah17	2810003K23Rik|Dnahc17|Dnahcl1|Gm1178|mKIAA3028	dynein, axonemal, heavy chain 17	protein-coding
mm_127739.1	chr15	103298931	103298972	+	1	NA	3' UTR (NM_019817, exon 9 of 9)	3' UTR (NM_019817, exon 9 of 9)	11487	NM_030720	80910	Mm.160369	NM_030720	ENSMUSG00000063234	Gpr84	EX33	G protein-coupled receptor 84	protein-coding
mm_11696.1	chr2	35883629	35883651	+	1	NA	intron (NM_029774, intron 6 of 9)	intron (NM_029774, intron 6 of 9)	64450	NR_040618	77665	Mm.400558	NR_040618	ENSMUSG00000086449	9030204H09Rik	-	RIKEN cDNA 9030204H09 gene	ncRNA
mm_21019.1	chr2	152397999	152398020	-	1	NA	promoter-TSS (NM_011438)	promoter-TSS (NM_011438)	37	NM_011438	20667	Mm.28424	NM_011438	ENSMUSG00000051817	Sox12	2010205A02Rik	SRY (sex determining region Y)-box 12	protein-coding
mm_114941.1	chr13	96542518	96542522	+	1	NA	promoter-TSS (NM_001164222)	promoter-TSS (NM_001164222)	59	NM_012048	27015	Mm.89926	NM_012048	ENSMUSG00000021668	Polk	DINP|Dinb1	polymerase (DNA directed), kappa	protein-coding
mm_111916.1	chr12	108873274	108873284	-	1	NA	intron (NM_011710, intron 6 of 10)	intron (NM_011710, intron 6 of 10)	19919	NM_001164488	22375	Mm.38433	NM_011710	ENSMUSG00000021266	Wars	TrpRS|WRS	tryptophanyl-tRNA synthetase	protein-coding
mm_24129.1	chr3	88207256	88207305	+	1	NA	Intergenic	Intergenic	-7891	NR_037276	100526540		NR_037276	ENSMUSG00000092988	Mir3093	mir-3093|mmu-mir-3093	microRNA 3093	ncRNA
mm_59135.1	chr7	24081889	24081948	+	1	NA	promoter-TSS (NM_172483)	promoter-TSS (NM_172483)	21	NM_001289637	210135	Mm.32254	NM_172483	ENSMUSG00000057101	Zfp180	2310040I01Rik|AI852378|D130011P11|HHZ168	zinc finger protein 180	protein-coding
mm_81546.1	chr9	110281260	110281266	+	1	NA	promoter-TSS (NR_105744)	promoter-TSS (NR_105744)	-24	NR_105744	102465959		NR_105744	ENSMUSG00000098973	Mir6236	Gm27547|mmu-mir-6236	microRNA 6236	ncRNA
mm_88272.1	chr10	74978633	74978635	+	1	NA	intron (NM_010311, intron 1 of 3)	intron (NM_010311, intron 1 of 3)	11403	NM_010311	14687	Mm.32595	NM_010311	ENSMUSG00000040009	Gnaz	AI847979|Gz	guanine nucleotide binding protein, alpha z subunit	protein-coding
mm_156641.1	chrX	157598827	157598846	+	1	NA	promoter-TSS (NM_172307)	promoter-TSS (NM_172307)	-121	NM_172307	270669	Mm.37577	NM_172307	ENSMUSG00000046873	Mbtps2	9630032G22Rik|AI662535	membrane-bound transcription factor peptidase, site 2	protein-coding
mm_93321.1	chr10	99132330	99132334	-	1	NA	intron (NM_027740, intron 4 of 11)	intron (NM_027740, intron 4 of 11)	24197	NM_015737	14426	Mm.314	NM_015737	ENSMUSG00000090035	Galnt4	AV011803	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 4	protein-coding
mm_108302.1	chr12	79303317	79303339	+	1	NA	intron (NM_001252562, intron 3 of 7)	intron (NM_001252562, intron 3 of 7)	5977	NM_001252562	19363	Mm.341756	NM_009014	ENSMUSG00000059060	Rad51b	AI553500|R51H2|Rad51l1|mREC2	RAD51 paralog B	protein-coding
mm_9154.1	chr1	170927568	170927583	-	1	NA	promoter-TSS (NM_001160215)	promoter-TSS (NM_001160215)	8	NM_001160215	98752	Mm.1850	NM_145141	ENSMUSG00000038421	Fcrla	BB219290|FCRL|FCRL1|FREB|Fcrlm1|Fcrx|Freb1|mFREB|mFcrX	Fc receptor-like A	protein-coding
mm_164248.1	chr15	97784512	97784532	+	1	NA	exon (NM_026353, exon 1 of 3)	exon (NM_026353, exon 1 of 3)	157	NM_026353	67739	Mm.28955	NM_026353	ENSMUSG00000081534	Slc48a1	4930570C03Rik	solute carrier family 48 (heme transporter), member 1	protein-coding
mm_76894.1	chr8	105708173	105708223	-	1	NA	promoter-TSS (NM_198299)	promoter-TSS (NM_198299)	-30	NM_198299	102124	Mm.276087	NM_198299	ENSMUSG00000013155	Enkd1	AI606951|E130303B06Rik	enkurin domain containing 1	protein-coding
mm_56622.1	chr6	112721703	112721706	-	1	NA	3' UTR (NM_080448, exon 22 of 22)	3' UTR (NM_080448, exon 22 of 22)	-25034	NM_001167730	58186	Mm.103812	NM_021385	ENSMUSG00000030254	Rad18	2810024C04Rik|Rad18sc	RAD18 E3 ubiquitin protein ligase	protein-coding
mm_76740.1	chr8	95202776	95202785	-	1	NA	Intergenic	Intergenic	-60240	NM_001145831	16582	Mm.378951	NM_010631	ENSMUSG00000031788	Kifc3	AI325457|BB123200	kinesin family member C3	protein-coding
mm_148648.1	chr19	5493413	5493427	+	1	NA	exon (NM_007687, exon 4 of 4)	exon (NM_007687, exon 4 of 4)	2965	NM_007687	12631	Mm.329655	NM_007687	ENSMUSG00000056201	Cfl1	AA959946|Cof	cofilin 1, non-muscle	protein-coding
mm_22010.1	chr2	167775391	167775401	-	1	NA	Intergenic	Intergenic	84219	NR_015500	329562	Mm.123101	NM_177851	ENSMUSG00000006462	A530013C23Rik	-	RIKEN cDNA A530013C23 gene	ncRNA
mm_139139.1	chr17	47509564	47509583	+	1	NA	intron (NM_001081635, intron 1 of 6)	intron (NM_001081635, intron 1 of 6)	4522	NM_001081635	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_84037.1	chr9	57765846	57765876	-	1	NA	promoter-TSS (NM_007713)	promoter-TSS (NM_007713)	-1	NM_007713	102414	Mm.25720	NM_007713	ENSMUSG00000032316	Clk3	AI256811	CDC-like kinase 3	protein-coding
mm_167620.1	chr9	57770665	57770668	+	1	NA	Intergenic	B1_Mm|SINE|Alu	-4806	NM_007713	102414	Mm.25720	NM_007713	ENSMUSG00000032316	Clk3	AI256811	CDC-like kinase 3	protein-coding
mm_1752.1	chr1	75507220	75507244	+	1	NA	promoter-TSS (NM_178884)	promoter-TSS (NM_178884)	155	NM_010564	16322	Mm.1100	NM_010564	ENSMUSG00000032968	Inha	AW555078	inhibin alpha	protein-coding
mm_144676.1	chr18	34751772	34751786	+	1	NA	promoter-TSS (NM_009860)	promoter-TSS (NM_009860)	-246	NM_009860	12532	Mm.286602	NM_009860	ENSMUSG00000044201	Cdc25c	Cdc25	cell division cycle 25C	protein-coding
mm_7211.1	chr1	93101811	93101821	-	1	NA	promoter-TSS (NM_008440)	promoter-TSS (NM_008440)	58	NM_001294149	16560	Mm.276408	NM_008440	ENSMUSG00000014602	Kif1a	ATSV|C630002N23Rik|Gm1626|Kns1	kinesin family member 1A	protein-coding
mm_22841.1	chr3	27938639	27938679	+	1	NA	promoter-TSS (NM_001164056)	promoter-TSS (NM_001164056)	-21	NM_001164056	18805	Mm.212039	NM_008875	ENSMUSG00000027695	Pld1	AA536939|C85393|Pld1a|Pld1b|mPLD1	phospholipase D1	protein-coding
mm_142138.1	chr17	35969529	35969569	-	1	NA	intron (NM_013854, intron 1 of 22)	CpG	201	NM_013854	224742	Mm.329022	NM_013854	ENSMUSG00000038762	Abcf1	AU041969|Abc50|D17Wsu166e|GCN20	ATP-binding cassette, sub-family F (GCN20), member 1	protein-coding
mm_26937.1	chr3	20263749	20263763	-	1	NA	exon (NM_029706, exon 7 of 11)	exon (NM_029706, exon 7 of 11)	11977	NM_029706	76703	Mm.34692	NM_029706	ENSMUSG00000011463	Cpb1	0910001A18Rik|1810063F02Rik|2210008M23Rik|AI504870	carboxypeptidase B1 (tissue)	protein-coding
mm_7733.1	chr1	130764096	130764109	-	1	NA	Intergenic	Intergenic	32126	NM_177604	212439	Mm.268547	NM_177604	ENSMUSG00000042510	AA986860	E030025M07|Sarg	expressed sequence AA986860	protein-coding
mm_47954.1	chr5	135545060	135545091	-	1	NA	promoter-TSS (NM_146001)	promoter-TSS (NM_146001)	47	NM_146001	215114	Mm.280805	NM_146001	ENSMUSG00000039959	Hip1	2610109B09Rik|A930014B11Rik|E130315I21Rik|mKIAA4113	huntingtin interacting protein 1	protein-coding
mm_124188.1	chr14	97052954	97052962	-	1	NA	Intergenic	Intergenic	-533924	NM_053105	93688	Mm.308735	NM_053105	ENSMUSG00000022076	Klhl1	mKIAA1490	kelch-like 1	protein-coding
mm_123285.1	chr14	61439810	61439828	-	1	NA	5' UTR (NM_008466, exon 1 of 17)	5' UTR (NM_008466, exon 1 of 17)	128	NM_008466	16648	Mm.25548	NM_008466	ENSMUSG00000021929	Kpna3	IPOA4	karyopherin (importin) alpha 3	protein-coding
mm_115305.1	chr13	112288497	112288507	+	1	NA	promoter-TSS (NM_029898)	promoter-TSS (NM_029898)	-16	NM_001168404	77318	Mm.159895	NM_029898	ENSMUSG00000049985	Ankrd55	C030011J08Rik	ankyrin repeat domain 55	protein-coding
mm_62329.1	chr7	100493320	100493324	+	1	NA	promoter-TSS (NM_011671)	promoter-TSS (NM_011671)	-36	NM_011671	22228	Mm.171378	NM_011671	ENSMUSG00000033685	Ucp2	Slc25a8	uncoupling protein 2 (mitochondrial, proton carrier)	protein-coding
mm_134570.1	chr16	20364107	20364136	-	1	NA	exon (NM_013790, exon 23 of 30)	exon (NM_013790, exon 23 of 30)	-38717	NM_183158	224044	Mm.276400	NM_183158	ENSMUSG00000022818	Cyp2ab1	EG224044|F730023N20	cytochrome P450, family 2, subfamily ab, polypeptide 1	protein-coding
mm_93611.1	chr10	117238590	117238614	-	1	NA	promoter-TSS (NM_029906)	promoter-TSS (NM_029906)	79	NM_029906	77397	Mm.118350	NM_029906	ENSMUSG00000020177	9530003J23Rik	Lyzf1	RIKEN cDNA 9530003J23 gene	protein-coding
mm_6391.1	chr1	72852279	72852313	-	1	NA	3' UTR (NM_008342, exon 4 of 4)	3' UTR (NM_008342, exon 4 of 4)	22569	NM_010518	16011	Mm.405761	NM_010518	ENSMUSG00000026185	Igfbp5	AI256729|AW208790|IGFBP-5|IGFBP-5P	insulin-like growth factor binding protein 5	protein-coding
mm_59909.1	chr7	30413745	30413831	+	1	NA	promoter-TSS (NM_011662)	promoter-TSS (NM_011662)	0	NM_011662	22177	Mm.46301	NM_011662	ENSMUSG00000030579	Tyrobp	DAP12|KARAP|Ly83	TYRO protein tyrosine kinase binding protein	protein-coding
mm_60987.1	chr7	49160700	49160712	+	1	NA	intron (NM_001111016, intron 2 of 38)	intron (NM_001111016, intron 2 of 38)	-85483	NM_175272	78286	Mm.333881	NM_175272	ENSMUSG00000052512	Nav2	5330421F07Rik|AU067780|BQ960892|HELAD1|POMFIL2|RAINB1|RAINB2|Unc53H2|mKIAA3015	neuron navigator 2	protein-coding
mm_165577.1	chr3	27222293	27222298	+	1	NA	intron (NM_178772, intron 1 of 4)	B1_Mur1|SINE|Alu	39291	NM_178772	320024	Mm.24576	NM_178772	ENSMUSG00000027698	Nceh1	Aadacl1|B230106I24Rik|CPO-BP|Nceh	neutral cholesterol ester hydrolase 1	protein-coding
mm_87309.1	chr10	42761484	42761490	+	1	NA	promoter-TSS (NM_153055)	promoter-TSS (NM_153055)	-9	NM_153055	140740	Mm.214344	NM_153055	ENSMUSG00000019802	Sec63	5730478J10Rik|AI649014|AW319215	SEC63-like (S. cerevisiae)	protein-coding
mm_83628.1	chr9	48911121	48911140	-	1	NA	promoter-TSS (NM_013561)	promoter-TSS (NM_013561)	-31	NM_001099644	15561	Mm.4831	NM_013561	ENSMUSG00000032269	Htr3a	5-HT3	5-hydroxytryptamine (serotonin) receptor 3A	protein-coding
mm_146765.1	chr18	17784371	17784371	-	1	NA	Intergenic	Intergenic	-203381	NR_045374	75162	Mm.60874	NR_045374		4930545E07Rik	-	RIKEN cDNA 4930545E07 gene	ncRNA
mm_100361.1	chr11	118476935	118476994	+	1	NA	promoter-TSS (NM_172573)	promoter-TSS (NM_172573)	4	NM_172573	217364	Mm.473963	NM_172573	ENSMUSG00000033857	Engase	C130099A03|D230014K01Rik	endo-beta-N-acetylglucosaminidase	protein-coding
mm_59080.1	chr7	19665450	19665482	+	1	NA	promoter-TSS (NM_019649)	promoter-TSS (NM_019649)	-436	NM_019649	56457	Mm.290960	NM_019649	ENSMUSG00000002981	Clptm1	HS9|N14	cleft lip and palate associated transmembrane protein 1	protein-coding
mm_32527.1	chr4	108879069	108879085	+	1	NA	promoter-TSS (NM_023537)	promoter-TSS (NM_023537)	7	NM_023537	69908	Mm.41580	NM_023537	ENSMUSG00000003411	Rab3b	2610528C18Rik	RAB3B, member RAS oncogene family	protein-coding
mm_88761.1	chr10	80330298	80330310	+	1	NA	promoter-TSS (NM_008793)	promoter-TSS (NM_008793)	159	NM_139292	70335	Mm.28147	NM_139292	ENSMUSG00000035504	Reep6	0610011M24Rik|Dp1l1	receptor accessory protein 6	protein-coding
mm_51790.1	chr6	88205858	88205880	+	1	NA	3' UTR (NM_008090, exon 6 of 6)	3' UTR (NM_008090, exon 6 of 6)	7205	NM_008090	14461	Mm.491156	NM_008090	ENSMUSG00000015053	Gata2	Gata-2	GATA binding protein 2	protein-coding
mm_99025.1	chr11	98938377	98938387	+	1	NA	intron (NM_009024, intron 1 of 8)	intron (NM_009024, intron 1 of 8)	664	NM_001177302	19401	Mm.439744	NM_009024	ENSMUSG00000037992	Rara	Nr1b1|RAR|RARalpha1	retinoic acid receptor, alpha	protein-coding
mm_34549.1	chr4	149586433	149586511	+	1	NA	promoter-TSS (NM_023051)	promoter-TSS (NM_023051)	4	NM_023051	65945	Mm.38993	NM_023051	ENSMUSG00000039953	Clstn1	1810034E21Rik|Cst-1|Cstn1	calsyntenin 1	protein-coding
mm_120518.1	chr14	66729112	66729133	+	1	NA	intron (NM_013461, intron 3 of 3)	intron (NM_013461, intron 3 of 3)	93871	NM_001271760	11549	Mm.57064	NM_013461	ENSMUSG00000045875	Adra1a	Adra1c	adrenergic receptor, alpha 1a	protein-coding
mm_67497.1	chr7	80768429	80768464	-	1	NA	exon (NM_016721, exon 3 of 38)	exon (NM_016721, exon 3 of 38)	34885	NM_016721	29875	Mm.207619	NM_016721	ENSMUSG00000030536	Iqgap1	AA682088|D7Ertd237e|D7Ertd257e|mKIAA0051	IQ motif containing GTPase activating protein 1	protein-coding
mm_20857.1	chr2	148408147	148408155	-	1	NA	promoter-TSS (NM_009378)	promoter-TSS (NM_009378)	37	NM_009378	21824	Mm.24096	NM_009378	ENSMUSG00000074743	Thbd	AI385582|CD141|TM	thrombomodulin	protein-coding
mm_160024.1	chr6	130231626	130231626	-	1	NA	promoter-TSS (NM_014194)	promoter-TSS (NM_014194)	61	NM_014194	16638	Mm.441781	NM_014194	ENSMUSG00000067599	Klra7	LGL-1|Ly-49G.1|Ly-49G.2|Ly-49G.3|Ly49G.4|Ly49g|Ly49g1|Ly49g2	killer cell lectin-like receptor, subfamily A, member 7	protein-coding
mm_49968.1	chr6	40768588	40768607	+	1	NA	3' UTR (NM_001171003, exon 48 of 48)	3' UTR (NM_001171003, exon 48 of 48)	118897	NM_139296	194357	Mm.207087	NM_139296	ENSMUSG00000029885	Moxd2	Dbhl1	monooxygenase, DBH-like 2	protein-coding
mm_136278.1	chr16	91069096	91069106	-	1	NA	promoter-TSS (NM_028905)	promoter-TSS (NM_028905)	44	NM_001163695	74387	Mm.236220	NM_028905	ENSMUSG00000039851	4932438H23Rik	4931406G06Rik|AI550392	RIKEN cDNA 4932438H23 gene	protein-coding
mm_23181.1	chr3	40810119	40810133	+	1	NA	intron (NM_173169, intron 7 of 15)	intron (NM_173169, intron 7 of 15)	10175	NR_045576	20873	Mm.3794	NM_011495	ENSMUSG00000025758	Plk4	1700028H20|AI385771|Sak|Stk18	polo-like kinase 4	protein-coding
mm_8509.1	chr1	154542382	154542414	-	1	NA	intron (NM_009782, intron 7 of 46)	intron (NM_009782, intron 7 of 46)	183522	NM_009782	12290	Mm.267517	NM_009782	ENSMUSG00000004110	Cacna1e	A430040I15|BII|Cach6|Cacnl1a6|Cav2.3|Cchra1|alpha1E	calcium channel, voltage-dependent, R type, alpha 1E subunit	protein-coding
mm_32736.1	chr4	116596732	116596746	+	1	NA	promoter-TSS (NM_001037916)	promoter-TSS (NM_001037916)	9	NM_001037916	622665	Mm.388905	NM_001037916	ENSMUSG00000034035	Ccdc17	-	coiled-coil domain containing 17	protein-coding
mm_134703.1	chr16	22857437	22857462	-	1	NA	promoter-TSS (NM_001190805)	promoter-TSS (NM_001190805)	220	NM_001081368	70573	Mm.68291	NM_001081368	ENSMUSG00000004462	Tbccd1	5730478M09Rik|AU015083|BB165076	TBCC domain containing 1	protein-coding
mm_35611.1	chr4	43384150	43384160	-	1	NA	intron (NM_001037709, intron 1 of 11)	intron (NM_001037709, intron 1 of 11)	2173	NM_001037709	100213	Mm.235730	NM_199057	ENSMUSG00000035969	Rusc2	AI840675|mKIAA0375	RUN and SH3 domain containing 2	protein-coding
mm_107163.1	chr12	24651422	24651432	+	1	NA	promoter-TSS (NM_178357)	promoter-TSS (NM_178357)	56	NM_178357	194655	Mm.9616	NM_178357	ENSMUSG00000020653	Klf11	9830142A17|D12Ertd427e|Tieg2|Tieg2b|Tieg3	Kruppel-like factor 11	protein-coding
mm_79473.1	chr9	56865108	56865115	+	1	NA	promoter-TSS (NM_139001)	promoter-TSS (NM_139001)	7	NM_139001	121021	Mm.41329	NM_139001	ENSMUSG00000032911	Cspg4	4732461B14Rik|AN2|NG2	chondroitin sulfate proteoglycan 4	protein-coding
mm_9278.1	chr1	171634323	171634343	-	1	NA	3' UTR (NM_144539, exon 8 of 8)	3' UTR (NM_144539, exon 8 of 8)	7567	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_155189.1	chrX	56374806	56374834	+	1	NA	non-coding (NR_028086, exon 1 of 2)	non-coding (NR_028086, exon 1 of 2)	234	NR_028086	320237	Mm.233168	NM_183030		Smim10l2a	6330419J24Rik|Ncrna00086	small integral membrane protein 10 like 2A	ncRNA
mm_54231.1	chr6	28228181	28228228	-	1	NA	Intergenic	Intergenic	33397	NM_001081678	627049	Mm.84441	NM_001081678	ENSMUSG00000039841	Zfp800	AA407452|Znf800	zinc finger protein 800	protein-coding
mm_26452.1	chr3	142701027	142701043	+	1	NA	promoter-TSS (NM_001293560)	promoter-TSS (NM_001293560)	-13	NM_173763	229905	Mm.289643	NM_173763	ENSMUSG00000040213	Kyat3	Ccbl2|KATIII|Kat3	kynurenine aminotransferase 3	protein-coding
mm_60712.1	chr7	45277479	45277493	+	1	NA	Intergenic	CpG	-5387	NM_001033176	76713	Mm.425445	NM_001033176	ENSMUSG00000070568	Slc6a21	1700039E15Rik|Gm19188	solute carrier family 6 member 21	protein-coding
mm_55909.1	chr6	83762489	83762498	-	1	NA	promoter-TSS (NR_105027)	promoter-TSS (NR_105027)	15	NR_105027	67934	Mm.126190	NR_105027	ENSMUSG00000099354	1700124L16Rik	-	RIKEN cDNA 1700124L16 gene	ncRNA
mm_170623.1	chr19	7217591	7217594	-	1	NA	promoter-TSS (NM_007750)	promoter-TSS (NM_007750)	24	NM_007750	12868	Mm.14022	NM_007750	ENSMUSG00000035885	Cox8a	COX8L	cytochrome c oxidase subunit VIIIa	protein-coding
mm_105006.1	chr11	100376921	100376940	-	1	NA	exon (NM_010593, exon 9 of 14)	exon (NM_010593, exon 9 of 14)	-20789	NM_010404	15114	Mm.281700	NM_010404	ENSMUSG00000006930	Hap1	HAP-1	huntingtin-associated protein 1	protein-coding
mm_173354.1	chrY	90813968	90813975	+	1	NA	intron (NM_133362, intron 2 of 3)	(CAGAGA)n|Simple_repeat|Simple_repeat	25435	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_22656.1	chr3	14871637	14871653	+	1	NA	exon (NM_007606, exon 7 of 7)	exon (NM_007606, exon 7 of 7)	8107	NM_007606	12350	Mm.300	NM_007606	ENSMUSG00000027559	Car3	BB219044|Ca3|Car-3	carbonic anhydrase 3	protein-coding
mm_130838.1	chr15	101850779	101850792	-	1	NA	promoter-TSS (NM_008473)	promoter-TSS (NM_008473)	1	NM_008473	16678	Mm.183137	NM_008473	ENSMUSG00000046834	Krt1	Krt-2.1|Krt2-1|Krt86	keratin 1	protein-coding
mm_24925.1	chr3	96528613	96528614	+	1	NA	exon (NM_027126, exon 4 of 4)	exon (NM_027126, exon 4 of 4)	3428	NM_027126	69585	Mm.171314	NM_027126	ENSMUSG00000038403	Hfe2	2310035L15Rik|5230400G09Rik|AI414844|AI789733|DL-M|HJV|Rgmc|hemojuvelin	hemochromatosis type 2 (juvenile)	protein-coding
mm_12058.1	chr2	59338715	59338729	+	1	NA	exon (NM_026361, exon 14 of 22)	exon (NM_026361, exon 14 of 22)	47960	NR_040510	76676	Mm.110038	NR_040510	ENSMUSG00000087455	5330411J11Rik	-	RIKEN cDNA 5330411J11 gene	ncRNA
mm_93843.1	chr10	121626392	121626418	-	1	NA	promoter-TSS (NM_001081056)	promoter-TSS (NM_001081056)	-89	NM_001081056	73192	Mm.25042	NM_001081056	ENSMUSG00000034667	Xpot	1110004L07Rik|3110065H13Rik|AI452076|C79645|EXPORTIN-T	exportin, tRNA (nuclear export receptor for tRNAs)	protein-coding
mm_172365.1	chr7	121015659	121015685	-	1	NA	TTS (NM_028955)	TTS (NM_028955)	-18773	NM_021554	59052	Mm.29122	NM_021554	ENSMUSG00000030876	Mettl9	0610012D09Rik|AA517660|Drev|MNCb-5680	methyltransferase like 9	protein-coding
mm_108939.1	chr12	102005535	102005582	+	1	NA	3' UTR (NM_016856, exon 15 of 15)	3' UTR (NM_016856, exon 15 of 15)	29584	NM_016856	51786	Mm.716	NM_016856	ENSMUSG00000041781	Cpsf2	100kDa|2610024B04Rik|AI662483|Cpsf|MCPSF|mKIAA1367	cleavage and polyadenylation specific factor 2	protein-coding
mm_87938.1	chr10	62885647	62885672	+	1	NA	Intergenic	Intergenic	-5645	NM_001253857	52463	Mm.17774	NM_027384	ENSMUSG00000047146	Tet1	2510010B09Rik|AA517754|BB001228|Cxxc6|D10Ertd17e|LCX|mKIAA1676	tet methylcytosine dioxygenase 1	protein-coding
mm_31025.1	chr4	40845773	40845775	+	1	NA	intron (NM_022305, intron 1 of 5)	intron (NM_022305, intron 1 of 5)	4364	NR_039584	100628614		NR_039584	ENSMUSG00000096377	Mir5123	mmu-mir-5123|mu-mir-5123	microRNA 5123	ncRNA
mm_125178.1	chr15	31572180	31572197	+	1	NA	intron (NM_181588, intron 1 of 5)	intron (NM_181588, intron 1 of 5)	3276	NM_181588	69574	Mm.28108	NM_181588	ENSMUSG00000022235	Cmbl	2310016A09Rik	carboxymethylenebutenolidase-like (Pseudomonas)	protein-coding
mm_60808.1	chr7	45640426	45640439	+	1	NA	intron (NM_172418, intron 1 of 9)	intron (NM_172418, intron 1 of 9)	455	NM_172418	74490	Mm.107442	NM_172418	ENSMUSG00000042918	Mamstr	2810022D01Rik|5430432N15Rik|AW743872|Mastr	MEF2 activating motif and SAP domain containing transcriptional regulator	protein-coding
mm_72714.1	chr8	84995984	84995985	+	1	NA	intron (NM_133255, intron 11 of 21)	intron (NM_133255, intron 11 of 21)	5389	NM_001167991	170833	Mm.247775	NM_133255	ENSMUSG00000052566	Hook2	A630054I03Rik	hook microtubule tethering protein 2	protein-coding
mm_147269.1	chr18	38929149	38929168	-	1	NA	intron (NM_001033789, intron 3 of 4)	intron (NM_001033789, intron 3 of 4)	-10459	NM_010197	14164	Mm.241282	NM_010197	ENSMUSG00000036585	Fgf1	Dffrx|Fam|Fgf-1|Fgfa	fibroblast growth factor 1	protein-coding
mm_42933.1	chr5	122942599	122942612	+	1	NA	intron (NM_001003953, intron 8 of 22)	intron (NM_001003953, intron 8 of 22)	-42255	NM_013910	30841	Mm.86406	NM_013910	ENSMUSG00000029475	Kdm2b	Cxxc2|Fbl10|Fbxl10|Jhdm1b|PCCX2	lysine (K)-specific demethylase 2B	protein-coding
mm_38321.1	chr4	137336127	137336139	-	1	NA	intron (NM_009861, intron 1 of 5)	intron (NM_009861, intron 1 of 5)	21626	NM_009861	12540	Mm.1022	NM_009861	ENSMUSG00000006699	Cdc42	AI747189|AU018915	cell division cycle 42	protein-coding
mm_56112.1	chr6	87511058	87511081	-	1	NA	intron (NM_001037727, intron 1 of 10)	RSINE1|SINE|B4	-14742	NM_175476	232201	Mm.119564	NM_175476	ENSMUSG00000030047	Arhgap25	A130039I20Rik	Rho GTPase activating protein 25	protein-coding
mm_51441.1	chr6	80070711	80070741	+	1	NA	intron (NM_001347261, intron 2 of 2)	intron (NM_001347261, intron 2 of 2)	51083	NM_178731	243499	Mm.483425	NM_178731	ENSMUSG00000052581	Lrrtm4	7530419J18Rik|A230052N11	leucine rich repeat transmembrane neuronal 4	protein-coding
mm_22423.1	chr2	181592699	181592727	-	1	NA	promoter-TSS (NM_001164597)	promoter-TSS (NM_001164597)	-252	NM_001164597	269401	Mm.386888	NM_001164597	ENSMUSG00000000823	Zfp512b	Gm632|Znf512b	zinc finger protein 512B	protein-coding
mm_22285.1	chr2	180203708	180203725	-	1	NA	intron (NM_001081171, intron 6 of 78)	L1MEd|LINE|L1	22143	NM_001081171	16776	Mm.4339	NM_001081171	ENSMUSG00000015647	Lama5	AA408760|AA408762|AI853660|[a]5|laminin-511|mKIAA0533	laminin, alpha 5	protein-coding
mm_74788.1	chr8	22185486	22185520	-	1	NA	intron (NM_001004140, intron 1 of 8)	intron (NM_001004140, intron 1 of 8)	316	NM_001004140	80986	Mm.22448	NM_001004140	ENSMUSG00000037725	Ckap2	AI461656|AW228814|LB1	cytoskeleton associated protein 2	protein-coding
mm_58351.1	chr6	147389787	147389817	-	1	NA	Intergenic	Intergenic	-86069	NM_025911	67015	Mm.209774	NM_025911	ENSMUSG00000030301	Ccdc91	1700086G08Rik|1810060J02Rik|AU045683|AW555238|p56	coiled-coil domain containing 91	protein-coding
mm_18966.1	chr2	76807439	76807468	-	1	NA	intron (NM_028004, intron 67 of 191)	intron (NM_028004, intron 67 of 191)	132138	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_140755.1	chr17	17416414	17416418	-	1	NA	intron (NM_025681, intron 1 of 5)	RMER17C|LTR|ERVK	13730	NM_025681	66643	Mm.268018	NM_025681	ENSMUSG00000047786	Lix1	5730466L18Rik	limb and CNS expressed 1	protein-coding
mm_112339.1	chr12	116256033	116256046	-	1	NA	exon (NM_146039, exon 3 of 22)	exon (NM_146039, exon 3 of 22)	6986	NM_146039	217935	Mm.31382	NM_146039	ENSMUSG00000042050	Wdr60	D430033N04Rik	WD repeat domain 60	protein-coding
mm_111981.1	chr12	110435030	110435035	-	1	NA	Intergenic	Intergenic	-12147	NM_001135001	26931	Mm.240396	NM_012023	ENSMUSG00000017843	Ppp2r5c	2610043M05Rik|2700063L20Rik|AI060890|AW545884|C85228|D12Bwg0916e|mKIAA0044	protein phosphatase 2, regulatory subunit B', gamma	protein-coding
mm_160867.1	chr11	61762034	61762034	-	1	NA	promoter-TSS (NM_144806)	promoter-TSS (NM_144806)	54	NM_144806	212627	Mm.27703	NM_144806	ENSMUSG00000020528	Prpsap2	A230054F23Rik	phosphoribosyl pyrophosphate synthetase-associated protein 2	protein-coding
mm_13763.1	chr2	118388675	118388683	+	1	NA	promoter-TSS (NM_013719)	promoter-TSS (NM_013719)	62	NM_013719	27103	Mm.217616	NM_013719	ENSMUSG00000005102	Eif2ak4	2610011M03|GCN2|MGCN2	eukaryotic translation initiation factor 2 alpha kinase 4	protein-coding
mm_163217.1	chr11	101246938	101246957	+	1	NA	intron (NM_019444, intron 1 of 3)	intron (NM_019444, intron 1 of 3)	613	NM_019444	54409	Mm.260698	NM_019444	ENSMUSG00000001240	Ramp2	-	receptor (calcitonin) activity modifying protein 2	protein-coding
mm_30967.1	chr4	33945515	33945519	+	1	NA	3' UTR (NM_007726, exon 2 of 2)	3' UTR (NM_007726, exon 2 of 2)	20885	NM_007726	12801	Mm.7992	NM_007726	ENSMUSG00000044288	Cnr1	CB-R|CB1|CB1R	cannabinoid receptor 1 (brain)	protein-coding
mm_130029.1	chr15	88954391	88954397	-	1	NA	promoter-TSS (NM_172818)	promoter-TSS (NM_172818)	24	NM_172818	239591	Mm.86807	NM_172818	ENSMUSG00000022388	Ttll8	1700019P01Rik|4933401B17	tubulin tyrosine ligase-like family, member 8	protein-coding
mm_166277.1	chr5	90768534	90768544	+	1	NA	promoter-TSS (NM_023785)	promoter-TSS (NM_023785)	21	NM_023785	57349	Mm.293614	NM_023785	ENSMUSG00000029372	Ppbp	2400003M24Rik|AI854500|CTAP3|CTAPIII|Cxcl7|LA-PF4|LDGF|MDGF|NAP-2|NAP-2-L1|Scyb7|TGB|TGB1|THBGB1|b-TG1|beta-TG	pro-platelet basic protein	protein-coding
mm_27057.1	chr3	27605703	27605717	-	1	NA	intron (NM_173182, intron 3 of 25)	B4|SINE|B4	-20715	NR_037275	100526525		NR_037275	ENSMUSG00000092695	Mir3092	mir-3092|mmu-mir-3092	microRNA 3092	ncRNA
mm_8387.1	chr1	151344443	151344449	-	1	NA	promoter-TSS (NM_001039512)	promoter-TSS (NM_001039512)	-52	NM_001039512	117198	Mm.33764	NM_028582	ENSMUSG00000023150	Ivns1abp	1190004M08Rik|1700126I16Rik|AA960440|HSPC068|ND1|NS-1|NS1-BP|Nd1-L|Nd1-S|mKIAA0850	influenza virus NS1A binding protein	protein-coding
mm_156666.1	chrX	158452537	158452539	+	1	NA	Intergenic	MERV1_LTR|LTR|ERV1	-409341	NM_177751	245684	Mm.197074	NM_177751	ENSMUSG00000025658	Cnksr2	Cnk2|Ksr2	connector enhancer of kinase suppressor of Ras 2	protein-coding
mm_135687.1	chr16	52427003	52427009	-	1	NA	intron (NM_009655, intron 1 of 15)	intron (NM_009655, intron 1 of 15)	26075	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_97279.1	chr11	76012135	76012135	+	1	NA	Intergenic	MT2B2|LTR|ERVL	12223	NM_198637	74230	Mm.271247	NM_198637	ENSMUSG00000053783	1700016K19Rik	Liat1	RIKEN cDNA 1700016K19 gene	protein-coding
mm_103596.1	chr11	78379035	78379040	-	1	NA	intron (NM_001277290, intron 1 of 8)	intron (NM_001277290, intron 1 of 8)	7571	NM_008238	15218	Mm.4496	NM_008238	ENSMUSG00000002057	Foxn1	D11Bhm185e|Fkh19|HFH-11|Hfh11|Whn|nu|nude	forkhead box N1	protein-coding
mm_99628.1	chr11	105092214	105092244	+	1	NA	promoter-TSS (NM_001081046)	promoter-TSS (NM_001081046)	10	NM_001081046	70894	Mm.87320	NM_001081046	ENSMUSG00000020690	Efcab3	4921510J17Rik	EF-hand calcium binding domain 3	protein-coding
mm_129854.1	chr15	83173008	83173023	-	1	NA	promoter-TSS (NM_029787)	promoter-TSS (NM_029787)	-807	NM_029787	109754	Mm.22560	NM_029787	ENSMUSG00000018042	Cyb5r3	0610016L08Rik|2500002N19Rik|C85115|Dia-1|Dia1|WU:AL591952.1-001|WU:AL591952.1-002|WU:AL591952.1-003|WU:Cyb5r3	cytochrome b5 reductase 3	protein-coding
mm_102037.1	chr11	51857600	51857610	-	1	NA	promoter-TSS (NM_199299)	promoter-TSS (NM_199299)	-124	NM_199299	76901	Mm.259996	NM_199299	ENSMUSG00000020387	Jade2	1200017K05Rik|AI480685|Phf15|mKIAA0239	jade family PHD finger 2	protein-coding
mm_121092.1	chr14	99301804	99301814	+	1	NA	exon (NM_009769, exon 2 of 4)	exon (NM_009769, exon 2 of 4)	3118	NM_009769	12224	Mm.30262	NM_009769	ENSMUSG00000005148	Klf5	4930520J07Rik|Bteb2|CKLF|IKLF	Kruppel-like factor 5	protein-coding
mm_110604.1	chr12	56536100	56536122	-	1	NA	intron (NM_009385, intron 1 of 2)	CpG	797	NM_009385	21869	Mm.89972	NM_009385	ENSMUSG00000001496	Nkx2-1	AV026640|Nkx2.1|T/EBP|Titf1|Ttf-1	NK2 homeobox 1	protein-coding
mm_155762.1	chrX	96167994	96168008	+	1	NA	3' UTR (NM_010833, exon 13 of 13)	3' UTR (NM_010833, exon 13 of 13)	-71925	NR_030718	100038363	Mm.30815	NR_030718	ENSMUSG00000078122	F630028O10Rik	ENSMUSG00000065522|Gm14924|OTTMUSG00000018496|mir-223	RIKEN cDNA F630028O10 gene	ncRNA
mm_45896.1	chr5	88675543	88675563	-	1	NA	promoter-TSS (NM_001098476)	promoter-TSS (NM_001098476)	27	NM_001098476	231413	Mm.332474	NM_178700	ENSMUSG00000044221	Grsf1	BB232551|C80280|D5Wsu31e	G-rich RNA sequence binding factor 1	protein-coding
mm_43670.1	chr5	138774270	138774285	+	1	NA	intron (NM_030565, intron 3 of 9)	MTD|LTR|ERVL-MaLR	19196	NM_030565	80752	Mm.320355	NM_030565	ENSMUSG00000025854	Fam20c	C76981|DMP-4|DMP4|GEF-CK|mKIAA4081	family with sequence similarity 20, member C	protein-coding
mm_120613.1	chr14	70207727	70207761	+	1	NA	promoter-TSS (NM_011366)	promoter-TSS (NM_011366)	-73	NM_011366	20410	Mm.5068	NM_011366	ENSMUSG00000022091	Sorbs3	SCAM-1|SH3P3|Sh3d4|vinexin-g	sorbin and SH3 domain containing 3	protein-coding
mm_108025.1	chr12	73649274	73649293	+	1	NA	intron (NM_001313977, intron 2 of 14)	intron (NM_001313977, intron 2 of 14)	64487	NM_008856	18755	Mm.341677	NM_008856	ENSMUSG00000021108	Prkch	Pkch	protein kinase C, eta	protein-coding
mm_86709.1	chr10	18845097	18845112	+	1	NA	promoter-TSS (NM_022032)	promoter-TSS (NM_022032)	33	NM_022032	64058	Mm.28209	NM_022032	ENSMUSG00000019851	Perp	1110017A08Rik|KCP1|KRTCAP1|PIGPC1|THW	PERP, TP53 apoptosis effector	protein-coding
mm_93975.1	chr10	127336131	127336133	-	1	NA	intron (NM_010296, intron 8 of 12)	intron (NM_010296, intron 8 of 12)	5447	NM_010296	14632	Mm.391450	NM_010296	ENSMUSG00000025407	Gli1	AV235269|Zfp-5|Zfp5	GLI-Kruppel family member GLI1	protein-coding
mm_102007.1	chr11	51604457	51604487	-	1	NA	exon (NM_010448, exon 5 of 7)	exon (NM_010448, exon 5 of 7)	2409	NM_001048061	15384	Mm.256875	NM_010448	ENSMUSG00000020358	Hnrnpab	3010025C11Rik|CBF-A|Cgbfa|Hnrpab	heterogeneous nuclear ribonucleoprotein A/B	protein-coding
mm_45060.1	chr5	41832566	41832587	-	1	NA	exon (NM_001081422, exon 4 of 27)	exon (NM_001081422, exon 4 of 27)	11739	NM_001310601	665775	Mm.158726	NM_001081422	ENSMUSG00000061755	Bod1l	A230054D04Rik|AI853319|FAM44A|mKIAA1327	biorientation of chromosomes in cell division 1-like	protein-coding
mm_66233.1	chr7	35215249	35215413	-	1	NA	promoter-TSS (NM_001024707)	promoter-TSS (NM_001024707)	14	NM_001024707	435965	Mm.333783	NM_001024707	ENSMUSG00000001802	Lrp3	-	low density lipoprotein receptor-related protein 3	protein-coding
mm_50069.1	chr6	41227537	41227549	+	1	NA	Intergenic	Intergenic	-74729	NM_011646	22074	Mm.383263	NM_011646	ENSMUSG00000054106	Try4	0910001B19Rik|Td	trypsin 4	protein-coding
mm_89042.1	chr10	82859199	82859217	+	1	NA	promoter-TSS (NM_015762)	promoter-TSS (NM_015762)	2	NM_015762	50493	Mm.210155	NM_015762	ENSMUSG00000020250	Txnrd1	TR|TR1|TrxR1	thioredoxin reductase 1	protein-coding
mm_133888.1	chr16	97356722	97356732	+	1	NA	promoter-TSS (NM_019517)	promoter-TSS (NM_019517)	-1	NM_019517	56175	Mm.97885	NM_019517	ENSMUSG00000040605	Bace2	1110059C24Rik|AEPLC|AI850424|ALP56|ARP1|ASP1|ASP21|BAE2|CDA13|CEAP1|DRAP	beta-site APP-cleaving enzyme 2	protein-coding
mm_138706.1	chr17	36042957	36042984	+	1	NA	promoter-TSS (NM_001034909)	promoter-TSS (NM_001034909)	9	NM_001034909	547347	Mm.484641	NM_001034909	ENSMUSG00000073407	Gm6034	EG547347|H2-gs14-2	predicted gene 6034	protein-coding
mm_70983.1	chr8	27260333	27260370	+	1	NA	promoter-TSS (NM_007918)	promoter-TSS (NM_007918)	24	NM_007918	13685	Mm.6700	NM_007918	ENSMUSG00000031490	Eif4ebp1	4e-bp1|AA959816|PHAS-I	eukaryotic translation initiation factor 4E binding protein 1	protein-coding
mm_141802.1	chr17	34497369	34497398	-	1	NA	promoter-TSS (NR_004051)	promoter-TSS (NR_004051)	46	NR_004051	81497	Mm.484231	NR_004051		Btnl5-ps	Btnl5|ENSMUSG00000073420|Gm15330|NG12|OTTMUSG00000020237	butyrophilin-like 5, pseudogene	pseudo
mm_46462.1	chr5	105119979	105120011	-	1	NA	exon (NM_001256005, exon 9 of 11)	exon (NM_001256005, exon 9 of 11)	-9703	NM_172777	236573	Mm.425261	NM_172777	ENSMUSG00000029298	Gbp9	-	guanylate-binding protein 9	protein-coding
mm_165000.1	chr19	20967810	20967829	+	1	NA	Intergenic	Intergenic	-13617	NM_028953	13409	Mm.219585	NM_028953	ENSMUSG00000024749	Tmc1	4933416G09Rik|Beethoven|Bth|CWEA1|dn	transmembrane channel-like gene family 1	protein-coding
mm_47381.1	chr5	122990286	122990290	-	1	NA	intron (NR_045820, intron 1 of 2)	intron (NR_045820, intron 1 of 2)	934	NR_045820	109202	Mm.30769	NM_175405	ENSMUSG00000056735	A930024E05Rik	-	RIKEN cDNA A930024E05 gene	ncRNA
mm_120870.1	chr14	75230314	75230326	+	1	NA	3' UTR (NM_001247984, exon 16 of 16)	3' UTR (NM_001247984, exon 16 of 16)	-11967	NM_019775	56373	Mm.24242	NM_019775	ENSMUSG00000021999	Cpb2	1110032P04Rik|4930405E17Rik|AI255929|CPR|Cpu|TAFI	carboxypeptidase B2 (plasma)	protein-coding
mm_155598.1	chrX	82513209	82513213	+	1	NA	Intergenic	Intergenic	-435659	NM_007868	13405	Mm.275608	NM_007868	ENSMUSG00000045103	Dmd	DXSmh7|DXSmh9|Dp427|Dp71|dys|mdx|pke	dystrophin, muscular dystrophy	protein-coding
mm_97755.1	chr11	80509315	80509331	+	1	NA	promoter-TSS (NR_126552)	promoter-TSS (NR_126552)	-217	NR_126552	77417	Mm.437510	NR_126552	ENSMUSG00000085078	C030013C21Rik	-	RIKEN cDNA C030013C21 gene	ncRNA
mm_18275.1	chr2	52372561	52372569	-	1	NA	Intergenic	Intergenic	-33767	NM_010889	17996	Mm.389247	NM_010889	ENSMUSG00000026950	Neb	AI595938	nebulin	protein-coding
mm_54162.1	chr6	23098090	23098097	-	1	NA	intron (NM_013930, intron 11 of 23)	intron (NM_013930, intron 11 of 23)	34893	NM_013930	30956	Mm.18651	NM_013930	ENSMUSG00000029695	Aass	LKR|LKR/SDH|LOR|LOR/SDH|Lorsdh|SDH	aminoadipate-semialdehyde synthase	protein-coding
mm_136285.1	chr16	91362778	91362788	-	1	NA	Intergenic	Intergenic	-10000	NM_010509	15976	Mm.6834	NM_010509	ENSMUSG00000022971	Ifnar2	AI747302|Ifnar-2	interferon (alpha and beta) receptor 2	protein-coding
mm_130015.1	chr15	88600207	88600213	-	1	NA	promoter-TSS (NM_027306)	promoter-TSS (NM_027306)	-92	NM_027306	70073	Mm.45306	NM_027306	ENSMUSG00000054117	Zdhhc25	1700030J15Rik	zinc finger, DHHC domain containing 25	protein-coding
mm_144817.1	chr18	36289424	36289442	+	1	NA	Intergenic	Intergenic	8271	NM_008989	19290	Mm.231802	NM_008989	ENSMUSG00000043991	Pura	CAGER-1|Pur-alpha|ssCRE-BP	purine rich element binding protein A	protein-coding
mm_108730.1	chr12	87420465	87420468	+	1	NA	Intergenic	Intergenic	17291	NR_037228	100526546		NR_037228	ENSMUSG00000105428	Mir3068	mir-3068|mmu-mir-3068	microRNA 3068	ncRNA
mm_50197.1	chr6	41951626	41951629	+	1	NA	promoter-TSS (NM_027832)	promoter-TSS (NM_027832)	-1	NM_027832	71578	Mm.96996	NM_027832	ENSMUSG00000029865	Sval1	9130404C18Rik|SLP-C	seminal vesicle antigen-like 1	protein-coding
mm_86348.1	chr9	123632458	123632462	-	1	NA	5' UTR (NM_011731, exon 1 of 11)	5' UTR (NM_011731, exon 1 of 11)	105	NM_011731	22599	Mm.41963	NM_011731	ENSMUSG00000025243	Slc6a20b	AA986306|Sit1|Slc6a20|XT3|Xtrp3	solute carrier family 6 (neurotransmitter transporter), member 20B	protein-coding
mm_43708.1	chr5	139364965	139364996	+	1	NA	intron (NM_028469, intron 2 of 4)	intron (NM_028469, intron 2 of 4)	4765	NR_029768	723898		NR_029768	ENSMUSG00000065593	Mir339	Mirn339|mir-339|mmu-mir-339	microRNA 339	ncRNA
mm_116351.1	chr13	38960543	38960554	-	1	NA	promoter-TSS (NM_001170430)	promoter-TSS (NM_001170430)	-11	NM_134060	108652	Mm.255506	NM_134060	ENSMUSG00000021432	Slc35b3	4921526O06Rik|AI428480|CGI-19|PABST2|PAPST2	solute carrier family 35, member B3	protein-coding
mm_110124.1	chr12	26444175	26444177	-	1	NA	3' UTR (NM_021384, exon 6 of 6)	3' UTR (NM_021384, exon 6 of 6)	12276	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_66413.1	chr7	44496411	44496452	-	1	NA	promoter-TSS (NM_197991)	promoter-TSS (NM_197991)	82	NM_197991	69683	Mm.294759	NM_197991	ENSMUSG00000008140	Emc10	2310044H10Rik|5430410O10Rik|Inm02|Mirta22	ER membrane protein complex subunit 10	protein-coding
mm_123910.1	chr14	73325774	73325836	-	1	NA	promoter-TSS (NM_009029)	promoter-TSS (NM_009029)	-14	NM_009029	19645	Mm.273862	NM_009029	ENSMUSG00000022105	Rb1	Rb|Rb-1|pRb	retinoblastoma 1	protein-coding
mm_97298.1	chr11	76494028	76494045	+	1	NA	intron (NM_198895, intron 2 of 22)	intron (NM_198895, intron 2 of 22)	459	NM_001346670	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_121877.1	chr14	21051540	21051563	-	1	NA	intron (NM_018829, intron 1 of 8)	intron (NM_018829, intron 1 of 8)	891	NM_018829	55946	Mm.376269	NM_018829	ENSMUSG00000021824	Ap3m1	1200013D09Rik|C78982|R75378	adaptor-related protein complex 3, mu 1 subunit	protein-coding
mm_41297.1	chr5	90464498	90464570	+	1	NA	intron (NM_009654, intron 4 of 14)	intron (NM_009654, intron 4 of 14)	3664	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_72767.1	chr8	85602067	85602073	+	1	NA	Intergenic	Intergenic	-46799	NM_019794	56445	Mm.475573	NM_019794	ENSMUSG00000031701	Dnaja2	1500017M13Rik|2010206B19Rik|DNAJ|DNJ3|Dnaj3|HIRIP4|PRO3015|mDj3	DnaJ heat shock protein family (Hsp40) member A2	protein-coding
mm_73573.1	chr8	109778556	109778558	+	1	NA	promoter-TSS (NM_009677)	promoter-TSS (NM_009677)	-26	NM_009677	11765	Mm.37210	NM_009677	ENSMUSG00000031731	Ap1g1	AA409002|AU041323|AW551707|Adtg|D8Ertd374e	adaptor protein complex AP-1, gamma 1 subunit	protein-coding
mm_37628.1	chr4	127350700	127350710	-	1	NA	TTS (NM_008127)	TTS (NM_008127)	3376	NM_008127	14621	Mm.56906	NM_008127	ENSMUSG00000046623	Gjb4	Cnx30.3|Cx30.3|Gjb-4	gap junction protein, beta 4	protein-coding
mm_87950.1	chr10	63060631	63060657	+	1	NA	promoter-TSS (NM_026701)	promoter-TSS (NM_026701)	-973	NM_026701	68371	Mm.261389	NM_026701	ENSMUSG00000020072	Pbld1	0610038K03Rik|Mawbp|Pbld	phenazine biosynthesis-like protein domain containing 1	protein-coding
mm_143444.1	chr17	70853643	70853645	-	1	NA	promoter-TSS (NM_001164074)	promoter-TSS (NM_001164074)	-112	NM_001164074	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_139205.1	chr17	47695172	47695204	+	1	NA	promoter-TSS (NM_144939)	promoter-TSS (NM_144939)	-19	NM_144939	107971	Mm.392206	NM_144939	ENSMUSG00000023266	Frs3	4930417B13Rik|AI449674|Frs2beta|Snt2	fibroblast growth factor receptor substrate 3	protein-coding
mm_31248.1	chr4	44953270	44953309	+	1	NA	Intergenic	Intergenic	-28105	NM_080289	76238	Mm.196574	NM_080289	ENSMUSG00000035637	Grhpr	1110059D05Rik|6430629L09Rik|Glxr	glyoxylate reductase/hydroxypyruvate reductase	protein-coding
mm_168921.1	chr12	59094570	59094579	-	1	NA	Intergenic	Intergenic	-1226	NM_001329047	338320	Mm.213215	NM_146034	ENSMUSG00000021000	Mia2	Ctage5|D12Bwg0579e|Mea6|Mgea|Mgea6	melanoma inhibitory activity 2	protein-coding
mm_43010.1	chr5	123749697	123749735	+	1	NA	promoter-TSS (NM_001042421)	promoter-TSS (NM_001042421)	-10	NM_001042421	208628	Mm.441089	NM_001042421	ENSMUSG00000029414	Kntc1	D330012D13|jgl	kinetochore associated 1	protein-coding
mm_70580.1	chr8	13167255	13167309	+	1	NA	exon (NM_010684, exon 3 of 9)	exon (NM_010684, exon 3 of 9)	8121	NM_010684	16783	Mm.16716	NM_010684	ENSMUSG00000031447	Lamp1	CD107a|LGP-120|LGP-A|Lamp-1|P2B	lysosomal-associated membrane protein 1	protein-coding
mm_153715.1	chr19	44403229	44403238	-	1	NA	exon (NM_009127, exon 3 of 6)	exon (NM_009127, exon 3 of 6)	4476	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_160272.1	chr7	118740173	118740173	+	1	NA	promoter-TSS (NM_027815)	promoter-TSS (NM_027815)	-98	NM_027815	71517	Mm.213298	NM_027815	ENSMUSG00000030982	9030624J02Rik	2610029J22Rik	RIKEN cDNA 9030624J02 gene	protein-coding
mm_80875.1	chr9	98955450	98955476	+	1	NA	promoter-TSS (NR_003248)	promoter-TSS (NR_003248)	-144	NM_012020	26927	Mm.151239	NM_012020	ENSMUSG00000050397	Foxl2	AU045128|BPES|PINTO|Pfrk	forkhead box L2	protein-coding
mm_159720.1	chr5	34410466	34410466	+	1	NA	intron (NM_001243123, intron 1 of 20)	intron (NM_001243123, intron 1 of 20)	40533	NM_001243123	231128	Mm.286885	NM_001030306	ENSMUSG00000037210	Fam193a	-	family with sequence similarity 193, member A	protein-coding
mm_132272.1	chr16	32906446	32906459	+	1	NA	3' UTR (NM_001159349, exon 8 of 8)	3' UTR (NM_001159349, exon 8 of 8)	-7648	NM_001310673	70144	Mm.491178	NM_001081255	ENSMUSG00000022801	Lrch3	2210409B11Rik|AW215594|Gm1742	leucine-rich repeats and calponin homology (CH) domain containing 3	protein-coding
mm_70384.1	chr8	10481125	10481136	+	1	NA	intron (NM_001319151, intron 23 of 34)	intron (NM_001319151, intron 23 of 34)	327219	NM_001319151	244281	Mm.422761	NM_001081397	ENSMUSG00000039057	Myo16	BM140241|C230040D10Rik|Gm1105|NYAP3|mKIAA0865	myosin XVI	protein-coding
mm_64049.1	chr7	140835467	140835476	+	1	NA	promoter-TSS (NM_029821)	promoter-TSS (NM_029821)	-25	NM_029821	76974	Mm.272359	NM_029821	ENSMUSG00000025481	Urah	1190003J15Rik|2810420C16Rik	urate (5-hydroxyiso-) hydrolase	protein-coding
mm_60116.1	chr7	35591764	35591771	+	1	NA	5' UTR (NM_178263, exon 2 of 12)	5' UTR (NM_178263, exon 2 of 12)	5520	NM_178263	245886	Mm.272620	NM_145633	ENSMUSG00000034867	Ankrd27	AA408090|BC016493|D330003H11Rik|Varp	ankyrin repeat domain 27 (VPS9 domain)	protein-coding
mm_68781.1	chr7	122955675	122955699	-	1	NA	Intergenic	Lx8|LINE|L1	14772	NR_045614	73951	Mm.389936	NR_045614		4930413G21Rik	-	RIKEN cDNA 4930413G21 gene	ncRNA
mm_59487.1	chr7	27473783	27473819	+	1	NA	promoter-TSS (NM_133210)	promoter-TSS (NM_133210)	-39	NM_133210	170742	Mm.200120	NM_133210	ENSMUSG00000055200	Sertad3	AW124805|D1Mgi51|Rbt1|Sei3	SERTA domain containing 3	protein-coding
mm_139862.1	chr17	70521657	70521698	+	1	NA	promoter-TSS (NM_001128180)	promoter-TSS (NM_001128180)	-217	NM_001347414	224997	Mm.311840	NM_027712	ENSMUSG00000003279	Dlgap1	4933422O14Rik|9630002F18|AI845682|AI848168|BB075781|D17Bwg0511e|GKAP/SAPAP|GKPA/SAPAP|Gkap|Sapap1|mKIAA4162	discs, large (Drosophila) homolog-associated protein 1	protein-coding
mm_23271.1	chr3	51590708	51590714	+	1	NA	Intergenic	Intergenic	-29888	NM_080793	73251	Mm.192111	NM_080793	ENSMUSG00000037111	Setd7	1600028F23Rik|H3K4MT|KMT7|Set7|Set7/9|mKIAA1717	SET domain containing (lysine methyltransferase) 7	protein-coding
mm_31894.1	chr4	83023798	83023802	+	1	NA	intron (NM_001198811, intron 1 of 36)	intron (NM_001198811, intron 1 of 36)	-2698	NM_177863	329872	Mm.242337	NM_177863	ENSMUSG00000059049	Frem1	BC037594|D430009N09|D630008K06|crf11|eye<m02Jus>|eyes2|heb|qbrick	Fras1 related extracellular matrix protein 1	protein-coding
mm_135431.1	chr16	45382800	45382846	-	1	NA	3' UTR (NM_010818, exon 6 of 6)	3' UTR (NM_010818, exon 6 of 6)	26230	NM_010818	17470	Mm.245851	NM_010818	ENSMUSG00000022661	Cd200	Mox2|OX2	CD200 antigen	protein-coding
mm_63001.1	chr7	120842744	120842758	+	1	NA	promoter-TSS (NM_001267710)	promoter-TSS (NM_001267710)	-80	NM_007908	13631	Mm.25997	NM_007908	ENSMUSG00000035064	Eef2k	C86191|eEF-2K	eukaryotic elongation factor-2 kinase	protein-coding
mm_111600.1	chr12	102253686	102253687	-	1	NA	intron (NM_172152, intron 12 of 16)	U3|snRNA|snRNA	-29388	NM_177620	217835	Mm.24145	NM_177620	ENSMUSG00000044456	Rin3	6430500K07|C86933	Ras and Rab interactor 3	protein-coding
mm_73053.1	chr8	94366100	94366113	+	1	NA	3' UTR (NM_001205311, exon 25 of 25)	3' UTR (NM_001205311, exon 25 of 25)	-20394	NM_022331	64209	Mm.29151	NM_022331	ENSMUSG00000031770	Herpud1	Herp|Mifl|SUP	homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1	protein-coding
mm_168956.1	chr12	78350974	78350975	+	1	NA	intron (NM_145965, intron 2 of 22)	LSU-rRNA_Hsa|rRNA|rRNA	124319	NM_145965	268566	Mm.341742	NM_145965	ENSMUSG00000047454	Gphn	5730552E08Rik|AI662856|BC027112|C230040D23|GPH|GPHRYN|geph	gephyrin	protein-coding
mm_89980.1	chr10	111595959	111595971	+	1	NA	Intergenic	Intergenic	-1692	NR_045344	71321	Mm.410785	NR_045344	ENSMUSG00000097082	4933440J02Rik	-	RIKEN cDNA 4933440J02 gene	ncRNA
mm_18677.1	chr2	71334085	71334109	-	1	NA	intron (NM_172436, intron 3 of 17)	intron (NM_172436, intron 3 of 17)	33457	NM_172436	78830	Mm.30928	NM_172436	ENSMUSG00000027010	Slc25a12	2610002D09Rik|AI839531|B230107K20Rik|BB129864	solute carrier family 25 (mitochondrial carrier, Aralar), member 12	protein-coding
mm_152084.1	chr19	6906853	6906878	-	1	NA	TTS (NM_012021)	TTS (NM_012021)	2780	NM_012021	54683	Mm.279782	NM_012021	ENSMUSG00000024953	Prdx5	AOEB166|AOPP|Pmp20|Prdx6|PrxV	peroxiredoxin 5	protein-coding
mm_78843.1	chr9	44327525	44327540	+	1	NA	intron (NM_007875, intron 1 of 8)	intron (NM_007875, intron 1 of 8)	687	NM_007875	13478	Mm.18353	NM_007875	ENSMUSG00000032123	Dpagt1	AU021132|Dpagt2|GPT|Gnpta	dolichyl-phosphate (UDP-N-acetylglucosamine) acetylglucosaminephosphotransferase 1 (GlcNAc-1-P transferase)	protein-coding
mm_170503.1	chr19	24290387	24290403	-	1	NA	Intergenic	Intergenic	-9809	NM_008044	14297	Mm.7319	NM_008044	ENSMUSG00000059363	Fxn	FA|FARR|Frda|X25	frataxin	protein-coding
mm_126501.1	chr15	81772292	81772320	+	1	NA	intron (NM_001081016, intron 5 of 22)	intron (NM_001081016, intron 5 of 22)	27458	NM_001081016	20286	Mm.432075	NM_001081016	ENSMUSG00000022390	Zc3h7b	Gm627|Scrg3|Zc2h7b|mKIAA1031	zinc finger CCCH type containing 7B	protein-coding
mm_150811.1	chr19	44388835	44388845	+	1	NA	Intergenic	Intergenic	18869	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_1403.1	chr1	67144994	67144998	+	1	NA	intron (NM_001080809, intron 4 of 37)	CT-rich|Low_complexity|Low_complexity	21969	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_17013.1	chr2	18897964	18897974	-	1	NA	intron (NM_008845, intron 3 of 9)	intron (NM_008845, intron 3 of 9)	-96151	NR_131254	66774	Mm.87075	NR_131254	ENSMUSG00000097638	Carlr	4933439G12Rik|Carl	cardiac and apoptosis-related long non-coding RNA	ncRNA
mm_168434.1	chr1	135232974	135232983	+	1	NA	Intergenic	Intergenic	25494	NM_001163131	13710	Mm.441439	NM_007921	ENSMUSG00000003051	Elf3	ESE-1|ESX|jen	E74-like factor 3	protein-coding
mm_70247.1	chr8	3393019	3393053	+	1	NA	promoter-TSS (NM_133962)	promoter-TSS (NM_133962)	28	NM_133962	102098	Mm.170461	NM_133962	ENSMUSG00000004568	Arhgef18	AI467246|D030053O22Rik	rho/rac guanine nucleotide exchange factor (GEF) 18	protein-coding
mm_119697.1	chr14	53644182	53644186	+	1	NA	Intergenic	LTRIS2|LTR|ERV1	609745	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_153249.1	chr19	36349288	36349319	-	1	NA	Intergenic	CpG	-29764	NM_029508	76073	Mm.259180	NM_029508	ENSMUSG00000024805	Pcgf5	0610009F02Rik|1110054A01Rik|5830406C17Rik|5830443C21Rik|9530023M17Rik|AI324127	polycomb group ring finger 5	protein-coding
mm_164357.1	chr16	21697371	21697373	+	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-2707	NM_001001881	72190	Mm.131606	NM_001001881	ENSMUSG00000043391	2510009E07Rik	AI194952	RIKEN cDNA 2510009E07 gene	protein-coding
mm_106844.1	chr12	8007575	8007577	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	29899	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_105739.1	chr11	109362443	109362450	-	1	NA	promoter-TSS (NM_010303)	promoter-TSS (NM_010303)	-348	NM_010303	14674	Mm.193925	NM_010303	ENSMUSG00000020611	Gna13	AU024132|AU043124|Galpha13	guanine nucleotide binding protein, alpha 13	protein-coding
mm_53038.1	chr6	124570351	124570361	+	1	NA	promoter-TSS (NM_001113356)	promoter-TSS (NM_001113356)	-74	NM_001113356	667277	Mm.481484	NM_001113356	ENSMUSG00000098470	C1rb	Gm8551|mC1rB	complement component 1, r subcomponent B	protein-coding
mm_119447.1	chr14	46882959	46882973	+	1	NA	promoter-TSS (NM_028966)	promoter-TSS (NM_028966)	1	NM_001037221	74480	Mm.214454	NM_028966	ENSMUSG00000021838	Samd4	1700024G08Rik|1700111L17Rik|4933436G17Rik|Samd4a|Smaug|Smaug1|sunk	sterile alpha motif domain containing 4	protein-coding
mm_150512.1	chr19	39030233	39030247	+	1	NA	intron (NM_028089, intron 4 of 8)	L1_Mur1|LINE|L1	23221	NM_028089	72082	Mm.142581	NM_028089	ENSMUSG00000025002	Cyp2c55	2010318C06Rik	cytochrome P450, family 2, subfamily c, polypeptide 55	protein-coding
mm_111610.1	chr12	102400217	102400242	-	1	NA	exon (NM_011175, exon 9 of 14)	exon (NM_011175, exon 9 of 14)	39584	NM_011175	19141	Mm.17185	NM_011175	ENSMUSG00000021190	Lgmn	AEP|AI746452|AU022324|Prsc1	legumain	protein-coding
mm_118857.1	chr14	25841874	25841882	+	1	NA	promoter-TSS (NM_013469)	promoter-TSS (NM_013469)	-277	NM_013469	11744	Mm.294083	NM_013469	ENSMUSG00000021866	Anxa11	A830099O17Rik|Anx11	annexin A11	protein-coding
mm_100514.1	chr11	120530568	120530577	+	1	NA	promoter-TSS (NM_008101)	promoter-TSS (NM_008101)	-155	NM_008101	14527	Mm.22329	NM_008101	ENSMUSG00000025127	Gcgr	GR	glucagon receptor	protein-coding
mm_151246.1	chr19	53903385	53903403	+	1	NA	promoter-TSS (NM_001168492)	promoter-TSS (NM_001168492)	43	NM_001168491	18569	Mm.1605	NM_011050	ENSMUSG00000024975	Pdcd4	D19Ucla1|Ma3|Tis	programmed cell death 4	protein-coding
mm_95847.1	chr11	57649569	57649571	+	1	NA	intron (NM_134189, intron 1 of 11)	MIRc|SINE|MIR	4128	NM_134189	171212	Mm.271670	NM_134189	ENSMUSG00000020520	Galnt10	AU018154|C330012K04Rik|GalNAc-T10|GalNAc-T9|Galnt9|ppGaNTase	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 10	protein-coding
mm_100428.1	chr11	119454585	119454625	+	1	NA	Intergenic	Intergenic	-36742	NM_001164636	338371	Mm.271946	NM_177394	ENSMUSG00000039850	Endov	A730011L01Rik	endonuclease V	protein-coding
mm_40859.1	chr5	73558060	73558064	+	1	NA	3' UTR (NM_001190734, exon 12 of 12)	3' UTR (NM_001190734, exon 12 of 12)	67036	NM_178896	100737	Mm.220312	NM_178896	ENSMUSG00000051674	Dcun1d4	AI836376	DCN1, defective in cullin neddylation 1, domain containing 4 (S. cerevisiae)	protein-coding
mm_51957.1	chr6	91756595	91756624	+	1	NA	3' UTR (NM_009320, exon 15 of 15)	3' UTR (NM_009320, exon 15 of 15)	50784	NM_001159507	243547	Mm.333264	NM_001033353	ENSMUSG00000030098	Grip2	-	glutamate receptor interacting protein 2	protein-coding
mm_64617.1	chr7	3616106	3616116	-	1	NA	promoter-TSS (NM_001290377)	promoter-TSS (NM_001290377)	46	NM_175632	232790	Mm.358882	NM_175632	ENSMUSG00000054594	Oscar	mOSCAR|mOSCAR-M1|mOSCAR-M2|mOSCAR-M3	osteoclast associated receptor	protein-coding
mm_73995.1	chr8	120736353	120736364	+	1	NA	promoter-TSS (NM_008320)	promoter-TSS (NM_008320)	0	NM_008320	15900	Mm.334861	NM_008320	ENSMUSG00000041515	Irf8	AI893568|ICSBP|IRF-8|Icsbp1|Myls	interferon regulatory factor 8	protein-coding
mm_149703.1	chr19	21396637	21396657	+	1	NA	intron (NM_010266, intron 12 of 13)	intron (NM_010266, intron 12 of 13)	76014	NM_010266	14544	Mm.45054	NM_010266	ENSMUSG00000058624	Gda	AU015411|AW047581|GAH	guanine deaminase	protein-coding
mm_144730.1	chr18	35553437	35553445	+	1	NA	promoter-TSS (NR_038073)	promoter-TSS (NR_038073)	31	NR_038073	100503380	Mm.482118	NR_038073	ENSMUSG00000097769	Snhg4	Gm17457	small nucleolar RNA host gene 4	ncRNA
mm_107339.1	chr12	32379132	32379178	+	1	NA	exon (NM_001162903, exon 1 of 1)	exon (NM_001162903, exon 1 of 1)	366	NM_001162903	72123	Mm.341352	NM_028111	ENSMUSG00000090946	Ccdc71l	2010109K11Rik|AV375874	coiled-coil domain containing 71 like	protein-coding
mm_121514.1	chr14	122009815	122009828	+	1	NA	intron (NM_026861, intron 8 of 8)	ORR1D2|LTR|ERVL-MaLR	-24853	NM_001037744	223262	Mm.297637	NM_001037744	ENSMUSG00000071229	Timm8a2	-	translocase of inner mitochondrial membrane 8A2	protein-coding
mm_44365.1	chr5	17807887	17807891	-	1	NA	intron (NM_007643, intron 8 of 14)	ORR1C1|LTR|ERVL-MaLR	28007	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_18626.1	chr2	68582306	68582350	-	1	NA	promoter-TSS (NM_177651)	promoter-TSS (NM_177651)	-85	NM_177651	227998	Mm.67562	NM_177651	ENSMUSG00000053896	4933409G03Rik	-	RIKEN cDNA 4933409G03 gene	protein-coding
mm_113329.1	chr13	30792637	30792647	+	1	NA	Intergenic	Intergenic	43409	NM_013674	16364	Mm.4677	NM_013674	ENSMUSG00000021356	Irf4	AI385587|IRF-4|LSIRF|NF-EM5|Spip	interferon regulatory factor 4	protein-coding
mm_77310.1	chr8	117673633	117673655	-	1	NA	Intergenic	Intergenic	-2129	NM_028725	74032	Mm.296302	NM_028725	ENSMUSG00000034308	Sdr42e1	4632417N05Rik|AI117603	short chain dehydrogenase/reductase family 42E, member 1	protein-coding
mm_69377.1	chr7	131312263	131312273	-	1	NA	intron (NM_008411, intron 6 of 8)	B1F|SINE|Alu	10024	NM_008411	16433	Mm.142717	NM_008411	ENSMUSG00000040205	Cuzd1	Erg-1|Itmap1|Uo-44|Usg|Utczp	CUB and zona pellucida-like domains 1	protein-coding
mm_15721.1	chr2	164077383	164077410	+	1	NA	intron (NM_021420, intron 1 of 10)	intron (NM_021420, intron 1 of 10)	3218	NM_021420	58231	Mm.234472	NM_021420	ENSMUSG00000018209	Stk4	AI447339|AU020804|Kas-2|Mst1|Ysk3	serine/threonine kinase 4	protein-coding
mm_112737.1	chr13	19257104	19257107	+	1	NA	Intergenic	Intergenic	138708	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_87075.1	chr10	29211638	29211649	+	1	NA	promoter-TSS (NM_001162537)	promoter-TSS (NM_001162537)	0	NM_001162537	212448	Mm.132789	NM_001162537	ENSMUSG00000004360	9330159F19Rik	-	RIKEN cDNA 9330159F19 gene	protein-coding
mm_106433.1	chr11	119392779	119392786	-	1	NA	Intergenic	B1_Mus2|SINE|Alu	2310	NR_035453	100316690		NR_035453	ENSMUSG00000088015	Mir1932	mir-1932|mmu-mir-1932	microRNA 1932	ncRNA
mm_27896.1	chr3	79450549	79450553	-	1	NA	intron (NM_001142953, intron 4 of 4)	intron (NM_001142953, intron 4 of 4)	105175	NM_001142953	100233207	Mm.373801	NM_001142953	ENSMUSG00000091685	Gm17359	-	predicted gene, 17359	protein-coding
mm_93391.1	chr10	107483793	107483796	-	1	NA	3' UTR (NM_008656, exon 3 of 3)	3' UTR (NM_008656, exon 3 of 3)	2340	NM_008656	17877	Mm.4984	NM_008656	ENSMUSG00000000435	Myf5	B130010J22Rik|Myf-5|bHLHc2	myogenic factor 5	protein-coding
mm_61384.1	chr7	72442804	72442804	+	1	NA	Intergenic	Intergenic	-136209	NM_001024703	244049	Mm.217412	NM_001024703	ENSMUSG00000032776	Mctp2	Gm489	multiple C2 domains, transmembrane 2	protein-coding
mm_78546.1	chr9	35354723	35354727	+	1	NA	Intergenic	Intergenic	73620	NR_040715	71133	Mm.158577	NR_040715	ENSMUSG00000111746	4933422A05Rik	-	RIKEN cDNA 4933422A05 gene	ncRNA
mm_154300.1	chr19	61224902	61224911	-	1	NA	3' UTR (NM_009970, exon 12 of 12)	3' UTR (NM_009970, exon 12 of 12)	3512	NM_009970	12982	Mm.287228	NM_009970	ENSMUSG00000059326	Csf2ra	CD116|Csfgmra|GM-CSF-Ra|GM-CSFR	colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)	protein-coding
mm_89821.1	chr10	105238489	105238516	+	1	NA	intron (NM_177368, intron 11 of 11)	LSU-rRNA_Hsa|rRNA|rRNA	335977	NM_177368	278279	Mm.25225	NM_177368	ENSMUSG00000036019	Tmtc2	8430438D04Rik|D330034A10Rik	transmembrane and tetratricopeptide repeat containing 2	protein-coding
mm_124374.1	chr14	106101181	106101189	-	1	NA	Intergenic	Intergenic	-5013	NM_198601	212085	Mm.78128	NM_198601	ENSMUSG00000022113	Trim52	4921513B05Rik	tripartite motif-containing 52	protein-coding
mm_61367.1	chr7	69909721	69909723	+	1	NA	Intergenic	Intergenic	413628	NR_045940	73796	Mm.410832	NR_045940	ENSMUSG00000108885	4930402F11Rik	-	RIKEN cDNA 4930402F11 gene	ncRNA
mm_102201.1	chr11	54727497	54727521	-	1	NA	intron (NM_178626, intron 3 of 5)	intron (NM_178626, intron 3 of 5)	60194	NM_178626	72729	Mm.29476	NM_178626	ENSMUSG00000052298	Cdc42se2	2810404F18Rik|AA408783|AA536669|SPEC2	CDC42 small effector 2	protein-coding
mm_168393.1	chr1	127283068	127283073	-	1	NA	intron (NM_145128, intron 2 of 17)	intron (NM_145128, intron 2 of 17)	78084	NM_145128	107895	Mm.214682	NM_145128	ENSMUSG00000036155	Mgat5	4930471A21Rik|5330407H02Rik|AI480971|GlcNAc-TV	mannoside acetylglucosaminyltransferase 5	protein-coding
mm_111706.1	chr12	103694687	103694703	-	1	NA	promoter-TSS (NM_001164742)	promoter-TSS (NM_001164742)	-6	NM_001164742	68348	Mm.20149	NM_026687	ENSMUSG00000021081	Serpina1f	0610012A11Rik|AI327419|Serpina2|epserin	serine (or cysteine) peptidase inhibitor, clade A, member 1F	protein-coding
mm_122521.1	chr14	47276852	47276864	-	1	NA	promoter-TSS (NM_080843)	promoter-TSS (NM_080843)	-1	NM_172598	218973	Mm.265615	NM_172598	ENSMUSG00000037572	Wdhd1	A630092E18|AND-1|D630024B06Rik	WD repeat and HMG-box DNA binding protein 1	protein-coding
mm_116188.1	chr13	31241093	31241099	-	1	NA	promoter-TSS (NR_045957)	promoter-TSS (NR_045957)	-10	NR_045957	73924	Mm.417825	NR_045957	ENSMUSG00000087460	4930401O12Rik	-	RIKEN cDNA 4930401O12 gene	ncRNA
mm_158651.1	chrX	155623482	155623502	-	1	NA	promoter-TSS (NM_001093750)	promoter-TSS (NM_001093750)	-165	NM_001093750	211612	Mm.218811	NM_001093750	ENSMUSG00000041552	Ptchd1	9630036J22Rik|AI848149|Gm387	patched domain containing 1	protein-coding
mm_108392.1	chr12	80948643	80948654	+	1	NA	intron (NM_009159, intron 5 of 7)	intron (NM_009159, intron 5 of 7)	3149	NM_001347415	20384	Mm.43331	NM_009159	ENSMUSG00000021134	Srsf5	Sfrs5	serine/arginine-rich splicing factor 5	protein-coding
mm_23038.1	chr3	34758375	34758380	+	1	NA	Intergenic	B1_Mur3|SINE|Alu	-13698	NR_110488	102638436	Mm.261793	NR_110488	ENSMUSG00000106519	Gm38509	Peril	predicted gene, 38509	ncRNA
mm_103584.1	chr11	78183173	78183216	-	1	NA	promoter-TSS (NR_037683)	promoter-TSS (NR_037683)	-81	NR_037683	100529077		NR_037683		Snord42b	MBII-287|U42B	small nucleolar RNA, C/D box 42B	snoRNA
mm_5350.1	chr1	25228762	25228776	-	1	NA	intron (NM_175642, intron 16 of 30)	intron (NM_175642, intron 16 of 30)	49185	NM_001204913	100504323	Mm.484176	NM_001204913		Gm20172	-	predicted gene, 20172	protein-coding
mm_168306.1	chr11	107131568	107131578	-	1	NA	exon (NM_176850, exon 1 of 28)	exon (NM_176850, exon 1 of 28)	349	NM_176850	207165	Mm.343986	NM_176850	ENSMUSG00000040481	Bptf	9430093H17Rik|Falz	bromodomain PHD finger transcription factor	protein-coding
mm_115474.1	chr13	119488426	119488478	+	1	NA	promoter-TSS (NR_027974)	promoter-TSS (NR_027974)	-68	NR_027974	67304	Mm.474382	NM_026084	ENSMUSG00000074635	3110070M22Rik	-	RIKEN cDNA 3110070M22 gene	ncRNA
mm_55734.1	chr6	77377465	77377468	-	1	NA	intron (NM_001109764, intron 8 of 19)	intron (NM_001109764, intron 8 of 19)	5009	NR_045141	70753	Mm.490700	NR_045141	ENSMUSG00000108077	6330415B21Rik	-	RIKEN cDNA 6330415B21 gene	ncRNA
mm_81202.1	chr9	107567904	107567941	+	1	NA	Intergenic	Intergenic	-1241	NM_010489	15587	Mm.4834	NM_010489	ENSMUSG00000010047	Hyal2	AI256841|AU020858|AW555733	hyaluronoglucosaminidase 2	protein-coding
mm_26216.1	chr3	138783346	138783346	+	1	NA	intron (NM_019571, intron 1 of 7)	intron (NM_019571, intron 1 of 7)	41138	NM_019571	56224	Mm.31927	NM_019571	ENSMUSG00000028152	Tspan5	2810455A09Rik|4930505M03Rik|NET-4|Tm4sf9	tetraspanin 5	protein-coding
mm_132616.1	chr16	38712959	38712962	+	1	NA	promoter-TSS (NM_020260)	promoter-TSS (NM_020260)	75	NM_020260	12549	Mm.370848	NM_020260	ENSMUSG00000022799	Arhgap31	5830477L08Rik|AU041750|Cdgap|D330026I07Rik	Rho GTPase activating protein 31	protein-coding
mm_81043.1	chr9	105395565	105395602	+	1	NA	promoter-TSS (NM_172461)	promoter-TSS (NM_172461)	191	NM_025651	66595	Mm.84941	NM_025651	ENSMUSG00000032567	Aste1	1100001A21Rik|AV006403	asteroid homolog 1 (Drosophila)	protein-coding
mm_18635.1	chr2	69382986	69383004	-	1	NA	intron (NM_175512, intron 1 of 4)	intron (NM_175512, intron 1 of 4)	2533	NM_175512	241452	Mm.211655	NM_175512	ENSMUSG00000027068	Dhrs9	C730025I08Rik|Rdh15	dehydrogenase/reductase (SDR family) member 9	protein-coding
mm_149148.1	chr19	9006460	9006471	+	1	NA	exon (NM_009643, exon 5 of 5)	exon (NM_009643, exon 5 of 5)	-11439	NR_105786	102465190		NR_105786	ENSMUSG00000099308	Mir6367	Gm27467|mmu-mir-6367	microRNA 6367	ncRNA
mm_147205.1	chr18	37896142	37896155	-	1	NA	exon (NM_001305981, exon 12 of 29)	exon (NM_001305981, exon 12 of 29)	39328	NM_001305980	13367	Mm.195916	NM_007858	ENSMUSG00000024456	Diaph1	D18Wsu154e|Dia1|Diap1|Drf1|p140mDia	diaphanous related formin 1	protein-coding
mm_152403.1	chr19	10577368	10577407	-	1	NA	promoter-TSS (NM_028411)	promoter-TSS (NM_028411)	-1	NR_126092	72982	Mm.391194	NM_028411	ENSMUSG00000024666	Tmem138	1700113I01Rik|2900055D14Rik	transmembrane protein 138	protein-coding
mm_100139.1	chr11	115975111	115975113	+	1	NA	5' UTR (NM_133663, exon 1 of 39)	5' UTR (NM_133663, exon 1 of 39)	387	NM_133663	192897	Mm.213873	NM_133663	ENSMUSG00000020758	Itgb4	AA407042|C230078O20|CD104	integrin beta 4	protein-coding
mm_79243.1	chr9	50528744	50528773	+	1	NA	promoter-TSS (NM_011220)	promoter-TSS (NM_011220)	-117	NM_011220	19286	Mm.35856	NM_011220	ENSMUSG00000032067	Pts	PTPS	6-pyruvoyl-tetrahydropterin synthase	protein-coding
mm_39729.1	chr5	28368241	28368284	+	1	NA	exon (NM_028234, exon 10 of 19)	exon (NM_028234, exon 10 of 19)	51073	NM_028234	381626	Mm.304075	NM_028234	ENSMUSG00000048271	Rbm33	3200001K10Rik|6430512A10Rik|AA386890|Prr8	RNA binding motif protein 33	protein-coding
mm_154551.1	chrM	15038	15053	-	1	NA	NA	Intergenic	NA	NA								
mm_28844.1	chr3	96667024	96667033	-	1	NA	Intergenic	Intergenic	-3103	NM_001081139	213121	Mm.39732	NM_001081139	ENSMUSG00000038354	Ankrd35	4732436F15Rik	ankyrin repeat domain 35	protein-coding
mm_158.1	chr1	12692543	12692554	+	1	NA	5' UTR (NM_001198566, exon 1 of 21)	5' UTR (NM_001198566, exon 1 of 21)	118	NM_001198566	240725	Mm.45563	NM_172294	ENSMUSG00000016918	Sulf1	AI467640|AW121680|mKIAA1077	sulfatase 1	protein-coding
mm_156147.1	chrX	129865153	129865160	+	1	NA	intron (NM_172493, intron 4 of 26)	intron (NM_172493, intron 4 of 26)	115414	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diaph2	Dia3|Diap2|Drf2|E430022I22Rik	diaphanous related formin 2	protein-coding
mm_3299.1	chr1	136696261	136696271	+	1	NA	promoter-TSS (NR_037986)	promoter-TSS (NR_037986)	55	NR_037986	100503474	Mm.428276	NR_037986		Platr22	Gm16880	pluripotency associated transcript 22	ncRNA
mm_97637.1	chr11	78973781	78973791	+	1	NA	intron (NM_001159301, intron 2 of 9)	MTD|LTR|ERVL-MaLR	11138	NM_001159301	16859	Mm.341434	NM_010708	ENSMUSG00000001123	Lgals9	AA407335|AI194909|AI265545|LGALS35|Lgals5|gal-9|galectin-9	lectin, galactose binding, soluble 9	protein-coding
mm_113863.1	chr13	48261162	48261168	+	1	NA	promoter-TSS (NM_031166)	promoter-TSS (NM_031166)	-262	NM_031166	15904	Mm.458006	NM_031166	ENSMUSG00000021379	Id4	Idb4|bHLHb27	inhibitor of DNA binding 4	protein-coding
mm_20598.1	chr2	131337635	131337643	-	1	NA	intron (NM_178607, intron 1 of 5)	intron (NM_178607, intron 1 of 5)	15253	NM_178607	51902	Mm.477523	NM_178607	ENSMUSG00000048911	Rnf24	2810473M14Rik|4930505A13Rik|AI317164|C86507|D2Ertd504e	ring finger protein 24	protein-coding
mm_75070.1	chr8	33834423	33834459	-	1	NA	exon (NM_019733, exon 5 of 9)	exon (NM_019733, exon 5 of 9)	-86671	NM_001206849	72632	Mm.443483	NM_001206849	ENSMUSG00000094500	Smim18	2700090O03Rik|AI835723	small integral membrane protein 18	protein-coding
mm_46680.1	chr5	109557800	109557805	-	1	NA	intron (NM_001310694, intron 1 of 7)	intron (NM_001310694, intron 1 of 7)	1191	NM_016715	57914	Mm.35771	NM_016715	ENSMUSG00000033467	Crlf2	CRLM2|Ly114|Tpte2|Tslpr	cytokine receptor-like factor 2	protein-coding
mm_150068.1	chr19	29386489	29386516	+	1	NA	3' UTR (NM_021893, exon 7 of 7)	3' UTR (NM_021893, exon 7 of 7)	19064	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_20052.1	chr2	120252268	120252294	-	1	NA	Intergenic	Intergenic	-6946	NM_177845	329502	Mm.330505	NM_177845	ENSMUSG00000050211	Pla2g4e	2310026J01Rik|C230096D22|Pla2epsilon	phospholipase A2, group IVE	protein-coding
mm_8958.1	chr1	164884981	164884990	-	1	NA	Intergenic	Intergenic	21864	NR_040303	433374	Mm.251149	NR_040303	ENSMUSG00000104117	Gm20743	-	predicted gene, 20743	ncRNA
mm_155353.1	chrX	68761891	68761901	+	1	NA	promoter-TSS (NM_001166620)	promoter-TSS (NM_001166620)	57	NM_001166619	207854	Mm.284945	NM_174993	ENSMUSG00000062170	Fmr1nb	3830422N12Rik|NY-SAR-35|NYSAR35	fragile X mental retardation 1 neighbor	protein-coding
mm_18927.1	chr2	76745627	76745640	-	1	NA	exon (NM_011652, exon 275 of 313)	exon (NM_011652, exon 275 of 313)	70318	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_33665.1	chr4	133176015	133176029	+	1	NA	intron (NM_153423, intron 1 of 8)	ID_B1|SINE|B4	-19633	NR_105984	102466215		NR_105984	ENSMUSG00000099202	Mir7017	Gm27945|mmu-mir-7017	microRNA 7017	ncRNA
mm_112082.1	chr12	112672029	112672044	-	1	NA	intron (NM_001331107, intron 1 of 13)	intron (NM_001331107, intron 1 of 13)	2240	NM_001165894	11651	Mm.6645	NM_009652	ENSMUSG00000001729	Akt1	Akt|LTR-akt|PKB|PKB/Akt|PKBalpha|Rac	thymoma viral proto-oncogene 1	protein-coding
mm_73240.1	chr8	104144249	104144269	+	1	NA	3' UTR (NM_009868, exon 12 of 12)	3' UTR (NM_009868, exon 12 of 12)	-26254	NM_001141924	65115	Mm.41849	NM_001141922	ENSMUSG00000031872	Bean1	Bean	brain expressed, associated with Nedd4, 1	protein-coding
mm_61238.1	chr7	65371423	65371433	+	1	NA	promoter-TSS (NM_001163574)	promoter-TSS (NM_001163574)	-184	NM_009386	21872	Mm.4342	NM_009386	ENSMUSG00000030516	Tjp1	ZO1	tight junction protein 1	protein-coding
mm_75552.1	chr8	57653024	57653039	-	1	NA	promoter-TSS (NM_144731)	promoter-TSS (NM_144731)	24	NM_001167981	108150	Mm.62886	NM_144731	ENSMUSG00000031608	Galnt7	AI225872	UDP-N-acetyl-alpha-D-galactosamine: polypeptide N-acetylgalactosaminyltransferase 7	protein-coding
mm_84006.1	chr9	57627028	57627072	-	1	NA	3' UTR (NM_007783, exon 13 of 13)	3' UTR (NM_007783, exon 13 of 13)	-6276	NM_199222	235416	Mm.295630	NM_199222	ENSMUSG00000056271	Lman1l	BC020188|slamp	lectin, mannose-binding 1 like	protein-coding
mm_126833.1	chr15	88982895	88982962	+	1	NA	promoter-TSS (NM_031260)	promoter-TSS (NM_031260)	-66	NM_031260	83456	Mm.358791	NM_031260	ENSMUSG00000015365	Mov10l1	CHAMP|Csm	Moloney leukemia virus 10-like 1	protein-coding
mm_30150.1	chr3	142572546	142572580	-	1	NA	exon (NM_018734, exon 11 of 11)	exon (NM_018734, exon 11 of 11)	12067	NM_001289493	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_139503.1	chr17	56303397	56303418	+	1	NA	promoter-TSS (NM_001111080)	promoter-TSS (NM_001111080)	70	NM_001111079	18140	Mm.42196	NM_010931	ENSMUSG00000001228	Uhrf1	AL022808|ICBP90|Np95|RNF106	ubiquitin-like, containing PHD and RING finger domains, 1	protein-coding
mm_7560.1	chr1	124723326	124723344	-	1	NA	Intergenic	Intergenic	-677776	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_120992.1	chr14	79397755	79397830	+	1	NA	promoter-TSS (NM_145960)	promoter-TSS (NM_145960)	20	NM_145960	211253	Mm.35306	NM_145960	ENSMUSG00000022022	Mtrf1	A830062K05Rik|MtRF-1	mitochondrial translational release factor 1	protein-coding
mm_23159.1	chr3	40531641	40531653	+	1	NA	Intergenic	CpG	-8735	NR_040445	100040882	Mm.272869	NR_040445	ENSMUSG00000037884	1700017G19Rik	-	RIKEN cDNA 1700017G19 gene	ncRNA
mm_27641.1	chr3	63854098	63854103	-	1	NA	Intergenic	Intergenic	-3109	NM_001177732	269437	Mm.316391	NM_183191	ENSMUSG00000036834	Plch1	BC042549|PLC-eta-1|PLCeta1|Plcl3	phospholipase C, eta 1	protein-coding
mm_94475.1	chr11	6560168	6560190	+	1	NA	promoter-TSS (NM_001190344)	promoter-TSS (NM_001190344)	-4	NM_001190344	216527	Mm.221271	NM_146014	ENSMUSG00000000378	Ccm2	BC029157	cerebral cavernous malformation 2	protein-coding
mm_61645.1	chr7	80387997	80388018	+	1	NA	promoter-TSS (NM_010194)	promoter-TSS (NM_010194)	-61	NM_010194	14159	Mm.48757	NM_010194	ENSMUSG00000053158	Fes	AI586313|BB137047|FPS|c-fes	feline sarcoma oncogene	protein-coding
mm_53321.1	chr6	129187526	129187538	+	1	NA	TTS (NM_053109)	TTS (NM_053109)	6917	NM_053109	93694	Mm.197536	NM_053109	ENSMUSG00000030157	Clec2d	Clr-b|Clrb|Ocil	C-type lectin domain family 2, member d	protein-coding
mm_102273.1	chr11	55395349	55395419	-	1	NA	3' UTR (NM_009242, exon 10 of 10)	3' UTR (NM_009242, exon 10 of 10)	24696	NM_009242	20692	Mm.291442	NM_009242	ENSMUSG00000018593	Sparc	BM-40|ON	secreted acidic cysteine rich glycoprotein	protein-coding
mm_59839.1	chr7	29519147	29519156	+	1	NA	Intergenic	CpG	-13691	NM_001081028	74206	Mm.447042	NM_001081028	ENSMUSG00000030583	Sipa1l3	2610511M17Rik	signal-induced proliferation-associated 1 like 3	protein-coding
mm_159162.1	chr2	90782738	90782738	+	1	NA	promoter-TSS (NM_178755)	promoter-TSS (NM_178755)	-6	NM_178755	271813	Mm.61146	NM_178755	ENSMUSG00000040812	Agbl2	4930524K04|A430081C19Rik|CCP2	ATP/GTP binding protein-like 2	protein-coding
mm_164077.1	chr14	122375409	122375419	+	1	NA	intron (NM_029556, intron 3 of 7)	intron (NM_029556, intron 3 of 7)	75701	NR_033325	328479	Mm.86095	NR_033325	ENSMUSG00000064052	Gm5089	6530402A20|C030005G22Rik|EG328479	predicted gene 5089	ncRNA
mm_130915.1	chr15	102625062	102625100	-	1	NA	5' UTR (NM_001310070, exon 1 of 12)	5' UTR (NM_001310070, exon 1 of 12)	383	NM_001310070	223922	Mm.208714	NM_146065	ENSMUSG00000052414	Atf7	1110012F10Rik|9430065F09Rik|AI549878|C130020M04Rik	activating transcription factor 7	protein-coding
mm_156617.1	chrX	153500332	153500362	+	1	NA	exon (NM_018798, exon 1 of 1)	exon (NM_018798, exon 1 of 1)	2115	NM_018798	54609	Mm.430772	NM_018798	ENSMUSG00000050148	Ubqln2	Chap1|Dsk2|HRIHFB2157|Plic-2|Plic2	ubiquilin 2	protein-coding
mm_109257.1	chr12	109459951	109459962	+	1	NA	exon (NM_010052, exon 5 of 5)	exon (NM_010052, exon 5 of 5)	6501	NM_010052	13386	Mm.157069	NM_010052	ENSMUSG00000040856	Dlk1	AW742678|DLK-1|DlkI|FA1|Ly107|Peg9|SCP1|ZOG|pG2|pref-1	delta-like 1 homolog (Drosophila)	protein-coding
mm_3943.1	chr1	163779812	163779865	+	1	NA	5' UTR (NM_010629, exon 1 of 21)	5' UTR (NM_010629, exon 1 of 21)	255	NM_010629	16579	Mm.4651	NM_010629	ENSMUSG00000026585	Kifap3	KAP-3|KAP3|SMAP	kinesin-associated protein 3	protein-coding
mm_118498.1	chr14	13454011	13454123	+	1	NA	5' UTR (NM_001163032, exon 1 of 5)	5' UTR (NM_001163032, exon 1 of 5)	109	NM_001163032	72003	Mm.317515	NM_028052	ENSMUSG00000056296	Synpr	1500003F20Rik|SPO	synaptoporin	protein-coding
mm_104015.1	chr11	85312054	85312097	-	1	NA	intron (NM_016910, intron 1 of 5)	intron (NM_016910, intron 1 of 5)	821	NM_016910	53892	Mm.45609	NM_016910	ENSMUSG00000020525	Ppm1d	AV338790|Wip1	protein phosphatase 1D magnesium-dependent, delta isoform	protein-coding
mm_94571.1	chr11	11689945	11689947	+	1	NA	promoter-TSS (NM_001301865)	promoter-TSS (NM_001301865)	-231	NM_001301865	22778	Mm.103545	NM_009578	ENSMUSG00000018654	Ikzf1	5832432G11Rik|Ikaros|LyF-1|Zfpn1a1|Znfn1a1|hlk-1|mKIAA4227	IKAROS family zinc finger 1	protein-coding
mm_133618.1	chr16	91560544	91560559	+	1	NA	exon (NM_008338, exon 5 of 7)	exon (NM_008338, exon 5 of 7)	13457	NM_008338	15980	Mm.249364	NM_008338	ENSMUSG00000022965	Ifngr2	Ifgr2|Ifgt	interferon gamma receptor 2	protein-coding
mm_90834.1	chr10	8453020	8453048	-	1	NA	intron (NM_177387, intron 1 of 7)	intron (NM_177387, intron 1 of 7)	65791	NM_177387	338362	Mm.41163	NM_177387	ENSMUSG00000047712	Ust	D930010O20Rik|UA2OST	uronyl-2-sulfotransferase	protein-coding
mm_172819.1	chr9	12655376	12655376	+	1	NA	Intergenic	Intergenic	450479	NR_040755	78219	Mm.414868	NR_040755	ENSMUSG00000111830	4930568E12Rik	-	RIKEN cDNA 4930568E12 gene	ncRNA
mm_61332.1	chr7	68275869	68275879	+	1	NA	promoter-TSS (NR_040341)	promoter-TSS (NR_040341)	720	NR_040340	100504026	Mm.426764	NR_040340	ENSMUSG00000086628	Gm16157	OTTMUSG00000031023	predicted gene 16157	ncRNA
mm_23971.1	chr3	85581134	85581148	+	1	NA	intron (NM_144896, intron 2 of 12)	intron (NM_144896, intron 2 of 12)	7012	NM_144896	229487	Mm.52275	NM_144896	ENSMUSG00000028085	Gatb	9430026F02Rik|Pet112|Pet112l	glutamyl-tRNA(Gln) amidotransferase, subunit B	protein-coding
mm_128369.1	chr15	42585539	42585543	-	1	NA	intron (NM_009640, intron 1 of 8)	intron (NM_009640, intron 1 of 8)	91436	NM_001286062	11600	Mm.309336	NM_009640	ENSMUSG00000022309	Angpt1	1110046O21Rik|Ang-1|Ang1	angiopoietin 1	protein-coding
mm_19831.1	chr2	112203366	112203373	-	1	NA	Intergenic	Lx9|LINE|L1	-36472	NM_207206	99010	Mm.33438	NM_207206	ENSMUSG00000027134	Lpcat4	AI505034|Agpat7|Aytl3|LPEAT2	lysophosphatidylcholine acyltransferase 4	protein-coding
mm_131295.1	chr16	11399598	11399611	+	1	NA	intron (NM_028964, intron 5 of 20)	intron (NM_028964, intron 5 of 20)	-6044	NM_001290148	74478	Mm.325831	NM_028964	ENSMUSG00000071669	Snx29	4933437K13Rik|ENSMUSG00000079738|Gm11170|Gm1737|Gm930|Rundc2a	sorting nexin 29	protein-coding
mm_169354.1	chr14	24487214	24487223	+	1	NA	promoter-TSS (NM_001081247)	promoter-TSS (NM_001081247)	-172	NM_001081247	218832	Mm.343610	NM_183157	ENSMUSG00000025280	Polr3a	9330175N20Rik|BC053071|RPC1|RPC155	polymerase (RNA) III (DNA directed) polypeptide A	protein-coding
mm_29294.1	chr3	107829585	107829599	-	1	NA	Intergenic	Intergenic	-47638	NM_133867	99662	Mm.108491	NM_133867	ENSMUSG00000040600	Eps8l3	AI504489|Eps8r3	EPS8-like 3	protein-coding
mm_106008.1	chr11	115813564	115813593	-	1	NA	promoter-TSS (NM_080643)	promoter-TSS (NM_080643)	14	NM_080643	140721	Mm.383737	NM_080643	ENSMUSG00000034471	Caskin2	1600028L06Rik|mKIAA1139	CASK-interacting protein 2	protein-coding
mm_53493.1	chr6	135203441	135203444	+	1	NA	intron (NM_028982, intron 1 of 12)	PB1D10|SINE|Alu	5455	NM_028982	74525	Mm.34182	NM_028982	ENSMUSG00000030207	Fam234b	8430419L09Rik|Kiaa1467|mKIAA1467	family with sequence similarity 234, member B	protein-coding
mm_54892.1	chr6	46147892	46147902	-	1	NA	intron (NM_001004357, intron 8 of 23)	intron (NM_001004357, intron 8 of 23)	1087836	NM_001004357	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding
mm_169546.1	chr15	102510663	102510677	-	1	NA	intron (NM_001163643, intron 1 of 15)	CpG	6334	NM_001163643	26404	Mm.172897	NM_009582	ENSMUSG00000023050	Map3k12	DLK|MUK|Zpk	mitogen-activated protein kinase kinase kinase 12	protein-coding
mm_142585.1	chr17	46726345	46726355	-	1	NA	TTS (NM_145488)	TTS (NM_145488)	2815	NM_010321	14711	Mm.29395	NM_010321	ENSMUSG00000002769	Gnmt	-	glycine N-methyltransferase	protein-coding
mm_26634.1	chr3	152930045	152930048	+	1	NA	intron (NM_012028, intron 2 of 4)	RLTR17|LTR|ERVK	52161	NM_012028	26938	Mm.40915	NM_012028	ENSMUSG00000039037	St6galnac5	AI851940|Siat7e	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 5	protein-coding
mm_120047.1	chr14	56620914	56620918	+	1	NA	intron (NM_001145978, intron 22 of 34)	intron (NM_001145978, intron 22 of 34)	45297	NM_001145978	328417	Mm.379357	NM_001145978	ENSMUSG00000054509	Parp4	Adprtl1|C030027K23Rik|E230037B21Rik|Gm743|PARPL|PH5P|VAULT3|VPARP|p193	poly (ADP-ribose) polymerase family, member 4	protein-coding
mm_115604.1	chr13	11969925	11969927	-	1	NA	intron (NM_023868, intron 1 of 104)	intron (NM_023868, intron 1 of 104)	137019	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding
mm_98444.1	chr11	94942792	94942822	+	1	NA	exon (NM_007742, exon 21 of 51)	exon (NM_007742, exon 21 of 51)	6583	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_61364.1	chr7	69496098	69496132	+	1	NA	promoter-TSS (NR_045940)	promoter-TSS (NR_045940)	21	NR_045940	73796	Mm.410832	NR_045940	ENSMUSG00000108885	4930402F11Rik	-	RIKEN cDNA 4930402F11 gene	ncRNA
mm_166256.1	chr5	87670883	87670897	+	1	NA	intron (NM_001286015, intron 5 of 32)	intron (NM_001286015, intron 5 of 32)	4682	NM_001286016	12990	Mm.427467	NM_007784	ENSMUSG00000070702	Csn1s1	AA959832|AW212882|Csna	casein alpha s1	protein-coding
mm_112110.1	chr12	112795782	112795794	-	1	NA	Intergenic	Intergenic	-13187	NM_145450	217887	Mm.186678	NM_145450	ENSMUSG00000037594	BC022687	AW050009|C130001I08Rik|Flj20080	cDNA sequence BC022687	protein-coding
mm_172148.1	chr6	3820705	3820707	-	1	NA	Intergenic	L1Md_T|LINE|L1	-55993	NM_007588	12311	Mm.4642	NM_007588	ENSMUSG00000023964	Calcr	Clr	calcitonin receptor	protein-coding
mm_82959.1	chr9	35570476	35570476	-	1	NA	promoter-TSS (NM_029762)	promoter-TSS (NM_029762)	-407	NM_029762	76832	Mm.482285	NM_029762	ENSMUSG00000050555	Hyls1	3010015K02Rik	hydrolethalus syndrome 1	protein-coding
mm_140816.1	chr17	22867159	22867190	-	1	NA	promoter-TSS (NM_177358)	promoter-TSS (NM_177358)	-40	NM_001110254	240041	Mm.328828	NM_177358	ENSMUSG00000059142	Zfp945	A630033E08Rik|C730040L01Rik	zinc finger protein 945	protein-coding
mm_166008.1	chr4	117445852	117445859	+	1	NA	intron (NM_025739, intron 2 of 14)	intron (NM_025739, intron 2 of 14)	51197	NM_025739	66743	Mm.318331	NM_025739	ENSMUSG00000028677	Rnf220	4732477A13|4931406I20Rik|5730503K05Rik|AV302541	ring finger protein 220	protein-coding
mm_141237.1	chr17	27436999	27437008	-	1	NA	intron (NM_001013385, intron 7 of 8)	intron (NM_001013385, intron 7 of 8)	66530	NM_001013385	268934	Mm.358940	NM_001013385	ENSMUSG00000063239	Grm4	Gprc1d|mGluR4	glutamate receptor, metabotropic 4	protein-coding
mm_152119.1	chr19	6987461	6987517	-	1	NA	TTS (NM_020566)	TTS (NM_020566)	162	NM_001185164	22340	Mm.15607	NM_011697	ENSMUSG00000024962	Vegfb	VEGF-B|Vrf	vascular endothelial growth factor B	protein-coding
mm_67399.1	chr7	79884612	79884614	-	1	NA	intron (NM_009682, intron 4 of 5)	B1_Mus2|SINE|Alu	36027	NM_009682	11778	Mm.220173	NM_009682	ENSMUSG00000063801	Ap3s2	[s]3B	adaptor-related protein complex 3, sigma 2 subunit	protein-coding
mm_20759.1	chr2	140671463	140671476	-	1	NA	promoter-TSS (NM_178382)	promoter-TSS (NM_178382)	7	NM_001172160	71436	Mm.426781	NM_178382	ENSMUSG00000051379	Flrt3	5530600M07Rik|C430047I10Rik|mKIAA1469	fibronectin leucine rich transmembrane protein 3	protein-coding
mm_6898.1	chr1	84745162	84745200	-	1	NA	exon (NM_133975, exon 26 of 41)	exon (NM_133975, exon 26 of 41)	-48960	NM_152915	227325	Mm.292560	NM_152915	ENSMUSG00000036766	Dner	A930026D19Rik|BET|Bret	delta/notch-like EGF repeat containing	protein-coding
mm_114845.1	chr13	92693258	92693259	+	1	NA	intron (NM_172588, intron 7 of 11)	intron (NM_172588, intron 7 of 11)	82120	NM_172588	218442	Mm.297970	NM_172588	ENSMUSG00000021703	Serinc5	A130038L21Rik|AIGP3|C86123|TPO1	serine incorporator 5	protein-coding
mm_9104.1	chr1	170110426	170110440	-	1	NA	Intergenic	Intergenic	-21489	NM_022563	18214	Mm.229249	NM_022563	ENSMUSG00000026674	Ddr2	AW495251|Ntrkr3|tyro10	discoidin domain receptor family, member 2	protein-coding
mm_66179.1	chr7	34022779	34022791	-	1	NA	TTS (NM_009596)	TTS (NM_009596)	1218	NM_009596	11354	Mm.8025	NM_009596	ENSMUSG00000066583	Scgb1b27	Abp|Abpa|Abpa27|Sal-1|Tcp	secretoglobin, family 1B, member 27	protein-coding
mm_134085.1	chr16	8738962	8738975	-	1	NA	promoter-TSS (NM_001003918)	promoter-TSS (NM_001003918)	-626	NM_001003918	252870	Mm.295330	NM_001003918	ENSMUSG00000022710	Usp7	2210010O09Rik|AA409944|AA617399|AU019296|AW548146|C80752|Hausp	ubiquitin specific peptidase 7	protein-coding
mm_81795.1	chr9	115200396	115200438	+	1	NA	intron (NM_148958, intron 4 of 9)	intron (NM_148958, intron 4 of 9)	81653	NR_029430	111186	Mm.484753	NR_029430		Stmn1-rs1	Lag-rs1|Lap18-rs1	stathmin 1, related sequence 1	pseudo
mm_64628.1	chr7	3692762	3692828	-	1	NA	promoter-TSS (NM_001164205)	promoter-TSS (NM_001164205)	730	NM_029934	77582	Mm.397541	NM_029934	ENSMUSG00000035596	Mboat7	5730589L02Rik|BB1|Leng4|Lpiat|Lpiat1|mBB1	membrane bound O-acyltransferase domain containing 7	protein-coding
mm_92774.1	chr10	81167897	81167905	-	1	NA	promoter-TSS (NM_021501)	promoter-TSS (NM_021501)	-181	NM_021501	59004	Mm.34428	NM_021501	ENSMUSG00000004934	Pias4	PIASY|Pias-gamma|Piasg	protein inhibitor of activated STAT 4	protein-coding
mm_88598.1	chr10	79793323	79793334	+	1	NA	promoter-TSS (NM_001161747)	promoter-TSS (NM_001161747)	-244	NM_023128	18483	Mm.34650	NM_023128	ENSMUSG00000035863	Palm	-	paralemmin	protein-coding
mm_35310.1	chr4	25281753	25281800	-	1	NA	promoter-TSS (NM_026194)	promoter-TSS (NM_026194)	45	NM_026194	67490	Mm.226295	NM_026194	ENSMUSG00000040359	Ufl1	1810074P20Rik|AI429228|Kiaa0776|Maxer|Rcad|mKIAA0776	UFM1 specific ligase 1	protein-coding
mm_125085.1	chr15	27025297	27025298	+	1	NA	Intergenic	Intergenic	-129733	NM_176959	448987	Mm.253378	NM_176959	ENSMUSG00000043556	Fbxl7	AL023057|D230018M15Rik|FBL7|Fbl6	F-box and leucine-rich repeat protein 7	protein-coding
mm_85089.1	chr9	91961129	91961141	-	1	NA	Intergenic	Intergenic	-231801	NM_001195693	100504689	Mm.464262	NM_001195693	ENSMUSG00000095654	Plscr5	331000	phospholipid scramblase family, member 5	protein-coding
mm_12074.1	chr2	59776030	59776054	+	1	NA	intron (NM_198294, intron 7 of 26)	intron (NM_198294, intron 7 of 26)	106564	NM_001159636	72137	Mm.288734	NM_028118	ENSMUSG00000026988	Wdsub1	1700048E19Rik|2610014F08Rik	WD repeat, SAM and U-box domain containing 1	protein-coding
mm_113004.1	chr13	21833737	21833751	+	1	NA	promoter-TSS (NM_001110555)	promoter-TSS (NM_001110555)	1	NM_001097979	665596	Mm.371766	NM_001097979	ENSMUSG00000069307	Hist1h2bq	Gm13646|OTTMUSG00000013203	histone cluster 1, H2bq	protein-coding
mm_136486.1	chr16	96082514	96082573	-	1	NA	promoter-TSS (NM_145125)	promoter-TSS (NM_145125)	-115	NM_145125	93871	Mm.240871	NM_145125	ENSMUSG00000022914	Brwd1	5330419I02Rik|D530019K20Rik|G1-403-16|Wdr9|repro5	bromodomain and WD repeat domain containing 1	protein-coding
mm_19340.1	chr2	90636865	90636874	-	1	NA	Intergenic	Intergenic	-40346	NM_021512	59015	Mm.24532	NM_021512	ENSMUSG00000051329	Nup160	160kDa|2810011M03Rik|AA414952|AU020188|Gtl-13|Gtl1-13|Gtl13|mKIAA0197	nucleoporin 160	protein-coding
mm_18086.1	chr2	44927207	44927239	-	1	NA	Intergenic	CpG	-65601	NM_172662	227835	Mm.314312	NM_172662	ENSMUSG00000036890	Gtdc1	E330008O22Rik	glycosyltransferase-like domain containing 1	protein-coding
mm_63572.1	chr7	128117749	128117759	+	1	NA	3' UTR (NM_008401, exon 30 of 30)	3' UTR (NM_008401, exon 30 of 30)	-11814	NM_021334	16411	Mm.22378	NM_021334	ENSMUSG00000030789	Itgax	AI449405|Cd11c|Cr4|N418	integrin alpha X	protein-coding
mm_33672.1	chr4	133192188	133192209	+	1	NA	exon (NM_153423, exon 7 of 9)	exon (NM_153423, exon 7 of 9)	-3457	NR_105984	102466215		NR_105984	ENSMUSG00000099202	Mir7017	Gm27945|mmu-mir-7017	microRNA 7017	ncRNA
mm_68258.1	chr7	105591775	105591821	-	1	NA	exon (NM_017371, exon 10 of 10)	exon (NM_017371, exon 10 of 10)	8318	NM_017371	15458	Mm.3485	NM_017371	ENSMUSG00000030895	Hpx	Hpxn|hx	hemopexin	protein-coding
mm_110802.1	chr12	72212340	72212405	-	1	NA	non-coding (NR_104446, exon 7 of 7)	non-coding (NR_104446, exon 7 of 7)	23374	NR_104446	104001	Mm.221275	NM_153457	ENSMUSG00000021087	Rtn1	Nsp	reticulon 1	protein-coding
mm_73291.1	chr8	104947349	104947363	+	1	NA	promoter-TSS (NM_001079865)	promoter-TSS (NM_001079865)	0	NM_001079865	71903	Mm.442371	NM_001079865	ENSMUSG00000062826	Ces2f	2310038E17Rik|A430088E12	carboxylesterase 2F	protein-coding
mm_152495.1	chr19	11081067	11081077	-	1	NA	promoter-TSS (NM_022430)	promoter-TSS (NM_022430)	31	NM_022430	64381	Mm.34460	NM_022430	ENSMUSG00000024730	Ms4a8a	2010004L09Rik|AI481240|CD20L5|Ms4a8	membrane-spanning 4-domains, subfamily A, member 8A	protein-coding
mm_82836.1	chr9	31150758	31150785	-	1	NA	3' UTR (NM_009691, exon 16 of 16)	3' UTR (NM_009691, exon 16 of 16)	-18972	NM_011176	19143	Mm.243926	NM_011176	ENSMUSG00000031995	St14	Epithin|MT-SP1|Prss14|Tmprss14|mCAP3|matriptase	suppression of tumorigenicity 14 (colon carcinoma)	protein-coding
mm_141689.1	chr17	33951792	33951803	-	1	NA	promoter-TSS (NM_019420)	promoter-TSS (NM_019420)	-309	NM_019420	54218	Mm.11132	NM_019420	ENSMUSG00000067370	B3galt4	Gal-T2|Galt2	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 4	protein-coding
mm_8163.1	chr1	136949592	136949599	-	1	NA	intron (NM_030676, intron 2 of 8)	intron (NM_030676, intron 2 of 8)	4035	NM_001159769	26424	Mm.16794	NM_030676	ENSMUSG00000026398	Nr5a2	AU020803|D1Ertd308e|Ftf|LRH-1|UF2-H3B	nuclear receptor subfamily 5, group A, member 2	protein-coding
mm_46471.1	chr5	105126714	105126716	-	1	NA	intron (NM_008620, intron 3 of 10)	L1Md_F2|LINE|L1	12837	NM_008620	17472	Mm.440525	NM_008620	ENSMUSG00000079363	Gbp4	AW228052|Mag-2|Mpa-2|Mpa2	guanylate binding protein 4	protein-coding
mm_156946.1	chrX	169980727	169980751	+	1	NA	intron (NM_001290512, intron 4 of 9)	intron (NM_001290512, intron 4 of 9)	-1822	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_136755.1	chr17	8582639	8582649	+	1	NA	intron (NM_001290707, intron 1 of 22)	intron (NM_001290707, intron 1 of 22)	55843	NM_001290707	23984	Mm.87161	NM_011866	ENSMUSG00000023868	Pde10a	-	phosphodiesterase 10A	protein-coding
mm_72020.1	chr8	70724110	70724122	+	1	NA	promoter-TSS (NM_201607)	promoter-TSS (NM_201607)	52	NM_201607	110385	Mm.255180	NM_201607	ENSMUSG00000031842	Pde4c	Dpde1|E130301F19Rik|dunce	phosphodiesterase 4C, cAMP specific	protein-coding
mm_172309.1	chr7	104543320	104543326	-	1	NA	Intergenic	L1Md_T|LINE|L1	-7962	NR_033673	625321	Mm.367236	NM_001037924	ENSMUSG00000073929	Trim30e-ps1	EG625321|Gm6577|Trim30-4	tripartite motif-containing 30E, pseudogene 1	pseudo
mm_6470.1	chr1	74048830	74048840	-	1	NA	intron (NM_027884, intron 3 of 34)	MIR|SINE|MIR	75612	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_127464.1	chr15	101272722	101272736	+	1	NA	exon (NM_010444, exon 5 of 7)	exon (NM_010444, exon 5 of 7)	5883	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_74395.1	chr8	3200430	3200461	-	1	NA	intron (NM_010568, intron 5 of 20)	intron (NM_010568, intron 5 of 20)	79172	NM_010568	16337	Mm.268003	NM_010568	ENSMUSG00000005534	Insr	4932439J01Rik|CD220|D630014A15Rik|IR|IR-A|IR-B	insulin receptor	protein-coding
mm_113923.1	chr13	49582709	49582734	+	1	NA	promoter-TSS (NM_012050)	promoter-TSS (NM_012050)	-26	NM_012050	27047	Mm.390589	NM_012050	ENSMUSG00000048368	Omd	OSAD|SLRR2C	osteomodulin	protein-coding
mm_55150.1	chr6	51466952	51466992	-	1	NA	exon (NM_182650, exon 3 of 10)	exon (NM_182650, exon 3 of 10)	2922	NM_182650	53379	Mm.155896	NM_016806	ENSMUSG00000004980	Hnrnpa2b1	9130414A06Rik|Hnrpa2|Hnrpa2b1|hnrnp-A	heterogeneous nuclear ribonucleoprotein A2/B1	protein-coding
mm_21129.1	chr2	154202691	154202732	-	1	NA	exon (NM_153418, exon 2 of 16)	exon (NM_153418, exon 2 of 16)	2331	NM_153418	228801	Mm.3783	NM_153418	ENSMUSG00000027485	Bpifb1	Lplunc1	BPI fold containing family B, member 1	protein-coding
mm_46709.1	chr5	110342964	110343007	-	1	NA	promoter-TSS (NM_153400)	promoter-TSS (NM_153400)	50	NM_153400	231602	Mm.55948	NM_153400	ENSMUSG00000029503	P2rx2	P2X2a|P2x2	purinergic receptor P2X, ligand-gated ion channel, 2	protein-coding
mm_121991.1	chr14	26442875	26442877	-	1	NA	intron (NM_001347494, intron 10 of 19)	intron (NM_001347494, intron 10 of 19)	85329	NR_038005	71106	Mm.158564	NR_038005	ENSMUSG00000021874	4933413J09Rik	GCSE	RIKEN cDNA 4933413J09 gene	ncRNA
mm_37758.1	chr4	129672698	129672708	-	1	NA	promoter-TSS (NM_008468)	promoter-TSS (NM_008468)	64	NM_008468	16650	Mm.202358	NM_008468	ENSMUSG00000003731	Kpna6	IPOA7|Kpna5|NPI-2	karyopherin (importin) alpha 6	protein-coding
mm_24866.1	chr3	95934802	95934836	+	1	NA	exon (NM_001253757, exon 3 of 7)	exon (NM_001253757, exon 3 of 7)	5562	NM_023210	66471	Mm.218657	NM_023210	ENSMUSG00000015749	Anp32e	2810018A15Rik|AI047746|AI326868|CPD1|LANP-L|LANPL|mLANP-L	acidic (leucine-rich) nuclear phosphoprotein 32 family, member E	protein-coding
mm_153034.1	chr19	31910422	31910435	-	1	NA	intron (NM_001081074, intron 3 of 11)	intron (NM_001081074, intron 3 of 11)	41667	NM_001081074	69865	Mm.87538	NM_001081074	ENSMUSG00000052595	A1cf	1810073H04Rik|ACF64|ACF65|ASP|Acf|MCM|MerCreMer|Tg(Myh6-cre/Esr1*)1Jmk|mer	APOBEC1 complementation factor	protein-coding
mm_7549.1	chr1	124536603	124536614	-	1	NA	Intergenic	Intergenic	-491049	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_80883.1	chr9	99183619	99183643	+	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	-43420	NM_029094	74769	Mm.213128	NM_029094	ENSMUSG00000032462	Pik3cb	1110001J02Rik|AI447572|p110beta	phosphatidylinositol 3-kinase, catalytic, beta polypeptide	protein-coding
mm_86340.1	chr9	123260757	123260773	-	1	NA	promoter-TSS (NM_001002267)	promoter-TSS (NM_001002267)	24	NM_001002267	72309	Mm.8569	NM_001002267	ENSMUSG00000054871	Tmem158	2310037P21Rik|Ris1	transmembrane protein 158	protein-coding
mm_43700.1	chr5	139252315	139252329	+	1	NA	promoter-TSS (NM_026269)	promoter-TSS (NM_026269)	-2	NM_026269	67604	Mm.270137	NM_026269	ENSMUSG00000025858	Get4	1110007L15Rik|AW412535|Cee	golgi to ER traffic protein 4	protein-coding
mm_34313.1	chr4	141817975	141817982	+	1	NA	exon (NM_007919, exon 7 of 8)	exon (NM_007919, exon 7 of 8)	8027	NM_007919	13706	Mm.45316	NM_007919	ENSMUSG00000058579	Cela2a	Ela-2|Ela2|Ela2a	chymotrypsin-like elastase family, member 2A	protein-coding
mm_93383.1	chr10	105574437	105574451	-	1	NA	promoter-TSS (NM_177368)	promoter-TSS (NM_177368)	35	NM_177368	278279	Mm.25225	NM_177368	ENSMUSG00000036019	Tmtc2	8430438D04Rik|D330034A10Rik	transmembrane and tetratricopeptide repeat containing 2	protein-coding
mm_96446.1	chr11	67479762	67479774	+	1	NA	Intergenic	Intergenic	-53230	NM_008088	14457	Mm.40338	NM_008088	ENSMUSG00000033066	Gas7	AW124766|B230343A10Rik|Gas7-cb	growth arrest specific 7	protein-coding
mm_148594.1	chr19	5069825	5069835	+	1	NA	exon (NM_054042, exon 1 of 1)	exon (NM_054042, exon 1 of 1)	1752	NM_054042	70445	Mm.29597	NM_054042	ENSMUSG00000056481	Cd248	2610111G01Rik|AI842296|Cd164l1|Tem1	CD248 antigen, endosialin	protein-coding
mm_64760.1	chr7	4866132	4866150	-	1	NA	promoter-TSS (NM_026158)	promoter-TSS (NM_026158)	38	NM_026158	67441	Mm.41385	NM_026158	ENSMUSG00000052605	Isoc2b	0610042E07Rik|AI553388|Isoc2	isochorismatase domain containing 2b	protein-coding
mm_62334.1	chr7	100494045	100494088	+	1	NA	intron (NM_011671, intron 1 of 7)	intron (NM_011671, intron 1 of 7)	708	NM_011671	22228	Mm.171378	NM_011671	ENSMUSG00000033685	Ucp2	Slc25a8	uncoupling protein 2 (mitochondrial, proton carrier)	protein-coding
mm_16129.1	chr2	170285329	170285346	+	1	NA	Intergenic	Intergenic	-71024	NR_040610	73303	Mm.443297	NR_040610	ENSMUSG00000086999	Bcas1os2	1700040N02Rik	breast carcinoma amplified sequence 1, opposite strand 2	ncRNA
mm_14684.1	chr2	140056053	140056063	+	1	NA	intron (NR_110350, intron 2 of 12)	intron (NR_110350, intron 2 of 12)	10747	NM_001159640	75812	Mm.293449	NM_175225	ENSMUSG00000039033	Tasp1	4930485D02Rik|AW986064	taspase, threonine aspartase 1	protein-coding
mm_86303.1	chr9	122351398	122351444	-	1	NA	promoter-TSS (NM_026179)	promoter-TSS (NM_026179)	-195	NM_026179	67469	Mm.280254	NM_026179	ENSMUSG00000032540	Abhd5	1300003D03Rik|2010002J10Rik|CDS|CGI-58|IECN5|NCIE2	abhydrolase domain containing 5	protein-coding
mm_169208.1	chr13	66473030	66473046	-	1	NA	Intergenic	RLTR27|LTR|ERVK	-31920	NM_001290196	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
mm_13689.1	chr2	117120861	117120882	+	1	NA	promoter-TSS (NM_001277256)	promoter-TSS (NM_001277256)	-200	NM_001277256	114715	Mm.245890	NM_033524	ENSMUSG00000027351	Spred1	5730461F13Rik|AL024345|AW047647	sprouty protein with EVH-1 domain 1, related sequence	protein-coding
mm_25901.1	chr3	131111368	131111405	+	1	NA	5' UTR (NM_001276402, exon 1 of 10)	5' UTR (NM_001276402, exon 1 of 10)	1089	NM_001276402	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_154021.1	chr19	53389672	53389675	-	1	NA	intron (NM_172429, intron 1 of 5)	intron (NM_172429, intron 1 of 5)	900	NM_172429	76479	Mm.313687	NM_172429	ENSMUSG00000025024	Smndc1	2410004J23Rik|4933440I19Rik	survival motor neuron domain containing 1	protein-coding
mm_114337.1	chr13	60738152	60738162	+	1	NA	intron (NM_029653, intron 18 of 25)	intron (NM_029653, intron 18 of 25)	48207	NM_199148	218275	Mm.222427	NM_199148	ENSMUSG00000042243	BC051665	-	cDNA sequence BC051665	protein-coding
mm_50215.1	chr6	42286677	42286687	+	1	NA	promoter-TSS (NM_013491)	promoter-TSS (NM_013491)	-3	NM_013491	12723	Mm.386757	NM_013491	ENSMUSG00000029862	Clcn1	Clc-1|Clc1|SMCC1|adr|mto|myotonia|nmf355	chloride channel, voltage-sensitive 1	protein-coding
mm_36718.1	chr4	98699138	98699148	-	1	NA	intron (NM_172696, intron 42 of 43)	intron (NM_172696, intron 42 of 43)	-27611	NM_001081202	381591	Mm.34340	NM_001081202	ENSMUSG00000087166	L1td1	AA546746|AB211064|D76865|ECAT11	LINE-1 type transposase domain containing 1	protein-coding
mm_65461.1	chr7	25471823	25471828	-	1	NA	exon (NM_001039186, exon 5 of 8)	exon (NM_001039186, exon 5 of 8)	5800	NM_001039185	26365	Mm.322502	NM_011926	ENSMUSG00000074272	Ceacam1	Bgp|Bgp1|C-CAM|CD66a|Cc1|Cea-1|Cea-7|Cea1|Cea7|Hv-2|Hv2|MHVR|MHVR1|Mhv-1|bb-1|mCEA1|mmCGM1|mmCGM1a|mmCGM2	carcinoembryonic antigen-related cell adhesion molecule 1	protein-coding
mm_36839.1	chr4	106617233	106617240	-	1	NA	promoter-TSS (NM_183182)	promoter-TSS (NM_183182)	2	NM_183182	242602	Mm.235591	NM_183182	ENSMUSG00000054362	Lexm	-	lymphocyte expansion molecule	protein-coding
mm_50222.1	chr6	42350083	42350091	+	1	NA	5' UTR (NM_001289618, exon 1 of 10)	5' UTR (NM_001289618, exon 1 of 10)	259	NM_001289619	22793	Mm.282303	NM_011777	ENSMUSG00000029860	Zyx	9530098H06Rik|R75157	zyxin	protein-coding
mm_36654.1	chr4	94650093	94650127	-	1	NA	promoter-TSS (NM_175305)	promoter-TSS (NM_175305)	34	NM_175305	100061	Mm.26760	NM_175305	ENSMUSG00000049799	Lrrc19	9130022A01Rik|AI314124|AL022954|AW261791	leucine rich repeat containing 19	protein-coding
mm_26190.1	chr3	138443086	138443176	+	1	NA	promoter-TSS (NM_007410)	promoter-TSS (NM_007410)	38	NM_007410	11532	Mm.3874	NM_007410	ENSMUSG00000028138	Adh5	Adh-5|Adh3|GSNOR	alcohol dehydrogenase 5 (class III), chi polypeptide	protein-coding
mm_34787.1	chr4	154191134	154191145	+	1	NA	intron (NM_001162977, intron 3 of 36)	BC1_Mm|scRNA|scRNA	20426	NM_001162977	230971	Mm.275216	NM_172273	ENSMUSG00000057751	Megf6	2600001P17Rik|Egfl3	multiple EGF-like-domains 6	protein-coding
mm_73543.1	chr8	108715059	108715098	+	1	NA	5' UTR (NM_007496, exon 1 of 10)	5' UTR (NM_007496, exon 1 of 10)	434	NM_007496	11906	Mm.416972	NM_007496	ENSMUSG00000038872	Zfhx3	A230102L03Rik|Atbf1|Sci|WBP9|mKIAA4228	zinc finger homeobox 3	protein-coding
mm_53411.1	chr6	132572146	132572156	+	1	NA	exon (NM_011174, exon 2 of 2)	exon (NM_011174, exon 2 of 2)	2309	NM_011174	19131	Mm.425348	NM_011174	ENSMUSG00000059934	Prh1	MP2|Prp	proline rich protein HaeIII subfamily 1	protein-coding
mm_98479.1	chr11	94950750	94950838	+	1	NA	exon (NM_007742, exon 49 of 51)	exon (NM_007742, exon 49 of 51)	14570	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_55782.1	chr6	81965926	81965962	-	1	NA	promoter-TSS (NM_026490)	promoter-TSS (NM_026490)	5	NM_026490	56284	Mm.276293	NM_026490	ENSMUSG00000030045	Mrpl19	9030416F12Rik|9130412E02Rik|D6Ertd157e|MRP-L15|RLX1|Rpml15	mitochondrial ribosomal protein L19	protein-coding
mm_35812.1	chr4	46749027	46749030	-	1	NA	intron (NM_001081141, intron 8 of 18)	L1MC5a|LINE|L1	-98829	NM_198664	381605	Mm.331595	NM_198664	ENSMUSG00000039813	Tbc1d2	A630005A06Rik|BC022630|Gm1037|PARIS-1|PARIS1	TBC1 domain family, member 2	protein-coding
mm_129965.1	chr15	85581837	85581913	-	1	NA	promoter-TSS (NM_009528)	promoter-TSS (NM_009528)	-54	NM_009528	22422	Mm.306946	NM_009528	ENSMUSG00000022382	Wnt7b	Wnt-7b	wingless-type MMTV integration site family, member 7B	protein-coding
mm_37357.1	chr4	120570217	120570234	-	1	NA	promoter-TSS (NM_016748)	promoter-TSS (NM_016748)	51	NM_016748	51797	Mm.1815	NM_016748	ENSMUSG00000028633	Ctps	Ctps1	cytidine 5'-triphosphate synthase	protein-coding
mm_145870.1	chr18	65465944	65465970	+	1	NA	intron (NM_172833, intron 12 of 15)	PB1D7|SINE|Alu	34960	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_148057.1	chr18	72148281	72148291	-	1	NA	intron (NM_007831, intron 1 of 28)	Lx7|LINE|L1	202783	NM_007831	13176	Mm.167882	NM_007831	ENSMUSG00000060534	Dcc	C030036D22Rik|Igdcc1	deleted in colorectal carcinoma	protein-coding
mm_85515.1	chr9	106399704	106399705	-	1	NA	Intergenic	Intergenic	-29707	NM_001324533	19944	Mm.288696	NM_009082	ENSMUSG00000048758	Rpl29	Rpl43	ribosomal protein L29	protein-coding
mm_69756.1	chr7	140999270	140999306	-	1	NA	Intergenic	Intergenic	11456	NM_025378	66141	Mm.141021	NM_025378	ENSMUSG00000025492	Ifitm3	1110004C05Rik|Cd225|Cdw217|DSPA2b|Fgls|IP15|mil-1	interferon induced transmembrane protein 3	protein-coding
mm_155683.1	chrX	93675344	93675376	+	1	NA	exon (NM_211138, exon 1 of 8)	exon (NM_211138, exon 1 of 8)	248	NM_211138	236899	Mm.166467	NM_177546	ENSMUSG00000035246	Pcyt1b	AW045697|CTTbeta	phosphate cytidylyltransferase 1, choline, beta isoform	protein-coding
mm_14606.1	chr2	136502051	136502061	+	1	NA	Intergenic	Intergenic	-30265	NM_175667	319196	Mm.477841	NM_175667	ENSMUSG00000074771	Ankef1	AV276460|Ankrd5	ankyrin repeat and EF-hand domain containing 1	protein-coding
mm_118313.1	chr13	113101987	113101993	-	1	NA	Intergenic	Intergenic	-1009	NM_010370	14938	Mm.15510	NM_010370	ENSMUSG00000023132	Gzma	AW494114|Ctla-3|Ctla3|Hf|Hf1|SE1|TSP-1|TSP1	granzyme A	protein-coding
mm_168824.1	chr12	22467008	22467018	-	1	NA	Intergenic	CpG	-310367	NR_136920	100043416		NM_001004167	ENSMUSG00000093846	Gm4425	EG432637|Gm5433	KRAB-domain protein pseudogene	pseudo
mm_159762.1	chr5	92388233	92388233	+	1	NA	promoter-TSS (NM_181728)	promoter-TSS (NM_181728)	99	NM_001310665	109979	Mm.263514	NM_181728	ENSMUSG00000034842	Art3	4930569O04Rik|ARTC3	ADP-ribosyltransferase 3	protein-coding
mm_88840.1	chr10	80871801	80871824	+	1	NA	Intergenic	Intergenic	-8004	NM_001081688	432478	Mm.235302	NM_001081688	ENSMUSG00000059406	Tmprss9	Serase-1B	transmembrane protease, serine 9	protein-coding
mm_34864.1	chr4	155557164	155557200	+	1	NA	exon (NM_008142, exon 11 of 12)	exon (NM_008142, exon 11 of 12)	-5210	NM_138671	192185	Mm.28347	NM_138671	ENSMUSG00000029063	Nadk	4432404C02Rik|BC004012	NAD kinase	protein-coding
mm_93608.1	chr10	117234423	117234431	-	1	NA	exon (NM_029906, exon 4 of 4)	exon (NM_029906, exon 4 of 4)	4254	NM_029906	77397	Mm.118350	NM_029906	ENSMUSG00000020177	9530003J23Rik	Lyzf1	RIKEN cDNA 9530003J23 gene	protein-coding
mm_123302.1	chr14	61648812	61648814	-	1	NA	intron (NR_028264, intron 1 of 6)	CpG	-16703	NR_029733	387174		NR_029733	ENSMUSG00000093007	Mir15a	Mirn15a|mir-15a|mmu-mir-15a	microRNA 15a	ncRNA
mm_168017.1	chrY	90737527	90737539	+	1	NA	Intergenic	IMPB_01|Satellite|Satellite	17517	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_111123.1	chr12	81333130	81333220	-	1	NA	promoter-TSS (NM_080440)	promoter-TSS (NM_080440)	5	NM_001167920	110893	Mm.443748	NM_080440	ENSMUSG00000079055	Slc8a3	AW742262|Ncx3	solute carrier family 8 (sodium/calcium exchanger), member 3	protein-coding
mm_4250.1	chr1	171408114	171408133	+	1	NA	exon (NM_001005508, exon 12 of 12)	exon (NM_001005508, exon 12 of 12)	-3190	NM_001305678	22278	Mm.8	NM_009480	ENSMUSG00000026641	Usf1	bHLHb11	upstream transcription factor 1	protein-coding
mm_110566.1	chr12	55821158	55821195	-	1	NA	5' UTR (NM_019994, exon 1 of 41)	5' UTR (NM_019994, exon 1 of 41)	340	NM_019994	56784	Mm.292180	NM_019994	ENSMUSG00000021027	Ralgapa1	2310003F20Rik|4930400K19Rik|AI563624|GRIPE|Garnl1|Tulip1|mKIAA0884	Ral GTPase activating protein, alpha subunit 1	protein-coding
mm_105503.1	chr11	106160709	106160721	-	1	NA	promoter-TSS (NM_172397)	promoter-TSS (NM_172397)	-573	NM_172397	67803	Mm.21687	NM_172397	ENSMUSG00000040699	Limd2	0610025L06Rik|AI413966	LIM domain containing 2	protein-coding
mm_148887.1	chr19	6871126	6871138	+	1	NA	Intergenic	ID_B1|SINE|B4	-12921	NM_001081291	78317	Mm.329596	NM_198008	ENSMUSG00000047810	Ccdc88b	2610041P08Rik|Ccdc88	coiled-coil domain containing 88B	protein-coding
mm_116343.1	chr13	38503589	38503601	-	1	NA	intron (NM_001289598, intron 8 of 9)	intron (NM_001289598, intron 8 of 9)	24319	NM_001289599	105245	Mm.28622	NM_145367	ENSMUSG00000038991	Txndc5	AL022641|ERp46|PC-TRP	thioredoxin domain containing 5	protein-coding
mm_7151.1	chr1	91406042	91406072	-	1	NA	promoter-TSS (NR_026924)	promoter-TSS (NR_026924)	-28	NR_026924	67086	Mm.396158	NR_026924	ENSMUSG00000100253	1700020N18Rik	-	RIKEN cDNA 1700020N18 gene	ncRNA
mm_39357.1	chr5	9101237	9101302	+	1	NA	5' UTR (NM_001081029, exon 2 of 5)	5' UTR (NM_001081029, exon 2 of 5)	532	NM_001081029	652925	Mm.439954	NM_001081029	ENSMUSG00000079659	Tmem243	4930420K17Rik|E030031F02Rik	transmembrane protein 243, mitochondrial	protein-coding
mm_164468.1	chr16	61947320	61947320	-	1	NA	Intergenic	Intergenic	839396	NM_178925	106338	Mm.26321	NM_178925	ENSMUSG00000050312	Nsun3	6720484A09Rik|AU022521	NOL1/NOP2/Sun domain family member 3	protein-coding
mm_39334.1	chr5	8798140	8798164	+	1	NA	promoter-TSS (NM_011075)	promoter-TSS (NM_011075)	5	NM_011075	18669	Mm.146649	NM_011075	ENSMUSG00000028970	Abcb1b	Abcb1|Mdr1|Mdr1b|Pgy-1|Pgy1|mdr	ATP-binding cassette, sub-family B (MDR/TAP), member 1B	protein-coding
mm_93260.1	chr10	95564066	95564091	-	1	NA	promoter-TSS (NM_027722)	promoter-TSS (NM_027722)	89	NM_027722	71207	Mm.24397	NM_027722	ENSMUSG00000020029	Nudt4	4933436C10Rik|DIPP2|DIPP2alpha|DIPP2beta|HDCMB47P	nudix (nucleoside diphosphate linked moiety X)-type motif 4	protein-coding
mm_151080.1	chr19	47619752	47619816	+	1	NA	exon (NM_001164639, exon 9 of 18)	exon (NM_001164639, exon 9 of 18)	39765	NM_001164639	20874	Mm.281011	NM_009289	ENSMUSG00000025060	Slk	9A2|AV021402|AW411554|Etk4|SMAK|Stk2|mKIAA0204|mSLK	STE20-like kinase	protein-coding
mm_34752.1	chr4	152318724	152318759	+	1	NA	promoter-TSS (NM_001033489)	promoter-TSS (NM_001033489)	-116	NM_001033489	433809	Mm.156205	NM_001033489	ENSMUSG00000058498	Rnf207	D330010C22Rik|Gm143	ring finger protein 207	protein-coding
mm_107030.1	chr12	13303251	13303262	+	1	NA	intron (NM_027706, intron 10 of 51)	intron (NM_027706, intron 10 of 51)	34129	NM_027706	71169	Mm.177520	NM_027706	ENSMUSG00000020576	Nbas	4933425L03Rik|Nag	neuroblastoma amplified sequence	protein-coding
mm_97395.1	chr11	77811215	77811227	+	1	NA	intron (NM_001291214, intron 1 of 38)	intron (NM_001291214, intron 1 of 38)	9923	NM_001291215	360013	Mm.341248	NM_011586	ENSMUSG00000000631	Myo18a	MAJN|MyoPDZ|MysPDZ|SP-R210	myosin XVIIIA	protein-coding
mm_88319.1	chr10	75564169	75564179	+	1	NA	Intergenic	Intergenic	-3844	NM_198860	192734	Mm.259320	NM_198860	ENSMUSG00000046807	Lrrc75b	AI646023|Fam211b	leucine rich repeat containing 75B	protein-coding
mm_59171.1	chr7	24402862	24402873	+	1	NA	intron (NM_028047, intron 1 of 13)	intron (NM_028047, intron 1 of 13)	3239	NM_028047	71997	Mm.150977	NM_028047	ENSMUSG00000002210	Smg9	1500002O20Rik|AI429693|N28092	smg-9 homolog, nonsense mediated mRNA decay factor (C. elegans)	protein-coding
mm_147062.1	chr18	34954303	34954359	-	1	NA	promoter-TSS (NM_010481)	promoter-TSS (NM_010481)	20	NM_010481	15526	Mm.209419	NM_010481	ENSMUSG00000024359	Hspa9	74kDa|Csa|Grp75|Hsc74|Hsp74|Hsp74a|Hspa9a|Mortalin|Mot-2|Mot2|Mthsp70|Pbp74	heat shock protein 9	protein-coding
mm_52344.1	chr6	110776553	110776556	+	1	NA	intron (NM_001346640, intron 1 of 10)	B3A|SINE|B2	130956	NM_177328	108073	Mm.240881	NM_177328	ENSMUSG00000056755	Grm7	6330570A01Rik|BB176677|C030018L03|E130018M02Rik|Gpr1g|Gprc1g|SMN2|Tg(SMN2)89Ahmb|mGluR7	glutamate receptor, metabotropic 7	protein-coding
mm_58668.1	chr7	7171347	7171373	+	1	NA	promoter-TSS (NM_146179)	promoter-TSS (NM_146179)	7	NM_146179	232854	Mm.184857	NM_146179	ENSMUSG00000034538	Zfp418	A230102I05Rik	zinc finger protein 418	protein-coding
mm_145652.1	chr18	61129274	61129296	+	1	NA	exon (NM_001037859, exon 19 of 22)	exon (NM_001037859, exon 19 of 22)	11817	NR_105949	102466212		NR_105949	ENSMUSG00000098389	Mir6983	Gm27496|mmu-mir-6983	microRNA 6983	ncRNA
mm_59485.1	chr7	27465716	27465732	+	1	NA	exon (NM_144923, exon 5 of 5)	exon (NM_144923, exon 5 of 5)	-8116	NM_133210	170742	Mm.200120	NM_133210	ENSMUSG00000055200	Sertad3	AW124805|D1Mgi51|Rbt1|Sei3	SERTA domain containing 3	protein-coding
mm_103270.1	chr11	72037475	72037495	-	1	NA	promoter-TSS (NM_053245)	promoter-TSS (NM_053245)	24	NM_053245	114230	Mm.95707	NM_053245	ENSMUSG00000040554	Aipl1	A930007I01Rik	aryl hydrocarbon receptor-interacting protein-like 1	protein-coding
mm_149720.1	chr19	21778308	21778318	+	1	NA	promoter-TSS (NM_031997)	promoter-TSS (NM_031997)	-27	NM_001033759	83921	Mm.329776	NM_031997	ENSMUSG00000024754	Tmem2	-	transmembrane protein 2	protein-coding
mm_73774.1	chr8	116537981	116537983	+	1	NA	Intergenic	Intergenic	32967	NM_029297	75465	Mm.23114	NM_029297	ENSMUSG00000034467	Dynlrb2	1700009A04Rik|DNLC2B|Dncl2b	dynein light chain roadblock-type 2	protein-coding
mm_137408.1	chr17	26111395	26111423	+	1	NA	Intergenic	Intergenic	-1907	NM_021793	60455	Mm.304656	NM_021793	ENSMUSG00000024180	Tmem8	AW490096|M83|Tmem8a	transmembrane protein 8 (five membrane-spanning domains)	protein-coding
mm_9065.1	chr1	167689038	167689049	-	1	NA	promoter-TSS (NM_033652)	promoter-TSS (NM_033652)	-515	NM_033652	110648	Mm.330081	NM_033652	ENSMUSG00000026686	Lmx1a	Lmx1.1|dr|dreher|sst	LIM homeobox transcription factor 1 alpha	protein-coding
mm_36145.1	chr4	59474818	59474843	-	1	NA	3' UTR (NM_144904, exon 15 of 15)	3' UTR (NM_144904, exon 15 of 15)	-36197	NM_001163288	634731	Mm.483589	NM_001163288	ENSMUSG00000038578	Susd1	A530080P10|Gm12528|OTTMUSG00000007332	sushi domain containing 1	protein-coding
mm_86586.1	chr10	13060700	13060723	+	1	NA	Intergenic	Intergenic	-30077	NM_009538	22634	Mm.287857	NM_009538	ENSMUSG00000019817	Plagl1	Lot1|Zac1	pleiomorphic adenoma gene-like 1	protein-coding
mm_42430.1	chr5	115341316	115341324	+	1	NA	promoter-TSS (NM_026933)	promoter-TSS (NM_026933)	73	NM_026933	69076	Mm.27951	NM_026933	ENSMUSG00000029535	Triap1	1810015M01Rik|AU020874|AU043831|P53csv|Wf-1	TP53 regulated inhibitor of apoptosis 1	protein-coding
mm_104880.1	chr11	99493113	99493129	-	1	NA	promoter-TSS (NM_033373)	promoter-TSS (NM_033373)	-11	NM_033373	94179	Mm.290657	NM_033373	ENSMUSG00000006777	Krt23	CK23|Haik1|K23|Krt1-23	keratin 23	protein-coding
mm_40709.1	chr5	65863654	65863656	+	1	NA	promoter-TSS (NM_001081105)	promoter-TSS (NM_001081105)	86	NM_001081105	74734	Mm.20323	NM_001081105	ENSMUSG00000029204	Rhoh	5830400A04Rik|AU019774|Arhh	ras homolog family member H	protein-coding
mm_163463.1	chr12	101145537	101145552	+	1	NA	promoter-TSS (NR_033653)	promoter-TSS (NR_033653)	-65	NR_033653	74947	Mm.488905	NR_033653	ENSMUSG00000092054	Kif4-ps	4930463M05Rik|Kif4b	kinesin family member 4, pseudogene	pseudo
mm_110628.1	chr12	57197312	57197330	-	1	NA	5' UTR (NM_172577, exon 1 of 10)	5' UTR (NM_172577, exon 1 of 10)	151	NM_172577	217593	Mm.32835	NM_172577	ENSMUSG00000035472	Slc25a21	9930033G19Rik|A630030I10|BB158148	solute carrier family 25 (mitochondrial oxodicarboxylate carrier), member 21	protein-coding
mm_9343.1	chr1	172057590	172057598	-	1	NA	promoter-TSS (NM_010916)	promoter-TSS (NM_010916)	2	NM_010916	18071	Mm.2474	NM_010916	ENSMUSG00000051251	Nhlh1	Hen1|Nscl|Tal2|bHLHa35	nescient helix loop helix 1	protein-coding
mm_133253.1	chr16	77329196	77329245	+	1	NA	promoter-TSS (NR_015543)	promoter-TSS (NR_015543)	-108	NR_015543	77994	Mm.394688	NR_015543	ENSMUSG00000090386	Mir99ahg	2810055G20Rik|D730043B02Rik	Mir99a and Mirlet7c-1 host gene (non-protein coding)	ncRNA
mm_127577.1	chr15	102296408	102296408	+	1	NA	5' UTR (NM_001014976, exon 1 of 31)	5' UTR (NM_001014976, exon 1 of 31)	115	NM_001014976	105988	Mm.288324	NM_001014976	ENSMUSG00000058290	Espl1	AL024103|AU045071|Cerp|ESP1|PRCE|SSE	extra spindle pole bodies 1, separase	protein-coding
mm_75921.1	chr8	71486038	71486056	-	1	NA	promoter-TSS (NM_001164679)	promoter-TSS (NM_001164679)	20	NM_001164679	382014	Mm.260360	NM_001164679	ENSMUSG00000034863	Ano8	BC053460|Tmem16h	anoctamin 8	protein-coding
mm_79755.1	chr9	62373604	62373630	+	1	NA	exon (NM_009672, exon 4 of 7)	exon (NM_009672, exon 4 of 7)	32274	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	protein-coding
mm_166750.1	chr6	125321813	125321833	+	1	NA	5' UTR (NM_011324, exon 1 of 12)	5' UTR (NM_011324, exon 1 of 12)	483	NM_011324	20276	Mm.144114	NM_011324	ENSMUSG00000030340	Scnn1a	ENaC|SCNEA|Scnn1|mENaC	sodium channel, nonvoltage-gated 1 alpha	protein-coding
mm_82073.1	chr9	122923051	122923092	+	1	NA	promoter-TSS (NM_009544)	promoter-TSS (NM_009544)	-7	NM_009544	22646	Mm.290595	NM_009544	ENSMUSG00000057895	Zfp105	AW557864	zinc finger protein 105	protein-coding
mm_72071.1	chr8	71534264	71534266	+	1	NA	TTS (NM_198095)	TTS (NM_198095)	3172	NM_198095	69550	Mm.260325	NM_198095	ENSMUSG00000046718	Bst2	2310015I10Rik|Bst-2|C87040|CD317|DAMP-1|GREG	bone marrow stromal cell antigen 2	protein-coding
mm_78693.1	chr9	40806639	40806642	+	1	NA	Intergenic	Intergenic	5367	NM_031165	15481	Mm.290774	NM_031165	ENSMUSG00000015656	Hspa8	2410008N15Rik|Hsc70|Hsc71|Hsc73|Hsp73|Hspa10	heat shock protein 8	protein-coding
mm_73229.1	chr8	104101655	104101708	+	1	NA	promoter-TSS (NM_009868)	promoter-TSS (NM_009868)	56	NM_009868	12562	Mm.21767	NM_009868	ENSMUSG00000031871	Cdh5	7B4|AA408225|Cd144|VE-Cad|VECD|VEcad|Vec	cadherin 5	protein-coding
mm_162989.1	chr11	23633673	23633675	-	1	NA	promoter-TSS (NM_001347242)	promoter-TSS (NM_001347242)	-43	NM_027860	71675	Mm.48031	NM_027860	ENSMUSG00000042208	0610010F05Rik	Kiaa1841|mKIAA1841	RIKEN cDNA 0610010F05 gene	protein-coding
mm_168587.1	chr1	173535794	173535794	-	1	NA	5' UTR (NM_001024721, exon 1 of 5)	5' UTR (NM_001024721, exon 1 of 5)	163	NM_001024721	545384	Mm.371698	NM_001024721	ENSMUSG00000070501	Ifi214	Pyhin-B|p214	interferon activated gene 214	protein-coding
mm_130055.1	chr15	89178064	89178074	-	1	NA	intron (NM_138749, intron 1 of 37)	intron (NM_138749, intron 1 of 37)	2719	NM_001284506	140570	Mm.267514	NM_138749	ENSMUSG00000036606	Plxnb2	Debt|plexin-B2	plexin B2	protein-coding
mm_129203.1	chr15	76512184	76512194	-	1	NA	promoter-TSS (NM_010046)	promoter-TSS (NM_010046)	-371	NM_010046	13350	Mm.22633	NM_010046	ENSMUSG00000022555	Dgat1	ARAT|C75990|D15Ertd23e|Dgat	diacylglycerol O-acyltransferase 1	protein-coding
mm_126380.1	chr15	80173251	80173267	+	1	NA	promoter-TSS (NM_010795)	promoter-TSS (NM_010795)	-462	NM_010795	17309	Mm.299693	NM_010795	ENSMUSG00000042428	Mgat3	1110038J12Rik|AI848272|GnT-III	mannoside acetylglucosaminyltransferase 3	protein-coding
mm_60320.1	chr7	44216457	44216466	+	1	NA	promoter-TSS (NM_008456)	promoter-TSS (NM_008456)	-13	NM_008456	16622	Mm.443373	NM_008456	ENSMUSG00000066512	Klk1b5	Klk5|kallikrein|mGK-5	kallikrein 1-related peptidase b5	protein-coding
mm_160157.1	chr7	44188237	44188237	+	1	NA	promoter-TSS (NM_010643)	promoter-TSS (NM_010643)	1	NM_010643	16617	Mm.483098	NM_010643	ENSMUSG00000063713	Klk1b24	Klk24|mGk-24	kallikrein 1-related peptidase b24	protein-coding
mm_30407.1	chr3	152253756	152253766	-	1	NA	intron (NM_199465, intron 2 of 12)	intron (NM_199465, intron 2 of 12)	12559	NM_199465	68810	Mm.200188	NM_199465	ENSMUSG00000039103	Nexn	1110046H09Rik|AA553326|NELIN	nexilin	protein-coding
mm_162036.1	chr19	55311755	55311755	-	1	NA	exon (NM_025883, exon 4 of 11)	exon (NM_025883, exon 4 of 11)	4277	NM_025883	66980	Mm.386789	NM_025883	ENSMUSG00000024982	Zdhhc6	2400007G07Rik|5930409M18Rik|AI462345|C77369	zinc finger, DHHC domain containing 6	protein-coding
mm_137995.1	chr17	33638131	33638141	+	1	NA	promoter-TSS (NR_028279)	promoter-TSS (NR_028279)	41	NR_028279	378460	Mm.272606	NM_001002842	ENSMUSG00000032739	Pram1	AY665714	PML-RAR alpha-regulated adaptor molecule 1	protein-coding
mm_74585.1	chr8	11314024	11314027	-	1	NA	intron (NM_009932, intron 3 of 47)	intron (NM_009932, intron 3 of 47)	-1199	NM_009931	12826	Mm.738	NM_009931	ENSMUSG00000031502	Col4a1	Bru|Col4a-1|Raw|Svc	collagen, type IV, alpha 1	protein-coding
mm_20435.1	chr2	129306596	129306621	-	1	NA	exon (NM_010554, exon 4 of 7)	exon (NM_010554, exon 4 of 7)	3364	NM_010554	16175	Mm.15534	NM_010554	ENSMUSG00000027399	Il1a	Il-1a	interleukin 1 alpha	protein-coding
mm_168894.1	chr1	25016779	25016795	+	1	NA	Intergenic	Intergenic	261167	NM_001204913	100504323	Mm.484176	NM_001204913		Gm20172	-	predicted gene, 20172	protein-coding
mm_142693.1	chr17	47833226	47833254	-	1	NA	promoter-TSS (NM_010783)	promoter-TSS (NM_010783)	51	NM_001276391	17240	Mm.329100	NM_010783	ENSMUSG00000032717	Mdfi	I-mf|I-mfa	MyoD family inhibitor	protein-coding
mm_66715.1	chr7	46059140	46059195	-	1	NA	intron (NM_153057, intron 15 of 30)	intron (NM_153057, intron 15 of 30)	25471	NM_153057	211548	Mm.274811	NM_153057	ENSMUSG00000030835	Nomo1	D7Ertd156e|Nomo|pM5	nodal modulator 1	protein-coding
mm_16898.1	chr2	13271439	13271446	-	1	NA	promoter-TSS (NM_009105)	promoter-TSS (NM_009105)	-27	NM_009105	20163	Mm.905	NM_009105	ENSMUSG00000026727	Rsu1	RsuI|rsp-1	Ras suppressor protein 1	protein-coding
mm_172296.1	chr7	100285577	100285580	+	1	NA	promoter-TSS (NM_177161)	promoter-TSS (NM_177161)	58	NM_177161	320452	Mm.150294	NM_177161	ENSMUSG00000051048	P4ha3	D930031A02Rik	procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide III	protein-coding
mm_72271.1	chr8	75099957	75099971	+	1	NA	exon (NM_010442, exon 5 of 5)	exon (NM_010442, exon 5 of 5)	6346	NM_010442	15368	Mm.276389	NM_010442	ENSMUSG00000005413	Hmox1	D8Wsu38e|HO-1|HO1|Hemox|Hmox|Hsp32	heme oxygenase 1	protein-coding
mm_60337.1	chr7	44335766	44335783	+	1	NA	intron (NM_001034115, intron 15 of 24)	intron (NM_001034115, intron 15 of 24)	25510	NM_001034115	243961	Mm.360368	NM_001034115	ENSMUSG00000038738	Shank1	-	SH3/ankyrin domain gene 1	protein-coding
mm_151092.1	chr19	47732946	47732950	+	1	NA	exon (NM_026377, exon 2 of 4)	exon (NM_026377, exon 2 of 4)	1192	NM_026377	67788	Mm.181610	NM_026377	ENSMUSG00000025066	Sfr1	6330577E15Rik|Meir5	SWI5 dependent recombination repair 1	protein-coding
mm_55052.1	chr6	49045364	49045392	-	1	NA	exon (NM_053110, exon 4 of 11)	exon (NM_053110, exon 4 of 11)	8860	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_19750.1	chr2	104849729	104849745	-	1	NA	5' UTR (NM_178695, exon 1 of 6)	5' UTR (NM_178695, exon 1 of 6)	113	NM_178695	228413	Mm.259609	NM_178695	ENSMUSG00000027171	Prrg4	9930111I18Rik|TMG4	proline rich Gla (G-carboxyglutamic acid) 4 (transmembrane)	protein-coding
mm_133245.1	chr16	77115619	77115631	+	1	NA	3' UTR (NM_013918, exon 24 of 24)	3' UTR (NM_013918, exon 24 of 24)	101556	NM_013918	30940	Mm.40986	NM_013918	ENSMUSG00000022867	Usp25	-	ubiquitin specific peptidase 25	protein-coding
mm_137324.1	chr17	24932847	24932847	+	1	NA	intron (NM_013931, intron 1 of 31)	intron (NM_013931, intron 1 of 31)	4130	NM_001163448	30957	Mm.43081	NM_013931	ENSMUSG00000024163	Mapk8ip3	BB120594|D17Wsu15e|JIP-3|JSAP1|JSAP1a|JSAP1b|JSAP1c|JSAP1d|Jip3|Syd2|mKIAA1066	mitogen-activated protein kinase 8 interacting protein 3	protein-coding
mm_128542.1	chr15	54986858	54986868	-	1	NA	Intergenic	Intergenic	-66717	NM_001285994	18606	Mm.250256	NM_015744	ENSMUSG00000022425	Enpp2	ATX|E-NPP 2|Npps2|PD-Ialpha|Pdnp2|lysoPLD	ectonucleotide pyrophosphatase/phosphodiesterase 2	protein-coding
mm_164816.1	chr18	34409398	34409407	+	1	NA	promoter-TSS (NM_016927)	promoter-TSS (NM_016927)	-21	NM_001163004	53871	Mm.445792	NM_016927	ENSMUSG00000014503	Pkd2l2	TRPP5	polycystic kidney disease 2-like 2	protein-coding
mm_149213.1	chr19	9984248	9984292	+	1	NA	TTS (NM_011913)	TTS (NM_011913)	1624	NM_010239	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
mm_27308.1	chr3	50366434	50366453	-	1	NA	3' UTR (NM_011990, exon 12 of 12)	3' UTR (NM_011990, exon 12 of 12)	77170	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_131618.1	chr16	19760796	19760798	+	1	NA	5' UTR (NM_001159407, exon 2 of 6)	5' UTR (NM_001159407, exon 2 of 6)	563	NM_001159407	108105	Mm.33935	NM_054052	ENSMUSG00000022686	B3gnt5	beta3GnT5	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5	protein-coding
mm_107778.1	chr12	60721759	60721762	+	1	NA	Intergenic	IAPEY_LTR|LTR|ERVK	800060	NR_045049	100504101	Mm.235026	NR_045049		Gm20063	-	predicted gene, 20063	ncRNA
mm_122639.1	chr14	51198941	51198946	-	1	NA	Intergenic	Intergenic	-3020	NM_007449	11731	Mm.377077	NM_007449	ENSMUSG00000047894	Ang2	Angrp|Raa3|Rnase5b	angiogenin, ribonuclease A family, member 2	protein-coding
mm_20676.1	chr2	132264214	132264224	-	1	NA	intron (NM_138651, intron 1 of 12)	intron (NM_138651, intron 1 of 12)	1071	NM_138651	110911	Mm.284503	NM_138651	ENSMUSG00000058793	Cds2	5730450N06Rik|5730460C18Rik|AI854580|D2Wsu127e	CDP-diacylglycerol synthase (phosphatidate cytidylyltransferase) 2	protein-coding
mm_120035.1	chr14	56206374	56206400	+	1	NA	exon (NM_010374, exon 3 of 5)	exon (NM_010374, exon 3 of 5)	5020	NM_010374	14943	Mm.457976	NM_010374	ENSMUSG00000015441	Gzmf	CCP4|Ctla-7|Ctla7|MCSP-3	granzyme F	protein-coding
mm_164390.1	chr16	32539114	32539118	+	1	NA	Intergenic	RMER17C2|LTR|ERVK	42835	NM_199309	245308	Mm.76859	NM_199309	ENSMUSG00000052363	Zdhhc19	Gm1744|Gm616	zinc finger, DHHC domain containing 19	protein-coding
mm_125229.1	chr15	34134316	34134324	+	1	NA	exon (NM_026002, exon 9 of 12)	exon (NM_026002, exon 9 of 12)	51601	NM_026002	67154	Mm.130883	NM_026002	ENSMUSG00000022255	Mtdh	2610103J23Rik|3D3|3D3/Lyric|AEG-1|AV353288|D8Bwg1112e|Lyric	metadherin	protein-coding
mm_165365.1	chr2	126556523	126556532	+	1	NA	intron (NM_011978, intron 1 of 9)	intron (NM_011978, intron 1 of 9)	3503	NM_011978	26458	Mm.290044	NM_011978	ENSMUSG00000027359	Slc27a2	ACSVL1|FATP2|VLCS|Vlac|Vlacs	solute carrier family 27 (fatty acid transporter), member 2	protein-coding
mm_26736.1	chr3	5576234	5576244	-	1	NA	promoter-TSS (NM_008994)	promoter-TSS (NM_008994)	9	NM_001163301	19302	Mm.132336	NM_008994	ENSMUSG00000040374	Pex2	D3Ertd138e|PAF-1|PMP35|Pxmp3	peroxisomal biogenesis factor 2	protein-coding
mm_108269.1	chr12	78749028	78749041	+	1	NA	promoter-TSS (NM_019579)	promoter-TSS (NM_019579)	87	NM_019579	56217	Mm.425777	NM_019579	ENSMUSG00000021112	Mpp5	3830420B02Rik|AI255216|AI644496|Pals1	membrane protein, palmitoylated 5 (MAGUK p55 subfamily member 5)	protein-coding
mm_2274.1	chr1	91250483	91250508	+	1	NA	intron (NM_026454, intron 1 of 9)	CpG	176	NM_026454	67921	Mm.337238	NM_026454	ENSMUSG00000034343	Ube2f	2510010F15Rik|AI851109	ubiquitin-conjugating enzyme E2F (putative)	protein-coding
mm_107118.1	chr12	18514466	18514486	+	1	NA	promoter-TSS (NM_001201330)	promoter-TSS (NM_001201330)	-34	NM_001033157	236366	Mm.352227	NM_001033157	ENSMUSG00000073197	5730507C01Rik	-	RIKEN cDNA 5730507C01 gene	protein-coding
mm_42579.1	chr5	117273781	117273808	+	1	NA	exon (NM_001199685, exon 21 of 21)	exon (NM_001199685, exon 21 of 21)	13770	NM_018858	23980	Mm.195898	NM_018858	ENSMUSG00000032959	Pebp1	HCNP|Pbp|Pbp1|Pbpr|Rkip	phosphatidylethanolamine binding protein 1	protein-coding
mm_46751.1	chr5	112121069	112121069	-	1	NA	Intergenic	Intergenic	-85694	NR_045377	75569	Mm.243721	NR_045377	ENSMUSG00000101683	1700028D13Rik	-	RIKEN cDNA 1700028D13 gene	ncRNA
mm_101387.1	chr11	24075701	24075702	-	1	NA	Intergenic	Intergenic	-2355	NM_016707	14025	Mm.53687	NM_016707	ENSMUSG00000000861	Bcl11a	2810047E18Rik|BCL-11A|Ctip1|D930021L15Rik|Evi9|Evi9a|Evi9b|Evi9c|mKIAA1809	B cell CLL/lymphoma 11A (zinc finger protein)	protein-coding
mm_45668.1	chr5	77211219	77211241	-	1	NA	promoter-TSS (NM_001289764)	promoter-TSS (NM_001289764)	-25	NM_001289767	69982	Mm.46106	NM_183284	ENSMUSG00000053030	Spink2	1700007F22Rik|AV038945|HUSI-II	serine peptidase inhibitor, Kazal type 2	protein-coding
mm_32492.1	chr4	108165450	108165524	+	1	NA	promoter-TSS (NM_026728)	promoter-TSS (NM_026728)	50	NM_001254754	52430	Mm.270783	NM_026728	ENSMUSG00000028601	Echdc2	1300017C12Rik|2610009M20Rik|D4Ertd765e	enoyl Coenzyme A hydratase domain containing 2	protein-coding
mm_93871.1	chr10	123196468	123196468	-	1	NA	intron (NM_001301628, intron 1 of 20)	CpG	551	NM_027604	14479	Mm.244209	NM_027604	ENSMUSG00000020124	Usp15	4921514G19Rik|AI327321|E430033I05Rik|Gcap18	ubiquitin specific peptidase 15	protein-coding
mm_22908.1	chr3	31017896	31017918	+	1	NA	intron (NM_008857, intron 1 of 17)	intron (NM_008857, intron 1 of 17)	-21059	NR_105975	102465610		NR_105975	ENSMUSG00000098890	Mir7008	Gm27752|mmu-mir-7008	microRNA 7008	ncRNA
mm_139403.1	chr17	52351511	52351543	+	1	NA	Intergenic	Intergenic	-251182	NM_001031811	211468	Mm.399068	NM_001031811	ENSMUSG00000035580	Kcnh8	C130090D05Rik|ELK|ELK1|ELK3|Kv12.1	potassium voltage-gated channel, subfamily H (eag-related), member 8	protein-coding
mm_120293.1	chr14	63138028	63138096	+	1	NA	exon (NM_007798, exon 6 of 10)	exon (NM_007798, exon 6 of 10)	15600	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_140630.1	chr17	12507097	12507107	-	1	NA	exon (NM_011395, exon 1 of 11)	exon (NM_011395, exon 1 of 11)	602	NM_011395	20519	Mm.99252	NM_011395	ENSMUSG00000023828	Slc22a3	EMT|Oct3|Orct3|Slca22a3	solute carrier family 22 (organic cation transporter), member 3	protein-coding
mm_80421.1	chr9	77917209	77917223	+	1	NA	promoter-TSS (NM_134255)	promoter-TSS (NM_134255)	-149	NM_134255	68801	Mm.430736	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	ELOVL family member 5, elongation of long chain fatty acids (yeast)	protein-coding
mm_11839.1	chr2	45112237	45112255	+	1	NA	promoter-TSS (NR_110571)	promoter-TSS (NR_110571)	-14	NR_110571	433424	Mm.441408	NR_110571	ENSMUSG00000052248	Zeb2os	Gm13476|OTTMUSG00000012358|Zeb2nat	zinc finger E-box binding homeobox 2, opposite strand	ncRNA
mm_67007.1	chr7	65338358	65338362	-	1	NA	intron (NM_009386, intron 5 of 27)	B1_Mur4|SINE|Alu	32884	NM_001163574	21872	Mm.4342	NM_009386	ENSMUSG00000030516	Tjp1	ZO1	tight junction protein 1	protein-coding
mm_58445.1	chr7	3299076	3299085	+	1	NA	3' UTR (NM_016969, exon 3 of 3)	3' UTR (NM_016969, exon 3 of 3)	-4452	NM_001291434	18752	Mm.7980	NM_011102	ENSMUSG00000078816	Prkcg	PKCgamma|Pkcc|Prkcc	protein kinase C, gamma	protein-coding
mm_63762.1	chr7	131116715	131116726	+	1	NA	exon (NM_007769, exon 45 of 47)	exon (NM_007769, exon 45 of 47)	29563	NM_173409	233918	Mm.78341	NM_173409	ENSMUSG00000013668	4933402N03Rik	4930412O05	RIKEN cDNA 4933402N03 gene	protein-coding
mm_64389.1	chr7	142488835	142488850	+	1	NA	intron (NM_001271508, intron 4 of 10)	intron (NM_001271508, intron 4 of 10)	-9994	NM_001347549	21957	Mm.389992	NM_011620	ENSMUSG00000061723	Tnnt3	fTnT	troponin T3, skeletal, fast	protein-coding
mm_96512.1	chr11	68473817	68473855	+	1	NA	exon (NM_177320, exon 2 of 19)	exon (NM_177320, exon 2 of 19)	-29183	NM_001004435	104709	Mm.234573	NM_001004435	ENSMUSG00000046207	Pik3r6	BB220380|p84|p84 PIKAP|p87(PIKAP)|p87PIKAP	phosphoinositide-3-kinase, regulatory subunit 6	protein-coding
mm_7594.1	chr1	125435892	125435900	-	1	NA	promoter-TSS (NM_023735)	promoter-TSS (NM_023735)	-169	NM_001205386	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding
mm_141669.1	chr17	33890585	33890652	-	1	NA	promoter-TSS (NM_001195298)	promoter-TSS (NM_001195298)	15	NM_001195298	100502766	Mm.335713	NM_001195298	ENSMUSG00000079553	Kifc1	100042970|Gm4137|HSET|KNSL2|Kifc5a|Knsl2a|Tctex-7|Tctex-7A|Tctex7|Tctex7a	kinesin family member C1	protein-coding
mm_33322.1	chr4	129084048	129084065	+	1	NA	exon (NM_029219, exon 9 of 9)	exon (NM_029219, exon 9 of 9)	-21474	NM_025452	66260	Mm.25295	NM_025452	ENSMUSG00000028786	Tmem54	1810017F10Rik|AI507302	transmembrane protein 54	protein-coding
mm_73848.1	chr8	117701065	117701084	+	1	NA	promoter-TSS (NM_008290)	promoter-TSS (NM_008290)	-872	NM_008290	15486	Mm.276466	NM_008290	ENSMUSG00000031844	Hsd17b2	AI194836|AI194967|AI255511	hydroxysteroid (17-beta) dehydrogenase 2	protein-coding
mm_1031.1	chr1	58755223	58755234	+	1	NA	3' UTR (NM_207653, exon 10 of 10)	3' UTR (NM_207653, exon 10 of 10)	24676	NM_001293805	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_28403.1	chr3	90242557	90242567	-	1	NA	promoter-TSS (NM_001307935)	promoter-TSS (NM_001307935)	-12	NM_001307935	78284	Mm.299952	NM_030080	ENSMUSG00000027938	Creb3l4	1700012K17Rik|5330432F22Rik|AIBZIP|AV040530|AV258827|CREB4|JAL|TISP40|acre1	cAMP responsive element binding protein 3-like 4	protein-coding
mm_15658.1	chr2	163205654	163205658	+	1	NA	Intergenic	Intergenic	-19798	NM_001098799	269389	Mm.207709	NM_001098799	ENSMUSG00000074607	Tox2	AI851523|AV026525|BI987407|Gcx1|RxHMG1	TOX high mobility group box family member 2	protein-coding
mm_165169.1	chr2	26476450	26476490	+	1	NA	exon (NM_008714, exon 14 of 34)	exon (NM_008714, exon 14 of 34)	-6351	NR_105962	102465602		NR_105962	ENSMUSG00000098548	Mir6996	Gm27531|mmu-mir-6996	microRNA 6996	ncRNA
mm_80502.1	chr9	78615483	78615493	+	1	NA	promoter-TSS (NM_153098)	promoter-TSS (NM_153098)	-58	NM_153098	235505	Mm.32955	NM_153098	ENSMUSG00000046186	Cd109	9930012E15Rik|AI480638|GARP	CD109 antigen	protein-coding
mm_109140.1	chr12	106527894	106527896	+	1	NA	Intergenic	Intergenic	-80229	NR_036593	76639	Mm.375609	NR_036593	ENSMUSG00000092066	1700121N20Rik	-	RIKEN cDNA 1700121N20 gene	ncRNA
mm_37742.1	chr4	129595169	129595193	-	1	NA	exon (NM_018799, exon 6 of 11)	exon (NM_018799, exon 6 of 11)	5467	NM_018799	54709	Mm.250874	NM_018799	ENSMUSG00000028798	Eif3i	36kDa|D4Ertd632e|Eif3s2|Trip1	eukaryotic translation initiation factor 3, subunit I	protein-coding
mm_133840.1	chr16	96200536	96200556	+	1	NA	promoter-TSS (NM_015825)	promoter-TSS (NM_015825)	76	NM_015825	50795	Mm.28638	NM_015825	ENSMUSG00000040666	Sh3bgr	5430437A18Rik	SH3-binding domain glutamic acid-rich protein	protein-coding
mm_98755.1	chr11	96545584	96545598	+	1	NA	intron (NM_001033186, intron 4 of 12)	intron (NM_001033186, intron 4 of 12)	81000	NM_001177898	78473	Mm.395840	NM_001033186	ENSMUSG00000057058	Skap1	1700091G21Rik|Scap1|Skap-55	src family associated phosphoprotein 1	protein-coding
mm_13342.1	chr2	102787672	102787682	+	1	NA	3' UTR (NM_001077514, exon 11 of 11)	3' UTR (NM_001077514, exon 11 of 11)	81239	NM_001077515	20511	Mm.267547	NM_011393	ENSMUSG00000005089	Slc1a2	1700091C19Rik|2900019G14Rik|AI159670|Eaat2|GLT-1|GLT1|MGLT1	solute carrier family 1 (glial high affinity glutamate transporter), member 2	protein-coding
mm_80388.1	chr9	75625708	75625770	+	1	NA	promoter-TSS (NM_027309)	promoter-TSS (NM_027309)	7	NM_027309	70082	Mm.19119	NM_027309	ENSMUSG00000032184	Lysmd2	2210402C18Rik|AV033872|AW538442	LysM, putative peptidoglycan-binding, domain containing 2	protein-coding
mm_115612.1	chr13	12022285	12022298	-	1	NA	intron (NM_023868, intron 1 of 104)	B3A|SINE|B2	84654	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding
mm_76675.1	chr8	93812732	93812740	-	1	NA	non-coding (NR_026888, exon 1 of 1)	non-coding (NR_026888, exon 1 of 1)	819	NR_026888	75809	Mm.443272	NM_029449		4930488L21Rik	4930452J22Rik	RIKEN cDNA 4930488L21 gene	ncRNA
mm_47557.1	chr5	124393825	124393856	-	1	NA	exon (NM_001081203, exon 17 of 32)	exon (NM_001081203, exon 17 of 32)	32074	NM_001081203	243272	Mm.23879	NM_001081203	ENSMUSG00000038095	Sbno1	9330180L10Rik|AI849128|AW557836|BC021875|Sbno|mSno1|sno	strawberry notch homolog 1 (Drosophila)	protein-coding
mm_17772.1	chr2	32824959	32824962	-	1	NA	intron (NM_009295, intron 1 of 18)	intron (NM_009295, intron 1 of 18)	22272	NM_009295	20910	Mm.278865	NM_009295	ENSMUSG00000026797	Stxbp1	AI317162|AI326233|MMS10-G|Ms10g|Munc-18a|Munc18-1|N-sec1|Rb-sec1|Sxtbp1|Unc18-1|Unc18h|nsec1	syntaxin binding protein 1	protein-coding
mm_114768.1	chr13	88821475	88821520	+	1	NA	promoter-TSS (NM_001037987)	promoter-TSS (NM_001037987)	25	NM_001037987	13612	Mm.125580	NM_010103	ENSMUSG00000034488	Edil3	Del-1|Del1	EGF-like repeats and discoidin I-like domains 3	protein-coding
mm_7766.1	chr1	131199960	131199975	-	1	NA	exon (NM_001311094, exon 1 of 5)	exon (NM_001311094, exon 1 of 5)	218	NM_001311094	54354	Mm.248291	NM_018750	ENSMUSG00000026430	Rassf5	1300019G20Rik|Maxp1|Nore1|Nore1A|Nore1B|Rapl	Ras association (RalGDS/AF-6) domain family member 5	protein-coding
mm_102528.1	chr11	60932942	60932985	-	1	NA	intron (NM_008928, intron 1 of 11)	intron (NM_008928, intron 1 of 11)	906	NM_008928	26397	Mm.18494	NM_008928	ENSMUSG00000018932	Map2k3	AW212142|MEK3|MKK3|Prkmk3|mMKK3b	mitogen-activated protein kinase kinase 3	protein-coding
mm_103644.1	chr11	78965803	78965834	-	1	NA	exon (NM_010708, exon 10 of 11)	exon (NM_010708, exon 10 of 11)	19106	NM_001159301	16859	Mm.341434	NM_010708	ENSMUSG00000001123	Lgals9	AA407335|AI194909|AI265545|LGALS35|Lgals5|gal-9|galectin-9	lectin, galactose binding, soluble 9	protein-coding
mm_69650.1	chr7	139582793	139582808	-	1	NA	promoter-TSS (NM_183248)	promoter-TSS (NM_183248)	-3	NR_027857	14912	Mm.28308	NM_183248	ENSMUSG00000041309	Nkx6-2	Gtx|Nkx6.2	NK6 homeobox 2	protein-coding
mm_76085.1	chr8	79399452	79399462	-	1	NA	promoter-TSS (NM_008539)	promoter-TSS (NM_008539)	11	NM_008539	17125	Mm.223717	NM_008539	ENSMUSG00000031681	Smad1	AI528653|Madh1|Madr1|Mlp1|MusMLP	SMAD family member 1	protein-coding
mm_96018.1	chr11	59543033	59543039	+	1	NA	intron (NM_145827, intron 1 of 9)	intron (NM_145827, intron 1 of 9)	350	NM_145827	216799	Mm.54174	NM_145827	ENSMUSG00000032691	Nlrp3	AGTAVPRL|AII/AVP|Cias1|FCAS|FCU|MWS|Mmig1|NALP3|Pypaf1	NLR family, pyrin domain containing 3	protein-coding
mm_150352.1	chr19	34644577	34644599	+	1	NA	intron (NM_008331, intron 1 of 1)	intron (NM_008331, intron 1 of 1)	3699	NM_008331	15957	Mm.439751	NM_008331	ENSMUSG00000034459	Ifit1	ISG56|Ifi56|P56	interferon-induced protein with tetratricopeptide repeats 1	protein-coding
mm_78235.1	chr9	21616231	21616281	+	1	NA	promoter-TSS (NM_001174078)	promoter-TSS (NM_001174078)	87	NM_001174078	20586	Mm.286593	NM_011417	ENSMUSG00000032187	Smarca4	Brg1|HP1-BP72|SNF2beta|SW1/SNF|b2b508.1Clo|b2b692Clo	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	protein-coding
mm_109147.1	chr12	107159729	107159732	+	1	NA	Intergenic	Intergenic	-443406	NR_015512	71033	Mm.159404	NR_015512	ENSMUSG00000085820	4933406K04Rik	4930426M03Rik|4930485I22Rik|4933427G14Rik	RIKEN cDNA 4933406K04 gene	ncRNA
mm_68436.1	chr7	109960122	109960128	-	1	NA	exon (NM_021494, exon 1 of 23)	exon (NM_021494, exon 1 of 23)	297	NM_021494	19347	Mm.21904	NM_021494	ENSMUSG00000035901	Dennd5a	1500012B19Rik|AJ245569|AW496491|ORF37|Rab6ip1|mKIAA1091	DENN/MADD domain containing 5A	protein-coding
mm_132088.1	chr16	30692259	30692308	+	1	NA	Intergenic	Intergenic	92560	NM_177632	224093	Mm.28244	NM_177632	ENSMUSG00000046546	Fam43a	Tuf1	family with sequence similarity 43, member A	protein-coding
mm_150971.1	chr19	46501168	46501197	+	1	NA	promoter-TSS (NM_053100)	promoter-TSS (NM_053100)	-466	NM_053100	93679	Mm.392177	NM_053100	ENSMUSG00000025034	Trim8	AA408830|BB006755|GERP|Rnf27	tripartite motif-containing 8	protein-coding
mm_119901.1	chr14	54948135	54948150	+	1	NA	TTS (NR_029724)	TTS (NR_029724)	1000	NR_029724	387204		NR_029724	ENSMUSG00000065432	Mir208a	Mirn208|Mirn208a|mir-208|mir-208a|mmu-mir-208	microRNA 208a	ncRNA
mm_79237.1	chr9	50501066	50501091	+	1	NA	exon (NM_029639, exon 3 of 4)	exon (NM_029639, exon 3 of 4)	3727	NR_040714	69631	Mm.414996	NR_040714	ENSMUSG00000101304	Plet1os	2310014F07Rik	placenta expressed transcript 1, opposite strand	ncRNA
mm_76898.1	chr8	105816863	105816868	-	1	NA	intron (NM_145824, intron 2 of 13)	intron (NM_145824, intron 2 of 13)	10485	NM_145824	74334	Mm.4206	NM_145824	ENSMUSG00000037415	Ranbp10	4432417N03Rik	RAN binding protein 10	protein-coding
mm_165756.1	chr3	112489212	112489217	+	1	NA	Intergenic	MTC|LTR|ERVL-MaLR	607311	NR_045362	625585	Mm.389497	NR_045362	ENSMUSG00000104543	Gm6602	-	predicted gene 6602	ncRNA
mm_144362.1	chr18	20376724	20376740	+	1	NA	promoter-TSS (NM_181682)	promoter-TSS (NM_181682)	3	NM_181682	225256	Mm.269128	NM_181682	ENSMUSG00000061928	Dsg1b	Dsg5|dsg1-beta	desmoglein 1 beta	protein-coding
mm_4632.1	chr1	179668277	179668287	+	1	NA	promoter-TSS (NM_178653)	promoter-TSS (NM_178653)	51	NM_178653	109232	Mm.136458	NM_178653	ENSMUSG00000038936	Sccpdh	AW214504|C330023F11Rik	saccharopine dehydrogenase (putative)	protein-coding
mm_108968.1	chr12	102469167	102469181	+	1	NA	promoter-TSS (NM_013747)	promoter-TSS (NM_013747)	40	NM_001199004	27277	Mm.273370	NM_013747	ENSMUSG00000021192	Golga5	Ret-II	golgi autoantigen, golgin subfamily a, 5	protein-coding
mm_3807.1	chr1	158362331	158362411	+	1	NA	promoter-TSS (NM_001205204)	promoter-TSS (NM_001205204)	67	NM_001205204	11899	Mm.329586	NM_007495	ENSMUSG00000026587	Astn1	Astn|GC14|mKIAA0289	astrotactin 1	protein-coding
mm_172999.1	chrM	1614	1616	+	1	NA	NA	Intergenic	NA	NA								
mm_97642.1	chr11	79306657	79306676	+	1	NA	Intergenic	Intergenic	-33226	NM_010897	18015	Mm.255596	NM_010897	ENSMUSG00000020716	Nf1	AW494271|Dsk9|E030030H24Rik|Mhdadsk9|Nf-1	neurofibromin 1	protein-coding
mm_153969.1	chr19	47857993	47858028	-	1	NA	exon (NM_010362, exon 3 of 6)	exon (NM_010362, exon 3 of 6)	3037	NM_010362	14873	Mm.378931	NM_010362	ENSMUSG00000025068	Gsto1	AA407097|AI194287|AU018802|Gsto-1|Gstx|Spg-r|p28	glutathione S-transferase omega 1	protein-coding
mm_83128.1	chr9	40430877	40430880	-	1	NA	intron (NM_172768, intron 1 of 19)	intron (NM_172768, intron 1 of 19)	24886	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_70517.1	chr8	12947982	12948010	+	1	NA	promoter-TSS (NR_128567)	promoter-TSS (NR_128567)	55	NR_128567	104797311		NR_128567	ENSMUSG00000105030	Gm38671	Mir9768|mmu-mir-9768	predicted gene, 38671	ncRNA
mm_160338.1	chr8	14727163	14727163	+	1	NA	exon (NM_001145965, exon 5 of 15)	exon (NM_001145965, exon 5 of 15)	-161373	NM_012000	26889	Mm.254027	NM_012000	ENSMUSG00000026317	Cln8	mnd	ceroid-lipofuscinosis, neuronal 8	protein-coding
mm_171843.1	chr5	16755293	16755312	+	1	NA	Intergenic	L1Md_T|LINE|L1	201401	NM_001289461	15234	Mm.267078	NM_010427	ENSMUSG00000028864	Hgf	C230052L06Rik|HGF/SF|NK1|NK2|SF|SF/HGF	hepatocyte growth factor	protein-coding
mm_69261.1	chr7	127893450	127893456	-	1	NA	exon (NM_178600, exon 3 of 3)	exon (NM_178600, exon 3 of 3)	2164	NM_178600	27973	Mm.29703	NM_178600	ENSMUSG00000096145	Vkorc1	D7Wsu86e	vitamin K epoxide reductase complex, subunit 1	protein-coding
mm_38634.1	chr4	142453533	142453536	-	1	NA	Intergenic	B4|SINE|B4	-214133	NM_001109685	71529	Mm.255986	NM_144531	ENSMUSG00000040606	Kazn	2310007B04Rik|9030409G11Rik|AI256607|AI666764|AW061099|Kaz|Kazrin	kazrin, periplakin interacting protein	protein-coding
mm_13797.1	chr2	118901622	118901663	+	1	NA	promoter-TSS (NM_001045523)	promoter-TSS (NM_001045523)	27	NM_001045523	228536	Mm.330487	NM_001045523	ENSMUSG00000040007	Bahd1	AL022997|AW541238|Gm117|mKIAA0945	bromo adjacent homology domain containing 1	protein-coding
mm_134645.1	chr16	21780323	21780326	-	1	NA	intron (NM_023737, intron 1 of 6)	PB1D9|SINE|Alu	7510	NM_023737	74147	Mm.28100	NM_023737	ENSMUSG00000022853	Ehhadh	1300002P22Rik|HD|L-PBE|LBFP|LBP|MFP|MFP1|PBFE	enoyl-Coenzyme A, hydratase/3-hydroxyacyl Coenzyme A dehydrogenase	protein-coding
mm_23970.1	chr3	85574110	85574148	+	1	NA	promoter-TSS (NM_144896)	promoter-TSS (NM_144896)	0	NM_144896	229487	Mm.52275	NM_144896	ENSMUSG00000028085	Gatb	9430026F02Rik|Pet112|Pet112l	glutamyl-tRNA(Gln) amidotransferase, subunit B	protein-coding
mm_27550.1	chr3	58132121	58132149	-	1	NA	Intergenic	Intergenic	31672	NR_040538	67850	Mm.416968	NR_040538	ENSMUSG00000100666	1700007F19Rik	-	RIKEN cDNA 1700007F19 gene	ncRNA
mm_45995.1	chr5	90506701	90506722	-	1	NA	exon (NM_007423, exon 12 of 15)	exon (NM_007423, exon 12 of 15)	-12238	NM_145146	280662	Mm.348786	NM_145146	ENSMUSG00000029369	Afm	Alf|alpha-Alb	afamin	protein-coding
mm_150867.1	chr19	45047558	45047572	+	1	NA	promoter-TSS (NM_053197)	promoter-TSS (NM_053197)	-11	NM_053197	94280	Mm.36169	NM_053197	ENSMUSG00000025212	Sfxn3	-	sideroflexin 3	protein-coding
mm_50053.1	chr6	41178309	41178317	+	1	NA	Intergenic	Intergenic	-123959	NM_011646	22074	Mm.383263	NM_011646	ENSMUSG00000054106	Try4	0910001B19Rik|Td	trypsin 4	protein-coding
mm_24450.1	chr3	90612870	90612881	+	1	NA	promoter-TSS (NM_011313)	promoter-TSS (NM_011313)	-19	NM_011313	20200	Mm.100144	NM_011313	ENSMUSG00000001025	S100a6	2A9|5B10|CALCYCLIN|Cacy|PRA	S100 calcium binding protein A6 (calcyclin)	protein-coding
mm_130033.1	chr15	88977924	88977949	-	1	NA	exon (NM_133241, exon 2 of 12)	exon (NM_133241, exon 2 of 12)	617	NM_133241	170790	Mm.32780	NM_133241	ENSMUSG00000035805	Mlc1	AW048630|BB074274|Kiaa0027-hp|LVM|MLC|VL|WKL1|mKIAA0027	megalencephalic leukoencephalopathy with subcortical cysts 1 homolog (human)	protein-coding
mm_128299.1	chr15	37459328	37459380	-	1	NA	promoter-TSS (NM_001170868)	promoter-TSS (NM_001170868)	28	NM_001170867	52589	Mm.283370	NM_134094	ENSMUSG00000051359	Ncald	AI848120|D030020D09Rik|D15Ertd412e	neurocalcin delta	protein-coding
mm_53824.1	chr6	147264099	147264103	+	1	NA	promoter-TSS (NM_008970)	promoter-TSS (NM_008970)	-88	NM_008970	19227	Mm.28440	NM_008970	ENSMUSG00000048776	Pthlh	PLP|PTH-like|Pthrp	parathyroid hormone-like peptide	protein-coding
mm_77905.1	chr9	7349108	7349118	+	1	NA	intron (NM_001320077, intron 3 of 10)	B4A|SINE|B4	1739	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_36078.1	chr4	58206505	58206520	-	1	NA	promoter-TSS (NM_022814)	promoter-TSS (NM_022814)	84	NM_022814	64817	Mm.261024	NM_022814	ENSMUSG00000028369	Svep1	1110021D17Rik|4833413O10Rik|AA387071|D430029O09Rik|Polydom	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	protein-coding
mm_40856.1	chr5	73502679	73502689	+	1	NA	intron (NM_001190733, intron 1 of 9)	intron (NM_001190733, intron 1 of 9)	11658	NM_178896	100737	Mm.220312	NM_178896	ENSMUSG00000051674	Dcun1d4	AI836376	DCN1, defective in cullin neddylation 1, domain containing 4 (S. cerevisiae)	protein-coding
mm_11174.1	chr2	28698853	28698863	+	1	NA	intron (NM_027283, intron 1 of 4)	intron (NM_027283, intron 1 of 4)	793	NM_027283	69987	Mm.239376	NM_027283	ENSMUSG00000026809	Spaca9	1700026L06Rik|MAST	sperm acrosome associated 9	protein-coding
mm_116491.1	chr13	44704505	44704514	-	1	NA	Intergenic	RMER17C|LTR|ERVK	-26265	NM_021878	16468	Mm.25059	NM_021878	ENSMUSG00000038518	Jarid2	Jmj|jumonji	jumonji, AT rich interactive domain 2	protein-coding
mm_109712.1	chr12	113896920	113896922	+	1	NA	Intergenic	Intergenic	353013	NM_174885	238406	Mm.188683	NM_174885	ENSMUSG00000043945	Adam6a	Adam6|tMDCIV	a disintegrin and metallopeptidase domain 6A	protein-coding
mm_58919.1	chr7	17716230	17716232	+	1	NA	intron (NM_028480, intron 2 of 8)	intron (NM_028480, intron 2 of 8)	2979	NM_028480	73250	Mm.244138	NM_028480	ENSMUSG00000008789	Ceacam5	1600029H12Rik|Psg30	carcinoembryonic antigen-related cell adhesion molecule 5	protein-coding
mm_20010.1	chr2	119229829	119229844	-	1	NA	promoter-TSS (NM_028104)	promoter-TSS (NM_028104)	29	NM_028104	72112	Mm.46317	NM_028104	ENSMUSG00000027317	Ppp1r14d	2010107K19Rik|GBPI-1|Ppp1r14	protein phosphatase 1, regulatory (inhibitor) subunit 14D	protein-coding
mm_119561.1	chr14	48798109	48798111	+	1	NA	Intergenic	Intergenic	-80763	NR_033783	66770	Mm.136954	NR_033783		4933429O19Rik	1700031B11Rik	RIKEN cDNA 4933429O19 gene	ncRNA
mm_22586.1	chr3	13472024	13472030	+	1	NA	intron (NM_001163328, intron 1 of 8)	T-rich|Low_complexity|Low_complexity	372	NM_001163328	76897	Mm.422625	NM_178631	ENSMUSG00000039717	Ralyl	0710005M24Rik	RALY RNA binding protein-like	protein-coding
mm_87083.1	chr10	29313622	29313630	+	1	NA	5' UTR (NM_025855, exon 1 of 6)	5' UTR (NM_025855, exon 1 of 6)	126	NM_025855	52665	Mm.28930	NM_025855	ENSMUSG00000019883	Echdc1	1700028A24Rik|AI314462|AI930038|D10Ertd667e|MMCD	enoyl Coenzyme A hydratase domain containing 1	protein-coding
mm_20888.1	chr2	148871952	148871960	-	1	NA	3' UTR (NM_009976, exon 3 of 3)	3' UTR (NM_009976, exon 3 of 3)	3556	NM_009976	13010	Mm.4263	NM_009976	ENSMUSG00000027447	Cst3	CysC	cystatin C	protein-coding
mm_73320.1	chr8	105264657	105264697	+	1	NA	promoter-TSS (NM_015821)	promoter-TSS (NM_015821)	29	NM_015821	50788	Mm.334764	NM_015821	ENSMUSG00000033313	Fbxl8	FBL8	F-box and leucine-rich repeat protein 8	protein-coding
mm_45402.1	chr5	66151904	66151962	-	1	NA	promoter-TSS (NM_001127382)	promoter-TSS (NM_001127382)	21	NM_001127382	245945	Mm.36863	NM_139065	ENSMUSG00000070780	Rbm47	9530077J19Rik	RNA binding motif protein 47	protein-coding
mm_78875.1	chr9	44483143	44483167	+	1	NA	Intergenic	CpG	-15981	NM_030256	80288	Mm.370270	NM_030256	ENSMUSG00000063382	Bcl9l	B9L|BC003321|BCL9-2|DLNB11	B cell CLL/lymphoma 9-like	protein-coding
mm_168545.1	chr1	162740367	162740371	-	1	NA	5' UTR (NM_001081290, exon 1 of 35)	5' UTR (NM_001081290, exon 1 of 35)	187	NM_001081290	226562	Mm.245446	NM_001081290	ENSMUSG00000040225	Prrc2c	1810043M20Rik|9630039I18Rik|A630006J20|Bat2d|Bat2d1|Bat2l2|E130112L15Rik|Prrc3|mKIAA1096	proline-rich coiled-coil 2C	protein-coding
mm_81412.1	chr9	109052883	109052903	+	1	NA	intron (NM_025858, intron 3 of 5)	intron (NM_025858, intron 3 of 5)	-1973	NM_026381	66940	Mm.196533	NM_025858	ENSMUSG00000025647	Shisa5	2310008D10Rik|6430628I05Rik|Scotin|mShisa5	shisa family member 5	protein-coding
mm_163018.1	chr11	46707089	46707091	-	1	NA	promoter-TSS (NM_134249)	promoter-TSS (NM_134249)	14	NM_134249	171284	Mm.234654	NM_134249	ENSMUSG00000040413	Timd2	AA816106|AU019358|AU019662|C78111|G9D3|TIM-2|Tim2	T cell immunoglobulin and mucin domain containing 2	protein-coding
mm_129607.1	chr15	79932512	79932546	-	1	NA	5' UTR (NM_144811, exon 1 of 7)	5' UTR (NM_144811, exon 1 of 7)	117	NM_144811	52609	Mm.323442	NM_144811	ENSMUSG00000053411	Cbx7	1600014J01Rik|AI851678|D15Ertd417e	chromobox 7	protein-coding
mm_120499.1	chr14	65981489	65981517	+	1	NA	TTS (NM_013492)	TTS (NM_013492)	13020	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_108399.1	chr12	81152422	81152432	+	1	NA	intron (NM_022316, intron 6 of 12)	intron (NM_022316, intron 6 of 12)	-13724	NR_037227	100526532		NR_037227	ENSMUSG00000092673	Mir3067	mir-3067|mmu-mir-3067	microRNA 3067	ncRNA
mm_164691.1	chr17	47731484	47731488	+	1	NA	intron (NM_025973, intron 5 of 8)	intron (NM_025973, intron 5 of 8)	4644	NM_025973	109820	Mm.22957	NM_025973	ENSMUSG00000023987	Pgc	2210410L06Rik|Upg-1|Upg1	progastricsin (pepsinogen C)	protein-coding
mm_102892.1	chr11	69416189	69416227	-	1	NA	Intergenic	Intergenic	-2533	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_118858.1	chr14	25842129	25842139	+	1	NA	promoter-TSS (NM_013469)	promoter-TSS (NM_013469)	-21	NM_013469	11744	Mm.294083	NM_013469	ENSMUSG00000021866	Anxa11	A830099O17Rik|Anx11	annexin A11	protein-coding
mm_72145.1	chr8	72135843	72135866	+	1	NA	intron (NM_001001491, intron 1 of 7)	intron (NM_001001491, intron 1 of 7)	562	NM_001001491	326618	Mm.295124	NM_001001491	ENSMUSG00000031799	Tpm4	2610528G24Rik|Tpm4.2|Tpm4.2cy	tropomyosin 4	protein-coding
mm_75208.1	chr8	39605290	39605306	-	1	NA	3' UTR (NM_031195, exon 9 of 9)	3' UTR (NM_031195, exon 9 of 9)	37380	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_81401.1	chr9	109038576	109038644	+	1	NA	promoter-TSS (NM_001284332)	promoter-TSS (NM_001284332)	43	NM_001284332	66940	Mm.196533	NM_025858	ENSMUSG00000025647	Shisa5	2310008D10Rik|6430628I05Rik|Scotin|mShisa5	shisa family member 5	protein-coding
mm_142433.1	chr17	45570582	45570611	-	1	NA	intron (NM_008302, intron 5 of 10)	intron (NM_008302, intron 5 of 10)	2665	NM_008302	15516	Mm.2180	NM_008302	ENSMUSG00000023944	Hsp90ab1	90kDa|AL022974|C81438|Hsp84|Hsp84-1|Hsp90|Hspcb	heat shock protein 90 alpha (cytosolic), class B member 1	protein-coding
mm_41068.1	chr5	87666966	87666976	+	1	NA	intron (NM_001286015, intron 1 of 32)	RSINE1|SINE|B4	763	NM_001286016	12990	Mm.427467	NM_007784	ENSMUSG00000070702	Csn1s1	AA959832|AW212882|Csna	casein alpha s1	protein-coding
mm_88787.1	chr10	80609337	80609351	+	1	NA	promoter-TSS (NR_105877)	promoter-TSS (NR_105877)	84	NR_105877	102465550		NR_105877	ENSMUSG00000099283	Mir6912	Gm27990|mmu-mir-6912	microRNA 6912	ncRNA
mm_156740.1	chrX	159943001	159943033	+	1	NA	5' UTR (NM_001290664, exon 1 of 6)	5' UTR (NM_001290664, exon 1 of 6)	324	NM_001290664	58194	Mm.286495	NM_021389	ENSMUSG00000040990	Sh3kbp1	1200007H22Rik|1700125L08Rik|5830464D22Rik|AI447724|Cin85|IN85|Ruk|Seta	SH3-domain kinase binding protein 1	protein-coding
mm_95414.1	chr11	50025377	50025385	+	1	NA	promoter-TSS (NM_021540)	promoter-TSS (NM_021540)	50	NM_001290750	59044	Mm.359004	NM_021540	ENSMUSG00000020376	Rnf130	2510042A13Rik|G1RZFP|G1rp|GOLIATH|GP	ring finger protein 130	protein-coding
mm_32154.1	chr4	99955490	99955509	+	1	NA	intron (NM_028132, intron 1 of 10)	intron (NM_028132, intron 1 of 10)	26048	NM_028132	72157	Mm.217764	NM_028132	ENSMUSG00000025791	Pgm2	2610020G18Rik|AA407108|AI098105|Pgm-2|Pgm1	phosphoglucomutase 2	protein-coding
mm_127193.1	chr15	99033748	99033756	+	1	NA	intron (NM_009448, intron 1 of 3)	intron (NM_009448, intron 1 of 3)	3861	NM_009448	22146	Mm.88212	NM_009448	ENSMUSG00000043091	Tuba1c	M[a]6|Tuba6	tubulin, alpha 1C	protein-coding
mm_126748.1	chr15	85736108	85736122	+	1	NA	intron (NM_011144, intron 1 of 7)	intron (NM_011144, intron 1 of 7)	339	NM_011144	19013	Mm.212789	NM_011144	ENSMUSG00000022383	Ppara	4933429D07Rik|AW742785|Nr1c1|PPAR-alpha|PPARalpha|Ppar	peroxisome proliferator activated receptor alpha	protein-coding
mm_100638.1	chr11	121748544	121748552	+	1	NA	Intergenic	Intergenic	46121	NM_144797	210029	Mm.153566	NM_144797	ENSMUSG00000039208	Metrnl	9430048M07Rik|BC019776	meteorin, glial cell differentiation regulator-like	protein-coding
mm_148919.1	chr19	6976416	6976453	+	1	NA	intron (NM_008889, intron 1 of 3)	intron (NM_008889, intron 1 of 3)	1386	NM_008889	18938	Mm.140	NM_008889	ENSMUSG00000056612	Ppp1r14b	AOM172|PHI-1|PLCB3N|Png	protein phosphatase 1, regulatory (inhibitor) subunit 14B	protein-coding
mm_134156.1	chr16	10790903	10790919	-	1	NA	promoter-TSS (NM_013638)	promoter-TSS (NM_013638)	3	NM_013638	19120	Mm.291887	NM_013638	ENSMUSG00000050058	Prm3	BC061127|PX|Pxg	protamine 3	protein-coding
mm_69158.1	chr7	127162611	127162646	-	1	NA	Intergenic	Intergenic	-24805	NM_001037810	20737	Mm.283714	NM_009259	ENSMUSG00000051457	Spn	A630014B01Rik|Cd43|Galgp|Ly-48|Ly48	sialophorin	protein-coding
mm_145152.1	chr18	46404945	46404958	+	1	NA	Intergenic	Intergenic	60865	NR_045438	72076	Mm.82766	NM_028086		Mospd4	2010013H21Rik	motile sperm domain containing 4	pseudo
mm_42436.1	chr5	115429550	115429568	+	1	NA	promoter-TSS (NM_008629)	promoter-TSS (NM_008629)	-126	NM_008629	17690	Mm.5077	NM_008629	ENSMUSG00000054256	Msi1	Msi1h|Musahi1|m-Msi-1	musashi RNA-binding protein 1	protein-coding
mm_25039.1	chr3	98287008	98287008	+	1	NA	intron (NM_008256, intron 1 of 9)	intron (NM_008256, intron 1 of 9)	6577	NM_008256	15360	Mm.289131	NM_008256	ENSMUSG00000027875	Hmgcs2	1300002P16|mHS	3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2	protein-coding
mm_74729.1	chr8	17535635	17535645	-	1	NA	promoter-TSS (NM_053171)	promoter-TSS (NM_053171)	-255	NM_053171	94109	Mm.436988	NM_053171	ENSMUSG00000060924	Csmd1	B930082H09|mKIAA1890	CUB and Sushi multiple domains 1	protein-coding
mm_46395.1	chr5	104072912	104072920	-	1	NA	intron (NM_001163772, intron 6 of 9)	intron (NM_001163772, intron 6 of 9)	4692	NM_001163772	100271704	Mm.366664	NM_001163772	ENSMUSG00000091034	Gm17660	Scpppq1	predicted gene, 17660	protein-coding
mm_153858.1	chr19	46502937	46502950	-	1	NA	exon (NM_053100, exon 1 of 6)	exon (NM_053100, exon 1 of 6)	1295	NM_053100	93679	Mm.392177	NM_053100	ENSMUSG00000025034	Trim8	AA408830|BB006755|GERP|Rnf27	tripartite motif-containing 8	protein-coding
mm_90556.1	chr10	128110812	128110838	+	1	NA	exon (NM_054078, exon 4 of 30)	exon (NM_054078, exon 4 of 30)	18042	NM_054078	116848	Mm.252213	NM_054078	ENSMUSG00000040054	Baz2a	AA415431|C030005G16Rik|C78388|Tip5|Walp3|mKIAA0314	bromodomain adjacent to zinc finger domain, 2A	protein-coding
mm_161004.1	chr11	116593697	116593697	+	1	NA	promoter-TSS (NM_009591)	promoter-TSS (NM_009591)	10	NM_009591	11298	Mm.42233	NM_009591	ENSMUSG00000020804	Aanat	AA-NAT|Nat-2|Nat4|Snat	arylalkylamine N-acetyltransferase	protein-coding
mm_2508.1	chr1	106214425	106214438	+	1	NA	intron (NM_133821, intron 1 of 16)	intron (NM_133821, intron 1 of 16)	42562	NM_133821	98432	Mm.24115	NM_133821	ENSMUSG00000044340	Phlpp1	AI836256|Phlpp|Plekhe1|SCOP|mKIAA0606	PH domain and leucine rich repeat protein phosphatase 1	protein-coding
mm_78249.1	chr9	21695622	21695625	+	1	NA	intron (NM_001174079, intron 29 of 33)	intron (NM_001174079, intron 29 of 33)	-27953	NM_001252658	16835	Mm.3213	NM_010700	ENSMUSG00000032193	Ldlr	Hlb301	low density lipoprotein receptor	protein-coding
mm_24185.1	chr3	88593170	88593187	+	1	NA	Intergenic	Intergenic	13507	NM_025448	66256	Mm.7091	NM_025448	ENSMUSG00000041355	Ssr2	1500032E05Rik|AI315033|AU020133|TLAP|TRAPB|TRAPbeta	signal sequence receptor, beta	protein-coding
mm_136236.1	chr16	90727330	90727386	-	1	NA	promoter-TSS (NM_025642)	promoter-TSS (NM_025642)	13	NM_025642	66578	Mm.180363	NM_025642	ENSMUSG00000022978	Mis18a	2610039C10Rik|2810018N07Rik	MIS18 kinetochore protein A	protein-coding
mm_112036.1	chr12	111574310	111574342	-	1	NA	promoter-TSS (NM_021516)	promoter-TSS (NM_021516)	76	NR_045295	100504687	Mm.26072	NR_045295	ENSMUSG00000096995	2810029C07Rik	AU017849	RIKEN cDNA 2810029C07 gene	ncRNA
mm_100704.1	chr11	3648721	3648730	-	1	NA	promoter-TSS (NM_001159288)	promoter-TSS (NM_001159288)	89	NR_002321	544752	Mm.390314	NR_002321	ENSMUSG00000056579	Tug1	AI316828	taurine upregulated gene 1	ncRNA
mm_33602.1	chr4	132568814	132568824	+	1	NA	intron (NM_001081211, intron 1 of 1)	(CA)n|Simple_repeat|Simple_repeat	4752	NM_001081211	19204	Mm.89389	NM_001081211	ENSMUSG00000056529	Ptafr	PAFR	platelet-activating factor receptor	protein-coding
mm_87811.1	chr10	60301906	60301916	+	1	NA	TTS (NM_001252635)	TTS (NM_001252635)	17450	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_166225.1	chr5	65080962	65080965	+	1	NA	Intergenic	Intergenic	-26605	NM_001347355	71778	Mm.10281	NM_175174	ENSMUSG00000054920	Klhl5	1300013C10Rik	kelch-like 5	protein-coding
mm_38706.1	chr4	145215495	145215526	-	1	NA	3' UTR (NM_011610, exon 10 of 10)	3' UTR (NM_011610, exon 10 of 10)	-20505	NM_001276465	230895	Mm.240310	NM_001033190	ENSMUSG00000020220	Vps13d	-	vacuolar protein sorting 13D	protein-coding
mm_38073.1	chr4	134127688	134127720	-	1	NA	TTS (NM_026257)	TTS (NM_026257)	1049	NM_080559	73723	Mm.22240	NM_080559	ENSMUSG00000028843	Sh3bgrl3	1110004L05Rik|AU022188	SH3 domain binding glutamic acid-rich protein-like 3	protein-coding
mm_138592.1	chr17	35509411	35509424	+	1	NA	exon (NM_001252452, exon 3 of 5)	exon (NM_001252452, exon 3 of 5)	610	NM_001252452	18999	Mm.17031	NM_013633	ENSMUSG00000024406	Pou5f1	NF-A3|Oct-3|Oct-3/4|Oct-4|Oct3|Oct3/4|Oct4|Otf-3|Otf-4|Otf3|Otf3-rs7|Otf3g|Otf4	POU domain, class 5, transcription factor 1	protein-coding
mm_22022.1	chr2	168003560	168003566	-	1	NA	intron (NM_001080708, intron 2 of 21)	intron (NM_001080708, intron 2 of 21)	7030	NM_001080708	69553	Mm.68454	NM_001080708	ENSMUSG00000074577	Fam65c	2310033K02Rik|Gm124	family with sequence similarity 65, member C	protein-coding
mm_171484.1	chr4	146097241	146097241	+	1	NA	promoter-TSS (NM_001037926)	promoter-TSS (NM_001037926)	-71	NM_001037926	626316	Mm.270762	NM_001037926	ENSMUSG00000066009	Zfp987	Gm13051|OTTMUSG00000010104|OTTMUSG00000010173	zinc finger protein 987	protein-coding
mm_124889.1	chr15	10314033	10314059	+	1	NA	intron (NM_001253781, intron 2 of 9)	intron (NM_001253781, intron 2 of 9)	20395	NM_001253782	19116	Mm.10516	NM_011169	ENSMUSG00000005268	Prlr	AI987712|Pr-1|Pr-3|Prlr-rs1	prolactin receptor	protein-coding
mm_147101.1	chr18	35655173	35655181	-	1	NA	promoter-TSS (NM_001270646)	promoter-TSS (NM_001270646)	22	NM_001270646	381148	Mm.297784	NM_001270646	ENSMUSG00000073600	Prob1	Gm1614	proline rich basic protein 1	protein-coding
mm_55854.1	chr6	83441675	83441684	-	1	NA	promoter-TSS (NM_183138)	promoter-TSS (NM_183138)	-1	NM_183138	194388	Mm.211030	NM_183138	ENSMUSG00000034832	Tet3	B430006D22Rik|BC037432|D230004J03Rik	tet methylcytosine dioxygenase 3	protein-coding
mm_40258.1	chr5	38230584	38230600	+	1	NA	exon (NM_025281, exon 6 of 9)	exon (NM_025281, exon 6 of 9)	10110	NM_025281	17089	Mm.28560	NM_025281	ENSMUSG00000067367	Lyar	MLZ-264	Ly1 antibody reactive clone	protein-coding
mm_113929.1	chr13	49609100	49609113	+	1	NA	intron (NM_008760, intron 1 of 6)	intron (NM_008760, intron 1 of 6)	1035	NM_008760	18295	Mm.4258	NM_008760	ENSMUSG00000021390	Ogn	3110079A16Rik|OG|OIF|SLRR3A|mimecan|mimican	osteoglycin	protein-coding
mm_36650.1	chr4	94587346	94587361	-	1	NA	exon (NM_172695, exon 4 of 14)	exon (NM_172695, exon 4 of 14)	-6297	NM_001081019	667250	Mm.449778	NM_001081019		Gm12657	H3mm12|OTTMUSG00000007855	predicted gene 12657	protein-coding
mm_149818.1	chr19	24197554	24197560	+	1	NA	intron (NM_011597, intron 1 of 22)	intron (NM_011597, intron 1 of 22)	-23417	NM_001198985	21873	Mm.104744	NM_011597	ENSMUSG00000024812	Tjp2	ZO-2	tight junction protein 2	protein-coding
mm_123952.1	chr14	73797333	73797333	-	1	NA	Intergenic	L1MA8|LINE|L1	244547	NM_011506	20916	Mm.38951	NM_011506	ENSMUSG00000022110	Sucla2	4930547K18Rik|A-SCS	succinate-Coenzyme A ligase, ADP-forming, beta subunit	protein-coding
mm_40806.1	chr5	70086574	70086576	+	1	NA	Intergenic	Intergenic	-494271	NM_001347363	67980	Mm.33830	NM_027681	ENSMUSG00000029209	Gnpda2	4921523I18Rik|4933412A11Rik|BB189630|GNPDA|Gnp2|Sb52|mKIAA4008	glucosamine-6-phosphate deaminase 2	protein-coding
mm_69479.1	chr7	133776682	133776704	-	1	NA	promoter-TSS (NM_025850)	promoter-TSS (NM_025850)	110	NM_001286032	101437	Mm.199223	NM_133941	ENSMUSG00000030986	Dhx32	3110079L04Rik|4732469F02Rik|AA408140|Ddx32	DEAH (Asp-Glu-Ala-His) box polypeptide 32	protein-coding
mm_172963.1	chr9	88719545	88719551	-	1	NA	intron (NM_001128601, intron 1 of 2)	CpG	250	NM_001128601	100039707	Mm.347377	NM_001128601	ENSMUSG00000079427	Mthfsl	Gm2382	5, 10-methenyltetrahydrofolate synthetase-like	protein-coding
mm_12501.1	chr2	71868515	71868526	+	1	NA	intron (NR_039557, intron 3 of 3).2	RLTR11C_MM|LTR|ERVK	-4704	NM_172665	228026	Mm.34411	NM_172665	ENSMUSG00000006494	Pdk1	B830012B01|D530020C15Rik	pyruvate dehydrogenase kinase, isoenzyme 1	protein-coding
mm_92616.1	chr10	80141311	80141322	-	1	NA	promoter-TSS (NM_025313)	promoter-TSS (NM_025313)	-959	NM_001347092	66043	Mm.278560	NM_025313	ENSMUSG00000003072	Atp5d	0610008F14Rik|1500000I11Rik|AA960090|AI876556|AU020773|C85518	ATP synthase, H+ transporting, mitochondrial F1 complex, delta subunit	protein-coding
mm_149895.1	chr19	25423903	25423905	+	1	NA	intron (NM_181404, intron 7 of 13)	intron (NM_181404, intron 7 of 13)	-81802	NM_015826	50796	Mm.391208	NM_015826	ENSMUSG00000024837	Dmrt1	-	doublesex and mab-3 related transcription factor 1	protein-coding
mm_76706.1	chr8	94591384	94591388	-	1	NA	intron (NM_028221, intron 1 of 7)	intron (NM_028221, intron 1 of 7)	10340	NM_028221	102122	Mm.250425	NM_028221	ENSMUSG00000031774	Fam192a	1700001O11Rik|2310065K24Rik|AI596259|Nip30	family with sequence similarity 192, member A	protein-coding
mm_57205.1	chr6	122851011	122851062	-	1	NA	exon (NM_009779, exon 2 of 2)	exon (NM_009779, exon 2 of 2)	5121	NM_009779	12267	Mm.2408	NM_009779	ENSMUSG00000040552	C3ar1	AZ3B|C3AR|HNFAG09	complement component 3a receptor 1	protein-coding
mm_104497.1	chr11	95842433	95842450	-	1	NA	promoter-TSS (NM_001284397)	promoter-TSS (NM_001284397)	-2	NM_025659	66610	Mm.485545	NM_025659	ENSMUSG00000018381	Abi3	2210414K06Rik|AI987680|NESH	ABI gene family, member 3	protein-coding
mm_20769.1	chr2	142879626	142879636	-	1	NA	intron (NM_001081133, intron 1 of 25)	intron (NM_001081133, intron 1 of 25)	21833	NM_001081133	16558	Mm.251934	NM_001081133	ENSMUSG00000038844	Kif16b	8430434E15Rik|AA623607|AI789011|C80253|C80902|mKIAA1590	kinesin family member 16B	protein-coding
mm_76774.1	chr8	95888365	95888375	-	1	NA	promoter-TSS (NM_010325)	promoter-TSS (NM_010325)	-5	NM_010325	14719	Mm.230169	NM_010325	ENSMUSG00000031672	Got2	AL022787|FABP-pm|Got-2|Kyat4|mAspAT	glutamatic-oxaloacetic transaminase 2, mitochondrial	protein-coding
mm_79636.1	chr9	59542822	59542832	+	1	NA	intron (NM_010421, intron 1 of 13)	intron (NM_010421, intron 1 of 13)	3287	NM_010421	15211	Mm.2284	NM_010421	ENSMUSG00000025232	Hexa	Hex-1	hexosaminidase A	protein-coding
mm_141682.1	chr17	33940290	33940296	-	1	NA	promoter-TSS (NM_010385)	promoter-TSS (NM_010385)	37	NM_001185182	14976	Mm.2948	NM_010385	ENSMUSG00000024309	Pfdn6	H-2Ke2|H2-Ke2|Ke-2	prefoldin subunit 6	protein-coding
mm_80310.1	chr9	74354083	74354084	+	1	NA	Intergenic	B4|SINE|B4	243749	NM_001033500	546144	Mm.335289	NM_177908	ENSMUSG00000044976	Wdr72	AW558070|D230040E23	WD repeat domain 72	protein-coding
mm_171894.1	chr5	3943174	3943190	-	1	NA	intron (NM_194462, intron 1 of 47)	RLTR9D|LTR|ERVK	14996	NM_194462	100986	Mm.46044	NM_194462	ENSMUSG00000040407	Akap9	5730481H23Rik|AKAP-9|AKAP450|AW545847|C79026|G1-448-15|PRKA9|mKIAA0803|mei2-5|repro12	A kinase (PRKA) anchor protein (yotiao) 9	protein-coding
mm_10387.1	chr2	12924121	12924134	+	1	NA	promoter-TSS (NM_008961)	promoter-TSS (NM_008961)	86	NM_001305437	19212	Mm.229322	NM_008961	ENSMUSG00000026730	Pter	AI790318|Mpr56-1	phosphotriesterase related	protein-coding
mm_157285.1	chrX	20861132	20861168	-	1	NA	TTS (NM_009703)	TTS (NM_009703)	2032	NR_049190	100885829		NR_049190	ENSMUSG00000093408	Mir5617	Gm25192|mir-5617|mmu-mir-5617	microRNA 5617	ncRNA
mm_154034.1	chr19	53528873	53528881	-	1	NA	promoter-TSS (NM_001085390)	promoter-TSS (NM_001085390)	-441	NM_001085390	240672	Mm.482424	NM_001085390	ENSMUSG00000034765	Dusp5	Gm337	dual specificity phosphatase 5	protein-coding
mm_173203.1	chrX	69606007	69606009	-	1	NA	intron (NM_008032, intron 3 of 19)	intron (NM_008032, intron 3 of 19)	245677	NM_008032	14266	Mm.466576	NM_008032	ENSMUSG00000031189	Aff2	FMR2P|Fmr2|Ox19|Oxh	AF4/FMR2 family, member 2	protein-coding
mm_136003.1	chr16	75586018	75586037	-	1	NA	promoter-TSS (NM_001252513)	promoter-TSS (NM_001252513)	34	NM_001252513	320355	Mm.99517	NM_177142	ENSMUSG00000032948	Lipi	D930038D03Rik|lpd1	lipase, member I	protein-coding
mm_87055.1	chr10	28836732	28836735	+	1	NA	intron (NM_001305663, intron 5 of 5)	intron (NM_001305663, intron 5 of 5)	86774	NR_033601	114676	Mm.390292	NR_033601		4930519F09Rik	-	pyruvate dehydrogenase E1 alpha 1 pseudogene	pseudo
mm_118348.1	chr13	114931937	114931948	-	1	NA	promoter-TSS (NM_008396)	promoter-TSS (NM_008396)	99	NM_008396	16398	Mm.5007	NM_008396	ENSMUSG00000015533	Itga2	CD49B|DX5	integrin alpha 2	protein-coding
mm_171123.1	chr3	144156818	144156826	+	1	NA	Intergenic	B4|SINE|B4	45510	NM_001161770	16911	Mm.29187	NM_010723	ENSMUSG00000028266	Lmo4	A730077C12Rik|Crp3|Etohi4	LIM domain only 4	protein-coding
mm_136047.1	chr16	78559550	78559552	-	1	NA	promoter-TSS (NR_040569)	promoter-TSS (NR_040569)	-765	NR_040569	75818	Mm.410817	NR_040569		4930478L05Rik	-	RIKEN cDNA 4930478L05 gene	ncRNA
mm_73312.1	chr8	105175368	105175385	+	1	NA	intron (NM_001161456, intron 2 of 4)	AT_rich|Low_complexity|Low_complexity	4702	NM_001161458	12400	Mm.2018	NM_022309	ENSMUSG00000031885	Cbfb	AI893578|PEA2|PEBP2b|Pebp2|Pebpb2	core binding factor beta	protein-coding
mm_65542.1	chr7	27121855	27121867	-	1	NA	exon (NM_007817, exon 3 of 10)	exon (NM_007817, exon 3 of 10)	1906	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_120222.1	chr14	62837760	62837770	+	1	NA	promoter-TSS (NR_106174)	promoter-TSS (NR_106174)	44	NR_106174	102465889		NR_106174	ENSMUSG00000099245	Mir8098	Gm27462|mmu-mir-8098	microRNA 8098	ncRNA
mm_156128.1	chrX	119386240	119386258	+	1	NA	Intergenic	Intergenic	-540947	NM_053114	93728	Mm.125979	NM_053114	ENSMUSG00000034732	Pabpc5	C820015E17	poly(A) binding protein, cytoplasmic 5	protein-coding
mm_47082.1	chr5	117115883	117115906	-	1	NA	promoter-TSS (NM_178622)	promoter-TSS (NM_178622)	99	NM_001122666	71954	Mm.34456	NM_178622	ENSMUSG00000066900	Suds3	2400003N08Rik|2410008L21Rik|AU067672|mSds3	suppressor of defective silencing 3 homolog (S. cerevisiae)	protein-coding
mm_67264.1	chr7	75780264	75780304	-	1	NA	Intergenic	(TTGGGG)n|Simple_repeat|Simple_repeat	-68054	NM_001122780	207952	Mm.206223	NM_029652	ENSMUSG00000055652	Klhl25	2810402K13Rik|BC027373|Enc-1	kelch-like 25	protein-coding
mm_20624.1	chr2	131909776	131909781	-	1	NA	promoter-TSS (NM_001278256)	promoter-TSS (NM_001278256)	-150	NM_011170	19122	Mm.648	NM_011170	ENSMUSG00000079037	Prnp	AA960666|AI325101|CD230|PrP|PrP<C>|PrPC|PrPSc|Prn-i|Prn-p|Sinc|prP27-30|prP33-35C	prion protein	protein-coding
mm_155389.1	chrX	71932434	71932444	+	1	NA	promoter-TSS (NR_027801)	promoter-TSS (NR_027801)	1	NR_027801	382221	Mm.295937	NM_001033470	ENSMUSG00000073130	Gm1141	Pasd1	predicted gene 1141	ncRNA
mm_55752.1	chr6	78373462	78373464	-	1	NA	TTS (NM_011036)	TTS (NM_011036)	2578	NM_011036	18489	Mm.2553	NM_011036	ENSMUSG00000071356	Reg3b	HIP|PAP1|Pap|REG-III	regenerating islet-derived 3 beta	protein-coding
mm_25843.1	chr3	129217584	129217603	+	1	NA	intron (NM_011098, intron 4 of 4)	intron (NM_011098, intron 4 of 4)	3661	NM_001287048	18741	Mm.246804	NM_011098	ENSMUSG00000028023	Pitx2	9430085M16Rik|Brx1|Brx1b|Munc30|Otlx2|Ptx2|Rieg	paired-like homeodomain transcription factor 2	protein-coding
mm_4986.1	chr1	191718256	191718313	+	1	NA	promoter-TSS (NM_001134829)	promoter-TSS (NM_001134829)	-111	NM_001134829	226856	Mm.277958	NM_172266	ENSMUSG00000026623	Lpgat1	AI649174|AW112037|BC013667	lysophosphatidylglycerol acyltransferase 1	protein-coding
mm_157185.1	chrX	10216919	10216921	-	1	NA	promoter-TSS (NM_001177954)	promoter-TSS (NM_001177954)	-125	NM_011285	19893	Mm.247556	NM_011285	ENSMUSG00000031174	Rpgr	Rp3h	retinitis pigmentosa GTPase regulator	protein-coding
mm_83746.1	chr9	51105875	51105888	-	1	NA	Intergenic	Intergenic	-2236	NR_029655	723849		NR_029655	ENSMUSG00000065492	Mir34b	Mirn34b|mir-34b|mmu-mir-34b	microRNA 34b	ncRNA
mm_51303.1	chr6	72310485	72310488	+	1	NA	intron (NM_147779, intron 8 of 11)	intron (NM_147779, intron 8 of 11)	5876	NM_147779	20388	Mm.46033	NM_147779	ENSMUSG00000056370	Sftpb	AI562151|SF-B|SP-B|Sftp-3|Sftp3	surfactant associated protein B	protein-coding
mm_56056.1	chr6	86765810	86765834	-	1	NA	intron (NM_013471, intron 1 of 12)	intron (NM_013471, intron 1 of 12)	9292	NM_001331120	11746	Mm.259702	NM_013471	ENSMUSG00000029994	Anxa4	AI265406|AIV|AW106930|Anx4|Xanx-4	annexin A4	protein-coding
mm_74869.1	chr8	25016324	25016335	-	1	NA	promoter-TSS (NM_027194)	promoter-TSS (NM_027194)	593	NM_001270996	11502	Mm.28908	NM_007404	ENSMUSG00000031555	Adam9	AU020942|MDC9|Mltng|mKIAA0021	a disintegrin and metallopeptidase domain 9 (meltrin gamma)	protein-coding
mm_106307.1	chr11	118301410	118301429	-	1	NA	3' UTR (NM_011594, exon 5 of 5)	3' UTR (NM_011594, exon 5 of 5)	-11175	NM_001033528	72344	Mm.232293	NM_001033528	ENSMUSG00000033909	Usp36	2700002L06Rik|mKIAA1453	ubiquitin specific peptidase 36	protein-coding
mm_133749.1	chr16	94370732	94370784	+	1	NA	promoter-TSS (NM_001159620)	promoter-TSS (NM_001159620)	19	NM_009441	22129	Mm.213408	NM_009441	ENSMUSG00000040785	Ttc3	2610202A04Rik|AA409221|D16Ium21|D16Ium21e|TPRD|mKIAA4119	tetratricopeptide repeat domain 3	protein-coding
mm_63651.1	chr7	128744937	128745020	+	1	NA	5' UTR (NM_001029982, exon 1 of 19)	5' UTR (NM_001029982, exon 1 of 19)	108	NM_001029982	207352	Mm.297105	NM_001029982	ENSMUSG00000055319	Sec23ip	D7Ertd373e|p125	Sec23 interacting protein	protein-coding
mm_114512.1	chr13	72628803	72628825	+	1	NA	promoter-TSS (NR_030701)	promoter-TSS (NR_030701)	17	NM_010574	16372	Mm.28888	NM_010574	ENSMUSG00000001504	Irx2	-	Iroquois related homeobox 2 (Drosophila)	protein-coding
mm_19736.1	chr2	104502576	104502586	-	1	NA	Intergenic	Intergenic	-8092	NM_001145824	15259	Mm.257925	NM_010434	ENSMUSG00000027177	Hipk3	DYRK6|FIST3|PKY|mir-1902	homeodomain interacting protein kinase 3	protein-coding
mm_54487.1	chr6	35308111	35308136	-	1	NA	promoter-TSS (NM_172892)	promoter-TSS (NM_172892)	3	NM_172892	243755	Mm.23666	NM_172892	ENSMUSG00000029843	Slc13a4	9630060C05Rik|SUT-1|SUT1	solute carrier family 13 (sodium/sulfate symporters), member 4	protein-coding
mm_165524.1	chr2	174346335	174346350	+	1	NA	non-coding (NR_003258, exon 13 of 13)	non-coding (NR_003258, exon 13 of 13)	16253	NM_001077510	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_162764.1	chr10	62339330	62339338	-	1	NA	intron (NM_010438, intron 4 of 21)	intron (NM_010438, intron 4 of 21)	1087	NM_001146100	15275	Mm.196605	NM_010438	ENSMUSG00000037012	Hk1	BB404130|Hk-1|Hk1-s|dea|mHk1-s	hexokinase 1	protein-coding
mm_36961.1	chr4	109156923	109156934	-	1	NA	intron (NM_001346502, intron 2 of 23)	intron (NM_001346502, intron 2 of 23)	-38892	NM_001134791	100273	Mm.366315	NM_133885	ENSMUSG00000028559	Osbpl9	2600011I06Rik|AU015843|Orp-9	oxysterol binding protein-like 9	protein-coding
mm_16720.1	chr2	7301913	7301919	-	1	NA	intron (NM_001110231, intron 2 of 15)	intron (NM_001110231, intron 2 of 15)	94084	NM_001110232	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_108372.1	chr12	80827714	80827724	+	1	NA	intron (NM_001242419, intron 1 of 6)	intron (NM_001242419, intron 1 of 6)	37187	NM_001242419	217684	Mm.341776	NM_178682	ENSMUSG00000021133	Susd6	4933426M11Rik|mKIAA0247	sushi domain containing 6	protein-coding
mm_97605.1	chr11	78949987	78950008	+	1	NA	exon (NM_010927, exon 20 of 27)	exon (NM_010927, exon 20 of 27)	24706	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_144026.1	chr17	90036745	90036758	-	1	NA	3' UTR (NM_001347419, exon 3 of 3)	3' UTR (NM_001347419, exon 3 of 3)	51617	NM_001346962	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_23481.1	chr3	60489336	60489346	+	1	NA	intron (NM_001253713, intron 2 of 9)	(GGGA)n|Simple_repeat|Simple_repeat	-11838	NM_001253711	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_124421.1	chr14	118108589	118108594	-	1	NA	Intergenic	Intergenic	24174	NM_029578	76355	Mm.251537	NM_029578	ENSMUSG00000022130	Tgds	2610017J16Rik|2610025M23Rik|AI648925	TDP-glucose 4,6-dehydratase	protein-coding
mm_145536.1	chr18	60805943	60805968	+	1	NA	intron (NM_001042605, intron 1 of 8)	intron (NM_001042605, intron 1 of 8)	2106	NM_010545	16149	Mm.439737	NM_010545	ENSMUSG00000024610	Cd74	CLIP|DHLAG|HLADG|Ia-GAMMA|Ii	CD74 antigen (invariant polypeptide of major histocompatibility complex, class II antigen-associated)	protein-coding
mm_5705.1	chr1	43502847	43502850	-	1	NA	intron (NM_010879, intron 1 of 4)	intron (NM_010879, intron 1 of 4)	57097	NM_010879	17974	Mm.389903	NM_010879	ENSMUSG00000066877	Nck2	4833426I10Rik|Grb4|NCKbeta|Nck-2	non-catalytic region of tyrosine kinase adaptor protein 2	protein-coding
mm_122278.1	chr14	34422715	34422724	-	1	NA	exon (NM_009758, exon 10 of 13)	exon (NM_009758, exon 10 of 13)	47215	NM_153127	105450	Mm.272673	NM_153127	ENSMUSG00000041445	Mmrn2	AA986839|ENDOGLYX1|Emilin3|EndoGlyx-1	multimerin 2	protein-coding
mm_165433.1	chr2	153539689	153539690	+	1	NA	Intergenic	Intergenic	-9718	NM_001134300	329540	Mm.50600	NM_001001986	ENSMUSG00000061411	Nol4l	4931410H15|8430427H17Rik|AI429157|Gm1636	nucleolar protein 4-like	protein-coding
mm_152982.1	chr19	29500362	29500384	-	1	NA	Intergenic	PB1|SINE|Alu	21614	NR_015567	77779	Mm.458738	NR_015567	ENSMUSG00000097855	A930007I19Rik	-	RIKEN cDNA A930007I19 gene	ncRNA
mm_165222.1	chr2	49787667	49787675	+	1	NA	promoter-TSS (NM_027990)	promoter-TSS (NM_027990)	-15	NM_027990	71897	Mm.41381	NM_027990	ENSMUSG00000026765	Lypd6b	2310010M24Rik|AW049525	LY6/PLAUR domain containing 6B	protein-coding
mm_150404.1	chr19	36834197	36834208	+	1	NA	promoter-TSS (NM_001163635)	promoter-TSS (NM_001163635)	-30	NM_001163635	74493	Mm.249310	NM_001163635	ENSMUSG00000024811	Tnks2	5430432P15Rik|AA517131|AI662480|ARTD6|TNKS-2|Tank2	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase 2	protein-coding
mm_107462.1	chr12	37241767	37241784	+	1	NA	5' UTR (NM_178767, exon 1 of 13)	5' UTR (NM_178767, exon 1 of 13)	136	NM_178767	319660	Mm.485540	NM_178767	ENSMUSG00000050103	Agmo	A530016O06Rik|AI790538|Tmem195	alkylglycerol monooxygenase	protein-coding
mm_109935.1	chr12	11204287	11204303	-	1	NA	intron (NR_131083, intron 1 of 2)	MIRb|SINE|MIR	207	NR_131084	77442	Mm.159922	NR_131083		9530020I12Rik	-	RIKEN cDNA 9530020I12 gene	ncRNA
mm_51554.1	chr6	83327734	83327760	+	1	NA	intron (NM_145571, intron 1 of 5)	B1_Mur2|SINE|Alu	1708	NM_145571	232157	Mm.29500	NM_145571	ENSMUSG00000043131	Mob1a	4022402H07Rik|MOB1|MOB4B|Mobk1b|Mobkl1b	MOB kinase activator 1A	protein-coding
mm_52031.1	chr6	96113119	96113127	+	1	NA	promoter-TSS (NM_182808)	promoter-TSS (NM_182808)	-31	NM_182808	320265	Mm.489890	NM_182808	ENSMUSG00000059187	Fam19a1	C630007B19Rik|FAM19A1 TAFA-1|TAFA1|Tafa-1	family with sequence similarity 19, member A1	protein-coding
mm_38291.1	chr4	136890505	136890507	-	1	NA	exon (NM_007574, exon 3 of 3)	exon (NM_007574, exon 3 of 3)	2408	NM_007574	12262	Mm.439732	NM_007574	ENSMUSG00000036896	C1qc	AI385742|C1qg|Ciqc	complement component 1, q subcomponent, C chain	protein-coding
mm_114675.1	chr13	80885666	80885680	+	1	NA	intron (NM_001042591, intron 1 of 7)	CpG	2251	NM_001042591	105171	Mm.423137	NM_001042591	ENSMUSG00000074794	Arrdc3	AI450344|mKIAA1376	arrestin domain containing 3	protein-coding
mm_110872.1	chr12	73779720	73779726	-	1	NA	Intergenic	Intergenic	-121601	NM_001313920	15251	Mm.3879	NM_010431	ENSMUSG00000021109	Hif1a	AA959795|HIF-1-alpha|HIF1-alpha|HIF1alpha|MOP1|bHLHe78	hypoxia inducible factor 1, alpha subunit	protein-coding
mm_57888.1	chr6	131367821	131367864	-	1	NA	exon (NM_011733, exon 8 of 9)	exon (NM_011733, exon 8 of 9)	20608	NM_139117	56449	Mm.458000	NM_011733	ENSMUSG00000030189	Ybx3	Csda|Dpba|MSY3|MSY4|Yb2|dbpA|oxyR	Y box protein 3	protein-coding
mm_12003.1	chr2	57265102	57265130	+	1	NA	intron (NM_010274, intron 1 of 16)	intron (NM_010274, intron 1 of 16)	26734	NM_010274	14571	Mm.3711	NM_010274	ENSMUSG00000026827	Gpd2	AA408484|AI448216|AU021455|AW494132|GPDH|Gdm1|Gpd-m|Gpdh-m|TISP38	glycerol phosphate dehydrogenase 2, mitochondrial	protein-coding
mm_107096.1	chr12	17690794	17690823	+	1	NA	promoter-TSS (NM_016677)	promoter-TSS (NM_016677)	-6	NM_016677	53602	Mm.313619	NM_016677	ENSMUSG00000071379	Hpcal1	NVP-3|Nvp3|VILIP3|Vnsl3|Vsnl3	hippocalcin-like 1	protein-coding
mm_100959.1	chr11	6635569	6635572	-	1	NA	TTS (NM_011709)	TTS (NM_011709)	3079	NM_011709	22373	Mm.268094	NM_011709	ENSMUSG00000000381	Wap	-	whey acidic protein	protein-coding
mm_6981.1	chr1	86356453	86356464	-	1	NA	promoter-TSS (NR_002851)	promoter-TSS (NR_002851)	-131	NR_002851	80828		NR_002851	ENSMUSG00000064823	Snord82	Rnu82|U82|Z25	small nucleolar RNA, C/D box 82	snoRNA
mm_59338.1	chr7	25463677	25463698	+	1	NA	3' UTR (NM_001039186, exon 8 of 8)	3' UTR (NM_001039186, exon 8 of 8)	13938	NM_001039185	26365	Mm.322502	NM_011926	ENSMUSG00000074272	Ceacam1	Bgp|Bgp1|C-CAM|CD66a|Cc1|Cea-1|Cea-7|Cea1|Cea7|Hv-2|Hv2|MHVR|MHVR1|Mhv-1|bb-1|mCEA1|mmCGM1|mmCGM1a|mmCGM2	carcinoembryonic antigen-related cell adhesion molecule 1	protein-coding
mm_129957.1	chr15	85131950	85131987	-	1	NA	promoter-TSS (NM_080470)	promoter-TSS (NM_080470)	-11	NM_080470	140557	Mm.182737	NM_080470	ENSMUSG00000022432	Smc1b	SMC-1B|SMC1beta|Smc1l2	structural maintenance of chromosomes 1B	protein-coding
mm_7638.1	chr1	127976445	127976457	-	1	NA	exon (NM_001285945, exon 13 of 21)	exon (NM_001285945, exon 13 of 21)	107678	NM_178690	226407	Mm.489713	NM_178690	ENSMUSG00000036104	Rab3gap1	1700003B17Rik|4732493F09Rik|AL117896|Rab3gap|p130	RAB3 GTPase activating protein subunit 1	protein-coding
mm_79252.1	chr9	50617517	50617561	+	1	NA	promoter-TSS (NM_001134902)	promoter-TSS (NM_001134902)	-75	NM_212449	270156	Mm.335149	NM_212449	ENSMUSG00000059820	AU019823	Gm639	expressed sequence AU019823	protein-coding
mm_171238.1	chr3	69182851	69182870	+	1	NA	Intergenic	(TTAGGG)n|Simple_repeat|Simple_repeat	-39559	NM_027843	71619	Mm.98122	NM_027843	ENSMUSG00000098207	Arl14	9130014L17Rik|Arf7	ADP-ribosylation factor-like 14	protein-coding
mm_106025.1	chr11	116027935	116027945	-	1	NA	Intergenic	Intergenic	-2376	NM_001286006	217331	Mm.297706	NM_172569	ENSMUSG00000020770	Unk	B230379M23Rik|Zc3h5|Zc3hdc5|mKIAA1753	unkempt family zinc finger	protein-coding
mm_80488.1	chr9	78369629	78369641	+	1	NA	Intergenic	Intergenic	-1436	NM_025274	434423	Mm.139314	NM_025274	ENSMUSG00000060461	Dppa5a	AA536857|Dppa5|Esg1|ecat2	developmental pluripotency associated 5A	protein-coding
mm_80071.1	chr9	69479547	69479579	+	1	NA	intron (NM_007585, intron 4 of 12)	intron (NM_007585, intron 4 of 12)	22619	NR_037296	100526560		NR_037296	ENSMUSG00000093042	Mir3109	mir-3109|mmu-mir-3109	microRNA 3109	ncRNA
mm_126635.1	chr15	83563572	83563580	+	1	NA	promoter-TSS (NM_009775)	promoter-TSS (NM_009775)	3	NM_009775	12257	Mm.1508	NM_009775	ENSMUSG00000041736	Tspo	Bzrp|IBP|PBR|Tspo1	translocator protein	protein-coding
mm_90148.1	chr10	118141803	118141870	+	1	NA	promoter-TSS (NM_010785)	promoter-TSS (NM_010785)	49	NM_010785	17245	Mm.101191	NM_010785	ENSMUSG00000020212	Mdm1	Arrd2|Mdm-1	transformed mouse 3T3 cell double minute 1	protein-coding
mm_104273.1	chr11	89095270	89095284	-	1	NA	Intergenic	ID_B1|SINE|B4	21436	NM_001033266	217071	Mm.342127	NM_001033266	ENSMUSG00000072553	Gm525	-	predicted gene 525	protein-coding
mm_140162.1	chr17	80224517	80224525	+	1	NA	promoter-TSS (NM_026053)	promoter-TSS (NM_026053)	32	NM_026053	67242	Mm.279985	NM_026053	ENSMUSG00000055760	Gemin6	2610019B15Rik|2810470M17Rik	gem (nuclear organelle) associated protein 6	protein-coding
mm_114520.1	chr13	73317815	73317830	+	1	NA	Intergenic	Intergenic	10660	NR_033306	407785	Mm.29897	NM_010888	ENSMUSG00000021606	Ndufs6	BC059730|IP13	NADH dehydrogenase (ubiquinone) Fe-S protein 6	protein-coding
mm_86666.1	chr10	17920190	17920205	+	1	NA	intron (NM_001033432, intron 1 of 3)	B4A|SINE|B4	27870	NM_001033432	380629	Mm.276430	NM_001033432	ENSMUSG00000039879	Heca	Gm869|HDC|HDCL	hdc homolog, cell cycle regulator	protein-coding
mm_98792.1	chr11	96944143	96944222	+	1	NA	promoter-TSS (NR_003293)	promoter-TSS (NR_003293)	36	NR_003293	319371	Mm.436865	NR_003293	ENSMUSG00000078700	D030028A08Rik	-	RIKEN cDNA D030028A08 gene	ncRNA
mm_49683.1	chr6	33249113	33249152	+	1	NA	promoter-TSS (NM_009148)	promoter-TSS (NM_009148)	-18	NM_009148	20336	Mm.265512	NM_009148	ENSMUSG00000029763	Exoc4	C78892|Sec8|Sec8l1	exocyst complex component 4	protein-coding
mm_154737.1	chrX	10252335	10252357	+	1	NA	promoter-TSS (NM_008769)	promoter-TSS (NM_008769)	41	NM_008769	18416	Mm.2611	NM_008769	ENSMUSG00000031173	Otc	AI265390|Sf|spf	ornithine transcarbamylase	protein-coding
mm_71714.1	chr8	61947405	61947416	+	1	NA	intron (NM_001293783, intron 6 of 37)	B3|SINE|B2	19323	NM_001293783	234311	Mm.275233	NM_144928	ENSMUSG00000037921	Ddx60	9830118M07	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	protein-coding
mm_38762.1	chr4	147903722	147903726	-	1	NA	intron (NM_001285920, intron 1 of 19)	intron (NM_001285920, intron 1 of 19)	974	NM_001285923	170731	Mm.154312	NM_133201	ENSMUSG00000029020	Mfn2	D630023P19Rik|Fzo	mitofusin 2	protein-coding
mm_13792.1	chr2	118870376	118870402	+	1	NA	intron (NM_019826, intron 3 of 11)	(T)n|Simple_repeat|Simple_repeat	8389	NM_019826	56357	Mm.6635	NM_019826	ENSMUSG00000027332	Ivd	1300016K07Rik|6720455E18Rik|AI463340	isovaleryl coenzyme A dehydrogenase	protein-coding
mm_37812.1	chr4	130934789	130934832	-	1	NA	3' UTR (NM_010686, exon 8 of 8)	3' UTR (NM_010686, exon 8 of 8)	-9575	NM_010769	17180	Mm.271796	NM_010769	ENSMUSG00000040533	Matn1	CMP|Crtm|Mat1|matrilin-1	matrilin 1, cartilage matrix protein	protein-coding
mm_14955.1	chr2	152080820	152080830	+	1	NA	promoter-TSS (NM_001160410)	promoter-TSS (NM_001160410)	-704	NM_001160410	545474	Mm.214317	NM_001160410	ENSMUSG00000060257	Scrt2	AW060659	scratch family zinc finger 2	protein-coding
mm_16610.1	chr2	5296202	5296214	-	1	NA	3' UTR (NM_001290375, exon 11 of 11)	3' UTR (NM_001290375, exon 11 of 11)	-83182	NR_030601	100124465		NR_030601	ENSMUSG00000078031	Mir466d	Mirn466d	microRNA 466d	ncRNA
mm_50212.1	chr6	42280846	42280848	+	1	NA	3' UTR (NM_007610, exon 11 of 11)	3' UTR (NM_007610, exon 11 of 11)	-5838	NM_013491	12723	Mm.386757	NM_013491	ENSMUSG00000029862	Clcn1	Clc-1|Clc1|SMCC1|adr|mto|myotonia|nmf355	chloride channel, voltage-sensitive 1	protein-coding
mm_94783.1	chr11	21953104	21953112	+	1	NA	Intergenic	Intergenic	48543	NM_011023	18423	Mm.129663	NM_011023	ENSMUSG00000005917	Otx1	A730044F23Rik|jv	orthodenticle homeobox 1	protein-coding
mm_31281.1	chr4	45848676	45848696	+	1	NA	promoter-TSS (NM_028788)	promoter-TSS (NM_028788)	-130	NM_001305421	74152	Mm.63645	NM_028788	ENSMUSG00000028327	Stra6l	1300002K09Rik|Rbpr2	STRA6-like	protein-coding
mm_51576.1	chr6	83758848	83758865	+	1	NA	TTS (NM_134157)	TTS (NM_134157)	3652	NR_105027	67934	Mm.126190	NR_105027	ENSMUSG00000099354	1700124L16Rik	-	RIKEN cDNA 1700124L16 gene	ncRNA
mm_36303.1	chr4	68954257	68954267	-	1	NA	5' UTR (NM_019967, exon 1 of 8)	5' UTR (NM_019967, exon 1 of 8)	135	NM_019967	56710	Mm.248788	NM_019967	ENSMUSG00000028351	Brinp1	BRINP|Dbc1|Dbccr1|Fam5a	bone morphogenic protein/retinoic acid inducible neural specific 1	protein-coding
mm_65551.1	chr7	27132507	27132534	-	1	NA	exon (NM_007817, exon 9 of 10)	exon (NM_007817, exon 9 of 10)	12565	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_35558.1	chr4	41569475	41569481	-	1	NA	promoter-TSS (NM_027993)	promoter-TSS (NM_027993)	49	NM_001159583	71901	Mm.39215	NM_027993	ENSMUSG00000028439	Fam219a	2310028H24Rik	family with sequence similarity 219, member A	protein-coding
mm_164210.1	chr15	82298936	82298938	+	1	NA	promoter-TSS (NM_029066)	promoter-TSS (NM_029066)	-47	NM_029066	74716	Mm.159315	NM_029066	ENSMUSG00000022455	Wbp2nl	4930521I23Rik|PAWP	WBP2 N-terminal like	protein-coding
mm_8813.1	chr1	161969160	161969190	-	1	NA	promoter-TSS (NM_026078)	promoter-TSS (NM_026078)	-13	NM_001039045	67292	Mm.45106	NM_026078	ENSMUSG00000026698	Pigc	3110030E07Rik|AW212108	phosphatidylinositol glycan anchor biosynthesis, class C	protein-coding
mm_59496.1	chr7	27535805	27535825	+	1	NA	exon (NM_011116, exon 11 of 14)	exon (NM_011116, exon 11 of 14)	12554	NM_001033315	233020	Mm.429716	NM_001033315	ENSMUSG00000040424	Hipk4	Gm162	homeodomain interacting protein kinase 4	protein-coding
mm_14509.1	chr2	132263274	132263318	+	1	NA	5' UTR (NM_001291040, exon 1 of 4)	5' UTR (NM_001291040, exon 1 of 4)	148	NM_138651	110911	Mm.284503	NM_138651	ENSMUSG00000058793	Cds2	5730450N06Rik|5730460C18Rik|AI854580|D2Wsu127e	CDP-diacylglycerol synthase (phosphatidate cytidylyltransferase) 2	protein-coding
mm_24001.1	chr3	86863215	86863221	+	1	NA	intron (NM_001195497, intron 2 of 15)	RMER17B|LTR|ERVK	57666	NM_001195496	70762	Mm.44490	NM_027539	ENSMUSG00000028078	Dclk2	6330415M09Rik|AU044875|CL2|CLICK2|Click-II|Dcamkl2	doublecortin-like kinase 2	protein-coding
mm_132046.1	chr16	29150170	29150181	+	1	NA	Intergenic	Intergenic	-59520	NM_013751	27281	Mm.103650	NM_013751	ENSMUSG00000022525	Hrasls	2810012B06Rik|A-C1|HRSL1|Hrasrs	HRAS-like suppressor	protein-coding
mm_123811.1	chr14	70522731	70522765	-	1	NA	exon (NM_011359, exon 2 of 6)	exon (NM_011359, exon 2 of 6)	1333	NM_011359	20389	Mm.24040	NM_011359	ENSMUSG00000022097	Sftpc	Bricd6|SP-C|SP5|SPC|Sftp-2|Sftp2|pro-SpC	surfactant associated protein C	protein-coding
mm_113003.1	chr13	21811761	21811766	+	1	NA	promoter-TSS (NM_175657)	promoter-TSS (NM_175657)	17	NM_001195421	100041230	Mm.442307	NM_001195421	ENSMUSG00000069306	Hist1h4m	Gm11275|OTTMUSG00000000446	histone cluster 1, H4m	protein-coding
mm_20418.1	chr2	129300940	129300946	-	1	NA	intron (NM_010554, intron 6 of 6)	intron (NM_010554, intron 6 of 6)	3573	NR_040371	100503468	Mm.446943	NR_040371	ENSMUSG00000085498	Gm14023	OTTMUSG00000015408	predicted gene 14023	ncRNA
mm_56583.1	chr6	106794593	106794616	-	1	NA	intron (NM_175357, intron 3 of 10)	intron (NM_175357, intron 3 of 10)	5483	NM_021449	58799	Mm.290085	NM_021449	ENSMUSG00000005362	Crbn	2610203G15Rik|2900045O07Rik|AF229032|AW108261|piL	cereblon	protein-coding
mm_36401.1	chr4	77826247	77826260	-	1	NA	intron (NM_011211, intron 2 of 39)	intron (NM_011211, intron 2 of 39)	385642	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding
mm_299.1	chr1	23291716	23291717	+	1	NA	promoter-TSS (NR_029717)	promoter-TSS (NR_029717)	15	NR_029717	723964		NR_029717	ENSMUSG00000065567	Mir30c-2	Mirn30c-2|mir-30c-2	microRNA 30c-2	ncRNA
mm_155669.1	chrX	90744659	90744711	+	1	NA	Intergenic	Intergenic	-147457	NM_001101450	212952	Mm.477436	NM_001101450	ENSMUSG00000091497	Gm44	-	predicted gene 44	protein-coding
mm_153107.1	chr19	32906185	32906205	-	1	NA	Intergenic	Intergenic	148618	NM_008960	19211	Mm.245395	NM_008960	ENSMUSG00000013663	Pten	2310035O07Rik|A130070J02Rik|AI463227|B430203M17Rik|MMAC1|TEP1	phosphatase and tensin homolog	protein-coding
mm_169683.1	chr15	72480268	72480274	+	1	NA	Intergenic	MTA_Mm|LTR|ERVL-MaLR	66008	NM_001033876	223604	Mm.386856	NM_001033876	ENSMUSG00000036760	Kcnk9	Task3	potassium channel, subfamily K, member 9	protein-coding
mm_107430.1	chr12	35712946	35712949	+	1	NA	Intergenic	Intergenic	-17829	NR_045050	71581	Mm.100110	NR_045050		9130015A21Rik	100043575|Gm4527	RIKEN cDNA 9130015A21 gene	ncRNA
mm_171964.1	chr5	85263866	85263870	+	1	NA	Intergenic	Intergenic	801715	NM_001345902	12617	Mm.4649	NM_007683	ENSMUSG00000029253	Cenpc1	CENP-C|Cenpc	centromere protein C1	protein-coding
mm_96650.1	chr11	69364011	69364041	+	1	NA	exon (NM_146019, exon 3 of 40)	exon (NM_146019, exon 3 of 40)	5400	NM_146019	216848	Mm.178246	NM_146019	ENSMUSG00000018474	Chd3	2600010P09Rik|AF020312|Chd7|Prp7|Prp9-1	chromodomain helicase DNA binding protein 3	protein-coding
mm_172415.1	chr7	23534850	23534850	-	1	NA	Intergenic	ERVB7_1-LTR_MM|LTR|ERVK	-5870	NM_001166842	100043101	Mm.480247	NM_001166842	ENSMUSG00000074291	Vmn1r168	ENSMUSG00000074291|Gm10659	vomeronasal 1 receptor 168	protein-coding
mm_166399.1	chr5	135957883	135957899	+	1	NA	Intergenic	Intergenic	16585	NM_001160366	109267	Mm.332750	NM_001160366	ENSMUSG00000029699	Ssc4d	C330016E03Rik|S4D-SRCRB|SRCRB-S4D|Srcrb4d	scavenger receptor cysteine rich family, 4 domains	protein-coding
mm_149964.1	chr19	28995204	28995213	+	1	NA	exon (NM_025950, exon 2 of 7)	exon (NM_025950, exon 2 of 7)	4856	NM_025950	67072	Mm.78875	NM_025950	ENSMUSG00000024780	Cdc37l1	2700033A15Rik|BB159850|Cdc37l|Harc	cell division cycle 37-like 1	protein-coding
mm_134463.1	chr16	18426452	18426462	-	1	NA	promoter-TSS (NM_013711)	promoter-TSS (NM_013711)	40	NM_013711	26462	Mm.390906	NM_013711	ENSMUSG00000075704	Txnrd2	AA118373|ESTM573010|TGR|Tr3|Trxr2|Trxrd2	thioredoxin reductase 2	protein-coding
mm_2028.1	chr1	87183311	87183316	+	1	NA	promoter-TSS (NM_027084)	promoter-TSS (NM_027084)	-1	NM_027084	69453	Mm.84618	NM_027084	ENSMUSG00000036480	Prss56	1700027L20Rik	protease, serine 56	protein-coding
mm_51571.1	chr6	83743011	83743038	+	1	NA	promoter-TSS (NM_134157)	promoter-TSS (NM_134157)	7	NM_134157	110935	Mm.220823	NM_134157	ENSMUSG00000006269	Atp6v1b1	AW208839|Atp6b1|D630003L15|D630030L16Rik|D630039P21Rik|Vpp-3|Vpp3	ATPase, H+ transporting, lysosomal V1 subunit B1	protein-coding
mm_88624.1	chr10	79879658	79879669	+	1	NA	promoter-TSS (NM_011178)	promoter-TSS (NM_011178)	-4	NM_011178	19152	Mm.2364	NM_011178	ENSMUSG00000057729	Prtn3	PR3|mPR3	proteinase 3	protein-coding
mm_154905.1	chrX	21068428	21068433	+	1	NA	promoter-TSS (NM_001085393)	promoter-TSS (NM_001085393)	-58	NM_001085393	278203		NM_001085393	ENSMUSG00000037167	Spaca5	Gm718|Lyze	sperm acrosome associated 5	protein-coding
mm_43037.1	chr5	123998676	123998720	+	1	NA	intron (NM_145070, intron 18 of 31)	intron (NM_145070, intron 18 of 31)	1846	NR_105999	102465625		NR_105999	ENSMUSG00000098454	Mir7032	Gm27309|mmu-mir-7032	microRNA 7032	ncRNA
mm_103812.1	chr11	83002577	83002593	-	1	NA	3' UTR (NM_001167743, exon 4 of 4)	3' UTR (NM_001167743, exon 4 of 4)	-10755	NM_172796	237886	Mm.270253	NM_172796	ENSMUSG00000069793	Slfn9	9830137M10Rik	schlafen 9	protein-coding
mm_39403.1	chr5	14514930	14514951	+	1	NA	promoter-TSS (NM_011995)	promoter-TSS (NM_011995)	22	NM_001110796	26875	Mm.146275	NM_011995	ENSMUSG00000061601	Pclo	Acz|Pico	piccolo (presynaptic cytomatrix protein)	protein-coding
mm_115188.1	chr13	108498642	108498665	+	1	NA	Intergenic	Intergenic	-155524	NM_011056	238871	Mm.434429	NM_011056	ENSMUSG00000021699	Pde4d	9630011N22Rik|Dpde3	phosphodiesterase 4D, cAMP specific	protein-coding
mm_4651.1	chr1	180333987	180334009	+	1	NA	exon (NM_001081175, exon 2 of 8)	exon (NM_001081175, exon 2 of 8)	-3449	NR_003623	277333	Mm.389223	NM_199472		Gm5069	EG277333	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_167627.1	chr9	61156919	61156937	+	1	NA	Intergenic	Lx8b|LINE|L1	18413	NR_045705	619328	Mm.325722	NR_045705	ENSMUSG00000110998	I730028E13Rik	-	RIKEN cDNA I730028E13 gene	ncRNA
mm_68320.1	chr7	106502126	106502136	-	1	NA	Intergenic	A-rich|Low_complexity|Low_complexity	-61058	NR_003967	209380	Mm.461779	NM_001001318		Gm4759	EG209380	GTPase, very large interferon inducible 1 pseudogene	pseudo
mm_145141.1	chr18	45559561	45559569	+	1	NA	promoter-TSS (NM_080465)	promoter-TSS (NM_080465)	-589	NM_080465	140492	Mm.411614	NM_080465	ENSMUSG00000054477	Kcnn2	KCa2.2|SK2|SKCA2|bc|fri	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2	protein-coding
mm_7166.1	chr1	92048955	92049000	-	1	NA	intron (NM_207225, intron 3 of 26)	MIRc|SINE|MIR	131364	NM_207225	208727	Mm.318567	NM_207225	ENSMUSG00000026313	Hdac4	4932408F19Rik|HD4	histone deacetylase 4	protein-coding
mm_117946.1	chr13	99435137	99435154	-	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-22319	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_79788.1	chr9	63690769	63690816	+	1	NA	intron (NM_016769, intron 1 of 8)	intron (NM_016769, intron 1 of 8)	67202	NM_016769	17127	Mm.7320	NM_016769	ENSMUSG00000032402	Smad3	AU022421|Madh3	SMAD family member 3	protein-coding
mm_84582.1	chr9	69491773	69491791	-	1	NA	TTS (NM_007585)	TTS (NM_007585)	34838	NR_037296	100526560		NR_037296	ENSMUSG00000093042	Mir3109	mir-3109|mmu-mir-3109	microRNA 3109	ncRNA
mm_41942.1	chr5	105731735	105731752	+	1	NA	intron (NM_178701, intron 1 of 2)	intron (NM_178701, intron 1 of 2)	30933	NM_178701	231549	Mm.23837	NM_178701	ENSMUSG00000046079	Lrrc8d	2810473G09Rik|4930525N13Rik|A930019F03|Lrrc5	leucine rich repeat containing 8D	protein-coding
mm_46009.1	chr5	90786603	90786631	-	1	NA	exon (NM_203320, exon 3 of 4)	exon (NM_203320, exon 3 of 4)	516	NM_203320	330122	Mm.244289	NM_203320	ENSMUSG00000029379	Cxcl3	Dcip1|Gm1960	chemokine (C-X-C motif) ligand 3	protein-coding
mm_123083.1	chr14	55745525	55745642	-	1	NA	promoter-TSS (NM_026403)	promoter-TSS (NM_026403)	101	NM_026819	52585	Mm.21623	NM_026819	ENSMUSG00000002332	Dhrs1	1110029G07Rik|AW112170|D14Ertd484e	dehydrogenase/reductase (SDR family) member 1	protein-coding
mm_587.1	chr1	39478849	39478867	+	1	NA	promoter-TSS (NM_018775)	promoter-TSS (NM_018775)	-111	NM_018775	54610	Mm.387293	NM_018775	ENSMUSG00000003134	Tbc1d8	AD3|HBLP1|VRP	TBC1 domain family, member 8	protein-coding
mm_163765.1	chr13	120017026	120017045	+	1	NA	Intergenic	L1_Mus3|LINE|L1	35169	NM_001302966	100861753	Mm.165042	NM_001302966	ENSMUSG00000095609	Gm21188	-	predicted gene, 21188	protein-coding
mm_132139.1	chr16	31940826	31940849	+	1	NA	intron (NM_172822, intron 1 of 2)	intron (NM_172822, intron 1 of 2)	6986	NM_172822	239827	Mm.440388	NM_172822	ENSMUSG00000045625	Pigz	F630022B06Rik	phosphatidylinositol glycan anchor biosynthesis, class Z	protein-coding
mm_136370.1	chr16	92822065	92822069	-	1	NA	intron (NM_001111022, intron 2 of 6)	intron (NM_001111022, intron 2 of 6)	4007	NM_001111021	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_80768.1	chr9	95559662	95559705	+	1	NA	promoter-TSS (NM_198414)	promoter-TSS (NM_198414)	-134	NM_198414	75552	Mm.151485	NM_198414	ENSMUSG00000064225	Paqr9	1700020G04Rik	progestin and adipoQ receptor family member IX	protein-coding
mm_131791.1	chr16	22898926	22898934	+	1	NA	exon (NM_001276450, exon 7 of 7)	exon (NM_001276450, exon 7 of 7)	-4544	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_164280.1	chr15	102315412	102315426	+	1	NA	exon (NM_001014976, exon 18 of 31)	exon (NM_001014976, exon 18 of 31)	-10697	NM_027044	56612	Mm.158264	NM_020031	ENSMUSG00000001289	Pfdn5	1190001O17Rik|1700010A06Rik|D15Ertd697e|Eig1|MM-1	prefoldin 5	protein-coding
mm_117826.1	chr13	98206138	98206148	-	1	NA	promoter-TSS (NM_012026)	promoter-TSS (NM_012026)	22	NM_012026	110596	Mm.252718	NM_012026	ENSMUSG00000021662	Arhgef28	9230110L08Rik|AI323540|D13Bwg1089e|RIP2|Rgnef|RhoGEF|Rhoip2|p190RhoGEF	Rho guanine nucleotide exchange factor (GEF) 28	protein-coding
mm_73629.1	chr8	110721423	110721444	+	1	NA	promoter-TSS (NM_198625)	promoter-TSS (NM_198625)	-43	NM_198625	244654	Mm.490385	NM_198625	ENSMUSG00000033763	Mtss1l	ABBA	metastasis suppressor 1-like	protein-coding
mm_168186.1	chr10	60277645	60277652	+	1	NA	promoter-TSS (NM_011179)	promoter-TSS (NM_011179)	20	NM_001146121	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_139099.1	chr17	46919849	46919857	+	1	NA	exon (NM_008938, exon 2 of 3)	exon (NM_008938, exon 2 of 3)	9368	NM_008938	19133	Mm.291370	NM_008938	ENSMUSG00000023978	Prph2	AOFMD|AVMD|Nmf193|PRPH|RP7|Rd-2|Rd2|Rds|Tspan22|rds	peripherin 2	protein-coding
mm_161766.1	chr17	36269094	36269094	-	1	NA	intron (NM_024468, intron 1 of 6)	intron (NM_024468, intron 1 of 6)	2339	NM_178281	79263	Mm.40624	NM_024468	ENSMUSG00000045409	Trim39	1100001D15Rik|E130103K13Rik|RBCC-B30.2|Rnf23|mKIAA4179|tfp	tripartite motif-containing 39	protein-coding
mm_73970.1	chr8	120488822	120488840	+	1	NA	promoter-TSS (NM_198671)	promoter-TSS (NM_198671)	-35	NM_198671	382034	Mm.334856	NM_198671	ENSMUSG00000031822	Gse1	2210013I18Rik|mKIAA0182	genetic suppressor element 1, coiled-coil protein	protein-coding
mm_139776.1	chr17	65642322	65642328	+	1	NA	promoter-TSS (NM_001146002)	promoter-TSS (NM_001146002)	-121	NM_001146002	213272	Mm.255732	NM_153519	ENSMUSG00000050612	Txndc2	AU021712|Sptrx-1|Sptrx1|Trx4	thioredoxin domain containing 2 (spermatozoa)	protein-coding
mm_123770.1	chr14	70212410	70212416	-	1	NA	Intergenic	Intergenic	-4742	NM_011366	20410	Mm.5068	NM_011366	ENSMUSG00000022091	Sorbs3	SCAM-1|SH3P3|Sh3d4|vinexin-g	sorbin and SH3 domain containing 3	protein-coding
mm_55012.1	chr6	48840553	48840583	-	1	NA	promoter-TSS (NM_025326)	promoter-TSS (NM_025326)	420	NM_023056	65963	Mm.28385	NM_023056	ENSMUSG00000029810	Tmem176b	1810009M01Rik|Clast1|Lr8	transmembrane protein 176B	protein-coding
mm_45869.1	chr5	88008108	88008125	-	1	NA	exon (NM_011422, exon 3 of 3)	exon (NM_011422, exon 3 of 3)	5591	NM_011422	20599	Mm.261199	NM_011422	ENSMUSG00000029280	Smr3a	AA589601|MSG1|MSG3|Smr1|Smr3	submaxillary gland androgen regulated protein 3A	protein-coding
mm_7911.1	chr1	133690062	133690072	-	1	NA	promoter-TSS (NM_001159649)	promoter-TSS (NM_001159649)	41	NM_001159649	240754	Mm.36534	NM_172842	ENSMUSG00000051998	Lax1	A530029E09|E430019B13Rik	lymphocyte transmembrane adaptor 1	protein-coding
mm_160290.1	chr7	127195629	127195629	-	1	NA	intron (NM_001285905, intron 1 of 6)	CpG	448	NM_001285907	70233	Mm.28050	NM_027353	ENSMUSG00000042502	Cd2bp2	1500011B02Rik|2410024K20Rik|AW048183	CD2 antigen (cytoplasmic tail) binding protein 2	protein-coding
mm_8217.1	chr1	138157619	138157637	-	1	NA	intron (NM_001111316, intron 1 of 31)	(GA)n|Simple_repeat|Simple_repeat	17498	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_115913.1	chr13	23465863	23465870	-	1	NA	promoter-TSS (NM_013483)	promoter-TSS (NM_013483)	35	NM_013483	12231	Mm.1420	NM_013483	ENSMUSG00000000706	Btn1a1	Btn	butyrophilin, subfamily 1, member A1	protein-coding
mm_144320.1	chr18	12734810	12734813	+	1	NA	intron (NM_028341, intron 11 of 13)	intron (NM_028341, intron 11 of 13)	-6544	NM_001042419	71132	Mm.179740	NM_027687	ENSMUSG00000024430	Cabyr	1700016C01Rik|4933421A18Rik|CBP86|FSP-2	calcium-binding tyrosine-(Y)-phosphorylation regulated (fibrousheathin 2)	protein-coding
mm_129016.1	chr15	74926765	74926783	-	1	NA	Intergenic	Intergenic	-28277	NM_001164039	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_164853.1	chr18	47901684	47901700	+	1	NA	Intergenic	B4A|SINE|B4	-21149	NR_045404	414127	Mm.450768	NR_045404		G630055G22Rik	-	RIKEN cDNA G630055G22 gene	ncRNA
mm_40347.1	chr5	45669885	45669901	+	1	NA	promoter-TSS (NM_019438)	promoter-TSS (NM_019438)	-32	NM_019438	54392	Mm.32012	NM_019438	ENSMUSG00000015880	Ncapg	5730507H05Rik|Hcapg|MFT.M05.13	non-SMC condensin I complex, subunit G	protein-coding
mm_27291.1	chr3	41742472	41742548	-	1	NA	promoter-TSS (NM_001081411)	promoter-TSS (NM_001081411)	4	NM_001081411	67161	Mm.331001	NM_026008	ENSMUSG00000059834	Sclt1	2610207F23Rik|4931421F20Rik	sodium channel and clathrin linker 1	protein-coding
mm_45143.1	chr5	49132027	49132029	-	1	NA	intron (NM_001199244, intron 1 of 7)	U2|snRNA|snRNA	153631	NM_001199244	80334	Mm.160172	NM_030265	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding
mm_135293.1	chr16	38550174	38550235	-	1	NA	promoter-TSS (NM_172380)	promoter-TSS (NM_172380)	52	NM_172380	224143	Mm.284366	NM_172380	ENSMUSG00000034064	Poglut1	9630046K23Rik|Clp46|Ktelc1|Rumi	protein O-glucosyltransferase 1	protein-coding
mm_5209.1	chr1	13587826	13587830	-	1	NA	intron (NM_028173, intron 1 of 10)	B1_Mur4|SINE|Alu	2082	NM_028173	72265	Mm.28765	NM_028173	ENSMUSG00000025935	Tram1	1810049E02Rik|TRAMP	translocating chain-associating membrane protein 1	protein-coding
mm_10208.1	chr2	5230054	5230062	+	1	NA	3' UTR (NM_028804, exon 3 of 3)	3' UTR (NM_028804, exon 3 of 3)	92282	NM_028804	74186	Mm.274715	NM_028804	ENSMUSG00000026676	Ccdc3	2310045O21Rik	coiled-coil domain containing 3	protein-coding
mm_164109.1	chr15	27855699	27855723	+	1	NA	intron (NM_001081302, intron 12 of 56)	intron (NM_001081302, intron 12 of 56)	170137	NM_001081302	223435	Mm.485422	NM_001081302	ENSMUSG00000022263	Trio	6720464I07Rik|AA408740|Solo	triple functional domain (PTPRF interacting)	protein-coding
mm_157745.1	chrX	73401695	73401709	-	1	NA	Intergenic	Intergenic	-9394	NM_009566	22754	Mm.5060	NM_009566	ENSMUSG00000031374	Zfp92	-	zinc finger protein 92	protein-coding
mm_73349.1	chr8	105427623	105427633	+	1	NA	promoter-TSS (NM_001170789)	promoter-TSS (NM_001170789)	-12	NM_001033371	270091	Mm.212709	NM_001033371	ENSMUSG00000054320	Lrrc36	BC036564	leucine rich repeat containing 36	protein-coding
mm_146378.1	chr18	82585126	82585139	+	1	NA	3' UTR (NM_010777, exon 7 of 7)	3' UTR (NM_010777, exon 7 of 7)	30624	NM_001025254	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_121332.1	chr14	115040295	115040329	+	1	NA	Intergenic	Intergenic	-3359	NR_029785	723905		NR_029785	ENSMUSG00000065508	Mir17	Mirn17|mir-17|mmu-mir-17	microRNA 17	ncRNA
mm_48132.1	chr5	137149975	137149984	-	1	NA	Intergenic	Intergenic	-33772	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_164710.1	chr17	53145590	53145592	+	1	NA	Intergenic	Lx5c|LINE|L1	317730	NM_172497	211482	Mm.60887	NM_172497	ENSMUSG00000023931	Efhb	4921525D22Rik	EF hand domain family, member B	protein-coding
mm_46596.1	chr5	107787256	107787259	-	1	NA	intron (NM_007964, intron 16 of 17)	intron (NM_007964, intron 16 of 17)	-42905	NM_001276397	73318	Mm.441500	NM_028502	ENSMUSG00000063447	Ube2d2b	1700013N18Rik	ubiquitin-conjugating enzyme E2D 2B	protein-coding
mm_14816.1	chr2	146222094	146222111	+	1	NA	5' UTR (NM_016889, exon 1 of 1)	5' UTR (NM_016889, exon 1 of 1)	105	NM_016889	53626	Mm.379070	NM_016889	ENSMUSG00000068154	Insm1	IA-1	insulinoma-associated 1	protein-coding
mm_146267.1	chr18	77870267	77870306	+	1	NA	intron (NM_013831, intron 6 of 14)	intron (NM_013831, intron 6 of 14)	-68181	NM_001195633	100502841	Mm.297782	NM_001195633	ENSMUSG00000039840	Epg5	4732475F16|5430411K18Rik|AI661957|AW456499|mKIAA1632	ectopic P-granules autophagy protein 5 homolog (C. elegans)	protein-coding
mm_111743.1	chr12	103897207	103897238	-	1	NA	exon (NM_009245, exon 3 of 5)	exon (NM_009245, exon 3 of 5)	7728	NM_009245	20702	Mm.439692	NM_009245	ENSMUSG00000079015	Serpina1c	Pi3|Pi6|Skalp|Spi1-3|Spi1-6|Wap3	serine (or cysteine) peptidase inhibitor, clade A, member 1C	protein-coding
mm_52432.1	chr6	113483585	113483618	+	1	NA	promoter-TSS (NM_133930)	promoter-TSS (NM_133930)	32	NM_133930	171508	Mm.41593	NM_133930	ENSMUSG00000030284	Creld1	AI843811	cysteine-rich with EGF-like domains 1	protein-coding
mm_54250.1	chr6	28261908	28261943	-	1	NA	promoter-TSS (NM_001081678)	promoter-TSS (NM_001081678)	-324	NM_001081678	627049	Mm.84441	NM_001081678	ENSMUSG00000039841	Zfp800	AA407452|Znf800	zinc finger protein 800	protein-coding
mm_45152.1	chr5	49323144	49323154	-	1	NA	Intergenic	Intergenic	-37490	NM_001199244	80334	Mm.160172	NM_030265	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding
mm_110635.1	chr12	57546150	57546158	-	1	NA	promoter-TSS (NM_008259)	promoter-TSS (NM_008259)	-33	NM_008259	15375	Mm.4578	NM_008259	ENSMUSG00000035451	Foxa1	Hnf-3a|Hnf3a|Tcf-3a|Tcf3a	forkhead box A1	protein-coding
mm_69038.1	chr7	126799164	126799191	-	1	NA	promoter-TSS (NM_001177307)	promoter-TSS (NM_001177307)	1	NM_001177307	11674	Mm.275831	NM_007438	ENSMUSG00000030695	Aldoa	Aldo-1|Aldo1	aldolase A, fructose-bisphosphate	protein-coding
mm_70392.1	chr8	11007430	11007466	+	1	NA	promoter-TSS (NR_046017)	promoter-TSS (NR_046017)	-402	NR_046017	619321	Mm.403007	NR_046017	ENSMUSG00000096938	9530052E02Rik	-	RIKEN cDNA 9530052E02 gene	ncRNA
mm_143330.1	chr17	66449625	66449650	-	1	NA	5' UTR (NM_172963, exon 1 of 14)	5' UTR (NM_172963, exon 1 of 14)	113	NM_172963	68617	Mm.33421	NM_172963	ENSMUSG00000052105	Mtcl1	1110012J17Rik|Ccdc165|D130071O13|Kiaa0802|Soga2|mKIAA0802|t8219b25	microtubule crosslinking factor 1	protein-coding
mm_114161.1	chr13	55413185	55413191	+	1	NA	exon (NM_011392, exon 13 of 13)	exon (NM_011392, exon 13 of 13)	2044	NM_029303	75477	Mm.432537	NM_029303	ENSMUSG00000044444	Pfn3	1700012P12Rik	profilin 3	protein-coding
mm_83810.1	chr9	53592025	53592036	-	1	NA	exon (NM_144784, exon 6 of 12)	exon (NM_144784, exon 6 of 12)	18320	NM_144784	110446	Mm.293233	NM_144784	ENSMUSG00000032047	Acat1	6330585C21Rik|Acat	acetyl-Coenzyme A acetyltransferase 1	protein-coding
mm_22432.1	chr2	181671623	181671645	-	1	NA	promoter-TSS (NM_009236)	promoter-TSS (NM_009236)	6	NM_009236	20672	Mm.264904	NM_009236	ENSMUSG00000046470	Sox18	AI385749|Ra|Ragl	SRY (sex determining region Y)-box 18	protein-coding
mm_44010.1	chr5	147077526	147077542	+	1	NA	promoter-TSS (NM_080795)	promoter-TSS (NM_080795)	188	NM_009087	20018	Mm.317557	NM_009087	ENSMUSG00000029642	Polr1d	1110003G10Rik|AC19|RPA16|Rpo1-3	polymerase (RNA) I polypeptide D	protein-coding
mm_23468.1	chr3	60476019	60476050	+	1	NA	intron (NM_001253713, intron 2 of 9)	intron (NM_001253713, intron 2 of 9)	3204	NM_001253713	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_110211.1	chr12	28582518	28582533	-	1	NA	promoter-TSS (NM_053156)	promoter-TSS (NM_053156)	-42	NM_053156	94041	Mm.84927	NM_053156	ENSMUSG00000020636	Allc	1700012B22Rik|Alc	allantoicase	protein-coding
mm_148611.1	chr19	5366388	5366421	+	1	NA	promoter-TSS (NM_027236)	promoter-TSS (NM_027236)	-41	NM_001038231	23825	Mm.358649	NM_011793	ENSMUSG00000024844	Banf1	Baf|Bcrp1|L2bp1/Baf	barrier to autointegration factor 1	protein-coding
mm_63670.1	chr7	130002206	130002209	+	1	NA	Intergenic	Intergenic	40042	NR_046077	100043150	Mm.334264	NR_046077	ENSMUSG00000108504	Gm4265	-	predicted gene 4265	ncRNA
mm_83374.1	chr9	44526398	44526423	-	1	NA	promoter-TSS (NM_007551)	promoter-TSS (NM_007551)	11	NM_007551	12145	Mm.6246	NM_007551	ENSMUSG00000047880	Cxcr5	Blr1|CXC-R5|CXCR-5|Gpcr6|MDR15	chemokine (C-X-C motif) receptor 5	protein-coding
mm_45373.1	chr5	66048520	66048523	-	1	NA	intron (NM_178446, intron 2 of 6)	intron (NM_178446, intron 2 of 6)	-44236	NR_027961	231253	Mm.436542	NM_177679	ENSMUSG00000054598	9130230L23Rik	-	RIKEN cDNA 9130230L23 gene	ncRNA
mm_33925.1	chr4	136653233	136653243	+	1	NA	3' UTR (NM_010142, exon 16 of 16)	3' UTR (NM_010142, exon 16 of 16)	30617	NM_001243262	242707	Mm.448979	NM_001243262	ENSMUSG00000070683	Lactbl1	-	lactamase, beta-like 1	protein-coding
mm_50083.1	chr6	41523731	41523754	+	1	NA	intron (NM_009430, intron 2 of 4)	intron (NM_009430, intron 2 of 4)	1966	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_5850.1	chr1	52992680	52992688	-	1	NA	Intergenic	L1Md_F2|LINE|L1	-39844	NM_144953	67080	Mm.236287	NM_144953	ENSMUSG00000043629	1700019D03Rik	2410136C24Rik|AA410151|smAKAP	RIKEN cDNA 1700019D03 gene	protein-coding
mm_11129.1	chr2	28230103	28230114	+	1	NA	3' UTR (NM_001038613, exon 6 of 6)	3' UTR (NM_001038613, exon 6 of 6)	24419	NM_019498	56177	Mm.43278	NM_019498	ENSMUSG00000026833	Olfm1	AMY|AW742568|Noe1|OlfA|Pancortin|Pancortin3	olfactomedin 1	protein-coding
mm_90350.1	chr10	127164772	127164786	+	1	NA	promoter-TSS (NM_008080)	promoter-TSS (NM_008080)	-377	NR_045166	14421	Mm.386762	NM_008080	ENSMUSG00000006731	B4galnt1	4933429D13Rik|Gal-NAc-T|GalNAc-T|GalNAcT|Galgt1|Ggm-2|Ggm2	beta-1,4-N-acetyl-galactosaminyl transferase 1	protein-coding
mm_72370.1	chr8	80950108	80950111	+	1	NA	Intergenic	Intergenic	64797	NM_027554	74841	Mm.246018	NM_027554	ENSMUSG00000038250	Usp38	4631402N15Rik|4833420O05Rik|AA536967|AU044701|AW544820|mKIAA1891	ubiquitin specific peptidase 38	protein-coding
mm_42698.1	chr5	119881343	119881346	+	1	NA	intron (NM_011537, intron 8 of 8)	RMER12C|LTR|ERVK	46681	NM_011537	21388	Mm.103636	NM_011537	ENSMUSG00000018263	Tbx5	-	T-box 5	protein-coding
mm_144378.1	chr18	20603352	20603364	+	1	NA	3' UTR (NM_007883, exon 15 of 15)	3' UTR (NM_007883, exon 15 of 15)	45284	NM_007883	13511	Mm.345891	NM_007883	ENSMUSG00000044393	Dsg2	AA408168|D18Ertd293e	desmoglein 2	protein-coding
mm_153626.1	chr19	44012428	44012442	-	1	NA	exon (NM_001167905, exon 7 of 8)	exon (NM_001167905, exon 7 of 8)	16812	NM_001001446	226143	Mm.329866	NM_001001446	ENSMUSG00000025197	Cyp2c44	AW107714|BC034834|b2b386Clo	cytochrome P450, family 2, subfamily c, polypeptide 44	protein-coding
mm_129118.1	chr15	76091595	76091653	-	1	NA	Intergenic	CpG	-1611	NM_144847	223649	Mm.101946	NM_144847	ENSMUSG00000075590	Nrbp2	BC011468	nuclear receptor binding protein 2	protein-coding
mm_42802.1	chr5	121714176	121714180	+	1	NA	intron (NM_009125, intron 1 of 24)	intron (NM_009125, intron 1 of 24)	2569	NM_009125	20239	Mm.260900	NM_009125	ENSMUSG00000042605	Atxn2	9630045M23Rik|ATX2|AW544490|Sca2	ataxin 2	protein-coding
mm_123144.1	chr14	57057568	57057589	-	1	NA	5' UTR (NM_001271623, exon 1 of 2)	5' UTR (NM_001271623, exon 1 of 2)	145	NM_001271623	14611	Mm.57207	NM_016975	ENSMUSG00000048582	Gja3	Cnx46|Cx43|Cx46|Gja-3	gap junction protein, alpha 3	protein-coding
mm_159823.1	chr5	123482107	123482107	-	1	NA	promoter-TSS (NM_029594)	promoter-TSS (NM_029594)	-6	NM_029594	76399	Mm.75049	NM_029594	ENSMUSG00000029437	Il31	1700013B14Rik	interleukin 31	protein-coding
mm_18190.1	chr2	45113218	45113238	-	1	NA	promoter-TSS (NM_015753)	promoter-TSS (NM_015753)	51	NM_015753	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_156688.1	chrX	159414579	159414589	+	1	NA	promoter-TSS (NM_001081124)	promoter-TSS (NM_001081124)	12	NM_001313751	78283	Mm.160079	NM_001081124	ENSMUSG00000041020	Map7d2	1600028E09Rik|2900002G04Rik|5330432J06Rik|C030036K04Rik|Mtap7d2	MAP7 domain containing 2	protein-coding
mm_18521.1	chr2	63080104	63080111	-	1	NA	intron (NM_133207, intron 2 of 15)	B3A|SINE|B2	104180	NM_133207	170738	Mm.242532	NM_133207	ENSMUSG00000059742	Kcnh7	9330137I11Rik|Kv11.3|erg3	potassium voltage-gated channel, subfamily H (eag-related), member 7	protein-coding
mm_161405.1	chr14	122983414	122983414	-	1	NA	promoter-TSS (NM_028651)	promoter-TSS (NM_028651)	-153	NM_028651	70551	Mm.271988	NM_028651	ENSMUSG00000041594	Tmtc4	4930403J22Rik|5730419O14Rik	transmembrane and tetratricopeptide repeat containing 4	protein-coding
mm_170034.1	chr17	22739839	22739842	-	1	NA	Intergenic	Intergenic	77907	NR_030709	100042679	Mm.484007	NR_030709		Gm16386	EG545191|ENSMUSG00000073442|Gm21017	zinc finger protein 946 pseudogene	pseudo
mm_120840.1	chr14	75187282	75187294	+	1	NA	intron (NM_008879, intron 2 of 16)	intron (NM_008879, intron 2 of 16)	50863	NM_008879	18826	Mm.153911	NM_008879	ENSMUSG00000021998	Lcp1	AW536232|D14Ertd310e|LCP-1|Pls2|pp65	lymphocyte cytosolic protein 1	protein-coding
mm_63561.1	chr7	128107683	128107695	+	1	NA	exon (NM_008401, exon 15 of 30)	exon (NM_008401, exon 15 of 30)	-21879	NM_021334	16411	Mm.22378	NM_021334	ENSMUSG00000030789	Itgax	AI449405|Cd11c|Cr4|N418	integrin alpha X	protein-coding
mm_11995.1	chr2	55597349	55597362	+	1	NA	3' UTR (NM_001304810, exon 3 of 3)	3' UTR (NM_001304810, exon 3 of 3)	161385	NM_008426	16519	Mm.5127	NM_008426	ENSMUSG00000026824	Kcnj3	GIRK-1|GIRK1|Kcnf3|Kir3.1	potassium inwardly-rectifying channel, subfamily J, member 3	protein-coding
mm_152565.1	chr19	11587835	11587837	-	1	NA	intron (NM_026835, intron 6 of 6)	intron (NM_026835, intron 6 of 6)	16968	NM_026835	68774	Mm.290390	NM_026835	ENSMUSG00000024679	Ms4a6d	1110058E16Rik|AI447446|Ms4a11	membrane-spanning 4-domains, subfamily A, member 6D	protein-coding
mm_171705.1	chr4	74643781	74643782	-	1	NA	Intergenic	L1Md_A|LINE|L1	391902	NM_144787	76804	Mm.209059	NM_144787	ENSMUSG00000028397	Kdm4c	2410141F18Rik|AA517467|Gasc1|Jmjd2c	lysine (K)-specific demethylase 4C	protein-coding
mm_65291.1	chr7	24450627	24450636	-	1	NA	Intergenic	Intergenic	-4949	NM_199013	210145	Mm.33811	NM_199013	ENSMUSG00000062028	Irgc1	F630044M05Rik|Gm1102|Gm474|Ifgge|Iigp5|Irgc	immunity-related GTPase family, cinema 1	protein-coding
mm_152227.1	chr19	8707861	8707872	-	1	NA	exon (NM_008577, exon 9 of 9)	exon (NM_008577, exon 9 of 9)	6031	NM_008577	17254	Mm.4114	NM_008577	ENSMUSG00000010095	Slc3a2	4F2|4F2HC|AI314110|Cd98|Ly-10|Ly-m10|Ly10|Mdu1|Mgp-2hc|NACAE	solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2	protein-coding
mm_534.1	chr1	37997957	37997963	+	1	NA	promoter-TSS (NM_172054)	promoter-TSS (NM_172054)	-50	NM_198303	226982	Mm.260943	NM_198303	ENSMUSG00000026083	Eif5b	A030003E17Rik|BC018347|IF2	eukaryotic translation initiation factor 5B	protein-coding
mm_101851.1	chr11	48866230	48866265	-	1	NA	exon (NM_008326, exon 3 of 3)	exon (NM_008326, exon 3 of 3)	5099	NM_008326	15944	Mm.29938	NM_008326	ENSMUSG00000046879	Irgm1	Ifggd3|Ifi1|Iigp3|Iipg3|Irgm|LRG-47	immunity-related GTPase family M member 1	protein-coding
mm_73557.1	chr8	108961161	108961173	+	1	NA	3' UTR (NM_007496, exon 10 of 10)	3' UTR (NM_007496, exon 10 of 10)	24307	NR_037295	100526511		NR_037295	ENSMUSG00000093241	Mir3108	mir-3108|mmu-mir-3108	microRNA 3108	ncRNA
mm_6458.1	chr1	74016766	74016778	-	1	NA	intron (NM_027884, intron 3 of 34)	intron (NM_027884, intron 3 of 34)	107675	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_77171.1	chr8	111690310	111690333	-	1	NA	promoter-TSS (NR_106044)	promoter-TSS (NR_106044)	-647	NR_106044	102466993		NR_106044	ENSMUSG00000099129	Mir7076	Gm27318|mmu-mir-7076	microRNA 7076	ncRNA
mm_61437.1	chr7	74529488	74529492	+	1	NA	intron (NM_001038643, intron 1 of 10)	intron (NM_001038643, intron 1 of 10)	25290	NM_023908	108116	Mm.425467	NM_023908	ENSMUSG00000025790	Slco3a1	5830414C08Rik|Anr1|MJAM|OATP-D|R75096|Slc21a11	solute carrier organic anion transporter family, member 3a1	protein-coding
mm_164668.1	chr17	44736087	44736181	-	1	NA	promoter-TSS (NM_001271631)	promoter-TSS (NM_001271631)	42	NR_073425	12393	Mm.391013	NM_009820	ENSMUSG00000039153	Runx2	AML3|Cbf|Cbfa-1|Cbfa1|LS3|Osf2|PEBP2aA|Pebp2a1|Pebpa2a	runt related transcription factor 2	protein-coding
mm_62029.1	chr7	91672487	91672497	+	1	NA	intron (NM_011807, intron 2 of 22)	intron (NM_011807, intron 2 of 22)	-389902	NM_001243046	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_29364.1	chr3	108686495	108686500	-	1	NA	intron (NM_029522, intron 12 of 14)	intron (NM_029522, intron 12 of 14)	32507	NM_001177770	229725	Mm.214545	NM_145543	ENSMUSG00000027884	Clcc1	Mclc	chloride channel CLIC-like 1	protein-coding
mm_4389.1	chr1	172340908	172340935	+	1	NA	promoter-TSS (NM_001039484)	promoter-TSS (NM_001039484)	-289	NM_001039484	16513	Mm.254563	NM_020269	ENSMUSG00000044708	Kcnj10	BIR10|BIRK-1|Kir1.2|Kir4.1	potassium inwardly-rectifying channel, subfamily J, member 10	protein-coding
mm_171776.1	chr5	109845002	109845002	-	1	NA	Intergenic	Intergenic	-10860	NR_027964	667213	Mm.454429	NR_027964	ENSMUSG00000105044	Gm10416	EG667213|ENSMUSG00000072761	zinc finger protein pseudogene	pseudo
mm_114833.1	chr13	92425921	92425929	+	1	NA	promoter-TSS (NM_175455)	promoter-TSS (NM_175455)	-44	NM_175455	218440	Mm.213623	NM_175455	ENSMUSG00000045034	Ankrd34b	6430502M16Rik|DP58	ankyrin repeat domain 34B	protein-coding
mm_131724.1	chr16	21693051	21693067	+	1	NA	intron (NM_001001881, intron 1 of 1)	intron (NM_001001881, intron 1 of 1)	1606	NM_001001881	72190	Mm.131606	NM_001001881	ENSMUSG00000043391	2510009E07Rik	AI194952	RIKEN cDNA 2510009E07 gene	protein-coding
mm_128732.1	chr15	64156260	64156264	-	1	NA	intron (NM_010026, intron 11 of 30)	intron (NM_010026, intron 11 of 30)	-95814	NM_144846	223601	Mm.246108	NM_144846	ENSMUSG00000022378	Fam49b	0910001A06Rik|AW122079	family with sequence similarity 49, member B	protein-coding
mm_84013.1	chr9	57645562	57645672	-	1	NA	promoter-TSS (NM_007783)	promoter-TSS (NM_007783)	36	NM_007783	12988	Mm.21974	NM_007783	ENSMUSG00000032312	Csk	AW212630|p50CSK	c-src tyrosine kinase	protein-coding
mm_79762.1	chr9	62677834	62677843	+	1	NA	promoter-TSS (NM_176922)	promoter-TSS (NM_176922)	-17	NM_176922	319480	Mm.34883	NM_176922	ENSMUSG00000032243	Itga11	4732459H24Rik	integrin alpha 11	protein-coding
mm_73254.1	chr8	104340293	104340341	+	1	NA	promoter-TSS (NM_024217)	promoter-TSS (NM_024217)	-277	NM_024217	68119	Mm.390108	NM_024217	ENSMUSG00000031875	Cmtm3	9430096L06Rik|AI413895|BNAS2|Cklfsf3	CKLF-like MARVEL transmembrane domain containing 3	protein-coding
mm_101853.1	chr11	48866983	48867009	-	1	NA	exon (NM_008326, exon 3 of 3)	exon (NM_008326, exon 3 of 3)	4350	NM_008326	15944	Mm.29938	NM_008326	ENSMUSG00000046879	Irgm1	Ifggd3|Ifi1|Iigp3|Iipg3|Irgm|LRG-47	immunity-related GTPase family M member 1	protein-coding
mm_43470.1	chr5	136693668	136693683	+	1	NA	promoter-TSS (NM_001303021)	promoter-TSS (NM_001303021)	-1	NM_001303021	59310	Mm.5178	NM_021611	ENSMUSG00000005474	Myl10	1700027I08Rik|Mylc2pl|PLRLC	myosin, light chain 10, regulatory	protein-coding
mm_24191.1	chr3	88607483	88607485	+	1	NA	Intergenic	Intergenic	-8723	NM_001198911	16800	Mm.239329	NM_008487	ENSMUSG00000028059	Arhgef2	AA408978|GEF|GEF-H1|GEFH1|LFP40|Lbcl1|Lfc|P40|mKIAA0651	rho/rac guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_139278.1	chr17	48247760	48247782	+	1	NA	promoter-TSS (NM_021407)	promoter-TSS (NM_021407)	42	NM_021407	58218	Mm.302438	NM_021407	ENSMUSG00000041754	Trem3	BB134760	triggering receptor expressed on myeloid cells 3	protein-coding
mm_148920.1	chr19	6976457	6976466	+	1	NA	intron (NM_008889, intron 1 of 3)	intron (NM_008889, intron 1 of 3)	1413	NM_008889	18938	Mm.140	NM_008889	ENSMUSG00000056612	Ppp1r14b	AOM172|PHI-1|PLCB3N|Png	protein phosphatase 1, regulatory (inhibitor) subunit 14B	protein-coding
mm_75804.1	chr8	70188859	70188886	-	1	NA	exon (NM_001007570, exon 6 of 8)	exon (NM_001007570, exon 6 of 8)	16464	NR_122028	234371	Mm.23488	NM_145597	ENSMUSG00000002342	Tmem161a	AI428876|BB161850|BC021367	transmembrane protein 161A	protein-coding
mm_70947.1	chr8	26724487	26724491	+	1	NA	Intergenic	Intergenic	99934	NR_045904	72316	Mm.490534	NR_045904	ENSMUSG00000100335	2310008N11Rik	-	RIKEN cDNA 2310008N11 gene	ncRNA
mm_31273.1	chr4	45409109	45409111	+	1	NA	promoter-TSS (NM_001009949)	promoter-TSS (NM_001009949)	-344	NM_001009949	230125	Mm.260210	NM_001009949	ENSMUSG00000045973	Slc25a51	9130208E07Rik|D130005A03Rik|Gm138|Mcart1	solute carrier family 25, member 51	protein-coding
mm_58875.1	chr7	16986961	16986988	+	1	NA	Intergenic	RSINE1|SINE|B4	-7614	NM_001101535	434130	Mm.459162	NM_001101535	ENSMUSG00000041117	Ccdc8	ENSMUSG00000041117	coiled-coil domain containing 8	protein-coding
mm_50843.1	chr6	54817511	54817526	+	1	NA	intron (NM_199143, intron 1 of 4)	CpG	602	NM_199143	387524	Mm.286149	NM_199143	ENSMUSG00000058446	Znrf2	1190002C14Rik|AU044205|D6Ertd365e	zinc and ring finger 2	protein-coding
mm_165264.1	chr2	74673903	74673926	+	1	NA	Intergenic	Intergenic	-1099	NM_008274	15432	Mm.57124	NM_008274	ENSMUSG00000001823	Hoxd12	Hox-4.7|Hox-5.6	homeobox D12	protein-coding
mm_86061.1	chr9	114640125	114640135	-	1	NA	promoter-TSS (NM_153585)	promoter-TSS (NM_153585)	70	NM_153585	78893	Mm.283708	NM_153585	ENSMUSG00000056167	Cnot10	2600001P13Rik	CCR4-NOT transcription complex, subunit 10	protein-coding
mm_43421.1	chr5	136039087	136039114	+	1	NA	exon (NM_175309, exon 2 of 6)	exon (NM_175309, exon 2 of 6)	604	NM_175309	100647	Mm.3089	NM_175309	ENSMUSG00000042985	Upk3b	AI447729|AI957187|P35|PMS2L14|UpIIIb	uroplakin 3B	protein-coding
mm_125995.1	chr15	76380469	76380479	+	1	NA	promoter-TSS (NM_175457)	promoter-TSS (NM_175457)	-39	NM_175457	223658	Mm.123240	NM_175457	ENSMUSG00000022558	Mroh1	D330001F17Rik|Heatr7a	maestro heat-like repeat family member 1	protein-coding
mm_146607.1	chr18	9619461	9619482	-	1	NA	promoter-TSS (NM_007593)	promoter-TSS (NM_007593)	-2	NM_007593	26369	Mm.195831	NM_007593	ENSMUSG00000050996	Cetn1	caltractin	centrin 1	protein-coding
mm_114078.1	chr13	54517505	54517508	+	1	NA	intron (NM_176987, intron 1 of 9)	MYSERV6-int|LTR|ERVK	13701	NM_176987	319719	Mm.376151	NM_176987	ENSMUSG00000043183	Simc1	4732471D19Rik	SUMO-interacting motifs containing 1	protein-coding
mm_158476.1	chrX	141474035	141474091	-	1	NA	promoter-TSS (NM_053185)	promoter-TSS (NM_053185)	13	NM_053185	94216	Mm.155586	NM_053185	ENSMUSG00000031273	Col4a6	BB116301	collagen, type IV, alpha 6	protein-coding
mm_54021.1	chr6	8759380	8759385	-	1	NA	promoter-TSS (NM_001252266)	promoter-TSS (NM_001252266)	-924	NM_001252266	15893	Mm.275683	NM_010492	ENSMUSG00000062995	Ica1	69kDa|ICA69	islet cell autoantigen 1	protein-coding
mm_111845.1	chr12	107938753	107938768	-	1	NA	intron (NM_001286343, intron 1 of 1)	intron (NM_001286343, intron 1 of 1)	64654	NM_001079883	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_5923.1	chr1	55215531	55215574	-	1	NA	intron (NM_028713, intron 1 of 8)	intron (NM_028713, intron 1 of 8)	11230	NM_028713	74013	Mm.292050	NM_028713	ENSMUSG00000025978	Rftn2	2700010E02Rik|3222401M22Rik	raftlin family member 2	protein-coding
mm_53950.1	chr6	5256227	5256278	-	1	NA	promoter-TSS (NM_173006)	promoter-TSS (NM_173006)	-19	NM_173006	269823	Mm.9122	NM_173006	ENSMUSG00000029759	Pon3	2810004E20|AI786302	paraoxonase 3	protein-coding
mm_93993.1	chr10	127531523	127531533	-	1	NA	intron (NM_183297, intron 1 of 1)	intron (NM_183297, intron 1 of 1)	3031	NM_183297	104080	Mm.437200	NM_183297	ENSMUSG00000040258	Nxph4	1110036M10Rik|AI851051	neurexophilin 4	protein-coding
mm_104923.1	chr11	99858745	99858754	-	1	NA	3' UTR (NM_001205030, exon 1 of 1)	3' UTR (NM_001205030, exon 1 of 1)	832	NM_001205030	432600	Mm.60039	NM_001205030	ENSMUSG00000069717	Gm11568	OTTMUSG00000002207	predicted gene 11568	protein-coding
mm_12172.1	chr2	62664307	62664311	+	1	NA	promoter-TSS (NM_145523)	promoter-TSS (NM_145523)	-18	NM_145523	227960	Mm.219877	NM_145523	ENSMUSG00000026893	Gca	5133401E04Rik|AI573844	grancalcin	protein-coding
mm_102770.1	chr11	68270845	68270885	-	1	NA	intron (NM_008744, intron 3 of 6)	intron (NM_008744, intron 3 of 6)	49973	NR_105833	102465219		NR_105833	ENSMUSG00000099174	Mir6406	Gm27981|mmu-mir-6406	microRNA 6406	ncRNA
mm_73965.1	chr8	120488417	120488490	+	1	NA	promoter-TSS (NM_198671)	promoter-TSS (NM_198671)	-413	NM_198671	382034	Mm.334856	NM_198671	ENSMUSG00000031822	Gse1	2210013I18Rik|mKIAA0182	genetic suppressor element 1, coiled-coil protein	protein-coding
mm_108408.1	chr12	81709104	81709138	+	1	NA	Intergenic	Intergenic	72049	NM_177395	338372	Mm.35284	NM_177395	ENSMUSG00000042724	Map3k9	E130314H24Rik|Mlk1|Prke1	mitogen-activated protein kinase kinase kinase 9	protein-coding
mm_43663.1	chr5	138754526	138754607	+	1	NA	promoter-TSS (NM_030565)	promoter-TSS (NM_030565)	-515	NM_030565	80752	Mm.320355	NM_030565	ENSMUSG00000025854	Fam20c	C76981|DMP-4|DMP4|GEF-CK|mKIAA4081	family with sequence similarity 20, member C	protein-coding
mm_167144.1	chr7	128205772	128205794	+	1	NA	TTS (NM_001029872)	TTS (NM_001029872)	583	NM_009943	12862	Mm.43824	NM_009943	ENSMUSG00000030785	Cox6a2	CoxVIaH|VIaH	cytochrome c oxidase subunit VIa polypeptide 2	protein-coding
mm_17133.1	chr2	24935149	24935215	-	1	NA	promoter-TSS (NM_001162485)	promoter-TSS (NM_001162485)	99	NR_027876	215705	Mm.45275	NM_178408	ENSMUSG00000026972	Arrdc1	AI957342|BC004091	arrestin domain containing 1	protein-coding
mm_77959.1	chr9	7692087	7692103	+	1	NA	promoter-TSS (NM_010810)	promoter-TSS (NM_010810)	5	NM_010810	17393	Mm.4825	NM_010810	ENSMUSG00000018623	Mmp7	MAT|MMP-7	matrix metallopeptidase 7	protein-coding
mm_4842.1	chr1	186960434	186960436	+	1	NA	Intergenic	RMER19B2|LTR|ERVK	-6981	NM_033077	110957	Mm.108054	NM_033077	ENSMUSG00000039224	D1Pas1	Pl10	DNA segment, Chr 1, Pasteur Institute 1	protein-coding
mm_116402.1	chr13	41423228	41423243	-	1	NA	intron (NM_001111324, intron 2 of 7)	intron (NM_001111324, intron 2 of 7)	64125	NM_001111324	18003	Mm.288980	NM_017464	ENSMUSG00000021365	Nedd9	Cas-L|CasL|HEF1|MEF1|Nedd-9|p105	neural precursor cell expressed, developmentally down-regulated gene 9	protein-coding
mm_28749.1	chr3	95818748	95818801	-	1	NA	5' UTR (NM_001081293, exon 1 of 11)	5' UTR (NM_001081293, exon 1 of 11)	179	NM_001081293	75137	Mm.196275	NM_028328	ENSMUSG00000028106	Rprd2	2810036A19Rik|4930535B03Rik|6720469I21Rik|AL022841|AL022940|AU021304|BB077382|mKIAA0460	regulation of nuclear pre-mRNA domain containing 2	protein-coding
mm_5406.1	chr1	33757961	33757977	-	1	NA	promoter-TSS (NM_145392)	promoter-TSS (NM_145392)	-219	NM_145392	213539	Mm.247037	NM_145392	ENSMUSG00000042215	Bag2	2610042A13Rik|BC016230	BCL2-associated athanogene 2	protein-coding
mm_118792.1	chr14	24119028	24119032	+	1	NA	Intergenic	B1_Mur1|SINE|Alu	30153	NR_106069	102465697		NR_106069	ENSMUSG00000105723	Mir7210	mir-7210|mmu-mir-7210	microRNA 7210	ncRNA
mm_140550.1	chr17	7169722	7169744	-	1	NA	promoter-TSS (NM_011299)	promoter-TSS (NM_011299)	-382	NM_011299	20112	Mm.268383	NM_011299	ENSMUSG00000023809	Rps6ka2	90kDa|D17Wsu134e|Rps6ka-rs1|Rsk3|p90rsk|pp90rsk	ribosomal protein S6 kinase, polypeptide 2	protein-coding
mm_4960.1	chr1	191267053	191267061	+	1	NA	Intergenic	Intergenic	51061	NM_025424	66208	Mm.46444	NM_025424	ENSMUSG00000037499	Nenf	1110060M21Rik|SCIRP10|Spuf	neuron derived neurotrophic factor	protein-coding
mm_2126.1	chr1	87909074	87909111	+	1	NA	intron (NM_177646, intron 3 of 29)	intron (NM_177646, intron 3 of 29)	-54793	NR_136921	100503175	Mm.426422	NR_136921	ENSMUSG00000101942	Gm19582	-	predicted gene, 19582	ncRNA
mm_144114.1	chr18	4366924	4366934	+	1	NA	intron (NR_040328, intron 2 of 3)	intron (NR_040328, intron 2 of 3)	-8663	NM_026157	67440	Mm.49826	NM_026157	ENSMUSG00000024234	Mtpap	0610027A18Rik|AW551379|Papd1	mitochondrial poly(A) polymerase	protein-coding
mm_91983.1	chr10	61783962	61783974	-	1	NA	promoter-TSS (NM_207000)	promoter-TSS (NM_207000)	-104	NM_207000	404634	Mm.272870	NM_207000	ENSMUSG00000020086	H2afy2	macroH2A2	H2A histone family, member Y2	protein-coding
mm_46887.1	chr5	113972962	113972976	-	1	NA	intron (NM_198109, intron 2 of 14)	intron (NM_198109, intron 2 of 14)	20788	NM_198109	231637	Mm.389682	NM_198109	ENSMUSG00000042121	Ssh1	AW551225|Gm1394|Gm1395|SSH-1|SSH-1L	slingshot homolog 1 (Drosophila)	protein-coding
mm_143903.1	chr17	84860017	84860030	-	1	NA	Intergenic	Intergenic	-69237	NM_028233	72416	Mm.217027	NM_028233	ENSMUSG00000024120	Lrpprc	3110001K13Rik|C76645|Gp130|Lrp130|Lsfc	leucine-rich PPR-motif containing	protein-coding
mm_110362.1	chr12	40038211	40038222	-	1	NA	promoter-TSS (NM_007487)	promoter-TSS (NM_007487)	-229	NM_001039515	11861	Mm.12723	NM_007487	ENSMUSG00000047446	Arl4a	AI467555|Arl4	ADP-ribosylation factor-like 4A	protein-coding
mm_127122.1	chr15	98108454	98108464	+	1	NA	promoter-TSS (NM_001163487)	promoter-TSS (NM_001163487)	-12	NM_001163487	18642	Mm.272582	NM_021514	ENSMUSG00000033065	Pfkm	AI131669|ATP-PFK|PFK-A|PFK-M|Pfk-4|Pfk4|Pfka|Pfkx	phosphofructokinase, muscle	protein-coding
mm_125284.1	chr15	36725272	36725277	+	1	NA	Intergenic	IAPLTR2a2_Mm|LTR|ERVK	65658	NM_001253807	22631	Mm.3360	NM_011740	ENSMUSG00000022285	Ywhaz	1110013I11Rik|14-3-3zeta|AI596267|AL022924|AU020854	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide	protein-coding
mm_80721.1	chr9	92275909	92275919	+	1	NA	5' UTR (NM_001195084, exon 1 of 8)	5' UTR (NM_001195084, exon 1 of 8)	312	NM_001195084	18828	Mm.10306	NM_008880	ENSMUSG00000032372	Plscr2	-	phospholipid scramblase 2	protein-coding
mm_162826.1	chr10	81302054	81302056	-	1	NA	intron (NM_008844, intron 1 of 17)	intron (NM_008844, intron 1 of 17)	9092	NM_001146687	18717	Mm.24222	NM_008844	ENSMUSG00000034902	Pip5k1c	AI115456|AI835305|Pip5kIgamma	phosphatidylinositol-4-phosphate 5-kinase, type 1 gamma	protein-coding
mm_54436.1	chr6	34317443	34317499	-	1	NA	promoter-TSS (NM_009658)	promoter-TSS (NM_009658)	18	NM_009658	11677	Mm.451	NM_009658	ENSMUSG00000001642	Akr1b3	ALR2|AR|Ahr-1|Ahr1|Akr1b1|Aldor1|Aldr1	aldo-keto reductase family 1, member B3 (aldose reductase)	protein-coding
mm_14780.1	chr2	145851027	145851040	+	1	NA	intron (NM_028724, intron 6 of 12)	intron (NM_028724, intron 6 of 12)	-52208	NM_026425	67877	Mm.151168	NM_026425	ENSMUSG00000002728	Naa20	1500004D14Rik|2900026I01Rik|AU041458|D2Ertd186e|Nat5	N(alpha)-acetyltransferase 20, NatB catalytic subunit	protein-coding
mm_118190.1	chr13	107767967	107767978	-	1	NA	intron (NM_145456, intron 5 of 14)	intron (NM_145456, intron 5 of 14)	-6885	NR_029759	723929		NR_029759	ENSMUSG00000065425	Mir325	Mirn325|mmu-mir-325	microRNA 325	ncRNA
mm_158833.1	chrX	168349231	168349256	-	1	NA	intron (NM_001033330, intron 3 of 19)	intron (NM_001033330, intron 3 of 19)	-226246	NM_001290427	333605	Mm.426168	NM_001033330	ENSMUSG00000049176	Frmpd4	Gm196|PKAP1|Pdzd10|Pdzk10|Preso1|preso	FERM and PDZ domain containing 4	protein-coding
mm_119921.1	chr14	54962045	54962084	+	1	NA	exon (NM_010856, exon 9 of 39)	exon (NM_010856, exon 9 of 39)	4543	NM_001164171	17888	Mm.290003	NM_010856	ENSMUSG00000040752	Myh6	A830009F23Rik|AA517445|Myhc-a|Myhca|alpha-MHC	myosin, heavy polypeptide 6, cardiac muscle, alpha	protein-coding
mm_65178.1	chr7	19692909	19692911	-	1	NA	promoter-TSS (NM_001110009)	promoter-TSS (NM_001110009)	-251	NM_007469	11812	Mm.182440	NM_007469	ENSMUSG00000040564	Apoc1	Apo-CIB|ApoC-IB|apo-CI|apoC-I	apolipoprotein C-I	protein-coding
mm_161729.1	chr17	29184020	29184020	-	1	NA	exon (NM_153166, exon 10 of 21)	exon (NM_153166, exon 10 of 21)	48964	NM_001002786	442827	Mm.440341	NM_001002786	ENSMUSG00000064147	Rab44	9830134C10Rik	RAB44, member RAS oncogene family	protein-coding
mm_84093.1	chr9	58241053	58241068	-	1	NA	intron (NM_001311088, intron 2 of 8)	C-rich|Low_complexity|Low_complexity	8726	NM_178087	18854	Mm.392123	NM_008884	ENSMUSG00000036986	Pml	1200009E24Rik|AI661194|Trim19	promyelocytic leukemia	protein-coding
mm_32550.1	chr4	109394206	109394246	+	1	NA	Intergenic	Intergenic	12031	NR_131195	102635290	Mm.427859	NR_131195		Ttc39aos1	Gm12750|OTTMUSG00000008290|lincRNA-EPS	Ttc39a opposite strand RNA 1	ncRNA
mm_140145.1	chr17	80061553	80061558	+	1	NA	intron (NM_144802, intron 1 of 12)	CpG	713	NM_144802	72692	Mm.64579	NM_144802	ENSMUSG00000024095	Hnrnpll	2510028H02Rik|2810036L13Rik|AI256697|AI852082|Hnrpll	heterogeneous nuclear ribonucleoprotein L-like	protein-coding
mm_42908.1	chr5	122513995	122514023	+	1	NA	Intergenic	GC_rich|Low_complexity|Low_complexity	-11784	NR_027838	11938	Mm.227583	NM_009722	ENSMUSG00000029467	Atp2a2	9530097L16Rik|D5Wsu150e|SERCA2|SERCA2B|Serca2a|mKIAA4195	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	protein-coding
mm_160793.1	chr11	3356184	3356184	-	1	NA	promoter-TSS (NM_001034030)	promoter-TSS (NM_001034030)	-43	NM_001034030	16886	Mm.124176	NM_010718	ENSMUSG00000020451	Limk2	Limk-2|whe	LIM motif-containing protein kinase 2	protein-coding
mm_62415.1	chr7	101317053	101317057	+	1	NA	Intergenic	Intergenic	-4264	NM_019990	56018	Mm.28896	NM_019990	ENSMUSG00000030688	Stard10	AV048538|CGI-52|NY-C0-28|PC-TP2|PCTP2|Pctpl|Sdccag28|SdccagG28|TISP-81	START domain containing 10	protein-coding
mm_57766.1	chr6	129234756	129234770	-	1	NA	intron (NR_040265, intron 1 of 2)	intron (NR_040265, intron 1 of 2)	3282	NR_040265	76432	Mm.261738	NR_040265	ENSMUSG00000097354	2310001H17Rik	AI646108	RIKEN cDNA 2310001H17 gene	ncRNA
mm_162024.1	chr19	46317747	46317747	-	1	NA	intron (NM_028627, intron 11 of 17)	CpG	9119	NM_001347454	73728	Mm.268532	NM_028627	ENSMUSG00000037126	Psd	1110007H17Rik|A930015K15|Efa6|Efa6a|Psdl|mKIAA2011	pleckstrin and Sec7 domain containing	protein-coding
mm_173054.1	chrX	124283292	124283303	-	1	NA	Intergenic	MMVL30-int|LTR|ERV1	-147387	NM_001100616	100038941	Mm.388852	NM_001100616	ENSMUSG00000072049	Vmn2r121	EG625699	vomeronasal 2, receptor 121	protein-coding
mm_164678.1	chr17	46680777	46680781	-	1	NA	promoter-TSS (NM_010787)	promoter-TSS (NM_010787)	-4	NM_001277311	17256	Mm.329083	NM_010787	ENSMUSG00000002768	Mea1	Mea-1	male enhanced antigen 1	protein-coding
mm_150342.1	chr19	34607524	34607536	+	1	NA	promoter-TSS (NM_001005858)	promoter-TSS (NM_001005858)	-427	NM_001005858	667370	Mm.271850	NM_001005858	ENSMUSG00000062488	Ifit3b	I830012O16Rik	interferon-induced protein with tetratricopeptide repeats 3B	protein-coding
mm_153339.1	chr19	38358477	38358480	-	1	NA	Intergenic	Intergenic	-37502	NM_175507	240660	Mm.262085	NM_175507	ENSMUSG00000044026	Slc35g1	AA590464|D330039I19Rik|Tmem20	solute carrier family 35, member G1	protein-coding
mm_143659.1	chr17	79714092	79714107	-	1	NA	exon (NM_009994, exon 2 of 3)	exon (NM_009994, exon 2 of 3)	942	NM_009994	13078	Mm.214016	NM_009994	ENSMUSG00000024087	Cyp1b1	CP1B|P4501b1	cytochrome P450, family 1, subfamily b, polypeptide 1	protein-coding
mm_167250.1	chr8	24725742	24725748	-	1	NA	exon (NM_009619, exon 1 of 22)	exon (NM_009619, exon 1 of 22)	107	NM_009619	11497	Mm.5168	NM_009619	ENSMUSG00000031553	Adam3	Cyrn1|Taz83|tMDC	a disintegrin and metallopeptidase domain 3 (cyritestin)	protein-coding
mm_45604.1	chr5	75044464	75044500	-	1	NA	5' UTR (NM_028850, exon 1 of 6)	5' UTR (NM_028850, exon 1 of 6)	159	NM_028850	74277	Mm.239814	NM_028850	ENSMUSG00000029229	Chic2	1700081B18Rik|4930502K01Rik|BTL	cysteine-rich hydrophobic domain 2	protein-coding
mm_149722.1	chr19	21778366	21778374	+	1	NA	promoter-TSS (NM_031997)	promoter-TSS (NM_031997)	30	NM_031997	83921	Mm.329776	NM_031997	ENSMUSG00000024754	Tmem2	-	transmembrane protein 2	protein-coding
mm_161429.1	chr15	51865483	51865483	-	1	NA	promoter-TSS (NM_080635)	promoter-TSS (NM_080635)	-22	NM_080635	68135	Mm.289800	NM_080635	ENSMUSG00000022312	Eif3h	1110008A16Rik|40kD|9430017H16Rik|EIF3-P40|EIF3-gamma|Eif3s3	eukaryotic translation initiation factor 3, subunit H	protein-coding
mm_143651.1	chr17	79451715	79451726	-	1	NA	Intergenic	Intergenic	26165	NR_033463	74622	Mm.311921	NR_033463		4930429F11Rik	-	RIKEN cDNA 4930429F11 gene	ncRNA
mm_127981.1	chr15	12491849	12491853	-	1	NA	intron (NM_001081064, intron 1 of 23)	MER58B|DNA|hAT-Charlie	100705	NM_001081064	68070	Mm.423205	NM_001081064	ENSMUSG00000022197	Pdzd2	4930537L06Rik|A930022H17Rik|Gm21706|Gm82|Pdzk3|mKIAA0300	PDZ domain containing 2	protein-coding
mm_23502.1	chr3	60528264	60528316	+	1	NA	intron (NM_001253710, intron 1 of 7)	intron (NM_001253710, intron 1 of 7)	27111	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_118993.1	chr14	28505760	28505772	+	1	NA	5' UTR (NM_009524, exon 1 of 5)	5' UTR (NM_009524, exon 1 of 5)	293	NM_009524	22418	Mm.287544	NM_009524	ENSMUSG00000021994	Wnt5a	8030457G12Rik|Wnt-5a	wingless-type MMTV integration site family, member 5A	protein-coding
mm_132254.1	chr16	32751714	32751734	+	1	NA	exon (NM_080457, exon 2 of 27)	exon (NM_080457, exon 2 of 27)	15838	NM_080457	140474	Mm.214599	NM_080457	ENSMUSG00000079620	Muc4	4933405I11Rik|Asgp	mucin 4	protein-coding
mm_16747.1	chr2	9691630	9691634	-	1	NA	Intergenic	Intergenic	186968	NM_008091	14462	Mm.313866	NM_008091	ENSMUSG00000015619	Gata3	Gata-3|jal	GATA binding protein 3	protein-coding
mm_109967.1	chr12	12788695	12788704	-	1	NA	Intergenic	Intergenic	-118782	NR_136889	102637952	Mm.421393	NR_136889		Gm34637	-	predicted gene, 34637	ncRNA
mm_79922.1	chr9	65629611	65629683	+	1	NA	promoter-TSS (NM_028030)	promoter-TSS (NM_028030)	-935	NM_028030	71973	Mm.29148	NM_028030	ENSMUSG00000032387	Rbpms2	2400008B06Rik|AI316523	RNA binding protein with multiple splicing 2	protein-coding
mm_131654.1	chr16	20539975	20540022	+	1	NA	intron (NM_001302970, intron 3 of 10)	intron (NM_001302970, intron 3 of 10)	4518	NM_009679	11773	Mm.18946	NM_009679	ENSMUSG00000022841	Ap2m1	-	adaptor-related protein complex 2, mu 1 subunit	protein-coding
mm_173077.1	chrX	137300686	137300687	-	1	NA	Intergenic	L1Md_T|LINE|L1	-180360	NM_007957	13984	Mm.8017	NM_007957	ENSMUSG00000023443	Esx1	Spx1	extraembryonic, spermatogenesis, homeobox 1	protein-coding
mm_97401.1	chr11	77840255	77840264	+	1	NA	intron (NM_001291214, intron 19 of 38)	intron (NM_001291214, intron 19 of 38)	38961	NM_001291215	360013	Mm.341248	NM_011586	ENSMUSG00000000631	Myo18a	MAJN|MyoPDZ|MysPDZ|SP-R210	myosin XVIIIA	protein-coding
mm_139992.1	chr17	72918299	72918316	+	1	NA	promoter-TSS (NM_029999)	promoter-TSS (NM_029999)	2	NM_029999	77889	Mm.154109	NM_029999	ENSMUSG00000024063	Lbh	1810009F10Rik|6720416L16Rik	limb-bud and heart	protein-coding
mm_71822.1	chr8	68895758	68895770	+	1	NA	exon (NM_008509, exon 5 of 10)	exon (NM_008509, exon 5 of 10)	15209	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_138275.1	chr17	34605490	34605498	+	1	NA	promoter-TSS (NM_001163379)	promoter-TSS (NM_001163379)	-367	NM_001163379	55979	Mm.8684	NM_018862	ENSMUSG00000034254	Agpat1	1-AGP|1-AGPAT|AW047140	1-acylglycerol-3-phosphate O-acyltransferase 1 (lysophosphatidic acid acyltransferase, alpha)	protein-coding
mm_154054.1	chr19	55103126	55103146	-	1	NA	Intergenic	MLT1L|LTR|ERVL-MaLR	-3689	NM_008149	14732	Mm.210196	NM_008149	ENSMUSG00000024978	Gpam	GPAT|GPAT1	glycerol-3-phosphate acyltransferase, mitochondrial	protein-coding
mm_142388.1	chr17	44814605	44814637	-	1	NA	promoter-TSS (NM_009820)	promoter-TSS (NM_009820)	6	NM_009820	12393	Mm.391013	NM_009820	ENSMUSG00000039153	Runx2	AML3|Cbf|Cbfa-1|Cbfa1|LS3|Osf2|PEBP2aA|Pebp2a1|Pebpa2a	runt related transcription factor 2	protein-coding
mm_85470.1	chr9	105764654	105764664	-	1	NA	intron (NM_001102607, intron 10 of 36)	intron (NM_001102607, intron 10 of 36)	44989	NM_172927	245026	Mm.482507	NM_172927	ENSMUSG00000043719	Col6a6	E330019B14|E330026B02Rik	collagen, type VI, alpha 6	protein-coding
mm_146320.1	chr18	80609816	80609835	+	1	NA	intron (NM_198429, intron 9 of 9)	intron (NM_198429, intron 9 of 9)	-65279	NR_028424	100039348	Mm.254722	NR_028424		Gm2176	A430076E10Rik	glucosamine-6-phosphate deaminase 1 pseudogene	pseudo
mm_73964.1	chr8	120488233	120488241	+	1	NA	promoter-TSS (NM_198671)	promoter-TSS (NM_198671)	-629	NM_198671	382034	Mm.334856	NM_198671	ENSMUSG00000031822	Gse1	2210013I18Rik|mKIAA0182	genetic suppressor element 1, coiled-coil protein	protein-coding
mm_83201.1	chr9	41579513	41579523	-	1	NA	intron (NR_131930, intron 3 of 3)	intron (NR_131930, intron 3 of 3)	-1735	NR_015483	73144	Mm.38166	NM_001033153	ENSMUSG00000074415	3110039I08Rik	2610203C20Rik|AI848448|D230004N17Rik|D3Mgi9|Mir100hg	RIKEN cDNA 3110039I08 gene	ncRNA
mm_164169.1	chr15	74672608	74672616	-	1	NA	promoter-TSS (NM_018790)	promoter-TSS (NM_018790)	-42	NM_018790	11838	Mm.491310	NM_018790	ENSMUSG00000022602	Arc	Arc3.1|C86064|arg3.1|mArc	activity regulated cytoskeletal-associated protein	protein-coding
mm_121112.1	chr14	101823072	101823090	+	1	NA	intron (NM_201529, intron 3 of 30)	L2b|LINE|L2	-17542	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_148748.1	chr19	6047082	6047103	+	1	NA	promoter-TSS (NM_001164709)	promoter-TSS (NM_001164709)	-53	NM_001164709	74126	Mm.149870	NM_028769	ENSMUSG00000024807	Syvn1	1200010C09Rik|AW211966|C85322|D530017H19Rik|Hrd1	synovial apoptosis inhibitor 1, synoviolin	protein-coding
mm_64121.1	chr7	141088122	141088184	+	1	NA	intron (NM_019762, intron 6 of 12)	intron (NM_019762, intron 6 of 12)	8384	NM_019762	56460	Mm.350037	NM_019762	ENSMUSG00000054065	Pkp3	2310056L12Rik	plakophilin 3	protein-coding
mm_111928.1	chr12	108885800	108885808	-	1	NA	intron (NM_011710, intron 2 of 10)	intron (NM_011710, intron 2 of 10)	7394	NM_001164488	22375	Mm.38433	NM_011710	ENSMUSG00000021266	Wars	TrpRS|WRS	tryptophanyl-tRNA synthetase	protein-coding
mm_151467.1	chr19	58670426	58670430	+	1	NA	promoter-TSS (NM_026925)	promoter-TSS (NM_026925)	63	NM_026925	69060	Mm.20407	NM_026925	ENSMUSG00000046008	Pnlip	1810007A24Rik|PL|PTL	pancreatic lipase	protein-coding
mm_160955.1	chr11	98152934	98152934	-	1	NA	TTS (NM_013634)	TTS (NM_013634)	-3318	NM_028149	72194	Mm.218350	NM_028149	ENSMUSG00000020883	Fbxl20	2610511F20Rik|4632423N09Rik|AI849362|AL117906|C86145|Fbl2|Scr|mKIAA4147	F-box and leucine-rich repeat protein 20	protein-coding
mm_64839.1	chr7	12998141	12998171	-	1	NA	promoter-TSS (NM_009512)	promoter-TSS (NM_009512)	36	NM_009512	26459	Mm.10984	NM_009512	ENSMUSG00000030382	Slc27a5	FACVL3|FATP5|VLCS-H2|VLCSH2|Vlacsr	solute carrier family 27 (fatty acid transporter), member 5	protein-coding
mm_134828.1	chr16	26095908	26095915	-	1	NA	intron (NM_173379, intron 1 of 14)	intron (NM_173379, intron 1 of 14)	9873	NM_173379	210530	Mm.326869	NM_173379	ENSMUSG00000038168	P3h2	4832416N06|AW553532|Leprel1|Mlat4	prolyl 3-hydroxylase 2	protein-coding
mm_5735.1	chr1	45335161	45335189	-	1	NA	exon (NM_009930, exon 27 of 51)	exon (NM_009930, exon 27 of 51)	23637	NM_009930	12825	Mm.249555	NM_009930	ENSMUSG00000026043	Col3a1	AW550625|Col3a-1|Tsk-2|Tsk2	collagen, type III, alpha 1	protein-coding
mm_93801.1	chr10	120898965	120898988	-	1	NA	promoter-TSS (NM_177092)	promoter-TSS (NM_177092)	-5	NM_177092	320183	Mm.169755	NM_177092	ENSMUSG00000051236	Msrb3	D430026P16Rik|I-8-23|MsrB2	methionine sulfoxide reductase B3	protein-coding
mm_17800.1	chr2	33304841	33304847	-	1	NA	intron (NM_001290570, intron 3 of 16)	intron (NM_001290570, intron 3 of 16)	66650	NM_001290570	241308	Mm.274249	NM_175211	ENSMUSG00000038831	Ralgps1	5830418G11Rik|AI853783|AI854138|RALGEF2|RALGPS1A|RalGEF 2|mKIAA0351	Ral GEF with PH domain and SH3 binding motif 1	protein-coding
mm_75811.1	chr8	70302880	70302892	-	1	NA	promoter-TSS (NM_001024922)	promoter-TSS (NM_001024922)	101	NM_021538	59042	Mm.28668	NM_021538	ENSMUSG00000055681	Cope	1110005D17Rik|Cope1	coatomer protein complex, subunit epsilon	protein-coding
mm_44795.1	chr5	32746273	32746313	-	1	NA	promoter-TSS (NM_001347332)	promoter-TSS (NM_001347332)	49	NM_001347332	320951	Mm.273765	NM_177298	ENSMUSG00000023452	Pisd	9030221M09Rik	phosphatidylserine decarboxylase	protein-coding
mm_84924.1	chr9	81632280	81632293	-	1	NA	promoter-TSS (NR_040397)	promoter-TSS (NR_040397)	-72	NR_040397	319405	Mm.246494	NR_040393	ENSMUSG00000097466	D430036J16Rik	-	RIKEN cDNA D430036J16 gene	ncRNA
mm_116224.1	chr13	32940626	32940638	-	1	NA	Intergenic	Intergenic	-24881	NM_011454	20708	Mm.36526	NM_011454	ENSMUSG00000042842	Serpinb6b	NK13|Spi12|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 6b	protein-coding
mm_171796.1	chr5	120893160	120893160	-	1	NA	Intergenic	RLTR1B|LTR|ERV1	-5547	NR_126529	23960	Mm.389688	NM_011852	ENSMUSG00000066861	Oas1g	AI449562|L2|Mmu-L|Mmu-L2|Oas1b|Oias-1|Oias1	2'-5' oligoadenylate synthetase 1G	protein-coding
mm_138310.1	chr17	34647188	34647216	+	1	NA	promoter-TSS (NM_017406)	promoter-TSS (NM_017406)	56	NM_017406	12915	Mm.4068	NM_017406	ENSMUSG00000015461	Atf6b	AA617266|ATF6beta|Creb-rp|Crebl1	activating transcription factor 6 beta	protein-coding
mm_13088.1	chr2	91210880	91210905	+	1	NA	TTS (NM_028119)	TTS (NM_028119)	7980	NM_007387	11432	Mm.45570	NM_007387	ENSMUSG00000002103	Acp2	Acp-2|LAP	acid phosphatase 2, lysosomal	protein-coding
mm_146823.1	chr18	21300117	21300123	-	1	NA	promoter-TSS (NM_001033445)	promoter-TSS (NM_001033445)	19	NM_001033445	381126	Mm.312276	NM_001033445	ENSMUSG00000042680	Garem1	C86169|Fam59a|Garem|Gm944|mKIAA4238	GRB2 associated regulator of MAPK1 subtype 1	protein-coding
mm_6319.1	chr1	71603842	71603853	-	1	NA	exon (NM_010233, exon 33 of 46)	exon (NM_010233, exon 33 of 46)	46691	NM_026195	108147	Mm.38010	NM_026195	ENSMUSG00000026192	Atic	2610509C24Rik|AA536954|AW212393	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	protein-coding
mm_163647.1	chr13	63946543	63946552	-	1	NA	Intergenic	Intergenic	131213	NM_023507	76251	Mm.186610	NM_023507	ENSMUSG00000021470	Ercc6l2	0610007P08Rik|1700019D06Rik|9330134C04Rik|Rad26l|Sr278	excision repair cross-complementing rodent repair deficiency, complementation group 6 like 2	protein-coding
mm_129782.1	chr15	82794268	82794284	-	1	NA	promoter-TSS (NM_029562)	promoter-TSS (NM_029562)	-31	NM_029562	76279	Mm.439931	NM_029562	ENSMUSG00000022445	Cyp2d26	1300006E06Rik	cytochrome P450, family 2, subfamily d, polypeptide 26	protein-coding
mm_122750.1	chr14	54181231	54181249	-	1	NA	Intergenic	Intergenic	72689	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_90820.1	chr10	7920025	7920073	-	1	NA	exon (NM_138667, exon 3 of 7)	exon (NM_138667, exon 3 of 7)	36074	NM_138667	68652	Mm.193041	NM_138667	ENSMUSG00000015755	Tab2	1110030N06Rik|A530078N03Rik|Map3k7ip2|mKIAA0733	TGF-beta activated kinase 1/MAP3K7 binding protein 2	protein-coding
mm_156179.1	chrX	130395818	130395822	+	1	NA	intron (NM_172493, intron 26 of 26)	intron (NM_172493, intron 26 of 26)	646078	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diaph2	Dia3|Diap2|Drf2|E430022I22Rik	diaphanous related formin 2	protein-coding
mm_138848.1	chr17	40727105	40727110	+	1	NA	promoter-TSS (NM_001038500)	promoter-TSS (NM_001038500)	-13	NM_001038500	619517	Mm.391018	NM_001038500	ENSMUSG00000073396	Esp1	EG619517|Gm6084	exocrine gland secreted peptide 1	protein-coding
mm_50834.1	chr6	54816632	54816701	+	1	NA	promoter-TSS (NM_199143)	promoter-TSS (NM_199143)	-250	NM_199143	387524	Mm.286149	NM_199143	ENSMUSG00000058446	Znrf2	1190002C14Rik|AU044205|D6Ertd365e	zinc and ring finger 2	protein-coding
mm_84581.1	chr9	69467357	69467401	-	1	NA	exon (NM_007585, exon 3 of 13)	exon (NM_007585, exon 3 of 13)	10435	NR_037296	100526560		NR_037296	ENSMUSG00000093042	Mir3109	mir-3109|mmu-mir-3109	microRNA 3109	ncRNA
mm_41941.1	chr5	105731702	105731708	+	1	NA	intron (NM_178701, intron 1 of 2)	intron (NM_178701, intron 1 of 2)	30895	NM_178701	231549	Mm.23837	NM_178701	ENSMUSG00000046079	Lrrc8d	2810473G09Rik|4930525N13Rik|A930019F03|Lrrc5	leucine rich repeat containing 8D	protein-coding
mm_132180.1	chr16	32400772	32400785	+	1	NA	5' UTR (NM_001160402, exon 1 of 5)	5' UTR (NM_001160402, exon 1 of 5)	272	NM_001160402	277203	Mm.484240	NM_001160402	ENSMUSG00000079625	Tm4sf19	EG277203	transmembrane 4 L six family member 19	protein-coding
mm_149762.1	chr19	22869850	22869853	+	1	NA	intron (NM_001035243, intron 9 of 23)	L1_Rod|LINE|L1	119246	NR_029591	387200		NR_029591	ENSMUSG00000065507	Mir204	Mirn204|mir-204|mmu-mir-204	microRNA 204	ncRNA
mm_18356.1	chr2	58195502	58195552	-	1	NA	Intergenic	Intergenic	31553	NR_045895	100042926	Mm.446515	NR_045895	ENSMUSG00000086862	Gm13546	OTTMUSG00000012675	predicted gene 13546	ncRNA
mm_9575.1	chr1	173982261	173982286	-	1	NA	intron (NM_008327, intron 1 of 6)	intron (NM_008327, intron 1 of 6)	571	NM_008327	26388	Mm.218770	NM_008327	ENSMUSG00000026535	Ifi202b	Ifbip-1|Ifi202|Ifi202a|p202	interferon activated gene 202B	protein-coding
mm_138975.1	chr17	45367733	45367745	+	1	NA	Intergenic	Intergenic	65968	NM_152810	71702	Mm.28270	NM_152810	ENSMUSG00000023932	Cdc5l	1200002I02Rik|AA408004|PCDC5RP	cell division cycle 5-like (S. pombe)	protein-coding
mm_24874.1	chr3	95982409	95982438	+	1	NA	Intergenic	Intergenic	-3087	NR_045872	668224	Mm.357766	NR_045872		Gm9054	EG668224	predicted gene 9054	ncRNA
mm_38033.1	chr4	133875229	133875239	-	1	NA	promoter-TSS (NM_001285506)	promoter-TSS (NM_001285506)	-503	NM_001285506	20111	Mm.301827	NM_009097	ENSMUSG00000003644	Rps6ka1	Mapkapk-1a|Rsk|Rsk-1|Rsk1|S6K-alpha-1|p90-Rsk1|p90Rsk1|p90S6K|p90rsk	ribosomal protein S6 kinase polypeptide 1	protein-coding
mm_165187.1	chr2	29890039	29890045	+	1	NA	promoter-TSS (NM_013615)	promoter-TSS (NM_013615)	-21	NM_013615	18286	Mm.330116	NM_013615	ENSMUSG00000026790	Odf2	AI848335|MMTEST29	outer dense fiber of sperm tails 2	protein-coding
mm_113753.1	chr13	44731569	44731583	+	1	NA	5' UTR (NM_001205043, exon 1 of 18)	5' UTR (NM_001205043, exon 1 of 18)	305	NM_001205043	16468	Mm.25059	NM_021878	ENSMUSG00000038518	Jarid2	Jmj|jumonji	jumonji, AT rich interactive domain 2	protein-coding
mm_104603.1	chr11	97187593	97187616	-	1	NA	5' UTR (NM_008379, exon 1 of 22)	5' UTR (NM_008379, exon 1 of 22)	288	NM_008379	16211	Mm.251013	NM_008379	ENSMUSG00000001440	Kpnb1	AA409963|IPOB|Impnb	karyopherin (importin) beta 1	protein-coding
mm_131752.1	chr16	22439952	22439965	+	1	NA	promoter-TSS (NM_023794)	promoter-TSS (NM_023794)	-388	NM_023794	104156	Mm.155708	NM_023794	ENSMUSG00000013089	Etv5	1110005E01Rik|8430401F14Rik|ERM	ets variant 5	protein-coding
mm_9603.1	chr1	175625553	175625576	-	1	NA	promoter-TSS (NM_010209)	promoter-TSS (NM_010209)	71	NM_010209	14194	Mm.41502	NM_010209	ENSMUSG00000026526	Fh1	Fh|Fh-1	fumarate hydratase 1	protein-coding
mm_74638.1	chr8	13254105	13254119	-	1	NA	promoter-TSS (NM_172750)	promoter-TSS (NM_172750)	50	NM_172750	234072	Mm.132785	NM_172750	ENSMUSG00000031448	Adprhl1	Arh2|D330008N11Rik	ADP-ribosylhydrolase like 1	protein-coding
mm_61333.1	chr7	68275965	68275966	+	1	NA	promoter-TSS (NR_040341)	promoter-TSS (NR_040341)	629	NR_040340	100504026	Mm.426764	NR_040340	ENSMUSG00000086628	Gm16157	OTTMUSG00000031023	predicted gene 16157	ncRNA
mm_100701.1	chr11	3633462	3633506	-	1	NA	Intergenic	Intergenic	14052	NR_110490	544752	Mm.390314	NR_002321	ENSMUSG00000056579	Tug1	AI316828	taurine upregulated gene 1	ncRNA
mm_156803.1	chrX	163909176	163909184	+	1	NA	5' UTR (NM_026887, exon 1 of 5)	5' UTR (NM_026887, exon 1 of 5)	163	NM_001290379	108012	Mm.426783	NM_026887	ENSMUSG00000031367	Ap1s2	1500012A13Rik|AI853648|EST1	adaptor-related protein complex 1, sigma 2 subunit	protein-coding
mm_29204.1	chr3	106767956	106768005	-	1	NA	exon (NM_007651, exon 4 of 8)	exon (NM_007651, exon 4 of 8)	22169	NM_007651	12508	Mm.316861	NM_007651	ENSMUSG00000040747	Cd53	AI323659|Ox-44|Tspan25	CD53 antigen	protein-coding
mm_45234.1	chr5	53594322	53594334	-	1	NA	intron (NM_001080927, intron 1 of 10)	intron (NM_001080927, intron 1 of 10)	3842	NM_001080927	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_69779.1	chr7	141060844	141060867	-	1	NA	promoter-TSS (NM_177897)	promoter-TSS (NM_177897)	-419	NM_177897	330671	Mm.133741	NM_177897	ENSMUSG00000055629	B4galnt4	BC038881|Gm1095|beta4GalNAcT4	beta-1,4-N-acetyl-galactosaminyl transferase 4	protein-coding
mm_26711.1	chr3	157993606	157993620	+	1	NA	intron (NM_001013806, intron 8 of 12)	intron (NM_001013806, intron 8 of 12)	38141	NM_001093753	69207	Mm.223946	NM_026989	ENSMUSG00000055436	Srsf11	0610009J05Rik|2610019N13Rik|BF642805|Sfrs11	serine/arginine-rich splicing factor 11	protein-coding
mm_88032.1	chr10	67285476	67285513	+	1	NA	promoter-TSS (NM_001036293)	promoter-TSS (NM_001036293)	-213	NM_001036293	641340	Mm.136223	NM_001036293	ENSMUSG00000075000	Nrbf2	NRBF-2	nuclear receptor binding factor 2	protein-coding
mm_43376.1	chr5	135671495	135671500	+	1	NA	Intergenic	Intergenic	-17648	NM_008898	18984	Mm.3863	NM_008898	ENSMUSG00000005514	Por	4933424M13Rik|CPR|CYPOR|P450R	P450 (cytochrome) oxidoreductase	protein-coding
mm_92302.1	chr10	75052984	75053006	-	1	NA	3' UTR (NM_029781, exon 11 of 11)	3' UTR (NM_029781, exon 11 of 11)	-7901	NM_001081412	110279	Mm.333722	NM_001081412	ENSMUSG00000009681	Bcr	5133400C09Rik|AI561783|AI853148|mKIAA3017	breakpoint cluster region	protein-coding
mm_85524.1	chr9	106464886	106464895	-	1	NA	TTS (NM_021567)	TTS (NM_021567)	1050	NM_001159652	436090	Mm.482905	NM_001159652	ENSMUSG00000091735	Gpr62	4933402E03Rik	G protein-coupled receptor 62	protein-coding
mm_69374.1	chr7	130998450	130998453	-	1	NA	Intergenic	MLTR18D_MM|LTR|ERVK	-33625	NM_001347632	12945	Mm.4138	NM_007769	ENSMUSG00000047517	Dmbt1	CRP|CRP-[a]|CRP-[b]|Crpd|DBMT1|gp300|p80	deleted in malignant brain tumors 1	protein-coding
mm_82407.1	chr9	14771190	14771202	-	1	NA	promoter-TSS (NM_029306)	promoter-TSS (NM_029306)	-166	NM_029306	69325	Mm.440453	NM_029306	ENSMUSG00000031927	1700012B09Rik	1700007P19Rik	RIKEN cDNA 1700012B09 gene	protein-coding
mm_76314.1	chr8	84663009	84663015	-	1	NA	promoter-TSS (NM_010499)	promoter-TSS (NM_010499)	-160	NM_010499	15936	Mm.399	NM_010499	ENSMUSG00000053560	Ier2	AI317238|Ch1|Pip92	immediate early response 2	protein-coding
mm_126398.1	chr15	80221891	80221895	+	1	NA	Intergenic	Intergenic	-12187	NM_178719	239555	Mm.307163	NM_178719	ENSMUSG00000022412	Mief1	A230016E22|AI452372|Smcr7l	mitochondrial elongation factor 1	protein-coding
mm_81434.1	chr9	109095428	109095453	+	1	NA	promoter-TSS (NM_172775)	promoter-TSS (NM_172775)	4	NM_172775	235611	Mm.53862	NM_172775	ENSMUSG00000053646	Plxnb1	2900002G15Rik|AU042020|mKIAA0407	plexin B1	protein-coding
mm_167520.1	chr9	20642116	20642120	+	1	NA	intron (NM_001286529, intron 1 of 2)	CpG-14732	688	NM_013911	30843	Mm.24608	NM_013911	ENSMUSG00000066892	Fbxl12	3110048D16Rik|Fbl12	F-box and leucine-rich repeat protein 12	protein-coding
mm_39514.1	chr5	21256817	21256828	+	1	NA	intron (NM_175437, intron 18 of 30)	B1_Mur4|SINE|Alu	70555	NM_175437	212167	Mm.121705	NM_175437	ENSMUSG00000039934	Gsap	A530088I07Rik|Pion	gamma-secretase activating protein	protein-coding
mm_36931.1	chr4	108451363	108451371	-	1	NA	Intergenic	Intergenic	-8059	NM_175472	230594	Mm.25181	NM_175472	ENSMUSG00000034610	Zcchc11	6030404K05Rik|9230115F04Rik|PPAPD3|mKIAA0191	zinc finger, CCHC domain containing 11	protein-coding
mm_122737.1	chr14	53961595	53961634	-	1	NA	Intergenic	Intergenic	292315	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_143057.1	chr17	57004865	57004892	-	1	NA	intron (NM_133801, intron 6 of 12)	ZP3AR|Satellite|Satellite	-4773	NM_008954	19197	Mm.86487	NM_008954	ENSMUSG00000002664	Pspn	PSP	persephin	protein-coding
mm_128665.1	chr15	60164556	60164558	-	1	NA	Intergenic	AT_rich|Low_complexity|Low_complexity	-147939	NM_027668	71088	Mm.425950	NM_027668	ENSMUSG00000071749	4933412E24Rik	-	RIKEN cDNA 4933412E24 gene	protein-coding
mm_2173.1	chr1	88406940	88406950	+	1	NA	promoter-TSS (NM_029269)	promoter-TSS (NM_029269)	-65	NM_029269	75396	Mm.173058	NM_029269	ENSMUSG00000026295	Spp2	0610038O04Rik|pp-24|spp24	secreted phosphoprotein 2	protein-coding
mm_75925.1	chr8	71504429	71504436	-	1	NA	intron (NM_032398, intron 5 of 5)	intron (NM_032398, intron 5 of 5)	7337	NM_032398	84094	Mm.260768	NM_032398	ENSMUSG00000034845	Plvap	MECA32|Pv1	plasmalemma vesicle associated protein	protein-coding
mm_162403.1	chr1	85699534	85699538	+	1	NA	intron (NM_001313713, intron 13 of 15)	intron (NM_001313713, intron 13 of 15)	37070	NM_177055	319997	Mm.116691	NM_177055	ENSMUSG00000052760	A630001G21Rik	-	RIKEN cDNA A630001G21 gene	protein-coding
mm_27042.1	chr3	27153807	27153842	-	1	NA	promoter-TSS (NM_001177626)	promoter-TSS (NM_001177626)	30	NM_007900	13605	Mm.261453	NM_007900	ENSMUSG00000027699	Ect2	AI528536|mKIAA4037	ect2 oncogene	protein-coding
mm_10675.1	chr2	21367548	21367548	+	1	NA	promoter-TSS (NM_001004761)	promoter-TSS (NM_001004761)	-19	NM_001004761	241263	Mm.166647	NM_175706	ENSMUSG00000045967	Gpr158	5330427M13Rik|mKIAA1136	G protein-coupled receptor 158	protein-coding
mm_147532.1	chr18	53246654	53246684	-	1	NA	intron (NM_029394, intron 1 of 6)	intron (NM_029394, intron 1 of 6)	1007	NM_029394	69226	Mm.32414	NM_029394	ENSMUSG00000024535	Snx24	2810011K15Rik|5730433I16Rik|AI451341	sorting nexing 24	protein-coding
mm_120027.1	chr14	55824906	55824919	+	1	NA	5' UTR (NM_001168346, exon 1 of 9)	5' UTR (NM_001168346, exon 1 of 9)	117	NM_023699	73181	Mm.27908	NM_023699	ENSMUSG00000023411	Nfatc4	3110041H08Rik|AW107667|AW546455|Nfat3	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 4	protein-coding
mm_159788.1	chr5	107597380	107597380	+	1	NA	promoter-TSS (NM_001163462)	promoter-TSS (NM_001163462)	7	NM_001163462	231571	Mm.482420	NM_144911	ENSMUSG00000033773	Rpap2	AW060207	RNA polymerase II associated protein 2	protein-coding
mm_116140.1	chr13	29654274	29654282	-	1	NA	intron (NR_131896, intron 8 of 16)	intron (NR_131896, intron 8 of 16)	201395	NR_131896	68916	Mm.212227	NM_144536	ENSMUSG00000006191	Cdkal1	1190005B03Rik|6620401C13Rik	CDK5 regulatory subunit associated protein 1-like 1	protein-coding
mm_77124.1	chr8	111325725	111325738	-	1	NA	intron (NM_029005, intron 4 of 10)	intron (NM_029005, intron 4 of 10)	12474	NM_001310613	74568	Mm.207971	NM_029005	ENSMUSG00000012519	Mlkl	9130019I15Rik	mixed lineage kinase domain-like	protein-coding
mm_37543.1	chr4	125122578	125122588	-	1	NA	intron (NM_153159, intron 2 of 5)	intron (NM_153159, intron 2 of 5)	5298	NM_153159	230738	Mm.402	NM_153159	ENSMUSG00000042677	Zc3h12a	BC036563|MCPIP|MCPIP-1|Mcpip1|Reg1	zinc finger CCCH type containing 12A	protein-coding
mm_162516.1	chr1	156500400	156500411	+	1	NA	Intergenic	RLTR10B|LTR|ERVK	-26077	NM_009230	20652	Mm.28099	NM_009230	ENSMUSG00000026600	Soat1	8430426K15Rik|ACAT-1|AW550831|Acact|ald|hid	sterol O-acyltransferase 1	protein-coding
mm_81526.1	chr9	110062629	110062671	+	1	NA	intron (NM_001311163, intron 1 of 10)	intron (NM_001311163, intron 1 of 10)	10629	NM_001311164	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_151258.1	chr19	53945917	53945918	+	1	NA	intron (NM_019658, intron 1 of 8)	intron (NM_019658, intron 1 of 8)	1041	NM_019658	56392	Mm.228669	NM_019658	ENSMUSG00000024976	Shoc2	AU017287|Sur8|mKIAA0862	soc-2 (suppressor of clear) homolog (C. elegans)	protein-coding
mm_136262.1	chr16	91024364	91024376	-	1	NA	intron (NM_026110, intron 12 of 17)	intron (NM_026110, intron 12 of 17)	-13062	NM_001164483	104015	Mm.187079	NM_001045515	ENSMUSG00000022973	Synj1	A930006D20Rik|AA675315|mKIAA0910	synaptojanin 1	protein-coding
mm_102611.1	chr11	62457575	62457594	-	1	NA	promoter-TSS (NM_177229)	promoter-TSS (NM_177229)	-252	NM_177229	20185	Mm.271814	NM_011308	ENSMUSG00000018501	Ncor1	5730405M06Rik|A230020K14Rik|N-CoR|RIP13|Rxrip13|mKIAA1047	nuclear receptor co-repressor 1	protein-coding
mm_73196.1	chr8	95534134	95534143	+	1	NA	promoter-TSS (NM_172914)	promoter-TSS (NM_172914)	38	NM_172914	244608	Mm.248902	NM_172914	ENSMUSG00000036598	Ccdc113	4933409I22|BC060957	coiled-coil domain containing 113	protein-coding
mm_53300.1	chr6	129045938	129045938	+	1	NA	promoter-TSS (NM_153094)	promoter-TSS (NM_153094)	37	NR_024263	232408	Mm.259262	NM_153094	ENSMUSG00000030154	Klrb1f	A630024B12Rik|Nkr-p1f|Nkrp1-f|Nkrp1f	killer cell lectin-like receptor subfamily B member 1F	protein-coding
mm_163559.1	chr13	24417129	24417139	+	1	NA	intron (NM_007717, intron 2 of 15)	intron (NM_007717, intron 2 of 15)	2012	NM_001284520	12763	Mm.8396	NM_007717	ENSMUSG00000016756	Cmah	-	cytidine monophospho-N-acetylneuraminic acid hydroxylase	protein-coding
mm_131916.1	chr16	23308110	23308112	+	1	NA	intron (NM_001252506, intron 1 of 6)	intron (NM_001252506, intron 1 of 6)	17641	NM_001252506	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_131938.1	chr16	23613370	23613413	+	1	NA	exon (NM_023386, exon 2 of 2)	exon (NM_023386, exon 2 of 2)	3472	NM_023386	67775	Mm.475107	NM_023386	ENSMUSG00000033355	Rtp4	5830458K16Rik|Ifrg28	receptor transporter protein 4	protein-coding
mm_8932.1	chr1	164181411	164181412	-	1	NA	intron (NM_007976, intron 6 of 24)	intron (NM_007976, intron 6 of 24)	-29194	NR_037987	100503816	Mm.398579	NR_037987	ENSMUSG00000086593	Gm16548	-	predicted gene 16548	ncRNA
mm_47699.1	chr5	129787176	129787259	-	1	NA	promoter-TSS (NM_009838)	promoter-TSS (NM_009838)	36	NM_133900	100678	Mm.271784	NM_133900	ENSMUSG00000029446	Psph	AI480570|PSP|PSPase	phosphoserine phosphatase	protein-coding
mm_134585.1	chr16	20424325	20424371	-	1	NA	intron (NM_176839, intron 1 of 6)	intron (NM_176839, intron 1 of 6)	2046	NM_013790	27416	Mm.20845	NM_013790	ENSMUSG00000022822	Abcc5	2900011L11Rik|AI132311|Abcc5a|Abcc5b|Mrp5	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	protein-coding
mm_119986.1	chr14	55578423	55578437	+	1	NA	promoter-TSS (NM_011189)	promoter-TSS (NM_011189)	-64	NM_011189	19186	Mm.830	NM_011189	ENSMUSG00000022216	Psme1	AW413925|PA28a	proteasome (prosome, macropain) activator subunit 1 (PA28 alpha)	protein-coding
mm_44356.1	chr5	17795672	17795682	-	1	NA	exon (NM_001159558, exon 12 of 16)	exon (NM_001159558, exon 12 of 16)	40219	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_135567.1	chr16	50192811	50192835	-	1	NA	3' UTR (NM_027444, exon 17 of 17)	3' UTR (NM_027444, exon 17 of 17)	-119971	NR_045935	224180	Mm.146439	NM_175010		Gm4827	B130050K08|EG224180	predicted gene 4827	ncRNA
mm_92899.1	chr10	83322893	83322912	-	1	NA	intron (NM_177388, intron 1 of 10)	MTEb|LTR|ERVL-MaLR	14915	NM_177388	338365	Mm.67073	NM_177388	ENSMUSG00000034591	Slc41a2	A230035L05Rik|SLC41A1-L1	solute carrier family 41, member 2	protein-coding
mm_33487.1	chr4	130822723	130822726	+	1	NA	exon (NM_011520, exon 5 of 5)	exon (NM_011520, exon 5 of 5)	30187	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_121759.1	chr14	19646075	19646079	-	1	NA	Intergenic	Intergenic	-43490	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_29879.1	chr3	131019683	131019696	-	1	NA	Intergenic	Intergenic	-90608	NM_010703	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_64966.1	chr7	16614959	16615021	-	1	NA	promoter-TSS (NM_172739)	promoter-TSS (NM_172739)	3	NM_172739	232906	Mm.28646	NM_172739	ENSMUSG00000058230	Arhgap35	6430596G11Rik|AI841135|Grlf1|mKIAA1722|p190A|p190RhoGAP	Rho GTPase activating protein 35	protein-coding
mm_1382.1	chr1	66816458	66816461	+	1	NA	intron (NM_177645, intron 1 of 13)	CpG	1136	NM_177645	68691	Mm.240912	NM_177645	ENSMUSG00000026004	Kansl1l	1110028C15Rik|1190030G24|AI427598|C430010P07Rik|mKIAA4189	KAT8 regulatory NSL complex subunit 1-like	protein-coding
mm_133235.1	chr16	77026598	77026628	+	1	NA	intron (NM_013918, intron 1 of 23)	B1_Mus1|SINE|Alu	12544	NM_013918	30940	Mm.40986	NM_013918	ENSMUSG00000022867	Usp25	-	ubiquitin specific peptidase 25	protein-coding
mm_57842.1	chr6	129467546	129467564	-	1	NA	exon (NM_020008, exon 4 of 6)	exon (NM_020008, exon 4 of 6)	5224	NM_001309637	56644	Mm.239516	NM_020008	ENSMUSG00000079293	Clec7a	BGR|Clecsf12|beta-GR	C-type lectin domain family 7, member a	protein-coding
mm_64828.1	chr7	12803608	12803644	-	1	NA	TTS (NM_026046)	TTS (NM_026046)	15234	NM_026046	67230	Mm.333574	NM_026046	ENSMUSG00000057894	Zfp329	2810439M05Rik|4632409L22Rik|ZNF329	zinc finger protein 329	protein-coding
mm_2842.1	chr1	131638307	131638338	+	1	NA	promoter-TSS (NM_007799)	promoter-TSS (NM_007799)	8	NM_007799	13034	Mm.230249	NM_007799	ENSMUSG00000004552	Ctse	A430072O03Rik|C920004C08Rik|CE|CatE	cathepsin E	protein-coding
mm_80311.1	chr9	74362611	74362612	+	1	NA	Intergenic	U4|snRNA|snRNA	252277	NM_001033500	546144	Mm.335289	NM_177908	ENSMUSG00000044976	Wdr72	AW558070|D230040E23	WD repeat domain 72	protein-coding
mm_15375.1	chr2	156475689	156475693	+	1	NA	5' UTR (NM_001006664, exon 1 of 22)	5' UTR (NM_001006664, exon 1 of 22)	157	NM_001006664	13821	Mm.20852	NM_013510	ENSMUSG00000027624	Epb41l1	4.1N|Epb4.1l1|NBL1|mKIAA0338	erythrocyte membrane protein band 4.1 like 1	protein-coding
mm_134665.1	chr16	22252384	22252387	-	1	NA	intron (NM_009186, intron 4 of 8)	B2_Mm1a|SINE|B2	13620	NM_001330554	20462	Mm.210352	NM_009186	ENSMUSG00000022858	Tra2b	5730405G21Rik|D16Ertd266e|SIG-41|Sfrs10|Silg41|TRA2beta	transformer 2 beta homolog (Drosophila)	protein-coding
mm_147791.1	chr18	61647825	61647828	-	1	NA	promoter-TSS (NR_029557)	promoter-TSS (NR_029557)	68	NR_029557	387163		NR_029557	ENSMUSG00000065592	Mir145a	Mir145|Mirn145|mir-145a|mmu-mir-145|mmu-mir-145a	microRNA 145a	ncRNA
mm_126884.1	chr15	89454108	89454114	+	1	NA	5' UTR (NM_021921, exon 1 of 12)	5' UTR (NM_021921, exon 1 of 12)	200	NM_021921	60597	Mm.173337	NM_021921	ENSMUSG00000022619	Mapk8ip2	3230402N03Rik|AI847694|AW049958|IB2|Jip2|R75148	mitogen-activated protein kinase 8 interacting protein 2	protein-coding
mm_81110.1	chr9	106453354	106453413	+	1	NA	promoter-TSS (NM_021567)	promoter-TSS (NM_021567)	-455	NM_021567	59092	Mm.286394	NM_021567	ENSMUSG00000023495	Pcbp4	1200003L19Rik|AlphaCP-4	poly(rC) binding protein 4	protein-coding
mm_41981.1	chr5	107534716	107534732	+	1	NA	promoter-TSS (NM_175241)	promoter-TSS (NM_175241)	13	NM_175241	76421	Mm.67037	NM_175241	ENSMUSG00000089798	1700028K03Rik	-	RIKEN cDNA 1700028K03 gene	protein-coding
mm_138481.1	chr17	35195079	35195089	+	1	NA	TTS (NR_105939)	TTS (NR_105939)	112	NR_105939	102465588		NR_105939	ENSMUSG00000098291	Mir6973a	Gm27967|mmu-mir-6973a	microRNA 6973a	ncRNA
mm_122296.1	chr14	34588655	34588669	-	1	NA	promoter-TSS (NM_001039071)	promoter-TSS (NM_001039071)	19	NM_001039076	24131	Mm.29733	NM_011918	ENSMUSG00000021798	Ldb3	AW742271|PDLIM6|ZASP	LIM domain binding 3	protein-coding
mm_158900.1	chr1	31222876	31222876	+	1	NA	promoter-TSS (NM_029062)	promoter-TSS (NM_029062)	37	NM_029062	74708	Mm.246796	NM_029062	ENSMUSG00000026063	Pih1d3	4930521A18Rik	PIH1 domain containing 3	protein-coding
mm_11345.1	chr2	30807929	30807999	+	1	NA	promoter-TSS (NM_170592)	promoter-TSS (NM_170592)	-13	NM_170592	66617	Mm.33167	NM_170592	ENSMUSG00000026857	Ntmt1	2610205E22Rik|AL033331|AL033332|Mettl11a|NTM1A	N-terminal Xaa-Pro-Lys N-methyltransferase 1	protein-coding
mm_21196.1	chr2	155451063	155451068	-	1	NA	Intergenic	Intergenic	-10282	NM_019825	56406	Mm.27592	NM_019825	ENSMUSG00000038369	Ncoa6	AIB3|ASC-2|ASC2|NRC|Ncoa7|PRIP|RAP250|mKIAA0181	nuclear receptor coactivator 6	protein-coding
mm_23548.1	chr3	61366379	61366395	+	1	NA	3' UTR (NM_028712, exon 1 of 1)	3' UTR (NM_028712, exon 1 of 1)	1880	NM_028712	74012	Mm.422674	NM_028712	ENSMUSG00000036894	Rap2b	4021402C18Rik|AA408554	RAP2B, member of RAS oncogene family	protein-coding
mm_91933.1	chr10	60687234	60687271	-	1	NA	intron (NR_045556, intron 1 of 68)	CpG-1084	9238	NM_001252635	22295	Mm.440327	NM_023370	ENSMUSG00000012819	Cdh23	4930542A03Rik|USH1D|ahl|ahl1|bob|bus|mdfw|nmf112|nmf181|nmf252|sals|v	cadherin 23 (otocadherin)	protein-coding
mm_13921.1	chr2	120609403	120609442	+	1	NA	promoter-TSS (NM_025475)	promoter-TSS (NM_025475)	40	NM_025475	66296	Mm.221900	NM_025475	ENSMUSG00000027285	Haus2	1700101G24Rik|2410007P03Rik|AU020217|Cep27	HAUS augmin-like complex, subunit 2	protein-coding
mm_102138.1	chr11	53480179	53480216	-	1	NA	promoter-TSS (NM_183173)	promoter-TSS (NM_183173)	-2	NM_183173	237761	Mm.145208	NM_183173	ENSMUSG00000044352	Sowaha	A830006N08Rik|Ankrd43	sosondowah ankyrin repeat domain family member A	protein-coding
mm_8924.1	chr1	163725124	163725136	-	1	NA	5' UTR (NM_001143956, exon 1 of 4)	5' UTR (NM_001143956, exon 1 of 4)	102	NM_001143956	240879	Mm.484621	NM_001143956	ENSMUSG00000040113	Mettl11b	Gm207|NTM1B	methyltransferase like 11B	protein-coding
mm_89985.1	chr10	111985457	111985463	+	1	NA	TTS (NM_028608)	TTS (NM_028608)	11804	NM_028608	73690	Mm.173790	NM_028608	ENSMUSG00000056888	Glipr1	2410114O14Rik|RTVP-1|RTVP1|mRTVP-1	GLI pathogenesis-related 1 (glioma)	protein-coding
mm_11075.1	chr2	27677298	27677308	+	1	NA	5' UTR (NM_011305, exon 1 of 10)	5' UTR (NM_011305, exon 1 of 10)	102	NM_011305	20181	Mm.24624	NM_011305	ENSMUSG00000015846	Rxra	9530071D11Rik|Nr2b1|RXRalpha1	retinoid X receptor alpha	protein-coding
mm_123787.1	chr14	70351355	70351435	-	1	NA	promoter-TSS (NM_144808)	promoter-TSS (NM_144808)	29	NM_144808	213053	Mm.270647	NM_144808	ENSMUSG00000022094	Slc39a14	FAD-123|ZIP-14|Zip14|fad123	solute carrier family 39 (zinc transporter), member 14	protein-coding
mm_43291.1	chr5	134227277	134227298	+	1	NA	exon (NM_001286037, exon 4 of 11)	exon (NM_001286037, exon 4 of 11)	2338	NM_001286037	17969	Mm.425296	NM_010876	ENSMUSG00000015950	Ncf1	NCF-47K|NOXO2|Ncf-1|p47-phox|p47<phox>|p47phox	neutrophil cytosolic factor 1	protein-coding
mm_95155.1	chr11	35769821	35769869	+	1	NA	5' UTR (NM_145962, exon 1 of 7)	5' UTR (NM_145962, exon 1 of 7)	350	NM_145962	211347	Mm.255044	NM_145962	ENSMUSG00000018846	Pank3	-	pantothenate kinase 3	protein-coding
mm_172422.1	chr7	26707289	26707289	+	1	NA	Intergenic	MMETn-int|LTR|ERVK	-20859	NM_001081148	243881	Mm.294678	NM_001081148	ENSMUSG00000040650	Cyp2b23	EG243881	cytochrome P450, family 2, subfamily b, polypeptide 23	protein-coding
mm_168079.1	chr10	11609222	11609223	+	1	NA	promoter-TSS (NM_013898)	promoter-TSS (NM_013898)	-2	NM_013898	30058	Mm.214504	NM_013898	ENSMUSG00000048007	Timm8a1	DXHXS1274E|Ddp1|Fci-12|Tim8a|Timm8a	translocase of inner mitochondrial membrane 8A1	protein-coding
mm_152136.1	chr19	7039903	7039925	-	1	NA	5' UTR (NM_016737, exon 1 of 14)	5' UTR (NM_016737, exon 1 of 14)	112	NM_016737	20867	Mm.258633	NM_016737	ENSMUSG00000024966	Stip1	Hop|Sti1|p60	stress-induced phosphoprotein 1	protein-coding
mm_93222.1	chr10	95175994	95176025	-	1	NA	intron (NM_009950, intron 2 of 2)	intron (NM_009950, intron 2 of 2)	-30184	NR_131146	628062		NR_131146		Gm29684	-	predicted gene, 29684	ncRNA
mm_54312.1	chr6	30157566	30157569	-	1	NA	Intergenic	Intergenic	8425	NR_029569	387177		NR_029569	ENSMUSG00000076361	Mir182	Mirn182|mir-182|mmu-mir-182	microRNA 182	ncRNA
mm_47599.1	chr5	125037547	125037594	-	1	NA	intron (NM_001253905, intron 21 of 42)	intron (NM_001253905, intron 21 of 42)	34095	NM_028443	73121	Mm.296138	NM_028443	ENSMUSG00000037962	Rflna	3110032G18Rik|Fam101a|cfm|cfm2	refilin A	protein-coding
mm_142976.1	chr17	56140390	56140408	-	1	NA	promoter-TSS (NM_001130456)	promoter-TSS (NM_001130456)	-56	NM_001130456	20359	Mm.8029	NM_013662	ENSMUSG00000001227	Sema6b	Sema|Seman|VIb|semaZ	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B	protein-coding
mm_100876.1	chr11	5971764	5971775	-	1	NA	3' UTR (NM_001174054, exon 21 of 21)	3' UTR (NM_001174054, exon 21 of 21)	16011	NM_019661	56418	Mm.294821	NM_019661	ENSMUSG00000002741	Ykt6	0610042I15Rik|1810013M05Rik|AW105923	YKT6 v-SNARE homolog (S. cerevisiae)	protein-coding
mm_22727.1	chr3	19644569	19644573	+	1	NA	5' UTR (NM_001081281, exon 1 of 10)	5' UTR (NM_001081281, exon 1 of 10)	111	NM_001081281	381485	Mm.35419	NM_001081281	ENSMUSG00000060913	Trim55	D830041C10Rik|Murf2|Rnf29	tripartite motif-containing 55	protein-coding
mm_125693.1	chr15	66891364	66891375	+	1	NA	promoter-TSS (NM_018865)	promoter-TSS (NM_018865)	-24	NM_018865	22402	Mm.10222	NM_018865	ENSMUSG00000005124	Wisp1	AW146261|CCN4|Elm1	WNT1 inducible signaling pathway protein 1	protein-coding
mm_49282.1	chr6	17637896	17637911	+	1	NA	intron (NM_007604, intron 1 of 9)	intron (NM_007604, intron 1 of 9)	805	NM_007604	12343	Mm.392504	NM_007604	ENSMUSG00000015733	Capza2	1110053K06Rik|AW208808|Cappa2	capping protein (actin filament) muscle Z-line, alpha 2	protein-coding
mm_113298.1	chr13	30731750	30731757	+	1	NA	Intergenic	Intergenic	-17480	NM_001347508	16364	Mm.4677	NM_013674	ENSMUSG00000021356	Irf4	AI385587|IRF-4|LSIRF|NF-EM5|Spip	interferon regulatory factor 4	protein-coding
mm_27427.1	chr3	51554052	51554060	-	1	NA	intron (NM_080793, intron 1 of 7)	intron (NM_080793, intron 1 of 7)	-5701	NR_033624	100039684	Mm.387178	NR_033624		5031434O11Rik	AI481280|Gm2370	RIKEN cDNA 5031434O11 gene	ncRNA
mm_150791.1	chr19	44303240	44303255	+	1	NA	promoter-TSS (NR_039574)	promoter-TSS (NR_039574)	76	NR_039574	100628619		NR_039574	ENSMUSG00000093315	Mir5114	mmu-mir-5114|mu-mir-5114	microRNA 5114	ncRNA
mm_108042.1	chr12	73901436	73901442	+	1	NA	5' UTR (NM_001313920, exon 1 of 15)	5' UTR (NM_001313920, exon 1 of 15)	115	NM_001313920	15251	Mm.3879	NM_010431	ENSMUSG00000021109	Hif1a	AA959795|HIF-1-alpha|HIF1-alpha|HIF1alpha|MOP1|bHLHe78	hypoxia inducible factor 1, alpha subunit	protein-coding
mm_48931.1	chr6	4533738	4533768	+	1	NA	exon (NM_007743, exon 40 of 52)	exon (NM_007743, exon 40 of 52)	28135	NM_007743	12843	Mm.277792	NM_007743	ENSMUSG00000029661	Col1a2	AA960264|AI325291|Col1a-2|Cola-2|Cola2|oim	collagen, type I, alpha 2	protein-coding
mm_79069.1	chr9	46240741	46240745	+	1	NA	promoter-TSS (NM_007468)	promoter-TSS (NM_007468)	-101	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_76403.1	chr8	84846323	84846334	-	1	NA	exon (NM_007591, exon 2 of 9)	exon (NM_007591, exon 2 of 9)	603	NM_007591	12317	Mm.1971	NM_007591	ENSMUSG00000003814	Calr	CRT|Calregulin	calreticulin	protein-coding
mm_124248.1	chr14	101637551	101637557	-	1	NA	intron (NM_001168592, intron 1 of 2)	intron (NM_001168592, intron 1 of 2)	2917	NM_001033132	66200	Mm.250474	NM_001033132	ENSMUSG00000075486	Commd6	1110059J08Rik|1700063H17Rik	COMM domain containing 6	protein-coding
mm_27292.1	chr3	45309878	45309881	-	1	NA	intron (NR_045172, intron 6 of 8)	intron (NR_045172, intron 6 of 8)	68381	NR_045172	72511	Mm.140700	NR_045172	ENSMUSG00000097040	2610316D01Rik	-	RIKEN cDNA 2610316D01 gene	ncRNA
mm_122173.1	chr14	31494993	31495054	-	1	NA	promoter-TSS (NM_025907)	promoter-TSS (NM_025907)	-46	NM_025907	67011	Mm.291731	NM_025907	ENSMUSG00000021891	Mettl6	1600013P15Rik|AI467521|AU020711	methyltransferase like 6	protein-coding
mm_101383.1	chr11	23818953	23818974	-	1	NA	Intergenic	L4_C_Mam|LINE|RTE-X	-47993	NM_009044	19696	Mm.4869	NM_009044	ENSMUSG00000020275	Rel	c-Rel	reticuloendotheliosis oncogene	protein-coding
mm_47675.1	chr5	128600643	128600673	-	1	NA	promoter-TSS (NM_175284)	promoter-TSS (NM_175284)	29	NR_015517	319616	Mm.387738	NR_015517	ENSMUSG00000072591	5930412G12Rik	-	RIKEN cDNA 5930412G12 gene	ncRNA
mm_52019.1	chr6	94665537	94665551	+	1	NA	intron (NM_008377, intron 1 of 18)	MER20|DNA|hAT-Charlie	34601	NM_008377	16206	Mm.245210	NM_008377	ENSMUSG00000030029	Lrig1	D6Bwg0781e|Img|LIG-1	leucine-rich repeats and immunoglobulin-like domains 1	protein-coding
mm_114044.1	chr13	54073730	54073740	+	1	NA	intron (NM_027324, intron 1 of 10)	B3A|SINE|B2	1890	NM_027324	14057	Mm.134191	NM_027324	ENSMUSG00000021474	Sfxn1	2810002O05Rik|A930015P12Rik|f	sideroflexin 1	protein-coding
mm_39175.1	chr4	155774504	155774555	-	1	NA	promoter-TSS (NM_147776)	promoter-TSS (NM_147776)	32	NM_147776	246228	Mm.26515	NM_147776	ENSMUSG00000042116	Vwa1	4932416A11Rik|WARP	von Willebrand factor A domain containing 1	protein-coding
mm_107245.1	chr12	26479240	26479260	+	1	NA	3' UTR (NM_020557, exon 5 of 5)	3' UTR (NM_020557, exon 5 of 5)	10035	NM_020557	22169	Mm.271839	NM_020557	ENSMUSG00000020638	Cmpk2	1200004E04Rik|TDKI|Tyki	cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial	protein-coding
mm_103613.1	chr11	78541471	78541474	-	1	NA	TTS (NM_018854)	TTS (NM_018854)	5036	NM_018854	55978	Mm.358671	NM_018854	ENSMUSG00000001105	Ift20	0610009H04Rik|AU015496	intraflagellar transport 20	protein-coding
mm_150693.1	chr19	42159629	42159635	+	1	NA	Intergenic	Intergenic	-10935	NM_177319	319740	Mm.287359	NM_177319	ENSMUSG00000018820	Zfyve27	2210011N02Rik|9530077C24Rik|AI426636|AI593546|AI835681	zinc finger, FYVE domain containing 27	protein-coding
mm_155205.1	chrX	56731780	56731798	+	1	NA	promoter-TSS (NM_010211)	promoter-TSS (NM_010211)	28	NM_010211	14199	Mm.3126	NM_010211	ENSMUSG00000023092	Fhl1	FHL-1|KyoT|RAM14-1|SLIM|SLIM-1	four and a half LIM domains 1	protein-coding
mm_18318.1	chr2	57108314	57108321	-	1	NA	exon (NM_013613, exon 8 of 8)	exon (NM_013613, exon 8 of 8)	6721	NM_013613	18227	Mm.3507	NM_013613	ENSMUSG00000026826	Nr4a2	HZF-3|NOT|Nurr1|RNR-1|TINOR|TINUR	nuclear receptor subfamily 4, group A, member 2	protein-coding
mm_94675.1	chr11	17460157	17460165	+	1	NA	Intergenic	Intergenic	202473	NM_001330649	57316	Mm.287982	NM_020558	ENSMUSG00000000581	C1d	1110036E10Rik|AI875855|SUN-CoR	C1D nuclear receptor co-repressor	protein-coding
mm_51411.1	chr6	78380768	78380780	+	1	NA	promoter-TSS (NM_011259)	promoter-TSS (NM_011259)	65	NM_011259	19694	Mm.2552	NM_011259	ENSMUSG00000079516	Reg3a	AV063448	regenerating islet-derived 3 alpha	protein-coding
mm_43813.1	chr5	142905348	142905359	+	1	NA	exon (NM_007393, exon 3 of 6)	exon (NM_007393, exon 3 of 6)	1401	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_134121.1	chr16	10313913	10313919	-	1	NA	promoter-TSS (NM_007929)	promoter-TSS (NM_007929)	52	NM_007929	13731	Mm.246009	NM_007929	ENSMUSG00000022505	Emp2	XMP	epithelial membrane protein 2	protein-coding
mm_84733.1	chr9	75071425	75071447	-	1	NA	5' UTR (NM_010864, exon 1 of 41)	5' UTR (NM_010864, exon 1 of 41)	230	NM_010864	17918	Mm.3645	NM_010864	ENSMUSG00000034593	Myo5a	9630007J19Rik|AI413174|AI661011|Dbv|MVa|Myo5|MyoVA|Sev-1|d|d-120J|flail|flr	myosin VA	protein-coding
mm_106612.1	chr11	120816210	120816233	-	1	NA	exon (NM_007988, exon 17 of 43)	exon (NM_007988, exon 17 of 43)	8326	NM_007988	14104	Mm.236443	NM_007988	ENSMUSG00000025153	Fasn	A630082H08Rik|FAS	fatty acid synthase	protein-coding
mm_114292.1	chr13	58807862	58807883	+	1	NA	5' UTR (NM_001025074, exon 1 of 18)	5' UTR (NM_001025074, exon 1 of 18)	175	NM_001025074	18212	Mm.130054	NM_008745	ENSMUSG00000055254	Ntrk2	GP145-TrkB/GP95-TrkB|Tkrb|trk-B|trkB	neurotrophic tyrosine kinase, receptor, type 2	protein-coding
mm_72542.1	chr8	83997371	83997381	+	1	NA	promoter-TSS (NM_001081415)	promoter-TSS (NM_001081415)	-296	NM_001081415	666704	Mm.298091	NM_001081415	ENSMUSG00000079003	Samd1	AA589507	sterile alpha motif domain containing 1	protein-coding
mm_109760.1	chr12	117843874	117843923	+	1	NA	promoter-TSS (NM_146040)	promoter-TSS (NM_146040)	37	NM_146040	217946	Mm.281149	NM_146040	ENSMUSG00000021175	Cdca7l	BC006933|JPO2	cell division cycle associated 7 like	protein-coding
mm_69389.1	chr7	131362728	131362737	-	1	NA	promoter-TSS (NM_026655)	promoter-TSS (NM_026655)	-34	NM_026655	68277	Mm.121122	NM_026655	ENSMUSG00000040177	2310057M21Rik	3110040E10Rik|AI429544	RIKEN cDNA 2310057M21 gene	protein-coding
mm_67973.1	chr7	100656832	100656834	-	1	NA	5' UTR (NM_001163187, exon 1 of 6)	5' UTR (NM_001163187, exon 1 of 6)	132	NM_001163187	27276	Mm.491216	NM_013746	ENSMUSG00000030701	Plekhb1	AI315628|PHR1|Phret1|evt-1	pleckstrin homology domain containing, family B (evectins) member 1	protein-coding
mm_85015.1	chr9	87731275	87731285	-	1	NA	promoter-TSS (NM_023814)	promoter-TSS (NM_023814)	-20	NM_023814	76365	Mm.158789	NM_023814	ENSMUSG00000032419	Tbx18	2810012F10Rik|2810404D13Rik	T-box18	protein-coding
mm_68593.1	chr7	116038805	116038818	-	1	NA	promoter-TSS (NM_001025559)	promoter-TSS (NM_001025559)	-67	NM_001025559	20679	Mm.323365	NM_011445	ENSMUSG00000051910	Sox6	AI987981|SOX-LZ	SRY (sex determining region Y)-box 6	protein-coding
mm_72643.1	chr8	84701873	84701882	+	1	NA	5' UTR (NM_008535, exon 1 of 4)	5' UTR (NM_008535, exon 1 of 4)	420	NM_008535	17095	Mm.4925	NM_008535	ENSMUSG00000034041	Lyl1	Lyl-1|bHLHa18	lymphoblastomic leukemia 1	protein-coding
mm_12066.1	chr2	59598563	59598598	+	1	NA	Intergenic	Intergenic	-13462	NM_198294	66860	Mm.27917	NM_198294	ENSMUSG00000035168	Tanc1	1200003E16Rik|Tanc|mKIAA1728	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	protein-coding
mm_77553.1	chr8	123284093	123284113	-	1	NA	exon (NM_016925, exon 28 of 43)	exon (NM_016925, exon 28 of 43)	-29881	NM_028200	72325	Mm.276193	NM_028200	ENSMUSG00000001062	Vps9d1	1300018I17Rik|2410004N05Rik|5DOS1|Vsp9d1	VPS9 domain containing 1	protein-coding
mm_30723.1	chr4	13743480	13743510	+	1	NA	5' UTR (NM_001111026, exon 1 of 11)	5' UTR (NM_001111026, exon 1 of 11)	193	NM_001111026	12395	Mm.4909	NM_009822	ENSMUSG00000006586	Runx1t1	Cbfa2t1h|ETO|MTG8	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	protein-coding
mm_118678.1	chr14	22079848	22079876	+	1	NA	intron (NM_028275, intron 2 of 6)	B3|SINE|B2	60150	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_61556.1	chr7	79500019	79500035	+	1	NA	promoter-TSS (NR_040314)	promoter-TSS (NR_040314)	1	NR_040313	101694	Mm.41661	NR_040311	ENSMUSG00000097023	Mir9-3hg	AI854517	Mir9-3 host gene	ncRNA
mm_18395.1	chr2	60210467	60210484	-	1	NA	intron (NM_020575, intron 1 of 9)	intron (NM_020575, intron 1 of 9)	539	NM_020575	57438	Mm.260635	NM_020575	ENSMUSG00000026977	March7	Axo|Axot|Gtrgeo17	membrane-associated ring finger (C3HC4) 7	protein-coding
mm_49679.1	chr6	32112114	32112130	+	1	NA	Intergenic	Intergenic	61834	NM_029587	76382	Mm.23510	NM_029587	ENSMUSG00000029766	1700012A03Rik	AI429084	RIKEN cDNA 1700012A03 gene	protein-coding
mm_6839.1	chr1	84233306	84233317	-	1	NA	intron (NM_001003948, intron 1 of 2)	intron (NM_001003948, intron 1 of 2)	-14350	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_83319.1	chr9	44144714	44144733	-	1	NA	Intergenic	Intergenic	10065	NM_023061	84004	Mm.275003	NM_023061	ENSMUSG00000032135	Mcam	1-gicerin|AV025631|CD146|CD149|Muc18|s-endo|s-gicerin	melanoma cell adhesion molecule	protein-coding
mm_71097.1	chr8	35208772	35208781	+	1	NA	Intergenic	Intergenic	-166965	NM_177741	244416	Mm.247126	NM_177741	ENSMUSG00000046794	Ppp1r3b	6430576E21|AW821953|GL|PTG	protein phosphatase 1, regulatory (inhibitor) subunit 3B	protein-coding
mm_128201.1	chr15	35932286	35932286	-	1	NA	intron (NM_053071, intron 3 of 3)	L1M3|LINE|L1	5960	NM_053071	12864	Mm.548	NM_053071	ENSMUSG00000014313	Cox6c	-	cytochrome c oxidase subunit VIc	protein-coding
mm_45339.1	chr5	65752142	65752186	-	1	NA	Intergenic	HAL1|LINE|L1	-11357	NM_001024917	333789	Mm.332398	NM_001024917	ENSMUSG00000037795	N4bp2	B3bp|E430014I16|Gm1791|Gm868	NEDD4 binding protein 2	protein-coding
mm_143127.1	chr17	57212717	57212735	-	1	NA	exon (NM_009778, exon 28 of 41)	exon (NM_009778, exon 28 of 41)	4502	NR_105944	102465591		NR_105944	ENSMUSG00000099066	Mir6978	Gm27858|mmu-mir-6978	microRNA 6978	ncRNA
mm_138569.1	chr17	35380404	35380435	+	1	NA	exon (NM_001143689, exon 3 of 6)	exon (NM_001143689, exon 3 of 6)	802	NM_001143689	15015	Mm.464284	NM_001143689	ENSMUSG00000035929	H2-Q4	H-2Q4|H2-Gs10|Qa-4|Qa4|Qat-4|Qb-1|Qb1	histocompatibility 2, Q region locus 4	protein-coding
mm_48300.1	chr5	138264123	138264147	-	1	NA	promoter-TSS (NM_153161)	promoter-TSS (NM_153161)	-83	NM_153161	231807	Mm.164493	NM_153161	ENSMUSG00000036948	BC037034	-	cDNA sequence BC037034	protein-coding
mm_58608.1	chr7	5057162	5057188	+	1	NA	5' UTR (NM_146178, exon 1 of 5)	5' UTR (NM_146178, exon 1 of 5)	449	NM_146178	232821	Mm.482157	NM_146178	ENSMUSG00000035228	Ccdc106	BC018462	coiled-coil domain containing 106	protein-coding
mm_64614.1	chr7	3502588	3502592	-	1	NA	promoter-TSS (NM_177363)	promoter-TSS (NM_177363)	-38	NM_177363	245126	Mm.245747	NM_177363	ENSMUSG00000053338	Tarm1	9930022N03Rik|ENSMUSG00000053338|Gm9904|OLT-2	T cell-interacting, activating receptor on myeloid cells 1	protein-coding
mm_155645.1	chrX	85573984	85574017	+	1	NA	promoter-TSS (NM_025729)	promoter-TSS (NM_025729)	-22	NM_025729	66724	Mm.119646	NM_025729	ENSMUSG00000035476	Tab3	4921526G09Rik|Map3k7ip3|mKIAA4135	TGF-beta activated kinase 1/MAP3K7 binding protein 3	protein-coding
mm_47023.1	chr5	115491887	115491902	-	1	NA	Intergenic	Intergenic	-7410	NM_133760	75387	Mm.332616	NM_133760	ENSMUSG00000029524	Sirt4	4930596O17Rik	sirtuin 4	protein-coding
mm_43881.1	chr5	143758392	143758400	+	1	NA	promoter-TSS (NR_015486)	promoter-TSS (NR_015486)	42	NR_015486	320064	Mm.332820	NR_015486		D130017N08Rik	1700012G11Rik	RIKEN cDNA D130017N08 gene	ncRNA
mm_37162.1	chr4	117155845	117155848	-	1	NA	promoter-TSS (NR_030704)	promoter-TSS (NR_030704)	2	NR_030704	100216533		NR_030704	ENSMUSG00000092680	Snord55	-	small nucleolar RNA, C/D box 55	snoRNA
mm_82110.1	chr9	123150818	123150851	+	1	NA	promoter-TSS (NM_011606)	promoter-TSS (NM_011606)	-112	NM_011606	21922	Mm.34588	NM_011606	ENSMUSG00000025784	Clec3b	Tna	C-type lectin domain family 3, member b	protein-coding
mm_8703.1	chr1	158712931	158712941	-	1	NA	3' UTR (NM_001085376, exon 22 of 22)	3' UTR (NM_001085376, exon 22 of 22)	207311	NR_030441	735253		NR_030441	ENSMUSG00000070103	Mir488	Mirn488|mir-488|mmu-mir-488	microRNA 488	ncRNA
mm_127518.1	chr15	101999487	101999493	+	1	NA	exon (NM_031170, exon 4 of 9)	exon (NM_031170, exon 4 of 9)	4852	NM_031170	16691	Mm.358618	NM_031170	ENSMUSG00000049382	Krt8	AA960620|AL022697|AU019895|Card2|EndoA|K8|Krt-2.8|Krt2-8	keratin 8	protein-coding
mm_167669.1	chr9	74015879	74015879	-	1	NA	Intergenic	Intergenic	-82312	NM_001081153	208898	Mm.41035	NM_001081153	ENSMUSG00000062151	Unc13c	1500037O19Rik|AU019458|D9Ertd414e|Munc13-3|Unc13h3	unc-13 homolog C (C. elegans)	protein-coding
mm_52752.1	chr6	120742755	120742755	+	1	NA	intron (NM_001128151, intron 7 of 18)	intron (NM_001128151, intron 7 of 18)	-31013	NM_001081048	71803	Mm.425340	NM_001081048	ENSMUSG00000004902	Slc25a18	1500015I14Rik|AW125787	solute carrier family 25 (mitochondrial carrier), member 18	protein-coding
mm_135986.1	chr16	75092755	75092773	-	1	NA	Intergenic	Intergenic	493297	NM_001252513	320355	Mm.99517	NM_177142	ENSMUSG00000032948	Lipi	D930038D03Rik|lpd1	lipase, member I	protein-coding
mm_9606.1	chr1	175692591	175692615	-	1	NA	promoter-TSS (NM_010098)	promoter-TSS (NM_010098)	29	NM_010098	13603	Mm.32744	NM_010098	ENSMUSG00000026525	Opn3	ERO|Ecpn	opsin 3	protein-coding
mm_60224.1	chr7	43579578	43579640	+	1	NA	promoter-TSS (NM_172482)	promoter-TSS (NM_172482)	23	NM_172482	210105	Mm.234422	NM_172482	ENSMUSG00000030469	Zfp719	8030458J18|9430094P17Rik|C630016O21Rik|mszf6	zinc finger protein 719	protein-coding
mm_22025.1	chr2	168039411	168039415	-	1	NA	Intergenic	ID4_|SINE|ID	-28820	NM_001080708	69553	Mm.68454	NM_001080708	ENSMUSG00000074577	Fam65c	2310033K02Rik|Gm124	family with sequence similarity 65, member C	protein-coding
mm_171104.1	chr3	133544320	133544321	-	1	NA	promoter-TSS (NM_001346736)	promoter-TSS (NM_001346736)	70	NM_001346736	214133	Mm.347816	NM_145989	ENSMUSG00000040943	Tet2	Ayu17-449|E130014J05Rik|mKIAA1546	tet methylcytosine dioxygenase 2	protein-coding
mm_119241.1	chr14	33471584	33471593	+	1	NA	Intergenic	Intergenic	-24430	NM_016700	26419	Mm.21495	NM_016700	ENSMUSG00000021936	Mapk8	AI849689|JNK|JNK1|Prkm8|SAPK1	mitogen-activated protein kinase 8	protein-coding
mm_17948.1	chr2	36136603	36136625	-	1	NA	promoter-TSS (NM_026434)	promoter-TSS (NM_026434)	90	NM_026434	67889	Mm.205937	NM_026434	ENSMUSG00000026889	Rbm18	2010004P11Rik|AU015530	RNA binding motif protein 18	protein-coding
mm_83821.1	chr9	53912814	53912817	-	1	NA	exon (NM_177769, exon 11 of 11)	exon (NM_177769, exon 11 of 11)	62486	NM_177769	270162	Mm.259791	NM_177769	ENSMUSG00000041986	Elmod1	4831417L10|AI428506|AI834991	ELMO/CED-12 domain containing 1	protein-coding
mm_79103.1	chr9	46243405	46243422	+	1	NA	TTS (NM_007468)	TTS (NM_007468)	2569	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_106972.1	chr12	8974004	8974079	+	1	NA	promoter-TSS (NM_172470)	promoter-TSS (NM_172470)	40	NM_172470	74682	Mm.87389	NM_172470	ENSMUSG00000066643	Wdr35	4930459M12Rik|4931430C06|mKIAA1336	WD repeat domain 35	protein-coding
mm_49369.1	chr6	23251159	23251162	+	1	NA	Intergenic	Intergenic	-2896	NM_028462	73191	Mm.55115	NM_028462	ENSMUSG00000029697	Fezf1	3110069A13Rik|Fez|Zfp312-like|fez-like	Fez family zinc finger 1	protein-coding
mm_91400.1	chr10	30803076	30803154	-	1	NA	promoter-TSS (NM_172495)	promoter-TSS (NM_172495)	-8	NM_172495	211329	Mm.297903	NM_172495	ENSMUSG00000039697	Ncoa7	9030406N13Rik	nuclear receptor coactivator 7	protein-coding
mm_149616.1	chr19	16435617	16435630	+	1	NA	promoter-TSS (NM_008137)	promoter-TSS (NM_008137)	-44	NM_008137	14675	Mm.313181	NM_008137	ENSMUSG00000024697	Gna14	AU023208	guanine nucleotide binding protein, alpha 14	protein-coding
mm_2991.1	chr1	133163975	133164039	+	1	NA	Intergenic	CpG	32841	NM_133819	108954	Mm.293628	NM_133819	ENSMUSG00000046062	Ppp1r15b	1810033K10Rik|AI606441|C530022L24Rik|CReP	protein phosphatase 1, regulatory (inhibitor) subunit 15b	protein-coding
mm_62101.1	chr7	96211896	96211921	+	1	NA	5' UTR (NM_001310760, exon 1 of 33)	5' UTR (NM_001310760, exon 1 of 33)	237	NM_001310760	23966	Mm.254610	NM_011858	ENSMUSG00000048078	Tenm4	Doc4|ELM2|Odz4|R75022|Ten-m4|l(7)-3Rn|l7Rn3|mKIAA1302	teneurin transmembrane protein 4	protein-coding
mm_58520.1	chr7	4139944	4139967	+	1	NA	exon (NM_172736, exon 4 of 15)	exon (NM_172736, exon 4 of 15)	2899	NM_172736	232798	Mm.22831	NM_172736	ENSMUSG00000035545	Leng8	AW049671	leukocyte receptor cluster (LRC) member 8	protein-coding
mm_21062.1	chr2	152779040	152779058	-	1	NA	intron (NM_001289739, intron 2 of 4)	intron (NM_001289739, intron 2 of 4)	24876	NM_053091	84682	Mm.196668	NM_053091	ENSMUSG00000009876	Cox4i2	Cox4b|CoxIV-2	cytochrome c oxidase subunit IV isoform 2	protein-coding
mm_72555.1	chr8	84066825	84066882	+	1	NA	promoter-TSS (NM_009055)	promoter-TSS (NM_009055)	17	NM_009055	19724	Mm.7892	NM_009055	ENSMUSG00000031706	Rfx1	AI047719|AI385641	regulatory factor X, 1 (influences HLA class II expression)	protein-coding
mm_121888.1	chr14	21741464	21741470	-	1	NA	intron (NM_001007268, intron 5 of 7)	intron (NM_001007268, intron 5 of 7)	1412	NM_013849	27389	Mm.390674	NM_013849	ENSMUSG00000021768	Dusp13	DUSP13A|DUSP13B|Gm1203|LMW-DSP6|MDSP|TMDP|TS-DSP6	dual specificity phosphatase 13	protein-coding
mm_73030.1	chr8	94179235	94179248	+	1	NA	5' UTR (NM_013602, exon 1 of 3)	5' UTR (NM_013602, exon 1 of 3)	152	NM_013602	17748	Mm.192991	NM_013602	ENSMUSG00000031765	Mt1	MT-I|Mt-1	metallothionein 1	protein-coding
mm_85974.1	chr9	112160682	112160688	-	1	NA	3' UTR (NM_001177623, exon 10 of 10)	3' UTR (NM_001177623, exon 10 of 10)	25264	NM_001177618	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_102384.1	chr11	58904174	58904217	-	1	NA	promoter-TSS (NM_011758)	promoter-TSS (NM_011758)	30	NM_011758	22698	Mm.127646	NM_011758	ENSMUSG00000037001	Zfp39	CTfin33|Zfp-39	zinc finger protein 39	protein-coding
mm_123020.1	chr14	55116398	55116408	-	1	NA	5' UTR (NM_177049, exon 1 of 6)	5' UTR (NM_177049, exon 1 of 6)	532	NM_177049	319984	Mm.19047	NM_177049	ENSMUSG00000022208	Jph4	9330157P13Rik|JP-4|JPHL1	junctophilin 4	protein-coding
mm_98016.1	chr11	84880309	84880373	+	1	NA	promoter-TSS (NM_001077636)	promoter-TSS (NM_001077636)	-56	NM_001077636	70325	Mm.390414	NM_027388	ENSMUSG00000045140	Pigw	2610044A17Rik|Gwt1	phosphatidylinositol glycan anchor biosynthesis, class W	protein-coding
mm_67320.1	chr7	79617643	79617659	-	1	NA	promoter-TSS (NM_019799)	promoter-TSS (NM_019799)	6	NM_019799	56315	Mm.10909	NM_019799	ENSMUSG00000030549	Rhcg	BB065800	Rhesus blood group-associated C glycoprotein	protein-coding
mm_125664.1	chr15	65787024	65787090	+	1	NA	promoter-TSS (NM_133766)	promoter-TSS (NM_133766)	16	NM_133766	76740	Mm.260647	NM_133766	ENSMUSG00000015002	Efr3a	A130089M23Rik|BB071175|C76891|C920006C10Rik|D030063F01Rik|mKIAA0143	EFR3 homolog A	protein-coding
mm_112575.1	chr13	13628426	13628445	+	1	NA	intron (NM_010748, intron 3 of 52)	intron (NM_010748, intron 3 of 52)	38026	NM_010748	17101	Mm.342337	NM_010748	ENSMUSG00000019726	Lyst	D13Sfk13|beige|bg	lysosomal trafficking regulator	protein-coding
mm_3500.1	chr1	150106980	150106985	+	1	NA	3' UTR (NM_011198, exon 10 of 10)	3' UTR (NM_011198, exon 10 of 10)	6951	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_151696.1	chr19	4397053	4397098	-	1	NA	promoter-TSS (NM_001001984)	promoter-TSS (NM_001001984)	2	NM_001001984	225876	Mm.31941	NM_001001984	ENSMUSG00000054611	Kdm2a	100043628|5530401A10Rik|AA589516|AW536790|Cxxc8|Fbl11|Fbl7|Fbxl11|Gm4560|Jhdm1|Jhdm1a|lalina	lysine (K)-specific demethylase 2A	protein-coding
mm_172062.1	chr6	132767705	132767710	-	1	NA	Intergenic	BGLII|LTR|ERVK	5576	NM_199153	387339	Mm.377902	NM_199153	ENSMUSG00000056901	Tas2r102	Tas2r2|mGR02|mt2r51	taste receptor, type 2, member 102	protein-coding
mm_49500.1	chr6	29768275	29768290	+	1	NA	promoter-TSS (NM_021414)	promoter-TSS (NM_021414)	-161	NM_021414	74340	Mm.210899	NM_021414	ENSMUSG00000029772	Ahcyl2	4631427C17Rik|AI227036|Adohcyase3|mKIAA0828	S-adenosylhomocysteine hydrolase-like 2	protein-coding
mm_84763.1	chr9	75599125	75599141	-	1	NA	promoter-TSS (NM_001038710)	promoter-TSS (NM_001038710)	0	NM_001038710	50876	Mm.291880	NM_016711	ENSMUSG00000032186	Tmod2	N-Tmod|NTMOD	tropomodulin 2	protein-coding
mm_97015.1	chr11	71019642	71019653	+	1	NA	promoter-TSS (NM_001291148)	promoter-TSS (NM_001291148)	36	NM_025993	67139	Mm.28227	NM_025993	ENSMUSG00000040599	Mis12	2510025F08Rik|AU044651|Misc12	MIS12 kinetochore complex component	protein-coding
mm_99265.1	chr11	101246357	101246370	+	1	NA	promoter-TSS (NM_019444)	promoter-TSS (NM_019444)	29	NM_019444	54409	Mm.260698	NM_019444	ENSMUSG00000001240	Ramp2	-	receptor (calcitonin) activity modifying protein 2	protein-coding
mm_163478.1	chr12	105013114	105013140	-	1	NA	Intergenic	Intergenic	-3318	NM_172500	212073	Mm.212688	NM_172500	ENSMUSG00000054150	Syne3	nesprin-3	spectrin repeat containing, nuclear envelope family member 3	protein-coding
mm_104754.1	chr11	98463777	98463798	-	1	NA	TTS (NM_011771)	TTS (NM_011771)	16953	NM_010346	14786	Mm.276702	NM_010346	ENSMUSG00000019312	Grb7	mKIAA4028	growth factor receptor bound protein 7	protein-coding
mm_94398.1	chr11	5595436	5595438	+	1	NA	intron (NM_023816, intron 7 of 26)	RLTR40|LTR|ERVK	25753	NM_023816	76389	Mm.67300	NM_023816	ENSMUSG00000020481	Ankrd36	1700008J08Rik|1700012M14Rik|Ankrd48	ankyrin repeat domain 36	protein-coding
mm_154635.1	chrX	7762904	7762914	+	1	NA	5' UTR (NM_001271489, exon 1 of 10)	5' UTR (NM_001271489, exon 1 of 10)	248	NM_172472	209446	Mm.249142	NM_172472	ENSMUSG00000000134	Tfe3	F830016E06Rik|Tcfe3|Tfe-3|bHLHe33	transcription factor E3	protein-coding
mm_18476.1	chr2	62412301	62412309	-	1	NA	promoter-TSS (NM_010074)	promoter-TSS (NM_010074)	-74	NM_001159543	13482	Mm.1151	NM_010074	ENSMUSG00000035000	Dpp4	Cd26|Dpp-4|THAM	dipeptidylpeptidase 4	protein-coding
mm_11878.1	chr2	49516804	49516804	+	1	NA	intron (NM_172663, intron 3 of 13)	intron (NM_172663, intron 3 of 13)	65318	NM_172663	227867	Mm.29167	NM_172663	ENSMUSG00000069495	Epc2	5830499L14|D2Ertd694e	enhancer of polycomb homolog 2 (Drosophila)	protein-coding
mm_150487.1	chr19	39006949	39006972	+	1	NA	promoter-TSS (NM_028089)	promoter-TSS (NM_028089)	-59	NM_028089	72082	Mm.142581	NM_028089	ENSMUSG00000025002	Cyp2c55	2010318C06Rik	cytochrome P450, family 2, subfamily c, polypeptide 55	protein-coding
mm_45889.1	chr5	88527842	88527852	-	1	NA	promoter-TSS (NM_152839)	promoter-TSS (NM_152839)	50	NM_152839	16069	Mm.1192	NM_152839	ENSMUSG00000067149	Jchain	9530090F24Rik|AI323815|Igj|Jch	immunoglobulin joining chain	protein-coding
mm_97532.1	chr11	78536356	78536368	+	1	NA	promoter-TSS (NM_018854)	promoter-TSS (NM_018854)	-74	NM_018854	55978	Mm.358671	NM_018854	ENSMUSG00000001105	Ift20	0610009H04Rik|AU015496	intraflagellar transport 20	protein-coding
mm_94435.1	chr11	6292556	6292580	+	1	NA	promoter-TSS (NM_001252288)	promoter-TSS (NM_001252288)	10	NM_001252288	18293	Mm.276348	NM_010956	ENSMUSG00000020456	Ogdh	2210403E04Rik|2210412K19Rik|AA409584|d1401|mKIAA4192	oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)	protein-coding
mm_56307.1	chr6	91807425	91807456	-	1	NA	promoter-TSS (NM_001159507)	promoter-TSS (NM_001159507)	-47	NM_001159507	243547	Mm.333264	NM_001033353	ENSMUSG00000030098	Grip2	-	glutamate receptor interacting protein 2	protein-coding
mm_38720.1	chr4	145234793	145234803	-	1	NA	intron (NM_011610, intron 1 of 9)	intron (NM_011610, intron 1 of 9)	12072	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_64652.1	chr7	4120434	4120466	-	1	NA	non-coding (NR_033568, exon 1 of 9)	non-coding (NR_033568, exon 1 of 9)	278	NR_033568	77323	Mm.378791	NR_033568	ENSMUSG00000086155	9430041J12Rik	-	RIKEN cDNA 9430041J12 gene	ncRNA
mm_142758.1	chr17	49009742	49009775	-	1	NA	intron (NM_027452, intron 1 of 2)	intron (NM_027452, intron 1 of 2)	77176	NM_027452	70530	Mm.133607	NM_027452	ENSMUSG00000040490	Lrfn2	5730420O05Rik|SALM1|mKIAA1246	leucine rich repeat and fibronectin type III domain containing 2	protein-coding
mm_131435.1	chr16	15888136	15888152	+	1	NA	3' UTR (NM_007679, exon 1 of 1)	3' UTR (NM_007679, exon 1 of 1)	858	NM_007679	12609	Mm.347407	NM_007679	ENSMUSG00000071637	Cebpd	c/EBPdelta	CCAAT/enhancer binding protein (C/EBP), delta	protein-coding
mm_114347.1	chr13	60928083	60928088	+	1	NA	Intergenic	L1_Mus3|LINE|L1	8481	NM_001145799	13024	Mm.482089	NM_007796	ENSMUSG00000044258	Ctla2a	Ctla-2a	cytotoxic T lymphocyte-associated protein 2 alpha	protein-coding
mm_41236.1	chr5	88764984	88764995	+	1	NA	promoter-TSS (NM_007832)	promoter-TSS (NM_007832)	-24	NM_007832	13178	Mm.298892	NM_007832	ENSMUSG00000029366	Dck	-	deoxycytidine kinase	protein-coding
mm_146442.1	chr18	84936207	84936210	+	1	NA	intron (NM_015798, intron 1 of 9)	(T)n|Simple_repeat|Simple_repeat	1183	NM_015798	50764	Mm.28369	NM_015798	ENSMUSG00000034391	Fbxo15	AU019763|Fbx15|ecat3	F-box protein 15	protein-coding
mm_132099.1	chr16	31422269	31422278	+	1	NA	promoter-TSS (NM_175177)	promoter-TSS (NM_175177)	-24	NM_175177	71911	Mm.293470	NM_175177	ENSMUSG00000046598	Bdh1	2310032J20Rik|AI327223|Bdh	3-hydroxybutyrate dehydrogenase, type 1	protein-coding
mm_159018.1	chr1	171285432	171285432	-	1	NA	intron (NM_013919, intron 3 of 12)	intron (NM_013919, intron 3 of 12)	2529	NM_013919	30941	Mm.27510	NM_013919	ENSMUSG00000053483	Usp21	ESTM28|Usp16|Usp23|W53272	ubiquitin specific peptidase 21	protein-coding
mm_115739.1	chr13	17804983	17805025	-	1	NA	promoter-TSS (NM_001081058)	promoter-TSS (NM_001081058)	93	NM_001081058	69562	Mm.193924	NM_027118	ENSMUSG00000041297	Cdk13	2310015O17Rik|Cdc2l5	cyclin-dependent kinase 13	protein-coding
mm_9330.1	chr1	171849543	171849548	-	1	NA	intron (NM_001289470, intron 2 of 8)	intron (NM_001289470, intron 2 of 8)	9848	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_31329.1	chr4	46451081	46451111	+	1	NA	5' UTR (NM_130889, exon 1 of 7)	5' UTR (NM_130889, exon 1 of 7)	170	NM_130889	67628	Mm.263913	NM_130889	ENSMUSG00000028333	Anp32b	2410015B15Rik|PAL31|PHAPI2a|Ssp29	acidic (leucine-rich) nuclear phosphoprotein 32 family, member B	protein-coding
mm_16433.1	chr2	180394356	180394372	+	1	NA	intron (NR_045331, intron 3 of 3)	intron (NR_045331, intron 3 of 3)	-4015	NR_029901	723954		NR_029901	ENSMUSG00000065460	Mir133a-2	Mirn133a-2|mir-133a-2	microRNA 133a-2	ncRNA
mm_78049.1	chr9	14704507	14704515	+	1	NA	intron (NM_177905, intron 17 of 18)	intron (NM_177905, intron 17 of 18)	36222	NM_177905	330890	Mm.334969	NM_177905	ENSMUSG00000036912	Piwil4	9230101H05Rik|Miwi2	piwi-like RNA-mediated gene silencing 4	protein-coding
mm_5402.1	chr1	33720355	33720363	-	1	NA	promoter-TSS (NM_001159729)	promoter-TSS (NM_001159729)	-60	NM_001159729	19335	Mm.86744	NM_008999	ENSMUSG00000004768	Rab23	AW545388|opb|opb2	RAB23, member RAS oncogene family	protein-coding
mm_56736.1	chr6	115759005	115759020	-	1	NA	promoter-TSS (NM_144805)	promoter-TSS (NM_144805)	-13	NM_144805	94346	Mm.29739	NM_144805	ENSMUSG00000059900	Tmem40	9030407H20Rik|AV091463|W64236	transmembrane protein 40	protein-coding
mm_22065.1	chr2	168712854	168712935	-	1	NA	intron (NM_001289446, intron 1 of 27)	intron (NM_001289446, intron 1 of 27)	21445	NM_001289445	11981	Mm.330819	NM_015731	ENSMUSG00000027546	Atp9a	IIa	ATPase, class II, type 9A	protein-coding
mm_4056.1	chr1	165838673	165838676	+	1	NA	intron (NM_001113391, intron 1 of 7)	intron (NM_001113391, intron 1 of 7)	49993	NM_001113392	12503	Mm.217308	NM_031162	ENSMUSG00000005763	Cd247	4930549J05Rik|A430104F18Rik|AW552088|Cd3|Cd3-eta|Cd3-zeta|Cd3h|Cd3z|Cd3zeta|T3z|Tcrk|Tcrz	CD247 antigen	protein-coding
mm_35262.1	chr4	19892358	19892375	-	1	NA	intron (NM_175406, intron 2 of 7)	intron (NM_175406, intron 2 of 7)	30200	NM_175406	242341	Mm.19298	NM_175406	ENSMUSG00000028238	Atp6v0d2	1620401A02Rik|AI324824|V-ATPase	ATPase, H+ transporting, lysosomal V0 subunit D2	protein-coding
mm_85265.1	chr9	99420371	99420394	-	1	NA	intron (NM_008624, intron 1 of 5)	intron (NM_008624, intron 1 of 5)	16330	NM_008624	17532	Mm.2045	NM_008624	ENSMUSG00000032470	Mras	2900078C09Rik|AI326250	muscle and microspikes RAS	protein-coding
mm_159737.1	chr5	65862977	65862977	+	1	NA	promoter-TSS (NM_001081105)	promoter-TSS (NM_001081105)	-592	NM_001081105	74734	Mm.20323	NM_001081105	ENSMUSG00000029204	Rhoh	5830400A04Rik|AU019774|Arhh	ras homolog family member H	protein-coding
mm_78085.1	chr9	17395299	17395302	+	1	NA	Intergenic	Intergenic	-896967	NM_025844	66917	Mm.103534	NM_025844	ENSMUSG00000001774	Chordc1	1110001O09Rik|AA409036|Chp-1|morgana	cysteine and histidine-rich domain (CHORD)-containing, zinc-binding protein 1	protein-coding
mm_48434.1	chr5	140623238	140623248	-	1	NA	3' UTR (NM_175274, exon 14 of 14)	3' UTR (NM_175274, exon 14 of 14)	15902	NM_008494	16848	Mm.12834	NM_008494	ENSMUSG00000029570	Lfng	AW061165	LFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	protein-coding
mm_26144.1	chr3	138065144	138065156	+	1	NA	intron (NR_037975, intron 1 of 3)	intron (NR_037975, intron 1 of 3)	2238	NR_037975	329763	Mm.169710	NM_177860	ENSMUSG00000049349	Gm5105	D830013H12|EG329763	predicted gene 5105	ncRNA
mm_6911.1	chr1	84839323	84839391	-	1	NA	promoter-TSS (NM_025386)	promoter-TSS (NM_025386)	-53	NM_133975	14897	Mm.209265	NM_133975	ENSMUSG00000026219	Trip12	1110036I07Rik|6720416K24Rik|AA410158|Gtl6|TRIP-12	thyroid hormone receptor interactor 12	protein-coding
mm_169183.1	chr13	65848633	65848649	-	1	NA	Intergenic	RLTR27|LTR|ERVK	-264812	NM_001177832	628709	Mm.390595	NM_001177832	ENSMUSG00000095909	Gm10324	ENSMUSG00000071302	predicted gene 10324	protein-coding
mm_82054.1	chr9	122601156	122601163	+	1	NA	Intergenic	Intergenic	28658	NR_015610	319626	Mm.186748	NR_015610	ENSMUSG00000097736	9530059O14Rik	-	RIKEN cDNA 9530059O14 gene	ncRNA
mm_85665.1	chr9	107675562	107675567	-	1	NA	3' UTR (NM_008140, exon 9 of 9)	3' UTR (NM_008140, exon 9 of 9)	4028	NM_008140	14685	Mm.284853	NM_008140	ENSMUSG00000034837	Gnat1	Gnat-1|Ird1|Ird2|Tralpha|irdc|irdr|transducin	guanine nucleotide binding protein, alpha transducing 1	protein-coding
mm_171429.1	chr4	135300851	135300857	-	1	NA	Intergenic	RLTR1B|LTR|ERV1	-28094	NM_013885	29876	Mm.257765	NM_013885	ENSMUSG00000037242	Clic4	D0Jmb3|TU-74|mc3s5|mtCLIC	chloride intracellular channel 4 (mitochondrial)	protein-coding
mm_133338.1	chr16	81200665	81200680	+	1	NA	promoter-TSS (NM_010954)	promoter-TSS (NM_010954)	-25	NM_001113208	17968	Mm.433941	NM_010954	ENSMUSG00000022762	Ncam2	Ncam-2|Ocam|RNCAM	neural cell adhesion molecule 2	protein-coding
mm_44991.1	chr5	38158912	38158921	-	1	NA	exon (NM_010942, exon 2 of 5)	exon (NM_010942, exon 2 of 5)	551	NM_010942	18196	Mm.7414	NM_010942	ENSMUSG00000029126	Nsg1	Neep21|m234|p21	neuron specific gene family member 1	protein-coding
mm_116878.1	chr13	55021545	55021556	-	1	NA	promoter-TSS (NM_001206391)	promoter-TSS (NM_001206391)	-165	NM_001033245	212032	Mm.267479	NM_001033245	ENSMUSG00000025877	Hk3	HK III|HK-III	hexokinase 3	protein-coding
mm_120056.1	chr14	56673916	56673928	+	1	NA	exon (NM_023773, exon 3 of 14)	exon (NM_023773, exon 3 of 14)	5674	NM_023773	75339	Mm.152466	NM_023773	ENSMUSG00000079184	Mphosph8	1500035L22Rik|4930548G07Rik|AU040635	M-phase phosphoprotein 8	protein-coding
mm_93407.1	chr10	107912363	107912367	-	1	NA	promoter-TSS (NM_001177567)	promoter-TSS (NM_001177567)	-231	NM_001177567	628870	Mm.336090	NM_001177567	ENSMUSG00000091455	Otogl	EG628870|Gm6924	otogelin-like	protein-coding
mm_37134.1	chr4	116807575	116807617	-	1	NA	promoter-TSS (NM_026654)	promoter-TSS (NM_026654)	-37	NM_026654	68276	Mm.30534	NM_026654	ENSMUSG00000028688	Toe1	4930584N22Rik|4933424D16Rik|AI413517	target of EGR1, member 1 (nuclear)	protein-coding
mm_66012.1	chr7	30588940	30588989	-	1	NA	promoter-TSS (NR_106134)	promoter-TSS (NR_106134)	-238	NM_029274	75410	Mm.168688	NM_029274	ENSMUSG00000006307	Kmt2b	2610014H22Rik|Mll2|Wbp7|mKIAA0304	lysine (K)-specific methyltransferase 2B	protein-coding
mm_148817.1	chr19	6298290	6298294	+	1	NA	exon (NM_010119, exon 5 of 5)	exon (NM_010119, exon 5 of 5)	-8165	NM_001033342	240505	Mm.329622	NM_001033342	ENSMUSG00000024769	Cdc42bpg	BC046418|MRCKgamma	CDC42 binding protein kinase gamma (DMPK-like)	protein-coding
mm_17304.1	chr2	26352068	26352115	-	1	NA	promoter-TSS (NM_001139504)	promoter-TSS (NM_001139504)	19	NM_026828	52838	Mm.31239	NM_026828	ENSMUSG00000075467	Dnlz	1110034G11Rik|D2Bwg1335e|HEP1	DNL-type zinc finger	protein-coding
mm_127166.1	chr15	98708226	98708247	+	1	NA	promoter-TSS (NM_153518)	promoter-TSS (NM_153518)	9	NM_153518	105833	Mm.26205	NM_153518	ENSMUSG00000003354	Ccdc65	4933417K04Rik|AI428139|AU020178|NYD-SP28	coiled-coil domain containing 65	protein-coding
mm_145364.1	chr18	56707726	56707940	+	1	NA	promoter-TSS (NM_010721)	promoter-TSS (NM_010721)	20	NM_010721	16906	Mm.4105	NM_010721	ENSMUSG00000024590	Lmnb1	-	lamin B1	protein-coding
mm_171560.1	chr4	147230222	147230227	+	1	NA	intron (NM_001039209, intron 1 of 2)	intron (NM_001039209, intron 1 of 2)	54358	NM_001039209	195531	Mm.270762	NM_001039209	ENSMUSG00000078496	Zfp982	Gm13152|OTTMUSG00000010671	zinc finger protein 982	protein-coding
mm_18844.1	chr2	75467813	75467824	-	1	NA	Intergenic	Intergenic	-23639	NR_040635	77269	Mm.389278	NR_040635		9430019J16Rik	-	RIKEN cDNA 9430019J16 gene	ncRNA
mm_53523.1	chr6	136518867	136518875	+	1	NA	promoter-TSS (NM_019426)	promoter-TSS (NM_019426)	20	NM_019426	54343	Mm.173271	NM_019426	ENSMUSG00000030213	Atf7ip	2610204M12Rik|AM|Mcaf1	activating transcription factor 7 interacting protein	protein-coding
mm_35591.1	chr4	43003891	43003893	-	1	NA	exon (NM_053081, exon 12 of 14)	exon (NM_053081, exon 12 of 14)	-3385	NM_009503	269523	Mm.245976	NM_009503	ENSMUSG00000028452	Vcp	3110001E05|CDC48|p97|p97/VCP	valosin containing protein	protein-coding
mm_128009.1	chr15	13173587	13173602	-	1	NA	promoter-TSS (NM_007666)	promoter-TSS (NM_007666)	81	NM_007666	12563	Mm.57048	NM_007666	ENSMUSG00000039385	Cdh6	cad6	cadherin 6	protein-coding
mm_129874.1	chr15	83423781	83423793	-	1	NA	intron (NM_001159509, intron 1 of 10)	intron (NM_001159509, intron 1 of 10)	9063	NM_011862	23970	Mm.23978	NM_011862	ENSMUSG00000016664	Pacsin2	AI197433	protein kinase C and casein kinase substrate in neurons 2	protein-coding
mm_89612.1	chr10	96036668	96036683	+	1	NA	exon (NM_001001932, exon 23 of 29)	exon (NM_001001932, exon 23 of 29)	96012	NM_001001932	216238	Mm.210035	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding
mm_170869.1	chr2	20180669	20180687	-	1	NA	Intergenic	RLTR9D|LTR|ERVK	-109235	NM_001081006	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding
mm_161556.1	chr16	13930275	13930275	+	1	NA	intron (NM_001289562, intron 1 of 3)	IAPLTR2_Mm|LTR|ERVK	-10354	NM_001289563	93734	Mm.76554	NM_033564	ENSMUSG00000022679	Mpv17l	M-LP	Mpv17 transgene, kidney disease mutant-like	protein-coding
mm_65610.1	chr7	27486227	27486231	-	1	NA	promoter-TSS (NM_018820)	promoter-TSS (NM_018820)	-724	NM_018820	55942	Mm.153684	NM_018820	ENSMUSG00000008384	Sertad1	1110032C13Rik|AV000455|AW456625|Sei-1|Sei1|TRIP-Br1	SERTA domain containing 1	protein-coding
mm_92743.1	chr10	80957830	80957848	-	1	NA	intron (NM_001038655, intron 2 of 3)	intron (NM_001038655, intron 2 of 3)	27748	NM_008655	17873	Mm.1360	NM_008655	ENSMUSG00000015312	Gadd45b	AI323528|Myd118	growth arrest and DNA-damage-inducible 45 beta	protein-coding
mm_78597.1	chr9	37434173	37434211	+	1	NA	Intergenic	Intergenic	-1017	NM_001164767	19649	Mm.212826	NM_011248	ENSMUSG00000032128	Robo3	Rbig1|Rig-1|Rig1|Robo3a|Robo3b	roundabout guidance receptor 3	protein-coding
mm_97133.1	chr11	75063116	75063116	+	1	NA	intron (NM_001002764, intron 13 of 18)	ID_B1|SINE|B4	2875	NR_030454	735274		NR_030454	ENSMUSG00000106252	Mir684-1	Mirn684-1	microRNA 684-1	ncRNA
mm_104708.1	chr11	98022595	98022671	-	1	NA	promoter-TSS (NM_031173)	promoter-TSS (NM_031173)	-6	NM_001282978	12295	Mm.41252	NM_031173	ENSMUSG00000020882	Cacnb1	CAB1|Cchb1|Cchlb1	calcium channel, voltage-dependent, beta 1 subunit	protein-coding
mm_70332.1	chr8	4493444	4493472	+	1	NA	promoter-TSS (NM_026058)	promoter-TSS (NM_026058)	53	NM_026058	67260	Mm.35511	NM_026058	ENSMUSG00000008206	Cers4	2900019C14Rik|Lass4|Trh1	ceramide synthase 4	protein-coding
mm_60248.1	chr7	43774625	43774636	+	1	NA	promoter-TSS (NM_001177373)	promoter-TSS (NM_001177373)	13	NM_001177373	56538	Mm.154276	NM_019974	ENSMUSG00000067616	Klk11	2310015I08Rik|Prss20|TLSP	kallikrein related-peptidase 11	protein-coding
mm_71523.1	chr8	46852657	46852662	+	1	NA	Intergenic	Intergenic	112914	NM_008391	16363	Mm.1149	NM_008391	ENSMUSG00000031627	Irf2	9830146E22Rik|AI646973|Irf-2	interferon regulatory factor 2	protein-coding
mm_18690.1	chr2	71530591	71530601	-	1	NA	TTS (NR_002854)	TTS (NR_002854)	1151	NM_010053	13390	Mm.475101	NM_010053	ENSMUSG00000041911	Dlx1	Dlx|Dlx-1	distal-less homeobox 1	protein-coding
mm_109762.1	chr12	117916098	117916106	+	1	NA	intron (NM_010060, intron 71 of 81)	intron (NM_010060, intron 71 of 81)	72241	NM_146040	217946	Mm.281149	NM_146040	ENSMUSG00000021175	Cdca7l	BC006933|JPO2	cell division cycle associated 7 like	protein-coding
mm_52996.1	chr6	123267989	123268010	+	1	NA	exon (NM_010819, exon 4 of 6)	exon (NM_010819, exon 4 of 6)	5892	NM_010819	17474	Mm.441101	NM_010819	ENSMUSG00000030144	Clec4d	Clecsf8|Mpcl|mcl	C-type lectin domain family 4, member d	protein-coding
mm_101804.1	chr11	46312070	46312119	-	1	NA	5' UTR (NM_001252460, exon 1 of 31)	5' UTR (NM_001252460, exon 1 of 31)	264	NM_001252460	76884	Mm.154358	NM_133769	ENSMUSG00000020340	Cyfip2	1500004I01Rik|6430511D02Rik|AA930218|AU022376|Pir121|mKIAA1168	cytoplasmic FMR1 interacting protein 2	protein-coding
mm_141072.1	chr17	25837110	25837199	-	1	NA	promoter-TSS (NM_144816)	promoter-TSS (NM_144816)	-27	NM_144816	214951	Mm.490018	NM_144816	ENSMUSG00000025735	Rhbdl1	Rhbdl	rhomboid, veinlet-like 1 (Drosophila)	protein-coding
mm_171630.1	chr4	19137941	19137943	+	1	NA	Intergenic	RLTR9E|LTR|ERVK	-142908	NM_013927	30952	Mm.445778	NM_013927	ENSMUSG00000056494	Cngb3	CCNC2|CNG6|Cngbeta2	cyclic nucleotide gated channel beta 3	protein-coding
mm_142515.1	chr17	46264596	46264596	-	1	NA	intron (NM_001252473, intron 3 of 9)	PB1D10|SINE|Alu	10431	NM_001111142	224813	Mm.70999	NM_001111142	ENSMUSG00000071073	Lrrc73	Gm88	leucine rich repeat containing 73	protein-coding
mm_147941.1	chr18	66153417	66153427	-	1	NA	intron (NM_178793, intron 2 of 10)	L1_Mur3|LINE|L1	65911	NR_030467	751558		NR_030467	ENSMUSG00000076147	Mir694	Mirn694|mir-694|mmu-mir-694	microRNA 694	ncRNA
mm_149876.1	chr19	25236769	25236790	+	1	NA	promoter-TSS (NM_181404)	promoter-TSS (NM_181404)	-423	NM_181404	107351	Mm.260722	NM_181404	ENSMUSG00000032702	Kank1	A930031B09Rik|AU015049|AW121052|Ankrd15|D330024H06Rik|mKIAA0172	KN motif and ankyrin repeat domains 1	protein-coding
mm_157053.1	chrX	8074721	8074736	-	1	NA	promoter-TSS (NM_001290716)	promoter-TSS (NM_001290716)	32	NM_011514	20937	Mm.9244	NM_011514	ENSMUSG00000039231	Suv39h1	AI852103|AL022883|DXHXS7466e|H3-K9-HMTase 1|KMT1A|mIS6	suppressor of variegation 3-9 homolog 1 (Drosophila)	protein-coding
mm_155455.1	chrX	73502743	73502753	+	1	NA	promoter-TSS (NM_177236)	promoter-TSS (NM_177236)	-338	NM_001310537	320707	Mm.210095	NM_177236	ENSMUSG00000031376	Atp2b3	6430519O13Rik|Pmca3	ATPase, Ca++ transporting, plasma membrane 3	protein-coding
mm_23807.1	chr3	79885184	79885197	+	1	NA	promoter-TSS (NM_133187)	promoter-TSS (NM_133187)	-740	NM_133187	68659	Mm.427274	NM_133187	ENSMUSG00000027955	Fam198b	1110032E23Rik|2210419I08Rik|AV011458|Ened	family with sequence similarity 198, member B	protein-coding
mm_145947.1	chr18	67401701	67401721	+	1	NA	exon (NM_026473, exon 4 of 4)	exon (NM_026473, exon 4 of 4)	10980	NM_026473	67951	Mm.181860	NM_026473	ENSMUSG00000001473	Tubb6	2310057H16Rik|BB220206	tubulin, beta 6 class V	protein-coding
mm_79448.1	chr9	56112136	56112148	+	1	NA	intron (NM_011193, intron 1 of 14)	intron (NM_011193, intron 1 of 14)	22166	NM_011193	19200	Mm.2534	NM_011193	ENSMUSG00000032322	Pstpip1	CD2BP1|def-2	proline-serine-threonine phosphatase-interacting protein 1	protein-coding
mm_52014.1	chr6	94500314	94500353	+	1	NA	promoter-TSS (NM_026255)	promoter-TSS (NM_026255)	19	NM_026255	67582	Mm.280725	NM_026255	ENSMUSG00000045100	Slc25a26	4930433D19Rik|4933433F13Rik|AW557176|D6Bwg0781e|Slc25a6	solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 26	protein-coding
mm_88823.1	chr10	80803664	80803682	+	1	NA	exon (NM_013651, exon 7 of 9)	exon (NM_013651, exon 7 of 9)	-1575	NM_007445	11705	Mm.376094	NM_007445	ENSMUSG00000035262	Amh	MIS	anti-Mullerian hormone	protein-coding
mm_162337.1	chr1	45925600	45925604	-	1	NA	promoter-TSS (NM_016917)	promoter-TSS (NM_016917)	-8	NM_016917	53945	Mm.28756	NM_016917	ENSMUSG00000025993	Slc40a1	Dusg|Fpn1|IREG1|MTP|MTP1|Ol5|Pcm|Slc11a3|Slc39a1	solute carrier family 40 (iron-regulated transporter), member 1	protein-coding
mm_159702.1	chr5	27501391	27501391	-	1	NA	promoter-TSS (NM_028561)	promoter-TSS (NM_028561)	1	NM_028561	73526	Mm.389608	NM_028561	ENSMUSG00000048703	Speer4b	1700081O22Rik|SPEER-4B	spermatogenesis associated glutamate (E)-rich protein 4B	protein-coding
mm_138150.1	chr17	34208753	34208773	+	1	NA	exon (NM_011530, exon 4 of 12)	exon (NM_011530, exon 4 of 12)	4284	NM_011530	21355	Mm.14814	NM_011530	ENSMUSG00000024339	Tap2	ABC18|AI462429|APT2|Abcb3|Ham-2|Ham2|MTP2|PSF2|RING11|Tap-2|Y1|jas	transporter 2, ATP-binding cassette, sub-family B (MDR/TAP)	protein-coding
mm_4073.1	chr1	166165835	166165843	+	1	NA	3' UTR (NM_021610, exon 7 of 7)	3' UTR (NM_021610, exon 7 of 7)	35379	NM_021610	59290	Mm.46357	NM_021610	ENSMUSG00000000544	Gpa33	2010310L10Rik|2210401D16Rik|BB116197	glycoprotein A33 (transmembrane)	protein-coding
mm_123388.1	chr14	63371143	63371153	-	1	NA	Intergenic	Intergenic	46039	NM_007549	12143	Mm.3962	NM_007549	ENSMUSG00000014453	Blk	-	B lymphoid kinase	protein-coding
mm_162506.1	chr1	150102801	150102805	+	1	NA	intron (NM_011198, intron 5 of 9)	intron (NM_011198, intron 5 of 9)	2772	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_94362.1	chr11	5009516	5009526	+	1	NA	intron (NM_007454, intron 1 of 20)	intron (NM_007454, intron 1 of 20)	22697	NM_007454	11764	Mm.274816	NM_007454	ENSMUSG00000009090	Ap1b1	Adtb1|b2b1660Clo	adaptor protein complex AP-1, beta 1 subunit	protein-coding
mm_33796.1	chr4	134924417	134924427	+	1	NA	exon (NM_023665, exon 2 of 5)	exon (NM_023665, exon 2 of 5)	797	NM_023665	27981	Mm.331964	NM_023665	ENSMUSG00000037266	Rsrp1	2700043I21Rik|D4Ucla2|D4Wsu53e	arginine/serine rich protein 1	protein-coding
mm_44377.1	chr5	17820483	17820535	-	1	NA	exon (NM_001159558, exon 5 of 16)	exon (NM_001159558, exon 5 of 16)	15387	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_96370.1	chr11	67236186	67236196	+	1	NA	Intergenic	Intergenic	-1621	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_150739.1	chr19	43782182	43782193	+	1	NA	promoter-TSS (NM_013806)	promoter-TSS (NM_013806)	-121	NM_013806	12780	Mm.39054	NM_013806	ENSMUSG00000025194	Abcc2	AI173996|Abc30|Cmoat|Mrp2|cMRP	ATP-binding cassette, sub-family C (CFTR/MRP), member 2	protein-coding
mm_43883.1	chr5	143817820	143817843	+	1	NA	Intergenic	CpG	-54031	NM_013557	15467	Mm.389709	NM_013557	ENSMUSG00000029613	Eif2ak1	HCR|Hri	eukaryotic translation initiation factor 2 alpha kinase 1	protein-coding
mm_42065.1	chr5	109547328	109547336	+	1	NA	Intergenic	B1_Mur2|SINE|Alu	11661	NM_016715	57914	Mm.35771	NM_016715	ENSMUSG00000033467	Crlf2	CRLM2|Ly114|Tpte2|Tslpr	cytokine receptor-like factor 2	protein-coding
mm_101708.1	chr11	42000670	42000676	-	1	NA	promoter-TSS (NM_008073)	promoter-TSS (NM_008073)	41	NM_177408	14406	Mm.5309	NM_008073	ENSMUSG00000020436	Gabrg2	GABAA-R|Gabrg-2|gamma2	gamma-aminobutyric acid (GABA) A receptor, subunit gamma 2	protein-coding
mm_62494.1	chr7	101969797	101969840	+	1	NA	promoter-TSS (NM_133947)	promoter-TSS (NM_133947)	-25	NM_133947	101706	Mm.27259	NM_133947	ENSMUSG00000066306	Numa1	6720401E04Rik|AA764025|AL022610|AU014979|NuMA	nuclear mitotic apparatus protein 1	protein-coding
mm_27789.1	chr3	75269968	75270007	-	1	NA	promoter-TSS (NM_026460)	promoter-TSS (NM_026460)	91	NM_026460	67931	Mm.259446	NM_026460	ENSMUSG00000034139	Serpini2	Spi14	serine (or cysteine) peptidase inhibitor, clade I, member 2	protein-coding
mm_16280.1	chr2	173788355	173788360	+	1	NA	Intergenic	B1_Mur1|SINE|Alu	50786	NM_019806	56491	Mm.260456	NM_019806	ENSMUSG00000054455	Vapb	AI225786|AI840687|AI848259|D2Abb2e|R75548|VAP33b|Vamp33b	vesicle-associated membrane protein, associated protein B and C	protein-coding
mm_103321.1	chr11	73199014	73199056	-	1	NA	promoter-TSS (NM_031251)	promoter-TSS (NM_031251)	-16	NM_031251	83429	Mm.259852	NM_031251	ENSMUSG00000005949	Ctns	AI195360|AW049661	cystinosis, nephropathic	protein-coding
mm_148751.1	chr19	6057893	6057914	+	1	NA	promoter-TSS (NM_001190436)	promoter-TSS (NM_001190436)	15	NM_001160239	14109	Mm.329631	NM_007990	ENSMUSG00000038274	Fau	MNSFbeta	Finkel-Biskis-Reilly murine sarcoma virus (FBR-MuSV) ubiquitously expressed (fox derived)	protein-coding
mm_50492.1	chr6	48988888	48988899	+	1	NA	exon (NM_172888, exon 1 of 5)	exon (NM_172888, exon 1 of 5)	2032	NM_172888	243377	Mm.446302	NM_172888	ENSMUSG00000039215	Svs1	9530003A11	seminal vesicle secretory protein 1	protein-coding
mm_42884.1	chr5	122372446	122372477	+	1	NA	promoter-TSS (NM_026883)	promoter-TSS (NM_026883)	-47	NM_024216	68080	Mm.266328	NM_024216	ENSMUSG00000029464	Gpn3	A930018B01Rik|Atpbd1c|D5Ertd708e	GPN-loop GTPase 3	protein-coding
mm_48630.1	chr5	145136955	145136985	-	1	NA	exon (NM_001033313, exon 2 of 6)	exon (NM_001033313, exon 2 of 6)	3119	NM_001033313	231887	Mm.188851	NM_001033313	ENSMUSG00000029623	Pdap1	HASPP28|PAP|PAP1	PDGFA associated protein 1	protein-coding
mm_29095.1	chr3	104780988	104781002	-	1	NA	promoter-TSS (NM_027982)	promoter-TSS (NM_027982)	-61	NM_027982	71887	Mm.379204	NM_027982	ENSMUSG00000002228	Ppm1j	2310008J22Rik|PP2Czeta|Ppp2cz	protein phosphatase 1J	protein-coding
mm_165481.1	chr2	164333450	164333459	+	1	NA	exon (NM_009301, exon 2 of 3)	exon (NM_009301, exon 2 of 3)	689	NM_009301	20944	Mm.140154	NM_009301	ENSMUSG00000017004	Svs5	BB115186|Semg1|Svp-1|Svp1|Svp5	seminal vesicle secretory protein 5	protein-coding
mm_26080.1	chr3	136670680	136670728	+	1	NA	5' UTR (NM_001293622, exon 1 of 13)	5' UTR (NM_001293622, exon 1 of 13)	638	NM_001293622	19055	Mm.331389	NM_008913	ENSMUSG00000028161	Ppp3ca	2900074D19Rik|CN|Caln|Calna|CnA	protein phosphatase 3, catalytic subunit, alpha isoform	protein-coding
mm_97634.1	chr11	78961967	78961978	+	1	NA	Intergenic	Intergenic	22952	NM_001159301	16859	Mm.341434	NM_010708	ENSMUSG00000001123	Lgals9	AA407335|AI194909|AI265545|LGALS35|Lgals5|gal-9|galectin-9	lectin, galactose binding, soluble 9	protein-coding
mm_173321.1	chrY	90736991	90736993	+	1	NA	Intergenic	IMPB_01|Satellite|Satellite	18058	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_82034.1	chr9	121996098	121996115	+	1	NA	promoter-TSS (NM_153540)	promoter-TSS (NM_153540)	-80	NM_153540	215494	Mm.402151	NM_153540	ENSMUSG00000066235	Pomgnt2	Ago61|C85492|Gtdc2	protein O-linked mannose beta 1,4-N-acetylglucosaminyltransferase 2	protein-coding
mm_77967.1	chr9	7786797	7786803	+	1	NA	intron (NM_133739, intron 2 of 4)	intron (NM_133739, intron 2 of 4)	2410	NR_049191	100885830		NR_049191	ENSMUSG00000093615	Mir5618	Gm23685|mmu-mir-5618	microRNA 5618	ncRNA
mm_101497.1	chr11	31824519	31824535	-	1	NA	promoter-TSS (NR_102314)	promoter-TSS (NR_102314)	20	NR_102310	414116	Mm.150222	NR_102310	ENSMUSG00000085772	D630024D03Rik	-	RIKEN cDNA D630024D03 gene	ncRNA
mm_118080.1	chr13	103334430	103334500	-	1	NA	promoter-TSS (NM_175171)	promoter-TSS (NM_175171)	27	NM_175171	328329	Mm.202606	NM_175171	ENSMUSG00000034751	Mast4	4930420O11Rik|AI642422|mKIAA0303	microtubule associated serine/threonine kinase family member 4	protein-coding
mm_81429.1	chr9	109082486	109082535	+	1	NA	promoter-TSS (NM_183250)	promoter-TSS (NM_183250)	14	NM_025689	66658	Mm.128227	NM_025689	ENSMUSG00000025645	Ccdc51	5730568A12Rik|AI551049	coiled-coil domain containing 51	protein-coding
mm_76851.1	chr8	105347886	105347940	-	1	NA	promoter-TSS (NM_001081332)	promoter-TSS (NM_001081332)	57	NM_177699	234686	Mm.87724	NM_177699	ENSMUSG00000014778	Fhod1	BC017144|FHOS|FHOS1	formin homology 2 domain containing 1	protein-coding
mm_31257.1	chr4	45018620	45018675	+	1	NA	promoter-TSS (NM_022811)	promoter-TSS (NM_022811)	38	NM_001285800	64424	Mm.282932	NM_022811	ENSMUSG00000028318	Polr1e	53kDa|AU042259|D030019D19Rik|Paf53|Praf1	polymerase (RNA) I polypeptide E	protein-coding
mm_157504.1	chrX	48594611	48594635	-	1	NA	promoter-TSS (NM_001166649)	promoter-TSS (NM_001166649)	-171	NM_001166649	208968	Mm.293819	NM_153532	ENSMUSG00000036916	Zfp280c	BC028839|Suhw3|Zfp633|Znf280c|mKIAA1584	zinc finger protein 280C	protein-coding
mm_72605.1	chr8	84420871	84420875	+	1	NA	intron (NM_001252061, intron 1 of 46)	ID4|SINE|ID	5509	NM_001252061	12286	Mm.334658	NM_007578	ENSMUSG00000034656	Cacna1a	APCA|BI|Caca1a|Cacnl1a4|Cav2.1|Ccha1a|EA2|FHM|HPCA|MHP|MHP1|SCA6|alpha1A|la|nmf352|rkr|smrl|tg	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	protein-coding
mm_4761.1	chr1	182436309	182436311	+	1	NA	intron (NM_173378, intron 4 of 17)	B1F2|SINE|Alu	27143	NM_173378	209456	Mm.287450	NM_173378	ENSMUSG00000026510	Trp53bp2	53BP2|AI746547|ASPP2|PPP1R13A|Tp53bp2|X98550	transformation related protein 53 binding protein 2	protein-coding
mm_161309.1	chr14	37098165	37098165	-	1	NA	5' UTR (NM_130878, exon 1 of 17)	5' UTR (NM_130878, exon 1 of 17)	146	NM_130878	170677	Mm.156506	NM_130878	ENSMUSG00000021803	Cdhr1	Pcdh21|Prcad|mKIAA1775	cadherin-related family member 1	protein-coding
mm_101171.1	chr11	16983221	16983269	-	1	NA	exon (NM_019549, exon 8 of 10)	exon (NM_019549, exon 8 of 10)	25473	NM_019549	56193	Mm.98232	NM_019549	ENSMUSG00000020120	Plek	2010300B13Rik	pleckstrin	protein-coding
mm_45211.1	chr5	52992354	52992371	-	1	NA	promoter-TSS (NR_040413)	promoter-TSS (NR_040413)	-70	NR_040413	75954	Mm.258937	NR_040413	ENSMUSG00000106352	5033403H07Rik	-	RIKEN cDNA 5033403H07 gene	ncRNA
mm_107294.1	chr12	30584430	30584466	+	1	NA	promoter-TSS (NM_172049)	promoter-TSS (NM_172049)	5	NM_172049	211986	Mm.34035	NM_172049	ENSMUSG00000043061	Tmem18	BC024093	transmembrane protein 18	protein-coding
mm_141420.1	chr17	29435430	29435440	-	1	NA	Intergenic	Intergenic	-55610	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_78835.1	chr9	44240708	44240717	+	1	NA	promoter-TSS (NM_001081369)	promoter-TSS (NM_001081369)	35	NM_001081369	270150	Mm.347681	NM_001081369	ENSMUSG00000070306	Ccdc153	-	coiled-coil domain containing 153	protein-coding
mm_41792.1	chr5	103753563	103753579	+	1	NA	promoter-TSS (NM_133919)	promoter-TSS (NM_133919)	-591	NM_133919	17355	Mm.6949	NM_133919	ENSMUSG00000029313	Aff1	9630032B01Rik|AW319193|Af4|Mllt2h|Rob	AF4/FMR2 family, member 1	protein-coding
mm_99885.1	chr11	109440098	109440173	+	1	NA	promoter-TSS (NR_040680)	promoter-TSS (NR_040680)	57	NR_040680	100503496	Mm.265874	NR_040680		LOC100503496	-	uncharacterized LOC100503496	ncRNA
mm_15760.1	chr2	164289217	164289227	+	1	NA	promoter-TSS (NM_021363)	promoter-TSS (NM_021363)	-45	NM_001311114	64335	Mm.389393	NM_021363	ENSMUSG00000017003	Svs3a	9530026M05Rik|BB121242|Semg2|Svp-3|Svp3|Svs3	seminal vesicle secretory protein 3A	protein-coding
mm_73685.1	chr8	111556395	111556398	+	1	NA	intron (NM_001168623, intron 1 of 4)	intron (NM_001168623, intron 1 of 4)	18053	NM_001168623	170737	Mm.271578	NM_133206	ENSMUSG00000033545	Znrf1	B830022L21Rik|Rnf42|Zrfp1|nin283	zinc and ring finger 1	protein-coding
mm_64023.1	chr7	140353565	140353569	+	1	NA	Intergenic	Lx6|LINE|L1	-7580	NM_146955	18361	Mm.222844	NM_146955	ENSMUSG00000060112	Olfr60	IH6|MOR253-6	olfactory receptor 60	protein-coding
mm_142293.1	chr17	40794064	40794091	-	1	NA	promoter-TSS (NM_009420)	promoter-TSS (NM_009420)	69	NM_001204071	22024	Mm.1296	NM_009420	ENSMUSG00000023930	Crisp2	CRISP-2|GAPDL5|Tpx-1|Tpx1	cysteine-rich secretory protein 2	protein-coding
mm_83656.1	chr9	49515264	49515266	-	1	NA	3' UTR (NM_010875, exon 16 of 16)	3' UTR (NM_010875, exon 16 of 16)	-3023	NR_029465	100036537	Mm.437541	NR_029465	ENSMUSG00000079564	Gm11149	ENSMUSG00000060603|ENSMUSG00000079564	predicted gene 11149	ncRNA
mm_44286.1	chr5	8368050	8368107	-	1	NA	promoter-TSS (NM_001007221)	promoter-TSS (NM_001007221)	82	NM_001007221	11496	Mm.275895	NM_001007220	ENSMUSG00000040537	Adam22	2900022I03Rik|AI854032|MDC2	a disintegrin and metallopeptidase domain 22	protein-coding
mm_41534.1	chr5	92825812	92825851	+	1	NA	intron (NM_001077595, intron 1 of 9)	intron (NM_001077595, intron 1 of 9)	16449	NM_001077595	27428	Mm.46014	NM_015756	ENSMUSG00000029381	Shroom3	AL022960|D5Ertd287e|Shrm|Shrm3	shroom family member 3	protein-coding
mm_16456.1	chr2	180582727	180582742	+	1	NA	5' UTR (NM_028479, exon 2 of 6)	5' UTR (NM_028479, exon 2 of 6)	1430	NM_028479	73247	Mm.426558	NM_028479	ENSMUSG00000027569	Mrgbp	1600027N09Rik|AW060503|C80444	MRG/MORF4L binding protein	protein-coding
mm_110063.1	chr12	21373502	21373518	-	1	NA	non-coding (NR_102380, exon 1 of 16)	non-coding (NR_102380, exon 1 of 16)	122	NR_102380	11491	Mm.27681	NM_009615	ENSMUSG00000052593	Adam17	CD156b|Tace	a disintegrin and metallopeptidase domain 17	protein-coding
mm_118517.1	chr14	14686400	14686432	+	1	NA	Intergenic	Intergenic	-16609	NM_001033270	218756	Mm.258893	NM_001033270	ENSMUSG00000021733	Slc4a7	E430014N10Rik|NBC3|NBCn1|NBCn1-G	solute carrier family 4, sodium bicarbonate cotransporter, member 7	protein-coding
mm_61520.1	chr7	78913910	78913918	+	1	NA	promoter-TSS (NM_001113527)	promoter-TSS (NM_001113527)	149	NM_020583	57444	Mm.322843	NM_020583	ENSMUSG00000039236	Isg20	1600023I01Rik|2010107M23Rik|20kDa|DnaQL|HEM45	interferon-stimulated protein	protein-coding
mm_6448.1	chr1	74008492	74008512	-	1	NA	intron (NM_027884, intron 4 of 34)	intron (NM_027884, intron 4 of 34)	115945	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_81033.1	chr9	104569796	104569800	+	1	NA	promoter-TSS (NM_028719)	promoter-TSS (NM_028719)	10	NM_028719	74020	Mm.326240	NM_028719	ENSMUSG00000032564	Cpne4	3632411M23Rik|4933406O10Rik	copine IV	protein-coding
mm_168717.1	chr12	10738502	10738510	-	1	NA	Intergenic	RLTR9D|LTR|ERVK	292118	NR_110487	328061	Mm.56067	NR_110487		Gm38407	4931412M21	predicted gene, 38407	ncRNA
mm_159418.1	chr3	106167536	106167536	-	1	NA	promoter-TSS (NM_009892)	promoter-TSS (NM_009892)	28	NM_009892	12655	Mm.387173	NM_009892	ENSMUSG00000040809	Chil3	AI505981|Chi3l3|ECF-L|Ym1	chitinase-like 3	protein-coding
mm_139982.1	chr17	72836679	72836717	+	1	NA	promoter-TSS (NM_027166)	promoter-TSS (NM_027166)	-6	NM_027166	383295	Mm.277533	NM_027166	ENSMUSG00000039770	Ypel5	2310076K21Rik|CGI-127	yippee-like 5 (Drosophila)	protein-coding
mm_63818.1	chr7	134022815	134022834	+	1	NA	intron (NM_007400, intron 3 of 22)	intron (NM_007400, intron 3 of 22)	202273	NM_007400	11489	Mm.439714	NM_007400	ENSMUSG00000054555	Adam12	Mltna	a disintegrin and metallopeptidase domain 12 (meltrin alpha)	protein-coding
mm_95714.1	chr11	54516716	54516728	+	1	NA	3' UTR (NM_173753, exon 18 of 18)	3' UTR (NM_173753, exon 18 of 18)	-6123	NM_001252494	192786	Mm.254404	NM_175258	ENSMUSG00000037533	Rapgef6	A530068K01|AI844632|BB085664|C030018K18Rik|PDZ-GEF2|Pdzgef2|RA-GEF-2|Ragef2|mKIAA4052	Rap guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_113473.1	chr13	36727325	36727348	+	1	NA	intron (NM_153529, intron 2 of 2)	C-rich|Low_complexity|Low_complexity	7141	NM_153529	68404	Mm.232930	NM_153529	ENSMUSG00000039114	Nrn1	0710008J23Rik|Cpg15|Nrn	neuritin 1	protein-coding
mm_53084.1	chr6	124996792	124996842	+	1	NA	promoter-TSS (NM_175696)	promoter-TSS (NM_175696)	97	NM_175696	319352	Mm.295327	NM_175696	ENSMUSG00000030329	Pianp	AI255183|AU067746|C530028O21Rik|Panp	PILR alpha associated neural protein	protein-coding
mm_53978.1	chr6	6818026	6818029	-	1	NA	Intergenic	Intergenic	-45307	NM_010057	13396	Mm.439763	NM_010057	ENSMUSG00000029754	Dlx6	-	distal-less homeobox 6	protein-coding
mm_2350.1	chr1	92910806	92910834	+	1	NA	promoter-TSS (NM_181405)	promoter-TSS (NM_181405)	-5	NM_181405	108657	Mm.200971	NM_181405	ENSMUSG00000026269	Rnpepl1	1110014H17Rik|AI894167	arginyl aminopeptidase (aminopeptidase B)-like 1	protein-coding
mm_12914.1	chr2	84916124	84916129	+	1	NA	Intergenic	MT2B1|LTR|ERVL	-20520	NM_021398	58207	Mm.290729	NM_021398	ENSMUSG00000027074	Slc43a3	Eeg1|SEEEG-1	solute carrier family 43, member 3	protein-coding
mm_133414.1	chr16	85152777	85152794	+	1	NA	intron (NM_007471, intron 1 of 15)	intron (NM_007471, intron 1 of 15)	20922	NM_001198825	11820	Mm.277585	NM_007471	ENSMUSG00000022892	App	Abeta|Abpp|Adap|Ag|Cvap|E030013M08Rik|betaApp	amyloid beta (A4) precursor protein	protein-coding
mm_151699.1	chr19	4440399	4440409	-	1	NA	promoter-TSS (NM_001329989)	promoter-TSS (NM_001329989)	845	NR_045989	319314	Mm.393810	NR_045989	ENSMUSG00000087132	A930001C03Rik	-	RIKEN cDNA A930001C03 gene	ncRNA
mm_142507.1	chr17	46144157	46144218	-	1	NA	promoter-TSS (NM_029338)	promoter-TSS (NM_029338)	11	NM_029338	75564	Mm.17993	NM_029338	ENSMUSG00000023966	Rsph9	1700027N10Rik	radial spoke head 9 homolog (Chlamydomonas)	protein-coding
mm_99204.1	chr11	101022903	101022924	+	1	NA	intron (NM_001243050, intron 5 of 20)	intron (NM_001243050, intron 5 of 20)	-7427	NR_105893	102466767		NR_105893	ENSMUSG00000098415	Mir6928	Gm27728|mmu-mir-6928	microRNA 6928	ncRNA
mm_41400.1	chr5	90786333	90786361	+	1	NA	exon (NM_203320, exon 2 of 4)	exon (NM_203320, exon 2 of 4)	246	NM_203320	330122	Mm.244289	NM_203320	ENSMUSG00000029379	Cxcl3	Dcip1|Gm1960	chemokine (C-X-C motif) ligand 3	protein-coding
mm_127198.1	chr15	99099452	99099482	+	1	NA	promoter-TSS (NM_176835)	promoter-TSS (NM_176835)	-17	NM_176835	72778	Mm.30544	NM_176835	ENSMUSG00000038009	Dnajc22	2810451A06Rik|AI506245	DnaJ heat shock protein family (Hsp40) member C22	protein-coding
mm_131230.1	chr16	10447413	10447450	+	1	NA	promoter-TSS (NM_001013778)	promoter-TSS (NM_001013778)	-81	NM_001013778	383103	Mm.325732	NM_001013778	ENSMUSG00000050908	Tvp23a	Fam18a	trans-golgi network vesicle protein 23A	protein-coding
mm_57050.1	chr6	122345854	122345879	-	1	NA	Intergenic	Intergenic	-5639	NM_001271579	13619	Mm.6822	NM_007905	ENSMUSG00000040669	Phc1	AW557034|Edr|Edr1|Mph1|Rae-28|rae28	polyhomeotic-like 1 (Drosophila)	protein-coding
mm_35477.1	chr4	40852104	40852108	-	1	NA	intron (NM_022305, intron 1 of 5)	MIRb|SINE|MIR	-1968	NR_039584	100628614		NR_039584	ENSMUSG00000096377	Mir5123	mmu-mir-5123|mu-mir-5123	microRNA 5123	ncRNA
mm_153198.1	chr19	34527397	34527481	-	1	NA	promoter-TSS (NM_021460)	promoter-TSS (NM_021460)	35	NM_001111100	16889	Mm.157545	NM_021460	ENSMUSG00000024781	Lipa	AA960673|Lal|Lip-1|Lip1	lysosomal acid lipase A	protein-coding
mm_130160.1	chr15	91192033	91192050	-	1	NA	promoter-TSS (NM_011994)	promoter-TSS (NM_011994)	-234	NM_011994	26874	Mm.295456	NM_011994	ENSMUSG00000055782	Abcd2	ABC39|ALDL1|ALDR|ALDRP	ATP-binding cassette, sub-family D (ALD), member 2	protein-coding
mm_4963.1	chr1	191272613	191272617	+	1	NA	Intergenic	L1MC4|LINE|L1	45503	NM_025424	66208	Mm.46444	NM_025424	ENSMUSG00000037499	Nenf	1110060M21Rik|SCIRP10|Spuf	neuron derived neurotrophic factor	protein-coding
mm_48404.1	chr5	140235448	140235453	-	1	NA	intron (NM_010752, intron 10 of 17)	ID_B1|SINE|B4	86102	NM_010752	17120	Mm.27250	NM_010752	ENSMUSG00000029554	Mad1l1	AI173502|AW550425|Mad1	MAD1 mitotic arrest deficient 1-like 1	protein-coding
mm_59838.1	chr7	29446386	29446394	+	1	NA	intron (NM_001081028, intron 2 of 22)	intron (NM_001081028, intron 2 of 22)	59070	NM_001081028	74206	Mm.447042	NM_001081028	ENSMUSG00000030583	Sipa1l3	2610511M17Rik	signal-induced proliferation-associated 1 like 3	protein-coding
mm_158283.1	chrX	111537958	111537964	-	1	NA	promoter-TSS (NM_025949)	promoter-TSS (NM_025949)	-2	NM_025949	67071	Mm.37617	NM_025949	ENSMUSG00000025665	Rps6ka6	2610524K04Rik|RSK4|S6K-alpha-6	ribosomal protein S6 kinase polypeptide 6	protein-coding
mm_73693.1	chr8	111582648	111582652	+	1	NA	intron (NM_001168623, intron 1 of 4)	intron (NM_001168623, intron 1 of 4)	44307	NM_001168623	170737	Mm.271578	NM_133206	ENSMUSG00000033545	Znrf1	B830022L21Rik|Rnf42|Zrfp1|nin283	zinc and ring finger 1	protein-coding
mm_13012.1	chr2	90917773	90917874	+	1	NA	exon (NM_025576, exon 1 of 5)	exon (NM_025576, exon 1 of 5)	227	NM_025576	66461	Mm.23926	NM_025576		Ptpmt1	1110001D10Rik|2810004N20Rik|PLIP	protein tyrosine phosphatase, mitochondrial 1	protein-coding
mm_165138.1	chr2	11332812	11332829	+	1	NA	Intergenic	Intergenic	-6669	NR_040369	100503147	Mm.91961	NR_040369	ENSMUSG00000086006	Gm13293	OTTMUSG00000011311	predicted gene 13293	ncRNA
mm_121284.1	chr14	105043413	105043428	+	1	NA	Intergenic	Intergenic	71256	NR_040628	100502987	Mm.124957	NR_040628		Gm17066	-	predicted gene 17066	ncRNA
mm_6286.1	chr1	69686224	69686238	-	1	NA	promoter-TSS (NM_011770)	promoter-TSS (NM_011770)	-271	NM_011770	22779	Mm.106343	NM_011770	ENSMUSG00000025997	Ikzf2	A730095J18Rik|Helios|Zfpn1a2|Znfn1a2	IKAROS family zinc finger 2	protein-coding
mm_163243.1	chr11	105975221	105975227	+	1	NA	promoter-TSS (NM_009598)	promoter-TSS (NM_009598)	16	NM_009598	11421	Mm.754	NM_009598	ENSMUSG00000020681	Ace	AW208573|CD143	angiotensin I converting enzyme (peptidyl-dipeptidase A) 1	protein-coding
mm_145829.1	chr18	65438660	65438673	+	1	NA	intron (NM_172833, intron 2 of 15)	intron (NM_172833, intron 2 of 15)	7669	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_57529.1	chr6	126535265	126535277	-	1	NA	5' UTR (NM_145983, exon 1 of 1)	5' UTR (NM_145983, exon 1 of 1)	284	NM_145983	16493	Mm.222831	NM_145983	ENSMUSG00000045534	Kcna5	Kv1.5	potassium voltage-gated channel, shaker-related subfamily, member 5	protein-coding
mm_48688.1	chr5	146758439	146758439	-	1	NA	intron (NM_011669, intron 3 of 8)	intron (NM_011669, intron 3 of 8)	36517	NM_011669	22217	Mm.167971	NM_011669	ENSMUSG00000029640	Usp12	Ubh1	ubiquitin specific peptidase 12	protein-coding
mm_100025.1	chr11	114903636	114903650	+	1	NA	3' UTR (NM_170758, exon 7 of 7)	3' UTR (NM_170758, exon 7 of 7)	13602	NM_170758	217303	Mm.294439	NM_170758	ENSMUSG00000034652	Cd300a	B230315M08Rik|Clm8|LMIR1|MAIR-I|MAIR-Ia|MMAC8|Pigr4|mcpir1	CD300A molecule	protein-coding
mm_160564.1	chr9	54951012	54951012	-	1	NA	promoter-TSS (NM_145229)	promoter-TSS (NM_145229)	-58	NM_145229	246735	Mm.473773	NM_145229	ENSMUSG00000044820	AY074887	Mcpr1	cDNA sequence AY074887	protein-coding
mm_10762.1	chr2	24186394	24186402	+	1	NA	promoter-TSS (NM_153511)	promoter-TSS (NM_153511)	-78	NM_153511	215257	Mm.249379	NM_153511	ENSMUSG00000044103	Il1f9	Il36g	interleukin 1 family, member 9	protein-coding
mm_147776.1	chr18	61531996	61531996	-	1	NA	intron (NM_177828, intron 1 of 12)	L3|LINE|CR1	4540	NM_177828	328967	Mm.488098	NM_177828	ENSMUSG00000045094	Arhgef37	4933429F08Rik	Rho guanine nucleotide exchange factor (GEF) 37	protein-coding
mm_2478.1	chr1	105846705	105846719	+	1	NA	3' UTR (NM_009399, exon 10 of 10)	3' UTR (NM_009399, exon 10 of 10)	65989	NM_009399	21934	Mm.6251	NM_009399	ENSMUSG00000026321	Tnfrsf11a	Ly109|ODFR|OFE|Rank|TRANCE-R|mRANK	tumor necrosis factor receptor superfamily, member 11a, NFKB activator	protein-coding
mm_55098.1	chr6	49543769	49543770	-	1	NA	Intergenic	Lx2A1|LINE|L1	148165	NM_029916	77485	Mm.128054	NM_029916	ENSMUSG00000023403	Stk31	C330007K24Rik	serine threonine kinase 31	protein-coding
mm_139842.1	chr17	69262277	69262286	+	1	NA	exon (NM_013813, exon 12 of 22)	exon (NM_013813, exon 12 of 22)	14925	NR_045428	69750	Mm.439063	NR_045428	ENSMUSG00000100572	2410021H03Rik	-	RIKEN cDNA 2410021H03 gene	ncRNA
mm_60161.1	chr7	39588513	39588524	+	1	NA	Intergenic	Intergenic	70752	NM_001004139	70227	Mm.333800	NM_001004139	ENSMUSG00000068959	Zfp619	3000002G13Rik	zinc finger protein 619	protein-coding
mm_53569.1	chr6	137252505	137252515	+	1	NA	5' UTR (NM_011216, exon 1 of 27)	5' UTR (NM_011216, exon 1 of 27)	211	NM_011216	19277	Mm.186361	NM_011216	ENSMUSG00000030223	Ptpro	D28|GLEPP1|PTPBK|PTPROt|PTPU2|PTPoc|PTPphi|Ptpn15|R-PTP-O	protein tyrosine phosphatase, receptor type, O	protein-coding
mm_102468.1	chr11	59976941	59976946	-	1	NA	exon (NM_001290013, exon 4 of 7)	exon (NM_001290013, exon 4 of 7)	-11999	NM_009026	19416	Mm.3903	NM_009026	ENSMUSG00000049892	Rasd1	Dexras1	RAS, dexamethasone-induced 1	protein-coding
mm_50058.1	chr6	41178732	41178748	+	1	NA	Intergenic	Intergenic	-123532	NM_011646	22074	Mm.383263	NM_011646	ENSMUSG00000054106	Try4	0910001B19Rik|Td	trypsin 4	protein-coding
mm_89108.1	chr10	84622281	84622303	+	1	NA	promoter-TSS (NM_027423)	promoter-TSS (NM_027423)	-145	NM_027423	70428	Mm.335007	NM_027423	ENSMUSG00000034453	Polr3b	2700078H01Rik|A330032P03Rik|C85372|RPC2	polymerase (RNA) III (DNA directed) polypeptide B	protein-coding
mm_171538.1	chr4	146971905	146971906	+	1	NA	Intergenic	Intergenic	-49945	NM_001177767	100043034	Mm.422606	NM_001177767	ENSMUSG00000067919	Rex2	Gm13138|OTTMUSG00000010655	reduced expression 2	protein-coding
mm_6220.1	chr1	66863301	66863315	-	1	NA	promoter-TSS (NM_007381)	promoter-TSS (NM_007381)	1	NM_007381	11363	Mm.2445	NM_007381	ENSMUSG00000026003	Acadl	AA960361|AU018452|C79855|LCAD	acyl-Coenzyme A dehydrogenase, long-chain	protein-coding
mm_14626.1	chr2	136777378	136777448	+	1	NA	exon (NM_001291056, exon 7 of 8)	exon (NM_001291056, exon 7 of 8)	63963	NM_001291056	20614	Mm.45953	NM_011428	ENSMUSG00000027273	Snap25	Bdr|GENA70|SNAP-25|SUP|sp	synaptosomal-associated protein 25	protein-coding
mm_103497.1	chr11	76571528	76571558	-	1	NA	promoter-TSS (NM_198895)	promoter-TSS (NM_198895)	-159	NM_198895	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_63044.1	chr7	121734426	121734440	+	1	NA	promoter-TSS (NM_011326)	promoter-TSS (NM_011326)	-46	NM_011326	20278	Mm.35247	NM_011326	ENSMUSG00000000216	Scnn1g	SCNEG	sodium channel, nonvoltage-gated 1 gamma	protein-coding
mm_167992.1	chrX	170009799	170009818	+	1	NA	Intergenic	CpG	-30891	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_88163.1	chr10	69706327	69706382	+	1	NA	intron (NM_170730, intron 1 of 17)	intron (NM_170730, intron 1 of 17)	172646	NM_146005	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_52062.1	chr6	97385199	97385203	+	1	NA	intron (NM_001346639, intron 5 of 22)	intron (NM_001346639, intron 5 of 22)	74085	NM_001346639	232288	Mm.27789	NM_145148	ENSMUSG00000030064	Frmd4b	6030440G05Rik|C87375|GOBLIN|GRSP1|R74720	FERM domain containing 4B	protein-coding
mm_60145.1	chr7	38183805	38183869	+	1	NA	promoter-TSS (NM_028166)	promoter-TSS (NM_028166)	50	NM_028166	72244	Mm.187554	NM_028166		1600014C10Rik	AI428873	RIKEN cDNA 1600014C10 gene	protein-coding
mm_152189.1	chr19	7441561	7441579	-	1	NA	intron (NM_053076, intron 1 of 6)	intron (NM_053076, intron 1 of 6)	18997	NR_105957	102466781		NR_105957	ENSMUSG00000098293	Mir6991	Gm27966|mmu-mir-6991	microRNA 6991	ncRNA
mm_59284.1	chr7	24918640	24918648	+	1	NA	intron (NM_001130150, intron 14 of 30)	intron (NM_001130150, intron 14 of 30)	14298	NM_001130152	16801	Mm.3181	NM_008488	ENSMUSG00000040940	Arhgef1	Lbcl2|Lsc	Rho guanine nucleotide exchange factor (GEF) 1	protein-coding
mm_12246.1	chr2	68875068	68875070	+	1	NA	intron (NM_172856, intron 1 of 9)	intron (NM_172856, intron 1 of 9)	13628	NM_001347161	241447	Mm.222222	NM_172856	ENSMUSG00000027035	Cers6	4732462C07Rik|AW544719|Lass6|T1L	ceramide synthase 6	protein-coding
mm_88533.1	chr10	78400889	78400935	+	1	NA	exon (NM_010925, exon 13 of 13)	exon (NM_010925, exon 13 of 13)	7633	NR_105872	102465547		NR_105872	ENSMUSG00000098376	Mir6907	Gm27351|mmu-mir-6907	microRNA 6907	ncRNA
mm_2501.1	chr1	106171898	106171911	+	1	NA	promoter-TSS (NM_133821)	promoter-TSS (NM_133821)	35	NM_133821	98432	Mm.24115	NM_133821	ENSMUSG00000044340	Phlpp1	AI836256|Phlpp|Plekhe1|SCOP|mKIAA0606	PH domain and leucine rich repeat protein phosphatase 1	protein-coding
mm_114191.1	chr13	55784559	55784564	+	1	NA	promoter-TSS (NM_001252487)	promoter-TSS (NM_001252487)	-18	NM_029772	76856	Mm.159795	NM_029772	ENSMUSG00000021499	Catsper3	4921522D01Rik|CACRC	cation channel, sperm associated 3	protein-coding
mm_101374.1	chr11	23770865	23770877	-	1	NA	promoter-TSS (NM_009044)	promoter-TSS (NM_009044)	99	NM_009044	19696	Mm.4869	NM_009044	ENSMUSG00000020275	Rel	c-Rel	reticuloendotheliosis oncogene	protein-coding
mm_131395.1	chr16	14317486	14317502	+	1	NA	promoter-TSS (NM_025345)	promoter-TSS (NM_025345)	-162	NM_025345	66086	Mm.42072	NM_025345	ENSMUSG00000022677	Fopnl	0610037P05Rik	Fgfr1op N-terminal like	protein-coding
mm_151318.1	chr19	55888933	55888943	+	1	NA	intron (NR_138565, intron 4 of 15)	intron (NR_138565, intron 4 of 15)	-6383	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_26245.1	chr3	141510122	141510133	+	1	NA	intron (NM_001293561, intron 1 of 16)	intron (NM_001293561, intron 1 of 16)	44563	NM_001293561	22253	Mm.24430	NM_009472	ENSMUSG00000059921	Unc5c	B130051O18Rik|Unc5h3|rcm	unc-5 netrin receptor C	protein-coding
mm_10614.1	chr2	19199267	19199316	+	1	NA	5' UTR (NM_001271565, exon 1 of 18)	5' UTR (NM_001271565, exon 1 of 18)	173	NM_001081083	70882	Mm.276696	NM_001081083	ENSMUSG00000037683	Armc3	4921513G22Rik	armadillo repeat containing 3	protein-coding
mm_110840.1	chr12	72939589	72939606	-	1	NA	promoter-TSS (NM_011384)	promoter-TSS (NM_011384)	-285	NM_011384	20476	Mm.57138	NM_011384	ENSMUSG00000021099	Six6	Optx2|Six9	sine oculis-related homeobox 6	protein-coding
mm_151971.1	chr19	5822284	5822298	-	1	NA	Intergenic	Intergenic	-19619	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_88664.1	chr10	80016736	80016758	+	1	NA	promoter-TSS (NM_001142701)	promoter-TSS (NM_001142701)	75	NM_001142701	70719	Mm.243954	NM_027521	ENSMUSG00000035697	Hmha1	6330406L22Rik|AW539505|Ha-1	histocompatibility (minor) HA-1	protein-coding
mm_98703.1	chr11	96304025	96304041	+	1	NA	exon (NM_008268, exon 1 of 2)	exon (NM_008268, exon 1 of 2)	521	NM_008268	15413	Mm.207	NM_008268	ENSMUSG00000038700	Hoxb5	AI385717|Hox-2.1	homeobox B5	protein-coding
mm_42493.1	chr5	115474613	115474638	+	1	NA	TTS (NM_011107)	TTS (NM_011107)	8359	NM_011107	18778	Mm.20190	NM_011107	ENSMUSG00000029522	Pla2g1b	Pla2a|sPLA2IB	phospholipase A2, group IB, pancreas	protein-coding
mm_67841.1	chr7	98533813	98533845	-	1	NA	Intergenic	Intergenic	39607	NM_001113379	434215	Mm.323057	NM_001113379	ENSMUSG00000090958	Lrrc32	AI426318|D11S833Eh|D7H11S833E|EG434215|Garp	leucine rich repeat containing 32	protein-coding
mm_3719.1	chr1	154078233	154078242	+	1	NA	Intergenic	Intergenic	-122950	NM_001204908	100503355	Mm.484410	NM_001204908	ENSMUSG00000066797	Zfp648	ENSMUSG00000066797|Gm10178|Gm203	zinc finger protein 648	protein-coding
mm_58803.1	chr7	16308331	16308361	+	1	NA	Intergenic	B1F|SINE|Alu	-1237	NM_133234	170770	Mm.7660	NM_133234	ENSMUSG00000002083	Bbc3	PUMA|PUMA/JFY1	BCL2 binding component 3	protein-coding
mm_9328.1	chr1	171849513	171849522	-	1	NA	intron (NM_001289470, intron 2 of 8)	intron (NM_001289470, intron 2 of 8)	9820	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_170365.1	chr1	85272357	85272361	+	1	NA	Intergenic	Intergenic	-1793	NM_001037909	620078	Mm.386456	NM_175219	ENSMUSG00000052477	C130026I21Rik	4930565N07Rik|OTTMUSG00000029174	RIKEN cDNA C130026I21 gene	protein-coding
mm_110103.1	chr12	26346590	26346608	-	1	NA	promoter-TSS (NR_130981)	promoter-TSS (NR_130981)	-111	NR_130981	75243	Mm.444753	NR_130981		4930549C15Rik	-	RIKEN cDNA 4930549C15 gene	ncRNA
mm_88779.1	chr10	80546908	80546914	+	1	NA	intron (NM_025852, intron 4 of 14)	intron (NM_025852, intron 4 of 14)	-7787	NM_026094	67331	Mm.52511	NM_026094	ENSMUSG00000003341	Atp8b3	1700042F02Rik|1700056N23Rik|ATPIK|SAPLT	ATPase, class I, type 8B, member 3	protein-coding
mm_16483.1	chr2	180890835	180890853	+	1	NA	Intergenic	Intergenic	-3196	NR_029538	723951		NR_029538	ENSMUSG00000065454	Mir124a-3	Mirn124a-3|mir-124-3|mir-124a-3	microRNA 124a-3	ncRNA
mm_63568.1	chr7	128117313	128117323	+	1	NA	exon (NM_008401, exon 30 of 30)	exon (NM_008401, exon 30 of 30)	-12250	NM_021334	16411	Mm.22378	NM_021334	ENSMUSG00000030789	Itgax	AI449405|Cd11c|Cr4|N418	integrin alpha X	protein-coding
mm_104966.1	chr11	100193100	100193103	-	1	NA	exon (NM_201255, exon 1 of 8)	exon (NM_201255, exon 1 of 8)	145	NM_201255	107656	Mm.445335	NM_201255	ENSMUSG00000051617	Krt9	EPPK|K9|Krt1-9	keratin 9	protein-coding
mm_69660.1	chr7	139978749	139978768	-	1	NA	promoter-TSS (NM_001033465)	promoter-TSS (NM_001033465)	-3	NM_001347613	381933	Mm.440431	NM_001033465	ENSMUSG00000073795	6430531B16Rik	Gm1093	RIKEN cDNA 6430531B16 gene	protein-coding
mm_42762.1	chr5	121204562	121204566	+	1	NA	promoter-TSS (NM_011290)	promoter-TSS (NM_011290)	63	NM_011290	19988	Mm.262021	NM_011290	ENSMUSG00000029614	Rpl6	Taxreb107	ribosomal protein L6	protein-coding
mm_34491.1	chr4	148591556	148591587	+	1	NA	promoter-TSS (NM_009272)	promoter-TSS (NM_009272)	58	NM_009272	20810	Mm.10	NM_009272	ENSMUSG00000006442	Srm	AA407669|SpdST|SpdSy	spermidine synthase	protein-coding
mm_130356.1	chr15	97767511	97767576	-	1	NA	5' UTR (NM_001177811, exon 1 of 27)	5' UTR (NM_001177811, exon 1 of 27)	123	NM_001177810	223864	Mm.24028	NM_144850	ENSMUSG00000022469	Rapgef3	2310016P22Rik|9330170P05Rik|Epac|Epac1	Rap guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_127773.1	chr15	3279563	3279575	-	1	NA	exon (NM_009155, exon 5 of 5)	exon (NM_009155, exon 5 of 5)	8592	NM_009155	20363	Mm.392203	NM_009155	ENSMUSG00000064373	Selenop	AU018766|D15Ucla1|Se-P|Sepp1|selp	selenoprotein P	protein-coding
mm_148912.1	chr19	6975049	6975071	+	1	NA	promoter-TSS (NM_008889)	promoter-TSS (NM_008889)	12	NM_008889	18938	Mm.140	NM_008889	ENSMUSG00000056612	Ppp1r14b	AOM172|PHI-1|PLCB3N|Png	protein phosphatase 1, regulatory (inhibitor) subunit 14B	protein-coding
mm_123397.1	chr14	63418821	63418835	-	1	NA	Intergenic	Intergenic	-1641	NM_007549	12143	Mm.3962	NM_007549	ENSMUSG00000014453	Blk	-	B lymphoid kinase	protein-coding
mm_162718.1	chr10	35911190	35911192	+	1	NA	Intergenic	B3A|SINE|B2	-595616	NM_001253355	319415	Mm.332442	NM_001081208	ENSMUSG00000044499	Hs3st5	D930005L05Rik|Gm1151|Hs3ost5	heparan sulfate (glucosamine) 3-O-sulfotransferase 5	protein-coding
mm_52565.1	chr6	116264187	116264225	+	1	NA	promoter-TSS (NM_001290338)	promoter-TSS (NM_001290338)	-13	NM_001309446	67492	Mm.272772	NM_001081317	ENSMUSG00000042213	Zfand4	Anubl1	zinc finger, AN1-type domain 4	protein-coding
mm_67013.1	chr7	65371211	65371287	-	1	NA	promoter-TSS (NM_001163574)	promoter-TSS (NM_001163574)	-5	NM_009386	21872	Mm.4342	NM_009386	ENSMUSG00000030516	Tjp1	ZO1	tight junction protein 1	protein-coding
mm_168266.1	chr10	93589600	93589603	-	1	NA	promoter-TSS (NM_027246)	promoter-TSS (NM_027246)	57	NM_027246	69878	Mm.259642	NM_027246	ENSMUSG00000020018	Snrpf	2010013O18Rik|SMF|sm-F|snRNP-F	small nuclear ribonucleoprotein polypeptide F	protein-coding
mm_56191.1	chr6	88627423	88627454	-	1	NA	promoter-TSS (NM_001278671)	promoter-TSS (NM_001278671)	10	NM_001278671	74589	Mm.196226	NM_029013	ENSMUSG00000033182	Kbtbd12	4833415F11Rik|4933428M03Rik|Klhdc6	kelch repeat and BTB (POZ) domain containing 12	protein-coding
mm_134450.1	chr16	18400827	18400842	-	1	NA	intron (NM_033474, intron 9 of 18)	intron (NM_033474, intron 9 of 18)	8271	NM_001272032	11877	Mm.293599	NM_033474	ENSMUSG00000000325	Arvcf	-	armadillo repeat gene deleted in velo-cardio-facial syndrome	protein-coding
mm_61960.1	chr7	90302238	90302248	+	1	NA	promoter-TSS (NM_001040085)	promoter-TSS (NM_001040085)	-112	NM_001289583	83671	Mm.26751	NM_031394	ENSMUSG00000030616	Sytl2	AI266830|Slp2|mKIAA1597	synaptotagmin-like 2	protein-coding
mm_17388.1	chr2	27072117	27072170	-	1	NA	promoter-TSS (NM_025376)	promoter-TSS (NM_025376)	18	NM_025376	66139	Mm.330087	NM_025376	ENSMUSG00000009214	Tmem8c	1110002H13Rik|AI131587	transmembrane protein 8C	protein-coding
mm_145256.1	chr18	52529011	52529057	+	1	NA	exon (NM_010728, exon 1 of 7)	exon (NM_010728, exon 1 of 7)	687	NM_001286181	16948	Mm.172	NM_010728	ENSMUSG00000024529	Lox	AI893619|TSC-160|rrg	lysyl oxidase	protein-coding
mm_37231.1	chr4	117993971	117993976	-	1	NA	intron (NM_009176, intron 5 of 11)	intron (NM_009176, intron 5 of 11)	-64210	NM_001284192	11876	Mm.56897	NM_009711	ENSMUSG00000028539	Artn	neublastin	artemin	protein-coding
mm_106907.1	chr12	8015692	8015703	+	1	NA	exon (NM_009693, exon 29 of 29)	exon (NM_009693, exon 29 of 29)	38020	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_122876.1	chr14	54925997	54926021	-	1	NA	5' UTR (NM_010112, exon 1 of 6)	5' UTR (NM_010112, exon 1 of 6)	779	NM_010112	13644	Mm.236438	NM_010112	ENSMUSG00000022203	Efs	-	embryonal Fyn-associated substrate	protein-coding
mm_106449.1	chr11	119937808	119937818	-	1	NA	Intergenic	Intergenic	-5279	NM_001037754	108100	Mm.197534	NM_130862	ENSMUSG00000025372	Baiap2	IRSp53|R75030	brain-specific angiogenesis inhibitor 1-associated protein 2	protein-coding
mm_93885.1	chr10	125328455	125328470	-	1	NA	promoter-TSS (NM_011391)	promoter-TSS (NM_011391)	73	NM_011391	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|Mct2	solute carrier family 16 (monocarboxylic acid transporters), member 7	protein-coding
mm_106443.1	chr11	119834462	119834488	-	1	NA	promoter-TSS (NR_045313)	promoter-TSS (NR_045313)	-110	NR_045312	319454	Mm.442144	NR_045312	ENSMUSG00000085081	Rptoros	A430071A18Rik	regulatory associated protein of MTOR, complex 1, opposite strand	ncRNA
mm_1468.1	chr1	69826958	69826984	+	1	NA	promoter-TSS (NM_029160)	promoter-TSS (NM_029160)	1	NM_001271533	66722	Mm.440554	NM_025728	ENSMUSG00000053153	Spag16	4921511D23Rik|4930524F24Rik|4930585K05Rik|AV261009|Pf20|Wdr29	sperm associated antigen 16	protein-coding
mm_42467.1	chr5	115453943	115453975	+	1	NA	3' UTR (NM_008629, exon 15 of 15)	3' UTR (NM_008629, exon 15 of 15)	-12307	NM_011107	18778	Mm.20190	NM_011107	ENSMUSG00000029522	Pla2g1b	Pla2a|sPLA2IB	phospholipase A2, group IB, pancreas	protein-coding
mm_17698.1	chr2	32353284	32353311	-	1	NA	promoter-TSS (NR_125959)	promoter-TSS (NR_125959)	32	NM_001301737	13429	Mm.44736	NM_010065	ENSMUSG00000026825	Dnm1	AI838169|Dnm|Ftfl|mKIAA4093	dynamin 1	protein-coding
mm_72019.1	chr8	70724068	70724078	+	1	NA	promoter-TSS (NM_201607)	promoter-TSS (NM_201607)	9	NM_201607	110385	Mm.255180	NM_201607	ENSMUSG00000031842	Pde4c	Dpde1|E130301F19Rik|dunce	phosphodiesterase 4C, cAMP specific	protein-coding
mm_49827.1	chr6	37806299	37806343	+	1	NA	Intergenic	Intergenic	-64490	NM_001272064	21848	Mm.41063	NM_145076	ENSMUSG00000029833	Trim24	A130082H20Rik|AI447469|D430004I05Rik|TIF1|TIF1-alpha|TIF1alpha|Tif1a	tripartite motif-containing 24	protein-coding
mm_119935.1	chr14	54971908	54971911	+	1	NA	intron (NM_080728, intron 38 of 40)	PB1D10|SINE|Alu	3122	NR_033497	791403	Mm.319176	NR_033497	ENSMUSG00000097652	Mhrt	D830015G02Rik|ENSMUSG00000053118|Myheart	myosin heavy chain associated RNA transcript	ncRNA
mm_90447.1	chr10	127668392	127668409	+	1	NA	intron (NR_045171, intron 1 of 1)	intron (NR_045171, intron 1 of 1)	1277	NR_045171	72243	Mm.482902	NR_045171	ENSMUSG00000040195	1700012D01Rik	-	RIKEN cDNA 1700012D01 gene	ncRNA
mm_51116.1	chr6	67791024	67791027	+	1	NA	Intergenic	Intergenic	-225326	NR_003100	75070	Mm.463364	NR_003100		4930515G16Rik	-	myc induced nuclear antigen pseudogene	pseudo
mm_68011.1	chr7	100939953	100939971	-	1	NA	5' UTR (NM_183168, exon 2 of 3)	5' UTR (NM_183168, exon 2 of 3)	-7801	NM_001081116	207212	Mm.29954	NM_001081116	ENSMUSG00000032875	Arhgef17	8030463K16|AI428794|AW558066|BC035332|mKIAA0337	Rho guanine nucleotide exchange factor (GEF) 17	protein-coding
mm_171174.1	chr3	3326852	3326871	+	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	-181169	NM_013920	30942	Mm.330897	NM_013920	ENSMUSG00000017688	Hnf4g	NR2A2	hepatocyte nuclear factor 4, gamma	protein-coding
mm_58550.1	chr7	4690761	4690778	+	1	NA	promoter-TSS (NM_001003920)	promoter-TSS (NM_001003920)	-159	NM_001003920	381979	Mm.297064	NM_001003920	ENSMUSG00000035390	Brsk1	Gm1100|SAD-B|SADB	BR serine/threonine kinase 1	protein-coding
mm_27674.1	chr3	65658909	65658947	-	1	NA	promoter-TSS (NR_106200)	promoter-TSS (NR_106200)	-360	NR_106200	102465905		NR_106200	ENSMUSG00000098944	Mir8120	Gm27637|mmu-mir-8120	microRNA 8120	ncRNA
mm_157316.1	chrX	21089131	21089136	-	1	NA	promoter-TSS (NM_183185)	promoter-TSS (NM_183185)	96	NM_183185	245368	Mm.220470	NM_183185	ENSMUSG00000031079	Zfp300	D930016N04Rik	zinc finger protein 300	protein-coding
mm_75743.1	chr8	69791171	69791212	-	1	NA	promoter-TSS (NM_133224)	promoter-TSS (NM_133224)	28	NM_133224	170759	Mm.186066	NM_133224	ENSMUSG00000031862	Atp13a1	Atp13a|Cgi152|catp	ATPase type 13A1	protein-coding
mm_106769.1	chr12	4593861	4593864	+	1	NA	intron (NM_011365, intron 1 of 38)	intron (NM_011365, intron 1 of 38)	854	NM_001198968	20403	Mm.341204	NM_011365	ENSMUSG00000020640	Itsn2	AI327390|Ese2|Sh3d1B|Sh3p18|mKIAA1256	intersectin 2	protein-coding
mm_67793.1	chr7	97730642	97730660	-	1	NA	intron (NM_175105, intron 1 of 2)	MLT1H|LTR|ERVL-MaLR	7596	NM_175105	66333	Mm.29756	NM_175105	ENSMUSG00000042797	Aqp11	1700015P13Rik|AI648923|sjds	aquaporin 11	protein-coding
mm_96702.1	chr11	69645170	69645178	+	1	NA	intron (NM_011814, intron 7 of 16)	B2_Mm2|SINE|B2	-9863	NM_009235	20670	Mm.347499	NM_009235	ENSMUSG00000041287	Sox15	-	SRY (sex determining region Y)-box 15	protein-coding
mm_97575.1	chr11	78940307	78940315	+	1	NA	exon (NM_010927, exon 11 of 27)	exon (NM_010927, exon 11 of 27)	15020	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_77416.1	chr8	120668031	120668056	-	1	NA	promoter-TSS (NM_009941)	promoter-TSS (NM_009941)	69	NM_010926	18117	Mm.2136	NM_010926	ENSMUSG00000031819	Emc8	Cox4nb|Fam158b|Noc4	ER membrane protein complex subunit 8	protein-coding
mm_74678.1	chr8	13975046	13975074	-	1	NA	promoter-TSS (NM_173744)	promoter-TSS (NM_173744)	-283	NM_173744	72148	Mm.5727	NM_173744	ENSMUSG00000050052	Tdrp	2610019F03Rik	testis development related protein	protein-coding
mm_144650.1	chr18	34220891	34220931	+	1	NA	promoter-TSS (NM_007462)	promoter-TSS (NM_007462)	-73	NM_007462	11789	Mm.384171	NM_007462	ENSMUSG00000005871	Apc	AI047805|AU020952|AW124434|CC1|Min|mAPC	adenomatosis polyposis coli	protein-coding
mm_149614.1	chr19	16385952	16385967	+	1	NA	3' UTR (NM_008139, exon 7 of 7)	3' UTR (NM_008139, exon 7 of 7)	-49708	NM_008137	14675	Mm.313181	NM_008137	ENSMUSG00000024697	Gna14	AU023208	guanine nucleotide binding protein, alpha 14	protein-coding
mm_145477.1	chr18	60376446	60376490	+	1	NA	intron (NM_021792, intron 1 of 1)	RMER17A|LTR|ERVK	439	NM_001146275	60440	Mm.261140	NM_021792	ENSMUSG00000054072	Iigp1	2900074L10Rik|AI046432|AW111922|Ifgga1|Iigp|Irga6	interferon inducible GTPase 1	protein-coding
mm_30936.1	chr4	32983495	32983503	+	1	NA	exon (NM_027491, exon 1 of 7)	exon (NM_027491, exon 1 of 7)	501	NM_027491	52187	Mm.300814	NM_027491	ENSMUSG00000028278	Rragd	5730543C08Rik|AI467523|C030003H22Rik|D4Ertd174e	Ras-related GTP binding D	protein-coding
mm_154122.1	chr19	57197517	57197536	-	1	NA	5' UTR (NM_001103177, exon 1 of 22)	5' UTR (NM_001103177, exon 1 of 22)	105	NM_001103177	226251	Mm.217161	NM_178688	ENSMUSG00000025085	Ablim1	2210411C18Rik|2610209L21Rik|4833406P10Rik|9330196J19Rik|AV079770|AW060987|AW215784|Limab1|mKIAA0059	actin-binding LIM protein 1	protein-coding
mm_10449.1	chr2	14273584	14273588	+	1	NA	intron (NM_008625, intron 9 of 29)	intron (NM_008625, intron 9 of 29)	12583	NR_030609	100124488		NR_030609	ENSMUSG00000077897	Mir511	Mirn511|mir-511|mmu-mir-511	microRNA 511	ncRNA
mm_164886.1	chr18	60807672	60807684	+	1	NA	intron (NM_001042605, intron 1 of 8)	intron (NM_001042605, intron 1 of 8)	3829	NM_010545	16149	Mm.439737	NM_010545	ENSMUSG00000024610	Cd74	CLIP|DHLAG|HLADG|Ia-GAMMA|Ii	CD74 antigen (invariant polypeptide of major histocompatibility complex, class II antigen-associated)	protein-coding
mm_2658.1	chr1	125677197	125677209	+	1	NA	5' UTR (NM_027677, exon 1 of 2)	5' UTR (NM_027677, exon 1 of 2)	207	NM_027677	71111	Mm.32727	NM_027677	ENSMUSG00000026343	Gpr39	4933415E13Rik	G protein-coupled receptor 39	protein-coding
mm_31825.1	chr4	69691953	69691962	+	1	NA	Intergenic	Intergenic	718478	NM_001313762	214444	Mm.370777	NM_145990	ENSMUSG00000039298	Cdk5rap2	2900018K03Rik|an|mKIAA1633	CDK5 regulatory subunit associated protein 2	protein-coding
mm_105486.1	chr11	105955847	105955855	-	1	NA	Intergenic	Intergenic	-11704	NM_007805	13056	Mm.149403	NM_007805	ENSMUSG00000019590	Cyb561	-	cytochrome b-561	protein-coding
mm_136001.1	chr16	75447108	75447116	-	1	NA	Intergenic	Intergenic	138949	NM_001252513	320355	Mm.99517	NM_177142	ENSMUSG00000032948	Lipi	D930038D03Rik|lpd1	lipase, member I	protein-coding
mm_133042.1	chr16	57471336	57471348	+	1	NA	intron (NM_001040397, intron 1 of 4)	intron (NM_001040397, intron 1 of 4)	-77900	NM_001177871	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding
mm_734.1	chr1	43445715	43445722	+	1	NA	promoter-TSS (NM_010879)	promoter-TSS (NM_010879)	-33	NM_010879	17974	Mm.389903	NM_010879	ENSMUSG00000066877	Nck2	4833426I10Rik|Grb4|NCKbeta|Nck-2	non-catalytic region of tyrosine kinase adaptor protein 2	protein-coding
mm_168153.1	chr10	41410329	41410335	-	1	NA	Intergenic	RLTR9D|LTR|ERVK	-40026	NM_001277229	268294	Mm.258475	NM_153398	ENSMUSG00000019826	Zbtb24	BC055367|Bif1|Bsg1|ZNF450	zinc finger and BTB domain containing 24	protein-coding
mm_8935.1	chr1	164307230	164307290	-	1	NA	promoter-TSS (NM_001293313)	promoter-TSS (NM_001293313)	224	NM_001160209	66352	Mm.33285	NM_025505	ENSMUSG00000026577	Blzf1	1700030G05Rik|Blzf1l|Golgin-45|Jem-1	basic leucine zipper nuclear factor 1	protein-coding
mm_117554.1	chr13	84347885	84347906	-	1	NA	Intergenic	Intergenic	125599	NM_175187	72745	Mm.295063	NM_175187	ENSMUSG00000035762	Tmem161b	2810446P07Rik|AI843389	transmembrane protein 161B	protein-coding
mm_143209.1	chr17	62880871	62880885	-	1	NA	intron (NM_010109, intron 1 of 3)	CpG	439	NM_207654	13640	Mm.7978	NM_010109	ENSMUSG00000048915	Efna5	AL-1|AV158822|EFL-5|Ephrin-A5|Epl7|LERK-7|RAGS	ephrin A5	protein-coding
mm_148153.1	chr18	77565196	77565204	-	1	NA	promoter-TSS (NM_001164504)	promoter-TSS (NM_001164504)	-64	NM_001164504	225743	Mm.23293	NM_001164504	ENSMUSG00000025427	Rnf165	2900024M11Rik|AI427432|Akd2|Ark2c|G630064H08Rik|Gm96	ring finger protein 165	protein-coding
mm_95065.1	chr11	32533310	32533335	+	1	NA	promoter-TSS (NM_009288)	promoter-TSS (NM_009288)	56	NM_009288	20868	Mm.8235	NM_009288	ENSMUSG00000020272	Stk10	Gek1|Lok|mKIAA4026	serine/threonine kinase 10	protein-coding
mm_72284.1	chr8	75109512	75109522	+	1	NA	promoter-TSS (NM_008566)	promoter-TSS (NM_008566)	8	NM_008566	17218	Mm.5048	NM_008566	ENSMUSG00000005410	Mcm5	AA617332|AI324988|AL033333|Cdc46|Mcmd5|P1-CDC46	minichromosome maintenance complex component 5	protein-coding
mm_85541.1	chr9	106682171	106682185	-	1	NA	intron (NM_001286498, intron 2 of 5)	intron (NM_001286498, intron 2 of 5)	3638	NM_011573	21767	Mm.22266	NM_011573	ENSMUSG00000040813	Tex264	TEG-264	testis expressed gene 264	protein-coding
mm_59867.1	chr7	30184213	30184216	+	1	NA	promoter-TSS (NM_009944)	promoter-TSS (NM_009944)	43	NM_009944	12865	Mm.423030	NM_009944	ENSMUSG00000074218	Cox7a1	COX7A|COX7AH|COX7AM	cytochrome c oxidase subunit VIIa 1	protein-coding
mm_21075.1	chr2	152830559	152830586	-	1	NA	5' UTR (NM_001289716, exon 1 of 3)	5' UTR (NM_001289716, exon 1 of 3)	145	NM_001289716	12048	Mm.238213	NM_009743	ENSMUSG00000007659	Bcl2l1	Bcl(X)L|Bcl-XL|Bcl2l|BclX|bcl-x|bcl2-L-1	BCL2-like 1	protein-coding
mm_71794.1	chr8	67494844	67494883	+	1	NA	promoter-TSS (NM_010874)	promoter-TSS (NM_010874)	-12	NM_001168577	17961	Mm.4695	NM_010874	ENSMUSG00000051147	Nat2	AV377607	N-acetyltransferase 2 (arylamine N-acetyltransferase)	protein-coding
mm_162461.1	chr1	128712971	128712994	-	1	NA	Intergenic	Intergenic	-120683	NM_009911	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding
mm_10562.1	chr2	18049004	18049027	+	1	NA	promoter-TSS (NM_028317)	promoter-TSS (NM_028317)	-566	NM_028317	72668	Mm.102183	NM_028317	ENSMUSG00000054074	Skida1	2810030E01Rik|5730507N06Rik|BB088113	SKI/DACH domain containing 1	protein-coding
mm_58268.1	chr6	145340779	145340799	-	1	NA	Intergenic	CpG	-46836	NR_003625	381827	Mm.179075	NM_001001987		1700073E17Rik	-	ribosomal protein L7 pseudogene	pseudo
mm_115108.1	chr13	103397068	103397069	+	1	NA	Intergenic	Intergenic	-62576	NM_175171	328329	Mm.202606	NM_175171	ENSMUSG00000034751	Mast4	4930420O11Rik|AI642422|mKIAA0303	microtubule associated serine/threonine kinase family member 4	protein-coding
mm_142463.1	chr17	45599582	45599597	-	1	NA	promoter-TSS (NM_001199115)	promoter-TSS (NM_001199115)	14	NM_001199115	63959	Mm.29744	NM_022880	ENSMUSG00000023942	Slc29a1	1200014D21Rik|AA407560|ENT1	solute carrier family 29 (nucleoside transporters), member 1	protein-coding
mm_49526.1	chr6	29985358	29985366	+	1	NA	promoter-TSS (NR_040264)	promoter-TSS (NR_040264)	33	NR_040263	76419	Mm.84522	NR_040263	ENSMUSG00000045709	Smkr-ps	1700023L04Rik	smal lysine rich protein 1, pseudogene	ncRNA
mm_49174.1	chr6	14901441	14901497	+	1	NA	5' UTR (NM_053242, exon 1 of 19)	5' UTR (NM_053242, exon 1 of 19)	120	NM_053242	114142	Mm.332919	NM_053242	ENSMUSG00000029563	Foxp2	2810043D05Rik|AI449000|CAG-16|D0Kist7	forkhead box P2	protein-coding
mm_118370.1	chr13	116876371	116876384	-	1	NA	intron (NM_001081009, intron 18 of 26)	intron (NM_001081009, intron 18 of 26)	149139	NM_001081009	52552	Mm.274466	NM_027272	ENSMUSG00000021725	Parp8	2810430O08Rik|ARTD16|D13Ertd275e	poly (ADP-ribose) polymerase family, member 8	protein-coding
mm_145490.1	chr18	60389801	60389829	+	1	NA	exon (NM_001146275, exon 3 of 3)	exon (NM_001146275, exon 3 of 3)	13786	NM_001146275	60440	Mm.261140	NM_021792	ENSMUSG00000054072	Iigp1	2900074L10Rik|AI046432|AW111922|Ifgga1|Iigp|Irga6	interferon inducible GTPase 1	protein-coding
mm_31591.1	chr4	57854712	57854735	+	1	NA	exon (NM_001035533, exon 1 of 4)	exon (NM_001035533, exon 1 of 4)	161	NM_001035533	11641	Mm.467752	NM_009649	ENSMUSG00000038729	Akap2	AA959716|AI649048|Akap-2|Akap-kl|B230340M18Rik|Prka2	A kinase (PRKA) anchor protein 2	protein-coding
mm_33392.1	chr4	129814624	129814629	+	1	NA	Intergenic	Intergenic	-5853	NM_008974	19244	Mm.193688	NM_008974	ENSMUSG00000028788	Ptp4a2	Prl-2	protein tyrosine phosphatase 4a2	protein-coding
mm_123260.1	chr14	61258384	61258465	-	1	NA	promoter-TSS (NM_011892)	promoter-TSS (NM_011892)	66	NM_011892	24053	Mm.72173	NM_011892	ENSMUSG00000035296	Sgcg	35kDa|5430420E18Rik|AI642964|gamma-SG	sarcoglycan, gamma (dystrophin-associated glycoprotein)	protein-coding
mm_52312.1	chr6	108828735	108828744	+	1	NA	promoter-TSS (NM_138677)	promoter-TSS (NM_138677)	98	NM_138677	192193	Mm.21596	NM_138677	ENSMUSG00000030104	Edem1	A130059K23Rik|EDEM|mKIAA0212	ER degradation enhancer, mannosidase alpha-like 1	protein-coding
mm_76058.1	chr8	77724374	77724390	-	1	NA	promoter-TSS (NM_010332)	promoter-TSS (NM_010332)	70	NM_010332	13617	Mm.283168	NM_010332	ENSMUSG00000031616	Ednra	ET-AR|ETa|Gpcr10	endothelin receptor type A	protein-coding
mm_91389.1	chr10	30655774	30655810	-	1	NA	promoter-TSS (NM_001111267)	promoter-TSS (NM_001111267)	75	NM_001111267	211329	Mm.297903	NM_172495	ENSMUSG00000039697	Ncoa7	9030406N13Rik	nuclear receptor coactivator 7	protein-coding
mm_104669.1	chr11	97660297	97660351	-	1	NA	Intergenic	CpG	-3088	NM_139311	246198	Mm.23685	NM_139311	ENSMUSG00000038437	Mllt6	AI315037|Af17	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 6	protein-coding
mm_56605.1	chr6	112352991	112352991	-	1	NA	Intergenic	Intergenic	35032	NM_175525	243612	Mm.122653	NM_175525	ENSMUSG00000034387	Ssu2	D630042P16Rik|Fls485|Ssuh2	ssu-2 homolog (C. elegans)	protein-coding
mm_142380.1	chr17	44736363	44736373	-	1	NA	promoter-TSS (NM_001271631)	promoter-TSS (NM_001271631)	-192	NM_001271631	12393	Mm.391013	NM_009820	ENSMUSG00000039153	Runx2	AML3|Cbf|Cbfa-1|Cbfa1|LS3|Osf2|PEBP2aA|Pebp2a1|Pebpa2a	runt related transcription factor 2	protein-coding
mm_71366.1	chr8	45746618	45746628	+	1	NA	intron (NM_172752, intron 6 of 22)	intron (NM_172752, intron 6 of 22)	72674	NR_045739	319940	Mm.441720	NR_045739	ENSMUSG00000085440	Sorbs2os	D330022K07Rik	sorbin and SH3 domain containing 2, opposite strand	ncRNA
mm_73805.1	chr8	117328875	117328878	+	1	NA	intron (NM_001163262, intron 1 of 20)	intron (NM_001163262, intron 1 of 20)	-20294	NM_028941	74440	Mm.233181	NM_028941	ENSMUSG00000034390	Cmip	4933407C03Rik|5830471E12Rik|AI314065|AI464126	c-Maf inducing protein	protein-coding
mm_115789.1	chr13	19337287	19337296	-	1	NA	Intergenic	Intergenic	58522	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_18714.1	chr2	72442882	72442893	-	1	NA	TTS (NM_023057)	TTS (NM_023057)	-33332	NM_025866	66953	Mm.270676	NM_025866	ENSMUSG00000055612	Cdca7	2310021G01Rik|AU044109|JPO1	cell division cycle associated 7	protein-coding
mm_28258.1	chr3	88570484	88570495	-	1	NA	TTS (NM_033526)	TTS (NM_033526)	-9182	NM_025448	66256	Mm.7091	NM_025448	ENSMUSG00000041355	Ssr2	1500032E05Rik|AI315033|AU020133|TLAP|TRAPB|TRAPbeta	signal sequence receptor, beta	protein-coding
mm_164289.1	chr15	103755506	103755510	-	1	NA	promoter-TSS (NR_126081)	promoter-TSS (NR_126081)	-10	NR_126081	20771	Mm.30276	NM_009268		Mucl1	Spt-2|Spt2	mucin-like 1	protein-coding
mm_131760.1	chr16	22884276	22884282	+	1	NA	intron (NR_110508, intron 2 of 3)	intron (NR_110508, intron 2 of 3)	-7736	NR_075099	11625	Mm.197554	NM_013465	ENSMUSG00000022868	Ahsg	-	alpha-2-HS-glycoprotein	protein-coding
mm_17325.1	chr2	26502815	26502823	-	1	NA	intron (NM_008714, intron 1 of 33)	CpG	1003	NM_008714	18128	Mm.290610	NM_008714	ENSMUSG00000026923	Notch1	9930111A19Rik|Mis6|N1|Tan1|lin-12	notch 1	protein-coding
mm_14359.1	chr2	129616223	129616261	+	1	NA	exon (NM_007547, exon 4 of 8)	exon (NM_007547, exon 4 of 8)	23073	NM_001291022	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_167515.1	chr9	14614866	14614884	-	1	NA	5' UTR (NM_001081395, exon 1 of 13)	5' UTR (NM_001081395, exon 1 of 13)	125	NM_001081395	75723	Mm.159552	NM_001081395	ENSMUSG00000013076	Amotl1	2310010G08Rik|2310067L22Rik|4932416D09Rik|JEAP|mFLJ00155	angiomotin-like 1	protein-coding
mm_168663.1	chr1	189277828	189277849	-	1	NA	intron (NM_001281848, intron 2 of 5)	intron (NM_001281848, intron 2 of 5)	65515	NM_001159850	16526	Mm.33304	NM_010607	ENSMUSG00000037624	Kcnk2	A430027H14Rik|AI848635|TREK-1	potassium channel, subfamily K, member 2	protein-coding
mm_61083.1	chr7	51622313	51622317	+	1	NA	5' UTR (NM_080853, exon 1 of 12)	5' UTR (NM_080853, exon 1 of 12)	485	NM_080853	140919	Mm.256618	NM_080853	ENSMUSG00000030500	Slc17a6	2900073D12Rik|DNPI|VGLUT2	solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 6	protein-coding
mm_24843.1	chr3	95662033	95662055	+	1	NA	3' UTR (NM_008562, exon 3 of 3)	3' UTR (NM_008562, exon 3 of 3)	3323	NM_008562	17210	Mm.1639	NM_008562	ENSMUSG00000038612	Mcl1	AW556805|Mcl-1	myeloid cell leukemia sequence 1	protein-coding
mm_131749.1	chr16	22266074	22266115	+	1	NA	promoter-TSS (NM_001330554)	promoter-TSS (NM_001330554)	-89	NM_001330555	20462	Mm.210352	NM_009186	ENSMUSG00000022858	Tra2b	5730405G21Rik|D16Ertd266e|SIG-41|Sfrs10|Silg41|TRA2beta	transformer 2 beta homolog (Drosophila)	protein-coding
mm_21160.1	chr2	154569846	154569874	-	1	NA	promoter-TSS (NM_001291105)	promoter-TSS (NM_001291105)	32	NM_007891	13555	Mm.18036	NM_007891	ENSMUSG00000027490	E2f1	E2F-1|mKIAA4009	E2F transcription factor 1	protein-coding
mm_168269.1	chr10	93792601	93792608	+	1	NA	Intergenic	RLTR45|LTR|ERVK	-38951	NM_183199	327799	Mm.491598	NM_183199	ENSMUSG00000020020	Usp44	E430004F17Rik	ubiquitin specific peptidase 44	protein-coding
mm_79846.1	chr9	64811532	64811538	+	1	NA	5' UTR (NM_001162917, exon 2 of 35)	5' UTR (NM_001162917, exon 2 of 35)	524	NM_001162917	102442	Mm.222473	NM_176935	ENSMUSG00000053641	Dennd4a	AI115600|AI851943|F730015K02Rik	DENN/MADD domain containing 4A	protein-coding
mm_144852.1	chr18	36641616	36641630	+	1	NA	exon (NM_175375, exon 24 of 34)	exon (NM_175375, exon 24 of 34)	-22437	NM_201256	108112	Mm.24790	NM_201256	ENSMUSG00000090264	Eif4ebp3	4e-bp3	eukaryotic translation initiation factor 4E binding protein 3	protein-coding
mm_132901.1	chr16	48872025	48872049	+	1	NA	promoter-TSS (NM_181596)	promoter-TSS (NM_181596)	-571	NM_181596	245195	Mm.231288	NM_181596	ENSMUSG00000022651	Retnlg	Fizz3|Relmg|Xcp1	resistin like gamma	protein-coding
mm_818.1	chr1	46425443	46425447	+	1	NA	promoter-TSS (NM_001310335)	promoter-TSS (NM_001310335)	-73	NM_001310335	100101919	Mm.383402	NM_001310335	ENSMUSG00000101337	Dnah7c	Dnahc7c	dynein, axonemal, heavy chain 7C	protein-coding
mm_160016.1	chr6	129643343	129643343	-	1	NA	promoter-TSS (NM_021378)	promoter-TSS (NM_021378)	-55	NM_021378	58179	Mm.358684	NM_021378	ENSMUSG00000033027	Klrc3	Klrc2|Nkg2e	killer cell lectin-like receptor subfamily C, member 3	protein-coding
mm_153226.1	chr19	34879202	34879212	-	1	NA	5' UTR (NM_001114339, exon 1 of 7)	5' UTR (NM_001114339, exon 1 of 7)	248	NM_001114339	75735	Mm.24742	NM_023792	ENSMUSG00000033610	Pank1	Pank|Pank1b	pantothenate kinase 1	protein-coding
mm_154637.1	chrX	7764251	7764263	+	1	NA	intron (NM_001271491, intron 1 of 8)	intron (NM_001271491, intron 1 of 8)	216	NM_001271491	209446	Mm.249142	NM_172472	ENSMUSG00000000134	Tfe3	F830016E06Rik|Tcfe3|Tfe-3|bHLHe33	transcription factor E3	protein-coding
mm_82552.1	chr9	20959786	20959792	-	1	NA	promoter-TSS (NM_001199432)	promoter-TSS (NM_001199432)	99	NM_001199432	13433	Mm.128580	NM_010066	ENSMUSG00000004099	Dnmt1	Cxxc9|Dnmt|Dnmt1o|MCMT|MTase|Met-1|Met1|MommeD2|m.MmuI	DNA methyltransferase (cytosine-5) 1	protein-coding
mm_66768.1	chr7	46732563	46732571	-	1	NA	promoter-TSS (NM_011316)	promoter-TSS (NM_011316)	36	NM_011316	20211	Mm.3489	NM_011316	ENSMUSG00000040017	Saa4	Saa-4|Saa-5	serum amyloid A 4	protein-coding
mm_67611.1	chr7	83884155	83884170	-	1	NA	5' UTR (NM_030705, exon 1 of 1)	5' UTR (NM_030705, exon 1 of 1)	179	NM_030705	80889	Mm.272998	NM_030705	ENSMUSG00000070462	Mesdc1	AW061151	mesoderm development candidate 1	protein-coding
mm_40876.1	chr5	74195282	74195294	+	1	NA	promoter-TSS (NM_026878)	promoter-TSS (NM_026878)	-38	NM_026878	68939	Mm.293316	NM_026878	ENSMUSG00000049907	Rasl11b	1190017B18Rik	RAS-like, family 11, member B	protein-coding
mm_147544.1	chr18	54496577	54496587	-	1	NA	Intergenic	RMER13B|LTR|ERVK	74287	NR_040338	77433	Mm.159919	NR_040338		Redrum	9430076G02Rik	Redrum, erythroid developmental long intergenic non-protein coding transcript	ncRNA
mm_65591.1	chr7	27328306	27328341	-	1	NA	exon (NM_175641, exon 10 of 33)	exon (NM_175641, exon 10 of 33)	5325	NM_001113549	108075	Mm.272251	NM_175641	ENSMUSG00000040488	Ltbp4	2310046A13Rik	latent transforming growth factor beta binding protein 4	protein-coding
mm_77259.1	chr8	115707189	115707272	-	1	NA	promoter-TSS (NM_001025577)	promoter-TSS (NM_001025577)	-336	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_42447.1	chr5	115432021	115432040	+	1	NA	intron (NM_008629, intron 4 of 14)	intron (NM_008629, intron 4 of 14)	2345	NM_008629	17690	Mm.5077	NM_008629	ENSMUSG00000054256	Msi1	Msi1h|Musahi1|m-Msi-1	musashi RNA-binding protein 1	protein-coding
mm_36240.1	chr4	63172051	63172079	-	1	NA	promoter-TSS (NM_010616)	promoter-TSS (NM_010616)	66	NM_010616	16552	Mm.216057	NM_010616	ENSMUSG00000028357	Kif12	-	kinesin family member 12	protein-coding
mm_169186.1	chr13	66027348	66027353	-	1	NA	Intergenic	Intergenic	-86103	NM_001177832	628709	Mm.390595	NM_001177832	ENSMUSG00000095909	Gm10324	ENSMUSG00000071302	predicted gene 10324	protein-coding
mm_31073.1	chr4	41369588	41369590	+	1	NA	intron (NM_023305, intron 2 of 6)	B4A|SINE|B4	20593	NM_023305	67123	Mm.289795	NM_023305	ENSMUSG00000028437	Ubap1	2700092A01Rik|NAG20|UBAP-1|Ubap	ubiquitin-associated protein 1	protein-coding
mm_57938.1	chr6	134792341	134792359	-	1	NA	5' UTR (NM_130447, exon 1 of 7)	5' UTR (NM_130447, exon 1 of 7)	278	NM_130447	70686	Mm.491182	NM_130447	ENSMUSG00000030203	Dusp16	3830417M17Rik|AW558566|D6Ertd213e|MKP-7|MKP7|Mkpm	dual specificity phosphatase 16	protein-coding
mm_156108.1	chrX	114474313	114474353	+	1	NA	promoter-TSS (NM_001290478)	promoter-TSS (NM_001290478)	0	NM_001290478	237010	Mm.132583	NM_172781	ENSMUSG00000025597	Klhl4	B130014A11|C130018J01Rik	kelch-like 4	protein-coding
mm_57471.1	chr6	125231773	125231824	-	1	NA	promoter-TSS (NM_145391)	promoter-TSS (NM_145391)	62	NM_145391	213233	Mm.296902	NM_145391	ENSMUSG00000038213	Tapbpl	BC017613|TAPBPL-R|Tapbplr	TAP binding protein-like	protein-coding
mm_12315.1	chr2	69355615	69355628	+	1	NA	Intergenic	L1Md_F2|LINE|L1	-13005	NM_021022	27413	Mm.439855	NM_021022	ENSMUSG00000027048	Abcb11	ABC16|Bsep|Lith1|PFIC2|PGY4|SPGP	ATP-binding cassette, sub-family B (MDR/TAP), member 11	protein-coding
mm_46996.1	chr5	115341113	115341139	-	1	NA	promoter-TSS (NM_026933)	promoter-TSS (NM_026933)	35	NM_029645	384281	Mm.229308	NM_029645	ENSMUSG00000029536	Gatc	2010003O18Rik	glutamyl-tRNA(Gln) amidotransferase, subunit C	protein-coding
mm_75838.1	chr8	70598425	70598441	-	1	NA	intron (NM_133772, intron 14 of 16)	CpG	3952	NM_023627	71780	Mm.29357	NM_023627	ENSMUSG00000019139	Isyna1	1300017C10Rik|AU018670	myo-inositol 1-phosphate synthase A1	protein-coding
mm_144638.1	chr18	32994975	32994978	+	1	NA	intron (NM_009793, intron 1 of 10)	intron (NM_009793, intron 1 of 10)	55935	NM_009793	12326	Mm.222329	NM_009793	ENSMUSG00000038128	Camk4	A430110E23Rik|AI666733|CaMKIV|CaMKIV/Gr|D18Bwg0362e	calcium/calmodulin-dependent protein kinase IV	protein-coding
mm_427.1	chr1	34472766	34472772	+	1	NA	exon (NM_011206, exon 13 of 15)	exon (NM_011206, exon 13 of 15)	13023	NM_011206	19253	Mm.361	NM_011206	ENSMUSG00000026126	Ptpn18	FLP1|HSCF|PTP-HSCF|PTP-K1|Ptpk1	protein tyrosine phosphatase, non-receptor type 18	protein-coding
mm_142653.1	chr17	47611212	47611244	-	1	NA	promoter-TSS (NM_020048)	promoter-TSS (NM_020048)	264	NM_016859	53414	Mm.472101	NM_016859	ENSMUSG00000023988	Bysl	Bys|Enp1	bystin-like	protein-coding
mm_100351.1	chr11	118428402	118428451	+	1	NA	promoter-TSS (NM_001204129)	promoter-TSS (NM_001204129)	-31	NM_001204129	56745	Mm.23845	NM_019959	ENSMUSG00000017446	C1qtnf1	1600017K21Rik|CTRP1|Zsig37	C1q and tumor necrosis factor related protein 1	protein-coding
mm_60595.1	chr7	44496693	44496704	+	1	NA	promoter-TSS (NM_197991)	promoter-TSS (NM_197991)	110	NM_028169	75538	Mm.258841	NM_028169	ENSMUSG00000051113	Fam71e1	0610007G24Rik|1700021N13Rik|1700021P22Rik|GARI-L5	family with sequence similarity 71, member E1	protein-coding
mm_65018.1	chr7	17655929	17655938	-	1	NA	Intergenic	RMER17A2|LTR|ERVK	-16380	NR_002857	232919	Mm.153893	NR_002857	ENSMUSG00000108558	Psg-ps1	AV036018|Cea-6|Cea6	pregnancy specific glycoprotein pseudogene 1	pseudo
mm_33439.1	chr4	130127677	130127697	+	1	NA	3' UTR (NM_026441, exon 5 of 5)	3' UTR (NM_026441, exon 5 of 5)	10864	NM_001163027	230777	Mm.246595	NM_198959	ENSMUSG00000028778	Hcrtr1	Ox1r|ox-1-R|ox1-R	hypocretin (orexin) receptor 1	protein-coding
mm_26847.1	chr3	14767513	14767522	-	1	NA	exon (NM_001083957, exon 6 of 7)	exon (NM_001083957, exon 6 of 7)	10943	NM_001083957	12346	Mm.273195	NM_009799	ENSMUSG00000027556	Car1	AW555628|Ca1|Car-1	carbonic anhydrase 1	protein-coding
mm_91646.1	chr10	42388328	42388331	-	1	NA	intron (NM_145743, intron 7 of 12)	intron (NM_145743, intron 7 of 12)	90236	NM_145743	215951	Mm.89646	NM_145743	ENSMUSG00000038302	Lace1	CG8520	lactation elevated 1	protein-coding
mm_62886.1	chr7	114846326	114846338	+	1	NA	intron (NM_173767, intron 11 of 12)	intron (NM_173767, intron 11 of 12)	100566	NM_173767	233752	Mm.83037	NM_173767	ENSMUSG00000048782	Insc	3830422K02Rik|C730020D23	inscuteable homolog (Drosophila)	protein-coding
mm_90908.1	chr10	11492002	11492013	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-117217	NM_013898	30058	Mm.214504	NM_013898	ENSMUSG00000048007	Timm8a1	DXHXS1274E|Ddp1|Fci-12|Tim8a|Timm8a	translocase of inner mitochondrial membrane 8A1	protein-coding
mm_6461.1	chr1	74028523	74028528	-	1	NA	intron (NM_027884, intron 3 of 34)	intron (NM_027884, intron 3 of 34)	95922	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_88762.1	chr10	80334005	80334018	+	1	NA	exon (NM_139292, exon 4 of 6)	exon (NM_139292, exon 4 of 6)	3866	NM_139292	70335	Mm.28147	NM_139292	ENSMUSG00000035504	Reep6	0610011M24Rik|Dp1l1	receptor accessory protein 6	protein-coding
mm_46056.1	chr5	92215346	92215354	-	1	NA	promoter-TSS (NR_033483)	promoter-TSS (NR_033483)	58	NR_033483	57425	Mm.2548	NM_020562	ENSMUSG00000029409	U90926	-	cDNA sequence U90926	ncRNA
mm_32694.1	chr4	116015780	116015812	+	1	NA	intron (NM_010173, intron 1 of 14)	intron (NM_010173, intron 1 of 14)	2106	NM_010173	14073	Mm.256025	NM_010173	ENSMUSG00000034171	Faah	AW412498	fatty acid amide hydrolase	protein-coding
mm_14844.1	chr2	148098755	148098759	+	1	NA	Intergenic	Intergenic	-51788	NM_010446	15376	Mm.938	NM_010446	ENSMUSG00000037025	Foxa2	HNF3-beta|HNF3beta|Hnf-3b|Hnf3b|Tcf-3b|Tcf3b	forkhead box A2	protein-coding
mm_158540.1	chrX	143933179	143933196	-	1	NA	promoter-TSS (NM_010025)	promoter-TSS (NM_010025)	32	NM_010025	13193	Mm.12871	NM_010025	ENSMUSG00000031285	Dcx	Dbct	doublecortin	protein-coding
mm_76580.1	chr8	89012451	89012463	-	1	NA	Intergenic	Intergenic	-12278	NR_106190	102465899		NR_106190	ENSMUSG00000099078	Mir8110	Gm27571|mmu-mir-8110	microRNA 8110	ncRNA
mm_45450.1	chr5	67608240	67608262	-	1	NA	5' UTR (NM_001033415, exon 1 of 2)	5' UTR (NM_001033415, exon 1 of 2)	368	NM_001033415	330096	Mm.442747	NM_001033415	ENSMUSG00000050010	Shisa3	D830007B15Rik	shisa family member 3	protein-coding
mm_33765.1	chr4	134397381	134397400	+	1	NA	promoter-TSS (NM_001285872)	promoter-TSS (NM_001285872)	-81	NM_001285872	100163	Mm.22116	NM_133880	ENSMUSG00000037366	Pafah2	2310074E22Rik|AI507170	platelet-activating factor acetylhydrolase 2	protein-coding
mm_57925.1	chr6	134517447	134517450	-	1	NA	intron (NM_008514, intron 3 of 22)	L1M4|LINE|L1	49465	NM_008514	16974	Mm.321990	NM_008514	ENSMUSG00000030201	Lrp6	C030016K15Rik|Cd|Gw|ska26|ska<m26Jus>|skax26	low density lipoprotein receptor-related protein 6	protein-coding
mm_14226.1	chr2	127425156	127425194	+	1	NA	promoter-TSS (NM_001081089)	promoter-TSS (NM_001081089)	-24	NM_001081089	215456	Mm.440454	NM_001081089	ENSMUSG00000046338	Gpat2	A530057A03Rik|Gm116|xGPAT1	glycerol-3-phosphate acyltransferase 2, mitochondrial	protein-coding
mm_104678.1	chr11	97690344	97690358	-	1	NA	exon (NM_009545, exon 13 of 13)	exon (NM_009545, exon 13 of 13)	4399	NM_001085500	217149	Mm.29659	NM_001085500	ENSMUSG00000078695	Cisd3	Mel-13|Mel13	CDGSH iron sulfur domain 3	protein-coding
mm_12849.1	chr2	83644565	83644577	+	1	NA	promoter-TSS (NM_026934)	promoter-TSS (NM_026934)	-7	NM_026934	69082	Mm.27804	NM_026934	ENSMUSG00000027091	Zc3h15	1700006A17Rik|1810012H02Rik|2610312B22Rik|FM22|Ierepo4	zinc finger CCCH-type containing 15	protein-coding
mm_82728.1	chr9	25151666	25151676	-	1	NA	5' UTR (NM_020586, exon 1 of 8)	5' UTR (NM_020586, exon 1 of 8)	110	NM_020586	80517	Mm.142843	NM_020586	ENSMUSG00000008429	Herpud2	5031400M07Rik|AB041580	HERPUD family member 2	protein-coding
mm_88172.1	chr10	69785606	69785637	+	1	NA	intron (NM_170730, intron 1 of 17)	intron (NM_170730, intron 1 of 17)	-139911	NM_170687	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_123870.1	chr14	72589794	72589822	-	1	NA	exon (NM_207636, exon 5 of 26)	exon (NM_207636, exon 5 of 26)	120195	NM_207636	319448	Mm.205421	NM_207636	ENSMUSG00000033487	Fndc3a	1700094E19Rik|D14Ertd453e|F730017H24Rik|Fndc3|sys	fibronectin type III domain containing 3A	protein-coding
mm_165193.1	chr2	32386008	32386014	-	1	NA	exon (NM_008491, exon 3 of 6)	exon (NM_008491, exon 3 of 6)	1728	NM_008491	16819	Mm.9537	NM_008491	ENSMUSG00000026822	Lcn2	24p3|AW212229|NRL|Sip24	lipocalin 2	protein-coding
mm_142583.1	chr17	46726315	46726323	-	1	NA	TTS (NM_145488)	TTS (NM_145488)	2846	NM_010321	14711	Mm.29395	NM_010321	ENSMUSG00000002769	Gnmt	-	glycine N-methyltransferase	protein-coding
mm_102630.1	chr11	62539092	62539131	-	1	NA	exon (NM_028448, exon 1 of 5)	exon (NM_028448, exon 1 of 5)	150	NM_028448	73139	Mm.390409	NM_028448	ENSMUSG00000018509	Cenpv	3110013H01Rik|AA671303|Prr6	centromere protein V	protein-coding
mm_172124.1	chr6	3201354	3201354	+	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	-87165	NR_036696	667335	Mm.380219	NR_036696	ENSMUSG00000106779	Gm8579	EG667335	spermatogenesis associated glutamate (E)-rich protein 4a pseudogene	pseudo
mm_65176.1	chr7	19692452	19692471	-	1	NA	exon (NM_001110009, exon 2 of 4)	exon (NM_001110009, exon 2 of 4)	198	NM_001110009	11812	Mm.182440	NM_007469	ENSMUSG00000040564	Apoc1	Apo-CIB|ApoC-IB|apo-CI|apoC-I	apolipoprotein C-I	protein-coding
mm_27544.1	chr3	57718304	57718320	-	1	NA	Intergenic	Intergenic	-17750	NM_001304456	24017	Mm.274360	NM_011883	ENSMUSG00000036503	Rnf13	2010001H16Rik|Rzf	ring finger protein 13	protein-coding
mm_19496.1	chr2	93453146	93453167	-	1	NA	promoter-TSS (NM_001271462)	promoter-TSS (NM_001271462)	337	NR_040533	100038525	Mm.440596	NR_040532	ENSMUSG00000075025	Gm10804	ENSMUSG00000075025	predicted gene 10804	ncRNA
mm_16582.1	chr2	3649272	3649286	-	1	NA	Intergenic	Intergenic	-64179	NM_025626	66540	Mm.277864	NM_025626	ENSMUSG00000026655	Fam107b	3110001A13Rik|AA589595|AA959793|AI132312	family with sequence similarity 107, member B	protein-coding
mm_154158.1	chr19	58455785	58455795	-	1	NA	promoter-TSS (NM_010279)	promoter-TSS (NM_010279)	-392	NM_010279	14585	Mm.88367	NM_010279	ENSMUSG00000025089	Gfra1	AU042498	glial cell line derived neurotrophic factor family receptor alpha 1	protein-coding
mm_114736.1	chr13	83732368	83732370	+	1	NA	intron (NR_015561, intron 2 of 3)	intron (NR_015561, intron 2 of 3)	4263	NR_015561	320203	Mm.245636	NM_177100	ENSMUSG00000050334	C130071C03Rik	2810449C10Rik	RIKEN cDNA C130071C03 gene	ncRNA
mm_96832.1	chr11	70000780	70000800	+	1	NA	TTS (NM_030064)	TTS (NM_030064)	164	NM_007888	13543	Mm.5114	NM_007888	ENSMUSG00000020888	Dvl2	-	dishevelled segment polarity protein 2	protein-coding
mm_97891.1	chr11	83299064	83299091	+	1	NA	promoter-TSS (NM_134025)	promoter-TSS (NM_134025)	-100	NM_134025	103737	Mm.102205	NM_134025	ENSMUSG00000018733	Pex12	AI451906	peroxisomal biogenesis factor 12	protein-coding
mm_69023.1	chr7	126792357	126792365	-	1	NA	intron (NM_019674, intron 1 of 8)	CpG-13569	110	NM_019674	56420	Mm.41998	NM_019674	ENSMUSG00000030697	Ppp4c	1110002D08Rik|AU016079|Ppx	protein phosphatase 4, catalytic subunit	protein-coding
mm_50818.1	chr6	54429679	54429694	+	1	NA	non-coding (NR_033635, exon 1 of 14)	non-coding (NR_033635, exon 1 of 14)	535	NR_033635	100042056	Mm.448157	NM_198118	ENSMUSG00000073067	9130019P16Rik	6430501H15Rik|OTTMUSG00000023151	RIKEN cDNA 9130019P16 gene	ncRNA
mm_120967.1	chr14	77904520	77904533	+	1	NA	exon (NM_029495, exon 1 of 12)	exon (NM_029495, exon 1 of 12)	287	NM_029495	108670	Mm.68134	NM_029495	ENSMUSG00000022014	Epsti1	2310046K10Rik|5033415K03Rik|BRESI1	epithelial stromal interaction 1 (breast)	protein-coding
mm_82898.1	chr9	32702879	32702894	-	1	NA	intron (NM_011808, intron 1 of 7)	intron (NM_011808, intron 1 of 7)	6844	NM_001038642	23871	Mm.292415	NM_011808	ENSMUSG00000032035	Ets1	AI196000|AI448617|D230050P06|Ets-1|Tpl1|vs	E26 avian leukemia oncogene 1, 5' domain	protein-coding
mm_26574.1	chr3	146630634	146630645	+	1	NA	3' UTR (NM_009474, exon 8 of 8)	3' UTR (NM_009474, exon 8 of 8)	-11293	NR_045949	100286843	Mm.475299	NR_045949	ENSMUSG00000085810	Gm16325	OTTMUSG00000033652	predicted gene 16325	ncRNA
mm_57749.1	chr6	129100905	129100925	-	1	NA	promoter-TSS (NM_153506)	promoter-TSS (NM_153506)	-12	NM_153506	232409	Mm.30870	NM_153506	ENSMUSG00000030155	Clec2e	Clra|clr-a	C-type lectin domain family 2, member e	protein-coding
mm_95289.1	chr11	45980256	45980273	+	1	NA	promoter-TSS (NM_173384)	promoter-TSS (NM_173384)	-46	NM_173384	214105	Mm.66708	NM_173384	ENSMUSG00000040489	Sox30	-	SRY (sex determining region Y)-box 30	protein-coding
mm_113468.1	chr13	36263151	36263153	+	1	NA	intron (NM_001039189, intron 3 of 5)	intron (NM_001039189, intron 3 of 5)	145509	NM_001039189	69955	Mm.70690	NM_024274	ENSMUSG00000021420	Fars2	Fars1|pheRS	phenylalanine-tRNA synthetase 2 (mitochondrial)	protein-coding
mm_46146.1	chr5	93205715	93205718	-	1	NA	promoter-TSS (NM_029363)	promoter-TSS (NM_029363)	779	NM_017367	12453	Mm.250419	NM_017367	ENSMUSG00000063015	Ccni	-	cyclin I	protein-coding
mm_144172.1	chr18	6733734	6733749	+	1	NA	Intergenic	Intergenic	-31426	NM_181070	19330	Mm.132802	NM_181070	ENSMUSG00000073639	Rab18	AA959686	RAB18, member RAS oncogene family	protein-coding
mm_68074.1	chr7	101869235	101869256	-	1	NA	5' UTR (NM_008034, exon 2 of 7)	5' UTR (NM_008034, exon 2 of 7)	1543	NM_001252554	14275	Mm.2135	NM_008034	ENSMUSG00000001827	Folr1	FBP1|Folbp-1|Folbp1	folate receptor 1 (adult)	protein-coding
mm_171116.1	chr3	138396939	138396952	+	1	NA	Intergenic	L1Md_Gf|LINE|L1	-18552	NM_011996	26876	Mm.158750	NM_011996	ENSMUSG00000037797	Adh4	Adh2	alcohol dehydrogenase 4 (class II), pi polypeptide	protein-coding
mm_60252.1	chr7	43781060	43781078	+	1	NA	promoter-TSS (NM_133712)	promoter-TSS (NM_133712)	15	NM_133712	69540	Mm.46421	NM_133712	ENSMUSG00000030693	Klk10	2300002A13Rik|NES1|PRSSL1	kallikrein related-peptidase 10	protein-coding
mm_12516.1	chr2	72054974	72054996	+	1	NA	5' UTR (NM_001204166, exon 1 of 28)	5' UTR (NM_001204166, exon 1 of 28)	368	NM_001204166	56508	Mm.196153	NM_019688	ENSMUSG00000049044	Rapgef4	1300003D15Rik|5730402K07Rik|6330581N18Rik|EPAC 2|Epac-2|Epac2|mKIAA4040	Rap guanine nucleotide exchange factor (GEF) 4	protein-coding
mm_82623.1	chr9	21804403	21804415	-	1	NA	intron (NM_177030, intron 43 of 49)	intron (NM_177030, intron 43 of 49)	5591	NR_106051	102465657		NR_106051	ENSMUSG00000098473	Mir7083	Gm27888|mmu-mir-7083	microRNA 7083	ncRNA
mm_154428.1	chrM	531	533	-	1	NA	NA	Intergenic	NA	NA								
mm_23861.1	chr3	83012769	83012775	+	1	NA	exon (NM_133862, exon 8 of 10)	exon (NM_133862, exon 8 of 10)	5048	NM_001317105	99571	Mm.16422	NM_133862	ENSMUSG00000033860	Fgg	3010002H13Rik|AI256424	fibrinogen gamma chain	protein-coding
mm_120847.1	chr14	75202660	75202694	+	1	NA	exon (NM_001247984, exon 5 of 16)	exon (NM_001247984, exon 5 of 16)	-39610	NM_019775	56373	Mm.24242	NM_019775	ENSMUSG00000021999	Cpb2	1110032P04Rik|4930405E17Rik|AI255929|CPR|Cpu|TAFI	carboxypeptidase B2 (plasma)	protein-coding
mm_95618.1	chr11	53519969	53519977	+	1	NA	5' UTR (NM_001252332, exon 1 of 10)	5' UTR (NM_001252332, exon 1 of 10)	237	NM_001347496	20362	Mm.274399	NM_033144	ENSMUSG00000018398	Sept8	AW046166|Sepl	septin 8	protein-coding
mm_147316.1	chr18	41999044	41999055	-	1	NA	promoter-TSS (NM_001033426)	promoter-TSS (NM_001033426)	0	NM_001033426	332309	Mm.240520	NM_001033426	ENSMUSG00000073574	Grxcr2	Gm851	glutaredoxin, cysteine rich 2	protein-coding
mm_58686.1	chr7	12834974	12835052	+	1	NA	5' UTR (NM_022981, exon 1 of 8)	5' UTR (NM_022981, exon 1 of 8)	203	NM_022981	65020	Mm.292297	NM_022981	ENSMUSG00000058638	Zfp110	2900024E01Rik|N28112|NRIF|Nrif1	zinc finger protein 110	protein-coding
mm_79328.1	chr9	53321746	53321752	+	1	NA	intron (NM_176846, intron 1 of 5)	intron (NM_176846, intron 1 of 5)	20079	NM_176846	320051	Mm.277540	NM_176846	ENSMUSG00000034584	Exph5	AC079869.22gm5|B130009M24Rik|E030050P12|Kiaa0624|Slac2b|slac2-b	exophilin 5	protein-coding
mm_153139.1	chr19	34246150	34246154	-	1	NA	exon (NM_007392, exon 6 of 9)	exon (NM_007392, exon 6 of 9)	9221	NM_007392	11475	Mm.213025	NM_007392	ENSMUSG00000035783	Acta2	0610041G09Rik|Actvs|SMalphaA|a-SMA|alphaSMA	actin, alpha 2, smooth muscle, aorta	protein-coding
mm_57029.1	chr6	122283230	122283242	-	1	NA	promoter-TSS (NM_016970)	promoter-TSS (NM_016970)	-403	NM_016970	50928	Mm.20434	NM_016970	ENSMUSG00000030114	Klrg1	2F1-Ag|MAFA|MAFA-L	killer cell lectin-like receptor subfamily G, member 1	protein-coding
mm_143840.1	chr17	84126000	84126040	-	1	NA	Intergenic	Intergenic	47360	NR_045458	74473	Mm.399575	NR_045458		4933433H22Rik	-	RIKEN cDNA 4933433H22 gene	ncRNA
mm_10242.1	chr2	8946946	8946954	+	1	NA	Intergenic	Intergenic	-242565	NR_038180	73438	Mm.23558	NR_038180	ENSMUSG00000085580	1700061F12Rik	-	RIKEN cDNA 1700061F12 gene	ncRNA
mm_103645.1	chr11	78966043	78966058	-	1	NA	exon (NM_010708, exon 9 of 11)	exon (NM_010708, exon 9 of 11)	18874	NM_001159301	16859	Mm.341434	NM_010708	ENSMUSG00000001123	Lgals9	AA407335|AI194909|AI265545|LGALS35|Lgals5|gal-9|galectin-9	lectin, galactose binding, soluble 9	protein-coding
mm_54474.1	chr6	34910824	34910863	-	1	NA	promoter-TSS (NM_001013366)	promoter-TSS (NM_001013366)	-12	NM_001013366	101240	Mm.152120	NM_001013366	ENSMUSG00000058486	Wdr91	9530020G05Rik|AI987683|AU018665	WD repeat domain 91	protein-coding
mm_16950.1	chr2	17202089	17202092	-	1	NA	Intergenic	RMER1C|Other|Other	-188364	NR_040632	75069	Mm.50378	NR_040632		4930515L03Rik	-	RIKEN cDNA 4930515L03 gene	ncRNA
mm_114523.1	chr13	73330983	73331057	+	1	NA	promoter-TSS (NM_053163)	promoter-TSS (NM_053163)	11	NM_053163	94066	Mm.26775	NM_053163	ENSMUSG00000021607	Mrpl36	AI646041	mitochondrial ribosomal protein L36	protein-coding
mm_110072.1	chr12	21417357	21417377	-	1	NA	promoter-TSS (NM_011739)	promoter-TSS (NM_011739)	69	NM_011739	22630	Mm.289630	NM_011739	ENSMUSG00000076432	Ywhaq	2700028P07Rik|AA409740|AU021156|R74690	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide	protein-coding
mm_60733.1	chr7	45434877	45434889	+	1	NA	promoter-TSS (NM_030678)	promoter-TSS (NM_030678)	44	NM_030678	14936	Mm.275654	NM_030678	ENSMUSG00000003865	Gys1	Gys3|MGS	glycogen synthase 1, muscle	protein-coding
mm_77507.1	chr8	122752184	122752207	-	1	NA	Intergenic	Intergenic	-23291	NM_144932	257633	Mm.334875	NM_144932	ENSMUSG00000015016	Acsf3	BB101783	acyl-CoA synthetase family member 3	protein-coding
mm_118324.1	chr13	113617634	113617644	-	1	NA	exon (NM_130796, exon 1 of 2)	exon (NM_130796, exon 1 of 2)	925	NM_130796	170625	Mm.33721	NM_130796	ENSMUSG00000042364	Snx18	Snag1	sorting nexin 18	protein-coding
mm_80997.1	chr9	103423567	103423579	+	1	NA	promoter-TSS (NR_040466)	promoter-TSS (NR_040466)	-5	NR_040466	100529079	Mm.437003	NR_040466	ENSMUSG00000086236	5830418P13Rik	-	RIKEN cDNA 5830418P13 gene	ncRNA
mm_152748.1	chr19	19110940	19110950	-	1	NA	5' UTR (NM_001043354, exon 1 of 10)	5' UTR (NM_001043354, exon 1 of 10)	251	NM_001043354	225998	Mm.234641	NM_146095	ENSMUSG00000036192	Rorb	Nr1f2|RZR-beta|RZRB|Rorbeta|hstp	RAR-related orphan receptor beta	protein-coding
mm_112808.1	chr13	20794129	20794179	+	1	NA	promoter-TSS (NM_001281854)	promoter-TSS (NM_001281854)	41	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_42605.1	chr5	117781018	117781075	+	1	NA	Intergenic	Intergenic	-85793	NM_008712	18125	Mm.44249	NM_008712	ENSMUSG00000029361	Nos1	2310005C01Rik|N-NOS|NC-NOS|NO|NOS|NOS-I|Nos-1|bNOS|nNOS	nitric oxide synthase 1, neuronal	protein-coding
mm_45571.1	chr5	73338581	73338640	-	1	NA	5' UTR (NM_001310636, exon 1 of 6)	5' UTR (NM_001310636, exon 1 of 6)	337	NM_026950	433904	Mm.274892	NM_026950	ENSMUSG00000029153	Ociad2	1810027I20Rik	OCIA domain containing 2	protein-coding
mm_91328.1	chr10	25220860	25220908	-	1	NA	intron (NM_018747, intron 6 of 7)	intron (NM_018747, intron 6 of 7)	-20714	NM_001347460	432442	Mm.485937	NM_018747	ENSMUSG00000039166	Akap7	6430401D08|AI662165|AKAP15|Akap18|BB170514	A kinase (PRKA) anchor protein 7	protein-coding
mm_42052.1	chr5	108630029	108630050	+	1	NA	promoter-TSS (NM_153569)	promoter-TSS (NM_153569)	229	NM_028223	72392	Mm.258324	NM_028223	ENSMUSG00000013495	Tmem175	3010001K23Rik|AI504381|mTMEM175	transmembrane protein 175	protein-coding
mm_56244.1	chr6	90731453	90731464	-	1	NA	intron (NM_001134384, intron 1 of 13)	intron (NM_001134384, intron 1 of 13)	-14929	NM_001134383	232227	Mm.196943	NM_182784	ENSMUSG00000034312	Iqsec1	AW561907|BC026481|BRAG2|D6Ertd349e|cI-43	IQ motif and Sec7 domain 1	protein-coding
mm_39099.1	chr4	154919914	154919948	-	1	NA	Intergenic	L1_Mus2|LINE|L1	8146	NM_178931	230979	Mm.215147	NM_178931	ENSMUSG00000042333	Tnfrsf14	Atar|HveA|Hvem|Tnfrs14	tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)	protein-coding
mm_21526.1	chr2	163643304	163643307	-	1	NA	intron (NM_012032, intron 1 of 9)	intron (NM_012032, intron 1 of 9)	-1545	NR_028113	68386	Mm.410649	NR_028113	ENSMUSG00000058812	0610039K10Rik	-	RIKEN cDNA 0610039K10 gene	ncRNA
mm_109870.1	chr12	4916134	4916140	-	1	NA	Intergenic	Intergenic	-1216	NM_001099628	320817	Mm.210966	NM_001099628	ENSMUSG00000052812	Atad2b	1110014E10Rik|BC032887|C79189|D530031C13Rik	ATPase family, AAA domain containing 2B	protein-coding
mm_109817.1	chr12	3646391	3646400	-	1	NA	intron (NR_027869, intron 7 of 20)	intron (NR_027869, intron 7 of 20)	73354	NM_007886	13528	Mm.286202	NM_007886	ENSMUSG00000071454	Dtnb	-	dystrobrevin, beta	protein-coding
mm_131273.1	chr16	11008936	11008946	+	1	NA	promoter-TSS (NR_040518)	promoter-TSS (NR_040518)	43	NR_040518	100043147	Mm.489001	NR_040518	ENSMUSG00000097056	Gm4262	-	predicted gene 4262	ncRNA
mm_22643.1	chr3	14864288	14864341	+	1	NA	exon (NM_007606, exon 2 of 7)	exon (NM_007606, exon 2 of 7)	776	NM_007606	12350	Mm.300	NM_007606	ENSMUSG00000027559	Car3	BB219044|Ca3|Car-3	carbonic anhydrase 3	protein-coding
mm_86819.1	chr10	20952494	20952504	+	1	NA	promoter-TSS (NM_026203)	promoter-TSS (NM_026203)	-48	NM_026203	52906	Mm.253280	NM_026203	ENSMUSG00000019986	Ahi1	1700015F03Rik|Ahi-1|D10Bwg0629e	Abelson helper integration site 1	protein-coding
mm_102824.1	chr11	69059455	69059501	-	1	NA	promoter-TSS (NM_028005)	promoter-TSS (NM_028005)	-297	NM_028005	71923	Mm.340257	NM_028005	ENSMUSG00000045176	Borcs6	2310047M10Rik	BLOC-1 related complex subunit 6	protein-coding
mm_161380.1	chr14	70554148	70554148	+	1	NA	promoter-TSS (NM_021877)	promoter-TSS (NM_021877)	92	NM_021877	15460	Mm.7598	NM_021877	ENSMUSG00000022096	Hr	ALUNC|AU|N|ba|bldy|hr|rh|rh-bmh|rhino	hairless	protein-coding
mm_50732.1	chr6	52570441	52570442	+	1	NA	intron (NM_145567, intron 4 of 7)	intron (NM_145567, intron 4 of 7)	69859	NM_145567	58875	Mm.286458	NM_145567	ENSMUSG00000029776	Hibadh	6430402H10Rik|AI265272	3-hydroxyisobutyrate dehydrogenase	protein-coding
mm_98349.1	chr11	93378501	93378505	+	1	NA	intron (NM_028296, intron 3 of 8)	L1MA5A|LINE|L1	279213	NM_028296	72605	Mm.342160	NM_028296	ENSMUSG00000056158	Car10	2700029L05Rik|BB085816|Ca10	carbonic anhydrase 10	protein-coding
mm_145804.1	chr18	65382075	65382098	+	1	NA	intron (NM_001037294, intron 1 of 12)	intron (NM_001037294, intron 1 of 12)	11802	NM_001037294	225638	Mm.296528	NM_001037294	ENSMUSG00000032845	Alpk2	Gm549|Hak	alpha-kinase 2	protein-coding
mm_100330.1	chr11	118244231	118244244	+	1	NA	intron (NM_001112699, intron 1 of 12)	intron (NM_001112699, intron 1 of 12)	4355	NM_001112699	19157	Mm.86413	NM_011180	ENSMUSG00000017132	Cyth1	CLM1|CTH-1|CYTIP|Pscd1	cytohesin 1	protein-coding
mm_13984.1	chr2	121509820	121509846	+	1	NA	intron (NM_001290987, intron 1 of 11)	intron (NM_001290987, intron 1 of 11)	3110	NM_001290986	241627	Mm.293284	NM_030234	ENSMUSG00000027242	Wdr76	5830411K18Rik|6030457D09|AA517836	WD repeat domain 76	protein-coding
mm_8810.1	chr1	161876835	161876854	-	1	NA	promoter-TSS (NM_172645)	promoter-TSS (NM_172645)	-183	NM_172645	226551	Mm.170002	NM_172645	ENSMUSG00000040297	Suco	4732491B11|AI848100|AU016931|Opt	SUN domain containing ossification factor	protein-coding
mm_101105.1	chr11	11932254	11932264	-	1	NA	3' UTR (NM_010345, exon 17 of 17)	3' UTR (NM_010345, exon 17 of 17)	-34115	NM_001190448	13195	Mm.12906	NM_016672	ENSMUSG00000020182	Ddc	Aadc	dopa decarboxylase	protein-coding
mm_71138.1	chr8	39045976	39045992	+	1	NA	intron (NM_030254, intron 1 of 7)	intron (NM_030254, intron 1 of 7)	40117	NM_030254	80286	Mm.272722	NM_030254	ENSMUSG00000039530	Tusc3	AU022242|BC003311|N33	tumor suppressor candidate 3	protein-coding
mm_11981.1	chr2	55292969	55292987	+	1	NA	Intergenic	Intergenic	-142992	NM_001304810	16519	Mm.5127	NM_008426	ENSMUSG00000026824	Kcnj3	GIRK-1|GIRK1|Kcnf3|Kir3.1	potassium inwardly-rectifying channel, subfamily J, member 3	protein-coding
mm_164762.1	chr17	85618564	85618568	-	1	NA	promoter-TSS (NR_015387)	promoter-TSS (NR_015387)	-170	NR_038082	100043902	Mm.150838	NR_015385	ENSMUSG00000093460	Six3os1	D17Mgi26|E130112H22Rik|Rncr1|Six3os	SIX homeobox 3, opposite strand 1	ncRNA
mm_134467.1	chr16	18426591	18426601	-	1	NA	5' UTR (NM_001111062, exon 1 of 6)	5' UTR (NM_001111062, exon 1 of 6)	120	NM_007744	12846	Mm.100940	NM_007744	ENSMUSG00000000326	Comt	Comt1|D16Wsu103e|D330014B15Rik	catechol-O-methyltransferase	protein-coding
mm_83828.1	chr9	54068347	54068416	-	1	NA	promoter-TSS (NM_001033535)	promoter-TSS (NM_001033535)	30	NM_001033535	244882	Mm.325589	NM_001033535	ENSMUSG00000074345	Tnfaip8l3	9930029P06Rik|Gm517	tumor necrosis factor, alpha-induced protein 8-like 3	protein-coding
mm_45588.1	chr5	74262711	74262722	-	1	NA	intron (NM_001286437, intron 5 of 7)	intron (NM_001286437, intron 5 of 7)	67390	NM_026878	68939	Mm.293316	NM_026878	ENSMUSG00000049907	Rasl11b	1190017B18Rik	RAS-like, family 11, member B	protein-coding
mm_109738.1	chr12	117154157	117154166	+	1	NA	intron (NM_011215, intron 12 of 22)	CpG	-2892	NR_033538	100038689	Mm.445351	NR_033538	ENSMUSG00000099907	Gm10421	ENSMUSG00000072792	predicted gene 10421	ncRNA
mm_5598.1	chr1	39564044	39564051	-	1	NA	intron (NM_001033135, intron 3 of 6)	intron (NM_001033135, intron 3 of 6)	13300	NM_001033135	67702	Mm.28614	NM_001033135	ENSMUSG00000048234	Rnf149	1600023E10Rik|AV037261|C76763|Gm15832|Greul4|OTTMUSG00000026591	ring finger protein 149	protein-coding
mm_79546.1	chr9	57911140	57911150	+	1	NA	intron (NM_001122873, intron 1 of 10)	intron (NM_001122873, intron 1 of 10)	159	NM_001122873	69459	Mm.41735	NM_027086	ENSMUSG00000055720	Ubl7	2300004C15Rik	ubiquitin-like 7 (bone marrow stromal cell-derived)	protein-coding
mm_62432.1	chr7	101361980	101361988	+	1	NA	intron (NM_001040111, intron 1 of 33)	intron (NM_001040111, intron 1 of 33)	13915	NM_001040111	69710	Mm.277687	NM_027180	ENSMUSG00000032812	Arap1	2410002L19Rik|Centd2|mKIAA0782	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	protein-coding
mm_93724.1	chr10	119239980	119239994	-	1	NA	promoter-TSS (NM_027994)	promoter-TSS (NM_027994)	68	NM_027994	71902	Mm.203965	NM_027994	ENSMUSG00000020114	Cand1	2310038O07Rik|6330512O03Rik|AI195005|AI846556|D10Ertd516e|Tp120a|mKIAA0829	cullin associated and neddylation disassociated 1	protein-coding
mm_162101.1	chrX	37831593	37831593	+	1	NA	promoter-TSS (NM_001025086)	promoter-TSS (NM_001025086)	-93	NM_001025086	547168	Mm.391251	NM_001025086	ENSMUSG00000071767	Rhox7a	Gm712|Rhox7	reproductive homeobox 7A	protein-coding
mm_19683.1	chr2	103454726	103454734	-	1	NA	3' UTR (NM_009804, exon 13 of 13)	3' UTR (NM_009804, exon 13 of 13)	30423	NM_009804	12359	Mm.4215	NM_009804	ENSMUSG00000027187	Cat	2210418N07|Cas-1|Cas1|Cs-1	catalase	protein-coding
mm_26107.1	chr3	137341180	137341190	+	1	NA	5' UTR (NM_016885, exon 1 of 11)	5' UTR (NM_016885, exon 1 of 11)	107	NM_016885	59308	Mm.27343	NM_016885	ENSMUSG00000054690	Emcn	0610012K22Rik|AI315669|Muc14	endomucin	protein-coding
mm_105578.1	chr11	106613371	106613384	-	1	NA	promoter-TSS (NM_198292)	promoter-TSS (NM_198292)	-447	NM_198292	21763	Mm.102407	NM_198292	ENSMUSG00000040548	Tex2	4930568E07Rik|AI553404|Def-5|Taz4	testis expressed gene 2	protein-coding
mm_142064.1	chr17	35673739	35673750	-	1	NA	promoter-TSS (NM_010364)	promoter-TSS (NM_010364)	-1	NM_010364	14885	Mm.10182	NM_010364	ENSMUSG00000001524	Gtf2h4	AW545633|BTF2 p52|p52	general transcription factor II H, polypeptide 4	protein-coding
mm_135152.1	chr16	35857809	35857823	-	1	NA	exon (NM_001039530, exon 6 of 17)	exon (NM_001039530, exon 6 of 17)	13566	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_166059.1	chr4	133378758	133378761	+	1	NA	intron (NM_016981, intron 1 of 11)	intron (NM_016981, intron 1 of 11)	8983	NR_039582	100628620		NR_039582	ENSMUSG00000092745	Mir5122	mmu-mir-5122|mu-mir-5122	microRNA 5122	ncRNA
mm_155469.1	chrX	73639415	73639436	+	1	NA	promoter-TSS (NM_029352)	promoter-TSS (NM_029352)	-16	NM_029352	75590	Mm.16479	NM_029352	ENSMUSG00000031383	Dusp9	Dusp4|Mpk4|Pyst3	dual specificity phosphatase 9	protein-coding
mm_49062.1	chr6	5390440	5390452	+	1	NA	intron (NM_023048, intron 1 of 5)	intron (NM_023048, intron 1 of 5)	7060	NM_023048	65255	Mm.51340	NM_023048	ENSMUSG00000042607	Asb4	8430401O13Rik|AV117194|AW060255	ankyrin repeat and SOCS box-containing 4	protein-coding
mm_190.1	chr1	15803239	15803249	+	1	NA	Intergenic	RLTR11D|LTR|ERVK	-2402	NM_009352	21749	Mm.4306	NM_009352	ENSMUSG00000025925	Terf1	Pin2|Trbf1|Trf1	telomeric repeat binding factor 1	protein-coding
mm_137926.1	chr17	32521732	32521735	+	1	NA	intron (NM_001101445, intron 5 of 12)	RMER6BA|LTR|ERVK	-14896	NM_024442	70101	Mm.30504	NM_024442	ENSMUSG00000048440	Cyp4f16	2310021J05Rik|AI746515	cytochrome P450, family 4, subfamily f, polypeptide 16	protein-coding
mm_19493.1	chr2	93424671	93424676	-	1	NA	intron (NM_001136055, intron 6 of 9)	intron (NM_001136055, intron 6 of 9)	-2666	NR_105967	102465605		NR_105967	ENSMUSG00000099238	Mir7001	Gm27886|mmu-mir-7001	microRNA 7001	ncRNA
mm_156879.1	chrX	166238902	166238914	+	1	NA	promoter-TSS (NM_001177961)	promoter-TSS (NM_001177961)	-35	NM_001177961	14758	Mm.222320	NM_023122	ENSMUSG00000031342	Gpm6b	AI593561|Gpm6|M6B	glycoprotein m6b	protein-coding
mm_28942.1	chr3	98893210	98893245	-	1	NA	promoter-TSS (NM_019545)	promoter-TSS (NM_019545)	3	NM_019545	56185	Mm.281874	NM_019545	ENSMUSG00000027870	Hao2	AI325478|Hao-2|Hao3|Haox3	hydroxyacid oxidase 2	protein-coding
mm_136980.1	chr17	16889255	16889263	+	1	NA	Intergenic	Intergenic	-174844	NM_001005358	449000	Mm.483718	NM_001005358	ENSMUSG00000096696	Zfp960	-	zinc finger protein 960	protein-coding
mm_144514.1	chr18	24709475	24709502	+	1	NA	5' UTR (NM_001289655, exon 1 of 26)	5' UTR (NM_001289655, exon 1 of 26)	865	NM_001289655	225288	Mm.329322	NM_175276	ENSMUSG00000034295	Fhod3	A930009H06Rik|FHOS2|mKIAA1695	formin homology 2 domain containing 3	protein-coding
mm_103032.1	chr11	69735389	69735399	-	1	NA	exon (NM_001291068, exon 29 of 29)	exon (NM_001291068, exon 29 of 29)	23239	NM_001291068	20020	Mm.16533	NM_009089	ENSMUSG00000005198	Polr2a	220kDa|Rpb1|Rpo2-1	polymerase (RNA) II (DNA directed) polypeptide A	protein-coding
mm_63827.1	chr7	134852986	134852999	+	1	NA	intron (NM_001033420, intron 25 of 51)	MTE2b|LTR|ERVL-MaLR	85438	NM_001143802	627214	Mm.323610	NM_001143802	ENSMUSG00000073805	Fam196a	B830028B13Rik	family with sequence similarity 196, member A	protein-coding
mm_98609.1	chr11	95842335	95842345	+	1	NA	promoter-TSS (NM_001284397)	promoter-TSS (NM_001284397)	45	NM_001284393	14710	Mm.46299	NM_023121	ENSMUSG00000038811	Gngt2	AV096488	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 2	protein-coding
mm_114509.1	chr13	71104801	71104807	+	1	NA	Intergenic	Intergenic	-2285	NR_130325	100316804		NR_130325	ENSMUSG00000080580	Mir466f-4	Mirn466f-4|mmu-mir-466f-4	microRNA 466f-4	ncRNA
mm_160951.1	chr11	97352066	97352066	-	1	NA	promoter-TSS (NM_001081220)	promoter-TSS (NM_001081220)	7	NM_001081220	217143	Mm.32622	NM_175453	ENSMUSG00000070337	Gpr179	5330439C02Rik|Gpr158l1	G protein-coupled receptor 179	protein-coding
mm_51687.1	chr6	86525423	86525448	+	1	NA	exon (NM_011865, exon 1 of 1)	exon (NM_011865, exon 1 of 1)	730	NM_011865	23983	Mm.274146	NM_011865	ENSMUSG00000051695	Pcbp1	WBP17|[a]CP-1|alphaCP-1|hnRNP E1	poly(rC) binding protein 1	protein-coding
mm_15747.1	chr2	164237524	164237528	+	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	815	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_34997.1	chr4	156110014	156110053	+	1	NA	promoter-TSS (NM_145557)	promoter-TSS (NM_145557)	35	NM_177205	230996	Mm.318925	NM_145557	ENSMUSG00000059939	9430015G10Rik	-	RIKEN cDNA 9430015G10 gene	protein-coding
mm_25004.1	chr3	97651973	97652046	+	1	NA	3' UTR (NM_001161763, exon 9 of 9)	3' UTR (NM_001161763, exon 9 of 9)	-6203	NM_182997	108097	Mm.31175	NM_182997	ENSMUSG00000038205	Prkab2	5730553K21Rik|AW049591|BB124140	protein kinase, AMP-activated, beta 2 non-catalytic subunit	protein-coding
mm_3427.1	chr1	150099737	150099757	+	1	NA	promoter-TSS (NM_011198)	promoter-TSS (NM_011198)	127	NR_015466	320019	Mm.353072	NR_015466	ENSMUSG00000097028	Ptgs2os	7530420F21Rik	prostaglandin-endoperoxide synthase 2, opposite strand	ncRNA
mm_40303.1	chr5	43711569	43711574	+	1	NA	intron (NM_172274, intron 21 of 39)	intron (NM_172274, intron 21 of 39)	49192	NM_172274	231214	Mm.44434	NM_172274	ENSMUSG00000039765	Cc2d2a	5730509K17Rik|b2b1035Clo	coiled-coil and C2 domain containing 2A	protein-coding
mm_62574.1	chr7	104314988	104315011	+	1	NA	promoter-TSS (NR_040749)	promoter-TSS (NR_040749)	-32	NR_040749	622070	Mm.486406	NR_040749	ENSMUSG00000087175	Gm15133	OTTMUSG00000019186	predicted gene 15133	ncRNA
mm_80064.1	chr9	69454085	69454116	+	1	NA	intron (NM_007585, intron 1 of 12)	CpG	417	NM_007585	12306	Mm.238343	NM_007585	ENSMUSG00000032231	Anxa2	AW215814|Cal1h	annexin A2	protein-coding
mm_37463.1	chr4	123473133	123473157	-	1	NA	exon (NM_001199136, exon 36 of 98)	exon (NM_001199136, exon 36 of 98)	-61234	NM_001167918	442834	Mm.483803	NM_001167918		D830031N03Rik	Kiaa0754|mKIAA0754	RIKEN cDNA D830031N03 gene	protein-coding
mm_24466.1	chr3	90654163	90654182	+	1	NA	promoter-TSS (NM_199422)	promoter-TSS (NM_199422)	-130	NM_199422	381493	Mm.291525	NM_199422	ENSMUSG00000063767	S100a7a	AY465109|Gm1020|S100A7L1|S100A7f|S100a15|S100a15a|S100a17l1	S100 calcium binding protein A7A	protein-coding
mm_82531.1	chr9	20726966	20726984	-	1	NA	intron (NM_173777, intron 1 of 5)	CpG	1239	NM_173777	244723	Mm.293552	NM_173777	ENSMUSG00000032172	Olfm2	A030009A06Rik	olfactomedin 2	protein-coding
mm_145292.1	chr18	53250931	53250934	+	1	NA	intron (NM_029394, intron 1 of 6)	intron (NM_029394, intron 1 of 6)	5270	NM_029394	69226	Mm.32414	NM_029394	ENSMUSG00000024535	Snx24	2810011K15Rik|5730433I16Rik|AI451341	sorting nexing 24	protein-coding
mm_73614.1	chr8	110117626	110117628	+	1	NA	Intergenic	Intergenic	37893	NM_175480	234725	Mm.87487	NM_175480	ENSMUSG00000044676	Zfp612	B230354B21Rik	zinc finger protein 612	protein-coding
mm_102538.1	chr11	61267075	61267086	-	1	NA	5' UTR (NM_007437, exon 1 of 10)	5' UTR (NM_007437, exon 1 of 10)	106	NM_001331114	11671	Mm.398221	NM_007437	ENSMUSG00000010025	Aldh3a2	AI194803|Ahd-3|Ahd-3r|Ahd3|Ahd3-r|Aldh4|Aldh4-r|FALDH	aldehyde dehydrogenase family 3, subfamily A2	protein-coding
mm_157473.1	chrX	48034843	48034858	-	1	NA	promoter-TSS (NM_013912)	promoter-TSS (NM_013912)	3	NM_013912	30878	Mm.29262	NM_013912	ENSMUSG00000037010	Apln	6030430G11Rik|Apel	apelin	protein-coding
mm_34432.1	chr4	145864066	145864098	+	1	NA	Intergenic	Intergenic	26863	NR_033612	236069	Mm.276881	NR_033612	ENSMUSG00000096233	Gm13238	OTTMUSG00000011065	carnitine deficiency-associated gene expressed in ventricle 3 pseudogene	pseudo
mm_105003.1	chr11	100374368	100374385	-	1	NA	exon (NM_010593, exon 10 of 14)	exon (NM_010593, exon 10 of 14)	-18235	NM_010404	15114	Mm.281700	NM_010404	ENSMUSG00000006930	Hap1	HAP-1	huntingtin-associated protein 1	protein-coding
mm_90141.1	chr10	118098250	118098251	+	1	NA	Intergenic	Intergenic	-43537	NM_001162904	17245	Mm.101191	NM_010785	ENSMUSG00000020212	Mdm1	Arrd2|Mdm-1	transformed mouse 3T3 cell double minute 1	protein-coding
mm_83792.1	chr9	52172658	52172685	-	1	NA	Intergenic	Intergenic	-4560	NM_001162921	244871	Mm.295686	NM_001162921	ENSMUSG00000035164	Zc3h12c	A230108E06|C230027N18Rik|mKIAA1726	zinc finger CCCH type containing 12C	protein-coding
mm_133185.1	chr16	72663117	72663127	+	1	NA	promoter-TSS (NM_019413)	promoter-TSS (NM_019413)	-27	NM_019413	19876	Mm.310772	NM_019413	ENSMUSG00000022883	Robo1	AW494633|AW742721|DUTT1|Gm310	roundabout guidance receptor 1	protein-coding
mm_135548.1	chr16	49801641	49801672	-	1	NA	Intergenic	Intergenic	-53998	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_168205.1	chr10	70378667	70378668	+	1	NA	Intergenic	Intergenic	-62001	NM_001143777	71721	Mm.477813	NM_024244	ENSMUSG00000043259	Fam13c	1200015N20Rik|C030038O19Rik|mKIAA1796	family with sequence similarity 13, member C	protein-coding
mm_44730.1	chr5	31048237	31048276	-	1	NA	promoter-TSS (NM_177870)	promoter-TSS (NM_177870)	-177	NM_177870	330064	Mm.205463	NM_177870	ENSMUSG00000006641	Slc5a6	E430023I20	solute carrier family 5 (sodium-dependent vitamin transporter), member 6	protein-coding
mm_153348.1	chr19	39741000	39741028	-	1	NA	promoter-TSS (NM_001039555)	promoter-TSS (NM_001039555)	87	NM_001039555	433247	Mm.335660	NM_001039555	ENSMUSG00000074882	Cyp2c68	9030012A22Rik	cytochrome P450, family 2, subfamily c, polypeptide 68	protein-coding
mm_140591.1	chr17	10244920	10244920	-	1	NA	intron (NM_021881, intron 3 of 6)	intron (NM_021881, intron 3 of 6)	74441	NM_021881	19317	Mm.130694	NM_021881	ENSMUSG00000062078	Qk	1110003F05Rik|1500005P18|QkI|l(17)-1Wis|l17Wis1	quaking	protein-coding
mm_81466.1	chr9	109875602	109875614	+	1	NA	promoter-TSS (NM_007658)	promoter-TSS (NM_007658)	29	NM_007658	12530	Mm.307103	NM_007658	ENSMUSG00000032477	Cdc25a	D9Ertd393e	cell division cycle 25A	protein-coding
mm_122883.1	chr14	54944741	54944774	-	1	NA	exon (NM_010856, exon 35 of 39)	exon (NM_010856, exon 35 of 39)	4385	NR_029724	387204		NR_029724	ENSMUSG00000065432	Mir208a	Mirn208|Mirn208a|mir-208|mir-208a|mmu-mir-208	microRNA 208a	ncRNA
mm_2385.1	chr1	93479199	93479234	+	1	NA	promoter-TSS (NM_133808)	promoter-TSS (NM_133808)	155	NM_001159719	18000	Mm.428652	NM_010891	ENSMUSG00000026276	Sept2	AW208991|Nedd-5|Nedd5|mKIAA0158	septin 2	protein-coding
mm_112824.1	chr13	20803114	20803132	+	1	NA	intron (NM_012054, intron 1 of 20)	G-rich|Low_complexity|Low_complexity	9010	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_68218.1	chr7	104410225	104410241	-	1	NA	3' UTR (NM_009099, exon 8 of 8)	3' UTR (NM_009099, exon 8 of 8)	-51587	NM_175648	244183	Mm.347647	NM_175648	ENSMUSG00000052749	Trim30b	A530023O14Rik|Trim30-1	tripartite motif-containing 30B	protein-coding
mm_35859.1	chr4	49473906	49473918	-	1	NA	Intergenic	Intergenic	-22803	NM_001164565	230161	Mm.30101	NM_001164565	ENSMUSG00000070985	Acnat1	AI132189	acyl-coenzyme A amino acid N-acyltransferase 1	protein-coding
mm_70558.1	chr8	13073961	13073972	+	1	NA	3' UTR (NM_025834, exon 8 of 8)	3' UTR (NM_025834, exon 8 of 8)	13058	NM_025834	66901	Mm.441140	NM_025834	ENSMUSG00000031445	Proz	1300015B06Rik	protein Z, vitamin K-dependent plasma glycoprotein	protein-coding
mm_48578.1	chr5	143506112	143506138	-	1	NA	3' UTR (NM_009007, exon 6 of 6)	3' UTR (NM_009007, exon 6 of 6)	21868	NM_009007	19353	Mm.292510	NM_009007	ENSMUSG00000001847	Rac1	AL023026|D5Ertd559e	RAS-related C3 botulinum substrate 1	protein-coding
mm_170532.1	chr19	3756228	3756228	-	1	NA	Intergenic	LTRIS3|LTR|ERV1	-11193	NM_001167889	225888	Mm.278578	NM_144871	ENSMUSG00000045098	Kmt5b	AA117471|C630029K18Rik|Suv4-20h1|Suv420h1	lysine methyltransferase 5B	protein-coding
mm_147988.1	chr18	67610859	67610915	-	1	NA	Intergenic	CpG	30449	NM_001081073	225659	Mm.111928	NM_001081073	ENSMUSG00000073542	Cep76	6230425F05Rik|9630013E05	centrosomal protein 76	protein-coding
mm_156488.1	chrX	144336048	144336054	+	1	NA	intron (NR_037145, intron 3 of 26)	intron (NR_037145, intron 3 of 26)	18085	NM_026247	67574	Mm.249084	NM_026247	ENSMUSG00000041718	Alg13	2810046O15Rik|4833435D08Rik|Glt28d1|MDS031|OTTMUSG00000018917	asparagine-linked glycosylation 13	protein-coding
mm_159640.1	chr4	141685746	141685746	-	1	NA	promoter-TSS (NM_023544)	promoter-TSS (NM_023544)	-30	NM_023544	69994	Mm.441022	NM_023544	ENSMUSG00000040715	Rsc1a1	1700027M01Rik|OTTMUSG00000010365|Rs1	regulatory solute carrier protein, family 1, member 1	protein-coding
mm_79421.1	chr9	55326960	55326980	+	1	NA	promoter-TSS (NM_172923)	promoter-TSS (NM_172923)	21	NM_172923	244886	Mm.24361	NM_172923	ENSMUSG00000032313	Tmem266	9630029F15|AI118078|HVRP1	transmembrane protein 266	protein-coding
mm_167837.1	chr9	124424627	124424697	-	1	NA	non-coding (NR_015516, exon 1 of 1)	non-coding (NR_015516, exon 1 of 1)	875	NR_015516	75135	Mm.476814	NR_015516		4930526I15Rik	1600027J15Rik	RIKEN cDNA 4930526I15 gene	ncRNA
mm_53298.1	chr6	129045894	129045906	+	1	NA	promoter-TSS (NM_153094)	promoter-TSS (NM_153094)	-1	NR_024262	232408	Mm.259262	NM_153094	ENSMUSG00000030154	Klrb1f	A630024B12Rik|Nkr-p1f|Nkrp1-f|Nkrp1f	killer cell lectin-like receptor subfamily B member 1F	protein-coding
mm_40734.1	chr5	66215760	66215807	+	1	NA	Intergenic	RMER10A|LTR|ERVL	-24448	NR_040695	73639	Mm.48851	NR_040695	ENSMUSG00000107014	1700126H18Rik	-	RIKEN cDNA 1700126H18 gene	ncRNA
mm_12052.1	chr2	59222211	59222214	+	1	NA	intron (NM_175464, intron 2 of 20)	RLTR16|LTR|ERVK	61362	NM_175464	227937	Mm.260938	NM_026361	ENSMUSG00000026991	Pkp4	5031422I09Rik|9430019K17Rik|Armrp|p0071	plakophilin 4	protein-coding
mm_144484.1	chr18	23999346	23999352	+	1	NA	intron (NM_011755, intron 2 of 2)	(T)n|Simple_repeat|Simple_repeat	9715	NM_011755	22694	Mm.290596	NM_011755	ENSMUSG00000063281	Zfp35	Zfp-35|Znf271|mszf13|mszf20-1|mszf28|mszf68	zinc finger protein 35	protein-coding
mm_82252.1	chr9	4796035	4796066	-	1	NA	5' UTR (NM_001113181, exon 1 of 11)	5' UTR (NM_001113181, exon 1 of 11)	184	NM_001113180	14802	Mm.209263	NM_019691	ENSMUSG00000025892	Gria4	GluA4|GluR-D|Glur-4|Glur4|Gluralpha4|spkw1	glutamate receptor, ionotropic, AMPA4 (alpha 4)	protein-coding
mm_105380.1	chr11	103267406	103267414	-	1	NA	promoter-TSS (NM_016896)	promoter-TSS (NM_016896)	-9	NM_016896	53859	Mm.158981	NM_016896	ENSMUSG00000020941	Map3k14	Nik|aly	mitogen-activated protein kinase kinase kinase 14	protein-coding
mm_132621.1	chr16	38828900	38828908	+	1	NA	promoter-TSS (NM_029042)	promoter-TSS (NM_029042)	-155	NM_029042	74663	Mm.50263	NM_029042	ENSMUSG00000022798	4930435E12Rik	TSCPA	RIKEN cDNA 4930435E12 gene	protein-coding
mm_29976.1	chr3	133663382	133663409	-	1	NA	Intergenic	RLTR12G|LTR|ERVK	-119005	NM_001040400	214133	Mm.347816	NM_145989	ENSMUSG00000040943	Tet2	Ayu17-449|E130014J05Rik|mKIAA1546	tet methylcytosine dioxygenase 2	protein-coding
mm_25828.1	chr3	128610971	128610995	+	1	NA	Intergenic	Intergenic	-379378	NR_045704	402774	Mm.209170	NR_045704	ENSMUSG00000105816	D030025E07Rik	-	RIKEN cDNA D030025E07 gene	ncRNA
mm_8332.1	chr1	150069960	150069960	-	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-17758	NR_106112	102465760		NR_106112	ENSMUSG00000098906	Mir7652	Gm27932|mmu-mir-7652	microRNA 7652	ncRNA
mm_51886.1	chr6	90601995	90602003	+	1	NA	Intergenic	Intergenic	-2881	NM_027868	71699	Mm.272633	NM_027868	ENSMUSG00000030089	Slc41a3	1010001P06Rik|AI480742|SLC41A1-L2	solute carrier family 41, member 3	protein-coding
mm_158274.1	chrX	111463064	111463081	-	1	NA	exon (NM_025949, exon 3 of 25)	exon (NM_025949, exon 3 of 25)	74887	NM_025949	67071	Mm.37617	NM_025949	ENSMUSG00000025665	Rps6ka6	2610524K04Rik|RSK4|S6K-alpha-6	ribosomal protein S6 kinase polypeptide 6	protein-coding
mm_50337.1	chr6	48508335	48508354	+	1	NA	non-coding (NR_027808, exon 2 of 7)	non-coding (NR_027808, exon 2 of 7)	4005	NR_027808	58894	Mm.31983	NR_015597	ENSMUSG00000107476	Zfp862-ps	4732460K03Rik|AI448302|Zfp862|mKIAA0543	zinc finger protein 862, pseudogene	pseudo
mm_29038.1	chr3	102782671	102782675	-	1	NA	promoter-TSS (NM_009432)	promoter-TSS (NM_009432)	41	NM_009432	22094	Mm.110730	NM_009432	ENSMUSG00000027857	Tshb	-	thyroid stimulating hormone, beta subunit	protein-coding
mm_10537.1	chr2	16438294	16438319	+	1	NA	intron (NM_026162, intron 1 of 13)	L1_Mm|LINE|L1	82002	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding
mm_139249.1	chr17	47734313	47734324	+	1	NA	exon (NM_025973, exon 9 of 9)	exon (NM_025973, exon 9 of 9)	-2719	NM_001161722	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_48410.1	chr5	140261779	140261789	-	1	NA	intron (NM_010752, intron 9 of 17)	intron (NM_010752, intron 9 of 17)	59768	NM_010752	17120	Mm.27250	NM_010752	ENSMUSG00000029554	Mad1l1	AI173502|AW550425|Mad1	MAD1 mitotic arrest deficient 1-like 1	protein-coding
mm_35177.1	chr4	15149012	15149045	-	1	NA	5' UTR (NM_178617, exon 1 of 13)	5' UTR (NM_178617, exon 1 of 13)	103	NM_178617	69352	Mm.389031	NM_178617	ENSMUSG00000040536	Necab1	1700003H21Rik|Efcbp1|STIP-1	N-terminal EF-hand calcium binding protein 1	protein-coding
mm_135338.1	chr16	42340505	42340564	-	1	NA	5' UTR (NM_008083, exon 1 of 3)	5' UTR (NM_008083, exon 1 of 3)	117	NM_008083	14432	Mm.1222	NM_008083	ENSMUSG00000047261	Gap43	B-50|Basp2|GAP-43	growth associated protein 43	protein-coding
mm_120932.1	chr14	76504186	76504249	+	1	NA	promoter-TSS (NM_009366)	promoter-TSS (NM_009366)	-9	NM_001310647	21807	Mm.153272	NM_009366	ENSMUSG00000022010	Tsc22d1	AA589566|AW105905|Egr5|TSC-22|Tgfb1i4|Tsc|Tsc22	TSC22 domain family, member 1	protein-coding
mm_169898.1	chr16	49293683	49293696	+	1	NA	Intergenic	RLTR9D|LTR|ERVK	236203	NM_001166210	667772	Mm.301387	NM_001166210	ENSMUSG00000092009	Myh15	EG667772	myosin, heavy chain 15	protein-coding
mm_51215.1	chr6	71353020	71353053	+	1	NA	Intergenic	Intergenic	-20391	NM_009857	12525	Mm.1858	NM_009857	ENSMUSG00000053977	Cd8a	BB154331|Ly-2|Ly-35|Ly-B|Lyt-2	CD8 antigen, alpha chain	protein-coding
mm_43566.1	chr5	137633566	137633576	+	1	NA	intron (NR_033148, intron 1 of 21)	intron (NR_033148, intron 1 of 21)	4448	NR_033148	100316903	Mm.200763	NR_033148		Gm20605	Lrch4-sap25	predicted gene 20605	ncRNA
mm_155174.1	chrX	53607919	53607954	+	1	NA	promoter-TSS (NM_028375)	promoter-TSS (NM_028375)	14	NM_028375	72865	Mm.158897	NM_028375	ENSMUSG00000051851	Cxx1c	2900027G03Rik|Mar8.1|Mart8a	CAAX box 1C	protein-coding
mm_51149.1	chr6	70671760	70671787	+	1	NA	Intergenic	Intergenic	120402	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_133490.1	chr16	90283220	90283230	+	1	NA	intron (NM_178923, intron 1 of 19)	intron (NM_178923, intron 1 of 19)	1278	NM_178923	224432	Mm.439811	NM_178923	ENSMUSG00000022983	Scaf4	AA517739|Sfrs15|Sra4|Srsf15	SR-related CTD-associated factor 4	protein-coding
mm_15889.1	chr2	164879359	164879398	+	1	NA	promoter-TSS (NM_146129)	promoter-TSS (NM_146129)	10	NM_146129	228866	Mm.241134	NM_146129	ENSMUSG00000039849	Pcif1	2310022K11Rik|C20orf67|F730014I05Rik	PDX1 C-terminal inhibiting factor 1	protein-coding
mm_138186.1	chr17	34268663	34268667	+	1	NA	intron (NM_207105, intron 5 of 5)	intron (NM_207105, intron 5 of 5)	5438	NM_207105	14961	Mm.254067	NM_207105	ENSMUSG00000073421	H2-Ab1	AI845868|Abeta|H-2Ab|H2-Ab|I-Abeta|IAb|Ia-2|Ia2|Rmcs1	histocompatibility 2, class II antigen A, beta 1	protein-coding
mm_120863.1	chr14	75229534	75229549	+	1	NA	3' UTR (NM_001247984, exon 16 of 16)	3' UTR (NM_001247984, exon 16 of 16)	-12746	NM_019775	56373	Mm.24242	NM_019775	ENSMUSG00000021999	Cpb2	1110032P04Rik|4930405E17Rik|AI255929|CPR|Cpu|TAFI	carboxypeptidase B2 (plasma)	protein-coding
mm_86001.1	chr9	112232369	112232386	-	1	NA	5' UTR (NM_001177616, exon 1 of 19)	5' UTR (NM_001177616, exon 1 of 19)	124	NM_001177616	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_26587.1	chr3	151294204	151294218	+	1	NA	Intergenic	Intergenic	-143671	NM_133222	170757	Mm.317261	NM_133222	ENSMUSG00000039167	Adgrl4	1110033N21Rik|ETL1|Eltd1|Etl	adhesion G protein-coupled receptor L4	protein-coding
mm_22968.1	chr3	32708256	32708260	+	1	NA	promoter-TSS (NM_019673)	promoter-TSS (NM_019673)	-288	NM_019673	56456	Mm.41077	NM_019673	ENSMUSG00000027671	Actl6a	2810432C06Rik|AI851094|ARP4|Actl6|Baf53a|C79802	actin-like 6A	protein-coding
mm_21597.1	chr2	164237820	164237831	-	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	516	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_153202.1	chr19	34629877	34629887	-	1	NA	intron (NM_053217, intron 1 of 2)	RLTR10|LTR|ERVK	10861	NM_053217	112419	Mm.440727	NM_053217	ENSMUSG00000067297	Ifit1bl2	2010002M12Rik|AW412491|Ifit1b	interferon induced protein with tetratricopeptide repeats 1B like 2	protein-coding
mm_110292.1	chr12	32208333	32208400	-	1	NA	promoter-TSS (NM_001146201)	promoter-TSS (NM_001146201)	-28	NM_001146201	30955	Mm.101369	NM_020272	ENSMUSG00000020573	Pik3cg	5830428L06Rik|PI3Kgamma|p110gamma	phosphoinositide-3-kinase, catalytic, gamma polypeptide	protein-coding
mm_38281.1	chr4	136890134	136890144	-	1	NA	exon (NM_007574, exon 3 of 3)	exon (NM_007574, exon 3 of 3)	2775	NM_007574	12262	Mm.439732	NM_007574	ENSMUSG00000036896	C1qc	AI385742|C1qg|Ciqc	complement component 1, q subcomponent, C chain	protein-coding
mm_73344.1	chr8	105348164	105348190	+	1	NA	promoter-TSS (NM_001081332)	promoter-TSS (NM_001081332)	-81	NM_001081332	277973	Mm.334766	NM_001081332	ENSMUSG00000014786	Slc9a5	Gm696	solute carrier family 9 (sodium/hydrogen exchanger), member 5	protein-coding
mm_51607.1	chr6	84154721	84154731	+	1	NA	intron (NM_001077694, intron 40 of 54)	intron (NM_001077694, intron 40 of 54)	135340	NM_021469	26903	Mm.220982	NM_021469	ENSMUSG00000033788	Dysf	2310004N10Rik|AI604795|D6Pas3	dysferlin	protein-coding
mm_48843.1	chr5	149367118	149367124	-	1	NA	Intergenic	Intergenic	-44685	NM_027519	70717	Mm.252139	NM_027519	ENSMUSG00000029659	Medag	6330406I15Rik|Awms3|MEDA-4|Meda4|mAWMS3	mesenteric estrogen dependent adipogenesis	protein-coding
mm_154315.1	chrM	1088	1106	+	1	NA	NA	Intergenic	NA	NA								
mm_82229.1	chr9	3029403	3029420	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	9332	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_72726.1	chr8	85071721	85071734	+	1	NA	promoter-TSS (NM_001039514)	promoter-TSS (NM_001039514)	-30	NM_001039514	330817	Mm.193086	NM_201408	ENSMUSG00000060038	Dhps	Dhs	deoxyhypusine synthase	protein-coding
mm_5645.1	chr1	40516448	40516453	-	1	NA	5' UTR (NM_010553, exon 3 of 13)	5' UTR (NM_010553, exon 3 of 13)	1088	NM_010553	16174	Mm.20466	NM_010553	ENSMUSG00000026068	Il18rap	AcPL|IL-18R-beta|IL-18RAcP|IL-18Rbeta|IL-1RAcPL	interleukin 18 receptor accessory protein	protein-coding
mm_45969.1	chr5	90468622	90468661	-	1	NA	exon (NM_009654, exon 8 of 15)	exon (NM_009654, exon 8 of 15)	7771	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_162949.1	chr11	3353381	3353383	-	1	NA	exon (NM_010718, exon 8 of 16)	exon (NM_010718, exon 8 of 16)	2759	NM_001034030	16886	Mm.124176	NM_010718	ENSMUSG00000020451	Limk2	Limk-2|whe	LIM motif-containing protein kinase 2	protein-coding
mm_67388.1	chr7	79842577	79842587	-	1	NA	promoter-TSS (NM_008486)	promoter-TSS (NM_008486)	-230	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_20748.1	chr2	140065826	140065847	-	1	NA	intron (NR_110351, intron 1 of 13)	B3|SINE|B2	969	NM_001159640	75812	Mm.293449	NM_175225	ENSMUSG00000039033	Tasp1	4930485D02Rik|AW986064	taspase, threonine aspartase 1	protein-coding
mm_134161.1	chr16	10791732	10791739	-	1	NA	promoter-TSS (NM_013638)	promoter-TSS (NM_013638)	370	NM_008933	19119	Mm.325769	NM_008933	ENSMUSG00000038015	Prm2	AI528784|Prm-2	protamine 2	protein-coding
mm_21899.1	chr2	166156169	166156180	-	1	NA	promoter-TSS (NM_028072)	promoter-TSS (NM_028072)	-491	NM_028072	72043	Mm.1011	NM_028072	ENSMUSG00000006800	Sulf2	2010004N24Rik|AU020235|MSulf-2|mKIAA1247	sulfatase 2	protein-coding
mm_95808.1	chr11	55110213	55110217	+	1	NA	3' UTR (NM_010299, exon 4 of 4)	3' UTR (NM_010299, exon 4 of 4)	12230	NM_010299	14667	Mm.287807	NM_010299	ENSMUSG00000000594	Gm2a	AA408702|AW215435|GM2-AP|SAP-3	GM2 ganglioside activator protein	protein-coding
mm_75976.1	chr8	72136799	72136815	-	1	NA	intron (NM_001001491, intron 1 of 7)	intron (NM_001001491, intron 1 of 7)	1515	NM_001001491	326618	Mm.295124	NM_001001491	ENSMUSG00000031799	Tpm4	2610528G24Rik|Tpm4.2|Tpm4.2cy	tropomyosin 4	protein-coding
mm_69742.1	chr7	140952182	140952185	-	1	NA	Intergenic	Intergenic	-1944	NM_053088	73835	Mm.389989	NM_053088	ENSMUSG00000025489	Ifitm5	1110003J06Rik|AW213665|Bril|DSPA1|Hrmp1|Hrtm1	interferon induced transmembrane protein 5	protein-coding
mm_31057.1	chr4	41191184	41191222	+	1	NA	3' UTR (NM_026275, exon 5 of 5)	3' UTR (NM_026275, exon 5 of 5)	55182	NM_026275	67615	Mm.389540	NM_026275	ENSMUSG00000036241	Ube2r2	1200003M11Rik|Cdc34b|Ubc3b	ubiquitin-conjugating enzyme E2R 2	protein-coding
mm_30725.1	chr4	13751336	13751358	+	1	NA	promoter-TSS (NM_001111027)	promoter-TSS (NM_001111027)	50	NM_001111027	12395	Mm.4909	NM_009822	ENSMUSG00000006586	Runx1t1	Cbfa2t1h|ETO|MTG8	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	protein-coding
mm_120991.1	chr14	79301199	79301205	+	1	NA	intron (NM_025427, intron 1 of 4)	CpG	433	NM_025427	66214	Mm.29811	NM_025427	ENSMUSG00000022018	Rgcc	1190002H23Rik|Rgc-32|Rgc32	regulator of cell cycle	protein-coding
mm_101829.1	chr11	47379307	47379344	-	1	NA	promoter-TSS (NM_011891)	promoter-TSS (NM_011891)	-23	NM_011891	24052	Mm.338890	NM_011891	ENSMUSG00000020354	Sgcd	35kDa|delta-SG	sarcoglycan, delta (dystrophin-associated glycoprotein)	protein-coding
mm_99471.1	chr11	102436165	102436189	+	1	NA	TTS (NM_199200)	TTS (NM_199200)	5855	NM_008175	14824	Mm.1568	NM_008175	ENSMUSG00000034708	Grn	Pgrn|epithelin	granulin	protein-coding
mm_91005.1	chr10	14545424	14545486	-	1	NA	promoter-TSS (NM_001002268)	promoter-TSS (NM_001002268)	-419	NM_001002268	215798	Mm.440142	NM_001002268	ENSMUSG00000039116	Adgrg6	1190004A11Rik|AI449247|AW045736|DREG|Gm222|Gpr126	adhesion G protein-coupled receptor G6	protein-coding
mm_4232.1	chr1	171370114	171370130	+	1	NA	promoter-TSS (NM_027893)	promoter-TSS (NM_027893)	-51	NM_027893	71740	Mm.263414	NM_027893	ENSMUSG00000006411	Nectin4	1200017F15Rik|Prr4|Pvrl4	nectin cell adhesion molecule 4	protein-coding
mm_105771.1	chr11	109676157	109676168	-	1	NA	intron (NM_153782, intron 7 of 10)	intron (NM_153782, intron 7 of 10)	25241	NM_001313976	19084	Mm.30039	NM_021880	ENSMUSG00000020612	Prkar1a	1300018C22Rik|RIalpha|Tse-1|Tse1	protein kinase, cAMP dependent regulatory, type I, alpha	protein-coding
mm_129419.1	chr15	78395900	78395914	-	1	NA	promoter-TSS (NM_028522)	promoter-TSS (NM_028522)	5	NM_028522	73376	Mm.73222	NM_028522	ENSMUSG00000062154	Tex33	1700061J05Rik|Ean57	testis expressed 33	protein-coding
mm_83715.1	chr9	50752349	50752373	-	1	NA	promoter-TSS (NM_001289784)	promoter-TSS (NM_001289784)	-7	NM_024441	69253	Mm.1980	NM_024441	ENSMUSG00000038086	Hspb2	27kDa|2810021G24Rik|HSP27|MKBP	heat shock protein 2	protein-coding
mm_77198.1	chr8	112032342	112032359	-	1	NA	Intergenic	Intergenic	20991	NM_020584	57321	Mm.213064	NM_020584	ENSMUSG00000033430	Terf2ip	Rap1	telomeric repeat binding factor 2, interacting protein	protein-coding
mm_17338.1	chr2	26596365	26596378	-	1	NA	exon (NM_026212, exon 3 of 6)	exon (NM_026212, exon 3 of 6)	-4951	NR_106155	102465787		NR_106155	ENSMUSG00000105799	Mir126b	mmu-mir-126b	microRNA 126b	ncRNA
mm_132000.1	chr16	25410739	25410755	+	1	NA	intron (NM_175165, intron 4 of 5)	intron (NM_175165, intron 4 of 5)	123930	NM_175165	71338	Mm.126851	NM_175165	ENSMUSG00000048399	Tprg	5430420C16Rik|Tprg1	transformation related protein 63 regulated	protein-coding
mm_49557.1	chr6	30551461	30551464	+	1	NA	intron (NM_001024698, intron 7 of 10)	intron (NM_001024698, intron 7 of 10)	9820	NM_001024698	232680	Mm.268855	NM_001024698	ENSMUSG00000071553	Cpa2	-	carboxypeptidase A2, pancreatic	protein-coding
mm_65783.1	chr7	28781335	28781380	-	1	NA	non-coding (NR_040339, exon 1 of 4)	non-coding (NR_040339, exon 1 of 4)	157	NR_040339	100503790	Mm.446894	NR_040339		Gm19897	-	predicted gene, 19897	ncRNA
mm_120975.1	chr14	78650893	78650905	+	1	NA	intron (NM_001081336, intron 3 of 28)	intron (NM_001081336, intron 3 of 28)	-6448	NR_104044	380921	Mm.89591	NM_001081336	ENSMUSG00000034731	Dgkh	5930402B05Rik|D130015C16|DGK	diacylglycerol kinase, eta	protein-coding
mm_163155.1	chr11	83605614	83605649	-	1	NA	intron (NR_036453, intron 2 of 8)	intron (NR_036453, intron 2 of 8)	-12544	NM_009139	20305	Mm.137	NM_009139	ENSMUSG00000018927	Ccl6	MRP-1|Scya6|c10	chemokine (C-C motif) ligand 6	protein-coding
mm_101239.1	chr11	20699582	20699594	-	1	NA	intron (NM_001290545, intron 6 of 9)	intron (NM_001290545, intron 6 of 9)	41968	NM_001290545	216549	Mm.356580	NM_181411	ENSMUSG00000049659	Aftph	-	aftiphilin	protein-coding
mm_17211.1	chr2	25478096	25478115	-	1	NA	Intergenic	Intergenic	-8356	NM_008963	19215	Mm.1008	NM_008963	ENSMUSG00000015090	Ptgds	21kDa|L-PGDS|PGD2|PGDS|PGDS2|Ptgs3	prostaglandin D2 synthase (brain)	protein-coding
mm_138752.1	chr17	37046095	37046135	+	1	NA	5' UTR (NM_019439, exon 1 of 23)	5' UTR (NM_019439, exon 1 of 23)	149	NM_019439	54393	Mm.32191	NM_019439	ENSMUSG00000024462	Gabbr1	GABAB1|GABAbR1|bM573K1.1	gamma-aminobutyric acid (GABA) B receptor, 1	protein-coding
mm_164335.1	chr16	10976613	10976644	+	1	NA	intron (NM_019980, intron 1 of 3)	intron (NM_019980, intron 1 of 3)	16493	NM_019980	56722	Mm.294753	NM_019980	ENSMUSG00000022500	Litaf	3222402J11Rik|C85531|N4WBP3|TBX1	LPS-induced TN factor	protein-coding
mm_105293.1	chr11	102470145	102470165	-	1	NA	promoter-TSS (NM_010575)	promoter-TSS (NM_010575)	-272	NM_010575	16399	Mm.26646	NM_010575	ENSMUSG00000034664	Itga2b	AI172977|CD41|CD41B|GpIIb|alphaIIb	integrin alpha 2b	protein-coding
mm_31761.1	chr4	63385478	63385488	+	1	NA	intron (NM_001305432, intron 5 of 20)	intron (NM_001305432, intron 5 of 20)	12757	NM_001305432	100182	Mm.387725	NM_001045514	ENSMUSG00000039158	Akna	AI597013	AT-hook transcription factor	protein-coding
mm_79787.1	chr9	63602651	63602703	+	1	NA	promoter-TSS (NM_025857)	promoter-TSS (NM_025857)	22	NM_025857	66939	Mm.34338	NM_025857	ENSMUSG00000037257	Aagab	2310007F21Rik|p34	alpha- and gamma-adaptin binding protein	protein-coding
mm_140631.1	chr17	12507173	12507187	-	1	NA	exon (NM_011395, exon 1 of 11)	exon (NM_011395, exon 1 of 11)	524	NM_011395	20519	Mm.99252	NM_011395	ENSMUSG00000023828	Slc22a3	EMT|Oct3|Orct3|Slca22a3	solute carrier family 22 (organic cation transporter), member 3	protein-coding
mm_12483.1	chr2	71529901	71529903	+	1	NA	TTS (NR_002854)	TTS (NR_002854)	457	NM_010053	13390	Mm.475101	NM_010053	ENSMUSG00000041911	Dlx1	Dlx|Dlx-1	distal-less homeobox 1	protein-coding
mm_92299.1	chr10	73691009	73691011	-	1	NA	Intergenic	Intergenic	-130857	NM_001142760	11994	Mm.338933	NM_023115	ENSMUSG00000052613	Pcdh15	BB078305|ENSMUSG00000046980|Gm9815|Ush1f|av|nmf19|roda	protocadherin 15	protein-coding
mm_98173.1	chr11	87755568	87755588	+	1	NA	Intergenic	Intergenic	-1286	NR_029555	387160		NR_029555	ENSMUSG00000105196	Mir142	Mirn142|miR-142|mir-142a|mmu-mir-142|mmu-mir-142a	microRNA 142	ncRNA
mm_56632.1	chr6	112947282	112947301	-	1	NA	promoter-TSS (NM_080448)	promoter-TSS (NM_080448)	-25	NM_080448	259302	Mm.236401	NM_080448	ENSMUSG00000030257	Srgap3	AI452337|Arhgap14|D130026O08Rik|Gbi|MEGAP|WRP|mKIAA0411	SLIT-ROBO Rho GTPase activating protein 3	protein-coding
mm_53697.1	chr6	142756759	142756775	+	1	NA	promoter-TSS (NM_009908)	promoter-TSS (NM_009908)	81	NM_009908	12764	Mm.3820	NM_009908	ENSMUSG00000030282	Cmas	AW208911|CMPNeu5Ac|D6Bwg0250e	cytidine monophospho-N-acetylneuraminic acid synthetase	protein-coding
mm_79809.1	chr9	64177713	64177738	+	1	NA	exon (NM_024212, exon 8 of 10)	exon (NM_024212, exon 8 of 10)	-1572	NM_183316	330959	Mm.24082	NM_183316	ENSMUSG00000032398	Snapc5	2010103A03Rik	small nuclear RNA activating complex, polypeptide 5	protein-coding
mm_47747.1	chr5	130255423	130255509	-	1	NA	promoter-TSS (NM_178897)	promoter-TSS (NM_178897)	64	NM_023248	66711	Mm.280484	NM_023248	ENSMUSG00000025337	Sbds	4733401P19Rik|AI836084|CGI-97|SDS	Shwachman-Bodian-Diamond syndrome homolog (human)	protein-coding
mm_97567.1	chr11	78937558	78937572	+	1	NA	exon (NM_010927, exon 8 of 27)	exon (NM_010927, exon 8 of 27)	12274	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_48340.1	chr5	139130171	139130181	-	1	NA	promoter-TSS (NM_008923)	promoter-TSS (NM_008923)	210	NM_001253890	19085	Mm.306163	NM_008923	ENSMUSG00000025855	Prkar1b	AI385716|RIbeta	protein kinase, cAMP dependent regulatory, type I beta	protein-coding
mm_166181.1	chr5	31494800	31494807	+	1	NA	promoter-TSS (NM_133756)	promoter-TSS (NM_133756)	42	NM_133756	74254	Mm.348649	NM_133756	ENSMUSG00000064037	Gpn1	2410004J02Rik|AI449615|MBDIN|NTPBP|Xab1	GPN-loop GTPase 1	protein-coding
mm_114115.1	chr13	55003214	55003228	+	1	NA	exon (NM_153131, exon 12 of 16)	exon (NM_153131, exon 12 of 16)	17598	NM_001206390	212032	Mm.267479	NM_001033245	ENSMUSG00000025877	Hk3	HK III|HK-III	hexokinase 3	protein-coding
mm_93284.1	chr10	96181505	96181509	-	1	NA	Intergenic	L2c|LINE|L2	-44700	NR_110448	74881	Mm.410819	NR_110448		4930459C07Rik	-	RIKEN cDNA 4930459C07 gene	ncRNA
mm_135817.1	chr16	58082951	58082984	-	1	NA	Intergenic	MTEa|LTR|ERVL-MaLR	-325568	NM_028523	73379	Mm.373589	NM_028523	ENSMUSG00000035107	Dcbld2	1700055P21Rik|AW146002|CLCP1|Esdn	discoidin, CUB and LCCL domain containing 2	protein-coding
mm_109913.1	chr12	8480245	8480252	-	1	NA	Intergenic	Intergenic	19737	NM_007483	11852	Mm.687	NM_007483	ENSMUSG00000054364	Rhob	AA017882|Arh6|Arhb	ras homolog family member B	protein-coding
mm_30367.1	chr3	152165880	152165966	-	1	NA	promoter-TSS (NM_016867)	promoter-TSS (NM_016867)	-23	NM_016867	54120	Mm.97	NM_016867	ENSMUSG00000039131	Gipc2	2200002N01Rik|AU021850|Semcap2	GIPC PDZ domain containing family, member 2	protein-coding
mm_56433.1	chr6	97354113	97354149	-	1	NA	intron (NM_001346639, intron 5 of 22)	intron (NM_001346639, intron 5 of 22)	-101351	NM_001081157	320502	Mm.68163	NM_001081157	ENSMUSG00000044086	Lmod3	5430424A14Rik	leiomodin 3 (fetal)	protein-coding
mm_17503.1	chr2	28915833	28915846	-	1	NA	5' UTR (NM_019446, exon 1 of 3)	5' UTR (NM_019446, exon 1 of 3)	582	NM_019446	54422	Mm.21390	NM_019446	ENSMUSG00000026805	Barhl1	Dres115|MBH2	BarH-like 1 (Drosophila)	protein-coding
mm_92417.1	chr10	76884463	76884466	-	1	NA	intron (NM_001347216, intron 2 of 15)	L1MEc|LINE|L1	77483	NM_001347216	59093	Mm.272803	NM_021568	ENSMUSG00000001120	Pcbp3	AlphaCP-3	poly(rC) binding protein 3	protein-coding
mm_157838.1	chrX	74304688	74304691	-	1	NA	promoter-TSS (NM_010273)	promoter-TSS (NM_010273)	-323	NM_010273	14567	Mm.205830	NM_010273	ENSMUSG00000015291	Gdi1	GDIA|GDIalpha	guanosine diphosphate (GDP) dissociation inhibitor 1	protein-coding
mm_127199.1	chr15	99099488	99099524	+	1	NA	promoter-TSS (NM_176835)	promoter-TSS (NM_176835)	22	NM_176835	72778	Mm.30544	NM_176835	ENSMUSG00000038009	Dnajc22	2810451A06Rik|AI506245	DnaJ heat shock protein family (Hsp40) member C22	protein-coding
mm_135718.1	chr16	55818300	55818337	-	1	NA	exon (NM_030612, exon 7 of 14)	exon (NM_030612, exon 7 of 14)	3820	NM_001159394	80859	Mm.247272	NM_030612	ENSMUSG00000035356	Nfkbiz	AA408868|INAP|Mail	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, zeta	protein-coding
mm_150859.1	chr19	45015199	45015224	+	1	NA	promoter-TSS (NM_001130525)	promoter-TSS (NM_001130525)	1	NM_001130525	226154	Mm.28204	NM_145503	ENSMUSG00000035342	Lzts2	BC014695|LAPSER1|mKIAA1813	leucine zipper, putative tumor suppressor 2	protein-coding
mm_128954.1	chr15	74784862	74784879	-	1	NA	Intergenic	Intergenic	-6011	NR_027837	78725	Mm.171357	NM_172433	ENSMUSG00000101026	D730001G18Rik	Ly6g6g	RIKEN cDNA D730001G18 gene	ncRNA
mm_590.1	chr1	39551300	39551305	+	1	NA	TTS (NM_001033135)	TTS (NM_001033135)	-2462	NR_028555	100217461		NR_028555	ENSMUSG00000077704	Snord89	MBII-289	small nucleolar RNA, C/D box 89	snoRNA
mm_111377.1	chr12	87266228	87266301	-	1	NA	promoter-TSS (NM_001142580)	promoter-TSS (NM_001142580)	22	NM_001142580	104799	Mm.208750	NM_134044	ENSMUSG00000021038	Vipas39	6720456H09Rik|9330175H22Rik|AI413782|SPE-39|Spe39|Vipar|hSPE-39	VPS33B interacting protein, apical-basolateral polarity regulator, spe-39 homolog	protein-coding
mm_52633.1	chr6	117174402	117174415	+	1	NA	3' UTR (NM_021704, exon 3 of 3)	3' UTR (NM_021704, exon 3 of 3)	5873	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_25804.1	chr3	127789298	127789310	+	1	NA	promoter-TSS (NM_145133)	promoter-TSS (NM_145133)	-609	NM_145133	211550	Mm.31852	NM_145133	ENSMUSG00000046688	Tifa	T2bp	TRAF-interacting protein with forkhead-associated domain	protein-coding
mm_138380.1	chr17	35024363	35024376	+	1	NA	exon (NM_138582, exon 14 of 17)	exon (NM_138582, exon 14 of 17)	3647	NR_028258	78376	Mm.390966	NM_023893	ENSMUSG00000036185	Sapcd1	2810436B06Rik|G7d|Ng23	suppressor APC domain containing 1	protein-coding
mm_159863.1	chr5	142776154	142776154	-	1	NA	intron (NM_178242, intron 6 of 15)	intron (NM_178242, intron 6 of 15)	41233	NM_178242	231861	Mm.354649	NM_178242	ENSMUSG00000039477	Tnrc18	BC025631|EG381742|Zfp469	trinucleotide repeat containing 18	protein-coding
mm_92580.1	chr10	79995384	79995402	-	1	NA	TTS (NM_007725)	TTS (NM_007725)	-2215	NM_001347081	27403	Mm.103351	NM_013850	ENSMUSG00000035722	Abca7	ABCX|Abc51	ATP-binding cassette, sub-family A (ABC1), member 7	protein-coding
mm_34562.1	chr4	149701710	149701750	+	1	NA	promoter-TSS (NM_001029837)	promoter-TSS (NM_001029837)	-101	NM_001029837	18707	Mm.229108	NM_008840	ENSMUSG00000039936	Pik3cd	2410099E07Rik|2610208K16Rik|AW545373|p110delta	phosphatidylinositol 3-kinase catalytic delta polypeptide	protein-coding
mm_99958.1	chr11	113619381	113619385	+	1	NA	promoter-TSS (NM_009217)	promoter-TSS (NM_009217)	-98	NM_009217	20606		NM_009217	ENSMUSG00000047904	Sstr2	SRIF-1|SS2R|SSTR-2|Smstr-2|Smstr2|sst2	somatostatin receptor 2	protein-coding
mm_130554.1	chr15	99088427	99088429	-	1	NA	promoter-TSS (NM_001024702)	promoter-TSS (NM_001024702)	-700	NM_001024702	239659	Mm.309917	NM_001024702	ENSMUSG00000001076	C1ql4	C1qtnf11|CTRP11	complement component 1, q subcomponent-like 4	protein-coding
mm_27570.1	chr3	58637202	58637221	-	1	NA	promoter-TSS (NM_001081262)	promoter-TSS (NM_001081262)	-4	NM_001081262	545527	Mm.357722	NM_001081262	ENSMUSG00000070471	Erich6	4932431H17Rik|Fam194a	glutamate rich 6	protein-coding
mm_29598.1	chr3	119783263	119783312	-	1	NA	5' UTR (NM_019550, exon 1 of 14)	5' UTR (NM_019550, exon 1 of 14)	101	NM_001310711	56195	Mm.29966	NM_019550	ENSMUSG00000028134	Ptbp2	Ptb2|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding
mm_124295.1	chr14	103055023	103055048	-	1	NA	exon (NM_008392, exon 5 of 5)	exon (NM_008392, exon 5 of 5)	8023	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_2973.1	chr1	133084153	133084165	+	1	NA	intron (NM_001099276, intron 12 of 32)	intron (NM_001099276, intron 12 of 32)	38147	NM_001099276	240752	Mm.387308	NM_001099276	ENSMUSG00000026447	Pik3c2b	C330011J12Rik|Gm199|PI3K-C2beta|PI3KC2beta	phosphoinositide-3-kinase, class 2, beta polypeptide	protein-coding
mm_149571.1	chr19	12805289	12805335	+	1	NA	intron (NM_134152, intron 2 of 8)	intron (NM_134152, intron 2 of 8)	6703	NM_134152	107321	Mm.313136	NM_134152	ENSMUSG00000024696	Lpxn	4933402K05Rik|A530083L21Rik|AV278559|LDPL	leupaxin	protein-coding
mm_13630.1	chr2	113655459	113655486	+	1	NA	intron (NM_001285458, intron 13 of 16)	intron (NM_001285458, intron 13 of 16)	-29618	NM_001287818	14260	Mm.4938	NM_010230	ENSMUSG00000044042	Fmn1	Fmn|formin-1|ld	formin 1	protein-coding
mm_137954.1	chr17	32965831	32965852	+	1	NA	promoter-TSS (NM_153063)	promoter-TSS (NM_153063)	10	NM_153063	224691	Mm.328953	NM_153063	ENSMUSG00000053600	Zfp472	KRIM-1|Krim-1A|Krim-1B|Krim1	zinc finger protein 472	protein-coding
mm_42231.1	chr5	113539075	113539090	+	1	NA	Intergenic	Intergenic	-11338	NM_177292	320916	Mm.102783	NM_177292	ENSMUSG00000063430	Wscd2	4933413A10Rik|C530024P05Rik|Gm450	WSC domain containing 2	protein-coding
mm_167971.1	chrX	154398210	154398248	+	1	NA	Intergenic	Intergenic	-54837	NM_001256259	75071	Mm.159415	NM_001256259	ENSMUSG00000059663	4930524N10Rik	-	RIKEN cDNA 4930524N10 gene	protein-coding
mm_90137.1	chr10	117861137	117861163	+	1	NA	Intergenic	Intergenic	-15176	NM_024457	215449	Mm.233009	NM_024457	ENSMUSG00000052681	Rap1b	2810443E11Rik	RAS related protein 1b	protein-coding
mm_31377.1	chr4	47413791	47413803	+	1	NA	3' UTR (NM_009370, exon 9 of 9)	3' UTR (NM_009370, exon 9 of 9)	27581	NM_001312869	21812	Mm.197552	NM_009370	ENSMUSG00000007613	Tgfbr1	ALK5|AU017191|Alk-5|ESK2|TGFR-1|TbetaR-I|TbetaRI	transforming growth factor, beta receptor I	protein-coding
mm_113441.1	chr13	34924414	34924426	+	1	NA	promoter-TSS (NM_025750)	promoter-TSS (NM_025750)	11	NM_025750	66761	Mm.157047	NM_025750	ENSMUSG00000021415	4933417A18Rik	-	RIKEN cDNA 4933417A18 gene	protein-coding
mm_146654.1	chr18	11051926	11051942	-	1	NA	promoter-TSS (NM_010258)	promoter-TSS (NM_010258)	-576	NM_010258	14465	Mm.329287	NM_010258	ENSMUSG00000005836	Gata6	AA410133|GATA-6	GATA binding protein 6	protein-coding
mm_136085.1	chr16	84835627	84835635	-	1	NA	promoter-TSS (NM_016755)	promoter-TSS (NM_016755)	-6	NM_001302213	11957	Mm.353	NM_016755	ENSMUSG00000022890	Atp5j	CF6	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit F	protein-coding
mm_47917.1	chr5	135000934	135000943	-	1	NA	non-coding (NR_026907, exon 1 of 5)	non-coding (NR_026907, exon 1 of 5)	412	NR_026907	71304	Mm.482317	NR_026907	ENSMUSG00000054909	Wbscr25	4933433J03Rik|4933439O14Rik	Williams Beuren syndrome chromosome region 25 (human)	ncRNA
mm_139854.1	chr17	69969107	69969125	+	1	NA	promoter-TSS (NM_001347412)	promoter-TSS (NM_001347412)	43	NM_001347411	224997	Mm.311840	NM_027712	ENSMUSG00000003279	Dlgap1	4933422O14Rik|9630002F18|AI845682|AI848168|BB075781|D17Bwg0511e|GKAP/SAPAP|GKPA/SAPAP|Gkap|Sapap1|mKIAA4162	discs, large (Drosophila) homolog-associated protein 1	protein-coding
mm_17391.1	chr2	27110561	27110575	-	1	NA	3' UTR (NM_175427, exon 3 of 3)	3' UTR (NM_175427, exon 3 of 3)	31187	NM_029981	77794	Mm.330088	NM_029981	ENSMUSG00000036040	Adamtsl2	A930008K15Rik|tcp-1	ADAMTS-like 2	protein-coding
mm_82547.1	chr9	20925845	20925854	-	1	NA	intron (NM_001314011, intron 16 of 38)	B1_Mur2|SINE|Alu	-11685	NR_106049	102466802		NR_106049	ENSMUSG00000099147	Mir7081	Gm27904|mmu-mir-7081	microRNA 7081	ncRNA
mm_58626.1	chr7	5080215	5080298	+	1	NA	promoter-TSS (NM_001252454)	promoter-TSS (NM_001252454)	21	NM_001252454	13854	Mm.3091	NM_010147	ENSMUSG00000035203	Epn1	AA269831|Ibp1	epsin 1	protein-coding
mm_158317.1	chrX	129614908	129614917	-	1	NA	Intergenic	Intergenic	-134830	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diaph2	Dia3|Diap2|Drf2|E430022I22Rik	diaphanous related formin 2	protein-coding
mm_58979.1	chr7	19054684	19054707	+	1	NA	promoter-TSS (NM_031255)	promoter-TSS (NM_031255)	8	NM_001159671	83434	Mm.84435	NM_031255	ENSMUSG00000040866	Rsph6a	RSP4|Rshl1	radial spoke head 6 homolog A (Chlamydomonas)	protein-coding
mm_4536.1	chr1	176754521	176754531	+	1	NA	intron (NM_001099637, intron 13 of 19)	intron (NM_001099637, intron 13 of 19)	17897	NR_029775	723921		NR_029775	ENSMUSG00000065573	Mir350	Mirn350|mir-350|mmu-mir-350	microRNA 350	ncRNA
mm_100114.1	chr11	115832805	115832820	+	1	NA	intron (NM_145438, intron 1 of 25)	intron (NM_145438, intron 1 of 25)	8754	NM_001252532	217325	Mm.290450	NM_145438	ENSMUSG00000020782	Llgl2	9130006H11Rik|Llglh2	lethal giant larvae homolog 2 (Drosophila)	protein-coding
mm_144422.1	chr18	21001247	21001266	+	1	NA	promoter-TSS (NM_207623)	promoter-TSS (NM_207623)	-44	NM_019706	56515	Mm.253542	NM_019706	ENSMUSG00000024317	Rnf138	2410015A17Rik|2810480D20Rik|STRIN|Trif|Trif-d	ring finger protein 138	protein-coding
mm_8851.1	chr1	162710417	162710428	-	1	NA	exon (NM_001081290, exon 12 of 35)	exon (NM_001081290, exon 12 of 35)	30134	NM_001081290	226562	Mm.245446	NM_001081290	ENSMUSG00000040225	Prrc2c	1810043M20Rik|9630039I18Rik|A630006J20|Bat2d|Bat2d1|Bat2l2|E130112L15Rik|Prrc3|mKIAA1096	proline-rich coiled-coil 2C	protein-coding
mm_128516.1	chr15	53346119	53346169	-	1	NA	promoter-TSS (NM_010162)	promoter-TSS (NM_010162)	39	NM_010162	14042	Mm.309395	NM_010162	ENSMUSG00000061731	Ext1	AA409028	exostoses (multiple) 1	protein-coding
mm_96657.1	chr11	69395786	69395828	+	1	NA	promoter-TSS (NM_030083)	promoter-TSS (NM_030083)	16	NM_030083	78304	Mm.45683	NM_030083	ENSMUSG00000059278	Naa38	1500034E06Rik|Lsmd1	N(alpha)-acetyltransferase 38, NatC auxiliary subunit	protein-coding
mm_139964.1	chr17	71673211	71673220	+	1	NA	promoter-TSS (NM_177087)	promoter-TSS (NM_177087)	-46	NM_177087	320159	Mm.187372	NM_177087	ENSMUSG00000045761	Fam179a	4632412N22Rik	family with sequence similarity 179, member A	protein-coding
mm_20285.1	chr2	126910367	126910387	-	1	NA	intron (NM_023220, intron 12 of 14)	intron (NM_023220, intron 12 of 14)	-7992	NR_106202	102466258		NR_106202	ENSMUSG00000098896	Mir3473g	Gm27751|mmu-mir-3473g	microRNA 3473g	ncRNA
mm_152894.1	chr19	24862181	24862197	-	1	NA	promoter-TSS (NM_175013)	promoter-TSS (NM_175013)	-347	NM_175013	226041	Mm.105222	NM_175013	ENSMUSG00000041731	Pgm5	4833423B07|9530034F03Rik|D830025G17|aciculin	phosphoglucomutase 5	protein-coding
mm_72487.1	chr8	83666828	83666882	+	1	NA	5' UTR (NM_013641, exon 1 of 3)	5' UTR (NM_013641, exon 1 of 3)	215	NM_013641	19216	Mm.213000	NM_013641	ENSMUSG00000019464	Ptger1	42kDa|EP1|Ptgerep1	prostaglandin E receptor 1 (subtype EP1)	protein-coding
mm_60960.1	chr7	47699937	47699950	+	1	NA	Intergenic	Intergenic	-98571	NM_153067	233222	Mm.240142	NM_153067	ENSMUSG00000078698	Mrgpra3	Mrga3	MAS-related GPR, member A3	protein-coding
mm_166997.1	chr7	46728565	46728605	+	1	NA	3' UTR (NM_011316, exon 4 of 4)	3' UTR (NM_011316, exon 4 of 4)	4018	NM_011316	20211	Mm.3489	NM_011316	ENSMUSG00000040017	Saa4	Saa-4|Saa-5	serum amyloid A 4	protein-coding
mm_120418.1	chr14	65358623	65358652	+	1	NA	promoter-TSS (NM_199029)	promoter-TSS (NM_199029)	-39	NM_199029	380912	Mm.270087	NM_199029	ENSMUSG00000034522	Zfp395	BC053701|Gm910	zinc finger protein 395	protein-coding
mm_29888.1	chr3	131234079	131234087	-	1	NA	3' UTR (NM_008212, exon 8 of 8)	3' UTR (NM_008212, exon 8 of 8)	38018	NM_008212	15107	Mm.260164	NM_008212	ENSMUSG00000027984	Hadh	AA409008|AU019341|AW742602|HCDH|Hadhsc|Schad	hydroxyacyl-Coenzyme A dehydrogenase	protein-coding
mm_28353.1	chr3	89683182	89683189	-	1	NA	Intergenic	Intergenic	-31837	NM_001038587	56417	Mm.316628	NM_019655	ENSMUSG00000027951	Adar	AV242451|Adar1|Adar1p110|Adar1p150|mZaADAR	adenosine deaminase, RNA-specific	protein-coding
mm_24305.1	chr3	89392238	89392251	+	1	NA	non-coding (NR_040403, exon 1 of 2)	non-coding (NR_040403, exon 1 of 2)	380	NR_040403	545539	Mm.393389	NR_040403	ENSMUSG00000074466	Gm15417	ENSMUSG00000074466|OTTMUSG00000021274	predicted gene 15417	ncRNA
mm_136640.1	chr17	5799617	5799649	+	1	NA	non-coding (NR_045079, exon 1 of 3)	non-coding (NR_045079, exon 1 of 3)	143	NR_045080	78512	Mm.23696	NR_045079	ENSMUSG00000096965	3300005D01Rik	-	RIKEN cDNA 3300005D01 gene	ncRNA
mm_84782.1	chr9	76362118	76362128	-	1	NA	Intergenic	Intergenic	-38545	NM_198962	387285	Mm.335300	NM_198962	ENSMUSG00000032360	Hcrtr2	OX2R|mOX2aR|mOX2bR|mOXR2	hypocretin (orexin) receptor 2	protein-coding
mm_167016.1	chr7	63889101	63889116	-	1	NA	3' UTR (NM_021366, exon 2 of 2)	3' UTR (NM_021366, exon 2 of 2)	-27749	NM_001256311	381994	Mm.425466	NM_001256311	ENSMUSG00000095061	E030018B13Rik	Gm1697	RIKEN cDNA E030018B13 gene	protein-coding
mm_130106.1	chr15	89429822	89429832	-	1	NA	promoter-TSS (NR_004843)	promoter-TSS (NR_004843)	100	NR_037154	12651	Mm.485045	NM_007692	ENSMUSG00000022617	Chkb	Chetk|Chkl|Ck|Ck/Ek|Ck/Ek-beta|Ckb|Ckekb|Ek	choline kinase beta	protein-coding
mm_26494.1	chr3	145576155	145576167	+	1	NA	promoter-TSS (NM_001081094)	promoter-TSS (NM_001081094)	-47	NM_001081094	229937	Mm.24586	NM_001081094	ENSMUSG00000074182	Znhit6	2410019A14Rik	zinc finger, HIT type 6	protein-coding
mm_151066.1	chr19	47455618	47455655	+	1	NA	intron (NM_001164717, intron 1 of 13)	intron (NM_001164717, intron 1 of 13)	8775	NM_001164717	14218	Mm.127560	NM_008018	ENSMUSG00000053617	Sh3pxd2a	2310014D11Rik|AA589508|AI256723|AI413738|C230050L11|EG329070|Fish|Gm5098|Sh3md1|TSK5|Tks5	SH3 and PX domains 2A	protein-coding
mm_10998.1	chr2	26389335	26389364	+	1	NA	promoter-TSS (NM_001085407)	promoter-TSS (NM_001085407)	1	NM_173180	66865	Mm.250359	NM_173180	ENSMUSG00000026926	Pmpca	1200002L24Rik|4933435E07Rik|Alpha-MPP|P-55	peptidase (mitochondrial processing) alpha	protein-coding
mm_157196.1	chrX	12128357	12128367	-	1	NA	intron (NM_001168321, intron 1 of 13)	CpG	31984	NR_045434	71458	Mm.196328	NM_029510	ENSMUSG00000040363	Bcor	2900008C10Rik|5830466J11Rik|8430401K06Rik|BcorR|D930024N20Rik|mKIAA1575	BCL6 interacting corepressor	protein-coding
mm_32859.1	chr4	118375497	118375502	+	1	NA	exon (NM_198170, exon 51 of 72)	exon (NM_198170, exon 51 of 72)	15500	NR_003946	68180	Mm.193212	NM_026601	ENSMUSG00000006395	Hyi	2700033B16Rik|6430559E15Rik|HT036	hydroxypyruvate isomerase (putative)	protein-coding
mm_137621.1	chr17	28299659	28299669	+	1	NA	exon (NM_011145, exon 8 of 8)	exon (NM_011145, exon 8 of 8)	-13866	NR_028297	72775	Mm.201859	NM_028348	ENSMUSG00000007570	Fance	2810451D06Rik|AI415634|AW209126	Fanconi anemia, complementation group E	protein-coding
mm_73632.1	chr8	110721497	110721504	+	1	NA	promoter-TSS (NM_198625)	promoter-TSS (NM_198625)	24	NM_198625	244654	Mm.490385	NM_198625	ENSMUSG00000033763	Mtss1l	ABBA	metastasis suppressor 1-like	protein-coding
mm_58172.1	chr6	142702300	142702319	-	1	NA	promoter-TSS (NM_011511)	promoter-TSS (NM_011511)	-35	NM_001310143	20928	Mm.35670	NM_011511	ENSMUSG00000030249	Abcc9	AI414027|AI449286|SUR2A|SUR2B|Sur2	ATP-binding cassette, sub-family C (CFTR/MRP), member 9	protein-coding
mm_88087.1	chr10	68276561	68276584	+	1	NA	intron (NM_023598, intron 2 of 9)	intron (NM_023598, intron 2 of 9)	2154	NM_023598	71371	Mm.440357	NM_023598	ENSMUSG00000019947	Arid5b	4930580B11|5430435G07Rik|AI467247|Desrt|Mrf2|Mrf2alpha|Mrf2beta	AT rich interactive domain 5B (MRF1-like)	protein-coding
mm_160259.1	chr7	108612277	108612277	+	1	NA	promoter-TSS (NM_001011871)	promoter-TSS (NM_001011871)	-32	NM_001011871	258215	Mm.377380	NM_001011871	ENSMUSG00000058244	Olfr506	MOR204-23	olfactory receptor 506	protein-coding
mm_88685.1	chr10	80075583	80075605	+	1	NA	intron (NM_183426, intron 4 of 31)	intron (NM_183426, intron 4 of 31)	21575	NM_001037741	625249	Mm.332810	NM_008162	ENSMUSG00000075706	Gpx4	GPx-4|GSHPx-4|PHGPx|mtPHGPx|snGPx	glutathione peroxidase 4	protein-coding
mm_167984.1	chrX	167330589	167330609	-	1	NA	promoter-TSS (NM_001290758)	promoter-TSS (NM_001290758)	-28	NM_001290756	170743	Mm.23979	NM_133211	ENSMUSG00000044583	Tlr7	-	toll-like receptor 7	protein-coding
mm_163534.1	chr13	10889047	10889047	-	1	NA	Intergenic	Lx8|LINE|L1	-528244	NM_033269	12671	Mm.342315	NM_033269	ENSMUSG00000046159	Chrm3	Chrm-3|M3|M3R	cholinergic receptor, muscarinic 3, cardiac	protein-coding
mm_56565.1	chr6	101377405	101377415	-	1	NA	exon (NM_018884, exon 1 of 10)	exon (NM_018884, exon 1 of 10)	487	NM_018884	55983	Mm.321654	NM_018884	ENSMUSG00000035357	Pdzrn3	1110020C07Rik|AI429718|AL023082|LNX3|SEMACAP3|Semcap3	PDZ domain containing RING finger 3	protein-coding
mm_44007.1	chr5	146948795	146948801	+	1	NA	exon (NM_025652, exon 1 of 9)	exon (NM_025652, exon 1 of 9)	141	NM_025652	66596	Mm.196528	NM_025652	ENSMUSG00000016503	Gtf3a	2010015D03Rik|2610111I01Rik|5330403M05Rik	general transcription factor III A	protein-coding
mm_20324.1	chr2	127444525	127444572	-	1	NA	promoter-TSS (NM_029629)	promoter-TSS (NM_029629)	17	NM_029629	68126	Mm.288676	NM_029629	ENSMUSG00000027371	Fahd2a	1500003K14Rik|B430104H02Rik|Cgi-105|Fahd2	fumarylacetoacetate hydrolase domain containing 2A	protein-coding
mm_120665.1	chr14	70545441	70545457	+	1	NA	5' UTR (NM_180588, exon 1 of 8)	5' UTR (NM_180588, exon 1 of 8)	198	NM_180588	72549	Mm.46742	NM_180588	ENSMUSG00000033589	Reep4	2700029E10Rik	receptor accessory protein 4	protein-coding
mm_163886.1	chr14	25011598	25011598	+	1	NA	Intergenic	Intergenic	131643	NR_045718	75862	Mm.109191	NR_045718		4930572O13Rik	-	RIKEN cDNA 4930572O13 gene	ncRNA
mm_128004.1	chr15	12824606	12824654	-	1	NA	promoter-TSS (NM_029998)	promoter-TSS (NM_029998)	27	NM_029998	77877	Mm.207311	NM_029998	ENSMUSG00000022195	6030458C11Rik	-	RIKEN cDNA 6030458C11 gene	protein-coding
mm_54195.1	chr6	24603405	24603469	-	1	NA	exon (NM_053098, exon 2 of 3)	exon (NM_053098, exon 2 of 3)	5666	NM_053098	93677	Mm.332941	NM_053098	ENSMUSG00000029683	Lmod2	C-Lmod	leiomodin 2 (cardiac)	protein-coding
mm_161945.1	chr19	4197704	4197704	-	1	NA	exon (NM_011237, exon 6 of 11)	exon (NM_011237, exon 6 of 11)	3899	NM_011237	19367	Mm.277629	NM_011237	ENSMUSG00000024824	Rad9a	Rad9	RAD9 checkpoint clamp component A	protein-coding
mm_91350.1	chr10	27616806	27616814	-	1	NA	5' UTR (NM_008481, exon 1 of 64)	5' UTR (NM_008481, exon 1 of 64)	132	NM_008481	16773	Mm.256087	NM_008481	ENSMUSG00000019899	Lama2	5830440B04|dy|mKIAA4087|mer|merosin	laminin, alpha 2	protein-coding
mm_97861.1	chr11	83116869	83116882	+	1	NA	promoter-TSS (NM_011407)	promoter-TSS (NM_011407)	30	NM_011407	20555	Mm.10948	NM_011407	ENSMUSG00000078763	Slfn1	AV316259	schlafen 1	protein-coding
mm_169525.1	chr14	90294871	90294873	+	1	NA	Intergenic	IAPLTR1_Mm|LTR|ERVK	167981	NR_045712	74967	Mm.390704	NR_045712		4930474H20Rik	-	RIKEN cDNA 4930474H20 gene	ncRNA
mm_68295.1	chr7	105737292	105737313	-	1	NA	promoter-TSS (NM_025897)	promoter-TSS (NM_025897)	83	NM_133951	101867	Mm.231400	NM_025897	ENSMUSG00000030888	Rrp8	1500003O22Rik|2900001K19Rik|AW538116	ribosomal RNA processing 8, methyltransferase, homolog (yeast)	protein-coding
mm_42024.1	chr5	108279032	108279044	+	1	NA	3' UTR (NM_026106, exon 3 of 3)	3' UTR (NM_026106, exon 3 of 3)	10141	NM_026106	13486	Mm.303534	NM_026106	ENSMUSG00000029265	Dr1	1700121L09Rik|Dr1l|NC2|NC2beta	down-regulator of transcription 1	protein-coding
mm_110251.1	chr12	31617167	31617180	-	1	NA	exon (NM_001164090, exon 6 of 8)	exon (NM_001164090, exon 6 of 8)	17424	NM_007530	12033	Mm.242379	NM_007530	ENSMUSG00000020650	Bcap29	AW208404|Bap29	B cell receptor associated protein 29	protein-coding
mm_148833.1	chr19	6342563	6342573	+	1	NA	intron (NM_009006, intron 5 of 31)	intron (NM_009006, intron 5 of 31)	1408	NR_117093	26412	Mm.25860	NM_009006	ENSMUSG00000024948	Map4k2	AI385662|BL44|GCK|Rab8ip	mitogen-activated protein kinase kinase kinase kinase 2	protein-coding
mm_96070.1	chr11	59810288	59810299	+	1	NA	promoter-TSS (NM_001271357)	promoter-TSS (NM_001271357)	213	NR_045686	100504104	Mm.391737	NR_045686	ENSMUSG00000087249	Gm16062	ENSMUSG00000072890|OTTMUSG00000029633	predicted gene 16062	ncRNA
mm_103838.1	chr11	83040194	83040219	-	1	NA	promoter-TSS (NR_073523)	promoter-TSS (NR_073523)	-164	NR_073523	237887	Mm.341645	NM_181542	ENSMUSG00000072621	Slfn10-ps	Slfn10|mFLJ00257	schlafen 10, pseudogene	pseudo
mm_74629.1	chr8	13171255	13171291	-	1	NA	exon (NM_010684, exon 5 of 9)	exon (NM_010684, exon 5 of 9)	12112	NM_010684	16783	Mm.16716	NM_010684	ENSMUSG00000031447	Lamp1	CD107a|LGP-120|LGP-A|Lamp-1|P2B	lysosomal-associated membrane protein 1	protein-coding
mm_150321.1	chr19	34574036	34574068	+	1	NA	exon (NM_008332, exon 3 of 3)	exon (NM_008332, exon 3 of 3)	-9477	NM_010501	15959	Mm.426079	NM_010501	ENSMUSG00000074896	Ifit3	Ifi49|P49	interferon-induced protein with tetratricopeptide repeats 3	protein-coding
mm_128462.1	chr15	50806689	50806716	-	1	NA	intron (NM_001310485, intron 5 of 7)	intron (NM_001310485, intron 5 of 7)	82347	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_34755.1	chr4	152338620	152338709	+	1	NA	promoter-TSS (NM_001081376)	promoter-TSS (NM_001081376)	13	NM_001081376	269610	Mm.40192	NM_029216	ENSMUSG00000005045	Chd5	4930532L22Rik|AW060752|B230399N07Rik|CHD-5	chromodomain helicase DNA binding protein 5	protein-coding
mm_150513.1	chr19	39030318	39030319	+	1	NA	intron (NM_028089, intron 4 of 8)	L1_Mur1|LINE|L1	23299	NM_028089	72082	Mm.142581	NM_028089	ENSMUSG00000025002	Cyp2c55	2010318C06Rik	cytochrome P450, family 2, subfamily c, polypeptide 55	protein-coding
mm_78562.1	chr9	35740971	35740971	+	1	NA	promoter-TSS (NM_001167588)	promoter-TSS (NM_001167588)	-78	NM_001167588	100312949	Mm.475848	NM_001167588	ENSMUSG00000091174	Gm17677	Pate-n|Pate10	predicted gene, 17677	protein-coding
mm_14926.1	chr2	151494184	151494203	+	1	NA	promoter-TSS (NM_198326)	promoter-TSS (NM_198326)	11	NM_198326	386649	Mm.419479	NM_198326	ENSMUSG00000027455	Nsfl1c	Munc-18c|Stxbp3a|p47	NSFL1 (p97) cofactor (p47)	protein-coding
mm_108663.1	chr12	86470110	86470122	+	1	NA	intron (NM_011934, intron 1 of 6)	CpG	48472	NM_011934	26380	Mm.235550	NM_011934	ENSMUSG00000021255	Esrrb	Err2|Errb|Estrrb|Nr3b2	estrogen related receptor, beta	protein-coding
mm_13.1	chr1	4857721	4857731	+	1	NA	promoter-TSS (NM_011541)	promoter-TSS (NM_011541)	32	NM_011541	21399	Mm.207263	NM_011541	ENSMUSG00000033813	Tcea1	S-II	transcription elongation factor A (SII) 1	protein-coding
mm_85992.1	chr9	112200018	112200028	-	1	NA	intron (NM_001177619, intron 1 of 10)	intron (NM_001177619, intron 1 of 10)	-12094	NM_028755	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_45739.1	chr5	86518550	86518561	-	1	NA	promoter-TSS (NM_177162)	promoter-TSS (NM_177162)	45	NM_177162	320454	Mm.184522	NM_177162	ENSMUSG00000079451	Tmprss11g	9930032O22Rik|Desc4	transmembrane protease, serine 11g	protein-coding
mm_170783.1	chr2	173984694	173984700	-	1	NA	Intergenic	L1VL4|LINE|L1	-92354	NM_172675	228960	Mm.277977	NM_172675	ENSMUSG00000027522	Stx16	4930401D03|5430410K23Rik|6330500A18Rik|AI648908|AW553605|Syn16	syntaxin 16	protein-coding
mm_63150.1	chr7	123369782	123369802	+	1	NA	exon (NM_001122643, exon 1 of 20)	exon (NM_001122643, exon 1 of 20)	123	NM_001122643	70497	Mm.403318	NM_144529	ENSMUSG00000030766	Arhgap17	5730403H17Rik|Nadrin|Nadrin2|Rich1|Wbp15	Rho GTPase activating protein 17	protein-coding
mm_3200.1	chr1	135818726	135818739	+	1	NA	5' UTR (NM_133664, exon 1 of 10)	5' UTR (NM_133664, exon 1 of 10)	134	NM_133664	16763	Mm.36726	NM_133664	ENSMUSG00000041782	Lad1	-	ladinin	protein-coding
mm_94898.1	chr11	29172935	29172943	+	1	NA	promoter-TSS (NM_134034)	promoter-TSS (NM_134034)	32	NM_134034	104570	Mm.276386	NM_134034	ENSMUSG00000020463	Smek2	AW011752|AW557776|Ppp4r3b|mKIAA1387	SMEK homolog 2, suppressor of mek1 (Dictyostelium)	protein-coding
mm_135216.1	chr16	36656749	36656757	-	1	NA	intron (NM_019388, intron 1 of 7)	intron (NM_019388, intron 1 of 7)	9324	NM_019388	12524	Mm.1452	NM_019388	ENSMUSG00000022901	Cd86	B7|B7-2|B7.2|B70|CLS1|Cd28l2|ETC-1|Ly-58|Ly58|MB7|MB7-2|TS/A-2	CD86 antigen	protein-coding
mm_33801.1	chr4	134926703	134926730	+	1	NA	intron (NM_023665, intron 3 of 4)	intron (NM_023665, intron 3 of 4)	3091	NM_023665	27981	Mm.331964	NM_023665	ENSMUSG00000037266	Rsrp1	2700043I21Rik|D4Ucla2|D4Wsu53e	arginine/serine rich protein 1	protein-coding
mm_44445.1	chr5	21664964	21664974	-	1	NA	3' UTR (NM_178728, exon 5 of 5)	3' UTR (NM_178728, exon 5 of 5)	18985	NM_026034	67211	Mm.260782	NM_026034	ENSMUSG00000038525	Armc10	2810037C14Rik|Svh	armadillo repeat containing 10	protein-coding
mm_68513.1	chr7	111593979	111593990	-	1	NA	intron (NM_173739, intron 3 of 10)	L2a|LINE|L2	185993	NM_173739	233733	Mm.323322	NM_173739	ENSMUSG00000038296	Galnt18	2900011G21Rik|BC024988|Galntl4	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 18	protein-coding
mm_119324.1	chr14	37135474	37135501	+	1	NA	promoter-TSS (NM_001199122)	promoter-TSS (NM_001199122)	-165	NM_078478	66092	Mm.182912	NM_078478	ENSMUSG00000041028	Ghitm	1010001P14Rik|C77840|MICS1|PTD010|Tmbim5	growth hormone inducible transmembrane protein	protein-coding
mm_74506.1	chr8	8617554	8617558	-	1	NA	3' UTR (NM_010111, exon 5 of 5)	3' UTR (NM_010111, exon 5 of 5)	43217	NM_010111	13642	Mm.209813	NM_010111	ENSMUSG00000001300	Efnb2	ELF-2|Epl5|Eplg5|Htk-L|LERK-5|Lerk5|NLERK-1	ephrin B2	protein-coding
mm_162266.1	chr1	6324644	6324646	+	1	NA	Intergenic	L1MC3|LINE|L1	-34686	NM_001195732	620393	Mm.388992	NM_001195732	ENSMUSG00000087247	Fam150a	EG620393	family with sequence similarity 150, member A	protein-coding
mm_46715.1	chr5	110448473	110448481	-	1	NA	promoter-TSS (NM_001142642)	promoter-TSS (NM_001142642)	26	NM_001317042	381668	Mm.348782	NM_028596	ENSMUSG00000043323	Fbrsl1	2410025L10Rik|AI467568|Gm1049|Gm29766|mKIAA1545	fibrosin-like 1	protein-coding
mm_149220.1	chr19	10015040	10015055	+	1	NA	intron (NM_001347429, intron 3 of 12)	intron (NM_001347429, intron 3 of 12)	-3147	NM_001347430	74760	Mm.281969	NM_144538	ENSMUSG00000024663	Rab3il1	1200014K04Rik|AI115013|C76746|Rab3ail1	RAB3A interacting protein (rabin3)-like 1	protein-coding
mm_47799.1	chr5	132509197	132509206	-	1	NA	intron (NM_177047, intron 1 of 18)	intron (NM_177047, intron 1 of 18)	33142	NM_177047	319974	Mm.409595	NM_177047	ENSMUSG00000029673	Auts2	2700063G02Rik|A730011F23Rik|D830032G16Rik	autism susceptibility candidate 2	protein-coding
mm_36325.1	chr4	70410306	70410323	-	1	NA	5' UTR (NM_001313762, exon 1 of 34)	5' UTR (NM_001313762, exon 1 of 34)	121	NM_001313762	214444	Mm.370777	NM_145990	ENSMUSG00000039298	Cdk5rap2	2900018K03Rik|an|mKIAA1633	CDK5 regulatory subunit associated protein 2	protein-coding
mm_53544.1	chr6	136827762	136827798	+	1	NA	intron (NM_021714, intron 1 of 11)	CpG	436	NM_021714	60321	Mm.141197	NM_021714	ENSMUSG00000030216	Wbp11	2510026P17Rik|D6Wsu113e|Npwbp|SIPP1	WW domain binding protein 11	protein-coding
mm_13565.1	chr2	112266457	112266504	+	1	NA	5' UTR (NM_133649, exon 1 of 25)	5' UTR (NM_133649, exon 1 of 25)	166	NM_133649	107723	Mm.491155	NM_133648	ENSMUSG00000027130	Slc12a6	9530023I19Rik|KCC3|gaxp	solute carrier family 12, member 6	protein-coding
mm_122561.1	chr14	49525841	49525903	-	1	NA	promoter-TSS (NM_029238)	promoter-TSS (NM_029238)	-35	NM_029238	75288	Mm.78738	NM_029238	ENSMUSG00000021852	Slc35f4	4930550L21Rik	solute carrier family 35, member F4	protein-coding
mm_45832.1	chr5	87694684	87694694	-	1	NA	exon (NM_001286023, exon 5 of 7)	exon (NM_001286023, exon 5 of 7)	4736	NM_001286020	12991	Mm.268737	NM_009972	ENSMUSG00000063157	Csn2	Csnb	casein beta	protein-coding
mm_15099.1	chr2	153346098	153346137	+	1	NA	promoter-TSS (NM_001039939)	promoter-TSS (NM_001039939)	-22	NM_001039939	228790	Mm.330677	NM_001039939	ENSMUSG00000042548	Asxl1	mKIAA0978	additional sex combs like 1	protein-coding
mm_99472.1	chr11	102436370	102436380	+	1	NA	TTS (NM_199200)	TTS (NM_199200)	6053	NM_008175	14824	Mm.1568	NM_008175	ENSMUSG00000034708	Grn	Pgrn|epithelin	granulin	protein-coding
mm_70670.1	chr8	14897199	14897228	+	1	NA	3' UTR (NM_012000, exon 3 of 3)	3' UTR (NM_012000, exon 3 of 3)	8677	NM_012000	26889	Mm.254027	NM_012000	ENSMUSG00000026317	Cln8	mnd	ceroid-lipofuscinosis, neuronal 8	protein-coding
mm_104524.1	chr11	96075368	96075402	-	1	NA	intron (NM_007506, intron 1 of 4)	intron (NM_007506, intron 1 of 4)	246	NM_001161419	11951	Mm.258	NM_007506	ENSMUSG00000006057	Atp5g1	-	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit C1 (subunit 9)	protein-coding
mm_77635.1	chr8	124152805	124152815	-	1	NA	Intergenic	Intergenic	-78584	NM_139272	108148	Mm.33808	NM_139272	ENSMUSG00000089704	Galnt2	AI480629	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2	protein-coding
mm_163429.1	chr12	83359252	83359254	-	1	NA	intron (NM_058212, intron 2 of 8)	intron (NM_058212, intron 2 of 8)	128483	NM_001267626	70127	Mm.151308	NM_058212	ENSMUSG00000021221	Dpf3	2810403B03Rik|6530402L11Rik|BAF45C|C78788|CERD4|cer-d4	D4, zinc and double PHD fingers, family 3	protein-coding
mm_119904.1	chr14	54949898	54949910	+	1	NA	promoter-TSS (NR_029724)	promoter-TSS (NR_029724)	-762	NR_029724	387204		NR_029724	ENSMUSG00000065432	Mir208a	Mirn208|Mirn208a|mir-208|mir-208a|mmu-mir-208	microRNA 208a	ncRNA
mm_146313.1	chr18	80468179	80468207	+	1	NA	intron (NM_026295, intron 1 of 12)	intron (NM_026295, intron 1 of 12)	1474	NM_026295	67655	Mm.312893	NM_026295	ENSMUSG00000033323	Ctdp1	4930563P03Rik|AW553592	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) phosphatase, subunit 1	protein-coding
mm_72483.1	chr8	83652671	83652711	+	1	NA	promoter-TSS (NM_018771)	promoter-TSS (NM_018771)	13	NM_018771	67903	Mm.20945	NM_018771	ENSMUSG00000019433	Gipc1	GIPC|Glut1CIP|Rgs19ip1|Semcap1|TIP-2|TaxIP2	GIPC PDZ domain containing family, member 1	protein-coding
mm_6460.1	chr1	74026961	74026971	-	1	NA	intron (NM_027884, intron 3 of 34)	intron (NM_027884, intron 3 of 34)	97481	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_97762.1	chr11	81587354	81587364	+	1	NA	intron (NM_001034013, intron 1 of 9)	L2|LINE|L2	-13820	NM_001033765	237880	Mm.435528	NM_001033765		1700071K01Rik	-	RIKEN cDNA 1700071K01 gene	protein-coding
mm_59568.1	chr7	28101255	28101263	+	1	NA	exon (NM_001122603, exon 11 of 20)	exon (NM_001122603, exon 11 of 20)	-28207	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_144733.1	chr18	35562181	35562197	+	1	NA	promoter-TSS (NM_010771)	promoter-TSS (NM_010771)	31	NM_010771	17184	Mm.215034	NM_010771	ENSMUSG00000037236	Matr3	1110061A14Rik|2810017I02Rik|AI841759|AW555618|D030046F20Rik|mKIAA0723	matrin 3	protein-coding
mm_40287.1	chr5	43233715	43233717	+	1	NA	exon (NM_001177379, exon 1 of 11)	exon (NM_001177379, exon 1 of 11)	253	NM_001177379	231207	Mm.7233	NM_175937	ENSMUSG00000039782	Cpeb2	A630055H10Rik|Cpe-bp2	cytoplasmic polyadenylation element binding protein 2	protein-coding
mm_64102.1	chr7	141020869	141020881	+	1	NA	Intergenic	Intergenic	-3983	NM_001033632	213002	Mm.276440	NM_001033632	ENSMUSG00000059108	Ifitm6	A330075D07|Dspa2f|Fgls5|fragilis5	interferon induced transmembrane protein 6	protein-coding
mm_221.1	chr1	17098091	17098130	+	1	NA	promoter-TSS (NM_020604)	promoter-TSS (NM_020604)	-221	NM_020604	57339	Mm.143761	NM_020604	ENSMUSG00000042686	Jph1	ENSMUSG00000054314|JP-1|Jp1	junctophilin 1	protein-coding
mm_51442.1	chr6	80149601	80149609	+	1	NA	intron (NM_001347261, intron 2 of 2)	RSINE1|SINE|B4	129962	NM_178731	243499	Mm.483425	NM_178731	ENSMUSG00000052581	Lrrtm4	7530419J18Rik|A230052N11	leucine rich repeat transmembrane neuronal 4	protein-coding
mm_77071.1	chr8	110039352	110039362	-	1	NA	promoter-TSS (NM_011998)	promoter-TSS (NM_011998)	-23	NM_011998	26887	Mm.89207	NM_011998	ENSMUSG00000035930	Chst4	GST-3|Gn6st-2|HEC-GlcNAc6ST	carbohydrate (chondroitin 6/keratan) sulfotransferase 4	protein-coding
mm_103021.1	chr11	69735019	69735023	-	1	NA	exon (NM_001291068, exon 29 of 29)	exon (NM_001291068, exon 29 of 29)	23612	NM_001291068	20020	Mm.16533	NM_009089	ENSMUSG00000005198	Polr2a	220kDa|Rpb1|Rpo2-1	polymerase (RNA) II (DNA directed) polypeptide A	protein-coding
mm_68994.1	chr7	126649525	126649535	-	1	NA	intron (NM_029339, intron 1 of 9)	CpG	221	NM_029339	75565	Mm.45686	NM_029339	ENSMUSG00000030714	Sgf29	1700023O11Rik|9530025I05Rik|Ccdc101	SAGA complex associated factor 29	protein-coding
mm_153953.1	chr19	47691885	47691904	-	1	NA	5' UTR (NM_007732, exon 1 of 53)	5' UTR (NM_007732, exon 1 of 53)	148	NM_007732	12821	Mm.1225	NM_007732	ENSMUSG00000025064	Col17a1	BP180|Bpag|Bpag2	collagen, type XVII, alpha 1	protein-coding
mm_85798.1	chr9	110101011	110101052	-	1	NA	promoter-TSS (NM_001252683)	promoter-TSS (NM_001252683)	56	NM_001252683	72831	Mm.276305	NM_133347	ENSMUSG00000032480	Dhx30	2810477H02Rik|C130058C04Rik|Ddx30|HELG|Ret-CoR	DEAH (Asp-Glu-Ala-His) box polypeptide 30	protein-coding
mm_40680.1	chr5	65539520	65539536	+	1	NA	intron (NM_001310618, intron 1 of 4)	intron (NM_001310618, intron 1 of 4)	2283	NM_001310619	53323	Mm.319512	NM_016786	ENSMUSG00000029203	Ube2k	AW492011|D5Ertd601e|E2-25k|HIP-2|Hip2|Hypg|Lig	ubiquitin-conjugating enzyme E2K	protein-coding
mm_161227.1	chr13	76384874	76384874	+	1	NA	promoter-TSS (NM_030174)	promoter-TSS (NM_030174)	-87	NM_030174	78771	Mm.316249	NM_030174	ENSMUSG00000021596	Mctp1	2810465F10Rik	multiple C2 domains, transmembrane 1	protein-coding
mm_101659.1	chr11	36677819	36677837	-	1	NA	intron (NM_011856, intron 2 of 28)	intron (NM_011856, intron 2 of 28)	266413	NM_001290702	23964	Mm.439889	NM_011856	ENSMUSG00000049336	Tenm2	Odz2|Odz3|Ten-2|Ten-m2	teneurin transmembrane protein 2	protein-coding
mm_99070.1	chr11	99168398	99168414	+	1	NA	Intergenic	Intergenic	-13329	NM_007719	12775	Mm.2932	NM_007719	ENSMUSG00000037944	Ccr7	CC-CKR-7|CCR-7|CD197|Cdw197|Cmkbr7|EBI1|Ebi1h	chemokine (C-C motif) receptor 7	protein-coding
mm_134547.1	chr16	19884232	19884252	-	1	NA	promoter-TSS (NR_015488)	promoter-TSS (NR_015488)	32	NR_027896	68162	Mm.35159	NR_015488		A930003A15Rik	AI853191	RIKEN cDNA A930003A15 gene	ncRNA
mm_167427.1	chr8	115705890	115705900	-	1	NA	exon (NM_001025577, exon 1 of 1)	exon (NM_001025577, exon 1 of 1)	999	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_141206.1	chr17	27043129	27043145	-	1	NA	Intergenic	Intergenic	13878	NM_027544	70772	Mm.440437	NM_027544	ENSMUSG00000048731	Ggnbp1	0610031G08Rik|mdf	gametogenetin binding protein 1	protein-coding
mm_101091.1	chr11	11873215	11873265	-	1	NA	exon (NM_016672, exon 4 of 15)	exon (NM_016672, exon 4 of 15)	5117	NR_045178	73321	Mm.443306	NR_045178	ENSMUSG00000086391	1700042O10Rik	-	RIKEN cDNA 1700042O10 gene	ncRNA
mm_81575.1	chr9	110422292	110422296	+	1	NA	exon (NM_008694, exon 4 of 4)	exon (NM_008694, exon 4 of 4)	2486	NM_008694	18054	Mm.236225	NM_008694	ENSMUSG00000032484	Ngp	bectenecin	neutrophilic granule protein	protein-coding
mm_83355.1	chr9	44379261	44379352	-	1	NA	promoter-TSS (NM_021395)	promoter-TSS (NM_021395)	-184	NM_021395	12282	Mm.116721	NM_021395	ENSMUSG00000032115	Hyou1	AI415631|CBP-140|Cab140|Grp170|Orp150	hypoxia up-regulated 1	protein-coding
mm_43914.1	chr5	144406526	144406551	+	1	NA	Intergenic	Intergenic	48013	NR_102373	100579137		NR_102372	ENSMUSG00000104600	Dmrt1i	Dmr	Dmrt1 interacting ncRNA	ncRNA
mm_68426.1	chr7	109781539	109781554	-	1	NA	promoter-TSS (NM_020610)	promoter-TSS (NM_020610)	-1	NM_020610	78593	Mm.275374	NM_020610	ENSMUSG00000034825	Nrip3	A330103B05Rik|D7H11orf14|ICRFP703B1614Q5.2	nuclear receptor interacting protein 3	protein-coding
mm_13576.1	chr2	112361745	112361752	+	1	NA	3' UTR (NM_133649, exon 25 of 25)	3' UTR (NM_133649, exon 25 of 25)	6279	NM_026519	68032	Mm.220942	NM_026519	ENSMUSG00000027131	Emc4	2610318K02Rik|Tmem85	ER membrane protein complex subunit 4	protein-coding
mm_118667.1	chr14	21848511	21848545	+	1	NA	5' UTR (NM_176925, exon 1 of 3)	5' UTR (NM_176925, exon 1 of 3)	382	NM_026965	69156	Mm.11827	NM_026965	ENSMUSG00000021773	Comtd1	1810030M08Rik|MT773	catechol-O-methyltransferase domain containing 1	protein-coding
mm_161902.1	chr18	59175197	59175197	+	1	NA	promoter-TSS (NM_001081328)	promoter-TSS (NM_001081328)	-143	NM_001081328	78923	Mm.84007	NM_001081328	ENSMUSG00000058152	Chsy3	4833446K15Rik|AI662215	chondroitin sulfate synthase 3	protein-coding
mm_126819.1	chr15	88751820	88751831	+	1	NA	intron (NM_181412, intron 1 of 2)	CpG	114	NM_181412	223773	Mm.396622	NM_181412	ENSMUSG00000034333	Zbed4	1700009F06Rik	zinc finger, BED type containing 4	protein-coding
mm_17366.1	chr2	26902786	26902828	-	1	NA	promoter-TSS (NM_009298)	promoter-TSS (NM_009298)	80	NM_009298	20935	Mm.245577	NM_009298	ENSMUSG00000036160	Surf6	D2Wsu129e|Surf-6	surfeit gene 6	protein-coding
mm_107865.1	chr12	69907794	69907808	+	1	NA	intron (NM_178628, intron 1 of 14)	intron (NM_178628, intron 1 of 14)	-14638	NM_201519	399510	Mm.291936	NM_201519	ENSMUSG00000034761	Map4k5	4432415E19Rik|GCKR|KHS|MAPKKKK5	mitogen-activated protein kinase kinase kinase kinase 5	protein-coding
mm_88902.1	chr10	81177694	81177737	+	1	NA	exon (NM_007907, exon 2 of 14)	exon (NM_007907, exon 2 of 14)	1084	NM_007907	13629	Mm.2903	NM_007907	ENSMUSG00000034994	Eef2	Ef-2	eukaryotic translation elongation factor 2	protein-coding
mm_79887.1	chr9	65294276	65294341	+	1	NA	promoter-TSS (NM_011802)	promoter-TSS (NM_011802)	48	NM_011802	270166	Mm.30088	NM_011802	ENSMUSG00000015357	Clpx	AU014732|E330029I21	caseinolytic mitochondrial matrix peptidase chaperone subunit	protein-coding
mm_158439.1	chrX	140062720	140062726	-	1	NA	promoter-TSS (NM_001081668)	promoter-TSS (NM_001081668)	-155	NM_001081668	279706	Mm.102590	NM_001081668	ENSMUSG00000072944	Nup62cl	Gm719	nucleoporin 62 C-terminal like	protein-coding
mm_89835.1	chr10	106632752	106632813	+	1	NA	intron (NM_001205341, intron 3 of 31)	intron (NM_001205341, intron 3 of 31)	-30302	NR_131026	75833	Mm.159596	NR_131026		4930532I03Rik	-	RIKEN cDNA 4930532I03 gene	ncRNA
mm_58825.1	chr7	16733666	16733679	+	1	NA	Intergenic	Intergenic	-4772	NM_198613	232910	Mm.333597	NM_198613	ENSMUSG00000008036	Ap2s1	AI043088	adaptor-related protein complex 2, sigma 1 subunit	protein-coding
mm_14064.1	chr2	122704232	122704247	+	1	NA	Intergenic	MLT1F|LTR|ERVL-MaLR	-1576	NM_001290993	22785	Mm.27801	NM_011774	ENSMUSG00000005802	Slc30a4	Znt4|lm|znT-4	solute carrier family 30 (zinc transporter), member 4	protein-coding
mm_58799.1	chr7	16248414	16248462	+	1	NA	exon (NM_001173550, exon 2 of 2)	exon (NM_001173550, exon 2 of 2)	-4284	NM_176912	319430	Mm.239570	NM_176912	ENSMUSG00000074361	C5ar2	C5L2|E030029A11Rik|Gpr77	complement component 5a receptor 2	protein-coding
mm_26334.1	chr3	142546510	142546520	+	1	NA	exon (NM_001083312, exon 11 of 11)	exon (NM_001083312, exon 11 of 11)	-13537	NM_018734	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_110253.1	chr12	31634503	31634514	-	1	NA	promoter-TSS (NM_007530)	promoter-TSS (NM_007530)	89	NM_007530	12033	Mm.242379	NM_007530	ENSMUSG00000020650	Bcap29	AW208404|Bap29	B cell receptor associated protein 29	protein-coding
mm_9349.1	chr1	172067835	172067858	-	1	NA	exon (NM_021607, exon 15 of 17)	exon (NM_021607, exon 15 of 17)	-10250	NM_010916	18071	Mm.2474	NM_010916	ENSMUSG00000051251	Nhlh1	Hen1|Nscl|Tal2|bHLHa35	nescient helix loop helix 1	protein-coding
mm_161975.1	chr19	12883668	12883668	+	1	NA	promoter-TSS (NM_146699)	promoter-TSS (NM_146699)	-215	NM_146699	258694	Mm.391190	NM_146699	ENSMUSG00000045126	Olfr1445	MOR202-7	olfactory receptor 1445	protein-coding
mm_40768.1	chr5	67054463	67054469	+	1	NA	3' UTR (NM_001001980, exon 26 of 26)	3' UTR (NM_001001980, exon 26 of 26)	44660	NM_008888	18935	Mm.62505	NM_008888	ENSMUSG00000012520	Phox2b	Dilp1|NBPhox|Pmx2b|Px2b	paired-like homeobox 2b	protein-coding
mm_59461.1	chr7	27233004	27233064	+	1	NA	promoter-TSS (NM_133770)	promoter-TSS (NM_133770)	21	NM_133770	76889	Mm.124728	NM_133770	ENSMUSG00000003762	Coq8b	0610012P18Rik|Adck4	coenzyme Q8B	protein-coding
mm_158009.1	chrX	95478077	95478087	-	1	NA	promoter-TSS (NM_080858)	promoter-TSS (NM_080858)	47	NM_080858	70392	Mm.79122	NM_080858	ENSMUSG00000031204	Asb12	2310036C05Rik|Asb-12	ankyrin repeat and SOCS box-containing 12	protein-coding
mm_136646.1	chr17	5841308	5841377	+	1	NA	promoter-TSS (NM_025664)	promoter-TSS (NM_025664)	-38	NM_025664	66616	Mm.89515	NM_025664	ENSMUSG00000002365	Snx9	2700073N08Rik|SDP1|SH3PX1	sorting nexin 9	protein-coding
mm_57618.1	chr6	128200577	128200592	-	1	NA	Intergenic	CpG	-16781	NR_077223	330427	Mm.426356	NR_077223	ENSMUSG00000107879	9330102E08Rik	-	RIKEN cDNA 9330102E08 gene	ncRNA
mm_4734.1	chr1	181576619	181576632	+	1	NA	Intergenic	Intergenic	-65174	NM_207280	403180	Mm.220754	NM_207280	ENSMUSG00000050625	Ccdc121	6530421E24Rik|Gm755	coiled-coil domain containing 121	protein-coding
mm_126932.1	chr15	91706594	91706605	+	1	NA	intron (NM_025730, intron 12 of 50)	intron (NM_025730, intron 12 of 50)	33375	NM_025730	66725	Mm.37558	NM_025730	ENSMUSG00000036273	Lrrk2	4921513O20Rik|9330188B09Rik|AW561911|D630001M17Rik|Gm927|cI-46	leucine-rich repeat kinase 2	protein-coding
mm_47106.1	chr5	118466470	118466485	-	1	NA	Intergenic	MIRb|SINE|MIR	-94242	NM_001347445	76199	Mm.206238	NM_172424	ENSMUSG00000018076	Med13l	2210413I17Rik|6330591G05Rik|9030618F05Rik|Thrap2|Trap240L|mKIAA1025	mediator complex subunit 13-like	protein-coding
mm_164373.1	chr16	24629607	24629618	+	1	NA	intron (NM_001145952, intron 4 of 11)	intron (NM_001145952, intron 4 of 11)	-92243	NM_001145954	210126	Mm.209385	NM_178665	ENSMUSG00000033306	Lpp	9430020K16Rik|AA959454|AU024130|B130055L10Rik|C79715|D630048H16	LIM domain containing preferred translocation partner in lipoma	protein-coding
mm_167729.1	chr9	103220937	103220951	+	1	NA	exon (NM_133977, exon 9 of 17)	exon (NM_133977, exon 9 of 17)	9342	NM_133977	22041	Mm.37214	NM_133977	ENSMUSG00000032554	Trf	AI266983|Cd176|HP|Tf|Tfn|hpx	transferrin	protein-coding
mm_93757.1	chr10	120175767	120175775	-	1	NA	intron (NM_028679, intron 5 of 11)	intron (NM_028679, intron 5 of 11)	25766	NM_028679	73914	Mm.146194	NM_028679	ENSMUSG00000020227	Irak3	4833428C18Rik|AI563835|IRAK-M	interleukin-1 receptor-associated kinase 3	protein-coding
mm_153029.1	chr19	31664655	31664690	-	1	NA	promoter-TSS (NM_011160)	promoter-TSS (NM_011160)	-302	NM_011160	19091	Mm.381170	NM_011160	ENSMUSG00000052920	Prkg1	AW125416|CGKI|Gm19690|Prkg1b|Prkgr1b	protein kinase, cGMP-dependent, type I	protein-coding
mm_47190.1	chr5	120754348	120754357	-	1	NA	3' UTR (NM_145226, exon 16 of 16)	3' UTR (NM_145226, exon 16 of 16)	-4504	NM_001347448	246728	Mm.260926	NM_145227	ENSMUSG00000032690	Oas2	Oasl11	2'-5' oligoadenylate synthetase 2	protein-coding
mm_22760.1	chr3	19989177	19989191	+	1	NA	exon (NM_007752, exon 18 of 19)	exon (NM_007752, exon 18 of 19)	32130	NM_007752	12870	Mm.13787	NM_007752	ENSMUSG00000003617	Cp	D3Ertd555e	ceruloplasmin	protein-coding
mm_147011.1	chr18	34508164	34508198	-	1	NA	Intergenic	Intergenic	-1358	NM_146084	225358	Mm.226899	NM_146084	ENSMUSG00000036501	Fam13b	2610024E20Rik|AW060714|AW546153	family with sequence similarity 13, member B	protein-coding
mm_125269.1	chr15	35653835	35653844	+	1	NA	intron (NM_177151, intron 30 of 61)	intron (NM_177151, intron 30 of 61)	7079	NR_035527	100316736		NR_035527	ENSMUSG00000076333	Mir599	mmu-mir-599	microRNA 599	ncRNA
mm_90765.1	chr10	5712003	5712009	-	1	NA	Intergenic	Intergenic	72788	NM_001313969	22353	Mm.98916	NM_011702	ENSMUSG00000019772	Vip	-	vasoactive intestinal polypeptide	protein-coding
mm_79283.1	chr9	50885489	50885498	+	1	NA	intron (NM_001286553, intron 15 of 16)	intron (NM_001286553, intron 15 of 16)	28569	NM_001286553	73699	Mm.7726	NM_028614	ENSMUSG00000032058	Ppp2r1b	2410091N08Rik|AI790395	protein phosphatase 2, regulatory subunit A, beta	protein-coding
mm_145258.1	chr18	52559194	52559198	+	1	NA	Intergenic	Intergenic	-29329	NM_001286182	16948	Mm.172	NM_010728	ENSMUSG00000024529	Lox	AI893619|TSC-160|rrg	lysyl oxidase	protein-coding
mm_131703.1	chr16	20717861	20717880	+	1	NA	promoter-TSS (NM_145632)	promoter-TSS (NM_145632)	44	NM_145632	245841	Mm.288730	NM_145632	ENSMUSG00000021018	Polr2h	-	polymerase (RNA) II (DNA directed) polypeptide H	protein-coding
mm_109761.1	chr12	117864910	117864937	+	1	NA	intron (NM_146040, intron 1 of 9)	intron (NM_146040, intron 1 of 9)	21062	NM_146040	217946	Mm.281149	NM_146040	ENSMUSG00000021175	Cdca7l	BC006933|JPO2	cell division cycle associated 7 like	protein-coding
mm_138913.1	chr17	43602828	43602847	+	1	NA	exon (NM_013737, exon 8 of 12)	exon (NM_013737, exon 8 of 12)	-11328	NR_045444	73504	Mm.9277	NR_045444	ENSMUSG00000090307	1700071M16Rik	-	RIKEN cDNA 1700071M16 gene	ncRNA
mm_127119.1	chr15	98092570	98092603	+	1	NA	promoter-TSS (NM_001163488)	promoter-TSS (NM_001163488)	-3	NM_001163488	18642	Mm.272582	NM_021514	ENSMUSG00000033065	Pfkm	AI131669|ATP-PFK|PFK-A|PFK-M|Pfk-4|Pfk4|Pfka|Pfkx	phosphofructokinase, muscle	protein-coding
mm_105496.1	chr11	106159903	106159913	-	1	NA	intron (NM_172397, intron 1 of 4)	CpG	234	NM_172397	67803	Mm.21687	NM_172397	ENSMUSG00000040699	Limd2	0610025L06Rik|AI413966	LIM domain containing 2	protein-coding
mm_64906.1	chr7	16047913	16047947	-	1	NA	Intergenic	CpG	-23915	NM_001347559	666528	Mm.290718	NM_001099277	ENSMUSG00000078796	Zfp541	EG666528|Znf541	zinc finger protein 541	protein-coding
mm_129444.1	chr15	78544644	78544658	-	1	NA	promoter-TSS (NM_009218)	promoter-TSS (NM_009218)	-306	NM_009218	20607	Mm.211411	NM_009218	ENSMUSG00000044933	Sstr3	Smstr-3|Smstr3|sst3	somatostatin receptor 3	protein-coding
mm_161097.1	chr12	98757103	98757103	+	1	NA	non-coding (NR_027648, exon 4 of 13)	non-coding (NR_027648, exon 4 of 13)	10135	NM_029334	75553	Mm.25549	NM_029334	ENSMUSG00000021012	Zc3h14	1010001P15Rik|1700016A15Rik|2700069A02Rik|AU014748	zinc finger CCCH type containing 14	protein-coding
mm_172234.1	chr6	67941699	67941718	-	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	-376009	NR_003100	75070	Mm.463364	NR_003100		4930515G16Rik	-	myc induced nuclear antigen pseudogene	pseudo
mm_78987.1	chr9	45399657	45399669	+	1	NA	promoter-TSS (NR_028499)	promoter-TSS (NR_028499)	-46	NR_028499	11936	Mm.22742	NM_007503	ENSMUSG00000059412	Fxyd2	Atp1g1	FXYD domain-containing ion transport regulator 2	protein-coding
mm_48848.1	chr5	149618996	149619014	-	1	NA	exon (NM_013559, exon 15 of 18)	exon (NM_013559, exon 15 of 18)	17310	NM_013559	15505	Mm.270681	NM_013559	ENSMUSG00000029657	Hsph1	105kDa|AI790491|Hsp105|Hsp110|hsp-E7I|hsp110/105	heat shock 105kDa/110kDa protein 1	protein-coding
mm_164692.1	chr17	47938252	47938252	-	1	NA	Intergenic	Intergenic	-13620	NM_001110825	74123	Mm.240062	NM_028767	ENSMUSG00000023991	Foxp4	1200010K03Rik|2310007G05Rik|mFKHLA	forkhead box P4	protein-coding
mm_134835.1	chr16	26358120	26358141	-	1	NA	3' UTR (NM_016674, exon 4 of 4)	3' UTR (NM_016674, exon 4 of 4)	13709	NM_016674	12737	Mm.289441	NM_016674	ENSMUSG00000022512	Cldn1	AI596271	claudin 1	protein-coding
mm_4142.1	chr1	170885084	170885098	+	1	NA	exon (NM_023173, exon 1 of 6)	exon (NM_023173, exon 1 of 6)	449	NM_023173	80915	Mm.34365	NM_023173	ENSMUSG00000026659	Dusp12	1190004O14Rik|AA027408|AW049275|ENSMUSG00000045460|ESTM36|LMW-DSP4|T-DSP4|VH1|mVH1	dual specificity phosphatase 12	protein-coding
mm_2685.1	chr1	127306677	127306696	+	1	NA	5' UTR (NM_145128, exon 3 of 18)	5' UTR (NM_145128, exon 3 of 18)	101700	NM_145128	107895	Mm.214682	NM_145128	ENSMUSG00000036155	Mgat5	4930471A21Rik|5330407H02Rik|AI480971|GlcNAc-TV	mannoside acetylglucosaminyltransferase 5	protein-coding
mm_57408.1	chr6	124865718	124865726	-	1	NA	3' UTR (NM_013488, exon 10 of 10)	3' UTR (NM_013488, exon 10 of 10)	-1805	NM_013533	14788	Mm.2514	NM_013533	ENSMUSG00000038390	Gpr162	A-2|BC031437|Grca	G protein-coupled receptor 162	protein-coding
mm_169752.1	chr15	90764668	90764685	-	1	NA	Intergenic	Intergenic	-85288	NM_001033851	66871	Mm.290991	NM_025815	ENSMUSG00000052560	Cpne8	1200003E11Rik|1500031E20Rik	copine VIII	protein-coding
mm_52827.1	chr6	121359249	121359292	+	1	NA	intron (NM_001347433, intron 9 of 14)	intron (NM_001347433, intron 9 of 14)	12573	NM_133661	14411	Mm.274506	NM_133661	ENSMUSG00000030109	Slc6a12	BGT1|GAT-2|GAT2|Gabt2	solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12	protein-coding
mm_53116.1	chr6	125096787	125096799	+	1	NA	promoter-TSS (NR_106012)	promoter-TSS (NR_106012)	-231	NR_106012	102466272		NR_106012	ENSMUSG00000098762	Mir7045	Gm27758|mmu-mir-7045	microRNA 7045	ncRNA
mm_133031.1	chr16	57352772	57352782	+	1	NA	promoter-TSS (NM_001040397)	promoter-TSS (NM_001040397)	-500	NM_001040397	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding
mm_111054.1	chr12	80110022	80110049	-	1	NA	exon (NM_007564, exon 2 of 2)	exon (NM_007564, exon 2 of 2)	2978	NM_007564	12192	Mm.235132	NM_007564	ENSMUSG00000021127	Zfp36l1	AW742437|AW743212|Berg36|Brf1|D530020L18Rik|ERF1|TIS11b|cMG1	zinc finger protein 36, C3H type-like 1	protein-coding
mm_162567.1	chr1	172856456	172856456	-	1	NA	Intergenic	Lx9|LINE|L1	38598	NM_011318	20219	Mm.330510	NM_011318	ENSMUSG00000026542	Apcs	Sap	serum amyloid P-component	protein-coding
mm_42300.1	chr5	114623661	114623661	+	1	NA	exon (NM_022017, exon 15 of 16)	exon (NM_022017, exon 15 of 16)	34760	NM_022017	63873	Mm.266450	NM_022017	ENSMUSG00000014158	Trpv4	0610033B08Rik|OTRPC4|Trp12|VR-OAC|VRL-2|VROAC	transient receptor potential cation channel, subfamily V, member 4	protein-coding
mm_24063.1	chr3	87915561	87915572	+	1	NA	3' UTR (NM_008231, exon 6 of 6)	3' UTR (NM_008231, exon 6 of 6)	-3978	NM_026591	67707	Mm.393802	NM_026591	ENSMUSG00000019710	Mrpl24	2010005E08Rik|2810470K06Rik|6720473G22Rik|AA407670	mitochondrial ribosomal protein L24	protein-coding
mm_28959.1	chr3	100684591	100684626	-	1	NA	exon (NM_010763, exon 1 of 13)	exon (NM_010763, exon 1 of 13)	865	NM_010763	17156	Mm.271617	NM_010763	ENSMUSG00000008763	Man1a2	AI428775|AI528764|AI854422|Man1b|PCR2	mannosidase, alpha, class 1A, member 2	protein-coding
mm_132984.1	chr16	52176084	52176086	+	1	NA	intron (NM_001033238, intron 13 of 17)	intron (NM_001033238, intron 13 of 17)	144536	NM_001033238	208650	Mm.328206	NM_001033238	ENSMUSG00000022637	Cblb	AI429560|AI851073|Cbl-b	Casitas B-lineage lymphoma b	protein-coding
mm_94497.1	chr11	7119743	7119745	+	1	NA	intron (NM_009622, intron 4 of 19)	L1MEc|LINE|L1	56255	NM_009622	432530	Mm.259733	NM_009622	ENSMUSG00000020431	Adcy1	AC1|D11Bwg1392e|I-AC|brl|mKIAA4070	adenylate cyclase 1	protein-coding
mm_46494.1	chr5	105132402	105132410	-	1	NA	intron (NM_008620, intron 3 of 10)	L1M2|LINE|L1	7146	NM_008620	17472	Mm.440525	NM_008620	ENSMUSG00000079363	Gbp4	AW228052|Mag-2|Mpa-2|Mpa2	guanylate binding protein 4	protein-coding
mm_165902.1	chr4	48279858	48279881	+	1	NA	promoter-TSS (NM_029572)	promoter-TSS (NM_029572)	109	NM_001281977	16348	Mm.317706	NM_010569	ENSMUSG00000028344	Invs	Nphp2|inv	inversin	protein-coding
mm_102196.1	chr11	54437933	54437948	-	1	NA	promoter-TSS (NM_173753)	promoter-TSS (NM_173753)	-239	NM_173753	216742	Mm.34087	NM_173753	ENSMUSG00000035992	Fnip1	A730024A03Rik|AI838773|AW557298	folliculin interacting protein 1	protein-coding
mm_147885.1	chr18	64692158	64692163	-	1	NA	Intergenic	MER33|DNA|hAT-Charlie	-31160	NM_001001488	54670	Mm.270043	NM_001001488	ENSMUSG00000039529	Atp8b1	AI451886|FIC1|Ic	ATPase, class I, type 8B, member 1	protein-coding
mm_69344.1	chr7	130192318	130192322	-	1	NA	intron (NM_001347638, intron 7 of 15)	intron (NM_001347638, intron 7 of 15)	74488	NM_010207	14183	Mm.16340	NM_010207	ENSMUSG00000030849	Fgfr2	AU043015|AW556123|Bek|Fgfr-2|Fgfr-7|Fgfr7|KGFR|KGFRTr|svs	fibroblast growth factor receptor 2	protein-coding
mm_161787.1	chr17	45659281	45659281	-	1	NA	promoter-TSS (NM_001013767)	promoter-TSS (NM_001013767)	28	NM_001013767	268958	Mm.426026	NM_001013767	ENSMUSG00000058626	Capn11	-	calpain 11	protein-coding
mm_126067.1	chr15	77356457	77356500	+	1	NA	Intergenic	Intergenic	42632	NM_029419	75761	Mm.232636	NM_029419	ENSMUSG00000010601	Apol7a	9130022K13Rik|Apol3	apolipoprotein L 7a	protein-coding
mm_59088.1	chr7	19696365	19696396	+	1	NA	exon (NM_009696, exon 4 of 4)	exon (NM_009696, exon 4 of 4)	2018	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_38776.1	chr4	148038770	148038816	-	1	NA	promoter-TSS (NM_010840)	promoter-TSS (NM_010840)	20	NM_011929	26372	Mm.89987	NM_011929	ENSMUSG00000029016	Clcn6	AI850629|Clc6	chloride channel, voltage-sensitive 6	protein-coding
mm_58525.1	chr7	4147801	4147826	+	1	NA	TTS (NM_175529)	TTS (NM_175529)	2059	NM_175529	243813	Mm.347643	NM_175529	ENSMUSG00000043432	Leng9	9530024C23Rik|F630035L11Rik	leukocyte receptor cluster (LRC) member 9	protein-coding
mm_120822.1	chr14	75136560	75136589	+	1	NA	5' UTR (NM_008879, exon 1 of 17)	5' UTR (NM_008879, exon 1 of 17)	149	NM_008879	18826	Mm.153911	NM_008879	ENSMUSG00000021998	Lcp1	AW536232|D14Ertd310e|LCP-1|Pls2|pp65	lymphocyte cytosolic protein 1	protein-coding
mm_113608.1	chr13	41249961	41249973	+	1	NA	5' UTR (NM_001135577, exon 1 of 2)	5' UTR (NM_001135577, exon 1 of 2)	123	NM_001135577	108934	Mm.38578	NM_001135577	ENSMUSG00000091264	Smim13	2900036K02Rik	small integral membrane protein 13	protein-coding
mm_69879.1	chr7	141636740	141636744	-	1	NA	intron (NM_001330001, intron 31 of 33)	intron (NM_001330001, intron 31 of 33)	16041	NR_106030	102466798		NR_106030	ENSMUSG00000098759	Mir7063	Gm27654|mmu-mir-7063	microRNA 7063	ncRNA
mm_56659.1	chr6	113483157	113483168	-	1	NA	promoter-TSS (NM_133930)	promoter-TSS (NM_133930)	-407	NM_133930	171508	Mm.41593	NM_133930	ENSMUSG00000030284	Creld1	AI843811	cysteine-rich with EGF-like domains 1	protein-coding
mm_12488.1	chr2	71719386	71719393	+	1	NA	promoter-TSS (NR_037979)	promoter-TSS (NR_037979)	-28	NR_037979	381371	Mm.330284	NM_201366	ENSMUSG00000064263	Platr26	Gm1631	pluripotency associated transcript 26	ncRNA
mm_45269.1	chr5	64603140	64603186	-	1	NA	intron (NR_045078, intron 2 of 3)	intron (NR_045078, intron 2 of 3)	7536	NR_045078	100042198	Mm.25191	NR_045078	ENSMUSG00000105402	Gm3716	Gm1683	predicted gene 3716	ncRNA
mm_61485.1	chr7	75698396	75698401	+	1	NA	intron (NM_029332, intron 16 of 36)	(T)n|Simple_repeat|Simple_repeat	-149940	NM_001122780	207952	Mm.206223	NM_029652	ENSMUSG00000055652	Klhl25	2810402K13Rik|BC027373|Enc-1	kelch-like 25	protein-coding
mm_27037.1	chr3	26331807	26331820	-	1	NA	promoter-TSS (NM_138666)	promoter-TSS (NM_138666)	96	NM_138666	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_110394.1	chr12	41878597	41878634	-	1	NA	intron (NM_053122, intron 6 of 6)	intron (NM_053122, intron 6 of 6)	-392558	NM_010733	16981	Mm.404786	NM_010733	ENSMUSG00000036295	Lrrn3	NLRR-3	leucine rich repeat protein 3, neuronal	protein-coding
mm_75797.1	chr8	70110234	70110244	-	1	NA	exon (NM_007789, exon 7 of 15)	exon (NM_007789, exon 7 of 15)	-7653	NR_106033	102465646		NR_106033	ENSMUSG00000099042	Mir7066	Gm27290|mmu-mir-7066	microRNA 7066	ncRNA
mm_161401.1	chr14	120297674	120297674	+	1	NA	intron (NM_175341, intron 1 of 8)	intron (NM_175341, intron 1 of 8)	22005	NM_175341	105559	Mm.238266	NM_175341	ENSMUSG00000022139	Mbnl2	1110002M11Rik|AI047808|AI837313|AI849185|AL118326|MBLL|R75232|mKIAA4072	muscleblind-like 2	protein-coding
mm_30857.1	chr4	28847310	28847313	+	1	NA	intron (NM_001290434, intron 3 of 16)	intron (NM_001290434, intron 3 of 16)	34166	NM_001122889	13841	Mm.257266	NM_010141	ENSMUSG00000028289	Epha7	Cek11|Ebk|Ehk3|Hek11|Mdk1	Eph receptor A7	protein-coding
mm_3631.1	chr1	152807828	152807876	+	1	NA	5' UTR (NM_010877, exon 2 of 16)	5' UTR (NM_010877, exon 2 of 16)	7699	NM_010877	17970	Mm.270307	NM_010877	ENSMUSG00000026480	Ncf2	NOXA2|Ncf-2|p67phox	neutrophil cytosolic factor 2	protein-coding
mm_25848.1	chr3	129532398	129532440	+	1	NA	promoter-TSS (NM_130450)	promoter-TSS (NM_130450)	33	NM_130450	170439	Mm.314113	NM_130450	ENSMUSG00000041220	Elovl6	C77826|FAE|LCE	ELOVL family member 6, elongation of long chain fatty acids (yeast)	protein-coding
mm_33988.1	chr4	137724447	137724475	+	1	NA	promoter-TSS (NR_138592)	promoter-TSS (NR_138592)	0	NR_138592	110351	Mm.180763	NM_029563	ENSMUSG00000041351	Rap1gap	1300019I11Rik|2310004O14Rik|AI427470|ARPP-90|Gap|Rap1GAP1|Rap1ga1	Rap1 GTPase-activating protein	protein-coding
mm_132244.1	chr16	32751059	32751069	+	1	NA	exon (NM_080457, exon 2 of 27)	exon (NM_080457, exon 2 of 27)	15178	NM_080457	140474	Mm.214599	NM_080457	ENSMUSG00000079620	Muc4	4933405I11Rik|Asgp	mucin 4	protein-coding
mm_11068.1	chr2	27676442	27676454	+	1	NA	promoter-TSS (NM_011305)	promoter-TSS (NM_011305)	-753	NM_011305	20181	Mm.24624	NM_011305	ENSMUSG00000015846	Rxra	9530071D11Rik|Nr2b1|RXRalpha1	retinoid X receptor alpha	protein-coding
mm_171645.1	chr4	32964847	32964852	+	1	NA	Intergenic	Intergenic	-14023	NM_001012451	140577	Mm.214766	NM_080471	ENSMUSG00000040183	Ankrd6	-	ankyrin repeat domain 6	protein-coding
mm_89697.1	chr10	97607167	97607244	+	1	NA	promoter-TSS (NM_008438)	promoter-TSS (NM_008438)	0	NM_008438	16545	Mm.6228	NM_008438	ENSMUSG00000019932	Kera	CNA2|SLRR2B	keratocan	protein-coding
mm_12329.1	chr2	69403967	69404014	+	1	NA	TTS (NM_175512)	TTS (NM_175512)	23528	NM_175512	241452	Mm.211655	NM_175512	ENSMUSG00000027068	Dhrs9	C730025I08Rik|Rdh15	dehydrogenase/reductase (SDR family) member 9	protein-coding
mm_98668.1	chr11	96282649	96282721	+	1	NA	5' UTR (NM_010461, exon 1 of 2)	5' UTR (NM_010461, exon 1 of 2)	780	NM_010461	15416	Mm.4822	NM_010461	ENSMUSG00000056648	Hoxb8	Hox-2.4	homeobox B8	protein-coding
mm_94085.1	chr10	128494137	128494151	-	1	NA	promoter-TSS (NM_010860)	promoter-TSS (NM_010860)	-258	NM_010860	17904	Mm.337074	NM_010860	ENSMUSG00000090841	Myl6	ESMLC|LC17|LC17-GI|MLC-3|MLC1SM|Myln	myosin, light polypeptide 6, alkali, smooth muscle and non-muscle	protein-coding
mm_85200.1	chr9	96732301	96732326	-	1	NA	promoter-TSS (NM_175537)	promoter-TSS (NM_175537)	-638	NM_175537	245007	Mm.485954	NM_175537	ENSMUSG00000040433	Zbtb38	A930014K01Rik|CIBZ	zinc finger and BTB domain containing 38	protein-coding
mm_84900.1	chr9	79831023	79831034	-	1	NA	intron (NM_001081243, intron 4 of 5)	intron (NM_001081243, intron 4 of 5)	37387	NR_040734	74633	Mm.262175	NR_040734	ENSMUSG00000086918	4930429F24Rik	-	RIKEN cDNA 4930429F24 gene	ncRNA
mm_114571.1	chr13	75089639	75089655	+	1	NA	promoter-TSS (NM_013628)	promoter-TSS (NM_013628)	-340	NM_013628	18548	Mm.1333	NM_013628	ENSMUSG00000021587	Pcsk1	Nec-1|Nec1|PC1|PC3|Phpp-1|SPC3	proprotein convertase subtilisin/kexin type 1	protein-coding
mm_59029.1	chr7	19304102	19304111	+	1	NA	3' UTR (NM_008036, exon 4 of 4)	3' UTR (NM_008036, exon 4 of 4)	5939	NM_008036	14282	Mm.248335	NM_008036	ENSMUSG00000003545	Fosb	-	FBJ osteosarcoma oncogene B	protein-coding
mm_16993.1	chr2	18307006	18307023	-	1	NA	exon (NM_001190817, exon 6 of 13)	exon (NM_001190817, exon 6 of 13)	85816	NM_001190817	13418	Mm.246674	NM_007869	ENSMUSG00000026740	Dnajc1	4733401K02Rik|AA960110|D230036H06Rik|Dnajl1|ERdj1|ERj1p|MTJ1	DnaJ heat shock protein family (Hsp40) member C1	protein-coding
mm_49540.1	chr6	30176482	30176485	+	1	NA	promoter-TSS (NR_038124)	promoter-TSS (NR_038124)	-140	NR_038124	100463519	Mm.361139	NR_038124		BB283400	BF465573|Rncr4	expressed sequence BB283400	ncRNA
mm_133483.1	chr16	90220535	90220537	+	1	NA	promoter-TSS (NM_011434)	promoter-TSS (NM_011434)	-206	NM_011434	20655	Mm.276325	NM_011434	ENSMUSG00000022982	Sod1	B430204E11Rik|Cu/Zn-SOD|CuZnSOD|Ipo-1|Ipo1|SODC|Sod-1	superoxide dismutase 1, soluble	protein-coding
mm_42038.1	chr5	108404858	108404881	+	1	NA	intron (NM_008806, intron 3 of 21)	intron (NM_008806, intron 3 of 21)	16496	NM_008806	18587	Mm.1372	NM_008806	ENSMUSG00000029491	Pde6b	Pdeb|r|rd|rd-1|rd1|rd10	phosphodiesterase 6B, cGMP, rod receptor, beta polypeptide	protein-coding
mm_27668.1	chr3	65381277	65381289	-	1	NA	3' UTR (NM_026155, exon 5 of 5)	3' UTR (NM_026155, exon 5 of 5)	11270	NM_026155	67437	Mm.232728	NM_026155	ENSMUSG00000027828	Ssr3	0610038P07Rik|AL022999|AU022074|AW553833|TRAPG	signal sequence receptor, gamma	protein-coding
mm_11420.1	chr2	31688526	31688560	+	1	NA	promoter-TSS (NM_001283047)	promoter-TSS (NM_001283047)	6	NM_001283046	11350	Mm.1318	NM_009594	ENSMUSG00000026842	Abl1	AI325092|Abl|E430008G22Rik|c-Abl	c-abl oncogene 1, non-receptor tyrosine kinase	protein-coding
mm_54842.1	chr6	42586576	42586578	-	1	NA	TTS (NM_203396)	TTS (NM_203396)	10795	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_10357.1	chr2	11690641	11690655	+	1	NA	3' UTR (NM_008367, exon 8 of 8)	3' UTR (NM_008367, exon 8 of 8)	-14645	NM_001271498	16169	Mm.200196	NM_008358	ENSMUSG00000023206	Il15ra	AA690181|IL-15RA	interleukin 15 receptor, alpha chain	protein-coding
mm_99923.1	chr11	110535904	110535940	+	1	NA	Intergenic	Intergenic	136800	NM_011943	26399	Mm.14487	NM_011943	ENSMUSG00000020623	Map2k6	MEK6|MKK6|Prkmk6|SAPKK3	mitogen-activated protein kinase kinase 6	protein-coding
mm_154595.1	chrX	7593079	7593079	+	1	NA	TTS (NM_138603)	TTS (NM_138603)	12341	NM_138603	54638	Mm.288192	NM_138603	ENSMUSG00000031143	Ccdc22	AI481216|DXImx40e|Ppp1r3f|Sfc22	coiled-coil domain containing 22	protein-coding
mm_12260.1	chr2	68940625	68940644	+	1	NA	intron (NM_172856, intron 2 of 9)	L1_Mus3|LINE|L1	79193	NM_001347161	241447	Mm.222222	NM_172856	ENSMUSG00000027035	Cers6	4732462C07Rik|AW544719|Lass6|T1L	ceramide synthase 6	protein-coding
mm_149522.1	chr19	12442814	12442827	+	1	NA	Intergenic	RMER1C|Other|Other	14915	NM_019540	56093	Mm.285849	NM_019540	ENSMUSG00000040065	Pfpl	Epcs5|Epcs50	pore forming protein-like	protein-coding
mm_137051.1	chr17	17917878	17917889	+	1	NA	Intergenic	Intergenic	30059	NM_008039	14289	Mm.378918	NM_008039	ENSMUSG00000052270	Fpr2	E330010I07Rik|Fpr-rs2	formyl peptide receptor 2	protein-coding
mm_94247.1	chr11	3330741	3330749	+	1	NA	promoter-TSS (NM_178149)	promoter-TSS (NM_178149)	14	NM_178149	216505	Mm.390323	NM_178149	ENSMUSG00000034614	Pik3ip1	1500004A08Rik|5830455E04Rik|Crkd|Hgfl	phosphoinositide-3-kinase interacting protein 1	protein-coding
mm_88331.1	chr10	75571543	75571551	+	1	NA	intron (NM_001305992, intron 1 of 13)	intron (NM_001305992, intron 1 of 13)	-1948	NM_008116	14598	Mm.4559	NM_008116	ENSMUSG00000006345	Ggt1	CD224|GGT|GGT 1|GGT-1|Ggtp|dwg	gamma-glutamyltransferase 1	protein-coding
mm_77402.1	chr8	120537265	120537276	-	1	NA	promoter-TSS (NM_001145896)	promoter-TSS (NM_001145896)	-139	NM_001145896	382034	Mm.334856	NM_198671	ENSMUSG00000031822	Gse1	2210013I18Rik|mKIAA0182	genetic suppressor element 1, coiled-coil protein	protein-coding
mm_53818.1	chr6	147091484	147091528	+	1	NA	5' UTR (NM_001081237, exon 1 of 3)	5' UTR (NM_001081237, exon 1 of 3)	431	NM_001081237	232539	Mm.491206	NM_001081237	ENSMUSG00000040102	Klhl42	A330079N23Rik|AI450355|C230080I20Rik|Ctb9|Klhdc5|mKIAA1340	kelch-like 42	protein-coding
mm_121569.1	chr14	122867845	122867848	+	1	NA	intron (NM_144844, intron 21 of 23)	intron (NM_144844, intron 21 of 23)	45319	NM_145466	223267	Mm.379358	NM_145466	ENSMUSG00000041625	Ggact	A2ld1	gamma-glutamylamine cyclotransferase	protein-coding
mm_95037.1	chr11	32221418	32221435	+	1	NA	intron (NM_010117, intron 1 of 17)	intron (NM_010117, intron 1 of 17)	867	NM_010117	13650	Mm.11545	NM_010117	ENSMUSG00000020282	Rhbdf1	C16ORF8|Dist|Dist1|Egfr-rs|mKIAA4242	rhomboid 5 homolog 1	protein-coding
mm_62442.1	chr7	101382815	101382840	+	1	NA	intron (NM_001040112, intron 1 of 30)	intron (NM_001040112, intron 1 of 30)	-2699	NM_027180	69710	Mm.277687	NM_027180	ENSMUSG00000032812	Arap1	2410002L19Rik|Centd2|mKIAA0782	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	protein-coding
mm_111154.1	chr12	83424906	83424912	-	1	NA	intron (NM_058212, intron 1 of 8)	intron (NM_058212, intron 1 of 8)	62827	NM_001267626	70127	Mm.151308	NM_058212	ENSMUSG00000021221	Dpf3	2810403B03Rik|6530402L11Rik|BAF45C|C78788|CERD4|cer-d4	D4, zinc and double PHD fingers, family 3	protein-coding
mm_132632.1	chr16	39025790	39025804	+	1	NA	3' UTR (NM_170599, exon 7 of 7)	3' UTR (NM_170599, exon 7 of 7)	123452	NM_170599	207683	Mm.245564	NM_170599	ENSMUSG00000022790	Igsf11	1700025L02Rik|BT-IgSF|Igsf13	immunoglobulin superfamily, member 11	protein-coding
mm_115457.1	chr13	119428383	119428385	+	1	NA	promoter-TSS (NM_001079849)	promoter-TSS (NM_001079849)	-216	NM_001079849	218693	Mm.490243	NM_145457	ENSMUSG00000025451	Paip1	PAIP-1	polyadenylate binding protein-interacting protein 1	protein-coding
mm_47725.1	chr5	130024281	130024357	-	1	NA	promoter-TSS (NM_133768)	promoter-TSS (NM_133768)	12	NM_133768	109900	Mm.23869	NM_133768	ENSMUSG00000025533	Asl	2510006M18Rik	argininosuccinate lyase	protein-coding
mm_64826.1	chr7	11988558	11988582	-	1	NA	Intergenic	Intergenic	-52729	NM_001166731	628946	Mm.484974	NM_001166731	ENSMUSG00000095864	Vmn1r77	Gm6935	vomeronasal 1 receptor 77	protein-coding
mm_137868.1	chr17	31322141	31322153	+	1	NA	exon (NM_153062, exon 8 of 20)	exon (NM_153062, exon 8 of 20)	25923	NM_001242427	224674	Mm.311395	NM_153062	ENSMUSG00000024036	Slc37a1	G3PP	solute carrier family 37 (glycerol-3-phosphate transporter), member 1	protein-coding
mm_150605.1	chr19	40830565	40830594	+	1	NA	promoter-TSS (NM_172839)	promoter-TSS (NM_172839)	-700	NM_172839	240665	Mm.309	NM_172839	ENSMUSG00000025010	Ccnj	D430039C20Rik	cyclin J	protein-coding
mm_97189.1	chr11	75572747	75572791	+	1	NA	3' UTR (NM_001199283, exon 14 of 14)	3' UTR (NM_001199283, exon 14 of 14)	-15310	NM_008850	18738	Mm.3128	NM_008850	ENSMUSG00000017781	Pitpna	Pitpn|vb|vibrator	phosphatidylinositol transfer protein, alpha	protein-coding
mm_51685.1	chr6	86525219	86525297	+	1	NA	exon (NM_011865, exon 1 of 1)	exon (NM_011865, exon 1 of 1)	907	NM_011865	23983	Mm.274146	NM_011865	ENSMUSG00000051695	Pcbp1	WBP17|[a]CP-1|alphaCP-1|hnRNP E1	poly(rC) binding protein 1	protein-coding
mm_55162.1	chr6	51871237	51871249	-	1	NA	intron (NM_018773, intron 11 of 12)	intron (NM_018773, intron 11 of 12)	141306	NM_018773	54353	Mm.221479	NM_018773	ENSMUSG00000059182	Skap2	2610021A10Rik|AA960083|BB137539|RA70|SKAP-HOM|Saps|Scap2|mSKAP55R	src family associated phosphoprotein 2	protein-coding
mm_148208.1	chr18	80151413	80151442	-	1	NA	promoter-TSS (NM_175028)	promoter-TSS (NM_175028)	55	NM_175028	240442	Mm.26594	NM_175028	ENSMUSG00000053950	Adnp2	8430420L05Rik|BC024969|Kiaa0863|Zfp508|mKIAA0863	ADNP homeobox 2	protein-coding
mm_143061.1	chr17	57011248	57011259	-	1	NA	promoter-TSS (NM_133801)	promoter-TSS (NM_133801)	35	NM_133801	98053	Mm.24632	NM_133801	ENSMUSG00000002658	Gtf2f1	2810405L04Rik|C76800|RAP74	general transcription factor IIF, polypeptide 1	protein-coding
mm_24686.1	chr3	94974729	94974753	+	1	NA	promoter-TSS (NM_001293716)	promoter-TSS (NM_001293716)	10	NM_001293716	107650	Mm.217222	NM_175356	ENSMUSG00000038861	Pi4kb	ESTM41|PI4K-beta|PI4Kbeta|Pik4cb	phosphatidylinositol 4-kinase, catalytic, beta polypeptide	protein-coding
mm_41278.1	chr5	90247270	90247274	+	1	NA	intron (NM_198010, intron 27 of 32)	ORR1A2-int|LTR|ERVL-MaLR	-23276	NM_001163456	231430	Mm.319697	NM_001033310	ENSMUSG00000035505	Cox18	BC038311	cytochrome c oxidase assembly protein 18	protein-coding
mm_59123.1	chr7	19911803	19911805	+	1	NA	intron (NM_027514, intron 4 of 7)	intron (NM_027514, intron 4 of 7)	9339	NM_027514	52118	Mm.227506	NM_027514	ENSMUSG00000040511	Pvr	3830421F03Rik|CD155|D7Ertd458e|HVED|PVS|Taa1|Tage4|mE4|necl-5	poliovirus receptor	protein-coding
mm_151740.1	chr19	4989965	4989972	-	1	NA	promoter-TSS (NM_153553)	promoter-TSS (NM_153553)	3	NM_153553	225872	Mm.287867	NM_153553	ENSMUSG00000045903	Npas4	LE-PAS|Nxf	neuronal PAS domain protein 4	protein-coding
mm_12547.1	chr2	72390757	72390772	+	1	NA	TTS (NM_178084)	TTS (NM_178084)	-85455	NM_025866	66953	Mm.270676	NM_025866	ENSMUSG00000055612	Cdca7	2310021G01Rik|AU044109|JPO1	cell division cycle associated 7	protein-coding
mm_56560.1	chr6	101297219	101297220	-	1	NA	intron (NM_018884, intron 3 of 9)	intron (NM_018884, intron 3 of 9)	80678	NM_018884	55983	Mm.321654	NM_018884	ENSMUSG00000035357	Pdzrn3	1110020C07Rik|AI429718|AL023082|LNX3|SEMACAP3|Semcap3	PDZ domain containing RING finger 3	protein-coding
mm_105562.1	chr11	106507069	106507106	-	1	NA	intron (NM_198292, intron 10 of 11)	intron (NM_198292, intron 10 of 11)	6096	NR_030703	100216537		NR_030703	ENSMUSG00000065126	Snord104	-	small nucleolar RNA, C/D box 104	snoRNA
mm_57086.1	chr6	122585129	122585151	-	1	NA	intron (NM_001134391, intron 5 of 7)	(CA)n|Simple_repeat|Simple_repeat	17304	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_69718.1	chr7	140208185	140208195	-	1	NA	Intergenic	Intergenic	-5422	NM_001011814	258055	Mm.377339	NM_001011814	ENSMUSG00000050366	Olfr524	MOR103-14P	olfactory receptor 524	protein-coding
mm_105399.1	chr11	103404021	103404029	-	1	NA	intron (NM_183034, intron 1 of 11)	intron (NM_183034, intron 1 of 11)	8639	NM_183034	353047	Mm.18556	NM_183034	ENSMUSG00000034247	Plekhm1	AP162|B2|BC038943|D330036J23Rik	pleckstrin homology domain containing, family M (with RUN domain) member 1	protein-coding
mm_32646.1	chr4	115057684	115057701	+	1	NA	promoter-TSS (NM_001287388)	promoter-TSS (NM_001287388)	-119	NM_001287388	21349	Mm.239869	NM_011527	ENSMUSG00000028717	Tal1	Hpt|SCL/tal-1|Scl|bHLHa17|tal-1	T cell acute lymphocytic leukemia 1	protein-coding
mm_84273.1	chr9	62796495	62796532	-	1	NA	exon (NM_010193, exon 2 of 2)	exon (NM_010193, exon 2 of 2)	15135	NM_010193	14155	Mm.24069	NM_010193	ENSMUSG00000032244	Fem1b	mKIAA0396	feminization 1 homolog b (C. elegans)	protein-coding
mm_55938.1	chr6	84970476	84970486	-	1	NA	intron (NM_177077, intron 6 of 21)	HAL1|LINE|L1	99032	NM_177077	75914	Mm.159621	NM_177077	ENSMUSG00000033769	Exoc6b	4930569O18Rik|G430127E12Rik|Sec15b|Sec15l2|mKIAA0919	exocyst complex component 6B	protein-coding
mm_41633.1	chr5	97090823	97090847	+	1	NA	3' UTR (NM_080708, exon 16 of 16)	3' UTR (NM_080708, exon 16 of 16)	20761	NM_198422	231474	Mm.332505	NM_198422	ENSMUSG00000055725	Paqr3	6330415A20Rik|AY424292|RKTG	progestin and adipoQ receptor family member III	protein-coding
mm_156275.1	chrX	136836623	136836631	+	1	NA	3' UTR (NM_011123, exon 7 of 7)	3' UTR (NM_011123, exon 7 of 7)	13881	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_77524.1	chr8	122962641	122962654	-	1	NA	intron (NM_001081379, intron 2 of 12)	intron (NM_001081379, intron 2 of 12)	79637	NR_037865	77087	Mm.31567	NM_001081379	ENSMUSG00000035569	Ankrd11	2410104C19Rik|3010027A04Rik|6330578C09Rik|9530048I21Rik|AA930108|Gm176|Yod	ankyrin repeat domain 11	protein-coding
mm_119671.1	chr14	52580585	52580590	+	1	NA	Intergenic	Intergenic	-84892	NM_001170918	57269	Mm.88822	NM_020512	ENSMUSG00000059887	Olfr1507	MOR244-1|Mor28|Or28	olfactory receptor 1507	protein-coding
mm_79758.1	chr9	62377295	62377334	+	1	NA	exon (NM_009672, exon 6 of 7)	exon (NM_009672, exon 6 of 7)	35971	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	protein-coding
mm_23346.1	chr3	54744496	54744511	+	1	NA	intron (NM_025442, intron 5 of 9)	intron (NM_025442, intron 5 of 9)	8964	NM_025442	66248	Mm.144218	NM_025442	ENSMUSG00000036632	Alg5	1500026A19Rik|2600005J22Rik|AV009521|AV170001|AW545564	asparagine-linked glycosylation 5 (dolichyl-phosphate beta-glucosyltransferase)	protein-coding
mm_89756.1	chr10	99306613	99306617	+	1	NA	Intergenic	L1_Mur3|LINE|L1	43384	NM_026268	67603	Mm.1791	NM_026268	ENSMUSG00000019960	Dusp6	1300019I03Rik|MKP-3|MKP3|PYST1	dual specificity phosphatase 6	protein-coding
mm_124072.1	chr14	78592027	78592031	-	1	NA	intron (NM_001081336, intron 20 of 28)	intron (NM_001081336, intron 20 of 28)	37261	NM_001253766	380921	Mm.89591	NM_001081336	ENSMUSG00000034731	Dgkh	5930402B05Rik|D130015C16|DGK	diacylglycerol kinase, eta	protein-coding
mm_10028.1	chr1	192099790	192099791	-	1	NA	3' UTR (NM_144814, exon 10 of 10)	3' UTR (NM_144814, exon 10 of 10)	-7191	NM_011633	22033	Mm.380491	NM_011633		Traf5	-	TNF receptor-associated factor 5	protein-coding
mm_135552.1	chr16	49848069	49848085	-	1	NA	Intergenic	Intergenic	-7577	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_147065.1	chr18	35118800	35118818	-	1	NA	promoter-TSS (NM_009818)	promoter-TSS (NM_009818)	-103	NM_009818	12385	Mm.18962	NM_009818	ENSMUSG00000037815	Ctnna1	2010010M04Rik|AA517462|AI988031|Catna1	catenin (cadherin associated protein), alpha 1	protein-coding
mm_36155.1	chr4	59781372	59781375	-	1	NA	intron (NM_001013577, intron 2 of 4)	B1_Mur2|SINE|Alu	2482	NM_001013577	66209	Mm.51988	NM_001013577	ENSMUSG00000038544	Inip	1110054O05Rik|2610312O17Rik|AA399876|Ssbip1	INTS3 and NABP interacting protein	protein-coding
mm_142048.1	chr17	35534160	35534166	-	1	NA	exon (NM_020576, exon 2 of 2)	exon (NM_020576, exon 2 of 2)	962	NM_020576	57390	Mm.34201	NM_020576	ENSMUSG00000024409	Psors1c2	AI448740|Pcg|SPR1	psoriasis susceptibility 1 candidate 2 (human)	protein-coding
mm_64920.1	chr7	16247773	16247787	-	1	NA	3' UTR (NM_001173550, exon 2 of 2)	3' UTR (NM_001173550, exon 2 of 2)	-3626	NM_176912	319430	Mm.239570	NM_176912	ENSMUSG00000074361	C5ar2	C5L2|E030029A11Rik|Gpr77	complement component 5a receptor 2	protein-coding
mm_141817.1	chr17	34606650	34606662	-	1	NA	intron (NM_001163379, intron 1 of 6)	intron (NM_001163379, intron 1 of 6)	795	NM_001163379	55979	Mm.8684	NM_018862	ENSMUSG00000034254	Agpat1	1-AGP|1-AGPAT|AW047140	1-acylglycerol-3-phosphate O-acyltransferase 1 (lysophosphatidic acid acyltransferase, alpha)	protein-coding
mm_67861.1	chr7	99049943	99049983	-	1	NA	intron (NM_178635, intron 6 of 14)	MTEa|LTR|ERVL-MaLR	91181	NM_178635	78610	Mm.323072	NM_178635	ENSMUSG00000035354	Uvrag	9530039D02Rik|AI648770|BB124205|Uvrag1|Uvragl	UV radiation resistance associated gene	protein-coding
mm_82692.1	chr9	22376219	22376229	-	1	NA	exon (NM_028390, exon 4 of 24)	exon (NM_028390, exon 4 of 24)	2999	NR_030448	751551		NR_030448	ENSMUSG00000076117	Mir680-2	Mirn680-2	microRNA 680-2	ncRNA
mm_95969.1	chr11	58918005	58918015	+	1	NA	promoter-TSS (NM_138678)	promoter-TSS (NM_138678)	-47	NM_138678	192194	Mm.22540	NM_138678	ENSMUSG00000020490	Btnl10	BUTR-1|Butr1	butyrophilin-like 10	protein-coding
mm_20675.1	chr2	132253228	132253236	-	1	NA	promoter-TSS (NM_011045)	promoter-TSS (NM_011045)	-52	NM_011045	18538	Mm.7141	NM_011045	ENSMUSG00000027342	Pcna	-	proliferating cell nuclear antigen	protein-coding
mm_87628.1	chr10	58255466	58255537	+	1	NA	promoter-TSS (NM_027375)	promoter-TSS (NM_027375)	-25	NM_027375	70297	Mm.25531	NM_027375	ENSMUSG00000038039	Gcc2	0610043A03Rik|2210420P05Rik|2600014C01Rik|AW112121|mKIAA0336	GRIP and coiled-coil domain containing 2	protein-coding
mm_38205.1	chr4	135855870	135855897	-	1	NA	promoter-TSS (NM_001284196)	promoter-TSS (NM_001284196)	-188	NM_001284196	14105	Mm.10229	NM_010178	ENSMUSG00000028676	Srsf10	FUSIP2|Fusip1|NSSR1|NSSR2|Nssr|SRrp40|Sfrs13a|Srsf13a|TASR|TASR1|TASR2	serine/arginine-rich splicing factor 10	protein-coding
mm_155404.1	chrX	73342588	73342606	+	1	NA	promoter-TSS (NM_031494)	promoter-TSS (NM_031494)	-23	NM_031494	27081	Mm.26595	NM_031494	ENSMUSG00000031365	Zfp275	5430431L06Rik|AI593314|DXBay20|DXHXS52|DXPas8	zinc finger protein 275	protein-coding
mm_114192.1	chr13	55784575	55784599	+	1	NA	promoter-TSS (NM_001252487)	promoter-TSS (NM_001252487)	8	NM_001252487	76856	Mm.159795	NM_029772	ENSMUSG00000021499	Catsper3	4921522D01Rik|CACRC	cation channel, sperm associated 3	protein-coding
mm_56291.1	chr6	91493165	91493181	-	1	NA	exon (NM_009531, exon 12 of 16)	exon (NM_009531, exon 12 of 16)	19422	NM_028766	74122	Mm.38801	NM_028766	ENSMUSG00000030095	Tmem43	1200015A22Rik|LUMA	transmembrane protein 43	protein-coding
mm_82561.1	chr9	21037776	21037795	-	1	NA	exon (NM_008319, exon 10 of 11)	exon (NM_008319, exon 10 of 11)	-5457	NR_035438	100316681		NR_035438	ENSMUSG00000084663	Mir1900	Mirn1900|mmu-mir-1900	microRNA 1900	ncRNA
mm_130046.1	chr15	89137583	89137600	-	1	NA	intron (NM_013871, intron 2 of 11)	intron (NM_013871, intron 2 of 11)	3112	NM_013871	29857	Mm.38343	NM_013871	ENSMUSG00000022610	Mapk12	AW123708|Erk6|P38gamma|Prkm12|Sapk3	mitogen-activated protein kinase 12	protein-coding
mm_151090.1	chr19	47731744	47731768	+	1	NA	promoter-TSS (NM_026377)	promoter-TSS (NM_026377)	0	NM_026377	67788	Mm.181610	NM_026377	ENSMUSG00000025066	Sfr1	6330577E15Rik|Meir5	SWI5 dependent recombination repair 1	protein-coding
mm_32196.1	chr4	101419336	101419349	+	1	NA	promoter-TSS (NM_009647)	promoter-TSS (NM_009647)	21	NM_001177604	11639	Mm.42040	NM_009647	ENSMUSG00000028527	Ak4	AK 4|Ak-3|Ak-4|Ak3|Ak3l1|D4Ertd274e	adenylate kinase 4	protein-coding
mm_25930.1	chr3	131223829	131223837	+	1	NA	3' UTR (NM_001276402, exon 10 of 10)	3' UTR (NM_001276402, exon 10 of 10)	48268	NM_008212	15107	Mm.260164	NM_008212	ENSMUSG00000027984	Hadh	AA409008|AU019341|AW742602|HCDH|Hadhsc|Schad	hydroxyacyl-Coenzyme A dehydrogenase	protein-coding
mm_118953.1	chr14	27379595	27379615	+	1	NA	exon (NM_027871, exon 4 of 11)	exon (NM_027871, exon 4 of 11)	18216	NM_001289688	71704	Mm.248606	NM_027871	ENSMUSG00000021895	Arhgef3	1200004I24Rik|9830169H03Rik|C76747|Xpln	Rho guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_35929.1	chr4	53032310	53032340	-	1	NA	3' UTR (NM_013454, exon 50 of 50)	3' UTR (NM_013454, exon 50 of 50)	20445	NM_025623	66536	Mm.38244	NM_025623	ENSMUSG00000015247	Nipsnap3b	2700063N13Rik|Nipsnap3a	nipsnap homolog 3B (C. elegans)	protein-coding
mm_172758.1	chr8	85949287	85949287	+	1	NA	intron (NM_199446, intron 13 of 31)	L1Md_T|LINE|L1	108285	NM_199446	102093	Mm.237296	NM_199446	ENSMUSG00000036879	Phkb	AI463271	phosphorylase kinase beta	protein-coding
mm_90943.1	chr10	12964253	12964278	-	1	NA	promoter-TSS (NM_029075)	promoter-TSS (NM_029075)	-6	NM_001163591	74732	Mm.248648	NM_029075	ENSMUSG00000039232	Stx11	5830405C08Rik	syntaxin 11	protein-coding
mm_27429.1	chr3	51554094	51554102	-	1	NA	intron (NM_080793, intron 1 of 7)	intron (NM_080793, intron 1 of 7)	-5659	NR_033624	100039684	Mm.387178	NR_033624		5031434O11Rik	AI481280|Gm2370	RIKEN cDNA 5031434O11 gene	ncRNA
mm_52688.1	chr6	118084128	118084132	+	1	NA	intron (NM_001316749, intron 3 of 12)	MER113|DNA|hAT-Charlie	-1062	NR_106011	102465632		NR_106011	ENSMUSG00000098583	Mir7044	Gm27354|mmu-mir-7044	microRNA 7044	ncRNA
mm_112794.1	chr13	20352938	20352942	+	1	NA	intron (NM_080288, intron 14 of 21)	Lx10|LINE|L1	-120050	NM_198093	140580	Mm.342392	NM_080288	ENSMUSG00000041112	Elmo1	6330578D22Rik|C230095H21Rik|CED-12	engulfment and cell motility 1	protein-coding
mm_16197.1	chr2	173000132	173000178	+	1	NA	promoter-TSS (NM_175112)	promoter-TSS (NM_175112)	38	NM_175112	66679	Mm.4113	NM_175112	ENSMUSG00000027509	Rae1	3230401I12Rik|D2Ertd342e|MNRP|MNRP41	ribonucleic acid export 1	protein-coding
mm_104796.1	chr11	98772952	98772971	-	1	NA	intron (NM_145434, intron 1 of 7)	intron (NM_145434, intron 1 of 7)	2416	NM_145434	217166	Mm.390397	NM_145434	ENSMUSG00000020889	Nr1d1	A530070C09Rik|R75201	nuclear receptor subfamily 1, group D, member 1	protein-coding
mm_153921.1	chr19	47314706	47314719	-	1	NA	intron (NM_001164717, intron 7 of 13)	intron (NM_001164717, intron 7 of 13)	-41123	NR_105961	102466782		NR_105961	ENSMUSG00000098786	Mir6995	Gm27576|mmu-mir-6995	microRNA 6995	ncRNA
mm_105325.1	chr11	102895921	102895939	-	1	NA	intron (NM_001131020, intron 1 of 7)	intron (NM_001131020, intron 1 of 7)	1270	NM_001131020	14580	Mm.1239	NM_010277	ENSMUSG00000020932	Gfap	AI836096	glial fibrillary acidic protein	protein-coding
mm_60351.1	chr7	44359737	44359763	+	1	NA	TTS (NM_027049)	TTS (NM_027049)	15280	NM_027049	69349	Mm.358922	NM_027049	ENSMUSG00000008028	1700008O03Rik	-	RIKEN cDNA 1700008O03 gene	protein-coding
mm_25616.1	chr3	118431527	118431538	+	1	NA	Intergenic	Intergenic	-2325	NR_029551	387155		NR_029551	ENSMUSG00000065569	Mir137	Mirn137|mir-137|mmu-mir-137	microRNA 137	ncRNA
mm_19991.1	chr2	118715451	118715458	-	1	NA	exon (NM_177568, exon 18 of 32)	exon (NM_177568, exon 18 of 32)	-11491	NM_001081971	383787	Mm.35758	NM_001081971	ENSMUSG00000078137	Ankrd63	Gm1337	ankyrin repeat domain 63	protein-coding
mm_49876.1	chr6	38592737	38592748	+	1	NA	exon (NM_001170849, exon 6 of 8)	exon (NM_001170849, exon 6 of 8)	37019	NM_001331223	192196	Mm.276133	NM_138680	ENSMUSG00000029823	Luc7l2	4930471C18Rik|AA522013|AU015269|CGI59|Cgi74	LUC7-like 2 (S. cerevisiae)	protein-coding
mm_27323.1	chr3	50367679	50367690	-	1	NA	3' UTR (NM_011990, exon 12 of 12)	3' UTR (NM_011990, exon 12 of 12)	75929	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_124504.1	chr14	121879607	121879635	-	1	NA	promoter-TSS (NR_130999)	promoter-TSS (NR_130999)	-213	NR_130999	78312	Mm.188743	NR_130999	ENSMUSG00000102112	1810041H14Rik	-	RIKEN cDNA 1810041H14 gene	ncRNA
mm_107234.1	chr12	26478219	26478231	+	1	NA	3' UTR (NM_020557, exon 5 of 5)	3' UTR (NM_020557, exon 5 of 5)	9010	NM_020557	22169	Mm.271839	NM_020557	ENSMUSG00000020638	Cmpk2	1200004E04Rik|TDKI|Tyki	cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial	protein-coding
mm_101041.1	chr11	8612230	8612236	-	1	NA	intron (NM_001083587, intron 2 of 30)	MLT1A0|LTR|ERVL-MaLR	52302	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_90180.1	chr10	119850735	119850755	+	1	NA	intron (NR_131760, intron 3 of 4)	intron (NR_131760, intron 3 of 4)	1645	NR_131760	78105	Mm.399086	NR_131760	ENSMUSG00000085418	Grip1os1	4930404E01Rik|4930483C13Rik	glutamate receptor interacting protein 1, opposite strand 1	ncRNA
mm_11606.1	chr2	33908672	33908686	+	1	NA	Intergenic	RSINE1|SINE|B4	-20733	NM_175184	72543	Mm.254914	NM_175184	ENSMUSG00000038740	Mvb12b	2610200O14Rik|2610528K11Rik|AI414895|Fam125b	multivesicular body subunit 12B	protein-coding
mm_108160.1	chr12	76367316	76367326	+	1	NA	intron (NM_028356, intron 1 of 2)	B3|SINE|B2	2143	NM_001172104	109929	Mm.41880	NM_028356	ENSMUSG00000056459	Zbtb25	2810462M08Rik|2900064P18Rik|AI842128|Kup|Zfp-50|Zfp50	zinc finger and BTB domain containing 25	protein-coding
mm_47032.1	chr5	115732258	115732283	-	1	NA	promoter-TSS (NM_001080808)	promoter-TSS (NM_001080808)	-711	NM_001080808	75665	Mm.233914	NM_001080808	ENSMUSG00000041609	Ccdc64	2210403N09Rik|BICDR-1|Bicdl1	coiled-coil domain containing 64	protein-coding
mm_144942.1	chr18	37768339	37768379	+	1	NA	exon (NM_033595, exon 1 of 4)	exon (NM_033595, exon 1 of 4)	2779	NM_033595	93724	Mm.247203	NM_033595	ENSMUSG00000102428	Pcdhga12	Pcdh13|pc2c	protocadherin gamma subfamily A, 12	protein-coding
mm_137353.1	chr17	25240167	25240220	+	1	NA	promoter-TSS (NM_001163718)	promoter-TSS (NM_001163718)	23	NM_026676	68327	Mm.180687	NM_026676	ENSMUSG00000015126	Tsr3	0610007P22Rik|1110014B11Rik|AL022759	TSR3 20S rRNA accumulation	protein-coding
mm_109008.1	chr12	103337113	103337121	+	1	NA	intron (NM_023049, intron 3 of 9)	intron (NM_023049, intron 3 of 9)	18884	NM_023049	65256	Mm.27159	NM_023049	ENSMUSG00000021200	Asb2	1110008E15Rik	ankyrin repeat and SOCS box-containing 2	protein-coding
mm_77096.1	chr8	110846771	110846798	-	1	NA	promoter-TSS (NM_133973)	promoter-TSS (NM_133973)	19	NM_133953	101943	Mm.236123	NM_133953	ENSMUSG00000033732	Sf3b3	1810061H24Rik|5730409A01Rik|AA409318|D8Ertd633e|RSE1|SAP130|mKIAA0017	splicing factor 3b, subunit 3	protein-coding
mm_162765.1	chr10	62553616	62553623	-	1	NA	Intergenic	Intergenic	24838	NM_028197	72320	Mm.258955	NM_028197	ENSMUSG00000036955	Kif1bp	0710007C18Rik|2510003E04Rik|KBP|mKIAA1279	KIF1 binding protein	protein-coding
mm_133544.1	chr16	91225447	91225455	+	1	NA	promoter-TSS (NM_016967)	promoter-TSS (NM_016967)	-99	NM_016967	50913	Mm.37289	NM_016967	ENSMUSG00000039830	Olig2	AI604895|Bhlhb1|Olg-2|Oligo2|RK17|bHLHe19	oligodendrocyte transcription factor 2	protein-coding
mm_83849.1	chr9	54501732	54501773	-	1	NA	promoter-TSS (NM_172771)	promoter-TSS (NM_172771)	-126	NM_172771	235380	Mm.93636	NM_172771	ENSMUSG00000041268	Dmxl2	6330586A12|6430411K14Rik|E130119P06Rik|mKIAA0856	Dmx-like 2	protein-coding
mm_105387.1	chr11	103363432	103363458	-	1	NA	5' UTR (NM_183288, exon 1 of 3)	5' UTR (NM_183288, exon 1 of 3)	247	NM_183288	544817	Mm.259113	NM_133715	ENSMUSG00000034255	Arhgap27	2310069I04Rik|5730442P18Rik|Gm21552|Sh3d20	Rho GTPase activating protein 27	protein-coding
mm_20681.1	chr2	132513903	132513919	-	1	NA	intron (NR_028286, intron 2 of 3)	(A)n|Simple_repeat|Simple_repeat	23183	NR_028286	70371	Mm.394667	NR_028286	ENSMUSG00000086379	1700026D11Rik	-	RIKEN cDNA 1700026D11 gene	ncRNA
mm_5048.1	chr1	194749468	194749480	+	1	NA	intron (NM_008882, intron 6 of 31)	intron (NM_008882, intron 6 of 31)	129645	NM_008882	18845	Mm.2251	NM_008882	ENSMUSG00000026640	Plxna2	2810428A13Rik|AA589422|AW457381|OCT|PlexA2|Plxn2|mKIAA0463	plexin A2	protein-coding
mm_173126.1	chrX	170002802	170002815	-	1	NA	Intergenic	Intergenic	-23891	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_70815.1	chr8	23095512	23095540	+	1	NA	intron (NR_102385, intron 11 of 45)	GSAT_MM|Satellite|Satellite	37267	NR_102385	11733	Mm.334444	NM_031158	ENSMUSG00000031543	Ank1	Ank-1|nb|pale	ankyrin 1, erythroid	protein-coding
mm_156033.1	chrX	107256173	107256173	+	1	NA	intron (NM_001177781, intron 1 of 4)	intron (NM_001177781, intron 1 of 4)	145	NM_001033251	213439	Mm.383562	NM_001033251	ENSMUSG00000073008	Gpr174	Gm376|Lypsr3	G protein-coupled receptor 174	protein-coding
mm_70324.1	chr8	4257764	4257803	+	1	NA	3' UTR (NM_183315, exon 2 of 2)	3' UTR (NM_183315, exon 2 of 2)	1491	NM_183315	330695	Mm.34210	NM_183315	ENSMUSG00000048644	Ctxn1	BC028881|Ctxn	cortexin 1	protein-coding
mm_51836.1	chr6	90301242	90301294	+	1	NA	promoter-TSS (NM_177738)	promoter-TSS (NM_177738)	-2	NM_177738	243535	Mm.233854	NM_177738	ENSMUSG00000049694	BC048671	-	cDNA sequence BC048671	protein-coding
mm_38460.1	chr4	140581918	140581957	-	1	NA	intron (NM_001290803, intron 9 of 28)	intron (NM_001290803, intron 9 of 28)	66819	NM_001112723	72754	Mm.29329	NM_172415	ENSMUSG00000040964	Arhgef10l	2810441C07Rik	Rho guanine nucleotide exchange factor (GEF) 10-like	protein-coding
mm_39455.1	chr5	17574668	17574686	+	1	NA	promoter-TSS (NM_013657)	promoter-TSS (NM_013657)	-139	NM_013657	20348	Mm.5071	NM_013657	ENSMUSG00000028780	Sema3c	1110036B02Rik|SemE|Semae	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	protein-coding
mm_37943.1	chr4	133103863	133103873	-	1	NA	Intergenic	Intergenic	-26765	NM_153423	242687	Mm.23566	NM_153423	ENSMUSG00000028868	Wasf2	AW742646|D4Ertd13e|WAVE2	WAS protein family, member 2	protein-coding
mm_69698.1	chr7	140036627	140036675	-	1	NA	promoter-TSS (NM_001286011)	promoter-TSS (NM_001286011)	23	NM_001286007	74237	Mm.40888	NM_133755	ENSMUSG00000025474	Tubgcp2	1700022B05Rik	tubulin, gamma complex associated protein 2	protein-coding
mm_126643.1	chr15	83780035	83780086	+	1	NA	promoter-TSS (NM_172610)	promoter-TSS (NM_172610)	37	NM_172610	223726	Mm.36395	NM_172610	ENSMUSG00000041708	Mpped1	6230403M19|AW456965|D15Bwg0669e	metallophosphoesterase domain containing 1	protein-coding
mm_108975.1	chr12	102647024	102647050	+	1	NA	intron (NM_172584, intron 2 of 9)	intron (NM_172584, intron 2 of 9)	37983	NR_035457	100316812		NR_035457	ENSMUSG00000089324	Mir1936	mir-1936|mmu-mir-1936	microRNA 1936	ncRNA
mm_85618.1	chr9	107614777	107614794	-	1	NA	3' UTR (NM_008138, exon 9 of 9)	3' UTR (NM_008138, exon 9 of 9)	-5544	NM_001291539	20347	Mm.4083	NM_009153	ENSMUSG00000057969	Sema3b	SemA|Semaa|sema5|semaV	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B	protein-coding
mm_90232.1	chr10	121376223	121376245	+	1	NA	exon (NM_029364, exon 4 of 14)	exon (NM_029364, exon 4 of 14)	11144	NM_029364	75612	Mm.207683	NM_029364	ENSMUSG00000034707	Gns	2610016K11Rik|AU042285|C87209|G6S|N28088	glucosamine (N-acetyl)-6-sulfatase	protein-coding
mm_145677.1	chr18	61568345	61568361	+	1	NA	exon (NM_146087, exon 3 of 10)	exon (NM_146087, exon 3 of 10)	12771	NM_146087	93687	Mm.26908	NM_146087	ENSMUSG00000024576	Csnk1a1	2610208K14Rik|4632404G05Rik|5430427P18Rik|CK1a|Csnk1a	casein kinase 1, alpha 1	protein-coding
mm_173188.1	chrX	6071212	6071219	+	1	NA	Intergenic	Intergenic	12205	NM_001166433	102991	Mm.199793	NM_001033211	ENSMUSG00000073294	AU022751	AU023811	expressed sequence AU022751	protein-coding
mm_117778.1	chr13	96671500	96671511	-	1	NA	promoter-TSS (NM_008255)	promoter-TSS (NM_008255)	-569	NM_008255	15357	Mm.316652	NM_008255	ENSMUSG00000021670	Hmgcr	HMG-CoAR|Red	3-hydroxy-3-methylglutaryl-Coenzyme A reductase	protein-coding
mm_46693.1	chr5	110086338	110086357	-	1	NA	Intergenic	Intergenic	-13622	NM_207279	403178	Mm.297057	NM_207279	ENSMUSG00000064247	Plcxd1	A330045H12Rik|Gm576	phosphatidylinositol-specific phospholipase C, X domain containing 1	protein-coding
mm_134592.1	chr16	20426389	20426399	-	1	NA	promoter-TSS (NM_013790)	promoter-TSS (NM_013790)	0	NM_013790	27416	Mm.20845	NM_013790	ENSMUSG00000022822	Abcc5	2900011L11Rik|AI132311|Abcc5a|Abcc5b|Mrp5	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	protein-coding
mm_147669.1	chr18	60624295	60624303	-	1	NA	promoter-TSS (NM_177340)	promoter-TSS (NM_177340)	6	NM_177340	104027	Mm.252321	NM_177340	ENSMUSG00000043079	Synpo	9030217H17Rik|9130229N11|9330140I15Rik|AW046661	synaptopodin	protein-coding
mm_35809.1	chr4	46650158	46650234	-	1	NA	promoter-TSS (NM_198664)	promoter-TSS (NM_198664)	3	NM_198664	381605	Mm.331595	NM_198664	ENSMUSG00000039813	Tbc1d2	A630005A06Rik|BC022630|Gm1037|PARIS-1|PARIS1	TBC1 domain family, member 2	protein-coding
mm_147346.1	chr18	43322668	43322670	-	1	NA	3' UTR (NM_001291455, exon 14 of 14)	3' UTR (NM_001291455, exon 14 of 14)	50603	NM_001136086	22240	Mm.8180	NM_009468	ENSMUSG00000024501	Dpysl3	CRMP-4|DRP-3|TUC4|ULIP-1|Ulip|Ulip1	dihydropyrimidinase-like 3	protein-coding
mm_160131.1	chr7	29231130	29231130	-	1	NA	intron (NM_001033525, intron 1 of 2)	A-rich|Low_complexity|Low_complexity	1392	NM_001033525	52150	Mm.24877	NM_001033525	ENSMUSG00000046410	Kcnk6	D7Ertd764e|Toss|Twik2	potassium inwardly-rectifying channel, subfamily K, member 6	protein-coding
mm_134091.1	chr16	9150856	9150859	-	1	NA	Intergenic	Intergenic	320757	NM_001081400	69053	Mm.390868	NM_001081400	ENSMUSG00000022507	1810013L24Rik	1110017P05Rik|3010002C02Rik|AA792997|AW124177|Gm19906|R74903	RIKEN cDNA 1810013L24 gene	protein-coding
mm_82598.1	chr9	21312256	21312332	-	1	NA	promoter-TSS (NM_009678)	promoter-TSS (NM_009678)	39	NM_009678	11768	Mm.22239	NM_009678	ENSMUSG00000003309	Ap1m2	D9Ertd818e|[m]1B|mu1B	adaptor protein complex AP-1, mu 2 subunit	protein-coding
mm_120728.1	chr14	73142961	73143041	+	1	NA	non-coding (NR_033185, exon 1 of 16)	non-coding (NR_033185, exon 1 of 16)	216	NR_033185	105670	Mm.280068	NM_134083	ENSMUSG00000022106	Rcbtb2	2610028E02Rik|2810420M18Rik|AI448345|AW240694|Chc1l|RC/BTB2	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 2	protein-coding
mm_85900.1	chr9	111055987	111056018	-	1	NA	exon (NM_017466, exon 2 of 2)	exon (NM_017466, exon 2 of 2)	1242	NM_001302377	54199	Mm.7336	NM_017466	ENSMUSG00000043953	Ccrl2	1810047I05Rik|Ackr5|CCR11|Cmkbr1l2|E01|L-CCR	chemokine (C-C motif) receptor-like 2	protein-coding
mm_103694.1	chr11	79515966	79515968	-	1	NA	exon (NM_001077496, exon 2 of 2)	exon (NM_001077496, exon 2 of 2)	7795	NM_001077496	216984	Mm.439665	NM_001077496	ENSMUSG00000093938	Evi2b	Evi-2|Evi2	ecotropic viral integration site 2b	protein-coding
mm_134061.1	chr16	8362728	8362737	-	1	NA	Intergenic	Intergenic	62404	NM_029070	74720	Mm.159318	NM_029070	ENSMUSG00000022715	Tmem114	4930511J11Rik|Cldn26	transmembrane protein 114	protein-coding
mm_137835.1	chr17	30901559	30901568	+	1	NA	promoter-TSS (NM_021332)	promoter-TSS (NM_021332)	-304	NM_021332	14652	Mm.390969	NM_021332	ENSMUSG00000024027	Glp1r	GLP-1R|GLP1Rc	glucagon-like peptide 1 receptor	protein-coding
mm_64387.1	chr7	142477048	142477057	+	1	NA	promoter-TSS (NM_001271523)	promoter-TSS (NM_001271523)	39	NM_001271523	16985	Mm.234003	NM_019391	ENSMUSG00000018819	Lsp1	Lsp-1|WP34|p50|pp52	lymphocyte specific 1	protein-coding
mm_108316.1	chr12	79643024	79643027	+	1	NA	intron (NM_009014, intron 7 of 10)	intron (NM_009014, intron 7 of 10)	281708	NR_131075	77290	Mm.395042	NR_131073		9430078K24Rik	-	RIKEN cDNA 9430078K24 gene	ncRNA
mm_128123.1	chr15	31318502	31318511	-	1	NA	intron (NM_027496, intron 2 of 3)	intron (NM_027496, intron 2 of 3)	49253	NM_001164441	67434	Mm.102470	NM_026153	ENSMUSG00000022237	Ankrd33b	0610012A05Rik|3021401C12Rik|5730557B15Rik	ankyrin repeat domain 33B	protein-coding
mm_86228.1	chr9	120136312	120136329	-	1	NA	Intergenic	Intergenic	5886	NR_002902	104433	Mm.453530	NR_002902	ENSMUSG00000064925	Snora62	E2|MBI-13|MBI-136|Rnu108	small nucleolar RNA, H/ACA box 62	snoRNA
mm_126632.1	chr15	83523977	83523987	+	1	NA	Intergenic	Intergenic	-2880	NM_007546	12124	Mm.267006	NM_007546	ENSMUSG00000016758	Bik	Biklk|Blk|Nbk	BCL2-interacting killer	protein-coding
mm_103284.1	chr11	72215088	72215094	-	1	NA	promoter-TSS (NM_001163728)	promoter-TSS (NM_001163728)	-47	NM_001163728	75304	Mm.340776	NM_001163728		4930563E22Rik	-	RIKEN cDNA 4930563E22 gene	protein-coding
mm_68730.1	chr7	120670240	120670255	-	1	NA	promoter-TSS (NM_001040137)	promoter-TSS (NM_001040137)	3	NM_001040137	67983	Mm.394441	NM_001040136	ENSMUSG00000030887	Pdzd9	4930408O21Rik	PDZ domain containing 9	protein-coding
mm_41009.1	chr5	81020882	81020892	+	1	NA	promoter-TSS (NM_198702)	promoter-TSS (NM_198702)	316	NM_001347369	319387	Mm.273631	NM_198702	ENSMUSG00000037605	Adgrl3	5430402I23Rik|CIRL-3|D130075K09Rik|Gm1379|LEC3|Lphn3|mKIAA0768	adhesion G protein-coupled receptor L3	protein-coding
mm_96940.1	chr11	70540172	70540194	+	1	NA	promoter-TSS (NM_001302476)	promoter-TSS (NM_001302476)	-89	NM_008876	18806	Mm.260177	NM_008876	ENSMUSG00000020828	Pld2	PLD1C	phospholipase D2	protein-coding
mm_100118.1	chr11	115882932	115882957	+	1	NA	Intergenic	Intergenic	-17195	NM_183259	66528	Mm.275740	NM_183259	ENSMUSG00000048442	Smim5	2210020M01Rik	small integral membrane protein 5	protein-coding
mm_57980.1	chr6	135731264	135731267	-	1	NA	3' UTR (NM_008171, exon 15 of 15)	3' UTR (NM_008171, exon 15 of 15)	72352	NR_126088	75024	Mm.399147	NR_126088	ENSMUSG00000107396	4930425L21Rik	4930473P14Rik	RIKEN cDNA 4930425L21 gene	ncRNA
mm_116334.1	chr13	38037942	38037952	-	1	NA	intron (NM_024242, intron 1 of 16)	intron (NM_024242, intron 1 of 16)	958	NM_024242	71340	Mm.297130	NM_024242	ENSMUSG00000021428	Riok1	3110046C13Rik|5430416A05Rik|Ad034	RIO kinase 1 (yeast)	protein-coding
mm_25580.1	chr3	116862821	116862824	+	1	NA	intron (NM_009146, intron 1 of 16)	intron (NM_009146, intron 1 of 16)	1142	NM_009146	20321	Mm.66293	NM_009146	ENSMUSG00000033386	Frrs1	AI131732|Sdfr2	ferric-chelate reductase 1	protein-coding
mm_50243.1	chr6	42351857	42351885	+	1	NA	exon (NM_001289618, exon 4 of 10)	exon (NM_001289618, exon 4 of 10)	2043	NM_001289619	22793	Mm.282303	NM_011777	ENSMUSG00000029860	Zyx	9530098H06Rik|R75157	zyxin	protein-coding
mm_112895.1	chr13	20885299	20885351	+	1	NA	intron (NM_012054, intron 4 of 20)	MLT1D|LTR|ERVL-MaLR	91212	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_86947.1	chr10	24842330	24842336	+	1	NA	Intergenic	MTD-int|LTR|ERVL-MaLR	-6138	NM_134005	209558	Mm.338425	NM_134005	ENSMUSG00000019989	Enpp3	AI876438|CD203c	ectonucleotide pyrophosphatase/phosphodiesterase 3	protein-coding
mm_127029.1	chr15	96288883	96288893	+	1	NA	intron (NM_175251, intron 2 of 20)	intron (NM_175251, intron 2 of 20)	1366	NM_175251	77044	Mm.17166	NM_175251	ENSMUSG00000033237	Arid2	1700124K17Rik|4432409D24Rik|zipzap/p200	AT rich interactive domain 2 (ARID, RFX-like)	protein-coding
mm_78272.1	chr9	22003411	22003461	+	1	NA	promoter-TSS (NM_029939)	promoter-TSS (NM_029939)	448	NM_008925	19089	Mm.214593	NM_008925	ENSMUSG00000003402	Prkcsh	80K-H|PKCSH	protein kinase C substrate 80K-H	protein-coding
mm_29894.1	chr3	131321382	131321384	-	1	NA	3' UTR (NM_028943, exon 6 of 6)	3' UTR (NM_028943, exon 6 of 6)	-18156	NM_027816	71519	Mm.473179	NM_027816	ENSMUSG00000027983	Cyp2u1	8430436A10Rik	cytochrome P450, family 2, subfamily u, polypeptide 1	protein-coding
mm_141185.1	chr17	26939264	26939307	-	1	NA	intron (NM_026948, intron 1 of 5)	intron (NM_026948, intron 1 of 5)	173	NR_104458	67675	Mm.439919	NM_026307	ENSMUSG00000024194	Cuta	0610039D01Rik|1810022E02Rik|1810060C03Rik|2700094G22Rik|AI326454	cutA divalent cation tolerance homolog	protein-coding
mm_146372.1	chr18	82584767	82584770	+	1	NA	3' UTR (NM_010777, exon 7 of 7)	3' UTR (NM_010777, exon 7 of 7)	30260	NM_001025254	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_73135.1	chr8	94976880	94976893	+	1	NA	promoter-TSS (NM_001198894)	promoter-TSS (NM_001198894)	-223	NM_001198894	14766	Mm.290834	NM_018882	ENSMUSG00000031785	Adgrg1	Cyt28|Gpr56|TM7LN4|TM7XN1	adhesion G protein-coupled receptor G1	protein-coding
mm_129997.1	chr15	86186003	86186027	-	1	NA	5' UTR (NM_145475, exon 1 of 13)	5' UTR (NM_145475, exon 1 of 13)	126	NM_145475	223753	Mm.222685	NM_145475	ENSMUSG00000035891	Cerk	AI848610|D330016D08Rik|mKIAA1646	ceramide kinase	protein-coding
mm_172318.1	chr7	106215363	106215363	-	1	NA	promoter-TSS (NM_001243039).2	promoter-TSS (NM_001243039).2	-23	NM_029000	74558	Mm.458429	NM_029000	ENSMUSG00000045868	Gvin1	9130002C22Rik|9830104F22Rik|Iigs1|VLIG|VLIG-1	GTPase, very large interferon inducible 1	protein-coding
mm_49719.1	chr6	34598519	34598529	+	1	NA	promoter-TSS (NM_001347100)	promoter-TSS (NM_001347100)	20	NM_001347100	109624	Mm.308134	NM_145575	ENSMUSG00000029761	Cald1	4833423D12Rik|AI195384|AV071549|AW536160|C920027I18Rik	caldesmon 1	protein-coding
mm_73426.1	chr8	106135436	106135457	+	1	NA	promoter-TSS (NR_040346)	promoter-TSS (NR_040346)	46	NR_040346	69771	Mm.393274	NR_040344		1810019D21Rik	-	RIKEN cDNA 1810019D21 gene	ncRNA
mm_33486.1	chr4	130822657	130822668	+	1	NA	exon (NM_011520, exon 5 of 5)	exon (NM_011520, exon 5 of 5)	30125	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_116374.1	chr13	40738374	40738386	-	1	NA	Intergenic	Intergenic	-3460	NM_001301674	21418	Mm.85544	NM_011547	ENSMUSG00000021359	Tfap2a	AP-2|AP2alpha|Ap-2 (a)|Ap2|Ap2tf|Tcfap2a	transcription factor AP-2, alpha	protein-coding
mm_117844.1	chr13	98693120	98693145	-	1	NA	intron (NM_001025606, intron 1 of 3)	intron (NM_001025606, intron 1 of 3)	1699	NM_001025606	380863	Mm.28264	NM_001025606	ENSMUSG00000052485	Tmem171	Gm905	transmembrane protein 171	protein-coding
mm_80753.1	chr9	95407426	95407439	+	1	NA	promoter-TSS (NM_018763)	promoter-TSS (NM_018763)	-162	NM_018763	54371	Mm.212446	NM_018763	ENSMUSG00000033350	Chst2	AI428561|AW121776|C130041E03Rik|Chts2|GST-2|GlcNAc6ST|Gn6st	carbohydrate sulfotransferase 2	protein-coding
mm_168344.1	chr11	120824079	120824080	-	1	NA	5' UTR (NM_007988, exon 1 of 43)	5' UTR (NM_007988, exon 1 of 43)	468	NM_007988	14104	Mm.236443	NM_007988	ENSMUSG00000025153	Fasn	A630082H08Rik|FAS	fatty acid synthase	protein-coding
mm_80130.1	chr9	70656230	70656245	+	1	NA	intron (NM_172772, intron 1 of 8)	intron (NM_172772, intron 1 of 8)	937	NM_172772	235461	Mm.170855	NM_172772	ENSMUSG00000042444	Fam63b	AI465301|B230380D07Rik|mKIAA1164	family with sequence similarity 63, member B	protein-coding
mm_74137.1	chr8	123213015	123213032	+	1	NA	promoter-TSS (NM_145606)	promoter-TSS (NM_145606)	165	NM_177279	320869	Mm.258354	NM_177279	ENSMUSG00000048478	Spata33	4732415M23Rik|AI847264	spermatogenesis associated 33	protein-coding
mm_143908.1	chr17	85088544	85088577	-	1	NA	5' UTR (NM_001163622, exon 2 of 15)	5' UTR (NM_001163622, exon 2 of 15)	1707	NM_145984	213760	Mm.259035	NM_145984	ENSMUSG00000024127	Prepl	2810457N15Rik|9530014L06Rik|D030028O16Rik|mKIAA0436	prolyl endopeptidase-like	protein-coding
mm_97375.1	chr11	77693577	77693580	+	1	NA	intron (NM_001024205, intron 2 of 3)	intron (NM_001024205, intron 2 of 3)	7439	NM_001024205	68564	Mm.428996	NM_001024205	ENSMUSG00000037857	Nufip2	1110001M19Rik|9530056D24Rik|AI256692|AI461731|PIG1|mKIAA1321	nuclear fragile X mental retardation protein interacting protein 2	protein-coding
mm_38103.1	chr4	134372576	134372589	-	1	NA	promoter-TSS (NM_019578)	promoter-TSS (NM_019578)	-35	NM_019578	56219	Mm.30978	NM_019578	ENSMUSG00000028838	Extl1	D430033M16Rik	exostoses (multiple)-like 1	protein-coding
mm_19374.1	chr2	91194768	91194789	-	1	NA	5' UTR (NM_013839, exon 1 of 10)	5' UTR (NM_013839, exon 1 of 10)	257	NM_013839	22259	Mm.22690	NM_013839	ENSMUSG00000002108	Nr1h3	AU018371|LXR|RLD1|Unr1	nuclear receptor subfamily 1, group H, member 3	protein-coding
mm_158420.1	chrX	139085212	139085225	-	1	NA	promoter-TSS (NM_177920)	promoter-TSS (NM_177920)	18	NM_177920	331535	Mm.211704	NM_177920	ENSMUSG00000031271	Serpina7	C730040N12Rik|Tbg	serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 7	protein-coding
mm_134403.1	chr16	17576217	17576237	-	1	NA	intron (NM_144852, intron 1 of 4)	intron (NM_144852, intron 1 of 4)	444	NM_144852	224022	Mm.298878	NM_144852	ENSMUSG00000022756	Slc7a4	AI853530	solute carrier family 7 (cationic amino acid transporter, y+ system), member 4	protein-coding
mm_16367.1	chr2	175869282	175869294	+	1	NA	promoter-TSS (NM_001099308).2	promoter-TSS (NM_001099308).2	43	NM_001164689	626832	Mm.441314	NM_001164689	ENSMUSG00000078887	Gm6710	1600017I02Rik|2310011F05Rik|2900089K14Rik|3100002L24Rik|WF-4	predicted gene 6710	protein-coding
mm_102638.1	chr11	62574083	62574085	-	1	NA	promoter-TSS (NM_011706)	promoter-TSS (NM_011706)	-402	NM_011706	22368	Mm.288064	NM_011706	ENSMUSG00000018507	Trpv2	GRC|OTRPC2|VRL-1|Vrl1	transient receptor potential cation channel, subfamily V, member 2	protein-coding
mm_137140.1	chr17	23610468	23610489	+	1	NA	exon (NM_001033425, exon 6 of 6)	exon (NM_001033425, exon 6 of 6)	9652	NM_001289482	332221	Mm.270315	NM_001033425	ENSMUSG00000023902	Zscan10	BC068284|Zfp206|Zkscan10|Znf206	zinc finger and SCAN domain containing 10	protein-coding
mm_129787.1	chr15	82806814	82806815	-	1	NA	Intergenic	L1MC1|LINE|L1	-12569	NM_029562	76279	Mm.439931	NM_029562	ENSMUSG00000022445	Cyp2d26	1300006E06Rik	cytochrome P450, family 2, subfamily d, polypeptide 26	protein-coding
mm_125916.1	chr15	76117792	76117798	+	1	NA	intron (NM_144848, intron 1 of 1)	intron (NM_144848, intron 1 of 1)	2400	NM_144848	223650	Mm.259929	NM_144848		Eppk1	6230424I18Rik|EPIPL|EPIPL1|EPPK	epiplakin 1	protein-coding
mm_101848.1	chr11	48826725	48826747	-	1	NA	intron (NM_053166, intron 1 of 6)	intron (NM_053166, intron 1 of 6)	598	NM_053166	94089	Mm.390335	NM_053166	ENSMUSG00000040350	Trim7	AI790312	tripartite motif-containing 7	protein-coding
mm_11669.1	chr2	35283993	35284014	+	1	NA	exon (NM_001206369, exon 2 of 17)	exon (NM_001206369, exon 2 of 17)	1623	NM_146120	227753	Mm.443	NM_146120	ENSMUSG00000026879	Gsn	ADF	gelsolin	protein-coding
mm_172027.1	chr6	122794293	122794298	+	1	NA	Intergenic	B2_Mm2|SINE|B2	-25889	NM_021899	60611	Mm.87142	NM_021899	ENSMUSG00000003154	Foxj2	Fhx	forkhead box J2	protein-coding
mm_132975.1	chr16	52049652	52049662	+	1	NA	intron (NM_001033238, intron 3 of 17)	intron (NM_001033238, intron 3 of 17)	18108	NM_001033238	208650	Mm.328206	NM_001033238	ENSMUSG00000022637	Cblb	AI429560|AI851073|Cbl-b	Casitas B-lineage lymphoma b	protein-coding
mm_163270.1	chr11	115187569	115187571	+	1	NA	promoter-TSS (NM_025400)	promoter-TSS (NM_025400)	83	NM_001033393	320534	Mm.260587	NM_001033393	ENSMUSG00000045980	Tmem104	C630005D06Rik|mFLJ00021	transmembrane protein 104	protein-coding
mm_92722.1	chr10	80807634	80807660	-	1	NA	TTS (NM_007445)	TTS (NM_007445)	2399	NM_007445	11705	Mm.376094	NM_007445	ENSMUSG00000035262	Amh	MIS	anti-Mullerian hormone	protein-coding
mm_172888.1	chr9	53690301	53690321	-	1	NA	intron (NM_175562, intron 1 of 1)	intron (NM_175562, intron 1 of 1)	15921	NM_175562	270160	Mm.290285	NM_175562	ENSMUSG00000055069	Rab39	C230094F14Rik|Rab39a	RAB39, member RAS oncogene family	protein-coding
mm_93721.1	chr10	119239518	119239532	-	1	NA	intron (NM_027994, intron 1 of 14)	CpG	530	NM_027994	71902	Mm.203965	NM_027994	ENSMUSG00000020114	Cand1	2310038O07Rik|6330512O03Rik|AI195005|AI846556|D10Ertd516e|Tp120a|mKIAA0829	cullin associated and neddylation disassociated 1	protein-coding
mm_122311.1	chr14	36906317	36906323	-	1	NA	intron (NM_001347503, intron 3 of 7)	intron (NM_001347503, intron 3 of 7)	13215	NM_001347503	72972	Mm.27621	NM_027045	ENSMUSG00000058690	Ccser2	1700012P13Rik|2900054P12Rik|AI035535|AW108503|Fam190b|Gcap14	coiled-coil serine rich 2	protein-coding
mm_86788.1	chr10	20203606	20203616	+	1	NA	intron (NM_001198635, intron 1 of 17)	intron (NM_001198635, intron 1 of 17)	-1757	NR_045350	73811	Mm.55644	NR_045350	ENSMUSG00000110754	4930405J17Rik	-	RIKEN cDNA 4930405J17 gene	ncRNA
mm_121492.1	chr14	121830949	121830954	+	1	NA	Intergenic	Intergenic	-33217	NM_134074	105445	Mm.378591	NM_134074	ENSMUSG00000025558	Dock9	AA959601|AW538057|B230309H04Rik|D14Wsu89e|Zizimin1|mKIAA1058	dedicator of cytokinesis 9	protein-coding
mm_54884.1	chr6	43076983	43076983	-	1	NA	Intergenic	Intergenic	-38761	NM_146655	258649	Mm.271494	NM_146655	ENSMUSG00000094669	Olfr441	MOR261-3	olfactory receptor 441	protein-coding
mm_53125.1	chr6	125130471	125130473	+	1	NA	TTS (NM_145979)	TTS (NM_145979)	-1411	NM_138747	110109	Mm.29203	NM_138747	ENSMUSG00000038279	Nop2	120kDa|A530002O17|Nol1	NOP2 nucleolar protein	protein-coding
mm_5496.1	chr1	36943811	36943842	-	1	NA	Intergenic	L2|LINE|L2	-4299	NM_018872	56030	Mm.186943	NM_018872	ENSMUSG00000026116	Tmem131	2610524E03Rik|CC28|D1Bwg0491e|Neg|RW1|YR-23|mKIAA0257	transmembrane protein 131	protein-coding
mm_3790.1	chr1	157412372	157412390	+	1	NA	promoter-TSS (NR_027984)	promoter-TSS (NR_027984)	29	NR_027984	69953	Mm.286863	NM_027274	ENSMUSG00000049881	2810025M15Rik	AI429618	RIKEN cDNA 2810025M15 gene	ncRNA
mm_114577.1	chr13	75640157	75640164	+	1	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	-4886	NR_030451	751556		NR_030451	ENSMUSG00000076236	Mir682	Mirn682|mir-682|mmu-mir-682	microRNA 682	ncRNA
mm_112912.1	chr13	20922940	20922951	+	1	NA	intron (NM_012054, intron 11 of 20)	B4A|SINE|B4	128832	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_156920.1	chrX	169122293	169122307	+	1	NA	intron (NM_001287530, intron 1 of 12)	B3|SINE|B2	9422	NM_001287530	11856	Mm.441810	NM_009707	ENSMUSG00000031355	Arhgap6	AI504284|RhoGAPX-1	Rho GTPase activating protein 6	protein-coding
mm_154365.1	chrM	8601	8616	+	1	NA	NA	Intergenic	NA	NA								
mm_49687.1	chr6	33375221	33375223	+	1	NA	intron (NM_001347089, intron 7 of 9)	intron (NM_001347089, intron 7 of 9)	126072	NM_009148	20336	Mm.265512	NM_009148	ENSMUSG00000029763	Exoc4	C78892|Sec8|Sec8l1	exocyst complex component 4	protein-coding
mm_165295.1	chr2	91096912	91096920	+	1	NA	5' UTR (NM_011355, exon 1 of 5)	5' UTR (NM_011355, exon 1 of 5)	238	NM_011355	20375	Mm.1302	NM_011355	ENSMUSG00000002111	Spi1	Dis-1|Dis1|PU.1|Sfpi-1|Sfpi1|Spi-1|Tcfpu1|Tfpu.1	spleen focus forming virus (SFFV) proviral integration oncogene	protein-coding
mm_140795.1	chr17	21450257	21450273	-	1	NA	promoter-TSS (NM_009558)	promoter-TSS (NM_009558)	-109	NM_001308323	22709	Mm.293030	NM_009558	ENSMUSG00000023892	Zfp51	Zfp-51|zfec12	zinc finger protein 51	protein-coding
mm_67133.1	chr7	72248958	72248961	-	1	NA	intron (NM_001024703, intron 2 of 22)	B3|SINE|B2	57636	NM_001024703	244049	Mm.217412	NM_001024703	ENSMUSG00000032776	Mctp2	Gm489	multiple C2 domains, transmembrane 2	protein-coding
mm_159301.1	chr2	177464770	177464770	+	1	NA	promoter-TSS (NM_001177568)	promoter-TSS (NM_001177568)	28	NM_001177568	628308	Mm.460436	NM_001177568	ENSMUSG00000078866	Zfp970	Gm14420|OTTMUSG00000016588	zinc finger protein 970	protein-coding
mm_26985.1	chr3	25697963	25697987	-	1	NA	intron (NM_001163387, intron 3 of 5)	intron (NM_001163387, intron 3 of 5)	455332	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_124453.1	chr14	118937740	118937772	-	1	NA	promoter-TSS (NM_008929)	promoter-TSS (NM_008929)	-176	NM_008929	100037258	Mm.12616	NM_008929	ENSMUSG00000022136	Dnajc3	AA408985|AU067833|Dnajc3a|Dnajc3b|Prkri|mp58|p58|p58IPK	DnaJ heat shock protein family (Hsp40) member C3	protein-coding
mm_114263.1	chr13	57282346	57282365	+	1	NA	Intergenic	Intergenic	-386566	NM_001302373	26946	Mm.62409	NM_012035	ENSMUSG00000021541	Trpc7	TRP7|Trrp8	transient receptor potential cation channel, subfamily C, member 7	protein-coding
mm_163359.1	chr12	29528118	29528133	-	1	NA	promoter-TSS (NM_008666)	promoter-TSS (NM_008666)	-259	NM_001093775	17933	Mm.253067	NM_008666	ENSMUSG00000061911	Myt1l	2900046C06Rik|2900093J19Rik|C630034G21Rik|Nztf1|Pmng1|Png-1|mKIAA1106	myelin transcription factor 1-like	protein-coding
mm_48556.1	chr5	143112972	143112987	-	1	NA	promoter-TSS (NM_207110)	promoter-TSS (NM_207110)	41	NM_207110	108086	Mm.381440	NM_080561	ENSMUSG00000045078	Rnf216	2810055G22Rik|AI647468|AU019462|C86502|F830018F18Rik|TRIAD3|UIP83|Ubce7ip1	ring finger protein 216	protein-coding
mm_11270.1	chr2	30061848	30061859	+	1	NA	promoter-TSS (NM_023871)	promoter-TSS (NM_023871)	-143	NM_023871	56086	Mm.326055	NM_023871	ENSMUSG00000054766	Set	2610030F17Rik|5730420M11Rik|AA407739|I-2PP2A|StF-IT-1|TAF-I	SET nuclear oncogene	protein-coding
mm_78070.1	chr9	15313803	15313824	+	1	NA	intron (NR_028401, intron 7 of 11)	intron (NR_028401, intron 7 of 11)	1202	NR_106108	102465758		NR_106108	ENSMUSG00000105847	Gm25500	Mir7650|mmu-mir-7650	predicted gene, 25500	ncRNA
mm_74224.1	chr8	124066778	124066788	+	1	NA	Intergenic	Intergenic	43310	NM_001029876	382038	Mm.334891	NM_001029876	ENSMUSG00000031976	Urb2	C77575|mKIAA0133	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	protein-coding
mm_172189.1	chr6	50566528	50566528	-	1	NA	promoter-TSS (NM_007808)	promoter-TSS (NM_007808)	-54	NM_007808	13063	Mm.35389	NM_007808	ENSMUSG00000063694	Cycs	-	cytochrome c, somatic	protein-coding
mm_135660.1	chr16	52404436	52404438	-	1	NA	intron (NM_009655, intron 1 of 15)	intron (NM_009655, intron 1 of 15)	48644	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_21403.1	chr2	157997147	157997179	-	1	NA	exon (NM_029282, exon 3 of 7)	exon (NM_029282, exon 3 of 7)	12197	NM_029282	75425	Mm.29068	NM_029282	ENSMUSG00000027650	Tti1	2610036D13Rik|AI449463	TELO2 interacting protein 1	protein-coding
mm_124938.1	chr15	12240455	12240458	+	1	NA	intron (NM_172958, intron 6 of 15)	B4|SINE|B4	35362	NM_172958	268783	Mm.54460	NM_172958	ENSMUSG00000039458	Mtmr12	3Pap|4932703C11|C730015A02Rik|Pip3ap|mKIAA1682	myotubularin related protein 12	protein-coding
mm_146932.1	chr18	32036942	32037019	-	1	NA	promoter-TSS (NM_032394)	promoter-TSS (NM_032394)	-49	NM_032394	17922	Mm.440013	NM_032394	ENSMUSG00000024388	Myo7b	-	myosin VIIB	protein-coding
mm_156368.1	chrX	139610613	139610632	+	1	NA	promoter-TSS (NM_023270)	promoter-TSS (NM_023270)	2	NM_023270	66889	Mm.27764	NM_023270	ENSMUSG00000031438	Rnf128	1300002C13Rik|AI987883|GRAIL|Greul1	ring finger protein 128	protein-coding
mm_144605.1	chr18	32397618	32397678	+	1	NA	intron (NM_001083334, intron 1 of 14)	intron (NM_001083334, intron 1 of 14)	-19364	NR_045403	402767	Mm.385109	NR_045403	ENSMUSG00000097413	A830052D11Rik	-	RIKEN cDNA A830052D11 gene	ncRNA
mm_63445.1	chr7	127490060	127490072	+	1	NA	TTS (NR_106027)	TTS (NR_106027)	815	NR_106027	102465642		NR_106027	ENSMUSG00000098267	Mir7060	Gm27515|mmu-mir-7060	microRNA 7060	ncRNA
mm_7460.1	chr1	120449675	120449678	-	1	NA	Intergenic	Intergenic	55408	NM_010766	17167	Mm.1856	NM_010766	ENSMUSG00000026390	Marco	AI323439|Ly112|Scara2	macrophage receptor with collagenous structure	protein-coding
mm_76533.1	chr8	87959535	87959558	-	1	NA	promoter-TSS (NM_033327)	promoter-TSS (NM_033327)	49	NM_033327	94187	Mm.23452	NM_033327	ENSMUSG00000045333	Zfp423	Ebfaz|Roaz|Zfp104|Znf423|ataxia1|mKIAA0760|nur12	zinc finger protein 423	protein-coding
mm_137381.1	chr17	25756654	25756665	+	1	NA	Intergenic	MER54B|LTR|ERVL	-2332	NM_018857	56047	Mm.17510	NM_018857	ENSMUSG00000063011	Msln	MPF	mesothelin	protein-coding
mm_173367.1	chrY	90820700	90820701	+	1	NA	Intergenic	IMPB_01|Satellite|Satellite	18706	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_158870.1	chrY	1245754	1245766	-	1	NA	promoter-TSS (NM_001326682)	promoter-TSS (NM_001326682)	-1	NM_009484	22290	Mm.20477	NM_009484	ENSMUSG00000068457	Uty	Hydb|mKIAA4057	ubiquitously transcribed tetratricopeptide repeat gene, Y chromosome	protein-coding
mm_104963.1	chr11	100145919	100145935	-	1	NA	promoter-TSS (NM_008471)	promoter-TSS (NM_008471)	-1	NM_008471	16669	Mm.439699	NM_008471	ENSMUSG00000020911	Krt19	AI663979|CK-19|EndoC|K19|Krt-1.19|Krt1-19	keratin 19	protein-coding
mm_167067.1	chr7	98112731	98112739	-	1	NA	intron (NM_001256081, intron 2 of 48)	intron (NM_001256081, intron 2 of 48)	-3487	NM_001256083	17921	Mm.1403	NM_008663	ENSMUSG00000030761	Myo7a	Hdb|Myo7|USH1B|nmf371|polka|sh-1|sh1	myosin VIIA	protein-coding
mm_72437.1	chr8	83087902	83087947	+	1	NA	3' UTR (NM_177378, exon 7 of 7)	3' UTR (NM_177378, exon 7 of 7)	-77428	NM_001111304	71310	Mm.24031	NM_027758	ENSMUSG00000031709	Tbc1d9	4933431N12Rik|AI847101|AW490653|C76116	TBC1 domain family, member 9	protein-coding
mm_94960.1	chr11	30771816	30771818	+	1	NA	promoter-TSS (NM_134013)	promoter-TSS (NM_134013)	42	NM_134013	103554	Mm.240066	NM_134013	ENSMUSG00000040850	Psme4	AA409398|AU041366|TEMO|mKIAA0077	proteasome (prosome, macropain) activator subunit 4	protein-coding
mm_86304.1	chr9	122351485	122351502	-	1	NA	promoter-TSS (NM_026179)	promoter-TSS (NM_026179)	-123	NM_026179	67469	Mm.280254	NM_026179	ENSMUSG00000032540	Abhd5	1300003D03Rik|2010002J10Rik|CDS|CGI-58|IECN5|NCIE2	abhydrolase domain containing 5	protein-coding
mm_28214.1	chr3	88384454	88384471	-	1	NA	promoter-TSS (NM_007541)	promoter-TSS (NM_007541)	4	NM_007541	12096	Mm.389459	NM_007541	ENSMUSG00000074483	Bglap	BGP|Bglap1|OC|OG1|mOC-A	bone gamma carboxyglutamate protein	protein-coding
mm_51364.1	chr6	72636289	72636321	+	1	NA	intron (NM_009332, intron 4 of 11)	intron (NM_009332, intron 4 of 11)	6474	NR_040421	100038714	Mm.321330	NR_040421		Gm15401	ENSMUSG00000072999|OTTMUSG00000021199	predicted gene 15401	ncRNA
mm_146978.1	chr18	33832742	33832756	-	1	NA	intron (NM_013512, intron 13 of 23)	intron (NM_013512, intron 13 of 23)	37857	NR_038151	69749	Mm.248787	NR_038151	ENSMUSG00000087590	Epb41l4aos	2410004N09Rik|Epb4.1l4aos	erythrocyte membrane protein band 4.1 like 4a, opposite strand	ncRNA
mm_110372.1	chr12	40199498	40199511	-	1	NA	promoter-TSS (NM_001033437)	promoter-TSS (NM_001033437)	-189	NM_001033437	380755	Mm.390463	NM_001033437	ENSMUSG00000071342	Lsmem1	Gm889	leucine-rich single-pass membrane protein 1	protein-coding
mm_58158.1	chr6	142472845	142472882	-	1	NA	5' UTR (NM_145572, exon 1 of 17)	5' UTR (NM_145572, exon 1 of 17)	246	NM_145572	232493	Mm.275975	NM_145572	ENSMUSG00000030244	Gys2	BC021322|LGS	glycogen synthase 2	protein-coding
mm_50982.1	chr6	62165964	62165967	+	1	NA	intron (NM_001164316, intron 10 of 10)	intron (NM_001164316, intron 10 of 10)	-985155	NR_040287	100504262	Mm.438066	NR_040287		A730020E08Rik	-	RIKEN cDNA A730020E08 gene	ncRNA
mm_37648.1	chr4	128786217	128786227	-	1	NA	intron (NM_001081098, intron 5 of 8)	intron (NM_001081098, intron 5 of 8)	19890	NM_001081098	230761	Mm.22616	NM_001081098	ENSMUSG00000028799	Zfp362	-	zinc finger protein 362	protein-coding
mm_76010.1	chr8	72835984	72836020	-	1	NA	intron (NM_001317391, intron 13 of 15)	intron (NM_001317391, intron 13 of 15)	74343	NM_007975	14065	Mm.12948	NM_007975	ENSMUSG00000050147	F2rl3	PAR4	coagulation factor II (thrombin) receptor-like 3	protein-coding
mm_35151.1	chr4	11966369	11966461	-	1	NA	promoter-TSS (NM_001290387)	promoter-TSS (NM_001290387)	35	NM_001098230	381511	Mm.331489	NM_001033453	ENSMUSG00000049225	Pdp1	Gm1024|Ppm2c	pyruvate dehyrogenase phosphatase catalytic subunit 1	protein-coding
mm_144665.1	chr18	34408486	34408494	+	1	NA	promoter-TSS (NM_016927)	promoter-TSS (NM_016927)	-933	NM_001163004	53871	Mm.445792	NM_016927	ENSMUSG00000014503	Pkd2l2	TRPP5	polycystic kidney disease 2-like 2	protein-coding
mm_15650.1	chr2	163122648	163122693	+	1	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	-33069	NM_026630	68236	Mm.33648	NM_026630	ENSMUSG00000070708	Gtsf1l	2410116G06Rik	gametocyte specific factor 1-like	protein-coding
mm_69945.1	chr7	142190450	142190453	-	1	NA	Intergenic	Intergenic	-10913	NM_023860	77215	Mm.462993	NM_023860	ENSMUSG00000046248	Krtap5-3	A030007E19Rik	keratin associated protein 5-3	protein-coding
mm_114700.1	chr13	83504304	83504310	+	1	NA	5' UTR (NM_025282, exon 1 of 11)	5' UTR (NM_025282, exon 1 of 11)	273	NM_001347564	17260	Mm.24001	NM_025282	ENSMUSG00000005583	Mef2c	5430401D19Rik|9930028G15Rik|AV011172|Mef2	myocyte enhancer factor 2C	protein-coding
mm_29146.1	chr3	105932639	105932647	-	1	NA	promoter-TSS (NM_001033780)	promoter-TSS (NM_001033780)	21	NM_001033780	433638	Mm.239081	NM_001033780	ENSMUSG00000074342	I830077J02Rik	-	RIKEN cDNA I830077J02 gene	protein-coding
mm_1146.1	chr1	60746486	60746496	+	1	NA	exon (NM_007642, exon 1 of 4)	exon (NM_007642, exon 1 of 4)	103	NM_007642	12487	Mm.255003	NM_007642	ENSMUSG00000026012	Cd28	-	CD28 antigen	protein-coding
mm_43120.1	chr5	124796373	124796375	+	1	NA	intron (NM_019536, intron 44 of 78)	intron (NM_019536, intron 44 of 78)	65847	NM_144819	215707	Mm.389693	NM_144819	ENSMUSG00000037979	Ccdc92	AW050178|D5Bwg0834e	coiled-coil domain containing 92	protein-coding
mm_143782.1	chr17	81730926	81730943	-	1	NA	intron (NR_104580, intron 1 of 8)	B4|SINE|B4	7453	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_105410.1	chr11	103627643	103627656	-	1	NA	Intergenic	Intergenic	11225	NM_027083	69444	Mm.275677	NM_027083	ENSMUSG00000020945	Lyzl6	1700023H08Rik|Lyc1|Lyzb	lysozyme-like 6	protein-coding
mm_107876.1	chr12	69963453	69963474	+	1	NA	promoter-TSS (NR_036607)	promoter-TSS (NR_036607)	54	NR_036607	100040999	Mm.394588	NR_036607	ENSMUSG00000079076	Gm3086	-	RuvB-like protein 1 pseudogene	pseudo
mm_83779.1	chr9	52141753	52141764	-	1	NA	intron (NM_001162921, intron 2 of 5)	intron (NM_001162921, intron 2 of 5)	26135	NR_105750	102465150		NR_105750	ENSMUSG00000099311	Mir6244	Gm27368|mmu-mir-6244	microRNA 6244	ncRNA
mm_113817.1	chr13	46725447	46725471	+	1	NA	intron (NM_175749, intron 1 of 21)	intron (NM_175749, intron 1 of 21)	2390	NM_175749	218210	Mm.255398	NM_175749	ENSMUSG00000021374	Nup153	B130015D15Rik|C88147	nucleoporin 153	protein-coding
mm_57481.1	chr6	125236997	125237025	-	1	NA	promoter-TSS (NM_001042564)	promoter-TSS (NM_001042564)	16	NM_001033126	21940	Mm.367714	NM_001033126	ENSMUSG00000030336	Cd27	S152|Tnfrsf7|Tp55	CD27 antigen	protein-coding
mm_159885.1	chr6	24108629	24108629	-	1	NA	intron (NM_019481, intron 7 of 14)	intron (NM_019481, intron 7 of 14)	59463	NM_019481	55961	Mm.19299	NM_019481	ENSMUSG00000029700	Slc13a1	AI314066|AI987826|NaSi-1|Nas1	solute carrier family 13 (sodium/sulfate symporters), member 1	protein-coding
mm_64723.1	chr7	4658984	4659026	-	1	NA	promoter-TSS (NM_172894)	promoter-TSS (NM_172894)	-55	NM_172894	243819	Mm.258670	NM_172894	ENSMUSG00000052296	Ppp6r1	2010309P17Rik|AI836219|B430201G11Rik|D030074N20Rik|Pp6r1|Saps1|mKIAA1115	protein phosphatase 6, regulatory subunit 1	protein-coding
mm_129704.1	chr15	81726230	81726270	-	1	NA	intron (NM_001146174, intron 1 of 15)	intron (NM_001146174, intron 1 of 15)	3669	NM_011241	19387	Mm.270975	NM_011241	ENSMUSG00000022391	Rangap1	C79654|Fug1|mKIAA1835	RAN GTPase activating protein 1	protein-coding
mm_163514.1	chr12	113427511	113427513	-	1	NA	Intergenic	Intergenic	-62053	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_81330.1	chr9	108516977	108517006	+	1	NA	promoter-TSS (NM_175143)	promoter-TSS (NM_175143)	-96	NM_001114119	69232	Mm.335449	NM_175143	ENSMUSG00000006673	Qrich1	2610028H07Rik	glutamine-rich 1	protein-coding
mm_171617.1	chr4	150570260	150570267	+	1	NA	exon (NM_001085492, exon 12 of 23)	exon (NM_001085492, exon 12 of 23)	81911	NM_173774	242773	Mm.29280	NM_173774	ENSMUSG00000039838	Slc45a1	C230078B22|Dnb5	solute carrier family 45, member 1	protein-coding
mm_76966.1	chr8	106210925	106210942	-	1	NA	promoter-TSS (NM_001007567)	promoter-TSS (NM_001007567)	0	NM_001007567	66432	Mm.269029	NM_001007567	ENSMUSG00000033106	Slc7a6os	2010007L18Rik|2400002F02Rik	solute carrier family 7, member 6 opposite strand	protein-coding
mm_102849.1	chr11	69369800	69369853	-	1	NA	promoter-TSS (NM_146019)	promoter-TSS (NM_146019)	-400	NM_146019	216848	Mm.178246	NM_146019	ENSMUSG00000018474	Chd3	2600010P09Rik|AF020312|Chd7|Prp7|Prp9-1	chromodomain helicase DNA binding protein 3	protein-coding
mm_154785.1	chrX	13071147	13071169	+	1	NA	promoter-TSS (NM_009481)	promoter-TSS (NM_009481)	-340	NM_009481	22284	Mm.242646	NM_009481	ENSMUSG00000031010	Usp9x	5730589N07Rik|AA407302|AA407699|AL022658|AL022749|Dffrx|FAF-X|Fafl	ubiquitin specific peptidase 9, X chromosome	protein-coding
mm_25185.1	chr3	103356810	103356816	+	1	NA	3' UTR (NM_053170, exon 20 of 20)	3' UTR (NM_053170, exon 20 of 20)	77520	NM_001079830	94093	Mm.195036	NM_053170	ENSMUSG00000033014	Trim33	8030451N04Rik|AI413936|Ecto|Tif1g	tripartite motif-containing 33	protein-coding
mm_115279.1	chr13	111797254	111797258	+	1	NA	intron (NM_011945, intron 1 of 19)	intron (NM_011945, intron 1 of 19)	11727	NM_011945	26401	Mm.15918	NM_011945	ENSMUSG00000021754	Map3k1	MAPKKK1|MEKK1|Mekk	mitogen-activated protein kinase kinase kinase 1	protein-coding
mm_125406.1	chr15	41710600	41710652	+	1	NA	intron (NM_001130166, intron 3 of 16)	intron (NM_001130166, intron 3 of 16)	-78408	NM_001130165	170719	Mm.254267	NM_130885	ENSMUSG00000022307	Oxr1	2210416C20Rik|C7|C7B	oxidation resistance 1	protein-coding
mm_2742.1	chr1	128590955	128590999	+	1	NA	intron (NM_009911, intron 1 of 1)	CpG	1322	NM_009911	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding
mm_89289.1	chr10	87892495	87892513	+	1	NA	intron (NM_001314010, intron 3 of 4)	B4A|SINE|B4	31393	NM_001111276	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_151679.1	chr19	4257605	4257611	-	1	NA	Intergenic	Intergenic	6270	NR_105951	102465595		NR_105951	ENSMUSG00000099290	Mir6985	Gm27719|mmu-mir-6985	microRNA 6985	ncRNA
mm_33786.1	chr4	134923051	134923081	+	1	NA	promoter-TSS (NM_023665)	promoter-TSS (NM_023665)	-559	NM_023665	27981	Mm.331964	NM_023665	ENSMUSG00000037266	Rsrp1	2700043I21Rik|D4Ucla2|D4Wsu53e	arginine/serine rich protein 1	protein-coding
mm_22250.1	chr2	174853219	174853223	-	1	NA	Intergenic	Intergenic	92602	NM_007903	13616	Mm.9478	NM_007903	ENSMUSG00000027524	Edn3	ET-3|PPET3|ls|tmgc48	endothelin 3	protein-coding
mm_164643.1	chr17	35122729	35122732	+	1	NA	promoter-TSS (NM_032460)	promoter-TSS (NM_032460)	-222	NM_032460	81845	Mm.7405	NM_032460	ENSMUSG00000092417	Gpank1	Bat-4|Bat4|D17H6S54E|G5	G patch domain and ankyrin repeats 1	protein-coding
mm_123918.1	chr14	73363118	73363149	-	1	NA	exon (NM_008410, exon 6 of 6)	exon (NM_008410, exon 6 of 6)	22138	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_79641.1	chr9	59558069	59558097	+	1	NA	exon (NM_010421, exon 6 of 14)	exon (NM_010421, exon 6 of 14)	18543	NM_010421	15211	Mm.2284	NM_010421	ENSMUSG00000025232	Hexa	Hex-1	hexosaminidase A	protein-coding
mm_153343.1	chr19	38819157	38819242	-	1	NA	promoter-TSS (NM_021315)	promoter-TSS (NM_021315)	38	NM_021315	57753	Mm.86482	NM_021315	ENSMUSG00000024999	Noc3l	AF233884|Fad24	NOC3 like DNA replication regulator	protein-coding
mm_136861.1	chr17	12821538	12821555	+	1	NA	intron (NR_027773, intron 1 of 2)	Lx3B|LINE|L1	46597	NM_008552	17171	Mm.425994	NM_008552	ENSMUSG00000068037	Mas1	Mas-1|Mgra	MAS1 oncogene	protein-coding
mm_131226.1	chr16	10170217	10170227	+	1	NA	promoter-TSS (NM_026594)	promoter-TSS (NM_026594)	-6	NM_026594	68172	Mm.23690	NM_026594	ENSMUSG00000039209	Rpl39l	4930517K11Rik	ribosomal protein L39-like	protein-coding
mm_15886.1	chr2	164839715	164839774	+	1	NA	exon (NM_011125, exon 16 of 16)	exon (NM_011125, exon 16 of 16)	5971	NM_008906	19025	Mm.359633	NM_008906	ENSMUSG00000017760	Ctsa	AU019505|PPCA|Ppgb	cathepsin A	protein-coding
mm_65640.1	chr7	27929469	27929487	-	1	NA	promoter-TSS (NM_028538)	promoter-TSS (NM_028538)	-48	NM_028538	73430	Mm.379224	NM_028538	ENSMUSG00000070709	Zfp974	1700049G17Rik|AV321011|BB026409	zinc finger protein 974	protein-coding
mm_35646.1	chr4	43523675	43523699	-	1	NA	promoter-TSS (NM_009416)	promoter-TSS (NM_009416)	-133	NM_001277875	22004	Mm.646	NM_009416	ENSMUSG00000028464	Tpm2	Tpm-2|Trop-2	tropomyosin 2, beta	protein-coding
mm_94512.1	chr11	8569850	8569858	+	1	NA	intron (NM_001083587, intron 4 of 30)	intron (NM_001083587, intron 4 of 30)	94681	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_65761.1	chr7	28631587	28631594	-	1	NA	promoter-TSS (NM_175319)	promoter-TSS (NM_175319)	-575	NM_175319	101744	Mm.26022	NM_175319	ENSMUSG00000037469	Acp7	AU017076|C330005M16Rik|Papl	acid phosphatase 7, tartrate resistant	protein-coding
mm_157574.1	chrX	52613914	52613924	-	1	NA	promoter-TSS (NM_016697)	promoter-TSS (NM_016697)	55	NM_016697	14734	Mm.22515	NM_016697	ENSMUSG00000055653	Gpc3	OCI-5	glypican 3	protein-coding
mm_13030.1	chr2	91054137	91054141	+	1	NA	5' UTR (NM_008948, exon 1 of 12)	5' UTR (NM_008948, exon 1 of 12)	123	NM_008948	19182	Mm.289832	NM_008948	ENSMUSG00000002102	Psmc3	TBP-1	proteasome (prosome, macropain) 26S subunit, ATPase 3	protein-coding
mm_3459.1	chr1	150103992	150104015	+	1	NA	exon (NM_011198, exon 7 of 10)	exon (NM_011198, exon 7 of 10)	3972	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_97186.1	chr11	75572460	75572485	+	1	NA	exon (NM_001199283, exon 14 of 14)	exon (NM_001199283, exon 14 of 14)	-15607	NM_008850	18738	Mm.3128	NM_008850	ENSMUSG00000017781	Pitpna	Pitpn|vb|vibrator	phosphatidylinositol transfer protein, alpha	protein-coding
mm_101962.1	chr11	50301017	50301031	-	1	NA	exon (NM_001110500, exon 10 of 15)	exon (NM_001110500, exon 10 of 15)	-8688	NM_175334	103806	Mm.51116	NM_175334	ENSMUSG00000050567	Maml1	AI644666|AW743257|D930008C07Rik|Mam-1|Mam1|mKIAA0200	mastermind like 1 (Drosophila)	protein-coding
mm_25584.1	chr3	116878498	116878527	+	1	NA	intron (NM_009146, intron 3 of 16)	B1_Mus1|SINE|Alu	16832	NM_009146	20321	Mm.66293	NM_009146	ENSMUSG00000033386	Frrs1	AI131732|Sdfr2	ferric-chelate reductase 1	protein-coding
mm_119588.1	chr14	50930141	50930160	+	1	NA	exon (NM_001033271, exon 2 of 7)	exon (NM_001033271, exon 2 of 7)	699	NM_001310506	219024	Mm.239117	NM_001033271	ENSMUSG00000035953	Tmem55b	BC039161	transmembrane protein 55b	protein-coding
mm_82731.1	chr9	25151773	25151840	-	1	NA	promoter-TSS (NM_020586)	promoter-TSS (NM_020586)	-25	NM_020586	80517	Mm.142843	NM_020586	ENSMUSG00000008429	Herpud2	5031400M07Rik|AB041580	HERPUD family member 2	protein-coding
mm_40618.1	chr5	64803551	64803561	+	1	NA	promoter-TSS (NM_008453)	promoter-TSS (NM_008453)	33	NM_008453	16599	Mm.392759	NM_008453	ENSMUSG00000029178	Klf3	9930027G08Rik|AL024007|Bklf|Tef-2	Kruppel-like factor 3 (basic)	protein-coding
mm_141021.1	chr17	25136493	25136507	-	1	NA	promoter-TSS (NM_001317404)	promoter-TSS (NM_001317404)	-131	NM_001317404	26373	Mm.270587	NM_011930	ENSMUSG00000036636	Clcn7	ClC-7|D17Wsu51e	chloride channel, voltage-sensitive 7	protein-coding
mm_39799.1	chr5	30622505	30622527	+	1	NA	exon (NM_010608, exon 2 of 2)	exon (NM_010608, exon 2 of 2)	-25420	NR_049199	100885838		NR_049199	ENSMUSG00000093710	Mir5625	Gm23930|mmu-mir-5625	microRNA 5625	ncRNA
mm_37144.1	chr4	116993688	116993703	-	1	NA	exon (NM_009478, exon 2 of 10)	exon (NM_009478, exon 2 of 10)	718	NM_009478	22275	Mm.46484	NM_009478	ENSMUSG00000028684	Urod	AI323803|UPD|Uro-d	uroporphyrinogen decarboxylase	protein-coding
mm_40135.1	chr5	35045276	35045285	+	1	NA	exon (NM_019447, exon 10 of 14)	exon (NM_019447, exon 10 of 14)	3771	NM_019447	54426	Mm.27369	NM_019447	ENSMUSG00000029102	Hgfac	HGFA	hepatocyte growth factor activator	protein-coding
mm_66892.1	chr7	59288673	59288691	-	1	NA	intron (NM_173010, intron 8 of 8)	intron (NM_173010, intron 8 of 8)	35467	NR_015479	330544	Mm.9002	NR_015479	ENSMUSG00000100826	C230091D08Rik	-	RIKEN cDNA C230091D08 gene	ncRNA
mm_151715.1	chr19	4625613	4625658	-	1	NA	promoter-TSS (NM_023131)	promoter-TSS (NM_023131)	-18	NM_023131	19671	Mm.391143	NM_023131	ENSMUSG00000024889	Rce1	D19Ertd283e|D19Ertd98e	Ras converting CAAX endopeptidase 1	protein-coding
mm_114659.1	chr13	78118231	78118237	+	1	NA	intron (NM_001163420, intron 8 of 8)	intron (NM_001163420, intron 8 of 8)	78215	NM_001347538	13865	Mm.439653	NM_010151	ENSMUSG00000069171	Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR-3|EAR3|Erbal3|SVP44|Tcfcoup1	nuclear receptor subfamily 2, group F, member 1	protein-coding
mm_120835.1	chr14	75177810	75177845	+	1	NA	intron (NM_008879, intron 2 of 16)	intron (NM_008879, intron 2 of 16)	41402	NM_008879	18826	Mm.153911	NM_008879	ENSMUSG00000021998	Lcp1	AW536232|D14Ertd310e|LCP-1|Pls2|pp65	lymphocyte cytosolic protein 1	protein-coding
mm_13021.1	chr2	91035576	91035610	+	1	NA	promoter-TSS (NM_009023)	promoter-TSS (NM_009023)	-34	NM_009023	19400	Mm.1272	NM_009023	ENSMUSG00000002104	Rapsn	43kDa|Nraps|Raps|rapsyn	receptor-associated protein of the synapse	protein-coding
mm_73275.1	chr8	104595357	104595361	+	1	NA	3' UTR (NM_001024606, exon 2 of 2)	3' UTR (NM_001024606, exon 2 of 2)	3891	NM_001024606	382051	Mm.290750	NM_001024606	ENSMUSG00000048371	Pdp2	4833426J09Rik|Gm1705|mKIAA1348	pyruvate dehyrogenase phosphatase catalytic subunit 2	protein-coding
mm_32573.1	chr4	109978838	109978859	+	1	NA	intron (NM_172296, intron 1 of 2)	intron (NM_172296, intron 1 of 2)	823	NM_172296	242620	Mm.32825	NM_172296	ENSMUSG00000047143	Dmrta2	Dmrt5	doublesex and mab-3 related transcription factor like family A2	protein-coding
mm_9273.1	chr1	171634109	171634119	-	1	NA	3' UTR (NM_144539, exon 8 of 8)	3' UTR (NM_144539, exon 8 of 8)	7786	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_107431.1	chr12	35724577	35724625	+	1	NA	Intergenic	Lx8|LINE|L1	-29483	NR_045050	71581	Mm.100110	NR_045050		9130015A21Rik	100043575|Gm4527	RIKEN cDNA 9130015A21 gene	ncRNA
mm_100788.1	chr11	4849346	4849473	-	1	NA	5' UTR (NM_001252252, exon 1 of 16)	5' UTR (NM_001252252, exon 1 of 16)	135	NM_001252250	18016	Mm.297109	NM_010898	ENSMUSG00000009073	Nf2	merlin	neurofibromin 2	protein-coding
mm_68720.1	chr7	120103215	120103225	-	1	NA	intron (NM_145586, intron 1 of 4)	intron (NM_145586, intron 1 of 4)	794	NM_145586	233806	Mm.257952	NM_145586	ENSMUSG00000030917	Tmem159	8430420C20Rik	transmembrane protein 159	protein-coding
mm_36787.1	chr4	103026710	103026752	-	1	NA	promoter-TSS (NM_011831)	promoter-TSS (NM_011831)	-3	NM_011831	23919	Mm.100163	NM_011831	ENSMUSG00000066090	Insl5	RIF2	insulin-like 5	protein-coding
mm_160328.1	chr8	3854285	3854285	-	1	NA	promoter-TSS (NM_130905)	promoter-TSS (NM_130905)	1	NM_130905	170780	Mm.52281	NM_130905	ENSMUSG00000040197	Cd209e	SIGNR4|mSIGNR4	CD209e antigen	protein-coding
mm_142955.1	chr17	56117578	56117588	-	1	NA	promoter-TSS (NM_001077348)	promoter-TSS (NM_001077348)	-35	NM_025874	66968	Mm.254985	NM_025874	ENSMUSG00000011305	Plin5	2310076L09Rik|AI415325|AW109675|Lsdp5|MLDP|PAT-1	perilipin 5	protein-coding
mm_89398.1	chr10	90314753	90314756	+	1	NA	intron (NM_001128086, intron 11 of 24)	L1ME2z|LINE|L1	-260973	NM_001177397	77531	Mm.440605	NM_181398	ENSMUSG00000058589	Anks1b	AIDA-1b|C030032C09Rik|E530015N03Rik|ENSMUSG00000078431|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding
mm_116314.1	chr13	37103970	37104001	-	1	NA	Intergenic	Intergenic	-53741	NM_001166391	74145	Mm.235105	NM_028784	ENSMUSG00000039109	F13a1	1200014I03Rik|AI462306|F13a	coagulation factor XIII, A1 subunit	protein-coding
mm_22611.1	chr3	14533818	14533866	+	1	NA	promoter-TSS (NM_028915)	promoter-TSS (NM_028915)	54	NM_028915	71710	Mm.257449	NM_028915	ENSMUSG00000027550	Lrrcc1	1200008A14Rik|4932441F23Rik|AI195358|AI447421	leucine rich repeat and coiled-coil domain containing 1	protein-coding
mm_102887.1	chr11	69411697	69411721	-	1	NA	intron (NM_001017426, intron 1 of 22)	CpG	1966	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_128605.1	chr15	58352729	58352749	-	1	NA	exon (NM_027211, exon 4 of 9)	exon (NM_027211, exon 4 of 9)	-28570	NM_177755	268807	Mm.124498	NM_177755	ENSMUSG00000022357	Klhl38	8230402K04Rik	kelch-like 38	protein-coding
mm_15716.1	chr2	164047346	164047401	+	1	NA	intron (NM_001114079, intron 11 of 13)	intron (NM_001114079, intron 11 of 13)	22149	NM_001114079	381404	Mm.82301	NM_001114079	ENSMUSG00000054582	Pabpc1l	1810053B01Rik|Epab	poly(A) binding protein, cytoplasmic 1-like	protein-coding
mm_48656.1	chr5	145873502	145873532	-	1	NA	exon (NM_007818, exon 4 of 13)	exon (NM_007818, exon 4 of 13)	6337	NM_007818	13112	Mm.332844	NM_007818	ENSMUSG00000056035	Cyp3a11	AI256190|Cyp3a|IIIAm1|Pcn	cytochrome P450, family 3, subfamily a, polypeptide 11	protein-coding
mm_148148.1	chr18	77498197	77498209	-	1	NA	intron (NM_001164504, intron 1 of 7)	intron (NM_001164504, intron 1 of 7)	66933	NM_001164504	225743	Mm.23293	NM_001164504	ENSMUSG00000025427	Rnf165	2900024M11Rik|AI427432|Akd2|Ark2c|G630064H08Rik|Gm96	ring finger protein 165	protein-coding
mm_142785.1	chr17	50157400	50157407	-	1	NA	intron (NM_181397, intron 2 of 9)	intron (NM_181397, intron 2 of 9)	33094	NM_181397	76438	Mm.41854	NM_181397	ENSMUSG00000039316	Rftn1	2310015N21Rik|AI853526	raftlin lipid raft linker 1	protein-coding
mm_95816.1	chr11	55137024	55137033	+	1	NA	intron (NM_172258, intron 6 of 10)	intron (NM_172258, intron 6 of 10)	14678	NM_172258	215332	Mm.87054	NM_172258	ENSMUSG00000049491	Slc36a3	PAT3|TRAMD2|tramdorin2	solute carrier family 36 (proton/amino acid symporter), member 3	protein-coding
mm_73849.1	chr8	117701821	117701850	+	1	NA	promoter-TSS (NM_008290)	promoter-TSS (NM_008290)	-111	NM_008290	15486	Mm.276466	NM_008290	ENSMUSG00000031844	Hsd17b2	AI194836|AI194967|AI255511	hydroxysteroid (17-beta) dehydrogenase 2	protein-coding
mm_37470.1	chr4	123564626	123564632	-	1	NA	intron (NM_001199136, intron 1 of 97)	intron (NM_001199136, intron 1 of 97)	-51791	NR_105824	102465214		NR_105824	ENSMUSG00000099005	Mir6398	Gm27657|mmu-mir-6398	microRNA 6398	ncRNA
mm_98548.1	chr11	95010473	95010483	+	1	NA	5' UTR (NM_146025, exon 1 of 10)	5' UTR (NM_146025, exon 1 of 10)	599	NM_146025	217125	Mm.297199	NM_146025	ENSMUSG00000047181	Samd14	AI839049|AI854782|BC034054	sterile alpha motif domain containing 14	protein-coding
mm_69603.1	chr7	137125701	137125712	-	1	NA	intron (NM_008598, intron 4 of 4)	intron (NM_008598, intron 4 of 4)	-108977	NR_045885	100038555	Mm.444788	NR_045885	ENSMUSG00000109722	Gm10578	ENSMUSG00000073800	predicted gene 10578	ncRNA
mm_163211.1	chr11	99772915	99772916	-	1	NA	promoter-TSS (NM_001126322)	promoter-TSS (NM_001126322)	-2	NM_001126322	100040276	Mm.475095	NM_001126322	ENSMUSG00000078668	Gm11595	OTTMUSG00000002543	predicted gene 11595	protein-coding
mm_48058.1	chr5	136566091	136566107	-	1	NA	promoter-TSS (NM_001291240)	promoter-TSS (NM_001291240)	-118	NM_001291233	13047	Mm.320317	NM_009986	ENSMUSG00000029705	Cux1	CDP|Cutl1|Cux|Cux-1	cut-like homeobox 1	protein-coding
mm_6398.1	chr1	72861497	72861519	-	1	NA	3' UTR (NM_010518, exon 4 of 4)	3' UTR (NM_010518, exon 4 of 4)	13357	NM_010518	16011	Mm.405761	NM_010518	ENSMUSG00000026185	Igfbp5	AI256729|AW208790|IGFBP-5|IGFBP-5P	insulin-like growth factor binding protein 5	protein-coding
mm_74695.1	chr8	15046048	15046091	-	1	NA	promoter-TSS (NR_037972)	promoter-TSS (NR_037972)	9	NR_037972	434285	Mm.334425	NM_001007591	ENSMUSG00000049008	BB014433	-	expressed sequence BB014433	ncRNA
mm_128468.1	chr15	50821720	50821730	-	1	NA	intron (NM_001310485, intron 5 of 7)	intron (NM_001310485, intron 5 of 7)	67324	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_3735.1	chr1	155117069	155117071	+	1	NA	Intergenic	MIR3|SINE|MIR	-17434	NM_010500	15939	Mm.12246	NM_010500	ENSMUSG00000056708	Ier5	-	immediate early response 5	protein-coding
mm_34109.1	chr4	139193235	139193252	+	1	NA	promoter-TSS (NM_001271405)	promoter-TSS (NM_001271405)	344	NM_001037761	12345	Mm.2945	NM_009798	ENSMUSG00000028745	Capzb	1700120C01Rik|AI325129|CPB1|CPB2|CPbeat2|CPbeta1|CPbeta2|Cappb1	capping protein (actin filament) muscle Z-line, beta	protein-coding
mm_48178.1	chr5	137314176	137314212	-	1	NA	promoter-TSS (NM_011639)	promoter-TSS (NM_011639)	47	NM_011639	22051	Mm.27063	NM_011639	ENSMUSG00000023348	Trip6	-	thyroid hormone receptor interactor 6	protein-coding
mm_35363.1	chr4	32406081	32406083	-	1	NA	Intergenic	Intergenic	-11353	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_130315.1	chr15	97247243	97247257	-	1	NA	promoter-TSS (NM_001164602)	promoter-TSS (NM_001164602)	37	NM_001164563	105827	Mm.24005	NM_178114	ENSMUSG00000048218	Amigo2	AI415330|AMIGO-2|AW208913|Ali1	adhesion molecule with Ig like domain 2	protein-coding
mm_97456.1	chr11	78194807	78194821	+	1	NA	intron (NM_001045516, intron 1 of 3)	intron (NM_001045516, intron 1 of 3)	1422	NM_001045516	216974	Mm.50974	NM_001045516	ENSMUSG00000044122	Proca1	4933404M19Rik	protein interacting with cyclin A1	protein-coding
mm_171066.1	chr3	112840368	112840377	-	1	NA	Intergenic	L1Md_T|LINE|L1	316355	NM_001190404	545562	Mm.462977	NM_001190403		Amy2b	Amy-X|Amy2-2|OTTMUSG00000022462|mAmy2-1	amylase 2b	protein-coding
mm_101507.1	chr11	32205688	32205692	-	1	NA	intron (NM_030093, intron 1 of 4)	intron (NM_030093, intron 1 of 4)	275	NM_030093	78372	Mm.29952	NM_030093	ENSMUSG00000040767	Snrnp25	3300001G02Rik|AL033324|C16ORF33	small nuclear ribonucleoprotein 25 (U11/U12)	protein-coding
mm_45703.1	chr5	83354980	83355060	-	1	NA	5' UTR (NM_153801, exon 1 of 12)	5' UTR (NM_153801, exon 1 of 12)	175	NM_153801	243078	Mm.126783	NM_153801	ENSMUSG00000049537	Tecrl	D330017N19Rik|Srd5a2l2	trans-2,3-enoyl-CoA reductase-like	protein-coding
mm_2203.1	chr1	89580205	89580215	+	1	NA	intron (NM_001037136, intron 1 of 16)	intron (NM_001037136, intron 1 of 16)	103682	NR_015540	74403	Mm.444291	NR_015540		4933400F21Rik	1700091C04Rik|4930565K10Rik	RIKEN cDNA 4933400F21 gene	ncRNA
mm_22721.1	chr3	19508607	19508641	+	1	NA	promoter-TSS (NM_001163536)	promoter-TSS (NM_001163536)	29	NM_025489	66326	Mm.45615	NM_025489	ENSMUSG00000027606	Dnajc5b	1700008A05Rik	DnaJ heat shock protein family (Hsp40) member C5 beta	protein-coding
mm_26752.1	chr3	7613772	7613785	-	1	NA	promoter-TSS (NM_001313889)	promoter-TSS (NM_001313889)	-18	NM_001313888	16196	Mm.3825	NM_008371	ENSMUSG00000040329	Il7	A630026I06Rik|Il-7|hlb368	interleukin 7	protein-coding
mm_81285.1	chr9	108306311	108306315	+	1	NA	promoter-TSS (NM_133986)	promoter-TSS (NM_133986)	153	NM_016802	11848	Mm.757	NM_016802	ENSMUSG00000007815	Rhoa	Arha|Arha1|Arha2	ras homolog family member A	protein-coding
mm_172319.1	chr7	106215374	106215374	-	1	NA	promoter-TSS (NM_001243039).2	promoter-TSS (NM_001243039).2	-34	NM_029000	74558	Mm.458429	NM_029000	ENSMUSG00000045868	Gvin1	9130002C22Rik|9830104F22Rik|Iigs1|VLIG|VLIG-1	GTPase, very large interferon inducible 1	protein-coding
mm_50986.1	chr6	63255893	63255903	+	1	NA	promoter-TSS (NM_008167)	promoter-TSS (NM_008167)	-959	NM_008167	14804	Mm.439651	NM_008167	ENSMUSG00000071424	Grid2	B230104L07Rik|GluD2|GluRdelta2|Lc|Lc<J>|MMS10-AC|Ms10ac|cpr|ho|nmf408|tpr	glutamate receptor, ionotropic, delta 2	protein-coding
mm_136504.1	chr16	96702789	96702794	-	1	NA	intron (NM_031174, intron 15 of 32)	intron (NM_031174, intron 15 of 32)	235185	NM_008791	18546	Mm.5023	NM_008791	ENSMUSG00000090223	Pcp4	P16Rimb19|Pcp-4|Pep19	Purkinje cell protein 4	protein-coding
mm_4574.1	chr1	177740920	177740996	+	1	NA	intron (NM_027077, intron 2 of 5)	intron (NM_027077, intron 2 of 5)	11144	NM_027077	69428	Mm.84467	NM_027077	ENSMUSG00000015962	1700016C15Rik	-	RIKEN cDNA 1700016C15 gene	protein-coding
mm_155215.1	chrX	56787875	56787883	+	1	NA	intron (NM_001287800, intron 1 of 5)	intron (NM_001287800, intron 1 of 5)	1352	NM_001287800	14199	Mm.3126	NM_010211	ENSMUSG00000023092	Fhl1	FHL-1|KyoT|RAM14-1|SLIM|SLIM-1	four and a half LIM domains 1	protein-coding
mm_121309.1	chr14	106106184	106106205	+	1	NA	promoter-TSS (NM_198601)	promoter-TSS (NM_198601)	-4	NM_198601	212085	Mm.78128	NM_198601	ENSMUSG00000022113	Trim52	4921513B05Rik	tripartite motif-containing 52	protein-coding
mm_88467.1	chr10	77581731	77581741	+	1	NA	promoter-TSS (NM_145925)	promoter-TSS (NM_145925)	-31	NM_145925	108705	Mm.28853	NM_145925	ENSMUSG00000009291	Pttg1ip	1810010L20Rik|AI314311|AU018448|C79540	pituitary tumor-transforming 1 interacting protein	protein-coding
mm_38971.1	chr4	150902225	150902246	-	1	NA	intron (NM_020569, intron 5 of 6)	intron (NM_020569, intron 5 of 6)	7686	NM_020569	57320	Mm.277349	NM_020569	ENSMUSG00000028964	Park7	DJ-1|Dj1	Parkinson disease (autosomal recessive, early onset) 7	protein-coding
mm_69648.1	chr7	139234581	139234602	-	1	NA	intron (NM_027164, intron 8 of 10)	intron (NM_027164, intron 8 of 10)	-13891	NM_001033206	101631	Mm.334300	NM_001033206	ENSMUSG00000060260	Pwwp2b	AI594893|D7Ertd517e|D930023J19Rik|Pwwp2	PWWP domain containing 2B	protein-coding
mm_145143.1	chr18	45559807	45559816	+	1	NA	promoter-TSS (NM_080465)	promoter-TSS (NM_080465)	-343	NM_080465	140492	Mm.411614	NM_080465	ENSMUSG00000054477	Kcnn2	KCa2.2|SK2|SKCA2|bc|fri	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2	protein-coding
mm_159042.1	chr1	180944104	180944104	+	1	NA	intron (NM_144794, intron 1 of 22)	intron (NM_144794, intron 1 of 22)	1586	NM_144794	208795	Mm.185518	NM_144794	ENSMUSG00000026519	Tmem63a	BC014795|Tmem64a	transmembrane protein 63a	protein-coding
mm_98790.1	chr11	96929410	96929421	+	1	NA	promoter-TSS (NM_146026)	promoter-TSS (NM_146026)	91	NM_146026	217138	Mm.342551	NM_146026	ENSMUSG00000047040	Prr15l	Atad4|BC022765|E230006A12Rik	proline rich 15-like	protein-coding
mm_120880.1	chr14	75315964	75315968	+	1	NA	exon (NM_026083, exon 8 of 19)	exon (NM_026083, exon 8 of 19)	31593	NM_026083	67302	Mm.74704	NM_026083	ENSMUSG00000022000	Zc3h13	2600010B19Rik|3110050K21Rik|4930570G11Rik|C87618	zinc finger CCCH type containing 13	protein-coding
mm_21288.1	chr2	156970554	156970573	-	1	NA	intron (NM_013865, intron 1 of 15)	MLT1F2|LTR|ERVL-MaLR	21548	NM_013865	29812	Mm.279256	NM_013865	ENSMUSG00000027634	Ndrg3	4833415O14Rik|AI747193|Ndr3	N-myc downstream regulated gene 3	protein-coding
mm_73528.1	chr8	108585048	108585051	+	1	NA	promoter-TSS (NR_077224)	promoter-TSS (NR_077224)	-372	NR_077224	109215	Mm.65282	NR_077224	ENSMUSG00000110613	Lncbate1	3010033K07Rik|Lnc-BATE1	brown adipose tissue enriched long non-coding RNA 1	ncRNA
mm_15064.1	chr2	153014586	153014627	+	1	NA	intron (NM_178939, intron 1 of 4)	intron (NM_178939, intron 1 of 4)	777	NM_178939	68559	Mm.12746	NM_178939	ENSMUSG00000027472	Pdrg1	1110004D19Rik|AU020945|AV006589|Pdrg	p53 and DNA damage regulated 1	protein-coding
mm_57152.1	chr6	122730005	122730048	-	1	NA	exon (NM_011401, exon 10 of 10)	exon (NM_011401, exon 10 of 10)	12719	NM_011401	20527	Mm.395108	NM_011401	ENSMUSG00000003153	Slc2a3	AA408729|AL023014|AL024341|AU040424|C78366|Glut-3|Glut3	solute carrier family 2 (facilitated glucose transporter), member 3	protein-coding
mm_64100.1	chr7	141009702	141009772	+	1	NA	exon (NM_025378, exon 2 of 2)	exon (NM_025378, exon 2 of 2)	1007	NM_025378	66141	Mm.141021	NM_025378	ENSMUSG00000025492	Ifitm3	1110004C05Rik|Cd225|Cdw217|DSPA2b|Fgls|IP15|mil-1	interferon induced transmembrane protein 3	protein-coding
mm_20177.1	chr2	122562349	122562357	-	1	NA	Intergenic	Intergenic	48924	NM_025961	67092	Mm.29975	NM_025961	ENSMUSG00000027199	Gatm	1810003P21Rik|AI314789|AT	glycine amidinotransferase (L-arginine:glycine amidinotransferase)	protein-coding
mm_125542.1	chr15	58245824	58245841	+	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	-30940	NM_026346	67731	Mm.25683	NM_026346	ENSMUSG00000022358	Fbxo32	4833442G10Rik|AI430017|ATROGIN1|Gm20361|MAFbx	F-box protein 32	protein-coding
mm_157305.1	chrX	20929856	20929870	-	1	NA	intron (NM_008823, intron 2 of 8)	intron (NM_008823, intron 2 of 8)	1692	NM_008823	18636	Mm.3064	NM_008823	ENSMUSG00000001128	Cfp	BCFG|Pfc	complement factor properdin	protein-coding
mm_16369.1	chr2	177460195	177460196	+	1	NA	Intergenic	RLTR45-int|LTR|ERVK	-4547	NM_001177568	628308	Mm.460436	NM_001177568	ENSMUSG00000078866	Zfp970	Gm14420|OTTMUSG00000016588	zinc finger protein 970	protein-coding
mm_81077.1	chr9	106223663	106223723	+	1	NA	exon (NM_031178, exon 2 of 2)	exon (NM_031178, exon 2 of 2)	1095	NM_031178	81897	Mm.44889	NM_031178	ENSMUSG00000045322	Tlr9	-	toll-like receptor 9	protein-coding
mm_12337.1	chr2	69670161	69670167	+	1	NA	promoter-TSS (NM_001081087)	promoter-TSS (NM_001081087)	44	NM_001081087	228003	Mm.178784	NM_001081087	ENSMUSG00000075307	Klhl41	Gm112|Kbtbd10|SARCOSIN	kelch-like 41	protein-coding
mm_1285.1	chr1	64121851	64121866	+	1	NA	promoter-TSS (NM_033563)	promoter-TSS (NM_033563)	-469	NM_033563	93691	Mm.29466	NM_033563	ENSMUSG00000025959	Klf7	9830124P08Rik	Kruppel-like factor 7 (ubiquitous)	protein-coding
mm_29481.1	chr3	115712856	115712867	-	1	NA	exon (NM_007901, exon 2 of 2)	exon (NM_007901, exon 2 of 2)	2194	NM_007901	13609	Mm.982	NM_007901	ENSMUSG00000045092	S1pr1	AI849002|Edg1|Lpb1|S1p|S1p1	sphingosine-1-phosphate receptor 1	protein-coding
mm_10506.1	chr2	16356036	16356053	+	1	NA	promoter-TSS (NM_026162)	promoter-TSS (NM_026162)	-260	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding
mm_6539.1	chr1	74951663	74951678	-	1	NA	promoter-TSS (NM_010544)	promoter-TSS (NM_010544)	2	NM_001313683	16147	Mm.439736	NM_010544	ENSMUSG00000006538	Ihh	HHG-2	Indian hedgehog	protein-coding
mm_117553.1	chr13	84340185	84340188	-	1	NA	Intergenic	Intergenic	117890	NM_175187	72745	Mm.295063	NM_175187	ENSMUSG00000035762	Tmem161b	2810446P07Rik|AI843389	transmembrane protein 161B	protein-coding
mm_75262.1	chr8	40598015	40598026	-	1	NA	intron (NM_001040699, intron 3 of 13)	intron (NM_001040699, intron 3 of 13)	36772	NM_001040699	54384	Mm.294871	NM_019433	ENSMUSG00000039431	Mtmr7	-	myotubularin related protein 7	protein-coding
mm_95572.1	chr11	52396586	52396601	+	1	NA	exon (NM_153117, exon 1 of 3)	exon (NM_153117, exon 1 of 3)	165	NM_153117	213673	Mm.291979	NM_153117	ENSMUSG00000036275	9530068E07Rik	C85061|Kct2	RIKEN cDNA 9530068E07 gene	protein-coding
mm_23996.1	chr3	86539885	86539907	+	1	NA	intron (NM_001077687, intron 38 of 50)	intron (NM_001077687, intron 38 of 50)	8387	NM_011839	23937	Mm.389466	NM_011839	ENSMUSG00000057777	Mab21l2	-	mab-21-like 2 (C. elegans)	protein-coding
mm_60574.1	chr7	44481615	44481641	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-2889	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_3361.1	chr1	138175692	138175700	+	1	NA	promoter-TSS (NM_001268286)	promoter-TSS (NM_001268286)	-391	NM_001268286	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_173311.1	chrY	90734929	90734938	+	1	NA	Intergenic	IMPB_01|Satellite|Satellite	20117	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_50370.1	chr6	48676194	48676209	+	1	NA	promoter-TSS (NM_174960)	promoter-TSS (NM_174960)	66	NM_174960	317758	Mm.116971	NM_174960	ENSMUSG00000051124	Gimap9	A630002K24|BB145400	GTPase, IMAP family member 9	protein-coding
mm_21952.1	chr2	167101577	167101578	-	1	NA	3' UTR (NM_008420, exon 2 of 2)	3' UTR (NM_008420, exon 2 of 2)	36284	NR_028540	100217443		NR_028540		Snord12	MBII-99	small nucleolar RNA, C/D box 12	snoRNA
mm_49885.1	chr6	38663279	38663296	+	1	NA	exon (NM_001101507, exon 1 of 5)	exon (NM_001101507, exon 1 of 5)	218	NM_001101507	665180	Mm.349066	NM_001101507	ENSMUSG00000079598	Clec2l	AI414054|AW122724|Gm1064	C-type lectin domain family 2, member L	protein-coding
mm_6090.1	chr1	63178859	63178896	-	1	NA	promoter-TSS (NR_028558)	promoter-TSS (NR_028558)	-146	NR_028558	100217464	Mm.484706	NR_028558	ENSMUSG00000064602	Snora41	MBI-83	small nucleolar RNA, H/ACA box 41	snoRNA
mm_79138.1	chr9	47643573	47643576	+	1	NA	intron (NM_001025600, intron 1 of 8)	intron (NM_001025600, intron 1 of 8)	113222	NM_018770	54725	Mm.234832	NM_018770	ENSMUSG00000032076	Cadm1	2900073G06Rik|3100001I08Rik|AI987920|Bl2|Igsf4|Igsf4a|Necl2|RA175|RA175A|RA175B|RA175C|RA175N|ST17|SgIGSF|SynCam|Tslc1	cell adhesion molecule 1	protein-coding
mm_49088.1	chr6	6955994	6956049	+	1	NA	promoter-TSS (NM_001077713)	promoter-TSS (NM_001077713)	3	NM_001077713	71238	Mm.389086	NM_001077713	ENSMUSG00000042505	Sdhaf3	0610005M07Rik|4933430A16Rik|Acn9	succinate dehydrogenase complex assembly factor 3	protein-coding
mm_22191.1	chr2	173276198	173276208	-	1	NA	5' UTR (NM_022995, exon 1 of 4)	5' UTR (NM_022995, exon 1 of 4)	330	NM_022995	65112	Mm.73682	NM_022995	ENSMUSG00000038400	Pmepa1	2210418I02Rik|AW455466|Erg1.2|N4wbp4|Stag1|Tmepai	prostate transmembrane protein, androgen induced 1	protein-coding
mm_115148.1	chr13	105082118	105082127	+	1	NA	promoter-TSS (NM_025751)	promoter-TSS (NM_025751)	0	NM_025751	66763	Mm.109093	NM_025751	ENSMUSG00000021718	4933425L06Rik	-	RIKEN cDNA 4933425L06 gene	protein-coding
mm_144836.1	chr18	36529224	36529241	+	1	NA	exon (NM_001271545, exon 3 of 21)	exon (NM_001271545, exon 3 of 21)	1080	NM_001271544	240215	Mm.135463	NM_172830	ENSMUSG00000024485	Slc4a9	AE4|D630003B07|D630024F24Rik	solute carrier family 4, sodium bicarbonate cotransporter, member 9	protein-coding
mm_116069.1	chr13	27640762	27640779	-	1	NA	exon (NM_001164058, exon 2 of 7)	exon (NM_001164058, exon 2 of 7)	1723	NM_001164058	19113	Mm.196424	NM_008930	ENSMUSG00000006488	Prl7a1	AA407021|AA409971|AA410116|PLP-E|PLP-G|Prlpe|Prlpg	prolactin family 7, subfamily a, member 1	protein-coding
mm_18536.1	chr2	64097995	64098023	-	1	NA	promoter-TSS (NM_021716)	promoter-TSS (NM_021716)	29	NM_001267846	60344	Mm.130769	NM_021716	ENSMUSG00000075324	Fign	fi|fidget	fidgetin	protein-coding
mm_145450.1	chr18	60213145	60213167	+	1	NA	intron (NM_001033767, intron 2 of 2)	Lx8|LINE|L1	1079	NM_001033767	240327	Mm.357104	NM_001033767	ENSMUSG00000073555	Gm4951	EG240327|Ifgga2	predicted gene 4951	protein-coding
mm_111053.1	chr12	80109913	80109955	-	1	NA	exon (NM_007564, exon 2 of 2)	exon (NM_007564, exon 2 of 2)	3079	NM_007564	12192	Mm.235132	NM_007564	ENSMUSG00000021127	Zfp36l1	AW742437|AW743212|Berg36|Brf1|D530020L18Rik|ERF1|TIS11b|cMG1	zinc finger protein 36, C3H type-like 1	protein-coding
mm_63799.1	chr7	132931229	132931246	+	1	NA	Intergenic	CpG	-18385	NM_207302	360216	Mm.389984	NM_207302	ENSMUSG00000030967	Zranb1	9330160G10Rik|D7Wsu87e|Gm1956|Trabid	zinc finger, RAN-binding domain containing 1	protein-coding
mm_114515.1	chr13	72702846	72702853	+	1	NA	Intergenic	Intergenic	74052	NM_010574	16372	Mm.28888	NM_010574	ENSMUSG00000001504	Irx2	-	Iroquois related homeobox 2 (Drosophila)	protein-coding
mm_61654.1	chr7	80472450	80472464	+	1	NA	intron (NM_001042527, intron 15 of 21)	PB1D7|SINE|Alu	62541	NM_007550	12144	Mm.12932	NM_007550	ENSMUSG00000030528	Blm	-	Bloom syndrome, RecQ helicase-like	protein-coding
mm_24523.1	chr3	92992214	92992221	+	1	NA	promoter-TSS (NM_001018079)	promoter-TSS (NM_001018079)	-9	NM_001018079	69520	Mm.439968	NM_001018079	ENSMUSG00000068885	Lce3f	2310002A05Rik	late cornified envelope 3F	protein-coding
mm_39284.1	chr5	3957737	3957754	+	1	NA	exon (NM_194462, exon 6 of 48)	exon (NM_194462, exon 6 of 48)	29559	NM_194462	100986	Mm.46044	NM_194462	ENSMUSG00000040407	Akap9	5730481H23Rik|AKAP-9|AKAP450|AW545847|C79026|G1-448-15|PRKA9|mKIAA0803|mei2-5|repro12	A kinase (PRKA) anchor protein (yotiao) 9	protein-coding
mm_103679.1	chr11	79250973	79250992	-	1	NA	exon (NM_019653, exon 2 of 9)	exon (NM_019653, exon 2 of 9)	3713	NM_019653	78889	Mm.307022	NM_019653	ENSMUSG00000017677	Wsb1	1110056B13Rik|2700038M07Rik	WD repeat and SOCS box-containing 1	protein-coding
mm_135595.1	chr16	50723383	50723397	-	1	NA	Intergenic	ERV3-16A3_I-int|LTR|ERVL	-3742	NR_105782	102466634		NR_105782	ENSMUSG00000098482	Mir6363	Gm28026|mmu-mir-6363	microRNA 6363	ncRNA
mm_52394.1	chr6	113301621	113301629	+	1	NA	intron (NM_170673, intron 17 of 19)	intron (NM_170673, intron 17 of 19)	-5512	NM_030178	78783	Mm.356059	NM_030178	ENSMUSG00000001632	Brpf1	4833438B11Rik|4930540D11Rik|Brpf2	bromodomain and PHD finger containing, 1	protein-coding
mm_80145.1	chr9	70852546	70852574	+	1	NA	intron (NM_001324473, intron 1 of 8)	intron (NM_001324473, intron 1 of 8)	82248	NM_008280	15450	Mm.390187	NM_008280	ENSMUSG00000032207	Lipc	AI256194|HL|Hpl	lipase, hepatic	protein-coding
mm_60159.1	chr7	39552475	39552512	+	1	NA	Intergenic	CpG	34727	NM_001004139	70227	Mm.333800	NM_001004139	ENSMUSG00000068959	Zfp619	3000002G13Rik	zinc finger protein 619	protein-coding
mm_79767.1	chr9	62825571	62825581	+	1	NA	Intergenic	RMER17C|LTR|ERVK	-13211	NM_001033175	76524	Mm.283636	NM_001033175	ENSMUSG00000032245	Cln6	1810065L06Rik|AW743417|D9Bwg1455e|nclf	ceroid-lipofuscinosis, neuronal 6	protein-coding
mm_132593.1	chr16	38452885	38452911	+	1	NA	promoter-TSS (NM_007414)	promoter-TSS (NM_007414)	-209	NM_007414	11544	Mm.20047	NM_007414	ENSMUSG00000002844	Adprh	Arh1	ADP-ribosylarginine hydrolase	protein-coding
mm_18159.1	chr2	45096783	45096798	-	1	NA	intron (NM_001289521, intron 1 of 8)	intron (NM_001289521, intron 1 of 8)	13487	NM_001289521	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_83558.1	chr9	46242865	46242871	-	1	NA	exon (NM_007468, exon 3 of 3)	exon (NM_007468, exon 3 of 3)	2024	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_12308.1	chr2	69113583	69113603	+	1	NA	3' UTR (NM_001347161, exon 11 of 11)	3' UTR (NM_001347161, exon 11 of 11)	-22207	NM_181547	329416	Mm.90047	NM_181547	ENSMUSG00000034738	Nostrin	Daip2|mDaIP2	nitric oxide synthase trafficker	protein-coding
mm_145973.1	chr18	67933998	67934017	+	1	NA	intron (NM_172631, intron 1 of 5)	CpG	750	NM_172631	52662	Mm.440183	NM_172631	ENSMUSG00000024544	Ldlrad4	8230401C20Rik|A430083H02|A430108L08Rik|C18orf1|D18Ertd653e|D330030L18Rik	low density lipoprotein receptor class A domain containing 4	protein-coding
mm_3737.1	chr1	155145851	155145855	+	1	NA	intron (NM_008209, intron 1 of 5)	intron (NM_008209, intron 1 of 5)	927	NM_008209	15064	Mm.7580	NM_008209	ENSMUSG00000026471	Mr1	H2ls	major histocompatibility complex, class I-related	protein-coding
mm_113825.1	chr13	47000106	47000131	+	1	NA	Intergenic	MTEa|LTR|ERVL-MaLR	14732	NM_175340	105193	Mm.25593	NM_175340	ENSMUSG00000044231	Nhlrc1	AI505271|B230309E09Rik|EPM2B	NHL repeat containing 1	protein-coding
mm_87956.1	chr10	63243761	63243771	+	1	NA	promoter-TSS (NM_026101)	promoter-TSS (NM_026101)	-31	NM_030114	67345	Mm.234437	NM_026101	ENSMUSG00000020064	Herc4	1700056O17Rik|4921531D01Rik|9530080M15Rik|mKIAA1593	hect domain and RLD 4	protein-coding
mm_85104.1	chr9	94702354	94702376	-	1	NA	intron (NM_177909, intron 2 of 15)	intron (NM_177909, intron 2 of 15)	32473	NM_177909	331004	Mm.326125	NM_177909	ENSMUSG00000031129	Slc9a9	5730527A11Rik|9930105B05|AI854429|Nhe9	solute carrier family 9 (sodium/hydrogen exchanger), member 9	protein-coding
mm_30800.1	chr4	20008462	20008472	+	1	NA	exon (NM_015767, exon 1 of 5)	exon (NM_015767, exon 1 of 5)	138	NM_015767	50500	Mm.24375	NM_015767	ENSMUSG00000073988	Ttpa	alpha-TTP	tocopherol (alpha) transfer protein	protein-coding
mm_102125.1	chr11	53351995	53352006	-	1	NA	intron (NM_033565, intron 1 of 20)	intron (NM_033565, intron 1 of 20)	1233	NM_033565	93736	Mm.395281	NM_033565	ENSMUSG00000049470	Aff4	AF5Q31|Alf4|Laf4l|MCEF	AF4/FMR2 family, member 4	protein-coding
mm_16654.1	chr2	6546067	6546077	-	1	NA	3' UTR (NM_010160, exon 12 of 12)	3' UTR (NM_010160, exon 12 of 12)	175590	NM_001310447	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_96907.1	chr11	70458979	70458989	+	1	NA	promoter-TSS (NM_001029929)	promoter-TSS (NM_001029929)	-638	NM_001029929	574428	Mm.472771	NM_001029929	ENSMUSG00000040829	Zmynd15	-	zinc finger, MYND-type containing 15	protein-coding
mm_52113.1	chr6	97904704	97904715	+	1	NA	intron (NM_001113198, intron 1 of 9)	intron (NM_001113198, intron 1 of 9)	-25108	NM_001178049	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_150316.1	chr19	34573590	34573623	+	1	NA	exon (NM_008332, exon 3 of 3)	exon (NM_008332, exon 3 of 3)	-9923	NM_010501	15959	Mm.426079	NM_010501	ENSMUSG00000074896	Ifit3	Ifi49|P49	interferon-induced protein with tetratricopeptide repeats 3	protein-coding
mm_119224.1	chr14	33250378	33250411	+	1	NA	intron (NM_153800, intron 2 of 10)	intron (NM_153800, intron 2 of 10)	33571	NM_153800	239027	Mm.318350	NM_153800	ENSMUSG00000063506	Arhgap22	B230341L19Rik|RHOGAP2|p68RacGAP	Rho GTPase activating protein 22	protein-coding
mm_101113.1	chr11	11957049	11957086	-	1	NA	intron (NM_010345, intron 4 of 16)	Tigger7|DNA|TcMar-Tigger	-58923	NM_001190448	13195	Mm.12906	NM_016672	ENSMUSG00000020182	Ddc	Aadc	dopa decarboxylase	protein-coding
mm_38320.1	chr4	137329090	137329127	-	1	NA	exon (NM_001243769, exon 4 of 6)	exon (NM_001243769, exon 4 of 6)	28651	NM_009861	12540	Mm.1022	NM_009861	ENSMUSG00000006699	Cdc42	AI747189|AU018915	cell division cycle 42	protein-coding
mm_9130.1	chr1	170761840	170761840	-	1	NA	intron (NM_001081304, intron 14 of 15)	L1M2|LINE|L1	105931	NM_001081304	226641	Mm.377046	NM_001081304	ENSMUSG00000026663	Atf6	9130025P16Rik|9630036G24|AA789574|Atf6alpha|ESTM49	activating transcription factor 6	protein-coding
mm_61631.1	chr7	80246448	80246456	+	1	NA	promoter-TSS (NM_177765)	promoter-TSS (NM_177765)	76	NM_177765	269954	Mm.276780	NM_177765	ENSMUSG00000045467	Ttll13	1700111A04Rik|4921538O11|BC024578	tubulin tyrosine ligase-like family, member 13	protein-coding
mm_70163.1	chr7	143592466	143592474	-	1	NA	exon (NM_013742, exon 2 of 23)	exon (NM_013742, exon 2 of 23)	7620	NM_001252593	27267	Mm.125659	NM_013742	ENSMUSG00000010755	Cars	CA3	cysteinyl-tRNA synthetase	protein-coding
mm_39362.1	chr5	9118579	9118595	+	1	NA	TTS (NM_001110327)	TTS (NM_001110327)	17850	NM_001081029	652925	Mm.439954	NM_001081029	ENSMUSG00000079659	Tmem243	4930420K17Rik|E030031F02Rik	transmembrane protein 243, mitochondrial	protein-coding
mm_117759.1	chr13	96081364	96081376	-	1	NA	intron (NM_029210, intron 2 of 12)	intron (NM_029210, intron 2 of 12)	51207	NM_029210	75209	Mm.40436	NM_029210	ENSMUSG00000051111	Sv2c	4930527L09Rik|AI841971	synaptic vesicle glycoprotein 2c	protein-coding
mm_169597.1	chr1	53328870	53328880	-	1	NA	Intergenic	BGLII|LTR|ERVK	15251	NR_104360	72085	Mm.482256	NM_028091	ENSMUSG00000026096	Osgepl1	2610001M19Rik|AA416452	O-sialoglycoprotein endopeptidase-like 1	protein-coding
mm_21801.1	chr2	164911259	164911299	-	1	NA	intron (NM_199027, intron 1 of 27)	CpG	471	NM_199027	329559	Mm.330776	NM_199027	ENSMUSG00000039834	Zfp335	1810045J01Rik|NIF-1|Nif1|Znf335	zinc finger protein 335	protein-coding
mm_135397.1	chr16	44558778	44558799	-	1	NA	promoter-TSS (NR_037242)	promoter-TSS (NR_037242)	82	NM_172506	117606	Mm.41561	NM_172506	ENSMUSG00000022687	Boc	4732455C11|mFLJ00376	biregional cell adhesion molecule-related/down-regulated by oncogenes (Cdon) binding protein	protein-coding
mm_169838.1	chr16	26866740	26866744	-	1	NA	Intergenic	L1Md_T|LINE|L1	101503	NM_001285916	239789	Mm.326909	NM_001013761	ENSMUSG00000068428	Gmnc	Gemc1|Gm1778|Gm606	geminin coiled-coil domain containing	protein-coding
mm_8579.1	chr1	155812891	155812906	-	1	NA	promoter-TSS (NM_023268)	promoter-TSS (NM_023268)	1	NM_023268	104009	Mm.27035	NM_023268	ENSMUSG00000033684	Qsox1	1300003H02Rik|QSOX|Qscn6|SOx	quiescin Q6 sulfhydryl oxidase 1	protein-coding
mm_28659.1	chr3	95241131	95241146	-	1	NA	promoter-TSS (NM_001024841)	promoter-TSS (NM_001024841)	-29	NM_001024841	229588	Mm.387177	NM_001024841	ENSMUSG00000068860	Gm128	Ment|pmis1	predicted gene 128	protein-coding
mm_100632.1	chr11	121717096	121717132	+	1	NA	3' UTR (NM_144797, exon 4 of 4)	3' UTR (NM_144797, exon 4 of 4)	14687	NM_144797	210029	Mm.153566	NM_144797	ENSMUSG00000039208	Metrnl	9430048M07Rik|BC019776	meteorin, glial cell differentiation regulator-like	protein-coding
mm_62252.1	chr7	99268339	99268388	+	1	NA	promoter-TSS (NM_001043355)	promoter-TSS (NM_001043355)	17	NM_001043355	17760	Mm.154087	NM_010837	ENSMUSG00000055407	Map6	2810411E12Rik|Map-6|Mtap6|STOP	microtubule-associated protein 6	protein-coding
mm_48127.1	chr5	137149810	137149841	-	1	NA	Intergenic	Intergenic	-33618	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_153533.1	chr19	41896161	41896207	-	1	NA	promoter-TSS (NM_199447)	promoter-TSS (NM_199447)	-31	NM_199447	107094	Mm.276044	NM_199447	ENSMUSG00000035049	Rrp12	AA408556|AA536972|mKIAA0690	ribosomal RNA processing 12 homolog (S. cerevisiae)	protein-coding
mm_11628.1	chr2	34775534	34775578	+	1	NA	exon (NM_001163434, exon 9 of 9)	exon (NM_001163434, exon 9 of 9)	3466	NM_022310	14828	Mm.330160	NM_022310	ENSMUSG00000026864	Hspa5	AL022860|AU019543|Bip|D2Wsu141e|D2Wsu17e|Grp78|Hsce70|SEZ-7|Sez7|baffled|mBiP	heat shock protein 5	protein-coding
mm_102015.1	chr11	51615730	51615765	-	1	NA	Intergenic	Intergenic	-4026	NM_026631	52530	Mm.28203	NM_026631	ENSMUSG00000001056	Nhp2	2410130M07Rik|D11Ertd175e|Nola2	NHP2 ribonucleoprotein	protein-coding
mm_44664.1	chr5	29195796	29195827	-	1	NA	promoter-TSS (NM_021470)	promoter-TSS (NM_021470)	-182	NM_001289757	56874	Mm.87352	NM_021470	ENSMUSG00000029130	Rnf32	1700009J01Rik|2700025B22Rik|4930542N22Rik|Lmbr2	ring finger protein 32	protein-coding
mm_34675.1	chr4	150932383	150932393	+	1	NA	exon (NM_001077508, exon 4 of 7)	exon (NM_001077508, exon 4 of 7)	4389	NM_001077509	21942	Mm.244187	NM_011612	ENSMUSG00000028965	Tnfrsf9	4-1BB|A930040I11Rik|AA408498|AI325004|CDw137|Cd137|ILA|Ly63	tumor necrosis factor receptor superfamily, member 9	protein-coding
mm_1329.1	chr1	65186728	65186738	+	1	NA	promoter-TSS (NM_001310624)	promoter-TSS (NM_001310624)	48	NM_001310624	18711	Mm.38370	NM_011086	ENSMUSG00000025949	Pikfyve	5230400C17Rik|Pip5k|Pip5k3|Pipk5k3|PipkIII|p235	phosphoinositide kinase, FYVE finger containing	protein-coding
mm_126430.1	chr15	80572713	80572713	+	1	NA	5' UTR (NM_001289442, exon 1 of 8)	5' UTR (NM_001289442, exon 1 of 8)	116	NM_001289442	17444	Mm.12947	NM_010815	ENSMUSG00000042351	Grap2	GRAP-2|GRB2L|GRBLG|GRID|Gads|GrbX|Grf40|GrpL|Mona|P38	GRB2-related adaptor protein 2	protein-coding
mm_105058.1	chr11	100712430	100712476	-	1	NA	promoter-TSS (NM_020004)	promoter-TSS (NM_020004)	14	NM_001038010	14534	Mm.218837	NM_020004	ENSMUSG00000020918	Kat2a	1110051E14Rik|AW212720|Gcn5|Gcn5l2|mmGCN5	K(lysine) acetyltransferase 2A	protein-coding
mm_105091.1	chr11	100889553	100889577	-	1	NA	exon (NM_213659, exon 23 of 24)	exon (NM_213659, exon 23 of 24)	29081	NM_001164062	20850	Mm.277403	NM_011488	ENSMUSG00000004043	Stat5a	AA959963|STAT5	signal transducer and activator of transcription 5A	protein-coding
mm_17114.1	chr2	24434103	24434105	-	1	NA	intron (NM_011040, intron 9 of 11)	intron (NM_011040, intron 9 of 11)	41495	NM_011040	18510	Mm.2533	NM_011040	ENSMUSG00000026976	Pax8	Pax-8	paired box 8	protein-coding
mm_16188.1	chr2	172977701	172977711	+	1	NA	Intergenic	Intergenic	-2136	NM_012046	26972	Mm.23495	NM_012046	ENSMUSG00000005883	Spo11	AI449549|Spo11a|Spo11b	SPO11 meiotic protein covalently bound to DSB	protein-coding
mm_155202.1	chrX	56731443	56731471	+	1	NA	promoter-TSS (NM_010211)	promoter-TSS (NM_010211)	-304	NM_010211	14199	Mm.3126	NM_010211	ENSMUSG00000023092	Fhl1	FHL-1|KyoT|RAM14-1|SLIM|SLIM-1	four and a half LIM domains 1	protein-coding
mm_112934.1	chr13	20978046	20978048	+	1	NA	intron (NM_012054, intron 12 of 20)	Lx9|LINE|L1	95252	NM_146535	258528	Mm.377554	NM_146535	ENSMUSG00000042869	Olfr1370	MOR256-14	olfactory receptor 1370	protein-coding
mm_16629.1	chr2	5698013	5698020	-	1	NA	intron (NM_001290374, intron 1 of 9)	intron (NM_001290374, intron 1 of 9)	16746	NM_001290374	227541	Mm.191949	NM_177343	ENSMUSG00000039145	Camk1d	A630059D12Rik|CKLiK|CaMKIdelta|E030025C11Rik|mCKLiK	calcium/calmodulin-dependent protein kinase ID	protein-coding
mm_162046.1	chr19	61069328	61069328	+	1	NA	exon (NM_018869, exon 6 of 16)	exon (NM_018869, exon 6 of 16)	71512	NR_131956	414758	Mm.100056	NM_001001737	ENSMUSG00000074733	Zfp950	5830428H23Rik|AU016073|BC055757|Gm34518|Zfp826|mszf84	zinc finger protein 950	protein-coding
mm_47104.1	chr5	118422001	118422005	-	1	NA	Intergenic	Intergenic	-138716	NM_001347445	76199	Mm.206238	NM_172424	ENSMUSG00000018076	Med13l	2210413I17Rik|6330591G05Rik|9030618F05Rik|Thrap2|Trap240L|mKIAA1025	mediator complex subunit 13-like	protein-coding
mm_39634.1	chr5	24471867	24471870	+	1	NA	intron (NM_139153, intron 1 of 17)	intron (NM_139153, intron 1 of 17)	19691	NM_139153	213990	Mm.250703	NM_139153	ENSMUSG00000023353	Agap3	AGAP-3|AV028425|Centg3|Crag|Crag.|MRIP-1|cnt-g3	ArfGAP with GTPase domain, ankyrin repeat and PH domain 3	protein-coding
mm_124660.1	chr15	5554748	5554756	+	1	NA	intron (NR_045274, intron 2 of 4)	ORR1D2|LTR|ERVL-MaLR	58434	NR_045274	71432	Mm.291087	NR_045274		5430437J10Rik	-	RIKEN cDNA 5430437J10 gene	ncRNA
mm_50882.1	chr6	55836879	55836900	+	1	NA	promoter-TSS (NM_001081665)	promoter-TSS (NM_001081665)	-129	NM_001081665	232016	Mm.333084	NM_001081665	ENSMUSG00000037973	Ccdc129	D530004J12Rik|Gm458	coiled-coil domain containing 129	protein-coding
mm_120391.1	chr14	64590482	64590488	+	1	NA	promoter-TSS (NR_029813)	promoter-TSS (NR_029813)	-172	NR_029813	387233		NR_029813	ENSMUSG00000065597	Mir124a-1	Mirn124a|Mirn124a-1	microRNA 124a-1	ncRNA
mm_152065.1	chr19	6532346	6532367	-	1	NA	3' UTR (NM_020253, exon 23 of 23)	3' UTR (NM_020253, exon 23 of 23)	10714	NM_009203	20521	Mm.391146	NM_009203	ENSMUSG00000061742	Slc22a12	AI987855|OAT4L|Rst|Slc22al2|URAT1	solute carrier family 22 (organic anion/cation transporter), member 12	protein-coding
mm_165361.1	chr2	123487614	123487620	-	1	NA	Intergenic	Intergenic	-602352	NM_001290997	214968	Mm.330536	NM_172537	ENSMUSG00000027200	Sema6d	1110067B02Rik|AA409156|D330011G23|mKIAA1479	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	protein-coding
mm_134173.1	chr16	10835335	10835369	-	1	NA	exon (NM_001162932, exon 1 of 2)	exon (NM_001162932, exon 1 of 2)	293	NM_001162932	223970	Mm.325777	NM_001033278	ENSMUSG00000037991	Rmi2	A630055G03Rik|Gm537|Gm929	RecQ mediated genome instability 2	protein-coding
mm_172377.1	chr7	128013227	128013243	-	1	NA	Intergenic	Intergenic	8857	NM_001079932	434246	Mm.389924	NM_001079932	ENSMUSG00000042828	Trim72	BC067209|MG53	tripartite motif-containing 72	protein-coding
mm_111749.1	chr12	103949151	103949172	-	1	NA	exon (NM_009247, exon 3 of 5)	exon (NM_009247, exon 3 of 5)	7736	NM_009247	20704	Mm.312593	NM_009247	ENSMUSG00000072849	Serpina1e	Dom5|PI5|Spi1-5	serine (or cysteine) peptidase inhibitor, clade A, member 1E	protein-coding
mm_5608.1	chr1	39615688	39615690	-	1	NA	Intergenic	Intergenic	35493	NM_170597	263764	Mm.122091	NM_170597	ENSMUSG00000050967	Creg2	A830098L22Rik	cellular repressor of E1A-stimulated genes 2	protein-coding
mm_82828.1	chr9	31149673	31149699	-	1	NA	3' UTR (NM_009691, exon 16 of 16)	3' UTR (NM_009691, exon 16 of 16)	-17887	NM_011176	19143	Mm.243926	NM_011176	ENSMUSG00000031995	St14	Epithin|MT-SP1|Prss14|Tmprss14|mCAP3|matriptase	suppression of tumorigenicity 14 (colon carcinoma)	protein-coding
mm_143313.1	chr17	66101549	66101559	-	1	NA	promoter-TSS (NM_028388)	promoter-TSS (NM_028388)	5	NM_001278415	72900	Mm.2206	NM_028388	ENSMUSG00000024099	Ndufv2	2900010C23Rik	NADH dehydrogenase (ubiquinone) flavoprotein 2	protein-coding
mm_29847.1	chr3	129901479	129901489	-	1	NA	promoter-TSS (NM_009811)	promoter-TSS (NM_009811)	69	NM_009811	12368	Mm.281379	NM_009811	ENSMUSG00000027997	Casp6	CASP-6|Mch2	caspase 6	protein-coding
mm_76413.1	chr8	84937348	84937367	-	1	NA	promoter-TSS (NM_019945)	promoter-TSS (NM_019945)	-4	NM_019945	56527	Mm.154614	NM_019945	ENSMUSG00000053693	Mast1	9430008B02Rik|SAST|SAST170	microtubule associated serine/threonine kinase 1	protein-coding
mm_43832.1	chr5	142972336	142972354	+	1	NA	3' UTR (NM_007984, exon 5 of 5)	3' UTR (NM_007984, exon 5 of 5)	11990	NM_007984	14086	Mm.289707	NM_007984	ENSMUSG00000029581	Fscn1	AI663989|Fan1|fascin-1	fascin actin-bundling protein 1	protein-coding
mm_90181.1	chr10	119992898	119992904	+	1	NA	promoter-TSS (NM_001277295)	promoter-TSS (NM_001277295)	-21	NM_001277295	74053	Mm.196692	NM_028736	ENSMUSG00000034813	Grip1	4931400F03Rik|GRIP|eb	glutamate receptor interacting protein 1	protein-coding
mm_73726.1	chr8	112698445	112698459	+	1	NA	intron (NM_130457, intron 3 of 23)	RLTR17|LTR|ERVK	128409	NM_130457	170571	Mm.209232	NM_130457	ENSMUSG00000031772	Cntnap4	Caspr4|E130114F09Rik	contactin associated protein-like 4	protein-coding
mm_90611.1	chr10	128361294	128361341	+	1	NA	3' UTR (NM_026444, exon 11 of 11)	3' UTR (NM_026444, exon 11 of 11)	8720	NM_001081040	210582	Mm.296876	NM_001081040	ENSMUSG00000039914	Coq10a	Gm1	coenzyme Q10A	protein-coding
mm_101264.1	chr11	21207036	21207049	-	1	NA	Intergenic	Intergenic	-31990	NM_139061	245944	Mm.170103	NM_139061	ENSMUSG00000020128	Vps54	Hcc8|Vps54l|mSLP8|wr	VPS54 GARP complex subunit	protein-coding
mm_124350.1	chr14	104464657	104464662	-	1	NA	intron (NM_011143, intron 2 of 2)	intron (NM_011143, intron 2 of 2)	3340	NM_011143	18996	Mm.246550	NM_011143	ENSMUSG00000048349	Pou4f1	Brn-3|Brn-3.0|Brn3|Brn3.0|Brn3a|E130119J07Rik	POU domain, class 4, transcription factor 1	protein-coding
mm_119484.1	chr14	47367769	47367796	+	1	NA	Intergenic	Intergenic	-6078	NM_010705	16854	Mm.248615	NM_010705	ENSMUSG00000050335	Lgals3	GBP|L-34|Mac-2|gal3	lectin, galactose binding, soluble 3	protein-coding
mm_18111.1	chr2	44994465	44994482	-	1	NA	intron (NM_001289521, intron 8 of 8)	intron (NM_001289521, intron 8 of 8)	28704	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_121053.1	chr14	85478991	85478991	+	1	NA	Intergenic	Intergenic	-766979	NR_040457	75155	Mm.399239	NR_040457		4930529K09Rik	4930507G21Rik	RIKEN cDNA 4930529K09 gene	ncRNA
mm_67779.1	chr7	97332018	97332095	-	1	NA	promoter-TSS (NM_001039039)	promoter-TSS (NM_001039039)	-267	NM_001039039	622320	Mm.334029	NM_001039039	ENSMUSG00000044952	Kctd21	EG622320	potassium channel tetramerisation domain containing 21	protein-coding
mm_112341.1	chr12	116405104	116405154	-	1	NA	promoter-TSS (NR_028421)	promoter-TSS (NR_028421)	32	NR_028421	319545	Mm.390543	NR_028421		D430020J02Rik	-	RIKEN cDNA D430020J02 gene	ncRNA
mm_41307.1	chr5	90468552	90468613	+	1	NA	exon (NM_009654, exon 8 of 15)	exon (NM_009654, exon 8 of 15)	7712	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_12068.1	chr2	59623001	59623004	+	1	NA	intron (NM_198294, intron 1 of 26)	intron (NM_198294, intron 1 of 26)	10960	NM_198294	66860	Mm.27917	NM_198294	ENSMUSG00000035168	Tanc1	1200003E16Rik|Tanc|mKIAA1728	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	protein-coding
mm_83338.1	chr9	44268183	44268229	-	1	NA	promoter-TSS (NM_001163743)	promoter-TSS (NM_001163743)	-19	NM_001163743	270151	Mm.3957	NM_178420	ENSMUSG00000032109	Nlrx1	BC034204|NOD9	NLR family member X1	protein-coding
mm_123549.1	chr14	66831639	66831669	-	1	NA	intron (NM_009955, intron 4 of 13)	RSINE1|SINE|B4	36946	NM_009955	12934	Mm.352648	NM_009955	ENSMUSG00000022048	Dpysl2	AI851130|Crmp2|DRP2|Musunc33|TOAD-64|Ulip2	dihydropyrimidinase-like 2	protein-coding
mm_158746.1	chrX	164381577	164381582	-	1	NA	intron (NM_001308489, intron 1 of 5)	intron (NM_001308489, intron 1 of 5)	8057	NM_010216	14205	Mm.297978	NM_010216	ENSMUSG00000031380	Vegfd	AI325264|Figf|VEGF-D	vascular endothelial growth factor D	protein-coding
mm_112538.1	chr13	9684558	9684562	+	1	NA	TTS (NM_001347480)	TTS (NM_001347480)	79250	NM_001347471	66505	Mm.397307	NM_144516	ENSMUSG00000021156	Zmynd11	2210402G22Rik|BS69	zinc finger, MYND domain containing 11	protein-coding
mm_101585.1	chr11	34543988	34544001	-	1	NA	intron (NM_033374, intron 22 of 51)	RLTR44-int|LTR|ERVK	229172	NM_001025382	574403	Mm.444796	NM_001025382	ENSMUSG00000069911	Fam196b	EG574403|Gm6041	family with sequence similarity 196, member B	protein-coding
mm_166226.1	chr5	65247323	65247329	+	1	NA	intron (NM_153391, intron 27 of 36)	B1_Mur1|SINE|Alu	47630	NM_153391	213081	Mm.127550	NM_153391	ENSMUSG00000037890	Wdr19	C330027H04Rik|D330023L08Rik|DYF2|Ift144|PWDMP|mKIAA1638	WD repeat domain 19	protein-coding
mm_160840.1	chr11	49204110	49204110	+	1	NA	intron (NM_009562, intron 1 of 3)	intron (NM_009562, intron 1 of 3)	610	NM_009562	22720	Mm.16650	NM_009562	ENSMUSG00000046311	Zfp62	-	zinc finger protein 62	protein-coding
mm_8221.1	chr1	138165189	138165200	-	1	NA	intron (NM_001111316, intron 1 of 31)	B1_Mur2|SINE|Alu	9932	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_48605.1	chr5	144255674	144255696	-	1	NA	intron (NM_018772, intron 1 of 2)	CpG	460	NM_018772	55950	Mm.38011	NM_018772	ENSMUSG00000047843	Bri3	I3	brain protein I3	protein-coding
mm_107157.1	chr12	24572434	24572458	+	1	NA	exon (NM_001161406, exon 1 of 16)	exon (NM_001161406, exon 1 of 16)	159	NM_001161406	195733	Mm.263068	NM_145890	ENSMUSG00000020656	Grhl1	LBP-32|MGR|Tcfcp2l2	grainyhead-like 1 (Drosophila)	protein-coding
mm_14470.1	chr2	131393090	131393100	+	1	NA	intron (NR_037281, intron 2 of 2)	intron (NR_037281, intron 2 of 2)	-40203	NM_178607	51902	Mm.477523	NM_178607	ENSMUSG00000048911	Rnf24	2810473M14Rik|4930505A13Rik|AI317164|C86507|D2Ertd504e	ring finger protein 24	protein-coding
mm_107546.1	chr12	40718376	40718378	+	1	NA	intron (NM_172803, intron 16 of 52)	Lx6|LINE|L1	272324	NM_172803	238130	Mm.341423	NM_172803	ENSMUSG00000035954	Dock4	5330406C03|6330411N01Rik|AF263288|C030023J22|mKIAA0716	dedicator of cytokinesis 4	protein-coding
mm_138051.1	chr17	33926313	33926326	+	1	NA	exon (NM_009318, exon 5 of 8)	exon (NM_009318, exon 5 of 8)	-3575	NM_009059	19732	Mm.43777	NM_009059	ENSMUSG00000041354	Rgl2	KE1.5|Rab2l|Rgt2|Rlf	ral guanine nucleotide dissociation stimulator-like 2	protein-coding
mm_113663.1	chr13	42682002	42682011	+	1	NA	intron (NM_001302635, intron 1 of 13)	intron (NM_001302635, intron 1 of 13)	1207	NM_001302635	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding
mm_65020.1	chr7	17973631	17973671	-	1	NA	exon (NM_023289, exon 2 of 4)	exon (NM_023289, exon 2 of 4)	1484	NM_023289	66996	Mm.36666	NM_023289	ENSMUSG00000030368	Ceacam11	1600015D01Rik	carcinoembryonic antigen-related cell adhesion molecule 11	protein-coding
mm_25959.1	chr3	132629834	132629888	+	1	NA	promoter-TSS (NM_001270430)	promoter-TSS (NM_001270430)	-330	NM_001270430	433653		NM_001270430	ENSMUSG00000091721	Gimd1	EG433653|Gm5549	GIMAP family P-loop NTPase domain containing 1	protein-coding
mm_103599.1	chr11	78386694	78386709	-	1	NA	promoter-TSS (NM_008238)	promoter-TSS (NM_008238)	-93	NM_001277290	15218	Mm.4496	NM_008238	ENSMUSG00000002057	Foxn1	D11Bhm185e|Fkh19|HFH-11|Hfh11|Whn|nu|nude	forkhead box N1	protein-coding
mm_138995.1	chr17	45555728	45555746	+	1	NA	promoter-TSS (NM_008690)	promoter-TSS (NM_008690)	37	NM_001304956	18037	Mm.57043	NM_008690	ENSMUSG00000023947	Nfkbie	I-kappa-B-epsilon|IKBE|IkB-E|NF-kappa-BIE|ikB-epsilon	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, epsilon	protein-coding
mm_173147.1	chrX	23534808	23534809	+	1	NA	Intergenic	L1M4|LINE|L1	-158243	NM_175180	72404	Mm.423	NM_175180	ENSMUSG00000036769	Wdr44	2610034K17Rik|RAB11BP|RPH11	WD repeat domain 44	protein-coding
mm_146929.1	chr18	31949871	31949884	-	1	NA	promoter-TSS (NM_001025381)	promoter-TSS (NM_001025381)	-241	NM_001025381	574402	Mm.391108	NM_001025381	ENSMUSG00000052229	Gpr17	AI853548	G protein-coupled receptor 17	protein-coding
mm_76598.1	chr8	89824662	89824674	-	1	NA	Intergenic	RLTR9B2|LTR|ERVK	523584	NM_172913	244579	Mm.302755	NM_172913	ENSMUSG00000043668	Tox3	500-9|BC052044|C230068E13|CAGF9|Tnrc9	TOX high mobility group box family member 3	protein-coding
mm_53759.1	chr6	145746586	145746606	+	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	-61787	NM_027760	71323	Mm.158669	NM_027760	ENSMUSG00000030259	Rassf8	5133400D11Rik|AA815821|AW123240|Hoj1|mHoj-1	Ras association (RalGDS/AF-6) domain family (N-terminal) member 8	protein-coding
mm_54527.1	chr6	36388916	36388918	-	1	NA	promoter-TSS (NR_015589)	promoter-TSS (NR_015589)	-683	NR_015589	319472	Mm.226434	NR_015589	ENSMUSG00000073154	9330158H04Rik	-	RIKEN cDNA 9330158H04 gene	ncRNA
mm_24411.1	chr3	90476122	90476220	+	1	NA	promoter-TSS (NM_026374)	promoter-TSS (NM_026374)	-30	NM_026374	67781	Mm.227258	NM_026374	ENSMUSG00000001016	Ilf2	6230405A16Rik|TEG-267|Tex261|Tex267	interleukin enhancer binding factor 2	protein-coding
mm_81739.1	chr9	113793029	113793069	+	1	NA	promoter-TSS (NM_001286603)	promoter-TSS (NM_001286603)	-281	NM_001286603	76499	Mm.222272	NM_029633	ENSMUSG00000033392	Clasp2	1500004F14Rik|8030404L10Rik|C77448|CLASP2beta|mKIAA0627	CLIP associating protein 2	protein-coding
mm_75858.1	chr8	70700197	70700233	-	1	NA	3' UTR (NM_001286944, exon 1 of 1)	3' UTR (NM_001286944, exon 1 of 1)	2476	NM_001286944	16478	Mm.419851	NM_010592	ENSMUSG00000071076	Jund	Jund1	jun D proto-oncogene	protein-coding
mm_11675.1	chr2	35340338	35340366	+	1	NA	Intergenic	Intergenic	-3343	NM_013515	13830	Mm.295284	NM_013515	ENSMUSG00000026880	Stom	Epb7.2	stomatin	protein-coding
mm_26248.1	chr3	141592065	141592068	+	1	NA	intron (NM_001293561, intron 1 of 16)	intron (NM_001293561, intron 1 of 16)	126502	NM_001293561	22253	Mm.24430	NM_009472	ENSMUSG00000059921	Unc5c	B130051O18Rik|Unc5h3|rcm	unc-5 netrin receptor C	protein-coding
mm_24266.1	chr3	89187975	89187997	+	1	NA	intron (NM_001014995, intron 9 of 11)	intron (NM_001014995, intron 9 of 11)	4761	NM_001014995	68521	Mm.274708	NM_001014995	ENSMUSG00000032657	Fam189b	1110013L07Rik	family with sequence similarity 189, member B	protein-coding
mm_152953.1	chr19	29048077	29048081	-	1	NA	promoter-TSS (NM_021299)	promoter-TSS (NM_021299)	-177	NM_021299	56248	Mm.196067	NM_021299	ENSMUSG00000024782	Ak3	AA407498|AI506714|AK-3|Ak3l|Ak3l1|Akl3l	adenylate kinase 3	protein-coding
mm_99777.1	chr11	107201973	107201983	+	1	NA	Intergenic	Intergenic	-12597	NM_001161329	68979	Mm.294617	NM_133702	ENSMUSG00000018433	Nol11	1500002M01Rik|AU015220|AU019874	nucleolar protein 11	protein-coding
mm_64038.1	chr7	140773031	140773061	+	1	NA	exon (NM_021282, exon 7 of 9)	exon (NM_021282, exon 7 of 9)	9214	NM_021282	13106	Mm.21758	NM_021282	ENSMUSG00000025479	Cyp2e1	Cyp2e	cytochrome P450, family 2, subfamily e, polypeptide 1	protein-coding
mm_18742.1	chr2	73038392	73038395	-	1	NA	Intergenic	Intergenic	-57947	NM_001018042	20687	Mm.124328	NM_011450	ENSMUSG00000027109	Sp3	D130027J01Rik	trans-acting transcription factor 3	protein-coding
mm_104860.1	chr11	99385327	99385339	-	1	NA	TTS (NM_010660)	TTS (NM_010660)	4031	NM_010660	16661	Mm.22662	NM_010660	ENSMUSG00000019761	Krt10	D130054E02Rik|K10|K1C1|Krt-1.10|Krt1-10	keratin 10	protein-coding
mm_73051.1	chr8	94365849	94365860	+	1	NA	exon (NM_001205311, exon 25 of 25)	exon (NM_001205311, exon 25 of 25)	-20646	NM_022331	64209	Mm.29151	NM_022331	ENSMUSG00000031770	Herpud1	Herp|Mifl|SUP	homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1	protein-coding
mm_66360.1	chr7	43530312	43530330	-	1	NA	intron (NM_021293, intron 3 of 5)	intron (NM_021293, intron 3 of 5)	2850	NM_001111058	12489	Mm.140157	NM_021293	ENSMUSG00000004609	Cd33	Siglec-3|gp67	CD33 antigen	protein-coding
mm_12461.1	chr2	71347956	71347974	+	1	NA	intron (NM_172436, intron 2 of 17)	RLTR16C_MM|LTR|ERVK	19589	NM_172436	78830	Mm.30928	NM_172436	ENSMUSG00000027010	Slc25a12	2610002D09Rik|AI839531|B230107K20Rik|BB129864	solute carrier family 25 (mitochondrial carrier, Aralar), member 12	protein-coding
mm_16562.1	chr2	3332448	3332460	-	1	NA	intron (NM_001013376, intron 1 of 1)	CpG	174	NM_001013376	227522	Mm.293948	NM_001013376	ENSMUSG00000049950	Rpp38	C330006A15Rik	ribonuclease P/MRP 38 subunit	protein-coding
mm_11779.1	chr2	39005231	39005277	+	1	NA	promoter-TSS (NM_025592)	promoter-TSS (NM_025592)	-123	NM_025592	66489	Mm.345333	NM_025592	ENSMUSG00000062997	Rpl35	2410039E09Rik	ribosomal protein L35	protein-coding
mm_77683.1	chr8	125734105	125734133	-	1	NA	promoter-TSS (NM_025636)	promoter-TSS (NM_025636)	-84	NM_025636	66566	Mm.25296	NM_025636	ENSMUSG00000031851	Ntpcr	2310079N02Rik|AI449709	nucleoside-triphosphatase, cancer-related	protein-coding
mm_172417.1	chr7	25264076	25264090	-	1	NA	Intergenic	Intergenic	-3616	NM_001302811	71722	Mm.28833	NM_027882	ENSMUSG00000005442	Cic	1200010B10Rik|mKIAA0306	capicua transcriptional repressor	protein-coding
mm_95492.1	chr11	51619732	51619813	+	1	NA	promoter-TSS (NM_026631)	promoter-TSS (NM_026631)	-1	NM_026631	52530	Mm.28203	NM_026631	ENSMUSG00000001056	Nhp2	2410130M07Rik|D11Ertd175e|Nola2	NHP2 ribonucleoprotein	protein-coding
mm_74461.1	chr8	4216006	4216011	-	1	NA	exon (NM_207203, exon 4 of 7)	exon (NM_207203, exon 4 of 7)	1304	NM_207203	73072	Mm.477379	NM_207203	ENSMUSG00000064125	Prr36	-	proline rich 36	protein-coding
mm_42699.1	chr5	119881928	119881935	+	1	NA	intron (NM_011537, intron 8 of 8)	intron (NM_011537, intron 8 of 8)	47268	NM_011537	21388	Mm.103636	NM_011537	ENSMUSG00000018263	Tbx5	-	T-box 5	protein-coding
mm_129896.1	chr15	83595112	83595162	-	1	NA	promoter-TSS (NM_183017)	promoter-TSS (NM_183017)	20	NM_183017	223723	Mm.46778	NM_183017	ENSMUSG00000016757	Ttll12	BC055368|D430005B17	tubulin tyrosine ligase-like family, member 12	protein-coding
mm_7634.1	chr1	127732932	127732977	-	1	NA	intron (NM_001033041, intron 1 of 9)	intron (NM_001033041, intron 1 of 9)	3541	NM_001033041	266645	Mm.25735	NM_001033041	ENSMUSG00000026348	Acmsd	-	amino carboxymuconate semialdehyde decarboxylase	protein-coding
mm_143326.1	chr17	66413241	66413241	-	1	NA	intron (NM_001114098, intron 3 of 14)	intron (NM_001114098, intron 3 of 14)	36509	NM_172963	68617	Mm.33421	NM_172963	ENSMUSG00000052105	Mtcl1	1110012J17Rik|Ccdc165|D130071O13|Kiaa0802|Soga2|mKIAA0802|t8219b25	microtubule crosslinking factor 1	protein-coding
mm_149256.1	chr19	10426145	10426157	+	1	NA	intron (NM_173067, intron 4 of 9)	intron (NM_173067, intron 4 of 9)	31296	NM_001111140	278795	Mm.490638	NM_001111140	ENSMUSG00000090291	Lrrc10b	Gm705|SerdinR	leucine rich repeat containing 10B	protein-coding
mm_171608.1	chr4	149457290	149457308	+	1	NA	Intergenic	CpG	-2331	NM_022020	63954	Mm.46023	NM_022020	ENSMUSG00000028996	Rbp7	1110002J23Rik|CRBP-III	retinol binding protein 7, cellular	protein-coding
mm_98518.1	chr11	94952688	94952702	+	1	NA	3' UTR (NM_007742, exon 51 of 51)	3' UTR (NM_007742, exon 51 of 51)	-14898	NM_018792	54388	Mm.30482	NM_018792	ENSMUSG00000038994	Hils1	H1.9|TISP64	histone H1-like protein in spermatids 1	protein-coding
mm_31185.1	chr4	43555625	43555642	+	1	NA	exon (NM_011602, exon 5 of 57)	exon (NM_011602, exon 5 of 57)	6950	NM_011602	21894	Mm.208601	NM_011602	ENSMUSG00000028465	Tln1	Tln	talin 1	protein-coding
mm_126397.1	chr15	80219579	80219602	+	1	NA	Intergenic	Intergenic	-14490	NM_178719	239555	Mm.307163	NM_178719	ENSMUSG00000022412	Mief1	A230016E22|AI452372|Smcr7l	mitochondrial elongation factor 1	protein-coding
mm_56514.1	chr6	99429016	99429043	-	1	NA	intron (NM_001347345, intron 2 of 19)	intron (NM_001347345, intron 2 of 19)	6316	NM_053202	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_54555.1	chr6	37207665	37207672	-	1	NA	intron (NM_001347104, intron 1 of 32)	intron (NM_001347104, intron 1 of 32)	92308	NM_001081206	320127	Mm.119469	NM_001081206	ENSMUSG00000038665	Dgki	C130010K08Rik	diacylglycerol kinase, iota	protein-coding
mm_3840.1	chr1	160044518	160044524	+	1	NA	non-coding (NR_028111, exon 1 of 3)	non-coding (NR_028111, exon 1 of 3)	141	NM_001162896	67647	Mm.171518	NM_001024470	ENSMUSG00000090394	4930523C07Rik	-	RIKEN cDNA 4930523C07 gene	protein-coding
mm_73609.1	chr8	110079759	110079774	+	1	NA	promoter-TSS (NM_175480)	promoter-TSS (NM_175480)	32	NM_175480	234725	Mm.87487	NM_175480	ENSMUSG00000044676	Zfp612	B230354B21Rik	zinc finger protein 612	protein-coding
mm_92419.1	chr10	76961869	76961944	-	1	NA	promoter-TSS (NM_021568)	promoter-TSS (NM_021568)	41	NM_001347216	59093	Mm.272803	NM_021568	ENSMUSG00000001120	Pcbp3	AlphaCP-3	poly(rC) binding protein 3	protein-coding
mm_18333.1	chr2	57297561	57297627	-	1	NA	intron (NM_001145820, intron 3 of 16)	intron (NM_001145820, intron 3 of 16)	59212	NM_010274	14571	Mm.3711	NM_010274	ENSMUSG00000026827	Gpd2	AA408484|AI448216|AU021455|AW494132|GPDH|Gdm1|Gpd-m|Gpdh-m|TISP38	glycerol phosphate dehydrogenase 2, mitochondrial	protein-coding
mm_10813.1	chr2	24350319	24350327	+	1	NA	3' UTR (NM_031167, exon 5 of 5)	3' UTR (NM_031167, exon 5 of 5)	4952	NM_001039701	16181	Mm.882	NM_031167	ENSMUSG00000026981	Il1rn	F630041P17Rik|IL-1ra	interleukin 1 receptor antagonist	protein-coding
mm_168230.1	chr10	80107196	80107196	+	1	NA	intron (NR_038088, intron 1 of 4)	B1_Mm|SINE|Alu	-4494	NM_183426	216161	Mm.262102	NM_183426	ENSMUSG00000035673	Sbno2	BC019206|F730040C21|Sno|Stno	strawberry notch homolog 2 (Drosophila)	protein-coding
mm_62352.1	chr7	100498840	100498852	+	1	NA	exon (NM_011671, exon 7 of 8)	exon (NM_011671, exon 7 of 8)	5488	NM_011671	22228	Mm.171378	NM_011671	ENSMUSG00000033685	Ucp2	Slc25a8	uncoupling protein 2 (mitochondrial, proton carrier)	protein-coding
mm_55542.1	chr6	70792156	70792199	-	1	NA	promoter-TSS (NM_009075)	promoter-TSS (NM_009075)	-2	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_89856.1	chr10	107495264	107495296	+	1	NA	promoter-TSS (NM_008657)	promoter-TSS (NM_008657)	-551	NM_008657	17878	Mm.11	NM_008657	ENSMUSG00000035923	Myf6	MRF4|bHLHc4|herculin	myogenic factor 6	protein-coding
mm_60538.1	chr7	44480425	44480447	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-4081	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_141737.1	chr17	34121945	34121972	-	1	NA	promoter-TSS (NM_010238)	promoter-TSS (NM_010238)	-211	NM_010238	14312	Mm.3444	NM_010238	ENSMUSG00000024335	Brd2	AW228947|D17H6S113E|Frg-1|Fsrg-1|Fsrg1|Nat|Ring3|Rnf3|mKIAA4005	bromodomain containing 2	protein-coding
mm_108510.1	chr12	83987855	83987898	+	1	NA	promoter-TSS (NM_134188)	promoter-TSS (NM_134188)	15	NM_134188	171210	Mm.371675	NM_134188	ENSMUSG00000021226	Acot2	AA571646|MTE-I|Mte1	acyl-CoA thioesterase 2	protein-coding
mm_165589.1	chr3	32906750	32906752	+	1	NA	intron (NM_001013024, intron 13 of 20)	intron (NM_001013024, intron 13 of 20)	78328	NM_001163517	58869	Mm.151332	NM_021483	ENSMUSG00000027674	Pex5l	1700016J08Rik|PXR2|Pex2|TRIP8b|pex5Rp	peroxisomal biogenesis factor 5-like	protein-coding
mm_60451.1	chr7	44477440	44477460	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-7067	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_27238.1	chr3	36521392	36521416	-	1	NA	promoter-TSS (NR_040411)	promoter-TSS (NR_040411)	41	NR_040411	100503068	Mm.389423	NR_040411	ENSMUSG00000085007	Gm11549	OTTMUSG00000002111	predicted gene 11549	ncRNA
mm_4849.1	chr1	187215502	187215547	+	1	NA	promoter-TSS (NM_029067)	promoter-TSS (NM_029067)	13	NM_026367	67769	Mm.138321	NM_026367	ENSMUSG00000039210	Gpatch2	5830433G22Rik|5830436K05Rik|AI427714|AI447508|AW107440|AW491060|Gpatc2	G patch domain containing 2	protein-coding
mm_32153.1	chr4	99929534	99929544	+	1	NA	promoter-TSS (NM_028132)	promoter-TSS (NM_028132)	88	NM_028132	72157	Mm.217764	NM_028132	ENSMUSG00000025791	Pgm2	2610020G18Rik|AA407108|AI098105|Pgm-2|Pgm1	phosphoglucomutase 2	protein-coding
mm_121194.1	chr14	103051291	103051301	+	1	NA	intron (NM_008392, intron 3 of 4)	intron (NM_008392, intron 3 of 4)	4284	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_107545.1	chr12	40712043	40712048	+	1	NA	intron (NM_172803, intron 16 of 52)	MTA_Mm|LTR|ERVL-MaLR	265992	NM_172803	238130	Mm.341423	NM_172803	ENSMUSG00000035954	Dock4	5330406C03|6330411N01Rik|AF263288|C030023J22|mKIAA0716	dedicator of cytokinesis 4	protein-coding
mm_77374.1	chr8	119833513	119833538	-	1	NA	intron (NM_028071, intron 2 of 3)	B1_Mur1|SINE|Alu	7054	NM_028071	72042	Mm.393405	NM_028071	ENSMUSG00000031827	Cotl1	1810074P22Rik|2010004C08Rik|Clp	coactosin-like 1 (Dictyostelium)	protein-coding
mm_61128.1	chr7	55849367	55849371	+	1	NA	intron (NM_011370, intron 1 of 30)	intron (NM_011370, intron 1 of 30)	7298	NM_001164661	20430	Mm.37249	NM_011370	ENSMUSG00000030447	Cyfip1	E030028J09Rik|P140SRA-1|P140sra1|Shyc|Sra-1|Sra1|l(7)1Rl|l71Rl|l7Rl1|mKIAA0068|pl-1	cytoplasmic FMR1 interacting protein 1	protein-coding
mm_17508.1	chr2	29099652	29099677	-	1	NA	Intergenic	MLTR13|LTR|ERVK	-25328	NM_198033	269254	Mm.41867	NM_198033	ENSMUSG00000043535	Setx	A130090N03|A930037J23Rik|AOA2|AW060766|Als4|SCAR1|Sen1|mKIAA0625	senataxin	protein-coding
mm_61574.1	chr7	79811201	79811215	+	1	NA	exon (NM_008589, exon 1 of 2)	exon (NM_008589, exon 1 of 2)	481	NM_008589	17293	Mm.31472	NM_008589	ENSMUSG00000030543	Mesp2	bHLHc6	mesoderm posterior 2	protein-coding
mm_104523.1	chr11	96073024	96073039	-	1	NA	3' UTR (NM_001161419, exon 5 of 5)	3' UTR (NM_001161419, exon 5 of 5)	2600	NM_001161419	11951	Mm.258	NM_007506	ENSMUSG00000006057	Atp5g1	-	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit C1 (subunit 9)	protein-coding
mm_112882.1	chr13	20857773	20857786	+	1	NA	intron (NM_012054, intron 4 of 20)	intron (NM_012054, intron 4 of 20)	63666	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_4151.1	chr1	171018942	171018979	+	1	NA	promoter-TSS (NM_144559)	promoter-TSS (NM_144559)	34	NM_144559	246256	Mm.251254	NM_144559	ENSMUSG00000059089	Fcgr4	4833442P21Rik|CD16-2|FcgRIV|FcgammaRIV|Fcgr3a|Fcrl3	Fc receptor, IgG, low affinity IV	protein-coding
mm_53892.1	chr6	3377175	3377198	-	1	NA	exon (NM_010156, exon 2 of 2)	exon (NM_010156, exon 2 of 2)	22385	NM_010156	209086	Mm.196013	NM_010156	ENSMUSG00000047735	Samd9l	AA175286|ESTM25|mKIAA2005	sterile alpha motif domain containing 9-like	protein-coding
mm_24922.1	chr3	96520454	96520462	+	1	NA	Intergenic	RMER17B|LTR|ERVK	-4727	NM_027126	69585	Mm.171314	NM_027126	ENSMUSG00000038403	Hfe2	2310035L15Rik|5230400G09Rik|AI414844|AI789733|DL-M|HJV|Rgmc|hemojuvelin	hemochromatosis type 2 (juvenile)	protein-coding
mm_66087.1	chr7	30971918	30971928	-	1	NA	exon (NM_017405, exon 2 of 10)	exon (NM_017405, exon 2 of 10)	1546	NM_001164185	54135	Mm.4067	NM_017405	ENSMUSG00000001247	Lsr	ILDR3|Lisch7	lipolysis stimulated lipoprotein receptor	protein-coding
mm_111751.1	chr12	103951083	103951084	-	1	NA	exon (NM_009247, exon 2 of 5)	exon (NM_009247, exon 2 of 5)	5814	NM_009247	20704	Mm.312593	NM_009247	ENSMUSG00000072849	Serpina1e	Dom5|PI5|Spi1-5	serine (or cysteine) peptidase inhibitor, clade A, member 1E	protein-coding
mm_23238.1	chr3	51210313	51210340	+	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	-14121	NM_009834	12457	Mm.86541	NM_009834	ENSMUSG00000023087	Noct	AU043840|Ccr4|Ccrn4l	nocturnin	protein-coding
mm_89538.1	chr10	94550915	94550934	+	1	NA	intron (NM_172051, intron 1 of 3)	intron (NM_172051, intron 1 of 3)	-24333	NM_001168684	319880	Mm.23047	NM_172051	ENSMUSG00000020023	Tmcc3	AW488095|C630016B22Rik|C88213|Tmcc1	transmembrane and coiled coil domains 3	protein-coding
mm_13656.1	chr2	114055163	114055182	+	1	NA	non-coding (NR_028422, exon 1 of 3)	non-coding (NR_028422, exon 1 of 3)	776	NR_028422	100303644	Mm.330469	NR_028422	ENSMUSG00000092397	C130080G10Rik	-	RIKEN cDNA C130080G10 gene	ncRNA
mm_134321.1	chr16	16073405	16073450	-	1	NA	intron (NM_146068, intron 5 of 19)	intron (NM_146068, intron 5 of 19)	73424	NM_146068	224008	Mm.244703	NM_146068	ENSMUSG00000041974	Spidr	2310008H04Rik|Kiaa0146	scaffolding protein involved in DNA repair	protein-coding
mm_93446.1	chr10	109903912	109903927	-	1	NA	intron (NM_001081035, intron 1 of 38)	intron (NM_001081035, intron 1 of 38)	96300	NM_001081035	260315	Mm.225050	NM_177797	ENSMUSG00000020181	Nav3	4732483H20Rik|9630020C08Rik|POMFIL1|Pomfil1p|mKIAA0938|unc53H3	neuron navigator 3	protein-coding
mm_80187.1	chr9	72389943	72389945	+	1	NA	Intergenic	L1M2|LINE|L1	-48585	NM_008613	17427	Mm.387671	NM_008613	ENSMUSG00000032221	Mns1	AW546487	meiosis-specific nuclear structural protein 1	protein-coding
mm_59019.1	chr7	19271678	19271704	+	1	NA	non-coding (NR_104069, exon 1 of 11)	non-coding (NR_104069, exon 1 of 11)	163	NM_001282021	22323	Mm.9684	NM_009499	ENSMUSG00000030403	Vasp	-	vasodilator-stimulated phosphoprotein	protein-coding
mm_146835.1	chr18	22828539	22828551	-	1	NA	intron (NM_001347510, intron 5 of 9)	intron (NM_001347510, intron 5 of 9)	210118	NM_001161483	319211	Mm.209896	NM_199024	ENSMUSG00000041923	Nol4	1700013J13Rik|4930568N03Rik|Gm1262	nucleolar protein 4	protein-coding
mm_111905.1	chr12	108765848	108765858	-	1	NA	Intergenic	Intergenic	-27458	NM_009537	22632	Mm.3868	NM_009537	ENSMUSG00000021264	Yy1	AW488674|NF-E1	YY1 transcription factor	protein-coding
mm_38203.1	chr4	135573624	135573643	-	1	NA	promoter-TSS (NM_001013756)	promoter-TSS (NM_001013756)	-13	NM_001013756	230824	Mm.331972	NM_001013756	ENSMUSG00000037188	Grhl3	AI561912|Get1|Som|Tfcp2l4|ct	grainyhead-like 3 (Drosophila)	protein-coding
mm_161146.1	chr13	22327934	22327934	+	1	NA	promoter-TSS (NM_134244)	promoter-TSS (NM_134244)	23	NM_134244	171278	Mm.378582	NM_134244	ENSMUSG00000069294	Vmn1r197	V1rh21	vomeronasal 1 receptor 197	protein-coding
mm_163524.1	chr12	116047828	116047836	+	1	NA	5' UTR (NM_019565, exon 1 of 3)	5' UTR (NM_019565, exon 1 of 3)	108	NM_019565	56220	Mm.254997	NM_019565	ENSMUSG00000042063	Zfp386	Kzf1|mKIAA4205	zinc finger protein 386 (Kruppel-like)	protein-coding
mm_110927.1	chr12	76369587	76369598	-	1	NA	promoter-TSS (NM_001172104)	promoter-TSS (NM_001172104)	-32	NM_028356	109929	Mm.41880	NM_028356	ENSMUSG00000056459	Zbtb25	2810462M08Rik|2900064P18Rik|AI842128|Kup|Zfp-50|Zfp50	zinc finger and BTB domain containing 25	protein-coding
mm_79295.1	chr9	51315894	51315899	+	1	NA	intron (NM_027217, intron 2 of 4)	Lx8|LINE|L1	13021	NM_027217	69809	Mm.75315	NM_027217	ENSMUSG00000036027	1810046K07Rik	-	RIKEN cDNA 1810046K07 gene	protein-coding
mm_112316.1	chr12	114946414	114946438	-	1	NA	Intergenic	Intergenic	-432732	NR_106063	102465664		NR_106063	ENSMUSG00000098357	Mir7094-2	Gm27508|mmu-mir-7094-2	microRNA 7094-2	ncRNA
mm_98332.1	chr11	90639602	90639602	+	1	NA	intron (NM_199008, intron 1 of 3)	intron (NM_199008, intron 1 of 3)	1418	NM_199008	69802	Mm.151940	NM_199008	ENSMUSG00000020544	Cox11	2010004I09Rik	cytochrome c oxidase assembly protein 11	protein-coding
mm_1520.1	chr1	72824531	72824541	+	1	NA	promoter-TSS (NM_008342)	promoter-TSS (NM_008342)	56	NM_008342	16008	Mm.141936	NM_008342	ENSMUSG00000039323	Igfbp2	AI255832|IBP-2|Igfbp-2|mIGFBP-2	insulin-like growth factor binding protein 2	protein-coding
mm_101855.1	chr11	48868610	48868630	-	1	NA	5' UTR (NM_008326, exon 2 of 3)	5' UTR (NM_008326, exon 2 of 3)	2726	NM_008326	15944	Mm.29938	NM_008326	ENSMUSG00000046879	Irgm1	Ifggd3|Ifi1|Iigp3|Iipg3|Irgm|LRG-47	immunity-related GTPase family M member 1	protein-coding
mm_11393.1	chr2	31454479	31454556	+	1	NA	Intergenic	Intergenic	-15753	NM_007494	11898	Mm.3217	NM_007494	ENSMUSG00000076441	Ass1	AA408052|ASS|Ass-1|fold	argininosuccinate synthetase 1	protein-coding
mm_46734.1	chr5	110808418	110808464	-	1	NA	intron (NM_001347394, intron 3 of 27)	intron (NM_001347394, intron 3 of 27)	1640	NM_009469	22241	Mm.271898	NM_009469	ENSMUSG00000029512	Ulk1	AU041434|Unc51.1|mKIAA0722	unc-51 like kinase 1	protein-coding
mm_62346.1	chr7	100498363	100498373	+	1	NA	exon (NM_011671, exon 6 of 8)	exon (NM_011671, exon 6 of 8)	5010	NM_011671	22228	Mm.171378	NM_011671	ENSMUSG00000033685	Ucp2	Slc25a8	uncoupling protein 2 (mitochondrial, proton carrier)	protein-coding
mm_169000.1	chr13	100786494	100786509	-	1	NA	promoter-TSS (NM_172301)	promoter-TSS (NM_172301)	-15	NM_172301	268697	Mm.260114	NM_172301	ENSMUSG00000041431	Ccnb1	Ccnb1-rs1|Ccnb1-rs13|CycB1|Cycb-4|Cycb-5|Cycb1-rs1	cyclin B1	protein-coding
mm_7244.1	chr1	93635642	93635652	-	1	NA	promoter-TSS (NM_021537)	promoter-TSS (NM_021537)	80	NM_021537	59041	Mm.28761	NM_021537	ENSMUSG00000026277	Stk25	1500019J11Rik|AU018434|C86992|Ste20-like|Ysk1	serine/threonine kinase 25 (yeast)	protein-coding
mm_166264.1	chr5	87963335	87963335	+	1	NA	intron (NR_045924, intron 1 of 4)	intron (NR_045924, intron 1 of 4)	16016	NR_045924	73471	Mm.396240	NR_045924	ENSMUSG00000099605	1700066N21Rik	-	RIKEN cDNA 1700066N21 gene	ncRNA
mm_153331.1	chr19	38124802	38124816	-	1	NA	promoter-TSS (NM_011255)	promoter-TSS (NM_011255)	2	NM_011255	19662	Mm.2605	NM_011255	ENSMUSG00000024990	Rbp4	Rbp-4	retinol binding protein 4, plasma	protein-coding
mm_91562.1	chr10	40025178	40025194	-	1	NA	promoter-TSS (NM_144821)	promoter-TSS (NM_144821)	82	NM_144821	215929	Mm.55513	NM_144821	ENSMUSG00000038522	Mfsd4b1	AI317395|AI482555|Naglt1a	major facilitator superfamily domain containing 4B1	protein-coding
mm_133554.1	chr16	91386001	91386039	+	1	NA	exon (NM_010509, exon 4 of 9)	exon (NM_010509, exon 4 of 9)	13237	NM_001110498	15976	Mm.6834	NM_010509	ENSMUSG00000022971	Ifnar2	AI747302|Ifnar-2	interferon (alpha and beta) receptor 2	protein-coding
mm_9535.1	chr1	173872883	173872920	-	1	NA	exon (NM_001170853, exon 5 of 10)	exon (NM_001170853, exon 5 of 10)	7286	NM_001170853	100040462	Mm.463437	NM_001170853	ENSMUSG00000090272	Mndal	Gm2785|Ifi212	myeloid nuclear differentiation antigen like	protein-coding
mm_108947.1	chr12	102283204	102283234	+	1	NA	promoter-TSS (NM_001161365)	promoter-TSS (NM_001161365)	145	NM_177620	217835	Mm.24145	NM_177620	ENSMUSG00000044456	Rin3	6430500K07|C86933	Ras and Rab interactor 3	protein-coding
mm_63756.1	chr7	131106975	131106983	+	1	NA	intron (NM_001347632, intron 40 of 47)	intron (NM_001347632, intron 40 of 47)	39304	NM_173409	233918	Mm.78341	NM_173409	ENSMUSG00000013668	4933402N03Rik	4930412O05	RIKEN cDNA 4933402N03 gene	protein-coding
mm_160671.1	chr10	4429196	4429196	-	1	NA	promoter-TSS (NR_002891)	promoter-TSS (NR_002891)	-30	NR_002891	433224	Mm.153111	NR_002891		Gm5512	EG433224	required for meiotic nuclear division 1 pseudogene	pseudo
mm_100920.1	chr11	6367112	6367161	-	1	NA	Intergenic	RLTR23|LTR|ERV1	-27989	NM_001005867	52915	Mm.1144	NM_028601	ENSMUSG00000041164	Zmiz2	Zimp7	zinc finger, MIZ-type containing 2	protein-coding
mm_100262.1	chr11	117332399	117332401	+	1	NA	promoter-TSS (NM_001113488)	promoter-TSS (NM_001113488)	87	NM_001113488	53860	Mm.38450	NM_017380	ENSMUSG00000059248	Sept9	MSF1|Msf|PNUTL4|Sint1	septin 9	protein-coding
mm_167919.1	chrX	101847447	101847449	-	1	NA	Intergenic	Intergenic	-1937	NM_001163610	100042480	Mm.232	NM_001163610	ENSMUSG00000079481	Nhsl2	1110062M06Rik|6430511F03|AI225852|AW488865|EG621083|ENSMUSG00000073037|Gm10456	NHS-like 2	protein-coding
mm_29287.1	chr3	107741467	107741496	-	1	NA	3' UTR (NM_007778, exon 9 of 9)	3' UTR (NM_007778, exon 9 of 9)	18988	NM_001113530	12977	Mm.795	NM_007778	ENSMUSG00000014599	Csf1	C87615|Csfm|MCSF|op	colony stimulating factor 1 (macrophage)	protein-coding
mm_161622.1	chr16	58929355	58929355	-	1	NA	promoter-TSS (NM_146999)	promoter-TSS (NM_146999)	-711	NM_146999	259001	Mm.223388	NM_146999	ENSMUSG00000090951	Olfr181	MOR184-4	olfactory receptor 181	protein-coding
mm_153163.1	chr19	34493140	34493179	-	1	NA	3' UTR (NM_021460, exon 10 of 10)	3' UTR (NM_021460, exon 10 of 10)	-18024	NM_009890	12642	Mm.30824	NM_009890	ENSMUSG00000050370	Ch25h	AI462618|m25OH	cholesterol 25-hydroxylase	protein-coding
mm_101414.1	chr11	29172728	29172756	-	1	NA	promoter-TSS (NM_134034)	promoter-TSS (NM_134034)	-165	NM_134034	104570	Mm.276386	NM_134034	ENSMUSG00000020463	Smek2	AW011752|AW557776|Ppp4r3b|mKIAA1387	SMEK homolog 2, suppressor of mek1 (Dictyostelium)	protein-coding
mm_134396.1	chr16	17530689	17530789	-	1	NA	intron (NM_026909, intron 2 of 4)	CpG	313	NM_026909	69009	Mm.10174	NM_026909	ENSMUSG00000022760	Thap7	1810004B07Rik	THAP domain containing 7	protein-coding
mm_74081.1	chr8	122523575	122523627	+	1	NA	intron (NM_001037298, intron 1 of 50)	intron (NM_001037298, intron 1 of 50)	27728	NM_001037298	234839	Mm.37324	NM_001037298	ENSMUSG00000014444	Piezo1	9630020g22|Fam38a|mKIAA0233	piezo-type mechanosensitive ion channel component 1	protein-coding
mm_41762.1	chr5	103375446	103375448	+	1	NA	Intergenic	Intergenic	-49745	NM_011204	19249	Mm.3414	NM_011204	ENSMUSG00000034573	Ptpn13	AI324989|PTP-BL|PTPL1|Ptpri|RIP	protein tyrosine phosphatase, non-receptor type 13	protein-coding
mm_123338.1	chr14	63133445	63133482	-	1	NA	exon (NM_007798, exon 2 of 10)	exon (NM_007798, exon 2 of 10)	11001	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_107378.1	chr12	32954281	32954292	+	1	NA	promoter-TSS (NM_198710)	promoter-TSS (NM_198710)	100	NM_198710	19027	Mm.246304	NM_013635	ENSMUSG00000020570	Sypl	AI314763|AI604763|D12Ertd446e|PanI|Pphn|Sypl1	synaptophysin-like protein	protein-coding
mm_117119.1	chr13	60848858	60848869	-	1	NA	intron (NM_178098, intron 5 of 7)	intron (NM_178098, intron 5 of 7)	15553	NM_178098	214639	Mm.19839	NM_178098	ENSMUSG00000050345	4930486L24Rik	AW545031	RIKEN cDNA 4930486L24 gene	protein-coding
mm_17461.1	chr2	28557796	28557822	-	1	NA	exon (NM_009885, exon 9 of 11)	exon (NM_009885, exon 9 of 11)	5594	NM_009885	12613	Mm.236017	NM_009885	ENSMUSG00000026818	Cel	1810036E18Rik|BAL	carboxyl ester lipase	protein-coding
mm_3694.1	chr1	153752811	153752831	+	1	NA	intron (NM_011882, intron 2 of 8)	intron (NM_011882, intron 2 of 8)	3395	NM_011882	24014	Mm.259254	NM_011882	ENSMUSG00000066800	Rnasel	E230029I04Rik	ribonuclease L (2', 5'-oligoisoadenylate synthetase-dependent)	protein-coding
mm_65631.1	chr7	27553015	27553070	-	1	NA	promoter-TSS (NM_175107)	promoter-TSS (NM_175107)	176	NM_011116	18807	Mm.6483	NM_011116	ENSMUSG00000003363	Pld3	Sam-9	phospholipase D family, member 3	protein-coding
mm_11826.1	chr2	44956607	44956644	+	1	NA	Intergenic	Intergenic	66552	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_96668.1	chr11	69409799	69409812	+	1	NA	intron (NM_001017426, intron 1 of 22)	intron (NM_001017426, intron 1 of 22)	3870	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_126435.1	chr15	80611754	80611767	+	1	NA	intron (NM_001289442, intron 1 of 7)	intron (NM_001289442, intron 1 of 7)	-11723	NM_010815	17444	Mm.12947	NM_010815	ENSMUSG00000042351	Grap2	GRAP-2|GRB2L|GRBLG|GRID|Gads|GrbX|Grf40|GrpL|Mona|P38	GRB2-related adaptor protein 2	protein-coding
mm_49457.1	chr6	29398921	29398931	+	1	NA	promoter-TSS (NM_001201378)	promoter-TSS (NM_001201378)	0	NM_145574	232664	Mm.251303	NM_145574	ENSMUSG00000029769	Ccdc136	4921511K06Rik|BC006583	coiled-coil domain containing 136	protein-coding
mm_104146.1	chr11	87045912	87045931	-	1	NA	intron (NM_025638, intron 4 of 9)	intron (NM_025638, intron 4 of 9)	28216	NM_025638	66569	Mm.281887	NM_025638	ENSMUSG00000061666	Gdpd1	2610020H15Rik	glycerophosphodiester phosphodiesterase domain containing 1	protein-coding
mm_145589.1	chr18	60985917	60985927	+	1	NA	3' UTR (NM_001286809, exon 6 of 6)	3' UTR (NM_001286809, exon 6 of 6)	22368	NM_001286809	12322	Mm.131530	NM_009792	ENSMUSG00000024617	Camk2a	CaMKII|R74975|mKIAA0968	calcium/calmodulin-dependent protein kinase II alpha	protein-coding
mm_163078.1	chr11	68864762	68864762	+	1	NA	Intergenic	Intergenic	-11631	NM_023668	83431	Mm.31979	NM_023668	ENSMUSG00000018736	Ndel1	2600006O07Rik|MITAP1|NUDEL|mNudel	nudE neurodevelopment protein 1 like 1	protein-coding
mm_53907.1	chr6	3966407	3966409	-	1	NA	intron (NR_138566, intron 2 of 4)	intron (NR_138566, intron 2 of 4)	1967	NM_009364	21789	Mm.25612	NM_009364	ENSMUSG00000029664	Tfpi2	AV000670|PP5/TFPI-2	tissue factor pathway inhibitor 2	protein-coding
mm_106135.1	chr11	116479728	116479750	-	1	NA	exon (NM_026364, exon 4 of 10)	exon (NM_026364, exon 4 of 10)	10607	NM_026364	67763	Mm.25125	NM_026364	ENSMUSG00000015869	Prpsap1	5730409F23Rik|PAP39	phosphoribosyl pyrophosphate synthetase-associated protein 1	protein-coding
mm_74864.1	chr8	24948772	24948829	-	1	NA	promoter-TSS (NM_001293693)	promoter-TSS (NM_001293693)	4	NM_001293693	353188	Mm.269223	NM_153397	ENSMUSG00000037437	Adam32	-	a disintegrin and metallopeptidase domain 32	protein-coding
mm_94980.1	chr11	31796434	31796461	+	1	NA	Intergenic	Intergenic	28100	NR_102310	414116	Mm.150222	NR_102310	ENSMUSG00000085772	D630024D03Rik	-	RIKEN cDNA D630024D03 gene	ncRNA
mm_156535.1	chrX	151066743	151066753	+	1	NA	exon (NM_008001, exon 3 of 18)	exon (NM_008001, exon 3 of 18)	19578	NM_008001	14163	Mm.8142	NM_008001	ENSMUSG00000025265	Fgd1	ZFYVE3	FYVE, RhoGEF and PH domain containing 1	protein-coding
mm_102220.1	chr11	54909793	54909803	-	1	NA	TTS (NM_021327)	TTS (NM_021327)	6944	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_15260.1	chr2	155013558	155013561	+	1	NA	promoter-TSS (NM_015770)	promoter-TSS (NM_015770)	-11	NM_015770	50518	Mm.315593	NM_015770	ENSMUSG00000027596	a	A<y>|ASIP|ASP|As	nonagouti	protein-coding
mm_103985.1	chr11	84827647	84827656	-	1	NA	intron (NM_177564, intron 1 of 6)	intron (NM_177564, intron 1 of 6)	1352	NM_177564	192970	Mm.192213	NM_177564	ENSMUSG00000034449	Dhrs11	-	dehydrogenase/reductase (SDR family) member 11	protein-coding
mm_13485.1	chr2	106382711	106382711	+	1	NA	Intergenic	Intergenic	140392	NR_040637	329483	Mm.246777	NR_040637	ENSMUSG00000087226	Gm14015	9330126M15|OTTMUSG00000015366	predicted gene 14015	ncRNA
mm_67065.1	chr7	67720185	67720189	-	1	NA	intron (NM_001168475, intron 9 of 10)	intron (NM_001168475, intron 9 of 10)	39555	NM_183312	233335	Mm.60526	NM_183312	ENSMUSG00000030554	Synm	4930412K21Rik|AI852401|Dmn|E130104F11|Syn|Synemin	synemin, intermediate filament protein	protein-coding
mm_69074.1	chr7	126976093	126976105	-	1	NA	5' UTR (NM_026638, exon 1 of 6)	5' UTR (NM_026638, exon 1 of 6)	185	NM_001347656	52858	Mm.28219	NM_026638	ENSMUSG00000030682	Cdipt	9530042F15Rik|D7Bwg0575e|Pis|Pis1	CDP-diacylglycerol--inositol 3-phosphatidyltransferase (phosphatidylinositol synthase)	protein-coding
mm_3178.1	chr1	135751092	135751107	+	1	NA	exon (NM_007791, exon 6 of 6)	exon (NM_007791, exon 6 of 6)	-14986	NM_013750	27280	Mm.34346	NM_013750	ENSMUSG00000041801	Phlda3	Tih1	pleckstrin homology like domain, family A, member 3	protein-coding
mm_13182.1	chr2	93030424	93030445	+	1	NA	non-coding (NR_110333, exon 3 of 6)	non-coding (NR_110333, exon 3 of 6)	1086	NR_110333	433456	Mm.235231	NM_001002794	ENSMUSG00000075027	4631405J19Rik	-	RIKEN cDNA 4631405J19 gene	ncRNA
mm_29443.1	chr3	110143681	110143691	-	1	NA	promoter-TSS (NM_001163350)	promoter-TSS (NM_001163350)	-214	NM_030699	80883	Mm.39262	NM_030699	ENSMUSG00000059857	Ntng1	A930010C08Rik|AI853992|Lmnt1	netrin G1	protein-coding
mm_97219.1	chr11	75631087	75631100	+	1	NA	promoter-TSS (NM_008916)	promoter-TSS (NM_008916)	73	NM_008916	19062	Mm.1458	NM_008916	ENSMUSG00000006127	Inpp5k	C62|Pps|SKIP	inositol polyphosphate 5-phosphatase K	protein-coding
mm_22583.1	chr3	13471609	13471635	+	1	NA	promoter-TSS (NM_001163328)	promoter-TSS (NM_001163328)	-33	NM_178631	76897	Mm.422625	NM_178631	ENSMUSG00000039717	Ralyl	0710005M24Rik	RALY RNA binding protein-like	protein-coding
mm_15431.1	chr2	157135802	157135806	+	1	NA	promoter-TSS (NM_001139520)	promoter-TSS (NM_001139520)	-582	NM_018851	56045	Mm.248478	NM_018851	ENSMUSG00000027639	Samhd1	E330031J07Rik|Mg11	SAM domain and HD domain, 1	protein-coding
mm_1691.1	chr1	75141788	75141798	+	1	NA	promoter-TSS (NM_170755)	promoter-TSS (NM_170755)	575	NM_026977	69171	Mm.28193	NM_026977	ENSMUSG00000033159	Cnppd1	1810031K17Rik|AU043960	cyclin Pas1/PHO80 domain containing 1	protein-coding
mm_161011.1	chr11	118513302	118513302	-	1	NA	exon (NM_001039167, exon 5 of 15)	exon (NM_001039167, exon 5 of 15)	36342	NM_172573	217364	Mm.473963	NM_172573	ENSMUSG00000033857	Engase	C130099A03|D230014K01Rik	endo-beta-N-acetylglucosaminidase	protein-coding
mm_106529.1	chr11	120572916	120572921	-	1	NA	promoter-TSS (NM_011032)	promoter-TSS (NM_011032)	18	NM_011032	18453	Mm.16660	NM_011032	ENSMUSG00000025130	P4hb	ERp59|PDI|Pdia1|Thbp	prolyl 4-hydroxylase, beta polypeptide	protein-coding
mm_105111.1	chr11	100970606	100970631	-	1	NA	promoter-TSS (NM_008986)	promoter-TSS (NM_008986)	-1	NM_008986	19285	Mm.21864	NM_008986	ENSMUSG00000004044	Ptrf	2310075E07Rik|AW546441|Cav-p60|Cavin	polymerase I and transcript release factor	protein-coding
mm_79619.1	chr9	58803526	58803537	+	1	NA	Intergenic	Intergenic	-19981	NM_001081192	330953	Mm.151967	NM_001081192	ENSMUSG00000032338	Hcn4	Bcng3|Hcn3	hyperpolarization-activated, cyclic nucleotide-gated K+ 4	protein-coding
mm_72772.1	chr8	86064800	86064803	+	1	NA	Intergenic	Intergenic	223799	NM_199446	102093	Mm.237296	NM_199446	ENSMUSG00000036879	Phkb	AI463271	phosphorylase kinase beta	protein-coding
mm_62589.1	chr7	105640523	105640586	+	1	NA	promoter-TSS (NM_019502)	promoter-TSS (NM_019502)	14	NM_019502	14356	Mm.220330	NM_019502	ENSMUSG00000089847	Timm10b	Fxc1|Tim10b|Tim9b	translocase of inner mitochondrial membrane 10B	protein-coding
mm_117791.1	chr13	97137923	97137942	-	1	NA	promoter-TSS (NM_001271464)	promoter-TSS (NM_001271464)	-5	NM_001146043	320806	Mm.219675	NM_177266	ENSMUSG00000021666	Gfm2	6530419G12Rik|A930009M04Rik|EF-G2mt|EFG2|MST027|RRF2mt	G elongation factor, mitochondrial 2	protein-coding
mm_7955.1	chr1	133921362	133921392	-	1	NA	promoter-TSS (NM_054077)	promoter-TSS (NM_054077)	24	NM_054077	116847	Mm.214514	NM_054077	ENSMUSG00000041577	Prelp	7330409J17Rik|SLRR2A	proline arginine-rich end leucine-rich repeat	protein-coding
mm_56474.1	chr6	99044415	99044426	-	1	NA	intron (NM_001347345, intron 6 of 19)	intron (NM_001347345, intron 6 of 19)	-16122	NM_001197322	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_15151.1	chr2	154000438	154000461	+	1	NA	TTS (NM_001080811)	TTS (NM_001080811)	-7827	NM_008953	19194	Mm.29197	NM_008953	ENSMUSG00000042459	Bpifa2	Bpifa2e|Psp	BPI fold containing family A, member 2	protein-coding
mm_16709.1	chr2	7085602	7085619	-	1	NA	intron (NM_001110231, intron 3 of 15)	(TATG)n|Simple_repeat|Simple_repeat	-4308	NM_001160292	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_46216.1	chr5	98513192	98513233	-	1	NA	intron (NM_001024614, intron 3 of 5)	RLTR11A2|LTR|ERVK	-37548	NR_030484	735265		NR_030484	ENSMUSG00000105814	Mir703	Mirn703|mir-703|mmu-mir-703	microRNA 703	ncRNA
mm_17261.1	chr2	25983178	25983234	-	1	NA	promoter-TSS (NM_001276361)	promoter-TSS (NM_001276361)	76	NM_001276360	227634	Mm.36834	NM_001115076	ENSMUSG00000026933	Camsap1	9530003A05Rik|C77823|PRO2405	calmodulin regulated spectrin-associated protein 1	protein-coding
mm_166615.1	chr6	71371308	71371323	+	1	NA	Intergenic	B4A|SINE|B4	-2112	NM_009857	12525	Mm.1858	NM_009857	ENSMUSG00000053977	Cd8a	BB154331|Ly-2|Ly-35|Ly-B|Lyt-2	CD8 antigen, alpha chain	protein-coding
mm_170727.1	chr2	150933496	150933509	+	1	NA	Intergenic	Intergenic	23908	NM_001163476	69270	Mm.271603	NM_027014	ENSMUSG00000027454	Gins1	2810418N01Rik|Gins4|PSF1|mKIAA0186	GINS complex subunit 1 (Psf1 homolog)	protein-coding
mm_120725.1	chr14	73138814	73138832	+	1	NA	Intergenic	Intergenic	-3687	NM_001170694	105670	Mm.280068	NM_134083	ENSMUSG00000022106	Rcbtb2	2610028E02Rik|2810420M18Rik|AI448345|AW240694|Chc1l|RC/BTB2	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 2	protein-coding
mm_119762.1	chr14	54171801	54171811	+	1	NA	Intergenic	Intergenic	82123	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_71903.1	chr8	70072811	70072822	+	1	NA	promoter-TSS (NM_001293795)	promoter-TSS (NM_001293795)	-108	NM_001293795	107770	Mm.37974	NM_181540	ENSMUSG00000036151	Tm6sf2	-	transmembrane 6 superfamily member 2	protein-coding
mm_97235.1	chr11	75655929	75655937	+	1	NA	promoter-TSS (NM_001080775)	promoter-TSS (NM_001080775)	-82	NM_001080775	17913	Mm.234502	NM_008659	ENSMUSG00000017774	Myo1c	C80397|MMIb|MYO1E|NMI|mm1beta|myr2	myosin IC	protein-coding
mm_38070.1	chr4	134098668	134098676	-	1	NA	Intergenic	Intergenic	-3599	NM_013706	23833	Mm.24130	NM_013706	ENSMUSG00000000682	Cd52	AI463198|B7|B7-Ag|CAMPATH-1|CLS1|MB7	CD52 antigen	protein-coding
mm_143028.1	chr17	56609676	56609686	-	1	NA	promoter-TSS (NM_153152)	promoter-TSS (NM_153152)	90	NM_153152	224904	Mm.34002	NM_153152	ENSMUSG00000049760	2410015M20Rik	Mic13|QIL1|sr104	RIKEN cDNA 2410015M20 gene	protein-coding
mm_148162.1	chr18	77713979	77714002	-	1	NA	promoter-TSS (NM_178670)	promoter-TSS (NM_178670)	20	NM_178670	212163	Mm.23293	NM_178670	ENSMUSG00000047466	8030462N17Rik	Akd2|Ark2N	RIKEN cDNA 8030462N17 gene	protein-coding
mm_99024.1	chr11	98937670	98937735	+	1	NA	promoter-TSS (NM_009024)	promoter-TSS (NM_009024)	6	NM_009024	19401	Mm.439744	NM_009024	ENSMUSG00000037992	Rara	Nr1b1|RAR|RARalpha1	retinoic acid receptor, alpha	protein-coding
mm_127543.1	chr15	102113026	102113061	+	1	NA	exon (NM_153533, exon 20 of 29)	exon (NM_153533, exon 20 of 29)	10055	NM_153533	209039	Mm.29389	NM_153533	ENSMUSG00000037003	Tns2	C1-ten|Tenc1|nep|nph	tensin 2	protein-coding
mm_26176.1	chr3	138288845	138288856	+	1	NA	exon (NM_007409, exon 7 of 9)	exon (NM_007409, exon 7 of 9)	11205	NM_007409	11522	Mm.2409	NM_007409	ENSMUSG00000074207	Adh1	ADH-AA|AI194826|Adh-1|Adh-1-t|Adh-1e|Adh-1t|Adh-3e|Adh1-e|Adh1-t|Adh1tl|Adh3-e	alcohol dehydrogenase 1 (class I)	protein-coding
mm_164222.1	chr15	85121815	85121818	-	1	NA	exon (NM_080470, exon 6 of 25)	exon (NM_080470, exon 6 of 25)	10141	NM_080470	140557	Mm.182737	NM_080470	ENSMUSG00000022432	Smc1b	SMC-1B|SMC1beta|Smc1l2	structural maintenance of chromosomes 1B	protein-coding
mm_138908.1	chr17	43592525	43592533	+	1	NA	intron (NM_013737, intron 2 of 11)	intron (NM_013737, intron 2 of 11)	-1020	NR_045444	73504	Mm.9277	NR_045444	ENSMUSG00000090307	1700071M16Rik	-	RIKEN cDNA 1700071M16 gene	ncRNA
mm_119728.1	chr14	54074968	54074981	+	1	NA	Intergenic	Intergenic	178955	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_62298.1	chr7	100100288	100100334	+	1	NA	intron (NM_133692, intron 6 of 11)	intron (NM_133692, intron 6 of 11)	21189	NM_133692	67967	Mm.37562	NM_133692	ENSMUSG00000030726	Pold3	2410142G14Rik|C85233|P66|P68	polymerase (DNA-directed), delta 3, accessory subunit	protein-coding
mm_145484.1	chr18	60382715	60382747	+	1	NA	5' UTR (NM_001146275, exon 2 of 3)	5' UTR (NM_001146275, exon 2 of 3)	6702	NM_001146275	60440	Mm.261140	NM_021792	ENSMUSG00000054072	Iigp1	2900074L10Rik|AI046432|AW111922|Ifgga1|Iigp|Irga6	interferon inducible GTPase 1	protein-coding
mm_64645.1	chr7	4024508	4024534	-	1	NA	intron (NM_001302676, intron 1 of 5)	(A)n|Simple_repeat|Simple_repeat	38683	NM_001302677	52855	Mm.290880	NM_178611	ENSMUSG00000055541	Lair1	5133400O11Rik|BB115266|D7Bwg0421e|Lair-1	leukocyte-associated Ig-like receptor 1	protein-coding
mm_4462.1	chr1	172930039	172930053	+	1	NA	Intergenic	MTE-int|LTR|ERVL-MaLR	-26722	NM_008763	18313	Mm.377103	NM_008763	ENSMUSG00000037924	Olfr16	MOR23|MOR26713	olfactory receptor 16	protein-coding
mm_10323.1	chr2	11250476	11250485	+	1	NA	intron (NM_008859, intron 8 of 17)	intron (NM_008859, intron 8 of 17)	78098	NM_008859	18761	Mm.329993	NM_008859	ENSMUSG00000026778	Prkcq	A130035A12Rik|AW494342|PKC-0|PKC-theta|PKCtheta|Pkcq	protein kinase C, theta	protein-coding
mm_87159.1	chr10	36628264	36628280	+	1	NA	5' UTR (NM_001253356, exon 2 of 5)	5' UTR (NM_001253356, exon 2 of 5)	121465	NM_001253356	319415	Mm.332442	NM_001081208	ENSMUSG00000044499	Hs3st5	D930005L05Rik|Gm1151|Hs3ost5	heparan sulfate (glucosamine) 3-O-sulfotransferase 5	protein-coding
mm_94561.1	chr11	11684951	11684955	+	1	NA	promoter-TSS (NM_009578)	promoter-TSS (NM_009578)	-972	NM_009578	22778	Mm.103545	NM_009578	ENSMUSG00000018654	Ikzf1	5832432G11Rik|Ikaros|LyF-1|Zfpn1a1|Znfn1a1|hlk-1|mKIAA4227	IKAROS family zinc finger 1	protein-coding
mm_136808.1	chr17	12384391	12384404	+	1	NA	exon (NM_008877, exon 3 of 19)	exon (NM_008877, exon 3 of 19)	5788	NM_008877	18815	Mm.971	NM_008877	ENSMUSG00000059481	Plg	AI649309|Pg	plasminogen	protein-coding
mm_35631.1	chr4	43499618	43499677	-	1	NA	promoter-TSS (NM_001013377)	promoter-TSS (NM_001013377)	13	NM_001013377	230098	Mm.331567	NM_001013377	ENSMUSG00000051517	Arhgef39	E130306D19Rik	Rho guanine nucleotide exchange factor (GEF) 39	protein-coding
mm_122651.1	chr14	51910706	51910739	-	1	NA	exon (NM_001145959, exon 3 of 15)	exon (NM_001145959, exon 3 of 15)	2766	NM_001145959	29811	Mm.26722	NM_013864	ENSMUSG00000004558	Ndrg2	AI182517|AU040374|Ndr2|SYLD	N-myc downstream regulated gene 2	protein-coding
mm_59489.1	chr7	27497336	27497346	+	1	NA	Intergenic	Intergenic	-1983	NM_198048	19153	Mm.10119	NM_019412	ENSMUSG00000053198	Prx	L-Periaxin	periaxin	protein-coding
mm_135962.1	chr16	74760712	74760725	-	1	NA	Intergenic	Intergenic	-349806	NM_175549	268902	Mm.171736	NM_175549	ENSMUSG00000052516	Robo2	2600013A04Rik|9430089E08Rik|BB097918|D230004I22Rik|mKIAA1568	roundabout guidance receptor 2	protein-coding
mm_149751.1	chr19	22692601	22692609	+	1	NA	promoter-TSS (NM_001035246)	promoter-TSS (NM_001035246)	-14	NM_001035245	226025	Mm.131943	NM_177341	ENSMUSG00000052387	Trpm3	6330504P12Rik|9330180E14|AU018608|B930001P07Rik|LTRPC3|MLSN2	transient receptor potential cation channel, subfamily M, member 3	protein-coding
mm_3699.1	chr1	153762548	153762574	+	1	NA	3' UTR (NM_011882, exon 9 of 9)	3' UTR (NM_011882, exon 9 of 9)	13135	NM_011882	24014	Mm.259254	NM_011882	ENSMUSG00000066800	Rnasel	E230029I04Rik	ribonuclease L (2', 5'-oligoisoadenylate synthetase-dependent)	protein-coding
mm_31548.1	chr4	55651678	55651712	+	1	NA	Intergenic	CpG	-119220	NM_010637	16600	Mm.4325	NM_010637	ENSMUSG00000003032	Klf4	EZF|Gklf|Zie	Kruppel-like factor 4 (gut)	protein-coding
mm_163064.1	chr11	66956593	66956597	+	1	NA	promoter-TSS (NR_130315)	promoter-TSS (NR_130315)	-43	NR_130645	71576	Mm.340077	NR_130315	ENSMUSG00000085683	9130409J20Rik	-	RIKEN cDNA 9130409J20 gene	ncRNA
mm_147546.1	chr18	54840032	54840040	-	1	NA	Intergenic	Intergenic	150144	NM_175751	269023	Mm.192984	NM_175751	ENSMUSG00000052713	Zfp608	4932417D18Rik|D430007A19Rik|Znf608	zinc finger protein 608	protein-coding
mm_43823.1	chr5	142961189	142961200	+	1	NA	exon (NM_007984, exon 1 of 5)	exon (NM_007984, exon 1 of 5)	839	NM_007984	14086	Mm.289707	NM_007984	ENSMUSG00000029581	Fscn1	AI663989|Fan1|fascin-1	fascin actin-bundling protein 1	protein-coding
mm_41447.1	chr5	90905351	90905374	+	1	NA	3' UTR (NM_009140, exon 4 of 4)	3' UTR (NM_009140, exon 4 of 4)	1463	NM_009140	20310	Mm.4979	NM_009140	ENSMUSG00000058427	Cxcl2	CINC-2a|GROb|Gro2|MIP-2|MIP-2a|Mgsa-b|Mip2|Scyb|Scyb2	chemokine (C-X-C motif) ligand 2	protein-coding
mm_36044.1	chr4	57262662	57262670	-	1	NA	intron (NM_011207, intron 4 of 25)	intron (NM_011207, intron 4 of 25)	39171	NM_011207	545622	Mm.246552	NM_011207	ENSMUSG00000038764	Ptpn3	9530011I20Rik|PTP-H1|PTPCL	protein tyrosine phosphatase, non-receptor type 3	protein-coding
mm_4756.1	chr1	182288082	182288118	+	1	NA	Intergenic	LTR33A_|LTR|ERVL	-5341	NM_007853	13244	Mm.29648	NM_007853	ENSMUSG00000038633	Degs1	AA536663|Degs|Des1|Mdes	delta(4)-desaturase, sphingolipid 1	protein-coding
mm_109675.1	chr12	113074806	113074818	+	1	NA	TTS (NM_001291445)	TTS (NM_001291445)	310	NM_029381	75671	Mm.23377	NM_029381	ENSMUSG00000012211	Tex22	1700028O09Rik|AV210422|Tep22	testis expressed gene 22	protein-coding
mm_71690.1	chr8	61293780	61293783	+	1	NA	intron (NM_021506, intron 2 of 11)	intron (NM_021506, intron 2 of 11)	-4909	NR_045475	69279	Mm.417857	NR_045475	ENSMUSG00000099419	1700001D01Rik	-	RIKEN cDNA 1700001D01 gene	ncRNA
mm_45278.1	chr5	64865546	64865560	-	1	NA	Intergenic	Intergenic	62030	NM_008453	16599	Mm.392759	NM_008453	ENSMUSG00000029178	Klf3	9930027G08Rik|AL024007|Bklf|Tef-2	Kruppel-like factor 3 (basic)	protein-coding
mm_9507.1	chr1	173738111	173738122	-	1	NA	intron (NM_001204910, intron 1 of 7)	intron (NM_001204910, intron 1 of 7)	3693	NM_001204910	226691	Mm.440876	NM_001204910	ENSMUSG00000073490	Ifi207	AI607873|Pyhin-A	interferon activated gene 207	protein-coding
mm_80949.1	chr9	102864513	102864523	+	1	NA	intron (NM_001042607, intron 2 of 14)	intron (NM_001042607, intron 2 of 14)	29598	NM_001042607	20187	Mm.335391	NM_013649	ENSMUSG00000032547	Ryk	AW536699|ERK-3|Vik	receptor-like tyrosine kinase	protein-coding
mm_72560.1	chr8	84073940	84073946	+	1	NA	exon (NM_009055, exon 2 of 21)	exon (NM_009055, exon 2 of 21)	7107	NM_009055	19724	Mm.7892	NM_009055	ENSMUSG00000031706	Rfx1	AI047719|AI385641	regulatory factor X, 1 (influences HLA class II expression)	protein-coding
mm_72768.1	chr8	85700997	85701025	+	1	NA	TTS (NR_106189)	TTS (NR_106189)	106	NR_106189	102465898		NR_106189	ENSMUSG00000098388	Mir8109	Gm27495|mmu-mir-8109	microRNA 8109	ncRNA
mm_9585.1	chr1	174031713	174031728	-	1	NA	promoter-TSS (NM_172648)	promoter-TSS (NM_172648)	35	NM_172648	226695	Mm.425061	NM_172648	ENSMUSG00000054203	Ifi205	D3|D3cDNA|Ifi205a	interferon activated gene 205	protein-coding
mm_3622.1	chr1	152750528	152750553	+	1	NA	promoter-TSS (NM_001081197)	promoter-TSS (NM_001081197)	-11	NM_001081197	71281	Mm.158650	NM_001081197	ENSMUSG00000055547	Apobec4	4933431M11Rik	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 4 (putative)	protein-coding
mm_95264.1	chr11	44962905	44962910	+	1	NA	intron (NM_007897, intron 10 of 15)	intron (NM_007897, intron 10 of 15)	154021	NR_045100	100504255	Mm.123608	NR_045100	ENSMUSG00000084773	Gm12159	OTTMUSG00000005475	predicted gene 12159	ncRNA
mm_82702.1	chr9	22468255	22468277	-	1	NA	promoter-TSS (NM_018739)	promoter-TSS (NM_018739)	90	NM_018739	55934	Mm.38235	NM_018739	ENSMUSG00000032239	Rp9	PAP-1|Rp9h	retinitis pigmentosa 9 (human)	protein-coding
mm_150728.1	chr19	43689673	43689695	+	1	NA	promoter-TSS (NM_053103)	promoter-TSS (NM_053103)	-5	NM_053103	93685	Mm.248237	NM_053103	ENSMUSG00000025192	Entpd7	1810012B13Rik|1810020C02Rik|2810003F23Rik|LALP1|Lysal2	ectonucleoside triphosphate diphosphohydrolase 7	protein-coding
mm_80581.1	chr9	84104229	84104233	+	1	NA	intron (NM_001305935, intron 9 of 10)	(CA)n|Simple_repeat|Simple_repeat	155450	NM_199195	12040	Mm.12819	NM_199195	ENSMUSG00000032263	Bckdhb	BCKDE1B|BCKDH E1-beta	branched chain ketoacid dehydrogenase E1, beta polypeptide	protein-coding
mm_40289.1	chr5	43233887	43233895	+	1	NA	exon (NM_001177379, exon 1 of 11)	exon (NM_001177379, exon 1 of 11)	428	NM_001177379	231207	Mm.7233	NM_175937	ENSMUSG00000039782	Cpeb2	A630055H10Rik|Cpe-bp2	cytoplasmic polyadenylation element binding protein 2	protein-coding
mm_117218.1	chr13	64107182	64107192	-	1	NA	intron (NM_001001321, intron 7 of 11)	intron (NM_001001321, intron 7 of 11)	-17986	NM_008291	15487	Mm.5109	NM_008291	ENSMUSG00000033122	Hsd17b3	-	hydroxysteroid (17-beta) dehydrogenase 3	protein-coding
mm_151719.1	chr19	4801357	4801370	-	1	NA	3' UTR (NM_019869, exon 3 of 3)	3' UTR (NM_019869, exon 3 of 3)	-7354	NM_001290123	19653	Mm.426069	NM_009032	ENSMUSG00000094936	Rbm4	4921506I22Rik|Lark1|Mlark|Rbm4a|lark	RNA binding motif protein 4	protein-coding
mm_26145.1	chr3	138065170	138065197	+	1	NA	intron (NR_037975, intron 1 of 3)	intron (NR_037975, intron 1 of 3)	2205	NR_037975	329763	Mm.169710	NM_177860	ENSMUSG00000049349	Gm5105	D830013H12|EG329763	predicted gene 5105	ncRNA
mm_56411.1	chr6	97212290	97212300	-	1	NA	intron (NM_022992, intron 1 of 2)	intron (NM_022992, intron 1 of 2)	1503	NM_022992	65106	Mm.291014	NM_022992	ENSMUSG00000035199	Arl6ip5	5930404D22Rik|AV001879|Aip-5|Gtrap3-18|addiscin	ADP-ribosylation factor-like 6 interacting protein 5	protein-coding
mm_48681.1	chr5	146261344	146261362	-	1	NA	intron (NM_153599, intron 2 of 12)	LSU-rRNA_Hsa|rRNA|rRNA	29678	NM_153599	264064	Mm.260576	NM_153599	ENSMUSG00000029635	Cdk8	-	cyclin-dependent kinase 8	protein-coding
mm_25594.1	chr3	116899803	116899822	+	1	NA	intron (NM_009146, intron 12 of 16)	intron (NM_009146, intron 12 of 16)	38132	NM_009146	20321	Mm.66293	NM_009146	ENSMUSG00000033386	Frrs1	AI131732|Sdfr2	ferric-chelate reductase 1	protein-coding
mm_128875.1	chr15	73038791	73038815	-	1	NA	intron (NM_180662, intron 4 of 21)	L1MB8|LINE|L1	17009	NM_029640	76510	Mm.158902	NM_029640	ENSMUSG00000047921	Trappc9	1810044A24Rik|2900005P22Rik|4632408O18Rik|Ibp|Nibp|TRS130|mKIAA1882	trafficking protein particle complex 9	protein-coding
mm_10132.1	chr2	4017707	4017722	+	1	NA	promoter-TSS (NM_001347086)	promoter-TSS (NM_001347086)	31	NM_001347086	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding
mm_121054.1	chr14	86172929	86172946	+	1	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	-73033	NR_040457	75155	Mm.399239	NR_040457		4930529K09Rik	4930507G21Rik	RIKEN cDNA 4930529K09 gene	ncRNA
mm_101815.1	chr11	46389472	46389505	-	1	NA	promoter-TSS (NM_001281968)	promoter-TSS (NM_001281968)	27	NM_001281968	16428	Mm.339927	NM_010583	ENSMUSG00000020395	Itk	Emt|Tcsk|Tsk	IL2 inducible T cell kinase	protein-coding
mm_2370.1	chr1	93227520	93227530	+	1	NA	intron (NM_001310428, intron 31 of 31)	intron (NM_001310428, intron 31 of 31)	-8372	NM_172463	208777	Mm.271897	NM_172463	ENSMUSG00000047793	Sned1	6720455I24Rik|AI197264|AI642697|D430044C15Rik|SST3|Snep	sushi, nidogen and EGF-like domains 1	protein-coding
mm_8463.1	chr1	153302452	153302459	-	1	NA	intron (NM_010683, intron 1 of 27)	intron (NM_010683, intron 1 of 27)	30331	NM_010683	226519	Mm.1249	NM_010683	ENSMUSG00000026478	Lamc1	Lamb2	laminin, gamma 1	protein-coding
mm_100135.1	chr11	115974908	115974917	+	1	NA	5' UTR (NM_133663, exon 1 of 39)	5' UTR (NM_133663, exon 1 of 39)	187	NM_133663	192897	Mm.213873	NM_133663	ENSMUSG00000020758	Itgb4	AA407042|C230078O20|CD104	integrin beta 4	protein-coding
mm_72439.1	chr8	83155772	83155793	+	1	NA	Intergenic	Intergenic	-9570	NM_001111304	71310	Mm.24031	NM_027758	ENSMUSG00000031709	Tbc1d9	4933431N12Rik|AI847101|AW490653|C76116	TBC1 domain family, member 9	protein-coding
mm_75431.1	chr8	47288448	47288476	-	1	NA	5' UTR (NM_001286376, exon 1 of 5)	5' UTR (NM_001286376, exon 1 of 5)	940	NM_001286376	71069	Mm.23973	NM_175162	ENSMUSG00000038143	Stox2	4933409N07Rik|AI449080|AI835114|mKIAA1392	storkhead box 2	protein-coding
mm_50557.1	chr6	49047806	49047813	+	1	NA	exon (NM_053110, exon 6 of 11)	exon (NM_053110, exon 6 of 11)	11291	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_35683.1	chr4	43669205	43669215	-	1	NA	promoter-TSS (NM_175517)	promoter-TSS (NM_175517)	239	NM_001085508	242409	Mm.171489	NM_001085508	ENSMUSG00000078716	Tmem8b	4930500O05Rik	transmembrane protein 8B	protein-coding
mm_152739.1	chr19	19005240	19005262	-	1	NA	intron (NM_001043354, intron 1 of 9)	MER5A|DNA|hAT-Charlie	-4134	NM_001289921	225998	Mm.234641	NM_146095	ENSMUSG00000036192	Rorb	Nr1f2|RZR-beta|RZRB|Rorbeta|hstp	RAR-related orphan receptor beta	protein-coding
mm_1596.1	chr1	74375236	74375257	+	1	NA	promoter-TSS (NM_013612)	promoter-TSS (NM_013612)	43	NM_013612	18173	Mm.2913	NM_013612	ENSMUSG00000026177	Slc11a1	Bcg|Ity|Ity1|Lsh|Nramp|Nramp1|ity	solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1	protein-coding
mm_4901.1	chr1	189827214	189827228	+	1	NA	intron (NM_008976, intron 5 of 18)	intron (NM_008976, intron 5 of 18)	95067	NM_026796	226830	Mm.156895	NM_026796	ENSMUSG00000026603	Smyd2	1110020E07Rik|4930402C15|KMT3C|Zmynd14	SET and MYND domain containing 2	protein-coding
mm_29100.1	chr3	104818083	104818105	-	1	NA	exon (NM_001163440, exon 2 of 21)	exon (NM_001163440, exon 2 of 21)	211	NM_008619	17454	Mm.1597	NM_008619	ENSMUSG00000002227	Mov10	C77703|Mov-10	Moloney leukemia virus 10	protein-coding
mm_42735.1	chr5	120630083	120630089	+	1	NA	exon (NM_001195094, exon 5 of 7)	exon (NM_001195094, exon 5 of 7)	4149	NM_001195094	546886	Mm.464847	NM_001195094	ENSMUSG00000094282	Cfap73	Ccdc42b|Gm5988	cilia and flagella associated protein 73	protein-coding
mm_111585.1	chr12	101886941	101886955	-	1	NA	exon (NM_028446, exon 10 of 21)	exon (NM_028446, exon 10 of 21)	26223	NM_028446	109181	Mm.208618	NM_028446	ENSMUSG00000021188	Trip11	2610511G22Rik|3110031G15Rik|6030460N08Rik|AI450776|GMAP-210|TRIP230	thyroid hormone receptor interactor 11	protein-coding
mm_154684.1	chrX	7922295	7922319	+	1	NA	exon (NM_013892, exon 2 of 3)	exon (NM_013892, exon 2 of 3)	2485	NM_013892	30052	Mm.4881	NM_013892	ENSMUSG00000039278	Pcsk1n	AI848336|KEP|PEN|PEN19|PEN20|Pan3|SAAS|SAASCT|bLEN|lLEN|proSAAS	proprotein convertase subtilisin/kexin type 1 inhibitor	protein-coding
mm_50937.1	chr6	57703061	57703093	+	1	NA	exon (NM_133737, exon 1 of 9)	exon (NM_133737, exon 1 of 9)	622	NM_133737	71835	Mm.274904	NM_133737	ENSMUSG00000062190	Lancl2	1700003F10Rik	LanC (bacterial lantibiotic synthetase component C)-like 2	protein-coding
mm_69009.1	chr7	126704128	126704172	-	1	NA	promoter-TSS (NM_001301374)	promoter-TSS (NM_001301374)	70	NM_001301374	12721	Mm.290482	NM_009898	ENSMUSG00000030707	Coro1a	Clabp|Lmb3|TACO|p57	coronin, actin binding protein 1A	protein-coding
mm_107958.1	chr12	72620674	72620716	+	1	NA	Intergenic	Intergenic	44133	NM_025522	66375	Mm.289653	NM_025522	ENSMUSG00000021094	Dhrs7	2310016E22Rik|5730564L20Rik|AW061210|Retdsr4|Retsdr4	dehydrogenase/reductase (SDR family) member 7	protein-coding
mm_162356.1	chr1	58449527	58449532	+	1	NA	intron (NM_022988, intron 2 of 6)	RSINE1|SINE|B4	-4043	NM_001285827	70225	Mm.340195	NM_027351	ENSMUSG00000026035	Ppil3	2310076N22Rik|2510026K04Rik|Cyp10l	peptidylprolyl isomerase (cyclophilin)-like 3	protein-coding
mm_64025.1	chr7	140764912	140764932	+	1	NA	exon (NM_021282, exon 2 of 9)	exon (NM_021282, exon 2 of 9)	1090	NM_021282	13106	Mm.21758	NM_021282	ENSMUSG00000025479	Cyp2e1	Cyp2e	cytochrome P450, family 2, subfamily e, polypeptide 1	protein-coding
mm_153201.1	chr19	34629853	34629870	-	1	NA	intron (NM_053217, intron 1 of 2)	intron (NM_053217, intron 1 of 2)	10882	NM_053217	112419	Mm.440727	NM_053217	ENSMUSG00000067297	Ifit1bl2	2010002M12Rik|AW412491|Ifit1b	interferon induced protein with tetratricopeptide repeats 1B like 2	protein-coding
mm_81046.1	chr9	105470536	105470540	+	1	NA	intron (NM_001253831, intron 1 of 26)	intron (NM_001253831, intron 1 of 26)	24595	NM_175025	235574	Mm.326247	NM_175025	ENSMUSG00000032570	Atp2c1	1700121J11Rik|ATP2C1A|AW061228|BCPM|D930003G21Rik|HHD|SPCA|pmr1	ATPase, Ca++-sequestering	protein-coding
mm_96398.1	chr11	67250565	67250569	+	1	NA	exon (NM_010855, exon 21 of 40)	exon (NM_010855, exon 21 of 40)	12755	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_82875.1	chr9	32451379	32451385	-	1	NA	intron (NM_008026, intron 5 of 8)	(TG)n|Simple_repeat|Simple_repeat	57397	NM_001168354	56379	Mm.390168	NM_019659	ENSMUSG00000041248	Kcnj1	Kir1.1|ROMK|Romk2	potassium inwardly-rectifying channel, subfamily J, member 1	protein-coding
mm_53742.1	chr6	145160898	145160909	+	1	NA	exon (NM_001281981, exon 12 of 20)	exon (NM_001281981, exon 12 of 20)	39164	NM_008511	16970	Mm.843	NM_008511	ENSMUSG00000030263	Lrmp	D6Int3|D6Int4|D6Int5|D6Int7|D6Int8|Jaw1	lymphoid-restricted membrane protein	protein-coding
mm_35273.1	chr4	19920193	19920208	-	1	NA	intron (NM_175406, intron 1 of 7)	B4A|SINE|B4	2366	NM_175406	242341	Mm.19298	NM_175406	ENSMUSG00000028238	Atp6v0d2	1620401A02Rik|AI324824|V-ATPase	ATPase, H+ transporting, lysosomal V0 subunit D2	protein-coding
mm_89524.1	chr10	94406189	94406225	+	1	NA	Intergenic	MER113|DNA|hAT-Charlie	-107504	NR_033209	215472	Mm.255656	NM_174999	ENSMUSG00000053420	Gm4792	E130012K09|EG215472	predicted gene 4792	ncRNA
mm_141019.1	chr17	25129338	25129349	-	1	NA	Intergenic	Intergenic	-4048	NM_011930	26373	Mm.270587	NM_011930	ENSMUSG00000036636	Clcn7	ClC-7|D17Wsu51e	chloride channel, voltage-sensitive 7	protein-coding
mm_75587.1	chr8	61574146	61574149	-	1	NA	intron (NM_001293772, intron 10 of 21)	B4A|SINE|B4	17022	NM_001293774	72333	Mm.29933	NM_001081390	ENSMUSG00000058056	Palld	2410003B16Rik|6030492A02	palladin, cytoskeletal associated protein	protein-coding
mm_124280.1	chr14	103048364	103048382	-	1	NA	intron (NM_008392, intron 1 of 4)	intron (NM_008392, intron 1 of 4)	1361	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_62529.1	chr7	102238091	102238115	+	1	NA	non-coding (NR_111938, exon 5 of 5)	non-coding (NR_111938, exon 5 of 5)	12015	NM_019566	56212	Mm.259795	NM_019566	ENSMUSG00000073982	Rhog	2810426G09Rik|Arhg|Sid10750	ras homolog family member G	protein-coding
mm_99083.1	chr11	99417142	99417152	+	1	NA	intron (NM_010661, intron 6 of 7)	intron (NM_010661, intron 6 of 7)	5112	NM_010661	268482	Mm.436651	NM_010661	ENSMUSG00000020912	Krt12	AI835216|K12|Krt-12|Krt1-12	keratin 12	protein-coding
mm_105313.1	chr11	102880926	102880977	-	1	NA	promoter-TSS (NM_001109995)	promoter-TSS (NM_001109995)	24	NM_011431	20624	Mm.873	NM_011431	ENSMUSG00000020929	Eftud2	116kDa|Snrp116|U5-116kD	elongation factor Tu GTP binding domain containing 2	protein-coding
mm_46622.1	chr5	108390955	108390958	-	1	NA	intron (NM_008806, intron 1 of 21)	intron (NM_008806, intron 1 of 21)	2583	NM_008806	18587	Mm.1372	NM_008806	ENSMUSG00000029491	Pde6b	Pdeb|r|rd|rd-1|rd1|rd10	phosphodiesterase 6B, cGMP, rod receptor, beta polypeptide	protein-coding
mm_14707.1	chr2	143063032	143063077	+	1	NA	promoter-TSS (NM_021335)	promoter-TSS (NM_021335)	-15	NM_021335	20639	Mm.1323	NM_021335	ENSMUSG00000008333	Snrpb2	2810052G09Rik	U2 small nuclear ribonucleoprotein B	protein-coding
mm_5448.1	chr1	36244123	36244131	-	1	NA	exon (NM_198899, exon 1 of 41)	exon (NM_198899, exon 1 of 41)	175	NM_198899	320011	Mm.261022	NM_198899	ENSMUSG00000037470	Uggt1	0910001L17Rik|A930007H10Rik|AA589501|AI414429|AI448372|C820010P03Rik|GT|UGT1|Ugcgl1	UDP-glucose glycoprotein glucosyltransferase 1	protein-coding
mm_73700.1	chr8	111686514	111686526	+	1	NA	TTS (NM_025583)	TTS (NM_025583)	3154	NR_106044	102466993		NR_106044	ENSMUSG00000099129	Mir7076	Gm27318|mmu-mir-7076	microRNA 7076	ncRNA
mm_45056.1	chr5	41819008	41819024	-	1	NA	exon (NM_001081422, exon 10 of 27)	exon (NM_001081422, exon 10 of 27)	25299	NM_001310601	665775	Mm.158726	NM_001081422	ENSMUSG00000061755	Bod1l	A230054D04Rik|AI853319|FAM44A|mKIAA1327	biorientation of chromosomes in cell division 1-like	protein-coding
mm_53408.1	chr6	132507759	132507762	+	1	NA	Intergenic	Intergenic	-62082	NM_011174	19131	Mm.425348	NM_011174	ENSMUSG00000059934	Prh1	MP2|Prp	proline rich protein HaeIII subfamily 1	protein-coding
mm_23163.1	chr3	40708917	40708937	+	1	NA	promoter-TSS (NM_178386)	promoter-TSS (NM_178386)	56	NM_178386	73333	Mm.78691	NM_178386	ENSMUSG00000069041	Slc25a31	1700034J06Rik|Ant4|Sfec	solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 31	protein-coding
mm_105835.1	chr11	113565741	113565792	-	1	NA	promoter-TSS (NM_027216)	promoter-TSS (NM_027216)	49	NM_001166503	69806	Mm.341021	NM_027216	ENSMUSG00000041654	Slc39a11	1810074D23Rik	solute carrier family 39 (metal ion transporter), member 11	protein-coding
mm_139377.1	chr17	51833243	51833261	+	1	NA	promoter-TSS (NM_001163632)	promoter-TSS (NM_001163632)	38	NM_001163632	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_84289.1	chr9	63149179	63149183	-	1	NA	promoter-TSS (NM_001163758)	promoter-TSS (NM_001163758)	-220	NM_001163758	207667	Mm.36349	NM_172446	ENSMUSG00000022245	Skor1	AV273001|C230094B15Rik|Corl1|Lbxcor1	SKI family transcriptional corepressor 1	protein-coding
mm_41649.1	chr5	98254147	98254158	+	1	NA	promoter-TSS (NM_001277268)	promoter-TSS (NM_001277268)	-32	NM_010203	14176	Mm.5055	NM_010203	ENSMUSG00000029337	Fgf5	Fgf-5|HBGF-5|angora|go	fibroblast growth factor 5	protein-coding
mm_135585.1	chr16	50578497	50578509	-	1	NA	Intergenic	Intergenic	-12000	NR_040566	75211	Mm.399337	NR_040566		4930542D17Rik	-	RIKEN cDNA 4930542D17 gene	ncRNA
mm_100888.1	chr11	6065540	6065635	-	1	NA	5' UTR (NM_001174054, exon 1 of 21)	5' UTR (NM_001174054, exon 1 of 21)	161	NM_001174054	12323	Mm.439733	NM_007595	ENSMUSG00000057897	Camk2b	CaMKII	calcium/calmodulin-dependent protein kinase II, beta	protein-coding
mm_4568.1	chr1	177467285	177467308	+	1	NA	Intergenic	Intergenic	21475	NM_013915	30928	Mm.330700	NM_013915	ENSMUSG00000063659	Zbtb18	RP58|Zfp238|Znf238	zinc finger and BTB domain containing 18	protein-coding
mm_63833.1	chr7	135396331	135396362	+	1	NA	Intergenic	Intergenic	-14021	NM_183193	270004	Mm.132547	NM_183193	ENSMUSG00000048377	Foxi2	B130055A05Rik	forkhead box I2	protein-coding
mm_135410.1	chr16	44999759	44999775	-	1	NA	Intergenic	Intergenic	56089	NM_001128132	74603	Mm.297337	NM_027578	ENSMUSG00000036172	Cd200r3	4733401I18Rik|4833409J19Rik|AI505817|BB106877|mCD200RLb	CD200 receptor 3	protein-coding
mm_62174.1	chr7	97400045	97400047	+	1	NA	promoter-TSS (NM_024220)	promoter-TSS (NM_024220)	43	NM_024220	68197	Mm.334031	NM_024220	ENSMUSG00000030647	Ndufc2	1810004I06Rik|2010300P09Rik|G1|R75094	NADH dehydrogenase (ubiquinone) 1, subcomplex unknown, 2	protein-coding
mm_166046.1	chr4	130914088	130914108	-	1	NA	intron (NM_010686, intron 1 of 7)	intron (NM_010686, intron 1 of 7)	764	NM_010686	16792	Mm.271868	NM_010686	ENSMUSG00000028581	Laptm5	E3	lysosomal-associated protein transmembrane 5	protein-coding
mm_35073.1	chr4	6989636	6989644	-	1	NA	intron (NM_145711, intron 1 of 8)	intron (NM_145711, intron 1 of 8)	1083	NM_145711	252838	Mm.435828	NM_145711	ENSMUSG00000041272	Tox	1700007F02Rik	thymocyte selection-associated high mobility group box	protein-coding
mm_96158.1	chr11	61486108	61486130	+	1	NA	exon (NM_029568, exon 3 of 6)	exon (NM_029568, exon 3 of 6)	675	NM_029568	76293	Mm.272278	NM_029568	ENSMUSG00000042436	Mfap4	1110007F23Rik	microfibrillar-associated protein 4	protein-coding
mm_29903.1	chr3	131470965	131470974	-	1	NA	Intergenic	Intergenic	-93799	NM_001289479	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_33511.1	chr4	130916013	130916019	+	1	NA	intron (NM_010686, intron 1 of 7)	intron (NM_010686, intron 1 of 7)	2682	NM_010686	16792	Mm.271868	NM_010686	ENSMUSG00000028581	Laptm5	E3	lysosomal-associated protein transmembrane 5	protein-coding
mm_156084.1	chrX	110811368	110811383	+	1	NA	Intergenic	Intergenic	-3004	NM_008901	18994	Mm.56946	NM_008901	ENSMUSG00000056854	Pou3f4	Brn-4|Brn4|OTF-9|Otf9|Slf|oct-9	POU domain, class 3, transcription factor 4	protein-coding
mm_62523.1	chr7	102230826	102230835	+	1	NA	intron (NR_111937, intron 2 of 5)	intron (NR_111937, intron 2 of 5)	7802	NR_111937	233575	Mm.302013	NM_145583	ENSMUSG00000030990	Pgap2	1810006G21Rik|C76649|Frag1	post-GPI attachment to proteins 2	protein-coding
mm_121913.1	chr14	22452689	22452699	-	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	90104	NR_046307	74896	Mm.444661	NR_046307		4930405A10Rik	4930456G20Rik	RIKEN cDNA 4930405A10 gene	ncRNA
mm_76573.1	chr8	88949982	88949994	-	1	NA	Intergenic	Intergenic	-74747	NR_106190	102465899		NR_106190	ENSMUSG00000099078	Mir8110	Gm27571|mmu-mir-8110	microRNA 8110	ncRNA
mm_24893.1	chr3	96162050	96162063	+	1	NA	promoter-TSS (NM_181409)	promoter-TSS (NM_181409)	86	NM_181409	194126	Mm.268536	NM_181409	ENSMUSG00000045934	Mtmr11	AI035306|BC051083|Cra	myotubularin related protein 11	protein-coding
mm_81419.1	chr9	109055973	109055991	+	1	NA	exon (NM_026381, exon 2 of 4)	exon (NM_026381, exon 2 of 4)	1116	NM_026381	66940	Mm.196533	NM_025858	ENSMUSG00000025647	Shisa5	2310008D10Rik|6430628I05Rik|Scotin|mShisa5	shisa family member 5	protein-coding
mm_51668.1	chr6	86371490	86371550	+	1	NA	promoter-TSS (NM_026506)	promoter-TSS (NM_026506)	-20	NM_026506	68011	Mm.276802	NM_026506	ENSMUSG00000057278	Snrpg	2810024K17Rik|AL022803|SMG|sm-G|snRNP-G	small nuclear ribonucleoprotein polypeptide G	protein-coding
mm_163627.1	chr13	57332011	57332011	+	1	NA	Intergenic	Intergenic	-436222	NM_001302373	26946	Mm.62409	NM_012035	ENSMUSG00000021541	Trpc7	TRP7|Trrp8	transient receptor potential cation channel, subfamily C, member 7	protein-coding
mm_82333.1	chr9	9239020	9239042	-	1	NA	promoter-TSS (NM_027823)	promoter-TSS (NM_027823)	-18	NM_027823	71544	Mm.334955	NM_027823	ENSMUSG00000050730	Arhgap42	9030420J04Rik|BE136619	Rho GTPase activating protein 42	protein-coding
mm_111249.1	chr12	84876471	84876474	-	1	NA	promoter-TSS (NM_013589)	promoter-TSS (NM_013589)	23	NM_013589	16997	Mm.3900	NM_013589	ENSMUSG00000002020	Ltbp2	AW208642	latent transforming growth factor beta binding protein 2	protein-coding
mm_78150.1	chr9	21015976	21015991	+	1	NA	promoter-TSS (NM_010493)	promoter-TSS (NM_010493)	43	NM_010493	15894	Mm.435508	NM_010493	ENSMUSG00000037405	Icam1	CD54|Icam-1|Ly-47|MALA-2	intercellular adhesion molecule 1	protein-coding
mm_37959.1	chr4	133352834	133352851	-	1	NA	Intergenic	Intergenic	-13527	NM_199306	230796	Mm.226576	NM_199306	ENSMUSG00000037622	Wdtc1	Gm695|adipose|adp	WD and tetratricopeptide repeats 1	protein-coding
mm_148943.1	chr19	7206684	7206713	+	1	NA	promoter-TSS (NM_134150)	promoter-TSS (NM_134150)	-414	NM_134150	107260	Mm.203921	NM_134150	ENSMUSG00000024767	Otub1	AI850305	OTU domain, ubiquitin aldehyde binding 1	protein-coding
mm_111904.1	chr12	108765808	108765828	-	1	NA	Intergenic	Intergenic	-27493	NM_009537	22632	Mm.3868	NM_009537	ENSMUSG00000021264	Yy1	AW488674|NF-E1	YY1 transcription factor	protein-coding
mm_87038.1	chr10	28672278	28672306	+	1	NA	intron (NR_131208, intron 1 of 3)	intron (NR_131208, intron 1 of 3)	3932	NM_178666	210757	Mm.123021	NM_178666	ENSMUSG00000049109	Themis	E430004N04Rik|Gasp|Spot|Tsepa|thylex	thymocyte selection associated	protein-coding
mm_77642.1	chr8	124406384	124406388	-	1	NA	intron (NM_171824, intron 1 of 6)	B3|SINE|B2	27550	NM_171824	209966	Mm.234233	NM_171824	ENSMUSG00000050751	Pgbd5	2900019M05Rik|AI854313	piggyBac transposable element derived 5	protein-coding
mm_100188.1	chr11	116680279	116680293	+	1	NA	intron (NM_009180, intron 6 of 8)	intron (NM_009180, intron 6 of 8)	5689	NR_028570	100216538		NR_028570	ENSMUSG00000065094	Snord1a	snR38	small nucleolar RNA, C/D box 1A	snoRNA
mm_40463.1	chr5	53634077	53634080	+	1	NA	intron (NM_001080928, intron 2 of 10)	intron (NM_001080928, intron 2 of 10)	43592	NM_001080927	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_115052.1	chr13	100651308	100651310	+	1	NA	promoter-TSS (NM_001015889)	promoter-TSS (NM_001015889)	-34	NM_027139	108143	Mm.301148	NM_027139	ENSMUSG00000052293	Taf9	2310012M09Rik|AA673500|AU045423|TAFII31|TAFII32|Taf2g	TATA-box binding protein associated factor 9	protein-coding
mm_35592.1	chr4	43005901	43005906	-	1	NA	intron (NM_001163233, intron 8 of 13)	intron (NM_001163233, intron 8 of 13)	4398	NM_001163233	60534	Mm.23122	NM_053081	ENSMUSG00000028453	Fancg	AU041407|Xrcc9	Fanconi anemia, complementation group G	protein-coding
mm_102732.1	chr11	67248652	67248674	-	1	NA	exon (NM_010855, exon 16 of 40)	exon (NM_010855, exon 16 of 40)	10851	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_61290.1	chr7	67647459	67647482	+	1	NA	promoter-TSS (NM_025905)	promoter-TSS (NM_025905)	60	NM_025905	67009	Mm.249356	NM_025905	ENSMUSG00000030555	Ttc23	1600012K10Rik	tetratricopeptide repeat domain 23	protein-coding
mm_166755.1	chr6	126853124	126853128	+	1	NA	promoter-TSS (NM_009650)	promoter-TSS (NM_009650)	28	NM_009650	11642	Mm.87748	NM_009650	ENSMUSG00000030344	Akap3	Prka3	A kinase (PRKA) anchor protein 3	protein-coding
mm_104363.1	chr11	94321899	94321909	-	1	NA	promoter-TSS (NM_026313)	promoter-TSS (NM_026313)	7	NM_026313	67684	Mm.30927	NM_026313	ENSMUSG00000020863	Luc7l3	3300001P08Rik|Luc7a	LUC7-like 3 (S. cerevisiae)	protein-coding
mm_143063.1	chr17	57011391	57011405	-	1	NA	promoter-TSS (NM_133801)	promoter-TSS (NM_133801)	-110	NM_133801	98053	Mm.24632	NM_133801	ENSMUSG00000002658	Gtf2f1	2810405L04Rik|C76800|RAP74	general transcription factor IIF, polypeptide 1	protein-coding
mm_17980.1	chr2	37703300	37703382	-	1	NA	Intergenic	CpG	-56056	NM_009261	20744	Mm.237095	NM_009261	ENSMUSG00000026915	Strbp	6430510M02Rik|AI852513|C230082I21Rik|C86322|Spnr	spermatid perinuclear RNA binding protein	protein-coding
mm_154170.1	chr19	58730054	58730065	-	1	NA	exon (NM_018874, exon 3 of 13)	exon (NM_018874, exon 3 of 13)	1172	NM_018874	18946	Mm.10753	NM_018874	ENSMUSG00000042179	Pnliprp1	Plrp1	pancreatic lipase related protein 1	protein-coding
mm_3434.1	chr1	150101296	150101313	+	1	NA	exon (NM_011198, exon 3 of 10)	exon (NM_011198, exon 3 of 10)	1273	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_163263.1	chr11	113180846	113180848	+	1	NA	intron (NR_015556, intron 1 of 2)	intron (NR_015556, intron 1 of 2)	20991	NR_015556	72386	Mm.266961	NR_015556	ENSMUSG00000087259	2610035D17Rik	-	RIKEN cDNA 2610035D17 gene	ncRNA
mm_32152.1	chr4	99929445	99929532	+	1	NA	promoter-TSS (NM_028132)	promoter-TSS (NM_028132)	37	NM_028132	72157	Mm.217764	NM_028132	ENSMUSG00000025791	Pgm2	2610020G18Rik|AA407108|AI098105|Pgm-2|Pgm1	phosphoglucomutase 2	protein-coding
mm_104600.1	chr11	97150026	97150084	-	1	NA	promoter-TSS (NM_198100)	promoter-TSS (NM_198100)	-343	NM_198100	73174	Mm.27882	NM_198100	ENSMUSG00000038517	Tbkbp1	3110043L15Rik|ProSAPiP2|SINTBAD	TBK1 binding protein 1	protein-coding
mm_14446.1	chr2	131068713	131068733	+	1	NA	TTS (NM_011426)	TTS (NM_011426)	-4909	NM_001163529	110751	Mm.108550	NM_033615	ENSMUSG00000027318	Adam33	Adaml	a disintegrin and metallopeptidase domain 33	protein-coding
mm_136148.1	chr16	87554235	87554246	-	1	NA	intron (NM_144854, intron 1 of 4)	intron (NM_144854, intron 1 of 4)	910	NM_144854	224419	Mm.194466	NM_144854	ENSMUSG00000025610	Map3k7cl	C21orf7|ORF63|Tak1l	Map3k7 C-terminal like	protein-coding
mm_130609.1	chr15	99853690	99853694	-	1	NA	intron (NM_001113545, intron 1 of 10)	B3A|SINE|B2	21764	NM_001113545	65970	Mm.33207	NM_023063	ENSMUSG00000023022	Lima1	Eplin	LIM domain and actin binding 1	protein-coding
mm_80184.1	chr9	72306670	72306679	+	1	NA	intron (NM_001311105, intron 6 of 20)	(TTTTTG)n|Simple_repeat|Simple_repeat	31786	NM_001311105	235469	Mm.242791	NM_146224	ENSMUSG00000038535	Zfp280d	A930005F02Rik|BC027163|Suhw4|ZNF634|Znf280d	zinc finger protein 280D	protein-coding
mm_91129.1	chr10	19594597	19594616	-	1	NA	intron (NM_010511, intron 1 of 6)	intron (NM_010511, intron 1 of 6)	2657	NM_010511	15979	Mm.549	NM_010511	ENSMUSG00000020009	Ifngr1	CD119|IFN-gammaR|Ifgr|Ifngr|Nktar	interferon gamma receptor 1	protein-coding
mm_69054.1	chr7	126883966	126884000	-	1	NA	5' UTR (NM_001163775, exon 1 of 16)	5' UTR (NM_001163775, exon 1 of 16)	984	NM_001163775	381921	Mm.259634	NM_001163774	ENSMUSG00000059981	Taok2	1110033K02Rik|B230344N16|MAP3K17|PSK|PSK1|TAO1|TAO2|mKIAA0881	TAO kinase 2	protein-coding
mm_153835.1	chr19	46326221	46326277	-	1	NA	intron (NM_028627, intron 1 of 17)	intron (NM_028627, intron 1 of 17)	617	NM_001347454	73728	Mm.268532	NM_028627	ENSMUSG00000037126	Psd	1110007H17Rik|A930015K15|Efa6|Efa6a|Psdl|mKIAA2011	pleckstrin and Sec7 domain containing	protein-coding
mm_140013.1	chr17	73204120	73204136	+	1	NA	intron (NM_001177967, intron 5 of 5)	intron (NM_001177967, intron 5 of 5)	96143	NM_001177967	225010	Mm.329194	NM_001081071	ENSMUSG00000054469	Lclat1	AI181996|Agpat8|Alcat1|Gm91|Lycat	lysocardiolipin acyltransferase 1	protein-coding
mm_137319.1	chr17	24895118	24895167	+	1	NA	promoter-TSS (NM_001163102)	promoter-TSS (NM_001163102)	22	NM_023260	79044	Mm.328851	NM_023260	ENSMUSG00000038880	Mrps34	0610007F04Rik|5330430D13Rik|AV001970|Tce2	mitochondrial ribosomal protein S34	protein-coding
mm_52961.1	chr6	123123515	123123528	+	1	NA	5' UTR (NM_001170333, exon 1 of 7)	5' UTR (NM_001170333, exon 1 of 7)	205	NM_001170333	26888	Mm.47384	NM_011999	ENSMUSG00000030148	Clec4a2	Clec4a|Clecsf6|DCIR|Dcir1	C-type lectin domain family 4, member a2	protein-coding
mm_168450.1	chr1	14113237	14113238	+	1	NA	Intergenic	Intergenic	196962	NM_001310459	14048	Mm.250185	NM_010164	ENSMUSG00000025932	Eya1	bor	EYA transcriptional coactivator and phosphatase 1	protein-coding
mm_102288.1	chr11	55405212	55405283	-	1	NA	exon (NM_009242, exon 5 of 10)	exon (NM_009242, exon 5 of 10)	14833	NM_009242	20692	Mm.291442	NM_009242	ENSMUSG00000018593	Sparc	BM-40|ON	secreted acidic cysteine rich glycoprotein	protein-coding
mm_121024.1	chr14	79587800	79587820	+	1	NA	5' UTR (NM_026474, exon 1 of 13)	5' UTR (NM_026474, exon 1 of 13)	119	NM_026474	67955	Mm.18972	NM_026474	ENSMUSG00000022024	Sugt1	2410174K12Rik|SGT1	SGT1, suppressor of G2 allele of SKP1 (S. cerevisiae)	protein-coding
mm_78380.1	chr9	27791197	27791207	+	1	NA	promoter-TSS (NM_177906)	promoter-TSS (NM_177906)	-67	NM_177906	330908	Mm.379474	NM_177906	ENSMUSG00000062257	Opcml	2900075O15Rik|3732419F12|AI844366|B930023M13Rik|C230027C17|Gm181|Obcam	opioid binding protein/cell adhesion molecule-like	protein-coding
mm_168425.1	chr11	33428468	33428491	-	1	NA	intron (NR_110973, intron 14 of 28)	intron (NR_110973, intron 14 of 28)	85267	NR_110973	66011	Mm.383775	NM_023146	ENSMUSG00000040594	Ranbp17	-	RAN binding protein 17	protein-coding
mm_156097.1	chrX	112497065	112497068	+	1	NA	intron (NM_001168590, intron 1 of 6)	Lx2B|LINE|L1	1792	NM_001168590	67715	Mm.45323	NM_026333	ENSMUSG00000025528	2010106E10Rik	-	RIKEN cDNA 2010106E10 gene	protein-coding
mm_155484.1	chrX	73681218	73681238	+	1	NA	3' UTR (NM_001142809, exon 13 of 13)	3' UTR (NM_001142809, exon 13 of 13)	8095	NM_001142809	102857	Mm.274553	NM_133987	ENSMUSG00000019558	Slc6a8	AA589632|CRT|CRTR|CT1|CTR5|Creat	solute carrier family 6 (neurotransmitter transporter, creatine), member 8	protein-coding
mm_14051.1	chr2	122377576	122377597	+	1	NA	Intergenic	Intergenic	-8668	NM_001013829	435684	Mm.458215	NM_001013829	ENSMUSG00000033256	Shf	-	Src homology 2 domain containing F	protein-coding
mm_13177.1	chr2	92954478	92954486	+	1	NA	3' UTR (NM_030725, exon 6 of 6)	3' UTR (NM_030725, exon 6 of 6)	39381	NM_030725	80976	Mm.33490	NM_030725	ENSMUSG00000027220	Syt13	5730409J20Rik|AI549909|mKIAA1427	synaptotagmin XIII	protein-coding
mm_84619.1	chr9	70503719	70503805	-	1	NA	promoter-TSS (NM_033604)	promoter-TSS (NM_033604)	-37	NM_033604	93836	Mm.29783	NM_033604	ENSMUSG00000032217	Rnf111	ARK|Arkadia	ring finger 111	protein-coding
mm_67371.1	chr7	79841686	79841705	-	1	NA	exon (NM_008486, exon 1 of 20)	exon (NM_008486, exon 1 of 20)	657	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_20731.1	chr2	137082009	137082022	-	1	NA	3' UTR (NM_013822, exon 26 of 26)	3' UTR (NM_013822, exon 26 of 26)	34505	NM_013822	16449	Mm.22398	NM_013822	ENSMUSG00000027276	Jag1	ABE2|Gsfabe2|Htu|Ozz|Ser-1	jagged 1	protein-coding
mm_136017.1	chr16	76226595	76226607	-	1	NA	Intergenic	Intergenic	103988	NR_040575	78215	Mm.243885	NR_040575		4930578N18Rik	-	RIKEN cDNA 4930578N18 gene	ncRNA
mm_122194.1	chr14	31780973	31780987	-	1	NA	intron (NM_001024604, intron 1 of 27)	intron (NM_001024604, intron 1 of 27)	49435	NM_001024604	105522	Mm.37660	NM_001024604	ENSMUSG00000014496	Ankrd28	AI465466|AI604979|E430019N21Rik|mKIAA0379	ankyrin repeat domain 28	protein-coding
mm_24418.1	chr3	90526826	90526832	+	1	NA	promoter-TSS (NM_001163526)	promoter-TSS (NM_001163526)	-20	NM_025393	66166	Mm.24006	NM_025393	ENSMUSG00000042306	S100a14	1110013O05Rik|S100a15|S114	S100 calcium binding protein A14	protein-coding
mm_103630.1	chr11	78936433	78936472	-	1	NA	exon (NM_010927, exon 7 of 27)	exon (NM_010927, exon 7 of 27)	11161	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_34742.1	chr4	152274091	152274163	+	1	NA	promoter-TSS (NM_178406)	promoter-TSS (NM_178406)	-235	NM_178406	100129	Mm.23235	NM_178406	ENSMUSG00000042804	Gpr153	1110065N12Rik|AI449320|PGR1	G protein-coupled receptor 153	protein-coding
mm_149719.1	chr19	21777526	21777530	+	1	NA	promoter-TSS (NM_031997)	promoter-TSS (NM_031997)	-812	NM_001033759	83921	Mm.329776	NM_031997	ENSMUSG00000024754	Tmem2	-	transmembrane protein 2	protein-coding
mm_90393.1	chr10	127322915	127322924	+	1	NA	promoter-TSS (NM_146011)	promoter-TSS (NM_146011)	-808	NM_146011	216445	Mm.227198	NM_146011	ENSMUSG00000040345	Arhgap9	AU043488	Rho GTPase activating protein 9	protein-coding
mm_105596.1	chr11	106750274	106750346	-	1	NA	promoter-TSS (NM_001271373)	promoter-TSS (NM_001271373)	-916	NM_001271375	380732	Mm.343952	NM_001033435	ENSMUSG00000040528	Milr1	Allergin-1|Gm885|Mca32	mast cell immunoglobulin like receptor 1	protein-coding
mm_172159.1	chr6	43625915	43625934	+	1	NA	intron (NM_001311111, intron 2 of 7)	L1Md_T|LINE|L1	40354	NM_001311111	29807	Mm.320979	NM_013861	ENSMUSG00000029735	Tpk1	-	thiamine pyrophosphokinase	protein-coding
mm_155539.1	chrX	74304993	74305036	+	1	NA	promoter-TSS (NM_010273)	promoter-TSS (NM_010273)	2	NM_010273	14567	Mm.205830	NM_010273	ENSMUSG00000015291	Gdi1	GDIA|GDIalpha	guanosine diphosphate (GDP) dissociation inhibitor 1	protein-coding
mm_103522.1	chr11	76846969	76847045	-	1	NA	promoter-TSS (NM_007754)	promoter-TSS (NM_007754)	1	NM_007754	12874	Mm.276736	NM_007754	ENSMUSG00000020841	Cpd	AA960140|AW322530|D830034L15Rik	carboxypeptidase D	protein-coding
mm_71833.1	chr8	68899476	68899521	+	1	NA	exon (NM_008509, exon 7 of 10)	exon (NM_008509, exon 7 of 10)	18943	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_77820.1	chr9	3335509	3335531	+	1	NA	intron (NM_026303, intron 1 of 11)	intron (NM_026303, intron 1 of 11)	289	NM_026303	67667	Mm.116968	NM_026303	ENSMUSG00000025899	Alkbh8	4930562C03Rik|8030431D03Rik|9430088N01Rik|Abh8	alkB homolog 8, tRNA methyltransferase	protein-coding
mm_121126.1	chr14	101840795	101840809	+	1	NA	5' UTR (NM_001347628, exon 1 of 27)	5' UTR (NM_001347628, exon 1 of 27)	179	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_128454.1	chr15	50773154	50773187	-	1	NA	intron (NM_001310485, intron 5 of 7)	intron (NM_001310485, intron 5 of 7)	115879	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_12913.1	chr2	84851442	84851462	+	1	NA	intron (NM_001081349, intron 5 of 14)	intron (NM_001081349, intron 5 of 14)	10826	NM_001083809	72401	Mm.22716	NM_024497	ENSMUSG00000027075	Slc43a1	2610016F07Rik|AA986141|Lat3|PB39|Pov1|R00504	solute carrier family 43, member 1	protein-coding
mm_40121.1	chr5	34989384	34989403	+	1	NA	intron (NM_173402, intron 3 of 16)	intron (NM_173402, intron 3 of 16)	-9685	NM_001163512	71729	Mm.196208	NM_173402	ENSMUSG00000029101	Rgs12	1200016K18Rik|4632412M04Rik|AI481290|E130309H11	regulator of G-protein signaling 12	protein-coding
mm_49214.1	chr6	15728101	15728145	+	1	NA	intron (NM_175088, intron 2 of 4)	intron (NM_175088, intron 2 of 4)	7462	NM_175088	16543	Mm.1314	NM_175088	ENSMUSG00000041390	Mdfic	Kdt1|Mdfid	MyoD family inhibitor domain containing	protein-coding
mm_43206.1	chr5	129160759	129160761	+	1	NA	intron (NM_001347486, intron 13 of 24)	intron (NM_001347486, intron 13 of 24)	64010	NM_001347486	243277	Mm.440501	NM_177734	ENSMUSG00000044017	Adgrd1	E230012M21Rik|Gpr133	adhesion G protein-coupled receptor D1	protein-coding
mm_153251.1	chr19	36625999	36626035	-	1	NA	intron (NR_033510, intron 3 of 4)	RMER1B|Other|Other	63462	NR_033510	668215	Mm.394223	NR_033510	ENSMUSG00000087579	1500017E21Rik	-	RIKEN cDNA 1500017E21 gene	ncRNA
mm_167715.1	chr9	98033175	98033181	-	1	NA	promoter-TSS (NM_022319)	promoter-TSS (NM_022319)	-11	NM_022319	64085	Mm.440903	NM_022319	ENSMUSG00000032452	Clstn2	2900042C18Rik|AI448973|CSTN2|Cs2|Cst-2|mKIAA4134	calsyntenin 2	protein-coding
mm_79718.1	chr9	61417810	61417817	+	1	NA	3' UTR (NM_009389, exon 20 of 20)	3' UTR (NM_009389, exon 20 of 20)	45447	NM_001083927	21887	Mm.24255	NM_009389	ENSMUSG00000032280	Tle3	2610103N05Rik|ESG|Grg3a|Grg3b|mKIAA1547	transducin-like enhancer of split 3	protein-coding
mm_159832.1	chr5	125532464	125532464	+	1	NA	promoter-TSS (NM_001190352)	promoter-TSS (NM_001190352)	46	NM_001190352	208151	Mm.40397	NM_001190352	ENSMUSG00000070498	Tmem132b	AK220418|mKIAA1786	transmembrane protein 132B	protein-coding
mm_159688.1	chr5	17476122	17476122	+	1	NA	promoter-TSS (NM_027609)	promoter-TSS (NM_027609)	0	NM_027609	70935	Mm.332225	NM_027609	ENSMUSG00000058643	Speer4f1	4922502J04Rik|SPEER-4F|Speer4f	spermatogenesis associated glutamate (E)-rich protein 4F1	protein-coding
mm_41359.1	chr5	90506595	90506599	+	1	NA	exon (NM_007423, exon 12 of 15)	exon (NM_007423, exon 12 of 15)	-12352	NM_145146	280662	Mm.348786	NM_145146	ENSMUSG00000029369	Afm	Alf|alpha-Alb	afamin	protein-coding
mm_10299.1	chr2	10523312	10523321	+	1	NA	intron (NM_001198808, intron 10 of 22)	intron (NM_001198808, intron 10 of 22)	5712	NR_035417	100316668		NR_035417	ENSMUSG00000080657	Mir669i	Mirn669i|mir-669i|mmu-mir-669i	microRNA 669i	ncRNA
mm_38905.1	chr4	149955029	149955048	-	1	NA	promoter-TSS (NM_029035)	promoter-TSS (NM_029035)	-32	NM_029035	74646	Mm.30	NM_029035	ENSMUSG00000039911	Spsb1	1110014L01Rik|4930422J18Rik|AI596360|AI854583|SSB-1|SSB1	splA/ryanodine receptor domain and SOCS box containing 1	protein-coding
mm_106080.1	chr11	116174818	116174821	-	1	NA	intron (NM_001271898, intron 11 of 13)	intron (NM_001271898, intron 11 of 13)	-6641	NM_172571	217335	Mm.35241	NM_172571	ENSMUSG00000020776	Fbf1	1110033G01Rik|5930413D20|mKIAA1863	Fas (TNFRSF6) binding factor 1	protein-coding
mm_132201.1	chr16	32550318	32550335	+	1	NA	Intergenic	Intergenic	54045	NM_199309	245308	Mm.76859	NM_199309	ENSMUSG00000052363	Zdhhc19	Gm1744|Gm616	zinc finger, DHHC domain containing 19	protein-coding
mm_111989.1	chr12	110601942	110601972	-	1	NA	intron (NM_030238, intron 1 of 76)	CpG	562	NM_030238	13424	Mm.181430	NM_030238	ENSMUSG00000018707	Dync1h1	9930018I23Rik|AI894280|DHC1|DHC1a|DNCL|Dnchc1|Dnec1|Dnecl|Loa|MAP1C|P22|Swl|mKIAA0325	dynein cytoplasmic 1 heavy chain 1	protein-coding
mm_131137.1	chr16	6348525	6348549	+	1	NA	intron (NM_021477, intron 2 of 16)	intron (NM_021477, intron 2 of 16)	372950	NR_045799	68238	Mm.434605	NR_045799	ENSMUSG00000101481	1700123O21Rik	-	RIKEN cDNA 1700123O21 gene	ncRNA
mm_169017.1	chr13	109902605	109902617	+	1	NA	intron (NM_011056, intron 7 of 16)	CpG	-1198	NR_035442	100316683		NR_035442	ENSMUSG00000084651	Mir1904	Mirn1904|mmu-mir-1904	microRNA 1904	ncRNA
mm_153000.1	chr19	30105337	30105346	-	1	NA	intron (NM_138595, intron 21 of 24)	intron (NM_138595, intron 21 of 24)	70100	NM_138595	104174	Mm.274852	NM_138595	ENSMUSG00000024827	Gldc	D030049L12Rik|D19Wsu57e	glycine decarboxylase	protein-coding
mm_82785.1	chr9	28996098	28996112	-	1	NA	3' UTR (NM_172290, exon 8 of 8)	3' UTR (NM_172290, exon 8 of 8)	967024	NM_172290	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding
mm_46030.1	chr5	91761610	91761647	-	1	NA	Intergenic	Intergenic	5672	NR_045383	73452	Mm.396233	NR_045383	ENSMUSG00000101978	1700063O14Rik	-	RIKEN cDNA 1700063O14 gene	ncRNA
mm_103735.1	chr11	80053313	80053316	-	1	NA	intron (NM_018776, intron 6 of 7)	RMER30|DNA|hAT-Charlie	27677	NM_001277106	54394	Mm.272093	NM_018776	ENSMUSG00000017561	Crlf3	BB164954|Creme9|Cytor4	cytokine receptor-like factor 3	protein-coding
mm_151454.1	chr19	57950535	57950545	+	1	NA	intron (NM_181415, intron 27 of 28)	intron (NM_181415, intron 27 of 28)	-100627	NR_049196	100885835		NR_049196	ENSMUSG00000093757	Mir5623	Gm26068|mir-5623|mmu-mir-5623	microRNA 5623	ncRNA
mm_36628.1	chr4	91376434	91376477	-	1	NA	promoter-TSS (NM_001177883)	promoter-TSS (NM_001177883)	36	NM_001347149	15569	Mm.318042	NM_010486	ENSMUSG00000008489	Elavl2	Hub|mel-N1	ELAV (embryonic lethal, abnormal vision, Drosophila)-like 2 (Hu antigen B)	protein-coding
mm_37951.1	chr4	133263043	133263135	-	1	NA	promoter-TSS (NM_031393)	promoter-TSS (NM_031393)	-2	NM_031393	269589	Mm.25660	NM_031393	ENSMUSG00000028860	Sytl1	9030417L18|PSGL-1|Slp1	synaptotagmin-like 1	protein-coding
mm_50408.1	chr6	48737365	48737394	+	1	NA	Intergenic	Intergenic	-1668	NM_175860	16205	Mm.252599	NM_008376	ENSMUSG00000090019	Gimap1	IAP38|Imap38|imap	GTPase, IMAP family member 1	protein-coding
mm_46301.1	chr5	100500587	100500597	-	1	NA	promoter-TSS (NM_172714)	promoter-TSS (NM_172714)	47	NM_172714	231506	Mm.212568	NM_172714	ENSMUSG00000035310	Lin54	AI461788	lin-54 homolog (C. elegans)	protein-coding
mm_28060.1	chr3	84259585	84259596	-	1	NA	5' UTR (NM_001271727, exon 1 of 12)	5' UTR (NM_001271727, exon 1 of 12)	189	NM_001271727	80890	Mm.44876	NM_030706	ENSMUSG00000027993	Trim2	mKIAA0517|narf	tripartite motif-containing 2	protein-coding
mm_53922.1	chr6	4086915	4086960	-	1	NA	promoter-TSS (NM_009748)	promoter-TSS (NM_009748)	-10	NM_009748	12068	Mm.286457	NM_009748	ENSMUSG00000032757	Bet1	AW555236|Bet-1	Bet1 golgi vesicular membrane trafficking protein	protein-coding
mm_110478.1	chr12	51851768	51851783	-	1	NA	Intergenic	Intergenic	-22239	NM_144788	207304	Mm.249391	NM_144788	ENSMUSG00000035247	Hectd1	A630086P08Rik|AI844876|b2b327Clo|opm	HECT domain containing 1	protein-coding
mm_89535.1	chr10	94515007	94515017	+	1	NA	5' UTR (NM_172051, exon 1 of 4)	5' UTR (NM_172051, exon 1 of 4)	155	NM_172051	319880	Mm.23047	NM_172051	ENSMUSG00000020023	Tmcc3	AW488095|C630016B22Rik|C88213|Tmcc1	transmembrane and coiled coil domains 3	protein-coding
mm_161396.1	chr14	105160532	105160532	-	1	NA	exon (NM_134077, exon 2 of 21)	exon (NM_134077, exon 2 of 21)	16795	NM_134077	74213	Mm.474531	NM_134077	ENSMUSG00000022119	Rbm26	1700009P03Rik|AI447318|C230097K14Rik|C86225|MLZ-393|Pro1777|Se70-2	RNA binding motif protein 26	protein-coding
mm_27244.1	chr3	36599412	36599440	-	1	NA	intron (NM_027810, intron 8 of 18)	intron (NM_027810, intron 8 of 18)	13963	NM_027810	71492	Mm.286187	NM_027810	ENSMUSG00000037325	Bbs7	8430406N16Rik	Bardet-Biedl syndrome 7 (human)	protein-coding
mm_116592.1	chr13	48536019	48536023	-	1	NA	promoter-TSS (NR_029656)	promoter-TSS (NR_029656)	93	NR_029656	387247		NR_029656	ENSMUSG00000065453	Mirlet7d	Mirnlet7d|let-7d|mmu-let-7d	microRNA let7d	ncRNA
mm_88714.1	chr10	80156729	80156763	+	1	NA	3' UTR (NM_001305798, exon 8 of 8)	3' UTR (NM_001305798, exon 8 of 8)	7064	NM_001305799	59090	Mm.143813	NM_021565	ENSMUSG00000035621	Midn	3000003C15Rik	midnolin	protein-coding
mm_111218.1	chr12	84448976	84449007	-	1	NA	promoter-TSS (NM_001313967)	promoter-TSS (NM_001313967)	-674	NM_001313967	104776	Mm.247510	NM_134042	ENSMUSG00000021238	Aldh6a1	1110038I05Rik|Mmsdh	aldehyde dehydrogenase family 6, subfamily A1	protein-coding
mm_1675.1	chr1	74794714	74794716	+	1	NA	intron (NM_009518, intron 2 of 3)	intron (NM_009518, intron 2 of 3)	2696	NM_009518	22409	Mm.5130	NM_009518	ENSMUSG00000026167	Wnt10a	-	wingless-type MMTV integration site family, member 10A	protein-coding
mm_14872.1	chr2	148799705	148799717	+	1	NA	intron (NM_009978, intron 1 of 3)	intron (NM_009978, intron 1 of 3)	872	NM_009978	13012	Mm.20435	NM_009978	ENSMUSG00000027442	Cst8	Cres|Cst-rs1	cystatin 8 (cystatin-related epididymal spermatogenic)	protein-coding
mm_93257.1	chr10	95548924	95548934	-	1	NA	3' UTR (NM_027722, exon 5 of 5)	3' UTR (NM_027722, exon 5 of 5)	10392	NR_037212	100526463		NR_037212	ENSMUSG00000092867	Mir3058	mir-3058|mmu-mir-3058	microRNA 3058	ncRNA
mm_17386.1	chr2	27072029	27072042	-	1	NA	5' UTR (NM_025376, exon 1 of 5)	5' UTR (NM_025376, exon 1 of 5)	126	NM_025376	66139	Mm.330087	NM_025376	ENSMUSG00000009214	Tmem8c	1110002H13Rik|AI131587	transmembrane protein 8C	protein-coding
mm_14311.1	chr2	129198758	129198769	+	1	NA	promoter-TSS (NM_015747)	promoter-TSS (NM_015747)	-10	NM_015747	20515	Mm.272675	NM_015747	ENSMUSG00000027397	Slc20a1	AI607883|Glvr-1|Glvr1	solute carrier family 20, member 1	protein-coding
mm_4283.1	chr1	171638992	171639039	+	1	NA	exon (NM_144539, exon 4 of 8)	exon (NM_144539, exon 4 of 8)	2885	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_65716.1	chr7	28378387	28378398	-	1	NA	exon (NM_011756, exon 2 of 2)	exon (NM_011756, exon 2 of 2)	836	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_31875.1	chr4	80834364	80834376	+	1	NA	5' UTR (NM_031202, exon 1 of 8)	5' UTR (NM_031202, exon 1 of 8)	157	NM_001282015	22178	Mm.30438	NM_031202	ENSMUSG00000005994	Tyrp1	Oca3|TRP-1|TRP1|Tyrp|b|brown|isa	tyrosinase-related protein 1	protein-coding
mm_94411.1	chr11	5803270	5803280	+	1	NA	exon (NM_018870, exon 1 of 3)	exon (NM_018870, exon 1 of 3)	521	NM_018870	56012	Mm.219627	NM_018870	ENSMUSG00000020475	Pgam2	-	phosphoglycerate mutase 2	protein-coding
mm_76440.1	chr8	85019566	85019580	-	1	NA	exon (NM_019652, exon 4 of 7)	exon (NM_019652, exon 4 of 7)	-5042	NR_052011	212989	Mm.215154	NM_001130194	ENSMUSG00000052819	Best2	Vmd2l1	bestrophin 2	protein-coding
mm_16782.1	chr2	9889536	9889544	-	1	NA	promoter-TSS (NR_040511)	promoter-TSS (NR_040511)	0	NR_040511	77682	Mm.488621	NR_040511	ENSMUSG00000079602	9230102O04Rik	-	RIKEN cDNA 9230102O04 gene	ncRNA
mm_621.1	chr1	40086092	40086094	+	1	NA	promoter-TSS (NR_037980)	promoter-TSS (NR_037980)	-242	NR_037980	100047133	Mm.447052	NR_037980	ENSMUSG00000097899	Gm16894	-	predicted gene, 16894	ncRNA
mm_115629.1	chr13	12106858	12106868	-	1	NA	promoter-TSS (NM_023868)	promoter-TSS (NM_023868)	82	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding
mm_166650.1	chr6	86605571	86605610	+	1	NA	Intergenic	Intergenic	-22584	NM_026414	67855	Mm.183043	NM_026414	ENSMUSG00000033508	Asprv1	2300003P22Rik|AA986851|SASP|SASPase|Taps	aspartic peptidase, retroviral-like 1	protein-coding
mm_134243.1	chr16	13189864	13189868	-	1	NA	Intergenic	Intergenic	-66615	NM_001122667	239719	Mm.270643	NM_153588	ENSMUSG00000009569	Mkl2	ENSMUSG00000075401|Gt4-1|MRTF-B|Mrtfb|mKIAA1243	MKL/myocardin-like 2	protein-coding
mm_131294.1	chr16	11398270	11398296	+	1	NA	intron (NM_028964, intron 5 of 20)	B1_Mm|SINE|Alu	-7365	NM_001290148	74478	Mm.325831	NM_028964	ENSMUSG00000071669	Snx29	4933437K13Rik|ENSMUSG00000079738|Gm11170|Gm1737|Gm930|Rundc2a	sorting nexin 29	protein-coding
mm_30504.1	chr3	158016420	158016435	-	1	NA	exon (NM_001093753, exon 8 of 12)	exon (NM_001093753, exon 8 of 12)	15327	NM_001093753	69207	Mm.223946	NM_026989	ENSMUSG00000055436	Srsf11	0610009J05Rik|2610019N13Rik|BF642805|Sfrs11	serine/arginine-rich splicing factor 11	protein-coding
mm_92665.1	chr10	80433584	80433594	-	1	NA	promoter-TSS (NM_011548)	promoter-TSS (NM_011548)	64	NM_001164150	21423	Mm.3406	NM_011548	ENSMUSG00000020167	Tcf3	A1|AA408400|ALF2|AW209082|E12|E12/E47|E2A|E47|KA1|ME2|Pan1|Pan2|TCF-3|Tcfe2a|VDIR|bHLHb21	transcription factor 3	protein-coding
mm_167737.1	chr9	106396646	106396648	+	1	NA	Intergenic	RSINE1|SINE|B4	28015	NM_153459	235584	Mm.275584	NM_153459	ENSMUSG00000053716	Dusp7	AU015694|Mkpx|Pyst2	dual specificity phosphatase 7	protein-coding
mm_124276.1	chr14	103033517	103033525	-	1	NA	intron (NR_045657, intron 1 of 2)	intron (NR_045657, intron 1 of 2)	282	NR_045657	71264	Mm.399572	NR_045657		4933432I03Rik	-	RIKEN cDNA 4933432I03 gene	ncRNA
mm_13050.1	chr2	91099623	91099634	+	1	NA	intron (NM_011355, intron 2 of 4)	intron (NM_011355, intron 2 of 4)	2950	NM_011355	20375	Mm.1302	NM_011355	ENSMUSG00000002111	Spi1	Dis-1|Dis1|PU.1|Sfpi-1|Sfpi1|Spi-1|Tcfpu1|Tfpu.1	spleen focus forming virus (SFFV) proviral integration oncogene	protein-coding
mm_150031.1	chr19	29374362	29374383	+	1	NA	intron (NM_021893, intron 3 of 6)	intron (NM_021893, intron 3 of 6)	6934	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_84895.1	chr9	79793522	79793541	-	1	NA	promoter-TSS (NR_040734)	promoter-TSS (NR_040734)	-101	NM_133718	69981	Mm.486324	NM_133718	ENSMUSG00000032328	Tmem30a	2010200I23Rik|AW540225|Cdc50a|D9Wsu20e	transmembrane protein 30A	protein-coding
mm_156492.1	chrX	144336125	144336138	+	1	NA	non-coding (NR_037145, exon 4 of 27)	non-coding (NR_037145, exon 4 of 27)	18165	NM_026247	67574	Mm.249084	NM_026247	ENSMUSG00000041718	Alg13	2810046O15Rik|4833435D08Rik|Glt28d1|MDS031|OTTMUSG00000018917	asparagine-linked glycosylation 13	protein-coding
mm_70149.1	chr7	143459382	143459420	-	1	NA	intron (NM_009876, intron 2 of 3)	CpG-13764	1649	NM_009876	12577	Mm.168789	NM_009876	ENSMUSG00000037664	Cdkn1c	AL024410|CDKI|Kip2|p57(kip2)|p57Kip2	cyclin-dependent kinase inhibitor 1C (P57)	protein-coding
mm_85401.1	chr9	103364971	103364996	-	1	NA	promoter-TSS (NM_001134427)	promoter-TSS (NM_001134427)	-4	NM_001134427	321022	Mm.261025	NM_175565	ENSMUSG00000032803	Cdv3	2510010F10Rik|C230084J24Rik|C79446|TPP36	carnitine deficiency-associated gene expressed in ventricle 3	protein-coding
mm_35718.1	chr4	44526748	44526749	-	1	NA	Intergenic	Intergenic	-176052	NR_073462	70602	Mm.491142	NR_073462	ENSMUSG00000103995	5730488B01Rik	-	RIKEN cDNA 5730488B01 gene	ncRNA
mm_97164.1	chr11	75489394	75489397	+	1	NA	intron (NM_138659, intron 2 of 41)	intron (NM_138659, intron 2 of 41)	2618	NM_138659	192159	Mm.3757	NM_138659	ENSMUSG00000020850	Prpf8	AU019467|D11Bwg0410e|DBF3/PRP8|Prp8|Sfprp8l	pre-mRNA processing factor 8	protein-coding
mm_134422.1	chr16	17893456	17893480	-	1	NA	promoter-TSS (NM_009435)	promoter-TSS (NM_009435)	-735	NM_009435	22114	Mm.439725	NM_009435	ENSMUSG00000041566	Tssk1	Stk22a|TSK-1|Tsk1|Tssk|Tssk1b	testis-specific serine kinase 1	protein-coding
mm_88560.1	chr10	79633605	79633609	+	1	NA	intron (NM_001024539, intron 1 of 12)	intron (NM_001024539, intron 1 of 12)	4311	NM_001024539	216148	Mm.39424	NM_001024539	ENSMUSG00000020312	Shc2	6720466E06|SCK|ShcB|Sli	SHC (Src homology 2 domain containing) transforming protein 2	protein-coding
mm_22702.1	chr3	18054497	18054515	+	1	NA	5' UTR (NM_021560, exon 1 of 1)	5' UTR (NM_021560, exon 1 of 1)	181	NM_021560	59058	Mm.149938	NM_021560	ENSMUSG00000025128	Bhlhe22	Beta3|Beta3a|Bhlhb5	basic helix-loop-helix family, member e22	protein-coding
mm_93447.1	chr10	109903953	109903966	-	1	NA	intron (NM_001081035, intron 1 of 38)	intron (NM_001081035, intron 1 of 38)	96260	NM_001081035	260315	Mm.225050	NM_177797	ENSMUSG00000020181	Nav3	4732483H20Rik|9630020C08Rik|POMFIL1|Pomfil1p|mKIAA0938|unc53H3	neuron navigator 3	protein-coding
mm_94218.1	chr11	3193563	3193578	+	1	NA	promoter-TSS (NM_030207)	promoter-TSS (NM_030207)	-107	NM_030207	78887	Mm.394071	NM_030207	ENSMUSG00000023764	Sfi1	-	Sfi1 homolog, spindle assembly associated (yeast)	protein-coding
mm_143727.1	chr17	81379047	81379060	-	1	NA	non-coding (NR_104580, exon 9 of 9)	non-coding (NR_104580, exon 9 of 9)	-313968	NM_028138	72167	Mm.273257	NM_028138	ENSMUSG00000024246	Thumpd2	2810025A12Rik	THUMP domain containing 2	protein-coding
mm_42926.1	chr5	122724985	122725010	+	1	NA	exon (NM_011026, exon 7 of 12)	exon (NM_011026, exon 7 of 12)	17453	NM_001310718	18438	Mm.290884	NM_011026	ENSMUSG00000029470	P2rx4	AI504491|AW555605|D5Ertd444e|P2X4	purinergic receptor P2X, ligand-gated ion channel 4	protein-coding
mm_72911.1	chr8	90955399	90955415	+	1	NA	intron (NM_001310530, intron 1 of 37)	intron (NM_001310530, intron 1 of 37)	23158	NM_001310530	109151	Mm.100615	NM_177224	ENSMUSG00000056608	Chd9	1810014J18Rik|9030205D12Rik|A330063D19Rik|AD013|PRIC320|mKIAA0308	chromodomain helicase DNA binding protein 9	protein-coding
mm_132087.1	chr16	30601751	30601763	+	1	NA	exon (NM_177632, exon 1 of 1)	exon (NM_177632, exon 1 of 1)	2034	NM_177632	224093	Mm.28244	NM_177632	ENSMUSG00000046546	Fam43a	Tuf1	family with sequence similarity 43, member A	protein-coding
mm_163710.1	chr13	109260651	109260680	+	1	NA	intron (NM_011056, intron 3 of 16)	intron (NM_011056, intron 3 of 16)	-64079	NR_030644	100124489		NR_030644	ENSMUSG00000076946	Mir582	Mirn582|mir-582|mmu-mir-582	microRNA 582	ncRNA
mm_157380.1	chrX	37901368	37901379	-	1	NA	exon (NM_023894, exon 2 of 4)	exon (NM_023894, exon 2 of 4)	397	NM_023894	104384	Mm.156958	NM_023894	ENSMUSG00000068048	Rhox9	1600026O01Rik|Gpbox|Psx2	reproductive homeobox 9	protein-coding
mm_45883.1	chr5	88328536	88328580	-	1	NA	exon (NM_008644, exon 3 of 3)	exon (NM_008644, exon 3 of 3)	11246	NM_008644	17830	Mm.200411	NM_008644	ENSMUSG00000064156	Prol1	Muc10	proline rich, lacrimal 1	protein-coding
mm_101651.1	chr11	36628775	36628798	-	1	NA	intron (NM_011856, intron 2 of 28)	B3A|SINE|B2	315455	NM_001290702	23964	Mm.439889	NM_011856	ENSMUSG00000049336	Tenm2	Odz2|Odz3|Ten-2|Ten-m2	teneurin transmembrane protein 2	protein-coding
mm_49038.1	chr6	4759979	4759987	+	1	NA	3' UTR (NM_130877, exon 2 of 2)	3' UTR (NM_130877, exon 2 of 2)	12677	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_142412.1	chr17	45549547	45549583	-	1	NA	5' UTR (NM_001013749, exon 1 of 3)	5' UTR (NM_001013749, exon 1 of 3)	112	NM_001013749	210573	Mm.329064	NM_001013749	ENSMUSG00000096847	Tmem151b	Gm323	transmembrane protein 151B	protein-coding
mm_78886.1	chr9	44603695	44603719	+	1	NA	Intergenic	MER89|LTR|ERV1	-1185	NM_001110826	13209	Mm.267061	NM_007841	ENSMUSG00000032097	Ddx6	1110001P04Rik|E230023J21Rik|HLR2|mRCK/P54|p54|rck	DEAD (Asp-Glu-Ala-Asp) box polypeptide 6	protein-coding
mm_40690.1	chr5	65764013	65764035	+	1	NA	intron (NM_001024917, intron 1 of 19)	CpG	503	NM_001024917	333789	Mm.332398	NM_001024917	ENSMUSG00000037795	N4bp2	B3bp|E430014I16|Gm1791|Gm868	NEDD4 binding protein 2	protein-coding
mm_165921.1	chr4	59890787	59890801	+	1	NA	intron (NM_172468, intron 6 of 8)	intron (NM_172468, intron 6 of 8)	24262	NM_021053	30936	Mm.284433	NM_021053	ENSMUSG00000028386	Slc46a2	5430429N04Rik|Ly110|TSO-1C12|Tscot	solute carrier family 46, member 2	protein-coding
mm_117562.1	chr13	85282896	85282901	-	1	NA	intron (NM_145452, intron 1 of 24)	intron (NM_145452, intron 1 of 24)	6588	NM_145452	218397	Mm.259653	NM_145452	ENSMUSG00000021549	Rasa1	Gap|RasGAP|Rasa	RAS p21 protein activator 1	protein-coding
mm_150143.1	chr19	31868755	31868787	+	1	NA	promoter-TSS (NM_001081074)	promoter-TSS (NM_001081074)	10	NM_001081074	69865	Mm.87538	NM_001081074	ENSMUSG00000052595	A1cf	1810073H04Rik|ACF64|ACF65|ASP|Acf|MCM|MerCreMer|Tg(Myh6-cre/Esr1*)1Jmk|mer	APOBEC1 complementation factor	protein-coding
mm_56909.1	chr6	119330569	119330583	-	1	NA	5' UTR (NM_172492, exon 1 of 5)	5' UTR (NM_172492, exon 1 of 5)	190	NM_172492	211187	Mm.121498	NM_172492	ENSMUSG00000055003	Lrtm2	A230084J22|AI841794	leucine-rich repeats and transmembrane domains 2	protein-coding
mm_123102.1	chr14	55882194	55882196	-	1	NA	3' UTR (NM_019820, exon 3 of 3)	3' UTR (NM_019820, exon 3 of 3)	2061	NM_019820	56410	Mm.97163	NM_019820	ENSMUSG00000040380	Cbln3	-	cerebellin 3 precursor protein	protein-coding
mm_22964.1	chr3	32529558	32529560	+	1	NA	promoter-TSS (NM_024200)	promoter-TSS (NM_024200)	77	NM_024200	67414	Mm.290414	NM_024200	ENSMUSG00000027668	Mfn1	2310002F04Rik|6330416C07Rik|D3Ertd265e|HR2|mKIAA4032	mitofusin 1	protein-coding
mm_72843.1	chr8	88300443	88300460	+	1	NA	intron (NM_001037723, intron 3 of 27)	intron (NM_001037723, intron 3 of 27)	6247	NM_001037724	11513	Mm.288206	NM_007406	ENSMUSG00000031659	Adcy7	AA407758	adenylate cyclase 7	protein-coding
mm_79855.1	chr9	64960847	64960891	+	1	NA	promoter-TSS (NM_001077631)	promoter-TSS (NM_001077631)	37	NM_001077631	69882	Mm.272616	NM_175153	ENSMUSG00000034263	Vwa9	2010321M09Rik	von Willebrand factor A domain containing 9	protein-coding
mm_160625.1	chr9	98856480	98856480	+	1	NA	promoter-TSS (NM_001134661)	promoter-TSS (NM_001134661)	-111	NM_001134661	623186	Mm.477438	NM_001134661	ENSMUSG00000063058	Prr23a2	EG623186|Gm6406	proline rich 23A, member 2	protein-coding
mm_49403.1	chr6	28426493	28426501	+	1	NA	TTS (NM_007480)	TTS (NM_007480)	-1404	NM_019569	56223	Mm.31708	NM_019569	ENSMUSG00000029707	Fscn3	-	fascin actin-bundling protein 3	protein-coding
mm_124502.1	chr14	121879542	121879560	-	1	NA	promoter-TSS (NR_130999)	promoter-TSS (NR_130999)	-143	NR_130999	78312	Mm.188743	NR_130999	ENSMUSG00000102112	1810041H14Rik	-	RIKEN cDNA 1810041H14 gene	ncRNA
mm_162964.1	chr11	9049034	9049043	+	1	NA	promoter-TSS (NM_001290520)	promoter-TSS (NM_001290520)	-47	NM_177576	194974	Mm.79210	NM_177576	ENSMUSG00000040985	Sun3	Sunc1	Sad1 and UNC84 domain containing 3	protein-coding
mm_94670.1	chr11	17248169	17248177	+	1	NA	Intergenic	MT2C_Mm|LTR|ERVL	-9374	NM_020558	57316	Mm.287982	NM_020558	ENSMUSG00000000581	C1d	1110036E10Rik|AI875855|SUN-CoR	C1D nuclear receptor co-repressor	protein-coding
mm_64409.1	chr7	142512053	142512070	+	1	NA	exon (NM_001163669, exon 13 of 17)	exon (NM_001163669, exon 13 of 17)	-5290	NR_033261	677289	Mm.350054	NR_033261	ENSMUSG00000043795	Prr33	ENSMUSG00000043795|Gm14492|OTTMUSG00000016823	proline rich 33	ncRNA
mm_60353.1	chr7	44384099	44384146	+	1	NA	promoter-TSS (NM_016663)	promoter-TSS (NM_016663)	-4	NM_001114116	20981	Mm.4824	NM_016663	ENSMUSG00000030731	Syt3	AI385753|sytIII	synaptotagmin III	protein-coding
mm_149272.1	chr19	10582316	10582325	+	1	NA	exon (NM_201351, exon 4 of 8)	exon (NM_201351, exon 4 of 8)	-4934	NR_126092	72982	Mm.391194	NM_028411	ENSMUSG00000024666	Tmem138	1700113I01Rik|2900055D14Rik	transmembrane protein 138	protein-coding
mm_4225.1	chr1	171344947	171344965	+	1	NA	promoter-TSS (NM_011070)	promoter-TSS (NM_011070)	689	NM_001242580	27045	Mm.12915	NM_012049	ENSMUSG00000013997	Nit1	AI255805|ESTM30|W57327	nitrilase 1	protein-coding
mm_65352.1	chr7	24997573	24997636	-	1	NA	exon (NM_001290469, exon 7 of 23)	exon (NM_001290469, exon 7 of 23)	8333	NM_001290469	232975	Mm.44101	NM_144921	ENSMUSG00000040907	Atp1a3	Atpa-2	ATPase, Na+/K+ transporting, alpha 3 polypeptide	protein-coding
mm_106270.1	chr11	117970344	117970354	-	1	NA	promoter-TSS (NM_007707)	promoter-TSS (NM_007707)	-983	NM_007707	12702	Mm.3468	NM_007707	ENSMUSG00000053113	Socs3	Cis3|Cish3|EF-10|Ef10|SSI-3|Ssi3	suppressor of cytokine signaling 3	protein-coding
mm_80437.1	chr9	77935377	77935382	+	1	NA	intron (NM_134255, intron 1 of 7)	intron (NM_134255, intron 1 of 7)	18014	NM_134255	68801	Mm.430736	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	ELOVL family member 5, elongation of long chain fatty acids (yeast)	protein-coding
mm_59412.1	chr7	27121537	27121549	+	1	NA	intron (NM_007817, intron 1 of 9)	intron (NM_007817, intron 1 of 9)	1588	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_132334.1	chr16	33819579	33819587	+	1	NA	3' UTR (NM_010739, exon 13 of 13)	3' UTR (NM_010739, exon 13 of 13)	-10082	NM_010580	16419	Mm.6424	NM_010580	ENSMUSG00000022817	Itgb5	AA475909|AI874634|ESTM23|[b]-5|[b]5|[b]5A|[b]5B|beta-5|beta5	integrin beta 5	protein-coding
mm_113368.1	chr13	32996999	32997011	+	1	NA	Intergenic	Intergenic	-7536	NM_009256	20723	Mm.245041	NM_009256	ENSMUSG00000045827	Serpinb9	BB283241|CAP-3|CAP3|PI-9|PI9|Spi6|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 9	protein-coding
mm_19418.1	chr2	91929893	91929904	-	1	NA	TTS (NM_007699)	TTS (NM_007699)	1804	NM_001291481	17242	Mm.906	NM_010784	ENSMUSG00000027239	Mdk	MK|Mek	midkine	protein-coding
mm_65106.1	chr7	19307194	19307204	-	1	NA	exon (NM_008036, exon 2 of 4)	exon (NM_008036, exon 2 of 4)	2846	NM_008036	14282	Mm.248335	NM_008036	ENSMUSG00000003545	Fosb	-	FBJ osteosarcoma oncogene B	protein-coding
mm_56805.1	chr6	116657414	116657453	-	1	NA	intron (NM_178045, intron 3 of 10)	intron (NM_178045, intron 3 of 10)	6749	NM_001166580	213393	Mm.38231	NM_145980	ENSMUSG00000048489	8430408G22Rik	Depp|Fseg	RIKEN cDNA 8430408G22 gene	protein-coding
mm_36264.1	chr4	63558731	63558742	-	1	NA	Intergenic	CpG	-1624	NM_144905	230279	Mm.41523	NM_144905	ENSMUSG00000045917	Tmem268	6330416G13Rik|AW492431|bM230C2.2	transmembrane protein 268	protein-coding
mm_140098.1	chr17	78272441	78272450	+	1	NA	intron (NM_015800, intron 2 of 16)	MER5B|DNA|hAT-Charlie	72197	NM_015800	50766	Mm.311912	NM_015800	ENSMUSG00000024074	Crim1	AU015004	cysteine rich transmembrane BMP regulator 1 (chordin like)	protein-coding
mm_66459.1	chr7	44892359	44892429	-	1	NA	promoter-TSS (NM_001331208)	promoter-TSS (NM_001331208)	30	NM_001331208	75613	Mm.157778	NM_029365	ENSMUSG00000002968	Med25	2610034E13Rik|2610529E18Rik|ESTM2	mediator complex subunit 25	protein-coding
mm_171835.1	chr5	149050733	149050734	-	1	NA	exon (NM_001313894, exon 2 of 5)	exon (NM_001313894, exon 2 of 5)	883	NM_001313894	15289	Mm.207047	NM_010439	ENSMUSG00000066551	Hmgb1	HMG-1|Hmg1|SBP-1|p30	high mobility group box 1	protein-coding
mm_93432.1	chr10	109010691	109010723	-	1	NA	5' UTR (NM_001252342, exon 1 of 11)	5' UTR (NM_001252342, exon 1 of 11)	268	NM_009306	20979	Mm.289702	NM_009306	ENSMUSG00000035864	Syt1	AW124717|G630098F17Rik|SytI	synaptotagmin I	protein-coding
mm_129999.1	chr15	86186137	86186185	-	1	NA	promoter-TSS (NM_145475)	promoter-TSS (NM_145475)	-20	NM_145475	223753	Mm.222685	NM_145475	ENSMUSG00000035891	Cerk	AI848610|D330016D08Rik|mKIAA1646	ceramide kinase	protein-coding
mm_23221.1	chr3	48954724	48954724	+	1	NA	Intergenic	Intergenic	-345624	NR_003617	66332	Mm.46124	NM_025493		1700018B24Rik	-	enhancer of rudimentary homolog pseudogene	pseudo
mm_36049.1	chr4	57300363	57300404	-	1	NA	intron (NM_011207, intron 1 of 25)	intron (NM_011207, intron 1 of 25)	1454	NM_011207	545622	Mm.246552	NM_011207	ENSMUSG00000038764	Ptpn3	9530011I20Rik|PTP-H1|PTPCL	protein tyrosine phosphatase, non-receptor type 3	protein-coding
mm_83129.1	chr9	40430953	40430971	-	1	NA	intron (NM_172768, intron 1 of 19)	intron (NM_172768, intron 1 of 19)	24802	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_158560.1	chrX	150435483	150435490	-	1	NA	intron (NM_001164683, intron 1 of 2)	intron (NM_001164683, intron 1 of 2)	5419	NM_001164686	382245	Mm.277309	NM_001164683	ENSMUSG00000041353	Tmem29	2700081K05Rik|6330540D07Rik|CXorf44-like	transmembrane protein 29	protein-coding
mm_29875.1	chr3	130930779	130930779	-	1	NA	Intergenic	Intergenic	-179518	NM_010703	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_63405.1	chr7	127326312	127326345	+	1	NA	intron (NM_001253874, intron 24 of 30)	intron (NM_001253874, intron 24 of 30)	18986	NM_146202	233890	Mm.23031	NM_146202	ENSMUSG00000047371	Zfp768	BC026432|Znf768	zinc finger protein 768	protein-coding
mm_13572.1	chr2	112284981	112284982	+	1	NA	intron (NM_133648, intron 1 of 24)	intron (NM_133648, intron 1 of 24)	293	NM_133648	107723	Mm.491155	NM_133648	ENSMUSG00000027130	Slc12a6	9530023I19Rik|KCC3|gaxp	solute carrier family 12, member 6	protein-coding
mm_126285.1	chr15	79229364	79229439	+	1	NA	promoter-TSS (NM_001045558)	promoter-TSS (NM_001045558)	19	NM_001045558	18693	Mm.259464	NM_008837	ENSMUSG00000068206	Pick1	Prkcabp	protein interacting with C kinase 1	protein-coding
mm_90771.1	chr10	5823881	5823937	-	1	NA	promoter-TSS (NM_175374)	promoter-TSS (NM_175374)	34	NM_175374	108853	Mm.55082	NM_175374	ENSMUSG00000019774	Mtrf1l	9130004K12Rik	mitochondrial translational release factor 1-like	protein-coding
mm_152798.1	chr19	21630785	21630803	-	1	NA	intron (NM_025423, intron 1 of 3)	intron (NM_025423, intron 1 of 3)	21997	NM_025423	66206	Mm.272430	NM_025423	ENSMUSG00000035171	1110059E24Rik	-	RIKEN cDNA 1110059E24 gene	protein-coding
mm_93345.1	chr10	100445037	100445040	-	1	NA	3' UTR (NM_001110013, exon 14 of 14)	3' UTR (NM_001110013, exon 14 of 14)	42309	NM_001033332	237500	Mm.296805	NM_001033332	ENSMUSG00000036676	Tmtc3	9130014E20Rik|B130008E12Rik|mSmile	transmembrane and tetratricopeptide repeat containing 3	protein-coding
mm_106305.1	chr11	118290189	118290200	-	1	NA	promoter-TSS (NM_001033528)	promoter-TSS (NM_001033528)	50	NM_001033528	72344	Mm.232293	NM_001033528	ENSMUSG00000033909	Usp36	2700002L06Rik|mKIAA1453	ubiquitin specific peptidase 36	protein-coding
mm_70030.1	chr7	142576548	142576564	-	1	NA	TTS (NR_030416)	TTS (NR_030416)	591	NR_030416	735280		NR_030416	ENSMUSG00000076275	Mir675	Mirn675|mir-675|mmu-mir-675	microRNA 675	ncRNA
mm_140448.1	chr17	88597664	88597704	+	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	-28871	NM_029858	77057	Mm.482203	NM_029858	ENSMUSG00000033855	Ston1	4921524J06Rik|C86231|Salf|Sblf	stonin 1	protein-coding
mm_34543.1	chr4	149518289	149518308	+	1	NA	promoter-TSS (NM_023465)	promoter-TSS (NM_023465)	57	NM_023465	67087	Mm.299735	NM_023465	ENSMUSG00000028988	Ctnnbip1	1110008O09Rik|2310001I19Rik|AW457332|Catnbip1|Icat	catenin beta interacting protein 1	protein-coding
mm_31988.1	chr4	89294863	89294903	+	1	NA	promoter-TSS (NR_132431)	promoter-TSS (NR_132431)	-264	NM_009877	12578	Mm.4733	NM_009877	ENSMUSG00000044303	Cdkn2a	ARF-INK4a|Arf|INK4a-ARF|Ink4a/Arf|MTS1|Pctr1|p16|p16(INK4a)|p16INK4a|p19<ARF>|p19ARF	cyclin-dependent kinase inhibitor 2A	protein-coding
mm_164905.1	chr18	68629305	68629312	+	1	NA	Intergenic	RMER30|DNA|hAT-Charlie	-110092	NR_105774	102465183		NR_105774	ENSMUSG00000099300	Mir6356	Gm27461|mmu-mir-6356	microRNA 6356	ncRNA
mm_66080.1	chr7	30956722	30956737	-	1	NA	promoter-TSS (NM_011680)	promoter-TSS (NM_011680)	74	NM_011680	22282	Mm.322453	NM_011680	ENSMUSG00000058239	Usf2	Usf-2|bHLHb12	upstream transcription factor 2	protein-coding
mm_50491.1	chr6	48988849	48988858	+	1	NA	exon (NM_172888, exon 1 of 5)	exon (NM_172888, exon 1 of 5)	1992	NM_172888	243377	Mm.446302	NM_172888	ENSMUSG00000039215	Svs1	9530003A11	seminal vesicle secretory protein 1	protein-coding
mm_37618.1	chr4	127061086	127061125	-	1	NA	promoter-TSS (NM_026670)	promoter-TSS (NM_026670)	27	NM_026670	68310	Mm.273806	NM_026670	ENSMUSG00000043872	Zmym1	5830412B09Rik|AW209050	zinc finger, MYM domain containing 1	protein-coding
mm_90157.1	chr10	118714437	118714453	+	1	NA	Intergenic	Intergenic	154458	NM_001014390	69181	Mm.45565	NM_001014390	ENSMUSG00000028630	Dyrk2	1810038L18Rik	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 2	protein-coding
mm_12757.1	chr2	79255450	79255470	+	1	NA	promoter-TSS (NM_010576)	promoter-TSS (NM_010576)	34	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D|Itga4B	integrin alpha 4	protein-coding
mm_40357.1	chr5	47990791	47990794	+	1	NA	intron (NR_111900, intron 3 of 35)	intron (NR_111900, intron 3 of 35)	7637	NM_001291228	20563	Mm.289739	NM_178804	ENSMUSG00000031558	Slit2	Drad-1|E030015M03Rik|E130320P19Rik|Slil3|mKIAA4141|slit-2	slit homolog 2 (Drosophila)	protein-coding
mm_108410.1	chr12	81859882	81859924	+	1	NA	promoter-TSS (NM_018814)	promoter-TSS (NM_018814)	-127	NM_018814	54604	Mm.86584	NM_018814	ENSMUSG00000021140	Pcnx	2900024E21Rik|3526401J03Rik|AF096286|AI327143|AI413187|Pcnx1|Pcnxl1	pecanex homolog (Drosophila)	protein-coding
mm_116810.1	chr13	54378914	54378941	-	1	NA	exon (NM_009946, exon 3 of 4)	exon (NM_009946, exon 3 of 4)	7578	NM_009946	12890	Mm.268902	NM_009946	ENSMUSG00000025867	Cplx2	921-L|AI413745|AW492120	complexin 2	protein-coding
mm_17544.1	chr2	29846303	29846316	-	1	NA	promoter-TSS (NR_029838)	promoter-TSS (NR_029838)	-582	NR_029838	723904		NR_029838	ENSMUSG00000065485	Mir219a-2	Mir219-2|Mirn219-2|mir-219a-2|mmu-mir-219a-2	microRNA 219a-2	ncRNA
mm_134142.1	chr16	10784688	10784704	-	1	NA	exon (NM_001271603, exon 2 of 2)	exon (NM_001271603, exon 2 of 2)	840	NM_009896	12703	Mm.130	NM_009896	ENSMUSG00000038037	Socs1	Cish1|Cish7|JAB|SOCS-1|SSI-1	suppressor of cytokine signaling 1	protein-coding
mm_139017.1	chr17	45758250	45758258	+	1	NA	Intergenic	MER117|DNA|hAT-Charlie	-24410	NM_028164	72240	Mm.482897	NM_028164	ENSMUSG00000094690	1600014C23Rik	-	RIKEN cDNA 1600014C23 gene	protein-coding
mm_65124.1	chr7	19458673	19458685	-	1	NA	promoter-TSS (NM_172279)	promoter-TSS (NM_172279)	-185	NM_172279	232944	Mm.260504	NM_172279	ENSMUSG00000030397	Mark4	2410090P21Rik|C79806|Markl1	MAP/microtubule affinity regulating kinase 4	protein-coding
mm_15594.1	chr2	160645882	160645896	+	1	NA	promoter-TSS (NM_009408)	promoter-TSS (NM_009408)	-8	NM_009408	21969	Mm.217233	NM_009408	ENSMUSG00000070544	Top1	AI467334|D130064I21Rik|Top-1	topoisomerase (DNA) I	protein-coding
mm_40486.1	chr5	56050424	56050426	+	1	NA	Intergenic	Lx7|LINE|L1	1667494	NR_015588	319216	Mm.332387	NR_015588	ENSMUSG00000097216	4932441J04Rik	-	RIKEN cDNA 4932441J04 gene	ncRNA
mm_116870.1	chr13	55018532	55018545	-	1	NA	intron (NM_001206392, intron 1 of 17)	intron (NM_001206392, intron 1 of 17)	2281	NM_001206390	212032	Mm.267479	NM_001033245	ENSMUSG00000025877	Hk3	HK III|HK-III	hexokinase 3	protein-coding
mm_132002.1	chr16	25523389	25523393	+	1	NA	Intergenic	Intergenic	-160374	NM_001127259	22061	Mm.20894	NM_011641	ENSMUSG00000022510	Trp63	AI462811|Ket|P51/P63|P63|P73l|Tp63|Trp53rp1	transformation related protein 63	protein-coding
mm_141094.1	chr17	25985774	25985795	-	1	NA	promoter-TSS (NM_001347334)	promoter-TSS (NM_001347334)	90	NM_001347334	50817	Mm.216072	NM_015830	ENSMUSG00000037326	Capn15	Solh	calpain 15	protein-coding
mm_52824.1	chr6	121356899	121356903	+	1	NA	intron (NM_001347433, intron 6 of 14)	intron (NM_001347433, intron 6 of 14)	10204	NM_133661	14411	Mm.274506	NM_133661	ENSMUSG00000030109	Slc6a12	BGT1|GAT-2|GAT2|Gabt2	solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12	protein-coding
mm_102641.1	chr11	62648459	62648514	-	1	NA	promoter-TSS (NM_175002)	promoter-TSS (NM_175002)	37	NM_198861	192976	Mm.339972	NM_198861	ENSMUSG00000046417	Lrrc75a	Fam211a	leucine rich repeat containing 75A	protein-coding
mm_171594.1	chr4	147698447	147698462	-	1	NA	intron (NM_001127188, intron 1 of 3)	intron (NM_001127188, intron 1 of 3)	4177	NM_001127188	100503584	Mm.276881	NM_001127188	ENSMUSG00000062518	Zfp534	Gm13159|OTTMUSG00000010681	zinc finger protein 534	protein-coding
mm_125487.1	chr15	54745616	54745632	+	1	NA	promoter-TSS (NM_010930)	promoter-TSS (NM_010930)	-304	NM_010930	18133	Mm.5167	NM_010930	ENSMUSG00000037362	Nov	C130088N23Rik|CCN3	nephroblastoma overexpressed gene	protein-coding
mm_155091.1	chrX	48146490	48146535	+	1	NA	promoter-TSS (NM_028773)	promoter-TSS (NM_028773)	76	NM_028773	74131	Mm.276131	NM_028773	ENSMUSG00000031101	Sash3	1200013B08Rik|AW413946|SLY1	SAM and SH3 domain containing 3	protein-coding
mm_63698.1	chr7	130645455	130645476	+	1	NA	intron (NM_001004468, intron 3 of 21)	intron (NM_001004468, intron 3 of 21)	-47091	NM_001347637	57752	Mm.86322	NM_021314	ENSMUSG00000030852	Tacc2	mKIAA4180	transforming, acidic coiled-coil containing protein 2	protein-coding
mm_28051.1	chr3	84041982	84042000	-	1	NA	Intergenic	Intergenic	-1830	NM_172681	229473	Mm.28838	NM_172681	ENSMUSG00000033767	D930015E06Rik	Kiaa0922|mKIAA0922	RIKEN cDNA D930015E06 gene	protein-coding
mm_105268.1	chr11	102365112	102365168	-	1	NA	5' UTR (NM_011403, exon 1 of 20)	5' UTR (NM_011403, exon 1 of 20)	141	NM_011403	20533	Mm.7248	NM_011403	ENSMUSG00000006574	Slc4a1	Ae1|CD233|Empb3|l11Jus51	solute carrier family 4 (anion exchanger), member 1	protein-coding
mm_73996.1	chr8	120736491	120736501	+	1	NA	intron (NM_008320, intron 1 of 8)	intron (NM_008320, intron 1 of 8)	138	NM_008320	15900	Mm.334861	NM_008320	ENSMUSG00000041515	Irf8	AI893568|ICSBP|IRF-8|Icsbp1|Myls	interferon regulatory factor 8	protein-coding
mm_147158.1	chr18	36679471	36679497	-	1	NA	promoter-TSS (NM_146085)	promoter-TSS (NM_146085)	-118	NM_146085	225372	Mm.89673	NM_146085	ENSMUSG00000006050	Apbb3	Fe65l2|Rirl2|TR2S	amyloid beta (A4) precursor protein-binding, family B, member 3	protein-coding
mm_35595.1	chr4	43025766	43025788	-	1	NA	promoter-TSS (NM_020035)	promoter-TSS (NM_020035)	-3	NM_020035	56703	Mm.143738	NM_020035	ENSMUSG00000028454	Pigo	PIG-O	phosphatidylinositol glycan anchor biosynthesis, class O	protein-coding
mm_80917.1	chr9	100847058	100847062	+	1	NA	intron (NM_009282, intron 11 of 33)	intron (NM_009282, intron 11 of 33)	187824	NM_001311149	66904	Mm.335385	NM_025835	ENSMUSG00000032527	Pccb	1300012P06Rik|AI314687|R74805	propionyl Coenzyme A carboxylase, beta polypeptide	protein-coding
mm_62104.1	chr7	96279193	96279195	+	1	NA	intron (NM_001310760, intron 1 of 32)	intron (NM_001310760, intron 1 of 32)	-26473	NR_105818	102465210		NR_105818	ENSMUSG00000099030	Mir6394	Gm27929|mmu-mir-6394	microRNA 6394	ncRNA
mm_87478.1	chr10	51492894	51492914	+	1	NA	intron (NM_001291894, intron 4 of 8)	intron (NM_001291894, intron 4 of 8)	2006	NM_013532	14728	Mm.34408	NM_013532	ENSMUSG00000062593	Lilrb4a	CD85K|Gp49b|HM18|ILT3|LIR-5|Lilrb4|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4A	protein-coding
mm_147292.1	chr18	39490650	39490717	-	1	NA	Intergenic	CpG	-3438	NM_008173	14815	Mm.129481	NM_008173	ENSMUSG00000024431	Nr3c1	GR|Grl-1|Grl1	nuclear receptor subfamily 3, group C, member 1	protein-coding
mm_38287.1	chr4	136890355	136890365	-	1	NA	exon (NM_007574, exon 3 of 3)	exon (NM_007574, exon 3 of 3)	2554	NM_007574	12262	Mm.439732	NM_007574	ENSMUSG00000036896	C1qc	AI385742|C1qg|Ciqc	complement component 1, q subcomponent, C chain	protein-coding
mm_70659.1	chr8	14777768	14777789	+	1	NA	intron (NM_172910, intron 8 of 15)	intron (NM_172910, intron 8 of 15)	-110758	NM_012000	26889	Mm.254027	NM_012000	ENSMUSG00000026317	Cln8	mnd	ceroid-lipofuscinosis, neuronal 8	protein-coding
mm_165254.1	chr2	72480033	72480048	+	1	NA	intron (NM_025866, intron 2 of 8)	intron (NM_025866, intron 2 of 8)	3821	NM_025866	66953	Mm.270676	NM_025866	ENSMUSG00000055612	Cdca7	2310021G01Rik|AU044109|JPO1	cell division cycle associated 7	protein-coding
mm_64713.1	chr7	4630474	4630485	-	1	NA	promoter-TSS (NM_023440)	promoter-TSS (NM_023440)	3	NM_023440	68255	Mm.389784	NM_023440	ENSMUSG00000045282	Tmem86b	C330014O21Rik	transmembrane protein 86B	protein-coding
mm_17768.1	chr2	32789499	32789508	-	1	NA	3' UTR (NM_001113569, exon 20 of 20)	3' UTR (NM_001113569, exon 20 of 20)	-5098	NM_025619	227736	Mm.441499	NM_025619	ENSMUSG00000038987	Cfap157	1700019L03Rik	cilia and flagella associated protein 157	protein-coding
mm_167988.1	chrX	170009609	170009622	+	1	NA	Intergenic	CpG	-30698	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_68589.1	chr7	116034391	116034417	-	1	NA	intron (NM_001025559, intron 1 of 15)	intron (NM_001025559, intron 1 of 15)	-3357	NM_001025560	20679	Mm.323365	NM_011445	ENSMUSG00000051910	Sox6	AI987981|SOX-LZ	SRY (sex determining region Y)-box 6	protein-coding
mm_49625.1	chr6	30804101	30804109	+	1	NA	intron (NM_017478, intron 20 of 23)	intron (NM_017478, intron 20 of 23)	62806	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_17054.1	chr2	21024161	21024166	-	1	NA	Intergenic	Intergenic	55289	NR_033225	433408	Mm.386941	NR_033225		Gm13375	OTTMUSG00000011664	predicted gene 13375	ncRNA
mm_13094.1	chr2	91256156	91256170	+	1	NA	promoter-TSS (NM_030880)	promoter-TSS (NM_030880)	-2	NM_001289677	80708	Mm.236650	NM_028733	ENSMUSG00000027257	Pacsin3	4921507A02Rik|6330413E15Rik|AW413130	protein kinase C and casein kinase substrate in neurons 3	protein-coding
mm_108455.1	chr12	82617103	82617116	+	1	NA	promoter-TSS (NM_001282061)	promoter-TSS (NM_001282061)	184	NM_015812	50779	Mm.126176	NM_015812	ENSMUSG00000021219	Rgs6	-	regulator of G-protein signaling 6	protein-coding
mm_12561.1	chr2	72545183	72545186	+	1	NA	Intergenic	Intergenic	68965	NM_025866	66953	Mm.270676	NM_025866	ENSMUSG00000055612	Cdca7	2310021G01Rik|AU044109|JPO1	cell division cycle associated 7	protein-coding
mm_129748.1	chr15	82337010	82337020	-	1	NA	intron (NM_008669, intron 3 of 9)	intron (NM_008669, intron 3 of 9)	1811	NM_008669	17939	Mm.20325	NM_008669	ENSMUSG00000022453	Naga	-	N-acetyl galactosaminidase, alpha	protein-coding
mm_137466.1	chr17	26655920	26655955	+	1	NA	3' UTR (NM_026170, exon 10 of 10)	3' UTR (NM_026170, exon 10 of 10)	-20459	NM_025272	11974	Mm.22602	NM_025272	ENSMUSG00000015575	Atp6v0e	Atp6k|Atp6v0e1|M9.2	ATPase, H+ transporting, lysosomal V0 subunit E	protein-coding
mm_139262.1	chr17	47761511	47761538	+	1	NA	intron (NM_001161723, intron 1 of 8)	intron (NM_001161723, intron 1 of 8)	23593	NM_001161723	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_107170.1	chr12	24708726	24708771	+	1	NA	intron (NM_009104, intron 2 of 9)	intron (NM_009104, intron 2 of 9)	494	NM_009104	20135	Mm.99	NM_009104	ENSMUSG00000020649	Rrm2	AA407299|R2	ribonucleotide reductase M2	protein-coding
mm_61308.1	chr7	67952818	67952828	+	1	NA	5' UTR (NM_010513, exon 1 of 21)	5' UTR (NM_010513, exon 1 of 21)	566	NM_010513	16001	Mm.275742	NM_010513	ENSMUSG00000005533	Igf1r	A330103N21Rik|CD221|D930020L01|IGF-1R|hyft	insulin-like growth factor I receptor	protein-coding
mm_40377.1	chr5	52368453	52368464	+	1	NA	exon (NM_011435, exon 2 of 2)	exon (NM_011435, exon 2 of 2)	4654	NM_011435	20657	Mm.2407	NM_011435	ENSMUSG00000072941	Sod3	AI314465|EC-SOD	superoxide dismutase 3, extracellular	protein-coding
mm_170791.1	chr2	175142020	175142022	-	1	NA	Intergenic	Intergenic	64896	NM_001164689	626832	Mm.441314	NM_001164689	ENSMUSG00000078887	Gm6710	1600017I02Rik|2310011F05Rik|2900089K14Rik|3100002L24Rik|WF-4	predicted gene 6710	protein-coding
mm_66612.1	chr7	45466551	45466587	-	1	NA	intron (NM_007527, intron 1 of 5)	CpG	329	NM_007527	12028	Mm.19904	NM_007527	ENSMUSG00000003873	Bax	-	BCL2-associated X protein	protein-coding
mm_34023.1	chr4	138041757	138041786	+	1	NA	intron (NM_172703, intron 2 of 34)	intron (NM_172703, intron 2 of 34)	48315	NM_172703	230861	Mm.268903	NM_172703	ENSMUSG00000028760	Eif4g3	1500002J22Rik|4930523M17Rik|G1-419-52|eIF4GII|repro8	eukaryotic translation initiation factor 4 gamma, 3	protein-coding
mm_107053.1	chr12	16653534	16653544	+	1	NA	promoter-TSS (NM_008747)	promoter-TSS (NM_008747)	69	NM_008747	18217	Mm.281715	NM_008747	ENSMUSG00000020591	Ntsr2	NT2R|NTRL	neurotensin receptor 2	protein-coding
mm_88068.1	chr10	67703366	67703375	+	1	NA	Intergenic	MIR3|SINE|MIR	-154415	NM_001005419	211488	Mm.297250	NM_001005419	ENSMUSG00000057134	Ado	Gm237	2-aminoethanethiol (cysteamine) dioxygenase	protein-coding
mm_89589.1	chr10	95892513	95892528	+	1	NA	Intergenic	B4A|SINE|B4	-48143	NM_001001932	216238	Mm.210035	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding
mm_117434.1	chr13	74617266	74617284	-	1	NA	Intergenic	Intergenic	-22597	NM_030711	80898	Mm.83526	NM_030711	ENSMUSG00000021583	Erap1	Arts1|ERAAP|PILSA|PILSAP	endoplasmic reticulum aminopeptidase 1	protein-coding
mm_132802.1	chr16	45158379	45158390	+	1	NA	promoter-TSS (NM_026402)	promoter-TSS (NM_026402)	289	NM_028756	74102	Mm.264984	NM_028756	ENSMUSG00000022664	Slc35a5	1010001J06Rik|AU021179|BB097433|D16Ertd450e|D730043G07Rik	solute carrier family 35, member A5	protein-coding
mm_111361.1	chr12	87048745	87048746	-	1	NA	intron (NM_172583, intron 2 of 24)	intron (NM_172583, intron 2 of 24)	22181	NM_172583	217733	Mm.110032	NM_172583	ENSMUSG00000034145	Tmem63c	4932420N09|9330187M14Rik	transmembrane protein 63c	protein-coding
mm_20466.1	chr2	129368131	129368162	-	1	NA	exon (NM_008361, exon 4 of 7)	exon (NM_008361, exon 4 of 7)	-1756	NR_015474	329514	Mm.207315	NM_177848	ENSMUSG00000074805	Il1bos	9430083I22|Gm14047|OTTMUSG00000015529	interleukin 1 beta, opposite strand	ncRNA
mm_4469.1	chr1	173419221	173419231	+	1	NA	Intergenic	Intergenic	-1378	NM_001013779	383619	Mm.131453	NM_001013779	ENSMUSG00000037860	Aim2	Gm1313|Ifi210	absent in melanoma 2	protein-coding
mm_150208.1	chr19	32800049	32800066	+	1	NA	exon (NM_008960, exon 5 of 9)	exon (NM_008960, exon 5 of 9)	42480	NM_008960	19211	Mm.245395	NM_008960	ENSMUSG00000013663	Pten	2310035O07Rik|A130070J02Rik|AI463227|B430203M17Rik|MMAC1|TEP1	phosphatase and tensin homolog	protein-coding
mm_115862.1	chr13	21441045	21441069	-	1	NA	promoter-TSS (NM_001162920)	promoter-TSS (NM_001162920)	-4	NM_001162920	319207	Mm.434384	NM_001012311	ENSMUSG00000055313	Pgbd1	4921509E05Rik	piggyBac transposable element derived 1	protein-coding
mm_54282.1	chr6	29212456	29212468	-	1	NA	promoter-TSS (NM_011829)	promoter-TSS (NM_011829)	-165	NM_011829	23917	Mm.260707	NM_011829	ENSMUSG00000003500	Impdh1	B930086D20Rik|IMPDH-I	inosine 5'-phosphate dehydrogenase 1	protein-coding
mm_152062.1	chr19	6532013	6532023	-	1	NA	exon (NM_020253, exon 23 of 23)	exon (NM_020253, exon 23 of 23)	11052	NM_009203	20521	Mm.391146	NM_009203	ENSMUSG00000061742	Slc22a12	AI987855|OAT4L|Rst|Slc22al2|URAT1	solute carrier family 22 (organic anion/cation transporter), member 12	protein-coding
mm_165747.1	chr3	107760259	107760282	-	1	NA	5' UTR (NM_007778, exon 1 of 9)	5' UTR (NM_007778, exon 1 of 9)	199	NM_001113530	12977	Mm.795	NM_007778	ENSMUSG00000014599	Csf1	C87615|Csfm|MCSF|op	colony stimulating factor 1 (macrophage)	protein-coding
mm_172733.1	chr8	78139956	78139960	-	1	NA	Intergenic	ERVB7_1-LTR_MM|LTR|ERVK	-73384	NM_183096	73301	Mm.61243	NM_183096	ENSMUSG00000037101	Ttc29	1700031F13Rik	tetratricopeptide repeat domain 29	protein-coding
mm_170720.1	chr2	14739181	14739182	+	1	NA	intron (NM_023116, intron 2 of 13)	intron (NM_023116, intron 2 of 13)	18539	NR_028497	625342	Mm.484784	NR_028497		Gm13315	OTTMUSG00000011384	lactate dehydrogenase A pseudogene	pseudo
mm_28052.1	chr3	84155736	84155754	-	1	NA	promoter-TSS (NM_029797)	promoter-TSS (NM_029797)	41	NM_029797	76915	Mm.274829	NM_029797	ENSMUSG00000033752	Mnd1	2610034E18Rik|AI591601|Gaj	meiotic nuclear divisions 1	protein-coding
mm_128603.1	chr15	58324120	58324143	-	1	NA	promoter-TSS (NM_177755)	promoter-TSS (NM_177755)	38	NM_177755	268807	Mm.124498	NM_177755	ENSMUSG00000022357	Klhl38	8230402K04Rik	kelch-like 38	protein-coding
mm_113068.1	chr13	23751204	23751207	+	1	NA	exon (NM_175660, exon 1 of 1)	exon (NM_175660, exon 1 of 1)	117	NM_175660	319172	Mm.423402	NM_175660	ENSMUSG00000061615	Hist1h2ab	H2A.1|H2a-53	histone cluster 1, H2ab	protein-coding
mm_78319.1	chr9	24368144	24368150	+	1	NA	Intergenic	Intergenic	134993	NM_172920	244745	Mm.38526	NM_172920	ENSMUSG00000043067	Dpy19l1	1100001I19Rik|6030402K12|AI225861|AW558481	dpy-19-like 1 (C. elegans)	protein-coding
mm_52036.1	chr6	96140781	96140802	+	1	NA	intron (NM_182808, intron 2 of 4)	intron (NM_182808, intron 2 of 4)	25414	NR_003643	78482	Mm.391486	NM_030107	ENSMUSG00000072878	1700123L14Rik	-	nucleoporin 50 pseudogene	pseudo
mm_17387.1	chr2	27072084	27072093	-	1	NA	promoter-TSS (NM_025376)	promoter-TSS (NM_025376)	73	NM_025376	66139	Mm.330087	NM_025376	ENSMUSG00000009214	Tmem8c	1110002H13Rik|AI131587	transmembrane protein 8C	protein-coding
mm_48024.1	chr5	136244866	136244908	-	1	NA	promoter-TSS (NM_018825)	promoter-TSS (NM_018825)	53	NM_001302939	23921	Mm.425294	NM_018825	ENSMUSG00000005057	Sh2b2	Aps	SH2B adaptor protein 2	protein-coding
mm_138851.1	chr17	40811184	40811188	+	1	NA	promoter-TSS (NM_011269)	promoter-TSS (NM_011269)	37	NM_011269	19743	Mm.12961	NM_011269	ENSMUSG00000023926	Rhag	CD241|Rh50|Rh50A	Rhesus blood group-associated A glycoprotein	protein-coding
mm_142817.1	chr17	51746966	51746970	-	1	NA	intron (NM_009122, intron 9 of 10)	intron (NM_009122, intron 9 of 10)	65086	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_132197.1	chr16	32496273	32496284	+	1	NA	promoter-TSS (NM_199309)	promoter-TSS (NM_199309)	-3	NM_199309	245308	Mm.76859	NM_199309	ENSMUSG00000052363	Zdhhc19	Gm1744|Gm616	zinc finger, DHHC domain containing 19	protein-coding
mm_67802.1	chr7	98111432	98111445	-	1	NA	intron (NM_001256081, intron 2 of 48)	CpG	-2190	NM_001256083	17921	Mm.1403	NM_008663	ENSMUSG00000030761	Myo7a	Hdb|Myo7|USH1B|nmf371|polka|sh-1|sh1	myosin VIIA	protein-coding
mm_50405.1	chr6	48728164	48728174	+	1	NA	Intergenic	Intergenic	9548	NM_146167	231932	Mm.30479	NM_146167	ENSMUSG00000043931	Gimap7	IAN7|Ian3	GTPase, IMAP family member 7	protein-coding
mm_133372.1	chr16	84709383	84709394	+	1	NA	Intergenic	Intergenic	-3635	NR_132106	100653389	Mm.261808	NR_132106	ENSMUSG00000097418	Mir155hg	Bic|Gm26667	Mir155 host gene (non-protein coding)	ncRNA
mm_19898.1	chr2	114052805	114052818	-	1	NA	promoter-TSS (NM_009608)	promoter-TSS (NM_009608)	64	NM_009608	11464	Mm.686	NM_009608	ENSMUSG00000068614	Actc1	Actc-1	actin, alpha, cardiac muscle 1	protein-coding
mm_26917.1	chr3	20242159	20242167	-	1	NA	promoter-TSS (NM_007753)	promoter-TSS (NM_007753)	18	NM_007753	12873	Mm.1135	NM_007753	ENSMUSG00000001865	Cpa3	MC-CPA	carboxypeptidase A3, mast cell	protein-coding
mm_87227.1	chr10	40477681	40477727	+	1	NA	exon (NM_001168304, exon 12 of 13)	exon (NM_001168304, exon 12 of 13)	-92658	NM_027572	70840	Mm.332570	NM_027572	ENSMUSG00000019834	Slc22a16	4921504E14Rik|CT2|FLIPT2|OCT6|OKB1	solute carrier family 22 (organic cation transporter), member 16	protein-coding
mm_93639.1	chr10	117288411	117288420	-	1	NA	3' UTR (NM_013590, exon 4 of 4)	3' UTR (NM_013590, exon 4 of 4)	4453	NM_013590	17110	Mm.177539	NM_013590	ENSMUSG00000069515	Lyz1	Lyz|Lyzf3|Lzp-s	lysozyme 1	protein-coding
mm_83389.1	chr9	44604743	44604757	-	1	NA	promoter-TSS (NM_001110826)	promoter-TSS (NM_001110826)	-142	NM_001110826	13209	Mm.267061	NM_007841	ENSMUSG00000032097	Ddx6	1110001P04Rik|E230023J21Rik|HLR2|mRCK/P54|p54|rck	DEAD (Asp-Glu-Ala-Asp) box polypeptide 6	protein-coding
mm_1899.1	chr1	85709594	85709617	+	1	NA	3' UTR (NM_013673, exon 20 of 20)	3' UTR (NM_013673, exon 20 of 20)	27001	NM_177055	319997	Mm.116691	NM_177055	ENSMUSG00000052760	A630001G21Rik	-	RIKEN cDNA A630001G21 gene	protein-coding
mm_167150.1	chr7	131199068	131199074	+	1	NA	intron (NM_175166, intron 5 of 22)	intron (NM_175166, intron 5 of 22)	24669	NM_175166	71395	Mm.118845	NM_175166	ENSMUSG00000006204	5430419D17Rik	-	RIKEN cDNA 5430419D17 gene	protein-coding
mm_4356.1	chr1	171917513	171917517	+	1	NA	promoter-TSS (NM_030710)	promoter-TSS (NM_030710)	-22	NM_030710	30925	Mm.486404	NM_030710	ENSMUSG00000015314	Slamf6	KAL1|KAL1b|Ly108|NTB-A|NTBA|SF2000	SLAM family member 6	protein-coding
mm_8816.1	chr1	161979701	161979705	-	1	NA	promoter-TSS (NM_001204904)	promoter-TSS (NM_001204904)	-67	NM_001204904	75368	Mm.108728	NM_001204904	ENSMUSG00000086277	4930558K02Rik	-	RIKEN cDNA 4930558K02 gene	protein-coding
mm_95303.1	chr11	46124998	46125017	+	1	NA	intron (NM_001291890, intron 10 of 22)	intron (NM_001291890, intron 10 of 22)	-2897	NM_001311209	11492	Mm.89940	NM_009616	ENSMUSG00000011256	Adam19	AL024287|MADDAM|MTLNB|Mltnb	a disintegrin and metallopeptidase domain 19 (meltrin beta)	protein-coding
mm_39752.1	chr5	29735726	29735737	+	1	NA	promoter-TSS (NM_001037941)	promoter-TSS (NM_001037941)	-167	NM_001037940	23950	Mm.290110	NM_011847	ENSMUSG00000029131	Dnajb6	Mrj|mDj4	DnaJ heat shock protein family (Hsp40) member B6	protein-coding
mm_96379.1	chr11	67242827	67242837	+	1	NA	exon (NM_010855, exon 8 of 40)	exon (NM_010855, exon 8 of 40)	5020	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_66487.1	chr7	45027932	45027967	-	1	NA	3' UTR (NM_175022, exon 14 of 14)	3' UTR (NM_175022, exon 14 of 14)	9942	NM_009101	20130	Mm.389894	NM_009101	ENSMUSG00000038387	Rras	AI573426	related RAS viral (r-ras) oncogene	protein-coding
mm_51558.1	chr6	83351250	83351264	+	1	NA	intron (NM_175277, intron 1 of 3)	intron (NM_175277, intron 1 of 3)	1773	NM_175277	78653	Mm.391470	NM_175277	ENSMUSG00000045160	Bola3	1810056O20Rik	bolA-like 3 (E. coli)	protein-coding
mm_125065.1	chr15	25941018	25941024	+	1	NA	5' UTR (NM_001277315, exon 1 of 7)	5' UTR (NM_001277315, exon 1 of 7)	195	NM_025459	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_93612.1	chr10	117238631	117238641	-	1	NA	promoter-TSS (NM_029906)	promoter-TSS (NM_029906)	45	NM_029906	77397	Mm.118350	NM_029906	ENSMUSG00000020177	9530003J23Rik	Lyzf1	RIKEN cDNA 9530003J23 gene	protein-coding
mm_42104.1	chr5	110514886	110514931	+	1	NA	promoter-TSS (NR_102290)	promoter-TSS (NR_102290)	-15	NR_102290	231603	Mm.22836	NM_173766	ENSMUSG00000048215	A630023P12Rik	-	RIKEN cDNA A630023P12 gene	ncRNA
mm_84343.1	chr9	64214634	64214638	-	1	NA	intron (NM_008927, intron 1 of 10)	intron (NM_008927, intron 1 of 10)	-20565	NM_033607	93841	Mm.390180	NM_033607	ENSMUSG00000035337	Uchl4	-	ubiquitin carboxyl-terminal esterase L4	protein-coding
mm_41703.1	chr5	101659207	101659215	+	1	NA	TTS (NM_144955)	TTS (NM_144955)	5500	NM_144955	18096	Mm.193072	NM_144955	ENSMUSG00000035187	Nkx6-1	NKX6A|Nkx6.1	NK6 homeobox 1	protein-coding
mm_160674.1	chr10	7691302	7691302	+	1	NA	intron (NM_010690, intron 1 of 7)	intron (NM_010690, intron 1 of 7)	10093	NM_010690	16798	Mm.34083	NM_010690	ENSMUSG00000040021	Lats1	AW208599	large tumor suppressor	protein-coding
mm_165945.1	chr4	82373911	82373949	-	1	NA	intron (NM_001113210, intron 3 of 11)	B4A|SINE|B4	131849	NM_001286127	18028	Mm.317947	NM_008687	ENSMUSG00000008575	Nfib	6720429L07Rik|CTF|E030026I10Rik|NF-I/B|NF1-B|NFI-B	nuclear factor I/B	protein-coding
mm_81201.1	chr9	107563287	107563297	+	1	NA	promoter-TSS (NM_019742)	promoter-TSS (NM_019742)	37	NM_019742	80385	Mm.21739	NM_019742	ENSMUSG00000010054	Tusc2	1190001E22Rik|AA407686|Fus1|Lgcc|PAP|Pdap2	tumor suppressor candidate 2	protein-coding
mm_40425.1	chr5	53532275	53532287	+	1	NA	Intergenic	MTE2b|LTR|ERVL-MaLR	-23498	NM_001080928	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_101084.1	chr11	11808924	11808967	-	1	NA	promoter-TSS (NM_021891)	promoter-TSS (NM_021891)	17	NM_021891	60530	Mm.236114	NM_021891	ENSMUSG00000035455	Fignl1	-	fidgetin-like 1	protein-coding
mm_133838.1	chr16	96156674	96156683	+	1	NA	3' UTR (NM_207301, exon 5 of 5)	3' UTR (NM_207301, exon 5 of 5)	11259	NM_207301	71446	Mm.255063	NM_207301	ENSMUSG00000023147	Wrb	5530402J05Rik|C030018G21Rik|Chd5	tryptophan rich basic protein	protein-coding
mm_102684.1	chr11	65269985	65270002	-	1	NA	promoter-TSS (NM_145136)	promoter-TSS (NM_145136)	-4	NM_146386	214384	Mm.32257	NM_145136	ENSMUSG00000020542	Myocd	BSAC2A|Srfcp	myocardin	protein-coding
mm_44971.1	chr5	36807859	36807870	-	1	NA	exon (NM_008550, exon 18 of 19)	exon (NM_008550, exon 18 of 19)	-11110	NM_026242	67568	Mm.332336	NM_026242	ENSMUSG00000055302	Mrfap1	9130413I22Rik|AL022827|Pam14	Morf4 family associated protein 1	protein-coding
mm_155061.1	chrX	42502206	42502207	+	1	NA	promoter-TSS (NM_011364)	promoter-TSS (NM_011364)	-359	NM_011364	20400	Mm.441197	NM_011364	ENSMUSG00000005696	Sh2d1a	Gm686|SAP	SH2 domain containing 1A	protein-coding
mm_57391.1	chr6	124840059	124840069	-	1	NA	5' UTR (NM_013530, exon 1 of 10)	5' UTR (NM_013530, exon 1 of 10)	211	NM_013530	14695	Mm.68889	NM_013530	ENSMUSG00000023439	Gnb3	Gnb-3	guanine nucleotide binding protein (G protein), beta 3	protein-coding
mm_22028.1	chr2	168050390	168050400	-	1	NA	Intergenic	CpG	-30609	NM_021409	58220	Mm.292834	NM_021409	ENSMUSG00000044641	Pard6b	AV025615|Par6b	par-6 family cell polarity regulator beta	protein-coding
mm_80752.1	chr9	95392804	95392806	+	1	NA	Intergenic	B4A|SINE|B4	14465	NM_018763	54371	Mm.212446	NM_018763	ENSMUSG00000033350	Chst2	AI428561|AW121776|C130041E03Rik|Chts2|GST-2|GlcNAc6ST|Gn6st	carbohydrate sulfotransferase 2	protein-coding
mm_132867.1	chr16	48611686	48611720	+	1	NA	intron (NM_010816, intron 20 of 26)	intron (NM_010816, intron 20 of 26)	160253	NM_198297	77647	Mm.167298	NM_198297	ENSMUSG00000030775	Trat1	C030046M14Rik|Tcrim|Trim	T cell receptor associated transmembrane adaptor 1	protein-coding
mm_167065.1	chr7	97032828	97032831	+	1	NA	intron (NM_153591, intron 9 of 13)	intron (NM_153591, intron 9 of 13)	-48922	NM_001162477	14389	Mm.42033	NM_010248	ENSMUSG00000004508	Gab2	AI463667|D130058I17Rik|p97	growth factor receptor bound protein 2-associated protein 2	protein-coding
mm_42433.1	chr5	115404538	115404580	+	1	NA	Intergenic	Intergenic	-25126	NM_008629	17690	Mm.5077	NM_008629	ENSMUSG00000054256	Msi1	Msi1h|Musahi1|m-Msi-1	musashi RNA-binding protein 1	protein-coding
mm_166729.1	chr6	122513576	122513580	+	1	NA	promoter-TSS (NM_015776)	promoter-TSS (NM_015776)	-6	NM_001347434	50530	Mm.41931	NM_015776	ENSMUSG00000030116	Mfap5	MAGP-2|MFAP-5	microfibrillar associated protein 5	protein-coding
mm_118534.1	chr14	16173681	16173696	+	1	NA	Intergenic	Intergenic	-75626	NM_021504	59007	Mm.258381	NM_021504	ENSMUSG00000021785	Ngly1	1110002C09Rik|PNGase|Png1	N-glycanase 1	protein-coding
mm_64677.1	chr7	4501716	4501722	-	1	NA	promoter-TSS (NM_029834)	promoter-TSS (NM_029834)	-39	NM_029834	232807	Mm.360391	NM_029834	ENSMUSG00000019254	Ppp1r12c	2410197A17Rik|AI839747|B430101M08|Mbs85	protein phosphatase 1, regulatory (inhibitor) subunit 12C	protein-coding
mm_85857.1	chr9	110743640	110743646	-	1	NA	promoter-TSS (NM_001083935)	promoter-TSS (NM_001083935)	43	NM_001083935	19228	Mm.3542	NM_011199	ENSMUSG00000032492	Pth1r	PPR|Pthr|Pthr1	parathyroid hormone 1 receptor	protein-coding
mm_42551.1	chr5	116438713	116438723	+	1	NA	promoter-TSS (NR_015595)	promoter-TSS (NR_015595)	-4	NR_015595	76798	Mm.444322	NR_015595	ENSMUSG00000086219	Srrm4os	2410137F16Rik	serine/arginine repetitive matrix 4, opposite strand	ncRNA
mm_118759.1	chr14	22394250	22394257	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	148545	NR_046307	74896	Mm.444661	NR_046307		4930405A10Rik	4930456G20Rik	RIKEN cDNA 4930405A10 gene	ncRNA
mm_67246.1	chr7	75309189	75309199	-	1	NA	promoter-TSS (NM_153579)	promoter-TSS (NM_153579)	68	NM_153579	64176	Mm.273082	NM_153579	ENSMUSG00000053025	Sv2b	A830038F04Rik|AI850768|mKIAA0735	synaptic vesicle glycoprotein 2 b	protein-coding
mm_42514.1	chr5	115544107	115544145	+	1	NA	intron (NM_133915, intron 1 of 11)	intron (NM_133915, intron 1 of 11)	-15341	NM_007475	11837	Mm.5286	NM_007475	ENSMUSG00000067274	Rplp0	36B4|Arbp|L10E	ribosomal protein, large, P0	protein-coding
mm_166118.1	chr4	150799592	150799611	-	1	NA	Intergenic	Intergenic	55348	NR_040649	73348	Mm.396218	NR_040649	ENSMUSG00000078492	1700045H11Rik	-	RIKEN cDNA 1700045H11 gene	ncRNA
mm_20606.1	chr2	131491685	131491714	-	1	NA	promoter-TSS (NM_001177840)	promoter-TSS (NM_001177840)	-163	NM_001177834	228608	Mm.136586	NM_145533	ENSMUSG00000027333	Smox	B130066H01Rik|PAO|PAOh1|SMO	spermine oxidase	protein-coding
mm_7418.1	chr1	119504737	119504795	-	1	NA	promoter-TSS (NM_022327)	promoter-TSS (NM_022327)	16	NM_022327	64143	Mm.27832	NM_022327	ENSMUSG00000004451	Ralb	5730472O18Rik	v-ral simian leukemia viral oncogene B	protein-coding
mm_65227.1	chr7	19715256	19715280	-	1	NA	5' UTR (NM_001109748, exon 1 of 9)	5' UTR (NM_001109748, exon 1 of 9)	161	NM_001109748	53333	Mm.61682	NM_016871	ENSMUSG00000002984	Tomm40	AW539759|Mom35|Tom40	translocase of outer mitochondrial membrane 40 homolog (yeast)	protein-coding
mm_52693.1	chr6	118348412	118348430	+	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-39702	NR_110507	102632423	Mm.261755	NR_110507	ENSMUSG00000107933	Gm30498	-	predicted gene, 30498	ncRNA
mm_163984.1	chr14	60379423	60379452	-	1	NA	exon (NM_001164705, exon 2 of 2)	exon (NM_001164705, exon 2 of 2)	1151	NM_001164705	72125	Mm.275499	NM_028113	ENSMUSG00000021986	Amer2	2600011E07Rik|Fam123a	APC membrane recruitment 2	protein-coding
mm_111459.1	chr12	98419625	98419644	-	1	NA	Intergenic	Intergenic	-104210	NR_136759	105245437	Mm.446375	NR_136759		Gm40893	-	predicted gene, 40893	ncRNA
mm_140498.1	chr17	3663563	3663567	-	1	NA	intron (NM_198958, intron 10 of 12)	intron (NM_198958, intron 10 of 12)	32696	NM_198958	224480	Mm.328756	NM_198958	ENSMUSG00000023802	Nox3	GP91-3|het|nmf250	NADPH oxidase 3	protein-coding
mm_53883.1	chr6	3345975	3345992	-	1	NA	Intergenic	Intergenic	53588	NM_010156	209086	Mm.196013	NM_010156	ENSMUSG00000047735	Samd9l	AA175286|ESTM25|mKIAA2005	sterile alpha motif domain containing 9-like	protein-coding
mm_30900.1	chr4	32336029	32336035	+	1	NA	Intergenic	Intergenic	-81403	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_131506.1	chr16	17451982	17452034	+	1	NA	promoter-TSS (NM_007764)	promoter-TSS (NM_007764)	23	NM_007764	12929	Mm.21048	NM_007764	ENSMUSG00000006134	Crkl	1110025F07Rik|AA589403|AI325100|Crkol	v-crk avian sarcoma virus CT10 oncogene homolog-like	protein-coding
mm_142973.1	chr17	56133933	56133941	-	1	NA	promoter-TSS (NM_013662)	promoter-TSS (NM_013662)	-85	NM_013662	20359	Mm.8029	NM_013662	ENSMUSG00000001227	Sema6b	Sema|Seman|VIb|semaZ	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B	protein-coding
mm_115389.1	chr13	113211322	113211325	+	1	NA	intron (NM_023612, intron 1 of 2)	(T)n|Simple_repeat|Simple_repeat	1664	NM_023612	71690	Mm.38929	NM_023612	ENSMUSG00000042379	Esm1	0610042H23Rik|AV004503|ESM-1	endothelial cell-specific molecule 1	protein-coding
mm_19647.1	chr2	102865358	102865408	-	1	NA	exon (NM_009851, exon 2 of 19)	exon (NM_009851, exon 2 of 19)	36282	NM_001177785	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_71461.1	chr8	46530377	46530405	+	1	NA	exon (NM_007981, exon 16 of 21)	exon (NM_007981, exon 16 of 21)	-21678	NM_027973	71876	Mm.22108	NM_027973	ENSMUSG00000031629	Cenpu	1700029A22Rik|Mlf1ip	centromere protein U	protein-coding
mm_91929.1	chr10	60358250	60358266	-	1	NA	exon (NM_001159572, exon 2 of 7)	exon (NM_001159572, exon 2 of 7)	11407	NM_028732	74048	Mm.273584	NM_028732	ENSMUSG00000020101	Vsir	4632428N05Rik|Dies1|PD-1H|VISTA	V-set immunoregulatory receptor	protein-coding
mm_42608.1	chr5	117841931	117841939	+	1	NA	Intergenic	CpG	-24904	NM_008712	18125	Mm.44249	NM_008712	ENSMUSG00000029361	Nos1	2310005C01Rik|N-NOS|NC-NOS|NO|NOS|NOS-I|Nos-1|bNOS|nNOS	nitric oxide synthase 1, neuronal	protein-coding
mm_164153.1	chr15	63998136	63998138	-	1	NA	intron (NM_144846, intron 1 of 11)	CpG	62311	NM_144846	223601	Mm.246108	NM_144846	ENSMUSG00000022378	Fam49b	0910001A06Rik|AW122079	family with sequence similarity 49, member B	protein-coding
mm_100549.1	chr11	120713979	120713999	+	1	NA	promoter-TSS (NM_016665)	promoter-TSS (NM_016665)	36	NM_153545	217366	Mm.347545	NM_153545	ENSMUSG00000025145	Lrrc45	BC023296	leucine rich repeat containing 45	protein-coding
mm_127971.1	chr15	12106904	12106910	-	1	NA	Intergenic	Intergenic	-10944	NM_011767	22763	Mm.273496	NM_011767	ENSMUSG00000022201	Zfr	C920030H05Rik	zinc finger RNA binding protein	protein-coding
mm_73766.1	chr8	115708505	115708529	+	1	NA	Intergenic	Intergenic	-1623	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_15356.1	chr2	156312429	156312481	+	1	NA	promoter-TSS (NM_027585)	promoter-TSS (NM_027585)	-18	NM_027585	70873	Mm.475234	NM_027585	ENSMUSG00000038085	Cnbd2	4921517L17Rik|5430421B09Rik|Cris	cyclic nucleotide binding domain containing 2	protein-coding
mm_127235.1	chr15	99408529	99408553	+	1	NA	3' UTR (NM_026669, exon 10 of 10)	3' UTR (NM_026669, exon 10 of 10)	15322	NM_001171035	110213	Mm.16769	NM_026669	ENSMUSG00000023010	Tmbim6	5031406P05Rik|Bi1|Tegt	transmembrane BAX inhibitor motif containing 6	protein-coding
mm_78862.1	chr9	44398345	44398361	+	1	NA	5' UTR (NM_008063, exon 1 of 8)	5' UTR (NM_008063, exon 1 of 8)	177	NM_008063	14385	Mm.30087	NM_008063	ENSMUSG00000032114	Slc37a4	100043178|G6PT|G6pt1|GSD-1b|mG6PT	solute carrier family 37 (glucose-6-phosphate transporter), member 4	protein-coding
mm_16303.1	chr2	174289644	174289677	+	1	NA	intron (NR_002846, intron 1 of 4)	(CA)n|Simple_repeat|Simple_repeat	5340	NM_022000	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_142297.1	chr17	40934450	40934493	-	1	NA	promoter-TSS (NM_031863)	promoter-TSS (NM_031863)	80	NM_031863	83815	Mm.9870	NM_031863	ENSMUSG00000023919	Cenpq	2610528M18Rik	centromere protein Q	protein-coding
mm_155608.1	chrX	83043220	83043226	+	1	NA	intron (NM_007868, intron 1 of 78)	intron (NM_007868, intron 1 of 78)	94353	NM_007868	13405	Mm.275608	NM_007868	ENSMUSG00000045103	Dmd	DXSmh7|DXSmh9|Dp427|Dp71|dys|mdx|pke	dystrophin, muscular dystrophy	protein-coding
mm_50873.1	chr6	55452256	55452267	+	1	NA	5' UTR (NM_001025372, exon 1 of 16)	5' UTR (NM_001025372, exon 1 of 16)	283	NM_007407	11517	Mm.44245	NM_007407	ENSMUSG00000029778	Adcyap1r1	2900024I10Rik|AI846590|PAC1|PAC1R|PACAP1-R	adenylate cyclase activating polypeptide 1 receptor 1	protein-coding
mm_56838.1	chr6	117179828	117179849	-	1	NA	3' UTR (NM_001012477, exon 4 of 4)	3' UTR (NM_001012477, exon 4 of 4)	11303	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_52294.1	chr6	108697810	108697819	+	1	NA	Intergenic	RSINE1|SINE|B4	-36880	NR_104577	75394	Mm.395061	NR_040757	ENSMUSG00000087341	0610040F04Rik	-	RIKEN cDNA 0610040F04 gene	ncRNA
mm_152989.1	chr19	29648343	29648353	-	1	NA	promoter-TSS (NM_001081213)	promoter-TSS (NM_001081213)	72	NM_001081213	226090	Mm.267131	NM_146098	ENSMUSG00000046324	Ermp1	D19Ertd410e|D19Wsu12e|Fxna|mKIAA1815	endoplasmic reticulum metallopeptidase 1	protein-coding
mm_102739.1	chr11	67251898	67251910	-	1	NA	exon (NM_010855, exon 23 of 40)	exon (NM_010855, exon 23 of 40)	14092	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_114361.1	chr13	61712976	61712998	+	1	NA	Intergenic	Intergenic	-58593	NR_028430	432812	Mm.317358	NR_028430		BC052688	-	cDNA sequence BC052688	pseudo
mm_166950.1	chr7	43980298	43980344	+	1	NA	TTS (NM_010116)	TTS (NM_010116)	4260	NM_010116	13648	Mm.440884	NM_010116	ENSMUSG00000059042	Klk1b9	EGF-BP C|Egfbp-3|Egfbp3|KAL|Klk9|kallikrein|mGk-9	kallikrein 1-related peptidase b9	protein-coding
mm_121344.1	chr14	115994944	115994947	+	1	NA	intron (NM_175500, intron 7 of 7)	intron (NM_175500, intron 7 of 7)	-585393	NR_045761	75088	Mm.444706	NR_045761	ENSMUSG00000093551	4930505G20Rik	-	RIKEN cDNA 4930505G20 gene	ncRNA
mm_154437.1	chrM	873	884	-	1	NA	NA	Intergenic	NA	NA								
mm_41974.1	chr5	107431542	107431558	+	1	NA	promoter-TSS (NM_027599)	promoter-TSS (NM_027599)	1	NM_027599	70902	Mm.55870	NM_027599	ENSMUSG00000033794	Lpcat2b	4921521K07Rik|Aytl1b	lysophosphatidylcholine acyltransferase 2B	protein-coding
mm_90306.1	chr10	126978929	126978973	+	1	NA	5' UTR (NM_001113470, exon 1 of 8)	5' UTR (NM_001113470, exon 1 of 8)	234	NM_001113470	52468	Mm.29490	NM_146012	ENSMUSG00000078429	Ctdsp2	AI586070|D10Ertd73e|OS-4|OS4|SCP2	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 2	protein-coding
mm_3045.1	chr1	134040420	134040430	+	1	NA	exon (NM_021355, exon 2 of 3)	exon (NM_021355, exon 2 of 3)	2910	NM_021355	14264	Mm.287146	NM_021355	ENSMUSG00000041559	Fmod	AI131919|AU041740|SLRR2E	fibromodulin	protein-coding
mm_100226.1	chr11	117115260	117115285	+	1	NA	promoter-TSS (NM_001166506)	promoter-TSS (NM_001166506)	100	NM_001166506	74136	Mm.272312	NM_028777	ENSMUSG00000020823	Sec14l1	1200017E04Rik|2810012L19Rik|Naa-35	SEC14-like lipid binding 1	protein-coding
mm_40386.1	chr5	52719855	52719856	+	1	NA	Intergenic	Lx8|LINE|L1	-21719	NM_028744	67073	Mm.248647	NM_025951	ENSMUSG00000029186	Pi4k2b	2610042N09Rik|4933409G22Rik	phosphatidylinositol 4-kinase type 2 beta	protein-coding
mm_4434.1	chr1	172506718	172506735	+	1	NA	3' UTR (NM_178598, exon 5 of 5)	3' UTR (NM_178598, exon 5 of 5)	6480	NM_178598	21346	Mm.271711	NM_178598	ENSMUSG00000026547	Tagln2	2700094C18Rik|SM22beta|Sm22B|Sm22a	transgelin 2	protein-coding
mm_80608.1	chr9	86757870	86757871	+	1	NA	TTS (NM_178738)	TTS (NM_178738)	14237	NM_178738	244954	Mm.257629	NM_178738	ENSMUSG00000033491	Prss35	6030424L22Rik|P3D9	protease, serine 35	protein-coding
mm_72052.1	chr8	71367497	71367540	+	1	NA	intron (NM_001145780, intron 2 of 8)	intron (NM_001145780, intron 2 of 8)	301	NM_025917	67023	Mm.41890	NM_025917	ENSMUSG00000002395	Use1	2010315L10Rik|5730403H22Rik|AV002165|D12|Ed2|Q-snare|p31	unconventional SNARE in the ER 1 homolog (S. cerevisiae)	protein-coding
mm_161717.1	chr17	25944927	25944927	-	1	NA	promoter-TSS (NM_001039038)	promoter-TSS (NM_001039038)	4	NM_001039038	621239	Mm.381070	NM_001039038	ENSMUSG00000090113	Nhlrc4	F430201B04Rik	NHL repeat containing 4	protein-coding
mm_170320.1	chr18	40308090	40308094	-	1	NA	intron (NM_026135, intron 1 of 1)	intron (NM_026135, intron 1 of 1)	49731	NM_026135	383348	Mm.76366	NM_026135	ENSMUSG00000051401	Kctd16	4930434H12Rik|Gm1267	potassium channel tetramerisation domain containing 16	protein-coding
mm_16800.1	chr2	10117439	10117450	-	1	NA	exon (NM_010582, exon 7 of 21)	exon (NM_010582, exon 7 of 21)	13239	NM_010582	16425	Mm.182043	NM_010582	ENSMUSG00000037254	Itih2	AI747202|Intin2|Itih-2	inter-alpha trypsin inhibitor, heavy chain 2	protein-coding
mm_131217.1	chr16	8835965	8835970	+	1	NA	intron (NM_001081400, intron 2 of 3)	intron (NM_001081400, intron 2 of 3)	5867	NM_001081400	69053	Mm.390868	NM_001081400	ENSMUSG00000022507	1810013L24Rik	1110017P05Rik|3010002C02Rik|AA792997|AW124177|Gm19906|R74903	RIKEN cDNA 1810013L24 gene	protein-coding
mm_127075.1	chr15	97383959	97383972	+	1	NA	intron (NM_172293, intron 5 of 5)	intron (NM_172293, intron 5 of 5)	-136678	NM_001164602	105827	Mm.24005	NM_178114	ENSMUSG00000048218	Amigo2	AI415330|AMIGO-2|AW208913|Ali1	adhesion molecule with Ig like domain 2	protein-coding
mm_143050.1	chr17	56906219	56906234	-	1	NA	intron (NM_022328, intron 3 of 11)	intron (NM_022328, intron 3 of 11)	29162	NM_022328	64144	Mm.148748	NM_022328	ENSMUSG00000024212	Mllt1	AA407901|BAM11|ENL|LTG19	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 1	protein-coding
mm_118398.1	chr13	119389284	119389285	-	1	NA	intron (NM_001308506, intron 4 of 16)	intron (NM_001308506, intron 4 of 16)	19727	NM_008710	18115	Mm.132584	NM_008710	ENSMUSG00000025453	Nnt	4930423F13Rik|AI323702|BB168308	nicotinamide nucleotide transhydrogenase	protein-coding
mm_170890.1	chr2	24985946	24985950	+	1	NA	intron (NM_146251, intron 7 of 34)	intron (NM_146251, intron 7 of 34)	9915	NM_146251	241274	Mm.389243	NM_146251	ENSMUSG00000036833	Pnpla7	BC027342|E430013P11Rik|Nre	patatin-like phospholipase domain containing 7	protein-coding
mm_145711.1	chr18	62937210	62937220	+	1	NA	exon (NM_133237, exon 3 of 5)	exon (NM_133237, exon 3 of 5)	14888	NM_133237	494504	Mm.391102	NM_133237	ENSMUSG00000071847	Apcdd1	AB023957|AU041258|Drapc1|EIG180	adenomatosis polyposis coli down-regulated 1	protein-coding
mm_167657.1	chr9	70768714	70768721	+	1	NA	intron (NM_007399, intron 13 of 15)	intron (NM_007399, intron 13 of 15)	89735	NM_007399	11487	Mm.3037	NM_007399	ENSMUSG00000054693	Adam10	1700031C13Rik|MADM|kuz|kuzbanian	a disintegrin and metallopeptidase domain 10	protein-coding
mm_76156.1	chr8	82357396	82357406	-	1	NA	intron (NM_008357, intron 2 of 7)	Lx9|LINE|L1	45185	NM_001254747	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_87326.1	chr10	42861579	42861588	+	1	NA	intron (NM_172938, intron 1 of 8)	intron (NM_172938, intron 1 of 8)	1071	NM_172938	268297	Mm.98731	NM_172938	ENSMUSG00000044770	Scml4	9330161D17|mFLJ00197	sex comb on midleg-like 4 (Drosophila)	protein-coding
mm_163956.1	chr14	54711904	54711949	-	1	NA	exon (NM_207131, exon 1 of 2)	exon (NM_207131, exon 1 of 2)	248	NM_207131	110794	Mm.236223	NM_207131	ENSMUSG00000052435	Cebpe	C/EBPe|CRP1|Gm294	CCAAT/enhancer binding protein (C/EBP), epsilon	protein-coding
mm_38013.1	chr4	133753861	133753869	-	1	NA	promoter-TSS (NM_001080819)	promoter-TSS (NM_001080819)	-254	NM_001080819	93760	Mm.22478	NM_001080819	ENSMUSG00000007880	Arid1a	1110030E03Rik|BAF250a|Osa1|Smarcf1	AT rich interactive domain 1A (SWI-like)	protein-coding
mm_19955.1	chr2	117342820	117342822	-	1	NA	promoter-TSS (NM_011246)	promoter-TSS (NM_011246)	56	NM_011246	19419	Mm.42150	NM_011246	ENSMUSG00000027347	Rasgrp1	Rasgrp	RAS guanyl releasing protein 1	protein-coding
mm_3533.1	chr1	150319408	150319449	+	1	NA	promoter-TSS (NM_024458)	promoter-TSS (NM_024458)	11	NM_001159730	20028	Mm.440883	NM_024458	ENSMUSG00000006007	Pdc	Rpr-1|Rpr1	phosducin	protein-coding
mm_99835.1	chr11	109011832	109011859	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	91496	NM_015732	12006	Mm.71710	NM_015732	ENSMUSG00000000142	Axin2	Axi1|Axil|Conductin	axin 2	protein-coding
mm_51286.1	chr6	72304593	72304623	+	1	NA	promoter-TSS (NM_001282071)	promoter-TSS (NM_001282071)	-2	NM_001282071	20388	Mm.46033	NM_147779	ENSMUSG00000056370	Sftpb	AI562151|SF-B|SP-B|Sftp-3|Sftp3	surfactant associated protein B	protein-coding
mm_3613.1	chr1	152229858	152229858	+	1	NA	Intergenic	Intergenic	-139538	NM_197990	69399	Mm.278031	NM_197990	ENSMUSG00000032666	1700025G04Rik	2610510E02Rik|2900042O04Rik|ENSMUSG00000073540	RIKEN cDNA 1700025G04 gene	protein-coding
mm_60188.1	chr7	43351379	43351412	+	1	NA	promoter-TSS (NM_145581)	promoter-TSS (NM_145581)	54	NM_145581	233186	Mm.290569	NM_145581	ENSMUSG00000039013	Siglecf	Siglec5|mSiglec-F	sialic acid binding Ig-like lectin F	protein-coding
mm_137318.1	chr17	24891358	24891362	+	1	NA	TTS (NM_001163102)	TTS (NM_001163102)	3727	NM_001163102	193838	Mm.440199	NM_001163102	ENSMUSG00000073436	Eme2	2810013J18Rik	essential meiotic structure-specific endonuclease subunit 2	protein-coding
mm_142332.1	chr17	43504329	43504331	-	1	NA	Intergenic	Intergenic	-1557	NM_008585	17287	Mm.5346	NM_008585	ENSMUSG00000023914	Mep1a	AI098089|AW107200|Mep-1|Mep-1a|Mep1	meprin 1 alpha	protein-coding
mm_36674.1	chr4	96348574	96348583	-	1	NA	5' UTR (NM_001004141, exon 1 of 9)	5' UTR (NM_001004141, exon 1 of 9)	102	NM_001004141	100066	Mm.26915	NM_001004141	ENSMUSG00000066097	Cyp2j11	AI314783|Cyp2j11-ps	cytochrome P450, family 2, subfamily j, polypeptide 11	protein-coding
mm_104281.1	chr11	89777678	89777697	-	1	NA	Intergenic	Intergenic	-80751	NM_001327810	382543	Mm.60997	NM_172534	ENSMUSG00000047773	Ankfn1	4932411E22Rik|Gm1175|nmf9	ankyrin-repeat and fibronectin type III domain containing 1	protein-coding
mm_67235.1	chr7	75308280	75308338	-	1	NA	promoter-TSS (NM_001109753)	promoter-TSS (NM_001109753)	77	NM_001109753	64176	Mm.273082	NM_153579	ENSMUSG00000053025	Sv2b	A830038F04Rik|AI850768|mKIAA0735	synaptic vesicle glycoprotein 2 b	protein-coding
mm_37038.1	chr4	115492115	115492127	-	1	NA	exon (NM_007822, exon 6 of 12)	exon (NM_007822, exon 6 of 12)	4020	NM_007822	13119	Mm.250901	NM_007822	ENSMUSG00000028715	Cyp4a14	AI314743	cytochrome P450, family 4, subfamily a, polypeptide 14	protein-coding
mm_12333.1	chr2	69647212	69647272	+	1	NA	promoter-TSS (NM_028284)	promoter-TSS (NM_028284)	-13	NM_028284	72569	Mm.252136	NM_028284	ENSMUSG00000063145	Bbs5	1700049I01Rik|2700023J09Rik	Bardet-Biedl syndrome 5 (human)	protein-coding
mm_42509.1	chr5	115519685	115519746	+	1	NA	intron (NM_133915, intron 1 of 11)	B3|SINE|B2	13039	NM_133915	19303	Mm.18714	NM_011223	ENSMUSG00000029528	Pxn	AW108311|AW123232|Pax	paxillin	protein-coding
mm_96562.1	chr11	69020906	69020908	+	1	NA	intron (NM_001143790, intron 1 of 22)	U4|snRNA|snRNA	4996	NM_001013256	68964	Mm.285785	NM_001013256	ENSMUSG00000020898	Ctc1	1500010J02Rik|AAF-132|AAF132	CTS telomere maintenance complex component 1	protein-coding
mm_6715.1	chr1	82291598	82291617	-	1	NA	promoter-TSS (NM_010570)	promoter-TSS (NM_010570)	-168	NM_010570	16367	Mm.4952	NM_010570	ENSMUSG00000055980	Irs1	G972R|IRS-1	insulin receptor substrate 1	protein-coding
mm_2051.1	chr1	87404948	87404960	+	1	NA	intron (NM_001110212, intron 9 of 28)	intron (NM_001110212, intron 9 of 28)	-10225	NM_001110227	100040591	Mm.443539	NM_001110227	ENSMUSG00000079436	Kcnj13	-	potassium inwardly-rectifying channel, subfamily J, member 13	protein-coding
mm_126791.1	chr15	86333773	86333784	+	1	NA	intron (NM_145476, intron 8 of 12)	intron (NM_145476, intron 8 of 12)	119319	NM_145476	223754	Mm.28904	NM_145476	ENSMUSG00000051864	Tbc1d22a	BC023106|D15Ertd781e	TBC1 domain family, member 22a	protein-coding
mm_134962.1	chr16	31429647	31429691	-	1	NA	intron (NM_001122683, intron 1 of 6)	CpG	916	NM_001122683	71911	Mm.293470	NM_175177	ENSMUSG00000046598	Bdh1	2310032J20Rik|AI327223|Bdh	3-hydroxybutyrate dehydrogenase, type 1	protein-coding
mm_97526.1	chr11	78501850	78501882	+	1	NA	exon (NM_011707, exon 7 of 8)	exon (NM_011707, exon 7 of 8)	-1647	NM_008759	18292	Mm.134360	NM_008759	ENSMUSG00000001103	Sebox	OG9|Og9x	SEBOX homeobox	protein-coding
mm_149581.1	chr19	15599253	15599256	+	1	NA	Intergenic	Intergenic	325368	NM_001205339	107272	Mm.289936	NM_177420	ENSMUSG00000024640	Psat1	D8Ertd814e|EPIP|PSA|Psat	phosphoserine aminotransferase 1	protein-coding
mm_16675.1	chr2	6858002	6858009	-	1	NA	intron (NM_001110229, intron 2 of 14)	L1_Mur3|LINE|L1	14030	NM_001347094	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_127892.1	chr15	9155361	9155378	-	1	NA	promoter-TSS (NM_001285980)	promoter-TSS (NM_001285980)	56	NM_001285980	27401	Mm.35584	NM_013787	ENSMUSG00000054115	Skp2	4930500A04Rik|FBXL1|FWD1|p45	S-phase kinase-associated protein 2 (p45)	protein-coding
mm_99324.1	chr11	101442694	101442718	+	1	NA	intron (NM_011289, intron 1 of 4)	CpG	461	NM_011289	19942	Mm.340658	NM_011289	ENSMUSG00000063316	Rpl27	-	ribosomal protein L27	protein-coding
mm_3715.1	chr1	153909230	153909241	+	1	NA	3' UTR (NM_008131, exon 7 of 7)	3' UTR (NM_008131, exon 7 of 7)	9306	NM_008131	14645	Mm.210745	NM_008131	ENSMUSG00000026473	Glul	GS|Glns	glutamate-ammonia ligase (glutamine synthetase)	protein-coding
mm_72528.1	chr8	83982796	83982803	+	1	NA	intron (NM_001277898, intron 3 of 9)	intron (NM_001277898, intron 3 of 9)	5916	NM_001277898	18747	Mm.19111	NM_008854	ENSMUSG00000005469	Prkaca	PKCD|Pkaca	protein kinase, cAMP dependent, catalytic, alpha	protein-coding
mm_11274.1	chr2	30061921	30061929	+	1	NA	promoter-TSS (NM_023871)	promoter-TSS (NM_023871)	-71	NM_023871	56086	Mm.326055	NM_023871	ENSMUSG00000054766	Set	2610030F17Rik|5730420M11Rik|AA407739|I-2PP2A|StF-IT-1|TAF-I	SET nuclear oncogene	protein-coding
mm_41219.1	chr5	88583592	88583602	+	1	NA	promoter-TSS (NM_027530)	promoter-TSS (NM_027530)	84	NM_027530	52822	Mm.270469	NM_027530	ENSMUSG00000029291	Rufy3	2810428M05Rik|6330416M07Rik|AW455998|AW538594|D5Bwg0860e|Ripx|Rpipx	RUN and FYVE domain containing 3	protein-coding
mm_33007.1	chr4	120666615	120666623	+	1	NA	promoter-TSS (NM_019563)	promoter-TSS (NM_019563)	56	NM_019563	56222	Mm.272646	NM_019563	ENSMUSG00000070803	Cited4	MRG-2|Mrg2	Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 4	protein-coding
mm_27682.1	chr3	65958200	65958222	-	1	NA	promoter-TSS (NM_019937)	promoter-TSS (NM_019937)	14	NM_019937	56706	Mm.175612	NM_019937	ENSMUSG00000027829	Ccnl1	2610030E23Rik|AU018493|Ccnl|ania-6a	cyclin L1	protein-coding
mm_112136.1	chr12	113000393	113000466	-	1	NA	5' UTR (NM_028193, exon 1 of 18)	5' UTR (NM_028193, exon 1 of 18)	192	NM_028193	72308	Mm.196721	NM_028193	ENSMUSG00000011158	Brf1	2510002F24Rik|GTF3B|TAF3C|TAFIII90|TFIIIB90|mTFIIIB90	BRF1, RNA polymerase III transcription initiation factor 90 kDa subunit	protein-coding
mm_55657.1	chr6	72390486	72390583	-	1	NA	5' UTR (NM_016794, exon 1 of 3)	5' UTR (NM_016794, exon 1 of 3)	133	NM_016794	22320	Mm.1838	NM_016794	ENSMUSG00000050732	Vamp8	AU041171|Edb|endobrevin	vesicle-associated membrane protein 8	protein-coding
mm_48986.1	chr6	4755724	4755751	+	1	NA	exon (NM_130877, exon 2 of 2)	exon (NM_130877, exon 2 of 2)	8431	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_129418.1	chr15	78395877	78395893	-	1	NA	promoter-TSS (NM_028522)	promoter-TSS (NM_028522)	27	NM_028522	73376	Mm.73222	NM_028522	ENSMUSG00000062154	Tex33	1700061J05Rik|Ean57	testis expressed 33	protein-coding
mm_159231.1	chr2	136532288	136532288	+	1	NA	promoter-TSS (NM_175667)	promoter-TSS (NM_175667)	-33	NM_175667	319196	Mm.477841	NM_175667	ENSMUSG00000074771	Ankef1	AV276460|Ankrd5	ankyrin repeat and EF-hand domain containing 1	protein-coding
mm_136434.1	chr16	94370968	94370990	-	1	NA	promoter-TSS (NM_001159620)	promoter-TSS (NM_001159620)	36	NM_019543	56176	Mm.474449	NM_019543	ENSMUSG00000022940	Pigp	Dcrc|Dscr5	phosphatidylinositol glycan anchor biosynthesis, class P	protein-coding
mm_30388.1	chr3	152247226	152247236	-	1	NA	exon (NM_199465, exon 8 of 13)	exon (NM_199465, exon 8 of 13)	19089	NM_199465	68810	Mm.200188	NM_199465	ENSMUSG00000039103	Nexn	1110046H09Rik|AA553326|NELIN	nexilin	protein-coding
mm_96806.1	chr11	69990452	69990483	+	1	NA	promoter-TSS (NM_019749)	promoter-TSS (NM_019749)	-903	NM_019749	56486	Mm.272460	NM_019749	ENSMUSG00000018567	Gabarap	-	gamma-aminobutyric acid receptor associated protein	protein-coding
mm_4955.1	chr1	191247908	191247941	+	1	NA	Intergenic	Intergenic	-64591	NM_007498	11910	Mm.2706	NM_007498	ENSMUSG00000026628	Atf3	LRG-21	activating transcription factor 3	protein-coding
mm_53846.1	chr6	148992716	148992721	+	1	NA	3' UTR (NM_177192, exon 21 of 21)	3' UTR (NM_177192, exon 21 of 21)	-46286	NM_019643	56306	Mm.18637	NM_019643	ENSMUSG00000039985	Fam60a	Ppcs1|Pptcs1|Tera	family with sequence similarity 60, member A	protein-coding
mm_51597.1	chr6	84008363	84008404	+	1	NA	promoter-TSS (NM_001077694)	promoter-TSS (NM_001077694)	-215	NM_001077694	26903	Mm.220982	NM_021469	ENSMUSG00000033788	Dysf	2310004N10Rik|AI604795|D6Pas3	dysferlin	protein-coding
mm_64841.1	chr7	13009796	13009856	-	1	NA	promoter-TSS (NM_001024699)	promoter-TSS (NM_001024699)	-26	NM_001024699	232879	Mm.279272	NM_001024699	ENSMUSG00000049600	Zbtb45	BB161562|Gm157|Zfp499	zinc finger and BTB domain containing 45	protein-coding
mm_23060.1	chr3	35855836	35855844	+	1	NA	3' UTR (NM_029570, exon 30 of 30)	3' UTR (NM_029570, exon 30 of 30)	74234	NM_033623	114893	Mm.374810	NM_033623	ENSMUSG00000027708	Dcun1d1	Rp42|SCCRO|Tes3|pTes3	DCN1, defective in cullin neddylation 1, domain containing 1 (S. cerevisiae)	protein-coding
mm_112986.1	chr13	21362930	21362937	+	1	NA	intron (NM_016684, intron 1 of 3)	CpG	113	NM_016684	22758	Mm.24124	NM_016684	ENSMUSG00000036721	Zscan12	2510038J07Rik|FPM315|Zfp96|mKIAA0426|zfp-96	zinc finger and SCAN domain containing 12	protein-coding
mm_112959.1	chr13	21180163	21180176	+	1	NA	5' UTR (NM_009054, exon 1 of 8)	5' UTR (NM_009054, exon 1 of 8)	238	NM_009054	19720	Mm.314056	NM_009054	ENSMUSG00000021326	Trim27	AW538890|Gm19403|Rfp	tripartite motif-containing 27	protein-coding
mm_70499.1	chr8	12826194	12826215	+	1	NA	intron (NR_121603, intron 9 of 29)	intron (NR_121603, intron 9 of 29)	5715	NR_045775	100504249	Mm.441494	NR_045775	ENSMUSG00000084780	Gm15350	OTTMUSG00000020611	predicted gene 15350	ncRNA
mm_68759.1	chr7	121520617	121520619	-	1	NA	Intergenic	Intergenic	69218	NR_102286	75793	Mm.23397	NR_102286		4933432K03Rik	1700001C18Rik|4930433G11Rik|AI428127	RIKEN cDNA 4933432K03 gene	ncRNA
mm_19337.1	chr2	90580542	90580548	-	1	NA	exon (NM_008982, exon 1 of 24)	exon (NM_008982, exon 1 of 24)	102	NM_008982	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_43386.1	chr5	135732748	135732774	+	1	NA	exon (NM_008898, exon 10 of 16)	exon (NM_008898, exon 10 of 16)	3128	NR_106001	102466791		NR_106001	ENSMUSG00000099197	Mir7034	Gm27372|mmu-mir-7034	microRNA 7034	ncRNA
mm_133640.1	chr16	91729403	91729435	+	1	NA	promoter-TSS (NM_001110276)	promoter-TSS (NM_001110276)	48	NM_010587	16443	Mm.40546	NM_010587	ENSMUSG00000022957	Itsn1	AA517634|AA545208|AI316805|AI839402|AI848451|Ehsh1|Ese1|Itsn|Sh3p17	intersectin 1 (SH3 domain protein 1A)	protein-coding
mm_96003.1	chr11	59450131	59450140	+	1	NA	promoter-TSS (NM_178659)	promoter-TSS (NM_178659)	90	NM_001205068	194952	Mm.295954	NM_178659	ENSMUSG00000036819	Jmjd4	6430559I23	jumonji domain containing 4	protein-coding
mm_72138.1	chr8	71951055	71951130	+	1	NA	promoter-TSS (NM_001164581)	promoter-TSS (NM_001164581)	26	NM_001164581	234413	Mm.334607	NM_001164581	ENSMUSG00000052446	Zfp961	A230105L22Rik|BC065788|mszf37|mszf55-2	zinc finger protein 961	protein-coding
mm_63989.1	chr7	140096721	140096731	+	1	NA	exon (NM_009475, exon 4 of 5)	exon (NM_009475, exon 4 of 5)	3330	NM_009475	22264	Mm.439707	NM_009475	ENSMUSG00000025467	Prap1	Upa	proline-rich acidic protein 1	protein-coding
mm_159921.1	chr6	54452976	54452976	+	1	NA	promoter-TSS (NM_001167861)	promoter-TSS (NM_001167861)	93	NM_001167861	330319	Mm.434326	NM_001167860	ENSMUSG00000086040	Wipf3	9030621G03|BQ952480	WAS/WASL interacting protein family, member 3	protein-coding
mm_37986.1	chr4	133623070	133623076	-	1	NA	intron (NM_001017968, intron 2 of 7)	B3|SINE|B2	10356	NM_001017968	503610	Mm.331948	NM_001017968	ENSMUSG00000037553	Zdhhc18	-	zinc finger, DHHC domain containing 18	protein-coding
mm_19143.1	chr2	80447408	80447425	-	1	NA	promoter-TSS (NM_011356)	promoter-TSS (NM_011356)	-20	NM_011356	20378	Mm.427436	NM_011356	ENSMUSG00000027004	Frzb	Frp|Sfrp3|frezzled|fritz|frzb-1	frizzled-related protein	protein-coding
mm_161542.1	chr15	103240454	103240454	+	1	NA	promoter-TSS (NM_010447)	promoter-TSS (NM_010447)	0	NR_002883	434858	Mm.391346	NR_002883		Gm5643	EG434858	heterogeneous nuclear ribonucleoprotein A1 pseudogene	pseudo
mm_9649.1	chr1	177443082	177443085	-	1	NA	Intergenic	Intergenic	-1578	NM_001012330	30928	Mm.330700	NM_013915	ENSMUSG00000063659	Zbtb18	RP58|Zfp238|Znf238	zinc finger and BTB domain containing 18	protein-coding
mm_130281.1	chr15	96747712	96747727	-	1	NA	Intergenic	Charlie4z|DNA|hAT-Charlie	-48021	NM_175121	67760	Mm.46754	NM_175121	ENSMUSG00000022462	Slc38a2	5033402L14Rik|AI316867|ATA2|SAT2|mKIAA1382	solute carrier family 38, member 2	protein-coding
mm_3153.1	chr1	135154625	135154640	+	1	NA	intron (NM_026823, intron 5 of 6)	intron (NM_026823, intron 5 of 6)	7798	NM_026823	68724	Mm.174998	NM_026823	ENSMUSG00000026426	Arl8a	1110033P22Rik|Arl10b|gie2	ADP-ribosylation factor-like 8A	protein-coding
mm_46418.1	chr5	104113450	104113472	-	1	NA	5' UTR (NM_010097, exon 1 of 11)	5' UTR (NM_010097, exon 1 of 11)	627	NM_010097	13602	Mm.29027	NM_010097	ENSMUSG00000029309	Sparcl1	Ecm2|Sc1|hevin|mast9	SPARC-like 1	protein-coding
mm_164863.1	chr18	54990655	54990683	-	1	NA	promoter-TSS (NM_175751)	promoter-TSS (NM_175751)	-489	NM_175751	269023	Mm.192984	NM_175751	ENSMUSG00000052713	Zfp608	4932417D18Rik|D430007A19Rik|Znf608	zinc finger protein 608	protein-coding
mm_135232.1	chr16	36897135	36897141	-	1	NA	promoter-TSS (NR_040476)	promoter-TSS (NR_040476)	51	NR_040476	68306	Mm.399193	NR_040476	ENSMUSG00000084834	4930565N06Rik	4930428L02Rik	RIKEN cDNA 4930565N06 gene	ncRNA
mm_19723.1	chr2	104441301	104441313	-	1	NA	exon (NM_001145824, exon 4 of 16)	exon (NM_001145824, exon 4 of 16)	-12367	NR_035432	100316678		NR_035432	ENSMUSG00000084516	Mir1902	Mirn1902|mmu-mir-1902	microRNA 1902	ncRNA
mm_109977.1	chr12	12940377	12940388	-	1	NA	exon (NM_008709, exon 2 of 3)	exon (NM_008709, exon 2 of 3)	1454	NM_008709	18109	Mm.16469	NM_008709	ENSMUSG00000037169	Mycn	N-myc|Nmyc|Nmyc-1|Nmyc1|bHLHe37|c-nmyc	v-myc avian myelocytomatosis viral related oncogene, neuroblastoma derived	protein-coding
mm_109940.1	chr12	11326192	11326215	-	1	NA	3' UTR (NM_012038, exon 4 of 4)	3' UTR (NM_012038, exon 4 of 4)	26316	NR_106136	102465775		NR_106136	ENSMUSG00000098879	Mir7675	Gm27965|mmu-mir-7675	microRNA 7675	ncRNA
mm_166936.1	chr7	36729443	36729447	+	1	NA	intron (NM_172298, intron 1 of 1)	intron (NM_172298, intron 1 of 1)	31327	NM_172298	243931	Mm.44141	NM_172298	ENSMUSG00000021217	Tshz3	A630038G13Rik|Tsh3|Zfp537|mKIAA1474|teashirt3	teashirt zinc finger family member 3	protein-coding
mm_15735.1	chr2	164237210	164237210	+	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	1131	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_128880.1	chr15	73061224	73061234	-	1	NA	promoter-TSS (NM_001164643)	promoter-TSS (NM_001164643)	-25	NM_001164643	76510	Mm.158902	NM_029640	ENSMUSG00000047921	Trappc9	1810044A24Rik|2900005P22Rik|4632408O18Rik|Ibp|Nibp|TRS130|mKIAA1882	trafficking protein particle complex 9	protein-coding
mm_36311.1	chr4	69758504	69758524	-	1	NA	Intergenic	Intergenic	651921	NM_001313762	214444	Mm.370777	NM_145990	ENSMUSG00000039298	Cdk5rap2	2900018K03Rik|an|mKIAA1633	CDK5 regulatory subunit associated protein 2	protein-coding
mm_129939.1	chr15	84856066	84856091	-	1	NA	promoter-TSS (NM_001081166)	promoter-TSS (NM_001081166)	51	NM_001081166	271305	Mm.101022	NM_001081166	ENSMUSG00000016624	Phf21b	A730032D07Rik	PHD finger protein 21B	protein-coding
mm_49302.1	chr6	17749141	17749151	+	1	NA	promoter-TSS (NM_001083315)	promoter-TSS (NM_001083315)	-24	NM_001083315	64213	Mm.12051	NM_022332	ENSMUSG00000029534	St7	9430001H04Rik|Fam4a2|HELG|RAY1|SEN4|TSG7	suppression of tumorigenicity 7	protein-coding
mm_150691.1	chr19	42147414	42147426	+	1	NA	promoter-TSS (NM_183195)	promoter-TSS (NM_183195)	31	NM_183195	277010	Mm.206250	NM_183195	ENSMUSG00000044345	Marveld1	AI504298|Mrvldc1	MARVEL (membrane-associating) domain containing 1	protein-coding
mm_6209.1	chr1	66816936	66816968	-	1	NA	intron (NM_177645, intron 1 of 13)	CpG	643	NM_177645	68691	Mm.240912	NM_177645	ENSMUSG00000026004	Kansl1l	1110028C15Rik|1190030G24|AI427598|C430010P07Rik|mKIAA4189	KAT8 regulatory NSL complex subunit 1-like	protein-coding
mm_99052.1	chr11	99051440	99051453	+	1	NA	exon (NM_010517, exon 4 of 4)	exon (NM_010517, exon 4 of 4)	10186	NM_010517	16010	Mm.233799	NM_010517	ENSMUSG00000017493	Igfbp4	AI875747|Deb2|IGFBP-4	insulin-like growth factor binding protein 4	protein-coding
mm_142206.1	chr17	36988575	36988587	-	1	NA	exon (NM_001115075, exon 3 of 6)	exon (NM_001115075, exon 3 of 6)	923	NM_001115075	240095	Mm.246609	NM_001115075	ENSMUSG00000024459	H2-M5	CRW2|D130003B22Rik|H-2M5	histocompatibility 2, M region locus 5	protein-coding
mm_25414.1	chr3	107368385	107368389	+	1	NA	Intergenic	Intergenic	-35098	NM_001045807	229700	Mm.27966	NM_001045807	ENSMUSG00000048109	Rbm15	C230088J01Rik|mKIAA1438	RNA binding motif protein 15	protein-coding
mm_84485.1	chr9	66845662	66845681	-	1	NA	3' UTR (NM_173413, exon 8 of 8)	3' UTR (NM_173413, exon 8 of 8)	-10965	NM_026674	68318	Mm.284229	NM_026674	ENSMUSG00000053040	Aph1c	0610008A10Rik|APH-1b|Aph1b	aph1 homolog C, gamma secretase subunit	protein-coding
mm_41845.1	chr5	104435113	104435128	+	1	NA	promoter-TSS (NM_001204203)	promoter-TSS (NM_001204203)	9	NM_001204203	20750	Mm.288474	NM_009263	ENSMUSG00000029304	Spp1	2AR|Apl-1|BNSP|BSPI|Bsp|ETA-1|Eta|OP|Opn|Opnl|Ric|Spp-1	secreted phosphoprotein 1	protein-coding
mm_150077.1	chr19	29386912	29386914	+	1	NA	3' UTR (NM_021893, exon 7 of 7)	3' UTR (NM_021893, exon 7 of 7)	19475	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_91859.1	chr10	59441709	59441713	-	1	NA	promoter-TSS (NM_010959)	promoter-TSS (NM_010959)	68	NM_010959	18302	Mm.123013	NM_010959	ENSMUSG00000009654	Oit3	EF-9|LZP	oncoprotein induced transcript 3	protein-coding
mm_21615.1	chr2	164275979	164275996	-	1	NA	TTS (NM_009300)	TTS (NM_009300)	2320	NM_009300	20941	Mm.1286	NM_009300	ENSMUSG00000016998	Svs4	SVS-IV|Svp-2|Svp-4|Svp2|Svp4	seminal vesicle secretory protein 4	protein-coding
mm_93972.1	chr10	127311618	127311722	-	1	NA	5' UTR (NM_001171582, exon 1 of 22)	5' UTR (NM_001171582, exon 1 of 22)	116	NM_001003913	216443	Mm.28173	NM_001003913	ENSMUSG00000040354	Mars	Metrs|Mtrns	methionine-tRNA synthetase	protein-coding
mm_53781.1	chr6	146577513	146577531	+	1	NA	promoter-TSS (NM_026218)	promoter-TSS (NM_026218)	313	NM_138757	71177	Mm.271774	NM_138757	ENSMUSG00000040250	Asun	4933424B01Rik|Spata30	asunder, spermatogenesis regulator	protein-coding
mm_119809.1	chr14	54222739	54222754	+	1	NA	Intergenic	Intergenic	31183	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_100564.1	chr11	120730615	120730641	+	1	NA	exon (NM_007621, exon 4 of 8)	exon (NM_007621, exon 4 of 8)	1393	NM_007621	12409	Mm.21454	NM_007621	ENSMUSG00000025150	Cbr2	MLCR	carbonyl reductase 2	protein-coding
mm_130007.1	chr15	86365098	86365101	-	1	NA	intron (NM_145476, intron 9 of 12)	intron (NM_145476, intron 9 of 12)	150640	NM_145476	223754	Mm.28904	NM_145476	ENSMUSG00000051864	Tbc1d22a	BC023106|D15Ertd781e	TBC1 domain family, member 22a	protein-coding
mm_29607.1	chr3	121262872	121262922	-	1	NA	intron (NM_178936, intron 1 of 7)	CpG	419	NM_178936	99887	Mm.26088	NM_178936	ENSMUSG00000028132	Tmem56	4930577M16Rik|AU018104|AW109744|C730036B01Rik	transmembrane protein 56	protein-coding
mm_165766.1	chr3	121547851	121547855	-	1	NA	Intergenic	Intergenic	-15509	NM_145394	213603	Mm.33062	NM_145394	ENSMUSG00000039865	Slc44a3	BC010552	solute carrier family 44, member 3	protein-coding
mm_122726.1	chr14	52316186	52316199	-	1	NA	5' UTR (NM_001244916, exon 1 of 2)	5' UTR (NM_001244916, exon 1 of 2)	131	NM_001244916	50524	Mm.39487	NM_015772	ENSMUSG00000049532	Sall2	AI225809|AW559097|Msal-2|Sal-2|mKIAA0360|p150(Sal2)	sal-like 2 (Drosophila)	protein-coding
mm_161202.1	chr13	58398049	58398049	-	1	NA	intron (NM_001301340, intron 4 of 15)	intron (NM_001301340, intron 4 of 15)	4120	NM_001301343	15387	Mm.142872	NM_025279	ENSMUSG00000021546	Hnrnpk	Hnrpk|KBBP|NOVA	heterogeneous nuclear ribonucleoprotein K	protein-coding
mm_92320.1	chr10	75560109	75560124	-	1	NA	exon (NM_198860, exon 1 of 4)	exon (NM_198860, exon 1 of 4)	214	NM_198860	192734	Mm.259320	NM_198860	ENSMUSG00000046807	Lrrc75b	AI646023|Fam211b	leucine rich repeat containing 75B	protein-coding
mm_7642.1	chr1	128102413	128102485	-	1	NA	promoter-TSS (NM_181750)	promoter-TSS (NM_181750)	22	NM_027678	226409	Mm.425048	NM_027678	ENSMUSG00000036086	Zranb3	4933425L19Rik|AH2|AI316834|C730006D09	zinc finger, RAN-binding domain containing 3	protein-coding
mm_168416.1	chr11	32283669	32283686	+	1	NA	promoter-TSS (NM_008218)	promoter-TSS (NM_008218)	2	NM_001083955	110257	Mm.196110	NM_001083955	ENSMUSG00000069917	Hba-a2	-	hemoglobin alpha, adult chain 2	protein-coding
mm_150270.1	chr19	34241693	34241709	+	1	NA	exon (NM_007392, exon 9 of 9)	exon (NM_007392, exon 9 of 9)	13672	NM_007392	11475	Mm.213025	NM_007392	ENSMUSG00000035783	Acta2	0610041G09Rik|Actvs|SMalphaA|a-SMA|alphaSMA	actin, alpha 2, smooth muscle, aorta	protein-coding
mm_77359.1	chr8	119635554	119635575	-	1	NA	5' UTR (NM_025734, exon 1 of 3)	5' UTR (NM_025734, exon 1 of 3)	116	NM_025734	66733	Mm.358699	NM_025734	ENSMUSG00000045246	Kcng4	4921535I01Rik|AW049024|KV6.3|KV6.4	potassium voltage-gated channel, subfamily G, member 4	protein-coding
mm_71692.1	chr8	61329359	61329376	+	1	NA	exon (NM_021506, exon 3 of 12)	exon (NM_021506, exon 3 of 12)	-40495	NR_045475	69279	Mm.417857	NR_045475	ENSMUSG00000099419	1700001D01Rik	-	RIKEN cDNA 1700001D01 gene	ncRNA
mm_1289.1	chr1	64295604	64295629	+	1	NA	Intergenic	Intergenic	-174227	NM_033563	93691	Mm.29466	NM_033563	ENSMUSG00000025959	Klf7	9830124P08Rik	Kruppel-like factor 7 (ubiquitous)	protein-coding
mm_95036.1	chr11	32205484	32205504	+	1	NA	promoter-TSS (NM_030093)	promoter-TSS (NM_030093)	79	NM_030093	78372	Mm.29952	NM_030093	ENSMUSG00000040767	Snrnp25	3300001G02Rik|AL033324|C16ORF33	small nuclear ribonucleoprotein 25 (U11/U12)	protein-coding
mm_104184.1	chr11	87797374	87797380	-	1	NA	exon (NM_010824, exon 8 of 14)	exon (NM_010824, exon 8 of 14)	3593	NM_010824	17523	Mm.4668	NM_010824	ENSMUSG00000009350	Mpo	mKIAA4033	myeloperoxidase	protein-coding
mm_78680.1	chr9	40784975	40784985	+	1	NA	TTS (NM_133733)	TTS (NM_133733)	-16293	NM_031165	15481	Mm.290774	NM_031165	ENSMUSG00000015656	Hspa8	2410008N15Rik|Hsc70|Hsc71|Hsc73|Hsp73|Hspa10	heat shock protein 8	protein-coding
mm_47188.1	chr5	120754177	120754224	-	1	NA	3' UTR (NM_145226, exon 16 of 16)	3' UTR (NM_145226, exon 16 of 16)	-4352	NM_001347448	246728	Mm.260926	NM_145227	ENSMUSG00000032690	Oas2	Oasl11	2'-5' oligoadenylate synthetase 2	protein-coding
mm_51907.1	chr6	91157252	91157262	+	1	NA	intron (NM_144919, intron 1 of 9)	intron (NM_144919, intron 1 of 9)	442	NM_144919	232232	Mm.206218	NM_144919	ENSMUSG00000034245	Hdac11	-	histone deacetylase 11	protein-coding
mm_149508.1	chr19	11965818	11965887	+	1	NA	promoter-TSS (NM_001033174)	promoter-TSS (NM_001033174)	8	NM_001033174	76303	Mm.291279	NM_001033174	ENSMUSG00000024687	Osbp	1110018F06Rik|AW559088|mKIAA4220	oxysterol binding protein	protein-coding
mm_69077.1	chr7	127001894	127001919	-	1	NA	exon (NM_080638, exon 2 of 15)	exon (NM_080638, exon 2 of 15)	12688	NM_080638	78388	Mm.228797	NM_080638	ENSMUSG00000030681	Mvp	2310009M24Rik|LRP|VAULT1	major vault protein	protein-coding
mm_58336.1	chr6	146634589	146634611	-	1	NA	promoter-TSS (NM_026281)	promoter-TSS (NM_026281)	-8	NM_026281	67623	Mm.278037	NM_026281	ENSMUSG00000040234	Tm7sf3	2010003B14Rik|NARP1	transmembrane 7 superfamily member 3	protein-coding
mm_124669.1	chr15	6387069	6387071	+	1	NA	intron (NM_001310446, intron 1 of 13)	intron (NM_001310446, intron 1 of 13)	322	NM_001310446	13132	Mm.240830	NM_023118	ENSMUSG00000022150	Dab2	5730435J12Rik|AA960054|AI957090|D15Wsu122e|D630005B22Rik|Doc-2|Doc2|p96	disabled 2, mitogen-responsive phosphoprotein	protein-coding
mm_114796.1	chr13	89739452	89739471	+	1	NA	intron (NM_172955, intron 1 of 5)	CpG	3051	NM_001081249	13003	Mm.158700	NM_019389	ENSMUSG00000021614	Vcan	5430420N07Rik|9430051N09|Cspg2|DPEAAE|NG2|PG-M|PG-M(V0)|PG-M(V1)|hdf	versican	protein-coding
mm_154616.1	chrX	7657440	7657450	+	1	NA	promoter-TSS (NM_001290624)	promoter-TSS (NM_001290624)	66	NM_001290624	54630	Mm.232232	NM_175097	ENSMUSG00000031145	Prickle3	Lmo6|Sfc16	prickle planar cell polarity protein 3	protein-coding
mm_47302.1	chr5	122371988	122371998	-	1	NA	promoter-TSS (NM_026883)	promoter-TSS (NM_026883)	-30	NM_026883	68948	Mm.474469	NM_026883	ENSMUSG00000029463	Fam216a	1500011H22Rik	family with sequence similarity 216, member A	protein-coding
mm_86752.1	chr10	19592423	19592448	+	1	NA	intron (NM_010511, intron 1 of 6)	intron (NM_010511, intron 1 of 6)	486	NM_010511	15979	Mm.549	NM_010511	ENSMUSG00000020009	Ifngr1	CD119|IFN-gammaR|Ifgr|Ifngr|Nktar	interferon gamma receptor 1	protein-coding
mm_144819.1	chr18	36291116	36291127	+	1	NA	Intergenic	Intergenic	-8980	NM_001267796	109169	Mm.426423	NM_001267796	ENSMUSG00000110185	Igip	6330403M23Rik	IgA inducing protein	protein-coding
mm_91260.1	chr10	23349861	23349881	-	1	NA	promoter-TSS (NM_001347372)	promoter-TSS (NM_001347372)	19	NM_001347372	14051	Mm.332128	NM_010167	ENSMUSG00000010461	Eya4	B130023L16Rik	EYA transcriptional coactivator and phosphatase 4	protein-coding
mm_158179.1	chrX	103981135	103981148	-	1	NA	5' UTR (NM_011276, exon 1 of 5)	5' UTR (NM_011276, exon 1 of 5)	143	NM_011276	19820	Mm.427762	NM_011276	ENSMUSG00000056537	Rlim	AL022832|AW743871|Ha1r|Rlim1|Rnf12	ring finger protein, LIM domain interacting	protein-coding
mm_173029.1	chrX	10531296	10531308	-	1	NA	intron (NM_019634, intron 1 of 7)	intron (NM_019634, intron 1 of 7)	46186	NM_019634	21912	Mm.18590	NM_019634	ENSMUSG00000058254	Tspan7	1200014P11Rik|A15|AI323365|Cd231|Mxs1|PE31|R74651|TALLA|Tm4sf2	tetraspanin 7	protein-coding
mm_139379.1	chr17	51853155	51853161	+	1	NA	Intergenic	Lx5c|LINE|L1	-19868	NM_001163632	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_119767.1	chr14	54173598	54173604	+	1	NA	Intergenic	Intergenic	80328	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_37853.1	chr4	132212142	132212153	-	1	NA	5' UTR (NM_145393, exon 1 of 5)	5' UTR (NM_145393, exon 1 of 5)	109	NM_145393	213541	Mm.23998	NM_145393	ENSMUSG00000040025	Ythdf2	9430020E02Rik|HGRG8|NY-REN-2	YTH domain family 2	protein-coding
mm_89555.1	chr10	94961676	94961686	+	1	NA	Intergenic	Intergenic	-17103	NM_018797	54712	Mm.256712	NM_018797	ENSMUSG00000074785	Plxnc1	2510048K12Rik|AW742158|CD232|Vespr	plexin C1	protein-coding
mm_49273.1	chr6	17552062	17552062	+	1	NA	intron (NM_008591, intron 15 of 21)	B4A|SINE|B4	-85036	NM_007604	12343	Mm.392504	NM_007604	ENSMUSG00000015733	Capza2	1110053K06Rik|AW208808|Cappa2	capping protein (actin filament) muscle Z-line, alpha 2	protein-coding
mm_112187.1	chr12	113422632	113422641	-	1	NA	Intergenic	Intergenic	-66929	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_120942.1	chr14	76674349	76674362	+	1	NA	Intergenic	Intergenic	-3213	NR_015485	73272	Mm.116804	NR_015485	ENSMUSG00000101009	1700108F19Rik	1700020I02Rik|BB065030	RIKEN cDNA 1700108F19 gene	ncRNA
mm_154984.1	chrX	38180598	38180613	+	1	NA	Intergenic	RLTR6B_Mm|LTR|ERV1	-9188	NM_020256	56805	Mm.391248	NM_020256	ENSMUSG00000048047	Zbtb33	AW260253|E130014G12Rik|Kaiso|Znf-kaiso	zinc finger and BTB domain containing 33	protein-coding
mm_99034.1	chr11	98959783	98959801	+	1	NA	promoter-TSS (NM_001176528)	promoter-TSS (NM_001176528)	-679	NM_001176528	19401	Mm.439744	NM_009024	ENSMUSG00000037992	Rara	Nr1b1|RAR|RARalpha1	retinoic acid receptor, alpha	protein-coding
mm_97760.1	chr11	80858385	80858394	+	1	NA	promoter-TSS (NM_029367)	promoter-TSS (NM_029367)	0	NM_029367	75622	Mm.26988	NM_029367	ENSMUSG00000053184	Spaca3	1700025M08Rik|ALLP17|Lyc3|SLLP1|mSLLP1	sperm acrosome associated 3	protein-coding
mm_137129.1	chr17	23564270	23564299	+	1	NA	promoter-TSS (NM_001033496)	promoter-TSS (NM_001033496)	-58	NM_001033496	449521	Mm.268582	NM_001033496	ENSMUSG00000071256	Zfp213	BC038178|D17Ertd197e	zinc finger protein 213	protein-coding
mm_93900.1	chr10	125390027	125390039	-	1	NA	Intergenic	Intergenic	-61498	NM_011391	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|Mct2	solute carrier family 16 (monocarboxylic acid transporters), member 7	protein-coding
mm_15785.1	chr2	164404371	164404400	+	1	NA	intron (NM_009036, intron 1 of 11)	intron (NM_009036, intron 1 of 11)	433	NM_013592	17183	Mm.29428	NM_013592	ENSMUSG00000016995	Matn4	matrilin-4	matrilin 4	protein-coding
mm_63177.1	chr7	125444636	125444709	+	1	NA	promoter-TSS (NM_029842)	promoter-TSS (NM_029842)	52	NM_029842	77035	Mm.307239	NM_029842	ENSMUSG00000030752	Kdm8	3110005O21Rik|Jmjd5	lysine (K)-specific demethylase 8	protein-coding
mm_71944.1	chr8	70374983	70375004	+	1	NA	intron (NM_016685, intron 4 of 18)	CpG-14087	1445	NM_016685	12845	Mm.45071	NM_016685	ENSMUSG00000031849	Comp	TSP5	cartilage oligomeric matrix protein	protein-coding
mm_125900.1	chr15	75969119	75969160	+	1	NA	promoter-TSS (NM_001081065)	promoter-TSS (NM_001081065)	-46	NM_001081065	69020	Mm.294295	NM_001081065	ENSMUSG00000034429	Zfp707	1500031N24Rik|AI451708|AW495315	zinc finger protein 707	protein-coding
mm_96672.1	chr11	69411102	69411116	+	1	NA	intron (NM_001017426, intron 1 of 22)	CpG	2566	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_15883.1	chr2	164839514	164839546	+	1	NA	TTS (NM_011125)	TTS (NM_011125)	5757	NM_008906	19025	Mm.359633	NM_008906	ENSMUSG00000017760	Ctsa	AU019505|PPCA|Ppgb	cathepsin A	protein-coding
mm_13213.1	chr2	96317784	96317805	+	1	NA	promoter-TSS (NM_001289742)	promoter-TSS (NM_001289742)	-375	NM_001289742	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_71922.1	chr8	70172384	70172424	+	1	NA	promoter-TSS (NM_001293797)	promoter-TSS (NM_001293797)	-4	NM_145597	234371	Mm.23488	NM_145597	ENSMUSG00000002342	Tmem161a	AI428876|BB161850|BC021367	transmembrane protein 161A	protein-coding
mm_168880.1	chr12	43037462	43037463	+	1	NA	Intergenic	L1Md_T|LINE|L1	1172606	NM_013760	27362	Mm.27432	NM_013760	ENSMUSG00000014905	Dnajb9	AA408011|AA673251|AA673481|AW556981|ERdj4|Mdg1|mDj7	DnaJ heat shock protein family (Hsp40) member B9	protein-coding
mm_49267.1	chr6	17491217	17491242	+	1	NA	5' UTR (NM_008591, exon 3 of 22)	5' UTR (NM_008591, exon 3 of 22)	27272	NM_008591	17295	Mm.86844	NM_008591	ENSMUSG00000009376	Met	AI838057|HGF|HGFR|Par4|c-Met	met proto-oncogene	protein-coding
mm_17587.1	chr2	30416004	30416045	-	1	NA	promoter-TSS (NM_007760)	promoter-TSS (NM_007760)	-26	NM_138748	110854	Mm.275393	NM_138748	ENSMUSG00000039515	Ptpa	2610042B21Rik|C77440|N28142|PR53|Ppp2r4	protein phosphatase 2 protein activator	protein-coding
mm_107003.1	chr12	11289610	11289646	+	1	NA	intron (NM_025695, intron 11 of 26)	intron (NM_025695, intron 11 of 26)	-10259	NR_106136	102465775		NR_106136	ENSMUSG00000098879	Mir7675	Gm27965|mmu-mir-7675	microRNA 7675	ncRNA
mm_15086.1	chr2	153240916	153240926	+	1	NA	promoter-TSS (NM_080463)	promoter-TSS (NM_080463)	437	NM_018807	54711	Mm.103199	NM_018807	ENSMUSG00000051413	Plagl2	AU018672|AW552839|mKIAA0198	pleiomorphic adenoma gene-like 2	protein-coding
mm_129733.1	chr15	82146790	82146819	-	1	NA	promoter-TSS (NM_033218)	promoter-TSS (NM_033218)	-465	NM_033218	20788	Mm.9002	NM_033218	ENSMUSG00000022463	Srebf2	AI608257|SREBP-2|SREBP2|SREBP2gc|bHLHd2|lop13|nuc	sterol regulatory element binding factor 2	protein-coding
mm_163081.1	chr11	69088607	69088607	+	1	NA	promoter-TSS (NM_009497)	promoter-TSS (NM_009497)	79	NM_009497	22318	Mm.28643	NM_009497	ENSMUSG00000020894	Vamp2	Syb-2|Syb2|sybII	vesicle-associated membrane protein 2	protein-coding
mm_52514.1	chr6	115362344	115362360	+	1	NA	promoter-TSS (NM_001308354)	promoter-TSS (NM_001308354)	3	NM_001308354	19016	Mm.3020	NM_011146	ENSMUSG00000000440	Pparg	Nr1c3|PPAR-gamma|PPAR-gamma2|PPARgamma|PPARgamma2	peroxisome proliferator activated receptor gamma	protein-coding
mm_52215.1	chr6	103510670	103510697	+	1	NA	promoter-TSS (NM_007697)	promoter-TSS (NM_007697)	-193	NM_007697	12661	Mm.251288	NM_007697	ENSMUSG00000030077	Chl1	A530023M13Rik|AI465420|CALL|LICAM2	cell adhesion molecule L1-like	protein-coding
mm_26584.1	chr3	150401912	150401947	+	1	NA	Intergenic	Intergenic	-1035953	NM_133222	170757	Mm.317261	NM_133222	ENSMUSG00000039167	Adgrl4	1110033N21Rik|ETL1|Eltd1|Etl	adhesion G protein-coupled receptor L4	protein-coding
mm_170045.1	chr17	24693979	24693980	+	1	NA	3' UTR (NM_023040, exon 3 of 3)	3' UTR (NM_023040, exon 3 of 3)	2177	NM_023040	11692	Mm.28124	NM_023040	ENSMUSG00000040888	Gfer	Alr|ERV1	growth factor, erv1 (S. cerevisiae)-like (augmenter of liver regeneration)	protein-coding
mm_66299.1	chr7	38107491	38107509	-	1	NA	promoter-TSS (NM_007633)	promoter-TSS (NM_007633)	-10	NM_007633	12447	Mm.16110	NM_007633	ENSMUSG00000002068	Ccne1	AW538188|CycE1	cyclin E1	protein-coding
mm_17512.1	chr2	29159756	29159756	-	1	NA	intron (NM_198033, intron 15 of 25)	intron (NM_198033, intron 15 of 25)	34764	NM_198033	269254	Mm.41867	NM_198033	ENSMUSG00000043535	Setx	A130090N03|A930037J23Rik|AOA2|AW060766|Als4|SCAR1|Sen1|mKIAA0625	senataxin	protein-coding
mm_112584.1	chr13	13712773	13712787	+	1	NA	exon (NM_010748, exon 39 of 53)	exon (NM_010748, exon 39 of 53)	-71279	NM_001302997	14706	Mm.215394	NM_010317	ENSMUSG00000021303	Gng4	-	guanine nucleotide binding protein (G protein), gamma 4	protein-coding
mm_169259.1	chr13	81065175	81065176	+	1	NA	intron (NR_015587, intron 1 of 1)	intron (NR_015587, intron 1 of 1)	101101	NR_015587	319983	Mm.343027	NR_015587	ENSMUSG00000097098	9330111N05Rik	-	RIKEN cDNA 9330111N05 gene	ncRNA
mm_15764.1	chr2	164316719	164316727	+	1	NA	promoter-TSS (NM_013679)	promoter-TSS (NM_013679)	-28	NM_013679	20945	Mm.439686	NM_013679	ENSMUSG00000017000	Svs6	MSVSP99|Svp6	seminal vesicle secretory protein 6	protein-coding
mm_171345.1	chr4	10813766	10813790	+	1	NA	Intergenic	Intergenic	-15976	NR_045185	73624	Mm.67392	NR_045185	ENSMUSG00000086080	1700123O12Rik	-	RIKEN cDNA 1700123O12 gene	ncRNA
mm_6464.1	chr1	74030882	74030894	-	1	NA	intron (NM_027884, intron 3 of 34)	L2c|LINE|L2	93559	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_45139.1	chr5	49012153	49012156	-	1	NA	intron (NM_001199244, intron 1 of 7)	ORR1A3-int|LTR|ERVL-MaLR	-122597	NM_030265	80334	Mm.160172	NM_030265	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding
mm_157559.1	chrX	52053445	52053448	-	1	NA	3' UTR (NM_008150, exon 9 of 9)	3' UTR (NM_008150, exon 9 of 9)	-80674	NM_028851	74279	Mm.159154	NM_028851	ENSMUSG00000031118	1700080O16Rik	-	RIKEN cDNA 1700080O16 gene	protein-coding
mm_19041.1	chr2	77014202	77014207	-	1	NA	intron (NM_001025576, intron 23 of 23)	intron (NM_001025576, intron 23 of 23)	-31657	NM_011652	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_36988.1	chr4	109666817	109666846	-	1	NA	promoter-TSS (NM_001301368)	promoter-TSS (NM_001301368)	-75	NM_001301368	12580	Mm.1912	NM_007671	ENSMUSG00000028551	Cdkn2c	C77269|INK4c|p18|p18-INK4c|p18-INK6|p18INK4c	cyclin-dependent kinase inhibitor 2C (p18, inhibits CDK4)	protein-coding
mm_154232.1	chr19	60226667	60226706	-	1	NA	promoter-TSS (NM_029648)	promoter-TSS (NM_029648)	11	NM_029648	76539	Mm.290183	NM_029648	ENSMUSG00000057858	Fam204a	2310065H12Rik|2610015K05Rik|D19Ertd737e	family with sequence similarity 204, member A	protein-coding
mm_13470.1	chr2	105682506	105682530	+	1	NA	promoter-TSS (NM_001310145)	promoter-TSS (NM_001310145)	55	NM_001310145	18508	Mm.3608	NM_013627	ENSMUSG00000027168	Pax6	1500038E17Rik|AEY11|Dey|Gsfaey11|Pax-6|Sey	paired box 6	protein-coding
mm_110925.1	chr12	76369475	76369517	-	1	NA	promoter-TSS (NM_001172104)	promoter-TSS (NM_001172104)	-32	NM_001172104	109929	Mm.41880	NM_028356	ENSMUSG00000056459	Zbtb25	2810462M08Rik|2900064P18Rik|AI842128|Kup|Zfp-50|Zfp50	zinc finger and BTB domain containing 25	protein-coding
mm_77056.1	chr8	109579057	109579072	-	1	NA	5' UTR (NM_017370, exon 1 of 5)	5' UTR (NM_017370, exon 1 of 5)	108	NM_017370	15439	Mm.26730	NM_017370	ENSMUSG00000031722	Hp	HP-1|preHP2	haptoglobin	protein-coding
mm_93685.1	chr10	117815566	117815581	-	1	NA	3' UTR (NM_024457, exon 8 of 8)	3' UTR (NM_024457, exon 8 of 8)	-22868	NM_134010	103468	Mm.12568	NM_134010	ENSMUSG00000052798	Nup107	AW541137|C76801	nucleoporin 107	protein-coding
mm_72728.1	chr8	85071771	85071794	+	1	NA	promoter-TSS (NM_001039514)	promoter-TSS (NM_001039514)	25	NM_001039514	330817	Mm.193086	NM_201408	ENSMUSG00000060038	Dhps	Dhs	deoxyhypusine synthase	protein-coding
mm_9387.1	chr1	172213946	172213961	-	1	NA	intron (NM_009813, intron 6 of 10)	intron (NM_009813, intron 6 of 10)	5942	NM_009813	12372	Mm.12829	NM_009813	ENSMUSG00000007122	Casq1	CSQ|CSQ-1|CSQ1|sCSQ	calsequestrin 1	protein-coding
mm_76787.1	chr8	102681506	102681509	-	1	NA	intron (NM_009866, intron 2 of 12)	intron (NM_009866, intron 2 of 12)	103604	NM_009866	12552	Mm.1571	NM_009866	ENSMUSG00000031673	Cdh11	Cad11|OSF-4	cadherin 11	protein-coding
mm_76055.1	chr8	77724266	77724276	-	1	NA	5' UTR (NM_010332, exon 1 of 8)	5' UTR (NM_010332, exon 1 of 8)	181	NM_010332	13617	Mm.283168	NM_010332	ENSMUSG00000031616	Ednra	ET-AR|ETa|Gpcr10	endothelin receptor type A	protein-coding
mm_52568.1	chr6	116286553	116286582	+	1	NA	intron (NM_001309446, intron 4 of 9)	intron (NM_001309446, intron 4 of 9)	20035	NM_001290339	67492	Mm.272772	NM_001081317	ENSMUSG00000042213	Zfand4	Anubl1	zinc finger, AN1-type domain 4	protein-coding
mm_33213.1	chr4	126609820	126609896	+	1	NA	promoter-TSS (NM_001145950)	promoter-TSS (NM_001145950)	4	NM_001145950	230757	Mm.296838	NM_001013755	ENSMUSG00000073755	5730409E04Rik	7530403E16Rik|AI849033	RIKEN cDNA 5730409E04Rik gene	protein-coding
mm_29576.1	chr3	116969013	116969027	-	1	NA	promoter-TSS (NM_023245)	promoter-TSS (NM_023245)	-68	NM_023245	114301	Mm.253736	NM_023245	ENSMUSG00000033377	Palmd	4631423C22Rik|PALML	palmdelphin	protein-coding
mm_46551.1	chr5	106624355	106624361	-	1	NA	intron (NM_026856, intron 5 of 6)	MLT1A0-int|LTR|ERVL-MaLR	72472	NM_026856	52397	Mm.249474	NM_026856	ENSMUSG00000049606	Zfp644	1110068L01Rik|AA408882|BM-005|D5Ertd689e|Zep-2	zinc finger protein 644	protein-coding
mm_35713.1	chr4	44233858	44233875	-	1	NA	Intergenic	CpG	-12599	NR_039565	100628618		NR_039565	ENSMUSG00000092677	Mir5106	mir-5106|mmu-mir-5106|mu-mir-5106	microRNA 5106	ncRNA
mm_23067.1	chr3	36066065	36066102	+	1	NA	promoter-TSS (NM_172678)	promoter-TSS (NM_172678)	83	NM_172678	229211	Mm.260997	NM_172678	ENSMUSG00000027710	Acad9	2600017P15Rik|4732402K02|C630012L17Rik|NPD002	acyl-Coenzyme A dehydrogenase family, member 9	protein-coding
mm_11160.1	chr2	28555857	28555863	+	1	NA	TTS (NM_009885)	TTS (NM_009885)	7543	NM_009885	12613	Mm.236017	NM_009885	ENSMUSG00000026818	Cel	1810036E18Rik|BAL	carboxyl ester lipase	protein-coding
mm_128699.1	chr15	63470894	63470897	-	1	NA	intron (NR_045279, intron 1 of 5)	intron (NR_045279, intron 1 of 5)	8713	NR_045279	432958	Mm.255105	NR_045279		Gm20740	-	predicted gene, 20740	ncRNA
mm_163858.1	chr14	19418588	19418598	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	183994	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_101409.1	chr11	28365565	28365575	-	1	NA	Intergenic	Intergenic	218754	NM_001166661	216613	Mm.93759	NM_181577	ENSMUSG00000032878	Ccdc85a	-	coiled-coil domain containing 85A	protein-coding
mm_61692.1	chr7	81087179	81087201	+	1	NA	intron (NM_054085, intron 5 of 13)	intron (NM_054085, intron 5 of 13)	-27609	NM_001004184	434203	Mm.389909	NM_001004184	ENSMUSG00000025726	Slc28a1	Cnt1	solute carrier family 28 (sodium-coupled nucleoside transporter), member 1	protein-coding
mm_33958.1	chr4	137485164	137485174	+	1	NA	intron (NM_008305, intron 1 of 96)	intron (NM_008305, intron 1 of 96)	16366	NM_008305	15530	Mm.273662	NM_008305	ENSMUSG00000028763	Hspg2	AI852380|Pcn|Plc|per	perlecan (heparan sulfate proteoglycan 2)	protein-coding
mm_90984.1	chr10	13832622	13832659	-	1	NA	intron (NM_001347362, intron 1 of 5)	intron (NM_001347362, intron 1 of 5)	36317	NM_025446	66253	Mm.45755	NM_025446	ENSMUSG00000019806	Aig1	1500031O19Rik|AV064870|AW413422|CGI-103	androgen-induced 1	protein-coding
mm_12941.1	chr2	85136471	85136481	+	1	NA	5' UTR (NM_011784, exon 1 of 1)	5' UTR (NM_011784, exon 1 of 1)	116	NM_011784	23796	Mm.29368	NM_011784	ENSMUSG00000044338	Aplnr	APJ|Agtrl1|msr/apj	apelin receptor	protein-coding
mm_113212.1	chr13	25127252	25127257	+	1	NA	intron (NM_177577, intron 7 of 9)	B1F|SINE|Alu	71250	NM_177577	195208	Mm.284719	NM_177577	ENSMUSG00000035910	Dcdc2a	AW492955|Dcdc2|RU2	doublecortin domain containing 2a	protein-coding
mm_79131.1	chr9	47547938	47547947	+	1	NA	intron (NM_001025600, intron 1 of 8)	intron (NM_001025600, intron 1 of 8)	17590	NM_018770	54725	Mm.234832	NM_018770	ENSMUSG00000032076	Cadm1	2900073G06Rik|3100001I08Rik|AI987920|Bl2|Igsf4|Igsf4a|Necl2|RA175|RA175A|RA175B|RA175C|RA175N|ST17|SgIGSF|SynCam|Tslc1	cell adhesion molecule 1	protein-coding
mm_158880.1	chr1	5588470	5588470	+	1	NA	promoter-TSS (NM_001204371)	promoter-TSS (NM_001204371)	-23	NM_011011	18387	Mm.7977	NM_011011	ENSMUSG00000025905	Oprk1	K-OR-1|KOR|KOR-1|MSL-1|Oprk2|R21	opioid receptor, kappa 1	protein-coding
mm_139834.1	chr17	69156554	69156564	+	1	NA	promoter-TSS (NM_013813)	promoter-TSS (NM_013813)	-251	NM_013813	13823	Mm.131135	NM_013813	ENSMUSG00000024044	Epb41l3	4.1B|DAL1P|Dal1|Epb4.1l3|NBL3	erythrocyte membrane protein band 4.1 like 3	protein-coding
mm_65582.1	chr7	27232873	27232888	-	1	NA	promoter-TSS (NM_133770)	promoter-TSS (NM_133770)	-133	NM_133770	76889	Mm.124728	NM_133770	ENSMUSG00000003762	Coq8b	0610012P18Rik|Adck4	coenzyme Q8B	protein-coding
mm_140464.1	chr17	92309216	92309231	+	1	NA	Intergenic	Intergenic	-889794	NM_001315503	11516	Mm.3407	NM_009625	ENSMUSG00000024256	Adcyap1	PACAP	adenylate cyclase activating polypeptide 1	protein-coding
mm_11537.1	chr2	32630320	32630331	+	1	NA	exon (NM_001198792, exon 3 of 6)	exon (NM_001198792, exon 3 of 6)	825	NM_021515	11636	Mm.29189	NM_021515	ENSMUSG00000026817	Ak1	Ak-1|B430205N08Rik	adenylate kinase 1	protein-coding
mm_96222.1	chr11	62511710	62511731	+	1	NA	intron (NM_001039536, intron 5 of 6)	MLTR25A|LTR|ERVK	27541	NM_028448	73139	Mm.390409	NM_028448	ENSMUSG00000018509	Cenpv	3110013H01Rik|AA671303|Prr6	centromere protein V	protein-coding
mm_57069.1	chr6	122577992	122578002	-	1	NA	3' UTR (NM_031159, exon 8 of 8)	3' UTR (NM_031159, exon 8 of 8)	24188	NM_009645	11628	Mm.391503	NM_009645	ENSMUSG00000040627	Aicda	Aid|Arp2	activation-induced cytidine deaminase	protein-coding
mm_158233.1	chrX	106485138	106485164	-	1	NA	promoter-TSS (NM_001007580)	promoter-TSS (NM_001007580)	78	NM_001007580	333564	Mm.298000	NM_001007580	ENSMUSG00000033737	Fndc3c1	Fndc3c|Gm784	fibronectin type III domain containing 3C1	protein-coding
mm_100922.1	chr11	6444360	6444370	-	1	NA	promoter-TSS (NM_029938)	promoter-TSS (NM_029938)	78	NM_029938	77605	Mm.27624	NM_029938	ENSMUSG00000041126	H2afv	C530002L11Rik|H2a.z-2|H2av	H2A histone family, member V	protein-coding
mm_96939.1	chr11	70540046	70540069	+	1	NA	promoter-TSS (NM_001302476)	promoter-TSS (NM_001302476)	-215	NM_008876	18806	Mm.260177	NM_008876	ENSMUSG00000020828	Pld2	PLD1C	phospholipase D2	protein-coding
mm_49194.1	chr6	15186852	15186896	+	1	NA	intron (NM_212435, intron 1 of 16)	intron (NM_212435, intron 1 of 16)	1368	NM_001286607	114142	Mm.332919	NM_053242	ENSMUSG00000029563	Foxp2	2810043D05Rik|AI449000|CAG-16|D0Kist7	forkhead box P2	protein-coding
mm_23935.1	chr3	84071999	84072004	+	1	NA	Intergenic	Intergenic	-31840	NM_172681	229473	Mm.28838	NM_172681	ENSMUSG00000033767	D930015E06Rik	Kiaa0922|mKIAA0922	RIKEN cDNA D930015E06 gene	protein-coding
mm_111192.1	chr12	84193741	84193758	-	1	NA	5' UTR (NM_001163502, exon 1 of 13)	5' UTR (NM_001163502, exon 1 of 13)	266	NM_001163502	238317	Mm.31256	NM_001163501	ENSMUSG00000042507	Elmsan1	9430029N19Rik|C130039O16Rik|Gm260	ELM2 and Myb/SANT-like domain containing 1	protein-coding
mm_111507.1	chr12	99563719	99563729	-	1	NA	promoter-TSS (NR_136760)	promoter-TSS (NR_136760)	-117	NR_136760	102639404	Mm.396324	NR_136760	ENSMUSG00000097917	Gm26839	-	predicted gene, 26839	ncRNA
mm_120858.1	chr14	75229233	75229249	+	1	NA	exon (NM_001247984, exon 16 of 16)	exon (NM_001247984, exon 16 of 16)	-13046	NM_019775	56373	Mm.24242	NM_019775	ENSMUSG00000021999	Cpb2	1110032P04Rik|4930405E17Rik|AI255929|CPR|Cpu|TAFI	carboxypeptidase B2 (plasma)	protein-coding
mm_86505.1	chr10	7589789	7589876	+	1	NA	promoter-TSS (NM_172784)	promoter-TSS (NM_172784)	32	NM_172784	237253	Mm.206759	NM_172784	ENSMUSG00000019796	Lrp11	1700034J19Rik|6330533B21|9830160H19Rik	low density lipoprotein receptor-related protein 11	protein-coding
mm_81657.1	chr9	110960928	110960941	+	1	NA	exon (NM_028838, exon 3 of 9)	exon (NM_028838, exon 3 of 9)	9389	NM_028838	74249	Mm.307615	NM_028838	ENSMUSG00000032495	Lrrc2	2400002D05Rik|4933431K03Rik	leucine rich repeat containing 2	protein-coding
mm_82412.1	chr9	14784507	14784577	-	1	NA	promoter-TSS (NM_018736)	promoter-TSS (NM_018736)	-112	NM_001310728	17535	Mm.149071	NM_018736	ENSMUSG00000031928	Mre11a	Mre11|Mre11b	MRE11A homolog A, double strand break repair nuclease	protein-coding
mm_138974.1	chr17	45298624	45298634	+	1	NA	Intergenic	Intergenic	135078	NM_152810	71702	Mm.28270	NM_152810	ENSMUSG00000023932	Cdc5l	1200002I02Rik|AA408004|PCDC5RP	cell division cycle 5-like (S. pombe)	protein-coding
mm_66336.1	chr7	43313097	43313116	-	1	NA	5' UTR (NM_027264, exon 1 of 5)	5' UTR (NM_027264, exon 1 of 5)	155	NM_027264	69930	Mm.45367	NM_027264	ENSMUSG00000012640	Zfp715	2610041B18Rik|mszf15	zinc finger protein 715	protein-coding
mm_22431.1	chr2	181671605	181671605	-	1	NA	promoter-TSS (NM_009236)	promoter-TSS (NM_009236)	35	NM_009236	20672	Mm.264904	NM_009236	ENSMUSG00000046470	Sox18	AI385749|Ra|Ragl	SRY (sex determining region Y)-box 18	protein-coding
mm_86784.1	chr10	20171903	20171927	+	1	NA	intron (NM_001198635, intron 1 of 17)	intron (NM_001198635, intron 1 of 17)	22995	NM_001198635	17761	Mm.20928	NM_008635	ENSMUSG00000019996	Map7	E-MAP-115|MAP-7|Mtap7|R75000|mshi|mste|ste	microtubule-associated protein 7	protein-coding
mm_137866.1	chr17	31296987	31296999	+	1	NA	intron (NM_001242427, intron 1 of 19)	intron (NM_001242427, intron 1 of 19)	769	NM_001242427	224674	Mm.311395	NM_153062	ENSMUSG00000024036	Slc37a1	G3PP	solute carrier family 37 (glycerol-3-phosphate transporter), member 1	protein-coding
mm_3983.1	chr1	164275670	164275686	+	1	NA	promoter-TSS (NM_029115)	promoter-TSS (NM_029115)	80	NM_029115	74895	Mm.167258	NM_029115	ENSMUSG00000026578	Ccdc181	4930455F23Rik|AI427889	coiled-coil domain containing 181	protein-coding
mm_105573.1	chr11	106612929	106612973	-	1	NA	promoter-TSS (NM_198292)	promoter-TSS (NM_198292)	-21	NM_198292	21763	Mm.102407	NM_198292	ENSMUSG00000040548	Tex2	4930568E07Rik|AI553404|Def-5|Taz4	testis expressed gene 2	protein-coding
mm_170997.1	chr2	75661779	75661797	+	1	NA	exon (NM_198090, exon 3 of 11)	exon (NM_198090, exon 3 of 11)	2498	NR_033513	627828	Mm.459502	NR_033513	ENSMUSG00000092086	Gm6793	EG627828	heterogeneous nuclear ribonucleoprotein A3 pseudogene	pseudo
mm_121089.1	chr14	99301635	99301662	+	1	NA	exon (NM_009769, exon 2 of 4)	exon (NM_009769, exon 2 of 4)	2957	NM_009769	12224	Mm.30262	NM_009769	ENSMUSG00000005148	Klf5	4930520J07Rik|Bteb2|CKLF|IKLF	Kruppel-like factor 5	protein-coding
mm_139548.1	chr17	56770259	56770305	+	1	NA	promoter-TSS (NM_001195673)	promoter-TSS (NM_001195673)	6	NM_001195673	100504446	Mm.46157	NM_001195673	ENSMUSG00000090273	Prr22	Gm546	proline rich 22	protein-coding
mm_123189.1	chr14	57890243	57890320	-	1	NA	promoter-TSS (NM_029492)	promoter-TSS (NM_029492)	-19	NM_029492	75965	Mm.29044	NM_029492	ENSMUSG00000021969	Zdhhc20	4930542A17Rik|5033406L14Rik|AI448102|B230110O18Rik|ENSMUSG00000055956|HK11	zinc finger, DHHC domain containing 20	protein-coding
mm_63997.1	chr7	140115874	140115889	+	1	NA	intron (NM_053119, intron 1 of 7)	intron (NM_053119, intron 1 of 7)	542	NM_053119	93747	Mm.24452	NM_053119	ENSMUSG00000025465	Echs1	C80529	enoyl Coenzyme A hydratase, short chain, 1, mitochondrial	protein-coding
mm_30878.1	chr4	32238981	32238996	+	1	NA	Intergenic	CpG	-178447	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_24917.1	chr3	96269696	96269703	+	1	NA	promoter-TSS (NM_175666)	promoter-TSS (NM_175666)	-1	NM_175666	319189	Mm.297655	NM_175666	ENSMUSG00000105827	Hist2h2bb	H2b-616	histone cluster 2, H2bb	protein-coding
mm_115505.1	chr13	4279337	4279353	-	1	NA	promoter-TSS (NM_013777)	promoter-TSS (NM_013777)	54	NM_013777	622402	Mm.27447	NM_013777	ENSMUSG00000021211	Akr1c12	AI266976|Akra	aldo-keto reductase family 1, member C12	protein-coding
mm_17212.1	chr2	25478351	25478356	-	1	NA	Intergenic	Intergenic	-8604	NM_008963	19215	Mm.1008	NM_008963	ENSMUSG00000015090	Ptgds	21kDa|L-PGDS|PGD2|PGDS|PGDS2|Ptgs3	prostaglandin D2 synthase (brain)	protein-coding
mm_20396.1	chr2	129183778	129183838	-	1	NA	Intergenic	Intergenic	-3135	NR_045264	100048701	Mm.428544	NR_045264	ENSMUSG00000084826	AI847159	OTTMUSG00000015420	expressed sequence AI847159	ncRNA
mm_151360.1	chr19	55910632	55910652	+	1	NA	exon (NM_001142918, exon 6 of 15)	exon (NM_001142918, exon 6 of 15)	15321	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_5597.1	chr1	39558962	39558973	-	1	NA	intron (NM_001033135, intron 4 of 6)	intron (NM_001033135, intron 4 of 6)	-10127	NR_028555	100217461		NR_028555	ENSMUSG00000077704	Snord89	MBII-289	small nucleolar RNA, C/D box 89	snoRNA
mm_51263.1	chr6	72097732	72097751	+	1	NA	exon (NM_001035228, exon 1 of 7)	exon (NM_001035228, exon 1 of 7)	133	NM_011375	20454	Mm.38248	NM_011375	ENSMUSG00000056091	St3gal5	3S-T|Siat9|[a]2	ST3 beta-galactoside alpha-2,3-sialyltransferase 5	protein-coding
mm_112471.1	chr13	5868479	5868497	+	1	NA	3' UTR (NM_011803, exon 4 of 4)	3' UTR (NM_011803, exon 4 of 4)	6999	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_106333.1	chr11	118355370	118355377	-	1	NA	promoter-TSS (NM_011594)	promoter-TSS (NM_011594)	38	NM_011594	21858	Mm.206505	NM_011594	ENSMUSG00000017466	Timp2	D11Bwg1104e|Timp-2	tissue inhibitor of metalloproteinase 2	protein-coding
mm_163103.1	chr11	69735435	69735443	-	1	NA	exon (NM_001291068, exon 29 of 29)	exon (NM_001291068, exon 29 of 29)	23194	NM_001291068	20020	Mm.16533	NM_009089	ENSMUSG00000005198	Polr2a	220kDa|Rpb1|Rpo2-1	polymerase (RNA) II (DNA directed) polypeptide A	protein-coding
mm_169810.1	chr16	19035992	19035996	+	1	NA	Intergenic	RLTR9D|LTR|ERVK	159244	NM_010435	15260	Mm.15694	NM_010435	ENSMUSG00000022702	Hira	AA138857|D16Ertd95e|Gm15797|N28177|OTTMUSG00000026264|Tuple1	histone cell cycle regulator	protein-coding
mm_154449.1	chrM	1966	2009	-	1	NA	NA	Intergenic	NA	NA								
mm_16059.1	chr2	167863096	167863124	+	1	NA	Intergenic	RCHARR1|DNA|hAT-Charlie	-69217	NM_011201	19246	Mm.277916	NM_011201	ENSMUSG00000027540	Ptpn1	PTP-1B|PTP-HA2|PTP1B	protein tyrosine phosphatase, non-receptor type 1	protein-coding
mm_46468.1	chr5	105122940	105122954	-	1	NA	exon (NM_001256005, exon 6 of 11)	exon (NM_001256005, exon 6 of 11)	-12655	NM_172777	236573	Mm.425261	NM_172777	ENSMUSG00000029298	Gbp9	-	guanylate-binding protein 9	protein-coding
mm_123002.1	chr14	54993336	54993354	-	1	NA	5' UTR (NM_080728, exon 3 of 41)	5' UTR (NM_080728, exon 3 of 41)	1204	NM_080728	140781	Mm.457983	NM_080728	ENSMUSG00000053093	Myh7	B-MHC|MyHC-I|Myhc-b|Myhcb|beta-MHC	myosin, heavy polypeptide 7, cardiac muscle, beta	protein-coding
mm_160315.1	chr7	142090202	142090202	-	1	NA	5' UTR (NM_008748, exon 2 of 7)	5' UTR (NM_008748, exon 2 of 7)	5082	NM_008748	18218	Mm.39725	NM_008748	ENSMUSG00000037887	Dusp8	5530400B01Rik|AI593498|Nttp1	dual specificity phosphatase 8	protein-coding
mm_99729.1	chr11	106301104	106301134	+	1	NA	exon (NM_008117, exon 3 of 5)	exon (NM_008117, exon 3 of 5)	777	NM_008117	14599	Mm.343934	NM_008117	ENSMUSG00000020713	Gh	Gh1|Ghb1	growth hormone	protein-coding
mm_62519.1	chr7	102230027	102230046	+	1	NA	intron (NR_111937, intron 2 of 5)	intron (NR_111937, intron 2 of 5)	7008	NR_111937	233575	Mm.302013	NM_145583	ENSMUSG00000030990	Pgap2	1810006G21Rik|C76649|Frag1	post-GPI attachment to proteins 2	protein-coding
mm_28342.1	chr3	89402521	89402527	-	1	NA	TTS (NM_177041)	TTS (NM_177041)	126	NM_020517	57275	Mm.482283	NM_020517	ENSMUSG00000078173	Lenep	AU018355|Lep503	lens epithelial protein	protein-coding
mm_138656.1	chr17	35868456	35868459	+	1	NA	exon (NM_001146711, exon 2 of 4)	exon (NM_001146711, exon 2 of 4)	1842	NM_175242	76448	Mm.359982	NM_175242	ENSMUSG00000034595	Ppp1r18	2310014H01Rik|AA407849|AI450394	protein phosphatase 1, regulatory subunit 18	protein-coding
mm_5365.1	chr1	25830091	25830189	-	1	NA	promoter-TSS (NM_175642)	promoter-TSS (NM_175642)	-433	NM_175642	210933	Mm.336569	NM_175642	ENSMUSG00000033569	Adgrb3	A830096D10Rik|Bai3	adhesion G protein-coupled receptor B3	protein-coding
mm_61002.1	chr7	49343422	49343435	+	1	NA	intron (NM_175272, intron 1 of 37)	intron (NM_175272, intron 1 of 37)	97239	NM_175272	78286	Mm.333881	NM_175272	ENSMUSG00000052512	Nav2	5330421F07Rik|AU067780|BQ960892|HELAD1|POMFIL2|RAINB1|RAINB2|Unc53H2|mKIAA3015	neuron navigator 2	protein-coding
mm_111118.1	chr12	80967996	80968032	-	1	NA	promoter-TSS (NM_001177561)	promoter-TSS (NM_001177561)	65	NM_011387	20493	Mm.486361	NM_011387	ENSMUSG00000021135	Slc10a1	Ntcp	solute carrier family 10 (sodium/bile acid cotransporter family), member 1	protein-coding
mm_15588.1	chr2	160365780	160365808	+	1	NA	exon (NM_010658, exon 1 of 1)	exon (NM_010658, exon 1 of 1)	1271	NM_010658	16658	Mm.330745	NM_010658	ENSMUSG00000074622	Mafb	Kreisler|Krml|Krml1|kr	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein B (avian)	protein-coding
mm_91393.1	chr10	30745846	30745888	-	1	NA	intron (NM_172495, intron 2 of 15)	intron (NM_172495, intron 2 of 15)	57240	NM_172495	211329	Mm.297903	NM_172495	ENSMUSG00000039697	Ncoa7	9030406N13Rik	nuclear receptor coactivator 7	protein-coding
mm_82213.1	chr9	3000219	3000238	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	38515	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_52157.1	chr6	98018666	98018678	+	1	NA	3' UTR (NM_001178049, exon 10 of 10)	3' UTR (NM_001178049, exon 10 of 10)	26889	NM_008601	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_39193.1	chr4	155992332	155992342	-	1	NA	promoter-TSS (NM_011341)	promoter-TSS (NM_011341)	341	NM_080445	117592	Mm.440185	NM_080445	ENSMUSG00000050796	B3galt6	BB129894|GalTII	UDP-Gal:betaGal beta 1,3-galactosyltransferase, polypeptide 6	protein-coding
mm_141994.1	chr17	35177454	35177456	-	1	NA	Intergenic	B1_Mur1|SINE|Alu	-1454	NM_019467	11629	Mm.10747	NM_019467	ENSMUSG00000024397	Aif1	AI607846|AIF-1|D17H6S50E|G1|Iba1	allograft inflammatory factor 1	protein-coding
mm_51463.1	chr6	82070762	82070769	+	1	NA	intron (NM_145570, intron 1 of 2)	intron (NM_145570, intron 1 of 2)	29137	NM_145570	232146	Mm.489683	NM_145570	ENSMUSG00000035104	Eva1a	BC014699|Fam176a|Tmem166	eva-1 homolog A (C. elegans)	protein-coding
mm_140934.1	chr17	24414471	24414484	-	1	NA	promoter-TSS (NM_001080128)	promoter-TSS (NM_001080128)	36	NR_033554	654822	Mm.489806	NM_001039561	ENSMUSG00000073437	D330041H03Rik	-	RIKEN cDNA D330041H03 gene	ncRNA
mm_53744.1	chr6	145182262	145182308	+	1	NA	intron (NM_177222, intron 11 of 15)	intron (NM_177222, intron 11 of 15)	28685	NM_177222	320662	Mm.207779	NM_177222	ENSMUSG00000043541	Casc1	A230084G12Rik|Las1	cancer susceptibility candidate 1	protein-coding
mm_127723.1	chr15	103239948	103239993	+	1	NA	promoter-TSS (NM_010447)	promoter-TSS (NM_010447)	-154	NM_001076789	12419	Mm.262059	NM_007626	ENSMUSG00000009575	Cbx5	2610029O15Rik|C75991|HP1|Hp1a|Hp1alpha	chromobox 5	protein-coding
mm_77338.1	chr8	119558795	119558807	-	1	NA	promoter-TSS (NM_001167910)	promoter-TSS (NM_001167910)	-40	NM_019709	56453	Mm.206934	NM_019709	ENSMUSG00000031835	Mbtps1	0610038M03Rik|AV003995|S1P|SKI-1|Ski1|mKIAA0091	membrane-bound transcription factor peptidase, site 1	protein-coding
mm_167070.1	chr7	99579756	99579764	+	1	NA	intron (NM_177231, intron 1 of 15)	MLT1O|LTR|ERVL-MaLR	27491	NR_029760	723840		NR_029760	ENSMUSG00000065571	Mir326	Mirn326|mir-326|mmu-mir-326	microRNA 326	ncRNA
mm_3866.1	chr1	160989409	160989430	+	1	NA	exon (NM_080844, exon 3 of 8)	exon (NM_080844, exon 3 of 8)	10813	NM_080844	11905	Mm.260770	NM_080844	ENSMUSG00000026715	Serpinc1	AI114908|ATIII|At-3|At3	serine (or cysteine) peptidase inhibitor, clade C (antithrombin), member 1	protein-coding
mm_109560.1	chr12	111814179	111814245	+	1	NA	promoter-TSS (NM_028875)	promoter-TSS (NM_028875)	42	NM_026752	68520	Mm.390497	NM_026752	ENSMUSG00000021286	Zfyve21	1110013H04Rik|AW558780|C85416	zinc finger, FYVE domain containing 21	protein-coding
mm_99921.1	chr11	110479349	110479365	+	1	NA	intron (NM_011943, intron 1 of 11)	intron (NM_011943, intron 1 of 11)	80235	NM_011943	26399	Mm.14487	NM_011943	ENSMUSG00000020623	Map2k6	MEK6|MKK6|Prkmk6|SAPKK3	mitogen-activated protein kinase kinase 6	protein-coding
mm_48239.1	chr5	137741360	137741370	-	1	NA	promoter-TSS (NM_001347505)	promoter-TSS (NM_001347505)	-197	NM_001347505	243300	Mm.74750	NM_175521	ENSMUSG00000045348	Nyap1	6430598A04Rik	neuronal tyrosine-phosphorylated phosphoinositide 3-kinase adaptor 1	protein-coding
mm_37223.1	chr4	117926762	117926770	-	1	NA	exon (NM_001284191, exon 6 of 6)	exon (NM_001284191, exon 6 of 6)	2997	NM_001284191	11876	Mm.56897	NM_009711	ENSMUSG00000028539	Artn	neublastin	artemin	protein-coding
mm_169274.1	chr13	89861985	89861988	+	1	NA	intron (NM_028012, intron 7 of 7)	L1_Mus3|LINE|L1	-119474	NM_001134475	13003	Mm.158700	NM_019389	ENSMUSG00000021614	Vcan	5430420N07Rik|9430051N09|Cspg2|DPEAAE|NG2|PG-M|PG-M(V0)|PG-M(V1)|hdf	versican	protein-coding
mm_96960.1	chr11	70640362	70640372	+	1	NA	exon (NM_010326, exon 2 of 2)	exon (NM_010326, exon 2 of 2)	1245	NM_010326	14723	Mm.377085	NM_010326	ENSMUSG00000050675	Gp1ba	GPIba|GPIbalpha	glycoprotein 1b, alpha polypeptide	protein-coding
mm_89518.1	chr10	94338746	94338755	+	1	NA	Intergenic	Intergenic	-40047	NR_033209	215472	Mm.255656	NM_174999	ENSMUSG00000053420	Gm4792	E130012K09|EG215472	predicted gene 4792	ncRNA
mm_92916.1	chr10	83648632	83648682	-	1	NA	promoter-TSS (NM_145220)	promoter-TSS (NM_145220)	7	NM_145220	216190	Mm.282985	NM_145220	ENSMUSG00000020263	Appl2	Dip3b	adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 2	protein-coding
mm_10308.1	chr2	11172162	11172172	+	1	NA	promoter-TSS (NM_008859)	promoter-TSS (NM_008859)	-215	NM_008859	18761	Mm.329993	NM_008859	ENSMUSG00000026778	Prkcq	A130035A12Rik|AW494342|PKC-0|PKC-theta|PKCtheta|Pkcq	protein kinase C, theta	protein-coding
mm_129725.1	chr15	82016088	82016129	-	1	NA	promoter-TSS (NM_010247)	promoter-TSS (NM_010247)	32	NM_134095	28075	Mm.474453	NM_134095	ENSMUSG00000022472	Desi1	AI427858|AI850401|D15Wsu75e|DeSI-1|Fam152b|Pppde2	desumoylating isopeptidase 1	protein-coding
mm_140327.1	chr17	86753901	86753914	+	1	NA	promoter-TSS (NM_010137)	promoter-TSS (NM_010137)	43	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_96711.1	chr11	69656523	69656532	+	1	NA	TTS (NR_125917)	TTS (NR_125917)	1490	NM_009235	20670	Mm.347499	NM_009235	ENSMUSG00000041287	Sox15	-	SRY (sex determining region Y)-box 15	protein-coding
mm_67609.1	chr7	83883518	83883570	-	1	NA	5' UTR (NM_030705, exon 1 of 1)	5' UTR (NM_030705, exon 1 of 1)	797	NM_030705	80889	Mm.272998	NM_030705	ENSMUSG00000070462	Mesdc1	AW061151	mesoderm development candidate 1	protein-coding
mm_64699.1	chr7	4547332	4547396	-	1	NA	promoter-TSS (NM_016908)	promoter-TSS (NM_016908)	-797	NM_016908	53420	Mm.358663	NM_016908	ENSMUSG00000004961	Syt5	SytV	synaptotagmin V	protein-coding
mm_103782.1	chr11	82764304	82764329	-	1	NA	promoter-TSS (NM_025884)	promoter-TSS (NM_025884)	5	NM_009839	12467	Mm.4126	NM_009839	ENSMUSG00000020698	Cct6b	CCT-zeta-2|CCTzeta-2|Cctz-2|TCP-1-zeta-2	chaperonin containing Tcp1, subunit 6b (zeta)	protein-coding
mm_164688.1	chr17	47687995	47688001	-	1	NA	TTS (NM_001290337)	TTS (NM_001290337)	388	NR_045945	100415787	Mm.392206	NR_045945	ENSMUSG00000084880	Tomm6os	Gm14872|OTTMUSG00000018355|Prickle4os	translocase of outer mitochondrial membrane 6, opposite strand	ncRNA
mm_134504.1	chr16	19063267	19063285	-	1	NA	Intergenic	Intergenic	186526	NM_010435	15260	Mm.15694	NM_010435	ENSMUSG00000022702	Hira	AA138857|D16Ertd95e|Gm15797|N28177|OTTMUSG00000026264|Tuple1	histone cell cycle regulator	protein-coding
mm_129556.1	chr15	79505811	79505831	-	1	NA	promoter-TSS (NM_008427)	promoter-TSS (NM_008427)	-580	NM_008427	16520	Mm.39759	NM_008427	ENSMUSG00000044216	Kcnj4	IRK3|Kcnf2|MB-IRK3	potassium inwardly-rectifying channel, subfamily J, member 4	protein-coding
mm_126217.1	chr15	78913908	78913910	+	1	NA	promoter-TSS (NM_020271)	promoter-TSS (NM_020271)	-10	NM_020271	57028	Mm.263169	NM_020271	ENSMUSG00000022436	Pdxp	1600027H05Rik|AB041662|PLPP	pyridoxal (pyridoxine, vitamin B6) phosphatase	protein-coding
mm_46940.1	chr5	114823441	114823457	-	1	NA	promoter-TSS (NM_181075)	promoter-TSS (NM_181075)	19	NM_181075	330173	Mm.482205	NM_181075	ENSMUSG00000092486	2610524H06Rik	-	RIKEN cDNA 2610524H06 gene	protein-coding
mm_150022.1	chr19	29372346	29372359	+	1	NA	intron (NM_021893, intron 1 of 6)	intron (NM_021893, intron 1 of 6)	4914	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_8814.1	chr1	161979657	161979681	-	1	NA	promoter-TSS (NM_001204904)	promoter-TSS (NM_001204904)	-33	NM_001204904	75368	Mm.108728	NM_001204904	ENSMUSG00000086277	4930558K02Rik	-	RIKEN cDNA 4930558K02 gene	protein-coding
mm_115287.1	chr13	111936207	111936233	+	1	NA	Intergenic	Intergenic	68284	NR_130345	102636620	Mm.402328	NR_130345	ENSMUSG00000086111	Gm15326	OTTMUSG00000020187	predicted gene 15326	ncRNA
mm_23412.1	chr3	58517538	58517546	+	1	NA	Intergenic	Intergenic	-8279	NM_001005509	229317	Mm.21617	NM_001005509	ENSMUSG00000027810	Eif2a	D030048D22|D3Ertd194e	eukaryotic translation initiation factor 2A	protein-coding
mm_20451.1	chr2	129364899	129364941	-	1	NA	3' UTR (NM_008361, exon 7 of 7)	3' UTR (NM_008361, exon 7 of 7)	-4982	NR_015474	329514	Mm.207315	NM_177848	ENSMUSG00000074805	Il1bos	9430083I22|Gm14047|OTTMUSG00000015529	interleukin 1 beta, opposite strand	ncRNA
mm_33924.1	chr4	136640049	136640051	+	1	NA	Intergenic	ID_B1|SINE|B4	17429	NM_001243262	242707	Mm.448979	NM_001243262	ENSMUSG00000070683	Lactbl1	-	lactamase, beta-like 1	protein-coding
mm_152467.1	chr19	10948569	10948574	-	1	NA	exon (NM_023731, exon 1 of 4)	exon (NM_023731, exon 1 of 4)	695	NM_023731	108673	Mm.294908	NM_023731	ENSMUSG00000024732	Ccdc86	4933411H20Rik|6720480F16Rik|D19Ertd678e	coiled-coil domain containing 86	protein-coding
mm_164514.1	chr16	95612596	95612597	+	1	NA	Intergenic	Intergenic	-26003	NM_001302152	13876	Mm.164531	NM_133659	ENSMUSG00000040732	Erg	D030036I24Rik	avian erythroblastosis virus E-26 (v-ets) oncogene related	protein-coding
mm_62856.1	chr7	114502424	114502429	+	1	NA	intron (NM_011055, intron 4 of 15)	AT_rich|Low_complexity|Low_complexity	60546	NR_110407	244209	Mm.108037	NM_177382	ENSMUSG00000030670	Cyp2r1	-	cytochrome P450, family 2, subfamily r, polypeptide 1	protein-coding
mm_65878.1	chr7	29555600	29555614	-	1	NA	Intergenic	Intergenic	-50147	NM_001081028	74206	Mm.447042	NM_001081028	ENSMUSG00000030583	Sipa1l3	2610511M17Rik	signal-induced proliferation-associated 1 like 3	protein-coding
mm_148037.1	chr18	70244481	70244496	-	1	NA	promoter-TSS (NM_029346)	promoter-TSS (NM_029346)	96	NM_029346	75577	Mm.58214	NM_029346	ENSMUSG00000024512	Dynap	2310002L13Rik	dynactin associated protein	protein-coding
mm_122175.1	chr14	31545784	31545791	-	1	NA	intron (NM_009937, intron 6 of 16)	ID_B1|SINE|B4	31596	NM_009937	382864	Mm.239821	NM_009937	ENSMUSG00000057606	Colq	A130034K24Rik	collagen-like tail subunit (single strand of homotrimer) of asymmetric acetylcholinesterase	protein-coding
mm_11047.1	chr2	27165564	27165570	+	1	NA	promoter-TSS (NM_138942)	promoter-TSS (NM_138942)	60	NM_138942	13166	Mm.167781	NM_138942	ENSMUSG00000000889	Dbh	-	dopamine beta hydroxylase	protein-coding
mm_138143.1	chr17	34204093	34204110	+	1	NA	promoter-TSS (NM_011530)	promoter-TSS (NM_011530)	-378	NM_011530	21355	Mm.14814	NM_011530	ENSMUSG00000024339	Tap2	ABC18|AI462429|APT2|Abcb3|Ham-2|Ham2|MTP2|PSF2|RING11|Tap-2|Y1|jas	transporter 2, ATP-binding cassette, sub-family B (MDR/TAP)	protein-coding
mm_35730.1	chr4	45011655	45011698	-	1	NA	5' UTR (NM_001163284, exon 1 of 2)	5' UTR (NM_001163284, exon 1 of 2)	736	NM_001163284	230119	Mm.44222	NM_173399	ENSMUSG00000049657	Zbtb5	5930421I10|9430083K24Rik|AI646847|mKIAA0354	zinc finger and BTB domain containing 5	protein-coding
mm_170602.1	chr19	5802613	5802617	-	1	NA	promoter-TSS (NR_002847)	promoter-TSS (NR_002847)	57	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_54790.1	chr6	41636311	41636313	-	1	NA	promoter-TSS (NM_022413)	promoter-TSS (NM_022413)	93	NM_022413	64177	Mm.296889	NM_022413	ENSMUSG00000029868	Trpv6	CAT|CaT1|Cac|Ecac2|Otrpc3	transient receptor potential cation channel, subfamily V, member 6	protein-coding
mm_111604.1	chr12	102395677	102395711	-	1	NA	exon (NM_011175, exon 12 of 14)	exon (NM_011175, exon 12 of 14)	44119	NM_011175	19141	Mm.17185	NM_011175	ENSMUSG00000021190	Lgmn	AEP|AI746452|AU022324|Prsc1	legumain	protein-coding
mm_67500.1	chr7	80778651	80778652	-	1	NA	intron (NM_016721, intron 2 of 37)	MIR|SINE|MIR	24680	NM_016721	29875	Mm.207619	NM_016721	ENSMUSG00000030536	Iqgap1	AA682088|D7Ertd237e|D7Ertd257e|mKIAA0051	IQ motif containing GTPase activating protein 1	protein-coding
mm_53750.1	chr6	145307050	145307050	+	1	NA	Intergenic	Intergenic	56498	NR_045598	100039495	Mm.121014	NR_045598	ENSMUSG00000086013	Gm15706	OTTMUSG00000025463	predicted gene 15706	ncRNA
mm_149966.1	chr19	29047490	29047527	+	1	NA	promoter-TSS (NR_028360)	promoter-TSS (NR_028360)	25	NR_028360	67329	Mm.394933	NR_028360		1700018L02Rik	-	RIKEN cDNA 1700018L02 gene	ncRNA
mm_104580.1	chr11	96956224	96956236	-	1	NA	exon (NM_030220, exon 5 of 7)	exon (NM_030220, exon 5 of 7)	12084	NR_003293	319371	Mm.436865	NR_003293	ENSMUSG00000078700	D030028A08Rik	-	RIKEN cDNA D030028A08 gene	ncRNA
mm_82143.1	chr9	123769899	123769908	+	1	NA	intron (NM_009913, intron 1 of 2)	intron (NM_009913, intron 1 of 2)	2692	NM_001166625	12769	Mm.440604	NM_009913	ENSMUSG00000029530	Ccr9	A130091K22Rik|Cmkbr10|GPR-9-6	chemokine (C-C motif) receptor 9	protein-coding
mm_90964.1	chr10	13375059	13375075	-	1	NA	intron (NM_001195065, intron 1 of 12)	(TG)n|Simple_repeat|Simple_repeat	13903	NM_001195066	215789	Mm.283359	NM_001033257	ENSMUSG00000062866	Phactr2	AV158170|BC012871	phosphatase and actin regulator 2	protein-coding
mm_104260.1	chr11	88924700	88924710	-	1	NA	exon (NM_029023, exon 13 of 13)	exon (NM_029023, exon 13 of 13)	18777	NR_045955	73921	Mm.439148	NR_045955	ENSMUSG00000087338	Scpep1os	4930405P13Rik	serine carboxypeptidase 1, opposite strand	ncRNA
mm_98105.1	chr11	86758229	86758232	+	1	NA	promoter-TSS (NM_001003908)	promoter-TSS (NM_001003908)	-738	NM_001003908	67300	Mm.254588	NM_001003908	ENSMUSG00000047126	Cltc	3110065L21Rik|CHC|R74732	clathrin, heavy polypeptide (Hc)	protein-coding
mm_99278.1	chr11	101279093	101279111	+	1	NA	promoter-TSS (NM_026618)	promoter-TSS (NM_026618)	-101	NM_026562	68107	Mm.262369	NM_026562	ENSMUSG00000078653	Cntd1	1700051C09Rik|4921513J16Rik|5430417M23Rik|Cntd	cyclin N-terminal domain containing 1	protein-coding
mm_168734.1	chr12	115085602	115085620	-	1	NA	Intergenic	Intergenic	-571917	NR_106063	102465664		NR_106063	ENSMUSG00000098357	Mir7094-2	Gm27508|mmu-mir-7094-2	microRNA 7094-2	ncRNA
mm_106845.1	chr12	8007802	8007819	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	30133	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_101854.1	chr11	48868097	48868113	-	1	NA	intron (NM_008326, intron 2 of 2)	(TCCC)n|Simple_repeat|Simple_repeat	3241	NM_008326	15944	Mm.29938	NM_008326	ENSMUSG00000046879	Irgm1	Ifggd3|Ifi1|Iigp3|Iipg3|Irgm|LRG-47	immunity-related GTPase family M member 1	protein-coding
mm_88695.1	chr10	80142296	80142311	+	1	NA	promoter-TSS (NM_025313)	promoter-TSS (NM_025313)	-12	NM_025313	66043	Mm.278560	NM_025313	ENSMUSG00000003072	Atp5d	0610008F14Rik|1500000I11Rik|AA960090|AI876556|AU020773|C85518	ATP synthase, H+ transporting, mitochondrial F1 complex, delta subunit	protein-coding
mm_68030.1	chr7	101012197	101012246	-	1	NA	promoter-TSS (NM_001302347)	promoter-TSS (NM_001302347)	-168	NM_001302346	18442	Mm.3000	NM_008773	ENSMUSG00000032860	P2ry2	P2U1|P2Y2	purinergic receptor P2Y, G-protein coupled 2	protein-coding
mm_58489.1	chr7	3657736	3657740	+	1	NA	intron (NM_146176, intron 13 of 17)	intron (NM_146176, intron 13 of 17)	1776	NR_039587	100628594		NR_039587	ENSMUSG00000093290	Mir3572	mir-3572|mmu-mir-3572	microRNA 3572	ncRNA
mm_70802.1	chr8	22938225	22938237	+	1	NA	exon (NM_001081149, exon 18 of 18)	exon (NM_001081149, exon 18 of 18)	-36605	NM_001110783	11733	Mm.334444	NM_031158	ENSMUSG00000031543	Ank1	Ank-1|nb|pale	ankyrin 1, erythroid	protein-coding
mm_38676.1	chr4	144980793	144980827	-	1	NA	intron (NM_001276502, intron 67 of 68)	intron (NM_001276502, intron 67 of 68)	87673	NM_011303	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding
mm_63598.1	chr7	128144608	128144626	+	1	NA	exon (NM_021334, exon 21 of 30)	exon (NM_021334, exon 21 of 30)	15049	NM_021334	16411	Mm.22378	NM_021334	ENSMUSG00000030789	Itgax	AI449405|Cd11c|Cr4|N418	integrin alpha X	protein-coding
mm_22259.1	chr2	177939018	177939020	-	1	NA	intron (NM_001282028, intron 4 of 4)	RLTR13C2|LTR|ERVK	-13369	NM_183135	78703		NM_183135	ENSMUSG00000074529	Zfp972	C330013J21Rik	zinc finger protein 972	protein-coding
mm_120930.1	chr14	76487760	76487772	+	1	NA	promoter-TSS (NM_001177751)	promoter-TSS (NM_001177751)	-670	NM_001177751	21807	Mm.153272	NM_009366	ENSMUSG00000022010	Tsc22d1	AA589566|AW105905|Egr5|TSC-22|Tgfb1i4|Tsc|Tsc22	TSC22 domain family, member 1	protein-coding
mm_74910.1	chr8	25240863	25240923	-	1	NA	Intergenic	CpG	-39351	NM_177089	320165	Mm.308452	NM_177089	ENSMUSG00000065954	Tacc1	4833447E04Rik|AA960202|B230378H13Rik	transforming, acidic coiled-coil containing protein 1	protein-coding
mm_14909.1	chr2	150570410	150570420	+	1	NA	promoter-TSS (NM_009977)	promoter-TSS (NM_009977)	0	NM_009977	13011	Mm.12965	NM_009977	ENSMUSG00000068129	Cst7	Cmap	cystatin F (leukocystatin)	protein-coding
mm_51868.1	chr6	90550864	90550871	+	1	NA	promoter-TSS (NM_027406)	promoter-TSS (NM_027406)	19	NM_027406	107747	Mm.30035	NM_027406	ENSMUSG00000030088	Aldh1l1	1810048F20Rik|FDH|Fthfd|Neut2	aldehyde dehydrogenase 1 family, member L1	protein-coding
mm_36042.1	chr4	57249140	57249150	-	1	NA	intron (NM_011207, intron 8 of 25)	intron (NM_011207, intron 8 of 25)	52692	NM_011207	545622	Mm.246552	NM_011207	ENSMUSG00000038764	Ptpn3	9530011I20Rik|PTP-H1|PTPCL	protein tyrosine phosphatase, non-receptor type 3	protein-coding
mm_130659.1	chr15	100641512	100641521	-	1	NA	3' UTR (NM_001270537, exon 11 of 11)	3' UTR (NM_001270537, exon 11 of 11)	-4576	NM_001033872	207818	Mm.26282	NM_174992	ENSMUSG00000053559	Smagp	-	small cell adhesion glycoprotein	protein-coding
mm_1040.1	chr1	58795463	58795559	+	1	NA	5' UTR (NM_009812, exon 1 of 9)	5' UTR (NM_009812, exon 1 of 9)	137	NM_009812	12370	Mm.336851	NM_009812	ENSMUSG00000026029	Casp8	CASP-8|FLICE|MACH|Mch5	caspase 8	protein-coding
mm_156460.1	chrX	142832521	142832548	+	1	NA	exon (NM_001199357, exon 5 of 7)	exon (NM_001199357, exon 5 of 7)	93534	NR_030523	723976		NR_030523	ENSMUSG00000076011	Mir652	Mirn652|miRX|mmu-mir-652	microRNA 652	ncRNA
mm_47202.1	chr5	120906650	120906658	-	1	NA	intron (NM_145211, intron 1 of 6)	B3A|SINE|B2	871	NM_145211	246730	Mm.14301	NM_145211	ENSMUSG00000052776	Oas1a	L3	2'-5' oligoadenylate synthetase 1A	protein-coding
mm_141810.1	chr17	34603523	34603626	-	1	NA	promoter-TSS (NM_019403)	promoter-TSS (NM_019403)	-13	NM_019403	54197	Mm.274542	NM_019403	ENSMUSG00000015478	Rnf5	2410131O05Rik|AA407576|NG2	ring finger protein 5	protein-coding
mm_137296.1	chr17	24804292	24804309	+	1	NA	promoter-TSS (NM_029197)	promoter-TSS (NM_029197)	-82	NM_029197	75178	Mm.52592	NM_029197	ENSMUSG00000024155	Meiob	4930528F23Rik|MLZ-675	meiosis specific with OB domains	protein-coding
mm_136219.1	chr16	89960816	89960828	-	1	NA	promoter-TSS (NM_009384)	promoter-TSS (NM_009384)	5	NM_009384	21844	Mm.310902	NM_009384	ENSMUSG00000002489	Tiam1	AI847750|D16Ium10|D16Ium10e	T cell lymphoma invasion and metastasis 1	protein-coding
mm_71987.1	chr8	70616148	70616161	+	1	NA	promoter-TSS (NM_153074)	promoter-TSS (NM_153074)	-690	NM_153074	211228	Mm.132939	NM_153074	ENSMUSG00000049988	Lrrc25	Mapa	leucine rich repeat containing 25	protein-coding
mm_66131.1	chr7	31055595	31055659	-	1	NA	promoter-TSS (NM_019503)	promoter-TSS (NM_019503)	29	NM_052992	56188	Mm.1491	NM_019503	ENSMUSG00000036570	Fxyd1	0610012C17Rik|1110006M24Rik|Plm|Pml	FXYD domain-containing ion transport regulator 1	protein-coding
mm_15125.1	chr2	153805016	153805019	+	1	NA	Intergenic	Intergenic	24138	NR_036629	100504221	Mm.246778	NM_177849	ENSMUSG00000044083	Efcab8	A630008I04|EG329541	EF-hand calcium binding domain 8	ncRNA
mm_128751.1	chr15	64571165	64571168	-	1	NA	Intergenic	Lx5|LINE|L1	-188247	NM_010026	13196	Mm.277236	NM_010026	ENSMUSG00000022377	Asap1	AV239055|DEF-1|Ddef1|PAP|mKIAA1249|s19	ArfGAP with SH3 domain, ankyrin repeat and PH domain1	protein-coding
mm_152222.1	chr19	8518976	8518998	-	1	NA	Intergenic	IAPLTR4|LTR|ERVK	-72267	NM_001164634	19879	Mm.285294	NM_031194	ENSMUSG00000063796	Slc22a8	Oat3|Roct	solute carrier family 22 (organic anion transporter), member 8	protein-coding
mm_161934.1	chr18	86712977	86712977	+	1	NA	5' UTR (NM_001302356, exon 3 of 5)	5' UTR (NM_001302356, exon 3 of 5)	912	NM_172633	12405	Mm.70775	NM_172633	ENSMUSG00000024647	Cbln2	6330593N19Rik|A730004O05	cerebellin 2 precursor protein	protein-coding
mm_142473.1	chr17	45674231	45674233	-	1	NA	exon (NM_198167, exon 7 of 24)	exon (NM_198167, exon 7 of 24)	11986	NM_198167	224807	Mm.157904	NM_198167	ENSMUSG00000036026	Tmem63b	BC026370	transmembrane protein 63b	protein-coding
mm_122858.1	chr14	54877533	54877552	-	1	NA	promoter-TSS (NM_001167908)	promoter-TSS (NM_001167908)	-4	NM_001167908	105651	Mm.297365	NM_001167908	ENSMUSG00000072494	Ppp1r3e	A630071A11Rik|AW049239|Gm1211	protein phosphatase 1, regulatory (inhibitor) subunit 3E	protein-coding
mm_131202.1	chr16	8619509	8619515	+	1	NA	3' UTR (NM_001170978, exon 15 of 15)	3' UTR (NM_001170978, exon 15 of 15)	18189	NM_025708	66690	Mm.10068	NM_025708	ENSMUSG00000043140	Tmem186	2810440M13Rik|4432406C05Rik|AI648175|AW210586	transmembrane protein 186	protein-coding
mm_106578.1	chr11	120727294	120727306	-	1	NA	promoter-TSS (NM_026428)	promoter-TSS (NM_026428)	-16	NM_001347608	67880	Mm.231091	NM_026428	ENSMUSG00000039450	Dcxr	0610038K04Rik|1810027P18Rik|XR	dicarbonyl L-xylulose reductase	protein-coding
mm_27713.1	chr3	68494047	68494070	-	1	NA	promoter-TSS (NM_001282044)	promoter-TSS (NM_001282044)	-123	NM_001282044	30953	Mm.331064	NM_013928	ENSMUSG00000027777	Schip1	Nf2ip|Schip-1	schwannomin interacting protein 1	protein-coding
mm_79167.1	chr9	47850534	47850554	+	1	NA	3' UTR (NM_018770, exon 10 of 10)	3' UTR (NM_018770, exon 10 of 10)	-32336	NR_046048	100038460	Mm.447649	NR_046048		Gm10677	ENSMUSG00000074363	predicted gene 10677	ncRNA
mm_21602.1	chr2	164238259	164238273	-	1	NA	promoter-TSS (NM_017390)	promoter-TSS (NM_017390)	75	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_29210.1	chr3	106790074	106790084	-	1	NA	promoter-TSS (NM_007651)	promoter-TSS (NM_007651)	70	NM_007651	12508	Mm.316861	NM_007651	ENSMUSG00000040747	Cd53	AI323659|Ox-44|Tspan25	CD53 antigen	protein-coding
mm_114287.1	chr13	58756513	58756523	+	1	NA	intron (NR_045469, intron 1 of 2)	intron (NR_045469, intron 1 of 2)	5793	NR_045469	67585	Mm.84751	NR_045469		4930455J16Rik	-	RIKEN cDNA 4930455J16 gene	ncRNA
mm_107634.1	chr12	52097730	52097736	+	1	NA	promoter-TSS (NM_029760)	promoter-TSS (NM_029760)	-13	NM_029760	76826	Mm.244781	NM_029760	ENSMUSG00000035142	Nubpl	2410170E07Rik	nucleotide binding protein-like	protein-coding
mm_168316.1	chr11	109012114	109012122	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	91769	NM_015732	12006	Mm.71710	NM_015732	ENSMUSG00000000142	Axin2	Axi1|Axil|Conductin	axin 2	protein-coding
mm_38993.1	chr4	151129349	151129389	-	1	NA	intron (NM_001081557, intron 11 of 23)	CpG	39799	NM_001308446	105704528	Mm.415128	NM_001308446	ENSMUSG00000078491	Gm13090	OTTMUSG00000010356	predicted gene 13090	protein-coding
mm_106891.1	chr12	8012284	8012307	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	34618	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_2611.1	chr1	120340761	120340769	+	1	NA	5' UTR (NM_207233, exon 1 of 2)	5' UTR (NM_207233, exon 1 of 2)	183	NM_207233	226359	Mm.337409	NM_207233	ENSMUSG00000036907	C1ql2	BC040774|CTRP10	complement component 1, q subcomponent-like 2	protein-coding
mm_132692.1	chr16	43236021	43236041	+	1	NA	intron (NM_001285805, intron 3 of 10)	intron (NM_001285805, intron 3 of 10)	-11253	NM_181058	56490	Mm.136238	NM_019778	ENSMUSG00000022708	Zbtb20	1300017A20Rik|7330412A13Rik|A930017C21Rik|D16Wsu73e|DPZF|HOF|ODA-8S|Oda8|Zfp288	zinc finger and BTB domain containing 20	protein-coding
mm_157829.1	chrX	74244045	74244061	-	1	NA	intron (NM_010227, intron 1 of 45)	intron (NM_010227, intron 1 of 45)	2481	NM_010227	192176	Mm.295533	NM_010227	ENSMUSG00000031328	Flna	ABP-280|Dilp2|F730004A14Rik|Fln1|GENA 379|filamin-1	filamin, alpha	protein-coding
mm_111017.1	chr12	79007277	79007346	-	1	NA	promoter-TSS (NM_178745)	promoter-TSS (NM_178745)	-34	NM_178745	268567	Mm.341747	NM_178745	ENSMUSG00000046157	Tmem229b	6330442E10Rik|9830138K24|AU019070	transmembrane protein 229B	protein-coding
mm_47399.1	chr5	123049381	123049419	-	1	NA	Intergenic	Intergenic	-2384	NM_001347456	74890	Mm.141383	NM_029112	ENSMUSG00000029477	Morn3	4930438O03Rik	MORN repeat containing 3	protein-coding
mm_150875.1	chr19	45058696	45058750	+	1	NA	Intergenic	Intergenic	11147	NM_001178013	94280	Mm.36169	NM_053197	ENSMUSG00000025212	Sfxn3	-	sideroflexin 3	protein-coding
mm_169177.1	chr13	65703888	65703899	+	1	NA	Intergenic	Intergenic	-409560	NM_001177832	628709	Mm.390595	NM_001177832	ENSMUSG00000095909	Gm10324	ENSMUSG00000071302	predicted gene 10324	protein-coding
mm_85840.1	chr9	110532833	110532846	-	1	NA	intron (NM_001081340, intron 1 of 20)	CpG	242	NM_001081340	235626	Mm.288949	NM_001081340	ENSMUSG00000044791	Setd2	4921524K10Rik|BC031601|KMT3A	SET domain containing 2	protein-coding
mm_26819.1	chr3	10331359	10331425	-	1	NA	promoter-TSS (NM_018864)	promoter-TSS (NM_018864)	47	NM_018864	55980	Mm.183042	NM_018864	ENSMUSG00000027531	Impa1	2610002K09Rik|2900059K10Rik|AI325909	inositol (myo)-1(or 4)-monophosphatase 1	protein-coding
mm_26203.1	chr3	138528595	138528598	+	1	NA	intron (NM_007917, intron 2 of 7)	intron (NM_007917, intron 2 of 7)	1328	NM_001313980	13684	Mm.3941	NM_007917	ENSMUSG00000028156	Eif4e	EG668879|Eif4e-ps|If4e|eIF-4E	eukaryotic translation initiation factor 4E	protein-coding
mm_70433.1	chr8	11556470	11556491	+	1	NA	promoter-TSS (NM_011919)	promoter-TSS (NM_011919)	23	NM_011919	26356	Mm.25709	NM_011919	ENSMUSG00000045969	Ing1	2610028J21Rik|AA407184|AI875420|mING1h|p33Ing1|p37Ing1b	inhibitor of growth family, member 1	protein-coding
mm_137103.1	chr17	21707743	21707765	+	1	NA	promoter-TSS (NM_001008501)	promoter-TSS (NM_001008501)	13	NM_001008501	240034	Mm.34723	NM_001008501	ENSMUSG00000067928	Zfp760	9430018I06|BC029103	zinc finger protein 760	protein-coding
mm_133805.1	chr16	95698790	95698795	+	1	NA	Intergenic	MIR3|SINE|MIR	-3615	NM_011809	23872	Mm.290207	NM_011809	ENSMUSG00000022895	Ets2	AU022856|Ets-2	E26 avian leukemia oncogene 2, 3' domain	protein-coding
mm_167551.1	chr9	33867942	33867945	+	1	NA	Intergenic	Intergenic	-174428	NR_040744	77119	Mm.367930	NR_040744	ENSMUSG00000098758	7630403G23Rik	-	RIKEN cDNA 7630403G23 gene	ncRNA
mm_138322.1	chr17	34849885	34849901	+	1	NA	promoter-TSS (NM_138580)	promoter-TSS (NM_138580)	311	NM_021337	108077	Mm.18845	NM_021337	ENSMUSG00000040356	Skiv2l	4930534J06Rik|AW214248|Ddx13|SKI|Ski2w	superkiller viralicidic activity 2-like (S. cerevisiae)	protein-coding
mm_131833.1	chr16	22959203	22959219	+	1	NA	exon (NM_053176, exon 6 of 7)	exon (NM_053176, exon 6 of 7)	8139	NM_053176	94175	Mm.358794	NM_053176	ENSMUSG00000022877	Hrg	AI265597|AW413091|D16jh2|D18020|Hprg|Hrgp	histidine-rich glycoprotein	protein-coding
mm_12383.1	chr2	69867449	69867462	+	1	NA	exon (NM_001110145, exon 6 of 12)	exon (NM_001110145, exon 6 of 12)	5893	NM_009278	20823	Mm.10508	NM_009278	ENSMUSG00000068882	Ssb	SS-B	Sjogren syndrome antigen B	protein-coding
mm_122017.1	chr14	27379461	27379477	-	1	NA	intron (NM_001289686, intron 5 of 12)	intron (NM_001289686, intron 5 of 12)	18080	NM_001289688	71704	Mm.248606	NM_027871	ENSMUSG00000021895	Arhgef3	1200004I24Rik|9830169H03Rik|C76747|Xpln	Rho guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_163001.1	chr11	32237239	32237239	-	1	NA	intron (NR_104306, intron 10 of 13)	intron (NR_104306, intron 10 of 13)	10734	NM_010822	268395	Mm.263161	NM_010822	ENSMUSG00000020287	Mpg	9830006D05|AI326268|APNG|Aag|Mid1	N-methylpurine-DNA glycosylase	protein-coding
mm_162876.1	chr10	97509952	97510026	+	1	NA	exon (NM_007833, exon 6 of 8)	exon (NM_007833, exon 6 of 8)	27658	NM_007833	13179	Mm.56769	NM_007833	ENSMUSG00000019929	Dcn	DC|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding
mm_64467.1	chr7	143005059	143005105	+	1	NA	promoter-TSS (NM_001128082)	promoter-TSS (NM_001128082)	36	NM_001128080	27027	Mm.28172	NM_020286	ENSMUSG00000000244	Tspan32	AW208513|Art-1|BB235973|D7Wsu37e|Phemx|Tssc6	tetraspanin 32	protein-coding
mm_98324.1	chr11	90257396	90257407	+	1	NA	intron (NM_026178, intron 1 of 6)	intron (NM_026178, intron 1 of 6)	7925	NM_026178	67468	Mm.277518	NM_026178	ENSMUSG00000003948	Mmd	1200017E07Rik|1810073C06Rik|AA690185	monocyte to macrophage differentiation-associated	protein-coding
mm_40736.1	chr5	66259891	66259904	+	1	NA	promoter-TSS (NM_027602)	promoter-TSS (NM_027602)	-1	NM_001302833	70918	Mm.23166	NM_027602	ENSMUSG00000029206	Nsun7	4921525L17Rik	NOL1/NOP2/Sun domain family, member 7	protein-coding
mm_28934.1	chr3	98882076	98882090	-	1	NA	exon (NM_019545, exon 5 of 9)	exon (NM_019545, exon 5 of 9)	11147	NM_019545	56185	Mm.281874	NM_019545	ENSMUSG00000027870	Hao2	AI325478|Hao-2|Hao3|Haox3	hydroxyacid oxidase 2	protein-coding
mm_130520.1	chr15	98872187	98872233	-	1	NA	Intergenic	CpG	-1005	NM_001033276	381022	Mm.264889	NM_001033276	ENSMUSG00000048154	Kmt2d	ALR|BC032281|BC058659|C430014K11Rik|KMT2B|Mll2|Mll4	lysine (K)-specific methyltransferase 2D	protein-coding
mm_104070.1	chr11	86586399	86586403	-	1	NA	intron (NM_029478, intron 11 of 11)	intron (NM_029478, intron 11 of 11)	-2243	NR_029738	387140		NR_029738	ENSMUSG00000065455	Mir21a	Mir21|Mirn21|mmu-mir-21|mmu-mir-21a	microRNA 21a	ncRNA
mm_122531.1	chr14	47384624	47384655	-	1	NA	exon (NM_010705, exon 5 of 6)	exon (NM_010705, exon 5 of 6)	10779	NM_001145953	16854	Mm.248615	NM_010705	ENSMUSG00000050335	Lgals3	GBP|L-34|Mac-2|gal3	lectin, galactose binding, soluble 3	protein-coding
mm_59139.1	chr7	24134186	24134212	+	1	NA	promoter-TSS (NM_019941)	promoter-TSS (NM_019941)	36	NM_019941	56525	Mm.295595	NM_019941	ENSMUSG00000047603	Zfp235	0610030O19Rik|AI428448	zinc finger protein 235	protein-coding
mm_169069.1	chr13	28188802	28188805	+	1	NA	Intergenic	BGLII|LTR|ERVK	46319	NM_023746	28078	Mm.155058	NM_023746	ENSMUSG00000017064	Prl5a1	1600013P04Rik|D13Wsu14e|Ghd24|PLP-L|Prlpl	prolactin family 5, subfamily a, member 1	protein-coding
mm_82435.1	chr9	15112146	15112157	-	1	NA	promoter-TSS (NM_001164797)	promoter-TSS (NM_001164797)	-43	NM_001164797	244698	Mm.325134	NM_001164797	ENSMUSG00000031936	Hephl1	Gm509|Zp|zyklopen	hephaestin-like 1	protein-coding
mm_77281.1	chr8	116713856	116713864	-	1	NA	intron (NM_029441, intron 1 of 6)	Lx9|LINE|L1	19131	NM_029441	75796	Mm.159575	NM_029441	ENSMUSG00000031758	Cdyl2	1700029M19Rik|4930453I21Rik|Gm20194	chromodomain protein, Y chromosome-like 2	protein-coding
mm_76060.1	chr8	77724499	77724515	-	1	NA	promoter-TSS (NM_010332)	promoter-TSS (NM_010332)	-55	NM_010332	13617	Mm.283168	NM_010332	ENSMUSG00000031616	Ednra	ET-AR|ETa|Gpcr10	endothelin receptor type A	protein-coding
mm_51332.1	chr6	72357954	72357966	+	1	NA	exon (NM_144916, exon 5 of 8)	exon (NM_144916, exon 5 of 8)	2477	NM_144916	232086	Mm.491165	NM_144916	ENSMUSG00000055912	Tmem150a	BC014685|Tmem150	transmembrane protein 150A	protein-coding
mm_116913.1	chr13	55488039	55488089	-	1	NA	promoter-TSS (NM_019813)	promoter-TSS (NM_019813)	12	NM_001177371	56320	Mm.19016	NM_019813	ENSMUSG00000034675	Dbn1	-	drebrin 1	protein-coding
mm_83287.1	chr9	43107103	43107109	-	1	NA	Intergenic	Intergenic	-1388	NM_027144	69632	Mm.275266	NM_027144	ENSMUSG00000059495	Arhgef12	2310014B11Rik|AU019857|Larg|mKIAA0382	Rho guanine nucleotide exchange factor (GEF) 12	protein-coding
mm_6846.1	chr1	84238173	84238190	-	1	NA	intron (NM_001003948, intron 1 of 2)	ORR1E|LTR|ERVL-MaLR	-19220	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_2194.1	chr1	89235189	89235193	+	1	NA	Intergenic	Intergenic	164729	NM_133816	98402	Mm.170983	NM_133816	ENSMUSG00000036206	Sh3bp4	AI594717|AW227605|BOG25	SH3-domain binding protein 4	protein-coding
mm_29310.1	chr3	107969163	107969177	-	1	NA	promoter-TSS (NM_010359)	promoter-TSS (NM_010359)	4	NM_010359	14864	Mm.440885	NM_010359	ENSMUSG00000004038	Gstm3	Fsc2|mGSTM5	glutathione S-transferase, mu 3	protein-coding
mm_155027.1	chrX	42067960	42067998	+	1	NA	promoter-TSS (NR_125870)	promoter-TSS (NR_125870)	143	NM_009688	11798	Mm.259879	NM_009688	ENSMUSG00000025860	Xiap	1110015C02Rik|Aipa|Api3|Birc4|IAP3|ILP-1|MIHA	X-linked inhibitor of apoptosis	protein-coding
mm_136030.1	chr16	76403674	76403717	-	1	NA	Intergenic	Intergenic	-30646	NM_173440	268903	Mm.74711	NM_173440	ENSMUSG00000048490	Nrip1	6030458L20Rik|8430438I05Rik|9630050P12|AA959574|AW456757|RIP140	nuclear receptor interacting protein 1	protein-coding
mm_27583.1	chr3	59101811	59101826	-	1	NA	promoter-TSS (NM_173398)	promoter-TSS (NM_173398)	3	NM_173398	229323	Mm.123648	NM_173398	ENSMUSG00000050075	Gpr171	A630006E05|F730001G15Rik|H963	G protein-coupled receptor 171	protein-coding
mm_119978.1	chr14	55561061	55561071	+	1	NA	intron (NM_001199009, intron 1 of 14)	intron (NM_001199009, intron 1 of 14)	143	NM_001199009	28199	Mm.11535	NM_133734	ENSMUSG00000022214	Dcaf11	0710008A13Rik|C76035|D14Ucla1|Dacf11|GLO14|Wdr23	DDB1 and CUL4 associated factor 11	protein-coding
mm_123566.1	chr14	66871660	66871708	-	1	NA	TTS (NM_001034881)	TTS (NM_001034881)	2834	NM_001034881	432870	Mm.425890	NM_001034881	ENSMUSG00000075553	Gm5464	EG432870	predicted gene 5464	protein-coding
mm_23783.1	chr3	79336651	79336686	+	1	NA	Intergenic	MLTR14|LTR|ERV1	-8708	NM_001142953	100233207	Mm.373801	NM_001142953	ENSMUSG00000091685	Gm17359	-	predicted gene, 17359	protein-coding
mm_72198.1	chr8	72548500	72548583	+	1	NA	promoter-TSS (NM_027485)	promoter-TSS (NM_027485)	-231	NM_027485	70625	Mm.235885	NM_027485	ENSMUSG00000045248	Med26	5730493L18Rik|AI414941|AW495270|Crsp7	mediator complex subunit 26	protein-coding
mm_71970.1	chr8	70535000	70535035	+	1	NA	3' UTR (NM_001199631, exon 9 of 9)	3' UTR (NM_001199631, exon 9 of 9)	-4658	NM_007924	13716	Mm.271973	NM_007924	ENSMUSG00000070002	Ell	Ell1|Men	elongation factor RNA polymerase II	protein-coding
mm_675.1	chr1	40466070	40466078	+	1	NA	promoter-TSS (NM_008365)	promoter-TSS (NM_008365)	68	NM_008365	16182	Mm.253664	NM_008365	ENSMUSG00000026070	Il18r1	Il18ralpha|Il1rrp	interleukin 18 receptor 1	protein-coding
mm_116453.1	chr13	43250824	43250835	-	1	NA	intron (NM_001033399, intron 1 of 1)	intron (NM_001033399, intron 1 of 1)	53343	NM_001033399	328232	Mm.441399	NM_001033399	ENSMUSG00000051335	Gfod1	9630032O13|AI850995	glucose-fructose oxidoreductase domain containing 1	protein-coding
mm_652.1	chr1	40429564	40429586	+	1	NA	promoter-TSS (NM_001294171)	promoter-TSS (NM_001294171)	5	NM_001294171	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_71857.1	chr8	68906359	68906366	+	1	NA	3' UTR (NM_008509, exon 10 of 10)	3' UTR (NM_008509, exon 10 of 10)	25807	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_169437.1	chr14	56261216	56261226	-	1	NA	exon (NM_013542, exon 2 of 5)	exon (NM_013542, exon 2 of 5)	1113	NM_013542	14939	Mm.14874	NM_013542	ENSMUSG00000015437	Gzmb	AI553453|CCP-1/C11|CCP1|Ctla-1|Ctla1|GZB	granzyme B	protein-coding
mm_80202.1	chr9	72408587	72408593	+	1	NA	Intergenic	Intergenic	-29939	NM_008613	17427	Mm.387671	NM_008613	ENSMUSG00000032221	Mns1	AW546487	meiosis-specific nuclear structural protein 1	protein-coding
mm_61392.1	chr7	73127869	73127878	+	1	NA	Intergenic	Intergenic	-25805	NR_046024	625243	Mm.261798	NR_046024	ENSMUSG00000108383	Gm6567	-	predicted gene 6567	ncRNA
mm_159368.1	chr3	88493274	88493274	-	1	NA	promoter-TSS (NM_019390)	promoter-TSS (NM_019390)	38	NM_019390	16905	Mm.243014	NM_019390	ENSMUSG00000028063	Lmna	Dhe	lamin A	protein-coding
mm_112705.1	chr13	18717290	18717316	+	1	NA	promoter-TSS (NM_172120)	promoter-TSS (NM_172120)	11	NM_172120	218035	Mm.27389	NM_172120	ENSMUSG00000041236	Vps41	AI317346|Vam2|mVam2	VPS41 HOPS complex subunit	protein-coding
mm_64631.1	chr7	3693534	3693552	-	1	NA	promoter-TSS (NM_029934)	promoter-TSS (NM_029934)	-18	NM_029934	77582	Mm.397541	NM_029934	ENSMUSG00000035596	Mboat7	5730589L02Rik|BB1|Leng4|Lpiat|Lpiat1|mBB1	membrane bound O-acyltransferase domain containing 7	protein-coding
mm_115170.1	chr13	108044422	108044497	+	1	NA	promoter-TSS (NM_001048250)	promoter-TSS (NM_001048250)	-15	NM_001048250	75616	Mm.491164	NM_001048250	ENSMUSG00000071180	Smim15	2810008M24Rik	small integral membrane protein 15	protein-coding
mm_96604.1	chr11	69091417	69091423	+	1	NA	3' UTR (NM_009497, exon 5 of 5)	3' UTR (NM_009497, exon 5 of 5)	2892	NM_009497	22318	Mm.28643	NM_009497	ENSMUSG00000020894	Vamp2	Syb-2|Syb2|sybII	vesicle-associated membrane protein 2	protein-coding
mm_60919.1	chr7	46838455	46838477	+	1	NA	Intergenic	Intergenic	-7338	NM_010699	16828	Mm.29324	NM_010699	ENSMUSG00000063229	Ldha	Ldh1|Ldhm|l7R2	lactate dehydrogenase A	protein-coding
mm_124950.1	chr15	12824823	12824833	+	1	NA	promoter-TSS (NM_029998)	promoter-TSS (NM_029998)	13	NM_001130149	14000	Mm.293142	NM_026799	ENSMUSG00000022191	Drosha	1110013A17Rik|AI874853|Etohi2|Rn3|Rnasen	drosha, ribonuclease type III	protein-coding
mm_151813.1	chr19	5488961	5488972	-	1	NA	promoter-TSS (NM_027877)	promoter-TSS (NM_027877)	-630	NM_027877	71711	Mm.27697	NM_027877	ENSMUSG00000024906	Mus81	1200008A18Rik|AI182501|AW045863	MUS81 structure-specific endonuclease subunit	protein-coding
mm_136409.1	chr16	93794836	93794845	-	1	NA	intron (NM_027293, intron 27 of 36)	Lx7|LINE|L1	-37281	NM_001045529	338467	Mm.287329	NM_001045529	ENSMUSG00000039456	Morc3	1110051N18Rik|AI452146|BF318192|D16Jhu32e|NXP2|Zcwcc3	microrchidia 3	protein-coding
mm_92802.1	chr10	81365785	81365801	-	1	NA	promoter-TSS (NM_001014836)	promoter-TSS (NM_001014836)	27	NM_001014836	432479	Mm.440450	NM_001014836	ENSMUSG00000020234	4930404N11Rik	2210409H10Rik|5730551K18Rik|AI854616	RIKEN cDNA 4930404N11 gene	protein-coding
mm_31194.1	chr4	43631418	43631437	+	1	NA	promoter-TSS (NM_173788)	promoter-TSS (NM_173788)	-508	NM_173788	230103	Mm.103477	NM_173788	ENSMUSG00000028469	Npr2	GC-B|GC-B2|GC-B3|cn|mNPR-B|pwe	natriuretic peptide receptor 2	protein-coding
mm_97280.1	chr11	76089431	76089439	+	1	NA	intron (NM_026664, intron 13 of 21)	intron (NM_026664, intron 13 of 21)	-61653	NM_029658	76566	Mm.34131	NM_029658	ENSMUSG00000020846	Rflnb	1500005K14Rik|Fam101b|RefilinB|cfm	refilin B	protein-coding
mm_153036.1	chr19	31910466	31910478	-	1	NA	intron (NM_001081074, intron 3 of 11)	intron (NM_001081074, intron 3 of 11)	41711	NM_001081074	69865	Mm.87538	NM_001081074	ENSMUSG00000052595	A1cf	1810073H04Rik|ACF64|ACF65|ASP|Acf|MCM|MerCreMer|Tg(Myh6-cre/Esr1*)1Jmk|mer	APOBEC1 complementation factor	protein-coding
mm_3794.1	chr1	157412686	157412697	+	1	NA	promoter-TSS (NM_177644)	promoter-TSS (NM_177644)	-96	NM_177644	226525	Mm.235028	NM_177644	ENSMUSG00000070565	Rasal2	6530401P13|A330066M24Rik	RAS protein activator like 2	protein-coding
mm_169182.1	chr13	65817898	65817917	+	1	NA	Intergenic	Intergenic	-295546	NM_001177832	628709	Mm.390595	NM_001177832	ENSMUSG00000095909	Gm10324	ENSMUSG00000071302	predicted gene 10324	protein-coding
mm_70012.1	chr7	142444067	142444093	-	1	NA	exon (NM_009405, exon 5 of 6)	exon (NM_009405, exon 5 of 6)	1612	NM_009405	21953	Mm.39469	NM_009405	ENSMUSG00000031097	Tnni2	-	troponin I, skeletal, fast 2	protein-coding
mm_9207.1	chr1	171229818	171229832	-	1	NA	3' UTR (NM_010185, exon 5 of 5)	3' UTR (NM_010185, exon 5 of 5)	4524	NM_010185	14127	Mm.22673	NM_010185	ENSMUSG00000058715	Fcer1g	AI573376|CD23|FcR-gamma|FcR[g]|FcRgamma|Fce1g|FcepsilonRI|Ly-50	Fc receptor, IgE, high affinity I, gamma polypeptide	protein-coding
mm_8632.1	chr1	156303586	156303616	-	1	NA	promoter-TSS (NM_001277730)	promoter-TSS (NM_001277730)	5	NM_001277730	214575	Mm.252800	NM_001134741	ENSMUSG00000060985	Tdrd5	Gm103	tudor domain containing 5	protein-coding
mm_68164.1	chr7	103812580	103812600	-	1	NA	TTS (NM_016956)	TTS (NM_016956)	1333	NM_016956	15130	Mm.288567	NM_016956		Hbb-b2	AI036344|Hbb2|Hbbt2|beta2	hemoglobin, beta adult minor chain	protein-coding
mm_39626.1	chr5	24427508	24427518	+	1	NA	promoter-TSS (NM_001253892)	promoter-TSS (NM_001253892)	-8	NM_001253892	20535	Mm.4580	NM_009207	ENSMUSG00000028962	Slc4a2	Ae2|B3RP	solute carrier family 4 (anion exchanger), member 2	protein-coding
mm_148385.1	chr19	3352501	3352516	+	1	NA	exon (NM_013495, exon 3 of 19)	exon (NM_013495, exon 3 of 19)	29207	NM_013495	12894	Mm.18522	NM_013495	ENSMUSG00000024900	Cpt1a	C730027G07|CPTI|Cpt1	carnitine palmitoyltransferase 1a, liver	protein-coding
mm_105164.1	chr11	101675466	101675496	-	1	NA	Intergenic	Intergenic	9940	NM_025404	80981	Mm.266840	NM_025404	ENSMUSG00000034936	Arl4d	1110036H21Rik|ARL6|AW456149|Arf4l|Arfl4|Arl5	ADP-ribosylation factor-like 4D	protein-coding
mm_27577.1	chr3	58822370	58822376	-	1	NA	Intergenic	Intergenic	62839	NM_153386	229320	Mm.131502	NM_153384	ENSMUSG00000043850	Clrn1	A130002D11Rik|USH3|Ush3a|clarin-1	clarin 1	protein-coding
mm_159814.1	chr5	120861426	120861426	+	1	NA	promoter-TSS (NM_001159934)	promoter-TSS (NM_001159934)	4	NM_145228	246729	Mm.115351	NM_145228	ENSMUSG00000001168	Oas1h	-	2'-5' oligoadenylate synthetase 1H	protein-coding
mm_132384.1	chr16	34929279	34929281	+	1	NA	intron (NM_139300, intron 16 of 31)	B1_Mm|SINE|Alu	10049	NR_040536	76649	Mm.420532	NR_040536	ENSMUSG00000100593	1700119H24Rik	-	RIKEN cDNA 1700119H24 gene	ncRNA
mm_154181.1	chr19	58792818	58792832	-	1	NA	intron (NM_026208, intron 1 of 5)	intron (NM_026208, intron 1 of 5)	1589	NM_026208	67507	Mm.27027	NM_026208	ENSMUSG00000026931	1700019N19Rik	-	RIKEN cDNA 1700019N19 gene	protein-coding
mm_143145.1	chr17	57221916	57221929	-	1	NA	exon (NM_009778, exon 15 of 41)	exon (NM_009778, exon 15 of 41)	-4694	NR_105944	102465591		NR_105944	ENSMUSG00000099066	Mir6978	Gm27858|mmu-mir-6978	microRNA 6978	ncRNA
mm_159539.1	chr4	88522849	88522849	-	1	NA	promoter-TSS (NM_010510)	promoter-TSS (NM_010510)	-55	NM_010510	15977	Mm.1245	NM_010510	ENSMUSG00000048806	Ifnb1	IFN-beta|IFNB|Ifb	interferon beta 1, fibroblast	protein-coding
mm_122592.1	chr14	50917323	50917336	-	1	NA	intron (NM_133676, intron 5 of 10)	intron (NM_133676, intron 5 of 10)	7564	NM_133676	66246	Mm.274791	NM_133676	ENSMUSG00000006289	Osgep	1500019L24Rik|GCPL-1|PRSMG1	O-sialoglycoprotein endopeptidase	protein-coding
mm_17608.1	chr2	30920281	30920305	-	1	NA	Intergenic	Intergenic	-16996	NM_022415	64292	Mm.28768	NM_022415	ENSMUSG00000050737	Ptges	2410099E23Rik|D2Ertd369e|Pges|mPGES|mPGES-1	prostaglandin E synthase	protein-coding
mm_38260.1	chr4	136880333	136880343	-	1	NA	exon (NM_009777, exon 3 of 3)	exon (NM_009777, exon 3 of 3)	5839	NM_009777	12260	Mm.2570	NM_009777	ENSMUSG00000036905	C1qb	-	complement component 1, q subcomponent, beta polypeptide	protein-coding
mm_15257.1	chr2	154892961	154892969	+	1	NA	promoter-TSS (NM_026030)	promoter-TSS (NM_026030)	-59	NM_026030	67204	Mm.377134	NM_026030	ENSMUSG00000074656	Eif2s2	2810026E11Rik|38kDa|AA408636|AA571381|AA986487|AW822225|D2Ertd303e|EIF2|EIF2B	eukaryotic translation initiation factor 2, subunit 2 (beta)	protein-coding
mm_70104.1	chr7	142661306	142661314	-	1	NA	promoter-TSS (NM_001122736)	promoter-TSS (NM_001122736)	-39	NM_001122736	16002	Mm.3862	NM_010514	ENSMUSG00000048583	Igf2	AL033362|Igf-2|Igf-II|M6pr|Mpr|Peg2	insulin-like growth factor 2	protein-coding
mm_156285.1	chrX	136837334	136837361	+	1	NA	3' UTR (NM_011123, exon 7 of 7)	3' UTR (NM_011123, exon 7 of 7)	14601	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_15580.1	chr2	158700972	158700972	+	1	NA	intron (NM_153089, intron 2 of 10)	L1MB7|LINE|L1	33837	NM_001159662	228852	Mm.150540	NM_153089	ENSMUSG00000037754	Ppp1r16b	ANKRD4|C130078N17Rik|TIMAP|Wdt4	protein phosphatase 1, regulatory (inhibitor) subunit 16B	protein-coding
mm_149705.1	chr19	21471335	21471348	+	1	NA	intron (NM_010266, intron 1 of 13)	RSINE1|SINE|B4	1320	NM_010266	14544	Mm.45054	NM_010266	ENSMUSG00000058624	Gda	AU015411|AW047581|GAH	guanine deaminase	protein-coding
mm_25935.1	chr3	131466539	131466544	+	1	NA	Intergenic	Intergenic	-98227	NM_001289479	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_79882.1	chr9	65235880	65235884	+	1	NA	intron (NM_177460, intron 5 of 6)	B1_Mur2|SINE|Alu	21192	NM_177460	214424	Mm.31129	NM_177460	ENSMUSG00000032392	Parp16	ARTD15|BC055447|C79952|PARP-16	poly (ADP-ribose) polymerase family, member 16	protein-coding
mm_84422.1	chr9	65691394	65691397	-	1	NA	TTS (NM_172536)	TTS (NM_172536)	14847	NM_001301307	18247	Mm.116749	NM_010952	ENSMUSG00000040652	Oaz2	AZ-2|AZ2|Oaz2-ps|Sez15	ornithine decarboxylase antizyme 2	protein-coding
mm_103560.1	chr11	77722678	77722697	-	1	NA	exon (NM_009965, exon 3 of 6)	exon (NM_009965, exon 3 of 6)	2606	NM_001313933	12957	Mm.22830	NM_009965	ENSMUSG00000000724	Cryba1	BA3/A1|Cryb	crystallin, beta A1	protein-coding
mm_83095.1	chr9	40321248	40321252	-	1	NA	intron (NM_172768, intron 4 of 19)	intron (NM_172768, intron 4 of 19)	-12222	NR_040728	73558	Mm.398307	NR_040728		1700110K17Rik	-	RIKEN cDNA 1700110K17 gene	ncRNA
mm_155801.1	chrX	99042605	99042613	+	1	NA	promoter-TSS (NM_199018)	promoter-TSS (NM_199018)	28	NM_199018	236920	Mm.236928	NM_199018	ENSMUSG00000031216	Stard8	Dlc3|mKIAA0189	START domain containing 8	protein-coding
mm_70651.1	chr8	14354455	14354457	+	1	NA	intron (NM_172910, intron 3 of 15)	intron (NM_172910, intron 3 of 15)	258581	NM_172910	244310	Mm.404697	NM_172910	ENSMUSG00000047495	Dlgap2	6430596N04Rik|Dap-2|Dap2|Sapap2	discs, large (Drosophila) homolog-associated protein 2	protein-coding
mm_1275.1	chr1	63445843	63445943	+	1	NA	promoter-TSS (NM_011780)	promoter-TSS (NM_011780)	2	NM_011780	23792	Mm.124892	NM_011780	ENSMUSG00000025964	Adam23	AW046396|MDC3	a disintegrin and metallopeptidase domain 23	protein-coding
mm_10952.1	chr2	25652995	25653019	+	1	NA	promoter-TSS (NM_033145)	promoter-TSS (NM_033145)	-111	NM_033145	78076	Mm.196708	NM_033145	ENSMUSG00000036449	Lcn8	9230106L18Rik|EP17|Lcn5|mEP17	lipocalin 8	protein-coding
mm_91722.1	chr10	44464196	44464215	-	1	NA	Intergenic	Intergenic	-5457	NM_007548	12142	Mm.4800	NM_007548	ENSMUSG00000038151	Prdm1	Blimp-1|Blimp1|PRDI-BF1|ZNFPR1A1|b2b1765Clo	PR domain containing 1, with ZNF domain	protein-coding
mm_82057.1	chr9	122682173	122682184	+	1	NA	promoter-TSS (NR_029819)	promoter-TSS (NR_029819)	-698	NR_029819	387156		NR_029819	ENSMUSG00000065414	Mir138-1	Mirn138|Mirn138-1|mir-138-1	microRNA 138-1	ncRNA
mm_125105.1	chr15	27771095	27771111	+	1	NA	intron (NM_001081302, intron 36 of 56)	intron (NM_001081302, intron 36 of 56)	-89561	NM_001242423	223433	Mm.266485	NM_198301	ENSMUSG00000056069	Fam105a	9830126M18	family with sequence similarity 105, member A	protein-coding
mm_8293.1	chr1	143344579	143344589	-	1	NA	Intergenic	Intergenic	-296113	NM_020025	26878	Mm.285580	NM_020025	ENSMUSG00000033849	B3galt2	-	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 2	protein-coding
mm_42063.1	chr5	109055644	109055653	+	1	NA	intron (NM_001104622, intron 1 of 5)	RLTR9A3B|LTR|ERVK	3804	NM_001104622	384219	Mm.469885	NM_001104622	ENSMUSG00000091450	Vmn2r11	EG384219	vomeronasal 2, receptor 11	protein-coding
mm_114795.1	chr13	89584652	89584708	+	1	NA	intron (NM_013500, intron 1 of 4)	intron (NM_013500, intron 1 of 4)	44044	NM_013500	12950	Mm.266790	NM_013500	ENSMUSG00000021613	Hapln1	BB099155|CLP|Crtl1|Crtl1l|LP|LP-1	hyaluronan and proteoglycan link protein 1	protein-coding
mm_62359.1	chr7	100499360	100499381	+	1	NA	3' UTR (NM_011671, exon 8 of 8)	3' UTR (NM_011671, exon 8 of 8)	6012	NM_011671	22228	Mm.171378	NM_011671	ENSMUSG00000033685	Ucp2	Slc25a8	uncoupling protein 2 (mitochondrial, proton carrier)	protein-coding
mm_49768.1	chr6	34863219	34863241	+	1	NA	promoter-TSS (NM_197986)	promoter-TSS (NM_197986)	84	NM_197986	68487	Mm.248440	NM_197986	ENSMUSG00000057137	Tmem140	1110007F12Rik	transmembrane protein 140	protein-coding
mm_146992.1	chr18	34221634	34221659	-	1	NA	non-coding (NR_040534, exon 1 of 2)	non-coding (NR_040534, exon 1 of 2)	126	NR_040534	633395	Mm.414290	NR_040534	ENSMUSG00000073607	Gm10548	ENSMUSG00000073607	ribosomal protein L29 pseudogene	pseudo
mm_165551.1	chr3	9997553	9997566	+	1	NA	Intergenic	L1VL1|LINE|L1	-15026	NM_001272097	16592	Mm.741	NM_010634	ENSMUSG00000027533	Fabp5	E-FABP|Fabpe|Klbp|PA-FABP|mal1	fatty acid binding protein 5, epidermal	protein-coding
mm_36235.1	chr4	63154131	63154150	-	1	NA	promoter-TSS (NM_007443)	promoter-TSS (NM_007443)	32	NM_007443	11699	Mm.2197	NM_007443	ENSMUSG00000028356	Ambp	AI194774|ASPI|HI-30|Intin4|Itil|UTI	alpha 1 microglobulin/bikunin	protein-coding
mm_125442.1	chr15	46324570	46324577	+	1	NA	promoter-TSS (NR_045509)	promoter-TSS (NR_045509)	-12	NR_045509	71120	Mm.158571	NR_045509	ENSMUSG00000099751	1700022A22Rik	4933413D07Rik	RIKEN cDNA 1700022A22 gene	ncRNA
mm_82574.1	chr9	21131162	21131168	-	1	NA	intron (NM_001205312, intron 1 of 24)	intron (NM_001205312, intron 1 of 24)	110	NM_018793	54721	Mm.20249	NM_018793	ENSMUSG00000032175	Tyk2	JTK1	tyrosine kinase 2	protein-coding
mm_102214.1	chr11	54908625	54908635	-	1	NA	exon (NM_008161, exon 3 of 5)	exon (NM_008161, exon 3 of 5)	5776	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_168748.1	chr12	115593585	115593601	-	1	NA	Intergenic	Intergenic	102201	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
mm_171931.1	chr5	6401156	6401158	-	1	NA	Intergenic	L1Md_T|LINE|L1	-651840	NM_027399	70358	Mm.85429	NM_027399	ENSMUSG00000015652	Steap1	2410007B19Rik|Prss24|Steap	six transmembrane epithelial antigen of the prostate 1	protein-coding
mm_7721.1	chr1	130661585	130661609	-	1	NA	promoter-TSS (NM_007576)	promoter-TSS (NM_007576)	21	NM_007576	12269	Mm.306720	NM_007576	ENSMUSG00000026405	C4bp	AI195242|C4bpa	complement component 4 binding protein	protein-coding
mm_68100.1	chr7	102015809	102015833	-	1	NA	TTS (NM_133947)	TTS (NM_133947)	2334	NM_010531	16068	Mm.422756	NM_010531	ENSMUSG00000070427	Il18bp	IL-18BP|Igifbp|MC54L	interleukin 18 binding protein	protein-coding
mm_98567.1	chr11	95384920	95384944	+	1	NA	promoter-TSS (NM_016752)	promoter-TSS (NM_016752)	10	NM_016752	110172	Mm.4593	NM_016752	ENSMUSG00000020873	Slc35b1	Ugalt2	solute carrier family 35, member B1	protein-coding
mm_117994.1	chr13	100467211	100467214	-	1	NA	Intergenic	Intergenic	-14348	NM_008670	17940	Mm.6898	NM_008670	ENSMUSG00000021640	Naip1	AV364616|Birc1a|D13Lsd1|Naip|Naip-rs1	NLR family, apoptosis inhibitory protein 1	protein-coding
mm_145249.1	chr18	52331522	52331545	+	1	NA	promoter-TSS (NM_026286)	promoter-TSS (NM_026286)	-3	NM_026286	67634	Mm.179144	NM_026286	ENSMUSG00000024510	Ftmt	4930447C24Rik|FerH|Fth3|MtF	ferritin mitochondrial	protein-coding
mm_126325.1	chr15	79878966	79878990	+	1	NA	Intergenic	Intergenic	-13430	NM_001160415	80287	Mm.284059	NM_030255	ENSMUSG00000009585	Apobec3	Apobec|Arp3|BC003314|Cem15|Rfv3	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 3	protein-coding
mm_77592.1	chr8	123891906	123891918	-	1	NA	3' UTR (NM_009606, exon 7 of 7)	3' UTR (NM_009606, exon 7 of 7)	2863	NM_001272041	11459	Mm.214950	NM_009606	ENSMUSG00000031972	Acta1	AA959943|Acta-2|Acts|Actsk-1	actin, alpha 1, skeletal muscle	protein-coding
mm_40442.1	chr5	53591249	53591260	+	1	NA	intron (NM_001080927, intron 1 of 10)	intron (NM_001080927, intron 1 of 10)	768	NM_001080927	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_32205.1	chr4	101507785	101507800	+	1	NA	promoter-TSS (NM_001164585)	promoter-TSS (NM_001164585)	-184	NM_001164585	72685	Mm.76494	NM_198412	ENSMUSG00000028528	Dnajc6	2810027M23Rik|mKIAA0473	DnaJ heat shock protein family (Hsp40) member C6	protein-coding
mm_109333.1	chr12	109581013	109581016	+	1	NA	TTS (NR_030573)	TTS (NR_030573)	781	NR_030573	100124466		NR_030573	ENSMUSG00000077025	Mir493	Mirn493|mmu-mir-493	microRNA 493	ncRNA
mm_136923.1	chr17	13846173	13846183	+	1	NA	intron (NM_010806, intron 13 of 32)	intron (NM_010806, intron 13 of 32)	-84784	NM_022311	21646	Mm.486358	NM_022311	ENSMUSG00000038347	Tcte2	AI429268|Tcte-2	t-complex-associated testis expressed 2	protein-coding
mm_158704.1	chrX	162125825	162125870	-	1	NA	intron (NM_001081052, intron 1 of 7)	intron (NM_001081052, intron 1 of 7)	33594	NM_001081052	195727	Mm.336313	NM_001081052	ENSMUSG00000059493	Nhs	Gm389|Gm48|Nhs1|Xcat	Nance-Horan syndrome (human)	protein-coding
mm_31873.1	chr4	80834299	80834313	+	1	NA	promoter-TSS (NM_031202)	promoter-TSS (NM_031202)	93	NM_001282015	22178	Mm.30438	NM_031202	ENSMUSG00000005994	Tyrp1	Oca3|TRP-1|TRP1|Tyrp|b|brown|isa	tyrosinase-related protein 1	protein-coding
mm_905.1	chr1	53824175	53824210	+	1	NA	intron (NM_001001883, intron 28 of 28)	intron (NM_001001883, intron 28 of 28)	-25232	NR_106149	102465783		NR_106149	ENSMUSG00000098443	Mir7681	Gm27806|mmu-mir-7681	microRNA 7681	ncRNA
mm_33360.1	chr4	129490861	129490878	+	1	NA	promoter-TSS (NM_080442)	promoter-TSS (NM_080442)	-99	NM_080442	58864	Mm.143802	NM_080442	ENSMUSG00000000411	Tssk3	1700014N07Rik|4930594I21Rik|Stk22c|Stk22d|Tsk-3|Tssk-3|Tssk3b	testis-specific serine kinase 3	protein-coding
mm_30888.1	chr4	32252261	32252288	+	1	NA	Intergenic	Intergenic	-165161	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_121320.1	chr14	111675520	111675532	+	1	NA	5' UTR (NM_198865, exon 1 of 2)	5' UTR (NM_198865, exon 1 of 2)	411	NM_198865	75409	Mm.235097	NM_029273	ENSMUSG00000033214	Slitrk5	2610019D03Rik	SLIT and NTRK-like family, member 5	protein-coding
mm_154501.1	chrM	11817	11825	-	1	NA	NA	Intergenic	NA	NA								
mm_113968.1	chr13	51645371	51645392	+	1	NA	5' UTR (NM_025415, exon 1 of 3)	5' UTR (NM_025415, exon 1 of 3)	149	NM_025415	66197	Mm.222228	NM_025415	ENSMUSG00000062248	Cks2	1110038L14Rik|CKSHS2	CDC28 protein kinase regulatory subunit 2	protein-coding
mm_146206.1	chr18	76856134	76856148	+	1	NA	promoter-TSS (NM_001109743)	promoter-TSS (NM_001109743)	-264	NM_001109743	664805	Mm.329543	NM_001109743	ENSMUSG00000091519	Skor2	Corl2|EG664805|Fussel18|Gm7348	SKI family transcriptional corepressor 2	protein-coding
mm_120707.1	chr14	71251265	71251284	+	1	NA	promoter-TSS (NR_046076)	promoter-TSS (NR_046076)	1	NR_046076	100043132	Mm.399336	NR_046075		Gm4251	-	predicted gene 4251	ncRNA
mm_62013.1	chr7	91344511	91344515	+	1	NA	intron (NM_011807, intron 1 of 22)	intron (NM_011807, intron 1 of 22)	253727	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_86655.1	chr10	17724309	17724341	+	1	NA	exon (NM_010828, exon 2 of 2)	exon (NM_010828, exon 2 of 2)	1097	NM_010828	17684	Mm.272321	NM_010828	ENSMUSG00000039910	Cited2	AI835299|ER154-like|Mrg1|Msg2|p35srj	Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 2	protein-coding
mm_154239.1	chr19	60581014	60581025	-	1	NA	promoter-TSS (NM_001172096)	promoter-TSS (NM_001172096)	4	NM_001172097	78832	Mm.259026	NM_030197	ENSMUSG00000033417	Cacul1	2700078E11Rik|2810417M16Rik|9830127L17Rik|AI450346|D130033C15Rik	CDK2 associated, cullin domain 1	protein-coding
mm_144348.1	chr18	15195251	15195261	+	1	NA	Intergenic	Intergenic	-43810	NM_134112	106931	Mm.329299	NM_134112	ENSMUSG00000036225	Kctd1	4933402K10Rik|AI661543|AW553000	potassium channel tetramerisation domain containing 1	protein-coding
mm_26119.1	chr3	137864536	137864564	+	1	NA	promoter-TSS (NM_016750)	promoter-TSS (NM_016750)	63	NM_016750	51788	Mm.117541	NM_016750	ENSMUSG00000037894	H2afz	H2A.Z|H2a.z-1	H2A histone family, member Z	protein-coding
mm_55107.1	chr6	50261944	50261955	-	1	NA	promoter-TSS (NM_018769)	promoter-TSS (NM_018769)	-180	NM_018769	54722	Mm.248361	NM_018769	ENSMUSG00000029821	Dfna5	2310037D07Rik|4932441K13Rik|Dfna5h|EG14210|Fin15	deafness, autosomal dominant 5 (human)	protein-coding
mm_27333.1	chr3	50398524	50398541	-	1	NA	intron (NM_011990, intron 6 of 11)	intron (NM_011990, intron 6 of 11)	45081	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_79610.1	chr9	58614369	58614372	+	1	NA	intron (NM_001293673, intron 1 of 7)	intron (NM_001293673, intron 1 of 7)	32130	NM_009145	20320	Mm.15125	NM_009145	ENSMUSG00000032336	Nptn	AW554172|SDR-1|Sdfr1	neuroplastin	protein-coding
mm_6113.1	chr1	64121192	64121203	-	1	NA	5' UTR (NM_033563, exon 1 of 4)	5' UTR (NM_033563, exon 1 of 4)	192	NM_033563	93691	Mm.29466	NM_033563	ENSMUSG00000025959	Klf7	9830124P08Rik	Kruppel-like factor 7 (ubiquitous)	protein-coding
mm_18990.1	chr2	76863497	76863517	-	1	NA	exon (NM_011652, exon 111 of 313)	exon (NM_011652, exon 111 of 313)	119040	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_50340.1	chr6	48537632	48537733	+	1	NA	promoter-TSS (NR_130985)	promoter-TSS (NR_130985)	113	NM_133764	76252	Mm.30214	NM_133764	ENSMUSG00000039347	Atp6v0e2	0610006O14Rik|NM9.2	ATPase, H+ transporting, lysosomal V0 subunit E2	protein-coding
mm_125960.1	chr15	76266585	76266593	+	1	NA	TTS (NR_045747)	TTS (NR_045747)	-1500	NM_028852	74281	Mm.159156	NM_028852	ENSMUSG00000049653	Spatc1	1700084J23Rik|speriolin	spermatogenesis and centriole associated 1	protein-coding
mm_162272.1	chr1	10315271	10315286	+	1	NA	Intergenic	Intergenic	-82608	NM_001102430	211673	Mm.229141	NM_001102430	ENSMUSG00000067851	Arfgef1	ARFGEP1|BIG1|D130059B05Rik|D730028O18Rik|P200	ADP-ribosylation factor guanine nucleotide-exchange factor 1(brefeldin A-inhibited)	protein-coding
mm_117571.1	chr13	85289191	85289236	-	1	NA	5' UTR (NM_145452, exon 1 of 25)	5' UTR (NM_145452, exon 1 of 25)	273	NM_145452	218397	Mm.259653	NM_145452	ENSMUSG00000021549	Rasa1	Gap|RasGAP|Rasa	RAS p21 protein activator 1	protein-coding
mm_118102.1	chr13	103920374	103920423	-	1	NA	5' UTR (NM_001289475, exon 1 of 26)	5' UTR (NM_001289475, exon 1 of 26)	188	NM_001289473	59079	Mm.277354	NM_021563	ENSMUSG00000021709	Erbin	1700028E05Rik|Erbb2ip|mKIAA1225	Erbb2 interacting protein	protein-coding
mm_24687.1	chr3	94974758	94974768	+	1	NA	promoter-TSS (NM_001293716)	promoter-TSS (NM_001293716)	32	NM_001293716	107650	Mm.217222	NM_175356	ENSMUSG00000038861	Pi4kb	ESTM41|PI4K-beta|PI4Kbeta|Pik4cb	phosphatidylinositol 4-kinase, catalytic, beta polypeptide	protein-coding
mm_98888.1	chr11	97836354	97836368	+	1	NA	3' UTR (NM_010688, exon 7 of 7)	3' UTR (NM_010688, exon 7 of 7)	-4419	NM_001080935	68127	Mm.110270	NM_001080935	ENSMUSG00000050538	B230217C12Rik	AI840637	RIKEN cDNA B230217C12 gene	protein-coding
mm_20238.1	chr2	126321466	126321475	-	1	NA	3' UTR (NM_001080944, exon 28 of 28)	3' UTR (NM_001080944, exon 28 of 28)	169329	NM_026981	69185	Mm.29019	NM_026981	ENSMUSG00000023330	Dtwd1	1810033A06Rik	DTW domain containing 1	protein-coding
mm_152240.1	chr19	8712968	8713023	-	1	NA	intron (NM_001161413, intron 2 of 9)	intron (NM_001161413, intron 2 of 9)	902	NM_008577	17254	Mm.4114	NM_008577	ENSMUSG00000010095	Slc3a2	4F2|4F2HC|AI314110|Cd98|Ly-10|Ly-m10|Ly10|Mdu1|Mgp-2hc|NACAE	solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2	protein-coding
mm_103248.1	chr11	70812540	70812554	-	1	NA	promoter-TSS (NM_001045526)	promoter-TSS (NM_001045526)	14	NM_001045526	327957	Mm.164325	NM_001045526	ENSMUSG00000057135	Scimp	A430084P05Rik	SLP adaptor and CSK interacting membrane protein	protein-coding
mm_155980.1	chrX	106126941	106126984	+	1	NA	3' UTR (NM_009726, exon 23 of 23)	3' UTR (NM_009726, exon 23 of 23)	-16313	NM_205820	279572	Mm.336203	NM_205820	ENSMUSG00000033777	Tlr13	AI666735|Gm713	toll-like receptor 13	protein-coding
mm_158028.1	chrX	96293457	96293465	-	1	NA	promoter-TSS (NM_177789)	promoter-TSS (NM_177789)	-23	NM_177789	278180	Mm.26781	NM_177789	ENSMUSG00000044206	Vsig4	A530061A11|BC025105|CRIg|Z39IG	V-set and immunoglobulin domain containing 4	protein-coding
mm_1074.1	chr1	59449275	59449281	+	1	NA	Intergenic	Intergenic	-32869	NM_008057	14369	Mm.297906	NM_008057	ENSMUSG00000041075	Fzd7	Fz7	frizzled class receptor 7	protein-coding
mm_136490.1	chr16	96124943	96124945	-	1	NA	intron (NM_008251, intron 4 of 5)	intron (NM_008251, intron 4 of 5)	2781	NM_008251	15312	Mm.2756	NM_008251	ENSMUSG00000040681	Hmgn1	HMG-14|Hmg14	high mobility group nucleosomal binding domain 1	protein-coding
mm_55394.1	chr6	60687306	60687316	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	141693	NM_001042451	20617	Mm.17484	NM_009221	ENSMUSG00000025889	Snca	NACP|alphaSYN	synuclein, alpha	protein-coding
mm_165659.1	chr3	87906071	87906091	+	1	NA	promoter-TSS (NM_008231)	promoter-TSS (NM_008231)	-240	NM_008231	15191	Mm.292208	NM_008231	ENSMUSG00000004897	Hdgf	AI118077|D3Ertd299e	hepatoma-derived growth factor	protein-coding
mm_161335.1	chr14	51007751	51007751	+	1	NA	promoter-TSS (NM_001162863)	promoter-TSS (NM_001162863)	0	NM_001162863	75019	Mm.318775	NM_029145	ENSMUSG00000021872	Rnase10	4930474F22Rik|Rah1	ribonuclease, RNase A family, 10 (non-active)	protein-coding
mm_118060.1	chr13	102706716	102706736	-	1	NA	TTS (NM_008533)	TTS (NM_008533)	13168	NM_008533	17079	Mm.373974	NM_008533	ENSMUSG00000021624	Cd180	F630107B15|Ly78|RP105	CD180 antigen	protein-coding
mm_173353.1	chrY	90813959	90813961	+	1	NA	intron (NM_133362, intron 2 of 3)	(CAGAGA)n|Simple_repeat|Simple_repeat	25446	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_104338.1	chr11	94053558	94053571	-	1	NA	intron (NM_001025429, intron 2 of 26)	intron (NM_001025429, intron 2 of 26)	9359	NM_001025429	70834	Mm.260737	NM_027569	ENSMUSG00000020859	Spag9	3110018C07Rik|4733401I23Rik|4831406C20Rik|AW552012|JLP|JSAP2|JSAP2a|Jip4|Mapk8ip4|syd1	sperm associated antigen 9	protein-coding
mm_159875.1	chr5	150518089	150518089	-	1	NA	promoter-TSS (NM_001159693)	promoter-TSS (NM_001159693)	70	NM_001159693	545824	Mm.380068	NM_001159693	ENSMUSG00000056586	Zar1l	XM_359419	zygote arrest 1-like	protein-coding
mm_109478.1	chr12	111423249	111423264	+	1	NA	intron (NM_001289487, intron 4 of 13)	intron (NM_001289487, intron 4 of 13)	5811	NM_001289488	74190	Mm.248640	NM_028807	ENSMUSG00000021280	Exoc3l4	1200009I06Rik|1600013K19Rik	exocyst complex component 3-like 4	protein-coding
mm_137474.1	chr17	26715645	26715702	+	1	NA	promoter-TSS (NM_029870)	promoter-TSS (NM_029870)	23	NM_029870	77128	Mm.275414	NM_029870	ENSMUSG00000048249	Crebrf	A930001N09Rik|LRF	CREB3 regulatory factor	protein-coding
mm_35732.1	chr4	45012060	45012078	-	1	NA	5' UTR (NM_001163284, exon 1 of 2)	5' UTR (NM_001163284, exon 1 of 2)	343	NM_001163284	230119	Mm.44222	NM_173399	ENSMUSG00000049657	Zbtb5	5930421I10|9430083K24Rik|AI646847|mKIAA0354	zinc finger and BTB domain containing 5	protein-coding
mm_6186.1	chr1	65110131	65110166	-	1	NA	intron (NM_175293, intron 5 of 7)	intron (NM_175293, intron 5 of 7)	-6785	NM_007774	12964	Mm.26904	NM_007774	ENSMUSG00000044429	Cryga	Cryg-4|DGcry-4	crystallin, gamma A	protein-coding
mm_60795.1	chr7	45587944	45587950	+	1	NA	exon (NM_001243053, exon 9 of 12)	exon (NM_001243053, exon 9 of 12)	-12771	NR_038165	71661	Mm.439894	NR_038165	ENSMUSG00000109644	0610005C13Rik	AI182092	RIKEN cDNA 0610005C13 gene	ncRNA
mm_15127.1	chr2	153826082	153826086	+	1	NA	Intergenic	Intergenic	45000	NM_001305048	76407	Mm.33629	NM_029599	ENSMUSG00000027480	Sun5	1700021O15Rik|SPAG4L-2|SRG4|Spag4l	Sad1 and UNC84 domain containing 5	protein-coding
mm_102237.1	chr11	54962904	54962953	-	1	NA	promoter-TSS (NM_021327)	promoter-TSS (NM_021327)	12	NM_021327	57783	Mm.259671	NM_021327	ENSMUSG00000020400	Tnip1	ABIN|ABIN-1|ABIN1|AU018810|Naf1|Nef|VAN	TNFAIP3 interacting protein 1	protein-coding
mm_83141.1	chr9	40455419	40455435	-	1	NA	exon (NM_172768, exon 1 of 20)	exon (NM_172768, exon 1 of 20)	337	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_132129.1	chr16	31754824	31754832	+	1	NA	exon (NM_001252436, exon 1 of 23)	exon (NM_001252436, exon 1 of 23)	478	NM_001252436	13383	Mm.382	NM_007862	ENSMUSG00000022770	Dlg1	B130052P05Rik|Dlgh1|E-dlg/SAP97|SAP-97|SAP97|mKIAA4187	discs, large homolog 1 (Drosophila)	protein-coding
mm_32945.1	chr4	119539653	119539698	+	1	NA	promoter-TSS (NM_001290696)	promoter-TSS (NM_001290696)	14	NM_172699	230700	Mm.259227	NM_172699	ENSMUSG00000032998	Foxj3	C330039G02Rik|Fhd6	forkhead box J3	protein-coding
mm_6691.1	chr1	80710395	80710402	-	1	NA	intron (NM_175291, intron 1 of 55)	intron (NM_175291, intron 1 of 55)	-45046	NM_001285927	210293	Mm.133473	NM_175291	ENSMUSG00000038608	Dock10	9330153B10Rik|A630054M16Rik|Jr4|Jr5|R75174|ZIZ3|Zizimin3|mKIAA0694	dedicator of cytokinesis 10	protein-coding
mm_163814.1	chr14	19416379	19416390	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	186203	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_134327.1	chr16	16358904	16359009	-	1	NA	promoter-TSS (NM_152816)	promoter-TSS (NM_152816)	75	NM_152816	74006	Mm.218820	NM_152816	ENSMUSG00000022789	Dnm1l	6330417M19Rik|AI450666|Dlp1|Dnmlp1|Drp1|python	dynamin 1-like	protein-coding
mm_30216.1	chr3	145018683	145018696	-	1	NA	exon (NM_017474, exon 5 of 14)	exon (NM_017474, exon 5 of 14)	14087	NM_017474	23844	Mm.33483	NM_017474	ENSMUSG00000028255	Clca1	Clca2|Clca3|gob-5|gob5	chloride channel accessory 1	protein-coding
mm_110266.1	chr12	31950187	31950197	-	1	NA	intron (NM_177993, intron 1 of 8)	CpG	343	NM_177993	73389	Mm.390461	NM_153198	ENSMUSG00000002996	Hbp1	1700058O05Rik|BE629963|C330012F01Rik|C86454	high mobility group box transcription factor 1	protein-coding
mm_77540.1	chr8	123042272	123042302	-	1	NA	promoter-TSS (NR_045268)	promoter-TSS (NR_045268)	-3	NM_001081379	77087	Mm.31567	NM_001081379	ENSMUSG00000035569	Ankrd11	2410104C19Rik|3010027A04Rik|6330578C09Rik|9530048I21Rik|AA930108|Gm176|Yod	ankyrin repeat domain 11	protein-coding
mm_50138.1	chr6	41543199	41543205	+	1	NA	Intergenic	Intergenic	21426	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_97844.1	chr11	83065313	83065317	+	1	NA	exon (NM_011408, exon 1 of 2)	exon (NM_011408, exon 1 of 2)	203	NM_011408	20556	Mm.278689	NM_011408	ENSMUSG00000072620	Slfn2	Shlf2	schlafen 2	protein-coding
mm_25978.1	chr3	133092571	133092611	+	1	NA	promoter-TSS (NM_026231)	promoter-TSS (NM_026231)	736	NM_027927	71793	Mm.246726	NM_027927	ENSMUSG00000028016	Ints12	1110020M19Rik|2810027J24Rik|4930529N21Rik|A230056J18Rik|AI666778|Phf22|int12	integrator complex subunit 12	protein-coding
mm_97256.1	chr11	75758839	75758851	+	1	NA	intron (NM_009536, intron 4 of 5)	intron (NM_009536, intron 4 of 5)	25958	NM_009536	22627	Mm.234700	NM_009536	ENSMUSG00000020849	Ywhae	AU019196	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide	protein-coding
mm_15926.1	chr2	165067187	165067195	+	1	NA	intron (NM_170702, intron 6 of 7)	RSINE1|SINE|B4	11555	NM_011611	21939	Mm.271833	NM_011611	ENSMUSG00000017652	Cd40	AI326936|Bp50|GP39|HIGM1|IGM|IMD3|T-BAM|TRAP|Tnfrsf5|p50	CD40 antigen	protein-coding
mm_59219.1	chr7	24608339	24608369	+	1	NA	exon (NM_023154, exon 7 of 8)	exon (NM_023154, exon 7 of 8)	-2974	NM_001102613	232970	Mm.333663	NM_001102613	ENSMUSG00000074277	Phldb3	EG232970|ENSMUSG00000061511|Gm10102	pleckstrin homology like domain, family B, member 3	protein-coding
mm_48052.1	chr5	136510719	136510740	-	1	NA	intron (NM_001291234, intron 1 of 22)	intron (NM_001291234, intron 1 of 22)	55252	NM_001291239	13047	Mm.320317	NM_009986	ENSMUSG00000029705	Cux1	CDP|Cutl1|Cux|Cux-1	cut-like homeobox 1	protein-coding
mm_162935.1	chr10	127368947	127368950	+	1	NA	intron (NM_010565, intron 1 of 1)	MLT1A0|LTR|ERVL-MaLR	1600	NM_010565	16325	Mm.2594	NM_010565	ENSMUSG00000025405	Inhbc	-	inhibin beta-C	protein-coding
mm_165425.1	chr2	151980074	151980092	-	1	NA	5' UTR (NM_146127, exon 1 of 2)	5' UTR (NM_146127, exon 1 of 2)	136	NM_146127	73847	Mm.272444	NM_028666	ENSMUSG00000027459	Fam110a	1700008J10Rik|5430432M24Rik|AI747080	family with sequence similarity 110, member A	protein-coding
mm_58288.1	chr6	145863645	145863665	-	1	NA	exon (NM_024469, exon 5 of 5)	exon (NM_024469, exon 5 of 5)	1765	NM_001271768	79362	Mm.154529	NM_024469	ENSMUSG00000030256	Bhlhe41	6430520M22Rik|Bhlhb2l|Bhlhb3|DEC2|Sharp1	basic helix-loop-helix family, member e41	protein-coding
mm_55470.1	chr6	68768591	68768605	-	1	NA	Intergenic	Intergenic	558576	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_170600.1	chr19	5802459	5802459	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	213	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_127778.1	chr15	3523216	3523219	-	1	NA	intron (NM_001048178, intron 1 of 8)	B4A|SINE|B4	58625	NM_001286370	14600	Mm.3986	NM_010284	ENSMUSG00000055737	Ghr	GHBP|GHR/BP	growth hormone receptor	protein-coding
mm_154496.1	chrM	11339	11364	-	1	NA	NA	Intergenic	NA	NA								
mm_79360.1	chr9	54286480	54286494	+	1	NA	promoter-TSS (NM_177350)	promoter-TSS (NM_177350)	1	NM_177350	235379	Mm.123549	NM_177350	ENSMUSG00000046167	Gldn	CRG-L2|Clom|Colm|Crgl2|Crlg2	gliomedin	protein-coding
mm_105959.1	chr11	115420457	115420516	-	1	NA	promoter-TSS (NM_027862)	promoter-TSS (NM_027862)	360	NM_183285	70382	Mm.276299	NM_183285	ENSMUSG00000016940	Kctd2	2310012I15Rik	potassium channel tetramerisation domain containing 2	protein-coding
mm_65814.1	chr7	29113889	29113920	-	1	NA	intron (NM_009109, intron 7 of 105)	B3|SINE|B2	11247	NM_009109	20190	Mm.439745	NM_009109	ENSMUSG00000030592	Ryr1	AI528790|RYR-1|Ryr|skrr	ryanodine receptor 1, skeletal muscle	protein-coding
mm_137925.1	chr17	32506475	32506501	+	1	NA	promoter-TSS (NM_001101445)	promoter-TSS (NM_001101445)	26	NM_001101445	208285	Mm.311422	NM_001101445	ENSMUSG00000091586	Cyp4f17	EG208285	cytochrome P450, family 4, subfamily f, polypeptide 17	protein-coding
mm_71406.1	chr8	46471082	46471109	+	1	NA	promoter-TSS (NM_007981)	promoter-TSS (NM_007981)	58	NM_007981	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_152145.1	chr19	7202339	7202356	-	1	NA	intron (NM_134150, intron 3 of 6)	PB1D10|SINE|Alu	3937	NM_134150	107260	Mm.203921	NM_134150	ENSMUSG00000024767	Otub1	AI850305	OTU domain, ubiquitin aldehyde binding 1	protein-coding
mm_148335.1	chr18	84301281	84301314	-	1	NA	intron (NM_001033341, intron 8 of 8)	intron (NM_001033341, intron 8 of 8)	213139	NM_146090	225791	Mm.147052	NM_146090	ENSMUSG00000049090	Zadh2	C530046K17Rik|PTGR-3|Pthr3	zinc binding alcohol dehydrogenase, domain containing 2	protein-coding
mm_7394.1	chr1	112957554	112957554	-	1	NA	Intergenic	Intergenic	-1092636	NM_001081316	319901	Mm.103468	NM_001081316	ENSMUSG00000038702	Dsel	9330132E09Rik|DS-epi2	dermatan sulfate epimerase-like	protein-coding
mm_27887.1	chr3	79181357	79181372	-	1	NA	Intergenic	Intergenic	-31555	NR_045502	70924	Mm.444622	NR_045502	ENSMUSG00000104585	4921511C10Rik	-	RIKEN cDNA 4921511C10 gene	ncRNA
mm_118411.1	chr14	7791416	7791422	+	1	NA	Intergenic	Intergenic	-26538	NM_001081427	286940	Mm.489652	NM_134080	ENSMUSG00000025278	Flnb	AL024016|Fln-b	filamin, beta	protein-coding
mm_129652.1	chr15	80798453	80798465	-	1	NA	promoter-TSS (NM_177124)	promoter-TSS (NM_177124)	-151	NM_177124	213988	Mm.131328	NM_144812	ENSMUSG00000047888	Tnrc6b	2700090M07Rik|A730065C02Rik|AI848765|D230019K20Rik	trinucleotide repeat containing 6b	protein-coding
mm_129220.1	chr15	76576749	76576752	-	1	NA	intron (NR_073123, intron 1 of 14)	intron (NR_073123, intron 1 of 14)	391	NR_073123	268822	Mm.181624	NM_172960	ENSMUSG00000022550	Adck5	A230108P17	aarF domain containing kinase 5	protein-coding
mm_131832.1	chr16	22959162	22959172	+	1	NA	exon (NM_053176, exon 6 of 7)	exon (NM_053176, exon 6 of 7)	8095	NM_053176	94175	Mm.358794	NM_053176	ENSMUSG00000022877	Hrg	AI265597|AW413091|D16jh2|D18020|Hprg|Hrgp	histidine-rich glycoprotein	protein-coding
mm_172788.1	chr9	106476583	106476583	-	1	NA	promoter-TSS (NM_145620)	promoter-TSS (NM_145620)	366	NM_001311150	235587	Mm.273659	NM_145619	ENSMUSG00000023249	Parp3	A930002C11Rik|AW990611|Adprt3|Adprtl3|PARP-3|pADPRT-3	poly (ADP-ribose) polymerase family, member 3	protein-coding
mm_161266.1	chr14	6875222	6875222	-	1	NA	Intergenic	Intergenic	-118165	NM_001309401	100041151	Mm.396155	NM_001309401	ENSMUSG00000091754	Gm3636	100042043	predicted gene 3636	protein-coding
mm_73098.1	chr8	94568338	94568358	+	1	NA	intron (NM_153507, intron 14 of 15)	intron (NM_153507, intron 14 of 15)	33378	NM_028221	102122	Mm.250425	NM_028221	ENSMUSG00000031774	Fam192a	1700001O11Rik|2310065K24Rik|AI596259|Nip30	family with sequence similarity 192, member A	protein-coding
mm_152061.1	chr19	6531980	6531994	-	1	NA	exon (NM_020253, exon 23 of 23)	exon (NM_020253, exon 23 of 23)	11083	NM_009203	20521	Mm.391146	NM_009203	ENSMUSG00000061742	Slc22a12	AI987855|OAT4L|Rst|Slc22al2|URAT1	solute carrier family 22 (organic anion/cation transporter), member 12	protein-coding
mm_126749.1	chr15	85736342	85736352	+	1	NA	intron (NM_011144, intron 1 of 7)	intron (NM_011144, intron 1 of 7)	571	NM_011144	19013	Mm.212789	NM_011144	ENSMUSG00000022383	Ppara	4933429D07Rik|AW742785|Nr1c1|PPAR-alpha|PPARalpha|Ppar	peroxisome proliferator activated receptor alpha	protein-coding
mm_115565.1	chr13	9764944	9764994	-	1	NA	promoter-TSS (NM_001347480)	promoter-TSS (NM_001347480)	-13	NM_001347473	66505	Mm.397307	NM_144516	ENSMUSG00000021156	Zmynd11	2210402G22Rik|BS69	zinc finger, MYND domain containing 11	protein-coding
mm_22507.1	chr3	7503424	7503503	+	1	NA	promoter-TSS (NM_173181)	promoter-TSS (NM_173181)	37	NM_173181	67306	Mm.332366	NM_173181	ENSMUSG00000043542	Zc2hc1a	3110050N22Rik|AI790358|AU023959|Fam164a	zinc finger, C2HC-type containing 1A	protein-coding
mm_113687.1	chr13	42866436	42866450	+	1	NA	5' UTR (NM_001302636, exon 1 of 13)	5' UTR (NM_001302636, exon 1 of 13)	196	NM_001302636	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding
mm_47852.1	chr5	134552140	134552233	-	1	NA	5' UTR (NM_001039162, exon 1 of 16)	5' UTR (NM_001039162, exon 1 of 16)	248	NM_001039162	269713	Mm.255138	NM_009990	ENSMUSG00000063146	Clip2	B230327O20|CLIP-115|Clip1|Cyln2|WSCR4|mKIAA0291|wbscr4	CAP-GLY domain containing linker protein 2	protein-coding
mm_19569.1	chr2	101629027	101629034	-	1	NA	promoter-TSS (NM_026592)	promoter-TSS (NM_026592)	-44	NM_026592	68170	Mm.31263	NM_026592	ENSMUSG00000027165	B230118H07Rik	NWC	RIKEN cDNA B230118H07 gene	protein-coding
mm_119030.1	chr14	30131550	30131557	+	1	NA	intron (NM_001302637, intron 9 of 48)	intron (NM_001302637, intron 9 of 48)	108920	NM_175343	218865	Mm.259916	NM_172264	ENSMUSG00000015970	Chdh	AU041472|D630034H06Rik	choline dehydrogenase	protein-coding
mm_118270.1	chr13	112595186	112595186	-	1	NA	Intergenic	Intergenic	-14524	NM_139299	218624	Mm.380801	NM_139299	ENSMUSG00000050377	Il31ra	CRL3|GLM-R|GPL|Glmr|NR10	interleukin 31 receptor A	protein-coding
mm_19084.1	chr2	78973025	78973035	-	1	NA	Intergenic	Intergenic	103983	NM_009454	22193	Mm.1485	NM_009454	ENSMUSG00000027011	Ube2e3	Ubce4|ubcM2	ubiquitin-conjugating enzyme E2E 3	protein-coding
mm_153282.1	chr19	37210704	37210733	-	1	NA	exon (NM_027314, exon 2 of 6)	exon (NM_027314, exon 2 of 6)	3173	NM_001164336	69104	Mm.175989	NM_027314	ENSMUSG00000023307	March5	1810015H18Rik|2310008I22Rik|2700055A20Rik|5730499H23Rik|E130202O05Rik|MARCH-V|MITOL|Marchv|Rnf153	membrane-associated ring finger (C3HC4) 5	protein-coding
mm_173362.1	chrY	90819632	90819635	+	1	NA	Intergenic	IMPB_01|Satellite|Satellite	19773	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_48854.1	chr5	149636234	149636253	-	1	NA	promoter-TSS (NM_013559)	promoter-TSS (NM_013559)	72	NM_013559	15505	Mm.270681	NM_013559	ENSMUSG00000029657	Hsph1	105kDa|AI790491|Hsp105|Hsp110|hsp-E7I|hsp110/105	heat shock 105kDa/110kDa protein 1	protein-coding
mm_77547.1	chr8	123236167	123236195	-	1	NA	promoter-TSS (NM_030176)	promoter-TSS (NM_030176)	28	NM_030176	78779	Mm.41459	NM_030176	ENSMUSG00000033594	Spata2l	2610039E05Rik|AI648233|mKIAA4138	spermatogenesis associated 2-like	protein-coding
mm_152442.1	chr19	10760066	10760080	-	1	NA	intron (NR_027805, intron 1 of 3)	intron (NR_027805, intron 1 of 3)	19126	NR_027805	403202	Mm.34482	NM_207529	ENSMUSG00000067577	A430093F15Rik	Gm674	RIKEN cDNA A430093F15 gene	ncRNA
mm_152786.1	chr19	21457501	21457501	-	1	NA	intron (NM_010266, intron 1 of 13)	intron (NM_010266, intron 1 of 13)	15160	NM_010266	14544	Mm.45054	NM_010266	ENSMUSG00000058624	Gda	AU015411|AW047581|GAH	guanine deaminase	protein-coding
mm_22994.1	chr3	34019933	34019939	+	1	NA	promoter-TSS (NM_001113188)	promoter-TSS (NM_001113188)	-143	NM_001113189	14359	Mm.259021	NM_008053	ENSMUSG00000027680	Fxr1	1110050J02Rik|9530073J07Rik|AI851072|Fxr1h|Fxr1p	fragile X mental retardation gene 1, autosomal homolog	protein-coding
mm_78958.1	chr9	45152937	45152939	+	1	NA	3' UTR (NM_001013390, exon 5 of 5)	3' UTR (NM_001013390, exon 5 of 5)	13896	NM_001013390	399548	Mm.335112	NM_001013390	ENSMUSG00000046480	Scn4b	Gm1471	sodium channel, type IV, beta	protein-coding
mm_94089.1	chr10	128517281	128517316	-	1	NA	exon (NM_011843, exon 17 of 31)	exon (NM_011843, exon 17 of 31)	-5268	NR_105881	102465552		NR_105881	ENSMUSG00000099292	Mir6916	Gm27721|mmu-mir-6916	microRNA 6916	ncRNA
mm_75253.1	chr8	40511259	40511274	-	1	NA	promoter-TSS (NM_033560)	promoter-TSS (NM_033560)	488	NM_001271543	18983	Mm.272551	NM_011135	ENSMUSG00000031601	Cnot7	AU022737|CAF-1|Caf1|Pop2	CCR4-NOT transcription complex, subunit 7	protein-coding
mm_133759.1	chr16	94459954	94459966	+	1	NA	exon (NM_009441, exon 42 of 46)	exon (NM_009441, exon 42 of 46)	66669	NM_007834	13185	Mm.7472	NM_007834	ENSMUSG00000022898	Dscr3	AW538125|Dcra	Down syndrome critical region gene 3	protein-coding
mm_112965.1	chr13	21183764	21183784	+	1	NA	exon (NM_009054, exon 3 of 8)	exon (NM_009054, exon 3 of 8)	3843	NM_009054	19720	Mm.314056	NM_009054	ENSMUSG00000021326	Trim27	AW538890|Gm19403|Rfp	tripartite motif-containing 27	protein-coding
mm_70905.1	chr8	25640902	25640948	+	1	NA	exon (NM_001081269, exon 1 of 23)	exon (NM_001081269, exon 1 of 23)	348	NM_001081269	234135	Mm.217337	NM_001001735	ENSMUSG00000054823	Whsc1l1	6720429E03|A530023P05|AI528490|NSD3|WHISTLE	Wolf-Hirschhorn syndrome candidate 1-like 1 (human)	protein-coding
mm_54185.1	chr6	24092360	24092361	-	1	NA	exon (NM_019481, exon 13 of 15)	exon (NM_019481, exon 13 of 15)	75732	NM_019481	55961	Mm.19299	NM_019481	ENSMUSG00000029700	Slc13a1	AI314066|AI987826|NaSi-1|Nas1	solute carrier family 13 (sodium/sulfate symporters), member 1	protein-coding
mm_36617.1	chr4	89294609	89294611	-	1	NA	promoter-TSS (NR_132431)	promoter-TSS (NR_132431)	9	NM_009877	12578	Mm.4733	NM_009877	ENSMUSG00000044303	Cdkn2a	ARF-INK4a|Arf|INK4a-ARF|Ink4a/Arf|MTS1|Pctr1|p16|p16(INK4a)|p16INK4a|p19<ARF>|p19ARF	cyclin-dependent kinase inhibitor 2A	protein-coding
mm_82351.1	chr9	13827030	13827129	-	1	NA	promoter-TSS (NM_001310721)	promoter-TSS (NM_001310721)	-26	NR_037622	74360	Mm.157212	NM_026665	ENSMUSG00000031922	Cep57	3110002L15Rik|4921510P06Rik|4931428M20Rik|AI467480|Tsp57|mKIAA0092	centrosomal protein 57	protein-coding
mm_56982.1	chr6	120364318	120364328	-	1	NA	promoter-TSS (NR_045558)	promoter-TSS (NR_045558)	46	NR_045558	67200	Mm.45767	NM_026028	ENSMUSG00000030177	Ccdc77	2400002C23Rik|2700091N06Rik|AV168274	coiled-coil domain containing 77	protein-coding
mm_48034.1	chr5	136268797	136268801	-	1	NA	3' UTR (NM_009986, exon 24 of 24)	3' UTR (NM_009986, exon 24 of 24)	-23859	NM_018825	23921	Mm.425294	NM_018825	ENSMUSG00000005057	Sh2b2	Aps	SH2B adaptor protein 2	protein-coding
mm_108274.1	chr12	78862026	78862071	+	1	NA	promoter-TSS (NM_026114)	promoter-TSS (NM_026114)	-24	NM_026114	13665	Mm.196220	NM_026114	ENSMUSG00000021116	Eif2s1	0910001O23Rik|2410026C18Rik|35kDa|Eif2a|eIF2alpha	eukaryotic translation initiation factor 2, subunit 1 alpha	protein-coding
mm_54428.1	chr6	33992373	33992376	-	1	NA	Intergenic	Intergenic	-37074	NM_028886	74354	Mm.127952	NM_028886	ENSMUSG00000056215	Lrguk	4921528H16Rik	leucine-rich repeats and guanylate kinase domain containing	protein-coding
mm_23360.1	chr3	55242531	55242555	+	1	NA	promoter-TSS (NM_001195538)	promoter-TSS (NM_001195538)	17	NM_001195538	13175	Mm.393242	NM_019978	ENSMUSG00000027797	Dclk1	1700113D08Rik|2810480F11Rik|AI836758|Click-I|Cpg16|Dcamkl1|Dcl|Dclk|mKIAA0369	doublecortin-like kinase 1	protein-coding
mm_123941.1	chr14	73375963	73375995	-	1	NA	intron (NM_008410, intron 1 of 5)	intron (NM_008410, intron 1 of 5)	9292	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_37833.1	chr4	132048961	132048972	-	1	NA	5' UTR (NM_001128606, exon 1 of 18)	5' UTR (NM_001128606, exon 1 of 18)	112	NM_001128606	269587	Mm.30038	NM_183428	ENSMUSG00000028906	Epb41	4.1R|AI415518|D4Ertd442e|Elp-1|Elp1|Epb4.1|mKIAA4056	erythrocyte membrane protein band 4.1	protein-coding
mm_13933.1	chr2	121015937	121015940	+	1	NA	intron (NM_010761, intron 9 of 10)	intron (NM_010761, intron 9 of 10)	7530	NM_010761	17151	Mm.7838	NM_010761	ENSMUSG00000023572	Ccndbp1	AU022347|DIP1|GCIP|Maid|SECC-8|SSEC-8	cyclin D-type binding-protein 1	protein-coding
mm_45968.1	chr5	90468589	90468617	-	1	NA	exon (NM_009654, exon 8 of 15)	exon (NM_009654, exon 8 of 15)	7733	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_168882.1	chr12	43175472	43175474	+	1	NA	Intergenic	L1Md_T|LINE|L1	1034595	NM_013760	27362	Mm.27432	NM_013760	ENSMUSG00000014905	Dnajb9	AA408011|AA673251|AA673481|AW556981|ERdj4|Mdg1|mDj7	DnaJ heat shock protein family (Hsp40) member B9	protein-coding
mm_120552.1	chr14	67793390	67793399	+	1	NA	intron (NM_177780, intron 29 of 51)	intron (NM_177780, intron 29 of 51)	48213	NR_133010	14714	Mm.358309	NM_008145	ENSMUSG00000015812	Gnrh1	Gnrh|Gnrh2|LHRH|Lhrh1|Lnrh|hpg	gonadotropin releasing hormone 1	protein-coding
mm_35007.1	chr4	3089795	3089820	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	-82276	NM_001167534	100312470	Mm.480297	NM_001167534	ENSMUSG00000094798	Vmn1r2	Gm11776|OTTMUSG00000004179	vomeronasal 1 receptor 2	protein-coding
mm_129740.1	chr15	82212829	82212848	-	1	NA	promoter-TSS (NM_001207021)	promoter-TSS (NM_001207021)	-23	NM_001207021	435145	Mm.41289	NM_001207021	ENSMUSG00000096883	Shisa8	Orf26|ckamp39	shisa family member 8	protein-coding
mm_62416.1	chr7	101317074	101317132	+	1	NA	Intergenic	Intergenic	-4216	NM_019990	56018	Mm.28896	NM_019990	ENSMUSG00000030688	Stard10	AV048538|CGI-52|NY-C0-28|PC-TP2|PCTP2|Pctpl|Sdccag28|SdccagG28|TISP-81	START domain containing 10	protein-coding
mm_60918.1	chr7	46832436	46832463	+	1	NA	Intergenic	Intergenic	-13355	NM_010699	16828	Mm.29324	NM_010699	ENSMUSG00000063229	Ldha	Ldh1|Ldhm|l7R2	lactate dehydrogenase A	protein-coding
mm_168557.1	chr1	166141947	166141960	+	1	NA	intron (NM_021610, intron 1 of 6)	B1_Mus2|SINE|Alu	11493	NM_021610	59290	Mm.46357	NM_021610	ENSMUSG00000000544	Gpa33	2010310L10Rik|2210401D16Rik|BB116197	glycoprotein A33 (transmembrane)	protein-coding
mm_90490.1	chr10	128015235	128015249	+	1	NA	promoter-TSS (NM_008921)	promoter-TSS (NM_008921)	27	NM_008921	19075	Mm.2903	NM_008921	ENSMUSG00000025395	Prim1	AI324982	DNA primase, p49 subunit	protein-coding
mm_50949.1	chr6	58643997	58644007	+	1	NA	intron (NM_011920, intron 1 of 15)	intron (NM_011920, intron 1 of 15)	47330	NM_011920	26357	Mm.333096	NM_011920	ENSMUSG00000029802	Abcg2	ABC15|ABCP|AI428558|BCRP|Bcrp1|MXR|MXR1	ATP-binding cassette, sub-family G (WHITE), member 2	protein-coding
mm_4748.1	chr1	182163338	182163342	+	1	NA	Intergenic	Intergenic	-5242	NM_001166728	625823	Mm.479992	NM_001166728	ENSMUSG00000091013	Vmn1r1	EG625823|Gm6628	vomeronasal 1 receptor 1	protein-coding
mm_101455.1	chr11	30248503	30248509	-	1	NA	Intergenic	Intergenic	-28734	NM_175836	20742	Mm.123110	NM_009260	ENSMUSG00000020315	Sptbn1	9930031C03Rik|AL033301|SPTB2|Spnb-2|Spnb2|elf1|elf3|mKIAA4049	spectrin beta, non-erythrocytic 1	protein-coding
mm_109034.1	chr12	104101088	104101098	+	1	NA	promoter-TSS (NM_172953)	promoter-TSS (NM_172953)	-20	NM_172953	268591	Mm.73172	NM_172953	ENSMUSG00000041550	Serpina5	4933415L04|PAI-3|Pci	serine (or cysteine) peptidase inhibitor, clade A, member 5	protein-coding
mm_110359.1	chr12	40037656	40037667	-	1	NA	promoter-TSS (NM_007487)	promoter-TSS (NM_007487)	-285	NM_007487	11861	Mm.12723	NM_007487	ENSMUSG00000047446	Arl4a	AI467555|Arl4	ADP-ribosylation factor-like 4A	protein-coding
mm_74619.1	chr8	13027702	13027735	-	1	NA	intron (NM_010172, intron 1 of 7)	intron (NM_010172, intron 1 of 7)	1684	NM_010172	14068	Mm.4827	NM_010172	ENSMUSG00000031443	F7	AI132620|Cf7|FVII	coagulation factor VII	protein-coding
mm_118418.1	chr14	7817975	7817994	+	1	NA	promoter-TSS (NM_001081427)	promoter-TSS (NM_001081427)	27	NM_134080	286940	Mm.489652	NM_134080	ENSMUSG00000025278	Flnb	AL024016|Fln-b	filamin, beta	protein-coding
mm_101467.1	chr11	30576919	30576922	-	1	NA	intron (NM_029344, intron 3 of 3)	intron (NM_029344, intron 3 of 3)	72476	NM_029344	75572	Mm.390319	NM_029344	ENSMUSG00000060923	Acyp2	2310004B09Rik	acylphosphatase 2, muscle type	protein-coding
mm_24547.1	chr3	93393697	93393699	+	1	NA	promoter-TSS (NM_009100)	promoter-TSS (NM_009100)	-1	NM_009100	20129	Mm.1417	NM_009100	ENSMUSG00000041984	Rptn	-	repetin	protein-coding
mm_123983.1	chr14	75593011	75593019	-	1	NA	exon (NM_001164139, exon 1 of 3)	exon (NM_001164139, exon 1 of 3)	101	NM_001164140	67926	Mm.23361	NM_026457	ENSMUSG00000034913	Spert	1700086N05Rik|AI596460|Nurit	spermatid associated	protein-coding
mm_162321.1	chr1	39467917	39467935	-	1	NA	intron (NM_018775, intron 1 of 19)	MER21C|LTR|ERVL	10821	NM_018775	54610	Mm.387293	NM_018775	ENSMUSG00000003134	Tbc1d8	AD3|HBLP1|VRP	TBC1 domain family, member 8	protein-coding
mm_146490.1	chr18	90534900	90534911	+	1	NA	intron (NM_198295, intron 13 of 15)	RSINE1|SINE|B4	24751	NM_198295	67988	Mm.268041	NM_198295	ENSMUSG00000024614	Tmx3	6430411B10Rik|A730024F05Rik|AV259382|Txndc10|mKIAA1830	thioredoxin-related transmembrane protein 3	protein-coding
mm_114929.1	chr13	95707468	95707489	+	1	NA	intron (NM_027711, intron 13 of 35)	intron (NM_027711, intron 13 of 35)	10558	NM_010170	14064	Mm.440952	NM_010170	ENSMUSG00000021675	F2rl2	F730031A08|PAR3	coagulation factor II (thrombin) receptor-like 2	protein-coding
mm_46824.1	chr5	113188662	113188704	-	1	NA	Intergenic	MIRc|SINE|MIR	-25370	NM_172884	243219	Mm.160131	NM_172884	ENSMUSG00000051339	2900026A02Rik	8430408O14Rik|A530094D01|AW539426|Gm449|Kiaa1671|mKIAA1671	RIKEN cDNA 2900026A02 gene	protein-coding
mm_135812.1	chr16	57421055	57421059	-	1	NA	intron (NM_001040397, intron 1 of 4)	intron (NM_001040397, intron 1 of 4)	67780	NM_001040397	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding
mm_134240.1	chr16	12762026	12762030	-	1	NA	Intergenic	Intergenic	-49362	NR_040507	75493	Mm.396146	NR_040507	ENSMUSG00000101565	1700003L19Rik	-	RIKEN cDNA 1700003L19 gene	ncRNA
mm_100941.1	chr11	6528421	6528433	-	1	NA	intron (NR_045893, intron 1 of 3)	intron (NR_045893, intron 1 of 3)	333	NR_045893	100041286	Mm.459507	NR_045893	ENSMUSG00000085156	Snhg15	Gm11974|OTTMUSG00000005115	small nucleolar RNA host gene 15	ncRNA
mm_7483.1	chr1	120993655	120993685	-	1	NA	Intergenic	Intergenic	-93735	NR_038008	98452	Mm.131017	NR_038008	ENSMUSG00000097881	Celrr	AI848258|B230209K01Rik|Celr|Gm818	cerebellum expressed regulatory RNA	ncRNA
mm_149516.1	chr19	12436324	12436331	+	1	NA	Intergenic	Lx8|LINE|L1	8422	NM_019540	56093	Mm.285849	NM_019540	ENSMUSG00000040065	Pfpl	Epcs5|Epcs50	pore forming protein-like	protein-coding
mm_161956.1	chr19	6934553	6934553	-	1	NA	promoter-TSS (NM_008431)	promoter-TSS (NM_008431)	-38	NM_008431	16528	Mm.12894	NM_008431	ENSMUSG00000024957	Kcnk4	MLZ-622|TRAAK|TRAAKt|Tex40	potassium channel, subfamily K, member 4	protein-coding
mm_71276.1	chr8	40919644	40919654	+	1	NA	3' UTR (NM_001044740, exon 12 of 12)	3' UTR (NM_001044740, exon 12 of 12)	-6584	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_85508.1	chr9	106247428	106247459	-	1	NA	5' UTR (NM_001291835, exon 1 of 11)	5' UTR (NM_001291835, exon 1 of 11)	287	NM_001291835	11655	Mm.290578	NM_020559	ENSMUSG00000032786	Alas1	ALAS|ALAS-N|Alas-1|Alas-h	aminolevulinic acid synthase 1	protein-coding
mm_69147.1	chr7	127100594	127100615	-	1	NA	Intergenic	Intergenic	9168	NM_178901	101602	Mm.490357	NM_178901	ENSMUSG00000045165	AI467606	-	expressed sequence AI467606	protein-coding
mm_18358.1	chr2	58357779	58357817	-	1	NA	promoter-TSS (NM_001111030)	promoter-TSS (NM_001111030)	-40	NM_001111030	269275	Mm.77751	NM_001033369	ENSMUSG00000026834	Acvr1c	ACTR-IC|ACVRLK7|ALK7|Alk-7|C230097P10	activin A receptor, type IC	protein-coding
mm_164780.1	chr18	5273313	5273318	-	1	NA	intron (NM_178722, intron 2 of 4)	intron (NM_178722, intron 2 of 4)	61124	NM_178722	240186	Mm.118257	NM_178722	ENSMUSG00000050945	Zfp438	9430031G09|9430091M14Rik|B830013J05Rik	zinc finger protein 438	protein-coding
mm_124313.1	chr14	103218971	103218990	-	1	NA	intron (NM_207215, intron 33 of 84)	RSINE1|SINE|B4	-119414	NM_001347600	50789	Mm.214746	NM_015822	ENSMUSG00000022124	Fbxl3	AU041772|AW212966|FBK|Fbl3a|Fbxl3a|Ovtm|Play68	F-box and leucine-rich repeat protein 3	protein-coding
mm_171458.1	chr4	145514958	145514962	+	1	NA	intron (NM_001324553, intron 1 of 3)	intron (NM_001324553, intron 1 of 3)	4201	NM_001324553	101056073	Mm.276881	NM_001324553	ENSMUSG00000078503	LOC101056073	-	zinc finger protein 501-like	protein-coding
mm_113907.1	chr13	49341453	49341463	+	1	NA	promoter-TSS (NM_029791)	promoter-TSS (NM_029791)	-91	NM_001039179	76895	Mm.197387	NM_029791	ENSMUSG00000037933	Bicd2	-	bicaudal D homolog 2 (Drosophila)	protein-coding
mm_135616.1	chr16	52271331	52271363	-	1	NA	intron (NM_009655, intron 11 of 15)	intron (NM_009655, intron 11 of 15)	181734	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_148758.1	chr19	6061238	6061252	+	1	NA	promoter-TSS (NM_013859)	promoter-TSS (NM_013859)	38	NM_013859	29805	Mm.2310	NM_013859	ENSMUSG00000075227	Znhit2	C11orf5|Fon|ORF6|Znhit2-ps	zinc finger, HIT domain containing 2	protein-coding
mm_84929.1	chr9	81633844	81633849	-	1	NA	intron (NR_040396, intron 1 of 4)	intron (NR_040396, intron 1 of 4)	-1294	NM_010482	15551	Mm.445308	NM_010482	ENSMUSG00000049511	Htr1b	-	5-hydroxytryptamine (serotonin) receptor 1B	protein-coding
mm_86774.1	chr10	20148458	20148478	+	1	NA	promoter-TSS (NM_008635)	promoter-TSS (NM_008635)	-452	NM_008635	17761	Mm.20928	NM_008635	ENSMUSG00000019996	Map7	E-MAP-115|MAP-7|Mtap7|R75000|mshi|mste|ste	microtubule-associated protein 7	protein-coding
mm_160767.1	chr10	97607421	97607421	+	1	NA	intron (NM_008438, intron 1 of 2)	intron (NM_008438, intron 1 of 2)	216	NM_008438	16545	Mm.6228	NM_008438	ENSMUSG00000019932	Kera	CNA2|SLRR2B	keratocan	protein-coding
mm_115104.1	chr13	103332582	103332589	+	1	NA	intron (NM_175171, intron 1 of 28)	intron (NM_175171, intron 1 of 28)	1907	NM_175171	328329	Mm.202606	NM_175171	ENSMUSG00000034751	Mast4	4930420O11Rik|AI642422|mKIAA0303	microtubule associated serine/threonine kinase family member 4	protein-coding
mm_165990.1	chr4	109156659	109156669	-	1	NA	exon (NM_133885, exon 3 of 23)	exon (NM_133885, exon 3 of 23)	-38628	NM_001134791	100273	Mm.366315	NM_133885	ENSMUSG00000028559	Osbpl9	2600011I06Rik|AU015843|Orp-9	oxysterol binding protein-like 9	protein-coding
mm_81214.1	chr9	107587643	107587656	+	1	NA	promoter-TSS (NM_025903)	promoter-TSS (NM_025903)	-69	NM_025903	15983	Mm.215335	NM_025903	ENSMUSG00000010048	Ifrd2	1810034A24Rik|AA470234|AI838527|SKMc15	interferon-related developmental regulator 2	protein-coding
mm_55723.1	chr6	73471065	73471075	-	1	NA	promoter-TSS (NR_108032)	promoter-TSS (NR_108032)	-49	NR_108032	73408	Mm.233629	NR_108032	ENSMUSG00000107408	1700065L07Rik	-	RIKEN cDNA 1700065L07 gene	ncRNA
mm_146096.1	chr18	73863693	73863713	+	1	NA	intron (NM_001305882, intron 2 of 8)	intron (NM_001305882, intron 2 of 8)	4318	NM_001305882	71263	Mm.126220	NM_027741	ENSMUSG00000064036	Mro	4930507C04Rik|4933435E20Rik	maestro	protein-coding
mm_47195.1	chr5	120773992	120774003	-	1	NA	exon (NM_145226, exon 2 of 16)	exon (NM_145226, exon 2 of 16)	3662	NM_145226	246727	Mm.204887	NM_145226	ENSMUSG00000032661	Oas3	Oasl10	2'-5' oligoadenylate synthetase 3	protein-coding
mm_58778.1	chr7	16061841	16061867	+	1	NA	Intergenic	GC_rich|Low_complexity|Low_complexity	-9991	NM_001347559	666528	Mm.290718	NM_001099277	ENSMUSG00000078796	Zfp541	EG666528|Znf541	zinc finger protein 541	protein-coding
mm_128597.1	chr15	58135112	58135122	-	1	NA	promoter-TSS (NM_027435)	promoter-TSS (NM_027435)	-35	NM_027435	70472	Mm.221758	NM_027435	ENSMUSG00000022360	Atad2	2610509G12Rik	ATPase family, AAA domain containing 2	protein-coding
mm_59185.1	chr7	24472580	24472621	+	1	NA	exon (NM_011113, exon 5 of 7)	exon (NM_011113, exon 5 of 7)	-9423	NM_153112	260299	Mm.178322	NM_153112	ENSMUSG00000054793	Cadm4	Igdf4c|Igsf4c|Tsll2	cell adhesion molecule 4	protein-coding
mm_170572.1	chr1	95238548	95238550	-	1	NA	Intergenic	L1Md_A|LINE|L1	-75079	NM_026321	67698	Mm.272705	NM_026321	ENSMUSG00000051185	Fam174a	2310044D20Rik|Fam174|Naa6|Tmem157	family with sequence similarity 174, member A	protein-coding
mm_2954.1	chr1	132477362	132477412	+	1	NA	promoter-TSS (NM_172517)	promoter-TSS (NM_172517)	20	NM_172517	213464	Mm.132868	NM_172517	ENSMUSG00000026439	Rbbp5	4933411J24Rik|C330016J05	retinoblastoma binding protein 5	protein-coding
mm_58915.1	chr7	17672347	17672349	+	1	NA	promoter-TSS (NR_002857)	promoter-TSS (NR_002857)	35	NR_002857	232919	Mm.153893	NR_002857	ENSMUSG00000108558	Psg-ps1	AV036018|Cea-6|Cea6	pregnancy specific glycoprotein pseudogene 1	pseudo
mm_169144.1	chr13	62161689	62161690	-	1	NA	intron (NM_001039239, intron 1 of 3)	L1Md_F2|LINE|L1	31799	NM_001039239	630579	Mm.440905	NM_001039239	ENSMUSG00000074867	Zfp808	EG630579|Gm7036	zinc finger protein 80	protein-coding
mm_120430.1	chr14	65805833	65805846	+	1	NA	promoter-TSS (NM_023209)	promoter-TSS (NM_023209)	-72	NM_023209	52033	Mm.24337	NM_023209	ENSMUSG00000022033	Pbk	2810434B10Rik|AW538537|D14Ertd732e|TOPK	PDZ binding kinase	protein-coding
mm_99741.1	chr11	106416797	106416805	+	1	NA	intron (NM_023913, intron 10 of 21)	intron (NM_023913, intron 10 of 21)	-34020	NM_010494	15896	Mm.394	NM_010494	ENSMUSG00000001029	Icam2	CD102|Icam-2|Ly-60	intercellular adhesion molecule 2	protein-coding
mm_172586.1	chr8	123446145	123446152	+	1	NA	5' UTR (NM_001253784, exon 2 of 13)	5' UTR (NM_001253784, exon 2 of 13)	2889	NM_001281803	23854	Mm.275127	NM_054046	ENSMUSG00000001482	Def8	AI449518|D8Ertd713e|DEF-8	differentially expressed in FDCP 8	protein-coding
mm_165243.1	chr2	67173950	67173997	+	1	NA	5' UTR (NM_001033477, exon 1 of 2)	5' UTR (NM_001033477, exon 1 of 2)	139	NM_001033477	383709	Mm.244520	NM_001033477		Gm1322	-	predicted gene 1322	protein-coding
mm_102071.1	chr11	52261543	52261565	-	1	NA	exon (NM_009331, exon 3 of 10)	exon (NM_009331, exon 3 of 10)	21041	NM_009331	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_81794.1	chr9	115167244	115167245	+	1	NA	exon (NM_148958, exon 3 of 10)	exon (NM_148958, exon 3 of 10)	99965	NM_148958	74486	Mm.458474	NM_148958	ENSMUSG00000040875	Osbpl10	4933433D06Rik|C820004B04Rik|OPR-10|ORP-10	oxysterol binding protein-like 10	protein-coding
mm_74296.1	chr8	125995408	125995473	+	1	NA	5' UTR (NM_008430, exon 1 of 3)	5' UTR (NM_008430, exon 1 of 3)	338	NM_008430	16525	Mm.10800	NM_008430	ENSMUSG00000033998	Kcnk1	AI788889|TWIK-1	potassium channel, subfamily K, member 1	protein-coding
mm_146699.1	chr18	12955751	12955778	-	1	NA	Intergenic	Intergenic	-13923	NM_207530	64291	Mm.259470	NM_020573	ENSMUSG00000044252	Osbpl1a	G430090F17Rik|Gm753|ORP-1|Osbpl1b	oxysterol binding protein-like 1A	protein-coding
mm_129430.1	chr15	78493727	78493747	-	1	NA	intron (NM_008368, intron 1 of 9)	intron (NM_008368, intron 1 of 9)	1329	NM_008368	16185	Mm.35287	NM_008368	ENSMUSG00000068227	Il2rb	CD122|IL-15Rbeta|IL15Rbeta|Il-2/15Rbeta|Il-2Rbeta|p70	interleukin 2 receptor, beta chain	protein-coding
mm_93335.1	chr10	99467663	99467674	-	1	NA	Intergenic	Intergenic	-141503	NR_038019	100504202	Mm.403801	NR_038019		Gm20110	-	predicted gene, 20110	ncRNA
mm_98702.1	chr11	96303898	96303916	+	1	NA	exon (NM_008268, exon 1 of 2)	exon (NM_008268, exon 1 of 2)	395	NM_008268	15413	Mm.207	NM_008268	ENSMUSG00000038700	Hoxb5	AI385717|Hox-2.1	homeobox B5	protein-coding
mm_51381.1	chr6	74050233	74050234	+	1	NA	Intergenic	Intergenic	-579212	NR_108032	73408	Mm.233629	NR_108032	ENSMUSG00000107408	1700065L07Rik	-	RIKEN cDNA 1700065L07 gene	ncRNA
mm_84236.1	chr9	62122678	62122688	-	1	NA	promoter-TSS (NR_039595)	promoter-TSS (NR_039595)	-89	NR_039595	100628602		NR_039595	ENSMUSG00000092696	Mir5133	mir-5133|mmu-mir-5133|mu-mir-5133	microRNA 5133	ncRNA
mm_7862.1	chr1	132542935	132542954	-	1	NA	promoter-TSS (NM_177129)	promoter-TSS (NM_177129)	-4	NM_177129	21367	Mm.260861	NM_011531	ENSMUSG00000053024	Cntn2	D130012K04Rik|TAG-1|Tax	contactin 2	protein-coding
mm_124425.1	chr14	118223898	118223947	-	1	NA	Intergenic	Intergenic	-12310	NR_131969	105245869	Mm.460408	NR_131969	ENSMUSG00000090534	LOC105245869	-	uncharacterized LOC105245869	ncRNA
mm_118782.1	chr14	24082133	24082152	+	1	NA	Intergenic	Intergenic	-6735	NR_106069	102465697		NR_106069	ENSMUSG00000105723	Mir7210	mir-7210|mmu-mir-7210	microRNA 7210	ncRNA
mm_95633.1	chr11	53632068	53632085	+	1	NA	exon (NM_008355, exon 4 of 4)	exon (NM_008355, exon 4 of 4)	2626	NM_008355	16163	Mm.1284	NM_008355	ENSMUSG00000020383	Il13	Il-13	interleukin 13	protein-coding
mm_40236.1	chr5	37392015	37392019	+	1	NA	exon (NM_145920, exon 13 of 20)	exon (NM_145920, exon 13 of 20)	53539	NM_145920	68525	Mm.25506	NM_145920	ENSMUSG00000050248	Evc2	1110017L09Rik|Lbn|limbin	Ellis van Creveld syndrome 2	protein-coding
mm_26519.1	chr3	145924304	145924378	+	1	NA	promoter-TSS (NM_009740)	promoter-TSS (NM_009740)	79	NM_009740	12042	Mm.239141	NM_009740	ENSMUSG00000028191	Bcl10	AI132454|BCL-10|C81403|CARMEN|CIPER|CLAP|ME10|cE10	B cell leukemia/lymphoma 10	protein-coding
mm_63031.1	chr7	121074634	121074648	+	1	NA	promoter-TSS (NM_030691)	promoter-TSS (NM_030691)	-111	NM_030691	80719	Mm.160384	NM_030691	ENSMUSG00000035004	Igsf6	-	immunoglobulin superfamily, member 6	protein-coding
mm_137727.1	chr17	29274079	29274129	+	1	NA	intron (NM_030561, intron 1 of 8)	L2|LINE|L2	5316	NM_030561	80748	Mm.290116	NM_030561	ENSMUSG00000052712	BC004004	2400006G15Rik	cDNA sequence BC004004	protein-coding
mm_155245.1	chrX	57223610	57223633	+	1	NA	3' UTR (NM_011616, exon 5 of 5)	3' UTR (NM_011616, exon 5 of 5)	11478	NM_011616	21947	Mm.4861	NM_011616	ENSMUSG00000031132	Cd40lg	CD154|CD40-L|Cd40l|HIGM1|IGM|IMD3|Ly-62|Ly62|T-BAM|TRAP|Tnfsf5|Tnlg8b|gp39	CD40 ligand	protein-coding
mm_37220.1	chr4	117915130	117915175	-	1	NA	promoter-TSS (NM_146152)	promoter-TSS (NM_146152)	-153	NM_146152	230673	Mm.287810	NM_146152	ENSMUSG00000033365	Ipo13	Imp13|Kap13|Ranbp13	importin 13	protein-coding
mm_72713.1	chr8	84995981	84995981	+	1	NA	intron (NM_133255, intron 11 of 21)	intron (NM_133255, intron 11 of 21)	5386	NM_001167991	170833	Mm.247775	NM_133255	ENSMUSG00000052566	Hook2	A630054I03Rik	hook microtubule tethering protein 2	protein-coding
mm_96772.1	chr11	69935846	69935854	+	1	NA	promoter-TSS (NM_016875)	promoter-TSS (NM_016875)	-49	NM_016875	53422	Mm.29286	NM_016875	ENSMUSG00000018554	Ybx2	Msy2	Y box protein 2	protein-coding
mm_50621.1	chr6	50125302	50125305	+	1	NA	intron (NM_019939, intron 1 of 12)	B1_Mur1|SINE|Alu	15062	NM_001164733	56524	Mm.41288	NM_008016	ENSMUSG00000038388	Mpp6	P55t|Pals2	membrane protein, palmitoylated 6 (MAGUK p55 subfamily member 6)	protein-coding
mm_50274.1	chr6	45317830	45317833	+	1	NA	intron (NM_001004357, intron 1 of 23)	intron (NM_001004357, intron 1 of 23)	257770	NM_001004357	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding
mm_35527.1	chr4	41275323	41275336	-	1	NA	promoter-TSS (NM_026872)	promoter-TSS (NM_026872)	-194	NM_026872	68926	Mm.41864	NM_026872	ENSMUSG00000028433	Ubap2	1190005K07Rik|AA408600|AU045235|UBAP-2|mKIAA1491	ubiquitin-associated protein 2	protein-coding
mm_53324.1	chr6	129221934	129221955	+	1	NA	Intergenic	Lx5|LINE|L1	16101	NR_040265	76432	Mm.261738	NR_040265	ENSMUSG00000097354	2310001H17Rik	AI646108	RIKEN cDNA 2310001H17 gene	ncRNA
mm_13737.1	chr2	118113050	118113063	+	1	NA	exon (NM_011580, exon 3 of 22)	exon (NM_011580, exon 3 of 22)	1180	NM_001313914	21825	Mm.4159	NM_011580	ENSMUSG00000040152	Thbs1	TSP-1|TSP1|Thbs-1|tbsp1	thrombospondin 1	protein-coding
mm_10093.1	chr2	3327293	3327296	+	1	NA	3' UTR (NM_008708, exon 14 of 14)	3' UTR (NM_008708, exon 14 of 14)	5334	NM_001013376	227522	Mm.293948	NM_001013376	ENSMUSG00000049950	Rpp38	C330006A15Rik	ribonuclease P/MRP 38 subunit	protein-coding
mm_161855.1	chr18	20247387	20247387	+	1	NA	promoter-TSS (NM_181680)	promoter-TSS (NM_181680)	47	NM_181680	211924	Mm.391118	NM_181680	ENSMUSG00000034774	Dsg1c	Dsg1gamma|Dsg6|dsg1g	desmoglein 1 gamma	protein-coding
mm_114854.1	chr13	93301218	93301248	+	1	NA	Intergenic	Intergenic	-2524	NM_147176	26556	Mm.37533	NM_011982	ENSMUSG00000007617	Homer1	PSD-Zip45|SYN47|Ves-1|homer-1|vesl-1	homer scaffolding protein 1	protein-coding
mm_27582.1	chr3	59101762	59101777	-	1	NA	promoter-TSS (NM_173398)	promoter-TSS (NM_173398)	52	NM_173398	229323	Mm.123648	NM_173398	ENSMUSG00000050075	Gpr171	A630006E05|F730001G15Rik|H963	G protein-coupled receptor 171	protein-coding
mm_152637.1	chr19	12501903	12501931	-	1	NA	promoter-TSS (NM_172442)	promoter-TSS (NM_172442)	79	NM_172442	207521	Mm.247695	NM_172442	ENSMUSG00000039982	Dtx4	AI449438|BC044798|D930042H13|RNF155	deltex 4, E3 ubiquitin ligase	protein-coding
mm_93121.1	chr10	91170642	91170645	-	1	NA	promoter-TSS (NM_001283048)	promoter-TSS (NM_001283048)	-93	NM_001283048	21917	Mm.159684	NM_011605	ENSMUSG00000019961	Tmpo	5630400D24Rik|AI195756|AI606875|AW214352|AW547477|LAP2|TP	thymopoietin	protein-coding
mm_129423.1	chr15	78406411	78406416	-	1	NA	promoter-TSS (NM_138670)	promoter-TSS (NM_138670)	-299	NM_001162493	246221	Mm.294215	NM_138670	ENSMUSG00000071711	Mpst	Mst	mercaptopyruvate sulfurtransferase	protein-coding
mm_17561.1	chr2	30194137	30194143	-	1	NA	intron (NM_172404, intron 2 of 13)	intron (NM_172404, intron 2 of 13)	11559	NM_172404	70266	Mm.216089	NM_172404	ENSMUSG00000039648	Kyat1	2010009K05Rik|AI182306|Ccbl1|Gtk|Kat1|KatI	kynurenine aminotransferase 1	protein-coding
mm_136543.1	chr16	97922583	97922613	-	1	NA	promoter-TSS (NM_174847)	promoter-TSS (NM_174847)	35	NM_174847	207781	Mm.1465	NM_174847	ENSMUSG00000045975	C2cd2	5730563M15|5830404H04Rik|AI314146|AI449533|BF168443|ORF25|mKIAA4045	C2 calcium-dependent domain containing 2	protein-coding
mm_156221.1	chrX	135008844	135008857	+	1	NA	intron (NM_175446, intron 1 of 6)	CpG	359	NM_175446	215693	Mm.336238	NM_175446	ENSMUSG00000052676	Zmat1	A230096A06|AW990744|B930008K04Rik	zinc finger, matrin type 1	protein-coding
mm_25319.1	chr3	106486060	106486092	+	1	NA	promoter-TSS (NM_028110)	promoter-TSS (NM_028110)	36	NM_028110	72121	Mm.14816	NM_028110	ENSMUSG00000027901	Dennd2d	2010308M01Rik|AI451421	DENN/MADD domain containing 2D	protein-coding
mm_62990.1	chr7	120504610	120504621	+	1	NA	intron (NM_001278943, intron 14 of 26)	CpG	82914	NM_001278944	233810		NM_001278943	ENSMUSG00000051900	Abca16	AY243472	ATP-binding cassette, sub-family A (ABC1), member 16	protein-coding
mm_160451.1	chr8	105690755	105690755	+	1	NA	promoter-TSS (NM_001033320)	promoter-TSS (NM_001033320)	-151	NM_001033320	234695	Mm.471640	NM_001033320	ENSMUSG00000050357	Carmil2	CG1399-PB|D130029J02Rik|Gm585|Rltpr	capping protein regulator and myosin 1 linker 2	protein-coding
mm_52094.1	chr6	97850133	97850144	+	1	NA	intron (NM_001113198, intron 1 of 9)	intron (NM_001113198, intron 1 of 9)	43080	NM_001113198	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_171011.1	chr2	83556552	83556556	+	1	NA	Intergenic	L1Md_F3|LINE|L1	-88024	NM_026934	69082	Mm.27804	NM_026934	ENSMUSG00000027091	Zc3h15	1700006A17Rik|1810012H02Rik|2610312B22Rik|FM22|Ierepo4	zinc finger CCCH-type containing 15	protein-coding
mm_44522.1	chr5	24391965	24392007	-	1	NA	5' UTR (NM_001002897, exon 1 of 14)	5' UTR (NM_001002897, exon 1 of 14)	157	NM_001002897	213948	Mm.332252	NM_001002897	ENSMUSG00000038295	Atg9b	Apg912|Apg9l2|Apgdc2|Gm574|Nos3as|eONE|sONE	autophagy related 9B	protein-coding
mm_82016.1	chr9	121719843	121719846	+	1	NA	intron (NM_010918, intron 2 of 16)	CpG-15515	663	NM_010918	18087	Mm.32842	NM_010918	ENSMUSG00000032525	Nktr	5330401F18Rik|D9Wsu172e	natural killer tumor recognition sequence	protein-coding
mm_83191.1	chr9	41014098	41014112	-	1	NA	3' UTR (NM_176860, exon 14 of 14)	3' UTR (NM_176860, exon 14 of 14)	-9477	NM_019465	54698	Mm.42791	NM_019465	ENSMUSG00000032021	Crtam	-	cytotoxic and regulatory T cell molecule	protein-coding
mm_12077.1	chr2	59779700	59779721	+	1	NA	intron (NM_198294, intron 7 of 26)	intron (NM_198294, intron 7 of 26)	102896	NM_001159636	72137	Mm.288734	NM_028118	ENSMUSG00000026988	Wdsub1	1700048E19Rik|2610014F08Rik	WD repeat, SAM and U-box domain containing 1	protein-coding
mm_132235.1	chr16	32750478	32750521	+	1	NA	exon (NM_080457, exon 2 of 27)	exon (NM_080457, exon 2 of 27)	14613	NM_080457	140474	Mm.214599	NM_080457	ENSMUSG00000079620	Muc4	4933405I11Rik|Asgp	mucin 4	protein-coding
mm_123327.1	chr14	62984503	62984512	-	1	NA	promoter-TSS (NM_001037751)	promoter-TSS (NM_001037751)	3	NM_001037751	432867	Mm.99387	NM_001037751	ENSMUSG00000075574	Defb48	Defb42|EG432867	defensin beta 48	protein-coding
mm_97747.1	chr11	80472684	80472686	+	1	NA	TTS (NM_178616)	TTS (NM_178616)	-4361	NM_009871	12569	Mm.142275	NM_009871	ENSMUSG00000048895	Cdk5r1	Cdk5r|D11Bwg0379e|p25|p35	cyclin-dependent kinase 5, regulatory subunit 1 (p35)	protein-coding
mm_119757.1	chr14	54168551	54168561	+	1	NA	Intergenic	Intergenic	85373	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_5246.1	chr1	16520024	16520039	-	1	NA	promoter-TSS (NM_025303)	promoter-TSS (NM_025303)	-729	NM_001111272	29819	Mm.216257	NM_025303	ENSMUSG00000025920	Stau2	-	staufen (RNA binding protein) homolog 2 (Drosophila)	protein-coding
mm_27933.1	chr3	79567806	79567863	-	1	NA	promoter-TSS (NM_001162999)	promoter-TSS (NM_001162999)	-155	NM_001162999	329679	Mm.244005	NM_001162999	ENSMUSG00000061175	Fnip2	D630023B12Rik|mKIAA1450	folliculin interacting protein 2	protein-coding
mm_121503.1	chr14	121930765	121930795	+	1	NA	intron (NM_026861, intron 4 of 8)	L1ME3A|LINE|L1	-15006	NM_182806	110168	Mm.37405	NM_182806	ENSMUSG00000050350	Gpr18	-	G protein-coupled receptor 18	protein-coding
mm_156259.1	chrX	136822738	136822780	+	1	NA	promoter-TSS (NM_011123)	promoter-TSS (NM_011123)	13	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_83868.1	chr9	55026459	55026486	-	1	NA	promoter-TSS (NM_145129)	promoter-TSS (NM_145129)	87	NM_145129	110834	Mm.63569	NM_145129	ENSMUSG00000032303	Chrna3	(a)3|A730007P14Rik|Acra-3|Acra3	cholinergic receptor, nicotinic, alpha polypeptide 3	protein-coding
mm_128401.1	chr15	44427795	44427813	-	1	NA	promoter-TSS (NM_175009)	promoter-TSS (NM_175009)	-307	NM_175009	223527	Mm.291828	NM_175009	ENSMUSG00000022338	Eny2	1810057B09Rik|6720481I12|DC6|Ey2	enhancer of yellow 2 homolog (Drosophila)	protein-coding
mm_139028.1	chr17	46161022	46161072	+	1	NA	promoter-TSS (NM_019581)	promoter-TSS (NM_019581)	15	NM_001145979	56055	Mm.22147	NM_019581	ENSMUSG00000023952	Gtpbp2	nmf205	GTP binding protein 2	protein-coding
mm_87374.1	chr10	44270249	44270253	+	1	NA	intron (NM_001314013, intron 1 of 6)	PB1D9|SINE|Alu	1912	NM_053069	11793	Mm.22264	NM_053069	ENSMUSG00000038160	Atg5	2010107M05Rik|3110067M24Rik|AW319544|Apg5l|Atg5l|C88337|Paddy	autophagy related 5	protein-coding
mm_143187.1	chr17	58934613	58934620	-	1	NA	intron (NM_027001, intron 6 of 12)	MLT1J1|LTR|ERVL-MaLR	56759	NM_027001	69239	Mm.246732	NM_027001	ENSMUSG00000024227	Pdzph1	2610034M16Rik|AV114557	PDZ and pleckstrin homology domains 1	protein-coding
mm_101588.1	chr11	34681736	34681762	-	1	NA	intron (NM_033374, intron 22 of 51)	RLTR44-int|LTR|ERVK	102156	NM_033374	94176	Mm.380679	NM_033374	ENSMUSG00000020143	Dock2	AI662014|AW122239|CED-5|Hch|MBC	dedicator of cyto-kinesis 2	protein-coding
mm_63534.1	chr7	127971807	127971810	+	1	NA	intron (NM_001347649, intron 3 of 14)	intron (NM_001347649, intron 3 of 14)	4329	NM_139149	233908	Mm.277680	NM_139149	ENSMUSG00000030795	Fus	D430004D17Rik|D930039C12Rik|Fus1|Tls	fused in sarcoma	protein-coding
mm_80959.1	chr9	103031468	103031472	+	1	NA	intron (NM_033314, intron 1 of 13)	intron (NM_033314, intron 1 of 13)	22981	NM_033314	24059	Mm.207106	NM_033314	ENSMUSG00000032548	Slco2a1	2310021C19Rik|Pgt|Slc21a2|mPgt	solute carrier organic anion transporter family, member 2a1	protein-coding
mm_57718.1	chr6	128788599	128788614	-	1	NA	promoter-TSS (NM_001159904)	promoter-TSS (NM_001159904)	35	NM_008527	17059	Mm.480764	NM_008527	ENSMUSG00000030325	Klrb1c	AI462337|CD161|Ly-59|Ly55c|Ly59|NK-RP1|NK1.1|NKR-P1.9|NKRP1|NKRP140|Nk-1|Nk-1.2|Nk1|Nk1.2|Nkrp1c|ly-55c	killer cell lectin-like receptor subfamily B member 1C	protein-coding
mm_100221.1	chr11	117091990	117092000	+	1	NA	Intergenic	Intergenic	14647	NR_105853	102465258		NR_105853	ENSMUSG00000104740	Mir6516	mmu-mir-6516	microRNA 6516	ncRNA
mm_89347.1	chr10	88135928	88135930	+	1	NA	intron (NM_029249, intron 3 of 10)	intron (NM_029249, intron 3 of 10)	11012	NM_029249	75317	Mm.179378	NM_029249	ENSMUSG00000035365	Parpbp	4930547N16Rik|AI503644|PARI	PARP1 binding protein	protein-coding
mm_172736.1	chr8	78147114	78147118	-	1	NA	Intergenic	ERVB7_1-LTR_MM|LTR|ERVK	-66226	NM_183096	73301	Mm.61243	NM_183096	ENSMUSG00000037101	Ttc29	1700031F13Rik	tetratricopeptide repeat domain 29	protein-coding
mm_144195.1	chr18	7901491	7901506	+	1	NA	exon (NM_001146298, exon 4 of 13)	exon (NM_001146298, exon 4 of 13)	32301	NM_153085	225131	Mm.204524	NM_153085	ENSMUSG00000024283	Wac	1110067P07Rik|A230035H12Rik|AI256735|AI256776|Wwp4	WW domain containing adaptor with coiled-coil	protein-coding
mm_55886.1	chr6	83527987	83527993	-	1	NA	intron (NM_009610, intron 1 of 8)	RMER4A|LTR|ERVK	8261	NM_009610	11468	Mm.292865	NM_009610	ENSMUSG00000059430	Actg2	ACTA3|Act-4|Act4|SMGA	actin, gamma 2, smooth muscle, enteric	protein-coding
mm_28877.1	chr3	97762735	97762739	-	1	NA	intron (NM_001039376, intron 8 of 46)	intron (NM_001039376, intron 8 of 46)	5277	NR_110360	83679	Mm.129840	NM_031401	ENSMUSG00000038170	Pde4dip	4732458A06Rik|9430063L05Rik|C87016|D130016K21Rik|D3Bwg1078e|Usmg4|mKIAA0454	phosphodiesterase 4D interacting protein (myomegalin)	protein-coding
mm_164576.1	chr17	24696557	24696565	-	1	NA	promoter-TSS (NM_023040)	promoter-TSS (NM_023040)	327	NM_027988	71893	Mm.390971	NM_027988	ENSMUSG00000019320	Noxo1	2310034C04Rik|P41NOX|P41NOXA|P41NOXB|P41NOXC|Snx28|hslt	NADPH oxidase organizer 1	protein-coding
mm_61550.1	chr7	79365122	79365125	+	1	NA	Intergenic	Intergenic	21904	NM_020599	19771	Mm.41653	NM_020599	ENSMUSG00000039194	Rlbp1	3110056M11Rik|CRALBP	retinaldehyde binding protein 1	protein-coding
mm_18778.1	chr2	73580289	73580353	-	1	NA	promoter-TSS (NM_007389)	promoter-TSS (NM_007389)	17	NM_007389	11435	Mm.4583	NM_007389	ENSMUSG00000027107	Chrna1	AI385656|AI608266|Achr-1|Acra	cholinergic receptor, nicotinic, alpha polypeptide 1 (muscle)	protein-coding
mm_2621.1	chr1	120602406	120602414	+	1	NA	promoter-TSS (NM_010133)	promoter-TSS (NM_010133)	-77	NM_010133	13798	Mm.2657	NM_010133	ENSMUSG00000058665	En1	En-1|Mo-en.1|engrailed-1	engrailed 1	protein-coding
mm_9306.1	chr1	171639629	171639631	-	1	NA	intron (NM_001347184, intron 2 of 5)	B1_Mur4|SINE|Alu	2270	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_5616.1	chr1	39720990	39721015	-	1	NA	promoter-TSS (NM_001145660)	promoter-TSS (NM_001145660)	-13	NM_001145660	619289	Mm.334107	NM_001145660	ENSMUSG00000057173	Rfx8	4933400N17Rik	regulatory factor X 8	protein-coding
mm_40366.1	chr5	48676431	48676436	+	1	NA	intron (NM_001199244, intron 1 of 7)	intron (NM_001199244, intron 1 of 7)	-76751	NM_001199245	80334	Mm.160172	NM_030265	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding
mm_102064.1	chr11	52256977	52256998	-	1	NA	exon (NM_009331, exon 7 of 10)	exon (NM_009331, exon 7 of 10)	24992	NM_011543	21402	Mm.42944	NM_011543	ENSMUSG00000036309	Skp1a	15kDa|2610043E24Rik|2610206H23Rik|EMC19|OCP-II|OCP2|SKP1|Tceb1l|p19A|p19Skp1	S-phase kinase-associated protein 1A	protein-coding
mm_168544.1	chr1	162721437	162721441	-	1	NA	exon (NM_001081290, exon 4 of 35)	exon (NM_001081290, exon 4 of 35)	19117	NM_001081290	226562	Mm.245446	NM_001081290	ENSMUSG00000040225	Prrc2c	1810043M20Rik|9630039I18Rik|A630006J20|Bat2d|Bat2d1|Bat2l2|E130112L15Rik|Prrc3|mKIAA1096	proline-rich coiled-coil 2C	protein-coding
mm_133963.1	chr16	4092257	4092267	-	1	NA	exon (NM_001025432, exon 27 of 31)	exon (NM_001025432, exon 27 of 31)	-14452	NM_026508	68015	Mm.123366	NM_026508	ENSMUSG00000005981	Trap1	2410002K23Rik|HSP75	TNF receptor-associated protein 1	protein-coding
mm_144822.1	chr18	36342945	36342950	+	1	NA	Intergenic	Intergenic	-5677	NM_001081365	66060	Mm.272527	NM_001081365	ENSMUSG00000046727	Cystm1	0610010O12Rik	cysteine-rich transmembrane module containing 1	protein-coding
mm_62320.1	chr7	100319405	100319433	+	1	NA	3' UTR (NM_177161, exon 13 of 13)	3' UTR (NM_177161, exon 13 of 13)	33899	NM_177161	320452	Mm.150294	NM_177161	ENSMUSG00000051048	P4ha3	D930031A02Rik	procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide III	protein-coding
mm_65731.1	chr7	28381925	28381929	-	1	NA	Intergenic	Intergenic	-2699	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_168299.1	chr11	106224129	106224148	+	1	NA	exon (NM_028074, exon 2 of 18)	exon (NM_028074, exon 2 of 18)	7212	NM_028074	72047	Mm.41367	NM_028074	ENSMUSG00000020705	Ddx42	1810047H21Rik|AW319508|AW556242|B430002H05Rik|RHELP|RNAHP|SF3b125	DEAD (Asp-Glu-Ala-Asp) box polypeptide 42	protein-coding
mm_35079.1	chr4	6990825	6990853	-	1	NA	promoter-TSS (NM_145711)	promoter-TSS (NM_145711)	-116	NM_145711	252838	Mm.435828	NM_145711	ENSMUSG00000041272	Tox	1700007F02Rik	thymocyte selection-associated high mobility group box	protein-coding
mm_18894.1	chr2	76712521	76712531	-	1	NA	exon (NM_011652, exon 307 of 313)	exon (NM_011652, exon 307 of 313)	37211	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_104142.1	chr11	87025405	87025425	-	1	NA	intron (NR_106195, intron 4 of 8)	ID_B1|SINE|B4	-31653	NM_001005341	77864	Mm.191894	NM_001005341	ENSMUSG00000018427	Ypel2	6430570G24|E130113K08Rik	yippee-like 2 (Drosophila)	protein-coding
mm_69121.1	chr7	127026297	127026310	-	1	NA	exon (NM_010772, exon 1 of 5)	exon (NM_010772, exon 1 of 5)	176	NM_010772	17188	Mm.378964	NM_010772	ENSMUSG00000030678	Maz	MAZI|PUR1|Pur-1|SAF-1|SAF-2	MYC-associated zinc finger protein (purine-binding transcription factor)	protein-coding
mm_20682.1	chr2	132574144	132574147	-	1	NA	intron (NM_001042672, intron 1 of 18)	intron (NM_001042672, intron 1 of 18)	4103	NM_001291050	74182	Mm.211211	NM_027096	ENSMUSG00000027346	Gpcpd1	2310004G06Rik|2310032D16Rik|AU015213|Gde5|Prei4|mKIAA1434	glycerophosphocholine phosphodiesterase 1	protein-coding
mm_95606.1	chr11	53372476	53372501	+	1	NA	exon (NM_033565, exon 3 of 21)	exon (NM_033565, exon 3 of 21)	21721	NM_033565	93736	Mm.395281	NM_033565	ENSMUSG00000049470	Aff4	AF5Q31|Alf4|Laf4l|MCEF	AF4/FMR2 family, member 4	protein-coding
mm_77940.1	chr9	7355825	7355835	+	1	NA	intron (NM_001320077, intron 9 of 10)	intron (NM_001320077, intron 9 of 10)	8456	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_127203.1	chr15	99126737	99126770	+	1	NA	promoter-TSS (NM_139140)	promoter-TSS (NM_139140)	-92	NM_139140	72572	Mm.276650	NM_139140	ENSMUSG00000051934	Spats2	2700012F11Rik|59kDa|Scr59|p59	spermatogenesis associated, serine-rich 2	protein-coding
mm_110698.1	chr12	69198402	69198416	-	1	NA	promoter-TSS (NM_027269)	promoter-TSS (NM_027269)	20	NM_027269	109065	Mm.107180	NM_027269	ENSMUSG00000020973	Dnaaf2	Ktu|TU54|kintoun|mknt	dynein, axonemal assembly factor 2	protein-coding
mm_45950.1	chr5	90366177	90366192	-	1	NA	promoter-TSS (NM_030886)	promoter-TSS (NM_030886)	1	NM_030886	81702	Mm.245522	NM_030886	ENSMUSG00000055204	Ankrd17	4933425K22Rik|A130069E23Rik|A930008M01|AA407558|AA516750|AU040470|Foe|Gtar|Mask|mKIAA0697	ankyrin repeat domain 17	protein-coding
mm_64772.1	chr7	4996045	4996094	-	1	NA	promoter-TSS (NM_026741)	promoter-TSS (NM_026741)	32	NM_026741	68490	Mm.76400	NM_026741	ENSMUSG00000051550	Zfp579	1110003A17Rik|Znf579	zinc finger protein 579	protein-coding
mm_62210.1	chr7	97843089	97843108	+	1	NA	5' UTR (NM_011035, exon 1 of 15)	5' UTR (NM_011035, exon 1 of 15)	159	NM_011035	18479	Mm.260227	NM_011035	ENSMUSG00000030774	Pak1	AW045634|PAK-1|Paka	p21 protein (Cdc42/Rac)-activated kinase 1	protein-coding
mm_61725.1	chr7	81859064	81859125	+	1	NA	promoter-TSS (NM_145375)	promoter-TSS (NM_145375)	93	NM_145375	107769	Mm.221412	NM_145375	ENSMUSG00000038623	Tm6sf1	AI428514|BC023123|C630016D09Rik	transmembrane 6 superfamily member 1	protein-coding
mm_165227.1	chr2	53486358	53486358	+	1	NA	Intergenic	Intergenic	294274	NM_022989	65103	Mm.37623	NM_022989	ENSMUSG00000026960	Arl6ip6	2310057C01Rik|2610529A11Rik|Aip-6	ADP-ribosylation factor-like 6 interacting protein 6	protein-coding
mm_62958.1	chr7	119730736	119730740	+	1	NA	Intergenic	MURVY-LTR|LTR|ERV1	-9940	NM_145585	233802	Mm.26392	NM_145585	ENSMUSG00000030942	Thumpd1	6330575P11Rik	THUMP domain containing 1	protein-coding
mm_2561.1	chr1	115826323	115826327	+	1	NA	intron (NM_001077425, intron 1 of 23)	intron (NM_001077425, intron 1 of 23)	141188	NM_001077425	636808	Mm.101576	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding
mm_96608.1	chr11	69095238	69095289	+	1	NA	Intergenic	CpG	-3693	NM_011065	18626	Mm.7373	NM_011065	ENSMUSG00000020893	Per1	Hftm|Per|m-rigui|mPer1	period circadian clock 1	protein-coding
mm_21841.1	chr2	165808274	165808289	-	1	NA	intron (NM_027230, intron 15 of 23)	intron (NM_027230, intron 15 of 23)	49892	NM_001252585	228880	Mm.227598	NM_027230	ENSMUSG00000039671	Zmynd8	1110013E22Rik|2010005I16Rik|3632413B07Rik|AI316811|AL024039|Prkcbp1|RACK7	zinc finger, MYND-type containing 8	protein-coding
mm_106640.1	chr11	120991261	120991278	-	1	NA	promoter-TSS (NM_139059)	promoter-TSS (NM_139059)	64	NM_139059	104318	Mm.216227	NM_027874	ENSMUSG00000025162	Csnk1d	1200006A05Rik|AA409348|D930010H05Rik	casein kinase 1, delta	protein-coding
mm_125389.1	chr15	40969325	40969327	+	1	NA	intron (NM_011766, intron 5 of 7)	intron (NM_011766, intron 5 of 7)	314284	NM_011766	22762	Mm.39496	NM_011766	ENSMUSG00000022306	Zfpm2	B330005D23Rik|FOG-2|FOG2	zinc finger protein, multitype 2	protein-coding
mm_168692.1	chr11	97166105	97166109	-	1	NA	exon (NM_008379, exon 16 of 22)	exon (NM_008379, exon 16 of 22)	-16395	NM_198100	73174	Mm.27882	NM_198100	ENSMUSG00000038517	Tbkbp1	3110043L15Rik|ProSAPiP2|SINTBAD	TBK1 binding protein 1	protein-coding
mm_8745.1	chr1	160251438	160251481	-	1	NA	intron (NM_001038621, intron 3 of 8)	intron (NM_001038621, intron 3 of 8)	-38567	NM_009786	12301	Mm.10702	NM_009786	ENSMUSG00000014226	Cacybp	SIP	calcyclin binding protein	protein-coding
mm_81761.1	chr9	114057459	114057479	+	1	NA	5' UTR (NM_001101510, exon 1 of 5)	5' UTR (NM_001101510, exon 1 of 5)	115	NM_001101510	382111	Mm.376140	NM_001101510	ENSMUSG00000086596	Susd5	Gm1126	sushi domain containing 5	protein-coding
mm_26571.1	chr3	146602498	146602512	+	1	NA	intron (NM_009474, intron 1 of 7)	intron (NM_009474, intron 1 of 7)	5356	NM_009474	22262	Mm.10865	NM_009474	ENSMUSG00000028186	Uox	AI663847	urate oxidase	protein-coding
mm_9076.1	chr1	168431503	168431513	-	1	NA	5' UTR (NM_001291509, exon 1 of 7)	5' UTR (NM_001291509, exon 1 of 7)	661	NM_001291508	18514	Mm.43358	NM_008783	ENSMUSG00000052534	Pbx1	2310056B04Rik|D230003C07Rik|Pbx-1	pre B cell leukemia homeobox 1	protein-coding
mm_42435.1	chr5	115429523	115429535	+	1	NA	promoter-TSS (NM_008629)	promoter-TSS (NM_008629)	-156	NM_008629	17690	Mm.5077	NM_008629	ENSMUSG00000054256	Msi1	Msi1h|Musahi1|m-Msi-1	musashi RNA-binding protein 1	protein-coding
mm_72963.1	chr8	92830765	92830807	+	1	NA	exon (NM_008610, exon 2 of 13)	exon (NM_008610, exon 2 of 13)	3489	NM_008610	17390	Mm.29564	NM_008610	ENSMUSG00000031740	Mmp2	Clg4a|GelA|MMP-2	matrix metallopeptidase 2	protein-coding
mm_151402.1	chr19	56510563	56510618	+	1	NA	Intergenic	Intergenic	37632	NM_018831	55947	Mm.2805	NM_018831	ENSMUSG00000025077	Dclre1a	2810043H12Rik|AU022226|Pso2|Smn1a|Snm1|mKIAA0086	DNA cross-link repair 1A	protein-coding
mm_104885.1	chr11	99550862	99550867	-	1	NA	promoter-TSS (NM_025524)	promoter-TSS (NM_025524)	-1	NM_025524	66380	Mm.30539	NM_025524	ENSMUSG00000069722	Krtap3-3	2310020D06Rik|KAP3.3|KRTAP3.3	keratin associated protein 3-3	protein-coding
mm_27322.1	chr3	50367449	50367465	-	1	NA	3' UTR (NM_011990, exon 12 of 12)	3' UTR (NM_011990, exon 12 of 12)	76156	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_6724.1	chr1	82586782	82586842	-	1	NA	promoter-TSS (NM_007735)	promoter-TSS (NM_007735)	37	NM_007735	12829	Mm.40253	NM_007735	ENSMUSG00000067158	Col4a4	E130010M05Rik|[a]4(IV)	collagen, type IV, alpha 4	protein-coding
mm_2060.1	chr1	87551263	87551268	+	1	NA	intron (NM_001111314, intron 1 of 14)	intron (NM_001111314, intron 1 of 14)	22605	NM_001111314	53972	Mm.435439	NM_019867	ENSMUSG00000026259	Ngef	Tims2|ephexin	neuronal guanine nucleotide exchange factor	protein-coding
mm_127411.1	chr15	101256386	101256393	+	1	NA	Intergenic	Intergenic	-10457	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_44834.1	chr5	34105805	34105820	-	1	NA	intron (NM_181857, intron 13 of 24)	RMER19B|LTR|ERVK	-12928	NR_040703	75357	Mm.410806	NR_040703	ENSMUSG00000106902	4930557J02Rik	-	RIKEN cDNA 4930557J02 gene	ncRNA
mm_126586.1	chr15	82298987	82298987	+	1	NA	promoter-TSS (NM_029066)	promoter-TSS (NM_029066)	3	NM_029066	74716	Mm.159315	NM_029066	ENSMUSG00000022455	Wbp2nl	4930521I23Rik|PAWP	WBP2 N-terminal like	protein-coding
mm_111561.1	chr12	101115275	101115289	-	1	NA	Intergenic	Intergenic	-30327	NR_033653	74947	Mm.488905	NR_033653	ENSMUSG00000092054	Kif4-ps	4930463M05Rik|Kif4b	kinesin family member 4, pseudogene	pseudo
mm_168497.1	chr11	51606420	51606427	-	1	NA	exon (NM_010448, exon 2 of 7)	exon (NM_010448, exon 2 of 7)	458	NM_001048061	15384	Mm.256875	NM_010448	ENSMUSG00000020358	Hnrnpab	3010025C11Rik|CBF-A|Cgbfa|Hnrpab	heterogeneous nuclear ribonucleoprotein A/B	protein-coding
mm_119296.1	chr14	34677076	34677090	+	1	NA	exon (NM_001301330, exon 2 of 19)	exon (NM_001301330, exon 2 of 19)	3155	NM_001301330	218914	Mm.27957	NM_001004436	ENSMUSG00000041408	Wapl	A530089A20Rik|BC037674|DIF-2|FOE|Wapal	WAPL cohesin release factor	protein-coding
mm_31567.1	chr4	57578299	57578311	+	1	NA	intron (NM_001304544, intron 1 of 8)	B4|SINE|B4	10057	NM_172868	242481	Mm.331630	NM_172868	ENSMUSG00000090053	Palm2	53-H12|B130066I24|R75368|pEN70	paralemmin 2	protein-coding
mm_79577.1	chr9	58134896	58134900	+	1	NA	intron (NM_001162479, intron 1 of 18)	intron (NM_001162479, intron 1 of 18)	233	NM_001162479	20897	Mm.10801	NM_009291	ENSMUSG00000032327	Stra6	AI891933	stimulated by retinoic acid gene 6	protein-coding
mm_65861.1	chr7	29354283	29354299	-	1	NA	intron (NM_001081028, intron 13 of 22)	intron (NM_001081028, intron 13 of 22)	50286	NM_013874	29861	Mm.101885	NM_013874	ENSMUSG00000030584	Dpf1	Neud4	D4, zinc and double PHD fingers family 1	protein-coding
mm_13297.1	chr2	102039647	102039659	+	1	NA	intron (NM_001290784, intron 4 of 5)	intron (NM_001290784, intron 4 of 5)	146807	NM_178886	241576	Mm.489740	NM_178886	ENSMUSG00000048058	Ldlrad3	6430500P08|AI194318|Lrad3	low density lipoprotein receptor class A domain containing 3	protein-coding
mm_130036.1	chr15	88978774	88978809	-	1	NA	promoter-TSS (NM_133241)	promoter-TSS (NM_133241)	-238	NM_133241	170790	Mm.32780	NM_133241	ENSMUSG00000035805	Mlc1	AW048630|BB074274|Kiaa0027-hp|LVM|MLC|VL|WKL1|mKIAA0027	megalencephalic leukoencephalopathy with subcortical cysts 1 homolog (human)	protein-coding
mm_1122.1	chr1	59977963	59977964	+	1	NA	intron (NM_001037725, intron 7 of 7)	intron (NM_001037725, intron 7 of 7)	64957	NM_001037725	72750	Mm.258250	NM_001037725	ENSMUSG00000041040	Fam117b	2810425F24Rik|6330416D14Rik|Als2cr13	family with sequence similarity 117, member B	protein-coding
mm_160905.1	chr11	77722792	77722792	-	1	NA	intron (NM_001313933, intron 2 of 4)	intron (NM_001313933, intron 2 of 4)	2501	NM_001313933	12957	Mm.22830	NM_009965	ENSMUSG00000000724	Cryba1	BA3/A1|Cryb	crystallin, beta A1	protein-coding
mm_62657.1	chr7	107693882	107693893	+	1	NA	intron (NM_001163557, intron 5 of 25)	intron (NM_001163557, intron 5 of 25)	64145	NM_001205227	320635	Mm.132828	NM_177216	ENSMUSG00000048065	Cyb5r2	D630003K02Rik|b5R.2	cytochrome b5 reductase 2	protein-coding
mm_136947.1	chr17	14512855	14512856	+	1	NA	Intergenic	Intergenic	-113913	NR_027986	74917	Mm.32228	NM_183107		4930474M22Rik	-	RIKEN cDNA 4930474M22 gene	ncRNA
mm_9182.1	chr1	171059391	171059405	-	1	NA	promoter-TSS (NM_010188)	promoter-TSS (NM_010188)	5	NM_010188	14131	Mm.22119	NM_010188	ENSMUSG00000059498	Fcgr3	CD16	Fc receptor, IgG, low affinity III	protein-coding
mm_63188.1	chr7	125581429	125581450	+	1	NA	Intergenic	CpG	-21990	NM_021887	60504	Mm.155643	NM_021887	ENSMUSG00000030745	Il21r	NILR	interleukin 21 receptor	protein-coding
mm_60090.1	chr7	34743947	34743950	+	1	NA	intron (NM_175140, intron 2 of 3)	ORR1B2|LTR|ERVL-MaLR	68763	NM_175140	68947	Mm.29380	NM_175140	ENSMUSG00000060402	Chst8	1500011J21Rik|AI426009	carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 8	protein-coding
mm_14364.1	chr2	129616555	129616570	+	1	NA	intron (NM_001291019, intron 4 of 7)	intron (NM_001291019, intron 4 of 7)	23393	NM_001291022	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_20465.1	chr2	129368009	129368125	-	1	NA	exon (NM_008361, exon 4 of 7)	exon (NM_008361, exon 4 of 7)	-1835	NR_015474	329514	Mm.207315	NM_177848	ENSMUSG00000074805	Il1bos	9430083I22|Gm14047|OTTMUSG00000015529	interleukin 1 beta, opposite strand	ncRNA
mm_151949.1	chr19	5801144	5801158	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	1521	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_1870.1	chr1	85600651	85600661	+	1	NA	promoter-TSS (NM_001013817)	promoter-TSS (NM_001013817)	-47	NM_001013817	434484	Mm.445821	NM_001013817	ENSMUSG00000070031	Sp140	-	Sp140 nuclear body protein	protein-coding
mm_84376.1	chr9	65037043	65037076	-	1	NA	exon (NM_028906, exon 3 of 21)	exon (NM_028906, exon 3 of 21)	4601	NM_028906	74388	Mm.202749	NM_028906	ENSMUSG00000032393	Dpp8	2310004I03Rik|4932434F09Rik|AI666706|DPP VIII	dipeptidylpeptidase 8	protein-coding
mm_41736.1	chr5	102718476	102718498	+	1	NA	intron (NM_146161, intron 2 of 8)	intron (NM_146161, intron 2 of 8)	-50323	NM_001286468	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding
mm_89694.1	chr10	97568354	97568381	+	1	NA	exon (NM_008524, exon 2 of 3)	exon (NM_008524, exon 2 of 3)	2866	NM_008524	17022	Mm.18888	NM_008524	ENSMUSG00000036446	Lum	Ldc|SLRR2D	lumican	protein-coding
mm_79210.1	chr9	49030877	49030883	+	1	NA	exon (NM_175482, exon 17 of 24)	exon (NM_175482, exon 17 of 24)	-24701	NM_012039	26951	Mm.24791	NM_012039	ENSMUSG00000032264	Zw10	6330566F14Rik|MmZw10	zw10 kinetochore protein	protein-coding
mm_6338.1	chr1	71629385	71629416	-	1	NA	exon (NM_001276413, exon 15 of 44)	exon (NM_001276413, exon 15 of 44)	23834	NM_010233	14268	Mm.193099	NM_010233	ENSMUSG00000026193	Fn1	E330027I09|Fn|Fn-1	fibronectin 1	protein-coding
mm_113284.1	chr13	30136638	30136650	+	1	NA	5' UTR (NM_153546, exon 1 of 13)	5' UTR (NM_153546, exon 1 of 13)	154	NM_153546	218121	Mm.89682	NM_153546	ENSMUSG00000038732	Mboat1	9130215M02Rik|BC023845|LPEAT1|Moact1|Oact1	membrane bound O-acyltransferase domain containing 1	protein-coding
mm_110321.1	chr12	34714547	34714568	-	1	NA	intron (NM_001271386, intron 3 of 27)	intron (NM_001271386, intron 3 of 27)	-185668	NM_024124	79221	Mm.310551	NM_024124	ENSMUSG00000004698	Hdac9	AV022454|D030072B18Rik|HD7B|HD9|HDRP|Hdac7b|Mitr|mKIAA0744	histone deacetylase 9	protein-coding
mm_57016.1	chr6	121245758	121245802	-	1	NA	promoter-TSS (NM_011909)	promoter-TSS (NM_011909)	-126	NM_011909	24110	Mm.326911	NM_011909	ENSMUSG00000030107	Usp18	1110058H21Rik|AW047653|UBP43|Ubp15	ubiquitin specific peptidase 18	protein-coding
mm_58697.1	chr7	12925730	12925742	+	1	NA	intron (NM_009095, intron 3 of 5)	intron (NM_009095, intron 3 of 5)	-1680	NM_029809	381845	Mm.439896	NM_029809	ENSMUSG00000033967	Rnf225	2310014L17Rik|AV237412|C77118	ring finger protein 225	protein-coding
mm_21932.1	chr2	167056634	167056650	-	1	NA	exon (NM_001033196, exon 3 of 14)	exon (NM_001033196, exon 3 of 14)	-6292	NR_138563	68949	Mm.391959	NM_001081005		Zfas1	1500012F01Rik|Zfos1	zinc finger, NFX1-type containing 1, antisense RNA 1	ncRNA
mm_13517.1	chr2	109917724	109917736	+	1	NA	promoter-TSS (NM_172671)	promoter-TSS (NM_172671)	83	NM_172671	107515	Mm.277351	NM_172671	ENSMUSG00000050199	Lgr4	9130225G07|A330106J01Rik|A930009A08Rik|Gpr48	leucine-rich repeat-containing G protein-coupled receptor 4	protein-coding
mm_50517.1	chr6	49040672	49040684	+	1	NA	intron (NM_053110, intron 1 of 10)	L1MEg|LINE|L1	4160	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_132040.1	chr16	27435059	27435066	+	1	NA	intron (NM_001025615, intron 5 of 9)	(T)n|Simple_repeat|Simple_repeat	46106	NM_001289436	67501	Mm.258985	NM_026202	ENSMUSG00000038127	Ccdc50	C3orf6	coiled-coil domain containing 50	protein-coding
mm_166655.1	chr6	87346197	87346203	-	1	NA	3' UTR (NM_025466, exon 6 of 6)	3' UTR (NM_025466, exon 6 of 6)	4715	NM_025466	66283	Mm.46414	NM_025466	ENSMUSG00000030050	Gkn1	2200002K21Rik|AMP-18|BRICD1|Fov	gastrokine 1	protein-coding
mm_162554.1	chr1	171439317	171439321	+	1	NA	intron (NM_172647, intron 1 of 9)	intron (NM_172647, intron 1 of 9)	1758	NM_172647	16456	Mm.294882	NM_172647	ENSMUSG00000038235	F11r	9130004G24|AA638916|ESTM33|JAM|JAM-1|JAM-A|Jcam|Jcam1|Ly106	F11 receptor	protein-coding
mm_119873.1	chr14	54686374	54686398	+	1	NA	5' UTR (NM_021437, exon 1 of 2)	5' UTR (NM_021437, exon 1 of 2)	215	NM_021437	58248	Mm.197509	NM_021437	ENSMUSG00000040822	1700123O20Rik	MNCb-2990	RIKEN cDNA 1700123O20 gene	protein-coding
mm_8546.1	chr1	155128503	155128533	-	1	NA	3' UTR (NM_008209, exon 6 of 6)	3' UTR (NM_008209, exon 6 of 6)	18262	NM_008209	15064	Mm.7580	NM_008209	ENSMUSG00000026471	Mr1	H2ls	major histocompatibility complex, class I-related	protein-coding
mm_99842.1	chr11	109353700	109353721	+	1	NA	TTS (NR_027883)	TTS (NR_027883)	6843	NR_027883	67927	Mm.394490	NR_027883	ENSMUSG00000099630	1700096J18Rik	-	RIKEN cDNA 1700096J18 gene	ncRNA
mm_91550.1	chr10	39894085	39894105	-	1	NA	non-coding (NR_033628, exon 3 of 4)	non-coding (NR_033628, exon 3 of 4)	5143	NR_033628	213332	Mm.484359	NR_033628		Mfsd4b4	AA474331	major facilitator superfamily domain containing 4B4	pseudo
mm_82271.1	chr9	7348792	7348820	-	1	NA	exon (NM_008605, exon 2 of 10)	exon (NM_008605, exon 2 of 10)	1432	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_156834.1	chrX	164373364	164373375	+	1	NA	promoter-TSS (NM_010216)	promoter-TSS (NM_010216)	-153	NM_001308489	14205	Mm.297978	NM_010216	ENSMUSG00000031380	Vegfd	AI325264|Figf|VEGF-D	vascular endothelial growth factor D	protein-coding
mm_114202.1	chr13	56006029	56006037	+	1	NA	Intergenic	Intergenic	129517	NM_012015	26914	Mm.283802	NM_012015	ENSMUSG00000015937	H2afy	H2AF12M|mH2a1|macroH2A1	H2A histone family, member Y	protein-coding
mm_115574.1	chr13	11572894	11572905	-	1	NA	intron (NM_023868, intron 97 of 104)	RSINE1|SINE|B4	50847	NR_027813	664793	Mm.410565	NR_027813		Zp4-ps	EG664793|Zp4|Zpb	zona pellucida glycoprotein 4, pseudogene	pseudo
mm_8355.1	chr1	150392722	150392757	-	1	NA	promoter-TSS (NM_133780)	promoter-TSS (NM_133780)	-99	NM_133780	108989	Mm.174256	NM_133780	ENSMUSG00000006005	Tpr	2610029M07Rik|C77892	translocated promoter region, nuclear basket protein	protein-coding
mm_171523.1	chr4	146610956	146610956	+	1	NA	Intergenic	Intergenic	-64083	NR_045468	67524	Mm.444300	NR_045468	ENSMUSG00000086046	1700095A21Rik	-	RIKEN cDNA 1700095A21 gene	ncRNA
mm_36062.1	chr4	57915741	57915774	-	1	NA	exon (NM_178727, exon 1 of 2)	exon (NM_178727, exon 1 of 2)	507	NM_178727	242484	Mm.23214	NM_178727	ENSMUSG00000052117	D630039A03Rik	-	RIKEN cDNA D630039A03 gene	protein-coding
mm_42333.1	chr5	114902839	114902850	+	1	NA	intron (NM_011854, intron 3 of 5)	B4|SINE|B4	5910	NM_011854	23962	Mm.228363	NM_011854	ENSMUSG00000029561	Oasl2	M1204|Mmu-OASL|Oasl	2'-5' oligoadenylate synthetase-like 2	protein-coding
mm_153315.1	chr19	38043636	38043646	-	1	NA	promoter-TSS (NM_001099634)	promoter-TSS (NM_001099634)	-64	NM_001302140	226101	Mm.34674	NM_177035	ENSMUSG00000048612	Myof	2310004N10Rik|2310051D19Rik|E030042N20Rik|Fer1l3	myoferlin	protein-coding
mm_138227.1	chr17	34354843	34354865	+	1	NA	promoter-TSS (NM_079835)	promoter-TSS (NM_079835)	32	NM_079835	547431	Mm.441007	NM_079835	ENSMUSG00000024340	Btnl2	BTL-II|BTLN2|Btl2|Gm315|NG9	butyrophilin-like 2	protein-coding
mm_77515.1	chr8	122894502	122894522	-	1	NA	non-coding (NR_037865, exon 10 of 14)	non-coding (NR_037865, exon 10 of 14)	46138	NM_007662	12555	Mm.1976	NM_007662	ENSMUSG00000031962	Cdh15	AI323380|Cdh14|Mcad	cadherin 15	protein-coding
mm_63622.1	chr7	128266327	128266335	+	1	NA	intron (NM_133254, intron 1 of 13)	intron (NM_133254, intron 1 of 13)	634	NM_133254	246787	Mm.38870	NM_133254	ENSMUSG00000030781	Slc5a2	Sglt2	solute carrier family 5 (sodium/glucose cotransporter), member 2	protein-coding
mm_27969.1	chr3	80717489	80717490	-	1	NA	intron (NM_001083806, intron 6 of 15)	L1MEd|LINE|L1	85302	NM_013540	14800	Mm.220224	NM_013540	ENSMUSG00000033981	Gria2	GluA2|GluR-B|Glur-2|Glur2	glutamate receptor, ionotropic, AMPA2 (alpha 2)	protein-coding
mm_5726.1	chr1	44118712	44118722	-	1	NA	promoter-TSS (NM_023645)	promoter-TSS (NM_023645)	56	NM_023645	72050	Mm.281714	NM_023645	ENSMUSG00000026047	Kdelc1	1810049A15Rik|5730416C13Rik|EP58|Kdel1	KDEL (Lys-Asp-Glu-Leu) containing 1	protein-coding
mm_62146.1	chr7	97111681	97111685	+	1	NA	intron (NM_001162477, intron 1 of 9)	intron (NM_001162477, intron 1 of 9)	29932	NM_010248	14389	Mm.42033	NM_010248	ENSMUSG00000004508	Gab2	AI463667|D130058I17Rik|p97	growth factor receptor bound protein 2-associated protein 2	protein-coding
mm_17014.1	chr2	18923875	18923880	-	1	NA	intron (NM_008845, intron 1 of 9)	intron (NM_008845, intron 1 of 9)	74244	NM_008845	18718	Mm.313977	NM_008845	ENSMUSG00000026737	Pip4k2a	AW742916|Pip5k2a	phosphatidylinositol-5-phosphate 4-kinase, type II, alpha	protein-coding
mm_147265.1	chr18	38881428	38881455	-	1	NA	intron (NM_010197, intron 1 of 3)	intron (NM_010197, intron 1 of 3)	-11015	NM_001033789	545253	Mm.244585	NM_001033789	ENSMUSG00000036452	Gm5820	EG545253	predicted gene 5820	protein-coding
mm_13029.1	chr2	91054120	91054132	+	1	NA	5' UTR (NM_008948, exon 1 of 12)	5' UTR (NM_008948, exon 1 of 12)	110	NM_008948	19182	Mm.289832	NM_008948	ENSMUSG00000002102	Psmc3	TBP-1	proteasome (prosome, macropain) 26S subunit, ATPase 3	protein-coding
mm_90925.1	chr10	12813602	12813612	-	1	NA	intron (NM_011682, intron 1 of 73)	intron (NM_011682, intron 1 of 73)	48128	NM_011682	22288	Mm.331784	NM_011682	ENSMUSG00000019820	Utrn	AA589569|DRP|Dmdl	utrophin	protein-coding
mm_1161.1	chr1	60909086	60909102	+	1	NA	promoter-TSS (NM_009843)	promoter-TSS (NM_009843)	69	NM_001281976	12477	Mm.390	NM_009843	ENSMUSG00000026011	Ctla4	Cd152|Ctla-4|Ly-56	cytotoxic T-lymphocyte-associated protein 4	protein-coding
mm_123905.1	chr14	73253523	73253525	-	1	NA	intron (NM_009029, intron 17 of 26)	intron (NM_009029, intron 17 of 26)	15633	NM_175116	67168	Mm.390681	NM_175116	ENSMUSG00000033446	Lpar6	2610302I02Rik|P2ry5|P2y5	lysophosphatidic acid receptor 6	protein-coding
mm_76407.1	chr8	84855674	84855675	-	1	NA	Intergenic	Intergenic	-1312	NM_025648	66590	Mm.292517	NM_025648	ENSMUSG00000003808	Farsa	0610012A19Rik|Farsla	phenylalanyl-tRNA synthetase, alpha subunit	protein-coding
mm_101358.1	chr11	23740833	23740842	-	1	NA	TTS (NM_009044)	TTS (NM_009044)	30133	NM_009044	19696	Mm.4869	NM_009044	ENSMUSG00000020275	Rel	c-Rel	reticuloendotheliosis oncogene	protein-coding
mm_154502.1	chrM	11884	11894	-	1	NA	NA	Intergenic	NA	NA								
mm_95556.1	chr11	52311004	52311022	+	1	NA	Intergenic	Intergenic	-27999	NM_001313981	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_62510.1	chr7	102210169	102210177	+	1	NA	promoter-TSS (NM_001291358)	promoter-TSS (NM_001291358)	-7	NM_001287164	269966	Mm.439800	NM_022979	ENSMUSG00000063550	Nup98	4732457F17|AI849286|Nup96	nucleoporin 98	protein-coding
mm_123530.1	chr14	66804503	66804520	-	1	NA	3' UTR (NM_009955, exon 14 of 14)	3' UTR (NM_009955, exon 14 of 14)	64089	NM_009955	12934	Mm.352648	NM_009955	ENSMUSG00000022048	Dpysl2	AI851130|Crmp2|DRP2|Musunc33|TOAD-64|Ulip2	dihydropyrimidinase-like 2	protein-coding
mm_95304.1	chr11	46127266	46127269	+	1	NA	promoter-TSS (NM_001311209)	promoter-TSS (NM_001311209)	-637	NM_001311209	11492	Mm.89940	NM_009616	ENSMUSG00000011256	Adam19	AL024287|MADDAM|MTLNB|Mltnb	a disintegrin and metallopeptidase domain 19 (meltrin beta)	protein-coding
mm_4778.1	chr1	182959115	182959123	+	1	NA	intron (NM_016928, intron 1 of 3)	intron (NM_016928, intron 1 of 3)	4331	NM_016928	53791	Mm.116894	NM_016928	ENSMUSG00000079164	Tlr5	-	toll-like receptor 5	protein-coding
mm_144714.1	chr18	35048294	35048294	+	1	NA	Intergenic	Intergenic	-70618	NM_009818	12385	Mm.18962	NM_009818	ENSMUSG00000037815	Ctnna1	2010010M04Rik|AA517462|AI988031|Catna1	catenin (cadherin associated protein), alpha 1	protein-coding
mm_92804.1	chr10	81365835	81365843	-	1	NA	promoter-TSS (NM_001014836)	promoter-TSS (NM_001014836)	-19	NM_001014836	432479	Mm.440450	NM_001014836	ENSMUSG00000020234	4930404N11Rik	2210409H10Rik|5730551K18Rik|AI854616	RIKEN cDNA 4930404N11 gene	protein-coding
mm_52393.1	chr6	113301613	113301619	+	1	NA	intron (NM_170673, intron 17 of 19)	intron (NM_170673, intron 17 of 19)	-5521	NM_030178	78783	Mm.356059	NM_030178	ENSMUSG00000001632	Brpf1	4833438B11Rik|4930540D11Rik|Brpf2	bromodomain and PHD finger containing, 1	protein-coding
mm_95964.1	chr11	58884102	58884113	+	1	NA	3' UTR (NM_172403, exon 5 of 5)	3' UTR (NM_172403, exon 5 of 5)	16867	NM_172403	69944	Mm.32118	NM_172403	ENSMUSG00000020491	2810021J22Rik	AI449137	RIKEN cDNA 2810021J22 gene	protein-coding
mm_6166.1	chr1	65062184	65062194	-	1	NA	intron (NM_007776, intron 2 of 2)	intron (NM_007776, intron 2 of 2)	1251	NM_007776	12967	Mm.425031	NM_007776	ENSMUSG00000067299	Crygd	Aey4|Cryg-1|DGcry-1|Lop12	crystallin, gamma D	protein-coding
mm_94066.1	chr10	128400449	128400473	-	1	NA	promoter-TSS (NM_028092)	promoter-TSS (NM_028092)	5	NM_028051	72002	Mm.22983	NM_028051	ENSMUSG00000039878	Slc39a5	1810013D05Rik|2010205A06Rik|Zip5	solute carrier family 39 (metal ion transporter), member 5	protein-coding
mm_40232.1	chr5	37288913	37288933	+	1	NA	exon (NM_001136058, exon 13 of 14)	exon (NM_001136058, exon 13 of 14)	43159	NM_007765	12933	Mm.290995	NM_007765	ENSMUSG00000029121	Crmp1	CRMP-1|DRP-1|Dpysl1|ULIP-3|Ulip3	collapsin response mediator protein 1	protein-coding
mm_18693.1	chr2	71543874	71543878	-	1	NA	3' UTR (NM_010054, exon 3 of 3)	3' UTR (NM_010054, exon 3 of 3)	2878	NM_010054	13392	Mm.3896	NM_010054	ENSMUSG00000023391	Dlx2	AW121999|Dlx-2|Tes-1	distal-less homeobox 2	protein-coding
mm_139237.1	chr17	47732971	47732973	+	1	NA	exon (NM_025973, exon 7 of 9)	exon (NM_025973, exon 7 of 9)	-4065	NM_001161722	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_35454.1	chr4	40702789	40702803	-	1	NA	5' UTR (NM_025545, exon 1 of 8)	5' UTR (NM_025545, exon 1 of 8)	120	NM_025545	66408	Mm.430710	NM_025545	ENSMUSG00000028411	Aptx	2410016G21Rik|AA388047|FHA-HIT	aprataxin	protein-coding
mm_92517.1	chr10	78464970	78464987	-	1	NA	promoter-TSS (NM_172134)	promoter-TSS (NM_172134)	-30	NM_172134	216134	Mm.206159	NM_172134	ENSMUSG00000032788	Pdxk	2310036D04Rik|AA119688|C77999	pyridoxal (pyridoxine, vitamin B6) kinase	protein-coding
mm_154657.1	chrX	7842012	7842022	+	1	NA	promoter-TSS (NM_001290537)	promoter-TSS (NM_001290537)	-65	NM_001290537	54644	Mm.142827	NM_138604	ENSMUSG00000031154	Otud5	AA407879|AI553596|BB114028|DUBA|DXImx46e|Sfc7	OTU domain containing 5	protein-coding
mm_66282.1	chr7	37770758	37770796	-	1	NA	Intergenic	CpG-13025	-1025	NM_172385	243937	Mm.322505	NM_172385	ENSMUSG00000043456	Zfp536	9630010P11Rik|Znf536|mKIAA0390	zinc finger protein 536	protein-coding
mm_139312.1	chr17	48351835	48351846	+	1	NA	exon (NM_031254, exon 4 of 5)	exon (NM_031254, exon 4 of 5)	5439	NM_001272078	83433	Mm.261623	NM_031254	ENSMUSG00000023992	Trem2	TREM-2|Trem2a|Trem2b|Trem2c	triggering receptor expressed on myeloid cells 2	protein-coding
mm_90803.1	chr10	7663697	7663721	-	1	NA	promoter-TSS (NM_008786)	promoter-TSS (NM_008786)	-101	NM_001347228	18537	Mm.258431	NM_008786	ENSMUSG00000019795	Pcmt1	C79501|PIMT	protein-L-isoaspartate (D-aspartate) O-methyltransferase 1	protein-coding
mm_66575.1	chr7	45334524	45334567	-	1	NA	promoter-TSS (NM_010473)	promoter-TSS (NM_010473)	-724	NM_010473	15464	Mm.39968	NM_010473	ENSMUSG00000038239	Hrc	-	histidine rich calcium binding protein	protein-coding
mm_112207.1	chr12	113427286	113427294	-	1	NA	Intergenic	Intergenic	-62275	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_133648.1	chr16	91794088	91794091	+	1	NA	intron (NM_001110275, intron 5 of 28)	Lx9|LINE|L1	64718	NM_010587	16443	Mm.40546	NM_010587	ENSMUSG00000022957	Itsn1	AA517634|AA545208|AI316805|AI839402|AI848451|Ehsh1|Ese1|Itsn|Sh3p17	intersectin 1 (SH3 domain protein 1A)	protein-coding
mm_115162.1	chr13	107687389	107687402	+	1	NA	promoter-TSS (NR_045900)	promoter-TSS (NR_045900)	-2	NR_045900	72257	Mm.234155	NR_045900	ENSMUSG00000102000	1700006H21Rik	-	RIKEN cDNA 1700006H21 gene	ncRNA
mm_86516.1	chr10	7681198	7681225	+	1	NA	promoter-TSS (NR_033219)	promoter-TSS (NR_033219)	2	NM_010690	16798	Mm.34083	NM_010690	ENSMUSG00000040021	Lats1	AW208599	large tumor suppressor	protein-coding
mm_18256.1	chr2	52271130	52271143	-	1	NA	exon (NM_010889, exon 50 of 157)	exon (NM_010889, exon 50 of 157)	-19866	NR_040620	78049	Mm.243883	NR_040620		4930573O16Rik	-	RIKEN cDNA 4930573O16 gene	ncRNA
mm_115749.1	chr13	18378456	18378458	-	1	NA	exon (NM_175006, exon 2 of 8)	exon (NM_175006, exon 2 of 8)	3582	NM_175006	218030	Mm.352263	NM_175006	ENSMUSG00000009734	Pou6f2	D130006K24Rik|RPF-1	POU domain, class 6, transcription factor 2	protein-coding
mm_84044.1	chr9	57946577	57946587	-	1	NA	intron (NM_011352, intron 1 of 13)	intron (NM_011352, intron 1 of 13)	6447	NM_011352	20361	Mm.335187	NM_011352	ENSMUSG00000038264	Sema7a	2900057C09Rik|CDw108|H-Sema-L|M-Sema-L|Semal	sema domain, immunoglobulin domain (Ig), and GPI membrane anchor, (semaphorin) 7A	protein-coding
mm_144447.1	chr18	22721608	22721612	+	1	NA	intron (NM_001347510, intron 8 of 9)	intron (NM_001347510, intron 8 of 9)	317053	NM_001161483	319211	Mm.209896	NM_199024	ENSMUSG00000041923	Nol4	1700013J13Rik|4930568N03Rik|Gm1262	nucleolar protein 4	protein-coding
mm_167736.1	chr9	106197469	106197476	-	1	NA	intron (NM_198931, intron 3 of 9)	intron (NM_198931, intron 3 of 9)	1467	NM_198931	67905	Mm.23018	NM_026447	ENSMUSG00000020253	Ppm1m	2810423O19Rik|AW610647|C77250|PP2Ceta	protein phosphatase 1M	protein-coding
mm_54322.1	chr6	30390998	30391029	-	1	NA	promoter-TSS (NM_172735)	promoter-TSS (NM_172735)	-3	NM_172735	232679	Mm.29780	NM_172735	ENSMUSG00000039130	Zc3hc1	1110054L24Rik|AU018540|AU019789|HSPC216|Nipa	zinc finger, C3HC type 1	protein-coding
mm_101434.1	chr11	30100362	30100364	-	1	NA	3' UTR (NM_175836, exon 35 of 35)	3' UTR (NM_175836, exon 35 of 35)	-74330	NM_146016	237711	Mm.445271	NM_146016	ENSMUSG00000044072	Eml6	2900083P10Rik|C230094A16Rik|EMAP-6	echinoderm microtubule associated protein like 6	protein-coding
mm_130395.1	chr15	97975669	97975687	-	1	NA	TTS (NM_001113515)	TTS (NM_001113515)	11449	NM_001252153	380967	Mm.196630	NM_201359	ENSMUSG00000052369	Tmem106c	AI046681|BC046621|D15Ertd405e	transmembrane protein 106C	protein-coding
mm_60905.1	chr7	46712668	46712701	+	1	NA	exon (NM_011315, exon 3 of 4)	exon (NM_011315, exon 3 of 4)	-2033	NM_030233	78935	Mm.289866	NM_030233	ENSMUSG00000006763	Saal1	5031425D22Rik|SPACIA1	serum amyloid A-like 1	protein-coding
mm_15947.1	chr2	165917375	165917406	+	1	NA	Intergenic	RMER20C_Mm|LTR|ERVK	-32552	NM_001252587	228880	Mm.227598	NM_027230	ENSMUSG00000039671	Zmynd8	1110013E22Rik|2010005I16Rik|3632413B07Rik|AI316811|AL024039|Prkcbp1|RACK7	zinc finger, MYND-type containing 8	protein-coding
mm_77072.1	chr8	110039372	110039396	-	1	NA	promoter-TSS (NM_011998)	promoter-TSS (NM_011998)	-50	NM_011998	26887	Mm.89207	NM_011998	ENSMUSG00000035930	Chst4	GST-3|Gn6st-2|HEC-GlcNAc6ST	carbohydrate (chondroitin 6/keratan) sulfotransferase 4	protein-coding
mm_51617.1	chr6	85187512	85187523	+	1	NA	promoter-TSS (NM_010131)	promoter-TSS (NM_010131)	-414	NM_010131	13796	Mm.391473	NM_010131	ENSMUSG00000033726	Emx1	-	empty spiracles homeobox 1	protein-coding
mm_33219.1	chr4	126677642	126677646	+	1	NA	promoter-TSS (NM_011970)	promoter-TSS (NM_011970)	1	NM_011970	26445	Mm.22233	NM_011970	ENSMUSG00000028837	Psmb2	AU045357|AW108089|C7-I|D4Wsu33e|HC7-I	proteasome (prosome, macropain) subunit, beta type 2	protein-coding
mm_168318.1	chr11	11436886	11436900	+	1	NA	intron (NM_001185153, intron 2 of 7)	intron (NM_001185153, intron 2 of 7)	25526	NM_015785	53604	Mm.9500	NM_015785	ENSMUSG00000020193	Zpbp	4930486K01Rik|Iam38|Sp38	zona pellucida binding protein	protein-coding
mm_85981.1	chr9	112166687	112166702	-	1	NA	intron (NM_001177623, intron 9 of 9)	intron (NM_001177623, intron 9 of 9)	19255	NM_001177618	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_104738.1	chr11	98384798	98384812	-	1	NA	3' UTR (NM_011540, exon 2 of 2)	3' UTR (NM_011540, exon 2 of 2)	994	NM_011540	21393	Mm.10762	NM_011540	ENSMUSG00000007877	Tcap	AI503981|AJ223855	titin-cap	protein-coding
mm_28378.1	chr3	89963274	89963286	-	1	NA	promoter-TSS (NM_001081182)	promoter-TSS (NM_001081182)	52	NM_001081182	54667	Mm.30455	NM_001081182	ENSMUSG00000060671	Atp8b2	Id	ATPase, class I, type 8B, member 2	protein-coding
mm_122567.1	chr14	50795690	50795705	-	1	NA	promoter-TSS (NM_001111119)	promoter-TSS (NM_001111119)	31	NM_001111119	239083	Mm.343880	NM_001111119	ENSMUSG00000071470	Ccnb1ip1	Gm288|Hei10|mei4	cyclin B1 interacting protein 1	protein-coding
mm_78244.1	chr9	21637273	21637310	+	1	NA	exon (NM_001174078, exon 6 of 34)	exon (NM_001174078, exon 6 of 34)	21122	NM_001174078	20586	Mm.286593	NM_011417	ENSMUSG00000032187	Smarca4	Brg1|HP1-BP72|SNF2beta|SW1/SNF|b2b508.1Clo|b2b692Clo	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	protein-coding
mm_84591.1	chr9	70036729	70036739	-	1	NA	5' UTR (NM_028087, exon 2 of 3)	5' UTR (NM_028087, exon 2 of 3)	1354	NM_028087	72077	Mm.195555	NM_028087	ENSMUSG00000032226	Gcnt3	2010013H22Rik|2210021I22Rik|2210401J11Rik	glucosaminyl (N-acetyl) transferase 3, mucin type	protein-coding
mm_41951.1	chr5	105741864	105741870	+	1	NA	intron (NM_001122768, intron 2 of 2)	intron (NM_001122768, intron 2 of 2)	41057	NM_178701	231549	Mm.23837	NM_178701	ENSMUSG00000046079	Lrrc8d	2810473G09Rik|4930525N13Rik|A930019F03|Lrrc5	leucine rich repeat containing 8D	protein-coding
mm_18528.1	chr2	63184299	63184335	-	1	NA	promoter-TSS (NM_133207)	promoter-TSS (NM_133207)	-30	NM_133207	170738	Mm.242532	NM_133207	ENSMUSG00000059742	Kcnh7	9330137I11Rik|Kv11.3|erg3	potassium voltage-gated channel, subfamily H (eag-related), member 7	protein-coding
mm_151724.1	chr19	4839287	4839338	-	1	NA	promoter-TSS (NM_016892)	promoter-TSS (NM_016892)	10	NM_016892	12460	Mm.434411	NM_016892	ENSMUSG00000034108	Ccs	Ccsd	copper chaperone for superoxide dismutase	protein-coding
mm_137433.1	chr17	26414821	26414895	+	1	NA	promoter-TSS (NM_001081656)	promoter-TSS (NM_001081656)	-107	NM_001081656	240055	Mm.133211	NM_001081656	ENSMUSG00000034413	Neurl1b	C230078M08Rik|EG240055	neuralized E3 ubiquitin protein ligase 1B	protein-coding
mm_27439.1	chr3	51788648	51788654	-	1	NA	intron (NM_001004176, intron 2 of 4)	intron (NM_001004176, intron 2 of 4)	127472	NM_001310482	211666	Mm.24679	NM_174995	ENSMUSG00000074604	Mgst2	GST2|MGST-II	microsomal glutathione S-transferase 2	protein-coding
mm_9382.1	chr1	172213065	172213075	-	1	NA	exon (NM_009813, exon 9 of 11)	exon (NM_009813, exon 9 of 11)	-6266	NM_011063	18611	Mm.544	NM_011063	ENSMUSG00000013698	Pea15a	Mat1|PEA-15|Pea15|Pkcs15	phosphoprotein enriched in astrocytes 15A	protein-coding
mm_66640.1	chr7	45575183	45575190	-	1	NA	promoter-TSS (NR_038166)	promoter-TSS (NR_038166)	-10	NR_038165	71661	Mm.439894	NR_038165	ENSMUSG00000109644	0610005C13Rik	AI182092	RIKEN cDNA 0610005C13 gene	ncRNA
mm_165147.1	chr2	19300515	19300573	+	1	NA	exon (NM_001271565, exon 17 of 18)	exon (NM_001271565, exon 17 of 18)	-43773	NR_126563	108871	Mm.107666	NR_126563		4930447M23Rik	-	RIKEN cDNA 4930447M23 gene	ncRNA
mm_152365.1	chr19	10101553	10101559	-	1	NA	promoter-TSS (NM_019699)	promoter-TSS (NM_019699)	-53	NM_019699	56473	Mm.38901	NM_019699	ENSMUSG00000024665	Fads2	2900042M13Rik|Fadsd2	fatty acid desaturase 2	protein-coding
mm_114766.1	chr13	88521191	88521203	+	1	NA	Intergenic	IAPLTR2b|LTR|ERVK	-300275	NM_010103	13612	Mm.125580	NM_010103	ENSMUSG00000034488	Edil3	Del-1|Del1	EGF-like repeats and discoidin I-like domains 3	protein-coding
mm_26192.1	chr3	138488870	138488881	+	1	NA	intron (NM_175224, intron 1 of 10)	intron (NM_175224, intron 1 of 10)	507	NM_175224	75624	Mm.26833	NM_175224	ENSMUSG00000005813	Metap1	1700029C17Rik|AW047992|mKIAA0094	methionyl aminopeptidase 1	protein-coding
mm_111665.1	chr12	103336380	103336421	-	1	NA	intron (NM_023049, intron 3 of 9)	intron (NM_023049, intron 3 of 9)	19601	NM_023049	65256	Mm.27159	NM_023049	ENSMUSG00000021200	Asb2	1110008E15Rik	ankyrin repeat and SOCS box-containing 2	protein-coding
mm_140888.1	chr17	23955330	23955357	-	1	NA	promoter-TSS (NM_001077421)	promoter-TSS (NM_001077421)	-70	NM_001077421	638345	Mm.46428	NM_001077421	ENSMUSG00000024125	Sbpl	2310068J22Rik	spermine binding protein-like	protein-coding
mm_166527.1	chr6	25931381	25931420	+	1	NA	promoter-TSS (NR_040771)	promoter-TSS (NR_040771)	-26	NR_040771	626904	Mm.126787	NR_040771	ENSMUSG00000106799	Gm20756	-	predicted gene, 20756	ncRNA
mm_60839.1	chr7	45725857	45725879	+	1	NA	promoter-TSS (NM_027055)	promoter-TSS (NM_027055)	-52	NM_027055	69363	Mm.45607	NM_027055	ENSMUSG00000070563	Spaca4	1700008E09Rik|AV043694|Samp14	sperm acrosome associated 4	protein-coding
mm_45395.1	chr5	66151363	66151375	-	1	NA	promoter-TSS (NM_001291226)	promoter-TSS (NM_001291226)	-391	NM_178446	245945	Mm.36863	NM_139065	ENSMUSG00000070780	Rbm47	9530077J19Rik	RNA binding motif protein 47	protein-coding
mm_3753.1	chr1	156036189	156036258	+	1	NA	exon (NM_144791, exon 1 of 7)	intron (NM_172843, intron 1 of 6)	187	NM_001160182	240832	Mm.253335	NM_022329	ENSMUSG00000050565	Tor1aip2	1110020D10Rik|15kDa|A130072J07|AA103493|AW060462|AW610675|C77739|Ifrg15|Lull1	torsin A interacting protein 2	protein-coding
mm_8296.1	chr1	143679690	143679715	-	1	NA	intron (NM_145991, intron 6 of 16)	intron (NM_145991, intron 6 of 16)	23191	NM_145991	214498	Mm.156727	NM_145991	ENSMUSG00000026361	Cdc73	8430414L16Rik|C130030P16Rik|C81219|Hrpt2	cell division cycle 73, Paf1/RNA polymerase II complex component	protein-coding
mm_170936.1	chr2	47200376	47200384	-	1	NA	Intergenic	Lx2A1|LINE|L1	1503775	NR_040497	69405	Mm.396184	NR_040497	ENSMUSG00000086202	1700019E08Rik	-	RIKEN cDNA 1700019E08 gene	ncRNA
mm_170870.1	chr2	20547978	20547979	+	1	NA	intron (NM_029895, intron 3 of 18)	intron (NM_029895, intron 3 of 18)	28465	NM_001177631	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding
mm_5919.1	chr1	55088104	55088117	-	1	NA	promoter-TSS (NM_010477)	promoter-TSS (NM_010477)	-38	NM_008303	15528	Mm.215667	NM_008303	ENSMUSG00000073676	Hspe1	10kDa|Hsp10|mt-cpn10	heat shock protein 1 (chaperonin 10)	protein-coding
mm_137729.1	chr17	29274186	29274203	+	1	NA	intron (NM_030561, intron 1 of 8)	intron (NM_030561, intron 1 of 8)	5406	NM_030561	80748	Mm.290116	NM_030561	ENSMUSG00000052712	BC004004	2400006G15Rik	cDNA sequence BC004004	protein-coding
mm_150163.1	chr19	32388519	32388530	+	1	NA	promoter-TSS (NM_144792)	promoter-TSS (NM_144792)	-70	NM_144792	208449	Mm.329810	NM_144792	ENSMUSG00000040451	Sgms1	9530058O11Rik|AI841905|C80702|Mob|Sms1|Sor1|Tmem23	sphingomyelin synthase 1	protein-coding
mm_54716.1	chr6	39844358	39844401	-	1	NA	Intergenic	Intergenic	-33443	NM_001010930	14548	Mm.377071	NM_010270	ENSMUSG00000029918	Mrps33	AI841153|CGI-139|Gdap3|MRP-S33|PTD003	mitochondrial ribosomal protein S33	protein-coding
mm_126540.1	chr15	82022924	82022934	+	1	NA	exon (NM_010247, exon 5 of 13)	exon (NM_010247, exon 5 of 13)	6560	NM_010247	14375	Mm.288809	NM_010247	ENSMUSG00000022471	Xrcc6	70kDa|G22p1|Ku70	X-ray repair complementing defective repair in Chinese hamster cells 6	protein-coding
mm_115719.1	chr13	15914378	15914393	-	1	NA	Intergenic	ORR1B2|LTR|ERVL-MaLR	-97466	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_103639.1	chr11	78963234	78963250	-	1	NA	3' UTR (NM_010708, exon 11 of 11)	3' UTR (NM_010708, exon 11 of 11)	21682	NM_001159301	16859	Mm.341434	NM_010708	ENSMUSG00000001123	Lgals9	AA407335|AI194909|AI265545|LGALS35|Lgals5|gal-9|galectin-9	lectin, galactose binding, soluble 9	protein-coding
mm_126778.1	chr15	86182905	86182916	+	1	NA	intron (NM_145475, intron 1 of 12)	intron (NM_145475, intron 1 of 12)	3231	NM_145475	223753	Mm.222685	NM_145475	ENSMUSG00000035891	Cerk	AI848610|D330016D08Rik|mKIAA1646	ceramide kinase	protein-coding
mm_34223.1	chr4	140992417	140992427	+	1	NA	exon (NM_029097, exon 3 of 29)	exon (NM_029097, exon 3 of 29)	5549	NM_001164366	74772	Mm.205625	NM_029097	ENSMUSG00000036622	Atp13a2	1110012E06Rik|AA589443	ATPase type 13A2	protein-coding
mm_163168.1	chr11	86758165	86758189	+	1	NA	promoter-TSS (NM_001003908)	promoter-TSS (NM_001003908)	-685	NM_001003908	67300	Mm.254588	NM_001003908	ENSMUSG00000047126	Cltc	3110065L21Rik|CHC|R74732	clathrin, heavy polypeptide (Hc)	protein-coding
mm_23212.1	chr3	41564998	41565008	+	1	NA	5' UTR (NM_001130186, exon 1 of 11)	5' UTR (NM_001130186, exon 1 of 11)	123	NM_001130186	269424	Mm.286285	NM_172303	ENSMUSG00000025764	Jade1	AU041499|D530048A03Rik|Phf17|mKIAA1807	jade family PHD finger 1	protein-coding
mm_20471.1	chr2	129410387	129410399	-	1	NA	Intergenic	L1MD|LINE|L1	-39254	NM_008361	16176	Mm.222830	NM_008361	ENSMUSG00000027398	Il1b	IL-1beta|Il-1b	interleukin 1 beta	protein-coding
mm_137301.1	chr17	24850655	24850683	+	1	NA	promoter-TSS (NM_023480)	promoter-TSS (NM_023480)	2	NM_001159626	14651	Mm.43784	NM_024284	ENSMUSG00000024158	Hagh	BC019817|Glo-2|Glo2|Rsp29	hydroxyacyl glutathione hydrolase	protein-coding
mm_87808.1	chr10	60301761	60301769	+	1	NA	TTS (NM_001252635)	TTS (NM_001252635)	17304	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_112842.1	chr13	20831106	20831116	+	1	NA	intron (NM_012054, intron 2 of 20)	MER57D|LTR|ERV1	36998	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_47494.1	chr5	124010713	124010718	-	1	NA	exon (NM_177876, exon 2 of 4)	exon (NM_177876, exon 2 of 4)	13863	NR_105999	102465625		NR_105999	ENSMUSG00000098454	Mir7032	Gm27309|mmu-mir-7032	microRNA 7032	ncRNA
mm_90728.1	chr10	5194860	5194871	-	1	NA	promoter-TSS (NM_001079686)	promoter-TSS (NM_001079686)	-158	NM_001079686	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_39171.1	chr4	155697030	155697042	-	1	NA	TTS (NM_178699)	TTS (NM_178699)	2694	NM_178699	230991	Mm.29083	NM_178699	ENSMUSG00000074738	Fndc10	B930041F14Rik|MNCb-3966	fibronectin type III domain containing 10	protein-coding
mm_31355.1	chr4	47207582	47207595	+	1	NA	promoter-TSS (NM_009928)	promoter-TSS (NM_009928)	-424	NM_009928	12819	Mm.233547	NM_009928	ENSMUSG00000028339	Col15a1	-	collagen, type XV, alpha 1	protein-coding
mm_164057.1	chr14	106217847	106217862	+	1	NA	Intergenic	RLTR9A2|LTR|ERVK	111656	NR_073203	212085	Mm.78128	NM_198601	ENSMUSG00000022113	Trim52	4921513B05Rik	tripartite motif-containing 52	protein-coding
mm_18772.1	chr2	73486457	73486461	-	1	NA	promoter-TSS (NM_001289723)	promoter-TSS (NM_001289723)	-706	NM_001289723	215280	Mm.223504	NM_153138	ENSMUSG00000075284	Wipf1	AI115543|D2Ertd120e|WIP|Waspip	WAS/WASL interacting protein family, member 1	protein-coding
mm_849.1	chr1	52008665	52008678	+	1	NA	5' UTR (NM_011487, exon 1 of 24)	5' UTR (NM_011487, exon 1 of 24)	431	NM_011487	20849	Mm.1550	NM_011487	ENSMUSG00000062939	Stat4	-	signal transducer and activator of transcription 4	protein-coding
mm_41595.1	chr5	95958717	95958738	+	1	NA	exon (NM_018866, exon 2 of 4)	exon (NM_018866, exon 2 of 4)	1788	NM_018866	55985	Mm.10116	NM_018866	ENSMUSG00000023078	Cxcl13	4631412M08Rik|ANGIE2|Angie|BCA-1|BLC|BLR1L|Scyb13	chemokine (C-X-C motif) ligand 13	protein-coding
mm_23830.1	chr3	81208994	81209001	+	1	NA	intron (NM_019971, intron 4 of 5)	intron (NM_019971, intron 4 of 5)	172581	NM_019971	54635	Mm.331089	NM_019971	ENSMUSG00000028019	Pdgfc	1110064L01Rik|AI647969|PDGF-C	platelet-derived growth factor, C polypeptide	protein-coding
mm_96021.1	chr11	59543356	59543364	+	1	NA	exon (NM_145827, exon 2 of 10)	exon (NM_145827, exon 2 of 10)	674	NM_145827	216799	Mm.54174	NM_145827	ENSMUSG00000032691	Nlrp3	AGTAVPRL|AII/AVP|Cias1|FCAS|FCU|MWS|Mmig1|NALP3|Pypaf1	NLR family, pyrin domain containing 3	protein-coding
mm_133845.1	chr16	96200667	96200706	+	1	NA	5' UTR (NM_015825, exon 1 of 8)	5' UTR (NM_015825, exon 1 of 8)	216	NM_015825	50795	Mm.28638	NM_015825	ENSMUSG00000040666	Sh3bgr	5430437A18Rik	SH3-binding domain glutamic acid-rich protein	protein-coding
mm_105171.1	chr11	101784461	101784481	-	1	NA	intron (NM_008815, intron 2 of 12)	G-rich|Low_complexity|Low_complexity	839	NM_008815	18612	Mm.5025	NM_008815	ENSMUSG00000017724	Etv4	AW414408|Pea-3|Pea3	ets variant 4	protein-coding
mm_80554.1	chr9	83100656	83100677	+	1	NA	Intergenic	RLTR31A_Mm|LTR|ERVK	45941	NM_175074	94353	Mm.244426	NM_026122	ENSMUSG00000066456	Hmgn3	1110002A15Rik|6330514M13Rik|BB071015|TRIP7	high mobility group nucleosomal binding domain 3	protein-coding
mm_72743.1	chr8	85087178	85087204	+	1	NA	exon (NM_010764, exon 6 of 24)	exon (NM_010764, exon 6 of 24)	3922	NM_010764	17159	Mm.4219	NM_010764	ENSMUSG00000005142	Man2b1	AW107687|LAMAN	mannosidase 2, alpha B1	protein-coding
mm_104279.1	chr11	89733681	89733708	-	1	NA	Intergenic	Intergenic	-36758	NM_001327810	382543	Mm.60997	NM_172534	ENSMUSG00000047773	Ankfn1	4932411E22Rik|Gm1175|nmf9	ankyrin-repeat and fibronectin type III domain containing 1	protein-coding
mm_25652.1	chr3	121457333	121457352	+	1	NA	exon (NM_028044, exon 7 of 7)	exon (NM_028044, exon 7 of 7)	30801	NM_028044	71994	Mm.275555	NM_028044	ENSMUSG00000053931	Cnn3	1600014M03Rik|C85854|Calpo3	calponin 3, acidic	protein-coding
mm_25423.1	chr3	107873899	107873904	+	1	NA	Intergenic	Intergenic	-3329	NM_133867	99662	Mm.108491	NM_133867	ENSMUSG00000040600	Eps8l3	AI504489|Eps8r3	EPS8-like 3	protein-coding
mm_154648.1	chrX	7794391	7794414	+	1	NA	intron (NM_207670, intron 4 of 24)	intron (NM_207670, intron 4 of 24)	4409	NM_207670	54645	Mm.194811	NM_207670	ENSMUSG00000031153	Gripap1	AI854681|DXImx47e|GRASP-1|Sfc10|mKIAA1167	GRIP1 associated protein 1	protein-coding
mm_41587.1	chr5	93267548	93267556	+	1	NA	promoter-TSS (NM_007635)	promoter-TSS (NM_007635)	-21	NM_007635	12452	Mm.3527	NM_007635	ENSMUSG00000029385	Ccng2	-	cyclin G2	protein-coding
mm_77328.1	chr8	119428929	119428937	-	1	NA	Intergenic	Intergenic	-8229	NM_027950	71839	Mm.272357	NM_027950	ENSMUSG00000074063	Osgin1	1700012B18Rik|Okl38	oxidative stress induced growth inhibitor 1	protein-coding
mm_16340.1	chr2	174341812	174341868	+	1	NA	non-coding (NR_003258, exon 6 of 13)	non-coding (NR_003258, exon 6 of 13)	11751	NM_001077510	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_156329.1	chrX	138936324	138936329	+	1	NA	intron (NM_013724, intron 2 of 27)	intron (NM_013724, intron 2 of 27)	21896	NM_013724	27206	Mm.482319	NM_013724	ENSMUSG00000052854	Nrk	AA407323|AA409510|AI225895|AV168563|AW538185|Nesk	Nik related kinase	protein-coding
mm_61413.1	chr7	73558828	73558884	+	1	NA	promoter-TSS (NR_037569)	promoter-TSS (NR_037569)	-461	NR_037569	69170	Mm.34539	NR_037569	ENSMUSG00000101970	1810026B05Rik	-	RIKEN cDNA 1810026B05 gene	ncRNA
mm_26732.1	chr3	5576095	5576110	-	1	NA	5' UTR (NM_008994, exon 1 of 6)	5' UTR (NM_008994, exon 1 of 6)	146	NM_001163301	19302	Mm.132336	NM_008994	ENSMUSG00000040374	Pex2	D3Ertd138e|PAF-1|PMP35|Pxmp3	peroxisomal biogenesis factor 2	protein-coding
mm_135624.1	chr16	52274169	52274176	-	1	NA	exon (NM_001331110, exon 10 of 15)	exon (NM_001331110, exon 10 of 15)	178909	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_89055.1	chr10	82881749	82881781	+	1	NA	exon (NM_001042523, exon 8 of 15)	exon (NM_001042523, exon 8 of 15)	15139	NM_025499	66341	Mm.443284	NM_025499	ENSMUSG00000109864	Eid3	1700027M21Rik|NS4EB	EP300 interacting inhibitor of differentiation 3	protein-coding
mm_128227.1	chr15	36555557	36555579	-	1	NA	promoter-TSS (NM_025712)	promoter-TSS (NM_025712)	0	NM_001347022	66696	Mm.253627	NM_025712	ENSMUSG00000013611	Snx31	4631426E05Rik	sorting nexin 31	protein-coding
mm_121927.1	chr14	23729388	23729394	-	1	NA	intron (NM_001253374, intron 1 of 28)	intron (NM_001253374, intron 1 of 28)	274814	NM_001253375	16531	Mm.343607	NM_010610	ENSMUSG00000063142	Kcnma1	5730414M22Rik|BKCa|MaxiK|Slo|Slo1|mSlo|mSlo1	potassium large conductance calcium-activated channel, subfamily M, alpha member 1	protein-coding
mm_64551.1	chr7	144422973	144422995	+	1	NA	TTS (NM_001081370)	TTS (NM_001081370)	20449	NR_037302	100499519		NR_037302	ENSMUSG00000093912	Mir3470b	mmu-mir-3470b	microRNA 3470b	ncRNA
mm_32426.1	chr4	107127946	107127949	+	1	NA	Intergenic	Intergenic	31056	NM_172873	242603	Mm.257231	NM_172873	ENSMUSG00000047636	Cdcp2	D030010E02Rik	CUB domain containing protein 2	protein-coding
mm_33103.1	chr4	124703717	124703726	+	1	NA	intron (NM_010213, intron 1 of 5)	intron (NM_010213, intron 1 of 5)	3022	NM_010213	14201	Mm.331856	NM_010213	ENSMUSG00000032643	Fhl3	SLIM2	four and a half LIM domains 3	protein-coding
mm_781.1	chr1	44789398	44789400	+	1	NA	intron (NM_028450, intron 10 of 10)	intron (NM_028450, intron 10 of 10)	-44450	NR_040602	75066	Mm.416932	NR_040602	ENSMUSG00000101701	4930521E06Rik	-	RIKEN cDNA 4930521E06 gene	ncRNA
mm_102731.1	chr11	67244704	67244726	-	1	NA	exon (NM_010855, exon 12 of 40)	exon (NM_010855, exon 12 of 40)	6903	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_65828.1	chr7	29179320	29179343	-	1	NA	intron (NM_026545, intron 1 of 6)	intron (NM_026545, intron 1 of 6)	1342	NM_026545	57296	Mm.273152	NM_026545	ENSMUSG00000030591	Psmd8	6720456J22Rik|AA407360|AL033291|AL033322|AL033323|C76433	proteasome (prosome, macropain) 26S subunit, non-ATPase, 8	protein-coding
mm_85714.1	chr9	108208790	108208803	-	1	NA	exon (NM_001276486, exon 4 of 4)	exon (NM_001276486, exon 4 of 4)	-18413	NM_007567	12217	Mm.20425	NM_007567	ENSMUSG00000032589	Bsn	-	bassoon	protein-coding
mm_10418.1	chr2	13580176	13580196	+	1	NA	exon (NM_011701, exon 6 of 9)	exon (NM_011701, exon 6 of 9)	5875	NM_011701	22352	Mm.268000	NM_011701	ENSMUSG00000026728	Vim	-	vimentin	protein-coding
mm_111226.1	chr12	84756530	84756597	-	1	NA	3' UTR (NM_023409, exon 4 of 4)	3' UTR (NM_023409, exon 4 of 4)	16549	NM_023409	67963	Mm.282556	NM_023409	ENSMUSG00000021242	Npc2	2700012J19Rik|AA408070|AU045843|HE1	Niemann-Pick type C2	protein-coding
mm_138267.1	chr17	34604185	34604195	+	1	NA	promoter-TSS (NM_019403)	promoter-TSS (NM_019403)	-629	NM_019403	54197	Mm.274542	NM_019403	ENSMUSG00000015478	Rnf5	2410131O05Rik|AA407576|NG2	ring finger protein 5	protein-coding
mm_49117.1	chr6	8509802	8509815	+	1	NA	promoter-TSS (NR_040452)	promoter-TSS (NR_040452)	208	NM_133236	170772	Mm.210787	NM_133236	ENSMUSG00000029638	Glcci1	2310047L21Rik|A130036A18Rik|Fam117c|Gig18|Tssn1	glucocorticoid induced transcript 1	protein-coding
mm_4223.1	chr1	171331363	171331374	+	1	NA	intron (NM_001128609, intron 2 of 5)	intron (NM_001128609, intron 2 of 5)	2223	NM_011615	21945	Mm.270139	NM_011615	ENSMUSG00000013973	Dedd	CASP8IP1|DEFT|Dedpro1|FLDED1|KE05	death effector domain-containing	protein-coding
mm_87448.1	chr10	51481786	51481798	+	1	NA	exon (NM_008147, exon 4 of 9)	exon (NM_008147, exon 4 of 9)	1180	NM_001291892	14727	Mm.439661	NM_008147	ENSMUSG00000062593	Lilr4b	Gp49a|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4B	protein-coding
mm_21302.1	chr2	157058729	157058753	-	1	NA	intron (NM_001164663, intron 2 of 14)	intron (NM_001164663, intron 2 of 14)	20524	NM_001164663	320706	Mm.79466	NM_001164663	ENSMUSG00000055485	Soga1	9830001H06Rik|AI426038|D430036N24Rik|Soga	suppressor of glucose, autophagy associated 1	protein-coding
mm_127919.1	chr15	9572552	9572566	-	1	NA	Intergenic	Intergenic	-42683	NM_008372	16197	Mm.389	NM_008372	ENSMUSG00000003882	Il7r	CD127|IL-7Ralpha	interleukin 7 receptor	protein-coding
mm_160182.1	chr7	46713504	46713504	-	1	NA	intron (NM_011315, intron 2 of 3)	intron (NM_011315, intron 2 of 3)	2172	NM_011315	20210	Mm.14277	NM_011315	ENSMUSG00000040026	Saa3	AV098916|Saa-3|l7R3	serum amyloid A 3	protein-coding
mm_106838.1	chr12	8006652	8006660	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	28979	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_53025.1	chr6	124474858	124474868	+	1	NA	Intergenic	RLTR16C_MM|LTR|ERVK	-10079	NM_153508	232370	Mm.193701	NM_153508	ENSMUSG00000008153	Clstn3	CSTN3|Cs3|Cst-3|alc-beta	calsyntenin 3	protein-coding
mm_171528.1	chr4	146611068	146611068	+	1	NA	Intergenic	Intergenic	-64195	NR_045468	67524	Mm.444300	NR_045468	ENSMUSG00000086046	1700095A21Rik	-	RIKEN cDNA 1700095A21 gene	ncRNA
mm_34043.1	chr4	138216466	138216503	+	1	NA	promoter-TSS (NM_001122896)	promoter-TSS (NM_001122896)	-128	NM_001122896	15441	Mm.348429	NM_010470	ENSMUSG00000028759	Hp1bp3	Hp1bp74	heterochromatin protein 1, binding protein 3	protein-coding
mm_151763.1	chr19	5158600	5158603	-	1	NA	intron (NM_153129, intron 4 of 23)	RMER4B|LTR|ERVK	-40193	NM_008451	16594	Mm.271648	NM_008451	ENSMUSG00000024862	Klc2	8030455F02Rik|AW212649|KLC 2|KLC-2	kinesin light chain 2	protein-coding
mm_88484.1	chr10	77630153	77630158	+	1	NA	intron (NM_019803, intron 1 of 5)	intron (NM_019803, intron 1 of 5)	7834	NM_019803	22213	Mm.458125	NM_019803	ENSMUSG00000009293	Ube2g2	1110003O05Rik|D10Xrf369|UBC7|Ubc7p	ubiquitin-conjugating enzyme E2G 2	protein-coding
mm_44209.1	chr5	4104484	4104492	-	1	NA	5' UTR (NM_020010, exon 1 of 10)	5' UTR (NM_020010, exon 1 of 10)	209	NM_020010	13121	Mm.140158	NM_020010	ENSMUSG00000001467	Cyp51	AI426508|CYPLI|Cyp51a1|Ldm|P450-14DM|P450LI	cytochrome P450, family 51	protein-coding
mm_91990.1	chr10	61979145	61979161	-	1	NA	promoter-TSS (NM_007731)	promoter-TSS (NM_007731)	-45	NM_007731	12817	Mm.300931	NM_007731	ENSMUSG00000058806	Col13a1	-	collagen, type XIII, alpha 1	protein-coding
mm_66828.1	chr7	48843642	48843662	-	1	NA	promoter-TSS (NM_013808)	promoter-TSS (NM_013808)	19	NM_013808	13009	Mm.17235	NM_013808	ENSMUSG00000030470	Csrp3	CRP3|MLP|MMLP	cysteine and glycine-rich protein 3	protein-coding
mm_71789.1	chr8	66704549	66704593	+	1	NA	exon (NM_010934, exon 2 of 3)	exon (NM_010934, exon 2 of 3)	7149	NM_010934	18166	Mm.5112	NM_010934	ENSMUSG00000036437	Npy1r	Npyr|Y1-R	neuropeptide Y receptor Y1	protein-coding
mm_48490.1	chr5	142564495	142564499	-	1	NA	3' UTR (NM_175217, exon 7 of 7)	3' UTR (NM_175217, exon 7 of 7)	-13399	NM_001289588	231858	Mm.33766	NM_178702	ENSMUSG00000029576	Radil	AI536456|D930005D10Rik	Ras association and DIL domains	protein-coding
mm_31114.1	chr4	42949862	42949923	+	1	NA	Intergenic	CpG	-3202	NM_019874	56323	Mm.20437	NM_019874	ENSMUSG00000036052	Dnajb5	1110058L06Rik|AI462558|Hsc40|Hsp40-3	DnaJ heat shock protein family (Hsp40) member B5	protein-coding
mm_135168.1	chr16	35928884	35928903	-	1	NA	3' UTR (NM_001013371, exon 5 of 5)	3' UTR (NM_001013371, exon 5 of 5)	-9577	NM_030253	80285	Mm.49074	NM_030253	ENSMUSG00000022906	Parp9	ARTD9|AW214463|BC003281|Bagl|Bal|PARP-9	poly (ADP-ribose) polymerase family, member 9	protein-coding
mm_115470.1	chr13	119462836	119462856	+	1	NA	promoter-TSS (NM_026127)	promoter-TSS (NM_026127)	87	NM_026127	67392	Mm.390641	NM_026127	ENSMUSG00000062822	4833420G17Rik	2210017J06Rik|5730533D17Rik|AW107518|C85193	RIKEN cDNA 4833420G17 gene	protein-coding
mm_37982.1	chr4	133620689	133620710	-	1	NA	intron (NM_001017968, intron 2 of 7)	intron (NM_001017968, intron 2 of 7)	12730	NM_001017968	503610	Mm.331948	NM_001017968	ENSMUSG00000037553	Zdhhc18	-	zinc finger, DHHC domain containing 18	protein-coding
mm_128403.1	chr15	44428304	44428337	-	1	NA	promoter-TSS (NM_026149)	promoter-TSS (NM_026149)	-13	NM_026149	67429	Mm.490404	NM_026149	ENSMUSG00000038736	Nudcd1	4921532K09Rik|AA407246|AW260430|AW556235|CML66-L|Cml66	NudC domain containing 1	protein-coding
mm_113785.1	chr13	45507599	45507650	+	1	NA	5' UTR (NM_025508, exon 1 of 9)	5' UTR (NM_025508, exon 1 of 9)	180	NM_025508	66355	Mm.290802	NM_025508	ENSMUSG00000000253	Gmpr	2310004P21Rik|AV028449|GMPR 1	guanosine monophosphate reductase	protein-coding
mm_71694.1	chr8	61479415	61479422	+	1	NA	Intergenic	Intergenic	-8316	NM_145595	234309	Mm.29059	NM_145595	ENSMUSG00000031641	Cbr4	A730083J17Rik|BC009118	carbonyl reductase 4	protein-coding
mm_71107.1	chr8	35602156	35602159	+	1	NA	intron (NM_001081279, intron 1 of 2)	intron (NM_001081279, intron 1 of 2)	-13137	NR_040376	100504714	Mm.381744	NR_040376	ENSMUSG00000097357	Gm16793	-	predicted gene, 16793	ncRNA
mm_96009.1	chr11	59542667	59542677	+	1	NA	promoter-TSS (NM_145827)	promoter-TSS (NM_145827)	-14	NM_145827	216799	Mm.54174	NM_145827	ENSMUSG00000032691	Nlrp3	AGTAVPRL|AII/AVP|Cias1|FCAS|FCU|MWS|Mmig1|NALP3|Pypaf1	NLR family, pyrin domain containing 3	protein-coding
mm_126981.1	chr15	93453574	93453589	+	1	NA	intron (NM_175363, intron 5 of 8)	URR1A|DNA|hAT-Charlie	55117	NM_001285863	223828	Mm.74208	NM_146062	ENSMUSG00000036167	Pphln1	CR|HSPC206|HSPC232	periphilin 1	protein-coding
mm_107527.1	chr12	40472868	40472871	+	1	NA	intron (NM_172803, intron 1 of 52)	ORR1B2|LTR|ERVL-MaLR	26816	NM_172803	238130	Mm.341423	NM_172803	ENSMUSG00000035954	Dock4	5330406C03|6330411N01Rik|AF263288|C030023J22|mKIAA0716	dedicator of cytokinesis 4	protein-coding
mm_170677.1	chr2	121956410	121956410	+	1	NA	promoter-TSS (NM_008545)	promoter-TSS (NM_008545)	-318	NM_008545	17147	Mm.389349	NM_008545	ENSMUSG00000074881	Mageb3	Mage-b3|Mage-ps1|Mage-rs3|Smage3	melanoma antigen, family B, 3	protein-coding
mm_54606.1	chr6	38341201	38341205	-	1	NA	intron (NM_001347122, intron 1 of 12)	MT2B|LTR|ERVL	13400	NM_028864	78781	Mm.25243	NM_028421	ENSMUSG00000029826	Zc3hav1	1200014N16Rik|2900058M19Rik|9130009D18Rik|9830115L13Rik|ARTD13|D6Bwg1452e|ZAP	zinc finger CCCH type, antiviral 1	protein-coding
mm_107975.1	chr12	72939909	72939929	+	1	NA	promoter-TSS (NM_011384)	promoter-TSS (NM_011384)	37	NM_011384	20476	Mm.57138	NM_011384	ENSMUSG00000021099	Six6	Optx2|Six9	sine oculis-related homeobox 6	protein-coding
mm_8129.1	chr1	136230335	136230355	-	1	NA	intron (NM_028872, intron 1 of 9)	intron (NM_028872, intron 1 of 9)	3935	NM_028872	67313	Mm.36763	NM_028872	ENSMUSG00000041605	5730559C18Rik	1700034M08Rik|4933426C09Rik|AI586180|D1Mgi54	RIKEN cDNA 5730559C18 gene	protein-coding
mm_36031.1	chr4	57143106	57143161	-	1	NA	promoter-TSS (NM_019427)	promoter-TSS (NM_019427)	23	NM_019427	54357	Mm.28217	NM_019427	ENSMUSG00000028434	Epb41l4b	6430543G08Rik|AA589614|AU021054|BB007528|D4Ertd346e|Ehm2|Epb4.1l4b|Lulu2	erythrocyte membrane protein band 4.1 like 4b	protein-coding
mm_4824.1	chr1	185454981	185454995	+	1	NA	5' UTR (NM_001033286, exon 1 of 4)	5' UTR (NM_001033286, exon 1 of 4)	140	NM_001033286	226781	Mm.227117	NM_001033286	ENSMUSG00000026614	Slc30a10	E130106K10Rik|Gm212	solute carrier family 30, member 10	protein-coding
mm_145161.1	chr18	46601976	46601990	+	1	NA	intron (NM_010120, intron 2 of 2)	intron (NM_010120, intron 2 of 2)	4279	NM_010120	13664	Mm.262037	NM_010120	ENSMUSG00000057561	Eif1a	C76390|Ef1a|Eftu|Eif4c|eIF-1A|eIF-4C	eukaryotic translation initiation factor 1A	protein-coding
mm_163122.1	chr11	76902021	76902037	+	1	NA	Intergenic	Intergenic	-2516	NM_025655	66601	Mm.25138	NM_025655	ENSMUSG00000020839	Tmigd1	2010002A20Rik|Tmigd	transmembrane and immunoglobulin domain containing 1	protein-coding
mm_26086.1	chr3	136692324	136692333	+	1	NA	intron (NM_008913, intron 1 of 13)	intron (NM_008913, intron 1 of 13)	22262	NM_001293622	19055	Mm.331389	NM_008913	ENSMUSG00000028161	Ppp3ca	2900074D19Rik|CN|Caln|Calna|CnA	protein phosphatase 3, catalytic subunit, alpha isoform	protein-coding
mm_128472.1	chr15	50882811	50882822	-	1	NA	intron (NM_032000, intron 1 of 5)	intron (NM_032000, intron 1 of 5)	6233	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_112009.1	chr12	110978621	110978643	-	1	NA	intron (NM_175207, intron 1 of 2)	intron (NM_175207, intron 1 of 2)	389	NM_175207	74251	Mm.250989	NM_175207	ENSMUSG00000037904	Ankrd9	2500003O20Rik	ankyrin repeat domain 9	protein-coding
mm_17609.1	chr2	30920377	30920379	-	1	NA	Intergenic	Intergenic	-17081	NM_022415	64292	Mm.28768	NM_022415	ENSMUSG00000050737	Ptges	2410099E23Rik|D2Ertd369e|Pges|mPGES|mPGES-1	prostaglandin E synthase	protein-coding
mm_92939.1	chr10	84554352	84554353	-	1	NA	Intergenic	Lx8|LINE|L1	-1014	NR_040658	442847	Mm.128292	NR_040658	ENSMUSG00000097076	Platr7	C330046G13Rik	pluripotency associated transcript 7	ncRNA
mm_112795.1	chr13	20406343	20406358	+	1	NA	intron (NM_080288, intron 15 of 21)	(T)n|Simple_repeat|Simple_repeat	-66640	NM_198093	140580	Mm.342392	NM_080288	ENSMUSG00000041112	Elmo1	6330578D22Rik|C230095H21Rik|CED-12	engulfment and cell motility 1	protein-coding
mm_70834.1	chr8	23153428	23153436	+	1	NA	5' UTR (NM_029002, exon 1 of 3)	5' UTR (NM_029002, exon 1 of 3)	161	NM_029002	74561	Mm.290028	NM_029002	ENSMUSG00000063672	Nkx6-3	9130417I07Rik|Nkx6.3	NK6 homeobox 3	protein-coding
mm_144357.1	chr18	17019063	17019093	+	1	NA	Intergenic	RMER17B|LTR|ERVK	-16430	NR_130158	75433	Mm.60907	NR_130158	ENSMUSG00000087170	1700001G01Rik	-	RIKEN cDNA 1700001G01 gene	ncRNA
mm_8196.1	chr1	138119806	138119822	-	1	NA	intron (NM_001111316, intron 4 of 31)	intron (NM_001111316, intron 4 of 31)	55312	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_95525.1	chr11	52232029	52232041	+	1	NA	promoter-TSS (NM_011543)	promoter-TSS (NM_011543)	40	NM_011543	21402	Mm.42944	NM_011543	ENSMUSG00000036309	Skp1a	15kDa|2610043E24Rik|2610206H23Rik|EMC19|OCP-II|OCP2|SKP1|Tceb1l|p19A|p19Skp1	S-phase kinase-associated protein 1A	protein-coding
mm_103684.1	chr11	79482339	79482347	-	1	NA	non-coding (NR_045305, exon 4 of 4)	non-coding (NR_045305, exon 4 of 4)	1688	NR_045305	104522	Mm.436987	NR_045305	ENSMUSG00000091523	AU040972	AU040954	expressed sequence AU040972	ncRNA
mm_16964.1	chr2	17689772	17689784	-	1	NA	intron (NM_028757, intron 2 of 6)	IMPB_01|Satellite|Satellite	41290	NM_028757	74103	Mm.120298	NM_028757	ENSMUSG00000053702	Nebl	1200007O21Rik|A630080F05Rik|BB140644|D830029A09Rik|Lnebl	nebulette	protein-coding
mm_50029.1	chr6	41130087	41130101	+	1	NA	Intergenic	Intergenic	-94585	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_134510.1	chr16	19067116	19067165	-	1	NA	Intergenic	Intergenic	190390	NM_010435	15260	Mm.15694	NM_010435	ENSMUSG00000022702	Hira	AA138857|D16Ertd95e|Gm15797|N28177|OTTMUSG00000026264|Tuple1	histone cell cycle regulator	protein-coding
mm_34736.1	chr4	152199806	152199821	+	1	NA	promoter-TSS (NM_001146058)	promoter-TSS (NM_001146058)	-31	NM_001146058	70025	Mm.296191	NM_133348	ENSMUSG00000028937	Acot7	2410041A17Rik|Ach1|Act|Bach|CTE-IIa|Cte-II|Lach1	acyl-CoA thioesterase 7	protein-coding
mm_170256.1	chr18	12898396	12898415	+	1	NA	intron (NM_207530, intron 11 of 27)	intron (NM_207530, intron 11 of 27)	-18426	NM_001252489	64291	Mm.259470	NM_020573	ENSMUSG00000044252	Osbpl1a	G430090F17Rik|Gm753|ORP-1|Osbpl1b	oxysterol binding protein-like 1A	protein-coding
mm_123076.1	chr14	55722193	55722211	-	1	NA	promoter-TSS (NM_019519)	promoter-TSS (NM_019519)	-26	NM_019519	56187	Mm.87216	NM_019519	ENSMUSG00000040472	Rabggta	gm	Rab geranylgeranyl transferase, a subunit	protein-coding
mm_56645.1	chr6	113377377	113377396	-	1	NA	promoter-TSS (NM_026552)	promoter-TSS (NM_026552)	134	NM_133932	101206	Mm.266811	NM_133932	ENSMUSG00000048930	Tada3	1110004B19Rik|ADA3|AI987856|Tada3l	transcriptional adaptor 3	protein-coding
mm_107312.1	chr12	31264988	31265002	+	1	NA	promoter-TSS (NM_008482)	promoter-TSS (NM_008482)	-299	NM_008482	16777	Mm.172674	NM_008482	ENSMUSG00000002900	Lamb1	C77966|C80098|C81607|D130003D08Rik|Lamb-1|Lamb1-1	laminin B1	protein-coding
mm_55408.1	chr6	61180177	61180210	-	1	NA	promoter-TSS (NM_183310)	promoter-TSS (NM_183310)	-132	NM_001164316	232035	Mm.150324	NM_183310	ENSMUSG00000039578	Ccser1	6230405M12Rik|C130092O11Rik|Fam190a	coiled-coil serine rich 1	protein-coding
mm_134702.1	chr16	22811400	22811413	-	1	NA	promoter-TSS (NM_009967)	promoter-TSS (NM_009967)	4	NM_009967	12970	Mm.6253	NM_009967	ENSMUSG00000033501	Crygs	AI327013|Opj|rncat	crystallin, gamma S	protein-coding
mm_91139.1	chr10	19850883	19850895	-	1	NA	exon (NM_029529, exon 1 of 2)	exon (NM_029529, exon 1 of 2)	570	NM_029529	76157	Mm.74324	NM_029529	ENSMUSG00000050473	Slc35d3	6230421J19Rik|Frcl1	solute carrier family 35, member D3	protein-coding
mm_121821.1	chr14	20471445	20471461	-	1	NA	exon (NM_001110794, exon 3 of 13)	exon (NM_001110794, exon 3 of 13)	8680	NM_001110794	11750	Mm.280231	NM_009674	ENSMUSG00000021814	Anxa7	AI265384|AI316497|Anx7|synexin	annexin A7	protein-coding
mm_153164.1	chr19	34493197	34493211	-	1	NA	3' UTR (NM_021460, exon 10 of 10)	3' UTR (NM_021460, exon 10 of 10)	-18069	NM_009890	12642	Mm.30824	NM_009890	ENSMUSG00000050370	Ch25h	AI462618|m25OH	cholesterol 25-hydroxylase	protein-coding
mm_128703.1	chr15	63611213	63611224	-	1	NA	Intergenic	Intergenic	-131610	NR_045279	432958	Mm.255105	NR_045279		Gm20740	-	predicted gene, 20740	ncRNA
mm_168710.1	chr11	99932509	99932519	+	1	NA	Intergenic	Intergenic	-3777	NM_001025244	432602	Mm.246878	NM_001025244	ENSMUSG00000051481	Krtap31-2	OTTMUSG00000002177	keratin associated protein 31-2	protein-coding
mm_89494.1	chr10	93833819	93833830	+	1	NA	intron (NM_001206851, intron 1 of 6)	CpG	2269	NM_001206851	327799	Mm.491598	NM_183199	ENSMUSG00000020020	Usp44	E430004F17Rik	ubiquitin specific peptidase 44	protein-coding
mm_29142.1	chr3	105928761	105928780	-	1	NA	exon (NM_001033780, exon 2 of 6)	exon (NM_001033780, exon 2 of 6)	3894	NM_001033780	433638	Mm.239081	NM_001033780	ENSMUSG00000074342	I830077J02Rik	-	RIKEN cDNA I830077J02 gene	protein-coding
mm_70690.1	chr8	15011442	15011457	+	1	NA	intron (NM_029116, intron 1 of 1)	CpG	424	NM_029116	74901	Mm.46675	NM_029116	ENSMUSG00000055675	Kbtbd11	2900016B01Rik|4930465M17Rik|mKIAA0711	kelch repeat and BTB (POZ) domain containing 11	protein-coding
mm_92112.1	chr10	63203867	63203877	-	1	NA	promoter-TSS (NM_182992)	promoter-TSS (NM_182992)	80	NM_182992	68802	Mm.259767	NM_182992	ENSMUSG00000020067	Mypn	1110056A04Rik|9830112J03|AI853556|mKIAA4170	myopalladin	protein-coding
mm_64216.1	chr7	141539771	141539795	+	1	NA	promoter-TSS (NM_001142681)	promoter-TSS (NM_001142681)	74	NM_026522	68038	Mm.245355	NM_026522	ENSMUSG00000025512	Chid1	3110023E09Rik|AI841869	chitinase domain containing 1	protein-coding
mm_38263.1	chr4	136880409	136880422	-	1	NA	exon (NM_009777, exon 3 of 3)	exon (NM_009777, exon 3 of 3)	5762	NM_009777	12260	Mm.2570	NM_009777	ENSMUSG00000036905	C1qb	-	complement component 1, q subcomponent, beta polypeptide	protein-coding
mm_29109.1	chr3	104863819	104863828	-	1	NA	promoter-TSS (NM_001253703)	promoter-TSS (NM_001253703)	682	NM_009797	12340	Mm.19142	NM_009797	ENSMUSG00000070372	Capza1	CAPZ|CAZ1|Cappa1	capping protein (actin filament) muscle Z-line, alpha 1	protein-coding
mm_89090.1	chr10	84110058	84110062	+	1	NA	Intergenic	Intergenic	330411	NM_001004363	77976	Mm.25874	NM_001004363	ENSMUSG00000020032	Nuak1	AU014801|AW494241|B230104P22Rik|Omphk1	NUAK family, SNF1-like kinase, 1	protein-coding
mm_14142.1	chr2	126545609	126545619	+	1	NA	Intergenic	Intergenic	-7410	NM_011978	26458	Mm.290044	NM_011978	ENSMUSG00000027359	Slc27a2	ACSVL1|FATP2|VLCS|Vlac|Vlacs	solute carrier family 27 (fatty acid transporter), member 2	protein-coding
mm_134774.1	chr16	23973227	23973232	-	1	NA	intron (NM_009744, intron 4 of 9)	intron (NM_009744, intron 4 of 9)	15383	NM_009744	12053	Mm.347398	NM_009744	ENSMUSG00000022508	Bcl6	Bcl5	B cell leukemia/lymphoma 6	protein-coding
mm_159224.1	chr2	129800548	129800548	+	1	NA	promoter-TSS (NM_183262)	promoter-TSS (NM_183262)	31	NM_001038635	67333	Mm.389329	NM_183262	ENSMUSG00000037885	Stk35	1700054C12Rik|CLIK1|Stk35l1	serine/threonine kinase 35	protein-coding
mm_60352.1	chr7	44374306	44374316	+	1	NA	intron (NM_027049, intron 2 of 5)	intron (NM_027049, intron 2 of 5)	719	NM_027049	69349	Mm.358922	NM_027049	ENSMUSG00000008028	1700008O03Rik	-	RIKEN cDNA 1700008O03 gene	protein-coding
mm_8263.1	chr1	139255756	139255765	-	1	NA	intron (NM_133239, intron 5 of 11)	intron (NM_133239, intron 5 of 11)	121316	NM_133239	170788	Mm.95700	NM_133239	ENSMUSG00000063681	Crb1	7530426H14Rik|A930008G09Rik	crumbs family member 1, photoreceptor morphogenesis associated	protein-coding
mm_441.1	chr1	34849695	34849720	+	1	NA	promoter-TSS (NM_145516)	promoter-TSS (NM_145516)	-252	NM_175421	226971	Mm.292751	NM_145516	ENSMUSG00000026123	Plekhb2	2310009M15Rik|AU018239|Evt2|Phdc|evt-2	pleckstrin homology domain containing, family B (evectins) member 2	protein-coding
mm_25226.1	chr3	103860021	103860045	+	1	NA	promoter-TSS (NM_008979)	promoter-TSS (NM_008979)	238	NR_104070	19260	Mm.395	NM_008979	ENSMUSG00000027843	Ptpn22	70zpep|PEP|Ptpn8	protein tyrosine phosphatase, non-receptor type 22 (lymphoid)	protein-coding
mm_4061.1	chr1	165864630	165864634	+	1	NA	TTS (NM_198933)	TTS (NM_198933)	70316	NM_198933	18986	Mm.245261	NM_011137	ENSMUSG00000026565	Pou2f1	2810482H01Rik|NF-A1|Oct-1|Oct1|Otf-1|Otf1	POU domain, class 2, transcription factor 1	protein-coding
mm_93439.1	chr10	109790173	109790185	-	1	NA	intron (NM_001081035, intron 12 of 38)	intron (NM_001081035, intron 12 of 38)	210040	NM_001081035	260315	Mm.225050	NM_177797	ENSMUSG00000020181	Nav3	4732483H20Rik|9630020C08Rik|POMFIL1|Pomfil1p|mKIAA0938|unc53H3	neuron navigator 3	protein-coding
mm_90144.1	chr10	118141524	118141528	+	1	NA	promoter-TSS (NM_010785)	promoter-TSS (NM_010785)	-261	NM_001162904	17245	Mm.101191	NM_010785	ENSMUSG00000020212	Mdm1	Arrd2|Mdm-1	transformed mouse 3T3 cell double minute 1	protein-coding
mm_121845.1	chr14	20618340	20618365	-	1	NA	promoter-TSS (NM_030180)	promoter-TSS (NM_030180)	2	NM_030180	78787	Mm.301173	NM_030180	ENSMUSG00000034235	Usp54	4930429G18Rik|AI115571|C030002J06Rik	ubiquitin specific peptidase 54	protein-coding
mm_130533.1	chr15	98934448	98934505	-	1	NA	promoter-TSS (NM_011654)	promoter-TSS (NM_011654)	-86	NM_011654	22143	Mm.392113	NM_011654	ENSMUSG00000023004	Tuba1b	Tuba2	tubulin, alpha 1B	protein-coding
mm_31192.1	chr4	43578922	43578974	+	1	NA	promoter-TSS (NM_172692)	promoter-TSS (NM_172692)	-84	NM_172692	230101	Mm.229444	NM_172692	ENSMUSG00000028467	Gba2	F630034E04	glucosidase beta 2	protein-coding
mm_120235.1	chr14	62887251	62887265	+	1	NA	intron (NM_175546, intron 2 of 11)	intron (NM_175546, intron 2 of 11)	21716	NR_105860	102465311		NR_105860	ENSMUSG00000098858	Mir6541	Gm27311|mmu-mir-6541	microRNA 6541	ncRNA
mm_69380.1	chr7	131322053	131322069	-	1	NA	5' UTR (NM_008411, exon 1 of 9)	5' UTR (NM_008411, exon 1 of 9)	231	NM_008411	16433	Mm.142717	NM_008411	ENSMUSG00000040205	Cuzd1	Erg-1|Itmap1|Uo-44|Usg|Utczp	CUB and zona pellucida-like domains 1	protein-coding
mm_68496.1	chr7	111076385	111076398	-	1	NA	exon (NM_013507, exon 14 of 22)	exon (NM_013507, exon 14 of 22)	6639	NM_001040131	13690	Mm.185453	NM_013507	ENSMUSG00000005610	Eif4g2	DAP-5|E130105L11Rik|Nat1|Natm1|p97	eukaryotic translation initiation factor 4, gamma 2	protein-coding
mm_62571.1	chr7	104244787	104244791	+	1	NA	intron (NM_030684, intron 1 of 7)	intron (NM_030684, intron 1 of 7)	332	NM_030684	94094	Mm.326945	NM_030684	ENSMUSG00000056144	Trim34a	Trim34|Trim34-1	tripartite motif-containing 34A	protein-coding
mm_108565.1	chr12	84773252	84773261	+	1	NA	promoter-TSS (NM_028863)	promoter-TSS (NM_028863)	-14	NM_028863	74316	Mm.25719	NM_028863	ENSMUSG00000021241	Isca2	0710001C05Rik|5730594E03Rik|Hbld1	iron-sulfur cluster assembly 2	protein-coding
mm_142591.1	chr17	46752075	46752090	-	1	NA	exon (NM_001305988, exon 1 of 5)	exon (NM_001305988, exon 1 of 5)	132	NM_001305989	72029	Mm.240325	NM_028065	ENSMUSG00000023973	Cnpy3	1600025D17Rik|2410050O22Rik|AI413153|CAG4A|ERDA5|PRAT4A|Tnrc5	canopy FGF signaling regulator 3	protein-coding
mm_3388.1	chr1	140246050	140246061	+	1	NA	promoter-TSS (NM_001081027)	promoter-TSS (NM_001081027)	-202	NM_001081027	240776	Mm.483845	NM_001081027	ENSMUSG00000052726	Kcnt2	E330038N15Rik|Slick	potassium channel, subfamily T, member 2	protein-coding
mm_136364.1	chr16	92793947	92793954	-	1	NA	intron (NM_001111022, intron 2 of 6)	intron (NM_001111022, intron 2 of 6)	32124	NM_001111021	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_3612.1	chr1	151947713	151947720	+	1	NA	intron (NM_197990, intron 3 of 5)	intron (NM_197990, intron 3 of 5)	142604	NM_197990	69399	Mm.278031	NM_197990	ENSMUSG00000032666	1700025G04Rik	2610510E02Rik|2900042O04Rik|ENSMUSG00000073540	RIKEN cDNA 1700025G04 gene	protein-coding
mm_83892.1	chr9	56027431	56027449	-	1	NA	promoter-TSS (NR_033529)	promoter-TSS (NR_033529)	-196	NR_033529	665005	Mm.384788	NR_033529		Gm7444	EG665005	ring finger protein 19A pseudogene	pseudo
mm_35954.1	chr4	53128115	53128134	-	1	NA	intron (NM_013454, intron 4 of 49)	intron (NM_013454, intron 4 of 49)	31771	NM_013454	11303	Mm.277376	NM_013454	ENSMUSG00000015243	Abca1	ABC-1|Abc1	ATP-binding cassette, sub-family A (ABC1), member 1	protein-coding
mm_14307.1	chr2	129129783	129129791	+	1	NA	promoter-TSS (NM_025395)	promoter-TSS (NM_025395)	87	NM_025395	66170	Mm.40621	NM_025395	ENSMUSG00000037938	Chchd5	1110027L01Rik|AW045710	coiled-coil-helix-coiled-coil-helix domain containing 5	protein-coding
mm_79601.1	chr9	58488569	58488578	+	1	NA	promoter-TSS (NM_176921)	promoter-TSS (NM_176921)	-30	NM_176921	319477	Mm.153674	NM_176921	ENSMUSG00000066607	6030419C18Rik	-	RIKEN cDNA 6030419C18 gene	protein-coding
mm_130713.1	chr15	101047363	101047376	-	1	NA	Intergenic	CpG	7030	NM_001214911	668225	Mm.385011	NM_001214911	ENSMUSG00000095440	Fignl2	EG668225	fidgetin-like 2	protein-coding
mm_26307.1	chr3	142512126	142512137	+	1	NA	intron (NM_153564, intron 10 of 10)	intron (NM_153564, intron 10 of 10)	15197	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_158645.1	chrX	155338476	155338486	-	1	NA	promoter-TSS (NM_016764)	promoter-TSS (NM_016764)	-21	NM_001313711	53381	Mm.247542	NM_016764	ENSMUSG00000025289	Prdx4	AOE372|Prx-iv|Prx4|TRANK	peroxiredoxin 4	protein-coding
mm_167892.1	chrX	64483166	64483169	+	1	NA	Intergenic	Intergenic	-206171	NM_178740	245446	Mm.101707	NM_178740	ENSMUSG00000046699	Slitrk4	6430513G13|D930039I09Rik	SLIT and NTRK-like family, member 4	protein-coding
mm_156794.1	chrX	162901227	162901261	+	1	NA	promoter-TSS (NM_001168569)	promoter-TSS (NM_001168569)	-316	NM_001168568	55936	Mm.2065	NM_018737	ENSMUSG00000031360	Ctps2	A830031M15Rik|AI326475|Ctpsh	cytidine 5'-triphosphate synthase 2	protein-coding
mm_19929.1	chr2	116064760	116064771	-	1	NA	promoter-TSS (NM_001346038)	promoter-TSS (NM_001346038)	-146	NM_001159570	17536	Mm.247566	NM_010825	ENSMUSG00000027210	Meis2	A430109D20Rik|Mrg1|Stra10	Meis homeobox 2	protein-coding
mm_64464.1	chr7	142665804	142665820	+	1	NA	intron (NR_002855, intron 2 of 3)	intron (NR_002855, intron 2 of 3)	1004	NM_001315488	16002	Mm.3862	NM_010514	ENSMUSG00000048583	Igf2	AL033362|Igf-2|Igf-II|M6pr|Mpr|Peg2	insulin-like growth factor 2	protein-coding
mm_21556.1	chr2	164083753	164083784	-	1	NA	intron (NM_021420, intron 3 of 10)	intron (NM_021420, intron 3 of 10)	9590	NM_021420	58231	Mm.234472	NM_021420	ENSMUSG00000018209	Stk4	AI447339|AU020804|Kas-2|Mst1|Ysk3	serine/threonine kinase 4	protein-coding
mm_35417.1	chr4	35035611	35035614	-	1	NA	intron (NM_178061, intron 2 of 3)	intron (NM_178061, intron 2 of 3)	-116443	NM_199157	387510	Mm.386929	NM_199157	ENSMUSG00000042993	Ifnk	-	interferon kappa	protein-coding
mm_96204.1	chr11	62131085	62131088	+	1	NA	intron (NM_001029936, intron 3 of 12)	intron (NM_001029936, intron 3 of 12)	54062	NM_001029936	432572	Mm.438022	NM_001029936	ENSMUSG00000042331	Specc1	2810012G08Rik|B230396K10Rik|Cytsb	sperm antigen with calponin homology and coiled-coil domains 1	protein-coding
mm_51041.1	chr6	65601583	65601629	+	1	NA	intron (NM_001001495, intron 5 of 7)	RMER17C|LTR|ERVK	11208	NM_001001495	414084	Mm.117558	NM_001001495	ENSMUSG00000044162	Tnip3	9030611K07Rik|ABIN-3|LIND	TNFAIP3 interacting protein 3	protein-coding
mm_127008.1	chr15	95830092	95830124	+	1	NA	intron (NM_175344, intron 1 of 19)	MER5B|DNA|hAT-Charlie	39265	NM_001253813	105722	Mm.38087	NM_175344	ENSMUSG00000064210	Ano6	2900059G15Rik|AA407480|AW554778|F730003B03Rik|Tmem16f	anoctamin 6	protein-coding
mm_50934.1	chr6	57702648	57702658	+	1	NA	5' UTR (NM_133737, exon 1 of 9)	5' UTR (NM_133737, exon 1 of 9)	198	NM_133737	71835	Mm.274904	NM_133737	ENSMUSG00000062190	Lancl2	1700003F10Rik	LanC (bacterial lantibiotic synthetase component C)-like 2	protein-coding
mm_50085.1	chr6	41523775	41523785	+	1	NA	intron (NM_009430, intron 2 of 4)	intron (NM_009430, intron 2 of 4)	2004	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_151287.1	chr19	55286410	55286418	+	1	NA	intron (NM_027976, intron 12 of 21)	intron (NM_027976, intron 12 of 21)	29618	NM_025883	66980	Mm.386789	NM_025883	ENSMUSG00000024982	Zdhhc6	2400007G07Rik|5930409M18Rik|AI462345|C77369	zinc finger, DHHC domain containing 6	protein-coding
mm_163863.1	chr14	19418821	19418847	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	183753	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_90136.1	chr10	117846121	117846170	+	1	NA	promoter-TSS (NM_024457)	promoter-TSS (NM_024457)	-171	NM_024457	215449	Mm.233009	NM_024457	ENSMUSG00000052681	Rap1b	2810443E11Rik	RAS related protein 1b	protein-coding
mm_71777.1	chr8	66471545	66471557	+	1	NA	TTS (NM_001293784)	TTS (NM_001293784)	14956	NM_025465	66282	Mm.294985	NM_025465	ENSMUSG00000025591	Tma16	1810029B16Rik	translation machinery associated 16	protein-coding
mm_72841.1	chr8	88300375	88300384	+	1	NA	intron (NM_001037723, intron 3 of 27)	intron (NM_001037723, intron 3 of 27)	6175	NM_001037724	11513	Mm.288206	NM_007406	ENSMUSG00000031659	Adcy7	AA407758	adenylate cyclase 7	protein-coding
mm_3720.1	chr1	154201553	154201560	+	1	NA	intron (NM_001204908, intron 1 of 1)	GA-rich|Low_complexity|Low_complexity	369	NM_001204908	100503355	Mm.484410	NM_001204908	ENSMUSG00000066797	Zfp648	ENSMUSG00000066797|Gm10178|Gm203	zinc finger protein 648	protein-coding
mm_139500.1	chr17	56289577	56289579	+	1	NA	intron (NM_025836, intron 1 of 7)	intron (NM_025836, intron 1 of 7)	933	NM_025836	66905	Mm.311696	NM_025836	ENSMUSG00000024197	Plin3	1300012C15Rik|M6prbp1|Tip47	perilipin 3	protein-coding
mm_113897.1	chr13	49195929	49195953	+	1	NA	3' UTR (NM_013610, exon 4 of 4)	3' UTR (NM_013610, exon 4 of 4)	8394	NM_013610	18081	Mm.18503	NM_013610	ENSMUSG00000037966	Ninj1	AU024536	ninjurin 1	protein-coding
mm_99336.1	chr11	101468182	101468192	+	1	NA	promoter-TSS (NM_009708)	promoter-TSS (NM_009708)	-151	NM_009708	11858	Mm.378883	NM_009708	ENSMUSG00000001313	Rnd2	Arhn|Rohn	Rho family GTPase 2	protein-coding
mm_57255.1	chr6	123283599	123283618	-	1	NA	exon (NM_019948, exon 6 of 6)	exon (NM_019948, exon 6 of 6)	6263	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_81815.1	chr9	118040595	118040604	+	1	NA	promoter-TSS (NM_013727)	promoter-TSS (NM_013727)	77	NM_013727	27215	Mm.92705	NM_013727	ENSMUSG00000039285	Azi2	AA410145|AZ2	5-azacytidine induced gene 2	protein-coding
mm_477.1	chr1	36511869	36511903	+	1	NA	promoter-TSS (NM_001039551)	promoter-TSS (NM_001039551)	19	NM_053186	94218	Mm.256323	NM_053186	ENSMUSG00000001138	Cnnm3	Acdp3|Clp3|mACDP3	cyclin M3	protein-coding
mm_89031.1	chr10	82699230	82699238	+	1	NA	exon (NM_001081218, exon 1 of 15)	exon (NM_001081218, exon 1 of 15)	227	NM_001081218	67933	Mm.127405	NM_026462	ENSMUSG00000020246	Hcfc2	1700129L13Rik|AU019838	host cell factor C2	protein-coding
mm_9932.1	chr1	189922339	189922357	-	1	NA	promoter-TSS (NM_026796)	promoter-TSS (NM_026796)	-60	NM_026796	226830	Mm.156895	NM_026796	ENSMUSG00000026603	Smyd2	1110020E07Rik|4930402C15|KMT3C|Zmynd14	SET and MYND domain containing 2	protein-coding
mm_14441.1	chr2	130906506	130906558	+	1	NA	promoter-TSS (NR_015523)	promoter-TSS (NR_015523)	37	NM_009730	11990	Mm.119936	NM_009730	ENSMUSG00000027312	Atrn	AW558010|Mgca|mg	attractin	protein-coding
mm_119701.1	chr14	53738304	53738307	+	1	NA	Intergenic	Intergenic	515624	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_155552.1	chrX	74429679	74429716	+	1	NA	promoter-TSS (NM_178590)	promoter-TSS (NM_178590)	16	NM_010547	16151	Mm.12967	NM_010547	ENSMUSG00000004221	Ikbkg	1110037D23Rik|AI848108|AI851264|AW124339|IKK[g]|NEMO	inhibitor of kappaB kinase gamma	protein-coding
mm_172667.1	chr8	43306946	43306946	-	1	NA	promoter-TSS (NM_009556)	promoter-TSS (NM_009556)	63	NM_009556	22702	Mm.285848	NM_009556	ENSMUSG00000051176	Zfp42	Rex-1|Rex1|Zfp-42	zinc finger protein 42	protein-coding
mm_123826.1	chr14	70626839	70626849	-	1	NA	5' UTR (NM_001252663, exon 1 of 14)	5' UTR (NM_001252663, exon 1 of 14)	221	NM_001252662	13829	Mm.210863	NM_013514	ENSMUSG00000022099	Dmtn	AI325486|Epb4.9|Epb49|dematin	dematin actin binding protein	protein-coding
mm_46541.1	chr5	105720634	105720665	-	1	NA	intron (NM_178701, intron 1 of 2)	intron (NM_178701, intron 1 of 2)	19839	NM_178701	231549	Mm.23837	NM_178701	ENSMUSG00000046079	Lrrc8d	2810473G09Rik|4930525N13Rik|A930019F03|Lrrc5	leucine rich repeat containing 8D	protein-coding
mm_171073.1	chr3	116597622	116597641	-	1	NA	intron (NM_030016, intron 1 of 11)	intron (NM_030016, intron 1 of 11)	2673	NM_001289571	72776	Mm.440836	NM_028349	ENSMUSG00000027959	Sass6	2810453L12Rik	SAS-6 centriolar assembly protein	protein-coding
mm_10182.1	chr2	4739317	4739320	+	1	NA	intron (NM_178663, intron 2 of 8)	intron (NM_178663, intron 2 of 8)	21487	NM_178663	209645	Mm.149539	NM_178663	ENSMUSG00000048186	Bend7	1110017O21Rik|E130319B15Rik	BEN domain containing 7	protein-coding
mm_29789.1	chr3	127553020	127553033	-	1	NA	promoter-TSS (NM_197997)	promoter-TSS (NM_197997)	323	NM_138593	28036	Mm.291032	NM_138593	ENSMUSG00000027968	Larp7	C330027G06Rik|D3Wsu161e	La ribonucleoprotein domain family, member 7	protein-coding
mm_16372.1	chr2	178119113	178119158	+	1	NA	5' UTR (NM_001177790, exon 1 of 13)	5' UTR (NM_001177790, exon 1 of 13)	160	NM_001177790	74189	Mm.44413	NM_028806	ENSMUSG00000027525	Phactr3	1500003N10Rik|4930415A02Rik|H17739|Scapin1|Scapinin|mKIAA4224	phosphatase and actin regulator 3	protein-coding
mm_103275.1	chr11	72135806	72135836	-	1	NA	promoter-TSS (NM_001081641)	promoter-TSS (NM_001081641)	68	NM_001024927	327958	Mm.351793	NM_001024927	ENSMUSG00000040543	Pitpnm3	A330068P14Rik|AI848332|Ackr6|Gm880	PITPNM family member 3	protein-coding
mm_12080.1	chr2	59811725	59811733	+	1	NA	intron (NM_198294, intron 16 of 26)	intron (NM_198294, intron 16 of 26)	70877	NM_001159636	72137	Mm.288734	NM_028118	ENSMUSG00000026988	Wdsub1	1700048E19Rik|2610014F08Rik	WD repeat, SAM and U-box domain containing 1	protein-coding
mm_153829.1	chr19	46317983	46318062	-	1	NA	intron (NM_028627, intron 11 of 17)	CpG	8844	NM_001347454	73728	Mm.268532	NM_028627	ENSMUSG00000037126	Psd	1110007H17Rik|A930015K15|Efa6|Efa6a|Psdl|mKIAA2011	pleckstrin and Sec7 domain containing	protein-coding
mm_110878.1	chr12	74317075	74317118	-	1	NA	Intergenic	Intergenic	19622	NM_198866	386753	Mm.341686	NM_198866	ENSMUSG00000029878	Dbpht2	Spot2	DNA binding protein with his-thr domain	protein-coding
mm_145169.1	chr18	46906973	46906980	+	1	NA	Intergenic	Intergenic	-14839	NM_001033446	381142	Mm.329423	NM_001033446	ENSMUSG00000073568	Arl14epl	Gm949	ADP-ribosylation factor-like 14 effector protein-like	protein-coding
mm_73616.1	chr8	110122595	110122598	+	1	NA	Intergenic	Intergenic	42862	NM_175480	234725	Mm.87487	NM_175480	ENSMUSG00000044676	Zfp612	B230354B21Rik	zinc finger protein 612	protein-coding
mm_155414.1	chrX	73490764	73490787	+	1	NA	intron (NM_007542, intron 1 of 7)	intron (NM_007542, intron 1 of 7)	7174	NM_007542	12111	Mm.2608	NM_007542	ENSMUSG00000031375	Bgn	BG|DSPG1|PG-S1|PGI|SLRR1A	biglycan	protein-coding
mm_58355.1	chr6	147675737	147675763	-	1	NA	Intergenic	Intergenic	-14491	NR_033636	100039727	Mm.396220	NR_033636	ENSMUSG00000085077	1700049E15Rik	Gm15761|OTTMUSG00000026044	RIKEN cDNA 1700049E15 gene	ncRNA
mm_57380.1	chr6	124814270	124814278	-	1	NA	promoter-TSS (NM_009415)	promoter-TSS (NM_009415)	22	NM_009415	21991	Mm.4222	NM_009415	ENSMUSG00000023456	Tpi1	AI255506|Tpi|Tpi-1	triosephosphate isomerase 1	protein-coding
mm_172825.1	chr9	17030228	17030229	+	1	NA	Intergenic	Intergenic	-651997	NM_001080814	270120	Mm.195010	NM_001080814	ENSMUSG00000074505	Fat3	9430076A06Rik|D430038H04Rik|Gm1132|Gm510|MFAT3F	FAT atypical cadherin 3	protein-coding
mm_165903.1	chr4	49536803	49536806	-	1	NA	exon (NM_144903, exon 9 of 9)	exon (NM_144903, exon 9 of 9)	12742	NM_144903	230163	Mm.482116	NM_144903	ENSMUSG00000028307	Aldob	Aldo-2|Aldo2|BC016435	aldolase B, fructose-bisphosphate	protein-coding
mm_130678.1	chr15	100675439	100675447	-	1	NA	exon (NM_033612, exon 7 of 8)	exon (NM_033612, exon 7 of 8)	-5943	NM_001270537	668218	Mm.451225	NM_001270537	ENSMUSG00000098112	Bin2	-	bridging integrator 2	protein-coding
mm_26249.1	chr3	141615255	141615259	+	1	NA	intron (NM_001293561, intron 1 of 16)	intron (NM_001293561, intron 1 of 16)	149693	NM_001293561	22253	Mm.24430	NM_009472	ENSMUSG00000059921	Unc5c	B130051O18Rik|Unc5h3|rcm	unc-5 netrin receptor C	protein-coding
mm_26560.1	chr3	146500072	146500092	+	1	NA	promoter-TSS (NM_001316756)	promoter-TSS (NM_001316756)	246	NM_010318	14707	Mm.140804	NM_010318	ENSMUSG00000068523	Gng5	G(y)5	guanine nucleotide binding protein (G protein), gamma 5	protein-coding
mm_88727.1	chr10	80179689	80179755	+	1	NA	5' UTR (NM_007909, exon 1 of 4)	5' UTR (NM_007909, exon 1 of 4)	240	NM_007909	13637	Mm.1478	NM_007909	ENSMUSG00000003070	Efna2	CEK7L|Elf1|Epl6|Eplg6|Lerk6	ephrin A2	protein-coding
mm_173013.1	chrM	617	618	+	1	NA	NA	Intergenic	NA	NA								
mm_165130.1	chr2	7395949	7395955	-	1	NA	promoter-TSS (NM_001110232)	promoter-TSS (NM_001110232)	48	NM_001110232	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_150350.1	chr19	34644245	34644255	+	1	NA	intron (NM_008331, intron 1 of 1)	intron (NM_008331, intron 1 of 1)	3361	NM_008331	15957	Mm.439751	NM_008331	ENSMUSG00000034459	Ifit1	ISG56|Ifi56|P56	interferon-induced protein with tetratricopeptide repeats 1	protein-coding
mm_136165.1	chr16	88563131	88563141	-	1	NA	promoter-TSS (NM_018778)	promoter-TSS (NM_018778)	47	NM_018778	54420	Mm.25836	NM_018778	ENSMUSG00000050520	Cldn8	AI648025	claudin 8	protein-coding
mm_131751.1	chr16	22402871	22402893	+	1	NA	intron (NM_023794, intron 7 of 12)	B1_Mus2|SINE|Alu	36688	NM_023794	104156	Mm.155708	NM_023794	ENSMUSG00000013089	Etv5	1110005E01Rik|8430401F14Rik|ERM	ets variant 5	protein-coding
mm_53458.1	chr6	134830320	134830337	+	1	NA	5' UTR (NM_177687, exon 1 of 5)	5' UTR (NM_177687, exon 1 of 5)	129	NM_177687	232430	Mm.267010	NM_177687	ENSMUSG00000032652	Crebl2	AI046348|B230205M03	cAMP responsive element binding protein-like 2	protein-coding
mm_158418.1	chrX	137122136	137122171	-	1	NA	Intergenic	Tigger7|DNA|TcMar-Tigger	-1827	NM_007957	13984	Mm.8017	NM_007957	ENSMUSG00000023443	Esx1	Spx1	extraembryonic, spermatogenesis, homeobox 1	protein-coding
mm_50849.1	chr6	54866455	54866466	+	1	NA	intron (NM_199143, intron 2 of 4)	intron (NM_199143, intron 2 of 4)	49544	NM_199143	387524	Mm.286149	NM_199143	ENSMUSG00000058446	Znrf2	1190002C14Rik|AU044205|D6Ertd365e	zinc and ring finger 2	protein-coding
mm_29087.1	chr3	104523685	104523700	-	1	NA	Intergenic	Intergenic	-11774	NM_001025067	269473	Mm.34855	NM_001025067	ENSMUSG00000032913	Lrig2	4632419I10Rik|BB096938|LIG-2	leucine-rich repeats and immunoglobulin-like domains 2	protein-coding
mm_23596.1	chr3	65108969	65108987	+	1	NA	promoter-TSS (NM_010597)	promoter-TSS (NM_010597)	-390	NM_010597	16497	Mm.316402	NM_010597	ENSMUSG00000027827	Kcnab1	Akr8a8|Kvbeta1.1|mKv(beta)1	potassium voltage-gated channel, shaker-related subfamily, beta member 1	protein-coding
mm_52128.1	chr6	97943326	97943337	+	1	NA	intron (NM_001113198, intron 2 of 9)	intron (NM_001113198, intron 2 of 9)	13514	NM_001178049	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_144727.1	chr18	35235500	35235517	+	1	NA	intron (NM_009818, intron 9 of 17)	intron (NM_009818, intron 9 of 17)	-20484	NM_178005	107065	Mm.39900	NM_178005	ENSMUSG00000071862	Lrrtm2	AI851755|BB129880|C630011A14Rik|mKIAA0416	leucine rich repeat transmembrane neuronal 2	protein-coding
mm_109711.1	chr12	113446407	113446410	+	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-43157	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_31280.1	chr4	45848327	45848374	+	1	NA	promoter-TSS (NM_028788)	promoter-TSS (NM_028788)	-466	NM_001305421	74152	Mm.63645	NM_028788	ENSMUSG00000028327	Stra6l	1300002K09Rik|Rbpr2	STRA6-like	protein-coding
mm_134710.1	chr16	22894351	22894392	-	1	NA	promoter-TSS (NR_110508)	promoter-TSS (NR_110508)	15	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_16645.1	chr2	6130118	6130167	-	1	NA	promoter-TSS (NM_001159657)	promoter-TSS (NM_001159657)	43	NM_144883	227545	Mm.133542	NM_144883	ENSMUSG00000045319	Proser2	5430407P10Rik|AU067770	proline and serine rich 2	protein-coding
mm_76047.1	chr8	77610676	77610730	-	1	NA	promoter-TSS (NM_145599)	promoter-TSS (NM_145599)	-50	NM_145599	234463	Mm.273578	NM_145599	ENSMUSG00000031617	Tmem184c	8430433H16Rik|AI645453|AL033298|BC004056|Tmem34	transmembrane protein 184C	protein-coding
mm_114107.1	chr13	54789501	54789509	+	1	NA	promoter-TSS (NM_028841)	promoter-TSS (NM_028841)	100	NM_028841	74257	Mm.32883	NM_028841	ENSMUSG00000025875	Tspan17	2210021G21Rik|AI047581|Fbxo23|Tm4sf17	tetraspanin 17	protein-coding
mm_137015.1	chr17	17832972	17832975	+	1	NA	intron (NM_001162909, intron 2 of 8)	intron (NM_001162909, intron 2 of 8)	1998	NM_001162909	75202	Mm.227456	NM_029205	ENSMUSG00000080316	Spaca6	4930546H06Rik|9530079D04Rik|B230206P06Rik|Ncrna00085|SPACA6A|let-7e|mir-125a|mir-99b	sperm acrosome associated 6	protein-coding
mm_78638.1	chr9	40269203	40269265	+	1	NA	promoter-TSS (NM_001083917)	promoter-TSS (NM_001083917)	18	NM_178227	235281	Mm.290083	NM_153522	ENSMUSG00000049281	Scn3b	1110001K16Rik|4833414B02Rik|Scnb3	sodium channel, voltage-gated, type III, beta	protein-coding
mm_16323.1	chr2	174304728	174304730	+	1	NA	intron (NM_001310085, intron 2 of 12)	(CA)n|Simple_repeat|Simple_repeat	6870	NM_001310085	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_29004.1	chr3	101592489	101592499	-	1	NA	exon (NM_144900, exon 4 of 23)	exon (NM_144900, exon 4 of 23)	12213	NM_144900	11928	Mm.193670	NM_144900	ENSMUSG00000033161	Atp1a1	Atpa-1|BC010319	ATPase, Na+/K+ transporting, alpha 1 polypeptide	protein-coding
mm_11704.1	chr2	36136443	36136470	+	1	NA	promoter-TSS (NM_026422)	promoter-TSS (NM_026422)	58	NM_026422	67871	Mm.378232	NM_026422	ENSMUSG00000026887	Mrrf	2400002D02Rik|MRFF|MTRRF|RRF	mitochondrial ribosome recycling factor	protein-coding
mm_136832.1	chr17	12741386	12741399	+	1	NA	promoter-TSS (NR_027784)	promoter-TSS (NR_027784)	81	NR_027784	104103	Mm.26553	NR_002853	ENSMUSG00000078247	Airn	2810051F02Rik|2810434M15Rik|AI256653|AI597500|AW049873|Air|B930018I07Rik|D17Ertd663e|IGF2RAS	antisense Igf2r RNA	ncRNA
mm_52808.1	chr6	121342883	121342924	+	1	NA	promoter-TSS (NM_001347433)	promoter-TSS (NM_001347433)	-173	NM_001347433	14411	Mm.274506	NM_133661	ENSMUSG00000030109	Slc6a12	BGT1|GAT-2|GAT2|Gabt2	solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12	protein-coding
mm_92400.1	chr10	76623319	76623332	-	1	NA	promoter-TSS (NM_146007)	promoter-TSS (NM_146007)	79	NM_146007	12834	Mm.1949	NM_146007	ENSMUSG00000020241	Col6a2	Col6a-2	collagen, type VI, alpha 2	protein-coding
mm_13704.1	chr2	117145201	117145212	+	1	NA	intron (NM_033524, intron 1 of 6)	intron (NM_033524, intron 1 of 6)	24135	NM_033524	114715	Mm.245890	NM_033524	ENSMUSG00000027351	Spred1	5730461F13Rik|AL024345|AW047647	sprouty protein with EVH-1 domain 1, related sequence	protein-coding
mm_69227.1	chr7	127649346	127649355	-	1	NA	Intergenic	Intergenic	-34917	NM_177226	320683	Mm.156718	NM_177226	ENSMUSG00000045639	Zfp629	9330199A09Rik|Znf629	zinc finger protein 629	protein-coding
mm_46584.1	chr5	107597596	107597625	-	1	NA	promoter-TSS (NM_133248)	promoter-TSS (NM_133248)	29	NM_133248	170823	Mm.41417	NM_133248	ENSMUSG00000029276	Glmn	9330160J16Rik|AW227515|Fap48|Fap68	glomulin, FKBP associated protein	protein-coding
mm_143818.1	chr17	83846747	83846757	-	1	NA	promoter-TSS (NM_025325)	promoter-TSS (NM_025325)	38	NM_025325	107766	Mm.30100	NM_025325	ENSMUSG00000000673	Haao	0610007K21Rik|0610012J07Rik|3-HAO|3-HAOxase|3HAO	3-hydroxyanthranilate 3,4-dioxygenase	protein-coding
mm_61736.1	chr7	82174799	82174825	+	1	NA	Intergenic	CpG	-85096	NM_001277955	20408	Mm.736	NM_017400	ENSMUSG00000030638	Sh3gl3	EEN-B2|SH3P13|Sh3d2c|Sh3d2c2	SH3-domain GRB2-like 3	protein-coding
mm_42561.1	chr5	117141884	117141896	+	1	NA	intron (NM_001081308, intron 1 of 19)	intron (NM_001081308, intron 1 of 19)	8302	NM_183306	330177	Mm.24343	NM_183306	ENSMUSG00000061288	Taok3	2900006A08Rik|A130052D22|A430105I05Rik	TAO kinase 3	protein-coding
mm_136357.1	chr16	92775298	92775302	-	1	NA	intron (NM_001111022, intron 2 of 6)	intron (NM_001111022, intron 2 of 6)	50774	NM_001111021	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_169610.1	chr15	37271446	37271447	+	1	NA	intron (NM_026496, intron 2 of 15)	B1_Mm|SINE|Alu	38410	NM_026496	252973	Mm.244612	NM_026496	ENSMUSG00000022286	Grhl2	0610015A08Rik|BOM|Tcfcp2l3|clft3	grainyhead-like 2 (Drosophila)	protein-coding
mm_118669.1	chr14	21995754	21995766	+	1	NA	Intergenic	Intergenic	-6159	NM_145459	218820	Mm.292401	NM_145459	ENSMUSG00000039081	Zfp503	AI181838|B830002A16Rik|Nolz-1|Nolz1|Znf503	zinc finger protein 503	protein-coding
mm_93319.1	chr10	99117151	99117154	-	1	NA	intron (NM_027740, intron 2 of 11)	intron (NM_027740, intron 2 of 11)	9017	NM_015737	14426	Mm.314	NM_015737	ENSMUSG00000090035	Galnt4	AV011803	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 4	protein-coding
mm_104684.1	chr11	97718410	97718420	-	1	NA	3' UTR (NM_054051, exon 10 of 10)	3' UTR (NM_054051, exon 10 of 10)	14981	NM_011971	26446	Mm.21874	NM_011971	ENSMUSG00000069744	Psmb3	AL033320|C10-II	proteasome (prosome, macropain) subunit, beta type 3	protein-coding
mm_57196.1	chr6	122850314	122850332	-	1	NA	exon (NM_009779, exon 2 of 2)	exon (NM_009779, exon 2 of 2)	5834	NM_009779	12267	Mm.2408	NM_009779	ENSMUSG00000040552	C3ar1	AZ3B|C3AR|HNFAG09	complement component 3a receptor 1	protein-coding
mm_41190.1	chr5	88327905	88327920	+	1	NA	exon (NM_008644, exon 3 of 3)	exon (NM_008644, exon 3 of 3)	10600	NM_008644	17830	Mm.200411	NM_008644	ENSMUSG00000064156	Prol1	Muc10	proline rich, lacrimal 1	protein-coding
mm_89148.1	chr10	86021994	86022015	+	1	NA	promoter-TSS (NM_153195)	promoter-TSS (NM_153195)	75	NM_153195	69754	Mm.44236	NM_153195	ENSMUSG00000001786	Fbxo7	2410015K21Rik|A230052G17Rik|AI117679|AW260462|C85118	F-box protein 7	protein-coding
mm_48306.1	chr5	138564672	138564707	-	1	NA	promoter-TSS (NM_029693)	promoter-TSS (NM_029693)	5	NM_029693	76658	Mm.73235	NM_029693	ENSMUSG00000029526	1700123K08Rik	-	RIKEN cDNA 1700123K08 gene	protein-coding
mm_168962.1	chr12	80317956	80317959	-	1	NA	Intergenic	RLTR1B|LTR|ERV1	-57576	NM_001346669	109711	Mm.253564	NM_134156	ENSMUSG00000015143	Actn1	3110023F10Rik|Actn1a	actinin, alpha 1	protein-coding
mm_130397.1	chr15	97975913	97975921	-	1	NA	3' UTR (NM_001113515, exon 53 of 53)	3' UTR (NM_001113515, exon 53 of 53)	11688	NM_001252153	380967	Mm.196630	NM_201359	ENSMUSG00000052369	Tmem106c	AI046681|BC046621|D15Ertd405e	transmembrane protein 106C	protein-coding
mm_152573.1	chr19	11592452	11592464	-	1	NA	intron (NM_026835, intron 4 of 6)	intron (NM_026835, intron 4 of 6)	12346	NM_026835	68774	Mm.290390	NM_026835	ENSMUSG00000024679	Ms4a6d	1110058E16Rik|AI447446|Ms4a11	membrane-spanning 4-domains, subfamily A, member 6D	protein-coding
mm_6578.1	chr1	75217295	75217304	-	1	NA	exon (NM_009447, exon 2 of 4)	exon (NM_009447, exon 2 of 4)	1995	NM_001313723	22145	Mm.1155	NM_009447	ENSMUSG00000026202	Tuba4a	M[a]4|Tuba4	tubulin, alpha 4A	protein-coding
mm_12980.1	chr2	90783214	90783224	+	1	NA	intron (NM_178755, intron 1 of 17)	CpG	475	NM_178755	271813	Mm.61146	NM_178755	ENSMUSG00000040812	Agbl2	4930524K04|A430081C19Rik|CCP2	ATP/GTP binding protein-like 2	protein-coding
mm_30714.1	chr4	12906786	12906817	+	1	NA	promoter-TSS (NM_001171801)	promoter-TSS (NM_001171801)	-36	NM_173746	208820	Mm.12057	NM_173746	ENSMUSG00000055963	Triqk	C130086A10|Gm11818|OTTMUSG00000004461	triple QxxK/R motif containing	protein-coding
mm_76089.1	chr8	79399514	79399532	-	1	NA	promoter-TSS (NM_008539)	promoter-TSS (NM_008539)	-55	NM_008539	17125	Mm.223717	NM_008539	ENSMUSG00000031681	Smad1	AI528653|Madh1|Madr1|Mlp1|MusMLP	SMAD family member 1	protein-coding
mm_107836.1	chr12	69296677	69296798	+	1	NA	promoter-TSS (NM_027117)	promoter-TSS (NM_027117)	56	NM_027117	69554	Mm.234368	NM_027117	ENSMUSG00000020978	Klhdc2	2310022K15Rik|D12Ertd522e|HCLP-1|LCP	kelch domain containing 2	protein-coding
mm_165641.1	chr3	75270109	75270119	-	1	NA	promoter-TSS (NM_026460)	promoter-TSS (NM_026460)	-36	NM_026460	67931	Mm.259446	NM_026460	ENSMUSG00000034139	Serpini2	Spi14	serine (or cysteine) peptidase inhibitor, clade I, member 2	protein-coding
mm_150620.1	chr19	41050408	41050421	+	1	NA	intron (NM_009345, intron 8 of 11)	B1F2|SINE|Alu	21139	NM_009345	21673	Mm.25620	NM_009345	ENSMUSG00000025014	Dntt	Tdt	deoxynucleotidyltransferase, terminal	protein-coding
mm_35967.1	chr4	53144226	53144241	-	1	NA	intron (NM_013454, intron 1 of 49)	intron (NM_013454, intron 1 of 49)	15662	NM_013454	11303	Mm.277376	NM_013454	ENSMUSG00000015243	Abca1	ABC-1|Abc1	ATP-binding cassette, sub-family A (ABC1), member 1	protein-coding
mm_14808.1	chr2	145903891	145903903	+	1	NA	intron (NM_026425, intron 1 of 5)	intron (NM_026425, intron 1 of 5)	656	NM_001141965	67877	Mm.151168	NM_026425	ENSMUSG00000002728	Naa20	1500004D14Rik|2900026I01Rik|AU041458|D2Ertd186e|Nat5	N(alpha)-acetyltransferase 20, NatB catalytic subunit	protein-coding
mm_37778.1	chr4	130168055	130168058	-	1	NA	intron (NM_023476, intron 5 of 11)	intron (NM_023476, intron 5 of 11)	6746	NM_001168333	94242	Mm.15801	NM_023476	ENSMUSG00000028776	Tinagl1	1110021J17Rik|AZ-1|AZ1|Arg1|Lcn7|TARP|Tinagl	tubulointerstitial nephritis antigen-like 1	protein-coding
mm_80233.1	chr9	72676565	72676573	+	1	NA	intron (NM_010890, intron 3 of 28)	RMER1B|Other|Other	14222	NM_010890	17999	Mm.279923	NM_010890	ENSMUSG00000032216	Nedd4	AA959633|AL023035|AU019897|E430025J12Rik|Nedd4-1|Nedd4a|mKIAA0093	neural precursor cell expressed, developmentally down-regulated 4	protein-coding
mm_146471.1	chr18	88894458	88894466	+	1	NA	promoter-TSS (NM_018821)	promoter-TSS (NM_018821)	-255	NM_018821	54607	Mm.91920	NM_018821	ENSMUSG00000056153	Socs6	1500012M23Rik|5830401B18Rik|AI447482|Cis4|Cish4|HSPC060|SOCS-4|SOCS-6|SSI4|STAI4|STATI4|Socs4	suppressor of cytokine signaling 6	protein-coding
mm_55360.1	chr6	56923822	56923926	-	1	NA	promoter-TSS (NM_026004)	promoter-TSS (NM_026004)	58	NM_026004	107569	Mm.158936	NM_026004	ENSMUSG00000029780	Nt5c3	1600024P05Rik|2610206B05Rik|3110004A18Rik|AI842776|Nt5c3a|Nt5y|PN-1|PN-I|PSN1|UMPH|Umph-1|Umph1|cN-III|lupin|p36	5'-nucleotidase, cytosolic III	protein-coding
mm_89406.1	chr10	90632069	90632071	+	1	NA	intron (NM_001177396, intron 1 of 11)	intron (NM_001177396, intron 1 of 11)	55379	NM_181398	77531	Mm.440605	NM_181398	ENSMUSG00000058589	Anks1b	AIDA-1b|C030032C09Rik|E530015N03Rik|ENSMUSG00000078431|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding
mm_25413.1	chr3	107368377	107368383	+	1	NA	Intergenic	Intergenic	-35091	NM_001045807	229700	Mm.27966	NM_001045807	ENSMUSG00000048109	Rbm15	C230088J01Rik|mKIAA1438	RNA binding motif protein 15	protein-coding
mm_169934.1	chr16	60747187	60747194	-	1	NA	Intergenic	L1Md_T|LINE|L1	-141659	NM_007938	13840	Mm.455790	NM_007938	ENSMUSG00000055540	Epha6	Ehk2|Hek12|m-ehk2	Eph receptor A6	protein-coding
mm_99672.1	chr11	105974640	105974658	+	1	NA	promoter-TSS (NM_009598)	promoter-TSS (NM_009598)	-559	NM_009598	11421	Mm.754	NM_009598	ENSMUSG00000020681	Ace	AW208573|CD143	angiotensin I converting enzyme (peptidyl-dipeptidase A) 1	protein-coding
mm_115390.1	chr13	113293157	113293204	+	1	NA	Intergenic	CpG	83521	NM_023612	71690	Mm.38929	NM_023612	ENSMUSG00000042379	Esm1	0610042H23Rik|AV004503|ESM-1	endothelial cell-specific molecule 1	protein-coding
mm_108187.1	chr12	76571545	76571567	+	1	NA	intron (NM_153804, intron 13 of 18)	intron (NM_153804, intron 13 of 18)	-23631	NR_046044	100504549	Mm.440349	NR_046044		AI463170	-	expressed sequence AI463170	ncRNA
mm_35893.1	chr4	49549222	49549228	-	1	NA	intron (NM_144903, intron 1 of 8)	intron (NM_144903, intron 1 of 8)	321	NM_144903	230163	Mm.482116	NM_144903	ENSMUSG00000028307	Aldob	Aldo-2|Aldo2|BC016435	aldolase B, fructose-bisphosphate	protein-coding
mm_29342.1	chr3	108226599	108226683	-	1	NA	promoter-TSS (NM_008596)	promoter-TSS (NM_008596)	-42	NM_008596	17306	Mm.316885	NM_008596	ENSMUSG00000027887	Sypl2	AI552439|Mg29	synaptophysin-like 2	protein-coding
mm_104859.1	chr11	99385280	99385303	-	1	NA	TTS (NM_010660)	TTS (NM_010660)	4073	NM_010660	16661	Mm.22662	NM_010660	ENSMUSG00000019761	Krt10	D130054E02Rik|K10|K1C1|Krt-1.10|Krt1-10	keratin 10	protein-coding
mm_172117.1	chr6	3201063	3201063	+	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	-87456	NR_036696	667335	Mm.380219	NR_036696	ENSMUSG00000106779	Gm8579	EG667335	spermatogenesis associated glutamate (E)-rich protein 4a pseudogene	pseudo
mm_128474.1	chr15	50889056	50889084	-	1	NA	promoter-TSS (NR_035444)	promoter-TSS (NR_035444)	-21	NM_001310485	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_25955.1	chr3	132085780	132085814	+	1	NA	5' UTR (NM_020265, exon 1 of 4)	5' UTR (NM_020265, exon 1 of 4)	505	NM_020265	56811	Mm.103593	NM_020265	ENSMUSG00000028031	Dkk2	-	dickkopf WNT signaling pathway inhibitor 2	protein-coding
mm_62473.1	chr7	101837064	101837094	+	1	NA	intron (NM_010567, intron 1 of 28)	CpG-13418	745	NM_001122739	16332	Mm.476000	NM_010567	ENSMUSG00000032737	Inppl1	51C|SHIP2	inositol polyphosphate phosphatase-like 1	protein-coding
mm_3441.1	chr1	150102687	150102705	+	1	NA	exon (NM_011198, exon 5 of 10)	exon (NM_011198, exon 5 of 10)	2665	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_35116.1	chr4	10988252	10988252	-	1	NA	TTS (NM_175175)	TTS (NM_175175)	19367	NM_175175	71801	Mm.34351	NM_175175	ENSMUSG00000049969	Plekhf2	1110070J07Rik|AA673237|ZFYVE18	pleckstrin homology domain containing, family F (with FYVE domain) member 2	protein-coding
mm_117854.1	chr13	98803786	98803808	-	1	NA	intron (NM_172591, intron 2 of 25)	intron (NM_172591, intron 2 of 25)	11652	NM_172591	218503	Mm.23928	NM_172591	ENSMUSG00000041685	Fcho2	5832424M12Rik|AA387320	FCH domain only 2	protein-coding
mm_107859.1	chr12	69724940	69724986	+	1	NA	promoter-TSS (NM_026536)	promoter-TSS (NM_026536)	1	NM_026536	68055	Mm.27844	NM_026536	ENSMUSG00000054894	Atp5s	1110015E18Rik|ATPW	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit S	protein-coding
mm_26907.1	chr3	19312193	19312213	-	1	NA	promoter-TSS (NM_001122759)	promoter-TSS (NM_001122759)	-881	NM_001122759	18583	Mm.355614	NM_008802	ENSMUSG00000069094	Pde7a	AU015378|AW047537	phosphodiesterase 7A	protein-coding
mm_90838.1	chr10	8518783	8518800	-	1	NA	promoter-TSS (NM_177387)	promoter-TSS (NM_177387)	34	NM_177387	338362	Mm.41163	NM_177387	ENSMUSG00000047712	Ust	D930010O20Rik|UA2OST	uronyl-2-sulfotransferase	protein-coding
mm_49958.1	chr6	40634808	40634864	+	1	NA	intron (NM_001171003, intron 1 of 47)	intron (NM_001171003, intron 1 of 47)	6005	NM_001171003	232714	Mm.33401	NM_001171003	ENSMUSG00000068587	Mgam	6030407P20Rik|MGA	maltase-glucoamylase	protein-coding
mm_39802.1	chr5	30623162	30623183	+	1	NA	3' UTR (NM_010608, exon 2 of 2)	3' UTR (NM_010608, exon 2 of 2)	-24764	NR_049199	100885838		NR_049199	ENSMUSG00000093710	Mir5625	Gm23930|mmu-mir-5625	microRNA 5625	ncRNA
mm_74916.1	chr8	25544993	25545007	-	1	NA	intron (NM_001079909, intron 2 of 16)	intron (NM_001079909, intron 2 of 16)	11083	NR_110510	102633315	Mm.437828	NR_110510	ENSMUSG00000086134	Gm16159	OTTMUSG00000031030	predicted gene 16159	ncRNA
mm_140182.1	chr17	80944651	80944671	+	1	NA	promoter-TSS (NM_026516)	promoter-TSS (NM_026516)	29	NM_026516	68027	Mm.357108	NM_026516	ENSMUSG00000024245	Tmem178	2810417M05Rik|Tmem178a	transmembrane protein 178	protein-coding
mm_165220.1	chr2	47742043	47742044	+	1	NA	Intergenic	RMER1B|Other|Other	-1072066	NM_007396	11480	Mm.314338	NM_007396	ENSMUSG00000052155	Acvr2a	ActrIIa|Acvr2|TactrII	activin receptor IIA	protein-coding
mm_117112.1	chr13	60177499	60177574	-	1	NA	promoter-TSS (NM_008086)	promoter-TSS (NM_008086)	-1	NM_008086	14451	Mm.22701	NM_008086	ENSMUSG00000052957	Gas1	AW554192|Gas-1	growth arrest specific 1	protein-coding
mm_93818.1	chr10	121472776	121472779	-	1	NA	intron (NM_138956, intron 1 of 4)	ID_B1|SINE|B4	3473	NM_138956	192678	Mm.41265	NM_138956	ENSMUSG00000025795	Rassf3	AW212023|AW322379	Ras association (RalGDS/AF-6) domain family member 3	protein-coding
mm_57323.1	chr6	124733177	124733187	-	1	NA	promoter-TSS (NM_013545)	promoter-TSS (NM_013545)	-28	NM_013545	15170	Mm.271799	NM_013545	ENSMUSG00000004266	Ptpn6	70Z-SHP|Hcph|PTPTY-42|Ptp1C|SH-PTP1|SHP-1|hcp|me	protein tyrosine phosphatase, non-receptor type 6	protein-coding
mm_35071.1	chr4	6903765	6903778	-	1	NA	intron (NM_145711, intron 1 of 8)	intron (NM_145711, intron 1 of 8)	86952	NM_145711	252838	Mm.435828	NM_145711	ENSMUSG00000041272	Tox	1700007F02Rik	thymocyte selection-associated high mobility group box	protein-coding
mm_91150.1	chr10	20312240	20312278	-	1	NA	promoter-TSS (NM_001025393)	promoter-TSS (NM_001025393)	-210	NM_001025392	72567	Mm.294783	NM_153787	ENSMUSG00000037608	Bclaf1	2610102K23Rik|2700025J07Rik|2810454G14Rik|5730534O06Rik|AI450190|AW556225|Btf|mKIAA0164	BCL2-associated transcription factor 1	protein-coding
mm_129665.1	chr15	81247960	81247996	-	1	NA	promoter-TSS (NR_077231)	promoter-TSS (NR_077231)	-7	NR_077231	78102	Mm.296832	NR_077229		8430426J06Rik	-	RIKEN cDNA 8430426J06 gene	ncRNA
mm_151967.1	chr19	5802668	5802675	-	1	NA	promoter-TSS (NR_002847)	promoter-TSS (NR_002847)	1	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_79535.1	chr9	57777830	57777867	+	1	NA	Intergenic	Intergenic	-11988	NM_007713	102414	Mm.25720	NM_007713	ENSMUSG00000032316	Clk3	AI256811	CDC-like kinase 3	protein-coding
mm_148332.1	chr18	84087703	84087716	-	1	NA	promoter-TSS (NM_146090)	promoter-TSS (NM_146090)	-449	NM_146090	225791	Mm.147052	NM_146090	ENSMUSG00000049090	Zadh2	C530046K17Rik|PTGR-3|Pthr3	zinc binding alcohol dehydrogenase, domain containing 2	protein-coding
mm_7810.1	chr1	131688586	131688611	-	1	NA	promoter-TSS (NM_145509)	promoter-TSS (NM_145509)	-97	NM_145509	226421	Mm.44508	NM_145509	ENSMUSG00000052688	Rab7b	5430435G22Rik	RAB7B, member RAS oncogene family	protein-coding
mm_123345.1	chr14	63139030	63139072	-	1	NA	exon (NM_007798, exon 8 of 10)	exon (NM_007798, exon 8 of 10)	16589	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_151705.1	chr19	4498548	4498572	-	1	NA	promoter-TSS (NM_027237)	promoter-TSS (NM_027237)	23	NM_027237	69861	Mm.282978	NM_027237	ENSMUSG00000042041	2010003K11Rik	-	RIKEN cDNA 2010003K11 gene	protein-coding
mm_11069.1	chr2	27676960	27676989	+	1	NA	promoter-TSS (NM_011305)	promoter-TSS (NM_011305)	-227	NM_011305	20181	Mm.24624	NM_011305	ENSMUSG00000015846	Rxra	9530071D11Rik|Nr2b1|RXRalpha1	retinoid X receptor alpha	protein-coding
mm_87176.1	chr10	38965617	38965630	+	1	NA	5' UTR (NM_010681, exon 1 of 38)	5' UTR (NM_010681, exon 1 of 38)	108	NM_010681	16775	Mm.258065	NM_010681	ENSMUSG00000019846	Lama4	-	laminin, alpha 4	protein-coding
mm_156496.1	chrX	144336213	144336229	+	1	NA	non-coding (NR_037145, exon 4 of 27)	non-coding (NR_037145, exon 4 of 27)	18255	NM_026247	67574	Mm.249084	NM_026247	ENSMUSG00000041718	Alg13	2810046O15Rik|4833435D08Rik|Glt28d1|MDS031|OTTMUSG00000018917	asparagine-linked glycosylation 13	protein-coding
mm_111976.1	chr12	110086378	110086393	-	1	NA	Intergenic	MLT1A0|LTR|ERVL-MaLR	71688	NR_045466	67280	Mm.390495	NR_045466		3110009F21Rik	-	RIKEN cDNA 3110009F21 gene	ncRNA
mm_173000.1	chrM	169	169	+	1	NA	NA	Intergenic	NA	NA								
mm_71423.1	chr8	46491003	46491007	+	1	NA	promoter-TSS (NM_001302163)	promoter-TSS (NM_001302163)	39	NM_001302163	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_32881.1	chr4	118875268	118875271	+	1	NA	Intergenic	RMER19B|LTR|ERVK	6486	NM_001011856	258159	Mm.388910	NM_001011856	ENSMUSG00000073769	Olfr1331	MOR259-3P	olfactory receptor 1331	protein-coding
mm_46552.1	chr5	106624395	106624404	-	1	NA	intron (NM_026856, intron 5 of 6)	MLT1A0-int|LTR|ERVL-MaLR	72431	NM_026856	52397	Mm.249474	NM_026856	ENSMUSG00000049606	Zfp644	1110068L01Rik|AA408882|BM-005|D5Ertd689e|Zep-2	zinc finger protein 644	protein-coding
mm_14929.1	chr2	151540794	151540798	+	1	NA	Intergenic	RLTR24|LTR|ERV1	-1687	NR_126058	14225	Mm.278458	NM_008019	ENSMUSG00000032966	Fkbp1a	FKBP12|Fkbp|Fkbp1	FK506 binding protein 1a	protein-coding
mm_73710.1	chr8	111688588	111688633	+	1	NA	TTS (NR_106044)	TTS (NR_106044)	1064	NR_106044	102466993		NR_106044	ENSMUSG00000099129	Mir7076	Gm27318|mmu-mir-7076	microRNA 7076	ncRNA
mm_118346.1	chr13	114854134	114854145	-	1	NA	intron (NM_008396, intron 21 of 29)	intron (NM_008396, intron 21 of 29)	35902	NM_001113374	17434	Mm.19027	NM_013826	ENSMUSG00000015536	Mocs2	AI415403	molybdenum cofactor synthesis 2	protein-coding
mm_145811.1	chr18	65414997	65415008	+	1	NA	intron (NR_105742, intron 3 of 6)	intron (NR_105742, intron 3 of 6)	-15995	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_131810.1	chr16	22918379	22918385	+	1	NA	promoter-TSS (NM_001083905)	promoter-TSS (NM_001083905)	0	NM_001083905	59083	Mm.28461	NM_021564	ENSMUSG00000022871	Fetub	2310011O17Rik|AI255764|D17980|Gugu	fetuin beta	protein-coding
mm_54252.1	chr6	28262408	28262429	-	1	NA	promoter-TSS (NM_001081678)	promoter-TSS (NM_001081678)	-817	NM_001081678	627049	Mm.84441	NM_001081678	ENSMUSG00000039841	Zfp800	AA407452|Znf800	zinc finger protein 800	protein-coding
mm_158555.1	chrX	147554098	147554110	-	1	NA	promoter-TSS (NM_001081173)	promoter-TSS (NM_001081173)	-23	NM_001081173	210297	Mm.30506	NM_001081173	ENSMUSG00000031290	Lrch2	AI316885|mKIAA1495	leucine-rich repeats and calponin homology (CH) domain containing 2	protein-coding
mm_166520.1	chr6	21986254	21986264	+	1	NA	5' UTR (NM_001081351, exon 1 of 22)	5' UTR (NM_001081351, exon 1 of 22)	349	NM_001081351	214642	Mm.221404	NM_001081351	ENSMUSG00000062980	Cped1	6720481P07|A430107O13Rik|AI552584	cadherin-like and PC-esterase domain containing 1	protein-coding
mm_34604.1	chr4	150237695	150237705	+	1	NA	intron (NM_023119, intron 1 of 11)	intron (NM_023119, intron 1 of 11)	376	NM_001025388	433182	Mm.70666	NM_001025388	ENSMUSG00000059040	Eno1b	EG433182|Eno1|Gm5506	enolase 1B, retrotransposed	protein-coding
mm_78452.1	chr9	32264661	32264664	+	1	NA	3' UTR (NM_177379, exon 13 of 13)	3' UTR (NM_177379, exon 13 of 13)	40413	NM_177379	330914	Mm.46683	NM_177379	ENSMUSG00000041444	Arhgap32	3426406O18Rik|Gc-gap|Grit|Px-rics|Rics|mKIAA0712|p200Rhogap|p250Gap	Rho GTPase activating protein 32	protein-coding
mm_63195.1	chr7	125603641	125603651	+	1	NA	5' UTR (NM_021887, exon 1 of 9)	5' UTR (NM_021887, exon 1 of 9)	217	NM_021887	60504	Mm.155643	NM_021887	ENSMUSG00000030745	Il21r	NILR	interleukin 21 receptor	protein-coding
mm_57911.1	chr6	133105649	133105679	-	1	NA	3' UTR (NM_001163445, exon 1 of 1)	3' UTR (NM_001163445, exon 1 of 1)	425	NR_073368	381820	Mm.291762	NM_001163445	ENSMUSG00000072704	Smim10l1	2700089E24Rik|AI662692	small integral membrane protein 10 like 1	protein-coding
mm_117882.1	chr13	99344621	99344631	-	1	NA	promoter-TSS (NM_026873)	promoter-TSS (NM_026873)	52	NM_026873	68927	Mm.276502	NM_026873	ENSMUSG00000021650	Ptcd2	1190005P08Rik	pentatricopeptide repeat domain 2	protein-coding
mm_140780.1	chr17	17883921	17883954	-	1	NA	promoter-TSS (NM_013521)	promoter-TSS (NM_013521)	2	NM_013521	14293	Mm.56951	NM_013521	ENSMUSG00000045551	Fpr1	FPR|LXA4R|fMLF-R	formyl peptide receptor 1	protein-coding
mm_111788.1	chr12	104761507	104761524	-	1	NA	Intergenic	RLTR17|LTR|ERVK	-9563	NM_148948	192119	Mm.21135	NM_148948	ENSMUSG00000041415	Dicer1	1110006F08Rik|D12Ertd7e|mKIAA0928	dicer 1, ribonuclease type III	protein-coding
mm_166713.1	chr6	118011498	118011511	+	1	NA	promoter-TSS (NM_001316749)	promoter-TSS (NM_001316749)	-33	NM_001316749	70727	Mm.87660	NM_027526	ENSMUSG00000030134	Rasgef1a	6330404M18Rik|AI835194	RasGEF domain family, member 1A	protein-coding
mm_139030.1	chr17	46161127	46161148	+	1	NA	5' UTR (NM_019581, exon 1 of 12)	5' UTR (NM_019581, exon 1 of 12)	105	NM_001145979	56055	Mm.22147	NM_019581	ENSMUSG00000023952	Gtpbp2	nmf205	GTP binding protein 2	protein-coding
mm_76427.1	chr8	84978102	84978116	-	1	NA	exon (NM_008416, exon 1 of 1)	exon (NM_008416, exon 1 of 1)	639	NM_008416	16477	Mm.1167	NM_008416	ENSMUSG00000052837	Junb	-	jun B proto-oncogene	protein-coding
mm_112467.1	chr13	5868084	5868094	+	1	NA	3' UTR (NM_011803, exon 4 of 4)	3' UTR (NM_011803, exon 4 of 4)	6600	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_169150.1	chr13	62778932	62778951	+	1	NA	intron (NM_001256065, intron 1 of 3)	intron (NM_001256065, intron 1 of 3)	6867	NM_001256065	380850	Mm.439823	NM_001256065	ENSMUSG00000091183	Gm5141	-	predicted gene 5141	protein-coding
mm_7154.1	chr1	91456463	91456473	-	1	NA	intron (NM_011066, intron 1 of 22)	intron (NM_011066, intron 1 of 22)	2860	NM_011066	18627	Mm.482463	NM_011066	ENSMUSG00000055866	Per2	mKIAA0347|mPer2	period circadian clock 2	protein-coding
mm_102209.1	chr11	54850490	54850524	-	1	NA	intron (NM_029327, intron 2 of 4)	intron (NM_029327, intron 2 of 4)	10084	NM_029327	75530	Mm.83578	NM_029327	ENSMUSG00000020268	Lyrm7	1700024C24Rik|9330147L21Rik	LYR motif containing 7	protein-coding
mm_90109.1	chr10	117268260	117268262	+	1	NA	Intergenic	MT2B1|LTR|ERVL	14011	NM_017372	17105	Mm.45436	NM_017372	ENSMUSG00000069516	Lyz2	AI326280|Lys|Lysm|Lyzf2|Lyzs|Lzm|Lzm-s1|Lzp	lysozyme 2	protein-coding
mm_73698.1	chr8	111643494	111643540	+	1	NA	promoter-TSS (NM_011742)	promoter-TSS (NM_011742)	74	NM_011742	22640	Mm.4184	NM_011742	ENSMUSG00000055835	Zfp1	Fnp-1|Zfp-1|mkr-1	zinc finger protein 1	protein-coding
mm_54943.1	chr6	48572661	48572677	-	1	NA	5' UTR (NM_001347167, exon 1 of 6)	5' UTR (NM_001347167, exon 1 of 6)	133	NM_001347168	71660	Mm.28231	NM_027852	ENSMUSG00000009281	Rarres2	0610007L05Rik|AI303516	retinoic acid receptor responder (tazarotene induced) 2	protein-coding
mm_133935.1	chr16	3872379	3872411	-	1	NA	promoter-TSS (NM_001033159)	promoter-TSS (NM_001033159)	-21	NM_001033159	71063	Mm.379190	NM_001033159	ENSMUSG00000039789	Zfp597	4933407K12Rik|AI462383|AI666357	zinc finger protein 597	protein-coding
mm_23076.1	chr3	36469241	36469248	+	1	NA	intron (NM_009673, intron 2 of 12)	MTB_Mm|LTR|ERVL-MaLR	6280	NR_105976	102466786		NR_105976	ENSMUSG00000098808	Mir7009	Gm27472|mmu-mir-7009	microRNA 7009	ncRNA
mm_125866.1	chr15	75474502	75474532	+	1	NA	Intergenic	Intergenic	25065	NM_001347049	102637705		NM_001347049	ENSMUSG00000093626	Ly6l	Gm20654	lymphocyte antigen 6 complex, locus L	protein-coding
mm_114801.1	chr13	90923123	90923170	+	1	NA	promoter-TSS (NM_024175)	promoter-TSS (NM_024175)	24	NM_024175	66475	Mm.306302	NM_024175	ENSMUSG00000049517	Rps23	2410044J15Rik	ribosomal protein S23	protein-coding
mm_37773.1	chr4	129819916	129819933	-	1	NA	promoter-TSS (NM_001164745)	promoter-TSS (NM_001164745)	-555	NM_008974	19244	Mm.193688	NM_008974	ENSMUSG00000028788	Ptp4a2	Prl-2	protein tyrosine phosphatase 4a2	protein-coding
mm_38261.1	chr4	136880345	136880353	-	1	NA	exon (NM_009777, exon 3 of 3)	exon (NM_009777, exon 3 of 3)	5828	NM_009777	12260	Mm.2570	NM_009777	ENSMUSG00000036905	C1qb	-	complement component 1, q subcomponent, beta polypeptide	protein-coding
mm_153668.1	chr19	44396027	44396042	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	11675	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_86847.1	chr10	21593113	21593122	+	1	NA	promoter-TSS (NR_027968)	promoter-TSS (NR_027968)	-28	NR_027968	67692	Mm.54306	NM_183266	ENSMUSG00000050844	1700020N01Rik	-	RIKEN cDNA 1700020N01 gene	ncRNA
mm_121316.1	chr14	109546056	109546057	+	1	NA	Intergenic	L1MDa|LINE|L1	85826	NR_039542	100628607		NR_039542	ENSMUSG00000092639	Mir3964	mmu-mir-3964|mu-mir-3964	microRNA 3964	ncRNA
mm_92652.1	chr10	80399479	80399516	-	1	NA	promoter-TSS (NM_013595)	promoter-TSS (NM_013595)	34	NM_013595	17192	Mm.7142	NM_013595	ENSMUSG00000035478	Mbd3	AI181826|AU019209	methyl-CpG binding domain protein 3	protein-coding
mm_157322.1	chrX	23266752	23266806	-	1	NA	promoter-TSS (NM_001310466)	promoter-TSS (NM_001310466)	23	NM_001310466	67455	Mm.224306	NM_026167	ENSMUSG00000036782	Klhl13	1200009K10Rik|AI451128|Bklhd2|D130072F20Rik	kelch-like 13	protein-coding
mm_32458.1	chr4	107381102	107381119	+	1	NA	intron (NM_028355, intron 6 of 17)	intron (NM_028355, intron 6 of 17)	13326	NM_028355	72787	Mm.28478	NM_028355	ENSMUSG00000028614	Ndc1	2810475A17Rik|AI450313|Tmem48|sks	NDC1 transmembrane nucleoporin	protein-coding
mm_133491.1	chr16	90284558	90284626	+	1	NA	promoter-TSS (NM_001346799)	promoter-TSS (NM_001346799)	-89	NM_001346799	224432	Mm.439811	NM_178923	ENSMUSG00000022983	Scaf4	AA517739|Sfrs15|Sra4|Srsf15	SR-related CTD-associated factor 4	protein-coding
mm_19463.1	chr2	92392635	92392654	-	1	NA	promoter-TSS (NM_001202446)	promoter-TSS (NM_001202446)	39	NM_001202446	19099	Mm.2720	NM_011162	ENSMUSG00000027223	Mapk8ip1	IB1|JIP-1|Jip1|Prkm8ip|Skip|mjip-2a	mitogen-activated protein kinase 8 interacting protein 1	protein-coding
mm_27389.1	chr3	50637424	50637428	-	1	NA	Intergenic	Intergenic	-193813	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_163227.1	chr11	102440616	102440618	+	1	NA	intron (NM_199200, intron 3 of 7)	B3|SINE|B2	7046	NM_199200	217219	Mm.259924	NM_199200	ENSMUSG00000034685	Fam171a2	-	family with sequence similarity 171, member A2	protein-coding
mm_101857.1	chr11	48871177	48871190	-	1	NA	5' UTR (NM_008326, exon 1 of 3)	5' UTR (NM_008326, exon 1 of 3)	163	NM_008326	15944	Mm.29938	NM_008326	ENSMUSG00000046879	Irgm1	Ifggd3|Ifi1|Iigp3|Iipg3|Irgm|LRG-47	immunity-related GTPase family M member 1	protein-coding
mm_148488.1	chr19	4151665	4151683	+	1	NA	exon (NM_011778, exon 8 of 11)	exon (NM_011778, exon 8 of 11)	-2972	NM_016933	19265	Mm.271937	NM_016933	ENSMUSG00000045826	Ptprcap	AI605264|CD-45-AP|LPAP|LSM-1	protein tyrosine phosphatase, receptor type, C polypeptide-associated protein	protein-coding
mm_117118.1	chr13	60843018	60843032	-	1	NA	intron (NM_178098, intron 7 of 7)	intron (NM_178098, intron 7 of 7)	21391	NM_178098	214639	Mm.19839	NM_178098	ENSMUSG00000050345	4930486L24Rik	AW545031	RIKEN cDNA 4930486L24 gene	protein-coding
mm_155989.1	chrX	106143686	106143694	+	1	NA	intron (NM_205820, intron 1 of 2)	ID_B1|SINE|B4	415	NM_205820	279572	Mm.336203	NM_205820	ENSMUSG00000033777	Tlr13	AI666735|Gm713	toll-like receptor 13	protein-coding
mm_164554.1	chr17	13867566	13867596	+	1	NA	intron (NM_010806, intron 22 of 32)	intron (NM_010806, intron 22 of 32)	-80792	NM_001122977	635895	Mm.388844	NM_001122977	ENSMUSG00000067941	Gm7168	EG635895	predicted gene 7168	protein-coding
mm_66576.1	chr7	45336247	45336255	-	1	NA	exon (NM_010473, exon 1 of 6)	exon (NM_010473, exon 1 of 6)	982	NM_010473	15464	Mm.39968	NM_010473	ENSMUSG00000038239	Hrc	-	histidine rich calcium binding protein	protein-coding
mm_103641.1	chr11	78963410	78963437	-	1	NA	exon (NM_010708, exon 11 of 11)	exon (NM_010708, exon 11 of 11)	21501	NM_001159301	16859	Mm.341434	NM_010708	ENSMUSG00000001123	Lgals9	AA407335|AI194909|AI265545|LGALS35|Lgals5|gal-9|galectin-9	lectin, galactose binding, soluble 9	protein-coding
mm_159739.1	chr5	66337621	66337621	-	1	NA	promoter-TSS (NM_001201416)	promoter-TSS (NM_001201416)	44	NM_001201416	11787	Mm.5159	NM_009686	ENSMUSG00000029207	Apbb2	2310007D03Rik|FE65L1|Rirl1|TR2L|Zfra	amyloid beta (A4) precursor protein-binding, family B, member 2	protein-coding
mm_83009.1	chr9	36767573	36767586	-	1	NA	promoter-TSS (NM_008408)	promoter-TSS (NM_008408)	-1	NM_008408	16430	Mm.2863	NM_008408	ENSMUSG00000032116	Stt3a	AA408947|BB081708|Itm1	STT3, subunit of the oligosaccharyltransferase complex, homolog A (S. cerevisiae)	protein-coding
mm_118780.1	chr14	24082078	24082083	+	1	NA	Intergenic	Intergenic	-6797	NR_106069	102465697		NR_106069	ENSMUSG00000105723	Mir7210	mir-7210|mmu-mir-7210	microRNA 7210	ncRNA
mm_137864.1	chr17	31296723	31296794	+	1	NA	5' UTR (NM_001242427, exon 1 of 20)	5' UTR (NM_001242427, exon 1 of 20)	534	NM_001242427	224674	Mm.311395	NM_153062	ENSMUSG00000024036	Slc37a1	G3PP	solute carrier family 37 (glycerol-3-phosphate transporter), member 1	protein-coding
mm_22386.1	chr2	181157022	181157042	-	1	NA	promoter-TSS (NM_007906)	promoter-TSS (NM_007906)	-17	NM_007906	13628	Mm.2645	NM_007906	ENSMUSG00000016349	Eef1a2	Eef1a|S1|wasted|wst	eukaryotic translation elongation factor 1 alpha 2	protein-coding
mm_119174.1	chr14	32165529	32165541	+	1	NA	promoter-TSS (NM_001284319)	promoter-TSS (NM_001284319)	-51	NM_001284319	27057	Mm.371598	NM_019744	ENSMUSG00000056234	Ncoa4	ARA70|Rfg	nuclear receptor coactivator 4	protein-coding
mm_102617.1	chr11	62458509	62458548	-	1	NA	promoter-TSS (NM_001039536)	promoter-TSS (NM_001039536)	68	NM_001039536	327942	Mm.390358	NM_199026	ENSMUSG00000014245	Pigl	Gm737	phosphatidylinositol glycan anchor biosynthesis, class L	protein-coding
mm_60970.1	chr7	48789018	48789060	+	1	NA	promoter-TSS (NM_028031)	promoter-TSS (NM_028031)	36	NM_028031	243983	Mm.279116	NM_028031	ENSMUSG00000030471	Zdhhc13	2410004E01Rik|C530010M18|HIP3RP|Hip14l|kojak|skc4	zinc finger, DHHC domain containing 13	protein-coding
mm_64172.1	chr7	141457003	141457009	+	1	NA	intron (NR_028142, intron 2 of 9)	intron (NR_028142, intron 2 of 9)	1818	NM_001163689	66853	Mm.29998	NM_025802	ENSMUSG00000025509	Pnpla2	0610039C21Rik|1110001C14Rik|Atgl|TTS-2.2	patatin-like phospholipase domain containing 2	protein-coding
mm_5918.1	chr1	55088031	55088102	-	1	NA	promoter-TSS (NM_010477)	promoter-TSS (NM_010477)	-82	NM_008303	15528	Mm.215667	NM_008303	ENSMUSG00000073676	Hspe1	10kDa|Hsp10|mt-cpn10	heat shock protein 1 (chaperonin 10)	protein-coding
mm_51869.1	chr6	90552152	90552165	+	1	NA	intron (NM_027406, intron 1 of 22)	B1F1|SINE|Alu	1310	NM_027406	107747	Mm.30035	NM_027406	ENSMUSG00000030088	Aldh1l1	1810048F20Rik|FDH|Fthfd|Neut2	aldehyde dehydrogenase 1 family, member L1	protein-coding
mm_26894.1	chr3	19238481	19238485	-	1	NA	intron (NM_001122759, intron 5 of 12)	B1_Mur2|SINE|Alu	26525	NM_008802	18583	Mm.355614	NM_008802	ENSMUSG00000069094	Pde7a	AU015378|AW047537	phosphodiesterase 7A	protein-coding
mm_126986.1	chr15	94543606	94543658	+	1	NA	promoter-TSS (NM_029926)	promoter-TSS (NM_029926)	-28	NM_029926	266632	Mm.422858	NM_029926	ENSMUSG00000059883	Irak4	8430405M07Rik|9330209D03Rik|IRAK-4|NY-REN-64	interleukin-1 receptor-associated kinase 4	protein-coding
mm_36992.1	chr4	110286520	110286530	-	1	NA	5' UTR (NM_010488, exon 1 of 7)	5' UTR (NM_010488, exon 1 of 7)	309	NM_010488	15572	Mm.3970	NM_010488	ENSMUSG00000028546	Elavl4	Elav|Hud|PNEM	ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4 (Hu antigen D)	protein-coding
mm_61232.1	chr7	64505361	64505364	+	1	NA	intron (NM_001291166, intron 1 of 14)	intron (NM_001291166, intron 1 of 14)	3224	NM_001291167	11784	Mm.4657	NM_007461	ENSMUSG00000030519	Apba2	X11-like|X11L|XllL|mXllL	amyloid beta (A4) precursor protein-binding, family A, member 2	protein-coding
mm_75022.1	chr8	31168700	31168746	-	1	NA	promoter-TSS (NM_026453)	promoter-TSS (NM_026453)	1	NM_026453	67920	Mm.289818	NM_026453	ENSMUSG00000031578	Mak16	2600016B03Rik|AI314911|Rbm13	MAK16 homolog	protein-coding
mm_62018.1	chr7	91509145	91509149	+	1	NA	intron (NM_011807, intron 2 of 22)	intron (NM_011807, intron 2 of 22)	418361	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_134863.1	chr16	28447018	28447033	-	1	NA	promoter-TSS (NM_183064)	promoter-TSS (NM_183064)	-950	NM_001276420	14167	Mm.7996	NM_010199	ENSMUSG00000022523	Fgf12	AV114868|B230343J05Rik|FGF-12|FHF-1|Fhf1	fibroblast growth factor 12	protein-coding
mm_21512.1	chr2	163625471	163625534	-	1	NA	exon (NM_012032, exon 10 of 10)	exon (NM_012032, exon 10 of 10)	18290	NM_001305803	76080	Mm.89828	NM_029512	ENSMUSG00000017679	Ttpal	3110080A02Rik|5830472M02Rik	tocopherol (alpha) transfer protein-like	protein-coding
mm_65933.1	chr7	30323036	30323049	-	1	NA	promoter-TSS (NM_001033140)	promoter-TSS (NM_001033140)	-667	NM_001033140	68332	Mm.6844	NM_001033140	ENSMUSG00000074211	Sdhaf1	0610010E21Rik|AI430885|AW490662|Lyrm8	succinate dehydrogenase complex assembly factor 1	protein-coding
mm_42634.1	chr5	118486951	118486994	+	1	NA	Intergenic	Intergenic	-73747	NM_001347445	76199	Mm.206238	NM_172424	ENSMUSG00000018076	Med13l	2210413I17Rik|6330591G05Rik|9030618F05Rik|Thrap2|Trap240L|mKIAA1025	mediator complex subunit 13-like	protein-coding
mm_56689.1	chr6	114041954	114042003	-	1	NA	5' UTR (NM_009723, exon 1 of 22)	5' UTR (NM_009723, exon 1 of 22)	102	NM_009723	11941	Mm.321755	NM_009723	ENSMUSG00000030302	Atp2b2	D6Abb2e|Gena300|PMCA2|Tmy|dfw|jog|wms|wri	ATPase, Ca++ transporting, plasma membrane 2	protein-coding
mm_139361.1	chr17	50530918	50530929	+	1	NA	intron (NM_013880, intron 1 of 5)	intron (NM_013880, intron 1 of 5)	21376	NM_013880	224860	Mm.217362	NM_013880	ENSMUSG00000038910	Plcl2	PLC-L2|PRIP-2|Plce2|mKIAA1092	phospholipase C-like 2	protein-coding
mm_124358.1	chr14	105138998	105139002	-	1	NA	intron (NM_134077, intron 13 of 20)	intron (NM_134077, intron 13 of 20)	-24324	NR_040628	100502987	Mm.124957	NR_040628		Gm17066	-	predicted gene 17066	ncRNA
mm_82676.1	chr9	22131876	22131885	-	1	NA	promoter-TSS (NM_001102404)	promoter-TSS (NM_001102404)	-15	NM_001102404	11433	Mm.46354	NM_007388	ENSMUSG00000001348	Acp5	TRACP|TRAP	acid phosphatase 5, tartrate resistant	protein-coding
mm_136788.1	chr17	10840423	10840437	+	1	NA	promoter-TSS (NM_016694)	promoter-TSS (NM_016694)	71	NM_016694	50873	Mm.311110	NM_016694	ENSMUSG00000023826	Park2	PRKN	Parkinson disease (autosomal recessive, juvenile) 2, parkin	protein-coding
mm_169668.1	chr15	62032321	62032336	+	1	NA	Intergenic	Intergenic	-5658	NR_132747	19296	Mm.4608	NM_011222	ENSMUSG00000097039	Pvt1	Ayu21-84Imeg|Gt(pU21)84Imeg|Mis-1|Mlvi-1|Pvt-1	plasmacytoma variant translocation 1	ncRNA
mm_36604.1	chr4	88938436	88938479	-	1	NA	intron (NR_132735, intron 1 of 2)	L1M4b|LINE|L1	3585	NR_132734	106557447	Mm.484668	NR_132734		LOC106557447	-	uncharacterized LOC106557447	ncRNA
mm_125807.1	chr15	74926164	74926177	+	1	NA	Intergenic	Intergenic	-28881	NM_001164039	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_30400.1	chr3	152252919	152252963	-	1	NA	exon (NM_199465, exon 4 of 13)	exon (NM_199465, exon 4 of 13)	13379	NM_199465	68810	Mm.200188	NM_199465	ENSMUSG00000039103	Nexn	1110046H09Rik|AA553326|NELIN	nexilin	protein-coding
mm_82490.1	chr9	18473568	18473582	-	1	NA	promoter-TSS (NM_028935)	promoter-TSS (NM_028935)	-16	NM_028935	72230	Mm.289689	NM_028935	ENSMUSG00000074500	Zfp558	1700007A21Rik|4932704I17Rik|Zfp558-ps	zinc finger protein 558	protein-coding
mm_68766.1	chr7	121946281	121946326	-	1	NA	intron (NM_001033318, intron 9 of 16)	intron (NM_001033318, intron 9 of 16)	35390	NM_001033318	233824	Mm.442015	NM_001033318	ENSMUSG00000034951	Cog7	5630400E24Rik|Gm167	component of oligomeric golgi complex 7	protein-coding
mm_123046.1	chr14	55591078	55591118	-	1	NA	promoter-TSS (NM_011190)	promoter-TSS (NM_011190)	3	NM_001029855	19188	Mm.371573	NM_011190	ENSMUSG00000079197	Psme2	AA589371|AI788882|PA28b	proteasome (prosome, macropain) activator subunit 2 (PA28 beta)	protein-coding
mm_27350.1	chr3	50415717	50415731	-	1	NA	intron (NM_011990, intron 6 of 11)	intron (NM_011990, intron 6 of 11)	27889	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_56545.1	chr6	99726420	99726426	-	1	NA	promoter-TSS (NM_001170419)	promoter-TSS (NM_001170419)	-31	NM_001170419	50501	Mm.87365	NM_015768	ENSMUSG00000030069	Prok2	Bv8|PK2|Prok1	prokineticin 2	protein-coding
mm_117717.1	chr13	95375306	95375321	-	1	NA	promoter-TSS (NM_025630)	promoter-TSS (NM_025630)	44	NM_025630	66549	Mm.36785	NM_025630	ENSMUSG00000021681	Aggf1	2010009L17Rik|2310029P06Rik|AW112072|Peg3|VG5Q	angiogenic factor with G patch and FHA domains 1	protein-coding
mm_105311.1	chr11	102846167	102846180	-	1	NA	exon (NM_001109995, exon 18 of 28)	exon (NM_001109995, exon 18 of 28)	9877	NM_080846	75689	Mm.44408	NM_080846	ENSMUSG00000020928	Higd1b	2310056K19Rik	HIG1 domain family, member 1B	protein-coding
mm_150784.1	chr19	44296633	44296653	+	1	NA	intron (NM_009128, intron 2 of 5)	intron (NM_009128, intron 2 of 5)	2967	NM_009128	20250	Mm.487021	NM_009128	ENSMUSG00000025203	Scd2	Mir5114|Scd-2|mir-5114|swty	stearoyl-Coenzyme A desaturase 2	protein-coding
mm_158434.1	chrX	139998520	139998566	-	1	NA	promoter-TSS (NM_001290630)	promoter-TSS (NM_001290630)	52	NM_153586	237073	Mm.256670	NM_153586	ENSMUSG00000031433	Rbm41	BB131279|D330023I21Rik	RNA binding motif protein 41	protein-coding
mm_95798.1	chr11	55103709	55103724	+	1	NA	exon (NM_010299, exon 2 of 4)	exon (NM_010299, exon 2 of 4)	5731	NM_010299	14667	Mm.287807	NM_010299	ENSMUSG00000000594	Gm2a	AA408702|AW215435|GM2-AP|SAP-3	GM2 ganglioside activator protein	protein-coding
mm_55101.1	chr6	49867768	49867773	-	1	NA	Intergenic	Intergenic	45060	NM_023456	109648	Mm.154796	NM_023456	ENSMUSG00000029819	Npy	0710005A05Rik	neuropeptide Y	protein-coding
mm_158931.1	chr1	65926514	65926514	+	1	NA	promoter-TSS (NM_027010)	promoter-TSS (NM_027010)	-8	NM_027010	12969	Mm.275362	NM_027010	ENSMUSG00000025945	Crygf	3110001K11Rik|Cryg-2|DGcry-2|Len-2	crystallin, gamma F	protein-coding
mm_80989.1	chr9	103305157	103305255	+	1	NA	promoter-TSS (NM_176979)	promoter-TSS (NM_176979)	-121	NM_176979	235559	Mm.259893	NM_176979	ENSMUSG00000032555	Topbp1	1110031N14Rik|2810429C13Rik|AI256758|D430026L04Rik|mKIAA0259	topoisomerase (DNA) II binding protein 1	protein-coding
mm_152034.1	chr19	6117844	6117860	-	1	NA	exon (NM_133678, exon 1 of 2)	exon (NM_133678, exon 1 of 2)	734	NM_133678	66406	Mm.303924	NM_133678	ENSMUSG00000024790	Sac3d1	2410004C24Rik|AU015683|shd1	SAC3 domain containing 1	protein-coding
mm_127864.1	chr15	8359257	8359273	-	1	NA	exon (NM_027707, exon 9 of 47)	exon (NM_027707, exon 9 of 47)	85198	NM_027707	71175	Mm.240329	NM_027707	ENSMUSG00000022141	Nipbl	Idn3	Nipped-B homolog (Drosophila)	protein-coding
mm_33013.1	chr4	120854848	120854867	+	1	NA	Intergenic	CpG	-23012	NM_182929	242662	Mm.192502	NM_182929	ENSMUSG00000032890	Rims3	A730060M23Rik|Nim3|Rim3|mKIAA0237	regulating synaptic membrane exocytosis 3	protein-coding
mm_141173.1	chr17	26572243	26572258	-	1	NA	intron (NM_026170, intron 1 of 9)	intron (NM_026170, intron 1 of 9)	10738	NM_026170	67458	Mm.30496	NM_026170	ENSMUSG00000001576	Ergic1	1200007D18Rik|maa-136	endoplasmic reticulum-golgi intermediate compartment (ERGIC) 1	protein-coding
mm_55978.1	chr6	85869108	85869123	-	1	NA	promoter-TSS (NM_053096)	promoter-TSS (NM_053096)	22	NM_053096	93673	Mm.24251	NM_053096	ENSMUSG00000033634	Nat8f2	Cml2	N-acetyltransferase 8 (GCN5-related) family member 2	protein-coding
mm_13913.1	chr2	120502320	120502332	+	1	NA	intron (NM_001109761, intron 14 of 20)	intron (NM_001109761, intron 14 of 20)	25417	NM_001109761	12335	Mm.458021	NM_007601	ENSMUSG00000079110	Capn3	AI323605|Capa-3|Capa3|Lp82|p94	calpain 3	protein-coding
mm_82808.1	chr9	29963113	29963141	-	1	NA	promoter-TSS (NM_172290)	promoter-TSS (NM_172290)	2	NM_172290	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding
mm_17147.1	chr2	25196743	25196755	-	1	NA	promoter-TSS (NM_146115)	promoter-TSS (NM_146115)	64	NM_146115	227612	Mm.119747	NM_146115	ENSMUSG00000059555	Tor4a	A830007P12Rik	torsin family 4, member A	protein-coding
mm_8419.1	chr1	152288036	152288046	-	1	NA	Intergenic	Intergenic	98641	NM_025677	66637	Mm.379120	NM_025677	ENSMUSG00000014980	Tsen15	5730449L18Rik|AL023077|Sen15	tRNA splicing endonuclease subunit 15	protein-coding
mm_149675.1	chr19	20405252	20405261	+	1	NA	promoter-TSS (NR_045817)	promoter-TSS (NR_045817)	-32	NR_045817	68994	Mm.261028	NM_183277	ENSMUSG00000094732	1500015L24Rik	-	RIKEN cDNA 1500015L24 gene	ncRNA
mm_59720.1	chr7	28781565	28781577	+	1	NA	promoter-TSS (NR_040339)	promoter-TSS (NR_040339)	-57	NR_040339	100503790	Mm.446894	NR_040339		Gm19897	-	predicted gene, 19897	ncRNA
mm_58965.1	chr7	18962561	18962564	+	1	NA	3' UTR (NM_001029877, exon 4 of 4)	3' UTR (NM_001029877, exon 4 of 4)	-24962	NM_194064	378430	Mm.277153	NM_194064	ENSMUSG00000051965	Nanos2	nos2	nanos homolog 2 (Drosophila)	protein-coding
mm_13866.1	chr2	119799543	119799572	+	1	NA	promoter-TSS (NM_019392)	promoter-TSS (NM_019392)	43	NM_019392	22174	Mm.2901	NM_019392	ENSMUSG00000027298	Tyro3	AI323366|Brt|Dtk|Etk-2|Rse|Sky|TK19-2|Tif|etk2/tyro3|tk19-1	TYRO3 protein tyrosine kinase 3	protein-coding
mm_71881.1	chr8	69812338	69812353	+	1	NA	intron (NM_198101, intron 7 of 20)	B2_Mm1t|SINE|B2	3658	NM_198101	78816	Mm.324305	NM_198101	ENSMUSG00000036246	Gmip	5031419I10Rik	Gem-interacting protein	protein-coding
mm_51299.1	chr6	72309756	72309771	+	1	NA	exon (NM_147779, exon 7 of 12)	exon (NM_147779, exon 7 of 12)	5153	NM_147779	20388	Mm.46033	NM_147779	ENSMUSG00000056370	Sftpb	AI562151|SF-B|SP-B|Sftp-3|Sftp3	surfactant associated protein B	protein-coding
mm_15976.1	chr2	166447542	166447578	+	1	NA	non-coding (NR_015558, exon 1 of 3)	non-coding (NR_015558, exon 1 of 3)	109	NR_015558	319684	Mm.399746	NR_015558		5031425F14Rik	-	RIKEN cDNA 5031425F14 gene	ncRNA
mm_139386.1	chr17	52163133	52163139	+	1	NA	Intergenic	Intergenic	280409	NR_045095	100504169	Mm.417731	NR_045095		Gm20098	-	predicted gene, 20098	ncRNA
mm_3155.1	chr1	135155293	135155304	+	1	NA	3' UTR (NM_026823, exon 7 of 7)	3' UTR (NM_026823, exon 7 of 7)	8464	NM_026823	68724	Mm.174998	NM_026823	ENSMUSG00000026426	Arl8a	1110033P22Rik|Arl10b|gie2	ADP-ribosylation factor-like 8A	protein-coding
mm_93666.1	chr10	117701617	117701625	-	1	NA	intron (NM_001288586, intron 4 of 10)	intron (NM_001288586, intron 4 of 10)	9137	NM_010786	17246	Mm.22670	NM_010786	ENSMUSG00000020184	Mdm2	1700007J15Rik|AA415488|Mdm-2	transformed mouse 3T3 cell double minute 2	protein-coding
mm_70192.1	chr7	143822794	143822857	-	1	NA	promoter-TSS (NM_007856)	promoter-TSS (NM_007856)	27	NM_001308095	78914	Mm.35104	NM_030221	ENSMUSG00000031090	Nadsyn1	9130012B15Rik	NAD synthetase 1	protein-coding
mm_94721.1	chr11	20632049	20632059	+	1	NA	promoter-TSS (NM_001038625)	promoter-TSS (NM_001038625)	77	NM_001038625	58172	Mm.339676	NM_021372	ENSMUSG00000049800	Sertad2	AB041541|AU021878|Kiaa0127|MNCb-1504|SEI-2|Sei2|TRIP-Br2|mKIAA0127	SERTA domain containing 2	protein-coding
mm_67423.1	chr7	80340153	80340210	-	1	NA	promoter-TSS (NM_133952)	promoter-TSS (NM_133952)	38	NM_133952	101869	Mm.243024	NM_133952	ENSMUSG00000030533	Unc45a	AW538196	unc-45 myosin chaperone A	protein-coding
mm_123112.1	chr14	55885979	55885987	-	1	NA	exon (NM_027143, exon 2 of 8)	exon (NM_027143, exon 2 of 8)	1041	NR_138134	219094	Mm.37592	NM_027143	ENSMUSG00000047153	Khnyn	6330555F21|9130227C08Rik|AI605259|Kiaa0323|mKIAA0323	KH and NYN domain containing	protein-coding
mm_84475.1	chr9	66804327	66804341	-	1	NA	Intergenic	MTE2a|LTR|ERVL-MaLR	-8911	NM_177583	208117	Mm.41291	NM_177583	ENSMUSG00000032375	Aph1b	2310057K14Rik|Aph1c	aph1 homolog B, gamma secretase subunit	protein-coding
mm_41835.1	chr5	104309312	104309322	+	1	NA	exon (NM_008318, exon 6 of 7)	exon (NM_008318, exon 6 of 7)	10030	NM_008318	15891	Mm.4987	NM_008318	ENSMUSG00000029306	Ibsp	BSP|BSP II|BSPII|Bsp2	integrin binding sialoprotein	protein-coding
mm_64093.1	chr7	140968271	140968273	+	1	NA	exon (NM_001112715, exon 1 of 2)	exon (NM_001112715, exon 1 of 2)	196	NM_001112715	68713	Mm.175661	NM_026820	ENSMUSG00000025491	Ifitm1	1110036C17Rik|DSPA2a|Mil-2|Mil2	interferon induced transmembrane protein 1	protein-coding
mm_38396.1	chr4	138836475	138836485	-	1	NA	intron (NM_001122954, intron 1 of 5)	intron (NM_001122954, intron 1 of 5)	4604	NM_001082531	18780	Mm.4675	NM_011108	ENSMUSG00000058908	Pla2g2a	EF|Mom1|Pla2|sPLA2|sPla2-IIA	phospholipase A2, group IIA (platelets, synovial fluid)	protein-coding
mm_96964.1	chr11	70647542	70647581	+	1	NA	promoter-TSS (NM_024211)	promoter-TSS (NM_024211)	274	NM_027445	70510	Mm.261818	NM_027445	ENSMUSG00000040746	Rnf167	0610010G05Rik|5730408C10Rik|AU019305|AV328608	ring finger protein 167	protein-coding
mm_82330.1	chr9	9227504	9227507	-	1	NA	intron (NM_027823, intron 1 of 22)	intron (NM_027823, intron 1 of 22)	-8783	NR_045754	100579151	Mm.412450	NR_045754	ENSMUSG00000085253	Gm16833	-	predicted gene, 16833	ncRNA
mm_166013.1	chr4	119232886	119232888	+	1	NA	promoter-TSS (NM_019782)	promoter-TSS (NM_019782)	-28	NM_001286148	56401	Mm.27961	NM_019782	ENSMUSG00000028641	P3h1	2410024C15Rik|Gros1|Lepre1	prolyl 3-hydroxylase 1	protein-coding
mm_46391.1	chr5	104021949	104021967	-	1	NA	promoter-TSS (NM_053262)	promoter-TSS (NM_053262)	-162	NM_053262	114664	Mm.46019	NM_053262	ENSMUSG00000029311	Hsd17b11	Dhrs8|Pan1b|SDR2|retSDR2	hydroxysteroid (17-beta) dehydrogenase 11	protein-coding
mm_142017.1	chr17	35200565	35200573	-	1	NA	intron (NM_001278601, intron 2 of 2)	intron (NM_001278601, intron 2 of 2)	1438	NM_013693	21926	Mm.1293	NM_013693	ENSMUSG00000024401	Tnf	DIF|TNF-a|TNF-alpha|TNFSF2|TNFalpha|Tnfa|Tnfsf1a|Tnlg1f	tumor necrosis factor	protein-coding
mm_81572.1	chr9	110421694	110421707	+	1	NA	exon (NM_008694, exon 3 of 4)	exon (NM_008694, exon 3 of 4)	1892	NM_008694	18054	Mm.236225	NM_008694	ENSMUSG00000032484	Ngp	bectenecin	neutrophilic granule protein	protein-coding
mm_152040.1	chr19	6127826	6127842	-	1	NA	intron (NM_026912, intron 1 of 7)	intron (NM_026912, intron 1 of 7)	381	NM_026912	69024	Mm.329629	NM_026912	ENSMUSG00000024787	Snx15	1500032B08Rik|E130013C21Rik	sorting nexin 15	protein-coding
mm_75745.1	chr8	69887382	69887401	-	1	NA	promoter-TSS (NM_026818)	promoter-TSS (NM_026818)	1	NM_026818	68709	Mm.334584	NM_026818	ENSMUSG00000044006	Cilp2	1110031K21Rik|AA407300|CLIP-2	cartilage intermediate layer protein 2	protein-coding
mm_126766.1	chr15	85879307	85879372	+	1	NA	promoter-TSS (NM_028063)	promoter-TSS (NM_028063)	12	NM_028063	72026	Mm.158211	NM_028063	ENSMUSG00000022386	Trmu	1110005N20Rik|1600025P05Rik|AI314320|Trmt1	tRNA 5-methylaminomethyl-2-thiouridylate methyltransferase	protein-coding
mm_117446.1	chr13	74770599	74770618	-	1	NA	5' UTR (NM_001301157, exon 1 of 28)	5' UTR (NM_001301157, exon 1 of 28)	128	NM_001301156	12380	Mm.29163	NM_009817	ENSMUSG00000021585	Cast	-	calpastatin	protein-coding
mm_106088.1	chr11	116189543	116189550	-	1	NA	exon (NM_001271898, exon 3 of 14)	exon (NM_001271898, exon 3 of 14)	-9309	NM_027107	69535	Mm.390347	NM_027107	ENSMUSG00000020778	Ten1	2310004N24Rik	TEN1 telomerase capping complex subunit	protein-coding
mm_2977.1	chr1	133108396	133108400	+	1	NA	3' UTR (NM_001099276, exon 33 of 33)	3' UTR (NM_001099276, exon 33 of 33)	-22768	NM_133819	108954	Mm.293628	NM_133819	ENSMUSG00000046062	Ppp1r15b	1810033K10Rik|AI606441|C530022L24Rik|CReP	protein phosphatase 1, regulatory (inhibitor) subunit 15b	protein-coding
mm_163296.1	chr11	120014388	120014400	-	1	NA	promoter-TSS (NR_037225)	promoter-TSS (NR_037225)	-373	NR_037225	100526518		NR_037225	ENSMUSG00000105524	Mir3065	mir-3065|mmu-mir-3065	microRNA 3065	ncRNA
mm_159317.1	chr3	13471555	13471555	+	1	NA	promoter-TSS (NM_001163328)	promoter-TSS (NM_001163328)	-100	NM_178631	76897	Mm.422625	NM_178631	ENSMUSG00000039717	Ralyl	0710005M24Rik	RALY RNA binding protein-like	protein-coding
mm_172800.1	chr9	115432428	115432440	-	1	NA	Intergenic	RLTR9D|LTR|ERVK	50615	NR_130329	100316675		NR_130329	ENSMUSG00000080409	Mir467h	Mirn467h|mmu-mir-467h	microRNA 467h	ncRNA
mm_87003.1	chr10	26799754	26799765	+	1	NA	intron (NM_176837, intron 1 of 14)	intron (NM_176837, intron 1 of 14)	27247	NM_176837	73910	Mm.356496	NM_176837	ENSMUSG00000039031	Arhgap18	4833419J07Rik|AI314906|AI843501	Rho GTPase activating protein 18	protein-coding
mm_128673.1	chr15	60187372	60187383	-	1	NA	Intergenic	Intergenic	-170759	NM_027668	71088	Mm.425950	NM_027668	ENSMUSG00000071749	4933412E24Rik	-	RIKEN cDNA 4933412E24 gene	protein-coding
mm_33445.1	chr4	130663213	130663224	+	1	NA	promoter-TSS (NM_001159603)	promoter-TSS (NM_001159603)	-141	NM_030722	80912	Mm.440206	NM_030722	ENSMUSG00000028580	Pum1	AA517475|Pumm|mKIAA0099	pumilio RNA-binding family member 1	protein-coding
mm_76379.1	chr8	84838600	84838623	-	1	NA	exon (NM_001297607, exon 3 of 9)	exon (NM_001297607, exon 3 of 9)	2054	NM_001297607	19358	Mm.255539	NM_009010	ENSMUSG00000003813	Rad23a	2310040P19Rik|AL024030|HR23A|mHR23A	RAD23 homolog A, nucleotide excision repair protein	protein-coding
mm_145370.1	chr18	56733212	56733227	+	1	NA	exon (NM_010721, exon 5 of 11)	exon (NM_010721, exon 5 of 11)	25406	NM_010721	16906	Mm.4105	NM_010721	ENSMUSG00000024590	Lmnb1	-	lamin B1	protein-coding
mm_98730.1	chr11	96352055	96352070	+	1	NA	exon (NM_134032, exon 1 of 2)	exon (NM_134032, exon 1 of 2)	430	NM_134032	103889	Mm.281153	NM_134032	ENSMUSG00000075588	Hoxb2	AI894218|Hox-2.8|Hoxbes2	homeobox B2	protein-coding
mm_23374.1	chr3	55527876	55527886	+	1	NA	intron (NM_001111052, intron 13 of 13)	intron (NM_001111052, intron 13 of 13)	66123	NM_001195540	13175	Mm.393242	NM_019978	ENSMUSG00000027797	Dclk1	1700113D08Rik|2810480F11Rik|AI836758|Click-I|Cpg16|Dcamkl1|Dcl|Dclk|mKIAA0369	doublecortin-like kinase 1	protein-coding
mm_167915.1	chrX	99459052	99459061	+	1	NA	Intergenic	Intergenic	11679	NM_001083110	18744	Mm.8211	NM_008853	ENSMUSG00000034403	Pja1	praja-1	praja ring finger 1, E3 ubiquitin protein ligase	protein-coding
mm_105270.1	chr11	102406610	102406622	-	1	NA	exon (NM_026542, exon 2 of 12)	exon (NM_026542, exon 2 of 12)	901	NM_026542	68066	Mm.44226	NM_026542	ENSMUSG00000018677	Slc25a39	3010027G13Rik|D11Ertd333e	solute carrier family 25, member 39	protein-coding
mm_154676.1	chrX	7899351	7899362	+	1	NA	promoter-TSS (NM_001252528)	promoter-TSS (NM_001252528)	20	NR_132589	21855	Mm.27393	NM_011591	ENSMUSG00000031158	Timm17b	17kDa|Sfc3|mTim17b	translocase of inner mitochondrial membrane 17b	protein-coding
mm_52065.1	chr6	97509654	97509698	+	1	NA	intron (NM_145148, intron 2 of 23)	intron (NM_145148, intron 2 of 23)	-21856	NM_001346637	232288	Mm.27789	NM_145148	ENSMUSG00000030064	Frmd4b	6030440G05Rik|C87375|GOBLIN|GRSP1|R74720	FERM domain containing 4B	protein-coding
mm_23456.1	chr3	60472595	60472608	+	1	NA	promoter-TSS (NM_001253713)	promoter-TSS (NM_001253713)	-229	NM_001253713	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_65988.1	chr7	30526459	30526464	-	1	NA	exon (NM_001289670, exon 17 of 21)	exon (NM_001289670, exon 17 of 21)	8599	NM_001289670	233071	Mm.190704	NM_178252	ENSMUSG00000036882	Arhgap33	AW324378|NOMA-GAP|Snx26|TCGAP	Rho GTPase activating protein 33	protein-coding
mm_81641.1	chr9	110895771	110895781	+	1	NA	exon (NM_001146059, exon 22 of 27)	exon (NM_001146059, exon 22 of 27)	15454	NM_001146060	235633	Mm.86338	NM_146228	ENSMUSG00000044037	Als2cl	79H19D|79H19E|BC022645|D930044G19Rik|mRn.49018	ALS2 C-terminal like	protein-coding
mm_122042.1	chr14	30009302	30009340	-	1	NA	promoter-TSS (NM_019583)	promoter-TSS (NM_019583)	321	NM_001136240	218865	Mm.259916	NM_172264	ENSMUSG00000015970	Chdh	AU041472|D630034H06Rik	choline dehydrogenase	protein-coding
mm_49173.1	chr6	14901404	14901422	+	1	NA	promoter-TSS (NM_053242)	promoter-TSS (NM_053242)	64	NM_053242	114142	Mm.332919	NM_053242	ENSMUSG00000029563	Foxp2	2810043D05Rik|AI449000|CAG-16|D0Kist7	forkhead box P2	protein-coding
mm_92294.1	chr10	72654707	72654727	-	1	NA	promoter-TSS (NM_025635)	promoter-TSS (NM_025635)	-129	NM_025635	52696	Mm.62876	NM_025635	ENSMUSG00000019923	Zwint	2010007E07Rik|2600001N01Rik|D10Ertd749e|Zwint-1	ZW10 interactor	protein-coding
mm_25265.1	chr3	104789027	104789046	+	1	NA	promoter-TSS (NM_007484)	promoter-TSS (NM_007484)	2	NM_007484	11853	Mm.262	NM_007484	ENSMUSG00000002233	Rhoc	AI324259|Arh9|Arhc	ras homolog family member C	protein-coding
mm_169305.1	chr14	104121979	104121982	+	1	NA	Intergenic	L1Md_T|LINE|L1	-94838	NR_045953	73877	Mm.399172	NR_045953		4930432J09Rik	-	RIKEN cDNA 4930432J09 gene	ncRNA
mm_56800.1	chr6	116656737	116656768	-	1	NA	intron (NM_178045, intron 3 of 10)	(TG)n|Simple_repeat|Simple_repeat	6068	NM_001166580	213393	Mm.38231	NM_145980	ENSMUSG00000048489	8430408G22Rik	Depp|Fseg	RIKEN cDNA 8430408G22 gene	protein-coding
mm_107290.1	chr12	29938043	29938059	+	1	NA	promoter-TSS (NM_181395)	promoter-TSS (NM_181395)	15	NM_181395	69675	Mm.251774	NM_181395	ENSMUSG00000020674	Pxdn	2310075M15Rik|C85409|E330004E07|VPO1|mKIAA0230	peroxidasin	protein-coding
mm_165714.1	chr3	99296546	99296554	+	1	NA	intron (NM_009323, intron 1 of 7)	intron (NM_009323, intron 1 of 7)	42790	NM_009323	21384	Mm.88761	NM_009323	ENSMUSG00000027868	Tbx15	Tbx14|Tbx8|de	T-box 15	protein-coding
mm_60025.1	chr7	30956928	30956963	+	1	NA	promoter-TSS (NM_011680)	promoter-TSS (NM_011680)	-142	NM_011680	22282	Mm.322453	NM_011680	ENSMUSG00000058239	Usf2	Usf-2|bHLHb12	upstream transcription factor 2	protein-coding
mm_2223.1	chr1	90519793	90519824	+	1	NA	Intergenic	Intergenic	-83617	NM_133805	108679	Mm.119177	NM_133805	ENSMUSG00000034432	Cops8	9430009J09Rik|AA408242|Csn8|Sgn8	COP9 signalosome subunit 8	protein-coding
mm_78054.1	chr9	14810666	14810670	+	1	NA	intron (NM_018736, intron 10 of 19)	intron (NM_018736, intron 10 of 19)	26014	NM_018736	17535	Mm.149071	NM_018736	ENSMUSG00000031928	Mre11a	Mre11|Mre11b	MRE11A homolog A, double strand break repair nuclease	protein-coding
mm_119234.1	chr14	33337407	33337415	+	1	NA	intron (NM_153800, intron 4 of 10)	intron (NM_153800, intron 4 of 10)	73613	NM_001310452	26419	Mm.21495	NM_016700	ENSMUSG00000021936	Mapk8	AI849689|JNK|JNK1|Prkm8|SAPK1	mitogen-activated protein kinase 8	protein-coding
mm_13205.1	chr2	93600094	93600114	+	1	NA	Intergenic	MIRb|SINE|MIR	-42330	NM_007442	11695	Mm.389389	NM_007442	ENSMUSG00000040310	Alx4	lst	aristaless-like homeobox 4	protein-coding
mm_117643.1	chr13	92530814	92530858	-	1	NA	promoter-TSS (NM_173392)	promoter-TSS (NM_173392)	-26	NM_173392	218441	Mm.259585	NM_173392	ENSMUSG00000021706	Zfyve16	AI035632|B130024H06Rik|B130031L15|mKIAA0305	zinc finger, FYVE domain containing 16	protein-coding
mm_5146.1	chr1	9748331	9748353	-	1	NA	promoter-TSS (NM_173443)	promoter-TSS (NM_173443)	40	NM_173443	70675	Mm.274493	NM_173443	ENSMUSG00000045210	Vcpip1	4932442A08|5730421J18Rik|5730538E15Rik|VCIP135|mKIAA1850	valosin containing protein (p97)/p47 complex interacting protein 1	protein-coding
mm_375.1	chr1	34011229	34011250	+	1	NA	promoter-TSS (NM_134448)	promoter-TSS (NM_134448)	-586	NM_133833	13518	Mm.336625	NM_010081	ENSMUSG00000026131	Dst	2310001O04Rik|A830042E19Rik|AW554249|BP230|BPAG1-n|Bpag|Bpag1|Macf2|ah|athetoid|dt|mKIAA0728|nmf203|nmf339	dystonin	protein-coding
mm_64622.1	chr7	3666918	3666941	-	1	NA	exon (NM_181820, exon 13 of 15)	exon (NM_181820, exon 13 of 15)	-1089	NM_027203	69757	Mm.389782	NM_027203	ENSMUSG00000078813	Leng1	1500001K17Rik	leukocyte receptor cluster (LRC) member 1	protein-coding
mm_54202.1	chr6	24953645	24953650	-	1	NA	3' UTR (NM_177013, exon 1 of 1)	3' UTR (NM_177013, exon 1 of 1)	2478	NM_177013	319832	Mm.127446	NM_177013	ENSMUSG00000048022	Tmem229a	6332401O19Rik	transmembrane protein 229A	protein-coding
mm_48443.1	chr5	140648939	140648949	-	1	NA	promoter-TSS (NM_175274)	promoter-TSS (NM_175274)	87	NM_001308040	78339	Mm.28947	NM_175274	ENSMUSG00000036565	Ttyh3	2900029G13Rik|AI414930|TTY3|mTTY3	tweety family member 3	protein-coding
mm_124192.1	chr14	98104912	98104914	-	1	NA	intron (NM_007826, intron 1 of 11)	intron (NM_007826, intron 1 of 11)	64852	NM_001038610	13134	Mm.320593	NM_007826	ENSMUSG00000055639	Dach1	Dac|Dach	dachshund 1 (Drosophila)	protein-coding
mm_73945.1	chr8	120114128	120114135	+	1	NA	promoter-TSS (NM_001163762)	promoter-TSS (NM_001163762)	-21	NM_001163762	234797	Mm.101958	NM_172286	ENSMUSG00000031824	6430548M08Rik	AW049007|Kiaa0513|mKIAA0513	RIKEN cDNA 6430548M08 gene	protein-coding
mm_56211.1	chr6	89317973	89317986	-	1	NA	3' UTR (NM_008881, exon 32 of 32)	3' UTR (NM_008881, exon 32 of 32)	-32254	NR_131021	75131	Mm.391482	NR_131021	ENSMUSG00000107622	4930512J16Rik	-	RIKEN cDNA 4930512J16 gene	ncRNA
mm_78619.1	chr9	37555672	37555688	+	1	NA	Intergenic	Intergenic	-2935	NM_022029	64011	Mm.335065	NM_022029	ENSMUSG00000053310	Nrgn	0710001B06Rik|AI838505|NG|NG/RC3|Pss1|R75334|RC3	neurogranin	protein-coding
mm_131089.1	chr16	4886201	4886205	+	1	NA	5' UTR (NM_029657, exon 1 of 17)	5' UTR (NM_029657, exon 1 of 17)	103	NM_001252437	17237	Mm.291326	NM_029657	ENSMUSG00000022517	Mgrn1	2610042J20Rik|mKIAA0544|md|nc	mahogunin, ring finger 1	protein-coding
mm_67209.1	chr7	74346956	74346980	-	1	NA	intron (NM_001038643, intron 3 of 10)	intron (NM_001038643, intron 3 of 10)	207812	NM_023908	108116	Mm.425467	NM_023908	ENSMUSG00000025790	Slco3a1	5830414C08Rik|Anr1|MJAM|OATP-D|R75096|Slc21a11	solute carrier organic anion transporter family, member 3a1	protein-coding
mm_15179.1	chr2	154190777	154190782	+	1	NA	promoter-TSS (NM_001012392)	promoter-TSS (NM_001012392)	-39	NM_001012392	228801	Mm.3783	NM_153418	ENSMUSG00000027485	Bpifb1	Lplunc1	BPI fold containing family B, member 1	protein-coding
mm_14373.1	chr2	129630186	129630199	+	1	NA	3' UTR (NM_001291022, exon 5 of 5)	3' UTR (NM_001291022, exon 5 of 5)	37023	NM_001291022	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_131288.1	chr16	11322877	11322911	+	1	NA	promoter-TSS (NM_028964)	promoter-TSS (NM_028964)	-10	NM_028964	74478	Mm.325831	NM_028964	ENSMUSG00000071669	Snx29	4933437K13Rik|ENSMUSG00000079738|Gm11170|Gm1737|Gm930|Rundc2a	sorting nexin 29	protein-coding
mm_158444.1	chrX	140542596	140542604	-	1	NA	promoter-TSS (NR_122039)	promoter-TSS (NR_122039)	68	NR_122039	14605	Mm.22216	NM_010286	ENSMUSG00000031431	Tsc22d3	DIP|Dsip1|Gilz|TSC-22R|Tilz3	TSC22 domain family, member 3	protein-coding
mm_135478.1	chr16	45986446	45986474	-	1	NA	intron (NM_001134480, intron 1 of 3)	(A)n|Simple_repeat|Simple_repeat	23953	NM_001134480	433022	Mm.380993	NM_001134480	ENSMUSG00000087141	Plcxd2	AW494639|EG433022	phosphatidylinositol-specific phospholipase C, X domain containing 2	protein-coding
mm_93248.1	chr10	95417251	95417269	-	1	NA	promoter-TSS (NM_007706)	promoter-TSS (NM_007706)	-115	NR_045339	70523	Mm.158398	NR_045338	ENSMUSG00000097766	5730420D15Rik	-	RIKEN cDNA 5730420D15 gene	ncRNA
mm_25174.1	chr3	103127528	103127541	+	1	NA	promoter-TSS (NM_177857)	promoter-TSS (NM_177857)	-22	NM_177857	329727	Mm.293641	NM_177857	ENSMUSG00000007379	Dennd2c	A930010I20Rik	DENN/MADD domain containing 2C	protein-coding
mm_119795.1	chr14	54196069	54196076	+	1	NA	Intergenic	Intergenic	57857	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_7552.1	chr1	124600920	124600922	-	1	NA	Intergenic	Intergenic	-555362	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_141622.1	chr17	32891571	32891646	-	1	NA	promoter-TSS (NM_207245)	promoter-TSS (NM_207245)	-5	NM_207245	240066	Mm.26636	NM_207245	ENSMUSG00000095325	Zfp870	AI173952	zinc finger protein 870	protein-coding
mm_57582.1	chr6	127151033	127151039	-	1	NA	promoter-TSS (NM_009829)	promoter-TSS (NM_009829)	12	NM_009829	12444	Mm.333406	NM_009829	ENSMUSG00000000184	Ccnd2	2600016F06Rik|AI256817|BF642806|C86853|Vin-1|Vin1|cD2	cyclin D2	protein-coding
mm_8934.1	chr1	164307201	164307226	-	1	NA	promoter-TSS (NM_001293313)	promoter-TSS (NM_001293313)	271	NM_001160209	66352	Mm.33285	NM_025505	ENSMUSG00000026577	Blzf1	1700030G05Rik|Blzf1l|Golgin-45|Jem-1	basic leucine zipper nuclear factor 1	protein-coding
mm_21779.1	chr2	164847894	164847905	-	1	NA	intron (NM_011125, intron 8 of 15)	B1F|SINE|Alu	9809	NM_011125	18830	Mm.6105	NM_011125	ENSMUSG00000017754	Pltp	Bpife|OD107	phospholipid transfer protein	protein-coding
mm_84195.1	chr9	60545845	60545869	-	1	NA	promoter-TSS (NR_040464)	promoter-TSS (NR_040464)	25	NR_040464	100504561	Mm.410770	NR_040463	ENSMUSG00000111761	9230112J17Rik	-	RIKEN cDNA 9230112J17 gene	ncRNA
mm_76232.1	chr8	83574666	83574676	-	1	NA	intron (NM_134118, intron 1 of 12)	intron (NM_134118, intron 1 of 12)	7913	NM_025843	66916	Mm.29683	NM_025843	ENSMUSG00000033938	Ndufb7	1110002H15Rik	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 7	protein-coding
mm_168997.1	chr13	100350188	100350190	+	1	NA	Intergenic	LTRIS2|LTR|ERV1	-32501	NM_021545	53880	Mm.218759	NM_021545		Naip7	Birc1g|Naip-rs4B|Naip6	NLR family, apoptosis inhibitory protein 7	protein-coding
mm_127802.1	chr15	3995709	3995760	-	1	NA	promoter-TSS (NR_045740)	promoter-TSS (NR_045740)	18	NM_145930	106064	Mm.21299	NM_145930	ENSMUSG00000041935	AW549877	AI195826	expressed sequence AW549877	protein-coding
mm_55500.1	chr6	69764664	69764689	-	1	NA	Intergenic	Intergenic	-437502	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_50570.1	chr6	49051022	49051091	+	1	NA	exon (NM_053110, exon 8 of 11)	exon (NM_053110, exon 8 of 11)	14538	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_90985.1	chr10	13832679	13832707	-	1	NA	intron (NM_001347362, intron 1 of 5)	intron (NM_001347362, intron 1 of 5)	36264	NM_025446	66253	Mm.45755	NM_025446	ENSMUSG00000019806	Aig1	1500031O19Rik|AV064870|AW413422|CGI-103	androgen-induced 1	protein-coding
mm_67837.1	chr7	98379267	98379272	-	1	NA	Intergenic	Intergenic	-17941	NM_001168539	244152	Mm.25317	NM_001024619	ENSMUSG00000049580	Tsku	9530051K01Rik|E2ig4|Lrrc54|Tsk	tsukushi, small leucine rich proteoglycan	protein-coding
mm_140514.1	chr17	5816700	5816701	-	1	NA	Intergenic	Intergenic	17210	NR_045080	78512	Mm.23696	NR_045079	ENSMUSG00000096965	3300005D01Rik	-	RIKEN cDNA 3300005D01 gene	ncRNA
mm_167631.1	chr9	62342339	62342359	+	1	NA	intron (NM_009672, intron 1 of 6)	CpG	1006	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	protein-coding
mm_170992.1	chr2	75191684	75191691	-	1	NA	Intergenic	Intergenic	252492	NR_040635	77269	Mm.389278	NR_040635		9430019J16Rik	-	RIKEN cDNA 9430019J16 gene	ncRNA
mm_121418.1	chr14	119749227	119749238	+	1	NA	promoter-TSS (NR_045621)	promoter-TSS (NR_045621)	5	NR_045621	75432	Mm.443277	NR_045621	ENSMUSG00000100274	1700006F04Rik	-	RIKEN cDNA 1700006F04 gene	ncRNA
mm_143468.1	chr17	71002805	71002854	-	1	NA	promoter-TSS (NM_026064)	promoter-TSS (NM_026064)	-296	NM_026064	67268	Mm.489605	NM_026064	ENSMUSG00000024048	Myl12a	2900073G15Rik|AI838292|C80200	myosin, light chain 12A, regulatory, non-sarcomeric	protein-coding
mm_109476.1	chr12	111421546	111421561	+	1	NA	5' UTR (NM_001289489, exon 2 of 13)	5' UTR (NM_001289489, exon 2 of 13)	4108	NM_001289488	74190	Mm.248640	NM_028807	ENSMUSG00000021280	Exoc3l4	1200009I06Rik|1600013K19Rik	exocyst complex component 3-like 4	protein-coding
mm_9129.1	chr1	170644380	170644392	-	1	NA	promoter-TSS (NM_177068)	promoter-TSS (NM_177068)	-146	NM_177068	320078	Mm.287131	NM_177068	ENSMUSG00000038463	Olfml2b	1110018N05Rik|4832415H08Rik|AI467542	olfactomedin-like 2B	protein-coding
mm_113079.1	chr13	23836898	23836910	+	1	NA	Intergenic	Intergenic	-2530	NM_001164743	105355	Mm.27038	NM_134069	ENSMUSG00000036083	Slc17a3	AW261723|Npt4	solute carrier family 17 (sodium phosphate), member 3	protein-coding
mm_145151.1	chr18	46337295	46337303	+	1	NA	Intergenic	Intergenic	-25371	NM_001160399	240261	Mm.329416	NM_001160399	ENSMUSG00000071855	Ccdc112	8430438M01Rik|AW108467	coiled-coil domain containing 112	protein-coding
mm_40540.1	chr5	57988019	57988041	+	1	NA	intron (NM_001310608, intron 3 of 3)	RMER15-int|LTR|ERVL	269949	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_152167.1	chr19	7297609	7297636	-	1	NA	intron (NM_007928, intron 1 of 17)	intron (NM_007928, intron 1 of 17)	-2175	NM_001080390	13728	Mm.258986	NM_007928	ENSMUSG00000024969	Mark2	EMK-1|Emk|Par-1|Par-1b	MAP/microtubule affinity regulating kinase 2	protein-coding
mm_157475.1	chrX	48139644	48139647	-	1	NA	Intergenic	Intergenic	-6791	NM_001313749	74131	Mm.276131	NM_028773	ENSMUSG00000031101	Sash3	1200013B08Rik|AW413946|SLY1	SAM and SH3 domain containing 3	protein-coding
mm_44589.1	chr5	24925407	24925420	-	1	NA	intron (NM_001310480, intron 2 of 13)	intron (NM_001310480, intron 2 of 13)	-16904	NM_001170555	108099	Mm.33649	NM_145401	ENSMUSG00000028944	Prkag2	2410051C13Rik|AAKG|AAKG2|AI854673|H91620p|WPWS	protein kinase, AMP-activated, gamma 2 non-catalytic subunit	protein-coding
mm_82691.1	chr9	22376200	22376214	-	1	NA	exon (NM_028390, exon 4 of 24)	exon (NM_028390, exon 4 of 24)	3016	NR_030448	751551		NR_030448	ENSMUSG00000076117	Mir680-2	Mirn680-2	microRNA 680-2	ncRNA
mm_3606.1	chr1	151678001	151678008	+	1	NA	intron (NM_022018, intron 5 of 13)	intron (NM_022018, intron 5 of 13)	-77370	NM_001311165	66967	Mm.337691	NM_001039644	ENSMUSG00000043019	Edem3	2310050N11Rik	ER degradation enhancer, mannosidase alpha-like 3	protein-coding
mm_150635.1	chr19	41483102	41483144	+	1	NA	Intergenic	CpG	-42129	NM_001326287	627352	Mm.395111	NM_001326287		Morf4l1b	EG627352|Gm6747	mortality factor 4 like 1B	protein-coding
mm_18087.1	chr2	44927285	44927317	-	1	NA	Intergenic	CpG	-65679	NM_172662	227835	Mm.314312	NM_172662	ENSMUSG00000036890	Gtdc1	E330008O22Rik	glycosyltransferase-like domain containing 1	protein-coding
mm_97055.1	chr11	72607314	72607324	+	1	NA	promoter-TSS (NM_025985)	promoter-TSS (NM_025985)	58	NM_025985	67128	Mm.458052	NM_025985	ENSMUSG00000020794	Ube2g1	2700059C12Rik|AI256795|AU014992|AW552068|D130023C12Rik	ubiquitin-conjugating enzyme E2G 1	protein-coding
mm_126701.1	chr15	85132081	85132121	+	1	NA	promoter-TSS (NM_080470)	promoter-TSS (NM_080470)	2	NM_026357	67747	Mm.158173	NM_026357	ENSMUSG00000022431	Ribc2	4930579A10Rik|Trib	RIB43A domain with coiled-coils 2	protein-coding
mm_127108.1	chr15	97869367	97869388	+	1	NA	exon (NM_009504, exon 6 of 10)	exon (NM_009504, exon 6 of 10)	-24875	NM_001204278	56233	Mm.384027	NM_019572	ENSMUSG00000022475	Hdac7	5830434K02Rik|HD7|HD7a|Hdac7a|mFLJ00062	histone deacetylase 7	protein-coding
mm_31738.1	chr4	63204139	63204167	+	1	NA	Intergenic	Intergenic	-11259	NM_025685	373864	Mm.194116	NM_025685	ENSMUSG00000045672	Col27a1	5730512J02Rik|AI449266	collagen, type XXVII, alpha 1	protein-coding
mm_164687.1	chr17	47611247	47611251	-	1	NA	promoter-TSS (NM_020048)	promoter-TSS (NM_020048)	243	NM_016859	53414	Mm.472101	NM_016859	ENSMUSG00000023988	Bysl	Bys|Enp1	bystin-like	protein-coding
mm_145844.1	chr18	65448202	65448216	+	1	NA	exon (NM_172833, exon 5 of 16)	exon (NM_172833, exon 5 of 16)	17212	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_59247.1	chr7	24784627	24784629	+	1	NA	TTS (NM_007675)	TTS (NM_007675)	7424	NM_007675	26366	Mm.30300	NM_007675	ENSMUSG00000054169	Ceacam10	Bgp3|Cea10	carcinoembryonic antigen-related cell adhesion molecule 10	protein-coding
mm_46106.1	chr5	92348112	92348151	-	1	NA	exon (NM_021274, exon 2 of 4)	exon (NM_021274, exon 2 of 4)	758	NM_021274	15945	Mm.877	NM_021274	ENSMUSG00000034855	Cxcl10	C7|CRG-2|INP10|IP-10|IP10|Ifi10|Scyb10|gIP-10|mob-1	chemokine (C-X-C motif) ligand 10	protein-coding
mm_5488.1	chr1	36892705	36892729	-	1	NA	intron (NM_018872, intron 1 of 40)	MTEa|LTR|ERVL-MaLR	46810	NM_018872	56030	Mm.186943	NM_018872	ENSMUSG00000026116	Tmem131	2610524E03Rik|CC28|D1Bwg0491e|Neg|RW1|YR-23|mKIAA0257	transmembrane protein 131	protein-coding
mm_33406.1	chr4	129847847	129847870	+	1	NA	3' UTR (NM_001164745, exon 6 of 6)	3' UTR (NM_001164745, exon 6 of 6)	27150	NM_001164745	19244	Mm.193688	NM_008974	ENSMUSG00000028788	Ptp4a2	Prl-2	protein tyrosine phosphatase 4a2	protein-coding
mm_57598.1	chr6	127794717	127794733	-	1	NA	Intergenic	Intergenic	-6582	NR_106092	102466996		NR_106092	ENSMUSG00000104804	Mir7233	mmu-mir-7233	microRNA 7233	ncRNA
mm_27678.1	chr3	65929416	65929442	-	1	NA	Intergenic	Intergenic	28796	NM_019937	56706	Mm.175612	NM_019937	ENSMUSG00000027829	Ccnl1	2610030E23Rik|AU018493|Ccnl|ania-6a	cyclin L1	protein-coding
mm_165201.1	chr2	32715392	32715401	+	1	NA	Intergenic	Intergenic	-2424	NR_039536	100628606		NR_039536	ENSMUSG00000105841	Mir3960	mmu-mir-3960	microRNA 3960	ncRNA
mm_130787.1	chr15	101628249	101628252	-	1	NA	promoter-TSS (NM_001003670)	promoter-TSS (NM_001003670)	-62	NM_001003670	406223	Mm.475602	NM_001003670	ENSMUSG00000064232	Gm5414	EG406223|Kb14	predicted gene 5414	protein-coding
mm_165146.1	chr2	18893724	18893724	+	1	NA	intron (NM_008845, intron 3 of 9)	intron (NM_008845, intron 3 of 9)	-91906	NR_131254	66774	Mm.87075	NR_131254	ENSMUSG00000097638	Carlr	4933439G12Rik|Carl	cardiac and apoptosis-related long non-coding RNA	ncRNA
mm_66643.1	chr7	45655628	45655636	-	1	NA	intron (NM_001271993, intron 1 of 2)	intron (NM_001271993, intron 1 of 2)	10762	NM_018876	14344	Mm.290046	NM_018876	ENSMUSG00000055978	Fut2	-	fucosyltransferase 2	protein-coding
mm_86856.1	chr10	21882215	21882239	+	1	NA	promoter-TSS (NM_001161845)	promoter-TSS (NM_001161845)	43	NM_001161845	20393	Mm.28405	NM_011361	ENSMUSG00000019970	Sgk1	Sgk	serum/glucocorticoid regulated kinase 1	protein-coding
mm_100843.1	chr11	5741142	5741182	-	1	NA	promoter-TSS (NM_178623)	promoter-TSS (NM_178623)	14	NM_178623	72046	Mm.271657	NM_178623	ENSMUSG00000049680	Urgcp	2010005J08Rik|9130001I21Rik|AW060359|Urg4|mKIAA1507	upregulator of cell proliferation	protein-coding
mm_79856.1	chr9	64960893	64960921	+	1	NA	promoter-TSS (NM_001077631)	promoter-TSS (NM_001077631)	-23	NM_175153	69882	Mm.272616	NM_175153	ENSMUSG00000034263	Vwa9	2010321M09Rik	von Willebrand factor A domain containing 9	protein-coding
mm_69862.1	chr7	141437797	141437805	-	1	NA	promoter-TSS (NM_026646)	promoter-TSS (NM_026646)	73	NM_026646	68267	Mm.33729	NM_026646	ENSMUSG00000019082	Slc25a22	1300006L01Rik|AI060884|Gc1	solute carrier family 25 (mitochondrial carrier, glutamate), member 22	protein-coding
mm_144138.1	chr18	4993838	4993854	+	1	NA	Intergenic	Intergenic	-52743	NM_153153	225115	Mm.136791	NM_153153	ENSMUSG00000024236	Svil	AU024053|B430302E16Rik	supervillin	protein-coding
mm_86843.1	chr10	21419469	21419481	+	1	NA	Intergenic	MTEa|LTR|ERVL-MaLR	42175	NM_178713	237320	Mm.90181	NM_178713	ENSMUSG00000037542	Aldh8a1	Raldh4	aldehyde dehydrogenase 8 family, member A1	protein-coding
mm_135513.1	chr16	48772010	48772030	-	1	NA	promoter-TSS (NM_198297)	promoter-TSS (NM_198297)	-64	NM_198297	77647	Mm.167298	NM_198297	ENSMUSG00000030775	Trat1	C030046M14Rik|Tcrim|Trim	T cell receptor associated transmembrane adaptor 1	protein-coding
mm_123180.1	chr14	57665193	57665260	-	1	NA	promoter-TSS (NM_020506)	promoter-TSS (NM_020506)	-270	NM_020506	57258	Mm.202747	NM_020506	ENSMUSG00000021952	Xpo4	B430309A01Rik|mKIAA1721	exportin 4	protein-coding
mm_60745.1	chr7	45458084	45458086	+	1	NA	3' UTR (NM_010240, exon 4 of 4)	3' UTR (NM_010240, exon 4 of 4)	1801	NM_010240	14325	Mm.30357	NM_010240	ENSMUSG00000050708	Ftl1	Ftl|Ftl-1|L-ferritin	ferritin light polypeptide 1	protein-coding
mm_94879.1	chr11	24255700	24255715	+	1	NA	Intergenic	Intergenic	175012	NM_001159290	14025	Mm.53687	NM_016707	ENSMUSG00000000861	Bcl11a	2810047E18Rik|BCL-11A|Ctip1|D930021L15Rik|Evi9|Evi9a|Evi9b|Evi9c|mKIAA1809	B cell CLL/lymphoma 11A (zinc finger protein)	protein-coding
mm_24695.1	chr3	95111014	95111087	+	1	NA	promoter-TSS (NM_009336)	promoter-TSS (NM_009336)	8	NM_009336	21427	Mm.133919	NM_009336	ENSMUSG00000008958	Vps72	Tcfl1|YL-1	vacuolar protein sorting 72	protein-coding
mm_112583.1	chr13	13712717	13712735	+	1	NA	exon (NM_010748, exon 39 of 53)	exon (NM_010748, exon 39 of 53)	-71333	NM_001302997	14706	Mm.215394	NM_010317	ENSMUSG00000021303	Gng4	-	guanine nucleotide binding protein (G protein), gamma 4	protein-coding
mm_133442.1	chr16	87729072	87729084	+	1	NA	intron (NM_007520, intron 4 of 4)	Lx8b|LINE|L1	30124	NM_007520	12013	Mm.26147	NM_007520	ENSMUSG00000025612	Bach1	6230421P05Rik|AI323795	BTB and CNC homology 1, basic leucine zipper transcription factor 1	protein-coding
mm_109376.1	chr12	109673366	109673369	+	1	NA	Intergenic	Intergenic	-8830	NR_030540	100124461		NR_030540	ENSMUSG00000077881	Mir882	Mirn882|mmu-mir-882	microRNA 882	ncRNA
mm_117305.1	chr13	67375730	67375757	-	1	NA	promoter-TSS (NM_001001186)	promoter-TSS (NM_001001186)	20	NM_001001186	408065	Mm.461583	NM_001001186	ENSMUSG00000078995	Zfp456	BC065418|Rslcan-13	zinc finger protein 456	protein-coding
mm_133171.1	chr16	72027603	72027613	+	1	NA	Intergenic	Intergenic	206719	NR_131116	319533	Mm.373754	NR_131115		8030451O07Rik	-	RIKEN cDNA 8030451O07 gene	ncRNA
mm_29369.1	chr3	108711418	108711430	-	1	NA	5' UTR (NM_029522, exon 2 of 15)	5' UTR (NM_029522, exon 2 of 15)	10875	NM_029522	76123	Mm.226941	NM_029522	ENSMUSG00000027883	Gpsm2	6230410J09Rik|LGN|Pins	G-protein signalling modulator 2 (AGS3-like, C. elegans)	protein-coding
mm_117121.1	chr13	60897398	60897414	-	1	NA	promoter-TSS (NM_007797)	promoter-TSS (NM_007797)	41	NM_007797	13025	Mm.30144	NM_007797	ENSMUSG00000074874	Ctla2b	AW545568|Ctla-2b	cytotoxic T lymphocyte-associated protein 2 beta	protein-coding
mm_93731.1	chr10	119850681	119850687	-	1	NA	intron (NR_131760, intron 3 of 4)	intron (NR_131760, intron 3 of 4)	1706	NR_131760	78105	Mm.399086	NR_131760	ENSMUSG00000085418	Grip1os1	4930404E01Rik|4930483C13Rik	glutamate receptor interacting protein 1, opposite strand 1	ncRNA
mm_118449.1	chr14	8299573	8299582	+	1	NA	exon (NM_183187, exon 3 of 4)	exon (NM_183187, exon 3 of 4)	10199	NM_183187	268709	Mm.256058	NM_183187	ENSMUSG00000021750	Fam107a	DRR1	family with sequence similarity 107, member A	protein-coding
mm_133012.1	chr16	56127373	56127395	+	1	NA	TTS (NM_001003973)	TTS (NM_001003973)	51904	NM_001304503	66315	Mm.255784	NM_025483	ENSMUSG00000052917	Senp7	2410152H17Rik|2810413I22Rik|2900036C23Rik|6030449K19Rik|AI790676	SUMO1/sentrin specific peptidase 7	protein-coding
mm_118642.1	chr14	21499832	21499883	+	1	NA	promoter-TSS (NM_001205241)	promoter-TSS (NM_001205241)	72	NM_017479	54169	Mm.248967	NM_017479	ENSMUSG00000021767	Kat6b	AI507552|B130044K16Rik|MYST-4|Morf|Myst4|mKIAA0383|qkf|querkopf	K(lysine) acetyltransferase 6B	protein-coding
mm_80399.1	chr9	77313722	77313725	+	1	NA	intron (NM_027150, intron 1 of 7)	intron (NM_027150, intron 1 of 7)	34147	NM_027150	69642	Mm.35008	NM_027150	ENSMUSG00000032355	Mlip	2310046A06Rik|AI931782|CIP	muscular LMNA-interacting protein	protein-coding
mm_149101.1	chr19	8942240	8942250	+	1	NA	TTS (NM_144872)	TTS (NM_144872)	325	NM_011842	23942	Mm.25339	NM_011842	ENSMUSG00000071646	Mta2	AW550797|Mata1l1|Mta1l1|mmta2	metastasis-associated gene family, member 2	protein-coding
mm_102332.1	chr11	57829236	57829246	-	1	NA	3' UTR (NM_008213, exon 2 of 2)	3' UTR (NM_008213, exon 2 of 2)	2906	NM_008213	15110	Mm.4746	NM_008213	ENSMUSG00000037335	Hand1	Ehand1|Hxt|Th1|Thing1|bHLHa27|eHAND	heart and neural crest derivatives expressed transcript 1	protein-coding
mm_144379.1	chr18	20665404	20665420	+	1	NA	5' UTR (NM_013697, exon 1 of 4)	5' UTR (NM_013697, exon 1 of 4)	162	NM_013697	22139	Mm.2108	NM_013697	ENSMUSG00000061808	Ttr	AA408768|AI787086|D17860|prealbumin	transthyretin	protein-coding
mm_167702.1	chr9	90243140	90243147	-	1	NA	intron (NM_194334, intron 2 of 12)	intron (NM_194334, intron 2 of 12)	27626	NM_194334	67016	Mm.335347	NM_194334	ENSMUSG00000037410	Tbc1d2b	1810061M12Rik|AI480956|AV021536|AV023399|AW491493|mKIAA1055	TBC1 domain family, member 2B	protein-coding
mm_150520.1	chr19	39036481	39036491	+	1	NA	intron (NM_028089, intron 7 of 8)	BC1_Mm|scRNA|scRNA	-24520	NM_028191	72303	Mm.482578	NM_028191	ENSMUSG00000067231	Cyp2c65	2210009K14Rik	cytochrome P450, family 2, subfamily c, polypeptide 65	protein-coding
mm_164055.1	chr14	103464383	103464407	+	1	NA	Intergenic	(CAGT)n|Simple_repeat|Simple_repeat	-48946	NM_022886	64929	Mm.244003	NM_022886	ENSMUSG00000022123	Scel	9230114I02Rik	sciellin	protein-coding
mm_27198.1	chr3	35662321	35662325	-	1	NA	intron (NR_040748, intron 2 of 18)	intron (NR_040748, intron 2 of 18)	3840	NR_040748	625963	Mm.251506	NR_040748	ENSMUSG00000105662	Gm6639	-	predicted gene 6639	ncRNA
mm_162945.1	chr10	129664865	129664869	+	1	NA	promoter-TSS (NR_030454).7	promoter-TSS (NR_030454).7	-888	NR_030454	735274		NR_030454	ENSMUSG00000106252	Mir684-1	Mirn684-1	microRNA 684-1	ncRNA
mm_21258.1	chr2	156348032	156348054	-	1	NA	intron (NM_001316755, intron 8 of 9)	intron (NM_001316755, intron 8 of 9)	-35339	NM_020255	19018	Mm.389346	NM_020255	ENSMUSG00000046229	Scand1	2310003H23Rik|Leap1|PGC-2|Ppargc2	SCAN domain-containing 1	protein-coding
mm_42779.1	chr5	121397966	121398004	+	1	NA	promoter-TSS (NM_172722)	promoter-TSS (NM_172722)	3	NM_172722	231713	Mm.33919	NM_172722	ENSMUSG00000042719	Naa25	4833422K13Rik|A630046C11|AI450868|C330023M02Rik|Mdm20	N(alpha)-acetyltransferase 25, NatB auxiliary subunit	protein-coding
mm_103824.1	chr11	83012212	83012289	-	1	NA	intron (NM_181545, intron 4 of 5)	Lx7|LINE|L1	8472	NM_001167743	276950	Mm.491599	NM_181545	ENSMUSG00000035208	Slfn8	-	schlafen 8	protein-coding
mm_39078.1	chr4	154334761	154334763	-	1	NA	intron (NM_001177995, intron 11 of 15)	intron (NM_001177995, intron 11 of 15)	-34867	NM_001112744	230972	Mm.38481	NM_001112744	ENSMUSG00000029032	Arhgef16	-	Rho guanine nucleotide exchange factor (GEF) 16	protein-coding
mm_9471.1	chr1	173334529	173334531	-	1	NA	3' UTR (NM_053199, exon 9 of 9)	3' UTR (NM_053199, exon 9 of 9)	-1027	NM_010045	13349	Mm.6393	NM_010045	ENSMUSG00000037872	Ackr1	AA162249|CCBP1|CD234|Darc|Dfy|ESTM35|FY|GPD	atypical chemokine receptor 1 (Duffy blood group)	protein-coding
mm_117821.1	chr13	98016187	98016200	-	1	NA	intron (NM_012026, intron 9 of 35)	intron (NM_012026, intron 9 of 35)	189972	NM_012026	110596	Mm.252718	NM_012026	ENSMUSG00000021662	Arhgef28	9230110L08Rik|AI323540|D13Bwg1089e|RIP2|Rgnef|RhoGEF|Rhoip2|p190RhoGEF	Rho guanine nucleotide exchange factor (GEF) 28	protein-coding
mm_137207.1	chr17	24038224	24038228	+	1	NA	promoter-TSS (NM_175440)	promoter-TSS (NM_175440)	-17	NM_175440	213171	Mm.133083	NM_175440	ENSMUSG00000050762	Prss27	CAPH2|Mpn|marapsin	protease, serine 27	protein-coding
mm_141181.1	chr17	26938805	26938816	-	1	NA	TTS (NM_009343)	TTS (NM_009343)	648	NR_104458	67675	Mm.439919	NM_026307	ENSMUSG00000024194	Cuta	0610039D01Rik|1810022E02Rik|1810060C03Rik|2700094G22Rik|AI326454	cutA divalent cation tolerance homolog	protein-coding
mm_45043.1	chr5	41701288	41701329	-	1	NA	intron (NM_027295, intron 2 of 6)	intron (NM_027295, intron 2 of 6)	6383	NM_001310592	100972	Mm.41555	NM_027295	ENSMUSG00000029128	Rab28	2700023P08Rik|AW496496	RAB28, member RAS oncogene family	protein-coding
mm_162855.1	chr10	89872923	89872943	+	1	NA	promoter-TSS (NM_001128086)	promoter-TSS (NM_001128086)	-576	NM_001128086	77531	Mm.440605	NM_181398	ENSMUSG00000058589	Anks1b	AIDA-1b|C030032C09Rik|E530015N03Rik|ENSMUSG00000078431|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding
mm_87922.1	chr10	62507902	62507914	+	1	NA	promoter-TSS (NM_011157)	promoter-TSS (NM_011157)	-153	NM_011157	19073	Mm.338790	NM_011157	ENSMUSG00000020077	Srgn	Prg|Prg1|Sgc	serglycin	protein-coding
mm_104721.1	chr11	98153561	98153570	-	1	NA	TTS (NM_013634)	TTS (NM_013634)	-3949	NM_028149	72194	Mm.218350	NM_028149	ENSMUSG00000020883	Fbxl20	2610511F20Rik|4632423N09Rik|AI849362|AL117906|C86145|Fbl2|Scr|mKIAA4147	F-box and leucine-rich repeat protein 20	protein-coding
mm_33390.1	chr4	129811214	129811259	+	1	NA	Intergenic	Intergenic	-9243	NM_008974	19244	Mm.193688	NM_008974	ENSMUSG00000028788	Ptp4a2	Prl-2	protein tyrosine phosphatase 4a2	protein-coding
mm_10253.1	chr2	9305328	9305332	+	1	NA	Intergenic	Intergenic	115815	NR_038180	73438	Mm.23558	NR_038180	ENSMUSG00000085580	1700061F12Rik	-	RIKEN cDNA 1700061F12 gene	ncRNA
mm_148964.1	chr19	7494464	7494474	+	1	NA	promoter-TSS (NM_146091)	promoter-TSS (NM_146091)	31	NM_146091	109168	Mm.264016	NM_146091	ENSMUSG00000024759	Atl3	4633402C03Rik|5730596K20Rik|AI465397|AW228836	atlastin GTPase 3	protein-coding
mm_90747.1	chr10	5424373	5424382	-	1	NA	exon (NM_153399, exon 8 of 32)	exon (NM_153399, exon 8 of 32)	63937	NM_001347711	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_12121.1	chr2	61617149	61617161	+	1	NA	intron (NM_001164072, intron 2 of 7)	L2a|LINE|L2	24058	NM_001164071	21353	Mm.244393	NM_011529	ENSMUSG00000064289	Tank	C86182|E430026L09Rik|I-TRAF	TRAF family member-associated Nf-kappa B activator	protein-coding
mm_18123.1	chr2	44997346	44997352	-	1	NA	exon (NM_015753, exon 8 of 10)	exon (NM_015753, exon 8 of 10)	25828	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_70592.1	chr8	13200777	13200787	+	1	NA	promoter-TSS (NM_025768)	promoter-TSS (NM_025768)	-158	NM_025768	66790	Mm.34901	NM_025768	ENSMUSG00000038515	Grtp1	5430401C05Rik|C81211|Tbc1d6	GH regulated TBC protein 1	protein-coding
mm_18270.1	chr2	52335242	52335252	-	1	NA	intron (NM_010889, intron 1 of 156)	intron (NM_010889, intron 1 of 156)	3551	NM_010889	17996	Mm.389247	NM_010889	ENSMUSG00000026950	Neb	AI595938	nebulin	protein-coding
mm_107442.1	chr12	36314427	36314438	+	1	NA	exon (NM_025312, exon 1 of 2)	exon (NM_025312, exon 1 of 2)	263	NM_025312	66042	Mm.43375	NM_025312	ENSMUSG00000036169	Sostdc1	0610006G05Rik|Sostl|USAG-1|Wise|ectodin	sclerostin domain containing 1	protein-coding
mm_55591.1	chr6	71555763	71555772	-	1	NA	intron (NM_025783, intron 2 of 5)	RMER19B|LTR|ERVK	11913	NM_025783	66700	Mm.181278	NM_025783	ENSMUSG00000053119	Chmp3	25.1|4921505F14Rik|9130011K15Rik|CGI-49|D6Ertd286e|NEDF|Vps24	charged multivesicular body protein 3	protein-coding
mm_83037.1	chr9	37255731	37255744	-	1	NA	promoter-TSS (NM_001145960)	promoter-TSS (NM_001145960)	1	NM_020258	56857	Mm.440037	NM_020258	ENSMUSG00000032122	Slc37a2	G3PP|Slc37a1|cI-2|ci2	solute carrier family 37 (glycerol-3-phosphate transporter), member 2	protein-coding
mm_11040.1	chr2	27009937	27009993	+	1	NA	promoter-TSS (NM_029862)	promoter-TSS (NM_029862)	39	NM_001243239	381356	Mm.150270	NM_029862	ENSMUSG00000015488	Cacfd1	5930434B04Rik|mFwe	calcium channel flower domain containing 1	protein-coding
mm_146009.1	chr18	69345761	69345811	+	1	NA	promoter-TSS (NM_001083967)	promoter-TSS (NM_001083967)	65	NM_001083967	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding
mm_19031.1	chr2	76969657	76969681	-	1	NA	exon (NM_011652, exon 7 of 313)	exon (NM_011652, exon 7 of 313)	12878	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_118345.1	chr13	114854120	114854126	-	1	NA	intron (NM_008396, intron 21 of 29)	intron (NM_008396, intron 21 of 29)	35886	NM_001113374	17434	Mm.19027	NM_013826	ENSMUSG00000015536	Mocs2	AI415403	molybdenum cofactor synthesis 2	protein-coding
mm_155106.1	chrX	48368143	48368157	+	1	NA	exon (NM_178782, exon 5 of 15)	exon (NM_178782, exon 5 of 15)	26792	NM_178782	320376	Mm.210146	NM_178782	ENSMUSG00000036959	Bcorl1	6720425J07Rik|B930011H20Rik	BCL6 co-repressor-like 1	protein-coding
mm_57993.1	chr6	136172377	136172396	-	1	NA	intron (NM_008171, intron 2 of 14)	intron (NM_008171, intron 2 of 14)	1125	NM_008171	14812	Mm.436649	NM_008171	ENSMUSG00000030209	Grin2b	AW490526|GluN2B|NR2B|Nmdar2b	glutamate receptor, ionotropic, NMDA2B (epsilon 2)	protein-coding
mm_83592.1	chr9	48480519	48480529	-	1	NA	promoter-TSS (NM_024233)	promoter-TSS (NM_024233)	87	NM_024233	104444	Mm.21911	NM_024233	ENSMUSG00000032026	Rexo2	1810038D15Rik|AW107347|Rex2|Sfn|Smfn	RNA exonuclease 2	protein-coding
mm_133407.1	chr16	84835361	84835421	+	1	NA	promoter-TSS (NM_001302216)	promoter-TSS (NM_001302216)	234	NM_016755	11957	Mm.353	NM_016755	ENSMUSG00000022890	Atp5j	CF6	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit F	protein-coding
mm_125966.1	chr15	76274224	76274230	+	1	NA	intron (NM_028852, intron 1 of 4)	RSINE1|SINE|B4	-4388	NR_045747	100038659	Mm.448549	NR_045747		Mirt2	ENSMUSG00000075583|Gm10872|Gm24562	myocardial infraction associated transcript 2	ncRNA
mm_29583.1	chr3	117360165	117360227	-	1	NA	exon (NM_177664, exon 1 of 7)	exon (NM_177664, exon 1 of 7)	680	NM_177664	229791	Mm.140138	NM_177664	ENSMUSG00000044667	Plppr4	A330086D10|D3Bwg0562e|Lppr4|PRG-1|mKIAA0455	phospholipid phosphatase related 4	protein-coding
mm_58551.1	chr7	4740112	4740120	+	1	NA	promoter-TSS (NM_001115018)	promoter-TSS (NM_001115018)	-11	NM_146177	232811	Mm.247844	NM_146177	ENSMUSG00000059851	Kmt5c	BC024816|Suv4-20h2|Suv420h2	lysine methyltransferase 5C	protein-coding
mm_47421.1	chr5	123141281	123141333	-	1	NA	promoter-TSS (NM_001040398)	promoter-TSS (NM_001040398)	-886	NM_001040398	208043	Mm.250391	NM_177581	ENSMUSG00000038384	Setd1b	AA516740|BC035291|KMT2G|mKIAA1076	SET domain containing 1B	protein-coding
mm_132463.1	chr16	36252873	36252877	+	1	NA	intron (NM_029733, intron 2 of 4)	intron (NM_029733, intron 2 of 4)	-24273	NM_001082543	20861	Mm.327618	NM_001082543	ENSMUSG00000071562	Stfa1	Stefin-3|Stf-3|Stf1|Stf3|Stfa3	stefin A1	protein-coding
mm_137366.1	chr17	25454528	25454553	+	1	NA	Intergenic	Intergenic	-17050	NM_027951	71840	Mm.282330	NM_027951	ENSMUSG00000024175	Tekt4	1700010L19Rik	tektin 4	protein-coding
mm_87797.1	chr10	60299946	60299970	+	1	NA	exon (NM_011179, exon 11 of 15)	exon (NM_011179, exon 11 of 15)	15497	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_79357.1	chr9	54266104	54266127	+	1	NA	Intergenic	Intergenic	-20371	NM_177350	235379	Mm.123549	NM_177350	ENSMUSG00000046167	Gldn	CRG-L2|Clom|Colm|Crgl2|Crlg2	gliomedin	protein-coding
mm_44275.1	chr5	5694560	5694581	-	1	NA	promoter-TSS (NM_001103156)	promoter-TSS (NM_001103156)	-2	NM_028734	74051	Mm.274956	NM_028734	ENSMUSG00000015653	Steap2	4921538B17Rik|AI930049|AW045895|IPCA-1|IPCA1|PCANAP1|STAMP1|STMP	six transmembrane epithelial antigen of prostate 2	protein-coding
mm_732.1	chr1	43204853	43204854	+	1	NA	Intergenic	Intergenic	-8092	NM_001289533	14200	Mm.6799	NM_010212	ENSMUSG00000008136	Fhl2	FHL-2|SLIM-3|SLIM3	four and a half LIM domains 2	protein-coding
mm_148109.1	chr18	74207815	74207823	-	1	NA	promoter-TSS (NM_001164355)	promoter-TSS (NM_001164355)	-1	NM_025581	66468	Mm.283406	NM_025581	ENSMUSG00000036223	Ska1	2810433K01Rik|AV117428	spindle and kinetochore associated complex subunit 1	protein-coding
mm_55715.1	chr6	73221609	73221622	-	1	NA	promoter-TSS (NM_001164669)	promoter-TSS (NM_001164669)	16	NM_001164669	330355	Mm.333166	NM_001164669	ENSMUSG00000052861	Dnah6	9830168K20|A730004I20Rik|Dnahc6|mKIAA1697|mdhc6	dynein, axonemal, heavy chain 6	protein-coding
mm_76075.1	chr8	78821079	78821119	-	1	NA	promoter-TSS (NM_030145)	promoter-TSS (NM_030145)	53	NM_001191004	78651	Mm.28694	NM_030145	ENSMUSG00000031683	Lsm6	1500031N17Rik|2410088K19Rik|AI747288	LSM6 homolog, U6 small nuclear RNA and mRNA degradation associated	protein-coding
mm_129180.1	chr15	76287751	76287771	-	1	NA	intron (NM_028852, intron 4 of 4)	ID_B1|SINE|B4	-6673	NM_001195537	100503915	Mm.393455	NM_001195537	ENSMUSG00000071724	Smpd5	ENSMUSG00000071724|Gm10345|MA-nSMase	sphingomyelin phosphodiesterase 5	protein-coding
mm_18216.1	chr2	49730293	49730307	-	1	NA	exon (NM_008449, exon 14 of 26)	exon (NM_008449, exon 14 of 26)	-57386	NM_027990	71897	Mm.41381	NM_027990	ENSMUSG00000026765	Lypd6b	2310010M24Rik|AW049525	LY6/PLAUR domain containing 6B	protein-coding
mm_118185.1	chr13	107414743	107414764	-	1	NA	Intergenic	Intergenic	-55069	NR_045083	105120	Mm.417700	NR_045083		AI197445	-	expressed sequence AI197445	ncRNA
mm_89727.1	chr10	98921021	98921029	+	1	NA	intron (NM_026482, intron 1 of 20)	intron (NM_026482, intron 1 of 20)	5873	NM_026482	67972	Mm.166944	NM_026482	ENSMUSG00000019943	Atp2b1	2810442I22Rik|E130111D10Rik|Pmca1	ATPase, Ca++ transporting, plasma membrane 1	protein-coding
mm_86287.1	chr9	121914681	121914701	-	1	NA	3' UTR (NM_010012, exon 1 of 1)	3' UTR (NM_010012, exon 1 of 1)	1614	NM_010012	13124	Mm.20889	NM_010012	ENSMUSG00000050445	Cyp8b1	-	cytochrome P450, family 8, subfamily b, polypeptide 1	protein-coding
mm_43647.1	chr5	138264058	138264097	+	1	NA	promoter-TSS (NM_153161)	promoter-TSS (NM_153161)	-25	NM_153161	231807	Mm.164493	NM_153161	ENSMUSG00000036948	BC037034	-	cDNA sequence BC037034	protein-coding
mm_155410.1	chrX	73420707	73420708	+	1	NA	intron (NM_009566, intron 4 of 5)	intron (NM_009566, intron 4 of 5)	9147	NM_001310531	22754	Mm.5060	NM_009566	ENSMUSG00000031374	Zfp92	-	zinc finger protein 92	protein-coding
mm_117988.1	chr13	100233336	100233340	-	1	NA	intron (NM_010870, intron 5 of 14)	intron (NM_010870, intron 5 of 14)	13998	NM_010870	17951	Mm.290476	NM_010870	ENSMUSG00000071203	Naip5	Birc1e|Lgn1|Naip-rs3	NLR family, apoptosis inhibitory protein 5	protein-coding
mm_87275.1	chr10	41887429	41887455	+	1	NA	promoter-TSS (NM_001013370)	promoter-TSS (NM_001013370)	3	NM_001013370	140742	Mm.139418	NM_001013370	ENSMUSG00000038332	Sesn1	1110002G11Rik|AU044290|Pa26|Sest1	sestrin 1	protein-coding
mm_37020.1	chr4	114470902	114470905	-	1	NA	intron (NM_001085549, intron 2 of 6)	intron (NM_001085549, intron 2 of 6)	64179	NM_001085549	666048	Mm.331779	NM_001085549	ENSMUSG00000070867	Trabd2b	Gm12824|Hkat|OTTMUSG00000008561	TraB domain containing 2B	protein-coding
mm_54337.1	chr6	30645231	30645247	-	1	NA	exon (NM_025350, exon 10 of 10)	exon (NM_025350, exon 10 of 10)	6021	NM_025350	109697	Mm.25377	NM_025350	ENSMUSG00000054446	Cpa1	0910001L12Rik|Cpa	carboxypeptidase A1, pancreatic	protein-coding
mm_95910.1	chr11	58206692	58206717	+	1	NA	exon (NM_018738, exon 3 of 3)	exon (NM_018738, exon 3 of 3)	7148	NM_018738	16145	Mm.33902	NM_018738	ENSMUSG00000078853	Igtp	AW558444|Irgm3	interferon gamma induced GTPase	protein-coding
mm_102555.1	chr11	61378104	61378108	-	1	NA	promoter-TSS (NM_026183)	promoter-TSS (NM_026183)	-31	NM_026183	67473	Mm.100741	NM_026183	ENSMUSG00000010122	Slc47a1	1300013J15Rik|AI036982|MATE1|mMATE1	solute carrier family 47, member 1	protein-coding
mm_49633.1	chr6	30804950	30804965	+	1	NA	intron (NM_017478, intron 20 of 23)	intron (NM_017478, intron 20 of 23)	63658	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_159741.1	chr5	71548292	71548292	-	1	NA	promoter-TSS (NM_030052)	promoter-TSS (NM_030052)	-87	NM_030052	78174	Mm.60690	NM_030052	ENSMUSG00000049387	Cox7b2	4930503B16Rik	cytochrome c oxidase subunit VIIb2	protein-coding
mm_13602.1	chr2	112712830	112712832	+	1	NA	intron (NM_177652, intron 65 of 103)	intron (NM_177652, intron 65 of 103)	153149	NM_001165935	74268	Mm.315125	NM_028844	ENSMUSG00000003604	Aven	1700013A01Rik|1700056A21Rik|mAven-L|mAven-S	apoptosis, caspase activation inhibitor	protein-coding
mm_120759.1	chr14	73366376	73366438	+	1	NA	exon (NM_008410, exon 3 of 6)	exon (NM_008410, exon 3 of 6)	18864	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_134007.1	chr16	4829284	4829319	-	1	NA	Intergenic	Intergenic	-6115	NM_030192	78809	Mm.325551	NM_030192	ENSMUSG00000022518	4930562C15Rik	-	RIKEN cDNA 4930562C15 gene	protein-coding
mm_55128.1	chr6	50596579	50596612	-	1	NA	promoter-TSS (NM_027564)	promoter-TSS (NM_027564)	-5	NM_027564	70821	Mm.157323	NM_027564	ENSMUSG00000029828	4921507P07Rik	TISP74	RIKEN cDNA 4921507P07 gene	protein-coding
mm_125200.1	chr15	32921105	32921123	+	1	NA	5' UTR (NM_008304, exon 1 of 5)	5' UTR (NM_008304, exon 1 of 5)	391	NM_008304	15529	Mm.234266	NM_008304	ENSMUSG00000022261	Sdc2	4833414L08Rik|AA960457|Hspg1|Synd2|syndecan-2	syndecan 2	protein-coding
mm_6815.1	chr1	84179109	84179126	-	1	NA	intron (NM_001003948, intron 1 of 2)	C-rich|Low_complexity|Low_complexity	39844	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_116168.1	chr13	30792251	30792261	-	1	NA	Intergenic	Intergenic	43023	NM_013674	16364	Mm.4677	NM_013674	ENSMUSG00000021356	Irf4	AI385587|IRF-4|LSIRF|NF-EM5|Spip	interferon regulatory factor 4	protein-coding
mm_73243.1	chr8	104250870	104250912	+	1	NA	promoter-TSS (NR_104433)	promoter-TSS (NR_104433)	30	NM_001286383	75458	Mm.269219	NM_029295	ENSMUSG00000054400	Cklf	1700001C14Rik|1810018M11Rik|A730028G07Rik|C32|CKLF1|CKLF3|CKLF4|CKLF5|Cklf2|Cklf6|HSPC224|UCK-1	chemokine-like factor	protein-coding
mm_108477.1	chr12	83659501	83659515	+	1	NA	exon (NM_027349, exon 7 of 19)	exon (NM_027349, exon 7 of 19)	27274	NM_027349	67039	Mm.46005	NM_027349	ENSMUSG00000010608	Rbm25	2600011C06Rik|2610015J01Rik|A130095G20Rik|AI159652|AL023075|AU043498|RNPC7	RNA binding motif protein 25	protein-coding
mm_126299.1	chr15	79357860	79357870	+	1	NA	3' UTR (NM_001304830, exon 3 of 3)	3' UTR (NM_001304830, exon 3 of 3)	9463	NM_001304832	17133	Mm.86646	NM_010755	ENSMUSG00000042622	Maff	-	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein F (avian)	protein-coding
mm_135074.1	chr16	34262895	34262920	-	1	NA	intron (NM_001164268, intron 10 of 33)	intron (NM_001164268, intron 10 of 33)	251120	NM_001164268	545156	Mm.82274	NM_177357	ENSMUSG00000061751	Kalrn	2210407G14Rik|AV235988|DUET|E530005C20Rik|Gm539|Hapip|TRAD	kalirin, RhoGEF kinase	protein-coding
mm_64118.1	chr7	141079760	141079781	+	1	NA	promoter-TSS (NM_019762)	promoter-TSS (NM_019762)	1	NM_019762	56460	Mm.350037	NM_019762	ENSMUSG00000054065	Pkp3	2310056L12Rik	plakophilin 3	protein-coding
mm_79978.1	chr9	66915649	66915691	+	1	NA	intron (NM_173413, intron 1 of 7)	intron (NM_173413, intron 1 of 7)	4035	NM_173413	235442	Mm.260376	NM_173413	ENSMUSG00000036943	Rab8b	5930437D16|D330025I23Rik	RAB8B, member RAS oncogene family	protein-coding
mm_3527.1	chr1	150165214	150165228	+	1	NA	promoter-TSS (NR_110420)	promoter-TSS (NR_110420)	-273	NR_110420	102639566	Mm.417208	NR_110420	ENSMUSG00000097754	Ptgs2os2	Gm26687|Linc-cox2|Lincrna-cox2	prostaglandin-endoperoxide synthase 2, opposite strand 2	ncRNA
mm_69898.1	chr7	141638032	141638048	-	1	NA	intron (NM_001330001, intron 31 of 33)	intron (NM_001330001, intron 31 of 33)	17279	NM_001330001	353328	Mm.246621	NM_181729	ENSMUSG00000048191	Muc6	-	mucin 6, gastric	protein-coding
mm_29268.1	chr3	107458923	107458975	-	1	NA	promoter-TSS (NM_145922)	promoter-TSS (NM_145922)	-51	NM_145922	99738	Mm.101976	NM_145922	ENSMUSG00000027895	Kcnc4	AI850292|KSHIIIC|Kcr2-4|Kv3.4	potassium voltage gated channel, Shaw-related subfamily, member 4	protein-coding
mm_12103.1	chr2	61578550	61578617	+	1	NA	promoter-TSS (NM_011529)	promoter-TSS (NM_011529)	-3	NM_011529	21353	Mm.244393	NM_011529	ENSMUSG00000064289	Tank	C86182|E430026L09Rik|I-TRAF	TRAF family member-associated Nf-kappa B activator	protein-coding
mm_109307.1	chr12	109560752	109560764	+	1	NA	non-coding (NR_003633, exon 5 of 5)	non-coding (NR_003633, exon 5 of 5)	-2934	NR_030427	791079		NR_030427	ENSMUSG00000076451	Mir770	Mirn770|mir-770|mmu-mir-770	microRNA 770	ncRNA
mm_132153.1	chr16	32142787	32142790	+	1	NA	TTS (NM_001347181)	TTS (NM_001347181)	22688	NM_146069	224109	Mm.33498	NM_146069	ENSMUSG00000052384	Nrros	E430025L02Rik|Lrcc33|Lrrc33	negative regulator of reactive oxygen species	protein-coding
mm_24708.1	chr3	95164310	95164333	+	1	NA	promoter-TSS (NM_011351)	promoter-TSS (NM_011351)	-18	NM_011351	20360	Mm.23662	NM_011351	ENSMUSG00000038777	Sema6c	Semay|mKIAA1869	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C	protein-coding
mm_165064.1	chr19	44057210	44057220	-	1	NA	intron (NM_145502, intron 5 of 10)	intron (NM_145502, intron 5 of 10)	12471	NM_145502	226144	Mm.279865	NM_145502	ENSMUSG00000025198	Erlin1	2810439N09Rik|C80197|Keo4|Spfh1	ER lipid raft associated 1	protein-coding
mm_82446.1	chr9	15306096	15306114	-	1	NA	promoter-TSS (NM_001199485)	promoter-TSS (NM_001199485)	62	NM_001199485	70984	Mm.261842	NM_133732	ENSMUSG00000031938	4931406C07Rik	-	RIKEN cDNA 4931406C07 gene	protein-coding
mm_62971.1	chr7	119896396	119896414	+	1	NA	promoter-TSS (NM_001163703)	promoter-TSS (NM_001163703)	113	NM_029610	73919	Mm.46381	NM_029610	ENSMUSG00000030922	Lyrm1	1110065L10Rik|2310004B22Rik|4930404J24Rik	LYR motif containing 1	protein-coding
mm_107676.1	chr12	54343702	54343716	+	1	NA	Intergenic	L1MA5|LINE|L1	47609	NR_033689	665239	Mm.26856	NR_033689		Gm7550	EG665239|Gm666	predicted gene 7550	ncRNA
mm_157109.1	chrX	9438033	9438037	-	1	NA	3' UTR (NM_007807, exon 13 of 13)	3' UTR (NM_007807, exon 13 of 13)	31289	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_142884.1	chr17	51829617	51829626	-	1	NA	intron (NM_001163632, intron 1 of 10)	intron (NM_001163632, intron 1 of 10)	3026	NM_009122	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_98553.1	chr11	95097227	95097268	+	1	NA	Intergenic	Intergenic	-20436	NM_001306162	16400	Mm.57035	NM_013565	ENSMUSG00000001507	Itga3	AA407068|CD49C|GAPB3	integrin alpha 3	protein-coding
mm_113094.1	chr13	24105603	24105613	+	1	NA	intron (NM_026825, intron 17 of 37)	intron (NM_026825, intron 17 of 37)	-114394	NM_145399	214189	Mm.255667	NM_145399	ENSMUSG00000021337	Scgn	-	secretagogin, EF-hand calcium binding protein	protein-coding
mm_64948.1	chr7	16372193	16372221	-	1	NA	intron (NM_001285892, intron 2 of 8)	MTD-int|LTR|ERVL-MaLR	15689	NM_001285892	56459	Mm.258530	NM_019748	ENSMUSG00000052833	Sae1	2400010M20Rik|2610044L12Rik|AL033372|AOS1|AW743391|D7Ertd177e|HSPC140|Sua1|Uble1a	SUMO1 activating enzyme subunit 1	protein-coding
mm_45105.1	chr5	44799644	44799666	-	1	NA	promoter-TSS (NM_010698)	promoter-TSS (NM_010698)	91	NM_001347349	16826	Mm.25785	NM_010698	ENSMUSG00000039706	Ldb2	AI035351|AW146358|CLIM1|CLP-36|Ldb3	LIM domain binding 2	protein-coding
mm_52655.1	chr6	117861945	117861972	+	1	NA	Intergenic	RMER30|DNA|hAT-Charlie	-1119	NM_008616	22685	Mm.249661	NM_008616	ENSMUSG00000042097	Zfp239	Mok-2|Mok2|Znf239	zinc finger protein 239	protein-coding
mm_113800.1	chr13	46420531	46420541	+	1	NA	intron (NM_001081425, intron 2 of 3)	intron (NM_001081425, intron 2 of 3)	2236	NM_001081425	666794	Mm.38269	NM_001081425	ENSMUSG00000038132	Rbm24	6330546B05Rik|AI606861	RNA binding motif protein 24	protein-coding
mm_134713.1	chr16	22895214	22895224	-	1	NA	promoter-TSS (NR_110508)	promoter-TSS (NR_110508)	-833	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_168542.1	chr11	62458644	62458659	-	1	NA	exon (NM_001039536, exon 1 of 7)	exon (NM_001039536, exon 1 of 7)	191	NM_001039536	327942	Mm.390358	NM_199026	ENSMUSG00000014245	Pigl	Gm737	phosphatidylinositol glycan anchor biosynthesis, class L	protein-coding
mm_105943.1	chr11	115267237	115267249	-	1	NA	promoter-TSS (NM_010350)	promoter-TSS (NM_010350)	0	NM_010350	14813	Mm.39090	NM_010350	ENSMUSG00000020734	Grin2c	GluN2C|NMDAR2C|NR2C	glutamate receptor, ionotropic, NMDA2C (epsilon 3)	protein-coding
mm_146217.1	chr18	77038376	77038387	+	1	NA	intron (NM_027721, intron 1 of 13)	MLTR25A|LTR|ERVK	8915	NM_027721	71206	Mm.35803	NM_027721	ENSMUSG00000025420	Katnal2	3110023G01Rik|4933439B08Rik	katanin p60 subunit A-like 2	protein-coding
mm_168973.1	chr12	86846500	86846513	-	1	NA	Intergenic	Intergenic	38308	NM_145836	238330	Mm.248358	NM_145836	ENSMUSG00000034168	Irf2bpl	6430527G18Rik|Eap1	interferon regulatory factor 2 binding protein-like	protein-coding
mm_142194.1	chr17	36951605	36951632	-	1	NA	5' UTR (NM_029632, exon 1 of 3)	5' UTR (NM_029632, exon 1 of 3)	174	NM_029632	76497	Mm.46176	NM_029632	ENSMUSG00000036398	Ppp1r11	1500041B02Rik|AV117883|Hcgv|Tcte5|Tctex-5|Tctex5	protein phosphatase 1, regulatory (inhibitor) subunit 11	protein-coding
mm_147192.1	chr18	37644122	37644136	-	1	NA	promoter-TSS (NM_175770)	promoter-TSS (NM_175770)	75	NM_175770	24074	Mm.236009	NM_175770	ENSMUSG00000051316	Taf7	55kDa|AI607308|BB007175|TAFII55|Taf2f	TATA-box binding protein associated factor 7	protein-coding
mm_89370.1	chr10	88731405	88731423	+	1	NA	promoter-TSS (NM_025859)	promoter-TSS (NM_025859)	0	NM_025859	104303	Mm.291247	NM_025859	ENSMUSG00000060904	Arl1	2310008D22Rik|AU019749	ADP-ribosylation factor-like 1	protein-coding
mm_51618.1	chr6	85187527	85187569	+	1	NA	promoter-TSS (NM_010131)	promoter-TSS (NM_010131)	-383	NM_010131	13796	Mm.391473	NM_010131	ENSMUSG00000033726	Emx1	-	empty spiracles homeobox 1	protein-coding
mm_86999.1	chr10	26778503	26778508	+	1	NA	intron (NM_176837, intron 1 of 14)	intron (NM_176837, intron 1 of 14)	5993	NM_176837	73910	Mm.356496	NM_176837	ENSMUSG00000039031	Arhgap18	4833419J07Rik|AI314906|AI843501	Rho GTPase activating protein 18	protein-coding
mm_121478.1	chr14	121035510	121035520	+	1	NA	promoter-TSS (NM_134082)	promoter-TSS (NM_134082)	-59	NM_134082	223254	Mm.223980	NM_134082	ENSMUSG00000025555	Farp1	AW228844|BC030329|Cdep	FERM, RhoGEF (Arhgef) and pleckstrin domain protein 1 (chondrocyte-derived)	protein-coding
mm_15918.1	chr2	165065009	165065025	+	1	NA	intron (NM_170703, intron 5 of 7)	intron (NM_170703, intron 5 of 7)	9381	NM_011611	21939	Mm.271833	NM_011611	ENSMUSG00000017652	Cd40	AI326936|Bp50|GP39|HIGM1|IGM|IMD3|T-BAM|TRAP|Tnfrsf5|p50	CD40 antigen	protein-coding
mm_163885.1	chr14	24446458	24446463	-	1	NA	Intergenic	Intergenic	40586	NM_001081247	218832	Mm.343610	NM_183157	ENSMUSG00000025280	Polr3a	9330175N20Rik|BC053071|RPC1|RPC155	polymerase (RNA) III (DNA directed) polypeptide A	protein-coding
mm_63817.1	chr7	134006613	134006614	+	1	NA	intron (NM_007400, intron 4 of 22)	intron (NM_007400, intron 4 of 22)	218484	NM_007400	11489	Mm.439714	NM_007400	ENSMUSG00000054555	Adam12	Mltna	a disintegrin and metallopeptidase domain 12 (meltrin alpha)	protein-coding
mm_22160.1	chr2	172940053	172940098	-	1	NA	5' UTR (NM_007557, exon 1 of 7)	5' UTR (NM_007557, exon 1 of 7)	246	NM_007557	12162	Mm.595	NM_007557	ENSMUSG00000008999	Bmp7	OP1	bone morphogenetic protein 7	protein-coding
mm_24963.1	chr3	96699252	96699267	+	1	NA	intron (NM_018812, intron 1 of 14)	intron (NM_018812, intron 1 of 14)	2183	NM_018812	229615	Mm.1635	NM_018812	ENSMUSG00000028101	Pias3	Pias3l	protein inhibitor of activated STAT 3	protein-coding
mm_153479.1	chr19	41275948	41275971	-	1	NA	intron (NM_031376, intron 16 of 16)	(GA)n|Simple_repeat|Simple_repeat	-11955	NM_133352	107358	Mm.246440	NM_133352	ENSMUSG00000025016	Tm9sf3	1810073M23Rik|2810031D16Rik|AI115521|AI413748|AW146116|AW549777|Smbp|mKIAA4036	transmembrane 9 superfamily member 3	protein-coding
mm_138522.1	chr17	35238379	35238404	+	1	NA	3' UTR (NM_023179, exon 3 of 3)	3' UTR (NM_023179, exon 3 of 3)	1795	NM_023179	66237	Mm.396107	NM_023179	ENSMUSG00000024403	Atp6v1g2	1500002D01Rik|Atp6g2|NG38|VAG2	ATPase, H+ transporting, lysosomal V1 subunit G2	protein-coding
mm_85623.1	chr9	107615021	107615060	-	1	NA	3' UTR (NM_008138, exon 9 of 9)	3' UTR (NM_008138, exon 9 of 9)	-5799	NM_001291539	20347	Mm.4083	NM_009153	ENSMUSG00000057969	Sema3b	SemA|Semaa|sema5|semaV	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B	protein-coding
mm_107906.1	chr12	70968333	70968352	+	1	NA	Intergenic	CpG	-6281	NM_001310595	19167	Mm.296338	NM_011184	ENSMUSG00000060073	Psma3	Lmpc8	proteasome (prosome, macropain) subunit, alpha type 3	protein-coding
mm_130933.1	chr15	103196806	103196824	-	1	NA	3' UTR (NM_001110216, exon 6 of 6)	3' UTR (NM_001110216, exon 6 of 6)	18537	NM_007626	12419	Mm.262059	NM_007626	ENSMUSG00000009575	Cbx5	2610029O15Rik|C75991|HP1|Hp1a|Hp1alpha	chromobox 5	protein-coding
mm_34214.1	chr4	140966511	140966515	+	1	NA	exon (NM_023374, exon 2 of 8)	exon (NM_023374, exon 2 of 8)	5242	NM_023374	67680	Mm.246965	NM_023374	ENSMUSG00000009863	Sdhb	0710008N11Rik	succinate dehydrogenase complex, subunit B, iron sulfur (Ip)	protein-coding
mm_3814.1	chr1	158969811	158969835	+	1	NA	Intergenic	MMERVK9E_I-int|LTR|ERVK	-12385	NM_001085376	23850	Mm.458621	NM_001085376	ENSMUSG00000073530	Pappa2	PAPP-A2|PLAC3|Pappe	pappalysin 2	protein-coding
mm_110274.1	chr12	32017611	32017617	-	1	NA	intron (NM_011158, intron 2 of 10)	intron (NM_011158, intron 2 of 10)	43665	NM_011158	19088	Mm.25594	NM_011158	ENSMUSG00000002997	Prkar2b	AI451071|AW061005|PKARIIbeta|Pkarb2|RII(beta)	protein kinase, cAMP dependent regulatory, type II beta	protein-coding
mm_65645.1	chr7	28050029	28050080	-	1	NA	promoter-TSS (NM_011874)	promoter-TSS (NM_011874)	38	NM_011874	23996	Mm.29582	NM_011874	ENSMUSG00000030603	Psmc4	CIP21|MIP224	proteasome (prosome, macropain) 26S subunit, ATPase, 4	protein-coding
mm_136260.1	chr16	91011130	91011170	-	1	NA	promoter-TSS (NM_001045515)	promoter-TSS (NM_001045515)	-55	NM_001045515	104015	Mm.187079	NM_001045515	ENSMUSG00000022973	Synj1	A930006D20Rik|AA675315|mKIAA0910	synaptojanin 1	protein-coding
mm_80765.1	chr9	95559534	95559544	+	1	NA	promoter-TSS (NM_198414)	promoter-TSS (NM_198414)	-278	NM_198414	75552	Mm.151485	NM_198414	ENSMUSG00000064225	Paqr9	1700020G04Rik	progestin and adipoQ receptor family member IX	protein-coding
mm_64749.1	chr7	4789542	4789614	-	1	NA	promoter-TSS (NM_029384)	promoter-TSS (NM_029384)	-18	NM_029384	664968	Mm.292837	NM_029384	ENSMUSG00000030431	Tmem238	2210411K11Rik	transmembrane protein 238	protein-coding
mm_113990.1	chr13	52583039	52583061	+	1	NA	promoter-TSS (NM_001198977)	promoter-TSS (NM_001198977)	-387	NM_001198977	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_87924.1	chr10	62508184	62508193	+	1	NA	promoter-TSS (NM_011157)	promoter-TSS (NM_011157)	-433	NM_011157	19073	Mm.338790	NM_011157	ENSMUSG00000020077	Srgn	Prg|Prg1|Sgc	serglycin	protein-coding
mm_21661.1	chr2	164425125	164425140	-	1	NA	3' UTR (NM_011521, exon 5 of 5)	3' UTR (NM_011521, exon 5 of 5)	18056	NM_011521	20971	Mm.3815	NM_011521	ENSMUSG00000017009	Sdc4	AA959608|AW108331|S4|Synd4|ryudocan|syndecan-4	syndecan 4	protein-coding
mm_146240.1	chr18	77196011	77196019	+	1	NA	intron (NM_153124, intron 1 of 6)	B1_Mur2|SINE|Alu	10168	NM_013666	225742	Mm.365178	NM_013666	ENSMUSG00000025425	St8sia5	ST8SiaV|Siat8e	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 5	protein-coding
mm_47080.1	chr5	117004719	117004723	-	1	NA	Intergenic	Intergenic	111272	NM_001122666	71954	Mm.34456	NM_178622	ENSMUSG00000066900	Suds3	2400003N08Rik|2410008L21Rik|AU067672|mSds3	suppressor of defective silencing 3 homolog (S. cerevisiae)	protein-coding
mm_8778.1	chr1	161156956	161156956	-	1	NA	3' UTR (NM_001195189, exon 2 of 2)	3' UTR (NM_001195189, exon 2 of 2)	2358	NM_001195189	100502590	Mm.449990	NM_001195189		4930469G21Rik	-	RIKEN cDNA 4930469G21 gene	protein-coding
mm_83010.1	chr9	36767596	36767638	-	1	NA	promoter-TSS (NM_008408)	promoter-TSS (NM_008408)	-39	NM_008408	16430	Mm.2863	NM_008408	ENSMUSG00000032116	Stt3a	AA408947|BB081708|Itm1	STT3, subunit of the oligosaccharyltransferase complex, homolog A (S. cerevisiae)	protein-coding
mm_152967.1	chr19	29367382	29367398	-	1	NA	promoter-TSS (NM_021893)	promoter-TSS (NM_021893)	-48	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_124364.1	chr14	105643666	105643687	-	1	NA	Intergenic	Intergenic	-19906	NR_105814	102465207		NR_105814	ENSMUSG00000098780	Mir6390	Gm27562|mmu-mir-6390	microRNA 6390	ncRNA
mm_168600.1	chr1	174254239	174254253	+	1	NA	Intergenic	L1Md_T|LINE|L1	-3270	NM_146715	258710	Mm.377647	NM_146715	ENSMUSG00000050788	Olfr419	MOR267-6	olfactory receptor 419	protein-coding
mm_72315.1	chr8	78066305	78066334	+	1	NA	Intergenic	Intergenic	-147023	NM_183096	73301	Mm.61243	NM_183096	ENSMUSG00000037101	Ttc29	1700031F13Rik	tetratricopeptide repeat domain 29	protein-coding
mm_57994.1	chr6	136172404	136172415	-	1	NA	intron (NM_008171, intron 2 of 14)	intron (NM_008171, intron 2 of 14)	1102	NM_008171	14812	Mm.436649	NM_008171	ENSMUSG00000030209	Grin2b	AW490526|GluN2B|NR2B|Nmdar2b	glutamate receptor, ionotropic, NMDA2B (epsilon 2)	protein-coding
mm_42149.1	chr5	111420161	111420188	+	1	NA	exon (NM_001081235, exon 1 of 2)	exon (NM_001081235, exon 1 of 2)	2008	NM_001081235	433938	Mm.332576	NM_001081235	ENSMUSG00000070576	Mn1	AA003644|AA009236	meningioma 1	protein-coding
mm_17187.1	chr2	25461022	25461040	-	1	NA	promoter-TSS (NM_153557)	promoter-TSS (NM_153557)	63	NM_153557	227622	Mm.261780	NM_153557	ENSMUSG00000047617	BC029214	D930050G13Rik|Paxx	cDNA sequence BC029214	protein-coding
mm_3119.1	chr1	134646571	134646587	+	1	NA	promoter-TSS (NM_009307)	promoter-TSS (NM_009307)	-102	NM_009307	20980	Mm.5102	NM_009307	ENSMUSG00000026452	Syt2	IP4BP|R74640|mKIAA4194	synaptotagmin II	protein-coding
mm_93632.1	chr10	117281003	117281005	-	1	NA	intron (NM_017372, intron 1 of 3)	PB1|SINE|Alu	1268	NM_017372	17105	Mm.45436	NM_017372	ENSMUSG00000069516	Lyz2	AI326280|Lys|Lysm|Lyzf2|Lyzs|Lzm|Lzm-s1|Lzp	lysozyme 2	protein-coding
mm_136045.1	chr16	78410175	78410190	-	1	NA	Intergenic	ORR1D2|LTR|ERVL-MaLR	-33001	NM_001297747	12228	Mm.392910	NM_009770	ENSMUSG00000022863	Btg3	ANA|tob5	B cell translocation gene 3	protein-coding
mm_50963.1	chr6	59209065	59209075	+	1	NA	5' UTR (NM_001081145, exon 1 of 2)	5' UTR (NM_001081145, exon 1 of 2)	200	NM_001081145	68140	Mm.25843	NM_001081145	ENSMUSG00000049232	Tigd2	3632410O17Rik	tigger transposable element derived 2	protein-coding
mm_24168.1	chr3	88563185	88563221	+	1	NA	exon (NM_033526, exon 6 of 11)	exon (NM_033526, exon 6 of 11)	9487	NM_033526	94232	Mm.303059	NM_033526	ENSMUSG00000008604	Ubqln4	A1Up|A1u|AI663987|CIP75|UBIN	ubiquilin 4	protein-coding
mm_66642.1	chr7	45638739	45638788	-	1	NA	exon (NM_028544, exon 12 of 12)	exon (NM_028544, exon 12 of 12)	-1214	NM_172418	74490	Mm.107442	NM_172418	ENSMUSG00000042918	Mamstr	2810022D01Rik|5430432N15Rik|AW743872|Mastr	MEF2 activating motif and SAP domain containing transcriptional regulator	protein-coding
mm_41691.1	chr5	100583408	100583443	+	1	NA	Intergenic	Intergenic	-11220	NM_139198	231507	Mm.34609	NM_139198	ENSMUSG00000029322	Plac8	C15|D5Wsu111e	placenta-specific 8	protein-coding
mm_55377.1	chr6	58780536	58780567	-	1	NA	Intergenic	MTD-int|LTR|ERVL-MaLR	-53149	NM_028705	73998	Mm.191892	NM_028705	ENSMUSG00000029804	Herc3	5730409F18Rik|AI646603|mKIAA0032	hect domain and RLD 3	protein-coding
mm_91615.1	chr10	41606451	41606456	-	1	NA	intron (NM_001303469, intron 1 of 20)	intron (NM_001303469, intron 1 of 20)	142	NM_001303469	75973	Mm.228517	NM_029493	ENSMUSG00000075225	Ccdc162	5033413D22Rik|Ccdc162p|Gm29096|Gm61|Gm6976	coiled-coil domain containing 162	protein-coding
mm_56913.1	chr6	119330724	119330800	-	1	NA	promoter-TSS (NM_172492)	promoter-TSS (NM_172492)	4	NM_172492	211187	Mm.121498	NM_172492	ENSMUSG00000055003	Lrtm2	A230084J22|AI841794	leucine-rich repeats and transmembrane domains 2	protein-coding
mm_80255.1	chr9	72807160	72807176	+	1	NA	promoter-TSS (NM_175485)	promoter-TSS (NM_175485)	-106	NM_175485	235472	Mm.31696	NM_175485	ENSMUSG00000036030	Prtg	A230098A12Rik|Igdcc5	protogenin	protein-coding
mm_39340.1	chr5	8893569	8893580	+	1	NA	promoter-TSS (NM_008830)	promoter-TSS (NM_008830)	-147	NM_008830	18670	Mm.297825	NM_008830	ENSMUSG00000042476	Abcb4	Mdr2|Pgy-2|Pgy2|mdr-2	ATP-binding cassette, sub-family B (MDR/TAP), member 4	protein-coding
mm_21677.1	chr2	164426074	164426098	-	1	NA	exon (NM_011521, exon 5 of 5)	exon (NM_011521, exon 5 of 5)	17102	NM_011521	20971	Mm.3815	NM_011521	ENSMUSG00000017009	Sdc4	AA959608|AW108331|S4|Synd4|ryudocan|syndecan-4	syndecan 4	protein-coding
mm_136743.1	chr17	8341028	8341047	+	1	NA	exon (NM_178774, exon 2 of 2)	exon (NM_178774, exon 2 of 2)	298	NM_178774	320111	Mm.442510	NM_178774	ENSMUSG00000055945	Prr18	9630019K15Rik	proline rich 18	protein-coding
mm_119238.1	chr14	33351315	33351349	+	1	NA	intron (NM_153800, intron 5 of 10)	CpG	59692	NM_001310452	26419	Mm.21495	NM_016700	ENSMUSG00000021936	Mapk8	AI849689|JNK|JNK1|Prkm8|SAPK1	mitogen-activated protein kinase 8	protein-coding
mm_23843.1	chr3	82380188	82380207	+	1	NA	exon (NM_001081230, exon 9 of 14)	exon (NM_001081230, exon 9 of 14)	22125	NM_001081230	213582	Mm.271269	NM_001081230	ENSMUSG00000033900	Map9	5033421J10Rik|5330427D05Rik|ASAP|Mtap9	microtubule-associated protein 9	protein-coding
mm_9878.1	chr1	185441742	185441761	-	1	NA	promoter-TSS (NR_038006)	promoter-TSS (NR_038006)	68	NR_038006	319562	Mm.184335	NM_176943	ENSMUSG00000051295	9630028B13Rik	-	RIKEN cDNA 9630028B13 gene	ncRNA
mm_90996.1	chr10	13967634	13967650	-	1	NA	intron (NM_010437, intron 1 of 8)	intron (NM_010437, intron 1 of 8)	1263	NM_010437	15273	Mm.42157	NM_010437	ENSMUSG00000015501	Hivep2	Gm20114|MIBP1|Schnurri-2|Shn-2	human immunodeficiency virus type I enhancer binding protein 2	protein-coding
mm_71286.1	chr8	40921397	40921426	+	1	NA	3' UTR (NM_001044740, exon 12 of 12)	3' UTR (NM_001044740, exon 12 of 12)	-4822	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_102857.1	chr11	69399308	69399313	-	1	NA	3' UTR (NM_001017426, exon 23 of 23)	3' UTR (NM_001017426, exon 23 of 23)	-1076	NM_025915	67020	Mm.390406	NM_025915	ENSMUSG00000045377	Tmem88	2600017H02Rik	transmembrane protein 88	protein-coding
mm_127039.1	chr15	96638672	96638675	+	1	NA	intron (NM_001166458, intron 1 of 15)	(T)n|Simple_repeat|Simple_repeat	3289	NM_134086	105727	Mm.103568	NM_134086	ENSMUSG00000023169	Slc38a1	AA408026|AA409865|AL022800|AU015942|NAT2	solute carrier family 38, member 1	protein-coding
mm_136633.1	chr17	5700083	5700121	+	1	NA	intron (NM_146073, intron 3 of 8)	B4|SINE|B4	-98555	NR_045081	78512	Mm.23696	NR_045079	ENSMUSG00000096965	3300005D01Rik	-	RIKEN cDNA 3300005D01 gene	ncRNA
mm_83774.1	chr9	52112983	52113019	-	1	NA	3' UTR (NM_001162921, exon 6 of 6)	3' UTR (NM_001162921, exon 6 of 6)	-2622	NR_105750	102465150		NR_105750	ENSMUSG00000099311	Mir6244	Gm27368|mmu-mir-6244	microRNA 6244	ncRNA
mm_131992.1	chr16	25043365	25043399	+	1	NA	Intergenic	Intergenic	-16257	NR_040374	319487	Mm.137341	NR_040374	ENSMUSG00000096960	A230028O05Rik	-	RIKEN cDNA A230028O05 gene	ncRNA
mm_108604.1	chr12	85472358	85472372	+	1	NA	Intergenic	CpG	-1536	NM_010234	14281	Mm.246513	NM_010234	ENSMUSG00000021250	Fos	D12Rfj1|c-fos|cFos	FBJ osteosarcoma oncogene	protein-coding
mm_1996.1	chr1	87126810	87126818	+	1	NA	exon (NM_007432, exon 8 of 11)	exon (NM_007432, exon 8 of 11)	1806	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_62742.1	chr7	111029020	111029030	+	1	NA	promoter-TSS (NM_009431)	promoter-TSS (NM_009431)	74	NM_009431	22083	Mm.255858	NM_009431	ENSMUSG00000005609	Ctr9	AA409336|Sh2bp1|Tsbp|Tsp|mKIAA0155	CTR9 homolog, Paf1/RNA polymerase II complex component	protein-coding
mm_47226.1	chr5	121374352	121374413	-	1	NA	intron (NM_172275, intron 8 of 11)	intron (NM_172275, intron 8 of 11)	11233	NM_001163470	231712	Mm.20488	NM_172275	ENSMUSG00000042726	Trafd1	1110008K06Rik|Fln29	TRAF type zinc finger domain containing 1	protein-coding
mm_143988.1	chr17	87641466	87641500	-	1	NA	exon (NM_008532, exon 5 of 10)	exon (NM_008532, exon 5 of 10)	5504	NM_008532	17075	Mm.4259	NM_008532	ENSMUSG00000045394	Epcam	CD326|EGP|EGP-2|Egp314|Ep-CAM|EpCAM1|GA733-2|Ly74|TROP1|Tacsd1|Tacstd1|gp40	epithelial cell adhesion molecule	protein-coding
mm_93586.1	chr10	116973222	116973231	-	1	NA	Intergenic	Intergenic	6952	NR_027846	103175	Mm.27138	NR_027846	ENSMUSG00000031294	D630029K05Rik	AI314111|AI875589	RIKEN cDNA D630029K05 gene	ncRNA
mm_73562.1	chr8	109494197	109494209	+	1	NA	intron (NM_019938, intron 1 of 20)	intron (NM_019938, intron 1 of 20)	176	NM_019938	56523	Mm.42166	NM_019938	ENSMUSG00000031727	Pmfbp1	1700016D22Rik|F77|Stap	polyamine modulated factor 1 binding protein 1	protein-coding
mm_127394.1	chr15	101128545	101128562	+	1	NA	promoter-TSS (NM_001277259)	promoter-TSS (NM_001277259)	31	NM_001277257	11482	Mm.279542	NM_009612	ENSMUSG00000000530	Acvrl1	AI115505|AI427544|Acvrlk1|Alk1	activin A receptor, type II-like 1	protein-coding
mm_41863.1	chr5	104440677	104440703	+	1	NA	3' UTR (NM_001204203, exon 7 of 7)	3' UTR (NM_001204203, exon 7 of 7)	4498	NM_001204233	20750	Mm.288474	NM_009263	ENSMUSG00000029304	Spp1	2AR|Apl-1|BNSP|BSPI|Bsp|ETA-1|Eta|OP|Opn|Opnl|Ric|Spp-1	secreted phosphoprotein 1	protein-coding
mm_15019.1	chr2	152669463	152669539	+	1	NA	promoter-TSS (NM_001159553)	promoter-TSS (NM_001159553)	40	NM_001159552	14950	Mm.277327	NM_010376	ENSMUSG00000019188	H13	1200006O09Rik|4930443L17Rik|5031424B04Rik|AV020344|H-13|Hm13|PSL3|Spp	histocompatibility 13	protein-coding
mm_140721.1	chr17	15433313	15433322	-	1	NA	non-coding (NR_033586, exon 11 of 11)	non-coding (NR_033586, exon 11 of 11)	37071	NM_024203	67544	Mm.35039	NM_024203	ENSMUSG00000014763	Fam120b	4932442K08Rik|AW049283|AW413338|CCPG|Pgcc1|mKIAA1838	family with sequence similarity 120, member B	protein-coding
mm_37002.1	chr4	110351911	110351945	-	1	NA	promoter-TSS (NM_001163397)	promoter-TSS (NM_001163397)	-17	NM_001163397	15572	Mm.3970	NM_010488	ENSMUSG00000028546	Elavl4	Elav|Hud|PNEM	ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4 (Hu antigen D)	protein-coding
mm_148801.1	chr19	6244837	6244843	+	1	NA	intron (NM_194348, intron 3 of 39)	intron (NM_194348, intron 3 of 39)	3172	NM_194348	329015	Mm.277384	NM_194348	ENSMUSG00000024773	Atg2a	1810013C15Rik|A830054M12|BC023754|mKIAA0404	autophagy related 2A	protein-coding
mm_118795.1	chr14	24487056	24487088	+	1	NA	promoter-TSS (NM_001081247)	promoter-TSS (NM_001081247)	-26	NM_001081247	218832	Mm.343610	NM_183157	ENSMUSG00000025280	Polr3a	9330175N20Rik|BC053071|RPC1|RPC155	polymerase (RNA) III (DNA directed) polypeptide A	protein-coding
mm_59798.1	chr7	29001599	29001625	+	1	NA	exon (NM_008279, exon 28 of 32)	exon (NM_008279, exon 28 of 32)	18758	NM_008279	26411	Mm.148278	NM_008279	ENSMUSG00000037337	Map4k1	Hpk1|mHPK1	mitogen-activated protein kinase kinase kinase kinase 1	protein-coding
mm_52375.1	chr6	113077568	113077623	+	1	NA	promoter-TSS (NR_027008)	promoter-TSS (NR_027008)	-44	NM_028385	72895	Mm.367159	NM_028385	ENSMUSG00000034269	Setd5	2900045N06Rik|C330007C20|C85544|mKIAA1757	SET domain containing 5	protein-coding
mm_132094.1	chr16	31275395	31275425	+	1	NA	promoter-TSS (NM_025800)	promoter-TSS (NM_025800)	-133	NM_025800	66849	Mm.291593	NM_025800	ENSMUSG00000047714	Ppp1r2	0610025N14Rik|2310007G06Rik|4930440J04Rik|5430408E15Rik|D16Ertd248e|IPP-2	protein phosphatase 1, regulatory (inhibitor) subunit 2	protein-coding
mm_104291.1	chr11	90388523	90388535	-	1	NA	intron (NM_172563, intron 1 of 3)	intron (NM_172563, intron 1 of 3)	2388	NM_172563	217082	Mm.158903	NM_172563	ENSMUSG00000003949	Hlf	E230015K02Rik	hepatic leukemia factor	protein-coding
mm_141911.1	chr17	34972151	34972158	-	1	NA	promoter-TSS (NM_013558)	promoter-TSS (NM_013558)	2	NM_010479	193740	Mm.6388	NM_010479	ENSMUSG00000091971	Hspa1a	Hsp70-3|Hsp70.3|Hsp72|hsp68|hsp70A1	heat shock protein 1A	protein-coding
mm_6524.1	chr1	74587965	74588041	-	1	NA	promoter-TSS (NM_025784)	promoter-TSS (NM_025784)	25	NM_001310668	77264	Mm.207298	NM_029888	ENSMUSG00000026135	Zfp142	9330177B18Rik|BB154236|mKIAA0236	zinc finger protein 142	protein-coding
mm_69784.1	chr7	141094874	141094884	-	1	NA	5' UTR (NM_023059, exon 2 of 10)	5' UTR (NM_023059, exon 2 of 10)	5667	NM_023059	24058	Mm.38017	NM_023059	ENSMUSG00000025494	Sigirr	AI256711|TIR8	single immunoglobulin and toll-interleukin 1 receptor (TIR) domain	protein-coding
mm_172006.1	chr6	109505230	109505230	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	676589	NM_138677	192193	Mm.21596	NM_138677	ENSMUSG00000030104	Edem1	A130059K23Rik|EDEM|mKIAA0212	ER degradation enhancer, mannosidase alpha-like 1	protein-coding
mm_100697.1	chr11	3531374	3531409	-	1	NA	exon (NM_001284428, exon 8 of 22)	exon (NM_001284428, exon 8 of 22)	7901	NM_013870	29856	Mm.188516	NM_013870	ENSMUSG00000020439	Smtn	smsmo	smoothelin	protein-coding
mm_115547.1	chr13	8870968	8870974	-	1	NA	promoter-TSS (NM_172445)	promoter-TSS (NM_172445)	73	NM_001039389	207615	Mm.284654	NM_172445	ENSMUSG00000021147	Wdr37	-	WD repeat domain 37	protein-coding
mm_167078.1	chr7	100706813	100706842	+	1	NA	5' UTR (NM_178764, exon 1 of 9)	5' UTR (NM_178764, exon 1 of 9)	125	NM_178764	319604	Mm.260362	NM_178764	ENSMUSG00000029461	Fam168a	2610030B18Rik|B930006L02Rik|mKIAA0280	family with sequence similarity 168, member A	protein-coding
mm_160487.1	chr8	125891107	125891107	-	1	NA	exon (NM_175561, exon 3 of 34)	exon (NM_175561, exon 3 of 34)	7210	NM_175561	270109	Mm.145535	NM_175561	ENSMUSG00000060212	Pcnx2	A830048P05|AU067631|E330039K12Rik|Pcnxl2|mKIAA0435	pecanex homolog 2	protein-coding
mm_75783.1	chr8	70029512	70029516	-	1	NA	intron (NM_028993, intron 5 of 18)	B1_Mur1|SINE|Alu	13220	NM_001167939	74549	Mm.269061	NM_028993	ENSMUSG00000031858	Mau2	9130404D08Rik|A930019L04Rik|C77863|C79014|Mau-2|mKIAA0892	MAU2 sister chromatid cohesion factor	protein-coding
mm_118480.1	chr14	11824363	11824367	+	1	NA	intron (NM_008981, intron 2 of 29)	intron (NM_008981, intron 2 of 29)	270812	NM_008981	19270	Mm.431266	NM_008981	ENSMUSG00000021745	Ptprg	5430405N12Rik|AW046354|AW549872|RPTPgamma	protein tyrosine phosphatase, receptor type, G	protein-coding
mm_13749.1	chr2	118124186	118124195	+	1	NA	exon (NM_011580, exon 21 of 22)	exon (NM_011580, exon 21 of 22)	12314	NM_001313914	21825	Mm.4159	NM_011580	ENSMUSG00000040152	Thbs1	TSP-1|TSP1|Thbs-1|tbsp1	thrombospondin 1	protein-coding
mm_167899.1	chrX	73495053	73495064	-	1	NA	3' UTR (NM_007542, exon 8 of 8)	3' UTR (NM_007542, exon 8 of 8)	-8028	NM_001310537	320707	Mm.210095	NM_177236	ENSMUSG00000031376	Atp2b3	6430519O13Rik|Pmca3	ATPase, Ca++ transporting, plasma membrane 3	protein-coding
mm_68077.1	chr7	101869308	101869344	-	1	NA	intron (NM_001252553, intron 1 of 6)	intron (NM_001252553, intron 1 of 6)	1462	NM_001252554	14275	Mm.2135	NM_008034	ENSMUSG00000001827	Folr1	FBP1|Folbp-1|Folbp1	folate receptor 1 (adult)	protein-coding
mm_10384.1	chr2	12301256	12301266	+	1	NA	promoter-TSS (NR_040353)	promoter-TSS (NR_040353)	15	NR_040353	338535	Mm.483275	NR_040353	ENSMUSG00000086843	E030013I19Rik	-	RIKEN cDNA E030013I19 gene	ncRNA
mm_133259.1	chr16	77329572	77329619	+	1	NA	non-coding (NR_015543, exon 1 of 5)	non-coding (NR_015543, exon 1 of 5)	267	NR_015543	77994	Mm.394688	NR_015543	ENSMUSG00000090386	Mir99ahg	2810055G20Rik|D730043B02Rik	Mir99a and Mirlet7c-1 host gene (non-protein coding)	ncRNA
mm_79393.1	chr9	54863824	54863842	+	1	NA	promoter-TSS (NM_022655)	promoter-TSS (NM_022655)	78	NM_022655	64602	Mm.208991	NM_022655	ENSMUSG00000032293	Ireb2	D9Ertd85e|Irp2	iron responsive element binding protein 2	protein-coding
mm_144742.1	chr18	35582790	35582811	+	1	NA	exon (NM_010771, exon 10 of 15)	exon (NM_010771, exon 10 of 15)	-15867	NM_026420	67869	Mm.126534	NM_026420	ENSMUSG00000037058	Paip2	2310050K10Rik|AU045972	polyadenylate-binding protein-interacting protein 2	protein-coding
mm_38757.1	chr4	147868470	147868551	-	1	NA	promoter-TSS (NM_010244)	promoter-TSS (NM_010244)	209	NM_001025365	28010	Mm.250504	NM_133873	ENSMUSG00000029022	Miip	AA553001|AI853621|D4Wsu114e|IIP45	migration and invasion inhibitory protein	protein-coding
mm_136993.1	chr17	17402819	17402829	+	1	NA	5' UTR (NM_025681, exon 1 of 6)	5' UTR (NM_025681, exon 1 of 6)	138	NM_025681	66643	Mm.268018	NM_025681	ENSMUSG00000047786	Lix1	5730466L18Rik	limb and CNS expressed 1	protein-coding
mm_4841.1	chr1	186926909	186926934	+	1	NA	Intergenic	Intergenic	-40495	NM_033077	110957	Mm.108054	NM_033077	ENSMUSG00000039224	D1Pas1	Pl10	DNA segment, Chr 1, Pasteur Institute 1	protein-coding
mm_144139.1	chr18	4993871	4993880	+	1	NA	Intergenic	Intergenic	-52714	NM_153153	225115	Mm.136791	NM_153153	ENSMUSG00000024236	Svil	AU024053|B430302E16Rik	supervillin	protein-coding
mm_63.1	chr1	6598501	6598504	+	1	NA	intron (NM_001244693, intron 2 of 22)	B1F|SINE|Alu	111271	NM_001244692	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding
mm_25014.1	chr3	97978923	97978986	+	1	NA	Intergenic	Intergenic	-34584	NM_010928	18129	Mm.485843	NM_010928	ENSMUSG00000027878	Notch2	AI853703|N2	notch 2	protein-coding
mm_72054.1	chr8	71367637	71367647	+	1	NA	intron (NM_001145780, intron 2 of 8)	intron (NM_001145780, intron 2 of 8)	425	NM_025917	67023	Mm.41890	NM_025917	ENSMUSG00000002395	Use1	2010315L10Rik|5730403H22Rik|AV002165|D12|Ed2|Q-snare|p31	unconventional SNARE in the ER 1 homolog (S. cerevisiae)	protein-coding
mm_146376.1	chr18	82584959	82584992	+	1	NA	3' UTR (NM_010777, exon 7 of 7)	3' UTR (NM_010777, exon 7 of 7)	30467	NM_001025254	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_77754.1	chr8	128488552	128488562	-	1	NA	intron (NM_008737, intron 12 of 16)	intron (NM_008737, intron 12 of 16)	129316	NR_035436	100316680		NR_035436	ENSMUSG00000084523	Mir1903	Mirn1903|mmu-mir-1903	microRNA 1903	ncRNA
mm_49987.1	chr6	41046842	41046872	+	1	NA	Intergenic	Intergenic	-11348	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_24388.1	chr3	90260283	90260285	+	1	NA	exon (NM_028881, exon 10 of 14)	exon (NM_028881, exon 10 of 14)	6003	NM_028881	74343	Mm.35627	NM_028881	ENSMUSG00000027936	Crtc2	4632407F12Rik|Torc2|mTORC2	CREB regulated transcription coactivator 2	protein-coding
mm_78074.1	chr9	15520831	15520834	+	1	NA	intron (NM_133214, intron 1 of 2)	CT-rich|Low_complexity|Low_complexity	15337	NM_133214	170748	Mm.86572	NM_133214	ENSMUSG00000058173	Smco4	Fn5	single-pass membrane protein with coiled-coil domains 4	protein-coding
mm_33522.1	chr4	130930837	130930847	+	1	NA	exon (NM_010686, exon 6 of 8)	exon (NM_010686, exon 6 of 8)	-13543	NM_010769	17180	Mm.271796	NM_010769	ENSMUSG00000040533	Matn1	CMP|Crtm|Mat1|matrilin-1	matrilin 1, cartilage matrix protein	protein-coding
mm_151133.1	chr19	50252576	50252608	+	1	NA	exon (NM_021377, exon 9 of 26)	exon (NM_021377, exon 9 of 26)	426054	NM_001252501	58178	Mm.313672	NM_021377	ENSMUSG00000043531	Sorcs1	Sorcs|mSorCS	sortilin-related VPS10 domain containing receptor 1	protein-coding
mm_144882.1	chr18	36796030	36796042	+	1	NA	intron (NM_025594, intron 3 of 5)	intron (NM_025594, intron 3 of 5)	2113	NM_025594	66492	Mm.251155	NM_025594	ENSMUSG00000001383	Zmat2	2610510D14Rik|2900082I05Rik	zinc finger, matrin type 2	protein-coding
mm_161558.1	chr16	14163411	14163411	-	1	NA	intron (NM_023317, intron 1 of 8)	CpG	136	NM_001114085	67203	Mm.24105	NM_023317	ENSMUSG00000022678	Nde1	2810027M15Rik|AU042936|AW822251|Nude|mNudE	nudE neurodevelopment protein 1	protein-coding
mm_84931.1	chr9	82903150	82903177	-	1	NA	exon (NM_001081216, exon 22 of 40)	exon (NM_001081216, exon 22 of 40)	72326	NM_001081216	83946	Mm.221688	NM_031879	ENSMUSG00000032253	Phip	2810004D21Rik|4632404O06Rik|Ndrp|Wdr11	pleckstrin homology domain interacting protein	protein-coding
mm_114712.1	chr13	83574476	83574484	+	1	NA	intron (NM_001347577, intron 1 of 10)	intron (NM_001347577, intron 1 of 10)	873	NM_001347569	17260	Mm.24001	NM_025282	ENSMUSG00000005583	Mef2c	5430401D19Rik|9930028G15Rik|AV011172|Mef2	myocyte enhancer factor 2C	protein-coding
mm_94667.1	chr11	17221287	17221305	+	1	NA	intron (NM_178909, intron 2 of 7)	LSU-rRNA_Hsa|rRNA|rRNA	9403	NM_178909	103784	Mm.298132	NM_178909	ENSMUSG00000078970	Wdr92	AI553587|HZGJ	WD repeat domain 92	protein-coding
mm_128080.1	chr15	27680118	27680158	-	1	NA	intron (NM_001242423, intron 1 of 7)	intron (NM_001242423, intron 1 of 7)	1404	NM_001242424	223433	Mm.266485	NM_198301	ENSMUSG00000056069	Fam105a	9830126M18	family with sequence similarity 105, member A	protein-coding
mm_160881.1	chr11	69405964	69405964	-	1	NA	exon (NM_001017426, exon 11 of 23)	exon (NM_001017426, exon 11 of 23)	7711	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_27167.1	chr3	33143295	33143312	-	1	NA	promoter-TSS (NM_001163516)	promoter-TSS (NM_001163516)	-112	NM_001163516	58869	Mm.151332	NM_021483	ENSMUSG00000027674	Pex5l	1700016J08Rik|PXR2|Pex2|TRIP8b|pex5Rp	peroxisomal biogenesis factor 5-like	protein-coding
mm_114225.1	chr13	56502089	56502101	+	1	NA	Intergenic	Intergenic	-19849	NM_008373	16198	Mm.3006	NM_008373	ENSMUSG00000021538	Il9	Il-9|P40	interleukin 9	protein-coding
mm_133653.1	chr16	91807191	91807209	+	1	NA	intron (NM_001110275, intron 8 of 28)	intron (NM_001110275, intron 8 of 28)	77829	NM_010587	16443	Mm.40546	NM_010587	ENSMUSG00000022957	Itsn1	AA517634|AA545208|AI316805|AI839402|AI848451|Ehsh1|Ese1|Itsn|Sh3p17	intersectin 1 (SH3 domain protein 1A)	protein-coding
mm_83286.1	chr9	43107019	43107023	-	1	NA	Intergenic	Intergenic	-1303	NM_027144	69632	Mm.275266	NM_027144	ENSMUSG00000059495	Arhgef12	2310014B11Rik|AU019857|Larg|mKIAA0382	Rho guanine nucleotide exchange factor (GEF) 12	protein-coding
mm_99187.1	chr11	100862156	100862179	+	1	NA	intron (NM_001164062, intron 3 of 17)	intron (NM_001164062, intron 3 of 17)	1683	NM_001164062	20850	Mm.277403	NM_011488	ENSMUSG00000004043	Stat5a	AA959963|STAT5	signal transducer and activator of transcription 5A	protein-coding
mm_142994.1	chr17	56300289	56300297	-	1	NA	promoter-TSS (NM_029799)	promoter-TSS (NM_029799)	-7	NM_029799	76920	Mm.329132	NM_029799	ENSMUSG00000073380	Arrdc5	1700013E09Rik	arrestin domain containing 5	protein-coding
mm_172641.1	chr8	25463631	25463633	+	1	NA	Intergenic	Intergenic	-55127	NM_001079909	14182	Mm.265716	NM_010206	ENSMUSG00000031565	Fgfr1	AW208770|Eask|FGFR-I|FLG|Fgfr-1|Flt-2|Hspy|MFR|bFGF-R-1|c-fgr	fibroblast growth factor receptor 1	protein-coding
mm_63559.1	chr7	128083674	128083687	+	1	NA	exon (NM_008401, exon 9 of 30)	exon (NM_008401, exon 9 of 30)	21040	NM_008401	16409	Mm.262106	NM_008401	ENSMUSG00000030786	Itgam	CD11b/CD18|CR3|CR3A|Cd11b|F730045J24Rik|Ly-40|MAC1|Mac-1|Mac-1a	integrin alpha M	protein-coding
mm_61794.1	chr7	83892242	83892290	+	1	NA	5' UTR (NM_023403, exon 1 of 3)	5' UTR (NM_023403, exon 1 of 3)	266	NM_023403	67943	Mm.117365	NM_023403	ENSMUSG00000038503	Mesdc2	2210015O11Rik|AW537813|mKIAA0081|mesd|msd	mesoderm development candidate 2	protein-coding
mm_39607.1	chr5	24105011	24105015	+	1	NA	intron (NM_001161800, intron 1 of 9)	B3A|SINE|B2	4423	NM_001161800	52323	Mm.273768	NM_026448	ENSMUSG00000028986	Klhl7	2700038B03Rik|D5Ertd363e|SBBI26	kelch-like 7	protein-coding
mm_100411.1	chr11	119426009	119426022	+	1	NA	Intergenic	Intergenic	35543	NR_035453	100316690		NR_035453	ENSMUSG00000088015	Mir1932	mir-1932|mmu-mir-1932	microRNA 1932	ncRNA
mm_161386.1	chr14	76415832	76415832	+	1	NA	promoter-TSS (NM_207652)	promoter-TSS (NM_207652)	11	NM_207652	21807	Mm.153272	NM_009366	ENSMUSG00000022010	Tsc22d1	AA589566|AW105905|Egr5|TSC-22|Tgfb1i4|Tsc|Tsc22	TSC22 domain family, member 1	protein-coding
mm_5018.1	chr1	193153108	193153116	+	1	NA	promoter-TSS (NM_016851)	promoter-TSS (NM_016851)	0	NM_016851	54139	Mm.273695	NM_016851	ENSMUSG00000026638	Irf6	AI876454|E230028I05Rik|mirf6	interferon regulatory factor 6	protein-coding
mm_97669.1	chr11	79660742	79660752	+	1	NA	intron (NM_175543, intron 3 of 14)	CpG	14339	NR_045898	72218	Mm.443271	NR_045898	ENSMUSG00000086569	Rab11fip4os2	1700020F10Rik|4930542H20Rik|Rab11fib4os2	RAB11 family interacting protein 4 (class II), opposite strand 2	ncRNA
mm_92096.1	chr10	62887413	62887440	-	1	NA	Intergenic	Intergenic	-7412	NM_001253857	52463	Mm.17774	NM_027384	ENSMUSG00000047146	Tet1	2510010B09Rik|AA517754|BB001228|Cxxc6|D10Ertd17e|LCX|mKIAA1676	tet methylcytosine dioxygenase 1	protein-coding
mm_83112.1	chr9	40376333	40376358	-	1	NA	intron (NM_172768, intron 2 of 19)	intron (NM_172768, intron 2 of 19)	42873	NR_040728	73558	Mm.398307	NR_040728		1700110K17Rik	-	RIKEN cDNA 1700110K17 gene	ncRNA
mm_97078.1	chr11	73009721	73009737	+	1	NA	intron (NM_008771, intron 6 of 11)	intron (NM_008771, intron 6 of 11)	-9279	NM_018883	55984	Mm.9998	NM_018883	ENSMUSG00000020785	Camkk1	AI846603|CaMKKalpha|Camkk	calcium/calmodulin-dependent protein kinase kinase 1, alpha	protein-coding
mm_11169.1	chr2	28560555	28560599	+	1	NA	exon (NM_009885, exon 4 of 11)	exon (NM_009885, exon 4 of 11)	2826	NM_009885	12613	Mm.236017	NM_009885	ENSMUSG00000026818	Cel	1810036E18Rik|BAL	carboxyl ester lipase	protein-coding
mm_52069.1	chr6	97807074	97807084	+	1	NA	promoter-TSS (NM_001113198)	promoter-TSS (NM_001113198)	21	NM_001113198	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_161472.1	chr15	79505287	79505287	-	1	NA	promoter-TSS (NM_008427)	promoter-TSS (NM_008427)	-46	NM_008427	16520	Mm.39759	NM_008427	ENSMUSG00000044216	Kcnj4	IRK3|Kcnf2|MB-IRK3	potassium inwardly-rectifying channel, subfamily J, member 4	protein-coding
mm_97859.1	chr11	83116789	83116797	+	1	NA	promoter-TSS (NM_011407)	promoter-TSS (NM_011407)	-52	NM_011407	20555	Mm.10948	NM_011407	ENSMUSG00000078763	Slfn1	AV316259	schlafen 1	protein-coding
mm_122765.1	chr14	54253844	54253904	-	1	NA	promoter-TSS (NM_001205181)	promoter-TSS (NM_001205181)	55	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_12400.1	chr2	70458946	70458956	+	1	NA	Intergenic	Intergenic	-15972	NM_022435	64406	Mm.423397	NM_022435	ENSMUSG00000075304	Sp5	-	trans-acting transcription factor 5	protein-coding
mm_119591.1	chr14	50947942	50947961	+	1	NA	exon (NM_013632, exon 2 of 6)	exon (NM_013632, exon 2 of 6)	3648	NM_013632	18950	Mm.17932	NM_013632	ENSMUSG00000021871	Pnp	AL024301|AU015798|Np|Np-1|Np-2|Pnp1	purine-nucleoside phosphorylase	protein-coding
mm_54696.1	chr6	39557707	39557742	-	1	NA	5' UTR (NM_172477, exon 1 of 19)	5' UTR (NM_172477, exon 1 of 19)	110	NM_172477	209773	Mm.440021	NM_172477	ENSMUSG00000038456	Dennd2a	B930096L08Rik|C130031G22|mKIAA1277	DENN/MADD domain containing 2A	protein-coding
mm_47288.1	chr5	122131989	122131989	-	1	NA	intron (NM_001289809, intron 1 of 11)	intron (NM_001289809, intron 1 of 11)	2904	NM_001289811	330188	Mm.386907	NM_183307	ENSMUSG00000043036	Ccdc63	4921511C16Rik	coiled-coil domain containing 63	protein-coding
mm_29566.1	chr3	116968539	116968551	-	1	NA	non-coding (NR_040596, exon 1 of 3)	non-coding (NR_040596, exon 1 of 3)	278	NR_040596	74654	Mm.410820	NR_040596	ENSMUSG00000080907	4930455H04Rik	-	RIKEN cDNA 4930455H04 gene	ncRNA
mm_16892.1	chr2	13223334	13223334	-	1	NA	intron (NM_009105, intron 4 of 8)	intron (NM_009105, intron 4 of 8)	48081	NM_009105	20163	Mm.905	NM_009105	ENSMUSG00000026727	Rsu1	RsuI|rsp-1	Ras suppressor protein 1	protein-coding
mm_44495.1	chr5	23684594	23684602	-	1	NA	Intergenic	MLT1F1|LTR|ERVL-MaLR	28069	NR_038090	433855	Mm.205125	NR_015554	ENSMUSG00000105987	AI506816	-	expressed sequence AI506816	ncRNA
mm_19251.1	chr2	84773373	84773405	-	1	NA	exon (NM_009776, exon 3 of 8)	exon (NM_009776, exon 3 of 8)	2040	NM_009776	12258	Mm.38888	NM_009776	ENSMUSG00000023224	Serping1	C1INH|C1nh	serine (or cysteine) peptidase inhibitor, clade G, member 1	protein-coding
mm_170999.1	chr2	75662916	75662921	+	1	NA	exon (NM_198090, exon 7 of 11)	exon (NM_198090, exon 7 of 11)	3628	NR_033513	627828	Mm.459502	NR_033513	ENSMUSG00000092086	Gm6793	EG627828	heterogeneous nuclear ribonucleoprotein A3 pseudogene	pseudo
mm_68123.1	chr7	102120304	102120323	-	1	NA	3' UTR (NM_001287164, exon 33 of 33)	3' UTR (NM_001287164, exon 33 of 33)	-3600	NM_001081424	504186	Mm.334074	NM_001081424	ENSMUSG00000066279	Chrna10	-	cholinergic receptor, nicotinic, alpha polypeptide 10	protein-coding
mm_48426.1	chr5	140565061	140565072	-	1	NA	promoter-TSS (NM_030022)	promoter-TSS (NM_030022)	1	NM_030022	77998	Mm.160040	NM_030022	ENSMUSG00000036586	Grifin	E130101O17Rik	galectin-related inter-fiber protein	protein-coding
mm_123529.1	chr14	66804012	66804025	-	1	NA	3' UTR (NM_009955, exon 14 of 14)	3' UTR (NM_009955, exon 14 of 14)	64582	NM_009955	12934	Mm.352648	NM_009955	ENSMUSG00000022048	Dpysl2	AI851130|Crmp2|DRP2|Musunc33|TOAD-64|Ulip2	dihydropyrimidinase-like 2	protein-coding
mm_25820.1	chr3	127861586	127861615	+	1	NA	Intergenic	Intergenic	-24108	NM_145964	211556	Mm.403486	NM_145964	ENSMUSG00000074238	Ap1ar	AA407621|C78909|Gadkin	adaptor-related protein complex 1 associated regulatory protein	protein-coding
mm_47765.1	chr5	131537940	131537963	-	1	NA	intron (NM_177047, intron 5 of 18)	CpG	-230429	NM_145218	212996	Mm.299204	NM_145218	ENSMUSG00000034040	Wbscr17	AA388321|E330012B09Rik	Williams-Beuren syndrome chromosome region 17 homolog (human)	protein-coding
mm_16648.1	chr2	6213036	6213044	-	1	NA	promoter-TSS (NM_024208)	promoter-TSS (NM_024208)	-46	NM_024208	67856	Mm.38342	NM_024208	ENSMUSG00000039063	Echdc3	2310005D12Rik|AI662097	enoyl Coenzyme A hydratase domain containing 3	protein-coding
mm_31643.1	chr4	59581618	59581629	+	1	NA	promoter-TSS (NM_024255)	promoter-TSS (NM_024255)	60	NM_024255	72479	Mm.272905	NM_024255	ENSMUSG00000028383	Hsdl2	2610207I16Rik	hydroxysteroid dehydrogenase like 2	protein-coding
mm_64021.1	chr7	140287965	140287978	+	1	NA	intron (NM_001128146, intron 6 of 15)	L1_Mur3|LINE|L1	-34730	NM_146956	258958	Mm.347648	NM_146956	ENSMUSG00000061489	Olfr525	MOR251-2	olfactory receptor 525	protein-coding
mm_10637.1	chr2	20370213	20370219	+	1	NA	intron (NM_001081006, intron 2 of 21)	intron (NM_001081006, intron 2 of 21)	80303	NM_001081006	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding
mm_74246.1	chr8	124831017	124831028	+	1	NA	3' UTR (NM_198632, exon 10 of 10)	3' UTR (NM_198632, exon 10 of 10)	32007	NM_025615	66523	Mm.436864	NM_025615	ENSMUSG00000031984	2810004N23Rik	3110004G14Rik|Ayu21-55|Gt(pU21)55Imeg|GtAyu21-55	RIKEN cDNA 2810004N23 gene	protein-coding
mm_83388.1	chr9	44604589	44604595	-	1	NA	promoter-TSS (NM_001110826)	promoter-TSS (NM_001110826)	-300	NM_001110826	13209	Mm.267061	NM_007841	ENSMUSG00000032097	Ddx6	1110001P04Rik|E230023J21Rik|HLR2|mRCK/P54|p54|rck	DEAD (Asp-Glu-Ala-Asp) box polypeptide 6	protein-coding
mm_105335.1	chr11	102946770	102946778	-	1	NA	promoter-TSS (NM_011795)	promoter-TSS (NM_011795)	-313	NM_011795	23829	Mm.57154	NM_011795	ENSMUSG00000045532	C1ql1	C1qrf|CRF|CTRP14|gliacolin	complement component 1, q subcomponent-like 1	protein-coding
mm_64046.1	chr7	140835205	140835241	+	1	NA	promoter-TSS (NM_029821)	promoter-TSS (NM_029821)	85	NM_001347605	76974	Mm.272359	NM_029821	ENSMUSG00000025481	Urah	1190003J15Rik|2810420C16Rik	urate (5-hydroxyiso-) hydrolase	protein-coding
mm_80370.1	chr9	75345107	75345112	+	1	NA	non-coding (NR_073186, exon 12 of 12)	non-coding (NR_073186, exon 12 of 12)	-2649	NM_013479	12049	Mm.25988	NM_013479	ENSMUSG00000032191	Bcl2l10	AA420380|AU023065|Boo|C85687|Diva	Bcl2-like 10	protein-coding
mm_10460.1	chr2	14305334	14305354	+	1	NA	exon (NM_008625, exon 17 of 30)	exon (NM_008625, exon 17 of 30)	44341	NR_030609	100124488		NR_030609	ENSMUSG00000077897	Mir511	Mirn511|mir-511|mmu-mir-511	microRNA 511	ncRNA
mm_80913.1	chr9	100645246	100645251	+	1	NA	intron (NM_009282, intron 1 of 33)	intron (NM_009282, intron 1 of 33)	1625	NM_009282	20842	Mm.42135	NM_009282	ENSMUSG00000037286	Stag1	AU045003|SA-1|Scc3	stromal antigen 1	protein-coding
mm_109366.1	chr12	109643352	109643357	+	1	NA	TTS (NR_046303)	TTS (NR_046303)	516	NR_046303	449561		NR_046303		AF357426	MBII-49	snoRNA AF357426	snoRNA
mm_54571.1	chr6	38046995	38046998	-	1	NA	promoter-TSS (NM_177200)	promoter-TSS (NM_177200)	0	NM_177200	320590	Mm.197449	NM_177200	ENSMUSG00000029830	Svopl	9430071P14Rik	SV2 related protein homolog (rat)-like	protein-coding
mm_29868.1	chr3	130709420	130709451	-	1	NA	promoter-TSS (NM_025509)	promoter-TSS (NM_025509)	9	NM_025509	66357	Mm.300697	NM_025509	ENSMUSG00000041084	Ostc	2310008M10Rik|5730557H03Rik	oligosaccharyltransferase complex subunit (non-catalytic)	protein-coding
mm_72809.1	chr8	87473251	87473257	+	1	NA	promoter-TSS (NM_019626)	promoter-TSS (NM_019626)	138	NR_125722	100040294	Mm.213632	NR_033430	ENSMUSG00000097248	Gm2694	C230036H16Rik|linc1582	predicted gene 2694	ncRNA
mm_106070.1	chr11	116168139	116168205	-	1	NA	promoter-TSS (NM_172571)	promoter-TSS (NM_172571)	6	NM_172571	217335	Mm.35241	NM_172571	ENSMUSG00000020776	Fbf1	1110033G01Rik|5930413D20|mKIAA1863	Fas (TNFRSF6) binding factor 1	protein-coding
mm_24586.1	chr3	93444968	93444975	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	2641	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_119015.1	chr14	30008894	30008901	+	1	NA	promoter-TSS (NM_001136240)	promoter-TSS (NM_001136240)	-1	NM_019583	50905	Mm.269363	NM_019583	ENSMUSG00000015966	Il17rb	Evi27|IL-17ER|IL-17Rh1|IL17RH1|Il17br	interleukin 17 receptor B	protein-coding
mm_53973.1	chr6	6217129	6217149	-	1	NA	promoter-TSS (NM_001177572)	promoter-TSS (NM_001177572)	34	NM_015829	50799	Mm.24513	NM_015829	ENSMUSG00000015112	Slc25a13	AI785475|Ctrn	solute carrier family 25 (mitochondrial carrier, adenine nucleotide translocator), member 13	protein-coding
mm_147138.1	chr18	36416594	36416598	-	1	NA	intron (NM_026027, intron 3 of 3)	intron (NM_026027, intron 3 of 3)	37899	NM_026027	67199	Mm.30184	NM_026027	ENSMUSG00000024346	Pfdn1	2700086I23Rik|AA408327|AU044714	prefoldin 1	protein-coding
mm_27943.1	chr3	79628860	79628870	-	1	NA	promoter-TSS (NM_025794)	promoter-TSS (NM_025794)	-98	NM_025794	66841	Mm.28336	NM_025794	ENSMUSG00000027809	Etfdh	0610010I20Rik|AV001013	electron transferring flavoprotein, dehydrogenase	protein-coding
mm_17564.1	chr2	30205700	30205716	-	1	NA	promoter-TSS (NM_172404)	promoter-TSS (NM_172404)	-9	NM_172404	70266	Mm.216089	NM_172404	ENSMUSG00000039648	Kyat1	2010009K05Rik|AI182306|Ccbl1|Gtk|Kat1|KatI	kynurenine aminotransferase 1	protein-coding
mm_4968.1	chr1	191281454	191281464	+	1	NA	Intergenic	Intergenic	36659	NM_025424	66208	Mm.46444	NM_025424	ENSMUSG00000037499	Nenf	1110060M21Rik|SCIRP10|Spuf	neuron derived neurotrophic factor	protein-coding
mm_152935.1	chr19	28680111	28680122	-	1	NA	promoter-TSS (NM_175459)	promoter-TSS (NM_175459)	-39	NM_175459	226075	Mm.223508	NM_175459	ENSMUSG00000052942	Glis3	4833409N03Rik|E330013K21Rik	GLIS family zinc finger 3	protein-coding
mm_729.1	chr1	43189101	43189115	+	1	NA	intron (NM_001289533, intron 1 of 5)	intron (NM_001289533, intron 1 of 5)	7653	NM_001289533	14200	Mm.6799	NM_010212	ENSMUSG00000008136	Fhl2	FHL-2|SLIM-3|SLIM3	four and a half LIM domains 2	protein-coding
mm_68542.1	chr7	114070173	114070192	-	1	NA	intron (NM_025846, intron 1 of 5)	intron (NM_025846, intron 1 of 5)	47599	NM_025846	66922	Mm.276572	NM_025846	ENSMUSG00000055723	Rras2	2610016H24Rik|C86394|TC21	related RAS viral (r-ras) oncogene 2	protein-coding
mm_43379.1	chr5	135689184	135689213	+	1	NA	promoter-TSS (NM_008898)	promoter-TSS (NM_008898)	53	NM_008898	18984	Mm.3863	NM_008898	ENSMUSG00000005514	Por	4933424M13Rik|CPR|CYPOR|P450R	P450 (cytochrome) oxidoreductase	protein-coding
mm_32433.1	chr4	107200573	107200609	+	1	NA	3' UTR (NM_029565, exon 8 of 8)	3' UTR (NM_029565, exon 8 of 8)	-8589	NM_001081272	546840	Mm.331755	NM_001081272	ENSMUSG00000070877	Ldlrad1	OTTMUSG00000008594	low density lipoprotein receptor class A domain containing 1	protein-coding
mm_36496.1	chr4	83285172	83285214	-	1	NA	intron (NM_027238, intron 2 of 19)	intron (NM_027238, intron 2 of 19)	38996	NM_027238	69863	Mm.5540	NM_025782	ENSMUSG00000038172	Ttc39b	1810054D07Rik|9130422G05Rik|AI450603|AV103077|AW215585	tetratricopeptide repeat domain 39B	protein-coding
mm_153335.1	chr19	38224066	38224095	-	1	NA	promoter-TSS (NM_001081075)	promoter-TSS (NM_001081075)	52	NM_001081075	70567	Mm.30607	NM_001081075	ENSMUSG00000054237	Fra10ac1	5730455O13Rik|AI448293	FRA10AC1 homolog (human)	protein-coding
mm_52916.1	chr6	122848159	122848196	+	1	NA	3' UTR (NM_009779, exon 2 of 2)	3' UTR (NM_009779, exon 2 of 2)	7980	NM_009779	12267	Mm.2408	NM_009779	ENSMUSG00000040552	C3ar1	AZ3B|C3AR|HNFAG09	complement component 3a receptor 1	protein-coding
mm_113481.1	chr13	37345289	37345303	+	1	NA	promoter-TSS (NM_010745)	promoter-TSS (NM_010745)	-49	NM_010745	17084	Mm.2639	NM_010745	ENSMUSG00000021423	Ly86	MD-1|MD1|ly86_tv2	lymphocyte antigen 86	protein-coding
mm_11617.1	chr2	34608499	34608507	+	1	NA	intron (NM_001290626, intron 9 of 10)	MLT1F2|LTR|ERVL-MaLR	146729	NM_025709	66691	Mm.156452	NM_025709	ENSMUSG00000026867	Gapvd1	2010005B09Rik|4432404J10Rik|AW108497|Gapex-5|RAP6|RME-6|mKIAA1521	GTPase activating protein and VPS9 domains 1	protein-coding
mm_170904.1	chr2	30071533	30071538	+	1	NA	3' UTR (NM_001204875, exon 8 of 8)	3' UTR (NM_001204875, exon 8 of 8)	5061	NM_001204875	56086	Mm.326055	NM_023871	ENSMUSG00000054766	Set	2610030F17Rik|5730420M11Rik|AA407739|I-2PP2A|StF-IT-1|TAF-I	SET nuclear oncogene	protein-coding
mm_82987.1	chr9	36533729	36533770	-	1	NA	3' UTR (NM_001033783, exon 3 of 3)	3' UTR (NM_001033783, exon 3 of 3)	8214	NM_001033783	434396	Mm.118836	NM_001033783	ENSMUSG00000074448	Gm5615	EG434396|Pate-H|Pate9	predicted gene 5615	protein-coding
mm_7337.1	chr1	105663642	105663660	-	1	NA	promoter-TSS (NM_013784)	promoter-TSS (NM_013784)	25	NM_013784	27392	Mm.268911	NM_013784	ENSMUSG00000056536	Pign	Gm20308|PIG-N	phosphatidylinositol glycan anchor biosynthesis, class N	protein-coding
mm_36619.1	chr4	89311022	89311025	-	1	NA	promoter-TSS (NM_007670)	promoter-TSS (NM_007670)	9	NM_007670	12579	Mm.423094	NM_007670	ENSMUSG00000073802	Cdkn2b	AV083695|INK4b|MTS2|p15|p15(INK4b)|p15INK4b	cyclin-dependent kinase inhibitor 2B (p15, inhibits CDK4)	protein-coding
mm_74704.1	chr8	16992980	16992983	-	1	NA	intron (NM_053171, intron 3 of 69)	intron (NM_053171, intron 3 of 69)	542404	NM_053171	94109	Mm.436988	NM_053171	ENSMUSG00000060924	Csmd1	B930082H09|mKIAA1890	CUB and Sushi multiple domains 1	protein-coding
mm_67311.1	chr7	79466128	79466136	-	1	NA	5' UTR (NM_017462, exon 1 of 23)	5' UTR (NM_017462, exon 1 of 23)	141	NM_017462	18975	Mm.3616	NM_017462	ENSMUSG00000039176	Polg	AA409516|PolgA	polymerase (DNA directed), gamma	protein-coding
mm_48018.1	chr5	136171166	136171176	-	1	NA	promoter-TSS (NM_178751)	promoter-TSS (NM_178751)	-515	NM_178751	269717	Mm.308396	NM_178751	ENSMUSG00000039747	Orai2	A730041O15Rik|Tmem142b	ORAI calcium release-activated calcium modulator 2	protein-coding
mm_161064.1	chr12	72071110	72071110	-	1	NA	promoter-TSS (NM_181752)	promoter-TSS (NM_181752)	-119	NM_181752	238252	Mm.390508	NM_181752	ENSMUSG00000043398	Gpr135	PAFR	G protein-coupled receptor 135	protein-coding
mm_67674.1	chr7	88308079	88308102	-	1	NA	exon (NM_009982, exon 6 of 7)	exon (NM_009982, exon 6 of 7)	30005	NM_001311790	13032	Mm.89295	NM_009982	ENSMUSG00000030560	Ctsc	AI047818|CatC|DPP1|DPPI	cathepsin C	protein-coding
mm_14624.1	chr2	136773974	136773999	+	1	NA	exon (NM_001291056, exon 6 of 8)	exon (NM_001291056, exon 6 of 8)	60536	NM_001291056	20614	Mm.45953	NM_011428	ENSMUSG00000027273	Snap25	Bdr|GENA70|SNAP-25|SUP|sp	synaptosomal-associated protein 25	protein-coding
mm_37519.1	chr4	124451320	124451320	-	1	NA	intron (NR_040774, intron 2 of 3)	intron (NR_040774, intron 2 of 3)	34639	NR_040774	78460	Mm.452060	NR_040774		1700057H15Rik	-	RIKEN cDNA 1700057H15 gene	ncRNA
mm_99956.1	chr11	113387623	113387624	+	1	NA	intron (NM_027216, intron 5 of 9)	intron (NM_027216, intron 5 of 9)	-177954	NR_040276	319871	Mm.383743	NR_040276	ENSMUSG00000085421	4732490B19Rik	-	RIKEN cDNA 4732490B19 gene	ncRNA
mm_23624.1	chr3	65958410	65958423	+	1	NA	promoter-TSS (NM_019937)	promoter-TSS (NM_019937)	-191	NM_019937	56706	Mm.175612	NM_019937	ENSMUSG00000027829	Ccnl1	2610030E23Rik|AU018493|Ccnl|ania-6a	cyclin L1	protein-coding
mm_78912.1	chr9	44981802	44981834	+	1	NA	promoter-TSS (NM_013487)	promoter-TSS (NM_013487)	32	NM_013487	12500	Mm.4527	NM_013487	ENSMUSG00000032094	Cd3d	T3d	CD3 antigen, delta polypeptide	protein-coding
mm_87533.1	chr10	53467941	53467946	+	1	NA	Intergenic	Intergenic	51046	NR_037973	100502868	Mm.297722	NR_037973		Gm20597	B230314j19	predicted gene, 20597	ncRNA
mm_98242.1	chr11	88164905	88164919	+	1	NA	intron (NM_198013, intron 1 of 10)	intron (NM_198013, intron 1 of 10)	-4653	NM_001172099	103841	Mm.374846	NM_198013	ENSMUSG00000018378	Cuedc1	AI841487|C330016O16Rik	CUE domain containing 1	protein-coding
mm_72231.1	chr8	74873128	74873137	+	1	NA	promoter-TSS (NM_027837)	promoter-TSS (NM_027837)	-42	NM_027837	71597	Mm.158735	NM_027837	ENSMUSG00000031621	Isx	9130012O13Rik|Pix-1	intestine specific homeobox	protein-coding
mm_153961.1	chr19	47787108	47787129	-	1	NA	intron (NM_027559, intron 13 of 37)	intron (NM_027559, intron 13 of 37)	-31961	NR_106165	102465883		NR_106165	ENSMUSG00000099069	Mir8090	Gm27862|mmu-mir-8090	microRNA 8090	ncRNA
mm_75484.1	chr8	48711037	48711037	-	1	NA	Intergenic	Intergenic	-36347	NM_011857	23965	Mm.42191	NM_011857	ENSMUSG00000031561	Tenm3	2610100B16Rik|Odz1|Odz3|Ten-m3|mKIAA1455	teneurin transmembrane protein 3	protein-coding
mm_35510.1	chr4	41094734	41094744	-	1	NA	exon (NM_016689, exon 3 of 6)	exon (NM_016689, exon 3 of 6)	3444	NM_016689	11828	Mm.34043	NM_016689	ENSMUSG00000028435	Aqp3	AQP-2	aquaporin 3	protein-coding
mm_70641.1	chr8	14017419	14017419	+	1	NA	Intergenic	Intergenic	18479	NR_131136	546036	Mm.31785	NR_131136	ENSMUSG00000110058	Gm5907	EG546036|Gm845	predicted gene 5907	ncRNA
mm_159276.1	chr2	165296964	165296964	-	1	NA	exon (NM_207706, exon 16 of 22)	exon (NM_207706, exon 16 of 22)	-9126	NR_045544	228875	Mm.21184	NM_144893	ENSMUSG00000017664	Slc35c2	C85957|CGI-15|D2Wsu58e|Ovcov1	solute carrier family 35, member C2	protein-coding
mm_18782.1	chr2	73659758	73659769	-	1	NA	exon (NM_175752, exon 1 of 7)	exon (NM_175752, exon 1 of 7)	660	NM_175752	108699	Mm.257073	NM_029716	ENSMUSG00000056486	Chn1	0610007I19Rik|0710001E19Rik|1700112L09Rik|2900046J01Rik|AI413815|ARHGAP2	chimerin 1	protein-coding
mm_89189.1	chr10	86347204	86347214	+	1	NA	3' UTR (NM_011595, exon 5 of 5)	3' UTR (NM_011595, exon 5 of 5)	46797	NM_011595	21859	Mm.4871	NM_011595	ENSMUSG00000020044	Timp3	Timp-3	tissue inhibitor of metalloproteinase 3	protein-coding
mm_112633.1	chr13	15994271	15994278	+	1	NA	Intergenic	RMER5|LTR|ERV1	-17577	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_148403.1	chr19	3851928	3851934	+	1	NA	non-coding (NR_073190, exon 1 of 13)	non-coding (NR_073190, exon 1 of 13)	158	NR_073190	12660	Mm.225505	NM_013490	ENSMUSG00000024843	Chka	CK|CK/EK-alpha|Chetk-alpha|Chk|ChoK|EK|EtnK-alpha	choline kinase alpha	protein-coding
mm_14836.1	chr2	147366140	147366159	+	1	NA	exon (NM_008780, exon 2 of 5)	exon (NM_008780, exon 2 of 5)	1155	NM_008780	18503	Mm.315502	NM_008780	ENSMUSG00000037034	Pax1	Pax-1|hbs|hunchback|un|undulated|wt	paired box 1	protein-coding
mm_143939.1	chr17	86230385	86230411	-	1	NA	intron (NM_011104, intron 1 of 14)	intron (NM_011104, intron 1 of 14)	56780	NR_045435	72104	Mm.443401	NR_045435	ENSMUSG00000100738	2010106C02Rik	-	RIKEN cDNA 2010106C02 gene	ncRNA
mm_75241.1	chr8	39637831	39637874	-	1	NA	intron (NM_001113326, intron 1 of 9)	intron (NM_001113326, intron 1 of 9)	4826	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_96239.1	chr11	62551757	62551770	+	1	NA	promoter-TSS (NM_001313984)	promoter-TSS (NM_001313984)	32	NM_001313984	22187	Mm.371592	NM_011664	ENSMUSG00000019505	Ubb	AL033289|Rps27a|Uba52|Ubb2|Ubc	ubiquitin B	protein-coding
mm_92659.1	chr10	80417387	80417418	-	1	NA	exon (NM_011548, exon 10 of 19)	exon (NM_011548, exon 10 of 19)	-10581	NM_025650	66594	Mm.379119	NM_025650	ENSMUSG00000020163	Uqcr11	0710008D09Rik|AL022707|Uqcr	ubiquinol-cytochrome c reductase, complex III subunit XI	protein-coding
mm_104499.1	chr11	95864641	95864648	-	1	NA	3' UTR (NM_008081, exon 11 of 11)	3' UTR (NM_008081, exon 11 of 11)	5827	NR_045187	73906	Mm.399894	NR_045187	ENSMUSG00000086015	4833417C18Rik	-	RIKEN cDNA 4833417C18 gene	ncRNA
mm_29468.1	chr3	113630069	113630147	-	1	NA	promoter-TSS (NM_001038696)	promoter-TSS (NM_001038696)	41	NM_026043	67225	Mm.316928	NM_026043	ENSMUSG00000027981	Rnpc3	2810441O16Rik|AI447568|C030014B17Rik	RNA-binding region (RNP1, RRM) containing 3	protein-coding
mm_114563.1	chr13	74494062	74494093	+	1	NA	promoter-TSS (NM_146231)	promoter-TSS (NM_146231)	-127	NM_146231	235956	Mm.296909	NM_146231	ENSMUSG00000069208	Zfp825	-	zinc finger protein 825	protein-coding
mm_20419.1	chr2	129301547	129301549	-	1	NA	intron (NM_010554, intron 6 of 6)	intron (NM_010554, intron 6 of 6)	4178	NR_040371	100503468	Mm.446943	NR_040371	ENSMUSG00000085498	Gm14023	OTTMUSG00000015408	predicted gene 14023	ncRNA
mm_134556.1	chr16	20241278	20241298	-	1	NA	promoter-TSS (NM_198599)	promoter-TSS (NM_198599)	70	NM_198599	208158	Mm.326383	NM_198599	ENSMUSG00000041205	Map6d1	A330066I15Rik	MAP6 domain containing 1	protein-coding
mm_136079.1	chr16	84835270	84835294	-	1	NA	promoter-TSS (NM_001302216)	promoter-TSS (NM_001302216)	158	NM_008065	14390	Mm.18974	NM_008065	ENSMUSG00000008976	Gabpa	GABPalpha	GA repeat binding protein, alpha	protein-coding
mm_52174.1	chr6	99204439	99204459	+	1	NA	intron (NM_001347345, intron 4 of 19)	intron (NM_001347345, intron 4 of 19)	62066	NM_001197321	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_7812.1	chr1	131760158	131760164	-	1	NA	intron (NM_177243, intron 12 of 20)	intron (NM_177243, intron 12 of 20)	16139	NM_177243	320718	Mm.482704	NM_177243	ENSMUSG00000042268	Slc26a9	E030002L01Rik	solute carrier family 26, member 9	protein-coding
mm_33606.1	chr4	132581119	132581129	+	1	NA	3' UTR (NM_001081211, exon 2 of 2)	3' UTR (NM_001081211, exon 2 of 2)	17057	NM_001081211	19204	Mm.89389	NM_001081211	ENSMUSG00000056529	Ptafr	PAFR	platelet-activating factor receptor	protein-coding
mm_54182.1	chr6	23839472	23839487	-	1	NA	promoter-TSS (NM_153163)	promoter-TSS (NM_153163)	-58	NM_001252105	320405	Mm.259632	NM_153163	ENSMUSG00000017978	Cadps2	A230044C21Rik|Caps-2|Caps2|Cpd2	Ca2+-dependent activator protein for secretion 2	protein-coding
mm_164745.1	chr17	73950335	73950354	+	1	NA	promoter-TSS (NM_011723)	promoter-TSS (NM_011723)	-148	NM_011723	22436	Mm.11223	NM_011723	ENSMUSG00000024066	Xdh	XO|Xor|Xox-1|Xox1	xanthine dehydrogenase	protein-coding
mm_97216.1	chr11	75630833	75630851	+	1	NA	promoter-TSS (NM_008916)	promoter-TSS (NM_008916)	-178	NM_008916	19062	Mm.1458	NM_008916	ENSMUSG00000006127	Inpp5k	C62|Pps|SKIP	inositol polyphosphate 5-phosphatase K	protein-coding
mm_18554.1	chr2	65188738	65188774	-	1	NA	intron (NM_027225, intron 1 of 12)	intron (NM_027225, intron 1 of 12)	49870	NM_177025	319876	Mm.34159	NM_027225	ENSMUSG00000034903	Cobll1	1810047P18Rik|Coblr1|D430044D16Rik	Cobl-like 1	protein-coding
mm_127916.1	chr15	9530312	9530322	-	1	NA	promoter-TSS (NM_008372)	promoter-TSS (NM_008372)	-441	NM_008372	16197	Mm.389	NM_008372	ENSMUSG00000003882	Il7r	CD127|IL-7Ralpha	interleukin 7 receptor	protein-coding
mm_38166.1	chr4	135216976	135216986	-	1	NA	3' UTR (NM_013885, exon 6 of 6)	3' UTR (NM_013885, exon 6 of 6)	55779	NM_013885	29876	Mm.257765	NM_013885	ENSMUSG00000037242	Clic4	D0Jmb3|TU-74|mc3s5|mtCLIC	chloride intracellular channel 4 (mitochondrial)	protein-coding
mm_13684.1	chr2	116972833	116972847	+	1	NA	Intergenic	Intergenic	72688	NR_040335	320975	Mm.132509	NR_040335	ENSMUSG00000085316	D330050G23Rik	-	RIKEN cDNA D330050G23 gene	ncRNA
mm_37196.1	chr4	117682217	117682225	-	1	NA	promoter-TSS (NM_023178)	promoter-TSS (NM_023178)	4	NM_023178	66233	Mm.29142	NM_023178	ENSMUSG00000009640	Dmap1	1500016M21Rik|DNMAP1|DNMTAP1|Dmtap1|mKIAA1425	DNA methyltransferase 1-associated protein 1	protein-coding
mm_46163.1	chr5	96162616	96162622	-	1	NA	promoter-TSS (NM_178854)	promoter-TSS (NM_178854)	-629	NM_144910	231464	Mm.28374	NM_144910	ENSMUSG00000034724	Cnot6l	4932442K20Rik	CCR4-NOT transcription complex, subunit 6-like	protein-coding
mm_32753.1	chr4	116686897	116686908	+	1	NA	promoter-TSS (NR_040442)	promoter-TSS (NR_040442)	-880	NR_040442	100502959	Mm.395400	NR_040442		AV051173	-	expressed sequence AV051173	ncRNA
mm_96178.1	chr11	61653225	61653235	+	1	NA	promoter-TSS (NM_027817)	promoter-TSS (NM_027817)	-91	NM_027817	71520	Mm.202760	NM_027817	ENSMUSG00000004837	Grap	8430435N19Rik|BB233594	GRB2-related adaptor protein	protein-coding
mm_76448.1	chr8	85080653	85080668	-	1	NA	promoter-TSS (NM_026399)	promoter-TSS (NM_026399)	86	NM_026399	67836	Mm.334680	NM_026399	ENSMUSG00000005150	Wdr83	1500041N16Rik|Morg1	WD repeat domain containing 83	protein-coding
mm_101718.1	chr11	42182240	42182281	-	1	NA	5' UTR (NM_010250, exon 1 of 10)	5' UTR (NM_010250, exon 1 of 10)	670	NM_010250	14394	Mm.439668	NM_010250	ENSMUSG00000010803	Gabra1	Gabra-1	gamma-aminobutyric acid (GABA) A receptor, subunit alpha 1	protein-coding
mm_102874.1	chr11	69409414	69409422	-	1	NA	intron (NM_001017426, intron 1 of 22)	intron (NM_001017426, intron 1 of 22)	4257	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_137810.1	chr17	30005030	30005098	+	1	NA	promoter-TSS (NM_148926)	promoter-TSS (NM_148926)	-23	NM_148926	21769	Mm.220972	NM_148926	ENSMUSG00000044477	Zfand3	AW539211|TEG-27|Tex27	zinc finger, AN1-type domain 3	protein-coding
mm_171496.1	chr4	146160126	146160142	+	1	NA	intron (NM_001177546, intron 2 of 4)	intron (NM_001177546, intron 2 of 4)	2444	NM_001177545	667666	Mm.459230	NM_001177545	ENSMUSG00000066007	Zfp600	Gm13164|OTTMUSG00000010694	zinc finger protein 600	protein-coding
mm_67844.1	chr7	98562354	98562366	-	1	NA	Intergenic	RLTR15|LTR|ERVK	68138	NM_001113379	434215	Mm.323057	NM_001113379	ENSMUSG00000090958	Lrrc32	AI426318|D11S833Eh|D7H11S833E|EG434215|Garp	leucine rich repeat containing 32	protein-coding
mm_67079.1	chr7	68264645	68264653	-	1	NA	promoter-TSS (NM_030101)	promoter-TSS (NM_030101)	-416	NM_030101	78444	Mm.425468	NM_030101	ENSMUSG00000030553	Pgpep1l	C330024D12Rik	pyroglutamyl-peptidase I-like	protein-coding
mm_73745.1	chr8	114417996	114418011	+	1	NA	promoter-TSS (NM_001007223)	promoter-TSS (NM_001007223)	-31	NM_001007223	403395	Mm.81117	NM_001007223	ENSMUSG00000008874	Clec3a	1110019O10Rik|Clecsf1|Gm796	C-type lectin domain family 3, member a	protein-coding
mm_15623.1	chr2	162661193	162661239	+	1	NA	promoter-TSS (NM_021464)	promoter-TSS (NM_021464)	53	NR_033569	77288	Mm.376571	NR_033569		9430021M05Rik	-	RIKEN cDNA 9430021M05 gene	ncRNA
mm_131846.1	chr16	23058534	23058544	+	1	NA	exon (NM_001102411, exon 1 of 10)	exon (NM_001102411, exon 1 of 10)	239	NM_001102412	16644	Mm.2160	NM_023125	ENSMUSG00000022875	Kng1	Kng	kininogen 1	protein-coding
mm_22123.1	chr2	170195851	170195873	-	1	NA	Intergenic	Intergenic	-53187	NM_001159683	228913	Mm.22858	NM_001033299	ENSMUSG00000052056	Zfp217	4933431C08Rik|AW987152|Gm562|ZABC1|Znf217	zinc finger protein 217	protein-coding
mm_133105.1	chr16	65473454	65473458	+	1	NA	Intergenic	Intergenic	-47173	NM_008849	18736	Mm.355440	NM_008849	ENSMUSG00000004842	Pou1f1	GHF-1|Hmp1|Pit-1|Pit1|Pit1-rs1|dw|dwarf	POU domain, class 1, transcription factor 1	protein-coding
mm_70107.1	chr7	142664664	142664690	-	1	NA	intron (NR_002855, intron 1 of 3)	intron (NR_002855, intron 1 of 3)	2139	NM_001315488	16002	Mm.3862	NM_010514	ENSMUSG00000048583	Igf2	AL033362|Igf-2|Igf-II|M6pr|Mpr|Peg2	insulin-like growth factor 2	protein-coding
mm_149846.1	chr19	25052511	25052519	+	1	NA	intron (NM_028785, intron 2 of 47)	intron (NM_028785, intron 2 of 47)	52986	NM_028785	76088	Mm.102485	NM_028785	ENSMUSG00000052085	Dock8	1200017A24Rik|5830472H07Rik|A130095G14Rik|AI461977	dedicator of cytokinesis 8	protein-coding
mm_79198.1	chr9	48495369	48495400	+	1	NA	promoter-TSS (NM_001004191)	promoter-TSS (NM_001004191)	41	NM_001004191	434402	Mm.386950	NM_001004191	ENSMUSG00000042293	Gm5617	EG434402	predicted gene 5617	protein-coding
mm_88878.1	chr10	81105934	81106004	+	1	NA	promoter-TSS (NM_001347144)	promoter-TSS (NM_001347144)	54	NM_001347144	26396	Mm.275436	NM_023138	ENSMUSG00000035027	Map2k2	AA589381|MEK2|MK2|Prkmk2	mitogen-activated protein kinase kinase 2	protein-coding
mm_122242.1	chr14	33382833	33382836	-	1	NA	intron (NM_001310452, intron 10 of 10)	intron (NM_001310452, intron 10 of 10)	28190	NM_001310452	26419	Mm.21495	NM_016700	ENSMUSG00000021936	Mapk8	AI849689|JNK|JNK1|Prkm8|SAPK1	mitogen-activated protein kinase 8	protein-coding
mm_53261.1	chr6	127913828	127913838	+	1	NA	intron (NM_026743, intron 2 of 7)	intron (NM_026743, intron 2 of 7)	26211	NM_026743	68498	Mm.174368	NM_026743	ENSMUSG00000030351	Tspan11	1110014F12Rik|AU067806	tetraspanin 11	protein-coding
mm_55793.1	chr6	82730840	82730851	-	1	NA	exon (NM_013820, exon 15 of 18)	exon (NM_013820, exon 15 of 18)	43609	NM_013820	15277	Mm.255848	NM_013820	ENSMUSG00000000628	Hk2	AI642394|HKII	hexokinase 2	protein-coding
mm_8865.1	chr1	162813874	162813883	-	1	NA	Intergenic	Intergenic	-1329	NM_144878	226564	Mm.155164	NM_144878	ENSMUSG00000026692	Fmo4	D1Ertd532e	flavin containing monooxygenase 4	protein-coding
mm_68643.1	chr7	118448173	118448227	-	1	NA	Intergenic	CpG	-4648	NM_138649	110058	Mm.156558	NM_138649	ENSMUSG00000058420	Syt17	Bk	synaptotagmin XVII	protein-coding
mm_125297.1	chr15	37071607	37071652	+	1	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	-64227	NM_026521	68036	Mm.371631	NM_026521	ENSMUSG00000062397	Zfp706	3110006P09Rik|AA793007|AW536850|C77232|Znf706	zinc finger protein 706	protein-coding
mm_78961.1	chr9	45245640	45245683	+	1	NA	intron (NM_001198971, intron 4 of 4)	intron (NM_001198971, intron 4 of 4)	21046	NR_106054	102466803		NR_106054	ENSMUSG00000098361	Mir7086	Gm27643|mmu-mir-7086	microRNA 7086	ncRNA
mm_146257.1	chr18	77794533	77794543	+	1	NA	promoter-TSS (NM_013831)	promoter-TSS (NM_013831)	-12	NM_013831	19201	Mm.57174	NM_013831	ENSMUSG00000025429	Pstpip2	MAYP|cmo	proline-serine-threonine phosphatase-interacting protein 2	protein-coding
mm_113074.1	chr13	23806987	23807012	+	1	NA	promoter-TSS (NM_144836)	promoter-TSS (NM_144836)	-28	NM_144836	218103	Mm.24030	NM_144836	ENSMUSG00000036110	Slc17a2	C730032N17Rik|NPT3	solute carrier family 17 (sodium phosphate), member 2	protein-coding
mm_57095.1	chr6	122588046	122588063	-	1	NA	intron (NM_001134391, intron 5 of 7)	B2_Mm2|SINE|B2	14390	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_23854.1	chr3	83010078	83010097	+	1	NA	exon (NM_133862, exon 5 of 10)	exon (NM_133862, exon 5 of 10)	2363	NM_001317105	99571	Mm.16422	NM_133862	ENSMUSG00000033860	Fgg	3010002H13Rik|AI256424	fibrinogen gamma chain	protein-coding
mm_30481.1	chr3	155025063	155025080	-	1	NA	intron (NM_177066, intron 5 of 24)	intron (NM_177066, intron 5 of 24)	30336	NM_177066	435766	Mm.210428	NM_177066	ENSMUSG00000040086	Tnni3k	Cark|D830019J24Rik	TNNI3 interacting kinase	protein-coding
mm_170341.1	chr18	48046687	48046688	+	1	NA	intron (NM_001025388, intron 1 of 1)	CpG	1352	NM_001025388	433182	Mm.70666	NM_001025388	ENSMUSG00000059040	Eno1b	EG433182|Eno1|Gm5506	enolase 1B, retrotransposed	protein-coding
mm_15085.1	chr2	153232542	153232572	+	1	NA	exon (NM_018807, exon 3 of 3)	exon (NM_018807, exon 3 of 3)	-7116	NM_198617	241732	Mm.277243	NM_198617	ENSMUSG00000074671	Tspyl3	AW212607|Gm36	TSPY-like 3	protein-coding
mm_71074.1	chr8	34155453	34155456	+	1	NA	intron (NM_026432, intron 1 of 5)	intron (NM_026432, intron 1 of 5)	891	NM_026432	67887	Mm.290353	NM_026432	ENSMUSG00000031532	Saraf	1810045K07Rik|Tmem66	store-operated calcium entry-associated regulatory factor	protein-coding
mm_117048.1	chr13	58385163	58385169	-	1	NA	promoter-TSS (NM_027335)	promoter-TSS (NM_027335)	59	NM_027335	70153	Mm.296610	NM_027335	ENSMUSG00000021550	2210016F16Rik	-	RIKEN cDNA 2210016F16 gene	protein-coding
mm_136951.1	chr17	14943190	14943201	+	1	NA	promoter-TSS (NM_001083881)	promoter-TSS (NM_001083881)	11	NM_026451	67912	Mm.390949	NM_026451	ENSMUSG00000050088	1600012H06Rik	-	RIKEN cDNA 1600012H06 gene	protein-coding
mm_113934.1	chr13	49653068	49653097	+	1	NA	promoter-TSS (NM_001271397)	promoter-TSS (NM_001271397)	4	NR_073167	70930	Mm.258915	NM_001081350	ENSMUSG00000021392	Nol8	4921532D18Rik|5730412B09Rik	nucleolar protein 8	protein-coding
mm_26734.1	chr3	5576173	5576183	-	1	NA	promoter-TSS (NM_008994)	promoter-TSS (NM_008994)	70	NM_001163301	19302	Mm.132336	NM_008994	ENSMUSG00000040374	Pex2	D3Ertd138e|PAF-1|PMP35|Pxmp3	peroxisomal biogenesis factor 2	protein-coding
mm_111247.1	chr12	84876437	84876445	-	1	NA	promoter-TSS (NM_013589)	promoter-TSS (NM_013589)	54	NM_013589	16997	Mm.3900	NM_013589	ENSMUSG00000002020	Ltbp2	AW208642	latent transforming growth factor beta binding protein 2	protein-coding
mm_116676.1	chr13	49240642	49240674	-	1	NA	exon (NM_028340, exon 2 of 5)	exon (NM_028340, exon 2 of 5)	7505	NM_025491	66329	Mm.34308	NM_025491	ENSMUSG00000021384	Susd3	1700017I11Rik|2810440J20Rik	sushi domain containing 3	protein-coding
mm_156474.1	chrX	143664366	143664399	+	1	NA	intron (NM_008778, intron 1 of 14)	intron (NM_008778, intron 1 of 14)	-1363	NM_001195049	18481	Mm.40035	NM_008778	ENSMUSG00000031284	Pak3	PAK-3|Pak65alpha|Pak65beta|Stk4	p21 protein (Cdc42/Rac)-activated kinase 3	protein-coding
mm_135029.1	chr16	32797414	32797461	-	1	NA	promoter-TSS (NM_146071)	promoter-TSS (NM_146071)	-2	NM_001145874	224116	Mm.153301	NM_146071	ENSMUSG00000035638	Muc20	BC026367	mucin 20	protein-coding
mm_132594.1	chr16	38457426	38457471	+	1	NA	Intergenic	Intergenic	-1485	NM_009855	12519	Mm.89474	NM_009855	ENSMUSG00000075122	Cd80	B71|Cd28l|Ly-53|Ly53|MIC17|TSA1	CD80 antigen	protein-coding
mm_40200.1	chr5	36936528	36936528	+	1	NA	intron (NM_172994, intron 5 of 8)	intron (NM_172994, intron 5 of 8)	52454	NM_011716	22393	Mm.20916	NM_011716	ENSMUSG00000039474	Wfs1	AI481085|wolframin	Wolfram syndrome 1 homolog (human)	protein-coding
mm_38768.1	chr4	147904809	147904864	-	1	NA	promoter-TSS (NM_001285923)	promoter-TSS (NM_001285923)	73	NM_001285922	170731	Mm.154312	NM_133201	ENSMUSG00000029020	Mfn2	D630023P19Rik|Fzo	mitofusin 2	protein-coding
mm_14612.1	chr2	136713445	136713492	+	1	NA	promoter-TSS (NM_001291056)	promoter-TSS (NM_001291056)	18	NM_001291056	20614	Mm.45953	NM_011428	ENSMUSG00000027273	Snap25	Bdr|GENA70|SNAP-25|SUP|sp	synaptosomal-associated protein 25	protein-coding
mm_72140.1	chr8	72008531	72008563	+	1	NA	intron (NM_024444, intron 2 of 12)	intron (NM_024444, intron 2 of 12)	1079	NM_024444	72054	Mm.160020	NM_024444	ENSMUSG00000003484	Cyp4f18	1810054N16Rik|Cyp4f3|Cypf18	cytochrome P450, family 4, subfamily f, polypeptide 18	protein-coding
mm_166711.1	chr6	117675162	117675188	-	1	NA	Intergenic	ORR1D2|LTR|ERVL-MaLR	76594	NR_045731	72263	Mm.443289	NR_045731	ENSMUSG00000099869	1700030F04Rik	-	RIKEN cDNA 1700030F04 gene	ncRNA
mm_79508.1	chr9	57483909	57483917	+	1	NA	Intergenic	Intergenic	-15853	NM_001301635	56807	Mm.102278	NM_020270	ENSMUSG00000040722	Scamp5	Sc5	secretory carrier membrane protein 5	protein-coding
mm_135512.1	chr16	48613839	48613865	-	1	NA	intron (NM_010816, intron 21 of 26)	intron (NM_010816, intron 21 of 26)	158104	NM_198297	77647	Mm.167298	NM_198297	ENSMUSG00000030775	Trat1	C030046M14Rik|Tcrim|Trim	T cell receptor associated transmembrane adaptor 1	protein-coding
mm_151238.1	chr19	53807535	53807543	+	1	NA	intron (NM_001170847, intron 1 of 13)	MLT1D|LTR|ERVL-MaLR	-84692	NM_011050	18569	Mm.1605	NM_011050	ENSMUSG00000024975	Pdcd4	D19Ucla1|Ma3|Tis	programmed cell death 4	protein-coding
mm_108552.1	chr12	84417236	84417254	+	1	NA	promoter-TSS (NM_025525)	promoter-TSS (NM_025525)	45	NM_025525	66381	Mm.24846	NM_025525	ENSMUSG00000098134	Rnf113a2	2310020H19Rik|AI426758|Rnf113a	ring finger protein 113A2	protein-coding
mm_69594.1	chr7	135716293	135716303	-	1	NA	promoter-TSS (NM_001081117)	promoter-TSS (NM_001081117)	81	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_62644.1	chr7	107665820	107665870	+	1	NA	intron (NM_001163557, intron 3 of 25)	intron (NM_001163557, intron 3 of 25)	59001	NM_001163557	19024	Mm.2817	NM_008905	ENSMUSG00000036528	Ppfibp2	Cclp1	PTPRF interacting protein, binding protein 2 (liprin beta 2)	protein-coding
mm_48520.1	chr5	142903254	142903287	-	1	NA	3' UTR (NM_007393, exon 6 of 6)	3' UTR (NM_007393, exon 6 of 6)	3484	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_112579.1	chr13	13698703	13698714	+	1	NA	intron (NM_010748, intron 31 of 52)	intron (NM_010748, intron 31 of 52)	-85351	NM_001302997	14706	Mm.215394	NM_010317	ENSMUSG00000021303	Gng4	-	guanine nucleotide binding protein (G protein), gamma 4	protein-coding
mm_17456.1	chr2	28556321	28556370	-	1	NA	exon (NM_009885, exon 11 of 11)	exon (NM_009885, exon 11 of 11)	7058	NM_009885	12613	Mm.236017	NM_009885	ENSMUSG00000026818	Cel	1810036E18Rik|BAL	carboxyl ester lipase	protein-coding
mm_89677.1	chr10	97517517	97517528	+	1	NA	exon (NM_007833, exon 8 of 8)	exon (NM_007833, exon 8 of 8)	35191	NM_007833	13179	Mm.56769	NM_007833	ENSMUSG00000019929	Dcn	DC|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding
mm_103406.1	chr11	75439588	75439592	-	1	NA	promoter-TSS (NM_008878)	promoter-TSS (NM_008878)	-89	NM_008878	18816	Mm.279733	NM_008878	ENSMUSG00000038224	Serpinf2	AI747498|Pli|Serpimf2	serine (or cysteine) peptidase inhibitor, clade F, member 2	protein-coding
mm_86000.1	chr9	112231170	112231184	-	1	NA	intron (NM_001177619, intron 1 of 10)	intron (NM_001177619, intron 1 of 10)	1324	NM_001177616	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_2865.1	chr1	131713097	131713111	+	1	NA	3' UTR (NM_145509, exon 6 of 6)	3' UTR (NM_145509, exon 6 of 6)	24409	NM_001311096	226421	Mm.44508	NM_145509	ENSMUSG00000052688	Rab7b	5430435G22Rik	RAB7B, member RAS oncogene family	protein-coding
mm_103091.1	chr11	69920850	69920875	-	1	NA	promoter-TSS (NM_001166592)	promoter-TSS (NM_001166592)	85	NM_001166594	276770	Mm.18026	NM_181582	ENSMUSG00000078812	Eif5a	AA410058|D19Wsu54e|Eif4d|Eif5a1|eIF-4D|eIF-5A|eIF-5A-1|eIF-5A1	eukaryotic translation initiation factor 5A	protein-coding
mm_144119.1	chr18	4590732	4590759	+	1	NA	Intergenic	Intergenic	-44184	NM_001081963	240185	Mm.33179	NM_001081963	ENSMUSG00000033960	9430020K01Rik	1110056P05Rik|Gm328|Jcad|mKIAA1462	RIKEN cDNA 9430020K01 gene	protein-coding
mm_91726.1	chr10	44866795	44866799	-	1	NA	Intergenic	Intergenic	-200417	NM_011156	19072	Mm.10281	NM_011156	ENSMUSG00000019849	Prep	AI047692|AI450383|D10Wsu136e|PEP|Pop	prolyl endopeptidase	protein-coding
mm_5758.1	chr1	46888134	46888140	-	1	NA	Intergenic	Intergenic	-34628	NM_172653	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|mKIAA1265	solute carrier family 39 (zinc transporter), member 10	protein-coding
mm_126661.1	chr15	84257162	84257172	+	1	NA	intron (NM_133167, intron 1 of 12)	intron (NM_133167, intron 1 of 12)	25124	NM_133167	170736	Mm.323892	NM_133167	ENSMUSG00000022438	Parvb	AI595373|AW742462|D15Gsk1|affixin	parvin, beta	protein-coding
mm_93040.1	chr10	88356991	88357122	-	1	NA	promoter-TSS (NM_027878)	promoter-TSS (NM_027878)	19	NM_027878	71712	Mm.35450	NM_027878	ENSMUSG00000020057	Dram1	1200002N14Rik|Dram	DNA-damage regulated autophagy modulator 1	protein-coding
mm_66116.1	chr7	31042338	31042353	-	1	NA	promoter-TSS (NM_001111073)	promoter-TSS (NM_001111073)	-14	NM_001287217	18301	Mm.1870	NM_008761	ENSMUSG00000009687	Fxyd5	EF-8|Oit2|RIC	FXYD domain-containing ion transport regulator 5	protein-coding
mm_157172.1	chrX	9469481	9469504	-	1	NA	promoter-TSS (NM_007807)	promoter-TSS (NM_007807)	-168	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_138840.1	chr17	40222310	40222336	+	1	NA	3' UTR (NM_009639, exon 8 of 8)	3' UTR (NM_009639, exon 8 of 8)	-13714	NM_031190	18663	Mm.717	NM_031190	ENSMUSG00000031233	Pgk2	Pgk-2|Tcp-2	phosphoglycerate kinase 2	protein-coding
mm_112027.1	chr12	111485774	111485804	-	1	NA	promoter-TSS (NM_001033248)	promoter-TSS (NM_001033248)	34	NM_001033248	212539	Mm.81916	NM_001033248	ENSMUSG00000010529	Gm266	-	predicted gene 266	protein-coding
mm_143974.1	chr17	87427774	87427778	-	1	NA	promoter-TSS (NM_029298)	promoter-TSS (NM_029298)	-35	NM_029298	75467	Mm.50108	NM_029298	ENSMUSG00000036557	Stpg4	1700011E24Rik|GSE	sperm tail PG rich repeat containing 4	protein-coding
mm_140164.1	chr17	80232745	80232748	+	1	NA	Intergenic	Intergenic	8257	NM_026053	67242	Mm.279985	NM_026053	ENSMUSG00000055760	Gemin6	2610019B15Rik|2810470M17Rik	gem (nuclear organelle) associated protein 6	protein-coding
mm_144386.1	chr18	20667617	20667627	+	1	NA	intron (NM_013697, intron 2 of 3)	B4A|SINE|B4	2372	NM_013697	22139	Mm.2108	NM_013697	ENSMUSG00000061808	Ttr	AA408768|AI787086|D17860|prealbumin	transthyretin	protein-coding
mm_127640.1	chr15	102473790	102473800	+	1	NA	intron (NM_001103165, intron 2 of 14)	L1_Mus3|LINE|L1	3163	NM_001174073	18521	Mm.236513	NM_011042	ENSMUSG00000056851	Pcbp2	AW412548|Hnrpx|alphaCP-2	poly(rC) binding protein 2	protein-coding
mm_29129.1	chr3	105687377	105687409	-	1	NA	exon (NM_017397, exon 1 of 11)	exon (NM_017397, exon 1 of 11)	178	NM_017397	53975	Mm.272826	NM_017397	ENSMUSG00000027905	Ddx20	GEMIN3|dp103	DEAD (Asp-Glu-Ala-Asp) box polypeptide 20	protein-coding
mm_117265.1	chr13	64370346	64370362	-	1	NA	5' UTR (NM_009984, exon 1 of 8)	5' UTR (NM_009984, exon 1 of 8)	166	NM_009984	13039	Mm.930	NM_009984	ENSMUSG00000021477	Ctsl	1190035F06Rik|CatL|Ctsl1|MEP|fs|nkt	cathepsin L	protein-coding
mm_33102.1	chr4	124703649	124703665	+	1	NA	intron (NM_010213, intron 1 of 5)	intron (NM_010213, intron 1 of 5)	2958	NM_010213	14201	Mm.331856	NM_010213	ENSMUSG00000032643	Fhl3	SLIM2	four and a half LIM domains 3	protein-coding
mm_79840.1	chr9	64810968	64810984	+	1	NA	promoter-TSS (NM_001162917)	promoter-TSS (NM_001162917)	-35	NM_001162917	102442	Mm.222473	NM_176935	ENSMUSG00000053641	Dennd4a	AI115600|AI851943|F730015K02Rik	DENN/MADD domain containing 4A	protein-coding
mm_71744.1	chr8	64947178	64947255	+	1	NA	promoter-TSS (NM_001163747)	promoter-TSS (NM_001163747)	31	NM_028427	73067	Mm.294445	NM_028427	ENSMUSG00000025521	Tmem192	3110005G23Rik	transmembrane protein 192	protein-coding
mm_159403.1	chr3	98510491	98510491	-	1	NA	promoter-TSS (NM_001111336).2	promoter-TSS (NM_001111336).2	-19	NM_001111336	15495	Mm.14309	NM_008294	ENSMUSG00000095143	Hsd3b4	-	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 4	protein-coding
mm_142508.1	chr17	46153498	46153511	-	1	NA	promoter-TSS (NM_025649)	promoter-TSS (NM_025649)	47	NM_025649	66591	Mm.272024	NM_025649	ENSMUSG00000034509	Mad2l1bp	0610009D16Rik|2510031P20Rik|AU018945|AW550977|C76045|CMT2A|CMT2B|Mad2lbp|mKIAA0110	MAD2L1 binding protein	protein-coding
mm_29959.1	chr3	133234940	133234961	-	1	NA	promoter-TSS (NM_029953)	promoter-TSS (NM_029953)	-61	NM_029953	77669	Mm.98630	NM_029953	ENSMUSG00000040969	Arhgef38	9130221D24Rik|D630013G24Rik	Rho guanine nucleotide exchange factor (GEF) 38	protein-coding
mm_151506.1	chr19	58732032	58732052	+	1	NA	exon (NM_018874, exon 5 of 13)	exon (NM_018874, exon 5 of 13)	3155	NM_018874	18946	Mm.10753	NM_018874	ENSMUSG00000042179	Pnliprp1	Plrp1	pancreatic lipase related protein 1	protein-coding
mm_117995.1	chr13	100490117	100490134	-	1	NA	exon (NM_022011, exon 2 of 16)	exon (NM_022011, exon 2 of 16)	2484	NM_022011	23894	Mm.272533	NM_022011	ENSMUSG00000021639	Gtf2h2	44kDa|BTF2 p44|BTF2-p44|Btf2p44|p44	general transcription factor II H, polypeptide 2	protein-coding
mm_56164.1	chr6	87992614	87992619	-	1	NA	Intergenic	Intergenic	10933	NR_026990	434064	Mm.371796	NR_026990	ENSMUSG00000084950	Gm5577	EG434064	predicted gene 5577	ncRNA
mm_140437.1	chr17	88441525	88441558	+	1	NA	intron (NM_180974, intron 1 of 5)	CpG	829	NM_180974	14236	Mm.112824	NM_180974	ENSMUSG00000034998	Foxn2	3230402J05Rik|6030465J18Rik|Fkh19|Foxn1|HTLF	forkhead box N2	protein-coding
mm_63270.1	chr7	126760648	126760653	+	1	NA	intron (NM_011952, intron 1 of 8)	intron (NM_011952, intron 1 of 8)	1024	NM_011952	26417	Mm.8385	NM_011952	ENSMUSG00000063065	Mapk3	Erk-1|Erk1|Ert2|Esrk1|Mnk1|Mtap2k|Prkm3|p44|p44erk1|p44mapk	mitogen-activated protein kinase 3	protein-coding
mm_44216.1	chr5	4757909	4757920	-	1	NA	5' UTR (NM_021457, exon 1 of 1)	5' UTR (NM_021457, exon 1 of 1)	302	NM_021457	14362	Mm.246003	NM_021457	ENSMUSG00000044674	Fzd1	AW227548|FZ-1|Fz1	frizzled class receptor 1	protein-coding
mm_122662.1	chr14	51913349	51913391	-	1	NA	5' UTR (NM_001145959, exon 1 of 15)	5' UTR (NM_001145959, exon 1 of 15)	118	NM_001145959	29811	Mm.26722	NM_013864	ENSMUSG00000004558	Ndrg2	AI182517|AU040374|Ndr2|SYLD	N-myc downstream regulated gene 2	protein-coding
mm_149842.1	chr19	25033130	25033136	+	1	NA	intron (NM_028785, intron 1 of 47)	intron (NM_028785, intron 1 of 47)	33604	NM_028785	76088	Mm.102485	NM_028785	ENSMUSG00000052085	Dock8	1200017A24Rik|5830472H07Rik|A130095G14Rik|AI461977	dedicator of cytokinesis 8	protein-coding
mm_145645.1	chr18	61122019	61122026	+	1	NA	intron (NM_001037859, intron 11 of 21)	B3|SINE|B2	4554	NR_105949	102466212		NR_105949	ENSMUSG00000098389	Mir6983	Gm27496|mmu-mir-6983	microRNA 6983	ncRNA
mm_147442.1	chr18	46525773	46525783	-	1	NA	5' UTR (NM_173423, exon 1 of 3)	5' UTR (NM_173423, exon 1 of 3)	193	NM_173423	240263	Mm.38249	NM_173423	ENSMUSG00000033319	Fem1c	2610312A07Rik|3632443A22Rik|AI646567	fem-1 homolog c (C.elegans)	protein-coding
mm_133584.1	chr16	91416050	91416065	+	1	NA	intron (NM_008349, intron 4 of 6)	intron (NM_008349, intron 4 of 6)	9822	NM_008349	16155	Mm.4154	NM_008349	ENSMUSG00000022969	Il10rb	6620401D04Rik|AI528744|CRF2-4|Crfb4|D16H21S58|D21S58h|IL-10R2|Il10r2	interleukin 10 receptor, beta	protein-coding
mm_10779.1	chr2	24336715	24336722	+	1	NA	promoter-TSS (NM_031167)	promoter-TSS (NM_031167)	-142	NM_031167	16181	Mm.882	NM_031167	ENSMUSG00000026981	Il1rn	F630041P17Rik|IL-1ra	interleukin 1 receptor antagonist	protein-coding
mm_48966.1	chr6	4601125	4601164	+	1	NA	promoter-TSS (NM_145398)	promoter-TSS (NM_145398)	78	NM_145398	213819	Mm.270703	NM_145398	ENSMUSG00000015189	Casd1	Cas1|Cast1	CAS1 domain containing 1	protein-coding
mm_14784.1	chr2	145860142	145860156	+	1	NA	exon (NM_028724, exon 9 of 13)	exon (NM_028724, exon 9 of 13)	-43092	NM_026425	67877	Mm.151168	NM_026425	ENSMUSG00000002728	Naa20	1500004D14Rik|2900026I01Rik|AU041458|D2Ertd186e|Nat5	N(alpha)-acetyltransferase 20, NatB catalytic subunit	protein-coding
mm_19170.1	chr2	84342794	84342804	-	1	NA	intron (NM_018782, intron 13 of 15)	Arthur1|DNA|hAT-Tip100	82467	NM_018782	54598	Mm.75467	NM_018782	ENSMUSG00000059588	Calcrl	AV071593|CRLR	calcitonin receptor-like	protein-coding
mm_151521.1	chr19	58740442	58740485	+	1	NA	exon (NM_018874, exon 11 of 13)	exon (NM_018874, exon 11 of 13)	11576	NM_018874	18946	Mm.10753	NM_018874	ENSMUSG00000042179	Pnliprp1	Plrp1	pancreatic lipase related protein 1	protein-coding
mm_162889.1	chr10	109309453	109309455	-	1	NA	Intergenic	L3|LINE|CR1	-298479	NM_001252341	20979	Mm.289702	NM_009306	ENSMUSG00000035864	Syt1	AW124717|G630098F17Rik|SytI	synaptotagmin I	protein-coding
mm_103847.1	chr11	83078159	83078182	-	1	NA	Intergenic	Intergenic	13058	NM_011408	20556	Mm.278689	NM_011408	ENSMUSG00000072620	Slfn2	Shlf2	schlafen 2	protein-coding
mm_147441.1	chr18	46525752	46525764	-	1	NA	5' UTR (NM_173423, exon 1 of 3)	5' UTR (NM_173423, exon 1 of 3)	213	NM_173423	240263	Mm.38249	NM_173423	ENSMUSG00000033319	Fem1c	2610312A07Rik|3632443A22Rik|AI646567	fem-1 homolog c (C.elegans)	protein-coding
mm_116735.1	chr13	51739773	51739781	-	1	NA	intron (NM_001281880, intron 2 of 16)	intron (NM_001281880, intron 2 of 16)	53970	NM_001281880	20354	Mm.33903	NM_013660	ENSMUSG00000021451	Sema4d	CD100|Semacl2|Semaj|Semcl2|coll-4	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D	protein-coding
mm_34513.1	chr4	148895908	148895924	+	1	NA	intron (NM_027195, intron 3 of 15)	intron (NM_027195, intron 3 of 15)	91524	NM_027195	69743	Mm.233879	NM_027195	ENSMUSG00000028977	Casz1	2410019P08Rik|AV096627|BC040081|Cst|D4Ertd432e	castor zinc finger 1	protein-coding
mm_141554.1	chr17	32205990	32205994	-	1	NA	TTS (NM_198094)	TTS (NM_198094)	-16443	NM_001347341	71932	Mm.176240	NM_001033163	ENSMUSG00000037577	Ephx3	2310063B19Rik|Abhd9	epoxide hydrolase 3	protein-coding
mm_32460.1	chr4	107381127	107381130	+	1	NA	intron (NM_028355, intron 6 of 17)	intron (NM_028355, intron 6 of 17)	13344	NM_028355	72787	Mm.28478	NM_028355	ENSMUSG00000028614	Ndc1	2810475A17Rik|AI450313|Tmem48|sks	NDC1 transmembrane nucleoporin	protein-coding
mm_110255.1	chr12	31634570	31634581	-	1	NA	promoter-TSS (NM_001164090)	promoter-TSS (NM_001164090)	22	NM_007530	12033	Mm.242379	NM_007530	ENSMUSG00000020650	Bcap29	AW208404|Bap29	B cell receptor associated protein 29	protein-coding
mm_155139.1	chrX	50841435	50841449	+	1	NA	promoter-TSS (NM_133729)	promoter-TSS (NM_133729)	71	NM_001313744	70415	Mm.46254	NM_133729	ENSMUSG00000031112	Stk26	2610018G03Rik|Mst4	serine/threonine kinase 26	protein-coding
mm_82175.1	chr9	123851285	123851314	+	1	NA	intron (NM_148925, intron 1 of 18)	intron (NM_148925, intron 1 of 18)	362	NM_148925	17281	Mm.252941	NM_148925	ENSMUSG00000025241	Fyco1	2810409M01Rik|Mem2|RUFY3|ZFYVE7	FYVE and coiled-coil domain containing 1	protein-coding
mm_146370.1	chr18	82584648	82584661	+	1	NA	3' UTR (NM_010777, exon 7 of 7)	3' UTR (NM_010777, exon 7 of 7)	30146	NM_001025254	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_110960.1	chr12	76795490	76795521	-	1	NA	promoter-TSS (NM_030677)	promoter-TSS (NM_030677)	49	NM_030677	14776	Mm.441856	NM_030677	ENSMUSG00000042808	Gpx2	GI-GPx|GPx-GI|GSHPx-2|GSHPx-GI	glutathione peroxidase 2	protein-coding
mm_123506.1	chr14	66235544	66235557	-	1	NA	intron (NM_001162365, intron 1 of 30)	intron (NM_001162365, intron 1 of 30)	-21998	NM_001162366	19229	Mm.21613	NM_172498	ENSMUSG00000059456	Ptk2b	CADTK|CAKB|CAKbeta|E430023O05Rik|FADK2|FAK2|PYK2|Raftk	PTK2 protein tyrosine kinase 2 beta	protein-coding
mm_95083.1	chr11	33163334	33163343	+	1	NA	promoter-TSS (NM_001252261)	promoter-TSS (NM_001252261)	-132	NM_008722	18148	Mm.485384	NM_008722	ENSMUSG00000057113	Npm1	B23|NO38|Npm	nucleophosmin 1	protein-coding
mm_87558.1	chr10	56083856	56083864	+	1	NA	intron (NM_001033385, intron 25 of 32)	L1MA9|LINE|L1	-23057	NM_001163833	73390	Mm.181475	NM_133751	ENSMUSG00000047669	Msl3l2	1700060H10Rik	male-specific lethal 3-like 2 (Drosophila)	protein-coding
mm_61904.1	chr7	90130357	90130367	+	1	NA	promoter-TSS (NR_046007)	promoter-TSS (NR_046007)	130	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_133377.1	chr16	84710557	84710570	+	1	NA	Intergenic	Intergenic	-2460	NR_132106	100653389	Mm.261808	NR_132106	ENSMUSG00000097418	Mir155hg	Bic|Gm26667	Mir155 host gene (non-protein coding)	ncRNA
mm_3669.1	chr1	153653107	153653176	+	1	NA	5' UTR (NM_026380, exon 1 of 7)	5' UTR (NM_026380, exon 1 of 7)	104	NM_026380	67792	Mm.379143	NM_026380	ENSMUSG00000042671	Rgs8	6530413N01Rik	regulator of G-protein signaling 8	protein-coding
mm_126134.1	chr15	78341628	78341647	+	1	NA	exon (NM_007780, exon 8 of 14)	exon (NM_007780, exon 8 of 14)	-6962	NR_106137	102465776		NR_106137	ENSMUSG00000098996	Mir7676-1	Gm27600|mmu-mir-7676-1	microRNA 7676-1	ncRNA
mm_33923.1	chr4	136622632	136622652	+	1	NA	promoter-TSS (NM_001243262)	promoter-TSS (NM_001243262)	21	NM_001243262	242707	Mm.448979	NM_001243262	ENSMUSG00000070683	Lactbl1	-	lactamase, beta-like 1	protein-coding
mm_165416.1	chr2	147531781	147531782	+	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	166787	NM_008780	18503	Mm.315502	NM_008780	ENSMUSG00000037034	Pax1	Pax-1|hbs|hunchback|un|undulated|wt	paired box 1	protein-coding
mm_113099.1	chr13	24376071	24376109	+	1	NA	intron (NM_001284519, intron 2 of 17)	intron (NM_001284519, intron 2 of 17)	-39032	NM_007717	12763	Mm.8396	NM_007717	ENSMUSG00000016756	Cmah	-	cytidine monophospho-N-acetylneuraminic acid hydroxylase	protein-coding
mm_52346.1	chr6	110940870	110940873	+	1	NA	intron (NM_001346640, intron 2 of 10)	intron (NM_001346640, intron 2 of 10)	295273	NM_177328	108073	Mm.240881	NM_177328	ENSMUSG00000056755	Grm7	6330570A01Rik|BB176677|C030018L03|E130018M02Rik|Gpr1g|Gprc1g|SMN2|Tg(SMN2)89Ahmb|mGluR7	glutamate receptor, metabotropic 7	protein-coding
mm_51057.1	chr6	65653082	65653109	+	1	NA	Intergenic	Intergenic	-18516	NM_172399	68169	Mm.52392	NM_172399	ENSMUSG00000049001	Ndnf	A930038C07Rik|epidermacan	neuron-derived neurotrophic factor	protein-coding
mm_43190.1	chr5	128736126	128736132	+	1	NA	promoter-TSS (NM_021311)	promoter-TSS (NM_021311)	-117	NM_021311	57749	Mm.272720	NM_021311	ENSMUSG00000029423	Piwil1	MIWI	piwi-like RNA-mediated gene silencing 1	protein-coding
mm_30313.1	chr3	151731347	151731369	-	1	NA	3' UTR (NM_133871, exon 8 of 8)	3' UTR (NM_133871, exon 8 of 8)	18601	NM_133871	99899	Mm.30756	NM_133871	ENSMUSG00000028037	Ifi44	A430056A10Rik|AW261460|MTAP44|p44	interferon-induced protein 44	protein-coding
mm_101721.1	chr11	42182390	42182437	-	1	NA	5' UTR (NM_010250, exon 1 of 10)	5' UTR (NM_010250, exon 1 of 10)	517	NM_010250	14394	Mm.439668	NM_010250	ENSMUSG00000010803	Gabra1	Gabra-1	gamma-aminobutyric acid (GABA) A receptor, subunit alpha 1	protein-coding
mm_45724.1	chr5	86065532	86065574	-	1	NA	promoter-TSS (NM_001345902)	promoter-TSS (NM_001345902)	30	NM_001345902	12617	Mm.4649	NM_007683	ENSMUSG00000029253	Cenpc1	CENP-C|Cenpc	centromere protein C1	protein-coding
mm_38802.1	chr4	148159572	148159602	-	1	NA	promoter-TSS (NM_001161851)	promoter-TSS (NM_001161851)	2	NM_001161851	230903	Mm.220327	NM_173401	ENSMUSG00000029001	Fbxo44	5730411K09|AV001623|FBG3|FBX30|Fbx6a|Fbxo6a	F-box protein 44	protein-coding
mm_15702.1	chr2	163995139	163995149	+	1	NA	promoter-TSS (NM_018753)	promoter-TSS (NM_018753)	-53	NM_018753	54401	Mm.34319	NM_018753	ENSMUSG00000018326	Ywhab	1300003C17Rik|14-3-3b	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta polypeptide	protein-coding
mm_161193.1	chr13	54055629	54055629	-	1	NA	promoter-TSS (NM_001291801)	promoter-TSS (NM_001291801)	29	NM_010076	13488	Mm.54161	NM_010076	ENSMUSG00000021478	Drd1	C030036C15Rik|Drd-1|Drd1a|Gpcr15	dopamine receptor D1	protein-coding
mm_115841.1	chr13	21287291	21287293	-	1	NA	3' UTR (NM_010343, exon 5 of 5)	3' UTR (NM_010343, exon 5 of 5)	5394	NM_010343	14780	Mm.1332	NM_010343	ENSMUSG00000004344	Gpx5	AV379049|Arep	glutathione peroxidase 5	protein-coding
mm_141721.1	chr17	34032046	34032061	-	1	NA	promoter-TSS (NM_001205216)	promoter-TSS (NM_001205216)	241	NM_001205214	20182	Mm.1243	NM_011306	ENSMUSG00000039656	Rxrb	AL023085|H-2RIIBP|Nr2b2|RCoR-1|Rub	retinoid X receptor beta	protein-coding
mm_28782.1	chr3	95993654	95993678	-	1	NA	intron (NM_023320, intron 2 of 5)	intron (NM_023320, intron 2 of 5)	2173	NM_023320	67220	Mm.458147	NM_023320	ENSMUSG00000015745	Plekho1	2810052M02Rik|CKIP-1|Ckip1|JZA-20|Jza2	pleckstrin homology domain containing, family O member 1	protein-coding
mm_31751.1	chr4	63345087	63345100	+	1	NA	exon (NM_008768, exon 2 of 6)	exon (NM_008768, exon 2 of 6)	537	NM_008768	18405	Mm.4777	NM_008768	ENSMUSG00000039196	Orm1	Agp-1|Agp-2|Orm-1	orosomucoid 1	protein-coding
mm_58300.1	chr6	145865565	145865572	-	1	NA	promoter-TSS (NM_001271768)	promoter-TSS (NM_001271768)	-148	NM_024469	79362	Mm.154529	NM_024469	ENSMUSG00000030256	Bhlhe41	6430520M22Rik|Bhlhb2l|Bhlhb3|DEC2|Sharp1	basic helix-loop-helix family, member e41	protein-coding
mm_111061.1	chr12	80113003	80113019	-	1	NA	promoter-TSS (NM_007564)	promoter-TSS (NM_007564)	2	NM_007564	12192	Mm.235132	NM_007564	ENSMUSG00000021127	Zfp36l1	AW742437|AW743212|Berg36|Brf1|D530020L18Rik|ERF1|TIS11b|cMG1	zinc finger protein 36, C3H type-like 1	protein-coding
mm_126387.1	chr15	80173694	80173704	+	1	NA	promoter-TSS (NM_010795)	promoter-TSS (NM_010795)	-22	NM_010795	17309	Mm.299693	NM_010795	ENSMUSG00000042428	Mgat3	1110038J12Rik|AI848272|GnT-III	mannoside acetylglucosaminyltransferase 3	protein-coding
mm_120585.1	chr14	69780620	69780630	+	1	NA	intron (NM_020275, intron 7 of 7)	intron (NM_020275, intron 7 of 7)	13153	NM_020275	21933	Mm.193430	NM_020275	ENSMUSG00000022074	Tnfrsf10b	DR5|KILLER|Ly98|MK|TRAILR2|TRICK2A|TRICK2B|TRICKB	tumor necrosis factor receptor superfamily, member 10b	protein-coding
mm_76852.1	chr8	105347942	105347975	-	1	NA	promoter-TSS (NM_001081332)	promoter-TSS (NM_001081332)	12	NM_177699	234686	Mm.87724	NM_177699	ENSMUSG00000014778	Fhod1	BC017144|FHOS|FHOS1	formin homology 2 domain containing 1	protein-coding
mm_164218.1	chr15	84923373	84923379	+	1	NA	promoter-TSS (NM_016714)	promoter-TSS (NM_016714)	-52	NM_016714	18141	Mm.28379	NM_016714	ENSMUSG00000016619	Nup50	1700030K07Rik|AI413123|Npap60	nucleoporin 50	protein-coding
mm_102675.1	chr11	65243637	65243651	-	1	NA	intron (NM_146386, intron 1 of 12)	intron (NM_146386, intron 1 of 12)	26345	NM_145136	214384	Mm.32257	NM_145136	ENSMUSG00000020542	Myocd	BSAC2A|Srfcp	myocardin	protein-coding
mm_112827.1	chr13	20813929	20813934	+	1	NA	intron (NM_012054, intron 1 of 20)	intron (NM_012054, intron 1 of 20)	19818	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_13811.1	chr2	119167783	119167835	+	1	NA	promoter-TSS (NM_177157)	promoter-TSS (NM_177157)	21	NM_177157	320415	Mm.86373	NM_177157	ENSMUSG00000046814	Gchfr	2010323F13Rik|GFRP|P35	GTP cyclohydrolase I feedback regulator	protein-coding
mm_170010.1	chr17	17121361	17121380	+	1	NA	promoter-TSS (NM_011765)	promoter-TSS (NM_011765)	-13	NM_011765	22759	Mm.436633	NM_011765	ENSMUSG00000095990	Zfp97	NGD16-4	zinc finger protein 97	protein-coding
mm_32510.1	chr4	108579419	108579427	+	1	NA	promoter-TSS (NM_172697)	promoter-TSS (NM_172697)	-31	NM_011015	18392	Mm.294154	NM_011015	ENSMUSG00000028587	Orc1	AA545195|MmORC1|Orc1l	origin recognition complex, subunit 1	protein-coding
mm_146007.1	chr18	69344542	69344559	+	1	NA	promoter-TSS (NM_013685)	promoter-TSS (NM_013685)	58	NM_013685	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding
mm_109086.1	chr12	104413873	104413879	+	1	NA	3' UTR (NM_009252, exon 5 of 5)	3' UTR (NM_009252, exon 5 of 5)	7168	NM_009252	20716	Mm.482074	NM_009252	ENSMUSG00000021091	Serpina3n	Spi2-2|Spi2.2|Spi2/eb.4	serine (or cysteine) peptidase inhibitor, clade A, member 3N	protein-coding
mm_87886.1	chr10	61726182	61726188	+	1	NA	intron (NM_001284300, intron 2 of 9)	intron (NM_001284300, intron 2 of 9)	5536	NM_153779	71361	Mm.286309	NM_153779	ENSMUSG00000020085	Aifm2	5430437E11Rik|Amid|D730001I10Rik|PRG3	apoptosis-inducing factor, mitochondrion-associated 2	protein-coding
mm_151866.1	chr19	5797719	5797727	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	-1742	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_99220.1	chr11	101033381	101033399	+	1	NA	intron (NM_001243050, intron 9 of 20)	intron (NM_001243050, intron 9 of 20)	3050	NR_105893	102466767		NR_105893	ENSMUSG00000098415	Mir6928	Gm27728|mmu-mir-6928	microRNA 6928	ncRNA
mm_84901.1	chr9	79860339	79860365	-	1	NA	intron (NM_001081243, intron 2 of 5)	intron (NM_001081243, intron 2 of 5)	66711	NR_040734	74633	Mm.262175	NR_040734	ENSMUSG00000086918	4930429F24Rik	-	RIKEN cDNA 4930429F24 gene	ncRNA
mm_10099.1	chr2	3442474	3442510	+	1	NA	intron (NM_001302684, intron 9 of 14)	B3A|SINE|B2	18361	NM_001302684	227525	Mm.23483	NM_146114	ENSMUSG00000026648	Dclre1c	9930121L06Rik|AI661365|Art|Snm1l	DNA cross-link repair 1C	protein-coding
mm_23364.1	chr3	55247066	55247084	+	1	NA	intron (NM_019978, intron 1 of 16)	intron (NM_019978, intron 1 of 16)	4549	NM_001195538	13175	Mm.393242	NM_019978	ENSMUSG00000027797	Dclk1	1700113D08Rik|2810480F11Rik|AI836758|Click-I|Cpg16|Dcamkl1|Dcl|Dclk|mKIAA0369	doublecortin-like kinase 1	protein-coding
mm_31228.1	chr4	44167582	44167622	+	1	NA	promoter-TSS (NM_175201)	promoter-TSS (NM_175201)	-64	NM_175201	73469	Mm.262859	NM_175201	ENSMUSG00000035696	Rnf38	1700065B19Rik|2610202O07Rik|AA673263|Oip1	ring finger protein 38	protein-coding
mm_107513.1	chr12	40223326	40223350	+	1	NA	promoter-TSS (NM_013562)	promoter-TSS (NM_013562)	-26	NR_045157	629820	Mm.435540	NR_045157	ENSMUSG00000035983	Gm7008	EG629820	predicted gene 7008	ncRNA
mm_166830.1	chr7	18686185	18686190	-	1	NA	promoter-TSS (NM_054058)	promoter-TSS (NM_054058)	-195	NM_054058	434540	Mm.479863	NM_054058	ENSMUSG00000063305	Psg20	Cea7|EG434540	pregnancy-specific glycoprotein 20	protein-coding
mm_143571.1	chr17	74295431	74295450	-	1	NA	promoter-TSS (NM_133771)	promoter-TSS (NM_133771)	-577	NM_133771	76890	Mm.311874	NM_133771	ENSMUSG00000058704	Memo1	0610016J10Rik|D930048L02Rik	mediator of cell motility 1	protein-coding
mm_59689.1	chr7	28444781	28444850	+	1	NA	intron (NM_001039192, intron 4 of 6)	intron (NM_001039192, intron 4 of 6)	3878	NM_001039192	63986	Mm.194536	NM_022024	ENSMUSG00000060791	Gmfg	0610039G16Rik|2310057N07Rik|AI324845	glia maturation factor, gamma	protein-coding
mm_54975.1	chr6	48739188	48739204	-	1	NA	intron (NM_175860, intron 1 of 2)	intron (NM_175860, intron 1 of 2)	149	NM_008376	16205	Mm.252599	NM_008376	ENSMUSG00000090019	Gimap1	IAP38|Imap38|imap	GTPase, IMAP family member 1	protein-coding
mm_89977.1	chr10	111595893	111595905	+	1	NA	Intergenic	Intergenic	-1626	NR_045344	71321	Mm.410785	NR_045344	ENSMUSG00000097082	4933440J02Rik	-	RIKEN cDNA 4933440J02 gene	ncRNA
mm_159961.1	chr6	88905937	88905937	+	1	NA	intron (NM_011906, intron 1 of 11)	MLT1J|LTR|ERVL-MaLR	3686	NM_011906	24100	Mm.284480	NM_011906	ENSMUSG00000002871	Tpra1	40kDa|Gpr175|Tpra40	transmembrane protein, adipocyte asscociated 1	protein-coding
mm_22017.1	chr2	167861265	167861266	-	1	NA	Intergenic	Intergenic	-71062	NM_011201	19246	Mm.277916	NM_011201	ENSMUSG00000027540	Ptpn1	PTP-1B|PTP-HA2|PTP1B	protein tyrosine phosphatase, non-receptor type 1	protein-coding
mm_168950.1	chr1	27755089	27755090	+	1	NA	Intergenic	Intergenic	1025163	NM_001013750	210962	Mm.214178	NM_001013750	ENSMUSG00000048411	Gm597	-	predicted gene 597	protein-coding
mm_102097.1	chr11	52332558	52332568	-	1	NA	Intergenic	B1F|SINE|Alu	-28299	NM_011694	22333	Mm.3555	NM_011694	ENSMUSG00000020402	Vdac1	AL033343|Vdac5|mVDAC1|mVDAC5	voltage-dependent anion channel 1	protein-coding
mm_108468.1	chr12	83632574	83632600	+	1	NA	intron (NM_027349, intron 1 of 18)	CpG	353	NM_027349	67039	Mm.46005	NM_027349	ENSMUSG00000010608	Rbm25	2600011C06Rik|2610015J01Rik|A130095G20Rik|AI159652|AL023075|AU043498|RNPC7	RNA binding motif protein 25	protein-coding
mm_150432.1	chr19	37536637	37536657	+	1	NA	Intergenic	Intergenic	-13771	NM_175353	107371	Mm.24865	NM_175353	ENSMUSG00000053799	Exoc6	4833405E05Rik|AW413330|C430002C19|Sec15|Sec15l1|hbd|msec15	exocyst complex component 6	protein-coding
mm_29104.1	chr3	104818267	104818293	-	1	NA	promoter-TSS (NM_008619)	promoter-TSS (NM_008619)	25	NM_008619	17454	Mm.1597	NM_008619	ENSMUSG00000002227	Mov10	C77703|Mov-10	Moloney leukemia virus 10	protein-coding
mm_112386.1	chr12	119238184	119238212	-	1	NA	promoter-TSS (NM_177290)	promoter-TSS (NM_177290)	78	NM_177290	320910	Mm.217000	NM_177290	ENSMUSG00000025321	Itgb8	4832412O06Rik	integrin beta 8	protein-coding
mm_79300.1	chr9	51853530	51853540	+	1	NA	TTS (NM_175535)	TTS (NM_175535)	22350	NR_033560	408028	Mm.393649	NR_033560	ENSMUSG00000074354	Arhgap20os	9230115E21Rik	Rho GTPase activating protein 20, opposite strand	ncRNA
mm_166164.1	chr5	20051012	20051022	+	1	NA	intron (NM_015823, intron 1 of 21)	intron (NM_015823, intron 1 of 21)	143499	NM_015823	50791	Mm.332231	NM_015823	ENSMUSG00000040003	Magi2	AIP-1|Acvri1|Acvrinp1|Acvrip1|Magi-2|S-SCAM|mKIAA0705	membrane associated guanylate kinase, WW and PDZ domain containing 2	protein-coding
mm_44408.1	chr5	17849689	17849703	-	1	NA	promoter-TSS (NM_001159557)	promoter-TSS (NM_001159557)	96	NM_001159557	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_170878.1	chr2	20900058	20900058	+	1	NA	intron (NM_001128084, intron 3 of 24)	LSU-rRNA_Hsa|rRNA|rRNA	67663	NM_001081364	71435	Mm.28507	NM_001081364	ENSMUSG00000036591	Arhgap21	5530401C11Rik|AA416458|ARHGAP10	Rho GTPase activating protein 21	protein-coding
mm_99759.1	chr11	106755116	106755135	+	1	NA	intron (NM_001271375, intron 3 of 6)	intron (NM_001271375, intron 3 of 6)	3899	NM_001033435	380732	Mm.343952	NM_001033435	ENSMUSG00000040528	Milr1	Allergin-1|Gm885|Mca32	mast cell immunoglobulin like receptor 1	protein-coding
mm_81020.1	chr9	104355959	104356003	+	1	NA	Intergenic	Intergenic	-18259	NM_207668	56318	Mm.19941	NM_019807	ENSMUSG00000032561	Acpp	5'-NT|A030005E02Rik|FRAP|Lap|PAP|Ppal	acid phosphatase, prostate	protein-coding
mm_70218.1	chr7	144939824	144939839	-	1	NA	promoter-TSS (NM_007631)	promoter-TSS (NM_007631)	94	NM_007631	12443	Mm.273049	NM_007631	ENSMUSG00000070348	Ccnd1	AI327039|CycD1|Cyl-1|PRAD1|bcl-1|cD1	cyclin D1	protein-coding
mm_105668.1	chr11	107454639	107454655	-	1	NA	intron (NM_145823, intron 1 of 9)	PB1D9|SINE|Alu	16073	NM_145823	71795	Mm.397413	NM_145823	ENSMUSG00000040430	Pitpnc1	1110020B03Rik|5830436L09Rik|AI662802|AI851387|C330017I21Rik|Dnr411|RDGBB|RDGBB1|rdgB-beta	phosphatidylinositol transfer protein, cytoplasmic 1	protein-coding
mm_107687.1	chr12	55302745	55302784	+	1	NA	5' UTR (NM_021529, exon 2 of 14)	5' UTR (NM_021529, exon 2 of 14)	127	NM_025373	66132	Mm.383213	NM_025373	ENSMUSG00000021023	1110008L16Rik	Kiaa0391|Mrpp3|mKIAA0391	RIKEN cDNA 1110008L16 gene	protein-coding
mm_122500.1	chr14	46821933	46821975	-	1	NA	intron (NM_022023, intron 1 of 6)	CpG	288	NM_022023	63985	Mm.87312	NM_022023	ENSMUSG00000062014	Gmfb	3110001H22Rik|3110001O16Rik|AI851627|C79176|D14Ertd630e	glia maturation factor, beta	protein-coding
mm_146236.1	chr18	77186041	77186048	+	1	NA	5' UTR (NM_013666, exon 1 of 8)	5' UTR (NM_013666, exon 1 of 8)	197	NM_013666	225742	Mm.365178	NM_013666	ENSMUSG00000025425	St8sia5	ST8SiaV|Siat8e	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 5	protein-coding
mm_4023.1	chr1	165763753	165763784	+	1	NA	promoter-TSS (NM_011804)	promoter-TSS (NM_011804)	-12	NM_011804	433375	Mm.294885	NM_011804	ENSMUSG00000040713	Creg1	AA755314|Creg	cellular repressor of E1A-stimulated genes 1	protein-coding
mm_2400.1	chr1	93719654	93719657	+	1	NA	intron (NM_001310761, intron 2 of 4)	RMER15-int|LTR|ERVL	12271	NM_001310761	67026	Mm.272356	NM_025920	ENSMUSG00000026279	Thap4	2010320B01Rik	THAP domain containing 4	protein-coding
mm_27474.1	chr3	53452180	53452191	-	1	NA	3' UTR (NM_172501, exon 7 of 7)	3' UTR (NM_172501, exon 7 of 7)	11073	NM_172501	212114	Mm.85744	NM_172501	ENSMUSG00000042997	Nhlrc3	4833441N19|8030451K01Rik|mKIAA4083	NHL repeat containing 3	protein-coding
mm_21215.1	chr2	155729360	155729443	-	1	NA	promoter-TSS (NM_145537)	promoter-TSS (NM_145537)	74	NM_145537	108687	Mm.273706	NM_145537	ENSMUSG00000038312	Edem2	9530090G24Rik|AI327354	ER degradation enhancer, mannosidase alpha-like 2	protein-coding
mm_120371.1	chr14	64587324	64587336	+	1	NA	promoter-TSS (NR_040709)	promoter-TSS (NR_040709)	-785	NR_040709	268755	Mm.194050	NR_040709	ENSMUSG00000097545	Mir124a-1hg	A930011O12Rik|Rncr3|mir-124-1|mir-3078	Mir124-1 host gene (non-protein coding)	ncRNA
mm_92568.1	chr10	79874652	79874660	-	1	NA	promoter-TSS (NM_001170935)	promoter-TSS (NM_001170935)	-22	NR_033210	216152	Mm.29678	NM_181681	ENSMUSG00000035835	Plppr3	Lppr3|Prg2	phospholipid phosphatase related 3	protein-coding
mm_114000.1	chr13	52583510	52583558	+	1	NA	promoter-TSS (NM_001198977)	promoter-TSS (NM_001198977)	97	NM_001198977	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_164707.1	chr17	52602723	52602760	+	1	NA	promoter-TSS (NM_001031811)	promoter-TSS (NM_001031811)	32	NM_001031811	211468	Mm.399068	NM_001031811	ENSMUSG00000035580	Kcnh8	C130090D05Rik|ELK|ELK1|ELK3|Kv12.1	potassium voltage-gated channel, subfamily H (eag-related), member 8	protein-coding
mm_57952.1	chr6	135118241	135118252	-	1	NA	promoter-TSS (NM_001205396)	promoter-TSS (NM_001205396)	37	NM_053118	93746	Mm.49902	NM_053118	ENSMUSG00000030205	Gprc5d	-	G protein-coupled receptor, family C, group 5, member D	protein-coding
mm_155828.1	chrX	100730120	100730122	+	1	NA	promoter-TSS (NM_001305941)	promoter-TSS (NM_001305941)	-65	NM_001305941	71584	Mm.283495	NM_023608	ENSMUSG00000019359	Gdpd2	9130017L10Rik|Gde3|Obdpf	glycerophosphodiester phosphodiesterase domain containing 2	protein-coding
mm_40814.1	chr5	72047128	72047139	+	1	NA	intron (NM_008069, intron 5 of 8)	intron (NM_008069, intron 5 of 8)	121050	NM_178599	27784	Mm.44223	NM_178599	ENSMUSG00000029213	Commd8	C77770|D5Buc26e	COMM domain containing 8	protein-coding
mm_53528.1	chr6	136551162	136551179	+	1	NA	intron (NM_019426, intron 1 of 14)	intron (NM_019426, intron 1 of 14)	32319	NM_019426	54343	Mm.173271	NM_019426	ENSMUSG00000030213	Atf7ip	2610204M12Rik|AM|Mcaf1	activating transcription factor 7 interacting protein	protein-coding
mm_96647.1	chr11	69340752	69340756	+	1	NA	promoter-TSS (NR_027827)	promoter-TSS (NR_027827)	-15	NR_027827	80515	Mm.5324	NM_020591	ENSMUSG00000043419	Chd3os	2310043C11Rik|A030009H04Rik|AA589459|AB041807|MNCb-2875|RNF21	chromodomain helicase DNA binding protein 3, opposite strand	ncRNA
mm_109842.1	chr12	4569535	4569547	-	1	NA	Intergenic	Lx5c|LINE|L1	-23467	NM_001198969	20403	Mm.341204	NM_011365	ENSMUSG00000020640	Itsn2	AI327390|Ese2|Sh3d1B|Sh3p18|mKIAA1256	intersectin 2	protein-coding
mm_118935.1	chr14	27141853	27141872	+	1	NA	Intergenic	Intergenic	-2131	NM_001289686	71704	Mm.248606	NM_027871	ENSMUSG00000021895	Arhgef3	1200004I24Rik|9830169H03Rik|C76747|Xpln	Rho guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_103798.1	chr11	82890502	82890534	-	1	NA	non-coding (NR_102720, exon 1 of 9)	non-coding (NR_102720, exon 1 of 9)	106	NR_102719	19364	Mm.9286	NM_011235	ENSMUSG00000018841	Rad51d	R51H3|Rad51l3|TRAD|Trad-d5	RAD51 paralog D	protein-coding
mm_38650.1	chr4	143276097	143276106	-	1	NA	exon (NM_010329, exon 2 of 6)	exon (NM_010329, exon 2 of 6)	23463	NM_010329	14726	Mm.2976	NM_010329	ENSMUSG00000028583	Pdpn	Gp38|OTS-8|RANDAM-2|T1-alpha|T1a|T1alpha	podoplanin	protein-coding
mm_93768.1	chr10	120201500	120201554	-	1	NA	promoter-TSS (NM_028679)	promoter-TSS (NM_028679)	10	NM_028679	73914	Mm.146194	NM_028679	ENSMUSG00000020227	Irak3	4833428C18Rik|AI563835|IRAK-M	interleukin-1 receptor-associated kinase 3	protein-coding
mm_44138.1	chr5	150142635	150142645	+	1	NA	Intergenic	Intergenic	-117290	NM_172887	320365	Mm.216590	NM_172887	ENSMUSG00000056602	Fry	13CDNA73|9330186A19Rik|AF346502|AI462658|C87180|D930046M03|cg003|mKIAA4143	FRY microtubule binding protein	protein-coding
mm_151049.1	chr19	47025254	47025269	+	1	NA	TTS (NM_146100)	TTS (NM_146100)	-10072	NM_001164363	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_4947.1	chr1	191194029	191194072	+	1	NA	Intergenic	Intergenic	-10717	NM_007498	11910	Mm.2706	NM_007498	ENSMUSG00000026628	Atf3	LRG-21	activating transcription factor 3	protein-coding
mm_75405.1	chr8	46210394	46210404	-	1	NA	intron (NM_007450, intron 1 of 3)	intron (NM_007450, intron 1 of 3)	610	NM_007450	11739	Mm.16228	NM_007450	ENSMUSG00000031633	Slc25a4	AU019225|Ant1	solute carrier family 25 (mitochondrial carrier, adenine nucleotide translocator), member 4	protein-coding
mm_11706.1	chr2	36136934	36136945	+	1	NA	promoter-TSS (NM_026434)	promoter-TSS (NM_026434)	-235	NR_027515	67889	Mm.205937	NM_026434	ENSMUSG00000026889	Rbm18	2010004P11Rik|AU015530	RNA binding motif protein 18	protein-coding
mm_140829.1	chr17	23645048	23645055	-	1	NA	5' UTR (NM_001033339, exon 1 of 10)	5' UTR (NM_001033339, exon 1 of 10)	218	NM_001033339	240047	Mm.235343	NM_001033339	ENSMUSG00000023903	Mmp25	F730048C11Rik|Leukolysin|MMP20|MT6-MMP	matrix metallopeptidase 25	protein-coding
mm_47814.1	chr5	134184428	134184439	-	1	NA	intron (NM_053266, intron 1 of 15)	CpG	395	NM_053266	114674	Mm.218744	NM_053266	ENSMUSG00000015942	Gtf2ird2	1700012P16Rik	GTF2I repeat domain containing 2	protein-coding
mm_93604.1	chr10	117234045	117234051	-	1	NA	3' UTR (NM_029906, exon 4 of 4)	3' UTR (NM_029906, exon 4 of 4)	4633	NM_029906	77397	Mm.118350	NM_029906	ENSMUSG00000020177	9530003J23Rik	Lyzf1	RIKEN cDNA 9530003J23 gene	protein-coding
mm_105924.1	chr11	115062125	115062156	-	1	NA	promoter-TSS (NM_172050)	promoter-TSS (NM_172050)	-101	NM_172050	217306	Mm.222667	NM_172050	ENSMUSG00000048498	Cd300e	BC034097|CLM2|Cd300le|TREM5	CD300E molecule	protein-coding
mm_155312.1	chrX	61709492	61709517	+	1	NA	promoter-TSS (NM_001018087)	promoter-TSS (NM_001018087)	-112	NM_001018087	434784	Mm.23468	NM_001018087	ENSMUSG00000057615	Ldoc1	Gm366|Mar7|Mart7|Sirh7	leucine zipper, down-regulated in cancer 1	protein-coding
mm_81355.1	chr9	108650114	108650120	+	1	NA	promoter-TSS (NM_011790)	promoter-TSS (NM_011790)	-737	NM_011790	23807	Mm.290447	NM_011790	ENSMUSG00000064145	Arih2	AI843547|ARI2|TRIAD1|UIP48	ariadne RBR E3 ubiquitin protein ligase 2	protein-coding
mm_41216.1	chr5	88583470	88583484	+	1	NA	promoter-TSS (NM_027530)	promoter-TSS (NM_027530)	-36	NM_001289777	52822	Mm.270469	NM_027530	ENSMUSG00000029291	Rufy3	2810428M05Rik|6330416M07Rik|AW455998|AW538594|D5Bwg0860e|Ripx|Rpipx	RUN and FYVE domain containing 3	protein-coding
mm_82654.1	chr9	22051964	22051983	-	1	NA	promoter-TSS (NM_010487)	promoter-TSS (NM_010487)	50	NM_010487	15571	Mm.390167	NM_010487	ENSMUSG00000003410	Elavl3	2600009P04Rik|Huc|PLE21|mHuC	ELAV (embryonic lethal, abnormal vision, Drosophila)-like 3 (Hu antigen C)	protein-coding
mm_31485.1	chr4	52596271	52596276	+	1	NA	promoter-TSS (NM_026652)	promoter-TSS (NM_026652)	-1	NM_026652	68274	Mm.85045	NM_026652	ENSMUSG00000028314	Toporsl	4930547C10Rik	topoisomerase I binding, arginine/serine-rich like	protein-coding
mm_149124.1	chr19	8990269	8990313	+	1	NA	intron (NR_104460, intron 1 of 6)	intron (NR_104460, intron 1 of 6)	1007	NM_001286518	66395	Mm.203866	NM_009643	ENSMUSG00000069833	Ahnak	DY6	AHNAK nucleoprotein (desmoyokin)	protein-coding
mm_19959.1	chr2	117342950	117342966	-	1	NA	promoter-TSS (NM_011246)	promoter-TSS (NM_011246)	-81	NM_011246	19419	Mm.42150	NM_011246	ENSMUSG00000027347	Rasgrp1	Rasgrp	RAS guanyl releasing protein 1	protein-coding
mm_149446.1	chr19	11484385	11484391	+	1	NA	Intergenic	Intergenic	-7650	NM_001164202	666926	Mm.486382	NM_001164202	ENSMUSG00000058470	Gm8369	EG666926	predicted gene 8369	protein-coding
mm_83658.1	chr9	49529525	49529535	-	1	NA	intron (NM_001081445, intron 13 of 17)	intron (NM_001081445, intron 13 of 17)	11242	NR_029465	100036537	Mm.437541	NR_029465	ENSMUSG00000079564	Gm11149	ENSMUSG00000060603|ENSMUSG00000079564	predicted gene 11149	ncRNA
mm_166217.1	chr5	63164575	63164577	+	1	NA	Intergenic	Intergenic	350753	NM_001170705	100322896	Mm.479821	NM_001170705	ENSMUSG00000090326	Dthd1	Gm17384	death domain containing 1	protein-coding
mm_138110.1	chr17	34122680	34122721	+	1	NA	promoter-TSS (NM_001204973)	promoter-TSS (NM_001204973)	-93	NM_001204973	14312	Mm.3444	NM_010238	ENSMUSG00000024335	Brd2	AW228947|D17H6S113E|Frg-1|Fsrg-1|Fsrg1|Nat|Ring3|Rnf3|mKIAA4005	bromodomain containing 2	protein-coding
mm_130250.1	chr15	96641483	96641556	-	1	NA	5' UTR (NM_134086, exon 1 of 16)	5' UTR (NM_134086, exon 1 of 16)	443	NM_134086	105727	Mm.103568	NM_134086	ENSMUSG00000023169	Slc38a1	AA408026|AA409865|AL022800|AU015942|NAT2	solute carrier family 38, member 1	protein-coding
mm_57024.1	chr6	122282788	122282798	-	1	NA	promoter-TSS (NM_016970)	promoter-TSS (NM_016970)	40	NM_016970	50928	Mm.20434	NM_016970	ENSMUSG00000030114	Klrg1	2F1-Ag|MAFA|MAFA-L	killer cell lectin-like receptor subfamily G, member 1	protein-coding
mm_15644.1	chr2	163062358	163062372	+	1	NA	intron (NM_008652, intron 3 of 13)	intron (NM_008652, intron 3 of 13)	-5725	NR_105970	102465607		NR_105970	ENSMUSG00000099091	Mir7003	Gm27340|mmu-mir-7003	microRNA 7003	ncRNA
mm_69686.1	chr7	139989401	139989429	-	1	NA	exon (NM_001291066, exon 6 of 24)	exon (NM_001291066, exon 6 of 24)	-2541	NR_106029	102465643		NR_106029	ENSMUSG00000099092	Mir7062	Gm27339|mmu-mir-7062	microRNA 7062	ncRNA
mm_91289.1	chr10	24836166	24836181	-	1	NA	promoter-TSS (NM_134005)	promoter-TSS (NM_134005)	22	NM_134005	209558	Mm.338425	NM_134005	ENSMUSG00000019989	Enpp3	AI876438|CD203c	ectonucleotide pyrophosphatase/phosphodiesterase 3	protein-coding
mm_100677.1	chr11	3452263	3452352	-	1	NA	promoter-TSS (NR_045276)	promoter-TSS (NR_045276)	-130	NR_028317	71523	Mm.72795	NM_027820	ENSMUSG00000034587	8430429K09Rik	-	RIKEN cDNA 8430429K09 gene	ncRNA
mm_27822.1	chr3	79076591	79076599	-	1	NA	intron (NM_001310536, intron 19 of 23)	RSINE1|SINE|B4	68292	NM_001310536	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_103478.1	chr11	76494861	76494883	-	1	NA	promoter-TSS (NM_001346670)	promoter-TSS (NM_001346670)	-377	NM_001346670	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_96461.1	chr11	67586751	67586761	+	1	NA	5' UTR (NM_001109657, exon 1 of 14)	5' UTR (NM_001109657, exon 1 of 14)	256	NM_001109657	14457	Mm.40338	NM_008088	ENSMUSG00000033066	Gas7	AW124766|B230343A10Rik|Gas7-cb	growth arrest specific 7	protein-coding
mm_64266.1	chr7	141751395	141751405	+	1	NA	exon (NM_023566, exon 38 of 46)	exon (NM_023566, exon 38 of 46)	-37611	NM_010844	17833	Mm.334332	NM_010844	ENSMUSG00000037974	Muc5ac	2210005L13Rik|MGM	mucin 5, subtypes A and C, tracheobronchial/gastric	protein-coding
mm_7006.1	chr1	86487332	86487369	-	1	NA	Intergenic	CpG	-39386	NM_008972	19231	Mm.19187	NM_008972	ENSMUSG00000026238	Ptma	Thym	prothymosin alpha	protein-coding
mm_9229.1	chr1	171247097	171247121	-	1	NA	promoter-TSS (NM_153064)	promoter-TSS (NM_153064)	13	NM_153064	226646	Mm.21669	NM_153064	ENSMUSG00000013593	Ndufs2	CI-49kD	NADH dehydrogenase (ubiquinone) Fe-S protein 2	protein-coding
mm_126874.1	chr15	89384876	89384884	+	1	NA	Intergenic	Intergenic	-2011	NM_001160178	546648	Mm.478787	NM_001160178	ENSMUSG00000091680	Klhdc7b	EG546648|Gm306	kelch domain containing 7B	protein-coding
mm_39315.1	chr5	8065120	8065135	+	1	NA	intron (NM_001080974, intron 7 of 7)	B4|SINE|B4	8585	NM_001080974	109552	Mm.96211	NM_025618	ENSMUSG00000003161	Sri	2210417O06Rik|2900070H08Rik|Sor	sorcin	protein-coding
mm_99957.1	chr11	113619319	113619346	+	1	NA	promoter-TSS (NM_009217)	promoter-TSS (NM_009217)	-149	NM_009217	20606		NM_009217	ENSMUSG00000047904	Sstr2	SRIF-1|SS2R|SSTR-2|Smstr-2|Smstr2|sst2	somatostatin receptor 2	protein-coding
mm_8364.1	chr1	150466161	150466170	-	1	NA	promoter-TSS (NM_021400)	promoter-TSS (NM_021400)	0	NM_021400	96875	Mm.174256	NM_021400	ENSMUSG00000006014	Prg4	CACP|DOL54|JCAP|MSF|SZP|lubricin	proteoglycan 4 (megakaryocyte stimulating factor, articular superficial zone protein)	protein-coding
mm_171721.1	chr4	86856256	86856259	-	1	NA	exon (NM_009096, exon 3 of 5)	exon (NM_009096, exon 3 of 5)	1110	NM_009096	20104	Mm.379007	NM_009096	ENSMUSG00000028495	Rps6	S6R	ribosomal protein S6	protein-coding
mm_76349.1	chr8	84746222	84746250	-	1	NA	intron (NM_001297601, intron 2 of 8)	(TG)n|Simple_repeat|Simple_repeat	28133	NM_001081981	18032	Mm.9394	NM_010906	ENSMUSG00000001911	Nfix	CTF|NF-I/X|NF1-X|NFI-X	nuclear factor I/X	protein-coding
mm_40867.1	chr5	73946903	73946909	+	1	NA	Intergenic	(T)n|Simple_repeat|Simple_repeat	121505	NM_177561	69727	Mm.48795	NM_177561	ENSMUSG00000054814	Usp46	1190009E20Rik|2410018I08Rik|AI451644	ubiquitin specific peptidase 46	protein-coding
mm_52037.1	chr6	96253811	96253813	+	1	NA	intron (NM_182808, intron 2 of 4)	intron (NM_182808, intron 2 of 4)	-87607	NR_003643	78482	Mm.391486	NM_030107	ENSMUSG00000072878	1700123L14Rik	-	nucleoporin 50 pseudogene	pseudo
mm_164270.1	chr15	101284177	101284178	+	1	NA	promoter-TSS (NM_026566)	promoter-TSS (NM_026566)	-124	NM_026566	68118	Mm.482360	NM_026566	ENSMUSG00000037204	Atg101	9430023L20Rik|AA407441|AU022967	autophagy related 101	protein-coding
mm_56043.1	chr6	86733269	86733394	-	1	NA	promoter-TSS (NM_011818)	promoter-TSS (NM_011818)	47	NM_011818	23885	Mm.321452	NM_011818	ENSMUSG00000001157	Gmcl1	2810049L19Rik|Btbd13|DIP|Gcl|Gcl-1|glc-1|mglc-1	germ cell-less, spermatogenesis associated 1	protein-coding
mm_82757.1	chr9	26860902	26860912	-	1	NA	promoter-TSS (NM_001113323)	promoter-TSS (NM_001113323)	-84	NM_001113323	70893	Mm.78118	NM_001113323	ENSMUSG00000031966	Glb1l3	4921509F24Rik	galactosidase, beta 1 like 3	protein-coding
mm_110248.1	chr12	31499542	31499563	-	1	NA	promoter-TSS (NM_001253847)	promoter-TSS (NM_001253847)	64	NM_134048	104836	Mm.273270	NM_134048	ENSMUSG00000020659	Cbll1	AI467391|Hakai|c-Cbl-like	Casitas B-lineage lymphoma-like 1	protein-coding
mm_52689.1	chr6	118163067	118163079	+	1	NA	intron (NM_001080780, intron 18 of 18)	intron (NM_001080780, intron 18 of 18)	-23933	NM_030165	78752	Mm.300317	NM_030165	ENSMUSG00000042042	Csgalnact2	4632415D10Rik|Galnact2	chondroitin sulfate N-acetylgalactosaminyltransferase 2	protein-coding
mm_150164.1	chr19	32389203	32389257	+	1	NA	promoter-TSS (NM_144792)	promoter-TSS (NM_144792)	14	NR_033198	67188	Mm.391160	NR_033198	ENSMUSG00000097787	2700046G09Rik	-	RIKEN cDNA 2700046G09 gene	ncRNA
mm_148310.1	chr18	83753406	83753409	-	1	NA	Intergenic	L1MD|LINE|L1	333155	NM_001081300	110796	Mm.102136	NM_001081300	ENSMUSG00000046982	Tshz1	5730407I04Rik|D18Bwg1409e|Mtsh1|NY-CO-33|Sdccag33|Tsh1|mKIAA4206|teashirt1	teashirt zinc finger family member 1	protein-coding
mm_119019.1	chr14	30009037	30009057	+	1	NA	promoter-TSS (NM_001136240)	promoter-TSS (NM_001136240)	47	NM_001136240	218865	Mm.259916	NM_172264	ENSMUSG00000015970	Chdh	AU041472|D630034H06Rik	choline dehydrogenase	protein-coding
mm_13994.1	chr2	121901189	121901220	+	1	NA	exon (NM_199038, exon 3 of 8)	exon (NM_199038, exon 3 of 8)	33499	NM_001205371	319996	Mm.292109	NM_177054	ENSMUSG00000060227	Casc4	D130060C09Rik|VGFG2573	cancer susceptibility candidate 4	protein-coding
mm_130964.1	chr15	103315998	103316017	-	1	NA	exon (NM_013866, exon 5 of 8)	exon (NM_013866, exon 5 of 8)	-5569	NM_030720	80910	Mm.160369	NM_030720	ENSMUSG00000063234	Gpr84	EX33	G protein-coupled receptor 84	protein-coding
mm_63043.1	chr7	121392267	121392286	+	1	NA	promoter-TSS (NM_001081327)	promoter-TSS (NM_001081327)	-20	NM_001081327	195646	Mm.247449	NM_177575	ENSMUSG00000046321	Hs3st2	6430516N12Rik|A830061E14Rik|AW491345	heparan sulfate (glucosamine) 3-O-sulfotransferase 2	protein-coding
mm_84735.1	chr9	75099173	75099176	-	1	NA	intron (NM_010864, intron 1 of 40)	intron (NM_010864, intron 1 of 40)	27968	NM_010864	17918	Mm.3645	NM_010864	ENSMUSG00000034593	Myo5a	9630007J19Rik|AI413174|AI661011|Dbv|MVa|Myo5|MyoVA|Sev-1|d|d-120J|flail|flr	myosin VA	protein-coding
mm_139778.1	chr17	65782702	65782726	+	1	NA	promoter-TSS (NM_001114131)	promoter-TSS (NM_001114131)	-641	NM_001114131	70351	Mm.48686	NM_146081	ENSMUSG00000061950	Ppp4r1	3110001J10Rik|Pp4r1	protein phosphatase 4, regulatory subunit 1	protein-coding
mm_55831.1	chr6	83124845	83124899	-	1	NA	intron (NM_023547, intron 1 of 4)	intron (NM_023547, intron 1 of 4)	157	NM_023547	70020	Mm.27814	NM_023547	ENSMUSG00000030034	Ino80b	2510009I23Rik|HMG1YL4|Hmga1l4|Papa1|Znhit4	INO80 complex subunit B	protein-coding
mm_35506.1	chr4	41093466	41093477	-	1	NA	3' UTR (NM_016689, exon 6 of 6)	3' UTR (NM_016689, exon 6 of 6)	4712	NM_016689	11828	Mm.34043	NM_016689	ENSMUSG00000028435	Aqp3	AQP-2	aquaporin 3	protein-coding
mm_18426.1	chr2	60752957	60752974	-	1	NA	3' UTR (NM_001141932, exon 15 of 15)	3' UTR (NM_001141932, exon 15 of 15)	-30362	NM_001159564	16420	Mm.98193	NM_021359	ENSMUSG00000026971	Itgb6	2210409C20Rik|4831415H04Rik	integrin beta 6	protein-coding
mm_167560.1	chr9	37609086	37609120	+	1	NA	intron (NM_001324545, intron 2 of 4)	intron (NM_001324545, intron 2 of 4)	4617	NM_011449	20686	Mm.8637	NM_011449	ENSMUSG00000001948	Spa17	Sp17	sperm autoantigenic protein 17	protein-coding
mm_32857.1	chr4	118360049	118360057	+	1	NA	promoter-TSS (NM_026601)	promoter-TSS (NM_026601)	54	NR_003946	68180	Mm.193212	NM_026601	ENSMUSG00000006395	Hyi	2700033B16Rik|6430559E15Rik|HT036	hydroxypyruvate isomerase (putative)	protein-coding
mm_845.1	chr1	51987140	51987151	+	1	NA	promoter-TSS (NM_001308266)	promoter-TSS (NM_001308266)	-3	NM_001308266	20849	Mm.1550	NM_011487	ENSMUSG00000062939	Stat4	-	signal transducer and activator of transcription 4	protein-coding
mm_4862.1	chr1	187662334	187662371	+	1	NA	intron (NM_001243792, intron 1 of 7)	intron (NM_001243792, intron 1 of 7)	53346	NM_001243792	26381	Mm.89989	NM_011935	ENSMUSG00000026610	Esrrg	ERR3|Errg|NR3B3|mKIAA0832	estrogen-related receptor gamma	protein-coding
mm_99087.1	chr11	99533463	99533468	+	1	NA	Intergenic	RMER17C|LTR|ERVK	9693	NM_001039666	406221	Mm.422372	NM_001039666	ENSMUSG00000059169	Krt40	CK-40|K40	keratin 40	protein-coding
mm_51073.1	chr6	66896430	66896440	+	1	NA	promoter-TSS (NM_001177559)	promoter-TSS (NM_001177559)	38	NM_001177556	14701	Mm.234342	NM_025278	ENSMUSG00000036402	Gng12	2010305F15Rik|AA536815|AI115529|AI314170|AI842738	guanine nucleotide binding protein (G protein), gamma 12	protein-coding
mm_98819.1	chr11	97315840	97315870	+	1	NA	5' UTR (NM_025927, exon 1 of 8)	5' UTR (NM_025927, exon 1 of 8)	139	NM_025927	67036	Mm.5381	NM_025927	ENSMUSG00000018882	Mrpl45	2600005P05Rik|AU043542|R75241	mitochondrial ribosomal protein L45	protein-coding
mm_6933.1	chr1	85591081	85591104	-	1	NA	intron (NM_175397, intron 5 of 12)	URR1B|DNA|hAT-Charlie	7718	NM_030194	109032	Mm.335802	NM_030194	ENSMUSG00000070034	Sp110	5031415C07Rik|52kDa|5830484A20Rik|ENSMUSG00000075603|Ifi75|Ipr1	Sp110 nuclear body protein	protein-coding
mm_77393.1	chr8	120228302	120228351	-	1	NA	promoter-TSS (NR_110496)	promoter-TSS (NR_110496)	-96	NR_110496	434353	Mm.411793	NR_110496	ENSMUSG00000097960	A330074K22Rik	-	RIKEN cDNA A330074K22 gene	ncRNA
mm_145558.1	chr18	60812182	60812261	+	1	NA	TTS (NR_039567)	TTS (NR_039567)	145	NR_039567	100628611		NR_039567	ENSMUSG00000093327	Mir5107	mir-5107|mmu-mir-5107|mu-mir-5107	microRNA 5107	ncRNA
mm_80447.1	chr9	77976843	77976854	+	1	NA	exon (NM_134255, exon 5 of 8)	exon (NM_134255, exon 5 of 8)	59483	NM_134255	68801	Mm.430736	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	ELOVL family member 5, elongation of long chain fatty acids (yeast)	protein-coding
mm_72531.1	chr8	83989555	83989575	+	1	NA	intron (NM_001277898, intron 5 of 9)	intron (NM_001277898, intron 5 of 9)	-8107	NM_001081415	666704	Mm.298091	NM_001081415	ENSMUSG00000079003	Samd1	AA589507	sterile alpha motif domain containing 1	protein-coding
mm_126963.1	chr15	92486671	92486702	+	1	NA	intron (NM_001164593, intron 3 of 9)	intron (NM_001164593, intron 3 of 9)	89876	NM_001164593	239618	Mm.309826	NM_001164593	ENSMUSG00000036218	Pdzrn4	1110017D07Rik|LNX4|SAMCAP3L|mKIAA3027	PDZ domain containing RING finger 4	protein-coding
mm_27677.1	chr3	65929356	65929377	-	1	NA	Intergenic	Intergenic	28859	NM_019937	56706	Mm.175612	NM_019937	ENSMUSG00000027829	Ccnl1	2610030E23Rik|AU018493|Ccnl|ania-6a	cyclin L1	protein-coding
mm_169630.1	chr15	44281867	44281877	+	1	NA	Intergenic	Intergenic	85737	NM_013696	22045	Mm.309350	NM_013696	ENSMUSG00000038760	Trhr	TRH-R1	thyrotropin releasing hormone receptor	protein-coding
mm_131590.1	chr16	18776840	18776856	+	1	NA	promoter-TSS (NM_013805)	promoter-TSS (NM_013805)	1	NM_013805	12741	Mm.22768	NM_013805	ENSMUSG00000041378	Cldn5	AI854493|MBEC1|Tmvcf	claudin 5	protein-coding
mm_22746.1	chr3	19957216	19957224	+	1	NA	5' UTR (NM_007752, exon 1 of 19)	5' UTR (NM_007752, exon 1 of 19)	166	NM_007752	12870	Mm.13787	NM_007752	ENSMUSG00000003617	Cp	D3Ertd555e	ceruloplasmin	protein-coding
mm_162797.1	chr10	76726199	76726245	-	1	NA	promoter-TSS (NM_009933)	promoter-TSS (NM_009933)	-178	NM_009933	12833	Mm.2509	NM_009933	ENSMUSG00000001119	Col6a1	AI747156|Col6a-1	collagen, type VI, alpha 1	protein-coding
mm_72565.1	chr8	84126025	84126045	+	1	NA	promoter-TSS (NM_001013384)	promoter-TSS (NM_001013384)	46	NM_001013384	244550	Mm.334654	NM_001013384	ENSMUSG00000012889	Podnl1	5832418A03Rik|Gm506	podocan-like 1	protein-coding
mm_98720.1	chr11	96323254	96323255	+	1	NA	5' UTR (NM_001079869, exon 1 of 4)	5' UTR (NM_001079869, exon 1 of 4)	128	NM_001079869	15410	Mm.342481	NM_010458	ENSMUSG00000048763	Hoxb3	Hox-2.7	homeobox B3	protein-coding
mm_116184.1	chr13	30974119	30974127	-	1	NA	promoter-TSS (NM_025588)	promoter-TSS (NM_025588)	-76	NM_025588	66482	Mm.293510	NM_025588	ENSMUSG00000021357	Exoc2	2410030I24Rik|AI648199|Sec5|Sec5l1	exocyst complex component 2	protein-coding
mm_110332.1	chr12	35534612	35534626	-	1	NA	exon (NM_013464, exon 1 of 11)	exon (NM_013464, exon 1 of 11)	370	NM_013464	11622	Mm.341377	NM_013464	ENSMUSG00000019256	Ahr	Ah|Ahh|Ahre|In|bHLHe76	aryl-hydrocarbon receptor	protein-coding
mm_130205.1	chr15	95528125	95528192	-	1	NA	promoter-TSS (NM_001289653)	promoter-TSS (NM_001289653)	94	NM_001289653	54003	Mm.3959	NM_016743	ENSMUSG00000022454	Nell2	A330108N19Rik|R75516|mel91	NEL-like 2	protein-coding
mm_159262.1	chr2	155440611	155440611	-	1	NA	intron (NM_001242558, intron 1 of 12)	B3|SINE|B2	172	NM_001242558	56406	Mm.27592	NM_019825	ENSMUSG00000038369	Ncoa6	AIB3|ASC-2|ASC2|NRC|Ncoa7|PRIP|RAP250|mKIAA0181	nuclear receptor coactivator 6	protein-coding
mm_11443.1	chr2	32047375	32047401	+	1	NA	intron (NM_172268, intron 32 of 35)	intron (NM_172268, intron 32 of 35)	-3558	NR_106135	102466844		NR_106135	ENSMUSG00000099075	Mir7674	Gm27563|mmu-mir-7674	microRNA 7674	ncRNA
mm_7553.1	chr1	124605733	124605763	-	1	NA	Intergenic	B4A|SINE|B4	-560189	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_163637.1	chr13	59770526	59770531	+	1	NA	promoter-TSS (NM_026921)	promoter-TSS (NM_026921)	562	NR_015349	13996	Mm.490435	NR_015349	ENSMUSG00000089875	Etohd2	AW491659	ethanol decreased 2	ncRNA
mm_54788.1	chr6	41558359	41558371	-	1	NA	Intergenic	Intergenic	36589	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_80774.1	chr9	95561560	95561562	+	1	NA	3' UTR (NM_198414, exon 1 of 1)	3' UTR (NM_198414, exon 1 of 1)	1744	NM_198414	75552	Mm.151485	NM_198414	ENSMUSG00000064225	Paqr9	1700020G04Rik	progestin and adipoQ receptor family member IX	protein-coding
mm_53956.1	chr6	5398327	5398365	-	1	NA	exon (NM_023048, exon 3 of 6)	exon (NM_023048, exon 3 of 6)	14960	NM_023048	65255	Mm.51340	NM_023048	ENSMUSG00000042607	Asb4	8430401O13Rik|AV117194|AW060255	ankyrin repeat and SOCS box-containing 4	protein-coding
mm_158275.1	chrX	111463104	111463139	-	1	NA	intron (NM_025949, intron 2 of 24)	CpG-15872	74838	NM_025949	67071	Mm.37617	NM_025949	ENSMUSG00000025665	Rps6ka6	2610524K04Rik|RSK4|S6K-alpha-6	ribosomal protein S6 kinase polypeptide 6	protein-coding
mm_58742.1	chr7	13037997	13038047	+	1	NA	promoter-TSS (NM_145578)	promoter-TSS (NM_145578)	-44	NM_145578	22192	Mm.196580	NM_145578	ENSMUSG00000005575	Ube2m	2510040H03Rik|UBC12|Ubc-rs2	ubiquitin-conjugating enzyme E2M	protein-coding
mm_127142.1	chr15	98398414	98398424	+	1	NA	promoter-TSS (NR_015496)	promoter-TSS (NR_015496)	-26	NR_015496	73302	Mm.272760	NR_015496	ENSMUSG00000099353	1700031M16Rik	4930413L20Rik	RIKEN cDNA 1700031M16 gene	ncRNA
mm_88652.1	chr10	79994846	79994858	+	1	NA	3' UTR (NM_007725, exon 7 of 7)	3' UTR (NM_007725, exon 7 of 7)	-2756	NM_001347081	27403	Mm.103351	NM_013850	ENSMUSG00000035722	Abca7	ABCX|Abc51	ATP-binding cassette, sub-family A (ABC1), member 7	protein-coding
mm_97739.1	chr11	80444902	80444905	+	1	NA	intron (NM_178616, intron 3 of 13)	B1_Mur2|SINE|Alu	16288	NM_178616	69077	Mm.260539	NM_178616	ENSMUSG00000017428	Psmd11	1700089D09Rik|1810019E17Rik|2610024G20Rik|2810055C24Rik|C78232|P44.5|S9	proteasome (prosome, macropain) 26S subunit, non-ATPase, 11	protein-coding
mm_128319.1	chr15	37985010	37985013	-	1	NA	intron (NM_001112721, intron 47 of 58)	intron (NM_001112721, intron 47 of 58)	-23956	NM_199476	382985	Mm.24738	NM_199476	ENSMUSG00000022292	Rrm2b	p53R2	ribonucleotide reductase M2 B (TP53 inducible)	protein-coding
mm_69384.1	chr7	131329471	131329486	-	1	NA	promoter-TSS (NM_027037)	promoter-TSS (NM_027037)	21	NM_027037	69318	Mm.233840	NM_027037	ENSMUSG00000030858	1700007K09Rik	-	RIKEN cDNA 1700007K09 gene	protein-coding
mm_37864.1	chr4	132329476	132329542	-	1	NA	promoter-TSS (NM_027925)	promoter-TSS (NM_027925)	29	NM_027925	71787	Mm.239183	NM_027925	ENSMUSG00000028898	Trnau1ap	1110007F05Rik|AA387999|Secp43|Trspap1|WI1-2643G14.2	tRNA selenocysteine 1 associated protein 1	protein-coding
mm_31462.1	chr4	49059440	49059465	+	1	NA	promoter-TSS (NM_178756)	promoter-TSS (NM_178756)	-10	NM_178756	272031	Mm.299460	NM_178756	ENSMUSG00000063446	Plppr1	E130309F12Rik|Lppr1|PRG-3|mKIAA4247	phospholipid phosphatase related 1	protein-coding
mm_21211.1	chr2	155668444	155668447	-	1	NA	exon (NM_001163452, exon 4 of 19)	exon (NM_001163452, exon 4 of 19)	23939	NM_019828	56407	Mm.234944	NM_019828	ENSMUSG00000038324	Trpc4ap	4833429F06Rik|D2Ertd113e|Trrp4ap|mFLJ00177|truss	transient receptor potential cation channel, subfamily C, member 4 associated protein	protein-coding
mm_63955.1	chr7	139907399	139907403	+	1	NA	intron (NM_177261, intron 3 of 30)	intron (NM_177261, intron 3 of 30)	12705	NM_177261	76484	Mm.44442	NM_177261	ENSMUSG00000066129	Kndc1	2410012C07Rik|B830014K08Rik|VKIND|very-kind	kinase non-catalytic C-lobe domain (KIND) containing 1	protein-coding
mm_93633.1	chr10	117282244	117282257	-	1	NA	promoter-TSS (NM_017372)	promoter-TSS (NM_017372)	22	NM_017372	17105	Mm.45436	NM_017372	ENSMUSG00000069516	Lyz2	AI326280|Lys|Lysm|Lyzf2|Lyzs|Lzm|Lzm-s1|Lzp	lysozyme 2	protein-coding
mm_121234.1	chr14	103055888	103055909	+	1	NA	3' UTR (NM_008392, exon 5 of 5)	3' UTR (NM_008392, exon 5 of 5)	8886	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_110116.1	chr12	26443873	26443883	-	1	NA	3' UTR (NM_021384, exon 6 of 6)	3' UTR (NM_021384, exon 6 of 6)	12574	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_16045.1	chr2	167721732	167721756	+	1	NA	Intergenic	Intergenic	30567	NR_015500	329562	Mm.123101	NM_177851	ENSMUSG00000006462	A530013C23Rik	-	RIKEN cDNA A530013C23 gene	ncRNA
mm_67089.1	chr7	68353197	68353221	-	1	NA	intron (NM_001013811, intron 6 of 8)	intron (NM_001013811, intron 6 of 8)	-64215	NR_046208	71244	Mm.410787	NR_046208	ENSMUSG00000108924	4933436H12Rik	-	RIKEN cDNA 4933436H12 gene	ncRNA
mm_60586.1	chr7	44482757	44482773	+	1	NA	Intergenic	Intergenic	-1752	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_114744.1	chr13	83832239	83832243	+	1	NA	Intergenic	Intergenic	-58967	NR_036594	72677	Mm.245636	NR_036594	ENSMUSG00000100891	2810049E08Rik	-	RIKEN cDNA 2810049E08 gene	ncRNA
mm_123964.1	chr14	74947796	74947804	-	1	NA	promoter-TSS (NM_001033439)	promoter-TSS (NM_001033439)	77	NM_001252132	380916	Mm.288868	NM_001033439	ENSMUSG00000068015	Lrch1	4832412D13Rik|AI552548|AW215503|Chdc1|mKIAA1016	leucine-rich repeats and calponin homology (CH) domain containing 1	protein-coding
mm_92653.1	chr10	80399533	80399547	-	1	NA	promoter-TSS (NM_013595)	promoter-TSS (NM_013595)	-9	NM_001306143	17192	Mm.7142	NM_013595	ENSMUSG00000035478	Mbd3	AI181826|AU019209	methyl-CpG binding domain protein 3	protein-coding
mm_62250.1	chr7	99267471	99267517	+	1	NA	promoter-TSS (NM_001043355)	promoter-TSS (NM_001043355)	47	NM_001048167	17760	Mm.154087	NM_010837	ENSMUSG00000055407	Map6	2810411E12Rik|Map-6|Mtap6|STOP	microtubule-associated protein 6	protein-coding
mm_52597.1	chr6	117170000	117170005	+	1	NA	intron (NM_013655, intron 1 of 3)	intron (NM_013655, intron 1 of 3)	1467	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_67667.1	chr7	86775969	86775978	-	1	NA	promoter-TSS (NM_001159706)	promoter-TSS (NM_001159706)	-109	NM_001159706	53320	Mm.269137	NM_016770	ENSMUSG00000001773	Folh1	GCP2|mopsm	folate hydrolase 1	protein-coding
mm_6435.1	chr1	73986795	73986802	-	1	NA	intron (NM_027884, intron 12 of 34)	intron (NM_027884, intron 12 of 34)	-122332	NR_045311	109198	Mm.359721	NR_045311	ENSMUSG00000100301	6030407O03Rik	-	RIKEN cDNA 6030407O03 gene	ncRNA
mm_129919.1	chr15	84217177	84217196	-	1	NA	Intergenic	Charlie1a|DNA|hAT-Charlie	-14857	NM_133167	170736	Mm.323892	NM_133167	ENSMUSG00000022438	Parvb	AI595373|AW742462|D15Gsk1|affixin	parvin, beta	protein-coding
mm_45736.1	chr5	86469056	86469062	-	1	NA	promoter-TSS (NM_001033233)	promoter-TSS (NM_001033233)	-69	NM_001033233	194597	Mm.249106	NM_001033233	ENSMUSG00000072845	Tmprss11a	Gm7	transmembrane protease, serine 11a	protein-coding
mm_97852.1	chr11	83069578	83069594	+	1	NA	exon (NM_011408, exon 2 of 2)	exon (NM_011408, exon 2 of 2)	4474	NM_011408	20556	Mm.278689	NM_011408	ENSMUSG00000072620	Slfn2	Shlf2	schlafen 2	protein-coding
mm_56809.1	chr6	116665952	116665963	-	1	NA	intron (NM_178045, intron 1 of 10)	L1_Mur2|LINE|L1	7879	NM_178045	213391	Mm.257931	NM_178045	ENSMUSG00000042129	Rassf4	3830411C14Rik|AD037|AI586137	Ras association (RalGDS/AF-6) domain family member 4	protein-coding
mm_6226.1	chr1	66935342	66935358	-	1	NA	promoter-TSS (NM_001113387)	promoter-TSS (NM_001113387)	16	NM_001113387	17901	Mm.1000	NM_021285	ENSMUSG00000061816	Myl1	AI325107|MLC1f|MLC3f|Mylf	myosin, light polypeptide 1	protein-coding
mm_113423.1	chr13	34046803	34046812	+	1	NA	exon (NM_026512, exon 3 of 7)	exon (NM_026512, exon 3 of 7)	9166	NM_026512	68021	Mm.140243	NM_026512	ENSMUSG00000038286	Bphl	2010012D11Rik|5730533B08Rik|AI115341	biphenyl hydrolase-like (serine hydrolase, breast epithelial mucin-associated antigen)	protein-coding
mm_158567.1	chrX	150459129	150459157	-	1	NA	promoter-TSS (NM_001164683)	promoter-TSS (NM_001164683)	7	NM_001164683	382245	Mm.277309	NM_001164683	ENSMUSG00000041353	Tmem29	2700081K05Rik|6330540D07Rik|CXorf44-like	transmembrane protein 29	protein-coding
mm_160578.1	chr9	58823304	58823304	+	1	NA	promoter-TSS (NM_001081192)	promoter-TSS (NM_001081192)	-208	NM_001081192	330953	Mm.151967	NM_001081192	ENSMUSG00000032338	Hcn4	Bcng3|Hcn3	hyperpolarization-activated, cyclic nucleotide-gated K+ 4	protein-coding
mm_64860.1	chr7	13037822	13037832	-	1	NA	promoter-TSS (NM_001243968)	promoter-TSS (NM_001243968)	151	NM_145578	22192	Mm.196580	NM_145578	ENSMUSG00000005575	Ube2m	2510040H03Rik|UBC12|Ubc-rs2	ubiquitin-conjugating enzyme E2M	protein-coding
mm_109657.1	chr12	113014386	113014470	+	1	NA	promoter-TSS (NM_001291445)	promoter-TSS (NM_001291445)	-80	NM_001291445	217893	Mm.35754	NM_198165	ENSMUSG00000021143	Pacs2	6720425G15Rik|AW208651|AW489976|E230011J22|Pacs1l|mKIAA0602	phosphofurin acidic cluster sorting protein 2	protein-coding
mm_10265.1	chr2	9693727	9693730	+	1	NA	Intergenic	Intergenic	184872	NM_008091	14462	Mm.313866	NM_008091	ENSMUSG00000015619	Gata3	Gata-3|jal	GATA binding protein 3	protein-coding
mm_125984.1	chr15	76343505	76343558	+	1	NA	promoter-TSS (NM_025567)	promoter-TSS (NM_025567)	8	NM_025567	66445	Mm.29196	NM_025567	ENSMUSG00000022551	Cyc1	2610002H19Rik|AA408921|Cyct1	cytochrome c-1	protein-coding
mm_153177.1	chr19	34493886	34493896	-	1	NA	3' UTR (NM_021460, exon 10 of 10)	3' UTR (NM_021460, exon 10 of 10)	-18756	NM_009890	12642	Mm.30824	NM_009890	ENSMUSG00000050370	Ch25h	AI462618|m25OH	cholesterol 25-hydroxylase	protein-coding
mm_55237.1	chr6	52245797	52245826	-	1	NA	promoter-TSS (NM_010450)	promoter-TSS (NM_010450)	-1	NM_010450	15396	Mm.26954	NM_010450	ENSMUSG00000038210	Hoxa11	Hox-1.9|Hoxa-11	homeobox A11	protein-coding
mm_169583.1	chr1	52431928	52431933	-	1	NA	Intergenic	RLTR17|LTR|ERVK	68518	NM_008667	17936	Mm.25903	NM_008667	ENSMUSG00000002881	Nab1	-	Ngfi-A binding protein 1	protein-coding
mm_168379.1	chr11	22287019	22287025	-	1	NA	promoter-TSS (NM_153078)	promoter-TSS (NM_153078)	-227	NM_001252515	216565	Mm.491265	NM_153078	ENSMUSG00000042302	Ehbp1	AF424697|Flj21950|NACSIN	EH domain binding protein 1	protein-coding
mm_142882.1	chr17	51826690	51826700	-	1	NA	promoter-TSS (NM_001163631)	promoter-TSS (NM_001163631)	-107	NM_001163631	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_142836.1	chr17	51790202	51790204	-	1	NA	intron (NM_009122, intron 5 of 10)	intron (NM_009122, intron 5 of 10)	21851	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_84705.1	chr9	72721384	72721398	-	1	NA	exon (NM_010890, exon 11 of 29)	exon (NM_010890, exon 11 of 29)	59044	NM_010890	17999	Mm.279923	NM_010890	ENSMUSG00000032216	Nedd4	AA959633|AL023035|AU019897|E430025J12Rik|Nedd4-1|Nedd4a|mKIAA0093	neural precursor cell expressed, developmentally down-regulated 4	protein-coding
mm_71426.1	chr8	46491126	46491142	+	1	NA	5' UTR (NM_001302163, exon 1 of 21)	5' UTR (NM_001302163, exon 1 of 21)	168	NM_001302163	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_63500.1	chr7	127800712	127800719	+	1	NA	TTS (NM_178029)	TTS (NM_178029)	106	NM_001040684	101502	Mm.157103	NM_133943	ENSMUSG00000042289	Hsd3b7	AI195443|BB098564	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 7	protein-coding
mm_161028.1	chr12	4274837	4274837	-	1	NA	exon (NM_010881, exon 16 of 23)	exon (NM_010881, exon 16 of 23)	-40543	NM_134046	52504	Mm.70546	NM_134046	ENSMUSG00000020652	Cenpo	2810429O05Rik|8430427C03Rik|D12Ertd482e	centromere protein O	protein-coding
mm_65824.1	chr7	29177181	29177201	-	1	NA	exon (NM_026545, exon 4 of 7)	exon (NM_026545, exon 4 of 7)	3482	NM_026545	57296	Mm.273152	NM_026545	ENSMUSG00000030591	Psmd8	6720456J22Rik|AA407360|AL033291|AL033322|AL033323|C76433	proteasome (prosome, macropain) 26S subunit, non-ATPase, 8	protein-coding
mm_147291.1	chr18	39490438	39490458	-	1	NA	Intergenic	CpG	-3203	NM_008173	14815	Mm.129481	NM_008173	ENSMUSG00000024431	Nr3c1	GR|Grl-1|Grl1	nuclear receptor subfamily 3, group C, member 1	protein-coding
mm_33862.1	chr4	135920732	135920801	+	1	NA	promoter-TSS (NM_024243)	promoter-TSS (NM_024243)	40	NM_024243	71665	Mm.439940	NM_024243	ENSMUSG00000028673	Fuca1	0610006A03Rik|9530055J05Rik|Afuc|Fuca	fucosidase, alpha-L- 1, tissue	protein-coding
mm_134167.1	chr16	10796275	10796278	-	1	NA	TTS (NM_013637)	TTS (NM_013637)	547	NM_013637	19118	Mm.42733	NM_013637	ENSMUSG00000022501	Prm1	Prm-1	protamine 1	protein-coding
mm_170240.1	chr17	89935781	89935795	+	1	NA	Intergenic	IAPLTR1_Mm|LTR|ERVK	152580	NM_001346962	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_6468.1	chr1	74036226	74036235	-	1	NA	intron (NM_027884, intron 3 of 34)	intron (NM_027884, intron 3 of 34)	88217	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_80973.1	chr9	103112095	103112149	+	1	NA	promoter-TSS (NM_173781)	promoter-TSS (NM_173781)	48	NM_173781	270192	Mm.490252	NM_173781	ENSMUSG00000032549	Rab6b	9630015C03|AI844641|C330006L04Rik|D9Bwg0185e	RAB6B, member RAS oncogene family	protein-coding
mm_77567.1	chr8	123429447	123429449	-	1	NA	Intergenic	MuLV-int|LTR|ERV1	-13508	NM_001253784	23854	Mm.275127	NM_054046	ENSMUSG00000001482	Def8	AI449518|D8Ertd713e|DEF-8	differentially expressed in FDCP 8	protein-coding
mm_82906.1	chr9	32924485	32924515	-	1	NA	intron (NR_131058, intron 1 of 3)	intron (NR_131058, intron 1 of 3)	4466	NR_131058	330917	Mm.488283	NR_131058		Gm27162	A430016B06	predicted gene 27162	ncRNA
mm_19735.1	chr2	104502533	104502543	-	1	NA	Intergenic	Intergenic	-8049	NM_001145824	15259	Mm.257925	NM_010434	ENSMUSG00000027177	Hipk3	DYRK6|FIST3|PKY|mir-1902	homeodomain interacting protein kinase 3	protein-coding
mm_18834.1	chr2	74716138	74716157	-	1	NA	promoter-TSS (NR_027899)	promoter-TSS (NR_027899)	-17	NR_027899	73429	Mm.443313	NR_027899		Hoxd3os1	1700064D17Rik|1700109F18Rik	homeobox D3, opposite strand 1	ncRNA
mm_90508.1	chr10	128040291	128040298	+	1	NA	exon (NM_001113199, exon 3 of 9)	exon (NM_001113199, exon 3 of 9)	4948	NM_001113199	17938	Mm.3746	NM_013608	ENSMUSG00000061315	Naca	AL022831|AL024382|Gm1878|mKIAA0363|skNAC	nascent polypeptide-associated complex alpha polypeptide	protein-coding
mm_54746.1	chr6	41032982	41032999	-	1	NA	exon (NM_023333, exon 3 of 5)	exon (NM_023333, exon 3 of 5)	2519	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_23953.1	chr3	84912472	84912483	+	1	NA	intron (NM_001177773, intron 4 of 13)	intron (NM_001177773, intron 4 of 13)	-39734	NM_080428	50754	Mm.196475	NM_080428	ENSMUSG00000028086	Fbxw7	1110001A17Rik|AGO|Cdc4|Fbw7|Fbwd6|Fbx30|Fbxo30|Fbxw6|SEL-10	F-box and WD-40 domain protein 7	protein-coding
mm_52944.1	chr6	122952633	122952650	+	1	NA	promoter-TSS (NM_153197)	promoter-TSS (NM_153197)	-3	NM_153197	73149	Mm.25684	NM_153197	ENSMUSG00000043832	Clec4a3	3110037K17Rik|Dcir3	C-type lectin domain family 4, member a3	protein-coding
mm_75826.1	chr8	70488477	70488507	-	1	NA	Intergenic	CpG	-1134	NM_182991	67937	Mm.23002	NM_182991	ENSMUSG00000035964	Tmem59l	5330410G16Rik	transmembrane protein 59-like	protein-coding
mm_128668.1	chr15	60187115	60187133	-	1	NA	Intergenic	Intergenic	-170506	NM_027668	71088	Mm.425950	NM_027668	ENSMUSG00000071749	4933412E24Rik	-	RIKEN cDNA 4933412E24 gene	protein-coding
mm_4596.1	chr1	178337972	178337987	+	1	NA	promoter-TSS (NM_016805)	promoter-TSS (NM_016805)	-195	NM_016805	51810	Mm.86589	NM_016805	ENSMUSG00000039630	Hnrnpu	AA408410|AI256620|AL024194|AL024437|AW557595|C86794|Hnrpu|SAFA|Sp120|hnRNP U	heterogeneous nuclear ribonucleoprotein U	protein-coding
mm_121706.1	chr14	15438870	15438876	-	1	NA	5' UTR (NM_146052, exon 1 of 2)	5' UTR (NM_146052, exon 1 of 2)	114	NM_146052	218763	Mm.138039	NM_146052	ENSMUSG00000045201	Lrrc3b	BC019794|LRP15	leucine rich repeat containing 3B	protein-coding
mm_105059.1	chr11	100715355	100715376	-	1	NA	TTS (NM_029307)	TTS (NM_029307)	1515	NM_029307	75482	Mm.46175	NM_029307	ENSMUSG00000017832	Hspb9	1700007H20Rik	heat shock protein, alpha-crystallin-related, B9	protein-coding
mm_31120.1	chr4	42952809	42952822	+	1	NA	promoter-TSS (NM_019874)	promoter-TSS (NM_019874)	-279	NM_019874	56323	Mm.20437	NM_019874	ENSMUSG00000036052	Dnajb5	1110058L06Rik|AI462558|Hsc40|Hsp40-3	DnaJ heat shock protein family (Hsp40) member B5	protein-coding
mm_140095.1	chr17	78200241	78200258	+	1	NA	promoter-TSS (NM_015800)	promoter-TSS (NM_015800)	1	NM_015800	50766	Mm.311912	NM_015800	ENSMUSG00000024074	Crim1	AU015004	cysteine rich transmembrane BMP regulator 1 (chordin like)	protein-coding
mm_105665.1	chr11	107417347	107417383	-	1	NA	intron (NM_145823, intron 1 of 9)	intron (NM_145823, intron 1 of 9)	53355	NM_145823	71795	Mm.397413	NM_145823	ENSMUSG00000040430	Pitpnc1	1110020B03Rik|5830436L09Rik|AI662802|AI851387|C330017I21Rik|Dnr411|RDGBB|RDGBB1|rdgB-beta	phosphatidylinositol transfer protein, cytoplasmic 1	protein-coding
mm_43830.1	chr5	142972243	142972258	+	1	NA	3' UTR (NM_007984, exon 5 of 5)	3' UTR (NM_007984, exon 5 of 5)	11895	NM_007984	14086	Mm.289707	NM_007984	ENSMUSG00000029581	Fscn1	AI663989|Fan1|fascin-1	fascin actin-bundling protein 1	protein-coding
mm_39114.1	chr4	154928586	154928600	-	1	NA	promoter-TSS (NM_178931)	promoter-TSS (NM_178931)	-516	NM_178931	230979	Mm.215147	NM_178931	ENSMUSG00000042333	Tnfrsf14	Atar|HveA|Hvem|Tnfrs14	tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)	protein-coding
mm_31404.1	chr4	48047325	48047327	+	1	NA	intron (NM_015743, intron 1 of 7)	CpG	2021	NM_015743	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_106489.1	chr11	120236053	120236058	-	1	NA	intron (NM_001347621, intron 1 of 27)	CpG	3108	NM_198423	268515	Mm.309498	NM_198423	ENSMUSG00000039741	Bahcc1	B930044J06|BC060615	BAH domain and coiled-coil containing 1	protein-coding
mm_81737.1	chr9	113792832	113792842	+	1	NA	promoter-TSS (NM_001286603)	promoter-TSS (NM_001286603)	-493	NM_001286603	76499	Mm.222272	NM_029633	ENSMUSG00000033392	Clasp2	1500004F14Rik|8030404L10Rik|C77448|CLASP2beta|mKIAA0627	CLIP associating protein 2	protein-coding
mm_84220.1	chr9	61925404	61925432	-	1	NA	intron (NM_024245, intron 15 of 22)	intron (NM_024245, intron 15 of 22)	-10908	NM_018853	56040	Mm.3158	NM_018853	ENSMUSG00000007892	Rplp1	2410042H16Rik|Arpp1|C430017H15Rik	ribosomal protein, large, P1	protein-coding
mm_145679.1	chr18	61587475	61587495	+	1	NA	3' UTR (NM_146087, exon 10 of 10)	3' UTR (NM_146087, exon 10 of 10)	31903	NM_146087	93687	Mm.26908	NM_146087	ENSMUSG00000024576	Csnk1a1	2610208K14Rik|4632404G05Rik|5430427P18Rik|CK1a|Csnk1a	casein kinase 1, alpha 1	protein-coding
mm_54139.1	chr6	21858135	21858139	-	1	NA	Intergenic	Intergenic	-5622	NM_173007	269831	Mm.21950	NM_173007	ENSMUSG00000029669	Tspan12	9030619E17|AI426782|AI663988|AW111457|Tm4sf12	tetraspanin 12	protein-coding
mm_58741.1	chr7	13037675	13037700	+	1	NA	promoter-TSS (NM_001243968)	promoter-TSS (NM_001243968)	-60	NM_001243968	22192	Mm.196580	NM_145578	ENSMUSG00000005575	Ube2m	2510040H03Rik|UBC12|Ubc-rs2	ubiquitin-conjugating enzyme E2M	protein-coding
mm_91336.1	chr10	25621556	25621568	-	1	NA	intron (NR_136909, intron 3 of 3)	intron (NR_136909, intron 3 of 3)	85176	NR_136909	102640597	Mm.412041	NR_136909	ENSMUSG00000101537	Gm29571	-	predicted gene 29571	ncRNA
mm_37352.1	chr4	120134632	120134649	-	1	NA	3' UTR (NM_010657, exon 9 of 9)	3' UTR (NM_010657, exon 9 of 9)	-26566	NM_007902	13615	Mm.284855	NM_007902	ENSMUSG00000028635	Edn2	ET-2|PPET2|VIC	endothelin 2	protein-coding
mm_16945.1	chr2	15049255	15049339	-	1	NA	promoter-TSS (NM_001165942)	promoter-TSS (NM_001165942)	15	NM_001165942	74455	Mm.478923	NM_028950	ENSMUSG00000026707	Nsun6	4933403D21Rik|4933414E04Rik|NOPD1	NOL1/NOP2/Sun domain family member 6	protein-coding
mm_135794.1	chr16	57196653	57196671	-	1	NA	intron (NM_026254, intron 8 of 17)	L1_Rod|LINE|L1	-29330	NM_023175	52633	Mm.383203	NM_023175	ENSMUSG00000022751	Nit2	1190017B19Rik|D16Ertd502e	nitrilase family, member 2	protein-coding
mm_136707.1	chr17	7925958	7925971	+	1	NA	promoter-TSS (NM_145968)	promoter-TSS (NM_145968)	-36	NM_145968	72536	Mm.119680	NM_145968	ENSMUSG00000033450	Tagap	2610315E15Rik	T cell activation Rho GTPase activating protein	protein-coding
mm_156493.1	chrX	144336148	144336150	+	1	NA	non-coding (NR_037145, exon 4 of 27)	non-coding (NR_037145, exon 4 of 27)	18183	NM_026247	67574	Mm.249084	NM_026247	ENSMUSG00000041718	Alg13	2810046O15Rik|4833435D08Rik|Glt28d1|MDS031|OTTMUSG00000018917	asparagine-linked glycosylation 13	protein-coding
mm_154572.1	chrX	7067497	7067515	+	1	NA	promoter-TSS (NM_009651)	promoter-TSS (NM_009651)	-9	NM_009651	11643	Mm.1498	NM_009651	ENSMUSG00000050089	Akap4	AKAP-4|AKAP82|Fsc1|PRKA4|mAKAP82|p82	A kinase (PRKA) anchor protein 4	protein-coding
mm_67614.1	chr7	83884290	83884315	-	1	NA	promoter-TSS (NM_030705)	promoter-TSS (NM_030705)	39	NM_030705	80889	Mm.272998	NM_030705	ENSMUSG00000070462	Mesdc1	AW061151	mesoderm development candidate 1	protein-coding
mm_40221.1	chr5	37242094	37242100	+	1	NA	promoter-TSS (NM_001136058)	promoter-TSS (NM_001136058)	39	NM_001136058	12933	Mm.290995	NM_007765	ENSMUSG00000029121	Crmp1	CRMP-1|DRP-1|Dpysl1|ULIP-3|Ulip3	collapsin response mediator protein 1	protein-coding
mm_144247.1	chr18	10782311	10782317	+	1	NA	TTS (NR_029547)	TTS (NR_029547)	662	NR_029547	387151		NR_029547	ENSMUSG00000065399	Mir133a-1	Mirn133|Mirn133a-1|mir-133a-1	microRNA 133a-1	ncRNA
mm_87559.1	chr10	56106884	56106937	+	1	NA	promoter-TSS (NM_001163833)	promoter-TSS (NM_001163833)	-7	NM_001163833	73390	Mm.181475	NM_133751	ENSMUSG00000047669	Msl3l2	1700060H10Rik	male-specific lethal 3-like 2 (Drosophila)	protein-coding
mm_86806.1	chr10	20326959	20326963	+	1	NA	intron (NM_001025392, intron 6 of 12)	intron (NM_001025392, intron 6 of 12)	14492	NM_001025393	72567	Mm.294783	NM_153787	ENSMUSG00000037608	Bclaf1	2610102K23Rik|2700025J07Rik|2810454G14Rik|5730534O06Rik|AI450190|AW556225|Btf|mKIAA0164	BCL2-associated transcription factor 1	protein-coding
mm_74217.1	chr8	123983022	123983033	+	1	NA	promoter-TSS (NM_019552)	promoter-TSS (NM_019552)	95	NM_019552	56199	Mm.274243	NM_019552	ENSMUSG00000031974	Abcb10	Abc-me|Abcb12	ATP-binding cassette, sub-family B (MDR/TAP), member 10	protein-coding
mm_80666.1	chr9	90113936	90113965	+	1	NA	intron (NM_001039147, intron 1 of 12)	CpG	870	NM_001039147	21761	Mm.426209	NM_024431	ENSMUSG00000062270	Morf4l1	MORFRG15|MRG15|TEG-189|Tex189|mKIAA4002	mortality factor 4 like 1	protein-coding
mm_49417.1	chr6	28888575	28888577	+	1	NA	3' UTR (NM_019776, exon 24 of 24)	3' UTR (NM_019776, exon 24 of 24)	-56829	NM_138682	192198	Mm.443660	NM_138682	ENSMUSG00000049939	Lrrc4	MBAG1|NGL-2|NGL2|NLG-2|Nag14	leucine rich repeat containing 4	protein-coding
mm_117706.1	chr13	95052999	95053002	-	1	NA	intron (NM_001170669, intron 7 of 18)	intron (NM_001170669, intron 7 of 18)	76656	NM_172590	218460	Mm.33856	NM_172590	ENSMUSG00000042015	Wdr41	B830029I03Rik|MSTP048	WD repeat domain 41	protein-coding
mm_70760.1	chr8	21529032	21529032	+	1	NA	promoter-TSS (NM_001177521)	promoter-TSS (NM_001177521)	2	NM_001177521	100041890	Mm.423382	NM_001177521	ENSMUSG00000094818	Defa32	ENSMUSG00000065957|Gm15308|OTTMUSG00000019860	defensin, alpha, 32	protein-coding
mm_54218.1	chr6	25809211	25809240	-	1	NA	promoter-TSS (NM_133931)	promoter-TSS (NM_133931)	1	NM_133931	101185	Mm.274589	NM_133931	ENSMUSG00000029676	Pot1a	1500031H18Rik|AI851169|Pot1	protection of telomeres 1A	protein-coding
mm_44468.1	chr5	23387034	23387061	-	1	NA	Intergenic	Intergenic	47306	NR_040469	269630	Mm.425231	NR_040469	ENSMUSG00000073147	5031425E22Rik	-	RIKEN cDNA 5031425E22 gene	ncRNA
mm_86927.1	chr10	24149445	24149467	+	1	NA	5' UTR (NM_016797, exon 1 of 10)	5' UTR (NM_016797, exon 1 of 10)	139	NM_016797	53331	Mm.248042	NM_016797	ENSMUSG00000019998	Stx7	AI315064|AI317144|AW107239|Syn7	syntaxin 7	protein-coding
mm_166099.1	chr4	143612106	143612136	-	1	NA	Intergenic	Intergenic	-2882	NM_001126324	279185	Mm.441604	NM_001126324	ENSMUSG00000066688	Gm13083	OTTMUSG00000010327	predicted gene 13083	protein-coding
mm_64289.1	chr7	141857524	141857532	+	1	NA	exon (NM_028801, exon 31 of 49)	exon (NM_028801, exon 31 of 49)	18456	NM_028801	74180	Mm.200752	NM_028801	ENSMUSG00000066108	Muc5b	2300002I04Rik|A130042M24|AV085033|MUC5|MUC9|mucin 5b	mucin 5, subtype B, tracheobronchial	protein-coding
mm_81344.1	chr9	108559858	108559862	+	1	NA	promoter-TSS (NM_011830)	promoter-TSS (NM_011830)	-641	NM_011830	23918	Mm.6065	NM_011830	ENSMUSG00000062867	Impdh2	IMPD	inosine 5'-phosphate dehydrogenase 2	protein-coding
mm_22258.1	chr2	177840345	177840354	-	1	NA	promoter-TSS (NM_001024849)	promoter-TSS (NM_001024849)	-13	NM_001024849	329575	Mm.425123	NM_001024849	ENSMUSG00000095362	Gm14325	OTTMUSG00000016325	predicted gene 14325	protein-coding
mm_4798.1	chr1	185204166	185204183	+	1	NA	promoter-TSS (NM_001163754)	promoter-TSS (NM_001163754)	6	NM_001163754	98732	Mm.275841	NM_172649	ENSMUSG00000039318	Rab3gap2	1110059F07Rik|2010002H18Rik|5830469C09|AI851069|AW743433|RAB3-GAP150|mKIAA0839	RAB3 GTPase activating protein subunit 2	protein-coding
mm_17700.1	chr2	32379427	32379476	-	1	NA	exon (NM_198001, exon 2 of 2)	exon (NM_198001, exon 2 of 2)	2464	NM_198001	73737	Mm.27608	NM_198001	ENSMUSG00000039195	1110008P14Rik	C79326	RIKEN cDNA 1110008P14 gene	protein-coding
mm_57348.1	chr6	124756479	124756527	-	1	NA	promoter-TSS (NM_007881)	promoter-TSS (NM_007881)	-16	NM_007881	13498	Mm.333380	NM_007881	ENSMUSG00000004263	Atn1	Atr1|Drpla|atrophin-1	atrophin 1	protein-coding
mm_126782.1	chr15	86194899	86194909	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-8763	NM_145475	223753	Mm.222685	NM_145475	ENSMUSG00000035891	Cerk	AI848610|D330016D08Rik|mKIAA1646	ceramide kinase	protein-coding
mm_146931.1	chr18	32035177	32035180	-	1	NA	intron (NM_032394, intron 1 of 46)	ID_B1|SINE|B4	1753	NM_032394	17922	Mm.440013	NM_032394	ENSMUSG00000024388	Myo7b	-	myosin VIIB	protein-coding
mm_167112.1	chr7	114667938	114667941	+	1	NA	Intergenic	Intergenic	-31582	NM_001305616	12310	Mm.4361	NM_007587	ENSMUSG00000030669	Calca	CA|CGRP-1|CGRP1|Calc|Calc1|Cgrp|Ct|Ctn	calcitonin/calcitonin-related polypeptide, alpha	protein-coding
mm_88374.1	chr10	76253849	76253866	+	1	NA	promoter-TSS (NM_009115)	promoter-TSS (NM_009115)	21	NM_009115	20203	Mm.235998	NM_009115	ENSMUSG00000033208	S100b	AI850290|Bpb	S100 protein, beta polypeptide, neural	protein-coding
mm_35682.1	chr4	43669147	43669200	-	1	NA	promoter-TSS (NM_175517)	promoter-TSS (NM_175517)	202	NM_001085508	242409	Mm.171489	NM_001085508	ENSMUSG00000078716	Tmem8b	4930500O05Rik	transmembrane protein 8B	protein-coding
mm_44722.1	chr5	30960237	30960320	-	1	NA	promoter-TSS (NM_001294302)	promoter-TSS (NM_001294302)	49	NM_001294302	50907	Mm.272414	NM_016703	ENSMUSG00000045302	Preb	C85705	prolactin regulatory element binding	protein-coding
mm_100471.1	chr11	119999109	119999124	+	1	NA	intron (NM_001037754, intron 11 of 13)	intron (NM_001037754, intron 11 of 13)	-15651	NR_037225	100526518		NR_037225	ENSMUSG00000105524	Mir3065	mir-3065|mmu-mir-3065	microRNA 3065	ncRNA
mm_61382.1	chr7	72306875	72306914	+	1	NA	promoter-TSS (NM_001024703)	promoter-TSS (NM_001024703)	-299	NM_001024703	244049	Mm.217412	NM_001024703	ENSMUSG00000032776	Mctp2	Gm489	multiple C2 domains, transmembrane 2	protein-coding
mm_57897.1	chr6	131379421	131379442	-	1	NA	exon (NM_011733, exon 5 of 9)	exon (NM_011733, exon 5 of 9)	9019	NM_139117	56449	Mm.458000	NM_011733	ENSMUSG00000030189	Ybx3	Csda|Dpba|MSY3|MSY4|Yb2|dbpA|oxyR	Y box protein 3	protein-coding
mm_128335.1	chr15	38455242	38455266	-	1	NA	Intergenic	MLT1N2|LTR|ERVL-MaLR	35293	NR_105916	102465574		NR_105916	ENSMUSG00000099110	Mir6951	Gm27765|mmu-mir-6951	microRNA 6951	ncRNA
mm_112689.1	chr13	16031087	16031105	+	1	NA	3' UTR (NM_008380, exon 5 of 5)	3' UTR (NM_008380, exon 5 of 5)	19245	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_167108.1	chr7	113621598	113621606	+	1	NA	Intergenic	Intergenic	-56615	NR_126544	69295	Mm.396150	NR_126544	ENSMUSG00000084984	Far1os	1700006P19Rik	fatty acyl CoA reductase 1, opposite strand	ncRNA
mm_97659.1	chr11	79578855	79578858	+	1	NA	3' UTR (NM_010897, exon 58 of 58)	3' UTR (NM_010897, exon 58 of 58)	-12356	NM_175543	268451	Mm.130656	NM_175543	ENSMUSG00000017639	Rab11fip4	A730072L08Rik|RAB11-FIP4|mKIAA1821	RAB11 family interacting protein 4 (class II)	protein-coding
mm_69709.1	chr7	140102368	140102378	-	1	NA	promoter-TSS (NR_104415)	promoter-TSS (NR_104415)	68	NM_001286217	69064	Mm.41915	NM_026928	ENSMUSG00000025466	Fuom	Fucu|Le51	fucose mutarotase	protein-coding
mm_32774.1	chr4	116699220	116699317	+	1	NA	3' UTR (NM_011034, exon 6 of 6)	3' UTR (NM_011034, exon 6 of 6)	9117	NM_025962	67096	Mm.252785	NM_025962	ENSMUSG00000028690	Mmachc	1810037K07Rik|CblC	methylmalonic aciduria cblC type, with homocystinuria	protein-coding
mm_23750.1	chr3	69548951	69548976	+	1	NA	intron (NM_178726, intron 2 of 3)	intron (NM_178726, intron 2 of 3)	49997	NM_020026	26879	Mm.153710	NM_020026	ENSMUSG00000043300	B3galnt1	B3galt3|b3GT3	UDP-GalNAc:betaGlcNAc beta 1,3-galactosaminyltransferase, polypeptide 1	protein-coding
mm_26739.1	chr3	6451665	6451675	-	1	NA	Intergenic	Intergenic	168773	NM_027048	69347	Mm.45822	NM_027048	ENSMUSG00000069118	1700008P02Rik	-	RIKEN cDNA 1700008P02 gene	protein-coding
mm_109043.1	chr12	104241253	104241264	+	1	NA	exon (NM_009251, exon 6 of 6)	exon (NM_009251, exon 6 of 6)	-6638	NR_033450	546546	Mm.390522	NM_001034870		Serpina3h	6C28|Spi2	serine (or cysteine) peptidase inhibitor, clade A, member 3H	pseudo
mm_55309.1	chr6	54972604	54972626	-	1	NA	promoter-TSS (NM_172729)	promoter-TSS (NM_172729)	-3	NM_172729	107607	Mm.28498	NM_172729	ENSMUSG00000038058	Nod1	C230079P11|Card4|F830007N14Rik|Nlrc1	nucleotide-binding oligomerization domain containing 1	protein-coding
mm_155607.1	chrX	83043102	83043125	+	1	NA	intron (NM_007868, intron 1 of 78)	intron (NM_007868, intron 1 of 78)	94243	NM_007868	13405	Mm.275608	NM_007868	ENSMUSG00000045103	Dmd	DXSmh7|DXSmh9|Dp427|Dp71|dys|mdx|pke	dystrophin, muscular dystrophy	protein-coding
mm_23437.1	chr3	59312865	59312887	+	1	NA	exon (NM_177855, exon 43 of 44)	exon (NM_177855, exon 43 of 44)	31380	NM_001162884	242050	Mm.228086	NM_001162884	ENSMUSG00000036334	Igsf10	6530405F15Rik|9030224D03|AA409708|AA536958|AI414626|Adlican2|CMF608	immunoglobulin superfamily, member 10	protein-coding
mm_37924.1	chr4	132842944	132842945	-	1	NA	intron (NM_146154, intron 1 of 6)	intron (NM_146154, intron 1 of 6)	225	NM_001290725	100336	Mm.105230	NM_146154	ENSMUSG00000028882	Ppp1r8	6330548N22Rik|AU044684|NIPP1	protein phosphatase 1, regulatory (inhibitor) subunit 8	protein-coding
mm_172191.1	chr6	51464545	51464548	-	1	NA	exon (NM_016806, exon 8 of 11)	exon (NM_016806, exon 8 of 11)	5348	NM_182650	53379	Mm.155896	NM_016806	ENSMUSG00000004980	Hnrnpa2b1	9130414A06Rik|Hnrpa2|Hnrpa2b1|hnrnp-A	heterogeneous nuclear ribonucleoprotein A2/B1	protein-coding
mm_27100.1	chr3	30491537	30491539	-	1	NA	intron (NM_021442, intron 1 of 2)	intron (NM_021442, intron 1 of 2)	17949	NM_021442	14013	Mm.56965	NM_007963	ENSMUSG00000027684	Mecom	D630039M04Rik|Evi-1|Evi1|Jbo|Mds|Mds1|Mds1-Evi1|Prdm3|Znfpr1b1	MDS1 and EVI1 complex locus	protein-coding
mm_60020.1	chr7	30787898	30787912	+	1	NA	promoter-TSS (NM_001033131)	promoter-TSS (NM_001033131)	0	NM_001033131	64661	Mm.268157	NM_001033131	ENSMUSG00000074199	Krtdap	Kdap|sk221	keratinocyte differentiation associated protein	protein-coding
mm_13721.1	chr2	117249779	117249779	+	1	NA	promoter-TSS (NM_026620)	promoter-TSS (NM_026620)	40	NM_026620	68215	Mm.219389	NM_026620	ENSMUSG00000027349	Fam98b	2610510H03Rik	family with sequence similarity 98, member B	protein-coding
mm_121445.1	chr14	120430562	120430574	+	1	NA	3' UTR (NM_207515, exon 8 of 8)	3' UTR (NM_207515, exon 8 of 8)	-47893	NM_029519	76108	Mm.261448	NM_029519	ENSMUSG00000051615	Rap2a	5830461H18Rik	RAS related protein 2a	protein-coding
mm_167219.1	chr8	11408105	11408115	+	1	NA	exon (NM_009932, exon 13 of 48)	exon (NM_009932, exon 13 of 48)	-69819	NR_126558	102132	Mm.37632	NR_126558	ENSMUSG00000096957	E230013L22Rik	AI645545	RIKEN cDNA E230013L22 gene	ncRNA
mm_37337.1	chr4	119657562	119657576	-	1	NA	exon (NM_008191, exon 2 of 3)	exon (NM_008191, exon 2 of 3)	1376	NM_008191	14916	Mm.278	NM_008191	ENSMUSG00000032978	Guca2b	AV066530|Gcap2|Ugn	guanylate cyclase activator 2b (retina)	protein-coding
mm_148875.1	chr19	6497933	6497943	+	1	NA	intron (NM_001205234, intron 17 of 22)	CpG	45132	NM_009203	20521	Mm.391146	NM_009203	ENSMUSG00000061742	Slc22a12	AI987855|OAT4L|Rst|Slc22al2|URAT1	solute carrier family 22 (organic anion/cation transporter), member 12	protein-coding
mm_104592.1	chr11	97041425	97041436	-	1	NA	promoter-TSS (NM_027026)	promoter-TSS (NM_027026)	-61	NM_027026	69297	Mm.250465	NM_027026	ENSMUSG00000020878	Lrrc46	1700006D24Rik	leucine rich repeat containing 46	protein-coding
mm_25712.1	chr3	122566720	122566739	+	1	NA	intron (NM_153118, intron 5 of 13)	intron (NM_153118, intron 5 of 13)	-25048	NR_106117	102465764		NR_106117	ENSMUSG00000104773	Mir7657	mmu-mir-7657	microRNA 7657	ncRNA
mm_103991.1	chr11	84840366	84840377	-	1	NA	exon (NM_153144, exon 8 of 14)	exon (NM_153144, exon 8 of 14)	11193	NR_046281	74995	Mm.84413	NR_046281	ENSMUSG00000086799	4930502E09Rik	-	RIKEN cDNA 4930502E09 gene	ncRNA
mm_29941.1	chr3	132857451	132857457	-	1	NA	intron (NR_102297, intron 1 of 3)	intron (NR_102297, intron 1 of 3)	21142	NR_102297	101243624	Mm.306256	NR_102297	ENSMUSG00000106230	Gm29811	-	predicted gene, 29811	ncRNA
mm_168021.1	chrY	90737862	90737880	+	1	NA	Intergenic	RLTR31D_MM|LTR|ERVK	17179	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_71915.1	chr8	70139348	70139364	+	1	NA	promoter-TSS (NM_001309841)	promoter-TSS (NM_001309841)	-143	NM_001145552	72368	Mm.644	NM_001145552	ENSMUSG00000002345	Borcs8	2310045N01Rik|Mef2bnb	BLOC-1 related complex subunit 8	protein-coding
mm_67131.1	chr7	70453238	70453243	-	1	NA	Intergenic	Intergenic	-86494	NM_183261	11819	Mm.158143	NM_009697	ENSMUSG00000030551	Nr2f2	2700033K02Rik|9430015G03Rik|ARP-1|Aporp1|COUP-TF2|COUP-TFII|COUPTFB|EAR3|SVP40|Tcfcoup2	nuclear receptor subfamily 2, group F, member 2	protein-coding
mm_57904.1	chr6	131388466	131388476	-	1	NA	promoter-TSS (NM_011733)	promoter-TSS (NM_011733)	-21	NM_011733	56449	Mm.458000	NM_011733	ENSMUSG00000030189	Ybx3	Csda|Dpba|MSY3|MSY4|Yb2|dbpA|oxyR	Y box protein 3	protein-coding
mm_154532.1	chrM	13750	13807	-	1	NA	NA	Intergenic	NA	NA								
mm_150987.1	chr19	46516188	46516203	+	1	NA	3' UTR (NM_053100, exon 6 of 6)	3' UTR (NM_053100, exon 6 of 6)	14547	NM_053100	93679	Mm.392177	NM_053100	ENSMUSG00000025034	Trim8	AA408830|BB006755|GERP|Rnf27	tripartite motif-containing 8	protein-coding
mm_462.1	chr1	36308060	36308075	+	1	NA	intron (NM_001172206, intron 1 of 6)	CpG	334	NM_001172205	214855	Mm.34316	NM_145996	ENSMUSG00000037447	Arid5a	D430024K22Rik|Mrf1	AT rich interactive domain 5A (MRF1-like)	protein-coding
mm_12522.1	chr2	72152524	72152528	+	1	NA	intron (NM_019688, intron 6 of 29)	intron (NM_019688, intron 6 of 29)	97909	NM_001204166	56508	Mm.196153	NM_019688	ENSMUSG00000049044	Rapgef4	1300003D15Rik|5730402K07Rik|6330581N18Rik|EPAC 2|Epac-2|Epac2|mKIAA4040	Rap guanine nucleotide exchange factor (GEF) 4	protein-coding
mm_81452.1	chr9	109816676	109816699	+	1	NA	promoter-TSS (NM_183136)	promoter-TSS (NM_183136)	60	NM_183136	78709	Mm.99613	NM_183136	ENSMUSG00000050074	Spink8	C630041L24Rik	serine peptidase inhibitor, Kazal type 8	protein-coding
mm_67401.1	chr7	79924845	79924847	-	1	NA	TTS (NM_027420)	TTS (NM_027420)	-4206	NM_009682	11778	Mm.220173	NM_009682	ENSMUSG00000063801	Ap3s2	[s]3B	adaptor-related protein complex 3, sigma 2 subunit	protein-coding
mm_153705.1	chr19	44397807	44397834	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	9889	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_62695.1	chr7	110122300	110122323	+	1	NA	5' UTR (NM_009516, exon 1 of 11)	5' UTR (NM_009516, exon 1 of 11)	252	NM_009516	22390	Mm.287173	NM_009516	ENSMUSG00000031016	Wee1	Wee1A	WEE 1 homolog 1 (S. pombe)	protein-coding
mm_143347.1	chr17	66694060	66694070	-	1	NA	intron (NM_008984, intron 22 of 30)	intron (NM_008984, intron 22 of 30)	-99443	NM_028998	74556	Mm.218634	NM_028998	ENSMUSG00000024105	Themis3	9130404H23Rik	thymocyte selection associated family member 3	protein-coding
mm_31987.1	chr4	89294757	89294769	+	1	NA	promoter-TSS (NR_132431)	promoter-TSS (NR_132431)	-144	NM_009877	12578	Mm.4733	NM_009877	ENSMUSG00000044303	Cdkn2a	ARF-INK4a|Arf|INK4a-ARF|Ink4a/Arf|MTS1|Pctr1|p16|p16(INK4a)|p16INK4a|p19<ARF>|p19ARF	cyclin-dependent kinase inhibitor 2A	protein-coding
mm_115189.1	chr13	108549191	108549191	+	1	NA	Intergenic	Intergenic	-104986	NM_011056	238871	Mm.434429	NM_011056	ENSMUSG00000021699	Pde4d	9630011N22Rik|Dpde3	phosphodiesterase 4D, cAMP specific	protein-coding
mm_162465.1	chr1	130851448	130851454	+	1	NA	3' UTR (NM_011082, exon 11 of 11)	3' UTR (NM_011082, exon 11 of 11)	-14326	NM_026976	69169	Mm.46042	NM_026976	ENSMUSG00000042474	Fcmr	1810037B05Rik|Faim3|FcmuR|Toso	Fc fragment of IgM receptor	protein-coding
mm_161063.1	chr12	71111330	71111330	+	1	NA	promoter-TSS (NM_029227)	promoter-TSS (NM_029227)	-98	NM_029227	75266	Mm.402075	NM_029227	ENSMUSG00000021078	Tomm20l	4930553D19Rik	translocase of outer mitochondrial membrane 20 homolog (yeast)-like	protein-coding
mm_163628.1	chr13	57882267	57882271	-	1	NA	intron (NM_001166464, intron 2 of 10)	intron (NM_001166464, intron 2 of 10)	26063	NM_009262	20745	Mm.379020	NM_009262	ENSMUSG00000056222	Spock1	Spock|Ticn1|testican	sparc/osteonectin, cwcv and kazal-like domains proteoglycan 1	protein-coding
mm_89540.1	chr10	94550966	94550976	+	1	NA	intron (NM_172051, intron 1 of 3)	intron (NM_172051, intron 1 of 3)	-24286	NM_001168684	319880	Mm.23047	NM_172051	ENSMUSG00000020023	Tmcc3	AW488095|C630016B22Rik|C88213|Tmcc1	transmembrane and coiled coil domains 3	protein-coding
mm_83223.1	chr9	42262137	42262141	-	1	NA	intron (NM_172769, intron 1 of 5)	intron (NM_172769, intron 1 of 5)	2161	NM_172769	235293	Mm.32700	NM_172769	ENSMUSG00000032018	Sc5d	A830037K02|A830073K23Rik|Sc5dl	sterol-C5-desaturase	protein-coding
mm_43024.1	chr5	123908179	123908188	+	1	NA	exon (NM_026603, exon 2 of 8)	exon (NM_026603, exon 2 of 8)	908	NM_026603	68184	Mm.28549	NM_026603	ENSMUSG00000023106	Denr	1500003K04Rik	density-regulated protein	protein-coding
mm_37726.1	chr4	129558777	129558792	-	1	NA	promoter-TSS (NM_010693)	promoter-TSS (NM_010693)	-412	NM_010693	16818	Mm.293753	NM_010693	ENSMUSG00000000409	Lck	Hck-3|Lsk|Lskt|p56<lck>|p56Lck	lymphocyte protein tyrosine kinase	protein-coding
mm_124720.1	chr15	6579964	6579974	+	1	NA	exon (NM_001278269, exon 1 of 17)	exon (NM_001278269, exon 1 of 17)	122	NM_011815	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_53902.1	chr6	3494550	3494563	-	1	NA	promoter-TSS (NM_178899)	promoter-TSS (NM_178899)	-58	NM_178899	101202	Mm.206911	NM_178899	ENSMUSG00000044156	Hepacam2	AI987662	HEPACAM family member 2	protein-coding
mm_107275.1	chr12	29534562	29534641	+	1	NA	promoter-TSS (NM_001093776)	promoter-TSS (NM_001093776)	-304	NM_001093776	17933	Mm.253067	NM_008666	ENSMUSG00000061911	Myt1l	2900046C06Rik|2900093J19Rik|C630034G21Rik|Nztf1|Pmng1|Png-1|mKIAA1106	myelin transcription factor 1-like	protein-coding
mm_7684.1	chr1	128590817	128590833	-	1	NA	intron (NM_009911, intron 1 of 1)	intron (NM_009911, intron 1 of 1)	1474	NM_009911	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding
mm_35507.1	chr4	41093521	41093532	-	1	NA	3' UTR (NM_016689, exon 6 of 6)	3' UTR (NM_016689, exon 6 of 6)	4657	NM_016689	11828	Mm.34043	NM_016689	ENSMUSG00000028435	Aqp3	AQP-2	aquaporin 3	protein-coding
mm_67397.1	chr7	79880044	79880068	-	1	NA	3' UTR (NM_009682, exon 6 of 6)	3' UTR (NM_009682, exon 6 of 6)	-37704	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_20757.1	chr2	140671429	140671439	-	1	NA	promoter-TSS (NM_178382)	promoter-TSS (NM_178382)	42	NM_001172160	71436	Mm.426781	NM_178382	ENSMUSG00000051379	Flrt3	5530600M07Rik|C430047I10Rik|mKIAA1469	fibronectin leucine rich transmembrane protein 3	protein-coding
mm_2667.1	chr1	127204990	127205051	+	1	NA	promoter-TSS (NM_145128)	promoter-TSS (NM_145128)	34	NM_145128	107895	Mm.214682	NM_145128	ENSMUSG00000036155	Mgat5	4930471A21Rik|5330407H02Rik|AI480971|GlcNAc-TV	mannoside acetylglucosaminyltransferase 5	protein-coding
mm_63058.1	chr7	122014577	122014579	+	1	NA	intron (NM_028758, intron 1 of 16)	intron (NM_028758, intron 1 of 16)	6620	NM_028758	74105	Mm.29619	NM_028758	ENSMUSG00000030872	Gga2	1200007E24Rik|mKIAA1080	golgi associated, gamma adaptin ear containing, ARF binding protein 2	protein-coding
mm_18077.1	chr2	42653294	42653302	-	1	NA	5' UTR (NM_053011, exon 1 of 91)	5' UTR (NM_053011, exon 1 of 91)	300	NM_053011	94217	Mm.441398	NM_053011	ENSMUSG00000049252	Lrp1b	9630004P12Rik|LRP-DIT	low density lipoprotein-related protein 1B (deleted in tumors)	protein-coding
mm_129812.1	chr15	82998917	82998930	-	1	NA	3' UTR (NM_028728, exon 6 of 6)	3' UTR (NM_028728, exon 6 of 6)	24215	NM_028728	74039	Mm.32584	NM_028728	ENSMUSG00000058099	Nfam1	4921501M20Rik|Cnaip	Nfat activating molecule with ITAM motif 1	protein-coding
mm_155942.1	chrX	104483122	104483157	+	1	NA	exon (NM_001081189, exon 1 of 7)	exon (NM_001081189, exon 1 of 7)	357	NM_001081189	331487	Mm.438275	NM_001081189	ENSMUSG00000073016	Uprt	Gm774	uracil phosphoribosyltransferase	protein-coding
mm_56624.1	chr6	112722273	112722277	-	1	NA	3' UTR (NM_080448, exon 22 of 22)	3' UTR (NM_080448, exon 22 of 22)	-25605	NM_001167730	58186	Mm.103812	NM_021385	ENSMUSG00000030254	Rad18	2810024C04Rik|Rad18sc	RAD18 E3 ubiquitin protein ligase	protein-coding
mm_2790.1	chr1	130850701	130850709	+	1	NA	intron (NM_011082, intron 10 of 10)	intron (NM_011082, intron 10 of 10)	-15072	NM_026976	69169	Mm.46042	NM_026976	ENSMUSG00000042474	Fcmr	1810037B05Rik|Faim3|FcmuR|Toso	Fc fragment of IgM receptor	protein-coding
mm_146928.1	chr18	31949823	31949835	-	1	NA	promoter-TSS (NM_001025381)	promoter-TSS (NM_001025381)	-193	NM_001025381	574402	Mm.391108	NM_001025381	ENSMUSG00000052229	Gpr17	AI853548	G protein-coupled receptor 17	protein-coding
mm_134853.1	chr16	28274309	28274313	-	1	NA	intron (NM_001276419, intron 3 of 4)	intron (NM_001276419, intron 3 of 4)	171764	NM_183064	14167	Mm.7996	NM_010199	ENSMUSG00000022523	Fgf12	AV114868|B230343J05Rik|FGF-12|FHF-1|Fhf1	fibroblast growth factor 12	protein-coding
mm_16015.1	chr2	167422038	167422050	+	1	NA	intron (NR_130767, intron 1 of 13)	intron (NR_130767, intron 1 of 13)	334	NM_001304542	77031	Mm.278924	NM_148929	ENSMUSG00000039463	Slc9a8	1200006P13Rik|6430709P13Rik|AI182282|NHE-8|NHE8	solute carrier family 9 (sodium/hydrogen exchanger), member 8	protein-coding
mm_92953.1	chr10	85266305	85266330	-	1	NA	Intergenic	Intergenic	-81263	NM_007771	12952	Mm.26237	NM_007771	ENSMUSG00000020038	Cry1	AU020726|AU021000|Phll1	cryptochrome 1 (photolyase-like)	protein-coding
mm_104116.1	chr11	86730807	86730817	-	1	NA	exon (NM_001003908, exon 5 of 32)	exon (NM_001003908, exon 5 of 32)	26680	NM_001003908	67300	Mm.254588	NM_001003908	ENSMUSG00000047126	Cltc	3110065L21Rik|CHC|R74732	clathrin, heavy polypeptide (Hc)	protein-coding
mm_86005.1	chr9	112233241	112233254	-	1	NA	promoter-TSS (NM_001177616)	promoter-TSS (NM_001177616)	-746	NM_001177616	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_74053.1	chr8	122282212	122282222	+	1	NA	promoter-TSS (NM_009569)	promoter-TSS (NM_009569)	76	NM_009569	22761	Mm.3105	NM_009569	ENSMUSG00000049577	Zfpm1	FOG|Fog1	zinc finger protein, multitype 1	protein-coding
mm_171749.1	chr5	101888107	101888113	-	1	NA	exon (NM_172882, exon 39 of 67)	exon (NM_172882, exon 39 of 67)	122980	NM_173370	74596	Mm.46764	NM_173370	ENSMUSG00000029330	Cds1	4833409J18Rik|AI314024|AW125888	CDP-diacylglycerol synthase 1	protein-coding
mm_31866.1	chr4	80003427	80003460	+	1	NA	Intergenic	Intergenic	-830770	NM_031202	22178	Mm.30438	NM_031202	ENSMUSG00000005994	Tyrp1	Oca3|TRP-1|TRP1|Tyrp|b|brown|isa	tyrosinase-related protein 1	protein-coding
mm_157963.1	chrX	88760319	88760319	-	1	NA	promoter-TSS (NR_035440)	promoter-TSS (NR_035440)	-766	NR_037313	100499530		NR_037313	ENSMUSG00000084559	Mir1906-2	mmu-mir-1906-2	microRNA 1906-2	ncRNA
mm_124708.1	chr15	6569453	6569459	+	1	NA	Intergenic	Intergenic	-10391	NM_001278269	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_90065.1	chr10	116301490	116301504	+	1	NA	5' UTR (NM_029928, exon 1 of 32)	5' UTR (NM_029928, exon 1 of 32)	123	NM_029928	19263	Mm.37213	NM_029928	ENSMUSG00000020154	Ptprb	3230402H02Rik|C130094E24|Ptpz|Rptpb|VE-PTP|Veptp	protein tyrosine phosphatase, receptor type, B	protein-coding
mm_7561.1	chr1	124723354	124723360	-	1	NA	Intergenic	Intergenic	-677798	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_149149.1	chr19	9006924	9006942	+	1	NA	exon (NM_009643, exon 5 of 5)	exon (NM_009643, exon 5 of 5)	-10971	NR_105786	102465190		NR_105786	ENSMUSG00000099308	Mir6367	Gm27467|mmu-mir-6367	microRNA 6367	ncRNA
mm_14673.1	chr2	139494054	139494063	+	1	NA	intron (NM_175467, intron 1 of 12)	intron (NM_175467, intron 1 of 12)	138	NM_175467	228677	Mm.100450	NM_175467	ENSMUSG00000039092	Sptlc3	C130053K05Rik	serine palmitoyltransferase, long chain base subunit 3	protein-coding
mm_89629.1	chr10	96371284	96371296	+	1	NA	Intergenic	Intergenic	145083	NR_110448	74881	Mm.410819	NR_110448		4930459C07Rik	-	RIKEN cDNA 4930459C07 gene	ncRNA
mm_49075.1	chr6	6118354	6118354	+	1	NA	intron (NM_015829, intron 5 of 17)	intron (NM_015829, intron 5 of 17)	98819	NM_015829	50799	Mm.24513	NM_015829	ENSMUSG00000015112	Slc25a13	AI785475|Ctrn	solute carrier family 25 (mitochondrial carrier, adenine nucleotide translocator), member 13	protein-coding
mm_132557.1	chr16	37963380	37963387	+	1	NA	intron (NM_153394, intron 3 of 9)	MLT1B|LTR|ERVL-MaLR	46887	NM_153394	239845	Mm.228018	NM_153394	ENSMUSG00000046961	Gpr156	Gababl	G protein-coupled receptor 156	protein-coding
mm_49317.1	chr6	18848585	18848600	+	1	NA	promoter-TSS (NM_133939)	promoter-TSS (NM_133939)	-43	NM_133939	76522	Mm.275158	NM_133939	ENSMUSG00000044155	Lsm8	2010003I05Rik|AW214405|Naa38	LSM8 homolog, U6 small nuclear RNA associated	protein-coding
mm_9391.1	chr1	172217936	172217948	-	1	NA	exon (NM_009813, exon 2 of 11)	exon (NM_009813, exon 2 of 11)	1953	NM_009813	12372	Mm.12829	NM_009813	ENSMUSG00000007122	Casq1	CSQ|CSQ-1|CSQ1|sCSQ	calsequestrin 1	protein-coding
mm_75185.1	chr8	36953140	36953160	-	1	NA	promoter-TSS (NM_001194940)	promoter-TSS (NM_001194940)	-708	NM_001194940	50768	Mm.125155	NM_015802	ENSMUSG00000031523	Dlc1	A730069N07Rik|Arhgap7|HP|STARD12|dlc-1	deleted in liver cancer 1	protein-coding
mm_59021.1	chr7	19279187	19279210	+	1	NA	exon (NM_177691, exon 1 of 5)	exon (NM_177691, exon 1 of 5)	851	NM_177691	232941	Mm.134068	NM_177691	ENSMUSG00000030402	Ppm1n	A930002H20|C79127	protein phosphatase, Mg2+/Mn2+ dependent, 1N (putative)	protein-coding
mm_100432.1	chr11	119469027	119469041	+	1	NA	Intergenic	Intergenic	-22313	NM_001164636	338371	Mm.271946	NM_177394	ENSMUSG00000039850	Endov	A730011L01Rik	endonuclease V	protein-coding
mm_2665.1	chr1	126844447	126844448	+	1	NA	Intergenic	Intergenic	-13815	NM_176957	210356	Mm.377234	NM_172484	ENSMUSG00000049690	Nckap5	8430408F21|D130011D22Rik|E030049G20Rik|Erih1|Erih2|Gm1548|Nap5	NCK-associated protein 5	protein-coding
mm_152150.1	chr19	7217530	7217543	-	1	NA	promoter-TSS (NM_007750)	promoter-TSS (NM_007750)	80	NM_007750	12868	Mm.14022	NM_007750	ENSMUSG00000035885	Cox8a	COX8L	cytochrome c oxidase subunit VIIIa	protein-coding
mm_124855.1	chr15	9533574	9533582	+	1	NA	Intergenic	Intergenic	-3702	NM_008372	16197	Mm.389	NM_008372	ENSMUSG00000003882	Il7r	CD127|IL-7Ralpha	interleukin 7 receptor	protein-coding
mm_62986.1	chr7	120204022	120204022	+	1	NA	promoter-TSS (NM_026458)	promoter-TSS (NM_026458)	58	NM_026458	67928	Mm.158178	NM_026458	ENSMUSG00000062017	Abca14	1700110B15Rik|4930539G24Rik	ATP-binding cassette, sub-family A (ABC1), member 14	protein-coding
mm_16604.1	chr2	5063997	5064048	-	1	NA	promoter-TSS (NM_181848)	promoter-TSS (NM_181848)	-84	NM_181848	71648	Mm.116942	NM_181848	ENSMUSG00000026672	Optn	4930441O07Rik|FIP2|HYPL|NRP	optineurin	protein-coding
mm_146664.1	chr18	12190380	12190398	-	1	NA	TTS (NM_029623)	TTS (NM_029623)	21659	NM_029623	76482	Mm.196596	NM_029623	ENSMUSG00000024410	3110002H16Rik	2400010D15Rik|Mic-1|Mic1	RIKEN cDNA 3110002H16 gene	protein-coding
mm_122553.1	chr14	48881845	48881855	-	1	NA	intron (NR_033783, intron 2 of 3)	intron (NR_033783, intron 2 of 3)	2977	NR_033783	66770	Mm.136954	NR_033783		4933429O19Rik	1700031B11Rik	RIKEN cDNA 4933429O19 gene	ncRNA
mm_41862.1	chr5	104440622	104440632	+	1	NA	3' UTR (NM_001204203, exon 7 of 7)	3' UTR (NM_001204203, exon 7 of 7)	4435	NM_001204233	20750	Mm.288474	NM_009263	ENSMUSG00000029304	Spp1	2AR|Apl-1|BNSP|BSPI|Bsp|ETA-1|Eta|OP|Opn|Opnl|Ric|Spp-1	secreted phosphoprotein 1	protein-coding
mm_131408.1	chr16	14451731	14451732	+	1	NA	intron (NM_008576, intron 19 of 30)	intron (NM_008576, intron 19 of 30)	90173	NM_008576	17250	Mm.196634	NM_008576	ENSMUSG00000023088	Abcc1	Abcc1a|Abcc1b|MRP|Mdrap|Mrp1	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	protein-coding
mm_43667.1	chr5	138755073	138755090	+	1	NA	promoter-TSS (NM_030565)	promoter-TSS (NM_030565)	0	NM_030565	80752	Mm.320355	NM_030565	ENSMUSG00000025854	Fam20c	C76981|DMP-4|DMP4|GEF-CK|mKIAA4081	family with sequence similarity 20, member C	protein-coding
mm_170040.1	chr17	24205514	24205514	-	1	NA	promoter-TSS (NM_001163849)	promoter-TSS (NM_001163849)	48	NM_001163851	224617	Mm.301585	NM_173186	ENSMUSG00000036473	Tbc1d24	9630033P11|C530046L02Rik|mKIAA1171	TBC1 domain family, member 24	protein-coding
mm_2358.1	chr1	92950895	92950903	+	1	NA	promoter-TSS (NR_015525)	promoter-TSS (NR_015525)	-309	NR_015525	100037260	Mm.442236	NR_015525	ENSMUSG00000100632	9430060I03Rik	-	RIKEN cDNA 9430060I03 gene	ncRNA
mm_30185.1	chr3	144689671	144689694	-	1	NA	3' UTR (NM_019464, exon 9 of 9)	3' UTR (NM_019464, exon 9 of 9)	30653	NM_001282042	54673	Mm.271775	NM_019464	ENSMUSG00000037062	Sh3glb1	AA409932|AI314629|AU015566|Bif-1|mKIAA0491	SH3-domain GRB2-like B1 (endophilin)	protein-coding
mm_14771.1	chr2	145786261	145786274	+	1	NA	intron (NM_028724, intron 1 of 12)	intron (NM_028724, intron 1 of 12)	151	NM_028724	74030	Mm.228799	NM_028724	ENSMUSG00000001768	Rin2	2010003K16Rik|4632403N06Rik|AW821980|RASSF4	Ras and Rab interactor 2	protein-coding
mm_99417.1	chr11	102309260	102309275	+	1	NA	intron (NM_001302955, intron 12 of 19)	CpG	8020	NM_001044383	21429	Mm.2845	NM_011551	ENSMUSG00000020923	Ubtf	A930005G04Rik|NOR-90|Tcfubf|UBF|UBF-1|UBF1	upstream binding transcription factor, RNA polymerase I	protein-coding
mm_111774.1	chr12	104044376	104044390	-	1	NA	promoter-TSS (NM_026535)	promoter-TSS (NM_026535)	60	NM_026535	68054	Mm.20286	NM_026535	ENSMUSG00000041567	Serpina12	4632419J12Rik	serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 12	protein-coding
mm_84807.1	chr9	77323829	77323832	-	1	NA	intron (NM_027150, intron 1 of 7)	intron (NM_027150, intron 1 of 7)	24040	NM_027150	69642	Mm.35008	NM_027150	ENSMUSG00000032355	Mlip	2310046A06Rik|AI931782|CIP	muscular LMNA-interacting protein	protein-coding
mm_4735.1	chr1	181576645	181576649	+	1	NA	Intergenic	Intergenic	-65196	NM_207280	403180	Mm.220754	NM_207280	ENSMUSG00000050625	Ccdc121	6530421E24Rik|Gm755	coiled-coil domain containing 121	protein-coding
mm_96868.1	chr11	70167185	70167198	+	1	NA	intron (NM_001204252, intron 1 of 9)	intron (NM_001204252, intron 1 of 9)	568	NM_010796	17312	Mm.252405	NM_010796	ENSMUSG00000000318	Clec10a	CD301a|M-ASGP-BP-1|Mgl|Mgl1	C-type lectin domain family 10, member A	protein-coding
mm_97317.1	chr11	76902153	76902167	+	1	NA	Intergenic	Intergenic	-2385	NM_025655	66601	Mm.25138	NM_025655	ENSMUSG00000020839	Tmigd1	2010002A20Rik|Tmigd	transmembrane and immunoglobulin domain containing 1	protein-coding
mm_14181.1	chr2	127008712	127008756	+	1	NA	promoter-TSS (NM_175550)	promoter-TSS (NM_175550)	23	NM_175550	108011	Mm.134045	NM_175550	ENSMUSG00000001998	Ap4e1	2310033A20Rik|9930028M04Rik|AV087807	adaptor-related protein complex AP-4, epsilon 1	protein-coding
mm_135753.1	chr16	55974542	55974607	-	1	NA	promoter-TSS (NR_027965)	promoter-TSS (NR_027965)	43	NR_027965	66391	Mm.472722	NM_133677	ENSMUSG00000102101	Zbtb11os1	2310061J03Rik	zinc finger and BTB domain containing 11, opposite strand 1	ncRNA
mm_100560.1	chr11	120730254	120730260	+	1	NA	exon (NM_007621, exon 6 of 8)	exon (NM_007621, exon 6 of 8)	1764	NM_007621	12409	Mm.21454	NM_007621	ENSMUSG00000025150	Cbr2	MLCR	carbonyl reductase 2	protein-coding
mm_27799.1	chr3	75881379	75881382	-	1	NA	intron (NM_001291069, intron 14 of 15)	intron (NM_001291069, intron 14 of 15)	75569	NM_175193	73124	Mm.249232	NM_175193	ENSMUSG00000034109	Golim4	3110027H23Rik|GIMPC|GPP130|Golph4|P138	golgi integral membrane protein 4	protein-coding
mm_143437.1	chr17	70852233	70852261	-	1	NA	promoter-TSS (NM_001164075)	promoter-TSS (NM_001164075)	-513	NM_001164075	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_107488.1	chr12	38780287	38780326	+	1	NA	5' UTR (NM_007960, exon 1 of 13)	5' UTR (NM_007960, exon 1 of 13)	224	NM_007960	14009	Mm.4866	NM_007960	ENSMUSG00000004151	Etv1	ER81|Etsrp81	ets variant 1	protein-coding
mm_45481.1	chr5	70842348	70842370	-	1	NA	5' UTR (NM_010252, exon 1 of 9)	5' UTR (NM_010252, exon 1 of 9)	258	NM_010252	14405	Mm.255292	NM_010252	ENSMUSG00000001260	Gabrg1	GabaA|GabaA/BZ	gamma-aminobutyric acid (GABA) A receptor, subunit gamma 1	protein-coding
mm_91262.1	chr10	23350192	23350251	-	1	NA	promoter-TSS (NM_001347372)	promoter-TSS (NM_001347372)	-278	NM_010167	14051	Mm.332128	NM_010167	ENSMUSG00000010461	Eya4	B130023L16Rik	EYA transcriptional coactivator and phosphatase 4	protein-coding
mm_111914.1	chr12	108835846	108835893	-	1	NA	promoter-TSS (NM_181328)	promoter-TSS (NM_181328)	7	NM_181328	214663	Mm.266264	NM_181328	ENSMUSG00000021265	Slc25a29	C030003J19Rik|CACL|mCACL	solute carrier family 25 (mitochondrial carrier, palmitoylcarnitine transporter), member 29	protein-coding
mm_49092.1	chr6	7562343	7562345	+	1	NA	intron (NM_009311, intron 6 of 6)	intron (NM_009311, intron 6 of 6)	7273	NM_009311	21333	Mm.1440	NM_009311	ENSMUSG00000061762	Tac1	4930528L02Rik|NK-1|NK1|Nkna|PPT-A|PPTA|SP	tachykinin 1	protein-coding
mm_25656.1	chr3	121531654	121531678	+	1	NA	intron (NM_145394, intron 2 of 14)	intron (NM_145394, intron 2 of 14)	678	NM_145394	213603	Mm.33062	NM_145394	ENSMUSG00000039865	Slc44a3	BC010552	solute carrier family 44, member 3	protein-coding
mm_151380.1	chr19	56072107	56072108	+	1	NA	Intergenic	Intergenic	176786	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_144283.1	chr18	11918060	11918063	+	1	NA	intron (NM_001146287, intron 4 of 9)	PB1D9|SINE|Alu	-77623	NR_035447	100316686		NR_035447	ENSMUSG00000084565	Mir1901	Mirn1901|mmu-mir-1901	microRNA 1901	ncRNA
mm_55454.1	chr6	67339662	67339674	-	1	NA	promoter-TSS (NM_001311141)	promoter-TSS (NM_001311141)	26	NM_001311141	16162	Mm.188337	NM_008354	ENSMUSG00000018341	Il12rb2	A930027I18Rik|IL-12RB2|Ifnm	interleukin 12 receptor, beta 2	protein-coding
mm_39562.1	chr5	23102390	23102413	+	1	NA	intron (NM_001081231, intron 1 of 3)	intron (NM_001081231, intron 1 of 3)	331952	NR_040469	269630	Mm.425231	NR_040469	ENSMUSG00000073147	5031425E22Rik	-	RIKEN cDNA 5031425E22 gene	ncRNA
mm_54955.1	chr6	48687536	48687570	-	1	NA	intron (NM_174990, intron 2 of 2)	intron (NM_174990, intron 2 of 2)	2975	NM_174990	107526	Mm.333048	NM_174990	ENSMUSG00000054435	Gimap4	AU019574|E430007K16Rik|Ian-1|Ian1|Imap4	GTPase, IMAP family member 4	protein-coding
mm_81514.1	chr9	110035317	110035349	+	1	NA	exon (NM_008633, exon 7 of 19)	exon (NM_008633, exon 7 of 19)	-16688	NM_001311163	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_60894.1	chr7	46397345	46397421	+	1	NA	5' UTR (NM_001112739, exon 1 of 4)	5' UTR (NM_001112739, exon 1 of 4)	915	NM_001112739	16502	Mm.249386	NM_008421	ENSMUSG00000058975	Kcnc1	C230009H10Rik|KShIIIB|KV4|Kcr2-1|Kv3.1|NGK2|Shaw	potassium voltage gated channel, Shaw-related subfamily, member 1	protein-coding
mm_106014.1	chr11	115933465	115933498	-	1	NA	promoter-TSS (NM_130454)	promoter-TSS (NM_130454)	11	NM_130454	170472	Mm.379351	NM_130454	ENSMUSG00000020752	Recql5	RecQ5|Recq5b|Recql5b	RecQ protein-like 5	protein-coding
mm_164881.1	chr18	58210586	58210594	-	1	NA	promoter-TSS (NM_010181)	promoter-TSS (NM_010181)	-664	NM_010181	14119	Mm.20271	NM_010181	ENSMUSG00000024598	Fbn2	BC063774|Fib-2|mKIAA4226|sne|sy	fibrillin 2	protein-coding
mm_88186.1	chr10	69994390	69994412	+	1	NA	exon (NM_170688, exon 37 of 43)	exon (NM_170688, exon 37 of 43)	68869	NM_009670	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_47630.1	chr5	125294108	125294136	-	1	NA	exon (NM_001205082, exon 7 of 12)	exon (NM_001205082, exon 7 of 12)	46972	NM_016741	20778	Mm.282242	NM_016741	ENSMUSG00000037936	Scarb1	AI120173|CD36|Cd36l1|Chohd1|Cla-1|Cla1|D5Ertd460e|Hdlq1|Hlb398|SR-B1|SR-BI|SRBI|Srb1|mSR-BI	scavenger receptor class B, member 1	protein-coding
mm_164420.1	chr16	43235954	43235963	+	1	NA	intron (NM_001285805, intron 3 of 10)	intron (NM_001285805, intron 3 of 10)	-11326	NM_181058	56490	Mm.136238	NM_019778	ENSMUSG00000022708	Zbtb20	1300017A20Rik|7330412A13Rik|A930017C21Rik|D16Wsu73e|DPZF|HOF|ODA-8S|Oda8|Zfp288	zinc finger and BTB domain containing 20	protein-coding
mm_79082.1	chr9	46242451	46242460	+	1	NA	exon (NM_007468, exon 3 of 3)	exon (NM_007468, exon 3 of 3)	1611	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_64441.1	chr7	142653702	142653722	+	1	NA	3' UTR (NM_010514, exon 4 of 4)	3' UTR (NM_010514, exon 4 of 4)	1284	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_153456.1	chr19	41206861	41206898	-	1	NA	promoter-TSS (NM_011904)	promoter-TSS (NM_011904)	-105	NM_011904	24087	Mm.89983	NM_011904	ENSMUSG00000025013	Tll2	-	tolloid-like 2	protein-coding
mm_142902.1	chr17	52213023	52213036	-	1	NA	Intergenic	Intergenic	330302	NR_045095	100504169	Mm.417731	NR_045095		Gm20098	-	predicted gene, 20098	ncRNA
mm_100742.1	chr11	4118699	4118705	-	1	NA	promoter-TSS (NM_144520)	promoter-TSS (NM_144520)	27	NM_144520	67815	Mm.253922	NM_144520	ENSMUSG00000003585	Sec14l2	1300013M05Rik|Spf|TAP	SEC14-like lipid binding 2	protein-coding
mm_103110.1	chr11	69981229	69981240	-	1	NA	promoter-TSS (NM_026017)	promoter-TSS (NM_026017)	1	NM_018740	54351	Mm.13430	NM_018740	ENSMUSG00000018565	Elp5	Derp6|Rai12	elongator acetyltransferase complex subunit 5	protein-coding
mm_54570.1	chr6	38023282	38023292	-	1	NA	intron (NM_177200, intron 7 of 15)	intron (NM_177200, intron 7 of 15)	23709	NM_177200	320590	Mm.197449	NM_177200	ENSMUSG00000029830	Svopl	9430071P14Rik	SV2 related protein homolog (rat)-like	protein-coding
mm_172134.1	chr6	34598952	34598956	+	1	NA	intron (NM_001347100, intron 1 of 13)	intron (NM_001347100, intron 1 of 13)	450	NM_001347100	109624	Mm.308134	NM_145575	ENSMUSG00000029761	Cald1	4833423D12Rik|AI195384|AV071549|AW536160|C920027I18Rik	caldesmon 1	protein-coding
mm_23780.1	chr3	79161646	79161673	+	1	NA	Intergenic	Intergenic	-15784	NM_001099624	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_75390.1	chr8	45630643	45630658	-	1	NA	intron (NM_001310707, intron 1 of 23)	intron (NM_001310707, intron 1 of 23)	2899	NM_001310707	234214	Mm.211096	NM_172752	ENSMUSG00000031626	Sorbs2	2010203O03Rik|9430041O17Rik|A530071H08|Argbp2|mKIAA0777|nArgBP2	sorbin and SH3 domain containing 2	protein-coding
mm_130096.1	chr15	89425535	89425551	-	1	NA	TTS (NM_007692)	TTS (NM_007692)	319	NM_009948	12895	Mm.227738	NM_009948	ENSMUSG00000078937	Cpt1b	Cpt1|Cpt1-m|Cpti|Cpti-m|M-cpti	carnitine palmitoyltransferase 1b, muscle	protein-coding
mm_36194.1	chr4	62329417	62329427	-	1	NA	exon (NM_001045528, exon 13 of 28)	exon (NM_001045528, exon 13 of 28)	31126	NM_001045528	338355	Mm.357792	NM_001045528	ENSMUSG00000066151	Fkbp15	BB131447|C430014M02Rik|FKBO133|FKBP-133|FKBP-15|FKBP133|mKIAA0674	FK506 binding protein 15	protein-coding
mm_169254.1	chr13	78357982	78357982	-	1	NA	Intergenic	L1Md_T|LINE|L1	-159109	NM_010151	13865	Mm.439653	NM_010151	ENSMUSG00000069171	Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR-3|EAR3|Erbal3|SVP44|Tcfcoup1	nuclear receptor subfamily 2, group F, member 1	protein-coding
mm_169802.1	chr16	18011740	18011747	+	1	NA	Intergenic	LTRIS2|LTR|ERV1	31178	NM_016983	22363	Mm.377118	NM_016983	ENSMUSG00000059280	Vpreb2	CD179b|VpreB1|Vpreb-2	pre-B lymphocyte gene 2	protein-coding
mm_130984.1	chr15	103347256	103347263	-	1	NA	intron (NM_001314041, intron 28 of 30)	B1_Mur1|SINE|Alu	3266	NR_105928	102466775		NR_105928	ENSMUSG00000098419	Mir6963	Gm27724|mmu-mir-6963	microRNA 6963	ncRNA
mm_132544.1	chr16	37882855	37882871	+	1	NA	3' UTR (NM_177093, exon 4 of 4)	3' UTR (NM_177093, exon 4 of 4)	14463	NM_177093	320184	Mm.390882	NM_177093	ENSMUSG00000034158	Lrrc58	1810012N18Rik|C330018J07Rik	leucine rich repeat containing 58	protein-coding
mm_108818.1	chr12	95695393	95695397	+	1	NA	intron (NM_201518, intron 1 of 1)	CpG	3169	NM_201518	399558	Mm.341948	NM_201518	ENSMUSG00000047414	Flrt2	-	fibronectin leucine rich transmembrane protein 2	protein-coding
mm_83082.1	chr9	40189510	40189514	-	1	NA	Intergenic	Intergenic	2433	NM_146615	258608	Mm.377590	NM_146615	ENSMUSG00000051095	Olfr986	MOR104-3	olfactory receptor 986	protein-coding
mm_32345.1	chr4	104775858	104775878	+	1	NA	intron (NM_001316671, intron 2 of 10)	intron (NM_001316671, intron 2 of 10)	9551	NM_001316671	110382	Mm.87072	NM_133882	ENSMUSG00000029656	C8b	4930439B20Rik|AI595927	complement component 8, beta polypeptide	protein-coding
mm_13892.1	chr2	120404758	120404785	+	1	NA	promoter-TSS (NM_173734)	promoter-TSS (NM_173734)	-655	NM_001110496	211499	Mm.260712	NM_173734	ENSMUSG00000033808	Tmem87a	A930025J12Rik	transmembrane protein 87A	protein-coding
mm_106576.1	chr11	120726660	120726667	-	1	NA	intron (NM_001347608, intron 2 of 6)	intron (NM_001347608, intron 2 of 6)	618	NM_026428	67880	Mm.231091	NM_026428	ENSMUSG00000039450	Dcxr	0610038K04Rik|1810027P18Rik|XR	dicarbonyl L-xylulose reductase	protein-coding
mm_46617.1	chr5	108132514	108132538	-	1	NA	promoter-TSS (NM_028481)	promoter-TSS (NM_028481)	65	NM_001347383	73130	Mm.363960	NM_028876	ENSMUSG00000063406	Tmed5	3110020O18Rik|4432412D15Rik	transmembrane p24 trafficking protein 5	protein-coding
mm_15668.1	chr2	163405823	163405826	+	1	NA	TTS (NM_025699)	TTS (NM_025699)	-7831	NM_001205076	59091	Mm.34459	NM_021566	ENSMUSG00000017817	Jph2	1110002E14Rik|JP-2|Jp2	junctophilin 2	protein-coding
mm_92284.1	chr10	71285428	71285445	-	1	NA	promoter-TSS (NM_145420)	promoter-TSS (NM_145420)	-174	NM_145420	216080	Mm.270530	NM_145420	ENSMUSG00000019927	Ube2d1	UBCH5	ubiquitin-conjugating enzyme E2D 1	protein-coding
mm_37332.1	chr4	119638791	119638812	-	1	NA	exon (NM_008190, exon 2 of 3)	exon (NM_008190, exon 2 of 3)	1069	NM_008190	14915	Mm.2614	NM_008190	ENSMUSG00000023247	Guca2a	Guca2	guanylate cyclase activator 2a (guanylin)	protein-coding
mm_164742.1	chr17	73871099	73871115	-	1	NA	Intergenic	Intergenic	66266	NM_020578	57440	Mm.18526	NM_020578	ENSMUSG00000024065	Ehd3	Ehd2	EH-domain containing 3	protein-coding
mm_126659.1	chr15	84232094	84232109	+	1	NA	promoter-TSS (NM_133167)	promoter-TSS (NM_133167)	58	NM_133167	170736	Mm.323892	NM_133167	ENSMUSG00000022438	Parvb	AI595373|AW742462|D15Gsk1|affixin	parvin, beta	protein-coding
mm_158267.1	chrX	109160919	109160943	-	1	NA	3' UTR (NM_019989, exon 4 of 4)	3' UTR (NM_019989, exon 4 of 4)	-35825	NM_001037917	622976	Mm.482747	NM_001037917	ENSMUSG00000048621	Gm6377	EG622976	predicted gene 6377	protein-coding
mm_108094.1	chr12	74298779	74298789	+	1	NA	5' UTR (NM_198866, exon 1 of 1)	5' UTR (NM_198866, exon 1 of 1)	1310	NM_198866	386753	Mm.341686	NM_198866	ENSMUSG00000029878	Dbpht2	Spot2	DNA binding protein with his-thr domain	protein-coding
mm_62570.1	chr7	104244497	104244552	+	1	NA	promoter-TSS (NM_030684)	promoter-TSS (NM_030684)	67	NM_030684	94094	Mm.326945	NM_030684	ENSMUSG00000056144	Trim34a	Trim34|Trim34-1	tripartite motif-containing 34A	protein-coding
mm_151417.1	chr19	56744451	56744467	+	1	NA	Intergenic	Intergenic	22087	NM_007419	11554	Mm.46797	NM_007419	ENSMUSG00000035283	Adrb1	Adrb-1|beta-AR	adrenergic receptor, beta 1	protein-coding
mm_90015.1	chr10	115315673	115315694	+	1	NA	promoter-TSS (NM_024454)	promoter-TSS (NM_024454)	-92	NM_024454	216344	Mm.21936	NM_024454	ENSMUSG00000020132	Rab21	9630024B22	RAB21, member RAS oncogene family	protein-coding
mm_128102.1	chr15	27968202	27968212	-	1	NA	intron (NM_001081302, intron 1 of 56)	intron (NM_001081302, intron 1 of 56)	57641	NM_001081302	223435	Mm.485422	NM_001081302	ENSMUSG00000022263	Trio	6720464I07Rik|AA408740|Solo	triple functional domain (PTPRF interacting)	protein-coding
mm_87211.1	chr10	39777588	39777590	+	1	NA	intron (NM_011264, intron 1 of 31)	L1M4|LINE|L1	45429	NM_011264	19714	Mm.439723	NM_011264	ENSMUSG00000019841	Rev3l	Rev|Rev3|Sez4	REV3 like, DNA directed polymerase zeta catalytic subunit	protein-coding
mm_52758.1	chr6	120776512	120776533	+	1	NA	intron (NM_001081048, intron 1 of 9)	intron (NM_001081048, intron 1 of 9)	2754	NM_001081048	71803	Mm.425340	NM_001081048	ENSMUSG00000004902	Slc25a18	1500015I14Rik|AW125787	solute carrier family 25 (mitochondrial carrier), member 18	protein-coding
mm_26393.1	chr3	142572930	142572946	+	1	NA	3' UTR (NM_018734, exon 11 of 11)	3' UTR (NM_018734, exon 11 of 11)	12442	NM_001289493	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_87882.1	chr10	61695504	61695576	+	1	NA	promoter-TSS (NM_027912)	promoter-TSS (NM_027912)	26	NM_001272091	71767	Mm.71514	NM_027912	ENSMUSG00000020087	Tysnd1	1300019N10Rik	trypsin domain containing 1	protein-coding
mm_132454.1	chr16	36041267	36041300	+	1	NA	promoter-TSS (NM_027113)	promoter-TSS (NM_027113)	93	NM_027113	69544	Mm.37802	NM_027113	ENSMUSG00000034379	Wdr5b	2310009C03Rik|AI606931	WD repeat domain 5B	protein-coding
mm_10540.1	chr2	16463845	16463856	+	1	NA	intron (NM_026162, intron 1 of 13)	intron (NM_026162, intron 1 of 13)	107546	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding
mm_6714.1	chr1	82291371	82291394	-	1	NA	promoter-TSS (NM_010570)	promoter-TSS (NM_010570)	57	NM_010570	16367	Mm.4952	NM_010570	ENSMUSG00000055980	Irs1	G972R|IRS-1	insulin receptor substrate 1	protein-coding
mm_2050.1	chr1	87403706	87403715	+	1	NA	exon (NM_001110212, exon 9 of 29)	exon (NM_001110212, exon 9 of 29)	-8981	NM_001110227	100040591	Mm.443539	NM_001110227	ENSMUSG00000079436	Kcnj13	-	potassium inwardly-rectifying channel, subfamily J, member 13	protein-coding
mm_97777.1	chr11	82167093	82167114	+	1	NA	Intergenic	L1_Mur3|LINE|L1	12709	NM_011329	20290	Mm.1283	NM_011329	ENSMUSG00000020702	Ccl1	BF534335|I-309|Scya1|Tca-3	chemokine (C-C motif) ligand 1	protein-coding
mm_135333.1	chr16	38828757	38828770	-	1	NA	promoter-TSS (NM_029042)	promoter-TSS (NM_029042)	-14	NM_029042	74663	Mm.50263	NM_029042	ENSMUSG00000022798	4930435E12Rik	TSCPA	RIKEN cDNA 4930435E12 gene	protein-coding
mm_57509.1	chr6	125468326	125468332	-	1	NA	intron (NM_007657, intron 2 of 7)	intron (NM_007657, intron 2 of 7)	26426	NM_007657	12527	Mm.210676	NM_007657	ENSMUSG00000030342	Cd9	Tspan29	CD9 antigen	protein-coding
mm_152449.1	chr19	10829906	10829910	-	1	NA	5' UTR (NM_009852, exon 1 of 13)	5' UTR (NM_009852, exon 1 of 13)	150	NM_001037801	12511	Mm.290897	NM_009852	ENSMUSG00000024670	Cd6	-	CD6 antigen	protein-coding
mm_57726.1	chr6	128933656	128933668	-	1	NA	promoter-TSS (NM_027562)	promoter-TSS (NM_027562)	-719	NM_027562	70809	Mm.439891	NM_027562	ENSMUSG00000000248	Clec2g	4632413B12Rik|Clr-c|Clr-d|Clrc|Clrd|Clrx|Ddv10|Ocilrp1	C-type lectin domain family 2, member g	protein-coding
mm_133976.1	chr16	4509592	4509596	-	1	NA	intron (NM_175347, intron 1 of 6)	intron (NM_175347, intron 1 of 6)	13459	NM_175347	106393	Mm.35811	NM_175347	ENSMUSG00000022519	Srl	9830004M20Rik|AW108387|sar	sarcalumenin	protein-coding
mm_152501.1	chr19	11165299	11165336	-	1	NA	promoter-TSS (NM_027074)	promoter-TSS (NM_027074)	3	NM_027074	69416	Mm.72491	NM_027074	ENSMUSG00000024728	1700025F22Rik	-	RIKEN cDNA 1700025F22 gene	protein-coding
mm_95098.1	chr11	34047079	34047093	+	1	NA	promoter-TSS (NM_010696)	promoter-TSS (NM_010696)	-115	NM_010696	16822	Mm.265350	NM_010696	ENSMUSG00000002699	Lcp2	AI323664|BB161688|SLP-76|SLP76|m1Khoe|twm	lymphocyte cytosolic protein 2	protein-coding
mm_50713.1	chr6	52175175	52175220	+	1	NA	intron (NM_010452, intron 3 of 4)	intron (NM_010452, intron 3 of 4)	9523	NR_131182	105242657	Mm.490651	NR_131182	ENSMUSG00000056445	Hoxaas2	2810043O09Rik|5730446D14Rik	Hoxa cluster antisense RNA 2	ncRNA
mm_109330.1	chr12	109566319	109566332	+	1	NA	non-coding (NR_003633, exon 5 of 5)	non-coding (NR_003633, exon 5 of 5)	2633	NR_030427	791079		NR_030427	ENSMUSG00000076451	Mir770	Mirn770|mir-770|mmu-mir-770	microRNA 770	ncRNA
mm_139384.1	chr17	52149286	52149295	+	1	NA	Intergenic	Intergenic	266563	NR_045095	100504169	Mm.417731	NR_045095		Gm20098	-	predicted gene, 20098	ncRNA
mm_114665.1	chr13	78201956	78202004	+	1	NA	intron (NR_045195, intron 1 of 2)	intron (NR_045195, intron 1 of 2)	-3107	NM_010151	13865	Mm.439653	NM_010151	ENSMUSG00000069171	Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR-3|EAR3|Erbal3|SVP44|Tcfcoup1	nuclear receptor subfamily 2, group F, member 1	protein-coding
mm_132654.1	chr16	41533329	41533360	+	1	NA	promoter-TSS (NM_175548)	promoter-TSS (NM_175548)	2	NM_175548	268890	Mm.310524	NM_175548	ENSMUSG00000061080	Lsamp	5430428I19|AW046674|B130007O04Rik|D930023J12Rik|Lam|Lamp	limbic system-associated membrane protein	protein-coding
mm_59131.1	chr7	19965476	19965486	+	1	NA	promoter-TSS (NM_027839)	promoter-TSS (NM_027839)	69	NM_027839	71601	Mm.98097	NM_027839	ENSMUSG00000070777	Ceacam20	9130012D09Rik	carcinoembryonic antigen-related cell adhesion molecule 20	protein-coding
mm_123375.1	chr14	63245274	63245278	-	1	NA	promoter-TSS (NM_008092)	promoter-TSS (NM_008092)	-5	NM_001310610	14463	Mm.247669	NM_008092	ENSMUSG00000021944	Gata4	Gata-4	GATA binding protein 4	protein-coding
mm_100651.1	chr11	3150340	3150369	-	1	NA	intron (NM_030207, intron 14 of 32)	intron (NM_030207, intron 14 of 32)	26333	NR_003517	236604	Mm.247625	NM_001004146		Pisd-ps1	-	phosphatidylserine decarboxylase, pseudogene 1	pseudo
mm_124041.1	chr14	77036617	77036693	-	1	NA	promoter-TSS (NM_172488)	promoter-TSS (NM_172488)	-38	NM_172488	210808	Mm.89278	NM_172488	ENSMUSG00000044350	Lacc1	9030625A04Rik	laccase (multicopper oxidoreductase) domain containing 1	protein-coding
mm_155078.1	chrX	46329005	46329015	+	1	NA	promoter-TSS (NR_045440)	promoter-TSS (NR_045440)	3	NM_028514	73360	Mm.60929	NM_028514	ENSMUSG00000046615	Actrt1	1700061J02Rik|Arp-T1	actin-related protein T1	protein-coding
mm_122094.1	chr14	30626411	30626427	-	1	NA	promoter-TSS (NM_011103)	promoter-TSS (NM_011103)	-211	NM_011103	18753	Mm.2314	NM_011103	ENSMUSG00000021948	Prkcd	AI385711|D14Ertd420e|PKC[d]|PKCdelta|Pkcd	protein kinase C, delta	protein-coding
mm_67301.1	chr7	79300945	79300954	-	1	NA	intron (NM_018811, intron 3 of 10)	intron (NM_018811, intron 3 of 10)	27683	NM_018811	54608	Mm.365490	NM_018811	ENSMUSG00000039202	Abhd2	2210009N18Rik|LABH2|Labh-2	abhydrolase domain containing 2	protein-coding
mm_40291.1	chr5	43233963	43233979	+	1	NA	exon (NM_001177379, exon 1 of 11)	exon (NM_001177379, exon 1 of 11)	508	NM_001177379	231207	Mm.7233	NM_175937	ENSMUSG00000039782	Cpeb2	A630055H10Rik|Cpe-bp2	cytoplasmic polyadenylation element binding protein 2	protein-coding
mm_98148.1	chr11	87592642	87592672	+	1	NA	intron (NM_133215, intron 1 of 18)	intron (NM_133215, intron 1 of 18)	440	NM_133215	170749	Mm.399376	NM_133215	ENSMUSG00000018401	Mtmr4	AA596759|ESTM44|FYVE-DSP2|ZFYVE11|mKIAA0647	myotubularin related protein 4	protein-coding
mm_87769.1	chr10	60293417	60293440	+	1	NA	exon (NM_011179, exon 4 of 15)	exon (NM_011179, exon 4 of 15)	8967	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_131170.1	chr16	7069729	7069737	+	1	NA	promoter-TSS (NM_183188)	promoter-TSS (NM_183188)	-102	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_38012.1	chr4	133753617	133753666	-	1	NA	promoter-TSS (NM_001080819)	promoter-TSS (NM_001080819)	-30	NM_001080819	93760	Mm.22478	NM_001080819	ENSMUSG00000007880	Arid1a	1110030E03Rik|BAF250a|Osa1|Smarcf1	AT rich interactive domain 1A (SWI-like)	protein-coding
mm_117032.1	chr13	58274341	58274364	-	1	NA	promoter-TSS (NM_019832)	promoter-TSS (NM_019832)	-164	NM_019832	56278	Mm.296625	NM_019832	ENSMUSG00000021552	Gkap1	42kDa|4933400B15Rik|D13Ertd340e|Gkap42	G kinase anchoring protein 1	protein-coding
mm_83887.1	chr9	55512157	55512230	-	1	NA	promoter-TSS (NM_145615)	promoter-TSS (NM_145615)	50	NM_145615	110842	Mm.290853	NM_145615	ENSMUSG00000032314	Etfa	2010200I21Rik|D9Ertd394e	electron transferring flavoprotein, alpha polypeptide	protein-coding
mm_128480.1	chr15	50889970	50889994	-	1	NA	promoter-TSS (NR_035444)	promoter-TSS (NR_035444)	59	NM_032000	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_88398.1	chr10	76581536	76581546	+	1	NA	exon (NM_080845, exon 7 of 14)	exon (NM_080845, exon 7 of 14)	5893	NM_080845	14317	Mm.36278	NM_080845	ENSMUSG00000001155	Ftcd	-	formiminotransferase cyclodeaminase	protein-coding
mm_113280.1	chr13	30136507	30136527	+	1	NA	promoter-TSS (NM_153546)	promoter-TSS (NM_153546)	27	NM_153546	218121	Mm.89682	NM_153546	ENSMUSG00000038732	Mboat1	9130215M02Rik|BC023845|LPEAT1|Moact1|Oact1	membrane bound O-acyltransferase domain containing 1	protein-coding
mm_29818.1	chr3	129216903	129216937	-	1	NA	intron (NM_011098, intron 4 of 4)	intron (NM_011098, intron 4 of 4)	2988	NM_001287048	18741	Mm.246804	NM_011098	ENSMUSG00000028023	Pitx2	9430085M16Rik|Brx1|Brx1b|Munc30|Otlx2|Ptx2|Rieg	paired-like homeodomain transcription factor 2	protein-coding
mm_136599.1	chr17	5103244	5103248	+	1	NA	intron (NM_001085355, intron 3 of 19)	intron (NM_001085355, intron 3 of 19)	108172	NM_001085355	239985	Mm.133401	NM_001085355	ENSMUSG00000069729	Arid1b	8030481M12|9330189K18Rik|AI836955|Ardi1b|B230217J03Rik|mKIAA1235	AT rich interactive domain 1B (SWI-like)	protein-coding
mm_51076.1	chr6	66912643	66912646	+	1	NA	intron (NM_001177558, intron 1 of 4)	intron (NM_001177558, intron 1 of 4)	15753	NM_001177558	14701	Mm.234342	NM_025278	ENSMUSG00000036402	Gng12	2010305F15Rik|AA536815|AI115529|AI314170|AI842738	guanine nucleotide binding protein (G protein), gamma 12	protein-coding
mm_155917.1	chrX	102037282	102037305	+	1	NA	intron (NM_001163610, intron 1 of 7)	intron (NM_001163610, intron 1 of 7)	34014	NM_001278534	331474	Mm.23297	NM_183318	ENSMUSG00000049191	Rgag4	6430402L03Rik|Mar5|Mart5|mKIAA2001	retrotransposon gag domain containing 4	protein-coding
mm_16607.1	chr2	5083817	5083827	-	1	NA	Intergenic	Intergenic	-19884	NM_181848	71648	Mm.116942	NM_181848	ENSMUSG00000026672	Optn	4930441O07Rik|FIP2|HYPL|NRP	optineurin	protein-coding
mm_154919.1	chrX	22461651	22461652	+	1	NA	promoter-TSS (NR_033731)	promoter-TSS (NR_033731)	55	NR_033731	76705	Mm.399727	NM_029707		Ppp1r2-ps7	1700023I07Rik	protein phosphatase 1, regulatory (inhibitor) subunit 2, pseudogene 7	pseudo
mm_65715.1	chr7	28378308	28378354	-	1	NA	exon (NM_011756, exon 2 of 2)	exon (NM_011756, exon 2 of 2)	897	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_10530.1	chr2	16404159	16404162	+	1	NA	intron (NM_026162, intron 1 of 13)	intron (NM_026162, intron 1 of 13)	47856	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding
mm_140627.1	chr17	12393126	12393136	-	1	NA	exon (NM_008877, exon 7 of 19)	exon (NM_008877, exon 7 of 19)	14522	NM_008877	18815	Mm.971	NM_008877	ENSMUSG00000059481	Plg	AI649309|Pg	plasminogen	protein-coding
mm_121458.1	chr14	120491012	120491013	+	1	NA	intron (NM_029519, intron 1 of 1)	MLT1A0|LTR|ERVL-MaLR	12551	NM_029519	76108	Mm.261448	NM_029519	ENSMUSG00000051615	Rap2a	5830461H18Rik	RAS related protein 2a	protein-coding
mm_61000.1	chr7	49304252	49304278	+	1	NA	intron (NM_175272, intron 1 of 37)	intron (NM_175272, intron 1 of 37)	58076	NM_175272	78286	Mm.333881	NM_175272	ENSMUSG00000052512	Nav2	5330421F07Rik|AU067780|BQ960892|HELAD1|POMFIL2|RAINB1|RAINB2|Unc53H2|mKIAA3015	neuron navigator 2	protein-coding
mm_39155.1	chr4	155414880	155414884	-	1	NA	intron (NR_102283, intron 1 of 4)	L1MC5a|LINE|L1	5692	NM_001166029	544678	Mm.472798	NM_177674	ENSMUSG00000078490	Cfap74	2010015L04Rik|A530045M11	cilia and flagella associated protein 74	protein-coding
mm_149560.1	chr19	12700108	12700117	+	1	NA	intron (NM_029550, intron 1 of 5)	Lx2|LINE|L1	4322	NM_029550	64697	Mm.218561	NM_029550	ENSMUSG00000024694	Keg1	0610008P16Rik|AI316519|GS4059	kidney expressed gene 1	protein-coding
mm_32535.1	chr4	109000915	109000925	+	1	NA	exon (NM_146150, exon 1 of 31)	exon (NM_146150, exon 1 of 31)	115	NM_146150	230598	Mm.274950	NM_146150	ENSMUSG00000053510	Nrd1	2600011I06Rik|AI875733|NRD-C|Nrdc	nardilysin, N-arginine dibasic convertase, NRD convertase 1	protein-coding
mm_135311.1	chr16	38713069	38713083	-	1	NA	promoter-TSS (NM_020260)	promoter-TSS (NM_020260)	-41	NM_020260	12549	Mm.370848	NM_020260	ENSMUSG00000022799	Arhgap31	5830477L08Rik|AU041750|Cdgap|D330026I07Rik	Rho GTPase activating protein 31	protein-coding
mm_115818.1	chr13	19824235	19824268	-	1	NA	promoter-TSS (NM_181754)	promoter-TSS (NM_181754)	6	NM_181754	353346	Mm.239268	NM_181754	ENSMUSG00000053101	Gpr141	PGR13	G protein-coupled receptor 141	protein-coding
mm_8027.1	chr1	135131156	135131164	-	1	NA	intron (NM_007955, intron 1 of 37)	intron (NM_007955, intron 1 of 37)	1415	NM_007955	13924	Mm.4450	NM_007955		Ptprv	Esp|OST|OST-PTP|mOST-PTP	protein tyrosine phosphatase, receptor type, V	protein-coding
mm_105130.1	chr11	101417393	101417407	-	1	NA	promoter-TSS (NM_144829)	promoter-TSS (NM_144829)	33	NM_144829	69684	Mm.146283	NM_144829	ENSMUSG00000075528	Aarsd1	1110069E20Rik|2310044P18Rik|AA589600|AlaX|AlaXp-II	alanyl-tRNA synthetase domain containing 1	protein-coding
mm_123234.1	chr14	60087398	60087404	-	1	NA	promoter-TSS (NM_015803)	promoter-TSS (NM_015803)	-567	NM_015803	50769	Mm.319599	NM_015803	ENSMUSG00000021983	Atp8a2	AI415030|Atpc1b|agil|wl	ATPase, aminophospholipid transporter-like, class I, type 8A, member 2	protein-coding
mm_66618.1	chr7	45474462	45474467	-	1	NA	3' UTR (NM_027903, exon 7 of 7)	3' UTR (NM_027903, exon 7 of 7)	-7566	NM_007527	12028	Mm.19904	NM_007527	ENSMUSG00000003873	Bax	-	BCL2-associated X protein	protein-coding
mm_60073.1	chr7	33743738	33743743	+	1	NA	promoter-TSS (NM_001099329)	promoter-TSS (NM_001099329)	-59	NM_001099329	100043860	Mm.389875	NM_001099329	ENSMUSG00000078753	Scgb1b24	Abpa24|Gm12769|OTTMUSG00000008385	secretoglobin, family 1B, member 24	protein-coding
mm_70220.1	chr7	144941528	144941544	-	1	NA	Intergenic	CpG	-1611	NM_007631	12443	Mm.273049	NM_007631	ENSMUSG00000070348	Ccnd1	AI327039|CycD1|Cyl-1|PRAD1|bcl-1|cD1	cyclin D1	protein-coding
mm_120144.1	chr14	60382769	60382771	+	1	NA	Intergenic	Intergenic	4484	NM_001164705	72125	Mm.275499	NM_028113	ENSMUSG00000021986	Amer2	2600011E07Rik|Fam123a	APC membrane recruitment 2	protein-coding
mm_148953.1	chr19	7297675	7297693	+	1	NA	intron (NM_007928, intron 1 of 17)	intron (NM_007928, intron 1 of 17)	-2237	NM_001080390	13728	Mm.258986	NM_007928	ENSMUSG00000024969	Mark2	EMK-1|Emk|Par-1|Par-1b	MAP/microtubule affinity regulating kinase 2	protein-coding
mm_5593.1	chr1	39557820	39557829	-	1	NA	intron (NM_001033135, intron 5 of 6)	intron (NM_001033135, intron 5 of 6)	-8984	NR_028555	100217461		NR_028555	ENSMUSG00000077704	Snord89	MBII-289	small nucleolar RNA, C/D box 89	snoRNA
mm_73977.1	chr8	120536560	120536573	+	1	NA	promoter-TSS (NM_001145896)	promoter-TSS (NM_001145896)	709	NM_001145897	382034	Mm.334856	NM_198671	ENSMUSG00000031822	Gse1	2210013I18Rik|mKIAA0182	genetic suppressor element 1, coiled-coil protein	protein-coding
mm_166754.1	chr6	126164971	126164983	-	1	NA	promoter-TSS (NM_001164035)	promoter-TSS (NM_001164035)	-17	NM_001164035	18205	Mm.267570	NM_008742	ENSMUSG00000049107	Ntf3	AI316846|AI835689|HDNF|NGF-2|Nt3|Ntf-3	neurotrophin 3	protein-coding
mm_135245.1	chr16	37384941	37384978	-	1	NA	promoter-TSS (NM_172440)	promoter-TSS (NM_172440)	-1	NM_172440	207227	Mm.80170	NM_172440	ENSMUSG00000022829	Stxbp5l	9430094L02|A830015P08Rik|LLGL4|T2dm1|t2md1|tomosyn-2	syntaxin binding protein 5-like	protein-coding
mm_64945.1	chr7	16366452	16366462	-	1	NA	intron (NM_001285892, intron 5 of 8)	intron (NM_001285892, intron 5 of 8)	21439	NM_001285892	56459	Mm.258530	NM_019748	ENSMUSG00000052833	Sae1	2400010M20Rik|2610044L12Rik|AL033372|AOS1|AW743391|D7Ertd177e|HSPC140|Sua1|Uble1a	SUMO1 activating enzyme subunit 1	protein-coding
mm_77039.1	chr8	109575354	109575368	-	1	NA	exon (NM_017370, exon 5 of 5)	exon (NM_017370, exon 5 of 5)	3811	NM_017370	15439	Mm.26730	NM_017370	ENSMUSG00000031722	Hp	HP-1|preHP2	haptoglobin	protein-coding
mm_61852.1	chr7	88299484	88299495	+	1	NA	exon (NM_009982, exon 4 of 7)	exon (NM_009982, exon 4 of 7)	21404	NM_001311790	13032	Mm.89295	NM_009982	ENSMUSG00000030560	Ctsc	AI047818|CatC|DPP1|DPPI	cathepsin C	protein-coding
mm_51074.1	chr6	66896445	66896479	+	1	NA	promoter-TSS (NM_001177559)	promoter-TSS (NM_001177559)	65	NM_001177556	14701	Mm.234342	NM_025278	ENSMUSG00000036402	Gng12	2010305F15Rik|AA536815|AI115529|AI314170|AI842738	guanine nucleotide binding protein (G protein), gamma 12	protein-coding
mm_50232.1	chr6	42351069	42351082	+	1	NA	exon (NM_001289618, exon 3 of 10)	exon (NM_001289618, exon 3 of 10)	1247	NM_001289619	22793	Mm.282303	NM_011777	ENSMUSG00000029860	Zyx	9530098H06Rik|R75157	zyxin	protein-coding
mm_166132.1	chr4	155624355	155624367	-	1	NA	promoter-TSS (NM_007661)	promoter-TSS (NM_007661)	394	NR_040441	100502734	Mm.306018	NR_040441	ENSMUSG00000086682	Gm16023	OTTMUSG00000029160	predicted gene 16023	ncRNA
mm_154227.1	chr19	59943583	59943595	-	1	NA	promoter-TSS (NM_001164367)	promoter-TSS (NM_001164367)	65	NM_001164367	74998	Mm.24167	NM_001033172	ENSMUSG00000040022	Rab11fip2	4930470G04Rik|A830046J09Rik|AW558126|Nrip11	RAB11 family interacting protein 2 (class I)	protein-coding
mm_7814.1	chr1	131910266	131910274	-	1	NA	promoter-TSS (NM_001145804)	promoter-TSS (NM_001145804)	-188	NM_175294	98415	Mm.246869	NM_175294	ENSMUSG00000026434	Nucks1	2700010L10Rik|8430423A01Rik|AI647518|C78391|Nucks	nuclear casein kinase and cyclin-dependent kinase substrate 1	protein-coding
mm_4665.1	chr1	180374939	180374941	+	1	NA	intron (NM_001081175, intron 2 of 7)	intron (NM_001081175, intron 2 of 7)	-44391	NR_003623	277333	Mm.389223	NM_199472		Gm5069	EG277333	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_161781.1	chr17	42315919	42315919	+	1	NA	promoter-TSS (NM_028474)	promoter-TSS (NM_028474)	-28	NM_028474	627626	Mm.390999	NM_028474	ENSMUSG00000042256	Ptchd4	3110082D06Rik|Gm321	patched domain containing 4	protein-coding
mm_76111.1	chr8	80739031	80739058	-	1	NA	exon (NM_053124, exon 1 of 24)	exon (NM_053124, exon 1 of 24)	415	NM_053124	93762	Mm.246803	NM_053124	ENSMUSG00000031715	Smarca5	4933427E24Rik|D030040M08Rik|D330027N15Rik|MommeD4|Snf2h	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5	protein-coding
mm_75665.1	chr8	66490741	66490779	-	1	NA	Intergenic	L1M2|LINE|L1	-4253	NM_025465	66282	Mm.294985	NM_025465	ENSMUSG00000025591	Tma16	1810029B16Rik	translation machinery associated 16	protein-coding
mm_172160.1	chr6	44420549	44420549	-	1	NA	Intergenic	Intergenic	-639512	NM_001004357	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding
mm_108753.1	chr12	88957422	88957430	+	1	NA	intron (NM_172544, intron 2 of 19)	intron (NM_172544, intron 2 of 19)	4036	NM_172544	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding
mm_134700.1	chr16	22657183	22657242	-	1	NA	promoter-TSS (NM_138650)	promoter-TSS (NM_138650)	19	NM_138650	110197	Mm.194986	NM_138650	ENSMUSG00000022861	Dgkg	2900055E17Rik|90kDa|AI854428|Dagk3|E430001K23Rik|mKIAA4131	diacylglycerol kinase, gamma	protein-coding
mm_50347.1	chr6	48589507	48589528	+	1	NA	promoter-TSS (NM_183309)	promoter-TSS (NM_183309)	72	NM_183309	330305	Mm.123868	NM_183309	ENSMUSG00000052730	Gm5111	A630038D02|EG330305	predicted gene 5111	protein-coding
mm_118243.1	chr13	111808685	111808701	-	1	NA	exon (NM_011945, exon 1 of 20)	exon (NM_011945, exon 1 of 20)	290	NM_011945	26401	Mm.15918	NM_011945	ENSMUSG00000021754	Map3k1	MAPKKK1|MEKK1|Mekk	mitogen-activated protein kinase kinase kinase 1	protein-coding
mm_135053.1	chr16	33787105	33787132	-	1	NA	Intergenic	Intergenic	-6919	NM_010739	17063	Mm.3177	NM_010739	ENSMUSG00000022824	Muc13	114/A10|14/A10|AI159736|Lrrp|Ly64|NJ-1	mucin 13, epithelial transmembrane	protein-coding
mm_145928.1	chr18	67133499	67133535	+	1	NA	promoter-TSS (NM_010307)	promoter-TSS (NM_010307)	-43	NM_010307	14680	Mm.440746	NM_010307	ENSMUSG00000024524	Gnal	2610011C15Rik|9630020G10Rik|Galphaolf|Gna10|Golf	guanine nucleotide binding protein, alpha stimulating, olfactory type	protein-coding
mm_93417.1	chr10	108690213	108690216	-	1	NA	intron (NM_001252341, intron 5 of 11)	intron (NM_001252341, intron 5 of 11)	9946	NM_203660	368203	Mm.452758	NM_203660		Gm5136	C6.1AL|EG368203	predicted gene 5136	protein-coding
mm_79484.1	chr9	56995127	56995139	+	1	NA	5' UTR (NM_019651, exon 1 of 13)	5' UTR (NM_019651, exon 1 of 13)	165	NM_019651	56294	Mm.325643	NM_019651	ENSMUSG00000032290	Ptpn9	MEG2	protein tyrosine phosphatase, non-receptor type 9	protein-coding
mm_85918.1	chr9	111119257	111119271	-	1	NA	intron (NM_027742, intron 1 of 13)	intron (NM_027742, intron 1 of 13)	1153	NM_001164838	71268	Mm.302287	NM_027742	ENSMUSG00000032497	Lrrfip2	5133400F20Rik|AI850587	leucine rich repeat (in FLII) interacting protein 2	protein-coding
mm_64570.1	chr7	144897117	144897135	+	1	NA	exon (NM_008003, exon 2 of 3)	exon (NM_008003, exon 2 of 3)	594	NM_008003	14170	Mm.3904	NM_008003	ENSMUSG00000031073	Fgf15	FGF19	fibroblast growth factor 15	protein-coding
mm_30919.1	chr4	32657185	32657194	+	1	NA	promoter-TSS (NM_001081392)	promoter-TSS (NM_001081392)	70	NM_001081392	100019	Mm.24627	NM_133874	ENSMUSG00000058006	Mdn1	4833432B22Rik|A130070M06|AA958993|D4Abb1e|Gm135	midasin AAA ATPase 1	protein-coding
mm_144328.1	chr18	12974419	12974437	+	1	NA	intron (NM_008378, intron 1 of 10)	intron (NM_008378, intron 1 of 10)	2176	NM_008378	16210	Mm.8154	NM_008378	ENSMUSG00000024423	Impact	E430016J11Rik	impact, RWD domain protein	protein-coding
mm_112208.1	chr12	113427318	113427330	-	1	NA	Intergenic	Intergenic	-62241	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_152778.1	chr19	21174852	21174860	-	1	NA	Intergenic	Intergenic	70146	NR_126458	75354	Mm.243873	NR_126458		4930554I06Rik	-	RIKEN cDNA 4930554I06 gene	ncRNA
mm_84902.1	chr9	79961962	79961976	-	1	NA	intron (NM_001081243, intron 1 of 5)	intron (NM_001081243, intron 1 of 5)	15913	NM_001081243	70598	Mm.23049	NM_001081243	ENSMUSG00000034898	Filip1	5730485H21Rik|AI843021	filamin A interacting protein 1	protein-coding
mm_18083.1	chr2	44920654	44920678	-	1	NA	Intergenic	Intergenic	-59044	NM_172662	227835	Mm.314312	NM_172662	ENSMUSG00000036890	Gtdc1	E330008O22Rik	glycosyltransferase-like domain containing 1	protein-coding
mm_60912.1	chr7	46795798	46795827	+	1	NA	promoter-TSS (NM_001167864)	promoter-TSS (NM_001167864)	69	NM_001005248	246694	Mm.379442	NM_178742	ENSMUSG00000014418	Hps5	AI646796|AL022647|C85120|haze|hz|maroon|mr|ru-2|ru2	Hermansky-Pudlak syndrome 5	protein-coding
mm_167254.1	chr8	24823980	24823986	-	1	NA	exon (NM_007401, exon 1 of 21)	exon (NM_007401, exon 1 of 21)	386	NM_001272058	11499	Mm.143889	NM_007401	ENSMUSG00000031554	Adam5	tMDC II|tMDCII	a disintegrin and metallopeptidase domain 5	protein-coding
mm_102900.1	chr11	69423992	69424012	-	1	NA	exon (NM_001081330, exon 78 of 86)	exon (NM_001081330, exon 78 of 86)	-10327	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_125316.1	chr15	38219308	38219320	+	1	NA	5' UTR (NM_008757, exon 1 of 2)	5' UTR (NM_008757, exon 1 of 2)	111	NM_008757	18285	Mm.252830	NM_008757	ENSMUSG00000061923	Odf1	-	outer dense fiber of sperm tails 1	protein-coding
mm_114642.1	chr13	76579671	76579678	+	1	NA	intron (NM_030174, intron 1 of 20)	intron (NM_030174, intron 1 of 20)	194713	NM_030174	78771	Mm.316249	NM_030174	ENSMUSG00000021596	Mctp1	2810465F10Rik	multiple C2 domains, transmembrane 1	protein-coding
mm_12875.1	chr2	84650902	84650945	+	1	NA	promoter-TSS (NM_001085449)	promoter-TSS (NM_001085449)	-183	NM_001085448	12388	Mm.35738	NM_007615	ENSMUSG00000034101	Ctnnd1	AA409437|AU019353|Catns|Ctnnd|P120|mKIAA0384	catenin (cadherin associated protein), delta 1	protein-coding
mm_162987.1	chr11	23020282	23020288	+	1	NA	exon (NM_028672, exon 3 of 4)	exon (NM_028672, exon 3 of 4)	6898	NM_028672	73873	Mm.252406	NM_028672	ENSMUSG00000049811	Fam161a	4930430E16Rik	family with sequence similarity 161, member A	protein-coding
mm_155470.1	chrX	73639440	73639442	+	1	NA	promoter-TSS (NM_029352)	promoter-TSS (NM_029352)	0	NM_029352	75590	Mm.16479	NM_029352	ENSMUSG00000031383	Dusp9	Dusp4|Mpk4|Pyst3	dual specificity phosphatase 9	protein-coding
mm_53263.1	chr6	127940273	127940315	+	1	NA	intron (NM_026743, intron 5 of 7)	intron (NM_026743, intron 5 of 7)	52672	NM_026743	68498	Mm.174368	NM_026743	ENSMUSG00000030351	Tspan11	1110014F12Rik|AU067806	tetraspanin 11	protein-coding
mm_57879.1	chr6	131247343	131247367	-	1	NA	promoter-TSS (NM_001170851)	promoter-TSS (NM_001170851)	7	NM_001170851	16633	Mm.4783	NM_008462	ENSMUSG00000030187	Klra2	Klra30|Ly49b	killer cell lectin-like receptor, subfamily A, member 2	protein-coding
mm_157818.1	chrX	74023909	74023917	-	1	NA	promoter-TSS (NM_001177976)	promoter-TSS (NM_001177976)	5	NM_001177975	16179	Mm.38241	NM_008363	ENSMUSG00000031392	Irak1	AA408924|IRAK|IRAK-1|IRAK1-S|IRAK1b|Il1rak|Plpk|mPLK	interleukin-1 receptor-associated kinase 1	protein-coding
mm_154435.1	chrM	836	846	-	1	NA	NA	Intergenic	NA	NA								
mm_77232.1	chr8	115704380	115704391	-	1	NA	3' UTR (NM_001025577, exon 1 of 1)	3' UTR (NM_001025577, exon 1 of 1)	2509	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_150695.1	chr19	42170605	42170631	+	1	NA	promoter-TSS (NM_001164531)	promoter-TSS (NM_001164531)	51	NM_001164531	319740	Mm.287359	NM_177319	ENSMUSG00000018820	Zfyve27	2210011N02Rik|9530077C24Rik|AI426636|AI593546|AI835681	zinc finger, FYVE domain containing 27	protein-coding
mm_77348.1	chr8	119574931	119574970	-	1	NA	promoter-TSS (NM_026648)	promoter-TSS (NM_026648)	250	NM_175185	72552	Mm.36756	NM_175185	ENSMUSG00000034189	Hsdl1	2700067E09Rik	hydroxysteroid dehydrogenase like 1	protein-coding
mm_115541.1	chr13	6648718	6648772	-	1	NA	promoter-TSS (NM_001291071)	promoter-TSS (NM_001291071)	26	NM_019703	56421	Mm.273874	NM_019703	ENSMUSG00000021196	Pfkp	1200015H23Rik|9330125N24Rik|ATP-PFK|PFK-C|PFK-P	phosphofructokinase, platelet	protein-coding
mm_51839.1	chr6	90302143	90302150	+	1	NA	intron (NM_177738, intron 2 of 4)	intron (NM_177738, intron 2 of 4)	876	NM_177738	243535	Mm.233854	NM_177738	ENSMUSG00000049694	BC048671	-	cDNA sequence BC048671	protein-coding
mm_169058.1	chr13	23329799	23329817	-	1	NA	intron (NR_131052, intron 2 of 3)	RLTRETN_Mm|LTR|ERVK	16283	NR_131052	75887	Mm.416957	NR_131052	ENSMUSG00000087097	4930586N03Rik	-	RIKEN cDNA 4930586N03 gene	ncRNA
mm_6280.1	chr1	69683305	69683317	-	1	NA	exon (NM_011770, exon 3 of 8)	exon (NM_011770, exon 3 of 8)	2649	NM_011770	22779	Mm.106343	NM_011770	ENSMUSG00000025997	Ikzf2	A730095J18Rik|Helios|Zfpn1a2|Znfn1a2	IKAROS family zinc finger 2	protein-coding
mm_43004.1	chr5	123489302	123489329	+	1	NA	promoter-TSS (NM_001289821)	promoter-TSS (NM_001289821)	-10	NM_001033461	381741	Mm.297826	NM_001033461	ENSMUSG00000063409	Lrrc43	Gm1061	leucine rich repeat containing 43	protein-coding
mm_126342.1	chr15	79900346	79900363	+	1	NA	intron (NM_001160415, intron 5 of 8)	intron (NM_001160415, intron 5 of 8)	5331	NM_001347041	80287	Mm.284059	NM_030255	ENSMUSG00000009585	Apobec3	Apobec|Arp3|BC003314|Cem15|Rfv3	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 3	protein-coding
mm_168412.1	chr11	3176683	3176686	-	1	NA	intron (NM_030207, intron 6 of 32)	B3|SINE|B2	16779	NM_030207	78887	Mm.394071	NM_030207	ENSMUSG00000023764	Sfi1	-	Sfi1 homolog, spindle assembly associated (yeast)	protein-coding
mm_70628.1	chr8	13705885	13705952	+	1	NA	promoter-TSS (NM_001101519)	promoter-TSS (NM_001101519)	29	NM_001101519	403185	Mm.252143	NM_001101519	ENSMUSG00000090336	4932443I19Rik	A230061C02Rik|Gm1106	RIKEN cDNA 4932443I19 gene	protein-coding
mm_5300.1	chr1	21298221	21298260	-	1	NA	promoter-TSS (NR_002858)	promoter-TSS (NR_002858)	72	NR_002858	241041	Mm.290634	NR_002858	ENSMUSG00000025936	Gm4956	EG241041	predicted gene 4956	pseudo
mm_87979.1	chr10	63800870	63800875	+	1	NA	intron (NM_177612, intron 5 of 17)	intron (NM_177612, intron 5 of 17)	-20183	NM_001164519	216033	Mm.444692	NM_177612	ENSMUSG00000060843	Ctnna3	4930429L08Rik|4933408A16|Catna3|Vr22	catenin (cadherin associated protein), alpha 3	protein-coding
mm_157281.1	chrX	20860926	20860939	-	1	NA	TTS (NM_009703)	TTS (NM_009703)	2250	NR_049190	100885829		NR_049190	ENSMUSG00000093408	Mir5617	Gm25192|mir-5617|mmu-mir-5617	microRNA 5617	ncRNA
mm_36021.1	chr4	56990307	56990329	-	1	NA	promoter-TSS (NM_001142965)	promoter-TSS (NM_001142965)	73	NM_001142965	230235	Mm.207654	NM_001142965	ENSMUSG00000045589	Frrs1l	6430704M03Rik	ferric-chelate reductase 1 like	protein-coding
mm_149637.1	chr19	17394097	17394122	+	1	NA	promoter-TSS (NM_019437)	promoter-TSS (NM_019437)	66	NM_019437	54391	Mm.7013	NM_019437	ENSMUSG00000024712	Rfk	0610038L10Rik|AF031381|KOI-4	riboflavin kinase	protein-coding
mm_133118.1	chr16	65815068	65815087	+	1	NA	promoter-TSS (NM_028572)	promoter-TSS (NM_028572)	-556	NM_028572	73569	Mm.25670	NM_028572	ENSMUSG00000091243	Vgll3	1700110N18Rik|4832416J22|C80713|Vgl-3|Vito-2	vestigial like family member 3	protein-coding
mm_106587.1	chr11	120729720	120729730	-	1	NA	exon (NM_007621, exon 8 of 8)	exon (NM_007621, exon 8 of 8)	2296	NM_007621	12409	Mm.21454	NM_007621	ENSMUSG00000025150	Cbr2	MLCR	carbonyl reductase 2	protein-coding
mm_160646.1	chr9	110115599	110115599	-	1	NA	promoter-TSS (NM_133347)	promoter-TSS (NM_133347)	-17	NM_133347	72831	Mm.276305	NM_133347	ENSMUSG00000032480	Dhx30	2810477H02Rik|C130058C04Rik|Ddx30|HELG|Ret-CoR	DEAH (Asp-Glu-Ala-His) box polypeptide 30	protein-coding
mm_67039.1	chr7	67222413	67222434	-	1	NA	promoter-TSS (NM_175215)	promoter-TSS (NM_175215)	35	NR_131044	76628	Mm.384589	NR_131043	ENSMUSG00000097527	1700112J16Rik	-	RIKEN cDNA 1700112J16 gene	ncRNA
mm_91831.1	chr10	56982131	56982137	-	1	NA	Intergenic	Intergenic	504219	NR_045353	74928	Mm.416643	NR_045353	ENSMUSG00000097370	4930467K11Rik	-	RIKEN cDNA 4930467K11 gene	ncRNA
mm_164494.1	chr16	90747317	90747323	+	1	NA	intron (NM_029844, intron 1 of 2)	intron (NM_029844, intron 1 of 2)	8996	NM_029844	77037	Mm.22455	NM_029844	ENSMUSG00000039956	Mrap	1110025G12Rik|Falp|ORF61	melanocortin 2 receptor accessory protein	protein-coding
mm_110170.1	chr12	27336405	27336439	-	1	NA	3' UTR (NM_009234, exon 1 of 1)	3' UTR (NM_009234, exon 1 of 1)	6296	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding
mm_158270.1	chrX	109623199	109623201	-	1	NA	Intergenic	Intergenic	426444	NM_001037917	622976	Mm.482747	NM_001037917	ENSMUSG00000048621	Gm6377	EG622976	predicted gene 6377	protein-coding
mm_38311.1	chr4	137015130	137015133	-	1	NA	intron (NM_198248, intron 3 of 18)	intron (NM_198248, intron 3 of 18)	33564	NM_198248	230848	Mm.31068	NM_198248	ENSMUSG00000060862	Zbtb40	BC059177|C230087D24|Gm571|mKIAA0478	zinc finger and BTB domain containing 40	protein-coding
mm_119026.1	chr14	30015478	30015496	+	1	NA	intron (NM_001136240, intron 1 of 7)	(T)n|Simple_repeat|Simple_repeat	-5816	NM_172264	218865	Mm.259916	NM_172264	ENSMUSG00000015970	Chdh	AU041472|D630034H06Rik	choline dehydrogenase	protein-coding
mm_21074.1	chr2	152830481	152830495	-	1	NA	5' UTR (NM_001289716, exon 1 of 3)	5' UTR (NM_001289716, exon 1 of 3)	229	NM_001289716	12048	Mm.238213	NM_009743	ENSMUSG00000007659	Bcl2l1	Bcl(X)L|Bcl-XL|Bcl2l|BclX|bcl-x|bcl2-L-1	BCL2-like 1	protein-coding
mm_167757.1	chr9	110422471	110422489	-	1	NA	3' UTR (NM_008694, exon 4 of 4)	3' UTR (NM_008694, exon 4 of 4)	2672	NM_008694	18054	Mm.236225	NM_008694	ENSMUSG00000032484	Ngp	bectenecin	neutrophilic granule protein	protein-coding
mm_80034.1	chr9	68824778	68824792	+	1	NA	intron (NM_013646, intron 1 of 10)	B4|SINE|B4	59439	NR_033299	320440	Mm.483129	NM_177159		9530091C08Rik	-	RIKEN cDNA 9530091C08 gene	ncRNA
mm_19547.1	chr2	98663881	98663891	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	1196229	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_66737.1	chr7	46672385	46672398	-	1	NA	5' UTR (NM_009414, exon 1 of 11)	5' UTR (NM_009414, exon 1 of 11)	146	NM_009414	21990	Mm.248684	NM_009414	ENSMUSG00000040046	Tph1	Tph	tryptophan hydroxylase 1	protein-coding
mm_12427.1	chr2	70563552	70563572	+	1	NA	promoter-TSS (NR_040496)	promoter-TSS (NR_040496)	-205	NR_040496	68986	Mm.437697	NR_040496	ENSMUSG00000087264	Gad1os	1500002O10Rik	glutamate decarboxylase 1, opposite strand	ncRNA
mm_18141.1	chr2	45056794	45056814	-	1	NA	intron (NM_001289521, intron 1 of 8)	intron (NM_001289521, intron 1 of 8)	-33627	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_68854.1	chr7	126369482	126369496	-	1	NA	promoter-TSS (NM_010689)	promoter-TSS (NM_010689)	79	NM_010689	16797	Mm.10280	NM_010689	ENSMUSG00000030742	Lat	p36-38|pp36	linker for activation of T cells	protein-coding
mm_98487.1	chr11	94951244	94951254	+	1	NA	exon (NM_007742, exon 50 of 51)	exon (NM_007742, exon 50 of 51)	15025	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_48096.1	chr5	137062653	137062662	-	1	NA	3' UTR (NM_008871, exon 9 of 9)	3' UTR (NM_008871, exon 9 of 9)	9615	NM_008871	18787	Mm.250422	NM_008871	ENSMUSG00000037411	Serpine1	PAI-1|PAI1|Planh1	serine (or cysteine) peptidase inhibitor, clade E, member 1	protein-coding
mm_113885.1	chr13	49188157	49188167	+	1	NA	intron (NM_013610, intron 1 of 3)	intron (NM_013610, intron 1 of 3)	615	NM_013610	18081	Mm.18503	NM_013610	ENSMUSG00000037966	Ninj1	AU024536	ninjurin 1	protein-coding
mm_66981.1	chr7	63938543	63938632	-	1	NA	5' UTR (NM_021366, exon 1 of 2)	5' UTR (NM_021366, exon 1 of 2)	328	NM_021366	50794	Mm.240473	NM_021366	ENSMUSG00000052040	Klf13	0610043C13Rik|9430029L20Rik|Bteb3|FKLF-2|FKLF2|NSLP1|RFLAT-1|RFLAT1	Kruppel-like factor 13	protein-coding
mm_25906.1	chr3	131112516	131112536	+	1	NA	promoter-TSS (NM_001276403)	promoter-TSS (NM_001276403)	-265	NM_001276403	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_22297.1	chr2	180273489	180273502	-	1	NA	promoter-TSS (NM_145851)	promoter-TSS (NM_145851)	-30	NM_145851	252966	Mm.386884	NM_145851	ENSMUSG00000038990	Cables2	ik3-2	CDK5 and Abl enzyme substrate 2	protein-coding
mm_152551.1	chr19	11393215	11393239	-	1	NA	TTS (NM_001310331)	TTS (NM_001310331)	-14434	NM_029499	64380	Mm.440715	NM_029499	ENSMUSG00000024675	Ms4a4c	5830413L19Rik|AI449185|Ms4a9	membrane-spanning 4-domains, subfamily A, member 4C	protein-coding
mm_87959.1	chr10	63243975	63243986	+	1	NA	5' UTR (NM_026101, exon 1 of 25)	5' UTR (NM_026101, exon 1 of 25)	183	NM_026101	67345	Mm.234437	NM_026101	ENSMUSG00000020064	Herc4	1700056O17Rik|4921531D01Rik|9530080M15Rik|mKIAA1593	hect domain and RLD 4	protein-coding
mm_92355.1	chr10	75921405	75921415	-	1	NA	5' UTR (NM_001161853, exon 1 of 9)	5' UTR (NM_001161853, exon 1 of 9)	204	NM_011418	20587	Mm.279751	NM_011418	ENSMUSG00000000902	Smarcb1	AU020204|Baf47|Ini1|SNF5/INI1|Snf5	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1	protein-coding
mm_74716.1	chr8	17354892	17354900	-	1	NA	intron (NM_053171, intron 1 of 69)	(A)n|Simple_repeat|Simple_repeat	180489	NM_053171	94109	Mm.436988	NM_053171	ENSMUSG00000060924	Csmd1	B930082H09|mKIAA1890	CUB and Sushi multiple domains 1	protein-coding
mm_170781.1	chr2	172509717	172509734	-	1	NA	Intergenic	Intergenic	37171	NM_029608	76426	Mm.46148	NM_029608	ENSMUSG00000027505	Fam209	1700029J11Rik	family with sequence similarity 209	protein-coding
mm_111331.1	chr12	86726440	86726475	-	1	NA	promoter-TSS (NM_144524)	promoter-TSS (NM_144524)	3	NM_144524	68737	Mm.63979	NM_144524	ENSMUSG00000021257	Angel1	1110030H02Rik|mKIAA0759	angel homolog 1	protein-coding
mm_34722.1	chr4	152177946	152177951	+	1	NA	promoter-TSS (NM_133348)	promoter-TSS (NM_133348)	-152	NM_133348	70025	Mm.296191	NM_133348	ENSMUSG00000028937	Acot7	2410041A17Rik|Ach1|Act|Bach|CTE-IIa|Cte-II|Lach1	acyl-CoA thioesterase 7	protein-coding
mm_15649.1	chr2	163122606	163122620	+	1	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	-33012	NM_026630	68236	Mm.33648	NM_026630	ENSMUSG00000070708	Gtsf1l	2410116G06Rik	gametocyte specific factor 1-like	protein-coding
mm_68043.1	chr7	101362814	101362818	-	1	NA	intron (NM_001040111, intron 1 of 33)	intron (NM_001040111, intron 1 of 33)	14747	NM_001040111	69710	Mm.277687	NM_027180	ENSMUSG00000032812	Arap1	2410002L19Rik|Centd2|mKIAA0782	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	protein-coding
mm_26746.1	chr3	7606534	7606550	-	1	NA	intron (NM_008371, intron 1 of 4)	intron (NM_008371, intron 1 of 4)	6351	NM_001313890	16196	Mm.3825	NM_008371	ENSMUSG00000040329	Il7	A630026I06Rik|Il-7|hlb368	interleukin 7	protein-coding
mm_104975.1	chr11	100207655	100207664	-	1	NA	promoter-TSS (NM_016958)	promoter-TSS (NM_016958)	-149	NM_001313956	16664	Mm.439898	NM_016958	ENSMUSG00000045545	Krt14	AI626930|CK-14|K14|Krt-1.14|Krt1-14	keratin 14	protein-coding
mm_152157.1	chr19	7261419	7261450	-	1	NA	Intergenic	Intergenic	-5960	NM_054048	104383	Mm.283859	NM_054048	ENSMUSG00000024968	Rcor2	1A13|AW122124|CoREST|Rcor|Rcor1	REST corepressor 2	protein-coding
mm_116723.1	chr13	51702175	51702194	-	1	NA	3' UTR (NM_001281880, exon 17 of 17)	3' UTR (NM_001281880, exon 17 of 17)	50476	NM_029279	75420	Mm.275981	NM_029279	ENSMUSG00000035139	Secisbp2	2210413N07Rik|2810012K13Rik|SBP2	SECIS binding protein 2	protein-coding
mm_66245.1	chr7	35555835	35555939	-	1	NA	promoter-TSS (NM_033080)	promoter-TSS (NM_033080)	41	NM_033080	110959	Mm.410206	NM_033080	ENSMUSG00000034875	Nudt19	D7Rp2|D7Rp2-r|D7Rp2-s|D7Rp2e|RP2-r|RP2-s	nudix (nucleoside diphosphate linked moiety X)-type motif 19	protein-coding
mm_48303.1	chr5	138272787	138272817	-	1	NA	promoter-TSS (NM_001033416)	promoter-TSS (NM_001033416)	10	NM_001347507	330217	Mm.332774	NM_001033416	ENSMUSG00000075593	Gal3st4	1500031A01Rik	galactose-3-O-sulfotransferase 4	protein-coding
mm_153898.1	chr19	47050824	47050915	-	1	NA	promoter-TSS (NM_027654)	promoter-TSS (NM_027654)	37	NM_027654	71041	Mm.35413	NM_027654	ENSMUSG00000025050	Pcgf6	4933407A11Rik|AI604840|MBLR|Rnf134	polycomb group ring finger 6	protein-coding
mm_26905.1	chr3	19311350	19311378	-	1	NA	promoter-TSS (NM_001122759)	promoter-TSS (NM_001122759)	-42	NM_001122759	18583	Mm.355614	NM_008802	ENSMUSG00000069094	Pde7a	AU015378|AW047537	phosphodiesterase 7A	protein-coding
mm_156591.1	chrX	152194244	152194253	+	1	NA	intron (NM_001005475, intron 2 of 13)	intron (NM_001005475, intron 2 of 13)	15239	NM_001005475	245666	Mm.33027	NM_001005475	ENSMUSG00000041115	Iqsec2	Brag1	IQ motif and Sec7 domain 2	protein-coding
mm_127535.1	chr15	102104348	102104358	+	1	NA	intron (NM_153533, intron 1 of 28)	intron (NM_153533, intron 1 of 28)	1365	NM_153533	209039	Mm.29389	NM_153533	ENSMUSG00000037003	Tns2	C1-ten|Tenc1|nep|nph	tensin 2	protein-coding
mm_140354.1	chr17	86831355	86831373	+	1	NA	3' UTR (NM_010137, exon 16 of 16)	3' UTR (NM_010137, exon 16 of 16)	77500	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_52267.1	chr6	108473034	108473043	+	1	NA	intron (NM_010585, intron 45 of 61)	intron (NM_010585, intron 45 of 61)	-16705	NR_106121	102465766		NR_106121	ENSMUSG00000105697	Mir7661	mmu-mir-7661	microRNA 7661	ncRNA
mm_171533.1	chr4	146750666	146750678	-	1	NA	Intergenic	Intergenic	-203799	NR_045468	67524	Mm.444300	NR_045468	ENSMUSG00000086046	1700095A21Rik	-	RIKEN cDNA 1700095A21 gene	ncRNA
mm_158397.1	chrX	136741434	136741449	-	1	NA	promoter-TSS (NM_001168229)	promoter-TSS (NM_001168229)	-89	NM_001168226	56397	Mm.27218	NM_019768	ENSMUSG00000031422	Morf4l2	2410017O14Rik|Mrgx|Sid393p|mKIAA0026	mortality factor 4 like 2	protein-coding
mm_81908.1	chr9	120002373	120002386	+	1	NA	Intergenic	Intergenic	-17721	NM_153287	215418	Mm.491094	NM_153287	ENSMUSG00000032515	Csrnp1	4931429D10Rik|Axud1|CSRNP-1|URAX1|taip-3	cysteine-serine-rich nuclear protein 1	protein-coding
mm_99414.1	chr11	102284933	102285033	+	1	NA	promoter-TSS (NM_028076)	promoter-TSS (NM_028076)	44	NM_001302505	72053	Mm.101274	NM_028076	ENSMUSG00000034757	Tmub2	2010008E23Rik	transmembrane and ubiquitin-like domain containing 2	protein-coding
mm_140849.1	chr17	23677433	23677456	-	1	NA	promoter-TSS (NM_013749)	promoter-TSS (NM_013749)	5	NM_001161746	27279	Mm.28518	NM_013749	ENSMUSG00000023905	Tnfrsf12a	AI255180|C87282|Fn14|HPIP|TWEAK-R|TweakR	tumor necrosis factor receptor superfamily, member 12a	protein-coding
mm_44357.1	chr5	17795684	17795701	-	1	NA	exon (NM_001159558, exon 12 of 16)	exon (NM_001159558, exon 12 of 16)	40204	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_65445.1	chr7	25395580	25395587	-	1	NA	exon (NM_010719, exon 1 of 10)	exon (NM_010719, exon 1 of 10)	404	NM_010719	16890	Mm.158548	NM_010719	ENSMUSG00000003123	Lipe	4933403G17Rik|HSL	lipase, hormone sensitive	protein-coding
mm_35761.1	chr4	45826964	45826974	-	1	NA	promoter-TSS (NM_018741)	promoter-TSS (NM_018741)	-142	NM_018741	75426	Mm.3919	NM_018741	ENSMUSG00000035551	Igfbpl1	2810011G06Rik|2810453O06Rik|IGFBPL	insulin-like growth factor binding protein-like 1	protein-coding
mm_116042.1	chr13	27245849	27245885	-	1	NA	exon (NM_008865, exon 3 of 5)	exon (NM_008865, exon 3 of 5)	3437	NM_008865	18776	Mm.37203	NM_008865	ENSMUSG00000038891	Prl3b1	Csh2|Ghd8|PL|Pl-2|Pl2|mPL-II|mplII	prolactin family 3, subfamily b, member 1	protein-coding
mm_5420.1	chr1	33907850	33907860	-	1	NA	promoter-TSS (NM_001310484)	promoter-TSS (NM_001310484)	-88	NM_001310484	320705	Mm.336619	NM_177235	ENSMUSG00000042182	Bend6	B230209C24Rik	BEN domain containing 6	protein-coding
mm_133085.1	chr16	62814688	62814703	+	1	NA	promoter-TSS (NM_026588)	promoter-TSS (NM_026588)	19	NM_026588	68159	Mm.386793	NM_026588	ENSMUSG00000047854	Stx19	A030009B12Rik	syntaxin 19	protein-coding
mm_54857.1	chr6	42593998	42594004	-	1	NA	exon (NM_203396, exon 2 of 7)	exon (NM_203396, exon 2 of 7)	3371	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_3101.1	chr1	134432199	134432209	+	1	NA	3' UTR (NM_001306069, exon 8 of 8)	3' UTR (NM_001306069, exon 8 of 8)	16540	NM_001306069	72674	Mm.259976	NM_028320	ENSMUSG00000026457	Adipor1	2810031L11Rik|ACDCR1|CGI-45|Paqr1	adiponectin receptor 1	protein-coding
mm_46895.1	chr5	114091191	114091223	-	1	NA	5' UTR (NM_026805, exon 1 of 16)	5' UTR (NM_026805, exon 1 of 16)	173	NM_026805	68666	Mm.63584	NM_026805	ENSMUSG00000042078	Svop	1110030H18Rik|AI415691|msvop	SV2 related protein	protein-coding
mm_72237.1	chr8	74935739	74935740	+	1	NA	Intergenic	Intergenic	-57911	NM_001316753	70823	Mm.261739	NM_178017	ENSMUSG00000034518	Hmgxb4	4733401K04Rik|AI316803|Hmgb2l1	HMG box domain containing 4	protein-coding
mm_161216.1	chr13	67099272	67099272	-	1	NA	intron (NM_001256052, intron 6 of 6)	intron (NM_001256052, intron 6 of 6)	-1296	NM_001012325	432769	Mm.458849	NM_001012325	ENSMUSG00000058883	Zfp708	Rslcan11	zinc finger protein 708	protein-coding
mm_143520.1	chr17	73399290	73399302	-	1	NA	promoter-TSS (NM_001033444)	promoter-TSS (NM_001033444)	0	NM_001033444	381122	Mm.81496	NM_001033444	ENSMUSG00000043705	Capn13	CANP 13|Gm943	calpain 13	protein-coding
mm_21447.1	chr2	160367941	160367951	-	1	NA	promoter-TSS (NM_010658)	promoter-TSS (NM_010658)	-881	NM_010658	16658	Mm.330745	NM_010658	ENSMUSG00000074622	Mafb	Kreisler|Krml|Krml1|kr	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein B (avian)	protein-coding
mm_84944.1	chr9	82975696	82975732	-	1	NA	promoter-TSS (NM_001081216)	promoter-TSS (NM_001081216)	-225	NM_001081216	83946	Mm.221688	NM_031879	ENSMUSG00000032253	Phip	2810004D21Rik|4632404O06Rik|Ndrp|Wdr11	pleckstrin homology domain interacting protein	protein-coding
mm_149236.1	chr19	10183038	10183048	+	1	NA	5' UTR (NM_146094, exon 1 of 12)	5' UTR (NM_146094, exon 1 of 12)	155	NM_146094	76267	Mm.30158	NM_146094	ENSMUSG00000010663	Fads1	0710001O03Rik|A930006B21Rik|AI317215|DSD	fatty acid desaturase 1	protein-coding
mm_33458.1	chr4	130792308	130792320	+	1	NA	promoter-TSS (NM_011520)	promoter-TSS (NM_011520)	-223	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_163365.1	chr12	33279450	33279450	-	1	NA	Intergenic	Intergenic	-23065	NM_001033436	380753	Mm.41540	NM_028139	ENSMUSG00000020564	Atxn7l1	2810423G08Rik|Atxn7l4	ataxin 7-like 1	protein-coding
mm_173193.1	chrX	62197571	62197571	+	1	NA	Intergenic	L1Md_T|LINE|L1	-85928	NM_001199997	74437	Mm.85792	NM_001199996	ENSMUSG00000045330	4933402E13Rik	-	RIKEN cDNA 4933402E13 gene	protein-coding
mm_10781.1	chr2	24336883	24336893	+	1	NA	promoter-TSS (NM_031167)	promoter-TSS (NM_031167)	28	NM_031167	16181	Mm.882	NM_031167	ENSMUSG00000026981	Il1rn	F630041P17Rik|IL-1ra	interleukin 1 receptor antagonist	protein-coding
mm_88192.1	chr10	70060188	70060194	+	1	NA	Intergenic	Intergenic	-36930	NM_001111121	76551	Mm.281741	NM_001111121	ENSMUSG00000048701	Ccdc6	2810012H18Rik|AA536681|AA960498|AW061011	coiled-coil domain containing 6	protein-coding
mm_102427.1	chr11	59449954	59450035	-	1	NA	promoter-TSS (NM_178659)	promoter-TSS (NM_178659)	-38	NM_144521	67826	Mm.26680	NM_144521	ENSMUSG00000009894	Snap47	1110031B06Rik|SNAP-47	synaptosomal-associated protein, 47	protein-coding
mm_121636.1	chr14	8378701	8378705	-	1	NA	promoter-TSS (NM_146050)	promoter-TSS (NM_146050)	60	NM_146050	18300	Mm.25351	NM_146050	ENSMUSG00000021749	Oit1	2310076N21Rik|AV067083|EF-7|Fam3d	oncoprotein induced transcript 1	protein-coding
mm_122637.1	chr14	51146780	51146790	-	1	NA	promoter-TSS (NM_011271)	promoter-TSS (NM_011271)	-18	NM_011271	19752	Mm.235538	NM_011271	ENSMUSG00000035896	Rnase1	AI574248|Rib-1|Rib1	ribonuclease, RNase A family, 1 (pancreatic)	protein-coding
mm_36510.1	chr4	83486416	83486439	-	1	NA	promoter-TSS (NM_001290527)	promoter-TSS (NM_001290527)	21	NM_001290527	101739	Mm.105331	NM_133948	ENSMUSG00000028484	Psip1	AA408851|AU015605|Dfs70|Ledgfa|Ledgfb|Psip2	PC4 and SFRS1 interacting protein 1	protein-coding
mm_152282.1	chr19	8880884	8880928	-	1	NA	promoter-TSS (NM_001160356)	promoter-TSS (NM_001160356)	27	NM_001160356	107197	Mm.381181	NM_001160356	ENSMUSG00000071654	Uqcc3	AI462493|Cbp4	ubiquinol-cytochrome c reductase complex assembly factor 3	protein-coding
mm_34744.1	chr4	152296167	152296180	+	1	NA	Intergenic	RMER17C2|LTR|ERVK	-1041	NR_037908	57295	Mm.277464	NM_133788	ENSMUSG00000039662	Icmt	1700008E11Rik|C80758|Gm13095|HSTE14|OTTMUSG00000010406|PPMT|STE14|pcCMT	isoprenylcysteine carboxyl methyltransferase	protein-coding
mm_78006.1	chr9	12059894	12059896	+	1	NA	Intergenic	Intergenic	1045960	NR_040755	78219	Mm.414868	NR_040755	ENSMUSG00000111830	4930568E12Rik	-	RIKEN cDNA 4930568E12 gene	ncRNA
mm_52209.1	chr6	101198522	101198545	+	1	NA	intron (NM_018884, intron 3 of 9)	intron (NM_018884, intron 3 of 9)	179364	NM_018884	55983	Mm.321654	NM_018884	ENSMUSG00000035357	Pdzrn3	1110020C07Rik|AI429718|AL023082|LNX3|SEMACAP3|Semcap3	PDZ domain containing RING finger 3	protein-coding
mm_1881.1	chr1	85650045	85650052	+	1	NA	promoter-TSS (NM_013673)	promoter-TSS (NM_013673)	60	NM_001313714	20684	Mm.290906	NM_013673	ENSMUSG00000026222	Sp100	A430075G10Rik	nuclear antigen Sp100	protein-coding
mm_96237.1	chr11	62551722	62551735	+	1	NA	promoter-TSS (NM_001313984)	promoter-TSS (NM_001313984)	-3	NM_001313984	22187	Mm.371592	NM_011664	ENSMUSG00000019505	Ubb	AL033289|Rps27a|Uba52|Ubb2|Ubc	ubiquitin B	protein-coding
mm_60455.1	chr7	44477579	44477599	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-6928	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_166693.1	chr6	113670092	113670096	+	1	NA	intron (NM_172161, intron 3 of 12)	intron (NM_172161, intron 3 of 12)	-26956	NM_001347356	381801	Mm.333322	NM_001033463	ENSMUSG00000056952	Tatdn2	AI646012|mKIAA0218	TatD DNase domain containing 2	protein-coding
mm_3313.1	chr1	137906087	137906097	+	1	NA	Intergenic	Intergenic	-60363	NR_029795	735252		NR_029795	ENSMUSG00000065565	Mir181a-1	Mirn181a-1|Mirn213|miR-213|mir-181a-1|mmu-mir-213	microRNA 181a-1	ncRNA
mm_89223.1	chr10	87205953	87205999	+	1	NA	intron (NM_029685, intron 4 of 5)	intron (NM_029685, intron 4 of 5)	147930	NM_029685	76640	Mm.78423	NM_029685	ENSMUSG00000047129	1700113H08Rik	-	RIKEN cDNA 1700113H08 gene	protein-coding
mm_84816.1	chr9	77544730	77544754	-	1	NA	promoter-TSS (NM_172528)	promoter-TSS (NM_172528)	110	NM_001146048	214345	Mm.28534	NM_172528	ENSMUSG00000032352	Lrrc1	A430093J20Rik|AU016091|D030059I21|mKIAA4018	leucine rich repeat containing 1	protein-coding
mm_139916.1	chr17	70963806	70963818	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	26704	NM_023402	67938	Mm.261329	NM_023402	ENSMUSG00000034868	Myl12b	1500001M02Rik|C77744|Mylc2b|RLC-B	myosin, light chain 12B, regulatory	protein-coding
mm_158408.1	chrX	136868538	136868606	-	1	NA	promoter-TSS (NM_176971)	promoter-TSS (NM_176971)	-32	NM_176971	319642	Mm.44557	NM_176971	ENSMUSG00000043463	Rab9b	9330195C02Rik	RAB9B, member RAS oncogene family	protein-coding
mm_7974.1	chr1	134063356	134063365	-	1	NA	Intergenic	Intergenic	15795	NM_007570	12227	Mm.392646	NM_007570	ENSMUSG00000020423	Btg2	AA959598|APRO1|Pc3|TIS21	B cell translocation gene 2, anti-proliferative	protein-coding
mm_54794.1	chr6	41680731	41680743	-	1	NA	promoter-TSS (NM_001007572)	promoter-TSS (NM_001007572)	-14	NM_001007572	194352	Mm.135734	NM_001007572	ENSMUSG00000036899	Trpv5	CAT2|D630033B11|ECAC1	transient receptor potential cation channel, subfamily V, member 5	protein-coding
mm_5607.1	chr1	39580894	39580904	-	1	NA	Intergenic	Intergenic	-3552	NM_001033135	67702	Mm.28614	NM_001033135	ENSMUSG00000048234	Rnf149	1600023E10Rik|AV037261|C76763|Gm15832|Greul4|OTTMUSG00000026591	ring finger protein 149	protein-coding
mm_48231.1	chr5	137684748	137684757	-	1	NA	promoter-TSS (NM_178162)	promoter-TSS (NM_178162)	1	NM_001303271	231801	Mm.260869	NM_145566	ENSMUSG00000029722	Agfg2	A630095P14Rik|Hrbl|RAB-R|RABR	ArfGAP with FG repeats 2	protein-coding
mm_104335.1	chr11	93997235	93997238	-	1	NA	intron (NM_001199203, intron 1 of 29)	intron (NM_001199203, intron 1 of 29)	1145	NM_027569	70834	Mm.260737	NM_027569	ENSMUSG00000020859	Spag9	3110018C07Rik|4733401I23Rik|4831406C20Rik|AW552012|JLP|JSAP2|JSAP2a|Jip4|Mapk8ip4|syd1	sperm associated antigen 9	protein-coding
mm_110797.1	chr12	72184991	72185033	-	1	NA	promoter-TSS (NM_028687)	promoter-TSS (NM_028687)	17	NM_028687	73936	Mm.475741	NM_028687	ENSMUSG00000021086	Ccdc175	4930403N07Rik	coiled-coil domain containing 175	protein-coding
mm_118295.1	chr13	113079107	113079113	-	1	NA	intron (NM_001281487, intron 7 of 11)	intron (NM_001281487, intron 7 of 11)	21871	NM_010370	14938	Mm.15510	NM_010370	ENSMUSG00000023132	Gzma	AW494114|Ctla-3|Ctla3|Hf|Hf1|SE1|TSP-1|TSP1	granzyme A	protein-coding
mm_45956.1	chr5	90462805	90462834	-	1	NA	exon (NM_009654, exon 3 of 15)	exon (NM_009654, exon 3 of 15)	1949	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_38226.1	chr4	135988076	135988117	-	1	NA	promoter-TSS (NM_025411)	promoter-TSS (NM_025411)	-852	NM_025411	66193	Mm.29131	NM_025411	ENSMUSG00000028669	Pithd1	1110049F12Rik|AA408179|Trp26	PITH (C-terminal proteasome-interacting domain of thioredoxin-like) domain containing 1	protein-coding
mm_37151.1	chr4	117120455	117120469	-	1	NA	non-coding (NR_024078, exon 7 of 7)	non-coding (NR_024078, exon 7 of 7)	5263	NR_024078	78611	Mm.446227	NM_001033187		Btbd19	9530048O09Rik|BB115071	BTB (POZ) domain containing 19	ncRNA
mm_56065.1	chr6	86783523	86783537	-	1	NA	intron (NM_013471, intron 1 of 12)	B2_Mm1a|SINE|B2	-8416	NM_001331120	11746	Mm.259702	NM_013471	ENSMUSG00000029994	Anxa4	AI265406|AIV|AW106930|Anx4|Xanx-4	annexin A4	protein-coding
mm_113478.1	chr13	36857568	36857577	+	1	NA	Intergenic	RMER19C|LTR|ERVK	-123095	NM_153529	68404	Mm.232930	NM_153529	ENSMUSG00000039114	Nrn1	0710008J23Rik|Cpg15|Nrn	neuritin 1	protein-coding
mm_123940.1	chr14	73370709	73370726	-	1	NA	intron (NM_008410, intron 1 of 5)	intron (NM_008410, intron 1 of 5)	14554	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_3602.1	chr1	151572242	151572245	+	1	NA	intron (NM_022018, intron 1 of 13)	intron (NM_022018, intron 1 of 13)	870	NM_022018	63913	Mm.157700	NM_022018	ENSMUSG00000026483	Fam129a	AI256368|AU019833|Niban	family with sequence similarity 129, member A	protein-coding
mm_155848.1	chrX	101274049	101274057	+	1	NA	promoter-TSS (NM_021521)	promoter-TSS (NM_021521)	-38	NM_021521	59024	Mm.20873	NM_021521	ENSMUSG00000079487	Med12	230kDa|Mopa|OPA-1|Tnrc11|Trap230	mediator complex subunit 12	protein-coding
mm_13863.1	chr2	119742307	119742331	+	1	NA	promoter-TSS (NM_146125)	promoter-TSS (NM_146125)	-18	NM_146125	228550	Mm.65337	NM_146125	ENSMUSG00000027296	Itpka	-	inositol 1,4,5-trisphosphate 3-kinase A	protein-coding
mm_13639.1	chr2	114048122	114048164	+	1	NA	exon (NM_009608, exon 6 of 7)	exon (NM_009608, exon 6 of 7)	4732	NM_009608	11464	Mm.686	NM_009608	ENSMUSG00000068614	Actc1	Actc-1	actin, alpha, cardiac muscle 1	protein-coding
mm_90854.1	chr10	8814426	8814461	-	1	NA	exon (NM_175155, exon 3 of 20)	exon (NM_175155, exon 3 of 20)	71627	NM_175155	70097	Mm.338275	NM_175155	ENSMUSG00000015305	Sash1	1100001C18Rik|2500002E12Rik|A330076K04Rik|mKIAA0790	SAM and SH3 domain containing 1	protein-coding
mm_148008.1	chr18	68214509	68214521	-	1	NA	intron (NM_172631, intron 3 of 5)	B1F|SINE|Alu	46458	NR_106078	102465702		NR_106078	ENSMUSG00000098253	Mir7219	Gm27613|mmu-mir-7219	microRNA 7219	ncRNA
mm_109907.1	chr12	8302007	8302018	-	1	NA	promoter-TSS (NM_013527)	promoter-TSS (NM_013527)	-58	NM_013527	238057	Mm.271308	NM_013527	ENSMUSG00000037660	Gdf7	BMP12	growth differentiation factor 7	protein-coding
mm_167344.1	chr8	79028352	79028366	+	1	NA	promoter-TSS (NM_178267)	promoter-TSS (NM_178267)	-78	NM_001294279	622675	Mm.48724	NM_178267	ENSMUSG00000071064	Zfp827	2810449M09Rik|D630040G17Rik|Znf827	zinc finger protein 827	protein-coding
mm_171321.1	chr3	96328417	96328422	+	1	NA	Intergenic	Intergenic	-34450	NM_010186	14129	Mm.150	NM_010186	ENSMUSG00000015947	Fcgr1	AI323638|AV092959|CD64|FcgammaRI|IGGHAFC	Fc receptor, IgG, high affinity I	protein-coding
mm_18787.1	chr2	73660402	73660410	-	1	NA	promoter-TSS (NM_175752)	promoter-TSS (NM_175752)	17	NM_175752	108699	Mm.257073	NM_029716	ENSMUSG00000056486	Chn1	0610007I19Rik|0710001E19Rik|1700112L09Rik|2900046J01Rik|AI413815|ARHGAP2	chimerin 1	protein-coding
mm_22225.1	chr2	174428661	174428682	-	1	NA	exon (NM_022325, exon 5 of 6)	exon (NM_022325, exon 5 of 6)	10368	NM_022325	64138	Mm.156919	NM_022325	ENSMUSG00000016256	Ctsz	AI787083|AU019819|CTSX|D2Wsu143e	cathepsin Z	protein-coding
mm_105517.1	chr11	106272707	106272814	-	1	NA	5' UTR (NM_001130187, exon 1 of 13)	5' UTR (NM_001130187, exon 1 of 13)	212	NM_001130187	83796	Mm.21772	NM_031878	ENSMUSG00000078619	Smarcd2	AW322457|Baf60b	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2	protein-coding
mm_167031.1	chr7	70354203	70354219	-	1	NA	3' UTR (NM_183261, exon 3 of 3)	3' UTR (NM_183261, exon 3 of 3)	6382	NM_009697	11819	Mm.158143	NM_009697	ENSMUSG00000030551	Nr2f2	2700033K02Rik|9430015G03Rik|ARP-1|Aporp1|COUP-TF2|COUP-TFII|COUPTFB|EAR3|SVP40|Tcfcoup2	nuclear receptor subfamily 2, group F, member 2	protein-coding
mm_60492.1	chr7	44478679	44478685	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-5835	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_15279.1	chr2	155276340	155276350	+	1	NA	promoter-TSS (NR_046364)	promoter-TSS (NR_046364)	-19	NM_025735	66734	Mm.196239	NM_025735	ENSMUSG00000027602	Map1lc3a	1010001H21Rik|4922501H04Rik|LC3|LC3a	microtubule-associated protein 1 light chain 3 alpha	protein-coding
mm_28311.1	chr3	89245160	89245193	-	1	NA	promoter-TSS (NM_001039466)	promoter-TSS (NM_001039466)	23	NM_001039466	360213	Mm.331156	NM_183037	ENSMUSG00000042766	Trim46	TRIFIC	tripartite motif-containing 46	protein-coding
mm_114082.1	chr13	54577903	54577918	+	1	NA	intron (NM_019968, intron 2 of 3)	L2b|LINE|L2	2897	NM_019968	56795	Mm.89484	NM_019968	ENSMUSG00000025870	Arl10	Arl10a|Arm1	ADP-ribosylation factor-like 10	protein-coding
mm_87171.1	chr10	37315386	37315390	+	1	NA	Intergenic	Intergenic	-176462	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_42485.1	chr5	115470889	115470917	+	1	NA	exon (NM_011107, exon 2 of 4)	exon (NM_011107, exon 2 of 4)	4637	NM_011107	18778	Mm.20190	NM_011107	ENSMUSG00000029522	Pla2g1b	Pla2a|sPLA2IB	phospholipase A2, group IB, pancreas	protein-coding
mm_55599.1	chr6	71633341	71633368	-	1	NA	promoter-TSS (NM_173001)	promoter-TSS (NM_173001)	-437	NM_001038695	104263	Mm.260479	NM_173001	ENSMUSG00000053470	Kdm3a	1700105C21Rik|C230043E16Rik|JHDM2a|Jmjd1|Jmjd1a|KDM2A|TGSA|Tsga	lysine (K)-specific demethylase 3A	protein-coding
mm_97771.1	chr11	82057846	82057856	+	1	NA	promoter-TSS (NM_011330)	promoter-TSS (NM_011330)	19	NM_011330	20292	Mm.4686	NM_011330	ENSMUSG00000020676	Ccl11	Scya11|eotaxin	chemokine (C-C motif) ligand 11	protein-coding
mm_160911.1	chr11	82911798	82911798	+	1	NA	exon (NM_178680, exon 2 of 20)	exon (NM_178680, exon 2 of 20)	545	NM_178680	217012	Mm.295205	NM_178680	ENSMUSG00000018845	Unc45b	AA445617|Cmya4|D230041A13Rik|Unc45	unc-45 myosin chaperone B	protein-coding
mm_123620.1	chr14	68120974	68120985	-	1	NA	exon (NM_008691, exon 3 of 3)	exon (NM_008691, exon 3 of 3)	-2773	NR_045897	100043072	Mm.242832	NR_045897		A230070E04Rik	Gm4210	RIKEN cDNA A230070E04 gene	ncRNA
mm_51004.1	chr6	63746564	63746566	+	1	NA	intron (NM_008167, intron 2 of 15)	intron (NM_008167, intron 2 of 15)	489708	NM_008167	14804	Mm.439651	NM_008167	ENSMUSG00000071424	Grid2	B230104L07Rik|GluD2|GluRdelta2|Lc|Lc<J>|MMS10-AC|Ms10ac|cpr|ho|nmf408|tpr	glutamate receptor, ionotropic, delta 2	protein-coding
mm_63731.1	chr7	130867518	130867523	+	1	NA	intron (NM_001346515, intron 1 of 12)	intron (NM_001346515, intron 1 of 12)	1610	NM_133942	101476	Mm.323554	NM_133942	ENSMUSG00000040268	Plekha1	AA960558|C920009D07Rik|TAPP1	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 1	protein-coding
mm_135051.1	chr16	33380718	33380755	-	1	NA	promoter-TSS (NM_011749)	promoter-TSS (NM_011749)	0	NR_045709	100502742	Mm.217880	NR_045709	ENSMUSG00000097318	1700007L15Rik	linc-Iqcg|linc1609	RIKEN cDNA 1700007L15 gene	ncRNA
mm_84131.1	chr9	59036281	59036293	-	1	NA	5' UTR (NM_008684, exon 1 of 29)	5' UTR (NM_008684, exon 1 of 29)	154	NM_008684	18007	Mm.42249	NM_008684	ENSMUSG00000032340	Neo1	2610028H22Rik|AI327052|D930014N22Rik|Igdcc2	neogenin	protein-coding
mm_68803.1	chr7	125491415	125491458	-	1	NA	exon (NM_026330, exon 1 of 8)	exon (NM_026330, exon 1 of 8)	106	NM_026330	67711	Mm.4467	NM_026330	ENSMUSG00000030750	Nsmce1	2510027N19Rik	NSE1 homolog, SMC5-SMC6 complex component	protein-coding
mm_12025.1	chr2	58160188	58160199	+	1	NA	promoter-TSS (NM_139200)	promoter-TSS (NM_139200)	-71	NM_139200	227929	Mm.273905	NM_139200	ENSMUSG00000026832	Cytip	A130053M09Rik|AI462064|C80816|Cbp|Cybr|Pscdbp	cytohesin 1 interacting protein	protein-coding
mm_34721.1	chr4	152177813	152177827	+	1	NA	promoter-TSS (NM_133348)	promoter-TSS (NM_133348)	-280	NM_133348	70025	Mm.296191	NM_133348	ENSMUSG00000028937	Acot7	2410041A17Rik|Ach1|Act|Bach|CTE-IIa|Cte-II|Lach1	acyl-CoA thioesterase 7	protein-coding
mm_144876.1	chr18	36760215	36760292	+	1	NA	promoter-TSS (NM_026464)	promoter-TSS (NM_026464)	14	NM_026464	67936	Mm.271719	NM_026464	ENSMUSG00000042660	Wdr55	2410080P20Rik|C80692	WD repeat domain 55	protein-coding
mm_171532.1	chr4	146750610	146750621	-	1	NA	Intergenic	Intergenic	-203742	NR_045468	67524	Mm.444300	NR_045468	ENSMUSG00000086046	1700095A21Rik	-	RIKEN cDNA 1700095A21 gene	ncRNA
mm_11965.1	chr2	53192102	53192128	+	1	NA	promoter-TSS (NM_018785)	promoter-TSS (NM_018785)	31	NM_022989	65103	Mm.37623	NM_022989	ENSMUSG00000026960	Arl6ip6	2310057C01Rik|2610529A11Rik|Aip-6	ADP-ribosylation factor-like 6 interacting protein 6	protein-coding
mm_100163.1	chr11	116434195	116434227	+	1	NA	promoter-TSS (NR_003376)	promoter-TSS (NR_003376)	-2	NR_003376	664849	Mm.258466	NR_003376		Gm7367	EG664849	1110014K08Rik pseudogene	pseudo
mm_7920.1	chr1	133800976	133800986	-	1	NA	Intergenic	Intergenic	-47234	NM_213616	381290	Mm.188617	NM_213616	ENSMUSG00000026463	Atp2b4	Pmca4	ATPase, Ca++ transporting, plasma membrane 4	protein-coding
mm_103631.1	chr11	78945252	78945300	-	1	NA	exon (NM_010927, exon 13 of 27)	exon (NM_010927, exon 13 of 27)	19985	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_60945.1	chr7	46983594	46983658	+	1	NA	non-coding (NR_033461, exon 2 of 5)	non-coding (NR_033461, exon 2 of 5)	6994	NR_033461	629141	Mm.229259	NR_033461	ENSMUSG00000056509	Gm9999	ENSMUSG00000056509	predicted gene 9999	ncRNA
mm_33349.1	chr4	129336017	129336041	+	1	NA	promoter-TSS (NM_009030)	promoter-TSS (NM_009030)	3	NM_025970	67106	Mm.36575	NM_025970	ENSMUSG00000057572	Zbtb8os	2010001H09Rik|2310028N13Rik|AI851226|Arch|Archm	zinc finger and BTB domain containing 8 opposite strand	protein-coding
mm_148672.1	chr19	5637737	5637766	+	1	NA	5' UTR (NM_009045, exon 1 of 11)	5' UTR (NM_009045, exon 1 of 11)	261	NM_009045	19697	Mm.249966	NM_009045	ENSMUSG00000024927	Rela	p65	v-rel reticuloendotheliosis viral oncogene homolog A (avian)	protein-coding
mm_101155.1	chr11	16972229	16972250	-	1	NA	3' UTR (NM_019549, exon 10 of 10)	3' UTR (NM_019549, exon 10 of 10)	20829	NM_176982	319701	Mm.120672	NM_176982	ENSMUSG00000044966	Fbxo48	A630050E13Rik	F-box protein 48	protein-coding
mm_72658.1	chr8	84856983	84857036	+	1	NA	promoter-TSS (NM_025648)	promoter-TSS (NM_025648)	23	NM_025648	66590	Mm.292517	NM_025648	ENSMUSG00000003808	Farsa	0610012A19Rik|Farsla	phenylalanyl-tRNA synthetase, alpha subunit	protein-coding
mm_156525.1	chrX	150594421	150594446	+	1	NA	intron (NM_008824, intron 1 of 13)	intron (NM_008824, intron 1 of 13)	4512	NM_008824	18639	Mm.249131	NM_008824	ENSMUSG00000025271	Pfkfb1	PFK/FBPase 1	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1	protein-coding
mm_146579.1	chr18	7583782	7583788	-	1	NA	intron (NM_001081287, intron 1 of 16)	LTRIS2|LTR|ERV1	43078	NM_001081287	75739	Mm.133293	NM_001081287	ENSMUSG00000057440	Mpp7	1110068J02Rik|2810038M04Rik|5430426E14Rik|AI415104|Gm955	membrane protein, palmitoylated 7 (MAGUK p55 subfamily member 7)	protein-coding
mm_164961.1	chr19	5800164	5800173	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	2504	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_102841.1	chr11	69364497	69364510	-	1	NA	intron (NM_146019, intron 2 of 39)	intron (NM_146019, intron 2 of 39)	4923	NM_146019	216848	Mm.178246	NM_146019	ENSMUSG00000018474	Chd3	2600010P09Rik|AF020312|Chd7|Prp7|Prp9-1	chromodomain helicase DNA binding protein 3	protein-coding
mm_94834.1	chr11	23497797	23497807	+	1	NA	exon (NM_172391, exon 1 of 9)	exon (NM_172391, exon 1 of 9)	237	NM_001290655	268390	Mm.13148	NM_172391	ENSMUSG00000020288	Ahsa2	-	AHA1, activator of heat shock protein ATPase 2	protein-coding
mm_76902.1	chr8	105827594	105827604	-	1	NA	promoter-TSS (NM_024445)	promoter-TSS (NM_024445)	-145	NM_024445	72236	Mm.386810	NM_024445	ENSMUSG00000031893	Tsnaxip1	1700016K08Rik|TXI1	translin-associated factor X (Tsnax) interacting protein 1	protein-coding
mm_145992.1	chr18	68337505	68337517	+	1	NA	promoter-TSS (NM_013596)	promoter-TSS (NM_013596)	-92	NM_013596	17203	Mm.8003	NM_013596	ENSMUSG00000007480	Mc5r	-	melanocortin 5 receptor	protein-coding
mm_74140.1	chr8	123235087	123235096	+	1	NA	promoter-TSS (NR_045849)	promoter-TSS (NR_045849)	0	NR_045849	71186	Mm.449984	NR_045849	ENSMUSG00000097637	4933417D19Rik	-	RIKEN cDNA 4933417D19 gene	ncRNA
mm_168137.1	chr10	29699373	29699379	-	1	NA	Intergenic	Lx6|LINE|L1	-163509	NM_028351	72780	Mm.45191	NM_028351	ENSMUSG00000019880	Rspo3	2810459H04Rik|AW742308|Cristin1|Thsd2	R-spondin 3	protein-coding
mm_105301.1	chr11	102556123	102556171	-	1	NA	promoter-TSS (NM_001159492)	promoter-TSS (NM_001159492)	11	NM_001159492	237943	Mm.260282	NM_001159492	ENSMUSG00000034621	Gpatch8	5430405G24Rik|AU018890|ENSMUSG00000075516|Fbm1|Gpatc8|mKIAA0553	G patch domain containing 8	protein-coding
mm_105261.1	chr11	102356890	102356911	-	1	NA	exon (NM_011403, exon 11 of 20)	exon (NM_011403, exon 11 of 20)	8381	NM_011403	20533	Mm.7248	NM_011403	ENSMUSG00000006574	Slc4a1	Ae1|CD233|Empb3|l11Jus51	solute carrier family 4 (anion exchanger), member 1	protein-coding
mm_3259.1	chr1	136259398	136259425	+	1	NA	3' UTR (NM_001101516, exon 1 of 1)	3' UTR (NM_001101516, exon 1 of 1)	1462	NM_001101516	383563	Mm.40367	NM_001101516	ENSMUSG00000052759	Gpr25	Gm1300	G protein-coupled receptor 25	protein-coding
mm_160761.1	chr10	89660113	89660113	-	1	NA	intron (NM_198021, intron 6 of 17)	intron (NM_198021, intron 6 of 17)	26172	NM_198021	213326	Mm.27651	NM_198021	ENSMUSG00000069539	Scyl2	AU015688|AW536445|BC030932|CVAK104|D10Ertd802e	SCY1-like 2 (S. cerevisiae)	protein-coding
mm_97288.1	chr11	76216339	76216342	+	1	NA	intron (NM_177367, intron 1 of 1)	intron (NM_177367, intron 1 of 1)	1232	NM_177367	276919	Mm.482713	NM_177367	ENSMUSG00000049396	Gemin4	4932415L08Rik|AU015359	gem (nuclear organelle) associated protein 4	protein-coding
mm_78173.1	chr9	21136750	21136769	+	1	NA	Intergenic	RSINE1|SINE|B4	-5484	NM_001205312	54721	Mm.20249	NM_018793	ENSMUSG00000032175	Tyk2	JTK1	tyrosine kinase 2	protein-coding
mm_169138.1	chr13	61532497	61532510	-	1	NA	Intergenic	Intergenic	9336	NM_022326	64139	Mm.279933	NM_022326	ENSMUSG00000074871	Ctsm	1600027J17Rik|AI324100|Catm	cathepsin M	protein-coding
mm_4764.1	chr1	182458602	182458612	+	1	NA	intron (NM_173378, intron 16 of 17)	intron (NM_173378, intron 16 of 17)	49440	NM_173378	209456	Mm.287450	NM_173378	ENSMUSG00000026510	Trp53bp2	53BP2|AI746547|ASPP2|PPP1R13A|Tp53bp2|X98550	transformation related protein 53 binding protein 2	protein-coding
mm_118075.1	chr13	103038776	103038781	-	1	NA	intron (NM_175171, intron 3 of 28)	B3|SINE|B2	278523	NR_130171	76624	Mm.426384	NR_130171	ENSMUSG00000091906	1700099I09Rik	-	RIKEN cDNA 1700099I09 gene	ncRNA
mm_101631.1	chr11	36271868	36271869	-	1	NA	intron (NM_011856, intron 5 of 28)	intron (NM_011856, intron 5 of 28)	-291779	NM_170779	211652	Mm.31267	NM_170779	ENSMUSG00000018849	Wwc1	AA408228|AU017197|BC037006|Kibra|mKIAA0869	WW, C2 and coiled-coil domain containing 1	protein-coding
mm_156943.1	chrX	169979049	169979091	+	1	NA	promoter-TSS (NR_029457)	promoter-TSS (NR_029457)	-153	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_141037.1	chr17	25273563	25273638	-	1	NA	promoter-TSS (NR_027452)	promoter-TSS (NR_027452)	-169	NM_001177610	22196	Mm.240044	NM_011665	ENSMUSG00000015120	Ube2i	5830467E05Rik|F830028O17Rik|UBC9|Ubce2i|Ubce9	ubiquitin-conjugating enzyme E2I	protein-coding
mm_12885.1	chr2	84742922	84742939	+	1	NA	Intergenic	Intergenic	-1752	NR_029544	387149		NR_029544	ENSMUSG00000065484	Mir130a	Mirn130|Mirn130a|mir-130a	microRNA 130a	ncRNA
mm_98121.1	chr11	87127173	87127264	+	1	NA	5' UTR (NM_197987, exon 1 of 24)	5' UTR (NM_197987, exon 1 of 24)	143	NM_197987	68729	Mm.17436	NM_197987	ENSMUSG00000018548	Trim37	1110032A10Rik|2810004E07Rik|AI848587|AU043018|MUL|TEF3|mKIAA0898	tripartite motif-containing 37	protein-coding
mm_148017.1	chr18	68429236	68429258	-	1	NA	promoter-TSS (NM_001271716)	promoter-TSS (NM_001271716)	73	NM_001301372	17200	Mm.426053	NM_008560	ENSMUSG00000045569	Mc2r	ACTH-R|ACTHR|MC2-R	melanocortin 2 receptor	protein-coding
mm_145163.1	chr18	46630909	46630914	+	1	NA	Intergenic	Intergenic	33207	NM_010120	13664	Mm.262037	NM_010120	ENSMUSG00000057561	Eif1a	C76390|Ef1a|Eftu|Eif4c|eIF-1A|eIF-4C	eukaryotic translation initiation factor 1A	protein-coding
mm_5891.1	chr1	54396946	54396951	-	1	NA	3' UTR (NM_001033194, exon 18 of 18)	3' UTR (NM_001033194, exon 18 of 18)	42078	NM_001033194	98488	Mm.25856	NM_001033194	ENSMUSG00000041303	Gtf3c3	TF3C-gamma|TFIIIC102	general transcription factor IIIC, polypeptide 3	protein-coding
mm_15704.1	chr2	163995236	163995246	+	1	NA	promoter-TSS (NM_018753)	promoter-TSS (NM_018753)	44	NM_018753	54401	Mm.34319	NM_018753	ENSMUSG00000018326	Ywhab	1300003C17Rik|14-3-3b	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta polypeptide	protein-coding
mm_63683.1	chr7	130553014	130553028	+	1	NA	Intergenic	Intergenic	-5640	NM_001162855	67872	Mm.21714	NM_001162855	ENSMUSG00000040331	Nsmce4a	2410003A14Rik	NSE4 homolog A, SMC5-SMC6 complex component	protein-coding
mm_95587.1	chr11	53300807	53300832	+	1	NA	promoter-TSS (NM_008300)	promoter-TSS (NM_008300)	-340	NM_008300	15525	Mm.239865	NM_008300	ENSMUSG00000020361	Hspa4	70kDa|AI317151|APG-2|Hsp110|Hsp70RY|mKIAA4025	heat shock protein 4	protein-coding
mm_84009.1	chr9	57645155	57645180	-	1	NA	5' UTR (NM_007783, exon 1 of 13)	5' UTR (NM_007783, exon 1 of 13)	486	NM_007783	12988	Mm.21974	NM_007783	ENSMUSG00000032312	Csk	AW212630|p50CSK	c-src tyrosine kinase	protein-coding
mm_93798.1	chr10	120898523	120898534	-	1	NA	intron (NM_177092, intron 1 of 6)	CpG	443	NM_177092	320183	Mm.169755	NM_177092	ENSMUSG00000051236	Msrb3	D430026P16Rik|I-8-23|MsrB2	methionine sulfoxide reductase B3	protein-coding
mm_149541.1	chr19	12564493	12564508	+	1	NA	Intergenic	Intergenic	-9010	NM_001346545	107373	Mm.1643	NM_026640	ENSMUSG00000024691	Fam111a	4632417K18Rik|AW413625	family with sequence similarity 111, member A	protein-coding
mm_141336.1	chr17	28510042	28510050	-	1	NA	Intergenic	Intergenic	-20815	NM_026290	67645	Mm.46170	NM_026290	ENSMUSG00000024223	Armc12	4930511I11Rik|AV041658	armadillo repeat containing 12	protein-coding
mm_40327.1	chr5	43910526	43910531	+	1	NA	3' UTR (NM_007646, exon 8 of 8)	3' UTR (NM_007646, exon 8 of 8)	41719	NM_007646	12494	Mm.249873	NM_007646	ENSMUSG00000029084	Cd38	ADPRC 1|Cd38-rs1|I-19	CD38 antigen	protein-coding
mm_102437.1	chr11	59506527	59506597	-	1	NA	promoter-TSS (NM_001130529)	promoter-TSS (NM_001130529)	78	NM_001291014	268417	Mm.239793	NM_172941	ENSMUSG00000020472	Zkscan17	Nizp1|Zfp496|Znf496	zinc finger with KRAB and SCAN domains 17	protein-coding
mm_29157.1	chr3	106032880	106032888	-	1	NA	promoter-TSS (NM_001080816)	promoter-TSS (NM_001080816)	11	NM_001080816	229687	Mm.39224	NM_170594	ENSMUSG00000043873	Chil5	Bclp|Bclp1|Bclp2|Chi3l7	chitinase-like 5	protein-coding
mm_15321.1	chr2	155750780	155750794	+	1	NA	promoter-TSS (NM_011171)	promoter-TSS (NM_011171)	-430	NM_011171	19124	Mm.3243	NM_011171	ENSMUSG00000027611	Procr	AI325044|Ccca|Ccd41|Epcr	protein C receptor, endothelial	protein-coding
mm_170933.1	chr2	46297062	46297063	-	1	NA	Intergenic	Intergenic	600457	NR_040497	69405	Mm.396184	NR_040497	ENSMUSG00000086202	1700019E08Rik	-	RIKEN cDNA 1700019E08 gene	ncRNA
mm_14274.1	chr2	128729292	128729305	+	1	NA	exon (NM_008587, exon 2 of 19)	exon (NM_008587, exon 2 of 19)	30301	NM_008587	17289	Mm.239655	NM_008587	ENSMUSG00000014361	Mertk	Eyk|Mer|Nyk|nmf12	c-mer proto-oncogene tyrosine kinase	protein-coding
mm_50463.1	chr6	48929892	48929897	+	1	NA	promoter-TSS (NM_001081273)	promoter-TSS (NM_001081273)	-2	NM_001081273	69761	Mm.333053	NM_001081273	ENSMUSG00000029813	1600015I10Rik	AI429442|Doxl1	RIKEN cDNA 1600015I10 gene	protein-coding
mm_38007.1	chr4	133722991	133723030	-	1	NA	exon (NM_001080819, exon 2 of 20)	exon (NM_001080819, exon 2 of 20)	-5902	NR_106086	102465707		NR_106086	ENSMUSG00000104566	Mir7227	mmu-mir-7227	microRNA 7227	ncRNA
mm_105886.1	chr11	114930720	114930730	-	1	NA	intron (NM_199221, intron 1 of 3)	intron (NM_199221, intron 1 of 3)	3661	NM_001347651	217304	Mm.185355	NM_199221	ENSMUSG00000063193	Cd300lb	CLM-7|Clm7|Gm253|LMIR5	CD300 molecule like family member B	protein-coding
mm_124111.1	chr14	79470134	79470174	-	1	NA	exon (NM_018765, exon 7 of 10)	exon (NM_018765, exon 7 of 10)	-11040	NM_007920	13709	Mm.20938	NM_007920	ENSMUSG00000036461	Elf1	Elf-1|Sts1|mElf-1|p70	E74-like factor 1	protein-coding
mm_123614.1	chr14	68120710	68120727	-	1	NA	exon (NM_008691, exon 3 of 3)	exon (NM_008691, exon 3 of 3)	-3034	NR_045897	100043072	Mm.242832	NR_045897		A230070E04Rik	Gm4210	RIKEN cDNA A230070E04 gene	ncRNA
mm_123016.1	chr14	55107137	55107150	-	1	NA	promoter-TSS (NM_007455)	promoter-TSS (NM_007455)	-550	NM_007455	11766	Mm.238879	NM_007455	ENSMUSG00000040701	Ap1g2	Adtg2|G2ad	adaptor protein complex AP-1, gamma 2 subunit	protein-coding
mm_170743.1	chr2	154892808	154892823	-	1	NA	promoter-TSS (NM_026030)	promoter-TSS (NM_026030)	91	NM_026030	67204	Mm.377134	NM_026030	ENSMUSG00000074656	Eif2s2	2810026E11Rik|38kDa|AA408636|AA571381|AA986487|AW822225|D2Ertd303e|EIF2|EIF2B	eukaryotic translation initiation factor 2, subunit 2 (beta)	protein-coding
mm_145549.1	chr18	60809023	60809066	+	1	NA	exon (NM_010545, exon 4 of 8)	exon (NM_010545, exon 4 of 8)	-3032	NR_039567	100628611		NR_039567	ENSMUSG00000093327	Mir5107	mir-5107|mmu-mir-5107|mu-mir-5107	microRNA 5107	ncRNA
mm_62155.1	chr7	97139944	97139993	+	1	NA	intron (NM_001162477, intron 1 of 9)	(TG)n|Simple_repeat|Simple_repeat	58217	NM_010248	14389	Mm.42033	NM_010248	ENSMUSG00000004508	Gab2	AI463667|D130058I17Rik|p97	growth factor receptor bound protein 2-associated protein 2	protein-coding
mm_152773.1	chr19	21170865	21170869	-	1	NA	Intergenic	Intergenic	66157	NR_126458	75354	Mm.243873	NR_126458		4930554I06Rik	-	RIKEN cDNA 4930554I06 gene	ncRNA
mm_125126.1	chr15	30172978	30173000	+	1	NA	5' UTR (NM_008729, exon 1 of 23)	5' UTR (NM_008729, exon 1 of 23)	396	NM_008729	18163	Mm.321648	NM_008729	ENSMUSG00000022240	Ctnnd2	Catnd2|Nprap|neurojugin	catenin (cadherin associated protein), delta 2	protein-coding
mm_98176.1	chr11	87756790	87756826	+	1	NA	promoter-TSS (NR_029555)	promoter-TSS (NR_029555)	-56	NR_029555	387160		NR_029555	ENSMUSG00000105196	Mir142	Mirn142|miR-142|mir-142a|mmu-mir-142|mmu-mir-142a	microRNA 142	ncRNA
mm_154469.1	chrM	3713	3736	-	1	NA	NA	Intergenic	NA	NA								
mm_68053.1	chr7	101620645	101620648	-	1	NA	Intergenic	Intergenic	-39485	NM_019915	11872	Mm.57008	NM_019915	ENSMUSG00000030651	Art2b	ART2.2|ARTC2|Art|Ly92b|Rt-6|Rt6|Rt6-2	ADP-ribosyltransferase 2b	protein-coding
mm_136827.1	chr17	12614708	12614716	+	1	NA	intron (NM_013667, intron 7 of 10)	intron (NM_013667, intron 7 of 10)	30523	NM_013667	20518	Mm.17322	NM_013667	ENSMUSG00000040966	Slc22a2	Oct2|Orct2	solute carrier family 22 (organic cation transporter), member 2	protein-coding
mm_169568.1	chr15	18144489	18144491	-	1	NA	intron (NR_045711, intron 9 of 11)	ORR1A0|LTR|ERVL-MaLR	225137	NR_045711	70886	Mm.399021	NR_045711		4921515E04Rik	-	RIKEN cDNA 4921515E04 gene	ncRNA
mm_39817.1	chr5	30711850	30711905	+	1	NA	promoter-TSS (NM_023047)	promoter-TSS (NM_023047)	-18	NM_023047	65254	Mm.27732	NM_023047	ENSMUSG00000029168	Dpysl5	CRAM|CRMP-5|Crmp5	dihydropyrimidinase-like 5	protein-coding
mm_97262.1	chr11	75764677	75764752	+	1	NA	3' UTR (NM_009536, exon 6 of 6)	3' UTR (NM_009536, exon 6 of 6)	-31095	NR_136933	102641247	Mm.411386	NR_136932		Gm12339	OTTMUSG00000006218	predicted gene 12339	ncRNA
mm_117728.1	chr13	95534163	95534205	-	1	NA	Intergenic	Intergenic	-8944	NM_007974	14063	Mm.1614	NM_007974	ENSMUSG00000021678	F2rl1	Gpcr11|PAR-2|Par2	coagulation factor II (thrombin) receptor-like 1	protein-coding
mm_56766.1	chr6	116181518	116181521	-	1	NA	intron (NM_177412, intron 1 of 5)	intron (NM_177412, intron 1 of 5)	11855	NM_177412	330401	Mm.425352	NM_177412	ENSMUSG00000030126	Tmcc1	3632431M01Rik|mKIAA0779	transmembrane and coiled coil domains 1	protein-coding
mm_65109.1	chr7	19309774	19309793	-	1	NA	5' UTR (NM_008036, exon 1 of 4)	5' UTR (NM_008036, exon 1 of 4)	262	NM_008036	14282	Mm.248335	NM_008036	ENSMUSG00000003545	Fosb	-	FBJ osteosarcoma oncogene B	protein-coding
mm_89880.1	chr10	108332664	108332689	+	1	NA	intron (NM_054056, intron 1 of 6)	CpG	487	NM_054056	114774	Mm.391419	NM_054056	ENSMUSG00000035873	Pawr	2310001G03Rik|PAR4|Par-4	PRKC, apoptosis, WT1, regulator	protein-coding
mm_131738.1	chr16	22009767	22009825	+	1	NA	intron (NR_027488, intron 1 of 16)	CpG	312	NR_027488	75826	Mm.297431	NM_029457	ENSMUSG00000022855	Senp2	2310007L05Rik|4930538C18Rik|AI646780|AW554757|Smt3ip2|SuPr-1|mKIAA1331	SUMO/sentrin specific peptidase 2	protein-coding
mm_19817.1	chr2	110363158	110363181	-	1	NA	promoter-TSS (NM_026271)	promoter-TSS (NM_026271)	-176	NM_026271	67606	Mm.291809	NM_026271	ENSMUSG00000074971	Fibin	1110018M03Rik	fin bud initiation factor homolog (zebrafish)	protein-coding
mm_133987.1	chr16	4624939	4624972	-	1	NA	promoter-TSS (NM_025571)	promoter-TSS (NM_025571)	-9	NM_025571	66449	Mm.354760	NM_025571	ENSMUSG00000014301	Pam16	2010110I09Rik|AV006767|CGI-136|Magmas|Tim16|Timm16	presequence translocase-asssociated motor 16 homolog (S. cerevisiae)	protein-coding
mm_25500.1	chr3	109452977	109452978	+	1	NA	intron (NM_020505, intron 2 of 26)	intron (NM_020505, intron 2 of 26)	112294	NM_020505	57257	Mm.282257	NM_020505	ENSMUSG00000033721	Vav3	A530094I06Rik|AA986410|Idd18.1	vav 3 oncogene	protein-coding
mm_12297.1	chr2	69091868	69091871	+	1	NA	intron (NM_172856, intron 8 of 9)	intron (NM_172856, intron 8 of 9)	-43931	NM_181547	329416	Mm.90047	NM_181547	ENSMUSG00000034738	Nostrin	Daip2|mDaIP2	nitric oxide synthase trafficker	protein-coding
mm_81018.1	chr9	104263274	104263293	+	1	NA	promoter-TSS (NM_001163026)	promoter-TSS (NM_001163026)	-353	NM_001163026	235567	Mm.217256	NM_001163026	ENSMUSG00000032560	Dnajc13	D030002L11Rik|Gm1124|RME-8|Rme8|mKIAA0678	DnaJ heat shock protein family (Hsp40) member C13	protein-coding
mm_112872.1	chr13	20853628	20853638	+	1	NA	intron (NM_012054, intron 4 of 20)	intron (NM_012054, intron 4 of 20)	59520	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_114732.1	chr13	83727371	83727387	+	1	NA	promoter-TSS (NR_015561)	promoter-TSS (NR_015561)	-727	NR_015561	320203	Mm.245636	NM_177100	ENSMUSG00000050334	C130071C03Rik	2810449C10Rik	RIKEN cDNA C130071C03 gene	ncRNA
mm_135305.1	chr16	38712829	38712839	-	1	NA	5' UTR (NM_020260, exon 1 of 12)	5' UTR (NM_020260, exon 1 of 12)	201	NM_020260	12549	Mm.370848	NM_020260	ENSMUSG00000022799	Arhgap31	5830477L08Rik|AU041750|Cdgap|D330026I07Rik	Rho GTPase activating protein 31	protein-coding
mm_23534.1	chr3	60631691	60631712	+	1	NA	Intergenic	Intergenic	130522	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_104958.1	chr11	100141828	100141857	-	1	NA	intron (NM_001313963, intron 3 of 5)	intron (NM_001313963, intron 3 of 5)	1857	NM_001313963	16669	Mm.439699	NM_008471	ENSMUSG00000020911	Krt19	AI663979|CK-19|EndoC|K19|Krt-1.19|Krt1-19	keratin 19	protein-coding
mm_91843.1	chr10	57532490	57532517	-	1	NA	promoter-TSS (NM_019760)	promoter-TSS (NM_019760)	26	NM_019760	56442	Mm.29344	NM_019760	ENSMUSG00000019877	Serinc1	1500011D18Rik|AI315070|AIGP-2|TMS-2|Tde1l|Tde2|Tms2|mKIAA1253	serine incorporator 1	protein-coding
mm_82304.1	chr9	7868039	7868067	-	1	NA	intron (NM_007464, intron 1 of 8)	MMERGLN-int|LTR|ERV1	5117	NM_007464	11796	Mm.2026	NM_007464	ENSMUSG00000032000	Birc3	AW107670|Api1|Api2|Birc2|C-IAP2|HIAP2|IAP1|IAP2|MIAP1|MIAP2|MIHB|MIHC|RNF49|cIAP-1|cIAP-2|cIAP1|cIAP2	baculoviral IAP repeat-containing 3	protein-coding
mm_117148.1	chr13	61164212	61164215	-	1	NA	promoter-TSS (NM_020284)	promoter-TSS (NM_020284)	-25	NM_020284	56835	Mm.315715	NM_020284	ENSMUSG00000055679	Ctsr	AI428350	cathepsin R	protein-coding
mm_166484.1	chr5	146661926	146661927	-	1	NA	Intergenic	RLTR17|LTR|ERVK	-76687	NM_001010941	14738	Mm.153539	NM_008151	ENSMUSG00000041468	Gpr12	Gpcr01|Gpcr12|Gpcr20|Gpcr21	G-protein coupled receptor 12	protein-coding
mm_142520.1	chr17	46282483	46282493	-	1	NA	intron (NM_001252474, intron 1 of 9)	intron (NM_001252474, intron 1 of 9)	538	NM_001252475	74094	Mm.284594	NM_028751	ENSMUSG00000012296	Tjap1	0610041D19Rik|AI415281|AW121008|Pilt|Tjp4	tight junction associated protein 1	protein-coding
mm_116293.1	chr13	36117244	36117254	-	1	NA	promoter-TSS (NM_024274)	promoter-TSS (NM_024274)	108	NM_201358	380840	Mm.390576	NM_201358	ENSMUSG00000046573	Lyrm4	BC034664|Gm903	LYR motif containing 4	protein-coding
mm_54046.1	chr6	13677931	13677974	-	1	NA	promoter-TSS (NM_175312)	promoter-TSS (NM_175312)	14	NM_175312	101148	Mm.354863	NM_175312	ENSMUSG00000042742	Bmt2	AI666701|B630005N14Rik	base methyltransferase of 25S rRNA 2	protein-coding
mm_11279.1	chr2	30062523	30062545	+	1	NA	intron (NM_023871, intron 1 of 7)	intron (NM_023871, intron 1 of 7)	538	NM_023871	56086	Mm.326055	NM_023871	ENSMUSG00000054766	Set	2610030F17Rik|5730420M11Rik|AA407739|I-2PP2A|StF-IT-1|TAF-I	SET nuclear oncogene	protein-coding
mm_28249.1	chr3	88509944	88509992	-	1	NA	Intergenic	Intergenic	-6616	NM_001002011	16905	Mm.243014	NM_019390	ENSMUSG00000028063	Lmna	Dhe	lamin A	protein-coding
mm_55833.1	chr6	83125138	83125146	-	1	NA	promoter-TSS (NM_023547)	promoter-TSS (NM_023547)	-113	NM_023547	70020	Mm.27814	NM_023547	ENSMUSG00000030034	Ino80b	2510009I23Rik|HMG1YL4|Hmga1l4|Papa1|Znhit4	INO80 complex subunit B	protein-coding
mm_131563.1	chr16	18127670	18127682	+	1	NA	promoter-TSS (NM_022982)	promoter-TSS (NM_022982)	-30	NM_022982	65079	Mm.40149	NM_022982	ENSMUSG00000043811	Rtn4r	NOGOR|NgR|NgR1	reticulon 4 receptor	protein-coding
mm_85219.1	chr9	96984237	96984246	-	1	NA	intron (NM_145134, intron 2 of 2)	intron (NM_145134, intron 2 of 2)	34114	NM_145134	211949	Mm.491271	NM_145134	ENSMUSG00000046997	Spsb4	D030068E18Rik|SSB-4|Ssb4	splA/ryanodine receptor domain and SOCS box containing 4	protein-coding
mm_76559.1	chr8	88362219	88362247	-	1	NA	promoter-TSS (NM_012047)	promoter-TSS (NM_012047)	-42	NM_012047	26992	Mm.5400	NM_012047	ENSMUSG00000031660	Brd7	BP75|CELTIX1|Ptpn13ip	bromodomain containing 7	protein-coding
mm_95461.1	chr11	50381505	50381552	+	1	NA	exon (NM_021510, exon 5 of 14)	exon (NM_021510, exon 5 of 14)	3809	NM_001347487	59013	Mm.21740	NM_021510	ENSMUSG00000007850	Hnrnph1	AI642080|E430005G16Rik|Hnrnph|Hnrph1	heterogeneous nuclear ribonucleoprotein H1	protein-coding
mm_89913.1	chr10	111176442	111176446	+	1	NA	intron (NM_175489, intron 1 of 23)	intron (NM_175489, intron 1 of 23)	11642	NM_175489	237542	Mm.220204	NM_175489	ENSMUSG00000020189	Osbpl8	AA536976|AA536995|C730029P18Rik|D330025H14Rik|ORP-8	oxysterol binding protein-like 8	protein-coding
mm_34966.1	chr4	156008682	156008692	+	1	NA	intron (NM_001302468, intron 4 of 6)	intron (NM_001302468, intron 4 of 6)	-5008	NM_011659	22163	Mm.13885	NM_011659	ENSMUSG00000029075	Tnfrsf4	ACT35|CD134|Ly-70|Ox40|TXGP1L|Txgp1	tumor necrosis factor receptor superfamily, member 4	protein-coding
mm_37838.1	chr4	132059161	132059171	-	1	NA	intron (NM_183428, intron 1 of 20)	intron (NM_183428, intron 1 of 20)	-10088	NM_001128606	269587	Mm.30038	NM_183428	ENSMUSG00000028906	Epb41	4.1R|AI415518|D4Ertd442e|Elp-1|Elp1|Epb4.1|mKIAA4056	erythrocyte membrane protein band 4.1	protein-coding
mm_161709.1	chr17	24889998	24889998	+	1	NA	intron (NM_027141, intron 2 of 6)	intron (NM_027141, intron 2 of 6)	2517	NM_027141	79043	Mm.274794	NM_027141	ENSMUSG00000024160	Spsb3	2310012N15Rik|3300001M01Rik|SSB3|Tce1|mKIAA4204	splA/ryanodine receptor domain and SOCS box containing 3	protein-coding
mm_36829.1	chr4	106167848	106167848	-	1	NA	Intergenic	MTEb|LTR|ERVL-MaLR	-148365	NM_183225	329908	Mm.234544	NM_183225	ENSMUSG00000028514	Usp24	2700066K03Rik|2810030C21Rik|AI414051|B130021E18|C79851	ubiquitin specific peptidase 24	protein-coding
mm_151748.1	chr19	5072498	5072523	-	1	NA	Intergenic	Intergenic	4432	NM_054042	70445	Mm.29597	NM_054042	ENSMUSG00000056481	Cd248	2610111G01Rik|AI842296|Cd164l1|Tem1	CD248 antigen, endosialin	protein-coding
mm_111996.1	chr12	110696310	110696319	-	1	NA	promoter-TSS (NM_010480)	promoter-TSS (NM_010480)	81	NM_010480	15519	Mm.1843	NM_010480	ENSMUSG00000021270	Hsp90aa1	86kDa|89kDa|AL024080|AL024147|Hsp86-1|Hsp89|Hsp90|Hspca|hsp4	heat shock protein 90, alpha (cytosolic), class A member 1	protein-coding
mm_33109.1	chr4	124724756	124724790	+	1	NA	exon (NM_029157, exon 10 of 17)	exon (NM_029157, exon 10 of 17)	-6921	NR_030479	735277		NR_030479	ENSMUSG00000076271	Mir697	Mirn697|mmu-mir-697	microRNA 697	ncRNA
mm_8510.1	chr1	154726377	154726387	-	1	NA	promoter-TSS (NM_009782)	promoter-TSS (NM_009782)	-462	NM_009782	12290	Mm.267517	NM_009782	ENSMUSG00000004110	Cacna1e	A430040I15|BII|Cach6|Cacnl1a6|Cav2.3|Cchra1|alpha1E	calcium channel, voltage-dependent, R type, alpha 1E subunit	protein-coding
mm_89117.1	chr10	84756151	84756164	+	1	NA	5' UTR (NM_001024918, exon 1 of 18)	5' UTR (NM_001024918, exon 1 of 18)	109	NM_001024918	71137	Mm.79070	NM_027689	ENSMUSG00000020037	Rfx4	4933412G19Rik|NYD-sp10	regulatory factor X, 4 (influences HLA class II expression)	protein-coding
mm_81663.1	chr9	111020944	111020960	+	1	NA	exon (NM_008522, exon 2 of 17)	exon (NM_008522, exon 2 of 17)	1660	NM_008522	17002	Mm.282359	NM_008522	ENSMUSG00000032496	Ltf	Csp82|Lf|MMS10R|Ms10r	lactotransferrin	protein-coding
mm_172972.1	chr9	90118881	90118901	+	1	NA	Intergenic	Intergenic	-4071	NM_024431	21761	Mm.426209	NM_024431	ENSMUSG00000062270	Morf4l1	MORFRG15|MRG15|TEG-189|Tex189|mKIAA4002	mortality factor 4 like 1	protein-coding
mm_81394.1	chr9	108989838	108989849	+	1	NA	Intergenic	Intergenic	-2059	NM_173019	270198	Mm.132391	NM_173019	ENSMUSG00000025648	Pfkfb4	C230090D14	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4	protein-coding
mm_157482.1	chrX	48208527	48208537	-	1	NA	5' UTR (NM_172465, exon 1 of 10)	5' UTR (NM_172465, exon 1 of 10)	170	NM_172465	208884	Mm.207367	NM_172465	ENSMUSG00000036985	Zdhhc9	6430508G22|9530098M12Rik	zinc finger, DHHC domain containing 9	protein-coding
mm_170704.1	chr2	138040142	138040158	+	1	NA	Intergenic	IAPLTR1_Mm|LTR|ERVK	-216434	NM_001025431	228662	Mm.153405	NM_145534	ENSMUSG00000062098	Btbd3	mKIAA0952	BTB (POZ) domain containing 3	protein-coding
mm_103612.1	chr11	78536236	78536248	-	1	NA	promoter-TSS (NM_018854)	promoter-TSS (NM_018854)	18	NM_001159392	21927	Mm.386774	NM_009395	ENSMUSG00000017615	Tnfaip1	Bacurd2|Edp-1|Edp1|Tnfip1	tumor necrosis factor, alpha-induced protein 1 (endothelial)	protein-coding
mm_18768.1	chr2	73485713	73485730	-	1	NA	promoter-TSS (NM_001289723)	promoter-TSS (NM_001289723)	32	NM_001289723	215280	Mm.223504	NM_153138	ENSMUSG00000075284	Wipf1	AI115543|D2Ertd120e|WIP|Waspip	WAS/WASL interacting protein family, member 1	protein-coding
mm_149416.1	chr19	11426283	11426309	+	1	NA	exon (NM_029499, exon 7 of 7)	exon (NM_029499, exon 7 of 7)	-17262	NM_021718	60361	Mm.33957	NM_021718	ENSMUSG00000056290	Ms4a4b	AI463180|Chandra|Ly116	membrane-spanning 4-domains, subfamily A, member 4B	protein-coding
mm_4646.1	chr1	180294732	180294734	+	1	NA	Intergenic	Intergenic	-35743	NM_001081175	320404	Mm.132535	NM_001081175	ENSMUSG00000038855	Itpkb	1110033J02Rik|E130307H12Rik	inositol 1,4,5-trisphosphate 3-kinase B	protein-coding
mm_67565.1	chr7	81904024	81904026	-	1	NA	intron (NM_013886, intron 2 of 5)	intron (NM_013886, intron 2 of 5)	30434	NM_013886	29877	Mm.392934	NM_013886	ENSMUSG00000025104	Hdgfrp3	2700022B06Rik|HRP-3	hepatoma-derived growth factor, related protein 3	protein-coding
mm_20925.1	chr2	150855650	150855701	-	1	NA	intron (NM_024465, intron 2 of 12)	(TG)n|Simple_repeat|Simple_repeat	49056	NM_024465	76192	Mm.112632	NM_024465	ENSMUSG00000032046	Abhd12	1500011G07Rik|6330583M11Rik|AI431047|AW547313	abhydrolase domain containing 12	protein-coding
mm_156180.1	chrX	130461552	130461571	+	1	NA	3' UTR (NM_172493, exon 27 of 27)	3' UTR (NM_172493, exon 27 of 27)	711819	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diaph2	Dia3|Diap2|Drf2|E430022I22Rik	diaphanous related formin 2	protein-coding
mm_106113.1	chr11	116335351	116335365	-	1	NA	promoter-TSS (NM_008240)	promoter-TSS (NM_008240)	-4	NM_008240	15223	Mm.378938	NM_008240	ENSMUSG00000034227	Foxj1	FKHL-13|HFH-4|Hfh4	forkhead box J1	protein-coding
mm_145678.1	chr18	61576175	61576179	+	1	NA	intron (NM_146087, intron 5 of 9)	intron (NM_146087, intron 5 of 9)	20595	NM_146087	93687	Mm.26908	NM_146087	ENSMUSG00000024576	Csnk1a1	2610208K14Rik|4632404G05Rik|5430427P18Rik|CK1a|Csnk1a	casein kinase 1, alpha 1	protein-coding
mm_65380.1	chr7	25090766	25090799	-	1	NA	TTS (NM_001163556)	TTS (NM_001163556)	6393	NR_105855	102465968		NR_105855	ENSMUSG00000098441	Mir6537	Gm27808|mmu-mir-6537	microRNA 6537	ncRNA
mm_165255.1	chr2	72480080	72480082	+	1	NA	intron (NM_025866, intron 2 of 8)	intron (NM_025866, intron 2 of 8)	3862	NM_025866	66953	Mm.270676	NM_025866	ENSMUSG00000055612	Cdca7	2310021G01Rik|AU044109|JPO1	cell division cycle associated 7	protein-coding
mm_34906.1	chr4	155694312	155694375	+	1	NA	promoter-TSS (NM_178699)	promoter-TSS (NM_178699)	1	NM_178699	230991	Mm.29083	NM_178699	ENSMUSG00000074738	Fndc10	B930041F14Rik|MNCb-3966	fibronectin type III domain containing 10	protein-coding
mm_140000.1	chr17	72941594	72941608	+	1	NA	3' UTR (NM_029999, exon 3 of 3)	3' UTR (NM_029999, exon 3 of 3)	23296	NM_029999	77889	Mm.154109	NM_029999	ENSMUSG00000024063	Lbh	1810009F10Rik|6720416L16Rik	limb-bud and heart	protein-coding
mm_106657.1	chr11	121204931	121204977	-	1	NA	promoter-TSS (NM_025402)	promoter-TSS (NM_025402)	-306	NM_025402	66179	Mm.390403	NM_025402	ENSMUSG00000025169	Ogfod3	1110031I02Rik	2-oxoglutarate and iron-dependent oxygenase domain containing 3	protein-coding
mm_28457.1	chr3	90682755	90682763	-	1	NA	Intergenic	Intergenic	12962	NM_001281852	20202	Mm.2128	NM_009114	ENSMUSG00000056071	S100a9	60B8Ag|AW546964|BEE22|Cagb|GAGB|L1Ag|MRP14|p14	S100 calcium binding protein A9 (calgranulin B)	protein-coding
mm_40286.1	chr5	43233695	43233703	+	1	NA	exon (NM_001177379, exon 1 of 11)	exon (NM_001177379, exon 1 of 11)	236	NM_001177379	231207	Mm.7233	NM_175937	ENSMUSG00000039782	Cpeb2	A630055H10Rik|Cpe-bp2	cytoplasmic polyadenylation element binding protein 2	protein-coding
mm_162912.1	chr10	119665145	119665145	+	1	NA	intron (NM_133442, intron 1 of 21)	intron (NM_133442, intron 1 of 21)	96554	NR_045359	75321	Mm.402041	NR_045359	ENSMUSG00000084764	Grip1os2	4930564G21Rik	glutamate receptor interacting protein 1, opposite strand 2	ncRNA
mm_123475.1	chr14	65975699	65975710	-	1	NA	exon (NM_013492, exon 5 of 9)	exon (NM_013492, exon 5 of 9)	7221	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_87378.1	chr10	44599817	44599868	+	1	NA	Intergenic	Intergenic	-141094	NM_007548	12142	Mm.4800	NM_007548	ENSMUSG00000038151	Prdm1	Blimp-1|Blimp1|PRDI-BF1|ZNFPR1A1|b2b1765Clo	PR domain containing 1, with ZNF domain	protein-coding
mm_72914.1	chr8	91070053	91070123	+	1	NA	promoter-TSS (NM_001282001)	promoter-TSS (NM_001282001)	31	NM_001282000	19651	Mm.235580	NM_011250	ENSMUSG00000031666	Rbl2	PRB2|RBR-2|Rb2|p130	retinoblastoma-like 2	protein-coding
mm_88891.1	chr10	81137981	81137992	+	1	NA	intron (NM_010731, intron 1 of 2)	CpG	1715	NM_010731	16969	Mm.20920	NM_010731	ENSMUSG00000035011	Zbtb7a	9030619K07Rik|9130006G12Rik|AI452336|FBI-1|Lrf|Pokemon|Zbtb7	zinc finger and BTB domain containing 7a	protein-coding
mm_105560.1	chr11	106488419	106488435	-	1	NA	promoter-TSS (NM_023913)	promoter-TSS (NM_023913)	-631	NM_023913	78943	Mm.340943	NM_023913	ENSMUSG00000020715	Ern1	9030414B18Rik|AI225830|C85377|Ire1a|Ire1alpha|Ire1p	endoplasmic reticulum (ER) to nucleus signalling 1	protein-coding
mm_136353.1	chr16	92697316	92697347	-	1	NA	promoter-TSS (NM_009821)	promoter-TSS (NM_009821)	-2	NM_009821	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_23781.1	chr3	79237912	79237922	+	1	NA	intron (NR_045502, intron 1 of 2)	ORR1A4|LTR|ERVL-MaLR	24998	NR_045502	70924	Mm.444622	NR_045502	ENSMUSG00000104585	4921511C10Rik	-	RIKEN cDNA 4921511C10 gene	ncRNA
mm_103473.1	chr11	76494396	76494438	-	1	NA	promoter-TSS (NM_001346670)	promoter-TSS (NM_001346670)	78	NM_001346670	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_5381.1	chr1	30949905	30949926	-	1	NA	promoter-TSS (NR_002688)	promoter-TSS (NR_002688)	-160	NM_011200	19243	Mm.491181	NM_011200	ENSMUSG00000026064	Ptp4a1	AA415290|AU019864|C130021B01|Prl-1	protein tyrosine phosphatase 4a1	protein-coding
mm_39191.1	chr4	155943598	155943640	-	1	NA	promoter-TSS (NM_001039158)	promoter-TSS (NM_001039158)	-194	NM_001039158	140499	Mm.371673	NM_021402	ENSMUSG00000023286	Ube2j2	1200007B18Rik|2400008G19Rik|5730472G04Rik|AL022923|NCUBE-2|Ubc6|Ubc6p	ubiquitin-conjugating enzyme E2J 2	protein-coding
mm_111166.1	chr12	83597112	83597121	-	1	NA	promoter-TSS (NM_183154)	promoter-TSS (NM_183154)	31	NM_183154	217695	Mm.59257	NM_183154	ENSMUSG00000042628	Zfyve1	DFCP1|G630053K23|TAFF1|ZNFN2A1|mKIAA1589	zinc finger, FYVE domain containing 1	protein-coding
mm_2372.1	chr1	93238870	93238873	+	1	NA	intron (NM_172463, intron 1 of 30)	intron (NM_172463, intron 1 of 30)	2974	NM_172463	208777	Mm.271897	NM_172463	ENSMUSG00000047793	Sned1	6720455I24Rik|AI197264|AI642697|D430044C15Rik|SST3|Snep	sushi, nidogen and EGF-like domains 1	protein-coding
mm_7379.1	chr1	107138610	107138610	-	1	NA	Intergenic	Intergenic	22504	NM_198680	383548	Mm.483991	NM_198680	ENSMUSG00000073602	Serpinb3b	Scca2-rs|Scca2-rs1	serine (or cysteine) peptidase inhibitor, clade B (ovalbumin), member 3B	protein-coding
mm_134078.1	chr16	8695062	8695064	-	1	NA	exon (NM_001003918, exon 22 of 31)	exon (NM_001003918, exon 22 of 31)	14293	NM_001324517	436336	Mm.357666	NM_001324517		Gm5767	EG436336	predicted gene 5767	protein-coding
mm_164396.1	chr16	33807860	33807885	+	1	NA	exon (NM_010739, exon 7 of 13)	exon (NM_010739, exon 7 of 13)	13835	NM_010739	17063	Mm.3177	NM_010739	ENSMUSG00000022824	Muc13	114/A10|14/A10|AI159736|Lrrp|Ly64|NJ-1	mucin 13, epithelial transmembrane	protein-coding
mm_150218.1	chr19	33391796	33391844	+	1	NA	intron (NM_001167818, intron 1 of 6)	CpG	475	NM_001167818	67795	Mm.204591	NM_001146342	ENSMUSG00000071573	Rnls	6530404N21Rik|AI452315|AW060440|C10orf59	renalase, FAD-dependent amine oxidase	protein-coding
mm_132381.1	chr16	34921839	34921847	+	1	NA	exon (NM_139300, exon 16 of 32)	exon (NM_139300, exon 16 of 32)	17486	NR_040536	76649	Mm.420532	NR_040536	ENSMUSG00000100593	1700119H24Rik	-	RIKEN cDNA 1700119H24 gene	ncRNA
mm_43050.1	chr5	124112299	124112351	+	1	NA	promoter-TSS (NM_001347478)	promoter-TSS (NM_001347478)	-13	NM_025671	66627	Mm.7050	NM_025671	ENSMUSG00000023707	Ogfod2	1300006G11Rik|5730405M13Rik|AU041636|AW552395	2-oxoglutarate and iron-dependent oxygenase domain containing 2	protein-coding
mm_57071.1	chr6	122578052	122578061	-	1	NA	3' UTR (NM_031159, exon 8 of 8)	3' UTR (NM_031159, exon 8 of 8)	24247	NM_009645	11628	Mm.391503	NM_009645	ENSMUSG00000040627	Aicda	Aid|Arp2	activation-induced cytidine deaminase	protein-coding
mm_38770.1	chr4	147910767	147910779	-	1	NA	exon (NM_011122, exon 19 of 19)	exon (NM_011122, exon 19 of 19)	-5864	NM_001285921	170731	Mm.154312	NM_133201	ENSMUSG00000029020	Mfn2	D630023P19Rik|Fzo	mitofusin 2	protein-coding
mm_20256.1	chr2	126598054	126598065	-	1	NA	intron (NM_008230, intron 9 of 11)	intron (NM_008230, intron 9 of 11)	20619	NM_008230	15186	Mm.18603	NM_008230	ENSMUSG00000027360	Hdc	AW108189|Hdc-a|Hdc-c|Hdc-e|Hdc-s	histidine decarboxylase	protein-coding
mm_64952.1	chr7	16387854	16387858	-	1	NA	promoter-TSS (NM_019748)	promoter-TSS (NM_019748)	40	NM_001285892	56459	Mm.258530	NM_019748	ENSMUSG00000052833	Sae1	2400010M20Rik|2610044L12Rik|AL033372|AOS1|AW743391|D7Ertd177e|HSPC140|Sua1|Uble1a	SUMO1 activating enzyme subunit 1	protein-coding
mm_53718.1	chr6	143409683	143409683	+	1	NA	Intergenic	Intergenic	163795	NR_027803	52285	Mm.354898	NM_001033129		D6Ertd474e	1700001I24Rik|AU023129	DNA segment, Chr 6, ERATO Doi 474, expressed	ncRNA
mm_75835.1	chr8	70527646	70527696	-	1	NA	promoter-TSS (NM_001199631)	promoter-TSS (NM_001199631)	-72	NM_001111066	14232	Mm.141864	NM_010223	ENSMUSG00000019428	Fkbp8	38kDa|FKBP-38|FKBP-8|Fkbp38	FK506 binding protein 8	protein-coding
mm_145170.1	chr18	46918890	46918911	+	1	NA	Intergenic	Intergenic	-2915	NM_001033446	381142	Mm.329423	NM_001033446	ENSMUSG00000073568	Arl14epl	Gm949	ADP-ribosylation factor-like 14 effector protein-like	protein-coding
mm_126960.1	chr15	92322074	92322076	+	1	NA	intron (NM_007727, intron 23 of 23)	intron (NM_007727, intron 23 of 23)	-74735	NM_001164593	239618	Mm.309826	NM_001164593	ENSMUSG00000036218	Pdzrn4	1110017D07Rik|LNX4|SAMCAP3L|mKIAA3027	PDZ domain containing RING finger 4	protein-coding
mm_37270.1	chr4	118544011	118544066	-	1	NA	promoter-TSS (NM_172383)	promoter-TSS (NM_172383)	-312	NM_172383	230678	Mm.23639	NM_172383	ENSMUSG00000050854	Tmem125	6330530A05Rik|AV223516	transmembrane protein 125	protein-coding
mm_64917.1	chr7	16240394	16240422	-	1	NA	intron (NM_176912, intron 1 of 1)	intron (NM_176912, intron 1 of 1)	1923	NM_001146005	319430	Mm.239570	NM_176912	ENSMUSG00000074361	C5ar2	C5L2|E030029A11Rik|Gpr77	complement component 5a receptor 2	protein-coding
mm_71845.1	chr8	68905065	68905139	+	1	NA	3' UTR (NM_008509, exon 10 of 10)	3' UTR (NM_008509, exon 10 of 10)	24547	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_1113.1	chr1	59872584	59872595	+	1	NA	3' UTR (NM_007561, exon 13 of 13)	3' UTR (NM_007561, exon 13 of 13)	-40417	NM_001037725	72750	Mm.258250	NM_001037725	ENSMUSG00000041040	Fam117b	2810425F24Rik|6330416D14Rik|Als2cr13	family with sequence similarity 117, member B	protein-coding
mm_171643.1	chr4	32046819	32046831	-	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	82718	NM_172688	26409	Mm.258589	NM_009316	ENSMUSG00000028284	Map3k7	B430101B05|C87327|Tak1	mitogen-activated protein kinase kinase kinase 7	protein-coding
mm_169765.1	chr15	99801501	99801501	-	1	NA	intron (NM_023063, intron 4 of 7)	B1_Mm|SINE|Alu	18648	NM_023063	65970	Mm.33207	NM_023063	ENSMUSG00000023022	Lima1	Eplin	LIM domain and actin binding 1	protein-coding
mm_69061.1	chr7	126897473	126897483	-	1	NA	intron (NM_026827, intron 1 of 5)	intron (NM_026827, intron 1 of 5)	800	NM_026827	68742	Mm.248646	NM_026827	ENSMUSG00000060538	Tmem219	1110032O16Rik|2900045G02Rik|IGFBP-3R	transmembrane protein 219	protein-coding
mm_98227.1	chr11	88068068	88068131	+	1	NA	promoter-TSS (NM_016686)	promoter-TSS (NM_016686)	-180	NM_016686	22344	Mm.46628	NM_016686	ENSMUSG00000018377	Vezf1	AI848691|AW046909|db1	vascular endothelial zinc finger 1	protein-coding
mm_81509.1	chr9	110034795	110034807	+	1	NA	exon (NM_008633, exon 7 of 19)	exon (NM_008633, exon 7 of 19)	-17220	NM_001311163	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_53929.1	chr6	4736422	4736441	-	1	NA	intron (NM_001130188, intron 1 of 11)	intron (NM_001130188, intron 1 of 11)	10773	NM_001130188	20392	Mm.8739	NM_011360	ENSMUSG00000004631	Sgce	e-SG	sarcoglycan, epsilon	protein-coding
mm_157721.1	chrX	70344639	70344648	-	1	NA	3' UTR (NM_010498, exon 9 of 9)	3' UTR (NM_010498, exon 9 of 9)	20442	NM_010498	15931	Mm.233083	NM_010498	ENSMUSG00000035847	Ids	AW214631	iduronate 2-sulfatase	protein-coding
mm_94630.1	chr11	16822828	16822834	+	1	NA	intron (NM_207655, intron 1 of 27)	intron (NM_207655, intron 1 of 27)	70628	NM_007912	13649	Mm.8534	NM_007912	ENSMUSG00000020122	Egfr	9030024J15Rik|AI552599|Erbb|Errb1|Errp|Wa5|wa-2|wa2	epidermal growth factor receptor	protein-coding
mm_166400.1	chr5	135974521	135974552	-	1	NA	promoter-TSS (NM_001160366)	promoter-TSS (NM_001160366)	-60	NM_001160366	109267	Mm.332750	NM_001160366	ENSMUSG00000029699	Ssc4d	C330016E03Rik|S4D-SRCRB|SRCRB-S4D|Srcrb4d	scavenger receptor cysteine rich family, 4 domains	protein-coding
mm_164932.1	chr18	82705050	82705073	+	1	NA	Intergenic	Intergenic	-12327	NM_177832	329002	Mm.34438	NM_177832	ENSMUSG00000041258	Zfp236	AI447957|Gm335	zinc finger protein 236	protein-coding
mm_3909.1	chr1	161896383	161896385	+	1	NA	Intergenic	Intergenic	-19723	NM_172645	226551	Mm.170002	NM_172645	ENSMUSG00000040297	Suco	4732491B11|AI848100|AU016931|Opt	SUN domain containing ossification factor	protein-coding
mm_107058.1	chr12	16653798	16653808	+	1	NA	exon (NM_008747, exon 1 of 4)	exon (NM_008747, exon 1 of 4)	333	NM_008747	18217	Mm.281715	NM_008747	ENSMUSG00000020591	Ntsr2	NT2R|NTRL	neurotensin receptor 2	protein-coding
mm_167491.1	chr9	7353544	7353546	+	1	NA	exon (NM_008605, exon 6 of 10)	exon (NM_008605, exon 6 of 10)	6171	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_24882.1	chr3	95996146	95996160	+	1	NA	promoter-TSS (NM_023320)	promoter-TSS (NM_023320)	-314	NM_023320	67220	Mm.458147	NM_023320	ENSMUSG00000015745	Plekho1	2810052M02Rik|CKIP-1|Ckip1|JZA-20|Jza2	pleckstrin homology domain containing, family O member 1	protein-coding
mm_1043.1	chr1	58795657	58795667	+	1	NA	5' UTR (NM_009812, exon 1 of 9)	5' UTR (NM_009812, exon 1 of 9)	288	NM_009812	12370	Mm.336851	NM_009812	ENSMUSG00000026029	Casp8	CASP-8|FLICE|MACH|Mch5	caspase 8	protein-coding
mm_156202.1	chrX	134427020	134427029	+	1	NA	intron (NM_010078, intron 2 of 22)	intron (NM_010078, intron 2 of 22)	22244	NM_010078	13497	Mm.121662	NM_010078	ENSMUSG00000000223	Drp2	AW495265|DRP-2	dystrophin related protein 2	protein-coding
mm_169860.1	chr16	3350825	3350839	+	1	NA	Intergenic	Intergenic	-241566	NM_146860	258859	Mm.377723	NM_146860	ENSMUSG00000051003	Olfr161	MOR131-1|OR912-47M6	olfactory receptor 161	protein-coding
mm_124885.1	chr15	10267153	10267157	+	1	NA	intron (NM_001253781, intron 1 of 9)	intron (NM_001253781, intron 1 of 9)	-26496	NM_001253782	19116	Mm.10516	NM_011169	ENSMUSG00000005268	Prlr	AI987712|Pr-1|Pr-3|Prlr-rs1	prolactin receptor	protein-coding
mm_49424.1	chr6	29248646	29248661	+	1	NA	Intergenic	Intergenic	-23835	NM_001190461	69573	Mm.45161	NM_023516	ENSMUSG00000043421	Hilpda	2310016C08Rik|AW049004|Hig2	hypoxia inducible lipid droplet associated	protein-coding
mm_88740.1	chr10	80276732	80276735	+	1	NA	intron (NM_001122605, intron 4 of 11)	intron (NM_001122605, intron 4 of 11)	-1431	NR_105876	102466207		NR_105876	ENSMUSG00000098672	Mir6911	Gm27822|mmu-mir-6911	microRNA 6911	ncRNA
mm_15063.1	chr2	152988630	152988632	+	1	NA	intron (NM_001083618, intron 5 of 14)	MTEa|LTR|ERVL-MaLR	26146	NM_001083618	74711	Mm.44746	NM_029064	ENSMUSG00000074673	Ttll9	1700016F23Rik|4930509O20Rik|AW046572	tubulin tyrosine ligase-like family, member 9	protein-coding
mm_94139.1	chr10	128720322	128720337	-	1	NA	TTS (NM_021882)	TTS (NM_021882)	14071	NM_021882	20431	Mm.16756	NM_021882	ENSMUSG00000025359	Pmel	D10H12S53E|D12S53Eh|Pmel17|Si|Silv|gp100|gp87	premelanosome protein	protein-coding
mm_13743.1	chr2	118119083	118119123	+	1	NA	exon (NM_011580, exon 11 of 22)	exon (NM_011580, exon 11 of 22)	7227	NM_001313914	21825	Mm.4159	NM_011580	ENSMUSG00000040152	Thbs1	TSP-1|TSP1|Thbs-1|tbsp1	thrombospondin 1	protein-coding
mm_3954.1	chr1	164063103	164063109	+	1	NA	exon (NM_001164059, exon 2 of 8)	exon (NM_001164059, exon 2 of 8)	1030	NM_001164059	20343	Mm.1461	NM_011346	ENSMUSG00000026581	Sell	AI528707|CD62L|L-selectin|LECAM-1|Lnhr|Ly-22|Ly-m22|Lyam-1|Lyam1	selectin, lymphocyte	protein-coding
mm_160824.1	chr11	33147388	33147388	-	1	NA	promoter-TSS (NM_008005)	promoter-TSS (NM_008005)	12	NM_008005	14172	Mm.339812	NM_008005	ENSMUSG00000057967	Fgf18	D130055P09Rik|FGF-18	fibroblast growth factor 18	protein-coding
mm_130824.1	chr15	101845888	101845899	-	1	NA	3' UTR (NM_008473, exon 9 of 9)	3' UTR (NM_008473, exon 9 of 9)	4893	NM_008473	16678	Mm.183137	NM_008473	ENSMUSG00000046834	Krt1	Krt-2.1|Krt2-1|Krt86	keratin 1	protein-coding
mm_97645.1	chr11	79339642	79339693	+	1	NA	promoter-TSS (NM_010897)	promoter-TSS (NM_010897)	-225	NM_010897	18015	Mm.255596	NM_010897	ENSMUSG00000020716	Nf1	AW494271|Dsk9|E030030H24Rik|Mhdadsk9|Nf-1	neurofibromin 1	protein-coding
mm_3225.1	chr1	135848060	135848077	+	1	NA	exon (NM_001130176, exon 7 of 13)	exon (NM_001130176, exon 7 of 13)	7207	NM_001130176	21956	Mm.247470	NM_011619	ENSMUSG00000026414	Tnnt2	Tnt|cTnT	troponin T2, cardiac	protein-coding
mm_106897.1	chr12	8012631	8012644	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	34960	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_18739.1	chr2	73012754	73012786	-	1	NA	Intergenic	Intergenic	-32324	NM_001018042	20687	Mm.124328	NM_011450	ENSMUSG00000027109	Sp3	D130027J01Rik	trans-acting transcription factor 3	protein-coding
mm_152952.1	chr19	29047848	29047977	-	1	NA	promoter-TSS (NM_021299)	promoter-TSS (NM_021299)	-10	NM_021299	56248	Mm.196067	NM_021299	ENSMUSG00000024782	Ak3	AA407498|AI506714|AK-3|Ak3l|Ak3l1|Akl3l	adenylate kinase 3	protein-coding
mm_109636.1	chr12	112768620	112768691	+	1	NA	3' UTR (NM_178911, exon 11 of 11)	3' UTR (NM_178911, exon 11 of 11)	8000	NM_178911	104759	Mm.203915	NM_178911	ENSMUSG00000052160	Pld4	AI132321|thss	phospholipase D family, member 4	protein-coding
mm_42021.1	chr5	108269445	108269470	+	1	NA	5' UTR (NM_026106, exon 1 of 3)	5' UTR (NM_026106, exon 1 of 3)	560	NM_026106	13486	Mm.303534	NM_026106	ENSMUSG00000029265	Dr1	1700121L09Rik|Dr1l|NC2|NC2beta	down-regulator of transcription 1	protein-coding
mm_137350.1	chr17	25188381	25188418	+	1	NA	promoter-TSS (NM_001197024)	promoter-TSS (NM_001197024)	-1	NM_001197024	74154	Mm.267353	NM_028789	ENSMUSG00000015127	Unkl	1300004G08Rik	unkempt family like zinc finger	protein-coding
mm_43260.1	chr5	130242158	130242160	+	1	NA	3' UTR (NM_001081394, exon 7 of 7)	3' UTR (NM_001081394, exon 7 of 7)	13371	NM_023248	66711	Mm.280484	NM_023248	ENSMUSG00000025337	Sbds	4733401P19Rik|AI836084|CGI-97|SDS	Shwachman-Bodian-Diamond syndrome homolog (human)	protein-coding
mm_77670.1	chr8	124863029	124863039	-	1	NA	promoter-TSS (NM_025615)	promoter-TSS (NM_025615)	1	NM_010322	14712	Mm.29114	NM_010322	ENSMUSG00000031985	Gnpat	AU019525|D1Ertd819e|DHAPAT	glyceronephosphate O-acyltransferase	protein-coding
mm_125758.1	chr15	73836131	73836138	+	1	NA	intron (NM_001033365, intron 1 of 10)	intron (NM_001033365, intron 1 of 10)	3537	NM_001033365	268816	Mm.440635	NM_001033365	ENSMUSG00000072487	Mroh5	Gm628	maestro heat-like repeat family member 5	protein-coding
mm_100952.1	chr11	6623981	6623991	-	1	NA	exon (NM_134011, exon 3 of 12)	exon (NM_134011, exon 3 of 12)	2081	NM_001130457	21379	Mm.247761	NM_134011	ENSMUSG00000000384	Tbrg4	2310042P22Rik|AA120735|AA408001|AI527316|Cpr2|R74877|Tb-12|mKIAA0948	transforming growth factor beta regulated gene 4	protein-coding
mm_109569.1	chr12	112106711	112106719	+	1	NA	promoter-TSS (NM_001081169)	promoter-TSS (NM_001081169)	32	NM_001081169	104816	Mm.77133	NM_001081169	ENSMUSG00000037686	Aspg	A530050D06Rik|AI429460|Gm690	asparaginase	protein-coding
mm_8674.1	chr1	156718895	156718935	-	1	NA	promoter-TSS (NM_145413)	promoter-TSS (NM_145413)	-5	NM_145413	215015	Mm.229107	NM_145413	ENSMUSG00000033557	Fam20b	C530043G21Rik|mKIAA0475	family with sequence similarity 20, member B	protein-coding
mm_151469.1	chr19	58671702	58671721	+	1	NA	exon (NM_026925, exon 3 of 13)	exon (NM_026925, exon 3 of 13)	1346	NM_026925	69060	Mm.20407	NM_026925	ENSMUSG00000046008	Pnlip	1810007A24Rik|PL|PTL	pancreatic lipase	protein-coding
mm_32711.1	chr4	116151427	116151448	+	1	NA	promoter-TSS (NM_001290658)	promoter-TSS (NM_001290658)	6	NM_001290658	68273	Mm.196045	NM_026651	ENSMUSG00000028700	Pomgnt1	0610016I07Rik|4930467B06Rik	protein O-linked mannose beta 1,2-N-acetylglucosaminyltransferase	protein-coding
mm_112046.1	chr12	111672291	111672306	-	1	NA	promoter-TSS (NM_021273)	promoter-TSS (NM_021273)	40	NM_021273	12709	Mm.16831	NM_021273	ENSMUSG00000001270	Ckb	B-CK|Bck|Ck-3|Ck3|Ckbb	creatine kinase, brain	protein-coding
mm_76931.1	chr8	105938017	105938042	-	1	NA	5' UTR (NM_013640, exon 1 of 8)	5' UTR (NM_013640, exon 1 of 8)	363	NM_013640	19171	Mm.787	NM_013640	ENSMUSG00000031897	Psmb10	Mecl-1|Mecl1	proteasome (prosome, macropain) subunit, beta type 10	protein-coding
mm_164581.1	chr17	25370615	25370633	+	1	NA	promoter-TSS (NM_012034)	promoter-TSS (NM_012034)	71	NM_012034	26945	Mm.180108	NM_012034	ENSMUSG00000033200	Tpsg1	Prss31|Tmt	tryptase gamma 1	protein-coding
mm_6682.1	chr1	80605820	80605835	-	1	NA	exon (NM_001285927, exon 7 of 56)	exon (NM_001285927, exon 7 of 56)	59525	NM_001285927	210293	Mm.133473	NM_175291	ENSMUSG00000038608	Dock10	9330153B10Rik|A630054M16Rik|Jr4|Jr5|R75174|ZIZ3|Zizimin3|mKIAA0694	dedicator of cytokinesis 10	protein-coding
mm_160936.1	chr11	94013705	94013705	+	1	NA	exon (NM_001199204, exon 2 of 30)	exon (NM_001199204, exon 2 of 30)	17614	NM_027569	70834	Mm.260737	NM_027569	ENSMUSG00000020859	Spag9	3110018C07Rik|4733401I23Rik|4831406C20Rik|AW552012|JLP|JSAP2|JSAP2a|Jip4|Mapk8ip4|syd1	sperm associated antigen 9	protein-coding
mm_3705.1	chr1	153891838	153891844	+	1	NA	exon (NM_178244, exon 1 of 1)	exon (NM_178244, exon 1 of 1)	195	NM_178244	240819	Mm.453236	NM_178244	ENSMUSG00000047053	Teddm1a	Epdd1|Teddm1|e9-1	transmembrane epididymal protein 1A	protein-coding
mm_28210.1	chr3	88336499	88336526	-	1	NA	intron (NM_178246, intron 1 of 21)	intron (NM_178246, intron 1 of 21)	252	NM_178246	229512	Mm.439830	NM_173188	ENSMUSG00000001415	Smg5	BC024683|mKIAA1089	Smg-5 homolog, nonsense mediated mRNA decay factor (C. elegans)	protein-coding
mm_165040.1	chr19	39023464	39023464	+	1	NA	intron (NM_028089, intron 4 of 8)	Lx6|LINE|L1	16445	NM_028089	72082	Mm.142581	NM_028089	ENSMUSG00000025002	Cyp2c55	2010318C06Rik	cytochrome P450, family 2, subfamily c, polypeptide 55	protein-coding
mm_120353.1	chr14	63992445	63992455	+	1	NA	promoter-TSS (NM_146246)	promoter-TSS (NM_146246)	19	NM_146246	271209	Mm.300655	NM_146246	ENSMUSG00000046049	Rp1l1	BC031365|BE983540|Dcdc4|Rp1hl1	retinitis pigmentosa 1 homolog like 1	protein-coding
mm_168322.1	chr11	115419916	115419921	-	1	NA	promoter-TSS (NM_027862)	promoter-TSS (NM_027862)	1	NM_027862	71679	Mm.371641	NM_027862	ENSMUSG00000034566	Atp5h	0610009D10Rik	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit D	protein-coding
mm_120695.1	chr14	70890100	70890130	+	1	NA	promoter-TSS (NM_008115)	promoter-TSS (NM_008115)	8	NM_001302094	14586	Mm.32619	NM_008115	ENSMUSG00000022103	Gfra2	-	glial cell line derived neurotrophic factor family receptor alpha 2	protein-coding
mm_150346.1	chr19	34641125	34641132	+	1	NA	promoter-TSS (NM_053217)	promoter-TSS (NM_053217)	239	NM_008331	15957	Mm.439751	NM_008331	ENSMUSG00000034459	Ifit1	ISG56|Ifi56|P56	interferon-induced protein with tetratricopeptide repeats 1	protein-coding
mm_20575.1	chr2	131086285	131086309	-	1	NA	5' UTR (NM_011426, exon 1 of 21)	5' UTR (NM_011426, exon 1 of 21)	468	NM_011426	20612	Mm.1374	NM_011426	ENSMUSG00000027322	Siglec1	Cd169|Siglec-1|Sn	sialic acid binding Ig-like lectin 1, sialoadhesin	protein-coding
mm_19042.1	chr2	77014389	77014392	-	1	NA	intron (NM_001025576, intron 23 of 23)	intron (NM_001025576, intron 23 of 23)	-31843	NM_011652	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_84274.1	chr9	62796913	62796928	-	1	NA	exon (NM_010193, exon 2 of 2)	exon (NM_010193, exon 2 of 2)	14728	NM_010193	14155	Mm.24069	NM_010193	ENSMUSG00000032244	Fem1b	mKIAA0396	feminization 1 homolog b (C. elegans)	protein-coding
mm_47714.1	chr5	130000817	130000852	-	1	NA	exon (NM_010368, exon 2 of 12)	exon (NM_010368, exon 2 of 12)	1994	NM_010368	110006	Mm.3317	NM_010368	ENSMUSG00000025534	Gusb	AI747421|Gur|Gus|Gus-r|Gus-s|Gus-t|Gus-u|Gut|asd|g	glucuronidase, beta	protein-coding
mm_41634.1	chr5	97091250	97091253	+	1	NA	TTS (NM_080708)	TTS (NM_080708)	20345	NM_198422	231474	Mm.332505	NM_198422	ENSMUSG00000055725	Paqr3	6330415A20Rik|AY424292|RKTG	progestin and adipoQ receptor family member III	protein-coding
mm_145882.1	chr18	65478476	65478505	+	1	NA	3' UTR (NM_172833, exon 16 of 16)	3' UTR (NM_172833, exon 16 of 16)	47493	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_97128.1	chr11	74927693	74927697	+	1	NA	intron (NM_001002764, intron 1 of 18)	intron (NM_001002764, intron 1 of 18)	1823	NM_001002764	103677	Mm.288460	NM_001002764	ENSMUSG00000038290	Smg6	AI317223|AU041178	Smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans)	protein-coding
mm_7581.1	chr1	125396581	125396593	-	1	NA	intron (NM_001205385, intron 11 of 12)	intron (NM_001205385, intron 11 of 12)	39140	NM_023735	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding
mm_152895.1	chr19	24862222	24862232	-	1	NA	promoter-TSS (NM_175013)	promoter-TSS (NM_175013)	-385	NM_175013	226041	Mm.105222	NM_175013	ENSMUSG00000041731	Pgm5	4833423B07|9530034F03Rik|D830025G17|aciculin	phosphoglucomutase 5	protein-coding
mm_84086.1	chr9	58202923	58202942	-	1	NA	promoter-TSS (NM_177193)	promoter-TSS (NM_177193)	35	NR_033522	665268	Mm.451475	NR_033522	ENSMUSG00000057818	1600029O15Rik	-	ribosomal protein L17 pseudogene	pseudo
mm_44187.1	chr5	151401114	151401134	+	1	NA	intron (NR_045700, intron 2 of 3)	B4A|SINE|B4	-5380	NR_131166	100042166	Mm.443286	NR_131166	ENSMUSG00000097321	Gm3704	-	predicted gene 3704	ncRNA
mm_121255.1	chr14	103057641	103057651	+	1	NA	Intergenic	B4A|SINE|B4	10634	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_24615.1	chr3	93470680	93470687	+	1	NA	exon (NM_027762, exon 3 of 3)	exon (NM_027762, exon 3 of 3)	1929	NM_027762	71325	Mm.68064	NM_027762	ENSMUSG00000027908	Tchhl1	5430400H23Rik|AA589420|S100a17|Thhl1	trichohyalin-like 1	protein-coding
mm_104105.1	chr11	86707093	86707106	-	1	NA	exon (NM_001003908, exon 20 of 32)	exon (NM_001003908, exon 20 of 32)	23018	NM_001098810	217057	Mm.24868	NM_175004	ENSMUSG00000072582	Ptrh2	A230072I16Rik|Bit1|CGI-147	peptidyl-tRNA hydrolase 2	protein-coding
mm_2025.1	chr1	87128690	87128697	+	1	NA	TTS (NM_007432)	TTS (NM_007432)	3685	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_60412.1	chr7	44476134	44476144	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	5792	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_116356.1	chr13	40725187	40725215	-	1	NA	intron (NM_001301674, intron 3 of 7)	intron (NM_001301674, intron 3 of 7)	-2607	NR_125899	102633805		NR_125899	ENSMUSG00000097752	Gm26688	Tfap2a-as1	predicted gene, 26688	ncRNA
mm_15486.1	chr2	157562109	157562144	+	1	NA	3' UTR (NM_010923, exon 3 of 3)	3' UTR (NM_010923, exon 3 of 3)	2048	NM_180960	18111	Mm.34330	NM_010923	ENSMUSG00000067786	Nnat	5730414I02Rik|AW107673|Peg5	neuronatin	protein-coding
mm_123145.1	chr14	57057669	57057726	-	1	NA	promoter-TSS (NM_001271623)	promoter-TSS (NM_001271623)	26	NM_001271623	14611	Mm.57207	NM_016975	ENSMUSG00000048582	Gja3	Cnx46|Cx43|Cx46|Gja-3	gap junction protein, alpha 3	protein-coding
mm_57592.1	chr6	127769175	127769196	-	1	NA	promoter-TSS (NM_201371)	promoter-TSS (NM_201371)	-26	NM_201371	381813	Mm.39750	NM_201371	ENSMUSG00000030350	Prmt8	Hrmt1l3|Hrmt1l4	protein arginine N-methyltransferase 8	protein-coding
mm_170109.1	chr17	39844966	39844974	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	1973	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_143387.1	chr17	68004076	68004140	-	1	NA	promoter-TSS (NM_172964)	promoter-TSS (NM_172964)	0	NM_172964	268970	Mm.9935	NM_172964	ENSMUSG00000024043	Arhgap28	AU044757|AW550892|E130310N06	Rho GTPase activating protein 28	protein-coding
mm_54478.1	chr6	35086133	35086136	-	1	NA	intron (NM_016877, intron 1 of 10)	intron (NM_016877, intron 1 of 10)	47603	NM_001164412	53621	Mm.214525	NM_016877	ENSMUSG00000038784	Cnot4	Not4|Not4h|Not4hp	CCR4-NOT transcription complex, subunit 4	protein-coding
mm_90511.1	chr10	128042691	128042695	+	1	NA	exon (NM_001113199, exon 3 of 9)	exon (NM_001113199, exon 3 of 9)	7347	NM_001113199	17938	Mm.3746	NM_013608	ENSMUSG00000061315	Naca	AL022831|AL024382|Gm1878|mKIAA0363|skNAC	nascent polypeptide-associated complex alpha polypeptide	protein-coding
mm_156248.1	chrX	136271450	136271467	+	1	NA	exon (NM_009750, exon 3 of 3)	exon (NM_009750, exon 3 of 3)	1205	NM_001110234	12070	Mm.90787	NM_009750	ENSMUSG00000046432	Bex3	AL033356|DXWsu67e|Gcap27|Nade|Ngfrap1	brain expressed X-linked 3	protein-coding
mm_28792.1	chr3	95997313	95997333	-	1	NA	Intergenic	Intergenic	-1484	NM_023320	67220	Mm.458147	NM_023320	ENSMUSG00000015745	Plekho1	2810052M02Rik|CKIP-1|Ckip1|JZA-20|Jza2	pleckstrin homology domain containing, family O member 1	protein-coding
mm_17498.1	chr2	28699662	28699688	-	1	NA	promoter-TSS (NM_027283)	promoter-TSS (NM_027283)	-24	NM_027283	69987	Mm.239376	NM_027283	ENSMUSG00000026809	Spaca9	1700026L06Rik|MAST	sperm acrosome associated 9	protein-coding
mm_170492.1	chr19	23056337	23056346	-	1	NA	Intergenic	U2|snRNA|snRNA	-84885	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_141263.1	chr17	27623442	27623495	-	1	NA	promoter-TSS (NM_001291046)	promoter-TSS (NM_001291046)	-16	NM_019837	56409	Mm.144699	NM_019837	ENSMUSG00000024213	Nudt3	1110011B09Rik|AA960325|Dipp|Dipp1	nudix (nucleotide diphosphate linked moiety X)-type motif 3	protein-coding
mm_166508.1	chr6	6578577	6578592	-	1	NA	promoter-TSS (NM_009169)	promoter-TSS (NM_009169)	74	NM_009169	20422	Mm.2469	NM_009169	ENSMUSG00000042541	Shfm1	DSS1|Shfdg1|Shfg	split hand/foot malformation (ectrodactyly) type 1	protein-coding
mm_123588.1	chr14	67072466	67072476	-	1	NA	promoter-TSS (NM_028032)	promoter-TSS (NM_028032)	0	NM_028032	71978	Mm.273997	NM_028032	ENSMUSG00000022052	Ppp2r2a	2410004D02Rik|mKIAA1541	protein phosphatase 2, regulatory subunit B, alpha	protein-coding
mm_159533.1	chr4	72852679	72852679	-	1	NA	promoter-TSS (NM_001199270)	promoter-TSS (NM_001199270)	-45	NM_001199270	353204	Mm.317892	NM_001199270	ENSMUSG00000059343	Aldoart1	4921524E03Rik|Aldo1-ps|Aldo1-ps2|Aldoa-ps2	aldolase 1 A, retrogene 1	protein-coding
mm_66024.1	chr7	30612732	30612744	-	1	NA	promoter-TSS (NM_026815)	promoter-TSS (NM_026815)	-4	NM_026815	109637	Mm.25471	NM_026815	ENSMUSG00000006313	Upk1a	1110031P12Rik|AU019298|C87192|Tspan21|Upk1	uroplakin 1A	protein-coding
mm_6739.1	chr1	83038822	83038825	-	1	NA	promoter-TSS (NM_030556)	promoter-TSS (NM_030556)	-375	NM_030556	80721	Mm.261542	NM_030556	ENSMUSG00000038496	Slc19a3	A230084E24Rik|AI788884|ThTr2	solute carrier family 19, member 3	protein-coding
mm_2075.1	chr1	87641176	87641178	+	1	NA	intron (NM_010566, intron 2 of 26)	intron (NM_010566, intron 2 of 26)	20865	NM_001110193	16331	Mm.15105	NM_010566	ENSMUSG00000026288	Inpp5d	SHIP|SHIP-1|SHIP1|SIP-145|p150Ship|s-SHIP	inositol polyphosphate-5-phosphatase D	protein-coding
mm_29948.1	chr3	132950224	132950226	-	1	NA	promoter-TSS (NM_001287103)	promoter-TSS (NM_001287103)	66	NM_001287102	114249	Mm.279310	NM_033525	ENSMUSG00000040998	Npnt	1110009H02Rik|AA682063|AI314031|Nctn|POEM	nephronectin	protein-coding
mm_46844.1	chr5	113413083	113413094	-	1	NA	Intergenic	Intergenic	55794	NM_001012726	503692	Mm.348794	NM_001012726	ENSMUSG00000053873	Aym1	-	activator of yeast meiotic promoters 1	protein-coding
mm_71809.1	chr8	68880651	68880672	+	1	NA	5' UTR (NM_008509, exon 1 of 10)	5' UTR (NM_008509, exon 1 of 10)	106	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_161680.1	chr17	17064078	17064078	+	1	NA	promoter-TSS (NM_001163919)	promoter-TSS (NM_001163919)	-25	NM_001005358	449000	Mm.483718	NM_001005358	ENSMUSG00000096696	Zfp960	-	zinc finger protein 960	protein-coding
mm_126017.1	chr15	76667480	76667496	+	1	NA	TTS (NM_007989)	TTS (NM_007989)	2460	NM_007989	14106	Mm.42011	NM_007989	ENSMUSG00000033837	Foxh1	Fast1|Fast2|fast-1|fast-2	forkhead box H1	protein-coding
mm_142089.1	chr17	35833974	35833974	-	1	NA	TTS (NM_011655)	TTS (NM_011655)	4327	NM_011655	22154	Mm.273538	NM_011655	ENSMUSG00000001525	Tubb5	AA408537|AI596182|B130022C14Rik|M(beta)5	tubulin, beta 5 class I	protein-coding
mm_111591.1	chr12	101975914	101975924	-	1	NA	promoter-TSS (NM_016856)	promoter-TSS (NM_016856)	-55	NM_016856	51786	Mm.716	NM_016856	ENSMUSG00000041781	Cpsf2	100kDa|2610024B04Rik|AI662483|Cpsf|MCPSF|mKIAA1367	cleavage and polyadenylation specific factor 2	protein-coding
mm_115294.1	chr13	111980627	111980655	+	1	NA	Intergenic	Intergenic	112705	NR_130345	102636620	Mm.402328	NR_130345	ENSMUSG00000086111	Gm15326	OTTMUSG00000020187	predicted gene 15326	ncRNA
mm_13181.1	chr2	93030374	93030416	+	1	NA	intron (NR_110333, intron 2 of 5)	intron (NR_110333, intron 2 of 5)	1047	NR_110333	433456	Mm.235231	NM_001002794	ENSMUSG00000075027	4631405J19Rik	-	RIKEN cDNA 4631405J19 gene	ncRNA
mm_15865.1	chr2	164833767	164833775	+	1	NA	promoter-TSS (NM_001082974)	promoter-TSS (NM_001082974)	-2	NM_008906	19025	Mm.359633	NM_008906	ENSMUSG00000017760	Ctsa	AU019505|PPCA|Ppgb	cathepsin A	protein-coding
mm_149119.1	chr19	8984837	8984882	+	1	NA	Intergenic	Intergenic	-4425	NR_104460	66395	Mm.203866	NM_009643	ENSMUSG00000069833	Ahnak	DY6	AHNAK nucleoprotein (desmoyokin)	protein-coding
mm_50049.1	chr6	41163015	41163030	+	1	NA	Intergenic	Intergenic	-127513	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_32993.1	chr4	120432853	120432858	+	1	NA	intron (NM_001159630, intron 1 of 17)	RLTR20A2|LTR|ERVK	27574	NM_013883	29871	Mm.427014	NM_013883	ENSMUSG00000000085	Scmh1	AI315320|AI851618|Scml1|Scml3	sex comb on midleg homolog 1	protein-coding
mm_144001.1	chr17	88065639	88065729	-	1	NA	promoter-TSS (NM_001081034)	promoter-TSS (NM_001081034)	-399	NM_001081034	225055	Mm.386857	NM_001081034	ENSMUSG00000005371	Fbxo11	C80048|Jf	F-box protein 11	protein-coding
mm_143816.1	chr17	83837331	83837333	-	1	NA	intron (NM_025325, intron 4 of 9)	intron (NM_025325, intron 4 of 9)	9458	NM_025325	107766	Mm.30100	NM_025325	ENSMUSG00000000673	Haao	0610007K21Rik|0610012J07Rik|3-HAO|3-HAOxase|3HAO	3-hydroxyanthranilate 3,4-dioxygenase	protein-coding
mm_63984.1	chr7	140049267	140049302	+	1	NA	promoter-TSS (NM_010836)	promoter-TSS (NM_010836)	-196	NM_001347609	17703	Mm.4816	NM_010836	ENSMUSG00000025469	Msx3	AI323377	msh homeobox 3	protein-coding
mm_55562.1	chr6	71352833	71352842	-	1	NA	Intergenic	Intergenic	-20590	NM_009857	12525	Mm.1858	NM_009857	ENSMUSG00000053977	Cd8a	BB154331|Ly-2|Ly-35|Ly-B|Lyt-2	CD8 antigen, alpha chain	protein-coding
mm_76471.1	chr8	85386311	85386345	-	1	NA	Intergenic	Intergenic	-5287	NM_001297612	213435	Mm.32804	NM_175441	ENSMUSG00000031698	Mylk3	D830007F02Rik|MLCK	myosin light chain kinase 3	protein-coding
mm_34968.1	chr4	156008724	156008736	+	1	NA	intron (NM_001302468, intron 4 of 6)	intron (NM_001302468, intron 4 of 6)	-4965	NM_011659	22163	Mm.13885	NM_011659	ENSMUSG00000029075	Tnfrsf4	ACT35|CD134|Ly-70|Ox40|TXGP1L|Txgp1	tumor necrosis factor receptor superfamily, member 4	protein-coding
mm_134902.1	chr16	30185907	30185913	-	1	NA	Intergenic	Intergenic	81622	NM_027904	71756	Mm.290614	NM_027904	ENSMUSG00000023176	Cpn2	1300018K11Rik	carboxypeptidase N, polypeptide 2	protein-coding
mm_158497.1	chrX	142369235	142369237	-	1	NA	intron (NM_019477, intron 1 of 15)	B1_Mus1|SINE|Alu	21299	NM_001033600	50790	Mm.391337	NM_019477	ENSMUSG00000031278	Acsl4	9430020A05Rik|ACS4|AU018108|Facl4|Lacs4	acyl-CoA synthetase long-chain family member 4	protein-coding
mm_148482.1	chr19	4126041	4126057	+	1	NA	promoter-TSS (NM_016666)	promoter-TSS (NM_016666)	89	NM_025889	66990	Mm.276255	NM_025889		Tmem134	2410001H17Rik|AI463452	transmembrane protein 134	protein-coding
mm_148593.1	chr19	5069738	5069753	+	1	NA	exon (NM_054042, exon 1 of 1)	exon (NM_054042, exon 1 of 1)	1667	NM_054042	70445	Mm.29597	NM_054042	ENSMUSG00000056481	Cd248	2610111G01Rik|AI842296|Cd164l1|Tem1	CD248 antigen, endosialin	protein-coding
mm_153375.1	chr19	40356693	40356717	-	1	NA	intron (NM_001034963, intron 8 of 22)	intron (NM_001034963, intron 8 of 22)	45605	NM_001034964	20411	Mm.210815	NM_009166	ENSMUSG00000025006	Sorbs1	2310065E01Rik|9530001P15Rik|CAP|SH3P12|Sh3d5|mKIAA1296	sorbin and SH3 domain containing 1	protein-coding
mm_45041.1	chr5	41636982	41636985	-	1	NA	intron (NR_132325, intron 3 of 5)	intron (NR_132325, intron 3 of 5)	70708	NM_001310592	100972	Mm.41555	NM_027295	ENSMUSG00000029128	Rab28	2700023P08Rik|AW496496	RAB28, member RAS oncogene family	protein-coding
mm_10163.1	chr2	4401394	4401500	+	1	NA	5' UTR (NM_001177843, exon 1 of 24)	5' UTR (NM_001177843, exon 1 of 24)	471	NM_001177843	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding
mm_108076.1	chr12	73945763	73945786	+	1	NA	3' UTR (NM_010431, exon 15 of 15)	3' UTR (NM_010431, exon 15 of 15)	-18756	NM_178392	75627	Mm.25937	NM_178392	ENSMUSG00000021113	Snapc1	2700033G17Rik|AU015787	small nuclear RNA activating complex, polypeptide 1	protein-coding
mm_61343.1	chr7	68283804	68283805	+	1	NA	intron (NM_001013811, intron 1 of 8)	intron (NM_001013811, intron 1 of 8)	-7210	NR_040340	100504026	Mm.426764	NR_040340	ENSMUSG00000086628	Gm16157	OTTMUSG00000031023	predicted gene 16157	ncRNA
mm_49517.1	chr6	29887919	29887921	+	1	NA	intron (NM_001347084, intron 9 of 17)	intron (NM_001347084, intron 9 of 17)	28324	NM_001171001	74340	Mm.210899	NM_021414	ENSMUSG00000029772	Ahcyl2	4631427C17Rik|AI227036|Adohcyase3|mKIAA0828	S-adenosylhomocysteine hydrolase-like 2	protein-coding
mm_127162.1	chr15	98634790	98634809	+	1	NA	promoter-TSS (NM_007581)	promoter-TSS (NM_007581)	32	NM_001286226	12297	Mm.3544	NM_007581	ENSMUSG00000003352	Cacnb3	Beta3|CAB3|Ca(v)beta3|Cchb3	calcium channel, voltage-dependent, beta 3 subunit	protein-coding
mm_117479.1	chr13	77047626	77047675	-	1	NA	intron (NM_134071, intron 18 of 20)	intron (NM_134071, intron 18 of 20)	87818	NM_134071	105377	Mm.209730	NM_134071	ENSMUSG00000021597	Slf1	2700017A04Rik|AW545819|Ankrd32|Brctd1|Brctx|C730024G01Rik	SMC5-SMC6 complex localization factor 1	protein-coding
mm_36414.1	chr4	78211686	78211696	-	1	NA	5' UTR (NM_011211, exon 1 of 40)	5' UTR (NM_011211, exon 1 of 40)	204	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding
mm_139208.1	chr17	47703207	47703247	+	1	NA	exon (NM_144939, exon 7 of 7)	exon (NM_144939, exon 7 of 7)	-1231	NR_045913	100126242	Mm.392746	NR_045912	ENSMUSG00000086930	Frs3os	4930417B13Rik|Gm14873|OTTMUSG00000018358	fibroblast growth factor receptor substrate 3, opposite strand	ncRNA
mm_45496.1	chr5	72165135	72165138	-	1	NA	intron (NM_178599, intron 2 of 4)	intron (NM_178599, intron 2 of 4)	3047	NM_178599	27784	Mm.44223	NM_178599	ENSMUSG00000029213	Commd8	C77770|D5Buc26e	COMM domain containing 8	protein-coding
mm_138677.1	chr17	35916542	35916562	+	1	NA	promoter-TSS (NM_025878)	promoter-TSS (NM_025878)	-112	NM_001347380	66973	Mm.29484	NM_025878	ENSMUSG00000024436	Mrps18b	2400002C15Rik	mitochondrial ribosomal protein S18B	protein-coding
mm_17398.1	chr2	27142531	27142556	-	1	NA	promoter-TSS (NM_175427)	promoter-TSS (NM_175427)	-66	NM_175427	109349	Mm.314080	NM_175427	ENSMUSG00000009216	Fam163b	C630035N08Rik	family with sequence similarity 163, member B	protein-coding
mm_170307.1	chr18	34952409	34952414	-	1	NA	exon (NM_010481, exon 3 of 17)	exon (NM_010481, exon 3 of 17)	1940	NM_010481	15526	Mm.209419	NM_010481	ENSMUSG00000024359	Hspa9	74kDa|Csa|Grp75|Hsc74|Hsp74|Hsp74a|Hspa9a|Mortalin|Mot-2|Mot2|Mthsp70|Pbp74	heat shock protein 9	protein-coding
mm_126638.1	chr15	83593000	83593025	+	1	NA	intron (NM_183017, intron 1 of 13)	intron (NM_183017, intron 1 of 13)	2145	NM_183017	223723	Mm.46778	NM_183017	ENSMUSG00000016757	Ttll12	BC055368|D430005B17	tubulin tyrosine ligase-like family, member 12	protein-coding
mm_63038.1	chr7	121075842	121075858	+	1	NA	intron (NM_021554, intron 4 of 4)	intron (NM_021554, intron 4 of 4)	-1320	NM_030691	80719	Mm.160384	NM_030691	ENSMUSG00000035004	Igsf6	-	immunoglobulin superfamily, member 6	protein-coding
mm_167880.1	chrX	43428927	43428929	-	1	NA	Intergenic	Intergenic	-154144	NM_011855	23963	Mm.327698	NM_011855	ENSMUSG00000016150	Tenm1	Odz1|Odz2|TCAP-1|Ten-m1|ten-1	teneurin transmembrane protein 1	protein-coding
mm_18468.1	chr2	62411696	62411706	-	1	NA	intron (NM_001159543, intron 1 of 24)	intron (NM_001159543, intron 1 of 24)	530	NM_010074	13482	Mm.1151	NM_010074	ENSMUSG00000035000	Dpp4	Cd26|Dpp-4|THAM	dipeptidylpeptidase 4	protein-coding
mm_16704.1	chr2	7044324	7044324	-	1	NA	intron (NM_001110231, intron 3 of 15)	intron (NM_001110231, intron 3 of 15)	36978	NM_001110230	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_134887.1	chr16	29441761	29441807	-	1	NA	intron (NM_172613, intron 14 of 29)	intron (NM_172613, intron 14 of 29)	-63052	NM_175650	268878	Mm.9823	NM_175650	ENSMUSG00000048939	Atp13a5	C630015F21Rik	ATPase type 13A5	protein-coding
mm_39442.1	chr5	16870256	16870263	+	1	NA	Intergenic	Intergenic	316358	NM_001289461	15234	Mm.267078	NM_010427	ENSMUSG00000028864	Hgf	C230052L06Rik|HGF/SF|NK1|NK2|SF|SF/HGF	hepatocyte growth factor	protein-coding
mm_85765.1	chr9	108854576	108854600	-	1	NA	5' UTR (NM_134420, exon 1 of 18)	5' UTR (NM_134420, exon 1 of 18)	545	NM_134420	171429	Mm.45201	NM_134420	ENSMUSG00000023259	Slc26a6	B930010B04Rik|CFEX|Pat-1|Pat1	solute carrier family 26, member 6	protein-coding
mm_107495.1	chr12	38783674	38783684	+	1	NA	promoter-TSS (NM_001163154)	promoter-TSS (NM_001163154)	-32	NM_001163154	14009	Mm.4866	NM_007960	ENSMUSG00000004151	Etv1	ER81|Etsrp81	ets variant 1	protein-coding
mm_44077.1	chr5	149016118	149016140	+	1	NA	Intergenic	Intergenic	9167	NR_040429	100503307	Mm.188008	NR_040429	ENSMUSG00000086610	Gm15408	OTTMUSG00000021225	predicted gene 15408	ncRNA
mm_3077.1	chr1	134290023	134290031	+	1	NA	promoter-TSS (NM_031189)	promoter-TSS (NM_031189)	23	NM_031189	17928	Mm.16528	NM_031189	ENSMUSG00000026459	Myog	MYF4|bHLHc3|myo	myogenin	protein-coding
mm_71711.1	chr8	61936256	61936286	+	1	NA	intron (NM_001293783, intron 1 of 37)	intron (NM_001293783, intron 1 of 37)	8184	NM_001293783	234311	Mm.275233	NM_144928	ENSMUSG00000037921	Ddx60	9830118M07	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	protein-coding
mm_77412.1	chr8	120628571	120628577	-	1	NA	intron (NM_001308449, intron 1 of 3)	intron (NM_001308449, intron 1 of 3)	5808	NM_197988	68918	Mm.473736	NM_197988	ENSMUSG00000043687	1190005I06Rik	-	RIKEN cDNA 1190005I06 gene	protein-coding
mm_77069.1	chr8	109991901	109991916	-	1	NA	exon (NM_146214, exon 3 of 12)	exon (NM_146214, exon 3 of 12)	1472	NM_146214	234724	Mm.28110	NM_146214	ENSMUSG00000001670	Tat	-	tyrosine aminotransferase	protein-coding
mm_147686.1	chr18	60723719	60723731	-	1	NA	Intergenic	Intergenic	-10336	NM_008306	15531	Mm.181862	NM_008306	ENSMUSG00000054008	Ndst1	1200015G06Rik|HSNST|HSNST 1|Hsst|N-HSST|N-HSST 1|NDST-1|b2b2230Clo	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 1	protein-coding
mm_130547.1	chr15	98953689	98953699	-	1	NA	promoter-TSS (NM_011653)	promoter-TSS (NM_011653)	-193	NM_011653	22142	Mm.405359	NM_011653	ENSMUSG00000072235	Tuba1a	Tuba-1|Tuba1	tubulin, alpha 1A	protein-coding
mm_142233.1	chr17	37481025	37481031	-	1	NA	3' UTR (NM_008204, exon 4 of 4)	3' UTR (NM_008204, exon 4 of 4)	2501	NM_008204	14990	Mm.329041	NM_008204	ENSMUSG00000016283	H2-M2	H-2M2|Thy19.4	histocompatibility 2, M region locus 2	protein-coding
mm_34127.1	chr4	139262021	139262043	+	1	NA	exon (NM_001271405, exon 4 of 9)	exon (NM_001271405, exon 4 of 9)	48668	NM_145384	212555	Mm.45131	NM_145384	ENSMUSG00000028744	Pqlc2	BC019216	PQ loop repeat containing 2	protein-coding
mm_77904.1	chr9	7349058	7349094	+	1	NA	intron (NM_001320077, intron 3 of 10)	B4A|SINE|B4	1702	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_37609.1	chr4	126753711	126753729	-	1	NA	promoter-TSS (NM_001035526)	promoter-TSS (NM_001035526)	-50	NM_133886	100317	Mm.206206	NM_133886	ENSMUSG00000028830	AU040320	A730047D20Rik|AAVR|Kiaa0319l	expressed sequence AU040320	protein-coding
mm_27070.1	chr3	28164745	28164748	-	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	-98468	NM_001163007	665113	Mm.126193	NM_026910	ENSMUSG00000027692	Tnik	1500031A17Rik|4831440I19Rik|AI451411|C530008O15Rik|C630040K21Rik	TRAF2 and NCK interacting kinase	protein-coding
mm_107394.1	chr12	33315394	33315411	+	1	NA	intron (NM_001033436, intron 1 of 7)	intron (NM_001033436, intron 1 of 7)	12887	NM_001033436	380753	Mm.41540	NM_028139	ENSMUSG00000020564	Atxn7l1	2810423G08Rik|Atxn7l4	ataxin 7-like 1	protein-coding
mm_75177.1	chr8	36952163	36952172	-	1	NA	5' UTR (NM_001194940, exon 1 of 18)	5' UTR (NM_001194940, exon 1 of 18)	275	NM_001194940	50768	Mm.125155	NM_015802	ENSMUSG00000031523	Dlc1	A730069N07Rik|Arhgap7|HP|STARD12|dlc-1	deleted in liver cancer 1	protein-coding
mm_29747.1	chr3	126997947	126997985	-	1	NA	intron (NM_001327938, intron 21 of 47)	intron (NM_001327938, intron 21 of 47)	486	NM_178655	109676	Mm.220242	NM_178655	ENSMUSG00000032826	Ank2	100043364|AI835472|AW491075|Ank-2|Gm4392	ankyrin 2, brain	protein-coding
mm_124784.1	chr15	7497494	7497500	+	1	NA	Intergenic	Intergenic	-99102	NM_001289498	268780	Mm.203208	NM_178748	ENSMUSG00000042961	Egflam	5930412K08|AU040377	EGF-like, fibronectin type III and laminin G domains	protein-coding
mm_70844.1	chr8	23446703	23446717	+	1	NA	3' UTR (NM_013834, exon 3 of 3)	3' UTR (NM_013834, exon 3 of 3)	35208	NM_013834	20377	Mm.281691	NM_013834	ENSMUSG00000031548	Sfrp1	2210415K03Rik|AW011917|AW107218|AW742929|sFRP-1	secreted frizzled-related protein 1	protein-coding
mm_155994.1	chrX	106156786	106156809	+	1	NA	exon (NM_205820, exon 3 of 3)	exon (NM_205820, exon 3 of 3)	13522	NM_205820	279572	Mm.336203	NM_205820	ENSMUSG00000033777	Tlr13	AI666735|Gm713	toll-like receptor 13	protein-coding
mm_154439.1	chrM	1249	1266	-	1	NA	NA	Intergenic	NA	NA								
mm_163830.1	chr14	19417550	19417571	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	185027	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_93340.1	chr10	99759606	99759616	-	1	NA	promoter-TSS (NM_027945)	promoter-TSS (NM_027945)	47	NM_027945	71832	Mm.483162	NM_027945	ENSMUSG00000046934	Csl	1700007H16Rik	citrate synthase like	protein-coding
mm_88488.1	chr10	77711418	77711423	+	1	NA	promoter-TSS (NM_001081452)	promoter-TSS (NM_001081452)	-26	NM_001081452	100009614	Mm.35821	NM_001081452	ENSMUSG00000094012	Gm10024	ENSMUSG00000057573	predicted gene 10024	protein-coding
mm_42379.1	chr5	114932742	114932768	+	1	NA	exon (NM_145209, exon 5 of 7)	exon (NM_145209, exon 5 of 7)	-9447	NM_028211	72357	Mm.292672	NM_028211	ENSMUSG00000029559	2210016L21Rik	-	RIKEN cDNA 2210016L21 gene	protein-coding
mm_12143.1	chr2	61804575	61804627	+	1	NA	5' UTR (NM_009322, exon 1 of 6)	5' UTR (NM_009322, exon 1 of 6)	148	NM_009322	21375	Mm.308525	NM_009322	ENSMUSG00000035033	Tbr1	-	T-box brain gene 1	protein-coding
mm_31675.1	chr4	62280400	62280421	+	1	NA	Intergenic	L1MB2|LINE|L1	-6019	NM_025286	20530	Mm.292539	NM_025286	ENSMUSG00000066152	Slc31a2	AI604396|CTR2	solute carrier family 31, member 2	protein-coding
mm_130238.1	chr15	96507196	96507201	-	1	NA	Intergenic	RLTR31C_MM|LTR|ERVK	-46355	NM_028148	72193	Mm.324474	NM_028148	ENSMUSG00000033228	Scaf11	1110061H03Rik|2610510E10Rik|AI462454|CASP11|SIP1|SRRP129|Sfrs2ip|Srsf2ip|mKIAA3013	SR-related CTD-associated factor 11	protein-coding
mm_66359.1	chr7	43528700	43528710	-	1	NA	3' UTR (NM_001111058, exon 7 of 7)	3' UTR (NM_001111058, exon 7 of 7)	4466	NM_001111058	12489	Mm.140157	NM_021293	ENSMUSG00000004609	Cd33	Siglec-3|gp67	CD33 antigen	protein-coding
mm_15136.1	chr2	153966392	153966438	+	1	NA	Intergenic	Intergenic	-8530	NM_001080811	545477	Mm.379973	NM_001080811	ENSMUSG00000078998	Bpifa6	EG545477|Gm5840|Splunc6	BPI fold containing family A, member 6	protein-coding
mm_124412.1	chr14	116947990	116947994	-	1	NA	intron (NM_001079844, intron 1 of 9)	intron (NM_001079844, intron 1 of 9)	22695	NM_011821	23888	Mm.440025	NM_011821	ENSMUSG00000058571	Gpc6	-	glypican 6	protein-coding
mm_150868.1	chr19	45047599	45047670	+	1	NA	promoter-TSS (NM_053197)	promoter-TSS (NM_053197)	58	NM_001178013	94280	Mm.36169	NM_053197	ENSMUSG00000025212	Sfxn3	-	sideroflexin 3	protein-coding
mm_14430.1	chr2	130563733	130563798	+	1	NA	promoter-TSS (NM_207207)	promoter-TSS (NM_207207)	8	NM_207207	99045	Mm.30057	NM_207207	ENSMUSG00000037740	Mrps26	AI648866|GI008|MRP-S13|MRP-S26|Rpms13	mitochondrial ribosomal protein S26	protein-coding
mm_132438.1	chr16	35938471	35938489	+	1	NA	promoter-TSS (NM_030253)	promoter-TSS (NM_030253)	10	NM_030253	80285	Mm.49074	NM_030253	ENSMUSG00000022906	Parp9	ARTD9|AW214463|BC003281|Bagl|Bal|PARP-9	poly (ADP-ribose) polymerase family, member 9	protein-coding
mm_6548.1	chr1	75133508	75133516	-	1	NA	exon (NM_194333, exon 2 of 12)	exon (NM_194333, exon 2 of 12)	378	NM_194333	22626	Mm.68157	NM_194333	ENSMUSG00000026205	Slc23a3	SVCT3|Yspl1	solute carrier family 23 (nucleobase transporters), member 3	protein-coding
mm_131132.1	chr16	5902594	5902595	+	1	NA	intron (NM_021477, intron 1 of 16)	Lx8b|LINE|L1	17801	NM_021477	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_28496.1	chr3	92484529	92484540	-	1	NA	exon (NM_009264, exon 2 of 2)	exon (NM_009264, exon 2 of 2)	1347	NM_009264	20753	Mm.331191	NM_009264	ENSMUSG00000050359	Sprr1a	AI528815|SPR1a|mSPRR1A	small proline-rich protein 1A	protein-coding
mm_7739.1	chr1	130911442	130911451	-	1	NA	promoter-TSS (NM_021380)	promoter-TSS (NM_021380)	-150	NM_021380	58181	Mm.103794	NM_021380	ENSMUSG00000026416	Il20	Zcyto10	interleukin 20	protein-coding
mm_22417.1	chr2	181498773	181498779	-	1	NA	intron (NR_111899, intron 1 of 5)	RMER15|LTR|ERVL	1634	NM_001291204	66314	Mm.136648	NM_025482	ENSMUSG00000000827	Tpd52l2	2810411G23Rik|AU016537|C86069|D54	tumor protein D52-like 2	protein-coding
mm_60585.1	chr7	44482724	44482740	+	1	NA	Intergenic	Intergenic	-1785	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_153353.1	chr19	40156838	40156865	-	1	NA	exon (NM_145499, exon 8 of 9)	exon (NM_145499, exon 8 of 9)	30435	NM_145499	226105	Mm.29119	NM_145499	ENSMUSG00000060613	Cyp2c70	-	cytochrome P450, family 2, subfamily c, polypeptide 70	protein-coding
mm_36525.1	chr4	84675414	84675428	-	1	NA	promoter-TSS (NM_172870)	promoter-TSS (NM_172870)	-335	NM_172870	242509	Mm.190774	NM_172870	ENSMUSG00000028487	Bnc2	5031434M05Rik|8430420F16Rik	basonuclin 2	protein-coding
mm_94820.1	chr11	23256002	23256105	+	1	NA	promoter-TSS (NM_134014)	promoter-TSS (NM_134014)	12	NM_134014	103573	Mm.217547	NM_134014	ENSMUSG00000020290	Xpo1	AA420417|Crm1|Exp1	exportin 1	protein-coding
mm_173338.1	chrY	90811573	90811574	+	1	NA	intron (NM_133362, intron 2 of 3)	IMPB_01|Satellite|Satellite	26131	NM_133362	170942	Mm.76062	NM_133362	ENSMUSG00000096768	Erdr1	edr	erythroid differentiation regulator 1	protein-coding
mm_156007.1	chrX	106920600	106920613	+	1	NA	promoter-TSS (NM_175271)	promoter-TSS (NM_175271)	-19	NM_175271	78134	Mm.90147	NM_175271	ENSMUSG00000049929	Lpar4	5730485F04Rik|Gpr23|LPA4|p2y9	lysophosphatidic acid receptor 4	protein-coding
mm_80695.1	chr9	91437850	91437854	+	1	NA	Intergenic	Intergenic	68880	NM_009576	22774	Mm.8062	NM_009576	ENSMUSG00000036972	Zic4	-	zinc finger protein of the cerebellum 4	protein-coding
mm_39270.1	chr5	3657188	3657205	+	1	NA	5' UTR (NM_029154, exon 1 of 11)	5' UTR (NM_029154, exon 1 of 11)	192	NM_029154	75010	Mm.85064	NM_029141	ENSMUSG00000014529	Tmbim7	4930403J02Rik|4930500J03Rik|4930511M11Rik|Lfg5|Lgf5|Tmbim1b	transmembrane BAX inhibitor motif containing 7	protein-coding
mm_118216.1	chr13	110280655	110280671	-	1	NA	promoter-TSS (NM_023852)	promoter-TSS (NM_023852)	-457	NM_023852	67295	Mm.151600	NM_023852	ENSMUSG00000021700	Rab3c	2700062I01Rik|3110015B08Rik|3110037E15Rik|AI850886	RAB3C, member RAS oncogene family	protein-coding
mm_130747.1	chr15	101261362	101261370	-	1	NA	Intergenic	Intergenic	-5480	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_105126.1	chr11	101232295	101232335	-	1	NA	Intergenic	Intergenic	-5852	NM_007970	14055	Mm.5027	NM_007970	ENSMUSG00000006920	Ezh1	ENX-2	enhancer of zeste 1 polycomb repressive complex 2 subunit	protein-coding
mm_102651.1	chr11	63313382	63313384	-	1	NA	intron (NR_105772, intron 4 of 6)	intron (NR_105772, intron 4 of 6)	72686	NR_105772	102466632		NR_105772	ENSMUSG00000098829	Mir6354	Gm27282|mmu-mir-6354	microRNA 6354	ncRNA
mm_56978.1	chr6	120294922	120294935	-	1	NA	promoter-TSS (NM_198884)	promoter-TSS (NM_198884)	-369	NM_198884	330406	Mm.321840	NM_198884	ENSMUSG00000041372	B4galnt3	AB114826|B4GalNAcT3|C330047A21	beta-1,4-N-acetyl-galactosaminyl transferase 3	protein-coding
mm_34316.1	chr4	141819086	141819102	+	1	NA	exon (NM_007919, exon 6 of 8)	exon (NM_007919, exon 6 of 8)	6911	NM_007919	13706	Mm.45316	NM_007919	ENSMUSG00000058579	Cela2a	Ela-2|Ela2|Ela2a	chymotrypsin-like elastase family, member 2A	protein-coding
mm_132580.1	chr16	38347074	38347084	+	1	NA	promoter-TSS (NM_001017429)	promoter-TSS (NM_001017429)	80	NM_001017429	12856	Mm.27396	NM_001017429	ENSMUSG00000046516	Cox17	AI037035	cytochrome c oxidase assembly protein 17	protein-coding
mm_165742.1	chr3	107218158	107218164	-	1	NA	exon (NM_001111143, exon 4 of 9)	exon (NM_001111143, exon 4 of 9)	3571	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_85632.1	chr9	107635331	107635353	-	1	NA	promoter-TSS (NM_008138)	promoter-TSS (NM_008138)	0	NM_008138	14678	Mm.196464	NM_008138	ENSMUSG00000032562	Gnai2	C76432|Galphai2|Gia|Gnai-2	guanine nucleotide binding protein (G protein), alpha inhibiting 2	protein-coding
mm_41203.1	chr5	88455989	88455993	+	1	NA	promoter-TSS (NM_009664)	promoter-TSS (NM_009664)	0	NM_001303431	11698	Mm.8437	NM_009664	ENSMUSG00000029288	Ambn	-	ameloblastin	protein-coding
mm_28412.1	chr3	90389282	90389319	-	1	NA	exon (NM_001316688, exon 1 of 10)	exon (NM_001316688, exon 1 of 10)	638	NM_001316688	26568	Mm.45519	NM_011988	ENSMUSG00000027932	Slc27a3	Acsvl3|FATP-3|FATP3|Vlcs-3	solute carrier family 27 (fatty acid transporter), member 3	protein-coding
mm_105864.1	chr11	114066987	114067064	-	1	NA	Intergenic	CpG	-1074	NM_172800	237979	Mm.130504	NM_172800	ENSMUSG00000041592	Sdk2	4632412F08Rik|5330435L01Rik|Sdk-2|mKIAA1514	sidekick cell adhesion molecule 2	protein-coding
mm_80823.1	chr9	96766812	96766836	+	1	NA	intron (NR_102294, intron 1 of 2)	MT2B1|LTR|ERVL	1262	NR_102296	319707	Mm.392191	NR_102293	ENSMUSG00000101581	C430002N11Rik	-	RIKEN cDNA C430002N11 gene	ncRNA
mm_127576.1	chr15	102296257	102296330	+	1	NA	promoter-TSS (NM_001014976)	promoter-TSS (NM_001014976)	0	NM_001014976	105988	Mm.288324	NM_001014976	ENSMUSG00000058290	Espl1	AL024103|AU045071|Cerp|ESP1|PRCE|SSE	extra spindle pole bodies 1, separase	protein-coding
mm_29384.1	chr3	108855980	108855984	-	1	NA	3' UTR (NM_177091, exon 13 of 13)	3' UTR (NM_177091, exon 13 of 13)	-15480	NM_011504	20912	Mm.316894	NM_011504	ENSMUSG00000027882	Stxbp3	Munc-18c|Stxbp3a|Sxtbp3|Unc18-3	syntaxin binding protein 3	protein-coding
mm_154038.1	chr19	53573320	53573331	-	1	NA	Intergenic	B1F2|SINE|Alu	-27071	NM_007790	13006	Mm.14910	NM_007790	ENSMUSG00000024974	Smc3	Bamacan|Cspg6|HCAP|Mmip1|SMC-3|SmcD	structural maintenance of chromosomes 3	protein-coding
mm_121552.1	chr14	122475959	122475980	+	1	NA	promoter-TSS (NR_045046)	promoter-TSS (NR_045046)	585	NM_009574	22772	Mm.308936	NM_009574	ENSMUSG00000061524	Zic2	HPE5|Ku	zinc finger protein of the cerebellum 2	protein-coding
mm_71161.1	chr8	40511417	40511444	+	1	NA	promoter-TSS (NM_033560)	promoter-TSS (NM_033560)	324	NM_001271543	18983	Mm.272551	NM_011135	ENSMUSG00000031601	Cnot7	AU022737|CAF-1|Caf1|Pop2	CCR4-NOT transcription complex, subunit 7	protein-coding
mm_170926.1	chr2	3958253	3958268	+	1	NA	Intergenic	ERVB7_2-LTR_MM|LTR|ERVK	-59423	NM_001347086	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding
mm_109708.1	chr12	113422083	113422101	+	1	NA	Intergenic	Intergenic	-67473	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_159460.1	chr3	156561889	156561889	+	1	NA	promoter-TSS (NM_001039094)	promoter-TSS (NM_001039094)	95	NM_001039094	320840	Mm.317293	NM_177274	ENSMUSG00000040037	Negr1	5330422G01Rik|KILON|Ntra	neuronal growth regulator 1	protein-coding
mm_28507.1	chr3	92573727	92573742	-	1	NA	promoter-TSS (NM_008412)	promoter-TSS (NM_008412)	1	NM_008412	16447	Mm.207365	NM_008412	ENSMUSG00000049128	Ivl	1110019C06Rik	involucrin	protein-coding
mm_71109.1	chr8	35620795	35620798	+	1	NA	intron (NM_001081279, intron 1 of 2)	intron (NM_001081279, intron 1 of 2)	-31776	NR_040376	100504714	Mm.381744	NR_040376	ENSMUSG00000097357	Gm16793	-	predicted gene, 16793	ncRNA
mm_44534.1	chr5	24475599	24475610	-	1	NA	intron (NM_139153, intron 1 of 17)	intron (NM_139153, intron 1 of 17)	23427	NM_139153	213990	Mm.250703	NM_139153	ENSMUSG00000023353	Agap3	AGAP-3|AV028425|Centg3|Crag|Crag.|MRIP-1|cnt-g3	ArfGAP with GTPase domain, ankyrin repeat and PH domain 3	protein-coding
mm_171740.1	chr4	96184923	96184926	+	1	NA	Intergenic	RLTR9D|LTR|ERVK	-43772	NM_001100182	242546	Mm.302562	NM_001100182	ENSMUSG00000081225	Cyp2j12	BB197342|Cyp2j12-ps|OTTMUSG00000007939	cytochrome P450, family 2, subfamily j, polypeptide 12	protein-coding
mm_124491.1	chr14	121739054	121739070	-	1	NA	promoter-TSS (NM_001128307)	promoter-TSS (NM_001128307)	-133	NM_001128307	105445	Mm.378591	NM_134074	ENSMUSG00000025558	Dock9	AA959601|AW538057|B230309H04Rik|D14Wsu89e|Zizimin1|mKIAA1058	dedicator of cytokinesis 9	protein-coding
mm_81817.1	chr9	118040624	118040630	+	1	NA	5' UTR (NM_013727, exon 1 of 8)	5' UTR (NM_013727, exon 1 of 8)	105	NM_013727	27215	Mm.92705	NM_013727	ENSMUSG00000039285	Azi2	AA410145|AZ2	5-azacytidine induced gene 2	protein-coding
mm_161246.1	chr13	100316600	100316600	-	1	NA	promoter-TSS (NM_010871)	promoter-TSS (NM_010871)	16	NM_010871	17952	Mm.218759	NM_010871	ENSMUSG00000078942	Naip6	Birc1f|Naip-rs4|Naip-rs4A	NLR family, apoptosis inhibitory protein 6	protein-coding
mm_53170.1	chr6	125342763	125342773	+	1	NA	intron (NM_011324, intron 8 of 11)	intron (NM_011324, intron 8 of 11)	-6955	NM_011609	21937	Mm.1258	NM_011609	ENSMUSG00000030341	Tnfrsf1a	CD120a|FPF|TNF-R|TNF-R-I|TNF-R1|TNF-R55|TNF-alphaR1|TNFAR|TNFR60|TNFRI|TNFRp55|TNFalpha-R1|Tnfr-2|Tnfr1|p55|p55-R	tumor necrosis factor receptor superfamily, member 1a	protein-coding
mm_89679.1	chr10	97517582	97517594	+	1	NA	exon (NM_007833, exon 8 of 8)	exon (NM_007833, exon 8 of 8)	35257	NM_007833	13179	Mm.56769	NM_007833	ENSMUSG00000019929	Dcn	DC|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding
mm_81524.1	chr9	110062562	110062591	+	1	NA	intron (NM_001311163, intron 1 of 10)	intron (NM_001311163, intron 1 of 10)	10555	NM_001311164	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_139859.1	chr17	69969362	69969378	+	1	NA	5' UTR (NM_001347412, exon 1 of 14)	5' UTR (NM_001347412, exon 1 of 14)	297	NM_001347411	224997	Mm.311840	NM_027712	ENSMUSG00000003279	Dlgap1	4933422O14Rik|9630002F18|AI845682|AI848168|BB075781|D17Bwg0511e|GKAP/SAPAP|GKPA/SAPAP|Gkap|Sapap1|mKIAA4162	discs, large (Drosophila) homolog-associated protein 1	protein-coding
mm_100679.1	chr11	3452888	3452899	-	1	NA	promoter-TSS (NM_001290473)	promoter-TSS (NM_001290473)	63	NM_001290472	193670	Mm.136973	NM_145355	ENSMUSG00000020448	Rnf185	-	ring finger protein 185	protein-coding
mm_30425.1	chr3	152845811	152845819	-	1	NA	intron (NM_012028, intron 3 of 4)	B4|SINE|B4	131715	NM_025662	329777	Mm.331447	NM_025662	ENSMUSG00000039047	Pigk	3000001O05Rik	phosphatidylinositol glycan anchor biosynthesis, class K	protein-coding
mm_19588.1	chr2	101950599	101950618	-	1	NA	3' UTR (NM_178886, exon 6 of 6)	3' UTR (NM_178886, exon 6 of 6)	64346	NM_029635	76501	Mm.330424	NM_029635	ENSMUSG00000027163	Commd9	1810029F08Rik|AA409293	COMM domain containing 9	protein-coding
mm_142390.1	chr17	44880831	44880831	-	1	NA	promoter-TSS (NM_029257)	promoter-TSS (NM_029257)	54	NM_029257	75341	Mm.386821	NM_029257		4930564C03Rik	-	RIKEN cDNA 4930564C03 gene	protein-coding
mm_158385.1	chrX	136085207	136085250	-	1	NA	promoter-TSS (NM_001024141)	promoter-TSS (NM_001024141)	27	NM_001024141	245610	Mm.336244	NM_001024141	ENSMUSG00000057000	Nxf3	Gm384	nuclear RNA export factor 3	protein-coding
mm_100062.1	chr11	115323546	115323573	+	1	NA	exon (NM_172801, exon 3 of 8)	exon (NM_172801, exon 3 of 8)	-1641	NM_176847	16470	Mm.451539	NM_176847	ENSMUSG00000045288	Ush1g	Sans|js	Usher syndrome 1G	protein-coding
mm_74202.1	chr8	123892307	123892382	+	1	NA	exon (NM_009606, exon 6 of 7)	exon (NM_009606, exon 6 of 7)	2431	NM_001272041	11459	Mm.214950	NM_009606	ENSMUSG00000031972	Acta1	AA959943|Acta-2|Acts|Actsk-1	actin, alpha 1, skeletal muscle	protein-coding
mm_125315.1	chr15	38219292	38219304	+	1	NA	promoter-TSS (NM_008757)	promoter-TSS (NM_008757)	95	NM_008757	18285	Mm.252830	NM_008757	ENSMUSG00000061923	Odf1	-	outer dense fiber of sperm tails 1	protein-coding
mm_93708.1	chr10	118715761	118715779	-	1	NA	Intergenic	RMER19B2|LTR|ERVK	153133	NM_001014390	69181	Mm.45565	NM_001014390	ENSMUSG00000028630	Dyrk2	1810038L18Rik	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 2	protein-coding
mm_34650.1	chr4	150853770	150853788	+	1	NA	intron (NR_040649, intron 1 of 3)	intron (NR_040649, intron 1 of 3)	1170	NR_040649	73348	Mm.396218	NR_040649	ENSMUSG00000078492	1700045H11Rik	-	RIKEN cDNA 1700045H11 gene	ncRNA
mm_119658.1	chr14	52136527	52136540	+	1	NA	intron (NM_023879, intron 10 of 24)	intron (NM_023879, intron 10 of 24)	25630	NM_023879	77945	Mm.21662	NM_023879	ENSMUSG00000057132	Rpgrip1	0610005A07Rik|4930401L23Rik|4930505G06Rik|A930002K18Rik|AA415034|nmf247	retinitis pigmentosa GTPase regulator interacting protein 1	protein-coding
mm_45206.1	chr5	52712795	52712808	-	1	NA	Intergenic	Intergenic	-28773	NM_028744	67073	Mm.248647	NM_025951	ENSMUSG00000029186	Pi4k2b	2610042N09Rik|4933409G22Rik	phosphatidylinositol 4-kinase type 2 beta	protein-coding
mm_156514.1	chrX	150554006	150554018	+	1	NA	exon (NM_009653, exon 4 of 11)	exon (NM_009653, exon 4 of 11)	-6567	NR_106147	102465782		NR_106147	ENSMUSG00000099172	Mir3620	Gm27984|mmu-mir-3620	microRNA 3620	ncRNA
mm_74845.1	chr8	24576277	24576283	-	1	NA	promoter-TSS (NM_145949)	promoter-TSS (NM_145949)	53	NM_145949	209176	Mm.219580	NM_145949	ENSMUSG00000031549	Ido2	AI265623|C230043N17Rik|Ido-2|Indol1	indoleamine 2,3-dioxygenase 2	protein-coding
mm_19931.1	chr2	116065218	116065238	-	1	NA	promoter-TSS (NM_010825)	promoter-TSS (NM_010825)	-170	NM_010825	17536	Mm.247566	NM_010825	ENSMUSG00000027210	Meis2	A430109D20Rik|Mrg1|Stra10	Meis homeobox 2	protein-coding
mm_148294.1	chr18	82585324	82585337	-	1	NA	3' UTR (NM_010777, exon 7 of 7)	3' UTR (NM_010777, exon 7 of 7)	30822	NM_001025254	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_89807.1	chr10	103029167	103029176	+	1	NA	promoter-TSS (NM_172553)	promoter-TSS (NM_172553)	-394	NM_172553	216285	Mm.19287	NM_172553	ENSMUSG00000036602	Alx1	AI314867|C130005I02|Cart1	ALX homeobox 1	protein-coding
mm_99963.1	chr11	113684426	113684480	+	1	NA	promoter-TSS (NM_138598)	promoter-TSS (NM_138598)	41	NM_177777	276852	Mm.239566	NM_177777	ENSMUSG00000041623	D11Wsu47e	-	DNA segment, Chr 11, Wayne State University 47, expressed	protein-coding
mm_170121.1	chr17	39846823	39846827	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	3828	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_31094.1	chr4	41755510	41755531	+	1	NA	promoter-TSS (NM_001302511)	promoter-TSS (NM_001302511)	292	NM_016658	14430	Mm.439669	NM_016658	ENSMUSG00000036073	Galt	AW553376	galactose-1-phosphate uridyl transferase	protein-coding
mm_36025.1	chr4	57073330	57073375	-	1	NA	exon (NM_019427, exon 12 of 16)	exon (NM_019427, exon 12 of 16)	69804	NM_019427	54357	Mm.28217	NM_019427	ENSMUSG00000028434	Epb41l4b	6430543G08Rik|AA589614|AU021054|BB007528|D4Ertd346e|Ehm2|Epb4.1l4b|Lulu2	erythrocyte membrane protein band 4.1 like 4b	protein-coding
mm_87616.1	chr10	57794528	57794528	+	1	NA	promoter-TSS (NM_020561)	promoter-TSS (NM_020561)	-16	NM_020561	57319	Mm.2379	NM_020561	ENSMUSG00000019872	Smpdl3a	0610010C24Rik|AI529588|ASM3A|ASML3|ASML3A	sphingomyelin phosphodiesterase, acid-like 3A	protein-coding
mm_96106.1	chr11	60538105	60538116	+	1	NA	5' UTR (NM_172943, exon 1 of 4)	5' UTR (NM_172943, exon 1 of 4)	427	NM_172943	268420	Mm.262056	NM_172943	ENSMUSG00000042650	Alkbh5	AW050020|AW215868|Abh5|E130207K11|Ofoxd	alkB homolog 5, RNA demethylase	protein-coding
mm_78015.1	chr9	13625681	13625685	+	1	NA	intron (NM_001013813, intron 1 of 3)	intron (NM_001013813, intron 1 of 3)	5694	NM_001013813	270118	Mm.116898	NM_173776	ENSMUSG00000031925	Maml2	5930431H10|BC032967	mastermind like 2 (Drosophila)	protein-coding
mm_156660.1	chrX	157711533	157711541	+	1	NA	intron (NR_045569, intron 3 of 6)	Lx9|LINE|L1	12564	NR_103722	66106	Mm.140340	NM_025357	ENSMUSG00000041476	Smpx	1010001C09Rik|Csl	small muscle protein, X-linked	protein-coding
mm_56443.1	chr6	97459358	97459375	-	1	NA	promoter-TSS (NM_001346639)	promoter-TSS (NM_001346639)	-80	NM_001346639	232288	Mm.27789	NM_145148	ENSMUSG00000030064	Frmd4b	6030440G05Rik|C87375|GOBLIN|GRSP1|R74720	FERM domain containing 4B	protein-coding
mm_99328.1	chr11	101460042	101460053	+	1	NA	3' UTR (NM_012037, exon 6 of 6)	3' UTR (NM_012037, exon 6 of 6)	6152	NM_012037	26949	Mm.29210	NM_012037	ENSMUSG00000034993	Vat1	VAT-1	vesicle amine transport 1	protein-coding
mm_11144.1	chr2	28513079	28513104	+	1	NA	promoter-TSS (NM_009058)	promoter-TSS (NM_009058)	-76	NM_009058	19730	Mm.5236	NM_009058	ENSMUSG00000026821	Ralgds	Gnds|Rgds|mKIAA1308	ral guanine nucleotide dissociation stimulator	protein-coding
mm_149437.1	chr19	11477921	11477938	+	1	NA	intron (NM_028595, intron 4 of 6)	intron (NM_028595, intron 4 of 6)	8561	NM_028595	73656	Mm.440719	NM_028595	ENSMUSG00000079419	Ms4a6c	2200009H22Rik|2210417N07Rik	membrane-spanning 4-domains, subfamily A, member 6C	protein-coding
mm_34563.1	chr4	149854529	149854566	+	1	NA	Intergenic	Intergenic	-80280	NM_027460	70556	Mm.41877	NM_027460	ENSMUSG00000028982	Slc25a33	5730438N18Rik|Pnc1	solute carrier family 25, member 33	protein-coding
mm_36995.1	chr4	110286855	110286886	-	1	NA	promoter-TSS (NM_010488)	promoter-TSS (NM_010488)	-36	NM_001163399	15572	Mm.3970	NM_010488	ENSMUSG00000028546	Elavl4	Elav|Hud|PNEM	ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4 (Hu antigen D)	protein-coding
mm_102197.1	chr11	54522648	54522660	-	1	NA	promoter-TSS (NM_001252494)	promoter-TSS (NM_001252494)	-191	NM_001252494	192786	Mm.254404	NM_175258	ENSMUSG00000037533	Rapgef6	A530068K01|AI844632|BB085664|C030018K18Rik|PDZ-GEF2|Pdzgef2|RA-GEF-2|Ragef2|mKIAA4052	Rap guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_7296.1	chr1	97910723	97910744	-	1	NA	intron (NM_013626, intron 7 of 25)	intron (NM_013626, intron 7 of 25)	137060	NR_037993	78603	Mm.442597	NR_037993	ENSMUSG00000089706	B230216N24Rik	-	RIKEN cDNA B230216N24 gene	ncRNA
mm_78252.1	chr9	21735668	21735674	+	1	NA	intron (NM_001252658, intron 5 of 16)	intron (NM_001252658, intron 5 of 16)	12095	NM_010700	16835	Mm.3213	NM_010700	ENSMUSG00000032193	Ldlr	Hlb301	low density lipoprotein receptor	protein-coding
mm_63190.1	chr7	125603421	125603437	+	1	NA	promoter-TSS (NM_021887)	promoter-TSS (NM_021887)	0	NM_021887	60504	Mm.155643	NM_021887	ENSMUSG00000030745	Il21r	NILR	interleukin 21 receptor	protein-coding
mm_114647.1	chr13	76935096	76935110	+	1	NA	intron (NM_030174, intron 17 of 20)	intron (NM_030174, intron 17 of 20)	200365	NM_134071	105377	Mm.209730	NM_134071	ENSMUSG00000021597	Slf1	2700017A04Rik|AW545819|Ankrd32|Brctd1|Brctx|C730024G01Rik	SMC5-SMC6 complex localization factor 1	protein-coding
mm_156784.1	chrX	161777942	161777959	+	1	NA	exon (NM_198409, exon 2 of 2)	exon (NM_198409, exon 2 of 2)	60397	NM_198409	24004	Mm.328503	NM_198409	ENSMUSG00000043518	Rai2	3f8	retinoic acid induced 2	protein-coding
mm_55664.1	chr6	72439550	72439564	-	1	NA	promoter-TSS (NM_145569)	promoter-TSS (NM_145569)	1	NM_145569	232087	Mm.29815	NM_145569	ENSMUSG00000053907	Mat2a	D630045P18Rik	methionine adenosyltransferase II, alpha	protein-coding
mm_27515.1	chr3	56183679	56183695	-	1	NA	promoter-TSS (NM_030595)	promoter-TSS (NM_030595)	14	NM_030595	26422	Mm.384353	NM_030595	ENSMUSG00000027799	Nbea	Lyst2|mKIAA1544	neurobeachin	protein-coding
mm_112079.1	chr12	112668109	112668126	-	1	NA	intron (NM_001331107, intron 2 of 13)	intron (NM_001331107, intron 2 of 13)	6159	NM_001165894	11651	Mm.6645	NM_009652	ENSMUSG00000001729	Akt1	Akt|LTR-akt|PKB|PKB/Akt|PKBalpha|Rac	thymoma viral proto-oncogene 1	protein-coding
mm_91558.1	chr10	39986596	39986608	-	1	NA	promoter-TSS (NM_001113385)	promoter-TSS (NM_001113385)	44	NM_001113385	215928	Mm.31744	NM_001001489	ENSMUSG00000038528	Mfsd4b5	Naglt1c	major facilitator superfamily domain containing 4B5	protein-coding
mm_52220.1	chr6	103510927	103510950	+	1	NA	promoter-TSS (NM_007697)	promoter-TSS (NM_007697)	62	NM_007697	12661	Mm.251288	NM_007697	ENSMUSG00000030077	Chl1	A530023M13Rik|AI465420|CALL|LICAM2	cell adhesion molecule L1-like	protein-coding
mm_83263.1	chr9	42461393	42461407	-	1	NA	intron (NM_173038, intron 1 of 7)	intron (NM_173038, intron 1 of 7)	10826	NM_173038	272589	Mm.34483	NM_173038	ENSMUSG00000037287	Tbcel	D330014K23|E130107N23Rik|Lrrc35	tubulin folding cofactor E-like	protein-coding
mm_124983.1	chr15	21035044	21035047	+	1	NA	Intergenic	Intergenic	-76407	NM_001008420	215654	Mm.300909	NM_001008420	ENSMUSG00000040452	Cdh12	Cdhb	cadherin 12	protein-coding
mm_163643.1	chr13	62812972	62813019	+	1	NA	Intergenic	CpG	-27187	NM_001256065	380850	Mm.439823	NM_001256065	ENSMUSG00000091183	Gm5141	-	predicted gene 5141	protein-coding
mm_87067.1	chr10	29143723	29143732	+	1	NA	promoter-TSS (NM_026138)	promoter-TSS (NM_026138)	-269	NM_026138	67412	Mm.390264	NM_026138	ENSMUSG00000038916	Soga3	6330407J23Rik	SOGA family member 3	protein-coding
mm_18830.1	chr2	74714264	74714296	-	1	NA	non-coding (NR_027899, exon 2 of 3)	non-coding (NR_027899, exon 2 of 3)	1850	NR_027899	73429	Mm.443313	NR_027899		Hoxd3os1	1700064D17Rik|1700109F18Rik	homeobox D3, opposite strand 1	ncRNA
mm_79879.1	chr9	65214664	65214701	+	1	NA	promoter-TSS (NM_177460)	promoter-TSS (NM_177460)	-8	NM_177460	214424	Mm.31129	NM_177460	ENSMUSG00000032392	Parp16	ARTD15|BC055447|C79952|PARP-16	poly (ADP-ribose) polymerase family, member 16	protein-coding
mm_44174.1	chr5	150953335	150953343	+	1	NA	exon (NM_013823, exon 1 of 5)	exon (NM_013823, exon 1 of 5)	732	NM_013823	16591	Mm.6500	NM_013823	ENSMUSG00000058488	Kl	alpha-kl	klotho	protein-coding
mm_152699.1	chr19	17278453	17278466	-	1	NA	Intergenic	Intergenic	61046	NM_001136484	14537	Mm.244825	NM_010265	ENSMUSG00000038843	Gcnt1	5630400D21Rik|B130048E03|C2 GlcNAcT|C2GNT|IGnT	glucosaminyl (N-acetyl) transferase 1, core 2	protein-coding
mm_2565.1	chr1	118321889	118321894	+	1	NA	promoter-TSS (NM_026472)	promoter-TSS (NM_026472)	48	NM_026472	67949	Mm.280311	NM_026472	ENSMUSG00000026377	Nifk	AI852665|C130020J04Rik|Mki67ip	nucleolar protein interacting with the FHA domain of MKI67	protein-coding
mm_26953.1	chr3	20367171	20367184	-	1	NA	promoter-TSS (NM_175086)	promoter-TSS (NM_175086)	0	NM_175086	11608	Mm.134863	NM_175086	ENSMUSG00000054988	Agtr1b	AT1B|AT2R1B|Agtr-1b|Angtr-1b	angiotensin II receptor, type 1b	protein-coding
mm_166185.1	chr5	32458958	32458968	+	1	NA	promoter-TSS (NM_172707)	promoter-TSS (NM_172707)	-7	NM_172707	19046	Mm.241931	NM_172707	ENSMUSG00000014956	Ppp1cb	1200010B19	protein phosphatase 1, catalytic subunit, beta isoform	protein-coding
mm_32085.1	chr4	98436805	98436820	+	1	NA	intron (NM_001005784, intron 11 of 19)	intron (NM_001005784, intron 11 of 19)	40986	NM_172696	12695	Mm.90218	NM_007704	ENSMUSG00000061859	Patj	Cipp|Inadl	PATJ, crumbs cell polarity complex component	protein-coding
mm_29869.1	chr3	130730280	130730288	-	1	NA	promoter-TSS (NM_001287581)	promoter-TSS (NM_001287581)	45	NM_001199350	619547	Mm.391636	NM_001199350		Rpl34-ps1	EG619547|ENSMUSG00000068396|Gm10239	ribosomal protein L34, pseudogene 1	protein-coding
mm_135192.1	chr16	36367624	36367637	-	1	NA	promoter-TSS (NM_001082546)	promoter-TSS (NM_001082546)	-60	NM_001082546	100034684	Mm.383561	NM_001082546	ENSMUSG00000071561	BC100530	-	cDNA sequence BC100530	protein-coding
mm_56063.1	chr6	86780936	86780964	-	1	NA	intron (NM_013471, intron 1 of 12)	ID_B1|SINE|B4	-5836	NM_001331120	11746	Mm.259702	NM_013471	ENSMUSG00000029994	Anxa4	AI265406|AIV|AW106930|Anx4|Xanx-4	annexin A4	protein-coding
mm_162467.1	chr1	132007396	132007418	+	1	NA	promoter-TSS (NM_007923)	promoter-TSS (NM_007923)	-198	NM_007923	13714	Mm.254233	NM_007923	ENSMUSG00000026436	Elk4	2310011G17Rik|A130026I01Rik|BB162516|SAP-1|Sap1	ELK4, member of ETS oncogene family	protein-coding
mm_128205.1	chr15	36010835	36010838	-	1	NA	intron (NM_001195748, intron 24 of 27)	intron (NM_001195748, intron 24 of 27)	-72590	NM_053071	12864	Mm.548	NM_053071	ENSMUSG00000014313	Cox6c	-	cytochrome c oxidase subunit VIc	protein-coding
mm_62814.1	chr7	113239664	113239670	+	1	NA	intron (NM_001243048, intron 2 of 16)	intron (NM_001243048, intron 2 of 16)	32202	NM_007489	11865	Mm.33970	NM_007489	ENSMUSG00000055116	Arntl	Arnt3|BMAL1b|Bmal1|MOP3|bHLHe5|bmal1b'	aryl hydrocarbon receptor nuclear translocator-like	protein-coding
mm_136985.1	chr17	17232142	17232147	+	1	NA	Intergenic	LTRIS2|LTR|ERV1	-62299	NM_001324550	100862203	Mm.484235	NM_001324550		Gm6712	EG626854	predicted gene 6712	protein-coding
mm_160397.1	chr8	69902683	69902683	-	1	NA	promoter-TSS (NM_023312)	promoter-TSS (NM_023312)	-125	NM_023312	67184	Mm.21162	NM_023312	ENSMUSG00000036199	Ndufa13	2700054G14Rik|AU022060|CDA016|CGI-39|GRIM-19|Grim19	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 13	protein-coding
mm_40508.1	chr5	57731724	57731737	+	1	NA	intron (NM_001310608, intron 1 of 3)	B1_Mur4|SINE|Alu	13649	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_52290.1	chr6	108665014	108665046	+	1	NA	exon (NM_011498, exon 5 of 5)	exon (NM_011498, exon 5 of 5)	-4096	NR_104577	75394	Mm.395061	NR_040757	ENSMUSG00000087341	0610040F04Rik	-	RIKEN cDNA 0610040F04 gene	ncRNA
mm_19550.1	chr2	98666282	98666287	-	1	NA	Intergenic	SYNREP_MM|Satellite|Satellite	1198627	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_109811.1	chr12	3426631	3426664	-	1	NA	promoter-TSS (NM_172421)	promoter-TSS (NM_172421)	100	NR_030694	100043040	Mm.415417	NR_030694	ENSMUSG00000071456	1110002L01Rik	-	RIKEN cDNA 1110002L01 gene	ncRNA
mm_556.1	chr1	38021668	38021686	+	1	NA	exon (NM_198303, exon 5 of 24)	exon (NM_198303, exon 5 of 24)	23667	NM_198303	226982	Mm.260943	NM_198303	ENSMUSG00000026083	Eif5b	A030003E17Rik|BC018347|IF2	eukaryotic translation initiation factor 5B	protein-coding
mm_164512.1	chr16	95464594	95464613	-	1	NA	intron (NM_001302152, intron 3 of 10)	RLTR17B_Mm|LTR|ERVK	-5255	NM_001302153	13876	Mm.164531	NM_133659	ENSMUSG00000040732	Erg	D030036I24Rik	avian erythroblastosis virus E-26 (v-ets) oncogene related	protein-coding
mm_170493.1	chr19	23075917	23075917	-	1	NA	Intergenic	MTEb-int|LTR|ERVL-MaLR	-65309	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_147168.1	chr18	36726572	36726586	-	1	NA	5' UTR (NM_009841, exon 1 of 2)	5' UTR (NM_009841, exon 1 of 2)	236	NM_009841	12475	Mm.3460	NM_009841	ENSMUSG00000051439	Cd14	-	CD14 antigen	protein-coding
mm_15549.1	chr2	158409921	158409935	+	1	NA	promoter-TSS (NM_001291138)	promoter-TSS (NM_001291138)	75	NM_001291138	228850	Mm.398185	NM_177227	ENSMUSG00000027652	Ralgapb	AI507211|B230339M05Rik|p170	Ral GTPase activating protein, beta subunit (non-catalytic)	protein-coding
mm_20421.1	chr2	129302979	129302990	-	1	NA	exon (NM_010554, exon 6 of 7)	exon (NM_010554, exon 6 of 7)	5614	NR_040371	100503468	Mm.446943	NR_040371	ENSMUSG00000085498	Gm14023	OTTMUSG00000015408	predicted gene 14023	ncRNA
mm_11845.1	chr2	45197734	45197744	+	1	NA	Intergenic	Intergenic	-84460	NM_015753	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_56159.1	chr6	87851530	87851565	-	1	NA	promoter-TSS (NM_013493)	promoter-TSS (NM_013493)	-441	NM_001347325	12785	Mm.290251	NM_013493	ENSMUSG00000030057	Cnbp	AA408710|Cnbp1|Znf9	cellular nucleic acid binding protein	protein-coding
mm_168853.1	chr12	24252453	24252461	-	1	NA	Intergenic	CpG	-155188	NM_001256489	66808	Mm.379124	NM_001256489	ENSMUSG00000073158	9030624G23Rik	-	RIKEN cDNA 9030624G23 gene	protein-coding
mm_140787.1	chr17	18959098	18959100	-	1	NA	Intergenic	Intergenic	44777	NM_001104549	627367	Mm.384131	NM_001104549	ENSMUSG00000091491	Vmn2r97	EG627367|Vn2r97	vomeronasal 2, receptor 97	protein-coding
mm_79491.1	chr9	57073859	57073872	+	1	NA	intron (NM_001110351, intron 1 of 21)	intron (NM_001110351, intron 1 of 21)	1825	NM_001110351	20466	Mm.15755	NM_011378	ENSMUSG00000042557	Sin3a	AW553200|Sin3|mKIAA4126|mSin3A	transcriptional regulator, SIN3A (yeast)	protein-coding
mm_2629.1	chr1	121087384	121087424	+	1	NA	promoter-TSS (NR_038008)	promoter-TSS (NR_038008)	-1	NR_038008	98452	Mm.131017	NR_038008	ENSMUSG00000097881	Celrr	AI848258|B230209K01Rik|Celr|Gm818	cerebellum expressed regulatory RNA	ncRNA
mm_37950.1	chr4	133241386	133241446	-	1	NA	exon (NM_016693, exon 1 of 29)	exon (NM_016693, exon 1 of 29)	598	NM_016693	53608	Mm.36640	NM_016693	ENSMUSG00000028862	Map3k6	Ask2|MAPKKK6|MEKK6	mitogen-activated protein kinase kinase kinase 6	protein-coding
mm_123486.1	chr14	66009205	66009235	-	1	NA	promoter-TSS (NM_178747)	promoter-TSS (NM_178747)	-10	NM_178747	268756	Mm.26207	NM_178747	ENSMUSG00000034450	Gulo	5730581M22|AU018375|BC028822|GLO|LGO|sfx|unh|unhip	gulonolactone (L-) oxidase	protein-coding
mm_50382.1	chr6	48686590	48686607	+	1	NA	intron (NM_174990, intron 1 of 2)	intron (NM_174990, intron 1 of 2)	2020	NM_174990	107526	Mm.333048	NM_174990	ENSMUSG00000054435	Gimap4	AU019574|E430007K16Rik|Ian-1|Ian1|Imap4	GTPase, IMAP family member 4	protein-coding
mm_8963.1	chr1	165160775	165160781	-	1	NA	promoter-TSS (NM_032005)	promoter-TSS (NM_032005)	-5	NM_032005	83993	Mm.190649	NM_032005	ENSMUSG00000026572	Tbx19	AU019250|D1Ertd754e|Tpit	T-box 19	protein-coding
mm_119342.1	chr14	41072937	41072943	+	1	NA	promoter-TSS (NM_027094)	promoter-TSS (NM_027094)	29	NM_027094	69496	Mm.55734	NM_027094	ENSMUSG00000021790	Dydc1	1700029M23Rik	DPY30 domain containing 1	protein-coding
mm_39686.1	chr5	26817410	26817428	+	1	NA	promoter-TSS (NM_010075)	promoter-TSS (NM_010075)	62	NM_010075	13483	Mm.42078	NM_010075	ENSMUSG00000061576	Dpp6	B930011P16Rik|D5Buc3|D5Buc4|D5Buc5|DPP VI|Dpp-6|Gm1377|In(5)6H-p|Peplb|Rw	dipeptidylpeptidase 6	protein-coding
mm_88289.1	chr10	75212159	75212187	+	1	NA	promoter-TSS (NM_001145826)	promoter-TSS (NM_001145826)	100	NM_153406	74392	Mm.27716	NM_153406	ENSMUSG00000033444	Specc1l	4930470P14Rik|4932439K10Rik|9530057A13Rik|AI317249|Cytsa|mKIAA0376	sperm antigen with calponin homology and coiled-coil domains 1-like	protein-coding
mm_9165.1	chr1	170971960	170971961	-	1	NA	intron (NM_010187, intron 1 of 6)	intron (NM_010187, intron 1 of 6)	4111	NM_001077189	14130	Mm.425062	NM_010187	ENSMUSG00000026656	Fcgr2b	AI528646|CD32|F630109E10Rik|Fc[g]RII|FcgRII|Fcgr2|Fcgr2a|Fcr-2|Fcr-3|Ly-17|Ly-m20|LyM-1|Lym-1|fcRII	Fc receptor, IgG, low affinity IIb	protein-coding
mm_80704.1	chr9	92250027	92250034	+	1	NA	promoter-TSS (NM_011636)	promoter-TSS (NM_011636)	-164	NM_011636	22038	Mm.421956	NM_011636	ENSMUSG00000032369	Plscr1	MmTRA1a|MmTRA1b|Nor1|Tra1|Tra1a|Tra1b|Tras1|Tras2	phospholipid scramblase 1	protein-coding
mm_40637.1	chr5	64906282	64906310	+	1	NA	Intergenic	Intergenic	26403	NM_030682	21897	Mm.273024	NM_030682	ENSMUSG00000044827	Tlr1	-	toll-like receptor 1	protein-coding
mm_63273.1	chr7	126762870	126762882	+	1	NA	intron (NM_011952, intron 2 of 8)	MIR3|SINE|MIR	3250	NM_011952	26417	Mm.8385	NM_011952	ENSMUSG00000063065	Mapk3	Erk-1|Erk1|Ert2|Esrk1|Mnk1|Mtap2k|Prkm3|p44|p44erk1|p44mapk	mitogen-activated protein kinase 3	protein-coding
mm_104409.1	chr11	94601826	94601851	-	1	NA	promoter-TSS (NM_153807)	promoter-TSS (NM_153807)	-52	NM_153807	264895	Mm.386885	NM_153807	ENSMUSG00000076435	Acsf2	-	acyl-CoA synthetase family member 2	protein-coding
mm_18337.1	chr2	58052833	58052870	-	1	NA	promoter-TSS (NM_029972)	promoter-TSS (NM_029972)	-99	NM_029972	77767	Mm.91712	NM_029972	ENSMUSG00000026830	Ermn	A330104H05Rik|AI854460|ermin|mKIAA1189	ermin, ERM-like protein	protein-coding
mm_104043.1	chr11	86349048	86349048	-	1	NA	intron (NM_001080931, intron 2 of 29)	intron (NM_001080931, intron 2 of 29)	8477	NM_001080931	327987	Mm.341886	NM_001080931	ENSMUSG00000034297	Med13	1110067M05Rik|D030023K18|Thrap1|Trap240	mediator complex subunit 13	protein-coding
mm_140722.1	chr17	15433330	15433337	-	1	NA	non-coding (NR_033586, exon 11 of 11)	non-coding (NR_033586, exon 11 of 11)	37087	NM_024203	67544	Mm.35039	NM_024203	ENSMUSG00000014763	Fam120b	4932442K08Rik|AW049283|AW413338|CCPG|Pgcc1|mKIAA1838	family with sequence similarity 120, member B	protein-coding
mm_157413.1	chrX	38442083	38442110	-	1	NA	exon (NM_001017959, exon 2 of 9)	exon (NM_001017959, exon 2 of 9)	14364	NM_010685	16784	Mm.486	NM_010685	ENSMUSG00000016534	Lamp2	CD107b|LGP-B|Lamp II|Lamp-2|Lamp-2a|Lamp-2b|Lamp-2c|Mac3	lysosomal-associated membrane protein 2	protein-coding
mm_119737.1	chr14	54121908	54121923	+	1	NA	Intergenic	Intergenic	132014	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_31180.1	chr4	43507086	43507096	+	1	NA	promoter-TSS (NM_139305)	promoter-TSS (NM_139305)	65	NM_139305	230099	Mm.283682	NM_139305	ENSMUSG00000028463	Car9	CAIX|Ca9|MN/CA9	carbonic anhydrase 9	protein-coding
mm_13678.1	chr2	116878699	116878743	+	1	NA	promoter-TSS (NM_026104)	promoter-TSS (NM_026104)	30	NM_026104	67356	Mm.131623	NM_026104	ENSMUSG00000027355	Tmco5	1700095F04Rik|Tmco5a	transmembrane and coiled-coil domains 5	protein-coding
mm_167073.1	chr7	99879735	99879744	-	1	NA	intron (NM_001164258, intron 7 of 18)	intron (NM_001164258, intron 7 of 18)	20521	NM_001164258	446101	Mm.440757	NM_001164258	ENSMUSG00000035211	Xrra1	AI449753	X-ray radiation resistance associated 1	protein-coding
mm_20215.1	chr2	125723658	125723691	-	1	NA	5' UTR (NM_199022, exon 1 of 12)	5' UTR (NM_199022, exon 1 of 12)	474	NM_199022	271849	Mm.425101	NM_199022	ENSMUSG00000035109	Shc4	6230417E10Rik|9930029B02Rik|Gm685|RaLP	SHC (Src homology 2 domain containing) family, member 4	protein-coding
mm_330.1	chr1	26156268	26156272	+	1	NA	Intergenic	Intergenic	-326563	NM_175642	210933	Mm.336569	NM_175642	ENSMUSG00000033569	Adgrb3	A830096D10Rik|Bai3	adhesion G protein-coupled receptor B3	protein-coding
mm_85285.1	chr9	99710006	99710022	-	1	NA	promoter-TSS (NM_001194922)	promoter-TSS (NM_001194922)	49	NM_019815	56492	Mm.386784	NM_019815	ENSMUSG00000032473	Cldn18	-	claudin 18	protein-coding
mm_172954.1	chr9	87952390	87952393	-	1	NA	Intergenic	L1Md_T|LINE|L1	-221131	NM_023814	76365	Mm.158789	NM_023814	ENSMUSG00000032419	Tbx18	2810012F10Rik|2810404D13Rik	T-box18	protein-coding
mm_125460.1	chr15	52295643	52295654	+	1	NA	promoter-TSS (NM_172816)	promoter-TSS (NM_172816)	95	NM_172816	239436	Mm.208831	NM_172816	ENSMUSG00000022315	Slc30a8	C820002P14Rik|ZnT-8|ZnT8	solute carrier family 30 (zinc transporter), member 8	protein-coding
mm_143699.1	chr17	80480479	80480487	-	1	NA	promoter-TSS (NM_009231)	promoter-TSS (NM_009231)	-30	NM_009231	20662	Mm.60975	NM_009231	ENSMUSG00000024241	Sos1	4430401P03Rik|9630010N06|AI449023	son of sevenless homolog 1 (Drosophila)	protein-coding
mm_157951.1	chrX	87238126	87238129	-	1	NA	intron (NM_001160403, intron 5 of 10)	L1_Mus3|LINE|L1	877496	NM_001160403	331461	Mm.121680	NM_001160403	ENSMUSG00000052372	Il1rapl1	6330532G10Rik|C030039N24|IL1R8|IL1RAPL|MRX34|OPHN4|TIGIRR-2	interleukin 1 receptor accessory protein-like 1	protein-coding
mm_39363.1	chr5	9118714	9118733	+	1	NA	TTS (NM_001110327)	TTS (NM_001110327)	17986	NM_001081029	652925	Mm.439954	NM_001081029	ENSMUSG00000079659	Tmem243	4930420K17Rik|E030031F02Rik	transmembrane protein 243, mitochondrial	protein-coding
mm_30356.1	chr3	151764164	151764180	-	1	NA	Intergenic	Intergenic	-1281	NM_031367	15061	Mm.219544	NM_031367	ENSMUSG00000039146	Ifi44l	H-28|H28|H28-1|NS1178	interferon-induced protein 44 like	protein-coding
mm_131103.1	chr16	5007364	5007376	+	1	NA	promoter-TSS (NM_001253803)	promoter-TSS (NM_001253803)	54	NR_045596	432995	Mm.271618	NM_001253796	ENSMUSG00000096215	Smim22	EG432995|Gm5480	small integral membrane protein 22	protein-coding
mm_131156.1	chr16	6889574	6889579	+	1	NA	intron (NM_021477, intron 5 of 16)	intron (NM_021477, intron 5 of 16)	-180259	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_42375.1	chr5	114929089	114929127	+	1	NA	intron (NM_145209, intron 3 of 6)	intron (NM_145209, intron 3 of 6)	5868	NM_145209	231655	Mm.95479	NM_145209	ENSMUSG00000041827	Oasl1	7530414C13Rik|oasl9	2'-5' oligoadenylate synthetase-like 1	protein-coding
mm_73444.1	chr8	106210994	106211011	+	1	NA	promoter-TSS (NM_001007567)	promoter-TSS (NM_001007567)	-52	NM_145404	214572	Mm.251804	NM_145404	ENSMUSG00000060098	Prmt7	4933402B05Rik|BC006705	protein arginine N-methyltransferase 7	protein-coding
mm_48365.1	chr5	139460502	139460549	-	1	NA	promoter-TSS (NM_028469)	promoter-TSS (NM_028469)	9	NM_028469	73212	Mm.84294	NM_028469	ENSMUSG00000053553	3110082I17Rik	AW411904	RIKEN cDNA 3110082I17 gene	protein-coding
mm_153179.1	chr19	34494081	34494161	-	1	NA	exon (NM_021460, exon 10 of 10)	exon (NM_021460, exon 10 of 10)	-18986	NM_009890	12642	Mm.30824	NM_009890	ENSMUSG00000050370	Ch25h	AI462618|m25OH	cholesterol 25-hydroxylase	protein-coding
mm_127304.1	chr15	100227859	100227869	+	1	NA	promoter-TSS (NM_007497)	promoter-TSS (NM_007497)	5	NM_007497	11908	Mm.676	NM_007497	ENSMUSG00000023027	Atf1	-	activating transcription factor 1	protein-coding
mm_61277.1	chr7	66743649	66743674	+	1	NA	exon (NM_001164201, exon 1 of 11)	exon (NM_001164201, exon 1 of 11)	157	NM_001164201	545975	Mm.380104	NM_001164201	ENSMUSG00000030510	Cers3	4930550L11Rik|Gm488|Lass3|T3L	ceramide synthase 3	protein-coding
mm_37992.1	chr4	133633619	133633631	-	1	NA	promoter-TSS (NM_001017968)	promoter-TSS (NM_001017968)	-196	NM_001017968	503610	Mm.331948	NM_001017968	ENSMUSG00000037553	Zdhhc18	-	zinc finger, DHHC domain containing 18	protein-coding
mm_83475.1	chr9	45828591	45828604	-	1	NA	promoter-TSS (NM_001081373)	promoter-TSS (NM_001081373)	41	NM_001081373	214552	Mm.260103	NM_172531	ENSMUSG00000043987	Cep164	AI450905|BC027092|D030051D21|mKIAA1052	centrosomal protein 164	protein-coding
mm_111107.1	chr12	80958051	80958061	-	1	NA	exon (NM_001177561, exon 3 of 5)	exon (NM_001177561, exon 3 of 5)	10023	NM_011387	20493	Mm.486361	NM_011387	ENSMUSG00000021135	Slc10a1	Ntcp	solute carrier family 10 (sodium/bile acid cotransporter family), member 1	protein-coding
mm_107595.1	chr12	49381975	49381995	+	1	NA	promoter-TSS (NM_001160112)	promoter-TSS (NM_001160112)	-898	NM_001160112	15228	Mm.4704	NM_008241	ENSMUSG00000020950	Foxg1	2900064B05Rik|BF-1|Bf1|Hfh9|Hfhbf1	forkhead box G1	protein-coding
mm_62340.1	chr7	100497100	100497127	+	1	NA	exon (NM_011671, exon 4 of 8)	exon (NM_011671, exon 4 of 8)	3755	NM_011671	22228	Mm.171378	NM_011671	ENSMUSG00000033685	Ucp2	Slc25a8	uncoupling protein 2 (mitochondrial, proton carrier)	protein-coding
mm_45734.1	chr5	86373439	86373450	-	1	NA	promoter-TSS (NM_145561)	promoter-TSS (NM_145561)	-57	NM_145561	231382	Mm.240139	NM_145561	ENSMUSG00000061259	Tmprss11d	AST|AsP|BC020151	transmembrane protease, serine 11d	protein-coding
mm_38547.1	chr4	141601613	141601663	-	1	NA	intron (NM_133754, intron 1 of 8)	intron (NM_133754, intron 1 of 8)	-1714	NM_001163256	74202	Mm.490327	NM_133754	ENSMUSG00000006219	Fblim1	2410043F08Rik|Cal|Fblp1|Gt10|migfilin|migfilin(s)	filamin binding LIM protein 1	protein-coding
mm_135307.1	chr16	38712863	38712903	-	1	NA	5' UTR (NM_020260, exon 1 of 12)	5' UTR (NM_020260, exon 1 of 12)	152	NM_020260	12549	Mm.370848	NM_020260	ENSMUSG00000022799	Arhgap31	5830477L08Rik|AU041750|Cdgap|D330026I07Rik	Rho GTPase activating protein 31	protein-coding
mm_78678.1	chr9	40784834	40784846	+	1	NA	TTS (NM_133733)	TTS (NM_133733)	-16433	NM_031165	15481	Mm.290774	NM_031165	ENSMUSG00000015656	Hspa8	2410008N15Rik|Hsc70|Hsc71|Hsc73|Hsp73|Hspa10	heat shock protein 8	protein-coding
mm_51880.1	chr6	90571746	90571759	+	1	NA	intron (NM_027406, intron 11 of 22)	intron (NM_027406, intron 11 of 22)	20904	NM_027406	107747	Mm.30035	NM_027406	ENSMUSG00000030088	Aldh1l1	1810048F20Rik|FDH|Fthfd|Neut2	aldehyde dehydrogenase 1 family, member L1	protein-coding
mm_94058.1	chr10	128303169	128303192	-	1	NA	promoter-TSS (NM_001252327)	promoter-TSS (NM_001252327)	-155	NM_133992	103135	Mm.244183	NM_133992	ENSMUSG00000005682	Pan2	1200014O24Rik|AI047843|AW742773|Usp52|mKIAA0710	PAN2 poly(A) specific ribonuclease subunit	protein-coding
mm_10319.1	chr2	11218450	11218462	+	1	NA	intron (NM_008859, intron 1 of 17)	intron (NM_008859, intron 1 of 17)	46074	NM_008859	18761	Mm.329993	NM_008859	ENSMUSG00000026778	Prkcq	A130035A12Rik|AW494342|PKC-0|PKC-theta|PKCtheta|Pkcq	protein kinase C, theta	protein-coding
mm_150506.1	chr19	39023551	39023561	+	1	NA	intron (NM_028089, intron 4 of 8)	Lx6|LINE|L1	16537	NM_028089	72082	Mm.142581	NM_028089	ENSMUSG00000025002	Cyp2c55	2010318C06Rik	cytochrome P450, family 2, subfamily c, polypeptide 55	protein-coding
mm_153210.1	chr19	34716916	34716923	-	1	NA	intron (NM_172838, intron 1 of 6)	MTD|LTR|ERVL-MaLR	30192	NM_172838	240638	Mm.74636	NM_172838	ENSMUSG00000009378	Slc16a12	3230401A21|AW210596	solute carrier family 16 (monocarboxylic acid transporters), member 12	protein-coding
mm_142230.1	chr17	37480849	37480869	-	1	NA	TTS (NM_008204)	TTS (NM_008204)	2670	NM_008204	14990	Mm.329041	NM_008204	ENSMUSG00000016283	H2-M2	H-2M2|Thy19.4	histocompatibility 2, M region locus 2	protein-coding
mm_76965.1	chr8	106137369	106137395	-	1	NA	promoter-TSS (NM_176838)	promoter-TSS (NM_176838)	-408	NM_176838	77411	Mm.183003	NM_176838	ENSMUSG00000084128	Esrp2	9530027K23Rik|Rbm35b	epithelial splicing regulatory protein 2	protein-coding
mm_115417.1	chr13	116309824	116309841	+	1	NA	promoter-TSS (NM_021459)	promoter-TSS (NM_021459)	-144	NM_021459	16392	Mm.42242	NM_021459	ENSMUSG00000042258	Isl1	-	ISL1 transcription factor, LIM/homeodomain	protein-coding
mm_75069.1	chr8	33832351	33832355	-	1	NA	intron (NM_001042674, intron 5 of 7)	intron (NM_001042674, intron 5 of 7)	-84583	NM_001206849	72632	Mm.443483	NM_001206849	ENSMUSG00000094500	Smim18	2700090O03Rik|AI835723	small integral membrane protein 18	protein-coding
mm_90275.1	chr10	122795165	122795167	+	1	NA	intron (NM_176919, intron 2 of 8)	B1_Mus1|SINE|Alu	115851	NR_106182	102466884		NR_106182	ENSMUSG00000099225	Mir8104	Gm27380|mmu-mir-8104	microRNA 8104	ncRNA
mm_81805.1	chr9	116314431	116314433	+	1	NA	Intergenic	Intergenic	-139069	NM_009371	21813	Mm.172346	NM_009371	ENSMUSG00000032440	Tgfbr2	1110020H15Rik|AU042018|DNIIR|RIIDN|TBR-II|TbetaR-II|TbetaRII	transforming growth factor, beta receptor II	protein-coding
mm_118259.1	chr13	112447259	112447290	-	1	NA	Intergenic	MLT1B|LTR|ERVL-MaLR	-16796	NM_010560	16195	Mm.4364	NM_010560	ENSMUSG00000021756	Il6st	5133400A03Rik|AA389424|BB405851|CD130|D13Ertd699e|gp130	interleukin 6 signal transducer	protein-coding
mm_85074.1	chr9	91361620	91361633	-	1	NA	exon (NM_009573, exon 3 of 3)	exon (NM_009573, exon 3 of 3)	4173	NM_009573	22771	Mm.335350	NM_009573	ENSMUSG00000032368	Zic1	ZIC|ZNF201	zinc finger protein of the cerebellum 1	protein-coding
mm_27955.1	chr3	79842858	79842932	-	1	NA	promoter-TSS (NM_027495)	promoter-TSS (NM_027495)	-233	NM_027495	70652	Mm.46635	NM_027495	ENSMUSG00000027956	Tmem144	1110057I03Rik|5730537D05Rik	transmembrane protein 144	protein-coding
mm_1879.1	chr1	85650009	85650020	+	1	NA	promoter-TSS (NM_013673)	promoter-TSS (NM_013673)	26	NM_001313714	20684	Mm.290906	NM_013673	ENSMUSG00000026222	Sp100	A430075G10Rik	nuclear antigen Sp100	protein-coding
mm_59752.1	chr7	28822052	28822053	+	1	NA	3' UTR (NM_177301, exon 13 of 13)	3' UTR (NM_177301, exon 13 of 13)	-3286	NM_016772	51798	Mm.291776	NM_016772	ENSMUSG00000053898	Ech1	AA617331	enoyl coenzyme A hydratase 1, peroxisomal	protein-coding
mm_131516.1	chr16	17511061	17511090	+	1	NA	intron (NM_001331226, intron 2 of 20)	intron (NM_001331226, intron 2 of 20)	1863	NM_001331226	66863	Mm.161726	NM_025808	ENSMUSG00000022761	Lztr1	1200003E21Rik|AI591627|AW550890	leucine-zipper-like transcriptional regulator, 1	protein-coding
mm_45253.1	chr5	62765619	62765632	-	1	NA	intron (NM_178407, intron 1 of 32)	intron (NM_178407, intron 1 of 32)	552	NM_178407	212285	Mm.244403	NM_178407	ENSMUSG00000037999	Arap2	Centd1|Gm148|mKIAA0580	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2	protein-coding
mm_44651.1	chr5	28210068	28210082	-	1	NA	promoter-TSS (NM_001310511)	promoter-TSS (NM_001310511)	93	NM_001310511	269637	Mm.68286	NM_175651	ENSMUSG00000044681	Cnpy1	1500012D20Rik|9630008K15Rik|AI853839	canopy FGF signaling regulator 1	protein-coding
mm_170343.1	chr18	48047908	48047915	+	1	NA	exon (NM_001025388, exon 2 of 2)	exon (NM_001025388, exon 2 of 2)	2576	NM_001025388	433182	Mm.70666	NM_001025388	ENSMUSG00000059040	Eno1b	EG433182|Eno1|Gm5506	enolase 1B, retrotransposed	protein-coding
mm_76677.1	chr8	93813578	93813588	-	1	NA	promoter-TSS (NR_026888)	promoter-TSS (NR_026888)	-28	NR_026888	75809	Mm.443272	NM_029449		4930488L21Rik	4930452J22Rik	RIKEN cDNA 4930488L21 gene	ncRNA
mm_43380.1	chr5	135697252	135697254	+	1	NA	intron (NM_008898, intron 1 of 15)	intron (NM_008898, intron 1 of 15)	8108	NM_008898	18984	Mm.3863	NM_008898	ENSMUSG00000005514	Por	4933424M13Rik|CPR|CYPOR|P450R	P450 (cytochrome) oxidoreductase	protein-coding
mm_49980.1	chr6	40891677	40891692	+	1	NA	intron (NR_035473, intron 2 of 3)	intron (NR_035473, intron 2 of 3)	-4190	NM_139296	194357	Mm.207087	NM_139296	ENSMUSG00000029885	Moxd2	Dbhl1	monooxygenase, DBH-like 2	protein-coding
mm_82762.1	chr9	26896995	26896997	-	1	NA	intron (NM_001281475, intron 9 of 20)	intron (NM_001281475, intron 9 of 20)	26085	NM_001281475	382064	Mm.335028	NM_001177509	ENSMUSG00000079644	Gm1110	-	predicted gene 1110	protein-coding
mm_152090.1	chr19	6908009	6908036	-	1	NA	exon (NM_012021, exon 2 of 6)	exon (NM_012021, exon 2 of 6)	1623	NM_012021	54683	Mm.279782	NM_012021	ENSMUSG00000024953	Prdx5	AOEB166|AOPP|Pmp20|Prdx6|PrxV	peroxiredoxin 5	protein-coding
mm_155095.1	chrX	48256882	48256928	+	1	NA	promoter-TSS (NM_028276)	promoter-TSS (NM_028276)	-29	NM_028276	72554	Mm.336045	NM_028276	ENSMUSG00000063785	Utp14a	2700066J21Rik|JsdX|NY-CO-16|SDCCAG16|T25628|mKIAA0266	UTP14A small subunit processome component	protein-coding
mm_7701.1	chr1	130422771	130422792	-	1	NA	intron (NM_001317361, intron 1 of 7)	intron (NM_001317361, intron 1 of 7)	262	NM_007827	13137	Mm.436759	NM_007827	ENSMUSG00000026401	Cd55b	AI323748|Daf|Daf-TM|Daf2|TM-DAF	CD55 molecule, decay accelerating factor for complement B	protein-coding
mm_8103.1	chr1	135849450	135849452	-	1	NA	exon (NM_001130176, exon 9 of 13)	exon (NM_001130176, exon 9 of 13)	8590	NM_001130176	21956	Mm.247470	NM_011619	ENSMUSG00000026414	Tnnt2	Tnt|cTnT	troponin T2, cardiac	protein-coding
mm_37856.1	chr4	132261527	132261572	-	1	NA	promoter-TSS (NM_020273)	promoter-TSS (NM_020273)	0	NM_020273	56809	Mm.103489	NM_020273	ENSMUSG00000028901	Gmeb1	1110050A04Rik|AI256615|AI481278	glucocorticoid modulatory element binding protein 1	protein-coding
mm_9805.1	chr1	181918480	181918508	-	1	NA	exon (NM_010135, exon 9 of 15)	exon (NM_010135, exon 9 of 15)	-76093	NM_133815	98386	Mm.4538	NM_133815	ENSMUSG00000004880	Lbr	AI505894|ic	lamin B receptor	protein-coding
mm_168906.1	chr12	55155374	55155376	+	1	NA	5' UTR (NM_001100109, exon 1 of 16).2	5' UTR (NM_001100109, exon 1 of 16).2	271	NM_001100109	665155	Mm.12848	NM_001100109	ENSMUSG00000079108	Srp54b	-	signal recognition particle 54B	protein-coding
mm_164124.1	chr15	38570768	38570774	-	1	NA	intron (NR_045757, intron 2 of 2)	intron (NR_045757, intron 2 of 2)	24163	NR_045757	69679	Mm.416890	NR_045757	ENSMUSG00000102106	2310043O21Rik	-	RIKEN cDNA 2310043O21 gene	ncRNA
mm_130918.1	chr15	102671034	102671086	-	1	NA	promoter-TSS (NM_026468)	promoter-TSS (NM_026468)	-13	NM_026468	67942	Mm.10314	NM_026468	ENSMUSG00000062683	Atp5g2	1810041M08Rik	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit C2 (subunit 9)	protein-coding
mm_65331.1	chr7	24978348	24978364	-	1	NA	3' UTR (NM_001290469, exon 23 of 23)	3' UTR (NM_001290469, exon 23 of 23)	-5628	NM_010261	14470	Mm.22473	NM_010261	ENSMUSG00000003380	Rabac1	2310040I06Rik|Gbpap1|PRA1|prenylin	Rab acceptor 1 (prenylated)	protein-coding
mm_59396.1	chr7	26764565	26764571	+	1	NA	intron (NM_007814, intron 6 of 8)	intron (NM_007814, intron 6 of 8)	7426	NM_007814	13090	Mm.14098	NM_007814	ENSMUSG00000066704	Cyp2b19	CYPIIB19	cytochrome P450, family 2, subfamily b, polypeptide 19	protein-coding
mm_75992.1	chr8	72393471	72393474	-	1	NA	intron (NM_001122832, intron 6 of 15)	ORR1B2-int|LTR|ERVL-MaLR	28002	NM_001122832	13859	Mm.288894	NM_007944	ENSMUSG00000006276	Eps15l1	9830147J04Rik|AI593686|Eps15-rs|Eps15R	epidermal growth factor receptor pathway substrate 15-like 1	protein-coding
mm_84359.1	chr9	64726584	64726587	-	1	NA	intron (NM_017382, intron 3 of 4)	intron (NM_017382, intron 3 of 4)	11171	NM_017382	53869	Mm.1387	NM_017382	ENSMUSG00000004771	Rab11a	-	RAB11A, member RAS oncogene family	protein-coding
mm_41719.1	chr5	102175322	102175335	+	1	NA	Intergenic	L1VL2|LINE|L1	-105407	NM_172882	72145	Mm.332522	NM_172882	ENSMUSG00000043940	Wdfy3	2610509D04Rik|ALFY|AW319683|B930017C24|BWF1|Bchs|D5Ertd66e|Ggtb3|ZFYVE25|mKIAA0993	WD repeat and FYVE domain containing 3	protein-coding
mm_79323.1	chr9	52683081	52683082	+	1	NA	intron (NR_045333, intron 1 of 4)	Lx5b|LINE|L1	3218	NR_045333	382139	Mm.335162	NR_045333	ENSMUSG00000111020	Gm1715	-	predicted gene 1715	ncRNA
mm_132081.1	chr16	30196120	30196124	+	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	71410	NM_027904	71756	Mm.290614	NM_027904	ENSMUSG00000023176	Cpn2	1300018K11Rik	carboxypeptidase N, polypeptide 2	protein-coding
mm_28096.1	chr3	86002496	86002507	-	1	NA	promoter-TSS (NM_001001650)	promoter-TSS (NM_001001650)	-10	NM_001001650	368202	Mm.253822	NM_001001650	ENSMUSG00000049013	Prss48	Esspl|Gm1019	protease, serine 48	protein-coding
mm_161641.1	chr16	94611445	94611445	+	1	NA	promoter-TSS (NM_001347731)	promoter-TSS (NM_001347731)	26	NM_001347731	13548	Mm.310973	NM_007890	ENSMUSG00000022897	Dyrk1a	2310043O08Rik|D16Ertd272e|D16Ertd493e|Dyrk|ENSMUSG00000074897|Gm10783|Mnbh|Mp86|mmb	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1a	protein-coding
mm_82771.1	chr9	26924187	26924195	-	1	NA	Intergenic	Intergenic	-1110	NM_001281475	382064	Mm.335028	NM_001177509	ENSMUSG00000079644	Gm1110	-	predicted gene 1110	protein-coding
mm_20094.1	chr2	120970598	120970636	-	1	NA	promoter-TSS (NM_009461)	promoter-TSS (NM_009461)	98	NM_009461	22222	Mm.389330	NM_009461	ENSMUSG00000027272	Ubr1	AI504731	ubiquitin protein ligase E3 component n-recognin 1	protein-coding
mm_128574.1	chr15	57708922	57708936	-	1	NA	intron (NM_199449, intron 1 of 3)	intron (NM_199449, intron 1 of 3)	14262	NM_199449	387609	Mm.36557	NM_199449	ENSMUSG00000071757	Zhx2	Afr-1|Afr1|Raf|mKIAA0854	zinc fingers and homeoboxes 2	protein-coding
mm_70207.1	chr7	144752025	144752027	-	1	NA	Intergenic	Intergenic	-13434	NM_001242349	101772	Mm.26700	NM_178642	ENSMUSG00000031075	Ano1	Tmem16a	anoctamin 1, calcium activated chloride channel	protein-coding
mm_101038.1	chr11	8605214	8605232	-	1	NA	intron (NM_001083587, intron 2 of 30)	intron (NM_001083587, intron 2 of 30)	59312	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_139630.1	chr17	57367418	57367451	+	1	NA	intron (NM_010130, intron 2 of 21)	intron (NM_010130, intron 2 of 21)	8748	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_168485.1	chr11	49198215	49198215	+	1	NA	Intergenic	RLTR10C|LTR|ERVK	-5285	NM_001024846	22720	Mm.16650	NM_009562	ENSMUSG00000046311	Zfp62	-	zinc finger protein 62	protein-coding
mm_136060.1	chr16	84583519	84583534	-	1	NA	Intergenic	Intergenic	-96263	NR_040537	78023	Mm.243853	NR_040537		4930529L06Rik	-	RIKEN cDNA 4930529L06 gene	ncRNA
mm_4760.1	chr1	182409248	182409259	+	1	NA	promoter-TSS (NM_173378)	promoter-TSS (NM_173378)	86	NM_173378	209456	Mm.287450	NM_173378	ENSMUSG00000026510	Trp53bp2	53BP2|AI746547|ASPP2|PPP1R13A|Tp53bp2|X98550	transformation related protein 53 binding protein 2	protein-coding
mm_10107.1	chr2	3649508	3649517	+	1	NA	Intergenic	Intergenic	-63946	NM_025626	66540	Mm.277864	NM_025626	ENSMUSG00000026655	Fam107b	3110001A13Rik|AA589595|AA959793|AI132312	family with sequence similarity 107, member B	protein-coding
mm_106754.1	chr12	4133422	4133426	+	1	NA	promoter-TSS (NM_138305)	promoter-TSS (NM_138305)	27	NM_001159536	104111	Mm.489807	NM_138305	ENSMUSG00000020654	Adcy3	AC3|mKIAA0511	adenylate cyclase 3	protein-coding
mm_143425.1	chr17	70849280	70849292	-	1	NA	intron (NM_001164074, intron 1 of 2)	intron (NM_001164074, intron 1 of 2)	504	NM_001164076	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_136703.1	chr17	7875358	7875367	+	1	NA	Intergenic	Intergenic	-50638	NM_145968	72536	Mm.119680	NM_145968	ENSMUSG00000033450	Tagap	2610315E15Rik	T cell activation Rho GTPase activating protein	protein-coding
mm_160217.1	chr7	100006166	100006166	+	1	NA	promoter-TSS (NM_133709)	promoter-TSS (NM_133709)	-238	NM_133709	69121	Mm.285295	NM_133709	ENSMUSG00000030732	Chrdl2	1810022C01Rik|Chl2	chordin-like 2	protein-coding
mm_23871.1	chr3	83029106	83029136	+	1	NA	exon (NM_010196, exon 3 of 5)	exon (NM_010196, exon 3 of 5)	2968	NM_001111048	14161	Mm.88793	NM_010196	ENSMUSG00000028001	Fga	ENSMUSG00000059807|Fib	fibrinogen alpha chain	protein-coding
mm_140349.1	chr17	86831234	86831244	+	1	NA	3' UTR (NM_010137, exon 16 of 16)	3' UTR (NM_010137, exon 16 of 16)	77375	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_26616.1	chr3	152395445	152395489	+	1	NA	promoter-TSS (NM_001080755)	promoter-TSS (NM_001080755)	-6	NM_001346655	108946	Mm.379292	NM_198416	ENSMUSG00000039068	Zzz3	3110065C23Rik|6430567E01Rik|AA408566|AI481057|AW556059|R75514	zinc finger, ZZ domain containing 3	protein-coding
mm_164699.1	chr17	49738733	49738745	+	1	NA	intron (NM_177052, intron 10 of 22)	intron (NM_177052, intron 10 of 22)	123567	NM_177052	319991	Mm.441340	NM_177052	ENSMUSG00000023999	Kif6	D130004B10Rik|D130084M03Rik	kinesin family member 6	protein-coding
mm_119395.1	chr14	41137863	41137873	+	1	NA	Intergenic	Intergenic	6080	NM_023134	20387	Mm.46062	NM_023134	ENSMUSG00000021789	Sftpa1	SP-A|Sftp-1|Sftp1	surfactant associated protein A1	protein-coding
mm_28076.1	chr3	84450771	84450771	-	1	NA	intron (NM_001033301, intron 10 of 11)	intron (NM_001033301, intron 10 of 11)	28720	NM_001205355	229474	Mm.331107	NM_001033301	ENSMUSG00000041842	Fhdc1	6330505N24Rik|Gm126	FH2 domain containing 1	protein-coding
mm_81032.1	chr9	104569755	104569793	+	1	NA	promoter-TSS (NM_028719)	promoter-TSS (NM_028719)	-14	NM_028719	74020	Mm.326240	NM_028719	ENSMUSG00000032564	Cpne4	3632411M23Rik|4933406O10Rik	copine IV	protein-coding
mm_112978.1	chr13	21312179	21312187	+	1	NA	promoter-TSS (NM_145451)	promoter-TSS (NM_145451)	-20	NM_145451	75512	Mm.46195	NM_145451	ENSMUSG00000004341	Gpx6	1700020G18Rik|Ry2d1|olfactory	glutathione peroxidase 6	protein-coding
mm_28383.1	chr3	90000554	90000581	-	1	NA	3' UTR (NM_001165983, exon 28 of 28)	3' UTR (NM_001165983, exon 28 of 28)	1807	NR_045749	100503469	Mm.440636	NR_045749	ENSMUSG00000105552	Gm19710	-	predicted gene, 19710	ncRNA
mm_109061.1	chr12	104343065	104343072	+	1	NA	exon (NM_011458, exon 3 of 5)	exon (NM_011458, exon 3 of 5)	4582	NM_011458	20714	Mm.291569	NM_011458	ENSMUSG00000058207	Serpina3k	1300001I07Rik|D12Rp54|MMCM2|MMSpi2|RP54|Spi-2|Spi2|contrapsin	serine (or cysteine) peptidase inhibitor, clade A, member 3K	protein-coding
mm_23012.1	chr3	34454382	34454399	+	1	NA	Intergenic	CpG	-105991	NR_015580	320478	Mm.444063	NR_015580	ENSMUSG00000105265	Sox2ot	B230215L15Rik	SOX2 overlapping transcript (non-protein coding)	ncRNA
mm_145979.1	chr18	68047021	68047024	+	1	NA	intron (NM_172631, intron 1 of 5)	intron (NM_172631, intron 1 of 5)	113765	NM_172631	52662	Mm.440183	NM_172631	ENSMUSG00000024544	Ldlrad4	8230401C20Rik|A430083H02|A430108L08Rik|C18orf1|D18Ertd653e|D330030L18Rik	low density lipoprotein receptor class A domain containing 4	protein-coding
mm_1254.1	chr1	63103150	63103150	+	1	NA	intron (NM_001081436, intron 2 of 11)	intron (NM_001081436, intron 2 of 11)	11117	NM_001081436	227195	Mm.74718	NM_001081436	ENSMUSG00000040865	Ino80d	7330405I11|A430093A21Rik|BC010584|OTTMUSG00000002594	INO80 complex subunit D	protein-coding
mm_88644.1	chr10	79948976	79949003	+	1	NA	exon (NM_001288626, exon 5 of 9)	exon (NM_001288626, exon 5 of 9)	-11163	NM_175450	216156	Mm.35828	NM_175450	ENSMUSG00000035754	Wdr18	2310012I10Rik|AU044733|AW122032	WD repeat domain 18	protein-coding
mm_121261.1	chr14	103070260	103070348	+	1	NA	promoter-TSS (NM_001033242)	promoter-TSS (NM_001033242)	88	NM_001033242	211286	Mm.295289	NM_001033242	ENSMUSG00000022125	Cln5	A730075N08Rik	ceroid-lipofuscinosis, neuronal 5	protein-coding
mm_91013.1	chr10	15263229	15263241	-	1	NA	Intergenic	RLTR13D6|LTR|ERVK	502946	NM_008703	18101	Mm.487342	NM_008703	ENSMUSG00000019865	Nmbr	BB182387	neuromedin B receptor	protein-coding
mm_96460.1	chr11	67586676	67586720	+	1	NA	5' UTR (NM_001109657, exon 1 of 14)	5' UTR (NM_001109657, exon 1 of 14)	198	NM_001109657	14457	Mm.40338	NM_008088	ENSMUSG00000033066	Gas7	AW124766|B230343A10Rik|Gas7-cb	growth arrest specific 7	protein-coding
mm_85382.1	chr9	103226888	103226920	-	1	NA	exon (NM_133977, exon 3 of 17)	exon (NM_133977, exon 3 of 17)	3382	NM_133977	22041	Mm.37214	NM_133977	ENSMUSG00000032554	Trf	AI266983|Cd176|HP|Tf|Tfn|hpx	transferrin	protein-coding
mm_127833.1	chr15	6600449	6600468	-	1	NA	intron (NM_011815, intron 1 of 17)	intron (NM_011815, intron 1 of 17)	20611	NM_011815	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_160816.1	chr11	23665451	23665451	+	1	NA	promoter-TSS (NM_001033654)	promoter-TSS (NM_001033654)	-223	NM_028956	74467	Mm.29536	NM_028304	ENSMUSG00000020280	Pus10	2810013G11Rik|4933435A13Rik|AU014648|C77560|Ccdc139	pseudouridylate synthase 10	protein-coding
mm_129735.1	chr15	82147492	82147500	-	1	NA	intron (NM_033218, intron 1 of 18)	CpG	227	NM_033218	20788	Mm.9002	NM_033218	ENSMUSG00000022463	Srebf2	AI608257|SREBP-2|SREBP2|SREBP2gc|bHLHd2|lop13|nuc	sterol regulatory element binding factor 2	protein-coding
mm_22126.1	chr2	170357107	170357120	-	1	NA	intron (NR_040610, intron 2 of 7)	intron (NR_040610, intron 2 of 7)	752	NR_040610	73303	Mm.443297	NR_040610	ENSMUSG00000086999	Bcas1os2	1700040N02Rik	breast carcinoma amplified sequence 1, opposite strand 2	ncRNA
mm_78548.1	chr9	35421542	35421616	+	1	NA	Intergenic	CpG	-30497	NM_021339	57810	Mm.80509	NM_021339	ENSMUSG00000038119	Cdon	CDO|Cd0|Orcam	cell adhesion molecule-related/down-regulated by oncogenes	protein-coding
mm_108492.1	chr12	83682548	83682560	+	1	NA	3' UTR (NM_027349, exon 19 of 19)	3' UTR (NM_027349, exon 19 of 19)	-6009	NM_008943	19164	Mm.998	NM_008943	ENSMUSG00000019969	Psen1	Ad3h|PS-1|PS1|S182	presenilin 1	protein-coding
mm_37056.1	chr4	116048656	116048685	-	1	NA	intron (NM_028142, intron 1 of 5)	intron (NM_028142, intron 1 of 5)	5206	NM_028142	72181	Mm.282560	NM_028142	ENSMUSG00000028706	Nsun4	2310010O12Rik|2810405F18Rik|AI507900|Shtap	NOL1/NOP2/Sun domain family, member 4	protein-coding
mm_10877.1	chr2	25242197	25242207	+	1	NA	promoter-TSS (NM_176834)	promoter-TSS (NM_176834)	-727	NM_176834	68846	Mm.24777	NM_176834	ENSMUSG00000044628	Rnf208	1110061N23Rik	ring finger protein 208	protein-coding
mm_80472.1	chr9	78175358	78175384	+	1	NA	promoter-TSS (NR_040401)	promoter-TSS (NR_040401)	-543	NR_040401	320295	Mm.131285	NR_040401	ENSMUSG00000097574	C920006O11Rik	-	RIKEN cDNA C920006O11 gene	ncRNA
mm_103328.1	chr11	74522739	74522808	-	1	NA	intron (NM_001015046, intron 2 of 24)	CpG	67385	NM_001015046	380711	Mm.425690	NM_001015046	ENSMUSG00000038807	Rap1gap2	AU067654|Garnl4|Gm1561|mKIAA1039	RAP1 GTPase activating protein 2	protein-coding
mm_98047.1	chr11	85713764	85713803	+	1	NA	intron (NR_045875, intron 1 of 5)	intron (NR_045875, intron 1 of 5)	5961	NR_045875	71489	Mm.442482	NR_045875	ENSMUSG00000086199	Bcas3os1	8430403D17Rik	breast carcinoma amplified sequence 3, opposite strand 1	ncRNA
mm_39022.1	chr4	152131748	152131763	-	1	NA	intron (NM_207688, intron 3 of 10)	CpG-10714	-2830	NM_019585	56226	Mm.264215	NM_019585	ENSMUSG00000028943	Espn	je	espin	protein-coding
mm_36546.1	chr4	86669987	86670025	-	1	NA	promoter-TSS (NM_007408)	promoter-TSS (NM_007408)	53	NM_007408	11520	Mm.381	NM_007408	ENSMUSG00000028494	Plin2	AA407157|ADPH|Adfp|Adrp	perilipin 2	protein-coding
mm_85936.1	chr9	112098004	112098012	-	1	NA	intron (NM_001177618, intron 17 of 18)	intron (NM_001177618, intron 17 of 18)	20703	NR_029823	723815		NR_029823	ENSMUSG00000065441	Mir128-2	Mirn128-2|Mirn128b|mir-128-2|mir-128b	microRNA 128-2	ncRNA
mm_73950.1	chr8	120228463	120228475	+	1	NA	promoter-TSS (NR_110496)	promoter-TSS (NR_110496)	-239	NR_110496	434353	Mm.411793	NR_110496	ENSMUSG00000097960	A330074K22Rik	-	RIKEN cDNA A330074K22 gene	ncRNA
mm_172494.1	chr7	59229256	59229261	+	1	NA	5' UTR (NM_001033962, exon 1 of 11)	5' UTR (NM_001033962, exon 1 of 11)	506	NM_011668	22215	Mm.9002	NM_011668	ENSMUSG00000025326	Ube3a	4732496B02|5830462N02Rik|A130086L21Rik|Hpve6a|mKIAA4216	ubiquitin protein ligase E3A	protein-coding
mm_47888.1	chr5	134703565	134703606	-	1	NA	3' UTR (NM_007925, exon 37 of 37)	3' UTR (NM_007925, exon 37 of 37)	-14995	NM_010717	16885	Mm.15409	NM_010717	ENSMUSG00000029674	Limk1	KIZ-1|LIMK-1|Limk	LIM-domain containing, protein kinase	protein-coding
mm_107680.1	chr12	54428036	54428044	+	1	NA	Intergenic	Intergenic	-36722	NR_033689	665239	Mm.26856	NR_033689		Gm7550	EG665239|Gm666	predicted gene 7550	ncRNA
mm_18236.1	chr2	51973191	51973216	-	1	NA	promoter-TSS (NM_001141948)	promoter-TSS (NM_001141948)	5	NM_001141949	64685	Mm.7491	NM_019401	ENSMUSG00000026946	Nmi	-	N-myc (and STAT) interactor	protein-coding
mm_156715.1	chrX	159697309	159697331	+	1	NA	intron (NM_001135727, intron 2 of 17)	intron (NM_001135727, intron 2 of 17)	-11281	NM_021389	58194	Mm.286495	NM_021389	ENSMUSG00000040990	Sh3kbp1	1200007H22Rik|1700125L08Rik|5830464D22Rik|AI447724|Cin85|IN85|Ruk|Seta	SH3-domain kinase binding protein 1	protein-coding
mm_52058.1	chr6	97233246	97233265	+	1	NA	TTS (NM_022992)	TTS (NM_022992)	19525	NM_001081157	320502	Mm.68163	NM_001081157	ENSMUSG00000044086	Lmod3	5430424A14Rik	leiomodin 3 (fetal)	protein-coding
mm_149192.1	chr19	9939280	9939291	+	1	NA	Intergenic	Intergenic	-39752	NM_016692	16319	Mm.29755	NM_016692	ENSMUSG00000024660	Incenp	2700067E22Rik|AU019509|C130081E20|C77457	inner centromere protein	protein-coding
mm_11549.1	chr2	32715416	32715427	+	1	NA	Intergenic	B1F1|SINE|Alu	-2449	NR_039536	100628606		NR_039536	ENSMUSG00000105841	Mir3960	mmu-mir-3960	microRNA 3960	ncRNA
mm_9512.1	chr1	173741718	173741755	-	1	NA	promoter-TSS (NM_001204910)	promoter-TSS (NM_001204910)	73	NM_001204910	226691	Mm.440876	NM_001204910	ENSMUSG00000073490	Ifi207	AI607873|Pyhin-A	interferon activated gene 207	protein-coding
mm_124539.1	chr14	122464164	122464191	-	1	NA	exon (NM_022987, exon 1 of 2)	exon (NM_022987, exon 1 of 2)	1481	NM_022987	65100	Mm.390761	NM_022987	ENSMUSG00000041703	Zic5	1700049L20Rik|Opr	zinc finger protein of the cerebellum 5	protein-coding
mm_167324.1	chr8	68772444	68772468	+	1	NA	Intergenic	RMER4B|LTR|ERVK	-21473	NM_001293791	70885	Mm.252421	NM_027590	ENSMUSG00000031864	Ints10	4921521J11Rik|AI462004	integrator complex subunit 10	protein-coding
mm_1705.1	chr1	75210833	75210910	+	1	NA	promoter-TSS (NM_011494)	promoter-TSS (NM_011494)	42	NM_011494	20872	Mm.1155	NM_011494	ENSMUSG00000026201	Stk16	EDPK|Krct|MPSK|PKL12|TSF-1	serine/threonine kinase 16	protein-coding
mm_118837.1	chr14	25607942	25607953	+	1	NA	intron (NM_001310666, intron 6 of 23)	CpG	4434	NM_001309430	100188919	Mm.473810	NM_001309430		Israa	-	immune system released activating agent	protein-coding
mm_16961.1	chr2	17460601	17460609	-	1	NA	intron (NM_028757, intron 4 of 6)	intron (NM_028757, intron 4 of 6)	-102909	NR_105847	102465964		NR_105847	ENSMUSG00000099161	Mir6419	Gm27713|mmu-mir-6419	microRNA 6419	ncRNA
mm_50858.1	chr6	55241154	55241154	+	1	NA	intron (NM_177883, intron 5 of 10)	B1_Mus2|SINE|Alu	37771	NM_001142781	330323	Mm.268997	NM_177883	ENSMUSG00000038022	Fam188b	C330043M08Rik|Gm1406	family with sequence similarity 188, member B	protein-coding
mm_2121.1	chr1	87896138	87896141	+	1	NA	intron (NM_177646, intron 3 of 29)	intron (NM_177646, intron 3 of 29)	-41840	NR_136921	100503175	Mm.426422	NR_136921	ENSMUSG00000101942	Gm19582	-	predicted gene, 19582	ncRNA
mm_59201.1	chr7	24507142	24507194	+	1	NA	promoter-TSS (NM_001290461)	promoter-TSS (NM_001290461)	81	NR_110958	232969	Mm.181332	NM_146183	ENSMUSG00000064264	Zfp428	2410005H09Rik|AV271806|AW047854|Znf428	zinc finger protein 428	protein-coding
mm_52098.1	chr6	97853503	97853518	+	1	NA	intron (NM_001113198, intron 1 of 9)	L1MB2|LINE|L1	46452	NM_001113198	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_10178.1	chr2	4597267	4597291	+	1	NA	intron (NM_001347086, intron 18 of 24)	intron (NM_001347086, intron 18 of 24)	37525	NM_001177844	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding
mm_48967.1	chr6	4623903	4623916	+	1	NA	intron (NM_145398, intron 8 of 17)	intron (NM_145398, intron 8 of 17)	22843	NM_145398	213819	Mm.270703	NM_145398	ENSMUSG00000015189	Casd1	Cas1|Cast1	CAS1 domain containing 1	protein-coding
mm_113216.1	chr13	25208387	25208391	+	1	NA	3' UTR (NM_177577, exon 10 of 10)	3' UTR (NM_177577, exon 10 of 10)	61607	NM_009513	22360	Mm.4766	NM_009513	ENSMUSG00000048978	Nrsn1	Neurensin-1|Neuro-p24|Vmp	neurensin 1	protein-coding
mm_4129.1	chr1	170308837	170308884	+	1	NA	promoter-TSS (NM_001039593)	promoter-TSS (NM_001039593)	-1	NM_001039593	76925	Mm.33631	NM_001039593	ENSMUSG00000042800	1700015E13Rik	-	RIKEN cDNA 1700015E13 gene	protein-coding
mm_6247.1	chr1	67116511	67116523	-	1	NA	Intergenic	Intergenic	-6510	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_30251.1	chr3	146596572	146596582	-	1	NA	promoter-TSS (NM_009474)	promoter-TSS (NM_009474)	-572	NM_009474	22262	Mm.10865	NM_009474	ENSMUSG00000028186	Uox	AI663847	urate oxidase	protein-coding
mm_106737.1	chr12	3897406	3897436	+	1	NA	exon (NM_153743, exon 6 of 18)	exon (NM_153743, exon 6 of 18)	5677	NM_153743	13435	Mm.5001	NM_007872	ENSMUSG00000020661	Dnmt3a	MmuIIIA	DNA methyltransferase 3A	protein-coding
mm_138963.1	chr17	44628190	44628193	+	1	NA	intron (NR_073392, intron 6 of 7)	intron (NR_073392, intron 6 of 7)	107985	NR_073425	12393	Mm.391013	NM_009820	ENSMUSG00000039153	Runx2	AML3|Cbf|Cbfa-1|Cbfa1|LS3|Osf2|PEBP2aA|Pebp2a1|Pebpa2a	runt related transcription factor 2	protein-coding
mm_170804.1	chr2	175703718	175703734	-	1	NA	promoter-TSS (NM_001177404)	promoter-TSS (NM_001177404)	-28	NM_001177404	100303732	Mm.484983	NM_001177404	ENSMUSG00000095199	Zfp967	Gm14431|OTTMUSG00000016608	zinc finger protein 967	protein-coding
mm_148564.1	chr19	4756528	4756556	+	1	NA	promoter-TSS (NM_025717)	promoter-TSS (NM_025717)	17	NM_025717	66704	Mm.396734	NM_025717	ENSMUSG00000033760	Rbm4b	4921506I22Rik|AI504630|AI506404|Lark2|Neosin	RNA binding motif protein 4B	protein-coding
mm_119457.1	chr14	47066418	47066439	+	1	NA	exon (NM_001163433, exon 5 of 12)	exon (NM_001163433, exon 5 of 12)	-2549	NM_001310544	74480	Mm.214454	NM_028966	ENSMUSG00000021838	Samd4	1700024G08Rik|1700111L17Rik|4933436G17Rik|Samd4a|Smaug|Smaug1|sunk	sterile alpha motif domain containing 4	protein-coding
mm_113852.1	chr13	47210845	47210848	+	1	NA	intron (NM_001170643, intron 2 of 7)	B1F|SINE|Alu	16843	NM_001170643	218215	Mm.287609	NM_146042	ENSMUSG00000038068	Rnf144b	BC025007|E130105P19Rik|Ibrdc2|Pir2	ring finger protein 144B	protein-coding
mm_156517.1	chrX	150588224	150588260	+	1	NA	promoter-TSS (NM_029943)	promoter-TSS (NM_029943)	-87	NM_029943	77622	Mm.440275	NM_029943	ENSMUSG00000025269	Apex2	C430040P13Rik|ape2	apurinic/apyrimidinic endonuclease 2	protein-coding
mm_15817.1	chr2	164523664	164523684	+	1	NA	Intergenic	RLTR44B|LTR|ERVK	26149	NM_133779	78928	Mm.28228	NM_133779	ENSMUSG00000017721	Pigt	2510012P17Rik|4930534E15Rik|CGI-06|NDAP|Ndap7	phosphatidylinositol glycan anchor biosynthesis, class T	protein-coding
mm_104629.1	chr11	97352349	97352363	-	1	NA	promoter-TSS (NM_001081220)	promoter-TSS (NM_001081220)	-283	NM_001081220	217143	Mm.32622	NM_175453	ENSMUSG00000070337	Gpr179	5330439C02Rik|Gpr158l1	G protein-coupled receptor 179	protein-coding
mm_108967.1	chr12	102469124	102469156	+	1	NA	promoter-TSS (NM_013747)	promoter-TSS (NM_013747)	6	NM_001199004	27277	Mm.273370	NM_013747	ENSMUSG00000021192	Golga5	Ret-II	golgi autoantigen, golgin subfamily a, 5	protein-coding
mm_43064.1	chr5	124328132	124328188	+	1	NA	promoter-TSS (NM_001134717)	promoter-TSS (NM_001134717)	71	NM_001134717	72650	Mm.121658	NM_028310	ENSMUSG00000047635	2810006K23Rik	-	RIKEN cDNA 2810006K23 gene	protein-coding
mm_14548.1	chr2	132847720	132847743	+	1	NA	promoter-TSS (NM_025646)	promoter-TSS (NM_025646)	-3	NM_025646	66586	Mm.357342	NM_025646	ENSMUSG00000027357	Crls1	0610009I22Rik|4930557M15Rik|5730490M08Rik	cardiolipin synthase 1	protein-coding
mm_106773.1	chr12	4600663	4600664	+	1	NA	intron (NM_011365, intron 1 of 38)	intron (NM_011365, intron 1 of 38)	7655	NM_001198968	20403	Mm.341204	NM_011365	ENSMUSG00000020640	Itsn2	AI327390|Ese2|Sh3d1B|Sh3p18|mKIAA1256	intersectin 2	protein-coding
mm_65396.1	chr7	25132441	25132455	-	1	NA	promoter-TSS (NM_001163556)	promoter-TSS (NM_001163556)	12	NM_011138	18987	Mm.76683	NM_011138	ENSMUSG00000008496	Pou2f2	Oct-2|Oct2a|Oct2b|Oct2c|Oct2d|Otf-2|Otf2	POU domain, class 2, transcription factor 2	protein-coding
mm_59120.1	chr7	19852055	19852061	+	1	NA	promoter-TSS (NM_001270489)	promoter-TSS (NM_001270489)	55	NM_001270489	100502736	Mm.445354	NM_001270489	ENSMUSG00000092216	Gm19345	-	predicted gene, 19345	protein-coding
mm_85699.1	chr9	108101931	108101934	-	1	NA	intron (NM_007567, intron 11 of 11)	B1_Mur3|SINE|Alu	-7452	NM_146226	235606	Mm.219639	NM_146226	ENSMUSG00000032590	Apeh	-	acylpeptide hydrolase	protein-coding
mm_78602.1	chr9	37528048	37528058	+	1	NA	promoter-TSS (NM_027102)	promoter-TSS (NM_027102)	-36	NR_136939	69524	Mm.41751	NM_027102	ENSMUSG00000001946	Esam	2310008D05Rik|Esam1|W117m	endothelial cell-specific adhesion molecule	protein-coding
mm_51636.1	chr6	85911868	85911885	+	1	NA	intron (NM_023160, intron 1 of 1)	intron (NM_023160, intron 1 of 1)	3801	NM_023160	66116	Mm.13036	NM_023160	ENSMUSG00000057103	Nat8f1	1110002I11Rik|AI266962|Cml1	N-acetyltransferase 8 (GCN5-related) family member 1	protein-coding
mm_26174.1	chr3	138288781	138288825	+	1	NA	exon (NM_007409, exon 7 of 9)	exon (NM_007409, exon 7 of 9)	11158	NM_007409	11522	Mm.2409	NM_007409	ENSMUSG00000074207	Adh1	ADH-AA|AI194826|Adh-1|Adh-1-t|Adh-1e|Adh-1t|Adh-3e|Adh1-e|Adh1-t|Adh1tl|Adh3-e	alcohol dehydrogenase 1 (class I)	protein-coding
mm_38628.1	chr4	142084666	142084683	-	1	NA	promoter-TSS (NM_145402)	promoter-TSS (NM_145402)	-370	NM_145402	214359	Mm.27587	NM_145402	ENSMUSG00000040616	Tmem51	BC003277	transmembrane protein 51	protein-coding
mm_152781.1	chr19	21383897	21383907	-	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	88759	NM_010266	14544	Mm.45054	NM_010266	ENSMUSG00000058624	Gda	AU015411|AW047581|GAH	guanine deaminase	protein-coding
mm_85762.1	chr9	108655868	108655872	-	1	NA	Intergenic	RLTR13B2|LTR|ERVK	-6228	NM_020520	57279	Mm.29666	NM_020520	ENSMUSG00000032602	Slc25a20	1110007P09Rik|C78826|Cact|mCAC	solute carrier family 25 (mitochondrial carnitine/acylcarnitine translocase), member 20	protein-coding
mm_23090.1	chr3	37062800	37062818	+	1	NA	promoter-TSS (NM_009350)	promoter-TSS (NM_009350)	-847	NM_009350	21744	Mm.8122	NM_009350	ENSMUSG00000027719	Adad1	Tenr	adenosine deaminase domain containing 1 (testis specific)	protein-coding
mm_173272.1	chrX	98033009	98033021	-	1	NA	Intergenic	L1_Mus1|LINE|L1	-115742	NM_013476	11835	Mm.39005	NM_013476	ENSMUSG00000046532	Ar	AW320017|Tfm	androgen receptor	protein-coding
mm_156063.1	chrX	109160454	109160475	+	1	NA	3' UTR (NM_019989, exon 4 of 4)	3' UTR (NM_019989, exon 4 of 4)	-36292	NM_001037917	622976	Mm.482747	NM_001037917	ENSMUSG00000048621	Gm6377	EG622976	predicted gene 6377	protein-coding
mm_86097.1	chr9	115293447	115293451	-	1	NA	intron (NM_024222, intron 1 of 15)	intron (NM_024222, intron 1 of 15)	-11379	NR_029430	111186	Mm.484753	NR_029430		Stmn1-rs1	Lag-rs1|Lap18-rs1	stathmin 1, related sequence 1	pseudo
mm_43457.1	chr5	136237029	136237061	+	1	NA	intron (NM_001302938, intron 1 of 8)	intron (NM_001302938, intron 1 of 8)	7895	NM_001302939	23921	Mm.425294	NM_018825	ENSMUSG00000005057	Sh2b2	Aps	SH2B adaptor protein 2	protein-coding
mm_16864.1	chr2	11777487	11777561	-	1	NA	promoter-TSS (NM_177268)	promoter-TSS (NM_177268)	3	NM_015792	50755	Mm.24088	NM_015792	ENSMUSG00000058594	Fbxo18	AU015756|Fbh1|Fbx18	F-box protein 18	protein-coding
mm_63269.1	chr7	126760592	126760599	+	1	NA	intron (NM_011952, intron 1 of 8)	intron (NM_011952, intron 1 of 8)	969	NM_011952	26417	Mm.8385	NM_011952	ENSMUSG00000063065	Mapk3	Erk-1|Erk1|Ert2|Esrk1|Mnk1|Mtap2k|Prkm3|p44|p44erk1|p44mapk	mitogen-activated protein kinase 3	protein-coding
mm_78802.1	chr9	44047603	44047650	+	1	NA	3' UTR (NM_009382, exon 4 of 4)	3' UTR (NM_009382, exon 4 of 4)	4242	NM_009382	21838	Mm.3951	NM_009382	ENSMUSG00000032011	Thy1	CD90|T25|Thy-1|Thy-1.2|Thy1.1|Thy1.2	thymus cell antigen 1, theta	protein-coding
mm_56947.1	chr6	119969280	119969323	-	1	NA	exon (NM_001185020, exon 7 of 26)	exon (NM_001185020, exon 7 of 26)	65010	NR_030487	735290		NR_030487	ENSMUSG00000076217	Mir706	Mirn706|mir-706|mmu-mir-706	microRNA 706	ncRNA
mm_125787.1	chr15	74716706	74716719	+	1	NA	3' UTR (NM_028216, exon 3 of 3)	3' UTR (NM_028216, exon 3 of 3)	1873	NM_028216	72373	Mm.46395	NM_028216	ENSMUSG00000022598	Psca	2210408B04Rik	prostate stem cell antigen	protein-coding
mm_167401.1	chr8	95713944	95713958	+	1	NA	3' UTR (NM_145602, exon 14 of 14)	3' UTR (NM_145602, exon 14 of 14)	-1962	NM_001035123	66083	Mm.261321	NM_001035123	ENSMUSG00000031671	Setd6	0610039J04Rik|3110004G14Rik|AI413388|C76402	SET domain containing 6	protein-coding
mm_47007.1	chr5	115474549	115474568	-	1	NA	exon (NM_011107, exon 4 of 4)	exon (NM_011107, exon 4 of 4)	8292	NM_011107	18778	Mm.20190	NM_011107	ENSMUSG00000029522	Pla2g1b	Pla2a|sPLA2IB	phospholipase A2, group IB, pancreas	protein-coding
mm_55659.1	chr6	72390660	72390670	-	1	NA	promoter-TSS (NM_016794)	promoter-TSS (NM_016794)	2	NM_016794	22320	Mm.1838	NM_016794	ENSMUSG00000050732	Vamp8	AU041171|Edb|endobrevin	vesicle-associated membrane protein 8	protein-coding
mm_30325.1	chr3	151731938	151731948	-	1	NA	3' UTR (NM_133871, exon 8 of 8)	3' UTR (NM_133871, exon 8 of 8)	18016	NM_133871	99899	Mm.30756	NM_133871	ENSMUSG00000028037	Ifi44	A430056A10Rik|AW261460|MTAP44|p44	interferon-induced protein 44	protein-coding
mm_150762.1	chr19	44237717	44237741	+	1	NA	intron (NM_024450, intron 4 of 5)	RMER17C2|LTR|ERVK	34441	NM_024450	30049	Mm.480594	NM_024450	ENSMUSG00000025202	Scd3	4930513N16Rik	stearoyl-coenzyme A desaturase 3	protein-coding
mm_135331.1	chr16	38828726	38828736	-	1	NA	promoter-TSS (NM_029042)	promoter-TSS (NM_029042)	18	NM_029042	74663	Mm.50263	NM_029042	ENSMUSG00000022798	4930435E12Rik	TSCPA	RIKEN cDNA 4930435E12 gene	protein-coding
mm_132501.1	chr16	36951184	36951194	+	1	NA	intron (NM_008225, intron 6 of 13)	intron (NM_008225, intron 6 of 13)	16206	NM_008225	15163	Mm.4091	NM_008225	ENSMUSG00000022831	Hcls1	AW213261|HS1	hematopoietic cell specific Lyn substrate 1	protein-coding
mm_136175.1	chr16	88774202	88774206	-	1	NA	promoter-TSS (NM_027170)	promoter-TSS (NM_027170)	2	NM_027170	69696	Mm.358728	NM_027170	ENSMUSG00000048830	2310057N15Rik	Krtap13-1	RIKEN cDNA 2310057N15 gene	protein-coding
mm_146838.1	chr18	22884253	22884256	-	1	NA	intron (NM_001347510, intron 5 of 9)	intron (NM_001347510, intron 5 of 9)	154409	NM_001161483	319211	Mm.209896	NM_199024	ENSMUSG00000041923	Nol4	1700013J13Rik|4930568N03Rik|Gm1262	nucleolar protein 4	protein-coding
mm_41557.1	chr5	93093429	93093444	+	1	NA	promoter-TSS (NM_001310669)	promoter-TSS (NM_001310669)	20	NM_001347377	52398	Mm.394184	NM_001009818	ENSMUSG00000058013	Sept11	6230410I01Rik|AW548875|D5Ertd606e	septin 11	protein-coding
mm_108418.1	chr12	81971203	81971221	+	1	NA	intron (NM_018814, intron 19 of 35)	intron (NM_018814, intron 19 of 35)	111182	NM_018814	54604	Mm.86584	NM_018814	ENSMUSG00000021140	Pcnx	2900024E21Rik|3526401J03Rik|AF096286|AI327143|AI413187|Pcnx1|Pcnxl1	pecanex homolog (Drosophila)	protein-coding
mm_127454.1	chr15	101270884	101270892	+	1	NA	exon (NM_010444, exon 2 of 7)	exon (NM_010444, exon 2 of 7)	4042	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_18247.1	chr2	52201462	52201474	-	1	NA	exon (NM_010889, exon 107 of 157)	exon (NM_010889, exon 107 of 157)	-89534	NR_040620	78049	Mm.243883	NR_040620		4930573O16Rik	-	RIKEN cDNA 4930573O16 gene	ncRNA
mm_47030.1	chr5	115652975	115652992	-	1	NA	intron (NM_001080808, intron 7 of 8)	intron (NM_001080808, intron 7 of 8)	7410	NR_105997	102465623		NR_105997	ENSMUSG00000099254	Mir7030	Gm27267|mmu-mir-7030	microRNA 7030	ncRNA
mm_99120.1	chr11	100145551	100145559	+	1	NA	exon (NM_008471, exon 1 of 6)	exon (NM_008471, exon 1 of 6)	371	NM_008471	16669	Mm.439699	NM_008471	ENSMUSG00000020911	Krt19	AI663979|CK-19|EndoC|K19|Krt-1.19|Krt1-19	keratin 19	protein-coding
mm_49711.1	chr6	34419462	34419468	+	1	NA	exon (NM_009731, exon 6 of 10)	exon (NM_009731, exon 6 of 10)	7103	NM_009731	11997	Mm.482073	NM_009731	ENSMUSG00000052131	Akr1b7	AR|Avdp|MVDP	aldo-keto reductase family 1, member B7	protein-coding
mm_136601.1	chr17	5152648	5152658	+	1	NA	intron (NM_001085355, intron 4 of 19)	B1_Mus2|SINE|Alu	157579	NM_001085355	239985	Mm.133401	NM_001085355	ENSMUSG00000069729	Arid1b	8030481M12|9330189K18Rik|AI836955|Ardi1b|B230217J03Rik|mKIAA1235	AT rich interactive domain 1B (SWI-like)	protein-coding
mm_165226.1	chr2	52424918	52424943	-	1	NA	promoter-TSS (NM_182994)	promoter-TSS (NM_182994)	-56	NM_182994	75423	Mm.314378	NM_182994	ENSMUSG00000036093	Arl5a	2410015N24Rik|2810410P22Rik|AA408731|AW610751|Arl5|T25534	ADP-ribosylation factor-like 5A	protein-coding
mm_86443.1	chr10	4106317	4106327	+	1	NA	intron (NM_172308, intron 25 of 27)	intron (NM_172308, intron 25 of 27)	133247	NM_172308	270685	Mm.184752	NM_172308	ENSMUSG00000040675	Mthfd1l	2410004L15Rik|AI647056|Fthfsdc1	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1-like	protein-coding
mm_42859.1	chr5	122219240	122219246	+	1	NA	intron (NM_028752, intron 2 of 6)	intron (NM_028752, intron 2 of 6)	8956	NM_028752	74096	Mm.28804	NM_028752	ENSMUSG00000064267	Hvcn1	0610039P13Rik|AI450555|BTS|HV1|Vsop.|mVSOP	hydrogen voltage-gated channel 1	protein-coding
mm_169224.1	chr13	66862125	66862135	-	1	NA	Intergenic	Intergenic	43220	NM_026219	67530	Mm.379136	NM_026219	ENSMUSG00000021520	Uqcrb	2210415M14Rik|QP-C|QPC|UQBC|UQBP|UQPC	ubiquinol-cytochrome c reductase binding protein	protein-coding
mm_170379.1	chr1	85598781	85598782	-	1	NA	promoter-TSS (NM_030194)	promoter-TSS (NM_030194)	29	NM_030194	109032	Mm.335802	NM_030194	ENSMUSG00000070034	Sp110	5031415C07Rik|52kDa|5830484A20Rik|ENSMUSG00000075603|Ifi75|Ipr1	Sp110 nuclear body protein	protein-coding
mm_18839.1	chr2	75133673	75133681	-	1	NA	Intergenic	Intergenic	307865	NM_016804	53375	Mm.292613	NM_016804	ENSMUSG00000027099	Mtx2	1500012G02Rik	metaxin 2	protein-coding
mm_130227.1	chr15	96285492	96285539	-	1	NA	Intergenic	CpG	-2007	NM_175251	77044	Mm.17166	NM_175251	ENSMUSG00000033237	Arid2	1700124K17Rik|4432409D24Rik|zipzap/p200	AT rich interactive domain 2 (ARID, RFX-like)	protein-coding
mm_73971.1	chr8	120489054	120489067	+	1	NA	5' UTR (NM_198671, exon 1 of 16)	5' UTR (NM_198671, exon 1 of 16)	194	NM_198671	382034	Mm.334856	NM_198671	ENSMUSG00000031822	Gse1	2210013I18Rik|mKIAA0182	genetic suppressor element 1, coiled-coil protein	protein-coding
mm_91997.1	chr10	62187487	62187491	-	1	NA	3' UTR (NM_197996, exon 8 of 8)	3' UTR (NM_197996, exon 8 of 8)	6738	NR_106122	102465767		NR_106122	ENSMUSG00000099185	Mir7662	Gm27876|mmu-mir-7662	microRNA 7662	ncRNA
mm_73847.1	chr8	117701008	117701054	+	1	NA	promoter-TSS (NM_008290)	promoter-TSS (NM_008290)	-915	NM_008290	15486	Mm.276466	NM_008290	ENSMUSG00000031844	Hsd17b2	AI194836|AI194967|AI255511	hydroxysteroid (17-beta) dehydrogenase 2	protein-coding
mm_170172.1	chr17	56462124	56462127	-	1	NA	promoter-TSS (NM_001252456)	promoter-TSS (NM_001252456)	96	NM_001252456	19280	Mm.258771	NM_011218	ENSMUSG00000013236	Ptprs	AL022616|PTP|PTP-NU3|PTPNU-3|PTPsigma|Ptpt9|R-PTP-S|RPTPsigma	protein tyrosine phosphatase, receptor type, S	protein-coding
mm_103705.1	chr11	79516623	79516633	-	1	NA	exon (NM_001077496, exon 2 of 2)	exon (NM_001077496, exon 2 of 2)	7134	NM_001077496	216984	Mm.439665	NM_001077496	ENSMUSG00000093938	Evi2b	Evi-2|Evi2	ecotropic viral integration site 2b	protein-coding
mm_37556.1	chr4	126163276	126163296	-	1	NA	promoter-TSS (NM_001162533)	promoter-TSS (NM_001162533)	55	NM_001162533	66938	Mm.29813	NM_025856	ENSMUSG00000073758	Sh3d21	1700029G01Rik|AU019788	SH3 domain containing 21	protein-coding
mm_34813.1	chr4	154936988	154937007	+	1	NA	Intergenic	Intergenic	-8920	NM_178931	230979	Mm.215147	NM_178931	ENSMUSG00000042333	Tnfrsf14	Atar|HveA|Hvem|Tnfrs14	tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)	protein-coding
mm_21357.1	chr2	157125070	157125082	-	1	NA	intron (NM_018851, intron 3 of 15)	RSINE1|SINE|B4	10146	NM_001139520	56045	Mm.248478	NM_018851	ENSMUSG00000027639	Samhd1	E330031J07Rik|Mg11	SAM domain and HD domain, 1	protein-coding
mm_19696.1	chr2	103760923	103760941	-	1	NA	intron (NM_153126, intron 1 of 28)	CpG	318	NM_153126	98956	Mm.288005	NM_153126	ENSMUSG00000027185	Nat10	AI429152	N-acetyltransferase 10	protein-coding
mm_8710.1	chr1	158968827	158968832	-	1	NA	Intergenic	Intergenic	-11391	NM_001085376	23850	Mm.458621	NM_001085376	ENSMUSG00000073530	Pappa2	PAPP-A2|PLAC3|Pappe	pappalysin 2	protein-coding
mm_96616.1	chr11	69099035	69099053	+	1	NA	promoter-TSS (NM_011065)	promoter-TSS (NM_011065)	88	NM_011065	18626	Mm.7373	NM_011065	ENSMUSG00000020893	Per1	Hftm|Per|m-rigui|mPer1	period circadian clock 1	protein-coding
mm_79905.1	chr9	65412772	65412796	+	1	NA	TTS (NM_178933)	TTS (NM_178933)	9989	NM_178933	330962	Mm.335247	NM_178933	ENSMUSG00000053862	Slc51b	Ostb	solute carrier family 51, beta subunit	protein-coding
mm_82541.1	chr9	20879696	20879706	-	1	NA	promoter-TSS (NM_145154)	promoter-TSS (NM_145154)	9	NM_145154	70726	Mm.34019	NM_145154	ENSMUSG00000038742	Angptl6	6330404E11Rik|AGF|ARP3|Arp5	angiopoietin-like 6	protein-coding
mm_49023.1	chr6	4759527	4759537	+	1	NA	3' UTR (NM_130877, exon 2 of 2)	3' UTR (NM_130877, exon 2 of 2)	12226	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_131347.1	chr16	13671923	13671937	+	1	NA	promoter-TSS (NM_001177552)	promoter-TSS (NM_001177552)	72	NM_025653	67118	Mm.223689	NM_025653	ENSMUSG00000022684	Bfar	3010001A07Rik|3110001I22Rik|AI666707|AW107665|Bar|Rnf47	bifunctional apoptosis regulator	protein-coding
mm_103073.1	chr11	69880972	69880985	-	1	NA	promoter-TSS (NM_153143)	promoter-TSS (NM_153143)	7	NM_153143	216858	Mm.239498	NM_153143	ENSMUSG00000046731	Kctd11	AF465352|Ren	potassium channel tetramerisation domain containing 11	protein-coding
mm_91475.1	chr10	34207828	34207849	-	1	NA	promoter-TSS (NM_172508)	promoter-TSS (NM_172508)	-287	NM_172508	212898	Mm.34557	NM_172508	ENSMUSG00000039497	Dse	6030499O08|AI480506|B130024B19Rik|DS-epi1|Sart2	dermatan sulfate epimerase	protein-coding
mm_149618.1	chr19	16781112	16781120	+	1	NA	promoter-TSS (NM_173028)	promoter-TSS (NM_173028)	-183	NM_173028	271564	Mm.211963	NM_173028	ENSMUSG00000046230	Vps13a	4930425F11|4930516E05Rik|4930543C13Rik|9930023P20|Chac|Chorein|D330038K10Rik|mKIAA0986	vacuolar protein sorting 13A	protein-coding
mm_110077.1	chr12	24493452	24493482	-	1	NA	Intergenic	Intergenic	-5114	NM_020614	21340	Mm.39082	NM_020614	ENSMUSG00000059669	Taf1b	4930408G01Rik|A230108M10Rik|TAFI68|Tafi86|p63	TATA-box binding protein associated factor, RNA polymerase I, B	protein-coding
mm_132875.1	chr16	48629989	48630011	+	1	NA	intron (NM_010816, intron 26 of 26)	RLTR23|LTR|ERV1	141956	NM_198297	77647	Mm.167298	NM_198297	ENSMUSG00000030775	Trat1	C030046M14Rik|Tcrim|Trim	T cell receptor associated transmembrane adaptor 1	protein-coding
mm_105720.1	chr11	108533695	108533697	-	1	NA	intron (NM_029606, intron 18 of 27)	intron (NM_029606, intron 18 of 27)	108430	NM_029606	76380	Mm.344071	NM_029586	ENSMUSG00000020728	Cep112	1700001M19Rik|1700029K01Rik|8430407H02Rik|AV043680|AV207351|Ccdc46|Macoco	centrosomal protein 112	protein-coding
mm_155449.1	chrX	73495310	73495332	+	1	NA	3' UTR (NM_007542, exon 8 of 8)	3' UTR (NM_007542, exon 8 of 8)	-7765	NM_001310537	320707	Mm.210095	NM_177236	ENSMUSG00000031376	Atp2b3	6430519O13Rik|Pmca3	ATPase, Ca++ transporting, plasma membrane 3	protein-coding
mm_131454.1	chr16	16870865	16870908	+	1	NA	5' UTR (NM_011624, exon 1 of 18)	5' UTR (NM_011624, exon 1 of 18)	150	NM_011624	21976	Mm.326089	NM_011624	ENSMUSG00000022779	Top3b	-	topoisomerase (DNA) III beta	protein-coding
mm_136069.1	chr16	84735808	84735818	-	1	NA	promoter-TSS (NM_017404)	promoter-TSS (NM_017404)	-511	NM_017404	27393	Mm.103655	NM_017404	ENSMUSG00000022889	Mrpl39	C21orf8|MRP-L5|ORF22|Rpml5	mitochondrial ribosomal protein L39	protein-coding
mm_112140.1	chr12	113140099	113140106	-	1	NA	promoter-TSS (NM_024223)	promoter-TSS (NM_024223)	-134	NM_024223	68337	Mm.133825	NM_024223	ENSMUSG00000006356	Crip2	0610010I23Rik|AW743261|C77570|CRP2|CRP4|Crp|ESP1|Hlp	cysteine rich protein 2	protein-coding
mm_133723.1	chr16	93711953	93712008	+	1	NA	promoter-TSS (NM_026700)	promoter-TSS (NM_026700)	73	NM_027293	70028	Mm.23230	NM_026700	ENSMUSG00000022946	Dopey2	0610038M01Rik|2610510B01Rik|AI503246|C21orf5|mKIAA0933	dopey family member 2	protein-coding
mm_6216.1	chr1	66849693	66849701	-	1	NA	intron (NM_007381, intron 4 of 10)	intron (NM_007381, intron 4 of 10)	13612	NM_007381	11363	Mm.2445	NM_007381	ENSMUSG00000026003	Acadl	AA960361|AU018452|C79855|LCAD	acyl-Coenzyme A dehydrogenase, long-chain	protein-coding
mm_93408.1	chr10	107912375	107912384	-	1	NA	promoter-TSS (NM_001177567)	promoter-TSS (NM_001177567)	-245	NM_001177567	628870	Mm.336090	NM_001177567	ENSMUSG00000091455	Otogl	EG628870|Gm6924	otogelin-like	protein-coding
mm_33989.1	chr4	137862239	137862249	+	1	NA	promoter-TSS (NM_199307)	promoter-TSS (NM_199307)	7	NM_199307	230857	Mm.401062	NM_199307	ENSMUSG00000057530	Ece1	AW322500|ECE-1|ECE-1a|ECE-1b|ECE-1d	endothelin converting enzyme 1	protein-coding
mm_88411.1	chr10	77032712	77032747	+	1	NA	promoter-TSS (NM_031196)	promoter-TSS (NM_031196)	-10	NM_001199271	20509	Mm.265060	NM_031196	ENSMUSG00000001436	Slc19a1	AI323572|RFC|RFC-1|RFC1	solute carrier family 19 (folate transporter), member 1	protein-coding
mm_43.1	chr1	6489176	6489200	+	1	NA	intron (NM_001244693, intron 2 of 22)	intron (NM_001244693, intron 2 of 22)	1957	NM_001244692	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding
mm_26479.1	chr3	144677674	144677706	+	1	NA	Intergenic	Intergenic	42645	NM_001282042	54673	Mm.271775	NM_019464	ENSMUSG00000037062	Sh3glb1	AA409932|AI314629|AU015566|Bif-1|mKIAA0491	SH3-domain GRB2-like B1 (endophilin)	protein-coding
mm_147217.1	chr18	37997529	37997540	-	1	NA	promoter-TSS (NM_139206)	promoter-TSS (NM_139206)	40	NM_139206	106952	Mm.247642	NM_139206	ENSMUSG00000024451	Arap3	Centd3|Drag1|E030006K04Rik|cnt-d3	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3	protein-coding
mm_57970.1	chr6	135346452	135346473	-	1	NA	Intergenic	Intergenic	-16469	NM_010128	13730	Mm.182785	NM_010128	ENSMUSG00000030208	Emp1	I-8-09|TMP	epithelial membrane protein 1	protein-coding
mm_35782.1	chr4	46413487	46413489	-	1	NA	Intergenic	Intergenic	-9305	NM_053149	93966	Mm.25793	NM_053149	ENSMUSG00000028332	Hemgn	4921524M03Rik|AI317176|EDAG|Hgn|mNDR	hemogen	protein-coding
mm_94759.1	chr11	21149090	21149102	+	1	NA	3' UTR (NM_023324, exon 7 of 7)	3' UTR (NM_023324, exon 7 of 7)	57772	NM_023324	67245	Mm.28957	NM_023324	ENSMUSG00000020134	Peli1	2810468L03Rik|A930031K15Rik|AA409794|AI586297|D11Ertd676e	pellino 1	protein-coding
mm_172681.1	chr8	52197132	52197132	-	1	NA	Intergenic	Intergenic	-1314570	NM_001205054	11593	Mm.334535	NM_001005847	ENSMUSG00000031521	Aga	AW060726	aspartylglucosaminidase	protein-coding
mm_67245.1	chr7	75309155	75309172	-	1	NA	promoter-TSS (NM_153579)	promoter-TSS (NM_153579)	99	NM_153579	64176	Mm.273082	NM_153579	ENSMUSG00000053025	Sv2b	A830038F04Rik|AI850768|mKIAA0735	synaptic vesicle glycoprotein 2 b	protein-coding
mm_20605.1	chr2	131454400	131454413	-	1	NA	intron (NR_037281, intron 1 of 2)	intron (NR_037281, intron 1 of 2)	-37456	NM_001177834	228608	Mm.136586	NM_145533	ENSMUSG00000027333	Smox	B130066H01Rik|PAO|PAOh1|SMO	spermine oxidase	protein-coding
mm_60366.1	chr7	44442070	44442080	+	1	NA	promoter-TSS (NM_198250)	promoter-TSS (NM_198250)	-412	NM_198250	272381	Mm.44173	NM_198250	ENSMUSG00000047085	Lrrc4b	A830007M12|Lrig4	leucine rich repeat containing 4B	protein-coding
mm_32348.1	chr4	104913514	104913524	+	1	NA	promoter-TSS (NM_001162980)	promoter-TSS (NM_001162980)	63	NM_001285952	242594	Mm.65181	NM_001162980	ENSMUSG00000078612	1700024P16Rik	C1orf168|Gm620	RIKEN cDNA 1700024P16 gene	protein-coding
mm_159178.1	chr2	111335924	111335924	-	1	NA	exon (NM_146907, exon 1 of 1)	exon (NM_146907, exon 1 of 1)	152	NM_146907	258909	Mm.377746	NM_146907	ENSMUSG00000096554	Olfr1282	MOR248-16|MOR248-2|Olfr1557	olfactory receptor 1282	protein-coding
mm_15162.1	chr2	154009862	154009872	+	1	NA	exon (NM_008953, exon 3 of 9)	exon (NM_008953, exon 3 of 9)	1591	NM_008953	19194	Mm.29197	NM_008953	ENSMUSG00000042459	Bpifa2	Bpifa2e|Psp	BPI fold containing family A, member 2	protein-coding
mm_51454.1	chr6	81911949	81911952	+	1	NA	Intergenic	RMER17C2|LTR|ERVK	-1150	NR_046040	74220	Mm.490521	NR_046040	ENSMUSG00000101404	1700009C05Rik	-	RIKEN cDNA 1700009C05 gene	ncRNA
mm_42214.1	chr5	113043428	113043428	+	1	NA	Intergenic	Intergenic	26689	NM_007773	12961	Mm.1215	NM_007773	ENSMUSG00000042240	Crybb2	Cryb-2	crystallin, beta B2	protein-coding
mm_32260.1	chr4	102581093	102581120	+	1	NA	intron (NM_019840, intron 6 of 14)	B4A|SINE|B4	-6452	NM_001177982	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_108484.1	chr12	83664133	83664172	+	1	NA	exon (NM_027349, exon 10 of 19)	exon (NM_027349, exon 10 of 19)	-24411	NM_008943	19164	Mm.998	NM_008943	ENSMUSG00000019969	Psen1	Ad3h|PS-1|PS1|S182	presenilin 1	protein-coding
mm_74519.1	chr8	9144532	9144555	-	1	NA	promoter-TSS (NR_073360)	promoter-TSS (NR_073360)	-126	NR_073360	74688	Mm.159298	NR_073360	ENSMUSG00000109215	4930453L07Rik	-	RIKEN cDNA 4930453L07 gene	ncRNA
mm_90572.1	chr10	128232097	128232101	+	1	NA	promoter-TSS (NM_001136082)	promoter-TSS (NM_001136082)	36	NM_001136082	21853	Mm.6458	NM_011589	ENSMUSG00000039994	Timeless	C77407|Debt69|tim	timeless circadian clock 1	protein-coding
mm_169343.1	chr14	14116389	14116407	-	1	NA	exon (NM_025550, exon 4 of 8)	exon (NM_025550, exon 4 of 8)	4506	NM_025550	66413	Mm.27591	NM_025550	ENSMUSG00000021737	Psmd6	2400006A19Rik	proteasome (prosome, macropain) 26S subunit, non-ATPase, 6	protein-coding
mm_44024.1	chr5	147429962	147429979	+	1	NA	promoter-TSS (NM_028291)	promoter-TSS (NM_028291)	-610	NM_028291	72587	Mm.320469	NM_028291	ENSMUSG00000029647	Pan3	2700050F09Rik|A430027N15Rik|AU014670	PAN3 poly(A) specific ribonuclease subunit	protein-coding
mm_148731.1	chr19	5877900	5877914	+	1	NA	promoter-TSS (NM_134154)	promoter-TSS (NM_134154)	-559	NM_134154	107375	Mm.5323	NM_134154	ENSMUSG00000024818	Slc25a45	AW491445	solute carrier family 25, member 45	protein-coding
mm_148515.1	chr19	4232409	4232425	+	1	NA	promoter-TSS (NR_132280)	promoter-TSS (NR_132280)	2	NR_132280	69745	Mm.32518	NM_027196	ENSMUSG00000024854	Pold4	2410012M21Rik|AI463381|AW060307|Polds|p12	polymerase (DNA-directed), delta 4	protein-coding
mm_124347.1	chr14	103998274	103998284	-	1	NA	intron (NR_045953, intron 1 of 2)	Lx9|LINE|L1	28863	NR_045953	73877	Mm.399172	NR_045953		4930432J09Rik	-	RIKEN cDNA 4930432J09 gene	ncRNA
mm_151912.1	chr19	5799676	5799690	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	2989	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_128393.1	chr15	43170954	43170995	-	1	NA	promoter-TSS (NM_172815)	promoter-TSS (NM_172815)	-156	NM_172815	239405	Mm.193274	NM_172815	ENSMUSG00000051920	Rspo2	2610028F08Rik|AA673245|D430027K22|ftls	R-spondin 2	protein-coding
mm_148811.1	chr19	6282746	6282761	+	1	NA	intron (NM_010119, intron 2 of 4)	ID4|SINE|ID	5857	NM_010119	13660	Mm.30169	NM_010119	ENSMUSG00000024772	Ehd1	AA409636|Past1|RME-1	EH-domain containing 1	protein-coding
mm_36805.1	chr4	103173485	103173495	-	1	NA	3' UTR (NM_177732, exon 10 of 10)	3' UTR (NM_177732, exon 10 of 10)	41394	NM_177732	242585	Mm.281800	NM_177732	ENSMUSG00000028521	Slc35d1	AI834976|C330011J09|UGTREL7|mKIAA0260	solute carrier family 35 (UDP-glucuronic acid/UDP-N-acetylgalactosamine dual transporter), member D1	protein-coding
mm_3214.1	chr1	135840672	135840696	+	1	NA	promoter-TSS (NM_001130176)	promoter-TSS (NM_001130176)	-177	NM_001130176	21956	Mm.247470	NM_011619	ENSMUSG00000026414	Tnnt2	Tnt|cTnT	troponin T2, cardiac	protein-coding
mm_166662.1	chr6	88798215	88798219	+	1	NA	intron (NM_011844, intron 3 of 7)	intron (NM_011844, intron 3 of 7)	43718	NM_030251	80283	Mm.166858	NM_030251	ENSMUSG00000030083	Abtb1	AI847549|BC003234|BPOZ|EF1ABP	ankyrin repeat and BTB (POZ) domain containing 1	protein-coding
mm_78354.1	chr9	25491130	25491135	+	1	NA	intron (NM_026189, intron 2 of 7)	Tigger13a|DNA|TcMar-Tigger	9535	NM_026189	67484	Mm.112977	NM_026189	ENSMUSG00000036611	Eepd1	2310005P05Rik|AI481005	endonuclease/exonuclease/phosphatase family domain containing 1	protein-coding
mm_145232.1	chr18	50134751	50134766	+	1	NA	intron (NM_008292, intron 2 of 23)	intron (NM_008292, intron 2 of 23)	6557	NM_008292	15488	Mm.277857	NM_008292	ENSMUSG00000024507	Hsd17b4	17-beta-HSD|17[b]-HSD|DBP|MFE-2|MFP2|MPF-2|Mfp-2|perMFE-2	hydroxysteroid (17-beta) dehydrogenase 4	protein-coding
mm_48864.1	chr5	149827663	149827666	-	1	NA	Intergenic	Intergenic	-15913	NR_077242	100861794	Mm.402054	NR_077242	ENSMUSG00000106740	Gm21221	-	predicted gene, 21221	ncRNA
mm_20178.1	chr2	122594906	122594913	-	1	NA	3' UTR (NM_025961, exon 9 of 9)	3' UTR (NM_025961, exon 9 of 9)	16368	NM_025961	67092	Mm.29975	NM_025961	ENSMUSG00000027199	Gatm	1810003P21Rik|AI314789|AT	glycine amidinotransferase (L-arginine:glycine amidinotransferase)	protein-coding
mm_81845.1	chr9	118556550	118556567	+	1	NA	exon (NM_018748, exon 15 of 24)	exon (NM_018748, exon 15 of 24)	-50151	NM_133721	104099	Mm.335520	NM_133721	ENSMUSG00000039115	Itga9	(alpha)9|2610002H11Rik|6720458D17Rik|AI461869|D130073C02|D9Ertd428e	integrin alpha 9	protein-coding
mm_89319.1	chr10	87930856	87930872	+	1	NA	3' UTR (NM_010512, exon 5 of 5)	3' UTR (NM_010512, exon 5 of 5)	-35807	NR_000040	22172	Mm.391420	NR_000040		Tyms-ps	-	thymidylate synthase, pseudogene	pseudo
mm_121982.1	chr14	25858160	25858166	-	1	NA	intron (NM_013469, intron 1 of 14)	intron (NM_013469, intron 1 of 14)	16008	NM_013469	11744	Mm.294083	NM_013469	ENSMUSG00000021866	Anxa11	A830099O17Rik|Anx11	annexin A11	protein-coding
mm_155784.1	chrX	96456405	96456441	+	1	NA	promoter-TSS (NM_001159627)	promoter-TSS (NM_001159627)	77	NM_001159627	15203	Mm.277092	NM_010417	ENSMUSG00000031209	Heph	C130006F04Rik|Cpl|mKIAA0698|sla	hephaestin	protein-coding
mm_7193.1	chr1	92919333	92919339	-	1	NA	intron (NM_181405, intron 10 of 10)	intron (NM_181405, intron 10 of 10)	8511	NM_181405	108657	Mm.200971	NM_181405	ENSMUSG00000026269	Rnpepl1	1110014H17Rik|AI894167	arginyl aminopeptidase (aminopeptidase B)-like 1	protein-coding
mm_89438.1	chr10	91170719	91170730	+	1	NA	promoter-TSS (NM_001283048)	promoter-TSS (NM_001283048)	-174	NM_001283048	21917	Mm.159684	NM_011605	ENSMUSG00000019961	Tmpo	5630400D24Rik|AI195756|AI606875|AW214352|AW547477|LAP2|TP	thymopoietin	protein-coding
mm_148717.1	chr19	5822348	5822351	+	1	NA	Intergenic	Intergenic	-19677	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_82460.1	chr9	15628284	15628311	-	1	NA	promoter-TSS (NM_181816)	promoter-TSS (NM_181816)	-364	NM_181816	234964	Mm.32237	NM_181816	ENSMUSG00000039977	Ccdc67	4933401K09Rik|Deup1	coiled-coil domain containing 67	protein-coding
mm_31644.1	chr4	59581676	59581682	+	1	NA	5' UTR (NM_024255, exon 1 of 11)	5' UTR (NM_024255, exon 1 of 11)	116	NM_024255	72479	Mm.272905	NM_024255	ENSMUSG00000028383	Hsdl2	2610207I16Rik	hydroxysteroid dehydrogenase like 2	protein-coding
mm_153637.1	chr19	44069691	44069708	-	1	NA	promoter-TSS (NM_001164360)	promoter-TSS (NM_001164360)	-13	NM_145502	226144	Mm.279865	NM_145502	ENSMUSG00000025198	Erlin1	2810439N09Rik|C80197|Keo4|Spfh1	ER lipid raft associated 1	protein-coding
mm_148211.1	chr18	80198477	80198488	-	1	NA	intron (NM_199197, intron 1 of 5)	intron (NM_199197, intron 1 of 5)	2137	NM_199197	68731	Mm.186936	NM_199197	ENSMUSG00000024570	Rbfa	1110032A13Rik|AI595940	ribosome binding factor A	protein-coding
mm_89984.1	chr10	111984830	111984847	+	1	NA	TTS (NM_028608)	TTS (NM_028608)	12143	NM_178610	52705	Mm.34606	NM_178610	ENSMUSG00000063334	Krr1	2610511F02Rik|AI255219|AI428520|D10Ertd773e|Hrb2	KRR1, small subunit (SSU) processome component, homolog (yeast)	protein-coding
mm_158728.1	chrX	163958087	163958132	-	1	NA	intron (NM_178794, intron 1 of 4)	intron (NM_178794, intron 1 of 4)	557	NM_009453	22184	Mm.426178	NM_009453	ENSMUSG00000031370	Zrsr2	35kDa|5031411E02Rik|A230052C13Rik|C77286|U2af1-rs2|URP	zinc finger (CCCH type), RNA binding motif and serine/arginine rich 2	protein-coding
mm_145463.1	chr18	60246715	60246735	+	1	NA	3' UTR (NM_001033767, exon 3 of 3)	3' UTR (NM_001033767, exon 3 of 3)	26542	NM_001034859	225594	Mm.329460	NM_001034859	ENSMUSG00000068606	Gm4841	EG225594|Ifgga3	predicted gene 4841	protein-coding
mm_37777.1	chr4	130139150	130139162	-	1	NA	promoter-TSS (NM_001305392)	promoter-TSS (NM_001305392)	6	NM_198959	230777	Mm.246595	NM_198959	ENSMUSG00000028778	Hcrtr1	Ox1r|ox-1-R|ox1-R	hypocretin (orexin) receptor 1	protein-coding
mm_167651.1	chr9	66060128	66060138	+	1	NA	promoter-TSS (NM_011149)	promoter-TSS (NM_011149)	-36	NM_011149	19035	Mm.335249	NM_011149	ENSMUSG00000032383	Ppib	AA408962|AA553318|AI844835|Cphn-2|Cphn2|CyP-20b	peptidylprolyl isomerase B	protein-coding
mm_172869.1	chr9	41911832	41911845	-	1	NA	Intergenic	RLTR4_Mm|LTR|ERV1	212451	NM_011436	20660	Mm.121920	NM_011436	ENSMUSG00000049313	Sorl1	2900010L19Rik|AI596264|AW261561|LR11|SorLA|gp250|mSorLA	sortilin-related receptor, LDLR class A repeats-containing	protein-coding
mm_36074.1	chr4	58009091	58009101	-	1	NA	promoter-TSS (NM_026132)	promoter-TSS (NM_026132)	28	NM_026132	67402	Mm.87357	NM_026132	ENSMUSG00000038709	Txndc8	4930429J24Rik|Sptrx-3|Sptrx3|Trx6	thioredoxin domain containing 8	protein-coding
mm_88379.1	chr10	76442369	76442393	+	1	NA	intron (NM_008787, intron 1 of 41)	CpG	531	NM_008787	18541	Mm.251794	NM_008787	ENSMUSG00000001151	Pcnt	AW476095|C86676|KEN|Pcnt2|kendrin|m239Asp|m275Asp	pericentrin (kendrin)	protein-coding
mm_57448.1	chr6	125049844	125049858	-	1	NA	promoter-TSS (NM_016845)	promoter-TSS (NM_016845)	2	NR_130997	78202	Mm.445941	NR_130997	ENSMUSG00000108034	4930557K07Rik	-	RIKEN cDNA 4930557K07 gene	ncRNA
mm_100686.1	chr11	3504767	3504833	-	1	NA	promoter-TSS (NM_172439)	promoter-TSS (NM_172439)	21	NM_172439	170835	Mm.24313	NM_172439	ENSMUSG00000034570	Inpp5j	Pib5pa|Pipp	inositol polyphosphate 5-phosphatase J	protein-coding
mm_67321.1	chr7	79715689	79715749	-	1	NA	Intergenic	CpG	-1533	NM_001291222	16576	Mm.101633	NM_010626	ENSMUSG00000050382	Kif7	-	kinesin family member 7	protein-coding
mm_132640.1	chr16	39984593	39984622	+	1	NA	Intergenic	CpG	1082262	NM_170599	207683	Mm.245564	NM_170599	ENSMUSG00000022790	Igsf11	1700025L02Rik|BT-IgSF|Igsf13	immunoglobulin superfamily, member 11	protein-coding
mm_25324.1	chr3	106562168	106562176	+	1	NA	intron (NM_001025582, intron 4 of 6)	intron (NM_001025582, intron 4 of 6)	-14370	NM_133869	99712	Mm.429443	NM_133869	ENSMUSG00000040774	Cept1	9930118K05Rik|mCEPT1	choline/ethanolaminephosphotransferase 1	protein-coding
mm_5844.1	chr1	52963224	52963234	-	1	NA	Intergenic	Intergenic	-10389	NM_144953	67080	Mm.236287	NM_144953	ENSMUSG00000043629	1700019D03Rik	2410136C24Rik|AA410151|smAKAP	RIKEN cDNA 1700019D03 gene	protein-coding
mm_168943.1	chr12	72442160	72442169	-	1	NA	promoter-TSS (NM_001142729)	promoter-TSS (NM_001142729)	-85	NM_001142729	78257	Mm.266280	NM_030070	ENSMUSG00000021090	Lrrc9	4921529O18Rik|4930432K16Rik	leucine rich repeat containing 9	protein-coding
mm_103815.1	chr11	83003097	83003109	-	1	NA	exon (NM_181545, exon 6 of 6)	exon (NM_181545, exon 6 of 6)	-11273	NM_172796	237886	Mm.270253	NM_172796	ENSMUSG00000069793	Slfn9	9830137M10Rik	schlafen 9	protein-coding
mm_140725.1	chr17	15476163	15476196	-	1	NA	exon (NM_011185, exon 6 of 6)	exon (NM_011185, exon 6 of 6)	22097	NM_011185	19170	Mm.32912	NM_011185	ENSMUSG00000014769	Psmb1	AA409053|C81484|Lmpc5	proteasome (prosome, macropain) subunit, beta type 1	protein-coding
mm_54877.1	chr6	42669859	42669872	-	1	NA	Intergenic	Intergenic	23194	NM_029930	77574	Mm.24652	NM_029930	ENSMUSG00000036667	Tcaf1	2810407D09Rik|3321401G04Rik|A230020K05Rik|AI848529|Fam115a	TRPM8 channel-associated factor 1	protein-coding
mm_24369.1	chr3	90104148	90104152	+	1	NA	promoter-TSS (NM_029937)	promoter-TSS (NM_029937)	18	NM_029937	77595	Mm.159949	NM_029937	ENSMUSG00000027939	Nup210l	4930548O11Rik|R26-EGFP|Tg(Gt(ROSA)26Sor-EGFP)130910Eps	nucleoporin 210-like	protein-coding
mm_14210.1	chr2	127270695	127270747	+	1	NA	exon (NM_139308, exon 1 of 8)	exon (NM_139308, exon 1 of 8)	492	NM_139308	99138	Mm.41271	NM_139308	ENSMUSG00000027367	Stard7	AI852671|AL022671|AW544915	START domain containing 7	protein-coding
mm_30715.1	chr4	12906841	12906881	+	1	NA	promoter-TSS (NM_001171801)	promoter-TSS (NM_001171801)	24	NM_001171801	208820	Mm.12057	NM_173746	ENSMUSG00000055963	Triqk	C130086A10|Gm11818|OTTMUSG00000004461	triple QxxK/R motif containing	protein-coding
mm_46474.1	chr5	105131373	105131386	-	1	NA	intron (NM_008620, intron 3 of 10)	GA-rich|Low_complexity|Low_complexity	8173	NM_008620	17472	Mm.440525	NM_008620	ENSMUSG00000079363	Gbp4	AW228052|Mag-2|Mpa-2|Mpa2	guanylate binding protein 4	protein-coding
mm_27949.1	chr3	79825493	79825506	-	1	NA	intron (NM_027495, intron 7 of 11)	intron (NM_027495, intron 7 of 11)	17163	NM_027495	70652	Mm.46635	NM_027495	ENSMUSG00000027956	Tmem144	1110057I03Rik|5730537D05Rik	transmembrane protein 144	protein-coding
mm_144949.1	chr18	37807841	37807861	+	1	NA	exon (NM_033581, exon 1 of 4)	exon (NM_033581, exon 1 of 4)	1441	NM_033581	93706	Mm.247203	NM_033581	ENSMUSG00000102918	Pcdhgc3	PC43|Pcdh2	protocadherin gamma subfamily C, 3	protein-coding
mm_15014.1	chr2	152604402	152604410	+	1	NA	promoter-TSS (NM_001037247)	promoter-TSS (NM_001037247)	79	NM_001037247	266620	Mm.330669	NM_001037247	ENSMUSG00000044863	Defb36	BD-36|Defb123|mBD-36	defensin beta 36	protein-coding
mm_5980.1	chr1	58392742	58392764	-	1	NA	promoter-TSS (NM_025824)	promoter-TSS (NM_025824)	-383	NM_025824	66882	Mm.21848	NM_025824	ENSMUSG00000051223	Bzw1	1200015E15Rik|mKIAA0005	basic leucine zipper and W2 domains 1	protein-coding
mm_94705.1	chr11	20248953	20248958	+	1	NA	intron (NM_172260, intron 1 of 6)	CpG	469	NM_172260	216543	Mm.260314	NM_172260	ENSMUSG00000044066	Cep68	6030463E10Rik|AI481761|BC027174|Kiaa0582	centrosomal protein 68	protein-coding
mm_146060.1	chr18	69683098	69683152	+	1	NA	3' UTR (NM_001083967, exon 20 of 20)	3' UTR (NM_001083967, exon 20 of 20)	-242434	NM_201362	381175	Mm.266831	NM_201362	ENSMUSG00000038903	Ccdc68	BC046343	coiled-coil domain containing 68	protein-coding
mm_89017.1	chr10	82083313	82083365	+	1	NA	Intergenic	Intergenic	35212	NM_001024626	408062	Mm.391409	NM_001024626	ENSMUSG00000061371	Zfp873	-	zinc finger protein 873	protein-coding
mm_83005.1	chr9	36757001	36757011	-	1	NA	intron (NM_008408, intron 5 of 17)	intron (NM_008408, intron 5 of 17)	10572	NM_008408	16430	Mm.2863	NM_008408	ENSMUSG00000032116	Stt3a	AA408947|BB081708|Itm1	STT3, subunit of the oligosaccharyltransferase complex, homolog A (S. cerevisiae)	protein-coding
mm_125742.1	chr15	73676662	73676675	+	1	NA	Intergenic	Intergenic	30837	NM_173365	239530	Mm.122997	NM_173365	ENSMUSG00000045281	Gpr20	A430106B11Rik	G protein-coupled receptor 20	protein-coding
mm_76818.1	chr8	104534569	104534624	-	1	NA	promoter-TSS (NM_144931)	promoter-TSS (NM_144931)	41	NM_144931	234664	Mm.237670	NM_144931	ENSMUSG00000031878	Nae1	59kDa|Appbp1	NEDD8 activating enzyme E1 subunit 1	protein-coding
mm_53039.1	chr6	124570367	124570399	+	1	NA	promoter-TSS (NM_001113356)	promoter-TSS (NM_001113356)	-47	NM_001113356	667277	Mm.481484	NM_001113356	ENSMUSG00000098470	C1rb	Gm8551|mC1rB	complement component 1, r subcomponent B	protein-coding
mm_12504.1	chr2	71873279	71873326	+	1	NA	promoter-TSS (NM_172665)	promoter-TSS (NM_172665)	78	NM_172665	228026	Mm.34411	NM_172665	ENSMUSG00000006494	Pdk1	B830012B01|D530020C15Rik	pyruvate dehydrogenase kinase, isoenzyme 1	protein-coding
mm_81132.1	chr9	106499984	106499995	+	1	NA	promoter-TSS (NM_001146701)	promoter-TSS (NM_001146701)	22	NM_001146701	74267	Mm.116682	NM_028843	ENSMUSG00000066383	Iqcf1	1700055J15Rik	IQ motif containing F1	protein-coding
mm_53529.1	chr6	136553973	136553996	+	1	NA	intron (NM_019426, intron 1 of 14)	intron (NM_019426, intron 1 of 14)	35133	NM_019426	54343	Mm.173271	NM_019426	ENSMUSG00000030213	Atf7ip	2610204M12Rik|AM|Mcaf1	activating transcription factor 7 interacting protein	protein-coding
mm_40145.1	chr5	35278912	35278926	+	1	NA	5' UTR (NM_007418, exon 1 of 1)	5' UTR (NM_007418, exon 1 of 1)	353	NM_007418	11553	Mm.57205	NM_007418	ENSMUSG00000045318	Adra2c	Adra-2c|[a]2C|alpha2-C4|alpha2C	adrenergic receptor, alpha 2c	protein-coding
mm_147314.1	chr18	41982539	41982574	-	1	NA	Intergenic	Intergenic	16493	NM_001033426	332309	Mm.240520	NM_001033426	ENSMUSG00000073574	Grxcr2	Gm851	glutaredoxin, cysteine rich 2	protein-coding
mm_37052.1	chr4	116018088	116018100	-	1	NA	promoter-TSS (NM_010173)	promoter-TSS (NM_010173)	-192	NM_010173	14073	Mm.256025	NM_010173	ENSMUSG00000034171	Faah	AW412498	fatty acid amide hydrolase	protein-coding
mm_40028.1	chr5	33417855	33417858	+	1	NA	3' UTR (NM_001081101, exon 14 of 14)	3' UTR (NM_001081101, exon 14 of 14)	16234	NM_011320	672284		NM_011320	ENSMUSG00000029112	Nkx1-1	Nkx-1.1|Sax2	NK1 transcription factor related, locus 1 (Drosophila)	protein-coding
mm_53390.1	chr6	129545398	129545423	+	1	NA	Intergenic	Intergenic	-12126	NR_045270	100504641	Mm.398286	NR_045270	ENSMUSG00000097675	1700101I11Rik	-	RIKEN cDNA 1700101I11 gene	ncRNA
mm_86953.1	chr10	24915694	24915727	+	1	NA	exon (NM_007482, exon 8 of 8)	exon (NM_007482, exon 8 of 8)	5046	NR_105870	102465545		NR_105870	ENSMUSG00000099181	Mir6905	Gm27879|mmu-mir-6905	microRNA 6905	ncRNA
mm_124799.1	chr15	8444966	8444973	+	1	NA	promoter-TSS (NM_027707)	promoter-TSS (NM_027707)	-506	NM_201232	71175	Mm.240329	NM_027707	ENSMUSG00000022141	Nipbl	Idn3	Nipped-B homolog (Drosophila)	protein-coding
mm_42318.1	chr5	114897499	114897514	+	1	NA	5' UTR (NM_011854, exon 1 of 6)	5' UTR (NM_011854, exon 1 of 6)	572	NM_011854	23962	Mm.228363	NM_011854	ENSMUSG00000029561	Oasl2	M1204|Mmu-OASL|Oasl	2'-5' oligoadenylate synthetase-like 2	protein-coding
mm_139521.1	chr17	56613393	56613425	+	1	NA	promoter-TSS (NM_018730)	promoter-TSS (NM_018730)	14	NM_018730	54217	Mm.11376	NM_018730	ENSMUSG00000057863	Rpl36	-	ribosomal protein L36	protein-coding
mm_4491.1	chr1	173641209	173641221	+	1	NA	exon (NM_175026, exon 4 of 7)	exon (NM_175026, exon 4 of 7)	10356	NM_175026	236312	Mm.447	NM_175026	ENSMUSG00000043263	Ifi209	4930422C14|AI447904|Ifix|Pyhin-1|Pyhin1	interferon activated gene 209	protein-coding
mm_58287.1	chr6	145863621	145863642	-	1	NA	exon (NM_024469, exon 5 of 5)	exon (NM_024469, exon 5 of 5)	1789	NM_001271768	79362	Mm.154529	NM_024469	ENSMUSG00000030256	Bhlhe41	6430520M22Rik|Bhlhb2l|Bhlhb3|DEC2|Sharp1	basic helix-loop-helix family, member e41	protein-coding
mm_20566.1	chr2	131081424	131081436	-	1	NA	exon (NM_011426, exon 6 of 21)	exon (NM_011426, exon 6 of 21)	5335	NM_011426	20612	Mm.1374	NM_011426	ENSMUSG00000027322	Siglec1	Cd169|Siglec-1|Sn	sialic acid binding Ig-like lectin 1, sialoadhesin	protein-coding
mm_116895.1	chr13	55362823	55362833	-	1	NA	promoter-TSS (NM_025828)	promoter-TSS (NM_025828)	-45	NM_025828	66890	Mm.38868	NM_025828	ENSMUSG00000021484	Lman2	1110003H06Rik|1300009F09Rik|AA408240|AL023023|AU040819|GP36B|VIP36	lectin, mannose-binding 2	protein-coding
mm_150238.1	chr19	34067391	34067402	+	1	NA	promoter-TSS (NM_027340)	promoter-TSS (NM_027340)	38	NM_027340	70166	Mm.75602	NM_027340	ENSMUSG00000024770	Lipn	2210418G03Rik|Lipl4	lipase, family member N	protein-coding
mm_160878.1	chr11	69100494	69100494	+	1	NA	intron (NM_001159367, intron 1 of 22)	intron (NM_001159367, intron 1 of 22)	336	NM_001159367	18626	Mm.7373	NM_011065	ENSMUSG00000020893	Per1	Hftm|Per|m-rigui|mPer1	period circadian clock 1	protein-coding
mm_36318.1	chr4	70252169	70252179	-	1	NA	intron (NM_145990, intron 27 of 36)	intron (NM_145990, intron 27 of 36)	158261	NM_001313762	214444	Mm.370777	NM_145990	ENSMUSG00000039298	Cdk5rap2	2900018K03Rik|an|mKIAA1633	CDK5 regulatory subunit associated protein 2	protein-coding
mm_138312.1	chr17	34648240	34648271	+	1	NA	exon (NM_017406, exon 3 of 18)	exon (NM_017406, exon 3 of 18)	1109	NM_017406	12915	Mm.4068	NM_017406	ENSMUSG00000015461	Atf6b	AA617266|ATF6beta|Creb-rp|Crebl1	activating transcription factor 6 beta	protein-coding
mm_116866.1	chr13	55006920	55006928	-	1	NA	TTS (NM_153131)	TTS (NM_153131)	13895	NM_001206390	212032	Mm.267479	NM_001033245	ENSMUSG00000025877	Hk3	HK III|HK-III	hexokinase 3	protein-coding
mm_11907.1	chr2	50910184	50910188	+	1	NA	non-coding (NR_033595, exon 1 of 1)	non-coding (NR_033595, exon 1 of 1)	502	NR_033595	227885	Mm.301654	NR_033595	ENSMUSG00000083270	Gm13498	OTTMUSG00000012426	heat shock protein 90 alpha (cytosolic), class B member 1 pseudogene	pseudo
mm_41420.1	chr5	90887911	90887915	+	1	NA	Intergenic	Intergenic	-3332	NM_008176	14825	Mm.21013	NM_008176	ENSMUSG00000029380	Cxcl1	Fsp|Gro1|KC|Mgsa|N51|Scyb1|gro	chemokine (C-X-C motif) ligand 1	protein-coding
mm_170051.1	chr17	28418512	28418518	-	1	NA	intron (NM_010220, intron 5 of 10)	BGLII|LTR|ERVK	-53372	NM_021478	22157	Mm.42102	NM_021478	ENSMUSG00000037446	Tulp1	Tulp1l	tubby like protein 1	protein-coding
mm_57520.1	chr6	125533349	125533357	-	1	NA	Intergenic	Intergenic	-19595	NM_011708	22371	Mm.22339	NM_011708	ENSMUSG00000001930	Vwf	6820430P06Rik|AI551257|B130011O06Rik|C630030D09|F8VWF|VWD	Von Willebrand factor	protein-coding
mm_43460.1	chr5	136564202	136564209	+	1	NA	intron (NM_001291234, intron 1 of 22)	intron (NM_001291234, intron 1 of 22)	1776	NM_001291239	13047	Mm.320317	NM_009986	ENSMUSG00000029705	Cux1	CDP|Cutl1|Cux|Cux-1	cut-like homeobox 1	protein-coding
mm_4579.1	chr1	178187680	178187713	+	1	NA	5' UTR (NM_024282, exon 1 of 5)	5' UTR (NM_024282, exon 1 of 5)	279	NM_024282	78825	Mm.440132	NM_024282	ENSMUSG00000026502	Desi2	5830417C01Rik|DeSI-2|Fam152a|Pppde1	desumoylating isopeptidase 2	protein-coding
mm_8659.1	chr1	156474468	156474520	-	1	NA	promoter-TSS (NM_009230)	promoter-TSS (NM_009230)	-166	NM_009230	20652	Mm.28099	NM_009230	ENSMUSG00000026600	Soat1	8430426K15Rik|ACAT-1|AW550831|Acact|ald|hid	sterol O-acyltransferase 1	protein-coding
mm_82461.1	chr9	15628327	15628341	-	1	NA	promoter-TSS (NM_181816)	promoter-TSS (NM_181816)	-401	NM_181816	234964	Mm.32237	NM_181816	ENSMUSG00000039977	Ccdc67	4933401K09Rik|Deup1	coiled-coil domain containing 67	protein-coding
mm_154802.1	chrX	13291478	13291493	+	1	NA	exon (NM_010028, exon 17 of 17)	exon (NM_010028, exon 17 of 17)	10463	NM_010028	13205	Mm.289662	NM_010028	ENSMUSG00000000787	Ddx3x	D1Pas1-rs2|Ddx3|Fin14	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 3, X-linked	protein-coding
mm_98078.1	chr11	86544945	86544978	+	1	NA	promoter-TSS (NM_001199045)	promoter-TSS (NM_001199045)	-30	NM_001199045	56427	Mm.383207	NM_019756	ENSMUSG00000020513	Tubd1	4930550G19Rik|Tubd	tubulin, delta 1	protein-coding
mm_2308.1	chr1	91541045	91541049	+	1	NA	promoter-TSS (NM_023046)	promoter-TSS (NM_023046)	-33	NM_023046	65247	Mm.234152	NM_023046	ENSMUSG00000026311	Asb1	1700029O08Rik|1700054C17Rik|AI426616|AI851378|mKIAA1146	ankyrin repeat and SOCS box-containing 1	protein-coding
mm_115673.1	chr13	12650184	12650222	-	1	NA	non-coding (NR_003568, exon 1 of 7)	non-coding (NR_003568, exon 1 of 7)	192	NR_003568	664862	Mm.415635	NR_003568		Gpr137b-ps	2310041G17Rik|ENSMUSG00000075118	G protein-coupled receptor 137B, pseudogene	pseudo
mm_69620.1	chr7	137314194	137314201	-	1	NA	5' UTR (NM_001113414, exon 1 of 16)	5' UTR (NM_001113414, exon 1 of 16)	248	NM_001113415	13593	Mm.258708	NM_010096	ENSMUSG00000010476	Ebf3	3110018A08Rik|O/E-2|mKIAA4201	early B cell factor 3	protein-coding
mm_65980.1	chr7	30445496	30445501	-	1	NA	promoter-TSS (NM_007467)	promoter-TSS (NM_007467)	84	NM_007467	11803	Mm.2381	NM_007467	ENSMUSG00000006651	Aplp1	-	amyloid beta (A4) precursor-like protein 1	protein-coding
mm_13056.1	chr2	91113258	91113278	+	1	NA	exon (NM_011355, exon 3 of 5)	exon (NM_011355, exon 3 of 5)	-4876	NM_008653	17868	Mm.10728	NM_008653	ENSMUSG00000002100	Mybpc3	-	myosin binding protein C, cardiac	protein-coding
mm_18201.1	chr2	45559933	45559938	-	1	NA	Intergenic	Intergenic	-136670	NR_040497	69405	Mm.396184	NR_040497	ENSMUSG00000086202	1700019E08Rik	-	RIKEN cDNA 1700019E08 gene	ncRNA
mm_8743.1	chr1	160250091	160250119	-	1	NA	intron (NM_001038621, intron 3 of 8)	intron (NM_001038621, intron 3 of 8)	-37213	NM_009786	12301	Mm.10702	NM_009786	ENSMUSG00000014226	Cacybp	SIP	calcyclin binding protein	protein-coding
mm_141517.1	chr17	31681596	31681603	-	1	NA	3' UTR (NM_001278570, exon 3 of 3)	3' UTR (NM_001278570, exon 3 of 3)	3668	NM_001278570	12954	Mm.1228	NM_013501	ENSMUSG00000024041	Cryaa	Acry-1|Crya-1|Crya1|DAcry-1|lop18	crystallin, alpha A	protein-coding
mm_99189.1	chr11	100884634	100884644	+	1	NA	3' UTR (NM_011488, exon 20 of 20)	3' UTR (NM_011488, exon 20 of 20)	24155	NM_001164062	20850	Mm.277403	NM_011488	ENSMUSG00000004043	Stat5a	AA959963|STAT5	signal transducer and activator of transcription 5A	protein-coding
mm_106676.1	chr11	121745657	121745685	-	1	NA	Intergenic	Intergenic	43244	NM_144797	210029	Mm.153566	NM_144797	ENSMUSG00000039208	Metrnl	9430048M07Rik|BC019776	meteorin, glial cell differentiation regulator-like	protein-coding
mm_140764.1	chr17	17624565	17624573	-	1	NA	promoter-TSS (NM_172827)	promoter-TSS (NM_172827)	-80	NM_172827	240028	Mm.328807	NM_172827	ENSMUSG00000023845	Lnpep	2010309L07Rik|4732490P18Rik|CAP|IRAP|PLAP|gp160|vp165	leucyl/cystinyl aminopeptidase	protein-coding
mm_125011.1	chr15	25622567	25622581	+	1	NA	promoter-TSS (NM_019472)	promoter-TSS (NM_019472)	24	NM_019472	17909	Mm.60590	NM_019472	ENSMUSG00000022272	Myo10	AW048724|D15Ertd600e|mKIAA0799|myosin-X	myosin X	protein-coding
mm_57033.1	chr6	122325688	122325700	-	1	NA	exon (NM_001271579, exon 7 of 15)	exon (NM_001271579, exon 7 of 15)	13963	NM_001042623	13619	Mm.6822	NM_007905	ENSMUSG00000040669	Phc1	AW557034|Edr|Edr1|Mph1|Rae-28|rae28	polyhomeotic-like 1 (Drosophila)	protein-coding
mm_138698.1	chr17	35980857	35980872	+	1	NA	intron (NM_008136, intron 2 of 11)	intron (NM_008136, intron 2 of 11)	909	NM_008136	14670	Mm.335754	NM_008136	ENSMUSG00000024429	Gnl1	Gna-rs1|Gnal1	guanine nucleotide binding protein-like 1	protein-coding
mm_64391.1	chr7	142489040	142489068	+	1	NA	intron (NM_001271508, intron 5 of 10)	intron (NM_001271508, intron 5 of 10)	-9782	NM_001347549	21957	Mm.389992	NM_011620	ENSMUSG00000061723	Tnnt3	fTnT	troponin T3, skeletal, fast	protein-coding
mm_38518.1	chr4	141416020	141416025	-	1	NA	promoter-TSS (NM_019701)	promoter-TSS (NM_019701)	-34	NM_019701	56365	Mm.24882	NM_019701	ENSMUSG00000006216	Clcnkb	CLCKB|Clc-Ka|Clck2|Clcnk1l	chloride channel, voltage-sensitive Kb	protein-coding
mm_55565.1	chr6	71360850	71360862	-	1	NA	Intergenic	Intergenic	-12571	NM_009857	12525	Mm.1858	NM_009857	ENSMUSG00000053977	Cd8a	BB154331|Ly-2|Ly-35|Ly-B|Lyt-2	CD8 antigen, alpha chain	protein-coding
mm_48212.1	chr5	137610426	137610452	-	1	NA	exon (NM_008788, exon 2 of 9)	exon (NM_008788, exon 2 of 9)	965	NM_008788	18542	Mm.262345	NM_008788	ENSMUSG00000029718	Pcolce	Astt-2|Astt2|P14|PCPE-1	procollagen C-endopeptidase enhancer protein	protein-coding
mm_150329.1	chr19	34574781	34574828	+	1	NA	3' UTR (NM_008332, exon 3 of 3)	3' UTR (NM_008332, exon 3 of 3)	-8725	NM_010501	15959	Mm.426079	NM_010501	ENSMUSG00000074896	Ifit3	Ifi49|P49	interferon-induced protein with tetratricopeptide repeats 3	protein-coding
mm_102435.1	chr11	59506420	59506442	-	1	NA	non-coding (NR_135273, exon 1 of 4)	non-coding (NR_135273, exon 1 of 4)	209	NM_001291014	268417	Mm.239793	NM_172941	ENSMUSG00000020472	Zkscan17	Nizp1|Zfp496|Znf496	zinc finger with KRAB and SCAN domains 17	protein-coding
mm_161998.1	chr19	39812745	39812745	-	1	NA	promoter-TSS (NM_010004)	promoter-TSS (NM_010004)	69	NM_010004	13099	Mm.353875	NM_010004	ENSMUSG00000025004	Cyp2c40	AI265721|AI662255	cytochrome P450, family 2, subfamily c, polypeptide 40	protein-coding
mm_1313.1	chr1	65048559	65048560	+	1	NA	TTS (NM_007777)	TTS (NM_007777)	2604	NM_007777	12968	Mm.258170	NM_007777	ENSMUSG00000070870	Cryge	Cryg-2|Cryg-6|DGcry-2|Elo	crystallin, gamma E	protein-coding
mm_147707.1	chr18	60812223	60812231	-	1	NA	TTS (NR_039567)	TTS (NR_039567)	151	NR_039567	100628611		NR_039567	ENSMUSG00000093327	Mir5107	mir-5107|mmu-mir-5107|mu-mir-5107	microRNA 5107	ncRNA
mm_162578.1	chr1	177729839	177729839	+	1	NA	promoter-TSS (NM_027077)	promoter-TSS (NM_027077)	25	NM_027077	69428	Mm.84467	NM_027077	ENSMUSG00000015962	1700016C15Rik	-	RIKEN cDNA 1700016C15 gene	protein-coding
mm_73771.1	chr8	116501701	116501705	+	1	NA	Intergenic	Intergenic	-3312	NM_029297	75465	Mm.23114	NM_029297	ENSMUSG00000034467	Dynlrb2	1700009A04Rik|DNLC2B|Dncl2b	dynein light chain roadblock-type 2	protein-coding
mm_26427.1	chr3	142618335	142618346	+	1	NA	3' UTR (NM_010259, exon 11 of 11)	3' UTR (NM_010259, exon 11 of 11)	-2323	NM_010260	14469	Mm.24038	NM_010260	ENSMUSG00000028270	Gbp2	-	guanylate binding protein 2	protein-coding
mm_24453.1	chr3	90613177	90613192	+	1	NA	5' UTR (NM_011313, exon 1 of 3)	5' UTR (NM_011313, exon 1 of 3)	290	NM_011313	20200	Mm.100144	NM_011313	ENSMUSG00000001025	S100a6	2A9|5B10|CALCYCLIN|Cacy|PRA	S100 calcium binding protein A6 (calcyclin)	protein-coding
mm_172753.1	chr8	85111940	85111955	-	1	NA	intron (NM_001037745, intron 4 of 4)	LSU-rRNA_Hsa|rRNA|rRNA	11148	NM_001037745	244556	Mm.334682	NM_001037745	ENSMUSG00000074194	Zfp791	EG244556	zinc finger protein 791	protein-coding
mm_72916.1	chr8	91073780	91073790	+	1	NA	intron (NM_011250, intron 1 of 21)	intron (NM_011250, intron 1 of 21)	3728	NM_001282000	19651	Mm.235580	NM_011250	ENSMUSG00000031666	Rbl2	PRB2|RBR-2|Rb2|p130	retinoblastoma-like 2	protein-coding
mm_141639.1	chr17	33139618	33139670	-	1	NA	promoter-TSS (NM_177719)	promoter-TSS (NM_177719)	39	NM_177719	240069	Mm.157765	NM_177719	ENSMUSG00000048602	Morc2b	4932411A10Rik|Tce6	microrchidia 2B	protein-coding
mm_96830.1	chr11	70000579	70000624	+	1	NA	promoter-TSS (NM_007888)	promoter-TSS (NM_007888)	-25	NM_007888	13543	Mm.5114	NM_007888	ENSMUSG00000020888	Dvl2	-	dishevelled segment polarity protein 2	protein-coding
mm_26314.1	chr3	142519501	142519516	+	1	NA	intron (NM_153564, intron 10 of 10)	RMER2|LTR|ERV1	-10828	NM_001083312	229900	Mm.45740	NM_145545	ENSMUSG00000040253	Gbp7	9830147J24Rik	guanylate binding protein 7	protein-coding
mm_76905.1	chr8	105827681	105827691	-	1	NA	promoter-TSS (NM_024445)	promoter-TSS (NM_024445)	-58	NM_024445	72236	Mm.386810	NM_024445	ENSMUSG00000031893	Tsnaxip1	1700016K08Rik|TXI1	translin-associated factor X (Tsnax) interacting protein 1	protein-coding
mm_65066.1	chr7	18910378	18910388	-	1	NA	promoter-TSS (NM_001033314)	promoter-TSS (NM_001033314)	21	NM_001033314	232933	Mm.333624	NM_001033314	ENSMUSG00000074358	Ccdc61	C530028I08Rik|Gm159	coiled-coil domain containing 61	protein-coding
mm_4923.1	chr1	190928830	190928888	+	1	NA	intron (NR_037579, intron 1 of 7)	CpG	354	NR_037579	52477	Mm.289914	NM_021421	ENSMUSG00000026634	Angel2	2610307I21Rik|5730410O10Rik|AI845692|D1Ertd396e|D1Ertd654e	angel homolog 2	protein-coding
mm_15450.1	chr2	157403074	157403102	+	1	NA	Intergenic	MLT1D|LTR|ERVL-MaLR	-21205	NM_009271	20779	Mm.22845	NM_009271	ENSMUSG00000027646	Src	AW259666|pp60c-src	Rous sarcoma oncogene	protein-coding
mm_122417.1	chr14	41134398	41134412	-	1	NA	exon (NM_023134, exon 6 of 6)	exon (NM_023134, exon 6 of 6)	2617	NM_023134	20387	Mm.46062	NM_023134	ENSMUSG00000021789	Sftpa1	SP-A|Sftp-1|Sftp1	surfactant associated protein A1	protein-coding
mm_59996.1	chr7	30563839	30563849	+	1	NA	promoter-TSS (NM_025498)	promoter-TSS (NM_025498)	504	NM_170760	233073	Mm.34790	NM_170760	ENSMUSG00000078765	U2af1l4	AA407033|AF419339|AI451269|AW553050|U2af26	U2 small nuclear RNA auxiliary factor 1-like 4	protein-coding
mm_54081.1	chr6	15728177	15728187	-	1	NA	intron (NM_175088, intron 2 of 4)	intron (NM_175088, intron 2 of 4)	7521	NM_175088	16543	Mm.1314	NM_175088	ENSMUSG00000041390	Mdfic	Kdt1|Mdfid	MyoD family inhibitor domain containing	protein-coding
mm_140694.1	chr17	13761417	13761425	-	1	NA	promoter-TSS (NM_022311)	promoter-TSS (NM_022311)	-27	NM_022311	21646	Mm.486358	NM_022311	ENSMUSG00000038347	Tcte2	AI429268|Tcte-2	t-complex-associated testis expressed 2	protein-coding
mm_104361.1	chr11	94309685	94309697	-	1	NA	exon (NM_026313, exon 2 of 11)	exon (NM_026313, exon 2 of 11)	12220	NM_026313	67684	Mm.30927	NM_026313	ENSMUSG00000020863	Luc7l3	3300001P08Rik|Luc7a	LUC7-like 3 (S. cerevisiae)	protein-coding
mm_56807.1	chr6	116657554	116657567	-	1	NA	intron (NM_178045, intron 3 of 10)	intron (NM_178045, intron 3 of 10)	6876	NM_001166580	213393	Mm.38231	NM_145980	ENSMUSG00000048489	8430408G22Rik	Depp|Fseg	RIKEN cDNA 8430408G22 gene	protein-coding
mm_168823.1	chr12	22466956	22466959	-	1	NA	Intergenic	CpG	-310311	NR_136920	100043416		NM_001004167	ENSMUSG00000093846	Gm4425	EG432637|Gm5433	KRAB-domain protein pseudogene	pseudo
mm_65746.1	chr7	28544229	28544240	-	1	NA	exon (NM_001081115, exon 6 of 6)	exon (NM_001081115, exon 6 of 6)	3020	NM_001081115	233038	Mm.224815	NM_001081115	ENSMUSG00000047586	Nccrp1	1190020J12Rik|Gm163|NCCRP-1	non-specific cytotoxic cell receptor protein 1 homolog (zebrafish)	protein-coding
mm_150159.1	chr19	32263114	32263115	+	1	NA	intron (NM_001168525, intron 2 of 9)	RLTR21|LTR|ERVK	-52101	NM_001168526	208449	Mm.329810	NM_144792	ENSMUSG00000040451	Sgms1	9530058O11Rik|AI841905|C80702|Mob|Sms1|Sor1|Tmem23	sphingomyelin synthase 1	protein-coding
mm_156604.1	chrX	153140013	153140045	+	1	NA	promoter-TSS (NM_001004154)	promoter-TSS (NM_001004154)	71	NM_001004154	245670	Mm.190922	NM_001004154	ENSMUSG00000041658	Rragb	-	Ras-related GTP binding B	protein-coding
mm_90433.1	chr10	127621299	127621323	+	1	NA	promoter-TSS (NM_008512)	promoter-TSS (NM_008512)	-163	NM_008512	16971	Mm.271854	NM_008512	ENSMUSG00000040249	Lrp1	A2mr|AI316852|CD91|Lrp|b2b1554Clo	low density lipoprotein receptor-related protein 1	protein-coding
mm_100162.1	chr11	116434088	116434106	+	1	NA	promoter-TSS (NR_003376)	promoter-TSS (NR_003376)	3	NM_176902	319370	Mm.258466	NM_176902	ENSMUSG00000050628	Ubald2	1110014K08Rik|D030012E24Rik|Fam100b	UBA-like domain containing 2	protein-coding
mm_154641.1	chrX	7764399	7764415	+	1	NA	intron (NM_001271491, intron 1 of 8)	ID2|SINE|ID	366	NM_001271491	209446	Mm.249142	NM_172472	ENSMUSG00000000134	Tfe3	F830016E06Rik|Tcfe3|Tfe-3|bHLHe33	transcription factor E3	protein-coding
mm_51169.1	chr6	70726590	70726596	+	1	NA	Intergenic	Intergenic	65582	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_33149.1	chr4	125176552	125176561	+	1	NA	Intergenic	Intergenic	-48675	NM_153159	230738	Mm.402	NM_153159	ENSMUSG00000042677	Zc3h12a	BC036563|MCPIP|MCPIP-1|Mcpip1|Reg1	zinc finger CCCH type containing 12A	protein-coding
mm_136257.1	chr16	91011006	91011023	-	1	NA	promoter-TSS (NM_001045515)	promoter-TSS (NM_001045515)	81	NM_001045515	104015	Mm.187079	NM_001045515	ENSMUSG00000022973	Synj1	A930006D20Rik|AA675315|mKIAA0910	synaptojanin 1	protein-coding
mm_156429.1	chrX	140979884	140979931	+	1	NA	Intergenic	Intergenic	-23196	NM_001164177	53380	Mm.17640	NM_016883	ENSMUSG00000031429	Psmd10	AW554874	proteasome (prosome, macropain) 26S subunit, non-ATPase, 10	protein-coding
mm_52342.1	chr6	110761045	110761047	+	1	NA	intron (NM_001346640, intron 1 of 10)	ORR1F|LTR|ERVL-MaLR	115448	NM_177328	108073	Mm.240881	NM_177328	ENSMUSG00000056755	Grm7	6330570A01Rik|BB176677|C030018L03|E130018M02Rik|Gpr1g|Gprc1g|SMN2|Tg(SMN2)89Ahmb|mGluR7	glutamate receptor, metabotropic 7	protein-coding
mm_48691.1	chr5	146794772	146794782	-	1	NA	5' UTR (NM_011669, exon 1 of 9)	5' UTR (NM_011669, exon 1 of 9)	179	NM_011669	22217	Mm.167971	NM_011669	ENSMUSG00000029640	Usp12	Ubh1	ubiquitin specific peptidase 12	protein-coding
mm_140177.1	chr17	80896813	80896841	+	1	NA	promoter-TSS (NR_131128)	promoter-TSS (NR_131128)	34	NR_131127	320784	Mm.474182	NR_131127		C230072F16Rik	-	RIKEN cDNA C230072F16 gene	ncRNA
mm_168791.1	chr12	19288584	19288588	+	1	NA	Intergenic	CpG	774076	NM_001201330	236366	Mm.352227	NM_001033157	ENSMUSG00000073197	5730507C01Rik	-	RIKEN cDNA 5730507C01 gene	protein-coding
mm_159918.1	chr6	50596404	50596404	-	1	NA	intron (NM_027564, intron 1 of 9)	CpG	186	NM_027564	70821	Mm.157323	NM_027564	ENSMUSG00000029828	4921507P07Rik	TISP74	RIKEN cDNA 4921507P07 gene	protein-coding
mm_140818.1	chr17	23193176	23193208	-	1	NA	promoter-TSS (NM_009555)	promoter-TSS (NM_009555)	36	NM_009555	22700	Mm.437934	NM_009555	ENSMUSG00000002617	Zfp40	CTfin12|NTfin12|Zfp-40	zinc finger protein 40	protein-coding
mm_142943.1	chr17	56074543	56074571	-	1	NA	intron (NM_024432, intron 1 of 10)	intron (NM_024432, intron 1 of 10)	432	NM_024432	66530	Mm.28000	NM_024432	ENSMUSG00000019578	Ubxn6	1200008L11Rik|2210415J11Rik|AU040909|Ubxd1|Ubxdc2	UBX domain protein 6	protein-coding
mm_146249.1	chr18	77778580	77778611	+	1	NA	exon (NM_007505, exon 4 of 12)	exon (NM_007505, exon 4 of 12)	4827	NM_007505	11946	Mm.276137	NM_007505	ENSMUSG00000025428	Atp5a1	AI035633|AL022851|AL023067|Atpm|D18Ertd206e|Mom2	ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1	protein-coding
mm_170406.1	chr1	86526941	86526947	+	1	NA	exon (NM_008972, exon 1 of 5)	exon (NM_008972, exon 1 of 5)	208	NM_008972	19231	Mm.19187	NM_008972	ENSMUSG00000026238	Ptma	Thym	prothymosin alpha	protein-coding
mm_162338.1	chr1	46427150	46427150	+	1	NA	intron (NM_001310335, intron 1 of 64)	intron (NM_001310335, intron 1 of 64)	1632	NM_001310335	100101919	Mm.383402	NM_001310335	ENSMUSG00000101337	Dnah7c	Dnahc7c	dynein, axonemal, heavy chain 7C	protein-coding
mm_145014.1	chr18	38632445	38632462	+	1	NA	Intergenic	Intergenic	-31185	NM_011898	24066	Mm.42038	NM_011898	ENSMUSG00000024427	Spry4	A030006O18Rik|sprouty4	sprouty homolog 4 (Drosophila)	protein-coding
mm_119789.1	chr14	54192712	54192722	+	1	NA	Intergenic	L3b|LINE|CR1	61212	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_91043.1	chr10	18546017	18546030	-	1	NA	promoter-TSS (NM_019487)	promoter-TSS (NM_019487)	53	NM_019487	56016	Mm.35551	NM_019487	ENSMUSG00000019853	Hebp2	SOUL	heme binding protein 2	protein-coding
mm_132450.1	chr16	36034938	36034959	+	1	NA	3' UTR (NM_008465, exon 14 of 14)	3' UTR (NM_008465, exon 14 of 14)	-6242	NM_027113	69544	Mm.37802	NM_027113	ENSMUSG00000034379	Wdr5b	2310009C03Rik|AI606931	WD repeat domain 5B	protein-coding
mm_167917.1	chrX	100741091	100741094	+	1	NA	Intergenic	Intergenic	10906	NM_001305941	71584	Mm.283495	NM_023608	ENSMUSG00000019359	Gdpd2	9130017L10Rik|Gde3|Obdpf	glycerophosphodiester phosphodiesterase domain containing 2	protein-coding
mm_141575.1	chr17	32321119	32321204	-	1	NA	promoter-TSS (NM_019774)	promoter-TSS (NM_019774)	77	NM_019774	56399	Mm.328945	NM_019774	ENSMUSG00000024045	Akap8	1200016A02Rik|AA673585|AKAP-8|AKAP95|AU015639	A kinase (PRKA) anchor protein 8	protein-coding
mm_73772.1	chr8	116504967	116504967	+	1	NA	promoter-TSS (NM_029297)	promoter-TSS (NM_029297)	-48	NM_029297	75465	Mm.23114	NM_029297	ENSMUSG00000034467	Dynlrb2	1700009A04Rik|DNLC2B|Dncl2b	dynein light chain roadblock-type 2	protein-coding
mm_48310.1	chr5	138619752	138619758	-	1	NA	promoter-TSS (NM_001163797)	promoter-TSS (NM_001163797)	-12	NM_001044747	24135	Mm.27575	NM_013844	ENSMUSG00000058291	Zfp68	KRAB3|KRAZ2|Zfp70|mszf22|mszf49	zinc finger protein 68	protein-coding
mm_123961.1	chr14	74933522	74933523	-	1	NA	intron (NM_001252132, intron 1 of 18)	intron (NM_001252132, intron 1 of 18)	14355	NM_001252132	380916	Mm.288868	NM_001033439	ENSMUSG00000068015	Lrch1	4832412D13Rik|AI552548|AW215503|Chdc1|mKIAA1016	leucine-rich repeats and calponin homology (CH) domain containing 1	protein-coding
mm_86402.1	chr9	123986631	123986639	-	1	NA	Intergenic	Intergenic	-8227	NM_007718	12770	Mm.423532	NM_007718	ENSMUSG00000064039	Ccr1l1	Cmkbr1l1	chemokine (C-C motif) receptor 1-like 1	protein-coding
mm_83423.1	chr9	44974240	44974250	-	1	NA	exon (NM_009850, exon 3 of 7)	exon (NM_009850, exon 3 of 7)	6186	NM_009850	12502	Mm.335106	NM_009850	ENSMUSG00000002033	Cd3g	Ctg-3|Ctg3|T3g	CD3 antigen, gamma polypeptide	protein-coding
mm_58000.1	chr6	136173493	136173523	-	1	NA	promoter-TSS (NM_008171)	promoter-TSS (NM_008171)	3	NM_008171	14812	Mm.436649	NM_008171	ENSMUSG00000030209	Grin2b	AW490526|GluN2B|NR2B|Nmdar2b	glutamate receptor, ionotropic, NMDA2B (epsilon 2)	protein-coding
mm_65084.1	chr7	19257612	19257626	-	1	NA	non-coding (NR_104069, exon 11 of 11)	non-coding (NR_104069, exon 11 of 11)	14235	NM_001282021	22323	Mm.9684	NM_009499	ENSMUSG00000030403	Vasp	-	vasodilator-stimulated phosphoprotein	protein-coding
mm_42688.1	chr5	119835116	119835118	+	1	NA	5' UTR (NM_011537, exon 1 of 9)	5' UTR (NM_011537, exon 1 of 9)	454	NM_011537	21388	Mm.103636	NM_011537	ENSMUSG00000018263	Tbx5	-	T-box 5	protein-coding
mm_94809.1	chr11	23020347	23020355	+	1	NA	exon (NM_028672, exon 3 of 4)	exon (NM_028672, exon 3 of 4)	6964	NM_028672	73873	Mm.252406	NM_028672	ENSMUSG00000049811	Fam161a	4930430E16Rik	family with sequence similarity 161, member A	protein-coding
mm_67227.1	chr7	74554727	74554791	-	1	NA	promoter-TSS (NM_023908)	promoter-TSS (NM_023908)	21	NM_023908	108116	Mm.425467	NM_023908	ENSMUSG00000025790	Slco3a1	5830414C08Rik|Anr1|MJAM|OATP-D|R75096|Slc21a11	solute carrier organic anion transporter family, member 3a1	protein-coding
mm_47676.1	chr5	128600675	128600706	-	1	NA	promoter-TSS (NM_175284)	promoter-TSS (NM_175284)	-3	NR_015517	319616	Mm.387738	NR_015517	ENSMUSG00000072591	5930412G12Rik	-	RIKEN cDNA 5930412G12 gene	ncRNA
mm_91157.1	chr10	20548321	20548333	-	1	NA	promoter-TSS (NM_001347366)	promoter-TSS (NM_001347366)	1	NM_001347366	29863	Mm.425617	NM_013875	ENSMUSG00000019990	Pde7b	-	phosphodiesterase 7B	protein-coding
mm_107818.1	chr12	66952225	66952236	+	1	NA	intron (NM_001193266, intron 1 of 16)	intron (NM_001193266, intron 1 of 16)	270319	NM_001193266	320772	Mm.227680	NM_207010	ENSMUSG00000034912	Mdga2	6720489L24Rik|9330209L04Rik|Adp|Mamdc1	MAM domain containing glycosylphosphatidylinositol anchor 2	protein-coding
mm_15518.1	chr2	158320296	158320312	+	1	NA	exon (NM_008489, exon 8 of 15)	exon (NM_008489, exon 8 of 15)	13811	NM_008489	16803	Mm.218846	NM_008489	ENSMUSG00000016024	Lbp	Bpifd2|Ly88	lipopolysaccharide binding protein	protein-coding
mm_145233.1	chr18	50134821	50134857	+	1	NA	intron (NM_008292, intron 2 of 23)	intron (NM_008292, intron 2 of 23)	6638	NM_008292	15488	Mm.277857	NM_008292	ENSMUSG00000024507	Hsd17b4	17-beta-HSD|17[b]-HSD|DBP|MFE-2|MFP2|MPF-2|Mfp-2|perMFE-2	hydroxysteroid (17-beta) dehydrogenase 4	protein-coding
mm_79649.1	chr9	59585786	59585795	+	1	NA	intron (NM_175235, intron 2 of 11)	intron (NM_175235, intron 2 of 11)	-3524	NM_001311092	76183	Mm.265415	NM_175235	ENSMUSG00000032297	Celf6	6330569O16Rik|Brunol6	CUGBP, Elav-like family member 6	protein-coding
mm_144417.1	chr18	20962807	20962818	+	1	NA	intron (NM_026301, intron 1 of 5)	intron (NM_026301, intron 1 of 5)	18187	NM_026301	67664	Mm.45980	NM_026301	ENSMUSG00000033107	Rnf125	4930553F04Rik	ring finger protein 125	protein-coding
mm_5992.1	chr1	58586241	58586318	-	1	NA	promoter-TSS (NM_172513)	promoter-TSS (NM_172513)	54	NM_001310598	213056	Mm.26272	NM_172513	ENSMUSG00000038174	Fam126b	C130065N10Rik|D1Ertd53e|D630010C10	family with sequence similarity 126, member B	protein-coding
mm_157008.1	chrX	7595443	7595450	-	1	NA	TTS (NM_054039)	TTS (NM_054039)	9974	NM_138603	54638	Mm.288192	NM_138603	ENSMUSG00000031143	Ccdc22	AI481216|DXImx40e|Ppp1r3f|Sfc22	coiled-coil domain containing 22	protein-coding
mm_123123.1	chr14	56159591	56159597	-	1	NA	promoter-TSS (NM_010375)	promoter-TSS (NM_010375)	-15	NM_010375	14944	Mm.14868	NM_010375	ENSMUSG00000040284	Gzmg	Ctla-7|Ctla7	granzyme G	protein-coding
mm_86888.1	chr10	22283059	22283070	+	1	NA	intron (NM_001177775, intron 1 of 5)	intron (NM_001177775, intron 1 of 5)	9590	NM_001177775	667281	Mm.484254	NM_001177775	ENSMUSG00000075297	H60b	EG667281	histocompatibility 60b	protein-coding
mm_46011.1	chr5	90789797	90789829	-	1	NA	Intergenic	Intergenic	3712	NM_203320	330122	Mm.244289	NM_203320	ENSMUSG00000029379	Cxcl3	Dcip1|Gm1960	chemokine (C-X-C motif) ligand 3	protein-coding
mm_126681.1	chr15	84720094	84720104	+	1	NA	promoter-TSS (NM_001164628)	promoter-TSS (NM_001164628)	47	NM_001205334	73167	Mm.128411	NM_028455	ENSMUSG00000078954	Arhgap8	3110043J09Rik	Rho GTPase activating protein 8	protein-coding
mm_107684.1	chr12	54862970	54862997	+	1	NA	promoter-TSS (NM_007688)	promoter-TSS (NM_007688)	-106	NM_007688	12632	Mm.276826	NM_007688	ENSMUSG00000062929	Cfl2	-	cofilin 2, muscle	protein-coding
mm_55643.1	chr6	72347681	72347753	-	1	NA	intron (NM_026696, intron 2 of 3)	CpG-12156	400	NM_026696	68364	Mm.52711	NM_026696	ENSMUSG00000058706	0610030E20Rik	1500031N04Rik|2810411C16Rik|AI461894	RIKEN cDNA 0610030E20 gene	protein-coding
mm_105045.1	chr11	100613392	100613400	-	1	NA	intron (NM_019795, intron 1 of 13)	intron (NM_019795, intron 1 of 13)	6772	NM_019795	56354	Mm.402409	NM_019795	ENSMUSG00000014195	Dnajc7	2010003F24Rik|2010004G07Rik|CCRP|Ttc2|mDj11|mTpr2	DnaJ heat shock protein family (Hsp40) member C7	protein-coding
mm_21231.1	chr2	156016748	156016765	-	1	NA	exon (NM_025516, exon 9 of 13)	exon (NM_025516, exon 9 of 13)	8631	NM_025516	66366	Mm.141276	NM_025516	ENSMUSG00000005881	Ergic3	2310015B14Rik|AV318804|CGI-54|D2Ucla1|NY-BR-84|Sdbcag84	ERGIC and golgi 3	protein-coding
mm_32627.1	chr4	114909272	114909322	+	1	NA	promoter-TSS (NM_008593)	promoter-TSS (NM_008593)	8	NR_030721	100040736	Mm.231287	NR_030721	ENSMUSG00000085399	Foxd2os	9130206I24Rik	forkhead box D2, opposite strand	ncRNA
mm_170648.1	chr2	100547096	100547098	-	1	NA	Intergenic	L1Md_T|LINE|L1	-1077651	NM_009020	19374	Mm.4988	NM_009020	ENSMUSG00000032864	Rag2	Rag-2	recombination activating gene 2	protein-coding
mm_154410.1	chrM	14744	14756	+	1	NA	NA	Intergenic	NA	NA								
mm_34895.1	chr4	155624968	155624977	+	1	NA	promoter-TSS (NR_040441)	promoter-TSS (NR_040441)	103	NM_007661	12537	Mm.267410	NM_007661	ENSMUSG00000029062	Cdk11b	AA989746|CDK11-p110|CDK11-p46|CDK11-p58|Cdc11b|Cdc2l1|Cdc2l2|Cdk11|p58	cyclin-dependent kinase 11B	protein-coding
mm_147590.1	chr18	56562502	56562535	-	1	NA	promoter-TSS (NM_138600)	promoter-TSS (NM_138600)	-51	NM_001162989	56698	Mm.214569	NM_019996	ENSMUSG00000008301	Phax	2810055C14Rik|4933427L19Rik|AU018701|AU018854|D18Ertd65e|Rnuxa|p55	phosphorylated adaptor for RNA export	protein-coding
mm_171736.1	chr4	94912617	94912617	+	1	NA	intron (NM_027089, intron 7 of 7)	intron (NM_027089, intron 7 of 7)	16226	NM_027089	67753	Mm.25097	NM_027089	ENSMUSG00000028575	Eqtn	1700028B15Rik|4930579C15Rik|Afaf|C81058|Eqtl|Eqts	equatorin, sperm acrosome associated	protein-coding
mm_83088.1	chr9	40320868	40320888	-	1	NA	intron (NM_172768, intron 4 of 19)	intron (NM_172768, intron 4 of 19)	-12594	NR_040728	73558	Mm.398307	NR_040728		1700110K17Rik	-	RIKEN cDNA 1700110K17 gene	ncRNA
mm_60043.1	chr7	31059424	31059439	+	1	NA	promoter-TSS (NM_144556)	promoter-TSS (NM_144556)	-504	NM_144556	243914	Mm.389870	NM_144556	ENSMUSG00000036560	Lgi4	Lgil3|clp	leucine-rich repeat LGI family, member 4	protein-coding
mm_158171.1	chrX	103706323	103706333	-	1	NA	exon (NM_009197, exon 4 of 6)	exon (NM_009197, exon 4 of 6)	75742	NM_029158	75064	Mm.159414	NM_029158	ENSMUSG00000031330	Zcchc13	4930513O09Rik|Cnbp2	zinc finger, CCHC domain containing 13	protein-coding
mm_26123.1	chr3	137865901	137865938	+	1	NA	intron (NM_001316995, intron 3 of 4)	intron (NM_001316995, intron 3 of 4)	1432	NM_016750	51788	Mm.117541	NM_016750	ENSMUSG00000037894	H2afz	H2A.Z|H2a.z-1	H2A histone family, member Z	protein-coding
mm_124655.1	chr15	5237514	5237524	+	1	NA	intron (NM_008965, intron 2 of 2)	intron (NM_008965, intron 2 of 2)	6668	NM_001136079	19219	Mm.18509	NM_008965	ENSMUSG00000039942	Ptger4	EP4|Ptgerep4	prostaglandin E receptor 4 (subtype EP4)	protein-coding
mm_134444.1	chr16	18249232	18249253	-	1	NA	promoter-TSS (NM_011239)	promoter-TSS (NM_011239)	359	NM_001081000	15547	Mm.271798	NM_008307	ENSMUSG00000022721	Trmt2a	Htf9c	TRM2 tRNA methyltransferase 2A	protein-coding
mm_16826.1	chr2	11475828	11475829	-	1	NA	intron (NM_001177757, intron 15 of 16)	intron (NM_001177757, intron 15 of 16)	26262	NM_001177754	170768	Mm.19669	NM_133232	ENSMUSG00000026773	Pfkfb3	E330010H22Rik|iPFK-2|uPFK-2	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	protein-coding
mm_69753.1	chr7	140956274	140956284	-	1	NA	promoter-TSS (NM_030694)	promoter-TSS (NM_030694)	-318	NM_030694	80876	Mm.379266	NM_030694	ENSMUSG00000060591	Ifitm2	DSPA2c|Ifitm3l|fragilis3|mil-3	interferon induced transmembrane protein 2	protein-coding
mm_80822.1	chr9	96765573	96765580	+	1	NA	promoter-TSS (NR_102294)	promoter-TSS (NR_102294)	14	NR_102296	319707	Mm.392191	NR_102293	ENSMUSG00000101581	C430002N11Rik	-	RIKEN cDNA C430002N11 gene	ncRNA
mm_80719.1	chr9	92275875	92275892	+	1	NA	5' UTR (NM_001195084, exon 1 of 8)	5' UTR (NM_001195084, exon 1 of 8)	281	NM_001195084	18828	Mm.10306	NM_008880	ENSMUSG00000032372	Plscr2	-	phospholipid scramblase 2	protein-coding
mm_116526.1	chr13	45806006	45806011	-	1	NA	intron (NM_001199304, intron 3 of 6)	intron (NM_001199304, intron 3 of 6)	158983	NM_001199304	20238	Mm.342683	NM_009124	ENSMUSG00000046876	Atxn1	2900016G23Rik|Atx1|C85907|ENSMUSG00000074917|Gm10786|Sca1	ataxin 1	protein-coding
mm_65017.1	chr7	17098514	17098521	-	1	NA	3' UTR (NM_007676, exon 5 of 5)	3' UTR (NM_007676, exon 5 of 5)	24477	NM_007676	26436	Mm.143686	NM_007676	ENSMUSG00000066760	Psg16	Cea11|PSG|bCEA	pregnancy specific glycoprotein 16	protein-coding
mm_53797.1	chr6	146757032	146757046	+	1	NA	intron (NM_001346666, intron 1 of 11)	intron (NM_001346666, intron 1 of 11)	32109	NM_172734	232533	Mm.322121	NM_172734	ENSMUSG00000001630	Stk38l	4930473A22Rik|Ndr2|Ndr54	serine/threonine kinase 38 like	protein-coding
mm_33547.1	chr4	130934733	130934739	+	1	NA	3' UTR (NM_010686, exon 8 of 8)	3' UTR (NM_010686, exon 8 of 8)	-9649	NM_010769	17180	Mm.271796	NM_010769	ENSMUSG00000040533	Matn1	CMP|Crtm|Mat1|matrilin-1	matrilin 1, cartilage matrix protein	protein-coding
mm_101074.1	chr11	11657227	11657262	-	1	NA	Intergenic	Intergenic	-28681	NM_009578	22778	Mm.103545	NM_009578	ENSMUSG00000018654	Ikzf1	5832432G11Rik|Ikaros|LyF-1|Zfpn1a1|Znfn1a1|hlk-1|mKIAA4227	IKAROS family zinc finger 1	protein-coding
mm_53399.1	chr6	129591756	129591767	+	1	NA	promoter-TSS (NM_010654)	promoter-TSS (NM_010654)	-50	NM_010654	16643	Mm.391515	NM_010654	ENSMUSG00000030165	Klrd1	CD94	killer cell lectin-like receptor, subfamily D, member 1	protein-coding
mm_120050.1	chr14	56647688	56647707	+	1	NA	exon (NM_001145978, exon 32 of 35)	exon (NM_001145978, exon 32 of 35)	-20551	NM_023773	75339	Mm.152466	NM_023773	ENSMUSG00000079184	Mphosph8	1500035L22Rik|4930548G07Rik|AU040635	M-phase phosphoprotein 8	protein-coding
mm_97601.1	chr11	78949599	78949628	+	1	NA	intron (NM_001313921, intron 17 of 25)	intron (NM_001313921, intron 17 of 25)	24322	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_13538.1	chr2	110721474	110721490	+	1	NA	promoter-TSS (NM_001290786)	promoter-TSS (NM_001290786)	-12	NM_001290786	269328	Mm.32566	NM_172979	ENSMUSG00000050808	Muc15	4732460E09|D730046L02Rik|MUC-15	mucin 15	protein-coding
mm_87358.1	chr10	43719633	43719634	+	1	NA	Intergenic	Intergenic	-26525	NR_040581	69443	Mm.484042	NR_040581	ENSMUSG00000111422	1700027J07Rik	-	RIKEN cDNA 1700027J07 gene	ncRNA
mm_101396.1	chr11	26578478	26578496	-	1	NA	intron (NM_001252447, intron 2 of 11)	L1MEf|LINE|L1	15433	NM_027260	69922	Mm.285351	NM_027260	ENSMUSG00000064090	Vrk2	2810003O05Rik|AI447698	vaccinia related kinase 2	protein-coding
mm_98575.1	chr11	95712669	95712704	+	1	NA	promoter-TSS (NR_045780)	promoter-TSS (NR_045780)	68	NR_045780	432396	Mm.426849	NR_045780	ENSMUSG00000086191	Zfp652os	1110035M17Rik	zinc finger protein 652, opposite strand	ncRNA
mm_36124.1	chr4	58915473	58915486	-	1	NA	Intergenic	Intergenic	-2754	NM_172381	230249	Mm.234801	NM_172381	ENSMUSG00000050812	AI314180	AW558785|BB181316|mKIAA0368	expressed sequence AI314180	protein-coding
mm_129051.1	chr15	75566265	75566276	-	1	NA	intron (NM_011837, intron 1 of 3)	intron (NM_011837, intron 1 of 3)	378	NM_001135689	23934	Mm.22154	NM_011837	ENSMUSG00000022577	Ly6h	-	lymphocyte antigen 6 complex, locus H	protein-coding
mm_62251.1	chr7	99267554	99267564	+	1	NA	promoter-TSS (NM_001043355)	promoter-TSS (NM_001043355)	112	NM_001048167	17760	Mm.154087	NM_010837	ENSMUSG00000055407	Map6	2810411E12Rik|Map-6|Mtap6|STOP	microtubule-associated protein 6	protein-coding
mm_99798.1	chr11	107546933	107546976	+	1	NA	Intergenic	CpG	-1006	NM_198298	78455	Mm.272047	NM_198298	ENSMUSG00000020721	Helz	3110078M01Rik|9430093I07Rik|9630002H22Rik|AI851979|DRHC	helicase with zinc finger domain	protein-coding
mm_121914.1	chr14	22542791	22542828	-	1	NA	promoter-TSS (NR_046307)	promoter-TSS (NR_046307)	-11	NR_046307	74896	Mm.444661	NR_046307		4930405A10Rik	4930456G20Rik	RIKEN cDNA 4930405A10 gene	ncRNA
mm_15406.1	chr2	156745826	156745841	+	1	NA	intron (NM_001042487, intron 1 of 6)	intron (NM_001042487, intron 1 of 6)	24554	NM_001042487	228836	Mm.22094	NM_146128	ENSMUSG00000061689	Dlgap4	AI225853|BC024558|DAP-4|DAP4|SAPAP-4|Sapap4|WBP16	discs, large homolog-associated protein 4 (Drosophila)	protein-coding
mm_53869.1	chr6	149334227	149334228	+	1	NA	intron (NM_026054, intron 4 of 4)	B1_Mur1|SINE|Alu	24813	NM_001289662	67246	Mm.333515	NM_026054	ENSMUSG00000032712	2810474O19Rik	6720435I21Rik|AA536804|AU020969|GET|Kiaa1551	RIKEN cDNA 2810474O19 gene	protein-coding
mm_50407.1	chr6	48737333	48737340	+	1	NA	Intergenic	Intergenic	-1711	NM_175860	16205	Mm.252599	NM_008376	ENSMUSG00000090019	Gimap1	IAP38|Imap38|imap	GTPase, IMAP family member 1	protein-coding
mm_10844.1	chr2	24975337	24975346	+	1	NA	promoter-TSS (NM_001031808)	promoter-TSS (NM_001031808)	-243	NM_001031808	107733	Mm.23010	NM_001031808	ENSMUSG00000036850	Mrpl41	MRP-L27|Rpml27	mitochondrial ribosomal protein L41	protein-coding
mm_52074.1	chr6	97827254	97827264	+	1	NA	intron (NM_001113198, intron 1 of 9)	intron (NM_001113198, intron 1 of 9)	20201	NM_001113198	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_10572.1	chr2	18064565	18064644	+	1	NA	promoter-TSS (NM_001252561)	promoter-TSS (NM_001252561)	19	NM_001252561	17354	Mm.209175	NM_010804	ENSMUSG00000026743	Mllt10	Af10|B130021D15Rik|D630001B22Rik|mKIAA4140	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 10	protein-coding
mm_133394.1	chr16	84774322	84774332	+	1	NA	5' UTR (NM_023844, exon 1 of 10)	5' UTR (NM_023844, exon 1 of 10)	204	NM_023844	67374	Mm.41758	NM_023844	ENSMUSG00000053062	Jam2	1110002N23Rik|2410030G21Rik|2410167M24Rik|JAM-2|JAM-B|Jcam2|VE-JAM	junction adhesion molecule 2	protein-coding
mm_160295.1	chr7	131543142	131543142	+	1	NA	exon (NM_008257, exon 1 of 2)	exon (NM_008257, exon 1 of 2)	179	NM_008257	15373	Mm.323562	NM_008257	ENSMUSG00000040148	Hmx3	Nkx-5.1|Nkx5-1|Nkx5.1	H6 homeobox 3	protein-coding
mm_42882.1	chr5	122354386	122354455	+	1	NA	promoter-TSS (NM_019780)	promoter-TSS (NM_019780)	7	NM_019780	56433	Mm.216528	NM_019780	ENSMUSG00000029462	Vps29	2010015D08Rik|AW049835|PEP11	VPS29 retromer complex component	protein-coding
mm_9083.1	chr1	168431897	168431905	-	1	NA	5' UTR (NM_001291509, exon 1 of 7)	5' UTR (NM_001291509, exon 1 of 7)	268	NM_001291508	18514	Mm.43358	NM_008783	ENSMUSG00000052534	Pbx1	2310056B04Rik|D230003C07Rik|Pbx-1	pre B cell leukemia homeobox 1	protein-coding
mm_57723.1	chr6	128890993	128891001	-	1	NA	5' UTR (NM_001254946, exon 1 of 3)	5' UTR (NM_001254946, exon 1 of 3)	127	NM_001254946	232406	Mm.30745	NM_001254946	ENSMUSG00000090164	BC035044	-	cDNA sequence BC035044	protein-coding
mm_102659.1	chr11	63975296	63975304	-	1	NA	intron (NM_178379, intron 6 of 6)	intron (NM_178379, intron 6 of 6)	11074	NR_131111	78883	Mm.410764	NR_131111	ENSMUSG00000086359	9630013K17Rik	-	RIKEN cDNA 9630013K17 gene	ncRNA
mm_145201.1	chr18	49979515	49979544	+	1	NA	5' UTR (NM_001177760, exon 1 of 3)	5' UTR (NM_001177760, exon 1 of 3)	102	NM_001177759	106869	Mm.27740	NM_134131	ENSMUSG00000062210	Tnfaip8	AA987150|E130304C20Rik|ENSMUSG00000073567|Gg2-1|Gm10539|Nded|Ssc-2|Tipe	tumor necrosis factor, alpha-induced protein 8	protein-coding
mm_2130.1	chr1	88055468	88055478	+	1	NA	promoter-TSS (NM_201641)	promoter-TSS (NM_201641)	62	NM_201641	394430	Mm.300095	NM_201641	ENSMUSG00000090165	Ugt1a10	A13|Ugt1a13	UDP glycosyltransferase 1 family, polypeptide A10	protein-coding
mm_7579.1	chr1	125197452	125197489	-	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	238257	NM_023735	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding
mm_98910.1	chr11	98202739	98202749	+	1	NA	promoter-TSS (NM_026952)	promoter-TSS (NM_026952)	-561	NM_001109628	69131	Mm.260516	NM_026952	ENSMUSG00000003119	Cdk12	1810022J16Rik|AI646528|Crk7|Crkrs|D11Ertd752e|Pksc	cyclin-dependent kinase 12	protein-coding
mm_83876.1	chr9	55149970	55150016	-	1	NA	promoter-TSS (NM_001346658)	promoter-TSS (NM_001346658)	-90	NM_001346658	109161	Mm.207894	NM_180600	ENSMUSG00000032307	Ube2q2	3010021M21Rik	ubiquitin-conjugating enzyme E2Q family member 2	protein-coding
mm_136871.1	chr17	12916495	12916515	+	1	NA	promoter-TSS (NM_026310)	promoter-TSS (NM_026310)	176	NM_013686	21454	Mm.229342	NM_013686	ENSMUSG00000068039	Tcp1	AI528772|CCT|Cct1|Ccta|TRic|Tcp-1|Tp63|c-cpn|p63	t-complex protein 1	protein-coding
mm_100154.1	chr11	116189415	116189460	+	1	NA	exon (NM_001271898, exon 3 of 14)	exon (NM_001271898, exon 3 of 14)	-9418	NM_027107	69535	Mm.390347	NM_027107	ENSMUSG00000020778	Ten1	2310004N24Rik	TEN1 telomerase capping complex subunit	protein-coding
mm_122377.1	chr14	39474049	39474079	-	1	NA	promoter-TSS (NM_008734)	promoter-TSS (NM_008734)	-976	NM_008734	18183	Mm.258705	NM_008734	ENSMUSG00000041014	Nrg3	ska	neuregulin 3	protein-coding
mm_418.1	chr1	34307769	34307783	+	1	NA	3' UTR (NM_134448, exon 98 of 98)	3' UTR (NM_134448, exon 98 of 98)	125423	NR_039562	100628580		NR_039562	ENSMUSG00000092852	Mir5103	mir-5103|mmu-mir-5103|mu-mir-5103	microRNA 5103	ncRNA
mm_169498.1	chr14	76495032	76495040	-	1	NA	intron (NM_001177751, intron 1 of 2)	intron (NM_001177751, intron 1 of 2)	6600	NM_001177751	21807	Mm.153272	NM_009366	ENSMUSG00000022010	Tsc22d1	AA589566|AW105905|Egr5|TSC-22|Tgfb1i4|Tsc|Tsc22	TSC22 domain family, member 1	protein-coding
mm_43146.1	chr5	125465996	125466038	+	1	NA	Intergenic	Intergenic	-9856	NM_030210	78894	Mm.431573	NM_030210	ENSMUSG00000029482	Aacs	2210408B16Rik|SUR5	acetoacetyl-CoA synthetase	protein-coding
mm_128920.1	chr15	73761076	73761090	-	1	NA	Intergenic	Intergenic	13057	NM_008975	19245	Mm.390807	NM_008975	ENSMUSG00000059895	Ptp4a3	AV088979|Prl-3|pPtp4a3	protein tyrosine phosphatase 4a3	protein-coding
mm_123719.1	chr14	70152432	70152462	-	1	NA	exon (NM_146055, exon 3 of 21)	exon (NM_146055, exon 3 of 21)	1344	NM_146055	219158	Mm.218284	NM_146055	ENSMUSG00000033712	Ccar2	2610301G19Rik|Dbc1|mKIAA1967	cell cycle activator and apoptosis regulator 2	protein-coding
mm_136842.1	chr17	12759190	12759201	+	1	NA	intron (NM_010515, intron 1 of 47)	PB1D9|SINE|Alu	10511	NM_010515	16004	Mm.26553	NM_010515	ENSMUSG00000023830	Igf2r	AI661837|CD222|CI-MPR|M6P/IGF2R|Mpr300	insulin-like growth factor 2 receptor	protein-coding
mm_43217.1	chr5	129727044	129727055	+	1	NA	intron (NM_008095, intron 1 of 9)	intron (NM_008095, intron 1 of 9)	1974	NM_008095	14467	Mm.12468	NM_008095	ENSMUSG00000029432	Gbas	AV006093|Nipsnap2	glioblastoma amplified sequence	protein-coding
mm_26552.1	chr3	146404845	146404877	+	1	NA	5' UTR (NM_001253768, exon 1 of 15)	5' UTR (NM_001253768, exon 1 of 15)	219	NM_138744	99167	Mm.200783	NM_138744	ENSMUSG00000036825	Ssx2ip	AU014939|AU042321|Adip	synovial sarcoma, X 2 interacting protein	protein-coding
mm_166097.1	chr4	142996197	142996200	+	1	NA	Intergenic	Intergenic	139964	NR_105988	102465618		NR_105988	ENSMUSG00000106597	Mir7021	mmu-mir-7021	microRNA 7021	ncRNA
mm_63585.1	chr7	128129537	128129574	+	1	NA	promoter-TSS (NM_021334)	promoter-TSS (NM_021334)	-13	NM_021334	16411	Mm.22378	NM_021334	ENSMUSG00000030789	Itgax	AI449405|Cd11c|Cr4|N418	integrin alpha X	protein-coding
mm_50073.1	chr6	41302266	41302279	+	1	NA	promoter-TSS (NM_011646)	promoter-TSS (NM_011646)	0	NM_011646	22074	Mm.383263	NM_011646	ENSMUSG00000054106	Try4	0910001B19Rik|Td	trypsin 4	protein-coding
mm_21139.1	chr2	154215294	154215313	-	1	NA	exon (NM_153418, exon 12 of 16)	exon (NM_153418, exon 12 of 16)	-8439	NM_144890	228802	Mm.167411	NM_144890	ENSMUSG00000038572	Bpifb5	Lplunc5	BPI fold containing family B, member 5	protein-coding
mm_6232.1	chr1	66944959	66944969	-	1	NA	promoter-TSS (NM_021285)	promoter-TSS (NM_021285)	92	NM_021285	17901	Mm.1000	NM_021285	ENSMUSG00000061816	Myl1	AI325107|MLC1f|MLC3f|Mylf	myosin, light polypeptide 1	protein-coding
mm_120776.1	chr14	74640871	74640887	+	1	NA	promoter-TSS (NM_172812)	promoter-TSS (NM_172812)	39	NM_172812	15558	Mm.214351	NM_172812	ENSMUSG00000034997	Htr2a	E030013E04|Htr-2|Htr2	5-hydroxytryptamine (serotonin) receptor 2A	protein-coding
mm_99096.1	chr11	99932021	99932029	+	1	NA	Intergenic	Intergenic	-4266	NM_001025244	432602	Mm.246878	NM_001025244	ENSMUSG00000051481	Krtap31-2	OTTMUSG00000002177	keratin associated protein 31-2	protein-coding
mm_150975.1	chr19	46501716	46501733	+	1	NA	promoter-TSS (NM_053100)	promoter-TSS (NM_053100)	76	NM_053100	93679	Mm.392177	NM_053100	ENSMUSG00000025034	Trim8	AA408830|BB006755|GERP|Rnf27	tripartite motif-containing 8	protein-coding
mm_150401.1	chr19	36554743	36554773	+	1	NA	5' UTR (NM_001163471, exon 1 of 21)	5' UTR (NM_001163471, exon 1 of 21)	119	NM_172637	226098	Mm.61107	NM_172637	ENSMUSG00000041180	Hectd2	4921524L07|A630025O09Rik|AW212605	HECT domain containing 2	protein-coding
mm_28577.1	chr3	93445446	93445557	-	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	3171	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_143871.1	chr17	84186959	84187004	-	1	NA	exon (NM_001001806, exon 2 of 2)	exon (NM_001001806, exon 2 of 2)	966	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_135432.1	chr16	45382852	45382882	-	1	NA	3' UTR (NM_010818, exon 6 of 6)	3' UTR (NM_010818, exon 6 of 6)	26186	NM_010818	17470	Mm.245851	NM_010818	ENSMUSG00000022661	Cd200	Mox2|OX2	CD200 antigen	protein-coding
mm_2777.1	chr1	130803083	130803091	+	1	NA	exon (NM_001170632, exon 2 of 7)	exon (NM_001170632, exon 2 of 7)	2185	NM_144960	64435	Mm.31821	NM_144960	ENSMUSG00000026415	Fcamr	-	Fc receptor, IgA, IgM, high affinity	protein-coding
mm_105227.1	chr11	102296752	102296812	-	1	NA	promoter-TSS (NM_001098836)	promoter-TSS (NM_001098836)	-153	NM_001098837	217218	Mm.390381	NM_001098836	ENSMUSG00000059995	Atxn7l3	E030022H21Rik	ataxin 7-like 3	protein-coding
mm_57830.1	chr6	129464503	129464513	-	1	NA	intron (NR_132130, intron 5 of 5)	L1M5|LINE|L1	8271	NM_001309637	56644	Mm.239516	NM_020008	ENSMUSG00000079293	Clec7a	BGR|Clecsf12|beta-GR	C-type lectin domain family 7, member a	protein-coding
mm_22005.1	chr2	167770445	167770476	-	1	NA	Intergenic	Intergenic	79283	NR_015500	329562	Mm.123101	NM_177851	ENSMUSG00000006462	A530013C23Rik	-	RIKEN cDNA A530013C23 gene	ncRNA
mm_125957.1	chr15	76249547	76249560	+	1	NA	3' UTR (NM_023168, exon 7 of 7)	3' UTR (NM_023168, exon 7 of 7)	1362	NR_105918	102465575		NR_105918	ENSMUSG00000098625	Mir6953	Gm27738|mmu-mir-6953	microRNA 6953	ncRNA
mm_86802.1	chr10	20312525	20312539	+	1	NA	promoter-TSS (NM_001025393)	promoter-TSS (NM_001025393)	63	NM_001025393	72567	Mm.294783	NM_153787	ENSMUSG00000037608	Bclaf1	2610102K23Rik|2700025J07Rik|2810454G14Rik|5730534O06Rik|AI450190|AW556225|Btf|mKIAA0164	BCL2-associated transcription factor 1	protein-coding
mm_106438.1	chr11	119547745	119547759	-	1	NA	promoter-TSS (NR_045099)	promoter-TSS (NR_045099)	68	NM_008730	18164	Mm.5142	NM_008730	ENSMUSG00000025582	Nptx1	D11Bwg1004e|Np1	neuronal pentraxin 1	protein-coding
mm_42773.1	chr5	121353965	121353968	+	1	NA	intron (NM_181421, intron 64 of 75)	intron (NM_181421, intron 64 of 75)	31649	NM_001163470	231712	Mm.20488	NM_172275	ENSMUSG00000042726	Trafd1	1110008K06Rik|Fln29	TRAF type zinc finger domain containing 1	protein-coding
mm_10867.1	chr2	25194807	25194820	+	1	NA	exon (NM_146115, exon 2 of 2)	exon (NM_146115, exon 2 of 2)	2000	NM_146115	227612	Mm.119747	NM_146115	ENSMUSG00000059555	Tor4a	A830007P12Rik	torsin family 4, member A	protein-coding
mm_11717.1	chr2	36241914	36241951	+	1	NA	intron (NM_008969, intron 7 of 10)	B3A|SINE|B2	11506	NM_008969	19224	Mm.275434	NM_008969	ENSMUSG00000047250	Ptgs1	COX1|Cox-1|Cox-3|PGHS-1|PHS 1|Pghs1	prostaglandin-endoperoxide synthase 1	protein-coding
mm_61817.1	chr7	87583949	87583957	+	1	NA	promoter-TSS (NM_001081414)	promoter-TSS (NM_001081414)	-215	NM_001081414	108071	Mm.235018	NM_001033224	ENSMUSG00000049583	Grm5	6430542K11Rik|AI850523|Glu5R|Gprc1e|mGluR5|mGluR5b	glutamate receptor, metabotropic 5	protein-coding
mm_155457.1	chrX	73502843	73502884	+	1	NA	promoter-TSS (NM_177236)	promoter-TSS (NM_177236)	-223	NM_001310537	320707	Mm.210095	NM_177236	ENSMUSG00000031376	Atp2b3	6430519O13Rik|Pmca3	ATPase, Ca++ transporting, plasma membrane 3	protein-coding
mm_114305.1	chr13	59625140	59625165	+	1	NA	intron (NM_030153, intron 16 of 22)	PB1|SINE|Alu	39819	NM_030153	78689	Mm.253902	NM_030153	ENSMUSG00000021555	Naa35	A330021G12Rik|A330027C19Rik|AI158944|C030004C14Rik|Mak10	N(alpha)-acetyltransferase 35, NatC auxiliary subunit	protein-coding
mm_28146.1	chr3	87377807	87377821	-	1	NA	intron (NM_001310545, intron 1 of 10)	intron (NM_001310545, intron 1 of 10)	1427	NM_001136236	229499	Mm.255203	NM_153090	ENSMUSG00000059994	Fcrl1	A230020G22Rik|Bxmas1|Bxmh1|Bxmh1b|Fcrh1|Fcrh1l|Fcrh1s|Ifgp1	Fc receptor-like 1	protein-coding
mm_87217.1	chr10	40257709	40257735	+	1	NA	promoter-TSS (NM_026113)	promoter-TSS (NM_026113)	-57	NM_026113	67371	Mm.64104	NM_026113	ENSMUSG00000019837	Gtf3c6	2410016F19Rik|AU019813	general transcription factor IIIC, polypeptide 6, alpha	protein-coding
mm_115401.1	chr13	113881188	113881220	+	1	NA	intron (NM_172595, intron 1 of 4)	intron (NM_172595, intron 1 of 4)	86696	NM_172595	218639	Mm.79837	NM_172595	ENSMUSG00000042348	Arl15	A430036I03|Arfrp2|C230032K13Rik	ADP-ribosylation factor-like 15	protein-coding
mm_23200.1	chr3	41495291	41495296	+	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	-2094	NR_040385	78706	Mm.366094	NR_040385	ENSMUSG00000097639	Platr4	C430002E04Rik	pluripotency associated transcript 4	ncRNA
mm_115646.1	chr13	12278938	12278948	-	1	NA	exon (NM_033268, exon 15 of 21)	exon (NM_033268, exon 15 of 21)	-20830	NM_001081128	238505	Mm.40335	NM_001081128	ENSMUSG00000021311	Mtr	AI894170|D830038K18Rik|MS	5-methyltetrahydrofolate-homocysteine methyltransferase	protein-coding
mm_70053.1	chr7	142651081	142651091	-	1	NA	3' UTR (NM_010514, exon 4 of 4)	3' UTR (NM_010514, exon 4 of 4)	3910	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_171160.1	chr3	22732256	22732258	-	1	NA	Intergenic	L1Md_A|LINE|L1	480887	NR_004439	19784		NR_004439		Rprl2	RPRH3|Rmrp3	ribonuclease P RNA-like 2	ncRNA
mm_120796.1	chr14	74735642	74735663	+	1	NA	intron (NM_001285423, intron 1 of 8)	intron (NM_001285423, intron 1 of 8)	3355	NM_016903	13885	Mm.38055	NM_016903	ENSMUSG00000021996	Esd	Es-10|Es10|FGH|sid478	esterase D/formylglutathione hydrolase	protein-coding
mm_166353.1	chr5	120629762	120629771	-	1	NA	exon (NM_001195094, exon 6 of 7)	exon (NM_001195094, exon 6 of 7)	4469	NM_001195094	546886	Mm.464847	NM_001195094	ENSMUSG00000094282	Cfap73	Ccdc42b|Gm5988	cilia and flagella associated protein 73	protein-coding
mm_167314.1	chr8	66330848	66330851	-	1	NA	intron (NM_175188, intron 4 of 7)	intron (NM_175188, intron 4 of 7)	-55452	NM_001166375	72925	Mm.380457	NM_175188	ENSMUSG00000036469	March1	2900024D24Rik|BB085186	membrane-associated ring finger (C3HC4) 1	protein-coding
mm_55259.1	chr6	53563919	53563938	-	1	NA	intron (NM_001327821, intron 5 of 10)	intron (NM_001327821, intron 5 of 10)	-9446	NM_172728	231991	Mm.227444	NM_172728	ENSMUSG00000053007	Creb5	9430076C15Rik|CRE-BPa|Crebpa|D430026C09Rik	cAMP responsive element binding protein 5	protein-coding
mm_36922.1	chr4	108144953	108144984	-	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-20469	NM_026728	52430	Mm.270783	NM_026728	ENSMUSG00000028601	Echdc2	1300017C12Rik|2610009M20Rik|D4Ertd765e	enoyl Coenzyme A hydratase domain containing 2	protein-coding
mm_117610.1	chr13	91262749	91262751	-	1	NA	Intergenic	Intergenic	-38763	NM_025770	66795	Mm.235385	NM_025770	ENSMUSG00000021619	Atg10	5330424L23Rik|5430428K15Rik|AI852123|APG10|Agp10|Apg10l|Apg10p|Atg10l	autophagy related 10	protein-coding
mm_161967.1	chr19	8999661	8999661	+	1	NA	intron (NR_104460, intron 1 of 6)	intron (NR_104460, intron 1 of 6)	10377	NM_001286518	66395	Mm.203866	NM_009643	ENSMUSG00000069833	Ahnak	DY6	AHNAK nucleoprotein (desmoyokin)	protein-coding
mm_158524.1	chrX	143860935	143860973	-	1	NA	3' UTR (NM_010025, exon 7 of 7)	3' UTR (NM_010025, exon 7 of 7)	-33542	NM_007603	12338	Mm.30290	NM_007603	ENSMUSG00000067276	Capn6	-	calpain 6	protein-coding
mm_114070.1	chr13	54382569	54382583	+	1	NA	3' UTR (NM_009946, exon 4 of 4)	3' UTR (NM_009946, exon 4 of 4)	11227	NM_009946	12890	Mm.268902	NM_009946	ENSMUSG00000025867	Cplx2	921-L|AI413745|AW492120	complexin 2	protein-coding
mm_73183.1	chr8	95113434	95113458	+	1	NA	promoter-TSS (NM_001145832)	promoter-TSS (NM_001145832)	-104	NM_001145832	16582	Mm.378951	NM_010631	ENSMUSG00000031788	Kifc3	AI325457|BB123200	kinesin family member C3	protein-coding
mm_96957.1	chr11	70615889	70615900	+	1	NA	promoter-TSS (NM_001145537)	promoter-TSS (NM_001145537)	0	NM_001145537	668433	Mm.425687	NM_001145537	ENSMUSG00000087279	4930544D05Rik	-	RIKEN cDNA 4930544D05 gene	protein-coding
mm_105732.1	chr11	109246916	109246926	-	1	NA	intron (NM_001165934, intron 12 of 16)	intron (NM_001165934, intron 12 of 16)	51260	NM_001165934	19739	Mm.38548	NM_011268	ENSMUSG00000020599	Rgs9	RGS9-1|Rgs9-2	regulator of G-protein signaling 9	protein-coding
mm_125214.1	chr15	34082765	34082775	+	1	NA	promoter-TSS (NM_026002)	promoter-TSS (NM_026002)	51	NM_026002	67154	Mm.130883	NM_026002	ENSMUSG00000022255	Mtdh	2610103J23Rik|3D3|3D3/Lyric|AEG-1|AV353288|D8Bwg1112e|Lyric	metadherin	protein-coding
mm_71480.1	chr8	46617427	46617446	+	1	NA	promoter-TSS (NM_001001184)	promoter-TSS (NM_001001184)	145	NM_009810	12367	Mm.34405	NM_009810	ENSMUSG00000031628	Casp3	A830040C14Rik|AC-3|CASP-3|CC3|CPP-32|CPP32|Caspase-3|Lice|SCA-1|Yama|mldy	caspase 3	protein-coding
mm_99416.1	chr11	102295470	102295474	+	1	NA	intron (NM_001098837, intron 1 of 12)	intron (NM_001098837, intron 1 of 12)	1157	NM_001098836	217218	Mm.390381	NM_001098836	ENSMUSG00000059995	Atxn7l3	E030022H21Rik	ataxin 7-like 3	protein-coding
mm_72013.1	chr8	70704040	70704044	+	1	NA	Intergenic	Intergenic	6303	NM_001286944	16478	Mm.419851	NM_010592	ENSMUSG00000071076	Jund	Jund1	jun D proto-oncogene	protein-coding
mm_58724.1	chr7	13024670	13024720	+	1	NA	5' UTR (NM_011588, exon 1 of 17)	5' UTR (NM_011588, exon 1 of 17)	543	NM_011588	21849	Mm.15701	NM_011588	ENSMUSG00000005566	Trim28	AA408787|KAP-1|KRIP-1|MommeD9|Tif1b|Tif1beta	tripartite motif-containing 28	protein-coding
mm_13407.1	chr2	104027824	104027868	+	1	NA	promoter-TSS (NM_212433)	promoter-TSS (NM_212433)	47	NM_212433	57443	Mm.143768	NM_020593	ENSMUSG00000027180	Fbxo3	1200002G09Rik|1700026K02Rik|AI046358|Fba	F-box protein 3	protein-coding
mm_127368.1	chr15	100749895	100749907	+	1	NA	Intergenic	Intergenic	-11846	NM_021530	59033	Mm.209856	NM_021530	ENSMUSG00000023032	Slc4a8	AW493845|C230026C11|NDCBE|kNBC-3	solute carrier family 4 (anion exchanger), member 8	protein-coding
mm_1023.1	chr1	58754075	58754121	+	1	NA	3' UTR (NM_207653, exon 10 of 10)	3' UTR (NM_207653, exon 10 of 10)	23546	NM_001293805	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_117834.1	chr13	98550772	98550776	-	1	NA	Intergenic	Intergenic	86636	NM_026685	68344	Mm.28766	NM_026685	ENSMUSG00000046082	Tmem174	0610009B10Rik|AA986094	transmembrane protein 174	protein-coding
mm_122031.1	chr14	29721836	29721886	-	1	NA	promoter-TSS (NM_009785)	promoter-TSS (NM_009785)	3	NM_009785	12294	Mm.386754	NM_009785	ENSMUSG00000021991	Cacna2d3	Cacnad3|alapha2delta3	calcium channel, voltage-dependent, alpha2/delta subunit 3	protein-coding
mm_109786.1	chr12	3248309	3248332	-	1	NA	3' UTR (NM_016676, exon 6 of 6)	3' UTR (NM_016676, exon 6 of 6)	12529	NR_015551	74173	Mm.309774	NM_028796	ENSMUSG00000079179	Rab10os	1700012B15Rik|1810036A22Rik	RAB10, member RAS oncogene family, opposite strand	ncRNA
mm_80914.1	chr9	100649225	100649230	+	1	NA	intron (NM_009282, intron 1 of 33)	intron (NM_009282, intron 1 of 33)	5604	NM_009282	20842	Mm.42135	NM_009282	ENSMUSG00000037286	Stag1	AU045003|SA-1|Scc3	stromal antigen 1	protein-coding
mm_65293.1	chr7	24457826	24457836	-	1	NA	Intergenic	Intergenic	-4652	NM_011113	18793	Mm.1359	NM_011113	ENSMUSG00000046223	Plaur	Cd87|u-PAR|uPAR	plasminogen activator, urokinase receptor	protein-coding
mm_120684.1	chr14	70773248	70773258	+	1	NA	Intergenic	MLTR25A|LTR|ERVK	-1128	NM_010071	13449	Mm.243323	NM_010071	ENSMUSG00000022102	Dok2	DokR|Frip	docking protein 2	protein-coding
mm_130199.1	chr15	94589808	94589828	-	1	NA	promoter-TSS (NM_008971)	promoter-TSS (NM_008971)	6	NM_008971	19230	Mm.490250	NM_008971	ENSMUSG00000022451	Twf1	A6|Ptk9|twinfilin	twinfilin actin binding protein 1	protein-coding
mm_9502.1	chr1	173730432	173730440	-	1	NA	exon (NM_001204910, exon 5 of 8)	exon (NM_001204910, exon 5 of 8)	11373	NM_001204910	226691	Mm.440876	NM_001204910	ENSMUSG00000073490	Ifi207	AI607873|Pyhin-A	interferon activated gene 207	protein-coding
mm_118859.1	chr14	25842147	25842170	+	1	NA	promoter-TSS (NM_013469)	promoter-TSS (NM_013469)	3	NM_013469	11744	Mm.294083	NM_013469	ENSMUSG00000021866	Anxa11	A830099O17Rik|Anx11	annexin A11	protein-coding
mm_54758.1	chr6	41035502	41035514	-	1	NA	promoter-TSS (NM_023333)	promoter-TSS (NM_023333)	1	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_44196.1	chr5	3640745	3640748	-	1	NA	3' UTR (NM_026033, exon 5 of 5)	3' UTR (NM_026033, exon 5 of 5)	7190	NM_026033	67210	Mm.178424	NM_026033	ENSMUSG00000007415	Gatad1	2310031E19Rik|2810047M21Rik|8430439A17Rik|9130430G15Rik|B330017N08Rik|ENSMUSG00000073241|Odag	GATA zinc finger domain containing 1	protein-coding
mm_55007.1	chr6	48836329	48836343	-	1	NA	exon (NM_001164209, exon 4 of 8)	exon (NM_001164209, exon 4 of 8)	4652	NM_023056	65963	Mm.28385	NM_023056	ENSMUSG00000029810	Tmem176b	1810009M01Rik|Clast1|Lr8	transmembrane protein 176B	protein-coding
mm_20395.1	chr2	129180663	129180671	-	1	NA	promoter-TSS (NR_045264)	promoter-TSS (NR_045264)	6	NR_045264	100048701	Mm.428544	NR_045264	ENSMUSG00000084826	AI847159	OTTMUSG00000015420	expressed sequence AI847159	ncRNA
mm_100034.1	chr11	114982612	114982630	+	1	NA	3' UTR (NM_145437, exon 4 of 4)	3' UTR (NM_145437, exon 4 of 4)	7265	NM_145437	217305	Mm.275986	NM_145437	ENSMUSG00000034641	Cd300ld	4732429D16Rik|CLM5|Cd300ld1|LMIR4|MAIR-IV|clm-5	CD300 molecule like family member d	protein-coding
mm_37407.1	chr4	122688959	122688963	-	1	NA	promoter-TSS (NM_023865)	promoter-TSS (NM_023865)	-298	NM_023865	77432	Mm.491436	NM_023865	ENSMUSG00000023263	9530002B09Rik	Aump|Vpp1|Vppl	RIKEN cDNA 9530002B09 gene	protein-coding
mm_104723.1	chr11	98193268	98193298	-	1	NA	promoter-TSS (NM_134027)	promoter-TSS (NM_134027)	10	NM_134027	19014	Mm.12926	NM_013634	ENSMUSG00000018160	Med1	AI480703|CRSP210|DRIP205|PBP|Pparbp|TRAP220|l11Jus15	mediator complex subunit 1	protein-coding
mm_128042.1	chr15	25390458	25390478	-	1	NA	intron (NM_027395, intron 1 of 1)	intron (NM_027395, intron 1 of 1)	23296	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	brain abundant, membrane attached signal protein 1	protein-coding
mm_152817.1	chr19	23134936	23134961	-	1	NA	Intergenic	CpG	-6278	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_149339.1	chr19	10850360	10850370	+	1	NA	intron (NM_023044, intron 2 of 7)	MTD|LTR|ERVL-MaLR	7821	NM_023044	65221	Mm.27387	NM_023044	ENSMUSG00000024737	Slc15a3	Ci1|cI-1	solute carrier family 15, member 3	protein-coding
mm_100849.1	chr11	5803559	5803569	-	1	NA	exon (NM_018870, exon 1 of 3)	exon (NM_018870, exon 1 of 3)	232	NM_018870	56012	Mm.219627	NM_018870	ENSMUSG00000020475	Pgam2	-	phosphoglycerate mutase 2	protein-coding
mm_113638.1	chr13	42052317	42052368	+	1	NA	intron (NM_007772, intron 1 of 8)	CpG	321	NM_007772	110521	Mm.4808	NM_007772	ENSMUSG00000021366	Hivep1	Cryabp1	human immunodeficiency virus type I enhancer binding protein 1	protein-coding
mm_101401.1	chr11	26593890	26593900	-	1	NA	promoter-TSS (NM_027260)	promoter-TSS (NM_027260)	25	NM_027260	69922	Mm.285351	NM_027260	ENSMUSG00000064090	Vrk2	2810003O05Rik|AI447698	vaccinia related kinase 2	protein-coding
mm_133286.1	chr16	77466039	77466058	+	1	NA	intron (NR_015543, intron 3 of 4)	Plat_L3|LINE|CR1	-132888	NR_029535	387229		NR_029535	ENSMUSG00000065530	Mir99a	Mirn99a|mir-99a|mmu-mir-99a	microRNA 99a	ncRNA
mm_78175.1	chr9	21167945	21167964	+	1	NA	TTS (NR_106127)	TTS (NR_106127)	2240	NM_183408	18577	Mm.191749	NM_019798	ENSMUSG00000032177	Pde4a	D9Ertd60e|Dpde2	phosphodiesterase 4A, cAMP specific	protein-coding
mm_138641.1	chr17	35866246	35866256	+	1	NA	promoter-TSS (NM_175242)	promoter-TSS (NM_175242)	123	NM_001146710	76448	Mm.359982	NM_175242	ENSMUSG00000034595	Ppp1r18	2310014H01Rik|AA407849|AI450394	protein phosphatase 1, regulatory subunit 18	protein-coding
mm_47637.1	chr5	125312245	125312252	-	1	NA	intron (NM_001205083, intron 1 of 10)	intron (NM_001205083, intron 1 of 10)	28846	NM_016741	20778	Mm.282242	NM_016741	ENSMUSG00000037936	Scarb1	AI120173|CD36|Cd36l1|Chohd1|Cla-1|Cla1|D5Ertd460e|Hdlq1|Hlb398|SR-B1|SR-BI|SRBI|Srb1|mSR-BI	scavenger receptor class B, member 1	protein-coding
mm_158952.1	chr1	87154894	87154894	-	1	NA	exon (NM_021306, exon 2 of 18)	exon (NM_021306, exon 2 of 18)	1242	NM_001277925	13599	Mm.140765	NM_021306	ENSMUSG00000026247	Ecel1	DINE|xce	endothelin converting enzyme-like 1	protein-coding
mm_62456.1	chr7	101451377	101451390	+	1	NA	exon (NM_001143849, exon 1 of 30)	exon (NM_001143849, exon 1 of 30)	131	NM_001243757	207728	Mm.247564	NM_001008548	ENSMUSG00000030653	Pde2a	CGS-PDE|cGSPDE	phosphodiesterase 2A, cGMP-stimulated	protein-coding
mm_136933.1	chr17	14169693	14169703	+	1	NA	Intergenic	Intergenic	34133	NM_172826	240025	Mm.79993	NM_172826	ENSMUSG00000048826	Dact2	2900084M21Rik|A630024E20|Dpr2|Frd2|dapper2	dishevelled-binding antagonist of beta-catenin 2	protein-coding
mm_125740.1	chr15	73518568	73518615	+	1	NA	intron (NM_001081066, intron 1 of 22)	intron (NM_001081066, intron 1 of 22)	6031	NM_001081066	105841	Mm.322557	NM_001081066	ENSMUSG00000036661	Dennd3	AI447457|E030003N15Rik	DENN/MADD domain containing 3	protein-coding
mm_141433.1	chr17	29492343	29492376	-	1	NA	intron (NM_008842, intron 4 of 5)	intron (NM_008842, intron 4 of 5)	1314	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_85068.1	chr9	91102175	91102184	-	1	NA	Intergenic	Intergenic	263620	NM_009573	22771	Mm.335350	NM_009573	ENSMUSG00000032368	Zic1	ZIC|ZNF201	zinc finger protein of the cerebellum 1	protein-coding
mm_63974.1	chr7	139950697	139950717	+	1	NA	Intergenic	Intergenic	6851	NM_009482	22286	Mm.10205	NM_009482	ENSMUSG00000047751	Utf1	AI505934	undifferentiated embryonic cell transcription factor 1	protein-coding
mm_123485.1	chr14	66009169	66009194	-	1	NA	promoter-TSS (NM_178747)	promoter-TSS (NM_178747)	29	NM_178747	268756	Mm.26207	NM_178747	ENSMUSG00000034450	Gulo	5730581M22|AU018375|BC028822|GLO|LGO|sfx|unh|unhip	gulonolactone (L-) oxidase	protein-coding
mm_126405.1	chr15	80255171	80255181	+	1	NA	promoter-TSS (NM_009716)	promoter-TSS (NM_009716)	-8	NM_001287180	11911	Mm.641	NM_009716	ENSMUSG00000042406	Atf4	Atf-4|C/ATF|CREB2|TAXREB67	activating transcription factor 4	protein-coding
mm_80194.1	chr9	72396301	72396318	+	1	NA	Intergenic	Intergenic	-42220	NM_008613	17427	Mm.387671	NM_008613	ENSMUSG00000032221	Mns1	AW546487	meiosis-specific nuclear structural protein 1	protein-coding
mm_56270.1	chr6	91023997	91024002	-	1	NA	intron (NM_018815, intron 33 of 39)	intron (NM_018815, intron 33 of 39)	92827	NM_018815	54563	Mm.28162	NM_018815	ENSMUSG00000030091	Nup210	9830001L10|AI836801|Pom210|gp190|gp210	nucleoporin 210	protein-coding
mm_138756.1	chr17	37050161	37050198	+	1	NA	intron (NM_019439, intron 5 of 22)	intron (NM_019439, intron 5 of 22)	4213	NM_019439	54393	Mm.32191	NM_019439	ENSMUSG00000024462	Gabbr1	GABAB1|GABAbR1|bM573K1.1	gamma-aminobutyric acid (GABA) B receptor, 1	protein-coding
mm_113480.1	chr13	37333758	37333773	+	1	NA	Intergenic	MTEa|LTR|ERVL-MaLR	-11580	NM_010745	17084	Mm.2639	NM_010745	ENSMUSG00000021423	Ly86	MD-1|MD1|ly86_tv2	lymphocyte antigen 86	protein-coding
mm_25626.1	chr3	118818162	118818181	+	1	NA	intron (NM_170778, intron 8 of 22)	Lx8|LINE|L1	255993	NM_170778	99586	Mm.27907	NM_170778	ENSMUSG00000033308	Dpyd	AI315208|DPD|E330028L06Rik	dihydropyrimidine dehydrogenase	protein-coding
mm_149471.1	chr19	11618949	11618951	+	1	NA	exon (NM_013516, exon 5 of 7)	exon (NM_013516, exon 5 of 7)	4769	NM_001276330	14126	Mm.329735	NM_013516	ENSMUSG00000024680	Ms4a2	FcRB|Fce1b|Fcer1b|Fcrbeta|Ms4a1|fcERI	membrane-spanning 4-domains, subfamily A, member 2	protein-coding
mm_70937.1	chr8	25849673	25849681	+	1	NA	promoter-TSS (NM_008432)	promoter-TSS (NM_008432)	54	NM_008432	16532	Mm.289679	NM_008432	ENSMUSG00000031576	Kcnu1	Kcnma3|Slo3|mSlo3	potassium channel, subfamily U, member 1	protein-coding
mm_3415.1	chr1	144317917	144317929	+	1	NA	Intergenic	Intergenic	-68819	NM_015811	50778	Mm.103701	NM_015811	ENSMUSG00000026358	Rgs1	BL34	regulator of G-protein signaling 1	protein-coding
mm_172833.1	chr9	23284376	23284379	-	1	NA	intron (NM_028472, intron 3 of 14)	intron (NM_028472, intron 3 of 14)	61301	NM_028472	73230	Mm.335020	NM_028472	ENSMUSG00000031963	Bmper	3110056H04Rik|CV-2|Crim3|Cv2	BMP-binding endothelial regulator	protein-coding
mm_36061.1	chr4	57915726	57915737	-	1	NA	exon (NM_178727, exon 1 of 2)	exon (NM_178727, exon 1 of 2)	533	NM_178727	242484	Mm.23214	NM_178727	ENSMUSG00000052117	D630039A03Rik	-	RIKEN cDNA D630039A03 gene	protein-coding
mm_28091.1	chr3	85887362	85887374	-	1	NA	5' UTR (NM_177130, exon 1 of 2)	5' UTR (NM_177130, exon 1 of 2)	150	NM_177130	320302	Mm.482978	NM_177130	ENSMUSG00000031286	Glt28d2	4732486J07Rik|Glt28d1l	glycosyltransferase 28 domain containing 2	protein-coding
mm_2241.1	chr1	91053546	91053550	+	1	NA	5' UTR (NM_008515, exon 1 of 23)	5' UTR (NM_008515, exon 1 of 23)	104	NM_008515	16978	Mm.45039	NM_008515	ENSMUSG00000026305	Lrrfip1	AU024550|Fliiap1	leucine rich repeat (in FLII) interacting protein 1	protein-coding
mm_36732.1	chr4	99121268	99121278	-	1	NA	promoter-TSS (NM_026082)	promoter-TSS (NM_026082)	-358	NM_026082	67299	Mm.260623	NM_026082	ENSMUSG00000028556	Dock7	3110056M06Rik|Gm430	dedicator of cytokinesis 7	protein-coding
mm_2170.1	chr1	88259392	88259414	+	1	NA	3' UTR (NM_198652, exon 8 of 8)	3' UTR (NM_198652, exon 8 of 8)	10005	NR_040291	78605	Mm.384762	NR_040291		6430706D22Rik	-	RIKEN cDNA 6430706D22 gene	ncRNA
mm_46714.1	chr5	110448440	110448454	-	1	NA	promoter-TSS (NM_001142642)	promoter-TSS (NM_001142642)	56	NM_001317042	381668	Mm.348782	NM_028596	ENSMUSG00000043323	Fbrsl1	2410025L10Rik|AI467568|Gm1049|Gm29766|mKIAA1545	fibrosin-like 1	protein-coding
mm_116399.1	chr13	41235098	41235102	-	1	NA	Intergenic	Intergenic	-14697	NM_019423	54326	Mm.2567	NM_019423	ENSMUSG00000021364	Elovl2	AI317360|Ssc2	elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 2	protein-coding
mm_52160.1	chr6	98019068	98019077	+	1	NA	3' UTR (NM_001178049, exon 10 of 10)	3' UTR (NM_001178049, exon 10 of 10)	27289	NM_008601	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_139650.1	chr17	57389131	57389138	+	1	NA	intron (NM_010130, intron 2 of 21)	RMER15|LTR|ERVL	30448	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_5396.1	chr1	33649154	33649173	-	1	NA	intron (NM_008922, intron 5 of 13)	intron (NM_008922, intron 5 of 13)	20631	NM_008922	19076	Mm.27705	NM_008922	ENSMUSG00000026134	Prim2	AI323589	DNA primase, p58 subunit	protein-coding
mm_133556.1	chr16	91388019	91388042	+	1	NA	exon (NM_010509, exon 5 of 9)	exon (NM_010509, exon 5 of 9)	15247	NM_001110498	15976	Mm.6834	NM_010509	ENSMUSG00000022971	Ifnar2	AI747302|Ifnar-2	interferon (alpha and beta) receptor 2	protein-coding
mm_101179.1	chr11	16995333	16995359	-	1	NA	exon (NM_019549, exon 2 of 10)	exon (NM_019549, exon 2 of 10)	13372	NM_019549	56193	Mm.98232	NM_019549	ENSMUSG00000020120	Plek	2010300B13Rik	pleckstrin	protein-coding
mm_3085.1	chr1	134405985	134406005	+	1	NA	promoter-TSS (NM_028057)	promoter-TSS (NM_028057)	5	NM_028057	72017	Mm.280230	NM_028057	ENSMUSG00000026456	Cyb5r1	1500005G05Rik|B5R.1|C80155|Nqo3a2	cytochrome b5 reductase 1	protein-coding
mm_160637.1	chr9	108461690	108461690	-	1	NA	promoter-TSS (NM_030075)	promoter-TSS (NM_030075)	-109	NM_030075	78267	Mm.283194	NM_030075	ENSMUSG00000032609	Klhdc8b	4931406O17Rik	kelch domain containing 8B	protein-coding
mm_138139.1	chr17	34198386	34198400	+	1	NA	5' UTR (NM_010724, exon 1 of 6)	5' UTR (NM_010724, exon 1 of 6)	198	NM_010724	16913	Mm.180191	NM_010724	ENSMUSG00000024338	Psmb8	Lmp-7|Lmp7	proteasome (prosome, macropain) subunit, beta type 8 (large multifunctional peptidase 7)	protein-coding
mm_61368.1	chr7	69909734	69909741	+	1	NA	Intergenic	Intergenic	413643	NR_045940	73796	Mm.410832	NR_045940	ENSMUSG00000108885	4930402F11Rik	-	RIKEN cDNA 4930402F11 gene	ncRNA
mm_48165.1	chr5	137152906	137152915	-	1	NA	Intergenic	Intergenic	-36703	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_79027.1	chr9	46009262	46009269	+	1	NA	Intergenic	RMER10A|LTR|ERVL	-3555	NM_027498	70661	Mm.219459	NM_027498	ENSMUSG00000034135	Sik3	5730525O22Rik|9030204A07Rik|AI447252|AI846254|AI849445|Qsk|SIK-3|mKIAA0999	SIK family kinase 3	protein-coding
mm_38669.1	chr4	144721432	144721439	-	1	NA	promoter-TSS (NM_001085536)	promoter-TSS (NM_001085536)	-31	NM_001085536	546849	Mm.457885	NM_001085536	ENSMUSG00000041735	Gm13178	Gm437|OTTMUSG00000010750	predicted gene 13178	protein-coding
mm_12863.1	chr2	83805139	83805169	+	1	NA	3' UTR (NM_008402, exon 30 of 30)	3' UTR (NM_008402, exon 30 of 30)	-7574	NM_175514	241520	Mm.330351	NM_175514	ENSMUSG00000048388	Fam171b	D430039N05Rik	family with sequence similarity 171, member B	protein-coding
mm_44125.1	chr5	149636528	149636539	+	1	NA	promoter-TSS (NM_013559)	promoter-TSS (NM_013559)	-197	NM_001347534	15505	Mm.270681	NM_013559	ENSMUSG00000029657	Hsph1	105kDa|AI790491|Hsp105|Hsp110|hsp-E7I|hsp110/105	heat shock 105kDa/110kDa protein 1	protein-coding
mm_66073.1	chr7	30909187	30909239	-	1	NA	exon (NM_001346084, exon 6 of 12)	exon (NM_001346084, exon 6 of 12)	5108	NM_001346089	17136	Mm.241355	NM_010758	ENSMUSG00000036634	Mag	Gma|siglec-4a	myelin-associated glycoprotein	protein-coding
mm_87302.1	chr10	42535043	42535053	+	1	NA	3' UTR (NM_017472, exon 4 of 4)	3' UTR (NM_017472, exon 4 of 4)	32994	NM_017472	54198	Mm.277870	NM_017472	ENSMUSG00000019804	Snx3	SDP3	sorting nexin 3	protein-coding
mm_79145.1	chr9	47700046	47700053	+	1	NA	intron (NM_001025600, intron 1 of 8)	(T)n|Simple_repeat|Simple_repeat	118159	NR_046048	100038460	Mm.447649	NR_046048		Gm10677	ENSMUSG00000074363	predicted gene 10677	ncRNA
mm_112102.1	chr12	112785420	112785449	-	1	NA	Intergenic	Intergenic	-23541	NM_145450	217887	Mm.186678	NM_145450	ENSMUSG00000037594	BC022687	AW050009|C130001I08Rik|Flj20080	cDNA sequence BC022687	protein-coding
mm_73377.1	chr8	105636510	105636589	+	1	NA	promoter-TSS (NM_181322)	promoter-TSS (NM_181322)	11	NM_181322	13018	Mm.269474	NM_181322	ENSMUSG00000005698	Ctcf	AW108038	CCCTC-binding factor	protein-coding
mm_99540.1	chr11	103197678	103197687	+	1	NA	exon (NM_001077698, exon 25 of 26)	exon (NM_001077698, exon 25 of 26)	10866	NM_001254724	69441	Mm.380648	NM_027082	ENSMUSG00000020940	1700023F06Rik	-	RIKEN cDNA 1700023F06 gene	protein-coding
mm_172772.1	chr8	94434341	94434342	+	1	NA	non-coding (NR_015514, exon 2 of 3)	non-coding (NR_015514, exon 2 of 3)	762	NR_015514	320377	Mm.486022	NR_015514		9330175E14Rik	A630085K21	RIKEN cDNA 9330175E14 gene	ncRNA
mm_73200.1	chr8	95677746	95677808	+	1	NA	Intergenic	CpG	-25260	NM_001195006	234593	Mm.29846	NM_145602	ENSMUSG00000036564	Ndrg4	D8Bwg1337e|Ndr1-rs|Ndr4|R74996|SMAP-8	N-myc downstream regulated gene 4	protein-coding
mm_66929.1	chr7	61530060	61530099	-	1	NA	non-coding (NR_045727, exon 5 of 5)	non-coding (NR_045727, exon 5 of 5)	85248	NR_045727	319752	Mm.294476	NR_045727		B230209E15Rik	-	RIKEN cDNA B230209E15 gene	ncRNA
mm_3392.1	chr1	141277714	141277715	+	1	NA	Intergenic	Intergenic	-621312	NR_040604	75910	Mm.483845	NR_040604	ENSMUSG00000102368	4930590L20Rik	-	RIKEN cDNA 4930590L20 gene	ncRNA
mm_118821.1	chr14	25529893	25529916	+	1	NA	intron (NM_001310666, intron 2 of 23)	intron (NM_001310666, intron 2 of 23)	-4535	NR_037236	100526533		NR_037236	ENSMUSG00000093081	Mir3075	mir-3075|mmu-mir-3075	microRNA 3075	ncRNA
mm_171201.1	chr3	54481412	54481424	+	1	NA	Intergenic	Intergenic	120311	NM_015784	50706	Mm.236067	NM_015784	ENSMUSG00000027750	Postn	A630052E07Rik|AI747096|OSF-2|Osf2|PLF|PN	periostin, osteoblast specific factor	protein-coding
mm_114534.1	chr13	73627166	73627183	+	1	NA	exon (NM_009354, exon 1 of 16)	exon (NM_009354, exon 1 of 16)	173	NM_009354	21752	Mm.10109	NM_009354	ENSMUSG00000021611	Tert	EST2|TCS1|TP2|TR|TRT	telomerase reverse transcriptase	protein-coding
mm_60555.1	chr7	44481149	44481174	+	1	NA	Intergenic	Intergenic	-3356	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_160722.1	chr10	69212634	69212634	+	1	NA	promoter-TSS (NM_001081347)	promoter-TSS (NM_001081347)	-23	NM_001081347	69288	Mm.26659	NM_001081347	ENSMUSG00000019944	Rhobtb1	1700008H16Rik|3110048G13Rik|AI173445|AI573858|AV350930	Rho-related BTB domain containing 1	protein-coding
mm_141158.1	chr17	26508190	26508207	-	1	NA	exon (NM_013642, exon 1 of 4)	exon (NM_013642, exon 1 of 4)	274	NM_013642	19252	Mm.239041	NM_013642	ENSMUSG00000024190	Dusp1	3CH134|MKP1|Ptpn16|U19515|erp|mkp-1	dual specificity phosphatase 1	protein-coding
mm_152364.1	chr19	10101502	10101532	-	1	NA	promoter-TSS (NM_019699)	promoter-TSS (NM_019699)	-14	NM_019699	56473	Mm.38901	NM_019699	ENSMUSG00000024665	Fads2	2900042M13Rik|Fadsd2	fatty acid desaturase 2	protein-coding
mm_51489.1	chr6	83056561	83056578	+	1	NA	non-coding (NR_125891, exon 8 of 12)	non-coding (NR_125891, exon 8 of 12)	-1275	NM_033606	93838	Mm.140332	NM_033606	ENSMUSG00000009145	Dqx1	2310066E11Rik	DEAQ RNA-dependent ATPase	protein-coding
mm_172619.1	chr8	20122351	20122374	+	1	NA	Intergenic	CpG	175070	NR_030708	547150	Mm.359054	NR_030708	ENSMUSG00000071796	6820431F20Rik	-	cadherin 11 pseudogene	pseudo
mm_21955.1	chr2	167188772	167188773	-	1	NA	promoter-TSS (NM_008420)	promoter-TSS (NM_008420)	46	NM_008420	16500	Mm.205341	NM_008420	ENSMUSG00000050556	Kcnb1	Kcr1-1|Kv2.1|Shab	potassium voltage gated channel, Shab-related subfamily, member 1	protein-coding
mm_163076.1	chr11	68176866	68176874	+	1	NA	intron (NM_018768, intron 7 of 7)	MER57C2|LTR|ERV1	-44022	NR_105833	102465219		NR_105833	ENSMUSG00000099174	Mir6406	Gm27981|mmu-mir-6406	microRNA 6406	ncRNA
mm_7902.1	chr1	133660807	133660818	-	1	NA	promoter-TSS (NM_001166552)	promoter-TSS (NM_001166552)	73	NM_001166552	667118	Mm.245357	NM_001166552	ENSMUSG00000094410	Zbed6	Gm8466|MGR	zinc finger, BED type containing 6	protein-coding
mm_49253.1	chr6	17340089	17340096	+	1	NA	3' UTR (NM_001243064, exon 2 of 2)	3' UTR (NM_001243064, exon 2 of 2)	32452	NM_001243064	12389	Mm.28278	NM_007616	ENSMUSG00000007655	Cav1	Cav|Cav-1	caveolin 1, caveolae protein	protein-coding
mm_76466.1	chr8	85380965	85380984	-	1	NA	promoter-TSS (NM_001297612)	promoter-TSS (NM_001297612)	67	NM_001297612	213435	Mm.32804	NM_175441	ENSMUSG00000031698	Mylk3	D830007F02Rik|MLCK	myosin light chain kinase 3	protein-coding
mm_63430.1	chr7	127478797	127478839	+	1	NA	Intergenic	Intergenic	-6403	NM_010183	14123	Mm.323505	NM_010183	ENSMUSG00000042423	Fbrs	Fbs|Fbs1	fibrosin	protein-coding
mm_129974.1	chr15	85811664	85811705	-	1	NA	promoter-TSS (NM_001164626)	promoter-TSS (NM_001164626)	13	NM_001164626	72355	Mm.33706	NM_197998	ENSMUSG00000064284	Cdpf1	2210021J22Rik	cysteine rich, DPF motif domain containing 1	protein-coding
mm_60258.1	chr7	43797568	43797586	+	1	NA	promoter-TSS (NM_008940)	promoter-TSS (NM_008940)	0	NM_001324398	259277	Mm.458023	NM_008940	ENSMUSG00000064023	Klk8	BSP1|NP|Nrpn|Prss19	kallikrein related-peptidase 8	protein-coding
mm_79398.1	chr9	54950783	54950797	+	1	NA	promoter-TSS (NM_011966)	promoter-TSS (NM_011966)	-69	NM_011966	26441	Mm.30270	NM_011966	ENSMUSG00000032301	Psma4	C9	proteasome (prosome, macropain) subunit, alpha type 4	protein-coding
mm_16477.1	chr2	180738198	180738223	+	1	NA	intron (NM_183161, intron 8 of 12)	intron (NM_183161, intron 8 of 12)	12871	NM_183161	228993	Mm.87189	NM_183161	ENSMUSG00000023393	Slc17a9	1700019H03Rik|BC019537|Vnut	solute carrier family 17, member 9	protein-coding
mm_155021.1	chrX	42060423	42060439	+	1	NA	Intergenic	ORR1A3|LTR|ERVL-MaLR	-7405	NM_009688	11798	Mm.259879	NM_009688	ENSMUSG00000025860	Xiap	1110015C02Rik|Aipa|Api3|Birc4|IAP3|ILP-1|MIHA	X-linked inhibitor of apoptosis	protein-coding
mm_38298.1	chr4	136896162	136896185	-	1	NA	exon (NM_007572, exon 3 of 3)	exon (NM_007572, exon 3 of 3)	2671	NM_007572	12259	Mm.439957	NM_007572	ENSMUSG00000036887	C1qa	AI255395|C1q	complement component 1, q subcomponent, alpha polypeptide	protein-coding
mm_19705.1	chr2	103783160	103783172	-	1	NA	exon (NM_016739, exon 3 of 19)	exon (NM_016739, exon 3 of 19)	13912	NM_001111290	53872	Mm.427589	NM_016739	ENSMUSG00000027184	Caprin1	AL022980|Caprin-1|Gpiap|Gpiap1|Mmgpip137|P137|rng105	cell cycle associated protein 1	protein-coding
mm_158782.1	chrX	167207283	167207294	-	1	NA	3' UTR (NM_021278, exon 3 of 3)	3' UTR (NM_021278, exon 3 of 3)	1930	NM_021278	19241	Mm.142729	NM_021278	ENSMUSG00000049775	Tmsb4x	Ptmb4|Tb4	thymosin, beta 4, X chromosome	protein-coding
mm_29228.1	chr3	107213436	107213450	-	1	NA	exon (NM_001111143, exon 7 of 9)	exon (NM_001111143, exon 7 of 9)	8289	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_52281.1	chr6	108660617	108660682	+	1	NA	promoter-TSS (NM_011498)	promoter-TSS (NM_011498)	20	NM_011498	20893	Mm.2436	NM_011498	ENSMUSG00000030103	Bhlhe40	Bhlhb2|C130042M06Rik|CR8|Clast5|Dec1|Sharp2|Stra13|Stra14	basic helix-loop-helix family, member e40	protein-coding
mm_132320.1	chr16	33794009	33794030	+	1	NA	promoter-TSS (NM_010739)	promoter-TSS (NM_010739)	-18	NM_010739	17063	Mm.3177	NM_010739	ENSMUSG00000022824	Muc13	114/A10|14/A10|AI159736|Lrrp|Ly64|NJ-1	mucin 13, epithelial transmembrane	protein-coding
mm_87221.1	chr10	40349266	40349387	+	1	NA	promoter-TSS (NM_001168304)	promoter-TSS (NM_001168304)	18	NM_001291816	78334	Mm.200924	NM_198164	ENSMUSG00000038481	Cdk19	2700084L06Rik|AI845279|AW228747|CDK11|Cdc2l6|mKIAA1028	cyclin-dependent kinase 19	protein-coding
mm_69175.1	chr7	127218372	127218380	-	1	NA	promoter-TSS (NM_017461)	promoter-TSS (NM_017461)	69	NM_017461	54204	Mm.18	NM_017461	ENSMUSG00000000486	Sept1	Diff6|Pnutl3	septin 1	protein-coding
mm_89832.1	chr10	106615781	106615795	+	1	NA	intron (NM_001205341, intron 3 of 31)	B4A|SINE|B4	-13308	NR_131026	75833	Mm.159596	NR_131026		4930532I03Rik	-	RIKEN cDNA 4930532I03 gene	ncRNA
mm_47455.1	chr5	123612154	123612178	-	1	NA	intron (NM_001347468, intron 15 of 24)	intron (NM_001347468, intron 15 of 24)	-39151	NM_029929	77573	Mm.41372	NM_029929	ENSMUSG00000029434	Vps33a	3830421M04Rik|AI503300|AW048546|AW554476|bf	VPS33A CORVET/HOPS core subunit	protein-coding
mm_9401.1	chr1	172234636	172234655	-	1	NA	intron (NM_013734, intron 14 of 22)	intron (NM_013734, intron 14 of 22)	-14750	NM_009813	12372	Mm.12829	NM_009813	ENSMUSG00000007122	Casq1	CSQ|CSQ-1|CSQ1|sCSQ	calsequestrin 1	protein-coding
mm_19864.1	chr2	113848656	113848744	-	1	NA	promoter-TSS (NM_181416)	promoter-TSS (NM_181416)	-39	NM_181416	228482	Mm.45753	NM_181416	ENSMUSG00000041219	Arhgap11a	6530401L14Rik|mKIAA0013	Rho GTPase activating protein 11A	protein-coding
mm_47011.1	chr5	115474711	115474717	-	1	NA	TTS (NM_011107)	TTS (NM_011107)	8448	NM_011107	18778	Mm.20190	NM_011107	ENSMUSG00000029522	Pla2g1b	Pla2a|sPLA2IB	phospholipase A2, group IB, pancreas	protein-coding
mm_160942.1	chr11	95145644	95145644	-	1	NA	5' UTR (NM_007867, exon 1 of 3)	5' UTR (NM_007867, exon 1 of 3)	157	NM_007867	13394	Mm.439766	NM_007867	ENSMUSG00000020871	Dlx4	Dlx-4|Dlx7	distal-less homeobox 4	protein-coding
mm_142301.1	chr17	42692245	42692289	-	1	NA	promoter-TSS (NM_001289499)	promoter-TSS (NM_001289499)	17	NM_001289501	78249	Mm.66217	NM_030067	ENSMUSG00000023918	Adgrf4	4632435A09Rik|AV239010|Gpr115	adhesion G protein-coupled receptor F4	protein-coding
mm_48584.1	chr5	143732216	143732272	-	1	NA	promoter-TSS (NM_029749)	promoter-TSS (NM_029749)	36	NM_029749	76800	Mm.259620	NM_029749	ENSMUSG00000051306	Usp42	2410140K03Rik|3110031A07Rik|A630018G05Rik|D5Ertd591e	ubiquitin specific peptidase 42	protein-coding
mm_130530.1	chr15	98918132	98918142	-	1	NA	promoter-TSS (NM_029098)	promoter-TSS (NM_029098)	-39	NM_029098	74775	Mm.385020	NM_029098	ENSMUSG00000022999	Lmbr1l	1110013E13Rik|AA415653|D15Ertd735e|Limr	limb region 1 like	protein-coding
mm_124792.1	chr15	8112663	8112665	+	1	NA	intron (NM_133227, intron 2 of 34)	intron (NM_133227, intron 2 of 34)	3351	NM_133227	170762	Mm.295168	NM_133227	ENSMUSG00000022142	Nup155	D930027M19Rik|mKIAA0791	nucleoporin 155	protein-coding
mm_65832.1	chr7	29180455	29180532	-	1	NA	exon (NM_026545, exon 1 of 7)	exon (NM_026545, exon 1 of 7)	180	NM_026545	57296	Mm.273152	NM_026545	ENSMUSG00000030591	Psmd8	6720456J22Rik|AA407360|AL033291|AL033322|AL033323|C76433	proteasome (prosome, macropain) 26S subunit, non-ATPase, 8	protein-coding
mm_141435.1	chr17	29519824	29519853	-	1	NA	Intergenic	Intergenic	28793	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_91819.1	chr10	55563561	55563563	-	1	NA	Intergenic	L1MA9|LINE|L1	-543355	NM_001163833	73390	Mm.181475	NM_133751	ENSMUSG00000047669	Msl3l2	1700060H10Rik	male-specific lethal 3-like 2 (Drosophila)	protein-coding
mm_149266.1	chr19	10577465	10577475	+	1	NA	promoter-TSS (NM_028411)	promoter-TSS (NM_028411)	-84	NR_126092	72982	Mm.391194	NM_028411	ENSMUSG00000024666	Tmem138	1700113I01Rik|2900055D14Rik	transmembrane protein 138	protein-coding
mm_159775.1	chr5	103911186	103911186	-	1	NA	promoter-TSS (NM_178741)	promoter-TSS (NM_178741)	43	NM_178741	246293	Mm.179871	NM_178741	ENSMUSG00000029312	Klhl8	2310001P09Rik|D5Ertd431e	kelch-like 8	protein-coding
mm_51861.1	chr6	90486378	90486388	+	1	NA	Intergenic	Intergenic	23757	NM_023184	66277	Mm.38343	NM_023184	ENSMUSG00000030087	Klf15	1810013I09Rik|AV048136|AW494632|CKLF|KKLF	Kruppel-like factor 15	protein-coding
mm_44063.1	chr5	148399634	148399639	+	1	NA	intron (NM_007513, intron 1 of 12)	CpG	268	NM_007513	11987	Mm.275489	NM_007513	ENSMUSG00000041313	Slc7a1	4831426K01Rik|AI447493|Atrc-1|Atrc1|Cat1|Rec-1|Rev-1|mCAT-1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 1	protein-coding
mm_67216.1	chr7	74448345	74448379	-	1	NA	intron (NM_001038643, intron 2 of 10)	B4|SINE|B4	106418	NM_023908	108116	Mm.425467	NM_023908	ENSMUSG00000025790	Slco3a1	5830414C08Rik|Anr1|MJAM|OATP-D|R75096|Slc21a11	solute carrier organic anion transporter family, member 3a1	protein-coding
mm_146598.1	chr18	9450067	9450075	-	1	NA	promoter-TSS (NM_026484)	promoter-TSS (NM_026484)	79	NM_026484	67974	Mm.86523	NM_026484	ENSMUSG00000024286	Ccny	1700025H17Rik|3110050L10Rik|4631402G10Rik|5730405I09Rik	cyclin Y	protein-coding
mm_109377.1	chr12	109700089	109700093	+	1	NA	Intergenic	HAL1|LINE|L1	-8969	NR_029880	723858		NR_029880	ENSMUSG00000065498	Mir379	Mirn379|mir-379|mmu-mir-379	microRNA 379	ncRNA
mm_57869.1	chr6	129678810	129678820	-	1	NA	exon (NM_001288664, exon 1 of 6)	exon (NM_001288664, exon 1 of 6)	158	NM_001288664	16641	Mm.56899	NM_010652	ENSMUSG00000030167	Klrc1	CD159a|NKG2A|NKG2B	killer cell lectin-like receptor subfamily C, member 1	protein-coding
mm_70607.1	chr8	13404941	13404950	+	1	NA	promoter-TSS (NM_011881)	promoter-TSS (NM_011881)	-136	NM_011881	24013	Mm.257501	NM_011881	ENSMUSG00000031450	Grk1	Gprk1|Rhok|Rk	G protein-coupled receptor kinase 1	protein-coding
mm_156023.1	chrX	107149033	107149051	+	1	NA	promoter-TSS (NM_175442)	promoter-TSS (NM_175442)	115	NM_001122596	213438	Mm.265244	NM_175442	ENSMUSG00000054293	A630033H20Rik	AI662791|P2ry10	RIKEN cDNA A630033H20 gene	protein-coding
mm_93924.1	chr10	127136646	127136654	-	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-15490	NM_001171026	216440	Mm.295246	NM_177614	ENSMUSG00000040462	Os9	4632413K17Rik|AU022351	amplified in osteosarcoma	protein-coding
mm_140569.1	chr17	8566582	8566621	-	1	NA	intron (NM_001290707, intron 1 of 22)	intron (NM_001290707, intron 1 of 22)	39800	NM_001290707	23984	Mm.87161	NM_011866	ENSMUSG00000023868	Pde10a	-	phosphodiesterase 10A	protein-coding
mm_158414.1	chrX	137117276	137117306	-	1	NA	exon (NM_007957, exon 4 of 5)	exon (NM_007957, exon 4 of 5)	3035	NM_007957	13984	Mm.8017	NM_007957	ENSMUSG00000023443	Esx1	Spx1	extraembryonic, spermatogenesis, homeobox 1	protein-coding
mm_3454.1	chr1	150103666	150103688	+	1	NA	exon (NM_011198, exon 6 of 10)	exon (NM_011198, exon 6 of 10)	3646	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_150036.1	chr19	29377251	29377261	+	1	NA	intron (NM_021893, intron 3 of 6)	intron (NM_021893, intron 3 of 6)	9818	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_4456.1	chr1	172699135	172699146	+	1	NA	3' UTR (NM_007768, exon 2 of 2)	3' UTR (NM_007768, exon 2 of 2)	1084	NM_007768	12944	Mm.28767	NM_007768	ENSMUSG00000037942	Crp	AI255847	C-reactive protein, pentraxin-related	protein-coding
mm_9622.1	chr1	176754413	176754423	-	1	NA	intron (NM_001099637, intron 13 of 19)	intron (NM_001099637, intron 13 of 19)	18005	NR_029775	723921		NR_029775	ENSMUSG00000065573	Mir350	Mirn350|mir-350|mmu-mir-350	microRNA 350	ncRNA
mm_60906.1	chr7	46751833	46751835	+	1	NA	promoter-TSS (NM_011314)	promoter-TSS (NM_011314)	1	NM_011314	20209	Mm.200941	NM_011314	ENSMUSG00000057465	Saa2	AW111173|Saa-2|Saa1	serum amyloid A 2	protein-coding
mm_50830.1	chr6	54681688	54681783	+	1	NA	5' UTR (NM_001289741, exon 1 of 5)	5' UTR (NM_001289741, exon 1 of 5)	111	NM_001289740	68235	Mm.233860	NM_026629	ENSMUSG00000038065	Mturn	2410066E13Rik|AI448550|B230212L03Rik	maturin, neural progenitor differentiation regulator homolog (Xenopus)	protein-coding
mm_113601.1	chr13	41236290	41236300	+	1	NA	Intergenic	Intergenic	-13549	NM_001135577	108934	Mm.38578	NM_001135577	ENSMUSG00000091264	Smim13	2900036K02Rik	small integral membrane protein 13	protein-coding
mm_83328.1	chr9	44233902	44233912	-	1	NA	5' UTR (NM_007619, exon 1 of 16)	5' UTR (NM_007619, exon 1 of 16)	139	NM_007619	12402	Mm.266871	NM_007619	ENSMUSG00000034342	Cbl	4732447J05Rik|Cbl-2|c-Cbl|cbl	Casitas B-lineage lymphoma	protein-coding
mm_89808.1	chr10	103334554	103334586	+	1	NA	Intergenic	Intergenic	-33238	NM_001252330	103098	Mm.458408	NM_175328	ENSMUSG00000019894	Slc6a15	AA536730|AI326450|AI326451|v7-3	solute carrier family 6 (neurotransmitter transporter), member 15	protein-coding
mm_156116.1	chrX	114897782	114897783	+	1	NA	Intergenic	MT2B2|LTR|ERVL	-7230	NM_001276396	237009	Mm.302216	NM_207241	ENSMUSG00000050435	Ube2dnl1	Ube2dnl	ubiquitin-conjugating enzyme E2D N-terminal like 1	protein-coding
mm_88993.1	chr10	81565959	81565977	+	1	NA	non-coding (NR_074087, exon 7 of 7)	non-coding (NR_074087, exon 7 of 7)	6524	NM_001276288	14797	Mm.180013	NM_010347	ENSMUSG00000054452	Aes	AL024115|Esp1|Grg|Grg-5|Grg5|Tle5	amino-terminal enhancer of split	protein-coding
mm_162836.1	chr10	84293201	84293203	-	1	NA	Intergenic	Intergenic	147269	NM_001004363	77976	Mm.25874	NM_001004363	ENSMUSG00000020032	Nuak1	AU014801|AW494241|B230104P22Rik|Omphk1	NUAK family, SNF1-like kinase, 1	protein-coding
mm_164347.1	chr16	17181637	17181647	+	1	NA	intron (NM_009456, intron 1 of 3)	L3|LINE|CR1	19850	NM_009456	22195	Mm.3074	NM_009456	ENSMUSG00000038965	Ube2l3	C79827|UbcM4|Ubce7	ubiquitin-conjugating enzyme E2L 3	protein-coding
mm_15673.1	chr2	163491656	163491677	+	1	NA	promoter-TSS (NM_001099331)	promoter-TSS (NM_001099331)	-652	NM_001099331	100043899	Mm.442535	NM_001099331	ENSMUSG00000078949	R3hdml	OTTMUSG00000001070	R3H domain containing-like	protein-coding
mm_104759.1	chr11	98477122	98477152	-	1	NA	intron (NM_011771, intron 6 of 7)	intron (NM_011771, intron 6 of 7)	30303	NM_010346	14786	Mm.276702	NM_010346	ENSMUSG00000019312	Grb7	mKIAA4028	growth factor receptor bound protein 7	protein-coding
mm_8875.1	chr1	162860061	162860077	-	1	NA	promoter-TSS (NM_001330291)	promoter-TSS (NM_001330291)	-69	NM_001330318	14261	Mm.976	NM_010231	ENSMUSG00000040181	Fmo1	-	flavin containing monooxygenase 1	protein-coding
mm_125565.1	chr15	59275357	59275374	+	1	NA	Intergenic	Intergenic	-31583	NR_045613	100416830	Mm.490788	NR_045613	ENSMUSG00000098528	Zfp572	4930472F24Rik	zinc finger protein 572	pseudo
mm_25742.1	chr3	122924421	122924459	+	1	NA	promoter-TSS (NM_024461)	promoter-TSS (NM_024461)	43	NM_024461	67704	Mm.24219	NM_024461	ENSMUSG00000054091	1810037I17Rik	5730414I01Rik	RIKEN cDNA 1810037I17 gene	protein-coding
mm_36075.1	chr4	58009118	58009133	-	1	NA	promoter-TSS (NM_026132)	promoter-TSS (NM_026132)	-1	NM_026132	67402	Mm.87357	NM_026132	ENSMUSG00000038709	Txndc8	4930429J24Rik|Sptrx-3|Sptrx3|Trx6	thioredoxin domain containing 8	protein-coding
mm_83541.1	chr9	46234515	46234533	-	1	NA	exon (NM_001289755, exon 3 of 4)	exon (NM_001289755, exon 3 of 4)	775	NM_001289833	11814	Mm.390161	NM_023114	ENSMUSG00000032081	Apoc3	apo-CIII|apoC-III	apolipoprotein C-III	protein-coding
mm_26020.1	chr3	135438475	135438485	+	1	NA	promoter-TSS (NM_025356)	promoter-TSS (NM_025356)	185	NR_030689	319587	Mm.358971	NR_030689	ENSMUSG00000097032	4930539J05Rik	8030475D13Rik	RIKEN cDNA 4930539J05 gene	ncRNA
mm_133545.1	chr16	91225564	91225579	+	1	NA	promoter-TSS (NM_016967)	promoter-TSS (NM_016967)	21	NM_016967	50913	Mm.37289	NM_016967	ENSMUSG00000039830	Olig2	AI604895|Bhlhb1|Olg-2|Oligo2|RK17|bHLHe19	oligodendrocyte transcription factor 2	protein-coding
mm_12353.1	chr2	69749529	69749550	+	1	NA	exon (NM_001081086, exon 14 of 14)	exon (NM_001081086, exon 14 of 14)	26451	NM_001081086	228005	Mm.11815	NM_001081086	ENSMUSG00000042133	Ppig	AU019516|AU022200|B230312B02Rik|CYP|SRCyp	peptidyl-prolyl isomerase G (cyclophilin G)	protein-coding
mm_108545.1	chr12	84362002	84362018	+	1	NA	promoter-TSS (NM_172581)	promoter-TSS (NM_172581)	42	NM_172582	217707	Mm.280062	NM_172582	ENSMUSG00000021235	Coq6	5930427M12Rik|AW742344	coenzyme Q6 monooxygenase	protein-coding
mm_78734.1	chr9	41583025	41583042	+	1	NA	intron (NR_015483, intron 1 of 1)	intron (NR_015483, intron 1 of 1)	1107	NR_029822	387236		NR_029822	ENSMUSG00000093354	Mir125b-1	Mirn125b|Mirn125b-1|mir-125b-1	microRNA 125b-1	ncRNA
mm_118698.1	chr14	22141504	22141548	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	121814	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_32009.1	chr4	94739277	94739298	+	1	NA	promoter-TSS (NM_001290551)	promoter-TSS (NM_001290551)	-2	NM_001290549	21687	Mm.14313	NM_013690	ENSMUSG00000006386	Tek	AA517024|Cd202b|Hyk|STK1|Tie-2|Tie2	endothelial-specific receptor tyrosine kinase	protein-coding
mm_108647.1	chr12	85960407	85960409	+	1	NA	intron (NM_001347395, intron 29 of 32)	intron (NM_001347395, intron 29 of 32)	118633	NM_009368	21809	Mm.3992	NM_009368	ENSMUSG00000021253	Tgfb3	TGF-beta-3|Tgfb-3	transforming growth factor, beta 3	protein-coding
mm_25904.1	chr3	131112227	131112249	+	1	NA	promoter-TSS (NM_001276403)	promoter-TSS (NM_001276403)	-553	NM_001276403	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_172945.1	chr9	81677936	81677952	+	1	NA	Intergenic	Intergenic	-45392	NM_010482	15551	Mm.445308	NM_010482	ENSMUSG00000049511	Htr1b	-	5-hydroxytryptamine (serotonin) receptor 1B	protein-coding
mm_144461.1	chr18	23472280	23472280	+	1	NA	intron (NM_010087, intron 1 of 11)	intron (NM_010087, intron 1 of 11)	-25202	NM_001285808	13527	Mm.94371	NM_010087	ENSMUSG00000024302	Dtna	2210407P21Rik|DTN-A|Dtn|Gm19389|a-DB-1|adbn	dystrobrevin alpha	protein-coding
mm_139369.1	chr17	51569481	51569481	+	1	NA	intron (NR_037250, intron 3 of 4)	PB1D10|SINE|Alu	-121212	NR_046166	328837	Mm.236143	NR_046166		C330011F03Rik	C330011F03	RIKEN cDNA C330011F03 gene	ncRNA
mm_80680.1	chr9	91097043	91097043	+	1	NA	Intergenic	Lx2|LINE|L1	268756	NM_009573	22771	Mm.335350	NM_009573	ENSMUSG00000032368	Zic1	ZIC|ZNF201	zinc finger protein of the cerebellum 1	protein-coding
mm_105465.1	chr11	105181368	105181387	-	1	NA	promoter-TSS (NR_027956)	promoter-TSS (NR_027956)	56	NR_027956	73431	Mm.351426	NM_028539		1700052K11Rik	AI840954	RIKEN cDNA 1700052K11 gene	ncRNA
mm_120998.1	chr14	79451792	79451840	+	1	NA	promoter-TSS (NM_001034882)	promoter-TSS (NM_001034882)	-19	NM_001034882	432879	Mm.308666	NM_001034882	ENSMUSG00000075502	Kbtbd6	EG432879|Gm5465|Zbtbd6	kelch repeat and BTB (POZ) domain containing 6	protein-coding
mm_118788.1	chr14	24118765	24118768	+	1	NA	Intergenic	Intergenic	29889	NR_106069	102465697		NR_106069	ENSMUSG00000105723	Mir7210	mir-7210|mmu-mir-7210	microRNA 7210	ncRNA
mm_3689.1	chr1	153751867	153751876	+	1	NA	5' UTR (NM_011882, exon 2 of 9)	5' UTR (NM_011882, exon 2 of 9)	2445	NM_011882	24014	Mm.259254	NM_011882	ENSMUSG00000066800	Rnasel	E230029I04Rik	ribonuclease L (2', 5'-oligoisoadenylate synthetase-dependent)	protein-coding
mm_6294.1	chr1	71029958	71029997	-	1	NA	3' UTR (NM_007525, exon 11 of 11)	3' UTR (NM_007525, exon 11 of 11)	72995	NM_007525	12021	Mm.10764	NM_007525	ENSMUSG00000026196	Bard1	ENSMUSG00000060893|ENSMUSG00000073653	BRCA1 associated RING domain 1	protein-coding
mm_107247.1	chr12	27183206	27183248	+	1	NA	Intergenic	Intergenic	-22711	NR_045870	636791	Mm.423496	NM_001039248	ENSMUSG00000094002	Gm9866	EG636791|ENSMUSG00000052076	predicted gene 9866	ncRNA
mm_54121.1	chr6	18109114	18109118	-	1	NA	promoter-TSS (NM_023729)	promoter-TSS (NM_023729)	-55	NM_023729	74068	Mm.73091	NM_023729	ENSMUSG00000010796	Asz1	4933400N19Rik|Gasz|ORF3	ankyrin repeat, SAM and basic leucine zipper domain containing 1	protein-coding
mm_146185.1	chr18	75820175	75820210	+	1	NA	promoter-TSS (NM_145356)	promoter-TSS (NM_145356)	14	NM_145356	207259	Mm.159332	NM_145356	ENSMUSG00000044646	Zbtb7c	B230208J24Rik|Kr-pok|Zbtb36	zinc finger and BTB domain containing 7C	protein-coding
mm_112613.1	chr13	15463596	15463607	+	1	NA	promoter-TSS (NM_008130)	promoter-TSS (NM_008130)	-122	NM_008130	14634	Mm.5098	NM_008130	ENSMUSG00000021318	Gli3	AI854843|AU023367|Bph|GLI3-190|GLI3FL|Pdn|Xt|add	GLI-Kruppel family member GLI3	protein-coding
mm_70986.1	chr8	27260498	27260509	+	1	NA	exon (NM_007918, exon 1 of 3)	exon (NM_007918, exon 1 of 3)	176	NM_007918	13685	Mm.6700	NM_007918	ENSMUSG00000031490	Eif4ebp1	4e-bp1|AA959816|PHAS-I	eukaryotic translation initiation factor 4E binding protein 1	protein-coding
mm_113420.1	chr13	34037620	34037655	+	1	NA	promoter-TSS (NM_026512)	promoter-TSS (NM_026512)	-4	NM_026512	68021	Mm.140243	NM_026512	ENSMUSG00000038286	Bphl	2010012D11Rik|5730533B08Rik|AI115341	biphenyl hydrolase-like (serine hydrolase, breast epithelial mucin-associated antigen)	protein-coding
mm_85230.1	chr9	97743591	97743593	-	1	NA	intron (NM_022319, intron 2 of 17)	intron (NM_022319, intron 2 of 17)	-259828	NR_110443	66737	Mm.445908	NR_110443	ENSMUSG00000090255	4921534H16Rik	-	RIKEN cDNA 4921534H16 gene	ncRNA
mm_172621.1	chr8	20148946	20148949	+	1	NA	Intergenic	B3|SINE|B2	148485	NR_030708	547150	Mm.359054	NR_030708	ENSMUSG00000071796	6820431F20Rik	-	cadherin 11 pseudogene	pseudo
mm_82001.1	chr9	121675244	121675259	+	1	NA	Intergenic	ORR1D2|LTR|ERVL-MaLR	29778	NM_001164562	215474	Mm.31421	NM_178677	ENSMUSG00000061536	Sec22c	4932412K21|5930407I15Rik|C530046H07|Sec22l3	SEC22 homolog C, vesicle trafficking protein	protein-coding
mm_103225.1	chr11	70669284	70669304	-	1	NA	TTS (NM_001190378)	TTS (NM_001190378)	122	NM_172561	216873	Mm.432524	NM_172561	ENSMUSG00000018287	Spag7	5730443G10|ACRP|FSA-1|Fsa1l	sperm associated antigen 7	protein-coding
mm_129902.1	chr15	83920172	83920189	-	1	NA	promoter-TSS (NM_001161629)	promoter-TSS (NM_001161629)	-807	NM_001161629	77627	Mm.196288	NM_029946	ENSMUSG00000022441	Efcab6	4931407K02Rik|4932408N08Rik|bM150J22.2|mKIAA1672	EF-hand calcium binding domain 6	protein-coding
mm_14945.1	chr2	151842913	151842934	+	1	NA	promoter-TSS (NM_001040689)	promoter-TSS (NM_001040689)	-4	NM_001040689	228770	Mm.159868	NM_001040689	ENSMUSG00000032852	Rspo4	A730099F22|A930029K19Rik	R-spondin 4	protein-coding
mm_150353.1	chr19	34647917	34647921	+	1	NA	exon (NM_008331, exon 2 of 2)	exon (NM_008331, exon 2 of 2)	7030	NM_008331	15957	Mm.439751	NM_008331	ENSMUSG00000034459	Ifit1	ISG56|Ifi56|P56	interferon-induced protein with tetratricopeptide repeats 1	protein-coding
mm_51885.1	chr6	90601976	90601987	+	1	NA	Intergenic	Intergenic	-2899	NM_027868	71699	Mm.272633	NM_027868	ENSMUSG00000030089	Slc41a3	1010001P06Rik|AI480742|SLC41A1-L2	solute carrier family 41, member 3	protein-coding
mm_165151.1	chr2	20598441	20598444	+	1	NA	intron (NM_029895, intron 3 of 18)	intron (NM_029895, intron 3 of 18)	78929	NM_001177631	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding
mm_117766.1	chr13	96471180	96471190	-	1	NA	promoter-TSS (NM_001042714)	promoter-TSS (NM_001042714)	-25	NM_001042714	271144	Mm.470057	NM_001042714	ENSMUSG00000047117	Ankdd1b	9330128J19Rik	ankyrin repeat and death domain containing 1B	protein-coding
mm_77060.1	chr8	109693203	109693211	-	1	NA	promoter-TSS (NM_028018)	promoter-TSS (NM_028018)	87	NM_028018	71955	Mm.290036	NM_028018	ENSMUSG00000031729	Ist1	2400003C14Rik|AW536298|mKIAA0174	increased sodium tolerance 1 homolog (yeast)	protein-coding
mm_51739.1	chr6	87277702	87277730	+	1	NA	intron (NM_054041, intron 8 of 17)	intron (NM_054041, intron 8 of 17)	58059	NM_054041	69538	Mm.232525	NM_054041	ENSMUSG00000033420	Antxr1	2310008J16Rik|2810405N18Rik|Antrx1|Tem8	anthrax toxin receptor 1	protein-coding
mm_161685.1	chr17	20502460	20502460	+	1	NA	exon (NM_134194, exon 1 of 1)	exon (NM_134194, exon 1 of 1)	161	NM_134194	171228	Mm.377186	NM_134194	ENSMUSG00000043537	Vmn1r225	V1re5	vomeronasal 1 receptor 225	protein-coding
mm_45130.1	chr5	48781026	48781061	-	1	NA	intron (NM_001199244, intron 1 of 7)	intron (NM_001199244, intron 1 of 7)	108514	NM_030265	80334	Mm.160172	NM_030265	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding
mm_126336.1	chr15	79897707	79897757	+	1	NA	exon (NM_001160415, exon 3 of 9)	exon (NM_001160415, exon 3 of 9)	2709	NM_001347041	80287	Mm.284059	NM_030255	ENSMUSG00000009585	Apobec3	Apobec|Arp3|BC003314|Cem15|Rfv3	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 3	protein-coding
mm_136252.1	chr16	90946859	90946861	-	1	NA	exon (NM_001045515, exon 29 of 33)	exon (NM_001045515, exon 29 of 33)	-12011	NM_026502	68001	Mm.45374	NM_026502	ENSMUSG00000022972	1110004E09Rik	-	RIKEN cDNA 1110004E09 gene	protein-coding
mm_22907.1	chr3	30995755	30995868	+	1	NA	promoter-TSS (NM_008857)	promoter-TSS (NM_008857)	40	NM_008857	18759	Mm.291554	NM_008857	ENSMUSG00000037643	Prkci	2310021H13Rik|AI427505|PKClambda|Pkci|Pkcl|Prkcl|aPKClambda|mKIAA4165	protein kinase C, iota	protein-coding
mm_16199.1	chr2	173021896	173021906	+	1	NA	promoter-TSS (NM_019547)	promoter-TSS (NM_019547)	-1	NM_019547	56190	Mm.485782	NM_019547	ENSMUSG00000027510	Rbm38	Rnpc1|Seb4|Seb4l	RNA binding motif protein 38	protein-coding
mm_97728.1	chr11	80389417	80389419	+	1	NA	intron (NM_001130170, intron 5 of 10)	intron (NM_001130170, intron 5 of 10)	6139	NM_001130171	22680	Mm.401332	NM_011751	ENSMUSG00000017421	Zfp207	8430401D15Rik|BuGZ|Zep|Znf207	zinc finger protein 207	protein-coding
mm_167496.1	chr9	13296585	13296601	+	1	NA	Intergenic	Intergenic	49637	NM_025534	66396	Mm.290620	NM_025534	ENSMUSG00000079084	Ccdc82	2310043N13Rik	coiled-coil domain containing 82	protein-coding
mm_169086.1	chr1	33680071	33680073	-	1	NA	Intergenic	LTRIS2|LTR|ERV1	10248	NR_033199	67503	Mm.87069	NM_026204	ENSMUSG00000103746	1700001G17Rik	-	RIKEN cDNA 1700001G17 gene	ncRNA
mm_115979.1	chr13	24222146	24222148	-	1	NA	intron (NM_001311122, intron 2 of 37)	ID_B1|SINE|B4	58643	NM_001311122	68732	Mm.211047	NM_026825	ENSMUSG00000021338	Carmil1	1110037D04Rik|AI425970|CARMIL|CARML1|D130057M20|Lrrc16|Lrrc16a	capping protein regulator and myosin 1 linker 1	protein-coding
mm_4961.1	chr1	191267078	191267091	+	1	NA	Intergenic	Intergenic	51034	NM_025424	66208	Mm.46444	NM_025424	ENSMUSG00000037499	Nenf	1110060M21Rik|SCIRP10|Spuf	neuron derived neurotrophic factor	protein-coding
mm_26674.1	chr3	154796268	154796276	+	1	NA	intron (NM_177066, intron 23 of 24)	intron (NM_177066, intron 23 of 24)	85139	NM_175176	209601	Mm.331454	NM_175176	ENSMUSG00000078161	Erich3	1700013E18Rik|4922501L14Rik|5031409G23Rik|AI596448|Gm133	glutamate rich 3	protein-coding
mm_19092.1	chr2	79369104	79369127	-	1	NA	intron (NM_001048176, intron 2 of 12)	intron (NM_001048176, intron 2 of 12)	59873	NM_001048176	228094	Mm.440704	NM_001033295	ENSMUSG00000075256	Cerkl	Gm1958|Rp26	ceramide kinase-like	protein-coding
mm_68962.1	chr7	126583178	126583255	-	1	NA	promoter-TSS (NM_009907)	promoter-TSS (NM_009907)	20	NM_001329789	12752	Mm.268930	NM_009907	ENSMUSG00000030720	Cln3	AI323623	ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease)	protein-coding
mm_13885.1	chr2	120013164	120013211	+	1	NA	intron (NM_011941, intron 7 of 29)	intron (NM_011941, intron 7 of 29)	-4330	NR_106125	102466842		NR_106125	ENSMUSG00000098632	Mir7665	Gm27478|mmu-mir-7665	microRNA 7665	ncRNA
mm_101282.1	chr11	21571787	21571797	-	1	NA	promoter-TSS (NM_145425)	promoter-TSS (NM_145425)	142	NM_008618	17449	Mm.212703	NM_008618	ENSMUSG00000020321	Mdh1	B230377B03Rik|D17921|MDH-s|MDHA|Mor-2|Mor2	malate dehydrogenase 1, NAD (soluble)	protein-coding
mm_130581.1	chr15	99534865	99534882	-	1	NA	Intergenic	Lx8|LINE|L1	-6708	NM_001038658	72393	Mm.39760	NM_028224	ENSMUSG00000023011	Faim2	2900002L20Rik|Lfg|Lfg2|NMP25|Nmp35|Tmbim2	Fas apoptotic inhibitory molecule 2	protein-coding
mm_66372.1	chr7	43656645	43656649	-	1	NA	intron (NM_031181, intron 4 of 6)	intron (NM_031181, intron 4 of 6)	3514	NM_031181	83382	Mm.157702	NM_031181	ENSMUSG00000030474	Siglece	Cd170|Siglec12|Siglec5|Siglec9|Siglecl1|mSiglec-E	sialic acid binding Ig-like lectin E	protein-coding
mm_111333.1	chr12	86734300	86734302	-	1	NA	promoter-TSS (NM_001195767)	promoter-TSS (NM_001195767)	-68	NM_001195767	627607	Mm.341880	NM_001195767	ENSMUSG00000059114	Lrrc74a	EG627607|Gm6772|Lrrc74	leucine rich repeat containing 74A	protein-coding
mm_137422.1	chr17	26203816	26203826	+	1	NA	intron (NM_001081069, intron 4 of 16)	intron (NM_001081069, intron 4 of 16)	859	NM_001081069	50782	Mm.109840	NM_001081069	ENSMUSG00000024186	Rgs11	C78048	regulator of G-protein signaling 11	protein-coding
mm_129275.1	chr15	77058552	77058563	-	1	NA	Intergenic	RLTR23|LTR|ERV1	-7889	NM_013593	17189	Mm.404074	NM_013593	ENSMUSG00000018893	Mb	AI325109	myoglobin	protein-coding
mm_122458.1	chr14	45388773	45388836	-	1	NA	promoter-TSS (NM_019425)	promoter-TSS (NM_019425)	-8	NM_019425	54342	Mm.312945	NM_019425	ENSMUSG00000037722	Gnpnat1	AU017428|AU040593|EMeg32|Gpnat1|Gsnpat	glucosamine-phosphate N-acetyltransferase 1	protein-coding
mm_169449.1	chr1	46075978	46075988	-	1	NA	intron (NM_001160386, intron 2 of 65)	L1Md_F2|LINE|L1	9245	NM_001160386	227058	Mm.296880	NM_001160386	ENSMUSG00000041144	Dnah7b	Dnahc7b|Gm107	dynein, axonemal, heavy chain 7B	protein-coding
mm_104252.1	chr11	88877089	88877091	-	1	NA	intron (NR_126433, intron 3 of 4)	RLTR26_Mus|LTR|ERVK	-12504	NM_001042541	11640	Mm.2969	NM_009648	ENSMUSG00000018428	Akap1	AKAP121|AKAP84|Akap|C76494|C81186|DAKAP1|S-AKAP84	A kinase (PRKA) anchor protein 1	protein-coding
mm_38703.1	chr4	145215239	145215251	-	1	NA	3' UTR (NM_011610, exon 10 of 10)	3' UTR (NM_011610, exon 10 of 10)	-20240	NM_001276465	230895	Mm.240310	NM_001033190	ENSMUSG00000020220	Vps13d	-	vacuolar protein sorting 13D	protein-coding
mm_154334.1	chrM	3435	3445	+	1	NA	NA	Intergenic	NA	NA								
mm_1620.1	chr1	74391806	74391829	+	1	NA	5' UTR (NM_153088, exon 1 of 7)	5' UTR (NM_153088, exon 1 of 7)	208	NM_153088	227292	Mm.165042	NM_153088	ENSMUSG00000026176	Ctdsp1	GIP|NLIIF|Nif3|SCP1	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 1	protein-coding
mm_29655.1	chr3	122408831	122408847	-	1	NA	Intergenic	Intergenic	-10941	NM_013867	29815	Mm.45815	NM_013867	ENSMUSG00000028121	Bcar3	AI131758|AND-34	breast cancer anti-estrogen resistance 3	protein-coding
mm_22037.1	chr2	168206801	168206809	-	1	NA	5' UTR (NM_009628, exon 1 of 4)	5' UTR (NM_009628, exon 1 of 4)	307	NM_009628	11538	Mm.201322	NM_009628	ENSMUSG00000051149	Adnp	AA589558|mKIAA0784	activity-dependent neuroprotective protein	protein-coding
mm_66396.1	chr7	44246691	44246710	-	1	NA	promoter-TSS (NM_025880)	promoter-TSS (NM_025880)	-22	NM_025880	668661	Mm.274492	NM_025880	ENSMUSG00000045411	2410002F23Rik	-	RIKEN cDNA 2410002F23 gene	protein-coding
mm_27555.1	chr3	58525114	58525160	-	1	NA	promoter-TSS (NM_001005509)	promoter-TSS (NM_001005509)	-684	NM_001005509	229317	Mm.21617	NM_001005509	ENSMUSG00000027810	Eif2a	D030048D22|D3Ertd194e	eukaryotic translation initiation factor 2A	protein-coding
mm_38024.1	chr4	133813295	133813305	-	1	NA	Intergenic	CpG	-59689	NM_001080819	93760	Mm.22478	NM_001080819	ENSMUSG00000007880	Arid1a	1110030E03Rik|BAF250a|Osa1|Smarcf1	AT rich interactive domain 1A (SWI-like)	protein-coding
mm_95341.1	chr11	47933918	47933921	+	1	NA	intron (NR_105801, intron 3 of 3)	MTD|LTR|ERVL-MaLR	140664	NR_105801	102466638		NR_105801	ENSMUSG00000099011	Mir6380	Gm27356|mmu-mir-6380	microRNA 6380	ncRNA
mm_32703.1	chr4	116075463	116075473	+	1	NA	promoter-TSS (NM_025641)	promoter-TSS (NM_025641)	199	NM_153521	230654	Mm.3655	NM_153521	ENSMUSG00000028703	Lrrc41	AA409966|AW555107|D630045E04Rik|D730026A16Rik|MUF1	leucine rich repeat containing 41	protein-coding
mm_101655.1	chr11	36677492	36677541	-	1	NA	intron (NM_011856, intron 2 of 28)	intron (NM_011856, intron 2 of 28)	266725	NM_001290702	23964	Mm.439889	NM_011856	ENSMUSG00000049336	Tenm2	Odz2|Odz3|Ten-2|Ten-m2	teneurin transmembrane protein 2	protein-coding
mm_132311.1	chr16	33720838	33720851	+	1	NA	intron (NM_175256, intron 2 of 14)	intron (NM_175256, intron 2 of 14)	36378	NM_175256	77446	Mm.245741	NM_172934	ENSMUSG00000075254	Heg1	4632417D23Rik|5530401I02Rik|9530025L16Rik|BC038614|Gm629|OTTMUSG00000027315	heart development protein with EGF-like domains 1	protein-coding
mm_160387.1	chr8	46294765	46294765	-	1	NA	promoter-TSS (NM_173789)	promoter-TSS (NM_173789)	-94	NM_173789	234219	Mm.145631	NM_173789	ENSMUSG00000047171	Helt	A830086M02|Hesl|Heslike|Mgn|megane	helt bHLH transcription factor	protein-coding
mm_144640.1	chr18	33007498	33007535	+	1	NA	intron (NM_009793, intron 1 of 10)	intron (NM_009793, intron 1 of 10)	68475	NM_009793	12326	Mm.222329	NM_009793	ENSMUSG00000038128	Camk4	A430110E23Rik|AI666733|CaMKIV|CaMKIV/Gr|D18Bwg0362e	calcium/calmodulin-dependent protein kinase IV	protein-coding
mm_83250.1	chr9	42400156	42400170	-	1	NA	promoter-TSS (NM_001324548)	promoter-TSS (NM_001324548)	-234	NM_001324548	21683	Mm.42209	NM_009347	ENSMUSG00000037705	Tecta	Tctna	tectorin alpha	protein-coding
mm_107167.1	chr12	24707812	24707824	+	1	NA	promoter-TSS (NM_009104)	promoter-TSS (NM_009104)	-436	NM_009104	20135	Mm.99	NM_009104	ENSMUSG00000020649	Rrm2	AA407299|R2	ribonucleotide reductase M2	protein-coding
mm_46841.1	chr5	113340090	113340099	-	1	NA	Intergenic	Intergenic	-2449	NR_106089	102466821		NR_106089	ENSMUSG00000104840	Mir7230	mmu-mir-7230	microRNA 7230	ncRNA
mm_96915.1	chr11	70460143	70460187	+	1	NA	promoter-TSS (NM_023158)	promoter-TSS (NM_023158)	-181	NM_023158	66102	Mm.425692	NM_023158	ENSMUSG00000018920	Cxcl16	0910001K24Rik|AV290116|BB024863|CXCL16v1|CXCL16v2|SR-PSOX|Zmynd15|b2b498Clo	chemokine (C-X-C motif) ligand 16	protein-coding
mm_86689.1	chr10	18431244	18431265	+	1	NA	intron (NM_173390, intron 1 of 6)	intron (NM_173390, intron 1 of 6)	23579	NM_173390	215819	Mm.297971	NM_173390	ENSMUSG00000039835	Nhsl1	5730409E15Rik|A630035H13Rik|A730096F01|BC013565|D10Bwg0940e|mKIAA1357	NHS-like 1	protein-coding
mm_124814.1	chr15	8968320	8968368	+	1	NA	5' UTR (NM_198024, exon 1 of 14)	5' UTR (NM_198024, exon 1 of 14)	395	NM_198024	223332	Mm.321371	NM_198024	ENSMUSG00000048424	Ranbp3l	C130037N17Rik	RAN binding protein 3-like	protein-coding
mm_69859.1	chr7	141434533	141434605	-	1	NA	promoter-TSS (NM_001177576)	promoter-TSS (NM_001177576)	25	NM_001177576	68267	Mm.33729	NM_026646	ENSMUSG00000019082	Slc25a22	1300006L01Rik|AI060884|Gc1	solute carrier family 25 (mitochondrial carrier, glutamate), member 22	protein-coding
mm_66802.1	chr7	47133698	47133720	-	1	NA	promoter-TSS (NM_013643)	promoter-TSS (NM_013643)	-25	NM_013643	19259	Mm.4654	NM_013643	ENSMUSG00000030854	Ptpn5	Step	protein tyrosine phosphatase, non-receptor type 5	protein-coding
mm_16952.1	chr2	17368616	17368651	-	1	NA	intron (NM_028757, intron 5 of 6)	intron (NM_028757, intron 5 of 6)	-194881	NR_105847	102465964		NR_105847	ENSMUSG00000099161	Mir6419	Gm27713|mmu-mir-6419	microRNA 6419	ncRNA
mm_88731.1	chr10	80226793	80226799	+	1	NA	intron (NM_023431, intron 1 of 13)	CpG	198	NM_023431	68114	Mm.273418	NM_023431	ENSMUSG00000020156	Mum1	2610019J09|9430059D04Rik|UBE-1C2	melanoma associated antigen (mutated) 1	protein-coding
mm_96111.1	chr11	60557895	60557903	+	1	NA	3' UTR (NM_172943, exon 4 of 4)	3' UTR (NM_172943, exon 4 of 4)	20216	NM_172943	268420	Mm.262056	NM_172943	ENSMUSG00000042650	Alkbh5	AW050020|AW215868|Abh5|E130207K11|Ofoxd	alkB homolog 5, RNA demethylase	protein-coding
mm_130689.1	chr15	100681959	100681974	-	1	NA	intron (NM_033612, intron 5 of 7)	B1_Mur2|SINE|Alu	5954	NM_033612	109901	Mm.2131	NM_033612	ENSMUSG00000023031	Cela1	1810009A17Rik|1810062B19Rik|Ela-1|Ela1|PC-TsF	chymotrypsin-like elastase family, member 1	protein-coding
mm_163197.1	chr11	95922506	95922521	+	1	NA	Intergenic	RLTR40|LTR|ERVK	-7642	NM_008081	14422	Mm.340702	NM_008081	ENSMUSG00000013418	B4galnt2	AI593864|Dlb-1|Dlb1|Galg2|Galgt2|Ggm3|Igf2bp1	beta-1,4-N-acetyl-galactosaminyl transferase 2	protein-coding
mm_141132.1	chr17	26206425	26206434	-	1	NA	intron (NM_001081069, intron 9 of 16)	intron (NM_001081069, intron 9 of 16)	3467	NM_001081069	50782	Mm.109840	NM_001081069	ENSMUSG00000024186	Rgs11	C78048	regulator of G-protein signaling 11	protein-coding
mm_115519.1	chr13	5845788	5845818	-	1	NA	Intergenic	Intergenic	12289	NR_045891	71867	Mm.179181	NR_045891	ENSMUSG00000100625	1700016G22Rik	-	RIKEN cDNA 1700016G22 gene	ncRNA
mm_39461.1	chr5	17814759	17814796	+	1	NA	exon (NM_001159558, exon 6 of 16)	exon (NM_001159558, exon 6 of 16)	21119	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_90262.1	chr10	122678633	122678641	+	1	NA	promoter-TSS (NR_106182)	promoter-TSS (NR_106182)	-125	NM_176919	319468	Mm.489703	NM_176919	ENSMUSG00000034613	Ppm1h	A430075L18Rik|ARHCL1|C030002B11Rik	protein phosphatase 1H (PP2C domain containing)	protein-coding
mm_57093.1	chr6	122587668	122587703	-	1	NA	intron (NM_001134391, intron 5 of 7)	intron (NM_001134391, intron 5 of 7)	14759	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_77110.1	chr8	111081814	111081824	-	1	NA	promoter-TSS (NM_181549)	promoter-TSS (NM_181549)	-111	NM_181549	353287	Mm.135495	NM_181549	ENSMUSG00000033633	Clec18a	Mrcl	C-type lectin domain family 18, member A	protein-coding
mm_10393.1	chr2	13573681	13573710	+	1	NA	promoter-TSS (NM_011701)	promoter-TSS (NM_011701)	-616	NM_011701	22352	Mm.268000	NM_011701	ENSMUSG00000026728	Vim	-	vimentin	protein-coding
mm_161853.1	chr18	15409410	15409410	-	1	NA	intron (NM_001308643, intron 1 of 5)	intron (NM_001308643, intron 1 of 5)	1572	NM_001308643	11829	Mm.250786	NM_009700	ENSMUSG00000024411	Aqp4	WCH4	aquaporin 4	protein-coding
mm_22482.1	chr3	5221226	5221245	+	1	NA	promoter-TSS (NR_045905)	promoter-TSS (NR_045905)	-412	NR_045905	72608	Mm.384359	NR_045905		2700069I18Rik	-	RIKEN cDNA 2700069I18 gene	ncRNA
mm_59298.1	chr7	25088468	25088476	+	1	NA	Intergenic	(T)n|Simple_repeat|Simple_repeat	8703	NR_105855	102465968		NR_105855	ENSMUSG00000098441	Mir6537	Gm27808|mmu-mir-6537	microRNA 6537	ncRNA
mm_11268.1	chr2	30061807	30061815	+	1	NA	promoter-TSS (NM_023871)	promoter-TSS (NM_023871)	-185	NM_023871	56086	Mm.326055	NM_023871	ENSMUSG00000054766	Set	2610030F17Rik|5730420M11Rik|AA407739|I-2PP2A|StF-IT-1|TAF-I	SET nuclear oncogene	protein-coding
mm_41516.1	chr5	92387871	92387892	+	1	NA	promoter-TSS (NM_181728)	promoter-TSS (NM_181728)	-253	NM_181728	109979	Mm.263514	NM_181728	ENSMUSG00000034842	Art3	4930569O04Rik|ARTC3	ADP-ribosyltransferase 3	protein-coding
mm_57610.1	chr6	128124332	128124355	-	1	NA	intron (NM_175414, intron 1 of 8)	intron (NM_175414, intron 1 of 8)	19235	NM_175414	109246	Mm.21814	NM_175414	ENSMUSG00000030352	Tspan9	6720474K14Rik|9430079M16Rik|AU018597	tetraspanin 9	protein-coding
mm_7507.1	chr1	123340934	123340980	-	1	NA	intron (NM_199021, intron 24 of 25)	intron (NM_199021, intron 24 of 25)	704602	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_153767.1	chr19	45591999	45592004	-	1	NA	intron (NM_013907, intron 5 of 8)	intron (NM_013907, intron 5 of 8)	31386	NM_172639	226162	Mm.21978	NM_172639	ENSMUSG00000041035	Dpcd	5330431N19Rik|Ndac	deleted in primary ciliary dyskinesia	protein-coding
mm_147836.1	chr18	62578927	62578935	-	1	NA	intron (NM_177829, intron 1 of 8)	intron (NM_177829, intron 1 of 8)	17333	NM_001001803	408198	Mm.478742	NM_001001803	ENSMUSG00000060201	Spink7	EG408198|Ecg2	serine peptidase inhibitor, Kazal type 7 (putative)	protein-coding
mm_62190.1	chr7	97579869	97579901	+	1	NA	promoter-TSS (NM_183251)	promoter-TSS (NM_183251)	-11	NM_001081267	233532	Mm.43977	NM_001081267	ENSMUSG00000035623	Rsf1	4832420A03Rik|C030033M12Rik|Gm164|Hbxap|XAP8|p325	remodeling and spacing factor 1	protein-coding
mm_5554.1	chr1	38664948	38665000	-	1	NA	Intergenic	Intergenic	-37730	NM_001290814	16764	Mm.336679	NM_010678	ENSMUSG00000037138	Aff3	3222402O04Rik|A730046J16|LAF-4|Laf4	AF4/FMR2 family, member 3	protein-coding
mm_7223.1	chr1	93342610	93342620	-	1	NA	5' UTR (NM_080850, exon 1 of 18)	5' UTR (NM_080850, exon 1 of 18)	173	NM_080850	269224	Mm.379454	NM_080850	ENSMUSG00000026274	Pask	mKIAA0135	PAS domain containing serine/threonine kinase	protein-coding
mm_135364.1	chr16	44027933	44027937	-	1	NA	promoter-TSS (NM_001172107)	promoter-TSS (NM_001172107)	10	NM_001172107	207798	Mm.19316	NM_153528	ENSMUSG00000036292	Gramd1c	4921521N14Rik	GRAM domain containing 1C	protein-coding
mm_54383.1	chr6	31217507	31217524	-	1	NA	intron (NR_110469, intron 1 of 3)	intron (NR_110469, intron 1 of 3)	959	NR_110470	232685	Mm.443019	NM_144555	ENSMUSG00000044471	Lncpint	Lincpint|MNCb-1768|Pint|linc-Pint	long non-protein coding RNA, Trp53 induced transcript	ncRNA
mm_96524.1	chr11	68496649	68496663	+	1	NA	3' UTR (NM_177320, exon 19 of 19)	3' UTR (NM_177320, exon 19 of 19)	-6363	NM_001004435	104709	Mm.234573	NM_001004435	ENSMUSG00000046207	Pik3r6	BB220380|p84|p84 PIKAP|p87(PIKAP)|p87PIKAP	phosphoinositide-3-kinase, regulatory subunit 6	protein-coding
mm_16046.1	chr2	167742766	167742785	+	1	NA	Intergenic	L1MB5|LINE|L1	51598	NR_015500	329562	Mm.123101	NM_177851	ENSMUSG00000006462	A530013C23Rik	-	RIKEN cDNA A530013C23 gene	ncRNA
mm_80660.1	chr9	90054599	90054606	+	1	NA	exon (NM_007801, exon 1 of 12)	exon (NM_007801, exon 1 of 12)	335	NM_001312649	13036	Mm.2277	NM_007801	ENSMUSG00000032359	Ctsh	AL022844	cathepsin H	protein-coding
mm_50530.1	chr6	49045450	49045455	+	1	NA	exon (NM_053110, exon 4 of 11)	exon (NM_053110, exon 4 of 11)	8934	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_73277.1	chr8	104624523	104624533	+	1	NA	promoter-TSS (NM_001252627)	promoter-TSS (NM_001252627)	-132	NM_001252628	12556	Mm.19423	NM_007663	ENSMUSG00000031881	Cdh16	-	cadherin 16	protein-coding
mm_22351.1	chr2	180920996	180921010	-	1	NA	promoter-TSS (NM_173761)	promoter-TSS (NM_173761)	-67	NM_173761	228994	Mm.30205	NM_173761	ENSMUSG00000038848	Ythdf1	2210410K23Rik|8030473O16	YTH domain family 1	protein-coding
mm_99962.1	chr11	113684022	113684026	+	1	NA	promoter-TSS (NM_177777)	promoter-TSS (NM_177777)	127	NM_138598	28081	Mm.351688	NM_138598	ENSMUSG00000041629	Fam104a	D11Wsu99e	family with sequence similarity 104, member A	protein-coding
mm_126311.1	chr15	79668542	79668546	+	1	NA	TTS (NM_028634)	TTS (NM_028634)	-2324	NM_172609	223696	Mm.246435	NM_172609	ENSMUSG00000022427	Tomm22	2310047D01|Tom22	translocase of outer mitochondrial membrane 22 homolog (yeast)	protein-coding
mm_108328.1	chr12	79891316	79891322	+	1	NA	Intergenic	Intergenic	33414	NR_131075	77290	Mm.395042	NR_131073		9430078K24Rik	-	RIKEN cDNA 9430078K24 gene	ncRNA
mm_99526.1	chr11	103170847	103170861	+	1	NA	promoter-TSS (NM_001077698)	promoter-TSS (NM_001077698)	-284	NM_001077698	57778	Mm.138913	NM_019679	ENSMUSG00000055805	Fmnl1	8030453N10Rik|AI553564|Fmnl|Fnrl|Frls	formin-like 1	protein-coding
mm_65415.1	chr7	25245520	25245532	-	1	NA	exon (NM_010155, exon 4 of 4)	exon (NM_010155, exon 4 of 4)	5232	NM_010155	13875	Mm.8068	NM_010155	ENSMUSG00000040857	Erf	-	Ets2 repressor factor	protein-coding
mm_90656.1	chr10	128799958	128799991	+	1	NA	TTS (NM_178066)	TTS (NM_178066)	4396	NM_178066	73827	Mm.24630	NM_178066	ENSMUSG00000047090	Tmem198b	1110012D08Rik	transmembrane protein 198b	protein-coding
mm_23973.1	chr3	85712320	85712320	+	1	NA	intron (NM_172682, intron 5 of 11)	MTE2b|LTR|ERVL-MaLR	33889	NM_172682	229488	Mm.119926	NM_172682	ENSMUSG00000051000	Fam160a1	9930021J17Rik	family with sequence similarity 160, member A1	protein-coding
mm_136610.1	chr17	5332545	5332582	+	1	NA	exon (NM_001085355, exon 16 of 20)	exon (NM_001085355, exon 16 of 20)	86204	NM_175349	106557	Mm.432764	NM_175349	ENSMUSG00000101959	Ldhal6b	4933402O15Rik|AI326310|LDHL|Ldhal	lactate dehydrogenase A-like 6B	protein-coding
mm_69096.1	chr7	127019496	127019498	-	1	NA	exon (NM_001102563, exon 2 of 4)	exon (NM_001102563, exon 2 of 4)	1714	NM_001102563	69017	Mm.392047	NM_001102563	ENSMUSG00000045114	Prrt2	1500031I19Rik|AI195361|DSPB3	proline-rich transmembrane protein 2	protein-coding
mm_55574.1	chr6	71396157	71396184	-	1	NA	intron (NM_024288, intron 7 of 8)	(CAG)n|Simple_repeat|Simple_repeat	22743	NM_001081110	12525	Mm.1858	NM_009857	ENSMUSG00000053977	Cd8a	BB154331|Ly-2|Ly-35|Ly-B|Lyt-2	CD8 antigen, alpha chain	protein-coding
mm_134758.1	chr16	23225335	23225347	-	1	NA	promoter-TSS (NM_001252505)	promoter-TSS (NM_001252505)	601	NM_145933	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_35815.1	chr4	46991537	46991650	-	1	NA	5' UTR (NM_001081141, exon 1 of 19)	5' UTR (NM_001081141, exon 1 of 19)	121	NM_001081141	242425	Mm.101909	NM_001081141	ENSMUSG00000039809	Gabbr2	GABABR2|Gb2|Gm425|Gpr51	gamma-aminobutyric acid (GABA) B receptor, 2	protein-coding
mm_127860.1	chr15	8351403	8351415	-	1	NA	exon (NM_027707, exon 10 of 47)	exon (NM_027707, exon 10 of 47)	93054	NM_027707	71175	Mm.240329	NM_027707	ENSMUSG00000022141	Nipbl	Idn3	Nipped-B homolog (Drosophila)	protein-coding
mm_29152.1	chr3	106001452	106001471	-	1	NA	promoter-TSS (NM_029604)	promoter-TSS (NM_029604)	36	NM_029604	100503311	Mm.386825	NM_029604	ENSMUSG00000010136	Pifo	1700027A23Rik	primary cilia formation	protein-coding
mm_24864.1	chr3	95929430	95929432	+	1	NA	5' UTR (NM_001253757, exon 1 of 7)	5' UTR (NM_001253757, exon 1 of 7)	174	NM_023210	66471	Mm.218657	NM_023210	ENSMUSG00000015749	Anp32e	2810018A15Rik|AI047746|AI326868|CPD1|LANP-L|LANPL|mLANP-L	acidic (leucine-rich) nuclear phosphoprotein 32 family, member E	protein-coding
mm_18989.1	chr2	76863366	76863403	-	1	NA	exon (NM_011652, exon 111 of 313)	exon (NM_011652, exon 111 of 313)	119163	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_109115.1	chr12	105513412	105513423	+	1	NA	promoter-TSS (NR_102381)	promoter-TSS (NR_102381)	-16	NR_102381	104932	Mm.274150	NR_102381		AU015791	-	expressed sequence AU015791	ncRNA
mm_27213.1	chr3	35932859	35932904	-	1	NA	promoter-TSS (NM_001205362)	promoter-TSS (NM_001205362)	85	NM_001205361	114893	Mm.374810	NM_033623	ENSMUSG00000027708	Dcun1d1	Rp42|SCCRO|Tes3|pTes3	DCN1, defective in cullin neddylation 1, domain containing 1 (S. cerevisiae)	protein-coding
mm_21718.1	chr2	164638598	164638609	-	1	NA	5' UTR (NM_001012723, exon 2 of 4)	5' UTR (NM_001012723, exon 2 of 4)	199	NM_001012723	277345	Mm.247244	NM_001012723	ENSMUSG00000070530	Wfdc16	BC043944|WAP16	WAP four-disulfide core domain 16	protein-coding
mm_152493.1	chr19	11055851	11055881	-	1	NA	Intergenic	Lx|LINE|L1	-5300	NR_102366	107350	Mm.6381	NM_001177351	ENSMUSG00000075010	AW112010	-	expressed sequence AW112010	ncRNA
mm_121996.1	chr14	26591568	26591574	-	1	NA	intron (NM_001134465, intron 1 of 19)	intron (NM_001134465, intron 1 of 19)	12021	NM_145969	211922	Mm.260512	NM_145969	ENSMUSG00000040818	Dennd6a	Fam116a	DENN/MADD domain containing 6A	protein-coding
mm_66474.1	chr7	44997222	44997276	-	1	NA	promoter-TSS (NM_016849)	promoter-TSS (NM_016849)	330	NM_029410	75736	Mm.261006	NM_029410	ENSMUSG00000003190	Bcl2l12	2810475P17Rik|5430429M05Rik|Bcl-L12|Bcl2-L12	BCL2-like 12 (proline rich)	protein-coding
mm_14275.1	chr2	128738267	128738277	+	1	NA	exon (NM_008587, exon 4 of 19)	exon (NM_008587, exon 4 of 19)	39275	NM_008587	17289	Mm.239655	NM_008587	ENSMUSG00000014361	Mertk	Eyk|Mer|Nyk|nmf12	c-mer proto-oncogene tyrosine kinase	protein-coding
mm_67107.1	chr7	70354534	70354538	-	1	NA	3' UTR (NM_183261, exon 3 of 3)	3' UTR (NM_183261, exon 3 of 3)	6057	NM_009697	11819	Mm.158143	NM_009697	ENSMUSG00000030551	Nr2f2	2700033K02Rik|9430015G03Rik|ARP-1|Aporp1|COUP-TF2|COUP-TFII|COUPTFB|EAR3|SVP40|Tcfcoup2	nuclear receptor subfamily 2, group F, member 2	protein-coding
mm_171612.1	chr4	150237302	150237303	+	1	NA	promoter-TSS (NM_001025388).2	promoter-TSS (NM_001025388).2	-22	NM_001025388	433182	Mm.70666	NM_001025388	ENSMUSG00000059040	Eno1b	EG433182|Eno1|Gm5506	enolase 1B, retrotransposed	protein-coding
mm_118828.1	chr14	25607312	25607349	+	1	NA	intron (NM_001310666, intron 6 of 23)	CpG	3817	NM_001309430	100188919	Mm.473810	NM_001309430		Israa	-	immune system released activating agent	protein-coding
mm_76164.1	chr8	82379072	82379081	-	1	NA	intron (NM_008357, intron 2 of 7)	intron (NM_008357, intron 2 of 7)	23510	NM_001254747	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_31994.1	chr4	89688173	89688180	+	1	NA	promoter-TSS (NM_175647)	promoter-TSS (NM_175647)	-22	NM_175647	242523	Mm.130167	NM_175647	ENSMUSG00000043753	Dmrta1	Dmrt4	doublesex and mab-3 related transcription factor like family A1	protein-coding
mm_9734.1	chr1	180230037	180230067	-	1	NA	intron (NM_001128605, intron 7 of 10)	intron (NM_001128605, intron 7 of 10)	15898	NM_011183	19165	Mm.330850	NM_011183	ENSMUSG00000010609	Psen2	ALG-3|Ad4h|Alg3|PS-2|PS2|Psnl2|STM2	presenilin 2	protein-coding
mm_101161.1	chr11	16973160	16973177	-	1	NA	3' UTR (NM_019549, exon 10 of 10)	3' UTR (NM_019549, exon 10 of 10)	21758	NM_176982	319701	Mm.120672	NM_176982	ENSMUSG00000044966	Fbxo48	A630050E13Rik	F-box protein 48	protein-coding
mm_157390.1	chrX	38405491	38405527	-	1	NA	exon (NM_001017959, exon 9 of 9)	exon (NM_001017959, exon 9 of 9)	50951	NM_010685	16784	Mm.486	NM_010685	ENSMUSG00000016534	Lamp2	CD107b|LGP-B|Lamp II|Lamp-2|Lamp-2a|Lamp-2b|Lamp-2c|Mac3	lysosomal-associated membrane protein 2	protein-coding
mm_162688.1	chr10	18235592	18235594	-	1	NA	promoter-TSS (NM_144820)	promoter-TSS (NM_144820)	-612	NM_144820	215814	Mm.296565	NM_144820	ENSMUSG00000059554	Ccdc28a	1700009P13Rik|AI480677	coiled-coil domain containing 28A	protein-coding
mm_135030.1	chr16	32810456	32810466	-	1	NA	promoter-TSS (NM_001256309)	promoter-TSS (NM_001256309)	-15	NM_001256309	381043	Mm.303864	NM_001256309	ENSMUSG00000094430	Gm933	Gm1743	predicted gene 933	protein-coding
mm_32655.1	chr4	115088906	115088909	+	1	NA	5' UTR (NM_001164557, exon 1 of 4)	5' UTR (NM_001164557, exon 1 of 4)	199	NM_001164557	67182	Mm.30181	NM_026018	ENSMUSG00000028716	Pdzk1ip1	0610007F13Rik|2700030M23Rik|AU046042|Map17	PDZK1 interacting protein 1	protein-coding
mm_95486.1	chr11	51577889	51577894	+	1	NA	intron (NM_153393, intron 27 of 28)	intron (NM_153393, intron 27 of 28)	-6866	NM_028398	72947	Mm.256875	NM_028398	ENSMUSG00000020359	Phykpl	2900006B13Rik|Agxt2l2	5-phosphohydroxy-L-lysine phospholyase	protein-coding
mm_46886.1	chr5	113961813	113961818	-	1	NA	intron (NM_198109, intron 5 of 14)	(TCTG)n|Simple_repeat|Simple_repeat	31942	NM_198109	231637	Mm.389682	NM_198109	ENSMUSG00000042121	Ssh1	AW551225|Gm1394|Gm1395|SSH-1|SSH-1L	slingshot homolog 1 (Drosophila)	protein-coding
mm_147470.1	chr18	46726930	46726931	-	1	NA	intron (NM_033037, intron 1 of 4)	B1_Mm|SINE|Alu	1412	NM_033037	12583	Mm.241056	NM_033037	ENSMUSG00000033022	Cdo1	1300002L19Rik|Cdo|D18Ucla3	cysteine dioxygenase 1, cytosolic	protein-coding
mm_156090.1	chrX	110837051	110837057	+	1	NA	Intergenic	Intergenic	22675	NM_008901	18994	Mm.56946	NM_008901	ENSMUSG00000056854	Pou3f4	Brn-4|Brn4|OTF-9|Otf9|Slf|oct-9	POU domain, class 3, transcription factor 4	protein-coding
mm_122034.1	chr14	29852348	29852370	-	1	NA	Intergenic	Intergenic	-116021	NM_019979	80795	Mm.104491	NM_019979	ENSMUSG00000042682	Selenok	1110001C03Rik|AA673253|HSPC030|Hsp30|Selk	selenoprotein K	protein-coding
mm_19553.1	chr2	98666626	98666636	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	1198974	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_96391.1	chr11	67249856	67249866	+	1	NA	exon (NM_010855, exon 18 of 40)	exon (NM_010855, exon 18 of 40)	12049	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_122795.1	chr14	54462797	54462799	-	1	NA	Intergenic	MIR|SINE|MIR	-1349	NM_022993	65107	Mm.472719	NM_022993	ENSMUSG00000022175	Lrp10	Lrp9	low-density lipoprotein receptor-related protein 10	protein-coding
mm_172152.1	chr6	41200400	41200411	-	1	NA	Intergenic	MMVL30-int|LTR|ERV1	-101867	NM_011646	22074	Mm.383263	NM_011646	ENSMUSG00000054106	Try4	0910001B19Rik|Td	trypsin 4	protein-coding
mm_69978.1	chr7	142377416	142377452	-	1	NA	exon (NM_009983, exon 6 of 9)	exon (NM_009983, exon 6 of 9)	-3688	NM_001347541	320802	Mm.154486	NM_177265	ENSMUSG00000045777	Ifitm10	6330512M04Rik|AI848576|DSPA3	interferon induced transmembrane protein 10	protein-coding
mm_70449.1	chr8	11758381	11758412	+	1	NA	promoter-TSS (NM_001113518)	promoter-TSS (NM_001113518)	66	NM_001113518	54126	Mm.244068	NM_017402	ENSMUSG00000031511	Arhgef7	Cool|PIX|Pak3bp|betaPix|betaPix-b|betaPix-c|cool-1|mKIAA0142|p85Cool1|p85SPR	Rho guanine nucleotide exchange factor (GEF7)	protein-coding
mm_95796.1	chr11	55098133	55098150	+	1	NA	5' UTR (NM_010299, exon 1 of 4)	5' UTR (NM_010299, exon 1 of 4)	156	NM_010299	14667	Mm.287807	NM_010299	ENSMUSG00000000594	Gm2a	AA408702|AW215435|GM2-AP|SAP-3	GM2 ganglioside activator protein	protein-coding
mm_124935.1	chr15	12230435	12230443	+	1	NA	intron (NM_172958, intron 2 of 15)	intron (NM_172958, intron 2 of 15)	25345	NM_172958	268783	Mm.54460	NM_172958	ENSMUSG00000039458	Mtmr12	3Pap|4932703C11|C730015A02Rik|Pip3ap|mKIAA1682	myotubularin related protein 12	protein-coding
mm_134030.1	chr16	5011757	5011778	-	1	NA	intron (NM_133185, intron 4 of 10)	intron (NM_133185, intron 4 of 10)	1786	NM_133185	66049	Mm.27792	NM_133185	ENSMUSG00000022540	Rogdi	0610011C19Rik|AU020118|C76152|Lzf	rogdi homolog	protein-coding
mm_4605.1	chr1	178448627	178448648	+	1	NA	intron (NM_026626, intron 2 of 6)	L2a|LINE|L2	42756	NM_026626	68226	Mm.252132	NM_026626	ENSMUSG00000026495	Efcab2	1700073K01Rik|D830011E08Rik	EF-hand calcium binding domain 2	protein-coding
mm_110724.1	chr12	69682184	69682226	-	1	NA	promoter-TSS (NM_001135559)	promoter-TSS (NM_001135559)	-353	NM_001135559	20663	Mm.3770	NM_001135559	ENSMUSG00000034801	Sos2	SOS-2|mSOS-2	son of sevenless homolog 2 (Drosophila)	protein-coding
mm_67060.1	chr7	67528974	67528996	-	1	NA	intron (NM_175124, intron 9 of 9)	intron (NM_175124, intron 9 of 9)	116251	NM_175124	67867	Mm.31247	NM_027413	ENSMUSG00000030556	Lrrc28	1300004K21Rik|2210012C09Rik|2310058O11Rik	leucine rich repeat containing 28	protein-coding
mm_4594.1	chr1	178337293	178337316	+	1	NA	exon (NM_016805, exon 1 of 14)	exon (NM_016805, exon 1 of 14)	480	NM_016805	51810	Mm.86589	NM_016805	ENSMUSG00000039630	Hnrnpu	AA408410|AI256620|AL024194|AL024437|AW557595|C86794|Hnrpu|SAFA|Sp120|hnRNP U	heterogeneous nuclear ribonucleoprotein U	protein-coding
mm_108603.1	chr12	85469008	85469014	+	1	NA	Intergenic	Intergenic	-4890	NM_010234	14281	Mm.246513	NM_010234	ENSMUSG00000021250	Fos	D12Rfj1|c-fos|cFos	FBJ osteosarcoma oncogene	protein-coding
mm_41588.1	chr5	93267563	93267605	+	1	NA	promoter-TSS (NM_007635)	promoter-TSS (NM_007635)	11	NM_007635	12452	Mm.3527	NM_007635	ENSMUSG00000029385	Ccng2	-	cyclin G2	protein-coding
mm_2357.1	chr1	92950845	92950877	+	1	NA	promoter-TSS (NR_015525)	promoter-TSS (NR_015525)	-271	NR_015525	100037260	Mm.442236	NR_015525	ENSMUSG00000100632	9430060I03Rik	-	RIKEN cDNA 9430060I03 gene	ncRNA
mm_14159.1	chr2	126602478	126602487	+	1	NA	intron (NM_008230, intron 7 of 11)	intron (NM_008230, intron 7 of 11)	16196	NM_008230	15186	Mm.18603	NM_008230	ENSMUSG00000027360	Hdc	AW108189|Hdc-a|Hdc-c|Hdc-e|Hdc-s	histidine decarboxylase	protein-coding
mm_159205.1	chr2	121351018	121351018	-	1	NA	promoter-TSS (NM_178795)	promoter-TSS (NM_178795)	-5	NM_178795	327655	Mm.386076	NM_178795	ENSMUSG00000033526	Ppip5k1	B430315C20Rik|Hisppd2a|mKIAA0377	diphosphoinositol pentakisphosphate kinase 1	protein-coding
mm_123703.1	chr14	69787119	69787120	-	1	NA	3' UTR (NM_153514, exon 10 of 10)	3' UTR (NM_153514, exon 10 of 10)	18426	NM_153514	246710	Mm.102367	NM_153514	ENSMUSG00000022075	Rhobtb2	Dbc2|E130206H14Rik|mKIAA0717	Rho-related BTB domain containing 2	protein-coding
mm_140374.1	chr17	86981084	86981097	+	1	NA	intron (NM_145491, intron 2 of 4)	B4A|SINE|B4	17979	NM_145491	104215	Mm.826	NM_145491	ENSMUSG00000024143	Rhoq	Arhq|TC10A|Tc10	ras homolog family member Q	protein-coding
mm_138981.1	chr17	45457013	45457021	+	1	NA	intron (NM_027649, intron 4 of 7)	intron (NM_027649, intron 4 of 7)	17921	NM_027649	71020	Mm.44257	NM_027649	ENSMUSG00000023935	Spats1	1700011H05Rik|4933400B06Rik|Daip2|Ddip|Srsp1	spermatogenesis associated, serine-rich 1	protein-coding
mm_7265.1	chr1	95626539	95626575	-	1	NA	TTS (NM_001159745)	TTS (NM_001159745)	41037	NM_009183	20452	Mm.306228	NM_009183	ENSMUSG00000040710	St8sia4	PST|PST-1|SIAT8-D|ST8SiaIV|Siat8d	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4	protein-coding
mm_85875.1	chr9	110947259	110947275	-	1	NA	Intergenic	Intergenic	-1109	NM_011562	21667	Mm.5090	NM_011562	ENSMUSG00000032494	Tdgf1	CR1|cripto	teratocarcinoma-derived growth factor 1	protein-coding
mm_66661.1	chr7	45717039	45717045	-	1	NA	5' UTR (NM_203280, exon 2 of 7)	5' UTR (NM_203280, exon 2 of 7)	960	NM_203280	56632	Mm.24222	NM_020011	ENSMUSG00000057342	Sphk2	C76851	sphingosine kinase 2	protein-coding
mm_34590.1	chr4	150189144	150189174	+	1	NA	exon (NM_009802, exon 7 of 8)	exon (NM_009802, exon 7 of 8)	11976	NM_009802	12353	Mm.232523	NM_009802	ENSMUSG00000028972	Car6	Ca6|DOC1	carbonic anhydrase 6	protein-coding
mm_97314.1	chr11	76891110	76891130	+	1	NA	Intergenic	Intergenic	-13425	NM_025655	66601	Mm.25138	NM_025655	ENSMUSG00000020839	Tmigd1	2010002A20Rik|Tmigd	transmembrane and immunoglobulin domain containing 1	protein-coding
mm_1658.1	chr1	74713211	74713221	+	1	NA	promoter-TSS (NM_024264)	promoter-TSS (NM_024264)	-319	NM_024264	104086	Mm.85083	NM_024264	ENSMUSG00000026170	Cyp27a1	1300013A03Rik|Cyp27	cytochrome P450, family 27, subfamily a, polypeptide 1	protein-coding
mm_149739.1	chr19	22447897	22447908	+	1	NA	promoter-TSS (NM_177341)	promoter-TSS (NM_177341)	-306	NM_177341	226025	Mm.131943	NM_177341	ENSMUSG00000052387	Trpm3	6330504P12Rik|9330180E14|AU018608|B930001P07Rik|LTRPC3|MLSN2	transient receptor potential cation channel, subfamily M, member 3	protein-coding
mm_100332.1	chr11	118319023	118319035	+	1	NA	intron (NM_011594, intron 2 of 4)	intron (NM_011594, intron 2 of 4)	23505	NM_021440	58251	Mm.439815	NM_021440	ENSMUSG00000076433	BC100451	Cep295nl|Ddc8|FS39|Kiaa1731nl	cDNA sequence BC100451	protein-coding
mm_17805.1	chr2	33371487	33371499	-	1	NA	promoter-TSS (NM_175211)	promoter-TSS (NM_175211)	1	NM_001290570	241308	Mm.274249	NM_175211	ENSMUSG00000038831	Ralgps1	5830418G11Rik|AI853783|AI854138|RALGEF2|RALGPS1A|RalGEF 2|mKIAA0351	Ral GEF with PH domain and SH3 binding motif 1	protein-coding
mm_149249.1	chr19	10389206	10389214	+	1	NA	5' UTR (NM_018801, exon 1 of 9)	5' UTR (NM_018801, exon 1 of 9)	120	NM_173068	54525	Mm.182654	NM_018801	ENSMUSG00000024743	Syt7	AI851541|B230112P13Rik	synaptotagmin VII	protein-coding
mm_65848.1	chr7	29256413	29256416	-	1	NA	TTS (NM_001082548)	TTS (NM_001082548)	-7947	NM_028179	72275	Mm.441142	NM_028179	ENSMUSG00000030587	2200002D01Rik	2010005J02Rik|H2RSP|IMUP|IMUP-1|IMUP-2	RIKEN cDNA 2200002D01 gene	protein-coding
mm_136489.1	chr16	96124917	96124925	-	1	NA	intron (NM_008251, intron 4 of 5)	intron (NM_008251, intron 4 of 5)	2804	NM_008251	15312	Mm.2756	NM_008251	ENSMUSG00000040681	Hmgn1	HMG-14|Hmg14	high mobility group nucleosomal binding domain 1	protein-coding
mm_28286.1	chr3	89089661	89089669	-	1	NA	intron (NM_028188, intron 4 of 10)	intron (NM_028188, intron 4 of 10)	366	NM_001083808	72296	Mm.27687	NM_028188	ENSMUSG00000041263	Rusc1	2210403N08Rik|AA408288|NESCA	RUN and SH3 domain containing 1	protein-coding
mm_145302.1	chr18	53345237	53345240	+	1	NA	intron (NM_029394, intron 3 of 6)	B1_Mur1|SINE|Alu	72769	NM_008908	19038	Mm.4587	NM_008908	ENSMUSG00000024538	Ppic	CyP-20c	peptidylprolyl isomerase C	protein-coding
mm_104181.1	chr11	87757266	87757269	-	1	NA	promoter-TSS (NR_106176)	promoter-TSS (NR_106176)	-312	NR_106176	102466883		NR_106176	ENSMUSG00000065420	Mir142b	Gm27750|mmu-mir-142b	microRNA 142b	ncRNA
mm_14431.1	chr2	130576171	130576176	+	1	NA	promoter-TSS (NM_011025)	promoter-TSS (NM_011025)	4	NM_011025	18429	Mm.16745	NM_011025	ENSMUSG00000027301	Oxt	OT|Oxy	oxytocin	protein-coding
mm_59764.1	chr7	28832379	28832392	+	1	NA	TTS (NM_016772)	TTS (NM_016772)	-1409	NM_010706	16855	Mm.210336	NM_010706	ENSMUSG00000053964	Lgals4	gal-4	lectin, galactose binding, soluble 4	protein-coding
mm_169950.1	chr16	76519639	76519642	-	1	NA	Intergenic	Intergenic	-146591	NM_173440	268903	Mm.74711	NM_173440	ENSMUSG00000048490	Nrip1	6030458L20Rik|8430438I05Rik|9630050P12|AA959574|AW456757|RIP140	nuclear receptor interacting protein 1	protein-coding
mm_132556.1	chr16	37916441	37916474	+	1	NA	promoter-TSS (NM_153394)	promoter-TSS (NM_153394)	-39	NM_153394	239845	Mm.228018	NM_153394	ENSMUSG00000046961	Gpr156	Gababl	G protein-coupled receptor 156	protein-coding
mm_105993.1	chr11	115628261	115628298	-	1	NA	promoter-TSS (NM_001252384)	promoter-TSS (NM_001252384)	16	NM_001252394	67283	Mm.383426	NM_026071	ENSMUSG00000020744	Slc25a19	2900089E13Rik|DNC|MUP1|TPC	solute carrier family 25 (mitochondrial thiamine pyrophosphate carrier), member 19	protein-coding
mm_129279.1	chr15	77153674	77153674	-	1	NA	5' UTR (NM_001110830, exon 1 of 13)	5' UTR (NM_001110830, exon 1 of 13)	138	NM_001110830	93686	Mm.202774	NM_053104	ENSMUSG00000033565	Rbfox2	Fbm2|Fxh|Hrnbp2|Rbm9	RNA binding protein, fox-1 homolog (C. elegans) 2	protein-coding
mm_68799.1	chr7	125349785	125349814	-	1	NA	promoter-TSS (NR_045804)	promoter-TSS (NR_045804)	-13	NR_045803	71208	Mm.159465	NM_172408	ENSMUSG00000045928	4933440M02Rik	-	RIKEN cDNA 4933440M02 gene	ncRNA
mm_2592.1	chr1	119453925	119453941	+	1	NA	Intergenic	Intergenic	-31685	NM_008381	16324	Mm.3092	NM_008381	ENSMUSG00000037035	Inhbb	-	inhibin beta-B	protein-coding
mm_55620.1	chr6	72235186	72235202	-	1	NA	5' UTR (NM_153778, exon 1 of 3)	5' UTR (NM_153778, exon 1 of 3)	383	NM_153778	71093	Mm.87449	NM_153778	ENSMUSG00000037621	Atoh8	4933425C05Rik|Hath6|Math6|bHLHa21|okadin	atonal bHLH transcription factor 8	protein-coding
mm_134147.1	chr16	10784898	10784912	-	1	NA	5' UTR (NM_001271603, exon 2 of 2)	5' UTR (NM_001271603, exon 2 of 2)	631	NM_009896	12703	Mm.130	NM_009896	ENSMUSG00000038037	Socs1	Cish1|Cish7|JAB|SOCS-1|SSI-1	suppressor of cytokine signaling 1	protein-coding
mm_154766.1	chrX	12157709	12157712	+	1	NA	intron (NR_045434, intron 1 of 3)	intron (NR_045434, intron 1 of 3)	2636	NR_045434	71458	Mm.196328	NM_029510	ENSMUSG00000040363	Bcor	2900008C10Rik|5830466J11Rik|8430401K06Rik|BcorR|D930024N20Rik|mKIAA1575	BCL6 interacting corepressor	protein-coding
mm_48189.1	chr5	137528889	137528914	-	1	NA	TTS (NM_031408)	TTS (NM_031408)	693	NR_105846	102465227		NR_105846	ENSMUSG00000098597	Mir6418	Gm27629|mir-6418|mmu-mir-6418	microRNA 6418	ncRNA
mm_147422.1	chr18	46212452	46212461	-	1	NA	5' UTR (NM_178872, exon 1 of 10)	5' UTR (NM_178872, exon 1 of 10)	151	NM_178872	28105	Mm.277382	NM_178872	ENSMUSG00000033949	Trim36	D18Wsu100e|haprin	tripartite motif-containing 36	protein-coding
mm_84023.1	chr9	57682207	57682216	-	1	NA	exon (NM_009993, exon 2 of 7)	exon (NM_009993, exon 2 of 7)	1444	NM_009993	13077	Mm.15537	NM_009993	ENSMUSG00000032310	Cyp1a2	CP12|Cyp1a1|P450-3	cytochrome P450, family 1, subfamily a, polypeptide 2	protein-coding
mm_89822.1	chr10	105573157	105573167	+	1	NA	intron (NM_177368, intron 1 of 11)	intron (NM_177368, intron 1 of 11)	1317	NM_177368	278279	Mm.25225	NM_177368	ENSMUSG00000036019	Tmtc2	8430438D04Rik|D330034A10Rik	transmembrane and tetratricopeptide repeat containing 2	protein-coding
mm_46616.1	chr5	108132491	108132503	-	1	NA	promoter-TSS (NM_028481)	promoter-TSS (NM_028481)	94	NM_001347383	73130	Mm.363960	NM_028876	ENSMUSG00000063406	Tmed5	3110020O18Rik|4432412D15Rik	transmembrane p24 trafficking protein 5	protein-coding
mm_43149.1	chr5	125495976	125495996	+	1	NA	intron (NM_030210, intron 5 of 17)	intron (NM_030210, intron 5 of 17)	20113	NM_030210	78894	Mm.431573	NM_030210	ENSMUSG00000029482	Aacs	2210408B16Rik|SUR5	acetoacetyl-CoA synthetase	protein-coding
mm_90158.1	chr10	118715888	118715927	+	1	NA	Intergenic	RMER19B2|LTR|ERVK	152996	NM_001014390	69181	Mm.45565	NM_001014390	ENSMUSG00000028630	Dyrk2	1810038L18Rik	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 2	protein-coding
mm_110307.1	chr12	33061807	33061818	-	1	NA	intron (NM_001024478, intron 6 of 19)	intron (NM_001024478, intron 6 of 19)	31063	NM_001024478	68764	Mm.60083	NM_001024478	ENSMUSG00000035860	Cdhr3	1110049B09Rik|BB172694|Cdh28	cadherin-related family member 3	protein-coding
mm_54006.1	chr6	7773671	7773677	-	1	NA	Intergenic	Intergenic	-71550	NM_052993	94192	Mm.102752	NM_052993	ENSMUSG00000042460	C1galt1	2210410E06Rik|AV284120|T-synthase	core 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase, 1	protein-coding
mm_31397.1	chr4	48045258	48045307	+	1	NA	promoter-TSS (NM_015743)	promoter-TSS (NM_015743)	-23	NM_015743	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_17987.1	chr2	37896597	37896618	-	1	NA	intron (NM_146122, intron 13 of 21)	A-rich|Low_complexity|Low_complexity	120358	NM_001163566	241324	Mm.392369	NM_001163566	ENSMUSG00000035403	Crb2	5930402A21|BC043114	crumbs family member 2	protein-coding
mm_101262.1	chr11	21091965	21091973	-	1	NA	intron (NM_023324, intron 1 of 6)	intron (NM_023324, intron 1 of 6)	645	NM_023324	67245	Mm.28957	NM_023324	ENSMUSG00000020134	Peli1	2810468L03Rik|A930031K15Rik|AA409794|AI586297|D11Ertd676e	pellino 1	protein-coding
mm_27889.1	chr3	79286697	79286726	-	1	NA	Intergenic	CpG	-58665	NM_001142953	100233207	Mm.373801	NM_001142953	ENSMUSG00000091685	Gm17359	-	predicted gene, 17359	protein-coding
mm_50395.1	chr6	48718603	48718613	+	1	NA	promoter-TSS (NM_146167)	promoter-TSS (NM_146167)	-13	NM_146167	231932	Mm.30479	NM_146167	ENSMUSG00000043931	Gimap7	IAN7|Ian3	GTPase, IMAP family member 7	protein-coding
mm_153945.1	chr19	47536998	47537049	-	1	NA	promoter-TSS (NM_175360)	promoter-TSS (NM_175360)	-3	NM_175360	108689	Mm.218048	NM_175360	ENSMUSG00000042694	Obfc1	0610009H20Rik|2310057J23Rik|AAF-44|AAF44|AI413458|RPA-32	oligonucleotide/oligosaccharide-binding fold containing 1	protein-coding
mm_142789.1	chr17	50164177	50164232	-	1	NA	intron (NM_181397, intron 2 of 9)	B4A|SINE|B4	26293	NM_181397	76438	Mm.41854	NM_181397	ENSMUSG00000039316	Rftn1	2310015N21Rik|AI853526	raftlin lipid raft linker 1	protein-coding
mm_161561.1	chr16	17406378	17406378	-	1	NA	promoter-TSS (NM_001001983)	promoter-TSS (NM_001001983)	-64	NM_001001983	224020	Mm.5718	NM_001001983	ENSMUSG00000041720	Pi4ka	Pik4ca	phosphatidylinositol 4-kinase, catalytic, alpha polypeptide	protein-coding
mm_110887.1	chr12	75549637	75549640	-	1	NA	intron (NM_012024, intron 2 of 13)	intron (NM_012024, intron 2 of 13)	46562	NM_012024	26932	Mm.259626	NM_012024	ENSMUSG00000021051	Ppp2r5e	4633401M22Rik|AI449017|B56beta	protein phosphatase 2, regulatory subunit B', epsilon	protein-coding
mm_127397.1	chr15	101134585	101134592	+	1	NA	intron (NM_001277255, intron 3 of 11)	intron (NM_001277255, intron 3 of 11)	6066	NM_001277257	11482	Mm.279542	NM_009612	ENSMUSG00000000530	Acvrl1	AI115505|AI427544|Acvrlk1|Alk1	activin A receptor, type II-like 1	protein-coding
mm_105564.1	chr11	106530098	106530121	-	1	NA	intron (NM_198292, intron 6 of 11)	intron (NM_198292, intron 6 of 11)	29118	NR_030703	100216537		NR_030703	ENSMUSG00000065126	Snord104	-	small nucleolar RNA, C/D box 104	snoRNA
mm_125108.1	chr15	27826614	27826618	+	1	NA	intron (NM_001081302, intron 28 of 56)	URR1B|DNA|hAT-Charlie	-145074	NM_001242423	223433	Mm.266485	NM_198301	ENSMUSG00000056069	Fam105a	9830126M18	family with sequence similarity 105, member A	protein-coding
mm_168133.1	chr10	27936335	27936355	+	1	NA	Intergenic	Intergenic	-138475	NM_008983	19272	Mm.332303	NM_008983	ENSMUSG00000019889	Ptprk	AI853699|PTPk|RPTPkappa	protein tyrosine phosphatase, receptor type, K	protein-coding
mm_145411.1	chr18	57533843	57533866	+	1	NA	promoter-TSS (NM_029290)	promoter-TSS (NM_029290)	28	NM_029290	75444	Mm.482900	NM_029290	ENSMUSG00000058925	1700011I03Rik	4930583I06Rik	RIKEN cDNA 1700011I03 gene	protein-coding
mm_156359.1	chrX	139480366	139480372	+	1	NA	promoter-TSS (NM_175326)	promoter-TSS (NM_175326)	2	NM_001346522	102871	Mm.26565	NM_175326	ENSMUSG00000042498	D330045A20Rik	AI132325	RIKEN cDNA D330045A20 gene	protein-coding
mm_66016.1	chr7	30598864	30598884	-	1	NA	Intergenic	Intergenic	-5932	NM_021397	58206	Mm.116789	NM_021397	ENSMUSG00000006310	Zbtb32	4930524C15Rik|FAXF|FAZF|PLZP|Rog|Tzfp	zinc finger and BTB domain containing 32	protein-coding
mm_51124.1	chr6	68219937	68219943	+	1	NA	Intergenic	Intergenic	-654241	NR_003100	75070	Mm.463364	NR_003100		4930515G16Rik	-	myc induced nuclear antigen pseudogene	pseudo
mm_54141.1	chr6	21858713	21858729	-	1	NA	Intergenic	Intergenic	-6206	NM_173007	269831	Mm.21950	NM_173007	ENSMUSG00000029669	Tspan12	9030619E17|AI426782|AI663988|AW111457|Tm4sf12	tetraspanin 12	protein-coding
mm_170225.1	chr17	80809312	80809315	+	1	NA	Intergenic	Intergenic	-81288	NM_001290345	225028	Mm.311948	NM_001081357	ENSMUSG00000024242	Map4k3	4833416M01Rik|4833416M07Rik|9530052P13Rik|Glk|MAPKKKK3|MEKKK 3|MEKKK3|RAB8IPL1	mitogen-activated protein kinase kinase kinase kinase 3	protein-coding
mm_120646.1	chr14	70530582	70530599	+	1	NA	promoter-TSS (NM_145219)	promoter-TSS (NM_145219)	-231	NM_145219	213469	Mm.41708	NM_145219	ENSMUSG00000033595	Lgi3	AI841179|AW049851	leucine-rich repeat LGI family, member 3	protein-coding
mm_151391.1	chr19	56425684	56425694	+	1	NA	intron (NM_007611, intron 2 of 6)	intron (NM_007611, intron 2 of 6)	28560	NM_007611	12369	Mm.35687	NM_007611	ENSMUSG00000025076	Casp7	AI314680|CMH-1|ICE-IAP3|Mch3|caspase-7|mCASP-7	caspase 7	protein-coding
mm_128325.1	chr15	38072408	38072409	-	1	NA	intron (NM_001112721, intron 1 of 58)	PB1D9|SINE|Alu	6446	NM_001112721	70790	Mm.476840	NM_027553	ENSMUSG00000037487	Ubr5	Edd|Edd1	ubiquitin protein ligase E3 component n-recognin 5	protein-coding
mm_1342.1	chr1	66175249	66175269	+	1	NA	promoter-TSS (NM_008632)	promoter-TSS (NM_008632)	-70	NM_008632	17756	Mm.256966	NM_008632	ENSMUSG00000015222	Map2	G1-397-34|MAP-2|Mtap-2|Mtap2|repro4	microtubule-associated protein 2	protein-coding
mm_6740.1	chr1	83059370	83059377	-	1	NA	Intergenic	Intergenic	-1557	NM_027778	71386	Mm.389133	NM_027778	ENSMUSG00000101315	Krtap28-13	5530401N06Rik	keratin associated protein 28-13	protein-coding
mm_144874.1	chr18	36751163	36751182	+	1	NA	exon (NM_011879, exon 9 of 20)	exon (NM_011879, exon 9 of 20)	6516	NM_011879	24010	Mm.30234	NM_011879	ENSMUSG00000024474	Ik	MuRED	IK cytokine	protein-coding
mm_99771.1	chr11	107025605	107025630	+	1	NA	Intergenic	Intergenic	-2606	NM_001163473	69066	Mm.40679	NM_001163473	ENSMUSG00000078607	1810010H24Rik	OTTMUSG00000003581	RIKEN cDNA 1810010H24 gene	protein-coding
mm_86883.1	chr10	22158396	22158405	+	1	NA	promoter-TSS (NM_009016)	promoter-TSS (NM_009016)	-209	NM_009016	19368	Mm.458004	NM_009016		Raet1a	RAE-1alpha|Rae1alpha|Raet1	retinoic acid early transcript 1, alpha	protein-coding
mm_11320.1	chr2	30396443	30396462	+	1	NA	exon (NM_020329, exon 5 of 8)	exon (NM_020329, exon 5 of 8)	4198	NM_001290508	57170	Mm.285167	NM_020329	ENSMUSG00000026856	Dolpp1	0610011H20Rik|AB030189|LSFR2	dolichyl pyrophosphate phosphatase 1	protein-coding
mm_22512.1	chr3	7617344	7617375	+	1	NA	Intergenic	Intergenic	-3599	NM_001313888	16196	Mm.3825	NM_008371	ENSMUSG00000040329	Il7	A630026I06Rik|Il-7|hlb368	interleukin 7	protein-coding
mm_102682.1	chr11	65269864	65269879	-	1	NA	5' UTR (NM_145136, exon 1 of 14)	5' UTR (NM_145136, exon 1 of 14)	118	NM_145136	214384	Mm.32257	NM_145136	ENSMUSG00000020542	Myocd	BSAC2A|Srfcp	myocardin	protein-coding
mm_59633.1	chr7	28157549	28157564	+	1	NA	exon (NM_001164655, exon 16 of 20)	exon (NM_001164655, exon 16 of 20)	-12192	NM_007991	14113	Mm.4595	NM_007991	ENSMUSG00000046865	Fbl	AL022665|FIB|FLRN|RNU3IP1	fibrillarin	protein-coding
mm_27168.1	chr3	33801684	33801694	-	1	NA	intron (NM_001290502, intron 3 of 9)	intron (NM_001290502, intron 3 of 9)	1506	NM_025978	67120	Mm.275710	NM_025978	ENSMUSG00000027677	Ttc14	2700016E08Rik|4930434D01Rik|4931403I22Rik|4933402I15Rik|AI662468|AU014779|AW561908|cI-44|mKIAA1980	tetratricopeptide repeat domain 14	protein-coding
mm_61627.1	chr7	80232863	80232945	+	1	NA	promoter-TSS (NM_178752)	promoter-TSS (NM_178752)	11	NM_178752	269952	Mm.187733	NM_178752	ENSMUSG00000050973	Gdpgp1	D330012F22Rik	GDP-D-glucose phosphorylase 1	protein-coding
mm_12601.1	chr2	74679553	74679564	+	1	NA	promoter-TSS (NR_073086)	promoter-TSS (NR_073086)	0	NR_073086	15431	Mm.207763	NM_008273	ENSMUSG00000042499	Hoxd11	E230017H14Rik|Hox-4.6|Hox-5.4|Hox-5.5	homeobox D11	protein-coding
mm_84046.1	chr9	58094327	58094328	-	1	NA	intron (NM_001311085, intron 2 of 18)	intron (NM_001311085, intron 2 of 18)	7898	NM_029212	382077	Mm.335193	NM_029212	ENSMUSG00000037716	Ccdc33	4930535E21Rik|Gm1117|Tzip1	coiled-coil domain containing 33	protein-coding
mm_57599.1	chr6	127794774	127794802	-	1	NA	Intergenic	Intergenic	-6645	NR_106092	102466996		NR_106092	ENSMUSG00000104804	Mir7233	mmu-mir-7233	microRNA 7233	ncRNA
mm_137988.1	chr17	33629409	33629448	+	1	NA	intron (NM_026712, intron 1 of 5)	intron (NM_026712, intron 1 of 5)	336	NM_026712	328801	Mm.181488	NM_026712	ENSMUSG00000073423	Zfp414	0610030H11Rik|Znf414	zinc finger protein 414	protein-coding
mm_10951.1	chr2	25617804	25617815	+	1	NA	promoter-TSS (NM_029859)	promoter-TSS (NM_029859)	-131	NM_029859	77058	Mm.478493	NM_029859	ENSMUSG00000026940	Ccdc183	4921530D09Rik|Cccd183|Kiaa1984	coiled-coil domain containing 183	protein-coding
mm_94801.1	chr11	22990581	22990584	+	1	NA	promoter-TSS (NM_009837)	promoter-TSS (NM_009837)	-11	NM_009837	12464	Mm.296985	NM_009837	ENSMUSG00000007739	Cct4	2610204B21Rik|A45|C78323|Cctd	chaperonin containing Tcp1, subunit 4 (delta)	protein-coding
mm_151332.1	chr19	55894478	55894501	+	1	NA	promoter-TSS (NM_001142924)	promoter-TSS (NM_001142924)	-832	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_668.1	chr1	40462232	40462249	+	1	NA	3' UTR (NM_001025602, exon 11 of 11)	3' UTR (NM_001025602, exon 11 of 11)	-3312	NM_001161842	16182	Mm.253664	NM_008365	ENSMUSG00000026070	Il18r1	Il18ralpha|Il1rrp	interleukin 18 receptor 1	protein-coding
mm_155119.1	chrX	48695051	48695095	+	1	NA	promoter-TSS (NM_173376)	promoter-TSS (NM_173376)	69	NM_173376	209003	Mm.32561	NM_173376	ENSMUSG00000031107	Rbmx2	2700089A17Rik|2810411A03Rik|CGI-79	RNA binding motif protein, X-linked 2	protein-coding
mm_112319.1	chr12	115068013	115068018	-	1	NA	Intergenic	Intergenic	-554321	NR_106063	102465664		NR_106063	ENSMUSG00000098357	Mir7094-2	Gm27508|mmu-mir-7094-2	microRNA 7094-2	ncRNA
mm_123493.1	chr14	66153397	66153449	-	1	NA	TTS (NM_144803)	TTS (NM_144803)	12463	NM_144803	110902	Mm.57350	NM_144803	ENSMUSG00000022041	Chrna2	Acra-2|Acra2|BC011490	cholinergic receptor, nicotinic, alpha polypeptide 2 (neuronal)	protein-coding
mm_38919.1	chr4	150001373	150001391	-	1	NA	intron (NM_173371, intron 1 of 4)	intron (NM_173371, intron 1 of 4)	1854	NM_001291004	100198	Mm.22183	NM_173371	ENSMUSG00000028980	H6pd	AI785303|G6pd1|Gpd-1|Gpd1	hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase)	protein-coding
mm_145035.1	chr18	39353672	39353677	+	1	NA	intron (NM_175164, intron 20 of 22)	intron (NM_175164, intron 20 of 22)	133571	NM_008173	14815	Mm.129481	NM_008173	ENSMUSG00000024431	Nr3c1	GR|Grl-1|Grl1	nuclear receptor subfamily 3, group C, member 1	protein-coding
mm_131700.1	chr16	20717755	20717784	+	1	NA	promoter-TSS (NM_145632)	promoter-TSS (NM_145632)	-57	NM_145632	245841	Mm.288730	NM_145632	ENSMUSG00000021018	Polr2h	-	polymerase (RNA) II (DNA directed) polypeptide H	protein-coding
mm_40550.1	chr5	58129402	58129405	+	1	NA	3' UTR (NM_001310606, exon 3 of 3)	3' UTR (NM_001310606, exon 3 of 3)	323595	NR_046190	78163	Mm.243828	NR_046190	ENSMUSG00000105234	4930459L07Rik	-	RIKEN cDNA 4930459L07 gene	ncRNA
mm_33375.1	chr4	129515620	129515642	+	1	NA	TTS (NM_008228)	TTS (NM_008228)	2050	NM_010807	17357	Mm.424974	NM_010807	ENSMUSG00000047945	Marcksl1	AL022768|AW215397|AW536807|D4Bc1|F52|MacMARCKS|Macs2|Macs3|Mlp|Mrp	MARCKS-like 1	protein-coding
mm_15561.1	chr2	158512748	158512771	+	1	NA	promoter-TSS (NM_001145015)	promoter-TSS (NM_001145015)	-37	NM_001145015	545481	Mm.125371	NM_001145015	ENSMUSG00000074625	Arhgap40	C20orf95|Gm14203|OTTMUSG00000015933	Rho GTPase activating protein 40	protein-coding
mm_55279.1	chr6	54292743	54292744	-	1	NA	intron (NM_023543, intron 3 of 6)	intron (NM_023543, intron 3 of 6)	19921	NM_023543	69993	Mm.321147	NM_023543	ENSMUSG00000004633	Chn2	1700026N20Rik|4930557O16Rik|ARHGAP3|Bch	chimerin 2	protein-coding
mm_88293.1	chr10	75273351	75273370	+	1	NA	intron (NM_153406, intron 10 of 15)	intron (NM_153406, intron 10 of 15)	-43517	NM_009630	11540	Mm.333734	NM_009630	ENSMUSG00000020178	Adora2a	A2AAR|A2aR|AA2AR	adenosine A2a receptor	protein-coding
mm_72593.1	chr8	84414264	84414274	+	1	NA	Intergenic	CpG	-1095	NM_001252060	12286	Mm.334658	NM_007578	ENSMUSG00000034656	Cacna1a	APCA|BI|Caca1a|Cacnl1a4|Cav2.1|Ccha1a|EA2|FHM|HPCA|MHP|MHP1|SCA6|alpha1A|la|nmf352|rkr|smrl|tg	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	protein-coding
mm_53017.1	chr6	123283455	123283531	+	1	NA	3' UTR (NM_019948, exon 6 of 6)	3' UTR (NM_019948, exon 6 of 6)	6378	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_118217.1	chr13	110280840	110280858	-	1	NA	promoter-TSS (NM_023852)	promoter-TSS (NM_023852)	-643	NM_023852	67295	Mm.151600	NM_023852	ENSMUSG00000021700	Rab3c	2700062I01Rik|3110015B08Rik|3110037E15Rik|AI850886	RAB3C, member RAS oncogene family	protein-coding
mm_102522.1	chr11	60913733	60913751	-	1	NA	promoter-TSS (NM_025294)	promoter-TSS (NM_025294)	50	NM_025294	24083	Mm.22780	NM_025294	ENSMUSG00000018931	Natd1	AI256713|F3-2|Gm16515|Gtlf3b	N-acetyltransferase domain containing 1	protein-coding
mm_127714.1	chr15	103014371	103014389	+	1	NA	promoter-TSS (NR_030526)	promoter-TSS (NR_030526)	372	NM_175730	15424	Mm.103825	NM_175730	ENSMUSG00000022485	Hoxc5	AI181837|Hox-3.4|Hox-6.2	homeobox C5	protein-coding
mm_78726.1	chr9	41580904	41580922	+	1	NA	promoter-TSS (NR_015483)	promoter-TSS (NR_015483)	-340	NR_015483	73144	Mm.38166	NM_001033153	ENSMUSG00000074415	3110039I08Rik	2610203C20Rik|AI848448|D230004N17Rik|D3Mgi9|Mir100hg	RIKEN cDNA 3110039I08 gene	ncRNA
mm_45446.1	chr5	67427795	67427813	-	1	NA	promoter-TSS (NM_001164806)	promoter-TSS (NM_001164806)	-5	NM_001164806	666938	Mm.101339	NM_001164806	ENSMUSG00000092060	Bend4	D330027G24Rik|EG666938	BEN domain containing 4	protein-coding
mm_129621.1	chr15	80083343	80083359	-	1	NA	promoter-TSS (NM_013762)	promoter-TSS (NM_013762)	55	NM_013762	27367	Mm.290771	NM_013762	ENSMUSG00000060036	Rpl3	F2|J1	ribosomal protein L3	protein-coding
mm_96548.1	chr11	68864161	68864199	+	1	NA	Intergenic	MLT1D|LTR|ERVL-MaLR	-11049	NM_023668	83431	Mm.31979	NM_023668	ENSMUSG00000018736	Ndel1	2600006O07Rik|MITAP1|NUDEL|mNudel	nudE neurodevelopment protein 1 like 1	protein-coding
mm_165460.1	chr2	158666399	158666439	+	1	NA	promoter-TSS (NM_001159662)	promoter-TSS (NM_001159662)	-314	NM_153089	228852	Mm.150540	NM_153089	ENSMUSG00000037754	Ppp1r16b	ANKRD4|C130078N17Rik|TIMAP|Wdt4	protein phosphatase 1, regulatory (inhibitor) subunit 16B	protein-coding
mm_133336.1	chr16	78930941	78930958	+	1	NA	promoter-TSS (NM_139134)	promoter-TSS (NM_139134)	1	NM_139134	246048	Mm.77895	NM_139134	ENSMUSG00000022860	Chodl	3110074E07Rik|MT75|PRED12	chondrolectin	protein-coding
mm_121033.1	chr14	79769927	79769935	+	1	NA	exon (NM_021543, exon 1 of 3)	exon (NM_021543, exon 1 of 3)	1381	NM_001042726	18530	Mm.390715	NM_021543	ENSMUSG00000036422	Pcdh8	1700080P15Rik|Papc	protocadherin 8	protein-coding
mm_45892.1	chr5	88564834	88564905	-	1	NA	promoter-TSS (NM_001289775)	promoter-TSS (NM_001289775)	-171	NM_001289774	52822	Mm.270469	NM_027530	ENSMUSG00000029291	Rufy3	2810428M05Rik|6330416M07Rik|AW455998|AW538594|D5Bwg0860e|Ripx|Rpipx	RUN and FYVE domain containing 3	protein-coding
mm_60481.1	chr7	44478384	44478398	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-6126	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_159987.1	chr6	114458521	114458521	+	1	NA	promoter-TSS (NM_001317124)	promoter-TSS (NM_001317124)	-1	NM_001317124	15465	Mm.333327	NM_008285	ENSMUSG00000053004	Hrh1	Bphs|H1R|HH1R|Hir	histamine receptor H1	protein-coding
mm_3976.1	chr1	164249024	164249051	+	1	NA	promoter-TSS (NM_054087)	promoter-TSS (NM_054087)	-9	NM_054087	116914	Mm.35444	NM_054087	ENSMUSG00000040918	Slc19a2	AV276020|AW322295|DDA1|THTR1|TRMA	solute carrier family 19 (thiamine transporter), member 2	protein-coding
mm_145835.1	chr18	65442365	65442380	+	1	NA	intron (NM_172833, intron 2 of 15)	intron (NM_172833, intron 2 of 15)	11375	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_75944.1	chr8	71569464	71569472	-	1	NA	intron (NM_011977, intron 2 of 13)	intron (NM_011977, intron 2 of 13)	541	NM_011977	26457	Mm.38165	NM_011977	ENSMUSG00000031808	Slc27a1	FATP1|Fatp	solute carrier family 27 (fatty acid transporter), member 1	protein-coding
mm_63305.1	chr7	126847909	126847919	+	1	NA	5' UTR (NM_010069, exon 1 of 11)	5' UTR (NM_010069, exon 1 of 11)	361	NM_010069	13446	Mm.266301	NM_010069	ENSMUSG00000052301	Doc2a	-	double C2, alpha	protein-coding
mm_132658.1	chr16	41666310	41666320	+	1	NA	intron (NM_001347236, intron 1 of 6)	intron (NM_001347236, intron 1 of 6)	132973	NM_175548	268890	Mm.310524	NM_175548	ENSMUSG00000061080	Lsamp	5430428I19|AW046674|B130007O04Rik|D930023J12Rik|Lam|Lamp	limbic system-associated membrane protein	protein-coding
mm_79617.1	chr9	58652419	58652448	+	1	NA	TTS (NM_028598)	TTS (NM_028598)	70193	NM_009145	20320	Mm.15125	NM_009145	ENSMUSG00000032336	Nptn	AW554172|SDR-1|Sdfr1	neuroplastin	protein-coding
mm_33959.1	chr4	137507247	137507250	+	1	NA	intron (NM_008305, intron 3 of 96)	L1MEg|LINE|L1	-31038	NR_105985	102465616		NR_105985	ENSMUSG00000099134	Mir7018	Gm27606|mmu-mir-7018	microRNA 7018	ncRNA
mm_132340.1	chr16	33829776	33829780	+	1	NA	5' UTR (NM_001145884, exon 1 of 15)	5' UTR (NM_001145884, exon 1 of 15)	113	NM_001145884	16419	Mm.6424	NM_010580	ENSMUSG00000022817	Itgb5	AA475909|AI874634|ESTM23|[b]-5|[b]5|[b]5A|[b]5B|beta-5|beta5	integrin beta 5	protein-coding
mm_9704.1	chr1	179381704	179381717	-	1	NA	intron (NM_027188, intron 5 of 11)	intron (NM_027188, intron 5 of 11)	136293	NM_027188	69726	Mm.222338	NM_027188	ENSMUSG00000055067	Smyd3	2410008A19Rik|Zmynd1	SET and MYND domain containing 3	protein-coding
mm_51814.1	chr6	88902387	88902414	+	1	NA	5' UTR (NM_011906, exon 1 of 12)	5' UTR (NM_011906, exon 1 of 12)	149	NM_011906	24100	Mm.284480	NM_011906	ENSMUSG00000002871	Tpra1	40kDa|Gpr175|Tpra40	transmembrane protein, adipocyte asscociated 1	protein-coding
mm_3381.1	chr1	139454846	139454869	+	1	NA	promoter-TSS (NM_009791)	promoter-TSS (NM_009791)	84	NM_009791	12316	Mm.168523	NM_009791	ENSMUSG00000033952	Aspm	Calmbp1|D330028K02Rik|MCPH5|Sha1	asp (abnormal spindle)-like, microcephaly associated (Drosophila)	protein-coding
mm_76884.1	chr8	105634855	105634872	-	1	NA	Intergenic	B1_Mur4|SINE|Alu	-1675	NM_181322	13018	Mm.269474	NM_181322	ENSMUSG00000005698	Ctcf	AW108038	CCCTC-binding factor	protein-coding
mm_40755.1	chr5	66890326	66890329	+	1	NA	intron (NM_001001980, intron 3 of 25)	intron (NM_001001980, intron 3 of 25)	-78089	NM_001256122	77569	Mm.374778	NM_001001980	ENSMUSG00000037736	Limch1	3732412D22Rik|mKIAA1102	LIM and calponin homology domains 1	protein-coding
mm_102735.1	chr11	67250938	67250958	-	1	NA	exon (NM_010855, exon 22 of 40)	exon (NM_010855, exon 22 of 40)	13136	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_77126.1	chr8	111337748	111337758	-	1	NA	intron (NM_029005, intron 1 of 10)	intron (NM_029005, intron 1 of 10)	452	NM_001310613	74568	Mm.207971	NM_029005	ENSMUSG00000012519	Mlkl	9130019I15Rik	mixed lineage kinase domain-like	protein-coding
mm_12471.1	chr2	71453324	71453370	+	1	NA	promoter-TSS (NM_025633)	promoter-TSS (NM_025633)	9	NM_025633	66559	Mm.152796	NM_025633	ENSMUSG00000041921	Metap1d	2310066F24Rik|3110033D18Rik|AV117938|MAP 1D|Map1d|MetAP 1D|Metapl1	methionyl aminopeptidase type 1D (mitochondrial)	protein-coding
mm_7967.1	chr1	134040361	134040385	-	1	NA	exon (NM_021355, exon 2 of 3)	exon (NM_021355, exon 2 of 3)	2858	NM_021355	14264	Mm.287146	NM_021355	ENSMUSG00000041559	Fmod	AI131919|AU041740|SLRR2E	fibromodulin	protein-coding
mm_21849.1	chr2	165861599	165861616	-	1	NA	intron (NM_027230, intron 2 of 23)	intron (NM_027230, intron 2 of 23)	-3434	NM_001252585	228880	Mm.227598	NM_027230	ENSMUSG00000039671	Zmynd8	1110013E22Rik|2010005I16Rik|3632413B07Rik|AI316811|AL024039|Prkcbp1|RACK7	zinc finger, MYND-type containing 8	protein-coding
mm_6483.1	chr1	74096850	74096864	-	1	NA	intron (NM_027884, intron 1 of 34)	intron (NM_027884, intron 1 of 34)	27590	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_27320.1	chr3	50366985	50367020	-	1	NA	3' UTR (NM_011990, exon 12 of 12)	3' UTR (NM_011990, exon 12 of 12)	76611	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_65117.1	chr7	19359478	19359488	-	1	NA	promoter-TSS (NM_145822)	promoter-TSS (NM_145822)	0	NM_145822	70333	Mm.171370	NM_145822	ENSMUSG00000047649	Cd3eap	1190028F09|2610103M17Rik|ASE-1|Ase1|CAST|PAF49	CD3E antigen, epsilon polypeptide associated protein	protein-coding
mm_133933.1	chr16	3872256	3872283	-	1	NA	5' UTR (NM_001033159, exon 1 of 3)	5' UTR (NM_001033159, exon 1 of 3)	105	NM_001033159	71063	Mm.379190	NM_001033159	ENSMUSG00000039789	Zfp597	4933407K12Rik|AI462383|AI666357	zinc finger protein 597	protein-coding
mm_26471.1	chr3	144570373	144570383	+	1	NA	promoter-TSS (NM_053102)	promoter-TSS (NM_053102)	-49	NM_053102	93684	Mm.29812	NM_053102	ENSMUSG00000037072	Selenof	9430015P09Rik|Sep15	selenoprotein F	protein-coding
mm_56798.1	chr6	116656329	116656341	-	1	NA	intron (NM_178045, intron 3 of 10)	(TG)n|Simple_repeat|Simple_repeat	5651	NM_001166580	213393	Mm.38231	NM_145980	ENSMUSG00000048489	8430408G22Rik	Depp|Fseg	RIKEN cDNA 8430408G22 gene	protein-coding
mm_38490.1	chr4	140835736	140835749	-	1	NA	intron (NM_011059, intron 1 of 15)	intron (NM_011059, intron 1 of 15)	10036	NM_011059	18599	Mm.20854	NM_011059	ENSMUSG00000025329	Padi1	AV236283|Pdi1	peptidyl arginine deiminase, type I	protein-coding
mm_143146.1	chr17	57222251	57222273	-	1	NA	exon (NM_009778, exon 14 of 41)	exon (NM_009778, exon 14 of 41)	-5034	NR_105944	102465591		NR_105944	ENSMUSG00000099066	Mir6978	Gm27858|mmu-mir-6978	microRNA 6978	ncRNA
mm_170583.1	chr1	9574531	9574534	+	1	NA	intron (NR_027664, intron 12 of 12)	PB1D10|SINE|Alu	26486	NR_027664	76187	Mm.28514	NM_175236	ENSMUSG00000025911	Adhfe1	6330565B14Rik|AI043035|Adh8	alcohol dehydrogenase, iron containing, 1	protein-coding
mm_44975.1	chr5	36825632	36825645	-	1	NA	intron (NM_008550, intron 4 of 18)	intron (NM_008550, intron 4 of 18)	5011	NM_008550	17160	Mm.761	NM_008550	ENSMUSG00000029119	Man2b2	mKIAA0935	mannosidase 2, alpha B2	protein-coding
mm_136822.1	chr17	12420929	12420933	+	1	NA	3' UTR (NM_011395, exon 11 of 11)	3' UTR (NM_011395, exon 11 of 11)	42322	NM_008877	18815	Mm.971	NM_008877	ENSMUSG00000059481	Plg	AI649309|Pg	plasminogen	protein-coding
mm_170425.1	chr18	72539207	72539211	+	1	NA	Intergenic	Intergenic	-188140	NM_007831	13176	Mm.167882	NM_007831	ENSMUSG00000060534	Dcc	C030036D22Rik|Igdcc1	deleted in colorectal carcinoma	protein-coding
mm_16711.1	chr2	7085695	7085702	-	1	NA	intron (NM_001110231, intron 3 of 15)	(TATG)n|Simple_repeat|Simple_repeat	-4396	NM_001160292	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_62915.1	chr7	117998530	117998534	+	1	NA	Intergenic	Intergenic	117615	NM_170669	267019	Mm.288212	NM_170669	ENSMUSG00000008683	Rps15a	A630031B11Rik	ribosomal protein S15A	protein-coding
mm_33337.1	chr4	129231790	129231804	+	1	NA	intron (NM_001285867, intron 1 of 6)	intron (NM_001285867, intron 1 of 6)	-3886	NM_001285866	97130	Mm.331907	NM_001033189	ENSMUSG00000050390	C77080	Kiaa1522|mKIAA1522	expressed sequence C77080	protein-coding
mm_54193.1	chr6	24527547	24527585	-	1	NA	promoter-TSS (NM_080847)	promoter-TSS (NM_080847)	119	NM_001311068	68202	Mm.275780	NM_026614	ENSMUSG00000023089	Ndufa5	2900002J19Rik	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 5	protein-coding
mm_147701.1	chr18	60808294	60808316	-	1	NA	exon (NM_010545, exon 3 of 8)	exon (NM_010545, exon 3 of 8)	-3771	NR_039567	100628611		NR_039567	ENSMUSG00000093327	Mir5107	mir-5107|mmu-mir-5107|mu-mir-5107	microRNA 5107	ncRNA
mm_3760.1	chr1	156052300	156052313	+	1	NA	3' UTR (NM_001160182, exon 3 of 3)	3' UTR (NM_001160182, exon 3 of 3)	11445	NM_022329	240832	Mm.253335	NM_022329	ENSMUSG00000050565	Tor1aip2	1110020D10Rik|15kDa|A130072J07|AA103493|AW060462|AW610675|C77739|Ifrg15|Lull1	torsin A interacting protein 2	protein-coding
mm_159680.1	chr5	3657148	3657148	+	1	NA	5' UTR (NM_029154, exon 1 of 11)	5' UTR (NM_029154, exon 1 of 11)	144	NM_029154	75010	Mm.85064	NM_029141	ENSMUSG00000014529	Tmbim7	4930403J02Rik|4930500J03Rik|4930511M11Rik|Lfg5|Lgf5|Tmbim1b	transmembrane BAX inhibitor motif containing 7	protein-coding
mm_15395.1	chr2	156721341	156721345	+	1	NA	promoter-TSS (NM_001042487)	promoter-TSS (NM_001042487)	64	NM_001042487	228836	Mm.22094	NM_146128	ENSMUSG00000061689	Dlgap4	AI225853|BC024558|DAP-4|DAP4|SAPAP-4|Sapap4|WBP16	discs, large homolog-associated protein 4 (Drosophila)	protein-coding
mm_156905.1	chrX	169036674	169036704	+	1	NA	promoter-TSS (NM_178754)	promoter-TSS (NM_178754)	78	NR_109847	11856	Mm.441810	NM_009707	ENSMUSG00000031355	Arhgap6	AI504284|RhoGAPX-1	Rho GTPase activating protein 6	protein-coding
mm_3154.1	chr1	135154642	135154686	+	1	NA	intron (NM_026823, intron 5 of 6)	intron (NM_026823, intron 5 of 6)	7830	NM_026823	68724	Mm.174998	NM_026823	ENSMUSG00000026426	Arl8a	1110033P22Rik|Arl10b|gie2	ADP-ribosylation factor-like 8A	protein-coding
mm_34255.1	chr4	141368117	141368179	+	1	NA	promoter-TSS (NM_001085513)	promoter-TSS (NM_001085513)	-44	NM_001085513	277743	Mm.294614	NM_001085513	ENSMUSG00000006218	Fam131c	Gm693	family with sequence similarity 131, member C	protein-coding
mm_70035.1	chr7	142577365	142577378	-	1	NA	promoter-TSS (NR_030416)	promoter-TSS (NR_030416)	-224	NR_030416	735280		NR_030416	ENSMUSG00000076275	Mir675	Mirn675|mir-675|mmu-mir-675	microRNA 675	ncRNA
mm_103637.1	chr11	78959898	78959923	-	1	NA	3' UTR (NM_010927, exon 27 of 27)	3' UTR (NM_010927, exon 27 of 27)	25014	NM_001159301	16859	Mm.341434	NM_010708	ENSMUSG00000001123	Lgals9	AA407335|AI194909|AI265545|LGALS35|Lgals5|gal-9|galectin-9	lectin, galactose binding, soluble 9	protein-coding
mm_167819.1	chr9	124312642	124312699	-	1	NA	promoter-TSS (NM_001243117)	promoter-TSS (NM_001243117)	24	NM_001243118	630836	Mm.458553	NM_001243117	ENSMUSG00000074829	2010315B03Rik	BC029716	RIKEN cDNA 2010315B03 gene	protein-coding
mm_78837.1	chr9	44255035	44255057	+	1	NA	intron (NM_178420, intron 8 of 9)	intron (NM_178420, intron 8 of 9)	-3582	NM_133226	170761	Mm.29872	NM_133226	ENSMUSG00000032105	Pdzd3	NaPi-Cap2|Pdzk2	PDZ domain containing 3	protein-coding
mm_92961.1	chr10	85957736	85957761	-	1	NA	promoter-TSS (NM_145422)	promoter-TSS (NM_145422)	45	NM_145422	28088	Mm.9257	NM_145422	ENSMUSG00000001783	Rtcb	AI255213|AI463255|D10Wsu52e|FAAP|HSPC117	RNA 2',3'-cyclic phosphate and 5'-OH ligase	protein-coding
mm_141732.1	chr17	34119318	34119340	-	1	NA	non-coding (NR_037970, exon 1 of 13)	non-coding (NR_037970, exon 1 of 13)	571	NR_037970	14312	Mm.3444	NM_010238	ENSMUSG00000024335	Brd2	AW228947|D17H6S113E|Frg-1|Fsrg-1|Fsrg1|Nat|Ring3|Rnf3|mKIAA4005	bromodomain containing 2	protein-coding
mm_81295.1	chr9	108337536	108337541	+	1	NA	3' UTR (NM_016802, exon 6 of 6)	3' UTR (NM_016802, exon 6 of 6)	-1542	NM_008160	14775	Mm.1090	NM_008160	ENSMUSG00000063856	Gpx1	AI195024|AL033363|CGPx|GPx-1|GSHPx-1|Gpx	glutathione peroxidase 1	protein-coding
mm_98772.1	chr11	96742956	96742959	+	1	NA	intron (NM_001177898, intron 10 of 10)	intron (NM_001177898, intron 10 of 10)	34598	NM_028965	74479	Mm.270781	NM_028965	ENSMUSG00000020876	Snx11	4933439F10Rik|A930041K09Rik|AI117694	sorting nexin 11	protein-coding
mm_1449.1	chr1	67230561	67230566	+	1	NA	3' UTR (NM_001080809, exon 38 of 38)	3' UTR (NM_001080809, exon 38 of 38)	107536	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_24913.1	chr3	96247831	96247874	+	1	NA	TTS (NM_178216)	TTS (NM_178216)	1152	NM_054045	97114	Mm.358797	NM_054045	ENSMUSG00000081058	Hist2h3c2	H3-614|H3.2-614|Hist2h3c2-ps|Hist2h3ca1|M32461	histone cluster 2, H3c2	protein-coding
mm_168923.1	chr12	61705610	61705616	-	1	NA	intron (NM_178714, intron 2 of 3)	intron (NM_178714, intron 2 of 3)	182446	NM_001310586	238205	Mm.28802	NM_178714	ENSMUSG00000035653	Lrfn5	AI427653|AI604817|C130061B21|mKIAA4208	leucine rich repeat and fibronectin type III domain containing 5	protein-coding
mm_98184.1	chr11	87793407	87793415	+	1	NA	promoter-TSS (NM_010824)	promoter-TSS (NM_010824)	-373	NM_010824	17523	Mm.4668	NM_010824	ENSMUSG00000009350	Mpo	mKIAA4033	myeloperoxidase	protein-coding
mm_38864.1	chr4	149446266	149446279	-	1	NA	Intergenic	Intergenic	8696	NM_022020	63954	Mm.46023	NM_022020	ENSMUSG00000028996	Rbp7	1110002J23Rik|CRBP-III	retinol binding protein 7, cellular	protein-coding
mm_97613.1	chr11	78952786	78952798	+	1	NA	intron (NM_001313921, intron 20 of 25)	intron (NM_001313921, intron 20 of 25)	27501	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_3142.1	chr1	135144329	135144353	+	1	NA	3' UTR (NM_177081, exon 10 of 10)	3' UTR (NM_177081, exon 10 of 10)	-2493	NM_026823	68724	Mm.174998	NM_026823	ENSMUSG00000026426	Arl8a	1110033P22Rik|Arl10b|gie2	ADP-ribosylation factor-like 8A	protein-coding
mm_160815.1	chr11	22956525	22956525	-	1	NA	exon (NM_144514, exon 2 of 3)	exon (NM_144514, exon 2 of 3)	-15480	NM_011663	22183	Mm.29542	NM_011663	ENSMUSG00000044068	Zrsr1	D11Ncvs75|Irlgs2|SP2|U2af1-rs1|U2afbp-rs	zinc finger (CCCH type), RNA binding motif and serine/arginine rich 1	protein-coding
mm_47909.1	chr5	134946440	134946443	-	1	NA	exon (NM_009903, exon 1 of 1)	exon (NM_009903, exon 1 of 1)	493	NM_009903	12740	Mm.7339	NM_009903	ENSMUSG00000047501	Cldn4	Cep-r|Cpetr|Cpetr1	claudin 4	protein-coding
mm_134919.1	chr16	30359247	30359250	-	1	NA	intron (NM_001128096, intron 7 of 33)	intron (NM_001128096, intron 7 of 33)	29282	NM_001128094	224088	Mm.8924	NM_001128094	ENSMUSG00000022533	Atp13a3	AU022875|Gm1745|Gm541|Gm542	ATPase type 13A3	protein-coding
mm_95469.1	chr11	50611297	50611298	+	1	NA	intron (NM_175643, intron 2 of 21)	intron (NM_175643, intron 2 of 21)	9212	NM_175643	216725	Mm.110597	NM_175643	ENSMUSG00000036545	Adamts2	ADAM-TS 2|ADAM-TS2|ADAMTS-2|PC I-NP|PCINP|pNPI	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 2	protein-coding
mm_14655.1	chr2	136944044	136944047	+	1	NA	intron (NM_001038641, intron 2 of 7)	B1_Mur1|SINE|Alu	44694	NM_001038641	74243	Mm.330612	NM_028201	ENSMUSG00000027281	Slx4ip	2210009G21Rik|2410004I22Rik|C85661|Slxip	SLX4 interacting protein	protein-coding
mm_21338.1	chr2	157107455	157107466	-	1	NA	exon (NM_001139520, exon 12 of 17)	exon (NM_001139520, exon 12 of 17)	20405	NM_001177439	383766	Mm.480305	NM_001177439	ENSMUSG00000074628	Tldc2	Gm1332	TBC/LysM associated domain containing 2	protein-coding
mm_114133.1	chr13	55212720	55212751	+	1	NA	intron (NM_008739, intron 1 of 22)	CpG	2953	NM_008739	18193	Mm.12964	NM_008739	ENSMUSG00000021488	Nsd1	AI528500|KMT3B	nuclear receptor-binding SET-domain protein 1	protein-coding
mm_75451.1	chr8	47675589	47675617	-	1	NA	promoter-TSS (NM_023503)	promoter-TSS (NM_023503)	-444	NM_023503	69260	Mm.430733	NM_023503	ENSMUSG00000063049	Ing2	2810011M06Rik|Ing1l|Ing2b|P33ING2	inhibitor of growth family, member 2	protein-coding
mm_118193.1	chr13	107823549	107823553	-	1	NA	intron (NM_145456, intron 2 of 14)	intron (NM_145456, intron 2 of 14)	-62464	NR_029759	723929		NR_029759	ENSMUSG00000065425	Mir325	Mirn325|mmu-mir-325	microRNA 325	ncRNA
mm_47261.1	chr5	121836248	121836279	-	1	NA	promoter-TSS (NM_001306126)	promoter-TSS (NM_001306126)	-159	NM_001306126	16923	Mm.65493	NM_008507	ENSMUSG00000042594	Sh2b3	AI429800|Lnk	SH2B adaptor protein 3	protein-coding
mm_62853.1	chr7	114416706	114416719	+	1	NA	intron (NM_011055, intron 1 of 15)	intron (NM_011055, intron 1 of 15)	1458	NM_011055	18576	Mm.430730	NM_011055	ENSMUSG00000030671	Pde3b	9830102A01Rik|AI847709	phosphodiesterase 3B, cGMP-inhibited	protein-coding
mm_65524.1	chr7	25786994	25787006	-	1	NA	intron (NM_009465, intron 2 of 19)	intron (NM_009465, intron 2 of 19)	1733	NM_001190974	26362	Mm.4128	NM_009465	ENSMUSG00000002602	Axl	AI323647|Ark|Tyro7|Ufo	AXL receptor tyrosine kinase	protein-coding
mm_43013.1	chr5	123907187	123907197	+	1	NA	promoter-TSS (NM_026603)	promoter-TSS (NM_026603)	-83	NM_026603	68184	Mm.28549	NM_026603	ENSMUSG00000023106	Denr	1500003K04Rik	density-regulated protein	protein-coding
mm_166401.1	chr5	136015187	136015203	+	1	NA	intron (NM_001256096, intron 4 of 10)	intron (NM_001256096, intron 4 of 10)	20395	NM_001256098	74198	Mm.275574	NM_023742	ENSMUSG00000004947	Dtx2	2610524D08Rik|AA408415|AU022494|Deltex2	deltex 2, E3 ubiquitin ligase	protein-coding
mm_29944.1	chr3	132906755	132906765	-	1	NA	exon (NM_001287103, exon 6 of 12)	exon (NM_001287103, exon 6 of 12)	-28164	NR_102298	101243624	Mm.306256	NR_102297	ENSMUSG00000106230	Gm29811	-	predicted gene, 29811	ncRNA
mm_90351.1	chr10	127165119	127165225	+	1	NA	promoter-TSS (NM_027739)	promoter-TSS (NM_027739)	16	NM_001244617	14421	Mm.386762	NM_008080	ENSMUSG00000006731	B4galnt1	4933429D13Rik|Gal-NAc-T|GalNAc-T|GalNAcT|Galgt1|Ggm-2|Ggm2	beta-1,4-N-acetyl-galactosaminyl transferase 1	protein-coding
mm_89715.1	chr10	98878066	98878073	+	1	NA	Intergenic	Intergenic	-37083	NM_026482	67972	Mm.166944	NM_026482	ENSMUSG00000019943	Atp2b1	2810442I22Rik|E130111D10Rik|Pmca1	ATPase, Ca++ transporting, plasma membrane 1	protein-coding
mm_59646.1	chr7	28162780	28162790	+	1	NA	exon (NM_001164655, exon 18 of 20)	exon (NM_001164655, exon 18 of 20)	-6963	NM_007991	14113	Mm.4595	NM_007991	ENSMUSG00000046865	Fbl	AL022665|FIB|FLRN|RNU3IP1	fibrillarin	protein-coding
mm_3011.1	chr1	133363565	133363581	+	1	NA	promoter-TSS (NM_175443)	promoter-TSS (NM_175443)	1	NM_175443	214253	Mm.52111	NM_175443	ENSMUSG00000070644	Etnk2	4933417N20Rik|AI197444|EKI 2|Eki2|Tuc1	ethanolamine kinase 2	protein-coding
mm_163662.1	chr13	75906863	75906863	+	1	NA	intron (NM_028493, intron 6 of 11)	intron (NM_028493, intron 6 of 11)	36961	NM_028493	73296	Mm.276200	NM_028493	ENSMUSG00000021589	Rhobtb3	1700040C17Rik|2610033K01Rik|4930503C18Rik|AI317148|AW208826|mKIAA0878	Rho-related BTB domain containing 3	protein-coding
mm_62367.1	chr7	100607661	100607823	+	1	NA	5' UTR (NM_024287, exon 1 of 8)	5' UTR (NM_024287, exon 1 of 8)	156	NM_001163663	19346	Mm.28650	NM_024287	ENSMUSG00000030704	Rab6a	2610028L11Rik|AA419671|Rab6	RAB6A, member RAS oncogene family	protein-coding
mm_102726.1	chr11	67240775	67240794	-	1	NA	exon (NM_010855, exon 3 of 40)	exon (NM_010855, exon 3 of 40)	2972	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_122077.1	chr14	30605167	30605175	-	1	NA	intron (NM_011103, intron 8 of 17)	intron (NM_011103, intron 8 of 17)	5139	NM_001310682	18753	Mm.2314	NM_011103	ENSMUSG00000021948	Prkcd	AI385711|D14Ertd420e|PKC[d]|PKCdelta|Pkcd	protein kinase C, delta	protein-coding
mm_71959.1	chr8	70527800	70527810	+	1	NA	promoter-TSS (NM_001199631)	promoter-TSS (NM_001199631)	-41	NM_001199631	14232	Mm.141864	NM_010223	ENSMUSG00000019428	Fkbp8	38kDa|FKBP-38|FKBP-8|Fkbp38	FK506 binding protein 8	protein-coding
mm_9636.1	chr1	177033707	177033709	-	1	NA	intron (NM_011785, intron 11 of 12)	intron (NM_011785, intron 11 of 12)	-197575	NR_037996	15365	Mm.441435	NR_037996		Hmga2-ps1	EG666235|Gm7996|Hmgic-ps1|[y]i-c	high mobility group AT-hook 2, pseudogene 1	pseudo
mm_45320.1	chr5	65454749	65454764	-	1	NA	intron (NM_133697, intron 3 of 4)	intron (NM_133697, intron 3 of 4)	-18914	NM_009466	22235	Mm.344831	NM_009466	ENSMUSG00000029201	Ugdh	Udpgdh	UDP-glucose dehydrogenase	protein-coding
mm_112641.1	chr13	16016329	16016340	+	1	NA	intron (NM_008380, intron 3 of 4)	intron (NM_008380, intron 3 of 4)	4483	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_4080.1	chr1	166379273	166379357	+	1	NA	5' UTR (NM_030245, exon 1 of 8)	5' UTR (NM_030245, exon 1 of 8)	148	NM_030245	27878	Mm.100665	NM_030245	ENSMUSG00000026563	Tada1	2900026B15Rik|D1Ertd251e|Staf42|Tada1l	transcriptional adaptor 1	protein-coding
mm_9668.1	chr1	178276637	178276651	-	1	NA	Intergenic	Intergenic	-42509	NM_025511	66359	Mm.489720	NM_025511	ENSMUSG00000026500	Cox20	2310005N03Rik|Fam36a	COX20 Cox2 chaperone	protein-coding
mm_75432.1	chr8	47289324	47289349	-	1	NA	promoter-TSS (NM_001286376)	promoter-TSS (NM_001286376)	66	NM_001286376	71069	Mm.23973	NM_175162	ENSMUSG00000038143	Stox2	4933409N07Rik|AI449080|AI835114|mKIAA1392	storkhead box 2	protein-coding
mm_145517.1	chr18	60443298	60443324	+	1	NA	Intergenic	(GA)n|Simple_repeat|Simple_repeat	58672	NM_134133	106878	Mm.273197	NM_134133	ENSMUSG00000038059	Smim3	2010002N04Rik|AI195350|AW561905|Nid67|cI-41	small integral membrane protein 3	protein-coding
mm_124700.1	chr15	6445364	6445376	+	1	NA	promoter-TSS (NM_013485)	promoter-TSS (NM_013485)	37	NM_013485	12279	Mm.29095	NM_013485	ENSMUSG00000022149	C9	-	complement component 9	protein-coding
mm_79558.1	chr9	58021950	58021964	+	1	NA	intron (NM_019779, intron 5 of 8)	MLT1B|LTR|ERVL-MaLR	7005	NM_019779	13070	Mm.302865	NM_019779	ENSMUSG00000032323	Cyp11a1	Cyp11a|Cypxia1|D9Ertd411e|P450scc|Scc|cscc	cytochrome P450, family 11, subfamily a, polypeptide 1	protein-coding
mm_37452.1	chr4	123411882	123411932	-	1	NA	promoter-TSS (NM_001167918)	promoter-TSS (NM_001167918)	4	NM_001167918	442834	Mm.483803	NM_001167918		D830031N03Rik	Kiaa0754|mKIAA0754	RIKEN cDNA D830031N03 gene	protein-coding
mm_39043.1	chr4	152418799	152418810	-	1	NA	intron (NM_001252654, intron 2 of 14)	intron (NM_001252654, intron 2 of 14)	30051	NM_001252655	16498	Mm.388924	NM_010598	ENSMUSG00000028931	Kcnab2	F5|I2rf5|Kcnb3|kv-beta-2	potassium voltage-gated channel, shaker-related subfamily, beta member 2	protein-coding
mm_38699.1	chr4	145214752	145214764	-	1	NA	3' UTR (NM_011610, exon 10 of 10)	3' UTR (NM_011610, exon 10 of 10)	-19753	NM_001276465	230895	Mm.240310	NM_001033190	ENSMUSG00000020220	Vps13d	-	vacuolar protein sorting 13D	protein-coding
mm_91401.1	chr10	30803286	30803376	-	1	NA	promoter-TSS (NM_172495)	promoter-TSS (NM_172495)	-224	NM_172495	211329	Mm.297903	NM_172495	ENSMUSG00000039697	Ncoa7	9030406N13Rik	nuclear receptor coactivator 7	protein-coding
mm_40284.1	chr5	43233486	43233491	+	1	NA	promoter-TSS (NM_001177379)	promoter-TSS (NM_001177379)	25	NM_001177379	231207	Mm.7233	NM_175937	ENSMUSG00000039782	Cpeb2	A630055H10Rik|Cpe-bp2	cytoplasmic polyadenylation element binding protein 2	protein-coding
mm_23821.1	chr3	80800526	80800532	+	1	NA	intron (NM_001083806, intron 2 of 15)	intron (NM_001083806, intron 2 of 15)	2262	NM_013540	14800	Mm.220224	NM_013540	ENSMUSG00000033981	Gria2	GluA2|GluR-B|Glur-2|Glur2	glutamate receptor, ionotropic, AMPA2 (alpha 2)	protein-coding
mm_108632.1	chr12	85686714	85686728	+	1	NA	promoter-TSS (NM_016767)	promoter-TSS (NM_016767)	1	NM_016767	53314	Mm.6672	NM_016767	ENSMUSG00000034266	Batf	B-ATF|SFA-2	basic leucine zipper transcription factor, ATF-like	protein-coding
mm_51021.1	chr6	65042808	65042900	+	1	NA	promoter-TSS (NM_001253392)	promoter-TSS (NM_001253392)	187	NM_007958	13990	Mm.99113	NM_007958	ENSMUSG00000029920	Smarcad1	AV081750|AW226546|D6Pas1|Etl1|mKIAA1122	SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1	protein-coding
mm_164123.1	chr15	38514826	38514830	-	1	NA	intron (NR_125913, intron 1 of 11)	PB1D10|SINE|Alu	4438	NM_001301688	54375	Mm.250214	NM_018745	ENSMUSG00000037458	Azin1	1700085L02Rik|AZI|Oazi|Oazin	antizyme inhibitor 1	protein-coding
mm_87597.1	chr10	57645839	57645857	+	1	NA	promoter-TSS (NM_001039053)	promoter-TSS (NM_001039053)	-21	NM_001039052	18768	Mm.262135	NM_008863	ENSMUSG00000019876	Pkib	Pkibeta|Prkacn2	protein kinase inhibitor beta, cAMP dependent, testis specific	protein-coding
mm_91582.1	chr10	40227817	40227824	-	1	NA	intron (NM_001042556, intron 7 of 9)	intron (NM_001042556, intron 7 of 9)	19159	NM_001042556	67239	Mm.11480	NM_023323	ENSMUSG00000038510	Rpf2	2810470K21Rik|AU040229|AU043242|Bxdc1	ribosome production factor 2 homolog	protein-coding
mm_10210.1	chr2	5603552	5603565	+	1	NA	intron (NM_001290374, intron 1 of 9)	intron (NM_001290374, intron 1 of 9)	72488	NM_001290376	227541	Mm.191949	NM_177343	ENSMUSG00000039145	Camk1d	A630059D12Rik|CKLiK|CaMKIdelta|E030025C11Rik|mCKLiK	calcium/calmodulin-dependent protein kinase ID	protein-coding
mm_28075.1	chr3	84305386	84305456	-	1	NA	promoter-TSS (NM_001271726)	promoter-TSS (NM_001271726)	-646	NM_001271726	80890	Mm.44876	NM_030706	ENSMUSG00000027993	Trim2	mKIAA0517|narf	tripartite motif-containing 2	protein-coding
mm_122138.1	chr14	31163923	31163938	-	1	NA	exon (NM_138672, exon 2 of 69)	exon (NM_138672, exon 2 of 69)	4711	NM_138672	192187	Mm.220821	NM_138672	ENSMUSG00000042286	Stab1	FEEL-1|FELE-1|MFEEL-1|MS-1|STAB-1|mKIAA0246	stabilin 1	protein-coding
mm_163175.1	chr11	87796314	87796339	+	1	NA	exon (NM_010824, exon 7 of 14)	exon (NM_010824, exon 7 of 14)	2542	NM_010824	17523	Mm.4668	NM_010824	ENSMUSG00000009350	Mpo	mKIAA4033	myeloperoxidase	protein-coding
mm_118603.1	chr14	20794195	20794230	+	1	NA	promoter-TSS (NM_178597)	promoter-TSS (NM_178597)	-124	NM_178597	12325	Mm.235182	NM_178597	ENSMUSG00000021820	Camk2g	Camkg	calcium/calmodulin-dependent protein kinase II gamma	protein-coding
mm_107777.1	chr12	59188445	59188459	+	1	NA	exon (NM_001165254, exon 22 of 23)	exon (NM_001165254, exon 22 of 23)	31031	NM_001033156	70611	Mm.311026	NM_001033156	ENSMUSG00000035329	Fbxo33	5730501N20Rik|AI642135	F-box protein 33	protein-coding
mm_47161.1	chr5	120711597	120711609	-	1	NA	promoter-TSS (NM_008052)	promoter-TSS (NM_008052)	66	NM_008052	14357	Mm.1645	NM_008052	ENSMUSG00000029603	Dtx1	Fxit1|mKIAA4160	deltex 1, E3 ubiquitin ligase	protein-coding
mm_167075.1	chr7	100658407	100658411	+	1	NA	promoter-TSS (NM_001291336)	promoter-TSS (NM_001291336)	47	NM_001163185	27276	Mm.491216	NM_013746	ENSMUSG00000030701	Plekhb1	AI315628|PHR1|Phret1|evt-1	pleckstrin homology domain containing, family B (evectins) member 1	protein-coding
mm_151193.1	chr19	53533811	53533821	+	1	NA	intron (NM_001085390, intron 1 of 3)	intron (NM_001085390, intron 1 of 3)	4498	NM_001085390	240672	Mm.482424	NM_001085390	ENSMUSG00000034765	Dusp5	Gm337	dual specificity phosphatase 5	protein-coding
mm_44707.1	chr5	30822920	30822946	-	1	NA	intron (NM_133350, intron 1 of 6)	intron (NM_133350, intron 1 of 6)	8292	NM_133350	100732	Mm.332295	NM_133350	ENSMUSG00000029166	Mapre3	AI790651|EB2|EB3|EBF3|RP3	microtubule-associated protein, RP/EB family, member 3	protein-coding
mm_168044.1	chrY	90811213	90811250	+	1	NA	intron (NM_133362, intron 2 of 3)	RLTR40|LTR|ERVK	25789	NM_133362	170942	Mm.76062	NM_133362	ENSMUSG00000096768	Erdr1	edr	erythroid differentiation regulator 1	protein-coding
mm_94626.1	chr11	16804414	16804424	+	1	NA	intron (NM_207655, intron 1 of 27)	intron (NM_207655, intron 1 of 27)	52216	NM_007912	13649	Mm.8534	NM_007912	ENSMUSG00000020122	Egfr	9030024J15Rik|AI552599|Erbb|Errb1|Errp|Wa5|wa-2|wa2	epidermal growth factor receptor	protein-coding
mm_119467.1	chr14	47287159	47287160	+	1	NA	intron (NM_080843, intron 1 of 1)	intron (NM_080843, intron 1 of 1)	10016	NM_080843	67296	Mm.23957	NM_080843	ENSMUSG00000048379	Socs4	3110032M18Rik|A730004F22Rik|AI427843|AU015727|AU015859|Socs7	suppressor of cytokine signaling 4	protein-coding
mm_3711.1	chr1	153908394	153908412	+	1	NA	3' UTR (NM_008131, exon 7 of 7)	3' UTR (NM_008131, exon 7 of 7)	8474	NM_008131	14645	Mm.210745	NM_008131	ENSMUSG00000026473	Glul	GS|Glns	glutamate-ammonia ligase (glutamine synthetase)	protein-coding
mm_125346.1	chr15	39197702	39197716	+	1	NA	promoter-TSS (NM_053271)	promoter-TSS (NM_053271)	-577	NM_001256382	116838	Mm.309296	NM_053271	ENSMUSG00000037386	Rims2	2810036I15Rik|AW048769|RIM2|Rab3ip2|Rim2(+40A)|Rim2(+44A)|Rim2(+4A)|Serg2|Syt3-rs|mKIAA0751	regulating synaptic membrane exocytosis 2	protein-coding
mm_4032.1	chr1	165773907	165773953	+	1	NA	3' UTR (NM_011804, exon 4 of 4)	3' UTR (NM_011804, exon 4 of 4)	10150	NM_011804	433375	Mm.294885	NM_011804	ENSMUSG00000040713	Creg1	AA755314|Creg	cellular repressor of E1A-stimulated genes 1	protein-coding
mm_113883.1	chr13	49013754	49013765	+	1	NA	Intergenic	Intergenic	45647	NR_015601	68128	Mm.426304	NR_015601		Fam120aos	C030044B11Rik	family with sequence similarity 120A, opposite strand	ncRNA
mm_167645.1	chr9	64830325	64830329	+	1	NA	intron (NM_001162917, intron 2 of 34)	intron (NM_001162917, intron 2 of 34)	19316	NM_001162917	102442	Mm.222473	NM_176935	ENSMUSG00000053641	Dennd4a	AI115600|AI851943|F730015K02Rik	DENN/MADD domain containing 4A	protein-coding
mm_136595.1	chr17	5057967	5057969	+	1	NA	intron (NM_001085355, intron 2 of 19)	intron (NM_001085355, intron 2 of 19)	62894	NM_001085355	239985	Mm.133401	NM_001085355	ENSMUSG00000069729	Arid1b	8030481M12|9330189K18Rik|AI836955|Ardi1b|B230217J03Rik|mKIAA1235	AT rich interactive domain 1B (SWI-like)	protein-coding
mm_104755.1	chr11	98463822	98463832	-	1	NA	TTS (NM_011771)	TTS (NM_011771)	16993	NM_010346	14786	Mm.276702	NM_010346	ENSMUSG00000019312	Grb7	mKIAA4028	growth factor receptor bound protein 7	protein-coding
mm_76484.1	chr8	85559436	85559439	-	1	NA	Intergenic	RSINE1|SINE|B4	-4166	NM_019794	56445	Mm.475573	NM_019794	ENSMUSG00000031701	Dnaja2	1500017M13Rik|2010206B19Rik|DNAJ|DNJ3|Dnaj3|HIRIP4|PRO3015|mDj3	DnaJ heat shock protein family (Hsp40) member A2	protein-coding
mm_164221.1	chr15	85017134	85017134	+	1	NA	promoter-TSS (NM_023478)	promoter-TSS (NM_023478)	-7	NM_023478	22270	Mm.46214	NM_023478	ENSMUSG00000022435	Upk3a	1110017C07Rik|UP3a|UPIII|Upk3	uroplakin 3A	protein-coding
mm_110388.1	chr12	40555114	40555125	-	1	NA	intron (NM_172803, intron 1 of 52)	intron (NM_172803, intron 1 of 52)	109066	NM_172803	238130	Mm.341423	NM_172803	ENSMUSG00000035954	Dock4	5330406C03|6330411N01Rik|AF263288|C030023J22|mKIAA0716	dedicator of cytokinesis 4	protein-coding
mm_127443.1	chr15	101270468	101270496	+	1	NA	exon (NM_010444, exon 2 of 7)	exon (NM_010444, exon 2 of 7)	3636	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_130308.1	chr15	97029275	97029277	-	1	NA	intron (NM_027052, intron 1 of 15)	B4|SINE|B4	26680	NM_027052	69354	Mm.250980	NM_027052	ENSMUSG00000022464	Slc38a4	1110012E16Rik|1700012A18Rik|Ata3|mATA3|mNAT3	solute carrier family 38, member 4	protein-coding
mm_99728.1	chr11	106300848	106300854	+	1	NA	exon (NM_008117, exon 4 of 5)	exon (NM_008117, exon 4 of 5)	1045	NM_008117	14599	Mm.343934	NM_008117	ENSMUSG00000020713	Gh	Gh1|Ghb1	growth hormone	protein-coding
mm_169179.1	chr13	65813088	65813091	-	1	NA	Intergenic	Intergenic	-300364	NM_001177832	628709	Mm.390595	NM_001177832	ENSMUSG00000095909	Gm10324	ENSMUSG00000071302	predicted gene 10324	protein-coding
mm_87933.1	chr10	62651713	62651726	+	1	NA	promoter-TSS (NM_053183)	promoter-TSS (NM_053183)	-521	NM_053183	94213	Mm.114116	NM_053183	ENSMUSG00000020076	Ddx50	4933429B04Rik|8430408E17Rik|GU2|RH-II	DEAD (Asp-Glu-Ala-Asp) box polypeptide 50	protein-coding
mm_24346.1	chr3	89831353	89831384	+	1	NA	promoter-TSS (NM_172530)	promoter-TSS (NM_172530)	-2	NM_172530	214547	Mm.225	NM_172530	ENSMUSG00000046280	She	9430022A14	src homology 2 domain-containing transforming protein E	protein-coding
mm_21031.1	chr2	152464605	152464608	-	1	NA	promoter-TSS (NM_001037933)	promoter-TSS (NM_001037933)	14	NM_001037933	629114	Mm.389372	NM_001037933	ENSMUSG00000074681	Defb23	EG629114	defensin beta 23	protein-coding
mm_71695.1	chr8	61487716	61487751	+	1	NA	promoter-TSS (NM_145595)	promoter-TSS (NM_145595)	-1	NM_145595	234309	Mm.29059	NM_145595	ENSMUSG00000031641	Cbr4	A730083J17Rik|BC009118	carbonyl reductase 4	protein-coding
mm_83771.1	chr9	52048794	52048800	-	1	NA	promoter-TSS (NR_023357)	promoter-TSS (NR_023357)	-92	NR_023357	629557	Mm.422775	NR_023357		Gm6981	EG629557	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_148225.1	chr18	80345846	80345880	-	1	NA	intron (NM_001190373, intron 1 of 3)	B4A|SINE|B4	18391	NM_001190373	240444	Mm.279568	NM_001190373	ENSMUSG00000059852	Kcng2	AA591524	potassium voltage-gated channel, subfamily G, member 2	protein-coding
mm_149687.1	chr19	20601959	20601974	+	1	NA	promoter-TSS (NM_013467)	promoter-TSS (NM_013467)	-16	NM_013467	11668	Mm.250866	NM_013467	ENSMUSG00000053279	Aldh1a1	Ahd-2|Ahd2|Aldh1|Aldh1a2|E1|Raldh1	aldehyde dehydrogenase family 1, subfamily A1	protein-coding
mm_129477.1	chr15	78718557	78718577	-	1	NA	promoter-TSS (NM_183141)	promoter-TSS (NM_183141)	-454	NM_183141	207393	Mm.323188	NM_183141	ENSMUSG00000043460	Elfn2	6330514E13|AW048948|BC094219|Lrrc62|Ppp1r29	leucine rich repeat and fibronectin type III, extracellular 2	protein-coding
mm_124993.1	chr15	22549065	22549082	+	1	NA	Intergenic	Intergenic	165911	NM_001165971	545091	Mm.475598	NM_001165971		Gm5803	EG545091	predicted gene 5803	protein-coding
mm_149944.1	chr19	27322519	27322532	+	1	NA	promoter-TSS (NM_183179)	promoter-TSS (NM_183179)	-94	NM_183179	240595	Mm.269759	NM_183179	ENSMUSG00000047298	Kcnv2	KV11.1	potassium channel, subfamily V, member 2	protein-coding
mm_46272.1	chr5	99978915	99978966	-	1	NA	promoter-TSS (NM_007516)	promoter-TSS (NM_007516)	-2	NM_001077267	11991	Mm.150231	NM_007516	ENSMUSG00000000568	Hnrnpd	Auf1|Hnrpd	heterogeneous nuclear ribonucleoprotein D	protein-coding
mm_170712.1	chr2	144149304	144149309	+	1	NA	Intergenic	ETnERV-int|LTR|ERVK	39984	NR_136884	433481	Mm.330630	NR_136884	ENSMUSG00000074758	Gm5535	EG433481	predicted gene 5535	ncRNA
mm_59705.1	chr7	28693998	28694012	+	1	NA	intron (NM_207238, intron 2 of 5)	intron (NM_207238, intron 2 of 5)	861	NM_001163702	233040	Mm.116116	NM_207238	ENSMUSG00000037463	Fbxo27	E130008B10Rik|FBG5|Gm161	F-box protein 27	protein-coding
mm_16276.1	chr2	173737556	173737601	+	1	NA	promoter-TSS (NM_019806)	promoter-TSS (NM_019806)	7	NM_019806	56491	Mm.260456	NM_019806	ENSMUSG00000054455	Vapb	AI225786|AI840687|AI848259|D2Abb2e|R75548|VAP33b|Vamp33b	vesicle-associated membrane protein, associated protein B and C	protein-coding
mm_123115.1	chr14	55944537	55944569	-	1	NA	exon (NM_010780, exon 1 of 5)	exon (NM_010780, exon 1 of 5)	122	NM_010780	17228	Mm.1252	NM_010780	ENSMUSG00000022225	Cma1	MMCP-5|Mcp-5|Mcp5|Mcpt5	chymase 1, mast cell	protein-coding
mm_121313.1	chr14	106881774	106881775	+	1	NA	Intergenic	Lx5b|LINE|L1	-395254	NR_045938	73631	Mm.48862	NR_045938	ENSMUSG00000099794	1700128A07Rik	-	RIKEN cDNA 1700128A07 gene	ncRNA
mm_119000.1	chr14	28649698	28649717	+	1	NA	Intergenic	Intergenic	138302	NM_001256224	22418	Mm.287544	NM_009524	ENSMUSG00000021994	Wnt5a	8030457G12Rik|Wnt-5a	wingless-type MMTV integration site family, member 5A	protein-coding
mm_28162.1	chr3	87795207	87795222	-	1	NA	promoter-TSS (NM_001033124)	promoter-TSS (NM_001033124)	-52	NM_001033124	18211	Mm.80682	NM_001033124	ENSMUSG00000028072	Ntrk1	C80751|Tkr|TrkA|trk	neurotrophic tyrosine kinase, receptor, type 1	protein-coding
mm_3607.1	chr1	151718597	151718646	+	1	NA	3' UTR (NM_022018, exon 14 of 14)	3' UTR (NM_022018, exon 14 of 14)	-36753	NM_001311165	66967	Mm.337691	NM_001039644	ENSMUSG00000043019	Edem3	2310050N11Rik	ER degradation enhancer, mannosidase alpha-like 3	protein-coding
mm_100292.1	chr11	117813816	117813835	+	1	NA	3' UTR (NM_009304, exon 4 of 4)	3' UTR (NM_009304, exon 4 of 4)	4158	NM_009304	20973	Mm.468228	NM_009304	ENSMUSG00000048277	Syngr2	Clast2|cellugyrin	synaptogyrin 2	protein-coding
mm_109444.1	chr12	110850305	110850325	+	1	NA	promoter-TSS (NM_028365)	promoter-TSS (NM_028365)	36	NM_028365	72805	Mm.443524	NM_028365	ENSMUSG00000021271	Zfp839	2810455K09Rik	zinc finger protein 839	protein-coding
mm_160794.1	chr11	3914667	3914667	-	1	NA	promoter-TSS (NM_153142)	promoter-TSS (NM_153142)	-3	NM_153142	103710	Mm.171514	NM_153142	ENSMUSG00000048807	Slc35e4	A330108F03Rik|AI414849|AI536442	solute carrier family 35, member E4	protein-coding
mm_37724.1	chr4	129558388	129558398	-	1	NA	promoter-TSS (NM_010693)	promoter-TSS (NM_010693)	-21	NM_010693	16818	Mm.293753	NM_010693	ENSMUSG00000000409	Lck	Hck-3|Lsk|Lskt|p56<lck>|p56Lck	lymphocyte protein tyrosine kinase	protein-coding
mm_33376.1	chr4	129515685	129515689	+	1	NA	TTS (NM_008228)	TTS (NM_008228)	2106	NM_010807	17357	Mm.424974	NM_010807	ENSMUSG00000047945	Marcksl1	AL022768|AW215397|AW536807|D4Bc1|F52|MacMARCKS|Macs2|Macs3|Mlp|Mrp	MARCKS-like 1	protein-coding
mm_78630.1	chr9	38742470	38742473	+	1	NA	3' UTR (NM_001145957, exon 19 of 19)	3' UTR (NM_001145957, exon 19 of 19)	-10325	NM_146787	258783	Mm.131149	NM_146787	ENSMUSG00000061039	Olfr920	MOR165-6	olfactory receptor 920	protein-coding
mm_47674.1	chr5	128433067	128433095	-	1	NA	promoter-TSS (NM_172885)	promoter-TSS (NM_172885)	-4	NM_172885	243274	Mm.447698	NM_172885	ENSMUSG00000034310	Tmem132d	C630028F04Rik	transmembrane protein 132D	protein-coding
mm_120496.1	chr14	65981375	65981400	+	1	NA	3' UTR (NM_013492, exon 9 of 9)	3' UTR (NM_013492, exon 9 of 9)	12904	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_126805.1	chr15	87625215	87625230	+	1	NA	promoter-TSS (NM_134096)	promoter-TSS (NM_134096)	-8	NM_134096	106014	Mm.244319	NM_134096	ENSMUSG00000054863	Fam19a5	TAFA5|Tafa-5|Tara-5	family with sequence similarity 19, member A5	protein-coding
mm_53661.1	chr6	141454742	141454745	+	1	NA	intron (NM_018779, intron 2 of 15)	intron (NM_018779, intron 2 of 15)	-69643	NM_001177772	58807	Mm.284495	NM_021471	ENSMUSG00000030235	Slco1c1	OATP-14|OATP-F|Oatp2|Oatpf|Slc21a14	solute carrier organic anion transporter family, member 1c1	protein-coding
mm_6392.1	chr1	72858463	72858489	-	1	NA	3' UTR (NM_010518, exon 4 of 4)	3' UTR (NM_010518, exon 4 of 4)	16389	NM_010518	16011	Mm.405761	NM_010518	ENSMUSG00000026185	Igfbp5	AI256729|AW208790|IGFBP-5|IGFBP-5P	insulin-like growth factor binding protein 5	protein-coding
mm_27211.1	chr3	35932571	35932596	-	1	NA	promoter-TSS (NM_001205362)	promoter-TSS (NM_001205362)	-249	NM_001205362	114893	Mm.374810	NM_033623	ENSMUSG00000027708	Dcun1d1	Rp42|SCCRO|Tes3|pTes3	DCN1, defective in cullin neddylation 1, domain containing 1 (S. cerevisiae)	protein-coding
mm_39889.1	chr5	31116723	31116727	+	1	NA	5' UTR (NM_021447, exon 1 of 9)	5' UTR (NM_021447, exon 1 of 9)	113	NM_021447	58522	Mm.143796	NM_021447	ENSMUSG00000062077	Trim54	4930486E09Rik|4930566I02Rik|MURF|MURF-3|MuRF3|Rnf30	tripartite motif-containing 54	protein-coding
mm_108999.1	chr12	103062379	103062379	+	1	NA	intron (NM_001081017, intron 13 of 48)	intron (NM_001081017, intron 13 of 48)	113520	NM_001081017	217843	Mm.387073	NM_177621	ENSMUSG00000021198	Unc79	9030205A07Rik|Mlca3	unc-79 homolog (C. elegans)	protein-coding
mm_141430.1	chr17	29467925	29467947	-	1	NA	Intergenic	Intergenic	-23109	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_7688.1	chr1	128607975	128607986	-	1	NA	Intergenic	Intergenic	-15681	NM_009911	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding
mm_141312.1	chr17	28358695	28358698	-	1	NA	intron (NM_021478, intron 10 of 14)	intron (NM_021478, intron 10 of 14)	6447	NM_021478	22157	Mm.42102	NM_021478	ENSMUSG00000037446	Tulp1	Tulp1l	tubby like protein 1	protein-coding
mm_58375.1	chr6	148992416	148992427	-	1	NA	3' UTR (NM_177192, exon 21 of 21)	3' UTR (NM_177192, exon 21 of 21)	-45989	NM_019643	56306	Mm.18637	NM_019643	ENSMUSG00000039985	Fam60a	Ppcs1|Pptcs1|Tera	family with sequence similarity 60, member A	protein-coding
mm_61324.1	chr7	68226580	68226591	+	1	NA	3' UTR (NM_010513, exon 21 of 21)	3' UTR (NM_010513, exon 21 of 21)	37648	NM_030101	78444	Mm.425468	NM_030101	ENSMUSG00000030553	Pgpep1l	C330024D12Rik	pyroglutamyl-peptidase I-like	protein-coding
mm_150461.1	chr19	38264836	38264848	+	1	NA	promoter-TSS (NM_020278)	promoter-TSS (NM_020278)	60	NM_020278	56839	Mm.298251	NM_020278	ENSMUSG00000067242	Lgi1	BB130740	leucine-rich repeat LGI family, member 1	protein-coding
mm_35346.1	chr4	32250354	32250359	-	1	NA	Intergenic	Intergenic	-167079	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_75859.1	chr8	70700404	70700418	-	1	NA	3' UTR (NM_001286944, exon 1 of 1)	3' UTR (NM_001286944, exon 1 of 1)	2672	NM_001286944	16478	Mm.419851	NM_010592	ENSMUSG00000071076	Jund	Jund1	jun D proto-oncogene	protein-coding
mm_6110.1	chr1	64078974	64078989	-	1	NA	exon (NM_033563, exon 2 of 4)	exon (NM_033563, exon 2 of 4)	-36480	NR_105864	102466760		NR_105864	ENSMUSG00000098487	Mir6899	Gm27384|mmu-mir-6899	microRNA 6899	ncRNA
mm_81028.1	chr9	104569602	104569631	+	1	NA	promoter-TSS (NM_028719)	promoter-TSS (NM_028719)	-172	NM_028719	74020	Mm.326240	NM_028719	ENSMUSG00000032564	Cpne4	3632411M23Rik|4933406O10Rik	copine IV	protein-coding
mm_30209.1	chr3	144827348	144827389	-	1	NA	exon (NM_139148, exon 11 of 14)	exon (NM_139148, exon 11 of 14)	-7874	NM_030601	80797	Mm.20897	NM_030601	ENSMUSG00000028262	Clca3a2	Clca2	chloride channel accessory 3A2	protein-coding
mm_121310.1	chr14	106106221	106106228	+	1	NA	promoter-TSS (NM_198601)	promoter-TSS (NM_198601)	26	NR_073203	212085	Mm.78128	NM_198601	ENSMUSG00000022113	Trim52	4921513B05Rik	tripartite motif-containing 52	protein-coding
mm_142912.1	chr17	53539386	53539407	-	1	NA	promoter-TSS (NM_173449)	promoter-TSS (NM_173449)	55	NM_173449	110332	Mm.444633	NM_173449	ENSMUSG00000044957	Pp2d1	4921523A10Rik	protein phosphatase 2C-like domain containing 1	protein-coding
mm_160914.1	chr11	83176207	83176207	+	1	NA	5' UTR (NM_011410, exon 4 of 8)	5' UTR (NM_011410, exon 4 of 8)	1021	NM_001302559	20558	Mm.38192	NM_011410	ENSMUSG00000000204	Slfn4	AI450778	schlafen 4	protein-coding
mm_163766.1	chr13	120017894	120017902	+	1	NA	Intergenic	Intergenic	34306	NM_001302966	100861753	Mm.165042	NM_001302966	ENSMUSG00000095609	Gm21188	-	predicted gene, 21188	protein-coding
mm_49624.1	chr6	30803918	30803929	+	1	NA	intron (NM_017478, intron 20 of 23)	B1_Mur4|SINE|Alu	62624	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_171920.1	chr5	5782748	5782753	-	1	NA	Intergenic	Intergenic	-33433	NM_027399	70358	Mm.85429	NM_027399	ENSMUSG00000015652	Steap1	2410007B19Rik|Prss24|Steap	six transmembrane epithelial antigen of the prostate 1	protein-coding
mm_117485.1	chr13	77439013	77439058	-	1	NA	intron (NM_001145676, intron 19 of 19)	GSAT_MM|Satellite|Satellite	-269655	NM_001163420	68675	Mm.343005	NM_138312	ENSMUSG00000064138	Fam172a	1110033M05Rik|2610318O14Rik|53-E6|9430037D06Rik|AF064782|pEN87	family with sequence similarity 172, member A	protein-coding
mm_99987.1	chr11	114717617	114717620	+	1	NA	intron (NM_053273, intron 13 of 13)	intron (NM_053273, intron 13 of 13)	-9794	NM_001034878	432611	Mm.212764	NM_001034878	ENSMUSG00000034706	Dnaic2	C030015H18Rik|Dnai2|Gm728	dynein, axonemal, intermediate chain 2	protein-coding
mm_58254.1	chr6	145076033	145076061	-	1	NA	5' UTR (NM_007532, exon 1 of 11)	5' UTR (NM_007532, exon 1 of 11)	110	NM_007532	12035	Mm.4606	NM_007532	ENSMUSG00000030268	Bcat1	BCATc|Eca39	branched chain aminotransferase 1, cytosolic	protein-coding
mm_91089.1	chr10	19015348	19015379	-	1	NA	promoter-TSS (NM_009397)	promoter-TSS (NM_009397)	47	NM_009397	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_96121.1	chr11	60775108	60775156	+	1	NA	intron (NM_009410, intron 1 of 18)	intron (NM_009410, intron 1 of 18)	2233	NM_009410	21975	Mm.10708	NM_009410	ENSMUSG00000002814	Top3a	-	topoisomerase (DNA) III alpha	protein-coding
mm_141204.1	chr17	27039530	27039552	-	1	NA	Intergenic	Intergenic	10282	NM_027544	70772	Mm.440437	NM_027544	ENSMUSG00000048731	Ggnbp1	0610031G08Rik|mdf	gametogenetin binding protein 1	protein-coding
mm_172149.1	chr6	3820899	3820900	-	1	NA	Intergenic	Intergenic	-56186	NM_007588	12311	Mm.4642	NM_007588	ENSMUSG00000023964	Calcr	Clr	calcitonin receptor	protein-coding
mm_138064.1	chr17	33931162	33931201	+	1	NA	intron (NM_009059, intron 2 of 17)	intron (NM_009059, intron 2 of 17)	1287	NM_009059	19732	Mm.43777	NM_009059	ENSMUSG00000041354	Rgl2	KE1.5|Rab2l|Rgt2|Rlf	ral guanine nucleotide dissociation stimulator-like 2	protein-coding
mm_154627.1	chrX	7728584	7728588	+	1	NA	promoter-TSS (NM_138602)	promoter-TSS (NM_138602)	15	NM_138602	54637	Mm.28850	NM_138602	ENSMUSG00000031149	Praf2	AA986329|C78013|DXImx39e|JM4|Sfc20	PRA1 domain family 2	protein-coding
mm_164092.1	chr15	9663677	9663677	+	1	NA	intron (NM_177123, intron 17 of 17)	RLTR1C|LTR|ERV1	85191	NM_177123	320277	Mm.127822	NM_177123	ENSMUSG00000072663	Spef2	C230086A09Rik	sperm flagellar 2	protein-coding
mm_79143.1	chr9	47693261	47693281	+	1	NA	intron (NM_001025600, intron 1 of 8)	intron (NM_001025600, intron 1 of 8)	124937	NR_046048	100038460	Mm.447649	NR_046048		Gm10677	ENSMUSG00000074363	predicted gene 10677	ncRNA
mm_141536.1	chr17	31855783	31855802	-	1	NA	promoter-TSS (NM_010831)	promoter-TSS (NM_010831)	0	NM_010831	17691	Mm.290941	NM_010831	ENSMUSG00000024042	Sik1	Msk|Sik|Snf1lk	salt inducible kinase 1	protein-coding
mm_167264.1	chr8	27945328	27945328	+	1	NA	Intergenic	Intergenic	139525	NR_033590	666422	Mm.484413	NR_033590	ENSMUSG00000110372	Gm8096	EG666422	3-phosphoglycerate dehydrogenase pseudogene	pseudo
mm_86233.1	chr9	120571388	120571420	-	1	NA	promoter-TSS (NM_025974)	promoter-TSS (NM_025974)	-113	NM_025974	67115	Mm.289810	NM_025974	ENSMUSG00000025794	Rpl14	3100001N19Rik|AA407502|AL022816|CAG-ISL-7|CTG-B33|L14	ribosomal protein L14	protein-coding
mm_148527.1	chr19	4510511	4510532	+	1	NA	promoter-TSS (NM_001162946)	promoter-TSS (NM_001162946)	49	NM_001162946	18563	Mm.1845	NM_008797	ENSMUSG00000024892	Pcx	Pc|Pcb	pyruvate carboxylase	protein-coding
mm_9067.1	chr1	168155778	168155793	-	1	NA	3' UTR (NM_001291509, exon 7 of 7)	3' UTR (NM_001291509, exon 7 of 7)	276384	NM_001291508	18514	Mm.43358	NM_008783	ENSMUSG00000052534	Pbx1	2310056B04Rik|D230003C07Rik|Pbx-1	pre B cell leukemia homeobox 1	protein-coding
mm_66649.1	chr7	45694370	45694406	-	1	NA	promoter-TSS (NM_001271578)	promoter-TSS (NM_001271578)	14	NM_001271578	56546	Mm.56914	NM_019934	ENSMUSG00000040364	Sec1	Fut10|Fut3	secretory blood group 1	protein-coding
mm_54855.1	chr6	42593452	42593456	-	1	NA	exon (NM_203396, exon 2 of 7)	exon (NM_203396, exon 2 of 7)	3918	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_144970.1	chr18	37826718	37826734	+	1	NA	intron (NM_001301259, intron 2 of 3)	intron (NM_001301259, intron 2 of 3)	7180	NM_033583	93708	Mm.247203	NM_033583	ENSMUSG00000102543	Pcdhgc5	-	protocadherin gamma subfamily C, 5	protein-coding
mm_139135.1	chr17	47509343	47509364	+	1	NA	intron (NM_001081635, intron 1 of 6)	intron (NM_001081635, intron 1 of 6)	4302	NM_001081635	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_99603.1	chr11	104550784	104550792	+	1	NA	promoter-TSS (NM_145436)	promoter-TSS (NM_145436)	125	NM_010858	17896	Mm.390355	NM_010858	ENSMUSG00000061086	Myl4	ALC1|AMLC|ELC|ELC1a|GT1|MLC1a|Myla	myosin, light polypeptide 4	protein-coding
mm_106105.1	chr11	116292476	116292476	-	1	NA	intron (NM_001347636, intron 13 of 18)	intron (NM_001347636, intron 13 of 18)	11537	NM_010254	14428	Mm.57149	NM_010254	ENSMUSG00000020793	Galr2	mGalR	galanin receptor 2	protein-coding
mm_3057.1	chr1	134066414	134066416	+	1	NA	Intergenic	MIRb|SINE|MIR	12740	NM_007570	12227	Mm.392646	NM_007570	ENSMUSG00000020423	Btg2	AA959598|APRO1|Pc3|TIS21	B cell translocation gene 2, anti-proliferative	protein-coding
mm_116175.1	chr13	30820633	30820643	-	1	NA	exon (NM_025588, exon 26 of 28)	exon (NM_025588, exon 26 of 28)	71405	NM_013674	16364	Mm.4677	NM_013674	ENSMUSG00000021356	Irf4	AI385587|IRF-4|LSIRF|NF-EM5|Spip	interferon regulatory factor 4	protein-coding
mm_66744.1	chr7	46712057	46712069	-	1	NA	TTS (NM_011315)	TTS (NM_011315)	-1412	NM_030233	78935	Mm.289866	NM_030233	ENSMUSG00000006763	Saal1	5031425D22Rik|SPACIA1	serum amyloid A-like 1	protein-coding
mm_135629.1	chr16	52301407	52301420	-	1	NA	intron (NM_009655, intron 3 of 15)	intron (NM_009655, intron 3 of 15)	151668	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_43851.1	chr5	143363891	143363919	+	1	NA	promoter-TSS (NM_133355)	promoter-TSS (NM_133355)	-3	NM_133355	170935	Mm.197460	NM_133355	ENSMUSG00000010825	Grid2ip	-	glutamate receptor, ionotropic, delta 2 (Grid2) interacting protein 1	protein-coding
mm_13680.1	chr2	116900201	116900216	+	1	NA	promoter-TSS (NR_040336)	promoter-TSS (NR_040336)	56	NR_040335	320975	Mm.132509	NR_040335	ENSMUSG00000085316	D330050G23Rik	-	RIKEN cDNA D330050G23 gene	ncRNA
mm_136321.1	chr16	91964620	91964660	-	1	NA	Intergenic	Intergenic	-33010	NM_138597	28080	Mm.41	NM_138597	ENSMUSG00000022956	Atp5o	ATPO|D12Wsu28e|OSCP	ATP synthase, H+ transporting, mitochondrial F1 complex, O subunit	protein-coding
mm_45732.1	chr5	86373402	86373407	-	1	NA	promoter-TSS (NM_145561)	promoter-TSS (NM_145561)	-17	NM_145561	231382	Mm.240139	NM_145561	ENSMUSG00000061259	Tmprss11d	AST|AsP|BC020151	transmembrane protease, serine 11d	protein-coding
mm_76131.1	chr8	80880464	80880471	-	1	NA	promoter-TSS (NM_001301298)	promoter-TSS (NM_001301298)	12	NM_021356	14388	Mm.277409	NM_021356	ENSMUSG00000031714	Gab1	AA408973|AW107238	growth factor receptor bound protein 2-associated protein 1	protein-coding
mm_95718.1	chr11	54522853	54522861	+	1	NA	promoter-TSS (NM_001252494)	promoter-TSS (NM_001252494)	12	NM_001252496	192786	Mm.254404	NM_175258	ENSMUSG00000037533	Rapgef6	A530068K01|AI844632|BB085664|C030018K18Rik|PDZ-GEF2|Pdzgef2|RA-GEF-2|Ragef2|mKIAA4052	Rap guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_99872.1	chr11	109399485	109399515	+	1	NA	3' UTR (NM_010303, exon 4 of 4)	3' UTR (NM_010303, exon 4 of 4)	-26446	NM_025275	13929	Mm.211850	NM_025275	ENSMUSG00000020610	Amz2	AA408420|ESTM12|X83328	archaelysin family metallopeptidase 2	protein-coding
mm_54704.1	chr6	39603690	39603712	-	1	NA	3' UTR (NM_139294, exon 22 of 22)	3' UTR (NM_139294, exon 22 of 22)	11118	NM_026612	68198	Mm.29415	NM_026612	ENSMUSG00000002416	Ndufb2	1810011O01Rik|8kDa|AGGG|AI325567|CI-AGGG	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 2	protein-coding
mm_1955.1	chr1	86359554	86359590	+	1	NA	promoter-TSS (NM_010880)	promoter-TSS (NM_010880)	-2	NR_015507	319336	Mm.389155	NR_015507	ENSMUSG00000073627	C130036L24Rik	ENSMUSG00000073627	RIKEN cDNA C130036L24 gene	ncRNA
mm_143224.1	chr17	63304175	63304190	-	1	NA	intron (NM_015794, intron 6 of 8)	RMER19B|LTR|ERVK	8791	NR_130176	414079	Mm.444282	NR_130176	ENSMUSG00000090565	4930405O22Rik	-	RIKEN cDNA 4930405O22 gene	ncRNA
mm_155398.1	chrX	72987353	72987366	+	1	NA	promoter-TSS (NM_001109043)	promoter-TSS (NM_001109043)	20	NM_001109043	22673	Mm.1161	NM_009549	ENSMUSG00000031351	Zfp185	P1|Znf185	zinc finger protein 185	protein-coding
mm_68582.1	chr7	115953346	115953355	-	1	NA	intron (NM_001025559, intron 1 of 15)	intron (NM_001025559, intron 1 of 15)	41736	NM_011445	20679	Mm.323365	NM_011445	ENSMUSG00000051910	Sox6	AI987981|SOX-LZ	SRY (sex determining region Y)-box 6	protein-coding
mm_17995.1	chr2	38166091	38166120	-	1	NA	intron (NM_146122, intron 2 of 21)	intron (NM_146122, intron 2 of 21)	121279	NM_146122	227801	Mm.314245	NM_146122	ENSMUSG00000035392	Dennd1a	6030446I19Rik|connecdenn	DENN/MADD domain containing 1A	protein-coding
mm_55993.1	chr6	86138434	86138434	-	1	NA	Intergenic	Intergenic	-56793	NM_031199	21802	Mm.137222	NM_031199	ENSMUSG00000029999	Tgfa	wa-1|wa1	transforming growth factor alpha	protein-coding
mm_78926.1	chr9	45055212	45055225	+	1	NA	promoter-TSS (NM_001093749)	promoter-TSS (NM_001093749)	37	NM_001093749	319742	Mm.49611	NM_176993	ENSMUSG00000070305	Mpzl3	5430427F17Rik|A530065I17Rik|rc	myelin protein zero-like 3	protein-coding
mm_51313.1	chr6	72314383	72314419	+	1	NA	TTS (NM_001282071)	TTS (NM_001282071)	9791	NM_147779	20388	Mm.46033	NM_147779	ENSMUSG00000056370	Sftpb	AI562151|SF-B|SP-B|Sftp-3|Sftp3	surfactant associated protein B	protein-coding
mm_141510.1	chr17	31658730	31658766	-	1	NA	promoter-TSS (NM_001163769)	promoter-TSS (NM_001163769)	6	NM_024187	108121	Mm.379289	NM_024187	ENSMUSG00000061613	U2af1	2010107D16Rik|35kDa	U2 small nuclear ribonucleoprotein auxiliary factor (U2AF) 1	protein-coding
mm_29136.1	chr3	105800676	105800687	-	1	NA	intron (NM_145541, intron 1 of 7)	intron (NM_145541, intron 1 of 7)	700	NM_145541	109905	Mm.101922	NM_145541	ENSMUSG00000068798	Rap1a	AI848598|G-22K|Krev-1|Rap1	RAS-related protein-1a	protein-coding
mm_99521.1	chr11	103134032	103134045	+	1	NA	5' UTR (NM_027658, exon 2 of 3)	5' UTR (NM_027658, exon 2 of 3)	679	NM_027658	71059	Mm.273871	NM_027658	ENSMUSG00000043372	Hexim2	4933402L21Rik	hexamethylene bis-acetamide inducible 2	protein-coding
mm_6348.1	chr1	71642081	71642106	-	1	NA	exon (NM_001276413, exon 8 of 44)	exon (NM_001276413, exon 8 of 44)	11141	NM_010233	14268	Mm.193099	NM_010233	ENSMUSG00000026193	Fn1	E330027I09|Fn|Fn-1	fibronectin 1	protein-coding
mm_55569.1	chr6	71373332	71373335	-	1	NA	promoter-TSS (NM_009857)	promoter-TSS (NM_009857)	-94	NM_009857	12525	Mm.1858	NM_009857	ENSMUSG00000053977	Cd8a	BB154331|Ly-2|Ly-35|Ly-B|Lyt-2	CD8 antigen, alpha chain	protein-coding
mm_115552.1	chr13	8974527	8974531	-	1	NA	intron (NM_027000, intron 15 of 16)	intron (NM_027000, intron 15 of 16)	21483	NM_027000	69237	Mm.41800	NM_027000	ENSMUSG00000021149	Gtpbp4	2610028C09Rik|Crfg|Gtpbp3|NGB|Nog1	GTP binding protein 4	protein-coding
mm_66532.1	chr7	45136311	45136340	-	1	NA	intron (NR_102725, intron 1 of 7)	intron (NR_102725, intron 1 of 7)	107	NM_013520	14256	Mm.1658	NM_013520	ENSMUSG00000110206	Flt3l	Flt3lg|Ly72L	FMS-like tyrosine kinase 3 ligand	protein-coding
mm_21007.1	chr2	152349923	152349942	-	1	NA	intron (NR_033505, intron 1 of 4)	intron (NR_033505, intron 1 of 4)	4263	NR_033505	791417	Mm.451219	NR_033505	ENSMUSG00000068062	Gm14164	OTTMUSG00000015846	predicted gene 14164	ncRNA
mm_60634.1	chr7	44816324	44816334	+	1	NA	promoter-TSS (NM_030693)	promoter-TSS (NM_030693)	-41	NM_001171024	100328588	Mm.2565	NM_001171024	ENSMUSG00000074141	Gm21948	Nup62-il4i1	predicted gene, 21948	protein-coding
mm_142229.1	chr17	37480800	37480812	-	1	NA	TTS (NM_008204)	TTS (NM_008204)	2723	NM_008204	14990	Mm.329041	NM_008204	ENSMUSG00000016283	H2-M2	H-2M2|Thy19.4	histocompatibility 2, M region locus 2	protein-coding
mm_114695.1	chr13	82295428	82295432	+	1	NA	Intergenic	Intergenic	402903	NR_039537	100628621		NR_039537	ENSMUSG00000106655	Mir3961	mmu-mir-3961	microRNA 3961	ncRNA
mm_155135.1	chrX	49499057	49499068	+	1	NA	exon (NM_001081123, exon 13 of 13)	exon (NM_001081123, exon 13 of 13)	28612	NM_001081123	75404	Mm.44305	NM_001081123	ENSMUSG00000036198	Arhgap36	1100001E04Rik|rho-gap	Rho GTPase activating protein 36	protein-coding
mm_120288.1	chr14	63134920	63134935	+	1	NA	intron (NM_007798, intron 3 of 9)	B3|SINE|B2	12465	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_147904.1	chr18	65382521	65382531	-	1	NA	intron (NM_001037294, intron 1 of 12)	intron (NM_001037294, intron 1 of 12)	11362	NM_001037294	225638	Mm.296528	NM_001037294	ENSMUSG00000032845	Alpk2	Gm549|Hak	alpha-kinase 2	protein-coding
mm_131735.1	chr16	21982354	21982363	+	1	NA	intron (NM_001289582, intron 2 of 9)	MIR3|SINE|MIR	13184	NM_001289582	239759	Mm.33192	NM_153404	ENSMUSG00000044626	Liph	C130037N08Rik|D16Wsu119e|H06|Lpdlr|P3|PLA1B|lpd1|lpd2|mPA-PLA1	lipase, member H	protein-coding
mm_57039.1	chr6	122339634	122339673	-	1	NA	promoter-TSS (NM_007905)	promoter-TSS (NM_007905)	4	NM_001042623	13619	Mm.6822	NM_007905	ENSMUSG00000040669	Phc1	AW557034|Edr|Edr1|Mph1|Rae-28|rae28	polyhomeotic-like 1 (Drosophila)	protein-coding
mm_91399.1	chr10	30802885	30802946	-	1	NA	5' UTR (NM_172495, exon 1 of 16)	5' UTR (NM_172495, exon 1 of 16)	192	NM_172495	211329	Mm.297903	NM_172495	ENSMUSG00000039697	Ncoa7	9030406N13Rik	nuclear receptor coactivator 7	protein-coding
mm_83366.1	chr9	44441192	44441230	-	1	NA	promoter-TSS (NM_001033469)	promoter-TSS (NM_001033469)	-343	NM_001033469	382074	Mm.335103	NM_001033469	ENSMUSG00000074397	Foxr1	Foxn5|Gm1115	forkhead box R1	protein-coding
mm_98103.1	chr11	86757880	86757911	+	1	NA	promoter-TSS (NM_001003908)	promoter-TSS (NM_001003908)	-403	NM_001003908	67300	Mm.254588	NM_001003908	ENSMUSG00000047126	Cltc	3110065L21Rik|CHC|R74732	clathrin, heavy polypeptide (Hc)	protein-coding
mm_105123.1	chr11	101171303	101171353	-	1	NA	promoter-TSS (NM_146030)	promoter-TSS (NM_146030)	-26	NM_146030	217198	Mm.273254	NM_146030	ENSMUSG00000035172	Plekhh3	BC020025	pleckstrin homology domain containing, family H (with MyTH4 domain) member 3	protein-coding
mm_70024.1	chr7	142576023	142576093	-	1	NA	non-coding (NR_130974, exon 5 of 5)	non-coding (NR_130974, exon 5 of 5)	1089	NR_030416	735280		NR_030416	ENSMUSG00000076275	Mir675	Mirn675|mir-675|mmu-mir-675	microRNA 675	ncRNA
mm_104394.1	chr11	94498171	94498191	-	1	NA	intron (NM_027984, intron 1 of 9)	intron (NM_027984, intron 1 of 9)	1793	NM_027984	71889	Mm.248620	NM_027984	ENSMUSG00000010080	Epn3	2310022G12Rik	epsin 3	protein-coding
mm_71829.1	chr8	68896734	68896741	+	1	NA	exon (NM_008509, exon 6 of 10)	exon (NM_008509, exon 6 of 10)	16182	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_123833.1	chr14	70628946	70629031	-	1	NA	promoter-TSS (NM_001252665)	promoter-TSS (NM_001252665)	59	NM_001252665	13829	Mm.210863	NM_013514	ENSMUSG00000022099	Dmtn	AI325486|Epb4.9|Epb49|dematin	dematin actin binding protein	protein-coding
mm_69448.1	chr7	133015470	133015482	-	1	NA	promoter-TSS (NM_001170744)	promoter-TSS (NM_001170744)	-229	NM_001170744	13017	Mm.246240	NM_009980	ENSMUSG00000030970	Ctbp2	AA407280|D7Ertd45e|Gtrgeo6|Ribeye	C-terminal binding protein 2	protein-coding
mm_26627.1	chr3	152884221	152884293	+	1	NA	intron (NM_012028, intron 2 of 4)	intron (NM_012028, intron 2 of 4)	97950	NM_012028	26938	Mm.40915	NM_012028	ENSMUSG00000039037	St6galnac5	AI851940|Siat7e	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 5	protein-coding
mm_110834.1	chr12	72761043	72761090	-	1	NA	promoter-TSS (NM_008910)	promoter-TSS (NM_008910)	-145	NM_008910	19042	Mm.261045	NM_008910	ENSMUSG00000021096	Ppm1a	2310003C21Rik|2900017D14Rik|AI427932|AU017636|MMPa-2|MPPa-1	protein phosphatase 1A, magnesium dependent, alpha isoform	protein-coding
mm_96449.1	chr11	67533039	67533059	+	1	NA	promoter-TSS (NM_008088)	promoter-TSS (NM_008088)	51	NM_008088	14457	Mm.40338	NM_008088	ENSMUSG00000033066	Gas7	AW124766|B230343A10Rik|Gas7-cb	growth arrest specific 7	protein-coding
mm_52343.1	chr6	110761135	110761149	+	1	NA	intron (NM_001346640, intron 1 of 10)	intron (NM_001346640, intron 1 of 10)	115544	NM_177328	108073	Mm.240881	NM_177328	ENSMUSG00000056755	Grm7	6330570A01Rik|BB176677|C030018L03|E130018M02Rik|Gpr1g|Gprc1g|SMN2|Tg(SMN2)89Ahmb|mGluR7	glutamate receptor, metabotropic 7	protein-coding
mm_158218.1	chrX	105929305	105929321	-	1	NA	promoter-TSS (NM_009530)	promoter-TSS (NM_009530)	59	NM_009530	22589	Mm.10141	NM_009530	ENSMUSG00000031229	Atrx	4833408C14Rik|AI447451|ATR2|DXHXS6677E|HP1-BP38|Hp1bp2|Hp1bp38|MRXS3|RAD54L|Rad54|XH2|Xnp|ZNF-HX	alpha thalassemia/mental retardation syndrome X-linked	protein-coding
mm_165023.1	chr19	32276963	32276965	-	1	NA	intron (NM_001168525, intron 2 of 9)	intron (NM_001168525, intron 2 of 9)	-65951	NM_001168526	208449	Mm.329810	NM_144792	ENSMUSG00000040451	Sgms1	9530058O11Rik|AI841905|C80702|Mob|Sms1|Sor1|Tmem23	sphingomyelin synthase 1	protein-coding
mm_147726.1	chr18	61008552	61008555	-	1	NA	intron (NM_201353, intron 2 of 13)	intron (NM_201353, intron 2 of 13)	5646	NM_201353	240332	Mm.39846	NM_201353	ENSMUSG00000052026	Slc6a7	AW455934|PROT	solute carrier family 6 (neurotransmitter transporter, L-proline), member 7	protein-coding
mm_71757.1	chr8	65967167	65967191	+	1	NA	exon (NM_175188, exon 3 of 8)	exon (NM_175188, exon 3 of 8)	348654	NM_175188	72925	Mm.380457	NM_175188	ENSMUSG00000036469	March1	2900024D24Rik|BB085186	membrane-associated ring finger (C3HC4) 1	protein-coding
mm_29885.1	chr3	131171440	131171442	-	1	NA	intron (NM_001276403, intron 3 of 11)	intron (NM_001276403, intron 3 of 11)	58650	NM_001276403	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_136363.1	chr16	92792296	92792303	-	1	NA	intron (NM_001111022, intron 2 of 6)	B4A|SINE|B4	33775	NM_001111021	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_6028.1	chr1	59316135	59316145	-	1	NA	intron (NM_001033373, intron 10 of 13)	intron (NM_001033373, intron 10 of 13)	59233	NM_001033373	271697	Mm.297713	NM_001033373	ENSMUSG00000026023	Cdk15	Als2cr7|Pftk2	cyclin-dependent kinase 15	protein-coding
mm_139218.1	chr17	47729276	47729291	+	1	NA	exon (NM_025973, exon 3 of 9)	exon (NM_025973, exon 3 of 9)	2441	NM_025973	109820	Mm.22957	NM_025973	ENSMUSG00000023987	Pgc	2210410L06Rik|Upg-1|Upg1	progastricsin (pepsinogen C)	protein-coding
mm_64495.1	chr7	143459853	143459898	+	1	NA	exon (NM_001161624, exon 2 of 4)	exon (NM_001161624, exon 2 of 4)	1175	NM_009876	12577	Mm.168789	NM_009876	ENSMUSG00000037664	Cdkn1c	AL024410|CDKI|Kip2|p57(kip2)|p57Kip2	cyclin-dependent kinase inhibitor 1C (P57)	protein-coding
mm_62281.1	chr7	99625953	99626018	+	1	NA	exon (NM_001195529, exon 1 of 1)	exon (NM_001195529, exon 1 of 1)	1118	NM_001195529	100503386	Mm.180719	NM_001195529	ENSMUSG00000096606	Tpbgl	EG245190|Gm4980	trophoblast glycoprotein-like	protein-coding
mm_109955.1	chr12	11882393	11882417	-	1	NA	non-coding (NR_003964, exon 1 of 1)	non-coding (NR_003964, exon 1 of 1)	494	NR_003964	627110	Mm.194735	NR_003964		Tubb2a-ps2	C79445	tubulin, beta 2a, pseudogene 2	pseudo
mm_49077.1	chr6	6299429	6299438	+	1	NA	intron (NR_136905, intron 1 of 3)	intron (NR_136905, intron 1 of 3)	50774	NR_136905	101056138	Mm.389085	NR_136904	ENSMUSG00000093482	Gm20619	-	predicted gene 20619	ncRNA
mm_7608.1	chr1	126492796	126492804	-	1	NA	5' UTR (NM_172484, exon 1 of 15)	5' UTR (NM_172484, exon 1 of 15)	127	NM_172484	210356	Mm.377234	NM_172484	ENSMUSG00000049690	Nckap5	8430408F21|D130011D22Rik|E030049G20Rik|Erih1|Erih2|Gm1548|Nap5	NCK-associated protein 5	protein-coding
mm_60154.1	chr7	39500559	39500562	+	1	NA	Intergenic	B3|SINE|B2	-17206	NM_001004139	70227	Mm.333800	NM_001004139	ENSMUSG00000068959	Zfp619	3000002G13Rik	zinc finger protein 619	protein-coding
mm_107015.1	chr12	12342175	12342178	+	1	NA	intron (NM_029758, intron 4 of 12)	intron (NM_029758, intron 4 of 12)	50299	NR_045829	70858	Mm.410838	NR_045829		4921511I17Rik	-	RIKEN cDNA 4921511I17 gene	ncRNA
mm_23322.1	chr3	53463780	53463822	+	1	NA	promoter-TSS (NM_172501)	promoter-TSS (NM_172501)	-16	NM_173382	212127	Mm.491292	NM_173382	ENSMUSG00000049504	Proser1	2810046L04Rik|9330161F11	proline and serine rich 1	protein-coding
mm_125364.1	chr15	39493652	39493655	+	1	NA	intron (NM_001256382, intron 13 of 26)	intron (NM_001256382, intron 13 of 26)	-165858	NM_001256384	116838	Mm.309296	NM_053271	ENSMUSG00000037386	Rims2	2810036I15Rik|AW048769|RIM2|Rab3ip2|Rim2(+40A)|Rim2(+44A)|Rim2(+4A)|Serg2|Syt3-rs|mKIAA0751	regulating synaptic membrane exocytosis 2	protein-coding
mm_45146.1	chr5	49176390	49176391	-	1	NA	intron (NM_001199244, intron 1 of 7)	intron (NM_001199244, intron 1 of 7)	109269	NM_001199244	80334	Mm.160172	NM_030265	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding
mm_45363.1	chr5	66003602	66003605	-	1	NA	intron (NR_027961, intron 1 of 6)	B1_Mur2|SINE|Alu	682	NR_027961	231253	Mm.436542	NM_177679	ENSMUSG00000054598	9130230L23Rik	-	RIKEN cDNA 9130230L23 gene	ncRNA
mm_26239.1	chr3	141465372	141465381	+	1	NA	promoter-TSS (NM_009472)	promoter-TSS (NM_009472)	-188	NM_009472	22253	Mm.24430	NM_009472	ENSMUSG00000059921	Unc5c	B130051O18Rik|Unc5h3|rcm	unc-5 netrin receptor C	protein-coding
mm_26504.1	chr3	145758751	145758764	+	1	NA	promoter-TSS (NM_026993)	promoter-TSS (NM_026993)	65	NM_026993	69219	Mm.234247	NM_026993	ENSMUSG00000028194	Ddah1	2410006N07Rik|2510015N06Rik|AI987801|AW050362	dimethylarginine dimethylaminohydrolase 1	protein-coding
mm_72982.1	chr8	92911767	92911777	+	1	NA	intron (NM_173014, intron 12 of 13)	intron (NM_173014, intron 12 of 13)	10377	NM_027112	69543	Mm.440514	NM_027112	ENSMUSG00000078144	Capns2	2310005G05Rik|30K-2	calpain, small subunit 2	protein-coding
mm_124645.1	chr15	4898679	4898757	+	1	NA	promoter-TSS (NM_001166066)	promoter-TSS (NM_001166066)	-19	NM_001166066	223825	Mm.159281	NM_001166066	ENSMUSG00000022155	Mroh2b	4930455B06Rik|Heatr7b2|SPIF	maestro heat-like repeat family member 2B	protein-coding
mm_86353.1	chr9	123650721	123650734	-	1	NA	intron (NM_139142, intron 7 of 10)	intron (NM_139142, intron 7 of 10)	-18162	NM_011731	22599	Mm.41963	NM_011731	ENSMUSG00000025243	Slc6a20b	AA986306|Sit1|Slc6a20|XT3|Xtrp3	solute carrier family 6 (neurotransmitter transporter), member 20B	protein-coding
mm_43713.1	chr5	139405279	139405297	+	1	NA	intron (NM_028469, intron 2 of 4)	intron (NM_028469, intron 2 of 4)	-1099	NM_177000	319772	Mm.440271	NM_177000	ENSMUSG00000044092	C130050O18Rik	-	RIKEN cDNA C130050O18 gene	protein-coding
mm_61671.1	chr7	80802883	80802889	+	1	NA	intron (NM_016721, intron 1 of 37)	intron (NM_016721, intron 1 of 37)	445	NM_016721	29875	Mm.207619	NM_016721	ENSMUSG00000030536	Iqgap1	AA682088|D7Ertd237e|D7Ertd257e|mKIAA0051	IQ motif containing GTPase activating protein 1	protein-coding
mm_75703.1	chr8	68852596	68852604	-	1	NA	Intergenic	Intergenic	-27955	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_165841.1	chr3	159495456	159495471	+	1	NA	promoter-TSS (NM_001172093)	promoter-TSS (NM_001172093)	30	NM_001172093	76131	Mm.371655	NM_029523	ENSMUSG00000028175	Depdc1a	5830484J08Rik|Depdc1	DEP domain containing 1a	protein-coding
mm_166738.1	chr6	124505246	124505253	+	1	NA	exon (NM_181344, exon 3 of 6)	exon (NM_181344, exon 3 of 6)	-7372	NM_023143	50909	Mm.333375	NM_023143	ENSMUSG00000055172	C1ra	AI132558|C1r|mC1rA	complement component 1, r subcomponent A	protein-coding
mm_19755.1	chr2	105126354	105126381	-	1	NA	promoter-TSS (NM_144783)	promoter-TSS (NM_144783)	143	NR_015462	329480	Mm.246679	NR_015462	ENSMUSG00000074987	Wt1os	6030498F17|AI314831|Wt1-as	Wilms tumor 1 homolog, opposite strand	ncRNA
mm_101730.1	chr11	42321059	42321072	-	1	NA	promoter-TSS (NM_008068)	promoter-TSS (NM_008068)	7	NM_008068	14399	Mm.4915	NM_008068	ENSMUSG00000020428	Gabra6	GABA-ARalpha6|Gabra-6|alpha6	gamma-aminobutyric acid (GABA) A receptor, subunit alpha 6	protein-coding
mm_124246.1	chr14	101609024	101609075	-	1	NA	5' UTR (NM_001081278, exon 1 of 19)	5' UTR (NM_001081278, exon 1 of 19)	142	NM_001081278	210789	Mm.320639	NM_173380	ENSMUSG00000033083	Tbc1d4	5930406J04Rik|A930035N22|AV295684|As160	TBC1 domain family, member 4	protein-coding
mm_3995.1	chr1	164458537	164458547	+	1	NA	promoter-TSS (NM_009721)	promoter-TSS (NM_009721)	-187	NM_009721	11931	Mm.4550	NM_009721	ENSMUSG00000026576	Atp1b1	Atp4b|Atpb|Atpb-1|NKbeta1	ATPase, Na+/K+ transporting, beta 1 polypeptide	protein-coding
mm_72104.1	chr8	71602171	71602208	+	1	NA	exon (NM_001166213, exon 5 of 15)	exon (NM_001166213, exon 5 of 15)	4543	NM_001166213	100037278	Mm.482159	NM_001166213	ENSMUSG00000043243	Fam129c	Bcnp1	family with sequence similarity 129, member C	protein-coding
mm_14962.1	chr2	152081233	152081252	+	1	NA	promoter-TSS (NM_001160410)	promoter-TSS (NM_001160410)	-287	NM_001160410	545474	Mm.214317	NM_001160410	ENSMUSG00000060257	Scrt2	AW060659	scratch family zinc finger 2	protein-coding
mm_92807.1	chr10	81378460	81378482	-	1	NA	promoter-TSS (NM_019757)	promoter-TSS (NM_019757)	-101	NM_019757	56371	Mm.24202	NM_019757	ENSMUSG00000020235	Fzr1	AW108046|Cdh1|FZR|FZR2|Fyr|HCDH|HCDH1	fizzy/cell division cycle 20 related 1 (Drosophila)	protein-coding
mm_120765.1	chr14	73381752	73381796	+	1	NA	intron (NM_008410, intron 1 of 5)	intron (NM_008410, intron 1 of 5)	3497	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_161716.1	chr17	25816566	25816566	+	1	NA	exon (NM_001164225, exon 2 of 6)	exon (NM_001164225, exon 2 of 6)	-7061	NM_173741	268933	Mm.95512	NM_173741	ENSMUSG00000025737	Wdr24	BC037651	WD repeat domain 24	protein-coding
mm_85931.1	chr9	112095127	112095139	-	1	NA	intron (NM_001177618, intron 17 of 18)	Tigger7|DNA|TcMar-Tigger	23578	NR_029823	723815		NR_029823	ENSMUSG00000065441	Mir128-2	Mirn128-2|Mirn128b|mir-128-2|mir-128b	microRNA 128-2	ncRNA
mm_165411.1	chr2	144331452	144331454	+	1	NA	promoter-TSS (NM_152947)	promoter-TSS (NM_152947)	-91	NM_152947	107586	Mm.252750	NM_026924	ENSMUSG00000037279	Ovol2	1700108N11Rik|1810007D21Rik|M-OVO|M-OVO-A|M-OVO-B|MOVO|Ovo2|Zfp339|movo2	ovo like zinc finger 2	protein-coding
mm_46130.1	chr5	92505519	92505666	-	1	NA	promoter-TSS (NM_007644)	promoter-TSS (NM_007644)	65	NM_007644	12492	Mm.297964	NM_007644	ENSMUSG00000029426	Scarb2	9330185J12Rik|Cd36l2|LGP85|LIMP II|LIMP-2|MLGP85	scavenger receptor class B, member 2	protein-coding
mm_161078.1	chr12	81917592	81917592	+	1	NA	intron (NM_018814, intron 5 of 35)	intron (NM_018814, intron 5 of 35)	57562	NM_018814	54604	Mm.86584	NM_018814	ENSMUSG00000021140	Pcnx	2900024E21Rik|3526401J03Rik|AF096286|AI327143|AI413187|Pcnx1|Pcnxl1	pecanex homolog (Drosophila)	protein-coding
mm_164887.1	chr18	60984135	60984143	+	1	NA	intron (NM_177407, intron 16 of 17)	intron (NM_177407, intron 16 of 17)	20585	NM_001286809	12322	Mm.131530	NM_009792	ENSMUSG00000024617	Camk2a	CaMKII|R74975|mKIAA0968	calcium/calmodulin-dependent protein kinase II alpha	protein-coding
mm_134630.1	chr16	21650386	21650407	-	1	NA	3' UTR (NM_001001881, exon 2 of 2)	3' UTR (NM_001001881, exon 2 of 2)	44269	NM_001001881	72190	Mm.131606	NM_001001881	ENSMUSG00000043391	2510009E07Rik	AI194952	RIKEN cDNA 2510009E07 gene	protein-coding
mm_73624.1	chr8	110618578	110618619	+	1	NA	promoter-TSS (NM_146216)	promoter-TSS (NM_146216)	-40	NM_146216	234729	Mm.274894	NM_146216	ENSMUSG00000010936	Vac14	AA959718|BC032215|D8Wsu151e|Tax1bp2|Trx|ingls	Vac14 homolog (S. cerevisiae)	protein-coding
mm_74037.1	chr8	121907084	121907097	+	1	NA	promoter-TSS (NM_001033485)	promoter-TSS (NM_001033485)	596	NM_011404	20539	Mm.22374	NM_011404	ENSMUSG00000040010	Slc7a5	4F2LC|D0H16S474E|LAT1|TA1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 5	protein-coding
mm_27707.1	chr3	67464135	67464167	-	1	NA	promoter-TSS (NM_016753)	promoter-TSS (NM_016753)	-244	NM_016753	17035	Mm.2632	NM_016753	ENSMUSG00000047557	Lxn	-	latexin	protein-coding
mm_54031.1	chr6	12706779	12706780	-	1	NA	intron (NM_001164805, intron 1 of 26)	intron (NM_001164805, intron 1 of 26)	42474	NM_001164805	330267	Mm.11989	NM_001164805	ENSMUSG00000032625	Thsd7a	Gm837	thrombospondin, type I, domain containing 7A	protein-coding
mm_48855.1	chr5	149636273	149636291	-	1	NA	promoter-TSS (NM_013559)	promoter-TSS (NM_013559)	33	NM_013559	15505	Mm.270681	NM_013559	ENSMUSG00000029657	Hsph1	105kDa|AI790491|Hsp105|Hsp110|hsp-E7I|hsp110/105	heat shock 105kDa/110kDa protein 1	protein-coding
mm_75203.1	chr8	39604587	39604605	-	1	NA	3' UTR (NM_031195, exon 9 of 9)	3' UTR (NM_031195, exon 9 of 9)	38082	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_60901.1	chr7	46711994	46712005	+	1	NA	TTS (NM_011315)	TTS (NM_011315)	-1348	NM_030233	78935	Mm.289866	NM_030233	ENSMUSG00000006763	Saal1	5031425D22Rik|SPACIA1	serum amyloid A-like 1	protein-coding
mm_37268.1	chr4	118542636	118542700	-	1	NA	5' UTR (NM_172383, exon 3 of 4)	5' UTR (NM_172383, exon 3 of 4)	1058	NM_172383	230678	Mm.23639	NM_172383	ENSMUSG00000050854	Tmem125	6330530A05Rik|AV223516	transmembrane protein 125	protein-coding
mm_3229.1	chr1	135849363	135849430	+	1	NA	exon (NM_001130176, exon 9 of 13)	exon (NM_001130176, exon 9 of 13)	8535	NM_001130176	21956	Mm.247470	NM_011619	ENSMUSG00000026414	Tnnt2	Tnt|cTnT	troponin T2, cardiac	protein-coding
mm_13609.1	chr2	113365495	113365506	+	1	NA	exon (NM_010230, exon 2 of 20)	exon (NM_010230, exon 2 of 20)	37764	NM_010230	14260	Mm.4938	NM_010230	ENSMUSG00000044042	Fmn1	Fmn|formin-1|ld	formin 1	protein-coding
mm_22729.1	chr3	19679034	19679042	+	1	NA	intron (NM_001081281, intron 9 of 9)	intron (NM_001081281, intron 9 of 9)	16358	NM_205769	12918	Mm.290689	NM_205769	ENSMUSG00000049796	Crh	CRF|Gm1347	corticotropin releasing hormone	protein-coding
mm_106293.1	chr11	118212760	118212775	-	1	NA	promoter-TSS (NM_001112700)	promoter-TSS (NM_001112700)	-25	NM_001112700	19157	Mm.86413	NM_011180	ENSMUSG00000017132	Cyth1	CLM1|CTH-1|CYTIP|Pscd1	cytohesin 1	protein-coding
mm_134014.1	chr16	4879790	4879803	-	1	NA	promoter-TSS (NM_145359)	promoter-TSS (NM_145359)	55	NM_145359	207740	Mm.268895	NM_145359	ENSMUSG00000039568	Ubald1	1500031H01Rik|BC013706|Fam100a	UBA-like domain containing 1	protein-coding
mm_116290.1	chr13	35211997	35212029	-	1	NA	promoter-TSS (NR_126478)	promoter-TSS (NR_126478)	35	NR_126478	75543	Mm.489052	NR_126478		1700019C18Rik	-	RIKEN cDNA 1700019C18 gene	ncRNA
mm_100934.1	chr11	6520845	6520851	-	1	NA	exon (NM_178440, exon 1 of 22)	exon (NM_178440, exon 1 of 22)	110	NM_178440	246177	Mm.239554	NM_178440	ENSMUSG00000020437	Myo1g	E430002D17Rik	myosin IG	protein-coding
mm_108514.1	chr12	84009482	84009503	+	1	NA	promoter-TSS (NM_012006)	promoter-TSS (NM_012006)	-10	NM_012006	26897	Mm.1978	NM_012006	ENSMUSG00000072949	Acot1	ACH2|CTE-1|CTE-I|Cte1|D12Ucla1	acyl-CoA thioesterase 1	protein-coding
mm_49532.1	chr6	30102154	30102160	+	1	NA	intron (NM_010938, intron 5 of 11)	intron (NM_010938, intron 5 of 11)	25836	NM_001164229	18181	Mm.259258	NM_010938	ENSMUSG00000058440	Nrf1	C87038|D6Ertd415e	nuclear respiratory factor 1	protein-coding
mm_109172.1	chr12	108371199	108371210	+	1	NA	promoter-TSS (NM_001286346)	promoter-TSS (NM_001286346)	51	NM_001286346	68519	Mm.236645	NM_001043335	ENSMUSG00000058070	Eml1	1110008N23Rik|A930030P13Rik|AA171013|AI847476|AI853955|ELP79|EMAP|EMAPL|heco	echinoderm microtubule associated protein like 1	protein-coding
mm_36511.1	chr4	83486458	83486478	-	1	NA	promoter-TSS (NM_001290527)	promoter-TSS (NM_001290527)	-20	NM_001347143	101739	Mm.105331	NM_133948	ENSMUSG00000028484	Psip1	AA408851|AU015605|Dfs70|Ledgfa|Ledgfb|Psip2	PC4 and SFRS1 interacting protein 1	protein-coding
mm_140449.1	chr17	88626531	88626548	+	1	NA	promoter-TSS (NM_029858)	promoter-TSS (NM_029858)	-16	NM_029858	77057	Mm.482203	NM_029858	ENSMUSG00000033855	Ston1	4921524J06Rik|C86231|Salf|Sblf	stonin 1	protein-coding
mm_155387.1	chrX	71816835	71816843	+	1	NA	promoter-TSS (NM_001081356)	promoter-TSS (NM_001081356)	81	NM_001290780	67048	Mm.41102	NM_001081356	ENSMUSG00000073131	Vma21	2610030H06Rik|AI840175	VMA21 vacuolar H+-ATPase homolog (S. cerevisiae)	protein-coding
mm_32067.1	chr4	97777900	97777916	+	1	NA	5' UTR (NM_001122953, exon 1 of 10)	5' UTR (NM_001122953, exon 1 of 10)	282	NM_010905	18027	Mm.31274	NM_010905	ENSMUSG00000028565	Nfia	1110047K16Rik|9430022M17Rik|CTF|NF1-A|NF1A	nuclear factor I/A	protein-coding
mm_167661.1	chr9	71215843	71215851	+	1	NA	promoter-TSS (NM_009022)	promoter-TSS (NM_009022)	58	NM_009022	19378	Mm.42016	NM_009022	ENSMUSG00000013584	Aldh1a2	AV116159|Aldh1a7|Raldh1|Raldh2	aldehyde dehydrogenase family 1, subfamily A2	protein-coding
mm_36726.1	chr4	99103797	99103833	-	1	NA	intron (NM_001290636, intron 1 of 48)	intron (NM_001290636, intron 1 of 48)	17100	NM_001290636	67299	Mm.260623	NM_026082	ENSMUSG00000028556	Dock7	3110056M06Rik|Gm430	dedicator of cytokinesis 7	protein-coding
mm_139103.1	chr17	47141738	47141773	+	1	NA	intron (NM_001097623, intron 2 of 19)	intron (NM_001097623, intron 2 of 19)	813	NM_001097623	224829	Mm.260989	NM_172622		Trerf1	9430096I18Rik|AI429294|B830015H24|RAPA|Trep-132|Trep132	transcriptional regulating factor 1	protein-coding
mm_167747.1	chr9	109847386	109847389	+	1	NA	TTS (NM_009921)	TTS (NM_009921)	2069	NM_009921	12796	Mm.3834	NM_009921	ENSMUSG00000038357	Camp	CAP18|Cnlp|Cramp|FALL39|MCLP	cathelicidin antimicrobial peptide	protein-coding
mm_105930.1	chr11	115125919	115125943	-	1	NA	intron (NM_001169153, intron 2 of 6)	(GA)n|Simple_repeat|Simple_repeat	8061	NM_001347648	246746	Mm.277387	NM_145634	ENSMUSG00000047798	Cd300lf	CLIM1|CLM-1|CLM1|Digr2|F730004D16Rik|IREM1|IgSF13|LMIR3|Pigr3	CD300 molecule like family member F	protein-coding
mm_111468.1	chr12	98574686	98574719	-	1	NA	promoter-TSS (NM_001316665)	promoter-TSS (NM_001316665)	10	NM_001316666	72258	Mm.196158	NM_029911	ENSMUSG00000033854	Kcnk10	1700024D23Rik|3010005K24Rik|Trek2	potassium channel, subfamily K, member 10	protein-coding
mm_136566.1	chr17	3326587	3326595	+	1	NA	promoter-TSS (NM_001122998)	promoter-TSS (NM_001122998)	18	NM_001122998	24001	Mm.137134	NM_011878	ENSMUSG00000023800	Tiam2	3000002F19Rik|STEF|mKIAA2016	T cell lymphoma invasion and metastasis 2	protein-coding
mm_12532.1	chr2	72212657	72212665	+	1	NA	intron (NM_001204165, intron 17 of 30)	intron (NM_001204165, intron 17 of 30)	-72976	NM_023057	65964	Mm.304143	NM_023057	ENSMUSG00000004085	Map3k20	AV006891|B230120H23Rik|MLTK|MLTKalpha|MLTKbeta|Zak	mitogen-activated protein kinase kinase kinase 20	protein-coding
mm_57400.1	chr6	124864083	124864093	-	1	NA	promoter-TSS (NM_013533)	promoter-TSS (NM_013533)	-171	NM_013533	14788	Mm.2514	NM_013533	ENSMUSG00000038390	Gpr162	A-2|BC031437|Grca	G protein-coupled receptor 162	protein-coding
mm_13670.1	chr2	115581766	115581792	+	1	NA	promoter-TSS (NM_207264)	promoter-TSS (NM_207264)	63	NM_001145898	399568	Mm.134929	NM_207264	ENSMUSG00000040282	BC052040	-	cDNA sequence BC052040	protein-coding
mm_132889.1	chr16	48842655	48842661	+	1	NA	intron (NM_020509, intron 1 of 3)	intron (NM_020509, intron 1 of 3)	106	NM_020509	57262	Mm.441868	NM_020509	ENSMUSG00000061100	Retnla	1810019L16Rik|Fizz-1|Fizz1|HIMF|RELM-alpha|RELMa|RELMalpha|Xcp2	resistin like alpha	protein-coding
mm_3927.1	chr1	162639149	162639158	+	1	NA	promoter-TSS (NM_010865)	promoter-TSS (NM_010865)	3	NM_010865	17926	Mm.10694	NM_010865	ENSMUSG00000026697	Myoc	AI957332|GLC1A|TIGR	myocilin	protein-coding
mm_4449.1	chr1	172588722	172588737	+	1	NA	intron (NM_029084, intron 1 of 4)	intron (NM_029084, intron 1 of 4)	1839	NM_029084	74748	Mm.179812	NM_029084	ENSMUSG00000053318	Slamf8	5830408F06Rik|Blame|SBBI42	SLAM family member 8	protein-coding
mm_118909.1	chr14	26656485	26656503	+	1	NA	3' UTR (NM_007479, exon 6 of 6)	3' UTR (NM_007479, exon 6 of 6)	13114	NR_106132	102465773		NR_106132	ENSMUSG00000098751	Mir7672	Gm27314|mmu-mir-7672	microRNA 7672	ncRNA
mm_151013.1	chr19	46761403	46761416	+	1	NA	promoter-TSS (NM_001102471)	promoter-TSS (NM_001102471)	-200	NM_033569	94219	Mm.306903	NM_033569	ENSMUSG00000064105	Cnnm2	AU015877|AW048635|Acdp2|Clp2	cyclin M2	protein-coding
mm_143482.1	chr17	71268590	71268604	-	1	NA	intron (NM_145158, intron 4 of 7)	intron (NM_145158, intron 4 of 7)	42368	NM_145158	246707	Mm.23462	NM_145158	ENSMUSG00000024053	Emilin2	FOAP-10	elastin microfibril interfacer 2	protein-coding
mm_172078.1	chr6	145932791	145932810	-	1	NA	intron (NM_001310837, intron 1 of 2)	LSU-rRNA_Hsa|rRNA|rRNA	927	NM_001310837	16651	Mm.49689	NM_010656	ENSMUSG00000030255	Sspn	Krag	sarcospan	protein-coding
mm_165534.1	chr2	180171575	180171581	+	1	NA	promoter-TSS (NM_019822)	promoter-TSS (NM_019822)	-10	NM_019822	56436	Mm.316654	NM_019822	ENSMUSG00000039041	Adrm1	1110063P18Rik|2510006J17Rik|AA408205|ARM-1|AU043535|Arm1|Gp110|Rpn13	adhesion regulating molecule 1	protein-coding
mm_5766.1	chr1	48698694	48698699	-	1	NA	Intergenic	RMER17B|LTR|ERVK	-1231571	NR_105768	102466969		NR_105768	ENSMUSG00000098876	Mir6350	Gm27958|mmu-mir-6350	microRNA 6350	ncRNA
mm_25236.1	chr3	103887261	103887263	+	1	NA	intron (NR_104070, intron 15 of 22)	BC1_Mm|scRNA|scRNA	-26858	NM_172684	229675	Mm.29366	NM_172684	ENSMUSG00000044098	Rsbn1	C230004D03Rik|E330004N01|Rosbin|Rsbn|Rsbp|mKIAA3002	rosbin, round spermatid basic protein 1	protein-coding
mm_74760.1	chr8	19197145	19197150	-	1	NA	Intergenic	Intergenic	-1557	NM_019728	56519	Mm.45276	NM_019728	ENSMUSG00000059230	Defb4	2310001F05Rik|BD-4	defensin beta 4	protein-coding
mm_36584.1	chr4	88033329	88033373	-	1	NA	promoter-TSS (NM_027326)	promoter-TSS (NM_027326)	56	NM_027326	70122	Mm.288898	NM_027326	ENSMUSG00000028496	Mllt3	2210011H10Rik|2610012I03Rik|3830408D16Rik|Af9|D4Ertd321e	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 3	protein-coding
mm_144834.1	chr18	36528146	36528154	+	1	NA	promoter-TSS (NM_001271545)	promoter-TSS (NM_001271545)	-2	NM_172830	240215	Mm.135463	NM_172830	ENSMUSG00000024485	Slc4a9	AE4|D630003B07|D630024F24Rik	solute carrier family 4, sodium bicarbonate cotransporter, member 9	protein-coding
mm_23878.1	chr3	83030934	83030938	+	1	NA	exon (NM_010196, exon 5 of 5)	exon (NM_010196, exon 5 of 5)	4783	NM_001111048	14161	Mm.88793	NM_010196	ENSMUSG00000028001	Fga	ENSMUSG00000059807|Fib	fibrinogen alpha chain	protein-coding
mm_158017.1	chrX	95965030	95965038	-	1	NA	Intergenic	Intergenic	-8060	NM_152822	76130	Mm.274318	NM_152822	ENSMUSG00000057421	Las1l	1810030A06Rik|5830482G23Rik	LAS1-like (S. cerevisiae)	protein-coding
mm_106997.1	chr12	11276300	11276317	+	1	NA	exon (NM_025695, exon 4 of 27)	exon (NM_025695, exon 4 of 27)	10422	NM_025695	67241	Mm.173953	NM_025695	ENSMUSG00000020608	Smc6	2810489L22Rik|3830418C19Rik|AA990493|AU018782|AW742439|SMC-6|Smc6l1|mKIAA4103	structural maintenance of chromosomes 6	protein-coding
mm_5147.1	chr1	9748356	9748367	-	1	NA	promoter-TSS (NM_173443)	promoter-TSS (NM_173443)	21	NM_173443	70675	Mm.274493	NM_173443	ENSMUSG00000045210	Vcpip1	4932442A08|5730421J18Rik|5730538E15Rik|VCIP135|mKIAA1850	valosin containing protein (p97)/p47 complex interacting protein 1	protein-coding
mm_163974.1	chr14	55757971	55757988	-	1	NA	exon (NM_009894, exon 2 of 5)	exon (NM_009894, exon 2 of 5)	445	NM_009894	12684	Mm.466766	NM_009894	ENSMUSG00000022219	Cideb	1110030C18Rik|AI790179|CIDE-B	cell death-inducing DNA fragmentation factor, alpha subunit-like effector B	protein-coding
mm_83633.1	chr9	49474427	49474440	-	1	NA	intron (NM_172770, intron 2 of 21)	L1M4|LINE|L1	11792	NM_172770	235330	Mm.177413	NM_172770	ENSMUSG00000040219	Ttc12	E330017O07Rik	tetratricopeptide repeat domain 12	protein-coding
mm_36003.1	chr4	56741447	56741447	-	1	NA	promoter-TSS (NM_025271)	promoter-TSS (NM_025271)	-22	NM_025271	11471	Mm.251434	NM_025271	ENSMUSG00000070980	Actl7b	Tact1	actin-like 7b	protein-coding
mm_28791.1	chr3	95996000	95996010	-	1	NA	promoter-TSS (NM_023320)	promoter-TSS (NM_023320)	-166	NM_023320	67220	Mm.458147	NM_023320	ENSMUSG00000015745	Plekho1	2810052M02Rik|CKIP-1|Ckip1|JZA-20|Jza2	pleckstrin homology domain containing, family O member 1	protein-coding
mm_101778.1	chr11	45465315	45465315	-	1	NA	Intergenic	Intergenic	-342768	NR_045876	100009664	Mm.415439	NR_045876		F630206G17Rik	-	RIKEN cDNA F630206G17 gene	ncRNA
mm_140635.1	chr17	12507723	12507727	-	1	NA	promoter-TSS (NM_011395)	promoter-TSS (NM_011395)	-21	NM_011395	20519	Mm.99252	NM_011395	ENSMUSG00000023828	Slc22a3	EMT|Oct3|Orct3|Slca22a3	solute carrier family 22 (organic cation transporter), member 3	protein-coding
mm_73375.1	chr8	105635782	105635802	+	1	NA	promoter-TSS (NM_181322)	promoter-TSS (NM_181322)	-746	NM_181322	13018	Mm.269474	NM_181322	ENSMUSG00000005698	Ctcf	AW108038	CCCTC-binding factor	protein-coding
mm_18091.1	chr2	44985190	44985200	-	1	NA	3' UTR (NM_015753, exon 10 of 10)	3' UTR (NM_015753, exon 10 of 10)	37982	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_105882.1	chr11	114930401	114930418	-	1	NA	intron (NM_199221, intron 1 of 3)	ID_B1|SINE|B4	3977	NM_001347651	217304	Mm.185355	NM_199221	ENSMUSG00000063193	Cd300lb	CLM-7|Clm7|Gm253|LMIR5	CD300 molecule like family member B	protein-coding
mm_25132.1	chr3	102262517	102262527	+	1	NA	non-coding (NR_040391, exon 1 of 4)	non-coding (NR_040391, exon 1 of 4)	117	NR_040391	319951	Mm.225196	NR_040391	ENSMUSG00000105891	A230001M10Rik	-	RIKEN cDNA A230001M10 gene	ncRNA
mm_172472.1	chr7	44553134	44553141	-	1	NA	intron (NM_001285518, intron 2 of 9)	intron (NM_001285518, intron 2 of 9)	828	NM_009473	22260	Mm.968	NM_009473	ENSMUSG00000060601	Nr1h2	AI194859|LXR|LXRB|LXRBSV|LXRbeta|NER1|OR-1|RIP15|UR|Unr|Unr2	nuclear receptor subfamily 1, group H, member 2	protein-coding
mm_25468.1	chr3	108653932	108653964	+	1	NA	promoter-TSS (NM_145543)	promoter-TSS (NM_145543)	8	NM_001177771	229725	Mm.214545	NM_145543	ENSMUSG00000027884	Clcc1	Mclc	chloride channel CLIC-like 1	protein-coding
mm_135868.1	chr16	60606489	60606517	-	1	NA	promoter-TSS (NM_007938)	promoter-TSS (NM_007938)	-972	NM_007938	13840	Mm.455790	NM_007938	ENSMUSG00000055540	Epha6	Ehk2|Hek12|m-ehk2	Eph receptor A6	protein-coding
mm_61861.1	chr7	88309974	88309981	+	1	NA	3' UTR (NM_009982, exon 7 of 7)	3' UTR (NM_009982, exon 7 of 7)	31892	NM_001311790	13032	Mm.89295	NM_009982	ENSMUSG00000030560	Ctsc	AI047818|CatC|DPP1|DPPI	cathepsin C	protein-coding
mm_110083.1	chr12	24681827	24681844	-	1	NA	promoter-TSS (NM_001161807)	promoter-TSS (NM_001161807)	-40	NM_001161807	12879	Mm.52265	NM_138686	ENSMUSG00000062563	Cys1	2900006B19Rik|AV218859|Ccap|ck|cpk	cystin 1	protein-coding
mm_67808.1	chr7	98117818	98117833	-	1	NA	intron (NM_001256081, intron 1 of 48)	intron (NM_001256081, intron 1 of 48)	1668	NM_001256081	17921	Mm.1403	NM_008663	ENSMUSG00000030761	Myo7a	Hdb|Myo7|USH1B|nmf371|polka|sh-1|sh1	myosin VIIA	protein-coding
mm_54122.1	chr6	18388055	18388077	-	1	NA	exon (NM_080285, exon 16 of 23)	exon (NM_080285, exon 16 of 23)	126759	NM_080285	30785	Mm.224189	NM_080285	ENSMUSG00000000416	Cttnbp2	3010022N24Rik|4732477G22Rik|6430526E05|9130022E09Rik|AU040881|Cortbp2|ORF4|mKIAA1758	cortactin binding protein 2	protein-coding
mm_28189.1	chr3	88078296	88078328	-	1	NA	promoter-TSS (NM_172526)	promoter-TSS (NM_172526)	-8	NM_172526	214191	Mm.229191	NM_172526	ENSMUSG00000051036	Ttc24	A430025D11Rik	tetratricopeptide repeat domain 24	protein-coding
mm_150423.1	chr19	37408726	37408741	+	1	NA	intron (NM_010615, intron 14 of 21)	(T)n|Simple_repeat|Simple_repeat	-26108	NM_008245	15242	Mm.33896	NM_008245	ENSMUSG00000024986	Hhex	Hex|Hex1|Hhex-rs2|Prh|Prhx	hematopoietically expressed homeobox	protein-coding
mm_69851.1	chr7	141427502	141427521	-	1	NA	exon (NM_021316, exon 2 of 2)	exon (NM_021316, exon 2 of 2)	1909	NM_021316	57754	Mm.87027	NM_021316	ENSMUSG00000060240	Cend1	1500001H12Rik|AI415214|BM88	cell cycle exit and neuronal differentiation 1	protein-coding
mm_15454.1	chr2	157424136	157424150	+	1	NA	promoter-TSS (NM_001025395)	promoter-TSS (NM_001025395)	-150	NM_009271	20779	Mm.22845	NM_009271	ENSMUSG00000027646	Src	AW259666|pp60c-src	Rous sarcoma oncogene	protein-coding
mm_146234.1	chr18	77144999	77145010	+	1	NA	exon (NM_001164168, exon 12 of 14)	exon (NM_001164168, exon 12 of 14)	-40843	NM_153124	225742	Mm.365178	NM_013666	ENSMUSG00000025425	St8sia5	ST8SiaV|Siat8e	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 5	protein-coding
mm_44118.1	chr5	149441842	149441851	+	1	NA	intron (NM_001310765, intron 1 of 5)	intron (NM_001310765, intron 1 of 5)	2186	NM_001310765	75860	Mm.159605	NM_029464	ENSMUSG00000029660	Tex26	4930588N13Rik	testis expressed 26	protein-coding
mm_78601.1	chr9	37489282	37489326	+	1	NA	promoter-TSS (NM_146222)	promoter-TSS (NM_146222)	-17	NM_146222	235184	Mm.127892	NM_146222	ENSMUSG00000042138	Msantd2	2810450G17Rik|9530092B10Rik	Myb/SANT-like DNA-binding domain containing 2	protein-coding
mm_142253.1	chr17	37569452	37569460	-	1	NA	promoter-TSS (NM_001013575)	promoter-TSS (NM_001013575)	-5	NM_001013575	258096	Mm.159619	NM_001013575	ENSMUSG00000051611	Olfr112	4930580F03Rik|MOR218-4	olfactory receptor 112	protein-coding
mm_78339.1	chr9	25288245	25288265	+	1	NA	exon (NM_001205367, exon 5 of 13)	exon (NM_001205367, exon 5 of 13)	35816	NM_001205367	235072	Mm.270259	NM_009859	ENSMUSG00000001833	Sept7	Cdc10|E430034N22	septin 7	protein-coding
mm_65304.1	chr7	24676671	24676679	-	1	NA	Intergenic	Intergenic	-4625	NM_019981	56746	Mm.23385	NM_019981	ENSMUSG00000062773	Tex101	1700008H15Rik|AI429076|TES101RP	testis expressed gene 101	protein-coding
mm_50889.1	chr6	56714959	56714971	+	1	NA	promoter-TSS (NM_030235)	promoter-TSS (NM_030235)	60	NM_030235	78937	Mm.105343	NM_030235	ENSMUSG00000029787	Avl9	5830411G16Rik|D730049P16Rik|mKIAA0241	AVL9 cell migration associated	protein-coding
mm_55093.1	chr6	49263980	49263990	-	1	NA	promoter-TSS (NM_198102)	promoter-TSS (NM_198102)	67	NM_001347209	101214	Mm.196598	NM_198102	ENSMUSG00000029817	Tra2a	1500010G04Rik|AL022798|G430041M01Rik|mAWMS1	transformer 2 alpha homolog (Drosophila)	protein-coding
mm_82884.1	chr9	32524507	32524510	-	1	NA	intron (NM_008026, intron 1 of 8)	intron (NM_008026, intron 1 of 8)	16944	NM_008026	14247	Mm.258908	NM_008026	ENSMUSG00000016087	Fli1	EWSR2|Fli-1|SIC-1|Sic1	Friend leukemia integration 1	protein-coding
mm_78718.1	chr9	41579661	41579669	+	1	NA	intron (NR_131930, intron 3 of 3)	intron (NR_131930, intron 3 of 3)	-1588	NR_015483	73144	Mm.38166	NM_001033153	ENSMUSG00000074415	3110039I08Rik	2610203C20Rik|AI848448|D230004N17Rik|D3Mgi9|Mir100hg	RIKEN cDNA 3110039I08 gene	ncRNA
mm_121283.1	chr14	104190989	104191008	+	1	NA	Intergenic	Intergenic	-163856	NR_045953	73877	Mm.399172	NR_045953		4930432J09Rik	-	RIKEN cDNA 4930432J09 gene	ncRNA
mm_118195.1	chr13	107857383	107857400	-	1	NA	intron (NM_145456, intron 2 of 14)	(A)n|Simple_repeat|Simple_repeat	32673	NM_145456	67263	Mm.490418	NM_145456	ENSMUSG00000032846	Zswim6	2900036G02Rik|mKIAA1577	zinc finger SWIM-type containing 6	protein-coding
mm_158581.1	chrX	150812449	150812489	-	1	NA	intron (NM_001199246, intron 2 of 12)	intron (NM_001199246, intron 2 of 12)	1234	NM_001199246	80884	Mm.22575	NM_030700	ENSMUSG00000025268	Maged2	4833439A22Rik|Mage-d2|ORF1	melanoma antigen, family D, 2	protein-coding
mm_33554.1	chr4	130936004	130936031	+	1	NA	3' UTR (NM_010686, exon 8 of 8)	3' UTR (NM_010686, exon 8 of 8)	-8368	NM_010769	17180	Mm.271796	NM_010769	ENSMUSG00000040533	Matn1	CMP|Crtm|Mat1|matrilin-1	matrilin 1, cartilage matrix protein	protein-coding
mm_15393.1	chr2	156721294	156721302	+	1	NA	promoter-TSS (NM_001042487)	promoter-TSS (NM_001042487)	19	NM_001042487	228836	Mm.22094	NM_146128	ENSMUSG00000061689	Dlgap4	AI225853|BC024558|DAP-4|DAP4|SAPAP-4|Sapap4|WBP16	discs, large homolog-associated protein 4 (Drosophila)	protein-coding
mm_107704.1	chr12	55489410	55489415	+	1	NA	TTS (NM_010907)	TTS (NM_010907)	3235	NM_010907	18035	Mm.170515	NM_010907	ENSMUSG00000021025	Nfkbia	AI462015|Nfkbi	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, alpha	protein-coding
mm_25903.1	chr3	131111556	131111569	+	1	NA	exon (NM_001276402, exon 1 of 10)	exon (NM_001276402, exon 1 of 10)	-1229	NM_001276403	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_131847.1	chr16	23058580	23058602	+	1	NA	exon (NM_001102411, exon 1 of 10)	exon (NM_001102411, exon 1 of 10)	291	NM_001102412	16644	Mm.2160	NM_023125	ENSMUSG00000022875	Kng1	Kng	kininogen 1	protein-coding
mm_77353.1	chr8	119586117	119586122	-	1	NA	intron (NM_026648, intron 5 of 11)	RLTR1B-int|LTR|ERV1	10884	NM_026648	68270	Mm.41977	NM_026648	ENSMUSG00000031831	Dnaaf1	4930457P18Rik|Lrrc50	dynein, axonemal assembly factor 1	protein-coding
mm_18116.1	chr2	44996567	44996583	-	1	NA	exon (NM_015753, exon 8 of 10)	exon (NM_015753, exon 8 of 10)	26602	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_23011.1	chr3	34202676	34202679	+	1	NA	Intergenic	ID_B1|SINE|B4	-121323	NM_026332	67713	Mm.274266	NM_026332	ENSMUSG00000027679	Dnajc19	1810055D05Rik|AA959924|Tim14	DnaJ heat shock protein family (Hsp40) member C19	protein-coding
mm_145184.1	chr18	49478949	49478952	+	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	-44339	NR_033785	67321	Mm.245802	NR_033785	ENSMUSG00000100297	1700044K03Rik	-	RIKEN cDNA 1700044K03 gene	ncRNA
mm_116257.1	chr13	34113259	34113267	-	1	NA	promoter-TSS (NR_046184)	promoter-TSS (NR_046184)	9	NR_046184	432745	Mm.159104	NR_046184		4930447K03Rik	-	RIKEN cDNA 4930447K03 gene	ncRNA
mm_875.1	chr1	52155199	52155217	+	1	NA	intron (NM_001205313, intron 23 of 24)	intron (NM_001205313, intron 23 of 24)	35586	NM_001205313	20846	Mm.277406	NM_009283	ENSMUSG00000026104	Stat1	2010005J02Rik|AA408197	signal transducer and activator of transcription 1	protein-coding
mm_118988.1	chr14	28504797	28504826	+	1	NA	promoter-TSS (NM_009524)	promoter-TSS (NM_009524)	-662	NM_009524	22418	Mm.287544	NM_009524	ENSMUSG00000021994	Wnt5a	8030457G12Rik|Wnt-5a	wingless-type MMTV integration site family, member 5A	protein-coding
mm_146684.1	chr18	12862205	12862269	-	1	NA	5' UTR (NM_001252492, exon 1 of 14)	5' UTR (NM_001252492, exon 1 of 14)	476	NM_001252493	64291	Mm.259470	NM_020573	ENSMUSG00000044252	Osbpl1a	G430090F17Rik|Gm753|ORP-1|Osbpl1b	oxysterol binding protein-like 1A	protein-coding
mm_171237.1	chr3	69005733	69005733	+	1	NA	intron (NM_133786, intron 1 of 23)	CpG	761	NM_133786	70099	Mm.206841	NM_133786	ENSMUSG00000034349	Smc4	2500002A22Rik|C79747|SMC-4|Smc4l1	structural maintenance of chromosomes 4	protein-coding
mm_149628.1	chr19	17136834	17136838	+	1	NA	intron (NM_181348, intron 9 of 19)	intron (NM_181348, intron 9 of 19)	180718	NM_181348	353211	Mm.257354	NM_181348	ENSMUSG00000039126	Prune2	6330414G02Rik|A230083H22Rik|A330102H22Rik|Bmcc1|mKIAA0367	prune homolog 2	protein-coding
mm_34714.1	chr4	152124864	152124891	+	1	NA	intron (NM_207688, intron 8 of 10)	intron (NM_207688, intron 8 of 10)	4048	NM_019585	56226	Mm.264215	NM_019585	ENSMUSG00000028943	Espn	je	espin	protein-coding
mm_89410.1	chr10	90829410	90829481	+	1	NA	promoter-TSS (NM_001347054)	promoter-TSS (NM_001347054)	-209	NM_001347054	77531	Mm.440605	NM_181398	ENSMUSG00000058589	Anks1b	AIDA-1b|C030032C09Rik|E530015N03Rik|ENSMUSG00000078431|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding
mm_167605.1	chr9	52164613	52164624	-	1	NA	intron (NM_001162921, intron 1 of 5)	intron (NM_001162921, intron 1 of 5)	3493	NM_001162921	244871	Mm.295686	NM_001162921	ENSMUSG00000035164	Zc3h12c	A230108E06|C230027N18Rik|mKIAA1726	zinc finger CCCH type containing 12C	protein-coding
mm_46396.1	chr5	104089682	104089693	-	1	NA	exon (NM_010097, exon 6 of 11)	exon (NM_010097, exon 6 of 11)	-12079	NM_001163772	100271704	Mm.366664	NM_001163772	ENSMUSG00000091034	Gm17660	Scpppq1	predicted gene, 17660	protein-coding
mm_87277.1	chr10	41893948	41893959	+	1	NA	intron (NM_001013370, intron 1 of 9)	intron (NM_001013370, intron 1 of 9)	6514	NM_001013370	140742	Mm.139418	NM_001013370	ENSMUSG00000038332	Sesn1	1110002G11Rik|AU044290|Pa26|Sest1	sestrin 1	protein-coding
mm_169848.1	chr1	63139001	63139020	+	1	NA	intron (NR_045914, intron 1 of 3)	B1_Mus1|SINE|Alu	24270	NR_045914	100380944	Mm.392955	NR_045914	ENSMUSG00000084799	Ino80dos	Gm11602|OTTMUSG00000002611	INO80 complex subunit D, opposite strand	ncRNA
mm_145000.1	chr18	38379340	38379350	+	1	NA	Intergenic	RMER10A|LTR|ERVL	-39630	NM_022996	65113	Mm.102496	NM_022996	ENSMUSG00000024425	Ndfip1	0610010M22Rik|N4wbp5	Nedd4 family interacting protein 1	protein-coding
mm_120663.1	chr14	70545349	70545359	+	1	NA	5' UTR (NM_180588, exon 1 of 8)	5' UTR (NM_180588, exon 1 of 8)	103	NM_180588	72549	Mm.46742	NM_180588	ENSMUSG00000033589	Reep4	2700029E10Rik	receptor accessory protein 4	protein-coding
mm_166159.1	chr5	15934892	15934900	+	1	NA	5' UTR (NM_001110843, exon 1 of 39)	5' UTR (NM_001110843, exon 1 of 39)	205	NM_001110844	12293	Mm.159842	NM_009784	ENSMUSG00000040118	Cacna2d1	Ca(v)alpha2delta1|Cacna2|Cchl2a	calcium channel, voltage-dependent, alpha2/delta subunit 1	protein-coding
mm_96631.1	chr11	69323964	69324043	+	1	NA	promoter-TSS (NM_001024206)	promoter-TSS (NM_001024206)	17	NM_001024206	245828	Mm.28073	NM_001024206	ENSMUSG00000049299	Trappc1	BET5|D11Ertd172e|MUM2	trafficking protein particle complex 1	protein-coding
mm_76489.1	chr8	85840609	85840642	-	1	NA	promoter-TSS (NM_199446)	promoter-TSS (NM_199446)	324	NM_028007	71927	Mm.61018	NM_028007	ENSMUSG00000031703	Itfg1	2310047C21Rik|AI314457|Cda08|D8Wsu49e	integrin alpha FG-GAP repeat containing 1	protein-coding
mm_32168.1	chr4	100305655	100305659	+	1	NA	intron (NM_001312690, intron 2 of 3)	intron (NM_001312690, intron 2 of 3)	-173210	NM_001033773	381534	Mm.318133	NM_001033773	ENSMUSG00000069733	Ube2u	-	ubiquitin-conjugating enzyme E2U (putative)	protein-coding
mm_52191.1	chr6	99770526	99770528	+	1	NA	Intergenic	Intergenic	-44135	NM_001170419	50501	Mm.87365	NM_015768	ENSMUSG00000030069	Prok2	Bv8|PK2|Prok1	prokineticin 2	protein-coding
mm_128321.1	chr15	38009661	38009685	-	1	NA	exon (NM_001081359, exon 23 of 59)	exon (NM_001081359, exon 23 of 59)	-48618	NM_199476	382985	Mm.24738	NM_199476	ENSMUSG00000022292	Rrm2b	p53R2	ribonucleotide reductase M2 B (TP53 inducible)	protein-coding
mm_116409.1	chr13	41425997	41426010	-	1	NA	5' UTR (NM_001111324, exon 2 of 8)	5' UTR (NM_001111324, exon 2 of 8)	61357	NM_001111324	18003	Mm.288980	NM_017464	ENSMUSG00000021365	Nedd9	Cas-L|CasL|HEF1|MEF1|Nedd-9|p105	neural precursor cell expressed, developmentally down-regulated gene 9	protein-coding
mm_122030.1	chr14	29721784	29721801	-	1	NA	promoter-TSS (NM_009785)	promoter-TSS (NM_009785)	72	NM_009785	12294	Mm.386754	NM_009785	ENSMUSG00000021991	Cacna2d3	Cacnad3|alapha2delta3	calcium channel, voltage-dependent, alpha2/delta subunit 3	protein-coding
mm_57917.1	chr6	133852008	133852019	-	1	NA	exon (NM_010594, exon 2 of 4)	exon (NM_010594, exon 2 of 4)	1654	NM_010594	16483	Mm.13052	NM_010594	ENSMUSG00000032758	Kap	AW146435|FKSG22	kidney androgen regulated protein	protein-coding
mm_68118.1	chr7	102116706	102116719	-	1	NA	promoter-TSS (NM_001081424)	promoter-TSS (NM_001081424)	1	NM_001081424	504186	Mm.334074	NM_001081424	ENSMUSG00000066279	Chrna10	-	cholinergic receptor, nicotinic, alpha polypeptide 10	protein-coding
mm_40991.1	chr5	77280787	77280796	+	1	NA	exon (NM_011263, exon 4 of 4)	exon (NM_011263, exon 4 of 4)	8034	NR_039557	100628577		NR_039557	ENSMUSG00000093061	Mir5098	mmu-mir-5098|mu-mir-5098	microRNA 5098	ncRNA
mm_135969.1	chr16	74925851	74925857	-	1	NA	Intergenic	Intergenic	-514942	NM_175549	268902	Mm.171736	NM_175549	ENSMUSG00000052516	Robo2	2600013A04Rik|9430089E08Rik|BB097918|D230004I22Rik|mKIAA1568	roundabout guidance receptor 2	protein-coding
mm_68085.1	chr7	101870779	101870787	-	1	NA	promoter-TSS (NM_008034)	promoter-TSS (NM_008034)	5	NM_001252554	14275	Mm.2135	NM_008034	ENSMUSG00000001827	Folr1	FBP1|Folbp-1|Folbp1	folate receptor 1 (adult)	protein-coding
mm_38477.1	chr4	140699666	140699683	-	1	NA	Intergenic	Intergenic	-1799	NM_173867	108911	Mm.253	NM_173867	ENSMUSG00000040945	Rcc2	2610510H01Rik|2610529N02Rik|AA536646|AA675016|Td60|mKIAA1470	regulator of chromosome condensation 2	protein-coding
mm_10801.1	chr2	24349683	24349700	+	1	NA	3' UTR (NM_031167, exon 5 of 5)	3' UTR (NM_031167, exon 5 of 5)	4320	NM_001039701	16181	Mm.882	NM_031167	ENSMUSG00000026981	Il1rn	F630041P17Rik|IL-1ra	interleukin 1 receptor antagonist	protein-coding
mm_113001.1	chr13	21810429	21810442	+	1	NA	promoter-TSS (NM_001110555).2	promoter-TSS (NM_001110555).2	-32	NM_178185	319171	Mm.250564	NM_178185	ENSMUSG00000094777	Hist1h2ap	ENSMUSG00000060262|Gm11276|OTTMUSG00000000448	histone cluster 1, H2ap	protein-coding
mm_166028.1	chr4	126047208	126047225	+	1	NA	intron (NM_025544, intron 1 of 7)	intron (NM_025544, intron 1 of 7)	288	NM_025544	66407	Mm.195628	NM_025544	ENSMUSG00000028861	Mrps15	1500003E24Rik|2410002B11Rik|Mprs15	mitochondrial ribosomal protein S15	protein-coding
mm_137218.1	chr17	24170907	24170936	+	1	NA	Intergenic	Intergenic	-1492	NM_009729	11984	Mm.30155	NM_009729	ENSMUSG00000024121	Atp6v0c	Atp6c|Atp6c2|Atp6l|Atpl|Atpl-rs1|PL16|VATL|Vma3	ATPase, H+ transporting, lysosomal V0 subunit C	protein-coding
mm_18888.1	chr2	76709507	76709520	-	1	NA	exon (NM_011652, exon 307 of 313)	exon (NM_011652, exon 307 of 313)	34198	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_16068.1	chr2	168081025	168081035	+	1	NA	promoter-TSS (NM_021409)	promoter-TSS (NM_021409)	26	NM_021409	58220	Mm.292834	NM_021409	ENSMUSG00000044641	Pard6b	AV025615|Par6b	par-6 family cell polarity regulator beta	protein-coding
mm_120525.1	chr14	66911221	66911228	+	1	NA	promoter-TSS (NM_175498)	promoter-TSS (NM_175498)	16	NM_175498	239157	Mm.44358	NM_175498	ENSMUSG00000046204	Pnma2	A830049P17Rik|mKIAA0883	paraneoplastic antigen MA2	protein-coding
mm_51360.1	chr6	72629285	72629304	+	1	NA	promoter-TSS (NR_040422)	promoter-TSS (NR_040422)	6	NR_040422	100038714	Mm.321330	NR_040421		Gm15401	ENSMUSG00000072999|OTTMUSG00000021199	predicted gene 15401	ncRNA
mm_154810.1	chrX	13632083	13632136	+	1	NA	promoter-TSS (NM_011823)	promoter-TSS (NM_011823)	-660	NM_011823	23890	Mm.487326	NM_011823	ENSMUSG00000040229	Gpr34	Lypsr1	G protein-coupled receptor 34	protein-coding
mm_154601.1	chrX	7607109	7607127	+	1	NA	promoter-TSS (NM_019582)	promoter-TSS (NM_019582)	15	NM_019582	54652	Mm.289647	NM_019582	ENSMUSG00000031142	Cacna1f	A930034B14|Cav1.4|Sfc17|nerg1|nob2	calcium channel, voltage-dependent, alpha 1F subunit	protein-coding
mm_15468.1	chr2	157470838	157470860	+	1	NA	3' UTR (NM_001025395, exon 14 of 14)	3' UTR (NM_001025395, exon 14 of 14)	46556	NM_001025395	20779	Mm.22845	NM_009271	ENSMUSG00000027646	Src	AW259666|pp60c-src	Rous sarcoma oncogene	protein-coding
mm_98405.1	chr11	94328263	94328278	+	1	NA	exon (NM_027799, exon 1 of 5)	exon (NM_027799, exon 1 of 5)	269	NM_146024	71452	Mm.141054	NM_027799	ENSMUSG00000020864	Ankrd40	1110011C06Rik|5530600A18Rik|Gcap15	ankyrin repeat domain 40	protein-coding
mm_122682.1	chr14	52014738	52014825	-	1	NA	promoter-TSS (NM_001253695)	promoter-TSS (NM_001253695)	-223	NM_001253695	69890	Mm.475652	NM_027248	ENSMUSG00000049295	Zfp219	2010302A17Rik	zinc finger protein 219	protein-coding
mm_136283.1	chr16	91355235	91355252	-	1	NA	Intergenic	Intergenic	-17540	NM_010509	15976	Mm.6834	NM_010509	ENSMUSG00000022971	Ifnar2	AI747302|Ifnar-2	interferon (alpha and beta) receptor 2	protein-coding
mm_10014.1	chr1	191990143	191990155	-	1	NA	Intergenic	Intergenic	8485	NR_039566	100628582		NR_039566	ENSMUSG00000093003	Mir3473c	mmu-mir-3473c	microRNA 3473c	ncRNA
mm_35997.1	chr4	56000787	56000816	-	1	NA	Intergenic	ERVL-B4-int|LTR|ERVL	-468326	NM_010637	16600	Mm.4325	NM_010637	ENSMUSG00000003032	Klf4	EZF|Gklf|Zie	Kruppel-like factor 4 (gut)	protein-coding
mm_115738.1	chr13	17804947	17804968	-	1	NA	5' UTR (NM_001081058, exon 1 of 14)	5' UTR (NM_001081058, exon 1 of 14)	140	NM_001081058	69562	Mm.193924	NM_027118	ENSMUSG00000041297	Cdk13	2310015O17Rik|Cdc2l5	cyclin-dependent kinase 13	protein-coding
mm_167920.1	chrX	102005055	102005075	+	1	NA	intron (NM_001163610, intron 1 of 7)	intron (NM_001163610, intron 1 of 7)	66242	NM_001278534	331474	Mm.23297	NM_183318	ENSMUSG00000049191	Rgag4	6430402L03Rik|Mar5|Mart5|mKIAA2001	retrotransposon gag domain containing 4	protein-coding
mm_16098.1	chr2	168981159	168981196	+	1	NA	Intergenic	Intergenic	2908	NR_040326	75508	Mm.271256	NR_040326	ENSMUSG00000086348	1700017J07Rik	-	RIKEN cDNA 1700017J07 gene	ncRNA
mm_50100.1	chr6	41533148	41533159	+	1	NA	Intergenic	Intergenic	11377	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_39588.1	chr5	23496080	23496095	+	1	NA	exon (NM_026984, exon 17 of 26)	exon (NM_026984, exon 17 of 26)	61658	NM_026984	69188	Mm.205190	NM_026984	ENSMUSG00000029004	Kmt2e	1810033J14Rik|9530077A04Rik|D230038D11Rik|Mll5|NKp44L	lysine (K)-specific methyltransferase 2E	protein-coding
mm_107989.1	chr12	73212079	73212083	+	1	NA	intron (NM_008612, intron 6 of 7)	intron (NM_008612, intron 6 of 7)	74630	NM_029580	76357	Mm.311344	NM_029580	ENSMUSG00000034442	Trmt5	2610027O18Rik|mKIAA1393	TRM5 tRNA methyltransferase 5	protein-coding
mm_97452.1	chr11	78194543	78194563	+	1	NA	intron (NM_001045516, intron 1 of 3)	intron (NM_001045516, intron 1 of 3)	1161	NM_001045516	216974	Mm.50974	NM_001045516	ENSMUSG00000044122	Proca1	4933404M19Rik	protein interacting with cyclin A1	protein-coding
mm_98298.1	chr11	90030296	90030359	+	1	NA	promoter-TSS (NM_026433)	promoter-TSS (NM_026433)	-21	NM_026433	67888	Mm.212428	NM_026433	ENSMUSG00000069763	Tmem100	1810057C19Rik|AV011897	transmembrane protein 100	protein-coding
mm_71025.1	chr8	33536603	33536621	+	1	NA	Intergenic	Intergenic	-33932	NM_031374	104271	Mm.280624	NM_031374	ENSMUSG00000009628	Tex15	2210014E14Rik|AL022622|AU022940	testis expressed gene 15	protein-coding
mm_79011.1	chr9	45595680	45595725	+	1	NA	intron (NM_001081270, intron 3 of 32)	RSINE1|SINE|B4	-164470	NR_040732	74602	Mm.394117	NR_040732	ENSMUSG00000097074	4833428L15Rik	-	RIKEN cDNA 4833428L15 gene	ncRNA
mm_32716.1	chr4	116221591	116221615	+	1	NA	promoter-TSS (NM_181585)	promoter-TSS (NM_181585)	-311	NM_181585	18710	Mm.253819	NM_181585	ENSMUSG00000028698	Pik3r3	AA414954|p55pik	phosphatidylinositol 3 kinase, regulatory subunit, polypeptide 3 (p55)	protein-coding
mm_110051.1	chr12	19175714	19175731	-	1	NA	Intergenic	CpG	661212	NM_001201330	236366	Mm.352227	NM_001033157	ENSMUSG00000073197	5730507C01Rik	-	RIKEN cDNA 5730507C01 gene	protein-coding
mm_132302.1	chr16	33523677	33523695	+	1	NA	intron (NM_001083902, intron 1 of 11)	intron (NM_001083902, intron 1 of 11)	5091	NM_001083902	171286	Mm.35253	NM_134251	ENSMUSG00000035506	Slc12a8	CCC9|E330020C02Rik	solute carrier family 12 (potassium/chloride transporters), member 8	protein-coding
mm_36178.1	chr4	62208414	62208424	-	1	NA	promoter-TSS (NM_001290353)	promoter-TSS (NM_001290353)	127	NM_001290351	22696	Mm.5011	NM_009554	ENSMUSG00000028389	Zfp37	Tzn|Zfp-37	zinc finger protein 37	protein-coding
mm_163256.1	chr11	109651005	109651009	+	1	NA	promoter-TSS (NM_021880)	promoter-TSS (NM_021880)	86	NM_001313976	19084	Mm.30039	NM_021880	ENSMUSG00000020612	Prkar1a	1300018C22Rik|RIalpha|Tse-1|Tse1	protein kinase, cAMP dependent regulatory, type I, alpha	protein-coding
mm_82471.1	chr9	16339459	16339462	-	1	NA	intron (NM_001080814, intron 1 of 24)	intron (NM_001080814, intron 1 of 24)	38771	NM_001080814	270120	Mm.195010	NM_001080814	ENSMUSG00000074505	Fat3	9430076A06Rik|D430038H04Rik|Gm1132|Gm510|MFAT3F	FAT atypical cadherin 3	protein-coding
mm_77302.1	chr8	117343678	117343691	-	1	NA	intron (NM_001163262, intron 1 of 20)	intron (NM_001163262, intron 1 of 20)	-5486	NM_028941	74440	Mm.233181	NM_028941	ENSMUSG00000034390	Cmip	4933407C03Rik|5830471E12Rik|AI314065|AI464126	c-Maf inducing protein	protein-coding
mm_100481.1	chr11	120232922	120232952	+	1	NA	promoter-TSS (NM_198423)	promoter-TSS (NM_198423)	-10	NM_001347621	268515	Mm.309498	NM_198423	ENSMUSG00000039741	Bahcc1	B930044J06|BC060615	BAH domain and coiled-coil containing 1	protein-coding
mm_123743.1	chr14	70191509	70191538	-	1	NA	exon (NM_001271407, exon 13 of 21)	exon (NM_001271407, exon 13 of 21)	723	NM_001271409	20410	Mm.5068	NM_011366	ENSMUSG00000022091	Sorbs3	SCAM-1|SH3P3|Sh3d4|vinexin-g	sorbin and SH3 domain containing 3	protein-coding
mm_171291.1	chr3	90087457	90087468	-	1	NA	exon (NM_001293748, exon 4 of 10)	exon (NM_001293748, exon 4 of 10)	7941	NM_001293749	59069	Mm.240839	NM_022314	ENSMUSG00000027940	Tpm3	TM30nm|TMnm|Tm5NM|Tpm-5|Tpm5|Trop-5|gamma-TM|hTM30nm|hTMnm	tropomyosin 3, gamma	protein-coding
mm_140295.1	chr17	85620847	85620855	+	1	NA	promoter-TSS (NM_011381)	promoter-TSS (NM_011381)	17	NM_011381	20473	Mm.370208	NM_011381	ENSMUSG00000038805	Six3	E130112M24Rik|Six3a|Six3alpha|Six3b|Six3beta	sine oculis-related homeobox 3	protein-coding
mm_172763.1	chr8	91601345	91601348	-	1	NA	intron (NM_011936, intron 8 of 8)	RLTR1B|LTR|ERV1	200308	NM_001253822	16373	Mm.238044	NM_008393	ENSMUSG00000031734	Irx3	AI894186	Iroquois related homeobox 3	protein-coding
mm_73232.1	chr8	104111440	104111457	+	1	NA	intron (NM_009868, intron 1 of 11)	intron (NM_009868, intron 1 of 11)	-5575	NR_131138	546096	Mm.252264	NR_131138	ENSMUSG00000110053	Gm29682	-	predicted gene, 29682	ncRNA
mm_21356.1	chr2	157124957	157124985	-	1	NA	intron (NM_018851, intron 3 of 15)	RSINE1|SINE|B4	10251	NM_001139520	56045	Mm.248478	NM_018851	ENSMUSG00000027639	Samhd1	E330031J07Rik|Mg11	SAM domain and HD domain, 1	protein-coding
mm_111104.1	chr12	80931446	80931451	-	1	NA	Intergenic	Intergenic	-7001	NR_033786	67340	Mm.386790	NR_033786	ENSMUSG00000101912	1700052I22Rik	-	RIKEN cDNA 1700052I22 gene	ncRNA
mm_75238.1	chr8	39631198	39631206	-	1	NA	intron (NM_001113326, intron 3 of 9)	intron (NM_001113326, intron 3 of 9)	11476	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_40083.1	chr5	34525778	34525788	+	1	NA	promoter-TSS (NM_011893)	promoter-TSS (NM_011893)	-1	NM_011893	24055	Mm.5012	NM_011893	ENSMUSG00000054520	Sh3bp2	3BP2	SH3-domain binding protein 2	protein-coding
mm_35131.1	chr4	11254249	11254266	-	1	NA	promoter-TSS (NM_001159595)	promoter-TSS (NM_001159595)	2	NM_178112	72656	Mm.246713	NM_178112	ENSMUSG00000040738	Ints8	2810013E07Rik|AV063769|D130008D20Rik	integrator complex subunit 8	protein-coding
mm_55745.1	chr6	77979516	77979622	-	1	NA	promoter-TSS (NM_145732)	promoter-TSS (NM_145732)	98	NM_145732	12386	Mm.34637	NM_009819	ENSMUSG00000063063	Ctnna2	AI481747|Catna|Catna2|cdf|chp	catenin (cadherin associated protein), alpha 2	protein-coding
mm_160711.1	chr10	60277653	60277653	+	1	NA	promoter-TSS (NM_011179)	promoter-TSS (NM_011179)	25	NM_001146121	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_122219.1	chr14	32388327	32388337	-	1	NA	promoter-TSS (NM_001034037)	promoter-TSS (NM_001034037)	41	NM_001034037	67085	Mm.109099	NM_001034037	ENSMUSG00000072473	1700024G13Rik	C10orf53	RIKEN cDNA 1700024G13 gene	protein-coding
mm_23550.1	chr3	61366518	61366522	+	1	NA	3' UTR (NM_028712, exon 1 of 1)	3' UTR (NM_028712, exon 1 of 1)	2013	NM_028712	74012	Mm.422674	NM_028712	ENSMUSG00000036894	Rap2b	4021402C18Rik|AA408554	RAP2B, member of RAS oncogene family	protein-coding
mm_136622.1	chr17	5522036	5522058	+	1	NA	intron (NM_146073, intron 1 of 8)	intron (NM_146073, intron 1 of 8)	29447	NM_146073	224454	Mm.487663	NM_146073	ENSMUSG00000034265	Zdhhc14	B530001K09Rik|New1cp	zinc finger, DHHC domain containing 14	protein-coding
mm_129784.1	chr15	82794447	82794462	-	1	NA	promoter-TSS (NM_029562)	promoter-TSS (NM_029562)	-209	NM_029562	76279	Mm.439931	NM_029562	ENSMUSG00000022445	Cyp2d26	1300006E06Rik	cytochrome P450, family 2, subfamily d, polypeptide 26	protein-coding
mm_154824.1	chrX	16634587	16634591	+	1	NA	intron (NM_173740, intron 2 of 14)	intron (NM_173740, intron 2 of 14)	14891	NM_173740	17161	Mm.21108	NM_173740	ENSMUSG00000025037	Maoa	1110061B18Rik|AA407771	monoamine oxidase A	protein-coding
mm_161925.1	chr18	76262429	76262429	+	1	NA	promoter-TSS (NM_001311070)	promoter-TSS (NM_001311070)	-16	NM_001311070	17126	Mm.152699	NM_010754	ENSMUSG00000024563	Smad2	7120426M23Rik|Madh2|Madr2|Smad-2|mMad2	SMAD family member 2	protein-coding
mm_121725.1	chr14	16575509	16575529	-	1	NA	promoter-TSS (NM_001289762)	promoter-TSS (NM_001289762)	-43	NM_001289762	218772	Mm.259318	NM_011243	ENSMUSG00000017491	Rarb	A830025K23|Hap|Nr1b2	retinoic acid receptor, beta	protein-coding
mm_3405.1	chr1	143916775	143916785	+	1	NA	Intergenic	Intergenic	87369	NM_009061	19735	Mm.28262	NM_009061	ENSMUSG00000026360	Rgs2	GOS8	regulator of G-protein signaling 2	protein-coding
mm_46099.1	chr5	92347353	92347374	-	1	NA	3' UTR (NM_021274, exon 4 of 4)	3' UTR (NM_021274, exon 4 of 4)	1526	NM_021274	15945	Mm.877	NM_021274	ENSMUSG00000034855	Cxcl10	C7|CRG-2|INP10|IP-10|IP10|Ifi10|Scyb10|gIP-10|mob-1	chemokine (C-X-C motif) ligand 10	protein-coding
mm_115004.1	chr13	98316363	98316368	+	1	NA	promoter-TSS (NR_137279)	promoter-TSS (NR_137279)	602	NM_145455	218490	Mm.371688	NM_145455	ENSMUSG00000021660	Btf3	1700054E11Rik	basic transcription factor 3	protein-coding
mm_123896.1	chr14	73049108	73049120	-	1	NA	promoter-TSS (NM_001162412)	promoter-TSS (NM_001162412)	0	NM_133720	70086	Mm.158324	NM_133720	ENSMUSG00000033470	Cysltr2	2300001H05Rik|CYSLT2R|Cltr2|Cyslt2	cysteinyl leukotriene receptor 2	protein-coding
mm_121799.1	chr14	20138548	20138566	-	1	NA	Intergenic	Intergenic	43225	NM_021542	16529	Mm.68998	NM_021542	ENSMUSG00000023243	Kcnk5	KCNK5b|TASK-2	potassium channel, subfamily K, member 5	protein-coding
mm_124101.1	chr14	79301015	79301026	-	1	NA	intron (NM_025427, intron 1 of 4)	CpG	615	NM_025427	66214	Mm.29811	NM_025427	ENSMUSG00000022018	Rgcc	1190002H23Rik|Rgc-32|Rgc32	regulator of cell cycle	protein-coding
mm_56299.1	chr6	91716344	91716370	-	1	NA	intron (NM_009320, intron 2 of 14)	intron (NM_009320, intron 2 of 14)	32290	NM_009320	21366	Mm.395650	NM_009320	ENSMUSG00000030096	Slc6a6	AA589629|C80501|Taut	solute carrier family 6 (neurotransmitter transporter, taurine), member 6	protein-coding
mm_26709.1	chr3	157947246	157947260	+	1	NA	promoter-TSS (NM_001013806)	promoter-TSS (NM_001013806)	-213	NM_001013806	433667	Mm.265806	NM_001013806	ENSMUSG00000039988	Ankrd13c	AI505652|AU022220	ankyrin repeat domain 13c	protein-coding
mm_173109.1	chrX	157492001	157492002	-	1	NA	promoter-TSS (NM_009214)	promoter-TSS (NM_009214)	45	NM_009214	20603	Mm.18652	NM_009214	ENSMUSG00000071708	Sms	AI427066|Gy|SPMSY|SpmST|gyro	spermine synthase	protein-coding
mm_71418.1	chr8	46488742	46488745	+	1	NA	intron (NM_007981, intron 1 of 20)	intron (NM_007981, intron 1 of 20)	-2223	NM_001302163	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_51322.1	chr6	72315983	72315998	+	1	NA	Intergenic	B1_Mus1|SINE|Alu	11380	NM_147779	20388	Mm.46033	NM_147779	ENSMUSG00000056370	Sftpb	AI562151|SF-B|SP-B|Sftp-3|Sftp3	surfactant associated protein B	protein-coding
mm_106187.1	chr11	116807145	116807153	-	1	NA	3' UTR (NM_001347633, exon 5 of 5)	3' UTR (NM_001347633, exon 5 of 5)	20897	NM_026280	67622	Mm.64962	NM_026280	ENSMUSG00000020814	Mxra7	1810057P16Rik|E130302J09Rik	matrix-remodelling associated 7	protein-coding
mm_155028.1	chrX	42068027	42068037	+	1	NA	promoter-TSS (NR_125870)	promoter-TSS (NR_125870)	196	NM_009688	11798	Mm.259879	NM_009688	ENSMUSG00000025860	Xiap	1110015C02Rik|Aipa|Api3|Birc4|IAP3|ILP-1|MIHA	X-linked inhibitor of apoptosis	protein-coding
mm_22134.1	chr2	170470012	170470012	-	1	NA	Intergenic	Intergenic	-26416	NM_001013369	109054	Mm.28808	NM_001013369	ENSMUSG00000052033	Pfdn4	0610025M10Rik|1810063B06Rik|C-1|C1|Pfd4	prefoldin 4	protein-coding
mm_58547.1	chr7	4658648	4658676	+	1	NA	5' UTR (NM_172894, exon 1 of 24)	5' UTR (NM_172894, exon 1 of 24)	288	NM_172894	243819	Mm.258670	NM_172894	ENSMUSG00000052296	Ppp6r1	2010309P17Rik|AI836219|B430201G11Rik|D030074N20Rik|Pp6r1|Saps1|mKIAA1115	protein phosphatase 6, regulatory subunit 1	protein-coding
mm_116638.1	chr13	49015284	49015292	-	1	NA	Intergenic	RMER17C2|LTR|ERVK	47176	NR_015601	68128	Mm.426304	NR_015601		Fam120aos	C030044B11Rik	family with sequence similarity 120A, opposite strand	ncRNA
mm_38404.1	chr4	138973550	138973565	-	1	NA	intron (NM_029857, intron 1 of 16)	intron (NM_029857, intron 1 of 16)	652	NM_029857	77056	Mm.122336	NM_029857	ENSMUSG00000041143	Tmco4	4632413C14Rik|AI430825	transmembrane and coiled-coil domains 4	protein-coding
mm_75969.1	chr8	72002550	72002561	-	1	NA	intron (NM_024444, intron 2 of 12)	intron (NM_024444, intron 2 of 12)	7071	NM_024444	72054	Mm.160020	NM_024444	ENSMUSG00000003484	Cyp4f18	1810054N16Rik|Cyp4f3|Cypf18	cytochrome P450, family 4, subfamily f, polypeptide 18	protein-coding
mm_56120.1	chr6	87532339	87532368	-	1	NA	intron (NM_001037727, intron 1 of 10)	intron (NM_001037727, intron 1 of 10)	906	NM_001037727	232201	Mm.119564	NM_175476	ENSMUSG00000030047	Arhgap25	A130039I20Rik	Rho GTPase activating protein 25	protein-coding
mm_135573.1	chr16	50331023	50331065	-	1	NA	5' UTR (NM_027444, exon 3 of 17)	5' UTR (NM_027444, exon 3 of 17)	101345	NM_027444	70508	Mm.28940	NM_027444	ENSMUSG00000022641	Bbx	5530401J07Rik|5730403O13Rik	bobby sox HMG box containing	protein-coding
mm_164119.1	chr15	36077560	36077581	-	1	NA	intron (NM_001195748, intron 14 of 27)	intron (NM_001195748, intron 14 of 27)	62830	NM_001195748	626596	Mm.321798	NM_001195748	ENSMUSG00000037627	Rgs22	-	regulator of G-protein signalling 22	protein-coding
mm_71099.1	chr8	35375720	35375766	+	1	NA	promoter-TSS (NM_177741)	promoter-TSS (NM_177741)	2	NM_177741	244416	Mm.247126	NM_177741	ENSMUSG00000046794	Ppp1r3b	6430576E21|AW821953|GL|PTG	protein phosphatase 1, regulatory (inhibitor) subunit 3B	protein-coding
mm_142747.1	chr17	48432847	48432854	-	1	NA	promoter-TSS (NM_009694)	promoter-TSS (NM_009694)	-122	NM_009694	11811	Mm.281793	NM_009694	ENSMUSG00000040694	Apobec2	Arp1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 2	protein-coding
mm_40605.1	chr5	64391556	64391582	+	1	NA	Intergenic	Intergenic	76373	NR_040681	69999	Mm.261413	NR_040681	ENSMUSG00000100911	1700027F09Rik	-	RIKEN cDNA 1700027F09 gene	ncRNA
mm_112122.1	chr12	112860973	112860981	-	1	NA	promoter-TSS (NM_019925)	promoter-TSS (NM_019925)	-61	NM_019925	56696	Mm.20455	NM_019925	ENSMUSG00000021298	Gpr132	G2a	G protein-coupled receptor 132	protein-coding
mm_62649.1	chr7	107685483	107685548	+	1	NA	intron (NM_001163557, intron 4 of 25)	intron (NM_001163557, intron 4 of 25)	72517	NM_001205227	320635	Mm.132828	NM_177216	ENSMUSG00000048065	Cyb5r2	D630003K02Rik|b5R.2	cytochrome b5 reductase 2	protein-coding
mm_146787.1	chr18	20114674	20114689	-	1	NA	promoter-TSS (NM_001291804)	promoter-TSS (NM_001291804)	92	NM_001291804	13505	Mm.33740	NM_013504	ENSMUSG00000044322	Dsc1	1110020A10Rik|AI507491	desmocollin 1	protein-coding
mm_170206.1	chr17	6961158	6961165	-	1	NA	promoter-TSS (NM_147155)	promoter-TSS (NM_147155)	-5	NM_147155	380608	Mm.371734	NM_147155	ENSMUSG00000052031	Tagap1	2610315E15Rik|AA415005|FKSG15	T cell activation GTPase activating protein 1	protein-coding
mm_120895.1	chr14	75845322	75845347	+	1	NA	promoter-TSS (NM_009429)	promoter-TSS (NM_009429)	78	NM_009429	22070	Mm.297482	NM_009429	ENSMUSG00000060126	Tpt1	TCTP|Trt|p21|p23	tumor protein, translationally-controlled 1	protein-coding
mm_17556.1	chr2	30124530	30124587	-	1	NA	promoter-TSS (NM_178694)	promoter-TSS (NM_178694)	53	NM_178694	227693	Mm.44526	NM_178694	ENSMUSG00000039686	Zer1	C230075L19Rik|Zyg11bl	zyg-11 related, cell cycle regulator	protein-coding
mm_52735.1	chr6	120419388	120419436	+	1	NA	exon (NM_145997, exon 22 of 28)	exon (NM_145997, exon 22 of 28)	-43785	NM_008359	16172	Mm.4481	NM_008359	ENSMUSG00000002897	Il17ra	AW538159|Cdw217|Il17r|VDw217	interleukin 17 receptor A	protein-coding
mm_54682.1	chr6	39419943	39419958	-	1	NA	promoter-TSS (NM_001311109)	promoter-TSS (NM_001311109)	-174	NM_001311109	54484	Mm.270484	NM_018810	ENSMUSG00000029922	Mkrn1	RFP	makorin, ring finger protein, 1	protein-coding
mm_167672.1	chr9	74861937	74861937	+	1	NA	promoter-TSS (NM_008262)	promoter-TSS (NM_008262)	16	NM_008262	15379	Mm.303355	NM_008262	ENSMUSG00000043013	Onecut1	D9Ertd423e|HNF-6|Hfh12|Hnf6|Hnf6b|OC-1|Oc1	one cut domain, family member 1	protein-coding
mm_1529.1	chr1	72849152	72849183	+	1	NA	exon (NM_008342, exon 2 of 4)	exon (NM_008342, exon 2 of 4)	23780	NM_001310659	16008	Mm.141936	NM_008342	ENSMUSG00000039323	Igfbp2	AI255832|IBP-2|Igfbp-2|mIGFBP-2	insulin-like growth factor binding protein 2	protein-coding
mm_133430.1	chr16	87553416	87553472	+	1	NA	5' UTR (NM_144854, exon 1 of 5)	5' UTR (NM_144854, exon 1 of 5)	114	NM_144854	224419	Mm.194466	NM_144854	ENSMUSG00000025610	Map3k7cl	C21orf7|ORF63|Tak1l	Map3k7 C-terminal like	protein-coding
mm_77152.1	chr8	111686542	111686602	-	1	NA	TTS (NM_025583)	TTS (NM_025583)	3102	NR_106044	102466993		NR_106044	ENSMUSG00000099129	Mir7076	Gm27318|mmu-mir-7076	microRNA 7076	ncRNA
mm_17361.1	chr2	26657220	26657241	-	1	NA	Intergenic	Intergenic	14052	NM_010695	16821	Mm.123925	NM_010695	ENSMUSG00000026919	Lcn4	A630045M08Rik|Vnsp2	lipocalin 4	protein-coding
mm_162499.1	chr1	139483523	139483527	+	1	NA	intron (NM_009791, intron 19 of 27)	MTB|LTR|ERVL-MaLR	-18182	NM_031164	14060	Mm.30105	NM_031164	ENSMUSG00000026368	F13b	Cf-13b|Cf13b	coagulation factor XIII, beta subunit	protein-coding
mm_129785.1	chr15	82794475	82794484	-	1	NA	promoter-TSS (NM_029562)	promoter-TSS (NM_029562)	-234	NM_029562	76279	Mm.439931	NM_029562	ENSMUSG00000022445	Cyp2d26	1300006E06Rik	cytochrome P450, family 2, subfamily d, polypeptide 26	protein-coding
mm_121967.1	chr14	25517291	25517301	-	1	NA	intron (NM_001310666, intron 2 of 23)	intron (NM_001310666, intron 2 of 23)	-17143	NR_037236	100526533		NR_037236	ENSMUSG00000093081	Mir3075	mir-3075|mmu-mir-3075	microRNA 3075	ncRNA
mm_46984.1	chr5	115300958	115300968	-	1	NA	promoter-TSS (NM_019682)	promoter-TSS (NM_019682)	27	NM_019682	56455	Mm.256858	NM_019682	ENSMUSG00000009013	Dynll1	Dlc8|Dnclc1|Pin	dynein light chain LC8-type 1	protein-coding
mm_11240.1	chr2	29889200	29889206	+	1	NA	promoter-TSS (NM_001113213)	promoter-TSS (NM_001113213)	-517	NM_001177661	18286	Mm.330116	NM_013615	ENSMUSG00000026790	Odf2	AI848335|MMTEST29	outer dense fiber of sperm tails 2	protein-coding
mm_146359.1	chr18	82584137	82584249	+	1	NA	3' UTR (NM_010777, exon 7 of 7)	3' UTR (NM_010777, exon 7 of 7)	29685	NM_001025254	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_36497.1	chr4	83316279	83316282	-	1	NA	intron (NM_027238, intron 1 of 19)	B4|SINE|B4	7909	NM_027238	69863	Mm.5540	NM_025782	ENSMUSG00000038172	Ttc39b	1810054D07Rik|9130422G05Rik|AI450603|AV103077|AW215585	tetratricopeptide repeat domain 39B	protein-coding
mm_170618.1	chr19	61266690	61266709	-	1	NA	Intergenic	CpG	-38281	NM_009970	12982	Mm.287228	NM_009970	ENSMUSG00000059326	Csf2ra	CD116|Csfgmra|GM-CSF-Ra|GM-CSFR	colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)	protein-coding
mm_131042.1	chr16	3884741	3884761	+	1	NA	5' UTR (NM_001290689, exon 1 of 6)	5' UTR (NM_001290689, exon 1 of 6)	132	NM_001290689	74763	Mm.28403	NM_029090	ENSMUSG00000005982	Naa60	1200013P24Rik|AI315146|Nat15	N(alpha)-acetyltransferase 60, NatF catalytic subunit	protein-coding
mm_127932.1	chr15	10485419	10485422	-	1	NA	promoter-TSS (NM_011232)	promoter-TSS (NM_011232)	517	NM_026396	67832	Mm.28057	NM_026396	ENSMUSG00000022247	Brix1	1110064N10Rik|Bxdc2|C76935	BRX1, biogenesis of ribosomes	protein-coding
mm_65329.1	chr7	24978302	24978310	-	1	NA	3' UTR (NM_001290469, exon 23 of 23)	3' UTR (NM_001290469, exon 23 of 23)	-5578	NM_010261	14470	Mm.22473	NM_010261	ENSMUSG00000003380	Rabac1	2310040I06Rik|Gbpap1|PRA1|prenylin	Rab acceptor 1 (prenylated)	protein-coding
mm_150420.1	chr19	37376360	37376422	+	1	NA	promoter-TSS (NM_010615)	promoter-TSS (NM_010615)	-12	NM_010615	16551	Mm.42203	NM_010615	ENSMUSG00000012443	Kif11	Eg5|Kif8|Kifl1|Knsl1	kinesin family member 11	protein-coding
mm_98036.1	chr11	85339669	85339677	+	1	NA	exon (NM_016910, exon 5 of 6)	exon (NM_016910, exon 5 of 6)	-13491	NM_001166642	192197	Mm.209989	NM_138681	ENSMUSG00000059439	Bcas3	1500019F07Rik|2610028P08Rik|AU021018|BC028339|K20D4|rudhira	breast carcinoma amplified sequence 3	protein-coding
mm_110179.1	chr12	27337488	27337498	-	1	NA	3' UTR (NM_009234, exon 1 of 1)	3' UTR (NM_009234, exon 1 of 1)	5225	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding
mm_83304.1	chr9	44033991	44034008	-	1	NA	Intergenic	L2a|LINE|L2	-9385	NM_009382	21838	Mm.3951	NM_009382	ENSMUSG00000032011	Thy1	CD90|T25|Thy-1|Thy-1.2|Thy1.1|Thy1.2	thymus cell antigen 1, theta	protein-coding
mm_81644.1	chr9	110948322	110948341	+	1	NA	Intergenic	Intergenic	-2173	NM_011562	21667	Mm.5090	NM_011562	ENSMUSG00000032494	Tdgf1	CR1|cripto	teratocarcinoma-derived growth factor 1	protein-coding
mm_42982.1	chr5	123239677	123239718	+	1	NA	exon (NM_026000, exon 3 of 6)	exon (NM_026000, exon 3 of 6)	11507	NM_026000	67151	Mm.278997	NM_026000	ENSMUSG00000029440	Psmd9	1500011J20Rik|2610202L11Rik|Bridge-1|P27	proteasome (prosome, macropain) 26S subunit, non-ATPase, 9	protein-coding
mm_116474.1	chr13	43525589	43525596	-	1	NA	Intergenic	Intergenic	34599	NM_001081059	76137	Mm.426290	NM_001081059	ENSMUSG00000021371	Mcur1	6230416A05Rik|AU015498|AV136929|AW554392|C88263|Ccdc90a	mitochondrial calcium uniporter regulator 1	protein-coding
mm_173062.1	chrX	129356920	129356924	+	1	NA	Intergenic	Intergenic	305398	NR_045441	75274	Mm.108718	NR_045441	ENSMUSG00000086244	4930558G05Rik	-	RIKEN cDNA 4930558G05 gene	ncRNA
mm_63886.1	chr7	137437592	137437649	+	1	NA	promoter-TSS (NM_023140)	promoter-TSS (NM_023140)	-28	NM_023140	30926	Mm.267692	NM_023140	ENSMUSG00000031068	Glrx3	PICOT|Txnl2	glutaredoxin 3	protein-coding
mm_153983.1	chr19	47914507	47914518	-	1	NA	intron (NM_001001738, intron 1 of 1)	intron (NM_001001738, intron 1 of 1)	4787	NM_001001738	414801	Mm.29457	NM_001001738	ENSMUSG00000044948	Itprip	4833424O12Rik|DANGER|mKIAA1754	inositol 1,4,5-triphosphate receptor interacting protein	protein-coding
mm_157801.1	chrX	73927997	73928020	-	1	NA	intron (NM_023132, intron 7 of 10)	intron (NM_023132, intron 7 of 10)	2842	NM_023132	19703	Mm.236969	NM_023132	ENSMUSG00000031387	Renbp	Age|Rnbp	renin binding protein	protein-coding
mm_16220.1	chr2	173110797	173110817	+	1	NA	intron (NM_001081387, intron 5 of 10)	intron (NM_001081387, intron 5 of 10)	8718	NM_001081387	664799	Mm.389396	NM_001081387	ENSMUSG00000070495	Ctcfl	Boris|OTTMUSG00000016680	CCCTC-binding factor (zinc finger protein)-like	protein-coding
mm_12238.1	chr2	68845130	68845137	+	1	NA	Intergenic	Intergenic	-16308	NM_172856	241447	Mm.222222	NM_172856	ENSMUSG00000027035	Cers6	4732462C07Rik|AW544719|Lass6|T1L	ceramide synthase 6	protein-coding
mm_47459.1	chr5	123661665	123661690	-	1	NA	intron (NM_001347468, intron 1 of 24)	intron (NM_001347468, intron 1 of 24)	22684	NM_019765	56430	Mm.241109	NM_019765	ENSMUSG00000049550	Clip1	1110007I12Rik|4631429H07Rik|AV017631|C81039|CLIP-170|CLIP170|CYLN1|Clip50|Rsn|mKIAA4046|restin	CAP-GLY domain containing linker protein 1	protein-coding
mm_37488.1	chr4	123612104	123612107	-	1	NA	intron (NM_001199136, intron 1 of 97)	intron (NM_001199136, intron 1 of 97)	-4315	NR_105824	102465214		NR_105824	ENSMUSG00000099005	Mir6398	Gm27657|mmu-mir-6398	microRNA 6398	ncRNA
mm_17760.1	chr2	32775626	32775649	-	1	NA	promoter-TSS (NM_001290563)	promoter-TSS (NM_001290563)	-4	NM_001290563	338348	Mm.475130	NM_177384	ENSMUSG00000039021	Ttc16	1200002K10Rik	tetratricopeptide repeat domain 16	protein-coding
mm_42248.1	chr5	113945451	113945466	+	1	NA	intron (NM_198109, intron 14 of 14)	intron (NM_198109, intron 14 of 14)	-36752	NM_011779	23790	Mm.260158	NM_011779	ENSMUSG00000004530	Coro1c	AL022675|AW455561|AW548837	coronin, actin binding protein 1C	protein-coding
mm_100492.1	chr11	120458094	120458147	+	1	NA	promoter-TSS (NM_025560)	promoter-TSS (NM_025560)	-9	NM_152807	67291	Mm.103384	NM_152807	ENSMUSG00000049957	Ccdc137	3110023B02Rik	coiled-coil domain containing 137	protein-coding
mm_116268.1	chr13	34652643	34652649	-	1	NA	promoter-TSS (NR_105041)	promoter-TSS (NR_105041)	35	NM_025831	66895	Mm.28943	NM_025831	ENSMUSG00000021411	Pxdc1	1300014I06Rik	PX domain containing 1	protein-coding
mm_39928.1	chr5	31613942	31613944	+	1	NA	promoter-TSS (NM_025796)	promoter-TSS (NM_025796)	-8	NM_025796	66845	Mm.120763	NM_025796	ENSMUSG00000106918	Mrpl33	0610009M10Rik|L33mt|MRP-L33	mitochondrial ribosomal protein L33	protein-coding
mm_92924.1	chr10	84440640	84440650	-	1	NA	promoter-TSS (NM_001004363)	promoter-TSS (NM_001004363)	-174	NM_001004363	77976	Mm.25874	NM_001004363	ENSMUSG00000020032	Nuak1	AU014801|AW494241|B230104P22Rik|Omphk1	NUAK family, SNF1-like kinase, 1	protein-coding
mm_93783.1	chr10	120476784	120476813	-	1	NA	promoter-TSS (NM_010441)	promoter-TSS (NM_010441)	-329	NM_010441	15364	Mm.157190	NM_010441	ENSMUSG00000056758	Hmga2	9430083A20Rik|HMGI-C|Hmgic|pg|pygmy	high mobility group AT-hook 2	protein-coding
mm_171399.1	chr4	12326081	12326081	-	1	NA	Intergenic	RLTR12E|LTR|ERVK	-154066	NM_026558	68099	Mm.25340	NM_026558	ENSMUSG00000028218	Fam92a	6720467C03Rik|Fam92a1	family with sequence similarity 92, member A	protein-coding
mm_82355.1	chr9	14381037	14381047	-	1	NA	5' UTR (NM_028013, exon 1 of 2)	5' UTR (NM_028013, exon 1 of 2)	200	NM_028013	71946	Mm.41423	NM_028013	ENSMUSG00000037419	Endod1	2210414F18Rik|2310067E08Rik|C85344	endonuclease domain containing 1	protein-coding
mm_171891.1	chr5	38225941	38225943	+	1	NA	exon (NM_025281, exon 3 of 9)	exon (NM_025281, exon 3 of 9)	5460	NM_025281	17089	Mm.28560	NM_025281	ENSMUSG00000067367	Lyar	MLZ-264	Ly1 antibody reactive clone	protein-coding
mm_6703.1	chr1	82236403	82236416	-	1	NA	3' UTR (NM_010570, exon 2 of 2)	3' UTR (NM_010570, exon 2 of 2)	55030	NM_010570	16367	Mm.4952	NM_010570	ENSMUSG00000055980	Irs1	G972R|IRS-1	insulin receptor substrate 1	protein-coding
mm_91711.1	chr10	44148942	44148950	-	1	NA	Intergenic	CpG	-21501	NR_001582	70365	Mm.87073	NR_001582	ENSMUSG00000091358	Speer5-ps1	1700007C10Rik|SPEER-5|Speer5-ps	spermatogenesis associated glutamate (E)-rich protein 5, pseudogene 1	pseudo
mm_26318.1	chr3	142521584	142521603	+	1	NA	3' UTR (NM_153564, exon 11 of 11)	3' UTR (NM_153564, exon 11 of 11)	-8743	NM_001083312	229900	Mm.45740	NM_145545	ENSMUSG00000040253	Gbp7	9830147J24Rik	guanylate binding protein 7	protein-coding
mm_158949.1	chr1	86156909	86156909	+	1	NA	intron (NM_030184, intron 1 of 24)	intron (NM_030184, intron 1 of 24)	2129	NM_001310702	78795	Mm.379264	NM_027456	ENSMUSG00000062590	Armc9	3830422A13Rik|4831423D23Rik|4930438O05Rik|5730415N24Rik	armadillo repeat containing 9	protein-coding
mm_83159.1	chr9	40465714	40465734	-	1	NA	Intergenic	Intergenic	-9960	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_119420.1	chr14	45329816	45329849	+	1	NA	promoter-TSS (NM_025959)	promoter-TSS (NM_025959)	8	NM_025959	67089	Mm.18472	NM_025959	ENSMUSG00000021832	Psmc6	2300001E01Rik|AI451058	proteasome (prosome, macropain) 26S subunit, ATPase, 6	protein-coding
mm_3950.1	chr1	164062048	164062058	+	1	NA	promoter-TSS (NM_001164059)	promoter-TSS (NM_001164059)	-23	NM_011346	20343	Mm.1461	NM_011346	ENSMUSG00000026581	Sell	AI528707|CD62L|L-selectin|LECAM-1|Lnhr|Ly-22|Ly-m22|Lyam-1|Lyam1	selectin, lymphocyte	protein-coding
mm_138753.1	chr17	37046556	37046600	+	1	NA	intron (NM_019439, intron 1 of 22)	CpG	612	NM_019439	54393	Mm.32191	NM_019439	ENSMUSG00000024462	Gabbr1	GABAB1|GABAbR1|bM573K1.1	gamma-aminobutyric acid (GABA) B receptor, 1	protein-coding
mm_35615.1	chr4	43429129	43429139	-	1	NA	promoter-TSS (NM_177377)	promoter-TSS (NM_177377)	0	NM_177377	329831	Mm.454466	NM_177377	ENSMUSG00000042788	Fam166b	4833436C18Rik	family with sequence similarity 166, member B	protein-coding
mm_130157.1	chr15	91191712	91191722	-	1	NA	promoter-TSS (NM_011994)	promoter-TSS (NM_011994)	90	NM_011994	26874	Mm.295456	NM_011994	ENSMUSG00000055782	Abcd2	ABC39|ALDL1|ALDR|ALDRP	ATP-binding cassette, sub-family D (ALD), member 2	protein-coding
mm_70272.1	chr8	3598340	3598349	+	1	NA	intron (NM_001347112, intron 2 of 17)	intron (NM_001347112, intron 2 of 17)	10894	NM_001347111	69697	Mm.390010	NM_027171	ENSMUSG00000044433	Camsap3	2310057J16Rik|Kiaa1543|Nezha	calmodulin regulated spectrin-associated protein family, member 3	protein-coding
mm_166023.1	chr4	123983389	123983397	+	1	NA	Intergenic	Intergenic	65960	NM_017475	54170	Mm.220922	NM_017475	ENSMUSG00000028646	Rragc	AU041672|Gtr2|RAGC|TIB929|YGR163W	Ras-related GTP binding C	protein-coding
mm_151153.1	chr19	53142786	53142803	+	1	NA	promoter-TSS (NM_001164100)	promoter-TSS (NM_001164100)	38	NM_001164100	27360	Mm.426080	NM_013758	ENSMUSG00000025026	Add3	AI463285|R75380	adducin 3 (gamma)	protein-coding
mm_46020.1	chr5	90905208	90905218	-	1	NA	3' UTR (NM_009140, exon 4 of 4)	3' UTR (NM_009140, exon 4 of 4)	1314	NM_009140	20310	Mm.4979	NM_009140	ENSMUSG00000058427	Cxcl2	CINC-2a|GROb|Gro2|MIP-2|MIP-2a|Mgsa-b|Mip2|Scyb|Scyb2	chemokine (C-X-C motif) ligand 2	protein-coding
mm_112799.1	chr13	20470116	20470120	+	1	NA	intron (NM_080288, intron 16 of 21)	intron (NM_080288, intron 16 of 21)	-2872	NM_198093	140580	Mm.342392	NM_080288	ENSMUSG00000041112	Elmo1	6330578D22Rik|C230095H21Rik|CED-12	engulfment and cell motility 1	protein-coding
mm_16924.1	chr2	13582547	13582570	-	1	NA	3' UTR (NM_011701, exon 9 of 9)	3' UTR (NM_011701, exon 9 of 9)	8247	NM_011701	22352	Mm.268000	NM_011701	ENSMUSG00000026728	Vim	-	vimentin	protein-coding
mm_163687.1	chr13	96470770	96470774	+	1	NA	intron (NM_001042714, intron 1 of 13)	intron (NM_001042714, intron 1 of 13)	388	NM_001042714	271144	Mm.470057	NM_001042714	ENSMUSG00000047117	Ankdd1b	9330128J19Rik	ankyrin repeat and death domain containing 1B	protein-coding
mm_62930.1	chr7	118633753	118633766	+	1	NA	promoter-TSS (NM_028930)	promoter-TSS (NM_028930)	23	NM_028930	74424	Mm.11068	NM_028930	ENSMUSG00000030650	Tmc5	4932443L08Rik|AU016085	transmembrane channel-like gene family 5	protein-coding
mm_129739.1	chr15	82212797	82212812	-	1	NA	promoter-TSS (NM_001207021)	promoter-TSS (NM_001207021)	11	NM_001207021	435145	Mm.41289	NM_001207021	ENSMUSG00000096883	Shisa8	Orf26|ckamp39	shisa family member 8	protein-coding
mm_127880.1	chr15	8636034	8636039	-	1	NA	3' UTR (NM_148938, exon 10 of 10)	3' UTR (NM_148938, exon 10 of 10)	74771	NM_148938	20512	Mm.204834	NM_148938	ENSMUSG00000005360	Slc1a3	AI504299|B430115D02Rik|Eaat1|GLAST|GLAST-1|GLU-T|GluT-1|Gmt1|MGluT1	solute carrier family 1 (glial high affinity glutamate transporter), member 3	protein-coding
mm_145617.1	chr18	61105818	61105828	+	1	NA	5' UTR (NM_001037859, exon 2 of 22)	5' UTR (NM_001037859, exon 2 of 22)	251	NM_001037859	12978	Mm.22574	NM_007779	ENSMUSG00000024621	Csf1r	AI323359|CD115|CSF-1R|Csfmr|Fim-2|Fim2|Fms|M-CSF-R|M-CSFR	colony stimulating factor 1 receptor	protein-coding
mm_86653.1	chr10	17724212	17724230	+	1	NA	exon (NM_010828, exon 2 of 2)	exon (NM_010828, exon 2 of 2)	993	NM_010828	17684	Mm.272321	NM_010828	ENSMUSG00000039910	Cited2	AI835299|ER154-like|Mrg1|Msg2|p35srj	Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 2	protein-coding
mm_127414.1	chr15	101258397	101258402	+	1	NA	Intergenic	Intergenic	-8447	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_158105.1	chrX	102050724	102050729	-	1	NA	intron (NM_001163610, intron 1 of 7)	intron (NM_001163610, intron 1 of 7)	20581	NM_001278534	331474	Mm.23297	NM_183318	ENSMUSG00000049191	Rgag4	6430402L03Rik|Mar5|Mart5|mKIAA2001	retrotransposon gag domain containing 4	protein-coding
mm_121022.1	chr14	79587701	79587712	+	1	NA	promoter-TSS (NM_026474)	promoter-TSS (NM_026474)	15	NM_026474	67955	Mm.18972	NM_026474	ENSMUSG00000022024	Sugt1	2410174K12Rik|SGT1	SGT1, suppressor of G2 allele of SKP1 (S. cerevisiae)	protein-coding
mm_52102.1	chr6	97874175	97874182	+	1	NA	intron (NM_001113198, intron 1 of 9)	intron (NM_001113198, intron 1 of 9)	-55639	NM_001178049	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_145590.1	chr18	60985963	60985969	+	1	NA	3' UTR (NM_001286809, exon 6 of 6)	3' UTR (NM_001286809, exon 6 of 6)	22412	NM_001286809	12322	Mm.131530	NM_009792	ENSMUSG00000024617	Camk2a	CaMKII|R74975|mKIAA0968	calcium/calmodulin-dependent protein kinase II alpha	protein-coding
mm_52301.1	chr6	108814986	108815006	+	1	NA	exon (NM_026011, exon 3 of 7)	exon (NM_026011, exon 3 of 7)	-13645	NM_138677	192193	Mm.21596	NM_138677	ENSMUSG00000030104	Edem1	A130059K23Rik|EDEM|mKIAA0212	ER degradation enhancer, mannosidase alpha-like 1	protein-coding
mm_114622.1	chr13	76018756	76018777	+	1	NA	promoter-TSS (NM_178916)	promoter-TSS (NM_178916)	-54	NM_001131069	218341	Mm.266515	NM_178916	ENSMUSG00000043190	Rfesd	AI256775|D030068K09	Rieske (Fe-S) domain containing	protein-coding
mm_69835.1	chr7	141279122	141279139	-	1	NA	promoter-TSS (NM_001287171)	promoter-TSS (NM_001287171)	3	NM_001287171	20287	Mm.4723	NM_011328	ENSMUSG00000038580	Sct	-	secretin	protein-coding
mm_11163.1	chr2	28556779	28556824	+	1	NA	exon (NM_009885, exon 10 of 11)	exon (NM_009885, exon 10 of 11)	6602	NM_009885	12613	Mm.236017	NM_009885	ENSMUSG00000026818	Cel	1810036E18Rik|BAL	carboxyl ester lipase	protein-coding
mm_34670.1	chr4	150924655	150924664	+	1	NA	intron (NM_011612, intron 1 of 7)	intron (NM_011612, intron 1 of 7)	-3340	NM_001077509	21942	Mm.244187	NM_011612	ENSMUSG00000028965	Tnfrsf9	4-1BB|A930040I11Rik|AA408498|AI325004|CDw137|Cd137|ILA|Ly63	tumor necrosis factor receptor superfamily, member 9	protein-coding
mm_13343.1	chr2	102787962	102787972	+	1	NA	3' UTR (NM_001077514, exon 11 of 11)	3' UTR (NM_001077514, exon 11 of 11)	81529	NM_001077515	20511	Mm.267547	NM_011393	ENSMUSG00000005089	Slc1a2	1700091C19Rik|2900019G14Rik|AI159670|Eaat2|GLT-1|GLT1|MGLT1	solute carrier family 1 (glial high affinity glutamate transporter), member 2	protein-coding
mm_3395.1	chr1	143640763	143640778	+	1	NA	promoter-TSS (NM_020025)	promoter-TSS (NM_020025)	73	NM_020025	26878	Mm.285580	NM_020025	ENSMUSG00000033849	B3galt2	-	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 2	protein-coding
mm_104764.1	chr11	98479452	98479460	-	1	NA	intron (NM_011771, intron 6 of 7)	intron (NM_011771, intron 6 of 7)	32622	NM_010346	14786	Mm.276702	NM_010346	ENSMUSG00000019312	Grb7	mKIAA4028	growth factor receptor bound protein 7	protein-coding
mm_154103.1	chr19	57045740	57045743	-	1	NA	intron (NM_001290813, intron 14 of 20)	intron (NM_001290813, intron 14 of 20)	-37166	NM_001177797	226250	Mm.226284	NM_146102	ENSMUSG00000025083	Afap1l2	AU041783|C86904|mKIAA1914	actin filament associated protein 1-like 2	protein-coding
mm_117495.1	chr13	78198797	78198808	-	1	NA	promoter-TSS (NM_010151)	promoter-TSS (NM_010151)	71	NM_010151	13865	Mm.439653	NM_010151	ENSMUSG00000069171	Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR-3|EAR3|Erbal3|SVP44|Tcfcoup1	nuclear receptor subfamily 2, group F, member 1	protein-coding
mm_7389.1	chr1	110977410	110977421	-	1	NA	promoter-TSS (NM_001081386)	promoter-TSS (NM_001081386)	-43	NM_001081386	227485	Mm.322070	NM_001081386	ENSMUSG00000047216	Cdh19	-	cadherin 19, type 2	protein-coding
mm_131281.1	chr16	11143904	11143905	+	1	NA	intron (NR_027502, intron 19 of 22)	LSU-rRNA_Hsa|rRNA|rRNA	-9372	NM_029582	106200	Mm.291015	NM_029582	ENSMUSG00000022498	Txndc11	2810408E11Rik|AI427833|EFP1|Txdc11	thioredoxin domain containing 11	protein-coding
mm_194.1	chr1	15804375	15804382	+	1	NA	Intergenic	RLTR11A2|LTR|ERVK	-1268	NM_009352	21749	Mm.4306	NM_009352	ENSMUSG00000025925	Terf1	Pin2|Trbf1|Trf1	telomeric repeat binding factor 1	protein-coding
mm_149013.1	chr19	8740703	8740707	+	1	NA	promoter-TSS (NM_001177347)	promoter-TSS (NM_001177347)	-13	NM_001177347	74307	Mm.48791	NM_001177347	ENSMUSG00000090840	1700092M07Rik	-	RIKEN cDNA 1700092M07 gene	protein-coding
mm_65219.1	chr7	19699046	19699063	-	1	NA	promoter-TSS (NM_001305819)	promoter-TSS (NM_001305819)	134	NM_001305843	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_1305.1	chr1	64690868	64690872	+	1	NA	promoter-TSS (NM_001097644)	promoter-TSS (NM_001097644)	-211	NR_038009	69941	Mm.69044	NR_038009	ENSMUSG00000087213	2810408I11Rik	-	RIKEN cDNA 2810408I11 gene	ncRNA
mm_167280.1	chr8	36248613	36248631	+	1	NA	exon (NM_001081150, exon 1 of 12)	exon (NM_001081150, exon 1 of 12)	894	NM_001081150	244421	Mm.324032	NM_001081150	ENSMUSG00000039633	Lonrf1	-	LON peptidase N-terminal domain and ring finger 1	protein-coding
mm_57370.1	chr6	124779747	124779763	-	1	NA	promoter-TSS (NM_001302555)	promoter-TSS (NM_001302555)	-28	NM_001302555	16977	Mm.3207	NM_013588	ENSMUSG00000030125	Lrrc23	4921537K05Rik|B7|Lrpb7	leucine rich repeat containing 23	protein-coding
mm_128307.1	chr15	37791994	37792005	-	1	NA	promoter-TSS (NM_001170866)	promoter-TSS (NM_001170866)	1	NM_001170866	52589	Mm.283370	NM_134094	ENSMUSG00000051359	Ncald	AI848120|D030020D09Rik|D15Ertd412e	neurocalcin delta	protein-coding
mm_145514.1	chr18	60443140	60443159	+	1	NA	Intergenic	MER73|LTR|ERVL	58834	NM_134133	106878	Mm.273197	NM_134133	ENSMUSG00000038059	Smim3	2010002N04Rik|AI195350|AW561905|Nid67|cI-41	small integral membrane protein 3	protein-coding
mm_78559.1	chr9	35672834	35672864	+	1	NA	TTS (NM_001033421)	TTS (NM_001033421)	3210	NM_001033421	330921	Mm.479701	NM_001033421	ENSMUSG00000074452	Pate2	Gm846|Pate-M|mANLP1	prostate and testis expressed 2	protein-coding
mm_84664.1	chr9	71975976	71975980	-	1	NA	intron (NM_001253862, intron 5 of 19)	intron (NM_001253862, intron 5 of 19)	12537	NR_029879	723889		NR_029879	ENSMUSG00000105200	Mir378a	Mir378|Mirn378|mmu-mir-378|mmu-mir-378a	microRNA 378a	ncRNA
mm_106234.1	chr11	117639739	117639784	-	1	NA	Intergenic	Intergenic	-14528	NM_198022	217351	Mm.40272	NM_198022	ENSMUSG00000025571	Tnrc6c	9930033H14Rik|mKIAA1582	trinucleotide repeat containing 6C	protein-coding
mm_101789.1	chr11	46058175	46058195	-	1	NA	intron (NM_001291891, intron 1 of 22)	intron (NM_001291891, intron 1 of 22)	2201	NM_001291891	11492	Mm.89940	NM_009616	ENSMUSG00000011256	Adam19	AL024287|MADDAM|MTLNB|Mltnb	a disintegrin and metallopeptidase domain 19 (meltrin beta)	protein-coding
mm_143547.1	chr17	74017200	74017208	-	1	NA	TTS (NM_053188)	TTS (NM_053188)	30712	NM_053188	94224	Mm.38933	NM_053188	ENSMUSG00000038541	Srd5a2	5ART2|S5AR 2	steroid 5 alpha-reductase 2	protein-coding
mm_167878.1	chrX	37805218	37805232	-	1	NA	exon (NM_008818, exon 3 of 5)	exon (NM_008818, exon 3 of 5)	-21830	NM_008955	19202	Mm.10105	NM_008955	ENSMUSG00000006200	Rhox6	AV213605|AW548842|Psx1	reproductive homeobox 6	protein-coding
mm_158892.1	chr1	20917758	20917758	+	1	NA	intron (NM_028829, intron 1 of 2)	intron (NM_028829, intron 1 of 2)	27136	NM_028829	74229	Mm.40780	NM_028829	ENSMUSG00000025931	Paqr8	1700019B16Rik|3110001D06Rik	progestin and adipoQ receptor family member VIII	protein-coding
mm_36594.1	chr4	88719102	88719106	-	1	NA	3' UTR (NM_172871, exon 1 of 1)	3' UTR (NM_172871, exon 1 of 1)	3404	NM_172871	242521	Mm.260601	NM_172871	ENSMUSG00000070923	Klhl9	8030469P05|C530050O22Rik|ENSMUSG00000070923|mKIAA1354	kelch-like 9	protein-coding
mm_99783.1	chr11	107337990	107338008	+	1	NA	intron (NM_145823, intron 1 of 9)	intron (NM_145823, intron 1 of 9)	132721	NM_145823	71795	Mm.397413	NM_145823	ENSMUSG00000040430	Pitpnc1	1110020B03Rik|5830436L09Rik|AI662802|AI851387|C330017I21Rik|Dnr411|RDGBB|RDGBB1|rdgB-beta	phosphatidylinositol transfer protein, cytoplasmic 1	protein-coding
mm_138526.1	chr17	35242169	35242198	+	1	NA	promoter-TSS (NM_001252457)	promoter-TSS (NM_001252457)	437	NM_019693	53817	Mm.439827	NM_019693	ENSMUSG00000019432	Ddx39b	0610030D10Rik|AI428441|Bat-1|Bat1|Bat1a|D17H6S81E|D17H6S81E-1|D6S81Eh	DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B	protein-coding
mm_1632.1	chr1	74506045	74506105	+	1	NA	promoter-TSS (NM_001310662)	promoter-TSS (NM_001310662)	15	NM_021383	58184	Mm.291708	NM_021383	ENSMUSG00000026174	Cnot9	2610007F23Rik|AI593551|Fl10|Rqcd1	CCR4-NOT transcription complex, subunit 9	protein-coding
mm_501.1	chr1	37029308	37029339	+	1	NA	Intergenic	CpG	-89796	NM_018872	56030	Mm.186943	NM_018872	ENSMUSG00000026116	Tmem131	2610524E03Rik|CC28|D1Bwg0491e|Neg|RW1|YR-23|mKIAA0257	transmembrane protein 131	protein-coding
mm_29125.1	chr3	105426535	105426541	-	1	NA	Intergenic	Intergenic	-25792	NM_001039347	56543	Mm.44530	NM_019931	ENSMUSG00000040896	Kcnd3	AW045978|Kncd3|Kv4.3	potassium voltage-gated channel, Shal-related family, member 3	protein-coding
mm_1574.1	chr1	74267768	74267794	+	1	NA	exon (NM_029711, exon 10 of 10)	exon (NM_029711, exon 10 of 10)	-10819	NM_174985	227289	Mm.246587	NM_174985	ENSMUSG00000064272	Gpbar1	BG37|GPCR|GPR131|M-BAR|TGR5	G protein-coupled bile acid receptor 1	protein-coding
mm_111756.1	chr12	103956892	103956901	-	1	NA	promoter-TSS (NM_009247)	promoter-TSS (NM_009247)	1	NM_009247	20704	Mm.312593	NM_009247	ENSMUSG00000072849	Serpina1e	Dom5|PI5|Spi1-5	serine (or cysteine) peptidase inhibitor, clade A, member 1E	protein-coding
mm_129416.1	chr15	78388758	78388776	-	1	NA	promoter-TSS (NM_001163613)	promoter-TSS (NM_001163613)	2	NM_001163613	73376	Mm.73222	NM_028522	ENSMUSG00000062154	Tex33	1700061J05Rik|Ean57	testis expressed 33	protein-coding
mm_67610.1	chr7	83883799	83883830	-	1	NA	5' UTR (NM_030705, exon 1 of 1)	5' UTR (NM_030705, exon 1 of 1)	527	NM_030705	80889	Mm.272998	NM_030705	ENSMUSG00000070462	Mesdc1	AW061151	mesoderm development candidate 1	protein-coding
mm_101922.1	chr11	50200873	50200903	-	1	NA	TTS (NM_026543)	TTS (NM_026543)	9932	NM_001290769	18412	Mm.40828	NM_011018	ENSMUSG00000015837	Sqstm1	A170|OSF-6|Osi|STAP|STONE14|p62	sequestosome 1	protein-coding
mm_103767.1	chr11	81867699	81867709	-	1	NA	intron (NR_038010, intron 2 of 4)	B4A|SINE|B4	7027	NR_038010	71388	Mm.158687	NR_038010	ENSMUSG00000020703	5530401A14Rik	-	RIKEN cDNA 5530401A14 gene	ncRNA
mm_123932.1	chr14	73366496	73366539	-	1	NA	exon (NM_008410, exon 3 of 6)	exon (NM_008410, exon 3 of 6)	18754	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_127914.1	chr15	9530033	9530036	-	1	NA	promoter-TSS (NM_008372)	promoter-TSS (NM_008372)	-158	NM_008372	16197	Mm.389	NM_008372	ENSMUSG00000003882	Il7r	CD127|IL-7Ralpha	interleukin 7 receptor	protein-coding
mm_20185.1	chr2	122600499	122600530	-	1	NA	exon (NM_025961, exon 6 of 9)	exon (NM_025961, exon 6 of 9)	10763	NM_025961	67092	Mm.29975	NM_025961	ENSMUSG00000027199	Gatm	1810003P21Rik|AI314789|AT	glycine amidinotransferase (L-arginine:glycine amidinotransferase)	protein-coding
mm_128156.1	chr15	32248653	32248653	-	1	NA	intron (NM_009154, intron 1 of 22)	intron (NM_009154, intron 1 of 22)	3840	NM_009154	20356	Mm.260374	NM_009154	ENSMUSG00000022231	Sema5a	5930434A13|9130201M22Rik|AI464145|Semaf|semF	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A	protein-coding
mm_143109.1	chr17	57172456	57172464	-	1	NA	Intergenic	RMER19B|LTR|ERVK	21721	NM_019418	50930	Mm.483369	NM_019418	ENSMUSG00000005824	Tnfsf14	HVEM-L|HVEML|LIGHT|LTg|Ly113|Tnlg1d	tumor necrosis factor (ligand) superfamily, member 14	protein-coding
mm_132791.1	chr16	45093612	45093622	+	1	NA	promoter-TSS (NM_026439)	promoter-TSS (NM_026439)	-436	NM_026439	67896	Mm.181074	NM_026439	ENSMUSG00000022665	Ccdc80	2610001E17Rik|DRO1|Ssg1|Urb	coiled-coil domain containing 80	protein-coding
mm_99797.1	chr11	107546903	107546923	+	1	NA	Intergenic	CpG	-1047	NM_198298	78455	Mm.272047	NM_198298	ENSMUSG00000020721	Helz	3110078M01Rik|9430093I07Rik|9630002H22Rik|AI851979|DRHC	helicase with zinc finger domain	protein-coding
mm_62377.1	chr7	100706774	100706785	+	1	NA	promoter-TSS (NM_178764)	promoter-TSS (NM_178764)	77	NM_178764	319604	Mm.260362	NM_178764	ENSMUSG00000029461	Fam168a	2610030B18Rik|B930006L02Rik|mKIAA0280	family with sequence similarity 168, member A	protein-coding
mm_26343.1	chr3	142547320	142547331	+	1	NA	3' UTR (NM_001083312, exon 11 of 11)	3' UTR (NM_001083312, exon 11 of 11)	-12727	NM_018734	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_61677.1	chr7	80993428	80993482	+	1	NA	promoter-TSS (NM_178707)	promoter-TSS (NM_178707)	-229	NM_178707	233410	Mm.29525	NM_178707	ENSMUSG00000005621	Zfp592	8430405N24|A730014M16Rik|Znf592|mKIAA0211	zinc finger protein 592	protein-coding
mm_24978.1	chr3	96829460	96829474	+	1	NA	promoter-TSS (NM_001163497)	promoter-TSS (NM_001163497)	-116	NM_001163496	54215	Mm.34693	NM_018767	ENSMUSG00000038304	Cd160	AU045688|By55	CD160 antigen	protein-coding
mm_129175.1	chr15	76269849	76269858	-	1	NA	promoter-TSS (NR_045747)	promoter-TSS (NR_045747)	-14	NR_045747	100038659	Mm.448549	NR_045747		Mirt2	ENSMUSG00000075583|Gm10872|Gm24562	myocardial infraction associated transcript 2	ncRNA
mm_96439.1	chr11	67321639	67321648	+	1	NA	Intergenic	Intergenic	-5460	NM_001081250	544791	Mm.461064	NM_001081250	ENSMUSG00000060180	Myh13	MyHC-eo	myosin, heavy polypeptide 13, skeletal muscle	protein-coding
mm_103647.1	chr11	78969359	78969377	-	1	NA	intron (NM_001159301, intron 4 of 9)	ID_B1|SINE|B4	15556	NM_001159301	16859	Mm.341434	NM_010708	ENSMUSG00000001123	Lgals9	AA407335|AI194909|AI265545|LGALS35|Lgals5|gal-9|galectin-9	lectin, galactose binding, soluble 9	protein-coding
mm_60328.1	chr7	44236191	44236202	+	1	NA	promoter-TSS (NR_029436)	promoter-TSS (NR_029436)	-74	NR_029436	70004	Mm.158317	NR_029436	ENSMUSG00000038782	1700028J19Rik	-	RIKEN cDNA 1700028J19 gene	ncRNA
mm_64978.1	chr7	16899352	16899358	-	1	NA	Intergenic	PB1D10|SINE|Alu	-7135	NM_008967	19222	Mm.287572	NM_008967	ENSMUSG00000043017	Ptgir	IP|PGI2	prostaglandin I receptor (IP)	protein-coding
mm_166732.1	chr6	122608702	122608708	+	1	NA	intron (NM_008108, intron 1 of 1)	intron (NM_008108, intron 1 of 1)	1382	NM_008108	14562	Mm.299742	NM_008108	ENSMUSG00000030117	Gdf3	C78318|Gdf-3|Vgr-2|Vgr2|ecat9	growth differentiation factor 3	protein-coding
mm_29914.1	chr3	131489036	131489050	-	1	NA	Intergenic	Intergenic	-75725	NM_001289479	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_124559.1	chr14	122983212	122983277	-	1	NA	promoter-TSS (NM_028651)	promoter-TSS (NM_028651)	17	NM_028651	70551	Mm.271988	NM_028651	ENSMUSG00000041594	Tmtc4	4930403J22Rik|5730419O14Rik	transmembrane and tetratricopeptide repeat containing 4	protein-coding
mm_63723.1	chr7	130847541	130847585	+	1	NA	Intergenic	L1MDa|LINE|L1	-18161	NM_001346515	101476	Mm.323554	NM_133942	ENSMUSG00000040268	Plekha1	AA960558|C920009D07Rik|TAPP1	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 1	protein-coding
mm_29532.1	chr3	116662538	116662548	-	1	NA	5' UTR (NM_008246, exon 1 of 12)	5' UTR (NM_008246, exon 1 of 12)	134	NM_008246	15247	Mm.280077	NM_008246	ENSMUSG00000089911	Mfsd14a	Hiat1	major facilitator superfamily domain containing 14A	protein-coding
mm_10533.1	chr2	16408692	16408715	+	1	NA	intron (NM_026162, intron 1 of 13)	Lx6|LINE|L1	52399	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding
mm_150038.1	chr19	29377437	29377449	+	1	NA	intron (NM_021893, intron 3 of 6)	MIR|SINE|MIR	10005	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_161199.1	chr13	55445393	55445393	+	1	NA	promoter-TSS (NM_001286064)	promoter-TSS (NM_001286064)	62	NM_001112711	26385	Mm.10193	NM_011938	ENSMUSG00000074886	Grk6	Gprk6	G protein-coupled receptor kinase 6	protein-coding
mm_46330.1	chr5	100916542	100916552	-	1	NA	Intergenic	Intergenic	70318	NM_172715	231510	Mm.271911	NM_172715	ENSMUSG00000029314	Agpat9	1-AGPAT|1-AGPAT 9|4933407I02Rik|4933408F15|A230097K15Rik|GPAT-3|Gpat3|mGPAT3	1-acylglycerol-3-phosphate O-acyltransferase 9	protein-coding
mm_123258.1	chr14	61173493	61173497	-	1	NA	intron (NM_172809, intron 3 of 9)	CpG-4552	35038	NM_172809	50720	Mm.440703	NM_015788	ENSMUSG00000048279	Sacs	A230052M14|DNAJC29|E130115J16Rik|mKIAA0730	sacsin	protein-coding
mm_45794.1	chr5	87538189	87538201	-	1	NA	promoter-TSS (NM_019878)	promoter-TSS (NM_019878)	0	NM_019878	56362	Mm.23502	NM_019878	ENSMUSG00000029269	Sult1b1	ST1B1|St2b2	sulfotransferase family 1B, member 1	protein-coding
mm_146062.1	chr18	69686733	69686742	+	1	NA	3' UTR (NM_001083967, exon 20 of 20)	3' UTR (NM_001083967, exon 20 of 20)	-238822	NM_201362	381175	Mm.266831	NM_201362	ENSMUSG00000038903	Ccdc68	BC046343	coiled-coil domain containing 68	protein-coding
mm_98795.1	chr11	96967020	96967033	+	1	NA	intron (NM_030220, intron 1 of 6)	intron (NM_030220, intron 1 of 6)	10662	NM_030220	78912	Mm.491183	NM_030220	ENSMUSG00000018678	Sp2	4930480I16Rik|mKIAA0048	Sp2 transcription factor	protein-coding
mm_130452.1	chr15	98543973	98543989	-	1	NA	exon (NM_009833, exon 9 of 9)	exon (NM_009833, exon 9 of 9)	-9712	NM_001289440	69612	Mm.229107	NM_133714	ENSMUSG00000022992	Kansl2	2310037I24Rik|B930009D17	KAT8 regulatory NSL complex subunit 2	protein-coding
mm_116075.1	chr13	27693324	27693332	-	1	NA	Intergenic	Intergenic	23409	NM_011120	18814	Mm.3258	NM_011120	ENSMUSG00000021348	Prl7d1	Ghd19|PLF-RP|PRP|Plfr	prolactin family 7, subfamily d, member 1	protein-coding
mm_100985.1	chr11	7213817	7213823	-	1	NA	5' UTR (NM_008343, exon 1 of 5)	5' UTR (NM_008343, exon 1 of 5)	103	NM_008343	16009	Mm.29254	NM_008343	ENSMUSG00000020427	Igfbp3	AI649005|IGFBP-3|IGgfbp3	insulin-like growth factor binding protein 3	protein-coding
mm_15771.1	chr2	164332785	164332789	+	1	NA	promoter-TSS (NM_009301)	promoter-TSS (NM_009301)	22	NM_009301	20944	Mm.140154	NM_009301	ENSMUSG00000017004	Svs5	BB115186|Semg1|Svp-1|Svp1|Svp5	seminal vesicle secretory protein 5	protein-coding
mm_170168.1	chr1	75506318	75506320	-	1	NA	promoter-TSS (NM_010564)	promoter-TSS (NM_010564)	133	NM_178884	98733	Mm.236454	NM_178884	ENSMUSG00000026211	Obsl1	AW822216	obscurin-like 1	protein-coding
mm_138088.1	chr17	33999764	33999775	+	1	NA	exon (NM_001001892, exon 2 of 8)	exon (NM_001001892, exon 2 of 8)	564	NM_001001892	14972	Mm.422886	NM_001001892	ENSMUSG00000061232	H2-K1	H-2K|H-2K(d)|H2-K|K-f	histocompatibility 2, K1, K region	protein-coding
mm_117725.1	chr13	95525240	95525252	-	1	NA	promoter-TSS (NM_007974)	promoter-TSS (NM_007974)	-6	NM_007974	14063	Mm.1614	NM_007974	ENSMUSG00000021678	F2rl1	Gpcr11|PAR-2|Par2	coagulation factor II (thrombin) receptor-like 1	protein-coding
mm_1485.1	chr1	71649197	71649235	+	1	NA	exon (NM_001276413, exon 4 of 44)	exon (NM_001276413, exon 4 of 44)	4018	NM_010233	14268	Mm.193099	NM_010233	ENSMUSG00000026193	Fn1	E330027I09|Fn|Fn-1	fibronectin 1	protein-coding
mm_160321.1	chr7	144838661	144838661	+	1	NA	promoter-TSS (NM_008007)	promoter-TSS (NM_008007)	49	NM_008007	14174	Mm.4947	NM_008007	ENSMUSG00000031074	Fgf3	Fgf-3|Int-2|Int-P	fibroblast growth factor 3	protein-coding
mm_142940.1	chr17	56036487	56036501	-	1	NA	5' UTR (NM_013664, exon 1 of 10)	5' UTR (NM_013664, exon 1 of 10)	143	NM_013664	20405	Mm.1773	NM_013664	ENSMUSG00000003200	Sh3gl1	C77078|EEN|SH3P8|Sh3d2b	SH3-domain GRB2-like 1	protein-coding
mm_5502.1	chr1	37418810	37418838	-	1	NA	3' UTR (NM_198006, exon 3 of 3)	3' UTR (NM_198006, exon 3 of 3)	11279	NM_198006	76178	Mm.28085	NM_198006	ENSMUSG00000026112	Coa5	1700001A24Rik|6330578E17Rik|Pet191	cytochrome C oxidase assembly factor 5	protein-coding
mm_29546.1	chr3	116804472	116804474	-	1	NA	intron (NM_001081326, intron 2 of 33)	intron (NM_001081326, intron 2 of 33)	3693	NM_001081326	77559	Mm.237099	NM_001081326	ENSMUSG00000033400	Agl	1110061O17Rik|9430004C13Rik|9630046L06Rik|AI850929|C77197	amylo-1,6-glucosidase, 4-alpha-glucanotransferase	protein-coding
mm_56273.1	chr6	91030081	91030084	-	1	NA	intron (NM_018815, intron 30 of 39)	intron (NM_018815, intron 30 of 39)	86744	NM_018815	54563	Mm.28162	NM_018815	ENSMUSG00000030091	Nup210	9830001L10|AI836801|Pom210|gp190|gp210	nucleoporin 210	protein-coding
mm_60249.1	chr7	43774643	43774648	+	1	NA	promoter-TSS (NM_001177373)	promoter-TSS (NM_001177373)	28	NM_001177373	56538	Mm.154276	NM_019974	ENSMUSG00000067616	Klk11	2310015I08Rik|Prss20|TLSP	kallikrein related-peptidase 11	protein-coding
mm_147092.1	chr18	35648508	35648516	-	1	NA	intron (NM_027222, intron 1 of 3)	intron (NM_027222, intron 1 of 3)	855	NM_027222	69816	Mm.27252	NM_027222	ENSMUSG00000024353	Mzb1	2010001M09Rik|AV064572|PACAP|pERp1	marginal zone B and B1 cell-specific protein 1	protein-coding
mm_163852.1	chr14	19418328	19418368	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	184239	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_62871.1	chr7	114745527	114745536	+	1	NA	promoter-TSS (NM_173767)	promoter-TSS (NM_173767)	-235	NM_173767	233752	Mm.83037	NM_173767	ENSMUSG00000048782	Insc	3830422K02Rik|C730020D23	inscuteable homolog (Drosophila)	protein-coding
mm_103667.1	chr11	79059873	79059879	-	1	NA	intron (NM_013571, intron 2 of 17)	intron (NM_013571, intron 2 of 17)	36279	NR_045873	790910	Mm.440410	NR_045873		Gm11201	ENSMUSG00000072637|OTTMUSG00000000169	predicted gene 11201	ncRNA
mm_16761.1	chr2	9877837	9877850	-	1	NA	5' UTR (NM_008091, exon 2 of 6)	5' UTR (NM_008091, exon 2 of 6)	757	NM_008091	14462	Mm.313866	NM_008091	ENSMUSG00000015619	Gata3	Gata-3|jal	GATA binding protein 3	protein-coding
mm_164964.1	chr19	6242374	6242396	-	1	NA	intron (NM_194348, intron 1 of 39)	intron (NM_194348, intron 1 of 39)	717	NM_194348	329015	Mm.277384	NM_194348	ENSMUSG00000024773	Atg2a	1810013C15Rik|A830054M12|BC023754|mKIAA0404	autophagy related 2A	protein-coding
mm_30657.1	chr4	8915756	8915791	+	1	NA	Intergenic	L2|LINE|L2	225367	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_17332.1	chr2	26516621	26516635	-	1	NA	Intergenic	Intergenic	12701	NR_132655	102639736		NR_132655		Gm35978	-	predicted gene, 35978	ncRNA
mm_28852.1	chr3	96832091	96832095	-	1	NA	promoter-TSS (NM_001146001)	promoter-TSS (NM_001146001)	-23	NR_015596	67583	Mm.444284	NR_015596	ENSMUSG00000087223	4930442L01Rik	-	RIKEN cDNA 4930442L01 gene	ncRNA
mm_11383.1	chr2	31278034	31278044	+	1	NA	intron (NM_019681, intron 2 of 7)	MIR3|SINE|MIR	32116	NM_019681	14299	Mm.249318	NM_019681	ENSMUSG00000062661	Ncs1	9430075O15Rik|A730032G13Rik|AI836659|Freq|Mfreq|NCS-1	neuronal calcium sensor 1	protein-coding
mm_128694.1	chr15	62092719	62092756	-	1	NA	intron (NR_132746, intron 1 of 6)	intron (NR_132746, intron 1 of 6)	53480	NR_132746	19296	Mm.4608	NM_011222	ENSMUSG00000097039	Pvt1	Ayu21-84Imeg|Gt(pU21)84Imeg|Mis-1|Mlvi-1|Pvt-1	plasmacytoma variant translocation 1	ncRNA
mm_23632.1	chr3	66225519	66225520	+	1	NA	3' UTR (NM_008987, exon 3 of 3)	3' UTR (NM_008987, exon 3 of 3)	5632	NM_008987	19288	Mm.276776	NM_008987	ENSMUSG00000027832	Ptx3	AI607804|TSG-14	pentraxin related gene	protein-coding
mm_169127.1	chr13	55246766	55246779	+	1	NA	exon (NM_008739, exon 5 of 23)	exon (NM_008739, exon 5 of 23)	36990	NM_008739	18193	Mm.12964	NM_008739	ENSMUSG00000021488	Nsd1	AI528500|KMT3B	nuclear receptor-binding SET-domain protein 1	protein-coding
mm_129778.1	chr15	82792926	82792940	-	1	NA	intron (NM_029562, intron 2 of 8)	intron (NM_029562, intron 2 of 8)	1312	NM_029562	76279	Mm.439931	NM_029562	ENSMUSG00000022445	Cyp2d26	1300006E06Rik	cytochrome P450, family 2, subfamily d, polypeptide 26	protein-coding
mm_79620.1	chr9	58822849	58822862	+	1	NA	promoter-TSS (NM_001081192)	promoter-TSS (NM_001081192)	-657	NM_001081192	330953	Mm.151967	NM_001081192	ENSMUSG00000032338	Hcn4	Bcng3|Hcn3	hyperpolarization-activated, cyclic nucleotide-gated K+ 4	protein-coding
mm_116031.1	chr13	25270037	25270050	-	1	NA	promoter-TSS (NM_009513)	promoter-TSS (NM_009513)	-47	NM_009513	22360	Mm.4766	NM_009513	ENSMUSG00000048978	Nrsn1	Neurensin-1|Neuro-p24|Vmp	neurensin 1	protein-coding
mm_130587.1	chr15	99632803	99632814	-	1	NA	intron (NM_012025, intron 7 of 17)	intron (NM_012025, intron 7 of 17)	18848	NM_001253808	26934	Mm.273804	NM_012025	ENSMUSG00000023015	Racgap1	AI227039|AI327394|Band25|GTPase|MgcRacGAP|gtl11|mKIAA1478	Rac GTPase-activating protein 1	protein-coding
mm_168792.1	chr12	19387785	19387795	+	1	NA	Intergenic	CpG	873280	NM_001201330	236366	Mm.352227	NM_001033157	ENSMUSG00000073197	5730507C01Rik	-	RIKEN cDNA 5730507C01 gene	protein-coding
mm_127565.1	chr15	102224715	102224717	+	1	NA	exon (NM_013566, exon 3 of 15)	exon (NM_013566, exon 3 of 15)	7219	NM_013566	16421	Mm.58	NM_013566	ENSMUSG00000001281	Itgb7	Ly69	integrin beta 7	protein-coding
mm_10755.1	chr2	23201937	23201942	+	1	NA	Intergenic	Intergenic	-5537	NM_027635	70981	Mm.314026	NM_027635	ENSMUSG00000026774	4931423N10Rik	-	RIKEN cDNA 4931423N10 gene	protein-coding
mm_5509.1	chr1	37488629	37488650	-	1	NA	promoter-TSS (NR_024017)	promoter-TSS (NR_024017)	-34	NR_024017	77633	Mm.483177	NR_024017	ENSMUSG00000103948	4930594C11Rik	-	G1 to S phase transition pseudogene	pseudo
mm_36203.1	chr4	62360525	62360552	-	1	NA	promoter-TSS (NM_001045528)	promoter-TSS (NM_001045528)	10	NM_001045528	338355	Mm.357792	NM_001045528	ENSMUSG00000066151	Fkbp15	BB131447|C430014M02Rik|FKBO133|FKBP-133|FKBP-15|FKBP133|mKIAA0674	FK506 binding protein 15	protein-coding
mm_83496.1	chr9	45946570	45946597	-	1	NA	intron (NM_001289668, intron 12 of 26)	intron (NM_001289668, intron 12 of 26)	-6993	NR_106055	102465659		NR_106055	ENSMUSG00000098327	Mir7087	Gm27273|mmu-mir-7087	microRNA 7087	ncRNA
mm_262.1	chr1	20890563	20890587	+	1	NA	promoter-TSS (NR_040492)	promoter-TSS (NR_040492)	-47	NM_028829	74229	Mm.40780	NM_028829	ENSMUSG00000025931	Paqr8	1700019B16Rik|3110001D06Rik	progestin and adipoQ receptor family member VIII	protein-coding
mm_123164.1	chr14	57133586	57133618	-	1	NA	promoter-TSS (NM_001271663)	promoter-TSS (NM_001271663)	9	NM_001271663	14623	Mm.25652	NM_008128	ENSMUSG00000040055	Gjb6	AA958971|Cx30|D14Bwg0506e	gap junction protein, beta 6	protein-coding
mm_155818.1	chrX	100572235	100572265	+	1	NA	promoter-TSS (NM_001081136)	promoter-TSS (NM_001081136)	3	NM_001081136	245533	Mm.77759	NM_001081136	ENSMUSG00000015665	Awat1	Dgat2l3	acyl-CoA wax alcohol acyltransferase 1	protein-coding
mm_131221.1	chr16	8856994	8857000	+	1	NA	3' UTR (NM_001081400, exon 4 of 4)	3' UTR (NM_001081400, exon 4 of 4)	26897	NM_001081400	69053	Mm.390868	NM_001081400	ENSMUSG00000022507	1810013L24Rik	1110017P05Rik|3010002C02Rik|AA792997|AW124177|Gm19906|R74903	RIKEN cDNA 1810013L24 gene	protein-coding
mm_135681.1	chr16	52420261	52420275	-	1	NA	intron (NM_009655, intron 1 of 15)	Lx9|LINE|L1	32813	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_124333.1	chr14	103843822	103843828	-	1	NA	promoter-TSS (NM_001276296)	promoter-TSS (NM_001276296)	-124	NM_001276296	13618	Mm.229532	NM_007904	ENSMUSG00000022122	Ednrb	ET-B|ET-BR|ETR-b|ETb|Sox10m1	endothelin receptor type B	protein-coding
mm_29856.1	chr3	130041347	130041358	-	1	NA	exon (NM_207209, exon 2 of 24)	exon (NM_207209, exon 2 of 24)	19555	NM_207209	99683	Mm.192303	NM_207209	ENSMUSG00000001052	Sec24b	AI605202|SEC24	Sec24 related gene family, member B (S. cerevisiae)	protein-coding
mm_68371.1	chr7	107801248	107801261	-	1	NA	promoter-TSS (NM_172908)	promoter-TSS (NM_172908)	-75	NM_172908	244199	Mm.99576	NM_172908	ENSMUSG00000048236	Ovch2	9230106D23Rik|Ovtn	ovochymase 2	protein-coding
mm_146918.1	chr18	31607522	31607527	-	1	NA	intron (NM_026165, intron 1 of 7)	intron (NM_026165, intron 1 of 7)	2378	NM_026165	67453	Mm.23896	NM_026165	ENSMUSG00000024259	Slc25a46	1200007B05Rik|AI325987	solute carrier family 25, member 46	protein-coding
mm_15949.1	chr2	165948105	165948106	+	1	NA	Intergenic	Intergenic	-44532	NM_008679	17979	Mm.469663	NM_008679	ENSMUSG00000027678	Ncoa3	2010305B15Rik|AW321064|Actr|Aib1|KAT13B|Rac3|Src3|Tram-1|Tram1|bHLHe42|p/Cip|pCip	nuclear receptor coactivator 3	protein-coding
mm_45463.1	chr5	67847361	67847375	-	1	NA	promoter-TSS (NM_009727)	promoter-TSS (NM_009727)	63	NM_009727	11980	Mm.153230	NM_009727	ENSMUSG00000037685	Atp8a1	AI481521|AI853962|APLT|AW743152|AW822227|Atp3a2|B230107D19Rik|ClassI	ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1	protein-coding
mm_126930.1	chr15	91673494	91673507	+	1	NA	intron (NM_025730, intron 1 of 50)	intron (NM_025730, intron 1 of 50)	276	NM_025730	66725	Mm.37558	NM_025730	ENSMUSG00000036273	Lrrk2	4921513O20Rik|9330188B09Rik|AW561911|D630001M17Rik|Gm927|cI-46	leucine-rich repeat kinase 2	protein-coding
mm_34142.1	chr4	139338093	139338103	+	1	NA	Intergenic	MLTR12|LTR|ERV1	14478	NM_001290810	69902	Mm.27871	NM_023536	ENSMUSG00000028741	Mrto4	2610012O22Rik|Mg684|Mrt4	mRNA turnover 4, ribosome maturation factor	protein-coding
mm_159050.1	chr1	186967308	186967308	+	1	NA	promoter-TSS (NM_033077)	promoter-TSS (NM_033077)	-108	NM_033077	110957	Mm.108054	NM_033077	ENSMUSG00000039224	D1Pas1	Pl10	DNA segment, Chr 1, Pasteur Institute 1	protein-coding
mm_172017.1	chr6	112702614	112702628	+	1	NA	Intergenic	RLTR9D|LTR|ERVK	-5951	NM_001167730	58186	Mm.103812	NM_021385	ENSMUSG00000030254	Rad18	2810024C04Rik|Rad18sc	RAD18 E3 ubiquitin protein ligase	protein-coding
mm_137209.1	chr17	24140916	24140936	+	1	NA	intron (NM_001286662, intron 1 of 13)	intron (NM_001286662, intron 1 of 13)	668	NM_011062	18607	Mm.10504	NM_011062	ENSMUSG00000024122	Pdpk1	Pdk1	3-phosphoinositide dependent protein kinase 1	protein-coding
mm_33793.1	chr4	134924259	134924289	+	1	NA	exon (NM_023665, exon 2 of 5)	exon (NM_023665, exon 2 of 5)	649	NM_023665	27981	Mm.331964	NM_023665	ENSMUSG00000037266	Rsrp1	2700043I21Rik|D4Ucla2|D4Wsu53e	arginine/serine rich protein 1	protein-coding
mm_7359.1	chr1	106705833	106705835	-	1	NA	intron (NM_009741, intron 1 of 1)	intron (NM_009741, intron 1 of 1)	8456	NM_009741	12043	Mm.257460	NM_009741	ENSMUSG00000057329	Bcl2	AW986256|Bcl-2|C430015F12Rik|D630044D05Rik|D830018M01Rik	B cell leukemia/lymphoma 2	protein-coding
mm_125864.1	chr15	75474471	75474477	+	1	NA	Intergenic	Intergenic	25022	NM_001347049	102637705		NM_001347049	ENSMUSG00000093626	Ly6l	Gm20654	lymphocyte antigen 6 complex, locus L	protein-coding
mm_40820.1	chr5	72602806	72602810	+	1	NA	TTS (NM_007723)	TTS (NM_007723)	-15258	NM_001024147	545758	Mm.332426	NM_001024147	ENSMUSG00000060204	Gm5868	EG545758	predicted gene 5868	protein-coding
mm_64134.1	chr7	141194108	141194118	+	1	NA	promoter-TSS (NM_001172065)	promoter-TSS (NM_001172065)	-17	NM_001172065	70552	Mm.45104	NM_153777	ENSMUSG00000038637	Lrrc56	5730427C23Rik|BB110509|mFLJ00101	leucine rich repeat containing 56	protein-coding
mm_40280.1	chr5	43062781	43062802	+	1	NA	Intergenic	Intergenic	-170672	NM_175937	231207	Mm.7233	NM_175937	ENSMUSG00000039782	Cpeb2	A630055H10Rik|Cpe-bp2	cytoplasmic polyadenylation element binding protein 2	protein-coding
mm_142344.1	chr17	43607378	43607400	-	1	NA	exon (NM_013737, exon 10 of 12)	exon (NM_013737, exon 10 of 12)	-15880	NR_045444	73504	Mm.9277	NR_045444	ENSMUSG00000090307	1700071M16Rik	-	RIKEN cDNA 1700071M16 gene	ncRNA
mm_706.1	chr1	40684075	40684077	+	1	NA	intron (NM_001033289, intron 1 of 11)	intron (NM_001033289, intron 1 of 11)	2364	NM_001033289	226999	Mm.256414	NM_001033289	ENSMUSG00000026062	Slc9a2	2210416H12Rik|4932415O19Rik|AV333884|NHE2	solute carrier family 9 (sodium/hydrogen exchanger), member 2	protein-coding
mm_29828.1	chr3	129726290	129726292	-	1	NA	intron (NM_010113, intron 5 of 23)	intron (NM_010113, intron 5 of 23)	-1205	NM_001329594	13645	Mm.252481	NM_010113	ENSMUSG00000028017	Egf	AI790464	epidermal growth factor	protein-coding
mm_120647.1	chr14	70530612	70530624	+	1	NA	promoter-TSS (NM_145219)	promoter-TSS (NM_145219)	-203	NM_145219	213469	Mm.41708	NM_145219	ENSMUSG00000033595	Lgi3	AI841179|AW049851	leucine-rich repeat LGI family, member 3	protein-coding
mm_143522.1	chr17	73710385	73710405	-	1	NA	promoter-TSS (NM_027864)	promoter-TSS (NM_027864)	56	NM_027864	71685	Mm.271953	NM_027864	ENSMUSG00000024064	Galnt14	0610033M06Rik	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 14	protein-coding
mm_31607.1	chr4	58644604	58644608	+	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	-91115	NM_010336	14745	Mm.4772	NM_010336	ENSMUSG00000038668	Lpar1	AI326300|Edg2|Gpcr26|Kdt2|lpA1|vzg-1	lysophosphatidic acid receptor 1	protein-coding
mm_106184.1	chr11	116725196	116725202	-	1	NA	Intergenic	Intergenic	-26968	NR_003364	193217	Mm.100084	NR_003364		BC018473	-	cDNA sequence BC018473	ncRNA
mm_44244.1	chr5	5346611	5346628	-	1	NA	intron (NM_011074, intron 2 of 14)	B1_Mus2|SINE|Alu	33632	NM_011074	18647	Mm.389061	NM_011074	ENSMUSG00000028926	Cdk14	Pftk1|mKIAA0834	cyclin-dependent kinase 14	protein-coding
mm_54705.1	chr6	39607667	39607670	-	1	NA	3' UTR (NM_139294, exon 22 of 22)	3' UTR (NM_139294, exon 22 of 22)	15085	NM_026612	68198	Mm.29415	NM_026612	ENSMUSG00000002416	Ndufb2	1810011O01Rik|8kDa|AGGG|AI325567|CI-AGGG	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 2	protein-coding
mm_84156.1	chr9	59525447	59525476	-	1	NA	promoter-TSS (NM_178388)	promoter-TSS (NM_178388)	40	NM_178388	73893	Mm.216135	NM_178388	ENSMUSG00000049526	Tmem202	4930425N13Rik	transmembrane protein 202	protein-coding
mm_14310.1	chr2	129196588	129196619	+	1	NA	Intergenic	MTE2a|LTR|ERVL-MaLR	-2170	NM_015747	20515	Mm.272675	NM_015747	ENSMUSG00000027397	Slc20a1	AI607883|Glvr-1|Glvr1	solute carrier family 20, member 1	protein-coding
mm_29163.1	chr3	106219478	106219483	-	1	NA	promoter-TSS (NM_145126)	promoter-TSS (NM_145126)	-1	NM_145126	104183	Mm.425140	NM_145126	ENSMUSG00000063779	Chil4	Chi3l4|Ym2	chitinase-like 4	protein-coding
mm_18191.1	chr2	45113256	45113275	-	1	NA	promoter-TSS (NM_015753)	promoter-TSS (NM_015753)	14	NM_015753	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_161515.1	chr15	98934436	98934436	-	1	NA	promoter-TSS (NM_011654)	promoter-TSS (NM_011654)	-46	NM_011654	22143	Mm.392113	NM_011654	ENSMUSG00000023004	Tuba1b	Tuba2	tubulin, alpha 1B	protein-coding
mm_20334.1	chr2	127538981	127538999	-	1	NA	intron (NM_138750, intron 6 of 23)	intron (NM_138750, intron 6 of 23)	2427	NM_178047	192212	Mm.34171	NM_138750	ENSMUSG00000027376	Prom2	AI507243|Prom-rp	prominin 2	protein-coding
mm_127606.1	chr15	102445388	102445403	+	1	NA	promoter-TSS (NM_144547)	promoter-TSS (NM_144547)	28	NM_144547	110542	Mm.60331	NM_144547	ENSMUSG00000023047	Amhr2	Misiir|Misrii|Mrii	anti-Mullerian hormone type 2 receptor	protein-coding
mm_10932.1	chr2	25467827	25467835	+	1	NA	exon (NM_008963, exon 5 of 7)	exon (NM_008963, exon 5 of 7)	1918	NM_008963	19215	Mm.1008	NM_008963	ENSMUSG00000015090	Ptgds	21kDa|L-PGDS|PGD2|PGDS|PGDS2|Ptgs3	prostaglandin D2 synthase (brain)	protein-coding
mm_34276.1	chr4	141424518	141424531	+	1	NA	3' UTR (NM_013868, exon 3 of 3)	3' UTR (NM_013868, exon 3 of 3)	3745	NM_013868	29818	Mm.46181	NM_013868	ENSMUSG00000006221	Hspb7	27kDa|Hsp25-2|cvHsp	heat shock protein family, member 7 (cardiovascular)	protein-coding
mm_99982.1	chr11	114668754	114668774	+	1	NA	promoter-TSS (NM_001048058)	promoter-TSS (NM_001048058)	-17	NM_001048058	67671	Mm.238817	NM_023372	ENSMUSG00000057322	Rpl38	0610025G13Rik|Rbt|Ts|Tss	ribosomal protein L38	protein-coding
mm_6730.1	chr1	82771308	82771310	-	1	NA	Intergenic	Intergenic	-2853	NM_025453	66261	Mm.46325	NM_025453	ENSMUSG00000026149	Tm4sf20	1810018L02Rik	transmembrane 4 L six family member 20	protein-coding
mm_143888.1	chr17	84380464	84380477	-	1	NA	intron (NM_183021, intron 26 of 37)	RSINE1|SINE|B4	85738	NM_183021	240174	Mm.246767	NM_177826	ENSMUSG00000024251	Thada	6530405K19|A930021O22|AU019899|BC052885|GITA	thyroid adenoma associated	protein-coding
mm_60936.1	chr7	46861453	46861461	+	1	NA	intron (NM_013580, intron 1 of 7)	intron (NM_013580, intron 1 of 7)	194	NM_013580	16833	Mm.16563	NM_013580	ENSMUSG00000030851	Ldhc	LDH-C4|Ldh-3|Ldh-x|Ldh3|Ldhc4	lactate dehydrogenase C	protein-coding
mm_72903.1	chr8	90884057	90884084	+	1	NA	intron (NM_177224, intron 2 of 39)	B1_Mur2|SINE|Alu	-48179	NM_001310530	109151	Mm.100615	NM_177224	ENSMUSG00000056608	Chd9	1810014J18Rik|9030205D12Rik|A330063D19Rik|AD013|PRIC320|mKIAA0308	chromodomain helicase DNA binding protein 9	protein-coding
mm_88166.1	chr10	69706657	69706669	+	1	NA	intron (NM_170730, intron 1 of 17)	intron (NM_170730, intron 1 of 17)	172955	NM_146005	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_39531.1	chr5	21372697	21372714	+	1	NA	promoter-TSS (NM_008013)	promoter-TSS (NM_008013)	32	NM_008013	14190	Mm.292100	NM_008013	ENSMUSG00000039899	Fgl2	AI385601|musfiblp	fibrinogen-like protein 2	protein-coding
mm_40745.1	chr5	66745397	66745407	+	1	NA	promoter-TSS (NM_001001980)	promoter-TSS (NM_001001980)	-438	NM_001001980	77569	Mm.374778	NM_001001980	ENSMUSG00000037736	Limch1	3732412D22Rik|mKIAA1102	LIM and calponin homology domains 1	protein-coding
mm_135747.1	chr16	55923864	55923881	-	1	NA	TTS (NM_001159365)	TTS (NM_001159365)	10976	NM_001159364	74201	Mm.178427	NM_028815	ENSMUSG00000022604	Cep97	2810403B08Rik|4932439K18Rik|AA437768|E130116N02Rik|Lrriq2	centrosomal protein 97	protein-coding
mm_149883.1	chr19	25377093	25377103	+	1	NA	intron (NM_181404, intron 3 of 13)	B4|SINE|B4	-128608	NM_015826	50796	Mm.391208	NM_015826	ENSMUSG00000024837	Dmrt1	-	doublesex and mab-3 related transcription factor 1	protein-coding
mm_89083.1	chr10	83562240	83562255	+	1	NA	intron (NM_001033375, intron 13 of 32)	intron (NM_001033375, intron 13 of 32)	18306	NM_001033375	319277	Mm.491194	NM_001033375	ENSMUSG00000034560	Washc4	A230046K03Rik|AA589518|Kiaa1033|mKIAA1033	WASH complex subunit 4	protein-coding
mm_117750.1	chr13	95897116	95897120	-	1	NA	Intergenic	U1|snRNA|snRNA	-5196	NM_027711	544963	Mm.38878	NM_027711	ENSMUSG00000021676	Iqgap2	4933417J23Rik|A630053O10|AI788777	IQ motif containing GTPase activating protein 2	protein-coding
mm_144456.1	chr18	23395984	23395985	+	1	NA	intron (NM_001285813, intron 1 of 21)	MLT1C|LTR|ERVL-MaLR	-19425	NM_010087	13527	Mm.94371	NM_010087	ENSMUSG00000024302	Dtna	2210407P21Rik|DTN-A|Dtn|Gm19389|a-DB-1|adbn	dystrobrevin alpha	protein-coding
mm_163496.1	chr12	110985406	110985417	+	1	NA	Intergenic	Intergenic	-6390	NM_175207	74251	Mm.250989	NM_175207	ENSMUSG00000037904	Ankrd9	2500003O20Rik	ankyrin repeat domain 9	protein-coding
mm_161836.1	chr17	84956537	84956537	+	1	NA	promoter-TSS (NM_001159497)	promoter-TSS (NM_001159497)	-204	NM_001159497	19043	Mm.249695	NM_011151	ENSMUSG00000061130	Ppm1b	PP2CB	protein phosphatase 1B, magnesium dependent, beta isoform	protein-coding
mm_96191.1	chr11	61956797	61956831	+	1	NA	promoter-TSS (NM_001281818)	promoter-TSS (NM_001281818)	51	NM_001310526	432572	Mm.438022	NM_001029936	ENSMUSG00000042331	Specc1	2810012G08Rik|B230396K10Rik|Cytsb	sperm antigen with calponin homology and coiled-coil domains 1	protein-coding
mm_96011.1	chr11	59542731	59542747	+	1	NA	promoter-TSS (NM_145827)	promoter-TSS (NM_145827)	53	NM_145827	216799	Mm.54174	NM_145827	ENSMUSG00000032691	Nlrp3	AGTAVPRL|AII/AVP|Cias1|FCAS|FCU|MWS|Mmig1|NALP3|Pypaf1	NLR family, pyrin domain containing 3	protein-coding
mm_32714.1	chr4	116173390	116173400	+	1	NA	promoter-TSS (NM_001099295)	promoter-TSS (NM_001099295)	23	NM_001099295	67323	Mm.45442	NM_001099295	ENSMUSG00000078593	1700042G07Rik	-	RIKEN cDNA 1700042G07 gene	protein-coding
mm_106097.1	chr11	116199041	116199090	-	1	NA	promoter-TSS (NM_015729)	promoter-TSS (NM_015729)	-20	NM_015729	11430	Mm.356689	NM_015729	ENSMUSG00000020777	Acox1	AOX|Acox|D130055E20Rik|Paox	acyl-Coenzyme A oxidase 1, palmitoyl	protein-coding
mm_122289.1	chr14	34541961	34541995	-	1	NA	exon (NM_001039071, exon 11 of 13)	exon (NM_001039071, exon 11 of 13)	-19177	NM_030062	78243	Mm.117483	NM_030062	ENSMUSG00000021797	9230112D13Rik	-	RIKEN cDNA 9230112D13 gene	protein-coding
mm_72549.1	chr8	84021363	84021374	+	1	NA	promoter-TSS (NM_028877)	promoter-TSS (NM_028877)	-106	NM_028877	74337	Mm.250943	NM_028877	ENSMUSG00000047986	Palm3	4432412L15Rik|AL024300	paralemmin 3	protein-coding
mm_87936.1	chr10	62699376	62699377	+	1	NA	intron (NM_001033260, intron 1 of 3)	L1_Rod|LINE|L1	16868	NR_106074	102465987		NR_106074	ENSMUSG00000105329	Mir7215	mmu-mir-7215	microRNA 7215	ncRNA
mm_51518.1	chr6	83147474	83147515	+	1	NA	exon (NM_133641, exon 3 of 12)	exon (NM_133641, exon 3 of 12)	8885	NM_023790	75659	Mm.130665	NM_023790	ENSMUSG00000030032	Wdr54	1700030E05Rik	WD repeat domain 54	protein-coding
mm_54756.1	chr6	41034376	41034389	-	1	NA	exon (NM_023333, exon 2 of 5)	exon (NM_023333, exon 2 of 5)	1127	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_68536.1	chr7	113369327	113369395	-	1	NA	promoter-TSS (NM_133700)	promoter-TSS (NM_133700)	-22	NM_133700	68815	Mm.238034	NM_133700	ENSMUSG00000038187	Btbd10	1110056N09Rik|Gmrp1	BTB (POZ) domain containing 10	protein-coding
mm_139177.1	chr17	47593445	47593475	+	1	NA	promoter-TSS (NM_007632)	promoter-TSS (NM_007632)	-7	NM_007632	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_121028.1	chr14	79704089	79704099	+	1	NA	intron (NR_045060, intron 1 of 3)	intron (NR_045060, intron 1 of 3)	1174	NR_045060	73989	Mm.107775	NR_045060		4930452G13Rik	-	RIKEN cDNA 4930452G13 gene	ncRNA
mm_153069.1	chr19	32238797	32238838	-	1	NA	intron (NM_001168525, intron 4 of 9)	intron (NM_001168525, intron 4 of 9)	-27804	NM_001168526	208449	Mm.329810	NM_144792	ENSMUSG00000040451	Sgms1	9530058O11Rik|AI841905|C80702|Mob|Sms1|Sor1|Tmem23	sphingomyelin synthase 1	protein-coding
mm_123946.1	chr14	73381332	73381344	-	1	NA	intron (NM_008410, intron 1 of 5)	B1F2|SINE|Alu	3933	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_128464.1	chr15	50809747	50809753	-	1	NA	intron (NM_001310485, intron 5 of 7)	intron (NM_001310485, intron 5 of 7)	79299	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_102326.1	chr11	57801412	57801432	-	1	NA	promoter-TSS (NM_001081168)	promoter-TSS (NM_001081168)	45	NR_131042	76516	Mm.28485	NR_131042	ENSMUSG00000087165	2010001A14Rik	-	RIKEN cDNA 2010001A14 gene	ncRNA
mm_134735.1	chr16	22899249	22899257	-	1	NA	non-coding (NR_075099, exon 6 of 6)	non-coding (NR_075099, exon 6 of 6)	-4867	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_20270.1	chr2	126676112	126676140	-	1	NA	promoter-TSS (NM_010249)	promoter-TSS (NM_010249)	211	NM_001271470	14391	Mm.293266	NM_010249	ENSMUSG00000027361	Gabpb1	BABPB2|E4TF1|E4TF1-47|E4TF1-53|E4Tf1B|GABPB|GABPB-1|GABPB-2|GABPB1-1|GABPB1-2|NRF2B1|NRF2B2	GA repeat binding protein, beta 1	protein-coding
mm_122787.1	chr14	54413988	54414084	-	1	NA	intron (NM_011405, intron 2 of 11)	intron (NM_011405, intron 2 of 11)	3643	NM_001253679	20540	Mm.142455	NM_011405	ENSMUSG00000000958	Slc7a7	AI790233|my+lat1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 7	protein-coding
mm_99701.1	chr11	106160124	106160145	+	1	NA	promoter-TSS (NM_172397)	promoter-TSS (NM_172397)	8	NM_172397	67803	Mm.21687	NM_172397	ENSMUSG00000040699	Limd2	0610025L06Rik|AI413966	LIM domain containing 2	protein-coding
mm_132858.1	chr16	48310166	48310188	+	1	NA	promoter-TSS (NM_028615)	promoter-TSS (NM_028615)	-97	NM_028615	73703	Mm.27857	NM_028615	ENSMUSG00000072419	Dppa2	2410088E07Rik|C80932|D19Mgi18|ECAT15-2	developmental pluripotency associated 2	protein-coding
mm_42412.1	chr5	115203989	115203997	+	1	NA	Intergenic	Intergenic	-9612	NM_001310712	29867	Mm.38551	NM_013879	ENSMUSG00000029544	Cabp1	caldendrin	calcium binding protein 1	protein-coding
mm_167796.1	chr9	123924976	123925017	+	1	NA	Intergenic	CpG	43696	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_78226.1	chr9	21588583	21588605	+	1	NA	TTS (NM_138303)	TTS (NM_138303)	-4128	NM_178619	69773	Mm.39704	NM_178619	ENSMUSG00000048429	Timm29	1810026J23Rik	translocase of inner mitochondrial membrane 29	protein-coding
mm_114847.1	chr13	92811805	92811805	+	1	NA	Intergenic	U2|snRNA|snRNA	-16987	NM_011582	21828	Mm.20865	NM_011582	ENSMUSG00000021702	Thbs4	TSP4	thrombospondin 4	protein-coding
mm_121119.1	chr14	101840482	101840492	+	1	NA	promoter-TSS (NM_001347628)	promoter-TSS (NM_001347628)	-136	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_121955.1	chr14	24429817	24429830	-	1	NA	Intergenic	Intergenic	57223	NM_001081247	218832	Mm.343610	NM_183157	ENSMUSG00000025280	Polr3a	9330175N20Rik|BC053071|RPC1|RPC155	polymerase (RNA) III (DNA directed) polypeptide A	protein-coding
mm_8247.1	chr1	138614414	138614424	-	1	NA	intron (NM_001311148, intron 1 of 7)	intron (NM_001311148, intron 1 of 7)	5338	NM_021605	59125	Mm.143817	NM_021605	ENSMUSG00000026393	Nek7	2810460C19Rik|AU020186	NIMA (never in mitosis gene a)-related expressed kinase 7	protein-coding
mm_1307.1	chr1	64927713	64927723	+	1	NA	intron (NM_001039493, intron 2 of 7)	PB1D10|SINE|Alu	29106	NM_001039493	241075	Mm.239534	NM_175509	ENSMUSG00000051344	Plekhm3	9430067K14Rik|A230102O09Rik|AI449570|DAPR|Plekhm1l	pleckstrin homology domain containing, family M, member 3	protein-coding
mm_3945.1	chr1	163929779	163929809	+	1	NA	promoter-TSS (NM_028776)	promoter-TSS (NM_028776)	29	NM_028776	240880	Mm.389213	NM_028776	ENSMUSG00000026584	Scyl3	1200016D23Rik|6030457O16|AW214499|Pace1	SCY1-like 3 (S. cerevisiae)	protein-coding
mm_135148.1	chr16	35857575	35857592	-	1	NA	exon (NM_001039530, exon 6 of 17)	exon (NM_001039530, exon 6 of 17)	13799	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_165942.1	chr4	79737197	79737200	-	1	NA	Intergenic	Intergenic	-1097015	NM_031202	22178	Mm.30438	NM_031202	ENSMUSG00000005994	Tyrp1	Oca3|TRP-1|TRP1|Tyrp|b|brown|isa	tyrosinase-related protein 1	protein-coding
mm_151122.1	chr19	47865574	47865581	+	1	NA	promoter-TSS (NM_026619)	promoter-TSS (NM_026619)	32	NM_030051	68214	Mm.63791	NM_026619	ENSMUSG00000025069	Gsto2	1700020F09Rik|4930425C18Rik|GSTO 2-2	glutathione S-transferase omega 2	protein-coding
mm_90209.1	chr10	120634864	120634872	+	1	NA	Intergenic	(T)n|Simple_repeat|Simple_repeat	-130864	NR_038000	70874	Mm.427286	NR_038000	ENSMUSG00000044544	4921513I03Rik	-	RIKEN cDNA 4921513I03 gene	ncRNA
mm_22276.1	chr2	178635826	178635830	-	1	NA	Intergenic	RMER17C|LTR|ERVK	205313	NM_198656	381409	Mm.330860	NM_198656	ENSMUSG00000039155	Cdh26	Gm1010	cadherin-like 26	protein-coding
mm_93785.1	chr10	120476919	120476936	-	1	NA	promoter-TSS (NM_010441)	promoter-TSS (NM_010441)	-458	NM_010441	15364	Mm.157190	NM_010441	ENSMUSG00000056758	Hmga2	9430083A20Rik|HMGI-C|Hmgic|pg|pygmy	high mobility group AT-hook 2	protein-coding
mm_95217.1	chr11	43838944	43838944	+	1	NA	intron (NM_001284380, intron 1 of 3)	B3|SINE|B2	-2455	NM_007416	11548	Mm.39086	NM_007416	ENSMUSG00000050541	Adra1b	[a]1b	adrenergic receptor, alpha 1b	protein-coding
mm_63356.1	chr7	126983480	126983480	+	1	NA	Intergenic	B1_Mur2|SINE|Alu	7566	NM_001347656	52858	Mm.28219	NM_026638	ENSMUSG00000030682	Cdipt	9530042F15Rik|D7Bwg0575e|Pis|Pis1	CDP-diacylglycerol--inositol 3-phosphatidyltransferase (phosphatidylinositol synthase)	protein-coding
mm_134185.1	chr16	10963356	10963409	-	1	NA	exon (NM_019980, exon 3 of 4)	exon (NM_019980, exon 3 of 4)	29739	NM_019980	56722	Mm.294753	NM_019980	ENSMUSG00000022500	Litaf	3222402J11Rik|C85531|N4WBP3|TBX1	LPS-induced TN factor	protein-coding
mm_15766.1	chr2	164316793	164316797	+	1	NA	promoter-TSS (NM_013679)	promoter-TSS (NM_013679)	44	NM_013679	20945	Mm.439686	NM_013679	ENSMUSG00000017000	Svs6	MSVSP99|Svp6	seminal vesicle secretory protein 6	protein-coding
mm_103830.1	chr11	83020116	83020146	-	1	NA	intron (NM_181545, intron 1 of 5)	intron (NM_181545, intron 1 of 5)	591	NM_001167743	276950	Mm.491599	NM_181545	ENSMUSG00000035208	Slfn8	-	schlafen 8	protein-coding
mm_32633.1	chr4	115000175	115000189	+	1	NA	promoter-TSS (NM_009185)	promoter-TSS (NM_009185)	64	NM_001304555	20460	Mm.3988	NM_009185	ENSMUSG00000028718	Stil	Sil	Scl/Tal1 interrupting locus	protein-coding
mm_109036.1	chr12	104101161	104101169	+	1	NA	promoter-TSS (NM_172953)	promoter-TSS (NM_172953)	52	NM_172953	268591	Mm.73172	NM_172953	ENSMUSG00000041550	Serpina5	4933415L04|PAI-3|Pci	serine (or cysteine) peptidase inhibitor, clade A, member 5	protein-coding
mm_133412.1	chr16	85072070	85072101	+	1	NA	intron (NM_007471, intron 5 of 15)	intron (NM_007471, intron 5 of 15)	99874	NR_045889	100038614	Mm.441351	NR_045889		Gm10791	ENSMUSG00000074933	predicted gene 10791	ncRNA
mm_117729.1	chr13	95604689	95604714	-	1	NA	exon (NM_010169, exon 2 of 2)	exon (NM_010169, exon 2 of 2)	13732	NM_010169	14062	Mm.24816	NM_010169	ENSMUSG00000048376	F2r	AI482343|Cf2r|Par1|ThrR	coagulation factor II (thrombin) receptor	protein-coding
mm_137232.1	chr17	24414641	24414691	+	1	NA	promoter-TSS (NM_001080128)	promoter-TSS (NM_001080128)	-9	NM_001080127	19826	Mm.1951	NM_009070	ENSMUSG00000034681	Rnps1	-	ribonucleic acid binding protein S1	protein-coding
mm_98903.1	chr11	98023072	98023085	+	1	NA	promoter-TSS (NM_031173)	promoter-TSS (NM_031173)	-451	NM_001282978	12295	Mm.41252	NM_031173	ENSMUSG00000020882	Cacnb1	CAB1|Cchb1|Cchlb1	calcium channel, voltage-dependent, beta 1 subunit	protein-coding
mm_86705.1	chr10	18844967	18844977	+	1	NA	promoter-TSS (NM_022032)	promoter-TSS (NM_022032)	-99	NM_022032	64058	Mm.28209	NM_022032	ENSMUSG00000019851	Perp	1110017A08Rik|KCP1|KRTCAP1|PIGPC1|THW	PERP, TP53 apoptosis effector	protein-coding
mm_69236.1	chr7	127708850	127708877	-	1	NA	promoter-TSS (NM_009746)	promoter-TSS (NM_009746)	-97	NM_001347652	12055	Mm.89667	NM_009746	ENSMUSG00000030814	Bcl7c	C230096E12Rik	B cell CLL/lymphoma 7C	protein-coding
mm_151852.1	chr19	5796384	5796483	-	1	NA	promoter-TSS (NR_144621)	promoter-TSS (NR_144621)	-452	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_147653.1	chr18	60502465	60502477	-	1	NA	promoter-TSS (NM_134133)	promoter-TSS (NM_134133)	-488	NM_134133	106878	Mm.273197	NM_134133	ENSMUSG00000038059	Smim3	2010002N04Rik|AI195350|AW561905|Nid67|cI-41	small integral membrane protein 3	protein-coding
mm_106926.1	chr12	8351572	8351576	+	1	NA	Intergenic	Intergenic	38141	NM_021429	58240	Mm.309954	NM_021429	ENSMUSG00000020605	Hs1bp3	-	HCLS1 binding protein 3	protein-coding
mm_103490.1	chr11	76541877	76541913	-	1	NA	intron (NM_198894, intron 1 of 22)	intron (NM_198894, intron 1 of 22)	29489	NM_198895	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_120179.1	chr14	61174882	61174904	+	1	NA	intron (NM_172809, intron 3 of 9)	RSINE1|SINE|B4	36436	NM_172809	50720	Mm.440703	NM_015788	ENSMUSG00000048279	Sacs	A230052M14|DNAJC29|E130115J16Rik|mKIAA0730	sacsin	protein-coding
mm_141089.1	chr17	25972085	25972088	-	1	NA	intron (NM_001347334, intron 2 of 11)	L1MB5|LINE|L1	-6581	NM_015830	50817	Mm.216072	NM_015830	ENSMUSG00000037326	Capn15	Solh	calpain 15	protein-coding
mm_146641.1	chr18	10735287	10735292	-	1	NA	intron (NM_144860, intron 1 of 20)	intron (NM_144860, intron 1 of 20)	9664	NM_144860	225164	Mm.21500	NM_144860	ENSMUSG00000024294	Mib1	DIP-1|E430019M12Rik|Mib|mKIAA1323	mindbomb E3 ubiquitin protein ligase 1	protein-coding
mm_42398.1	chr5	114942177	114942212	+	1	NA	promoter-TSS (NM_028211)	promoter-TSS (NM_028211)	-8	NM_028211	72357	Mm.292672	NM_028211	ENSMUSG00000029559	2210016L21Rik	-	RIKEN cDNA 2210016L21 gene	protein-coding
mm_118401.1	chr13	119408161	119408180	-	1	NA	intron (NM_001308506, intron 1 of 16)	intron (NM_001308506, intron 1 of 16)	841	NM_008710	18115	Mm.132584	NM_008710	ENSMUSG00000025453	Nnt	4930423F13Rik|AI323702|BB168308	nicotinamide nucleotide transhydrogenase	protein-coding
mm_147514.1	chr18	52517680	52517686	-	1	NA	3' UTR (NM_010728, exon 7 of 7)	3' UTR (NM_010728, exon 7 of 7)	12038	NM_001286181	16948	Mm.172	NM_010728	ENSMUSG00000024529	Lox	AI893619|TSC-160|rrg	lysyl oxidase	protein-coding
mm_131476.1	chr16	17070324	17070336	+	1	NA	5' UTR (NM_023249, exon 1 of 5)	5' UTR (NM_023249, exon 1 of 5)	191	NM_001291047	106369	Mm.237941	NM_023249	ENSMUSG00000022773	Ypel1	0610009L05Rik|1700016N17Rik|1700019O22Rik|4921520K19Rik|4930511F14Rik|AV118478|DGL-1|Dgl1|Ppil2|mdgl-1	yippee-like 1 (Drosophila)	protein-coding
mm_142036.1	chr17	35258269	35258291	-	1	NA	Intergenic	Intergenic	-4814	NM_010380	14964	Mm.439675	NM_010380	ENSMUSG00000073411	H2-D1	H-2D|H2-D	histocompatibility 2, D region locus 1	protein-coding
mm_124073.1	chr14	78610169	78610182	-	1	NA	intron (NM_001081336, intron 12 of 28)	intron (NM_001081336, intron 12 of 28)	19115	NM_001253766	380921	Mm.89591	NM_001081336	ENSMUSG00000034731	Dgkh	5930402B05Rik|D130015C16|DGK	diacylglycerol kinase, eta	protein-coding
mm_3507.1	chr1	150107226	150107233	+	1	NA	3' UTR (NM_011198, exon 10 of 10)	3' UTR (NM_011198, exon 10 of 10)	7198	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_163547.1	chr13	20660579	20660582	-	1	NA	Intergenic	U2|snRNA|snRNA	-133533	NM_001281854	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_170186.1	chr17	62882518	62882523	-	1	NA	Intergenic	CpG-6536	-1203	NM_010109	13640	Mm.7978	NM_010109	ENSMUSG00000048915	Efna5	AL-1|AV158822|EFL-5|Ephrin-A5|Epl7|LERK-7|RAGS	ephrin A5	protein-coding
mm_88358.1	chr10	75936275	75936292	+	1	NA	exon (NM_175329, exon 2 of 4)	exon (NM_175329, exon 2 of 4)	710	NM_175329	103172	Mm.333849	NM_175329	ENSMUSG00000049422	Chchd10	1620401E04Rik|AI267078|Ndg2	coiled-coil-helix-coiled-coil-helix domain containing 10	protein-coding
mm_46739.1	chr5	110810116	110810133	-	1	NA	promoter-TSS (NM_009469)	promoter-TSS (NM_009469)	-43	NM_001347394	22241	Mm.271898	NM_009469	ENSMUSG00000029512	Ulk1	AU041434|Unc51.1|mKIAA0722	unc-51 like kinase 1	protein-coding
mm_170808.1	chr2	175931120	175931136	-	1	NA	promoter-TSS (NM_001177404).2	promoter-TSS (NM_001177404).2	-28	NM_001177406	100303732	Mm.484983	NM_001177404	ENSMUSG00000095199	Zfp967	Gm14431|OTTMUSG00000016608	zinc finger protein 967	protein-coding
mm_91180.1	chr10	20891516	20891555	-	1	NA	Intergenic	Intergenic	-61012	NM_026203	52906	Mm.253280	NM_026203	ENSMUSG00000019986	Ahi1	1700015F03Rik|Ahi-1|D10Bwg0629e	Abelson helper integration site 1	protein-coding
mm_21731.1	chr2	164743156	164743181	-	1	NA	promoter-TSS (NM_027961)	promoter-TSS (NM_027961)	99	NM_027961	71856	Mm.330770	NM_027961	ENSMUSG00000076434	Wfdc3	1700015L13Rik|1700127F16Rik	WAP four-disulfide core domain 3	protein-coding
mm_451.1	chr1	36068644	36068672	+	1	NA	exon (NM_015818, exon 1 of 2)	exon (NM_015818, exon 1 of 2)	258	NM_015818	50785	Mm.213566	NM_015818	ENSMUSG00000045216	Hs6st1	6Ost1	heparan sulfate 6-O-sulfotransferase 1	protein-coding
mm_140060.1	chr17	74670277	74670308	+	1	NA	exon (NM_007566, exon 64 of 73)	exon (NM_007566, exon 64 of 73)	-47458	NM_152817	74196	Mm.209503	NM_152817	ENSMUSG00000024078	Ttc27	2610511O17Rik	tetratricopeptide repeat domain 27	protein-coding
mm_53310.1	chr6	129181923	129181933	+	1	NA	intron (NM_053109, intron 1 of 4)	intron (NM_053109, intron 1 of 4)	1313	NM_053109	93694	Mm.197536	NM_053109	ENSMUSG00000030157	Clec2d	Clr-b|Clrb|Ocil	C-type lectin domain family 2, member d	protein-coding
mm_17820.1	chr2	33781701	33781715	-	1	NA	intron (NM_175184, intron 7 of 9)	intron (NM_175184, intron 7 of 9)	-24108	NR_045729	320482	Mm.442057	NR_045729	ENSMUSG00000086484	Nron	A630071L07Rik|Gm24353	non-protein coding RNA, repressor of NFAT	ncRNA
mm_57424.1	chr6	124914036	124914044	-	1	NA	3' UTR (NM_026988, exon 5 of 5)	3' UTR (NM_026988, exon 5 of 5)	-2335	NM_008479	16768	Mm.4528	NM_008479	ENSMUSG00000030124	Lag3	CD223|LAG-3|Ly66	lymphocyte-activation gene 3	protein-coding
mm_72652.1	chr8	84842500	84842503	+	1	NA	3' UTR (NM_007591, exon 9 of 9)	3' UTR (NM_007591, exon 9 of 9)	-1836	NM_009010	19358	Mm.255539	NM_009010	ENSMUSG00000003813	Rad23a	2310040P19Rik|AL024030|HR23A|mHR23A	RAD23 homolog A, nucleotide excision repair protein	protein-coding
mm_57423.1	chr6	124914007	124914021	-	1	NA	3' UTR (NM_026988, exon 5 of 5)	3' UTR (NM_026988, exon 5 of 5)	-2309	NM_008479	16768	Mm.4528	NM_008479	ENSMUSG00000030124	Lag3	CD223|LAG-3|Ly66	lymphocyte-activation gene 3	protein-coding
mm_146337.1	chr18	82475134	82475151	+	1	NA	promoter-TSS (NM_010777)	promoter-TSS (NM_010777)	19	NM_001025245	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_151564.1	chr19	60712868	60712876	+	1	NA	Intergenic	MLT1H|LTR|ERVL-MaLR	-43115	NM_178421	332397	Mm.186390	NM_178421	ENSMUSG00000072437	Nanos1	NOS-1	nanos homolog 1 (Drosophila)	protein-coding
mm_139272.1	chr17	48146380	48146387	+	1	NA	promoter-TSS (NM_177824)	promoter-TSS (NM_177824)	-76	NM_001177896	328829	Mm.466999	NM_177824	ENSMUSG00000073386	9830107B12Rik	Trem5	RIKEN cDNA 9830107B12 gene	protein-coding
mm_132505.1	chr16	36955322	36955332	+	1	NA	exon (NM_008225, exon 7 of 14)	exon (NM_008225, exon 7 of 14)	20344	NM_008225	15163	Mm.4091	NM_008225	ENSMUSG00000022831	Hcls1	AW213261|HS1	hematopoietic cell specific Lyn substrate 1	protein-coding
mm_147231.1	chr18	38211958	38211995	-	1	NA	Intergenic	(CGG)n|Simple_repeat|Simple_repeat	-2214	NM_029357	75599	Mm.36560	NM_029357	ENSMUSG00000051375	Pcdh1	2010005A06Rik|AI585920	protocadherin 1	protein-coding
mm_23373.1	chr3	55503153	55503153	+	1	NA	intron (NM_019978, intron 14 of 16)	intron (NM_019978, intron 14 of 16)	41395	NM_001195540	13175	Mm.393242	NM_019978	ENSMUSG00000027797	Dclk1	1700113D08Rik|2810480F11Rik|AI836758|Click-I|Cpg16|Dcamkl1|Dcl|Dclk|mKIAA0369	doublecortin-like kinase 1	protein-coding
mm_117123.1	chr13	60897440	60897455	-	1	NA	promoter-TSS (NM_007797)	promoter-TSS (NM_007797)	0	NM_007797	13025	Mm.30144	NM_007797	ENSMUSG00000074874	Ctla2b	AW545568|Ctla-2b	cytotoxic T lymphocyte-associated protein 2 beta	protein-coding
mm_60178.1	chr7	42271097	42271098	+	1	NA	intron (NM_001105058, intron 3 of 5)	Lx3_Mus|LINE|L1	11044	NM_001105058	637873	Mm.469899	NM_001105058	ENSMUSG00000090967	Vmn2r61	Casr-rs2|EG637873|Gprc2a-rs2	vomeronasal 2, receptor 61	protein-coding
mm_91174.1	chr10	20725005	20725022	-	1	NA	promoter-TSS (NM_013875)	promoter-TSS (NM_013875)	65	NM_013875	29863	Mm.425617	NM_013875	ENSMUSG00000019990	Pde7b	-	phosphodiesterase 7B	protein-coding
mm_81588.1	chr9	110476986	110476999	+	1	NA	promoter-TSS (NM_001163569)	promoter-TSS (NM_001163569)	-2	NM_001163569	16578	Mm.42170	NM_010628	ENSMUSG00000032489	Kif9	-	kinesin family member 9	protein-coding
mm_119183.1	chr14	32201938	32201995	+	1	NA	promoter-TSS (NM_011960)	promoter-TSS (NM_011960)	-5	NM_011960	26430	Mm.15962	NM_011960	ENSMUSG00000021911	Parg	AI413217	poly (ADP-ribose) glycohydrolase	protein-coding
mm_171620.1	chr4	153153043	153153055	+	1	NA	Intergenic	(TTAGGG)n|Simple_repeat|Simple_repeat	329781	NM_001099299	230959	Mm.318874	NM_001099299	ENSMUSG00000039546	Ajap1	Gm573	adherens junction associated protein 1	protein-coding
mm_76295.1	chr8	84203522	84203527	-	1	NA	Intergenic	Intergenic	-4994	NR_029740	387216		NR_029740	ENSMUSG00000065611	Mir23a	Mirn23a|mir-23a|mmu-mir-23a	microRNA 23a	ncRNA
mm_146542.1	chr18	5593928	5593942	-	1	NA	intron (NM_011546, intron 1 of 7)	intron (NM_011546, intron 1 of 7)	-1498	NR_033552	791318	Mm.84339	NR_033552	ENSMUSG00000063087	Gm10125	ENSMUSG00000063087|Zeb1os	predicted gene 10125	ncRNA
mm_131174.1	chr16	7069826	7069846	+	1	NA	promoter-TSS (NM_183188)	promoter-TSS (NM_183188)	1	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_121270.1	chr14	103347064	103347081	+	1	NA	promoter-TSS (NM_207215)	promoter-TSS (NM_207215)	-272	NM_207215	105689	Mm.6478	NM_207215	ENSMUSG00000033004	Mycbp2	AU023734|AW107953|AW546647|C130061D10Rik|Pam|Phr1|R75243	MYC binding protein 2	protein-coding
mm_135485.1	chr16	46010356	46010437	-	1	NA	promoter-TSS (NM_001134480)	promoter-TSS (NM_001134480)	17	NM_001134480	433022	Mm.380993	NM_001134480	ENSMUSG00000087141	Plcxd2	AW494639|EG433022	phosphatidylinositol-specific phospholipase C, X domain containing 2	protein-coding
mm_142354.1	chr17	43630311	43630313	-	1	NA	promoter-TSS (NM_198418)	promoter-TSS (NM_198418)	-13	NM_001161367	210510	Mm.329058	NM_198418	ENSMUSG00000040140	Tdrd6	AB097085|Tdr2	tudor domain containing 6	protein-coding
mm_118699.1	chr14	22143127	22143138	+	1	NA	intron (NM_028275, intron 2 of 6)	L1_Rod|LINE|L1	123420	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_135472.1	chr16	45887488	45887530	-	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-43131	NM_001252442	208177	Mm.211477	NM_153412	ENSMUSG00000033149	Phldb2	AV253284|C820004H04Rik|LL5b|LL5beta	pleckstrin homology like domain, family B, member 2	protein-coding
mm_106712.1	chr12	3826579	3826591	+	1	NA	intron (NM_001271753, intron 1 of 22)	RSINE1|SINE|B4	19425	NM_001271753	13435	Mm.5001	NM_007872	ENSMUSG00000020661	Dnmt3a	MmuIIIA	DNA methyltransferase 3A	protein-coding
mm_99867.1	chr11	109397541	109397639	+	1	NA	3' UTR (NM_010303, exon 4 of 4)	3' UTR (NM_010303, exon 4 of 4)	-28356	NM_025275	13929	Mm.211850	NM_025275	ENSMUSG00000020610	Amz2	AA408420|ESTM12|X83328	archaelysin family metallopeptidase 2	protein-coding
mm_169592.1	chr15	30447639	30447646	-	1	NA	intron (NM_008729, intron 2 of 22)	L1Md_T|LINE|L1	275049	NM_008729	18163	Mm.321648	NM_008729	ENSMUSG00000022240	Ctnnd2	Catnd2|Nprap|neurojugin	catenin (cadherin associated protein), delta 2	protein-coding
mm_169560.1	chr15	12118740	12118745	+	1	NA	intron (NM_011767, intron 2 of 19)	CpG-4794	891	NM_011767	22763	Mm.273496	NM_011767	ENSMUSG00000022201	Zfr	C920030H05Rik	zinc finger RNA binding protein	protein-coding
mm_169284.1	chr13	97137865	97137876	-	1	NA	promoter-TSS (NM_001271464)	promoter-TSS (NM_001271464)	56	NM_021552	59050	Mm.390634	NM_021552	ENSMUSG00000060739	Nsa2	5730427N09Rik|LNR42|Nsa2p|Tinp1|Yr29	NSA2 ribosome biogenesis homolog	protein-coding
mm_15812.1	chr2	164501503	164501516	+	1	NA	exon (NM_133779, exon 8 of 12)	exon (NM_133779, exon 8 of 12)	3984	NM_133779	78928	Mm.28228	NM_133779	ENSMUSG00000017721	Pigt	2510012P17Rik|4930534E15Rik|CGI-06|NDAP|Ndap7	phosphatidylinositol glycan anchor biosynthesis, class T	protein-coding
mm_51321.1	chr6	72314897	72314917	+	1	NA	TTS (NM_001282071)	TTS (NM_001282071)	10297	NM_147779	20388	Mm.46033	NM_147779	ENSMUSG00000056370	Sftpb	AI562151|SF-B|SP-B|Sftp-3|Sftp3	surfactant associated protein B	protein-coding
mm_164821.1	chr18	35562332	35562357	+	1	NA	intron (NM_010771, intron 1 of 14)	CpG	186	NM_010771	17184	Mm.215034	NM_010771	ENSMUSG00000037236	Matr3	1110061A14Rik|2810017I02Rik|AI841759|AW555618|D030046F20Rik|mKIAA0723	matrin 3	protein-coding
mm_62154.1	chr7	97138513	97138524	+	1	NA	intron (NM_001162477, intron 1 of 9)	ORR1D2|LTR|ERVL-MaLR	56767	NM_010248	14389	Mm.42033	NM_010248	ENSMUSG00000004508	Gab2	AI463667|D130058I17Rik|p97	growth factor receptor bound protein 2-associated protein 2	protein-coding
mm_99505.1	chr11	103042985	103042993	+	1	NA	intron (NM_008707, intron 1 of 11)	intron (NM_008707, intron 1 of 11)	14427	NM_008707	18107	Mm.10265	NM_008707	ENSMUSG00000020936	Nmt1	AW536594	N-myristoyltransferase 1	protein-coding
mm_27623.1	chr3	59344347	59344367	-	1	NA	promoter-TSS (NM_001162884)	promoter-TSS (NM_001162884)	-101	NM_001162884	242050	Mm.228086	NM_001162884	ENSMUSG00000036334	Igsf10	6530405F15Rik|9030224D03|AA409708|AA536958|AI414626|Adlican2|CMF608	immunoglobulin superfamily, member 10	protein-coding
mm_92515.1	chr10	78464888	78464944	-	1	NA	promoter-TSS (NM_172134)	promoter-TSS (NM_172134)	32	NM_172134	216134	Mm.206159	NM_172134	ENSMUSG00000032788	Pdxk	2310036D04Rik|AA119688|C77999	pyridoxal (pyridoxine, vitamin B6) kinase	protein-coding
mm_156722.1	chrX	159840061	159840064	+	1	NA	promoter-TSS (NM_001135728)	promoter-TSS (NM_001135728)	-406	NM_001135728	58194	Mm.286495	NM_021389	ENSMUSG00000040990	Sh3kbp1	1200007H22Rik|1700125L08Rik|5830464D22Rik|AI447724|Cin85|IN85|Ruk|Seta	SH3-domain kinase binding protein 1	protein-coding
mm_59595.1	chr7	28137587	28137596	+	1	NA	exon (NM_001164655, exon 4 of 20)	exon (NM_001164655, exon 4 of 20)	8125	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_64985.1	chr7	16916041	16916060	-	1	NA	3' UTR (NM_007590, exon 6 of 6)	3' UTR (NM_007590, exon 6 of 6)	7982	NM_007590	12315	Mm.288630	NM_007590	ENSMUSG00000019370	Calm3	CaMA|R75142	calmodulin 3	protein-coding
mm_162880.1	chr10	99693127	99693128	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-51207	NR_038018	100417125	Mm.391428	NR_038018		Gm18409	-	mediator of cell motility 1 pseudogene	pseudo
mm_124928.1	chr15	12179653	12179664	+	1	NA	intron (NM_011767, intron 17 of 19)	intron (NM_011767, intron 17 of 19)	8166	NR_035443	100316684		NR_035443	ENSMUSG00000084592	Mir1898	Mirn1898|mmu-mir-1898	microRNA 1898	ncRNA
mm_107299.1	chr12	30910560	30910577	+	1	NA	intron (NM_001110239, intron 1 of 5)	intron (NM_001110239, intron 1 of 5)	1044	NM_021330	11431	Mm.359831	NM_021330	ENSMUSG00000044573	Acp1	4632432E04Rik|AI427468|Acp-1|LMW-PTP|Lmptp	acid phosphatase 1, soluble	protein-coding
mm_93467.1	chr10	111010267	111010273	-	1	NA	promoter-TSS (NM_172554)	promoter-TSS (NM_172554)	-204	NM_172554	320150	Mm.339281	NM_172554	ENSMUSG00000035798	Zdhhc17	A230053P19Rik|BB187739|D130071N24Rik|Hip14	zinc finger, DHHC domain containing 17	protein-coding
mm_118180.1	chr13	107021762	107021772	-	1	NA	promoter-TSS (NR_015471)	promoter-TSS (NR_015471)	347	NM_001145779	16563	Mm.355686	NM_008442	ENSMUSG00000021693	Kif2a	C530030B14Rik|Kif2|Kns2|M-kinesin	kinesin family member 2A	protein-coding
mm_70109.1	chr7	142664786	142664831	-	1	NA	intron (NR_002855, intron 1 of 3)	intron (NR_002855, intron 1 of 3)	2008	NM_001315488	16002	Mm.3862	NM_010514	ENSMUSG00000048583	Igf2	AL033362|Igf-2|Igf-II|M6pr|Mpr|Peg2	insulin-like growth factor 2	protein-coding
mm_88965.1	chr10	81394997	81395052	+	1	NA	TTS (NM_001099917)	TTS (NM_001099917)	1960	NM_001099917	72273	Mm.253147	NM_001099917	ENSMUSG00000078439	Smim24	2210404O07Rik	small integral membrane protein 24	protein-coding
mm_70506.1	chr8	12915880	12915966	+	1	NA	promoter-TSS (NM_178076)	promoter-TSS (NM_178076)	30	NM_178076	17207	Mm.334413	NM_178076	ENSMUSG00000031442	Mcf2l	C130040G20Rik|Dbs|Ost|mKIAA0362	mcf.2 transforming sequence-like	protein-coding
mm_61389.1	chr7	73105348	73105354	+	1	NA	Intergenic	Intergenic	-3283	NR_046024	625243	Mm.261798	NR_046024	ENSMUSG00000108383	Gm6567	-	predicted gene 6567	ncRNA
mm_49907.1	chr6	38983326	38983338	+	1	NA	intron (NM_011539, intron 4 of 12)	L3|LINE|CR1	64346	NM_011539	21391	Mm.4054	NM_011539	ENSMUSG00000029925	Tbxas1	CYP5|CYP5A1|THAS|TS|TXAS|TXS	thromboxane A synthase 1, platelet	protein-coding
mm_231.1	chr1	17946998	17947007	+	1	NA	Intergenic	MYSERV6-int|LTR|ERVK	190049	NM_030033	78081	Mm.319913	NM_030033	ENSMUSG00000025774	Crisp4	9230112K08Rik	cysteine-rich secretory protein 4	protein-coding
mm_154960.1	chrX	36874352	36874368	+	1	NA	promoter-TSS (NM_001313696)	promoter-TSS (NM_001313696)	65	NM_019668	22209	Mm.395649	NM_019668	ENSMUSG00000016308	Ube2a	HHR6A|HR6A|Mhr6a	ubiquitin-conjugating enzyme E2A	protein-coding
mm_127047.1	chr15	96642589	96642599	+	1	NA	promoter-TSS (NM_001166456)	promoter-TSS (NM_001166456)	-251	NM_001166456	105727	Mm.103568	NM_134086	ENSMUSG00000023169	Slc38a1	AA408026|AA409865|AL022800|AU015942|NAT2	solute carrier family 38, member 1	protein-coding
mm_135602.1	chr16	51930007	51930023	-	1	NA	Intergenic	RMER19C|LTR|ERVK	-101534	NM_001033238	208650	Mm.328206	NM_001033238	ENSMUSG00000022637	Cblb	AI429560|AI851073|Cbl-b	Casitas B-lineage lymphoma b	protein-coding
mm_79698.1	chr9	60837865	60837898	+	1	NA	intron (NM_028283, intron 1 of 18)	intron (NM_028283, intron 1 of 18)	43333	NM_028283	72565	Mm.68819	NM_028283	ENSMUSG00000034485	Uaca	2700059D02Rik|nucling	uveal autoantigen with coiled-coil domains and ankyrin repeats	protein-coding
mm_59336.1	chr7	25463448	25463470	+	1	NA	3' UTR (NM_001039186, exon 8 of 8)	3' UTR (NM_001039186, exon 8 of 8)	14166	NM_001039185	26365	Mm.322502	NM_011926	ENSMUSG00000074272	Ceacam1	Bgp|Bgp1|C-CAM|CD66a|Cc1|Cea-1|Cea-7|Cea1|Cea7|Hv-2|Hv2|MHVR|MHVR1|Mhv-1|bb-1|mCEA1|mmCGM1|mmCGM1a|mmCGM2	carcinoembryonic antigen-related cell adhesion molecule 1	protein-coding
mm_28826.1	chr3	96293954	96293985	-	1	NA	promoter-TSS (NM_010186)	promoter-TSS (NM_010186)	0	NM_010186	14129	Mm.150	NM_010186	ENSMUSG00000015947	Fcgr1	AI323638|AV092959|CD64|FcgammaRI|IGGHAFC	Fc receptor, IgG, high affinity I	protein-coding
mm_146367.1	chr18	82584567	82584578	+	1	NA	3' UTR (NM_010777, exon 7 of 7)	3' UTR (NM_010777, exon 7 of 7)	30064	NM_001025254	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_65473.1	chr7	25477608	25477634	-	1	NA	promoter-TSS (NM_001039186)	promoter-TSS (NM_001039186)	4	NM_001039185	26365	Mm.322502	NM_011926	ENSMUSG00000074272	Ceacam1	Bgp|Bgp1|C-CAM|CD66a|Cc1|Cea-1|Cea-7|Cea1|Cea7|Hv-2|Hv2|MHVR|MHVR1|Mhv-1|bb-1|mCEA1|mmCGM1|mmCGM1a|mmCGM2	carcinoembryonic antigen-related cell adhesion molecule 1	protein-coding
mm_147135.1	chr18	36280976	36280989	-	1	NA	promoter-TSS (NM_008989)	promoter-TSS (NM_008989)	-180	NM_008989	19290	Mm.231802	NM_008989	ENSMUSG00000043991	Pura	CAGER-1|Pur-alpha|ssCRE-BP	purine rich element binding protein A	protein-coding
mm_64311.1	chr7	141864585	141864595	+	1	NA	exon (NM_028801, exon 31 of 49)	exon (NM_028801, exon 31 of 49)	25518	NM_028801	74180	Mm.200752	NM_028801	ENSMUSG00000066108	Muc5b	2300002I04Rik|A130042M24|AV085033|MUC5|MUC9|mucin 5b	mucin 5, subtype B, tracheobronchial	protein-coding
mm_84915.1	chr9	80012852	80012855	-	1	NA	Intergenic	Intergenic	-34971	NM_001081243	70598	Mm.23049	NM_001081243	ENSMUSG00000034898	Filip1	5730485H21Rik|AI843021	filamin A interacting protein 1	protein-coding
mm_79711.1	chr9	61372360	61372383	+	1	NA	promoter-TSS (NM_009389)	promoter-TSS (NM_009389)	5	NM_001083927	21887	Mm.24255	NM_009389	ENSMUSG00000032280	Tle3	2610103N05Rik|ESG|Grg3a|Grg3b|mKIAA1547	transducin-like enhancer of split 3	protein-coding
mm_138683.1	chr17	35916952	35916958	+	1	NA	promoter-TSS (NM_025878)	promoter-TSS (NM_025878)	-241	NM_001163818	52040	Mm.29385	NM_175934	ENSMUSG00000039220	Ppp1r10	2610025H06Rik|Cat53|D17Ertd808e|Fb19|Pnuts	protein phosphatase 1, regulatory subunit 10	protein-coding
mm_5792.1	chr1	51915902	51915958	-	1	NA	promoter-TSS (NM_010863)	promoter-TSS (NM_010863)	48	NM_001290982	17912	Mm.3390	NM_010863	ENSMUSG00000018417	Myo1b	AA406997|MIH-L|MMIa	myosin IB	protein-coding
mm_52135.1	chr6	97951014	97951024	+	1	NA	intron (NM_001113198, intron 2 of 9)	intron (NM_001113198, intron 2 of 9)	21202	NM_001178049	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_3408.1	chr1	144004383	144004405	+	1	NA	promoter-TSS (NM_009061)	promoter-TSS (NM_009061)	-245	NM_009061	19735	Mm.28262	NM_009061	ENSMUSG00000026360	Rgs2	GOS8	regulator of G-protein signaling 2	protein-coding
mm_88795.1	chr10	80676779	80676799	+	1	NA	promoter-TSS (NM_021462)	promoter-TSS (NM_021462)	-496	NM_021462	17347	Mm.42126	NM_021462	ENSMUSG00000020190	Mknk2	2010016G11Rik|Gprk7|Mnk2	MAP kinase-interacting serine/threonine kinase 2	protein-coding
mm_167485.1	chr8	129253222	129253245	+	1	NA	Intergenic	Intergenic	-10397	NM_001346808	102635552		NM_001346808		Gm32856	-	predicted gene, 32856	protein-coding
mm_13826.1	chr2	119240632	119240647	+	1	NA	intron (NM_016907, intron 2 of 10)	(TG)n|Simple_repeat|Simple_repeat	3279	NM_016907	20732	Mm.104955	NM_016907	ENSMUSG00000027315	Spint1	HAI-1	serine protease inhibitor, Kunitz type 1	protein-coding
mm_134105.1	chr16	9995379	9995400	-	1	NA	Intergenic	CpG	-2856	NM_008170	14811	Mm.2953	NM_008170	ENSMUSG00000059003	Grin2a	GluN2A|NMDAR2A|NR2A	glutamate receptor, ionotropic, NMDA2A (epsilon 1)	protein-coding
mm_73478.1	chr8	106935721	106935776	+	1	NA	promoter-TSS (NM_009229)	promoter-TSS (NM_009229)	-2	NM_009229	20650	Mm.30228	NM_009229	ENSMUSG00000041308	Sntb2	Snt2	syntrophin, basic 2	protein-coding
mm_161095.1	chr12	91786436	91786436	-	1	NA	promoter-TSS (NM_175367)	promoter-TSS (NM_175367)	0	NM_175367	108800	Mm.23125	NM_175367	ENSMUSG00000020961	Ston2	4933401N24Rik|AI425999|AW544599	stonin 2	protein-coding
mm_101785.1	chr11	45955184	45955193	-	1	NA	promoter-TSS (NM_001290737)	promoter-TSS (NM_001290737)	0	NM_001290737	66628	Mm.269083	NM_001080969	ENSMUSG00000011254	Thg1l	-	tRNA-histidine guanylyltransferase 1-like (S. cerevisiae)	protein-coding
mm_66751.1	chr7	46712609	46712618	-	1	NA	exon (NM_011315, exon 3 of 4)	exon (NM_011315, exon 3 of 4)	-1962	NM_030233	78935	Mm.289866	NM_030233	ENSMUSG00000006763	Saal1	5031425D22Rik|SPACIA1	serum amyloid A-like 1	protein-coding
mm_97271.1	chr11	75765377	75765386	+	1	NA	3' UTR (NM_009536, exon 6 of 6)	3' UTR (NM_009536, exon 6 of 6)	-30428	NR_136933	102641247	Mm.411386	NR_136932		Gm12339	OTTMUSG00000006218	predicted gene 12339	ncRNA
mm_48660.1	chr5	145879858	145879872	-	1	NA	promoter-TSS (NM_007818)	promoter-TSS (NM_007818)	-11	NM_007818	13112	Mm.332844	NM_007818	ENSMUSG00000056035	Cyp3a11	AI256190|Cyp3a|IIIAm1|Pcn	cytochrome P450, family 3, subfamily a, polypeptide 11	protein-coding
mm_86664.1	chr10	17919312	17919314	+	1	NA	intron (NM_001033432, intron 1 of 3)	intron (NM_001033432, intron 1 of 3)	28754	NM_001033432	380629	Mm.276430	NM_001033432	ENSMUSG00000039879	Heca	Gm869|HDC|HDCL	hdc homolog, cell cycle regulator	protein-coding
mm_116898.1	chr13	55401188	55401197	-	1	NA	exon (NM_011392, exon 5 of 13)	exon (NM_011392, exon 5 of 13)	1544	NM_011392	20505	Mm.276355	NM_011392	ENSMUSG00000021490	Slc34a1	NaPi-IIa|Npt2|Npt2a|Slc17a2	solute carrier family 34 (sodium phosphate), member 1	protein-coding
mm_24443.1	chr3	90604642	90604660	+	1	NA	intron (NM_011311, intron 1 of 2)	intron (NM_011311, intron 1 of 2)	881	NM_011311	20198	Mm.3925	NM_011311	ENSMUSG00000001020	S100a4	18A2|42a|Capl|FSp1|Mts1|PeL98|metastasin|pk9a	S100 calcium binding protein A4	protein-coding
mm_154859.1	chrX	20658414	20658447	+	1	NA	promoter-TSS (NM_001276317)	promoter-TSS (NM_001276317)	-74	NM_001276317	22201	Mm.1104	NM_009457	ENSMUSG00000001924	Uba1	A1S9|Sbx|Ube-1|Ube1x	ubiquitin-like modifier activating enzyme 1	protein-coding
mm_2659.1	chr1	125677219	125677233	+	1	NA	5' UTR (NM_027677, exon 1 of 2)	5' UTR (NM_027677, exon 1 of 2)	230	NM_027677	71111	Mm.32727	NM_027677	ENSMUSG00000026343	Gpr39	4933415E13Rik	G protein-coupled receptor 39	protein-coding
mm_78842.1	chr9	44327042	44327058	+	1	NA	exon (NM_007875, exon 1 of 9)	exon (NM_007875, exon 1 of 9)	205	NM_007875	13478	Mm.18353	NM_007875	ENSMUSG00000032123	Dpagt1	AU021132|Dpagt2|GPT|Gnpta	dolichyl-phosphate (UDP-N-acetylglucosamine) acetylglucosaminephosphotransferase 1 (GlcNAc-1-P transferase)	protein-coding
mm_4451.1	chr1	172633065	172633075	+	1	NA	promoter-TSS (NM_026725)	promoter-TSS (NM_026725)	-96	NM_026725	68440	Mm.33024	NM_026725	ENSMUSG00000026544	Dusp23	1300005N15Rik|LDP-3	dual specificity phosphatase 23	protein-coding
mm_51926.1	chr6	91272102	91272113	+	1	NA	3' UTR (NM_001081437, exon 17 of 17)	3' UTR (NM_001081437, exon 17 of 17)	59343	NM_007992	14115	Mm.249146	NM_007992	ENSMUSG00000064080	Fbln2	5730577E14Rik|FIBL-2	fibulin 2	protein-coding
mm_56040.1	chr6	86684511	86684529	-	1	NA	promoter-TSS (NM_025665)	promoter-TSS (NM_025665)	-29	NM_025665	66618	Mm.182650	NM_025665	ENSMUSG00000001158	Snrnp27	2610209M04Rik|AI449063|AU022368|Ry1	small nuclear ribonucleoprotein 27 (U4/U6.U5)	protein-coding
mm_138952.1	chr17	44134814	44134822	+	1	NA	Intergenic	Intergenic	-29010	NM_199016	224794	Mm.255971	NM_199016	ENSMUSG00000023961	Enpp4	4933413N07Rik|AA986363|AI195364|E-NPP 4|Gm90|mKIAA0879	ectonucleotide pyrophosphatase/phosphodiesterase 4	protein-coding
mm_2706.1	chr1	128038523	128038525	+	1	NA	intron (NM_027678, intron 4 of 20)	intron (NM_027678, intron 4 of 20)	63947	NM_027678	226409	Mm.425048	NM_027678	ENSMUSG00000036086	Zranb3	4933425L19Rik|AH2|AI316834|C730006D09	zinc finger, RAN-binding domain containing 3	protein-coding
mm_156506.1	chrX	146962502	146962520	+	1	NA	promoter-TSS (NM_008312)	promoter-TSS (NM_008312)	-2	NM_008312	15560	Mm.439670	NM_008312	ENSMUSG00000041380	Htr2c	5-HT2C|5-HT2cR|5-HTR2C|5HT1c|Htr1c|SR1	5-hydroxytryptamine (serotonin) receptor 2C	protein-coding
mm_81098.1	chr9	106429387	106429397	+	1	NA	promoter-TSS (NM_001324533)	promoter-TSS (NM_001324533)	-19	NM_001324533	19944	Mm.288696	NM_009082	ENSMUSG00000048758	Rpl29	Rpl43	ribosomal protein L29	protein-coding
mm_29276.1	chr3	107555049	107555062	-	1	NA	promoter-TSS (NM_026261)	promoter-TSS (NM_026261)	18	NM_026261	67591	Mm.55982	NM_026261	ENSMUSG00000055891	Ubl4b	4930522D07Rik	ubiquitin-like 4B	protein-coding
mm_42678.1	chr5	119686858	119686865	+	1	NA	intron (NR_040416, intron 2 of 2)	intron (NR_040416, intron 2 of 2)	4357	NR_040416	433944	Mm.491053	NR_040416	ENSMUSG00000086847	Tbx3os2	Gm16065|OTTMUSG00000029666	T-box 3, opposite strand 2	ncRNA
mm_107533.1	chr12	40555701	40555713	+	1	NA	intron (NM_172803, intron 1 of 52)	MLT1F2|LTR|ERVL-MaLR	109654	NM_172803	238130	Mm.341423	NM_172803	ENSMUSG00000035954	Dock4	5330406C03|6330411N01Rik|AF263288|C030023J22|mKIAA0716	dedicator of cytokinesis 4	protein-coding
mm_124310.1	chr14	103154174	103154178	-	1	NA	intron (NM_207215, intron 59 of 84)	intron (NM_207215, intron 59 of 84)	-54610	NM_001347600	50789	Mm.214746	NM_015822	ENSMUSG00000022124	Fbxl3	AU041772|AW212966|FBK|Fbl3a|Fbxl3a|Ovtm|Play68	F-box and leucine-rich repeat protein 3	protein-coding
mm_56727.1	chr6	115661732	115661749	-	1	NA	intron (NM_029780, intron 1 of 16)	B1_Mus1|SINE|Alu	14895	NM_029780	110157	Mm.184163	NM_029780	ENSMUSG00000000441	Raf1	6430402F14Rik|AA990557|BB129353|Craf1|D830050J10Rik|Raf-1|c-Raf|v-Raf	v-raf-leukemia viral oncogene 1	protein-coding
mm_126753.1	chr15	85772226	85772250	+	1	NA	intron (NM_001113418, intron 2 of 7)	intron (NM_001113418, intron 2 of 7)	36462	NM_011144	19013	Mm.212789	NM_011144	ENSMUSG00000022383	Ppara	4933429D07Rik|AW742785|Nr1c1|PPAR-alpha|PPARalpha|Ppar	peroxisome proliferator activated receptor alpha	protein-coding
mm_27724.1	chr3	69004476	69004499	-	1	NA	promoter-TSS (NM_133786)	promoter-TSS (NM_133786)	83	NM_026641	68259	Mm.389451	NM_026641	ENSMUSG00000027778	Ift80	4921524P20Rik|Wdr56|mKIAA1374	intraflagellar transport 80	protein-coding
mm_44194.1	chr5	3596072	3596118	-	1	NA	promoter-TSS (NM_027777)	promoter-TSS (NM_027777)	29	NM_001293806	71382	Mm.379196	NM_027777	ENSMUSG00000005907	Pex1	5430414H02Rik|E330005K07Rik|ZWS1	peroxisomal biogenesis factor 1	protein-coding
mm_83530.1	chr9	46230277	46230290	-	1	NA	exon (NM_009692, exon 4 of 4)	exon (NM_009692, exon 4 of 4)	1653	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2|apo-AI|apoA-I	apolipoprotein A-I	protein-coding
mm_39290.1	chr5	4038984	4039001	+	1	NA	intron (NM_194462, intron 26 of 47)	intron (NM_194462, intron 26 of 47)	65705	NM_020010	13121	Mm.140158	NM_020010	ENSMUSG00000001467	Cyp51	AI426508|CYPLI|Cyp51a1|Ldm|P450-14DM|P450LI	cytochrome P450, family 51	protein-coding
mm_165454.1	chr2	157794226	157794232	-	1	NA	intron (NM_025680, intron 4 of 15)	intron (NM_025680, intron 4 of 15)	56828	NM_025680	66642	Mm.45193	NM_025680	ENSMUSG00000027649	Ctnnbl1	5730471K09Rik|NAP|NYD-SP19|P14L	catenin, beta like 1	protein-coding
mm_12362.1	chr2	69749981	69750002	+	1	NA	exon (NM_001081086, exon 14 of 14)	exon (NM_001081086, exon 14 of 14)	26903	NM_001081086	228005	Mm.11815	NM_001081086	ENSMUSG00000042133	Ppig	AU019516|AU022200|B230312B02Rik|CYP|SRCyp	peptidyl-prolyl isomerase G (cyclophilin G)	protein-coding
mm_101816.1	chr11	46389510	46389525	-	1	NA	promoter-TSS (NM_001281968)	promoter-TSS (NM_001281968)	-2	NM_001281965	16428	Mm.339927	NM_010583	ENSMUSG00000020395	Itk	Emt|Tcsk|Tsk	IL2 inducible T cell kinase	protein-coding
mm_45785.1	chr5	87337137	87337139	-	1	NA	promoter-TSS (NM_028094)	promoter-TSS (NM_028094)	57	NM_028094	72094	Mm.482739	NM_028094	ENSMUSG00000035780	Ugt2a3	2010321J07Rik	UDP glucuronosyltransferase 2 family, polypeptide A3	protein-coding
mm_141603.1	chr17	32787086	32787088	-	1	NA	intron (NM_172458, intron 1 of 3)	intron (NM_172458, intron 1 of 3)	460	NM_001346705	208292	Mm.38813	NM_172458	ENSMUSG00000024298	Zfp871	4732483N19|9030612M13Rik|AI118577|AI265322|mKIAA3006	zinc finger protein 871	protein-coding
mm_6300.1	chr1	71307508	71307516	-	1	NA	intron (NM_175210, intron 19 of 52)	intron (NM_175210, intron 19 of 52)	107398	NM_175210	74591	Mm.159251	NM_175210	ENSMUSG00000050296	Abca12	4832428G11Rik|4833417A11Rik	ATP-binding cassette, sub-family A (ABC1), member 12	protein-coding
mm_149907.1	chr19	25610565	25610576	+	1	NA	promoter-TSS (NM_177360)	promoter-TSS (NM_177360)	33	NM_177360	240590	Mm.62785	NM_177360	ENSMUSG00000042372	Dmrt3	-	doublesex and mab-3 related transcription factor 3	protein-coding
mm_145791.1	chr18	65244288	65244305	+	1	NA	intron (NR_105742, intron 4 of 6)	intron (NR_105742, intron 4 of 6)	-4565	NR_029600	387231		NR_029600	ENSMUSG00000065402	Mir122	Mir122a|Mirn122a|mir-122|mmu-mir-122	microRNA 122	ncRNA
mm_116137.1	chr13	29325711	29325724	-	1	NA	3' UTR (NM_144536, exon 16 of 16)	3' UTR (NM_144536, exon 16 of 16)	309462	NR_045075	77920	Mm.197051	NR_045073	ENSMUSG00000086363	A330102I10Rik	-	RIKEN cDNA A330102I10 gene	ncRNA
mm_25835.1	chr3	129202526	129202536	+	1	NA	intron (NM_011098, intron 1 of 4)	intron (NM_011098, intron 1 of 4)	2653	NM_001042504	18741	Mm.246804	NM_011098	ENSMUSG00000028023	Pitx2	9430085M16Rik|Brx1|Brx1b|Munc30|Otlx2|Ptx2|Rieg	paired-like homeodomain transcription factor 2	protein-coding
mm_114267.1	chr13	58128642	58128653	+	1	NA	promoter-TSS (NM_029872)	promoter-TSS (NM_029872)	-91	NM_029872	77134	Mm.490274	NM_029872	ENSMUSG00000007836	Hnrnpa0	1110055B05Rik|3010025E17Rik|Hnrpa0|hnRNP A0	heterogeneous nuclear ribonucleoprotein A0	protein-coding
mm_4905.1	chr1	189879930	189879941	+	1	NA	TTS (NM_026796)	TTS (NM_026796)	42353	NM_026796	226830	Mm.156895	NM_026796	ENSMUSG00000026603	Smyd2	1110020E07Rik|4930402C15|KMT3C|Zmynd14	SET and MYND domain containing 2	protein-coding
mm_130556.1	chr15	99136096	99136098	-	1	NA	intron (NM_139140, intron 1 of 12)	intron (NM_139140, intron 1 of 12)	9252	NM_139140	72572	Mm.276650	NM_139140	ENSMUSG00000051934	Spats2	2700012F11Rik|59kDa|Scr59|p59	spermatogenesis associated, serine-rich 2	protein-coding
mm_166272.1	chr5	90490669	90490678	+	1	NA	promoter-TSS (NM_007423)	promoter-TSS (NM_007423)	-41	NM_007423	11576	Mm.358570	NM_007423	ENSMUSG00000054932	Afp	-	alpha fetoprotein	protein-coding
mm_142908.1	chr17	52350014	52350022	-	1	NA	Intergenic	Intergenic	-252691	NM_001031811	211468	Mm.399068	NM_001031811	ENSMUSG00000035580	Kcnh8	C130090D05Rik|ELK|ELK1|ELK3|Kv12.1	potassium voltage-gated channel, subfamily H (eag-related), member 8	protein-coding
mm_38672.1	chr4	144786552	144786566	-	1	NA	promoter-TSS (NM_001126316)	promoter-TSS (NM_001126316)	24	NM_001126316	329993	Mm.297407	NM_001126316	ENSMUSG00000078504	Gm438	-	predicted gene 438	protein-coding
mm_64208.1	chr7	141475441	141475455	+	1	NA	promoter-TSS (NM_025593)	promoter-TSS (NM_025593)	212	NM_053082	64540	Mm.489619	NM_053082	ENSMUSG00000025511	Tspan4	AI325509|AI746565|D130042I01Rik|NAG-2|Tm4sf7|Tspan-4	tetraspanin 4	protein-coding
mm_128511.1	chr15	53327104	53327107	-	1	NA	intron (NM_010162, intron 1 of 10)	AT_rich|Low_complexity|Low_complexity	19078	NM_010162	14042	Mm.309395	NM_010162	ENSMUSG00000061731	Ext1	AA409028	exostoses (multiple) 1	protein-coding
mm_21832.1	chr2	165407798	165407811	-	1	NA	intron (NM_054055, intron 12 of 12)	intron (NM_054055, intron 12 of 12)	-7410	NM_029021	74614	Mm.72179	NM_029021	ENSMUSG00000027670	Ocstamp	4833422F24Rik|OC-STAMP	osteoclast stimulatory transmembrane protein	protein-coding
mm_131694.1	chr16	20693328	20693347	+	1	NA	TTS (NM_145941)	TTS (NM_145941)	-1720	NM_133778	78408	Mm.196512	NM_133778	ENSMUSG00000050821	Fam131a	2900046G09Rik	family with sequence similarity 131, member A	protein-coding
mm_130439.1	chr15	98480664	98480680	-	1	NA	3' UTR (NM_010679, exon 4 of 4)	3' UTR (NM_010679, exon 4 of 4)	2011	NM_010679	16770	Mm.5074	NM_010679	ENSMUSG00000022991	Lalba	AW208827|Lyzg	lactalbumin, alpha	protein-coding
mm_76554.1	chr8	88361942	88361976	-	1	NA	5' UTR (NM_012047, exon 1 of 17)	5' UTR (NM_012047, exon 1 of 17)	232	NM_012047	26992	Mm.5400	NM_012047	ENSMUSG00000031660	Brd7	BP75|CELTIX1|Ptpn13ip	bromodomain containing 7	protein-coding
mm_57942.1	chr6	134792500	134792508	-	1	NA	5' UTR (NM_130447, exon 1 of 7)	5' UTR (NM_130447, exon 1 of 7)	124	NM_130447	70686	Mm.491182	NM_130447	ENSMUSG00000030203	Dusp16	3830417M17Rik|AW558566|D6Ertd213e|MKP-7|MKP7|Mkpm	dual specificity phosphatase 16	protein-coding
mm_171343.1	chr4	104262773	104262783	+	1	NA	Intergenic	L1Md_T|LINE|L1	-104760	NR_104385	13131	Mm.289682	NM_010014	ENSMUSG00000028519	Dab1	AI956902|C630028C02Rik|scm|scr|scrambler|yot	disabled 1	protein-coding
mm_165624.1	chr3	65108900	65108911	+	1	NA	promoter-TSS (NM_010597)	promoter-TSS (NM_010597)	-463	NM_010597	16497	Mm.316402	NM_010597	ENSMUSG00000027827	Kcnab1	Akr8a8|Kvbeta1.1|mKv(beta)1	potassium voltage-gated channel, shaker-related subfamily, beta member 1	protein-coding
mm_114885.1	chr13	94285478	94285492	+	1	NA	promoter-TSS (NM_029153)	promoter-TSS (NM_029153)	-204	NM_029153	107767	Mm.201455	NM_029153	ENSMUSG00000021687	Scamp1	4930505M11Rik|AI415563|AW122395	secretory carrier membrane protein 1	protein-coding
mm_161300.1	chr14	30714724	30714724	+	1	NA	promoter-TSS (NM_019460)	promoter-TSS (NM_019460)	-125	NM_019460	54650	Mm.294662	NM_019460	ENSMUSG00000006527	Sfmbt1	4930442N21Rik|9330180L21Rik|AA536974|Sfmbt|Smr	Scm-like with four mbt domains 1	protein-coding
mm_145994.1	chr18	68340394	68340396	+	1	NA	TTS (NM_013596)	TTS (NM_013596)	2792	NM_013596	17203	Mm.8003	NM_013596	ENSMUSG00000007480	Mc5r	-	melanocortin 5 receptor	protein-coding
mm_6080.1	chr1	62735941	62735960	-	1	NA	intron (NM_001077405, intron 2 of 15)	intron (NM_001077405, intron 2 of 15)	32633	NM_001077405	18187	Mm.266341	NM_010939	ENSMUSG00000025969	Nrp2	1110048P06Rik|Np-2|Np2|Npn-2|Npn2	neuropilin 2	protein-coding
mm_157538.1	chrX	51204776	51204788	-	1	NA	intron (NM_134163, intron 1 of 7)	intron (NM_134163, intron 1 of 7)	1208	NM_001310515	171170	Mm.295324	NM_134163	ENSMUSG00000036109	Mbnl3	A530038J18Rik|AI661274|CHCR|E430034C16Rik|MBLX|MBLX39|MBXL	muscleblind-like 3 (Drosophila)	protein-coding
mm_89074.1	chr10	82987211	82987211	+	1	NA	intron (NM_021439, intron 1 of 2)	intron (NM_021439, intron 1 of 2)	1714	NM_021439	58250	Mm.360747	NM_021439	ENSMUSG00000034612	Chst11	1110020P09Rik|C4ST|C4ST-1|C4ST1|C4s	carbohydrate sulfotransferase 11	protein-coding
mm_54879.1	chr6	42693072	42693082	-	1	NA	promoter-TSS (NM_029930)	promoter-TSS (NM_029930)	-18	NM_029930	77574	Mm.24652	NM_029930	ENSMUSG00000036667	Tcaf1	2810407D09Rik|3321401G04Rik|A230020K05Rik|AI848529|Fam115a	TRPM8 channel-associated factor 1	protein-coding
mm_134106.1	chr16	9995413	9995443	-	1	NA	Intergenic	CpG	-2895	NM_008170	14811	Mm.2953	NM_008170	ENSMUSG00000059003	Grin2a	GluN2A|NMDAR2A|NR2A	glutamate receptor, ionotropic, NMDA2A (epsilon 1)	protein-coding
mm_115915.1	chr13	23465896	23465914	-	1	NA	promoter-TSS (NM_013483)	promoter-TSS (NM_013483)	-4	NM_013483	12231	Mm.1420	NM_013483	ENSMUSG00000000706	Btn1a1	Btn	butyrophilin, subfamily 1, member A1	protein-coding
mm_98598.1	chr11	95825160	95825179	+	1	NA	intron (NM_153104, intron 1 of 2)	intron (NM_153104, intron 1 of 2)	669	NM_153104	237928	Mm.133075	NM_153104	ENSMUSG00000050860	Phospho1	D11Moh36|Phospo1	phosphatase, orphan 1	protein-coding
mm_128356.1	chr15	39944608	39944626	-	1	NA	promoter-TSS (NM_172814)	promoter-TSS (NM_172814)	-623	NM_001347036	239393	Mm.39874	NM_172814	ENSMUSG00000022305	Lrp12	AI848829|C820005L12Rik|LRP-12	low density lipoprotein-related protein 12	protein-coding
mm_11604.1	chr2	33805855	33805875	+	1	NA	promoter-TSS (NR_045729)	promoter-TSS (NR_045729)	49	NR_045729	320482	Mm.442057	NR_045729	ENSMUSG00000086484	Nron	A630071L07Rik|Gm24353	non-protein coding RNA, repressor of NFAT	ncRNA
mm_135601.1	chr16	51736242	51736245	-	1	NA	Intergenic	Intergenic	-295306	NM_001033238	208650	Mm.328206	NM_001033238	ENSMUSG00000022637	Cblb	AI429560|AI851073|Cbl-b	Casitas B-lineage lymphoma b	protein-coding
mm_132078.1	chr16	30139400	30139409	+	1	NA	Intergenic	Intergenic	74047	NM_008235	15205	Mm.390859	NM_008235	ENSMUSG00000022528	Hes1	Hry|bHLHb39	hairy and enhancer of split 1 (Drosophila)	protein-coding
mm_9832.1	chr1	183524357	183524361	-	1	NA	Intergenic	RMER19B|LTR|ERVK	105111	NM_001308052	78772	Mm.29003	NM_030175	ENSMUSG00000053461	Hhipl2	4930507C10Rik|AW208802|Hhip3	hedgehog interacting protein-like 2	protein-coding
mm_61258.1	chr7	66060599	66060607	+	1	NA	5' UTR (NM_021336, exon 1 of 9)	5' UTR (NM_021336, exon 1 of 9)	267	NM_021336	68981	Mm.22362	NM_021336	ENSMUSG00000030512	Snrpa1	1500015N06Rik	small nuclear ribonucleoprotein polypeptide A'	protein-coding
mm_20563.1	chr2	131080413	131080424	-	1	NA	exon (NM_011426, exon 7 of 21)	exon (NM_011426, exon 7 of 21)	6347	NM_011426	20612	Mm.1374	NM_011426	ENSMUSG00000027322	Siglec1	Cd169|Siglec-1|Sn	sialic acid binding Ig-like lectin 1, sialoadhesin	protein-coding
mm_155016.1	chrX	41954380	41954387	+	1	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	-42482	NM_001033422	331401	Mm.259498	NM_001033422	ENSMUSG00000037475	Thoc2	6330441O12Rik|D130005M13Rik|Gm1139|Gm1793|Tho2	THO complex 2	protein-coding
mm_5568.1	chr1	38898067	38898077	-	1	NA	promoter-TSS (NM_145142)	promoter-TSS (NM_145142)	88	NM_145142	98388	Mm.260054	NM_145142	ENSMUSG00000026080	Chst10	AI507003|AU041319|Hnk-1st|ST	carbohydrate sulfotransferase 10	protein-coding
mm_38554.1	chr4	141623800	141623840	-	1	NA	promoter-TSS (NM_001013780)	promoter-TSS (NM_001013780)	14	NM_001013780	384071	Mm.295682	NM_001013780	ENSMUSG00000040740	Slc25a34	Gm1369	solute carrier family 25, member 34	protein-coding
mm_167230.1	chr8	13414300	13414308	+	1	NA	intron (NM_011881, intron 5 of 6)	intron (NM_011881, intron 5 of 6)	9223	NM_011881	24013	Mm.257501	NM_011881	ENSMUSG00000031450	Grk1	Gprk1|Rhok|Rk	G protein-coupled receptor kinase 1	protein-coding
mm_143400.1	chr17	70753452	70753461	-	1	NA	intron (NM_001347411, intron 9 of 14)	intron (NM_001347411, intron 9 of 14)	93321	NM_001164077	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_68846.1	chr7	126364930	126364951	-	1	NA	intron (NM_010689, intron 8 of 11)	intron (NM_010689, intron 8 of 11)	3105	NR_106025	102466797		NR_106025	ENSMUSG00000099017	Mir7058	Gm27766|mmu-mir-7058	microRNA 7058	ncRNA
mm_34707.1	chr4	152116018	152116028	+	1	NA	promoter-TSS (NM_033042)	promoter-TSS (NM_033042)	89	NM_001291010	85030	Mm.101198	NM_033042	ENSMUSG00000024793	Tnfrsf25	APO-3|DDR3|DR3|LARD|TR3|TRAMP|Tnfrsf12|WSL-1|WSL-LR|Wsl	tumor necrosis factor receptor superfamily, member 25	protein-coding
mm_97763.1	chr11	81985650	81985690	+	1	NA	Intergenic	Intergenic	-17274	NM_001034013	11418	Mm.234998	NM_007384	ENSMUSG00000020704	Asic2	ACIC2|Accn1|BNC1|BNaC1|BNaC1a|Mdeg	acid-sensing (proton-gated) ion channel 2	protein-coding
mm_23644.1	chr3	67374174	67374185	+	1	NA	promoter-TSS (NM_010801)	promoter-TSS (NM_010801)	82	NM_001039543	17349	Mm.10414	NM_010801	ENSMUSG00000048416	Mlf1	HLS7	myeloid leukemia factor 1	protein-coding
mm_151245.1	chr19	53903235	53903277	+	1	NA	promoter-TSS (NM_001168492)	promoter-TSS (NM_001168492)	-95	NM_001168492	18569	Mm.1605	NM_011050	ENSMUSG00000024975	Pdcd4	D19Ucla1|Ma3|Tis	programmed cell death 4	protein-coding
mm_119792.1	chr14	54194221	54194238	+	1	NA	Intergenic	Intergenic	59700	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_144369.1	chr18	20510254	20510267	+	1	NA	promoter-TSS (NM_030596)	promoter-TSS (NM_030596)	-14	NM_030596	13512	Mm.106811	NM_030596	ENSMUSG00000056632	Dsg3	bal	desmoglein 3	protein-coding
mm_118482.1	chr14	12046046	12046049	+	1	NA	intron (NM_008981, intron 5 of 29)	intron (NM_008981, intron 5 of 29)	-143896	NM_001347593	19270	Mm.431266	NM_008981	ENSMUSG00000021745	Ptprg	5430405N12Rik|AW046354|AW549872|RPTPgamma	protein tyrosine phosphatase, receptor type, G	protein-coding
mm_57354.1	chr6	124756998	124757008	-	1	NA	promoter-TSS (NM_007881)	promoter-TSS (NM_007881)	-516	NM_007881	13498	Mm.333380	NM_007881	ENSMUSG00000004263	Atn1	Atr1|Drpla|atrophin-1	atrophin 1	protein-coding
mm_47439.1	chr5	123181638	123181660	-	1	NA	intron (NM_008277, intron 3 of 13)	intron (NM_008277, intron 3 of 13)	1037	NM_008277	15445	Mm.439709	NM_008277	ENSMUSG00000029445	Hpd	Fla|Flp|Hppd|Laf	4-hydroxyphenylpyruvic acid dioxygenase	protein-coding
mm_107472.1	chr12	37880171	37880179	+	1	NA	promoter-TSS (NM_178681)	promoter-TSS (NM_178681)	-530	NM_178681	217480	Mm.126525	NM_178681	ENSMUSG00000036095	Dgkb	6430574F24|90kda|C630029D13Rik|DAGK2|DGK|DGK-beta|mKIAA0718	diacylglycerol kinase, beta	protein-coding
mm_34047.1	chr4	138221575	138221629	+	1	NA	5' UTR (NM_010470, exon 2 of 13)	5' UTR (NM_010470, exon 2 of 13)	4475	NM_001122897	15441	Mm.348429	NM_010470	ENSMUSG00000028759	Hp1bp3	Hp1bp74	heterochromatin protein 1, binding protein 3	protein-coding
mm_94911.1	chr11	29374577	29374581	+	1	NA	exon (NM_176841, exon 2 of 32)	exon (NM_176841, exon 2 of 32)	407	NM_176841	108686	Mm.338284	NM_176841	ENSMUSG00000032740	Ccdc88a	A430106J12Rik|AI848406|Ape|C130096N06Rik|C330012F17Rik|D130005J21Rik|Girdin|Giv|Grdn|Hkrp1	coiled coil domain containing 88A	protein-coding
mm_80810.1	chr9	96478346	96478361	+	1	NA	intron (NM_001311135, intron 1 of 2)	CpG	322	NM_011279	19823	Mm.28235	NM_011279	ENSMUSG00000051234	Rnf7	Rbx2|SAG	ring finger protein 7	protein-coding
mm_54599.1	chr6	38306304	38306305	-	1	NA	3' UTR (NM_001347122, exon 13 of 13)	3' UTR (NM_001347122, exon 13 of 13)	-7045	NM_172467	209032	Mm.101389	NM_172467	ENSMUSG00000047749	Zc3hav1l	B130055L09Rik|E430016P22Rik	zinc finger CCCH-type, antiviral 1-like	protein-coding
mm_46642.1	chr5	108548842	108548852	-	1	NA	intron (NM_007756, intron 1 of 3)	intron (NM_007756, intron 1 of 3)	1180	NM_007756	12889	Mm.5195	NM_007756	ENSMUSG00000033615	Cplx1	921-S	complexin 1	protein-coding
mm_125019.1	chr15	25655136	25655166	+	1	NA	intron (NM_019472, intron 1 of 40)	L1MC3|LINE|L1	32601	NM_019472	17909	Mm.60590	NM_019472	ENSMUSG00000022272	Myo10	AW048724|D15Ertd600e|mKIAA0799|myosin-X	myosin X	protein-coding
mm_108853.1	chr12	98445979	98446004	+	1	NA	intron (NM_029911, intron 4 of 6)	intron (NM_029911, intron 4 of 6)	-77853	NR_136759	105245437	Mm.446375	NR_136759		Gm40893	-	predicted gene, 40893	ncRNA
mm_153332.1	chr19	38125235	38125240	-	1	NA	promoter-TSS (NM_011255)	promoter-TSS (NM_011255)	84	NM_001159487	19662	Mm.2605	NM_011255	ENSMUSG00000024990	Rbp4	Rbp-4	retinol binding protein 4, plasma	protein-coding
mm_83780.1	chr9	52143921	52143932	-	1	NA	exon (NM_001162921, exon 2 of 6)	exon (NM_001162921, exon 2 of 6)	24185	NM_001162921	244871	Mm.295686	NM_001162921	ENSMUSG00000035164	Zc3h12c	A230108E06|C230027N18Rik|mKIAA1726	zinc finger CCCH type containing 12C	protein-coding
mm_14805.1	chr2	145887018	145887030	+	1	NA	3' UTR (NM_028724, exon 13 of 13)	3' UTR (NM_028724, exon 13 of 13)	-16217	NM_026425	67877	Mm.151168	NM_026425	ENSMUSG00000002728	Naa20	1500004D14Rik|2900026I01Rik|AU041458|D2Ertd186e|Nat5	N(alpha)-acetyltransferase 20, NatB catalytic subunit	protein-coding
mm_94625.1	chr11	16786078	16786086	+	1	NA	intron (NM_207655, intron 1 of 27)	intron (NM_207655, intron 1 of 27)	33879	NM_007912	13649	Mm.8534	NM_007912	ENSMUSG00000020122	Egfr	9030024J15Rik|AI552599|Erbb|Errb1|Errp|Wa5|wa-2|wa2	epidermal growth factor receptor	protein-coding
mm_143565.1	chr17	74294777	74294806	-	1	NA	promoter-TSS (NM_133771)	promoter-TSS (NM_133771)	72	NM_133771	76890	Mm.311874	NM_133771	ENSMUSG00000058704	Memo1	0610016J10Rik|D930048L02Rik	mediator of cell motility 1	protein-coding
mm_123899.1	chr14	73117212	73117220	-	1	NA	Intergenic	Intergenic	-25294	NM_001170694	105670	Mm.280068	NM_134083	ENSMUSG00000022106	Rcbtb2	2610028E02Rik|2810420M18Rik|AI448345|AW240694|Chc1l|RC/BTB2	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 2	protein-coding
mm_166343.1	chr5	115500668	115500676	+	1	NA	Intergenic	Intergenic	-6004	NM_011223	19303	Mm.18714	NM_011223	ENSMUSG00000029528	Pxn	AW108311|AW123232|Pax	paxillin	protein-coding
mm_154168.1	chr19	58681785	58681786	-	1	NA	TTS (NM_026925)	TTS (NM_026925)	11420	NM_026925	69060	Mm.20407	NM_026925	ENSMUSG00000046008	Pnlip	1810007A24Rik|PL|PTL	pancreatic lipase	protein-coding
mm_54010.1	chr6	8171359	8171359	-	1	NA	intron (NM_001037865, intron 3 of 34)	intron (NM_001037865, intron 3 of 34)	21258	NM_001037865	213945	Mm.297404	NM_001037865	ENSMUSG00000068794	Col28a1	Col28|Gm466	collagen, type XXVIII, alpha 1	protein-coding
mm_160712.1	chr10	60331729	60331729	-	1	NA	exon (NM_001252635, exon 41 of 69)	exon (NM_001252635, exon 41 of 69)	-15122	NM_001159572	74048	Mm.273584	NM_028732	ENSMUSG00000020101	Vsir	4632428N05Rik|Dies1|PD-1H|VISTA	V-set immunoregulatory receptor	protein-coding
mm_55042.1	chr6	48988064	48988076	-	1	NA	exon (NM_172888, exon 1 of 5)	exon (NM_172888, exon 1 of 5)	1209	NM_172888	243377	Mm.446302	NM_172888	ENSMUSG00000039215	Svs1	9530003A11	seminal vesicle secretory protein 1	protein-coding
mm_155530.1	chrX	74297121	74297178	+	1	NA	promoter-TSS (NM_018794)	promoter-TSS (NM_018794)	52	NM_018794	54411	Mm.21961	NM_018794	ENSMUSG00000019087	Atp6ap1	16A|AC45|AI316502|AW108110|Atp6ip1|Atp6s1|C7-1|CF2|VATPS1|XAP-3|mFLJ00383	ATPase, H+ transporting, lysosomal accessory protein 1	protein-coding
mm_29793.1	chr3	127690749	127690783	-	1	NA	intron (NM_027808, intron 4 of 13)	B3A|SINE|B2	57621	NM_009718	11924	Mm.42017	NM_009718	ENSMUSG00000027967	Neurog2	Atoh4|Math4A|bHLHa8|ngn-2|ngn2	neurogenin 2	protein-coding
mm_47352.1	chr5	122707418	122707445	-	1	NA	promoter-TSS (NM_011026)	promoter-TSS (NM_011026)	-113	NM_001310720	18438	Mm.290884	NM_011026	ENSMUSG00000029470	P2rx4	AI504491|AW555605|D5Ertd444e|P2X4	purinergic receptor P2X, ligand-gated ion channel 4	protein-coding
mm_106541.1	chr11	120578993	120579003	-	1	NA	3' UTR (NM_133796, exon 6 of 6)	3' UTR (NM_133796, exon 6 of 6)	2622	NM_133796	192662	Mm.30016	NM_133796	ENSMUSG00000025132	Arhgdia	5330430M07Rik|Gdi-1|Rho-GDI|RhoDGI|RhoGDI-1	Rho GDP dissociation inhibitor (GDI) alpha	protein-coding
mm_108457.1	chr12	82707537	82707581	+	1	NA	intron (NM_001310478, intron 2 of 17)	PB1D9|SINE|Alu	90060	NM_001282061	50779	Mm.126176	NM_015812	ENSMUSG00000021219	Rgs6	-	regulator of G-protein signaling 6	protein-coding
mm_124757.1	chr15	6644797	6644820	+	1	NA	exon (NM_011815, exon 11 of 18)	exon (NM_011815, exon 11 of 18)	-63573	NM_030168	78757	Mm.275811	NM_030168	ENSMUSG00000050310	Rictor	4921505C17Rik|6030405M08Rik|AVO3|AW492497|D530039E11Rik	RPTOR independent companion of MTOR, complex 2	protein-coding
mm_152205.1	chr19	7711087	7711106	-	1	NA	exon (NM_144785, exon 1 of 10)	exon (NM_144785, exon 1 of 10)	214	NM_144785	207151	Mm.21365	NM_144785	ENSMUSG00000024757	Slc22a19	D630043A20Rik|OAT-5|Oat5|Slc22a9	solute carrier family 22 (organic anion transporter), member 19	protein-coding
mm_162064.1	chrX	9572409	9572409	-	1	NA	promoter-TSS (NM_001085517)	promoter-TSS (NM_001085517)	-18	NM_001085517	333452	Mm.473671	NM_001085517	ENSMUSG00000061065	H2al1o	EG333452|Gm5132	H2A histone family member L1O	protein-coding
mm_33517.1	chr4	130928712	130928719	+	1	NA	exon (NM_010686, exon 4 of 8)	exon (NM_010686, exon 4 of 8)	15381	NM_010686	16792	Mm.271868	NM_010686	ENSMUSG00000028581	Laptm5	E3	lysosomal-associated protein transmembrane 5	protein-coding
mm_116959.1	chr13	56141135	56141148	-	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	-5591	NM_001159513	26914	Mm.283802	NM_012015	ENSMUSG00000015937	H2afy	H2AF12M|mH2a1|macroH2A1	H2A histone family, member Y	protein-coding
mm_53662.1	chr6	141524380	141524449	+	1	NA	promoter-TSS (NM_001177772)	promoter-TSS (NM_001177772)	28	NM_021471	58807	Mm.284495	NM_021471	ENSMUSG00000030235	Slco1c1	OATP-14|OATP-F|Oatp2|Oatpf|Slc21a14	solute carrier organic anion transporter family, member 1c1	protein-coding
mm_50805.1	chr6	54292900	54292909	+	1	NA	non-coding (NR_033635, exon 12 of 14)	non-coding (NR_033635, exon 12 of 14)	20082	NM_023543	69993	Mm.321147	NM_023543	ENSMUSG00000004633	Chn2	1700026N20Rik|4930557O16Rik|ARHGAP3|Bch	chimerin 2	protein-coding
mm_171527.1	chr4	146611047	146611048	+	1	NA	Intergenic	Intergenic	-64174	NR_045468	67524	Mm.444300	NR_045468	ENSMUSG00000086046	1700095A21Rik	-	RIKEN cDNA 1700095A21 gene	ncRNA
mm_24136.1	chr3	88228330	88228340	+	1	NA	Intergenic	Intergenic	12737	NR_029817	387133		NR_029817	ENSMUSG00000106493	Mir9-1	Mirn9|Mirn9-1|mir-9-1|mmu-mir-9-1	microRNA 9-1	ncRNA
mm_9250.1	chr1	171390179	171390205	-	1	NA	intron (NM_001005508, intron 1 of 11)	intron (NM_001005508, intron 1 of 11)	1232	NM_001005508	226652	Mm.251048	NM_001005508	ENSMUSG00000048865	Arhgap30	6030405P05Rik|Gm102|mFLJ00267	Rho GTPase activating protein 30	protein-coding
mm_159111.1	chr2	52110011	52110011	+	1	NA	exon (NM_175238, exon 30 of 36)	exon (NM_175238, exon 30 of 36)	37174	NM_175238	51869	Mm.254530	NM_175238	ENSMUSG00000036202	Rif1	5730435J01Rik|6530403D07Rik|AU016181|AW549474|D2Ertd145e	replication timing regulatory factor 1	protein-coding
mm_165854.1	chr4	13784750	13784791	+	1	NA	promoter-TSS (NM_009822)	promoter-TSS (NM_009822)	-12	NM_009822	12395	Mm.4909	NM_009822	ENSMUSG00000006586	Runx1t1	Cbfa2t1h|ETO|MTG8	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	protein-coding
mm_144545.1	chr18	28381305	28381307	+	1	NA	Intergenic	Intergenic	-178858	NR_045398	320624	Mm.50107	NR_045398		4930474G06Rik	-	RIKEN cDNA 4930474G06 gene	ncRNA
mm_90208.1	chr10	120625651	120625672	+	1	NA	Intergenic	Intergenic	-140071	NR_038000	70874	Mm.427286	NR_038000	ENSMUSG00000044544	4921513I03Rik	-	RIKEN cDNA 4921513I03 gene	ncRNA
mm_143578.1	chr17	74316365	74316377	-	1	NA	promoter-TSS (NM_001146223)	promoter-TSS (NM_001146223)	23	NM_001146222	66310	Mm.28536	NM_024428	ENSMUSG00000024067	Dpy30	2810410M20Rik|C87842	dpy-30, histone methyltransferase complex regulatory subunit	protein-coding
mm_66204.1	chr7	34234560	34234566	-	1	NA	Intergenic	Intergenic	-4227	NM_008155	14751	Mm.589	NM_008155	ENSMUSG00000036427	Gpi1	Amf|Gpi|Gpi-1|Gpi-1r|Gpi-1s|Gpi-1t|Gpi1-r|Gpi1-s|Gpi1-t|Gpi1s|MF|NK|NK/GPI|Nlk|Org|Pgi|Phi	glucose phosphate isomerase 1	protein-coding
mm_53094.1	chr6	125009233	125009253	+	1	NA	promoter-TSS (NM_175557)	promoter-TSS (NM_175557)	5	NM_001252083	269800	Mm.108677	NM_175557	ENSMUSG00000038346	Zfp384	BB163993|C130073D16Rik|Ciz|NP|Nmp4	zinc finger protein 384	protein-coding
mm_102269.1	chr11	55394727	55394738	-	1	NA	3' UTR (NM_009242, exon 10 of 10)	3' UTR (NM_009242, exon 10 of 10)	25348	NM_009242	20692	Mm.291442	NM_009242	ENSMUSG00000018593	Sparc	BM-40|ON	secreted acidic cysteine rich glycoprotein	protein-coding
mm_44314.1	chr5	9300111	9300118	-	1	NA	intron (NM_172706, intron 1 of 21)	intron (NM_172706, intron 1 of 21)	33921	NM_172706	231014	Mm.130063	NM_172706	ENSMUSG00000056004	9330182L06Rik	Eig121l	RIKEN cDNA 9330182L06 gene	protein-coding
mm_99787.1	chr11	107417513	107417532	+	1	NA	intron (NM_145823, intron 1 of 9)	intron (NM_145823, intron 1 of 9)	53198	NM_145823	71795	Mm.397413	NM_145823	ENSMUSG00000040430	Pitpnc1	1110020B03Rik|5830436L09Rik|AI662802|AI851387|C330017I21Rik|Dnr411|RDGBB|RDGBB1|rdgB-beta	phosphatidylinositol transfer protein, cytoplasmic 1	protein-coding
mm_153902.1	chr19	47090679	47090683	-	1	NA	promoter-TSS (NM_011053)	promoter-TSS (NM_011053)	-56	NM_023211	66477	Mm.29722	NM_023211	ENSMUSG00000071528	Usmg5	2010301L15Rik	upregulated during skeletal muscle growth 5	protein-coding
mm_61483.1	chr7	75684951	75684957	+	1	NA	intron (NM_029332, intron 12 of 36)	intron (NM_029332, intron 12 of 36)	-163384	NM_001122780	207952	Mm.206223	NM_029652	ENSMUSG00000055652	Klhl25	2810402K13Rik|BC027373|Enc-1	kelch-like 25	protein-coding
mm_118379.1	chr13	117025386	117025444	-	1	NA	exon (NM_001081009, exon 1 of 27)	exon (NM_001081009, exon 1 of 27)	101	NM_001081009	52552	Mm.274466	NM_027272	ENSMUSG00000021725	Parp8	2810430O08Rik|ARTD16|D13Ertd275e	poly (ADP-ribose) polymerase family, member 8	protein-coding
mm_133217.1	chr16	75907043	75907074	+	1	NA	intron (NM_023380, intron 1 of 7)	intron (NM_023380, intron 1 of 7)	2208	NM_023380	67742	Mm.131406	NM_023380	ENSMUSG00000022876	Samsn1	4930571B16Rik|930571B16Rik|Hacs1|SLy2	SAM domain, SH3 domain and nuclear localization signals, 1	protein-coding
mm_82724.1	chr9	25151206	25151239	-	1	NA	5' UTR (NM_020586, exon 1 of 8)	5' UTR (NM_020586, exon 1 of 8)	559	NM_020586	80517	Mm.142843	NM_020586	ENSMUSG00000008429	Herpud2	5031400M07Rik|AB041580	HERPUD family member 2	protein-coding
mm_44839.1	chr5	34169524	34169534	-	1	NA	promoter-TSS (NM_001289804)	promoter-TSS (NM_001289804)	-3	NM_001289803	272158	Mm.319286	NM_181857	ENSMUSG00000045102	Poln	POL4P	DNA polymerase N	protein-coding
mm_53668.1	chr6	141632601	141632611	+	1	NA	intron (NM_020495, intron 1 of 15)	B4|SINE|B4	3088	NM_020495	28253	Mm.272223	NM_020495	ENSMUSG00000030236	Slco1b2	7330442B20Rik|OATP-C|OATP2|Oatp1b2|Oatp4|Slc21a10|Slc21a6|lst-1|mlst-1	solute carrier organic anion transporter family, member 1b2	protein-coding
mm_19487.1	chr2	93203319	93203333	-	1	NA	3' UTR (NM_183180, exon 10 of 10)	3' UTR (NM_183180, exon 10 of 10)	15742	NM_001025246	277414	Mm.41033	NM_001025246	ENSMUSG00000068735	Trp53i11	Tp53i11	transformation related protein 53 inducible protein 11	protein-coding
mm_69451.1	chr7	133089112	133089115	-	1	NA	intron (NM_009980, intron 1 of 10)	intron (NM_009980, intron 1 of 10)	-7253	NM_001347623	13017	Mm.246240	NM_009980	ENSMUSG00000030970	Ctbp2	AA407280|D7Ertd45e|Gtrgeo6|Ribeye	C-terminal binding protein 2	protein-coding
mm_157012.1	chrX	7671342	7671397	-	1	NA	promoter-TSS (NM_019755)	promoter-TSS (NM_019755)	21	NM_019755	18824	Mm.18565	NM_019755	ENSMUSG00000031146	Plp2	mIMA4	proteolipid protein 2	protein-coding
mm_59225.1	chr7	24636567	24636589	+	1	NA	promoter-TSS (NM_133743)	promoter-TSS (NM_133743)	8	NM_133743	72434	Mm.281093	NM_133743	ENSMUSG00000057454	Lypd3	2310061G07Rik|C4.4a	Ly6/Plaur domain containing 3	protein-coding
mm_12792.1	chr2	79635371	79635410	+	1	NA	promoter-TSS (NM_080558)	promoter-TSS (NM_080558)	-35	NM_080558	70599	Mm.272881	NM_080558	ENSMUSG00000027007	Ssfa2	5730488C15Rik|CS-1|CS1|KRAP|SPAG13|mKIAA1927	sperm specific antigen 2	protein-coding
mm_3237.1	chr1	135850772	135850791	+	1	NA	exon (NM_001130176, exon 10 of 13)	exon (NM_001130176, exon 10 of 13)	9920	NM_001130176	21956	Mm.247470	NM_011619	ENSMUSG00000026414	Tnnt2	Tnt|cTnT	troponin T2, cardiac	protein-coding
mm_170982.1	chr2	72019438	72019443	+	1	NA	intron (NM_001204165, intron 1 of 30)	ORR1A2|LTR|ERVL-MaLR	-35177	NM_001204166	56508	Mm.196153	NM_019688	ENSMUSG00000049044	Rapgef4	1300003D15Rik|5730402K07Rik|6330581N18Rik|EPAC 2|Epac-2|Epac2|mKIAA4040	Rap guanine nucleotide exchange factor (GEF) 4	protein-coding
mm_161607.1	chr16	43979278	43979278	-	1	NA	promoter-TSS (NM_001007460)	promoter-TSS (NM_001007460)	-228	NM_001007460	332175	Mm.327852	NM_001007460	ENSMUSG00000036304	Zdhhc23	Gm1751|Gm779|nidd	zinc finger, DHHC domain containing 23	protein-coding
mm_55719.1	chr6	73221712	73221723	-	1	NA	promoter-TSS (NM_001164669)	promoter-TSS (NM_001164669)	-86	NM_001164669	330355	Mm.333166	NM_001164669	ENSMUSG00000052861	Dnah6	9830168K20|A730004I20Rik|Dnahc6|mKIAA1697|mdhc6	dynein, axonemal, heavy chain 6	protein-coding
mm_121977.1	chr14	25848338	25848348	-	1	NA	intron (NM_013469, intron 1 of 14)	intron (NM_013469, intron 1 of 14)	6188	NM_013469	11744	Mm.294083	NM_013469	ENSMUSG00000021866	Anxa11	A830099O17Rik|Anx11	annexin A11	protein-coding
mm_87683.1	chr10	59256872	59256876	+	1	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	34952	NM_172939	268301	Mm.3036	NM_172939	ENSMUSG00000098188	Sowahc	4921515A04Rik|9430099J10Rik|Ankrd57|C820004L04Rik	sosondowah ankyrin repeat domain family member C	protein-coding
mm_125042.1	chr15	25778120	25778140	+	1	NA	exon (NM_019472, exon 22 of 41)	exon (NM_019472, exon 22 of 41)	-65168	NM_001034851	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_67161.1	chr7	73541824	73541829	-	1	NA	promoter-TSS (NM_001081345)	promoter-TSS (NM_001081345)	-80	NM_001081345	244059	Mm.34539	NM_001081345	ENSMUSG00000078671	Chd2	2810013C04Rik|2810040A01Rik|5630401D06Rik|AI851092|BC029703|CHD-2	chromodomain helicase DNA binding protein 2	protein-coding
mm_20521.1	chr2	130839684	130839696	-	1	NA	promoter-TSS (NM_001311147)	promoter-TSS (NM_001311147)	-3	NM_001311147	228602	Mm.271990	NM_028367	ENSMUSG00000027309	4930402H24Rik	2810487F15Rik|AI413763|C78926	RIKEN cDNA 4930402H24 gene	protein-coding
mm_145282.1	chr18	53193138	53193148	+	1	NA	intron (NM_026386, intron 2 of 14)	intron (NM_026386, intron 2 of 14)	16778	NM_026386	67804	Mm.252171	NM_026386	ENSMUSG00000034484	Snx2	0610030A03Rik	sorting nexin 2	protein-coding
mm_170008.1	chr17	16889280	16889283	+	1	NA	Intergenic	Intergenic	-174822	NM_001005358	449000	Mm.483718	NM_001005358	ENSMUSG00000096696	Zfp960	-	zinc finger protein 960	protein-coding
mm_145787.1	chr18	65143699	65143724	+	1	NA	intron (NM_001114386, intron 5 of 30)	intron (NM_001114386, intron 5 of 30)	-105150	NR_029600	387231		NR_029600	ENSMUSG00000065402	Mir122	Mir122a|Mirn122a|mir-122|mmu-mir-122	microRNA 122	ncRNA
mm_34416.1	chr4	145274083	145274091	+	1	NA	intron (NM_009401, intron 12 of 12)	intron (NM_009401, intron 12 of 12)	-27217	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_119260.1	chr14	33954021	33954031	+	1	NA	promoter-TSS (NM_015745)	promoter-TSS (NM_015745)	4	NM_015745	19661	Mm.436622	NM_015745	ENSMUSG00000041534	Rbp3	Irbp|Rbp-3	retinol binding protein 3, interstitial	protein-coding
mm_10192.1	chr2	4919042	4919062	+	1	NA	promoter-TSS (NM_010726)	promoter-TSS (NM_010726)	56	NM_010726	16922	Mm.391704	NM_010726	ENSMUSG00000026664	Phyh	AI256161|AI265699|Lnap1|PAHX	phytanoyl-CoA hydroxylase	protein-coding
mm_6559.1	chr1	75141573	75141606	-	1	NA	intron (NM_026977, intron 1 of 8)	CpG	779	NM_026977	69171	Mm.28193	NM_026977	ENSMUSG00000033159	Cnppd1	1810031K17Rik|AU043960	cyclin Pas1/PHO80 domain containing 1	protein-coding
mm_103327.1	chr11	74522599	74522630	-	1	NA	intron (NM_001015046, intron 2 of 24)	CpG	67544	NM_001015046	380711	Mm.425690	NM_001015046	ENSMUSG00000038807	Rap1gap2	AU067654|Garnl4|Gm1561|mKIAA1039	RAP1 GTPase activating protein 2	protein-coding
mm_110539.1	chr12	55302646	55302725	-	1	NA	promoter-TSS (NM_025373)	promoter-TSS (NM_025373)	48	NM_025373	66132	Mm.383213	NM_025373	ENSMUSG00000021023	1110008L16Rik	Kiaa0391|Mrpp3|mKIAA0391	RIKEN cDNA 1110008L16 gene	protein-coding
mm_113798.1	chr13	46419021	46419037	+	1	NA	5' UTR (NM_001081425, exon 1 of 4)	5' UTR (NM_001081425, exon 1 of 4)	729	NM_001081425	666794	Mm.38269	NM_001081425	ENSMUSG00000038132	Rbm24	6330546B05Rik|AI606861	RNA binding motif protein 24	protein-coding
mm_115045.1	chr13	100104210	100104212	+	1	NA	promoter-TSS (NM_001081061)	promoter-TSS (NM_001081061)	-141	NM_001081061	544971	Mm.288546	NM_001081061	ENSMUSG00000049658	Bdp1	AI662220|AW049390|AW456745|B130055N23Rik|G630013P12Rik|TAF3B1|TFC5|TFIIIB150|TFIIIB90|Tfnr|mKIAA1241	B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB	protein-coding
mm_66985.1	chr7	63939689	63939707	-	1	NA	promoter-TSS (NM_021366)	promoter-TSS (NM_021366)	-783	NM_021366	50794	Mm.240473	NM_021366	ENSMUSG00000052040	Klf13	0610043C13Rik|9430029L20Rik|Bteb3|FKLF-2|FKLF2|NSLP1|RFLAT-1|RFLAT1	Kruppel-like factor 13	protein-coding
mm_103141.1	chr11	70238959	70238970	-	1	NA	exon (NM_173742, exon 2 of 3)	exon (NM_173742, exon 2 of 3)	888	NM_173742	52898	Mm.29852	NM_173742	ENSMUSG00000040904	Rnasek	2310033H11Rik|AA571397|D11Bwg0434e	ribonuclease, RNase K	protein-coding
mm_26804.1	chr3	10025537	10025540	-	1	NA	Intergenic	Intergenic	12953	NM_001272098	16592	Mm.741	NM_010634	ENSMUSG00000027533	Fabp5	E-FABP|Fabpe|Klbp|PA-FABP|mal1	fatty acid binding protein 5, epidermal	protein-coding
mm_34032.1	chr4	138097305	138097328	+	1	NA	exon (NM_001256198, exon 8 of 33)	exon (NM_001256198, exon 8 of 33)	41202	NR_126429	73563	Mm.444294	NR_126429	ENSMUSG00000084804	1700095J12Rik	-	RIKEN cDNA 1700095J12 gene	ncRNA
mm_29080.1	chr3	104171472	104171473	-	1	NA	intron (NM_001159354, intron 1 of 20)	L1Md_F2|LINE|L1	48934	NM_133853	99470	Mm.264849	NM_133853	ENSMUSG00000052539	Magi3	4732496O19Rik|6530407C02Rik|AA407180|AI120132|mKIAA1634	membrane associated guanylate kinase, WW and PDZ domain containing 3	protein-coding
mm_129199.1	chr15	76511825	76511851	-	1	NA	promoter-TSS (NM_010046)	promoter-TSS (NM_010046)	-20	NM_010046	13350	Mm.22633	NM_010046	ENSMUSG00000022555	Dgat1	ARAT|C75990|D15Ertd23e|Dgat	diacylglycerol O-acyltransferase 1	protein-coding
mm_58931.1	chr7	17975327	17975331	+	1	NA	exon (NM_023289, exon 3 of 4)	exon (NM_023289, exon 3 of 4)	3162	NM_023289	66996	Mm.36666	NM_023289	ENSMUSG00000030368	Ceacam11	1600015D01Rik	carcinoembryonic antigen-related cell adhesion molecule 11	protein-coding
mm_162409.1	chr1	87126345	87126352	+	1	NA	exon (NM_007432, exon 6 of 11)	exon (NM_007432, exon 6 of 11)	1340	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_79468.1	chr9	56477250	56477267	+	1	NA	exon (NM_025812, exon 4 of 10)	exon (NM_025812, exon 4 of 10)	58412	NM_025812	66867	Mm.150856	NM_025812	ENSMUSG00000032329	Hmg20a	1200004E06Rik|5730490E10Rik|Hmgxb1|Ibraf	high mobility group 20A	protein-coding
mm_19043.1	chr2	77123799	77123804	-	1	NA	intron (NM_001025576, intron 5 of 23)	intron (NM_001025576, intron 5 of 23)	46834	NM_001025576	545428	Mm.26579	NM_001025576	ENSMUSG00000044033	Ccdc141	2610301F02Rik|CAMDI|ENSMUSG00000075261	coiled-coil domain containing 141	protein-coding
mm_151320.1	chr19	55892691	55892699	+	1	NA	intron (NR_138565, intron 4 of 15)	intron (NR_138565, intron 4 of 15)	-2626	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_3704.1	chr1	153891733	153891740	+	1	NA	promoter-TSS (NM_178244)	promoter-TSS (NM_178244)	90	NM_178244	240819	Mm.453236	NM_178244	ENSMUSG00000047053	Teddm1a	Epdd1|Teddm1|e9-1	transmembrane epididymal protein 1A	protein-coding
mm_55283.1	chr6	54523722	54523725	-	1	NA	intron (NM_027268, intron 4 of 7)	L1MEg|LINE|L1	42659	NM_027268	69938	Mm.41557	NM_027268	ENSMUSG00000019124	Scrn1	2810019K23Rik|6330535A03Rik|AI852905|SES1|mKIAA0193	secernin 1	protein-coding
mm_141841.1	chr17	34729881	34729904	-	1	NA	exon (NM_009780, exon 36 of 41)	exon (NM_009780, exon 36 of 41)	14005	NM_009780	12268	Mm.477109	NM_009780	ENSMUSG00000073418	C4b	C4|Ss	complement component 4B (Chido blood group)	protein-coding
mm_14367.1	chr2	129618497	129618538	+	1	NA	exon (NM_001291022, exon 2 of 5)	exon (NM_001291022, exon 2 of 5)	25348	NM_001291022	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_154579.1	chrX	7572540	7572554	+	1	NA	intron (NM_138605, intron 1 of 3)	intron (NM_138605, intron 1 of 3)	-1053	NR_029473	78185	Mm.160055	NR_029473	ENSMUSG00000039545	Ppp1r3fos	4930524L23Rik	protein phosphatase 1, regulatory subunit 3F, opposite strand	ncRNA
mm_27445.1	chr3	51903357	51903369	-	1	NA	intron (NM_001004176, intron 1 of 4)	(TG)n|Simple_repeat|Simple_repeat	201643	NM_001004176	433586	Mm.234972	NM_001004176	ENSMUSG00000061143	Maml3	AV234550|BC049812|Mam-2|mKIAA1816	mastermind like 3 (Drosophila)	protein-coding
mm_20766.1	chr2	142778468	142778471	-	1	NA	intron (NM_001081133, intron 12 of 25)	intron (NM_001081133, intron 12 of 25)	122995	NM_001081133	16558	Mm.251934	NM_001081133	ENSMUSG00000038844	Kif16b	8430434E15Rik|AA623607|AI789011|C80253|C80902|mKIAA1590	kinesin family member 16B	protein-coding
mm_106802.1	chr12	4956670	4956673	+	1	NA	intron (NM_001099628, intron 10 of 30)	intron (NM_001099628, intron 10 of 30)	39318	NM_001099628	320817	Mm.210966	NM_001099628	ENSMUSG00000052812	Atad2b	1110014E10Rik|BC032887|C79189|D530031C13Rik	ATPase family, AAA domain containing 2B	protein-coding
mm_40738.1	chr5	66260122	66260170	+	1	NA	promoter-TSS (NM_027602)	promoter-TSS (NM_027602)	248	NM_001302834	70918	Mm.23166	NM_027602	ENSMUSG00000029206	Nsun7	4921525L17Rik	NOL1/NOP2/Sun domain family, member 7	protein-coding
mm_35496.1	chr4	41047600	41047638	-	1	NA	intron (NM_007473, intron 1 of 7)	intron (NM_007473, intron 1 of 7)	517	NM_007473	11832	Mm.8728	NM_007473	ENSMUSG00000028427	Aqp7	AQP7L|AQPap	aquaporin 7	protein-coding
mm_26509.1	chr3	145827700	145827731	+	1	NA	intron (NM_026993, intron 1 of 5)	intron (NM_026993, intron 1 of 5)	69023	NM_026993	69219	Mm.234247	NM_026993	ENSMUSG00000028194	Ddah1	2410006N07Rik|2510015N06Rik|AI987801|AW050362	dimethylarginine dimethylaminohydrolase 1	protein-coding
mm_140241.1	chr17	84142892	84142898	+	1	NA	Intergenic	Intergenic	45052	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_80393.1	chr9	75775669	75775687	+	1	NA	5' UTR (NM_007555, exon 1 of 7)	5' UTR (NM_007555, exon 1 of 7)	313	NM_007555	12160	Mm.428950	NM_007555	ENSMUSG00000032179	Bmp5	AU023399|se	bone morphogenetic protein 5	protein-coding
mm_101690.1	chr11	40733374	40733442	-	1	NA	promoter-TSS (NM_013552)	promoter-TSS (NM_013552)	29	NM_013552	15366	Mm.116997	NM_013552	ENSMUSG00000020330	Hmmr	AA386826|CD168|Rhamm	hyaluronan mediated motility receptor (RHAMM)	protein-coding
mm_53212.1	chr6	126718886	126718934	+	1	NA	intron (NM_013568, intron 1 of 1)	intron (NM_013568, intron 1 of 1)	21764	NM_013568	16494	Mm.62535	NM_013568	ENSMUSG00000038077	Kcna6	Kv1.6|MK1.6	potassium voltage-gated channel, shaker-related, subfamily, member 6	protein-coding
mm_152114.1	chr19	6979136	6979159	-	1	NA	5' UTR (NM_008020, exon 2 of 6)	5' UTR (NM_008020, exon 2 of 6)	1293	NM_008020	14227	Mm.4234	NM_008020	ENSMUSG00000056629	Fkbp2	13kDa|FKBP-2|mFKBP13|mFKBP2	FK506 binding protein 2	protein-coding
mm_39208.1	chr4	156050734	156050761	-	1	NA	promoter-TSS (NM_029264)	promoter-TSS (NM_029264)	70	NM_029264	330010	Mm.440232	NM_029264	ENSMUSG00000029074	Ttll10	4833412E22Rik|4930595O22Rik|AU022799|BC042775|Ttll5	tubulin tyrosine ligase-like family, member 10	protein-coding
mm_92987.1	chr10	86701803	86701818	-	1	NA	exon (NM_011631, exon 5 of 18)	exon (NM_011631, exon 5 of 18)	3634	NM_011631	22027	Mm.87773	NM_011631	ENSMUSG00000020048	Hsp90b1	ERp99|GRP94|TA-3|Targ2|Tra-1|Tra1|endoplasmin|gp96	heat shock protein 90, beta (Grp94), member 1	protein-coding
mm_90443.1	chr10	127658325	127658331	+	1	NA	intron (NM_009284, intron 17 of 21)	intron (NM_009284, intron 17 of 21)	8375	NM_001122895	17937	Mm.336898	NM_008668	ENSMUSG00000025402	Nab2	AI451907	Ngfi-A binding protein 2	protein-coding
mm_16871.1	chr2	12301915	12301922	-	1	NA	promoter-TSS (NM_001001309)	promoter-TSS (NM_001001309)	26	NR_138462	241226	Mm.329997	NM_001001309	ENSMUSG00000026768	Itga8	AI447669	integrin alpha 8	protein-coding
mm_70493.1	chr8	12573065	12573076	+	1	NA	promoter-TSS (NM_024279)	promoter-TSS (NM_024279)	21	NM_024279	78634	Mm.116871	NM_024279	ENSMUSG00000010435	Spaca7	1700094C09Rik	sperm acrosome associated 7	protein-coding
mm_116517.1	chr13	45744391	45744400	-	1	NA	intron (NM_001199304, intron 4 of 6)	ID_B1|SINE|B4	220596	NM_001199304	20238	Mm.342683	NM_009124	ENSMUSG00000046876	Atxn1	2900016G23Rik|Atx1|C85907|ENSMUSG00000074917|Gm10786|Sca1	ataxin 1	protein-coding
mm_106584.1	chr11	120729642	120729663	-	1	NA	3' UTR (NM_007621, exon 8 of 8)	3' UTR (NM_007621, exon 8 of 8)	-2368	NM_001347608	67880	Mm.231091	NM_026428	ENSMUSG00000039450	Dcxr	0610038K04Rik|1810027P18Rik|XR	dicarbonyl L-xylulose reductase	protein-coding
mm_171635.1	chr4	21579292	21579293	+	1	NA	Intergenic	L1Md_T|LINE|L1	106671	NM_001080771	230025	Mm.208541	NM_001080771	ENSMUSG00000040478	Prdm13	-	PR domain containing 13	protein-coding
mm_89536.1	chr10	94550820	94550833	+	1	NA	intron (NM_172051, intron 1 of 3)	intron (NM_172051, intron 1 of 3)	-24431	NM_001168684	319880	Mm.23047	NM_172051	ENSMUSG00000020023	Tmcc3	AW488095|C630016B22Rik|C88213|Tmcc1	transmembrane and coiled coil domains 3	protein-coding
mm_98440.1	chr11	94939693	94939718	+	1	NA	exon (NM_007742, exon 7 of 51)	exon (NM_007742, exon 7 of 51)	3481	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_131362.1	chr16	13780601	13780623	+	1	NA	promoter-TSS (NM_001039521)	promoter-TSS (NM_001039521)	-87	NM_001039521	106298	Mm.288606	NM_001039521	ENSMUSG00000022682	Rrn3	AL023001|E130302O19Rik|R75565|TIF-1A|Tif1a	RRN3 RNA polymerase I transcription factor homolog (yeast)	protein-coding
mm_10842.1	chr2	24975224	24975236	+	1	NA	promoter-TSS (NM_001031808)	promoter-TSS (NM_001031808)	-132	NM_001031808	107733	Mm.23010	NM_001031808	ENSMUSG00000036850	Mrpl41	MRP-L27|Rpml27	mitochondrial ribosomal protein L41	protein-coding
mm_80907.1	chr9	100643552	100643564	+	1	NA	promoter-TSS (NM_009282)	promoter-TSS (NM_009282)	-65	NM_009282	20842	Mm.42135	NM_009282	ENSMUSG00000037286	Stag1	AU045003|SA-1|Scc3	stromal antigen 1	protein-coding
mm_117420.1	chr13	74343385	74343404	-	1	NA	exon (NM_023281, exon 3 of 15)	exon (NM_023281, exon 3 of 15)	6846	NM_023281	66945	Mm.158231	NM_023281	ENSMUSG00000021577	Sdha	1500032O14Rik|2310034D06Rik|4921513A11|C81073|FP|SDH2|SDHF	succinate dehydrogenase complex, subunit A, flavoprotein (Fp)	protein-coding
mm_21546.1	chr2	164054824	164054838	-	1	NA	intron (NM_025996, intron 5 of 6)	intron (NM_025996, intron 5 of 6)	16271	NM_025996	67145	Mm.23173	NM_025996	ENSMUSG00000018322	Tomm34	2610100K07Rik|TOM34	translocase of outer mitochondrial membrane 34	protein-coding
mm_44090.1	chr5	149244913	149244937	+	1	NA	Intergenic	Intergenic	-20079	NM_001308462	11690	Mm.19844	NM_009663	ENSMUSG00000060063	Alox5ap	Flap	arachidonate 5-lipoxygenase activating protein	protein-coding
mm_81816.1	chr9	118040609	118040615	+	1	NA	promoter-TSS (NM_013727)	promoter-TSS (NM_013727)	90	NM_013727	27215	Mm.92705	NM_013727	ENSMUSG00000039285	Azi2	AA410145|AZ2	5-azacytidine induced gene 2	protein-coding
mm_83454.1	chr9	45204084	45204106	-	1	NA	promoter-TSS (NM_145403)	promoter-TSS (NM_145403)	-20	NM_145403	214523	Mm.436756	NM_145403	ENSMUSG00000032091	Tmprss4	mCAP2	transmembrane protease, serine 4	protein-coding
mm_17740.1	chr2	32712235	32712276	-	1	NA	TTS (NR_039536)	TTS (NR_039536)	529	NM_130860	107951	Mm.27557	NM_130860	ENSMUSG00000009555	Cdk9	PITALRE	cyclin-dependent kinase 9 (CDC2-related kinase)	protein-coding
mm_107168.1	chr12	24708275	24708292	+	1	NA	promoter-TSS (NM_009104)	promoter-TSS (NM_009104)	29	NM_009104	20135	Mm.99	NM_009104	ENSMUSG00000020649	Rrm2	AA407299|R2	ribonucleotide reductase M2	protein-coding
mm_64253.1	chr7	141744620	141744639	+	1	NA	exon (NM_023566, exon 28 of 46)	exon (NM_023566, exon 28 of 46)	-44382	NM_010844	17833	Mm.334332	NM_010844	ENSMUSG00000037974	Muc5ac	2210005L13Rik|MGM	mucin 5, subtypes A and C, tracheobronchial/gastric	protein-coding
mm_42863.1	chr5	122226856	122226866	+	1	NA	intron (NM_028752, intron 2 of 6)	intron (NM_028752, intron 2 of 6)	16574	NM_028752	74096	Mm.28804	NM_028752	ENSMUSG00000064267	Hvcn1	0610039P13Rik|AI450555|BTS|HV1|Vsop.|mVSOP	hydrogen voltage-gated channel 1	protein-coding
mm_16026.1	chr2	167539783	167539787	+	1	NA	intron (NM_011427, intron 2 of 2)	intron (NM_011427, intron 2 of 2)	1590	NM_011427	20613	Mm.2093	NM_011427	ENSMUSG00000042821	Snai1	Sna|Sna1|Snail|Snail1	snail family zinc finger 1	protein-coding
mm_34335.1	chr4	143350028	143350039	+	1	NA	5' UTR (NM_001162983, exon 1 of 2)	5' UTR (NM_001162983, exon 1 of 2)	283	NM_001162983	242735	Mm.94020	NM_001162983	ENSMUSG00000028584	Lrrc38	A230053A07Rik	leucine rich repeat containing 38	protein-coding
mm_39852.1	chr5	30913587	30913628	+	1	NA	promoter-TSS (NM_133918)	promoter-TSS (NM_133918)	-179	NM_133918	100952	Mm.286375	NM_133918	ENSMUSG00000029163	Emilin1	5830419M17Rik|AW229038|BB105748|EMILIN-1|gp115	elastin microfibril interfacer 1	protein-coding
mm_107614.1	chr12	49385653	49385658	+	1	NA	exon (NM_008241, exon 2 of 2)	exon (NM_008241, exon 2 of 2)	2648	NM_008241	15228	Mm.4704	NM_008241	ENSMUSG00000020950	Foxg1	2900064B05Rik|BF-1|Bf1|Hfh9|Hfhbf1	forkhead box G1	protein-coding
mm_22795.1	chr3	22214510	22214533	+	1	NA	3' UTR (NM_030732, exon 16 of 16)	3' UTR (NM_030732, exon 16 of 16)	-36849	NR_004439	19784		NR_004439		Rprl2	RPRH3|Rmrp3	ribonuclease P RNA-like 2	ncRNA
mm_94311.1	chr11	4220703	4220742	+	1	NA	exon (NM_028022, exon 5 of 9)	exon (NM_028022, exon 5 of 9)	2471	NM_028022	71962	Mm.7852	NM_028022	ENSMUSG00000020424	Gatsl3	2410008K03Rik	GATS protein-like 3	protein-coding
mm_139562.1	chr17	56981321	56981329	+	1	NA	intron (NM_175731, intron 1 of 5)	PB1D10|SINE|Alu	801	NM_175731	171168	Mm.218784	NM_175731	ENSMUSG00000045019	Acer1	2310024P18Rik|AI662009|Alkcdase1|Asah3|Cer1	alkaline ceramidase 1	protein-coding
mm_17965.1	chr2	37443097	37443178	-	1	NA	promoter-TSS (NM_146121)	promoter-TSS (NM_146121)	-16	NM_199025	320633	Mm.383299	NM_199025	ENSMUSG00000050714	Zbtb26	A630026F21Rik	zinc finger and BTB domain containing 26	protein-coding
mm_141515.1	chr17	31681271	31681294	-	1	NA	3' UTR (NM_001278570, exon 3 of 3)	3' UTR (NM_001278570, exon 3 of 3)	3351	NM_001278570	12954	Mm.1228	NM_013501	ENSMUSG00000024041	Cryaa	Acry-1|Crya-1|Crya1|DAcry-1|lop18	crystallin, alpha A	protein-coding
mm_170389.1	chr18	60774664	60774664	+	1	NA	promoter-TSS (NM_020600)	promoter-TSS (NM_020600)	68	NM_020600	20044	Mm.43778	NM_020600	ENSMUSG00000024608	Rps14	2600014J02Rik|AL023078	ribosomal protein S14	protein-coding
mm_101274.1	chr11	21370679	21370689	-	1	NA	promoter-TSS (NM_139297)	promoter-TSS (NM_139297)	-55	NM_139297	216558	Mm.28877	NM_139297	ENSMUSG00000001891	Ugp2	UDPGP|UGPase	UDP-glucose pyrophosphorylase 2	protein-coding
mm_25142.1	chr3	102724451	102724494	+	1	NA	intron (NR_040588, intron 3 of 3)	intron (NR_040588, intron 3 of 3)	-10298	NM_027533	70747	Mm.27469	NM_027533	ENSMUSG00000027858	Tspan2	6330415F13Rik|B230119D02Rik|tspan-2	tetraspanin 2	protein-coding
mm_54776.1	chr6	41539856	41539898	-	1	NA	Intergenic	Intergenic	18101	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_105262.1	chr11	102357085	102357096	-	1	NA	exon (NM_011403, exon 10 of 20)	exon (NM_011403, exon 10 of 20)	8191	NM_011403	20533	Mm.7248	NM_011403	ENSMUSG00000006574	Slc4a1	Ae1|CD233|Empb3|l11Jus51	solute carrier family 4 (anion exchanger), member 1	protein-coding
mm_146534.1	chr18	5404431	5404437	-	1	NA	Intergenic	Intergenic	-69995	NM_178722	240186	Mm.118257	NM_178722	ENSMUSG00000050945	Zfp438	9430031G09|9430091M14Rik|B830013J05Rik	zinc finger protein 438	protein-coding
mm_105786.1	chr11	109801778	109801780	-	1	NA	intron (NM_027038, intron 2 of 4)	Lx5|LINE|L1	26267	NM_027038	69324	Mm.31700	NM_027038	ENSMUSG00000020617	1700012B07Rik	1700069D21Rik	RIKEN cDNA 1700012B07 gene	protein-coding
mm_109605.1	chr12	112721106	112721127	+	1	NA	Intergenic	Intergenic	-1058	NM_001024602	217882	Mm.23689	NM_001024602	ENSMUSG00000072825	Cep170b	AI466840|AW555464|Kiaa0284|mKIAA0284	centrosomal protein 170B	protein-coding
mm_168833.1	chr12	23010180	23010184	-	1	NA	promoter-TSS (NR_015504)	promoter-TSS (NR_015504)	61	NR_015504	69732	Mm.391403	NM_028362	ENSMUSG00000073164	2410018L13Rik	2810480C08Rik	RIKEN cDNA 2410018L13 gene	ncRNA
mm_83040.1	chr9	37348370	37348391	-	1	NA	promoter-TSS (NM_001081429)	promoter-TSS (NM_001081429)	12	NM_001081429	245902	Mm.390150	NM_001081429	ENSMUSG00000034303	Ccdc15	A630039F14Rik|D030074L19	coiled-coil domain containing 15	protein-coding
mm_78193.1	chr9	21337871	21337877	+	1	NA	promoter-TSS (NM_152808)	promoter-TSS (NM_152808)	46	NM_152808	68682	Mm.148425	NM_152808	ENSMUSG00000057193	Slc44a2	1110028E10Rik|CTL2	solute carrier family 44, member 2	protein-coding
mm_133654.1	chr16	91807221	91807236	+	1	NA	intron (NM_001110275, intron 8 of 28)	intron (NM_001110275, intron 8 of 28)	77857	NM_010587	16443	Mm.40546	NM_010587	ENSMUSG00000022957	Itsn1	AA517634|AA545208|AI316805|AI839402|AI848451|Ehsh1|Ese1|Itsn|Sh3p17	intersectin 1 (SH3 domain protein 1A)	protein-coding
mm_96305.1	chr11	63158442	63158460	+	1	NA	3' UTR (NM_008885, exon 5 of 5)	3' UTR (NM_008885, exon 5 of 5)	25648	NM_001302260	18858	Mm.1237	NM_008885	ENSMUSG00000018217	Pmp22	22kDa|Gas-3|HNPP|Tr|trembler	peripheral myelin protein 22	protein-coding
mm_128674.1	chr15	60187399	60187415	-	1	NA	Intergenic	Intergenic	-170789	NM_027668	71088	Mm.425950	NM_027668	ENSMUSG00000071749	4933412E24Rik	-	RIKEN cDNA 4933412E24 gene	protein-coding
mm_6550.1	chr1	75133574	75133578	-	1	NA	intron (NM_194333, intron 1 of 11)	intron (NM_194333, intron 1 of 11)	314	NM_194333	22626	Mm.68157	NM_194333	ENSMUSG00000026205	Slc23a3	SVCT3|Yspl1	solute carrier family 23 (nucleobase transporters), member 3	protein-coding
mm_72960.1	chr8	92827397	92827429	+	1	NA	5' UTR (NM_008610, exon 1 of 13)	5' UTR (NM_008610, exon 1 of 13)	116	NM_008610	17390	Mm.29564	NM_008610	ENSMUSG00000031740	Mmp2	Clg4a|GelA|MMP-2	matrix metallopeptidase 2	protein-coding
mm_111010.1	chr12	78980674	78980680	-	1	NA	intron (NM_178745, intron 1 of 2)	intron (NM_178745, intron 1 of 2)	2801	NM_001170401	268567	Mm.341747	NM_178745	ENSMUSG00000046157	Tmem229b	6330442E10Rik|9830138K24|AU019070	transmembrane protein 229B	protein-coding
mm_109261.1	chr12	109462570	109462571	+	1	NA	non-coding (NR_033813, exon 6 of 6)	non-coding (NR_033813, exon 6 of 6)	9115	NM_010052	13386	Mm.157069	NM_010052	ENSMUSG00000040856	Dlk1	AW742678|DLK-1|DlkI|FA1|Ly107|Peg9|SCP1|ZOG|pG2|pref-1	delta-like 1 homolog (Drosophila)	protein-coding
mm_83035.1	chr9	37255670	37255683	-	1	NA	promoter-TSS (NM_001145960)	promoter-TSS (NM_001145960)	62	NM_020258	56857	Mm.440037	NM_020258	ENSMUSG00000032122	Slc37a2	G3PP|Slc37a1|cI-2|ci2	solute carrier family 37 (glycerol-3-phosphate transporter), member 2	protein-coding
mm_93164.1	chr10	93265835	93265876	-	1	NA	intron (NM_013508, intron 2 of 4)	intron (NM_013508, intron 2 of 4)	45304	NM_001322268	13713	Mm.4454	NM_013508	ENSMUSG00000008398	Elk3	D430049E23Rik|Erp|Etrp|Net|Sap-2	ELK3, member of ETS oncogene family	protein-coding
mm_28853.1	chr3	96905248	96905258	-	1	NA	promoter-TSS (NM_026229)	promoter-TSS (NM_026229)	45	NM_026229	67549	Mm.46722	NM_026229	ENSMUSG00000028096	Gpr89	4933412D19Rik|Gpr89a|SH120	G protein-coupled receptor 89	protein-coding
mm_142678.1	chr17	47732463	47732474	-	1	NA	exon (NM_025973, exon 6 of 9)	exon (NM_025973, exon 6 of 9)	-4569	NM_001161722	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_128733.1	chr15	64182424	64182428	-	1	NA	intron (NM_010026, intron 5 of 30)	intron (NM_010026, intron 5 of 30)	-121978	NM_144846	223601	Mm.246108	NM_144846	ENSMUSG00000022378	Fam49b	0910001A06Rik|AW122079	family with sequence similarity 49, member B	protein-coding
mm_16329.1	chr2	174327727	174327729	+	1	NA	promoter-TSS (NR_003258)	promoter-TSS (NR_003258)	-40	NM_001310083	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_149828.1	chr19	24500744	24500749	+	1	NA	intron (NM_008846, intron 1 of 14)	Charlie5|DNA|hAT-Charlie	-23272	NM_026520	68034	Mm.440181	NM_026520	ENSMUSG00000074922	Fam122a	2410124L17Rik|2900009I07Rik|ENSMUSG00000051082|Gm9849	family with sequence similarity 122, member A	protein-coding
mm_103939.1	chr11	83753634	83753653	-	1	NA	promoter-TSS (NM_145432)	promoter-TSS (NM_145432)	6	NM_145432	217026	Mm.117874	NM_145432	ENSMUSG00000000976	Heatr6	2700008B19Rik|BB135312|BB249351	HEAT repeat containing 6	protein-coding
mm_2500.1	chr1	106171883	106171896	+	1	NA	promoter-TSS (NM_133821)	promoter-TSS (NM_133821)	20	NM_133821	98432	Mm.24115	NM_133821	ENSMUSG00000044340	Phlpp1	AI836256|Phlpp|Plekhe1|SCOP|mKIAA0606	PH domain and leucine rich repeat protein phosphatase 1	protein-coding
mm_6393.1	chr1	72858735	72858758	-	1	NA	3' UTR (NM_010518, exon 4 of 4)	3' UTR (NM_010518, exon 4 of 4)	16119	NM_010518	16011	Mm.405761	NM_010518	ENSMUSG00000026185	Igfbp5	AI256729|AW208790|IGFBP-5|IGFBP-5P	insulin-like growth factor binding protein 5	protein-coding
mm_30938.1	chr4	33031372	33031524	+	1	NA	promoter-TSS (NM_019586)	promoter-TSS (NM_019586)	23	NM_019586	56228	Mm.259095	NM_019586	ENSMUSG00000028277	Ube2j1	0710008M05Rik|1110030I22Rik|NCUBE-1|Ncube|Ncube1|Ubc6p	ubiquitin-conjugating enzyme E2J 1	protein-coding
mm_85691.1	chr9	108079256	108079273	-	1	NA	promoter-TSS (NM_001311152)	promoter-TSS (NM_001311152)	37	NM_001311152	84585	Mm.379272	NM_032543	ENSMUSG00000041528	Rnf123	BC003945|Kpc1	ring finger protein 123	protein-coding
mm_16370.1	chr2	177759255	177759293	+	1	NA	promoter-TSS (NM_001243903)	promoter-TSS (NM_001243903)	-14	NM_001243903	626802	Mm.386029	NM_001243903	ENSMUSG00000078864	Gm14322	OTTMUSG00000016321	predicted gene 14322	protein-coding
mm_113749.1	chr13	44731266	44731276	+	1	NA	promoter-TSS (NM_001205043)	promoter-TSS (NM_001205043)	0	NM_001205043	16468	Mm.25059	NM_021878	ENSMUSG00000038518	Jarid2	Jmj|jumonji	jumonji, AT rich interactive domain 2	protein-coding
mm_139178.1	chr17	47593480	47593500	+	1	NA	promoter-TSS (NM_007632)	promoter-TSS (NM_007632)	23	NM_007632	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_108577.1	chr12	84996488	84996496	+	1	NA	exon (NM_001347421, exon 1 of 20)	exon (NM_001347421, exon 1 of 20)	171	NM_178363	56531	Mm.153183	NM_178363	ENSMUSG00000021244	Ylpm1	A930013E17Rik|ZAP|Zap3	YLP motif containing 1	protein-coding
mm_130585.1	chr15	99601584	99601589	-	1	NA	exon (NM_175087, exon 1 of 5)	exon (NM_175087, exon 1 of 5)	186	NM_175087	11831	Mm.202309	NM_175087	ENSMUSG00000043144	Aqp6	AI790337	aquaporin 6	protein-coding
mm_105722.1	chr11	109011772	109011782	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	91428	NM_015732	12006	Mm.71710	NM_015732	ENSMUSG00000000142	Axin2	Axi1|Axil|Conductin	axin 2	protein-coding
mm_138703.1	chr17	36020980	36021001	+	1	NA	promoter-TSS (NM_008207)	promoter-TSS (NM_008207)	-430	NM_008207	15042	Mm.439654	NM_008207	ENSMUSG00000053835	H2-T24	H-2T24	histocompatibility 2, T region locus 24	protein-coding
mm_118380.1	chr13	117025506	117025541	-	1	NA	promoter-TSS (NM_001081009)	promoter-TSS (NM_001081009)	-7	NM_001081009	52552	Mm.274466	NM_027272	ENSMUSG00000021725	Parp8	2810430O08Rik|ARTD16|D13Ertd275e	poly (ADP-ribose) polymerase family, member 8	protein-coding
mm_52309.1	chr6	108828596	108828604	+	1	NA	promoter-TSS (NM_138677)	promoter-TSS (NM_138677)	-41	NM_138677	192193	Mm.21596	NM_138677	ENSMUSG00000030104	Edem1	A130059K23Rik|EDEM|mKIAA0212	ER degradation enhancer, mannosidase alpha-like 1	protein-coding
mm_59169.1	chr7	24399978	24400011	+	1	NA	intron (NM_028047, intron 1 of 13)	CpG	366	NM_028047	71997	Mm.150977	NM_028047	ENSMUSG00000002210	Smg9	1500002O20Rik|AI429693|N28092	smg-9 homolog, nonsense mediated mRNA decay factor (C. elegans)	protein-coding
mm_48685.1	chr5	146687504	146687520	-	1	NA	Intergenic	Intergenic	-102273	NM_001010941	14738	Mm.153539	NM_008151	ENSMUSG00000041468	Gpr12	Gpcr01|Gpcr12|Gpcr20|Gpcr21	G-protein coupled receptor 12	protein-coding
mm_97921.1	chr11	83574689	83574730	+	1	NA	3' UTR (NM_011338, exon 4 of 4)	3' UTR (NM_011338, exon 4 of 4)	3927	NM_011338	20308	Mm.416125	NM_011338	ENSMUSG00000019122	Ccl9	CCF18|MRP-2|Scya10|Scya9	chemokine (C-C motif) ligand 9	protein-coding
mm_149779.1	chr19	23135111	23135130	+	1	NA	Intergenic	CpG	-6106	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_151607.1	chr19	3686550	3686586	-	1	NA	promoter-TSS (NM_008513)	promoter-TSS (NM_008513)	-4	NM_008513	16973	Mm.274581	NM_008513	ENSMUSG00000024913	Lrp5	BMND1|HBM|LR3|LRP7|OPPG|mKIAA4142	low density lipoprotein receptor-related protein 5	protein-coding
mm_2322.1	chr1	92058936	92058948	+	1	NA	intron (NM_207225, intron 2 of 26)	L1M5|LINE|L1	121399	NM_207225	208727	Mm.318567	NM_207225	ENSMUSG00000026313	Hdac4	4932408F19Rik|HD4	histone deacetylase 4	protein-coding
mm_166618.1	chr6	72314555	72314558	+	1	NA	TTS (NM_001282071)	TTS (NM_001282071)	9946	NM_147779	20388	Mm.46033	NM_147779	ENSMUSG00000056370	Sftpb	AI562151|SF-B|SP-B|Sftp-3|Sftp3	surfactant associated protein B	protein-coding
mm_150006.1	chr19	29289566	29289577	+	1	NA	intron (NM_001048177, intron 11 of 23)	intron (NM_001048177, intron 11 of 23)	35747	NM_013754	27356	Mm.306511	NM_013754	ENSMUSG00000050957	Insl6	RIF1	insulin-like 6	protein-coding
mm_97979.1	chr11	83882701	83882728	+	1	NA	exon (NM_001291268, exon 5 of 9)	exon (NM_001291268, exon 5 of 9)	29754	NM_001291269	21410	Mm.7226	NM_009330	ENSMUSG00000020679	Hnf1b	HNF-1-beta|HNF-1B|HNF-1Beta|Hnf1beta|LFB3|Tcf-2|Tcf2|vHNF1	HNF1 homeobox B	protein-coding
mm_169882.1	chr16	41861180	41861180	-	1	NA	intron (NM_001347236, intron 1 of 6)	intron (NM_001347236, intron 1 of 6)	327838	NM_175548	268890	Mm.310524	NM_175548	ENSMUSG00000061080	Lsamp	5430428I19|AW046674|B130007O04Rik|D930023J12Rik|Lam|Lamp	limbic system-associated membrane protein	protein-coding
mm_20068.1	chr2	120404104	120404115	-	1	NA	promoter-TSS (NM_173734)	promoter-TSS (NM_173734)	7	NM_173734	211499	Mm.260712	NM_173734	ENSMUSG00000033808	Tmem87a	A930025J12Rik	transmembrane protein 87A	protein-coding
mm_5103.1	chr1	5070294	5070304	-	1	NA	promoter-TSS (NM_001177795)	promoter-TSS (NM_001177795)	-14	NM_001177795	58175	Mm.103771	NM_021374	ENSMUSG00000002459	Rgs20	2900073E09Rik|Rgsz1	regulator of G-protein signaling 20	protein-coding
mm_5038.1	chr1	193334955	193334965	+	1	NA	exon (NM_001277928, exon 17 of 23)	exon (NM_001277928, exon 17 of 23)	32717	NM_001277928	16780	Mm.435441	NM_008484	ENSMUSG00000026639	Lamb3	-	laminin, beta 3	protein-coding
mm_65943.1	chr7	30413685	30413694	-	1	NA	promoter-TSS (NM_011662)	promoter-TSS (NM_011662)	-99	NM_011662	22177	Mm.46301	NM_011662	ENSMUSG00000030579	Tyrobp	DAP12|KARAP|Ly83	TYRO protein tyrosine kinase binding protein	protein-coding
mm_90278.1	chr10	122806076	122806079	+	1	NA	intron (NM_176919, intron 3 of 8)	intron (NM_176919, intron 3 of 8)	126762	NR_106182	102466884		NR_106182	ENSMUSG00000099225	Mir8104	Gm27380|mmu-mir-8104	microRNA 8104	ncRNA
mm_103475.1	chr11	76494598	76494609	-	1	NA	promoter-TSS (NM_001346670)	promoter-TSS (NM_001346670)	-108	NM_001346670	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_84208.1	chr9	60688066	60688082	-	1	NA	promoter-TSS (NM_001146047)	promoter-TSS (NM_001146047)	60	NM_145616	102747	Mm.269413	NM_145616	ENSMUSG00000047766	Lrrc49	AI430817|AW050057|D430025H09Rik|PGs4|p79	leucine rich repeat containing 49	protein-coding
mm_92321.1	chr10	75643972	75643986	-	1	NA	promoter-TSS (NM_001162913)	promoter-TSS (NM_001162913)	29	NM_001162913	71733	Mm.247956	NM_027890	ENSMUSG00000006342	Susd2	1200011D11Rik	sushi domain containing 2	protein-coding
mm_98948.1	chr11	98447065	98447082	+	1	NA	5' UTR (NM_010346, exon 1 of 15)	5' UTR (NM_010346, exon 1 of 15)	239	NM_010346	14786	Mm.276702	NM_010346	ENSMUSG00000019312	Grb7	mKIAA4028	growth factor receptor bound protein 7	protein-coding
mm_106898.1	chr12	8012667	8012677	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	34995	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_100977.1	chr11	7200822	7200829	-	1	NA	exon (NM_008341, exon 3 of 4)	exon (NM_008341, exon 3 of 4)	3038	NM_008341	16006	Mm.21300	NM_008341	ENSMUSG00000020429	Igfbp1	-	insulin-like growth factor binding protein 1	protein-coding
mm_103749.1	chr11	80429306	80429313	-	1	NA	intron (NM_178616, intron 1 of 13)	intron (NM_178616, intron 1 of 13)	694	NM_178616	69077	Mm.260539	NM_178616	ENSMUSG00000017428	Psmd11	1700089D09Rik|1810019E17Rik|2610024G20Rik|2810055C24Rik|C78232|P44.5|S9	proteasome (prosome, macropain) 26S subunit, non-ATPase, 11	protein-coding
mm_113971.1	chr13	51651574	51651582	+	1	NA	promoter-TSS (NM_029279)	promoter-TSS (NM_029279)	-130	NM_001308448	75420	Mm.275981	NM_029279	ENSMUSG00000035139	Secisbp2	2210413N07Rik|2810012K13Rik|SBP2	SECIS binding protein 2	protein-coding
mm_146289.1	chr18	78476897	78476901	+	1	NA	intron (NM_030683, intron 2 of 11)	intron (NM_030683, intron 2 of 11)	120051	NM_207651	27411	Mm.44158	NM_030683	ENSMUSG00000024552	Slc14a2	UT-A1|UT-A3	solute carrier family 14 (urea transporter), member 2	protein-coding
mm_91941.1	chr10	60831435	60831446	-	1	NA	5' UTR (NM_029770, exon 1 of 17)	5' UTR (NM_029770, exon 1 of 17)	141	NM_029770	107449	Mm.290433	NM_029770	ENSMUSG00000020099	Unc5b	6330415E02Rik|A630020F16|D10Bwg0792e|Unc5h2	unc-5 netrin receptor B	protein-coding
mm_18037.1	chr2	38854920	38854922	-	1	NA	intron (NM_010264, intron 3 of 10)	intron (NM_010264, intron 3 of 10)	1091	NR_029904	723903		NR_029904	ENSMUSG00000065578	Mir181b-2	Mirn181b-2|mir-181b-2	microRNA 181b-2	ncRNA
mm_92208.1	chr10	68191740	68191748	-	1	NA	intron (NM_023598, intron 3 of 9)	intron (NM_023598, intron 3 of 9)	86982	NM_023598	71371	Mm.440357	NM_023598	ENSMUSG00000019947	Arid5b	4930580B11|5430435G07Rik|AI467247|Desrt|Mrf2|Mrf2alpha|Mrf2beta	AT rich interactive domain 5B (MRF1-like)	protein-coding
mm_79467.1	chr9	56437586	56437609	+	1	NA	intron (NM_025812, intron 1 of 9)	GC_rich|Low_complexity|Low_complexity	18751	NM_025812	66867	Mm.150856	NM_025812	ENSMUSG00000032329	Hmg20a	1200004E06Rik|5730490E10Rik|Hmgxb1|Ibraf	high mobility group 20A	protein-coding
mm_90922.1	chr10	12615034	12615069	-	1	NA	intron (NM_011682, intron 50 of 73)	intron (NM_011682, intron 50 of 73)	246684	NM_011682	22288	Mm.331784	NM_011682	ENSMUSG00000019820	Utrn	AA589569|DRP|Dmdl	utrophin	protein-coding
mm_76322.1	chr8	84701677	84701726	-	1	NA	5' UTR (NM_008535, exon 1 of 4)	5' UTR (NM_008535, exon 1 of 4)	244	NM_008535	17095	Mm.4925	NM_008535	ENSMUSG00000034041	Lyl1	Lyl-1|bHLHa18	lymphoblastomic leukemia 1	protein-coding
mm_120033.1	chr14	55884961	55885010	+	1	NA	promoter-TSS (NM_019820)	promoter-TSS (NM_019820)	43	NR_138134	219094	Mm.37592	NM_027143	ENSMUSG00000047153	Khnyn	6330555F21|9130227C08Rik|AI605259|Kiaa0323|mKIAA0323	KH and NYN domain containing	protein-coding
mm_20298.1	chr2	127124951	127124966	-	1	NA	intron (NM_144818, intron 5 of 17)	intron (NM_144818, intron 5 of 17)	8996	NM_144818	215387	Mm.29786	NM_144818	ENSMUSG00000034906	Ncaph	A730011O11Rik|Brrn1|HCAP-H|mKIAA0074	non-SMC condensin I complex, subunit H	protein-coding
mm_31314.1	chr4	46114686	46114697	+	1	NA	TTS (NM_173033)	TTS (NM_173033)	23784	NM_173033	272027	Mm.331588	NM_173033	ENSMUSG00000035495	Tstd2	3010020C06	thiosulfate sulfurtransferase (rhodanese)-like domain containing 2	protein-coding
mm_166790.1	chr6	145307331	145307334	-	1	NA	Intergenic	Intergenic	56780	NR_045598	100039495	Mm.121014	NR_045598	ENSMUSG00000086013	Gm15706	OTTMUSG00000025463	predicted gene 15706	ncRNA
mm_118983.1	chr14	28443393	28443402	+	1	NA	intron (NM_001347497, intron 19 of 19)	intron (NM_001347497, intron 19 of 19)	-62076	NM_009524	22418	Mm.287544	NM_009524	ENSMUSG00000021994	Wnt5a	8030457G12Rik|Wnt-5a	wingless-type MMTV integration site family, member 5A	protein-coding
mm_150365.1	chr19	34649424	34649439	+	1	NA	3' UTR (NM_008331, exon 2 of 2)	3' UTR (NM_008331, exon 2 of 2)	8542	NM_008331	15957	Mm.439751	NM_008331	ENSMUSG00000034459	Ifit1	ISG56|Ifi56|P56	interferon-induced protein with tetratricopeptide repeats 1	protein-coding
mm_112878.1	chr13	20854810	20854821	+	1	NA	intron (NM_012054, intron 4 of 20)	intron (NM_012054, intron 4 of 20)	60702	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_79078.1	chr9	46242268	46242281	+	1	NA	intron (NM_007468, intron 2 of 2)	intron (NM_007468, intron 2 of 2)	1430	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_30070.1	chr3	137965993	137966001	-	1	NA	exon (NM_011932, exon 2 of 9)	exon (NM_011932, exon 2 of 9)	15552	NM_011932	26377	Mm.254835	NM_011932	ENSMUSG00000028159	Dapp1	Bam32	dual adaptor for phosphotyrosine and 3-phosphoinositides 1	protein-coding
mm_105574.1	chr11	106612992	106613007	-	1	NA	promoter-TSS (NM_198292)	promoter-TSS (NM_198292)	-69	NM_198292	21763	Mm.102407	NM_198292	ENSMUSG00000040548	Tex2	4930568E07Rik|AI553404|Def-5|Taz4	testis expressed gene 2	protein-coding
mm_68144.1	chr7	102247082	102247087	-	1	NA	intron (NM_019566, intron 1 of 1)	intron (NM_019566, intron 1 of 1)	3034	NM_019566	56212	Mm.259795	NM_019566	ENSMUSG00000073982	Rhog	2810426G09Rik|Arhg|Sid10750	ras homolog family member G	protein-coding
mm_171292.1	chr3	90287671	90287672	+	1	NA	Intergenic	B1_Mm|SINE|Alu	17522	NR_105979	102465612		NR_105979	ENSMUSG00000099199	Mir7012	Gm27370|mmu-mir-7012	microRNA 7012	ncRNA
mm_136984.1	chr17	17064043	17064077	+	1	NA	promoter-TSS (NM_001163919)	promoter-TSS (NM_001163919)	-43	NM_001005358	449000	Mm.483718	NM_001005358	ENSMUSG00000096696	Zfp960	-	zinc finger protein 960	protein-coding
mm_9467.1	chr1	173333460	173333471	-	1	NA	promoter-TSS (NM_010045)	promoter-TSS (NM_010045)	38	NM_010045	13349	Mm.6393	NM_010045	ENSMUSG00000037872	Ackr1	AA162249|CCBP1|CD234|Darc|Dfy|ESTM35|FY|GPD	atypical chemokine receptor 1 (Duffy blood group)	protein-coding
mm_125290.1	chr15	36726907	36726941	+	1	NA	Intergenic	RMER17C-int|LTR|ERVK	64008	NM_001253807	22631	Mm.3360	NM_011740	ENSMUSG00000022285	Ywhaz	1110013I11Rik|14-3-3zeta|AI596267|AL022924|AU020854	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide	protein-coding
mm_128709.1	chr15	63912288	63912297	-	1	NA	promoter-TSS (NM_028992)	promoter-TSS (NM_028992)	5	NM_028992	74548	Mm.273185	NM_028992	ENSMUSG00000055748	Gsdmc4	9030605I04Rik	gasdermin C4	protein-coding
mm_71078.1	chr8	34608274	34608311	+	1	NA	intron (NR_040706, intron 2 of 4)	intron (NR_040706, intron 2 of 4)	32024	NR_040706	330734	Mm.149998	NR_040706	ENSMUSG00000109819	B930018H19Rik	B930018H19	RIKEN cDNA B930018H19 gene	ncRNA
mm_16816.1	chr2	11375040	11375082	-	1	NA	intron (NR_040615, intron 1 of 2)	intron (NR_040615, intron 1 of 2)	23439	NR_040615	77543	Mm.490670	NR_040615	ENSMUSG00000102674	8030442B05Rik	-	RIKEN cDNA 8030442B05 gene	ncRNA
mm_53994.1	chr6	6881951	6881985	-	1	NA	promoter-TSS (NM_010056)	promoter-TSS (NM_010056)	100	NM_198854	13395	Mm.4873	NM_010056	ENSMUSG00000029755	Dlx5	AI385752	distal-less homeobox 5	protein-coding
mm_151551.1	chr19	59458674	59458695	+	1	NA	promoter-TSS (NM_010132)	promoter-TSS (NM_010132)	-6	NM_010132	13797	Mm.245394	NM_010132	ENSMUSG00000043969	Emx2	Pdo	empty spiracles homeobox 2	protein-coding
mm_143391.1	chr17	69417292	69417303	-	1	NA	non-coding (NR_026848, exon 1 of 1)	non-coding (NR_026848, exon 1 of 1)	850	NR_026848	77533	Mm.266592	NR_026848		C030034I22Rik	-	RIKEN cDNA C030034I22 gene	ncRNA
mm_149562.1	chr19	12795723	12795732	+	1	NA	non-coding (NR_024093, exon 1 of 13)	non-coding (NR_024093, exon 1 of 13)	396	NR_024093	664779	Mm.290924	NM_001039718	ENSMUSG00000024695	Gm44505	Zfp91-Cntf|Zfp91Cntf	predicted readthrough transcript (NMD candidate), 44505	ncRNA
mm_82571.1	chr9	21079799	21079809	-	1	NA	exon (NM_027911, exon 8 of 13)	exon (NM_027911, exon 8 of 13)	-4216	NR_106050	102465656		NR_106050	ENSMUSG00000098907	Mir7082	Gm27933|mmu-mir-7082	microRNA 7082	ncRNA
mm_34173.1	chr4	140395749	140395772	+	1	NA	Intergenic	Intergenic	-148949	NM_198610	230868	Mm.298731	NM_198610	ENSMUSG00000040972	Igsf21	BC055811|Gm141	immunoglobulin superfamily, member 21	protein-coding
mm_127745.1	chr15	103453906	103453915	+	1	NA	promoter-TSS (NM_153505)	promoter-TSS (NM_153505)	85	NM_153505	105855	Mm.30805	NM_153505	ENSMUSG00000022488	Nckap1l	4930568P13Rik|AI463083|Hem1|Hemp1	NCK associated protein 1 like	protein-coding
mm_12049.1	chr2	59161618	59161636	+	1	NA	intron (NM_175464, intron 1 of 20)	CpG	777	NM_175464	227937	Mm.260938	NM_026361	ENSMUSG00000026991	Pkp4	5031422I09Rik|9430019K17Rik|Armrp|p0071	plakophilin 4	protein-coding
mm_166253.1	chr5	86917000	86917004	-	1	NA	3' UTR (NM_152811, exon 6 of 6)	3' UTR (NM_152811, exon 6 of 6)	9501	NM_152811	71773	Mm.26741	NM_152811	ENSMUSG00000035836	Ugt2b1	1300012D20Rik	UDP glucuronosyltransferase 2 family, polypeptide B1	protein-coding
mm_60715.1	chr7	45277540	45277551	+	1	NA	Intergenic	CpG	-5328	NM_001033176	76713	Mm.425445	NM_001033176	ENSMUSG00000070568	Slc6a21	1700039E15Rik|Gm19188	solute carrier family 6 member 21	protein-coding
mm_146319.1	chr18	80608623	80608628	+	1	NA	intron (NM_198429, intron 9 of 9)	intron (NM_198429, intron 9 of 9)	-64079	NR_028424	100039348	Mm.254722	NR_028424		Gm2176	A430076E10Rik	glucosamine-6-phosphate deaminase 1 pseudogene	pseudo
mm_107314.1	chr12	31265280	31265322	+	1	NA	promoter-TSS (NM_008482)	promoter-TSS (NM_008482)	7	NM_008482	16777	Mm.172674	NM_008482	ENSMUSG00000002900	Lamb1	C77966|C80098|C81607|D130003D08Rik|Lamb-1|Lamb1-1	laminin B1	protein-coding
mm_117410.1	chr13	74009336	74009359	-	1	NA	promoter-TSS (NM_182839)	promoter-TSS (NM_182839)	-72	NM_182839	72948	Mm.39752	NM_182839	ENSMUSG00000021573	Tppp	2900041A09Rik|AI849835	tubulin polymerization promoting protein	protein-coding
mm_159406.1	chr3	98762375	98762375	-	1	NA	promoter-TSS (NM_001161745)	promoter-TSS (NM_001161745)	35	NM_001161745	15494	Mm.158717	NM_001012306	ENSMUSG00000062410	Hsd3b3	9030618K22Rik|AI790201	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 3	protein-coding
mm_145237.1	chr18	50278365	50278367	+	1	NA	promoter-TSS (NM_001004061)	promoter-TSS (NM_001004061)	-3	NM_001004061	225497	Mm.329435	NM_001004061	ENSMUSG00000035420	Fam170a	Gm93|Znfd	family with sequence similarity 170, member A	protein-coding
mm_142115.1	chr17	35838260	35838264	-	1	NA	promoter-TSS (NM_011655)	promoter-TSS (NM_011655)	39	NM_011655	22154	Mm.273538	NM_011655	ENSMUSG00000001525	Tubb5	AA408537|AI596182|B130022C14Rik|M(beta)5	tubulin, beta 5 class I	protein-coding
mm_161841.1	chr17	88065297	88065297	-	1	NA	promoter-TSS (NM_001081034)	promoter-TSS (NM_001081034)	-12	NM_001081034	225055	Mm.386857	NM_001081034	ENSMUSG00000005371	Fbxo11	C80048|Jf	F-box protein 11	protein-coding
mm_113223.1	chr13	27059499	27059507	+	1	NA	exon (NM_011164, exon 2 of 5)	exon (NM_011164, exon 2 of 5)	1933	NM_011164	19109	Mm.1270	NM_011164	ENSMUSG00000021342	Prl	AV290867|Gha1|Prl1a1	prolactin	protein-coding
mm_146525.1	chr18	4353336	4353352	-	1	NA	promoter-TSS (NM_007746)	promoter-TSS (NM_007746)	-203	NR_040328	73915	Mm.482777	NR_040328		4833419F23Rik	-	RIKEN cDNA 4833419F23 gene	ncRNA
mm_138535.1	chr17	35247175	35247177	+	1	NA	intron (NM_019693, intron 5 of 10)	intron (NM_019693, intron 5 of 10)	3101	NR_105941	102465589		NR_105941	ENSMUSG00000098499	Mir6975	Gm27693|mmu-mir-6975	microRNA 6975	ncRNA
mm_172502.1	chr7	67418003	67418003	+	1	NA	Intergenic	L1Md_T|LINE|L1	-45145	NM_001291195	17258	Mm.132788	NM_001033713	ENSMUSG00000030557	Mef2a	A430079H05Rik	myocyte enhancer factor 2A	protein-coding
mm_78056.1	chr9	14860233	14860246	+	1	NA	promoter-TSS (NM_010287)	promoter-TSS (NM_010287)	29	NM_010287	14608	Mm.4672	NM_010287	ENSMUSG00000031932	Gpr83	AW045253|Gir|Gpr72|RP105|RP39|RP82	G protein-coupled receptor 83	protein-coding
mm_59767.1	chr7	28834025	28834030	+	1	NA	promoter-TSS (NM_010707)	promoter-TSS (NM_010707)	-143	NM_010707	16857	Mm.210336	NM_010707		Lgals6	galectin-6	lectin, galactose binding, soluble 6	protein-coding
mm_102245.1	chr11	55078121	55078145	-	1	NA	promoter-TSS (NM_177471)	promoter-TSS (NM_177471)	-2	NM_177471	52570	Mm.22361	NM_177471	ENSMUSG00000049588	Ccdc69	2210021E03Rik|D11Ertd461e	coiled-coil domain containing 69	protein-coding
mm_63794.1	chr7	132859239	132859266	+	1	NA	promoter-TSS (NM_198017)	promoter-TSS (NM_198017)	27	NM_198017	109359	Mm.274824	NM_198017	ENSMUSG00000030965	Fam175b	AA589499|AI853413|Abro1|C430003P19Rik	family with sequence similarity 175, member B	protein-coding
mm_70857.1	chr8	24395792	24395794	+	1	NA	Intergenic	Intergenic	43153	NM_026931	69068	Mm.25775	NM_026931	ENSMUSG00000056313	1810011O10Rik	1110065B09Rik|AW121743|AW321058	RIKEN cDNA 1810011O10 gene	protein-coding
mm_33485.1	chr4	130822181	130822201	+	1	NA	intron (NM_011520, intron 4 of 4)	intron (NM_011520, intron 4 of 4)	29654	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_47464.1	chr5	123671053	123671063	-	1	NA	intron (NM_001347468, intron 1 of 24)	intron (NM_001347468, intron 1 of 24)	13303	NM_019765	56430	Mm.241109	NM_019765	ENSMUSG00000049550	Clip1	1110007I12Rik|4631429H07Rik|AV017631|C81039|CLIP-170|CLIP170|CYLN1|Clip50|Rsn|mKIAA4046|restin	CAP-GLY domain containing linker protein 1	protein-coding
mm_45007.1	chr5	38491924	38491935	-	1	NA	intron (NM_145559, intron 1 of 10)	intron (NM_145559, intron 1 of 10)	-8544	NM_001012363	117591	Mm.260137	NM_145559	ENSMUSG00000005107	Slc2a9	Glut9|SLC2A9B|SLC2a9A	solute carrier family 2 (facilitated glucose transporter), member 9	protein-coding
mm_151723.1	chr19	4839257	4839278	-	1	NA	promoter-TSS (NM_016892)	promoter-TSS (NM_016892)	55	NM_016892	12460	Mm.434411	NM_016892	ENSMUSG00000034108	Ccs	Ccsd	copper chaperone for superoxide dismutase	protein-coding
mm_112645.1	chr13	16017065	16017104	+	1	NA	intron (NM_008380, intron 3 of 4)	intron (NM_008380, intron 3 of 4)	5233	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_60172.1	chr7	40987577	40987590	+	1	NA	promoter-TSS (NM_207248)	promoter-TSS (NM_207248)	-26	NM_207248	243944	Mm.333806	NM_207248	ENSMUSG00000091692	4930433I11Rik	Gm481	RIKEN cDNA 4930433I11 gene	protein-coding
mm_170519.1	chr19	31723530	31723541	+	1	NA	intron (NM_001013833, intron 1 of 17)	L1_Mus2|LINE|L1	41498	NM_001013833	19091	Mm.381170	NM_011160	ENSMUSG00000052920	Prkg1	AW125416|CGKI|Gm19690|Prkg1b|Prkgr1b	protein kinase, cGMP-dependent, type I	protein-coding
mm_132441.1	chr16	35939862	35939872	+	1	NA	promoter-TSS (NM_001013371)	promoter-TSS (NM_001013371)	-840	NM_001013371	209200	Mm.390852	NM_001013371	ENSMUSG00000049502	Dtx3l	AU042200|BC023741	deltex 3-like, E3 ubiquitin ligase	protein-coding
mm_32482.1	chr4	107889831	107889880	+	1	NA	promoter-TSS (NM_028754)	promoter-TSS (NM_028754)	29	NM_001347160	74098	Mm.274853	NM_028754	ENSMUSG00000028608	0610037L13Rik	1110008H16Rik	RIKEN cDNA 0610037L13 gene	protein-coding
mm_41110.1	chr5	87777436	87777444	+	1	NA	intron (NM_007785, intron 2 of 13)	intron (NM_007785, intron 2 of 13)	2990	NM_007785	12993	Mm.4908	NM_007785	ENSMUSG00000061937	Csn1s2a	Csng|PP22	casein alpha s2-like A	protein-coding
mm_102042.1	chr11	51950087	51950122	-	1	NA	Intergenic	Intergenic	-17527	NM_029976	52626	Mm.289456	NM_029976	ENSMUSG00000020392	Cdkn2aipnl	A430101B06Rik|AA409260|D11Ertd497e|MNCb-1520	CDKN2A interacting protein N-terminal like	protein-coding
mm_102148.1	chr11	53632572	53632590	-	1	NA	exon (NM_008355, exon 3 of 4)	exon (NM_008355, exon 3 of 4)	2121	NM_008355	16163	Mm.1284	NM_008355	ENSMUSG00000020383	Il13	Il-13	interleukin 13	protein-coding
mm_139767.1	chr17	64634493	64634497	+	1	NA	intron (NM_008549, intron 3 of 21)	T-rich|Low_complexity|Low_complexity	32846	NM_008549	17158	Mm.2433	NM_008549	ENSMUSG00000024085	Man2a1	Mana-2|Mana2|Map-2	mannosidase 2, alpha 1	protein-coding
mm_90140.1	chr10	118098177	118098202	+	1	NA	Intergenic	Intergenic	-43598	NM_001162904	17245	Mm.101191	NM_010785	ENSMUSG00000020212	Mdm1	Arrd2|Mdm-1	transformed mouse 3T3 cell double minute 1	protein-coding
mm_65274.1	chr7	24299388	24299406	-	1	NA	5' UTR (NM_009561, exon 1 of 7)	5' UTR (NM_009561, exon 1 of 7)	152	NM_009561	22719	Mm.12832	NM_009561	ENSMUSG00000050605	Zfp61	-	zinc finger protein 61	protein-coding
mm_60993.1	chr7	49246813	49246817	+	1	NA	5' UTR (NM_175272, exon 1 of 38)	5' UTR (NM_175272, exon 1 of 38)	626	NM_175272	78286	Mm.333881	NM_175272	ENSMUSG00000052512	Nav2	5330421F07Rik|AU067780|BQ960892|HELAD1|POMFIL2|RAINB1|RAINB2|Unc53H2|mKIAA3015	neuron navigator 2	protein-coding
mm_171147.1	chr3	153912056	153912063	-	1	NA	TTS (NR_028525)	TTS (NR_028525)	130	NR_028525	100217425		NR_028525		Snord45c	MBII-401	small nucleolar RNA, C/D box 45C	snoRNA
mm_111070.1	chr12	80128460	80128466	-	1	NA	intron (NR_033514, intron 2 of 2)	intron (NR_033514, intron 2 of 2)	4381	NR_033514	69548	Mm.269712	NR_033514	ENSMUSG00000097729	2310015A10Rik	5330419I17Rik	RIKEN cDNA 2310015A10 gene	ncRNA
mm_61409.1	chr7	73538012	73538058	+	1	NA	intron (NM_001081345, intron 2 of 38)	intron (NM_001081345, intron 2 of 38)	3711	NM_001081345	244059	Mm.34539	NM_001081345	ENSMUSG00000078671	Chd2	2810013C04Rik|2810040A01Rik|5630401D06Rik|AI851092|BC029703|CHD-2	chromodomain helicase DNA binding protein 2	protein-coding
mm_98130.1	chr11	87433219	87433260	+	1	NA	intron (NM_001199293, intron 1 of 30)	B1_Mur4|SINE|Alu	5648	NM_001199293	83560	Mm.440758	NM_031386	ENSMUSG00000010342	Tex14	C85585	testis expressed gene 14	protein-coding
mm_18629.1	chr2	69206199	69206207	-	1	NA	promoter-TSS (NM_001199123)	promoter-TSS (NM_001199123)	10	NM_025565	66442	Mm.272969	NM_025565	ENSMUSG00000005233	Spc25	2600017H08Rik|2610205L13Rik|Spbc25	SPC25, NDC80 kinetochore complex component, homolog (S. cerevisiae)	protein-coding
mm_2466.1	chr1	105456545	105456551	+	1	NA	Intergenic	Intergenic	-99838	NM_001160368	320311	Mm.389162	NM_178779	ENSMUSG00000047496	Rnf152	A930029B02Rik	ring finger protein 152	protein-coding
mm_107992.1	chr12	73286799	73286805	+	1	NA	promoter-TSS (NM_029580)	promoter-TSS (NM_029580)	-46	NM_001037717	625098	Mm.32075	NM_001037717	ENSMUSG00000044712	Slc38a6	AW322671|EG625098	solute carrier family 38, member 6	protein-coding
mm_34115.1	chr4	139200498	139200505	+	1	NA	intron (NM_001271405, intron 1 of 8)	intron (NM_001271405, intron 1 of 8)	6390	NM_001271405	12345	Mm.2945	NM_009798	ENSMUSG00000028745	Capzb	1700120C01Rik|AI325129|CPB1|CPB2|CPbeat2|CPbeta1|CPbeta2|Cappb1	capping protein (actin filament) muscle Z-line, beta	protein-coding
mm_26926.1	chr3	20249815	20249840	-	1	NA	exon (NM_029706, exon 11 of 11)	exon (NM_029706, exon 11 of 11)	-7646	NM_007753	12873	Mm.1135	NM_007753	ENSMUSG00000001865	Cpa3	MC-CPA	carboxypeptidase A3, mast cell	protein-coding
mm_47596.1	chr5	124862369	124862410	-	1	NA	promoter-TSS (NM_001081750)	promoter-TSS (NM_001081750)	-168	NM_144819	215707	Mm.389693	NM_144819	ENSMUSG00000037979	Ccdc92	AW050178|D5Bwg0834e	coiled-coil domain containing 92	protein-coding
mm_28810.1	chr3	96256272	96256307	-	1	NA	Intergenic	Intergenic	7028	NM_033596	97122	Mm.227295	NM_033596	ENSMUSG00000091405	Hist2h4	H4|X04652	histone cluster 2, H4	protein-coding
mm_167488.1	chr9	5857244	5857248	+	1	NA	Intergenic	Intergenic	-311366	NM_027924	71785	Mm.390122	NM_027924	ENSMUSG00000032006	Pdgfd	1110003I09Rik	platelet-derived growth factor, D polypeptide	protein-coding
mm_132619.1	chr16	38761702	38761707	+	1	NA	intron (NM_001285793, intron 4 of 6)	ORR1F|LTR|ERVL-MaLR	19445	NM_001285793	56375	Mm.182377	NM_019804	ENSMUSG00000022793	B4galt4	9130402O08Rik|B4galt-IV|b4Gal-T4|beta4Gal-T4|beta4GalT-IV	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 4	protein-coding
mm_116571.1	chr13	47099398	47099434	-	1	NA	exon (NM_025900, exon 6 of 11)	exon (NM_025900, exon 6 of 11)	6805	NM_025900	110052	Mm.131150	NM_025900	ENSMUSG00000021377	Dek	1810019E15Rik|D13H6S231E	DEK oncogene (DNA binding)	protein-coding
mm_12629.1	chr2	74704862	74704914	+	1	NA	promoter-TSS (NM_001290730)	promoter-TSS (NM_001290730)	273	NM_001290731	15437	Mm.280673	NM_008276	ENSMUSG00000027102	Hoxd8	4921540P06Rik|AI047735|Hox-4.3|Hox-5.4	homeobox D8	protein-coding
mm_154111.1	chr19	57134644	57134656	-	1	NA	exon (NM_178688, exon 5 of 25)	exon (NM_178688, exon 5 of 25)	-15626	NM_001103178	226251	Mm.217161	NM_178688	ENSMUSG00000025085	Ablim1	2210411C18Rik|2610209L21Rik|4833406P10Rik|9330196J19Rik|AV079770|AW060987|AW215784|Limab1|mKIAA0059	actin-binding LIM protein 1	protein-coding
mm_14084.1	chr2	125068149	125068163	+	1	NA	promoter-TSS (NM_175034)	promoter-TSS (NM_175034)	29	NM_175034	317750	Mm.330538	NM_175034	ENSMUSG00000035183	Slc24a5	F630045L20Rik|JSX|NCKX5|NCX5|Oca6	solute carrier family 24, member 5	protein-coding
mm_88089.1	chr10	68530096	68530101	+	1	NA	intron (NM_028491, intron 2 of 7)	intron (NM_028491, intron 2 of 7)	11777	NM_028491	73287	Mm.141830	NM_028491	ENSMUSG00000019945	1700040L02Rik	-	RIKEN cDNA 1700040L02 gene	protein-coding
mm_51455.1	chr6	81923646	81923706	+	1	NA	promoter-TSS (NM_177884)	promoter-TSS (NM_177884)	7	NM_177884	330361	Mm.474487	NM_177884	ENSMUSG00000035125	Gcfc2	A130099G21|AW146020|GCF2|Tcf9	GC-rich sequence DNA binding factor 2	protein-coding
mm_121986.1	chr14	26439256	26439269	-	1	NA	intron (NM_001310445, intron 14 of 22)	intron (NM_001310445, intron 14 of 22)	81715	NR_038005	71106	Mm.158564	NR_038005	ENSMUSG00000021874	4933413J09Rik	GCSE	RIKEN cDNA 4933413J09 gene	ncRNA
mm_111087.1	chr12	80260497	80260505	-	1	NA	promoter-TSS (NM_134156)	promoter-TSS (NM_134156)	-120	NM_001346669	109711	Mm.253564	NM_134156	ENSMUSG00000015143	Actn1	3110023F10Rik|Actn1a	actinin, alpha 1	protein-coding
mm_162755.1	chr10	60479685	60479706	+	1	NA	intron (NM_023370, intron 12 of 68)	(TCTA)n|Simple_repeat|Simple_repeat	79969	NM_001164374	100302688	Mm.444135	NM_001164374	ENSMUSG00000090439	Gm17455	-	predicted gene, 17455	protein-coding
mm_52505.1	chr6	115360951	115360962	+	1	NA	promoter-TSS (NM_001127330)	promoter-TSS (NM_001127330)	5	NM_001127330	19016	Mm.3020	NM_011146	ENSMUSG00000000440	Pparg	Nr1c3|PPAR-gamma|PPAR-gamma2|PPARgamma|PPARgamma2	peroxisome proliferator activated receptor gamma	protein-coding
mm_10373.1	chr2	11725063	11725076	+	1	NA	intron (NR_073191, intron 4 of 5)	B3A|SINE|B2	19357	NM_001271500	16169	Mm.200196	NM_008358	ENSMUSG00000023206	Il15ra	AA690181|IL-15RA	interleukin 15 receptor, alpha chain	protein-coding
mm_14819.1	chr2	146855816	146855825	+	1	NA	promoter-TSS (NM_001033298)	promoter-TSS (NM_001033298)	-69	NM_001033298	228730	Mm.292352	NM_001033298	ENSMUSG00000074749	Kiz	Gm114|Ncrna00153|Plk1s1	kizuna centrosomal protein	protein-coding
mm_66506.1	chr7	45092185	45092196	-	1	NA	promoter-TSS (NM_026555)	promoter-TSS (NM_026555)	23	NM_026555	52377	Mm.29997	NM_026555	ENSMUSG00000019539	Rcn3	6030455P07Rik|D530026G20Rik|D7Ertd671e|RLP49	reticulocalbin 3, EF-hand calcium binding domain	protein-coding
mm_164705.1	chr17	51813487	51813519	-	1	NA	intron (NM_001163632, intron 1 of 10)	CpG	-1449	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_108147.1	chr12	76255484	76255494	+	1	NA	5' UTR (NM_138745, exon 1 of 28)	5' UTR (NM_138745, exon 1 of 28)	257	NM_138745	108156	Mm.29584	NM_138745	ENSMUSG00000021048	Mthfd1	Dcs|E430024A07Rik|Mthfd	methylenetetrahydrofolate dehydrogenase (NADP+ dependent), methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthase	protein-coding
mm_76019.1	chr8	75026057	75026059	-	1	NA	intron (NM_178017, intron 9 of 10)	RLTR13B1|LTR|ERVK	-7628	NM_001136259	21968	Mm.1967	NM_011622	ENSMUSG00000042870	Tom1	-	target of myb1 trafficking protein	protein-coding
mm_133697.1	chr16	92824600	92824613	+	1	NA	intron (NM_001111022, intron 2 of 6)	intron (NM_001111022, intron 2 of 6)	1468	NM_001111021	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_15685.1	chr2	163630963	163630978	+	1	NA	exon (NM_012032, exon 6 of 10)	exon (NM_012032, exon 6 of 10)	-13880	NR_028113	68386	Mm.410649	NR_028113	ENSMUSG00000058812	0610039K10Rik	-	RIKEN cDNA 0610039K10 gene	ncRNA
mm_134923.1	chr16	30389313	30389348	-	1	NA	promoter-TSS (NM_001128094)	promoter-TSS (NM_001128094)	-800	NM_001128096	224088	Mm.8924	NM_001128094	ENSMUSG00000022533	Atp13a3	AU022875|Gm1745|Gm541|Gm542	ATPase type 13A3	protein-coding
mm_155288.1	chrX	61183476	61183486	+	1	NA	3' UTR (NM_001166658, exon 1 of 1)	3' UTR (NM_001166658, exon 1 of 1)	2077	NM_001166658	631990	Mm.401324	NM_001166658	ENSMUSG00000090546	Cdr1	100039759|Cdr|Cdr34|EG631990|Gm2409|Gm7077	cerebellar degeneration related antigen 1	protein-coding
mm_111859.1	chr12	107959039	107959046	-	1	NA	intron (NM_001286343, intron 1 of 1)	MIR3|SINE|MIR	44372	NM_001079883	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_135117.1	chr16	35841159	35841173	-	1	NA	exon (NM_001039530, exon 14 of 17)	exon (NM_001039530, exon 14 of 17)	30216	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_35818.1	chr4	46991823	46991831	-	1	NA	promoter-TSS (NM_001081141)	promoter-TSS (NM_001081141)	-113	NM_001081141	242425	Mm.101909	NM_001081141	ENSMUSG00000039809	Gabbr2	GABABR2|Gb2|Gm425|Gpr51	gamma-aminobutyric acid (GABA) B receptor, 2	protein-coding
mm_79806.1	chr9	64176970	64177018	+	1	NA	exon (NM_024212, exon 6 of 10)	exon (NM_024212, exon 6 of 10)	1562	NR_028548	100217453		NR_028548	ENSMUSG00000094411	Snord16a	MBII-98	small nucleolar RNA, C/D box 16A	snoRNA
mm_116032.1	chr13	25270077	25270094	-	1	NA	promoter-TSS (NM_009513)	promoter-TSS (NM_009513)	-89	NM_009513	22360	Mm.4766	NM_009513	ENSMUSG00000048978	Nrsn1	Neurensin-1|Neuro-p24|Vmp	neurensin 1	protein-coding
mm_96713.1	chr11	69662639	69662646	+	1	NA	promoter-TSS (NR_035455)	promoter-TSS (NR_035455)	7	NR_125917	24070	Mm.89579	NM_011900	ENSMUSG00000018761	Mpdu1	LEC35|SL15|Supl15h	mannose-P-dolichol utilization defect 1	protein-coding
mm_28177.1	chr3	88000365	88000389	-	1	NA	promoter-TSS (NM_001109758)	promoter-TSS (NM_001109758)	-21	NM_001109758	12032	Mm.4598	NM_007529	ENSMUSG00000004892	Bcan	Cspg7	brevican	protein-coding
mm_140890.1	chr17	23975534	23975540	-	1	NA	promoter-TSS (NM_013921)	promoter-TSS (NM_013921)	-307	NM_013921	30943	Mm.142568	NM_013921	ENSMUSG00000024124	Prss30	2010015P21Rik|Disp|Disp1|Tmprss8	protease, serine 30	protein-coding
mm_13637.1	chr2	114047460	114047491	+	1	NA	exon (NM_009608, exon 7 of 7)	exon (NM_009608, exon 7 of 7)	5400	NM_009608	11464	Mm.686	NM_009608	ENSMUSG00000068614	Actc1	Actc-1	actin, alpha, cardiac muscle 1	protein-coding
mm_33842.1	chr4	135759755	135759759	+	1	NA	promoter-TSS (NM_001085509)	promoter-TSS (NM_001085509)	42	NM_001085509	242702	Mm.318639	NM_001085509	ENSMUSG00000037139	Myom3	8430427K15Rik|Gm434	myomesin family, member 3	protein-coding
mm_163374.1	chr12	44075498	44075498	+	1	NA	Intergenic	LTR33|LTR|ERVL	134570	NM_013760	27362	Mm.27432	NM_013760	ENSMUSG00000014905	Dnajb9	AA408011|AA673251|AA673481|AW556981|ERdj4|Mdg1|mDj7	DnaJ heat shock protein family (Hsp40) member B9	protein-coding
mm_69653.1	chr7	139683798	139683853	-	1	NA	promoter-TSS (NM_001302546)	promoter-TSS (NM_001302546)	-10	NM_001302546	212124	Mm.425507	NM_177212	ENSMUSG00000049571	Cfap46	9330101J02Rik|E030019B06Rik|Gm170|Ttc40	cilia and flagella associated protein 46	protein-coding
mm_42270.1	chr5	114146325	114146343	+	1	NA	Intergenic	Intergenic	15178	NM_011677	22256	Mm.1393	NM_011677	ENSMUSG00000029591	Ung	UNG1|UNG2	uracil DNA glycosylase	protein-coding
mm_125134.1	chr15	30457592	30457599	+	1	NA	intron (NM_008729, intron 2 of 22)	intron (NM_008729, intron 2 of 22)	285002	NM_008729	18163	Mm.321648	NM_008729	ENSMUSG00000022240	Ctnnd2	Catnd2|Nprap|neurojugin	catenin (cadherin associated protein), delta 2	protein-coding
mm_160559.1	chr9	52047131	52047131	+	1	NA	promoter-TSS (NM_009041)	promoter-TSS (NM_009041)	-19	NM_001104616	19684	Mm.245746	NM_009041	ENSMUSG00000032050	Rdx	AA516625	radixin	protein-coding
mm_58060.1	chr6	136857728	136857750	-	1	NA	promoter-TSS (NM_026639)	promoter-TSS (NM_026639)	-139	NM_026639	109978	Mm.31840	NM_026639	ENSMUSG00000030217	Art4	4432404K01Rik|ARTC4|DO|DOK1	ADP-ribosyltransferase 4	protein-coding
mm_94560.1	chr11	11667769	11667791	+	1	NA	Intergenic	MIR3|SINE|MIR	-18145	NM_009578	22778	Mm.103545	NM_009578	ENSMUSG00000018654	Ikzf1	5832432G11Rik|Ikaros|LyF-1|Zfpn1a1|Znfn1a1|hlk-1|mKIAA4227	IKAROS family zinc finger 1	protein-coding
mm_35745.1	chr4	45408909	45408937	-	1	NA	promoter-TSS (NM_001009949)	promoter-TSS (NM_001009949)	-157	NM_001009949	230125	Mm.260210	NM_001009949	ENSMUSG00000045973	Slc25a51	9130208E07Rik|D130005A03Rik|Gm138|Mcart1	solute carrier family 25, member 51	protein-coding
mm_13408.1	chr2	104042033	104042039	+	1	NA	intron (NM_020593, intron 3 of 9)	L1MEg|LINE|L1	14237	NM_212433	57443	Mm.143768	NM_020593	ENSMUSG00000027180	Fbxo3	1200002G09Rik|1700026K02Rik|AI046358|Fba	F-box protein 3	protein-coding
mm_40352.1	chr5	46034409	46034421	+	1	NA	Intergenic	Intergenic	-102006	NR_110478	78106	Mm.243807	NR_110478	ENSMUSG00000106602	4930405L22Rik	-	RIKEN cDNA 4930405L22 gene	ncRNA
mm_36937.1	chr4	108579249	108579308	-	1	NA	promoter-TSS (NM_172697)	promoter-TSS (NM_172697)	58	NM_172697	230596	Mm.157534	NM_172697	ENSMUSG00000063800	Prpf38a	2410002M20Rik	PRP38 pre-mRNA processing factor 38 (yeast) domain containing A	protein-coding
mm_140804.1	chr17	22081292	22081307	-	1	NA	Intergenic	CpG	84678	NM_177596	210853	Mm.441622	NM_177596	ENSMUSG00000063383	Zfp947	6720451E15|EG210853|Gm4769	zinc finger protein 947	protein-coding
mm_67312.1	chr7	79466168	79466240	-	1	NA	promoter-TSS (NM_017462)	promoter-TSS (NM_017462)	69	NM_017462	18975	Mm.3616	NM_017462	ENSMUSG00000039176	Polg	AA409516|PolgA	polymerase (DNA directed), gamma	protein-coding
mm_74362.1	chr8	128359243	128359291	+	1	NA	promoter-TSS (NR_035436)	promoter-TSS (NR_035436)	26	NR_035436	100316680		NR_035436	ENSMUSG00000084523	Mir1903	Mirn1903|mmu-mir-1903	microRNA 1903	ncRNA
mm_936.1	chr1	55796377	55796425	+	1	NA	Intergenic	Lx8|LINE|L1	-134840	NR_045837	329159	Mm.98697	NR_045837	ENSMUSG00000099950	9130227L01Rik	-	RIKEN cDNA 9130227L01 gene	ncRNA
mm_30208.1	chr3	144760860	144760868	-	1	NA	non-coding (NR_130895, exon 1 of 13)	non-coding (NR_130895, exon 1 of 13)	113	NR_130895	12722	Mm.454553	NM_009899	ENSMUSG00000056025	Clca3a1	Cacc|Clca1	chloride channel accessory 3A1	protein-coding
mm_77087.1	chr8	110776447	110776448	-	1	NA	intron (NM_029646, intron 1 of 7)	B1_Mur2|SINE|Alu	29477	NM_029646	76527	Mm.77697	NM_029646	ENSMUSG00000031750	Il34	2010004A03Rik|AI593503	interleukin 34	protein-coding
mm_107526.1	chr12	40472719	40472733	+	1	NA	intron (NM_172803, intron 1 of 52)	ORR1B2|LTR|ERVL-MaLR	26673	NM_172803	238130	Mm.341423	NM_172803	ENSMUSG00000035954	Dock4	5330406C03|6330411N01Rik|AF263288|C030023J22|mKIAA0716	dedicator of cytokinesis 4	protein-coding
mm_138284.1	chr17	34611808	34611820	+	1	NA	exon (NM_018862, exon 6 of 7)	exon (NM_018862, exon 6 of 7)	2800	NM_018862	55979	Mm.8684	NM_018862	ENSMUSG00000034254	Agpat1	1-AGP|1-AGPAT|AW047140	1-acylglycerol-3-phosphate O-acyltransferase 1 (lysophosphatidic acid acyltransferase, alpha)	protein-coding
mm_6881.1	chr1	84580700	84580710	-	1	NA	exon (NM_152915, exon 4 of 13)	exon (NM_152915, exon 4 of 13)	-115134	NR_039588	100628595		NR_039588	ENSMUSG00000093254	Mir5126	mir-5126|mmu-mir-5126|mu-mir-5126	microRNA 5126	ncRNA
mm_118231.1	chr13	111489836	111489890	-	1	NA	5' UTR (NM_028487, exon 1 of 13)	5' UTR (NM_028487, exon 1 of 13)	178	NM_028487	73274	Mm.57286	NM_028487	ENSMUSG00000032745	Gpbp1	1700034P14Rik|AU019836|D230035M11Rik|Gpbp|mGPBP	GC-rich promoter binding protein 1	protein-coding
mm_117531.1	chr13	83379059	83379060	-	1	NA	Intergenic	Intergenic	-124975	NM_001347572	17260	Mm.24001	NM_025282	ENSMUSG00000005583	Mef2c	5430401D19Rik|9930028G15Rik|AV011172|Mef2	myocyte enhancer factor 2C	protein-coding
mm_127196.1	chr15	99074969	99075005	+	1	NA	promoter-TSS (NM_030159)	promoter-TSS (NM_030159)	14	NM_030159	78733	Mm.124905	NM_030159	ENSMUSG00000032783	Troap	AW476063|E130301L11Rik|tastin	trophinin associated protein	protein-coding
mm_126613.1	chr15	83035492	83035496	+	1	NA	Intergenic	Intergenic	-2097	NM_001271411	74039	Mm.32584	NM_028728	ENSMUSG00000058099	Nfam1	4921501M20Rik|Cnaip	Nfat activating molecule with ITAM motif 1	protein-coding
mm_45822.1	chr5	87692826	87692832	-	1	NA	3' UTR (NM_001286023, exon 7 of 7)	3' UTR (NM_001286023, exon 7 of 7)	6596	NM_001286020	12991	Mm.268737	NM_009972	ENSMUSG00000063157	Csn2	Csnb	casein beta	protein-coding
mm_12598.1	chr2	74675008	74675032	+	1	NA	promoter-TSS (NM_008274)	promoter-TSS (NM_008274)	7	NM_008274	15432	Mm.57124	NM_008274	ENSMUSG00000001823	Hoxd12	Hox-4.7|Hox-5.6	homeobox D12	protein-coding
mm_119102.1	chr14	30951407	30951415	+	1	NA	promoter-TSS (NM_001308328)	promoter-TSS (NM_001308328)	34	NM_011849	23955	Mm.251494	NM_011849	ENSMUSG00000021918	Nek4	Stk2	NIMA (never in mitosis gene a)-related expressed kinase 4	protein-coding
mm_130049.1	chr15	89147150	89147195	-	1	NA	intron (NM_011161, intron 1 of 11)	intron (NM_011161, intron 1 of 11)	2434	NM_011161	19094	Mm.91969	NM_011161	ENSMUSG00000053137	Mapk11	P38b|Prkm11|Sapk2|Sapk2b|p38-2|p38beta|p38beta2	mitogen-activated protein kinase 11	protein-coding
mm_125773.1	chr15	74597818	74597828	+	1	NA	Intergenic	Intergenic	38495	NM_001177437	69439	Mm.263708	NM_001177437	ENSMUSG00000022603	Mroh4	1700016M24Rik	maestro heat-like repeat family member 4	protein-coding
mm_131837.1	chr16	22960922	22960932	+	1	NA	exon (NM_053176, exon 7 of 7)	exon (NM_053176, exon 7 of 7)	9855	NM_053176	94175	Mm.358794	NM_053176	ENSMUSG00000022877	Hrg	AI265597|AW413091|D16jh2|D18020|Hprg|Hrgp	histidine-rich glycoprotein	protein-coding
mm_117167.1	chr13	62858703	62858723	-	1	NA	promoter-TSS (NM_007994)	promoter-TSS (NM_007994)	-343	NM_007994	14120	Mm.391871	NM_007994	ENSMUSG00000021456	Fbp2	Fbp-1|Fbp1|Rae-30	fructose bisphosphatase 2	protein-coding
mm_18203.1	chr2	46442682	46442713	-	1	NA	Intergenic	Intergenic	746092	NR_040497	69405	Mm.396184	NR_040497	ENSMUSG00000086202	1700019E08Rik	-	RIKEN cDNA 1700019E08 gene	ncRNA
mm_171315.1	chr3	95427649	95427650	+	1	NA	intron (NR_033637, intron 1 of 2)	CpG	300	NR_033637	100043305	Mm.412052	NR_033637		Gm4349	-	SET domain, bifurcated 1 pseudogene	pseudo
mm_68580.1	chr7	115859848	115859864	-	1	NA	intron (NM_001025560, intron 2 of 15)	intron (NM_001025560, intron 2 of 15)	-13716	NM_001277326	20679	Mm.323365	NM_011445	ENSMUSG00000051910	Sox6	AI987981|SOX-LZ	SRY (sex determining region Y)-box 6	protein-coding
mm_75068.1	chr8	33826173	33826175	-	1	NA	intron (NM_001042674, intron 5 of 7)	Charlie1a|DNA|hAT-Charlie	-78404	NM_001206849	72632	Mm.443483	NM_001206849	ENSMUSG00000094500	Smim18	2700090O03Rik|AI835723	small integral membrane protein 18	protein-coding
mm_54516.1	chr6	35512161	35512224	-	1	NA	3' UTR (NM_008098, exon 4 of 4)	3' UTR (NM_008098, exon 4 of 4)	27696	NM_008098	14489	Mm.182746	NM_008098	ENSMUSG00000029840	Mtpn	5033418D15Rik|Gcdp|V1	myotrophin	protein-coding
mm_156614.1	chrX	153499346	153499358	+	1	NA	exon (NM_018798, exon 1 of 1)	exon (NM_018798, exon 1 of 1)	1120	NM_018798	54609	Mm.430772	NM_018798	ENSMUSG00000050148	Ubqln2	Chap1|Dsk2|HRIHFB2157|Plic-2|Plic2	ubiquilin 2	protein-coding
mm_76.1	chr1	6730106	6730117	+	1	NA	promoter-TSS (NR_045189)	promoter-TSS (NR_045189)	60	NR_045188	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding
mm_86967.1	chr10	25375200	25375234	+	1	NA	intron (NM_001199265, intron 1 of 19)	intron (NM_001199265, intron 1 of 19)	15419	NM_001199265	13822	Mm.306026	NM_013511	ENSMUSG00000019978	Epb41l2	4.1G|AW555191|D10Ertd398e|Epb4.1l2|NBL2	erythrocyte membrane protein band 4.1 like 2	protein-coding
mm_82089.1	chr9	123049379	123049425	+	1	NA	intron (NM_177911, intron 6 of 13)	intron (NM_177911, intron 6 of 13)	14661	NM_177911	331046	Mm.195309	NM_177911	ENSMUSG00000025787	Tgm4	9530008N10Rik|Eapa1|TGP	transglutaminase 4 (prostate)	protein-coding
mm_61839.1	chr7	88288972	88288984	+	1	NA	3' UTR (NM_001311790, exon 4 of 4)	3' UTR (NM_001311790, exon 4 of 4)	10893	NM_001311790	13032	Mm.89295	NM_009982	ENSMUSG00000030560	Ctsc	AI047818|CatC|DPP1|DPPI	cathepsin C	protein-coding
mm_53581.1	chr6	137425322	137425337	+	1	NA	intron (NM_001164402, intron 6 of 15)	(CA)n|Simple_repeat|Simple_repeat	14608	NM_001164403	19277	Mm.186361	NM_011216	ENSMUSG00000030223	Ptpro	D28|GLEPP1|PTPBK|PTPROt|PTPU2|PTPoc|PTPphi|Ptpn15|R-PTP-O	protein tyrosine phosphatase, receptor type, O	protein-coding
mm_164544.1	chr17	8506336	8506353	+	1	NA	Intergenic	Intergenic	-20457	NM_001290707	23984	Mm.87161	NM_011866	ENSMUSG00000023868	Pde10a	-	phosphodiesterase 10A	protein-coding
mm_99479.1	chr11	102604611	102604621	+	1	NA	5' UTR (NM_020510, exon 1 of 1)	5' UTR (NM_020510, exon 1 of 1)	185	NM_020510	57265	Mm.36416	NM_020510	ENSMUSG00000050288	Fzd2	AL033370|AW456835|Fz10|Fzd10|Mfz10|Mfz10a	frizzled class receptor 2	protein-coding
mm_5274.1	chr1	18237474	18237478	-	1	NA	promoter-TSS (NM_001039123)	promoter-TSS (NM_001039123)	-33	NM_001039123	654460	Mm.389000	NM_001039123	ENSMUSG00000073735	Defb18	BD-18|EG654460|mBD-18	defensin beta 18	protein-coding
mm_91848.1	chr10	58651693	58651696	-	1	NA	intron (NM_010100, intron 1 of 11)	intron (NM_010100, intron 1 of 11)	24002	NM_010100	13608	Mm.174523	NM_010100	ENSMUSG00000003227	Edar	ED1R|ED3|ED5|EDA-A1R|EDA3|dl	ectodysplasin-A receptor	protein-coding
mm_34002.1	chr4	137920783	137920830	+	1	NA	intron (NM_199307, intron 3 of 19)	intron (NM_199307, intron 3 of 19)	58569	NM_199307	230857	Mm.401062	NM_199307	ENSMUSG00000057530	Ece1	AW322500|ECE-1|ECE-1a|ECE-1b|ECE-1d	endothelin converting enzyme 1	protein-coding
mm_2759.1	chr1	130163857	130163867	+	1	NA	intron (NM_172485, intron 19 of 27)	intron (NM_172485, intron 19 of 27)	259181	NM_007827	13137	Mm.436759	NM_007827	ENSMUSG00000026401	Cd55b	AI323748|Daf|Daf-TM|Daf2|TM-DAF	CD55 molecule, decay accelerating factor for complement B	protein-coding
mm_70699.1	chr8	15032410	15032435	+	1	NA	3' UTR (NM_029116, exon 2 of 2)	3' UTR (NM_029116, exon 2 of 2)	13656	NR_037972	434285	Mm.334425	NM_001007591	ENSMUSG00000049008	BB014433	-	expressed sequence BB014433	ncRNA
mm_169250.1	chr13	76180421	76180428	+	1	NA	intron (NM_001081352, intron 41 of 43)	BGLII|LTR|ERVK	81690	NM_001081352	218343	Mm.277964	NM_001081352	ENSMUSG00000033991	Ttc37	mKIAA0372	tetratricopeptide repeat domain 37	protein-coding
mm_98778.1	chr11	96789236	96789254	+	1	NA	5' UTR (NM_007622, exon 1 of 6)	5' UTR (NM_007622, exon 1 of 6)	109	NM_007622	12412	Mm.29055	NM_007622	ENSMUSG00000018666	Cbx1	Cbx|Cbx-rs2|E430007M08Rik|HP1B|Hp1beta|M31|MOD1	chromobox 1	protein-coding
mm_171996.1	chr6	104263185	104263185	-	1	NA	Intergenic	L1Md_T|LINE|L1	-229859	NM_017383	53870	Mm.321671	NM_017383	ENSMUSG00000030092	Cntn6	NB-3	contactin 6	protein-coding
mm_138321.1	chr17	34837245	34837294	+	1	NA	promoter-TSS (NM_019442)	promoter-TSS (NM_019442)	250	NM_001163770	112403	Mm.275309	NM_033613	ENSMUSG00000040482	Dxo	Dom3z|NG6	decapping exoribonuclease	protein-coding
mm_13906.1	chr2	120484360	120484374	+	1	NA	intron (NM_001109761, intron 3 of 20)	intron (NM_001109761, intron 3 of 20)	7458	NM_001109761	12335	Mm.458021	NM_007601	ENSMUSG00000079110	Capn3	AI323605|Capa-3|Capa3|Lp82|p94	calpain 3	protein-coding
mm_138970.1	chr17	44839318	44839321	+	1	NA	intron (NM_178652, intron 2 of 11)	intron (NM_178652, intron 2 of 11)	-24522	NR_073392	12393	Mm.391013	NM_009820	ENSMUSG00000039153	Runx2	AML3|Cbf|Cbfa-1|Cbfa1|LS3|Osf2|PEBP2aA|Pebp2a1|Pebpa2a	runt related transcription factor 2	protein-coding
mm_149058.1	chr19	8839459	8839470	+	1	NA	promoter-TSS (NM_010316)	promoter-TSS (NM_010316)	136	NM_008144	14705	Mm.345134	NM_008144	ENSMUSG00000071657	Bscl2	2900097C17Rik|AI046355|Gng3lg	Berardinelli-Seip congenital lipodystrophy 2 (seipin)	protein-coding
mm_24810.1	chr3	95588961	95588988	+	1	NA	promoter-TSS (NM_001177669)	promoter-TSS (NM_001177669)	40	NM_001177670	229593	Mm.245830	NM_146133	ENSMUSG00000046519	Golph3l	2010204I15Rik|AU015439|AW549227|C77637|Gpp34r	golgi phosphoprotein 3-like	protein-coding
mm_124809.1	chr15	8967930	8967936	+	1	NA	promoter-TSS (NM_198024)	promoter-TSS (NM_198024)	-16	NM_198024	223332	Mm.321371	NM_198024	ENSMUSG00000048424	Ranbp3l	C130037N17Rik	RAN binding protein 3-like	protein-coding
mm_125757.1	chr15	73830074	73830095	+	1	NA	intron (NM_001033365, intron 1 of 10)	intron (NM_001033365, intron 1 of 10)	9587	NM_001033365	268816	Mm.440635	NM_001033365	ENSMUSG00000072487	Mroh5	Gm628	maestro heat-like repeat family member 5	protein-coding
mm_133829.1	chr16	95900493	95900503	+	1	NA	intron (NR_040484, intron 1 of 3)	L1MC5|LINE|L1	-1785	NR_040485	69776	Mm.120470	NR_040484	ENSMUSG00000086899	1600002D24Rik	-	RIKEN cDNA 1600002D24 gene	ncRNA
mm_115861.1	chr13	21440692	21440713	-	1	NA	promoter-TSS (NM_001162919)	promoter-TSS (NM_001162919)	8	NM_001162919	319207	Mm.434384	NM_001012311	ENSMUSG00000055313	Pgbd1	4921509E05Rik	piggyBac transposable element derived 1	protein-coding
mm_119435.1	chr14	46379448	46379466	+	1	NA	promoter-TSS (NR_037981)	promoter-TSS (NR_037981)	-67	NR_037981	100041724	Mm.383311	NM_001099324	ENSMUSG00000079261	Gm15217	OTTMUSG00000019524	predicted gene 15217	ncRNA
mm_45858.1	chr5	87788618	87788621	-	1	NA	3' UTR (NM_001304768, exon 13 of 13)	3' UTR (NM_001304768, exon 13 of 13)	14169	NM_007785	12993	Mm.4908	NM_007785	ENSMUSG00000061937	Csn1s2a	Csng|PP22	casein alpha s2-like A	protein-coding
mm_108808.1	chr12	92809671	92809681	+	1	NA	Intergenic	Lx7|LINE|L1	635147	NR_126436	75295	Mm.243878	NR_126436		4930559C10Rik	-	RIKEN cDNA 4930559C10 gene	ncRNA
mm_149679.1	chr19	20492578	20492588	+	1	NA	promoter-TSS (NR_015502)	promoter-TSS (NR_015502)	-132	NR_015502	320092	Mm.482524	NR_015502		E030003E18Rik	1700127G21Rik	RIKEN cDNA E030003E18 gene	ncRNA
mm_111673.1	chr12	103338315	103338399	-	1	NA	intron (NM_023049, intron 2 of 9)	intron (NM_023049, intron 2 of 9)	17644	NM_023049	65256	Mm.27159	NM_023049	ENSMUSG00000021200	Asb2	1110008E15Rik	ankyrin repeat and SOCS box-containing 2	protein-coding
mm_2794.1	chr1	130851460	130851465	+	1	NA	3' UTR (NM_011082, exon 11 of 11)	3' UTR (NM_011082, exon 11 of 11)	-14315	NM_026976	69169	Mm.46042	NM_026976	ENSMUSG00000042474	Fcmr	1810037B05Rik|Faim3|FcmuR|Toso	Fc fragment of IgM receptor	protein-coding
mm_132665.1	chr16	42166752	42166754	+	1	NA	intron (NM_001347236, intron 6 of 6)	intron (NM_001347236, intron 6 of 6)	136716	NR_105858	102466172		NR_105858	ENSMUSG00000098300	Mir6540	Gm27780|mir-6540|mmu-mir-6540	microRNA 6540	ncRNA
mm_73075.1	chr8	94450203	94450213	+	1	NA	Intergenic	B1_Mur1|SINE|Alu	-15105	NR_015514	320377	Mm.486022	NR_015514		9330175E14Rik	A630085K21	RIKEN cDNA 9330175E14 gene	ncRNA
mm_36537.1	chr4	86656153	86656164	-	1	NA	TTS (NM_007408)	TTS (NM_007408)	13901	NM_007408	11520	Mm.381	NM_007408	ENSMUSG00000028494	Plin2	AA407157|ADPH|Adfp|Adrp	perilipin 2	protein-coding
mm_5821.1	chr1	52727297	52727382	-	1	NA	promoter-TSS (NM_133829)	promoter-TSS (NM_133829)	-21	NM_133829	98682	Mm.491173	NM_133829	ENSMUSG00000041439	Mfsd6	2210010L05Rik|9630025I22Rik|AI836200|AW212394|MMR2	major facilitator superfamily domain containing 6	protein-coding
mm_106323.1	chr11	118303736	118303745	-	1	NA	exon (NM_011594, exon 5 of 5)	exon (NM_011594, exon 5 of 5)	-13496	NM_001033528	72344	Mm.232293	NM_001033528	ENSMUSG00000033909	Usp36	2700002L06Rik|mKIAA1453	ubiquitin specific peptidase 36	protein-coding
mm_125014.1	chr15	25626183	25626207	+	1	NA	intron (NM_019472, intron 1 of 40)	intron (NM_019472, intron 1 of 40)	3645	NM_019472	17909	Mm.60590	NM_019472	ENSMUSG00000022272	Myo10	AW048724|D15Ertd600e|mKIAA0799|myosin-X	myosin X	protein-coding
mm_54737.1	chr6	40954378	40954385	-	1	NA	Intergenic	Intergenic	-10391	NM_023707	73626	Mm.425319	NM_023707	ENSMUSG00000094808	1810009J06Rik	-	RIKEN cDNA 1810009J06 gene	protein-coding
mm_4613.1	chr1	178555887	178555899	+	1	NA	intron (NM_001161665, intron 2 of 14)	intron (NM_001161665, intron 2 of 14)	26768	NM_001161665	269152	Mm.129727	NM_177724	ENSMUSG00000026494	Kif26b	4832420M10|BC056349|D230039L06Rik	kinesin family member 26B	protein-coding
mm_165929.1	chr4	63634425	63634429	+	1	NA	Intergenic	Intergenic	-11998	NM_029324	75524	Mm.38543	NM_029324	ENSMUSG00000058935	1700018C11Rik	bM230C2.3	RIKEN cDNA 1700018C11 gene	protein-coding
mm_122265.1	chr14	34310540	34310560	-	1	NA	promoter-TSS (NM_008133)	promoter-TSS (NM_008133)	-47	NM_029389	75698	Mm.45406	NM_029389	ENSMUSG00000041471	Fam35a	3110001K24Rik	family with sequence similarity 35, member A	protein-coding
mm_78725.1	chr9	41580752	41580752	+	1	NA	promoter-TSS (NR_015483)	promoter-TSS (NR_015483)	-501	NR_015483	73144	Mm.38166	NM_001033153	ENSMUSG00000074415	3110039I08Rik	2610203C20Rik|AI848448|D230004N17Rik|D3Mgi9|Mir100hg	RIKEN cDNA 3110039I08 gene	ncRNA
mm_49691.1	chr6	33503287	33503287	+	1	NA	intron (NM_009148, intron 9 of 17)	intron (NM_009148, intron 9 of 17)	254137	NM_009148	20336	Mm.265512	NM_009148	ENSMUSG00000029763	Exoc4	C78892|Sec8|Sec8l1	exocyst complex component 4	protein-coding
mm_12236.1	chr2	68726889	68726913	+	1	NA	intron (NM_183113, intron 18 of 28)	RLTR48A|LTR|ERV1	69017	NM_183113	75721	Mm.65456	NM_183113	ENSMUSG00000079324	4932414N04Rik	-	RIKEN cDNA 4932414N04 gene	protein-coding
mm_37405.1	chr4	121518946	121518960	-	1	NA	Intergenic	Intergenic	-95854	NM_001144948	666921	Mm.477980	NM_001144948	ENSMUSG00000078576	Gm12886	OTTMUSG00000008908	predicted gene 12886	protein-coding
mm_130562.1	chr15	99287199	99287201	-	1	NA	promoter-TSS (NM_001081254)	promoter-TSS (NM_001081254)	-20	NM_001081254	545136	Mm.324745	NM_001081254	ENSMUSG00000078907	Fam186b	EG545136	family with sequence similarity 186, member B	protein-coding
mm_145135.1	chr18	45268854	45268864	+	1	NA	promoter-TSS (NM_001312905)	promoter-TSS (NM_001312905)	-1	NM_001312905	140492	Mm.411614	NM_080465	ENSMUSG00000054477	Kcnn2	KCa2.2|SK2|SKCA2|bc|fri	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2	protein-coding
mm_66069.1	chr7	30836597	30836626	-	1	NA	Intergenic	Intergenic	-12836	NM_146187	233079	Mm.97338	NM_146187	ENSMUSG00000051314	Ffar2	GPCR43|Gpr43	free fatty acid receptor 2	protein-coding
mm_5817.1	chr1	52726799	52726820	-	1	NA	intron (NM_178081, intron 1 of 5)	CpG	509	NM_178081	98682	Mm.491173	NM_133829	ENSMUSG00000041439	Mfsd6	2210010L05Rik|9630025I22Rik|AI836200|AW212394|MMR2	major facilitator superfamily domain containing 6	protein-coding
mm_86809.1	chr10	20339752	20339767	+	1	NA	exon (NM_001025393, exon 11 of 12)	exon (NM_001025393, exon 11 of 12)	-8060	NM_027930	71804	Mm.262151	NM_027930	ENSMUSG00000019992	Mtfr2	2610016C23Rik|4933412C16Rik|Dufd1|Fam54a	mitochondrial fission regulator 2	protein-coding
mm_76435.1	chr8	84985808	84985844	-	1	NA	Intergenic	Intergenic	-4769	NM_133255	170833	Mm.247775	NM_133255	ENSMUSG00000052566	Hook2	A630054I03Rik	hook microtubule tethering protein 2	protein-coding
mm_159897.1	chr6	34920722	34920722	+	1	NA	promoter-TSS (NM_009292)	promoter-TSS (NM_009292)	-238	NM_009292	20899	Mm.5171	NM_009292	ENSMUSG00000029848	Stra8	-	stimulated by retinoic acid gene 8	protein-coding
mm_45971.1	chr5	90469528	90469543	-	1	NA	exon (NM_009654, exon 9 of 15)	exon (NM_009654, exon 9 of 15)	8665	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_17707.1	chr2	32385465	32385493	-	1	NA	exon (NM_008491, exon 5 of 6)	exon (NM_008491, exon 5 of 6)	2260	NM_008491	16819	Mm.9537	NM_008491	ENSMUSG00000026822	Lcn2	24p3|AW212229|NRL|Sip24	lipocalin 2	protein-coding
mm_107104.1	chr12	17755325	17755336	+	1	NA	intron (NM_016677, intron 1 of 3)	RSINE1|SINE|B4	64516	NM_016677	53602	Mm.313619	NM_016677	ENSMUSG00000071379	Hpcal1	NVP-3|Nvp3|VILIP3|Vnsl3|Vsnl3	hippocalcin-like 1	protein-coding
mm_135382.1	chr16	44139758	44139766	-	1	NA	promoter-TSS (NM_007508)	promoter-TSS (NM_007508)	-29	NM_001347239	72117	Mm.278726	NM_028108	ENSMUSG00000022698	Naa50	2600005K24Rik|2810441M03Rik|AW112078|Mak3|Mak3p|Nat13|Nat5|San	N(alpha)-acetyltransferase 50, NatE catalytic subunit	protein-coding
mm_36962.1	chr4	109174256	109174276	-	1	NA	intron (NM_001346502, intron 1 of 23)	intron (NM_001346502, intron 1 of 23)	28006	NM_133885	100273	Mm.366315	NM_133885	ENSMUSG00000028559	Osbpl9	2600011I06Rik|AU015843|Orp-9	oxysterol binding protein-like 9	protein-coding
mm_171130.1	chr3	146838876	146838876	-	1	NA	Intergenic	Intergenic	-13491	NM_001302957	70892	Mm.187793	NM_027594	ENSMUSG00000036745	Ttll7	1110049N09Rik|4921517B04Rik|C630030B20|mTTLL7	tubulin tyrosine ligase-like family, member 7	protein-coding
mm_171064.1	chr3	111198401	111198403	-	1	NA	Intergenic	RLTR10E|LTR|ERVK	-683501	NR_045362	625585	Mm.389497	NR_045362	ENSMUSG00000104543	Gm6602	-	predicted gene 6602	ncRNA
mm_7340.1	chr1	105967037	105967082	-	1	NA	Intergenic	Lx9|LINE|L1	-23347	NM_001122676	227449	Mm.210188	NM_001122675	ENSMUSG00000038866	Zcchc2	9930114B20Rik|AW212015	zinc finger, CCHC domain containing 2	protein-coding
mm_73147.1	chr8	94992684	94992702	+	1	NA	intron (NM_018882, intron 1 of 13)	intron (NM_018882, intron 1 of 13)	8294	NM_018882	14766	Mm.290834	NM_018882	ENSMUSG00000031785	Adgrg1	Cyt28|Gpr56|TM7LN4|TM7XN1	adhesion G protein-coupled receptor G1	protein-coding
mm_25730.1	chr3	122834496	122834503	+	1	NA	intron (NM_153422, intron 14 of 20)	intron (NM_153422, intron 14 of 20)	-32519	NR_045168	71647	Mm.449992	NR_045168	ENSMUSG00000106583	4930447N08Rik	-	RIKEN cDNA 4930447N08 gene	ncRNA
mm_57744.1	chr6	129093352	129093355	-	1	NA	3' UTR (NM_153506, exon 5 of 5)	3' UTR (NM_153506, exon 5 of 5)	7550	NM_153506	232409	Mm.30870	NM_153506	ENSMUSG00000030155	Clec2e	Clra|clr-a	C-type lectin domain family 2, member e	protein-coding
mm_164478.1	chr16	73086445	73086445	+	1	NA	Intergenic	Intergenic	423296	NM_019413	19876	Mm.310772	NM_019413	ENSMUSG00000022883	Robo1	AW494633|AW742721|DUTT1|Gm310	roundabout guidance receptor 1	protein-coding
mm_50068.1	chr6	41227497	41227530	+	1	NA	Intergenic	Intergenic	-74759	NM_011646	22074	Mm.383263	NM_011646	ENSMUSG00000054106	Try4	0910001B19Rik|Td	trypsin 4	protein-coding
mm_12214.1	chr2	67445995	67446009	+	1	NA	promoter-TSS (NM_001083919)	promoter-TSS (NM_001083919)	0	NM_001083919	241431	Mm.261043	NM_001024618	ENSMUSG00000027022	Xirp2	2310003D02Rik|2310008C07Rik|A530024P18Rik|AI452089|Cmya3|Gm352|Xin2	xin actin-binding repeat containing 2	protein-coding
mm_156981.1	chrX	7235153	7235157	-	1	NA	intron (NM_001243762, intron 2 of 13)	ID_B1|SINE|B4	2619	NR_030495	723974		NR_030495	ENSMUSG00000070108	Mir500	Mirn500|mir-500|mmu-mir-500	microRNA 500	ncRNA
mm_22677.1	chr3	15056070	15056103	+	1	NA	Intergenic	RLTR13G|LTR|ERVK	84885	NR_040550	77127	Mm.195792	NR_040549	ENSMUSG00000098008	A930001A20Rik	-	RIKEN cDNA A930001A20 gene	ncRNA
mm_126825.1	chr15	88858589	88858597	+	1	NA	Intergenic	Intergenic	-3601	NM_145478	223775	Mm.400129	NM_145478	ENSMUSG00000035828	Pim3	BC026639|Kid1	proviral integration site 3	protein-coding
mm_131183.1	chr16	7193718	7193747	+	1	NA	intron (NM_183188, intron 1 of 12)	intron (NM_183188, intron 1 of 12)	123897	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_131673.1	chr16	20672922	20672942	+	1	NA	intron (NM_001304432, intron 1 of 31)	CpG	205	NM_001304432	208643	Mm.260256	NM_145941	ENSMUSG00000045983	Eif4g1	E030015G23Rik|eIF-4-gamma 1|eIF-4G 1|eIF-4G1|eIF4GI	eukaryotic translation initiation factor 4, gamma 1	protein-coding
mm_147355.1	chr18	43373194	43373204	-	1	NA	promoter-TSS (NM_001136086)	promoter-TSS (NM_001136086)	73	NM_001136086	22240	Mm.8180	NM_009468	ENSMUSG00000024501	Dpysl3	CRMP-4|DRP-3|TUC4|ULIP-1|Ulip|Ulip1	dihydropyrimidinase-like 3	protein-coding
mm_105810.1	chr11	110533226	110533275	-	1	NA	Intergenic	Intergenic	134128	NM_011943	26399	Mm.14487	NM_011943	ENSMUSG00000020623	Map2k6	MEK6|MKK6|Prkmk6|SAPKK3	mitogen-activated protein kinase kinase 6	protein-coding
mm_45044.1	chr5	41706913	41706916	-	1	NA	intron (NR_132325, intron 1 of 5)	intron (NR_132325, intron 1 of 5)	777	NM_001310592	100972	Mm.41555	NM_027295	ENSMUSG00000029128	Rab28	2700023P08Rik|AW496496	RAB28, member RAS oncogene family	protein-coding
mm_28617.1	chr3	94997098	94997120	-	1	NA	intron (NM_175356, intron 7 of 10)	intron (NM_175356, intron 7 of 10)	-7059	NR_105980	102465613		NR_105980	ENSMUSG00000099033	Mir7013	Gm27488|mmu-mir-7013	microRNA 7013	ncRNA
mm_82018.1	chr9	121730667	121730705	+	1	NA	intron (NM_010918, intron 5 of 16)	5S|rRNA|rRNA	11505	NM_010918	18087	Mm.32842	NM_010918	ENSMUSG00000032525	Nktr	5330401F18Rik|D9Wsu172e	natural killer tumor recognition sequence	protein-coding
mm_158158.1	chrX	103480784	103480796	-	1	NA	non-coding (NR_001570, exon 1 of 8)	non-coding (NR_001570, exon 1 of 8)	2443	NR_001570	213742	Mm.274770	NR_001463	ENSMUSG00000086503	Xist	A430022B11|AI314753	inactive X specific transcripts	ncRNA
mm_40062.1	chr5	33996749	33996763	+	1	NA	5' UTR (NM_001001985, exon 1 of 3)	5' UTR (NM_001001985, exon 1 of 3)	772	NM_001001985	269642	Mm.274610	NM_001001985	ENSMUSG00000048142	Nat8l	1110038O08Rik|Shati	N-acetyltransferase 8-like	protein-coding
mm_87034.1	chr10	28668490	28668498	+	1	NA	non-coding (NR_131208, exon 1 of 4)	non-coding (NR_131208, exon 1 of 4)	134	NM_178666	210757	Mm.123021	NM_178666	ENSMUSG00000049109	Themis	E430004N04Rik|Gasp|Spot|Tsepa|thylex	thymocyte selection associated	protein-coding
mm_94131.1	chr10	128696011	128696065	-	1	NA	intron (NM_177411, intron 1 of 5)	CpG	230	NM_177411	19344	Mm.12815	NM_011229	ENSMUSG00000000711	Rab5b	C030027M18Rik	RAB5B, member RAS oncogene family	protein-coding
mm_38514.1	chr4	141398683	141398726	-	1	NA	promoter-TSS (NM_024412)	promoter-TSS (NM_024412)	2	NM_024412	12733	Mm.167900	NM_024412	ENSMUSG00000033770	Clcnka	C75963|CLC-K1|Clcnk1	chloride channel, voltage-sensitive Ka	protein-coding
mm_107927.1	chr12	71111419	71111456	+	1	NA	promoter-TSS (NM_029227)	promoter-TSS (NM_029227)	9	NM_029227	75266	Mm.402075	NM_029227	ENSMUSG00000021078	Tomm20l	4930553D19Rik	translocase of outer mitochondrial membrane 20 homolog (yeast)-like	protein-coding
mm_5623.1	chr1	40163445	40163447	-	1	NA	Intergenic	Intergenic	-61634	NM_008362	16177	Mm.896	NM_008362	ENSMUSG00000026072	Il1r1	CD121a|CD121b|IL-1R1|IL-iR|Il1r-1	interleukin 1 receptor, type I	protein-coding
mm_92514.1	chr10	78440780	78440804	-	1	NA	3' UTR (NM_172134, exon 11 of 11)	3' UTR (NM_172134, exon 11 of 11)	4365	NR_105873	102466762		NR_105873	ENSMUSG00000098279	Mir6908	Gm27827|mmu-mir-6908	microRNA 6908	ncRNA
mm_104365.1	chr11	94321958	94321968	-	1	NA	promoter-TSS (NM_026313)	promoter-TSS (NM_026313)	-52	NM_026313	67684	Mm.30927	NM_026313	ENSMUSG00000020863	Luc7l3	3300001P08Rik|Luc7a	LUC7-like 3 (S. cerevisiae)	protein-coding
mm_172538.1	chr7	95187992	95187992	+	1	NA	Intergenic	L1Md_T|LINE|L1	-983252	NM_001310762	23966	Mm.254610	NM_011858	ENSMUSG00000048078	Tenm4	Doc4|ELM2|Odz4|R75022|Ten-m4|l(7)-3Rn|l7Rn3|mKIAA1302	teneurin transmembrane protein 4	protein-coding
mm_51910.1	chr6	91212800	91212844	+	1	NA	promoter-TSS (NM_001081437)	promoter-TSS (NM_001081437)	58	NM_007992	14115	Mm.249146	NM_007992	ENSMUSG00000064080	Fbln2	5730577E14Rik|FIBL-2	fibulin 2	protein-coding
mm_102652.1	chr11	63463922	63463932	-	1	NA	Intergenic	Intergenic	-77858	NR_105772	102466632		NR_105772	ENSMUSG00000098829	Mir6354	Gm27282|mmu-mir-6354	microRNA 6354	ncRNA
mm_42911.1	chr5	122648335	122648346	+	1	NA	intron (NM_001038845, intron 1 of 12)	intron (NM_001038845, intron 1 of 12)	-2084	NM_001284402	18439	Mm.42026	NM_011027	ENSMUSG00000029468	P2rx7	AI467586|P2X(7)|P2X7R	purinergic receptor P2X, ligand-gated ion channel, 7	protein-coding
mm_115625.1	chr13	12105395	12105406	-	1	NA	intron (NM_023868, intron 1 of 104)	intron (NM_023868, intron 1 of 104)	1545	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding
mm_151303.1	chr19	55741925	55741935	+	1	NA	non-coding (NR_138565, exon 1 of 16)	non-coding (NR_138565, exon 1 of 16)	120	NM_001142923	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_54049.1	chr6	13838433	13838442	-	1	NA	intron (NM_145066, intron 2 of 3)	intron (NM_145066, intron 2 of 3)	1505	NM_001330666	64450	Mm.167625	NM_145066	ENSMUSG00000048216	Gpr85	2900026B03Rik	G protein-coupled receptor 85	protein-coding
mm_49884.1	chr6	38663062	38663119	+	1	NA	promoter-TSS (NM_001101507)	promoter-TSS (NM_001101507)	21	NM_001101507	665180	Mm.349066	NM_001101507	ENSMUSG00000079598	Clec2l	AI414054|AW122724|Gm1064	C-type lectin domain family 2, member L	protein-coding
mm_153275.1	chr19	37176083	37176098	-	1	NA	promoter-TSS (NM_001290826)	promoter-TSS (NM_001290826)	-27	NM_001290826	208922	Mm.391176	NM_198300	ENSMUSG00000039652	Cpeb3	4831444O18Rik|CPE-BP3|mKIAA0940	cytoplasmic polyadenylation element binding protein 3	protein-coding
mm_87289.1	chr10	42502049	42502055	+	1	NA	promoter-TSS (NM_017472)	promoter-TSS (NM_017472)	-2	NM_017472	54198	Mm.277870	NM_017472	ENSMUSG00000019804	Snx3	SDP3	sorting nexin 3	protein-coding
mm_172679.1	chr8	51347464	51347467	+	1	NA	Intergenic	L1Md_T|LINE|L1	979353	NR_046067	100039954	Mm.400419	NR_046067	ENSMUSG00000110281	Gm2516	-	predicted gene 2516	ncRNA
mm_101229.1	chr11	20331305	20331308	-	1	NA	intron (NM_018861, intron 1 of 7)	intron (NM_018861, intron 1 of 7)	1407	NM_018861	55963	Mm.6379	NM_018861	ENSMUSG00000020142	Slc1a4	ASCT-1|ASCT1|AW045657|SATT	solute carrier family 1 (glutamate/neutral amino acid transporter), member 4	protein-coding
mm_163088.1	chr11	69734659	69734665	-	1	NA	exon (NM_001291068, exon 29 of 29)	exon (NM_001291068, exon 29 of 29)	23971	NM_001291068	20020	Mm.16533	NM_009089	ENSMUSG00000005198	Polr2a	220kDa|Rpb1|Rpo2-1	polymerase (RNA) II (DNA directed) polypeptide A	protein-coding
mm_111454.1	chr12	98385908	98385915	-	1	NA	Intergenic	Intergenic	117276	NM_008152	14744	Mm.378924	NM_008152	ENSMUSG00000021886	Gpr65	Dig1|Gpcr25|TDAG8	G-protein coupled receptor 65	protein-coding
mm_119376.1	chr14	41131778	41131794	+	1	NA	promoter-TSS (NM_023134)	promoter-TSS (NM_023134)	-2	NM_023134	20387	Mm.46062	NM_023134	ENSMUSG00000021789	Sftpa1	SP-A|Sftp-1|Sftp1	surfactant associated protein A1	protein-coding
mm_117185.1	chr13	63539339	63539352	-	1	NA	exon (NM_008957, exon 12 of 24)	exon (NM_008957, exon 12 of 24)	26390	NM_008957	19206	Mm.228798	NM_008957	ENSMUSG00000021466	Ptch1	A230106A15Rik|Ptc|Ptc1|Ptch|mes	patched 1	protein-coding
mm_69324.1	chr7	128523451	128523458	-	1	NA	promoter-TSS (NM_013863)	promoter-TSS (NM_013863)	-129	NM_013863	29810	Mm.84073	NM_013863	ENSMUSG00000030847	Bag3	AA407278|Bis|mg638	BCL2-associated athanogene 3	protein-coding
mm_42370.1	chr5	114924245	114924283	+	1	NA	intron (NM_145209, intron 2 of 6)	intron (NM_145209, intron 2 of 6)	1024	NM_145209	231655	Mm.95479	NM_145209	ENSMUSG00000041827	Oasl1	7530414C13Rik|oasl9	2'-5' oligoadenylate synthetase-like 1	protein-coding
mm_1877.1	chr1	85610861	85610871	+	1	NA	exon (NM_001013817, exon 3 of 17)	exon (NM_001013817, exon 3 of 17)	-6975	NM_175397	109032	Mm.335802	NM_030194	ENSMUSG00000070034	Sp110	5031415C07Rik|52kDa|5830484A20Rik|ENSMUSG00000075603|Ifi75|Ipr1	Sp110 nuclear body protein	protein-coding
mm_71780.1	chr8	66491008	66491028	+	1	NA	Intergenic	RLTR31B2|LTR|ERVK	-4511	NM_025465	66282	Mm.294985	NM_025465	ENSMUSG00000025591	Tma16	1810029B16Rik	translation machinery associated 16	protein-coding
mm_36522.1	chr4	84674990	84675006	-	1	NA	promoter-TSS (NM_172870)	promoter-TSS (NM_172870)	88	NM_172870	242509	Mm.190774	NM_172870	ENSMUSG00000028487	Bnc2	5031434M05Rik|8430420F16Rik	basonuclin 2	protein-coding
mm_33779.1	chr4	134535475	134535515	+	1	NA	promoter-TSS (NM_001256112)	promoter-TSS (NM_001256112)	-108	NM_029759	76824	Mm.30153	NM_029759	ENSMUSG00000046671	Mtfr1l	2410166I05Rik|AI480750|Fam54b	mitochondrial fission regulator 1-like	protein-coding
mm_50400.1	chr6	48720439	48720445	+	1	NA	intron (NM_146167, intron 1 of 1)	intron (NM_146167, intron 1 of 1)	1821	NM_146167	231932	Mm.30479	NM_146167	ENSMUSG00000043931	Gimap7	IAN7|Ian3	GTPase, IMAP family member 7	protein-coding
mm_59060.1	chr7	19415400	19415424	+	1	NA	exon (NM_007710, exon 4 of 8)	exon (NM_007710, exon 4 of 8)	4318	NM_007710	12715	Mm.2375	NM_007710	ENSMUSG00000030399	Ckm	Ckmm|M-CK|MCK	creatine kinase, muscle	protein-coding
mm_85023.1	chr9	88438910	88438936	-	1	NA	promoter-TSS (NM_172926)	promoter-TSS (NM_172926)	28	NM_172926	244962	Mm.439873	NM_172926	ENSMUSG00000032422	Snx14	B830022K16|C330035N22Rik|YR-14	sorting nexin 14	protein-coding
mm_77974.1	chr9	7868277	7868285	+	1	NA	intron (NM_007464, intron 1 of 8)	intron (NM_007464, intron 1 of 8)	4889	NM_007464	11796	Mm.2026	NM_007464	ENSMUSG00000032000	Birc3	AW107670|Api1|Api2|Birc2|C-IAP2|HIAP2|IAP1|IAP2|MIAP1|MIAP2|MIHB|MIHC|RNF49|cIAP-1|cIAP-2|cIAP1|cIAP2	baculoviral IAP repeat-containing 3	protein-coding
mm_34551.1	chr4	149586556	149586566	+	1	NA	promoter-TSS (NM_023051)	promoter-TSS (NM_023051)	93	NM_023051	65945	Mm.38993	NM_023051	ENSMUSG00000039953	Clstn1	1810034E21Rik|Cst-1|Cstn1	calsyntenin 1	protein-coding
mm_70877.1	chr8	25103486	25103489	+	1	NA	Intergenic	Intergenic	-1676	NM_031257	83436	Mm.261122	NM_031257	ENSMUSG00000031557	Plekha2	6430512N22Rik|AI851530|AU041791|TAPP2|W91773	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 2	protein-coding
mm_5315.1	chr1	22562535	22562535	-	1	NA	intron (NM_001012623, intron 5 of 14).2	intron (NM_001012623, intron 5 of 14).2	-129692	NM_183018	116837	Mm.60061	NM_053270	ENSMUSG00000041670	Rims1	C030033M19Rik|RIM1|RIM1a|RIM1alpha|Rab3ip1|Rim|Serg1|mKIAA0340	regulating synaptic membrane exocytosis 1	protein-coding
mm_7257.1	chr1	93799359	93799370	-	1	NA	intron (NM_001105667, intron 2 of 4)	intron (NM_001105667, intron 2 of 4)	2570	NM_023136	21915	Mm.250332	NM_023136	ENSMUSG00000026281	Dtymk	AU044245|CDC8|D10Ertd203e|TMPK|TYPK|Tmk|mtmk	deoxythymidylate kinase	protein-coding
mm_122499.1	chr14	46809274	46809285	-	1	NA	3' UTR (NM_022023, exon 7 of 7)	3' UTR (NM_022023, exon 7 of 7)	12963	NM_022023	63985	Mm.87312	NM_022023	ENSMUSG00000062014	Gmfb	3110001H22Rik|3110001O16Rik|AI851627|C79176|D14Ertd630e	glia maturation factor, beta	protein-coding
mm_148253.1	chr18	80743001	80743008	-	1	NA	intron (NM_001201569, intron 26 of 29)	intron (NM_001201569, intron 26 of 29)	-29933	NM_001164109	18018	Mm.329560	NM_016791	ENSMUSG00000033016	Nfatc1	2210017P03Rik|AI449492|AV076380|NF-ATc|NFAT2|NFATc|Nfatcb	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 1	protein-coding
mm_120564.1	chr14	68159865	68159866	+	1	NA	Intergenic	MTE2a|LTR|ERVL-MaLR	-34861	NM_008691	18040	Mm.242832	NM_008691	ENSMUSG00000022054	Nefm	NF-M|NF160|NF165|Nef3|Nfm	neurofilament, medium polypeptide	protein-coding
mm_133896.1	chr16	97536339	97536346	+	1	NA	intron (NM_013606, intron 1 of 13)	intron (NM_013606, intron 1 of 13)	259	NM_013606	17858	Mm.14157	NM_013606	ENSMUSG00000023341	Mx2	AI528743|Mx-2	MX dynamin-like GTPase 2	protein-coding
mm_63339.1	chr7	126959809	126959813	+	1	NA	exon (NM_001252566, exon 8 of 17)	exon (NM_001252566, exon 8 of 17)	9276	NM_001252566	233878	Mm.283926	NM_144926	ENSMUSG00000030683	Sez6l2	AI835913|AW121566|BSRP-A|Psk1	seizure related 6 homolog like 2	protein-coding
mm_67260.1	chr7	75774112	75774122	-	1	NA	Intergenic	MTC-int|LTR|ERVL-MaLR	-74221	NM_001122780	207952	Mm.206223	NM_029652	ENSMUSG00000055652	Klhl25	2810402K13Rik|BC027373|Enc-1	kelch-like 25	protein-coding
mm_20620.1	chr2	131855808	131855818	-	1	NA	3' UTR (NM_001166206, exon 2 of 2)	3' UTR (NM_001166206, exon 2 of 2)	3934	NM_001166206	71995	Mm.22	NM_028045	ENSMUSG00000037482	Erv3	1600014E20Rik|AA389086|AI426069|AI448024|D19349	endogenous retroviral sequence 3	protein-coding
mm_93898.1	chr10	125389560	125389570	-	1	NA	Intergenic	Intergenic	-61030	NM_011391	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|Mct2	solute carrier family 16 (monocarboxylic acid transporters), member 7	protein-coding
mm_7025.1	chr1	87098560	87098599	-	1	NA	3' UTR (NM_001081082, exon 11 of 11)	3' UTR (NM_001081082, exon 11 of 11)	3027	NM_001081082	76768	Mm.58068	NM_001081082	ENSMUSG00000079440	Alpi	2010001C14Rik|Akp6|gIAP	alkaline phosphatase, intestinal	protein-coding
mm_81042.1	chr9	105395520	105395563	+	1	NA	promoter-TSS (NM_172461)	promoter-TSS (NM_172461)	149	NM_025651	66595	Mm.84941	NM_025651	ENSMUSG00000032567	Aste1	1100001A21Rik|AV006403	asteroid homolog 1 (Drosophila)	protein-coding
mm_159161.1	chr2	90679174	90679174	+	1	NA	5' UTR (NM_021512, exon 2 of 37)	5' UTR (NM_021512, exon 2 of 37)	1959	NM_021512	59015	Mm.24532	NM_021512	ENSMUSG00000051329	Nup160	160kDa|2810011M03Rik|AA414952|AU020188|Gtl-13|Gtl1-13|Gtl13|mKIAA0197	nucleoporin 160	protein-coding
mm_154819.1	chrX	16522872	16522874	+	1	NA	promoter-TSS (NM_001039943)	promoter-TSS (NM_001039943)	4	NM_025738	66742	Mm.45302	NM_025738	ENSMUSG00000023257	Cypt1	4931420D14Rik|Ckt1r3|Cypt5|Cypt6|TISP55	cysteine-rich perinuclear theca 1	protein-coding
mm_92890.1	chr10	82814134	82814153	-	1	NA	intron (NR_038042, intron 1 of 2)	intron (NR_038042, intron 1 of 2)	2020	NR_038042	70003	Mm.48789	NR_038042	ENSMUSG00000056821	1700028I16Rik	-	RIKEN cDNA 1700028I16 gene	ncRNA
mm_100111.1	chr11	115814277	115814279	+	1	NA	promoter-TSS (NM_080643)	promoter-TSS (NM_080643)	-461	NM_029557	76265	Mm.275438	NM_029557	ENSMUSG00000020781	Tsen54	0610034P02Rik	tRNA splicing endonuclease subunit 54	protein-coding
mm_59205.1	chr7	24507313	24507402	+	1	NA	non-coding (NR_110958, exon 1 of 3)	non-coding (NR_110958, exon 1 of 3)	270	NR_110958	232969	Mm.181332	NM_146183	ENSMUSG00000064264	Zfp428	2410005H09Rik|AV271806|AW047854|Znf428	zinc finger protein 428	protein-coding
mm_23913.1	chr3	83043872	83043879	+	1	NA	exon (NM_181849, exon 6 of 8)	exon (NM_181849, exon 6 of 8)	5988	NM_181849	110135	Mm.30063	NM_181849	ENSMUSG00000033831	Fgb	2510049G14Rik	fibrinogen beta chain	protein-coding
mm_127761.1	chr15	103515245	103515254	+	1	NA	5' UTR (NM_001285890, exon 1 of 15)	5' UTR (NM_001285890, exon 1 of 15)	272	NM_001285890	18574	Mm.390792	NM_008800	ENSMUSG00000022489	Pde1b	Pde1b1	phosphodiesterase 1B, Ca2+-calmodulin dependent	protein-coding
mm_154898.1	chrX	20872778	20872820	+	1	NA	exon (NM_011593, exon 3 of 6)	exon (NM_011593, exon 3 of 6)	2633	NM_001294280	21857	Mm.8245	NM_011593	ENSMUSG00000001131	Timp1	Clgi|EPA|TIMP-1|TPA-S1|Timp	tissue inhibitor of metalloproteinase 1	protein-coding
mm_128571.1	chr15	57695341	57695376	-	1	NA	intron (NM_199449, intron 1 of 3)	CpG	691	NM_199449	387609	Mm.36557	NM_199449	ENSMUSG00000071757	Zhx2	Afr-1|Afr1|Raf|mKIAA0854	zinc fingers and homeoboxes 2	protein-coding
mm_76544.1	chr8	88118584	88118597	-	1	NA	promoter-TSS (NM_029074)	promoter-TSS (NM_029074)	-169	NM_029074	382030	Mm.216574	NM_029074	ENSMUSG00000036810	Cnep1r1	5033428A16Rik|NEP1-R1|Tmem188	CTD nuclear envelope phosphatase 1 regulatory subunit 1	protein-coding
mm_95927.1	chr11	58330713	58330735	+	1	NA	promoter-TSS (NM_024480)	promoter-TSS (NM_024480)	17	NM_001308167	79566	Mm.290534	NM_024480	ENSMUSG00000013646	Sh3bp5l	2310074E09Rik|BC003251|mKIAA1720	SH3 binding domain protein 5 like	protein-coding
mm_79216.1	chr9	49250486	49250532	+	1	NA	promoter-TSS (NM_177701)	promoter-TSS (NM_177701)	-22	NM_177701	235327	Mm.246604	NM_177701	ENSMUSG00000054156	Gm4894	A430041E03|EG235327	predicted gene 4894	protein-coding
mm_49902.1	chr6	38941394	38941408	+	1	NA	intron (NM_011539, intron 1 of 12)	intron (NM_011539, intron 1 of 12)	22415	NM_011539	21391	Mm.4054	NM_011539	ENSMUSG00000029925	Tbxas1	CYP5|CYP5A1|THAS|TS|TXAS|TXS	thromboxane A synthase 1, platelet	protein-coding
mm_88809.1	chr10	80763884	80763889	+	1	NA	intron (NM_199322, intron 1 of 27)	intron (NM_199322, intron 1 of 27)	8680	NM_199322	208266	Mm.152371	NM_199322	ENSMUSG00000061589	Dot1l	A630076O07|AW907654|Dot1|KMT4|mDot1	DOT1-like, histone H3 methyltransferase (S. cerevisiae)	protein-coding
mm_116882.1	chr13	55100249	55100321	-	1	NA	promoter-TSS (NM_001293660)	promoter-TSS (NM_001293660)	10	NM_011307	20184	Mm.259301	NM_011307	ENSMUSG00000025878	Uimc1	9430016E08Rik|D330018D10Rik|D630032M02Rik|RIP110|Rxrip110	ubiquitin interaction motif containing 1	protein-coding
mm_87434.1	chr10	51451804	51451808	+	1	NA	Intergenic	L1VL1|LINE|L1	-28806	NM_008147	14727	Mm.439661	NM_008147	ENSMUSG00000062593	Lilr4b	Gp49a|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4B	protein-coding
mm_18429.1	chr2	60780936	60780947	-	1	NA	intron (NM_020296, intron 5 of 13)	intron (NM_020296, intron 5 of 13)	-58338	NM_001159564	16420	Mm.98193	NM_021359	ENSMUSG00000026971	Itgb6	2210409C20Rik|4831415H04Rik	integrin beta 6	protein-coding
mm_113239.1	chr13	27312611	27312627	+	1	NA	promoter-TSS (NM_011166)	promoter-TSS (NM_011166)	-8	NM_011166	19111	Mm.7512	NM_011166	ENSMUSG00000069259	Prl6a1	Ghd10|PLP-B|Prlpb	prolactin family 6, subfamily a, member 1	protein-coding
mm_9770.1	chr1	180999846	180999860	-	1	NA	exon (NM_010145, exon 3 of 9)	exon (NM_010145, exon 3 of 9)	17716	NM_010145	13849	Mm.9075	NM_010145	ENSMUSG00000038776	Ephx1	EH|Eph-1|Eph1|Epxh1|mEH	epoxide hydrolase 1, microsomal	protein-coding
mm_121327.1	chr14	114946013	114946030	+	1	NA	promoter-TSS (NR_126551)	promoter-TSS (NR_126551)	-73	NR_126548	74982		NR_126548		1700100I10Rik	1700085D13Rik|4930481K08Rik	RIKEN cDNA 1700100I10 gene	ncRNA
mm_100949.1	chr11	6599436	6599445	-	1	NA	exon (NM_001081652, exon 2 of 8)	exon (NM_001081652, exon 2 of 8)	6614	NM_001081652	192950	Mm.337771	NM_001081652	ENSMUSG00000041073	Nacad	D230024G13Rik|mKIAA0363	NAC alpha domain containing	protein-coding
mm_80711.1	chr9	92250297	92250311	+	1	NA	5' UTR (NM_011636, exon 1 of 9)	5' UTR (NM_011636, exon 1 of 9)	110	NM_011636	22038	Mm.421956	NM_011636	ENSMUSG00000032369	Plscr1	MmTRA1a|MmTRA1b|Nor1|Tra1|Tra1a|Tra1b|Tras1|Tras2	phospholipid scramblase 1	protein-coding
mm_109010.1	chr12	103346243	103346259	+	1	NA	intron (NM_023049, intron 1 of 9)	intron (NM_023049, intron 1 of 9)	9750	NM_023049	65256	Mm.27159	NM_023049	ENSMUSG00000021200	Asb2	1110008E15Rik	ankyrin repeat and SOCS box-containing 2	protein-coding
mm_146389.1	chr18	82692930	82692950	+	1	NA	promoter-TSS (NM_177832)	promoter-TSS (NM_177832)	-206	NM_177832	329002	Mm.34438	NM_177832	ENSMUSG00000041258	Zfp236	AI447957|Gm335	zinc finger protein 236	protein-coding
mm_65987.1	chr7	30526163	30526182	-	1	NA	exon (NM_001289670, exon 18 of 21)	exon (NM_001289670, exon 18 of 21)	8888	NM_001289670	233071	Mm.190704	NM_178252	ENSMUSG00000036882	Arhgap33	AW324378|NOMA-GAP|Snx26|TCGAP	Rho GTPase activating protein 33	protein-coding
mm_100178.1	chr11	116534059	116534069	+	1	NA	promoter-TSS (NM_011451)	promoter-TSS (NM_011451)	-676	NM_011451	20698	Mm.20944	NM_011451	ENSMUSG00000061878	Sphk1	1110006G24Rik|Sk1|Spk1	sphingosine kinase 1	protein-coding
mm_168078.1	chr10	113503123	113503124	-	1	NA	Intergenic	RLTR10D2|LTR|ERVK	-83455	NR_035418	100316831		NR_035418	ENSMUSG00000080594	Mir669h	Mirn669h|mir-669h|mmu-mir-669h	microRNA 669h	ncRNA
mm_137797.1	chr17	29681170	29681181	+	1	NA	intron (NR_132314, intron 11 of 27)	intron (NR_132314, intron 11 of 27)	20580	NM_028791	74157	Mm.390979	NM_028791	ENSMUSG00000024019	Cmtr1	1300018I05Rik|AI451264|Ftsjd2|MTr1	cap methyltransferase 1	protein-coding
mm_63908.1	chr7	139214662	139214681	+	1	NA	intron (NM_001143755, intron 2 of 8)	intron (NM_001143755, intron 2 of 8)	-1364	NM_001162540	57740	Mm.65336	NM_021302	ENSMUSG00000015981	Stk32c	PKE|Pkek|YANK3	serine/threonine kinase 32C	protein-coding
mm_109182.1	chr12	108472753	108472777	+	1	NA	intron (NM_001043335, intron 3 of 21)	B4A|SINE|B4	49949	NM_001043335	68519	Mm.236645	NM_001043335	ENSMUSG00000058070	Eml1	1110008N23Rik|A930030P13Rik|AA171013|AI847476|AI853955|ELP79|EMAP|EMAPL|heco	echinoderm microtubule associated protein like 1	protein-coding
mm_10554.1	chr2	16751279	16751296	+	1	NA	exon (NM_026162, exon 14 of 14)	exon (NM_026162, exon 14 of 14)	262439	NR_040632	75069	Mm.50378	NR_040632		4930515L03Rik	-	RIKEN cDNA 4930515L03 gene	ncRNA
mm_99133.1	chr11	100319956	100319962	+	1	NA	promoter-TSS (NM_011508)	promoter-TSS (NM_011508)	10	NM_011508	20918	Mm.13886	NM_011508	ENSMUSG00000035530	Eif1	Sui1-rs1	eukaryotic translation initiation factor 1	protein-coding
mm_155110.1	chrX	48519413	48519474	+	1	NA	5' UTR (NM_011228, exon 1 of 2)	5' UTR (NM_011228, exon 1 of 2)	158	NM_011228	19337	Mm.2015	NM_011228	ENSMUSG00000031104	Rab33a	Rabs10	RAB33A, member RAS oncogene family	protein-coding
mm_82802.1	chr9	29769331	29769334	-	1	NA	intron (NM_172290, intron 1 of 7)	intron (NM_172290, intron 1 of 7)	193797	NM_172290	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding
mm_106816.1	chr12	7980561	7980576	+	1	NA	exon (NM_009693, exon 4 of 29)	exon (NM_009693, exon 4 of 29)	2891	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_3675.1	chr1	153667504	153667512	+	1	NA	intron (NM_001347115, intron 2 of 5)	intron (NM_001347115, intron 2 of 5)	1835	NM_001347115	67792	Mm.379143	NM_026380	ENSMUSG00000042671	Rgs8	6530413N01Rik	regulator of G-protein signaling 8	protein-coding
mm_144570.1	chr18	31789121	31789171	+	1	NA	promoter-TSS (NM_027002)	promoter-TSS (NM_027002)	-13	NM_027002	69241	Mm.279898	NM_027002	ENSMUSG00000024258	Polr2d	2310002G05Rik|2610028L19Rik|HSRBP4|RBP4	polymerase (RNA) II (DNA directed) polypeptide D	protein-coding
mm_57973.1	chr6	135349778	135349791	-	1	NA	Intergenic	Intergenic	-13147	NM_010128	13730	Mm.182785	NM_010128	ENSMUSG00000030208	Emp1	I-8-09|TMP	epithelial membrane protein 1	protein-coding
mm_70152.1	chr7	143460990	143461005	-	1	NA	promoter-TSS (NM_001161624)	promoter-TSS (NM_001161624)	53	NM_009876	12577	Mm.168789	NM_009876	ENSMUSG00000037664	Cdkn1c	AL024410|CDKI|Kip2|p57(kip2)|p57Kip2	cyclin-dependent kinase inhibitor 1C (P57)	protein-coding
mm_58637.1	chr7	6018979	6018979	+	1	NA	Intergenic	Intergenic	-7969	NM_030738	81013	Mm.160378	NM_030738	ENSMUSG00000066850	Vmn1r65	V1rd6|V3R6	vomeronasal 1 receptor 65	protein-coding
mm_119388.1	chr14	41137345	41137353	+	1	NA	TTS (NM_023134)	TTS (NM_023134)	5561	NM_023134	20387	Mm.46062	NM_023134	ENSMUSG00000021789	Sftpa1	SP-A|Sftp-1|Sftp1	surfactant associated protein A1	protein-coding
mm_164194.1	chr15	78899823	78899827	+	1	NA	promoter-TSS (NM_009164)	promoter-TSS (NM_009164)	57	NM_009164	20401	Mm.4462	NM_009164	ENSMUSG00000022436	Sh3bp1	3BP-1	SH3-domain binding protein 1	protein-coding
mm_125256.1	chr15	35313274	35313314	+	1	NA	intron (NR_045280, intron 1 of 2)	intron (NR_045280, intron 1 of 2)	15241	NR_045280	100126269	Mm.247402	NR_045280		BC048602	-	cDNA sequence BC048602	ncRNA
mm_16020.1	chr2	167503415	167503461	+	1	NA	5' UTR (NM_030743, exon 3 of 8)	5' UTR (NM_030743, exon 3 of 8)	-10564	NM_170756	263876	Mm.34342	NM_170756	ENSMUSG00000047030	Spata2	AI504642|mKIAA0757	spermatogenesis associated 2	protein-coding
mm_167137.1	chr7	127273992	127274000	-	1	NA	promoter-TSS (NM_009266)	promoter-TSS (NM_009266)	63	NM_009266	20768	Mm.20294	NM_009266	ENSMUSG00000049091	Sephs2	Sps2|Ysg3	selenophosphate synthetase 2	protein-coding
mm_1819.1	chr1	82342989	82342998	+	1	NA	intron (NM_029777, intron 3 of 6)	intron (NM_029777, intron 3 of 6)	3944	NM_001122685	76867	Mm.226994	NM_029777	ENSMUSG00000026142	Rhbdd1	4930418P06Rik|RRP4|mRHBDD1	rhomboid domain containing 1	protein-coding
mm_104814.1	chr11	98961529	98961549	-	1	NA	intron (NM_001176528, intron 1 of 7)	intron (NM_001176528, intron 1 of 7)	1068	NM_001176528	19401	Mm.439744	NM_009024	ENSMUSG00000037992	Rara	Nr1b1|RAR|RARalpha1	retinoic acid receptor, alpha	protein-coding
mm_6786.1	chr1	84140265	84140276	-	1	NA	intron (NM_001003948, intron 2 of 2)	L1_Mur3|LINE|L1	78691	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_71607.1	chr8	56297418	56297421	+	1	NA	intron (NM_008278, intron 2 of 6)	B1_Mm|SINE|Alu	2867	NM_008278	15446	Mm.18832	NM_008278	ENSMUSG00000031613	Hpgd	15-PGDH|AV026552	hydroxyprostaglandin dehydrogenase 15 (NAD)	protein-coding
mm_131775.1	chr16	22894828	22894837	+	1	NA	promoter-TSS (NR_110508)	promoter-TSS (NR_110508)	-446	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_161166.1	chr13	34002882	34002882	+	1	NA	promoter-TSS (NM_009068)	promoter-TSS (NM_009068)	8	NM_009068	19766	Mm.374799	NM_009068	ENSMUSG00000021408	Ripk1	D330015H01Rik|RIP|Rinp|Rip1	receptor (TNFRSF)-interacting serine-threonine kinase 1	protein-coding
mm_106474.1	chr11	120139428	120139432	-	1	NA	intron (NM_024249, intron 4 of 16)	intron (NM_024249, intron 4 of 16)	11921	NM_001164799	72055	Mm.253403	NM_024249	ENSMUSG00000061306	Slc38a10	1810073N04Rik	solute carrier family 38, member 10	protein-coding
mm_116245.1	chr13	33935759	33935769	-	1	NA	promoter-TSS (NR_040707)	promoter-TSS (NR_040707)	-268	NR_040707	68808	Mm.443347	NR_040707	ENSMUSG00000085457	1110046J04Rik	-	RIKEN cDNA 1110046J04 gene	ncRNA
mm_57779.1	chr6	129239745	129239771	-	1	NA	Intergenic	Intergenic	-1276	NR_040266	76432	Mm.261738	NR_040265	ENSMUSG00000097354	2310001H17Rik	AI646108	RIKEN cDNA 2310001H17 gene	ncRNA
mm_69727.1	chr7	140773155	140773209	-	1	NA	exon (NM_021282, exon 7 of 9)	exon (NM_021282, exon 7 of 9)	9350	NM_021282	13106	Mm.21758	NM_021282	ENSMUSG00000025479	Cyp2e1	Cyp2e	cytochrome P450, family 2, subfamily e, polypeptide 1	protein-coding
mm_9441.1	chr1	172588234	172588246	-	1	NA	intron (NM_029084, intron 1 of 4)	intron (NM_029084, intron 1 of 4)	2328	NM_029084	74748	Mm.179812	NM_029084	ENSMUSG00000053318	Slamf8	5830408F06Rik|Blame|SBBI42	SLAM family member 8	protein-coding
mm_30801.1	chr4	20008495	20008501	+	1	NA	exon (NM_015767, exon 1 of 5)	exon (NM_015767, exon 1 of 5)	169	NM_015767	50500	Mm.24375	NM_015767	ENSMUSG00000073988	Ttpa	alpha-TTP	tocopherol (alpha) transfer protein	protein-coding
mm_133657.1	chr16	91820445	91820453	+	1	NA	intron (NM_001110275, intron 12 of 28)	intron (NM_001110275, intron 12 of 28)	91078	NM_010587	16443	Mm.40546	NM_010587	ENSMUSG00000022957	Itsn1	AA517634|AA545208|AI316805|AI839402|AI848451|Ehsh1|Ese1|Itsn|Sh3p17	intersectin 1 (SH3 domain protein 1A)	protein-coding
mm_76140.1	chr8	81780570	81780574	-	1	NA	intron (NM_001024617, intron 7 of 24)	RMER17B|LTR|ERVK	438010	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_133401.1	chr16	84834902	84834941	+	1	NA	promoter-TSS (NM_001302216)	promoter-TSS (NM_001302216)	77	NM_001302216	11957	Mm.353	NM_016755	ENSMUSG00000022890	Atp5j	CF6	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit F	protein-coding
mm_149557.1	chr19	12633508	12633525	+	1	NA	5' UTR (NM_145935, exon 1 of 6)	5' UTR (NM_145935, exon 1 of 6)	208	NM_145935	107146	Mm.39974	NM_145935	ENSMUSG00000063683	Glyat	A330009E03Rik|ACGNAT|AI195249|AI315345|CAT|GAT	glycine-N-acyltransferase	protein-coding
mm_145990.1	chr18	68314552	68314563	+	1	NA	intron (NM_026440, intron 7 of 10)	(T)n|Simple_repeat|Simple_repeat	14202	NM_001170953	67897	Mm.27544	NM_026440	ENSMUSG00000009535	Rnmt	2610002P10Rik|AI848273|Rg7mt1|mKIAA0398	RNA (guanine-7-) methyltransferase	protein-coding
mm_46385.1	chr5	104017766	104017791	-	1	NA	intron (NM_053262, intron 2 of 6)	intron (NM_053262, intron 2 of 6)	4018	NM_053262	114664	Mm.46019	NM_053262	ENSMUSG00000029311	Hsd17b11	Dhrs8|Pan1b|SDR2|retSDR2	hydroxysteroid (17-beta) dehydrogenase 11	protein-coding
mm_10824.1	chr2	24379122	24379124	+	1	NA	Intergenic	Intergenic	-6274	NM_177611	215632	Mm.490434	NM_177611	ENSMUSG00000026979	Psd4	BC046518|EFA6B	pleckstrin and Sec7 domain containing 4	protein-coding
mm_13853.1	chr2	119675063	119675095	+	1	NA	promoter-TSS (NM_030112)	promoter-TSS (NM_030112)	11	NM_030112	76246	Mm.33437	NM_030112	ENSMUSG00000027304	Rtf1	2900005O08Rik|6530416A09Rik|AI853581|AU043144|AW553985|Gtl7|cbp82	RTF1, Paf1/RNA polymerase II complex component	protein-coding
mm_132554.1	chr16	37884064	37884078	+	1	NA	3' UTR (NM_177093, exon 4 of 4)	3' UTR (NM_177093, exon 4 of 4)	15671	NM_177093	320184	Mm.390882	NM_177093	ENSMUSG00000034158	Lrrc58	1810012N18Rik|C330018J07Rik	leucine rich repeat containing 58	protein-coding
mm_43008.1	chr5	123662226	123662231	+	1	NA	intron (NM_001347468, intron 1 of 24)	intron (NM_001347468, intron 1 of 24)	22133	NM_019765	56430	Mm.241109	NM_019765	ENSMUSG00000049550	Clip1	1110007I12Rik|4631429H07Rik|AV017631|C81039|CLIP-170|CLIP170|CYLN1|Clip50|Rsn|mKIAA4046|restin	CAP-GLY domain containing linker protein 1	protein-coding
mm_91676.1	chr10	43456541	43456549	-	1	NA	intron (NM_001168289, intron 7 of 7)	intron (NM_001168289, intron 7 of 7)	-22595	NM_199028	331623	Mm.490388	NM_199028	ENSMUSG00000038214	Bend3	mKIAA1553	BEN domain containing 3	protein-coding
mm_130985.1	chr15	103353758	103353784	-	1	NA	exon (NM_010577, exon 12 of 30)	exon (NM_010577, exon 12 of 30)	-3246	NR_105928	102466775		NR_105928	ENSMUSG00000098419	Mir6963	Gm27724|mmu-mir-6963	microRNA 6963	ncRNA
mm_86769.1	chr10	19934293	19934317	+	1	NA	promoter-TSS (NM_008580)	promoter-TSS (NM_008580)	-221	NM_008580	26408	Mm.6595	NM_008580	ENSMUSG00000071369	Map3k5	7420452D20Rik|ASK|ASK1|MAPKKK5|Mekk5	mitogen-activated protein kinase kinase kinase 5	protein-coding
mm_90475.1	chr10	127866443	127866455	+	1	NA	promoter-TSS (NM_145424)	promoter-TSS (NM_145424)	-27	NM_145424	216454	Mm.214923	NM_145424	ENSMUSG00000074639	BC089597	CRAD-L	cDNA sequence BC089597	protein-coding
mm_121164.1	chr14	103012871	103012887	+	1	NA	intron (NR_045657, intron 2 of 2)	intron (NR_045657, intron 2 of 2)	20924	NR_045657	71264	Mm.399572	NR_045657		4933432I03Rik	-	RIKEN cDNA 4933432I03 gene	ncRNA
mm_91705.1	chr10	44022283	44022291	-	1	NA	Intergenic	Intergenic	-17441	NM_172393	11630	Mm.292082	NM_172393	ENSMUSG00000019866	Aim1	AI462491|AI463325	absent in melanoma 1	protein-coding
mm_20878.1	chr2	148732458	148732463	-	1	NA	promoter-TSS (NM_019632)	promoter-TSS (NM_019632)	-40	NM_019632	17957	Mm.274308	NM_019632	ENSMUSG00000027438	Napb	Brp14|E161|I47|SNARE|b-SNAP	N-ethylmaleimide sensitive fusion protein attachment protein beta	protein-coding
mm_65283.1	chr7	24433580	24433603	-	1	NA	intron (NM_199013, intron 2 of 2)	PB1D7|SINE|Alu	12091	NM_199013	210145	Mm.33811	NM_199013	ENSMUSG00000062028	Irgc1	F630044M05Rik|Gm1102|Gm474|Ifgge|Iigp5|Irgc	immunity-related GTPase family, cinema 1	protein-coding
mm_62107.1	chr7	96456312	96456325	+	1	NA	intron (NM_001310760, intron 3 of 32)	intron (NM_001310760, intron 3 of 32)	-114354	NR_046043	670727	Mm.421352	NR_046043	ENSMUSG00000085751	Gm15412	OTTMUSG00000021245	predicted gene 15412	ncRNA
mm_90913.1	chr10	12406853	12406856	-	1	NA	intron (NM_011682, intron 68 of 73)	intron (NM_011682, intron 68 of 73)	454881	NM_011682	22288	Mm.331784	NM_011682	ENSMUSG00000019820	Utrn	AA589569|DRP|Dmdl	utrophin	protein-coding
mm_102459.1	chr11	59839777	59839794	-	1	NA	promoter-TSS (NM_011991)	promoter-TSS (NM_011991)	-18	NM_011991	26572	Mm.40	NM_011991	ENSMUSG00000019373	Cops3	Csn3|Sgn3	COP9 signalosome subunit 3	protein-coding
mm_60102.1	chr7	35334307	35334331	+	1	NA	promoter-TSS (NM_027897)	promoter-TSS (NM_027897)	82	NM_027897	52428	Mm.286600	NM_027897	ENSMUSG00000030494	Rhpn2	1300002E07Rik|AA536890|C85860|D7Ertd784e	rhophilin, Rho GTPase binding protein 2	protein-coding
mm_111294.1	chr12	85473349	85473351	-	1	NA	promoter-TSS (NM_010234)	promoter-TSS (NM_010234)	-551	NM_010234	14281	Mm.246513	NM_010234	ENSMUSG00000021250	Fos	D12Rfj1|c-fos|cFos	FBJ osteosarcoma oncogene	protein-coding
mm_11272.1	chr2	30061883	30061891	+	1	NA	promoter-TSS (NM_023871)	promoter-TSS (NM_023871)	-109	NM_023871	56086	Mm.326055	NM_023871	ENSMUSG00000054766	Set	2610030F17Rik|5730420M11Rik|AA407739|I-2PP2A|StF-IT-1|TAF-I	SET nuclear oncogene	protein-coding
mm_10086.1	chr2	3118336	3118392	+	1	NA	promoter-TSS (NM_001081161)	promoter-TSS (NM_001081161)	-24	NM_001081161	269233	Mm.23044	NM_001081161	ENSMUSG00000050530	Fam171a1	9630050M13Rik|AA409679	family with sequence similarity 171, member A1	protein-coding
mm_95791.1	chr11	54961703	54961709	+	1	NA	intron (NM_001199275, intron 1 of 18)	intron (NM_001199275, intron 1 of 18)	1234	NM_021327	57783	Mm.259671	NM_021327	ENSMUSG00000020400	Tnip1	ABIN|ABIN-1|ABIN1|AU018810|Naf1|Nef|VAN	TNFAIP3 interacting protein 1	protein-coding
mm_133751.1	chr16	94410824	94410861	+	1	NA	exon (NM_009441, exon 14 of 46)	exon (NM_009441, exon 14 of 46)	-39827	NM_001159617	56176	Mm.474449	NM_019543	ENSMUSG00000022940	Pigp	Dcrc|Dscr5	phosphatidylinositol glycan anchor biosynthesis, class P	protein-coding
mm_51046.1	chr6	65625426	65625441	+	1	NA	intron (NM_001001495, intron 7 of 7)	(TAGA)n|Simple_repeat|Simple_repeat	35035	NM_001001495	414084	Mm.117558	NM_001001495	ENSMUSG00000044162	Tnip3	9030611K07Rik|ABIN-3|LIND	TNFAIP3 interacting protein 3	protein-coding
mm_8627.1	chr1	156270823	156270829	-	1	NA	intron (NM_001134741, intron 12 of 17)	intron (NM_001134741, intron 12 of 17)	32522	NM_001134741	214575	Mm.252800	NM_001134741	ENSMUSG00000060985	Tdrd5	Gm103	tudor domain containing 5	protein-coding
mm_4363.1	chr1	172026858	172026866	+	1	NA	intron (NM_033509, intron 1 of 7)	intron (NM_033509, intron 1 of 7)	433	NM_033509	93840	Mm.36148	NM_033509	ENSMUSG00000026556	Vangl2	C530001F03Rik|Lootl|Lp|Lpp1|Ltap|Vang1l2|loop-tail|ska17|ska<m17Jus>|stbm|strabismus	vang-like 2 (van gogh, Drosophila)	protein-coding
mm_100608.1	chr11	121308369	121308370	+	1	NA	3' UTR (NM_001080932, exon 9 of 9)	3' UTR (NM_001080932, exon 9 of 9)	46078	NM_025793	66840	Mm.103986	NM_025793	ENSMUSG00000025173	Wdr45b	0610008N23Rik|AA408735|D16Bwg0193e|WIPI-3|Wdr45l	WD repeat domain 45B	protein-coding
mm_95719.1	chr11	54522873	54522895	+	1	NA	promoter-TSS (NM_001252494)	promoter-TSS (NM_001252494)	39	NM_001252496	192786	Mm.254404	NM_175258	ENSMUSG00000037533	Rapgef6	A530068K01|AI844632|BB085664|C030018K18Rik|PDZ-GEF2|Pdzgef2|RA-GEF-2|Ragef2|mKIAA4052	Rap guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_131882.1	chr16	23224873	23224923	+	1	NA	5' UTR (NM_145933, exon 1 of 8)	5' UTR (NM_145933, exon 1 of 8)	158	NM_145933	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_70577.1	chr8	13165934	13165940	+	1	NA	exon (NM_010684, exon 2 of 9)	exon (NM_010684, exon 2 of 9)	6776	NM_010684	16783	Mm.16716	NM_010684	ENSMUSG00000031447	Lamp1	CD107a|LGP-120|LGP-A|Lamp-1|P2B	lysosomal-associated membrane protein 1	protein-coding
mm_25274.1	chr3	105094992	105094996	+	1	NA	Intergenic	Intergenic	28150	NM_029228	75269	Mm.307994	NM_029228	ENSMUSG00000051788	4930564D02Rik	-	RIKEN cDNA 4930564D02 gene	protein-coding
mm_136402.1	chr16	93598361	93598361	-	1	NA	intron (NM_145482, intron 4 of 11)	L1_Rod|LINE|L1	5454	NM_145482	224440	Mm.10628	NM_145482	ENSMUSG00000022948	Setd4	AY037804|C21orf18|ORF21	SET domain containing 4	protein-coding
mm_11004.1	chr2	26498414	26498455	+	1	NA	intron (NM_008714, intron 2 of 33)	intron (NM_008714, intron 2 of 33)	5388	NM_008714	18128	Mm.290610	NM_008714	ENSMUSG00000026923	Notch1	9930111A19Rik|Mis6|N1|Tan1|lin-12	notch 1	protein-coding
mm_62543.1	chr7	102317449	102317451	+	1	NA	intron (NM_009287, intron 1 of 11)	intron (NM_009287, intron 1 of 11)	49626	NM_009287	20866	Mm.645	NM_009287	ENSMUSG00000030987	Stim1	SIM	stromal interaction molecule 1	protein-coding
mm_143419.1	chr17	70842507	70842508	-	1	NA	Intergenic	B1_Mur2|SINE|Alu	4270	NM_001164077	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_1960.1	chr1	86426324	86426349	+	1	NA	promoter-TSS (NM_027966)	promoter-TSS (NM_027966)	7	NM_027966	71863	Mm.179627	NM_027966	ENSMUSG00000036574	1700019O17Rik	-	RIKEN cDNA 1700019O17 gene	protein-coding
mm_154587.1	chrX	7573206	7573247	+	1	NA	promoter-TSS (NR_029473)	promoter-TSS (NR_029473)	-374	NR_029473	78185	Mm.160055	NR_029473	ENSMUSG00000039545	Ppp1r3fos	4930524L23Rik	protein phosphatase 1, regulatory subunit 3F, opposite strand	ncRNA
mm_118844.1	chr14	25661406	25661435	+	1	NA	exon (NM_183208, exon 23 of 24)	exon (NM_183208, exon 23 of 24)	-32750	NM_134084	105675	Mm.41656	NM_134084	ENSMUSG00000021868	Ppif	AW457192|CyP-D|CyP-F|CypD|PPIase	peptidylprolyl isomerase F (cyclophilin F)	protein-coding
mm_90905.1	chr10	11082288	11082372	-	1	NA	promoter-TSS (NM_001114333)	promoter-TSS (NM_001114333)	1	NM_001114333	14816	Mm.391904	NM_016976	ENSMUSG00000019828	Grm1	4930455H15Rik|ENSMUSG00000075319|Gm10828|Gprc1a|mGluR1|nmf373|rcw|wobl	glutamate receptor, metabotropic 1	protein-coding
mm_103208.1	chr11	70652949	70652988	-	1	NA	exon (NM_011072, exon 2 of 3)	exon (NM_011072, exon 2 of 3)	1682	NM_011072	18643	Mm.2647	NM_011072	ENSMUSG00000018293	Pfn1	Pfn	profilin 1	protein-coding
mm_58184.1	chr6	142964136	142964192	-	1	NA	5' UTR (NM_011374, exon 1 of 5)	5' UTR (NM_011374, exon 1 of 5)	288	NM_011374	20449	Mm.260838	NM_011374	ENSMUSG00000030283	St8sia1	9330109E03Rik|GD3S|Sia-T|Siat8|Siat8a	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 1	protein-coding
mm_126743.1	chr15	85734909	85734925	+	1	NA	promoter-TSS (NM_011144)	promoter-TSS (NM_011144)	-647	NM_001113418	19013	Mm.212789	NM_011144	ENSMUSG00000022383	Ppara	4933429D07Rik|AW742785|Nr1c1|PPAR-alpha|PPARalpha|Ppar	peroxisome proliferator activated receptor alpha	protein-coding
mm_30458.1	chr3	153944426	153944452	-	1	NA	5' UTR (NM_007382, exon 1 of 12)	5' UTR (NM_007382, exon 1 of 12)	204	NM_007382	11364	Mm.10530	NM_007382	ENSMUSG00000062908	Acadm	AU018656|MCAD	acyl-Coenzyme A dehydrogenase, medium chain	protein-coding
mm_36623.1	chr4	91371985	91372000	-	1	NA	promoter-TSS (NM_207686)	promoter-TSS (NM_207686)	63	NM_010486	15569	Mm.318042	NM_010486	ENSMUSG00000008489	Elavl2	Hub|mel-N1	ELAV (embryonic lethal, abnormal vision, Drosophila)-like 2 (Hu antigen B)	protein-coding
mm_31656.1	chr4	59873768	59873774	+	1	NA	intron (NM_172468, intron 3 of 8)	intron (NM_172468, intron 3 of 8)	41285	NM_021053	30936	Mm.284433	NM_021053	ENSMUSG00000028386	Slc46a2	5430429N04Rik|Ly110|TSO-1C12|Tscot	solute carrier family 46, member 2	protein-coding
mm_5802.1	chr1	52190902	52190915	-	1	NA	intron (NM_001081081, intron 12 of 17)	intron (NM_001081081, intron 12 of 17)	42324	NM_001081081	14660	Mm.398608	NM_001081081	ENSMUSG00000026103	Gls	6330442B14|AI314027|B230365M23Rik	glutaminase	protein-coding
mm_103031.1	chr11	69735376	69735386	-	1	NA	exon (NM_001291068, exon 29 of 29)	exon (NM_001291068, exon 29 of 29)	23252	NM_001291068	20020	Mm.16533	NM_009089	ENSMUSG00000005198	Polr2a	220kDa|Rpb1|Rpo2-1	polymerase (RNA) II (DNA directed) polypeptide A	protein-coding
mm_43489.1	chr5	136919595	136919623	+	1	NA	intron (NR_015555, intron 1 of 3)	intron (NR_015555, intron 1 of 3)	463	NR_015555	66752	Mm.135764	NR_015555	ENSMUSG00000097908	4933404O12Rik	AW494809	RIKEN cDNA 4933404O12 gene	ncRNA
mm_171080.1	chr3	121249964	121249964	-	1	NA	intron (NM_178936, intron 1 of 7)	LSU-rRNA_Hsa|rRNA|rRNA	13352	NM_178936	99887	Mm.26088	NM_178936	ENSMUSG00000028132	Tmem56	4930577M16Rik|AU018104|AW109744|C730036B01Rik	transmembrane protein 56	protein-coding
mm_60794.1	chr7	45575242	45575306	+	1	NA	promoter-TSS (NR_038166)	promoter-TSS (NR_038166)	-98	NR_038165	71661	Mm.439894	NR_038165	ENSMUSG00000109644	0610005C13Rik	AI182092	RIKEN cDNA 0610005C13 gene	ncRNA
mm_9344.1	chr1	172066493	172066535	-	1	NA	3' UTR (NM_021607, exon 17 of 17)	3' UTR (NM_021607, exon 17 of 17)	-8918	NM_010916	18071	Mm.2474	NM_010916	ENSMUSG00000051251	Nhlh1	Hen1|Nscl|Tal2|bHLHa35	nescient helix loop helix 1	protein-coding
mm_39772.1	chr5	30014089	30014105	+	1	NA	intron (NM_001314054, intron 2 of 4)	B1_Mur2|SINE|Alu	983	NM_031168	16193	Mm.1019	NM_031168	ENSMUSG00000025746	Il6	Il-6	interleukin 6	protein-coding
mm_154234.1	chr19	60537525	60537528	-	1	NA	intron (NM_030197, intron 5 of 8)	A-rich|Low_complexity|Low_complexity	43497	NM_001172097	78832	Mm.259026	NM_030197	ENSMUSG00000033417	Cacul1	2700078E11Rik|2810417M16Rik|9830127L17Rik|AI450346|D130033C15Rik	CDK2 associated, cullin domain 1	protein-coding
mm_95421.1	chr11	50131343	50131426	+	1	NA	promoter-TSS (NM_001290759)	promoter-TSS (NM_001290759)	24	NM_029745	76795	Mm.290975	NM_029745	ENSMUSG00000036644	Tbc1d9b	-	TBC1 domain family, member 9B	protein-coding
mm_19006.1	chr2	76889754	76889776	-	1	NA	exon (NM_011652, exon 73 of 313)	exon (NM_011652, exon 73 of 313)	92782	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_95766.1	chr11	54907205	54907246	+	1	NA	exon (NM_008161, exon 2 of 5)	exon (NM_008161, exon 2 of 5)	4371	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_68193.1	chr7	104369839	104369876	-	1	NA	Intergenic	Intergenic	-11211	NM_175648	244183	Mm.347647	NM_175648	ENSMUSG00000052749	Trim30b	A530023O14Rik|Trim30-1	tripartite motif-containing 30B	protein-coding
mm_57363.1	chr6	124766132	124766149	-	1	NA	exon (NM_013509, exon 7 of 12)	exon (NM_013509, exon 7 of 12)	3533	NM_001302642	13807	Mm.3913	NM_013509	ENSMUSG00000004267	Eno2	AI837106|D6Ertd375e|Eno-2|NSE	enolase 2, gamma neuronal	protein-coding
mm_168538.1	chr11	61930261	61930261	-	1	NA	promoter-TSS (NM_019921)	promoter-TSS (NM_019921)	-4	NM_019921	56697	Mm.274404	NM_019921	ENSMUSG00000047804	Akap10	1500031L16Rik|B130049N18Rik|D-AKAP-2|D-AKAP2|PRKA10	A kinase (PRKA) anchor protein 10	protein-coding
mm_41680.1	chr5	99978670	99978684	+	1	NA	5' UTR (NM_007516, exon 1 of 8)	5' UTR (NM_007516, exon 1 of 8)	261	NM_001077266	11991	Mm.150231	NM_007516	ENSMUSG00000000568	Hnrnpd	Auf1|Hnrpd	heterogeneous nuclear ribonucleoprotein D	protein-coding
mm_71574.1	chr8	54529607	54529633	+	1	NA	intron (NM_029701, intron 1 of 4)	CpG	378	NM_029701	76687	Mm.86437	NM_029701	ENSMUSG00000054408	Spcs3	1810011E08Rik|SPC22/23	signal peptidase complex subunit 3 homolog (S. cerevisiae)	protein-coding
mm_97203.1	chr11	75598275	75598302	+	1	NA	exon (NM_008850, exon 3 of 12)	exon (NM_008850, exon 3 of 12)	1943	NR_110477	654359	Mm.439961	NR_110477		Gm12338	OTTMUSG00000006216	cytochrome c oxidase, subunit VIIc pseudogene	pseudo
mm_25497.1	chr3	109371922	109371925	+	1	NA	intron (NM_020505, intron 1 of 26)	intron (NM_020505, intron 1 of 26)	31240	NM_020505	57257	Mm.282257	NM_020505	ENSMUSG00000033721	Vav3	A530094I06Rik|AA986410|Idd18.1	vav 3 oncogene	protein-coding
mm_8996.1	chr1	165709779	165709794	-	1	NA	Intergenic	Intergenic	-1692	NM_001038846	226594	Mm.265552	NM_178593	ENSMUSG00000040723	Rcsd1	A430105K13Rik|BC025872|CapZIP	RCSD domain containing 1	protein-coding
mm_163737.1	chr13	119690453	119690471	+	1	NA	5' UTR (NM_001291439, exon 1 of 10)	5' UTR (NM_001291439, exon 1 of 10)	111	NM_001291439	208715	Mm.61526	NM_145942	ENSMUSG00000093930	Hmgcs1	B130032C06Rik	3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1	protein-coding
mm_10542.1	chr2	16532053	16532079	+	1	NA	intron (NM_026162, intron 2 of 13)	intron (NM_026162, intron 2 of 13)	175762	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding
mm_152616.1	chr19	12434854	12434864	-	1	NA	Intergenic	Intergenic	6954	NM_019540	56093	Mm.285849	NM_019540	ENSMUSG00000040065	Pfpl	Epcs5|Epcs50	pore forming protein-like	protein-coding
mm_81712.1	chr9	111312109	111312121	+	1	NA	exon (NM_001164659, exon 1 of 22)	exon (NM_001164659, exon 1 of 22)	376	NM_001164659	320429	Mm.270754	NM_001164659	ENSMUSG00000062296	Trank1	A230061D21Rik|C030048J01Rik|Gm187|Lba1	tetratricopeptide repeat and ankyrin repeat containing 1	protein-coding
mm_53005.1	chr6	123270679	123270689	+	1	NA	intron (NM_001163161, intron 5 of 5)	intron (NM_001163161, intron 5 of 5)	8577	NM_010819	17474	Mm.441101	NM_010819	ENSMUSG00000030144	Clec4d	Clecsf8|Mpcl|mcl	C-type lectin domain family 4, member d	protein-coding
mm_61312.1	chr7	68059104	68059107	+	1	NA	intron (NM_010513, intron 2 of 20)	B1_Mur2|SINE|Alu	106848	NM_010513	16001	Mm.275742	NM_010513	ENSMUSG00000005533	Igf1r	A330103N21Rik|CD221|D930020L01|IGF-1R|hyft	insulin-like growth factor I receptor	protein-coding
mm_125783.1	chr15	74716515	74716517	+	1	NA	exon (NM_028216, exon 3 of 3)	exon (NM_028216, exon 3 of 3)	1677	NM_028216	72373	Mm.46395	NM_028216	ENSMUSG00000022598	Psca	2210408B04Rik	prostate stem cell antigen	protein-coding
mm_160069.1	chr7	6197302	6197302	+	1	NA	5' UTR (NM_178028, exon 1 of 6)	5' UTR (NM_178028, exon 1 of 6)	212	NM_178028	232836	Mm.246599	NM_178028	ENSMUSG00000034660	Galp	-	galanin-like peptide	protein-coding
mm_164586.1	chr17	26508952	26508964	+	1	NA	promoter-TSS (NM_013642)	promoter-TSS (NM_013642)	-486	NM_013642	19252	Mm.239041	NM_013642	ENSMUSG00000024190	Dusp1	3CH134|MKP1|Ptpn16|U19515|erp|mkp-1	dual specificity phosphatase 1	protein-coding
mm_101169.1	chr11	16981827	16981840	-	1	NA	exon (NM_019549, exon 9 of 10)	exon (NM_019549, exon 9 of 10)	26885	NM_019549	56193	Mm.98232	NM_019549	ENSMUSG00000020120	Plek	2010300B13Rik	pleckstrin	protein-coding
mm_90463.1	chr10	127759781	127759801	+	1	NA	promoter-TSS (NM_080436)	promoter-TSS (NM_080436)	28	NM_080436	107605	Mm.484271	NM_080436	ENSMUSG00000089789	Rdh1	-	retinol dehydrogenase 1 (all trans)	protein-coding
mm_109809.1	chr12	3357013	3357026	-	1	NA	Intergenic	Intergenic	-8113	NM_008445	16570	Mm.7688	NM_008445	ENSMUSG00000020668	Kif3c	mKIAA4058	kinesin family member 3C	protein-coding
mm_60446.1	chr7	44477213	44477241	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	6880	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_27924.1	chr3	79549538	79549544	-	1	NA	intron (NM_001162999, intron 1 of 16)	AT_rich|Low_complexity|Low_complexity	18138	NM_001162999	329679	Mm.244005	NM_001162999	ENSMUSG00000061175	Fnip2	D630023B12Rik|mKIAA1450	folliculin interacting protein 2	protein-coding
mm_167538.1	chr9	22003308	22003334	+	1	NA	promoter-TSS (NM_029939)	promoter-TSS (NM_029939)	333	NM_008925	19089	Mm.214593	NM_008925	ENSMUSG00000003402	Prkcsh	80K-H|PKCSH	protein kinase C substrate 80K-H	protein-coding
mm_118808.1	chr14	25459233	25459261	+	1	NA	promoter-TSS (NM_183208)	promoter-TSS (NM_183208)	62	NM_183208	328365	Mm.227484	NM_183208	ENSMUSG00000007817	Zmiz1	BC065120|E330020C23|ENSMUSG00000072684|Gm10397|I920194n01|Rai17|Zimp10	zinc finger, MIZ-type containing 1	protein-coding
mm_47665.1	chr5	126504972	126504979	-	1	NA	Intergenic	Intergenic	-525814	NR_040685	71247	Mm.399586	NR_040685	ENSMUSG00000105490	4933438B17Rik	-	RIKEN cDNA 4933438B17 gene	ncRNA
mm_159082.1	chr2	27067924	27067924	-	1	NA	promoter-TSS (NM_001159602)	promoter-TSS (NM_001159602)	-56	NM_001159602	66139	Mm.330087	NM_025376	ENSMUSG00000009214	Tmem8c	1110002H13Rik|AI131587	transmembrane protein 8C	protein-coding
mm_131744.1	chr16	22096024	22096069	+	1	NA	intron (NM_183029, intron 2 of 15)	ORR1F|LTR|ERVL-MaLR	67253	NM_183029	319765	Mm.489442	NM_183029	ENSMUSG00000033581	Igf2bp2	C330012H03Rik|IMP-2|Imp2|Neilsen	insulin-like growth factor 2 mRNA binding protein 2	protein-coding
mm_139804.1	chr17	66123599	66123617	+	1	NA	promoter-TSS (NM_001003919)	promoter-TSS (NM_001003919)	88	NM_001003919	320209	Mm.259605	NM_001003919	ENSMUSG00000035842	Ddx11	4732462I11Rik|CHL1|CHLR1|KRG2|essa15a	DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11	protein-coding
mm_135771.1	chr16	56831810	56831819	-	1	NA	intron (NM_019631, intron 1 of 5)	intron (NM_019631, intron 1 of 5)	-35956	NM_172825	239853	Mm.258979	NM_172825	ENSMUSG00000022755	Adgrg7	9130020O16Rik|Gpr128	adhesion G protein-coupled receptor G7	protein-coding
mm_126616.1	chr15	83100307	83100318	+	1	NA	5' UTR (NM_023475, exon 1 of 12)	5' UTR (NM_023475, exon 1 of 12)	107	NM_023475	68607	Mm.30056	NM_023475	ENSMUSG00000058586	Serhl	0610008B10Rik|1110019M09Rik|AU019786	serine hydrolase-like	protein-coding
mm_143987.1	chr17	87637100	87637109	-	1	NA	intron (NM_008532, intron 2 of 9)	CpG-6684	1125	NM_008532	17075	Mm.4259	NM_008532	ENSMUSG00000045394	Epcam	CD326|EGP|EGP-2|Egp314|Ep-CAM|EpCAM1|GA733-2|Ly74|TROP1|Tacsd1|Tacstd1|gp40	epithelial cell adhesion molecule	protein-coding
mm_8265.1	chr1	139376970	139376983	-	1	NA	promoter-TSS (NM_133239)	promoter-TSS (NM_133239)	100	NM_133239	170788	Mm.95700	NM_133239	ENSMUSG00000063681	Crb1	7530426H14Rik|A930008G09Rik	crumbs family member 1, photoreceptor morphogenesis associated	protein-coding
mm_76949.1	chr8	105989397	105989408	-	1	NA	intron (NM_001301205, intron 3 of 9)	intron (NM_001301205, intron 3 of 9)	2371	NM_001301204	319446	Mm.248357	NM_176913	ENSMUSG00000053687	Dpep2	F630103D06Rik|MBD-2	dipeptidase 2	protein-coding
mm_60457.1	chr7	44477620	44477643	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-6886	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_24213.1	chr3	88629464	88629479	+	1	NA	intron (NM_001198912, intron 1 of 21)	intron (NM_001198912, intron 1 of 21)	8077	NM_001198912	16800	Mm.239329	NM_008487	ENSMUSG00000028059	Arhgef2	AA408978|GEF|GEF-H1|GEFH1|LFP40|Lbcl1|Lfc|P40|mKIAA0651	rho/rac guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_172832.1	chr9	22903611	22903613	-	1	NA	Intergenic	L1Md_A|LINE|L1	-319464	NM_028472	73230	Mm.335020	NM_028472	ENSMUSG00000031963	Bmper	3110056H04Rik|CV-2|Crim3|Cv2	BMP-binding endothelial regulator	protein-coding
mm_99507.1	chr11	103043160	103043183	+	1	NA	exon (NM_008707, exon 2 of 12)	exon (NM_008707, exon 2 of 12)	14609	NM_008707	18107	Mm.10265	NM_008707	ENSMUSG00000020936	Nmt1	AW536594	N-myristoyltransferase 1	protein-coding
mm_119687.1	chr14	53530747	53530764	+	1	NA	Intergenic	Intergenic	723174	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_26925.1	chr3	20249744	20249805	-	1	NA	exon (NM_029706, exon 11 of 11)	exon (NM_029706, exon 11 of 11)	-7593	NM_007753	12873	Mm.1135	NM_007753	ENSMUSG00000001865	Cpa3	MC-CPA	carboxypeptidase A3, mast cell	protein-coding
mm_33598.1	chr4	132568498	132568508	+	1	NA	intron (NM_001081211, intron 1 of 1)	B4|SINE|B4	4436	NM_001081211	19204	Mm.89389	NM_001081211	ENSMUSG00000056529	Ptafr	PAFR	platelet-activating factor receptor	protein-coding
mm_20581.1	chr2	131146817	131146830	-	1	NA	TTS (NM_028306)	TTS (NM_028306)	13197	NM_026091	67326	Mm.27711	NM_026091	ENSMUSG00000027327	1700037H04Rik	-	RIKEN cDNA 1700037H04 gene	protein-coding
mm_82823.1	chr9	31120863	31120869	-	1	NA	intron (NM_011176, intron 1 of 18)	intron (NM_011176, intron 1 of 18)	10933	NM_011176	19143	Mm.243926	NM_011176	ENSMUSG00000031995	St14	Epithin|MT-SP1|Prss14|Tmprss14|mCAP3|matriptase	suppression of tumorigenicity 14 (colon carcinoma)	protein-coding
mm_167419.1	chr8	110962849	110962851	+	1	NA	intron (NM_009179, intron 3 of 6)	B3|SINE|B2	34973	NM_007916	13680	Mm.287901	NM_007916	ENSMUSG00000015023	Ddx19a	DBP5|Ddx19|Eif4a-rs1	DEAD (Asp-Glu-Ala-Asp) box polypeptide 19a	protein-coding
mm_33529.1	chr4	130932314	130932325	+	1	NA	intron (NM_010686, intron 7 of 7)	RMER1C|Other|Other	-12066	NM_010769	17180	Mm.271796	NM_010769	ENSMUSG00000040533	Matn1	CMP|Crtm|Mat1|matrilin-1	matrilin 1, cartilage matrix protein	protein-coding
mm_154088.1	chr19	56815769	56815777	-	1	NA	Intergenic	Intergenic	-2090	NM_170757	213993	Mm.469677	NM_170757	ENSMUSG00000035173	Ccdc186	1810028B20Rik|A630007B06Rik|AI159700|Otg1	coiled-coil domain containing 186	protein-coding
mm_117413.1	chr13	74208662	74208719	-	1	NA	promoter-TSS (NM_177333)	promoter-TSS (NM_177333)	10	NM_177333	211446	Mm.261859	NM_177333	ENSMUSG00000034152	Exoc3	2810050O03Rik|E430013E20Rik|Sec6|Sec6l1	exocyst complex component 3	protein-coding
mm_85279.1	chr9	99568850	99568911	-	1	NA	promoter-TSS (NM_001166138)	promoter-TSS (NM_001166138)	19	NM_001166138	74125	Mm.234823	NM_028768	ENSMUSG00000032468	Armc8	1200015K23Rik|Gid5|HSPC056	armadillo repeat containing 8	protein-coding
mm_159632.1	chr4	138250316	138250316	+	1	NA	promoter-TSS (NM_001099631)	promoter-TSS (NM_001099631)	-95	NM_001099631	230863	Mm.482408	NM_001099631	ENSMUSG00000045349	Sh2d5	BC036961	SH2 domain containing 5	protein-coding
mm_69556.1	chr7	135700000	135700023	-	1	NA	exon (NM_001081117, exon 12 of 14)	exon (NM_001081117, exon 12 of 14)	16368	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_111926.1	chr12	108884337	108884346	-	1	NA	intron (NM_011710, intron 2 of 10)	intron (NM_011710, intron 2 of 10)	8857	NM_001164488	22375	Mm.38433	NM_011710	ENSMUSG00000021266	Wars	TrpRS|WRS	tryptophanyl-tRNA synthetase	protein-coding
mm_125353.1	chr15	39391804	39391821	+	1	NA	intron (NM_001256382, intron 3 of 26)	intron (NM_001256382, intron 3 of 26)	193526	NM_053271	116838	Mm.309296	NM_053271	ENSMUSG00000037386	Rims2	2810036I15Rik|AW048769|RIM2|Rab3ip2|Rim2(+40A)|Rim2(+44A)|Rim2(+4A)|Serg2|Syt3-rs|mKIAA0751	regulating synaptic membrane exocytosis 2	protein-coding
mm_967.1	chr1	58122229	58122251	+	1	NA	intron (NM_023617, intron 5 of 34)	L3|LINE|CR1	9104	NM_023617	71724	Mm.20108	NM_023617	ENSMUSG00000064294	Aox3	1200011D03Rik|AI326299|Aoh1|Aoh2	aldehyde oxidase 3	protein-coding
mm_97065.1	chr11	72881792	72881792	+	1	NA	intron (NM_001045536, intron 32 of 54)	U1|snRNA|snRNA	-79377	NM_016745	53313	Mm.6306	NM_016745	ENSMUSG00000020788	Atp2a3	SERCA3b|Serca3	ATPase, Ca++ transporting, ubiquitous	protein-coding
mm_115995.1	chr13	24400346	24400346	-	1	NA	intron (NM_001284519, intron 3 of 17)	intron (NM_001284519, intron 3 of 17)	-14776	NM_007717	12763	Mm.8396	NM_007717	ENSMUSG00000016756	Cmah	-	cytidine monophospho-N-acetylneuraminic acid hydroxylase	protein-coding
mm_4209.1	chr1	171266726	171266731	+	1	NA	Intergenic	RMER4B|LTR|ERVK	-3600	NM_020579	57370	Mm.274011	NM_020579	ENSMUSG00000052423	B4galt3	9530061M23Rik|AA104562|AW125175|ESTM26|ESTM6|R74981	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 3	protein-coding
mm_69169.1	chr7	127215044	127215070	-	1	NA	TTS (NM_016754)	TTS (NM_016754)	3388	NM_017461	54204	Mm.18	NM_017461	ENSMUSG00000000486	Sept1	Diff6|Pnutl3	septin 1	protein-coding
mm_110508.1	chr12	54695814	54695828	-	1	NA	promoter-TSS (NM_001331162)	promoter-TSS (NM_001331162)	73	NM_001331162	66266	Mm.156440	NM_025456	ENSMUSG00000054302	Eapp	1810011O16Rik	E2F-associated phosphoprotein	protein-coding
mm_78132.1	chr9	20868724	20868741	+	1	NA	promoter-TSS (NM_175687)	promoter-TSS (NM_175687)	90	NM_175687	319278	Mm.249932	NM_175687	ENSMUSG00000038884	A230050P20Rik	RyDEN	RIKEN cDNA A230050P20 gene	protein-coding
mm_22748.1	chr3	19957342	19957356	+	1	NA	exon (NM_007752, exon 1 of 19)	exon (NM_007752, exon 1 of 19)	295	NM_007752	12870	Mm.13787	NM_007752	ENSMUSG00000003617	Cp	D3Ertd555e	ceruloplasmin	protein-coding
mm_158142.1	chrX	103428352	103428399	-	1	NA	Intergenic	B1_Mur1|SINE|Alu	-3142	NR_002844	22097	Mm.472939	NR_002844	ENSMUSG00000085715	Tsix	-	X (inactive)-specific transcript, opposite strand	ncRNA
mm_55062.1	chr6	49047998	49048007	-	1	NA	exon (NM_053110, exon 6 of 11)	exon (NM_053110, exon 6 of 11)	11484	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_111676.1	chr12	103355736	103355746	-	1	NA	5' UTR (NM_023049, exon 1 of 10)	5' UTR (NM_023049, exon 1 of 10)	260	NM_023049	65256	Mm.27159	NM_023049	ENSMUSG00000021200	Asb2	1110008E15Rik	ankyrin repeat and SOCS box-containing 2	protein-coding
mm_51447.1	chr6	80214754	80214784	+	1	NA	intron (NM_001347261, intron 2 of 2)	B3A|SINE|B2	195126	NM_178731	243499	Mm.483425	NM_178731	ENSMUSG00000052581	Lrrtm4	7530419J18Rik|A230052N11	leucine rich repeat transmembrane neuronal 4	protein-coding
mm_139080.1	chr17	46681039	46681184	+	1	NA	promoter-TSS (NM_010787)	promoter-TSS (NM_010787)	-10	NM_010787	17256	Mm.329083	NM_010787	ENSMUSG00000002768	Mea1	Mea-1	male enhanced antigen 1	protein-coding
mm_104334.1	chr11	93996826	93996835	-	1	NA	intron (NM_001199203, intron 1 of 29)	intron (NM_001199203, intron 1 of 29)	739	NM_027569	70834	Mm.260737	NM_027569	ENSMUSG00000020859	Spag9	3110018C07Rik|4733401I23Rik|4831406C20Rik|AW552012|JLP|JSAP2|JSAP2a|Jip4|Mapk8ip4|syd1	sperm associated antigen 9	protein-coding
mm_134473.1	chr16	18586984	18587013	-	1	NA	promoter-TSS (NM_011532)	promoter-TSS (NM_011532)	-29	NM_001285476	21380	Mm.295194	NM_011532	ENSMUSG00000009097	Tbx1	-	T-box 1	protein-coding
mm_139843.1	chr17	69289671	69289688	+	1	NA	3' UTR (NM_013813, exon 22 of 22)	3' UTR (NM_013813, exon 22 of 22)	-12473	NR_045428	69750	Mm.439063	NR_045428	ENSMUSG00000100572	2410021H03Rik	-	RIKEN cDNA 2410021H03 gene	ncRNA
mm_106357.1	chr11	118393668	118393696	-	1	NA	exon (NM_011150, exon 6 of 6)	exon (NM_011150, exon 6 of 6)	8249	NM_011150	19039	Mm.3152	NM_011150	ENSMUSG00000033880	Lgals3bp	90K|CyCAP|MAC-2BP|Ppicap|Tango10b	lectin, galactoside-binding, soluble, 3 binding protein	protein-coding
mm_117942.1	chr13	99434832	99434842	-	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-22011	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_79618.1	chr9	58653118	58653153	+	1	NA	TTS (NM_009145)	TTS (NM_009145)	70895	NM_009145	20320	Mm.15125	NM_009145	ENSMUSG00000032336	Nptn	AW554172|SDR-1|Sdfr1	neuroplastin	protein-coding
mm_143833.1	chr17	84083646	84083658	-	1	NA	intron (NR_045458, intron 2 of 5)	A-rich|Low_complexity|Low_complexity	4992	NR_045458	74473	Mm.399575	NR_045458		4933433H22Rik	-	RIKEN cDNA 4933433H22 gene	ncRNA
mm_78136.1	chr9	20888291	20888295	+	1	NA	5' UTR (NM_145610, exon 1 of 11)	5' UTR (NM_145610, exon 1 of 11)	118	NM_145610	235036	Mm.2930	NM_145610	ENSMUSG00000004100	Ppan	A230087P06Rik|SSF1	peter pan homolog (Drosophila)	protein-coding
mm_107369.1	chr12	32850674	32850691	+	1	NA	3' UTR (NM_021524, exon 11 of 11)	3' UTR (NM_021524, exon 11 of 11)	26566	NR_045032	100504486	Mm.440246	NR_045032		Gdap10	Gdap-ps	ganglioside-induced differentiation-associated-protein 10	ncRNA
mm_136088.1	chr16	84955416	84955438	-	1	NA	exon (NM_001198823, exon 18 of 18)	exon (NM_001198823, exon 18 of 18)	-16784	NR_045889	100038614	Mm.441351	NR_045889		Gm10791	ENSMUSG00000074933	predicted gene 10791	ncRNA
mm_147491.1	chr18	47368691	47368707	-	1	NA	5' UTR (NM_018744, exon 1 of 19)	5' UTR (NM_018744, exon 1 of 19)	169	NM_018744	20358	Mm.40909	NM_018744	ENSMUSG00000019647	Sema6a	A730020P05Rik|AI851735|Sema6A-1|Semaq|VIa	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A	protein-coding
mm_135356.1	chr16	43889606	43889641	-	1	NA	promoter-TSS (NM_029128)	promoter-TSS (NM_029128)	53	NM_029128	106248	Mm.275354	NM_029128	ENSMUSG00000022704	Qtrtd1	3110012M05Rik|4930470H18Rik|AI648807|Qtrt2	queuine tRNA-ribosyltransferase domain containing 1	protein-coding
mm_40173.1	chr5	35913710	35913712	+	1	NA	intron (NM_027373, intron 1 of 16)	intron (NM_027373, intron 1 of 16)	20392	NM_027373	70292	Mm.125167	NM_027373	ENSMUSG00000029094	Afap1	2600003E23Rik|9630044L16Rik|AI848729|Afap|mKIAA3018	actin filament associated protein 1	protein-coding
mm_116924.1	chr13	55536505	55536547	-	1	NA	5' UTR (NM_134059, exon 1 of 17)	5' UTR (NM_134059, exon 1 of 17)	132	NM_134059	72935	Mm.205045	NM_134059	ENSMUSG00000021494	Ddx41	2900024F02Rik|AA958953|ABS|AI324246	DEAD (Asp-Glu-Ala-Asp) box polypeptide 41	protein-coding
mm_18259.1	chr2	52286109	52286125	-	1	NA	exon (NM_010889, exon 38 of 157)	exon (NM_010889, exon 38 of 157)	-4885	NR_040620	78049	Mm.243883	NR_040620		4930573O16Rik	-	RIKEN cDNA 4930573O16 gene	ncRNA
mm_3497.1	chr1	150106812	150106818	+	1	NA	3' UTR (NM_011198, exon 10 of 10)	3' UTR (NM_011198, exon 10 of 10)	6784	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_16374.1	chr2	178141877	178141887	+	1	NA	promoter-TSS (NM_028806)	promoter-TSS (NM_028806)	-51	NM_028806	74189	Mm.44413	NM_028806	ENSMUSG00000027525	Phactr3	1500003N10Rik|4930415A02Rik|H17739|Scapin1|Scapinin|mKIAA4224	phosphatase and actin regulator 3	protein-coding
mm_37969.1	chr4	133498479	133498508	-	1	NA	promoter-TSS (NM_001081156)	promoter-TSS (NM_001081156)	57	NM_001081156	69539	Mm.151594	NM_001081156	ENSMUSG00000056596	Trnp1	2300002D11Rik|Trnp	TMF1-regulated nuclear protein 1	protein-coding
mm_69428.1	chr7	132813165	132813182	-	1	NA	promoter-TSS (NM_212473)	promoter-TSS (NM_212473)	23	NM_212473	77938	Mm.225649	NM_175268	ENSMUSG00000030956	Fam53b	A930008G19Rik|mKIAA0140	family with sequence similarity 53, member B	protein-coding
mm_109030.1	chr12	104084175	104084185	+	1	NA	intron (NR_002861, intron 3 of 3)	intron (NR_002861, intron 3 of 3)	6221	NR_002861	321018	Mm.297023	NR_002861		Serpina4-ps1	KALps|Klst	serine (or cysteine) peptidase inhibitor, clade A, member 4, pseudogene 1	pseudo
mm_5097.1	chr1	4880694	4880699	-	1	NA	intron (NM_001159750, intron 3 of 9)	intron (NM_001159750, intron 3 of 9)	22368	NM_001159751	21399	Mm.207263	NM_011541	ENSMUSG00000033813	Tcea1	S-II	transcription elongation factor A (SII) 1	protein-coding
mm_90888.1	chr10	10234845	10234854	-	1	NA	Intergenic	Intergenic	237465	NM_001127353	215772	Mm.246573	NM_172547	ENSMUSG00000050994	Adgb	9130014G24Rik	androglobin	protein-coding
mm_158322.1	chrX	133898293	133898377	-	1	NA	promoter-TSS (NM_019656)	promoter-TSS (NM_019656)	94	NM_019656	56496	Mm.46701	NM_019656	ENSMUSG00000067377	Tspan6	6720473L21Rik|AI316786|T245|TSPAN-6|Tm4sf|Tm4sf6	tetraspanin 6	protein-coding
mm_150185.1	chr19	32665430	32665438	+	1	NA	exon (NM_011864, exon 13 of 13)	exon (NM_011864, exon 13 of 13)	45429	NM_011864	23972	Mm.203916	NM_011864	ENSMUSG00000024899	Papss2	1810018P12Rik|AI159688|AtpsU2|Atpsk2|Sk2|bm	3'-phosphoadenosine 5'-phosphosulfate synthase 2	protein-coding
mm_21574.1	chr2	164237131	164237140	-	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	1206	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_20163.1	chr2	122151106	122151130	-	1	NA	exon (NM_009735, exon 2 of 4)	exon (NM_009735, exon 2 of 4)	3431	NM_009735	12010	Mm.163	NM_009735	ENSMUSG00000060802	B2m	Ly-m11|beta2-m|beta2m	beta-2 microglobulin	protein-coding
mm_37256.1	chr4	118436784	118436799	-	1	NA	exon (NM_023223, exon 2 of 10)	exon (NM_023223, exon 2 of 10)	552	NM_023223	107995	Mm.261764	NM_023223	ENSMUSG00000006398	Cdc20	2310042N09Rik|C87100|p55CDC	cell division cycle 20	protein-coding
mm_168985.1	chr12	95340543	95340546	+	1	NA	Intergenic	L1Md_T|LINE|L1	-351682	NM_201518	399558	Mm.341948	NM_201518	ENSMUSG00000047414	Flrt2	-	fibronectin leucine rich transmembrane protein 2	protein-coding
mm_166539.1	chr6	31165383	31165390	+	1	NA	TTS (NR_110469)	TTS (NR_110469)	53088	NR_110470	232685	Mm.443019	NM_144555	ENSMUSG00000044471	Lncpint	Lincpint|MNCb-1768|Pint|linc-Pint	long non-protein coding RNA, Trp53 induced transcript	ncRNA
mm_173010.1	chrM	315	331	+	1	NA	NA	Intergenic	NA	NA								
mm_136187.1	chr16	88981829	88981831	-	1	NA	Intergenic	Intergenic	-18957	NM_183296	71369	Mm.251757	NM_130872	ENSMUSG00000096534	Krtap16-3	5430404J20Rik|Krtap16-10	keratin associated protein 16-3	protein-coding
mm_154455.1	chrM	2361	2389	-	1	NA	NA	Intergenic	NA	NA								
mm_64321.1	chr7	141949689	141949797	+	1	NA	promoter-TSS (NM_029426)	promoter-TSS (NM_029426)	-8	NM_001009930	75770	Mm.274868	NM_029426	ENSMUSG00000053046	Brsk2	4833424K13Rik|SAD-A|SADA	BR serine/threonine kinase 2	protein-coding
mm_171212.1	chr3	5860491	5860494	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-284244	NM_001163305	19302	Mm.132336	NM_008994	ENSMUSG00000040374	Pex2	D3Ertd138e|PAF-1|PMP35|Pxmp3	peroxisomal biogenesis factor 2	protein-coding
mm_147285.1	chr18	39489158	39489164	-	1	NA	Intergenic	CpG	-1916	NM_008173	14815	Mm.129481	NM_008173	ENSMUSG00000024431	Nr3c1	GR|Grl-1|Grl1	nuclear receptor subfamily 3, group C, member 1	protein-coding
mm_61702.1	chr7	81213324	81213342	+	1	NA	promoter-TSS (NM_008803)	promoter-TSS (NM_008803)	-471	NM_008803	18584	Mm.371577	NM_008803	ENSMUSG00000025584	Pde8a	AI551852|Pde8	phosphodiesterase 8A	protein-coding
mm_95355.1	chr11	48837466	48837481	+	1	NA	promoter-TSS (NM_001347436)	promoter-TSS (NM_001347436)	2	NM_001347446	94089	Mm.390335	NM_053166	ENSMUSG00000040350	Trim7	AI790312	tripartite motif-containing 7	protein-coding
mm_65559.1	chr7	27166471	27166522	-	1	NA	intron (NM_053208, intron 1 of 5)	CpG	306	NM_053208	112406	Mm.29978	NM_053208	ENSMUSG00000058709	Egln2	0610011A13Rik|C85656|Hif-p4h-1|Ier4|Phd1|SM-20	egl-9 family hypoxia-inducible factor 2	protein-coding
mm_36435.1	chr4	82294887	82294959	-	1	NA	3' UTR (NM_001113209, exon 12 of 12)	3' UTR (NM_001113209, exon 12 of 12)	210856	NM_001286127	18028	Mm.317947	NM_008687	ENSMUSG00000008575	Nfib	6720429L07Rik|CTF|E030026I10Rik|NF-I/B|NF1-B|NFI-B	nuclear factor I/B	protein-coding
mm_94551.1	chr11	11462491	11462528	+	1	NA	promoter-TSS (NM_015785)	promoter-TSS (NM_015785)	-90	NM_001185153	53604	Mm.9500	NM_015785	ENSMUSG00000020193	Zpbp	4930486K01Rik|Iam38|Sp38	zona pellucida binding protein	protein-coding
mm_16881.1	chr2	13010816	13010864	-	1	NA	promoter-TSS (NM_153155)	promoter-TSS (NM_153155)	24	NM_153155	227580	Mm.229322	NM_153155	ENSMUSG00000049630	C1ql3	1110065A22Rik|AI661623|C1ql|C1qtnf13|CTRP13|K100	C1q-like 3	protein-coding
mm_152111.1	chr19	6951474	6951514	-	1	NA	exon (NM_007522, exon 4 of 4)	exon (NM_007522, exon 4 of 4)	8932	NM_001285453	12015	Mm.4387	NM_007522	ENSMUSG00000024959	Bad	AI325008|Bbc2	BCL2-associated agonist of cell death	protein-coding
mm_78191.1	chr9	21330358	21330365	+	1	NA	intron (NM_001199186, intron 1 of 21)	intron (NM_001199186, intron 1 of 21)	-7467	NM_152808	68682	Mm.148425	NM_152808	ENSMUSG00000057193	Slc44a2	1110028E10Rik|CTL2	solute carrier family 44, member 2	protein-coding
mm_20296.1	chr2	126933868	126933880	-	1	NA	promoter-TSS (NM_023220)	promoter-TSS (NM_023220)	-639	NM_023220	66552	Mm.269928	NM_023220	ENSMUSG00000027366	Sppl2a	2010106G01Rik|C130089K23Rik	signal peptide peptidase like 2A	protein-coding
mm_54880.1	chr6	42693092	42693100	-	1	NA	promoter-TSS (NM_029930)	promoter-TSS (NM_029930)	-37	NM_029930	77574	Mm.24652	NM_029930	ENSMUSG00000036667	Tcaf1	2810407D09Rik|3321401G04Rik|A230020K05Rik|AI848529|Fam115a	TRPM8 channel-associated factor 1	protein-coding
mm_54750.1	chr6	41033186	41033188	-	1	NA	exon (NM_023333, exon 3 of 5)	exon (NM_023333, exon 3 of 5)	2322	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_10983.1	chr2	25889216	25889218	+	1	NA	intron (NM_175462, intron 4 of 31)	intron (NM_175462, intron 4 of 31)	11434	NM_001302351	227632	Mm.119462	NM_175462	ENSMUSG00000058740	Kcnt1	C030030G16Rik|Slack|Slo2.2|slo2	potassium channel, subfamily T, member 1	protein-coding
mm_10652.1	chr2	20669712	20669726	+	1	NA	intron (NM_029895, intron 4 of 18)	RLTR41C|LTR|ERV1	150206	NM_001177631	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding
mm_14953.1	chr2	151999875	151999885	+	1	NA	promoter-TSS (NM_001164819)	promoter-TSS (NM_001164819)	14	NM_001164820	69698	Mm.258262	NM_027172	ENSMUSG00000027463	Slc52a3	2310046K01Rik|RFT2	solute carrier protein family 52, member 3	protein-coding
mm_108917.1	chr12	100729387	100729392	+	1	NA	Intergenic	B1_Mur2|SINE|Alu	-4269	NM_153587	73086	Mm.220417	NM_153587	ENSMUSG00000021180	Rps6ka5	3110005L17Rik|6330404E13Rik|AI854034|MSK1|MSPK1|RLPK|RLSK|S6K-alpha-5	ribosomal protein S6 kinase, polypeptide 5	protein-coding
mm_88576.1	chr10	79682233	79682247	+	1	NA	promoter-TSS (NM_177613)	promoter-TSS (NM_177613)	45	NM_177613	216150	Mm.21981	NM_177613	ENSMUSG00000020307	Cdc34	AI327276|UBE2R1	cell division cycle 34	protein-coding
mm_169681.1	chr15	70416624	70416635	+	1	NA	Intergenic	RLTR10D2|LTR|ERVK	492396	NR_045071	100503580	Mm.404646	NR_045071		Gm19782	-	predicted gene, 19782	ncRNA
mm_65372.1	chr7	25073073	25073125	-	1	NA	promoter-TSS (NM_008168)	promoter-TSS (NM_008168)	-730	NM_008168	14809	Mm.2879	NM_008168	ENSMUSG00000003378	Grik5	GluK5|GluRgamma2|KA2	glutamate receptor, ionotropic, kainate 5 (gamma 2)	protein-coding
mm_15254.1	chr2	154861837	154861863	+	1	NA	exon (NM_001139513, exon 5 of 9)	exon (NM_001139513, exon 5 of 9)	31056	NM_026030	67204	Mm.377134	NM_026030	ENSMUSG00000074656	Eif2s2	2810026E11Rik|38kDa|AA408636|AA571381|AA986487|AW822225|D2Ertd303e|EIF2|EIF2B	eukaryotic translation initiation factor 2, subunit 2 (beta)	protein-coding
mm_161740.1	chr17	32659572	32659572	+	1	NA	promoter-TSS (NM_001101588)	promoter-TSS (NM_001101588)	89	NM_001101588	631304	Mm.328950	NM_001101588	ENSMUSG00000090700	Cyp4f40	EG631304	cytochrome P450, family 4, subfamily f, polypeptide 40	protein-coding
mm_53301.1	chr6	129057208	129057256	+	1	NA	non-coding (NR_024263, exon 5 of 5)	non-coding (NR_024263, exon 5 of 5)	11331	NR_024263	232408	Mm.259262	NM_153094	ENSMUSG00000030154	Klrb1f	A630024B12Rik|Nkr-p1f|Nkrp1-f|Nkrp1f	killer cell lectin-like receptor subfamily B member 1F	protein-coding
mm_36790.1	chr4	103114223	103114233	-	1	NA	promoter-TSS (NM_027696)	promoter-TSS (NM_027696)	71	NM_146254	242584	Mm.374877	NM_146254	ENSMUSG00000035126	Wdr78	BC028975	WD repeat domain 78	protein-coding
mm_126365.1	chr15	80098181	80098203	+	1	NA	intron (NM_207708, intron 1 of 3)	intron (NM_207708, intron 1 of 3)	6858	NM_207708	20972	Mm.230301	NM_009303	ENSMUSG00000022415	Syngr1	R75468|Syngr1b|p29	synaptogyrin 1	protein-coding
mm_155000.1	chrX	39346265	39346266	+	1	NA	promoter-TSS (NM_001177380)	promoter-TSS (NM_001177380)	-1	NM_001177380	78631	Mm.243738	NM_001177380	ENSMUSG00000079619	Cypt15	1700085A12Rik	cysteine-rich perinuclear theca 15	protein-coding
mm_48549.1	chr5	142905817	142905832	-	1	NA	intron (NM_007393, intron 1 of 5)	CpG	930	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_9632.1	chr1	176814071	176814133	-	1	NA	promoter-TSS (NM_029756)	promoter-TSS (NM_029756)	-558	NM_029756	76816	Mm.171399	NM_029756	ENSMUSG00000026504	Sdccag8	2700048G21Rik|5730470G24Rik|Cccap	serologically defined colon cancer antigen 8	protein-coding
mm_121609.1	chr14	8258882	8258903	-	1	NA	promoter-TSS (NM_001161667)	promoter-TSS (NM_001161667)	-53	NM_001161667	93732	Mm.28700	NM_053115	ENSMUSG00000021751	Acox2	THCCox	acyl-Coenzyme A oxidase 2, branched chain	protein-coding
mm_131999.1	chr16	25385890	25385903	+	1	NA	intron (NM_175165, intron 4 of 5)	intron (NM_175165, intron 4 of 5)	99079	NM_175165	71338	Mm.126851	NM_175165	ENSMUSG00000048399	Tprg	5430420C16Rik|Tprg1	transformation related protein 63 regulated	protein-coding
mm_58556.1	chr7	4740933	4740949	+	1	NA	intron (NM_146177, intron 1 of 8)	intron (NM_146177, intron 1 of 8)	814	NM_001115018	232811	Mm.247844	NM_146177	ENSMUSG00000059851	Kmt5c	BC024816|Suv4-20h2|Suv420h2	lysine methyltransferase 5C	protein-coding
mm_166290.1	chr5	100660901	100660902	+	1	NA	intron (NM_027978, intron 4 of 6)	L2b|LINE|L2	13355	NM_027978	71883	Mm.260661	NM_027978	ENSMUSG00000029319	Coq2	2310002F18Rik|PHB:PPT	coenzyme Q2 4-hydroxybenzoate polyprenyltransferase	protein-coding
mm_19120.1	chr2	80038940	80038948	-	1	NA	intron (NM_001159582, intron 2 of 15)	intron (NM_001159582, intron 2 of 15)	90027	NM_016744	18573	Mm.40678	NM_016744	ENSMUSG00000059173	Pde1a	AI987702|AW125737	phosphodiesterase 1A, calmodulin-dependent	protein-coding
mm_82581.1	chr9	21149895	21149978	-	1	NA	promoter-TSS (NM_016742)	promoter-TSS (NM_016742)	-30	NM_016742	12539	Mm.32331	NM_016742	ENSMUSG00000019471	Cdc37	p50|p50Cdc37	cell division cycle 37	protein-coding
mm_2160.1	chr1	88212683	88212700	+	1	NA	exon (NM_201645, exon 1 of 5)	exon (NM_201645, exon 1 of 5)	732	NM_201645	394436	Mm.300095	NM_201645	ENSMUSG00000089960	Ugt1a1	Gnt1|UDPGT 1-1|UGT1A01|Udpgt-1a|UgtBr1	UDP glucuronosyltransferase 1 family, polypeptide A1	protein-coding
mm_109900.1	chr12	7901657	7901665	-	1	NA	Intergenic	Intergenic	-76016	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_111254.1	chr12	84951294	84951296	-	1	NA	5' UTR (NM_178065, exon 2 of 20)	5' UTR (NM_178065, exon 2 of 20)	19591	NM_178065	68497	Mm.24446	NM_178065	ENSMUSG00000042350	Arel1	1110018G07Rik|AI649076|AW610792|Kiaa0317|mKIAA0317	apoptosis resistant E3 ubiquitin protein ligase 1	protein-coding
mm_173298.1	chrY	50104317	50104317	+	1	NA	Intergenic	Intergenic	-259190	NM_001160143	100040031	Mm.463839	NM_001160143	ENSMUSG00000093950	Gm20823	-	predicted gene, 20823	protein-coding
mm_59992.1	chr7	30554942	30554952	+	1	NA	TTS (NM_001290569)	TTS (NM_001290569)	1645	NM_001012401	243912	Mm.34885	NM_001012401	ENSMUSG00000036854	Hspb6	AA387366|Gm479|Hsp20	heat shock protein, alpha-crystallin-related, B6	protein-coding
mm_144081.1	chr17	91093071	91093077	-	1	NA	promoter-TSS (NM_020252)	promoter-TSS (NM_020252)	-272	NM_020252	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_93418.1	chr10	108691140	108691149	-	1	NA	intron (NM_001252341, intron 4 of 11)	intron (NM_001252341, intron 4 of 11)	9016	NM_203660	368203	Mm.452758	NM_203660		Gm5136	C6.1AL|EG368203	predicted gene 5136	protein-coding
mm_15474.1	chr2	157560103	157560119	+	1	NA	promoter-TSS (NM_010923)	promoter-TSS (NM_010923)	33	NM_180960	18111	Mm.34330	NM_010923	ENSMUSG00000067786	Nnat	5730414I02Rik|AW107673|Peg5	neuronatin	protein-coding
mm_169417.1	chr14	53078456	53078460	+	1	NA	Intergenic	Intergenic	-582763	NM_001170918	57269	Mm.88822	NM_020512	ENSMUSG00000059887	Olfr1507	MOR244-1|Mor28|Or28	olfactory receptor 1507	protein-coding
mm_10916.1	chr2	25395911	25395935	+	1	NA	promoter-TSS (NM_009849)	promoter-TSS (NM_009849)	49	NM_009849	12496	Mm.482100	NM_009849	ENSMUSG00000015085	Entpd2	Cd39l1|NTPDase2	ectonucleoside triphosphate diphosphohydrolase 2	protein-coding
mm_147774.1	chr18	61484755	61484779	-	1	NA	promoter-TSS (NR_045419)	promoter-TSS (NR_045419)	-160	NR_045419	442846	Mm.417648	NR_045419		A530050N04Rik	-	RIKEN cDNA A530050N04 gene	ncRNA
mm_13462.1	chr2	105675479	105675504	+	1	NA	promoter-TSS (NM_013627)	promoter-TSS (NM_013627)	-253	NM_001244200	18508	Mm.3608	NM_013627	ENSMUSG00000027168	Pax6	1500038E17Rik|AEY11|Dey|Gsfaey11|Pax-6|Sey	paired box 6	protein-coding
mm_138343.1	chr17	34914246	34914276	+	1	NA	promoter-TSS (NM_023557)	promoter-TSS (NM_023557)	-205	NM_023557	70129	Mm.183126	NM_023557	ENSMUSG00000007034	Slc44a4	2210409B01Rik|NG22	solute carrier family 44, member 4	protein-coding
mm_137778.1	chr17	29493038	29493105	+	1	NA	intron (NM_008842, intron 4 of 5)	intron (NM_008842, intron 4 of 5)	2026	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_83986.1	chr9	57428015	57428025	-	1	NA	intron (NM_176831, intron 3 of 6)	intron (NM_176831, intron 3 of 6)	12094	NM_176831	66812	Mm.250508	NM_176831	ENSMUSG00000063849	Ppcdc	1810057I13Rik|8430432M10Rik	phosphopantothenoylcysteine decarboxylase	protein-coding
mm_58534.1	chr7	4460688	4460730	+	1	NA	Intergenic	Intergenic	-4026	NM_026146	67425	Mm.360392	NM_026146	ENSMUSG00000006154	Eps8l1	2310051G19Rik|4632407K17Rik|AW060268|DRC3|EPS8R1	EPS8-like 1	protein-coding
mm_15723.1	chr2	164078187	164078189	+	1	NA	intron (NM_021420, intron 1 of 10)	intron (NM_021420, intron 1 of 10)	4010	NM_021420	58231	Mm.234472	NM_021420	ENSMUSG00000018209	Stk4	AI447339|AU020804|Kas-2|Mst1|Ysk3	serine/threonine kinase 4	protein-coding
mm_27966.1	chr3	80688446	80688466	-	1	NA	3' UTR (NM_013540, exon 16 of 16)	3' UTR (NM_013540, exon 16 of 16)	114335	NM_013540	14800	Mm.220224	NM_013540	ENSMUSG00000033981	Gria2	GluA2|GluR-B|Glur-2|Glur2	glutamate receptor, ionotropic, AMPA2 (alpha 2)	protein-coding
mm_91547.1	chr10	39731919	39731929	-	1	NA	promoter-TSS (NM_011264)	promoter-TSS (NM_011264)	83	NR_038037	327744	Mm.295265	NM_183198	ENSMUSG00000087177	E130307A14Rik	-	RIKEN cDNA E130307A14 gene	ncRNA
mm_123806.1	chr14	70521459	70521478	-	1	NA	exon (NM_011359, exon 5 of 6)	exon (NM_011359, exon 5 of 6)	-1208	NR_033241	12153	Mm.27757	NM_009755	ENSMUSG00000022098	Bmp1	Pcp|Tld	bone morphogenetic protein 1	protein-coding
mm_172980.1	chr9	96895610	96895628	+	1	NA	Intergenic	Intergenic	-6145	NM_001289645	235534	Mm.233031	NM_153420	ENSMUSG00000043587	Pxylp1	9430094M07Rik|Acpl2|BB177120|C130099A20Rik	2-phosphoxylose phosphatase 1	protein-coding
mm_79031.1	chr9	46047967	46047970	+	1	NA	intron (NM_027498, intron 1 of 24)	intron (NM_027498, intron 1 of 24)	35148	NM_027498	70661	Mm.219459	NM_027498	ENSMUSG00000034135	Sik3	5730525O22Rik|9030204A07Rik|AI447252|AI846254|AI849445|Qsk|SIK-3|mKIAA0999	SIK family kinase 3	protein-coding
mm_62135.1	chr7	97081805	97081817	+	1	NA	promoter-TSS (NM_010248)	promoter-TSS (NM_010248)	60	NM_010248	14389	Mm.42033	NM_010248	ENSMUSG00000004508	Gab2	AI463667|D130058I17Rik|p97	growth factor receptor bound protein 2-associated protein 2	protein-coding
mm_11059.1	chr2	27505847	27505858	+	1	NA	Intergenic	Intergenic	-9295	NM_080848	140858	Mm.28265	NM_080848	ENSMUSG00000026917	Wdr5	2410008O07Rik|AA408785|AA960360|Big|Big-3	WD repeat domain 5	protein-coding
mm_143739.1	chr17	81498498	81498509	-	1	NA	intron (NR_104580, intron 2 of 8)	intron (NR_104580, intron 2 of 8)	239884	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_129081.1	chr15	75888755	75888785	-	1	NA	promoter-TSS (NM_001282443)	promoter-TSS (NM_001282443)	-47	NM_001282443	223645		NM_001282443	ENSMUSG00000098678	Mroh6	Gm19570	maestro heat-like repeat family member 6	protein-coding
mm_111177.1	chr12	83827619	83827645	-	1	NA	intron (NR_073564, intron 5 of 12)	B1_Mur4|SINE|Alu	14726	NM_001272055	18222	Mm.4390	NM_010949	ENSMUSG00000021224	Numb	Nb	numb homolog (Drosophila)	protein-coding
mm_36598.1	chr4	88744349	88744353	-	1	NA	Intergenic	Intergenic	-10517	NM_001085528	435791	Mm.473673	NM_001085528	ENSMUSG00000094618	Gm13271	Ifnz|OTTMUSG00000011262	predicted gene 13271	protein-coding
mm_138421.1	chr17	35069544	35069557	+	1	NA	3' UTR (NM_023463, exon 3 of 3)	3' UTR (NM_023463, exon 3 of 3)	2225	NM_023463	68468	Mm.215096	NM_023463	ENSMUSG00000092586	Ly6g6c	1110003M04Rik|AU016360|G6c|NG24	lymphocyte antigen 6 complex, locus G6C	protein-coding
mm_119378.1	chr14	41134101	41134111	+	1	NA	exon (NM_023134, exon 6 of 6)	exon (NM_023134, exon 6 of 6)	2318	NM_023134	20387	Mm.46062	NM_023134	ENSMUSG00000021789	Sftpa1	SP-A|Sftp-1|Sftp1	surfactant associated protein A1	protein-coding
mm_142833.1	chr17	51782894	51782904	-	1	NA	exon (NM_001163632, exon 7 of 11)	exon (NM_001163632, exon 7 of 11)	29155	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_46180.1	chr5	97111566	97111586	-	1	NA	promoter-TSS (NM_198422)	promoter-TSS (NM_198422)	20	NM_198422	231474	Mm.332505	NM_198422	ENSMUSG00000055725	Paqr3	6330415A20Rik|AY424292|RKTG	progestin and adipoQ receptor family member III	protein-coding
mm_19098.1	chr2	79453208	79453217	-	1	NA	3' UTR (NM_010894, exon 2 of 2)	3' UTR (NM_010894, exon 2 of 2)	3424	NM_010894	18012	Mm.4636	NM_010894	ENSMUSG00000034701	Neurod1	BETA2|BHF-1|Nd1|Neurod|bHLHa3	neurogenic differentiation 1	protein-coding
mm_94167.1	chr10	128804145	128804157	-	1	NA	intron (NM_178066, intron 1 of 4)	intron (NM_178066, intron 1 of 4)	219	NM_178066	73827	Mm.24630	NM_178066	ENSMUSG00000047090	Tmem198b	1110012D08Rik	transmembrane protein 198b	protein-coding
mm_146476.1	chr18	89197242	89197252	+	1	NA	promoter-TSS (NM_178687)	promoter-TSS (NM_178687)	-180	NM_178687	225825	Mm.139293	NM_178687	ENSMUSG00000034028	Cd226	BC051526|DNAM-1|DNAM1|Pta1|TLiSA1	CD226 antigen	protein-coding
mm_134346.1	chr16	16571109	16571115	-	1	NA	intron (NM_001301817, intron 1 of 16)	intron (NM_001301817, intron 1 of 16)	-10893	NM_139232	224014	Mm.256131	NM_139232	ENSMUSG00000022788	Fgd4	9030023J02Rik|9330209B17Rik|Frabp|ZFYVE6	FYVE, RhoGEF and PH domain containing 4	protein-coding
mm_53724.1	chr6	144672891	144672900	+	1	NA	promoter-TSS (NR_040519)	promoter-TSS (NR_040519)	27	NR_040519	66760	Mm.233631	NR_040519	ENSMUSG00000085785	Sox5os3	4933425H06Rik	SRY (sex determining region Y)-box 5, opposite strand 3	ncRNA
mm_19276.1	chr2	85518967	85518973	-	1	NA	promoter-TSS (NM_001081664)	promoter-TSS (NM_001081664)	-35	NM_001081664	228151	Mm.17636	NM_001081664	ENSMUSG00000075217	4833423E24Rik	Fads2p1|Gm113	RIKEN cDNA 4833423E24 gene	protein-coding
mm_71259.1	chr8	40917649	40917713	+	1	NA	3' UTR (NM_001044740, exon 12 of 12)	3' UTR (NM_001044740, exon 12 of 12)	-8552	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_98761.1	chr11	96572482	96572486	+	1	NA	intron (NM_001033186, intron 4 of 12)	intron (NM_001033186, intron 4 of 12)	107893	NM_001177898	78473	Mm.395840	NM_001033186	ENSMUSG00000057058	Skap1	1700091G21Rik|Scap1|Skap-55	src family associated phosphoprotein 1	protein-coding
mm_48242.1	chr5	137747986	137747990	-	1	NA	intron (NM_029805, intron 2 of 5)	intron (NM_029805, intron 2 of 5)	2019	NM_029805	78829	Mm.286399	NM_023910	ENSMUSG00000029723	Tsc22d4	0610009M14Rik|1700023B23Rik|AI415410|Thg-1pit|Tilz2	TSC22 domain family, member 4	protein-coding
mm_40459.1	chr5	53606912	53606942	+	1	NA	intron (NM_001277116, intron 3 of 12)	intron (NM_001277116, intron 3 of 12)	16441	NM_001080927	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_89129.1	chr10	85102698	85102719	+	1	NA	promoter-TSS (NM_001013028)	promoter-TSS (NM_001013028)	81	NM_001013028	103266	Mm.335025	NM_001013028	ENSMUSG00000060935	Tmem263	AI597468	transmembrane protein 263	protein-coding
mm_73925.1	chr8	119829653	119829659	+	1	NA	intron (NM_028071, intron 2 of 3)	intron (NM_028071, intron 2 of 3)	10923	NM_028071	72042	Mm.393405	NM_028071	ENSMUSG00000031827	Cotl1	1810074P22Rik|2010004C08Rik|Clp	coactosin-like 1 (Dictyostelium)	protein-coding
mm_71885.1	chr8	69822155	69822165	+	1	NA	promoter-TSS (NM_020028)	promoter-TSS (NM_020028)	-405	NM_020028	53978	Mm.23253	NM_020028	ENSMUSG00000031861	Lpar2	Edg4|IPA2|LPA2	lysophosphatidic acid receptor 2	protein-coding
mm_32352.1	chr4	105157258	105157268	+	1	NA	promoter-TSS (NM_080555)	promoter-TSS (NM_080555)	-84	NM_080555	67916	Mm.348326	NM_080555	ENSMUSG00000028517	Plpp3	1110003O22Rik|2610002D05Rik|AV025606|D4Bwg0538e|D4Bwg1535e|Lpp3|Ppab2b|Ppap2b	phospholipid phosphatase 3	protein-coding
mm_23845.1	chr3	83007851	83007868	+	1	NA	5' UTR (NM_133862, exon 1 of 10)	5' UTR (NM_133862, exon 1 of 10)	135	NM_001317105	99571	Mm.16422	NM_133862	ENSMUSG00000033860	Fgg	3010002H13Rik|AI256424	fibrinogen gamma chain	protein-coding
mm_88852.1	chr10	80930686	80930696	+	1	NA	intron (NM_008655, intron 2 of 3)	intron (NM_008655, intron 2 of 3)	600	NM_008655	17873	Mm.1360	NM_008655	ENSMUSG00000015312	Gadd45b	AI323528|Myd118	growth arrest and DNA-damage-inducible 45 beta	protein-coding
mm_119736.1	chr14	54121876	54121904	+	1	NA	Intergenic	Intergenic	132039	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_77082.1	chr8	110521937	110521952	-	1	NA	intron (NM_172916, intron 42 of 86)	intron (NM_172916, intron 42 of 86)	-19588	NR_105058	100861869	Mm.84499	NR_105058		Gm21283	-	predicted gene, 21283	ncRNA
mm_86650.1	chr10	17723974	17724011	+	1	NA	exon (NM_010828, exon 2 of 2)	exon (NM_010828, exon 2 of 2)	764	NM_010828	17684	Mm.272321	NM_010828	ENSMUSG00000039910	Cited2	AI835299|ER154-like|Mrg1|Msg2|p35srj	Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 2	protein-coding
mm_140991.1	chr17	24850291	24850319	-	1	NA	promoter-TSS (NM_024284)	promoter-TSS (NM_024284)	-3	NM_023480	68636	Mm.347964	NM_023480	ENSMUSG00000045316	Fahd1	1110025H10Rik|AV002085	fumarylacetoacetate hydrolase domain containing 1	protein-coding
mm_25417.1	chr3	107595139	107595164	+	1	NA	5' UTR (NM_007441, exon 1 of 4)	5' UTR (NM_007441, exon 1 of 4)	120	NM_007441	11694	Mm.10112	NM_007441	ENSMUSG00000014603	Alx3	-	aristaless-like homeobox 3	protein-coding
mm_136021.1	chr16	76337041	76337077	-	1	NA	intron (NM_173440, intron 2 of 3)	intron (NM_173440, intron 2 of 3)	35990	NM_173440	268903	Mm.74711	NM_173440	ENSMUSG00000048490	Nrip1	6030458L20Rik|8430438I05Rik|9630050P12|AA959574|AW456757|RIP140	nuclear receptor interacting protein 1	protein-coding
mm_25154.1	chr3	103020595	103020635	+	1	NA	promoter-TSS (NM_001310693)	promoter-TSS (NM_001310693)	69	NM_144901	229663	Mm.277713	NM_144901	ENSMUSG00000068823	Csde1	AA960392|BC016898|D3Jfr1|mKIAA0885|unr	cold shock domain containing E1, RNA binding	protein-coding
mm_145435.1	chr18	58836383	58836396	+	1	NA	promoter-TSS (NM_175506)	promoter-TSS (NM_175506)	26	NM_175506	240322	Mm.71963	NM_175506	ENSMUSG00000053441	Adamts19	4831407I23Rik|AU015154|D230034E10Rik	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 19	protein-coding
mm_55459.1	chr6	67491850	67491862	-	1	NA	promoter-TSS (NM_144548)	promoter-TSS (NM_144548)	-1	NM_144548	209590	Mm.221227	NM_144548	ENSMUSG00000049093	Il23r	IL-23R	interleukin 23 receptor	protein-coding
mm_160430.1	chr8	88696876	88696876	+	1	NA	promoter-TSS (NM_001128171)	promoter-TSS (NM_001128171)	-152	NM_001128170	74256	Mm.490395	NM_173369	ENSMUSG00000036712	Cyld	2010013M14Rik|2900009M21Rik|C130039D01Rik|CDMT|CYLD1|EAC|mKIAA0849	CYLD lysine 63 deubiquitinase	protein-coding
mm_130124.1	chr15	89591856	89591916	-	1	NA	promoter-TSS (NM_026817)	promoter-TSS (NM_026817)	37	NM_026817	68708	Mm.23258	NM_026817	ENSMUSG00000022621	Rabl2	1110031N17Rik|AW549303|Rabl2a	RAB, member RAS oncogene family-like 2	protein-coding
mm_21864.1	chr2	165885775	165885787	-	1	NA	promoter-TSS (NM_001252584)	promoter-TSS (NM_001252584)	-943	NM_001252587	228880	Mm.227598	NM_027230	ENSMUSG00000039671	Zmynd8	1110013E22Rik|2010005I16Rik|3632413B07Rik|AI316811|AL024039|Prkcbp1|RACK7	zinc finger, MYND-type containing 8	protein-coding
mm_117570.1	chr13	85289156	85289165	-	1	NA	5' UTR (NM_145452, exon 1 of 25)	5' UTR (NM_145452, exon 1 of 25)	326	NM_145452	218397	Mm.259653	NM_145452	ENSMUSG00000021549	Rasa1	Gap|RasGAP|Rasa	RAS p21 protein activator 1	protein-coding
mm_56748.1	chr6	115991632	115991667	-	1	NA	intron (NM_026376, intron 1 of 35)	intron (NM_026376, intron 1 of 35)	3356	NM_026376	67784	Mm.3085	NM_026376	ENSMUSG00000030123	Plxnd1	6230425C21Rik|b2b1863Clo|b2b553Clo	plexin D1	protein-coding
mm_168468.1	chr1	14840242	14840263	-	1	NA	Intergenic	Intergenic	78610	NM_177781	277328	Mm.186329	NM_177781	ENSMUSG00000032769	Trpa1	Anktm1|TRPA1b	transient receptor potential cation channel, subfamily A, member 1	protein-coding
mm_101380.1	chr11	23771280	23771293	-	1	NA	promoter-TSS (NM_009044)	promoter-TSS (NM_009044)	-316	NM_009044	19696	Mm.4869	NM_009044	ENSMUSG00000020275	Rel	c-Rel	reticuloendotheliosis oncogene	protein-coding
mm_87209.1	chr10	39732384	39732450	+	1	NA	promoter-TSS (NR_038037)	promoter-TSS (NR_038037)	257	NM_011264	19714	Mm.439723	NM_011264	ENSMUSG00000019841	Rev3l	Rev|Rev3|Sez4	REV3 like, DNA directed polymerase zeta catalytic subunit	protein-coding
mm_16721.1	chr2	7322649	7322651	-	1	NA	intron (NM_001110231, intron 2 of 15)	intron (NM_001110231, intron 2 of 15)	73350	NM_001110232	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_137251.1	chr17	24533886	24533900	+	1	NA	promoter-TSS (NM_177375)	promoter-TSS (NM_177375)	-146	NM_177375	328778	Mm.266033	NM_177375	ENSMUSG00000079657	Rab26	A830020M03Rik	RAB26, member RAS oncogene family	protein-coding
mm_142781.1	chr17	50136837	50136849	-	1	NA	intron (NM_181397, intron 2 of 9)	RSINE1|SINE|B4	53654	NM_181397	76438	Mm.41854	NM_181397	ENSMUSG00000039316	Rftn1	2310015N21Rik|AI853526	raftlin lipid raft linker 1	protein-coding
mm_142654.1	chr17	47611424	47611434	-	1	NA	promoter-TSS (NM_020048)	promoter-TSS (NM_020048)	63	NM_016859	53414	Mm.472101	NM_016859	ENSMUSG00000023988	Bysl	Bys|Enp1	bystin-like	protein-coding
mm_11186.1	chr2	29097718	29097722	+	1	NA	Intergenic	MT2A|LTR|ERVL	-27272	NM_198033	269254	Mm.41867	NM_198033	ENSMUSG00000043535	Setx	A130090N03|A930037J23Rik|AOA2|AW060766|Als4|SCAR1|Sen1|mKIAA0625	senataxin	protein-coding
mm_66462.1	chr7	44901312	44901330	-	1	NA	TTS (NM_027376)	TTS (NM_027376)	5242	NM_027376	70300	Mm.276298	NM_027376	ENSMUSG00000011658	Fuz	2600013E07Rik|b2b1273Clo	fuzzy planar cell polarity protein	protein-coding
mm_138239.1	chr17	34459890	34459900	+	1	NA	exon (NM_001163855, exon 23 of 24)	exon (NM_001163855, exon 23 of 24)	16042	NM_030746	632126	Mm.484958	NM_030746	ENSMUSG00000058435	Btnl4	Btn3a3|EG632126|NG11	butyrophilin-like 4	protein-coding
mm_98775.1	chr11	96789119	96789146	+	1	NA	promoter-TSS (NM_007622)	promoter-TSS (NM_007622)	-4	NM_007622	12412	Mm.29055	NM_007622	ENSMUSG00000018666	Cbx1	Cbx|Cbx-rs2|E430007M08Rik|HP1B|Hp1beta|M31|MOD1	chromobox 1	protein-coding
mm_124508.1	chr14	121915775	121915793	-	1	NA	promoter-TSS (NM_182806)	promoter-TSS (NM_182806)	-10	NM_182806	110168	Mm.37405	NM_182806	ENSMUSG00000050350	Gpr18	-	G protein-coupled receptor 18	protein-coding
mm_19541.1	chr2	98662259	98662282	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	1194613	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_57683.1	chr6	128512219	128512229	-	1	NA	exon (NM_007376, exon 12 of 36)	exon (NM_007376, exon 12 of 36)	14496	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_122217.1	chr14	32317970	32317989	-	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-4040	NM_001081130	239017	Mm.318302	NM_001081130	ENSMUSG00000021913	Ogdhl	-	oxoglutarate dehydrogenase-like	protein-coding
mm_90526.1	chr10	128083892	128083938	+	1	NA	exon (NM_016774, exon 2 of 10)	exon (NM_016774, exon 2 of 10)	608	NM_016774	11947	Mm.238973	NM_016774	ENSMUSG00000025393	Atp5b	-	ATP synthase, H+ transporting mitochondrial F1 complex, beta subunit	protein-coding
mm_157018.1	chrX	7740207	7740218	-	1	NA	intron (NM_207202, intron 1 of 9)	intron (NM_207202, intron 1 of 9)	1112	NM_207202	54648	Mm.63342	NM_207202	ENSMUSG00000031150	Ccdc120	AA030924|DXImx50e|Jm11|Sfc25	coiled-coil domain containing 120	protein-coding
mm_130084.1	chr15	89378950	89378962	-	1	NA	intron (NM_001013022, intron 1 of 4)	CpG-5245	298	NM_001013022	70113	Mm.247273	NM_001013022	ENSMUSG00000047394	Odf3b	2010001J22Rik	outer dense fiber of sperm tails 3B	protein-coding
mm_117471.1	chr13	76098607	76098658	-	1	NA	promoter-TSS (NM_001081352)	promoter-TSS (NM_001081352)	28	NM_029847	77041	Mm.196399	NM_029847	ENSMUSG00000021592	Arsk	2810429K17Rik|4833414G15Rik	arylsulfatase K	protein-coding
mm_150378.1	chr19	36083747	36083756	+	1	NA	promoter-TSS (NM_019428)	promoter-TSS (NM_019428)	35	NM_019428	54364	Mm.277891	NM_019428	ENSMUSG00000024800	Rpp30	Rnasep2|TSG15	ribonuclease P/MRP 30 subunit	protein-coding
mm_77714.1	chr8	126593919	126593929	-	1	NA	promoter-TSS (NM_001164598)	promoter-TSS (NM_001164598)	-488	NM_001164598	270110	Mm.334918	NM_001164598	ENSMUSG00000051495	Irf2bp2	E130305N23Rik|IRF-2BP2	interferon regulatory factor 2 binding protein 2	protein-coding
mm_75504.1	chr8	53638946	53639021	-	1	NA	promoter-TSS (NM_146208)	promoter-TSS (NM_146208)	82	NM_146208	234258	Mm.281749	NM_146208	ENSMUSG00000039396	Neil3	AI449477|BC034753|C85903	nei like 3 (E. coli)	protein-coding
mm_103520.1	chr11	76812443	76812454	-	1	NA	exon (NM_007754, exon 5 of 21)	exon (NM_007754, exon 5 of 21)	34560	NM_007754	12874	Mm.276736	NM_007754	ENSMUSG00000020841	Cpd	AA960140|AW322530|D830034L15Rik	carboxypeptidase D	protein-coding
mm_57887.1	chr6	131365348	131365374	-	1	NA	3' UTR (NM_011733, exon 9 of 9)	3' UTR (NM_011733, exon 9 of 9)	23089	NM_139117	56449	Mm.458000	NM_011733	ENSMUSG00000030189	Ybx3	Csda|Dpba|MSY3|MSY4|Yb2|dbpA|oxyR	Y box protein 3	protein-coding
mm_116278.1	chr13	34924344	34924367	-	1	NA	promoter-TSS (NM_025750)	promoter-TSS (NM_025750)	-54	NM_025750	66761	Mm.157047	NM_025750	ENSMUSG00000021415	4933417A18Rik	-	RIKEN cDNA 4933417A18 gene	protein-coding
mm_65952.1	chr7	30425398	30425407	-	1	NA	exon (NM_172142, exon 4 of 11)	exon (NM_172142, exon 4 of 11)	2098	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_140547.1	chr17	6948284	6948349	-	1	NA	promoter-TSS (NM_001083945)	promoter-TSS (NM_001083945)	40	NM_001083945	100037282	Mm.29830	NM_001083945	ENSMUSG00000023806	Rsph3b	Rshl2b	radial spoke 3B homolog (Chlamydomonas)	protein-coding
mm_83860.1	chr9	54661845	54661855	-	1	NA	promoter-TSS (NM_053178)	promoter-TSS (NM_053178)	35	NM_053178	94180	Mm.20592	NM_053178	ENSMUSG00000032281	Acsbg1	BG1|Bgm|E230019G03Rik|GR-LACS|Lpd|R75185	acyl-CoA synthetase bubblegum family member 1	protein-coding
mm_35560.1	chr4	41569503	41569551	-	1	NA	promoter-TSS (NM_027993)	promoter-TSS (NM_027993)	0	NM_001159583	71901	Mm.39215	NM_027993	ENSMUSG00000028439	Fam219a	2310028H24Rik	family with sequence similarity 219, member A	protein-coding
mm_133342.1	chr16	81201274	81201277	+	1	NA	intron (NM_001113208, intron 1 of 17)	intron (NM_001113208, intron 1 of 17)	578	NM_010954	17968	Mm.433941	NM_010954	ENSMUSG00000022762	Ncam2	Ncam-2|Ocam|RNCAM	neural cell adhesion molecule 2	protein-coding
mm_157711.1	chrX	66304144	66304165	-	1	NA	Intergenic	Intergenic	-345164	NM_001161431	245450	Mm.336081	NM_198863	ENSMUSG00000036790	Slitrk2	A930040J07	SLIT and NTRK-like family, member 2	protein-coding
mm_140096.1	chr17	78200340	78200383	+	1	NA	5' UTR (NM_015800, exon 1 of 17)	5' UTR (NM_015800, exon 1 of 17)	113	NM_015800	50766	Mm.311912	NM_015800	ENSMUSG00000024074	Crim1	AU015004	cysteine rich transmembrane BMP regulator 1 (chordin like)	protein-coding
mm_10270.1	chr2	9881504	9881512	+	1	NA	non-coding (NR_024257, exon 1 of 5)	non-coding (NR_024257, exon 1 of 5)	262	NR_024257	381347	Mm.441450	NR_024257		4930412O13Rik	ENSMUSG00000075535|Gm10853	RIKEN cDNA 4930412O13 gene	ncRNA
mm_146314.1	chr18	80468879	80468923	+	1	NA	intron (NM_026295, intron 1 of 12)	intron (NM_026295, intron 1 of 12)	766	NM_026295	67655	Mm.312893	NM_026295	ENSMUSG00000033323	Ctdp1	4930563P03Rik|AW553592	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) phosphatase, subunit 1	protein-coding
mm_154355.1	chrM	6146	6167	+	1	NA	NA	Intergenic	NA	NA								
mm_173115.1	chrX	159988201	159988216	+	1	NA	promoter-TSS (NM_001163085)	promoter-TSS (NM_001163085)	-225	NM_001163085	270672	Mm.386889	NM_001163085	ENSMUSG00000031303	Map3k15	BC031147|MEKK15	mitogen-activated protein kinase kinase kinase 15	protein-coding
mm_84135.1	chr9	59036873	59036885	-	1	NA	promoter-TSS (NM_008684)	promoter-TSS (NM_008684)	-438	NM_001042752	18007	Mm.42249	NM_008684	ENSMUSG00000032340	Neo1	2610028H22Rik|AI327052|D930014N22Rik|Igdcc2	neogenin	protein-coding
mm_159975.1	chr6	113077444	113077444	+	1	NA	promoter-TSS (NR_027008)	promoter-TSS (NR_027008)	-195	NM_028385	72895	Mm.367159	NM_028385	ENSMUSG00000034269	Setd5	2900045N06Rik|C330007C20|C85544|mKIAA1757	SET domain containing 5	protein-coding
mm_150484.1	chr19	38950256	38950280	+	1	NA	exon (NM_008234, exon 11 of 22)	exon (NM_008234, exon 11 of 22)	19278	NM_008234	15201	Mm.57223	NM_008234	ENSMUSG00000025001	Hells	AI323785|E130115I21Rik|LSH|Lysh|PASG|YFK8	helicase, lymphoid specific	protein-coding
mm_40426.1	chr5	53532303	53532309	+	1	NA	Intergenic	MTE2b|LTR|ERVL-MaLR	-23473	NM_001080928	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_64147.1	chr7	141263184	141263198	+	1	NA	TTS (NM_001081118)	TTS (NM_001081118)	3233	NM_001252601	54123	Mm.3233	NM_016850	ENSMUSG00000025498	Irf7	-	interferon regulatory factor 7	protein-coding
mm_149884.1	chr19	25382284	25382305	+	1	NA	intron (NM_181404, intron 4 of 13)	intron (NM_181404, intron 4 of 13)	-123412	NM_015826	50796	Mm.391208	NM_015826	ENSMUSG00000024837	Dmrt1	-	doublesex and mab-3 related transcription factor 1	protein-coding
mm_40305.1	chr5	43808006	43808010	+	1	NA	Intergenic	CpG	-10885	NM_009763	12182	Mm.246332	NM_009763	ENSMUSG00000029082	Bst1	114/A10|A530073F09|BP-3|Bp3|Bsta1|CD157|Ly65	bone marrow stromal cell antigen 1	protein-coding
mm_12889.1	chr2	84773431	84773479	+	1	NA	exon (NM_009776, exon 3 of 8)	exon (NM_009776, exon 3 of 8)	1974	NM_009776	12258	Mm.38888	NM_009776	ENSMUSG00000023224	Serping1	C1INH|C1nh	serine (or cysteine) peptidase inhibitor, clade G, member 1	protein-coding
mm_122597.1	chr14	50930882	50930890	-	1	NA	promoter-TSS (NM_001033271)	promoter-TSS (NM_001033271)	-37	NM_001310507	219024	Mm.239117	NM_001033271	ENSMUSG00000035953	Tmem55b	BC039161	transmembrane protein 55b	protein-coding
mm_71863.1	chr8	69088734	69088744	+	1	NA	promoter-TSS (NM_007509)	promoter-TSS (NM_007509)	3	NM_007509	11966	Mm.249096	NM_007509	ENSMUSG00000006273	Atp6v1b2	AI194269|AI790362|Atp6b2|HO57|R74844	ATPase, H+ transporting, lysosomal V1 subunit B2	protein-coding
mm_71437.1	chr8	46511399	46511416	+	1	NA	exon (NM_007981, exon 5 of 21)	exon (NM_007981, exon 5 of 21)	20441	NM_001302163	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_149375.1	chr19	11375538	11375554	+	1	NA	promoter-TSS (NM_001310331)	promoter-TSS (NM_001310331)	58	NM_001310331	666907		NM_001310331	ENSMUSG00000101389	Ms4a4a	EG666907	membrane-spanning 4-domains, subfamily A, member 4A	protein-coding
mm_156193.1	chrX	134059262	134059272	+	1	NA	promoter-TSS (NM_133196)	promoter-TSS (NM_133196)	91	NM_133196	108062	Mm.67938	NM_133196	ENSMUSG00000031256	Cstf2	C630034J23Rik|Cstf64|mir-3112	cleavage stimulation factor, 3' pre-RNA subunit 2	protein-coding
mm_81389.1	chr9	108983005	108983026	+	1	NA	intron (NM_007738, intron 113 of 117)	intron (NM_007738, intron 113 of 117)	-3148	NM_145077	171530	Mm.388865	NM_145077	ENSMUSG00000049699	Ucn2	Ucn II|Ucn-2|ucn-II	urocortin 2	protein-coding
mm_131500.1	chr16	17405982	17406098	+	1	NA	promoter-TSS (NM_023348)	promoter-TSS (NM_023348)	40	NM_023348	67474	Mm.271992	NM_023348	ENSMUSG00000022765	Snap29	1300018G05Rik|AI891940|AU020222|BB131856|Gs32	synaptosomal-associated protein 29	protein-coding
mm_159988.1	chr6	115238987	115238987	+	1	NA	promoter-TSS (NM_001326560)	promoter-TSS (NM_001326560)	-7	NM_001326560	20965	Mm.441431	NM_013681	ENSMUSG00000009394	Syn2	2900074L19Rik|AI836018|AI841723	synapsin II	protein-coding
mm_158791.1	chrX	167210314	167210324	-	1	NA	Intergenic	Intergenic	-1101	NM_021278	19241	Mm.142729	NM_021278	ENSMUSG00000049775	Tmsb4x	Ptmb4|Tb4	thymosin, beta 4, X chromosome	protein-coding
mm_154039.1	chr19	53600006	53600013	-	1	NA	promoter-TSS (NM_007790)	promoter-TSS (NM_007790)	-387	NM_007790	13006	Mm.14910	NM_007790	ENSMUSG00000024974	Smc3	Bamacan|Cspg6|HCAP|Mmip1|SMC-3|SmcD	structural maintenance of chromosomes 3	protein-coding
mm_115834.1	chr13	21287049	21287051	-	1	NA	3' UTR (NM_010343, exon 5 of 5)	3' UTR (NM_010343, exon 5 of 5)	5636	NM_010343	14780	Mm.1332	NM_010343	ENSMUSG00000004344	Gpx5	AV379049|Arep	glutathione peroxidase 5	protein-coding
mm_170242.1	chr17	91647753	91647753	-	1	NA	Intergenic	Intergenic	-554951	NM_020252	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_129732.1	chr15	82047583	82047610	-	1	NA	promoter-TSS (NM_011482)	promoter-TSS (NM_011482)	2	NM_011482	20826	Mm.299312	NM_011482	ENSMUSG00000063480	Nhp2l1	FA-1|Fta1|Snu13|Ssfa1	NHP2 non-histone chromosome protein 2-like 1 (S. cerevisiae)	protein-coding
mm_148273.1	chr18	81927476	81927484	-	1	NA	Intergenic	Intergenic	64600	NR_039589	100628596		NR_039589	ENSMUSG00000093036	Mir5127	mmu-mir-5127|mu-mir-5127	microRNA 5127	ncRNA
mm_52886.1	chr6	122553800	122553816	+	1	NA	promoter-TSS (NM_009645)	promoter-TSS (NM_009645)	-1	NM_009645	11628	Mm.391503	NM_009645	ENSMUSG00000040627	Aicda	Aid|Arp2	activation-induced cytidine deaminase	protein-coding
mm_113801.1	chr13	46429623	46429633	+	1	NA	3' UTR (NM_001081425, exon 4 of 4)	3' UTR (NM_001081425, exon 4 of 4)	11328	NM_001081425	666794	Mm.38269	NM_001081425	ENSMUSG00000038132	Rbm24	6330546B05Rik|AI606861	RNA binding motif protein 24	protein-coding
mm_136274.1	chr16	91061561	91061579	-	1	NA	intron (NM_028905, intron 1 of 2)	MLT1J2|LTR|ERVL-MaLR	7575	NM_001163695	74387	Mm.236220	NM_028905	ENSMUSG00000039851	4932438H23Rik	4931406G06Rik|AI550392	RIKEN cDNA 4932438H23 gene	protein-coding
mm_55058.1	chr6	49047898	49047906	-	1	NA	exon (NM_053110, exon 6 of 11)	exon (NM_053110, exon 6 of 11)	11384	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_116789.1	chr13	53377356	53377373	-	1	NA	promoter-TSS (NM_009269)	promoter-TSS (NM_009269)	-3	NM_009269	268656	Mm.240336	NM_009269	ENSMUSG00000021468	Sptlc1	AW552086|C77762|E030036H05|Lcb1	serine palmitoyltransferase, long chain base subunit 1	protein-coding
mm_172926.1	chr9	71114620	71114623	-	1	NA	intron (NR_073483, intron 6 of 6)	MT2_Mm|LTR|ERVL	48012	NM_001271843	64008	Mm.449427	NM_022026	ENSMUSG00000032204	Aqp9	1700020I22Rik|AI266899|AQP-9	aquaporin 9	protein-coding
mm_84474.1	chr9	66795470	66795521	-	1	NA	promoter-TSS (NM_177583)	promoter-TSS (NM_177583)	-72	NM_177583	208117	Mm.41291	NM_177583	ENSMUSG00000032375	Aph1b	2310057K14Rik|Aph1c	aph1 homolog B, gamma secretase subunit	protein-coding
mm_41834.1	chr5	104302451	104302462	+	1	NA	exon (NM_008318, exon 4 of 7)	exon (NM_008318, exon 4 of 7)	3169	NM_008318	15891	Mm.4987	NM_008318	ENSMUSG00000029306	Ibsp	BSP|BSP II|BSPII|Bsp2	integrin binding sialoprotein	protein-coding
mm_23993.1	chr3	86539739	86539747	+	1	NA	intron (NM_001077687, intron 38 of 50)	intron (NM_001077687, intron 38 of 50)	8540	NM_011839	23937	Mm.389466	NM_011839	ENSMUSG00000057777	Mab21l2	-	mab-21-like 2 (C. elegans)	protein-coding
mm_30255.1	chr3	146648299	146648312	-	1	NA	non-coding (NR_045949, exon 2 of 4)	non-coding (NR_045949, exon 2 of 4)	3012	NM_029144	75015	Mm.250432	NM_029144	ENSMUSG00000048652	4930503B20Rik	1700013A07Rik|1700095G21Rik|4930483N21Rik|Gm1652|Samd13	RIKEN cDNA 4930503B20 gene	protein-coding
mm_64710.1	chr7	4628525	4628533	-	1	NA	exon (NM_023440, exon 3 of 3)	exon (NM_023440, exon 3 of 3)	1953	NM_023440	68255	Mm.389784	NM_023440	ENSMUSG00000045282	Tmem86b	C330014O21Rik	transmembrane protein 86B	protein-coding
mm_20243.1	chr2	126491567	126491582	-	1	NA	promoter-TSS (NM_001080944)	promoter-TSS (NM_001080944)	-21	NM_001080944	241633	Mm.222235	NM_001080944	ENSMUSG00000060131	Atp8b4	A530043E15|Im	ATPase, class I, type 8B, member 4	protein-coding
mm_142095.1	chr17	35834692	35834700	-	1	NA	3' UTR (NM_011655, exon 4 of 4)	3' UTR (NM_011655, exon 4 of 4)	3605	NM_011655	22154	Mm.273538	NM_011655	ENSMUSG00000001525	Tubb5	AA408537|AI596182|B130022C14Rik|M(beta)5	tubulin, beta 5 class I	protein-coding
mm_89901.1	chr10	111160471	111160494	+	1	NA	Intergenic	RLTR28|LTR|ERVL	-4320	NM_001003717	237542	Mm.220204	NM_175489	ENSMUSG00000020189	Osbpl8	AA536976|AA536995|C730029P18Rik|D330025H14Rik|ORP-8	oxysterol binding protein-like 8	protein-coding
mm_122222.1	chr14	32464708	32464716	-	1	NA	5' UTR (NM_021712, exon 1 of 1)	5' UTR (NM_021712, exon 1 of 1)	138	NM_021712	20508	Mm.190503	NM_021712	ENSMUSG00000100241	Slc18a3	VAChT|VAT	solute carrier family 18 (vesicular monoamine), member 3	protein-coding
mm_169517.1	chr14	87441716	87441725	-	1	NA	intron (NM_172605, intron 1 of 13)	intron (NM_172605, intron 1 of 13)	25137	NM_001253755	219249	Mm.35168	NM_172605	ENSMUSG00000022019	Tdrd3	4732418C03Rik|6720468N18	tudor domain containing 3	protein-coding
mm_4658.1	chr1	180357206	180357210	+	1	NA	intron (NM_001081175, intron 2 of 7)	intron (NM_001081175, intron 2 of 7)	-26659	NR_003623	277333	Mm.389223	NM_199472		Gm5069	EG277333	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_141610.1	chr17	32809879	32809940	-	1	NA	promoter-TSS (NM_001267583)	promoter-TSS (NM_001267583)	22	NM_001267583	240063	Mm.30675	NM_183177	ENSMUSG00000055202	Zfp811	BC052046	zinc finger protein 811	protein-coding
mm_128213.1	chr15	36164841	36164851	-	1	NA	promoter-TSS (NM_001081253)	promoter-TSS (NM_001081253)	38	NM_001081253	78803	Mm.26393	NM_175281	ENSMUSG00000048230	Fbxo43	4930533G20Rik|Emi2	F-box protein 43	protein-coding
mm_61719.1	chr7	81765932	81765936	+	1	NA	intron (NM_025997, intron 1 of 2)	B1_Mus2|SINE|Alu	2981	NM_025997	67148	Mm.241472	NM_025997	ENSMUSG00000038646	Fam103a1	2410047I02Rik|2610204K14Rik|RAM	family with sequence similarity 103, member A1	protein-coding
mm_17862.1	chr2	34826077	34826087	-	1	NA	intron (NM_001164770, intron 1 of 7)	CpG-8028	153	NM_001164770	30050	Mm.4465	NM_013890	ENSMUSG00000035949	Fbxw2	2700071L08Rik|FBW2|Fwd2|MD6	F-box and WD-40 domain protein 2	protein-coding
mm_116566.1	chr13	47011038	47011061	-	1	NA	Intergenic	CpG	3801	NM_175340	105193	Mm.25593	NM_175340	ENSMUSG00000044231	Nhlrc1	AI505271|B230309E09Rik|EPM2B	NHL repeat containing 1	protein-coding
mm_101373.1	chr11	23770828	23770846	-	1	NA	5' UTR (NM_009044, exon 1 of 10)	5' UTR (NM_009044, exon 1 of 10)	133	NM_009044	19696	Mm.4869	NM_009044	ENSMUSG00000020275	Rel	c-Rel	reticuloendotheliosis oncogene	protein-coding
mm_161178.1	chr13	42301327	42301327	+	1	NA	promoter-TSS (NM_010104)	promoter-TSS (NM_010104)	-149	NM_010104	13614	Mm.14543	NM_010104	ENSMUSG00000021367	Edn1	ET-1|PPET1|preproET	endothelin 1	protein-coding
mm_129259.1	chr15	76723773	76723801	-	1	NA	promoter-TSS (NM_176828)	promoter-TSS (NM_176828)	58	NM_145472	223665	Mm.291713	NM_145472	ENSMUSG00000033707	C030006K11Rik	1110033I13Rik	RIKEN cDNA C030006K11 gene	protein-coding
mm_12799.1	chr2	79652002	79652024	+	1	NA	intron (NM_080558, intron 9 of 17)	intron (NM_080558, intron 9 of 17)	16588	NM_080558	70599	Mm.272881	NM_080558	ENSMUSG00000027007	Ssfa2	5730488C15Rik|CS-1|CS1|KRAP|SPAG13|mKIAA1927	sperm specific antigen 2	protein-coding
mm_24000.1	chr3	86845833	86845849	+	1	NA	intron (NM_001195497, intron 2 of 15)	intron (NM_001195497, intron 2 of 15)	75043	NM_001195496	70762	Mm.44490	NM_027539	ENSMUSG00000028078	Dclk2	6330415M09Rik|AU044875|CL2|CLICK2|Click-II|Dcamkl2	doublecortin-like kinase 2	protein-coding
mm_69139.1	chr7	127050323	127050340	-	1	NA	exon (NM_026918, exon 3 of 3)	exon (NM_026918, exon 3 of 3)	1646	NM_026918	69036	Mm.21835	NM_026918	ENSMUSG00000049350	Zg16	1810010M01Rik|AI593689|ZG16p	zymogen granule protein 16	protein-coding
mm_67292.1	chr7	78847207	78847255	-	1	NA	promoter-TSS (NM_029585)	promoter-TSS (NM_029585)	-20	NM_029585	76375	Mm.250541	NM_029585	ENSMUSG00000030610	Det1	2610034H20Rik	de-etiolated homolog 1 (Arabidopsis)	protein-coding
mm_20652.1	chr2	132094176	132094204	-	1	NA	exon (NM_018824, exon 3 of 16)	exon (NM_018824, exon 3 of 16)	50918	NM_018824	54338	Mm.103581	NM_018824	ENSMUSG00000027340	Slc23a2	AI844736|NBTL1|SVCT2|Slc23a1|YSPL2|YSPL3|mKIAA0238	solute carrier family 23 (nucleobase transporters), member 2	protein-coding
mm_105616.1	chr11	106788643	106788649	-	1	NA	promoter-TSS (NM_177088)	promoter-TSS (NM_177088)	-152	NM_007840	13207	Mm.491096	NM_007840	ENSMUSG00000020719	Ddx5	2600009A06Rik|G17P1|HUMP68|Hlr1|p68	DEAD (Asp-Glu-Ala-Asp) box polypeptide 5	protein-coding
mm_50335.1	chr6	48478699	48478711	+	1	NA	exon (NM_173428, exon 61 of 103)	exon (NM_173428, exon 61 of 103)	-25634	NR_015597	58894	Mm.31983	NR_015597	ENSMUSG00000107476	Zfp862-ps	4732460K03Rik|AI448302|Zfp862|mKIAA0543	zinc finger protein 862, pseudogene	pseudo
mm_123860.1	chr14	72538942	72538968	-	1	NA	3' UTR (NM_207636, exon 26 of 26)	3' UTR (NM_207636, exon 26 of 26)	171048	NM_207636	319448	Mm.205421	NM_207636	ENSMUSG00000033487	Fndc3a	1700094E19Rik|D14Ertd453e|F730017H24Rik|Fndc3|sys	fibronectin type III domain containing 3A	protein-coding
mm_117757.1	chr13	96011035	96011042	-	1	NA	intron (NM_029210, intron 4 of 12)	intron (NM_029210, intron 4 of 12)	-119116	NM_027711	544963	Mm.38878	NM_027711	ENSMUSG00000021676	Iqgap2	4933417J23Rik|A630053O10|AI788777	IQ motif containing GTPase activating protein 2	protein-coding
mm_104475.1	chr11	95514542	95514594	-	1	NA	promoter-TSS (NM_130858)	promoter-TSS (NM_130858)	-3	NM_130858	104079	Mm.22970	NM_130858	ENSMUSG00000046719	Nxph3	-	neurexophilin 3	protein-coding
mm_138166.1	chr17	34264243	34264284	+	1	NA	intron (NM_207105, intron 1 of 5)	intron (NM_207105, intron 1 of 5)	1036	NM_207105	14961	Mm.254067	NM_207105	ENSMUSG00000073421	H2-Ab1	AI845868|Abeta|H-2Ab|H2-Ab|I-Abeta|IAb|Ia-2|Ia2|Rmcs1	histocompatibility 2, class II antigen A, beta 1	protein-coding
mm_127019.1	chr15	96185735	96185772	+	1	NA	intron (NR_028311, intron 1 of 1)	intron (NR_028311, intron 1 of 1)	2953	NR_028311	100043335	Mm.247464	NR_028311		Gm4371	EG667874|Gm8854	eukaryotic translation initiation factor 3, subunit I pseudogene	pseudo
mm_79931.1	chr9	65659657	65659678	+	1	NA	3' UTR (NM_028030, exon 8 of 8)	3' UTR (NM_028030, exon 8 of 8)	-16881	NM_010952	18247	Mm.116749	NM_010952	ENSMUSG00000040652	Oaz2	AZ-2|AZ2|Oaz2-ps|Sez15	ornithine decarboxylase antizyme 2	protein-coding
mm_65545.1	chr7	27130330	27130380	-	1	NA	exon (NM_007817, exon 7 of 10)	exon (NM_007817, exon 7 of 10)	10400	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_114633.1	chr13	76384134	76384150	+	1	NA	promoter-TSS (NM_030174)	promoter-TSS (NM_030174)	-819	NM_030174	78771	Mm.316249	NM_030174	ENSMUSG00000021596	Mctp1	2810465F10Rik	multiple C2 domains, transmembrane 1	protein-coding
mm_121685.1	chr14	13778462	13778473	-	1	NA	Intergenic	Intergenic	107591	NM_177624	218739	Mm.39919	NM_177624	ENSMUSG00000044772	Sntn	A430083B19Rik	sentan, cilia apical structure protein	protein-coding
mm_162489.1	chr1	135847738	135847740	+	1	NA	exon (NM_001130176, exon 6 of 13)	exon (NM_001130176, exon 6 of 13)	6878	NM_001130176	21956	Mm.247470	NM_011619	ENSMUSG00000026414	Tnnt2	Tnt|cTnT	troponin T2, cardiac	protein-coding
mm_41671.1	chr5	99611789	99611795	+	1	NA	intron (NR_030692, intron 1 of 3)	intron (NR_030692, intron 1 of 3)	117268	NR_030692	319818	Mm.295233	NR_030692	ENSMUSG00000089809	A930011G23Rik	-	RIKEN cDNA A930011G23 gene	ncRNA
mm_69189.1	chr7	127273513	127273525	-	1	NA	exon (NM_009266, exon 1 of 1)	exon (NM_009266, exon 1 of 1)	540	NM_009266	20768	Mm.20294	NM_009266	ENSMUSG00000049091	Sephs2	Sps2|Ysg3	selenophosphate synthetase 2	protein-coding
mm_5378.1	chr1	30949298	30949337	-	1	NA	intron (NM_011200, intron 1 of 5)	CpG	393	NR_002688	433406	Mm.389003	NR_002688		Gm13363	OTTMUSG00000011595	predicted gene 13363	pseudo
mm_76831.1	chr8	104708270	104708272	-	1	NA	Intergenic	Intergenic	-25732	NM_001190330	102022	Mm.212983	NM_133960	ENSMUSG00000055730	Ces2a	9130231C15Rik|AI266984|Ces6	carboxylesterase 2A	protein-coding
mm_164794.1	chr18	18232272	18232277	+	1	NA	Intergenic	RLTR1F_Mm|LTR|ERVK	-651284	NR_045374	75162	Mm.60874	NR_045374		4930545E07Rik	-	RIKEN cDNA 4930545E07 gene	ncRNA
mm_99886.1	chr11	109452732	109452749	+	1	NA	non-coding (NR_040680, exon 2 of 2)	non-coding (NR_040680, exon 2 of 2)	12662	NR_040680	100503496	Mm.265874	NR_040680		LOC100503496	-	uncharacterized LOC100503496	ncRNA
mm_105071.1	chr11	100752906	100752907	-	1	NA	intron (NM_001081194, intron 6 of 16)	intron (NM_001081194, intron 6 of 16)	6872	NM_001081194	380728	Mm.297539	NM_001081194	ENSMUSG00000035355	Kcnh4	BEC2	potassium voltage-gated channel, subfamily H (eag-related), member 4	protein-coding
mm_27288.1	chr3	41565510	41565544	-	1	NA	intron (NM_001130186, intron 1 of 10)	CpG	647	NM_001130186	269424	Mm.286285	NM_172303	ENSMUSG00000025764	Jade1	AU041499|D530048A03Rik|Phf17|mKIAA1807	jade family PHD finger 1	protein-coding
mm_145951.1	chr18	67464861	67464922	+	1	NA	promoter-TSS (NM_144867)	promoter-TSS (NM_144867)	42	NM_144867	225655	Mm.221420	NM_144867	ENSMUSG00000024530	Slmo1	A230074A19Rik|BC019561|Prelid3a	slowmo homolog 1 (Drosophila)	protein-coding
mm_88850.1	chr10	80930352	80930360	+	1	NA	exon (NM_008655, exon 1 of 4)	exon (NM_008655, exon 1 of 4)	265	NM_008655	17873	Mm.1360	NM_008655	ENSMUSG00000015312	Gadd45b	AI323528|Myd118	growth arrest and DNA-damage-inducible 45 beta	protein-coding
mm_95874.1	chr11	58059227	58059248	+	1	NA	3' UTR (NM_028451, exon 19 of 19)	3' UTR (NM_028451, exon 19 of 19)	-44916	NM_026949	69125	Mm.28910	NM_026949	ENSMUSG00000020515	Cnot8	1500015I04Rik|1810022F04Rik|AA536816|AU015770|AU043059	CCR4-NOT transcription complex, subunit 8	protein-coding
mm_63370.1	chr7	127091459	127091467	+	1	NA	promoter-TSS (NM_178901)	promoter-TSS (NM_178901)	27	NM_178901	101602	Mm.490357	NM_178901	ENSMUSG00000045165	AI467606	-	expressed sequence AI467606	protein-coding
mm_18619.1	chr2	68472003	68472118	-	1	NA	promoter-TSS (NM_016866)	promoter-TSS (NM_016866)	-79	NM_016866	53416	Mm.198414	NM_016866	ENSMUSG00000027030	Stk39	AW227544|AW556857|DCHT|RF005|Rnl5|SPAK	serine/threonine kinase 39	protein-coding
mm_61094.1	chr7	51862007	51862035	+	1	NA	promoter-TSS (NM_001330608)	promoter-TSS (NM_001330608)	6	NM_001330608	14453	Mm.207360	NM_008087	ENSMUSG00000030498	Gas2	Gas-2	growth arrest specific 2	protein-coding
mm_30153.1	chr3	142619176	142619181	-	1	NA	TTS (NM_010259)	TTS (NM_010259)	-1485	NM_010260	14469	Mm.24038	NM_010260	ENSMUSG00000028270	Gbp2	-	guanylate binding protein 2	protein-coding
mm_138033.1	chr17	33919620	33919628	+	1	NA	TTS (NM_020625)	TTS (NM_020625)	146	NM_009318	21356	Mm.154457	NM_009318	ENSMUSG00000024308	Tapbp	D17Wsu91e|TPN	TAP binding protein	protein-coding
mm_27748.1	chr3	69289936	69289971	-	1	NA	Intergenic	Intergenic	-26965	NM_178726	242083	Mm.40577	NM_178726	ENSMUSG00000027784	Ppm1l	3222401G13|5930404J21Rik|AI481720|AW045850|PP2C|PP2Cepsilon|Pp2ce|Ppp2ce|mKIAA4175	protein phosphatase 1 (formerly 2C)-like	protein-coding
mm_155516.1	chrX	74254680	74254726	+	1	NA	promoter-TSS (NM_007927)	promoter-TSS (NM_007927)	16	NM_007927	13726	Mm.18892	NM_007927	ENSMUSG00000001964	Emd	AW550900|Sta	emerin	protein-coding
mm_72100.1	chr8	71592230	71592240	+	1	NA	promoter-TSS (NM_025396)	promoter-TSS (NM_025396)	51	NM_001294269	66171	Mm.282284	NM_025396	ENSMUSG00000031807	Pgls	1110030K05Rik|AI447866|Plgs	6-phosphogluconolactonase	protein-coding
mm_50384.1	chr6	48690647	48690658	+	1	NA	exon (NM_001243199, exon 3 of 4)	exon (NM_001243199, exon 3 of 4)	6074	NM_174990	107526	Mm.333048	NM_174990	ENSMUSG00000054435	Gimap4	AU019574|E430007K16Rik|Ian-1|Ian1|Imap4	GTPase, IMAP family member 4	protein-coding
mm_72569.1	chr8	84127539	84127558	+	1	NA	intron (NM_001013384, intron 3 of 9)	intron (NM_001013384, intron 3 of 9)	1559	NM_001013384	244550	Mm.334654	NM_001013384	ENSMUSG00000012889	Podnl1	5832418A03Rik|Gm506	podocan-like 1	protein-coding
mm_15770.1	chr2	164332760	164332776	+	1	NA	promoter-TSS (NM_009301)	promoter-TSS (NM_009301)	3	NM_009301	20944	Mm.140154	NM_009301	ENSMUSG00000017004	Svs5	BB115186|Semg1|Svp-1|Svp1|Svp5	seminal vesicle secretory protein 5	protein-coding
mm_106378.1	chr11	118426514	118426519	-	1	NA	Intergenic	Intergenic	-1941	NM_001204129	56745	Mm.23845	NM_019959	ENSMUSG00000017446	C1qtnf1	1600017K21Rik|CTRP1|Zsig37	C1q and tumor necrosis factor related protein 1	protein-coding
mm_167393.1	chr8	95062519	95062519	+	1	NA	intron (NM_001042715, intron 7 of 17)	intron (NM_001042715, intron 7 of 17)	7416	NM_001042715	330830	Mm.277112	NM_001042715	ENSMUSG00000031786	Drc7	Ccdc135|Gm770|SRG-L|SRG-S	dynein regulatory complex subunit 7	protein-coding
mm_164039.1	chr14	87159987	87160001	+	1	NA	Intergenic	Intergenic	-18880	NM_019670	56419	Mm.440585	NM_019670	ENSMUSG00000022021	Diaph3	4930417P13Rik|Dia2|Diap3|Drf3|mDia2|mKIAA4117|p134MDia2	diaphanous related formin 3	protein-coding
mm_151342.1	chr19	55895457	55895483	+	1	NA	5' UTR (NM_001142924, exon 1 of 12)	5' UTR (NM_001142924, exon 1 of 12)	149	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_110458.1	chr12	51692014	51692026	-	1	NA	promoter-TSS (NM_001172098)	promoter-TSS (NM_001172098)	-106	NM_052973	94186	Mm.65979	NM_052973	ENSMUSG00000020954	Strn3	Gs2na|SG2NA	striatin, calmodulin binding protein 3	protein-coding
mm_71192.1	chr8	40874402	40874415	+	1	NA	intron (NM_007514, intron 1 of 11)	LTR83|LTR|ERVL	12041	NM_001044740	11988	Mm.4676	NM_007514	ENSMUSG00000031596	Slc7a2	20.5|AI158848|Atrc2|CAT-2|Cat2|Tea	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	protein-coding
mm_143884.1	chr17	84313645	84313645	-	1	NA	intron (NM_183021, intron 28 of 37)	intron (NM_183021, intron 28 of 37)	-125698	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_108721.1	chr12	87163818	87163831	+	1	NA	exon (NM_001252556, exon 8 of 8)	exon (NM_001252556, exon 8 of 8)	-8339	NR_136901	625237	Mm.390529	NR_136901		Gm6566	EG625237	predicted gene 6566	ncRNA
mm_58218.1	chr6	144209374	144209385	-	1	NA	5' UTR (NM_011444, exon 1 of 15)	5' UTR (NM_011444, exon 1 of 15)	189	NM_001113559	20678	Mm.1752	NM_011444	ENSMUSG00000041540	Sox5	A730017D01Rik|AI528773	SRY (sex determining region Y)-box 5	protein-coding
mm_124856.1	chr15	9533599	9533627	+	1	NA	Intergenic	Intergenic	-3737	NM_008372	16197	Mm.389	NM_008372	ENSMUSG00000003882	Il7r	CD127|IL-7Ralpha	interleukin 7 receptor	protein-coding
mm_145472.1	chr18	60303827	60303838	+	1	NA	TTS (NM_001101475)	TTS (NM_001101475)	10452	NM_001101475	240328	Mm.329461	NM_001101475	ENSMUSG00000090942	F830016B08Rik	Ifgga4	RIKEN cDNA F830016B08 gene	protein-coding
mm_113513.1	chr13	37778474	37778500	+	1	NA	Intergenic	CpG	-47551	NM_026830	68750	Mm.491109	NM_026830	ENSMUSG00000039087	Rreb1	1110037N09Rik|AA414966|B930013M22Rik	ras responsive element binding protein 1	protein-coding
mm_115072.1	chr13	101655113	101655137	+	1	NA	Intergenic	Intergenic	37505	NM_001024955	18708	Mm.259333	NM_001024955	ENSMUSG00000041417	Pik3r1	PI3K|p50alpha|p55alpha|p85alpha	phosphatidylinositol 3-kinase, regulatory subunit, polypeptide 1 (p85 alpha)	protein-coding
mm_87212.1	chr10	39794923	39794932	+	1	NA	exon (NM_011264, exon 4 of 32)	exon (NM_011264, exon 4 of 32)	62767	NM_011264	19714	Mm.439723	NM_011264	ENSMUSG00000019841	Rev3l	Rev|Rev3|Sez4	REV3 like, DNA directed polymerase zeta catalytic subunit	protein-coding
mm_146080.1	chr18	70621684	70621687	+	1	NA	intron (NM_010773, intron 5 of 6)	intron (NM_010773, intron 5 of 6)	53393	NM_010773	17191	Mm.322	NM_010773	ENSMUSG00000024513	Mbd2	MBD2a	methyl-CpG binding domain protein 2	protein-coding
mm_92684.1	chr10	80622595	80622609	-	1	NA	promoter-TSS (NM_134002)	promoter-TSS (NM_134002)	-178	NM_134002	103236	Mm.29873	NM_134002	ENSMUSG00000003345	Csnk1g2	2810429I12Rik|AI463719	casein kinase 1, gamma 2	protein-coding
mm_80331.1	chr9	75037810	75037820	+	1	NA	promoter-TSS (NM_021548)	promoter-TSS (NM_021548)	83	NM_021548	59046	Mm.247837	NM_021548	ENSMUSG00000007656	Arpp19	19kDa|2700024H10Rik|ARPP-19|AW559096|Arpp12	cAMP-regulated phosphoprotein 19	protein-coding
mm_79200.1	chr9	48495904	48495910	+	1	NA	promoter-TSS (NR_037589)	promoter-TSS (NR_037589)	564	NM_001004191	434402	Mm.386950	NM_001004191	ENSMUSG00000042293	Gm5617	EG434402	predicted gene 5617	protein-coding
mm_28318.1	chr3	89279634	89279647	-	1	NA	promoter-TSS (NM_010107)	promoter-TSS (NM_010107)	5	NM_010107	13636	Mm.15675	NM_010107	ENSMUSG00000027954	Efna1	AI325262|B61|Efl1|Epl1|Eplg1|Lerk1	ephrin A1	protein-coding
mm_85682.1	chr9	107872749	107872781	-	1	NA	promoter-TSS (NM_029169)	promoter-TSS (NM_029169)	54	NM_011251	19654	Mm.139926	NM_011251	ENSMUSG00000032582	Rbm6	4930506F14Rik|Def-3|NY-LU-12|g16|mKIAA4015	RNA binding motif protein 6	protein-coding
mm_161409.1	chr15	5244010	5244010	-	1	NA	5' UTR (NM_001136079, exon 1 of 3)	5' UTR (NM_001136079, exon 1 of 3)	177	NM_001136079	19219	Mm.18509	NM_008965	ENSMUSG00000039942	Ptger4	EP4|Ptgerep4	prostaglandin E receptor 4 (subtype EP4)	protein-coding
mm_100444.1	chr11	119489233	119489271	+	1	NA	Intergenic	Intergenic	-2095	NM_001164636	338371	Mm.271946	NM_177394	ENSMUSG00000039850	Endov	A730011L01Rik	endonuclease V	protein-coding
mm_25247.1	chr3	103968630	103968661	+	1	NA	promoter-TSS (NR_030676)	promoter-TSS (NR_030676)	-329	NR_030676	100125931	Mm.400392	NR_030676	ENSMUSG00000089998	Phtf1os	A130049A11Rik	putative homeodomain transcription factor 1, opposite strand	ncRNA
mm_152131.1	chr19	7019424	7019463	-	1	NA	promoter-TSS (NM_153795)	promoter-TSS (NM_153795)	26	NM_153795	108101	Mm.157591	NM_153795	ENSMUSG00000024965	Fermt3	C79673|Kindlin3	fermitin family member 3	protein-coding
mm_78080.1	chr9	15730841	15730856	+	1	NA	intron (NM_172289, intron 8 of 10)	intron (NM_172289, intron 8 of 10)	21079	NM_172289	234967	Mm.138815	NM_172289	ENSMUSG00000043885	Slc36a4	6330573I15Rik|PAT4	solute carrier family 36 (proton/amino acid symporter), member 4	protein-coding
mm_153991.1	chr19	50030752	50030767	-	1	NA	Intergenic	Intergenic	647887	NM_001252501	58178	Mm.313672	NM_021377	ENSMUSG00000043531	Sorcs1	Sorcs|mSorCS	sortilin-related VPS10 domain containing receptor 1	protein-coding
mm_114474.1	chr13	68271034	68271037	+	1	NA	Intergenic	ERVB4_2-I_MM-int|LTR|ERVK	311069	NM_001308475	210009	Mm.205514	NM_172480	ENSMUSG00000034617	Mtrr	4732420G08|MSR	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	protein-coding
mm_51601.1	chr6	84008738	84008753	+	1	NA	5' UTR (NM_001077694, exon 1 of 55)	5' UTR (NM_001077694, exon 1 of 55)	147	NM_001077694	26903	Mm.220982	NM_021469	ENSMUSG00000033788	Dysf	2310004N10Rik|AI604795|D6Pas3	dysferlin	protein-coding
mm_99858.1	chr11	109365083	109365088	+	1	NA	intron (NM_010303, intron 1 of 3)	intron (NM_010303, intron 1 of 3)	-1431	NR_038097	100036768	Mm.467767	NR_038097	ENSMUSG00000056687	Gm11696	OTTMUSG00000003456	predicted gene 11696	ncRNA
mm_161595.1	chr16	36184127	36184127	+	1	NA	promoter-TSS (NM_001082547)	promoter-TSS (NM_001082547)	-85	NM_001082547	433016	Mm.235340	NM_001082547	ENSMUSG00000079597	Gm5483	EG433016	predicted gene 5483	protein-coding
mm_5987.1	chr1	58445162	58445202	-	1	NA	promoter-TSS (NM_022988)	promoter-TSS (NM_022988)	31	NM_022988	65102	Mm.340248	NM_022988	ENSMUSG00000026036	Nif3l1	1110030G24Rik	Ngg1 interacting factor 3-like 1 (S. pombe)	protein-coding
mm_120378.1	chr14	64588123	64588136	+	1	NA	promoter-TSS (NR_040709)	promoter-TSS (NR_040709)	14	NR_040709	268755	Mm.194050	NR_040709	ENSMUSG00000097545	Mir124a-1hg	A930011O12Rik|Rncr3|mir-124-1|mir-3078	Mir124-1 host gene (non-protein coding)	ncRNA
mm_167039.1	chr7	79261552	79261556	+	1	NA	Intergenic	Intergenic	-11712	NM_018811	54608	Mm.365490	NM_018811	ENSMUSG00000039202	Abhd2	2210009N18Rik|LABH2|Labh-2	abhydrolase domain containing 2	protein-coding
mm_99163.1	chr11	100624083	100624100	+	1	NA	intron (NM_028024, intron 1 of 3)	intron (NM_028024, intron 1 of 3)	1136	NM_028024	71966	Mm.274734	NM_028024	ENSMUSG00000017837	Nkiras2	2410003M04Rik|4930527H08Rik|D630018G21Rik|KBRAS2	NFKB inhibitor interacting Ras-like protein 2	protein-coding
mm_84610.1	chr9	70217370	70217409	-	1	NA	intron (NM_181072, intron 1 of 27)	intron (NM_181072, intron 1 of 27)	10039	NM_181072	71602	Mm.249311	NM_181072	ENSMUSG00000032220	Myo1e	2310020N23Rik|9130023P14Rik|AA407778|myosin-1e|myr 3	myosin IE	protein-coding
mm_173083.1	chrX	142298332	142298335	+	1	NA	non-coding (NR_002883, exon 1 of 1)	non-coding (NR_002883, exon 1 of 1)	828	NR_002883	434858	Mm.391346	NR_002883		Gm5643	EG434858	heterogeneous nuclear ribonucleoprotein A1 pseudogene	pseudo
mm_146632.1	chr18	10182184	10182223	-	1	NA	promoter-TSS (NM_009071)	promoter-TSS (NM_009071)	-411	NM_009071	19877	Mm.6710	NM_009071	ENSMUSG00000024290	Rock1	1110055K06Rik|Rock-I	Rho-associated coiled-coil containing protein kinase 1	protein-coding
mm_87269.1	chr10	41746750	41746758	+	1	NA	intron (NM_001243074, intron 2 of 10)	intron (NM_001243074, intron 2 of 10)	62909	NM_001243075	103268	Mm.338605	NM_026643	ENSMUSG00000019813	Cep57l1	2410017P07Rik|4930484D11Rik|AI607327|cep57R	centrosomal protein 57-like 1	protein-coding
mm_150160.1	chr19	32295861	32295864	+	1	NA	intron (NM_144792, intron 2 of 9)	L1MA4A|LINE|L1	53454	NM_001168525	208449	Mm.329810	NM_144792	ENSMUSG00000040451	Sgms1	9530058O11Rik|AI841905|C80702|Mob|Sms1|Sor1|Tmem23	sphingomyelin synthase 1	protein-coding
mm_95035.1	chr11	32205412	32205481	+	1	NA	promoter-TSS (NM_030093)	promoter-TSS (NM_030093)	31	NM_030093	78372	Mm.29952	NM_030093	ENSMUSG00000040767	Snrnp25	3300001G02Rik|AL033324|C16ORF33	small nuclear ribonucleoprotein 25 (U11/U12)	protein-coding
mm_85533.1	chr9	106544684	106544688	-	1	NA	intron (NM_026645, intron 6 of 7)	intron (NM_026645, intron 6 of 7)	16939	NM_026645	68265	Mm.141451	NM_026645	ENSMUSG00000023577	Iqcf3	1700012F17Rik|AV040440	IQ motif containing F3	protein-coding
mm_13744.1	chr2	118119999	118120012	+	1	NA	exon (NM_011580, exon 13 of 22)	exon (NM_011580, exon 13 of 22)	8129	NM_001313914	21825	Mm.4159	NM_011580	ENSMUSG00000040152	Thbs1	TSP-1|TSP1|Thbs-1|tbsp1	thrombospondin 1	protein-coding
mm_158310.1	chrX	126593118	126593127	-	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	240882	NM_177705	237029	Mm.60998	NM_177705	ENSMUSG00000058670	4932411N23Rik	-	RIKEN cDNA 4932411N23 gene	protein-coding
mm_103027.1	chr11	69735285	69735295	-	1	NA	exon (NM_001291068, exon 29 of 29)	exon (NM_001291068, exon 29 of 29)	23343	NM_001291068	20020	Mm.16533	NM_009089	ENSMUSG00000005198	Polr2a	220kDa|Rpb1|Rpo2-1	polymerase (RNA) II (DNA directed) polypeptide A	protein-coding
mm_64918.1	chr7	16244153	16244196	-	1	NA	promoter-TSS (NM_176912)	promoter-TSS (NM_176912)	-20	NM_176912	319430	Mm.239570	NM_176912	ENSMUSG00000074361	C5ar2	C5L2|E030029A11Rik|Gpr77	complement component 5a receptor 2	protein-coding
mm_21748.1	chr2	164805195	164805203	-	1	NA	promoter-TSS (NM_178375)	promoter-TSS (NM_178375)	85	NM_178375	67538	Mm.33184	NM_178375	ENSMUSG00000045822	Zswim3	4921517A06Rik|C86566	zinc finger SWIM-type containing 3	protein-coding
mm_149358.1	chr19	11047613	11047619	+	1	NA	TTS (NR_102366)	TTS (NR_102366)	2950	NR_102366	107350	Mm.6381	NM_001177351	ENSMUSG00000075010	AW112010	-	expressed sequence AW112010	ncRNA
mm_73729.1	chr8	113635620	113635630	+	1	NA	promoter-TSS (NM_001048143)	promoter-TSS (NM_001048143)	39	NM_001048143	270096	Mm.74689	NM_173015	ENSMUSG00000078908	Mon1b	5031407H10|5033413H12Rik	MON1 homolog B, secretory traffciking associated	protein-coding
mm_113464.1	chr13	36117849	36117910	+	1	NA	promoter-TSS (NM_201358)	promoter-TSS (NM_201358)	236	NM_001039189	69955	Mm.70690	NM_024274	ENSMUSG00000021420	Fars2	Fars1|pheRS	phenylalanine-tRNA synthetase 2 (mitochondrial)	protein-coding
mm_138234.1	chr17	34398854	34398858	+	1	NA	promoter-TSS (NM_001163855)	promoter-TSS (NM_001163855)	36	NM_001163855	407788	Mm.73205	NM_001001177	ENSMUSG00000057246	BC051142	NG8|TSBP|Tesb|Tesbp	cDNA sequence BC051142	protein-coding
mm_129738.1	chr15	82212694	82212706	-	1	NA	5' UTR (NM_001207021, exon 1 of 4)	5' UTR (NM_001207021, exon 1 of 4)	115	NM_001207021	435145	Mm.41289	NM_001207021	ENSMUSG00000096883	Shisa8	Orf26|ckamp39	shisa family member 8	protein-coding
mm_71512.1	chr8	46846428	46846438	+	1	NA	3' UTR (NM_008391, exon 9 of 9)	3' UTR (NM_008391, exon 9 of 9)	106688	NM_008391	16363	Mm.1149	NM_008391	ENSMUSG00000031627	Irf2	9830146E22Rik|AI646973|Irf-2	interferon regulatory factor 2	protein-coding
mm_148061.1	chr18	72202595	72202598	-	1	NA	intron (NM_007831, intron 1 of 28)	intron (NM_007831, intron 1 of 28)	148473	NM_007831	13176	Mm.167882	NM_007831	ENSMUSG00000060534	Dcc	C030036D22Rik|Igdcc1	deleted in colorectal carcinoma	protein-coding
mm_6207.1	chr1	66815928	66815954	-	1	NA	intron (NM_177645, intron 1 of 13)	intron (NM_177645, intron 1 of 13)	1654	NM_177645	68691	Mm.240912	NM_177645	ENSMUSG00000026004	Kansl1l	1110028C15Rik|1190030G24|AI427598|C430010P07Rik|mKIAA4189	KAT8 regulatory NSL complex subunit 1-like	protein-coding
mm_120434.1	chr14	65805984	65806030	+	1	NA	promoter-TSS (NM_023209)	promoter-TSS (NM_023209)	96	NM_023209	52033	Mm.24337	NM_023209	ENSMUSG00000022033	Pbk	2810434B10Rik|AW538537|D14Ertd732e|TOPK	PDZ binding kinase	protein-coding
mm_145862.1	chr18	65458159	65458179	+	1	NA	exon (NM_172833, exon 9 of 16)	exon (NM_172833, exon 9 of 16)	27172	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_51084.1	chr6	67019720	67019734	+	1	NA	3' UTR (NM_001177559, exon 5 of 5)	3' UTR (NM_001177559, exon 5 of 5)	-16872	NR_040278	320172	Mm.449039	NR_040278	ENSMUSG00000087231	E230016M11Rik	-	RIKEN cDNA E230016M11 gene	ncRNA
mm_56676.1	chr6	113719451	113719468	-	1	NA	promoter-TSS (NM_001286405)	promoter-TSS (NM_001286405)	-5	NM_001286404	58991	Mm.379095	NM_021488	ENSMUSG00000064177	Ghrl	2210006E23Rik|Ghr|MTLRP|MTLRPAP|m46	ghrelin	protein-coding
mm_140931.1	chr17	24351054	24351064	-	1	NA	promoter-TSS (NM_001039581)	promoter-TSS (NM_001039581)	-964	NM_013855	27410	Mm.239470	NM_013855	ENSMUSG00000024130	Abca3	1810036E22Rik|ABC-C|Abc3	ATP-binding cassette, sub-family A (ABC1), member 3	protein-coding
mm_64445.1	chr7	142653993	142654005	+	1	NA	TTS (NR_030251)	TTS (NR_030251)	997	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_112961.1	chr13	21180391	21180460	+	1	NA	5' UTR (NM_009054, exon 1 of 8)	5' UTR (NM_009054, exon 1 of 8)	494	NM_009054	19720	Mm.314056	NM_009054	ENSMUSG00000021326	Trim27	AW538890|Gm19403|Rfp	tripartite motif-containing 27	protein-coding
mm_106828.1	chr12	7996510	7996521	+	1	NA	intron (NM_009693, intron 18 of 28)	intron (NM_009693, intron 18 of 28)	18838	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_28875.1	chr3	97735512	97735552	-	1	NA	intron (NM_001039376, intron 24 of 46)	intron (NM_001039376, intron 24 of 46)	32482	NR_110360	83679	Mm.129840	NM_031401	ENSMUSG00000038170	Pde4dip	4732458A06Rik|9430063L05Rik|C87016|D130016K21Rik|D3Bwg1078e|Usmg4|mKIAA0454	phosphodiesterase 4D interacting protein (myomegalin)	protein-coding
mm_79105.1	chr9	46268602	46268619	+	1	NA	promoter-TSS (NM_080434)	promoter-TSS (NM_080434)	2	NM_080434	66113	Mm.29738	NM_080434	ENSMUSG00000032079	Apoa5	1300007O05Rik|Apoav|RAP3	apolipoprotein A-V	protein-coding
mm_22305.1	chr2	180381217	180381223	-	1	NA	intron (NR_040745, intron 4 of 6)	intron (NR_040745, intron 4 of 6)	-4384	NR_045331	622283	Mm.447602	NR_045331		Mir1a-1hg	EG622283|Gm6307	Mir1a-1 and Mir133a-2 host gene	ncRNA
mm_154019.1	chr19	53313293	53313310	-	1	NA	intron (NM_001008542, intron 1 of 5)	CpG	2795	NM_001008542	17859	Mm.2154	NM_010847	ENSMUSG00000025025	Mxi1	ENSMUSG00000067085|Gm10197|Mad2|bHLHc11	MAX interactor 1, dimerization protein	protein-coding
mm_6061.1	chr1	60517154	60517158	-	1	NA	intron (NM_001045513, intron 4 of 13)	intron (NM_001045513, intron 4 of 13)	49609	NM_001045513	77300	Mm.440325	NM_001045513	ENSMUSG00000026014	Raph1	9430025M21Rik|C730009O10Rik|Lpd	Ras association (RalGDS/AF-6) and pleckstrin homology domains 1	protein-coding
mm_102695.1	chr11	65788276	65788318	-	1	NA	promoter-TSS (NM_001316367)	promoter-TSS (NM_001316367)	62	NM_009157	26398	Mm.412922	NM_009157	ENSMUSG00000033352	Map2k4	JNKK1|MEK4|MKK4|PRKMK4|Sek1|Serk1	mitogen-activated protein kinase kinase 4	protein-coding
mm_54459.1	chr6	34873524	34873546	-	1	NA	3' UTR (NM_197986, exon 2 of 2)	3' UTR (NM_197986, exon 2 of 2)	4530	NM_199145	78412	Mm.248440	NM_199145	ENSMUSG00000046806	3110062M04Rik	AL023049|Mri	RIKEN cDNA 3110062M04 gene	protein-coding
mm_75100.1	chr8	34111727	34111738	-	1	NA	Intergenic	Intergenic	-3020	NM_011722	22428	Mm.150373	NM_011722	ENSMUSG00000031516	Dctn6	AU044699|WS-3|p27	dynactin 6	protein-coding
mm_81624.1	chr9	110834675	110834681	+	1	NA	promoter-TSS (NM_153172)	promoter-TSS (NM_153172)	90	NM_153172	260408	Mm.79114	NM_153172	ENSMUSG00000047257	Prss45	Tespl|Tessp5	protease, serine 45	protein-coding
mm_27097.1	chr3	30220428	30220431	-	1	NA	Intergenic	Intergenic	-207225	NM_007963	14013	Mm.56965	NM_007963	ENSMUSG00000027684	Mecom	D630039M04Rik|Evi-1|Evi1|Jbo|Mds|Mds1|Mds1-Evi1|Prdm3|Znfpr1b1	MDS1 and EVI1 complex locus	protein-coding
mm_132461.1	chr16	36184083	36184095	+	1	NA	promoter-TSS (NM_001082547)	promoter-TSS (NM_001082547)	-123	NM_001082547	433016	Mm.235340	NM_001082547	ENSMUSG00000079597	Gm5483	EG433016	predicted gene 5483	protein-coding
mm_137428.1	chr17	26270353	26270386	+	1	NA	intron (NR_037906, intron 5 of 8)	intron (NR_037906, intron 5 of 8)	17459	NR_037905	66978	Mm.440216	NM_025881	ENSMUSG00000024188	Luc7l	1810045C04Rik|2410018D03Rik	Luc7-like	protein-coding
mm_161535.1	chr15	102524592	102524592	-	1	NA	promoter-TSS (NM_018787)	promoter-TSS (NM_018787)	29	NM_018787	54615	Mm.445915	NM_018787	ENSMUSG00000023052	Npff	-	neuropeptide FF-amide peptide precursor	protein-coding
mm_154658.1	chrX	7842028	7842038	+	1	NA	promoter-TSS (NM_001290537)	promoter-TSS (NM_001290537)	-49	NM_001290537	54644	Mm.142827	NM_138604	ENSMUSG00000031154	Otud5	AA407879|AI553596|BB114028|DUBA|DXImx46e|Sfc7	OTU domain containing 5	protein-coding
mm_30680.1	chr4	11191418	11191424	+	1	NA	promoter-TSS (NM_009830)	promoter-TSS (NM_009830)	70	NM_001037134	12448	Mm.35867	NM_009830	ENSMUSG00000028212	Ccne2	-	cyclin E2	protein-coding
mm_37511.1	chr4	123896593	123896604	-	1	NA	Intergenic	Intergenic	-8415	NM_019660	56309	Mm.446553	NM_019660	ENSMUSG00000028647	Mycbp	5730488M09Rik|AW552132|AW742590|Amy-1	MYC binding protein	protein-coding
mm_105752.1	chr11	109473037	109473050	-	1	NA	promoter-TSS (NM_028710)	promoter-TSS (NM_028710)	186	NM_134038	104681	Mm.265874	NM_134038	ENSMUSG00000041920	Slc16a6	AW743111|ESTM12|MCT 6|MCT 7|MCT6	solute carrier family 16 (monocarboxylic acid transporters), member 6	protein-coding
mm_62796.1	chr7	112742071	112742080	+	1	NA	intron (NM_009346, intron 1 of 12)	intron (NM_009346, intron 1 of 12)	-17309	NM_001166585	21676	Mm.24685	NM_009346	ENSMUSG00000055320	Tead1	2610024B07Rik|B230114H05Rik|Gtrgeo5|TEAD-1|TEF-1|Tcf13|mTEF-1	TEA domain family member 1	protein-coding
mm_160376.1	chr8	40823022	40823022	+	1	NA	promoter-TSS (NM_001025380)	promoter-TSS (NM_001025380)	13	NM_001025380	546055	Mm.334503	NM_001025380	ENSMUSG00000054033	Adam39	1700056P18Rik	a disintegrin and metallopeptidase domain 39	protein-coding
mm_145874.1	chr18	65472676	65472692	+	1	NA	intron (NM_172833, intron 13 of 15)	intron (NM_172833, intron 13 of 15)	41687	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_166658.1	chr6	87791449	87791463	-	1	NA	non-coding (NR_104478, exon 3 of 3)	non-coding (NR_104478, exon 3 of 3)	13320	NM_018762	54368	Mm.12897	NM_018762	ENSMUSG00000030054	Gp9	Cd42|GPIX	glycoprotein 9 (platelet)	protein-coding
mm_36407.1	chr4	78003584	78003586	-	1	NA	intron (NM_011211, intron 1 of 39)	intron (NM_011211, intron 1 of 39)	208310	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding
mm_16524.1	chr2	181520534	181520563	+	1	NA	promoter-TSS (NM_001271585)	promoter-TSS (NM_001271585)	63	NM_001271584	13002	Mm.140761	NM_016775	ENSMUSG00000000826	Dnajc5	2610314I24Rik|AU018536|Csp	DnaJ heat shock protein family (Hsp40) member C5	protein-coding
mm_129737.1	chr15	82166925	82166933	-	1	NA	intron (NM_033218, intron 1 of 18)	intron (NM_033218, intron 1 of 18)	19660	NM_033218	20788	Mm.9002	NM_033218	ENSMUSG00000022463	Srebf2	AI608257|SREBP-2|SREBP2|SREBP2gc|bHLHd2|lop13|nuc	sterol regulatory element binding factor 2	protein-coding
mm_140428.1	chr17	88064781	88064801	+	1	NA	intron (NM_001081034, intron 1 of 22)	CpG	494	NM_001081034	225055	Mm.386857	NM_001081034	ENSMUSG00000005371	Fbxo11	C80048|Jf	F-box protein 11	protein-coding
mm_144344.1	chr18	15150416	15150426	+	1	NA	intron (NM_134112, intron 1 of 4)	CpG	1025	NM_134112	106931	Mm.329299	NM_134112	ENSMUSG00000036225	Kctd1	4933402K10Rik|AI661543|AW553000	potassium channel tetramerisation domain containing 1	protein-coding
mm_142237.1	chr17	37481209	37481219	-	1	NA	3' UTR (NM_008204, exon 4 of 4)	3' UTR (NM_008204, exon 4 of 4)	2315	NM_008204	14990	Mm.329041	NM_008204	ENSMUSG00000016283	H2-M2	H-2M2|Thy19.4	histocompatibility 2, M region locus 2	protein-coding
mm_120138.1	chr14	60377584	60377594	+	1	NA	promoter-TSS (NM_001164705)	promoter-TSS (NM_001164705)	-697	NM_028113	72125	Mm.275499	NM_028113	ENSMUSG00000021986	Amer2	2600011E07Rik|Fam123a	APC membrane recruitment 2	protein-coding
mm_136948.1	chr17	14546342	14546361	+	1	NA	Intergenic	Intergenic	-147409	NR_027986	74917	Mm.32228	NM_183107		4930474M22Rik	-	RIKEN cDNA 4930474M22 gene	ncRNA
mm_134478.1	chr16	18621605	18621615	-	1	NA	TTS (NM_213614)	TTS (NM_213614)	793	NM_001001999	14724	Mm.475622	NM_010327	ENSMUSG00000050761	Gp1bb	-	glycoprotein Ib, beta polypeptide	protein-coding
mm_134155.1	chr16	10788650	10788668	-	1	NA	promoter-TSS (NM_013694)	promoter-TSS (NM_013694)	-4	NM_013694	21959	Mm.206798	NM_013694	ENSMUSG00000043050	Tnp2	TP2|Tp-2	transition protein 2	protein-coding
mm_47669.1	chr5	127617344	127617354	-	1	NA	promoter-TSS (NM_133895)	promoter-TSS (NM_133895)	43	NM_133895	100561	Mm.28506	NM_133895	ENSMUSG00000029416	Slc15a4	AA987064|AW742963|C130069N12Rik|PHT1|PTR4	solute carrier family 15, member 4	protein-coding
mm_35785.1	chr4	46468760	46468790	-	1	NA	exon (NM_130889, exon 4 of 7)	exon (NM_130889, exon 4 of 7)	17849	NM_130889	67628	Mm.263913	NM_130889	ENSMUSG00000028333	Anp32b	2410015B15Rik|PAL31|PHAPI2a|Ssp29	acidic (leucine-rich) nuclear phosphoprotein 32 family, member B	protein-coding
mm_168231.1	chr10	80676221	80676225	-	1	NA	promoter-TSS (NM_021462)	promoter-TSS (NM_021462)	70	NM_021462	17347	Mm.42126	NM_021462	ENSMUSG00000020190	Mknk2	2010016G11Rik|Gprk7|Mnk2	MAP kinase-interacting serine/threonine kinase 2	protein-coding
mm_94860.1	chr11	24077743	24077794	+	1	NA	promoter-TSS (NM_001242934)	promoter-TSS (NM_001242934)	-288	NM_016707	14025	Mm.53687	NM_016707	ENSMUSG00000000861	Bcl11a	2810047E18Rik|BCL-11A|Ctip1|D930021L15Rik|Evi9|Evi9a|Evi9b|Evi9c|mKIAA1809	B cell CLL/lymphoma 11A (zinc finger protein)	protein-coding
mm_143015.1	chr17	56476367	56476460	-	1	NA	promoter-TSS (NM_001252453)	promoter-TSS (NM_001252453)	67	NM_001252455	19280	Mm.258771	NM_011218	ENSMUSG00000013236	Ptprs	AL022616|PTP|PTP-NU3|PTPNU-3|PTPsigma|Ptpt9|R-PTP-S|RPTPsigma	protein tyrosine phosphatase, receptor type, S	protein-coding
mm_11691.1	chr2	35663637	35663651	+	1	NA	intron (NM_001290637, intron 3 of 16)	intron (NM_001290637, intron 3 of 16)	-28350	NM_001001602	69601	Mm.29629	NM_001001602	ENSMUSG00000026883	Dab2ip	2310011D08Rik|AI480459|Aip1|mKIAA1743	disabled 2 interacting protein	protein-coding
mm_52385.1	chr6	113237877	113237907	+	1	NA	promoter-TSS (NM_026849)	promoter-TSS (NM_026849)	49	NM_026849	97287	Mm.197816	NM_026849	ENSMUSG00000030269	Mtmr14	1110061O04Rik|AW553738|C76151	myotubularin related protein 14	protein-coding
mm_11515.1	chr2	32587281	32587310	+	1	NA	5' UTR (NM_011373, exon 1 of 5)	5' UTR (NM_011373, exon 1 of 5)	217	NM_011373	20448	Mm.27446	NM_011373	ENSMUSG00000079442	St6galnac4	SIAT7-D|ST6GalNAcIV|Siat7d	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 4	protein-coding
mm_103741.1	chr11	80081179	80081205	-	1	NA	promoter-TSS (NM_018776)	promoter-TSS (NM_018776)	-201	NM_018776	54394	Mm.272093	NM_018776	ENSMUSG00000017561	Crlf3	BB164954|Creme9|Cytor4	cytokine receptor-like factor 3	protein-coding
mm_34534.1	chr4	149485216	149485254	+	1	NA	promoter-TSS (NM_026963)	promoter-TSS (NM_026963)	-93	NM_133435	66454	Mm.76062	NM_133435	ENSMUSG00000028992	Nmnat1	2610529L11Rik|5730441G13Rik|D4Cole1e|nmnat	nicotinamide nucleotide adenylyltransferase 1	protein-coding
mm_25669.1	chr3	121953186	121953198	+	1	NA	promoter-TSS (NM_172525)	promoter-TSS (NM_172525)	-134	NM_172525	214137	Mm.229287	NM_172525	ENSMUSG00000039831	Arhgap29	6720461J18Rik|A830014I19|AU040217|B130017I01Rik|C76601|Parg1	Rho GTPase activating protein 29	protein-coding
mm_44622.1	chr5	25705764	25705787	-	1	NA	promoter-TSS (NM_020570)	promoter-TSS (NM_020570)	22	NM_020570	57434	Mm.143767	NM_020570	ENSMUSG00000028933	Xrcc2	4921524O04Rik|8030409M04Rik|RAD51|RecA	X-ray repair complementing defective repair in Chinese hamster cells 2	protein-coding
mm_26792.1	chr3	9786519	9786526	-	1	NA	intron (NM_053182, intron 1 of 7)	intron (NM_053182, intron 1 of 7)	47157	NM_053182	94212	Mm.23897	NM_053182	ENSMUSG00000027508	Pag1	Cbp|F730007C19Rik|Pag	phosphoprotein associated with glycosphingolipid microdomains 1	protein-coding
mm_124441.1	chr14	118706441	118706469	-	1	NA	promoter-TSS (NM_001163676)	promoter-TSS (NM_001163676)	-236	NM_001033336	239273	Mm.40537	NM_001033336	ENSMUSG00000032849	Abcc4	ABCC4-N1|D630049P08Rik|MOATB|MRP4	ATP-binding cassette, sub-family C (CFTR/MRP), member 4	protein-coding
mm_50010.1	chr6	41059434	41059455	+	1	NA	Intergenic	Intergenic	-23935	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_172785.1	chr9	100969569	100969573	-	1	NA	Intergenic	BGLII_B|LTR|ERVK	65313	NM_001311149	66904	Mm.335385	NM_025835	ENSMUSG00000032527	Pccb	1300012P06Rik|AI314687|R74805	propionyl Coenzyme A carboxylase, beta polypeptide	protein-coding
mm_66122.1	chr7	31053124	31053152	-	1	NA	intron (NM_052991, intron 4 of 7)	intron (NM_052991, intron 4 of 7)	-1684	NM_022007	57780	Mm.41770	NM_022007	ENSMUSG00000036578	Fxyd7	1110035I01Rik	FXYD domain-containing ion transport regulator 7	protein-coding
mm_94673.1	chr11	17324968	17324990	+	1	NA	Intergenic	Intergenic	67291	NM_001330649	57316	Mm.287982	NM_020558	ENSMUSG00000000581	C1d	1110036E10Rik|AI875855|SUN-CoR	C1D nuclear receptor co-repressor	protein-coding
mm_45258.1	chr5	63939552	63939587	-	1	NA	intron (NM_145923, intron 1 of 6)	intron (NM_145923, intron 1 of 6)	29328	NM_145923	100532	Mm.243632	NM_145923	ENSMUSG00000047881	Rell1	AA536743	RELT-like 1	protein-coding
mm_63358.1	chr7	127016658	127016672	+	1	NA	TTS (NM_001102563)	TTS (NM_001102563)	687	NM_030240	67278	Mm.345385	NM_030240	ENSMUSG00000030680	Pagr1a	2900092E17Rik|C77040|PA1|PAGR1	PAXIP1 associated glutamate rich protein 1A	protein-coding
mm_32723.1	chr4	116507585	116507623	+	1	NA	promoter-TSS (NM_008389)	promoter-TSS (NM_008389)	55	NM_008389	16351	Mm.1350	NM_008389	ENSMUSG00000028696	Ipp	D4Jhu8|Mipp	IAP promoted placental gene	protein-coding
mm_11332.1	chr2	30445635	30445647	+	1	NA	intron (NM_138748, intron 9 of 9)	intron (NM_138748, intron 9 of 9)	28558	NM_030244	72500	Mm.295464	NM_030244	ENSMUSG00000089762	Ier5l	2610524G09Rik	immediate early response 5-like	protein-coding
mm_64112.1	chr7	141078127	141078137	+	1	NA	promoter-TSS (NM_001162924)	promoter-TSS (NM_001162924)	-97	NM_001162924	56460	Mm.350037	NM_019762	ENSMUSG00000054065	Pkp3	2310056L12Rik	plakophilin 3	protein-coding
mm_66714.1	chr7	46030335	46030341	-	1	NA	promoter-TSS (NM_018795)	promoter-TSS (NM_018795)	-52	NM_018795	27421	Mm.63514	NM_018795	ENSMUSG00000030834	Abcc6	Abcc1b|DCC|Dyscalc1|Mrp6|dyscalc	ATP-binding cassette, sub-family C (CFTR/MRP), member 6	protein-coding
mm_75476.1	chr8	48555258	48555268	-	1	NA	intron (NM_011857, intron 2 of 28)	CpG	119427	NM_001145937	23965	Mm.42191	NM_011857	ENSMUSG00000031561	Tenm3	2610100B16Rik|Odz1|Odz3|Ten-m3|mKIAA1455	teneurin transmembrane protein 3	protein-coding
mm_2248.1	chr1	91057889	91057898	+	1	NA	intron (NM_001310732, intron 1 of 24)	intron (NM_001310732, intron 1 of 24)	4449	NM_008515	16978	Mm.45039	NM_008515	ENSMUSG00000026305	Lrrfip1	AU024550|Fliiap1	leucine rich repeat (in FLII) interacting protein 1	protein-coding
mm_105628.1	chr11	106913628	106913631	-	1	NA	intron (NM_025481, intron 1 of 18)	intron (NM_025481, intron 1 of 18)	7086	NM_025481	66313	Mm.340955	NM_025481	ENSMUSG00000018363	Smurf2	2810411E22Rik|AI558114|AI649275	SMAD specific E3 ubiquitin protein ligase 2	protein-coding
mm_170213.1	chr17	72479606	72479606	+	1	NA	intron (NM_007439, intron 1 of 28)	LTRIS2|LTR|ERV1	124701	NM_007439	11682	Mm.311854	NM_007439	ENSMUSG00000055471	Alk	CD246|Tcrz	anaplastic lymphoma kinase	protein-coding
mm_134487.1	chr16	18629794	18629806	-	1	NA	intron (NM_213614, intron 1 of 11)	CpG-5592	138	NM_213614	18951	Mm.20365	NM_213614	ENSMUSG00000072214	Sept5	Cdcrel-1|Cdcrel1|Pnutl1	septin 5	protein-coding
mm_73532.1	chr8	108703455	108703501	+	1	NA	Intergenic	Intergenic	-11166	NM_007496	11906	Mm.416972	NM_007496	ENSMUSG00000038872	Zfhx3	A230102L03Rik|Atbf1|Sci|WBP9|mKIAA4228	zinc finger homeobox 3	protein-coding
mm_169892.1	chr16	48283720	48283736	+	1	NA	promoter-TSS (NM_028610)	promoter-TSS (NM_028610)	-7	NM_028610	73693	Mm.35597	NM_028610	ENSMUSG00000058550	Dppa4	2410091M23Rik|C76608|ECAT15-1	developmental pluripotency associated 4	protein-coding
mm_96510.1	chr11	68459528	68459531	+	1	NA	intron (NM_177320, intron 1 of 18)	L1ME2|LINE|L1	27404	NM_177320	320207	Mm.244960	NM_177320	ENSMUSG00000020901	Pik3r5	AV230647|F730038I15Rik	phosphoinositide-3-kinase, regulatory subunit 5, p101	protein-coding
mm_166316.1	chr5	110330693	110330701	+	1	NA	intron (NM_011132, intron 41 of 48)	intron (NM_011132, intron 41 of 48)	12338	NM_153400	231602	Mm.55948	NM_153400	ENSMUSG00000029503	P2rx2	P2X2a|P2x2	purinergic receptor P2X, ligand-gated ion channel, 2	protein-coding
mm_87382.1	chr10	44686247	44686250	+	1	NA	Intergenic	Intergenic	-227500	NM_007548	12142	Mm.4800	NM_007548	ENSMUSG00000038151	Prdm1	Blimp-1|Blimp1|PRDI-BF1|ZNFPR1A1|b2b1765Clo	PR domain containing 1, with ZNF domain	protein-coding
mm_649.1	chr1	40428290	40428320	+	1	NA	Intergenic	Intergenic	-1265	NM_001294171	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_64197.1	chr7	141467504	141467541	+	1	NA	TTS (NM_001025103)	TTS (NM_001025103)	160	NM_001111049	12476	Mm.30246	NM_009842	ENSMUSG00000025510	Cd151	PETA-3|SFA-1|Tspan24	CD151 antigen	protein-coding
mm_50296.1	chr6	47468351	47468355	+	1	NA	intron (NM_012042, intron 1 of 21)	L1MC5a|LINE|L1	14029	NM_012042	26965	Mm.87611	NM_012042	ENSMUSG00000029686	Cul1	-	cullin 1	protein-coding
mm_64268.1	chr7	141753368	141753383	+	1	NA	exon (NM_023566, exon 43 of 46)	exon (NM_023566, exon 43 of 46)	-35636	NM_010844	17833	Mm.334332	NM_010844	ENSMUSG00000037974	Muc5ac	2210005L13Rik|MGM	mucin 5, subtypes A and C, tracheobronchial/gastric	protein-coding
mm_16203.1	chr2	173033498	173033519	+	1	NA	exon (NM_019547, exon 4 of 4)	exon (NM_019547, exon 4 of 4)	11606	NM_019547	56190	Mm.485782	NM_019547	ENSMUSG00000027510	Rbm38	Rnpc1|Seb4|Seb4l	RNA binding motif protein 38	protein-coding
mm_23889.1	chr3	83031362	83031376	+	1	NA	exon (NM_010196, exon 5 of 5)	exon (NM_010196, exon 5 of 5)	5216	NM_001111048	14161	Mm.88793	NM_010196	ENSMUSG00000028001	Fga	ENSMUSG00000059807|Fib	fibrinogen alpha chain	protein-coding
mm_87431.1	chr10	50903090	50903099	+	1	NA	intron (NM_011376, intron 1 of 10)	intron (NM_011376, intron 1 of 10)	7443	NM_011376	20464	Mm.4774	NM_011376	ENSMUSG00000019913	Sim1	bHLHe14|mSIM1	single-minded homolog 1 (Drosophila)	protein-coding
mm_97163.1	chr11	75487134	75487150	+	1	NA	exon (NM_138659, exon 1 of 42)	exon (NM_138659, exon 1 of 42)	365	NM_138659	192159	Mm.3757	NM_138659	ENSMUSG00000020850	Prpf8	AU019467|D11Bwg0410e|DBF3/PRP8|Prp8|Sfprp8l	pre-mRNA processing factor 8	protein-coding
mm_171954.1	chr5	78473870	78473877	+	1	NA	Intergenic	Intergenic	1008385	NR_131050	69370	Mm.426881	NR_131050	ENSMUSG00000107232	1700017L05Rik	-	RIKEN cDNA 1700017L05 gene	ncRNA
mm_146344.1	chr18	82537125	82537135	+	1	NA	intron (NM_001025245, intron 3 of 3)	intron (NM_001025245, intron 3 of 3)	-17333	NM_001025256	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_2067.1	chr1	87620335	87620401	+	1	NA	promoter-TSS (NM_001110192)	promoter-TSS (NM_001110192)	56	NM_001110193	16331	Mm.15105	NM_010566	ENSMUSG00000026288	Inpp5d	SHIP|SHIP-1|SHIP1|SIP-145|p150Ship|s-SHIP	inositol polyphosphate-5-phosphatase D	protein-coding
mm_53393.1	chr6	129588058	129588067	+	1	NA	Intergenic	Intergenic	-3749	NM_010654	16643	Mm.391515	NM_010654	ENSMUSG00000030165	Klrd1	CD94	killer cell lectin-like receptor, subfamily D, member 1	protein-coding
mm_36700.1	chr4	96664113	96664162	-	1	NA	promoter-TSS (NM_010007)	promoter-TSS (NM_010007)	-18	NM_010007	13109	Mm.12838	NM_010007	ENSMUSG00000052520	Cyp2j5	-	cytochrome P450, family 2, subfamily j, polypeptide 5	protein-coding
mm_30865.1	chr4	31964082	31964160	+	1	NA	promoter-TSS (NM_009316)	promoter-TSS (NM_009316)	14	NM_172688	26409	Mm.258589	NM_009316	ENSMUSG00000028284	Map3k7	B430101B05|C87327|Tak1	mitogen-activated protein kinase kinase kinase 7	protein-coding
mm_59315.1	chr7	25289493	25289510	+	1	NA	exon (NM_027882, exon 11 of 20)	exon (NM_027882, exon 11 of 20)	7322	NM_027882	71722	Mm.28833	NM_027882	ENSMUSG00000005442	Cic	1200010B10Rik|mKIAA0306	capicua transcriptional repressor	protein-coding
mm_153477.1	chr19	41273872	41273882	-	1	NA	TTS (NM_031376)	TTS (NM_031376)	-9873	NM_133352	107358	Mm.246440	NM_133352	ENSMUSG00000025016	Tm9sf3	1810073M23Rik|2810031D16Rik|AI115521|AI413748|AW146116|AW549777|Smbp|mKIAA4036	transmembrane 9 superfamily member 3	protein-coding
mm_78026.1	chr9	13765971	13765983	+	1	NA	intron (NR_024025, intron 1 of 15)	intron (NR_024025, intron 1 of 15)	16796	NR_024025	77116	Mm.210405	NM_023858	ENSMUSG00000031918	Mtmr2	6030445P13Rik	myotubularin related protein 2	protein-coding
mm_68159.1	chr7	102687253	102687298	-	1	NA	promoter-TSS (NM_001307998)	promoter-TSS (NM_001307998)	52	NM_198012	101700	Mm.39043	NM_198012	ENSMUSG00000073968	Trim68	AI894158|F730114J12Rik|Rnf137|SS-56	tripartite motif-containing 68	protein-coding
mm_12292.1	chr2	69036028	69036034	+	1	NA	intron (NM_172856, intron 4 of 9)	intron (NM_172856, intron 4 of 9)	-99769	NM_181547	329416	Mm.90047	NM_181547	ENSMUSG00000034738	Nostrin	Daip2|mDaIP2	nitric oxide synthase trafficker	protein-coding
mm_93379.1	chr10	105568253	105568256	-	1	NA	intron (NM_177368, intron 1 of 11)	intron (NM_177368, intron 1 of 11)	6225	NM_177368	278279	Mm.25225	NM_177368	ENSMUSG00000036019	Tmtc2	8430438D04Rik|D330034A10Rik	transmembrane and tetratricopeptide repeat containing 2	protein-coding
mm_139475.1	chr17	55986539	55986549	+	1	NA	promoter-TSS (NM_183178)	promoter-TSS (NM_183178)	33	NM_183178	240121	Mm.270660	NM_183178	ENSMUSG00000011589	Fsd1	-	fibronectin type 3 and SPRY domain-containing protein	protein-coding
mm_81596.1	chr9	110529232	110529242	+	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-3360	NM_001081340	235626	Mm.288949	NM_001081340	ENSMUSG00000044791	Setd2	4921524K10Rik|BC031601|KMT3A	SET domain containing 2	protein-coding
mm_17496.1	chr2	28621933	28621963	-	1	NA	promoter-TSS (NM_001160406)	promoter-TSS (NM_001160406)	34	NM_008114	14582	Mm.373385	NM_008114	ENSMUSG00000026815	Gfi1b	Gfi-1B	growth factor independent 1B	protein-coding
mm_77560.1	chr8	123427559	123427566	-	1	NA	Intergenic	MuLV-int|LTR|ERV1	-15394	NM_001253784	23854	Mm.275127	NM_054046	ENSMUSG00000001482	Def8	AI449518|D8Ertd713e|DEF-8	differentially expressed in FDCP 8	protein-coding
mm_48884.1	chr5	151190155	151190219	-	1	NA	promoter-TSS (NM_001163493)	promoter-TSS (NM_001163493)	6	NM_001163493	243362	Mm.209272	NM_146258	ENSMUSG00000016128	Stard13	DLC2|GT650	StAR-related lipid transfer (START) domain containing 13	protein-coding
mm_51612.1	chr6	85076180	85076184	+	1	NA	promoter-TSS (NR_002702)	promoter-TSS (NR_002702)	41	NR_002702	108176	Mm.431982	NR_002702		Npm3-ps1	-	nucleoplasmin 3, pseudogene 1	pseudo
mm_23201.1	chr3	41496203	41496231	+	1	NA	Intergenic	RLTR23|LTR|ERV1	-3018	NR_040385	78706	Mm.366094	NR_040385	ENSMUSG00000097639	Platr4	C430002E04Rik	pluripotency associated transcript 4	ncRNA
mm_152096.1	chr19	6909634	6909691	-	1	NA	promoter-TSS (NM_026306)	promoter-TSS (NM_026306)	-17	NM_012021	54683	Mm.279782	NM_012021	ENSMUSG00000024953	Prdx5	AOEB166|AOPP|Pmp20|Prdx6|PrxV	peroxiredoxin 5	protein-coding
mm_116228.1	chr13	33040033	33040043	-	1	NA	3' UTR (NM_011452, exon 7 of 7)	3' UTR (NM_011452, exon 7 of 7)	12624	NM_011452	20706	Mm.45371	NM_011452	ENSMUSG00000021403	Serpinb9b	1600019A21Rik|R86|SPI-CI|Spi10|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 9b	protein-coding
mm_26613.1	chr3	152348571	152348574	+	1	NA	intron (NM_001076676, intron 1 of 23)	ID_B1|SINE|B4	2094	NM_001076676	170822	Mm.258320	NM_133247	ENSMUSG00000025437	Usp33	9830169D19Rik|AA409780|Vdu1	ubiquitin specific peptidase 33	protein-coding
mm_85172.1	chr9	96478661	96478669	-	1	NA	promoter-TSS (NM_011279)	promoter-TSS (NM_011279)	10	NM_011279	19823	Mm.28235	NM_011279	ENSMUSG00000051234	Rnf7	Rbx2|SAG	ring finger protein 7	protein-coding
mm_77052.1	chr8	109577511	109577529	-	1	NA	exon (NM_017370, exon 2 of 5)	exon (NM_017370, exon 2 of 5)	1652	NM_017370	15439	Mm.26730	NM_017370	ENSMUSG00000031722	Hp	HP-1|preHP2	haptoglobin	protein-coding
mm_58407.1	chr7	3249859	3249867	+	1	NA	promoter-TSS (NM_001033431)	promoter-TSS (NM_001033431)	-123	NM_001033431	378425	Mm.277152	NM_001033431	ENSMUSG00000078817	Nlrp12	Nalp12|PYPAF7	NLR family, pyrin domain containing 12	protein-coding
mm_159597.1	chr4	126753549	126753549	+	1	NA	promoter-TSS (NM_001035526)	promoter-TSS (NM_001035526)	-6	NM_001035525	100317	Mm.206206	NM_133886	ENSMUSG00000028830	AU040320	A730047D20Rik|AAVR|Kiaa0319l	expressed sequence AU040320	protein-coding
mm_159206.1	chr2	121413580	121413580	-	1	NA	promoter-TSS (NM_007952)	promoter-TSS (NM_007952)	212	NM_153075	212670	Mm.384318	NM_153075	ENSMUSG00000033486	Catsper2	-	cation channel, sperm associated 2	protein-coding
mm_55630.1	chr6	72314705	72314721	-	1	NA	TTS (NM_001282071)	TTS (NM_001282071)	10103	NM_147779	20388	Mm.46033	NM_147779	ENSMUSG00000056370	Sftpb	AI562151|SF-B|SP-B|Sftp-3|Sftp3	surfactant associated protein B	protein-coding
mm_2022.1	chr1	87128187	87128189	+	1	NA	TTS (NM_007432)	TTS (NM_007432)	3180	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_136893.1	chr17	13013182	13013202	+	1	NA	intron (NM_013671, intron 3 of 4)	intron (NM_013671, intron 3 of 4)	5353	NM_013671	20656	Mm.290876	NM_013671	ENSMUSG00000006818	Sod2	MnSOD|Sod-2	superoxide dismutase 2, mitochondrial	protein-coding
mm_171328.1	chr3	98339895	98339896	-	1	NA	promoter-TSS (NM_016966)	promoter-TSS (NM_016966)	74	NM_016966	236539	Mm.16898	NM_016966	ENSMUSG00000053398	Phgdh	3-PGDH|3PGDH|4930479N23|A10|PGAD|PGD|PGDH|SERA	3-phosphoglycerate dehydrogenase	protein-coding
mm_144333.1	chr18	13508382	13508400	+	1	NA	Intergenic	Intergenic	464342	NM_145492	225207	Mm.40325	NM_145492	ENSMUSG00000024420	Zfp521	B930086A16Rik|Evi3|Znf521	zinc finger protein 521	protein-coding
mm_150490.1	chr19	39007163	39007165	+	1	NA	exon (NM_028089, exon 1 of 9)	exon (NM_028089, exon 1 of 9)	145	NM_028089	72082	Mm.142581	NM_028089	ENSMUSG00000025002	Cyp2c55	2010318C06Rik	cytochrome P450, family 2, subfamily c, polypeptide 55	protein-coding
mm_100440.1	chr11	119486365	119486394	+	1	NA	Intergenic	Intergenic	-4968	NM_001164636	338371	Mm.271946	NM_177394	ENSMUSG00000039850	Endov	A730011L01Rik	endonuclease V	protein-coding
mm_81584.1	chr9	110422589	110422600	+	1	NA	3' UTR (NM_008694, exon 4 of 4)	3' UTR (NM_008694, exon 4 of 4)	2786	NM_008694	18054	Mm.236225	NM_008694	ENSMUSG00000032484	Ngp	bectenecin	neutrophilic granule protein	protein-coding
mm_137992.1	chr17	33637822	33637830	+	1	NA	promoter-TSS (NR_028279)	promoter-TSS (NR_028279)	-230	NM_001002842	378460	Mm.272606	NM_001002842	ENSMUSG00000032739	Pram1	AY665714	PML-RAR alpha-regulated adaptor molecule 1	protein-coding
mm_86608.1	chr10	13964627	13964647	+	1	NA	Intergenic	CpG	-1742	NM_010437	15273	Mm.42157	NM_010437	ENSMUSG00000015501	Hivep2	Gm20114|MIBP1|Schnurri-2|Shn-2	human immunodeficiency virus type I enhancer binding protein 2	protein-coding
mm_73583.1	chr8	109860263	109860281	+	1	NA	3' UTR (NM_009677, exon 24 of 24)	3' UTR (NM_009677, exon 24 of 24)	-8331	NM_001122594	244650	Mm.23494	NM_001122594	ENSMUSG00000031732	Phlpp2	AI481772|C130044A18Rik|Phlppl	PH domain and leucine rich repeat protein phosphatase 2	protein-coding
mm_59142.1	chr7	24270398	24270471	+	1	NA	promoter-TSS (NM_009567)	promoter-TSS (NM_009567)	16	NM_009567	22755	Mm.383535	NM_009567	ENSMUSG00000055305	Zfp93	Znf235	zinc finger protein 93	protein-coding
mm_42402.1	chr5	114968829	114968835	+	1	NA	intron (NM_009327, intron 1 of 9)	CT-rich|Low_complexity|Low_complexity	2230	NM_009327	21405	Mm.332607	NM_009327	ENSMUSG00000029556	Hnf1a	AI323641|HNF1|HNF1-alpha|HNF1[a]|Hnf-1|Hnf1alpha|LFB1|Tcf-1|Tcf1	HNF1 homeobox A	protein-coding
mm_87674.1	chr10	59016367	59016369	+	1	NA	intron (NM_172788, intron 3 of 9)	Lx8|LINE|L1	203009	NM_172788	237353	Mm.333078	NM_172788	ENSMUSG00000037990	Sh3rf3	4831416G18Rik|Igfbp5-ip|Sh3md4|Sh3rf31	SH3 domain containing ring finger 3	protein-coding
mm_114692.1	chr13	81783528	81783564	+	1	NA	intron (NM_007684, intron 1 of 4)	CpG	254	NM_007684	12626	Mm.12481	NM_007684	ENSMUSG00000021537	Cetn3	MmCEN3	centrin 3	protein-coding
mm_25484.1	chr3	109123177	109123196	+	1	NA	promoter-TSS (NM_172685)	promoter-TSS (NM_172685)	37	NM_172685	229731	Mm.33574	NM_172685	ENSMUSG00000040322	Slc25a24	2610016M12Rik	solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 24	protein-coding
mm_140761.1	chr17	17608210	17608212	-	1	NA	intron (NM_172827, intron 1 of 17)	intron (NM_172827, intron 1 of 17)	16278	NM_172827	240028	Mm.328807	NM_172827	ENSMUSG00000023845	Lnpep	2010309L07Rik|4732490P18Rik|CAP|IRAP|PLAP|gp160|vp165	leucyl/cystinyl aminopeptidase	protein-coding
mm_47780.1	chr5	131964725	131964731	-	1	NA	intron (NM_177047, intron 4 of 18)	intron (NM_177047, intron 4 of 18)	84459	NR_040704	75369	Mm.389696	NR_040704	ENSMUSG00000105773	4930563F08Rik	-	RIKEN cDNA 4930563F08 gene	ncRNA
mm_29835.1	chr3	129804123	129804140	-	1	NA	promoter-TSS (NM_001287224)	promoter-TSS (NM_001287224)	-101	NM_001287224	242235	Mm.302549	NM_001205102	ENSMUSG00000093865	Lrit3	Gm421	leucine-rich repeat, immunoglobulin-like and transmembrane domains 3	protein-coding
mm_126994.1	chr15	94629237	94629270	+	1	NA	promoter-TSS (NM_178789)	promoter-TSS (NM_178789)	68	NM_178789	320709	Mm.74873	NM_178789	ENSMUSG00000063296	Tmem117	B930062P21Rik	transmembrane protein 117	protein-coding
mm_31766.1	chr4	63544748	63544762	+	1	NA	promoter-TSS (NM_024173)	promoter-TSS (NM_024173)	-10	NM_024173	66290	Mm.371615	NM_024173	ENSMUSG00000039105	Atp6v1g1	1810024D14Rik|AA960677|ATP6J|Atp6g1|VAG1|Vma10	ATPase, H+ transporting, lysosomal V1 subunit G1	protein-coding
mm_153071.1	chr19	32242270	32242280	-	1	NA	intron (NM_001168525, intron 4 of 9)	intron (NM_001168525, intron 4 of 9)	-31262	NM_001168526	208449	Mm.329810	NM_144792	ENSMUSG00000040451	Sgms1	9530058O11Rik|AI841905|C80702|Mob|Sms1|Sor1|Tmem23	sphingomyelin synthase 1	protein-coding
mm_170087.1	chr17	35598687	35598687	-	1	NA	Intergenic	B1_Mus2|SINE|Alu	27950	NM_001244654	672682	Mm.454025	NM_001244654	ENSMUSG00000090588	Gm9573	Muc21	predicted gene 9573	protein-coding
mm_93907.1	chr10	126978532	126978569	-	1	NA	promoter-TSS (NM_001113470)	promoter-TSS (NM_001113470)	-167	NM_001113470	52468	Mm.29490	NM_146012	ENSMUSG00000078429	Ctdsp2	AI586070|D10Ertd73e|OS-4|OS4|SCP2	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 2	protein-coding
mm_125459.1	chr15	52295510	52295545	+	1	NA	promoter-TSS (NM_172816)	promoter-TSS (NM_172816)	-26	NM_172816	239436	Mm.208831	NM_172816	ENSMUSG00000022315	Slc30a8	C820002P14Rik|ZnT-8|ZnT8	solute carrier family 30 (zinc transporter), member 8	protein-coding
mm_24344.1	chr3	89799354	89799364	+	1	NA	Intergenic	RMER17B|LTR|ERVK	25750	NM_027315	70093	Mm.41438	NM_027315	ENSMUSG00000042572	Ube2q1	1110002C01Rik|2310012M18Rik|AI854014|Gtap|NICE-5|PRO3094|Ube2q	ubiquitin-conjugating enzyme E2Q family member 1	protein-coding
mm_122403.1	chr14	41004456	41004467	-	1	NA	intron (NM_001316735, intron 1 of 5)	intron (NM_001316735, intron 1 of 5)	2459	NM_001316739	70564	Mm.27227	NM_027464	ENSMUSG00000021792	Fam213a	5730469M10Rik|AU040822|Adrx|Pamm	family with sequence similarity 213, member A	protein-coding
mm_111580.1	chr12	101819065	101819078	-	1	NA	promoter-TSS (NM_011812)	promoter-TSS (NM_011812)	48	NM_011812	23876	Mm.288381	NM_011812	ENSMUSG00000021186	Fbln5	A55|DANCE|EVEC	fibulin 5	protein-coding
mm_88599.1	chr10	79793554	79793621	+	1	NA	promoter-TSS (NM_001161747)	promoter-TSS (NM_001161747)	15	NM_001161747	18483	Mm.34650	NM_023128	ENSMUSG00000035863	Palm	-	paralemmin	protein-coding
mm_52933.1	chr6	122933849	122933872	+	1	NA	exon (NM_199311, exon 6 of 6)	exon (NM_199311, exon 6 of 6)	12012	NM_199311	269799	Mm.297275	NM_199311	ENSMUSG00000049037	Clec4a1	BC049354|Dcir4	C-type lectin domain family 4, member a1	protein-coding
mm_75567.1	chr8	60503225	60503233	-	1	NA	Intergenic	L2c|LINE|L2	-2895	NM_011834	23923	Mm.35020	NM_011834	ENSMUSG00000057228	Aadat	AI875679|Aadt|KATII|Kat2|Kyat2|mKat-2	aminoadipate aminotransferase	protein-coding
mm_59128.1	chr7	19965366	19965420	+	1	NA	promoter-TSS (NM_027839)	promoter-TSS (NM_027839)	-19	NM_027839	71601	Mm.98097	NM_027839	ENSMUSG00000070777	Ceacam20	9130012D09Rik	carcinoembryonic antigen-related cell adhesion molecule 20	protein-coding
mm_96175.1	chr11	61617866	61617881	+	1	NA	Intergenic	MER53|DNA|hAT	-35448	NM_027817	71520	Mm.202760	NM_027817	ENSMUSG00000004837	Grap	8430435N19Rik|BB233594	GRB2-related adaptor protein	protein-coding
mm_18161.1	chr2	45098867	45098889	-	1	NA	intron (NM_001289521, intron 1 of 8)	intron (NM_001289521, intron 1 of 8)	11399	NM_001289521	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_6792.1	chr1	84144541	84144552	-	1	NA	intron (NM_001003948, intron 2 of 2)	MER2|DNA|TcMar-Tigger	74415	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_37185.1	chr4	117289436	117289455	-	1	NA	promoter-TSS (NM_001310731)	promoter-TSS (NM_001310731)	10	NM_001310730	66743	Mm.318331	NM_025739	ENSMUSG00000028677	Rnf220	4732477A13|4931406I20Rik|5730503K05Rik|AV302541	ring finger protein 220	protein-coding
mm_3563.1	chr1	150430628	150430641	+	1	NA	exon (NM_133780, exon 33 of 52)	exon (NM_133780, exon 33 of 52)	35531	NM_021400	96875	Mm.174256	NM_021400	ENSMUSG00000006014	Prg4	CACP|DOL54|JCAP|MSF|SZP|lubricin	proteoglycan 4 (megakaryocyte stimulating factor, articular superficial zone protein)	protein-coding
mm_153293.1	chr19	37413876	37413886	-	1	NA	intron (NM_010615, intron 19 of 21)	intron (NM_010615, intron 19 of 21)	-20960	NM_008245	15242	Mm.33896	NM_008245	ENSMUSG00000024986	Hhex	Hex|Hex1|Hhex-rs2|Prh|Prhx	hematopoietically expressed homeobox	protein-coding
mm_61688.1	chr7	81023840	81023862	+	1	NA	exon (NM_178707, exon 3 of 10)	exon (NM_178707, exon 3 of 10)	30167	NM_178707	233410	Mm.29525	NM_178707	ENSMUSG00000005621	Zfp592	8430405N24|A730014M16Rik|Znf592|mKIAA0211	zinc finger protein 592	protein-coding
mm_45966.1	chr5	90468513	90468536	-	1	NA	exon (NM_009654, exon 8 of 15)	exon (NM_009654, exon 8 of 15)	7654	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_11891.1	chr2	49744572	49744588	+	1	NA	intron (NM_008449, intron 20 of 25)	intron (NM_008449, intron 20 of 25)	-43106	NM_027990	71897	Mm.41381	NM_027990	ENSMUSG00000026765	Lypd6b	2310010M24Rik|AW049525	LY6/PLAUR domain containing 6B	protein-coding
mm_85476.1	chr9	105828087	105828100	-	1	NA	promoter-TSS (NM_001102607)	promoter-TSS (NM_001102607)	-8	NM_001102607	245026	Mm.482507	NM_172927	ENSMUSG00000043719	Col6a6	E330019B14|E330026B02Rik	collagen, type VI, alpha 6	protein-coding
mm_77382.1	chr8	120042762	120042768	-	1	NA	intron (NM_030209, intron 14 of 14)	ID_B1|SINE|B4	50327	NM_001310635	78892	Mm.264680	NM_030209	ENSMUSG00000031825	Crispld2	1810049K24Rik|Lcrisp2|Lgl1|coffeecrisp	cysteine-rich secretory protein LCCL domain containing 2	protein-coding
mm_116271.1	chr13	34652899	34652925	-	1	NA	promoter-TSS (NR_105041)	promoter-TSS (NR_105041)	-11	NR_105041	101056149	Mm.421309	NR_105041	ENSMUSG00000086786	Gm15908	OTTMUSG00000027716	predicted gene 15908	ncRNA
mm_44603.1	chr5	25100625	25100657	-	1	NA	promoter-TSS (NM_145401)	promoter-TSS (NM_145401)	1	NM_145401	108099	Mm.33649	NM_145401	ENSMUSG00000028944	Prkag2	2410051C13Rik|AAKG|AAKG2|AI854673|H91620p|WPWS	protein kinase, AMP-activated, gamma 2 non-catalytic subunit	protein-coding
mm_147275.1	chr18	39185105	39185111	-	1	NA	intron (NM_175164, intron 11 of 22)	intron (NM_175164, intron 11 of 22)	191963	NM_175164	71302	Mm.329396	NM_175164	ENSMUSG00000036452	Arhgap26	1810044B20Rik|2610010G17Rik|4933432P15Rik|AI853435|mKIAA0621	Rho GTPase activating protein 26	protein-coding
mm_35207.1	chr4	19570047	19570068	-	1	NA	promoter-TSS (NM_027769)	promoter-TSS (NM_027769)	47	NM_027769	70568	Mm.38390	NM_027769	ENSMUSG00000028228	Cpne3	5430428M23Rik|5730450C07Rik|C85108|CPN3	copine III	protein-coding
mm_15826.1	chr2	164643864	164643865	+	1	NA	Intergenic	Intergenic	-5062	NM_001012723	277345	Mm.247244	NM_001012723	ENSMUSG00000070530	Wfdc16	BC043944|WAP16	WAP four-disulfide core domain 16	protein-coding
mm_142876.1	chr17	51824792	51824802	-	1	NA	intron (NM_001163632, intron 1 of 10)	intron (NM_001163632, intron 1 of 10)	1791	NM_001163631	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_155485.1	chrX	73681667	73681680	+	1	NA	3' UTR (NM_001142809, exon 13 of 13)	3' UTR (NM_001142809, exon 13 of 13)	8540	NM_001142809	102857	Mm.274553	NM_133987	ENSMUSG00000019558	Slc6a8	AA589632|CRT|CRTR|CT1|CTR5|Creat	solute carrier family 6 (neurotransmitter transporter, creatine), member 8	protein-coding
mm_39507.1	chr5	21218417	21218423	+	1	NA	intron (NM_175437, intron 6 of 30)	intron (NM_175437, intron 6 of 30)	32153	NM_175437	212167	Mm.121705	NM_175437	ENSMUSG00000039934	Gsap	A530088I07Rik|Pion	gamma-secretase activating protein	protein-coding
mm_102232.1	chr11	54918652	54918683	-	1	NA	exon (NM_021327, exon 13 of 18)	exon (NM_021327, exon 13 of 18)	15813	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_63128.1	chr7	123001635	123001651	+	1	NA	exon (NM_011247, exon 18 of 18)	exon (NM_011247, exon 18 of 18)	31079	NM_175023	19647	Mm.4480	NM_011247	ENSMUSG00000030779	Rbbp6	4933422O15Rik|AI316869|BB233631|C030034J04Rik|C77662|P2P-R|PACT	retinoblastoma binding protein 6	protein-coding
mm_150586.1	chr19	40660652	40660664	+	1	NA	intron (NM_009848, intron 1 of 9)	intron (NM_009848, intron 1 of 9)	888	NM_009848	12495	Mm.2824	NM_009848	ENSMUSG00000048120	Entpd1	2610206B08Rik|AA408691|Cd39|NTPDase-1	ectonucleoside triphosphate diphosphohydrolase 1	protein-coding
mm_37859.1	chr4	132273756	132273758	-	1	NA	promoter-TSS (NM_025579)	promoter-TSS (NM_025579)	-618	NM_025579	66464	Mm.331926	NM_025579	ENSMUSG00000028899	Taf12	20kDa|2810422D08Rik|AW557038|Taf2J	TATA-box binding protein associated factor 12	protein-coding
mm_168981.1	chr12	92095074	92095086	-	1	NA	Intergenic	BGLII|LTR|ERVK	-245923	NM_011344	20338	Mm.250605	NM_011344	ENSMUSG00000020964	Sel1l	AW493766|Sel1h|mKIAA4137	sel-1 suppressor of lin-12-like (C. elegans)	protein-coding
mm_30513.1	chr3	158036631	158036647	-	1	NA	promoter-TSS (NM_001289525)	promoter-TSS (NM_001289525)	0	NM_001093752	69207	Mm.223946	NM_026989	ENSMUSG00000055436	Srsf11	0610009J05Rik|2610019N13Rik|BF642805|Sfrs11	serine/arginine-rich splicing factor 11	protein-coding
mm_32059.1	chr4	97777590	97777600	+	1	NA	promoter-TSS (NM_001122953)	promoter-TSS (NM_001122953)	-31	NM_001122953	18027	Mm.31274	NM_010905	ENSMUSG00000028565	Nfia	1110047K16Rik|9430022M17Rik|CTF|NF1-A|NF1A	nuclear factor I/A	protein-coding
mm_11184.1	chr2	28898796	28898800	+	1	NA	intron (NM_001033294, intron 19 of 19)	intron (NM_001033294, intron 19 of 19)	17623	NM_019446	54422	Mm.21390	NM_019446	ENSMUSG00000026805	Barhl1	Dres115|MBH2	BarH-like 1 (Drosophila)	protein-coding
mm_78048.1	chr9	14663071	14663078	+	1	NA	Intergenic	Intergenic	-48074	NM_001081395	75723	Mm.159552	NM_001081395	ENSMUSG00000013076	Amotl1	2310010G08Rik|2310067L22Rik|4932416D09Rik|JEAP|mFLJ00155	angiomotin-like 1	protein-coding
mm_159365.1	chr3	88334019	88334019	-	1	NA	intron (NM_024246, intron 1 of 3)	intron (NM_024246, intron 1 of 3)	414	NM_024246	71913	Mm.34256	NM_024246	ENSMUSG00000001420	Tmem79	2310042N02Rik|2310074C17Rik|Matt|ma	transmembrane protein 79	protein-coding
mm_94221.1	chr11	3202685	3202729	+	1	NA	promoter-TSS (NM_001166549)	promoter-TSS (NM_001166549)	124	NM_023743	74203	Mm.255649	NM_023743	ENSMUSG00000020454	Eif4enif1	2610509L04Rik|A930019J01Rik|AA410001|AU021239|Clast4|D11Ertd166e	eukaryotic translation initiation factor 4E nuclear import factor 1	protein-coding
mm_65505.1	chr7	25736956	25736960	-	1	NA	intron (NM_178089, intron 7 of 7)	B1_Mur1|SINE|Alu	17743	NM_178089	232989	Mm.254223	NM_144922	ENSMUSG00000040725	Hnrnpul1	E130317O14Rik|E1B-AP5|E1BAP5|Hnrnpul|Hnrpul1	heterogeneous nuclear ribonucleoprotein U-like 1	protein-coding
mm_107385.1	chr12	33147772	33147820	+	1	NA	promoter-TSS (NR_015602)	promoter-TSS (NR_015602)	110	NM_028139	380753	Mm.41540	NM_028139	ENSMUSG00000020564	Atxn7l1	2810423G08Rik|Atxn7l4	ataxin 7-like 1	protein-coding
mm_70894.1	chr8	25601467	25601477	+	1	NA	promoter-TSS (NM_001308482)	promoter-TSS (NM_001308482)	-129	NM_001308481	234135	Mm.217337	NM_001001735	ENSMUSG00000054823	Whsc1l1	6720429E03|A530023P05|AI528490|NSD3|WHISTLE	Wolf-Hirschhorn syndrome candidate 1-like 1 (human)	protein-coding
mm_166567.1	chr6	48988192	48988196	+	1	NA	exon (NM_172888, exon 1 of 5)	exon (NM_172888, exon 1 of 5)	1333	NM_172888	243377	Mm.446302	NM_172888	ENSMUSG00000039215	Svs1	9530003A11	seminal vesicle secretory protein 1	protein-coding
mm_49364.1	chr6	22999682	22999690	+	1	NA	exon (NM_001311064, exon 12 of 30)	exon (NM_001311064, exon 12 of 30)	124184	NM_001081306	19283	Mm.41639	NM_011219	ENSMUSG00000068748	Ptprz1	AI850339|DSD-1-PG|PTPbeta|PTPzeta|Ptprz|Ptpz|R-PTP-zeta|RPTPz|Rptpbeta	protein tyrosine phosphatase, receptor type Z, polypeptide 1	protein-coding
mm_127238.1	chr15	99579055	99579059	+	1	NA	promoter-TSS (NM_009699)	promoter-TSS (NM_009699)	1	NM_009699	11827	Mm.20206	NM_009699	ENSMUSG00000023013	Aqp2	AQP-CD|WCH-CD|cph|jpk	aquaporin 2	protein-coding
mm_13772.1	chr2	118663312	118663328	+	1	NA	promoter-TSS (NM_001033254)	promoter-TSS (NM_001033254)	-257	NM_001033254	214230	Mm.241857	NM_001033254	ENSMUSG00000074923	Pak6	4732456M09	p21 protein (Cdc42/Rac)-activated kinase 6	protein-coding
mm_11201.1	chr2	29125317	29125327	+	1	NA	5' UTR (NM_198033, exon 1 of 26)	5' UTR (NM_198033, exon 1 of 26)	330	NM_198033	269254	Mm.41867	NM_198033	ENSMUSG00000043535	Setx	A130090N03|A930037J23Rik|AOA2|AW060766|Als4|SCAR1|Sen1|mKIAA0625	senataxin	protein-coding
mm_68952.1	chr7	126564499	126564540	-	1	NA	exon (NM_146200, exon 4 of 21)	exon (NM_146200, exon 4 of 21)	1847	NM_146200	56347	Mm.22776	NM_146200	ENSMUSG00000030738	Eif3c	110kDa|3230401O13Rik|Eif3s8|NIPIL(A3)|NipilA3|Xs|Xsl	eukaryotic translation initiation factor 3, subunit C	protein-coding
mm_92127.1	chr10	64090179	64090192	-	1	NA	promoter-TSS (NM_178678)	promoter-TSS (NM_178678)	70	NM_178678	216028	Mm.431318	NM_178678	ENSMUSG00000042846	Lrrtm3	9630044H04Rik	leucine rich repeat transmembrane neuronal 3	protein-coding
mm_82470.1	chr9	16310352	16310372	-	1	NA	intron (NM_001080814, intron 1 of 24)	B4A|SINE|B4	67869	NM_001080814	270120	Mm.195010	NM_001080814	ENSMUSG00000074505	Fat3	9430076A06Rik|D430038H04Rik|Gm1132|Gm510|MFAT3F	FAT atypical cadherin 3	protein-coding
mm_97520.1	chr11	78500117	78500135	+	1	NA	exon (NM_011707, exon 4 of 8)	exon (NM_011707, exon 4 of 8)	1006	NM_011707	22370	Mm.3667	NM_011707	ENSMUSG00000017344	Vtn	AI256434|Vn	vitronectin	protein-coding
mm_63687.1	chr7	130574921	130574942	+	1	NA	Intergenic	Intergenic	-2553	NM_001004468	57752	Mm.86322	NM_021314	ENSMUSG00000030852	Tacc2	mKIAA4180	transforming, acidic coiled-coil containing protein 2	protein-coding
mm_143026.1	chr17	56584508	56584568	-	1	NA	promoter-TSS (NM_001163300)	promoter-TSS (NM_001163300)	45	NM_001029979	224902	Mm.214973	NM_001029979	ENSMUSG00000042625	Safb2	AA389433|AI255170|mKIAA0138	scaffold attachment factor B2	protein-coding
mm_165878.1	chr4	41138415	41138419	+	1	NA	intron (NM_026275, intron 1 of 4)	B1_Mus1|SINE|Alu	2396	NM_026275	67615	Mm.389540	NM_026275	ENSMUSG00000036241	Ube2r2	1200003M11Rik|Cdc34b|Ubc3b	ubiquitin-conjugating enzyme E2R 2	protein-coding
mm_6253.1	chr1	68966691	68966726	-	1	NA	intron (NM_010154, intron 1 of 26)	intron (NM_010154, intron 1 of 26)	141351	NM_010154	13869	Mm.442420	NM_010154	ENSMUSG00000062209	Erbb4	Her4|c-erbB-4	erb-b2 receptor tyrosine kinase 4	protein-coding
mm_37796.1	chr4	130520185	130520207	-	1	NA	Intergenic	Intergenic	53840	NM_025998	67149	Mm.423029	NM_025998	ENSMUSG00000078532	Nkain1	2610200G18Rik|2810426C15Rik	Na+/K+ transporting ATPase interacting 1	protein-coding
mm_2136.1	chr1	88070805	88070813	+	1	NA	promoter-TSS (NM_201644)	promoter-TSS (NM_201644)	30	NM_201644	394434	Mm.300095	NM_201644	ENSMUSG00000090175	Ugt1a9	UDPGT|UDPGT 1-9|UGT1-09|UGT1.9|UGTP4|Ugt1a12|mUGTBr/P	UDP glucuronosyltransferase 1 family, polypeptide A9	protein-coding
mm_145222.1	chr18	50056984	50056997	+	1	NA	intron (NM_134131, intron 1 of 1)	intron (NM_134131, intron 1 of 1)	3708	NM_134131	106869	Mm.27740	NM_134131	ENSMUSG00000062210	Tnfaip8	AA987150|E130304C20Rik|ENSMUSG00000073567|Gg2-1|Gm10539|Nded|Ssc-2|Tipe	tumor necrosis factor, alpha-induced protein 8	protein-coding
mm_133709.1	chr16	93368415	93368431	+	1	NA	Intergenic	Intergenic	-1297	NR_030429	791074		NR_030429	ENSMUSG00000076457	Mir802	Mirn802|mir-802|mmu-mir-802	microRNA 802	ncRNA
mm_170851.1	chr2	177897154	177897163	+	1	NA	promoter-TSS (NR_038101)	promoter-TSS (NR_038101)	-5	NR_038101	665205	Mm.440737	NR_038101		Gm14327	OTTMUSG00000016328	predicted gene 14327	pseudo
mm_115485.1	chr13	3610282	3610300	-	1	NA	intron (NM_134063, intron 1 of 19)	intron (NM_134063, intron 1 of 19)	817	NM_134063	105203	Mm.221609	NM_134063	ENSMUSG00000033799	Fam208b	AI645998|Pap20|mKIAA2006	family with sequence similarity 208, member B	protein-coding
mm_59950.1	chr7	30425800	30425810	+	1	NA	exon (NM_172142, exon 6 of 11)	exon (NM_172142, exon 6 of 11)	2501	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_145050.1	chr18	40256948	40256951	+	1	NA	promoter-TSS (NR_045177)	promoter-TSS (NR_045177)	-13	NR_045177	73001	Mm.428647	NR_045177	ENSMUSG00000071860	2900055J20Rik	-	RIKEN cDNA 2900055J20 gene	ncRNA
mm_105621.1	chr11	106789116	106789133	-	1	NA	promoter-TSS (NM_177088)	promoter-TSS (NM_177088)	-128	NM_177088	320162	Mm.30524	NM_177088	ENSMUSG00000018372	Cep95	4732496G21Rik|AI118346|AI448335|Ccdc45|D330027A14Rik|F630025I20Rik	centrosomal protein 95	protein-coding
mm_108567.1	chr12	84773322	84773335	+	1	NA	promoter-TSS (NM_028863)	promoter-TSS (NM_028863)	58	NM_028863	74316	Mm.25719	NM_028863	ENSMUSG00000021241	Isca2	0710001C05Rik|5730594E03Rik|Hbld1	iron-sulfur cluster assembly 2	protein-coding
mm_124879.1	chr15	10223975	10224034	+	1	NA	promoter-TSS (NM_001253781)	promoter-TSS (NM_001253781)	98	NM_001253781	19116	Mm.10516	NM_011169	ENSMUSG00000005268	Prlr	AI987712|Pr-1|Pr-3|Prlr-rs1	prolactin receptor	protein-coding
mm_128082.1	chr15	27681499	27681554	-	1	NA	promoter-TSS (NM_198301)	promoter-TSS (NM_198301)	16	NM_001242424	223433	Mm.266485	NM_198301	ENSMUSG00000056069	Fam105a	9830126M18	family with sequence similarity 105, member A	protein-coding
mm_12975.1	chr2	90775412	90775418	+	1	NA	intron (NM_018828, intron 12 of 16)	intron (NM_018828, intron 12 of 16)	-7329	NM_178755	271813	Mm.61146	NM_178755	ENSMUSG00000040812	Agbl2	4930524K04|A430081C19Rik|CCP2	ATP/GTP binding protein-like 2	protein-coding
mm_120919.1	chr14	76415350	76415374	+	1	NA	promoter-TSS (NM_207652)	promoter-TSS (NM_207652)	401	NM_001310646	21807	Mm.153272	NM_009366	ENSMUSG00000022010	Tsc22d1	AA589566|AW105905|Egr5|TSC-22|Tgfb1i4|Tsc|Tsc22	TSC22 domain family, member 1	protein-coding
mm_35889.1	chr4	49544880	49544908	-	1	NA	exon (NM_144903, exon 2 of 9)	exon (NM_144903, exon 2 of 9)	4652	NM_144903	230163	Mm.482116	NM_144903	ENSMUSG00000028307	Aldob	Aldo-2|Aldo2|BC016435	aldolase B, fructose-bisphosphate	protein-coding
mm_14050.1	chr2	122375695	122375721	+	1	NA	Intergenic	Intergenic	-6790	NM_001013829	435684	Mm.458215	NM_001013829	ENSMUSG00000033256	Shf	-	Src homology 2 domain containing F	protein-coding
mm_91838.1	chr10	57517238	57517250	-	1	NA	exon (NM_019760, exon 9 of 9)	exon (NM_019760, exon 9 of 9)	15285	NM_019760	56442	Mm.29344	NM_019760	ENSMUSG00000019877	Serinc1	1500011D18Rik|AI315070|AIGP-2|TMS-2|Tde1l|Tde2|Tms2|mKIAA1253	serine incorporator 1	protein-coding
mm_116102.1	chr13	28885289	28885320	-	1	NA	non-coding (NR_045054, exon 1 of 8)	non-coding (NR_045054, exon 1 of 8)	118	NR_045054	72518	Mm.37454	NR_045053		2610307P16Rik	AI666457	RIKEN cDNA 2610307P16 gene	ncRNA
mm_102642.1	chr11	62648564	62648591	-	1	NA	promoter-TSS (NM_175002)	promoter-TSS (NM_175002)	-54	NM_198861	192976	Mm.339972	NM_198861	ENSMUSG00000046417	Lrrc75a	Fam211a	leucine rich repeat containing 75A	protein-coding
mm_136167.1	chr16	88563150	88563164	-	1	NA	promoter-TSS (NM_018778)	promoter-TSS (NM_018778)	26	NM_018778	54420	Mm.25836	NM_018778	ENSMUSG00000050520	Cldn8	AI648025	claudin 8	protein-coding
mm_133684.1	chr16	92498114	92498118	+	1	NA	promoter-TSS (NM_172469)	promoter-TSS (NM_172469)	-31	NM_172469	209195	Mm.44747	NM_172469	ENSMUSG00000022949	Clic6	5730466J16Rik|AL022908|AW045520|CLIC1L	chloride intracellular channel 6	protein-coding
mm_37322.1	chr4	119404785	119404832	-	1	NA	intron (NM_029286, intron 1 of 14)	B2_Mm2|SINE|B2	10713	NM_001270435	73332	Mm.425204	NM_028506	ENSMUSG00000028637	Ccdc30	1700001O02Rik|1700041C02Rik|1700111D19Rik|4930445I03Rik	coiled-coil domain containing 30	protein-coding
mm_26716.1	chr3	158036695	158036728	+	1	NA	promoter-TSS (NM_001289525)	promoter-TSS (NM_001289525)	29	NM_001289524	67144	Mm.358704	NM_024194	ENSMUSG00000063052	Lrrc40	2610040E16Rik|AI837674	leucine rich repeat containing 40	protein-coding
mm_116117.1	chr13	28950341	28950351	-	1	NA	TTS (NM_009238)	TTS (NM_009238)	3336	NM_009238	20677	Mm.240627	NM_009238	ENSMUSG00000076431	Sox4	AA682046|Sox-4	SRY (sex determining region Y)-box 4	protein-coding
mm_64388.1	chr7	142481379	142481389	+	1	NA	intron (NM_001271523, intron 1 of 10)	intron (NM_001271523, intron 1 of 10)	4371	NM_001271523	16985	Mm.234003	NM_019391	ENSMUSG00000018819	Lsp1	Lsp-1|WP34|p50|pp52	lymphocyte specific 1	protein-coding
mm_130366.1	chr15	97791451	97791471	-	1	NA	3' UTR (NM_026353, exon 3 of 3)	3' UTR (NM_026353, exon 3 of 3)	7096	NM_026353	67739	Mm.28955	NM_026353	ENSMUSG00000081534	Slc48a1	4930570C03Rik	solute carrier family 48 (heme transporter), member 1	protein-coding
mm_162531.1	chr1	164949926	164949928	+	1	NA	Intergenic	Intergenic	-14417	NM_008510	16963	Mm.190	NM_008510	ENSMUSG00000026573	Xcl1	AI661682|ATAC|LTN|Lptn|SCM-1|SCM-1a|Scyc1	chemokine (C motif) ligand 1	protein-coding
mm_59432.1	chr7	27129830	27129863	+	1	NA	exon (NM_007817, exon 6 of 10)	exon (NM_007817, exon 6 of 10)	9891	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_2625.1	chr1	120621716	120621745	+	1	NA	Intergenic	Intergenic	19243	NM_010133	13798	Mm.2657	NM_010133	ENSMUSG00000058665	En1	En-1|Mo-en.1|engrailed-1	engrailed 1	protein-coding
mm_9174.1	chr1	171051822	171051864	-	1	NA	exon (NM_010188, exon 5 of 5)	exon (NM_010188, exon 5 of 5)	7560	NM_010188	14131	Mm.22119	NM_010188	ENSMUSG00000059498	Fcgr3	CD16	Fc receptor, IgG, low affinity III	protein-coding
mm_19200.1	chr2	84474591	84474600	-	1	NA	promoter-TSS (NM_011576)	promoter-TSS (NM_011576)	-421	NM_011576	21788	Mm.124316	NM_011576	ENSMUSG00000027082	Tfpi	A630013F22Rik|AW552122|EPI|LACI	tissue factor pathway inhibitor	protein-coding
mm_13715.1	chr2	117179366	117179380	+	1	NA	3' UTR (NM_033524, exon 7 of 7)	3' UTR (NM_033524, exon 7 of 7)	-5754	NR_030440	732489		NR_030440	ENSMUSG00000076376	Mir674	Mirn674|mir-674|mmu-mir-674	microRNA 674	ncRNA
mm_171738.1	chr4	95194602	95194602	+	1	NA	Intergenic	Intergenic	-142380	NM_010591	16476	Mm.275071	NM_010591	ENSMUSG00000052684	Jun	AP-1|Junc|c-jun	jun proto-oncogene	protein-coding
mm_143102.1	chr17	57081709	57081725	-	1	NA	exon (NM_009451, exon 4 of 4)	exon (NM_009451, exon 4 of 4)	-3207	NM_153551	70785	Mm.284447	NM_153551	ENSMUSG00000002668	Dennd1c	4432409M07Rik	DENN/MADD domain containing 1C	protein-coding
mm_151170.1	chr19	53251250	53251285	+	1	NA	intron (NR_036590, intron 1 of 2)	intron (NR_036590, intron 1 of 2)	3938	NR_036590	69319	Mm.57452	NR_036590		1700001K23Rik	-	RIKEN cDNA 1700001K23 gene	ncRNA
mm_89162.1	chr10	86124411	86124443	+	1	NA	intron (NM_013722, intron 7 of 13)	intron (NM_013722, intron 7 of 13)	28573	NR_038024	78170	Mm.444790	NR_038024		4930486F22Rik	-	RIKEN cDNA 4930486F22 gene	ncRNA
mm_129068.1	chr15	75664100	75664141	-	1	NA	exon (NM_028404, exon 11 of 14)	exon (NM_028404, exon 11 of 14)	14670	NM_028404	72960	Mm.182401	NM_028404	ENSMUSG00000000934	Top1mt	2900052H09Rik	DNA topoisomerase 1, mitochondrial	protein-coding
mm_173210.1	chrX	73026628	73026647	+	1	NA	intron (NM_009549, intron 17 of 18)	LSU-rRNA_Hsa|rRNA|rRNA	10466	NM_001100461	385377	Mm.327861	NM_001100461	ENSMUSG00000050424	Pnma5	mKIAA1934	paraneoplastic antigen family 5	protein-coding
mm_147756.1	chr18	61224331	61224336	-	1	NA	intron (NM_146086, intron 1 of 21)	intron (NM_146086, intron 1 of 21)	3834	NM_146086	225600	Mm.391106	NM_146086	ENSMUSG00000024575	Pde6a	Pdea|nmf282	phosphodiesterase 6A, cGMP-specific, rod, alpha	protein-coding
mm_140880.1	chr17	23829032	23829043	-	1	NA	promoter-TSS (NM_026305)	promoter-TSS (NM_026305)	72	NM_026305	67673	Mm.153758	NM_026305	ENSMUSG00000055839	Elob	0610040H15Rik|Tceb2	elongin B	protein-coding
mm_24463.1	chr3	90654110	90654123	+	1	NA	promoter-TSS (NM_199422)	promoter-TSS (NM_199422)	-186	NM_199422	381493	Mm.291525	NM_199422	ENSMUSG00000063767	S100a7a	AY465109|Gm1020|S100A7L1|S100A7f|S100a15|S100a15a|S100a17l1	S100 calcium binding protein A7A	protein-coding
mm_126774.1	chr15	86168468	86168510	+	1	NA	intron (NM_145475, intron 1 of 12)	intron (NM_145475, intron 1 of 12)	17652	NM_145475	223753	Mm.222685	NM_145475	ENSMUSG00000035891	Cerk	AI848610|D330016D08Rik|mKIAA1646	ceramide kinase	protein-coding
mm_130466.1	chr15	98609905	98609932	-	1	NA	Intergenic	CpG	-2285	NM_007405	11512	Mm.157091	NM_007405	ENSMUSG00000022994	Adcy6	AC6|mKIAA0422	adenylate cyclase 6	protein-coding
mm_25027.1	chr3	98146451	98146480	+	1	NA	exon (NM_010928, exon 34 of 34)	exon (NM_010928, exon 34 of 34)	-14169	NM_027665	71078	Mm.50711	NM_027665	ENSMUSG00000043468	Adam30	4933424D07Rik|svph4	a disintegrin and metallopeptidase domain 30	protein-coding
mm_146974.1	chr18	33464008	33464064	-	1	NA	promoter-TSS (NM_001267717)	promoter-TSS (NM_001267717)	-7	NM_001109988	27528	Mm.407415	NM_053078	ENSMUSG00000042834	Nrep	AI325076|D0H4S114|Harp|P311|PTZ17|SEZ17	neuronal regeneration related protein	protein-coding
mm_66013.1	chr7	30592942	30592954	-	1	NA	promoter-TSS (NM_021397)	promoter-TSS (NM_021397)	-6	NM_021397	58206	Mm.116789	NM_021397	ENSMUSG00000006310	Zbtb32	4930524C15Rik|FAXF|FAZF|PLZP|Rog|Tzfp	zinc finger and BTB domain containing 32	protein-coding
mm_56094.1	chr6	87379465	87379499	-	1	NA	TTS (NM_025467)	TTS (NM_025467)	6117	NM_025467	66284	Mm.46446	NM_025467	ENSMUSG00000030049	Gkn2	1810036H07Rik|Bricd1b	gastrokine 2	protein-coding
mm_80824.1	chr9	96782457	96782496	+	1	NA	Intergenic	Intergenic	16914	NR_102296	319707	Mm.392191	NR_102293	ENSMUSG00000101581	C430002N11Rik	-	RIKEN cDNA C430002N11 gene	ncRNA
mm_35163.1	chr4	14544215	14544231	-	1	NA	exon (NM_145947, exon 9 of 19)	exon (NM_145947, exon 9 of 19)	77555	NM_145947	208890	Mm.483839	NM_145947	ENSMUSG00000040569	Slc26a7	-	solute carrier family 26, member 7	protein-coding
mm_138250.1	chr17	34590057	34590104	+	1	NA	5' UTR (NM_134116, exon 1 of 4)	5' UTR (NM_134116, exon 1 of 4)	274	NM_134116	106512	Mm.26584	NM_134116	ENSMUSG00000034786	Gpsm3	AA960287|AGS4	G-protein signalling modulator 3 (AGS3-like, C. elegans)	protein-coding
mm_82928.1	chr9	35119191	35119212	-	1	NA	intron (NR_029475, intron 2 of 5)	intron (NR_029475, intron 2 of 5)	-2391	NM_009178	20443	Mm.275973	NM_009178	ENSMUSG00000032038	St3gal4	Siat4c	ST3 beta-galactoside alpha-2,3-sialyltransferase 4	protein-coding
mm_11325.1	chr2	30416188	30416221	+	1	NA	promoter-TSS (NM_007760)	promoter-TSS (NM_007760)	154	NM_138748	110854	Mm.275393	NM_138748	ENSMUSG00000039515	Ptpa	2610042B21Rik|C77440|N28142|PR53|Ppp2r4	protein phosphatase 2 protein activator	protein-coding
mm_19378.1	chr2	91195041	91195080	-	1	NA	promoter-TSS (NM_013839)	promoter-TSS (NM_013839)	-25	NM_013839	22259	Mm.22690	NM_013839	ENSMUSG00000002108	Nr1h3	AU018371|LXR|RLD1|Unr1	nuclear receptor subfamily 1, group H, member 3	protein-coding
mm_124208.1	chr14	99090157	99090168	-	1	NA	intron (NM_028315, intron 6 of 20)	intron (NM_028315, intron 6 of 20)	-9262	NM_029320	52023	Mm.22835	NM_029320	ENSMUSG00000022064	Pibf1	-	progesterone immunomodulatory binding factor 1	protein-coding
mm_157991.1	chrX	94537349	94537357	-	1	NA	exon (NM_019791, exon 10 of 13)	exon (NM_019791, exon 10 of 13)	4721	NM_019791	94275	Mm.27578	NM_019791	ENSMUSG00000025151	Maged1	2810433C11Rik|5430405L04Rik|DXBwg1492e|Dlixin|Dlxin-1|Dlxin1|MAGE-D1|NRAGE|mFLJ00163	melanoma antigen, family D, 1	protein-coding
mm_26850.1	chr3	14770207	14770247	-	1	NA	exon (NM_001083957, exon 5 of 7)	exon (NM_001083957, exon 5 of 7)	8233	NM_001083957	12346	Mm.273195	NM_009799	ENSMUSG00000027556	Car1	AW555628|Ca1|Car-1	carbonic anhydrase 1	protein-coding
mm_66979.1	chr7	63937685	63937711	-	1	NA	intron (NM_021366, intron 1 of 1)	CpG	1217	NM_021366	50794	Mm.240473	NM_021366	ENSMUSG00000052040	Klf13	0610043C13Rik|9430029L20Rik|Bteb3|FKLF-2|FKLF2|NSLP1|RFLAT-1|RFLAT1	Kruppel-like factor 13	protein-coding
mm_126301.1	chr15	79358441	79358453	+	1	NA	3' UTR (NM_001304830, exon 3 of 3)	3' UTR (NM_001304830, exon 3 of 3)	10045	NM_001304832	17133	Mm.86646	NM_010755	ENSMUSG00000042622	Maff	-	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein F (avian)	protein-coding
mm_129881.1	chr15	83464577	83464591	-	1	NA	promoter-TSS (NM_001159509)	promoter-TSS (NM_001159509)	22	NM_001159509	23970	Mm.23978	NM_011862	ENSMUSG00000016664	Pacsin2	AI197433	protein kinase C and casein kinase substrate in neurons 2	protein-coding
mm_132096.1	chr16	31297386	31297392	+	1	NA	exon (NM_007470, exon 6 of 6)	exon (NM_007470, exon 6 of 6)	17419	NM_001301353	11815	Mm.2082	NM_007470	ENSMUSG00000022548	Apod	-	apolipoprotein D	protein-coding
mm_130032.1	chr15	88977845	88977859	-	1	NA	exon (NM_133241, exon 2 of 12)	exon (NM_133241, exon 2 of 12)	701	NM_133241	170790	Mm.32780	NM_133241	ENSMUSG00000035805	Mlc1	AW048630|BB074274|Kiaa0027-hp|LVM|MLC|VL|WKL1|mKIAA0027	megalencephalic leukoencephalopathy with subcortical cysts 1 homolog (human)	protein-coding
mm_80838.1	chr9	97179154	97179163	+	1	NA	Intergenic	Intergenic	-68117	NM_138756	192287	Mm.228067	NM_138756	ENSMUSG00000032449	Slc25a36	C330005L02Rik	solute carrier family 25, member 36	protein-coding
mm_50894.1	chr6	56857732	56857740	+	1	NA	intron (NM_012056, intron 5 of 9)	(T)n|Simple_repeat|Simple_repeat	25677	NM_012056	27055	Mm.20943	NM_012056	ENSMUSG00000029781	Fkbp9	1810014L23|AW549641|FKBP-63|FKBP-9|FKBP60|FKBP63|FKBP65RS	FK506 binding protein 9	protein-coding
mm_40655.1	chr5	65131110	65131158	+	1	NA	promoter-TSS (NM_175174)	promoter-TSS (NM_175174)	-97	NM_175174	71778	Mm.10281	NM_175174	ENSMUSG00000054920	Klhl5	1300013C10Rik	kelch-like 5	protein-coding
mm_161713.1	chr17	25222721	25222721	+	1	NA	exon (NM_028789, exon 1 of 5)	exon (NM_028789, exon 1 of 5)	139	NM_028789	74154	Mm.267353	NM_028789	ENSMUSG00000015127	Unkl	1300004G08Rik	unkempt family like zinc finger	protein-coding
mm_165186.1	chr2	29890006	29890016	+	1	NA	promoter-TSS (NM_013615)	promoter-TSS (NM_013615)	-52	NM_013615	18286	Mm.330116	NM_013615	ENSMUSG00000026790	Odf2	AI848335|MMTEST29	outer dense fiber of sperm tails 2	protein-coding
mm_123130.1	chr14	56262173	56262187	-	1	NA	5' UTR (NM_013542, exon 1 of 5)	5' UTR (NM_013542, exon 1 of 5)	154	NM_013542	14939	Mm.14874	NM_013542	ENSMUSG00000015437	Gzmb	AI553453|CCP-1/C11|CCP1|Ctla-1|Ctla1|GZB	granzyme B	protein-coding
mm_53001.1	chr6	123270298	123270336	+	1	NA	exon (NM_010819, exon 5 of 6)	exon (NM_010819, exon 5 of 6)	8210	NM_010819	17474	Mm.441101	NM_010819	ENSMUSG00000030144	Clec4d	Clecsf8|Mpcl|mcl	C-type lectin domain family 4, member d	protein-coding
mm_40664.1	chr5	65348476	65348502	+	1	NA	promoter-TSS (NM_031180)	promoter-TSS (NM_031180)	78	NM_031180	83379	Mm.45274	NM_031180	ENSMUSG00000029195	Klb	AV071179|betaKlotho	klotho beta	protein-coding
mm_45854.1	chr5	87784584	87784598	-	1	NA	intron (NM_007785, intron 10 of 13)	intron (NM_007785, intron 10 of 13)	10141	NM_007785	12993	Mm.4908	NM_007785	ENSMUSG00000061937	Csn1s2a	Csng|PP22	casein alpha s2-like A	protein-coding
mm_10430.1	chr2	14073630	14073672	+	1	NA	promoter-TSS (NM_011484)	promoter-TSS (NM_011484)	283	NR_038162	70957	Mm.399049	NR_038162	ENSMUSG00000086657	Stamos	4921530L18Rik	signal transducing adaptor molecule (SH3 domain and ITAM motif) 1, opposite strand	ncRNA
mm_143527.1	chr17	73901813	73901824	-	1	NA	intron (NM_011723, intron 24 of 35)	intron (NM_011723, intron 24 of 35)	48378	NM_011723	22436	Mm.11223	NM_011723	ENSMUSG00000024066	Xdh	XO|Xor|Xox-1|Xox1	xanthine dehydrogenase	protein-coding
mm_75008.1	chr8	27296284	27296297	-	1	NA	non-coding (NR_003107, exon 1 of 1)	non-coding (NR_003107, exon 1 of 1)	245	NR_003107	732482	Mm.463248	NR_003107		Gm9731	-	Fam58a pseudogene	pseudo
mm_88078.1	chr10	67979738	67979760	+	1	NA	5' UTR (NM_001081346, exon 1 of 13)	5' UTR (NM_001081346, exon 1 of 13)	151	NM_001081346	170799	Mm.209844	NM_133244	ENSMUSG00000037846	Rtkn2	B130039D23Rik|Mbf|Plekhk1	rhotekin 2	protein-coding
mm_28178.1	chr3	88000404	88000420	-	1	NA	promoter-TSS (NM_001109758)	promoter-TSS (NM_001109758)	-56	NM_001109758	12032	Mm.4598	NM_007529	ENSMUSG00000004892	Bcan	Cspg7	brevican	protein-coding
mm_36713.1	chr4	98023063	98023101	-	1	NA	intron (NM_001122953, intron 6 of 9)	intron (NM_001122953, intron 6 of 9)	245456	NM_010905	18027	Mm.31274	NM_010905	ENSMUSG00000028565	Nfia	1110047K16Rik|9430022M17Rik|CTF|NF1-A|NF1A	nuclear factor I/A	protein-coding
mm_11807.1	chr2	43917269	43917272	+	1	NA	intron (NM_001301832, intron 7 of 14)	intron (NM_001301832, intron 7 of 14)	148054	NR_040622	320872	Mm.445023	NR_040622	ENSMUSG00000085089	Arhgap15os	A430092G05Rik	Rho GTPase activating protein 15, opposite strand	ncRNA
mm_5498.1	chr1	36985771	36985779	-	1	NA	Intergenic	Intergenic	-46248	NM_018872	56030	Mm.186943	NM_018872	ENSMUSG00000026116	Tmem131	2610524E03Rik|CC28|D1Bwg0491e|Neg|RW1|YR-23|mKIAA0257	transmembrane protein 131	protein-coding
mm_9070.1	chr1	168323273	168323276	-	1	NA	intron (NM_008783, intron 2 of 7)	intron (NM_008783, intron 2 of 7)	108895	NM_001291508	18514	Mm.43358	NM_008783	ENSMUSG00000052534	Pbx1	2310056B04Rik|D230003C07Rik|Pbx-1	pre B cell leukemia homeobox 1	protein-coding
mm_2434.1	chr1	96872260	96872297	+	1	NA	promoter-TSS (NM_172658)	promoter-TSS (NM_172658)	-107	NM_172658	227394	Mm.11662	NM_172658	ENSMUSG00000040693	Slco4c1	9530051F04|C330017E21Rik|OATP-H|OATP-M1|OATP4C1|OATPX|PRO2176|SLC21A20|oatp-R	solute carrier organic anion transporter family, member 4C1	protein-coding
mm_91920.1	chr10	60299963	60299998	-	1	NA	exon (NM_011179, exon 11 of 15)	exon (NM_011179, exon 11 of 15)	15519	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_81619.1	chr9	110798161	110798177	+	1	NA	promoter-TSS (NM_153099)	promoter-TSS (NM_153099)	-16	NM_153099	235628	Mm.292285	NM_153099	ENSMUSG00000044664	Prss42	Tessp2	protease, serine 42	protein-coding
mm_17537.1	chr2	29772223	29772233	-	1	NA	Intergenic	Intergenic	10700	NM_001177392	433416	Mm.330112	NM_001034887	ENSMUSG00000075425	Gm13547	OTTMUSG00000012686	predicted gene 13547	protein-coding
mm_14742.1	chr2	144369035	144369046	+	1	NA	promoter-TSS (NM_001166640)	promoter-TSS (NM_001166640)	5	NM_181417	228714	Mm.227925	NM_181417	ENSMUSG00000027425	Csrp2bp	2510008M08Rik|ATAC2|AU023459|D2Ertd473e|D2Wsu131e|E430020F17|Kat14	cysteine and glycine-rich protein 2 binding protein	protein-coding
mm_141478.1	chr17	31144272	31144288	-	1	NA	promoter-TSS (NM_009363)	promoter-TSS (NM_009363)	2	NM_009363	21785	Mm.1825	NM_009363	ENSMUSG00000024028	Tff2	SP|mSP	trefoil factor 2 (spasmolytic protein 1)	protein-coding
mm_51459.1	chr6	82052317	82052330	+	1	NA	intron (NM_145570, intron 1 of 2)	intron (NM_145570, intron 1 of 2)	10695	NM_145570	232146	Mm.489683	NM_145570	ENSMUSG00000035104	Eva1a	BC014699|Fam176a|Tmem166	eva-1 homolog A (C. elegans)	protein-coding
mm_100830.1	chr11	5421563	5421566	-	1	NA	intron (NM_001080924, intron 1 of 8)	intron (NM_001080924, intron 1 of 8)	23283	NM_001080924	407821	Mm.216313	NM_001080924	ENSMUSG00000041961	Znrf3	Gm1167	zinc and ring finger 3	protein-coding
mm_84462.1	chr9	66592818	66592826	-	1	NA	exon (NM_144937, exon 1 of 15)	exon (NM_144937, exon 1 of 15)	293	NM_144937	235441	Mm.32465	NM_144937	ENSMUSG00000032376	Usp3	AA409661|BC017156	ubiquitin specific peptidase 3	protein-coding
mm_41822.1	chr5	104046533	104046561	+	1	NA	promoter-TSS (NM_028794)	promoter-TSS (NM_028794)	-317	NM_028794	74167	Mm.241484	NM_028794	ENSMUSG00000029310	Nudt9	1190002C07Rik|ADPR-PPase|AI462474	nudix (nucleoside diphosphate linked moiety X)-type motif 9	protein-coding
mm_40365.1	chr5	48401018	48401024	+	1	NA	intron (NM_001199242, intron 4 of 7)	intron (NM_001199242, intron 4 of 7)	5448	NR_045500	70592	Mm.437183	NR_045500	ENSMUSG00000029089	5730480H06Rik	-	RIKEN cDNA 5730480H06 gene	ncRNA
mm_126031.1	chr15	76722907	76722955	+	1	NA	promoter-TSS (NM_198119)	promoter-TSS (NM_198119)	-758	NM_198119	378937	Mm.289666	NM_198119	ENSMUSG00000033707	Lrrc24	6430402H13Rik	leucine rich repeat containing 24	protein-coding
mm_724.1	chr1	42952950	42952983	+	1	NA	promoter-TSS (NM_053107)	promoter-TSS (NM_053107)	94	NM_053107	93690	Mm.444976	NM_053107	ENSMUSG00000041907	Gpr45	9230112G11Rik|AW046772	G protein-coupled receptor 45	protein-coding
mm_114609.1	chr13	75840003	75840044	+	1	NA	exon (NM_053108, exon 1 of 3)	exon (NM_053108, exon 1 of 3)	137	NM_053108	93692	Mm.25844	NM_053108	ENSMUSG00000021591	Glrx	C86710|D13Wsu156e|Glrx1|Grx1|TTase	glutaredoxin	protein-coding
mm_30644.1	chr4	8837711	8837722	+	1	NA	intron (NM_001277149, intron 15 of 37)	intron (NM_001277149, intron 15 of 37)	147310	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_116548.1	chr13	45971305	45971313	-	1	NA	Intergenic	Intergenic	-6318	NM_009124	20238	Mm.342683	NM_009124	ENSMUSG00000046876	Atxn1	2900016G23Rik|Atx1|C85907|ENSMUSG00000074917|Gm10786|Sca1	ataxin 1	protein-coding
mm_73378.1	chr8	105636591	105636612	+	1	NA	promoter-TSS (NM_181322)	promoter-TSS (NM_181322)	63	NM_181322	13018	Mm.269474	NM_181322	ENSMUSG00000005698	Ctcf	AW108038	CCCTC-binding factor	protein-coding
mm_146366.1	chr18	82584550	82584562	+	1	NA	3' UTR (NM_010777, exon 7 of 7)	3' UTR (NM_010777, exon 7 of 7)	30048	NM_001025254	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_26858.1	chr3	14864058	14864071	-	1	NA	intron (NM_007606, intron 1 of 6)	intron (NM_007606, intron 1 of 6)	526	NM_007606	12350	Mm.300	NM_007606	ENSMUSG00000027559	Car3	BB219044|Ca3|Car-3	carbonic anhydrase 3	protein-coding
mm_131729.1	chr16	21855111	21855126	+	1	NA	Intergenic	B4A|SINE|B4	-36851	NM_172821	71751	Mm.420837	NM_172821	ENSMUSG00000033618	Map3k13	C130026N12Rik|LZK	mitogen-activated protein kinase kinase kinase 13	protein-coding
mm_59107.1	chr7	19796919	19796933	+	1	NA	promoter-TSS (NM_023224)	promoter-TSS (NM_023224)	-117	NM_023224	80794	Mm.81698	NM_023224	ENSMUSG00000040525	Cblc	2310076I21Rik|2310079L19Rik|Cbl3	Casitas B-lineage lymphoma c	protein-coding
mm_82203.1	chr9	124102041	124102048	+	1	NA	promoter-TSS (NM_009915)	promoter-TSS (NM_009915)	-139	NM_009915	12772	Mm.6272	NM_009915	ENSMUSG00000049103	Ccr2	Cc-ckr-2|Ccr2a|Ccr2b|Ckr2|Ckr2a|Ckr2b|Cmkbr2|mJe-r	chemokine (C-C motif) receptor 2	protein-coding
mm_21202.1	chr2	155553085	155553090	-	1	NA	intron (NR_040613, intron 2 of 3)	intron (NR_040613, intron 2 of 3)	3843	NR_040613	74945	Mm.401956	NR_040613	ENSMUSG00000086529	Acss2os	4930471I20Rik	acyl-CoA synthetase short-chain family member 2, opposite strand	ncRNA
mm_72093.1	chr8	71580529	71580565	+	1	NA	intron (NM_011977, intron 6 of 13)	intron (NM_011977, intron 6 of 13)	11620	NM_011977	26457	Mm.38165	NM_011977	ENSMUSG00000031808	Slc27a1	FATP1|Fatp	solute carrier family 27 (fatty acid transporter), member 1	protein-coding
mm_112886.1	chr13	20859684	20859692	+	1	NA	intron (NM_012054, intron 4 of 20)	intron (NM_012054, intron 4 of 20)	65575	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_78583.1	chr9	37348444	37348502	+	1	NA	promoter-TSS (NM_001081429)	promoter-TSS (NM_001081429)	-81	NM_001081429	245902	Mm.390150	NM_001081429	ENSMUSG00000034303	Ccdc15	A630039F14Rik|D030074L19	coiled-coil domain containing 15	protein-coding
mm_64187.1	chr7	141460923	141460951	+	1	NA	promoter-TSS (NM_001025103)	promoter-TSS (NM_001025103)	-157	NM_001025103	213573	Mm.386851	NM_001025103	ENSMUSG00000048200	Cracr2b	6330520A15Rik|BC026645|Cracr2a|Efcab4|Efcab4a	calcium release activated channel regulator 2B	protein-coding
mm_4624.1	chr1	179546384	179546405	+	1	NA	promoter-TSS (NM_146105)	promoter-TSS (NM_146105)	-118	NM_001331054	15278	Mm.293529	NM_008249	ENSMUSG00000026492	Tfb2m	Hkp1	transcription factor B2, mitochondrial	protein-coding
mm_131589.1	chr16	18776101	18776139	+	1	NA	promoter-TSS (NM_013805)	promoter-TSS (NM_013805)	-727	NM_013805	12741	Mm.22768	NM_013805	ENSMUSG00000041378	Cldn5	AI854493|MBEC1|Tmvcf	claudin 5	protein-coding
mm_164941.1	chr19	3570685	3570685	+	1	NA	intron (NM_029456, intron 1 of 22)	RSINE1|SINE|B4	5064	NM_001164159	52036	Mm.284686	NM_028999	ENSMUSG00000024908	Ppp6r3	4930528G08Rik|9130026N02Rik|D19Bwg1430e|D19Ertd703e|Pp6r3|Ppcs3|Pptcs3|Sapl|Saps3|mKIAA1558	protein phosphatase 6, regulatory subunit 3	protein-coding
mm_158157.1	chrX	103480694	103480769	-	1	NA	non-coding (NR_001570, exon 1 of 8)	non-coding (NR_001570, exon 1 of 8)	2502	NR_001570	213742	Mm.274770	NR_001463	ENSMUSG00000086503	Xist	A430022B11|AI314753	inactive X specific transcripts	ncRNA
mm_124387.1	chr14	108914165	108914183	-	1	NA	promoter-TSS (NM_199065)	promoter-TSS (NM_199065)	65	NM_199065	76965	Mm.257268	NM_199065	ENSMUSG00000075478	Slitrk1	3200001I04Rik	SLIT and NTRK-like family, member 1	protein-coding
mm_158116.1	chrX	102250779	102250797	-	1	NA	promoter-TSS (NM_001276474)	promoter-TSS (NM_001276474)	-12	NM_001276474	12705	Mm.2390	NM_007709	ENSMUSG00000051159	Cited1	AI316840|AU019144|Msg1	Cbp/p300-interacting transactivator with Glu/Asp-rich carboxy-terminal domain 1	protein-coding
mm_155287.1	chrX	61183458	61183466	+	1	NA	3' UTR (NM_001166658, exon 1 of 1)	3' UTR (NM_001166658, exon 1 of 1)	2096	NM_001166658	631990	Mm.401324	NM_001166658	ENSMUSG00000090546	Cdr1	100039759|Cdr|Cdr34|EG631990|Gm2409|Gm7077	cerebellar degeneration related antigen 1	protein-coding
mm_98551.1	chr11	95057100	95057119	+	1	NA	exon (NM_001306162, exon 15 of 26)	exon (NM_001306162, exon 15 of 26)	12089	NM_001306071	16400	Mm.57035	NM_013565	ENSMUSG00000001507	Itga3	AA407068|CD49C|GAPB3	integrin alpha 3	protein-coding
mm_11379.1	chr2	31245802	31245900	+	1	NA	promoter-TSS (NM_019681)	promoter-TSS (NM_019681)	-72	NM_019681	14299	Mm.249318	NM_019681	ENSMUSG00000062661	Ncs1	9430075O15Rik|A730032G13Rik|AI836659|Freq|Mfreq|NCS-1	neuronal calcium sensor 1	protein-coding
mm_138153.1	chr17	34211973	34211994	+	1	NA	exon (NM_011530, exon 6 of 12)	exon (NM_011530, exon 6 of 12)	7504	NM_011530	21355	Mm.14814	NM_011530	ENSMUSG00000024339	Tap2	ABC18|AI462429|APT2|Abcb3|Ham-2|Ham2|MTP2|PSF2|RING11|Tap-2|Y1|jas	transporter 2, ATP-binding cassette, sub-family B (MDR/TAP)	protein-coding
mm_40182.1	chr5	36204037	36204043	+	1	NA	promoter-TSS (NM_175249)	promoter-TSS (NM_175249)	19	NM_175249	76943	Mm.44242	NM_175249	ENSMUSG00000043430	Psapl1	2310020A21Rik	prosaposin-like 1	protein-coding
mm_36710.1	chr4	97584664	97584677	-	1	NA	promoter-TSS (NR_015513)	promoter-TSS (NR_015513)	-79	NR_015513	319865	Mm.373807	NM_177023		E130114P18Rik	-	RIKEN cDNA E130114P18 gene	ncRNA
mm_45853.1	chr5	87781862	87781895	-	1	NA	exon (NM_001304768, exon 8 of 13)	exon (NM_001304768, exon 8 of 13)	7428	NM_007785	12993	Mm.4908	NM_007785	ENSMUSG00000061937	Csn1s2a	Csng|PP22	casein alpha s2-like A	protein-coding
mm_171637.1	chr4	23100947	23100949	-	1	NA	Intergenic	L1Md_T|LINE|L1	610400	NR_131335	105500046		NR_131335	ENSMUSG00000107859	Gm30731	Pnky|lnc-pou3f2	predicted gene, 30731	ncRNA
mm_164549.1	chr17	13010264	13010266	+	1	NA	intron (NM_013671, intron 2 of 4)	intron (NM_013671, intron 2 of 4)	2426	NM_013671	20656	Mm.290876	NM_013671	ENSMUSG00000006818	Sod2	MnSOD|Sod-2	superoxide dismutase 2, mitochondrial	protein-coding
mm_168472.1	chr11	48753600	48753601	-	1	NA	Intergenic	Intergenic	-46760	NM_008143	14694	Mm.5305	NM_008143	ENSMUSG00000020372	Rack1	AL033335|GB-like|Gnb2-rs1|Gnb2l1|p205	receptor for activated C kinase 1	protein-coding
mm_59787.1	chr7	28895238	28895257	+	1	NA	intron (NM_021895, intron 19 of 20)	intron (NM_021895, intron 19 of 20)	13591	NM_001110807	60594	Mm.476990	NM_021894	ENSMUSG00000054083	Capn12	CANP 12	calpain 12	protein-coding
mm_124470.1	chr14	121370498	121370501	-	1	NA	intron (NM_145465, intron 1 of 10)	HAL1|LINE|L1	8731	NM_145465	223255	Mm.390756	NM_145465	ENSMUSG00000063410	Stk24	1810013H02Rik|C76483|MST-3|Mst3|STE20	serine/threonine kinase 24	protein-coding
mm_37553.1	chr4	126058409	126058436	-	1	NA	promoter-TSS (NM_172701)	promoter-TSS (NM_172701)	-143	NM_172701	230751	Mm.38907	NM_172701	ENSMUSG00000042616	Oscp1	1810007P19Rik|5730415O04|6030436A01Rik	organic solute carrier partner 1	protein-coding
mm_20107.1	chr2	121116439	121116447	-	1	NA	Intergenic	Intergenic	-6652	NM_001160424	640543	Mm.478785	NM_001160424	ENSMUSG00000079103	Tgm7	TGMZ|TGz	transglutaminase 7	protein-coding
mm_100302.1	chr11	117849287	117849340	+	1	NA	promoter-TSS (NM_009689)	promoter-TSS (NM_009689)	76	NM_009689	11799	Mm.8552	NM_009689	ENSMUSG00000017716	Birc5	AAC-11|Api4|TIAP|survivin40	baculoviral IAP repeat-containing 5	protein-coding
mm_61726.1	chr7	81859148	81859152	+	1	NA	non-coding (NR_111910, exon 1 of 8)	non-coding (NR_111910, exon 1 of 8)	149	NM_145375	107769	Mm.221412	NM_145375	ENSMUSG00000038623	Tm6sf1	AI428514|BC023123|C630016D09Rik	transmembrane 6 superfamily member 1	protein-coding
mm_149730.1	chr19	21840256	21840260	+	1	NA	intron (NM_001033759, intron 18 of 23)	intron (NM_001033759, intron 18 of 23)	61918	NM_031997	83921	Mm.329776	NM_031997	ENSMUSG00000024754	Tmem2	-	transmembrane protein 2	protein-coding
mm_156656.1	chrX	157702950	157702964	+	1	NA	non-coding (NR_103722, exon 2 of 6)	non-coding (NR_103722, exon 2 of 6)	3984	NR_103722	66106	Mm.140340	NM_025357	ENSMUSG00000041476	Smpx	1010001C09Rik|Csl	small muscle protein, X-linked	protein-coding
mm_75611.1	chr8	62123145	62123155	-	1	NA	promoter-TSS (NM_001136089)	promoter-TSS (NM_001136089)	43	NM_001136089	26359	Mm.42179	NM_011922	ENSMUSG00000031635	Anxa10	-	annexin A10	protein-coding
mm_151191.1	chr19	53529101	53529105	+	1	NA	promoter-TSS (NM_001085390)	promoter-TSS (NM_001085390)	-215	NM_001085390	240672	Mm.482424	NM_001085390	ENSMUSG00000034765	Dusp5	Gm337	dual specificity phosphatase 5	protein-coding
mm_172604.1	chr8	15519974	15519974	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	462321	NM_008664	17930	Mm.272115	NM_008664	ENSMUSG00000031461	Myom2	AW146149	myomesin 2	protein-coding
mm_156651.1	chrX	157702792	157702827	+	1	NA	intron (NR_045569, intron 1 of 6)	intron (NR_045569, intron 1 of 6)	3836	NR_103722	66106	Mm.140340	NM_025357	ENSMUSG00000041476	Smpx	1010001C09Rik|Csl	small muscle protein, X-linked	protein-coding
mm_58129.1	chr6	140613928	140613933	-	1	NA	Intergenic	RMER15|LTR|ERVL	-8733	NM_178803	11569	Mm.86453	NM_009637	ENSMUSG00000030232	Aebp2	AU023766|B230313N05Rik	AE binding protein 2	protein-coding
mm_2296.1	chr1	91494597	91494624	+	1	NA	promoter-TSS (NM_028718)	promoter-TSS (NM_028718)	-58	NM_028718	74019	Mm.318430	NM_028718	ENSMUSG00000034292	Traf3ip1	3930402D05Rik|AU041749|MIP-T3	TRAF3 interacting protein 1	protein-coding
mm_87225.1	chr10	40433890	40433900	+	1	NA	intron (NM_198164, intron 2 of 11)	ORR1F|LTR|ERVL-MaLR	84587	NM_001291816	78334	Mm.200924	NM_198164	ENSMUSG00000038481	Cdk19	2700084L06Rik|AI845279|AW228747|CDK11|Cdc2l6|mKIAA1028	cyclin-dependent kinase 19	protein-coding
mm_100456.1	chr11	119729579	119729592	+	1	NA	intron (NM_028898, intron 4 of 33)	intron (NM_028898, intron 4 of 33)	104780	NR_045313	319454	Mm.442144	NR_045312	ENSMUSG00000085081	Rptoros	A430071A18Rik	regulatory associated protein of MTOR, complex 1, opposite strand	ncRNA
mm_82105.1	chr9	123067410	123067419	+	1	NA	3' UTR (NM_177911, exon 14 of 14)	3' UTR (NM_177911, exon 14 of 14)	32673	NM_177911	331046	Mm.195309	NM_177911	ENSMUSG00000025787	Tgm4	9530008N10Rik|Eapa1|TGP	transglutaminase 4 (prostate)	protein-coding
mm_149305.1	chr19	10732315	10732325	+	1	NA	intron (NM_007650, intron 1 of 10)	intron (NM_007650, intron 1 of 10)	6654	NM_007650	12507	Mm.779	NM_007650	ENSMUSG00000024669	Cd5	Ly-1|Ly-12|Ly-A|Lyt-1	CD5 antigen	protein-coding
mm_58421.1	chr7	3293074	3293122	+	1	NA	promoter-TSS (NM_001093766)	promoter-TSS (NM_001093766)	70	NM_001093766	50918	Mm.29874	NM_016969	ENSMUSG00000068566	Myadm	D7Wsu62e	myeloid-associated differentiation marker	protein-coding
mm_47514.1	chr5	124079073	124079083	-	1	NA	intron (NM_019875, intron 6 of 11)	intron (NM_019875, intron 6 of 11)	16720	NM_019875	56325	Mm.254839	NM_019875	ENSMUSG00000029408	Abcb9	TAPL|mKIAA1520	ATP-binding cassette, sub-family B (MDR/TAP), member 9	protein-coding
mm_80165.1	chr9	71293653	71293658	+	1	NA	exon (NM_009022, exon 13 of 14)	exon (NM_009022, exon 13 of 14)	77866	NM_009022	19378	Mm.42016	NM_009022	ENSMUSG00000013584	Aldh1a2	AV116159|Aldh1a7|Raldh1|Raldh2	aldehyde dehydrogenase family 1, subfamily A2	protein-coding
mm_44754.1	chr5	31295863	31295942	-	1	NA	promoter-TSS (NM_022424)	promoter-TSS (NM_022424)	-25	NM_022424	64339	Mm.292544	NM_022424	ENSMUSG00000038552	Fndc4	2810430J06Rik|6330410H20Rik|AB030187|AI838506|AW487863|FRCP1|Fnmp1	fibronectin type III domain containing 4	protein-coding
mm_168346.1	chr11	121925299	121925306	-	1	NA	Intergenic	Intergenic	95084	NM_029049	74675	Mm.61213	NM_029049	ENSMUSG00000039198	Ptchd3	4930451E13Rik|4933440L20Rik|RNDEu-3	patched domain containing 3	protein-coding
mm_32204.1	chr4	101507762	101507772	+	1	NA	promoter-TSS (NM_001164585)	promoter-TSS (NM_001164585)	-209	NM_001164585	72685	Mm.76494	NM_198412	ENSMUSG00000028528	Dnajc6	2810027M23Rik|mKIAA0473	DnaJ heat shock protein family (Hsp40) member C6	protein-coding
mm_108839.1	chr12	97124309	97124341	+	1	NA	Intergenic	Intergenic	-1077103	NR_103800	69423	Mm.46121	NM_027076		1700019M22Rik	-	NFX-like protein	pseudo
mm_66900.1	chr7	59976555	59976565	-	1	NA	Intergenic	Intergenic	-2129	NR_015456	52480	Mm.482346	NR_015456	ENSMUSG00000100826	Snhg14	AU018661|D7Ertd715e|Lncat	small nucleolar RNA host gene 14	ncRNA
mm_59110.1	chr7	19816579	19816594	+	1	NA	intron (NM_033601, intron 2 of 8)	intron (NM_033601, intron 2 of 8)	6169	NM_033601	12051	Mm.439658	NM_033601	ENSMUSG00000053175	Bcl3	AI528691|Bcl-3	B cell leukemia/lymphoma 3	protein-coding
mm_29277.1	chr3	107555070	107555079	-	1	NA	promoter-TSS (NM_026261)	promoter-TSS (NM_026261)	-1	NM_026261	67591	Mm.55982	NM_026261	ENSMUSG00000055891	Ubl4b	4930522D07Rik	ubiquitin-like 4B	protein-coding
mm_46625.1	chr5	108434360	108434370	-	1	NA	promoter-TSS (NM_007507)	promoter-TSS (NM_007507)	13	NM_007507	11958	Mm.136093	NM_007507	ENSMUSG00000050856	Atp5k	2610008D24Rik|Atp5i|Lfm1	ATP synthase, H+ transporting, mitochondrial F1F0 complex, subunit E	protein-coding
mm_72308.1	chr8	77549394	77549444	+	1	NA	promoter-TSS (NM_001081240)	promoter-TSS (NM_001081240)	22	NM_001081240	102182	Mm.197630	NM_178903	ENSMUSG00000037134	Prmt9	AI931714|Prmt10	protein arginine methyltransferase 9	protein-coding
mm_56897.1	chr6	119121271	119121275	-	1	NA	intron (NM_001255998, intron 1 of 47)	intron (NM_001255998, intron 1 of 47)	-12778	NM_001256002	12288	Mm.41628	NM_009781	ENSMUSG00000051331	Cacna1c	Cav1.2|Cchl1a1|D930026N18Rik|MBC|MELC-CC	calcium channel, voltage-dependent, L type, alpha 1C subunit	protein-coding
mm_5014.1	chr1	192841683	192841690	+	1	NA	promoter-TSS (NR_040468)	promoter-TSS (NR_040468)	-19	NR_040468	73455	Mm.414869	NR_040468		1700065J18Rik	-	RIKEN cDNA 1700065J18 gene	ncRNA
mm_72366.1	chr8	80859386	80859409	+	1	NA	intron (NM_021356, intron 1 of 9)	B1_Mur2|SINE|Alu	21082	NM_021356	14388	Mm.277409	NM_021356	ENSMUSG00000031714	Gab1	AA408973|AW107238	growth factor receptor bound protein 2-associated protein 1	protein-coding
mm_133743.1	chr16	94010963	94010975	+	1	NA	Intergenic	PB1D9|SINE|Alu	-2132	NM_019500	56173	Mm.328716	NM_019500	ENSMUSG00000047109	Cldn14	AI851731	claudin 14	protein-coding
mm_49208.1	chr6	15720825	15720847	+	1	NA	5' UTR (NM_175088, exon 1 of 5)	5' UTR (NM_175088, exon 1 of 5)	175	NM_175088	16543	Mm.1314	NM_175088	ENSMUSG00000041390	Mdfic	Kdt1|Mdfid	MyoD family inhibitor domain containing	protein-coding
mm_84563.1	chr9	67832326	67832331	-	1	NA	promoter-TSS (NM_001163143)	promoter-TSS (NM_001163143)	2	NM_001163143	244911	Mm.325849	NM_001163143	ENSMUSG00000047990	C2cd4a	EG244911|Fam148a	C2 calcium-dependent domain containing 4A	protein-coding
mm_41923.1	chr5	105610969	105610972	+	1	NA	Intergenic	Intergenic	-88999	NM_001122768	231549	Mm.23837	NM_178701	ENSMUSG00000046079	Lrrc8d	2810473G09Rik|4930525N13Rik|A930019F03|Lrrc5	leucine rich repeat containing 8D	protein-coding
mm_83960.1	chr9	57131234	57131252	-	1	NA	promoter-TSS (NR_102289)	promoter-TSS (NR_102289)	47	NR_102289	76794	Mm.472839	NR_102289	ENSMUSG00000086728	Man2c1os	2410133F24Rik|AI851351	mannosidase, alpha, class 2C, member 1, opposite strand	ncRNA
mm_49109.1	chr6	8363124	8363127	+	1	NA	intron (NM_001302353, intron 2 of 4)	intron (NM_001302353, intron 2 of 4)	103837	NM_001302353	100036521	Mm.446106	NM_001302353	ENSMUSG00000089862	Umad1	Gm16039|OTTMUSG00000029336	UMAP1-MVP12 associated (UMA) domain containing 1	protein-coding
mm_96306.1	chr11	63158472	63158482	+	1	NA	3' UTR (NM_008885, exon 5 of 5)	3' UTR (NM_008885, exon 5 of 5)	25674	NM_001302260	18858	Mm.1237	NM_008885	ENSMUSG00000018217	Pmp22	22kDa|Gas-3|HNPP|Tr|trembler	peripheral myelin protein 22	protein-coding
mm_169214.1	chr13	66680806	66680816	-	1	NA	Intergenic	Intergenic	224539	NM_026219	67530	Mm.379136	NM_026219	ENSMUSG00000021520	Uqcrb	2210415M14Rik|QP-C|QPC|UQBC|UQBP|UQPC	ubiquinol-cytochrome c reductase binding protein	protein-coding
mm_47263.1	chr5	121836788	121836798	-	1	NA	promoter-TSS (NM_001306128)	promoter-TSS (NM_001306128)	66	NM_001306128	16923	Mm.65493	NM_008507	ENSMUSG00000042594	Sh2b3	AI429800|Lnk	SH2B adaptor protein 3	protein-coding
mm_30230.1	chr3	145759588	145759592	-	1	NA	intron (NM_026993, intron 1 of 5)	intron (NM_026993, intron 1 of 5)	898	NM_026993	69219	Mm.234247	NM_026993	ENSMUSG00000028194	Ddah1	2410006N07Rik|2510015N06Rik|AI987801|AW050362	dimethylarginine dimethylaminohydrolase 1	protein-coding
mm_9176.1	chr1	171057972	171057981	-	1	NA	intron (NM_010188, intron 2 of 4)	intron (NM_010188, intron 2 of 4)	1427	NM_010188	14131	Mm.22119	NM_010188	ENSMUSG00000059498	Fcgr3	CD16	Fc receptor, IgG, low affinity III	protein-coding
mm_52562.1	chr6	116208186	116208197	+	1	NA	promoter-TSS (NR_131013)	promoter-TSS (NR_131013)	158	NM_026585	28006	Mm.28524	NM_026585	ENSMUSG00000024104	Washc2	A130095H06|C530005J20Rik|D6Wsu116e|Fam21	WASH complex subunit 2	protein-coding
mm_114912.1	chr13	94976436	94976452	+	1	NA	promoter-TSS (NM_172590)	promoter-TSS (NM_172590)	100	NM_172590	218460	Mm.33856	NM_172590	ENSMUSG00000042015	Wdr41	B830029I03Rik|MSTP048	WD repeat domain 41	protein-coding
mm_56701.1	chr6	114969005	114969022	-	1	NA	Intergenic	CpG	-47261	NM_177683	232334	Mm.268357	NM_177683	ENSMUSG00000030315	Vgll4	BC048841|VGL-4	vestigial like family member 4	protein-coding
mm_109821.1	chr12	3856166	3856170	-	1	NA	intron (NM_007872, intron 3 of 22)	intron (NM_007872, intron 3 of 22)	6076	NR_045884	100038522	Mm.417270	NR_045884	ENSMUSG00000073242	Dnmt3aos	ENSMUSG00000073242|Gm10485	DNA methyltransferase 3A, opposite strand	ncRNA
mm_147004.1	chr18	34373503	34373520	-	1	NA	promoter-TSS (NM_007874)	promoter-TSS (NM_007874)	-96	NM_007874	13476	Mm.280075	NM_007874	ENSMUSG00000005873	Reep5	AI324241|AU022809|AW495741|DP1/TB2|Dp1|R74856|TB2/DP1	receptor accessory protein 5	protein-coding
mm_153311.1	chr19	38032913	38032918	-	1	NA	intron (NM_001302140, intron 1 of 53)	intron (NM_001302140, intron 1 of 53)	10662	NM_001099634	226101	Mm.34674	NM_177035	ENSMUSG00000048612	Myof	2310004N10Rik|2310051D19Rik|E030042N20Rik|Fer1l3	myoferlin	protein-coding
mm_129446.1	chr15	78549353	78549384	-	1	NA	Intergenic	RMER1A|Other|Other	-5023	NM_009218	20607	Mm.211411	NM_009218	ENSMUSG00000044933	Sstr3	Smstr-3|Smstr3|sst3	somatostatin receptor 3	protein-coding
mm_39296.1	chr5	5481552	5481554	+	1	NA	Intergenic	Intergenic	-2410	NM_001200025	381716	Mm.276086	NM_001200025	ENSMUSG00000079666	1700015F17Rik	Gm1686	RIKEN cDNA 1700015F17 gene	protein-coding
mm_24827.1	chr3	95653897	95653907	+	1	NA	Intergenic	Intergenic	-4819	NM_008562	17210	Mm.1639	NM_008562	ENSMUSG00000038612	Mcl1	AW556805|Mcl-1	myeloid cell leukemia sequence 1	protein-coding
mm_145771.1	chr18	65023910	65023916	+	1	NA	5' UTR (NM_031881, exon 1 of 30)	5' UTR (NM_031881, exon 1 of 30)	386	NM_031881	83814	Mm.98668	NM_031881	ENSMUSG00000024589	Nedd4l	1300012C07Rik|Nedd4-2|Nedd4b	neural precursor cell expressed, developmentally down-regulated gene 4-like	protein-coding
mm_105393.1	chr11	103375963	103375969	-	1	NA	intron (NM_183034, intron 7 of 11)	PB1D10|SINE|Alu	-12274	NM_001205236	544817	Mm.259113	NM_133715	ENSMUSG00000034255	Arhgap27	2310069I04Rik|5730442P18Rik|Gm21552|Sh3d20	Rho GTPase activating protein 27	protein-coding
mm_28197.1	chr3	88177672	88177783	-	1	NA	promoter-TSS (NR_045997)	promoter-TSS (NR_045997)	58	NR_045997	76642	Mm.424420	NR_045997	ENSMUSG00000096935	1700113A16Rik	2210408E11Rik|AA408983	RIKEN cDNA 1700113A16 gene	ncRNA
mm_84033.1	chr9	57765541	57765555	-	1	NA	5' UTR (NM_007713, exon 1 of 13)	5' UTR (NM_007713, exon 1 of 13)	312	NM_007713	102414	Mm.25720	NM_007713	ENSMUSG00000032316	Clk3	AI256811	CDC-like kinase 3	protein-coding
mm_40115.1	chr5	34949365	34949369	+	1	NA	promoter-TSS (NM_173402)	promoter-TSS (NM_173402)	-81	NM_173402	71729	Mm.196208	NM_173402	ENSMUSG00000029101	Rgs12	1200016K18Rik|4632412M04Rik|AI481290|E130309H11	regulator of G-protein signaling 12	protein-coding
mm_121760.1	chr14	19653361	19653371	-	1	NA	Intergenic	Intergenic	-50779	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_97319.1	chr11	76902183	76902185	+	1	NA	Intergenic	Intergenic	-2361	NM_025655	66601	Mm.25138	NM_025655	ENSMUSG00000020839	Tmigd1	2010002A20Rik|Tmigd	transmembrane and immunoglobulin domain containing 1	protein-coding
mm_33548.1	chr4	130934815	130934825	+	1	NA	3' UTR (NM_010686, exon 8 of 8)	3' UTR (NM_010686, exon 8 of 8)	-9565	NM_010769	17180	Mm.271796	NM_010769	ENSMUSG00000040533	Matn1	CMP|Crtm|Mat1|matrilin-1	matrilin 1, cartilage matrix protein	protein-coding
mm_118333.1	chr13	113880393	113880398	-	1	NA	intron (NM_172595, intron 1 of 4)	AT_rich|Low_complexity|Low_complexity	85887	NM_172595	218639	Mm.79837	NM_172595	ENSMUSG00000042348	Arl15	A430036I03|Arfrp2|C230032K13Rik	ADP-ribosylation factor-like 15	protein-coding
mm_72971.1	chr8	92882121	92882146	+	1	NA	intron (NM_173014, intron 8 of 13)	intron (NM_173014, intron 8 of 13)	-19262	NM_027112	69543	Mm.440514	NM_027112	ENSMUSG00000078144	Capns2	2310005G05Rik|30K-2	calpain, small subunit 2	protein-coding
mm_167139.1	chr7	127561752	127561764	+	1	NA	TTS (NM_001304266)	TTS (NM_001304266)	535	NM_001304267	105180375	Mm.428042	NM_001304267	ENSMUSG00000106715	Tmem265	-	transmembrane protein 265	protein-coding
mm_29603.1	chr3	121205480	121205484	-	1	NA	3' UTR (NM_178936, exon 8 of 8)	3' UTR (NM_178936, exon 8 of 8)	-33787	NM_025637	66568	Mm.263163	NM_025637	ENSMUSG00000028133	Rwdd3	2510027J23Rik|3110037C01Rik|AI035684|AI662458|Rsume|X2CR1	RWD domain containing 3	protein-coding
mm_151623.1	chr19	3907088	3907117	-	1	NA	promoter-TSS (NM_001136091)	promoter-TSS (NM_001136091)	31	NM_001136091	27060	Mm.271689	NM_016921	ENSMUSG00000001750	Tcirg1	ATP6N1C|ATP6a3|Atp6i|OC-116|OPTB1|Stv1|TIRC7|Vph1|oc	T cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 protein A3	protein-coding
mm_134111.1	chr16	9995702	9995725	-	1	NA	Intergenic	CpG	-3180	NM_008170	14811	Mm.2953	NM_008170	ENSMUSG00000059003	Grin2a	GluN2A|NMDAR2A|NR2A	glutamate receptor, ionotropic, NMDA2A (epsilon 1)	protein-coding
mm_110201.1	chr12	27340754	27340764	-	1	NA	3' UTR (NM_009234, exon 1 of 1)	3' UTR (NM_009234, exon 1 of 1)	1959	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding
mm_113365.1	chr13	32965495	32965511	+	1	NA	promoter-TSS (NM_011454)	promoter-TSS (NM_011454)	-10	NM_011454	20708	Mm.36526	NM_011454	ENSMUSG00000042842	Serpinb6b	NK13|Spi12|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 6b	protein-coding
mm_67103.1	chr7	69909633	69909640	-	1	NA	Intergenic	Intergenic	413542	NR_045940	73796	Mm.410832	NR_045940	ENSMUSG00000108885	4930402F11Rik	-	RIKEN cDNA 4930402F11 gene	ncRNA
mm_10031.1	chr1	192137956	192137967	-	1	NA	promoter-TSS (NM_144814)	promoter-TSS (NM_144814)	79	NM_001290278	214742	Mm.207457	NM_144814	ENSMUSG00000037395	Rcor3	4921514E24Rik|C730034D20Rik|E130101E15Rik	REST corepressor 3	protein-coding
mm_143827.1	chr17	84004348	84004359	-	1	NA	intron (NR_130994, intron 1 of 1)	intron (NR_130994, intron 1 of 1)	5801	NR_130994	78148	Mm.243918	NR_130994		8430430B14Rik	-	RIKEN cDNA 8430430B14 gene	ncRNA
mm_3651.1	chr1	153090323	153090365	+	1	NA	intron (NM_175460, intron 6 of 10)	intron (NM_175460, intron 6 of 10)	96103	NM_008485	16782	Mm.329272	NM_008485	ENSMUSG00000026479	Lamc2	AA589349	laminin, gamma 2	protein-coding
mm_128121.1	chr15	31224760	31224767	-	1	NA	intron (NM_146057, intron 1 of 3)	intron (NM_146057, intron 1 of 3)	378	NM_146057	223453	Mm.222867	NM_146057	ENSMUSG00000039168	Dap	4921531N22Rik|AI789753|AU040360	death-associated protein	protein-coding
mm_29684.1	chr3	123026203	123026215	-	1	NA	exon (NM_021503, exon 3 of 6)	exon (NM_021503, exon 3 of 6)	8778	NM_021503	59006	Mm.141157	NM_021503	ENSMUSG00000028116	Myoz2	1110012I24Rik|Fatz-2|Myozl2	myozenin 2	protein-coding
mm_14890.1	chr2	149085560	149085562	+	1	NA	Intergenic	Intergenic	-210049	NM_009976	13010	Mm.4263	NM_009976	ENSMUSG00000027447	Cst3	CysC	cystatin C	protein-coding
mm_18604.1	chr2	68233029	68233047	-	1	NA	intron (NM_016866, intron 16 of 17)	intron (NM_016866, intron 16 of 17)	128366	NM_020283	26877	Mm.226435	NM_020283	ENSMUSG00000034780	B3galt1	beta3Gal-T1	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 1	protein-coding
mm_8691.1	chr1	157256692	157256701	-	1	NA	intron (NM_177644, intron 3 of 17)	intron (NM_177644, intron 3 of 17)	-148016	NM_001305063	73435	Mm.116705	NM_028540	ENSMUSG00000026592	Tex35	1700057K13Rik	testis expressed 35	protein-coding
mm_129832.1	chr15	83149271	83149304	-	1	NA	promoter-TSS (NM_178627)	promoter-TSS (NM_178627)	49	NM_178627	73826	Mm.23758	NM_178627	ENSMUSG00000041815	Poldip3	1110008P04Rik|AA408269|AL022852|C77954|PDIP46|SKAR|mKIAA1649	polymerase (DNA-directed), delta interacting protein 3	protein-coding
mm_83685.1	chr9	50507755	50507765	-	1	NA	Intergenic	Intergenic	-2955	NR_040714	69631	Mm.414996	NR_040714	ENSMUSG00000101304	Plet1os	2310014F07Rik	placenta expressed transcript 1, opposite strand	ncRNA
mm_10464.1	chr2	14314429	14314449	+	1	NA	intron (NM_008625, intron 21 of 29)	PB1|SINE|Alu	53436	NR_030609	100124488		NR_030609	ENSMUSG00000077897	Mir511	Mirn511|mir-511|mmu-mir-511	microRNA 511	ncRNA
mm_70047.1	chr7	142578043	142578068	-	1	NA	promoter-TSS (NR_130974)	promoter-TSS (NR_130974)	91	NR_130974	14955	Mm.14802	NR_001592	ENSMUSG00000000031	H19	AI747191	H19, imprinted maternally expressed transcript	ncRNA
mm_51428.1	chr6	78428552	78428562	+	1	NA	3' UTR (NM_009042, exon 6 of 6)	3' UTR (NM_009042, exon 6 of 6)	2574	NM_009042	19692	Mm.142731	NM_009042	ENSMUSG00000059654	Reg1	-	regenerating islet-derived 1	protein-coding
mm_58319.1	chr6	146460141	146460144	-	1	NA	intron (NM_010586, intron 2 of 55)	B4A|SINE|B4	42081	NM_010586	16439	Mm.7800	NM_010586	ENSMUSG00000030287	Itpr2	AI649341|InsP3R-2|InsP3R-5|Ip3r2|Itpr5|insP3R2	inositol 1,4,5-triphosphate receptor 2	protein-coding
mm_95712.1	chr11	54516157	54516167	+	1	NA	3' UTR (NM_173753, exon 18 of 18)	3' UTR (NM_173753, exon 18 of 18)	-6683	NM_001252494	192786	Mm.254404	NM_175258	ENSMUSG00000037533	Rapgef6	A530068K01|AI844632|BB085664|C030018K18Rik|PDZ-GEF2|Pdzgef2|RA-GEF-2|Ragef2|mKIAA4052	Rap guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_156448.1	chrX	142687221	142687236	+	1	NA	intron (NM_001199360, intron 2 of 6)	intron (NM_001199360, intron 2 of 6)	5502	NM_001199360	209497	Mm.249648	NM_177592	ENSMUSG00000047045	Tmem164	AI316850|AI852450|AW547186|F730011B02	transmembrane protein 164	protein-coding
mm_146091.1	chr18	73573477	73573503	+	1	NA	exon (NM_001039214, exon 1 of 2)	exon (NM_001039214, exon 1 of 2)	785	NM_001039214	240396	Mm.24131	NM_001039214	ENSMUSG00000037253	Mex3c	A130001D14Rik|BC035207|BM-013|Rkhd2	mex3 RNA binding family member C	protein-coding
mm_86181.1	chr9	119190415	119190420	-	1	NA	promoter-TSS (NM_001037749)	promoter-TSS (NM_001037749)	-24	NM_001037749	382113	Mm.335525	NM_001037749	ENSMUSG00000070280	Slc22a14	Gm1128	solute carrier family 22 (organic cation transporter), member 14	protein-coding
mm_43541.1	chr5	137510407	137510460	+	1	NA	Intergenic	CpG	-8004	NM_028753	74097	Mm.290242	NM_028753	ENSMUSG00000029715	Pop7	0610037N12Rik|AI852017|Rpp20	processing of precursor 7, ribonuclease P family, (S. cerevisiae)	protein-coding
mm_131625.1	chr16	20107538	20107560	+	1	NA	exon (NM_029436, exon 3 of 8)	exon (NM_029436, exon 3 of 8)	9995	NM_029436	75785	Mm.392450	NM_029436	ENSMUSG00000062901	Klhl24	1110046J11Rik|4930429H24Rik|6530402O20Rik|C85082	kelch-like 24	protein-coding
mm_16793.1	chr2	10080406	10080446	-	1	NA	promoter-TSS (NM_001112738)	promoter-TSS (NM_001112738)	84	NM_020615	11949	Mm.12677	NM_020615	ENSMUSG00000025781	Atp5c1	1700094F02Rik	ATP synthase, H+ transporting, mitochondrial F1 complex, gamma polypeptide 1	protein-coding
mm_135819.1	chr16	58415316	58415327	-	1	NA	intron (NM_028523, intron 1 of 15)	intron (NM_028523, intron 1 of 15)	6786	NM_028523	73379	Mm.373589	NM_028523	ENSMUSG00000035107	Dcbld2	1700055P21Rik|AW146002|CLCP1|Esdn	discoidin, CUB and LCCL domain containing 2	protein-coding
mm_113059.1	chr13	23735153	23735183	+	1	NA	Intergenic	Intergenic	-3639	NM_015786	50708	Mm.193539	NM_015786	ENSMUSG00000036181	Hist1h1c	0610008C09Rik|H1.2|H1c|H1f2|H1var1|His1a	histone cluster 1, H1c	protein-coding
mm_54381.1	chr6	31211208	31211222	-	1	NA	intron (NR_110469, intron 1 of 3)	MER5A|DNA|hAT-Charlie	7259	NR_110470	232685	Mm.443019	NM_144555	ENSMUSG00000044471	Lncpint	Lincpint|MNCb-1768|Pint|linc-Pint	long non-protein coding RNA, Trp53 induced transcript	ncRNA
mm_137358.1	chr17	25318650	25318657	+	1	NA	promoter-TSS (NM_053260)	promoter-TSS (NM_053260)	-1	NM_053260	114662	Mm.207082	NM_053260	ENSMUSG00000034039	Prss29	D19363|Isp2|mISP-2	protease, serine 29	protein-coding
mm_100615.1	chr11	121544198	121544221	+	1	NA	intron (NM_029878, intron 14 of 38)	intron (NM_029878, intron 14 of 38)	-24867	NM_178763	319530	Mm.11395	NM_178763	ENSMUSG00000039238	Zfp750	A030007D23Rik|Znf750	zinc finger protein 750	protein-coding
mm_111487.1	chr12	98901265	98901275	-	1	NA	5' UTR (NM_001081191, exon 1 of 44)	5' UTR (NM_001081191, exon 1 of 44)	214	NM_001081191	319670	Mm.390484	NM_001081191	ENSMUSG00000051166	Eml5	BC027154|C130068M19Rik	echinoderm microtubule associated protein like 5	protein-coding
mm_82912.1	chr9	34948787	34948799	-	1	NA	intron (NM_001190913, intron 4 of 13)	intron (NM_001190913, intron 4 of 13)	-167935	NR_029475	78934	Mm.391688	NR_029475	ENSMUSG00000070315	4930581F22Rik	-	RIKEN cDNA 4930581F22 gene	ncRNA
mm_63227.1	chr7	126429056	126429120	+	1	NA	5' UTR (NM_030566, exon 1 of 13)	5' UTR (NM_030566, exon 1 of 13)	321	NM_030566	70314	Mm.35467	NM_030566	ENSMUSG00000030727	Rabep2	2610011A08Rik|AI462746|Fra	rabaptin, RAB GTPase binding effector protein 2	protein-coding
mm_35492.1	chr4	40948197	40948296	-	1	NA	promoter-TSS (NM_001171739)	promoter-TSS (NM_001171739)	48	NM_009736	12017	Mm.688	NM_009736	ENSMUSG00000028416	Bag1	BAG-1|Rap46	BCL2-associated athanogene 1	protein-coding
mm_165438.1	chr2	154009206	154009210	+	1	NA	exon (NM_008953, exon 2 of 9)	exon (NM_008953, exon 2 of 9)	932	NM_008953	19194	Mm.29197	NM_008953	ENSMUSG00000042459	Bpifa2	Bpifa2e|Psp	BPI fold containing family A, member 2	protein-coding
mm_28629.1	chr3	95140084	95140121	-	1	NA	promoter-TSS (NR_106175)	promoter-TSS (NR_106175)	-916	NR_106175	102465890		NR_106175	ENSMUSG00000098498	Mir8099-1	Gm27917|mmu-mir-8099-1	microRNA 8099-1	ncRNA
mm_63867.1	chr7	135684366	135684381	+	1	NA	3' UTR (NM_011212, exon 21 of 21)	3' UTR (NM_011212, exon 21 of 21)	32006	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_4518.1	chr1	175036371	175036375	+	1	NA	Intergenic	Intergenic	-114554	NM_011825	23893	Mm.25760	NM_011825	ENSMUSG00000050069	Grem2	Gremlin2|Prdc	gremlin 2, DAN family BMP antagonist	protein-coding
mm_162763.1	chr10	62339296	62339315	-	1	NA	intron (NM_010438, intron 4 of 21)	intron (NM_010438, intron 4 of 21)	1116	NM_001146100	15275	Mm.196605	NM_010438	ENSMUSG00000037012	Hk1	BB404130|Hk-1|Hk1-s|dea|mHk1-s	hexokinase 1	protein-coding
mm_9437.1	chr1	172526833	172526834	-	1	NA	intron (NM_027972, intron 1 of 11)	MLT1N2|LTR|ERVL-MaLR	5703	NM_027972	71870	Mm.78373	NM_027972	ENSMUSG00000026546	Cfap45	1700028D05Rik|Ccdc19|Nesg1	cilia and flagella associated protein 45	protein-coding
mm_104559.1	chr11	96828177	96828191	-	1	NA	5' UTR (NM_008686, exon 2 of 5)	5' UTR (NM_008686, exon 2 of 5)	1318	NM_001130450	18023	Mm.6743	NM_008686	ENSMUSG00000038615	Nfe2l1	AA408798|AW212678|LCR-F1|Lcrf1|NRF1|TCF-11|TCF11	nuclear factor, erythroid derived 2,-like 1	protein-coding
mm_111621.1	chr12	102421331	102421341	-	1	NA	intron (NM_011175, intron 2 of 13)	(TG)n|Simple_repeat|Simple_repeat	18477	NM_011175	19141	Mm.17185	NM_011175	ENSMUSG00000021190	Lgmn	AEP|AI746452|AU022324|Prsc1	legumain	protein-coding
mm_135617.1	chr16	52271488	52271507	-	1	NA	intron (NM_009655, intron 11 of 15)	L1_Mur3|LINE|L1	181584	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_124148.1	chr14	90556749	90556776	-	1	NA	Intergenic	Intergenic	429871	NR_045712	74967	Mm.390704	NR_045712		4930474H20Rik	-	RIKEN cDNA 4930474H20 gene	ncRNA
mm_32507.1	chr4	108478893	108478909	+	1	NA	5' UTR (NM_175472, exon 3 of 31)	5' UTR (NM_175472, exon 3 of 31)	19475	NM_175472	230594	Mm.25181	NM_175472	ENSMUSG00000034610	Zcchc11	6030404K05Rik|9230115F04Rik|PPAPD3|mKIAA0191	zinc finger, CCHC domain containing 11	protein-coding
mm_38332.1	chr4	137437794	137437827	-	1	NA	Intergenic	LTR33|LTR|ERVL	-7290	NM_026419	67868	Mm.297477	NM_026419	ENSMUSG00000023433	Cela3b	0910001F22Rik|2310074F01Rik|AI504000|Ela3|Ela3b	chymotrypsin-like elastase family, member 3B	protein-coding
mm_110617.1	chr12	56978701	56978703	-	1	NA	intron (NM_172577, intron 1 of 9)	intron (NM_172577, intron 1 of 9)	181941	NM_001167976	217593	Mm.32835	NM_172577	ENSMUSG00000035472	Slc25a21	9930033G19Rik|A630030I10|BB158148	solute carrier family 25 (mitochondrial oxodicarboxylate carrier), member 21	protein-coding
mm_131963.1	chr16	24609282	24609285	+	1	NA	intron (NM_001145952, intron 4 of 11)	intron (NM_001145952, intron 4 of 11)	79969	NR_038091	624582	Mm.439775	NR_038091		Morf4l1-ps1	A730098P11Rik	mortality factor 4 like 1, pseudogene 1	pseudo
mm_94946.1	chr11	29718796	29718839	+	1	NA	5' UTR (NM_024226, exon 1 of 7)	5' UTR (NM_024226, exon 1 of 7)	254	NM_024226	68585	Mm.192580	NM_024226	ENSMUSG00000020458	Rtn4	1110020G17Rik|AA407876|AA409940|AA960376|ASY|C130026I10Rik|NOGO|NSP-CL|NgA|Nogo-A|Nogo-B|Nogo-C|mKIAA0886|mKIAA4153	reticulon 4	protein-coding
mm_74984.1	chr8	27142005	27142044	-	1	NA	promoter-TSS (NR_045840)	promoter-TSS (NR_045840)	-886	NR_045840	71082	Mm.395259	NR_045840		4933416M07Rik	-	RIKEN cDNA 4933416M07 gene	ncRNA
mm_130478.1	chr15	98738719	98738785	-	1	NA	3' UTR (NM_007478, exon 5 of 5)	3' UTR (NM_007478, exon 5 of 5)	-10554	NM_024169	66120	Mm.30729	NM_024169	ENSMUSG00000003355	Fkbp11	1110002O23Rik|FKBP-11	FK506 binding protein 11	protein-coding
mm_135150.1	chr16	35857726	35857766	-	1	NA	exon (NM_001039530, exon 6 of 17)	exon (NM_001039530, exon 6 of 17)	13636	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_158673.1	chrX	157598643	157598655	-	1	NA	promoter-TSS (NM_172307)	promoter-TSS (NM_172307)	66	NM_172307	270669	Mm.37577	NM_172307	ENSMUSG00000046873	Mbtps2	9630032G22Rik|AI662535	membrane-bound transcription factor peptidase, site 2	protein-coding
mm_52890.1	chr6	122578408	122578423	+	1	NA	3' UTR (NM_031159, exon 8 of 8)	3' UTR (NM_031159, exon 8 of 8)	24029	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_141165.1	chr17	26531683	26531697	-	1	NA	Intergenic	Intergenic	-23218	NM_013642	19252	Mm.239041	NM_013642	ENSMUSG00000024190	Dusp1	3CH134|MKP1|Ptpn16|U19515|erp|mkp-1	dual specificity phosphatase 1	protein-coding
mm_61822.1	chr7	87586473	87586490	+	1	NA	intron (NM_001143834, intron 1 of 10)	C-rich|Low_complexity|Low_complexity	2313	NM_001143834	108071	Mm.235018	NM_001033224	ENSMUSG00000049583	Grm5	6430542K11Rik|AI850523|Glu5R|Gprc1e|mGluR5|mGluR5b	glutamate receptor, metabotropic 5	protein-coding
mm_41423.1	chr5	90892481	90892491	+	1	NA	intron (NM_008176, intron 3 of 3)	intron (NM_008176, intron 3 of 3)	1241	NM_008176	14825	Mm.21013	NM_008176	ENSMUSG00000029380	Cxcl1	Fsp|Gro1|KC|Mgsa|N51|Scyb1|gro	chemokine (C-X-C motif) ligand 1	protein-coding
mm_67461.1	chr7	80403371	80403378	-	1	NA	promoter-TSS (NM_011046)	promoter-TSS (NM_011046)	-562	NM_011046	18550	Mm.5241	NM_011046	ENSMUSG00000030530	Furin	9130404I01Rik|Fur|PACE|Pcsk3|SPC1	furin (paired basic amino acid cleaving enzyme)	protein-coding
mm_66277.1	chr7	37769418	37769421	-	1	NA	intron (NM_172385, intron 1 of 5)	intron (NM_172385, intron 1 of 5)	333	NM_172385	243937	Mm.322505	NM_172385	ENSMUSG00000043456	Zfp536	9630010P11Rik|Znf536|mKIAA0390	zinc finger protein 536	protein-coding
mm_20821.1	chr2	145884906	145884914	-	1	NA	intron (NM_028724, intron 12 of 12)	intron (NM_028724, intron 12 of 12)	-18331	NM_026425	67877	Mm.151168	NM_026425	ENSMUSG00000002728	Naa20	1500004D14Rik|2900026I01Rik|AU041458|D2Ertd186e|Nat5	N(alpha)-acetyltransferase 20, NatB catalytic subunit	protein-coding
mm_68992.1	chr7	126625483	126625496	-	1	NA	promoter-TSS (NM_019738)	promoter-TSS (NM_019738)	-19	NM_019738	56312	Mm.18742	NM_019738	ENSMUSG00000030717	Nupr1	2310032H04Rik|Com1|p8	nuclear protein transcription regulator 1	protein-coding
mm_170818.1	chr2	176486767	176486786	-	1	NA	promoter-TSS (NM_001099349).3	promoter-TSS (NM_001099349).3	-27	NM_001099349	100043381		NM_001099349	ENSMUSG00000078880	Gm14308	OTTMUSG00000016254	predicted gene 14308	protein-coding
mm_99209.1	chr11	101023104	101023125	+	1	NA	intron (NM_001243050, intron 5 of 20)	ID_B1|SINE|B4	-7226	NR_105893	102466767		NR_105893	ENSMUSG00000098415	Mir6928	Gm27728|mmu-mir-6928	microRNA 6928	ncRNA
mm_55111.1	chr6	50382926	50382936	-	1	NA	promoter-TSS (NM_027881)	promoter-TSS (NM_027881)	-94	NM_027881	71720	Mm.44153	NM_027881	ENSMUSG00000029822	Osbpl3	1200014M06Rik|6720421I08Rik|A530055M08|ORP-3|ORP3|OSBP3	oxysterol binding protein-like 3	protein-coding
mm_169361.1	chr1	43189061	43189076	+	1	NA	intron (NM_001289533, intron 1 of 5)	intron (NM_001289533, intron 1 of 5)	7693	NM_001289533	14200	Mm.6799	NM_010212	ENSMUSG00000008136	Fhl2	FHL-2|SLIM-3|SLIM3	four and a half LIM domains 2	protein-coding
mm_160075.1	chr7	7136746	7136746	-	1	NA	promoter-TSS (NM_029584)	promoter-TSS (NM_029584)	9	NM_029584	76373	Mm.159732	NM_029584	ENSMUSG00000063535	Zfp773	2810409K11Rik	zinc finger protein 773	protein-coding
mm_94490.1	chr11	6676772	6676782	+	1	NA	3' UTR (NM_019511, exon 3 of 3)	3' UTR (NM_019511, exon 3 of 3)	-16541	NR_028586	100041311	Mm.388018	NR_028586	ENSMUSG00000086373	Gm11978	OTTMUSG00000005125|OTTMUSG00000005127	predicted gene 11978	pseudo
mm_34974.1	chr4	156012601	156012605	+	1	NA	3' UTR (NM_011341, exon 7 of 7)	3' UTR (NM_011341, exon 7 of 7)	-1092	NM_011659	22163	Mm.13885	NM_011659	ENSMUSG00000029075	Tnfrsf4	ACT35|CD134|Ly-70|Ox40|TXGP1L|Txgp1	tumor necrosis factor receptor superfamily, member 4	protein-coding
mm_94073.1	chr10	128409147	128409176	-	1	NA	intron (NM_027257, intron 2 of 6)	intron (NM_027257, intron 2 of 6)	635	NM_027257	69917	Mm.46614	NM_027257	ENSMUSG00000025374	Nabp2	2610036N15Rik|Obfc2b|SSB1	nucleic acid binding protein 2	protein-coding
mm_51997.1	chr6	92449188	92449197	+	1	NA	intron (NM_001081146, intron 3 of 8)	intron (NM_001081146, intron 3 of 8)	32200	NM_001134460	243548	Mm.248820	NM_001081146	ENSMUSG00000030020	Prickle2	6230400G14Rik|6720451F06Rik|mpk2	prickle planar cell polarity protein 2	protein-coding
mm_49849.1	chr6	38369367	38369372	+	1	NA	Intergenic	RMER19B|LTR|ERVK	-12155	NM_153600	264134	Mm.253446	NM_153600	ENSMUSG00000056832	Ttc26	9330141E21Rik|9430097H08Rik|hop|hpy	tetratricopeptide repeat domain 26	protein-coding
mm_146639.1	chr18	10610347	10610363	-	1	NA	promoter-TSS (NM_001081222)	promoter-TSS (NM_001081222)	-3	NM_001081222	77805	Mm.210996	NM_144542	ENSMUSG00000024293	Esco1	A930014I12Rik	establishment of sister chromatid cohesion N-acetyltransferase 1	protein-coding
mm_57573.1	chr6	127142271	127142278	-	1	NA	intron (NM_009829, intron 3 of 4)	intron (NM_009829, intron 3 of 4)	-7115	NR_040274	77558	Mm.358918	NR_040273	ENSMUSG00000097166	9330179D12Rik	-	RIKEN cDNA 9330179D12 gene	ncRNA
mm_18933.1	chr2	76750147	76750155	-	1	NA	exon (NM_011652, exon 275 of 313)	exon (NM_011652, exon 275 of 313)	74836	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_69297.1	chr7	128276082	128276086	-	1	NA	intron (NM_145590, intron 9 of 12)	intron (NM_145590, intron 9 of 12)	10387	NM_133254	246787	Mm.38870	NM_133254	ENSMUSG00000030781	Slc5a2	Sglt2	solute carrier family 5 (sodium/glucose cotransporter), member 2	protein-coding
mm_98133.1	chr11	87471667	87471674	+	1	NA	intron (NM_001199293, intron 2 of 30)	intron (NM_001199293, intron 2 of 30)	44079	NM_001199293	83560	Mm.440758	NM_031386	ENSMUSG00000010342	Tex14	C85585	testis expressed gene 14	protein-coding
mm_15637.1	chr2	163054571	163054583	+	1	NA	promoter-TSS (NM_008652)	promoter-TSS (NM_008652)	-58	NM_008652	17865	Mm.4594	NM_008652	ENSMUSG00000017861	Mybl2	B-Myb|Bmyb	myeloblastosis oncogene-like 2	protein-coding
mm_155323.1	chrX	62487785	62487787	+	1	NA	Intergenic	AT_rich|Low_complexity|Low_complexity	28283	NR_045443	75545	Mm.391270	NR_045442	ENSMUSG00000085757	1700019B21Rik	-	RIKEN cDNA 1700019B21 gene	ncRNA
mm_61570.1	chr7	79743143	79743169	+	1	NA	promoter-TSS (NM_001037927)	promoter-TSS (NM_001037927)	-7	NM_001037927	626359	Mm.387216	NM_001037927	ENSMUSG00000039099	Wdr93	EG626359	WD repeat domain 93	protein-coding
mm_21651.1	chr2	164334250	164334262	-	1	NA	3' UTR (NM_009301, exon 3 of 3)	3' UTR (NM_009301, exon 3 of 3)	1491	NM_009301	20944	Mm.140154	NM_009301	ENSMUSG00000017004	Svs5	BB115186|Semg1|Svp-1|Svp1|Svp5	seminal vesicle secretory protein 5	protein-coding
mm_107562.1	chr12	42028516	42028521	+	1	NA	Intergenic	Intergenic	-542461	NM_010733	16981	Mm.404786	NM_010733	ENSMUSG00000036295	Lrrn3	NLRR-3	leucine rich repeat protein 3, neuronal	protein-coding
mm_20430.1	chr2	129306166	129306179	-	1	NA	non-coding (NR_040371, exon 4 of 5)	non-coding (NR_040371, exon 4 of 5)	3800	NM_010554	16175	Mm.15534	NM_010554	ENSMUSG00000027399	Il1a	Il-1a	interleukin 1 alpha	protein-coding
mm_55495.1	chr6	69649357	69649387	-	1	NA	Intergenic	Intergenic	-322198	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_118855.1	chr14	25751413	25751424	+	1	NA	intron (NM_001101433, intron 2 of 3)	MIRb|SINE|MIR	17438	NM_001101433	71918	Mm.41904	NM_001101433	ENSMUSG00000055538	Zcchc24	2310047A01Rik	zinc finger, CCHC domain containing 24	protein-coding
mm_71927.1	chr8	70248056	70248072	+	1	NA	intron (NM_172755, intron 3 of 10)	B4A|SINE|B4	-13642	NM_133972	76813	Mm.383251	NM_133972	ENSMUSG00000002343	Armc6	2410153K17Rik|AW554412	armadillo repeat containing 6	protein-coding
mm_172001.1	chr6	107070878	107070889	+	1	NA	Intergenic	L1Md_F2|LINE|L1	-270796	NM_175357	58799	Mm.290085	NM_021449	ENSMUSG00000005362	Crbn	2610203G15Rik|2900045O07Rik|AF229032|AW108261|piL	cereblon	protein-coding
mm_88757.1	chr10	80329544	80329555	+	1	NA	promoter-TSS (NM_139292)	promoter-TSS (NM_139292)	-76	NM_008793	18551	Mm.299916	NM_008793	ENSMUSG00000020131	Pcsk4	AI647044|L21221|NEC 3|NEC3|PC4|SPC5	proprotein convertase subtilisin/kexin type 4	protein-coding
mm_72751.1	chr8	85221482	85221486	+	1	NA	Intergenic	RMER21A|LTR|ERV1	-9013	NM_146859	258858	Mm.354727	NM_146859	ENSMUSG00000051952	Olfr371	MOR141-3	olfactory receptor 371	protein-coding
mm_24635.1	chr3	94342118	94342124	+	1	NA	promoter-TSS (NM_025416)	promoter-TSS (NM_025416)	22	NM_025416	66198	Mm.180200	NM_025416	ENSMUSG00000028148	Them5	1110007B02Rik|1110038F21Rik	thioesterase superfamily member 5	protein-coding
mm_35329.1	chr4	26346808	26346840	-	1	NA	promoter-TSS (NM_172865)	promoter-TSS (NM_172865)	-172	NM_172865	242362	Mm.245602	NM_172865	ENSMUSG00000040520	Manea	4932703L02Rik	mannosidase, endo-alpha	protein-coding
mm_107555.1	chr12	41257285	41257285	+	1	NA	intron (NM_053122, intron 4 of 6)	intron (NM_053122, intron 4 of 6)	228772	NM_001271708	16981	Mm.404786	NM_010733	ENSMUSG00000036295	Lrrn3	NLRR-3	leucine rich repeat protein 3, neuronal	protein-coding
mm_66645.1	chr7	45655654	45655667	-	1	NA	intron (NM_001271993, intron 1 of 2)	intron (NM_001271993, intron 1 of 2)	10734	NM_018876	14344	Mm.290046	NM_018876	ENSMUSG00000055978	Fut2	-	fucosyltransferase 2	protein-coding
mm_92428.1	chr10	77112144	77112153	-	1	NA	intron (NM_009929, intron 2 of 41)	A-rich|Low_complexity|Low_complexity	1557	NM_001109991	12822	Mm.4352	NM_009929	ENSMUSG00000001435	Col18a1	-	collagen, type XVIII, alpha 1	protein-coding
mm_43227.1	chr5	129846981	129847036	+	1	NA	promoter-TSS (NM_026445)	promoter-TSS (NM_026445)	18	NM_026445	67902	Mm.103546	NM_026445	ENSMUSG00000025538	Sumf2	2610040F05Rik	sulfatase modifying factor 2	protein-coding
mm_118414.1	chr14	7791452	7791487	+	1	NA	Intergenic	CpG	-26488	NM_001081427	286940	Mm.489652	NM_134080	ENSMUSG00000025278	Flnb	AL024016|Fln-b	filamin, beta	protein-coding
mm_80930.1	chr9	102559293	102559307	+	1	NA	Intergenic	L1MEd|LINE|L1	53162	NM_024291	16716	Mm.101692	NM_024291	ENSMUSG00000035606	Ky	CD1|D9Mgc44e|ky	kyphoscoliosis peptidase	protein-coding
mm_99548.1	chr11	103360468	103360512	+	1	NA	exon (NM_183288, exon 3 of 3)	exon (NM_183288, exon 3 of 3)	3202	NM_183288	544817	Mm.259113	NM_133715	ENSMUSG00000034255	Arhgap27	2310069I04Rik|5730442P18Rik|Gm21552|Sh3d20	Rho GTPase activating protein 27	protein-coding
mm_159009.1	chr1	163951332	163951332	+	1	NA	intron (NM_001286002, intron 12 of 13)	intron (NM_001286002, intron 12 of 13)	21567	NM_028776	240880	Mm.389213	NM_028776	ENSMUSG00000026584	Scyl3	1200016D23Rik|6030457O16|AW214499|Pace1	SCY1-like 3 (S. cerevisiae)	protein-coding
mm_80668.1	chr9	90163058	90163101	+	1	NA	5' UTR (NM_001326351, exon 1 of 24)	5' UTR (NM_001326351, exon 1 of 24)	101	NM_001311115	108153	Mm.102141	NM_001003911	ENSMUSG00000032363	Adamts7	ADAM-TS7|ADAMTS7B	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 7	protein-coding
mm_88510.1	chr10	77978691	77978701	+	1	NA	promoter-TSS (NM_026431)	promoter-TSS (NM_026431)	46	NM_026431	67884	Mm.297512	NM_026431	ENSMUSG00000020284	1810043G02Rik	AV026620|D10Jhu13e	RIKEN cDNA 1810043G02 gene	protein-coding
mm_61994.1	chr7	91118310	91118314	+	1	NA	intron (NM_011807, intron 1 of 22)	intron (NM_011807, intron 1 of 22)	27526	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_140034.1	chr17	74338907	74338938	+	1	NA	promoter-TSS (NM_001162870)	promoter-TSS (NM_001162870)	-65	NM_001162870	50850	Mm.19804	NM_016962	ENSMUSG00000024068	Spast	Spg4|mKIAA1083	spastin	protein-coding
mm_135371.1	chr16	44085997	44086017	-	1	NA	3' UTR (NM_007508, exon 15 of 15)	3' UTR (NM_007508, exon 15 of 15)	53012	NM_007508	11964	Mm.217787	NM_007508	ENSMUSG00000052459	Atp6v1a	AI647066|Atp6a1|Atp6a2|Atp6v1a1|VA68|VPP2	ATPase, H+ transporting, lysosomal V1 subunit A	protein-coding
mm_76365.1	chr8	84773980	84774036	-	1	NA	5' UTR (NM_001081981, exon 1 of 11)	5' UTR (NM_001081981, exon 1 of 11)	361	NM_001081981	18032	Mm.9394	NM_010906	ENSMUSG00000001911	Nfix	CTF|NF-I/X|NF1-X|NFI-X	nuclear factor I/X	protein-coding
mm_46303.1	chr5	100500622	100500657	-	1	NA	promoter-TSS (NM_172714)	promoter-TSS (NM_172714)	0	NM_172714	231506	Mm.212568	NM_172714	ENSMUSG00000035310	Lin54	AI461788	lin-54 homolog (C. elegans)	protein-coding
mm_9187.1	chr1	171129721	171129745	-	1	NA	3' UTR (NM_025321, exon 6 of 6)	3' UTR (NM_025321, exon 6 of 6)	8072	NM_001081275	75472	Mm.32760	NM_029301	ENSMUSG00000026649	Cfap126	1700009P17Rik|AV282292|Flattop|Fltp	cilia and flagella associated protein 126	protein-coding
mm_122202.1	chr14	31781634	31781661	-	1	NA	intron (NM_001024604, intron 1 of 27)	intron (NM_001024604, intron 1 of 27)	48768	NM_001024604	105522	Mm.37660	NM_001024604	ENSMUSG00000014496	Ankrd28	AI465466|AI604979|E430019N21Rik|mKIAA0379	ankyrin repeat domain 28	protein-coding
mm_79151.1	chr9	47739705	47739708	+	1	NA	intron (NM_001025600, intron 1 of 8)	intron (NM_001025600, intron 1 of 8)	78502	NR_046048	100038460	Mm.447649	NR_046048		Gm10677	ENSMUSG00000074363	predicted gene 10677	ncRNA
mm_28100.1	chr3	86142685	86142689	-	1	NA	promoter-TSS (NM_016959)	promoter-TSS (NM_016959)	-19	NM_016959	20091	Mm.391785	NM_016959	ENSMUSG00000028081	Rps3a1	Rps3a	ribosomal protein S3A1	protein-coding
mm_133098.1	chr16	64852309	64852350	+	1	NA	promoter-TSS (NM_001347245)	promoter-TSS (NM_001347245)	244	NM_178647	106143	Mm.10160	NM_178647	ENSMUSG00000054604	Cggbp1	AA960172|AL023996|AW045841	CGG triplet repeat binding protein 1	protein-coding
mm_161648.1	chr17	6138393	6138393	+	1	NA	5' UTR (NM_054040, exon 1 of 14)	5' UTR (NM_054040, exon 1 of 14)	245	NM_054040	68842	Mm.449307	NM_054040	ENSMUSG00000034377	Tulp4	1110057P05Rik|2210038L17Rik|Tusp	tubby like protein 4	protein-coding
mm_162969.1	chr11	11462203	11462207	-	1	NA	exon (NM_015785, exon 1 of 8)	exon (NM_015785, exon 1 of 8)	214	NM_015785	53604	Mm.9500	NM_015785	ENSMUSG00000020193	Zpbp	4930486K01Rik|Iam38|Sp38	zona pellucida binding protein	protein-coding
mm_56621.1	chr6	112721267	112721289	-	1	NA	3' UTR (NM_080448, exon 22 of 22)	3' UTR (NM_080448, exon 22 of 22)	-24608	NM_001167730	58186	Mm.103812	NM_021385	ENSMUSG00000030254	Rad18	2810024C04Rik|Rad18sc	RAD18 E3 ubiquitin protein ligase	protein-coding
mm_6888.1	chr1	84695977	84695994	-	1	NA	TTS (NR_039588)	TTS (NR_039588)	146	NR_039588	100628595		NR_039588	ENSMUSG00000093254	Mir5126	mir-5126|mmu-mir-5126|mu-mir-5126	microRNA 5126	ncRNA
mm_4126.1	chr1	169969766	169969773	+	1	NA	promoter-TSS (NM_010476)	promoter-TSS (NM_010476)	360	NR_040438	67303	Mm.396611	NR_040438	ENSMUSG00000097503	3110045C21Rik	AI838577	RIKEN cDNA 3110045C21 gene	ncRNA
mm_43044.1	chr5	124075305	124075326	+	1	NA	intron (NM_019875, intron 9 of 11)	(CA)n|Simple_repeat|Simple_repeat	20483	NM_019875	56325	Mm.254839	NM_019875	ENSMUSG00000029408	Abcb9	TAPL|mKIAA1520	ATP-binding cassette, sub-family B (MDR/TAP), member 9	protein-coding
mm_15398.1	chr2	156721664	156721680	+	1	NA	promoter-TSS (NR_040505)	promoter-TSS (NR_040505)	393	NM_001042487	228836	Mm.22094	NM_146128	ENSMUSG00000061689	Dlgap4	AI225853|BC024558|DAP-4|DAP4|SAPAP-4|Sapap4|WBP16	discs, large homolog-associated protein 4 (Drosophila)	protein-coding
mm_153797.1	chr19	46039177	46039189	-	1	NA	5' UTR (NM_010697, exon 1 of 11)	5' UTR (NM_010697, exon 1 of 11)	438	NM_010697	16825	Mm.327442	NM_010697	ENSMUSG00000025223	Ldb1	CLIM2|NLI	LIM domain binding 1	protein-coding
mm_155278.1	chrX	61120823	61120843	+	1	NA	intron (NR_030706, intron 4 of 7)	intron (NR_030706, intron 4 of 7)	4455	NR_030706	331424	Mm.127263	NM_177916	ENSMUSG00000071753	C230004F18Rik	-	RIKEN cDNA C230004F18 gene	ncRNA
mm_62400.1	chr7	101108769	101108783	+	1	NA	promoter-TSS (NM_001146010)	promoter-TSS (NM_001146010)	1	NM_199012	207278	Mm.263041	NM_199012	ENSMUSG00000030691	Fchsd2	BC034086|R74866|Sh3md3|mKIAA0769	FCH and double SH3 domains 2	protein-coding
mm_57576.1	chr6	127148783	127148824	-	1	NA	promoter-TSS (NR_040275)	promoter-TSS (NR_040275)	-586	NR_040274	77558	Mm.358918	NR_040273	ENSMUSG00000097166	9330179D12Rik	-	RIKEN cDNA 9330179D12 gene	ncRNA
mm_48540.1	chr5	142905170	142905181	-	1	NA	intron (NM_007393, intron 3 of 5)	intron (NM_007393, intron 3 of 5)	1579	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_43182.1	chr5	128443552	128443560	+	1	NA	Intergenic	Intergenic	-10479	NM_172885	243274	Mm.447698	NM_172885	ENSMUSG00000034310	Tmem132d	C630028F04Rik	transmembrane protein 132D	protein-coding
mm_65087.1	chr7	19260989	19261007	-	1	NA	exon (NM_001282022, exon 6 of 13)	exon (NM_001282022, exon 6 of 13)	10856	NM_001282021	22323	Mm.9684	NM_009499	ENSMUSG00000030403	Vasp	-	vasodilator-stimulated phosphoprotein	protein-coding
mm_70731.1	chr8	18846492	18846512	+	1	NA	5' UTR (NM_026792, exon 1 of 8)	5' UTR (NM_026792, exon 1 of 8)	223	NM_026792	52123	Mm.24117	NM_026792	ENSMUSG00000031467	Agpat5	1110013A05Rik|D8Ertd319e	1-acylglycerol-3-phosphate O-acyltransferase 5 (lysophosphatidic acid acyltransferase, epsilon)	protein-coding
mm_60504.1	chr7	44479434	44479485	+	1	NA	Intergenic	L1MC4|LINE|L1	-5058	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_88517.1	chr10	78050640	78050658	+	1	NA	exon (NM_019448, exon 3 of 13)	exon (NM_019448, exon 3 of 13)	690	NM_001284197	54427	Mm.13433	NM_019448	ENSMUSG00000000730	Dnmt3l	D6Ertd14e|ecat7	DNA (cytosine-5-)-methyltransferase 3-like	protein-coding
mm_126991.1	chr15	94628907	94628922	+	1	NA	promoter-TSS (NM_178789)	promoter-TSS (NM_178789)	-271	NM_178789	320709	Mm.74873	NM_178789	ENSMUSG00000063296	Tmem117	B930062P21Rik	transmembrane protein 117	protein-coding
mm_117399.1	chr13	73692567	73692577	-	1	NA	intron (NM_028878, intron 2 of 11)	intron (NM_028878, intron 2 of 11)	-7254	NM_027780	71390	Mm.105251	NM_027780		Slc6a19os	5430425J12Rik	solute carrier family 6 (neurotransmitter transporter), member 19, opposite strand	protein-coding
mm_123594.1	chr14	67713211	67713229	-	1	NA	exon (NM_175384, exon 4 of 15)	exon (NM_175384, exon 4 of 15)	2390	NM_001110162	108912	Mm.33831	NM_175384	ENSMUSG00000048922	Cdca2	2610311M19Rik|AI586158	cell division cycle associated 2	protein-coding
mm_160973.1	chr11	100440953	100440953	-	1	NA	promoter-TSS (NM_025727)	promoter-TSS (NM_025727)	136	NM_026561	68106	Mm.28738	NM_026561	ENSMUSG00000017176	Nt5c3b	2610037D24Rik|AI841843|C330027I04Rik|Nt5c3l	5'-nucleotidase, cytosolic IIIB	protein-coding
mm_138676.1	chr17	35916429	35916479	+	1	NA	promoter-TSS (NM_025878)	promoter-TSS (NM_025878)	-14	NM_001347380	66973	Mm.29484	NM_025878	ENSMUSG00000024436	Mrps18b	2400002C15Rik	mitochondrial ribosomal protein S18B	protein-coding
mm_27399.1	chr3	51224597	51224625	-	1	NA	5' UTR (NM_009834, exon 1 of 3)	5' UTR (NM_009834, exon 1 of 3)	164	NM_009834	12457	Mm.86541	NM_009834	ENSMUSG00000023087	Noct	AU043840|Ccr4|Ccrn4l	nocturnin	protein-coding
mm_42257.1	chr5	114022284	114022292	+	1	NA	intron (NM_010018, intron 9 of 10)	RLTR17B_Mm|LTR|ERVK	17480	NM_001286396	13142	Mm.20115	NM_010018	ENSMUSG00000042096	Dao	AI987963|DAAO|DAMOX|Dao-1|Dao1	D-amino acid oxidase	protein-coding
mm_40998.1	chr5	77351226	77351251	+	1	NA	exon (NM_008048, exon 4 of 5)	exon (NM_008048, exon 4 of 5)	40754	NM_153798	231329	Mm.273217	NM_153798	ENSMUSG00000029250	Polr2b	Pol2rb|Rpb140|Rpb2	polymerase (RNA) II (DNA directed) polypeptide B	protein-coding
mm_111475.1	chr12	98683685	98683693	-	1	NA	intron (NM_011877, intron 13 of 18)	intron (NM_011877, intron 13 of 18)	50956	NM_011877	24000	Mm.4420	NM_011877	ENSMUSG00000021009	Ptpn21	PTPD1|PTPRL10	protein tyrosine phosphatase, non-receptor type 21	protein-coding
mm_135754.1	chr16	55994971	55994984	-	1	NA	intron (NM_173026, intron 5 of 10)	MTE2b|LTR|ERVL-MaLR	-20360	NR_027965	66391	Mm.472722	NM_133677	ENSMUSG00000102101	Zbtb11os1	2310061J03Rik	zinc finger and BTB domain containing 11, opposite strand 1	ncRNA
mm_500.1	chr1	36986258	36986269	+	1	NA	Intergenic	RMER10B|LTR|ERVL	-46736	NM_018872	56030	Mm.186943	NM_018872	ENSMUSG00000026116	Tmem131	2610524E03Rik|CC28|D1Bwg0491e|Neg|RW1|YR-23|mKIAA0257	transmembrane protein 131	protein-coding
mm_136056.1	chr16	78577204	78577219	-	1	NA	promoter-TSS (NM_001252440)	promoter-TSS (NM_001252440)	-523	NM_025967	67102	Mm.37332	NM_025967	ENSMUSG00000022864	D16Ertd472e	1700010I10Rik|2310009O17Rik|E330003K22Rik|Eurl	DNA segment, Chr 16, ERATO Doi 472, expressed	protein-coding
mm_60179.1	chr7	42488767	42488775	+	1	NA	intron (NM_001309389, intron 2 of 4)	intron (NM_001309389, intron 2 of 4)	16982	NM_001309389	434178	Mm.333810	NM_001309388	ENSMUSG00000092416	Zfp141	-	zinc finger protein 141	protein-coding
mm_57986.1	chr6	136003455	136003462	-	1	NA	intron (NM_008171, intron 4 of 14)	intron (NM_008171, intron 4 of 14)	170053	NM_008171	14812	Mm.436649	NM_008171	ENSMUSG00000030209	Grin2b	AW490526|GluN2B|NR2B|Nmdar2b	glutamate receptor, ionotropic, NMDA2B (epsilon 2)	protein-coding
mm_165390.1	chr2	131855247	131855273	-	1	NA	3' UTR (NM_001166206, exon 2 of 2)	3' UTR (NM_001166206, exon 2 of 2)	4487	NM_001166206	71995	Mm.22	NM_028045	ENSMUSG00000037482	Erv3	1600014E20Rik|AA389086|AI426069|AI448024|D19349	endogenous retroviral sequence 3	protein-coding
mm_142957.1	chr17	56120294	56120314	-	1	NA	exon (NM_029796, exon 2 of 2)	exon (NM_029796, exon 2 of 2)	1642	NM_029796	76905	Mm.348025	NM_029796	ENSMUSG00000037095	Lrg1	1300008B03Rik|2310031E04Rik|Lrg|Lrhg	leucine-rich alpha-2-glycoprotein 1	protein-coding
mm_79034.1	chr9	46119019	46119022	+	1	NA	intron (NM_027498, intron 1 of 24)	intron (NM_027498, intron 1 of 24)	106200	NM_027498	70661	Mm.219459	NM_027498	ENSMUSG00000034135	Sik3	5730525O22Rik|9030204A07Rik|AI447252|AI846254|AI849445|Qsk|SIK-3|mKIAA0999	SIK family kinase 3	protein-coding
mm_34937.1	chr4	155841147	155841167	+	1	NA	exon (NM_024263, exon 3 of 10)	exon (NM_024263, exon 3 of 10)	1477	NM_024263	74761	Mm.159028	NM_024263	ENSMUSG00000029070	Mxra8	1200013A08Rik|1700095D18Rik|AI131686|Asp3|Dicam	matrix-remodelling associated 8	protein-coding
mm_27137.1	chr3	32599375	32599383	-	1	NA	intron (NM_013531, intron 2 of 9)	MLTR11B|LTR|ERVK	17156	NM_013531	14696	Mm.139192	NM_013531	ENSMUSG00000027669	Gnb4	6720453A21Rik|G(beta)4	guanine nucleotide binding protein (G protein), beta 4	protein-coding
mm_1929.1	chr1	86110890	86110905	+	1	NA	5' UTR (NM_008311, exon 2 of 4)	5' UTR (NM_008311, exon 2 of 4)	1073	NM_008311	15559	Mm.439747	NM_008311	ENSMUSG00000026228	Htr2b	5-HT2B|AJ012488|AV377389	5-hydroxytryptamine (serotonin) receptor 2B	protein-coding
mm_155319.1	chrX	62287148	62287161	+	1	NA	promoter-TSS (NM_001199996)	promoter-TSS (NM_001199996)	12	NM_001199996	74437	Mm.85792	NM_001199996	ENSMUSG00000045330	4933402E13Rik	-	RIKEN cDNA 4933402E13 gene	protein-coding
mm_33840.1	chr4	135759706	135759720	+	1	NA	promoter-TSS (NM_001085509)	promoter-TSS (NM_001085509)	-2	NM_001085509	242702	Mm.318639	NM_001085509	ENSMUSG00000037139	Myom3	8430427K15Rik|Gm434	myomesin family, member 3	protein-coding
mm_61288.1	chr7	67645470	67645506	+	1	NA	promoter-TSS (NR_028144)	promoter-TSS (NR_028144)	-252	NR_028143	67867	Mm.31247	NM_027413	ENSMUSG00000030556	Lrrc28	1300004K21Rik|2210012C09Rik|2310058O11Rik	leucine rich repeat containing 28	protein-coding
mm_13338.1	chr2	102787464	102787474	+	1	NA	3' UTR (NM_001077514, exon 11 of 11)	3' UTR (NM_001077514, exon 11 of 11)	81031	NM_001077515	20511	Mm.267547	NM_011393	ENSMUSG00000005089	Slc1a2	1700091C19Rik|2900019G14Rik|AI159670|Eaat2|GLT-1|GLT1|MGLT1	solute carrier family 1 (glial high affinity glutamate transporter), member 2	protein-coding
mm_30684.1	chr4	11321931	11321937	+	1	NA	intron (NM_001081201, intron 1 of 18)	CpG	197	NM_001081201	381510	Mm.331486	NM_001081201	ENSMUSG00000045205	Dpy19l4	Gm1023|Narg3	dpy-19-like 4 (C. elegans)	protein-coding
mm_23147.1	chr3	39979737	39979743	+	1	NA	Intergenic	Intergenic	543172	NR_040445	100040882	Mm.272869	NR_040445	ENSMUSG00000037884	1700017G19Rik	-	RIKEN cDNA 1700017G19 gene	ncRNA
mm_107682.1	chr12	54656753	54656774	+	1	NA	promoter-TSS (NM_134054)	promoter-TSS (NM_134054)	-191	NM_134054	104725	Mm.485026	NM_134054	ENSMUSG00000044408	Sptssa	1110002B05Rik|AA407909|AA409588|AU041967|Ssspta	serine palmitoyltransferase, small subunit A	protein-coding
mm_60053.1	chr7	31149975	31149992	+	1	NA	intron (NM_027898, intron 1 of 18)	intron (NM_027898, intron 1 of 18)	1067	NM_027898	52857	Mm.27366	NM_027898	ENSMUSG00000001248	Gramd1a	1300003M23Rik|AI415002|AW547240|D7Bwg0611e	GRAM domain containing 1A	protein-coding
mm_75066.1	chr8	33806743	33806783	-	1	NA	exon (NM_019733, exon 6 of 9)	exon (NM_019733, exon 6 of 9)	-58993	NM_001206849	72632	Mm.443483	NM_001206849	ENSMUSG00000094500	Smim18	2700090O03Rik|AI835723	small integral membrane protein 18	protein-coding
mm_140961.1	chr17	24644983	24644994	-	1	NA	promoter-TSS (NM_023449)	promoter-TSS (NM_023449)	-31	NM_023449	65962	Mm.21587	NM_023055	ENSMUSG00000002504	Slc9a3r2	0610011L07Rik|1200011K07Rik|2010007A20Rik|E3karp|NHERF-2|Nherf2|Octs2|Sip-1|Sip1|Sryip1|Tka-1	solute carrier family 9 (sodium/hydrogen exchanger), member 3 regulator 2	protein-coding
mm_108963.1	chr12	102398324	102398357	+	1	NA	exon (NM_011175, exon 11 of 14)	exon (NM_011175, exon 11 of 14)	41473	NM_011175	19141	Mm.17185	NM_011175	ENSMUSG00000021190	Lgmn	AEP|AI746452|AU022324|Prsc1	legumain	protein-coding
mm_38153.1	chr4	134927369	134927371	-	1	NA	TTS (NM_023665)	TTS (NM_023665)	-3610	NM_026780	68592	Mm.29989	NM_026780	ENSMUSG00000028821	Syf2	1110018L13Rik|Cbpin|D4Bwg1551e|Gcipip|Ntc31|mp29|p29	SYF2 homolog, RNA splicing factor (S. cerevisiae)	protein-coding
mm_40979.1	chr5	77097454	77097460	+	1	NA	intron (NM_175606, intron 1 of 2)	intron (NM_175606, intron 1 of 2)	-2190	NM_001159900	74318	Mm.181852	NM_175606	ENSMUSG00000059325	Hopx	1110018K11Rik|1200015P04Rik|2300002F06Rik|AI848177|AW490897|Cameo|Hdop|Hod|Hop|Ob1|Obl|Toto	HOP homeobox	protein-coding
mm_96323.1	chr11	64079548	64079574	+	1	NA	promoter-TSS (NM_178379)	promoter-TSS (NM_178379)	77	NR_033780	66456	Mm.124828	NR_033780	ENSMUSG00000087497	2810001G20Rik	AW045514	RIKEN cDNA 2810001G20 gene	ncRNA
mm_169798.1	chr16	16820135	16820152	-	1	NA	promoter-TSS (NM_001258458)	promoter-TSS (NM_001258458)	53	NM_001258458	665562	Mm.444358	NM_001258458		Rpl31-ps12	EG665562|Gm7689	ribosomal protein L31, pseudogene 1 2	protein-coding
mm_157328.1	chrX	23318897	23318909	-	1	NA	intron (NM_026167, intron 2 of 8)	RLTR16B_MM|LTR|ERVK	-33344	NM_001290476	67455	Mm.224306	NM_026167	ENSMUSG00000036782	Klhl13	1200009K10Rik|AI451128|Bklhd2|D130072F20Rik	kelch-like 13	protein-coding
mm_126140.1	chr15	78348216	78348229	+	1	NA	promoter-TSS (NR_106138)	promoter-TSS (NR_106138)	-377	NR_106137	102465776		NR_106137	ENSMUSG00000098996	Mir7676-1	Gm27600|mmu-mir-7676-1	microRNA 7676-1	ncRNA
mm_81890.1	chr9	119402227	119402269	+	1	NA	promoter-TSS (NM_007397)	promoter-TSS (NM_007397)	70	NM_007397	11481	Mm.8940	NM_007397	ENSMUSG00000061393	Acvr2b	4930516B21Rik|ActRIIB	activin receptor IIB	protein-coding
mm_14922.1	chr2	151373933	151373941	+	1	NA	Intergenic	Intergenic	58512	NR_131976	100125594	Mm.381283	NR_131976	ENSMUSG00000087495	LOC100125594	-	uncharacterized LOC100125594	ncRNA
mm_160614.1	chr9	88719800	88719800	-	1	NA	promoter-TSS (NM_001128601)	promoter-TSS (NM_001128601)	-2	NM_001128601	100039707	Mm.347377	NM_001128601	ENSMUSG00000079427	Mthfsl	Gm2382	5, 10-methenyltetrahydrofolate synthetase-like	protein-coding
mm_16828.1	chr2	11484773	11484791	-	1	NA	exon (NM_001177754, exon 8 of 16)	exon (NM_001177754, exon 8 of 16)	17308	NM_001177754	170768	Mm.19669	NM_133232	ENSMUSG00000026773	Pfkfb3	E330010H22Rik|iPFK-2|uPFK-2	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	protein-coding
mm_106867.1	chr12	8009808	8009820	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	32137	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_69067.1	chr7	126928783	126928814	-	1	NA	promoter-TSS (NM_172747)	promoter-TSS (NM_172747)	-81	NM_172747	233877	Mm.245897	NM_172747	ENSMUSG00000030685	Kctd13	1500003N18Rik|AV259508|PDIP1alpha|Pdip1|Poldip1	potassium channel tetramerisation domain containing 13	protein-coding
mm_167049.1	chr7	82867785	82867794	+	1	NA	exon (NM_175366, exon 1 of 2)	exon (NM_175366, exon 1 of 2)	456	NM_175366	108797	Mm.306789	NM_175366	ENSMUSG00000057706	Mex3b	4931439A04Rik|M-04814|Rkhd3|mKIAA2009	mex3 RNA binding family member B	protein-coding
mm_23949.1	chr3	84843227	84843236	+	1	NA	intron (NM_001177773, intron 1 of 13)	intron (NM_001177773, intron 1 of 13)	-20914	NM_001177774	50754	Mm.196475	NM_080428	ENSMUSG00000028086	Fbxw7	1110001A17Rik|AGO|Cdc4|Fbw7|Fbwd6|Fbx30|Fbxo30|Fbxw6|SEL-10	F-box and WD-40 domain protein 7	protein-coding
mm_3789.1	chr1	157412255	157412263	+	1	NA	promoter-TSS (NR_027984)	promoter-TSS (NR_027984)	-93	NR_027984	69953	Mm.286863	NM_027274	ENSMUSG00000049881	2810025M15Rik	AI429618	RIKEN cDNA 2810025M15 gene	ncRNA
mm_50632.1	chr6	51171202	51171215	+	1	NA	Intergenic	Intergenic	98702	NR_029719	387166		NR_029719	ENSMUSG00000065505	Mir148a	Mirn148|Mirn148a|mir-148a	microRNA 148a	ncRNA
mm_137793.1	chr17	29660711	29660721	+	1	NA	5' UTR (NM_028791, exon 1 of 24)	5' UTR (NM_028791, exon 1 of 24)	121	NM_028791	74157	Mm.390979	NM_028791	ENSMUSG00000024019	Cmtr1	1300018I05Rik|AI451264|Ftsjd2|MTr1	cap methyltransferase 1	protein-coding
mm_81495.1	chr9	110032127	110032139	+	1	NA	exon (NM_008633, exon 6 of 19)	exon (NM_008633, exon 6 of 19)	-19888	NM_001311163	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_67416.1	chr7	80232557	80232633	-	1	NA	promoter-TSS (NM_178752)	promoter-TSS (NM_178752)	210	NM_001291276	23991	Mm.30217	NM_011870	ENSMUSG00000030538	Cib1	Cibkip|Kip|Prkdcip	calcium and integrin binding 1 (calmyrin)	protein-coding
mm_50809.1	chr6	54326829	54326845	+	1	NA	promoter-TSS (NM_030024)	promoter-TSS (NM_030024)	-175	NM_030024	78004	Mm.41984	NM_030024	ENSMUSG00000045725	Prr15	E130201N16Rik|G90	proline rich 15	protein-coding
mm_21920.1	chr2	166904534	166904538	-	1	NA	Intergenic	RSINE1|SINE|B4	-1560	NM_023565	110750	Mm.22417	NM_023565	ENSMUSG00000002718	Cse1l	2610100P18Rik|AA407533|Capts|Cas|Xpo2	chromosome segregation 1-like (S. cerevisiae)	protein-coding
mm_136204.1	chr16	89826412	89826418	-	1	NA	intron (NM_009384, intron 15 of 27)	intron (NM_009384, intron 15 of 27)	-8063	NM_001145887	21844	Mm.310902	NM_009384	ENSMUSG00000002489	Tiam1	AI847750|D16Ium10|D16Ium10e	T cell lymphoma invasion and metastasis 1	protein-coding
mm_66074.1	chr7	30914833	30914878	-	1	NA	promoter-TSS (NM_001346089)	promoter-TSS (NM_001346089)	67	NM_001346084	17136	Mm.241355	NM_010758	ENSMUSG00000036634	Mag	Gma|siglec-4a	myelin-associated glycoprotein	protein-coding
mm_106934.1	chr12	8674130	8674150	+	1	NA	promoter-TSS (NM_001160219)	promoter-TSS (NM_001160219)	6	NM_001160222	80913	Mm.341243	NM_030723	ENSMUSG00000020594	Pum2	5730503J23Rik|Pumm2	pumilio RNA-binding family member 2	protein-coding
mm_146144.1	chr18	74779191	74779199	+	1	NA	promoter-TSS (NR_028560)	promoter-TSS (NR_028560)	-17	NM_177470	52538	Mm.245724	NM_177470	ENSMUSG00000036880	Acaa2	0610011L04Rik|AI255831|AI265397|D18Ertd240e	acetyl-Coenzyme A acyltransferase 2 (mitochondrial 3-oxoacyl-Coenzyme A thiolase)	protein-coding
mm_90532.1	chr10	128086310	128086322	+	1	NA	TTS (NR_030442)	TTS (NR_030442)	1030	NR_030442	751518		NR_030442	ENSMUSG00000093245	Mir677	Mirn677|mir-677|mmu-mir-677	microRNA 677	ncRNA
mm_41389.1	chr5	90769452	90769464	+	1	NA	3' UTR (NM_023785, exon 3 of 3)	3' UTR (NM_023785, exon 3 of 3)	940	NM_023785	57349	Mm.293614	NM_023785	ENSMUSG00000029372	Ppbp	2400003M24Rik|AI854500|CTAP3|CTAPIII|Cxcl7|LA-PF4|LDGF|MDGF|NAP-2|NAP-2-L1|Scyb7|TGB|TGB1|THBGB1|b-TG1|beta-TG	pro-platelet basic protein	protein-coding
mm_37999.1	chr4	133673138	133673160	-	1	NA	promoter-TSS (NM_178698)	promoter-TSS (NM_178698)	-502	NM_001145956	230801	Mm.217004	NM_178698	ENSMUSG00000043257	Pigv	B330013B03|D430024F16Rik	phosphatidylinositol glycan anchor biosynthesis, class V	protein-coding
mm_4472.1	chr1	173419348	173419375	+	1	NA	Intergenic	Intergenic	-1243	NM_001013779	383619	Mm.131453	NM_001013779	ENSMUSG00000037860	Aim2	Gm1313|Ifi210	absent in melanoma 2	protein-coding
mm_116596.1	chr13	48546453	48546465	-	1	NA	Intergenic	CpG	-8187	NR_029725	387244		NR_029725	ENSMUSG00000065421	Mirlet7a-1	Let-7a|Mirnlet7a|Mirnlet7a-1|let-7a-1	microRNA let7a-1	ncRNA
mm_67411.1	chr7	80099092	80099102	-	1	NA	exon (NM_173011, exon 4 of 11)	exon (NM_173011, exon 4 of 11)	16253	NM_173011	269951	Mm.246432	NM_173011	ENSMUSG00000030541	Idh2	E430004F23|IDPm|Idh-2	isocitrate dehydrogenase 2 (NADP+), mitochondrial	protein-coding
mm_31655.1	chr4	59868485	59868497	+	1	NA	intron (NM_172468, intron 3 of 8)	intron (NM_172468, intron 3 of 8)	46565	NM_021053	30936	Mm.284433	NM_021053	ENSMUSG00000028386	Slc46a2	5430429N04Rik|Ly110|TSO-1C12|Tscot	solute carrier family 46, member 2	protein-coding
mm_133626.1	chr16	91563580	91563585	+	1	NA	3' UTR (NM_008338, exon 7 of 7)	3' UTR (NM_008338, exon 7 of 7)	16488	NM_008338	15980	Mm.249364	NM_008338	ENSMUSG00000022965	Ifngr2	Ifgr2|Ifgt	interferon gamma receptor 2	protein-coding
mm_5560.1	chr1	38824650	38824654	-	1	NA	Intergenic	Intergenic	-3437	NM_001029878	381338	Mm.487137	NM_028403	ENSMUSG00000048814	Lonrf2	2900060P06Rik|AI851349	LON peptidase N-terminal domain and ring finger 2	protein-coding
mm_129404.1	chr15	78285216	78285252	-	1	NA	promoter-TSS (NR_106137).2	promoter-TSS (NR_106137).2	-385	NR_106137	102465776		NR_106137	ENSMUSG00000098996	Mir7676-1	Gm27600|mmu-mir-7676-1	microRNA 7676-1	ncRNA
mm_164786.1	chr18	9212185	9212193	+	1	NA	promoter-TSS (NM_008058)	promoter-TSS (NM_008058)	-667	NM_008058	14370	Mm.184289	NM_008058	ENSMUSG00000036904	Fzd8	Fz8	frizzled class receptor 8	protein-coding
mm_8004.1	chr1	134556988	134557002	-	1	NA	Intergenic	CpG	-3183	NM_152895	75605	Mm.28995	NM_152895	ENSMUSG00000042207	Kdm5b	2010009J12Rik|2210016I17Rik|AW556288|D1Ertd202e|Jarid1b|PLU-1|PUT1|Plu1|RBBP2H1A|Rb-Bp2|mKIAA4034	lysine (K)-specific demethylase 5B	protein-coding
mm_132084.1	chr16	30510670	30510694	+	1	NA	Intergenic	CpG	39896	NM_172614	224090	Mm.241459	NM_172614	ENSMUSG00000022537	Tmem44	1700007N03Rik|9330161C17Rik|B230220N21	transmembrane protein 44	protein-coding
mm_161141.1	chr13	21478857	21478857	+	1	NA	promoter-TSS (NM_001039115)	promoter-TSS (NM_001039115)	8	NM_001039115	544922	Mm.441300	NM_001039115	ENSMUSG00000054931	Zkscan4	AI841875|Gm11272|OTTMUSG00000000421	zinc finger with KRAB and SCAN domains 4	protein-coding
mm_111685.1	chr12	103442360	103442378	-	1	NA	exon (NM_029803, exon 4 of 4)	exon (NM_029803, exon 4 of 4)	1311	NM_029803	76933	Mm.271275	NM_029803	ENSMUSG00000079017	Ifi27l2a	2310061N23Rik|Ifi27|Isg12|Isg12(b1)	interferon, alpha-inducible protein 27 like 2A	protein-coding
mm_170535.1	chr19	3851771	3851781	+	1	NA	promoter-TSS (NM_001271496)	promoter-TSS (NM_001271496)	3	NR_073190	12660	Mm.225505	NM_013490	ENSMUSG00000024843	Chka	CK|CK/EK-alpha|Chetk-alpha|Chk|ChoK|EK|EtnK-alpha	choline kinase alpha	protein-coding
mm_50090.1	chr6	41524928	41524937	+	1	NA	exon (NM_009430, exon 5 of 5)	exon (NM_009430, exon 5 of 5)	3156	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_21821.1	chr2	165287803	165287845	-	1	NA	promoter-TSS (NM_001252574)	promoter-TSS (NM_001252574)	14	NM_001252575	228875	Mm.21184	NM_144893	ENSMUSG00000017664	Slc35c2	C85957|CGI-15|D2Wsu58e|Ovcov1	solute carrier family 35, member C2	protein-coding
mm_59789.1	chr7	28972606	28972633	+	1	NA	exon (NM_028659, exon 7 of 8)	exon (NM_028659, exon 7 of 8)	9269	NM_001285943	73830	Mm.29714	NM_028659	ENSMUSG00000053565	Eif3k	1200009C21Rik|Eif3s12	eukaryotic translation initiation factor 3, subunit K	protein-coding
mm_131820.1	chr16	22920441	22920469	+	1	NA	5' UTR (NM_021564, exon 1 of 8)	5' UTR (NM_021564, exon 1 of 8)	233	NM_001083904	59083	Mm.28461	NM_021564	ENSMUSG00000022871	Fetub	2310011O17Rik|AI255764|D17980|Gugu	fetuin beta	protein-coding
mm_168228.1	chr10	80053682	80053691	+	1	NA	promoter-TSS (NM_001037741)	promoter-TSS (NM_001037741)	198	NM_008162	625249	Mm.332810	NM_008162	ENSMUSG00000075706	Gpx4	GPx-4|GSHPx-4|PHGPx|mtPHGPx|snGPx	glutathione peroxidase 4	protein-coding
mm_130329.1	chr15	97719681	97719693	-	1	NA	intron (NM_001168693, intron 4 of 9)	intron (NM_001168693, intron 4 of 9)	1463	NM_008902	19011	Mm.1001	NM_008902	ENSMUSG00000022468	Endou	Pp11r|Tcl-30	endonuclease, polyU-specific	protein-coding
mm_109133.1	chr12	105899857	105899866	+	1	NA	Intergenic	MLT1J|LTR|ERVL-MaLR	-110402	NM_011705	22367	Mm.2981	NM_011705	ENSMUSG00000021115	Vrk1	51PK	vaccinia related kinase 1	protein-coding
mm_123920.1	chr14	73364594	73364623	-	1	NA	exon (NM_008410, exon 5 of 6)	exon (NM_008410, exon 5 of 6)	20663	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_85004.1	chr9	86880492	86880502	-	1	NA	promoter-TSS (NM_001277986)	promoter-TSS (NM_001277986)	-48	NM_001277983	20616	Mm.281651	NM_013669	ENSMUSG00000033419	Snap91	91kDa|AP180|F1-20|mKIAA0656	synaptosomal-associated protein 91	protein-coding
mm_31930.1	chr4	86053688	86053721	+	1	NA	promoter-TSS (NM_029967)	promoter-TSS (NM_029967)	-211	NM_029967	77739	Mm.331690	NM_029967	ENSMUSG00000066113	Adamtsl1	5930437A14Rik|6720426B09Rik|ADAMTSL-1	ADAMTS-like 1	protein-coding
mm_143072.1	chr17	57023546	57023555	-	1	NA	exon (NM_010613, exon 15 of 18)	exon (NM_010613, exon 15 of 18)	7957	NM_010613	16549	Mm.34296	NM_010613	ENSMUSG00000007670	Khsrp	6330409F21Rik|Fbp2|Fubp2|Ksrp	KH-type splicing regulatory protein	protein-coding
mm_167286.1	chr8	40511478	40511488	+	1	NA	promoter-TSS (NM_033560)	promoter-TSS (NM_033560)	271	NM_001271543	18983	Mm.272551	NM_011135	ENSMUSG00000031601	Cnot7	AU022737|CAF-1|Caf1|Pop2	CCR4-NOT transcription complex, subunit 7	protein-coding
mm_71328.1	chr8	44961442	44961445	+	1	NA	intron (NM_001081286, intron 1 of 25)	AT_rich|Low_complexity|Low_complexity	11235	NM_001081286	14107	Mm.27365	NM_001081286	ENSMUSG00000070047	Fat1	2310038E12Rik|AU023433|Fath|mFat1	FAT atypical cadherin 1	protein-coding
mm_66059.1	chr7	30744170	30744199	-	1	NA	promoter-TSS (NM_001290631)	promoter-TSS (NM_001290631)	-503	NM_001290631	14447	Mm.436562	NM_008085	ENSMUSG00000061099	Gapdhs	Gapd-s|Gapds	glyceraldehyde-3-phosphate dehydrogenase, spermatogenic	protein-coding
mm_103722.1	chr11	79530476	79530488	-	1	NA	5' UTR (NM_010161, exon 1 of 2)	5' UTR (NM_010161, exon 1 of 2)	127	NM_146023	101488212	Mm.439665	NM_146023	ENSMUSG00000070354	Gm21975	Evi2a-evi2b	predicted gene 21975	protein-coding
mm_123871.1	chr14	72589827	72589885	-	1	NA	exon (NM_207636, exon 5 of 26)	exon (NM_207636, exon 5 of 26)	120147	NM_207636	319448	Mm.205421	NM_207636	ENSMUSG00000033487	Fndc3a	1700094E19Rik|D14Ertd453e|F730017H24Rik|Fndc3|sys	fibronectin type III domain containing 3A	protein-coding
mm_157197.1	chrX	12128387	12128412	-	1	NA	intron (NM_001168321, intron 1 of 13)	CpG	31947	NR_045434	71458	Mm.196328	NM_029510	ENSMUSG00000040363	Bcor	2900008C10Rik|5830466J11Rik|8430401K06Rik|BcorR|D930024N20Rik|mKIAA1575	BCL6 interacting corepressor	protein-coding
mm_167475.1	chr8	128359170	128359181	+	1	NA	promoter-TSS (NR_035436)	promoter-TSS (NR_035436)	-66	NR_035436	100316680		NR_035436	ENSMUSG00000084523	Mir1903	Mirn1903|mmu-mir-1903	microRNA 1903	ncRNA
mm_42924.1	chr5	122721792	122721812	+	1	NA	intron (NM_001310720, intron 5 of 10)	intron (NM_001310720, intron 5 of 10)	14258	NM_001310718	18438	Mm.290884	NM_011026	ENSMUSG00000029470	P2rx4	AI504491|AW555605|D5Ertd444e|P2X4	purinergic receptor P2X, ligand-gated ion channel 4	protein-coding
mm_137149.1	chr17	23679364	23679377	+	1	NA	promoter-TSS (NM_018777)	promoter-TSS (NM_018777)	5	NM_018777	54419	Mm.86421	NM_018777	ENSMUSG00000023906	Cldn6	AL024037	claudin 6	protein-coding
mm_98309.1	chr11	90033633	90033651	+	1	NA	5' UTR (NM_026433, exon 2 of 3)	5' UTR (NM_026433, exon 2 of 3)	3294	NM_026433	67888	Mm.212428	NM_026433	ENSMUSG00000069763	Tmem100	1810057C19Rik|AV011897	transmembrane protein 100	protein-coding
mm_33300.1	chr4	129007712	129007717	+	1	NA	exon (NM_016895, exon 5 of 7)	exon (NM_016895, exon 5 of 7)	14490	NM_001033966	11637	Mm.29460	NM_016895	ENSMUSG00000028792	Ak2	Ak-2|D4Ertd220e	adenylate kinase 2	protein-coding
mm_172295.1	chr6	97647898	97647900	-	1	NA	Intergenic	ERVB7_1-LTR_MM|LTR|ERVK	-30242	NM_145148	232288	Mm.27789	NM_145148	ENSMUSG00000030064	Frmd4b	6030440G05Rik|C87375|GOBLIN|GRSP1|R74720	FERM domain containing 4B	protein-coding
mm_20120.1	chr2	121235803	121235846	-	1	NA	exon (NM_013735, exon 12 of 28)	exon (NM_013735, exon 12 of 28)	35583	NM_001290830	27223	Mm.215389	NM_013735	ENSMUSG00000043909	Trp53bp1	53BP1|Tp53bp1|m53BP1|p53BP1	transformation related protein 53 binding protein 1	protein-coding
mm_100373.1	chr11	119145120	119145123	+	1	NA	3' UTR (NM_172443, exon 12 of 12)	3' UTR (NM_172443, exon 12 of 12)	9016	NR_105899	102465563		NR_105899	ENSMUSG00000098704	Mir6934	Gm27523|mmu-mir-6934	microRNA 6934	ncRNA
mm_52715.1	chr6	119481546	119481563	+	1	NA	3' UTR (NM_133940, exon 1 of 1)	3' UTR (NM_133940, exon 1 of 1)	1886	NM_133940	101358	Mm.125477	NM_133940	ENSMUSG00000030019	Fbxl14	AW322056|Fbx14l	F-box and leucine-rich repeat protein 14	protein-coding
mm_152629.1	chr19	12491939	12491983	-	1	NA	exon (NM_172442, exon 2 of 9)	exon (NM_172442, exon 2 of 9)	10035	NM_172442	207521	Mm.247695	NM_172442	ENSMUSG00000039982	Dtx4	AI449438|BC044798|D930042H13|RNF155	deltex 4, E3 ubiquitin ligase	protein-coding
mm_4091.1	chr1	167283914	167283923	+	1	NA	intron (NM_030724, intron 1 of 6)	CpG	1209	NM_030724	80914	Mm.280895	NM_030724	ENSMUSG00000026558	Uck2	AA407809|AI481316|AU018180|AU020720|TSA903|UK|UMK|Umpk	uridine-cytidine kinase 2	protein-coding
mm_94979.1	chr11	31733985	31733988	+	1	NA	Intergenic	Intergenic	-62124	NM_001024919	69556	Mm.34183	NM_001024919	ENSMUSG00000044502	Bod1	2310022M17Rik|BOD2.1|Fam44b	biorientation of chromosomes in cell division 1	protein-coding
mm_156058.1	chrX	109154300	109154315	+	1	NA	exon (NM_019989, exon 3 of 4)	exon (NM_019989, exon 3 of 4)	-42449	NM_001037917	622976	Mm.482747	NM_001037917	ENSMUSG00000048621	Gm6377	EG622976	predicted gene 6377	protein-coding
mm_61018.1	chr7	49398080	49398092	+	1	NA	exon (NM_001111016, exon 5 of 39)	exon (NM_001111016, exon 5 of 39)	151897	NM_175272	78286	Mm.333881	NM_175272	ENSMUSG00000052512	Nav2	5330421F07Rik|AU067780|BQ960892|HELAD1|POMFIL2|RAINB1|RAINB2|Unc53H2|mKIAA3015	neuron navigator 2	protein-coding
mm_48075.1	chr5	136695616	136695639	-	1	NA	intron (NM_001085387, intron 2 of 4)	intron (NM_001085387, intron 2 of 4)	1450	NM_001085387	59310	Mm.5178	NM_021611	ENSMUSG00000005474	Myl10	1700027I08Rik|Mylc2pl|PLRLC	myosin, light chain 10, regulatory	protein-coding
mm_111701.1	chr12	103676719	103676729	-	1	NA	promoter-TSS (NM_001310472)	promoter-TSS (NM_001310472)	38	NM_001310472	194604		NM_001310472	ENSMUSG00000071179	Serpina16	Gm46	serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 16	protein-coding
mm_167169.1	chr7	137314252	137314254	-	1	NA	5' UTR (NM_001113414, exon 1 of 16)	5' UTR (NM_001113414, exon 1 of 16)	192	NM_001113415	13593	Mm.258708	NM_010096	ENSMUSG00000010476	Ebf3	3110018A08Rik|O/E-2|mKIAA4201	early B cell factor 3	protein-coding
mm_61152.1	chr7	58658182	58658294	+	1	NA	promoter-TSS (NM_009728)	promoter-TSS (NM_009728)	36	NM_009728	11982	Mm.135129	NM_009728	ENSMUSG00000025324	Atp10a	Atp10c|pfatp	ATPase, class V, type 10A	protein-coding
mm_15555.1	chr2	158487946	158487948	+	1	NA	intron (NM_001291137, intron 27 of 30)	intron (NM_001291137, intron 27 of 30)	-14665	NM_145635	246747	Mm.28800	NM_145635	ENSMUSG00000044405	Adig	SMAF-1|Smaf1	adipogenin	protein-coding
mm_93574.1	chr10	116581825	116581875	-	1	NA	promoter-TSS (NM_028082)	promoter-TSS (NM_028082)	-339	NM_001037846	72068	Mm.351553	NM_028082	ENSMUSG00000020166	Cnot2	2600016M12Rik|2810470K03Rik|AA537049|AA959607|AW557563|C79650	CCR4-NOT transcription complex, subunit 2	protein-coding
mm_153867.1	chr19	46673064	46673072	-	1	NA	promoter-TSS (NM_007809)	promoter-TSS (NM_007809)	-68	NM_007809	13074	Mm.1262	NM_007809	ENSMUSG00000003555	Cyp17a1	Cyp17|p450c17	cytochrome P450, family 17, subfamily a, polypeptide 1	protein-coding
mm_132387.1	chr16	34994848	34994869	+	1	NA	intron (NM_139300, intron 29 of 31)	intron (NM_139300, intron 29 of 31)	-27563	NM_023587	70757	Mm.27286	NM_023587	ENSMUSG00000035376	Hacd2	6330408J20Rik|AI255777|AI481689|Hcad2|Ptplb	3-hydroxyacyl-CoA dehydratase 2	protein-coding
mm_143677.1	chr17	80053363	80053368	-	1	NA	intron (NM_144802, intron 2 of 12)	PB1D11|SINE|Alu	8903	NM_144802	72692	Mm.64579	NM_144802	ENSMUSG00000024095	Hnrnpll	2510028H02Rik|2810036L13Rik|AI256697|AI852082|Hnrpll	heterogeneous nuclear ribonucleoprotein L-like	protein-coding
mm_121756.1	chr14	19627442	19627447	-	1	NA	Intergenic	Intergenic	-24857	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_48834.1	chr5	149184955	149184977	-	1	NA	intron (NM_001115150, intron 1 of 7)	CpG	406	NM_001115149	231915	Mm.29402	NM_001013378	ENSMUSG00000041264	Uspl1	E430026A01Rik	ubiquitin specific peptidase like 1	protein-coding
mm_142961.1	chr17	56120794	56120818	-	1	NA	exon (NM_029796, exon 2 of 2)	exon (NM_029796, exon 2 of 2)	1140	NM_029796	76905	Mm.348025	NM_029796	ENSMUSG00000037095	Lrg1	1300008B03Rik|2310031E04Rik|Lrg|Lrhg	leucine-rich alpha-2-glycoprotein 1	protein-coding
mm_49118.1	chr6	8509829	8509848	+	1	NA	promoter-TSS (NR_040452)	promoter-TSS (NR_040452)	238	NM_133236	170772	Mm.210787	NM_133236	ENSMUSG00000029638	Glcci1	2310047L21Rik|A130036A18Rik|Fam117c|Gig18|Tssn1	glucocorticoid induced transcript 1	protein-coding
mm_50430.1	chr6	48844085	48844113	+	1	NA	exon (NM_025326, exon 5 of 7)	exon (NM_025326, exon 5 of 7)	2443	NM_001098271	66058	Mm.27061	NM_025326	ENSMUSG00000023367	Tmem176a	0610011I04Rik|AU040201|AU041743|Keg2	transmembrane protein 176A	protein-coding
mm_74226.1	chr8	124067133	124067139	+	1	NA	Intergenic	B1_Mur2|SINE|Alu	43663	NM_001029876	382038	Mm.334891	NM_001029876	ENSMUSG00000031976	Urb2	C77575|mKIAA0133	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	protein-coding
mm_69003.1	chr7	126700904	126700913	-	1	NA	intron (NM_001301374, intron 7 of 10)	intron (NM_001301374, intron 7 of 10)	3312	NM_001301374	12721	Mm.290482	NM_009898	ENSMUSG00000030707	Coro1a	Clabp|Lmb3|TACO|p57	coronin, actin binding protein 1A	protein-coding
mm_32377.1	chr4	106316078	106316119	+	1	NA	promoter-TSS (NM_183225)	promoter-TSS (NM_183225)	-115	NM_183225	329908	Mm.234544	NM_183225	ENSMUSG00000028514	Usp24	2700066K03Rik|2810030C21Rik|AI414051|B130021E18|C79851	ubiquitin specific peptidase 24	protein-coding
mm_173048.1	chrX	120385971	120385989	+	1	NA	intron (NR_073451, intron 2 of 7)	L1Md_T|LINE|L1	-72754	NM_001281531	624957		NM_001281531	ENSMUSG00000083616	H2afb3	EG624957|H2A.Bbd3|H2afb3-ps	H2A histone family, member B3	protein-coding
mm_136838.1	chr17	12748376	12748379	+	1	NA	intron (NR_027773, intron 1 of 2)	intron (NR_027773, intron 1 of 2)	7066	NR_027784	104103	Mm.26553	NR_002853	ENSMUSG00000078247	Airn	2810051F02Rik|2810434M15Rik|AI256653|AI597500|AW049873|Air|B930018I07Rik|D17Ertd663e|IGF2RAS	antisense Igf2r RNA	ncRNA
mm_119768.1	chr14	54174399	54174401	+	1	NA	Intergenic	Intergenic	79529	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_79851.1	chr9	64918720	64918749	+	1	NA	3' UTR (NM_001162917, exon 35 of 35)	3' UTR (NM_001162917, exon 35 of 35)	32873	NM_144813	214111	Mm.156124	NM_144813	ENSMUSG00000034452	Slc24a1	-	solute carrier family 24 (sodium/potassium/calcium exchanger), member 1	protein-coding
mm_43023.1	chr5	123908083	123908114	+	1	NA	intron (NM_026603, intron 1 of 7)	intron (NM_026603, intron 1 of 7)	823	NM_026603	68184	Mm.28549	NM_026603	ENSMUSG00000023106	Denr	1500003K04Rik	density-regulated protein	protein-coding
mm_20023.1	chr2	119440188	119440193	-	1	NA	intron (NM_026574, intron 13 of 35)	B1_Mus1|SINE|Alu	37439	NM_026574	68142	Mm.330496	NM_026574	ENSMUSG00000034154	Ino80	2310079N15Rik|4632409L19Rik|Inoc1	INO80 complex subunit	protein-coding
mm_42241.1	chr5	113827018	113827029	+	1	NA	intron (NM_009151, intron 1 of 1)	intron (NM_009151, intron 1 of 1)	3478	NM_009151	20345	Mm.332590	NM_009151	ENSMUSG00000048163	Selplg	CD162|Psgl-1|Psgl1|Selp1|Selpl	selectin, platelet (p-selectin) ligand	protein-coding
mm_34443.1	chr4	147985893	147985903	+	1	NA	5' UTR (NM_008726, exon 1 of 3)	5' UTR (NM_008726, exon 1 of 3)	110	NM_001287348	18158	Mm.2740	NM_008726	ENSMUSG00000029019	Nppb	AA408272|BNF|BNP	natriuretic peptide type B	protein-coding
mm_124086.1	chr14	78732629	78732647	-	1	NA	Intergenic	CpG	-7549	NM_001081336	380921	Mm.89591	NM_001081336	ENSMUSG00000034731	Dgkh	5930402B05Rik|D130015C16|DGK	diacylglycerol kinase, eta	protein-coding
mm_124861.1	chr15	10035815	10035820	+	1	NA	Intergenic	MIRb|SINE|MIR	-141421	NM_011169	19116	Mm.10516	NM_011169	ENSMUSG00000005268	Prlr	AI987712|Pr-1|Pr-3|Prlr-rs1	prolactin receptor	protein-coding
mm_79712.1	chr9	61372389	61372404	+	1	NA	promoter-TSS (NM_009389)	promoter-TSS (NM_009389)	30	NM_001083927	21887	Mm.24255	NM_009389	ENSMUSG00000032280	Tle3	2610103N05Rik|ESG|Grg3a|Grg3b|mKIAA1547	transducin-like enhancer of split 3	protein-coding
mm_78569.1	chr9	36431845	36431853	+	1	NA	promoter-TSS (NM_001167586)	promoter-TSS (NM_001167586)	-35	NM_001167586	639025	Mm.386535	NM_001167586	ENSMUSG00000023093	Gm7257	EG639025|Pate-q|Pate12	predicted gene 7257	protein-coding
mm_101647.1	chr11	36551402	36551415	-	1	NA	intron (NM_011856, intron 2 of 28)	intron (NM_011856, intron 2 of 28)	392833	NM_001290702	23964	Mm.439889	NM_011856	ENSMUSG00000049336	Tenm2	Odz2|Odz3|Ten-2|Ten-m2	teneurin transmembrane protein 2	protein-coding
mm_138510.1	chr17	35236651	35236668	+	1	NA	promoter-TSS (NM_010909)	promoter-TSS (NM_010909)	63	NM_023179	66237	Mm.396107	NM_023179	ENSMUSG00000024403	Atp6v1g2	1500002D01Rik|Atp6g2|NG38|VAG2	ATPase, H+ transporting, lysosomal V1 subunit G2	protein-coding
mm_61005.1	chr7	49347480	49347496	+	1	NA	intron (NM_175272, intron 1 of 37)	intron (NM_175272, intron 1 of 37)	101299	NM_175272	78286	Mm.333881	NM_175272	ENSMUSG00000052512	Nav2	5330421F07Rik|AU067780|BQ960892|HELAD1|POMFIL2|RAINB1|RAINB2|Unc53H2|mKIAA3015	neuron navigator 2	protein-coding
mm_165381.1	chr2	129198503	129198513	-	1	NA	promoter-TSS (NM_015747)	promoter-TSS (NM_015747)	-265	NM_015747	20515	Mm.272675	NM_015747	ENSMUSG00000027397	Slc20a1	AI607883|Glvr-1|Glvr1	solute carrier family 20, member 1	protein-coding
mm_76927.1	chr8	105936956	105936966	-	1	NA	exon (NM_013640, exon 5 of 8)	exon (NM_013640, exon 5 of 8)	1431	NM_013640	19171	Mm.787	NM_013640	ENSMUSG00000031897	Psmb10	Mecl-1|Mecl1	proteasome (prosome, macropain) subunit, beta type 10	protein-coding
mm_162845.1	chr10	86346884	86346924	+	1	NA	3' UTR (NM_011595, exon 5 of 5)	3' UTR (NM_011595, exon 5 of 5)	46492	NM_011595	21859	Mm.4871	NM_011595	ENSMUSG00000020044	Timp3	Timp-3	tissue inhibitor of metalloproteinase 3	protein-coding
mm_110516.1	chr12	54861083	54861099	-	1	NA	3' UTR (NM_007688, exon 4 of 4)	3' UTR (NM_007688, exon 4 of 4)	1786	NM_007688	12632	Mm.276826	NM_007688	ENSMUSG00000062929	Cfl2	-	cofilin 2, muscle	protein-coding
mm_111284.1	chr12	85373911	85373936	-	1	NA	intron (NM_026775, intron 1 of 4)	intron (NM_026775, intron 1 of 4)	794	NM_026775	68581	Mm.379159	NM_026775	ENSMUSG00000021248	Tmed10	1110014C03Rik|Tmp21|p23|p24delta1	transmembrane p24 trafficking protein 10	protein-coding
mm_83625.1	chr9	48836325	48836357	-	1	NA	promoter-TSS (NM_001033324)	promoter-TSS (NM_001033324)	-396	NM_001033324	235320	Mm.457803	NM_001033324	ENSMUSG00000066687	Zbtb16	AI467657|PLZF|Zfp145|lu	zinc finger and BTB domain containing 16	protein-coding
mm_25205.1	chr3	103809576	103809635	+	1	NA	promoter-TSS (NM_001163552)	promoter-TSS (NM_001163552)	88	NM_001163553	67489	Mm.197568	NM_026193	ENSMUSG00000032952	Ap4b1	1810038H16Rik|AV004952|Ap4b4	adaptor-related protein complex AP-4, beta 1	protein-coding
mm_134295.1	chr16	14275486	14275488	-	1	NA	intron (NM_001161775, intron 2 of 40)	intron (NM_001161775, intron 2 of 40)	15921	NM_001161775	17880	Mm.250705	NM_013607	ENSMUSG00000018830	Myh11	AV071570|SM1|SM2|smMHC	myosin, heavy polypeptide 11, smooth muscle	protein-coding
mm_53008.1	chr6	123270875	123270900	+	1	NA	intron (NM_001163161, intron 5 of 5)	B1F|SINE|Alu	8780	NM_010819	17474	Mm.441101	NM_010819	ENSMUSG00000030144	Clec4d	Clecsf8|Mpcl|mcl	C-type lectin domain family 4, member d	protein-coding
mm_105355.1	chr11	103028205	103028291	-	1	NA	promoter-TSS (NM_008707)	promoter-TSS (NM_008707)	-314	NM_008707	18107	Mm.10265	NM_008707	ENSMUSG00000020936	Nmt1	AW536594	N-myristoyltransferase 1	protein-coding
mm_90316.1	chr10	127063549	127063597	+	1	NA	promoter-TSS (NM_009870)	promoter-TSS (NM_009870)	-30	NM_009870	12567	Mm.6839	NM_009870	ENSMUSG00000006728	Cdk4	Crk3	cyclin-dependent kinase 4	protein-coding
mm_125876.1	chr15	75626266	75626311	+	1	NA	TTS (NM_011759)	TTS (NM_011759)	9604	NM_011759	22701	Mm.87210	NM_011759	ENSMUSG00000047003	Zfp41	CTfin92|Zfp-41	zinc finger protein 41	protein-coding
mm_122346.1	chr14	38617939	38617941	-	1	NA	intron (NM_001190188, intron 3 of 8)	intron (NM_001190188, intron 3 of 8)	-280362	NR_045713	75170	Mm.372967	NR_045713	ENSMUSG00000093528	Nrg3os	4930529F24Rik	neuregulin 3, opposite strand	ncRNA
mm_135637.1	chr16	52346930	52346944	-	1	NA	intron (NM_009655, intron 1 of 15)	intron (NM_009655, intron 1 of 15)	106144	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_54999.1	chr6	48834043	48834125	-	1	NA	exon (NM_001164209, exon 8 of 8)	exon (NM_001164209, exon 8 of 8)	6904	NM_023056	65963	Mm.28385	NM_023056	ENSMUSG00000029810	Tmem176b	1810009M01Rik|Clast1|Lr8	transmembrane protein 176B	protein-coding
mm_141333.1	chr17	28507475	28507489	-	1	NA	Intergenic	Intergenic	-21333	NM_010220	14229	Mm.276405	NM_010220	ENSMUSG00000024222	Fkbp5	D17Ertd592e|Dit1|FKBP-5|FKBP51	FK506 binding protein 5	protein-coding
mm_95038.1	chr11	32226482	32226545	+	1	NA	promoter-TSS (NM_010822)	promoter-TSS (NM_010822)	8	NM_010822	268395	Mm.263161	NM_010822	ENSMUSG00000020287	Mpg	9830006D05|AI326268|APNG|Aag|Mid1	N-methylpurine-DNA glycosylase	protein-coding
mm_27989.1	chr3	82093715	82093727	-	1	NA	3' UTR (NM_021896, exon 9 of 9)	3' UTR (NM_021896, exon 9 of 9)	12588	NR_105977	102466991		NR_105977	ENSMUSG00000098712	Mir7010	Gm28029|mmu-mir-7010	microRNA 7010	ncRNA
mm_526.1	chr1	37660770	37660787	+	1	NA	intron (NM_028096, intron 1 of 9)	L1M4c|LINE|L1	59033	NM_028096	72097	Mm.142607	NM_028096	ENSMUSG00000026090	2010300C02Rik	-	RIKEN cDNA 2010300C02 gene	protein-coding
mm_119276.1	chr14	34307934	34307941	+	1	NA	intron (NM_029389, intron 2 of 10)	PB1D9|SINE|Alu	2566	NM_029389	75698	Mm.45406	NM_029389	ENSMUSG00000041471	Fam35a	3110001K24Rik	family with sequence similarity 35, member A	protein-coding
mm_46859.1	chr5	113800357	113800412	-	1	NA	promoter-TSS (NM_146162)	promoter-TSS (NM_146162)	-32	NM_146162	231633	Mm.41681	NM_146162	ENSMUSG00000054675	Tmem119	AW208946|BC025600|obif	transmembrane protein 119	protein-coding
mm_104760.1	chr11	98477210	98477214	-	1	NA	intron (NM_011771, intron 6 of 7)	intron (NM_011771, intron 6 of 7)	30378	NM_010346	14786	Mm.276702	NM_010346	ENSMUSG00000019312	Grb7	mKIAA4028	growth factor receptor bound protein 7	protein-coding
mm_163503.1	chr12	112853138	112853148	-	1	NA	exon (NM_019925, exon 3 of 3)	exon (NM_019925, exon 3 of 3)	7773	NM_019925	56696	Mm.20455	NM_019925	ENSMUSG00000021298	Gpr132	G2a	G protein-coupled receptor 132	protein-coding
mm_143589.1	chr17	74459137	74459170	-	1	NA	promoter-TSS (NM_001033367)	promoter-TSS (NM_001033367)	-45	NM_001033367	268973	Mm.311884	NM_001033367	ENSMUSG00000039193	Nlrc4	9530011P19Rik|CLAN|CLAN1|CLANA|CLANB|CLANC|CLAND|Card12|IPAF	NLR family, CARD domain containing 4	protein-coding
mm_128533.1	chr15	54853365	54853377	-	1	NA	intron (NM_001285994, intron 19 of 25)	intron (NM_001285994, intron 19 of 25)	66775	NM_015744	18606	Mm.250256	NM_015744	ENSMUSG00000022425	Enpp2	ATX|E-NPP 2|Npps2|PD-Ialpha|Pdnp2|lysoPLD	ectonucleotide pyrophosphatase/phosphodiesterase 2	protein-coding
mm_165249.1	chr2	70476163	70476200	+	1	NA	exon (NM_022435, exon 2 of 2)	exon (NM_022435, exon 2 of 2)	1258	NM_022435	64406	Mm.423397	NM_022435	ENSMUSG00000075304	Sp5	-	trans-acting transcription factor 5	protein-coding
mm_63225.1	chr7	126395551	126395553	+	1	NA	intron (NM_010900, intron 2 of 7)	intron (NM_010900, intron 2 of 7)	1185	NM_010900	18020	Mm.1389	NM_010900	ENSMUSG00000030722	Nfatc2ip	D7Ertd304e|NIP45	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 2 interacting protein	protein-coding
mm_60625.1	chr7	44708789	44708800	+	1	NA	promoter-TSS (NM_029317)	promoter-TSS (NM_029317)	51	NM_029317	75510	Mm.273301	NM_029317	ENSMUSG00000066500	Izumo2	1700023D19Rik	IZUMO family member 2	protein-coding
mm_37097.1	chr4	116612058	116612070	-	1	NA	exon (NM_016777, exon 6 of 16)	exon (NM_016777, exon 6 of 16)	-14434	NR_029450	654318	Mm.255685	NR_029450	ENSMUSG00000085408	C530005A16Rik	D930044c15rik	RIKEN cDNA C530005A16 gene	ncRNA
mm_6883.1	chr1	84695553	84695563	-	1	NA	promoter-TSS (NR_039588)	promoter-TSS (NR_039588)	-281	NR_039588	100628595		NR_039588	ENSMUSG00000093254	Mir5126	mir-5126|mmu-mir-5126|mu-mir-5126	microRNA 5126	ncRNA
mm_72973.1	chr8	92887401	92887416	+	1	NA	intron (NM_173014, intron 9 of 13)	intron (NM_173014, intron 9 of 13)	-13987	NM_027112	69543	Mm.440514	NM_027112	ENSMUSG00000078144	Capns2	2310005G05Rik|30K-2	calpain, small subunit 2	protein-coding
mm_136960.1	chr17	15499962	15499976	+	1	NA	promoter-TSS (NM_013684)	promoter-TSS (NM_013684)	81	NM_013684	21374	Mm.244820	NM_013684	ENSMUSG00000014767	Tbp	GTF2D1|Gtf2d|SCA17|TFIID	TATA box binding protein	protein-coding
mm_166073.1	chr4	135898641	135898656	+	1	NA	intron (NM_009924, intron 1 of 1)	intron (NM_009924, intron 1 of 1)	3459	NM_009924	12802	Mm.297251	NM_009924	ENSMUSG00000062585	Cnr2	CB-2|CB2|CB2-R	cannabinoid receptor 2 (macrophage)	protein-coding
mm_103817.1	chr11	83003627	83003639	-	1	NA	exon (NM_181545, exon 6 of 6)	exon (NM_181545, exon 6 of 6)	-11803	NM_172796	237886	Mm.270253	NM_172796	ENSMUSG00000069793	Slfn9	9830137M10Rik	schlafen 9	protein-coding
mm_116295.1	chr13	36117352	36117393	-	1	NA	promoter-TSS (NM_024274)	promoter-TSS (NM_024274)	-15	NM_201358	380840	Mm.390576	NM_201358	ENSMUSG00000046573	Lyrm4	BC034664|Gm903	LYR motif containing 4	protein-coding
mm_29257.1	chr3	107219781	107219785	-	1	NA	intron (NM_001111143, intron 1 of 8)	intron (NM_001111143, intron 1 of 8)	1949	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_8573.1	chr1	155742002	155742046	-	1	NA	promoter-TSS (NM_010712)	promoter-TSS (NM_010712)	3	NM_010712	16872	Mm.103624	NM_010712	ENSMUSG00000026468	Lhx4	A330062J17Rik|Gsh-4|Gsh4	LIM homeobox protein 4	protein-coding
mm_27256.1	chr3	37232634	37232637	-	1	NA	promoter-TSS (NM_001291041)	promoter-TSS (NM_001291041)	1	NM_001291041	60505	Mm.157689	NM_021782	ENSMUSG00000027718	Il21	IL-21	interleukin 21	protein-coding
mm_157100.1	chrX	9437566	9437579	-	1	NA	3' UTR (NM_007807, exon 13 of 13)	3' UTR (NM_007807, exon 13 of 13)	31752	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_47873.1	chr5	134678191	134678254	-	1	NA	promoter-TSS (NR_131247)	promoter-TSS (NR_131247)	26	NM_001305875	16885	Mm.15409	NM_010717	ENSMUSG00000029674	Limk1	KIZ-1|LIMK-1|Limk	LIM-domain containing, protein kinase	protein-coding
mm_107127.1	chr12	20312216	20312263	+	1	NA	Intergenic	CpG	503540	NR_015521	69513	Mm.273972	NR_015521	ENSMUSG00000099759	1700030C10Rik	-	RIKEN cDNA 1700030C10 gene	ncRNA
mm_61784.1	chr7	83756083	83756095	+	1	NA	Intergenic	Intergenic	-20599	NM_010551	16170	Mm.10137	NM_010551	ENSMUSG00000001741	Il16	mKIAA4048	interleukin 16	protein-coding
mm_91414.1	chr10	31609719	31609732	-	1	NA	promoter-TSS (NM_001146349)	promoter-TSS (NM_001146349)	0	NM_001146349	268291	Mm.295212	NM_001146349	ENSMUSG00000063760	Rnf217	AU016819|Ibrdc1	ring finger protein 217	protein-coding
mm_79009.1	chr9	45476337	45476341	+	1	NA	intron (NM_001081270, intron 3 of 32)	intron (NM_001081270, intron 3 of 32)	-45107	NR_040732	74602	Mm.394117	NR_040732	ENSMUSG00000097074	4833428L15Rik	-	RIKEN cDNA 4833428L15 gene	ncRNA
mm_52012.1	chr6	94130645	94130663	+	1	NA	intron (NM_001029850, intron 1 of 23)	intron (NM_001029850, intron 1 of 23)	106788	NR_130996	78178	Mm.452749	NR_130996	ENSMUSG00000045095	4930511A08Rik	-	RIKEN cDNA 4930511A08 gene	ncRNA
mm_10788.1	chr2	24347455	24347512	+	1	NA	exon (NM_031167, exon 3 of 5)	exon (NM_031167, exon 3 of 5)	2112	NM_001039701	16181	Mm.882	NM_031167	ENSMUSG00000026981	Il1rn	F630041P17Rik|IL-1ra	interleukin 1 receptor antagonist	protein-coding
mm_16169.1	chr2	172546194	172546199	+	1	NA	Intergenic	Intergenic	-3397	NM_009335	21420	Mm.3629	NM_009335	ENSMUSG00000028640	Tfap2c	AA409384|AP2gamma|Ap-2.2|Stra2|Tcfap2c	transcription factor AP-2, gamma	protein-coding
mm_36933.1	chr4	108552416	108552416	-	1	NA	intron (NM_175472, intron 28 of 30)	MT2A|LTR|ERVL	26920	NM_172697	230596	Mm.157534	NM_172697	ENSMUSG00000063800	Prpf38a	2410002M20Rik	PRP38 pre-mRNA processing factor 38 (yeast) domain containing A	protein-coding
mm_1564.1	chr1	74155671	74155686	+	1	NA	intron (NM_009909, intron 1 of 1)	intron (NM_009909, intron 1 of 1)	1684	NM_009909	12765	Mm.234466	NM_009909	ENSMUSG00000026180	Cxcr2	CD128|CDw128|Cmkar2|Gpcr16|IL-8Rh|IL-8rb|IL8RA|Il8rb|mIL-8RH	chemokine (C-X-C motif) receptor 2	protein-coding
mm_49012.1	chr6	4758483	4758497	+	1	NA	3' UTR (NM_130877, exon 2 of 2)	3' UTR (NM_130877, exon 2 of 2)	11184	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_71292.1	chr8	41141716	41141740	+	1	NA	Intergenic	HAL1M8|LINE|L1	-8002	NM_001005863	102103	Mm.149438	NM_001005863	ENSMUSG00000045636	Mtus1	AI481402|ATBP135|Atip1|B430010I23Rik|B430305I03Rik|C85752|Cctsg1-440|MD44|MTSG1|mKIAA1288	mitochondrial tumor suppressor 1	protein-coding
mm_63558.1	chr7	128082629	128082647	+	1	NA	intron (NM_001082960, intron 8 of 29)	B3A|SINE|B2	19998	NM_008401	16409	Mm.262106	NM_008401	ENSMUSG00000030786	Itgam	CD11b/CD18|CR3|CR3A|Cd11b|F730045J24Rik|Ly-40|MAC1|Mac-1|Mac-1a	integrin alpha M	protein-coding
mm_99732.1	chr11	106301471	106301477	+	1	NA	exon (NM_008117, exon 2 of 5)	exon (NM_008117, exon 2 of 5)	422	NM_008117	14599	Mm.343934	NM_008117	ENSMUSG00000020713	Gh	Gh1|Ghb1	growth hormone	protein-coding
mm_156309.1	chrX	136838105	136838126	+	1	NA	3' UTR (NM_011123, exon 7 of 7)	3' UTR (NM_011123, exon 7 of 7)	15369	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_101060.1	chr11	9039619	9039625	-	1	NA	promoter-TSS (NM_001290519)	promoter-TSS (NM_001290519)	-31	NM_001290519	194974	Mm.79210	NM_177576	ENSMUSG00000040985	Sun3	Sunc1	Sad1 and UNC84 domain containing 3	protein-coding
mm_157279.1	chrX	20617575	20617618	-	1	NA	promoter-TSS (NM_145627)	promoter-TSS (NM_145627)	-32	NM_019435	104130	Mm.30084	NM_019435	ENSMUSG00000031059	Ndufb11	D5Bwg0566e|D5Bwg0577e|NP15.6|Np15	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 11	protein-coding
mm_44280.1	chr5	7186423	7186428	-	1	NA	intron (NM_001163223, intron 1 of 3)	intron (NM_001163223, intron 1 of 3)	-117739	NM_027603	70920	Mm.158494	NM_027603	ENSMUSG00000040514	4921511H03Rik	-	RIKEN cDNA 4921511H03 gene	protein-coding
mm_93289.1	chr10	96332945	96332957	-	1	NA	Intergenic	MIR3|SINE|MIR	106744	NR_110448	74881	Mm.410819	NR_110448		4930459C07Rik	-	RIKEN cDNA 4930459C07 gene	ncRNA
mm_72339.1	chr8	79304257	79304261	+	1	NA	intron (NR_045822, intron 2 of 2)	intron (NR_045822, intron 2 of 2)	9181	NR_045823	234479	Mm.238026	NR_045822		Gm4890	A630049P17	predicted gene 4890	ncRNA
mm_47181.1	chr5	120753689	120753699	-	1	NA	3' UTR (NM_145226, exon 16 of 16)	3' UTR (NM_145226, exon 16 of 16)	-3846	NM_001347448	246728	Mm.260926	NM_145227	ENSMUSG00000032690	Oas2	Oasl11	2'-5' oligoadenylate synthetase 2	protein-coding
mm_21706.1	chr2	164585456	164585458	-	1	NA	promoter-TSS (NM_001177848)	promoter-TSS (NM_001177848)	-10	NM_001033240	209351	Mm.293365	NM_001033240	ENSMUSG00000074595	Wfdc6a	Gm122	WAP four-disulfide core domain 6A	protein-coding
mm_42418.1	chr5	115301112	115301174	+	1	NA	promoter-TSS (NM_019682)	promoter-TSS (NM_019682)	23	NR_131932	102639268	Mm.319998	NR_131932		Gm13830	OTTMUSG00000014646	predicted gene 13830	ncRNA
mm_166384.1	chr5	131586519	131586520	+	1	NA	intron (NM_177047, intron 5 of 18)	intron (NM_177047, intron 5 of 18)	-278997	NM_145218	212996	Mm.299204	NM_145218	ENSMUSG00000034040	Wbscr17	AA388321|E330012B09Rik	Williams-Beuren syndrome chromosome region 17 homolog (human)	protein-coding
mm_90411.1	chr10	127420821	127420840	+	1	NA	promoter-TSS (NM_001168293)	promoter-TSS (NM_001168293)	-37	NM_027900	71750	Mm.29342	NM_027900	ENSMUSG00000025404	R3hdm2	1300003K24Rik|AU041262|mKIAA1002	R3H domain containing 2	protein-coding
mm_93641.1	chr10	117292864	117292870	-	1	NA	promoter-TSS (NM_013590)	promoter-TSS (NM_013590)	1	NM_013590	17110	Mm.177539	NM_013590	ENSMUSG00000069515	Lyz1	Lyz|Lyzf3|Lzp-s	lysozyme 1	protein-coding
mm_64683.1	chr7	4512839	4512842	-	1	NA	intron (NM_001277903, intron 5 of 13)	B1F|SINE|Alu	3135	NM_001277903	21955	Mm.358643	NM_011618	ENSMUSG00000064179	Tnnt1	AW146156|Tnt|sTnT|ssTnT	troponin T1, skeletal, slow	protein-coding
mm_156213.1	chrX	134685209	134685258	+	1	NA	non-coding (NR_045454, exon 3 of 3)	non-coding (NR_045454, exon 3 of 3)	1229	NR_045454	77983	Mm.153204	NR_045454	ENSMUSG00000087024	B230119M05Rik	-	RIKEN cDNA B230119M05 gene	ncRNA
mm_96024.1	chr11	59548566	59548575	+	1	NA	exon (NM_145827, exon 4 of 10)	exon (NM_145827, exon 4 of 10)	5884	NM_145827	216799	Mm.54174	NM_145827	ENSMUSG00000032691	Nlrp3	AGTAVPRL|AII/AVP|Cias1|FCAS|FCU|MWS|Mmig1|NALP3|Pypaf1	NLR family, pyrin domain containing 3	protein-coding
mm_52459.1	chr6	113697075	113697159	+	1	NA	promoter-TSS (NM_001347356)	promoter-TSS (NM_001347356)	67	NM_001033463	381801	Mm.333322	NM_001033463	ENSMUSG00000056952	Tatdn2	AI646012|mKIAA0218	TatD DNase domain containing 2	protein-coding
mm_26611.1	chr3	152290327	152290331	+	1	NA	intron (NM_001162375, intron 8 of 13)	intron (NM_001162375, intron 8 of 13)	-24009	NM_199465	68810	Mm.200188	NM_199465	ENSMUSG00000039103	Nexn	1110046H09Rik|AA553326|NELIN	nexilin	protein-coding
mm_152604.1	chr19	11818419	11818442	-	1	NA	intron (NM_001025307, intron 1 of 10)	intron (NM_001025307, intron 1 of 10)	973	NM_001286543	20908	Mm.272264	NM_011502	ENSMUSG00000041488	Stx3	Syn-3	syntaxin 3	protein-coding
mm_86624.1	chr10	13966269	13966284	+	1	NA	promoter-TSS (NM_010437)	promoter-TSS (NM_010437)	-103	NM_010437	15273	Mm.42157	NM_010437	ENSMUSG00000015501	Hivep2	Gm20114|MIBP1|Schnurri-2|Shn-2	human immunodeficiency virus type I enhancer binding protein 2	protein-coding
mm_106702.1	chr12	3643944	3643986	+	1	NA	exon (NM_007886, exon 7 of 19)	exon (NM_007886, exon 7 of 19)	70924	NM_007886	13528	Mm.286202	NM_007886	ENSMUSG00000071454	Dtnb	-	dystrobrevin, beta	protein-coding
mm_133688.1	chr16	92498674	92498742	+	1	NA	exon (NM_172469, exon 1 of 6)	exon (NM_172469, exon 1 of 6)	561	NM_172469	209195	Mm.44747	NM_172469	ENSMUSG00000022949	Clic6	5730466J16Rik|AL022908|AW045520|CLIC1L	chloride intracellular channel 6	protein-coding
mm_135377.1	chr16	44139034	44139050	-	1	NA	promoter-TSS (NM_007508)	promoter-TSS (NM_007508)	-23	NM_007508	11964	Mm.217787	NM_007508	ENSMUSG00000052459	Atp6v1a	AI647066|Atp6a1|Atp6a2|Atp6v1a1|VA68|VPP2	ATPase, H+ transporting, lysosomal V1 subunit A	protein-coding
mm_80867.1	chr9	98515520	98515526	+	1	NA	Intergenic	Intergenic	24986	NM_009034	19660	Mm.12825	NM_009034	ENSMUSG00000032454	Rbp2	Crbp-2|CrbpII|Rbp-2	retinol binding protein 2, cellular	protein-coding
mm_148331.1	chr18	84086747	84086758	-	1	NA	promoter-TSS (NM_001081300)	promoter-TSS (NM_001081300)	-190	NM_001081300	110796	Mm.102136	NM_001081300	ENSMUSG00000046982	Tshz1	5730407I04Rik|D18Bwg1409e|Mtsh1|NY-CO-33|Sdccag33|Tsh1|mKIAA4206|teashirt1	teashirt zinc finger family member 1	protein-coding
mm_89479.1	chr10	93554879	93554886	+	1	NA	intron (NM_175488, intron 4 of 15)	intron (NM_175488, intron 4 of 15)	14250	NM_175488	237465	Mm.477086	NM_175488	ENSMUSG00000036168	Ccdc38	4933417K05Rik	coiled-coil domain containing 38	protein-coding
mm_162389.1	chr1	75449724	75449724	+	1	NA	promoter-TSS (NM_183022)	promoter-TSS (NM_183022)	-786	NM_183022	241118	Mm.110790	NM_183022	ENSMUSG00000033007	Asic4	Accn4|BNAC4	acid-sensing (proton-gated) ion channel family member 4	protein-coding
mm_71841.1	chr8	68904833	68904854	+	1	NA	3' UTR (NM_008509, exon 10 of 10)	3' UTR (NM_008509, exon 10 of 10)	24288	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_162160.1	chrX	93654856	93654856	+	1	NA	promoter-TSS (NM_177546)	promoter-TSS (NM_177546)	-7	NM_177546	236899	Mm.166467	NM_177546	ENSMUSG00000035246	Pcyt1b	AW045697|CTTbeta	phosphate cytidylyltransferase 1, choline, beta isoform	protein-coding
mm_147898.1	chr18	65328629	65328644	-	1	NA	intron (NM_001037294, intron 4 of 12)	MIRb|SINE|MIR	65252	NM_001037294	225638	Mm.296528	NM_001037294	ENSMUSG00000032845	Alpk2	Gm549|Hak	alpha-kinase 2	protein-coding
mm_126344.1	chr15	79901188	79901198	+	1	NA	intron (NM_001160415, intron 5 of 8)	intron (NM_001160415, intron 5 of 8)	6170	NM_001347041	80287	Mm.284059	NM_030255	ENSMUSG00000009585	Apobec3	Apobec|Arp3|BC003314|Cem15|Rfv3	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 3	protein-coding
mm_131007.1	chr15	103562867	103562876	-	1	NA	3' UTR (NM_008134, exon 4 of 4)	3' UTR (NM_008134, exon 4 of 4)	2210	NM_001289587	14663	Mm.219621	NM_008134	ENSMUSG00000022491	Glycam1	MC26|Sgp50|glyCAM-1	glycosylation dependent cell adhesion molecule 1	protein-coding
mm_99905.1	chr11	109717273	109717277	+	1	NA	intron (NM_153782, intron 1 of 10)	intron (NM_153782, intron 1 of 10)	4981	NM_153782	208659	Mm.208662	NM_153782	ENSMUSG00000020614	Fam20a	AI606893	family with sequence similarity 20, member A	protein-coding
mm_107080.1	chr12	17033709	17033715	+	1	NA	Intergenic	Intergenic	-21985	NM_001201333	73667	Mm.159048	NM_001201332	ENSMUSG00000071398	2410004P03Rik	-	RIKEN cDNA 2410004P03 gene	protein-coding
mm_20182.1	chr2	122598884	122598923	-	1	NA	intron (NM_025961, intron 6 of 8)	L1Md_F2|LINE|L1	12374	NM_025961	67092	Mm.29975	NM_025961	ENSMUSG00000027199	Gatm	1810003P21Rik|AI314789|AT	glycine amidinotransferase (L-arginine:glycine amidinotransferase)	protein-coding
mm_48161.1	chr5	137152802	137152811	-	1	NA	Intergenic	Intergenic	-36599	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_159081.1	chr2	26441921	26441921	-	1	NA	exon (NM_153125, exon 2 of 30)	exon (NM_153125, exon 2 of 30)	3295	NM_153125	227648	Mm.206371	NM_153125	ENSMUSG00000026924	Sec16a	AU024582|C230052J16Rik	SEC16 homolog A, endoplasmic reticulum export factor	protein-coding
mm_156022.1	chrX	107149022	107149030	+	1	NA	promoter-TSS (NM_175442)	promoter-TSS (NM_175442)	99	NM_001122596	213438	Mm.265244	NM_175442	ENSMUSG00000054293	A630033H20Rik	AI662791|P2ry10	RIKEN cDNA A630033H20 gene	protein-coding
mm_135788.1	chr16	57163761	57163772	-	1	NA	intron (NM_023175, intron 3 of 9)	intron (NM_023175, intron 3 of 9)	3566	NM_023175	52633	Mm.383203	NM_023175	ENSMUSG00000022751	Nit2	1190017B19Rik|D16Ertd502e	nitrilase family, member 2	protein-coding
mm_122286.1	chr14	34503295	34503318	-	1	NA	promoter-TSS (NM_009758)	promoter-TSS (NM_009758)	-760	NM_009758	12166	Mm.237825	NM_009758	ENSMUSG00000021796	Bmpr1a	1110037I22Rik|ALK3|AU045487|BMPR-IA|Bmpr	bone morphogenetic protein receptor, type 1A	protein-coding
mm_141929.1	chr17	35027879	35027895	-	1	NA	TTS (NR_130641)	TTS (NR_130641)	129	NR_028258	78376	Mm.390966	NM_023893	ENSMUSG00000036185	Sapcd1	2810436B06Rik|G7d|Ng23	suppressor APC domain containing 1	protein-coding
mm_84764.1	chr9	75611077	75611102	-	1	NA	5' UTR (NM_016711, exon 1 of 10)	5' UTR (NM_016711, exon 1 of 10)	236	NM_016711	50876	Mm.291880	NM_016711	ENSMUSG00000032186	Tmod2	N-Tmod|NTMOD	tropomodulin 2	protein-coding
mm_48733.1	chr5	147557783	147557789	-	1	NA	Intergenic	MuRRS-int|LTR|ERV1	127206	NM_028291	72587	Mm.320469	NM_028291	ENSMUSG00000029647	Pan3	2700050F09Rik|A430027N15Rik|AU014670	PAN3 poly(A) specific ribonuclease subunit	protein-coding
mm_125528.1	chr15	57912225	57912278	+	1	NA	promoter-TSS (NM_001081396)	promoter-TSS (NM_001081396)	52	NM_001167679	210544	Mm.390835	NM_199300	ENSMUSG00000022364	Tbc1d31	4B3|D330013L20Rik|Gm85|Wdr67	TBC1 domain family, member 31	protein-coding
mm_71864.1	chr8	69088754	69088796	+	1	NA	promoter-TSS (NM_007509)	promoter-TSS (NM_007509)	39	NM_007509	11966	Mm.249096	NM_007509	ENSMUSG00000006273	Atp6v1b2	AI194269|AI790362|Atp6b2|HO57|R74844	ATPase, H+ transporting, lysosomal V1 subunit B2	protein-coding
mm_22973.1	chr3	32708766	32708772	+	1	NA	5' UTR (NM_019673, exon 1 of 14)	5' UTR (NM_019673, exon 1 of 14)	223	NM_019673	56456	Mm.41077	NM_019673	ENSMUSG00000027671	Actl6a	2810432C06Rik|AI851094|ARP4|Actl6|Baf53a|C79802	actin-like 6A	protein-coding
mm_138794.1	chr17	37492397	37492415	+	1	NA	promoter-TSS (NM_146328)	promoter-TSS (NM_146328)	-62	NM_146328	258325	Mm.484339	NM_146328	ENSMUSG00000090894	Olfr110	MOR249-2	olfactory receptor 110	protein-coding
mm_107388.1	chr12	33302247	33302266	+	1	NA	promoter-TSS (NM_001033436)	promoter-TSS (NM_001033436)	-259	NM_001033436	380753	Mm.41540	NM_028139	ENSMUSG00000020564	Atxn7l1	2810423G08Rik|Atxn7l4	ataxin 7-like 1	protein-coding
mm_73963.1	chr8	120488207	120488225	+	1	NA	promoter-TSS (NM_198671)	promoter-TSS (NM_198671)	-650	NM_198671	382034	Mm.334856	NM_198671	ENSMUSG00000031822	Gse1	2210013I18Rik|mKIAA0182	genetic suppressor element 1, coiled-coil protein	protein-coding
mm_11528.1	chr2	32626853	32626861	+	1	NA	intron (NM_001198791, intron 1 of 6)	intron (NM_001198791, intron 1 of 6)	1420	NM_001198791	11636	Mm.29189	NM_021515	ENSMUSG00000026817	Ak1	Ak-1|B430205N08Rik	adenylate kinase 1	protein-coding
mm_111823.1	chr12	106716324	106716336	-	1	NA	promoter-TSS (NR_015512)	promoter-TSS (NR_015512)	-6	NR_015512	71033	Mm.159404	NR_015512	ENSMUSG00000085820	4933406K04Rik	4930426M03Rik|4930485I22Rik|4933427G14Rik	RIKEN cDNA 4933406K04 gene	ncRNA
mm_58990.1	chr7	19094715	19094739	+	1	NA	TTS (NM_001190490)	TTS (NM_001190490)	183	NM_011383	20475	Mm.3410	NM_011383	ENSMUSG00000040841	Six5	Dmahp|MDMAHP|TrexBF	sine oculis-related homeobox 5	protein-coding
mm_75391.1	chr8	45975225	45975281	-	1	NA	promoter-TSS (NM_138668)	promoter-TSS (NM_138668)	-1	NM_001033148	69479	Mm.158282	NM_001033148	ENSMUSG00000071103	1700029J07Rik	-	RIKEN cDNA 1700029J07 gene	protein-coding
mm_97211.1	chr11	75620695	75620712	+	1	NA	intron (NM_008850, intron 10 of 11)	intron (NM_008850, intron 10 of 11)	-10317	NM_008916	19062	Mm.1458	NM_008916	ENSMUSG00000006127	Inpp5k	C62|Pps|SKIP	inositol polyphosphate 5-phosphatase K	protein-coding
mm_115092.1	chr13	102706900	102706912	+	1	NA	TTS (NM_008533)	TTS (NM_008533)	13348	NM_008533	17079	Mm.373974	NM_008533	ENSMUSG00000021624	Cd180	F630107B15|Ly78|RP105	CD180 antigen	protein-coding
mm_39642.1	chr5	24586799	24586822	+	1	NA	promoter-TSS (NM_133913)	promoter-TSS (NM_133913)	60	NM_133913	100910	Mm.140672	NM_133913	ENSMUSG00000038181	Chpf2	2010209O12Rik|AW060945|mKIAA1402|mir-671	chondroitin polymerizing factor 2	protein-coding
mm_113870.1	chr13	48662886	48662888	+	1	NA	promoter-TSS (NM_007526)	promoter-TSS (NM_007526)	-149	NM_007526	12022	Mm.42241	NM_007526	ENSMUSG00000021381	Barx1	-	BarH-like homeobox 1	protein-coding
mm_137489.1	chr17	26948617	26948640	+	1	NA	promoter-TSS (NR_037244)	promoter-TSS (NR_037244)	-509	NR_037244	100526534		NR_037244	ENSMUSG00000093118	Mir3083	mir-3083|mmu-mir-3083	microRNA 3083	ncRNA
mm_143018.1	chr17	56476508	56476517	-	1	NA	promoter-TSS (NM_001252453)	promoter-TSS (NM_001252453)	-32	NM_011218	19280	Mm.258771	NM_011218	ENSMUSG00000013236	Ptprs	AL022616|PTP|PTP-NU3|PTPNU-3|PTPsigma|Ptpt9|R-PTP-S|RPTPsigma	protein tyrosine phosphatase, receptor type, S	protein-coding
mm_166962.1	chr7	44480534	44480541	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-3980	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_53615.1	chr6	140041535	140041537	+	1	NA	promoter-TSS (NM_054066)	promoter-TSS (NM_054066)	11	NM_007605	12344	Mm.12817	NM_007605	ENSMUSG00000041791	Capza3	510-4|Cappa3|Gsg3|Tex8|repro32	capping protein (actin filament) muscle Z-line, alpha 3	protein-coding
mm_143767.1	chr17	81647855	81647865	-	1	NA	exon (NM_001112798, exon 2 of 9)	exon (NM_001112798, exon 2 of 9)	90527	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_10310.1	chr2	11172217	11172237	+	1	NA	promoter-TSS (NM_008859)	promoter-TSS (NM_008859)	-155	NM_008859	18761	Mm.329993	NM_008859	ENSMUSG00000026778	Prkcq	A130035A12Rik|AW494342|PKC-0|PKC-theta|PKCtheta|Pkcq	protein kinase C, theta	protein-coding
mm_10881.1	chr2	25243060	25243087	+	1	NA	5' UTR (NM_176834, exon 1 of 1)	5' UTR (NM_176834, exon 1 of 1)	144	NM_176834	68846	Mm.24777	NM_176834	ENSMUSG00000044628	Rnf208	1110061N23Rik	ring finger protein 208	protein-coding
mm_5636.1	chr1	40437432	40437442	-	1	NA	intron (NM_001294171, intron 1 of 7)	intron (NM_001294171, intron 1 of 7)	-2192	NM_001025602	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_42782.1	chr5	121452166	121452179	+	1	NA	promoter-TSS (NM_029912)	promoter-TSS (NM_029912)	302	NM_026129	67397	Mm.154570	NM_026129	ENSMUSG00000029616	Erp29	1200015M03Rik|2810446M09Rik|AW209030|Erp28|Erp31|PDI-Db	endoplasmic reticulum protein 29	protein-coding
mm_111159.1	chr12	83487732	83487740	-	1	NA	promoter-TSS (NM_001267626)	promoter-TSS (NM_001267626)	0	NM_001267626	70127	Mm.151308	NM_058212	ENSMUSG00000021221	Dpf3	2810403B03Rik|6530402L11Rik|BAF45C|C78788|CERD4|cer-d4	D4, zinc and double PHD fingers, family 3	protein-coding
mm_97981.1	chr11	83885495	83885504	+	1	NA	intron (NM_001291269, intron 5 of 8)	B4A|SINE|B4	32539	NM_001291269	21410	Mm.7226	NM_009330	ENSMUSG00000020679	Hnf1b	HNF-1-beta|HNF-1B|HNF-1Beta|Hnf1beta|LFB3|Tcf-2|Tcf2|vHNF1	HNF1 homeobox B	protein-coding
mm_157069.1	chrX	8193361	8193385	-	1	NA	TTS (NM_145907)	TTS (NM_145907)	139	NM_007898	13595	Mm.27183	NM_007898	ENSMUSG00000031168	Ebp	AI255399|Pabp|SI|Td|mSI	phenylalkylamine Ca2+ antagonist (emopamil) binding protein	protein-coding
mm_84919.1	chr9	80067768	80067778	-	1	NA	intron (NM_001311110, intron 1 of 23)	CpG	870	NM_146003	215351	Mm.28232	NM_146003	ENSMUSG00000034252	Senp6	2810017C20Rik|E130319N12Rik|Susp1|mKIAA0797	SUMO/sentrin specific peptidase 6	protein-coding
mm_90308.1	chr10	126997398	126997416	+	1	NA	3' UTR (NM_146012, exon 3 of 3)	3' UTR (NM_146012, exon 3 of 3)	-1033	NR_030259	723882		NR_030259	ENSMUSG00000072837	Mir546	Mirn546|mmu-mir-546	microRNA 546	ncRNA
mm_142176.1	chr17	36263491	36263491	-	1	NA	intron (NM_178281, intron 4 of 6)	intron (NM_178281, intron 4 of 6)	-5645	NM_026308	67676	Mm.27131	NM_026308	ENSMUSG00000024446	Rpp21	0610037N01Rik	ribonuclease P 21 subunit	protein-coding
mm_137872.1	chr17	31433100	31433156	+	1	NA	intron (NM_008804, intron 4 of 18)	intron (NM_008804, intron 4 of 18)	46894	NM_001163748	18585	Mm.10812	NM_008804	ENSMUSG00000041119	Pde9a	PDE9A1	phosphodiesterase 9A	protein-coding
mm_118985.1	chr14	28504635	28504656	+	1	NA	promoter-TSS (NM_009524)	promoter-TSS (NM_009524)	-828	NM_009524	22418	Mm.287544	NM_009524	ENSMUSG00000021994	Wnt5a	8030457G12Rik|Wnt-5a	wingless-type MMTV integration site family, member 5A	protein-coding
mm_136973.1	chr17	15751315	15751318	+	1	NA	intron (NM_007690, intron 22 of 35)	PB1D10|SINE|Alu	46349	NM_007690	12648	Mm.8137	NM_007690	ENSMUSG00000023852	Chd1	4930525N21Rik|AI851787|AW555109	chromodomain helicase DNA binding protein 1	protein-coding
mm_11831.1	chr2	45106193	45106213	+	1	NA	intron (NM_001289521, intron 1 of 8)	intron (NM_001289521, intron 1 of 8)	4074	NM_001289521	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_82387.1	chr9	14663015	14663076	-	1	NA	Intergenic	Intergenic	-48045	NM_001081395	75723	Mm.159552	NM_001081395	ENSMUSG00000013076	Amotl1	2310010G08Rik|2310067L22Rik|4932416D09Rik|JEAP|mFLJ00155	angiomotin-like 1	protein-coding
mm_113196.1	chr13	24943519	24943531	+	1	NA	5' UTR (NM_008156, exon 2 of 26)	5' UTR (NM_008156, exon 2 of 26)	373	NM_008156	14756	Mm.291831	NM_008156	ENSMUSG00000021340	Gpld1	6330541J12Rik|AW546131	glycosylphosphatidylinositol specific phospholipase D1	protein-coding
mm_169702.1	chr15	75086885	75086886	+	1	NA	Intergenic	Intergenic	25064	NM_001099217	100041546	Mm.482110	NM_001099217	ENSMUSG00000022584	Ly6c2	Ly-6C.2|Ly-6C2	lymphocyte antigen 6 complex, locus C2	protein-coding
mm_163753.1	chr13	119790694	119790710	-	1	NA	promoter-TSS (NM_001302548)	promoter-TSS (NM_001302548)	30	NM_001302548	72465	Mm.139115	NM_028245	ENSMUSG00000094870	Zfp131	2610109I01Rik|AW558871|Znf131	zinc finger protein 131	protein-coding
mm_28224.1	chr3	88453389	88453401	-	1	NA	intron (NM_001163491, intron 2 of 14)	intron (NM_001163491, intron 2 of 14)	2366	NM_013658	20351	Mm.439752	NM_013658	ENSMUSG00000028064	Sema4a	AI132332|SemB|Semab	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A	protein-coding
mm_136771.1	chr17	9030615	9030619	+	1	NA	Intergenic	Intergenic	42284	NM_001347544	66931	Mm.67591	NM_025851	ENSMUSG00000023873	1700010I14Rik	-	RIKEN cDNA 1700010I14 gene	protein-coding
mm_75440.1	chr8	47413780	47413826	-	1	NA	Intergenic	CpG	-61455	NM_175162	71069	Mm.23973	NM_175162	ENSMUSG00000038143	Stox2	4933409N07Rik|AI449080|AI835114|mKIAA1392	storkhead box 2	protein-coding
mm_60141.1	chr7	38183186	38183199	+	1	NA	promoter-TSS (NM_028166)	promoter-TSS (NM_028166)	-25	NM_001085385	72244	Mm.187554	NM_028166		1600014C10Rik	AI428873	RIKEN cDNA 1600014C10 gene	protein-coding
mm_59667.1	chr7	28376526	28376563	+	1	NA	TTS (NM_011756)	TTS (NM_011756)	2684	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_162110.1	chrX	50942923	50942923	-	1	NA	promoter-TSS (NM_001190332)	promoter-TSS (NM_001190332)	-213	NM_001190332	385354	Mm.393050	NM_001190332	ENSMUSG00000036131	Frmd7	EG665849|Gm1533	FERM domain containing 7	protein-coding
mm_111171.1	chr12	83632004	83632041	-	1	NA	promoter-TSS (NM_027349)	promoter-TSS (NM_027349)	-212	NM_027349	67039	Mm.46005	NM_027349	ENSMUSG00000010608	Rbm25	2600011C06Rik|2610015J01Rik|A130095G20Rik|AI159652|AL023075|AU043498|RNPC7	RNA binding motif protein 25	protein-coding
mm_38698.1	chr4	145214591	145214611	-	1	NA	3' UTR (NM_011610, exon 10 of 10)	3' UTR (NM_011610, exon 10 of 10)	-19596	NM_001276465	230895	Mm.240310	NM_001033190	ENSMUSG00000020220	Vps13d	-	vacuolar protein sorting 13D	protein-coding
mm_108153.1	chr12	76324839	76324841	+	1	NA	promoter-TSS (NM_001101471)	promoter-TSS (NM_001101471)	-51	NM_001101471	238276	Mm.311452	NM_001101471	ENSMUSG00000021057	Akap5	3526401B18Rik|AKAP 150|AKAP-5|AKAP150|BB098886|Gm258|P150	A kinase (PRKA) anchor protein 5	protein-coding
mm_57398.1	chr6	124863726	124863771	-	1	NA	TTS (NM_013488)	TTS (NM_013488)	169	NM_013533	14788	Mm.2514	NM_013533	ENSMUSG00000038390	Gpr162	A-2|BC031437|Grca	G protein-coupled receptor 162	protein-coding
mm_149421.1	chr19	11443578	11443593	+	1	NA	promoter-TSS (NM_021718)	promoter-TSS (NM_021718)	27	NM_021718	60361	Mm.33957	NM_021718	ENSMUSG00000056290	Ms4a4b	AI463180|Chandra|Ly116	membrane-spanning 4-domains, subfamily A, member 4B	protein-coding
mm_98024.1	chr11	85171075	85171086	+	1	NA	promoter-TSS (NM_028589)	promoter-TSS (NM_028589)	-16	NM_028589	73634	Mm.48850	NM_028589	ENSMUSG00000018479	1700125H20Rik	-	RIKEN cDNA 1700125H20 gene	protein-coding
mm_100204.1	chr11	116843652	116843677	+	1	NA	promoter-TSS (NM_033398)	promoter-TSS (NM_033398)	149	NM_028865	74319	Mm.429312	NM_028865	ENSMUSG00000090266	Mettl23	1110005A03Rik|1500035B17Rik|4933424L15Rik	methyltransferase like 23	protein-coding
mm_102226.1	chr11	54910086	54910096	-	1	NA	TTS (NM_021327)	TTS (NM_021327)	7237	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_99841.1	chr11	109346876	109346886	+	1	NA	promoter-TSS (NR_027883)	promoter-TSS (NR_027883)	14	NR_027883	67927	Mm.394490	NR_027883	ENSMUSG00000099630	1700096J18Rik	-	RIKEN cDNA 1700096J18 gene	ncRNA
mm_29420.1	chr3	108976551	108976566	-	1	NA	intron (NM_001163567, intron 10 of 10)	intron (NM_001163567, intron 10 of 10)	36001	NM_001078646	66715	Mm.158124	NM_025723	ENSMUSG00000045662	Henmt1	4921515J06Rik|Hen1|mHEN1	HEN1 methyltransferase homolog 1 (Arabidopsis)	protein-coding
mm_127693.1	chr15	102990482	102990492	+	1	NA	promoter-TSS (NM_010466)	promoter-TSS (NM_010466)	-52	NM_010466	15426	Mm.6167	NM_010466	ENSMUSG00000001657	Hoxc8	D130011F21Rik|Hox-3.1	homeobox C8	protein-coding
mm_76388.1	chr8	84842794	84842804	-	1	NA	exon (NM_007591, exon 9 of 9)	exon (NM_007591, exon 9 of 9)	-2134	NM_009010	19358	Mm.255539	NM_009010	ENSMUSG00000003813	Rad23a	2310040P19Rik|AL024030|HR23A|mHR23A	RAD23 homolog A, nucleotide excision repair protein	protein-coding
mm_29419.1	chr3	108976492	108976498	-	1	NA	intron (NM_001163567, intron 10 of 10)	intron (NM_001163567, intron 10 of 10)	35938	NM_001078646	66715	Mm.158124	NM_025723	ENSMUSG00000045662	Henmt1	4921515J06Rik|Hen1|mHEN1	HEN1 methyltransferase homolog 1 (Arabidopsis)	protein-coding
mm_45961.1	chr5	90464175	90464188	-	1	NA	exon (NM_009654, exon 4 of 15)	exon (NM_009654, exon 4 of 15)	3311	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_101232.1	chr11	20332690	20332774	-	1	NA	promoter-TSS (NM_018861)	promoter-TSS (NM_018861)	-19	NM_018861	55963	Mm.6379	NM_018861	ENSMUSG00000020142	Slc1a4	ASCT-1|ASCT1|AW045657|SATT	solute carrier family 1 (glutamate/neutral amino acid transporter), member 4	protein-coding
mm_6382.1	chr1	72780814	72780819	-	1	NA	Intergenic	Intergenic	-43664	NM_008342	16008	Mm.141936	NM_008342	ENSMUSG00000039323	Igfbp2	AI255832|IBP-2|Igfbp-2|mIGFBP-2	insulin-like growth factor binding protein 2	protein-coding
mm_59037.1	chr7	19332953	19332975	+	1	NA	Intergenic	CpG	-12107	NM_001127324	13870	Mm.280913	NM_007948	ENSMUSG00000003549	Ercc1	Ercc-1	excision repair cross-complementing rodent repair deficiency, complementation group 1	protein-coding
mm_3972.1	chr1	164193062	164193070	+	1	NA	exon (NM_007976, exon 13 of 25)	exon (NM_007976, exon 13 of 25)	-40849	NR_037987	100503816	Mm.398579	NR_037987	ENSMUSG00000086593	Gm16548	-	predicted gene 16548	ncRNA
mm_155009.1	chrX	41401159	41401200	+	1	NA	promoter-TSS (NM_001290451)	promoter-TSS (NM_001290451)	-122	NM_016886	53623	Mm.327681	NM_016886	ENSMUSG00000001986	Gria3	2900064I19Rik|GluA3|GluR-C|GluR-K3|Glur-3|Glur3|Gluralpha3	glutamate receptor, ionotropic, AMPA3 (alpha 3)	protein-coding
mm_113256.1	chr13	28021415	28021420	+	1	NA	exon (NM_011165, exon 4 of 5)	exon (NM_011165, exon 4 of 5)	5194	NM_011165	19110	Mm.18607	NM_011165	ENSMUSG00000005891	Prl4a1	AA409771|Ghd23|PLP-A|Prlpa	prolactin family 4, subfamily a, member 1	protein-coding
mm_164374.1	chr16	25799644	25799645	+	1	NA	intron (NM_001127259, intron 3 of 13)	intron (NM_001127259, intron 3 of 13)	-2272	NM_001127263	22061	Mm.20894	NM_011641	ENSMUSG00000022510	Trp63	AI462811|Ket|P51/P63|P63|P73l|Tp63|Trp53rp1	transformation related protein 63	protein-coding
mm_147870.1	chr18	64479397	64479407	-	1	NA	intron (NM_007998, intron 2 of 10)	intron (NM_007998, intron 2 of 10)	9664	NM_007998	14151	Mm.1070	NM_007998	ENSMUSG00000024588	Fech	AI894116|Fcl|fch	ferrochelatase	protein-coding
mm_14369.1	chr2	129630002	129630023	+	1	NA	exon (NM_001291022, exon 5 of 5)	exon (NM_001291022, exon 5 of 5)	36843	NM_001291022	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_4228.1	chr1	171356563	171356574	+	1	NA	exon (NM_011070, exon 2 of 4)	exon (NM_011070, exon 2 of 4)	4230	NM_001033039	68874	Mm.10756	NM_001033039	ENSMUSG00000045259	Klhdc9	1190002J23Rik|AA087357|ESTM31	kelch domain containing 9	protein-coding
mm_166801.1	chr7	3981810	3981813	+	1	NA	Intergenic	Intergenic	-66310	NR_028115	18726	Mm.440989	NM_011090	ENSMUSG00000030427	Lilra6	7M1|Pira3	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	protein-coding
mm_52663.1	chr6	117900443	117900473	+	1	NA	5' UTR (NM_001166432, exon 1 of 4)	5' UTR (NM_001166432, exon 1 of 4)	118	NM_001166432	98758	Mm.422979	NM_133834	ENSMUSG00000042079	Hnrnpf	4833420I20Rik|AA407306|Hnrpf	heterogeneous nuclear ribonucleoprotein F	protein-coding
mm_29103.1	chr3	104818225	104818237	-	1	NA	promoter-TSS (NM_008619)	promoter-TSS (NM_008619)	74	NM_008619	17454	Mm.1597	NM_008619	ENSMUSG00000002227	Mov10	C77703|Mov-10	Moloney leukemia virus 10	protein-coding
mm_54584.1	chr6	38125515	38125517	-	1	NA	promoter-TSS (NM_080467)	promoter-TSS (NM_080467)	-930	NM_080467	140494	Mm.462308	NM_080467	ENSMUSG00000038600	Atp6v0a4	Atp6n1b|a4	ATPase, H+ transporting, lysosomal V0 subunit A4	protein-coding
mm_112635.1	chr13	16011921	16011949	+	1	NA	promoter-TSS (NM_008380)	promoter-TSS (NM_008380)	84	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_27849.1	chr3	79156693	79156702	-	1	NA	Intergenic	L1_Mur3|LINE|L1	-10822	NM_001099624	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_91956.1	chr10	61100691	61100710	-	1	NA	3' UTR (NM_001316673, exon 15 of 15)	3' UTR (NM_001316673, exon 15 of 15)	11369	NM_025273	13180	Mm.39473	NM_025273	ENSMUSG00000020098	Pcbd1	Dcoh|Pcbd|Pcd|Phs	pterin 4 alpha carbinolamine dehydratase/dimerization cofactor of hepatocyte nuclear factor 1 alpha (TCF1) 1	protein-coding
mm_142562.1	chr17	46645764	46645786	-	1	NA	promoter-TSS (NM_029091)	promoter-TSS (NM_029091)	-446	NM_001316742	27398	Mm.391007	NM_025302	ENSMUSG00000002767	Mrpl2	CGI-22|L2mt|MRP-L14|MRP-L2|Rpml14	mitochondrial ribosomal protein L2	protein-coding
mm_72502.1	chr8	83740636	83740639	+	1	NA	intron (NM_001163031, intron 1 of 17)	B3|SINE|B2	674	NM_001163029	26364	Mm.334648	NM_011925	ENSMUSG00000002885	Adgre5	AA409984|Cd97|TM7LN1	adhesion G protein-coupled receptor E5	protein-coding
mm_69847.1	chr7	141414055	141414104	-	1	NA	promoter-TSS (NM_172116)	promoter-TSS (NM_172116)	46	NM_172116	213350	Mm.290953	NM_172116	ENSMUSG00000051007	Pddc1	BC023835|D230016J19Rik	Parkinson disease 7 domain containing 1	protein-coding
mm_61092.1	chr7	51725246	51725254	+	1	NA	Intergenic	Intergenic	103420	NM_080853	140919	Mm.256618	NM_080853	ENSMUSG00000030500	Slc17a6	2900073D12Rik|DNPI|VGLUT2	solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 6	protein-coding
mm_136904.1	chr17	13016279	13016289	+	1	NA	3' UTR (NM_013671, exon 5 of 5)	3' UTR (NM_013671, exon 5 of 5)	8445	NM_013671	20656	Mm.290876	NM_013671	ENSMUSG00000006818	Sod2	MnSOD|Sod-2	superoxide dismutase 2, mitochondrial	protein-coding
mm_69999.1	chr7	142386672	142386683	-	1	NA	intron (NM_009983, intron 1 of 8)	intron (NM_009983, intron 1 of 8)	1193	NM_009983	13033	Mm.231395	NM_009983	ENSMUSG00000007891	Ctsd	CD|CatD	cathepsin D	protein-coding
mm_67550.1	chr7	81498274	81498287	-	1	NA	promoter-TSS (NM_183143)	promoter-TSS (NM_183143)	50	NM_183143	210321	Mm.99511	NM_183143	ENSMUSG00000061877	BC048679	-	cDNA sequence BC048679	protein-coding
mm_20910.1	chr2	150600355	150600367	-	1	NA	intron (NM_027977, intron 1 of 8)	intron (NM_027977, intron 1 of 8)	8162	NM_027977	71881	Mm.26599	NM_027977	ENSMUSG00000033096	Apmap	2310001A20Rik|AI314817	adipocyte plasma membrane associated protein	protein-coding
mm_15597.1	chr2	160646012	160646026	+	1	NA	5' UTR (NM_009408, exon 1 of 21)	5' UTR (NM_009408, exon 1 of 21)	122	NM_009408	21969	Mm.217233	NM_009408	ENSMUSG00000070544	Top1	AI467334|D130064I21Rik|Top-1	topoisomerase (DNA) I	protein-coding
mm_146960.1	chr18	33213833	33213852	-	1	NA	promoter-TSS (NM_001347624)	promoter-TSS (NM_001347624)	20	NM_001347624	170459	Mm.127058	NM_133774	ENSMUSG00000024378	Stard4	4632419C16Rik|9030213J02Rik	StAR-related lipid transfer (START) domain containing 4	protein-coding
mm_120715.1	chr14	72710096	72710122	+	1	NA	promoter-TSS (NM_207636)	promoter-TSS (NM_207636)	-106	NM_207636	319448	Mm.205421	NM_207636	ENSMUSG00000033487	Fndc3a	1700094E19Rik|D14Ertd453e|F730017H24Rik|Fndc3|sys	fibronectin type III domain containing 3A	protein-coding
mm_172229.1	chr6	67494777	67494783	+	1	NA	Intergenic	L1Md_Gf|LINE|L1	-2925	NM_144548	209590	Mm.221227	NM_144548	ENSMUSG00000049093	Il23r	IL-23R	interleukin 23 receptor	protein-coding
mm_8830.1	chr1	162571369	162571375	-	1	NA	intron (NM_001347125, intron 1 of 7)	CpG	544	NM_001347125	53330	Mm.10699	NM_016796	ENSMUSG00000026696	Vamp4	D1Ertd147e	vesicle-associated membrane protein 4	protein-coding
mm_1954.1	chr1	86357232	86357294	+	1	NA	promoter-TSS (NR_002851)	promoter-TSS (NR_002851)	-936	NR_002851	80828		NR_002851	ENSMUSG00000064823	Snord82	Rnu82|U82|Z25	small nucleolar RNA, C/D box 82	snoRNA
mm_100726.1	chr11	3927515	3927525	-	1	NA	exon (NM_001130458, exon 3 of 10)	exon (NM_001130458, exon 3 of 10)	4441	NM_001130459	21452	Mm.20948	NM_015749	ENSMUSG00000020432	Tcn2	AW208754|Tcn-2	transcobalamin 2	protein-coding
mm_159080.1	chr2	26369551	26369551	-	1	NA	exon (NM_172339, exon 16 of 23)	exon (NM_172339, exon 16 of 23)	-10004	NM_001037747	332579	Mm.330064	NM_001037747	ENSMUSG00000026928	Card9	Gm782	caspase recruitment domain family, member 9	protein-coding
mm_142126.1	chr17	35897343	35897369	-	1	NA	promoter-TSS (NM_001033630)	promoter-TSS (NM_001033630)	22	NM_001033630	69662	Mm.260159	NM_001033630	ENSMUSG00000050705	2310061I04Rik	-	RIKEN cDNA 2310061I04 gene	protein-coding
mm_68753.1	chr7	121068282	121068357	-	1	NA	exon (NM_030691, exon 3 of 6)	exon (NM_030691, exon 3 of 6)	6211	NM_030691	80719	Mm.160384	NM_030691	ENSMUSG00000035004	Igsf6	-	immunoglobulin superfamily, member 6	protein-coding
mm_351.1	chr1	31253249	31253251	+	1	NA	Intergenic	ETnERV3-int|LTR|ERVK	-11597	NR_015347	226957	Mm.25966	NR_015347		Gm4850	EG226957	THO complex 4 pseudogene	pseudo
mm_119471.1	chr14	47298261	47298342	+	1	NA	promoter-TSS (NM_178684)	promoter-TSS (NM_178684)	-13	NM_178684	218975	Mm.212297	NM_178684	ENSMUSG00000021840	Mapk1ip1l	9130202B12|C130032J12Rik	mitogen-activated protein kinase 1 interacting protein 1-like	protein-coding
mm_53243.1	chr6	127561313	127561343	+	1	NA	Intergenic	CpG	-16647	NM_001033464	381812	Mm.296093	NM_001033464	ENSMUSG00000061414	Cracr2a	Efcab4b|Gm1073|Gm462	calcium release activated channel regulator 2A	protein-coding
mm_110527.1	chr12	54986304	54986308	-	1	NA	promoter-TSS (NM_013815)	promoter-TSS (NM_013815)	30	NM_013815	217578	Mm.479583	NM_013815	ENSMUSG00000035021	Baz1a	Acf1|B930060C03|BC065123|Gtl5|Wcrf180|cbp146	bromodomain adjacent to zinc finger domain 1A	protein-coding
mm_109029.1	chr12	104077937	104077952	+	1	NA	promoter-TSS (NR_002861)	promoter-TSS (NR_002861)	-15	NR_002861	321018	Mm.297023	NR_002861		Serpina4-ps1	KALps|Klst	serine (or cysteine) peptidase inhibitor, clade A, member 4, pseudogene 1	pseudo
mm_160416.1	chr8	83541201	83541201	+	1	NA	exon (NM_146270, exon 1 of 1)	exon (NM_146270, exon 1 of 1)	108	NM_146270	258267	Mm.377401	NM_146270	ENSMUSG00000047286	Olfr370	MOR267-16|MOR26716	olfactory receptor 370	protein-coding
mm_763.1	chr1	43983521	43983544	+	1	NA	exon (NM_009418, exon 23 of 30)	exon (NM_009418, exon 23 of 30)	36474	NM_001013799	433294	Mm.123621	NM_001013799	ENSMUSG00000047343	Mettl21c	A530098C11Rik	methyltransferase like 21C	protein-coding
mm_10284.1	chr2	10153550	10153560	+	1	NA	promoter-TSS (NM_172471)	promoter-TSS (NM_172471)	12	NM_172471	209378	Mm.313876	NM_172471	ENSMUSG00000025780	Itih5	4631408O11Rik|5430408M01Rik|E130106B02	inter-alpha (globulin) inhibitor H5	protein-coding
mm_122084.1	chr14	30618134	30618135	-	1	NA	intron (NM_011103, intron 1 of 17)	intron (NM_011103, intron 1 of 17)	-7824	NM_001310682	18753	Mm.2314	NM_011103	ENSMUSG00000021948	Prkcd	AI385711|D14Ertd420e|PKC[d]|PKCdelta|Pkcd	protein kinase C, delta	protein-coding
mm_172302.1	chr7	104288304	104288312	+	1	NA	promoter-TSS (NM_001310602)	promoter-TSS (NM_001310602)	-202	NM_001310602	667823	Mm.482375	NM_001310602	ENSMUSG00000060441	Trim5	EG667823|Gm8833	tripartite motif-containing 5	protein-coding
mm_118774.1	chr14	22829369	22829374	+	1	NA	intron (NM_028275, intron 6 of 6)	intron (NM_028275, intron 6 of 6)	265200	NR_033550	791307	Mm.364384	NR_033550	ENSMUSG00000068680	Gm10248	ENSMUSG00000068680	predicted gene 10248	ncRNA
mm_67628.1	chr7	84152018	84152022	-	1	NA	promoter-TSS (NM_133722)	promoter-TSS (NM_133722)	-127	NM_133722	70178	Mm.23914	NM_133722	ENSMUSG00000038459	Abhd17c	2210412D01Rik|AL023007|Fam108c|Fam108c1	abhydrolase domain containing 17C	protein-coding
mm_41892.1	chr5	105518725	105518738	+	1	NA	promoter-TSS (NM_133897)	promoter-TSS (NM_133897)	-740	NM_133897	100604	Mm.319847	NM_133897	ENSMUSG00000054720	Lrrc8c	AD158|AI326115|E430036I04Rik|fad158	leucine rich repeat containing 8 family, member C	protein-coding
mm_113533.1	chr13	37841611	37841658	+	1	NA	intron (NM_001039188, intron 1 of 9)	intron (NM_001039188, intron 1 of 9)	14241	NM_001039188	68750	Mm.491109	NM_026830	ENSMUSG00000039087	Rreb1	1110037N09Rik|AA414966|B930013M22Rik	ras responsive element binding protein 1	protein-coding
mm_138231.1	chr17	34377161	34377177	+	1	NA	promoter-TSS (NM_001111094)	promoter-TSS (NM_001111094)	37	NM_001111094	100038862	Mm.440426	NM_201405	ENSMUSG00000062638	Btnl1	Btnl3|Gm316|Gm33	butyrophilin-like 1	protein-coding
mm_118447.1	chr14	8214136	8214181	+	1	NA	promoter-TSS (NM_001305936)	promoter-TSS (NM_001305936)	77	NM_027782	71393	Mm.292712	NM_027782	ENSMUSG00000021752	Kctd6	5430433B02Rik|AU044285	potassium channel tetramerisation domain containing 6	protein-coding
mm_76324.1	chr8	84705163	84705175	-	1	NA	TTS (NM_008535)	TTS (NM_008535)	3712	NM_008535	17095	Mm.4925	NM_008535	ENSMUSG00000034041	Lyl1	Lyl-1|bHLHa18	lymphoblastomic leukemia 1	protein-coding
mm_146552.1	chr18	6220986	6220999	-	1	NA	exon (NM_008448, exon 12 of 26)	exon (NM_008448, exon 12 of 26)	20532	NM_008448	16573	Mm.223744	NM_008448	ENSMUSG00000006740	Kif5b	AL022807|Khc|Khcs|Kns1|Ukhc	kinesin family member 5B	protein-coding
mm_145842.1	chr18	65447685	65447695	+	1	NA	exon (NM_172833, exon 4 of 16)	exon (NM_172833, exon 4 of 16)	16693	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_169479.1	chr14	70723477	70723477	-	1	NA	intron (NM_023045, intron 1 of 27)	intron (NM_023045, intron 1 of 27)	43151	NM_023045	65246	Mm.152987	NM_023045	ENSMUSG00000022100	Xpo7	4930506C02Rik|BB164534|Ranbp16|mKIAA0745	exportin 7	protein-coding
mm_149993.1	chr19	29252555	29252590	+	1	NA	intron (NM_008413, intron 2 of 24)	intron (NM_008413, intron 2 of 24)	769	NM_008413	16452	Mm.275839	NM_008413	ENSMUSG00000024789	Jak2	Fd17	Janus kinase 2	protein-coding
mm_70137.1	chr7	143273771	143273775	-	1	NA	non-coding (NR_001461, exon 1 of 1)	non-coding (NR_001461, exon 1 of 1)	22774	NR_001461	63830	Mm.356096	NR_001461	ENSMUSG00000101609	Kcnq1ot1	Kvlqt1-as|Lit1|Tssc8	KCNQ1 overlapping transcript 1	ncRNA
mm_57289.1	chr6	124433470	124433485	-	1	NA	intron (NM_001346656, intron 16 of 17)	intron (NM_001346656, intron 16 of 17)	-18410	NM_001277805	19305	Mm.22418	NM_008995	ENSMUSG00000005069	Pex5	AW212715|ESTM1|PTS1R|Pxr1|X83306	peroxisomal biogenesis factor 5	protein-coding
mm_78108.1	chr9	20581346	20581359	+	1	NA	promoter-TSS (NM_172919)	promoter-TSS (NM_172919)	24	NM_172919	244721	Mm.86627	NM_172919	ENSMUSG00000058192	Zfp846	2210010B09Rik|9130221F13|Znf846	zinc finger protein 846	protein-coding
mm_59751.1	chr7	28822034	28822044	+	1	NA	3' UTR (NM_177301, exon 13 of 13)	3' UTR (NM_177301, exon 13 of 13)	-3299	NM_016772	51798	Mm.291776	NM_016772	ENSMUSG00000053898	Ech1	AA617331	enoyl coenzyme A hydratase 1, peroxisomal	protein-coding
mm_34062.1	chr4	138454306	138454327	+	1	NA	promoter-TSS (NM_025451)	promoter-TSS (NM_025451)	-832	NM_025451	66259	Mm.41603	NM_025451	ENSMUSG00000046447	Camk2n1	1810006K23Rik|AI848599|AI891706	calcium/calmodulin-dependent protein kinase II inhibitor 1	protein-coding
mm_39611.1	chr5	24164986	24165044	+	1	NA	promoter-TSS (NM_153092)	promoter-TSS (NM_153092)	52	NM_001346582	231042	Mm.45513	NM_153092	ENSMUSG00000048439	Nupl2	AV116043|CG1|NLP-1|Nlp1	nucleoporin like 2	protein-coding
mm_35623.1	chr4	43454583	43454587	-	1	NA	promoter-TSS (NM_001110320)	promoter-TSS (NM_001110320)	41	NM_001110320	12517	Mm.188157	NM_007654	ENSMUSG00000028459	Cd72	CD72c|Ly-19|Ly-32|Ly-m19|Lyb-2	CD72 antigen	protein-coding
mm_45622.1	chr5	75978448	75978463	-	1	NA	promoter-TSS (NM_010612)	promoter-TSS (NM_010612)	-27	NM_010612	16542	Mm.285	NM_010612	ENSMUSG00000062960	Kdr	6130401C07|Flk-1|Flk1|Krd-1|Ly73|VEGFR-2|VEGFR2|sVEGFR-2	kinase insert domain protein receptor	protein-coding
mm_143349.1	chr17	67061486	67061532	-	1	NA	intron (NM_008984, intron 5 of 30)	intron (NM_008984, intron 5 of 30)	-35274	NR_049205	100885844		NR_049205	ENSMUSG00000093508	Mir5709	Gm22041|mir-5709|mmu-mir-5709	microRNA 5709	ncRNA
mm_134561.1	chr16	20302325	20302345	-	1	NA	promoter-TSS (NM_001005767)	promoter-TSS (NM_001005767)	27	NM_001005767	381038	Mm.371737	NM_001005767	ENSMUSG00000033918	Parl	D16Ertd607e|PRO2207|PSARL1|PSENIP2|Psarl	presenilin associated, rhomboid-like	protein-coding
mm_80543.1	chr9	81631930	81631948	+	1	NA	promoter-TSS (NR_040393)	promoter-TSS (NR_040393)	9	NR_040393	319405	Mm.246494	NR_040393	ENSMUSG00000097466	D430036J16Rik	-	RIKEN cDNA D430036J16 gene	ncRNA
mm_147873.1	chr18	64489023	64489040	-	1	NA	promoter-TSS (NM_007998)	promoter-TSS (NM_007998)	35	NM_007998	14151	Mm.1070	NM_007998	ENSMUSG00000024588	Fech	AI894116|Fcl|fch	ferrochelatase	protein-coding
mm_138745.1	chr17	37003684	37003686	+	1	NA	promoter-TSS (NR_033137)	promoter-TSS (NR_033137)	19	NR_033137	22715	Mm.305561	NM_009559	ENSMUSG00000036036	Zfp57	G19|Zfp-57	zinc finger protein 57	protein-coding
mm_100956.1	chr11	6626031	6626072	-	1	NA	promoter-TSS (NM_134011)	promoter-TSS (NM_134011)	16	NM_001130457	21379	Mm.247761	NM_134011	ENSMUSG00000000384	Tbrg4	2310042P22Rik|AA120735|AA408001|AI527316|Cpr2|R74877|Tb-12|mKIAA0948	transforming growth factor beta regulated gene 4	protein-coding
mm_47206.1	chr5	120941882	120941893	-	1	NA	3' UTR (NM_011286, exon 22 of 22)	3' UTR (NM_011286, exon 22 of 22)	27069	NM_133893	100535	Mm.247620	NM_133893	ENSMUSG00000032623	Oas1d	AA536864|C85127|oasl8	2'-5' oligoadenylate synthetase 1D	protein-coding
mm_26551.1	chr3	146404816	146404833	+	1	NA	5' UTR (NM_001253768, exon 1 of 15)	5' UTR (NM_001253768, exon 1 of 15)	182	NM_138744	99167	Mm.200783	NM_138744	ENSMUSG00000036825	Ssx2ip	AU014939|AU042321|Adip	synovial sarcoma, X 2 interacting protein	protein-coding
mm_118357.1	chr13	115101559	115101573	-	1	NA	5' UTR (NM_001033228, exon 1 of 29)	5' UTR (NM_001033228, exon 1 of 29)	398	NM_001033228	109700	Mm.317280	NM_001033228	ENSMUSG00000042284	Itga1	CD49A|E130012M19Rik|Vla1	integrin alpha 1	protein-coding
mm_63425.1	chr7	127475116	127475128	+	1	NA	exon (NM_145589, exon 7 of 11)	exon (NM_145589, exon 7 of 11)	3508	NM_145589	233895	Mm.44183	NM_145589	ENSMUSG00000030822	Prr14	BC006909	proline rich 14	protein-coding
mm_34236.1	chr4	141147912	141147971	+	1	NA	promoter-TSS (NM_172518)	promoter-TSS (NM_172518)	19	NM_172518	213499	Mm.28865	NM_172518	ENSMUSG00000028920	Fbxo42	6720460I06Rik|mKIAA1332	F-box protein 42	protein-coding
mm_152758.1	chr19	20373706	20373739	-	1	NA	exon (NM_010730, exon 13 of 13)	exon (NM_010730, exon 13 of 13)	16949	NM_010730	16952	Mm.248360	NM_010730	ENSMUSG00000024659	Anxa1	Anx-1|Anx-A1|C430014K04Rik|Lpc-1|Lpc1	annexin A1	protein-coding
mm_92007.1	chr10	62337391	62337395	-	1	NA	intron (NM_010438, intron 4 of 21)	intron (NM_010438, intron 4 of 21)	3028	NM_001146100	15275	Mm.196605	NM_010438	ENSMUSG00000037012	Hk1	BB404130|Hk-1|Hk1-s|dea|mHk1-s	hexokinase 1	protein-coding
mm_146011.1	chr18	69346144	69346198	+	1	NA	intron (NM_001083967, intron 1 of 19)	CpG	450	NM_001083967	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding
mm_108848.1	chr12	98271782	98271824	+	1	NA	intron (NM_008152, intron 1 of 1)	Lx2B2|LINE|L1	3168	NM_008152	14744	Mm.378924	NM_008152	ENSMUSG00000021886	Gpr65	Dig1|Gpcr25|TDAG8	G-protein coupled receptor 65	protein-coding
mm_32124.1	chr4	99033232	99033243	+	1	NA	intron (NM_013913, intron 2 of 6)	intron (NM_013913, intron 2 of 6)	2283	NM_013913	30924	Mm.28341	NM_013913	ENSMUSG00000028553	Angptl3	hypl	angiopoietin-like 3	protein-coding
mm_98712.1	chr11	96314659	96314664	+	1	NA	Intergenic	CpG	-2504	NR_029784	723893		NR_029784	ENSMUSG00000065519	Mir10a	Mirn10a|miR-10a|mmu-mir-10a	microRNA 10a	ncRNA
mm_31564.1	chr4	57568012	57568093	+	1	NA	promoter-TSS (NM_172868)	promoter-TSS (NM_172868)	-196	NM_001304544	677884	Mm.331630	NM_001304544	ENSMUSG00000089945	Pakap	AF064781|Gm20459|Palm2-Akap2|Palm2Akap2|Palm2akap2	paralemmin A kinase anchor protein	protein-coding
mm_54867.1	chr6	42597687	42597702	-	1	NA	promoter-TSS (NM_203396)	promoter-TSS (NM_203396)	-322	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_6497.1	chr1	74281113	74281147	-	1	NA	exon (NM_146110, exon 9 of 11)	exon (NM_146110, exon 9 of 11)	2530	NM_174985	227289	Mm.246587	NM_174985	ENSMUSG00000064272	Gpbar1	BG37|GPCR|GPR131|M-BAR|TGR5	G protein-coupled bile acid receptor 1	protein-coding
mm_122619.1	chr14	51145456	51145462	-	1	NA	exon (NM_011271, exon 2 of 2)	exon (NM_011271, exon 2 of 2)	1308	NM_011271	19752	Mm.235538	NM_011271	ENSMUSG00000035896	Rnase1	AI574248|Rib-1|Rib1	ribonuclease, RNase A family, 1 (pancreatic)	protein-coding
mm_99462.1	chr11	102435279	102435297	+	1	NA	exon (NM_008175, exon 10 of 13)	exon (NM_008175, exon 10 of 13)	4966	NM_008175	14824	Mm.1568	NM_008175	ENSMUSG00000034708	Grn	Pgrn|epithelin	granulin	protein-coding
mm_67581.1	chr7	82867078	82867084	-	1	NA	promoter-TSS (NM_175366)	promoter-TSS (NM_175366)	-252	NM_175366	108797	Mm.306789	NM_175366	ENSMUSG00000057706	Mex3b	4931439A04Rik|M-04814|Rkhd3|mKIAA2009	mex3 RNA binding family member B	protein-coding
mm_20941.1	chr2	151432376	151432380	-	1	NA	promoter-TSS (NR_131976)	promoter-TSS (NR_131976)	71	NR_131976	100125594	Mm.381283	NR_131976	ENSMUSG00000087495	LOC100125594	-	uncharacterized LOC100125594	ncRNA
mm_5797.1	chr1	52155368	52155379	-	1	NA	intron (NM_001205313, intron 23 of 24)	intron (NM_001205313, intron 23 of 24)	35751	NM_001205313	20846	Mm.277406	NM_009283	ENSMUSG00000026104	Stat1	2010005J02Rik|AA408197	signal transducer and activator of transcription 1	protein-coding
mm_3475.1	chr1	150105385	150105405	+	1	NA	exon (NM_011198, exon 10 of 10)	exon (NM_011198, exon 10 of 10)	5364	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_26087.1	chr3	136696827	136696833	+	1	NA	intron (NM_008913, intron 1 of 13)	(T)n|Simple_repeat|Simple_repeat	26764	NM_001293622	19055	Mm.331389	NM_008913	ENSMUSG00000028161	Ppp3ca	2900074D19Rik|CN|Caln|Calna|CnA	protein phosphatase 3, catalytic subunit, alpha isoform	protein-coding
mm_142430.1	chr17	45569764	45569798	-	1	NA	exon (NM_008302, exon 7 of 11)	exon (NM_008302, exon 7 of 11)	3480	NM_008302	15516	Mm.2180	NM_008302	ENSMUSG00000023944	Hsp90ab1	90kDa|AL022974|C81438|Hsp84|Hsp84-1|Hsp90|Hspcb	heat shock protein 90 alpha (cytosolic), class B member 1	protein-coding
mm_19666.1	chr2	103303159	103303171	-	1	NA	promoter-TSS (NM_007914)	promoter-TSS (NM_007914)	31	NM_007914	13661	Mm.10724	NM_007914	ENSMUSG00000012350	Ehf	9030625L19Rik|AU019492	ets homologous factor	protein-coding
mm_61626.1	chr7	80220954	80220957	+	1	NA	intron (NM_013659, intron 13 of 14)	intron (NM_013659, intron 13 of 14)	11850	NM_001291276	23991	Mm.30217	NM_011870	ENSMUSG00000030538	Cib1	Cibkip|Kip|Prkdcip	calcium and integrin binding 1 (calmyrin)	protein-coding
mm_21985.1	chr2	167577179	167577182	-	1	NA	Intergenic	Intergenic	38985	NM_011427	20613	Mm.2093	NM_011427	ENSMUSG00000042821	Snai1	Sna|Sna1|Snail|Snail1	snail family zinc finger 1	protein-coding
mm_80292.1	chr9	73094827	73094834	+	1	NA	intron (NM_001301230, intron 6 of 6)	MLT1L|LTR|ERVL-MaLR	-7568	NM_025890	66991	Mm.471745	NM_025890	ENSMUSG00000092622	Khdc3	2410004A20Rik|AI467128|FILIA|OEEP48	KH domain containing 3, subcortical maternal complex member	protein-coding
mm_136352.1	chr16	92697110	92697117	-	1	NA	5' UTR (NM_009821, exon 1 of 5)	5' UTR (NM_009821, exon 1 of 5)	216	NM_001111023	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_82056.1	chr9	122682123	122682133	+	1	NA	promoter-TSS (NR_029819)	promoter-TSS (NR_029819)	-748	NR_029819	387156		NR_029819	ENSMUSG00000065414	Mir138-1	Mirn138|Mirn138-1|mir-138-1	microRNA 138-1	ncRNA
mm_64602.1	chr7	3212629	3212633	-	1	NA	Intergenic	B1F|SINE|Alu	-5995	NR_029640	100049710		NR_029640	ENSMUSG00000077815	Mir290a	Mir290|Mirn290|mir-290a|mmu-miR-290|mmu-mir-290a	microRNA 290a	ncRNA
mm_11802.1	chr2	43748803	43748875	+	1	NA	promoter-TSS (NM_153820)	promoter-TSS (NM_153820)	15	NM_001301831	76117	Mm.217350	NM_153820	ENSMUSG00000049744	Arhgap15	5830480G12Rik	Rho GTPase activating protein 15	protein-coding
mm_155070.1	chrX	43590938	43590944	+	1	NA	promoter-TSS (NM_001195271)	promoter-TSS (NM_001195271)	-48	NM_001195271	637093	Mm.368463	NM_001195271	ENSMUSG00000078320	Tex13c1	Gm362|Tex13c	TEX13 family member C1	protein-coding
mm_108992.1	chr12	102899272	102899321	+	1	NA	promoter-TSS (NM_001039049)	promoter-TSS (NM_001039049)	-10	NM_001039049	75483	Mm.660	NM_001039049	ENSMUSG00000043319	Cox8c	1700007F21Rik|COX8-3|COXVIII-3	cytochrome c oxidase subunit VIIIc	protein-coding
mm_112224.1	chr12	113430377	113430385	-	1	NA	Intergenic	Intergenic	-59184	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_87840.1	chr10	60399803	60399805	+	1	NA	promoter-TSS (NM_001164374)	promoter-TSS (NM_001164374)	78	NM_001164374	100302688	Mm.444135	NM_001164374	ENSMUSG00000090439	Gm17455	-	predicted gene, 17455	protein-coding
mm_166098.1	chr4	143450325	143450326	-	1	NA	promoter-TSS (NM_173773)	promoter-TSS (NM_173773)	-1	NM_001347238	242737	Mm.148643	NM_173773	ENSMUSG00000047799	Oog4	E330017M15	oogenesin 4	protein-coding
mm_4958.1	chr1	191266887	191266927	+	1	NA	Intergenic	Intergenic	51211	NM_025424	66208	Mm.46444	NM_025424	ENSMUSG00000037499	Nenf	1110060M21Rik|SCIRP10|Spuf	neuron derived neurotrophic factor	protein-coding
mm_100125.1	chr11	115912064	115912076	+	1	NA	promoter-TSS (NM_001162998)	promoter-TSS (NM_001162998)	53	NM_001162998	68528	Mm.441893	NM_001162998	ENSMUSG00000075420	Smim6	1110017F19Rik	small integral membrane protein 6	protein-coding
mm_73795.1	chr8	117258103	117258103	+	1	NA	intron (NM_001163262, intron 1 of 20)	intron (NM_001163262, intron 1 of 20)	1084	NM_001163262	74440	Mm.233181	NM_028941	ENSMUSG00000034390	Cmip	4933407C03Rik|5830471E12Rik|AI314065|AI464126	c-Maf inducing protein	protein-coding
mm_139187.1	chr17	47596074	47596104	+	1	NA	intron (NM_001081635, intron 4 of 6)	intron (NM_001081635, intron 4 of 6)	2622	NM_007632	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_121783.1	chr14	19976801	19976806	-	1	NA	promoter-TSS (NM_001285911)	promoter-TSS (NM_001285911)	-110	NM_001285911	14702	Mm.41737	NM_010315	ENSMUSG00000043004	Gng2	-	guanine nucleotide binding protein (G protein), gamma 2	protein-coding
mm_157260.1	chrX	19161580	19161592	-	1	NA	Intergenic	Intergenic	-14615	NR_029807	723828		NR_029807	ENSMUSG00000065471	Mir222	Mirn222|mir-222|mmu-mir-222	microRNA 222	ncRNA
mm_64968.1	chr7	16615074	16615138	-	1	NA	promoter-TSS (NM_172739)	promoter-TSS (NM_172739)	-113	NM_172739	232906	Mm.28646	NM_172739	ENSMUSG00000058230	Arhgap35	6430596G11Rik|AI841135|Grlf1|mKIAA1722|p190A|p190RhoGAP	Rho GTPase activating protein 35	protein-coding
mm_169526.1	chr14	90301708	90301710	+	1	NA	Intergenic	IAPLTR1_Mm|LTR|ERVK	174818	NR_045712	74967	Mm.390704	NR_045712		4930474H20Rik	-	RIKEN cDNA 4930474H20 gene	ncRNA
mm_83573.1	chr9	47474906	47474923	-	1	NA	Intergenic	Intergenic	-55256	NM_001310841	54725	Mm.234832	NM_018770	ENSMUSG00000032076	Cadm1	2900073G06Rik|3100001I08Rik|AI987920|Bl2|Igsf4|Igsf4a|Necl2|RA175|RA175A|RA175B|RA175C|RA175N|ST17|SgIGSF|SynCam|Tslc1	cell adhesion molecule 1	protein-coding
mm_104418.1	chr11	94760912	94760917	-	1	NA	5' UTR (NM_001105561, exon 1 of 5)	5' UTR (NM_001105561, exon 1 of 5)	268	NM_001105561	217122	Mm.24063	NM_183153		Gm11545	A430060F13Rik|C86086|OTTMUSG00000002043	predicted gene 11545	protein-coding
mm_84042.1	chr9	57796563	57796589	-	1	NA	exon (NM_019689, exon 5 of 8)	exon (NM_019689, exon 5 of 8)	-30716	NM_007713	102414	Mm.25720	NM_007713	ENSMUSG00000032316	Clk3	AI256811	CDC-like kinase 3	protein-coding
mm_67800.1	chr7	98096414	98096426	-	1	NA	intron (NM_001256081, intron 8 of 48)	intron (NM_001256081, intron 8 of 48)	12828	NM_001256082	17921	Mm.1403	NM_008663	ENSMUSG00000030761	Myo7a	Hdb|Myo7|USH1B|nmf371|polka|sh-1|sh1	myosin VIIA	protein-coding
mm_49839.1	chr6	38109409	38109417	+	1	NA	promoter-TSS (NM_029921)	promoter-TSS (NM_029921)	60	NM_029921	77522	Mm.387207	NM_029921	ENSMUSG00000029829	Tmem213	D630002J15Rik	transmembrane protein 213	protein-coding
mm_108055.1	chr12	73923103	73923105	+	1	NA	intron (NM_010431, intron 1 of 14)	B2_Mm2|SINE|B2	15237	NM_001313919	15251	Mm.3879	NM_010431	ENSMUSG00000021109	Hif1a	AA959795|HIF-1-alpha|HIF1-alpha|HIF1alpha|MOP1|bHLHe78	hypoxia inducible factor 1, alpha subunit	protein-coding
mm_162916.1	chr10	120160376	120160379	+	1	NA	intron (NM_028679, intron 8 of 11)	ORR1F|LTR|ERVL-MaLR	41160	NM_028679	73914	Mm.146194	NM_028679	ENSMUSG00000020227	Irak3	4833428C18Rik|AI563835|IRAK-M	interleukin-1 receptor-associated kinase 3	protein-coding
mm_47456.1	chr5	123621847	123621850	-	1	NA	exon (NM_019765, exon 13 of 24)	exon (NM_019765, exon 13 of 24)	-48833	NM_029929	77573	Mm.41372	NM_029929	ENSMUSG00000029434	Vps33a	3830421M04Rik|AI503300|AW048546|AW554476|bf	VPS33A CORVET/HOPS core subunit	protein-coding
mm_161381.1	chr14	70659224	70659224	-	1	NA	3' UTR (NM_023045, exon 28 of 28)	3' UTR (NM_023045, exon 28 of 28)	-6140	NM_181345	328440	Mm.347749	NM_181345	ENSMUSG00000047911	Npm2	-	nucleophosmin/nucleoplasmin 2	protein-coding
mm_48067.1	chr5	136581621	136581636	-	1	NA	Intergenic	Intergenic	-14138	NM_001291238	13047	Mm.320317	NM_009986	ENSMUSG00000029705	Cux1	CDP|Cutl1|Cux|Cux-1	cut-like homeobox 1	protein-coding
mm_146332.1	chr18	81200003	81200008	+	1	NA	Intergenic	Intergenic	-213427	NM_178280	20689	Mm.215917	NM_178280	ENSMUSG00000024565	Sall3	B130022O04Rik|Msal|Msal-1|Sal|Salt|Spalt	sal-like 3 (Drosophila)	protein-coding
mm_52365.1	chr6	112696773	112696786	+	1	NA	promoter-TSS (NM_021385)	promoter-TSS (NM_021385)	-109	NM_001167730	58186	Mm.103812	NM_021385	ENSMUSG00000030254	Rad18	2810024C04Rik|Rad18sc	RAD18 E3 ubiquitin protein ligase	protein-coding
mm_98437.1	chr11	94938500	94938538	+	1	NA	exon (NM_007742, exon 5 of 51)	exon (NM_007742, exon 5 of 51)	2295	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_171270.1	chr3	88772513	88772513	-	1	NA	promoter-TSS (NM_018804)	promoter-TSS (NM_018804)	86	NM_018804	229521	Mm.379376	NM_018804	ENSMUSG00000068923	Syt11	1500004A13Rik|3632445O20Rik|5430404N14Rik|6530420C11Rik|AI851970	synaptotagmin XI	protein-coding
mm_158498.1	chrX	142384778	142384781	-	1	NA	intron (NM_019477, intron 1 of 15)	intron (NM_019477, intron 1 of 15)	5756	NM_001033600	50790	Mm.391337	NM_019477	ENSMUSG00000031278	Acsl4	9430020A05Rik|ACS4|AU018108|Facl4|Lacs4	acyl-CoA synthetase long-chain family member 4	protein-coding
mm_110129.1	chr12	26444713	26444734	-	1	NA	3' UTR (NM_021384, exon 6 of 6)	3' UTR (NM_021384, exon 6 of 6)	11729	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_1076.1	chr1	59482121	59482131	+	1	NA	promoter-TSS (NM_008057)	promoter-TSS (NM_008057)	-21	NM_008057	14369	Mm.297906	NM_008057	ENSMUSG00000041075	Fzd7	Fz7	frizzled class receptor 7	protein-coding
mm_90318.1	chr10	127063657	127063670	+	1	NA	promoter-TSS (NM_009870)	promoter-TSS (NM_009870)	60	NM_009870	12567	Mm.6839	NM_009870	ENSMUSG00000006728	Cdk4	Crk3	cyclin-dependent kinase 4	protein-coding
mm_121966.1	chr14	25493468	25493476	-	1	NA	intron (NM_001310666, intron 1 of 23)	intron (NM_001310666, intron 1 of 23)	34287	NM_183208	328365	Mm.227484	NM_183208	ENSMUSG00000007817	Zmiz1	BC065120|E330020C23|ENSMUSG00000072684|Gm10397|I920194n01|Rai17|Zimp10	zinc finger, MIZ-type containing 1	protein-coding
mm_135665.1	chr16	52407701	52407711	-	1	NA	intron (NM_009655, intron 1 of 15)	B4A|SINE|B4	45375	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_62480.1	chr7	101871637	101871644	+	1	NA	promoter-TSS (NM_008034)	promoter-TSS (NM_008034)	-852	NM_001252552	14275	Mm.2135	NM_008034	ENSMUSG00000001827	Folr1	FBP1|Folbp-1|Folbp1	folate receptor 1 (adult)	protein-coding
mm_149957.1	chr19	28893041	28893043	+	1	NA	intron (NM_009199, intron 3 of 11)	intron (NM_009199, intron 3 of 11)	57876	NM_009199	20510	Mm.246670	NM_009199	ENSMUSG00000024935	Slc1a1	D130048G10Rik|EAAC1|EAAC2|EAAT3|MEAAC1	solute carrier family 1 (neuronal/epithelial high affinity glutamate transporter, system Xag), member 1	protein-coding
mm_127254.1	chr15	99702138	99702205	+	1	NA	promoter-TSS (NM_031842)	promoter-TSS (NM_031842)	-116	NM_031842	83797	Mm.273756	NM_031842	ENSMUSG00000023018	Smarcd1	AA407987|Baf60a|D15Kz1	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1	protein-coding
mm_79061.1	chr9	46230252	46230263	+	1	NA	exon (NM_009692, exon 4 of 4)	exon (NM_009692, exon 4 of 4)	1627	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2|apo-AI|apoA-I	apolipoprotein A-I	protein-coding
mm_72867.1	chr8	88658022	88658048	+	1	NA	intron (NM_145857, intron 2 of 12)	intron (NM_145857, intron 2 of 12)	10688	NM_145857	257632	Mm.222633	NM_145857	ENSMUSG00000055994	Nod2	ACUG|BLAU|CD|Card15|F830032C23Rik|IBD1|Nlrc2	nucleotide-binding oligomerization domain containing 2	protein-coding
mm_61108.1	chr7	52678910	52678910	+	1	NA	Intergenic	Intergenic	-663194	NM_001195601	100503036	Mm.279725	NM_001195601	ENSMUSG00000094445	1700015G11Rik	Ccdc179	RIKEN cDNA 1700015G11 gene	protein-coding
mm_127520.1	chr15	102028219	102028235	+	1	NA	promoter-TSS (NM_010664)	promoter-TSS (NM_010664)	11	NM_010664	16668	Mm.22479	NM_010664	ENSMUSG00000023043	Krt18	CK18|K18|Krt1-18	keratin 18	protein-coding
mm_15332.1	chr2	155778674	155778683	+	1	NA	intron (NM_010808, intron 1 of 8)	B4|SINE|B4	3336	NM_010808	17391	Mm.389325	NM_010808	ENSMUSG00000027612	Mmp24	AU040325|MMP-21|MT5-MMP|MT5MMP|MTMMP5	matrix metallopeptidase 24	protein-coding
mm_52867.1	chr6	122308970	122309018	+	1	NA	promoter-TSS (NM_010749)	promoter-TSS (NM_010749)	-16	NM_010749	17113	Mm.249225	NM_010749	ENSMUSG00000007458	M6pr	CD-MPR|Mpr46	mannose-6-phosphate receptor, cation dependent	protein-coding
mm_85573.1	chr9	107289392	107289422	-	1	NA	promoter-TSS (NM_001316691)	promoter-TSS (NM_001316691)	-11	NM_001316691	102626	Mm.222612	NM_178907	ENSMUSG00000032577	Mapkapk3	3PK|AI874665|MAPKAP-K3|MAPKAP3|MK-3|MK3|MapkKapk3	mitogen-activated protein kinase-activated protein kinase 3	protein-coding
mm_71667.1	chr8	60671574	60671585	+	1	NA	exon (NM_001177882, exon 3 of 3)	exon (NM_001177882, exon 3 of 3)	16022	NM_001177882	71306	Mm.23242	NM_027756	ENSMUSG00000031647	Mfap3l	4933428A15Rik|5430405D20Rik|AI461995|AW125052|NYD-sp9|mKIAA0626	microfibrillar-associated protein 3-like	protein-coding
mm_64433.1	chr7	142578038	142578056	+	1	NA	promoter-TSS (NR_130974)	promoter-TSS (NR_130974)	99	NR_130974	14955	Mm.14802	NR_001592	ENSMUSG00000000031	H19	AI747191	H19, imprinted maternally expressed transcript	ncRNA
mm_70287.1	chr8	3655763	3655781	+	1	NA	promoter-TSS (NM_001204959)	promoter-TSS (NM_001204959)	2	NM_022984	57264	Mm.1181	NM_022984	ENSMUSG00000012705	Retn	ADSF|Fizz3|Rstn|Xcp4	resistin	protein-coding
mm_171619.1	chr4	152327495	152327514	+	1	NA	exon (NM_001277114, exon 2 of 4)	exon (NM_001277114, exon 2 of 4)	1778	NR_102291	19934	Mm.307846	NM_009079	ENSMUSG00000028936	Rpl22	2700038K18Rik	ribosomal protein L22	protein-coding
mm_22744.1	chr3	19957120	19957131	+	1	NA	promoter-TSS (NM_007752)	promoter-TSS (NM_007752)	71	NM_007752	12870	Mm.13787	NM_007752	ENSMUSG00000003617	Cp	D3Ertd555e	ceruloplasmin	protein-coding
mm_40006.1	chr5	32979143	32979144	+	1	NA	intron (NM_001025426, intron 39 of 42)	MER58A|DNA|hAT-Charlie	-39673	NM_011738	22629	Mm.332314	NM_011738	ENSMUSG00000018965	Ywhah	-	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta polypeptide	protein-coding
mm_76054.1	chr8	77724159	77724169	-	1	NA	5' UTR (NM_010332, exon 1 of 8)	5' UTR (NM_010332, exon 1 of 8)	288	NM_010332	13617	Mm.283168	NM_010332	ENSMUSG00000031616	Ednra	ET-AR|ETa|Gpcr10	endothelin receptor type A	protein-coding
mm_61351.1	chr7	68289477	68289480	+	1	NA	intron (NM_001013811, intron 1 of 8)	intron (NM_001013811, intron 1 of 8)	-12884	NR_040340	100504026	Mm.426764	NR_040340	ENSMUSG00000086628	Gm16157	OTTMUSG00000031023	predicted gene 16157	ncRNA
mm_26425.1	chr3	142618289	142618314	+	1	NA	3' UTR (NM_010259, exon 11 of 11)	3' UTR (NM_010259, exon 11 of 11)	-2362	NM_010260	14469	Mm.24038	NM_010260	ENSMUSG00000028270	Gbp2	-	guanylate binding protein 2	protein-coding
mm_73064.1	chr8	94386524	94386534	+	1	NA	promoter-TSS (NM_022331)	promoter-TSS (NM_022331)	29	NM_022331	64209	Mm.29151	NM_022331	ENSMUSG00000031770	Herpud1	Herp|Mifl|SUP	homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1	protein-coding
mm_21646.1	chr2	164333499	164333507	-	1	NA	exon (NM_009301, exon 2 of 3)	exon (NM_009301, exon 2 of 3)	738	NM_009301	20944	Mm.140154	NM_009301	ENSMUSG00000017004	Svs5	BB115186|Semg1|Svp-1|Svp1|Svp5	seminal vesicle secretory protein 5	protein-coding
mm_45366.1	chr5	66018561	66018575	-	1	NA	3' UTR (NM_139065, exon 7 of 7)	3' UTR (NM_139065, exon 7 of 7)	-14283	NR_027961	231253	Mm.436542	NM_177679	ENSMUSG00000054598	9130230L23Rik	-	RIKEN cDNA 9130230L23 gene	ncRNA
mm_89719.1	chr10	98914427	98914437	+	1	NA	promoter-TSS (NM_026482)	promoter-TSS (NM_026482)	-720	NM_026482	67972	Mm.166944	NM_026482	ENSMUSG00000019943	Atp2b1	2810442I22Rik|E130111D10Rik|Pmca1	ATPase, Ca++ transporting, plasma membrane 1	protein-coding
mm_46456.1	chr5	105117920	105117929	-	1	NA	3' UTR (NM_001256005, exon 11 of 11)	3' UTR (NM_001256005, exon 11 of 11)	-7632	NM_172777	236573	Mm.425261	NM_172777	ENSMUSG00000029298	Gbp9	-	guanylate-binding protein 9	protein-coding
mm_159669.1	chr4	154299941	154299941	-	1	NA	promoter-TSS (NM_001112744)	promoter-TSS (NM_001112744)	-46	NM_001112744	230972	Mm.38481	NM_001112744	ENSMUSG00000029032	Arhgef16	-	Rho guanine nucleotide exchange factor (GEF) 16	protein-coding
mm_112215.1	chr12	113428653	113428662	-	1	NA	Intergenic	Intergenic	-60908	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_117650.1	chr13	92795004	92795029	-	1	NA	promoter-TSS (NM_011582)	promoter-TSS (NM_011582)	-198	NM_011582	21828	Mm.20865	NM_011582	ENSMUSG00000021702	Thbs4	TSP4	thrombospondin 4	protein-coding
mm_85249.1	chr9	99140111	99140124	-	1	NA	promoter-TSS (NM_029094)	promoter-TSS (NM_029094)	94	NM_029094	74769	Mm.213128	NM_029094	ENSMUSG00000032462	Pik3cb	1110001J02Rik|AI447572|p110beta	phosphatidylinositol 3-kinase, catalytic, beta polypeptide	protein-coding
mm_146522.1	chr18	4353227	4353238	-	1	NA	promoter-TSS (NM_007746)	promoter-TSS (NM_007746)	-279	NM_007746	26410	Mm.3275	NM_007746	ENSMUSG00000024235	Map3k8	Cot|Cot/Tpl2|Est|Estf|Tpl-2|Tpl2|c-COT	mitogen-activated protein kinase kinase kinase 8	protein-coding
mm_158896.1	chr1	23761899	23761899	+	1	NA	promoter-TSS (NM_172124)	promoter-TSS (NM_172124)	-27	NM_172124	280645	Mm.471661	NM_172124	ENSMUSG00000026156	B3gat2	GlcAT-S|Glcats	beta-1,3-glucuronyltransferase 2 (glucuronosyltransferase S)	protein-coding
mm_40198.1	chr5	36868694	36868716	+	1	NA	5' UTR (NM_172994, exon 1 of 9)	5' UTR (NM_172994, exon 1 of 9)	135	NM_172994	269643	Mm.41694	NM_172994	ENSMUSG00000029120	Ppp2r2c	6330548O06Rik|IMYPNO|IMYPNO1|PR52	protein phosphatase 2, regulatory subunit B, gamma	protein-coding
mm_76434.1	chr8	84985338	84985344	-	1	NA	Intergenic	Intergenic	-5254	NM_133255	170833	Mm.247775	NM_133255	ENSMUSG00000052566	Hook2	A630054I03Rik	hook microtubule tethering protein 2	protein-coding
mm_42658.1	chr5	119669944	119669954	+	1	NA	promoter-TSS (NM_198052)	promoter-TSS (NM_198052)	-913	NM_198052	21386	Mm.219139	NM_011535	ENSMUSG00000018604	Tbx3	D5Ertd189e	T-box 3	protein-coding
mm_113877.1	chr13	48968162	48968216	+	1	NA	promoter-TSS (NR_015601)	promoter-TSS (NR_015601)	77	NR_015601	68128	Mm.426304	NR_015601		Fam120aos	C030044B11Rik	family with sequence similarity 120A, opposite strand	ncRNA
mm_71793.1	chr8	67333257	67333260	+	1	NA	Intergenic	RLTR24B_MM|LTR|ERV1	-157500	NM_008673	17960	Mm.14125	NM_008673	ENSMUSG00000025588	Nat1	Nat-1	N-acetyl transferase 1	protein-coding
mm_164470.1	chr16	65520603	65520607	+	1	NA	promoter-TSS (NM_008849)	promoter-TSS (NM_008849)	-24	NM_008849	18736	Mm.355440	NM_008849	ENSMUSG00000004842	Pou1f1	GHF-1|Hmp1|Pit-1|Pit1|Pit1-rs1|dw|dwarf	POU domain, class 1, transcription factor 1	protein-coding
mm_25438.1	chr3	108093053	108093062	+	1	NA	promoter-TSS (NM_008141)	promoter-TSS (NM_008141)	-9	NM_008141	14686	Mm.439652	NM_008141	ENSMUSG00000009108	Gnat2	AW490837|Gnat-2|Gt-2|Tcalpha	guanine nucleotide binding protein, alpha transducing 2	protein-coding
mm_165636.1	chr3	70040496	70040498	+	1	NA	Intergenic	B4|SINE|B4	32884	NM_001018031	229389	Mm.331071	NM_001018031	ENSMUSG00000027788	Otol1	Gm414	otolin 1	protein-coding
mm_110023.1	chr12	16788667	16788678	-	1	NA	intron (NM_015764, intron 1 of 34)	intron (NM_015764, intron 1 of 34)	12214	NM_015764	268527	Mm.428062	NM_015764	ENSMUSG00000036523	Greb1	5730583K22Rik|9130004E13|AF180470|AU023194|mKIAA0575	gene regulated by estrogen in breast cancer protein	protein-coding
mm_86719.1	chr10	19015574	19015588	+	1	NA	promoter-TSS (NM_009397)	promoter-TSS (NM_009397)	-171	NM_009397	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_75536.1	chr8	57320737	57320769	-	1	NA	promoter-TSS (NM_010402)	promoter-TSS (NM_010402)	106	NR_110474	102636514		NR_110474	ENSMUSG00000100510	Uph	-	upperhand	ncRNA
mm_31047.1	chr4	41135813	41135898	+	1	NA	promoter-TSS (NM_026275)	promoter-TSS (NM_026275)	-166	NM_026275	67615	Mm.389540	NM_026275	ENSMUSG00000036241	Ube2r2	1200003M11Rik|Cdc34b|Ubc3b	ubiquitin-conjugating enzyme E2R 2	protein-coding
mm_30378.1	chr3	152242806	152242819	-	1	NA	exon (NM_199465, exon 10 of 13)	exon (NM_199465, exon 10 of 13)	23508	NM_199465	68810	Mm.200188	NM_199465	ENSMUSG00000039103	Nexn	1110046H09Rik|AA553326|NELIN	nexilin	protein-coding
mm_27435.1	chr3	51561783	51561818	-	1	NA	promoter-TSS (NM_080793)	promoter-TSS (NM_080793)	-977	NM_080793	73251	Mm.192111	NM_080793	ENSMUSG00000037111	Setd7	1600028F23Rik|H3K4MT|KMT7|Set7|Set7/9|mKIAA1717	SET domain containing (lysine methyltransferase) 7	protein-coding
mm_24684.1	chr3	94954120	94954220	+	1	NA	promoter-TSS (NM_017395)	promoter-TSS (NM_017395)	-845	NM_017395	53970	Mm.24308	NM_017395	ENSMUSG00000005774	Rfx5	-	regulatory factor X, 5 (influences HLA class II expression)	protein-coding
mm_153224.1	chr19	34877881	34877923	-	1	NA	promoter-TSS (NM_023792)	promoter-TSS (NM_023792)	15	NM_023792	75735	Mm.24742	NM_023792	ENSMUSG00000033610	Pank1	Pank|Pank1b	pantothenate kinase 1	protein-coding
mm_69889.1	chr7	141637231	141637237	-	1	NA	intron (NM_001330001, intron 31 of 33)	intron (NM_001330001, intron 31 of 33)	16533	NR_106030	102466798		NR_106030	ENSMUSG00000098759	Mir7063	Gm27654|mmu-mir-7063	microRNA 7063	ncRNA
mm_171815.1	chr5	137602071	137602074	+	1	NA	Intergenic	Intergenic	-1013	NM_030037	68929	Mm.41355	NM_030037	ENSMUSG00000037221	Mospd3	1190005J19Rik|5133401H10Rik|Gtig2|R124	motile sperm domain containing 3	protein-coding
mm_55169.1	chr6	51920062	51920109	-	1	NA	intron (NM_018773, intron 6 of 12)	intron (NM_018773, intron 6 of 12)	92464	NM_018773	54353	Mm.221479	NM_018773	ENSMUSG00000059182	Skap2	2610021A10Rik|AA960083|BB137539|RA70|SKAP-HOM|Saps|Scap2|mSKAP55R	src family associated phosphoprotein 2	protein-coding
mm_97296.1	chr11	76454403	76454407	+	1	NA	intron (NM_001346670, intron 13 of 21)	intron (NM_001346670, intron 13 of 21)	14060	NM_001291186	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_169551.1	chr15	103242421	103242429	+	1	NA	exon (NM_010447, exon 6 of 10)	exon (NM_010447, exon 6 of 10)	1971	NR_002883	434858	Mm.391346	NR_002883		Gm5643	EG434858	heterogeneous nuclear ribonucleoprotein A1 pseudogene	pseudo
mm_90589.1	chr10	128271935	128271942	+	1	NA	intron (NM_019963, intron 1 of 23)	B3|SINE|B2	1362	NM_019963	20847	Mm.293120	NM_019963	ENSMUSG00000040033	Stat2	1600010G07Rik|AW496480	signal transducer and activator of transcription 2	protein-coding
mm_72989.1	chr8	92994648	92994652	+	1	NA	exon (NM_009209, exon 10 of 14)	exon (NM_009209, exon 10 of 14)	33603	NM_009209	20538	Mm.57040	NM_009209	ENSMUSG00000055368	Slc6a2	NE-T|NET|Slc6a5	solute carrier family 6 (neurotransmitter transporter, noradrenalin), member 2	protein-coding
mm_115354.1	chr13	112800787	112800822	+	1	NA	promoter-TSS (NM_008903)	promoter-TSS (NM_008903)	27	NM_008247	19012	Mm.291029	NM_008247	ENSMUSG00000021759	Plpp1	Hic53|Hpic53|LPP-1|LPP1|PAP-2a|PAP2-alpha|PAP2a|Ppap2a|mPAP	phospholipid phosphatase 1	protein-coding
mm_158383.1	chrX	136085169	136085173	-	1	NA	promoter-TSS (NM_001024141)	promoter-TSS (NM_001024141)	84	NM_001024141	245610	Mm.336244	NM_001024141	ENSMUSG00000057000	Nxf3	Gm384	nuclear RNA export factor 3	protein-coding
mm_141383.1	chr17	29079095	29079133	-	1	NA	promoter-TSS (NR_036469)	promoter-TSS (NR_036469)	12	NR_036469	100504267	Mm.438550	NR_036469	ENSMUSG00000085912	Trp53cor1	Gm16197|OTTMUSG00000031656|linc-p21|lincRNA-p21	tumor protein p53 pathway corepressor 1	ncRNA
mm_9492.1	chr1	173729542	173729566	-	1	NA	exon (NM_001204910, exon 5 of 8)	exon (NM_001204910, exon 5 of 8)	12255	NM_001204910	226691	Mm.440876	NM_001204910	ENSMUSG00000073490	Ifi207	AI607873|Pyhin-A	interferon activated gene 207	protein-coding
mm_119291.1	chr14	34673949	34673965	+	1	NA	promoter-TSS (NM_001301330)	promoter-TSS (NM_001301330)	29	NM_001301330	218914	Mm.27957	NM_001004436	ENSMUSG00000041408	Wapl	A530089A20Rik|BC037674|DIF-2|FOE|Wapal	WAPL cohesin release factor	protein-coding
mm_27051.1	chr3	27240569	27240573	-	1	NA	intron (NM_178772, intron 4 of 4)	intron (NM_178772, intron 4 of 4)	57567	NM_178772	320024	Mm.24576	NM_178772	ENSMUSG00000027698	Nceh1	Aadacl1|B230106I24Rik|CPO-BP|Nceh	neutral cholesterol ester hydrolase 1	protein-coding
mm_5465.1	chr1	36534728	36534734	-	1	NA	intron (NM_001310521, intron 1 of 8)	intron (NM_001310521, intron 1 of 8)	1008	NM_153502	78321	Mm.41421	NM_153502	ENSMUSG00000067653	Ankrd23	1110058D09Rik|2310041C05Rik|AI853437|Darp|MARP3	ankyrin repeat domain 23	protein-coding
mm_158898.1	chr1	25826825	25826825	-	1	NA	intron (NM_175642, intron 1 of 30)	intron (NM_175642, intron 1 of 30)	2882	NM_175642	210933	Mm.336569	NM_175642	ENSMUSG00000033569	Adgrb3	A830096D10Rik|Bai3	adhesion G protein-coupled receptor B3	protein-coding
mm_159376.1	chr3	89391988	89391988	-	1	NA	non-coding (NR_040403, exon 1 of 2)	non-coding (NR_040403, exon 1 of 2)	124	NR_040403	545539	Mm.393389	NR_040403	ENSMUSG00000074466	Gm15417	ENSMUSG00000074466|OTTMUSG00000021274	predicted gene 15417	ncRNA
mm_151750.1	chr19	5093004	5093016	-	1	NA	TTS (NM_026553)	TTS (NM_026553)	4472	NM_026553	68090	Mm.44202	NM_026553	ENSMUSG00000024875	Yif1a	5330422J23Rik|54TM|Yif1|Yif1p	Yip1 interacting factor homolog A (S. cerevisiae)	protein-coding
mm_142776.1	chr17	50094255	50094274	-	1	NA	intron (NM_181397, intron 3 of 9)	intron (NM_181397, intron 3 of 9)	96233	NM_181397	76438	Mm.41854	NM_181397	ENSMUSG00000039316	Rftn1	2310015N21Rik|AI853526	raftlin lipid raft linker 1	protein-coding
mm_155271.1	chrX	59999437	59999495	+	1	NA	promoter-TSS (NM_001305797)	promoter-TSS (NM_001305797)	2	NM_001305797	14071	Mm.391283	NM_007979	ENSMUSG00000031138	F9	AW111646|Cf-9|Cf9	coagulation factor IX	protein-coding
mm_169528.1	chr14	91647652	91647653	+	1	NA	Intergenic	RLTR6_Mm|LTR|ERV1	1520761	NR_045712	74967	Mm.390704	NR_045712		4930474H20Rik	-	RIKEN cDNA 4930474H20 gene	ncRNA
mm_140895.1	chr17	24073258	24073276	-	1	NA	TTS (NM_011062)	TTS (NM_011062)	218	NM_027008	69259	Mm.28171	NM_027008	ENSMUSG00000016946	Kctd5	2610030N08Rik|mKIAA0176	potassium channel tetramerisation domain containing 5	protein-coding
mm_120527.1	chr14	66966791	66966799	+	1	NA	Intergenic	Intergenic	42082	NM_009761	12177	Mm.29820	NM_009761	ENSMUSG00000022051	Bnip3l	C86132|D14Ertd719e|Nip3L|Nix	BCL2/adenovirus E1B interacting protein 3-like	protein-coding
mm_125654.1	chr15	63255939	63255953	+	1	NA	Intergenic	Intergenic	223662	NR_045279	432958	Mm.255105	NR_045279		Gm20740	-	predicted gene, 20740	ncRNA
mm_78241.1	chr9	21627378	21627381	+	1	NA	intron (NM_001174079, intron 1 of 33)	intron (NM_001174079, intron 1 of 33)	11210	NM_001174078	20586	Mm.286593	NM_011417	ENSMUSG00000032187	Smarca4	Brg1|HP1-BP72|SNF2beta|SW1/SNF|b2b508.1Clo|b2b692Clo	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	protein-coding
mm_63868.1	chr7	135713108	135713133	+	1	NA	intron (NM_001081117, intron 3 of 13)	MLT1B|LTR|ERVL-MaLR	3259	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_52943.1	chr6	122952534	122952555	+	1	NA	promoter-TSS (NM_153197)	promoter-TSS (NM_153197)	29	NM_001204241	73149	Mm.25684	NM_153197	ENSMUSG00000043832	Clec4a3	3110037K17Rik|Dcir3	C-type lectin domain family 4, member a3	protein-coding
mm_108172.1	chr12	76404480	76404482	+	1	NA	5' UTR (NM_008301, exon 1 of 1)	5' UTR (NM_008301, exon 1 of 1)	111	NM_008301	15512	Mm.296181	NM_008301	ENSMUSG00000059970	Hspa2	70kDa|HSP70.2|HSP70A2|Hsp70-2	heat shock protein 2	protein-coding
mm_130012.1	chr15	86706437	86706447	-	1	NA	Intergenic	Intergenic	491983	NM_145476	223754	Mm.28904	NM_145476	ENSMUSG00000051864	Tbc1d22a	BC023106|D15Ertd781e	TBC1 domain family, member 22a	protein-coding
mm_170346.1	chr18	50135082	50135087	+	1	NA	intron (NM_008292, intron 2 of 23)	intron (NM_008292, intron 2 of 23)	6883	NM_008292	15488	Mm.277857	NM_008292	ENSMUSG00000024507	Hsd17b4	17-beta-HSD|17[b]-HSD|DBP|MFE-2|MFP2|MPF-2|Mfp-2|perMFE-2	hydroxysteroid (17-beta) dehydrogenase 4	protein-coding
mm_44044.1	chr5	147681910	147681918	+	1	NA	exon (NM_010228, exon 5 of 30)	exon (NM_010228, exon 5 of 30)	44074	NM_010228	14254	Mm.389712	NM_010228	ENSMUSG00000029648	Flt1	AI323757|Flt-1|VEGFR-1|VEGFR1|sFlt1	FMS-like tyrosine kinase 1	protein-coding
mm_139954.1	chr17	71259996	71260006	+	1	NA	intron (NM_145158, intron 4 of 7)	intron (NM_145158, intron 4 of 7)	50964	NM_145158	246707	Mm.23462	NM_145158	ENSMUSG00000024053	Emilin2	FOAP-10	elastin microfibril interfacer 2	protein-coding
mm_11281.1	chr2	30062719	30062732	+	1	NA	intron (NM_023871, intron 1 of 7)	intron (NM_023871, intron 1 of 7)	729	NM_023871	56086	Mm.326055	NM_023871	ENSMUSG00000054766	Set	2610030F17Rik|5730420M11Rik|AA407739|I-2PP2A|StF-IT-1|TAF-I	SET nuclear oncogene	protein-coding
mm_34657.1	chr4	150866377	150866396	+	1	NA	exon (NM_133753, exon 4 of 4)	exon (NM_133753, exon 4 of 4)	11295	NM_133753	74155	Mm.318841	NM_133753	ENSMUSG00000028967	Errfi1	1300002F13Rik|AI788755|Mig-6|Mig6|RALT	ERBB receptor feedback inhibitor 1	protein-coding
mm_21363.1	chr2	157131187	157131195	-	1	NA	intron (NM_018851, intron 1 of 15)	B1_Mus1|SINE|Alu	4031	NM_001139520	56045	Mm.248478	NM_018851	ENSMUSG00000027639	Samhd1	E330031J07Rik|Mg11	SAM domain and HD domain, 1	protein-coding
mm_39874.1	chr5	31077065	31077075	+	1	NA	intron (NM_023525, intron 39 of 43)	intron (NM_023525, intron 39 of 43)	16457	NM_011773	22784	Mm.1396	NM_011773	ENSMUSG00000029151	Slc30a3	Znt3	solute carrier family 30 (zinc transporter), member 3	protein-coding
mm_35926.1	chr4	53032224	53032265	-	1	NA	3' UTR (NM_013454, exon 50 of 50)	3' UTR (NM_013454, exon 50 of 50)	20364	NM_025623	66536	Mm.38244	NM_025623	ENSMUSG00000015247	Nipsnap3b	2700063N13Rik|Nipsnap3a	nipsnap homolog 3B (C. elegans)	protein-coding
mm_80910.1	chr9	100643631	100643637	+	1	NA	promoter-TSS (NM_009282)	promoter-TSS (NM_009282)	11	NM_009282	20842	Mm.42135	NM_009282	ENSMUSG00000037286	Stag1	AU045003|SA-1|Scc3	stromal antigen 1	protein-coding
mm_104495.1	chr11	95837578	95837584	-	1	NA	intron (NM_001163464, intron 1 of 7)	intron (NM_001163464, intron 1 of 7)	-4714	NM_023121	14710	Mm.46299	NM_023121	ENSMUSG00000038811	Gngt2	AV096488	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 2	protein-coding
mm_47139.1	chr5	120548296	120548309	-	1	NA	exon (NM_145853, exon 13 of 28)	exon (NM_145853, exon 13 of 28)	37110	NM_001177594	170756	Mm.291070	NM_133221	ENSMUSG00000032754	Slc8b1	AF261233|NCKX6|NCLX|Slc24a6	solute carrier family 8 (sodium/lithium/calcium exchanger), member B1	protein-coding
mm_118541.1	chr14	16410247	16410254	+	1	NA	intron (NM_009409, intron 21 of 35)	intron (NM_009409, intron 21 of 35)	45044	NM_009409	21974	Mm.130362	NM_009409	ENSMUSG00000017485	Top2b	D230016L12Rik|Top-2	topoisomerase (DNA) II beta	protein-coding
mm_97991.1	chr11	83964420	83964478	+	1	NA	promoter-TSS (NM_194341)	promoter-TSS (NM_194341)	18	NM_194341	217030	Mm.82680	NM_194341	ENSMUSG00000034940	Synrg	Ap1gbp1|SYNG	synergin, gamma	protein-coding
mm_104645.1	chr11	97539780	97539792	-	1	NA	intron (NM_018873, intron 4 of 19)	intron (NM_018873, intron 4 of 19)	35340	NM_018873	56013	Mm.342665	NM_018873	ENSMUSG00000038453	Srcin1	P140|SNIP|mKIAA1684|p140Cap	SRC kinase signaling inhibitor 1	protein-coding
mm_37343.1	chr4	119658632	119658646	-	1	NA	intron (NM_008191, intron 1 of 2)	intron (NM_008191, intron 1 of 2)	306	NM_008191	14916	Mm.278	NM_008191	ENSMUSG00000032978	Guca2b	AV066530|Gcap2|Ugn	guanylate cyclase activator 2b (retina)	protein-coding
mm_2929.1	chr1	132298499	132298505	+	1	NA	promoter-TSS (NM_144810)	promoter-TSS (NM_144810)	-124	NM_144810	213417	Mm.39723	NM_144810	ENSMUSG00000042115	Klhdc8a	A630065K24Rik	kelch domain containing 8A	protein-coding
mm_165256.1	chr2	72633844	72633847	+	1	NA	Intergenic	Intergenic	-69665	NR_040503	74541	Mm.410774	NR_040503	ENSMUSG00000085252	8430437L04Rik	-	RIKEN cDNA 8430437L04 gene	ncRNA
mm_13803.1	chr2	119034784	119034869	+	1	NA	promoter-TSS (NM_173450)	promoter-TSS (NM_173450)	36	NM_173450	271842	Mm.33617	NM_173450	ENSMUSG00000027324	Rpusd2	4921503C21Rik|9630001E10|BB231107	RNA pseudouridylate synthase domain containing 2	protein-coding
mm_519.1	chr1	37494576	37494589	+	1	NA	intron (NM_001290801, intron 3 of 14)	ID4_|SINE|ID	-5977	NR_024017	77633	Mm.483177	NR_024017	ENSMUSG00000103948	4930594C11Rik	-	G1 to S phase transition pseudogene	pseudo
mm_84069.1	chr9	58201526	58201544	-	1	NA	5' UTR (NM_001161537, exon 1 of 3)	5' UTR (NM_001161537, exon 1 of 3)	180	NM_001161535	320563	Mm.186499	NM_177193	ENSMUSG00000051243	Islr2	B930052A04Rik|Linx|Mbu-3|mKIAA1465	immunoglobulin superfamily containing leucine-rich repeat 2	protein-coding
mm_63746.1	chr7	130943475	130943493	+	1	NA	intron (NM_019564, intron 1 of 8)	intron (NM_019564, intron 1 of 8)	7281	NM_019564	56213	Mm.30156	NM_019564	ENSMUSG00000006205	Htra1	AI429470|HTRA|L56|Prss11|RSPP11	HtrA serine peptidase 1	protein-coding
mm_125109.1	chr15	27924244	27924256	+	1	NA	intron (NM_001081302, intron 1 of 56)	intron (NM_001081302, intron 1 of 56)	101598	NM_001081302	223435	Mm.485422	NM_001081302	ENSMUSG00000022263	Trio	6720464I07Rik|AA408740|Solo	triple functional domain (PTPRF interacting)	protein-coding
mm_66919.1	chr7	60097601	60097627	-	1	NA	promoter-TSS (NM_001082961)	promoter-TSS (NM_001082961)	-6	NM_001082961	20646	Mm.274995	NM_013670	ENSMUSG00000102252	Snrpn	2410045I01Rik|HCERN3|Peg4|Pwcr1|SMN	small nuclear ribonucleoprotein N	protein-coding
mm_16271.1	chr2	173685633	173685634	+	1	NA	intron (NM_024436, intron 2 of 6)	intron (NM_024436, intron 2 of 6)	15515	NR_105758	102465173		NR_105758	ENSMUSG00000098588	Mir6340	Gm27909|mmu-mir-6340	microRNA 6340	ncRNA
mm_101888.1	chr11	48994183	48994186	-	1	NA	Intergenic	Intergenic	-1938	NM_011579	21822	Mm.15793	NM_011579	ENSMUSG00000078922	Tgtp1	Gtp2|Irgb6|Mg21|Tgtp	T cell specific GTPase 1	protein-coding
mm_32732.1	chr4	116560148	116560152	+	1	NA	intron (NM_029868, intron 1 of 11)	T-rich|Low_complexity|Low_complexity	2423	NM_029868	77110	Mm.41715	NM_029868	ENSMUSG00000034042	Gpbp1l1	5330440M15Rik|BC002292	GC-rich promoter binding protein 1-like 1	protein-coding
mm_38380.1	chr4	138725263	138725267	-	1	NA	promoter-TSS (NM_178671)	promoter-TSS (NM_178671)	0	NR_104373	212190	Mm.292226	NM_178671	ENSMUSG00000043621	Ubxn10	5730509E04Rik|A830047D02|Ubxd3	UBX domain protein 10	protein-coding
mm_114790.1	chr13	89540688	89540698	+	1	NA	promoter-TSS (NM_013500)	promoter-TSS (NM_013500)	57	NM_013500	12950	Mm.266790	NM_013500	ENSMUSG00000021613	Hapln1	BB099155|CLP|Crtl1|Crtl1l|LP|LP-1	hyaluronan and proteoglycan link protein 1	protein-coding
mm_120754.1	chr14	73362405	73362414	+	1	NA	3' UTR (NM_008410, exon 6 of 6)	3' UTR (NM_008410, exon 6 of 6)	22862	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_144612.1	chr18	32816855	32816865	+	1	NA	promoter-TSS (NR_033206)	promoter-TSS (NR_033206)	0	NR_033206	53603	Mm.143716	NM_021367	ENSMUSG00000024379	Tslp	-	thymic stromal lymphopoietin	protein-coding
mm_21584.1	chr2	164237304	164237323	-	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	1028	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_162255.1	chrX	168577439	168577439	-	1	NA	promoter-TSS (NM_001033330)	promoter-TSS (NM_001033330)	-206	NM_001033330	333605	Mm.426168	NM_001033330	ENSMUSG00000049176	Frmpd4	Gm196|PKAP1|Pdzd10|Pdzk10|Preso1|preso	FERM and PDZ domain containing 4	protein-coding
mm_60003.1	chr7	30712211	30712227	+	1	NA	promoter-TSS (NM_018731)	promoter-TSS (NM_018731)	10	NM_001290627	11944	Mm.12821	NM_018731	ENSMUSG00000005553	Atp4a	-	ATPase, H+/K+ exchanging, gastric, alpha polypeptide	protein-coding
mm_82525.1	chr9	20644727	20644789	-	1	NA	promoter-TSS (NM_001310746)	promoter-TSS (NM_001310746)	9	NM_001286529	30843	Mm.24608	NM_013911	ENSMUSG00000066892	Fbxl12	3110048D16Rik|Fbl12	F-box and leucine-rich repeat protein 12	protein-coding
mm_151806.1	chr19	5425368	5425388	-	1	NA	promoter-TSS (NM_024176)	promoter-TSS (NM_024176)	234	NM_001256515	107242	Mm.329658	NM_134149	ENSMUSG00000047423	AI837181	Bles03|N28173	expressed sequence AI837181	protein-coding
mm_32731.1	chr4	116558057	116558090	+	1	NA	intron (NM_029868, intron 1 of 11)	CpG	346	NM_029868	77110	Mm.41715	NM_029868	ENSMUSG00000034042	Gpbp1l1	5330440M15Rik|BC002292	GC-rich promoter binding protein 1-like 1	protein-coding
mm_101526.1	chr11	33147809	33147828	-	1	NA	promoter-TSS (NM_008005)	promoter-TSS (NM_008005)	-418	NR_102395	14172	Mm.339812	NM_008005	ENSMUSG00000057967	Fgf18	D130055P09Rik|FGF-18	fibroblast growth factor 18	protein-coding
mm_103785.1	chr11	82804424	82804428	-	1	NA	TTS (NM_010716)	TTS (NM_010716)	23317	NM_010716	16882	Mm.277136	NM_010716	ENSMUSG00000020697	Lig3	D11Wsu78e	ligase III, DNA, ATP-dependent	protein-coding
mm_7427.1	chr1	119837289	119837299	-	1	NA	promoter-TSS (NM_019933)	promoter-TSS (NM_019933)	-223	NM_019933	19258	Mm.458796	NM_019933	ENSMUSG00000026384	Ptpn4	PTPMEG|Ptn4|TEP|TEP/mPTPMEG|hPTP-MEG	protein tyrosine phosphatase, non-receptor type 4	protein-coding
mm_105509.1	chr11	106210425	106210465	-	1	NA	exon (NM_026009, exon 4 of 13)	exon (NM_026009, exon 4 of 13)	5922	NM_026009	67163	Mm.22109	NM_026009	ENSMUSG00000078622	Ccdc47	2610204L23Rik|C88307|asp4|calumin	coiled-coil domain containing 47	protein-coding
mm_71175.1	chr8	40675049	40675056	+	1	NA	promoter-TSS (NM_010086)	promoter-TSS (NM_010086)	-25	NM_010086	13526	Mm.67403	NM_010086	ENSMUSG00000046723	Adam24	Dtgn5	a disintegrin and metallopeptidase domain 24 (testase 1)	protein-coding
mm_149311.1	chr19	10759799	10759840	+	1	NA	intron (NR_027805, intron 1 of 3)	intron (NR_027805, intron 1 of 3)	18872	NR_027805	403202	Mm.34482	NM_207529	ENSMUSG00000067577	A430093F15Rik	Gm674	RIKEN cDNA A430093F15 gene	ncRNA
mm_136770.1	chr17	8992240	8992274	+	1	NA	exon (NM_025851, exon 2 of 10)	exon (NM_025851, exon 2 of 10)	3924	NM_001347544	66931	Mm.67591	NM_025851	ENSMUSG00000023873	1700010I14Rik	-	RIKEN cDNA 1700010I14 gene	protein-coding
mm_24019.1	chr3	87526406	87526432	+	1	NA	intron (NM_001286844, intron 1 of 4)	intron (NM_001286844, intron 1 of 4)	841	NM_012051	27049	Mm.219460	NM_012051	ENSMUSG00000003382	Etv3	AI414410|METS|Pe1	ets variant 3	protein-coding
mm_64925.1	chr7	16273261	16273331	-	1	NA	TTS (NM_001136471)	TTS (NM_001136471)	396	NM_001136270	66300	Mm.218698	NM_001136270	ENSMUSG00000091811	Inafm1	2610014I16Rik|Prr24	InaF motif containing 1	protein-coding
mm_162660.1	chr10	5149016	5149019	+	1	NA	intron (NM_001347732, intron 103 of 145)	intron (NM_001347732, intron 103 of 145)	45690	NM_001079686	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_75922.1	chr8	71486333	71486339	-	1	NA	promoter-TSS (NM_001164679)	promoter-TSS (NM_001164679)	-269	NM_001164679	382014	Mm.260360	NM_001164679	ENSMUSG00000034863	Ano8	BC053460|Tmem16h	anoctamin 8	protein-coding
mm_1494.1	chr1	71888077	71888121	+	1	NA	promoter-TSS (NR_027659)	promoter-TSS (NR_027659)	-13	NR_027658	667931	Mm.214128	NR_027658	ENSMUSG00000099707	Gm8883	EG667931|Gm554	predicted gene 8883	ncRNA
mm_113077.1	chr13	23807096	23807102	+	1	NA	promoter-TSS (NM_144836)	promoter-TSS (NM_144836)	72	NM_144836	218103	Mm.24030	NM_144836	ENSMUSG00000036110	Slc17a2	C730032N17Rik|NPT3	solute carrier family 17 (sodium phosphate), member 2	protein-coding
mm_8922.1	chr1	163403605	163403619	-	1	NA	promoter-TSS (NM_178883)	promoter-TSS (NM_178883)	57	NM_001313738	98376	Mm.32901	NM_178883	ENSMUSG00000040124	Gorab	NTKL-BP1|SCYL1-BP1|Scyl1bp1	golgin, RAB6-interacting	protein-coding
mm_166958.1	chr7	44477939	44477945	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-6575	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_115057.1	chr13	100669699	100669754	+	1	NA	5' UTR (NM_001168386, exon 1 of 10)	5' UTR (NM_001168386, exon 1 of 10)	245	NM_001168386	76041	Mm.23977	NM_183115	ENSMUSG00000048924	Ccdc125	5830436D01Rik|AL023012	coiled-coil domain containing 125	protein-coding
mm_157790.1	chrX	73854392	73854451	-	1	NA	3' UTR (NM_008478, exon 29 of 29)	3' UTR (NM_008478, exon 29 of 29)	26413	NM_008478	16728	Mm.260568	NM_008478	ENSMUSG00000031391	L1cam	CD171|L1|N-CAM-L1|NCAM-L1	L1 cell adhesion molecule	protein-coding
mm_15038.1	chr2	152787798	152787827	+	1	NA	intron (NM_001289717, intron 2 of 2)	intron (NM_001289717, intron 2 of 2)	33639	NM_053091	84682	Mm.196668	NM_053091	ENSMUSG00000009876	Cox4i2	Cox4b|CoxIV-2	cytochrome c oxidase subunit IV isoform 2	protein-coding
mm_19568.1	chr2	101629017	101629025	-	1	NA	promoter-TSS (NM_026592)	promoter-TSS (NM_026592)	-35	NM_026592	68170	Mm.31263	NM_026592	ENSMUSG00000027165	B230118H07Rik	NWC	RIKEN cDNA B230118H07 gene	protein-coding
mm_65091.1	chr7	19265990	19266021	-	1	NA	intron (NR_104069, intron 1 of 10)	MIR3|SINE|MIR	5849	NM_001282021	22323	Mm.9684	NM_009499	ENSMUSG00000030403	Vasp	-	vasodilator-stimulated phosphoprotein	protein-coding
mm_148565.1	chr19	4756558	4756623	+	1	NA	promoter-TSS (NM_025717)	promoter-TSS (NM_025717)	65	NM_025717	66704	Mm.396734	NM_025717	ENSMUSG00000033760	Rbm4b	4921506I22Rik|AI504630|AI506404|Lark2|Neosin	RNA binding motif protein 4B	protein-coding
mm_98143.1	chr11	87581147	87581153	+	1	NA	promoter-TSS (NM_011129)	promoter-TSS (NM_011129)	89	NM_001284392	18952	Mm.2214	NM_011129	ENSMUSG00000020486	Sept4	ARTS|Bh5|OTTMUSG00000001265|Pnutl2	septin 4	protein-coding
mm_57698.1	chr6	128525171	128525209	-	1	NA	exon (NM_007376, exon 2 of 36)	exon (NM_007376, exon 2 of 36)	1530	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_24015.1	chr3	87435821	87435829	+	1	NA	promoter-TSS (NM_183222)	promoter-TSS (NM_183222)	43	NM_001113238	329693	Mm.331122	NM_183222	ENSMUSG00000048031	Fcrl5	Fcrh3|mBXMH2	Fc receptor-like 5	protein-coding
mm_26423.1	chr3	142618202	142618223	+	1	NA	3' UTR (NM_010259, exon 11 of 11)	3' UTR (NM_010259, exon 11 of 11)	-2451	NM_010260	14469	Mm.24038	NM_010260	ENSMUSG00000028270	Gbp2	-	guanylate binding protein 2	protein-coding
mm_162443.1	chr1	116182044	116182046	-	1	NA	intron (NM_001077425, intron 8 of 23)	Lx8|LINE|L1	496908	NM_001077425	636808	Mm.101576	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding
mm_115795.1	chr13	19343259	19343266	-	1	NA	Intergenic	Intergenic	52551	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_170796.1	chr2	175372476	175372482	+	1	NA	promoter-TSS (NM_001177405).2	promoter-TSS (NM_001177405).2	17	NM_001177404	100303732	Mm.484983	NM_001177404	ENSMUSG00000095199	Zfp967	Gm14431|OTTMUSG00000016608	zinc finger protein 967	protein-coding
mm_104698.1	chr11	97986385	97986472	-	1	NA	promoter-TSS (NM_028199)	promoter-TSS (NM_028199)	18	NM_028199	72324	Mm.39617	NM_028199	ENSMUSG00000017417	Plxdc1	2410003I07Rik|AI848450|Tem7	plexin domain containing 1	protein-coding
mm_125189.1	chr15	32481295	32481316	+	1	NA	intron (NM_009154, intron 5 of 22)	intron (NM_009154, intron 5 of 22)	236492	NM_009154	20356	Mm.260374	NM_009154	ENSMUSG00000022231	Sema5a	5930434A13|9130201M22Rik|AI464145|Semaf|semF	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A	protein-coding
mm_57675.1	chr6	128494768	128494778	-	1	NA	exon (NM_007376, exon 21 of 36)	exon (NM_007376, exon 21 of 36)	31947	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_16008.1	chr2	167375356	167375363	+	1	NA	Intergenic	Intergenic	-26181	NM_019835	56336	Mm.200886	NM_019835	ENSMUSG00000017929	B4galt5	9430078I07Rik|AW049941|AW539721	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 5	protein-coding
mm_155436.1	chrX	73494656	73494666	+	1	NA	exon (NM_007542, exon 8 of 8)	exon (NM_007542, exon 8 of 8)	-8425	NM_001310537	320707	Mm.210095	NM_177236	ENSMUSG00000031376	Atp2b3	6430519O13Rik|Pmca3	ATPase, Ca++ transporting, plasma membrane 3	protein-coding
mm_41563.1	chr5	93133551	93133570	+	1	NA	intron (NM_001347377, intron 1 of 10)	intron (NM_001347377, intron 1 of 10)	40144	NM_001347377	52398	Mm.394184	NM_001009818	ENSMUSG00000058013	Sept11	6230410I01Rik|AW548875|D5Ertd606e	septin 11	protein-coding
mm_55928.1	chr6	84587938	84587986	-	1	NA	exon (NM_175475, exon 2 of 7)	exon (NM_175475, exon 2 of 7)	5848	NM_175475	232174	Mm.255246	NM_175475	ENSMUSG00000063415	Cyp26b1	CP26|P450RAI-2	cytochrome P450, family 26, subfamily b, polypeptide 1	protein-coding
mm_132739.1	chr16	43889937	43889947	+	1	NA	promoter-TSS (NM_029128)	promoter-TSS (NM_029128)	40	NM_027801	212153	Mm.209835	NM_027801	ENSMUSG00000022701	Ccdc191	2610015P09Rik|8430422M09Rik|AU040712	coiled-coil domain containing 191	protein-coding
mm_11433.1	chr2	31974428	31974448	+	1	NA	promoter-TSS (NM_172268)	promoter-TSS (NM_172268)	-12	NM_172268	227720	Mm.289686	NM_172268	ENSMUSG00000001855	Nup214	BC039282|CAN|D2H9S46E	nucleoporin 214	protein-coding
mm_107831.1	chr12	69241842	69241901	+	1	NA	promoter-TSS (NM_178253)	promoter-TSS (NM_178253)	39	NM_178253	271005	Mm.180969	NM_178253	ENSMUSG00000051890	Klhdc1	-	kelch domain containing 1	protein-coding
mm_68886.1	chr7	126447995	126448004	-	1	NA	exon (NM_007504, exon 17 of 23)	exon (NM_007504, exon 17 of 23)	15074	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_165943.1	chr4	81452334	81452341	-	1	NA	Intergenic	L2a|LINE|L2	-9522	NM_001305284	17475	Mm.153039	NM_010820	ENSMUSG00000028402	Mpdz	AI225843|B930003D11Rik|MUPP1	multiple PDZ domain protein	protein-coding
mm_21040.1	chr2	152511777	152511791	-	1	NA	promoter-TSS (NM_001039120)	promoter-TSS (NM_001039120)	-48	NM_001039120	654457	Mm.389363	NM_001039120	ENSMUSG00000074680	Defb26	EG654457	defensin beta 26	protein-coding
mm_167305.1	chr8	60506178	60506184	+	1	NA	promoter-TSS (NM_011834)	promoter-TSS (NM_011834)	57	NM_011834	23923	Mm.35020	NM_011834	ENSMUSG00000057228	Aadat	AI875679|Aadt|KATII|Kat2|Kyat2|mKat-2	aminoadipate aminotransferase	protein-coding
mm_18870.1	chr2	75978165	75978206	-	1	NA	promoter-TSS (NM_001081228)	promoter-TSS (NM_001081228)	-6	NM_001081228	620631	Mm.389286	NM_001081228	ENSMUSG00000075272	Ttc30a2	OTTMUSG00000015167	tetratricopeptide repeat domain 30A2	protein-coding
mm_30038.1	chr3	135691489	135691511	-	1	NA	promoter-TSS (NM_008689)	promoter-TSS (NM_008689)	47	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_7505.1	chr1	121567907	121567952	-	1	NA	promoter-TSS (NM_025860)	promoter-TSS (NM_025860)	51	NM_025860	66942	Mm.44219	NM_025860	ENSMUSG00000001674	Ddx18	2310005B10Rik	DEAD (Asp-Glu-Ala-Asp) box polypeptide 18	protein-coding
mm_81397.1	chr9	108991983	108992002	+	1	NA	promoter-TSS (NM_173019)	promoter-TSS (NM_173019)	90	NM_173019	270198	Mm.132391	NM_173019	ENSMUSG00000025648	Pfkfb4	C230090D14	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4	protein-coding
mm_86410.1	chr10	3366171	3366207	+	1	NA	promoter-TSS (NM_133485)	promoter-TSS (NM_133485)	39	NM_133485	76142	Mm.308126	NM_133485	ENSMUSG00000040653	Ppp1r14c	6330514J04Rik|KEPI	protein phosphatase 1, regulatory (inhibitor) subunit 14c	protein-coding
mm_96208.1	chr11	62281425	62281434	+	1	NA	promoter-TSS (NM_028360)	promoter-TSS (NM_028360)	-34	NM_027198	69747	Mm.141150	NM_027198	ENSMUSG00000014243	Zswim7	2410012H22Rik	zinc finger SWIM-type containing 7	protein-coding
mm_82809.1	chr9	29963146	29963154	-	1	NA	promoter-TSS (NM_172290)	promoter-TSS (NM_172290)	-21	NM_172290	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding
mm_49101.1	chr6	7871560	7871563	+	1	NA	3' UTR (NM_052993, exon 4 of 4)	3' UTR (NM_052993, exon 4 of 4)	26337	NM_052993	94192	Mm.102752	NM_052993	ENSMUSG00000042460	C1galt1	2210410E06Rik|AV284120|T-synthase	core 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase, 1	protein-coding
mm_58269.1	chr6	145341755	145341779	-	1	NA	Intergenic	Intergenic	-45858	NR_003625	381827	Mm.179075	NM_001001987		1700073E17Rik	-	ribosomal protein L7 pseudogene	pseudo
mm_85752.1	chr9	108648616	108648624	-	1	NA	intron (NM_011790, intron 1 of 15)	MER3|DNA|hAT-Charlie	760	NM_011790	23807	Mm.290447	NM_011790	ENSMUSG00000064145	Arih2	AI843547|ARI2|TRIAD1|UIP48	ariadne RBR E3 ubiquitin protein ligase 2	protein-coding
mm_80249.1	chr9	72749097	72749114	+	1	NA	3' UTR (NM_010890, exon 29 of 29)	3' UTR (NM_010890, exon 29 of 29)	-58169	NM_175485	235472	Mm.31696	NM_175485	ENSMUSG00000036030	Prtg	A230098A12Rik|Igdcc5	protogenin	protein-coding
mm_109521.1	chr12	111454665	111454675	+	1	NA	3' UTR (NM_009396, exon 12 of 12)	3' UTR (NM_009396, exon 12 of 12)	12009	NM_009396	21928	Mm.255332	NM_009396	ENSMUSG00000021281	Tnfaip2	B94|Exoc3l3|M-sec|Tnfip2|tnfb94	tumor necrosis factor, alpha-induced protein 2	protein-coding
mm_81940.1	chr9	120401918	120401918	+	1	NA	intron (NM_144557, intron 3 of 16)	intron (NM_144557, intron 3 of 16)	-90688	NM_026892	68969	Mm.28753	NM_026892	ENSMUSG00000006941	Eif1b	1500010M16Rik|3110001N14Rik|Gc20	eukaryotic translation initiation factor 1B	protein-coding
mm_48938.1	chr6	4538692	4538777	+	1	NA	exon (NM_007743, exon 50 of 52)	exon (NM_007743, exon 50 of 52)	33116	NM_007743	12843	Mm.277792	NM_007743	ENSMUSG00000029661	Col1a2	AA960264|AI325291|Col1a-2|Cola-2|Cola2|oim	collagen, type I, alpha 2	protein-coding
mm_35960.1	chr4	53137049	53137050	-	1	NA	intron (NM_013454, intron 2 of 49)	L1MEd|LINE|L1	22846	NM_013454	11303	Mm.277376	NM_013454	ENSMUSG00000015243	Abca1	ABC-1|Abc1	ATP-binding cassette, sub-family A (ABC1), member 1	protein-coding
mm_27835.1	chr3	79140795	79140831	-	1	NA	intron (NM_001099624, intron 1 of 23)	tRNA-Ala-GCY_|tRNA|tRNA	4074	NM_001310536	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_114398.1	chr13	63293160	63293166	+	1	NA	intron (NR_045794, intron 1 of 2)	PB1D7|SINE|Alu	3984	NR_045794	100504114	Mm.437070	NR_045794	ENSMUSG00000097242	Gm16907	-	predicted gene, 16907	ncRNA
mm_166289.1	chr5	100650490	100650512	+	1	NA	Intergenic	Intergenic	23755	NM_027978	71883	Mm.260661	NM_027978	ENSMUSG00000029319	Coq2	2310002F18Rik|PHB:PPT	coenzyme Q2 4-hydroxybenzoate polyprenyltransferase	protein-coding
mm_82608.1	chr9	21592734	21592795	-	1	NA	promoter-TSS (NM_138303)	promoter-TSS (NM_138303)	42	NM_178619	69773	Mm.39704	NM_178619	ENSMUSG00000048429	Timm29	1810026J23Rik	translocase of inner mitochondrial membrane 29	protein-coding
mm_61718.1	chr7	81762948	81762997	+	1	NA	promoter-TSS (NM_025997)	promoter-TSS (NM_025997)	19	NM_025997	67148	Mm.241472	NM_025997	ENSMUSG00000038646	Fam103a1	2410047I02Rik|2610204K14Rik|RAM	family with sequence similarity 103, member A1	protein-coding
mm_44969.1	chr5	36796704	36796706	-	1	NA	promoter-TSS (NM_026242)	promoter-TSS (NM_026242)	49	NM_026242	67568	Mm.332336	NM_026242	ENSMUSG00000055302	Mrfap1	9130413I22Rik|AL022827|Pam14	Morf4 family associated protein 1	protein-coding
mm_8742.1	chr1	160247674	160247680	-	1	NA	intron (NM_001038621, intron 3 of 8)	intron (NM_001038621, intron 3 of 8)	-34785	NM_009786	12301	Mm.10702	NM_009786	ENSMUSG00000014226	Cacybp	SIP	calcyclin binding protein	protein-coding
mm_152914.1	chr19	27421382	27421427	-	1	NA	exon (NM_177474, exon 8 of 18)	exon (NM_177474, exon 8 of 18)	8504	NM_177474	52874	Mm.261027	NM_177474	ENSMUSG00000041360	Pum3	1110069H02Rik|AA675048|D19Bwg1357e|Kiaa0020	pumilio RNA-binding family member 3	protein-coding
mm_143268.1	chr17	65642160	65642182	-	1	NA	promoter-TSS (NM_001146002)	promoter-TSS (NM_001146002)	33	NM_001146002	213272	Mm.255732	NM_153519	ENSMUSG00000050612	Txndc2	AU021712|Sptrx-1|Sptrx1|Trx4	thioredoxin domain containing 2 (spermatozoa)	protein-coding
mm_15532.1	chr2	158382987	158382999	+	1	NA	3' UTR (NM_175692, exon 5 of 5)	3' UTR (NM_175692, exon 5 of 5)	7355	NM_175692	319317	Mm.294494	NM_175692	ENSMUSG00000044349	Snhg11	A930034L06Rik|AI854265|AL022637|AW319638|E130013N09Rik	small nucleolar RNA host gene 11	protein-coding
mm_129841.1	chr15	83154581	83154590	-	1	NA	exon (NM_029787, exon 9 of 9)	exon (NM_029787, exon 9 of 9)	4940	NR_004432	104307	Mm.471434	NR_004432	ENSMUSG00000065176	Rnu12	-	RNA U12, small nuclear	snRNA
mm_117874.1	chr13	98926297	98926308	-	1	NA	promoter-TSS (NM_178716)	promoter-TSS (NM_178716)	82	NM_178716	238799	Mm.173286	NM_178716	ENSMUSG00000009470	Tnpo1	AU021749|D13Ertd688e|IPO2|Kpnb2|MIP|MIP1|TRN	transportin 1	protein-coding
mm_69068.1	chr7	126949500	126949521	-	1	NA	promoter-TSS (NM_001039645)	promoter-TSS (NM_001039645)	71	NM_001347657	233879	Mm.444143	NM_001039645	ENSMUSG00000046378	Asphd1	A830007L07Rik|Gm168	aspartate beta-hydroxylase domain containing 1	protein-coding
mm_121704.1	chr14	15438820	15438833	-	1	NA	5' UTR (NM_146052, exon 1 of 2)	5' UTR (NM_146052, exon 1 of 2)	161	NM_146052	218763	Mm.138039	NM_146052	ENSMUSG00000045201	Lrrc3b	BC019794|LRP15	leucine rich repeat containing 3B	protein-coding
mm_167024.1	chr7	67167279	67167282	+	1	NA	Intergenic	Intergenic	55178	NR_131044	76628	Mm.384589	NR_131043	ENSMUSG00000097527	1700112J16Rik	-	RIKEN cDNA 1700112J16 gene	ncRNA
mm_7578.1	chr1	124846116	124846128	-	1	NA	Intergenic	Intergenic	589605	NM_023735	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding
mm_53446.1	chr6	134414460	134414485	+	1	NA	intron (NM_025778, intron 2 of 6)	intron (NM_025778, intron 2 of 6)	18143	NM_025778	66813	Mm.474472	NM_025778	ENSMUSG00000030200	Bcl2l14	4930452K23Rik|4933405K19Rik|9030625M01Rik|AI429211|Bclg	BCL2-like 14 (apoptosis facilitator)	protein-coding
mm_28775.1	chr3	95929599	95929624	-	1	NA	exon (NM_001253757, exon 1 of 7)	exon (NM_001253757, exon 1 of 7)	354	NM_023210	66471	Mm.218657	NM_023210	ENSMUSG00000015749	Anp32e	2810018A15Rik|AI047746|AI326868|CPD1|LANP-L|LANPL|mLANP-L	acidic (leucine-rich) nuclear phosphoprotein 32 family, member E	protein-coding
mm_150193.1	chr19	32665917	32665935	+	1	NA	3' UTR (NM_011864, exon 13 of 13)	3' UTR (NM_011864, exon 13 of 13)	45921	NM_011864	23972	Mm.203916	NM_011864	ENSMUSG00000024899	Papss2	1810018P12Rik|AI159688|AtpsU2|Atpsk2|Sk2|bm	3'-phosphoadenosine 5'-phosphosulfate synthase 2	protein-coding
mm_87162.1	chr10	36974559	36974579	+	1	NA	promoter-TSS (NM_008229)	promoter-TSS (NM_008229)	25	NM_008229	15182	Mm.19806	NM_008229	ENSMUSG00000019777	Hdac2	D10Wsu179e|YAF1|Yy1bp|mRPD3	histone deacetylase 2	protein-coding
mm_53206.1	chr6	125690397	125690409	+	1	NA	promoter-TSS (NM_153589)	promoter-TSS (NM_153589)	-16	NM_153589	243634	Mm.333398	NM_153589	ENSMUSG00000038115	Ano2	BC033409|Tmem16b	anoctamin 2	protein-coding
mm_1260.1	chr1	63176819	63176919	+	1	NA	promoter-TSS (NM_001160039)	promoter-TSS (NM_001160039)	38	NM_018796	55949	Mm.2718	NM_018796	ENSMUSG00000025967	Eef1b2	2810017J07Rik|Eef1b	eukaryotic translation elongation factor 1 beta 2	protein-coding
mm_70818.1	chr8	23123278	23123281	+	1	NA	intron (NR_102385, intron 37 of 45)	intron (NR_102385, intron 37 of 45)	-15751	NM_001310436	11733	Mm.334444	NM_031158	ENSMUSG00000031543	Ank1	Ank-1|nb|pale	ankyrin 1, erythroid	protein-coding
mm_67576.1	chr7	82174699	82174709	-	1	NA	Intergenic	Intergenic	-85204	NM_001277955	20408	Mm.736	NM_017400	ENSMUSG00000030638	Sh3gl3	EEN-B2|SH3P13|Sh3d2c|Sh3d2c2	SH3-domain GRB2-like 3	protein-coding
mm_20936.1	chr2	150875060	150875090	-	1	NA	intron (NM_024465, intron 1 of 12)	B1_Mus1|SINE|Alu	29656	NM_024465	76192	Mm.112632	NM_024465	ENSMUSG00000032046	Abhd12	1500011G07Rik|6330583M11Rik|AI431047|AW547313	abhydrolase domain containing 12	protein-coding
mm_84384.1	chr9	65422896	65422910	-	1	NA	promoter-TSS (NM_178933)	promoter-TSS (NM_178933)	-130	NM_178933	330962	Mm.335247	NM_178933	ENSMUSG00000053862	Slc51b	Ostb	solute carrier family 51, beta subunit	protein-coding
mm_66324.1	chr7	42505696	42505736	-	1	NA	promoter-TSS (NM_001309388)	promoter-TSS (NM_001309388)	37	NM_001309389	434178	Mm.333810	NM_001309388	ENSMUSG00000092416	Zfp141	-	zinc finger protein 141	protein-coding
mm_41744.1	chr5	102768896	102768927	+	1	NA	5' UTR (NM_001286468, exon 1 of 8)	5' UTR (NM_001286468, exon 1 of 8)	101	NM_001286468	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding
mm_138936.1	chr17	43909096	43909108	+	1	NA	intron (NM_001286653, intron 2 of 4)	intron (NM_001286653, intron 2 of 4)	-43897	NM_001286654	53901	Mm.251242	NM_030598	ENSMUSG00000039601	Rcan2	Csp2|Dscr1l1|MCIP2|ZAKI-4	regulator of calcineurin 2	protein-coding
mm_164047.1	chr14	99147868	99147868	+	1	NA	intron (NM_029320, intron 9 of 17)	ORR1E|LTR|ERVL-MaLR	-48098	NM_028315	72662	Mm.163339	NM_028315	ENSMUSG00000033166	Dis3	2810028N01Rik	DIS3 homolog, exosome endoribonuclease and 3'-5' exoribonuclease	protein-coding
mm_48724.1	chr5	147400280	147400288	-	1	NA	5' UTR (NM_010229, exon 1 of 24)	5' UTR (NM_010229, exon 1 of 24)	205	NM_010229	14255	Mm.194	NM_010229	ENSMUSG00000042817	Flt3	B230315G04|CD135|Flk-2|Flk2|Flt-3|Ly72|wmfl	FMS-like tyrosine kinase 3	protein-coding
mm_6156.1	chr1	65018426	65018432	-	1	NA	intron (NM_001310617, intron 5 of 8)	RLTR20A|LTR|ERVK	14330	NM_027582	70861	Mm.18725	NM_027582	ENSMUSG00000025955	Akr1cl	4921521F21Rik|AI451536|AI503553	aldo-keto reductase family 1, member C-like	protein-coding
mm_45090.1	chr5	44101669	44101745	-	1	NA	promoter-TSS (NM_008935)	promoter-TSS (NM_008935)	29	NM_008935	19126	Mm.6250	NM_008935	ENSMUSG00000029086	Prom1	4932416E19Rik|AC133|CD133|Prom|Prom-1|Proml1	prominin 1	protein-coding
mm_140207.1	chr17	83775557	83775603	+	1	NA	intron (NM_001171053, intron 8 of 13)	intron (NM_001171053, intron 8 of 13)	69417	NM_001171052	116871	Mm.277668	NM_054082	ENSMUSG00000055817	Mta3	1110002J22Rik|mKIAA1266	metastasis associated 3	protein-coding
mm_164891.1	chr18	61884674	61884676	-	1	NA	intron (NM_198649, intron 1 of 22)	intron (NM_198649, intron 1 of 22)	27149	NM_198649	319713	Mm.329478	NM_198649	ENSMUSG00000032735	Ablim3	AW990719|D930036B08Rik	actin binding LIM protein family, member 3	protein-coding
mm_86765.1	chr10	19933925	19933953	+	1	NA	promoter-TSS (NM_008580)	promoter-TSS (NM_008580)	-587	NM_008580	26408	Mm.6595	NM_008580	ENSMUSG00000071369	Map3k5	7420452D20Rik|ASK|ASK1|MAPKKK5|Mekk5	mitogen-activated protein kinase kinase kinase 5	protein-coding
mm_31182.1	chr4	43518411	43518441	+	1	NA	exon (NM_009416, exon 7 of 9)	exon (NM_009416, exon 7 of 9)	5128	NM_009416	22004	Mm.646	NM_009416	ENSMUSG00000028464	Tpm2	Tpm-2|Trop-2	tropomyosin 2, beta	protein-coding
mm_122928.1	chr14	54961425	54961446	-	1	NA	intron (NM_001164171, intron 10 of 38)	intron (NM_001164171, intron 10 of 38)	5172	NM_001164171	17888	Mm.290003	NM_010856	ENSMUSG00000040752	Myh6	A830009F23Rik|AA517445|Myhc-a|Myhca|alpha-MHC	myosin, heavy polypeptide 6, cardiac muscle, alpha	protein-coding
mm_68229.1	chr7	104446048	104446060	-	1	NA	intron (NM_009099, intron 1 of 7)	intron (NM_009099, intron 1 of 7)	19139	NM_009099	20128	Mm.295578	NM_009099	ENSMUSG00000030921	Trim30a	Rpt-1|Rpt1|Trim30	tripartite motif-containing 30A	protein-coding
mm_72137.1	chr8	71922886	71922901	+	1	NA	promoter-TSS (NM_133358)	promoter-TSS (NM_133358)	68	NM_133358	170938	Mm.480419	NM_133358	ENSMUSG00000066880	Zfp617	Zfps11-6	zinc finger protein 617	protein-coding
mm_82356.1	chr9	14381158	14381164	-	1	NA	promoter-TSS (NM_028013)	promoter-TSS (NM_028013)	81	NM_028013	71946	Mm.41423	NM_028013	ENSMUSG00000037419	Endod1	2210414F18Rik|2310067E08Rik|C85344	endonuclease domain containing 1	protein-coding
mm_72796.1	chr8	87101717	87101723	+	1	NA	Intergenic	Intergenic	98130	NR_040697	100038706	Mm.334690	NR_040697	ENSMUSG00000099207	Gm10637	ENSMUSG00000074176	predicted gene 10637	ncRNA
mm_135714.1	chr16	55798938	55798973	-	1	NA	Intergenic	Intergenic	23183	NM_001159394	80859	Mm.247272	NM_030612	ENSMUSG00000035356	Nfkbiz	AA408868|INAP|Mail	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, zeta	protein-coding
mm_67937.1	chr7	100121047	100121094	-	1	NA	intron (NM_133692, intron 1 of 11)	intron (NM_133692, intron 1 of 11)	430	NM_133692	67967	Mm.37562	NM_133692	ENSMUSG00000030726	Pold3	2410142G14Rik|C85233|P66|P68	polymerase (DNA-directed), delta 3, accessory subunit	protein-coding
mm_132919.1	chr16	49770613	49770623	+	1	NA	Intergenic	Intergenic	71324	NM_028680	73916	Mm.241276	NM_028680	ENSMUSG00000032965	Ift57	4833420A15Rik|Esrrbl1|Hippi|MHS4R2	intraflagellar transport 57	protein-coding
mm_64795.1	chr7	6685300	6685323	-	1	NA	intron (NM_011769, intron 5 of 7)	intron (NM_011769, intron 5 of 7)	11121	NM_011769	22776	Mm.89976	NM_011769	ENSMUSG00000002266	Zim1	-	zinc finger, imprinted 1	protein-coding
mm_752.1	chr1	43730667	43730718	+	1	NA	promoter-TSS (NM_024283)	promoter-TSS (NM_024283)	90	NM_024283	78896	Mm.50109	NM_024283	ENSMUSG00000026051	1500015O10Rik	Ecrg4	RIKEN cDNA 1500015O10 gene	protein-coding
mm_88508.1	chr10	77893436	77893442	+	1	NA	promoter-TSS (NR_015547)	promoter-TSS (NR_015547)	19	NR_015547	75188	Mm.348012	NM_029200	ENSMUSG00000096573	1700009J07Rik	4930535B06Rik	RIKEN cDNA 1700009J07 gene	ncRNA
mm_134040.1	chr16	5132459	5132483	-	1	NA	promoter-TSS (NM_008909)	promoter-TSS (NM_008909)	10	NM_008909	19041	Mm.266875	NM_008909	ENSMUSG00000039457	Ppl	AW553870	periplakin	protein-coding
mm_172031.1	chr6	124636969	124636984	-	1	NA	promoter-TSS (NM_173864)	promoter-TSS (NM_173864)	-891	NM_173864	317677	Mm.483270	NM_173864	ENSMUSG00000079343	C1s2	C1sb|EG317677|Gm5077	complement component 1, s subcomponent 2	protein-coding
mm_3208.1	chr1	135826892	135826917	+	1	NA	intron (NM_133664, intron 2 of 9)	intron (NM_133664, intron 2 of 9)	8306	NM_133664	16763	Mm.36726	NM_133664	ENSMUSG00000041782	Lad1	-	ladinin	protein-coding
mm_45776.1	chr5	87092536	87092542	-	1	NA	promoter-TSS (NM_001029867)	promoter-TSS (NM_001029867)	16	NM_001029867	231396	Mm.439851	NM_001029867	ENSMUSG00000070704	Ugt2b36	-	UDP glucuronosyltransferase 2 family, polypeptide B36	protein-coding
mm_3245.1	chr1	136052805	136052826	+	1	NA	promoter-TSS (NM_014193)	promoter-TSS (NM_014193)	-86	NM_001081023	12292	Mm.4418	NM_014193	ENSMUSG00000026407	Cacna1s	AW493108|Cav1.1|Cchl1a3|fmd|mdg|sj	calcium channel, voltage-dependent, L type, alpha 1S subunit	protein-coding
mm_98815.1	chr11	97309646	97309659	+	1	NA	Intergenic	Intergenic	-6064	NM_025927	67036	Mm.5381	NM_025927	ENSMUSG00000018882	Mrpl45	2600005P05Rik|AU043542|R75241	mitochondrial ribosomal protein L45	protein-coding
mm_133493.1	chr16	90385903	90385944	+	1	NA	promoter-TSS (NM_015755)	promoter-TSS (NM_015755)	-474	NM_015755	26559	Mm.125874	NM_015755	ENSMUSG00000053414	Hunk	Bstk1|Mak-v	hormonally upregulated Neu-associated kinase	protein-coding
mm_7305.1	chr1	97977285	97977298	-	1	NA	intron (NM_013626, intron 1 of 25)	intron (NM_013626, intron 1 of 25)	70502	NR_037993	78603	Mm.442597	NR_037993	ENSMUSG00000089706	B230216N24Rik	-	RIKEN cDNA B230216N24 gene	ncRNA
mm_110806.1	chr12	72212528	72212542	-	1	NA	exon (NM_001286448, exon 7 of 7)	exon (NM_001286448, exon 7 of 7)	23211	NR_104446	104001	Mm.221275	NM_153457	ENSMUSG00000021087	Rtn1	Nsp	reticulon 1	protein-coding
mm_159855.1	chr5	137871722	137871722	-	1	NA	promoter-TSS (NM_001024932)	promoter-TSS (NM_001024932)	36	NM_001024932	545812	Mm.332769	NM_001024932	ENSMUSG00000066682	Pilrb2	EG545812	paired immunoglobin-like type 2 receptor beta 2	protein-coding
mm_164608.1	chr17	30901844	30901846	+	1	NA	promoter-TSS (NM_021332)	promoter-TSS (NM_021332)	-22	NM_021332	14652	Mm.390969	NM_021332	ENSMUSG00000024027	Glp1r	GLP-1R|GLP1Rc	glucagon-like peptide 1 receptor	protein-coding
mm_99497.1	chr11	102885141	102885153	+	1	NA	promoter-TSS (NM_025766)	promoter-TSS (NM_025766)	-22	NM_025766	66784	Mm.483216	NM_025766	ENSMUSG00000075510	Fam187a	4933439F11Rik	family with sequence similarity 187, member A	protein-coding
mm_109343.1	chr12	109599281	109599284	+	1	NA	Intergenic	Intergenic	-3879	NM_184109	353326	Mm.23062	NM_184109	ENSMUSG00000085925	Rtl1	6430411K18Rik|Mar|Mart1|Mor1|Peg11	retrotransposon-like 1	protein-coding
mm_8133.1	chr1	136234114	136234134	-	1	NA	5' UTR (NM_028872, exon 1 of 10)	5' UTR (NM_028872, exon 1 of 10)	156	NM_028872	67313	Mm.36763	NM_028872	ENSMUSG00000041605	5730559C18Rik	1700034M08Rik|4933426C09Rik|AI586180|D1Mgi54	RIKEN cDNA 5730559C18 gene	protein-coding
mm_129529.1	chr15	79285421	79285435	-	1	NA	promoter-TSS (NM_177580)	promoter-TSS (NM_177580)	81	NM_177580	207495	Mm.309647	NM_177580	ENSMUSG00000018126	Baiap2l2	BC048937	BAI1-associated protein 2-like 2	protein-coding
mm_34324.1	chr4	141859349	141859376	+	1	NA	3' UTR (NM_025994, exon 4 of 4)	3' UTR (NM_025994, exon 4 of 4)	-13003	NM_001033875	76701	Mm.489680	NM_001033875	ENSMUSG00000062478	Ctrc	1810044E12Rik	chymotrypsin C (caldecrin)	protein-coding
mm_42623.1	chr5	118169713	118169743	+	1	NA	promoter-TSS (NM_007545)	promoter-TSS (NM_007545)	-36	NM_007545	12123	Mm.384468	NM_007545	ENSMUSG00000046607	Hrk	AI838259|Bid3|DP5|harakiri	harakiri, BCL2 interacting protein (contains only BH3 domain)	protein-coding
mm_105908.1	chr11	114983209	114983220	-	1	NA	3' UTR (NM_145437, exon 4 of 4)	3' UTR (NM_145437, exon 4 of 4)	6672	NM_145437	217305	Mm.275986	NM_145437	ENSMUSG00000034641	Cd300ld	4732429D16Rik|CLM5|Cd300ld1|LMIR4|MAIR-IV|clm-5	CD300 molecule like family member d	protein-coding
mm_92052.1	chr10	62503955	62503965	-	1	NA	intron (NM_011157, intron 1 of 2)	intron (NM_011157, intron 1 of 2)	3795	NM_011157	19073	Mm.338790	NM_011157	ENSMUSG00000020077	Srgn	Prg|Prg1|Sgc	serglycin	protein-coding
mm_7797.1	chr1	131525244	131525259	-	1	NA	5' UTR (NM_001081011, exon 2 of 23)	5' UTR (NM_001081011, exon 2 of 23)	2110	NM_001081011	14270	Mm.276259	NM_019520	ENSMUSG00000026425	Srgap2	9930124L22Rik|AI448945|FBP2|Fnbp2|srGAP3	SLIT-ROBO Rho GTPase activating protein 2	protein-coding
mm_1692.1	chr1	75142434	75142483	+	1	NA	promoter-TSS (NM_026977)	promoter-TSS (NM_026977)	-90	NM_026977	69171	Mm.28193	NM_026977	ENSMUSG00000033159	Cnppd1	1810031K17Rik|AU043960	cyclin Pas1/PHO80 domain containing 1	protein-coding
mm_133368.1	chr16	84708875	84708889	+	1	NA	Intergenic	Intergenic	-4141	NR_132106	100653389	Mm.261808	NR_132106	ENSMUSG00000097418	Mir155hg	Bic|Gm26667	Mir155 host gene (non-protein coding)	ncRNA
mm_91108.1	chr10	19170688	19170696	-	1	NA	intron (NR_038022, intron 1 of 1)	intron (NR_038022, intron 1 of 1)	3454	NR_038022	100504265	Mm.383417	NR_038021		Gm20139	-	predicted gene, 20139	ncRNA
mm_141853.1	chr17	34803010	34803026	-	1	NA	exon (NM_009995, exon 6 of 10)	exon (NM_009995, exon 6 of 10)	1408	NM_009995	13079	Mm.440407	NM_009995	ENSMUSG00000024365	Cyp21a1	21-OH|21OH|21OHA|21OHB|CYP21OH-A|Cyp21|Cyp21-ps1|Cyp21B|Cyp21a2-ps|Cyp21a2ps|Oh21-1|Oh21-2	cytochrome P450, family 21, subfamily a, polypeptide 1	protein-coding
mm_89617.1	chr10	96163560	96163561	+	1	NA	Intergenic	Intergenic	-62647	NR_110448	74881	Mm.410819	NR_110448		4930459C07Rik	-	RIKEN cDNA 4930459C07 gene	ncRNA
mm_123259.1	chr14	61257991	61258014	-	1	NA	intron (NM_011892, intron 1 of 7)	intron (NM_011892, intron 1 of 7)	488	NM_011892	24053	Mm.72173	NM_011892	ENSMUSG00000035296	Sgcg	35kDa|5430420E18Rik|AI642964|gamma-SG	sarcoglycan, gamma (dystrophin-associated glycoprotein)	protein-coding
mm_173310.1	chrY	90734895	90734898	+	1	NA	Intergenic	IMPB_01|Satellite|Satellite	20154	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_150628.1	chr19	41344906	41344918	+	1	NA	intron (NM_031376, intron 2 of 16)	intron (NM_031376, intron 2 of 16)	40158	NM_031376	83490	Mm.222266	NM_031376	ENSMUSG00000025017	Pik3ap1	1810044J04Rik|BCAP	phosphoinositide-3-kinase adaptor protein 1	protein-coding
mm_10413.1	chr2	13579567	13579579	+	1	NA	intron (NM_011701, intron 5 of 8)	intron (NM_011701, intron 5 of 8)	5262	NM_011701	22352	Mm.268000	NM_011701	ENSMUSG00000026728	Vim	-	vimentin	protein-coding
mm_7987.1	chr1	134234886	134234896	-	1	NA	promoter-TSS (NM_001291928)	promoter-TSS (NM_001291928)	-35	NM_001291928	11539	Mm.298908	NM_009629	ENSMUSG00000042429	Adora1	A1-AR|A1AR|A1R|AA1R|AI848715|BB176431|Ri	adenosine A1 receptor	protein-coding
mm_152780.1	chr19	21174885	21174905	-	1	NA	Intergenic	Intergenic	70185	NR_126458	75354	Mm.243873	NR_126458		4930554I06Rik	-	RIKEN cDNA 4930554I06 gene	ncRNA
mm_135784.1	chr16	56928090	56928127	-	1	NA	promoter-TSS (NM_001347042)	promoter-TSS (NM_001347042)	-169	NM_001347042	100503609	Mm.457937	NM_001347042	ENSMUSG00000109588	Lnp1	Gm19797	leukemia NUP98 fusion partner 1	protein-coding
mm_112678.1	chr13	16028014	16028032	+	1	NA	3' UTR (NM_008380, exon 5 of 5)	3' UTR (NM_008380, exon 5 of 5)	16172	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_42403.1	chr5	114969871	114969885	+	1	NA	intron (NM_009327, intron 1 of 9)	intron (NM_009327, intron 1 of 9)	1184	NM_009327	21405	Mm.332607	NM_009327	ENSMUSG00000029556	Hnf1a	AI323641|HNF1|HNF1-alpha|HNF1[a]|Hnf-1|Hnf1alpha|LFB1|Tcf-1|Tcf1	HNF1 homeobox A	protein-coding
mm_81022.1	chr9	104361837	104361846	+	1	NA	Intergenic	Intergenic	-24119	NM_207668	56318	Mm.19941	NM_019807	ENSMUSG00000032561	Acpp	5'-NT|A030005E02Rik|FRAP|Lap|PAP|Ppal	acid phosphatase, prostate	protein-coding
mm_93983.1	chr10	127370493	127370518	-	1	NA	promoter-TSS (NM_010565)	promoter-TSS (NM_010565)	43	NM_010565	16325	Mm.2594	NM_010565	ENSMUSG00000025405	Inhbc	-	inhibin beta-C	protein-coding
mm_5091.1	chr1	4602169	4602169	-	1	NA	Intergenic	Intergenic	-104815	NM_001289465	20671	Mm.279103	NM_011441	ENSMUSG00000025902	Sox17	-	SRY (sex determining region Y)-box 17	protein-coding
mm_12239.1	chr2	68861079	68861089	+	1	NA	promoter-TSS (NM_001347161)	promoter-TSS (NM_001347161)	-357	NM_172856	241447	Mm.222222	NM_172856	ENSMUSG00000027035	Cers6	4732462C07Rik|AW544719|Lass6|T1L	ceramide synthase 6	protein-coding
mm_10724.1	chr2	22855176	22855204	+	1	NA	intron (NM_019456, intron 9 of 13)	intron (NM_019456, intron 9 of 13)	-40332	NM_019501	56075	Mm.249752	NM_019501	ENSMUSG00000026784	Pdss1	2610203G20Rik|2700031G06Rik|TPT|TPT 1|Tprt|mDLP1|mSPS1	prenyl (solanesyl) diphosphate synthase, subunit 1	protein-coding
mm_107255.1	chr12	28675202	28675212	+	1	NA	promoter-TSS (NM_134052)	promoter-TSS (NM_134052)	0	NM_134052	104923	Mm.291504	NM_134052	ENSMUSG00000020629	Adi1	AL024210|Fe-ARD|MTCBP-1|Ni-ARD	acireductone dioxygenase 1	protein-coding
mm_47276.1	chr5	122019396	122019429	-	1	NA	intron (NM_001312908, intron 2 of 22)	intron (NM_001312908, intron 2 of 22)	28413	NM_007804	13048	Mm.156172	NM_007804	ENSMUSG00000042589	Cux2	1700051K22Rik|Cutl2|Cux-2|ENSMUSG00000072641	cut-like homeobox 2	protein-coding
mm_159248.1	chr2	151973935	151973935	-	1	NA	promoter-TSS (NM_001289151)	promoter-TSS (NM_001289151)	46	NM_001289150	73847	Mm.272444	NM_028666	ENSMUSG00000027459	Fam110a	1700008J10Rik|5430432M24Rik|AI747080	family with sequence similarity 110, member A	protein-coding
mm_92602.1	chr10	80105567	80105577	-	1	NA	intron (NR_038088, intron 1 of 4)	intron (NR_038088, intron 1 of 4)	-2870	NM_183426	216161	Mm.262102	NM_183426	ENSMUSG00000035673	Sbno2	BC019206|F730040C21|Sno|Stno	strawberry notch homolog 2 (Drosophila)	protein-coding
mm_161946.1	chr19	4305726	4305726	-	1	NA	intron (NM_130863, intron 1 of 21)	CpG	496	NM_130863	110355	Mm.254144	NM_130863	ENSMUSG00000024858	Grk2	Adrbk-1|Adrbk1|Bark-1|beta ARK|betaARK1	G protein-coupled receptor kinase 2	protein-coding
mm_18995.1	chr2	76868070	76868090	-	1	NA	exon (NM_011652, exon 105 of 313)	exon (NM_011652, exon 105 of 313)	114467	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_11976.1	chr2	55114232	55114244	+	1	NA	3' UTR (NM_173030, exon 13 of 13)	3' UTR (NM_173030, exon 13 of 13)	-321732	NM_001304810	16519	Mm.5127	NM_008426	ENSMUSG00000026824	Kcnj3	GIRK-1|GIRK1|Kcnf3|Kir3.1	potassium inwardly-rectifying channel, subfamily J, member 3	protein-coding
mm_94803.1	chr11	23007524	23007536	+	1	NA	Intergenic	Intergenic	-5857	NM_028672	73873	Mm.252406	NM_028672	ENSMUSG00000049811	Fam161a	4930430E16Rik	family with sequence similarity 161, member A	protein-coding
mm_81216.1	chr9	107587712	107587746	+	1	NA	promoter-TSS (NM_025903)	promoter-TSS (NM_025903)	11	NM_025903	15983	Mm.215335	NM_025903	ENSMUSG00000010048	Ifrd2	1810034A24Rik|AA470234|AI838527|SKMc15	interferon-related developmental regulator 2	protein-coding
mm_117589.1	chr13	89712275	89712288	-	1	NA	exon (NM_001134474, exon 6 of 14)	exon (NM_001134474, exon 6 of 14)	30231	NM_001081249	13003	Mm.158700	NM_019389	ENSMUSG00000021614	Vcan	5430420N07Rik|9430051N09|Cspg2|DPEAAE|NG2|PG-M|PG-M(V0)|PG-M(V1)|hdf	versican	protein-coding
mm_135215.1	chr16	36649006	36649012	-	1	NA	intron (NM_019388, intron 1 of 7)	intron (NM_019388, intron 1 of 7)	17068	NM_019388	12524	Mm.1452	NM_019388	ENSMUSG00000022901	Cd86	B7|B7-2|B7.2|B70|CLS1|Cd28l2|ETC-1|Ly-58|Ly58|MB7|MB7-2|TS/A-2	CD86 antigen	protein-coding
mm_146158.1	chr18	75018710	75018816	+	1	NA	promoter-TSS (NM_027727)	promoter-TSS (NM_027727)	-9	NM_027727	69190	Mm.173826	NM_027727	ENSMUSG00000035765	Dym	1810041M12Rik|4933427L07Rik|C030019K18Rik	dymeclin	protein-coding
mm_107029.1	chr12	13269112	13269154	+	1	NA	promoter-TSS (NM_027706)	promoter-TSS (NM_027706)	6	NM_027706	71169	Mm.177520	NM_027706	ENSMUSG00000020576	Nbas	4933425L03Rik|Nag	neuroblastoma amplified sequence	protein-coding
mm_48010.1	chr5	136165090	136165100	-	1	NA	intron (NM_178751, intron 1 of 2)	intron (NM_178751, intron 1 of 2)	5561	NM_178751	269717	Mm.308396	NM_178751	ENSMUSG00000039747	Orai2	A730041O15Rik|Tmem142b	ORAI calcium release-activated calcium modulator 2	protein-coding
mm_25194.1	chr3	103735854	103735869	+	1	NA	exon (NM_133859, exon 3 of 3)	exon (NM_133859, exon 3 of 3)	2140	NM_133859	99543	Mm.211535	NM_133859	ENSMUSG00000027848	Olfml3	2810002E22Rik|AI115209|AW550633|HNOEL-iso|ONT3|mONT3	olfactomedin-like 3	protein-coding
mm_165185.1	chr2	29889989	29889993	+	1	NA	promoter-TSS (NM_013615)	promoter-TSS (NM_013615)	-72	NM_013615	18286	Mm.330116	NM_013615	ENSMUSG00000026790	Odf2	AI848335|MMTEST29	outer dense fiber of sperm tails 2	protein-coding
mm_64566.1	chr7	144896524	144896539	+	1	NA	promoter-TSS (NM_008003)	promoter-TSS (NM_008003)	-1	NM_008003	14170	Mm.3904	NM_008003	ENSMUSG00000031073	Fgf15	FGF19	fibroblast growth factor 15	protein-coding
mm_54883.1	chr6	42774731	42774733	-	1	NA	Intergenic	Intergenic	12678	NM_146986	258988	Mm.377777	NM_146986	ENSMUSG00000095236	Olfr38	18A|MOR257-2	olfactory receptor 38	protein-coding
mm_12494.1	chr2	71787099	71787107	+	1	NA	5' UTR (NM_008397, exon 1 of 26)	5' UTR (NM_008397, exon 1 of 26)	164	NM_001277970	16403	Mm.225096	NM_008397	ENSMUSG00000027111	Itga6	5033401O05Rik|AI115430|Cd49f|VLA-6	integrin alpha 6	protein-coding
mm_136855.1	chr17	12798975	12799004	+	1	NA	intron (NR_027784, intron 2 of 2)	B4|SINE|B4	-29283	NM_010515	16004	Mm.26553	NM_010515	ENSMUSG00000023830	Igf2r	AI661837|CD222|CI-MPR|M6P/IGF2R|Mpr300	insulin-like growth factor 2 receptor	protein-coding
mm_107269.1	chr12	29533281	29533291	+	1	NA	intron (NM_001093778, intron 1 of 24)	intron (NM_001093778, intron 1 of 24)	-1619	NM_001093776	17933	Mm.253067	NM_008666	ENSMUSG00000061911	Myt1l	2900046C06Rik|2900093J19Rik|C630034G21Rik|Nztf1|Pmng1|Png-1|mKIAA1106	myelin transcription factor 1-like	protein-coding
mm_134724.1	chr16	22898858	22898875	-	1	NA	exon (NM_001276450, exon 7 of 7)	exon (NM_001276450, exon 7 of 7)	-4480	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_129476.1	chr15	78718516	78718555	-	1	NA	promoter-TSS (NM_183141)	promoter-TSS (NM_183141)	-422	NM_183141	207393	Mm.323188	NM_183141	ENSMUSG00000043460	Elfn2	6330514E13|AW048948|BC094219|Lrrc62|Ppp1r29	leucine rich repeat and fibronectin type III, extracellular 2	protein-coding
mm_64034.1	chr7	140770073	140770082	+	1	NA	exon (NM_021282, exon 5 of 9)	exon (NM_021282, exon 5 of 9)	6245	NM_021282	13106	Mm.21758	NM_021282	ENSMUSG00000025479	Cyp2e1	Cyp2e	cytochrome P450, family 2, subfamily e, polypeptide 1	protein-coding
mm_10795.1	chr2	24349525	24349531	+	1	NA	exon (NM_031167, exon 5 of 5)	exon (NM_031167, exon 5 of 5)	4157	NM_001039701	16181	Mm.882	NM_031167	ENSMUSG00000026981	Il1rn	F630041P17Rik|IL-1ra	interleukin 1 receptor antagonist	protein-coding
mm_164679.1	chr17	46680936	46680944	-	1	NA	promoter-TSS (NM_010787)	promoter-TSS (NM_010787)	-10	NM_027910	71765	Mm.254784	NM_027910	ENSMUSG00000063576	Klhdc3	1300011D16Rik|Peas	kelch domain containing 3	protein-coding
mm_120408.1	chr14	65172333	65172361	+	1	NA	Intergenic	Intergenic	-74241	NM_018788	54616	Mm.103748	NM_018788	ENSMUSG00000021978	Extl3	2900009G18Rik|AU040105|Ext1l|mKIAA0519	exostoses (multiple)-like 3	protein-coding
mm_33986.1	chr4	137719521	137719523	+	1	NA	intron (NM_001256218, intron 15 of 24)	intron (NM_001256218, intron 15 of 24)	-4939	NR_138592	110351	Mm.180763	NM_029563	ENSMUSG00000041351	Rap1gap	1300019I11Rik|2310004O14Rik|AI427470|ARPP-90|Gap|Rap1GAP1|Rap1ga1	Rap1 GTPase-activating protein	protein-coding
mm_113816.1	chr13	46725261	46725272	+	1	NA	intron (NM_175749, intron 1 of 21)	intron (NM_175749, intron 1 of 21)	2583	NM_175749	218210	Mm.255398	NM_175749	ENSMUSG00000021374	Nup153	B130015D15Rik|C88147	nucleoporin 153	protein-coding
mm_111758.1	chr12	103958895	103958919	-	1	NA	Intergenic	Intergenic	-2010	NM_009247	20704	Mm.312593	NM_009247	ENSMUSG00000072849	Serpina1e	Dom5|PI5|Spi1-5	serine (or cysteine) peptidase inhibitor, clade A, member 1E	protein-coding
mm_128272.1	chr15	36794199	36794209	-	1	NA	5' UTR (NM_011740, exon 1 of 7)	5' UTR (NM_011740, exon 1 of 7)	334	NM_011740	22631	Mm.3360	NM_011740	ENSMUSG00000022285	Ywhaz	1110013I11Rik|14-3-3zeta|AI596267|AL022924|AU020854	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide	protein-coding
mm_123869.1	chr14	72584818	72584828	-	1	NA	exon (NM_207636, exon 6 of 26)	exon (NM_207636, exon 6 of 26)	125180	NM_207636	319448	Mm.205421	NM_207636	ENSMUSG00000033487	Fndc3a	1700094E19Rik|D14Ertd453e|F730017H24Rik|Fndc3|sys	fibronectin type III domain containing 3A	protein-coding
mm_4705.1	chr1	180893108	180893108	+	1	NA	promoter-TSS (NM_177099)	promoter-TSS (NM_177099)	0	NM_177099	320202	Mm.87078	NM_177099	ENSMUSG00000066652	Lefty2	6030463A22Rik|Ebaf|Lefta|Leftb|lefty-2|lefty-B	left-right determination factor 2	protein-coding
mm_67591.1	chr7	83655492	83655498	-	1	NA	intron (NM_010551, intron 12 of 18)	intron (NM_010551, intron 12 of 18)	23478	NM_023377	170460	Mm.357953	NM_023377	ENSMUSG00000046027	Stard5	2310058G22Rik|AI607880|D7Ertd152e	StAR-related lipid transfer (START) domain containing 5	protein-coding
mm_20951.1	chr2	151729565	151729578	-	1	NA	exon (NM_001305244, exon 2 of 5)	exon (NM_001305244, exon 2 of 5)	11739	NM_212446	228769	Mm.146984	NM_144889	ENSMUSG00000032869	Psmf1	AW048666|BC012260|PI31	proteasome (prosome, macropain) inhibitor subunit 1	protein-coding
mm_64056.1	chr7	140847785	140847793	+	1	NA	promoter-TSS (NM_027019)	promoter-TSS (NM_027019)	-127	NM_027019	69287	Mm.56404	NM_027019	ENSMUSG00000025482	Odf3	1700011O04Rik|SHIPPO1	outer dense fiber of sperm tails 3	protein-coding
mm_73755.1	chr8	114973376	114973390	+	1	NA	intron (NM_019573, intron 8 of 8)	intron (NM_019573, intron 8 of 8)	533731	NM_019573	80707	Mm.440420	NM_019573	ENSMUSG00000004637	Wwox	5330426P09Rik|9030416C10Rik|WOX1	WW domain-containing oxidoreductase	protein-coding
mm_56284.1	chr6	91411364	91411373	-	1	NA	promoter-TSS (NM_009527)	promoter-TSS (NM_009527)	1	NM_009527	22421	Mm.56964	NM_009527	ENSMUSG00000030093	Wnt7a	AI849442|Wnt-7a|px|tw	wingless-type MMTV integration site family, member 7A	protein-coding
mm_7365.1	chr1	106713916	106713924	-	1	NA	5' UTR (NM_177410, exon 1 of 1)	5' UTR (NM_177410, exon 1 of 1)	370	NM_009741	12043	Mm.257460	NM_009741	ENSMUSG00000057329	Bcl2	AW986256|Bcl-2|C430015F12Rik|D630044D05Rik|D830018M01Rik	B cell leukemia/lymphoma 2	protein-coding
mm_102011.1	chr11	51606591	51606595	-	1	NA	intron (NM_001048061, intron 1 of 7)	CpG-1915	288	NM_001048061	15384	Mm.256875	NM_010448	ENSMUSG00000020358	Hnrnpab	3010025C11Rik|CBF-A|Cgbfa|Hnrpab	heterogeneous nuclear ribonucleoprotein A/B	protein-coding
mm_138434.1	chr17	35108289	35108308	+	1	NA	promoter-TSS (NM_148947)	promoter-TSS (NM_148947)	-2	NM_148947	114652	Mm.222643	NM_148947	ENSMUSG00000034482	Ly6g5c	G5c|NG33	lymphocyte antigen 6 complex, locus G5C	protein-coding
mm_110084.1	chr12	24681854	24681854	-	1	NA	promoter-TSS (NM_001161807)	promoter-TSS (NM_001161807)	-59	NM_001161807	12879	Mm.52265	NM_138686	ENSMUSG00000062563	Cys1	2900006B19Rik|AV218859|Ccap|ck|cpk	cystin 1	protein-coding
mm_163261.1	chr11	112785283	112785293	+	1	NA	exon (NM_011448, exon 3 of 3)	exon (NM_011448, exon 3 of 3)	3078	NM_011448	20682	Mm.286407	NM_011448	ENSMUSG00000000567	Sox9	2010306G03Rik|AV220920|mKIAA4243	SRY (sex determining region Y)-box 9	protein-coding
mm_145021.1	chr18	38993127	38993186	+	1	NA	promoter-TSS (NM_175164)	promoter-TSS (NM_175164)	11	NM_175164	71302	Mm.329396	NM_175164	ENSMUSG00000036452	Arhgap26	1810044B20Rik|2610010G17Rik|4933432P15Rik|AI853435|mKIAA0621	Rho GTPase activating protein 26	protein-coding
mm_54070.1	chr6	14754739	14754751	-	1	NA	exon (NM_080464, exon 1 of 4)	exon (NM_080464, exon 1 of 4)	529	NM_080464	140491	Mm.209429	NM_080464	ENSMUSG00000042717	Ppp1r3a	GM|RG1|RGL	protein phosphatase 1, regulatory (inhibitor) subunit 3A	protein-coding
mm_67707.1	chr7	89941137	89941174	-	1	NA	promoter-TSS (NM_001291289)	promoter-TSS (NM_001291289)	49	NM_001291289	67669	Mm.28679	NM_026304	ENSMUSG00000062797	Hikeshi	0610007P06Rik|1110002N09Rik|l(7)6Rn|l7Rn6	heat shock protein nuclear import factor	protein-coding
mm_76510.1	chr8	86885316	86885326	-	1	NA	promoter-TSS (NM_030563)	promoter-TSS (NM_030563)	-63	NM_030563	80750	Mm.25117	NM_030563	ENSMUSG00000031652	N4bp1	AI481586|C81621	NEDD4 binding protein 1	protein-coding
mm_25682.1	chr3	122173759	122173772	+	1	NA	intron (NM_007378, intron 47 of 49)	intron (NM_007378, intron 47 of 49)	-71792	NM_008129	14630	Mm.292676	NM_008129	ENSMUSG00000028124	Gclm	AI649393|Gcmc|Glclr	glutamate-cysteine ligase, modifier subunit	protein-coding
mm_125051.1	chr15	25843269	25843280	+	1	NA	promoter-TSS (NM_001034851)	promoter-TSS (NM_001034851)	-24	NM_001034851	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_35975.1	chr4	53403564	53403574	-	1	NA	Intergenic	B4A|SINE|B4	-36844	NM_001159633	100434	Mm.482207	NM_133891	ENSMUSG00000028412	Slc44a1	2210409B22Rik|4833416H08Rik|AW547365|CHTL1|CTL1|Cdw92	solute carrier family 44, member 1	protein-coding
mm_57053.1	chr6	122466555	122466597	-	1	NA	intron (NM_027664, intron 2 of 5)	RMER19B|LTR|ERVK	19729	NM_027664	108653	Mm.277939	NM_027664	ENSMUSG00000040649	Rimklb	4931417E21Rik|4933426K21Rik|AA097693|AI325948|AU015629|Naags	ribosomal modification protein rimK-like family member B	protein-coding
mm_74227.1	chr8	124197106	124197123	+	1	NA	Intergenic	Intergenic	-34280	NM_139272	108148	Mm.33808	NM_139272	ENSMUSG00000089704	Galnt2	AI480629	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2	protein-coding
mm_84166.1	chr9	59680789	59680814	-	1	NA	Intergenic	Intergenic	24433	NM_001253883	18746	Mm.326167	NM_011099	ENSMUSG00000032294	Pkm	AA414905|AL024370|AL024424|Pk-2|Pk-3|Pk3|Pkm2	pyruvate kinase, muscle	protein-coding
mm_103124.1	chr11	70220698	70220709	-	1	NA	5' UTR (NM_172371, exon 1 of 4)	5' UTR (NM_172371, exon 1 of 4)	291	NM_172371	69309	Mm.93266	NM_172371	ENSMUSG00000044367	Slc16a13	1700007D07Rik	solute carrier family 16 (monocarboxylic acid transporters), member 13	protein-coding
mm_142394.1	chr17	44880877	44880890	-	1	NA	promoter-TSS (NM_029257)	promoter-TSS (NM_029257)	2	NM_029257	75341	Mm.386821	NM_029257		4930564C03Rik	-	RIKEN cDNA 4930564C03 gene	protein-coding
mm_68005.1	chr7	100938800	100938819	-	1	NA	exon (NM_183168, exon 3 of 3)	exon (NM_183168, exon 3 of 3)	-6648	NM_001081116	207212	Mm.29954	NM_001081116	ENSMUSG00000032875	Arhgef17	8030463K16|AI428794|AW558066|BC035332|mKIAA0337	Rho guanine nucleotide exchange factor (GEF) 17	protein-coding
mm_24430.1	chr3	90541156	90541173	+	1	NA	promoter-TSS (NM_026416)	promoter-TSS (NM_026416)	-59	NM_026416	67860	Mm.331185	NM_026416	ENSMUSG00000074457	S100a16	2300002L21Rik|AI325039|AI663996|DT1P1A7|S100F	S100 calcium binding protein A16	protein-coding
mm_35016.1	chr4	3678983	3679029	-	1	NA	intron (NM_010747, intron 1 of 12)	intron (NM_010747, intron 1 of 12)	885	NM_010747	17096	Mm.317331	NM_010747	ENSMUSG00000042228	Lyn	AA407514|Hck-2|p53Lyn|p56Lyn	LYN proto-oncogene, Src family tyrosine kinase	protein-coding
mm_108744.1	chr12	88725596	88725607	+	1	NA	Intergenic	Intergenic	-68903	NM_001198587	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding
mm_5827.1	chr1	52799543	52799562	-	1	NA	intron (NM_008384, intron 1 of 5)	intron (NM_008384, intron 1 of 5)	18136	NM_008384	16329	Mm.917	NM_008384	ENSMUSG00000026102	Inpp1	2300002C06Rik|AV137389	inositol polyphosphate-1-phosphatase	protein-coding
mm_32965.1	chr4	119895455	119895460	+	1	NA	intron (NM_010657, intron 1 of 8)	intron (NM_010657, intron 1 of 8)	80779	NM_010657	16656	Mm.302758	NM_010657	ENSMUSG00000028634	Hivep3	2900056N03Rik|A130075N07|AI848000|E030045D18Rik|KBP-1|KBP1|Krc|Rc|Schnurri-3|Shn3|Zas3	human immunodeficiency virus type I enhancer binding protein 3	protein-coding
mm_17912.1	chr2	35367717	35367726	-	1	NA	promoter-TSS (NM_029463)	promoter-TSS (NM_029463)	8	NM_029463	75859	Mm.159604	NM_029463	ENSMUSG00000026882	4930568D16Rik	Ggta1l1	RIKEN cDNA 4930568D16 gene	protein-coding
mm_4830.1	chr1	186512107	186512108	+	1	NA	non-coding (NR_131124, exon 3 of 3)	non-coding (NR_131124, exon 3 of 3)	46574	NR_131124	320449	Mm.404477	NR_131124	ENSMUSG00000103690	A730004F24Rik	-	RIKEN cDNA A730004F24 gene	ncRNA
mm_128096.1	chr15	27840669	27840671	-	1	NA	intron (NM_001081302, intron 20 of 56)	intron (NM_001081302, intron 20 of 56)	-159128	NM_001242423	223433	Mm.266485	NM_198301	ENSMUSG00000056069	Fam105a	9830126M18	family with sequence similarity 105, member A	protein-coding
mm_159606.1	chr4	129992071	129992071	+	1	NA	promoter-TSS (NM_001290715)	promoter-TSS (NM_001290715)	17	NM_001290715	230775	Mm.262241	NM_173071	ENSMUSG00000028782	Adgrb2	Bai2	adhesion G protein-coupled receptor B2	protein-coding
mm_44124.1	chr5	149636501	149636524	+	1	NA	promoter-TSS (NM_013559)	promoter-TSS (NM_013559)	-176	NM_001347534	15505	Mm.270681	NM_013559	ENSMUSG00000029657	Hsph1	105kDa|AI790491|Hsp105|Hsp110|hsp-E7I|hsp110/105	heat shock 105kDa/110kDa protein 1	protein-coding
mm_14143.1	chr2	126545671	126545702	+	1	NA	Intergenic	Lx8|LINE|L1	-7338	NM_011978	26458	Mm.290044	NM_011978	ENSMUSG00000027359	Slc27a2	ACSVL1|FATP2|VLCS|Vlac|Vlacs	solute carrier family 27 (fatty acid transporter), member 2	protein-coding
mm_89594.1	chr10	95941055	95941071	+	1	NA	intron (NM_001001932, intron 1 of 28)	CpG	400	NM_001001932	216238	Mm.210035	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding
mm_3202.1	chr1	135818811	135818834	+	1	NA	5' UTR (NM_133664, exon 1 of 10)	5' UTR (NM_133664, exon 1 of 10)	224	NM_133664	16763	Mm.36726	NM_133664	ENSMUSG00000041782	Lad1	-	ladinin	protein-coding
mm_75018.1	chr8	31067833	31067837	-	1	NA	Intergenic	RMER20B|LTR|ERVK	-21827	NM_025869	66959	Mm.23916	NM_025869	ENSMUSG00000039661	Dusp26	2310043K02Rik|Skrp3	dual specificity phosphatase 26 (putative)	protein-coding
mm_49175.1	chr6	14901548	14901571	+	1	NA	5' UTR (NM_053242, exon 1 of 19)	5' UTR (NM_053242, exon 1 of 19)	210	NM_053242	114142	Mm.332919	NM_053242	ENSMUSG00000029563	Foxp2	2810043D05Rik|AI449000|CAG-16|D0Kist7	forkhead box P2	protein-coding
mm_128918.1	chr15	73735072	73735127	-	1	NA	intron (NM_001166388, intron 1 of 5)	intron (NM_001166388, intron 1 of 5)	10169	NM_001166388	19245	Mm.390807	NM_008975	ENSMUSG00000059895	Ptp4a3	AV088979|Prl-3|pPtp4a3	protein tyrosine phosphatase 4a3	protein-coding
mm_127483.1	chr15	101274683	101274689	+	1	NA	3' UTR (NM_010444, exon 7 of 7)	3' UTR (NM_010444, exon 7 of 7)	7840	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_155239.1	chrX	57212168	57212173	+	1	NA	promoter-TSS (NM_011616)	promoter-TSS (NM_011616)	27	NM_011616	21947	Mm.4861	NM_011616	ENSMUSG00000031132	Cd40lg	CD154|CD40-L|Cd40l|HIGM1|IGM|IMD3|Ly-62|Ly62|T-BAM|TRAP|Tnfsf5|Tnlg8b|gp39	CD40 ligand	protein-coding
mm_157941.1	chrX	85776538	85776548	-	1	NA	5' UTR (NM_212444, exon 1 of 20)	5' UTR (NM_212444, exon 1 of 20)	276	NM_001294140	14933	Mm.246682	NM_008194	ENSMUSG00000025059	Gk	D930012N15Rik|Gyk	glycerol kinase	protein-coding
mm_154324.1	chrM	2370	2380	+	1	NA	NA	Intergenic	NA	NA								
mm_159596.1	chr4	126566043	126566043	+	1	NA	exon (NM_175554, exon 8 of 26)	exon (NM_175554, exon 8 of 26)	6183	NR_106067	102465673		NR_106067	ENSMUSG00000098831	Mir7119	Gm27560|mmu-mir-7119	microRNA 7119	ncRNA
mm_27442.1	chr3	51796517	51796538	-	1	NA	intron (NM_001004176, intron 2 of 4)	intron (NM_001004176, intron 2 of 4)	135348	NM_001310482	211666	Mm.24679	NM_174995	ENSMUSG00000074604	Mgst2	GST2|MGST-II	microsomal glutathione S-transferase 2	protein-coding
mm_27375.1	chr3	50443457	50443465	-	1	NA	5' UTR (NM_011990, exon 1 of 12)	5' UTR (NM_011990, exon 1 of 12)	152	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_70979.1	chr8	27175312	27175318	+	1	NA	promoter-TSS (NM_001080813)	promoter-TSS (NM_001080813)	-669	NM_001080813	75767	Mm.205335	NM_029423	ENSMUSG00000031488	Rab11fip1	2010200K21Rik|4833414G05Rik|Rcp	RAB11 family interacting protein 1 (class I)	protein-coding
mm_68397.1	chr7	109557468	109557468	-	1	NA	intron (NM_001001326, intron 2 of 19)	intron (NM_001001326, intron 2 of 19)	37336	NR_028079	100302499	Mm.482651	NR_028079	ENSMUSG00000065016	Snora3	MBI-28	small nucleolar RNA, H/ACA box 3	snoRNA
mm_18998.1	chr2	76868451	76868459	-	1	NA	exon (NM_011652, exon 104 of 313)	exon (NM_011652, exon 104 of 313)	114092	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_75712.1	chr8	68905684	68905696	-	1	NA	3' UTR (NM_008509, exon 10 of 10)	3' UTR (NM_008509, exon 10 of 10)	25135	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_120655.1	chr14	70531678	70531693	+	1	NA	intron (NM_145219, intron 1 of 7)	intron (NM_145219, intron 1 of 7)	864	NM_145219	213469	Mm.41708	NM_145219	ENSMUSG00000033595	Lgi3	AI841179|AW049851	leucine-rich repeat LGI family, member 3	protein-coding
mm_130172.1	chr15	93336445	93336513	-	1	NA	intron (NR_028315, intron 1 of 4)	CpG-5264	456	NR_028315	67057	Mm.4714	NM_024189	ENSMUSG00000022634	Yaf2	2810021M11Rik	YY1 associated factor 2	protein-coding
mm_76213.1	chr8	83442657	83442667	-	1	NA	promoter-TSS (NM_019708)	promoter-TSS (NM_019708)	0	NM_001285992	56367	Mm.246911	NM_019708	ENSMUSG00000063253	Scoc	0610011C06Rik|2810002J11Rik|AA415030|SCOCO	short coiled-coil protein	protein-coding
mm_171542.1	chr4	147013186	147013188	+	1	NA	Intergenic	RLTR27|LTR|ERVK	-8663	NM_001177767	100043034	Mm.422606	NM_001177767	ENSMUSG00000067919	Rex2	Gm13138|OTTMUSG00000010655	reduced expression 2	protein-coding
mm_158118.1	chrX	102251859	102251868	-	1	NA	promoter-TSS (NM_007709)	promoter-TSS (NM_007709)	-20	NM_007709	12705	Mm.2390	NM_007709	ENSMUSG00000051159	Cited1	AI316840|AU019144|Msg1	Cbp/p300-interacting transactivator with Glu/Asp-rich carboxy-terminal domain 1	protein-coding
mm_4166.1	chr1	171051189	171051201	+	1	NA	TTS (NM_010188)	TTS (NM_010188)	8208	NM_010188	14131	Mm.22119	NM_010188	ENSMUSG00000059498	Fcgr3	CD16	Fc receptor, IgG, low affinity III	protein-coding
mm_13336.1	chr2	102787010	102787020	+	1	NA	3' UTR (NM_001077514, exon 11 of 11)	3' UTR (NM_001077514, exon 11 of 11)	80577	NM_001077515	20511	Mm.267547	NM_011393	ENSMUSG00000005089	Slc1a2	1700091C19Rik|2900019G14Rik|AI159670|Eaat2|GLT-1|GLT1|MGLT1	solute carrier family 1 (glial high affinity glutamate transporter), member 2	protein-coding
mm_75297.1	chr8	41054871	41054877	-	1	NA	promoter-TSS (NM_001005864)	promoter-TSS (NM_001005864)	-78	NM_001005864	102103	Mm.149438	NM_001005863	ENSMUSG00000045636	Mtus1	AI481402|ATBP135|Atip1|B430010I23Rik|B430305I03Rik|C85752|Cctsg1-440|MD44|MTSG1|mKIAA1288	mitochondrial tumor suppressor 1	protein-coding
mm_39551.1	chr5	21786740	21786784	+	1	NA	exon (NM_011188, exon 2 of 13)	exon (NM_011188, exon 2 of 13)	1479	NM_011188	19181	Mm.2462	NM_011188	ENSMUSG00000028932	Psmc2	-	proteasome (prosome, macropain) 26S subunit, ATPase 2	protein-coding
mm_118106.1	chr13	103920577	103920590	-	1	NA	promoter-TSS (NM_001289475)	promoter-TSS (NM_001289475)	3	NM_001289473	59079	Mm.277354	NM_021563	ENSMUSG00000021709	Erbin	1700028E05Rik|Erbb2ip|mKIAA1225	Erbb2 interacting protein	protein-coding
mm_55327.1	chr6	55681049	55681108	-	1	NA	5' UTR (NM_009717, exon 1 of 2)	5' UTR (NM_009717, exon 1 of 2)	185	NM_009717	11922	Mm.5106	NM_009717	ENSMUSG00000037984	Neurod6	Atoh2|Math-2|Math2|Nex|Nex1m|bHLHa2	neurogenic differentiation 6	protein-coding
mm_102820.1	chr11	69011973	69011996	-	1	NA	Intergenic	RLTR19|LTR|ERVK	-3524	NM_001159519	237823	Mm.340288	NM_001159519	ENSMUSG00000020899	Pfas	4432409B16Rik|FGAMS|FGAR-AT|FGARAT|Gm18|PURL|Sofa	phosphoribosylformylglycinamidine synthase (FGAR amidotransferase)	protein-coding
mm_114540.1	chr13	73763194	73763198	+	1	NA	promoter-TSS (NM_011390)	promoter-TSS (NM_011390)	-501	NM_011390	20499	Mm.275800	NM_011390	ENSMUSG00000017756	Slc12a7	AA408796|D13Ertd261e|Kcc4	solute carrier family 12, member 7	protein-coding
mm_156220.1	chrX	134756564	134756617	+	1	NA	promoter-TSS (NM_027870)	promoter-TSS (NM_027870)	22	NM_027870	71703	Mm.67949	NM_027870	ENSMUSG00000049047	Armcx3	1200004E24Rik|AI450003|ALEX3	armadillo repeat containing, X-linked 3	protein-coding
mm_168622.1	chr1	179464607	179464617	-	1	NA	intron (NM_027188, intron 1 of 11)	RLTR16B_MM|LTR|ERVK	53391	NM_027188	69726	Mm.222338	NM_027188	ENSMUSG00000055067	Smyd3	2410008A19Rik|Zmynd1	SET and MYND domain containing 3	protein-coding
mm_91488.1	chr10	37135603	37135607	-	1	NA	3' UTR (NM_008538, exon 2 of 2)	3' UTR (NM_008538, exon 2 of 2)	3321	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_74128.1	chr8	123186406	123186416	+	1	NA	5' UTR (NM_007876, exon 1 of 11)	5' UTR (NM_007876, exon 1 of 11)	176	NM_007876	13479	Mm.20388	NM_007876	ENSMUSG00000019278	Dpep1	AI327012|MBD	dipeptidase 1 (renal)	protein-coding
mm_90896.1	chr10	10475034	10475053	-	1	NA	Intergenic	RMER17B|LTR|ERVK	-2729	NM_001127353	215772	Mm.246573	NM_172547	ENSMUSG00000050994	Adgb	9130014G24Rik	androglobin	protein-coding
mm_73969.1	chr8	120488753	120488803	+	1	NA	promoter-TSS (NM_198671)	promoter-TSS (NM_198671)	-88	NM_198671	382034	Mm.334856	NM_198671	ENSMUSG00000031822	Gse1	2210013I18Rik|mKIAA0182	genetic suppressor element 1, coiled-coil protein	protein-coding
mm_115455.1	chr13	118790481	118790485	+	1	NA	3' UTR (NM_008002, exon 3 of 3)	3' UTR (NM_008002, exon 3 of 3)	75784	NM_008002	14165	Mm.317323	NM_008002	ENSMUSG00000021732	Fgf10	AEY17|BB213776|Fgf-10|Gsfaey17	fibroblast growth factor 10	protein-coding
mm_132781.1	chr16	44811739	44811767	+	1	NA	Intergenic	Intergenic	-8975	NM_207244	239849	Mm.445045	NM_207244	ENSMUSG00000062082	Cd200r4	F630107N04Rik|MCD200RLa	CD200 receptor 4	protein-coding
mm_110221.1	chr12	28635833	28635837	-	1	NA	intron (NM_011300, intron 1 of 6)	CpG-3104	118	NM_011300	20115	Mm.279839	NM_011300	ENSMUSG00000061477	Rps7	Mtu|Rps7A|S7	ribosomal protein S7	protein-coding
mm_35030.1	chr4	4019629	4019659	-	1	NA	promoter-TSS (NM_181989)	promoter-TSS (NM_181989)	19	NM_181989	242285	Mm.98096	NM_181989	ENSMUSG00000028236	Sdr16c5	Rdhe2|Scdr9	short chain dehydrogenase/reductase family 16C, member 5	protein-coding
mm_54014.1	chr6	8259099	8259153	-	1	NA	promoter-TSS (NM_026632)	promoter-TSS (NM_026632)	15	NM_026632	68240	Mm.29073	NM_026632	ENSMUSG00000012483	Rpa3	14kDa|C330026P08Rik	replication protein A3	protein-coding
mm_53857.1	chr6	149309392	149309438	+	1	NA	promoter-TSS (NM_001289662)	promoter-TSS (NM_001289662)	1	NM_001289662	67246	Mm.333515	NM_026054	ENSMUSG00000032712	2810474O19Rik	6720435I21Rik|AA536804|AU020969|GET|Kiaa1551	RIKEN cDNA 2810474O19 gene	protein-coding
mm_31337.1	chr4	46468709	46468736	+	1	NA	exon (NM_130889, exon 4 of 7)	exon (NM_130889, exon 4 of 7)	17796	NM_130889	67628	Mm.263913	NM_130889	ENSMUSG00000028333	Anp32b	2410015B15Rik|PAL31|PHAPI2a|Ssp29	acidic (leucine-rich) nuclear phosphoprotein 32 family, member B	protein-coding
mm_9831.1	chr1	182749176	182749189	-	1	NA	promoter-TSS (NM_001033547)	promoter-TSS (NM_001033547)	-2	NM_001033547	433386	Mm.338103	NM_001033547	ENSMUSG00000043429	Ccdc185	4922505E12Rik	coiled-coil domain containing 185	protein-coding
mm_132421.1	chr16	35211395	35211397	+	1	NA	intron (NM_001012765, intron 1 of 20)	intron (NM_001012765, intron 1 of 20)	55760	NM_001012765	224129	Mm.41137	NM_001012765	ENSMUSG00000022840	Adcy5	AW121902|Ac5	adenylate cyclase 5	protein-coding
mm_127298.1	chr15	100199281	100199296	+	1	NA	intron (NM_001159361, intron 29 of 37)	intron (NM_001159361, intron 29 of 37)	-11252	NR_037311	100499528		NR_037311	ENSMUSG00000092752	Mir3473a	Mir3473|mir-3473a|mmu-mir-3473|mmu-mir-3473a	microRNA 3473a	ncRNA
mm_157910.1	chrX	78477696	78477698	-	1	NA	intron (NM_027322, intron 3 of 3)	L1VL4|LINE|L1	106108	NM_001164275	546336	Mm.211712	NM_027322	ENSMUSG00000047996	Prrg1	2010007L08Rik	proline rich Gla (G-carboxyglutamic acid) 1	protein-coding
mm_151674.1	chr19	4191077	4191083	-	1	NA	promoter-TSS (NM_178650)	promoter-TSS (NM_178650)	-33	NM_178650	108995	Mm.288312	NM_178650	ENSMUSG00000040247	Tbc1d10c	1810062O14Rik|AI428527	TBC1 domain family, member 10c	protein-coding
mm_164889.1	chr18	61553583	61553585	+	1	NA	Intergenic	Intergenic	-1998	NM_146087	93687	Mm.26908	NM_146087	ENSMUSG00000024576	Csnk1a1	2610208K14Rik|4632404G05Rik|5430427P18Rik|CK1a|Csnk1a	casein kinase 1, alpha 1	protein-coding
mm_71567.1	chr8	54077137	54077152	+	1	NA	promoter-TSS (NM_009506)	promoter-TSS (NM_009506)	-388	NM_009506	22341	Mm.1402	NM_009506	ENSMUSG00000031520	Vegfc	AW228853|VEGF-C	vascular endothelial growth factor C	protein-coding
mm_33573.1	chr4	132308669	132308688	+	1	NA	promoter-TSS (NR_029468)	promoter-TSS (NR_029468)	0	NR_029468	100039864	Mm.258912	NR_029468	ENSMUSG00000086290	Snhg12	2310005L22Rik	small nucleolar RNA host gene 12	ncRNA
mm_114352.1	chr13	60939966	60939969	+	1	NA	exon (NM_009411, exon 4 of 5)	exon (NM_009411, exon 4 of 5)	1968	NM_009411	21984	Mm.2372	NM_009411	ENSMUSG00000033834	Tpbpa	AV033951|Tb-1|Tb1|Tpbp|b2b1247Clo	trophoblast specific protein alpha	protein-coding
mm_79630.1	chr9	59315161	59315173	+	1	NA	exon (NM_028121, exon 7 of 7)	exon (NM_028121, exon 7 of 7)	23595	NM_028121	72141	Mm.22456	NM_028121	ENSMUSG00000025236	Adpgk	2610017G09Rik|Adp-gk|C77577	ADP-dependent glucokinase	protein-coding
mm_27823.1	chr3	79078897	79078920	-	1	NA	intron (NM_001310536, intron 19 of 23)	intron (NM_001310536, intron 19 of 23)	65979	NM_001310536	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_47683.1	chr5	128989922	128989935	-	1	NA	intron (NM_001286033, intron 8 of 9)	intron (NM_001286033, intron 8 of 9)	18644	NM_001286034	13852	Mm.260716	NM_007941	ENSMUSG00000029428	Stx2	AW538950|Epim|G1-536-1|Syn-2|repro34	syntaxin 2	protein-coding
mm_130149.1	chr15	91049824	91049867	-	1	NA	5' UTR (NM_001109041, exon 1 of 36)	5' UTR (NM_001109041, exon 1 of 36)	106	NM_001109041	16564	Mm.41379	NM_016705	ENSMUSG00000022629	Kif21a	-	kinesin family member 21A	protein-coding
mm_166025.1	chr4	124802602	124802610	+	1	NA	promoter-TSS (NM_008636)	promoter-TSS (NM_008636)	57	NM_008636	17764	Mm.272397	NM_008636	ENSMUSG00000028890	Mtf1	MTF-1|Thyls	metal response element binding transcription factor 1	protein-coding
mm_117247.1	chr13	64364057	64364138	-	1	NA	3' UTR (NM_009984, exon 8 of 8)	3' UTR (NM_009984, exon 8 of 8)	6423	NM_009984	13039	Mm.930	NM_009984	ENSMUSG00000021477	Ctsl	1190035F06Rik|CatL|Ctsl1|MEP|fs|nkt	cathepsin L	protein-coding
mm_168343.1	chr11	120784275	120784284	+	1	NA	promoter-TSS (NM_145370)	promoter-TSS (NM_145370)	7	NM_001177874	209318	Mm.30195	NM_145370	ENSMUSG00000025156	Gps1	Cops1|Csn1|R75577|Sgn1	G protein pathway suppressor 1	protein-coding
mm_126462.1	chr15	80977781	80977845	+	1	NA	promoter-TSS (NM_134091)	promoter-TSS (NM_134091)	48	NM_134091	105835	Mm.274943	NM_134091	ENSMUSG00000042303	Sgsm3	1810012I01Rik|AI428557|BB175482|Cip85|R75178|RUSC3|Rutbc3	small G protein signaling modulator 3	protein-coding
mm_89447.1	chr10	93124561	93124570	+	1	NA	Intergenic	Intergenic	-36311	NM_146239	237459	Mm.217404	NM_146239	ENSMUSG00000020015	Cdk17	6430598J10Rik|Pctk2	cyclin-dependent kinase 17	protein-coding
mm_73182.1	chr8	95081207	95081286	+	1	NA	promoter-TSS (NM_028805)	promoter-TSS (NM_028805)	45	NM_028805	74187	Mm.28382	NM_028805	ENSMUSG00000031787	Katnb1	2410003J24Rik|KAT	katanin p80 (WD40-containing) subunit B 1	protein-coding
mm_16838.1	chr2	11499914	11499927	-	1	NA	intron (NM_001177758, intron 1 of 14)	intron (NM_001177758, intron 1 of 14)	2170	NM_001177754	170768	Mm.19669	NM_133232	ENSMUSG00000026773	Pfkfb3	E330010H22Rik|iPFK-2|uPFK-2	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	protein-coding
mm_152173.1	chr19	7341793	7341829	-	1	NA	promoter-TSS (NM_001080388)	promoter-TSS (NM_001080388)	49	NM_001080389	13728	Mm.258986	NM_007928	ENSMUSG00000024969	Mark2	EMK-1|Emk|Par-1|Par-1b	MAP/microtubule affinity regulating kinase 2	protein-coding
mm_104674.1	chr11	97664757	97664766	-	1	NA	intron (NM_139311, intron 1 of 19)	intron (NM_139311, intron 1 of 19)	1349	NM_139311	246198	Mm.23685	NM_139311	ENSMUSG00000038437	Mllt6	AI315037|Af17	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 6	protein-coding
mm_107869.1	chr12	69907883	69907889	+	1	NA	5' UTR (NM_178628, exon 2 of 15)	5' UTR (NM_178628, exon 2 of 15)	-14723	NM_201519	399510	Mm.291936	NM_201519	ENSMUSG00000034761	Map4k5	4432415E19Rik|GCKR|KHS|MAPKKKK5	mitogen-activated protein kinase kinase kinase kinase 5	protein-coding
mm_104056.1	chr11	86544755	86544781	-	1	NA	promoter-TSS (NM_001199045)	promoter-TSS (NM_001199045)	39	NM_028259	72508	Mm.394280	NM_028259	ENSMUSG00000020516	Rps6kb1	2610318I15Rik|4732464A07Rik|70kDa|AA959758|AI256796|AI314060|S6K1|p70/85s6k|p70s6k	ribosomal protein S6 kinase, polypeptide 1	protein-coding
mm_99930.1	chr11	110997510	110997542	+	1	NA	promoter-TSS (NM_001252209)	promoter-TSS (NM_001252209)	39	NM_001252209	16517	Mm.30176	NM_010604	ENSMUSG00000051497	Kcnj16	6430410F18Rik|AI132396|Kir5.1	potassium inwardly-rectifying channel, subfamily J, member 16	protein-coding
mm_145976.1	chr18	67934748	67934750	+	1	NA	intron (NM_172631, intron 1 of 5)	intron (NM_172631, intron 1 of 5)	1492	NM_172631	52662	Mm.440183	NM_172631	ENSMUSG00000024544	Ldlrad4	8230401C20Rik|A430083H02|A430108L08Rik|C18orf1|D18Ertd653e|D330030L18Rik	low density lipoprotein receptor class A domain containing 4	protein-coding
mm_68413.1	chr7	109665697	109665699	-	1	NA	Intergenic	L1_Mur3|LINE|L1	-38039	NM_020616	57373	Mm.334138	NM_020616	ENSMUSG00000031023	Akip1	BCA3|C11orf17|D7H11orf17|D930014E17Rik|ICRFP703B1614Q5.6|ORF27	A kinase (PRKA) interacting protein 1	protein-coding
mm_159612.1	chr4	132144453	132144453	-	1	NA	promoter-TSS (NM_013622)	promoter-TSS (NM_013622)	33	NM_013622	18386	Mm.5243	NM_013622	ENSMUSG00000050511	Oprd1	DOR|DOR-1|Nbor|mDOR	opioid receptor, delta 1	protein-coding
mm_10995.1	chr2	26339426	26339451	+	1	NA	intron (NM_153410, intron 9 of 13)	intron (NM_153410, intron 9 of 13)	12672	NM_026828	52838	Mm.31239	NM_026828	ENSMUSG00000075467	Dnlz	1110034G11Rik|D2Bwg1335e|HEP1	DNL-type zinc finger	protein-coding
mm_169927.1	chr16	57391511	57391520	-	1	NA	intron (NM_001040397, intron 1 of 4)	LSU-rRNA_Hsa|rRNA|rRNA	38238	NM_001040397	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding
mm_109012.1	chr12	103355279	103355295	+	1	NA	intron (NM_023049, intron 1 of 9)	intron (NM_023049, intron 1 of 9)	714	NM_023049	65256	Mm.27159	NM_023049	ENSMUSG00000021200	Asb2	1110008E15Rik	ankyrin repeat and SOCS box-containing 2	protein-coding
mm_60502.1	chr7	44479366	44479406	+	1	NA	Intergenic	B1_Mus2|SINE|Alu	-5131	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_137340.1	chr17	25136421	25136465	+	1	NA	promoter-TSS (NM_001317404)	promoter-TSS (NM_001317404)	-188	NM_001317404	26373	Mm.270587	NM_011930	ENSMUSG00000036636	Clcn7	ClC-7|D17Wsu51e	chloride channel, voltage-sensitive 7	protein-coding
mm_63860.1	chr7	135683793	135683803	+	1	NA	3' UTR (NM_011212, exon 21 of 21)	3' UTR (NM_011212, exon 21 of 21)	-31484	NR_015548	67765	Mm.445272	NR_015548	ENSMUSG00000097471	5830432E09Rik	-	RIKEN cDNA 5830432E09 gene	ncRNA
mm_28389.1	chr3	90017610	90017613	-	1	NA	intron (NM_153489, intron 16 of 26)	intron (NM_153489, intron 16 of 26)	-6401	NR_106129	102465771		NR_106129	ENSMUSG00000098397	Mir7669	Gm27996|mmu-mir-7669	microRNA 7669	ncRNA
mm_162044.1	chr19	59219882	59219882	+	1	NA	exon (NM_207261, exon 1 of 3)	exon (NM_207261, exon 1 of 3)	234	NM_207261	332396	Mm.329947	NM_207261	ENSMUSG00000040901	Kcnk18	Gm781|Tresk|Tresk-2|Trik	potassium channel, subfamily K, member 18	protein-coding
mm_130901.1	chr15	102405545	102405573	-	1	NA	promoter-TSS (NM_013672)	promoter-TSS (NM_013672)	-757	NM_013672	20683	Mm.4618	NM_013672	ENSMUSG00000001280	Sp1	1110003E12Rik|AA450830|AI845540|Sp1-1	trans-acting transcription factor 1	protein-coding
mm_53088.1	chr6	125002083	125002096	+	1	NA	3' UTR (NM_001145926, exon 6 of 6)	3' UTR (NM_001145926, exon 6 of 6)	3479	NM_001145926	319352	Mm.295327	NM_175696	ENSMUSG00000030329	Pianp	AI255183|AU067746|C530028O21Rik|Panp	PILR alpha associated neural protein	protein-coding
mm_55779.1	chr6	81910449	81910470	-	1	NA	intron (NR_046040, intron 1 of 5)	intron (NR_046040, intron 1 of 5)	341	NR_046040	74220	Mm.490521	NR_046040	ENSMUSG00000101404	1700009C05Rik	-	RIKEN cDNA 1700009C05 gene	ncRNA
mm_69270.1	chr7	127929976	127929980	-	1	NA	5' UTR (NM_133351, exon 1 of 6)	5' UTR (NM_133351, exon 1 of 6)	135	NM_133351	76560	Mm.5875	NM_133351	ENSMUSG00000030800	Prss8	2410039E18Rik|AI313909|C79772|CAP1|fr|mCAP1	protease, serine 8 (prostasin)	protein-coding
mm_19920.1	chr2	115919785	115919787	-	1	NA	intron (NM_001346047, intron 10 of 13)	intron (NM_001346047, intron 10 of 13)	144833	NM_001346044	17536	Mm.247566	NM_010825	ENSMUSG00000027210	Meis2	A430109D20Rik|Mrg1|Stra10	Meis homeobox 2	protein-coding
mm_149651.1	chr19	18670725	18670779	+	1	NA	promoter-TSS (NM_026120)	promoter-TSS (NM_026120)	-28	NM_026120	67383	Mm.306602	NM_026120	ENSMUSG00000024726	Carnmt1	2410127L17Rik	carnosine N-methyltransferase 1	protein-coding
mm_95590.1	chr11	53330613	53330619	+	1	NA	intron (NM_026479, intron 2 of 3)	intron (NM_026479, intron 2 of 3)	5927	NM_026479	67966	Mm.288072	NM_026479	ENSMUSG00000018239	Zcchc10	2410141K03Rik|AA675321|D11Ertd416e	zinc finger, CCHC domain containing 10	protein-coding
mm_82277.1	chr9	7355416	7355426	-	1	NA	exon (NM_008605, exon 8 of 10)	exon (NM_008605, exon 8 of 10)	8047	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_31230.1	chr4	44300941	44301002	+	1	NA	promoter-TSS (NM_010790)	promoter-TSS (NM_010790)	54	NM_010790	17279	Mm.268668	NM_010790	ENSMUSG00000035683	Melk	AI327312|MPK38|mKIAA0175	maternal embryonic leucine zipper kinase	protein-coding
mm_147616.1	chr18	57533716	57533720	-	1	NA	promoter-TSS (NM_029290)	promoter-TSS (NM_029290)	34	NR_015541	74916	Mm.444721	NR_015541	ENSMUSG00000085800	1700066O22Rik	4930500F21Rik|4930515O13Rik|4930542C11Rik	RIKEN cDNA 1700066O22 gene	ncRNA
mm_51491.1	chr6	83057011	83057032	+	1	NA	promoter-TSS (NM_033606)	promoter-TSS (NM_033606)	-823	NM_033606	93838	Mm.140332	NM_033606	ENSMUSG00000009145	Dqx1	2310066E11Rik	DEAQ RNA-dependent ATPase	protein-coding
mm_98561.1	chr11	95339926	95339938	+	1	NA	intron (NM_172543, intron 1 of 7)	intron (NM_172543, intron 1 of 7)	2914	NM_172543	215512	Mm.262113	NM_172543	ENSMUSG00000038893	Fam117a	5730593F17Rik|AW548096	family with sequence similarity 117, member A	protein-coding
mm_135523.1	chr16	48874491	48874496	-	1	NA	TTS (NM_181596)	TTS (NM_181596)	1885	NM_181596	245195	Mm.231288	NM_181596	ENSMUSG00000022651	Retnlg	Fizz3|Relmg|Xcp1	resistin like gamma	protein-coding
mm_44211.1	chr5	4104632	4104642	-	1	NA	promoter-TSS (NM_020010)	promoter-TSS (NM_020010)	60	NM_020010	13121	Mm.140158	NM_020010	ENSMUSG00000001467	Cyp51	AI426508|CYPLI|Cyp51a1|Ldm|P450-14DM|P450LI	cytochrome P450, family 51	protein-coding
mm_117363.1	chr13	70827444	70827448	-	1	NA	intron (NM_172053, intron 3 of 22)	intron (NM_172053, intron 3 of 22)	14365	NM_172053	271127	Mm.115970	NM_172053	ENSMUSG00000049538	Adamts16	-	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 16	protein-coding
mm_73157.1	chr8	94995592	94995621	+	1	NA	intron (NM_018882, intron 1 of 13)	intron (NM_018882, intron 1 of 13)	11207	NM_018882	14766	Mm.290834	NM_018882	ENSMUSG00000031785	Adgrg1	Cyt28|Gpr56|TM7LN4|TM7XN1	adhesion G protein-coupled receptor G1	protein-coding
mm_118562.1	chr14	17981889	17981900	+	1	NA	exon (NM_009380, exon 1 of 7)	exon (NM_009380, exon 1 of 7)	250	NM_009380	21834	Mm.32563	NM_009380	ENSMUSG00000021779	Thrb	Nr1a2|T3R[b]|T3Rbeta|Thrb1|Thrb2|c-erbAbeta	thyroid hormone receptor beta	protein-coding
mm_114375.1	chr13	63117050	63117060	+	1	NA	intron (NM_001289926, intron 5 of 15)	MER45B|DNA|hAT-Tip100	-122974	NR_110520	72061	Mm.188105	NM_028079	ENSMUSG00000021458	2010111I01Rik	2300006M17Rik|AP-O|AW742919|Aopep|ApO|mir-23b|mir-24-1|mir-27b	RIKEN cDNA 2010111I01 gene	protein-coding
mm_37396.1	chr4	121098252	121098262	-	1	NA	promoter-TSS (NM_172700)	promoter-TSS (NM_172700)	-14	NM_172700	230709	Mm.34399	NM_172700	ENSMUSG00000043207	Zmpste24	A530043O15Rik|D030046F19|FACE1|Face-1|MADB|STE24|Ste24p	zinc metallopeptidase, STE24	protein-coding
mm_51609.1	chr6	84185746	84185774	+	1	NA	intron (NM_001077694, intron 41 of 54)	intron (NM_001077694, intron 41 of 54)	166374	NM_021469	26903	Mm.220982	NM_021469	ENSMUSG00000033788	Dysf	2310004N10Rik|AI604795|D6Pas3	dysferlin	protein-coding
mm_82922.1	chr9	35099109	35099119	-	1	NA	intron (NM_009178, intron 1 of 10)	intron (NM_009178, intron 1 of 10)	-17614	NR_029475	78934	Mm.391688	NR_029475	ENSMUSG00000070315	4930581F22Rik	-	RIKEN cDNA 4930581F22 gene	ncRNA
mm_101639.1	chr11	36432994	36433014	-	1	NA	intron (NM_011856, intron 2 of 28)	intron (NM_011856, intron 2 of 28)	-452915	NM_170779	211652	Mm.31267	NM_170779	ENSMUSG00000018849	Wwc1	AA408228|AU017197|BC037006|Kibra|mKIAA0869	WW, C2 and coiled-coil domain containing 1	protein-coding
mm_142522.1	chr17	46282992	46283026	-	1	NA	promoter-TSS (NM_028751)	promoter-TSS (NM_028751)	17	NM_001252475	74094	Mm.284594	NM_028751	ENSMUSG00000012296	Tjap1	0610041D19Rik|AI415281|AW121008|Pilt|Tjp4	tight junction associated protein 1	protein-coding
mm_79176.1	chr9	47893259	47893307	+	1	NA	Intergenic	MLT1J1|LTR|ERVL-MaLR	-75075	NR_046048	100038460	Mm.447649	NR_046048		Gm10677	ENSMUSG00000074363	predicted gene 10677	ncRNA
mm_73307.1	chr8	105170729	105170759	+	1	NA	promoter-TSS (NM_001161458)	promoter-TSS (NM_001161458)	70	NM_001161458	12400	Mm.2018	NM_022309	ENSMUSG00000031885	Cbfb	AI893578|PEA2|PEBP2b|Pebp2|Pebpb2	core binding factor beta	protein-coding
mm_101466.1	chr11	30573116	30573144	-	1	NA	intron (NM_029344, intron 3 of 3)	intron (NM_029344, intron 3 of 3)	76266	NM_029344	75572	Mm.390319	NM_029344	ENSMUSG00000060923	Acyp2	2310004B09Rik	acylphosphatase 2, muscle type	protein-coding
mm_120161.1	chr14	60732995	60733009	+	1	NA	promoter-TSS (NM_001310594)	promoter-TSS (NM_001310594)	98	NM_001310594	219140	Mm.149776	NM_001033272	ENSMUSG00000021990	Spata13	C79050|ESTM11|X83327|mFLJ00298	spermatogenesis associated 13	protein-coding
mm_145618.1	chr18	61105845	61105890	+	1	NA	5' UTR (NM_001037859, exon 2 of 22)	5' UTR (NM_001037859, exon 2 of 22)	295	NM_001037859	12978	Mm.22574	NM_007779	ENSMUSG00000024621	Csf1r	AI323359|CD115|CSF-1R|Csfmr|Fim-2|Fim2|Fms|M-CSF-R|M-CSFR	colony stimulating factor 1 receptor	protein-coding
mm_25743.1	chr3	122984694	122984722	+	1	NA	promoter-TSS (NM_133857)	promoter-TSS (NM_133857)	-261	NM_133857	99526	Mm.491248	NM_133857	ENSMUSG00000039701	Usp53	AA939927|Phxr3|Sp6|mKIAA1350|mbo	ubiquitin specific peptidase 53	protein-coding
mm_149156.1	chr19	9015701	9015728	+	1	NA	exon (NM_009643, exon 5 of 5)	exon (NM_009643, exon 5 of 5)	-2190	NR_105786	102465190		NR_105786	ENSMUSG00000099308	Mir6367	Gm27467|mmu-mir-6367	microRNA 6367	ncRNA
mm_82593.1	chr9	21239311	21239339	-	1	NA	promoter-TSS (NM_016679)	promoter-TSS (NM_016679)	7	NM_016679	50868	Mm.248266	NM_016679	ENSMUSG00000003308	Keap1	INRF2|mKIAA0132	kelch-like ECH-associated protein 1	protein-coding
mm_104802.1	chr11	98775087	98775104	-	1	NA	5' UTR (NM_145434, exon 1 of 8)	5' UTR (NM_145434, exon 1 of 8)	282	NM_145434	217166	Mm.390397	NM_145434	ENSMUSG00000020889	Nr1d1	A530070C09Rik|R75201	nuclear receptor subfamily 1, group D, member 1	protein-coding
mm_127226.1	chr15	99399770	99399803	+	1	NA	5' UTR (NM_001171034, exon 2 of 11)	5' UTR (NM_001171034, exon 2 of 11)	6567	NM_001171035	110213	Mm.16769	NM_026669	ENSMUSG00000023010	Tmbim6	5031406P05Rik|Bi1|Tegt	transmembrane BAX inhibitor motif containing 6	protein-coding
mm_50165.1	chr6	41553565	41553595	+	1	NA	Intergenic	L3b|LINE|CR1	31804	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_56400.1	chr6	97060408	97060420	-	1	NA	promoter-TSS (NM_177233)	promoter-TSS (NM_177233)	-3	NM_177233	320701	Mm.131700	NM_177233	ENSMUSG00000046500	Fam19a4	C130034I18Rik|Fam19a4 Tafa-4|Tafa-4	family with sequence similarity 19, member A4	protein-coding
mm_31236.1	chr4	44701601	44701642	+	1	NA	intron (NM_008782, intron 1 of 9)	intron (NM_008782, intron 1 of 9)	-1179	NR_073462	70602	Mm.491142	NR_073462	ENSMUSG00000103995	5730488B01Rik	-	RIKEN cDNA 5730488B01 gene	ncRNA
mm_149912.1	chr19	26605126	26605156	+	1	NA	promoter-TSS (NM_011416)	promoter-TSS (NM_011416)	-19	NM_011416	67155	Mm.342988	NM_011416	ENSMUSG00000024921	Smarca2	2610209L14Rik|SNF2alpha|Snf2l2|brahma|brm	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	protein-coding
mm_103432.1	chr11	75796033	75796037	-	1	NA	promoter-TSS (NM_007873)	promoter-TSS (NM_007873)	25	NM_007873	13447	Mm.5137	NM_007873	ENSMUSG00000020848	Doc2b	-	double C2, beta	protein-coding
mm_67332.1	chr7	79742986	79742996	-	1	NA	promoter-TSS (NM_001037927)	promoter-TSS (NM_001037927)	34	NM_011068	18631	Mm.20615	NM_011068	ENSMUSG00000030545	Pex11a	PEX11alpha	peroxisomal biogenesis factor 11 alpha	protein-coding
mm_150407.1	chr19	36879261	36879279	+	1	NA	exon (NM_001163635, exon 19 of 27)	exon (NM_001163635, exon 19 of 27)	40329	NM_028263	72514	Mm.41674	NM_028263	ENSMUSG00000047632	Fgfbp3	2610306H15Rik|Fgf-bp3	fibroblast growth factor binding protein 3	protein-coding
mm_51858.1	chr6	90466282	90466292	+	1	NA	intron (NM_023184, intron 1 of 2)	intron (NM_023184, intron 1 of 2)	3661	NM_023184	66277	Mm.38343	NM_023184	ENSMUSG00000030087	Klf15	1810013I09Rik|AV048136|AW494632|CKLF|KKLF	Kruppel-like factor 15	protein-coding
mm_53356.1	chr6	129351424	129351437	+	1	NA	intron (NM_177686, intron 1 of 5)	intron (NM_177686, intron 1 of 5)	1186	NM_177686	232413	Mm.90241	NM_177686	ENSMUSG00000053063	Clec12a	CLL-1|D230024O04|KLRL1|Micl	C-type lectin domain family 12, member a	protein-coding
mm_148632.1	chr19	5460609	5460638	+	1	NA	promoter-TSS (NM_021438)	promoter-TSS (NM_021438)	16	NM_021438	58249	Mm.329656	NM_021438	ENSMUSG00000024911	Fibp	2010004G08Rik|2010005N21Rik|3010027N18Rik	fibroblast growth factor (acidic) intracellular binding protein	protein-coding
mm_139397.1	chr17	52304523	52304537	+	1	NA	Intergenic	Intergenic	-298179	NM_001031811	211468	Mm.399068	NM_001031811	ENSMUSG00000035580	Kcnh8	C130090D05Rik|ELK|ELK1|ELK3|Kv12.1	potassium voltage-gated channel, subfamily H (eag-related), member 8	protein-coding
mm_35224.1	chr4	19680353	19680383	-	1	NA	intron (NR_074089, intron 2 of 23)	intron (NR_074089, intron 2 of 23)	28636	NM_177327	107568	Mm.78312	NM_177327	ENSMUSG00000041058	Wwp1	8030445B08Rik|AIP5|SDRP1|Tiul1	WW domain containing E3 ubiquitin protein ligase 1	protein-coding
mm_56952.1	chr6	119992501	119992511	-	1	NA	exon (NM_001185020, exon 3 of 26)	exon (NM_001185020, exon 3 of 26)	41805	NR_030487	735290		NR_030487	ENSMUSG00000076217	Mir706	Mirn706|mir-706|mmu-mir-706	microRNA 706	ncRNA
mm_76900.1	chr8	105826306	105826332	-	1	NA	intron (NM_145824, intron 1 of 13)	intron (NM_145824, intron 1 of 13)	1031	NM_145824	74334	Mm.4206	NM_145824	ENSMUSG00000037415	Ranbp10	4432417N03Rik	RAN binding protein 10	protein-coding
mm_62521.1	chr7	102230152	102230167	+	1	NA	intron (NR_111937, intron 2 of 5)	intron (NR_111937, intron 2 of 5)	7131	NR_111937	233575	Mm.302013	NM_145583	ENSMUSG00000030990	Pgap2	1810006G21Rik|C76649|Frag1	post-GPI attachment to proteins 2	protein-coding
mm_53741.1	chr6	145145474	145145483	+	1	NA	intron (NM_008511, intron 3 of 18)	intron (NM_008511, intron 3 of 18)	23739	NM_008511	16970	Mm.843	NM_008511	ENSMUSG00000030263	Lrmp	D6Int3|D6Int4|D6Int5|D6Int7|D6Int8|Jaw1	lymphoid-restricted membrane protein	protein-coding
mm_104021.1	chr11	85775656	85775688	-	1	NA	promoter-TSS (NR_046194)	promoter-TSS (NR_046194)	8	NR_046194	78420	Mm.488197	NR_046194	ENSMUSG00000085514	Bcas3os2	9530048J24Rik	breast carcinoma amplified sequence 3 opposite strand 2	ncRNA
mm_86804.1	chr10	20320149	20320149	+	1	NA	intron (NM_001025392, intron 2 of 12)	Tigger2b|DNA|TcMar-Tigger	7680	NM_001025393	72567	Mm.294783	NM_153787	ENSMUSG00000037608	Bclaf1	2610102K23Rik|2700025J07Rik|2810454G14Rik|5730534O06Rik|AI450190|AW556225|Btf|mKIAA0164	BCL2-associated transcription factor 1	protein-coding
mm_69984.1	chr7	142380891	142380899	-	1	NA	exon (NM_009983, exon 5 of 9)	exon (NM_009983, exon 5 of 9)	6975	NM_009983	13033	Mm.231395	NM_009983	ENSMUSG00000007891	Ctsd	CD|CatD	cathepsin D	protein-coding
mm_130235.1	chr15	96474448	96474468	-	1	NA	Intergenic	Intergenic	-13615	NM_028148	72193	Mm.324474	NM_028148	ENSMUSG00000033228	Scaf11	1110061H03Rik|2610510E10Rik|AI462454|CASP11|SIP1|SRRP129|Sfrs2ip|Srsf2ip|mKIAA3013	SR-related CTD-associated factor 11	protein-coding
mm_43687.1	chr5	138976975	138977016	+	1	NA	TTS (NM_008808)	TTS (NM_008808)	17958	NM_008808	18590	Mm.2675	NM_008808	ENSMUSG00000025856	Pdgfa	-	platelet derived growth factor, alpha	protein-coding
mm_22212.1	chr2	174285165	174285184	-	1	NA	exon (NM_022000, exon 2 of 13)	exon (NM_022000, exon 2 of 13)	854	NM_022000	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_530.1	chr1	37872334	37872371	+	1	NA	intron (NM_001037918, intron 1 of 1)	intron (NM_001037918, intron 1 of 1)	146	NM_001037918	623661	Mm.138000	NM_001037918	ENSMUSG00000037216	Lipt1	EG623661	lipoyltransferase 1	protein-coding
mm_92814.1	chr10	81427123	81427179	-	1	NA	promoter-TSS (NM_008688)	promoter-TSS (NM_008688)	22	NM_008688	18029	Mm.426936	NM_008688	ENSMUSG00000055053	Nfic	1110019L22Rik|1500041O16Rik|AA589446|AI746521|NF1-C	nuclear factor I/C	protein-coding
mm_121238.1	chr14	103056205	103056239	+	1	NA	3' UTR (NM_008392, exon 5 of 5)	3' UTR (NM_008392, exon 5 of 5)	9210	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_85653.1	chr9	107658969	107658985	-	1	NA	exon (NM_001199218, exon 3 of 16)	exon (NM_001199218, exon 3 of 16)	8422	NM_023805	76257	Mm.296560	NM_023805	ENSMUSG00000010064	Slc38a3	0610012J02Rik|D9Ucla2|Nat1|Slc38-3|Sn1|Snat3|mNAT	solute carrier family 38, member 3	protein-coding
mm_18860.1	chr2	75703976	75703991	-	1	NA	intron (NR_132727, intron 1 of 1)	CpG	680	NR_132727	18024	Mm.1025	NM_010902	ENSMUSG00000015839	Nfe2l2	Nrf2	nuclear factor, erythroid derived 2, like 2	protein-coding
mm_155918.1	chrX	102050808	102050821	+	1	NA	intron (NM_001163610, intron 1 of 7)	intron (NM_001163610, intron 1 of 7)	20493	NM_001278534	331474	Mm.23297	NM_183318	ENSMUSG00000049191	Rgag4	6430402L03Rik|Mar5|Mart5|mKIAA2001	retrotransposon gag domain containing 4	protein-coding
mm_40616.1	chr5	64803482	64803499	+	1	NA	promoter-TSS (NM_008453)	promoter-TSS (NM_008453)	-33	NM_008453	16599	Mm.392759	NM_008453	ENSMUSG00000029178	Klf3	9930027G08Rik|AL024007|Bklf|Tef-2	Kruppel-like factor 3 (basic)	protein-coding
mm_133800.1	chr16	95297891	95297900	+	1	NA	non-coding (NR_073406, exon 6 of 6)	non-coding (NR_073406, exon 6 of 6)	40337	NM_001271690	16516	Mm.272239	NM_019664	ENSMUSG00000062609	Kcnj15	4930414N08Rik|AI182284|AI267127|IRKK|Kir4.2	potassium inwardly-rectifying channel, subfamily J, member 15	protein-coding
mm_127939.1	chr15	10589161	10589176	-	1	NA	intron (NM_001166408, intron 11 of 17)	intron (NM_001166408, intron 11 of 17)	-11125	NR_033541	100038608	Mm.450744	NR_033541		Gm10389	ENSMUSG00000072658	predicted gene 10389	ncRNA
mm_38084.1	chr4	134154388	134154415	-	1	NA	intron (NM_144527, intron 4 of 13)	intron (NM_144527, intron 4 of 13)	-25648	NM_080559	73723	Mm.22240	NM_080559	ENSMUSG00000028843	Sh3bgrl3	1110004L05Rik|AU022188	SH3 domain binding glutamic acid-rich protein-like 3	protein-coding
mm_153940.1	chr19	47464580	47464635	-	1	NA	promoter-TSS (NM_008018)	promoter-TSS (NM_008018)	-196	NM_008018	14218	Mm.127560	NM_008018	ENSMUSG00000053617	Sh3pxd2a	2310014D11Rik|AA589508|AI256723|AI413738|C230050L11|EG329070|Fish|Gm5098|Sh3md1|TSK5|Tks5	SH3 and PX domains 2A	protein-coding
mm_127664.1	chr15	102520819	102520838	+	1	NA	intron (NM_009319, intron 3 of 8)	intron (NM_009319, intron 3 of 8)	2636	NM_009319	21357	Mm.291485	NM_009319	ENSMUSG00000023051	Tarbp2	Prbp|TRBP	TARBP2, RISC loading complex RNA binding subunit	protein-coding
mm_158803.1	chrX	167255140	167255142	-	1	NA	intron (NM_001313761, intron 1 of 2)	L1VL4|LINE|L1	9188	NM_001313761	170744	Mm.196676	NM_133212	ENSMUSG00000040522	Tlr8	-	toll-like receptor 8	protein-coding
mm_136762.1	chr17	8801707	8801721	+	1	NA	promoter-TSS (NM_011866)	promoter-TSS (NM_011866)	-31	NM_011866	23984	Mm.87161	NM_011866	ENSMUSG00000023868	Pde10a	-	phosphodiesterase 10A	protein-coding
mm_173283.1	chrY	1641671	1641680	+	1	NA	Intergenic	L1Md_T|LINE|L1	-181893	NM_148943	107868	Mm.347376	NM_148943	ENSMUSG00000069044	Usp9y	Dffry|Fafl2	ubiquitin specific peptidase 9, Y chromosome	protein-coding
mm_68489.1	chr7	111074478	111074514	-	1	NA	exon (NM_013507, exon 19 of 22)	exon (NM_013507, exon 19 of 22)	8534	NM_001040131	13690	Mm.185453	NM_013507	ENSMUSG00000005610	Eif4g2	DAP-5|E130105L11Rik|Nat1|Natm1|p97	eukaryotic translation initiation factor 4, gamma 2	protein-coding
mm_105212.1	chr11	102163554	102163557	-	1	NA	TTS (NM_172947)	TTS (NM_172947)	-7148	NM_029649	76547	Mm.46529	NM_029649	ENSMUSG00000020921	Tmem101	2610511E22Rik	transmembrane protein 101	protein-coding
mm_33942.1	chr4	136953026	136953031	+	1	NA	intron (NM_007939, intron 1 of 16)	intron (NM_007939, intron 1 of 16)	3788	NM_007939	13842	Mm.1390	NM_007939	ENSMUSG00000028661	Epha8	AW047546|Eek|Hek3|mKIAA1459	Eph receptor A8	protein-coding
mm_168549.1	chr1	162893378	162893378	-	1	NA	intron (NM_018881, intron 2 of 8)	intron (NM_018881, intron 2 of 8)	5334	NM_018881	55990	Mm.10929	NM_018881	ENSMUSG00000040170	Fmo2	2310008D08Rik|2310042I22Rik|AW107733	flavin containing monooxygenase 2	protein-coding
mm_94061.1	chr10	128368891	128368897	-	1	NA	5' UTR (NM_001081040, exon 1 of 5)	5' UTR (NM_001081040, exon 1 of 5)	1143	NM_001081040	210582	Mm.296876	NM_001081040	ENSMUSG00000039914	Coq10a	Gm1	coenzyme Q10A	protein-coding
mm_56508.1	chr6	99339464	99339484	-	1	NA	intron (NM_001347345, intron 2 of 19)	intron (NM_001347345, intron 2 of 19)	-72959	NM_001197321	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_160868.1	chr11	62438459	62438459	-	1	NA	promoter-TSS (NM_001252313)	promoter-TSS (NM_001252313)	56	NM_001252313	20185	Mm.271814	NM_011308	ENSMUSG00000018501	Ncor1	5730405M06Rik|A230020K14Rik|N-CoR|RIP13|Rxrip13|mKIAA1047	nuclear receptor co-repressor 1	protein-coding
mm_77406.1	chr8	120537767	120537782	-	1	NA	promoter-TSS (NR_106159)	promoter-TSS (NR_106159)	365	NM_001145896	382034	Mm.334856	NM_198671	ENSMUSG00000031822	Gse1	2210013I18Rik|mKIAA0182	genetic suppressor element 1, coiled-coil protein	protein-coding
mm_1829.1	chr1	82718933	82718938	+	1	NA	3' UTR (NM_007734, exon 52 of 52)	3' UTR (NM_007734, exon 52 of 52)	-5955	NM_001310697	75734	Mm.396863	NM_029409	ENSMUSG00000026150	Mff	5230400G24Rik|AI314724	mitochondrial fission factor	protein-coding
mm_70635.1	chr8	13869674	13869740	+	1	NA	promoter-TSS (NM_181854)	promoter-TSS (NM_181854)	66	NM_181854	101994	Mm.289346	NM_181854	ENSMUSG00000047710	Champ1	AA675043|AI116001|D8Ertd457e|D8Ertd569e|Zfp828|Znf828|mKIAA1802	chromosome alignment maintaining phosphoprotein 1	protein-coding
mm_145885.1	chr18	65580757	65580798	+	1	NA	intron (NM_207255, intron 1 of 5)	CpG	547	NM_207255	328977	Mm.286232	NM_207255	ENSMUSG00000042439	Zfp532	C530030I18Rik|Znf532|mKIAA1629	zinc finger protein 532	protein-coding
mm_16343.1	chr2	174345393	174345451	+	1	NA	non-coding (NR_003258, exon 10 of 13)	non-coding (NR_003258, exon 10 of 13)	15333	NM_001077510	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_8519.1	chr1	154816957	154816973	-	1	NA	Intergenic	Intergenic	-91045	NM_009782	12290	Mm.267517	NM_009782	ENSMUSG00000004110	Cacna1e	A430040I15|BII|Cach6|Cacnl1a6|Cav2.3|Cchra1|alpha1E	calcium channel, voltage-dependent, R type, alpha 1E subunit	protein-coding
mm_59025.1	chr7	19291135	19291139	+	1	NA	promoter-TSS (NM_001025364)	promoter-TSS (NM_001025364)	68	NM_001025364	20167	Mm.24142	NM_013648	ENSMUSG00000030401	Rtn2	MMS10-P|Ms10p|NSPLI|Nspl1	reticulon 2 (Z-band associated protein)	protein-coding
mm_159225.1	chr2	130295874	130295874	+	1	NA	promoter-TSS (NM_001110513)	promoter-TSS (NM_001110513)	-65	NM_001110513	228598	Mm.32582	NM_152993	ENSMUSG00000053552	Ebf4	Ebf3|O/E-4|Olf-1	early B cell factor 4	protein-coding
mm_20123.1	chr2	121271316	121271322	-	1	NA	promoter-TSS (NM_013735)	promoter-TSS (NM_013735)	88	NM_001290830	27223	Mm.215389	NM_013735	ENSMUSG00000043909	Trp53bp1	53BP1|Tp53bp1|m53BP1|p53BP1	transformation related protein 53 binding protein 1	protein-coding
mm_6991.1	chr1	86357421	86357434	-	1	NA	exon (NM_010880, exon 3 of 14)	exon (NM_010880, exon 3 of 14)	-1100	NR_002851	80828		NR_002851	ENSMUSG00000064823	Snord82	Rnu82|U82|Z25	small nucleolar RNA, C/D box 82	snoRNA
mm_25442.1	chr3	108186411	108186424	+	1	NA	5' UTR (NM_001287093, exon 1 of 3)	5' UTR (NM_001287093, exon 1 of 3)	128	NM_001287093	229715	Mm.275752	NM_146137	ENSMUSG00000050947	Amigo1	Amigo|ali2	adhesion molecule with Ig like domain 1	protein-coding
mm_118415.1	chr14	7791489	7791493	+	1	NA	Intergenic	CpG	-26466	NM_001081427	286940	Mm.489652	NM_134080	ENSMUSG00000025278	Flnb	AL024016|Fln-b	filamin, beta	protein-coding
mm_18146.1	chr2	45066627	45066646	-	1	NA	intron (NM_001289521, intron 1 of 8)	intron (NM_001289521, intron 1 of 8)	-43459	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_33584.1	chr4	132544703	132544714	+	1	NA	exon (NM_172400, exon 5 of 9)	exon (NM_172400, exon 5 of 9)	9149	NM_172400	68598	Mm.29685	NM_172400	ENSMUSG00000054405	Dnajc8	1110021D09Rik|2010009J04Rik|AL024084|AU019262|AU044514	DnaJ heat shock protein family (Hsp40) member C8	protein-coding
mm_70091.1	chr7	142656122	142656167	-	1	NA	intron (NM_001315488, intron 1 of 3)	intron (NM_001315488, intron 1 of 3)	-1148	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_37156.1	chr4	117125637	117125683	-	1	NA	promoter-TSS (NR_024078)	promoter-TSS (NR_024078)	65	NR_024078	78611	Mm.446227	NM_001033187		Btbd19	9530048O09Rik|BB115071	BTB (POZ) domain containing 19	ncRNA
mm_115977.1	chr13	24206261	24206269	-	1	NA	intron (NM_001311122, intron 2 of 37)	intron (NM_001311122, intron 2 of 37)	74525	NM_001311122	68732	Mm.211047	NM_026825	ENSMUSG00000021338	Carmil1	1110037D04Rik|AI425970|CARMIL|CARML1|D130057M20|Lrrc16|Lrrc16a	capping protein regulator and myosin 1 linker 1	protein-coding
mm_131777.1	chr16	22895177	22895192	+	1	NA	promoter-TSS (NR_110508)	promoter-TSS (NR_110508)	-798	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_58961.1	chr7	18925918	18925924	+	1	NA	promoter-TSS (NM_001029877)	promoter-TSS (NM_001029877)	33	NM_001029877	384569	Mm.262724	NM_001029877	ENSMUSG00000030411	Nova2	Gm1424	neuro-oncological ventral antigen 2	protein-coding
mm_146258.1	chr18	77794558	77794610	+	1	NA	promoter-TSS (NM_013831)	promoter-TSS (NM_013831)	34	NM_013831	19201	Mm.57174	NM_013831	ENSMUSG00000025429	Pstpip2	MAYP|cmo	proline-serine-threonine phosphatase-interacting protein 2	protein-coding
mm_2732.1	chr1	128244258	128244325	+	1	NA	5' UTR (NM_026390, exon 1 of 13)	5' UTR (NM_026390, exon 1 of 13)	110	NM_026390	67812	Mm.293321	NM_026390	ENSMUSG00000026353	Ubxn4	1300013G12Rik|Ubxd2|mKIAA0242	UBX domain protein 4	protein-coding
mm_103814.1	chr11	83003057	83003076	-	1	NA	3' UTR (NM_001167743, exon 4 of 4)	3' UTR (NM_001167743, exon 4 of 4)	-11236	NM_172796	237886	Mm.270253	NM_172796	ENSMUSG00000069793	Slfn9	9830137M10Rik	schlafen 9	protein-coding
mm_171215.1	chr3	59286879	59286880	-	1	NA	intron (NM_177855, intron 38 of 43)	L1Md_A|LINE|L1	-24048	NM_027571	70839	Mm.422675	NM_027571	ENSMUSG00000036353	P2ry12	2900079B22Rik|4921504D23Rik|P2Y12	purinergic receptor P2Y, G-protein coupled 12	protein-coding
mm_28566.1	chr3	93444953	93444963	-	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	2628	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_41793.1	chr5	103753613	103753618	+	1	NA	promoter-TSS (NM_133919)	promoter-TSS (NM_133919)	-547	NM_133919	17355	Mm.6949	NM_133919	ENSMUSG00000029313	Aff1	9630032B01Rik|AW319193|Af4|Mllt2h|Rob	AF4/FMR2 family, member 1	protein-coding
mm_45012.1	chr5	38521490	38521498	-	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	-19342	NM_145559	117591	Mm.260137	NM_145559	ENSMUSG00000005107	Slc2a9	Glut9|SLC2A9B|SLC2a9A	solute carrier family 2 (facilitated glucose transporter), member 9	protein-coding
mm_121495.1	chr14	121878592	121878728	+	1	NA	promoter-TSS (NM_026861)	promoter-TSS (NM_026861)	54	NM_026861	68889	Mm.441151	NM_026861	ENSMUSG00000041765	Ubac2	1190008A14Rik|AW554959|Phgdhl1	ubiquitin associated domain containing 2	protein-coding
mm_172687.1	chr8	57511957	57511959	+	1	NA	5' UTR (NM_008252, exon 1 of 5)	5' UTR (NM_008252, exon 1 of 5)	115	NM_008252	97165	Mm.276881	NM_008252	ENSMUSG00000054717	Hmgb2	C80539|HMG-2|Hmg2	high mobility group box 2	protein-coding
mm_69277.1	chr7	127982027	127982030	-	1	NA	TTS (NM_139149)	TTS (NM_139149)	11839	NM_023258	66824	Mm.24163	NM_023258	ENSMUSG00000030793	Pycard	9130417A21Rik|Asc|CARD5|TMS-1|TNS1|masc	PYD and CARD domain containing	protein-coding
mm_42308.1	chr5	114851793	114851818	+	1	NA	promoter-TSS (NR_105748)	promoter-TSS (NR_105748)	-143	NR_105748	102466620		NR_105748	ENSMUSG00000098343	Mir6240	Gm27850|mmu-mir-6240	microRNA 6240	ncRNA
mm_104907.1	chr11	99650235	99650237	-	1	NA	Intergenic	Intergenic	-6147	NM_029613	76444	Mm.348022	NM_029613	ENSMUSG00000045109	Krtap4-7	2310037K05Rik|KAP4.7|KRTAP4.7	keratin associated protein 4-7	protein-coding
mm_156808.1	chrX	163927634	163927668	+	1	NA	3' UTR (NM_026887, exon 5 of 5)	3' UTR (NM_026887, exon 5 of 5)	18634	NM_001290379	108012	Mm.426783	NM_026887	ENSMUSG00000031367	Ap1s2	1500012A13Rik|AI853648|EST1	adaptor-related protein complex 1, sigma 2 subunit	protein-coding
mm_82029.1	chr9	121937286	121937297	+	1	NA	promoter-TSS (NR_033553)	promoter-TSS (NR_033553)	16	NR_033553	69430	Mm.482910	NR_033553	ENSMUSG00000043773	1700048O20Rik	1700022O21Rik	RIKEN cDNA 1700048O20 gene	ncRNA
mm_26648.1	chr3	153973626	153973690	+	1	NA	5' UTR (NM_001081263, exon 1 of 22)	5' UTR (NM_001081263, exon 1 of 22)	222	NM_001081263	242259	Mm.239962	NM_001081263	ENSMUSG00000028360	Slc44a5	AA117069|Gm422	solute carrier family 44, member 5	protein-coding
mm_93401.1	chr10	107719979	107719989	-	1	NA	promoter-TSS (NM_001081432)	promoter-TSS (NM_001081432)	43	NM_001081432	237523	Mm.391418	NM_001081432	ENSMUSG00000035916	Ptprq	-	protein tyrosine phosphatase, receptor type, Q	protein-coding
mm_117352.1	chr13	69739419	69739437	-	1	NA	5' UTR (NM_001145162, exon 1 of 2)	5' UTR (NM_001145162, exon 1 of 2)	469	NM_001145162	76980	Mm.23960	NM_001145162	ENSMUSG00000052981	Ube2ql1	3110006E14Rik	ubiquitin-conjugating enzyme E2Q family-like 1	protein-coding
mm_35204.1	chr4	19521563	19521597	-	1	NA	3' UTR (NM_027769, exon 16 of 16)	3' UTR (NM_027769, exon 16 of 16)	48524	NM_027769	70568	Mm.38390	NM_027769	ENSMUSG00000028228	Cpne3	5430428M23Rik|5730450C07Rik|C85108|CPN3	copine III	protein-coding
mm_76950.1	chr8	105990721	105990748	-	1	NA	exon (NM_176913, exon 2 of 12)	exon (NM_176913, exon 2 of 12)	1039	NM_001301204	319446	Mm.248357	NM_176913	ENSMUSG00000053687	Dpep2	F630103D06Rik|MBD-2	dipeptidase 2	protein-coding
mm_8090.1	chr1	135688095	135688149	-	1	NA	Intergenic	CpG	-41075	NM_007791	13007	Mm.196484	NM_007791	ENSMUSG00000026421	Csrp1	AA408841|AA959891|AW545626|CRP1|Csrp	cysteine and glycine-rich protein 1	protein-coding
mm_124944.1	chr15	12321617	12321625	+	1	NA	5' UTR (NM_025673, exon 1 of 4)	5' UTR (NM_025673, exon 1 of 4)	125	NM_025673	66629	Mm.157655	NM_025673	ENSMUSG00000022200	Golph3	4733401N08Rik|5730410D03Rik|AW413496	golgi phosphoprotein 3	protein-coding
mm_128094.1	chr15	27788571	27788589	-	1	NA	intron (NM_001081302, intron 34 of 56)	intron (NM_001081302, intron 34 of 56)	-107038	NM_001242423	223433	Mm.266485	NM_198301	ENSMUSG00000056069	Fam105a	9830126M18	family with sequence similarity 105, member A	protein-coding
mm_84868.1	chr9	78937071	78937072	-	1	NA	Intergenic	Intergenic	321525	NM_153098	235505	Mm.32955	NM_153098	ENSMUSG00000046186	Cd109	9930012E15Rik|AI480638|GARP	CD109 antigen	protein-coding
mm_117586.1	chr13	89662057	89662067	-	1	NA	intron (NM_001081249, intron 12 of 14)	intron (NM_001081249, intron 12 of 14)	80450	NM_001081249	13003	Mm.158700	NM_019389	ENSMUSG00000021614	Vcan	5430420N07Rik|9430051N09|Cspg2|DPEAAE|NG2|PG-M|PG-M(V0)|PG-M(V1)|hdf	versican	protein-coding
mm_141555.1	chr17	32211203	32211245	-	1	NA	exon (NM_001286630, exon 12 of 20)	exon (NM_001286630, exon 12 of 20)	-21675	NM_001347341	71932	Mm.176240	NM_001033163	ENSMUSG00000037577	Ephx3	2310063B19Rik|Abhd9	epoxide hydrolase 3	protein-coding
mm_70329.1	chr8	4391674	4391675	+	1	NA	Intergenic	Intergenic	42086	NM_009138	20300	Mm.7275	NM_009138	ENSMUSG00000023235	Ccl25	A130072A22Rik|AI852536|CKb15|Scya25|TECK	chemokine (C-C motif) ligand 25	protein-coding
mm_29447.1	chr3	110250964	110251015	-	1	NA	promoter-TSS (NM_178891)	promoter-TSS (NM_178891)	10	NM_178891	99890	Mm.36115	NM_178891	ENSMUSG00000049300	Prmt6	AW124876|BB233495|Hrmt1l6	protein arginine N-methyltransferase 6	protein-coding
mm_153694.1	chr19	44397276	44397312	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	10415	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_5675.1	chr1	43141856	43141872	-	1	NA	exon (NM_001289533, exon 3 of 6)	exon (NM_001289533, exon 3 of 6)	22097	NM_010212	14200	Mm.6799	NM_010212	ENSMUSG00000008136	Fhl2	FHL-2|SLIM-3|SLIM3	four and a half LIM domains 2	protein-coding
mm_109153.1	chr12	108002052	108002055	+	1	NA	intron (NM_001079883, intron 1 of 3)	intron (NM_001079883, intron 1 of 3)	1361	NM_001079883	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_47969.1	chr5	135908889	135909006	-	1	NA	3' UTR (NM_018871, exon 2 of 2)	3' UTR (NM_018871, exon 2 of 2)	21028	NM_013560	15507	Mm.13849	NM_013560	ENSMUSG00000004951	Hspb1	27kDa|Hsp25	heat shock protein 1	protein-coding
mm_112197.1	chr12	113425793	113425838	-	1	NA	Intergenic	Intergenic	-63750	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_153041.1	chr19	32061385	32061413	-	1	NA	5' UTR (NM_018830, exon 3 of 24)	5' UTR (NM_018830, exon 3 of 24)	41741	NM_018830	54447	Mm.491229	NM_018830	ENSMUSG00000024887	Asah2	AI585898	N-acylsphingosine amidohydrolase 2	protein-coding
mm_53524.1	chr6	136520404	136520407	+	1	NA	intron (NM_019426, intron 1 of 14)	intron (NM_019426, intron 1 of 14)	1554	NM_019426	54343	Mm.173271	NM_019426	ENSMUSG00000030213	Atf7ip	2610204M12Rik|AM|Mcaf1	activating transcription factor 7 interacting protein	protein-coding
mm_24698.1	chr3	95124483	95124560	+	1	NA	promoter-TSS (NM_016712)	promoter-TSS (NM_016712)	7	NM_016712	50874	Mm.71935	NM_016712	ENSMUSG00000005628	Tmod4	MTMOD|Sk-Tmod	tropomodulin 4	protein-coding
mm_83069.1	chr9	37613543	37613553	-	1	NA	promoter-TSS (NM_011734)	promoter-TSS (NM_011734)	172	NM_011449	20686	Mm.8637	NM_011449	ENSMUSG00000001948	Spa17	Sp17	sperm autoantigenic protein 17	protein-coding
mm_20797.1	chr2	144257131	144257159	-	1	NA	exon (NM_024225, exon 6 of 13)	exon (NM_024225, exon 6 of 13)	9057	NR_030762	100313519	Mm.453538	NR_030762	ENSMUSG00000077714	Snord17	MBI-43	small nucleolar RNA, C/D box 17	snoRNA
mm_88649.1	chr10	79967305	79967343	+	1	NA	exon (NM_175450, exon 9 of 10)	exon (NM_175450, exon 9 of 10)	-3400	NM_130455	170483	Mm.391566	NM_130455	ENSMUSG00000035745	Grin3b	GluN3B|NR3B	glutamate receptor, ionotropic, NMDA3B	protein-coding
mm_68186.1	chr7	104149419	104149421	-	1	NA	exon (NM_198624, exon 1 of 1)	exon (NM_198624, exon 1 of 1)	1136	NM_198624	244179	Mm.189668	NM_198624	ENSMUSG00000051437	Ubqlnl	4922504M18Rik|Gm490	ubiquilin-like	protein-coding
mm_92289.1	chr10	71344917	71344927	-	1	NA	promoter-TSS (NM_134007)	promoter-TSS (NM_134007)	-73	NM_134007	52637	Mm.254114	NM_134007	ENSMUSG00000037710	Cisd1	AU043990|AW743335|D10Ertd214e|Zcd1|mitoNEET	CDGSH iron sulfur domain 1	protein-coding
mm_40869.1	chr5	74014196	74014209	+	1	NA	intron (NM_177561, intron 5 of 8)	intron (NM_177561, intron 5 of 8)	54209	NM_177561	69727	Mm.48795	NM_177561	ENSMUSG00000054814	Usp46	1190009E20Rik|2410018I08Rik|AI451644	ubiquitin specific peptidase 46	protein-coding
mm_60971.1	chr7	48789063	48789081	+	1	NA	promoter-TSS (NM_028031)	promoter-TSS (NM_028031)	69	NM_028031	243983	Mm.279116	NM_028031	ENSMUSG00000030471	Zdhhc13	2410004E01Rik|C530010M18|HIP3RP|Hip14l|kojak|skc4	zinc finger, DHHC domain containing 13	protein-coding
mm_58713.1	chr7	12978345	12978355	+	1	NA	intron (NM_001168561, intron 1 of 4)	intron (NM_001168561, intron 1 of 4)	502	NM_001168561	269870	Mm.62083	NM_175558	ENSMUSG00000033961	Zfp446	A630035I11Rik|A930031C22|AA120513|AV306632	zinc finger protein 446	protein-coding
mm_54560.1	chr6	37362441	37362445	-	1	NA	exon (NM_178661, exon 4 of 12)	exon (NM_178661, exon 4 of 12)	-62467	NM_001347104	320127	Mm.119469	NM_001081206	ENSMUSG00000038665	Dgki	C130010K08Rik	diacylglycerol kinase, iota	protein-coding
mm_163362.1	chr12	32770885	32770890	-	1	NA	Intergenic	Intergenic	-49448	NM_021524	59027	Mm.202727	NM_021524	ENSMUSG00000020572	Nampt	1110035O14Rik|AI314458|AI480535|NAmPRTase|Pbef|Pbef1|Visfatin	nicotinamide phosphoribosyltransferase	protein-coding
mm_84710.1	chr9	73039608	73039636	-	1	NA	promoter-TSS (NM_018889)	promoter-TSS (NM_018889)	77	NM_018889	55981	Mm.139905	NM_018889	ENSMUSG00000079469	Pigb	Pig-b	phosphatidylinositol glycan anchor biosynthesis, class B	protein-coding
mm_105489.1	chr11	106065923	106065954	-	1	NA	promoter-TSS (NM_027346)	promoter-TSS (NM_027346)	-169	NM_027346	70207	Mm.343857	NM_027346	ENSMUSG00000001983	Taco1	2310066I18Rik|Ccdc44	translational activator of mitochondrially encoded cytochrome c oxidase I	protein-coding
mm_30365.1	chr3	152107198	152107201	-	1	NA	intron (NM_016867, intron 4 of 5)	intron (NM_016867, intron 4 of 5)	58701	NM_016867	54120	Mm.97	NM_016867	ENSMUSG00000039131	Gipc2	2200002N01Rik|AU021850|Semcap2	GIPC PDZ domain containing family, member 2	protein-coding
mm_6534.1	chr1	74893110	74893123	-	1	NA	promoter-TSS (NM_021541)	promoter-TSS (NM_021541)	27	NM_021541	12958	Mm.86656	NM_021541	ENSMUSG00000006546	Cryba2	E130107M19Rik	crystallin, beta A2	protein-coding
mm_4239.1	chr1	171388956	171389042	+	1	NA	promoter-TSS (NM_001005508)	promoter-TSS (NM_001005508)	39	NM_001005508	226652	Mm.251048	NM_001005508	ENSMUSG00000048865	Arhgap30	6030405P05Rik|Gm102|mFLJ00267	Rho GTPase activating protein 30	protein-coding
mm_94083.1	chr10	128493523	128493552	-	1	NA	promoter-TSS (NM_001317220)	promoter-TSS (NM_001317220)	349	NM_001317218	17904	Mm.337074	NM_010860	ENSMUSG00000090841	Myl6	ESMLC|LC17|LC17-GI|MLC-3|MLC1SM|Myln	myosin, light polypeptide 6, alkali, smooth muscle and non-muscle	protein-coding
mm_58733.1	chr7	13030080	13030103	+	1	NA	exon (NM_011588, exon 14 of 17)	exon (NM_011588, exon 14 of 17)	4686	NM_026885	68953	Mm.295670	NM_026885	ENSMUSG00000033916	Chmp2a	1500016L11Rik	charged multivesicular body protein 2A	protein-coding
mm_97388.1	chr11	77770882	77770885	+	1	NA	Intergenic	Intergenic	-6352	NM_001291213	360013	Mm.341248	NM_011586	ENSMUSG00000000631	Myo18a	MAJN|MyoPDZ|MysPDZ|SP-R210	myosin XVIIIA	protein-coding
mm_156340.1	chrX	139010045	139010054	+	1	NA	TTS (NM_013724)	TTS (NM_013724)	75187	NM_177920	331535	Mm.211704	NM_177920	ENSMUSG00000031271	Serpina7	C730040N12Rik|Tbg	serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 7	protein-coding
mm_99372.1	chr11	101984256	101984268	+	1	NA	intron (NM_028207, intron 1 of 2)	intron (NM_028207, intron 1 of 2)	529	NM_028207	72349	Mm.196295	NM_028207	ENSMUSG00000003518	Dusp3	2210015O03Rik|5031436O03Rik|T-DSP11|VHR	dual specificity phosphatase 3 (vaccinia virus phosphatase VH1-related)	protein-coding
mm_42339.1	chr5	114903682	114903697	+	1	NA	intron (NM_011854, intron 3 of 5)	ID4_|SINE|ID	6755	NM_011854	23962	Mm.228363	NM_011854	ENSMUSG00000029561	Oasl2	M1204|Mmu-OASL|Oasl	2'-5' oligoadenylate synthetase-like 2	protein-coding
mm_24133.1	chr3	88215673	88215680	+	1	NA	promoter-TSS (NR_029817)	promoter-TSS (NR_029817)	78	NR_029817	387133		NR_029817	ENSMUSG00000106493	Mir9-1	Mirn9|Mirn9-1|mir-9-1|mmu-mir-9-1	microRNA 9-1	ncRNA
mm_103383.1	chr11	75415145	75415151	-	1	NA	intron (NM_011340, intron 4 of 7)	intron (NM_011340, intron 4 of 7)	7475	NM_011340	20317	Mm.2044	NM_011340	ENSMUSG00000000753	Serpinf1	AI195227|EPC-1|Pedf|Pedfl|Sdf3	serine (or cysteine) peptidase inhibitor, clade F, member 1	protein-coding
mm_28449.1	chr3	90514357	90514366	-	1	NA	promoter-TSS (NM_009113)	promoter-TSS (NM_009113)	-31	NM_011309	20193	Mm.24662	NM_011309	ENSMUSG00000044080	S100a1	AI266795|S100|S100a	S100 calcium binding protein A1	protein-coding
mm_8643.1	chr1	156430313	156430324	-	1	NA	3' UTR (NM_009230, exon 16 of 16)	3' UTR (NM_009230, exon 16 of 16)	-9403	NM_001346967	77352	Mm.428709	NM_001033180	ENSMUSG00000026601	Axdnd1	9430070O13Rik|Gm979	axonemal dynein light chain domain containing 1	protein-coding
mm_157283.1	chrX	20861008	20861032	-	1	NA	TTS (NM_009703)	TTS (NM_009703)	2162	NR_049190	100885829		NR_049190	ENSMUSG00000093408	Mir5617	Gm25192|mir-5617|mmu-mir-5617	microRNA 5617	ncRNA
mm_116777.1	chr13	52981967	52981979	-	1	NA	promoter-TSS (NM_017373)	promoter-TSS (NM_017373)	-934	NM_017373	18030	Mm.136604	NM_017373	ENSMUSG00000056749	Nfil3	AV225605|E4BP4	nuclear factor, interleukin 3, regulated	protein-coding
mm_47364.1	chr5	122901699	122901720	-	1	NA	intron (NM_001003953, intron 12 of 22)	intron (NM_001003953, intron 12 of 22)	-1359	NM_013910	30841	Mm.86406	NM_013910	ENSMUSG00000029475	Kdm2b	Cxxc2|Fbl10|Fbxl10|Jhdm1b|PCCX2	lysine (K)-specific demethylase 2B	protein-coding
mm_159388.1	chr3	92285290	92285290	+	1	NA	promoter-TSS (NM_001309382)	promoter-TSS (NM_001309382)	-14	NM_001309382	100042514	Mm.6853	NM_001309382	ENSMUSG00000074445	Sprr2a3	-	small proline-rich protein 2A3	protein-coding
mm_2032.1	chr1	87205785	87205793	+	1	NA	promoter-TSS (NM_009604)	promoter-TSS (NM_009604)	-22	NM_009604	11449	Mm.2810	NM_009604	ENSMUSG00000026253	Chrng	Achr-3|Acrg	cholinergic receptor, nicotinic, gamma polypeptide	protein-coding
mm_125670.1	chr15	65926815	65926821	+	1	NA	intron (NM_001145096, intron 15 of 16)	RLTR13D6|LTR|ERVK	-14531	NM_010953	18256	Mm.41776	NM_010953	ENSMUSG00000015001	Oc90	Ocn-95|PLA2L|Pla2ll|oc95	otoconin 90	protein-coding
mm_132141.1	chr16	31948573	31948618	+	1	NA	promoter-TSS (NR_027897)	promoter-TSS (NR_027897)	49	NM_026554	68092	Mm.290027	NM_026554	ENSMUSG00000022774	Ncbp2	20kDa|5930413E18Rik|AA536802|AI843301|C79367	nuclear cap binding protein subunit 2	protein-coding
mm_61504.1	chr7	78077618	78077618	+	1	NA	Intergenic	Intergenic	500220	NM_008746	18213	Mm.33496	NM_008746	ENSMUSG00000059146	Ntrk3	AW125844|Ntrk3_tv3|TrkC	neurotrophic tyrosine kinase, receptor, type 3	protein-coding
mm_61219.1	chr7	64392737	64392763	+	1	NA	promoter-TSS (NM_026483)	promoter-TSS (NM_026483)	-21	NM_028626	73724	Mm.10093	NM_028626	ENSMUSG00000033429	Mcee	1110007A04Rik	methylmalonyl CoA epimerase	protein-coding
mm_50740.1	chr6	52721395	52721428	+	1	NA	exon (NM_025816, exon 2 of 18)	exon (NM_025816, exon 2 of 18)	7682	NM_025816	52440	Mm.389757	NM_025816	ENSMUSG00000004535	Tax1bp1	1200003J11Rik|1700069J21Rik|AA930106|D6Ertd404e|D6Ertd772e|T6bp|TXBP151	Tax1 (human T cell leukemia virus type I) binding protein 1	protein-coding
mm_21157.1	chr2	154569382	154569401	-	1	NA	promoter-TSS (NM_001291105)	promoter-TSS (NM_001291105)	35	NM_001291105	13555	Mm.18036	NM_007891	ENSMUSG00000027490	E2f1	E2F-1|mKIAA4009	E2F transcription factor 1	protein-coding
mm_29380.1	chr3	108840470	108840474	-	1	NA	promoter-TSS (NM_011504)	promoter-TSS (NM_011504)	30	NM_011504	20912	Mm.316894	NM_011504	ENSMUSG00000027882	Stxbp3	Munc-18c|Stxbp3a|Sxtbp3|Unc18-3	syntaxin binding protein 3	protein-coding
mm_60034.1	chr7	31002925	31002942	+	1	NA	Intergenic	Intergenic	21012	NM_001242647	76415	Mm.259739	NM_175240	ENSMUSG00000046826	Fam187b	1700020B09Rik|Tmem162	family with sequence similarity 187, member B	protein-coding
mm_42807.1	chr5	121753056	121753059	+	1	NA	intron (NM_009125, intron 5 of 24)	intron (NM_009125, intron 5 of 24)	41448	NM_009125	20239	Mm.260900	NM_009125	ENSMUSG00000042605	Atxn2	9630045M23Rik|ATX2|AW544490|Sca2	ataxin 2	protein-coding
mm_119601.1	chr14	51053539	51053564	+	1	NA	Intergenic	RMER17B|LTR|ERVK	-3388	NM_001011877	497113	Mm.379741	NM_001011877	ENSMUSG00000059648	Rnase11	Raj1	ribonuclease, RNase A family, 11 (non-active)	protein-coding
mm_18319.1	chr2	57113054	57113063	-	1	NA	5' UTR (NM_013613, exon 2 of 8)	5' UTR (NM_013613, exon 2 of 8)	1980	NM_013613	18227	Mm.3507	NM_013613	ENSMUSG00000026826	Nr4a2	HZF-3|NOT|Nurr1|RNR-1|TINOR|TINUR	nuclear receptor subfamily 4, group A, member 2	protein-coding
mm_148573.1	chr19	4869387	4869396	+	1	NA	exon (NM_013456, exon 8 of 21)	exon (NM_013456, exon 8 of 21)	8518	NM_013456	11474	Mm.5316	NM_013456	ENSMUSG00000006457	Actn3	-	actinin alpha 3	protein-coding
mm_28995.1	chr3	101426959	101426975	-	1	NA	intron (NM_207205, intron 3 of 10)	intron (NM_207205, intron 3 of 10)	49842	NM_207205	78908	Mm.257997	NM_207205	ENSMUSG00000042035	Igsf3	1700016K10Rik|2810035F16Rik|4833439O17Rik|mKIAA0466	immunoglobulin superfamily, member 3	protein-coding
mm_13954.1	chr2	121303726	121303743	+	1	NA	exon (NM_001173506, exon 4 of 6)	exon (NM_001173506, exon 4 of 6)	8280	NM_001173506	17754	Mm.36501	NM_032393	ENSMUSG00000027254	Map1a	6330416M19Rik|AI853608|Mtap-1|Mtap1|Mtap1a|moth1	microtubule-associated protein 1 A	protein-coding
mm_33434.1	chr4	130061167	130061186	+	1	NA	intron (NM_028266, intron 23 of 69)	intron (NM_028266, intron 23 of 69)	13336	NM_028266	107581	Mm.41860	NM_028266	ENSMUSG00000040690	Col16a1	2700007F12Rik|A530052M23Rik|AI838662|CA1F	collagen, type XVI, alpha 1	protein-coding
mm_28679.1	chr3	95315734	95315759	-	1	NA	intron (NM_029789, intron 1 of 10)	intron (NM_029789, intron 1 of 10)	556	NM_029789	76893	Mm.181009	NM_029789	ENSMUSG00000015714	Cers2	0610013I17Rik|AI225939|Lass2|TRH3	ceramide synthase 2	protein-coding
mm_157019.1	chrX	7741289	7741321	-	1	NA	promoter-TSS (NM_207202)	promoter-TSS (NM_207202)	19	NM_207202	54648	Mm.63342	NM_207202	ENSMUSG00000031150	Ccdc120	AA030924|DXImx50e|Jm11|Sfc25	coiled-coil domain containing 120	protein-coding
mm_166920.1	chr7	30743705	30743731	-	1	NA	promoter-TSS (NM_001290631)	promoter-TSS (NM_001290631)	-37	NM_001290631	14447	Mm.436562	NM_008085	ENSMUSG00000061099	Gapdhs	Gapd-s|Gapds	glyceraldehyde-3-phosphate dehydrogenase, spermatogenic	protein-coding
mm_94804.1	chr11	23008338	23008391	+	1	NA	Intergenic	CpG	-5023	NM_028672	73873	Mm.252406	NM_028672	ENSMUSG00000049811	Fam161a	4930430E16Rik	family with sequence similarity 161, member A	protein-coding
mm_87988.1	chr10	64090924	64090928	+	1	NA	promoter-TSS (NM_178678)	promoter-TSS (NM_178678)	-671	NM_178678	216028	Mm.431318	NM_178678	ENSMUSG00000042846	Lrrtm3	9630044H04Rik	leucine rich repeat transmembrane neuronal 3	protein-coding
mm_173328.1	chrY	90777138	90777151	-	1	NA	Intergenic	Intergenic	-8298	NR_137282	170942	Mm.76062	NM_133362	ENSMUSG00000096768	Erdr1	edr	erythroid differentiation regulator 1	protein-coding
mm_117991.1	chr13	100307023	100307027	-	1	NA	intron (NM_021545, intron 5 of 14)	intron (NM_021545, intron 5 of 14)	9591	NM_010871	17952	Mm.218759	NM_010871	ENSMUSG00000078942	Naip6	Birc1f|Naip-rs4|Naip-rs4A	NLR family, apoptosis inhibitory protein 6	protein-coding
mm_81424.1	chr9	109056638	109056720	+	1	NA	exon (NM_026381, exon 4 of 4)	exon (NM_026381, exon 4 of 4)	1813	NM_026381	66940	Mm.196533	NM_025858	ENSMUSG00000025647	Shisa5	2310008D10Rik|6430628I05Rik|Scotin|mShisa5	shisa family member 5	protein-coding
mm_89879.1	chr10	108332174	108332182	+	1	NA	promoter-TSS (NM_054056)	promoter-TSS (NM_054056)	-11	NM_054056	114774	Mm.391419	NM_054056	ENSMUSG00000035873	Pawr	2310001G03Rik|PAR4|Par-4	PRKC, apoptosis, WT1, regulator	protein-coding
mm_37474.1	chr4	123565437	123565453	-	1	NA	intron (NM_001199136, intron 1 of 97)	intron (NM_001199136, intron 1 of 97)	-50975	NR_105824	102465214		NR_105824	ENSMUSG00000099005	Mir6398	Gm27657|mmu-mir-6398	microRNA 6398	ncRNA
mm_104377.1	chr11	94392918	94392983	-	1	NA	promoter-TSS (NM_029600)	promoter-TSS (NM_029600)	26	NM_029600	76408	Mm.23942	NM_029600	ENSMUSG00000020865	Abcc3	1700019L09Rik|ABC31|MLP2|MOAT-D|MRP3	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	protein-coding
mm_98744.1	chr11	96464650	96464660	+	1	NA	promoter-TSS (NM_001177899)	promoter-TSS (NM_001177899)	64	NM_001177898	78473	Mm.395840	NM_001033186	ENSMUSG00000057058	Skap1	1700091G21Rik|Scap1|Skap-55	src family associated phosphoprotein 1	protein-coding
mm_160772.1	chr10	117675893	117675893	+	1	NA	intron (NM_027468, intron 6 of 8)	intron (NM_027468, intron 6 of 8)	34865	NM_010786	17246	Mm.22670	NM_010786	ENSMUSG00000020184	Mdm2	1700007J15Rik|AA415488|Mdm-2	transformed mouse 3T3 cell double minute 2	protein-coding
mm_4877.1	chr1	187919289	187919306	+	1	NA	intron (NM_001243792, intron 2 of 7)	intron (NM_001243792, intron 2 of 7)	-78530	NM_011935	26381	Mm.89989	NM_011935	ENSMUSG00000026610	Esrrg	ERR3|Errg|NR3B3|mKIAA0832	estrogen-related receptor gamma	protein-coding
mm_168707.1	chr11	99824802	99824802	+	1	NA	Intergenic	MERVL-int|LTR|ERVL	-9136	NM_001100614	670496	Mm.466614	NM_001100614	ENSMUSG00000078258	Gm11564	OTTMUSG00000002201	predicted gene 11564	protein-coding
mm_144246.1	chr18	10764565	10764568	+	1	NA	intron (NM_144860, intron 9 of 20)	L1M2|LINE|L1	18410	NR_029547	387151		NR_029547	ENSMUSG00000065399	Mir133a-1	Mirn133|Mirn133a-1|mir-133a-1	microRNA 133a-1	ncRNA
mm_135778.1	chr16	56885924	56885932	-	1	NA	5' UTR (NM_019631, exon 1 of 6)	5' UTR (NM_019631, exon 1 of 6)	235	NM_019631	56277	Mm.262328	NM_019631	ENSMUSG00000022754	Tmem45a	C630002M10Rik|M32486|p19.5	transmembrane protein 45a	protein-coding
mm_2064.1	chr1	87594584	87594597	+	1	NA	promoter-TSS (NM_015750)	promoter-TSS (NM_015750)	40	NM_015750	23956	Mm.143717	NM_015750	ENSMUSG00000079434	Neu2	MBS|MSS|MTS	neuraminidase 2	protein-coding
mm_6728.1	chr1	82767212	82767215	-	1	NA	intron (NM_025453, intron 1 of 3)	intron (NM_025453, intron 1 of 3)	1243	NM_025453	66261	Mm.46325	NM_025453	ENSMUSG00000026149	Tm4sf20	1810018L02Rik	transmembrane 4 L six family member 20	protein-coding
mm_40118.1	chr5	34974982	34974999	+	1	NA	intron (NM_173402, intron 2 of 16)	intron (NM_173402, intron 2 of 16)	-24088	NM_001163512	71729	Mm.196208	NM_173402	ENSMUSG00000029101	Rgs12	1200016K18Rik|4632412M04Rik|AI481290|E130309H11	regulator of G-protein signaling 12	protein-coding
mm_140188.1	chr17	83215272	83215289	+	1	NA	promoter-TSS (NM_134117)	promoter-TSS (NM_134117)	-3	NM_134117	106522	Mm.311974	NM_134117	ENSMUSG00000024247	Pkdcc	AI115348|AW548124|Adtk1|ESTM17|MAd1|Sgk493|Vlk|X83346	protein kinase domain containing, cytoplasmic	protein-coding
mm_98996.1	chr11	98795238	98795254	+	1	NA	promoter-TSS (NM_028722)	promoter-TSS (NM_028722)	-523	NM_028722	74026	Mm.258352	NM_028722	ENSMUSG00000052915	Msl1	2810017F12Rik|4121402D02Rik|4930463F05Rik|AA682082|Msl-1	male-specific lethal 1 homolog (Drosophila)	protein-coding
mm_156490.1	chrX	144336080	144336092	+	1	NA	intron (NR_037145, intron 3 of 26)	intron (NR_037145, intron 3 of 26)	18120	NM_026247	67574	Mm.249084	NM_026247	ENSMUSG00000041718	Alg13	2810046O15Rik|4833435D08Rik|Glt28d1|MDS031|OTTMUSG00000018917	asparagine-linked glycosylation 13	protein-coding
mm_112409.1	chr13	3564988	3565019	+	1	NA	exon (NM_008112, exon 11 of 11)	exon (NM_008112, exon 11 of 11)	26928	NM_008112	14569	Mm.153226	NM_008112	ENSMUSG00000021218	Gdi2	GDI-B|GDIB|Gdi3	guanosine diphosphate (GDP) dissociation inhibitor 2	protein-coding
mm_120102.1	chr14	58893466	58893469	+	1	NA	Intergenic	Lx4A|LINE|L1	249426	NM_026461	67932	Mm.65550	NM_026461	ENSMUSG00000021977	1700129C05Rik	-	RIKEN cDNA 1700129C05 gene	protein-coding
mm_18676.1	chr2	71317569	71317589	-	1	NA	intron (NM_172436, intron 5 of 17)	intron (NM_172436, intron 5 of 17)	49975	NM_172436	78830	Mm.30928	NM_172436	ENSMUSG00000027010	Slc25a12	2610002D09Rik|AI839531|B230107K20Rik|BB129864	solute carrier family 25 (mitochondrial carrier, Aralar), member 12	protein-coding
mm_150735.1	chr19	43732261	43732264	+	1	NA	TTS (NM_144874)	TTS (NM_144874)	20738	NM_144874	226139	Mm.248237	NM_144874	ENSMUSG00000040018	Cox15	2900026G05Rik	cytochrome c oxidase assembly protein 15	protein-coding
mm_134063.1	chr16	8425151	8425161	-	1	NA	promoter-TSS (NM_029070)	promoter-TSS (NM_029070)	-20	NM_029070	74720	Mm.159318	NM_029070	ENSMUSG00000022715	Tmem114	4930511J11Rik|Cldn26	transmembrane protein 114	protein-coding
mm_2166.1	chr1	88259148	88259168	+	1	NA	exon (NM_001281466, exon 40 of 42)	exon (NM_001281466, exon 40 of 42)	10250	NR_040291	78605	Mm.384762	NR_040291		6430706D22Rik	-	RIKEN cDNA 6430706D22 gene	ncRNA
mm_61576.1	chr7	79821802	79821811	+	1	NA	TTS (NM_008486)	TTS (NM_008486)	11079	NM_008589	17293	Mm.31472	NM_008589	ENSMUSG00000030543	Mesp2	bHLHc6	mesoderm posterior 2	protein-coding
mm_67081.1	chr7	68275108	68275120	-	1	NA	promoter-TSS (NR_040341)	promoter-TSS (NR_040341)	-16	NR_040341	100504026	Mm.426764	NR_040340	ENSMUSG00000086628	Gm16157	OTTMUSG00000031023	predicted gene 16157	ncRNA
mm_141849.1	chr17	34801762	34801773	-	1	NA	3' UTR (NM_009995, exon 10 of 10)	3' UTR (NM_009995, exon 10 of 10)	2659	NM_009995	13079	Mm.440407	NM_009995	ENSMUSG00000024365	Cyp21a1	21-OH|21OH|21OHA|21OHB|CYP21OH-A|Cyp21|Cyp21-ps1|Cyp21B|Cyp21a2-ps|Cyp21a2ps|Oh21-1|Oh21-2	cytochrome P450, family 21, subfamily a, polypeptide 1	protein-coding
mm_57049.1	chr6	122345390	122345412	-	1	NA	Intergenic	PB1D7|SINE|Alu	-5174	NM_001271579	13619	Mm.6822	NM_007905	ENSMUSG00000040669	Phc1	AW557034|Edr|Edr1|Mph1|Rae-28|rae28	polyhomeotic-like 1 (Drosophila)	protein-coding
mm_147410.1	chr18	44828884	44828894	-	1	NA	exon (NM_001163013, exon 1 of 30)	exon (NM_001163013, exon 1 of 30)	224	NM_001163013	240255	Mm.244482	NM_001163013	ENSMUSG00000034653	Ythdc2	3010002F02Rik|BC037178	YTH domain containing 2	protein-coding
mm_151355.1	chr19	55898946	55898978	+	1	NA	intron (NM_001142924, intron 1 of 11)	intron (NM_001142924, intron 1 of 11)	3641	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_144023.1	chr17	90036434	90036436	-	1	NA	3' UTR (NM_001347419, exon 3 of 3)	3' UTR (NM_001347419, exon 3 of 3)	51933	NM_001346962	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_4289.1	chr1	171762926	171762966	+	1	NA	Intergenic	Intergenic	-4186	NM_013730	27218	Mm.103648	NM_013730	ENSMUSG00000015316	Slamf1	4933415F16|AA177906|CD150|CDw150|ESTM51|IPO-3|Slam	signaling lymphocytic activation molecule family member 1	protein-coding
mm_134386.1	chr16	17222401	17222429	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-11172	NM_178922	58180	Mm.261602	NM_178922	ENSMUSG00000050240	Hic2	AA409108|HRG22|mKIAA1020	hypermethylated in cancer 2	protein-coding
mm_82505.1	chr9	20480867	20480888	-	1	NA	intron (NM_146221, intron 1 of 6)	B4|SINE|B4	11869	NM_146221	235028	Mm.297660	NM_146221	ENSMUSG00000059475	Zfp426	2900057C04Rik|KRAB1|Zfo61|Zfp68-rs1|Znf426|mKIAA4237	zinc finger protein 426	protein-coding
mm_133249.1	chr16	77247223	77247228	+	1	NA	Intergenic	MTEb-int|LTR|ERVL-MaLR	-82103	NR_015543	77994	Mm.394688	NR_015543	ENSMUSG00000090386	Mir99ahg	2810055G20Rik|D730043B02Rik	Mir99a and Mirlet7c-1 host gene (non-protein coding)	ncRNA
mm_38877.1	chr4	149689517	149689535	-	1	NA	intron (NM_001029837, intron 1 of 23)	B2_Mm1t|SINE|B2	9182	NM_001164050	18707	Mm.229108	NM_008840	ENSMUSG00000039936	Pik3cd	2410099E07Rik|2610208K16Rik|AW545373|p110delta	phosphatidylinositol 3-kinase catalytic delta polypeptide	protein-coding
mm_84053.1	chr9	58158499	58158551	-	1	NA	promoter-TSS (NM_001195431)	promoter-TSS (NM_001195431)	29	NM_001195431	26968	Mm.367887	NM_012043	ENSMUSG00000037206	Islr	AW553146|Meflin	immunoglobulin superfamily containing leucine-rich repeat	protein-coding
mm_113675.1	chr13	42753822	42753832	+	1	NA	intron (NM_001005740, intron 1 of 12)	(GGGAGA)n|Simple_repeat|Simple_repeat	44246	NM_001005740	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding
mm_69541.1	chr7	135695671	135695683	-	1	NA	exon (NM_001081117, exon 12 of 14)	exon (NM_001081117, exon 12 of 14)	20702	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_115880.1	chr13	21780149	21780185	-	1	NA	exon (NM_020034, exon 1 of 1)	exon (NM_020034, exon 1 of 1)	458	NM_020034	56702	Mm.221314	NM_020034	ENSMUSG00000058773	Hist1h1b	H1.5|H1B|H1f5|H1s-3	histone cluster 1, H1b	protein-coding
mm_122589.1	chr14	50897449	50897457	-	1	NA	Intergenic	Intergenic	-4198	NM_001166651	546611	Mm.390692	NM_001166651	ENSMUSG00000090799	Klhl33	EG546611	kelch-like 33	protein-coding
mm_134629.1	chr16	21650367	21650380	-	1	NA	3' UTR (NM_001001881, exon 2 of 2)	3' UTR (NM_001001881, exon 2 of 2)	44292	NM_001001881	72190	Mm.131606	NM_001001881	ENSMUSG00000043391	2510009E07Rik	AI194952	RIKEN cDNA 2510009E07 gene	protein-coding
mm_94706.1	chr11	20249576	20249594	+	1	NA	promoter-TSS (NM_172260)	promoter-TSS (NM_172260)	-161	NM_172260	216543	Mm.260314	NM_172260	ENSMUSG00000044066	Cep68	6030463E10Rik|AI481761|BC027174|Kiaa0582	centrosomal protein 68	protein-coding
mm_95536.1	chr11	52261506	52261531	+	1	NA	exon (NM_009331, exon 3 of 10)	exon (NM_009331, exon 3 of 10)	21077	NM_009331	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_158569.1	chrX	150583916	150583919	-	1	NA	intron (NM_029943, intron 5 of 5)	B1_Mus1|SINE|Alu	4238	NM_029943	77622	Mm.440275	NM_029943	ENSMUSG00000025269	Apex2	C430040P13Rik|ape2	apurinic/apyrimidinic endonuclease 2	protein-coding
mm_155302.1	chrX	61185781	61185796	+	1	NA	promoter-TSS (NM_001166658)	promoter-TSS (NM_001166658)	-230	NM_001166658	631990	Mm.401324	NM_001166658	ENSMUSG00000090546	Cdr1	100039759|Cdr|Cdr34|EG631990|Gm2409|Gm7077	cerebellar degeneration related antigen 1	protein-coding
mm_65202.1	chr7	19696948	19696969	-	1	NA	exon (NM_009696, exon 4 of 4)	exon (NM_009696, exon 4 of 4)	1440	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_13590.1	chr2	112492927	112493005	+	1	NA	promoter-TSS (NM_028844)	promoter-TSS (NM_028844)	2	NM_028844	74268	Mm.315125	NM_028844	ENSMUSG00000003604	Aven	1700013A01Rik|1700056A21Rik|mAven-L|mAven-S	apoptosis, caspase activation inhibitor	protein-coding
mm_148601.1	chr19	5298277	5298287	+	1	NA	promoter-TSS (NM_001024717)	promoter-TSS (NM_001024717)	-49	NM_001024717	545276	Mm.447174	NM_001024717	ENSMUSG00000047658	Gal3st3	-	galactose-3-O-sulfotransferase 3	protein-coding
mm_36813.1	chr4	103215340	103215389	-	1	NA	promoter-TSS (NM_177732)	promoter-TSS (NM_177732)	-480	NM_177732	242585	Mm.281800	NM_177732	ENSMUSG00000028521	Slc35d1	AI834976|C330011J09|UGTREL7|mKIAA0260	solute carrier family 35 (UDP-glucuronic acid/UDP-N-acetylgalactosamine dual transporter), member D1	protein-coding
mm_57729.1	chr6	128945854	128945859	-	1	NA	intron (NM_027562, intron 1 of 6)	B3|SINE|B2	11475	NM_027562	70809	Mm.439891	NM_027562	ENSMUSG00000000248	Clec2g	4632413B12Rik|Clr-c|Clr-d|Clrc|Clrd|Clrx|Ddv10|Ocilrp1	C-type lectin domain family 2, member g	protein-coding
mm_45171.1	chr5	51495799	51495809	-	1	NA	intron (NR_132764, intron 3 of 12)	intron (NR_132764, intron 3 of 12)	58117	NR_027710	19017	Mm.259072	NM_008904	ENSMUSG00000029167	Ppargc1a	A830037N07Rik|ENSMUSG00000079510|Gm11133|PGC-1|PPARGC-1-alpha|Pgc-1alpha|Pgc1|Pgco1|Ppargc1	peroxisome proliferative activated receptor, gamma, coactivator 1 alpha	protein-coding
mm_38617.1	chr4	141952239	141952262	-	1	NA	intron (NM_177868, intron 12 of 31)	intron (NM_177868, intron 12 of 31)	-30742	NR_040672	545691	Mm.332015	NR_040672	ENSMUSG00000085424	Fhad1os1	Gm13037|OTTMUSG00000010113	forkhead-associated (FHA) phosphopeptide binding domain 1, opposite strand 1	ncRNA
mm_112220.1	chr12	113429243	113429252	-	1	NA	Intergenic	Intergenic	-60318	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_76584.1	chr8	89025996	89026010	-	1	NA	Intergenic	Intergenic	1268	NR_106190	102465899		NR_106190	ENSMUSG00000099078	Mir8110	Gm27571|mmu-mir-8110	microRNA 8110	ncRNA
mm_87719.1	chr10	60106199	60106221	+	1	NA	promoter-TSS (NM_052994)	promoter-TSS (NM_052994)	-47	NM_052994	94214	Mm.153429	NM_052994	ENSMUSG00000058297	Spock2	AA407235|Gcap26|mKIAA0275	sparc/osteonectin, cwcv and kazal-like domains proteoglycan 2	protein-coding
mm_12406.1	chr2	70508698	70508706	+	1	NA	promoter-TSS (NM_025744)	promoter-TSS (NM_025744)	-117	NM_025744	66748	Mm.423014	NM_025744	ENSMUSG00000075302	Erich2	4933404M02Rik	glutamate rich 2	protein-coding
mm_54172.1	chr6	23650275	23650288	-	1	NA	promoter-TSS (NM_198251)	promoter-TSS (NM_198251)	24	NM_198251	386611	Mm.436547	NM_198251	ENSMUSG00000051956	Rnf133	Greul2	ring finger protein 133	protein-coding
mm_128425.1	chr15	48791984	48791998	-	1	NA	promoter-TSS (NM_001081391)	promoter-TSS (NM_001081391)	-2	NM_001081391	239420	Mm.309363	NM_001081391	ENSMUSG00000022311	Csmd3	4930500N14Rik|mKIAA1894	CUB and Sushi multiple domains 3	protein-coding
mm_159908.1	chr6	43309558	43309558	-	1	NA	promoter-TSS (NM_130869)	promoter-TSS (NM_130869)	-4	NM_130869	18291	Mm.17715	NM_130869	ENSMUSG00000029736	Nobox	OG2|Og2x	NOBOX oogenesis homeobox	protein-coding
mm_153796.1	chr19	46033203	46033225	-	1	NA	exon (NM_010697, exon 11 of 11)	exon (NM_010697, exon 11 of 11)	6407	NM_010697	16825	Mm.327442	NM_010697	ENSMUSG00000025223	Ldb1	CLIM2|NLI	LIM domain binding 1	protein-coding
mm_97202.1	chr11	75598234	75598265	+	1	NA	exon (NM_008850, exon 3 of 12)	exon (NM_008850, exon 3 of 12)	1982	NR_110477	654359	Mm.439961	NR_110477		Gm12338	OTTMUSG00000006216	cytochrome c oxidase, subunit VIIc pseudogene	pseudo
mm_108799.1	chr12	91590241	91590252	+	1	NA	promoter-TSS (NM_031391)	promoter-TSS (NM_031391)	241	NM_175335	83602	Mm.275728	NM_031391	ENSMUSG00000020962	Gtf2a1	6330549H03Rik|AA536742|AA959775|AW060250|TfIIAa/b|Tfiia1	general transcription factor II A, 1	protein-coding
mm_172915.1	chr9	64176164	64176165	+	1	NA	TTS (NR_028548)	TTS (NR_028548)	732	NR_028548	100217453		NR_028548	ENSMUSG00000094411	Snord16a	MBII-98	small nucleolar RNA, C/D box 16A	snoRNA
mm_157112.1	chrX	9438222	9438233	-	1	NA	exon (NM_007807, exon 13 of 13)	exon (NM_007807, exon 13 of 13)	31097	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_93169.1	chr10	93310847	93310878	-	1	NA	5' UTR (NM_001322268, exon 1 of 6)	5' UTR (NM_001322268, exon 1 of 6)	297	NM_001322268	13713	Mm.4454	NM_013508	ENSMUSG00000008398	Elk3	D430049E23Rik|Erp|Etrp|Net|Sap-2	ELK3, member of ETS oncogene family	protein-coding
mm_147614.1	chr18	57315119	57315121	-	1	NA	Intergenic	Intergenic	-39613	NM_028447	73137	Mm.29889	NM_028447	ENSMUSG00000024594	Prrc1	1190002C06Rik|2310058D16Rik|3110038B19Rik|9430085A19Rik	proline-rich coiled-coil 1	protein-coding
mm_91923.1	chr10	60300861	60300885	-	1	NA	exon (NM_011179, exon 14 of 15)	exon (NM_011179, exon 14 of 15)	16412	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_118056.1	chr13	102014315	102014331	-	1	NA	Intergenic	MLT1A0|LTR|ERVL-MaLR	-246106	NM_001077495	18708	Mm.259333	NM_001024955	ENSMUSG00000041417	Pik3r1	PI3K|p50alpha|p55alpha|p85alpha	phosphatidylinositol 3-kinase, regulatory subunit, polypeptide 1 (p85 alpha)	protein-coding
mm_115857.1	chr13	21292680	21292711	-	1	NA	promoter-TSS (NM_010343)	promoter-TSS (NM_010343)	-9	NM_010343	14780	Mm.1332	NM_010343	ENSMUSG00000004344	Gpx5	AV379049|Arep	glutathione peroxidase 5	protein-coding
mm_43788.1	chr5	142629727	142629763	+	1	NA	5' UTR (NM_178398, exon 1 of 12)	5' UTR (NM_178398, exon 1 of 12)	161	NM_178398	74781	Mm.29432	NM_178398	ENSMUSG00000029578	Wipi2	1110018O08Rik|2510001I10Rik	WD repeat domain, phosphoinositide interacting 2	protein-coding
mm_172660.1	chr8	41164591	41164591	+	1	NA	Intergenic	L1Md_T|LINE|L1	-30865	NM_001005863	102103	Mm.149438	NM_001005863	ENSMUSG00000045636	Mtus1	AI481402|ATBP135|Atip1|B430010I23Rik|B430305I03Rik|C85752|Cctsg1-440|MD44|MTSG1|mKIAA1288	mitochondrial tumor suppressor 1	protein-coding
mm_19430.1	chr2	91944820	91944839	-	1	NA	TTS (NR_105965)	TTS (NR_105965)	101	NR_105965	102465604		NR_105965	ENSMUSG00000098651	Mir6999	Gm27673|mmu-mir-6999	microRNA 6999	ncRNA
mm_1330.1	chr1	65230774	65230802	+	1	NA	intron (NM_001310624, intron 12 of 41)	intron (NM_001310624, intron 12 of 41)	44103	NM_001310624	18711	Mm.38370	NM_011086	ENSMUSG00000025949	Pikfyve	5230400C17Rik|Pip5k|Pip5k3|Pipk5k3|PipkIII|p235	phosphoinositide kinase, FYVE finger containing	protein-coding
mm_153588.1	chr19	43521360	43521364	-	1	NA	intron (NM_010324, intron 1 of 8)	intron (NM_010324, intron 1 of 8)	3243	NM_010324	14718	Mm.19039	NM_010324	ENSMUSG00000025190	Got1	AI789014|Got-1|cAspAT|cCAT	glutamic-oxaloacetic transaminase 1, soluble	protein-coding
mm_47189.1	chr5	120754314	120754320	-	1	NA	3' UTR (NM_145226, exon 16 of 16)	3' UTR (NM_145226, exon 16 of 16)	-4469	NM_001347448	246728	Mm.260926	NM_145227	ENSMUSG00000032690	Oas2	Oasl11	2'-5' oligoadenylate synthetase 2	protein-coding
mm_120015.1	chr14	55745894	55745918	+	1	NA	promoter-TSS (NM_026819)	promoter-TSS (NM_026819)	213	NM_026403	67842	Mm.180338	NM_026403	ENSMUSG00000019297	Nop9	2610027L16Rik	NOP9 nucleolar protein	protein-coding
mm_126449.1	chr15	80798587	80798608	+	1	NA	promoter-TSS (NM_177124)	promoter-TSS (NM_177124)	-13	NM_177124	213988	Mm.131328	NM_144812	ENSMUSG00000047888	Tnrc6b	2700090M07Rik|A730065C02Rik|AI848765|D230019K20Rik	trinucleotide repeat containing 6b	protein-coding
mm_128081.1	chr15	27681485	27681495	-	1	NA	promoter-TSS (NM_198301)	promoter-TSS (NM_198301)	52	NM_001242424	223433	Mm.266485	NM_198301	ENSMUSG00000056069	Fam105a	9830126M18	family with sequence similarity 105, member A	protein-coding
mm_150793.1	chr19	44303337	44303346	+	1	NA	TTS (NR_039574)	TTS (NR_039574)	170	NR_039574	100628619		NR_039574	ENSMUSG00000093315	Mir5114	mmu-mir-5114|mu-mir-5114	microRNA 5114	ncRNA
mm_72612.1	chr8	84601361	84601377	+	1	NA	intron (NM_001252059, intron 30 of 45)	intron (NM_001252059, intron 30 of 45)	61483	NM_010499	15936	Mm.399	NM_010499	ENSMUSG00000053560	Ier2	AI317238|Ch1|Pip92	immediate early response 2	protein-coding
mm_130827.1	chr15	101846035	101846046	-	1	NA	exon (NM_008473, exon 9 of 9)	exon (NM_008473, exon 9 of 9)	4746	NM_008473	16678	Mm.183137	NM_008473	ENSMUSG00000046834	Krt1	Krt-2.1|Krt2-1|Krt86	keratin 1	protein-coding
mm_55983.1	chr6	85915654	85915692	-	1	NA	promoter-TSS (NM_001170488)	promoter-TSS (NM_001170488)	4	NM_023160	66116	Mm.13036	NM_023160	ENSMUSG00000057103	Nat8f1	1110002I11Rik|AI266962|Cml1	N-acetyltransferase 8 (GCN5-related) family member 1	protein-coding
mm_15791.1	chr2	164425808	164425846	+	1	NA	3' UTR (NM_011521, exon 5 of 5)	3' UTR (NM_011521, exon 5 of 5)	17361	NM_011521	20971	Mm.3815	NM_011521	ENSMUSG00000017009	Sdc4	AA959608|AW108331|S4|Synd4|ryudocan|syndecan-4	syndecan 4	protein-coding
mm_13244.1	chr2	98662833	98662860	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	1195189	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_39767.1	chr5	30013559	30013564	+	1	NA	intron (NM_001314054, intron 2 of 4)	intron (NM_001314054, intron 2 of 4)	447	NM_031168	16193	Mm.1019	NM_031168	ENSMUSG00000025746	Il6	Il-6	interleukin 6	protein-coding
mm_95108.1	chr11	34071060	34071069	+	1	NA	exon (NM_010696, exon 7 of 21)	exon (NM_010696, exon 7 of 21)	23863	NM_010696	16822	Mm.265350	NM_010696	ENSMUSG00000002699	Lcp2	AI323664|BB161688|SLP-76|SLP76|m1Khoe|twm	lymphocyte cytosolic protein 2	protein-coding
mm_25527.1	chr3	114904214	114904224	+	1	NA	promoter-TSS (NM_001286750)	promoter-TSS (NM_001286750)	141	NM_153458	229759	Mm.54183	NM_153157	ENSMUSG00000027965	Olfm3	B230206G02Rik	olfactomedin 3	protein-coding
mm_64278.1	chr7	141809582	141809594	+	1	NA	intron (NM_010844, intron 31 of 49)	intron (NM_010844, intron 31 of 49)	20577	NM_010844	17833	Mm.334332	NM_010844	ENSMUSG00000037974	Muc5ac	2210005L13Rik|MGM	mucin 5, subtypes A and C, tracheobronchial/gastric	protein-coding
mm_8721.1	chr1	160044740	160044759	-	1	NA	non-coding (NR_028111, exon 1 of 3)	non-coding (NR_028111, exon 1 of 3)	369	NM_001162896	67647	Mm.171518	NM_001024470	ENSMUSG00000090394	4930523C07Rik	-	RIKEN cDNA 4930523C07 gene	protein-coding
mm_116784.1	chr13	53286196	53286213	-	1	NA	promoter-TSS (NM_013846)	promoter-TSS (NM_013846)	-95	NM_013846	26564	Mm.342774	NM_013846	ENSMUSG00000021464	Ror2	Ntrkr2|mRor2	receptor tyrosine kinase-like orphan receptor 2	protein-coding
mm_48401.1	chr5	140206047	140206057	-	1	NA	intron (NM_010752, intron 10 of 17)	intron (NM_010752, intron 10 of 17)	115500	NM_010752	17120	Mm.27250	NM_010752	ENSMUSG00000029554	Mad1l1	AI173502|AW550425|Mad1	MAD1 mitotic arrest deficient 1-like 1	protein-coding
mm_126059.1	chr15	77015779	77015787	+	1	NA	3' UTR (NM_013593, exon 4 of 4)	3' UTR (NM_013593, exon 4 of 4)	6944	NM_001164048	17189	Mm.404074	NM_013593	ENSMUSG00000018893	Mb	AI325109	myoglobin	protein-coding
mm_93313.1	chr10	98898006	98898028	-	1	NA	Intergenic	Intergenic	-17135	NM_026482	67972	Mm.166944	NM_026482	ENSMUSG00000019943	Atp2b1	2810442I22Rik|E130111D10Rik|Pmca1	ATPase, Ca++ transporting, plasma membrane 1	protein-coding
mm_80237.1	chr9	72693195	72693209	+	1	NA	intron (NM_010890, intron 6 of 28)	intron (NM_010890, intron 6 of 28)	30855	NM_010890	17999	Mm.279923	NM_010890	ENSMUSG00000032216	Nedd4	AA959633|AL023035|AU019897|E430025J12Rik|Nedd4-1|Nedd4a|mKIAA0093	neural precursor cell expressed, developmentally down-regulated 4	protein-coding
mm_73106.1	chr8	94666653	94666676	+	1	NA	promoter-TSS (NM_024269)	promoter-TSS (NM_024269)	64	NM_024191	107566	Mm.393247	NM_024191	ENSMUSG00000031776	Arl2bp	1700010P10Rik|1700027H16Rik|6330544B05Rik|AI482273|AI849834|BART|Bart1	ADP-ribosylation factor-like 2 binding protein	protein-coding
mm_58768.1	chr7	15885144	15885155	+	1	NA	intron (NR_038092, intron 2 of 4)	Lx6|LINE|L1	2532	NR_038092	546024	Mm.259041	NM_001033638	ENSMUSG00000074365	Crxos	AA606869|AY590891|Crxos1|Egam1	cone-rod homeobox, opposite strand	protein-coding
mm_23443.1	chr3	59533414	59533416	+	1	NA	Intergenic	Intergenic	-189159	NM_001162884	242050	Mm.228086	NM_001162884	ENSMUSG00000036334	Igsf10	6530405F15Rik|9030224D03|AA409708|AA536958|AI414626|Adlican2|CMF608	immunoglobulin superfamily, member 10	protein-coding
mm_111056.1	chr12	80110202	80110213	-	1	NA	exon (NM_007564, exon 2 of 2)	exon (NM_007564, exon 2 of 2)	2806	NM_007564	12192	Mm.235132	NM_007564	ENSMUSG00000021127	Zfp36l1	AW742437|AW743212|Berg36|Brf1|D530020L18Rik|ERF1|TIS11b|cMG1	zinc finger protein 36, C3H type-like 1	protein-coding
mm_140872.1	chr17	23789881	23789913	-	1	NA	Intergenic	RMER10A|LTR|ERVL	-3820	NM_029798	76917	Mm.269613	NM_029798	ENSMUSG00000023911	Flywch2	2810417J12Rik|3010014L17Rik|AW548203	FLYWCH family member 2	protein-coding
mm_128704.1	chr15	63647891	63647904	-	1	NA	Intergenic	Intergenic	160842	NM_031378	83492	Mm.335619	NM_031378	ENSMUSG00000079025	Gsdmc	Gsdmc1|Mlze	gasdermin C	protein-coding
mm_125838.1	chr15	74958595	74958605	+	1	NA	exon (NM_001164036, exon 4 of 4)	exon (NM_001164036, exon 4 of 4)	3494	NM_001164040	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_37069.1	chr4	116144543	116144598	-	1	NA	promoter-TSS (NM_026547)	promoter-TSS (NM_026547)	46	NM_026547	68075	Mm.132803	NM_026547	ENSMUSG00000028701	Lurap1	1520402A15Rik|Lrp35a	leucine rich adaptor protein 1	protein-coding
mm_115784.1	chr13	19336826	19336831	-	1	NA	Intergenic	Intergenic	58985	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_80942.1	chr9	102717797	102717815	+	1	NA	promoter-TSS (NM_019764)	promoter-TSS (NM_019764)	2	NM_019764	56332	Mm.21145	NM_019764	ENSMUSG00000032531	Amotl2	AW549739|C79691|Lccp|MASCOT|mKIAA0989	angiomotin-like 2	protein-coding
mm_116523.1	chr13	45789233	45789253	-	1	NA	intron (NM_001199304, intron 4 of 6)	intron (NM_001199304, intron 4 of 6)	175748	NM_001199304	20238	Mm.342683	NM_009124	ENSMUSG00000046876	Atxn1	2900016G23Rik|Atx1|C85907|ENSMUSG00000074917|Gm10786|Sca1	ataxin 1	protein-coding
mm_114471.1	chr13	67863325	67863328	+	1	NA	promoter-TSS (NM_001001185)	promoter-TSS (NM_001001185)	0	NM_001001185	408058	Mm.177840	NM_001001185	ENSMUSG00000064063	BC048507	-	cDNA sequence BC048507	protein-coding
mm_110353.1	chr12	39006944	39006951	-	1	NA	Intergenic	RMER19C|LTR|ERVK	223236	NM_001163154	14009	Mm.4866	NM_007960	ENSMUSG00000004151	Etv1	ER81|Etsrp81	ets variant 1	protein-coding
mm_149091.1	chr19	8929414	8929448	+	1	NA	promoter-TSS (NM_144872)	promoter-TSS (NM_144872)	-75	NM_009073	19881	Mm.426094	NM_009073	ENSMUSG00000071648	Rom1	M101156|Rgsc1156|Rom-1|Rosp1|Tspan23	rod outer segment membrane protein 1	protein-coding
mm_104717.1	chr11	98053342	98053362	-	1	NA	5' UTR (NM_146028, exon 1 of 11)	5' UTR (NM_146028, exon 1 of 11)	110	NM_146028	217154	Mm.181008	NM_146028	ENSMUSG00000017400	Stac2	24b2|24b2/STAC2|AW240854	SH3 and cysteine rich domain 2	protein-coding
mm_44381.1	chr5	17821471	17821483	-	1	NA	intron (NM_007643, intron 3 of 14)	MIR3|SINE|MIR	14419	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_8114.1	chr1	135919322	135919339	-	1	NA	promoter-TSS (NM_019645)	promoter-TSS (NM_019645)	-123	NM_019645	18772	Mm.4494	NM_019645	ENSMUSG00000026413	Pkp1	-	plakophilin 1	protein-coding
mm_131980.1	chr16	25021985	25021995	+	1	NA	Intergenic	RLTR12A|LTR|ERVK	-37649	NR_040374	319487	Mm.137341	NR_040374	ENSMUSG00000096960	A230028O05Rik	-	RIKEN cDNA A230028O05 gene	ncRNA
mm_165090.1	chr19	52264634	52264644	+	1	NA	exon (NM_008386, exon 2 of 2)	exon (NM_008386, exon 2 of 2)	342	NM_008386	16333	Mm.46269	NM_008386	ENSMUSG00000035804	Ins1	Ins-1|Ins2-rs1	insulin I	protein-coding
mm_162404.1	chr1	86039660	86039662	+	1	NA	Intergenic	Intergenic	-6202	NM_001144993	72792	Mm.54981	NM_001144992	ENSMUSG00000026227	2810459M11Rik	-	RIKEN cDNA 2810459M11 gene	protein-coding
mm_134316.1	chr16	15895766	15895795	-	1	NA	intron (NM_146068, intron 17 of 19)	intron (NM_146068, intron 17 of 19)	8494	NM_007679	12609	Mm.347407	NM_007679	ENSMUSG00000071637	Cebpd	c/EBPdelta	CCAAT/enhancer binding protein (C/EBP), delta	protein-coding
mm_151899.1	chr19	5799161	5799167	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	-3183	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_167539.1	chr9	22105411	22105423	+	1	NA	exon (NM_009922, exon 4 of 7)	exon (NM_009922, exon 4 of 7)	6164	NM_009922	12797	Mm.4356	NM_009922	ENSMUSG00000001349	Cnn1	CN|CnnI	calponin 1	protein-coding
mm_46572.1	chr5	107289364	107289378	-	1	NA	5' UTR (NM_011578, exon 1 of 17)	5' UTR (NM_011578, exon 1 of 17)	224	NM_011578	21814	Mm.200775	NM_011578	ENSMUSG00000029287	Tgfbr3	1110036H20Rik|AU015626|AW215636|TBRIII	transforming growth factor, beta receptor III	protein-coding
mm_41153.1	chr5	87929811	87929815	+	1	NA	exon (NM_007786, exon 4 of 5)	exon (NM_007786, exon 4 of 5)	4180	NM_007786	12994	Mm.296303	NM_007786	ENSMUSG00000001622	Csn3	AW208918|CSN10|Csnk	casein kappa	protein-coding
mm_19517.1	chr2	94010730	94010764	-	1	NA	promoter-TSS (NM_026944)	promoter-TSS (NM_026944)	-17	NM_026944	69113	Mm.272498	NM_026944	ENSMUSG00000040174	Alkbh3	1700108H04Rik|1810020C19Rik|Abh3|mABH3	alkB homolog 3, alpha-ketoglutarate-dependent dioxygenase	protein-coding
mm_101821.1	chr11	46698609	46698623	-	1	NA	5' UTR (NM_001161355, exon 1 of 9)	5' UTR (NM_001161355, exon 1 of 9)	214	NM_001161355	171284	Mm.234654	NM_134249	ENSMUSG00000040413	Timd2	AA816106|AU019358|AU019662|C78111|G9D3|TIM-2|Tim2	T cell immunoglobulin and mucin domain containing 2	protein-coding
mm_121995.1	chr14	26534871	26534929	-	1	NA	promoter-TSS (NM_032008)	promoter-TSS (NM_032008)	-276	NM_001310445	83997	Mm.36769	NM_032008	ENSMUSG00000021870	Slmap	D330001L02Rik|Miranda|Slap|mKIAA1601	sarcolemma associated protein	protein-coding
mm_101296.1	chr11	22171407	22171426	-	1	NA	intron (NM_001252515, intron 6 of 24)	intron (NM_001252515, intron 6 of 24)	115379	NM_153078	216565	Mm.491265	NM_153078	ENSMUSG00000042302	Ehbp1	AF424697|Flj21950|NACSIN	EH domain binding protein 1	protein-coding
mm_19670.1	chr2	103372726	103372737	-	1	NA	promoter-TSS (NR_040332)	promoter-TSS (NR_040332)	33	NR_040332	319854	Mm.403818	NR_040332	ENSMUSG00000087278	A930006I01Rik	-	RIKEN cDNA A930006I01 gene	ncRNA
mm_151173.1	chr19	53310476	53310494	+	1	NA	promoter-TSS (NM_001008542)	promoter-TSS (NM_001008542)	-21	NM_001008542	17859	Mm.2154	NM_010847	ENSMUSG00000025025	Mxi1	ENSMUSG00000067085|Gm10197|Mad2|bHLHc11	MAX interactor 1, dimerization protein	protein-coding
mm_145898.1	chr18	65626849	65626854	+	1	NA	intron (NM_207255, intron 3 of 5)	AT_rich|Low_complexity|Low_complexity	-7236	NR_105742	100526497		NR_105742	ENSMUSG00000077113	Mir466p	mmu-mir-466p	microRNA 466p	ncRNA
mm_135125.1	chr16	35843814	35843829	-	1	NA	intron (NM_001039530, intron 12 of 16)	RLTR17B_Mm|LTR|ERVK	27561	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_74879.1	chr8	25087534	25087538	-	1	NA	intron (NM_031257, intron 2 of 11)	B1_Mur3|SINE|Alu	14275	NM_031257	83436	Mm.261122	NM_031257	ENSMUSG00000031557	Plekha2	6430512N22Rik|AI851530|AU041791|TAPP2|W91773	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 2	protein-coding
mm_54754.1	chr6	41034311	41034314	-	1	NA	exon (NM_023333, exon 2 of 5)	exon (NM_023333, exon 2 of 5)	1197	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_10751.1	chr2	23191007	23191024	+	1	NA	exon (NM_013771, exon 13 of 19)	exon (NM_013771, exon 13 of 19)	-16461	NM_027635	70981	Mm.314026	NM_027635	ENSMUSG00000026774	4931423N10Rik	-	RIKEN cDNA 4931423N10 gene	protein-coding
mm_36871.1	chr4	107177624	107177634	-	1	NA	exon (NM_025617, exon 2 of 5)	exon (NM_025617, exon 2 of 5)	737	NM_025617	66526	Mm.246956	NM_025617	ENSMUSG00000028619	Tceanc2	2210010B22Rik|2210012G02Rik|6330404A07Rik|AU015593|Tdeanc2	transcription elongation factor A (SII) N-terminal and central domain containing 2	protein-coding
mm_44899.1	chr5	35525543	35525566	-	1	NA	promoter-TSS (NM_153107)	promoter-TSS (NM_153107)	72	NM_153107	242939	Mm.108557	NM_153107	ENSMUSG00000036596	Cpz	AV136066	carboxypeptidase Z	protein-coding
mm_124329.1	chr14	103843595	103843601	-	1	NA	5' UTR (NM_001276296, exon 1 of 8)	5' UTR (NM_001276296, exon 1 of 8)	103	NM_007904	13618	Mm.229532	NM_007904	ENSMUSG00000022122	Ednrb	ET-B|ET-BR|ETR-b|ETb|Sox10m1	endothelin receptor type B	protein-coding
mm_37084.1	chr4	116404520	116404524	-	1	NA	intron (NM_008641, intron 3 of 28)	intron (NM_008641, intron 3 of 28)	59659	NM_001042743	17776	Mm.9287	NM_008641	ENSMUSG00000003810	Mast2	MAST205|Mtssk	microtubule associated serine/threonine kinase 2	protein-coding
mm_28855.1	chr3	96905295	96905341	-	1	NA	promoter-TSS (NM_026229)	promoter-TSS (NM_026229)	-20	NM_026229	67549	Mm.46722	NM_026229	ENSMUSG00000028096	Gpr89	4933412D19Rik|Gpr89a|SH120	G protein-coupled receptor 89	protein-coding
mm_151180.1	chr19	53329508	53329518	+	1	NA	promoter-TSS (NM_010847)	promoter-TSS (NM_010847)	100	NM_010847	17859	Mm.2154	NM_010847	ENSMUSG00000025025	Mxi1	ENSMUSG00000067085|Gm10197|Mad2|bHLHc11	MAX interactor 1, dimerization protein	protein-coding
mm_75955.1	chr8	71701743	71701754	-	1	NA	promoter-TSS (NM_028189)	promoter-TSS (NM_028189)	52	NM_028189	72297	Mm.290837	NM_028189	ENSMUSG00000031803	B3gnt3	2210008L19Rik	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 3	protein-coding
mm_30544.1	chr4	3683256	3683261	+	1	NA	intron (NM_010747, intron 1 of 12)	G-rich|Low_complexity|Low_complexity	5137	NM_010747	17096	Mm.317331	NM_010747	ENSMUSG00000042228	Lyn	AA407514|Hck-2|p53Lyn|p56Lyn	LYN proto-oncogene, Src family tyrosine kinase	protein-coding
mm_52691.1	chr6	118163118	118163122	+	1	NA	intron (NM_001080780, intron 18 of 18)	intron (NM_001080780, intron 18 of 18)	-23980	NM_030165	78752	Mm.300317	NM_030165	ENSMUSG00000042042	Csgalnact2	4632415D10Rik|Galnact2	chondroitin sulfate N-acetylgalactosaminyltransferase 2	protein-coding
mm_304.1	chr1	23761847	23761866	+	1	NA	promoter-TSS (NM_172124)	promoter-TSS (NM_172124)	-70	NM_172124	280645	Mm.471661	NM_172124	ENSMUSG00000026156	B3gat2	GlcAT-S|Glcats	beta-1,3-glucuronyltransferase 2 (glucuronosyltransferase S)	protein-coding
mm_35824.1	chr4	47057297	47057356	-	1	NA	promoter-TSS (NM_001024136)	promoter-TSS (NM_001024136)	-20	NM_001024136	75691	Mm.86866	NM_001024136	ENSMUSG00000066191	Anks6	2210417J20Rik|Ankrd14|Gm635|SamCystin|Samd6|b2b1801.1Clo	ankyrin repeat and sterile alpha motif domain containing 6	protein-coding
mm_51892.1	chr6	90618479	90618510	+	1	NA	promoter-TSS (NM_001037493)	promoter-TSS (NM_001037493)	-752	NM_001037493	71699	Mm.272633	NM_027868	ENSMUSG00000030089	Slc41a3	1010001P06Rik|AI480742|SLC41A1-L2	solute carrier family 41, member 3	protein-coding
mm_37733.1	chr4	129573638	129573652	-	1	NA	promoter-TSS (NM_001162433)	promoter-TSS (NM_001162433)	-4	NM_001162433	16818	Mm.293753	NM_010693	ENSMUSG00000000409	Lck	Hck-3|Lsk|Lskt|p56<lck>|p56Lck	lymphocyte protein tyrosine kinase	protein-coding
mm_143047.1	chr17	56874422	56874460	-	1	NA	promoter-TSS (NM_001039114)	promoter-TSS (NM_001039114)	6	NM_001039114	328845	Mm.179421	NM_001039114	ENSMUSG00000024207	Acsbg2	Bgr	acyl-CoA synthetase bubblegum family member 2	protein-coding
mm_100459.1	chr11	119856201	119856215	+	1	NA	intron (NM_028898, intron 17 of 33)	intron (NM_028898, intron 17 of 33)	-21843	NR_045312	319454	Mm.442144	NR_045312	ENSMUSG00000085081	Rptoros	A430071A18Rik	regulatory associated protein of MTOR, complex 1, opposite strand	ncRNA
mm_99920.1	chr11	110479303	110479345	+	1	NA	intron (NM_011943, intron 1 of 11)	intron (NM_011943, intron 1 of 11)	80202	NM_011943	26399	Mm.14487	NM_011943	ENSMUSG00000020623	Map2k6	MEK6|MKK6|Prkmk6|SAPKK3	mitogen-activated protein kinase kinase 6	protein-coding
mm_84290.1	chr9	63197360	63197395	-	1	NA	intron (NM_011840, intron 19 of 21)	intron (NM_011840, intron 19 of 21)	-48416	NM_001163758	207667	Mm.36349	NM_172446	ENSMUSG00000022245	Skor1	AV273001|C230094B15Rik|Corl1|Lbxcor1	SKI family transcriptional corepressor 1	protein-coding
mm_41650.1	chr5	98254175	98254190	+	1	NA	promoter-TSS (NM_001277268)	promoter-TSS (NM_001277268)	-2	NM_010203	14176	Mm.5055	NM_010203	ENSMUSG00000029337	Fgf5	Fgf-5|HBGF-5|angora|go	fibroblast growth factor 5	protein-coding
mm_159556.1	chr4	107068696	107068696	+	1	NA	exon (NM_001346552, exon 2 of 7)	exon (NM_001346552, exon 2 of 7)	1708	NM_175471	230582	Mm.44608	NM_175471	ENSMUSG00000028621	Cyb5rl	2810410C14Rik	cytochrome b5 reductase-like	protein-coding
mm_163531.1	chr13	9152359	9152378	-	1	NA	intron (NM_001311117, intron 11 of 16)	intron (NM_001311117, intron 11 of 16)	58487	NM_172585	217980	Mm.234944	NM_172585	ENSMUSG00000033499	Larp4b	A630096F19|AI256361|D13Wsu64e|Larp5	La ribonucleoprotein domain family, member 4B	protein-coding
mm_157565.1	chrX	52397187	52397201	-	1	NA	exon (NM_016697, exon 4 of 8)	exon (NM_016697, exon 4 of 8)	-19013	NR_105805	102465202		NR_105805	ENSMUSG00000105738	Mir6384	mmu-mir-6384	microRNA 6384	ncRNA
mm_95944.1	chr11	58384741	58384746	+	1	NA	exon (NM_001083884, exon 5 of 7)	exon (NM_001083884, exon 5 of 7)	4097	NM_001330197	70163	Mm.24119	NM_027339	ENSMUSG00000013643	Lypd8	2210415F13Rik	LY6/PLAUR domain containing 8	protein-coding
mm_83212.1	chr9	42069938	42069977	-	1	NA	intron (NM_011436, intron 8 of 47)	intron (NM_011436, intron 8 of 47)	54332	NM_011436	20660	Mm.121920	NM_011436	ENSMUSG00000049313	Sorl1	2900010L19Rik|AI596264|AW261561|LR11|SorLA|gp250|mSorLA	sortilin-related receptor, LDLR class A repeats-containing	protein-coding
mm_50651.1	chr6	51470340	51470350	+	1	NA	promoter-TSS (NM_007624)	promoter-TSS (NM_007624)	-271	NM_007624	12417	Mm.280968	NM_007624	ENSMUSG00000029836	Cbx3	HP1g|M32	chromobox 3	protein-coding
mm_41508.1	chr5	92371678	92371691	+	1	NA	intron (NM_001310664, intron 2 of 10)	intron (NM_001310664, intron 2 of 10)	-8388	NR_038116	56066	Mm.131723	NM_019494	ENSMUSG00000060183	Cxcl11	Cxc11|H174|I-tac|Ip9|Itac|Scyb11|Scyb9b|b-R1|betaR1	chemokine (C-X-C motif) ligand 11	protein-coding
mm_82831.1	chr9	31150070	31150086	-	1	NA	3' UTR (NM_009691, exon 16 of 16)	3' UTR (NM_009691, exon 16 of 16)	-18279	NM_011176	19143	Mm.243926	NM_011176	ENSMUSG00000031995	St14	Epithin|MT-SP1|Prss14|Tmprss14|mCAP3|matriptase	suppression of tumorigenicity 14 (colon carcinoma)	protein-coding
mm_137080.1	chr17	21423487	21423516	+	1	NA	5' UTR (NM_011760, exon 1 of 4)	5' UTR (NM_011760, exon 1 of 4)	274	NM_011760	22712	Mm.12916	NM_011760	ENSMUSG00000023882	Zfp54	2810034D10Rik|KRAB10|Zfp-54|Zfp76|mszf83	zinc finger protein 54	protein-coding
mm_109932.1	chr12	10724095	10724119	-	1	NA	Intergenic	Intergenic	277719	NR_110487	328061	Mm.56067	NR_110487		Gm38407	4931412M21	predicted gene, 38407	ncRNA
mm_136197.1	chr16	89571172	89571190	-	1	NA	promoter-TSS (NM_001113406)	promoter-TSS (NM_001113406)	2	NM_001113406	16693	Mm.310906	NM_001113406	ENSMUSG00000091212	Krtap11-1	AA162070|AA589467|AV018433|Hacl1|KAP11.1|PRED29	keratin associated protein 11-1	protein-coding
mm_152018.1	chr19	6015490	6015505	-	1	NA	promoter-TSS (NM_007600)	promoter-TSS (NM_007600)	-250	NM_007600	12333	Mm.6221	NM_007600	ENSMUSG00000024942	Capn1	Capa-1|Capa1|mu-calpin	calpain 1	protein-coding
mm_109953.1	chr12	11436551	11436603	-	1	NA	promoter-TSS (NM_012038)	promoter-TSS (NM_012038)	72	NM_012038	26950	Mm.27005	NM_012038	ENSMUSG00000054459	Vsnl1	VILIP|Vnsl1	visinin-like 1	protein-coding
mm_3489.1	chr1	150105855	150105864	+	1	NA	3' UTR (NM_011198, exon 10 of 10)	3' UTR (NM_011198, exon 10 of 10)	5828	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_130343.1	chr15	97731514	97731524	-	1	NA	promoter-TSS (NM_001168693)	promoter-TSS (NM_001168693)	-114	NM_001168693	19011	Mm.1001	NM_008902	ENSMUSG00000022468	Endou	Pp11r|Tcl-30	endonuclease, polyU-specific	protein-coding
mm_104401.1	chr11	94509797	94509797	-	1	NA	exon (NM_170671, exon 9 of 19)	exon (NM_170671, exon 9 of 19)	-9823	NM_027984	71889	Mm.248620	NM_027984	ENSMUSG00000010080	Epn3	2310022G12Rik	epsin 3	protein-coding
mm_57790.1	chr6	129271811	129271822	-	1	NA	intron (NM_001033122, intron 1 of 4)	intron (NM_001033122, intron 1 of 4)	3553	NM_001033122	12515	Mm.74745	NM_001033122	ENSMUSG00000030156	Cd69	5830438K24Rik|AI452015|AIM|VEA	CD69 antigen	protein-coding
mm_125367.1	chr15	39687282	39687286	+	1	NA	Intergenic	Intergenic	27773	NM_001256384	116838	Mm.309296	NM_053271	ENSMUSG00000037386	Rims2	2810036I15Rik|AW048769|RIM2|Rab3ip2|Rim2(+40A)|Rim2(+44A)|Rim2(+4A)|Serg2|Syt3-rs|mKIAA0751	regulating synaptic membrane exocytosis 2	protein-coding
mm_75426.1	chr8	47220620	47220630	-	1	NA	intron (NM_175162, intron 1 of 4)	intron (NM_175162, intron 1 of 4)	68777	NM_001286376	71069	Mm.23973	NM_175162	ENSMUSG00000038143	Stox2	4933409N07Rik|AI449080|AI835114|mKIAA1392	storkhead box 2	protein-coding
mm_57840.1	chr6	129465552	129465564	-	1	NA	exon (NM_020008, exon 5 of 6)	exon (NM_020008, exon 5 of 6)	7221	NM_001309637	56644	Mm.239516	NM_020008	ENSMUSG00000079293	Clec7a	BGR|Clecsf12|beta-GR	C-type lectin domain family 7, member a	protein-coding
mm_19519.1	chr2	94066703	94066711	-	1	NA	intron (NM_019657, intron 4 of 10)	intron (NM_019657, intron 4 of 10)	-55977	NM_026944	69113	Mm.272498	NM_026944	ENSMUSG00000040174	Alkbh3	1700108H04Rik|1810020C19Rik|Abh3|mABH3	alkB homolog 3, alpha-ketoglutarate-dependent dioxygenase	protein-coding
mm_46959.1	chr5	115119278	115119345	-	1	NA	promoter-TSS (NM_007383)	promoter-TSS (NM_007383)	35	NM_007383	11409	Mm.18759	NM_007383	ENSMUSG00000029545	Acads	AI196007|Bcd-1|Bcd1|Hdlq8|SCAD	acyl-Coenzyme A dehydrogenase, short chain	protein-coding
mm_25047.1	chr3	98302610	98302637	+	1	NA	exon (NM_008256, exon 8 of 10)	exon (NM_008256, exon 8 of 10)	22192	NM_008256	15360	Mm.289131	NM_008256	ENSMUSG00000027875	Hmgcs2	1300002P16|mHS	3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2	protein-coding
mm_37000.1	chr4	110292720	110292732	-	1	NA	intron (NM_001163397, intron 1 of 5)	intron (NM_001163397, intron 1 of 5)	-5199	NM_001347178	15572	Mm.3970	NM_010488	ENSMUSG00000028546	Elavl4	Elav|Hud|PNEM	ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4 (Hu antigen D)	protein-coding
mm_116797.1	chr13	53639188	53639202	-	1	NA	promoter-TSS (NR_131079)	promoter-TSS (NR_131079)	6	NR_131079	77398	Mm.174307	NR_131079		9530014B07Rik	-	RIKEN cDNA 9530014B07 gene	ncRNA
mm_49932.1	chr6	39437883	39437885	+	1	NA	Intergenic	RLTR1B|LTR|ERV1	-17515	NM_018810	54484	Mm.270484	NM_018810	ENSMUSG00000029922	Mkrn1	RFP	makorin, ring finger protein, 1	protein-coding
mm_48731.1	chr5	147430061	147430115	-	1	NA	promoter-TSS (NM_028291)	promoter-TSS (NM_028291)	-492	NM_028291	72587	Mm.320469	NM_028291	ENSMUSG00000029647	Pan3	2700050F09Rik|A430027N15Rik|AU014670	PAN3 poly(A) specific ribonuclease subunit	protein-coding
mm_35460.1	chr4	40717010	40717011	-	1	NA	Intergenic	Intergenic	5307	NR_077221	622208	Mm.471544	NR_077221		Gm6297	-	predicted gene 6297	ncRNA
mm_28392.1	chr3	90019233	90019244	-	1	NA	exon (NM_001165987, exon 15 of 25)	exon (NM_001165987, exon 15 of 25)	-8028	NR_106129	102465771		NR_106129	ENSMUSG00000098397	Mir7669	Gm27996|mmu-mir-7669	microRNA 7669	ncRNA
mm_92392.1	chr10	76599334	76599381	-	1	NA	3' UTR (NM_001347207, exon 28 of 28)	3' UTR (NM_001347207, exon 28 of 28)	23709	NM_080845	14317	Mm.36278	NM_080845	ENSMUSG00000001155	Ftcd	-	formiminotransferase cyclodeaminase	protein-coding
mm_63844.1	chr7	135651958	135651972	+	1	NA	promoter-TSS (NM_001316681)	promoter-TSS (NM_001316681)	66	NM_001316681	19267	Mm.945	NM_011212	ENSMUSG00000041836	Ptpre	PTPe|PTPepsilon|RPTPepsilon	protein tyrosine phosphatase, receptor type, E	protein-coding
mm_125390.1	chr15	40993928	40993937	+	1	NA	intron (NM_011766, intron 5 of 7)	intron (NM_011766, intron 5 of 7)	338890	NM_011766	22762	Mm.39496	NM_011766	ENSMUSG00000022306	Zfpm2	B330005D23Rik|FOG-2|FOG2	zinc finger protein, multitype 2	protein-coding
mm_6144.1	chr1	64927500	64927540	-	1	NA	intron (NM_001039493, intron 2 of 7)	intron (NM_001039493, intron 2 of 7)	29304	NM_001039493	241075	Mm.239534	NM_175509	ENSMUSG00000051344	Plekhm3	9430067K14Rik|A230102O09Rik|AI449570|DAPR|Plekhm1l	pleckstrin homology domain containing, family M, member 3	protein-coding
mm_35547.1	chr4	41503047	41503122	-	1	NA	promoter-TSS (NM_001085515)	promoter-TSS (NM_001085515)	-9	NM_001085515	329828	Mm.27054	NM_001085515	ENSMUSG00000046312	AI464131	AA408153|AI604836|Gm762|Kiaa1161|NET37	expressed sequence AI464131	protein-coding
mm_21347.1	chr2	157112838	157112864	-	1	NA	exon (NM_001139520, exon 9 of 17)	exon (NM_001139520, exon 9 of 17)	22371	NM_001139520	56045	Mm.248478	NM_018851	ENSMUSG00000027639	Samhd1	E330031J07Rik|Mg11	SAM domain and HD domain, 1	protein-coding
mm_33358.1	chr4	129487088	129487098	+	1	NA	3' UTR (NM_133889, exon 11 of 11)	3' UTR (NM_133889, exon 11 of 11)	3677	NM_080442	58864	Mm.143802	NM_080442	ENSMUSG00000000411	Tssk3	1700014N07Rik|4930594I21Rik|Stk22c|Stk22d|Tsk-3|Tssk-3|Tssk3b	testis-specific serine kinase 3	protein-coding
mm_14320.1	chr2	129365146	129365164	+	1	NA	exon (NM_008361, exon 7 of 7)	exon (NM_008361, exon 7 of 7)	-4747	NR_015474	329514	Mm.207315	NM_177848	ENSMUSG00000074805	Il1bos	9430083I22|Gm14047|OTTMUSG00000015529	interleukin 1 beta, opposite strand	ncRNA
mm_141264.1	chr17	27623758	27623785	-	1	NA	promoter-TSS (NM_001291046)	promoter-TSS (NM_001291046)	-319	NM_019837	56409	Mm.144699	NM_019837	ENSMUSG00000024213	Nudt3	1110011B09Rik|AA960325|Dipp|Dipp1	nudix (nucleotide diphosphate linked moiety X)-type motif 3	protein-coding
mm_8562.1	chr1	155279408	155279424	-	1	NA	3' UTR (NM_011273, exon 15 of 15)	3' UTR (NM_011273, exon 15 of 15)	120713	NM_021433	58244	Mm.66264	NM_021433	ENSMUSG00000026470	Stx6	2310039E05Rik|2410005I16Rik|AA437559|AI415714|AI845861	syntaxin 6	protein-coding
mm_104770.1	chr11	98545808	98545819	-	1	NA	5' UTR (NM_011771, exon 1 of 8)	5' UTR (NM_011771, exon 1 of 8)	218	NM_011771	22780	Mm.133367	NM_011771	ENSMUSG00000018168	Ikzf3	5830411O07Rik|Aiolos|Zfpn1a3|Znfn1a3	IKAROS family zinc finger 3	protein-coding
mm_50890.1	chr6	56746549	56746559	+	1	NA	intron (NM_030235, intron 13 of 15)	B1_Mur1|SINE|Alu	31649	NM_030235	78937	Mm.105343	NM_030235	ENSMUSG00000029787	Avl9	5830411G16Rik|D730049P16Rik|mKIAA0241	AVL9 cell migration associated	protein-coding
mm_36601.1	chr4	88917245	88917254	-	1	NA	intron (NR_132735, intron 2 of 2)	intron (NR_132735, intron 2 of 2)	-6587	NR_029747	723895		NR_029747	ENSMUSG00000065408	Mir31	Mirn31|miR-31|mmu-mir-31	microRNA 31	ncRNA
mm_42712.1	chr5	120431970	120431980	+	1	NA	promoter-TSS (NM_008499)	promoter-TSS (NM_008499)	89	NM_008499	16873	Mm.5151	NM_008499	ENSMUSG00000029595	Lhx5	Lim2	LIM homeobox protein 5	protein-coding
mm_85924.1	chr9	111690215	111690240	-	1	NA	5' UTR (NM_001324546, exon 1 of 10)	5' UTR (NM_001324546, exon 1 of 10)	121	NM_016853	20840	Mm.1414	NM_016853	ENSMUSG00000032502	Stac	-	src homology three (SH3) and cysteine rich domain	protein-coding
mm_12183.1	chr2	65237834	65237846	+	1	NA	intron (NM_027225, intron 1 of 12)	intron (NM_027225, intron 1 of 12)	786	NM_177025	319876	Mm.34159	NM_027225	ENSMUSG00000034903	Cobll1	1810047P18Rik|Coblr1|D430044D16Rik	Cobl-like 1	protein-coding
mm_73424.1	chr8	106117832	106117835	+	1	NA	intron (NM_010901, intron 9 of 9)	ID_B1|SINE|B4	-17567	NR_040345	69771	Mm.393274	NR_040344		1810019D21Rik	-	RIKEN cDNA 1810019D21 gene	ncRNA
mm_148229.1	chr18	80363671	80363675	-	1	NA	intron (NM_001190373, intron 1 of 3)	CpG	581	NM_001190373	240444	Mm.279568	NM_001190373	ENSMUSG00000059852	Kcng2	AA591524	potassium voltage-gated channel, subfamily G, member 2	protein-coding
mm_57706.1	chr6	128543380	128543436	-	1	NA	intron (NM_001001179, intron 31 of 35)	intron (NM_001001179, intron 31 of 35)	-16688	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_88973.1	chr10	81419996	81420010	+	1	NA	intron (NM_026756, intron 2 of 8)	intron (NM_026756, intron 2 of 8)	-3706	NR_106141	102465778		NR_106141	ENSMUSG00000105379	Mir1191b	mmu-mir-1191b	microRNA 1191b	ncRNA
mm_11735.1	chr2	37532776	37532779	+	1	NA	intron (NM_001033960, intron 14 of 18)	intron (NM_001033960, intron 14 of 18)	16151	NM_177383	338346	Mm.445325	NM_177383	ENSMUSG00000053164	Gpr21	C230004C13Rik	G protein-coupled receptor 21	protein-coding
mm_151323.1	chr19	55893125	55893131	+	1	NA	intron (NR_138565, intron 4 of 15)	intron (NR_138565, intron 4 of 15)	-2193	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_114099.1	chr13	54720146	54720161	+	1	NA	exon (NM_001033364, exon 15 of 32)	exon (NM_001033364, exon 15 of 32)	18690	NM_001033364	268663	Mm.315382	NM_001033364	ENSMUSG00000034918	Cdhr2	Gm624|PC-LKC|Pcdh24	cadherin-related family member 2	protein-coding
mm_137309.1	chr17	24878695	24878705	+	1	NA	promoter-TSS (NM_008340)	promoter-TSS (NM_008340)	-70	NM_008340	16005	Mm.3135	NM_008340	ENSMUSG00000046070	Igfals	ALS|Albs|mKIAA4111	insulin-like growth factor binding protein, acid labile subunit	protein-coding
mm_69495.1	chr7	134225106	134225136	-	1	NA	promoter-TSS (NM_007400)	promoter-TSS (NM_007400)	-24	NM_007400	11489	Mm.439714	NM_007400	ENSMUSG00000054555	Adam12	Mltna	a disintegrin and metallopeptidase domain 12 (meltrin alpha)	protein-coding
mm_11449.1	chr2	32083280	32083290	+	1	NA	5' UTR (NM_175511, exon 1 of 2)	5' UTR (NM_175511, exon 1 of 2)	420	NM_175511	241303	Mm.250441	NM_175511	ENSMUSG00000050592	Fam78a	A130092J06Rik	family with sequence similarity 78, member A	protein-coding
mm_71488.1	chr8	46740290	46740308	+	1	NA	promoter-TSS (NR_045750)	promoter-TSS (NR_045750)	554	NM_008391	16363	Mm.1149	NM_008391	ENSMUSG00000031627	Irf2	9830146E22Rik|AI646973|Irf-2	interferon regulatory factor 2	protein-coding
mm_168986.1	chr12	95585399	95585403	-	1	NA	Intergenic	L1Md_T|LINE|L1	-106825	NM_201518	399558	Mm.341948	NM_201518	ENSMUSG00000047414	Flrt2	-	fibronectin leucine rich transmembrane protein 2	protein-coding
mm_83908.1	chr9	56259149	56259176	-	1	NA	exon (NM_172924, exon 4 of 7)	exon (NM_172924, exon 4 of 7)	-98092	NM_019793	56434	Mm.28484	NM_019793	ENSMUSG00000032324	Tspan3	1700055K04Rik|TM4-A|Tm4sf8	tetraspanin 3	protein-coding
mm_5106.1	chr1	5084524	5084544	-	1	NA	exon (NM_133826, exon 2 of 14)	exon (NM_133826, exon 2 of 14)	1448	NM_001310442	108664	Mm.27082	NM_133826	ENSMUSG00000033793	Atp6v1h	0710001F19Rik|AU022349|CGI-11|SFD|SFDalpha|SFDbeta|VMA13	ATPase, H+ transporting, lysosomal V1 subunit H	protein-coding
mm_106892.1	chr12	8012332	8012338	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	34658	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_31966.1	chr4	86930763	86930773	+	1	NA	intron (NM_001290543, intron 5 of 5)	intron (NM_001290543, intron 5 of 5)	56354	NM_139306	230379	Mm.45019	NM_139306	ENSMUSG00000038007	Acer2	2410116I05Rik|Asah3l|CRG-L1|maCER2	alkaline ceramidase 2	protein-coding
mm_108516.1	chr12	84038389	84038435	+	1	NA	promoter-TSS (NM_134247)	promoter-TSS (NM_134247)	33	NM_134247	171282	Mm.482217	NM_134247	ENSMUSG00000052392	Acot4	B430212I04Rik|PTE-Ib|Pte1b|Pte2b	acyl-CoA thioesterase 4	protein-coding
mm_133989.1	chr16	4634377	4634426	-	1	NA	exon (NM_030205, exon 14 of 28)	exon (NM_030205, exon 14 of 28)	-5544	NM_139307	246154	Mm.482140	NM_139307	ENSMUSG00000039646	Vasn	2610528G05Rik|Atia|Slitl2	vasorin	protein-coding
mm_113406.1	chr13	33964685	33964704	+	1	NA	promoter-TSS (NM_001163241)	promoter-TSS (NM_001163241)	35	NM_001163241	18105	Mm.264036	NM_020282	ENSMUSG00000046949	Nqo2	NMO2|Nmor2|Ox2	NAD(P)H dehydrogenase, quinone 2	protein-coding
mm_123505.1	chr14	66232403	66232419	-	1	NA	intron (NM_001162365, intron 1 of 30)	intron (NM_001162365, intron 1 of 30)	-18859	NM_001162366	19229	Mm.21613	NM_172498	ENSMUSG00000059456	Ptk2b	CADTK|CAKB|CAKbeta|E430023O05Rik|FADK2|FAK2|PYK2|Raftk	PTK2 protein tyrosine kinase 2 beta	protein-coding
mm_138248.1	chr17	34589915	34589928	+	1	NA	5' UTR (NM_134116, exon 1 of 4)	5' UTR (NM_134116, exon 1 of 4)	115	NM_134116	106512	Mm.26584	NM_134116	ENSMUSG00000034786	Gpsm3	AA960287|AGS4	G-protein signalling modulator 3 (AGS3-like, C. elegans)	protein-coding
mm_58415.1	chr7	3290554	3290586	+	1	NA	promoter-TSS (NM_016969)	promoter-TSS (NM_016969)	14	NM_001093765	50918	Mm.29874	NM_016969	ENSMUSG00000068566	Myadm	D7Wsu62e	myeloid-associated differentiation marker	protein-coding
mm_104700.1	chr11	97988709	97988723	-	1	NA	TTS (NM_207231)	TTS (NM_207231)	-2270	NM_001163608	72324	Mm.39617	NM_028199	ENSMUSG00000017417	Plxdc1	2410003I07Rik|AI848450|Tem7	plexin domain containing 1	protein-coding
mm_65534.1	chr7	25816501	25816535	-	1	NA	promoter-TSS (NM_028775)	promoter-TSS (NM_028775)	12	NM_028775	74134	Mm.275188	NM_028775	ENSMUSG00000040703	Cyp2s1	1200011C15Rik|AU041727|C79779	cytochrome P450, family 2, subfamily s, polypeptide 1	protein-coding
mm_166462.1	chr5	140830155	140830192	-	1	NA	exon (NM_010302, exon 1 of 4)	exon (NM_010302, exon 1 of 4)	258	NM_010302	14673	Mm.370185	NM_010302	ENSMUSG00000000149	Gna12	AI414047|AI504261|Galpha12	guanine nucleotide binding protein, alpha 12	protein-coding
mm_29737.1	chr3	126922753	126922773	-	1	NA	3' UTR (NM_178655, exon 25 of 25)	3' UTR (NM_178655, exon 25 of 25)	20623	NM_001034168	109676	Mm.220242	NM_178655	ENSMUSG00000032826	Ank2	100043364|AI835472|AW491075|Ank-2|Gm4392	ankyrin 2, brain	protein-coding
mm_142071.1	chr17	35697981	35698001	-	1	NA	intron (NM_007584, intron 1 of 17)	intron (NM_007584, intron 1 of 17)	2599	NM_001198833	12305	Mm.5021	NM_007584	ENSMUSG00000003534	Ddr1	6030432F18|AI323681|CD167a|Cak|Nep|PTK3A	discoidin domain receptor family, member 1	protein-coding
mm_51285.1	chr6	72304320	72304330	+	1	NA	promoter-TSS (NM_001282071)	promoter-TSS (NM_001282071)	-285	NM_001282071	20388	Mm.46033	NM_147779	ENSMUSG00000056370	Sftpb	AI562151|SF-B|SP-B|Sftp-3|Sftp3	surfactant associated protein B	protein-coding
mm_24731.1	chr3	95283014	95283056	+	1	NA	promoter-TSS (NM_133858)	promoter-TSS (NM_133858)	100	NM_199475	75007	Mm.279287	NM_133858	ENSMUSG00000038712	Fam63a	1810005H09Rik|4930504E06Rik|AA562754|AA960384|AW561904|cI-40|mKIAA1390|ni	family with sequence similarity 63, member A	protein-coding
mm_132581.1	chr16	38347256	38347260	+	1	NA	intron (NM_001017429, intron 1 of 2)	intron (NM_001017429, intron 1 of 2)	259	NM_001017429	12856	Mm.27396	NM_001017429	ENSMUSG00000046516	Cox17	AI037035	cytochrome c oxidase assembly protein 17	protein-coding
mm_35685.1	chr4	44012486	44012528	-	1	NA	promoter-TSS (NM_001080385)	promoter-TSS (NM_001080385)	-136	NM_016760	12757	Mm.298875	NM_016760	ENSMUSG00000028478	Clta	AV026556|Lca	clathrin, light polypeptide (Lca)	protein-coding
mm_21803.1	chr2	164911587	164911608	-	1	NA	5' UTR (NM_199027, exon 1 of 28)	5' UTR (NM_199027, exon 1 of 28)	153	NM_199027	329559	Mm.330776	NM_199027	ENSMUSG00000039834	Zfp335	1810045J01Rik|NIF-1|Nif1|Znf335	zinc finger protein 335	protein-coding
mm_115597.1	chr13	11833562	11833566	-	1	NA	intron (NM_023868, intron 13 of 104)	intron (NM_023868, intron 13 of 104)	273381	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding
mm_133971.1	chr16	4374985	4374998	-	1	NA	intron (NM_001291910, intron 3 of 11)	intron (NM_001291910, intron 3 of 11)	45507	NM_001291910	11515	Mm.439750	NM_009624	ENSMUSG00000005580	Adcy9	AC9|ACtp10|AW125421|D16Wsu65e|mKIAA0520	adenylate cyclase 9	protein-coding
mm_136525.1	chr16	97459882	97459899	-	1	NA	intron (NR_003520, intron 2 of 8)	MTD|LTR|ERVL-MaLR	3015	NM_010846	17857	Mm.33996	NM_010846	ENSMUSG00000000386	Mx1	AI893580|Mx|Mx-1	MX dynamin-like GTPase 1	protein-coding
mm_53127.1	chr6	125136678	125136681	+	1	NA	intron (NM_138747, intron 5 of 15)	intron (NM_138747, intron 5 of 15)	4796	NM_138747	110109	Mm.29203	NM_138747	ENSMUSG00000038279	Nop2	120kDa|A530002O17|Nol1	NOP2 nucleolar protein	protein-coding
mm_45626.1	chr5	76231301	76231303	-	1	NA	intron (NM_001305222, intron 18 of 21)	intron (NM_001305222, intron 18 of 21)	47422	NM_011626	21982	Mm.790	NM_011626	ENSMUSG00000029234	Tmem165	AV026557|Tpardl|Tparl|pFT27	transmembrane protein 165	protein-coding
mm_24587.1	chr3	93444986	93444992	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	2659	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_20211.1	chr2	125506396	125506408	-	1	NA	promoter-TSS (NM_007993)	promoter-TSS (NM_007993)	36	NM_007993	14118	Mm.271644	NM_007993	ENSMUSG00000027204	Fbn1	AI536462|B430209H23|Fib-1|Tsk	fibrillin 1	protein-coding
mm_54345.1	chr6	30710528	30710538	-	1	NA	Intergenic	Intergenic	-16784	NR_130781	83922	Mm.65389	NM_031998	ENSMUSG00000029790	Cep41	1700017E11Rik|2810431D15Rik|Tsga14	centrosomal protein 41	protein-coding
mm_147002.1	chr18	34373299	34373306	-	1	NA	exon (NM_007874, exon 1 of 5)	exon (NM_007874, exon 1 of 5)	113	NM_007874	13476	Mm.280075	NM_007874	ENSMUSG00000005873	Reep5	AI324241|AU022809|AW495741|DP1/TB2|Dp1|R74856|TB2/DP1	receptor accessory protein 5	protein-coding
mm_13093.1	chr2	91256114	91256124	+	1	NA	promoter-TSS (NM_030880)	promoter-TSS (NM_030880)	-46	NM_001289677	80708	Mm.236650	NM_028733	ENSMUSG00000027257	Pacsin3	4921507A02Rik|6330413E15Rik|AW413130	protein kinase C and casein kinase substrate in neurons 3	protein-coding
mm_133704.1	chr16	93124008	93124029	+	1	NA	Intergenic	Intergenic	229171	NR_040486	69857	Mm.81192	NR_040486	ENSMUSG00000100277	1810053B23Rik	1810008L18Rik|1810056K14Rik	RIKEN cDNA 1810053B23 gene	ncRNA
mm_30864.1	chr4	31963923	31963980	+	1	NA	promoter-TSS (NM_009316)	promoter-TSS (NM_009316)	-156	NM_009316	26409	Mm.258589	NM_009316	ENSMUSG00000028284	Map3k7	B430101B05|C87327|Tak1	mitogen-activated protein kinase kinase kinase 7	protein-coding
mm_62401.1	chr7	101108789	101108811	+	1	NA	promoter-TSS (NM_001146010)	promoter-TSS (NM_001146010)	25	NM_199012	207278	Mm.263041	NM_199012	ENSMUSG00000030691	Fchsd2	BC034086|R74866|Sh3md3|mKIAA0769	FCH and double SH3 domains 2	protein-coding
mm_50388.1	chr6	48700530	48700540	+	1	NA	Intergenic	Intergenic	7709	NM_153175	231931	Mm.321047	NM_153175	ENSMUSG00000047867	Gimap6	4833419H03Rik|Ian6|mFLJ00102	GTPase, IMAP family member 6	protein-coding
mm_110178.1	chr12	27337122	27337136	-	1	NA	3' UTR (NM_009234, exon 1 of 1)	3' UTR (NM_009234, exon 1 of 1)	5589	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding
mm_64497.1	chr7	143473751	143473808	+	1	NA	promoter-TSS (NM_008767)	promoter-TSS (NM_008767)	24	NM_008767	18400	Mm.271740	NM_008767	ENSMUSG00000000154	Slc22a18	AW260131|BWR1A|BWSCR1A|HET|ITM|Impt1|Orctl2|Slc22a1l|TSSC5|p45-BWR1A	solute carrier family 22 (organic cation transporter), member 18	protein-coding
mm_70681.1	chr8	14996129	14996144	+	1	NA	intron (NM_172751, intron 27 of 28)	intron (NM_172751, intron 27 of 28)	-14889	NM_029116	74901	Mm.46675	NM_029116	ENSMUSG00000055675	Kbtbd11	2900016B01Rik|4930465M17Rik|mKIAA0711	kelch repeat and BTB (POZ) domain containing 11	protein-coding
mm_141743.1	chr17	34129401	34129412	-	1	NA	intron (NM_010386, intron 1 of 5)	intron (NM_010386, intron 1 of 5)	6574	NM_010386	14998	Mm.16373	NM_010386	ENSMUSG00000037649	H2-DMa	H-2Ma|H2-Ma	histocompatibility 2, class II, locus DMa	protein-coding
mm_114624.1	chr13	76098764	76098774	+	1	NA	promoter-TSS (NM_001081352)	promoter-TSS (NM_001081352)	35	NM_001081352	218343	Mm.277964	NM_001081352	ENSMUSG00000033991	Ttc37	mKIAA0372	tetratricopeptide repeat domain 37	protein-coding
mm_138957.1	chr17	44188654	44188664	+	1	NA	promoter-TSS (NM_172621)	promoter-TSS (NM_172621)	87	NM_172621	224796	Mm.37666	NM_172621	ENSMUSG00000023959	Clic5	5730531E12Rik|B330005L24|Gm322|jbg	chloride intracellular channel 5	protein-coding
mm_136316.1	chr16	91729061	91729092	-	1	NA	promoter-TSS (NM_001110276)	promoter-TSS (NM_001110276)	-274	NM_133679	66609	Mm.109823	NM_026994	ENSMUSG00000058240	Cryzl1	2210407J23Rik|2410006O11Rik|QOH-1	crystallin, zeta (quinone reductase)-like 1	protein-coding
mm_37303.1	chr4	119257154	119257173	-	1	NA	exon (NM_153105, exon 3 of 4)	exon (NM_153105, exon 3 of 4)	1694	NM_001038590	242653	Mm.130701	NM_153105	ENSMUSG00000066058	Cldn19	-	claudin 19	protein-coding
mm_16234.1	chr2	173156277	173156291	+	1	NA	intron (NM_011044, intron 6 of 9)	intron (NM_011044, intron 6 of 9)	3211	NM_011044	18534	Mm.266867	NM_011044	ENSMUSG00000027513	Pck1	AI265463|PEPCK|Pck-1	phosphoenolpyruvate carboxykinase 1, cytosolic	protein-coding
mm_142366.1	chr17	44105888	44105896	-	1	NA	promoter-TSS (NM_199016)	promoter-TSS (NM_199016)	-84	NM_199016	224794	Mm.255971	NM_199016	ENSMUSG00000023961	Enpp4	4933413N07Rik|AA986363|AI195364|E-NPP 4|Gm90|mKIAA0879	ectonucleotide pyrophosphatase/phosphodiesterase 4	protein-coding
mm_158098.1	chrX	101734126	101734142	-	1	NA	promoter-TSS (NM_009910)	promoter-TSS (NM_009910)	13	NM_009910	12766	Mm.12876	NM_009910	ENSMUSG00000050232	Cxcr3	Cd183|Cmkar3	chemokine (C-X-C motif) receptor 3	protein-coding
mm_147252.1	chr18	38603094	38603113	-	1	NA	Intergenic	Intergenic	-1835	NM_011898	24066	Mm.42038	NM_011898	ENSMUSG00000024427	Spry4	A030006O18Rik|sprouty4	sprouty homolog 4 (Drosophila)	protein-coding
mm_93569.1	chr10	116559295	116559300	-	1	NA	intron (NM_001037846, intron 1 of 15)	Charlie4a|DNA|hAT-Charlie	22214	NM_001037848	72068	Mm.351553	NM_028082	ENSMUSG00000020166	Cnot2	2600016M12Rik|2810470K03Rik|AA537049|AA959607|AW557563|C79650	CCR4-NOT transcription complex, subunit 2	protein-coding
mm_22843.1	chr3	27984146	27984200	+	1	NA	promoter-TSS (NM_008875)	promoter-TSS (NM_008875)	2	NM_008875	18805	Mm.212039	NM_008875	ENSMUSG00000027695	Pld1	AA536939|C85393|Pld1a|Pld1b|mPLD1	phospholipase D1	protein-coding
mm_17633.1	chr2	31054198	31054209	-	1	NA	exon (NM_019406, exon 9 of 9)	exon (NM_019406, exon 9 of 9)	42297	NM_001177650	14269	Mm.52297	NM_019406	ENSMUSG00000075415	Fnbp1	1110057E06Rik|2210010H06Rik|FBP1|Fbp17	formin binding protein 1	protein-coding
mm_119173.1	chr14	32159902	32159989	+	1	NA	promoter-TSS (NM_001033988)	promoter-TSS (NM_001033988)	58	NM_001033988	27057	Mm.371598	NM_019744	ENSMUSG00000056234	Ncoa4	ARA70|Rfg	nuclear receptor coactivator 4	protein-coding
mm_24493.1	chr3	92365882	92365890	+	1	NA	5' UTR (NM_011472, exon 2 of 2)	5' UTR (NM_011472, exon 2 of 2)	699	NM_011472	20760	Mm.10692	NM_011472	ENSMUSG00000050635	Sprr2f	-	small proline-rich protein 2F	protein-coding
mm_145026.1	chr18	39031544	39031544	+	1	NA	intron (NM_175164, intron 1 of 22)	intron (NM_175164, intron 1 of 22)	38399	NM_175164	71302	Mm.329396	NM_175164	ENSMUSG00000036452	Arhgap26	1810044B20Rik|2610010G17Rik|4933432P15Rik|AI853435|mKIAA0621	Rho GTPase activating protein 26	protein-coding
mm_91358.1	chr10	28973965	28973968	-	1	NA	exon (NM_026336, exon 5 of 6)	exon (NM_026336, exon 5 of 6)	12340	NM_026336	67719	Mm.440480	NM_026336	ENSMUSG00000015519	2310057J18Rik	2210414P04Rik|Leg1	RIKEN cDNA 2310057J18 gene	protein-coding
mm_116059.1	chr13	27511570	27511574	-	1	NA	exon (NM_023741, exon 2 of 6)	exon (NM_023741, exon 2 of 6)	1641	NM_023741	74188	Mm.46090	NM_023741	ENSMUSG00000021346	Prl8a8	1600032B14Rik|Ghd14|PLP-Cgamma|Prlpc3	prolactin family 8, subfamily a, member 81	protein-coding
mm_89007.1	chr10	81628547	81628567	+	1	NA	promoter-TSS (NM_027480)	promoter-TSS (NM_027480)	17	NM_027480	70615	Mm.304382	NM_027480	ENSMUSG00000054708	Ankrd24	4631433D01Rik|5730519E19Rik|D10Bur2e	ankyrin repeat domain 24	protein-coding
mm_24720.1	chr3	95234705	95234722	+	1	NA	3' UTR (NM_172395, exon 5 of 5)	3' UTR (NM_172395, exon 5 of 5)	5770	NM_001038708	57912	Mm.28189	NM_172395	ENSMUSG00000046722	Cdc42se1	1300002M12Rik|AW558204|Cdcse1|SCIP1|Spec1	CDC42 small effector 1	protein-coding
mm_71731.1	chr8	61986904	61986913	+	1	NA	intron (NM_001293783, intron 22 of 37)	MIRb|SINE|MIR	58821	NM_001293783	234311	Mm.275233	NM_144928	ENSMUSG00000037921	Ddx60	9830118M07	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	protein-coding
mm_62414.1	chr7	101301869	101301901	+	1	NA	intron (NM_001111111, intron 1 of 17)	CpG	203	NM_001111111	73683	Mm.275744	NM_001111111	ENSMUSG00000047767	Atg16l2	2410118P20Rik	autophagy related 16-like 2 (S. cerevisiae)	protein-coding
mm_35490.1	chr4	40948132	40948150	-	1	NA	promoter-TSS (NM_029814)	promoter-TSS (NM_029814)	153	NM_009736	12017	Mm.688	NM_009736	ENSMUSG00000028416	Bag1	BAG-1|Rap46	BCL2-associated athanogene 1	protein-coding
mm_141295.1	chr17	28080061	28080100	-	1	NA	exon (NM_013687, exon 2 of 10)	exon (NM_013687, exon 2 of 10)	504	NM_013687	21463	Mm.29758	NM_013687	ENSMUSG00000062859	Tcp11	D17Ken1|Tcp-11	t-complex protein 11	protein-coding
mm_34674.1	chr4	150929711	150929757	+	1	NA	intron (NM_001077509, intron 1 of 7)	intron (NM_001077509, intron 1 of 7)	1735	NM_001077509	21942	Mm.244187	NM_011612	ENSMUSG00000028965	Tnfrsf9	4-1BB|A930040I11Rik|AA408498|AI325004|CDw137|Cd137|ILA|Ly63	tumor necrosis factor receptor superfamily, member 9	protein-coding
mm_50449.1	chr6	48904980	48904991	+	1	NA	promoter-TSS (NM_001161622)	promoter-TSS (NM_001161622)	-1	NM_001161622	76507	Mm.213898	NM_029638	ENSMUSG00000029811	Aoc1	1600012D06Rik|Abp1|DAO	amine oxidase, copper-containing 1	protein-coding
mm_138751.1	chr17	37045981	37046080	+	1	NA	promoter-TSS (NM_019439)	promoter-TSS (NM_019439)	64	NM_019439	54393	Mm.32191	NM_019439	ENSMUSG00000024462	Gabbr1	GABAB1|GABAbR1|bM573K1.1	gamma-aminobutyric acid (GABA) B receptor, 1	protein-coding
mm_134050.1	chr16	5367860	5367868	-	1	NA	Intergenic	MT2A|LTR|ERVL	-111908	NM_027446	70511	Mm.45780	NM_027446	ENSMUSG00000022544	Eef2kmt	5730409G15Rik|Fam86|Fam86a|eEF2-KMT	eukaryotic elongation factor 2 lysine methyltransferase	protein-coding
mm_36167.1	chr4	61780812	61780846	-	1	NA	exon (NM_001135127, exon 3 of 7)	exon (NM_001135127, exon 3 of 7)	1394	NM_001134644	100048885	Mm.422695	NM_001134644		Gm2083	-	major urinary protein LOC100048885	protein-coding
mm_35189.1	chr4	16013805	16013808	-	1	NA	promoter-TSS (NM_145950)	promoter-TSS (NM_145950)	71	NM_145950	209212	Mm.46455	NM_145950	ENSMUSG00000041153	Osgin2	BC010311|C230027H09Rik	oxidative stress induced growth inhibitor family member 2	protein-coding
mm_16753.1	chr2	9867554	9867557	-	1	NA	intron (NM_008091, intron 4 of 5)	intron (NM_008091, intron 4 of 5)	11045	NM_008091	14462	Mm.313866	NM_008091	ENSMUSG00000015619	Gata3	Gata-3|jal	GATA binding protein 3	protein-coding
mm_29161.1	chr3	106163370	106163375	-	1	NA	intron (NM_009892, intron 3 of 10)	B1_Mus1|SINE|Alu	4192	NM_009892	12655	Mm.387173	NM_009892	ENSMUSG00000040809	Chil3	AI505981|Chi3l3|ECF-L|Ym1	chitinase-like 3	protein-coding
mm_137966.1	chr17	33432891	33432911	+	1	NA	promoter-TSS (NM_183282)	promoter-TSS (NM_183282)	2	NM_183282	69481	Mm.154333	NM_183282	ENSMUSG00000092519	Actl9	1700029I08Rik|AV259599	actin-like 9	protein-coding
mm_160880.1	chr11	69324140	69324140	+	1	NA	promoter-TSS (NM_172560)	promoter-TSS (NM_172560)	154	NM_001024206	245828	Mm.28073	NM_001024206	ENSMUSG00000049299	Trappc1	BET5|D11Ertd172e|MUM2	trafficking protein particle complex 1	protein-coding
mm_71424.1	chr8	46491080	46491082	+	1	NA	5' UTR (NM_001302163, exon 1 of 21)	5' UTR (NM_001302163, exon 1 of 21)	115	NM_001302163	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_87404.1	chr10	45634638	45634640	+	1	NA	intron (NM_172473, intron 6 of 23)	intron (NM_172473, intron 6 of 23)	56810	NM_172473	209462	Mm.458633	NM_172473	ENSMUSG00000038822	Hace1	1700042J16Rik|A730034A22Rik|BC025474	HECT domain and ankyrin repeat containing, E3 ubiquitin protein ligase 1	protein-coding
mm_105580.1	chr11	106665446	106665449	-	1	NA	intron (NM_001305157, intron 14 of 15)	intron (NM_001305157, intron 14 of 15)	49834	NM_001305158	18613	Mm.343951	NM_008816	ENSMUSG00000020717	Pecam1	C85791|Cd31|PECAM-1|Pecam	platelet/endothelial cell adhesion molecule 1	protein-coding
mm_154879.1	chrX	20695505	20695529	+	1	NA	exon (NM_011049, exon 7 of 16)	exon (NM_011049, exon 7 of 16)	7091	NM_011049	18555	Mm.102574	NM_011049	ENSMUSG00000031065	Cdk16	Crk5|Pctaire1|Pctk1	cyclin-dependent kinase 16	protein-coding
mm_141699.1	chr17	33996385	33996430	-	1	NA	3' UTR (NM_001001892, exon 8 of 8)	3' UTR (NM_001001892, exon 8 of 8)	3926	NM_001001892	14972	Mm.422886	NM_001001892	ENSMUSG00000061232	H2-K1	H-2K|H-2K(d)|H2-K|K-f	histocompatibility 2, K1, K region	protein-coding
mm_141697.1	chr17	33996190	33996248	-	1	NA	3' UTR (NM_001001892, exon 8 of 8)	3' UTR (NM_001001892, exon 8 of 8)	4114	NM_001001892	14972	Mm.422886	NM_001001892	ENSMUSG00000061232	H2-K1	H-2K|H-2K(d)|H2-K|K-f	histocompatibility 2, K1, K region	protein-coding
mm_101436.1	chr11	30107362	30107365	-	1	NA	3' UTR (NM_009260, exon 31 of 31)	3' UTR (NM_009260, exon 31 of 31)	-81330	NM_146016	237711	Mm.445271	NM_146016	ENSMUSG00000044072	Eml6	2900083P10Rik|C230094A16Rik|EMAP-6	echinoderm microtubule associated protein like 6	protein-coding
mm_135557.1	chr16	49856117	49856128	-	1	NA	intron (NM_010581, intron 1 of 9)	intron (NM_010581, intron 1 of 9)	468	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_21389.1	chr2	157560863	157560883	-	1	NA	intron (NM_001291128, intron 2 of 2)	(A)n|Simple_repeat|Simple_repeat	795	NM_180960	18111	Mm.34330	NM_010923	ENSMUSG00000067786	Nnat	5730414I02Rik|AW107673|Peg5	neuronatin	protein-coding
mm_142830.1	chr17	51776535	51776539	-	1	NA	intron (NM_009122, intron 7 of 10)	intron (NM_009122, intron 7 of 10)	35517	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_75998.1	chr8	72474791	72474855	-	1	NA	intron (NM_138585, intron 1 of 17)	CpG	410	NM_138585	27967	Mm.30136	NM_138585	ENSMUSG00000052488	Cherp	5730408I11Rik|D8Wsu96e|DAN16|Scaf6	calcium homeostasis endoplasmic reticulum protein	protein-coding
mm_129261.1	chr15	76805088	76805091	-	1	NA	intron (NM_198420, intron 1 of 10)	B4|SINE|B4	13081	NM_001168288	223666	Mm.322931	NM_198420	ENSMUSG00000033697	Arhgap39	9530053N22|AI843066|D15Wsu169e|Kiaa1688|Porf-2	Rho GTPase activating protein 39	protein-coding
mm_26713.1	chr3	157993659	157993669	+	1	NA	intron (NM_001013806, intron 8 of 12)	intron (NM_001013806, intron 8 of 12)	38090	NM_001093753	69207	Mm.223946	NM_026989	ENSMUSG00000055436	Srsf11	0610009J05Rik|2610019N13Rik|BF642805|Sfrs11	serine/arginine-rich splicing factor 11	protein-coding
mm_78669.1	chr9	40731004	40731014	+	1	NA	intron (NM_133733, intron 1 of 6)	intron (NM_133733, intron 1 of 6)	45045	NM_133733	71566	Mm.280560	NM_133733	ENSMUSG00000032024	Clmp	9030425E11Rik|ACAM|ASP5|AW557819	CXADR-like membrane protein	protein-coding
mm_125048.1	chr15	25843193	25843241	+	1	NA	promoter-TSS (NM_001034851)	promoter-TSS (NM_001034851)	-81	NM_001034851	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_85367.1	chr9	103220964	103220974	-	1	NA	exon (NM_133977, exon 9 of 17)	exon (NM_133977, exon 9 of 17)	9317	NM_133977	22041	Mm.37214	NM_133977	ENSMUSG00000032554	Trf	AI266983|Cd176|HP|Tf|Tfn|hpx	transferrin	protein-coding
mm_146709.1	chr18	13972618	13972702	-	1	NA	promoter-TSS (NM_145492)	promoter-TSS (NM_145492)	73	NM_145492	225207	Mm.40325	NM_145492	ENSMUSG00000024420	Zfp521	B930086A16Rik|Evi3|Znf521	zinc finger protein 521	protein-coding
mm_63385.1	chr7	127214251	127214261	+	1	NA	TTS (NM_017461)	TTS (NM_017461)	2648	NM_016754	17907	Mm.14526	NM_016754	ENSMUSG00000030672	Mylpf	2410014J02Rik|MLC-2|Mlc2	myosin light chain, phosphorylatable, fast skeletal muscle	protein-coding
mm_102431.1	chr11	59500194	59500198	-	1	NA	intron (NM_001291014, intron 5 of 9)	intron (NM_001291014, intron 5 of 9)	-5457	NR_135273	74476	Mm.440257	NR_015585	ENSMUSG00000072893	4933439C10Rik	2610028M21Rik	RIKEN cDNA 4933439C10 gene	ncRNA
mm_66270.1	chr7	37231069	37231080	-	1	NA	Intergenic	Intergenic	532956	NM_172298	243931	Mm.44141	NM_172298	ENSMUSG00000021217	Tshz3	A630038G13Rik|Tsh3|Zfp537|mKIAA1474|teashirt3	teashirt zinc finger family member 3	protein-coding
mm_46422.1	chr5	104113741	104113756	-	1	NA	5' UTR (NM_010097, exon 1 of 11)	5' UTR (NM_010097, exon 1 of 11)	340	NM_010097	13602	Mm.29027	NM_010097	ENSMUSG00000029309	Sparcl1	Ecm2|Sc1|hevin|mast9	SPARC-like 1	protein-coding
mm_160148.1	chr7	41032519	41032519	+	1	NA	promoter-TSS (NM_183166)	promoter-TSS (NM_183166)	-200	NM_183166	233164	Mm.67238	NM_183166	ENSMUSG00000048312	Gm4884	4930549O06|EG233164	predicted gene 4884	protein-coding
mm_40607.1	chr5	64487853	64487873	+	1	NA	Intergenic	Intergenic	10855	NR_045413	77382	Mm.366742	NR_045411	ENSMUSG00000105352	C030018K13Rik	-	RIKEN cDNA C030018K13 gene	ncRNA
mm_5322.1	chr1	22806044	22806102	-	1	NA	promoter-TSS (NM_001012625)	promoter-TSS (NM_001012625)	-349	NM_001012624	116837	Mm.60061	NM_053270	ENSMUSG00000041670	Rims1	C030033M19Rik|RIM1|RIM1a|RIM1alpha|Rab3ip1|Rim|Serg1|mKIAA0340	regulating synaptic membrane exocytosis 1	protein-coding
mm_78648.1	chr9	40324532	40324544	+	1	NA	intron (NM_172768, intron 4 of 19)	intron (NM_172768, intron 4 of 19)	-8934	NR_040728	73558	Mm.398307	NR_040728		1700110K17Rik	-	RIKEN cDNA 1700110K17 gene	ncRNA
mm_19352.1	chr2	90918395	90918442	-	1	NA	promoter-TSS (NM_025576)	promoter-TSS (NM_025576)	-368	NM_025576	66461	Mm.23926	NM_025576		Ptpmt1	1110001D10Rik|2810004N20Rik|PLIP	protein tyrosine phosphatase, mitochondrial 1	protein-coding
mm_161528.1	chr15	101367658	101367658	-	1	NA	intron (NM_028770, intron 1 of 8)	intron (NM_028770, intron 1 of 8)	-1694	NR_035462	100316694		NR_035462	ENSMUSG00000088459	Mir1941	mmu-mir-1941	microRNA 1941	ncRNA
mm_67021.1	chr7	66049612	66049613	-	1	NA	3' UTR (NM_001291184, exon 21 of 21)	3' UTR (NM_001291184, exon 21 of 21)	-10724	NM_021336	68981	Mm.22362	NM_021336	ENSMUSG00000030512	Snrpa1	1500015N06Rik	small nuclear ribonucleoprotein polypeptide A'	protein-coding
mm_17206.1	chr2	25470097	25470110	-	1	NA	promoter-TSS (NM_008963)	promoter-TSS (NM_008963)	-354	NM_008963	19215	Mm.1008	NM_008963	ENSMUSG00000015090	Ptgds	21kDa|L-PGDS|PGD2|PGDS|PGDS2|Ptgs3	prostaglandin D2 synthase (brain)	protein-coding
mm_98689.1	chr11	96299047	96299083	+	1	NA	promoter-TSS (NM_008269)	promoter-TSS (NM_008269)	-106	NM_008269	15414	Mm.215	NM_008269	ENSMUSG00000000690	Hoxb6	Hox-2.2	homeobox B6	protein-coding
mm_168461.1	chr11	4441165	4441174	-	1	NA	promoter-TSS (NM_029458)	promoter-TSS (NM_029458)	-87	NM_029458	75828	Mm.159592	NM_029458	ENSMUSG00000020419	Hormad2	4930529M09Rik	HORMA domain containing 2	protein-coding
mm_129171.1	chr15	76249392	76249406	-	1	NA	3' UTR (NM_023168, exon 7 of 7)	3' UTR (NM_023168, exon 7 of 7)	1208	NR_105918	102465575		NR_105918	ENSMUSG00000098625	Mir6953	Gm27738|mmu-mir-6953	microRNA 6953	ncRNA
mm_166759.1	chr6	129036620	129036648	+	1	NA	Intergenic	RMER19A|LTR|ERVK	-9267	NR_024262	232408	Mm.259262	NM_153094	ENSMUSG00000030154	Klrb1f	A630024B12Rik|Nkr-p1f|Nkrp1-f|Nkrp1f	killer cell lectin-like receptor subfamily B member 1F	protein-coding
mm_167421.1	chr8	111561158	111561192	+	1	NA	intron (NM_001168623, intron 1 of 4)	B4A|SINE|B4	22832	NM_001168623	170737	Mm.271578	NM_133206	ENSMUSG00000033545	Znrf1	B830022L21Rik|Rnf42|Zrfp1|nin283	zinc and ring finger 1	protein-coding
mm_166398.1	chr5	135351955	135351961	+	1	NA	Intergenic	Intergenic	-1337	NM_001346745	215061	Mm.261834	NM_178240	ENSMUSG00000053388	Trim50	-	tripartite motif-containing 50	protein-coding
mm_151678.1	chr19	4216096	4216110	-	1	NA	intron (NM_001310038, intron 2 of 3)	intron (NM_001310038, intron 2 of 3)	1714	NM_001310039	56708	Mm.347919	NM_019952	ENSMUSG00000040663	Clcf1	BSF-3|Bsf3|CLC|NNT-1	cardiotrophin-like cytokine factor 1	protein-coding
mm_76305.1	chr8	84270359	84270405	-	1	NA	promoter-TSS (NM_001294281)	promoter-TSS (NM_001294281)	20	NM_001294281	67736	Mm.30095	NM_026350	ENSMUSG00000004994	Ccdc130	4930527D15Rik|C77430	coiled-coil domain containing 130	protein-coding
mm_11660.1	chr2	35132167	35132189	+	1	NA	promoter-TSS (NM_001290635)	promoter-TSS (NM_001290635)	-56	NM_001290635	26920	Mm.231332	NM_012018	ENSMUSG00000057110	Cntrl	6720467O09Rik|AA968343|Cep1|Cep110|IB3/5|Ma2a8|b2b1468.1Clo|b2b1468Clo	centriolin	protein-coding
mm_118103.1	chr13	103920432	103920484	-	1	NA	5' UTR (NM_001289475, exon 1 of 26)	5' UTR (NM_001289475, exon 1 of 26)	128	NM_001289473	59079	Mm.277354	NM_021563	ENSMUSG00000021709	Erbin	1700028E05Rik|Erbb2ip|mKIAA1225	Erbb2 interacting protein	protein-coding
mm_135193.1	chr16	36408350	36408362	-	1	NA	promoter-TSS (NM_001082545)	promoter-TSS (NM_001082545)	7	NM_001082545	20862	Mm.359610	NM_001082545	ENSMUSG00000022902	Stfa2	Stf2	stefin A2	protein-coding
mm_15566.1	chr2	158610979	158611048	+	1	NA	promoter-TSS (NR_040359)	promoter-TSS (NR_040359)	255	NM_009508	22348	Mm.143404	NM_009508	ENSMUSG00000037771	Slc32a1	R75019|VGAT|Viaat	solute carrier family 32 (GABA vesicular transporter), member 1	protein-coding
mm_6303.1	chr1	71414841	71414872	-	1	NA	promoter-TSS (NM_175210)	promoter-TSS (NM_175210)	54	NM_175210	74591	Mm.159251	NM_175210	ENSMUSG00000050296	Abca12	4832428G11Rik|4833417A11Rik	ATP-binding cassette, sub-family A (ABC1), member 12	protein-coding
mm_99734.1	chr11	106365496	106365499	+	1	NA	Intergenic	Intergenic	-9329	NM_029345	75573	Mm.159539	NM_029345	ENSMUSG00000009210	Prr29	2310007L24Rik	proline rich 29	protein-coding
mm_161278.1	chr14	16384504	16384504	+	1	NA	exon (NM_009409, exon 3 of 36)	exon (NM_009409, exon 3 of 36)	19298	NM_009409	21974	Mm.130362	NM_009409	ENSMUSG00000017485	Top2b	D230016L12Rik|Top-2	topoisomerase (DNA) II beta	protein-coding
mm_85311.1	chr9	101120729	101120732	-	1	NA	intron (NM_001161362, intron 13 of 13)	L1_Mur2|LINE|L1	45968	NM_001100451	77853	Mm.326206	NM_001100451	ENSMUSG00000066415	Msl2	E130103E02Rik|Msl2l1|Rnf184	male-specific lethal 2 homolog (Drosophila)	protein-coding
mm_47042.1	chr5	116024358	116024370	-	1	NA	promoter-TSS (NM_031869)	promoter-TSS (NM_031869)	64	NM_031869	19079	Mm.458152	NM_031869	ENSMUSG00000029513	Prkab1	1300015D22Rik|AU021155|E430008F22	protein kinase, AMP-activated, beta 1 non-catalytic subunit	protein-coding
mm_68062.1	chr7	101864094	101864156	-	1	NA	intron (NM_001252552, intron 3 of 6)	intron (NM_001252552, intron 3 of 6)	6663	NM_001252554	14275	Mm.2135	NM_008034	ENSMUSG00000001827	Folr1	FBP1|Folbp-1|Folbp1	folate receptor 1 (adult)	protein-coding
mm_109770.1	chr12	118847228	118847238	+	1	NA	intron (NM_177082, intron 1 of 2)	intron (NM_177082, intron 1 of 2)	904	NM_177082	320145	Mm.51682	NM_177082	ENSMUSG00000048562	Sp8	D930049B17Rik|mBtd	trans-acting transcription factor 8	protein-coding
mm_98552.1	chr11	95076946	95076951	+	1	NA	promoter-TSS (NM_001306162)	promoter-TSS (NM_001306162)	-137	NM_001306162	16400	Mm.57035	NM_013565	ENSMUSG00000001507	Itga3	AA407068|CD49C|GAPB3	integrin alpha 3	protein-coding
mm_132051.1	chr16	29533233	29533234	+	1	NA	intron (NM_172613, intron 1 of 29)	intron (NM_172613, intron 1 of 29)	8250	NM_172613	224079	Mm.54954	NM_172613	ENSMUSG00000038094	Atp13a4	4631413J11Rik|4832416L12|9330174J19Rik	ATPase type 13A4	protein-coding
mm_76684.1	chr8	94037036	94037046	-	1	NA	promoter-TSS (NM_026623)	promoter-TSS (NM_026623)	-2	NM_026623	68219	Mm.354445	NM_026623	ENSMUSG00000031754	Nudt21	25kDa|3110048P04Rik|5730530J16Rik|AU014860|AW549947|Cpsf5	nudix (nucleoside diphosphate linked moiety X)-type motif 21	protein-coding
mm_98364.1	chr11	93955317	93955328	+	1	NA	intron (NM_008705, intron 2 of 4)	intron (NM_008705, intron 2 of 4)	461	NM_001077529	18103	Mm.1260	NM_008705	ENSMUSG00000020857	Nme2	NM23-H2|NM23B|nm23-M2	NME/NM23 nucleoside diphosphate kinase 2	protein-coding
mm_66128.1	chr7	31054799	31054814	-	1	NA	promoter-TSS (NM_194321)	promoter-TSS (NM_194321)	47	NM_052991	56188	Mm.1491	NM_019503	ENSMUSG00000036570	Fxyd1	0610012C17Rik|1110006M24Rik|Plm|Pml	FXYD domain-containing ion transport regulator 1	protein-coding
mm_170965.1	chr2	58160056	58160061	-	1	NA	promoter-TSS (NM_139200)	promoter-TSS (NM_139200)	64	NM_139200	227929	Mm.273905	NM_139200	ENSMUSG00000026832	Cytip	A130053M09Rik|AI462064|C80816|Cbp|Cybr|Pscdbp	cytohesin 1 interacting protein	protein-coding
mm_85773.1	chr9	109051706	109051715	-	1	NA	intron (NM_025858, intron 3 of 5)	intron (NM_025858, intron 3 of 5)	-3156	NM_026381	66940	Mm.196533	NM_025858	ENSMUSG00000025647	Shisa5	2310008D10Rik|6430628I05Rik|Scotin|mShisa5	shisa family member 5	protein-coding
mm_57476.1	chr6	125234803	125234819	-	1	NA	promoter-TSS (NR_106193)	promoter-TSS (NR_106193)	1	NR_106193	102465901		NR_106193	ENSMUSG00000098856	Mir8113	Gm27394|mmu-mir-8113	microRNA 8113	ncRNA
mm_133867.1	chr16	96361806	96361816	+	1	NA	promoter-TSS (NM_028078)	promoter-TSS (NM_028078)	47	NM_028078	72058	Mm.119714	NM_028078	ENSMUSG00000000159	Igsf5	2010003D20Rik|JCAM|Jam4	immunoglobulin superfamily, member 5	protein-coding
mm_71017.1	chr8	33385617	33385681	+	1	NA	promoter-TSS (NM_001122822)	promoter-TSS (NM_001122822)	-122	NM_011721	22427	Mm.228805	NM_011721	ENSMUSG00000031583	Wrn	AI846146	Werner syndrome homolog (human)	protein-coding
mm_2257.1	chr1	91114795	91114806	+	1	NA	exon (NM_001111311, exon 8 of 8)	exon (NM_001111311, exon 8 of 8)	-30303	NM_001033408	329207	Mm.295940	NM_001033408	ENSMUSG00000070732	Rbm44	Gm817	RNA binding motif protein 44	protein-coding
mm_15354.1	chr2	156311754	156311766	+	1	NA	promoter-TSS (NM_027585)	promoter-TSS (NM_027585)	-713	NM_027585	70873	Mm.475234	NM_027585	ENSMUSG00000038085	Cnbd2	4921517L17Rik|5430421B09Rik|Cris	cyclic nucleotide binding domain containing 2	protein-coding
mm_13435.1	chr2	105126480	105126484	+	1	NA	promoter-TSS (NM_144783)	promoter-TSS (NM_144783)	28	NR_015462	329480	Mm.246679	NR_015462	ENSMUSG00000074987	Wt1os	6030498F17|AI314831|Wt1-as	Wilms tumor 1 homolog, opposite strand	ncRNA
mm_15331.1	chr2	155775334	155775392	+	1	NA	promoter-TSS (NM_010808)	promoter-TSS (NM_010808)	21	NM_010808	17391	Mm.389325	NM_010808	ENSMUSG00000027612	Mmp24	AU040325|MMP-21|MT5-MMP|MT5MMP|MTMMP5	matrix metallopeptidase 24	protein-coding
mm_147172.1	chr18	36726731	36726745	-	1	NA	promoter-TSS (NM_009841)	promoter-TSS (NM_009841)	77	NM_009841	12475	Mm.3460	NM_009841	ENSMUSG00000051439	Cd14	-	CD14 antigen	protein-coding
mm_160602.1	chr9	78155243	78155243	+	1	NA	intron (NM_019987, intron 7 of 13)	intron (NM_019987, intron 7 of 13)	-20671	NR_040401	320295	Mm.131285	NR_040401	ENSMUSG00000097574	C920006O11Rik	-	RIKEN cDNA C920006O11 gene	ncRNA
mm_135775.1	chr16	56831879	56831891	-	1	NA	intron (NM_019631, intron 1 of 5)	intron (NM_019631, intron 1 of 5)	-36027	NM_172825	239853	Mm.258979	NM_172825	ENSMUSG00000022755	Adgrg7	9130020O16Rik|Gpr128	adhesion G protein-coupled receptor G7	protein-coding
mm_11917.1	chr2	52071606	52071617	+	1	NA	Intergenic	PB1D7|SINE|Alu	-1226	NM_175238	51869	Mm.254530	NM_175238	ENSMUSG00000036202	Rif1	5730435J01Rik|6530403D07Rik|AU016181|AW549474|D2Ertd145e	replication timing regulatory factor 1	protein-coding
mm_129284.1	chr15	77162908	77162915	-	1	NA	intron (NM_053104, intron 2 of 13)	intron (NM_053104, intron 2 of 13)	-9099	NM_001286418	93686	Mm.202774	NM_053104	ENSMUSG00000033565	Rbfox2	Fbm2|Fxh|Hrnbp2|Rbm9	RNA binding protein, fox-1 homolog (C. elegans) 2	protein-coding
mm_62446.1	chr7	101384012	101384038	+	1	NA	intron (NM_001040112, intron 1 of 30)	intron (NM_001040112, intron 1 of 30)	-1501	NM_027180	69710	Mm.277687	NM_027180	ENSMUSG00000032812	Arap1	2410002L19Rik|Centd2|mKIAA0782	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	protein-coding
mm_58611.1	chr7	5061399	5061411	+	1	NA	promoter-TSS (NM_001205231)	promoter-TSS (NM_001205231)	-738	NM_133671	22185	Mm.360389	NM_133671	ENSMUSG00000030435	U2af2	65kDa	U2 small nuclear ribonucleoprotein auxiliary factor (U2AF) 2	protein-coding
mm_67415.1	chr7	80232480	80232498	-	1	NA	promoter-TSS (NM_178752)	promoter-TSS (NM_178752)	316	NM_001291276	23991	Mm.30217	NM_011870	ENSMUSG00000030538	Cib1	Cibkip|Kip|Prkdcip	calcium and integrin binding 1 (calmyrin)	protein-coding
mm_76937.1	chr8	105939903	105939913	-	1	NA	exon (NM_008490, exon 6 of 6)	exon (NM_008490, exon 6 of 6)	-1516	NM_013640	19171	Mm.787	NM_013640	ENSMUSG00000031897	Psmb10	Mecl-1|Mecl1	proteasome (prosome, macropain) subunit, beta type 10	protein-coding
mm_28243.1	chr3	88481908	88481915	-	1	NA	3' UTR (NM_001002011, exon 12 of 12)	3' UTR (NM_001002011, exon 12 of 12)	11401	NM_019390	16905	Mm.243014	NM_019390	ENSMUSG00000028063	Lmna	Dhe	lamin A	protein-coding
mm_29913.1	chr3	131489002	131489021	-	1	NA	Intergenic	Intergenic	-75757	NM_001289479	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_166641.1	chr6	83537143	83537149	-	1	NA	promoter-TSS (NM_009610)	promoter-TSS (NM_009610)	-895	NM_009610	11468	Mm.292865	NM_009610	ENSMUSG00000059430	Actg2	ACTA3|Act-4|Act4|SMGA	actin, gamma 2, smooth muscle, enteric	protein-coding
mm_149700.1	chr19	21278173	21278174	+	1	NA	intron (NM_009551, intron 4 of 5)	intron (NM_009551, intron 4 of 5)	5895	NM_009551	22682	Mm.292405	NM_009551	ENSMUSG00000024750	Zfand5	2310057A04Rik|5830475F03Rik|AA415485|Za20d2|Zfp216	zinc finger, AN1-type domain 5	protein-coding
mm_69759.1	chr7	141009653	141009681	-	1	NA	TTS (NM_025378)	TTS (NM_025378)	1077	NM_025378	66141	Mm.141021	NM_025378	ENSMUSG00000025492	Ifitm3	1110004C05Rik|Cd225|Cdw217|DSPA2b|Fgls|IP15|mil-1	interferon induced transmembrane protein 3	protein-coding
mm_155277.1	chrX	61120504	61120523	+	1	NA	intron (NR_030706, intron 4 of 7)	intron (NR_030706, intron 4 of 7)	4135	NR_030706	331424	Mm.127263	NM_177916	ENSMUSG00000071753	C230004F18Rik	-	RIKEN cDNA C230004F18 gene	ncRNA
mm_153844.1	chr19	46332800	46332810	-	1	NA	intron (NM_001164291, intron 1 of 8)	intron (NM_001164291, intron 1 of 8)	4621	NM_133694	68431	Mm.19973	NM_133694	ENSMUSG00000025226	Fbxl15	0710008C12Rik|Fbxo37	F-box and leucine-rich repeat protein 15	protein-coding
mm_138094.1	chr17	34039229	34039255	+	1	NA	TTS (NM_001205216)	TTS (NM_001205216)	104	NM_001317722	12815	Mm.20230	NM_009926	ENSMUSG00000024330	Col11a2	-	collagen, type XI, alpha 2	protein-coding
mm_101298.1	chr11	22286806	22286818	-	1	NA	promoter-TSS (NM_153078)	promoter-TSS (NM_153078)	-17	NM_001252515	216565	Mm.491265	NM_153078	ENSMUSG00000042302	Ehbp1	AF424697|Flj21950|NACSIN	EH domain binding protein 1	protein-coding
mm_137364.1	chr17	25370576	25370599	+	1	NA	promoter-TSS (NM_012034)	promoter-TSS (NM_012034)	34	NM_012034	26945	Mm.180108	NM_012034	ENSMUSG00000033200	Tpsg1	Prss31|Tmt	tryptase gamma 1	protein-coding
mm_163198.1	chr11	96124434	96124444	+	1	NA	Intergenic	CpG	-9347	NM_172799	237930	Mm.249912	NM_172799	ENSMUSG00000038756	Ttll6	4932418K24Rik|D11Moh43e|D11Moh44e|t8130b59	tubulin tyrosine ligase-like family, member 6	protein-coding
mm_28648.1	chr3	95228333	95228339	-	1	NA	promoter-TSS (NM_172395)	promoter-TSS (NM_172395)	-88	NM_172395	57912	Mm.28189	NM_172395	ENSMUSG00000046722	Cdc42se1	1300002M12Rik|AW558204|Cdcse1|SCIP1|Spec1	CDC42 small effector 1	protein-coding
mm_166907.1	chr7	28893702	28893708	-	1	NA	TTS (NM_001110807)	TTS (NM_001110807)	12049	NM_001110807	60594	Mm.476990	NM_021894	ENSMUSG00000054083	Capn12	CANP 12	calpain 12	protein-coding
mm_41272.1	chr5	89149354	89149369	+	1	NA	exon (NM_001136260, exon 13 of 25)	exon (NM_001136260, exon 13 of 25)	262101	NM_018760	54403	Mm.41044	NM_018760	ENSMUSG00000060961	Slc4a4	AI835705|NBC|NBC1	solute carrier family 4 (anion exchanger), member 4	protein-coding
mm_71906.1	chr8	70073032	70073040	+	1	NA	exon (NM_001293795, exon 1 of 10)	exon (NM_001293795, exon 1 of 10)	112	NM_181540	107770	Mm.37974	NM_181540	ENSMUSG00000036151	Tm6sf2	-	transmembrane 6 superfamily member 2	protein-coding
mm_136120.1	chr16	85900231	85900252	-	1	NA	exon (NM_011782, exon 1 of 8)	exon (NM_011782, exon 1 of 8)	884	NM_011782	23794	Mm.112933	NM_011782	ENSMUSG00000022894	Adamts5	9530092O11Rik|ADAM-TS5|ADAMTS1|ADAMTS11|ADMP-2|AI481094|ASMP-2	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)	protein-coding
mm_44058.1	chr5	148265203	148265263	+	1	NA	intron (NM_029920, intron 7 of 14)	intron (NM_029920, intron 7 of 14)	127582	NM_001301424	11987	Mm.275489	NM_007513	ENSMUSG00000041313	Slc7a1	4831426K01Rik|AI447493|Atrc-1|Atrc1|Cat1|Rec-1|Rev-1|mCAT-1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 1	protein-coding
mm_29226.1	chr3	107212863	107212877	-	1	NA	exon (NM_001111143, exon 8 of 9)	exon (NM_001111143, exon 8 of 9)	8862	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_146561.1	chr18	6241472	6241482	-	1	NA	promoter-TSS (NM_008448)	promoter-TSS (NM_008448)	47	NM_008448	16573	Mm.223744	NM_008448	ENSMUSG00000006740	Kif5b	AL022807|Khc|Khcs|Kns1|Ukhc	kinesin family member 5B	protein-coding
mm_136417.1	chr16	93929484	93929505	-	1	NA	promoter-TSS (NM_001165925)	promoter-TSS (NM_001165925)	73	NM_001165925	56173	Mm.328716	NM_019500	ENSMUSG00000047109	Cldn14	AI851731	claudin 14	protein-coding
mm_59008.1	chr7	19212522	19212546	+	1	NA	promoter-TSS (NM_175668)	promoter-TSS (NM_175668)	-4	NM_175668	319197	Mm.135984	NM_175668	ENSMUSG00000044317	Gpr4	-	G protein-coupled receptor 4	protein-coding
mm_142924.1	chr17	53846072	53846091	-	1	NA	promoter-TSS (NM_026935)	promoter-TSS (NM_026935)	-123	NM_026935	69083	Mm.19320	NM_026935	ENSMUSG00000023122	Sult1c2	1810008N17Rik|ST1C1|ST1C2|Sult1c1	sulfotransferase family, cytosolic, 1C, member 2	protein-coding
mm_11329.1	chr2	30441920	30441949	+	1	NA	intron (NM_138748, intron 8 of 9)	intron (NM_138748, intron 8 of 9)	25884	NM_138748	110854	Mm.275393	NM_138748	ENSMUSG00000039515	Ptpa	2610042B21Rik|C77440|N28142|PR53|Ppp2r4	protein phosphatase 2 protein activator	protein-coding
mm_76536.1	chr8	87960518	87960581	-	1	NA	promoter-TSS (NM_033327)	promoter-TSS (NM_033327)	-954	NM_033327	94187	Mm.23452	NM_033327	ENSMUSG00000045333	Zfp423	Ebfaz|Roaz|Zfp104|Znf423|ataxia1|mKIAA0760|nur12	zinc finger protein 423	protein-coding
mm_78418.1	chr9	31030622	31030700	+	1	NA	promoter-TSS (NM_001115130)	promoter-TSS (NM_001115130)	17	NM_172765	235132	Mm.239355	NM_172765	ENSMUSG00000047412	Zbtb44	6030404E16Rik|Btbd15|E230011F09	zinc finger and BTB domain containing 44	protein-coding
mm_11772.1	chr2	38880885	38880888	+	1	NA	intron (NM_010264, intron 2 of 10)	intron (NM_010264, intron 2 of 10)	27056	NR_029904	723903		NR_029904	ENSMUSG00000065578	Mir181b-2	Mirn181b-2|mir-181b-2	microRNA 181b-2	ncRNA
mm_32781.1	chr4	116708588	116708604	+	1	NA	promoter-TSS (NM_026714)	promoter-TSS (NM_026714)	-211	NM_025962	67096	Mm.252785	NM_025962	ENSMUSG00000028690	Mmachc	1810037K07Rik|CblC	methylmalonic aciduria cblC type, with homocystinuria	protein-coding
mm_35399.1	chr4	34687263	34687309	-	1	NA	5' UTR (NM_011895, exon 1 of 8)	5' UTR (NM_011895, exon 1 of 8)	152	NM_011895	24060	Mm.281885	NM_011895	ENSMUSG00000028293	Slc35a1	AA408150|AI314851	solute carrier family 35 (CMP-sialic acid transporter), member 1	protein-coding
mm_23448.1	chr3	59952186	59952200	+	1	NA	promoter-TSS (NR_037189)	promoter-TSS (NR_037189)	-116	NR_037189	676914	Mm.228502	NR_037189	ENSMUSG00000070465	Gm9696	-	arylacetamide deacetylase-like 2 pseudogene	pseudo
mm_61925.1	chr7	90161251	90161305	+	1	NA	exon (NM_001252521, exon 3 of 20)	exon (NM_001252521, exon 3 of 20)	31046	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_87218.1	chr10	40258464	40258470	+	1	NA	promoter-TSS (NM_026113)	promoter-TSS (NM_026113)	-802	NM_026113	67371	Mm.64104	NM_026113	ENSMUSG00000019837	Gtf3c6	2410016F19Rik|AU019813	general transcription factor IIIC, polypeptide 6, alpha	protein-coding
mm_105224.1	chr11	102230128	102230166	-	1	NA	promoter-TSS (NM_001284249)	promoter-TSS (NM_001284249)	3	NR_106179	102465892		NR_106179	ENSMUSG00000098863	Mir8101	Gm27705|mmu-mir-8101	microRNA 8101	ncRNA
mm_85009.1	chr9	87255464	87255535	-	1	NA	promoter-TSS (NM_199316)	promoter-TSS (NM_199316)	33	NM_199316	382090	Mm.335338	NM_199316	ENSMUSG00000056919	Cep162	4922501C03Rik|mKIAA1009	centrosomal protein 162	protein-coding
mm_130822.1	chr15	101845661	101845671	-	1	NA	3' UTR (NM_008473, exon 9 of 9)	3' UTR (NM_008473, exon 9 of 9)	5120	NM_008473	16678	Mm.183137	NM_008473	ENSMUSG00000046834	Krt1	Krt-2.1|Krt2-1|Krt86	keratin 1	protein-coding
mm_65959.1	chr7	30431911	30431914	-	1	NA	Intergenic	Intergenic	8608	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_4437.1	chr1	172506852	172506860	+	1	NA	3' UTR (NM_178598, exon 5 of 5)	3' UTR (NM_178598, exon 5 of 5)	6610	NM_178598	21346	Mm.271711	NM_178598	ENSMUSG00000026547	Tagln2	2700094C18Rik|SM22beta|Sm22B|Sm22a	transgelin 2	protein-coding
mm_27830.1	chr3	79097709	79097754	-	1	NA	intron (NM_001310536, intron 5 of 23)	L1M3|LINE|L1	47156	NM_001310536	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_72538.1	chr8	83997209	83997216	+	1	NA	promoter-TSS (NM_001081415)	promoter-TSS (NM_001081415)	-460	NM_001081415	666704	Mm.298091	NM_001081415	ENSMUSG00000079003	Samd1	AA589507	sterile alpha motif domain containing 1	protein-coding
mm_60413.1	chr7	44476154	44476164	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	5812	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_109768.1	chr12	118602649	118602656	+	1	NA	Intergenic	Intergenic	-72459	NR_045947	100384890	Mm.484658	NR_045947		D230030E09Rik	Npe	Riken cDNA D230030E09 gene	ncRNA
mm_92934.1	chr10	84533885	84533896	-	1	NA	promoter-TSS (NM_175451)	promoter-TSS (NM_175451)	-2	NM_175451	216197	Mm.334999	NM_175451	ENSMUSG00000046841	Ckap4	5630400A09Rik|CLIMP-63|P63	cytoskeleton-associated protein 4	protein-coding
mm_154092.1	chr19	56822081	56822087	-	1	NA	Intergenic	CpG	-4125	NM_001002238	83561	Mm.247541	NM_031387	ENSMUSG00000025081	Tdrd1	MTR-1	tudor domain containing 1	protein-coding
mm_160050.1	chr7	3249761	3249761	-	1	NA	promoter-TSS (NM_001033431)	promoter-TSS (NM_001033431)	-21	NM_001033431	378425	Mm.277152	NM_001033431	ENSMUSG00000078817	Nlrp12	Nalp12|PYPAF7	NLR family, pyrin domain containing 12	protein-coding
mm_64356.1	chr7	142390187	142390196	+	1	NA	Intergenic	Intergenic	-2321	NM_009983	13033	Mm.231395	NM_009983	ENSMUSG00000007891	Ctsd	CD|CatD	cathepsin D	protein-coding
mm_14410.1	chr2	130277697	130277700	+	1	NA	promoter-TSS (NR_028528)	promoter-TSS (NR_028528)	-328	NR_028528	100217428		NR_028528	ENSMUSG00000065272	Snord57	MBII-434	small nucleolar RNA, C/D box 57	snoRNA
mm_125498.1	chr15	55208768	55208783	+	1	NA	exon (NM_145470, exon 5 of 9)	exon (NM_145470, exon 5 of 9)	75339	NM_001037937	97998	Mm.295397	NM_145470	ENSMUSG00000022419	Deptor	Depdc6	DEP domain containing MTOR-interacting protein	protein-coding
mm_14653.1	chr2	136922292	136922298	+	1	NA	intron (NM_001038641, intron 2 of 7)	PB1D10|SINE|Alu	22944	NM_001038641	74243	Mm.330612	NM_028201	ENSMUSG00000027281	Slx4ip	2210009G21Rik|2410004I22Rik|C85661|Slxip	SLX4 interacting protein	protein-coding
mm_90799.1	chr10	7661983	7661991	-	1	NA	intron (NM_001347228, intron 1 of 7)	A-rich|Low_complexity|Low_complexity	-1384	NR_030698	320642	Mm.398806	NR_030698		A630066F11Rik	-	RIKEN cDNA A630066F11 gene	ncRNA
mm_114625.1	chr13	76098776	76098809	+	1	NA	promoter-TSS (NM_001081352)	promoter-TSS (NM_001081352)	58	NM_001081352	218343	Mm.277964	NM_001081352	ENSMUSG00000033991	Ttc37	mKIAA0372	tetratricopeptide repeat domain 37	protein-coding
mm_69940.1	chr7	142112407	142112413	-	1	NA	Intergenic	Intergenic	8490	NM_001347558	108167466	Mm.365101	NM_001347558	ENSMUSG00000109859	Gm45618	-	predicted gene 45618	protein-coding
mm_31833.1	chr4	70582417	70582423	+	1	NA	Intergenic	Lx5c|LINE|L1	-47492	NM_172694	230316	Mm.251188	NM_172694	ENSMUSG00000039270	Megf9	4933405H16Rik|9630025C07|Egfl5|mKIAA0818	multiple EGF-like-domains 9	protein-coding
mm_169475.1	chr14	69337181	69337184	+	1	NA	promoter-TSS (NM_026174).2	promoter-TSS (NM_026174).2	31	NM_026174	67464	Mm.489765	NM_026174	ENSMUSG00000095463	Entpd4	1200014F22Rik|4930513O14Rik|A430102M06Rik|AI414893|Lysal1|mKIAA0392	ectonucleoside triphosphate diphosphohydrolase 4	protein-coding
mm_122730.1	chr14	52316375	52316382	-	1	NA	promoter-TSS (NM_001244916)	promoter-TSS (NM_001244916)	-55	NM_001244916	50524	Mm.39487	NM_015772	ENSMUSG00000049532	Sall2	AI225809|AW559097|Msal-2|Sal-2|mKIAA0360|p150(Sal2)	sal-like 2 (Drosophila)	protein-coding
mm_104959.1	chr11	100142128	100142151	-	1	NA	exon (NM_008471, exon 3 of 6)	exon (NM_008471, exon 3 of 6)	1560	NM_001313963	16669	Mm.439699	NM_008471	ENSMUSG00000020911	Krt19	AI663979|CK-19|EndoC|K19|Krt-1.19|Krt1-19	keratin 19	protein-coding
mm_93474.1	chr10	111507374	111507397	-	1	NA	exon (NM_009344, exon 1 of 2)	exon (NM_009344, exon 1 of 2)	1099	NM_009344	21664	Mm.3117	NM_009344	ENSMUSG00000020205	Phlda1	DT1P1B11|TDAG51|Tdag	pleckstrin homology like domain, family A, member 1	protein-coding
mm_17025.1	chr2	19431851	19431870	-	1	NA	Intergenic	Intergenic	-13803	NM_018809	19213	Mm.69647	NM_018809	ENSMUSG00000026735	Ptf1a	PTF1-p48|PTF1p48|bHLHa29	pancreas specific transcription factor, 1a	protein-coding
mm_88904.1	chr10	81178050	81178088	+	1	NA	promoter-TSS (NR_028549)	promoter-TSS (NR_028549)	-892	NR_028549	100217454		NR_028549	ENSMUSG00000064441	Snord37	MBII-376	small nucleolar RNA, C/D box 37	snoRNA
mm_89914.1	chr10	111176971	111177013	+	1	NA	intron (NM_175489, intron 1 of 23)	intron (NM_175489, intron 1 of 23)	12190	NM_175489	237542	Mm.220204	NM_175489	ENSMUSG00000020189	Osbpl8	AA536976|AA536995|C730029P18Rik|D330025H14Rik|ORP-8	oxysterol binding protein-like 8	protein-coding
mm_162306.1	chr1	36780021	36780031	+	1	NA	intron (NM_009539, intron 9 of 12)	IMPB_01|Satellite|Satellite	1042	NM_001289612	22637	Mm.8038	NM_009539	ENSMUSG00000026117	Zap70	Srk|ZAP-70|mrtle|mur	zeta-chain (TCR) associated protein kinase	protein-coding
mm_77493.1	chr8	122576614	122576624	-	1	NA	exon (NM_009698, exon 2 of 5)	exon (NM_009698, exon 2 of 5)	288	NM_009698	11821	Mm.1786	NM_009698	ENSMUSG00000006589	Aprt	C85684	adenine phosphoribosyl transferase	protein-coding
mm_50154.1	chr6	41546078	41546095	+	1	NA	Intergenic	Intergenic	24310	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_15999.1	chr2	167189680	167189693	+	1	NA	promoter-TSS (NM_008420)	promoter-TSS (NM_008420)	-868	NM_008420	16500	Mm.205341	NM_008420	ENSMUSG00000050556	Kcnb1	Kcr1-1|Kv2.1|Shab	potassium voltage gated channel, Shab-related subfamily, member 1	protein-coding
mm_91514.1	chr10	37138554	37138572	-	1	NA	5' UTR (NM_008538, exon 1 of 2)	5' UTR (NM_008538, exon 1 of 2)	363	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_50589.1	chr6	49060226	49060236	+	1	NA	Intergenic	Intergenic	-13564	NM_029353	75593	Mm.439947	NM_029353	ENSMUSG00000029815	Malsu1	2410003K15Rik|Matsu1	mitochondrial assembly of ribosomal large subunit 1	protein-coding
mm_26337.1	chr3	142547139	142547139	+	1	NA	3' UTR (NM_001083312, exon 11 of 11)	3' UTR (NM_001083312, exon 11 of 11)	-12913	NM_018734	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_100168.1	chr11	116531844	116531874	+	1	NA	promoter-TSS (NM_001172472)	promoter-TSS (NM_001172472)	-52	NM_001172475	20698	Mm.20944	NM_011451	ENSMUSG00000061878	Sphk1	1110006G24Rik|Sk1|Spk1	sphingosine kinase 1	protein-coding
mm_107033.1	chr12	13438805	13438808	+	1	NA	intron (NM_027706, intron 36 of 51)	intron (NM_027706, intron 36 of 51)	169679	NM_027706	71169	Mm.177520	NM_027706	ENSMUSG00000020576	Nbas	4933425L03Rik|Nag	neuroblastoma amplified sequence	protein-coding
mm_154237.1	chr19	60580886	60580992	-	1	NA	promoter-TSS (NM_001172096)	promoter-TSS (NM_001172096)	84	NM_001172097	78832	Mm.259026	NM_030197	ENSMUSG00000033417	Cacul1	2700078E11Rik|2810417M16Rik|9830127L17Rik|AI450346|D130033C15Rik	CDK2 associated, cullin domain 1	protein-coding
mm_104383.1	chr11	94474298	94474308	-	1	NA	promoter-TSS (NM_001177890)	promoter-TSS (NM_001177890)	-105	NM_001112813	12291	Mm.29585	NM_009783	ENSMUSG00000020866	Cacna1g	Cav3.1d|[a]1G|a1G|alpha-1G|mKIAA1123	calcium channel, voltage-dependent, T type, alpha 1G subunit	protein-coding
mm_100305.1	chr11	117963653	117963686	+	1	NA	Intergenic	CpG	5697	NM_007707	12702	Mm.3468	NM_007707	ENSMUSG00000053113	Socs3	Cis3|Cish3|EF-10|Ef10|SSI-3|Ssi3	suppressor of cytokine signaling 3	protein-coding
mm_121611.1	chr14	8258962	8258977	-	1	NA	promoter-TSS (NM_053115)	promoter-TSS (NM_053115)	50	NM_053115	93732	Mm.28700	NM_053115	ENSMUSG00000021751	Acox2	THCCox	acyl-Coenzyme A oxidase 2, branched chain	protein-coding
mm_82194.1	chr9	123965080	123965090	+	1	NA	intron (NM_009912, intron 1 of 1)	intron (NM_009912, intron 1 of 1)	3607	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_169581.1	chr1	52320969	52320971	+	1	NA	Intergenic	MMERGLN_LTR|LTR|ERV1	-87738	NM_001113383	14660	Mm.398608	NM_001081081	ENSMUSG00000026103	Gls	6330442B14|AI314027|B230365M23Rik	glutaminase	protein-coding
mm_173243.1	chrX	89199840	89199840	+	1	NA	Intergenic	Intergenic	209849	NM_008821	18630	Mm.3086	NM_008821	ENSMUSG00000035395	Pet2	PC231|PC326|Pex3	plasmacytoma expressed transcript 2	protein-coding
mm_95954.1	chr11	58421104	58421118	+	1	NA	promoter-TSS (NM_027239)	promoter-TSS (NM_027239)	0	NM_027239	69864	Mm.45641	NM_027239	ENSMUSG00000013653	1810065E05Rik	AV047390	RIKEN cDNA 1810065E05 gene	protein-coding
mm_64364.1	chr7	142434773	142434789	+	1	NA	promoter-TSS (NM_001285857)	promoter-TSS (NM_001285857)	-196	NM_001285857	55925	Mm.213002	NM_018802	ENSMUSG00000031098	Syt8	-	synaptotagmin VIII	protein-coding
mm_144122.1	chr18	4636533	4636553	+	1	NA	intron (NM_001081963, intron 1 of 3)	intron (NM_001081963, intron 1 of 3)	1614	NM_001081963	240185	Mm.33179	NM_001081963	ENSMUSG00000033960	9430020K01Rik	1110056P05Rik|Gm328|Jcad|mKIAA1462	RIKEN cDNA 9430020K01 gene	protein-coding
mm_94683.1	chr11	19019115	19019140	+	1	NA	promoter-TSS (NM_010789)	promoter-TSS (NM_010789)	-158	NM_010789	17268	Mm.356578	NM_010789	ENSMUSG00000020160	Meis1	C530044H18Rik|Evi8	Meis homeobox 1	protein-coding
mm_124810.1	chr15	8967944	8967960	+	1	NA	promoter-TSS (NM_198024)	promoter-TSS (NM_198024)	3	NM_198024	223332	Mm.321371	NM_198024	ENSMUSG00000048424	Ranbp3l	C130037N17Rik	RAN binding protein 3-like	protein-coding
mm_85105.1	chr9	95401049	95401053	-	1	NA	3' UTR (NM_018763, exon 2 of 2)	3' UTR (NM_018763, exon 2 of 2)	6219	NM_018763	54371	Mm.212446	NM_018763	ENSMUSG00000033350	Chst2	AI428561|AW121776|C130041E03Rik|Chts2|GST-2|GlcNAc6ST|Gn6st	carbohydrate sulfotransferase 2	protein-coding
mm_43304.1	chr5	134676545	134676563	+	1	NA	intron (NM_010717, intron 2 of 15)	intron (NM_010717, intron 2 of 15)	1694	NM_001305875	16885	Mm.15409	NM_010717	ENSMUSG00000029674	Limk1	KIZ-1|LIMK-1|Limk	LIM-domain containing, protein kinase	protein-coding
mm_171688.1	chr4	6093395	6093397	-	1	NA	Intergenic	RLTR9D|LTR|ERVK	-97709	NM_026534	68053	Mm.404043	NM_026534	ENSMUSG00000028243	Ubxn2b	3110003A22Rik|6430407D20Rik|AI451665|p37	UBX domain protein 2B	protein-coding
mm_56844.1	chr6	117891569	117891595	-	1	NA	Intergenic	Intergenic	-8758	NM_001166432	98758	Mm.422979	NM_133834	ENSMUSG00000042079	Hnrnpf	4833420I20Rik|AA407306|Hnrpf	heterogeneous nuclear ribonucleoprotein F	protein-coding
mm_98457.1	chr11	94947631	94947635	+	1	NA	exon (NM_007742, exon 39 of 51)	exon (NM_007742, exon 39 of 51)	11409	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_17289.1	chr2	26204612	26204622	-	1	NA	intron (NM_010711, intron 1 of 5)	intron (NM_010711, intron 1 of 5)	1958	NM_001039653	16871	Mm.386765	NM_010711	ENSMUSG00000026934	Lhx3	Lim3|P-LIM|mLIM3|mLim-3	LIM homeobox protein 3	protein-coding
mm_23954.1	chr3	84912554	84912572	+	1	NA	intron (NM_001177773, intron 4 of 13)	intron (NM_001177773, intron 4 of 13)	-39648	NM_080428	50754	Mm.196475	NM_080428	ENSMUSG00000028086	Fbxw7	1110001A17Rik|AGO|Cdc4|Fbw7|Fbwd6|Fbx30|Fbxo30|Fbxw6|SEL-10	F-box and WD-40 domain protein 7	protein-coding
mm_147921.1	chr18	65873860	65873863	-	1	NA	intron (NM_175012, intron 1 of 2)	intron (NM_175012, intron 1 of 2)	375	NM_175012	225642	Mm.20298	NM_175012	ENSMUSG00000024517	Grp	BLP	gastrin releasing peptide	protein-coding
mm_15360.1	chr2	156401443	156401449	+	1	NA	Intergenic	Intergenic	-8467	NR_024329	347740	Mm.324242	NR_024329		2900097C17Rik	1810005K14Rik|4930563C06Rik	RIKEN cDNA 2900097C17 gene	ncRNA
mm_94972.1	chr11	30959008	30959018	+	1	NA	intron (NM_023906, intron 1 of 9)	L1_Mus3|LINE|L1	4615	NM_023906	65257	Mm.440539	NM_023906	ENSMUSG00000020305	Asb3	2400011J03Rik|Asb-3	ankyrin repeat and SOCS box-containing 3	protein-coding
mm_90299.1	chr10	125966190	125966207	+	1	NA	promoter-TSS (NM_177152)	promoter-TSS (NM_177152)	-21	NM_177152	320398	Mm.275586	NM_177152	ENSMUSG00000020105	Lrig3	9030421L11Rik|9130004I02Rik|9430095K15Rik|mKIAA3016	leucine-rich repeats and immunoglobulin-like domains 3	protein-coding
mm_74180.1	chr8	123477860	123477904	+	1	NA	promoter-TSS (NR_028260)	promoter-TSS (NR_028260)	20	NR_028260	114896	Mm.287475	NM_054070	ENSMUSG00000031967	Afg3l1	1700047G05Rik|3110061K15Rik	AFG3-like AAA ATPase 1	protein-coding
mm_92350.1	chr10	75893003	75893009	-	1	NA	promoter-TSS (NM_024440)	promoter-TSS (NM_024440)	-392	NM_024440	70377	Mm.275878	NM_024440	ENSMUSG00000009092	Derl3	1810006I20Rik|1810063P04Rik|IZP6|derlin-3	Der1-like domain family, member 3	protein-coding
mm_116246.1	chr13	33935783	33935832	-	1	NA	promoter-TSS (NR_040707)	promoter-TSS (NR_040707)	-225	NR_040707	68808	Mm.443347	NR_040707	ENSMUSG00000085457	1110046J04Rik	-	RIKEN cDNA 1110046J04 gene	ncRNA
mm_16411.1	chr2	180042729	180042739	+	1	NA	promoter-TSS (NM_001289476)	promoter-TSS (NM_001289476)	251	NM_178750	269397	Mm.63068	NM_178750	ENSMUSG00000039086	Ss18l1	A230053O16Rik|CREST	SS18, nBAF chromatin remodeling complex subunit like 1	protein-coding
mm_23944.1	chr3	84666230	84666288	+	1	NA	promoter-TSS (NM_177260)	promoter-TSS (NM_177260)	67	NM_177260	320782	Mm.107370	NM_177260	ENSMUSG00000056498	Tmem154	9930117H01Rik	transmembrane protein 154	protein-coding
mm_73828.1	chr8	117460222	117460236	+	1	NA	TTS (NR_106046)	TTS (NR_106046)	964	NR_106046	102465653		NR_106046	ENSMUSG00000098483	Mir7078	Gm27386|mmu-mir-7078	microRNA 7078	ncRNA
mm_85545.1	chr9	106685304	106685320	-	1	NA	5' UTR (NM_011573, exon 1 of 6)	5' UTR (NM_011573, exon 1 of 6)	504	NM_011573	21767	Mm.22266	NM_011573	ENSMUSG00000040813	Tex264	TEG-264	testis expressed gene 264	protein-coding
mm_79419.1	chr9	55310622	55310622	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-16327	NM_172923	244886	Mm.24361	NM_172923	ENSMUSG00000032313	Tmem266	9630029F15|AI118078|HVRP1	transmembrane protein 266	protein-coding
mm_171077.1	chr3	121249858	121249859	-	1	NA	intron (NM_178936, intron 1 of 7)	LSU-rRNA_Hsa|rRNA|rRNA	13458	NM_178936	99887	Mm.26088	NM_178936	ENSMUSG00000028132	Tmem56	4930577M16Rik|AU018104|AW109744|C730036B01Rik	transmembrane protein 56	protein-coding
mm_158030.1	chrX	97376457	97376465	-	1	NA	intron (NM_001161432, intron 1 of 7)	intron (NM_001161432, intron 1 of 7)	748	NM_001161432	245527	Mm.189270	NM_175540	ENSMUSG00000034457	Eda2r	9430060M22Rik|TNFRSF27|Xedar	ectodysplasin A2 receptor	protein-coding
mm_45809.1	chr5	87670911	87670928	-	1	NA	intron (NM_001286015, intron 6 of 32)	intron (NM_001286015, intron 6 of 32)	4711	NM_001286016	12990	Mm.427467	NM_007784	ENSMUSG00000070702	Csn1s1	AA959832|AW212882|Csna	casein alpha s1	protein-coding
mm_155444.1	chrX	73495014	73495024	+	1	NA	3' UTR (NM_007542, exon 8 of 8)	3' UTR (NM_007542, exon 8 of 8)	-8067	NM_001310537	320707	Mm.210095	NM_177236	ENSMUSG00000031376	Atp2b3	6430519O13Rik|Pmca3	ATPase, Ca++ transporting, plasma membrane 3	protein-coding
mm_56769.1	chr6	116414045	116414053	-	1	NA	intron (NM_009662, intron 9 of 13)	intron (NM_009662, intron 9 of 13)	47129	NM_009662	11689	Mm.41072	NM_009662	ENSMUSG00000025701	Alox5	5-LO|5-LOX|5LO|5LX|AI850497|F730011J02	arachidonate 5-lipoxygenase	protein-coding
mm_122416.1	chr14	41122530	41122556	-	1	NA	exon (NM_133653, exon 10 of 10)	exon (NM_133653, exon 10 of 10)	-9245	NM_023134	20387	Mm.46062	NM_023134	ENSMUSG00000021789	Sftpa1	SP-A|Sftp-1|Sftp1	surfactant associated protein A1	protein-coding
mm_50807.1	chr6	54300134	54300162	+	1	NA	exon (NM_001311133, exon 8 of 8)	exon (NM_001311133, exon 8 of 8)	-26864	NM_030024	78004	Mm.41984	NM_030024	ENSMUSG00000045725	Prr15	E130201N16Rik|G90	proline rich 15	protein-coding
mm_79583.1	chr9	58202856	58202866	+	1	NA	promoter-TSS (NM_177193)	promoter-TSS (NM_177193)	-36	NR_033522	665268	Mm.451475	NR_033522	ENSMUSG00000057818	1600029O15Rik	-	ribosomal protein L17 pseudogene	pseudo
mm_58561.1	chr7	4741840	4741852	+	1	NA	5' UTR (NM_001115018, exon 2 of 9)	5' UTR (NM_001115018, exon 2 of 9)	1719	NM_001115018	232811	Mm.247844	NM_146177	ENSMUSG00000059851	Kmt5c	BC024816|Suv4-20h2|Suv420h2	lysine methyltransferase 5C	protein-coding
mm_38307.1	chr4	136898827	136898838	-	1	NA	promoter-TSS (NM_007572)	promoter-TSS (NM_007572)	12	NM_007572	12259	Mm.439957	NM_007572	ENSMUSG00000036887	C1qa	AI255395|C1q	complement component 1, q subcomponent, alpha polypeptide	protein-coding
mm_96910.1	chr11	70459710	70459727	+	1	NA	promoter-TSS (NM_001029929)	promoter-TSS (NM_001029929)	96	NM_001029929	574428	Mm.472771	NM_001029929	ENSMUSG00000040829	Zmynd15	-	zinc finger, MYND-type containing 15	protein-coding
mm_151248.1	chr19	53906235	53906255	+	1	NA	intron (NM_001168491, intron 1 of 11)	intron (NM_001168491, intron 1 of 11)	2894	NM_001168491	18569	Mm.1605	NM_011050	ENSMUSG00000024975	Pdcd4	D19Ucla1|Ma3|Tis	programmed cell death 4	protein-coding
mm_102768.1	chr11	68196076	68196081	-	1	NA	intron (NM_018768, intron 7 of 7)	intron (NM_018768, intron 7 of 7)	-24814	NR_105833	102465219		NR_105833	ENSMUSG00000099174	Mir6406	Gm27981|mmu-mir-6406	microRNA 6406	ncRNA
mm_78715.1	chr9	41523853	41523883	+	1	NA	intron (NR_131930, intron 2 of 3)	intron (NR_131930, intron 2 of 3)	-7557	NR_029790	723892		NR_029790	ENSMUSG00000093011	Mir100	Mirn100|mir-100|mmu-mir-100	microRNA 100	ncRNA
mm_78743.1	chr9	42076510	42076544	+	1	NA	intron (NM_011436, intron 6 of 47)	Lx8|LINE|L1	47762	NM_011436	20660	Mm.121920	NM_011436	ENSMUSG00000049313	Sorl1	2900010L19Rik|AI596264|AW261561|LR11|SorLA|gp250|mSorLA	sortilin-related receptor, LDLR class A repeats-containing	protein-coding
mm_66602.1	chr7	45459432	45459457	-	1	NA	intron (NM_010240, intron 1 of 3)	intron (NM_010240, intron 1 of 3)	442	NM_010240	14325	Mm.30357	NM_010240	ENSMUSG00000050708	Ftl1	Ftl|Ftl-1|L-ferritin	ferritin light polypeptide 1	protein-coding
mm_155500.1	chrX	73774437	73774454	+	1	NA	promoter-TSS (NM_019684)	promoter-TSS (NM_019684)	40	NM_019684	56504	Mm.111904	NM_019684	ENSMUSG00000002007	Srpk3	Mssk1|Stk23	serine/arginine-rich protein specific kinase 3	protein-coding
mm_49029.1	chr6	4759715	4759719	+	1	NA	3' UTR (NM_130877, exon 2 of 2)	3' UTR (NM_130877, exon 2 of 2)	12411	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_30796.1	chr4	19852131	19852133	+	1	NA	Intergenic	Intergenic	33405	NM_028746	74087	Mm.173833	NM_028746	ENSMUSG00000041052	Slc7a13	0610009O04Rik|AGT-1|AGT1|XAT2	solute carrier family 7, (cationic amino acid transporter, y+ system) member 13	protein-coding
mm_11756.1	chr2	38511492	38511523	+	1	NA	promoter-TSS (NM_021606)	promoter-TSS (NM_021606)	-190	NM_021606	59126	Mm.143818	NM_021606	ENSMUSG00000026749	Nek6	1300007C09Rik	NIMA (never in mitosis gene a)-related expressed kinase 6	protein-coding
mm_95320.1	chr11	46437487	46437512	+	1	NA	intron (NM_001104556, intron 1 of 1)	CpG	538	NM_025426	66213	Mm.24159	NM_025426	ENSMUSG00000020397	Med7	1110063B05Rik|Crsp33|Crsp9	mediator complex subunit 7	protein-coding
mm_151838.1	chr19	5721812	5721853	-	1	NA	exon (NM_001114597, exon 5 of 19)	exon (NM_001114597, exon 5 of 19)	4485	NM_001114595	114601	Mm.210447	NM_053252	ENSMUSG00000024937	Ehbp1l1	G430002G23Rik	EH domain binding protein 1-like 1	protein-coding
mm_131510.1	chr16	17491421	17491434	+	1	NA	promoter-TSS (NM_001291070)	promoter-TSS (NM_001291070)	-494	NM_001291070	72168	Mm.40038	NM_175178	ENSMUSG00000022763	Aifm3	2810401C16Rik|AI840249|Aifl	apoptosis-inducing factor, mitochondrion-associated 3	protein-coding
mm_80320.1	chr9	74952853	74952935	+	1	NA	promoter-TSS (NM_001113283)	promoter-TSS (NM_001113283)	-159	NM_001113283	235493	Mm.208955	NM_153584	ENSMUSG00000034858	Fam214a	6330415I01Rik|AI553555|C130047D21Rik|Kiaa1370|mKIAA1370	family with sequence similarity 214, member A	protein-coding
mm_160427.1	chr8	88283224	88283224	+	1	NA	intron (NM_001109756, intron 1 of 27)	intron (NM_001109756, intron 1 of 27)	232	NM_001109756	11513	Mm.288206	NM_007406	ENSMUSG00000031659	Adcy7	AA407758	adenylate cyclase 7	protein-coding
mm_67920.1	chr7	99858993	99859007	-	1	NA	promoter-TSS (NM_001164258)	promoter-TSS (NM_001164258)	-117	NM_025668	66624	Mm.30043	NM_025668	ENSMUSG00000035227	Spcs2	5730406I15Rik|AA408713|mKIAA0102	signal peptidase complex subunit 2 homolog (S. cerevisiae)	protein-coding
mm_46179.1	chr5	97111546	97111554	-	1	NA	promoter-TSS (NM_198422)	promoter-TSS (NM_198422)	46	NM_198422	231474	Mm.332505	NM_198422	ENSMUSG00000055725	Paqr3	6330415A20Rik|AY424292|RKTG	progestin and adipoQ receptor family member III	protein-coding
mm_167595.1	chr9	48708777	48708777	+	1	NA	intron (NM_001033324, intron 4 of 6)	intron (NM_001033324, intron 4 of 6)	-103654	NM_010924	18113	Mm.8362	NM_010924	ENSMUSG00000032271	Nnmt	-	nicotinamide N-methyltransferase	protein-coding
mm_152367.1	chr19	10101810	10101820	-	1	NA	promoter-TSS (NM_019699)	promoter-TSS (NM_019699)	-312	NM_019699	56473	Mm.38901	NM_019699	ENSMUSG00000024665	Fads2	2900042M13Rik|Fadsd2	fatty acid desaturase 2	protein-coding
mm_134208.1	chr16	11175522	11175571	-	1	NA	intron (NM_145931, intron 1 of 22)	intron (NM_145931, intron 1 of 22)	847	NR_027502	106205	Mm.226860	NM_145931	ENSMUSG00000037965	Zc3h7a	A430104C18Rik|AI447294|AW556219|HSPC055|Zc3h7|Zc3hdc7	zinc finger CCCH type containing 7 A	protein-coding
mm_65222.1	chr7	19699956	19699961	-	1	NA	promoter-TSS (NM_009696)	promoter-TSS (NM_009696)	-770	NM_009696	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_65693.1	chr7	28372631	28372637	-	1	NA	promoter-TSS (NM_001083912)	promoter-TSS (NM_001083912)	28	NM_138752	101497	Mm.235700	NM_138752	ENSMUSG00000037552	Plekhg2	AI194308|Clg|Cslg	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	protein-coding
mm_51193.1	chr6	71224476	71224481	+	1	NA	intron (NM_009762, intron 5 of 8)	intron (NM_009762, intron 5 of 8)	24590	NM_017399	14080	Mm.22126	NM_017399	ENSMUSG00000054422	Fabp1	Fabpl|L-FABP	fatty acid binding protein 1, liver	protein-coding
mm_102810.1	chr11	68947374	68947412	-	1	NA	exon (NM_177566, exon 12 of 16)	exon (NM_177566, exon 12 of 16)	9465	NM_177566	442801	Mm.376147	NM_177566	ENSMUSG00000052921	Arhgef15	D130071N09|D530030K12Rik|E5	Rho guanine nucleotide exchange factor (GEF) 15	protein-coding
mm_7712.1	chr1	130462985	130463008	-	1	NA	promoter-TSS (NM_010016)	promoter-TSS (NM_010016)	-252	NM_010016	13136	Mm.101591	NM_010016	ENSMUSG00000026399	Cd55	Daf|Daf-GPI|Daf1|GPI-DAF	CD55 molecule, decay accelerating factor for complement	protein-coding
mm_151959.1	chr19	5801477	5801531	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	1168	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_11295.1	chr2	30134682	30134709	+	1	NA	intron (NM_146252, intron 1 of 11)	intron (NM_146252, intron 1 of 11)	949	NM_146252	70296	Mm.19172	NM_146252	ENSMUSG00000039678	Tbc1d13	2600014A06Rik|BC025586	TBC1 domain family, member 13	protein-coding
mm_30514.1	chr3	158171802	158171804	-	1	NA	intron (NM_001081358, intron 18 of 27)	intron (NM_001081358, intron 18 of 27)	135121	NM_001289524	67144	Mm.358704	NM_024194	ENSMUSG00000063052	Lrrc40	2610040E16Rik|AI837674	leucine rich repeat containing 40	protein-coding
mm_89734.1	chr10	99000788	99000823	+	1	NA	intron (NM_026482, intron 10 of 20)	intron (NM_026482, intron 10 of 20)	85653	NM_026482	67972	Mm.166944	NM_026482	ENSMUSG00000019943	Atp2b1	2810442I22Rik|E130111D10Rik|Pmca1	ATPase, Ca++ transporting, plasma membrane 1	protein-coding
mm_111063.1	chr12	80114472	80114486	-	1	NA	Intergenic	CpG	-1466	NM_007564	12192	Mm.235132	NM_007564	ENSMUSG00000021127	Zfp36l1	AW742437|AW743212|Berg36|Brf1|D530020L18Rik|ERF1|TIS11b|cMG1	zinc finger protein 36, C3H type-like 1	protein-coding
mm_171747.1	chr4	98733640	98733644	+	1	NA	exon (NM_001081202, exon 3 of 5)	exon (NM_001081202, exon 3 of 5)	6888	NM_001081202	381591	Mm.34340	NM_001081202	ENSMUSG00000087166	L1td1	AA546746|AB211064|D76865|ECAT11	LINE-1 type transposase domain containing 1	protein-coding
mm_19240.1	chr2	84715278	84715287	-	1	NA	promoter-TSS (NM_144887)	promoter-TSS (NM_144887)	-118	NM_144887	228136	Mm.288508	NM_144887	ENSMUSG00000034075	Zdhhc5	1110032A17Rik|AI451382|Zisp	zinc finger, DHHC domain containing 5	protein-coding
mm_138461.1	chr17	35142267	35142273	+	1	NA	intron (NM_057171, intron 10 of 24)	intron (NM_057171, intron 10 of 24)	6556	NM_001252469	224727	Mm.203962	NM_057171	ENSMUSG00000024392	Bag6	2410045D21Rik|AA408914|BAG-6|Bat3|D17H6S52E|G3|Scythe	BCL2-associated athanogene 6	protein-coding
mm_87816.1	chr10	60302109	60302122	+	1	NA	TTS (NM_001252635)	TTS (NM_001252635)	17654	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_127901.1	chr15	9507437	9507448	-	1	NA	3' UTR (NM_008372, exon 8 of 8)	3' UTR (NM_008372, exon 8 of 8)	22434	NM_008372	16197	Mm.389	NM_008372	ENSMUSG00000003882	Il7r	CD127|IL-7Ralpha	interleukin 7 receptor	protein-coding
mm_63119.1	chr7	122821599	122821637	+	1	NA	Intergenic	Intergenic	148841	NR_045614	73951	Mm.389936	NR_045614		4930413G21Rik	-	RIKEN cDNA 4930413G21 gene	ncRNA
mm_160117.1	chr7	27396425	27396425	-	1	NA	promoter-TSS (NM_001199234)	promoter-TSS (NM_001199234)	128	NM_001199236	80297	Mm.459123	NM_032610	ENSMUSG00000011751	Sptbn4	1700022P15Rik|5830426A08Rik|ROSA62|SpbIV|Spnb4|dyn|lnd|nmf261|nmf379|qv	spectrin beta, non-erythrocytic 4	protein-coding
mm_22972.1	chr3	32708758	32708764	+	1	NA	5' UTR (NM_019673, exon 1 of 14)	5' UTR (NM_019673, exon 1 of 14)	215	NM_019673	56456	Mm.41077	NM_019673	ENSMUSG00000027671	Actl6a	2810432C06Rik|AI851094|ARP4|Actl6|Baf53a|C79802	actin-like 6A	protein-coding
mm_29660.1	chr3	122559100	122559116	-	1	NA	exon (NM_001114665, exon 8 of 16)	exon (NM_001114665, exon 8 of 16)	-17427	NR_106117	102465764		NR_106117	ENSMUSG00000104773	Mir7657	mmu-mir-7657	microRNA 7657	ncRNA
mm_110141.1	chr12	26448201	26448225	-	1	NA	intron (NM_021384, intron 4 of 5)	intron (NM_021384, intron 4 of 5)	8239	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_68136.1	chr7	102239601	102239616	-	1	NA	3' UTR (NM_019566, exon 2 of 2)	3' UTR (NM_019566, exon 2 of 2)	10510	NM_019566	56212	Mm.259795	NM_019566	ENSMUSG00000073982	Rhog	2810426G09Rik|Arhg|Sid10750	ras homolog family member G	protein-coding
mm_116266.1	chr13	34628319	34628325	-	1	NA	3' UTR (NM_025831, exon 5 of 5)	3' UTR (NM_025831, exon 5 of 5)	24359	NM_025831	66895	Mm.28943	NM_025831	ENSMUSG00000021411	Pxdc1	1300014I06Rik	PX domain containing 1	protein-coding
mm_94842.1	chr11	23666480	23666496	+	1	NA	promoter-TSS (NM_023651)	promoter-TSS (NM_023651)	512	NM_028304	74467	Mm.29536	NM_028304	ENSMUSG00000020280	Pus10	2810013G11Rik|4933435A13Rik|AU014648|C77560|Ccdc139	pseudouridylate synthase 10	protein-coding
mm_51050.1	chr6	65631233	65631246	+	1	NA	3' UTR (NM_001001495, exon 8 of 8)	3' UTR (NM_001001495, exon 8 of 8)	-40372	NM_172399	68169	Mm.52392	NM_172399	ENSMUSG00000049001	Ndnf	A930038C07Rik|epidermacan	neuron-derived neurotrophic factor	protein-coding
mm_5320.1	chr1	22805904	22805914	-	1	NA	promoter-TSS (NM_001012625)	promoter-TSS (NM_001012625)	-185	NM_001012624	116837	Mm.60061	NM_053270	ENSMUSG00000041670	Rims1	C030033M19Rik|RIM1|RIM1a|RIM1alpha|Rab3ip1|Rim|Serg1|mKIAA0340	regulating synaptic membrane exocytosis 1	protein-coding
mm_132613.1	chr16	38712175	38712178	+	1	NA	intron (NM_020260, intron 1 of 11)	intron (NM_020260, intron 1 of 11)	859	NM_020260	12549	Mm.370848	NM_020260	ENSMUSG00000022799	Arhgap31	5830477L08Rik|AU041750|Cdgap|D330026I07Rik	Rho GTPase activating protein 31	protein-coding
mm_57216.1	chr6	122933994	122934004	-	1	NA	3' UTR (NM_199311, exon 6 of 6)	3' UTR (NM_199311, exon 6 of 6)	12151	NM_199311	269799	Mm.297275	NM_199311	ENSMUSG00000049037	Clec4a1	BC049354|Dcir4	C-type lectin domain family 4, member a1	protein-coding
mm_128208.1	chr15	36140394	36140406	-	1	NA	promoter-TSS (NM_001195748)	promoter-TSS (NM_001195748)	0	NM_001195748	626596	Mm.321798	NM_001195748	ENSMUSG00000037627	Rgs22	-	regulator of G-protein signalling 22	protein-coding
mm_55672.1	chr6	72550845	72550863	-	1	NA	intron (NM_001271395, intron 1 of 9)	L3|LINE|CR1	1207	NM_001271395	12332	Mm.18626	NM_007599	ENSMUSG00000056737	Capg	gCap39|mbh1	capping protein (actin filament), gelsolin-like	protein-coding
mm_30439.1	chr3	153633518	153633528	-	1	NA	intron (NM_011372, intron 1 of 4)	intron (NM_011372, intron 1 of 4)	91610	NM_011372	20447	Mm.296453	NM_011372	ENSMUSG00000052544	St6galnac3	Siat7c	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 3	protein-coding
mm_18394.1	chr2	60210430	60210453	-	1	NA	intron (NM_020575, intron 1 of 9)	intron (NM_020575, intron 1 of 9)	505	NM_020575	57438	Mm.260635	NM_020575	ENSMUSG00000026977	March7	Axo|Axot|Gtrgeo17	membrane-associated ring finger (C3HC4) 7	protein-coding
mm_62703.1	chr7	110237879	110237881	+	1	NA	intron (NM_009302, intron 1 of 11)	intron (NM_009302, intron 1 of 11)	16177	NM_009302	20947	Mm.334144	NM_009302	ENSMUSG00000031015	Swap70	70kDa|AV235546	SWA-70 protein	protein-coding
mm_143285.1	chr17	65864646	65864672	-	1	NA	exon (NM_001198949, exon 3 of 10)	exon (NM_001198949, exon 3 of 10)	20264	NM_001198949	19765	Mm.17009	NM_009067	ENSMUSG00000024096	Ralbp1	RLIP76|Rip1	ralA binding protein 1	protein-coding
mm_19733.1	chr2	104494558	104494578	-	1	NA	promoter-TSS (NM_001145824)	promoter-TSS (NM_001145824)	-79	NM_001145824	15259	Mm.257925	NM_010434	ENSMUSG00000027177	Hipk3	DYRK6|FIST3|PKY|mir-1902	homeodomain interacting protein kinase 3	protein-coding
mm_88976.1	chr10	81525375	81525387	+	1	NA	Intergenic	Intergenic	-1156	NM_010304	14676	Mm.1546	NM_010304	ENSMUSG00000034792	Gna15	G[a]15|Galpha15	guanine nucleotide binding protein, alpha 15	protein-coding
mm_23611.1	chr3	65528405	65528431	+	1	NA	promoter-TSS (NM_178892)	promoter-TSS (NM_178892)	-29	NM_178892	99929	Mm.246398	NM_178892	ENSMUSG00000034640	Tiparp	ARTD14|AW558171|PARP7	TCDD-inducible poly(ADP-ribose) polymerase	protein-coding
mm_5869.1	chr1	53783809	53783813	-	1	NA	intron (NM_133810, intron 1 of 7)	intron (NM_133810, intron 1 of 7)	1404	NM_133810	98267	Mm.25559	NM_133810	ENSMUSG00000026094	Stk17b	3110009A03Rik|AI120141|Drak2	serine/threonine kinase 17b (apoptosis-inducing)	protein-coding
mm_148936.1	chr19	7025639	7025652	+	1	NA	intron (NM_016737, intron 9 of 13)	intron (NM_016737, intron 9 of 13)	-6176	NM_153795	108101	Mm.157591	NM_153795	ENSMUSG00000024965	Fermt3	C79673|Kindlin3	fermitin family member 3	protein-coding
mm_128777.1	chr15	66792788	66792800	-	1	NA	intron (NM_009192, intron 4 of 8)	RSINE1|SINE|B4	39035	NM_001029841	20491	Mm.7601	NM_009192	ENSMUSG00000022372	Sla	Slap|Slap-1	src-like adaptor	protein-coding
mm_58675.1	chr7	11514287	11514287	+	1	NA	Intergenic	Intergenic	116372	NM_001110316	665902	Mm.425380	NM_001110316	ENSMUSG00000070828	Zscan4f	C330039H09Rik	zinc finger and SCAN domain containing 4F	protein-coding
mm_141043.1	chr17	25392492	25392493	-	1	NA	exon (NM_021415, exon 9 of 35)	exon (NM_021415, exon 9 of 35)	21939	NM_012034	26945	Mm.180108	NM_012034	ENSMUSG00000033200	Tpsg1	Prss31|Tmt	tryptase gamma 1	protein-coding
mm_40043.1	chr5	33828250	33828253	+	1	NA	Intergenic	Intergenic	-14861	NM_175231	107823	Mm.19892	NM_175231	ENSMUSG00000057406	Whsc1	5830445G22Rik|9430010A17Rik|AW555663|C130020C13Rik|D030027O06Rik|D930023B08Rik|MMSET|NSD2|Whsc1l|mKIAA1090	Wolf-Hirschhorn syndrome candidate 1 (human)	protein-coding
mm_117952.1	chr13	99444366	99444370	-	1	NA	intron (NM_008634, intron 2 of 6)	intron (NM_008634, intron 2 of 6)	-31542	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_6001.1	chr1	58972694	58972697	-	1	NA	promoter-TSS (NM_172656)	promoter-TSS (NM_172656)	787	NM_172406	70827	Mm.222887	NM_172406	ENSMUSG00000026028	Trak2	2900022D04Rik|4733401O11Rik|AI480836|AW046271|Als2cr3|CALS-C|GRIF-1|GRIF1|OIP98|mKIAA0549	trafficking protein, kinesin binding 2	protein-coding
mm_111394.1	chr12	90728112	90728133	-	1	NA	3' UTR (NM_010050, exon 2 of 2)	3' UTR (NM_010050, exon 2 of 2)	10915	NM_010050	13371	Mm.21389	NM_010050	ENSMUSG00000007682	Dio2	5DII|AI324267|DIOII	deiodinase, iodothyronine, type II	protein-coding
mm_19274.1	chr2	85196698	85196708	-	1	NA	promoter-TSS (NM_001033346)	promoter-TSS (NM_001033346)	-4	NM_001033346	241528	Mm.291095	NM_001033346	ENSMUSG00000075224	Lrrc55	A330097E02Rik|Gm351	leucine rich repeat containing 55	protein-coding
mm_19130.1	chr2	80129291	80129304	-	1	NA	promoter-TSS (NM_016744)	promoter-TSS (NM_016744)	115	NM_001159582	18573	Mm.40678	NM_016744	ENSMUSG00000059173	Pde1a	AI987702|AW125737	phosphodiesterase 1A, calmodulin-dependent	protein-coding
mm_86478.1	chr10	4710168	4710186	+	1	NA	promoter-TSS (NM_001302533)	promoter-TSS (NM_001302533)	19	NM_001302533	13982	Mm.9213	NM_007956	ENSMUSG00000019768	Esr1	ER|ER-alpha|ERa|ERalpha|ESR|Estr|Estra|Nr3a1	estrogen receptor 1 (alpha)	protein-coding
mm_131629.1	chr16	20141062	20141140	+	1	NA	promoter-TSS (NM_001145931)	promoter-TSS (NM_001145931)	38	NM_001145930	208146	Mm.390895	NM_001033237	ENSMUSG00000041215	Yeats2	BC042768|mKIAA1197	YEATS domain containing 2	protein-coding
mm_169258.1	chr1	37997205	37997217	-	1	NA	promoter-TSS (NM_172054)	promoter-TSS (NM_172054)	-3	NM_172054	98258	Mm.28438	NM_172054	ENSMUSG00000058407	Txndc9	AI098020|APACD	thioredoxin domain containing 9	protein-coding
mm_57247.1	chr6	123283366	123283374	-	1	NA	3' UTR (NM_019948, exon 6 of 6)	3' UTR (NM_019948, exon 6 of 6)	6501	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_78684.1	chr9	40798466	40798491	+	1	NA	Intergenic	Lx8|LINE|L1	-2795	NM_031165	15481	Mm.290774	NM_031165	ENSMUSG00000015656	Hspa8	2410008N15Rik|Hsc70|Hsc71|Hsc73|Hsp73|Hspa10	heat shock protein 8	protein-coding
mm_146475.1	chr18	89197192	89197198	+	1	NA	promoter-TSS (NM_178687)	promoter-TSS (NM_178687)	-232	NM_178687	225825	Mm.139293	NM_178687	ENSMUSG00000034028	Cd226	BC051526|DNAM-1|DNAM1|Pta1|TLiSA1	CD226 antigen	protein-coding
mm_156011.1	chrX	107088453	107088466	+	1	NA	promoter-TSS (NM_172435)	promoter-TSS (NM_172435)	-876	NM_172435	78826	Mm.74639	NM_172435	ENSMUSG00000050921	P2ry10	5830408N17Rik|Lypsr2|P2Y10	purinergic receptor P2Y, G-protein coupled 10	protein-coding
mm_135673.1	chr16	52417624	52417638	-	1	NA	intron (NM_009655, intron 1 of 15)	intron (NM_009655, intron 1 of 15)	35450	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_102507.1	chr11	60727258	60727268	-	1	NA	promoter-TSS (NM_022009)	promoter-TSS (NM_022009)	0	NM_022009	14248	Mm.339755	NM_022009	ENSMUSG00000002812	Flii	3632430F08Rik|Fliih	flightless I actin binding protein	protein-coding
mm_158784.1	chrX	167207413	167207537	-	1	NA	3' UTR (NM_021278, exon 3 of 3)	3' UTR (NM_021278, exon 3 of 3)	1743	NM_021278	19241	Mm.142729	NM_021278	ENSMUSG00000049775	Tmsb4x	Ptmb4|Tb4	thymosin, beta 4, X chromosome	protein-coding
mm_153525.1	chr19	41774565	41774591	-	1	NA	intron (NM_027667, intron 9 of 11)	intron (NM_027667, intron 9 of 11)	27506	NM_001163495	71085	Mm.21646	NM_027667	ENSMUSG00000025154	Arhgap19	4933411B03Rik|AI120128|AW546831|mFLJ00368	Rho GTPase activating protein 19	protein-coding
mm_62508.1	chr7	102107045	102107073	+	1	NA	exon (NM_009710, exon 3 of 5)	exon (NM_009710, exon 3 of 5)	5316	NM_009710	11870	Mm.261071	NM_009710	ENSMUSG00000030996	Art1	ADPRT|ARTC1|Yac-1	ADP-ribosyltransferase 1	protein-coding
mm_104081.1	chr11	86598612	86598651	-	1	NA	intron (NM_029478, intron 10 of 11)	intron (NM_029478, intron 10 of 11)	-14473	NR_029738	387140		NR_029738	ENSMUSG00000065455	Mir21a	Mir21|Mirn21|mmu-mir-21|mmu-mir-21a	microRNA 21a	ncRNA
mm_36334.1	chr4	72193342	72193353	-	1	NA	intron (NM_001285530, intron 4 of 17)	intron (NM_001285530, intron 4 of 17)	7546	NM_011599	21885	Mm.278444	NM_011599	ENSMUSG00000008305	Tle1	C230057C06Rik|Estm14|Grg-1|Grg1|Tle4l	transducin-like enhancer of split 1	protein-coding
mm_116587.1	chr13	47274494	47274500	-	1	NA	Intergenic	RMER17C|LTR|ERVK	80494	NM_001170643	218215	Mm.287609	NM_146042	ENSMUSG00000038068	Rnf144b	BC025007|E130105P19Rik|Ibrdc2|Pir2	ring finger protein 144B	protein-coding
mm_118542.1	chr14	16575630	16575634	+	1	NA	promoter-TSS (NM_001289762)	promoter-TSS (NM_001289762)	-156	NM_001289762	218772	Mm.259318	NM_011243	ENSMUSG00000017491	Rarb	A830025K23|Hap|Nr1b2	retinoic acid receptor, beta	protein-coding
mm_98001.1	chr11	84173473	84173494	+	1	NA	Intergenic	Intergenic	-6007	NM_001037932	628813	Mm.390389	NM_001037932	ENSMUSG00000051452	Gm11437	AI463690|OTTMUSG00000000997	predicted gene 11437	protein-coding
mm_117772.1	chr13	96542555	96542567	-	1	NA	promoter-TSS (NM_001164222)	promoter-TSS (NM_001164222)	18	NM_012048	27015	Mm.89926	NM_012048	ENSMUSG00000021668	Polk	DINP|Dinb1	polymerase (DNA directed), kappa	protein-coding
mm_5858.1	chr1	53751360	53751391	-	1	NA	Intergenic	Lx4A|LINE|L1	33840	NM_133810	98267	Mm.25559	NM_133810	ENSMUSG00000026094	Stk17b	3110009A03Rik|AI120141|Drak2	serine/threonine kinase 17b (apoptosis-inducing)	protein-coding
mm_87232.1	chr10	40629988	40630053	+	1	NA	promoter-TSS (NM_027442)	promoter-TSS (NM_027442)	9	NR_133568	70503	Mm.252862	NM_027442	ENSMUSG00000063428	Ddo	5330420D20Rik|5730402C02Rik|AI467244	D-aspartate oxidase	protein-coding
mm_134035.1	chr16	5040545	5040548	-	1	NA	intron (NM_001079814, intron 3 of 15)	B1_Mur1|SINE|Alu	9364	NM_001079814	74022	Mm.21652	NM_028720	ENSMUSG00000022536	Glyr1	2810419J22Rik|3930401K13Rik|AW545332|Npac	glyoxylate reductase 1 homolog (Arabidopsis)	protein-coding
mm_27381.1	chr3	50443779	50443780	-	1	NA	promoter-TSS (NM_011990)	promoter-TSS (NM_011990)	-166	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_157471.1	chrX	47892558	47892564	-	1	NA	promoter-TSS (NM_001290708)	promoter-TSS (NM_001290708)	-9	NM_001290708	93761	Mm.229151	NM_053123	ENSMUSG00000031099	Smarca1	5730494M04Rik|Snf2l	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1	protein-coding
mm_79820.1	chr9	64385647	64385657	+	1	NA	promoter-TSS (NM_001134399)	promoter-TSS (NM_001134399)	26	NM_001134399	214058	Mm.127721	NM_172522	ENSMUSG00000036466	Megf11	2410080H04Rik|D130061K05	multiple EGF-like-domains 11	protein-coding
mm_170710.1	chr2	14295743	14295751	+	1	NA	intron (NM_008625, intron 15 of 29)	intron (NM_008625, intron 15 of 29)	34744	NR_030609	100124488		NR_030609	ENSMUSG00000077897	Mir511	Mirn511|mir-511|mmu-mir-511	microRNA 511	ncRNA
mm_10514.1	chr2	16356582	16356615	+	1	NA	5' UTR (NM_026162, exon 1 of 14)	5' UTR (NM_026162, exon 1 of 14)	294	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding
mm_172374.1	chr7	126345704	126345706	-	1	NA	Intergenic	Intergenic	22340	NR_106025	102466797		NR_106025	ENSMUSG00000099017	Mir7058	Gm27766|mmu-mir-7058	microRNA 7058	ncRNA
mm_120170.1	chr14	60784559	60784675	+	1	NA	promoter-TSS (NM_027436)	promoter-TSS (NM_027436)	51	NR_040642	70478	Mm.274650	NM_027436	ENSMUSG00000021993	Mipep	5730405E07Rik|MIP	mitochondrial intermediate peptidase	protein-coding
mm_134565.1	chr16	20354711	20354719	-	1	NA	intron (NM_013790, intron 25 of 29)	intron (NM_013790, intron 25 of 29)	-29311	NM_183158	224044	Mm.276400	NM_183158	ENSMUSG00000022818	Cyp2ab1	EG224044|F730023N20	cytochrome P450, family 2, subfamily ab, polypeptide 1	protein-coding
mm_36362.1	chr4	76332466	76332467	-	1	NA	intron (NM_011211, intron 10 of 39)	intron (NM_011211, intron 10 of 39)	-1054180	NM_025849	66928	Mm.24332	NM_025849	ENSMUSG00000028398	Tmem261	1700027K24Rik|3110001D03Rik	transmembrane protein 261	protein-coding
mm_24608.1	chr3	93446196	93446205	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	3870	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_141630.1	chr17	32917321	32917342	-	1	NA	promoter-TSS (NM_001204336)	promoter-TSS (NM_001204336)	-2	NM_001204333	64385	Mm.486449	NM_022434	ENSMUSG00000024292	Cyp4f14	1300014O15Rik|cyp4f-14	cytochrome P450, family 4, subfamily f, polypeptide 14	protein-coding
mm_123767.1	chr14	70211883	70211890	-	1	NA	Intergenic	Intergenic	-4215	NM_011366	20410	Mm.5068	NM_011366	ENSMUSG00000022091	Sorbs3	SCAM-1|SH3P3|Sh3d4|vinexin-g	sorbin and SH3 domain containing 3	protein-coding
mm_31461.1	chr4	49059336	49059347	+	1	NA	promoter-TSS (NM_178756)	promoter-TSS (NM_178756)	-121	NM_178756	272031	Mm.299460	NM_178756	ENSMUSG00000063446	Plppr1	E130309F12Rik|Lppr1|PRG-3|mKIAA4247	phospholipid phosphatase related 1	protein-coding
mm_27423.1	chr3	51518354	51518369	-	1	NA	3' UTR (NM_080793, exon 8 of 8)	3' UTR (NM_080793, exon 8 of 8)	34395	NM_016858	19338	Mm.1664	NM_016858	ENSMUSG00000027739	Rab33b	-	RAB33B, member RAS oncogene family	protein-coding
mm_157984.1	chrX	94150632	94150638	-	1	NA	Intergenic	Intergenic	-27228	NM_001044386	22764	Mm.919	NM_011768	ENSMUSG00000079509	Zfx	Zfx5|Zfx5,6|Zfx6	zinc finger protein X-linked	protein-coding
mm_37921.1	chr4	132790879	132790884	-	1	NA	intron (NM_001033308, intron 2 of 5)	intron (NM_001033308, intron 2 of 5)	5483	NM_001033308	230787	Mm.290912	NM_001033308	ENSMUSG00000037731	Themis2	ICB-1	thymocyte selection associated family member 2	protein-coding
mm_122447.1	chr14	45295880	45295915	-	1	NA	intron (NM_015774, intron 9 of 15)	intron (NM_015774, intron 9 of 15)	22675	NM_015774	50527	Mm.387108	NM_015774	ENSMUSG00000021831	Ero1l	ERO1-L|Ero1a	ERO1-like (S. cerevisiae)	protein-coding
mm_99846.1	chr11	109362062	109362075	+	1	NA	promoter-TSS (NM_010303)	promoter-TSS (NM_010303)	-726	NM_010303	14674	Mm.193925	NM_010303	ENSMUSG00000020611	Gna13	AU024132|AU043124|Galpha13	guanine nucleotide binding protein, alpha 13	protein-coding
mm_105143.1	chr11	101459996	101460009	-	1	NA	3' UTR (NM_012037, exon 6 of 6)	3' UTR (NM_012037, exon 6 of 6)	6197	NM_012037	26949	Mm.29210	NM_012037	ENSMUSG00000034993	Vat1	VAT-1	vesicle amine transport 1	protein-coding
mm_131575.1	chr16	18388996	18389043	+	1	NA	intron (NM_001272028, intron 1 of 17)	intron (NM_001272028, intron 1 of 17)	-3544	NM_001272031	11877	Mm.293599	NM_033474	ENSMUSG00000000325	Arvcf	-	armadillo repeat gene deleted in velo-cardio-facial syndrome	protein-coding
mm_80725.1	chr9	92457787	92457896	+	1	NA	5' UTR (NM_178711, exon 1 of 9)	5' UTR (NM_178711, exon 1 of 9)	463	NM_178711	235527	Mm.55289	NM_178711	ENSMUSG00000032377	Plscr4	AV245873	phospholipid scramblase 4	protein-coding
mm_171423.1	chr4	133967892	133967916	-	1	NA	promoter-TSS (NM_016957)	promoter-TSS (NM_016957)	87	NM_016957	15331	Mm.319660	NM_016957	ENSMUSG00000003038	Hmgn2	HMG-17|Hmg17	high mobility group nucleosomal binding domain 2	protein-coding
mm_72131.1	chr8	71881962	71882006	+	1	NA	promoter-TSS (NM_145624)	promoter-TSS (NM_145624)	-84	NM_145624	236193	Mm.290790	NM_145624	ENSMUSG00000056019	Zfp709	BC021921|GIOT-4|HIT-40	zinc finger protein 709	protein-coding
mm_52239.1	chr6	104782731	104782734	+	1	NA	intron (NM_017383, intron 11 of 22)	intron (NM_017383, intron 11 of 22)	289688	NM_017383	53870	Mm.321671	NM_017383	ENSMUSG00000030092	Cntn6	NB-3	contactin 6	protein-coding
mm_7072.1	chr1	88008521	88008556	-	1	NA	promoter-TSS (NM_001198573)	promoter-TSS (NM_001198573)	13	NM_001198573	227334	Mm.80484	NM_001033291	ENSMUSG00000005501	Usp40	B230215L03Rik|C730029K03	ubiquitin specific peptidase 40	protein-coding
mm_68404.1	chr7	109616351	109616374	-	1	NA	non-coding (NR_037617, exon 1 of 20)	non-coding (NR_037617, exon 1 of 20)	206	NR_037617	76954	Mm.252009	NM_029811	ENSMUSG00000031024	St5	2010004M01Rik|2610305K15Rik	suppression of tumorigenicity 5	protein-coding
mm_103895.1	chr11	83575305	83575315	-	1	NA	3' UTR (NM_011338, exon 4 of 4)	3' UTR (NM_011338, exon 4 of 4)	3326	NM_011338	20308	Mm.416125	NM_011338	ENSMUSG00000019122	Ccl9	CCF18|MRP-2|Scya10|Scya9	chemokine (C-C motif) ligand 9	protein-coding
mm_115947.1	chr13	23710898	23710920	-	1	NA	promoter-TSS (NM_001347493)	promoter-TSS (NM_001347493)	-55	NM_010424	15216	Mm.2681	NM_010424	ENSMUSG00000006611	Hfe	MR2	hemochromatosis	protein-coding
mm_141561.1	chr17	32224191	32224202	-	1	NA	exon (NM_001286630, exon 5 of 20)	exon (NM_001286630, exon 5 of 20)	-17724	NR_102329	100043434		NR_102329		Gm4432	-	predicted gene 4432	pseudo
mm_6136.1	chr1	64734392	64734396	-	1	NA	3' UTR (NM_001042659, exon 2 of 2)	3' UTR (NM_001042659, exon 2 of 2)	3356	NM_001042659	14367	Mm.150813	NM_022721	ENSMUSG00000045005	Fzd5	5330434N09Rik|AI427138|Fz-5|Fz5|mFz5	frizzled class receptor 5	protein-coding
mm_148036.1	chr18	70244419	70244428	-	1	NA	5' UTR (NM_029346, exon 1 of 3)	5' UTR (NM_029346, exon 1 of 3)	161	NM_029346	75577	Mm.58214	NM_029346	ENSMUSG00000024512	Dynap	2310002L13Rik	dynactin associated protein	protein-coding
mm_105187.1	chr11	101984729	101984741	-	1	NA	promoter-TSS (NM_028207)	promoter-TSS (NM_028207)	56	NM_028207	72349	Mm.196295	NM_028207	ENSMUSG00000003518	Dusp3	2210015O03Rik|5031436O03Rik|T-DSP11|VHR	dual specificity phosphatase 3 (vaccinia virus phosphatase VH1-related)	protein-coding
mm_33505.1	chr4	130913121	130913137	+	1	NA	promoter-TSS (NM_010686)	promoter-TSS (NM_010686)	-205	NM_010686	16792	Mm.271868	NM_010686	ENSMUSG00000028581	Laptm5	E3	lysosomal-associated protein transmembrane 5	protein-coding
mm_23834.1	chr3	81995697	81995709	+	1	NA	Intergenic	Intergenic	-1219	NM_021370	58170	Mm.88839	NM_021370	ENSMUSG00000028008	Asic5	Accn5|Blinac|Inac	acid-sensing (proton-gated) ion channel family member 5	protein-coding
mm_6649.1	chr1	79761699	79761748	-	1	NA	promoter-TSS (NM_001111279)	promoter-TSS (NM_001111279)	46	NM_001111279	69368	Mm.293273	NM_027057	ENSMUSG00000073643	Wdfy1	1700013B03Rik|1700120F24Rik|FENS-1|Jr1|WDF1|ZFYVE17|mKIAA1435	WD repeat and FYVE domain containing 1	protein-coding
mm_149627.1	chr19	17136809	17136819	+	1	NA	intron (NM_181348, intron 9 of 19)	intron (NM_181348, intron 9 of 19)	180696	NM_181348	353211	Mm.257354	NM_181348	ENSMUSG00000039126	Prune2	6330414G02Rik|A230083H22Rik|A330102H22Rik|Bmcc1|mKIAA0367	prune homolog 2	protein-coding
mm_149512.1	chr19	11977022	11977032	+	1	NA	intron (NM_001033174, intron 3 of 13)	intron (NM_001033174, intron 3 of 13)	11183	NM_001033174	76303	Mm.291279	NM_001033174	ENSMUSG00000024687	Osbp	1110018F06Rik|AW559088|mKIAA4220	oxysterol binding protein	protein-coding
mm_156484.1	chrX	144335788	144335831	+	1	NA	intron (NR_037145, intron 3 of 26)	intron (NR_037145, intron 3 of 26)	17843	NM_026247	67574	Mm.249084	NM_026247	ENSMUSG00000041718	Alg13	2810046O15Rik|4833435D08Rik|Glt28d1|MDS031|OTTMUSG00000018917	asparagine-linked glycosylation 13	protein-coding
mm_57607.1	chr6	128028915	128028919	-	1	NA	intron (NM_175414, intron 3 of 8)	intron (NM_175414, intron 3 of 8)	114661	NM_175414	109246	Mm.21814	NM_175414	ENSMUSG00000030352	Tspan9	6720474K14Rik|9430079M16Rik|AU018597	tetraspanin 9	protein-coding
mm_57805.1	chr6	129386053	129386062	-	1	NA	promoter-TSS (NM_027709)	promoter-TSS (NM_027709)	-183	NM_001204223	71183	Mm.79402	NM_027709	ENSMUSG00000030158	Clec12b	4933425B16Rik	C-type lectin domain family 12, member B	protein-coding
mm_172578.1	chr8	119602628	119602646	-	1	NA	intron (NM_021441, intron 6 of 14)	intron (NM_021441, intron 6 of 14)	2603	NM_021441	21341	Mm.41977	NM_021441	ENSMUSG00000031832	Taf1c	Tafi95|mTAFI95	TATA-box binding protein associated factor, RNA polymerase I, C	protein-coding
mm_41870.1	chr5	104459644	104459654	+	1	NA	exon (NM_008861, exon 1 of 15)	exon (NM_008861, exon 1 of 15)	192	NM_008861	18764	Mm.6442	NM_008861	ENSMUSG00000034462	Pkd2	C030034P18Rik|PC2|TRPP2	polycystic kidney disease 2	protein-coding
mm_147469.1	chr18	46717095	46717117	-	1	NA	intron (NM_033037, intron 3 of 4)	HAL1|LINE|L1	11236	NM_033037	12583	Mm.241056	NM_033037	ENSMUSG00000033022	Cdo1	1300002L19Rik|Cdo|D18Ucla3	cysteine dioxygenase 1, cytosolic	protein-coding
mm_60087.1	chr7	34655278	34655301	+	1	NA	Intergenic	CpG	-2448	NM_146188	233107	Mm.486198	NM_146188	ENSMUSG00000030499	Kctd15	BC031749	potassium channel tetramerisation domain containing 15	protein-coding
mm_111725.1	chr12	103765731	103765753	-	1	NA	exon (NM_009246, exon 3 of 5)	exon (NM_009246, exon 3 of 5)	7891	NM_009246	20703	Mm.439695	NM_009246	ENSMUSG00000071177	Serpina1d	AI118301|Dom4|PI4|Spi1-4	serine (or cysteine) peptidase inhibitor, clade A, member 1D	protein-coding
mm_12017.1	chr2	58153873	58153886	+	1	NA	intron (NM_139200, intron 1 of 7)	intron (NM_139200, intron 1 of 7)	6243	NM_139200	227929	Mm.273905	NM_139200	ENSMUSG00000026832	Cytip	A130053M09Rik|AI462064|C80816|Cbp|Cybr|Pscdbp	cytohesin 1 interacting protein	protein-coding
mm_95720.1	chr11	54522899	54522909	+	1	NA	promoter-TSS (NM_001252494)	promoter-TSS (NM_001252494)	59	NM_001252496	192786	Mm.254404	NM_175258	ENSMUSG00000037533	Rapgef6	A530068K01|AI844632|BB085664|C030018K18Rik|PDZ-GEF2|Pdzgef2|RA-GEF-2|Ragef2|mKIAA4052	Rap guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_137098.1	chr17	21566989	21567043	+	1	NA	promoter-TSS (NM_001002008)	promoter-TSS (NM_001002008)	-30	NM_001002008	381066	Mm.441097	NM_001002008	ENSMUSG00000067931	Zfp948	-	zinc finger protein 948	protein-coding
mm_136715.1	chr17	7931378	7931388	+	1	NA	exon (NM_145968, exon 8 of 10)	exon (NM_145968, exon 8 of 10)	5383	NM_145968	72536	Mm.119680	NM_145968	ENSMUSG00000033450	Tagap	2610315E15Rik	T cell activation Rho GTPase activating protein	protein-coding
mm_49090.1	chr6	7301916	7301934	+	1	NA	Intergenic	Intergenic	-252960	NM_001311060	21333	Mm.1440	NM_009311	ENSMUSG00000061762	Tac1	4930528L02Rik|NK-1|NK1|Nkna|PPT-A|PPTA|SP	tachykinin 1	protein-coding
mm_1641.1	chr1	74542882	74542918	+	1	NA	promoter-TSS (NM_001081456)	promoter-TSS (NM_001081456)	11	NM_001081456	18802	Mm.290731	NM_148937	ENSMUSG00000026173	Plcd4	4921507K24Rik	phospholipase C, delta 4	protein-coding
mm_71417.1	chr8	46488381	46488415	+	1	NA	intron (NM_007981, intron 1 of 20)	intron (NM_007981, intron 1 of 20)	-2568	NM_001302163	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_74473.1	chr8	4259138	4259172	-	1	NA	TTS (NM_011592)	TTS (NM_011592)	119	NM_183315	330695	Mm.34210	NM_183315	ENSMUSG00000048644	Ctxn1	BC028881|Ctxn	cortexin 1	protein-coding
mm_72277.1	chr8	75100219	75100237	+	1	NA	3' UTR (NM_010442, exon 5 of 5)	3' UTR (NM_010442, exon 5 of 5)	6610	NM_010442	15368	Mm.276389	NM_010442	ENSMUSG00000005413	Hmox1	D8Wsu38e|HO-1|HO1|Hemox|Hmox|Hsp32	heme oxygenase 1	protein-coding
mm_167399.1	chr8	95311637	95311647	+	1	NA	promoter-TSS (NM_028532)	promoter-TSS (NM_028532)	44	NM_199455	73407	Mm.472783	NM_028532	ENSMUSG00000090206	Tepp	1700055M20Rik	testis, prostate and placenta expressed	protein-coding
mm_22453.1	chr3	3187993	3187997	+	1	NA	Intergenic	Intergenic	-320035	NM_013920	30942	Mm.330897	NM_013920	ENSMUSG00000017688	Hnf4g	NR2A2	hepatocyte nuclear factor 4, gamma	protein-coding
mm_109693.1	chr12	113146480	113146527	+	1	NA	TTS (NM_024223)	TTS (NM_024223)	-5509	NM_007763	12925	Mm.272368	NM_007763	ENSMUSG00000006360	Crip1	CRHP|CRP1|Crip	cysteine-rich protein 1 (intestinal)	protein-coding
mm_135974.1	chr16	75016426	75016434	-	1	NA	Intergenic	Lx2B2|LINE|L1	569631	NM_001252513	320355	Mm.99517	NM_177142	ENSMUSG00000032948	Lipi	D930038D03Rik|lpd1	lipase, member I	protein-coding
mm_15380.1	chr2	156530042	156530044	+	1	NA	intron (NM_001006664, intron 17 of 21)	intron (NM_001006664, intron 17 of 21)	-17533	NM_026661	68295	Mm.253648	NM_026661	ENSMUSG00000027628	Aar2	0610011L14Rik	AAR2 splicing factor homolog	protein-coding
mm_164577.1	chr17	24699800	24699807	+	1	NA	TTS (NM_145396)	TTS (NM_145396)	3569	NM_027988	71893	Mm.390971	NM_027988	ENSMUSG00000019320	Noxo1	2310034C04Rik|P41NOX|P41NOXA|P41NOXB|P41NOXC|Snx28|hslt	NADPH oxidase organizer 1	protein-coding
mm_98251.1	chr11	88294047	88294073	+	1	NA	promoter-TSS (NM_028859)	promoter-TSS (NM_028859)	17	NM_028859	74297	Mm.207320	NM_028859	ENSMUSG00000034031	Ccdc182	1700106J16Rik	coiled-coil domain containing 182	protein-coding
mm_116074.1	chr13	27668035	27668039	-	1	NA	promoter-TSS (NM_011168)	promoter-TSS (NM_011168)	-1	NM_011168	19114	Mm.153999	NM_011168	ENSMUSG00000046899	Prl7a2	Ghd18|PLP-F|Prlpf	prolactin family 7, subfamily a, member 2	protein-coding
mm_156785.1	chrX	162500331	162500365	+	1	NA	intron (NM_178256, intron 13 of 17)	L1M5|LINE|L1	143310	NM_001290633	194590	Mm.442441	NM_178256	ENSMUSG00000040855	Reps2	POB1	RALBP1 associated Eps domain containing protein 2	protein-coding
mm_14071.1	chr2	122765357	122765374	+	1	NA	promoter-TSS (NM_001162503)	promoter-TSS (NM_001162503)	6	NM_001162503	59010	Mm.28986	NM_021507	ENSMUSG00000005803	Sqrdl	0610039J17Rik|4930557M22Rik|SQOR	sulfide quinone reductase-like (yeast)	protein-coding
mm_9271.1	chr1	171633901	171633905	-	1	NA	3' UTR (NM_144539, exon 8 of 8)	3' UTR (NM_144539, exon 8 of 8)	7997	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_142016.1	chr17	35200539	35200544	-	1	NA	exon (NM_013693, exon 4 of 4)	exon (NM_013693, exon 4 of 4)	1466	NM_013693	21926	Mm.1293	NM_013693	ENSMUSG00000024401	Tnf	DIF|TNF-a|TNF-alpha|TNFSF2|TNFalpha|Tnfa|Tnfsf1a|Tnlg1f	tumor necrosis factor	protein-coding
mm_72783.1	chr8	86745656	86745660	+	1	NA	promoter-TSS (NR_027829)	promoter-TSS (NR_027829)	-41	NR_027829	666945	Mm.391806	NR_027829		Gm10638	ENSMUSG00000074178	predicted gene 10638	ncRNA
mm_13653.1	chr2	114054850	114054860	+	1	NA	non-coding (NR_028422, exon 1 of 3)	non-coding (NR_028422, exon 1 of 3)	459	NR_028422	100303644	Mm.330469	NR_028422	ENSMUSG00000092397	C130080G10Rik	-	RIKEN cDNA C130080G10 gene	ncRNA
mm_98396.1	chr11	94322077	94322108	+	1	NA	promoter-TSS (NM_026313)	promoter-TSS (NM_026313)	-181	NM_026313	67684	Mm.30927	NM_026313	ENSMUSG00000020863	Luc7l3	3300001P08Rik|Luc7a	LUC7-like 3 (S. cerevisiae)	protein-coding
mm_47537.1	chr5	124249712	124249722	-	1	NA	promoter-TSS (NM_011256)	promoter-TSS (NM_011256)	43	NM_011256	19679	Mm.44261	NM_011256	ENSMUSG00000029406	Pitpnm2	NIR3|RDGBA2|Rdgb2|mKIAA1457	phosphatidylinositol transfer protein, membrane-associated 2	protein-coding
mm_28779.1	chr3	95989397	95989414	-	1	NA	exon (NM_023320, exon 6 of 6)	exon (NM_023320, exon 6 of 6)	3895	NR_045872	668224	Mm.357766	NR_045872		Gm9054	EG668224	predicted gene 9054	ncRNA
mm_168767.1	chr12	12911984	12911995	+	1	NA	Intergenic	Intergenic	29847	NM_008709	18109	Mm.16469	NM_008709	ENSMUSG00000037169	Mycn	N-myc|Nmyc|Nmyc-1|Nmyc1|bHLHe37|c-nmyc	v-myc avian myelocytomatosis viral related oncogene, neuroblastoma derived	protein-coding
mm_158945.1	chr1	83159610	83159610	+	1	NA	promoter-TSS (NM_027725)	promoter-TSS (NM_027725)	-152	NR_027636	71227	Mm.256482	NM_027725	ENSMUSG00000053161	Daw1	4930563E19Rik|4933429D11Rik|Wdr69|b2b1116Clo|b2b1584Clo	dynein assembly factor with WDR repeat domains 1	protein-coding
mm_72657.1	chr8	84847238	84847250	+	1	NA	promoter-TSS (NM_007591)	promoter-TSS (NM_007591)	-313	NM_007591	12317	Mm.1971	NM_007591	ENSMUSG00000003814	Calr	CRT|Calregulin	calreticulin	protein-coding
mm_47020.1	chr5	115489992	115490036	-	1	NA	Intergenic	CpG	-5530	NM_133760	75387	Mm.332616	NM_133760	ENSMUSG00000029524	Sirt4	4930596O17Rik	sirtuin 4	protein-coding
mm_83476.1	chr9	45828619	45828680	-	1	NA	promoter-TSS (NM_001081373)	promoter-TSS (NM_001081373)	-11	NM_001081373	214552	Mm.260103	NM_172531	ENSMUSG00000043987	Cep164	AI450905|BC027092|D030051D21|mKIAA1052	centrosomal protein 164	protein-coding
mm_49495.1	chr6	29735632	29735663	+	1	NA	5' UTR (NM_176996, exon 1 of 12)	5' UTR (NM_176996, exon 1 of 12)	150	NM_176996	319757	Mm.29279	NM_176996	ENSMUSG00000001761	Smo	E130215L21Rik|Smoh|bnb|smoothened	smoothened, frizzled class receptor	protein-coding
mm_27531.1	chr3	57501776	57501802	-	1	NA	exon (NM_133784, exon 3 of 7)	exon (NM_133784, exon 3 of 7)	74087	NM_133784	97064	Mm.405029	NM_133784	ENSMUSG00000027803	Wwtr1	2310058J06Rik|2610021I22Rik|C78399|Taz	WW domain containing transcription regulator 1	protein-coding
mm_129715.1	chr15	81871645	81871709	-	1	NA	promoter-TSS (NM_080633)	promoter-TSS (NM_080633)	215	NM_026737	68479	Mm.271715	NM_026737	ENSMUSG00000061360	Phf5a	1110007B08Rik	PHD finger protein 5A	protein-coding
mm_81497.1	chr9	110032177	110032193	+	1	NA	exon (NM_008633, exon 6 of 19)	exon (NM_008633, exon 6 of 19)	-19836	NM_001311163	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_77727.1	chr8	126849988	126850009	-	1	NA	Intergenic	Intergenic	95923	NM_024214	67952	Mm.6932	NM_024214	ENSMUSG00000093904	Tomm20	1810060K07Rik|BB284719|Gm19268|MAS20|MOM19|TOM20|mKIAA0016	translocase of outer mitochondrial membrane 20 homolog (yeast)	protein-coding
mm_54281.1	chr6	29212297	29212313	-	1	NA	promoter-TSS (NM_011829)	promoter-TSS (NM_011829)	-8	NM_011829	23917	Mm.260707	NM_011829	ENSMUSG00000003500	Impdh1	B930086D20Rik|IMPDH-I	inosine 5'-phosphate dehydrogenase 1	protein-coding
mm_76500.1	chr8	86746094	86746123	-	1	NA	promoter-TSS (NM_009172)	promoter-TSS (NM_009172)	-102	NM_009172	20437	Mm.324553	NM_009172	ENSMUSG00000036840	Siah1a	AA982064|AI853500|Sinh1a	seven in absentia 1A	protein-coding
mm_3782.1	chr1	156672877	156672894	+	1	NA	intron (NM_023141, intron 2 of 5)	RMER17C|LTR|ERVK	1454	NM_023141	30935	Mm.206737	NM_023141	ENSMUSG00000060519	Tor3a	Adir	torsin family 3, member A	protein-coding
mm_43128.1	chr5	125300410	125300427	+	1	NA	exon (NM_001205082, exon 4 of 12)	exon (NM_001205082, exon 4 of 12)	40676	NM_016741	20778	Mm.282242	NM_016741	ENSMUSG00000037936	Scarb1	AI120173|CD36|Cd36l1|Chohd1|Cla-1|Cla1|D5Ertd460e|Hdlq1|Hlb398|SR-B1|SR-BI|SRBI|Srb1|mSR-BI	scavenger receptor class B, member 1	protein-coding
mm_98673.1	chr11	96284049	96284075	+	1	NA	intron (NM_010461, intron 1 of 1)	CpG	2157	NM_010461	15416	Mm.4822	NM_010461	ENSMUSG00000056648	Hoxb8	Hox-2.4	homeobox B8	protein-coding
mm_161147.1	chr13	22354373	22354373	+	1	NA	promoter-TSS (NM_134220)	promoter-TSS (NM_134220)	27	NM_134220	171254	Mm.377208	NM_134220	ENSMUSG00000095125	Vmn1r198	V1ri3	vomeronasal 1 receptor 198	protein-coding
mm_127862.1	chr15	8351636	8351668	-	1	NA	exon (NM_027707, exon 10 of 47)	exon (NM_027707, exon 10 of 47)	92811	NM_027707	71175	Mm.240329	NM_027707	ENSMUSG00000022141	Nipbl	Idn3	Nipped-B homolog (Drosophila)	protein-coding
mm_47962.1	chr5	135713516	135713523	-	1	NA	intron (NM_008898, intron 1 of 15)	intron (NM_008898, intron 1 of 15)	22370	NR_106001	102466791		NR_106001	ENSMUSG00000099197	Mir7034	Gm27372|mmu-mir-7034	microRNA 7034	ncRNA
mm_94345.1	chr11	4873961	4874005	+	1	NA	promoter-TSS (NM_008698)	promoter-TSS (NM_008698)	-20	NM_008698	18082	Mm.293716	NM_008698	ENSMUSG00000034285	Nipsnap1	-	nipsnap homolog 1 (C. elegans)	protein-coding
mm_84321.1	chr9	63838065	63838067	-	1	NA	Intergenic	Intergenic	-80072	NM_016769	17127	Mm.7320	NM_016769	ENSMUSG00000032402	Smad3	AU022421|Madh3	SMAD family member 3	protein-coding
mm_90396.1	chr10	127323789	127323794	+	1	NA	promoter-TSS (NM_146011)	promoter-TSS (NM_146011)	64	NM_146011	216445	Mm.227198	NM_146011	ENSMUSG00000040345	Arhgap9	AU043488	Rho GTPase activating protein 9	protein-coding
mm_39328.1	chr5	8660022	8660028	+	1	NA	promoter-TSS (NM_011076)	promoter-TSS (NM_011076)	-67	NM_011076	18671	Mm.207354	NM_011076	ENSMUSG00000040584	Abcb1a	Abcb4|Evi32|Mdr1a|Mdr3|P-gp|Pgp|Pgy-3|Pgy3|mdr-3	ATP-binding cassette, sub-family B (MDR/TAP), member 1A	protein-coding
mm_14465.1	chr2	131262043	131262047	+	1	NA	promoter-TSS (NM_153501)	promoter-TSS (NM_153501)	-455	NM_153501	74450	Mm.101264	NM_153501	ENSMUSG00000037514	Pank2	4933409I19Rik|AI642621	pantothenate kinase 2	protein-coding
mm_101746.1	chr11	43379383	43379393	-	1	NA	Intergenic	Intergenic	-4927	NR_029558	387164		NR_029558	ENSMUSG00000065601	Mir146	Mirn146|miR-146a|mmu-mir-146	microRNA 146	ncRNA
mm_6192.1	chr1	65159041	65159056	-	1	NA	3' UTR (NM_010497, exon 9 of 9)	3' UTR (NM_010497, exon 9 of 9)	20094	NM_010497	15926	Mm.9925	NM_010497	ENSMUSG00000025950	Idh1	AI314845|AI788952|E030024J03Rik|Id-1|Idh-1|Idpc	isocitrate dehydrogenase 1 (NADP+), soluble	protein-coding
mm_32608.1	chr4	112072659	112072674	+	1	NA	intron (NM_001347180, intron 1 of 11)	intron (NM_001347180, intron 1 of 11)	650	NM_001347180	320640	Mm.253775	NM_178786	ENSMUSG00000055960	Skint4	9530098N22Rik	selection and upkeep of intraepithelial T cells 4	protein-coding
mm_126030.1	chr15	76712278	76712281	+	1	NA	intron (NM_145471, intron 3 of 5)	intron (NM_145471, intron 3 of 5)	1539	NM_145471	223664	Mm.277582	NM_145471	ENSMUSG00000033728	Lrrc14	E130306I01Rik|mKIAA0014	leucine rich repeat containing 14	protein-coding
mm_83866.1	chr9	54824867	54824915	-	1	NA	Intergenic	Intergenic	-38864	NM_022655	64602	Mm.208991	NM_022655	ENSMUSG00000032293	Ireb2	D9Ertd85e|Irp2	iron responsive element binding protein 2	protein-coding
mm_104914.1	chr11	99740122	99740125	-	1	NA	Intergenic	Intergenic	32790	NM_001126322	100040276	Mm.475095	NM_001126322	ENSMUSG00000078668	Gm11595	OTTMUSG00000002543	predicted gene 11595	protein-coding
mm_77396.1	chr8	120333015	120333037	-	1	NA	Intergenic	Intergenic	-104796	NR_110496	434353	Mm.411793	NR_110496	ENSMUSG00000097960	A330074K22Rik	-	RIKEN cDNA A330074K22 gene	ncRNA
mm_67206.1	chr7	74302892	74302896	-	1	NA	intron (NM_001038643, intron 8 of 10)	intron (NM_001038643, intron 8 of 10)	251886	NM_023908	108116	Mm.425467	NM_023908	ENSMUSG00000025790	Slco3a1	5830414C08Rik|Anr1|MJAM|OATP-D|R75096|Slc21a11	solute carrier organic anion transporter family, member 3a1	protein-coding
mm_148709.1	chr19	5802185	5802207	+	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	476	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_65492.1	chr7	25689121	25689141	-	1	NA	intron (NM_011577, intron 1 of 6)	intron (NM_011577, intron 1 of 6)	2129	NM_011577	21803	Mm.248380	NM_011577	ENSMUSG00000002603	Tgfb1	TGF-beta1|TGFbeta1|Tgfb|Tgfb-1	transforming growth factor, beta 1	protein-coding
mm_8894.1	chr1	162898396	162898456	-	1	NA	intron (NM_018881, intron 1 of 8)	intron (NM_018881, intron 1 of 8)	286	NM_018881	55990	Mm.10929	NM_018881	ENSMUSG00000040170	Fmo2	2310008D08Rik|2310042I22Rik|AW107733	flavin containing monooxygenase 2	protein-coding
mm_159718.1	chr5	33821429	33821429	+	1	NA	Intergenic	CpG	-21683	NM_175231	107823	Mm.19892	NM_175231	ENSMUSG00000057406	Whsc1	5830445G22Rik|9430010A17Rik|AW555663|C130020C13Rik|D030027O06Rik|D930023B08Rik|MMSET|NSD2|Whsc1l|mKIAA1090	Wolf-Hirschhorn syndrome candidate 1 (human)	protein-coding
mm_154543.1	chrM	14577	14587	-	1	NA	NA	Intergenic	NA	NA								
mm_69262.1	chr7	127893465	127893481	-	1	NA	exon (NM_178600, exon 3 of 3)	exon (NM_178600, exon 3 of 3)	2144	NM_178600	27973	Mm.29703	NM_178600	ENSMUSG00000096145	Vkorc1	D7Wsu86e	vitamin K epoxide reductase complex, subunit 1	protein-coding
mm_26417.1	chr3	142611233	142611239	+	1	NA	intron (NM_010259, intron 9 of 10)	intron (NM_010259, intron 9 of 10)	-9427	NM_010260	14469	Mm.24038	NM_010260	ENSMUSG00000028270	Gbp2	-	guanylate binding protein 2	protein-coding
mm_33783.1	chr4	134897849	134897854	+	1	NA	TTS (NM_027935)	TTS (NM_027935)	17065	NM_027935	71817	Mm.88349	NM_027935	ENSMUSG00000028822	Tmem50a	3200001F09Rik|CAM|Smp1	transmembrane protein 50A	protein-coding
mm_53784.1	chr6	146577898	146577948	+	1	NA	promoter-TSS (NM_026218)	promoter-TSS (NM_026218)	12	NM_026218	67529	Mm.333499	NM_026218	ENSMUSG00000040242	Fgfr1op2	1500031J01Rik	FGFR1 oncogene partner 2	protein-coding
mm_71285.1	chr8	40920857	40920873	+	1	NA	3' UTR (NM_001044740, exon 12 of 12)	3' UTR (NM_001044740, exon 12 of 12)	-5368	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_45839.1	chr5	87696054	87696074	-	1	NA	exon (NM_001286023, exon 4 of 7)	exon (NM_001286023, exon 4 of 7)	3361	NM_001286020	12991	Mm.268737	NM_009972	ENSMUSG00000063157	Csn2	Csnb	casein beta	protein-coding
mm_162017.1	chr19	45075157	45075157	+	1	NA	promoter-TSS (NM_178929)	promoter-TSS (NM_178929)	-982	NM_178929	107250	Mm.24417	NM_178929	ENSMUSG00000025213	Kazald1	AI842353|Bono1|IGFBP-rP10	Kazal-type serine peptidase inhibitor domain 1	protein-coding
mm_141959.1	chr17	35118536	35118568	-	1	NA	exon (NM_009975, exon 4 of 7)	exon (NM_009975, exon 4 of 7)	2740	NM_001303476	13001	Mm.378901	NM_009975	ENSMUSG00000024387	Csnk2b	CK II beta	casein kinase 2, beta polypeptide	protein-coding
mm_117963.1	chr13	99516513	99516523	-	1	NA	promoter-TSS (NM_008634)	promoter-TSS (NM_008634)	84	NM_008634	17755	Mm.4173	NM_008634	ENSMUSG00000052727	Map1b	A230055D22|AI843217|LC1|MAP5|Mtap-5|Mtap1b|Mtap5	microtubule-associated protein 1B	protein-coding
mm_136994.1	chr17	17402853	17402863	+	1	NA	5' UTR (NM_025681, exon 1 of 6)	5' UTR (NM_025681, exon 1 of 6)	172	NM_025681	66643	Mm.268018	NM_025681	ENSMUSG00000047786	Lix1	5730466L18Rik	limb and CNS expressed 1	protein-coding
mm_123105.1	chr14	55882775	55882784	-	1	NA	3' UTR (NM_019820, exon 3 of 3)	3' UTR (NM_019820, exon 3 of 3)	1477	NM_019820	56410	Mm.97163	NM_019820	ENSMUSG00000040380	Cbln3	-	cerebellin 3 precursor protein	protein-coding
mm_150636.1	chr19	41483204	41483221	+	1	NA	Intergenic	CpG	-42040	NM_001326287	627352	Mm.395111	NM_001326287		Morf4l1b	EG627352|Gm6747	mortality factor 4 like 1B	protein-coding
mm_106983.1	chr12	9580842	9580850	+	1	NA	3' UTR (NM_011859, exon 3 of 3)	3' UTR (NM_011859, exon 3 of 3)	6404	NM_011859	23967	Mm.45055	NM_011859	ENSMUSG00000048387	Osr1	Odd1|Osr	odd-skipped related 1 (Drosophila)	protein-coding
mm_131788.1	chr16	22898808	22898856	+	1	NA	exon (NM_001276450, exon 7 of 7)	exon (NM_001276450, exon 7 of 7)	-4446	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_128239.1	chr15	36608625	36608635	-	1	NA	5' UTR (NM_008774, exon 1 of 15)	5' UTR (NM_008774, exon 1 of 15)	343	NM_008774	18458	Mm.371570	NM_008774	ENSMUSG00000022283	Pabpc1	PABP|Pabp1|PabpI|Pabpl1|ePAB	poly(A) binding protein, cytoplasmic 1	protein-coding
mm_141339.1	chr17	28517492	28517504	-	1	NA	Intergenic	Intergenic	-13363	NM_026290	67645	Mm.46170	NM_026290	ENSMUSG00000024223	Armc12	4930511I11Rik|AV041658	armadillo repeat containing 12	protein-coding
mm_96974.1	chr11	70652037	70652128	+	1	NA	TTS (NM_001316728)	TTS (NM_001316728)	2568	NM_011072	18643	Mm.2647	NM_011072	ENSMUSG00000018293	Pfn1	Pfn	profilin 1	protein-coding
mm_121393.1	chr14	119137545	119137551	+	1	NA	promoter-TSS (NM_015820)	promoter-TSS (NM_015820)	-717	NM_015820	50787	Mm.445777	NM_015820	ENSMUSG00000053465	Hs6st3	6OST3|HS6ST-3	heparan sulfate 6-O-sulfotransferase 3	protein-coding
mm_132601.1	chr16	38558665	38558684	+	1	NA	promoter-TSS (NM_001205286)	promoter-TSS (NM_001205286)	-24	NM_001205286	67846	Mm.310476	NM_026407	ENSMUSG00000002845	Tmem39a	2610033C09Rik	transmembrane protein 39a	protein-coding
mm_19974.1	chr2	118256930	118256973	-	1	NA	promoter-TSS (NM_027759)	promoter-TSS (NM_027759)	15	NM_027759	71313	Mm.85046	NM_027759	ENSMUSG00000027344	Fsip1	1700012M13Rik|4933432K11Rik	fibrous sheath-interacting protein 1	protein-coding
mm_129163.1	chr15	76243380	76243396	-	1	NA	promoter-TSS (NM_001163575)	promoter-TSS (NM_001163575)	52	NM_001163576	671535	Mm.373750	NM_001163575	ENSMUSG00000063268	Parp10	-	poly (ADP-ribose) polymerase family, member 10	protein-coding
mm_110230.1	chr12	29059623	29059624	-	1	NA	Intergenic	L1MCa|LINE|L1	307795	NM_201357	380752	Mm.273724	NM_201357	ENSMUSG00000036613	Tssc1	D12Ertd604e|Eipr1	tumor suppressing subtransferable candidate 1	protein-coding
mm_51426.1	chr6	78428152	78428161	+	1	NA	exon (NM_009042, exon 5 of 6)	exon (NM_009042, exon 5 of 6)	2173	NM_009042	19692	Mm.142731	NM_009042	ENSMUSG00000059654	Reg1	-	regenerating islet-derived 1	protein-coding
mm_79041.1	chr9	46210709	46210725	+	1	NA	exon (NM_027498, exon 20 of 25)	exon (NM_027498, exon 20 of 25)	-17913	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2|apo-AI|apoA-I	apolipoprotein A-I	protein-coding
mm_26089.1	chr3	136713702	136713714	+	1	NA	intron (NM_008913, intron 1 of 13)	intron (NM_008913, intron 1 of 13)	43642	NM_001293622	19055	Mm.331389	NM_008913	ENSMUSG00000028161	Ppp3ca	2900074D19Rik|CN|Caln|Calna|CnA	protein phosphatase 3, catalytic subunit, alpha isoform	protein-coding
mm_17170.1	chr2	25311504	25311529	-	1	NA	intron (NM_001177656, intron 3 of 19)	CpG-7818	7671	NM_008169	14810	Mm.278672	NM_008169	ENSMUSG00000026959	Grin1	GluN1|GluRdelta1|GluRzeta1|M100174|NMD-R1|NMDAR1|NR1|Nmdar|Rgsc174	glutamate receptor, ionotropic, NMDA1 (zeta 1)	protein-coding
mm_98274.1	chr11	89015529	89015556	+	1	NA	exon (NM_009546, exon 7 of 9)	exon (NM_009546, exon 7 of 9)	16139	NM_009546	217069	Mm.248445	NM_009546	ENSMUSG00000000275	Trim25	AA960166|AL022677|EFP|Zfp147	tripartite motif-containing 25	protein-coding
mm_85450.1	chr9	104328024	104328024	-	1	NA	intron (NM_207668, intron 1 of 10)	intron (NM_207668, intron 1 of 10)	9698	NM_019807	56318	Mm.19941	NM_019807	ENSMUSG00000032561	Acpp	5'-NT|A030005E02Rik|FRAP|Lap|PAP|Ppal	acid phosphatase, prostate	protein-coding
mm_88396.1	chr10	76575641	76575656	+	1	NA	promoter-TSS (NM_080845)	promoter-TSS (NM_080845)	0	NM_080845	14317	Mm.36278	NM_080845	ENSMUSG00000001155	Ftcd	-	formiminotransferase cyclodeaminase	protein-coding
mm_104093.1	chr11	86683500	86683548	-	1	NA	promoter-TSS (NM_001098810)	promoter-TSS (NM_001098810)	298	NM_029478	75909	Mm.390398	NM_029478	ENSMUSG00000018171	Vmp1	3110098I04Rik|4930579A11Rik|AI787464|Tango5|Tmem49|mir-21a|ni-2	vacuole membrane protein 1	protein-coding
mm_64830.1	chr7	12818838	12818865	-	1	NA	promoter-TSS (NM_026046)	promoter-TSS (NM_026046)	9	NM_026046	67230	Mm.333574	NM_026046	ENSMUSG00000057894	Zfp329	2810439M05Rik|4632409L22Rik|ZNF329	zinc finger protein 329	protein-coding
mm_30084.1	chr3	138131357	138131381	-	1	NA	promoter-TSS (NM_008642)	promoter-TSS (NM_008642)	8	NM_008642	17777	Mm.2941	NM_008642	ENSMUSG00000028158	Mttp	1810043K16Rik|MTP	microsomal triglyceride transfer protein	protein-coding
mm_168817.1	chr12	22030834	22030843	-	1	NA	Intergenic	CpG	125808	NR_136920	100043416		NM_001004167	ENSMUSG00000093846	Gm4425	EG432637|Gm5433	KRAB-domain protein pseudogene	pseudo
mm_61154.1	chr7	58658382	58658411	+	1	NA	5' UTR (NM_009728, exon 1 of 21)	5' UTR (NM_009728, exon 1 of 21)	194	NM_009728	11982	Mm.135129	NM_009728	ENSMUSG00000025324	Atp10a	Atp10c|pfatp	ATPase, class V, type 10A	protein-coding
mm_10972.1	chr2	25706933	25706941	+	1	NA	promoter-TSS (NM_023326)	promoter-TSS (NM_023326)	58	NM_023326	107771	Mm.330057	NM_023326	ENSMUSG00000049086	Bmyc	2900002K07Rik|AW060705|Mycb	brain expressed myelocytomatosis oncogene	protein-coding
mm_170713.1	chr2	144156325	144156343	+	1	NA	Intergenic	ERVB7_1-LTR_MM|LTR|ERVK	32956	NR_136884	433481	Mm.330630	NR_136884	ENSMUSG00000074758	Gm5535	EG433481	predicted gene 5535	ncRNA
mm_68777.1	chr7	122101828	122101859	-	1	NA	promoter-TSS (NM_028177)	promoter-TSS (NM_028177)	5	NM_028177	70316	Mm.3014	NM_028177	ENSMUSG00000030869	Ndufab1	2210401F17Rik|2310039H15Rik|2610003B19Rik|8kDa|9130423F15Rik|ACP|CI-SDAP|SDAP	NADH dehydrogenase (ubiquinone) 1, alpha/beta subcomplex, 1	protein-coding
mm_56264.1	chr6	90925096	90925098	-	1	NA	Intergenic	Intergenic	-114974	NM_001134384	232227	Mm.196943	NM_182784	ENSMUSG00000034312	Iqsec1	AW561907|BC026481|BRAG2|D6Ertd349e|cI-43	IQ motif and Sec7 domain 1	protein-coding
mm_104741.1	chr11	98400454	98400474	-	1	NA	promoter-TSS (NM_001033537)	promoter-TSS (NM_001033537)	26	NM_001033537	320655	Mm.86519	NM_001033537	ENSMUSG00000038208	Pgap3	CAB2|D430035D22Rik|Perld1	post-GPI attachment to proteins 3	protein-coding
mm_29471.1	chr3	115641544	115641554	-	1	NA	Intergenic	Lx8|LINE|L1	73506	NM_007901	13609	Mm.982	NM_007901	ENSMUSG00000045092	S1pr1	AI849002|Edg1|Lpb1|S1p|S1p1	sphingosine-1-phosphate receptor 1	protein-coding
mm_143126.1	chr17	57212670	57212691	-	1	NA	exon (NM_009778, exon 28 of 41)	exon (NM_009778, exon 28 of 41)	4548	NR_105944	102465591		NR_105944	ENSMUSG00000099066	Mir6978	Gm27858|mmu-mir-6978	microRNA 6978	ncRNA
mm_114349.1	chr13	60935628	60935640	+	1	NA	exon (NM_001145799, exon 3 of 5)	exon (NM_001145799, exon 3 of 5)	932	NM_001145799	13024	Mm.482089	NM_007796	ENSMUSG00000044258	Ctla2a	Ctla-2a	cytotoxic T lymphocyte-associated protein 2 alpha	protein-coding
mm_67360.1	chr7	79838469	79838482	-	1	NA	exon (NM_008486, exon 8 of 20)	exon (NM_008486, exon 8 of 20)	3877	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_20720.1	chr2	135583290	135583314	-	1	NA	promoter-TSS (NR_015544)	promoter-TSS (NR_015544)	-82	NR_015544	320684	Mm.421433	NR_015544	ENSMUSG00000085631	9630028H03Rik	-	RIKEN cDNA 9630028H03 gene	ncRNA
mm_70696.1	chr8	15027760	15027777	+	1	NA	exon (NM_029116, exon 2 of 2)	exon (NM_029116, exon 2 of 2)	16743	NM_029116	74901	Mm.46675	NM_029116	ENSMUSG00000055675	Kbtbd11	2900016B01Rik|4930465M17Rik|mKIAA0711	kelch repeat and BTB (POZ) domain containing 11	protein-coding
mm_48850.1	chr5	149619171	149619180	-	1	NA	intron (NM_001347534, intron 13 of 16)	intron (NM_001347534, intron 13 of 16)	17140	NM_013559	15505	Mm.270681	NM_013559	ENSMUSG00000029657	Hsph1	105kDa|AI790491|Hsp105|Hsp110|hsp-E7I|hsp110/105	heat shock 105kDa/110kDa protein 1	protein-coding
mm_38495.1	chr4	141053248	141053258	-	1	NA	intron (NM_001145958, intron 2 of 35)	intron (NM_001145958, intron 2 of 35)	408	NM_172122	230872	Mm.80685	NM_172122	ENSMUSG00000040860	Crocc	-	ciliary rootlet coiled-coil, rootletin	protein-coding
mm_119629.1	chr14	51162236	51162255	+	1	NA	promoter-TSS (NM_019398)	promoter-TSS (NM_019398)	-15	NM_019398	54159	Mm.377125	NM_019398	ENSMUSG00000059606	Rnase2b	Ear5|Raf4|mR5	ribonuclease, RNase A family, 2B (liver, eosinophil-derived neurotoxin)	protein-coding
mm_128346.1	chr15	39784823	39784836	-	1	NA	intron (NM_022722, intron 8 of 9)	intron (NM_022722, intron 8 of 9)	-12216	NR_045788	100503072	Mm.446661	NR_045788	ENSMUSG00000087695	Gm16291	OTTMUSG00000033244	predicted gene 16291	ncRNA
mm_47726.1	chr5	130081350	130081382	-	1	NA	intron (NM_001130476, intron 1 of 5)	intron (NM_001130476, intron 1 of 5)	1996	NM_001130476	22021	Mm.332720	NM_013837	ENSMUSG00000034118	Tpst1	R75054|Tango13a	protein-tyrosine sulfotransferase 1	protein-coding
mm_68654.1	chr7	118537857	118537861	-	1	NA	3' UTR (NM_172476, exon 16 of 16)	3' UTR (NM_172476, exon 16 of 16)	-4503	NM_009940	12850	Mm.20634	NM_009940	ENSMUSG00000030652	Coq7	clk-1	demethyl-Q 7	protein-coding
mm_137963.1	chr17	33432260	33432266	+	1	NA	promoter-TSS (NM_183282)	promoter-TSS (NM_183282)	-636	NM_183282	69481	Mm.154333	NM_183282	ENSMUSG00000092519	Actl9	1700029I08Rik|AV259599	actin-like 9	protein-coding
mm_119794.1	chr14	54196038	54196064	+	1	NA	Intergenic	Intergenic	57878	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_45431.1	chr5	67099108	67099118	-	1	NA	promoter-TSS (NM_008888)	promoter-TSS (NM_008888)	13	NM_008888	18935	Mm.62505	NM_008888	ENSMUSG00000012520	Phox2b	Dilp1|NBPhox|Pmx2b|Px2b	paired-like homeobox 2b	protein-coding
mm_46309.1	chr5	100564731	100564733	-	1	NA	intron (NM_139198, intron 1 of 4)	intron (NM_139198, intron 1 of 4)	7473	NM_139198	231507	Mm.34609	NM_139198	ENSMUSG00000029322	Plac8	C15|D5Wsu111e	placenta-specific 8	protein-coding
mm_14193.1	chr2	127087490	127087497	+	1	NA	intron (NM_026678, intron 5 of 7)	RMER6B|LTR|ERVK	16836	NM_026678	109778	Mm.22028	NM_026678	ENSMUSG00000001999	Blvra	0610006A11Rik|2500001N03Rik|Blvr	biliverdin reductase A	protein-coding
mm_62144.1	chr7	97101587	97101599	+	1	NA	intron (NM_001162477, intron 1 of 9)	B3A|SINE|B2	19842	NM_010248	14389	Mm.42033	NM_010248	ENSMUSG00000004508	Gab2	AI463667|D130058I17Rik|p97	growth factor receptor bound protein 2-associated protein 2	protein-coding
mm_60230.1	chr7	43634719	43634741	+	1	NA	promoter-TSS (NM_028236)	promoter-TSS (NM_028236)	-9	NM_028236	72431	Mm.158821	NM_028236	ENSMUSG00000030472	Ceacam18	2010110O04Rik	carcinoembryonic antigen-related cell adhesion molecule 18	protein-coding
mm_36185.1	chr4	62220300	62220303	-	1	NA	Intergenic	Intergenic	-11755	NM_001290350	22696	Mm.5011	NM_009554	ENSMUSG00000028389	Zfp37	Tzn|Zfp-37	zinc finger protein 37	protein-coding
mm_136166.1	chr16	88563145	88563147	-	1	NA	promoter-TSS (NM_018778)	promoter-TSS (NM_018778)	37	NM_018778	54420	Mm.25836	NM_018778	ENSMUSG00000050520	Cldn8	AI648025	claudin 8	protein-coding
mm_77314.1	chr8	117692282	117692298	-	1	NA	non-coding (NR_131057, exon 8 of 8)	non-coding (NR_131057, exon 8 of 8)	-9656	NM_008290	15486	Mm.276466	NM_008290	ENSMUSG00000031844	Hsd17b2	AI194836|AI194967|AI255511	hydroxysteroid (17-beta) dehydrogenase 2	protein-coding
mm_15962.1	chr2	166016250	166016254	+	1	NA	intron (NM_008679, intron 1 of 22)	B1_Mus1|SINE|Alu	23615	NM_008679	17979	Mm.469663	NM_008679	ENSMUSG00000027678	Ncoa3	2010305B15Rik|AW321064|Actr|Aib1|KAT13B|Rac3|Src3|Tram-1|Tram1|bHLHe42|p/Cip|pCip	nuclear receptor coactivator 3	protein-coding
mm_135327.1	chr16	38800236	38800246	-	1	NA	promoter-TSS (NM_178924)	promoter-TSS (NM_178924)	-38	NM_178924	22268	Mm.130793	NM_178924	ENSMUSG00000049436	Upk1b	AI413235|Tspan20|UPIb|Upk1	uroplakin 1B	protein-coding
mm_140050.1	chr17	74528423	74528433	+	1	NA	5' UTR (NM_007566, exon 1 of 73)	5' UTR (NM_007566, exon 1 of 73)	133	NM_007566	12211	Mm.442564	NM_007566	ENSMUSG00000024073	Birc6	A430032G04Rik|A430040A19Rik|AA501170|Bruce|D630005A10Rik|mKIAA1289	baculoviral IAP repeat-containing 6	protein-coding
mm_23959.1	chr3	84952189	84952200	+	1	NA	promoter-TSS (NM_080428)	promoter-TSS (NM_080428)	-17	NM_080428	50754	Mm.196475	NM_080428	ENSMUSG00000028086	Fbxw7	1110001A17Rik|AGO|Cdc4|Fbw7|Fbwd6|Fbx30|Fbxo30|Fbxw6|SEL-10	F-box and WD-40 domain protein 7	protein-coding
mm_11656.1	chr2	34963871	34963886	+	1	NA	Intergenic	Intergenic	-2106	NM_001326601	22029	Mm.239514	NM_009421	ENSMUSG00000026875	Traf1	4732496E14Rik	TNF receptor-associated factor 1	protein-coding
mm_58043.1	chr6	136827748	136827761	-	1	NA	intron (NM_021714, intron 1 of 11)	CpG	462	NM_021714	60321	Mm.141197	NM_021714	ENSMUSG00000030216	Wbp11	2510026P17Rik|D6Wsu113e|Npwbp|SIPP1	WW domain binding protein 11	protein-coding
mm_147737.1	chr18	61107008	61107015	-	1	NA	intron (NM_001037859, intron 2 of 21)	intron (NM_001037859, intron 2 of 21)	1439	NM_001037859	12978	Mm.22574	NM_007779	ENSMUSG00000024621	Csf1r	AI323359|CD115|CSF-1R|Csfmr|Fim-2|Fim2|Fms|M-CSF-R|M-CSFR	colony stimulating factor 1 receptor	protein-coding
mm_161810.1	chr17	63896002	63896002	+	1	NA	intron (NM_001286415, intron 1 of 17)	intron (NM_001286415, intron 1 of 17)	17936	NM_001286415	14158	Mm.23039	NM_008000	ENSMUSG00000000127	Fer	AV082135|C330004K01Rik|Fert|Fert2	fer (fms/fps related) protein kinase	protein-coding
mm_45422.1	chr5	66593519	66593532	-	1	NA	intron (NM_001310626, intron 1 of 15)	intron (NM_001310626, intron 1 of 15)	25292	NM_009686	11787	Mm.5159	NM_009686	ENSMUSG00000029207	Apbb2	2310007D03Rik|FE65L1|Rirl1|TR2L|Zfra	amyloid beta (A4) precursor protein-binding, family B, member 2	protein-coding
mm_132849.1	chr16	46113151	46113152	+	1	NA	intron (NM_032465, intron 2 of 14)	intron (NM_032465, intron 2 of 14)	7097	NM_032465	84544	Mm.29204	NM_032465	ENSMUSG00000022657	Cd96	1700109I12Rik|Tactile	CD96 antigen	protein-coding
mm_164196.1	chr15	78973056	78973063	+	1	NA	intron (NM_001039156, intron 9 of 24)	intron (NM_001039156, intron 9 of 24)	-9997	NM_001024716	110253	Mm.123714	NM_138579	ENSMUSG00000033088	Triobp	AI428493|EST478828|Tara|mKIAA1662	TRIO and F-actin binding protein	protein-coding
mm_70537.1	chr8	13039304	13039304	+	1	NA	intron (NM_001242368, intron 2 of 8)	MTEa|LTR|ERVL-MaLR	1996	NM_001242368	14058	Mm.262589	NM_007972	ENSMUSG00000031444	F10	Cf10|fX	coagulation factor X	protein-coding
mm_5287.1	chr1	20816758	20816771	-	1	NA	exon (NM_008563, exon 4 of 17)	exon (NM_008563, exon 4 of 17)	3449	NM_008563	17215	Mm.4502	NM_008563	ENSMUSG00000041859	Mcm3	AL033361|C80350|Mcmd|P1|p1.m	minichromosome maintenance complex component 3	protein-coding
mm_169495.1	chr14	75931516	75931516	-	1	NA	intron (NM_026816, intron 5 of 7)	intron (NM_026816, intron 5 of 7)	-23487	NM_026214	67516	Mm.390712	NM_026214	ENSMUSG00000046523	Kctd4	2210017A09Rik|AU017169	potassium channel tetramerisation domain containing 4	protein-coding
mm_36957.1	chr4	109156621	109156631	-	1	NA	intron (NM_001346502, intron 3 of 23)	intron (NM_001346502, intron 3 of 23)	-38590	NM_001134791	100273	Mm.366315	NM_133885	ENSMUSG00000028559	Osbpl9	2600011I06Rik|AU015843|Orp-9	oxysterol binding protein-like 9	protein-coding
mm_12436.1	chr2	70672475	70672491	+	1	NA	intron (NM_027352, intron 1 of 9)	(T)n|Simple_repeat|Simple_repeat	10974	NM_027352	70231	Mm.271950	NM_027352	ENSMUSG00000014959	Gorasp2	0610011A07Rik|2410043M02Rik|5730520M13Rik|9430094F20Rik|AW552058|ENSMUSG00000075299|GOLPH2|GRASP55|GRS2|p59	golgi reassembly stacking protein 2	protein-coding
mm_128903.1	chr15	73363784	73363788	-	1	NA	intron (NM_007982, intron 2 of 31)	AT_rich|Low_complexity|Low_complexity	59405	NM_007982	14083	Mm.254494	NM_007982	ENSMUSG00000022607	Ptk2	FAK|FRNK|Fadk|mKIAA4203|p125FAK	PTK2 protein tyrosine kinase 2	protein-coding
mm_54294.1	chr6	29281029	29281037	-	1	NA	promoter-TSS (NM_001101486)	promoter-TSS (NM_001101486)	-108	NM_001101486	245884	Mm.33683	NM_001101486	ENSMUSG00000079652	Fam71f2	AI507611|GARI	family with sequence similarity 71, member F2	protein-coding
mm_74442.1	chr8	3918217	3918219	-	1	NA	non-coding (NR_104430, exon 9 of 9)	non-coding (NR_104430, exon 9 of 9)	8623	NM_001037800	69165	Mm.175163	NM_026972	ENSMUSG00000065987	Cd209b	1810030I22Rik|DC-SIGNR1|OtB7|SIGNR1|mSIGNR1	CD209b antigen	protein-coding
mm_131739.1	chr16	22023802	22023816	+	1	NA	intron (NR_027488, intron 6 of 16)	intron (NR_027488, intron 6 of 16)	14325	NR_027488	75826	Mm.297431	NM_029457	ENSMUSG00000022855	Senp2	2310007L05Rik|4930538C18Rik|AI646780|AW554757|Smt3ip2|SuPr-1|mKIAA1331	SUMO/sentrin specific peptidase 2	protein-coding
mm_168422.1	chr11	33161205	33161216	-	1	NA	exon (NM_001252261, exon 3 of 10)	exon (NM_001252261, exon 3 of 10)	1996	NM_001252261	18148	Mm.485384	NM_008722	ENSMUSG00000057113	Npm1	B23|NO38|Npm	nucleophosmin 1	protein-coding
mm_128599.1	chr15	58182978	58182981	-	1	NA	intron (NM_026346, intron 7 of 8)	intron (NM_026346, intron 7 of 8)	31913	NM_026346	67731	Mm.25683	NM_026346	ENSMUSG00000022358	Fbxo32	4833442G10Rik|AI430017|ATROGIN1|Gm20361|MAFbx	F-box protein 32	protein-coding
mm_43970.1	chr5	145980955	145980972	+	1	NA	intron (NR_030782, intron 11 of 11)	ORR1D1|LTR|ERVL-MaLR	28654	NM_019792	56388	Mm.301900	NM_019792	ENSMUSG00000029630	Cyp3a25	AI327008	cytochrome P450, family 3, subfamily a, polypeptide 25	protein-coding
mm_139671.1	chr17	57412294	57412305	+	1	NA	intron (NM_010130, intron 9 of 21)	intron (NM_010130, intron 9 of 21)	53613	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_77287.1	chr8	116894765	116894775	-	1	NA	intron (NM_026844, intron 2 of 3)	B3A|SINE|B2	26666	NM_026844	66531	Mm.4011	NM_026844	ENSMUSG00000014633	Cmc2	1110046L09Rik|2310061C15Rik|DC13	COX assembly mitochondrial protein 2	protein-coding
mm_167311.1	chr8	61715531	61715544	+	1	NA	intron (NM_001081390, intron 3 of 19)	intron (NM_001081390, intron 3 of 19)	44561	NM_001293773	72333	Mm.29933	NM_001081390	ENSMUSG00000058056	Palld	2410003B16Rik|6030492A02	palladin, cytoskeletal associated protein	protein-coding
mm_123751.1	chr14	70192867	70192892	-	1	NA	promoter-TSS (NM_001271409)	promoter-TSS (NM_001271409)	-633	NM_001271409	20410	Mm.5068	NM_011366	ENSMUSG00000022091	Sorbs3	SCAM-1|SH3P3|Sh3d4|vinexin-g	sorbin and SH3 domain containing 3	protein-coding
mm_85837.1	chr9	110532776	110532778	-	1	NA	intron (NM_001081340, intron 1 of 20)	CpG	180	NM_001081340	235626	Mm.288949	NM_001081340	ENSMUSG00000044791	Setd2	4921524K10Rik|BC031601|KMT3A	SET domain containing 2	protein-coding
mm_104878.1	chr11	99433557	99433562	-	1	NA	intron (NM_023256, intron 2 of 7)	intron (NM_023256, intron 2 of 7)	4594	NM_023256	66809	Mm.28042	NM_023256	ENSMUSG00000035775	Krt20	9030623C06Rik|Ck-20|Ck20|K20|Krt21	keratin 20	protein-coding
mm_79192.1	chr9	48450328	48450336	+	1	NA	Intergenic	Intergenic	-4012	NR_026561	667933	Mm.491076	NR_026561		Gm8884	EG667933	predicted gene 8884	ncRNA
mm_153156.1	chr19	34254202	34254260	-	1	NA	intron (NM_007392, intron 1 of 8)	intron (NM_007392, intron 1 of 8)	1142	NM_007392	11475	Mm.213025	NM_007392	ENSMUSG00000035783	Acta2	0610041G09Rik|Actvs|SMalphaA|a-SMA|alphaSMA	actin, alpha 2, smooth muscle, aorta	protein-coding
mm_156075.1	chrX	109161735	109161745	+	1	NA	3' UTR (NM_019989, exon 4 of 4)	3' UTR (NM_019989, exon 4 of 4)	-35016	NM_001037917	622976	Mm.482747	NM_001037917	ENSMUSG00000048621	Gm6377	EG622976	predicted gene 6377	protein-coding
mm_168898.1	chr12	54694834	54694835	-	1	NA	intron (NM_025456, intron 1 of 5)	intron (NM_025456, intron 1 of 5)	1060	NM_001331162	66266	Mm.156440	NM_025456	ENSMUSG00000054302	Eapp	1810011O16Rik	E2F-associated phosphoprotein	protein-coding
mm_8985.1	chr1	165696740	165696750	-	1	NA	intron (NM_178593, intron 1 of 6)	intron (NM_178593, intron 1 of 6)	11349	NM_178593	226594	Mm.265552	NM_178593	ENSMUSG00000040723	Rcsd1	A430105K13Rik|BC025872|CapZIP	RCSD domain containing 1	protein-coding
mm_99487.1	chr11	102665613	102665633	+	1	NA	promoter-TSS (NM_001127576)	promoter-TSS (NM_001127576)	38	NM_001127576	268491	Mm.447643	NM_001127576	ENSMUSG00000051455	Meioc	Gm1564|Gm663	meiosis specific with coiled-coil domain	protein-coding
mm_53465.1	chr6	134920511	134920523	+	1	NA	5' UTR (NM_009875, exon 1 of 3)	5' UTR (NM_009875, exon 1 of 3)	116	NM_009875	12576	Mm.2958	NM_009875	ENSMUSG00000003031	Cdkn1b	AA408329|AI843786|Kip1|p27|p27Kip1	cyclin-dependent kinase inhibitor 1B	protein-coding
mm_81183.1	chr9	107505588	107505609	+	1	NA	intron (NM_001174047, intron 4 of 38)	intron (NM_001174047, intron 4 of 38)	-28347	NM_019704	56395	Mm.260153	NM_019704	ENSMUSG00000010045	Tmem115	C78915|Pl6|Pp6	transmembrane protein 115	protein-coding
mm_86901.1	chr10	22306742	22306770	+	1	NA	promoter-TSS (NR_015465)	promoter-TSS (NR_015465)	36	NR_015465	606736	Mm.387042	NR_015465	ENSMUSG00000097352	C920009B18Rik	-	RIKEN cDNA C920009B18 gene	ncRNA
mm_117740.1	chr13	95685826	95685865	-	1	NA	intron (NM_027711, intron 14 of 35)	intron (NM_027711, intron 14 of 35)	-11075	NM_010170	14064	Mm.440952	NM_010170	ENSMUSG00000021675	F2rl2	F730031A08|PAR3	coagulation factor II (thrombin) receptor-like 2	protein-coding
mm_121498.1	chr14	121879710	121879742	+	1	NA	promoter-TSS (NR_130999)	promoter-TSS (NR_130999)	-318	NR_130999	78312	Mm.188743	NR_130999	ENSMUSG00000102112	1810041H14Rik	-	RIKEN cDNA 1810041H14 gene	ncRNA
mm_58196.1	chr6	143099832	143099858	-	1	NA	intron (NM_001109688, intron 1 of 24)	CpG-12558	307	NM_001286578	74741	Mm.130260	NM_029081	ENSMUSG00000030279	C2cd5	5730419I09Rik|C030008B15Rik|CDP138	C2 calcium-dependent domain containing 5	protein-coding
mm_45997.1	chr5	90639673	90639683	-	1	NA	intron (NM_001310656, intron 1 of 10)	intron (NM_001310656, intron 1 of 10)	849	NM_028478	73246	Mm.30172	NM_028478	ENSMUSG00000029370	Rassf6	1600016B17Rik	Ras association (RalGDS/AF-6) domain family member 6	protein-coding
mm_20059.1	chr2	120352023	120352030	-	1	NA	intron (NR_027618, intron 1 of 25)	intron (NR_027618, intron 1 of 25)	1107	NM_178851	269338	Mm.246131	NM_147153	ENSMUSG00000027291	Vps39	A230065P22Rik|AW743070|Vam6|Vam6P|mVam6	VPS39 HOPS complex subunit	protein-coding
mm_92668.1	chr10	80433946	80434001	-	1	NA	promoter-TSS (NM_011548)	promoter-TSS (NM_011548)	-320	NM_001164148	21423	Mm.3406	NM_011548	ENSMUSG00000020167	Tcf3	A1|AA408400|ALF2|AW209082|E12|E12/E47|E2A|E47|KA1|ME2|Pan1|Pan2|TCF-3|Tcfe2a|VDIR|bHLHb21	transcription factor 3	protein-coding
mm_77392.1	chr8	120228222	120228297	-	1	NA	promoter-TSS (NR_110496)	promoter-TSS (NR_110496)	-29	NR_110496	434353	Mm.411793	NR_110496	ENSMUSG00000097960	A330074K22Rik	-	RIKEN cDNA A330074K22 gene	ncRNA
mm_152770.1	chr19	20964402	20964408	-	1	NA	Intergenic	Intergenic	-10203	NM_028953	13409	Mm.219585	NM_028953	ENSMUSG00000024749	Tmc1	4933416G09Rik|Beethoven|Bth|CWEA1|dn	transmembrane channel-like gene family 1	protein-coding
mm_113009.1	chr13	21910922	21910931	+	1	NA	Intergenic	B1_Mur1|SINE|Alu	-13877	NR_035500	100316716		NR_035500	ENSMUSG00000088148	Mir1983	mmu-mir-1983	microRNA 1983	ncRNA
mm_15973.1	chr2	166153996	166154036	+	1	NA	intron (NM_028072, intron 1 of 20)	intron (NM_028072, intron 1 of 20)	1269	NM_001252578	72043	Mm.1011	NM_028072	ENSMUSG00000006800	Sulf2	2010004N24Rik|AU020235|MSulf-2|mKIAA1247	sulfatase 2	protein-coding
mm_70496.1	chr8	12757031	12757065	+	1	NA	promoter-TSS (NM_001293667)	promoter-TSS (NM_001293667)	32	NM_001293667	50770	Mm.257837	NM_015804	ENSMUSG00000031441	Atp11a	4930558F19Rik|AU040868|Atpc1h|Ih	ATPase, class VI, type 11A	protein-coding
mm_147397.1	chr18	44380324	44380336	-	1	NA	promoter-TSS (NM_027490)	promoter-TSS (NM_027490)	-170	NM_027490	70640	Mm.87629	NM_027490	ENSMUSG00000024472	Dcp2	2410015D23Rik|5730537H01Rik|AL118268	decapping mRNA 2	protein-coding
mm_102108.1	chr11	53257743	53257758	-	1	NA	Intergenic	Intergenic	42729	NM_008300	15525	Mm.239865	NM_008300	ENSMUSG00000020361	Hspa4	70kDa|AI317151|APG-2|Hsp110|Hsp70RY|mKIAA4025	heat shock protein 4	protein-coding
mm_54362.1	chr6	31115017	31115051	-	1	NA	intron (NR_110471, intron 3 of 3)	intron (NR_110471, intron 3 of 3)	-51941	NR_029532	387223		NR_029532	ENSMUSG00000065604	Mir29b-1	Mirn29b|Mirn29b-1|mir-29b-1	microRNA 29b-1	ncRNA
mm_172651.1	chr8	33764697	33764701	-	1	NA	intron (NM_026584, intron 6 of 7)	RLTR10D2|LTR|ERVK	-16929	NM_001206849	72632	Mm.443483	NM_001206849	ENSMUSG00000094500	Smim18	2700090O03Rik|AI835723	small integral membrane protein 18	protein-coding
mm_67853.1	chr7	98702850	98702874	-	1	NA	promoter-TSS (NM_028410)	promoter-TSS (NM_028410)	66	NR_144495	100040769	Mm.126401	NR_144495		Gm15506	OTTMUSG00000023003	predicted gene 15506	ncRNA
mm_36563.1	chr4	87230415	87230432	-	1	NA	5' UTR (NM_172426, exon 1 of 11)	5' UTR (NM_172426, exon 1 of 11)	117	NM_172426	76376	Mm.490487	NM_172426	ENSMUSG00000037996	Slc24a2	2810021B17Rik|6330417K15Rik|AI847460|Nckx2	solute carrier family 24 (sodium/potassium/calcium exchanger), member 2	protein-coding
mm_126218.1	chr15	78913917	78913927	+	1	NA	promoter-TSS (NM_020271)	promoter-TSS (NM_020271)	3	NM_020271	57028	Mm.263169	NM_020271	ENSMUSG00000022436	Pdxp	1600027H05Rik|AB041662|PLPP	pyridoxal (pyridoxine, vitamin B6) phosphatase	protein-coding
mm_44640.1	chr5	28124039	28124046	-	1	NA	Intergenic	Intergenic	-41654	NM_010134	13799	Mm.4298	NM_010134	ENSMUSG00000039095	En2	BB131122|En-2	engrailed 2	protein-coding
mm_7527.1	chr1	124208393	124208405	-	1	NA	Intergenic	B3A|SINE|B2	-162840	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_36622.1	chr4	91371947	91371972	-	1	NA	promoter-TSS (NM_207686)	promoter-TSS (NM_207686)	96	NM_010486	15569	Mm.318042	NM_010486	ENSMUSG00000008489	Elavl2	Hub|mel-N1	ELAV (embryonic lethal, abnormal vision, Drosophila)-like 2 (Hu antigen B)	protein-coding
mm_113755.1	chr13	44731843	44731861	+	1	NA	5' UTR (NM_001205043, exon 1 of 18)	5' UTR (NM_001205043, exon 1 of 18)	581	NM_001205043	16468	Mm.25059	NM_021878	ENSMUSG00000038518	Jarid2	Jmj|jumonji	jumonji, AT rich interactive domain 2	protein-coding
mm_125161.1	chr15	31225157	31225196	+	1	NA	intron (NM_146057, intron 1 of 3)	intron (NM_146057, intron 1 of 3)	791	NM_146057	223453	Mm.222867	NM_146057	ENSMUSG00000039168	Dap	4921531N22Rik|AI789753|AU040360	death-associated protein	protein-coding
mm_131829.1	chr16	22951146	22951153	+	1	NA	promoter-TSS (NM_053176)	promoter-TSS (NM_053176)	77	NM_053176	94175	Mm.358794	NM_053176	ENSMUSG00000022877	Hrg	AI265597|AW413091|D16jh2|D18020|Hprg|Hrgp	histidine-rich glycoprotein	protein-coding
mm_62025.1	chr7	91647714	91647715	+	1	NA	intron (NM_011807, intron 2 of 22)	intron (NM_011807, intron 2 of 22)	-414680	NM_001243046	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_19848.1	chr2	113748874	113748920	-	1	NA	3' UTR (NM_011824, exon 2 of 2)	3' UTR (NM_011824, exon 2 of 2)	9751	NM_011824	23892	Mm.166318	NM_011824	ENSMUSG00000074934	Grem1	Cktsf1b1|Drm|Grem|ld	gremlin 1, DAN family BMP antagonist	protein-coding
mm_114879.1	chr13	94176761	94176762	+	1	NA	intron (NM_172589, intron 3 of 3)	intron (NM_172589, intron 3 of 3)	108520	NM_029153	107767	Mm.201455	NM_029153	ENSMUSG00000021687	Scamp1	4930505M11Rik|AI415563|AW122395	secretory carrier membrane protein 1	protein-coding
mm_108733.1	chr12	87874071	87874075	+	1	NA	promoter-TSS (NM_001122662)	promoter-TSS (NM_001122662)	1	NM_001122662	100039042	Mm.423010	NM_001122662	ENSMUSG00000072905	Gm2016	-	predicted gene 2016	protein-coding
mm_169839.1	chr16	28951421	28951421	-	1	NA	Intergenic	Intergenic	-21723	NM_177718	239796	Mm.155887	NM_177718	ENSMUSG00000051065	Mb21d2	1600021P15Rik|A430031N04|C87006	Mab-21 domain containing 2	protein-coding
mm_94450.1	chr11	6389331	6389397	+	1	NA	Intergenic	Intergenic	-5761	NM_001005867	52915	Mm.1144	NM_028601	ENSMUSG00000041164	Zmiz2	Zimp7	zinc finger, MIZ-type containing 2	protein-coding
mm_55080.1	chr6	49214666	49214676	-	1	NA	5' UTR (NM_023670, exon 1 of 15)	5' UTR (NM_023670, exon 1 of 15)	283	NM_023670	140488	Mm.281018	NM_023670	ENSMUSG00000029814	Igf2bp3	2610101N11Rik|AA522010|AL022933|AU045931|IMP-3|IMP3|Koc13|Neilsen|mimp3	insulin-like growth factor 2 mRNA binding protein 3	protein-coding
mm_127675.1	chr15	102889868	102889868	+	1	NA	Intergenic	L1ME3E|LINE|L1	-31263	NM_010464	15422	Mm.207062	NM_010464	ENSMUSG00000001655	Hoxc13	-	homeobox C13	protein-coding
mm_37376.1	chr4	120975007	120975023	-	1	NA	intron (NM_133716, intron 6 of 9)	intron (NM_133716, intron 6 of 9)	-1693	NR_105982	102465614		NR_105982	ENSMUSG00000106436	Mir7015	mmu-mir-7015	microRNA 7015	ncRNA
mm_116736.1	chr13	51739789	51739813	-	1	NA	intron (NM_001281880, intron 2 of 16)	intron (NM_001281880, intron 2 of 16)	53946	NM_001281880	20354	Mm.33903	NM_013660	ENSMUSG00000021451	Sema4d	CD100|Semacl2|Semaj|Semcl2|coll-4	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D	protein-coding
mm_155392.1	chrX	72825162	72825183	+	1	NA	promoter-TSS (NM_001290435)	promoter-TSS (NM_001290435)	-6	NM_001290435	57249	Mm.117125	NM_020488	ENSMUSG00000031344	Gabrq	-	gamma-aminobutyric acid (GABA) A receptor, subunit theta	protein-coding
mm_66520.1	chr7	45124334	45124354	-	1	NA	promoter-TSS (NM_013725)	promoter-TSS (NM_013725)	45	NM_013725	27207	Mm.196538	NM_013725	ENSMUSG00000003429	Rps11	-	ribosomal protein S11	protein-coding
mm_56883.1	chr6	119030940	119030980	-	1	NA	intron (NM_001256002, intron 3 of 47)	HAL1|LINE|L1	77535	NM_001159534	12288	Mm.41628	NM_009781	ENSMUSG00000051331	Cacna1c	Cav1.2|Cchl1a1|D930026N18Rik|MBC|MELC-CC	calcium channel, voltage-dependent, L type, alpha 1C subunit	protein-coding
mm_95571.1	chr11	52396541	52396543	+	1	NA	exon (NM_153117, exon 1 of 3)	exon (NM_153117, exon 1 of 3)	114	NM_153117	213673	Mm.291979	NM_153117	ENSMUSG00000036275	9530068E07Rik	C85061|Kct2	RIKEN cDNA 9530068E07 gene	protein-coding
mm_84604.1	chr9	70103118	70103142	-	1	NA	intron (NM_029784, intron 4 of 8)	RSINE1|SINE|B4	38427	NM_029784	76886	Mm.44355	NM_029784	ENSMUSG00000032224	Fam81a	6430514L14Rik	family with sequence similarity 81, member A	protein-coding
mm_60609.1	chr7	44587340	44587375	+	1	NA	TTS (NM_008437)	TTS (NM_008437)	-3529	NM_008422	16504	Mm.40312	NM_008422	ENSMUSG00000062785	Kcnc3	KShIIID|Kcr2-3|Kv3.3	potassium voltage gated channel, Shaw-related subfamily, member 3	protein-coding
mm_50596.1	chr6	49073817	49073861	+	1	NA	promoter-TSS (NM_029353)	promoter-TSS (NM_029353)	44	NM_029353	75593	Mm.439947	NM_029353	ENSMUSG00000029815	Malsu1	2410003K15Rik|Matsu1	mitochondrial assembly of ribosomal large subunit 1	protein-coding
mm_39038.1	chr4	152318570	152318654	-	1	NA	promoter-TSS (NM_001033489)	promoter-TSS (NM_001033489)	13	NM_001033489	433809	Mm.156205	NM_001033489	ENSMUSG00000058498	Rnf207	D330010C22Rik|Gm143	ring finger protein 207	protein-coding
mm_162510.1	chr1	152683072	152683091	+	1	NA	intron (NM_001346117, intron 1 of 18)	RSINE1|SINE|B4	-57864	NM_016846	19731	Mm.245270	NM_016846	ENSMUSG00000026482	Rgl1	Rgl|mKIAA0959	ral guanine nucleotide dissociation stimulator,-like 1	protein-coding
mm_120592.1	chr14	70075191	70075199	+	1	NA	Intergenic	CpG	-2250	NM_018781	13655	Mm.103737	NM_018781	ENSMUSG00000033730	Egr3	Pilot	early growth response 3	protein-coding
mm_82682.1	chr9	22135772	22135784	-	1	NA	promoter-TSS (NM_001102405)	promoter-TSS (NM_001102405)	-32	NM_001102405	11433	Mm.46354	NM_007388	ENSMUSG00000001348	Acp5	TRACP|TRAP	acid phosphatase 5, tartrate resistant	protein-coding
mm_58581.1	chr7	4922564	4922593	+	1	NA	TTS (NM_170759)	TTS (NM_170759)	327	NM_201355	269854	Mm.42652	NM_201355	ENSMUSG00000035285	Nat14	BC047219	N-acetyltransferase 14	protein-coding
mm_52799.1	chr6	121336384	121336408	+	1	NA	intron (NM_144512, intron 13 of 14)	intron (NM_144512, intron 13 of 14)	-6680	NM_001347433	14411	Mm.274506	NM_133661	ENSMUSG00000030109	Slc6a12	BGT1|GAT-2|GAT2|Gabt2	solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12	protein-coding
mm_141863.1	chr17	34804483	34804491	-	1	NA	promoter-TSS (NM_009995)	promoter-TSS (NM_009995)	-61	NM_009995	13079	Mm.440407	NM_009995	ENSMUSG00000024365	Cyp21a1	21-OH|21OH|21OHA|21OHB|CYP21OH-A|Cyp21|Cyp21-ps1|Cyp21B|Cyp21a2-ps|Cyp21a2ps|Oh21-1|Oh21-2	cytochrome P450, family 21, subfamily a, polypeptide 1	protein-coding
mm_58807.1	chr7	16313616	16313675	+	1	NA	exon (NM_133234, exon 3 of 4)	exon (NM_133234, exon 3 of 4)	4062	NM_133234	170770	Mm.7660	NM_133234	ENSMUSG00000002083	Bbc3	PUMA|PUMA/JFY1	BCL2 binding component 3	protein-coding
mm_39748.1	chr5	29569839	29569853	+	1	NA	intron (NM_133907, intron 1 of 22)	intron (NM_133907, intron 1 of 22)	604	NM_133907	100763	Mm.137746	NM_133907	ENSMUSG00000039000	Ube3c	AI853514|mKIAA0010	ubiquitin protein ligase E3C	protein-coding
mm_89994.1	chr10	112083346	112083371	+	1	NA	promoter-TSS (NM_026223)	promoter-TSS (NM_026223)	4	NM_026223	67537	Mm.292351	NM_026223	ENSMUSG00000020214	Glipr1l2	4921508O11Rik	GLI pathogenesis-related 1 like 2	protein-coding
mm_20097.1	chr2	121025743	121025744	-	1	NA	intron (NM_013513, intron 9 of 12)	intron (NM_013513, intron 9 of 12)	11134	NM_013513	13828	Mm.240051	NM_013513	ENSMUSG00000023216	Epb42	Epb4.2	erythrocyte membrane protein band 4.2	protein-coding
mm_120718.1	chr14	72851866	72851880	+	1	NA	Intergenic	Intergenic	-141870	NM_207636	319448	Mm.205421	NM_207636	ENSMUSG00000033487	Fndc3a	1700094E19Rik|D14Ertd453e|F730017H24Rik|Fndc3|sys	fibronectin type III domain containing 3A	protein-coding
mm_32798.1	chr4	117068094	117068118	+	1	NA	intron (NM_175135, intron 8 of 9)	intron (NM_175135, intron 8 of 9)	-27950	NM_001312903	19207	Mm.287037	NM_008958	ENSMUSG00000028681	Ptch2	ptc2	patched 2	protein-coding
mm_141878.1	chr17	34857029	34857043	-	1	NA	TTS (NM_138580)	TTS (NM_138580)	596	NR_105938	102465587		NR_105938	ENSMUSG00000098445	Mir6972	Gm27810|mmu-mir-6972	microRNA 6972	ncRNA
mm_50878.1	chr6	55491231	55491243	+	1	NA	exon (NM_007407, exon 14 of 17)	exon (NM_007407, exon 14 of 17)	39259	NM_007407	11517	Mm.44245	NM_007407	ENSMUSG00000029778	Adcyap1r1	2900024I10Rik|AI846590|PAC1|PAC1R|PACAP1-R	adenylate cyclase activating polypeptide 1 receptor 1	protein-coding
mm_118850.1	chr14	25674867	25674876	+	1	NA	Intergenic	Intergenic	-19299	NM_134084	105675	Mm.41656	NM_134084	ENSMUSG00000021868	Ppif	AW457192|CyP-D|CyP-F|CypD|PPIase	peptidylprolyl isomerase F (cyclophilin F)	protein-coding
mm_153843.1	chr19	46332777	46332791	-	1	NA	intron (NM_001164291, intron 1 of 8)	intron (NM_001164291, intron 1 of 8)	4600	NM_133694	68431	Mm.19973	NM_133694	ENSMUSG00000025226	Fbxl15	0710008C12Rik|Fbxo37	F-box and leucine-rich repeat protein 15	protein-coding
mm_24428.1	chr3	90539646	90539660	+	1	NA	Intergenic	Intergenic	-1570	NM_026416	67860	Mm.331185	NM_026416	ENSMUSG00000074457	S100a16	2300002L21Rik|AI325039|AI663996|DT1P1A7|S100F	S100 calcium binding protein A16	protein-coding
mm_46789.1	chr5	112766970	112766980	-	1	NA	intron (NM_028901, intron 34 of 43)	RLTR17B_Mm|LTR|ERVK	-26317	NR_040675	67360	Mm.59218	NR_040675	ENSMUSG00000098230	1700095B10Rik	-	RIKEN cDNA 1700095B10 gene	ncRNA
mm_95849.1	chr11	57717312	57717314	+	1	NA	intron (NM_134189, intron 1 of 11)	intron (NM_134189, intron 1 of 11)	71871	NM_134189	171212	Mm.271670	NM_134189	ENSMUSG00000020520	Galnt10	AU018154|C330012K04Rik|GalNAc-T10|GalNAc-T9|Galnt9|ppGaNTase	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 10	protein-coding
mm_105462.1	chr11	105126300	105126341	-	1	NA	promoter-TSS (NM_172567)	promoter-TSS (NM_172567)	-105	NM_172567	52686	Mm.270091	NM_172567	ENSMUSG00000020691	Mettl2	2810438F06Rik|AW493404|C130031G21Rik|D11Ertd768e|METL|PSENIP1	methyltransferase like 2	protein-coding
mm_168924.1	chr12	63047826	63047843	-	1	NA	Intergenic	L1Md_T|LINE|L1	360047	NR_131949	73309	Mm.276558	NR_131949		Spanxn4	1700047L15Rik	SPANX family, member N4	ncRNA
mm_42449.1	chr5	115435001	115435029	+	1	NA	intron (NM_008629, intron 5 of 14)	intron (NM_008629, intron 5 of 14)	5330	NM_008629	17690	Mm.5077	NM_008629	ENSMUSG00000054256	Msi1	Msi1h|Musahi1|m-Msi-1	musashi RNA-binding protein 1	protein-coding
mm_34081.1	chr4	138725283	138725309	+	1	NA	promoter-TSS (NM_178671)	promoter-TSS (NM_178671)	-29	NM_008868	18781	Mm.5189	NM_008868	ENSMUSG00000028750	Pla2g2c	-	phospholipase A2, group IIC	protein-coding
mm_18895.1	chr2	76712607	76712617	-	1	NA	exon (NM_011652, exon 307 of 313)	exon (NM_011652, exon 307 of 313)	37297	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_35625.1	chr4	43454877	43454900	-	1	NA	promoter-TSS (NM_001110320)	promoter-TSS (NM_001110320)	-262	NM_007654	12517	Mm.188157	NM_007654	ENSMUSG00000028459	Cd72	CD72c|Ly-19|Ly-32|Ly-m19|Lyb-2	CD72 antigen	protein-coding
mm_149069.1	chr19	8871513	8871559	+	1	NA	promoter-TSS (NM_146093)	promoter-TSS (NM_146093)	-23	NM_146093	225896	Mm.27839	NM_146093	ENSMUSG00000071655	Ubxn1	2B28|4930455J02Rik|D19Ertd721e|T25529	UBX domain protein 1	protein-coding
mm_26556.1	chr3	146451624	146451628	+	1	NA	intron (NM_028836, intron 1 of 5)	ORR1B1|LTR|ERVL-MaLR	1159	NM_001293672	74245	Mm.45396	NM_028836	ENSMUSG00000028189	Ctbs	2210401K11Rik|CTB	chitobiase, di-N-acetyl-	protein-coding
mm_104851.1	chr11	99321202	99321216	-	1	NA	exon (NM_133730, exon 3 of 8)	exon (NM_133730, exon 3 of 8)	1732	NM_133730	70810	Mm.268173	NM_133730	ENSMUSG00000035831	Krt25	4631426H08Rik|Ka38|Krt25a|mIRSa1	keratin 25	protein-coding
mm_112921.1	chr13	20933969	20934000	+	1	NA	intron (NM_012054, intron 11 of 20)	Lx8|LINE|L1	139315	NM_146535	258528	Mm.377554	NM_146535	ENSMUSG00000042869	Olfr1370	MOR256-14	olfactory receptor 1370	protein-coding
mm_94802.1	chr11	22990618	22990654	+	1	NA	promoter-TSS (NM_009837)	promoter-TSS (NM_009837)	43	NM_009837	12464	Mm.296985	NM_009837	ENSMUSG00000007739	Cct4	2610204B21Rik|A45|C78323|Cctd	chaperonin containing Tcp1, subunit 4 (delta)	protein-coding
mm_36638.1	chr4	93335815	93335825	-	1	NA	promoter-TSS (NM_026954)	promoter-TSS (NM_026954)	-309	NM_026954	69136	Mm.171558	NM_026954	ENSMUSG00000054000	Tusc1	2200001D17Rik|TSG-9	tumor suppressor candidate 1	protein-coding
mm_20204.1	chr2	125123619	125123648	-	1	NA	promoter-TSS (NM_001162417)	promoter-TSS (NM_001162417)	27	NM_001162417	17876	Mm.18535	NM_010852	ENSMUSG00000027201	Myef2	9430071B01|mKIAA1341	myelin basic protein expression factor 2, repressor	protein-coding
mm_42529.1	chr5	115631983	115632033	+	1	NA	promoter-TSS (NR_027810)	promoter-TSS (NR_027810)	21	NM_198163	77407	Mm.27553	NM_198163	ENSMUSG00000029518	Rab35	9530019H02Rik|AU040256|H-ray|RAB1C|RAY	RAB35, member RAS oncogene family	protein-coding
mm_74233.1	chr8	124318163	124318171	+	1	NA	intron (NM_139272, intron 3 of 15)	L1MB1|LINE|L1	86773	NM_139272	108148	Mm.33808	NM_139272	ENSMUSG00000089704	Galnt2	AI480629	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2	protein-coding
mm_837.1	chr1	51566574	51566599	+	1	NA	Intergenic	Intergenic	-88187	NM_001310549	109019	Mm.196290	NM_028696	ENSMUSG00000026107	Nabp1	4930434H03Rik|4930442A21Rik|4930488J04Rik|4933440J18Rik|5830411E10Rik|AI852561|Nbp1|Obfc2a|Ssb2	nucleic acid binding protein 1	protein-coding
mm_72723.1	chr8	85037215	85037227	+	1	NA	promoter-TSS (NM_001122843)	promoter-TSS (NM_001122843)	53	NM_001122843	212999	Mm.220357	NM_145390	ENSMUSG00000031691	Tnpo2	1110034O24Rik|AA414969|AI464345|AI852433|IPO3|Knpb2b|Kpnb2b|TRN2	transportin 2 (importin 3, karyopherin beta 2b)	protein-coding
mm_148086.1	chr18	73701755	73701757	-	1	NA	intron (NM_008540, intron 1 of 11)	intron (NM_008540, intron 1 of 11)	1985	NM_008540	17128	Mm.100399	NM_008540	ENSMUSG00000024515	Smad4	AW743858|D18Wsu70e|DPC4|Madh4	SMAD family member 4	protein-coding
mm_21541.1	chr2	163750170	163750183	-	1	NA	promoter-TSS (NM_001272052)	promoter-TSS (NM_001272052)	63	NM_007398	11486	Mm.388	NM_007398	ENSMUSG00000017697	Ada	-	adenosine deaminase	protein-coding
mm_120416.1	chr14	65358579	65358589	+	1	NA	promoter-TSS (NM_199029)	promoter-TSS (NM_199029)	-92	NM_199029	380912	Mm.270087	NM_199029	ENSMUSG00000034522	Zfp395	BC053701|Gm910	zinc finger protein 395	protein-coding
mm_99210.1	chr11	101023129	101023158	+	1	NA	intron (NM_001243050, intron 5 of 20)	ID_B1|SINE|B4	-7197	NR_105893	102466767		NR_105893	ENSMUSG00000098415	Mir6928	Gm27728|mmu-mir-6928	microRNA 6928	ncRNA
mm_37808.1	chr4	130839948	130839960	-	1	NA	Intergenic	Intergenic	47417	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_27646.1	chr3	63899397	63899407	-	1	NA	Intergenic	Intergenic	29983	NM_177856	329659	Mm.39342	NM_177856	ENSMUSG00000048581	E130311K13Rik	-	RIKEN cDNA E130311K13 gene	protein-coding
mm_24788.1	chr3	95545347	95545352	+	1	NA	exon (NM_021281, exon 5 of 8)	exon (NM_021281, exon 5 of 8)	-14328	NM_026489	67981	Mm.179050	NM_026489	ENSMUSG00000028109	Hormad1	4921522K05Rik|Nohma	HORMA domain containing 1	protein-coding
mm_121455.1	chr14	120478682	120478689	+	1	NA	5' UTR (NM_029519, exon 1 of 2)	5' UTR (NM_029519, exon 1 of 2)	224	NM_029519	76108	Mm.261448	NM_029519	ENSMUSG00000051615	Rap2a	5830461H18Rik	RAS related protein 2a	protein-coding
mm_138459.1	chr17	35140256	35140278	+	1	NA	exon (NM_001252469, exon 6 of 24)	exon (NM_001252469, exon 6 of 24)	4553	NM_001252469	224727	Mm.203962	NM_057171	ENSMUSG00000024392	Bag6	2410045D21Rik|AA408914|BAG-6|Bat3|D17H6S52E|G3|Scythe	BCL2-associated athanogene 6	protein-coding
mm_23131.1	chr3	37753434	37753441	+	1	NA	Intergenic	L2|LINE|L2	-29077	NM_198657	381438	Mm.490549	NM_198657	ENSMUSG00000058174	Gm5148	EG381438	predicted gene 5148	protein-coding
mm_69864.1	chr7	141443315	141443359	-	1	NA	promoter-TSS (NM_022654)	promoter-TSS (NM_022654)	18	NM_022654	57913	Mm.334321	NM_022654	ENSMUSG00000025507	Pidd1	1200011D09Rik|AU042446|Lrdd|Pidd	p53 induced death domain protein 1	protein-coding
mm_141249.1	chr17	27547347	27547357	-	1	NA	Intergenic	Intergenic	-9222	NM_001166536	15361	Mm.4438	NM_016660	ENSMUSG00000046711	Hmga1	AL023995|Hmga1a|Hmga1b|Hmgi|Hmgiy|Hmgy	high mobility group AT-hook 1	protein-coding
mm_77525.1	chr8	122981978	122981981	-	1	NA	intron (NM_001081379, intron 1 of 12)	intron (NM_001081379, intron 1 of 12)	60305	NR_037865	77087	Mm.31567	NM_001081379	ENSMUSG00000035569	Ankrd11	2410104C19Rik|3010027A04Rik|6330578C09Rik|9530048I21Rik|AA930108|Gm176|Yod	ankyrin repeat domain 11	protein-coding
mm_68058.1	chr7	101837876	101837958	-	1	NA	promoter-TSS (NM_001122739)	promoter-TSS (NM_001122739)	-93	NM_001122739	16332	Mm.476000	NM_010567	ENSMUSG00000032737	Inppl1	51C|SHIP2	inositol polyphosphate phosphatase-like 1	protein-coding
mm_38636.1	chr4	142656077	142656078	-	1	NA	Intergenic	Intergenic	-416676	NM_001109685	71529	Mm.255986	NM_144531	ENSMUSG00000040606	Kazn	2310007B04Rik|9030409G11Rik|AI256607|AI666764|AW061099|Kaz|Kazrin	kazrin, periplakin interacting protein	protein-coding
mm_37642.1	chr4	128260918	128260922	-	1	NA	promoter-TSS (NM_027036)	promoter-TSS (NM_027036)	-25	NM_027036	69317	Mm.331893	NM_027036	ENSMUSG00000048686	Hmgb4	1700001F22Rik|AI326135	high-mobility group box 4	protein-coding
mm_26910.1	chr3	19695326	19695336	-	1	NA	promoter-TSS (NM_205769)	promoter-TSS (NM_205769)	65	NM_205769	12918	Mm.290689	NM_205769	ENSMUSG00000049796	Crh	CRF|Gm1347	corticotropin releasing hormone	protein-coding
mm_145651.1	chr18	61129260	61129272	+	1	NA	intron (NM_001037859, intron 18 of 21)	intron (NM_001037859, intron 18 of 21)	11798	NR_105949	102466212		NR_105949	ENSMUSG00000098389	Mir6983	Gm27496|mmu-mir-6983	microRNA 6983	ncRNA
mm_160957.1	chr11	98350244	98350244	+	1	NA	TTS (NR_045477)	TTS (NR_045477)	248	NM_001313970	19049	Mm.45372	NM_144828	ENSMUSG00000061718	Ppp1r1b	AU040756|DARPP-32|Darpp32	protein phosphatase 1, regulatory (inhibitor) subunit 1B	protein-coding
mm_68652.1	chr7	118533270	118533274	-	1	NA	promoter-TSS (NM_009940)	promoter-TSS (NM_009940)	84	NM_001304758	12850	Mm.20634	NM_009940	ENSMUSG00000030652	Coq7	clk-1	demethyl-Q 7	protein-coding
mm_52185.1	chr6	99521407	99521419	+	1	NA	promoter-TSS (NM_001347345)	promoter-TSS (NM_001347345)	-420	NM_001347345	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_132486.1	chr16	36914589	36914602	+	1	NA	exon (NM_030035, exon 13 of 22)	exon (NM_030035, exon 13 of 22)	-17406	NR_040476	68306	Mm.399193	NR_040476	ENSMUSG00000084834	4930565N06Rik	4930428L02Rik	RIKEN cDNA 4930565N06 gene	ncRNA
mm_135999.1	chr16	75383702	75383705	-	1	NA	Intergenic	Lx8|LINE|L1	202358	NM_001252513	320355	Mm.99517	NM_177142	ENSMUSG00000032948	Lipi	D930038D03Rik|lpd1	lipase, member I	protein-coding
mm_150559.1	chr19	39330388	39330392	+	1	NA	exon (NM_007815, exon 9 of 9)	exon (NM_007815, exon 9 of 9)	43305	NM_007815	13095	Mm.20764	NM_007815	ENSMUSG00000003053	Cyp2c29	AHOH|AHOHase|AI159681|AI196010|Ah-2|Ahh-1|Cyp2c|P450-2C	cytochrome P450, family 2, subfamily c, polypeptide 29	protein-coding
mm_124000.1	chr14	75844936	75844948	-	1	NA	promoter-TSS (NM_009429)	promoter-TSS (NM_009429)	22	NR_045294	100043189	Mm.426329	NR_045294		Gm4285	-	predicted gene 4285	ncRNA
mm_27485.1	chr3	54634627	54634629	-	1	NA	Intergenic	Intergenic	-58477	NM_019995	56790	Mm.486375	NM_019995	ENSMUSG00000027751	Supt20	AA667204|AI450544|D3Ertd300e|Fam48a|Supt20h|p38IP	suppressor of Ty 20	protein-coding
mm_116620.1	chr13	48880014	48880052	-	1	NA	3' UTR (NM_001033268, exon 18 of 18)	3' UTR (NM_001033268, exon 18 of 18)	-9148	NM_011078	18676	Mm.486213	NM_011078	ENSMUSG00000038025	Phf2	GRC5	PHD finger protein 2	protein-coding
mm_64086.1	chr7	140967358	140967362	+	1	NA	promoter-TSS (NM_001112715)	promoter-TSS (NM_001112715)	-69	NM_026820	68713	Mm.175661	NM_026820	ENSMUSG00000025491	Ifitm1	1110036C17Rik|DSPA2a|Mil-2|Mil2	interferon induced transmembrane protein 1	protein-coding
mm_102093.1	chr11	52283303	52283394	-	1	NA	promoter-TSS (NM_009331)	promoter-TSS (NM_009331)	-334	NM_001313981	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_105172.1	chr11	101784517	101784567	-	1	NA	exon (NM_001316366, exon 2 of 13)	exon (NM_001316366, exon 2 of 13)	768	NM_008815	18612	Mm.5025	NM_008815	ENSMUSG00000017724	Etv4	AW414408|Pea-3|Pea3	ets variant 4	protein-coding
mm_123310.1	chr14	62346994	62347004	-	1	NA	intron (NM_026001, intron 2 of 10)	intron (NM_026001, intron 2 of 10)	14894	NM_026001	67153	Mm.26040	NM_026001	ENSMUSG00000021932	Rnaseh2b	1110019N06Rik|2610207P08Rik|Dleu8	ribonuclease H2, subunit B	protein-coding
mm_57012.1	chr6	121173715	121173748	-	1	NA	Intergenic	Intergenic	-9936	NM_001304774	74043	Mm.491240	NM_028730	ENSMUSG00000067825	Pex26	4632428M11Rik	peroxisomal biogenesis factor 26	protein-coding
mm_140918.1	chr17	24170827	24170852	-	1	NA	Intergenic	Intergenic	-1410	NM_009729	11984	Mm.30155	NM_009729	ENSMUSG00000024121	Atp6v0c	Atp6c|Atp6c2|Atp6l|Atpl|Atpl-rs1|PL16|VATL|Vma3	ATPase, H+ transporting, lysosomal V0 subunit C	protein-coding
mm_56630.1	chr6	112946905	112946915	-	1	NA	5' UTR (NM_080448, exon 1 of 22)	5' UTR (NM_080448, exon 1 of 22)	356	NM_080448	259302	Mm.236401	NM_080448	ENSMUSG00000030257	Srgap3	AI452337|Arhgap14|D130026O08Rik|Gbi|MEGAP|WRP|mKIAA0411	SLIT-ROBO Rho GTPase activating protein 3	protein-coding
mm_78012.1	chr9	13470004	13470009	+	1	NA	Intergenic	Intergenic	38645	NR_028271	18689	Mm.41972	NM_008835	ENSMUSG00000031802	Phxr4	Sp5	per-hexamer repeat gene 4	ncRNA
mm_134090.1	chr16	8823809	8823826	-	1	NA	Intergenic	MLT1J|LTR|ERVL-MaLR	-6283	NM_001081400	69053	Mm.390868	NM_001081400	ENSMUSG00000022507	1810013L24Rik	1110017P05Rik|3010002C02Rik|AA792997|AW124177|Gm19906|R74903	RIKEN cDNA 1810013L24 gene	protein-coding
mm_139664.1	chr17	57408340	57408468	+	1	NA	exon (NM_010130, exon 7 of 22)	exon (NM_010130, exon 7 of 22)	49718	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_2908.1	chr1	132007555	132007591	+	1	NA	promoter-TSS (NM_007923)	promoter-TSS (NM_007923)	-32	NM_007923	13714	Mm.254233	NM_007923	ENSMUSG00000026436	Elk4	2310011G17Rik|A130026I01Rik|BB162516|SAP-1|Sap1	ELK4, member of ETS oncogene family	protein-coding
mm_99001.1	chr11	98798654	98798664	+	1	NA	non-coding (NR_033551, exon 3 of 3)	non-coding (NR_033551, exon 3 of 3)	2890	NM_028722	74026	Mm.258352	NM_028722	ENSMUSG00000052915	Msl1	2810017F12Rik|4121402D02Rik|4930463F05Rik|AA682082|Msl-1	male-specific lethal 1 homolog (Drosophila)	protein-coding
mm_49860.1	chr6	38550774	38550807	+	1	NA	promoter-TSS (NM_001170849)	promoter-TSS (NM_001170849)	-544	NM_138680	192196	Mm.276133	NM_138680	ENSMUSG00000029823	Luc7l2	4930471C18Rik|AA522013|AU015269|CGI59|Cgi74	LUC7-like 2 (S. cerevisiae)	protein-coding
mm_165488.1	chr2	164523691	164523708	+	1	NA	Intergenic	RLTR44B|LTR|ERVK	26174	NM_133779	78928	Mm.28228	NM_133779	ENSMUSG00000017721	Pigt	2510012P17Rik|4930534E15Rik|CGI-06|NDAP|Ndap7	phosphatidylinositol glycan anchor biosynthesis, class T	protein-coding
mm_81162.1	chr9	107298357	107298371	+	1	NA	intron (NM_001317354, intron 1 of 1)	intron (NM_001317354, intron 1 of 1)	1705	NM_009895	12700	Mm.4592	NM_009895	ENSMUSG00000032578	Cish	CIS-1|CIS1|Cis|F17|F23|SOCS	cytokine inducible SH2-containing protein	protein-coding
mm_31103.1	chr4	41762356	41762373	+	1	NA	promoter-TSS (NM_010549)	promoter-TSS (NM_010549)	54	NM_010549	16157	Mm.193451	NM_010549	ENSMUSG00000073889	Il11ra1	AI314697|GP130|Il-11ra|Il11ra|Il11ra2|NR1	interleukin 11 receptor, alpha chain 1	protein-coding
mm_141297.1	chr17	28080145	28080170	-	1	NA	exon (NM_013687, exon 2 of 10)	exon (NM_013687, exon 2 of 10)	427	NM_013687	21463	Mm.29758	NM_013687	ENSMUSG00000062859	Tcp11	D17Ken1|Tcp-11	t-complex protein 11	protein-coding
mm_82874.1	chr9	32429704	32429706	-	1	NA	intron (NM_008026, intron 6 of 8)	intron (NM_008026, intron 6 of 8)	35720	NM_001168354	56379	Mm.390168	NM_019659	ENSMUSG00000041248	Kcnj1	Kir1.1|ROMK|Romk2	potassium inwardly-rectifying channel, subfamily J, member 1	protein-coding
mm_163970.1	chr14	55385461	55385464	+	1	NA	Intergenic	Intergenic	-93296	NM_001037938	28200	Mm.27427	NM_030686	ENSMUSG00000022210	Dhrs4	AI043103|AI790593|CR|D14Ucla2|NDRD|PHCR|PSCD|RRD|mouNRDR	dehydrogenase/reductase (SDR family) member 4	protein-coding
mm_48839.1	chr5	149267048	149267079	-	1	NA	intron (NM_001308462, intron 1 of 3)	intron (NM_001308462, intron 1 of 3)	2059	NM_009663	11690	Mm.19844	NM_009663	ENSMUSG00000060063	Alox5ap	Flap	arachidonate 5-lipoxygenase activating protein	protein-coding
mm_160861.1	chr11	59727628	59727628	+	1	NA	exon (NM_201245, exon 4 of 23)	exon (NM_201245, exon 4 of 23)	12526	NR_045476	69320	Mm.443242	NR_045476	ENSMUSG00000086330	1700007J10Rik	4930573L17Rik	RIKEN cDNA 1700007J10 gene	ncRNA
mm_33185.1	chr4	126117155	126117158	+	1	NA	intron (NM_028800, intron 1 of 10)	intron (NM_028800, intron 1 of 10)	13199	NM_001145827	74178	Mm.440269	NM_028800	ENSMUSG00000042608	Stk40	2310004N11Rik|AI428792	serine/threonine kinase 40	protein-coding
mm_135317.1	chr16	38713429	38713439	-	1	NA	promoter-TSS (NM_020260)	promoter-TSS (NM_020260)	-399	NM_020260	12549	Mm.370848	NM_020260	ENSMUSG00000022799	Arhgap31	5830477L08Rik|AU041750|Cdgap|D330026I07Rik	Rho GTPase activating protein 31	protein-coding
mm_122273.1	chr14	34374618	34374690	-	1	NA	promoter-TSS (NM_011430)	promoter-TSS (NM_011430)	15	NM_011430	20618	Mm.282800	NM_011430	ENSMUSG00000023064	Sncg	C79089|persyn	synuclein, gamma	protein-coding
mm_16420.1	chr2	180171950	180171962	+	1	NA	intron (NM_019822, intron 1 of 9)	CpG	368	NM_019822	56436	Mm.316654	NM_019822	ENSMUSG00000039041	Adrm1	1110063P18Rik|2510006J17Rik|AA408205|ARM-1|AU043535|Arm1|Gp110|Rpn13	adhesion regulating molecule 1	protein-coding
mm_131511.1	chr16	17499688	17499704	+	1	NA	exon (NM_001291070, exon 2 of 20)	exon (NM_001291070, exon 2 of 20)	7775	NM_001291070	72168	Mm.40038	NM_175178	ENSMUSG00000022763	Aifm3	2810401C16Rik|AI840249|Aifl	apoptosis-inducing factor, mitochondrion-associated 3	protein-coding
mm_71269.1	chr8	40919058	40919195	+	1	NA	3' UTR (NM_001044740, exon 12 of 12)	3' UTR (NM_001044740, exon 12 of 12)	-7107	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_99815.1	chr11	108425243	108425304	+	1	NA	promoter-TSS (NM_029606)	promoter-TSS (NM_029606)	7	NM_029606	76380	Mm.344071	NM_029586	ENSMUSG00000020728	Cep112	1700001M19Rik|1700029K01Rik|8430407H02Rik|AV043680|AV207351|Ccdc46|Macoco	centrosomal protein 112	protein-coding
mm_160356.1	chr8	21594510	21594510	-	1	NA	promoter-TSS (NM_001177526).2	promoter-TSS (NM_001177526).2	-45	NM_001177518	665927	Mm.422762	NM_001177518	ENSMUSG00000079114	Gm7849	EG665927	predicted gene 7849	protein-coding
mm_25833.1	chr3	129199920	129199943	+	1	NA	promoter-TSS (NM_001042504)	promoter-TSS (NM_001042504)	53	NM_001042504	18741	Mm.246804	NM_011098	ENSMUSG00000028023	Pitx2	9430085M16Rik|Brx1|Brx1b|Munc30|Otlx2|Ptx2|Rieg	paired-like homeodomain transcription factor 2	protein-coding
mm_36135.1	chr4	59349918	59349934	-	1	NA	exon (NM_001163288, exon 12 of 17)	exon (NM_001163288, exon 12 of 17)	88707	NM_001163288	634731	Mm.483589	NM_001163288	ENSMUSG00000038578	Susd1	A530080P10|Gm12528|OTTMUSG00000007332	sushi domain containing 1	protein-coding
mm_83344.1	chr9	44288536	44288601	-	1	NA	promoter-TSS (NM_138955)	promoter-TSS (NM_138955)	-324	NM_138955	192663	Mm.101876	NM_138955	ENSMUSG00000032131	Abcg4	6430517O04Rik	ATP-binding cassette, sub-family G (WHITE), member 4	protein-coding
mm_31562.1	chr4	57567817	57567836	+	1	NA	promoter-TSS (NM_172868)	promoter-TSS (NM_172868)	-422	NM_001304544	677884	Mm.331630	NM_001304544	ENSMUSG00000089945	Pakap	AF064781|Gm20459|Palm2-Akap2|Palm2Akap2|Palm2akap2	paralemmin A kinase anchor protein	protein-coding
mm_49808.1	chr6	36388210	36388221	+	1	NA	promoter-TSS (NR_015589)	promoter-TSS (NR_015589)	19	NR_015589	319472	Mm.226434	NR_015589	ENSMUSG00000073154	9330158H04Rik	-	RIKEN cDNA 9330158H04 gene	ncRNA
mm_146429.1	chr18	84851759	84851807	+	1	NA	intron (NM_025797, intron 1 of 4)	intron (NM_025797, intron 1 of 4)	369	NM_025797	109672	Mm.31018	NM_025797	ENSMUSG00000024646	Cyb5a	0610009N12Rik|Cyb5	cytochrome b5 type A (microsomal)	protein-coding
mm_62793.1	chr7	112682726	112682729	+	1	NA	intron (NM_009346, intron 1 of 12)	intron (NM_009346, intron 1 of 12)	3407	NM_009346	21676	Mm.24685	NM_009346	ENSMUSG00000055320	Tead1	2610024B07Rik|B230114H05Rik|Gtrgeo5|TEAD-1|TEF-1|Tcf13|mTEF-1	TEA domain family member 1	protein-coding
mm_18849.1	chr2	75658887	75658959	-	1	NA	promoter-TSS (NM_198090)	promoter-TSS (NM_198090)	-336	NM_146130	229279	Mm.316306	NM_053263	ENSMUSG00000059005	Hnrnpa3	2410013L13Rik|2610209F03Rik|2610510D13Rik|Hnrpa3	heterogeneous nuclear ribonucleoprotein A3	protein-coding
mm_17268.1	chr2	26062331	26062342	-	1	NA	intron (NM_026495, intron 3 of 5)	intron (NM_026495, intron 3 of 5)	30060	NM_001037098	67991	Mm.131074	NM_026495	ENSMUSG00000026932	Nacc2	0610020I02Rik|AI448087|Btbd14a|C030048H19Rik	nucleus accumbens associated 2, BEN and BTB (POZ) domain containing	protein-coding
mm_22564.1	chr3	9988260	9988278	+	1	NA	Intergenic	Intergenic	-24316	NM_001272097	16592	Mm.741	NM_010634	ENSMUSG00000027533	Fabp5	E-FABP|Fabpe|Klbp|PA-FABP|mal1	fatty acid binding protein 5, epidermal	protein-coding
mm_61243.1	chr7	65693448	65693477	+	1	NA	promoter-TSS (NM_178056)	promoter-TSS (NM_178056)	45	NM_026795	68634	Mm.476828	NM_026795	ENSMUSG00000078681	Tm2d3	1110025I09Rik|5930422O05Rik|Blp2	TM2 domain containing 3	protein-coding
mm_63182.1	chr7	125491529	125491565	+	1	NA	promoter-TSS (NM_026330)	promoter-TSS (NM_026330)	-5	NM_026330	67711	Mm.4467	NM_026330	ENSMUSG00000030750	Nsmce1	2510027N19Rik	NSE1 homolog, SMC5-SMC6 complex component	protein-coding
mm_118973.1	chr14	27876522	27876541	+	1	NA	intron (NM_177814, intron 3 of 15)	intron (NM_177814, intron 3 of 15)	254124	NM_177814	238988	Mm.318004	NM_177814	ENSMUSG00000040640	Erc2	6430531D06|CAST|CAST1/ERC2|D14Ertd171e|ELKS2alpha	ELKS/RAB6-interacting/CAST family member 2	protein-coding
mm_70743.1	chr8	19150757	19150760	+	1	NA	Intergenic	L1VL2|LINE|L1	-7129	NM_153115	78128	Mm.229357	NM_153115	ENSMUSG00000079842	Spag11a	9230111C08Rik|Bin1b|EP2Q|EP2e|Spag11	sperm associated antigen 11A	protein-coding
mm_36704.1	chr4	96786774	96786784	-	1	NA	Intergenic	Intergenic	-1619	NM_001081284	620779	Mm.439625	NM_001081284	ENSMUSG00000078639	Gm12695	OTTMUSG00000008003	predicted gene 12695	protein-coding
mm_134911.1	chr16	30267525	30267572	-	1	NA	promoter-TSS (NM_027904)	promoter-TSS (NM_027904)	-16	NM_027904	71756	Mm.290614	NM_027904	ENSMUSG00000023176	Cpn2	1300018K11Rik	carboxypeptidase N, polypeptide 2	protein-coding
mm_44331.1	chr5	14723682	14723698	-	1	NA	intron (NM_001110796, intron 9 of 19)	intron (NM_001110796, intron 9 of 19)	191199	NM_198666	381714	Mm.368256	NM_198666	ENSMUSG00000033219	Gm9758	ENSMUSG00000033219	predicted gene 9758	protein-coding
mm_17365.1	chr2	26864944	26864966	-	1	NA	promoter-TSS (NM_030718)	promoter-TSS (NM_030718)	40	NM_030718	80908	Mm.160386	NM_030718	ENSMUSG00000015787	Abo	NAGAT	ABO blood group (transferase A, alpha 1-3-N-acetylgalactosaminyltransferase, transferase B, alpha 1-3-galactosyltransferase)	protein-coding
mm_12794.1	chr2	79635445	79635463	+	1	NA	promoter-TSS (NM_080558)	promoter-TSS (NM_080558)	29	NM_080558	70599	Mm.272881	NM_080558	ENSMUSG00000027007	Ssfa2	5730488C15Rik|CS-1|CS1|KRAP|SPAG13|mKIAA1927	sperm specific antigen 2	protein-coding
mm_16922.1	chr2	13580214	13580233	-	1	NA	exon (NM_011701, exon 6 of 9)	exon (NM_011701, exon 6 of 9)	5912	NM_011701	22352	Mm.268000	NM_011701	ENSMUSG00000026728	Vim	-	vimentin	protein-coding
mm_72355.1	chr8	79711834	79711884	+	1	NA	promoter-TSS (NM_026904)	promoter-TSS (NM_026904)	39	NM_026904	68999	Mm.257445	NM_026904	ENSMUSG00000036977	Anapc10	1500026N15Rik|A830003M23Rik|APC10	anaphase promoting complex subunit 10	protein-coding
mm_95231.1	chr11	44520335	44520343	+	1	NA	intron (NM_001166553, intron 1 of 5)	intron (NM_001166553, intron 1 of 5)	962	NM_001166553	74315	Mm.156771	NM_028862	ENSMUSG00000019189	Rnf145	3732413I11Rik|TMRF1	ring finger protein 145	protein-coding
mm_19402.1	chr2	91636395	91636439	-	1	NA	promoter-TSS (NM_010168)	promoter-TSS (NM_010168)	40	NM_010168	14061	Mm.89048	NM_010168	ENSMUSG00000027249	F2	Cf-2|Cf2|FII	coagulation factor II	protein-coding
mm_143990.1	chr17	87682827	87682827	-	1	NA	intron (NM_008628, intron 4 of 15)	RSINE1|SINE|B4	10270	NM_008628	17685	Mm.4619	NM_008628	ENSMUSG00000024151	Msh2	AI788990	mutS homolog 2	protein-coding
mm_101958.1	chr11	50299153	50299225	-	1	NA	exon (NM_001110500, exon 11 of 15)	exon (NM_001110500, exon 11 of 15)	-6853	NM_175334	103806	Mm.51116	NM_175334	ENSMUSG00000050567	Maml1	AI644666|AW743257|D930008C07Rik|Mam-1|Mam1|mKIAA0200	mastermind like 1 (Drosophila)	protein-coding
mm_115217.1	chr13	109632627	109632701	+	1	NA	intron (NM_011056, intron 3 of 16)	intron (NM_011056, intron 3 of 16)	-271145	NR_035442	100316683		NR_035442	ENSMUSG00000084651	Mir1904	Mirn1904|mmu-mir-1904	microRNA 1904	ncRNA
mm_74526.1	chr8	9559184	9559206	-	1	NA	intron (NM_001347127, intron 1 of 3)	intron (NM_001347127, intron 1 of 3)	211828	NM_173446	270028	Mm.268163	NM_173446	ENSMUSG00000079157	Fam155a	6430500D16|AW121567|Tmem28	family with sequence similarity 155, member A	protein-coding
mm_149434.1	chr19	11472614	11472633	+	1	NA	3' UTR (NM_001166376, exon 3 of 3)	3' UTR (NM_001166376, exon 3 of 3)	3255	NM_028595	73656	Mm.440719	NM_028595	ENSMUSG00000079419	Ms4a6c	2200009H22Rik|2210417N07Rik	membrane-spanning 4-domains, subfamily A, member 6C	protein-coding
mm_8762.1	chr1	160792768	160792781	-	1	NA	5' UTR (NM_013862, exon 1 of 21)	5' UTR (NM_013862, exon 1 of 21)	164	NM_013862	29809	Mm.25833	NM_013862	ENSMUSG00000026721	Rabgap1l	5830411O09Rik|8430421H08Rik|9630005B12Rik|AW049894|HHL|Hh1|mKIAA0471	RAB GTPase activating protein 1-like	protein-coding
mm_116110.1	chr13	28950063	28950078	-	1	NA	TTS (NM_009238)	TTS (NM_009238)	3612	NM_009238	20677	Mm.240627	NM_009238	ENSMUSG00000076431	Sox4	AA682046|Sox-4	SRY (sex determining region Y)-box 4	protein-coding
mm_81725.1	chr9	112256293	112256341	+	1	NA	promoter-TSS (NR_033433)	promoter-TSS (NR_033433)	-257	NR_033433	620760	Mm.259863	NR_015468	ENSMUSG00000087038	2900079G21Rik	C130083B14|Gm6179	RIKEN cDNA 2900079G21 gene	ncRNA
mm_146222.1	chr18	77065196	77065250	+	1	NA	promoter-TSS (NM_001164168)	promoter-TSS (NM_001164168)	15	NM_001164167	17344	Mm.6370	NM_008602	ENSMUSG00000025423	Pias2	6330408K17Rik|AI462206|ARIP3|AU018068|Dib|Miz1|PIASxalpha|PIASxb|PIASxbeta|SIZ2	protein inhibitor of activated STAT 2	protein-coding
mm_78586.1	chr9	37367355	37367378	+	1	NA	promoter-TSS (NM_175189)	promoter-TSS (NM_175189)	-240	NM_175189	72927	Mm.266133	NM_175189	ENSMUSG00000046240	Hepacam	2900042E01Rik|Glialcam|Hepn1	hepatocyte cell adhesion molecule	protein-coding
mm_45814.1	chr5	87675036	87675062	-	1	NA	exon (NM_007784, exon 13 of 34)	exon (NM_007784, exon 13 of 34)	8841	NM_001286016	12990	Mm.427467	NM_007784	ENSMUSG00000070702	Csn1s1	AA959832|AW212882|Csna	casein alpha s1	protein-coding
mm_80556.1	chr9	83409620	83409621	+	1	NA	intron (NM_029434, intron 3 of 7)	intron (NM_029434, intron 3 of 7)	-21927	NR_102437	100039186	Mm.212721	NR_102437	ENSMUSG00000099718	Gm2087	-	predicted gene 2087	ncRNA
mm_64447.1	chr7	142658533	142658585	+	1	NA	5' UTR (NM_010514, exon 1 of 4)	5' UTR (NM_010514, exon 1 of 4)	245	NM_010514	16002	Mm.3862	NM_010514	ENSMUSG00000048583	Igf2	AL033362|Igf-2|Igf-II|M6pr|Mpr|Peg2	insulin-like growth factor 2	protein-coding
mm_68924.1	chr7	126472384	126472395	-	1	NA	exon (NM_001289538, exon 2 of 9)	exon (NM_001289538, exon 2 of 9)	705	NR_110346	20399	Mm.8538	NM_011363	ENSMUSG00000030733	Sh2b1	AI425885|C530001K22Rik|Irip|Psm|SH2-B|SH2-Bb|Sh2bpsm1|mKIAA1299	SH2B adaptor protein 1	protein-coding
mm_2035.1	chr1	87213925	87213990	+	1	NA	promoter-TSS (NM_001039169)	promoter-TSS (NM_001039169)	18	NM_001039169	26987	Mm.227183	NM_023314	ENSMUSG00000026254	Eif4e2	2700069E09Rik|AI036339|AV129531|D0H0S6743E|Eif4el3	eukaryotic translation initiation factor 4E member 2	protein-coding
mm_69935.1	chr7	142095090	142095098	-	1	NA	5' UTR (NM_008748, exon 1 of 7)	5' UTR (NM_008748, exon 1 of 7)	190	NM_008748	18218	Mm.39725	NM_008748	ENSMUSG00000037887	Dusp8	5530400B01Rik|AI593498|Nttp1	dual specificity phosphatase 8	protein-coding
mm_161961.1	chr19	7802610	7802610	-	1	NA	promoter-TSS (NM_146232)	promoter-TSS (NM_146232)	57	NM_146232	236149	Mm.207060	NM_146232	ENSMUSG00000053303	Slc22a26	-	solute carrier family 22 (organic cation transporter), member 26	protein-coding
mm_69178.1	chr7	127218732	127218736	-	1	NA	promoter-TSS (NM_017461)	promoter-TSS (NM_017461)	-289	NM_017461	54204	Mm.18	NM_017461	ENSMUSG00000000486	Sept1	Diff6|Pnutl3	septin 1	protein-coding
mm_39623.1	chr5	24423915	24423958	+	1	NA	promoter-TSS (NM_007668)	promoter-TSS (NM_007668)	-406	NM_007668	12568	Mm.298798	NM_007668	ENSMUSG00000028969	Cdk5	AW048668|Crk6	cyclin-dependent kinase 5	protein-coding
mm_160946.1	chr11	96318159	96318159	+	1	NA	promoter-TSS (NM_010459)	promoter-TSS (NM_010459)	-108	NM_010459	15412	Mm.3546	NM_010459	ENSMUSG00000038692	Hoxb4	Hox-2.6	homeobox B4	protein-coding
mm_115106.1	chr13	103344881	103344881	+	1	NA	Intergenic	Intergenic	-10389	NM_175171	328329	Mm.202606	NM_175171	ENSMUSG00000034751	Mast4	4930420O11Rik|AI642422|mKIAA0303	microtubule associated serine/threonine kinase family member 4	protein-coding
mm_6563.1	chr1	75142325	75142354	-	1	NA	promoter-TSS (NM_026977)	promoter-TSS (NM_026977)	29	NM_026977	69171	Mm.28193	NM_026977	ENSMUSG00000033159	Cnppd1	1810031K17Rik|AU043960	cyclin Pas1/PHO80 domain containing 1	protein-coding
mm_130579.1	chr15	99527675	99527745	-	1	NA	5' UTR (NM_028224, exon 1 of 12)	5' UTR (NM_028224, exon 1 of 12)	455	NM_028224	72393	Mm.39760	NM_028224	ENSMUSG00000023011	Faim2	2900002L20Rik|Lfg|Lfg2|NMP25|Nmp35|Tmbim2	Fas apoptotic inhibitory molecule 2	protein-coding
mm_26988.1	chr3	25700228	25700250	-	1	NA	intron (NM_001163387, intron 3 of 5)	intron (NM_001163387, intron 3 of 5)	453068	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_130411.1	chr15	97977834	97977847	-	1	NA	exon (NM_001113515, exon 50 of 53)	exon (NM_001113515, exon 50 of 53)	13611	NM_001252153	380967	Mm.196630	NM_201359	ENSMUSG00000052369	Tmem106c	AI046681|BC046621|D15Ertd405e	transmembrane protein 106C	protein-coding
mm_130230.1	chr15	96460712	96460742	-	1	NA	5' UTR (NM_028148, exon 1 of 15)	5' UTR (NM_028148, exon 1 of 15)	116	NM_028148	72193	Mm.324474	NM_028148	ENSMUSG00000033228	Scaf11	1110061H03Rik|2610510E10Rik|AI462454|CASP11|SIP1|SRRP129|Sfrs2ip|Srsf2ip|mKIAA3013	SR-related CTD-associated factor 11	protein-coding
mm_139547.1	chr17	56764806	56764845	+	1	NA	promoter-TSS (NM_144858)	promoter-TSS (NM_144858)	74	NM_144858	224907	Mm.293973	NM_144858	ENSMUSG00000007603	Dus3l	AI662135|AW557805	dihydrouridine synthase 3-like (S. cerevisiae)	protein-coding
mm_76169.1	chr8	82391920	82391938	-	1	NA	intron (NM_001254747, intron 1 of 7)	intron (NM_001254747, intron 1 of 7)	10657	NM_001254747	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_88282.1	chr10	75130982	75131001	+	1	NA	intron (NM_001081412, intron 2 of 22)	intron (NM_001081412, intron 2 of 22)	70095	NM_001081412	110279	Mm.333722	NM_001081412	ENSMUSG00000009681	Bcr	5133400C09Rik|AI561783|AI853148|mKIAA3017	breakpoint cluster region	protein-coding
mm_92338.1	chr10	75822522	75822548	-	1	NA	promoter-TSS (NM_029472)	promoter-TSS (NM_029472)	8	NM_029472	75886	Mm.268996	NM_029472	ENSMUSG00000009093	Gstt4	4930583C14Rik|AI507011	glutathione S-transferase, theta 4	protein-coding
mm_119306.1	chr14	34819841	34819856	+	1	NA	promoter-TSS (NM_008166)	promoter-TSS (NM_008166)	-288	NM_008166	14803	Mm.121569	NM_008166	ENSMUSG00000041078	Grid1	GluD1|GluRdelta1	glutamate receptor, ionotropic, delta 1	protein-coding
mm_96206.1	chr11	62249013	62249027	+	1	NA	promoter-TSS (NM_007413)	promoter-TSS (NM_007413)	36	NM_007413	11541	Mm.40740	NM_007413	ENSMUSG00000018500	Adora2b	A2BAR|A2BR|A2b|AA2BR|AI480866|AI605384	adenosine A2b receptor	protein-coding
mm_34547.1	chr4	149553190	149553193	+	1	NA	intron (NM_001141930, intron 3 of 3)	PB1D10|SINE|Alu	8074	NM_001141930	67087	Mm.299735	NM_023465	ENSMUSG00000028988	Ctnnbip1	1110008O09Rik|2310001I19Rik|AW457332|Catnbip1|Icat	catenin beta interacting protein 1	protein-coding
mm_63562.1	chr7	128112969	128112989	+	1	NA	exon (NM_008401, exon 20 of 30)	exon (NM_008401, exon 20 of 30)	-16589	NM_021334	16411	Mm.22378	NM_021334	ENSMUSG00000030789	Itgax	AI449405|Cd11c|Cr4|N418	integrin alpha X	protein-coding
mm_69066.1	chr7	126922888	126922926	-	1	NA	Intergenic	Intergenic	-5972	NM_172747	233877	Mm.245897	NM_172747	ENSMUSG00000030685	Kctd13	1500003N18Rik|AV259508|PDIP1alpha|Pdip1|Poldip1	potassium channel tetramerisation domain containing 13	protein-coding
mm_150675.1	chr19	42052260	42052275	+	1	NA	promoter-TSS (NM_025752)	promoter-TSS (NM_025752)	39	NM_025752	66765	Mm.440412	NM_025752	ENSMUSG00000090369	4933411K16Rik	-	RIKEN cDNA 4933411K16 gene	protein-coding
mm_116969.1	chr13	56178642	56178648	-	1	NA	5' UTR (NM_001168615, exon 1 of 3)	5' UTR (NM_001168615, exon 1 of 3)	240	NM_145976	212937	Mm.116697	NM_145976	ENSMUSG00000049625	Tifab	-	TRAF-interacting protein with forkhead-associated domain, family member B	protein-coding
mm_73812.1	chr8	117379349	117379385	+	1	NA	intron (NM_028941, intron 2 of 20)	intron (NM_028941, intron 2 of 20)	30197	NM_028941	74440	Mm.233181	NM_028941	ENSMUSG00000034390	Cmip	4933407C03Rik|5830471E12Rik|AI314065|AI464126	c-Maf inducing protein	protein-coding
mm_69180.1	chr7	127232632	127232654	-	1	NA	promoter-TSS (NM_146201)	promoter-TSS (NM_146201)	487	NR_030674	100043580	Mm.482209	NR_030674	ENSMUSG00000000486	Gm4532	-	predicted gene 4532	ncRNA
mm_90063.1	chr10	116301418	116301428	+	1	NA	promoter-TSS (NM_029928)	promoter-TSS (NM_029928)	49	NM_029928	19263	Mm.37213	NM_029928	ENSMUSG00000020154	Ptprb	3230402H02Rik|C130094E24|Ptpz|Rptpb|VE-PTP|Veptp	protein tyrosine phosphatase, receptor type, B	protein-coding
mm_149773.1	chr19	23087924	23087935	+	1	NA	Intergenic	B1_Mus1|SINE|Alu	-53297	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_144072.1	chr17	91057370	91057372	-	1	NA	intron (NM_001346957, intron 1 of 18)	ORR1A2|LTR|ERVL-MaLR	32234	NM_001346957	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_163909.1	chr14	31267910	31267923	+	1	NA	intron (NM_001033668, intron 61 of 77)	intron (NM_001033668, intron 61 of 77)	16427	NM_027088	104416	Mm.3779	NM_027088	ENSMUSG00000021901	Bap1	2300006C11Rik|AA989761|AW553466|mKIAA0272|uch-x4	Brca1 associated protein 1	protein-coding
mm_63297.1	chr7	126812668	126812686	+	1	NA	Intergenic	Intergenic	-4208	NM_026884	68952	Mm.440393	NM_026884	ENSMUSG00000058966	Fam57b	1500016O10Rik|A330104J06Rik|AI413816|AW060769	family with sequence similarity 57, member B	protein-coding
mm_39238.1	chr5	3236382	3236387	+	1	NA	Intergenic	Intergenic	-107509	NM_009873	12571	Mm.31672	NM_009873	ENSMUSG00000040274	Cdk6	AI504062|Crk2	cyclin-dependent kinase 6	protein-coding
mm_147876.1	chr18	64516044	64516048	-	1	NA	intron (NM_001142950, intron 1 of 14)	intron (NM_001142950, intron 1 of 14)	511	NM_027350	70223	Mm.29192	NM_027350	ENSMUSG00000024587	Nars	3010001M15Rik|AA960128|ASNRS|C78150	asparaginyl-tRNA synthetase	protein-coding
mm_122254.1	chr14	34117753	34117789	-	1	NA	Intergenic	Intergenic	-15017	NM_001251843	105518	Mm.246608	NM_001251843	ENSMUSG00000095493	A630023A22Rik	AI461879	RIKEN cDNA A630023A22 gene	protein-coding
mm_49718.1	chr6	34598328	34598334	+	1	NA	promoter-TSS (NM_001347100)	promoter-TSS (NM_001347100)	-173	NM_001347100	109624	Mm.308134	NM_145575	ENSMUSG00000029761	Cald1	4833423D12Rik|AI195384|AV071549|AW536160|C920027I18Rik	caldesmon 1	protein-coding
mm_11195.1	chr2	29124107	29124166	+	1	NA	promoter-TSS (NM_198033)	promoter-TSS (NM_198033)	-856	NM_198033	269254	Mm.41867	NM_198033	ENSMUSG00000043535	Setx	A130090N03|A930037J23Rik|AOA2|AW060766|Als4|SCAR1|Sen1|mKIAA0625	senataxin	protein-coding
mm_26108.1	chr3	137341213	137341223	+	1	NA	5' UTR (NM_016885, exon 1 of 11)	5' UTR (NM_016885, exon 1 of 11)	140	NM_016885	59308	Mm.27343	NM_016885	ENSMUSG00000054690	Emcn	0610012K22Rik|AI315669|Muc14	endomucin	protein-coding
mm_163394.1	chr12	66420995	66420999	+	1	NA	Intergenic	MYSERV6-int|LTR|ERVK	-136596	NM_001162933	238217	Mm.188575	NM_001162933	ENSMUSG00000060499	Rpl10l	EG238217	ribosomal protein L10-like	protein-coding
mm_122123.1	chr14	31128886	31128923	-	1	NA	promoter-TSS (NM_001308464)	promoter-TSS (NM_001308464)	26	NM_001308466	66487	Mm.379116	NM_001308091	ENSMUSG00000058351	Smim4	2010107H07Rik|Gm41122	small integral membrane protein 4	protein-coding
mm_64297.1	chr7	141861552	141861561	+	1	NA	exon (NM_028801, exon 31 of 49)	exon (NM_028801, exon 31 of 49)	22484	NM_028801	74180	Mm.200752	NM_028801	ENSMUSG00000066108	Muc5b	2300002I04Rik|A130042M24|AV085033|MUC5|MUC9|mucin 5b	mucin 5, subtype B, tracheobronchial	protein-coding
mm_90890.1	chr10	10234909	10234915	-	1	NA	Intergenic	Intergenic	237402	NM_001127353	215772	Mm.246573	NM_172547	ENSMUSG00000050994	Adgb	9130014G24Rik	androglobin	protein-coding
mm_116520.1	chr13	45777561	45777585	-	1	NA	intron (NM_001199304, intron 4 of 6)	B1_Mur1|SINE|Alu	187418	NM_001199304	20238	Mm.342683	NM_009124	ENSMUSG00000046876	Atxn1	2900016G23Rik|Atx1|C85907|ENSMUSG00000074917|Gm10786|Sca1	ataxin 1	protein-coding
mm_154108.1	chr19	57118898	57118979	-	1	NA	promoter-TSS (NM_001103178)	promoter-TSS (NM_001103178)	86	NM_001347459	226251	Mm.217161	NM_178688	ENSMUSG00000025085	Ablim1	2210411C18Rik|2610209L21Rik|4833406P10Rik|9330196J19Rik|AV079770|AW060987|AW215784|Limab1|mKIAA0059	actin-binding LIM protein 1	protein-coding
mm_83503.1	chr9	45955227	45955250	-	1	NA	promoter-TSS (NM_001289668)	promoter-TSS (NM_001289668)	11	NM_172257	214597	Mm.379345	NM_172257	ENSMUSG00000034908	Sidt2	B930096O19|BC023957|CGI-40	SID1 transmembrane family, member 2	protein-coding
mm_112642.1	chr13	16016685	16016706	+	1	NA	intron (NM_008380, intron 3 of 4)	RLTR31D_MM|LTR|ERVK	4844	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_19634.1	chr2	102814131	102814141	-	1	NA	exon (NM_009851, exon 19 of 19)	exon (NM_009851, exon 19 of 19)	87529	NM_001177785	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_84908.1	chr9	79977629	79977633	-	1	NA	5' UTR (NM_001081243, exon 1 of 6)	5' UTR (NM_001081243, exon 1 of 6)	251	NM_001081243	70598	Mm.23049	NM_001081243	ENSMUSG00000034898	Filip1	5730485H21Rik|AI843021	filamin A interacting protein 1	protein-coding
mm_57390.1	chr6	124840042	124840052	-	1	NA	5' UTR (NM_013530, exon 1 of 10)	5' UTR (NM_013530, exon 1 of 10)	228	NM_013530	14695	Mm.68889	NM_013530	ENSMUSG00000023439	Gnb3	Gnb-3	guanine nucleotide binding protein (G protein), beta 3	protein-coding
mm_3212.1	chr1	135838411	135838423	+	1	NA	intron (NM_001130181, intron 1 of 13)	intron (NM_001130181, intron 1 of 13)	2083	NM_001130179	21956	Mm.247470	NM_011619	ENSMUSG00000026414	Tnnt2	Tnt|cTnT	troponin T2, cardiac	protein-coding
mm_170456.1	chr18	88658760	88658773	-	1	NA	Intergenic	Intergenic	235441	NM_018821	54607	Mm.91920	NM_018821	ENSMUSG00000056153	Socs6	1500012M23Rik|5830401B18Rik|AI447482|Cis4|Cish4|HSPC060|SOCS-4|SOCS-6|SSI4|STAI4|STATI4|Socs4	suppressor of cytokine signaling 6	protein-coding
mm_78342.1	chr9	25297803	25297826	+	1	NA	exon (NM_001205367, exon 8 of 13)	exon (NM_001205367, exon 8 of 13)	45375	NM_001205367	235072	Mm.270259	NM_009859	ENSMUSG00000001833	Sept7	Cdc10|E430034N22	septin 7	protein-coding
mm_90546.1	chr10	128092754	128092769	+	1	NA	promoter-TSS (NM_054078)	promoter-TSS (NM_054078)	-22	NM_054078	116848	Mm.252213	NM_054078	ENSMUSG00000040054	Baz2a	AA415431|C030005G16Rik|C78388|Tip5|Walp3|mKIAA0314	bromodomain adjacent to zinc finger domain, 2A	protein-coding
mm_100904.1	chr11	6200412	6200446	-	1	NA	promoter-TSS (NM_173748)	promoter-TSS (NM_173748)	22	NM_173748	209586	Mm.25321	NM_173748	ENSMUSG00000053838	Nudcd3	AI427847|BC024322|mKIAA1068	NudC domain containing 3	protein-coding
mm_82627.1	chr9	21918112	21918158	-	1	NA	promoter-TSS (NM_001324531)	promoter-TSS (NM_001324531)	48	NM_031874	19340	Mm.260157	NM_031874	ENSMUSG00000019066	Rab3d	C130057E11Rik	RAB3D, member RAS oncogene family	protein-coding
mm_112264.1	chr12	114048749	114048769	-	1	NA	Intergenic	Intergenic	420707	NR_106062	102465663		NR_106062	ENSMUSG00000105438	Mir7094-1	mmu-mir-7094-1	microRNA 7094-1	ncRNA
mm_167888.1	chrX	60892519	60892567	-	1	NA	exon (NM_009237, exon 1 of 1)	exon (NM_009237, exon 1 of 1)	887	NM_009237	20675	Mm.35784	NM_009237	ENSMUSG00000045179	Sox3	Sox-3	SRY (sex determining region Y)-box 3	protein-coding
mm_70259.1	chr8	3516840	3516903	+	1	NA	intron (NM_001122818, intron 3 of 34)	CpG	1487	NM_015801	50767	Mm.23085	NM_015801	ENSMUSG00000004565	Pnpla6	AI661849|MSws|Nte	patatin-like phospholipase domain containing 6	protein-coding
mm_141599.1	chr17	32524062	32524086	-	1	NA	exon (NM_001101445, exon 7 of 13)	exon (NM_001101445, exon 7 of 13)	-12555	NM_024442	70101	Mm.30504	NM_024442	ENSMUSG00000048440	Cyp4f16	2310021J05Rik|AI746515	cytochrome P450, family 4, subfamily f, polypeptide 16	protein-coding
mm_69656.1	chr7	139974350	139974358	-	1	NA	intron (NM_001347613, intron 5 of 5)	intron (NM_001347613, intron 5 of 5)	4401	NM_001347614	381933	Mm.440431	NM_001033465	ENSMUSG00000073795	6430531B16Rik	Gm1093	RIKEN cDNA 6430531B16 gene	protein-coding
mm_21683.1	chr2	164431220	164431230	-	1	NA	exon (NM_011521, exon 2 of 5)	exon (NM_011521, exon 2 of 5)	11963	NM_011521	20971	Mm.3815	NM_011521	ENSMUSG00000017009	Sdc4	AA959608|AW108331|S4|Synd4|ryudocan|syndecan-4	syndecan 4	protein-coding
mm_8318.1	chr1	144609107	144609114	-	1	NA	Intergenic	U4|snRNA|snRNA	-41443	NR_110891	624910	Mm.389199	NM_001290269	ENSMUSG00000098509	Rgs21	EG624910	regulator of G-protein signalling 21	protein-coding
mm_135253.1	chr16	37654394	37654406	-	1	NA	promoter-TSS (NM_026610)	promoter-TSS (NM_026610)	-32	NM_026610	68194	Mm.379154	NM_026610	ENSMUSG00000022820	Ndufb4	0610006N12Rik|1300010H20Rik	NADH dehydrogenase (ubiquinone) 1 beta subcomplex 4	protein-coding
mm_76917.1	chr8	105933043	105933064	-	1	NA	exon (NM_023182, exon 3 of 7)	exon (NM_023182, exon 3 of 7)	809	NM_023182	109660	Mm.2745	NM_023182	ENSMUSG00000031896	Ctrl	0910001G08Rik|1810004D15Rik|AV005227|Ctra-1|Ctra1|chymopasin|mFLJ00366	chymotrypsin-like	protein-coding
mm_22832.1	chr3	27317060	27317084	+	1	NA	promoter-TSS (NM_009425)	promoter-TSS (NM_009425)	-5	NM_009425	22035	Mm.1062	NM_009425	ENSMUSG00000039304	Tnfsf10	A330042I21Rik|AI448571|APO-2L|Ly81|TL2|Tnlg6a|Trail	tumor necrosis factor (ligand) superfamily, member 10	protein-coding
mm_104513.1	chr11	96005962	96005972	-	1	NA	promoter-TSS (NM_009951)	promoter-TSS (NM_009951)	-23	NM_009951	140486	Mm.294769	NM_009951	ENSMUSG00000013415	Igf2bp1	AL024068|AW549074|CRD-BP|Crdbp|D030026A21Rik|D11Moh40e|D11Moh45|IMP-1|IMP1|Neilsen|ZBP-1|Zbp1|mir-3063	insulin-like growth factor 2 mRNA binding protein 1	protein-coding
mm_107059.1	chr12	16653904	16653976	+	1	NA	exon (NM_008747, exon 1 of 4)	exon (NM_008747, exon 1 of 4)	470	NM_008747	18217	Mm.281715	NM_008747	ENSMUSG00000020591	Ntsr2	NT2R|NTRL	neurotensin receptor 2	protein-coding
mm_115218.1	chr13	109632708	109632718	+	1	NA	intron (NM_011056, intron 3 of 16)	intron (NM_011056, intron 3 of 16)	-271096	NR_035442	100316683		NR_035442	ENSMUSG00000084651	Mir1904	Mirn1904|mmu-mir-1904	microRNA 1904	ncRNA
mm_68471.1	chr7	110769302	110769365	-	1	NA	intron (NM_001276301, intron 1 of 14)	intron (NM_001276301, intron 1 of 14)	1127	NM_001276301	11717	Mm.3238	NM_009667	ENSMUSG00000005686	Ampd3	-	adenosine monophosphate deaminase 3	protein-coding
mm_165364.1	chr2	126500016	126500029	+	1	NA	Intergenic	Intergenic	-8469	NM_001080944	241633	Mm.222235	NM_001080944	ENSMUSG00000060131	Atp8b4	A530043E15|Im	ATPase, class I, type 8B, member 4	protein-coding
mm_44512.1	chr5	24329557	24329598	-	1	NA	promoter-TSS (NM_001294162)	promoter-TSS (NM_001294162)	14	NM_001294162	16511	Mm.6539	NM_013569	ENSMUSG00000038319	Kcnh2	AI326795|ERG1|LQT|Lqt2|M-erg|Merg1|merg1a|merg1b	potassium voltage-gated channel, subfamily H (eag-related), member 2	protein-coding
mm_71393.1	chr8	46162278	46162286	+	1	NA	Intergenic	Intergenic	-7274	NM_025747	66756	Mm.133623	NM_025747	ENSMUSG00000031631	Cfap97	1110068E21Rik|4933411K20Rik|AW049273|Kiaa1430|mKIAA1430	cilia and flagella associated protein 97	protein-coding
mm_115845.1	chr13	21287403	21287405	-	1	NA	exon (NM_010343, exon 5 of 5)	exon (NM_010343, exon 5 of 5)	5282	NM_010343	14780	Mm.1332	NM_010343	ENSMUSG00000004344	Gpx5	AV379049|Arep	glutathione peroxidase 5	protein-coding
mm_34770.1	chr4	153955961	153955965	+	1	NA	Intergenic	Intergenic	-1274	NM_175287	97159	Mm.7066	NM_175287	ENSMUSG00000047613	A430005L14Rik	C79672	RIKEN cDNA A430005L14 gene	protein-coding
mm_6196.1	chr1	65179045	65179055	-	1	NA	promoter-TSS (NM_010497)	promoter-TSS (NM_010497)	92	NM_010497	15926	Mm.9925	NM_010497	ENSMUSG00000025950	Idh1	AI314845|AI788952|E030024J03Rik|Id-1|Idh-1|Idpc	isocitrate dehydrogenase 1 (NADP+), soluble	protein-coding
mm_54632.1	chr6	38695442	38695469	-	1	NA	Intergenic	Intergenic	32386	NM_001101507	665180	Mm.349066	NM_001101507	ENSMUSG00000079598	Clec2l	AI414054|AW122724|Gm1064	C-type lectin domain family 2, member L	protein-coding
mm_77379.1	chr8	119840532	119840549	-	1	NA	promoter-TSS (NM_028071)	promoter-TSS (NM_028071)	39	NM_028071	72042	Mm.393405	NM_028071	ENSMUSG00000031827	Cotl1	1810074P22Rik|2010004C08Rik|Clp	coactosin-like 1 (Dictyostelium)	protein-coding
mm_12256.1	chr2	68913670	68913677	+	1	NA	intron (NM_172856, intron 1 of 9)	intron (NM_172856, intron 1 of 9)	52232	NM_001347161	241447	Mm.222222	NM_172856	ENSMUSG00000027035	Cers6	4732462C07Rik|AW544719|Lass6|T1L	ceramide synthase 6	protein-coding
mm_123683.1	chr14	69523094	69523113	-	1	NA	Intergenic	Intergenic	-10554	NM_173420	239167	Mm.259889	NM_173420	ENSMUSG00000047977	Synb	D930020E02Rik|syncytin-B	syncytin b	protein-coding
mm_135859.1	chr16	59639125	59639191	-	1	NA	5' UTR (NM_019665, exon 1 of 8)	5' UTR (NM_019665, exon 1 of 8)	181	NM_019665	56297	Mm.392505	NM_019665	ENSMUSG00000022722	Arl6	1110018H24Rik|2210411E14Rik|BBS3	ADP-ribosylation factor-like 6	protein-coding
mm_145856.1	chr18	65454833	65454845	+	1	NA	intron (NM_172833, intron 8 of 15)	intron (NM_172833, intron 8 of 15)	23842	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_42510.1	chr5	115542907	115542937	+	1	NA	intron (NM_133915, intron 1 of 11)	intron (NM_133915, intron 1 of 11)	-16545	NM_007475	11837	Mm.5286	NM_007475	ENSMUSG00000067274	Rplp0	36B4|Arbp|L10E	ribosomal protein, large, P0	protein-coding
mm_13083.1	chr2	91206780	91206820	+	1	NA	exon (NM_007387, exon 7 of 11)	exon (NM_007387, exon 7 of 11)	3888	NM_007387	11432	Mm.45570	NM_007387	ENSMUSG00000002103	Acp2	Acp-2|LAP	acid phosphatase 2, lysosomal	protein-coding
mm_113524.1	chr13	37826019	37826044	+	1	NA	promoter-TSS (NM_001177868)	promoter-TSS (NM_001177868)	-7	NM_026830	68750	Mm.491109	NM_026830	ENSMUSG00000039087	Rreb1	1110037N09Rik|AA414966|B930013M22Rik	ras responsive element binding protein 1	protein-coding
mm_164209.1	chr15	82283140	82283150	+	1	NA	exon (NM_011889, exon 3 of 10)	exon (NM_011889, exon 3 of 10)	8210	NM_011889	24050	Mm.309707	NM_011889	ENSMUSG00000022456	Sept3	3110018K01Rik|AV154067|B530002E20Rik|Sep3	septin 3	protein-coding
mm_43817.1	chr5	142929214	142929223	+	1	NA	Intergenic	CpG	-22464	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_66912.1	chr7	60003967	60003994	-	1	NA	intron (NM_001082962, intron 2 of 10)	intron (NM_001082962, intron 2 of 10)	1176	NM_013670	20646	Mm.274995	NM_013670	ENSMUSG00000102252	Snrpn	2410045I01Rik|HCERN3|Peg4|Pwcr1|SMN	small nuclear ribonucleoprotein N	protein-coding
mm_12749.1	chr2	79231292	79231304	+	1	NA	Intergenic	Intergenic	-24128	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D|Itga4B	integrin alpha 4	protein-coding
mm_127089.1	chr15	97782196	97782206	+	1	NA	Intergenic	Intergenic	-2164	NM_026353	67739	Mm.28955	NM_026353	ENSMUSG00000081534	Slc48a1	4930570C03Rik	solute carrier family 48 (heme transporter), member 1	protein-coding
mm_91030.1	chr10	18023123	18023225	-	1	NA	promoter-TSS (NM_028440)	promoter-TSS (NM_028440)	78	NM_028440	73112	Mm.276041	NM_028440	ENSMUSG00000078453	Abracl	1700028I04Rik|3110003A17Rik	ABRA C-terminal like	protein-coding
mm_109353.1	chr12	109609697	109609700	+	1	NA	intron (NR_028261, intron 2 of 20)	intron (NR_028261, intron 2 of 20)	-1802	NR_029770	723846		NR_029770	ENSMUSG00000070101	Mir341	Mirn341|mmu-mir-341	microRNA 341	ncRNA
mm_110335.1	chr12	35676618	35676624	-	1	NA	intron (NR_045050, intron 3 of 4)	intron (NR_045050, intron 3 of 4)	9683	NR_045051	71581	Mm.100110	NR_045050		9130015A21Rik	100043575|Gm4527	RIKEN cDNA 9130015A21 gene	ncRNA
mm_82520.1	chr9	20642512	20642536	-	1	NA	promoter-TSS (NM_025401)	promoter-TSS (NM_025401)	282	NM_013911	30843	Mm.24608	NM_013911	ENSMUSG00000066892	Fbxl12	3110048D16Rik|Fbl12	F-box and leucine-rich repeat protein 12	protein-coding
mm_23479.1	chr3	60487440	60487454	+	1	NA	intron (NM_001253713, intron 2 of 9)	intron (NM_001253713, intron 2 of 9)	-13732	NM_001253711	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_102898.1	chr11	69423929	69423953	-	1	NA	exon (NM_001081330, exon 78 of 86)	exon (NM_001081330, exon 78 of 86)	-10266	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_117899.1	chr13	99425828	99425854	-	1	NA	exon (NM_008634, exon 7 of 7)	exon (NM_008634, exon 7 of 7)	-13015	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_52469.1	chr6	114248046	114248058	+	1	NA	3' UTR (NM_172890, exon 14 of 14)	3' UTR (NM_172890, exon 14 of 14)	-34583	NM_178703	232333	Mm.5260	NM_178703	ENSMUSG00000030310	Slc6a1	A730043E01|GABATHG|GABATR|GAT-1|Gabt|Gabt1|Gat1|XT-1|Xtrp1	solute carrier family 6 (neurotransmitter transporter, GABA), member 1	protein-coding
mm_49949.1	chr6	40325472	40325501	+	1	NA	promoter-TSS (NM_023538)	promoter-TSS (NM_023538)	8	NM_023538	69923	Mm.32840	NM_023538	ENSMUSG00000029916	Agk	2610037M15Rik|6720408I04Rik|AI465370|Mulk	acylglycerol kinase	protein-coding
mm_18449.1	chr2	60948271	60948281	-	1	NA	intron (NM_020296, intron 1 of 13)	intron (NM_020296, intron 1 of 13)	14928	NM_020296	56878	Mm.259667	NM_020296	ENSMUSG00000026970	Rbms1	2600014B10Rik|AI255215|MSSP-1|MSSP-2|MSSP-3|YC1	RNA binding motif, single stranded interacting protein 1	protein-coding
mm_66778.1	chr7	46919878	46919908	-	1	NA	promoter-TSS (NM_021884)	promoter-TSS (NM_021884)	37	NM_021884	22088	Mm.241334	NM_021884	ENSMUSG00000014402	Tsg101	AI255943|CC2	tumor susceptibility gene 101	protein-coding
mm_51100.1	chr6	67271928	67271956	+	1	NA	exon (NM_025814, exon 3 of 8)	exon (NM_025814, exon 3 of 8)	4963	NM_025814	66870	Mm.240490	NM_025814	ENSMUSG00000036371	Serbp1	1200009K13Rik|9330147J08Rik|AL022786|Pairbp1	serpine1 mRNA binding protein 1	protein-coding
mm_74784.1	chr8	22060020	22060056	-	1	NA	promoter-TSS (NM_001243161)	promoter-TSS (NM_001243161)	36	NM_007511	11979	Mm.87854	NM_007511	ENSMUSG00000006567	Atp7b	Atp7a|WND|tx	ATPase, Cu++ transporting, beta polypeptide	protein-coding
mm_36864.1	chr4	107057503	107057520	-	1	NA	exon (NM_025500, exon 6 of 7)	exon (NM_025500, exon 6 of 7)	9355	NM_025500	56280	Mm.29517	NM_025500	ENSMUSG00000028622	Mrpl37	2300004O14Rik|AI132596|MRP-L2|Rpml2	mitochondrial ribosomal protein L37	protein-coding
mm_87752.1	chr10	60277682	60277692	+	1	NA	promoter-TSS (NM_011179)	promoter-TSS (NM_011179)	59	NM_001146121	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_107884.1	chr12	70233865	70233898	+	1	NA	non-coding (NR_045174, exon 5 of 5)	non-coding (NR_045174, exon 5 of 5)	6040	NR_045174	414124	Mm.416164	NR_045174	ENSMUSG00000085298	F730035M05Rik	-	RIKEN cDNA F730035M05 gene	ncRNA
mm_126785.1	chr15	86214432	86214455	+	1	NA	promoter-TSS (NM_145476)	promoter-TSS (NM_145476)	-16	NM_145476	223754	Mm.28904	NM_145476	ENSMUSG00000051864	Tbc1d22a	BC023106|D15Ertd781e	TBC1 domain family, member 22a	protein-coding
mm_95234.1	chr11	44575215	44575218	+	1	NA	Intergenic	MT2B1|LTR|ERVL	-11101	NR_126460	75389	Mm.261421	NR_126460	ENSMUSG00000086501	4930597A21Rik	-	RIKEN cDNA 4930597A21 gene	ncRNA
mm_118297.1	chr13	113079149	113079155	-	1	NA	intron (NM_001281487, intron 7 of 11)	intron (NM_001281487, intron 7 of 11)	21829	NM_010370	14938	Mm.15510	NM_010370	ENSMUSG00000023132	Gzma	AW494114|Ctla-3|Ctla3|Hf|Hf1|SE1|TSP-1|TSP1	granzyme A	protein-coding
mm_56504.1	chr6	99339101	99339102	-	1	NA	intron (NM_001347345, intron 2 of 19)	intron (NM_001347345, intron 2 of 19)	-72586	NM_001197321	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_139271.1	chr17	48089661	48089686	+	1	NA	promoter-TSS (NM_026625)	promoter-TSS (NM_026625)	41	NM_026625	68224	Mm.138490	NM_026625	ENSMUSG00000021545	1700067P10Rik	-	RIKEN cDNA 1700067P10 gene	protein-coding
mm_165234.1	chr2	58830664	58830670	+	1	NA	intron (NM_001001178, intron 11 of 13)	RMER17C|LTR|ERVK	75483	NM_029692	76654	Mm.200370	NM_029692	ENSMUSG00000026839	Upp2	1700124F02Rik|AI266885|UDRPASE2|UP2|UPASE2	uridine phosphorylase 2	protein-coding
mm_162384.1	chr1	74249122	74249132	+	1	NA	intron (NM_029711, intron 3 of 9)	AmnSINE1|SINE|Deu	12577	NM_029711	76709	Mm.337038	NM_029711	ENSMUSG00000006304	Arpc2	2210023N03Rik|34kDa|p34-Arc	actin related protein 2/3 complex, subunit 2	protein-coding
mm_112199.1	chr12	113425993	113426030	-	1	NA	Intergenic	Intergenic	-63554	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_17920.1	chr2	35442090	35442123	-	1	NA	intron (NM_001308300, intron 1 of 6)	intron (NM_001308300, intron 1 of 6)	19343	NM_001308299	14594	Mm.281124	NM_010283	ENSMUSG00000035778	Ggta1	AW108479|GALT|Gal|Ggta|Ggta-1|alpha Gal|alpha3GalT	glycoprotein galactosyltransferase alpha 1, 3	protein-coding
mm_825.1	chr1	50927498	50927506	+	1	NA	promoter-TSS (NM_019790)	promoter-TSS (NM_019790)	-21	NM_019790	56363	Mm.245154	NM_019790	ENSMUSG00000026109	Tmeff2	4832418D20Rik|7630402F16Rik|TR-2	transmembrane protein with EGF-like and two follistatin-like domains 2	protein-coding
mm_70669.1	chr8	14889028	14889075	+	1	NA	5' UTR (NM_012000, exon 1 of 3)	5' UTR (NM_012000, exon 1 of 3)	515	NM_012000	26889	Mm.254027	NM_012000	ENSMUSG00000026317	Cln8	mnd	ceroid-lipofuscinosis, neuronal 8	protein-coding
mm_34112.1	chr4	139194087	139194133	+	1	NA	promoter-TSS (NM_001271405)	promoter-TSS (NM_001271405)	-1	NM_001271405	12345	Mm.2945	NM_009798	ENSMUSG00000028745	Capzb	1700120C01Rik|AI325129|CPB1|CPB2|CPbeat2|CPbeta1|CPbeta2|Cappb1	capping protein (actin filament) muscle Z-line, beta	protein-coding
mm_72886.1	chr8	89053203	89053252	+	1	NA	Intergenic	RLTR20B3|LTR|ERVK	-9065	NM_021390	58198	Mm.214361	NM_021390	ENSMUSG00000031665	Sall1	Msal-3	sal-like 1 (Drosophila)	protein-coding
mm_26403.1	chr3	142605183	142605194	+	1	NA	intron (NM_010259, intron 6 of 10)	intron (NM_010259, intron 6 of 10)	10341	NM_010259	14468	Mm.457978	NM_010259	ENSMUSG00000040264	Gbp2b	Gbp-1|Gbp1|Mag-1|Mpa-1|Mpa1	guanylate binding protein 2b	protein-coding
mm_165061.1	chr19	42177184	42177206	+	1	NA	intron (NM_177319, intron 2 of 12)	intron (NM_177319, intron 2 of 12)	6628	NM_001164531	319740	Mm.287359	NM_177319	ENSMUSG00000018820	Zfyve27	2210011N02Rik|9530077C24Rik|AI426636|AI593546|AI835681	zinc finger, FYVE domain containing 27	protein-coding
mm_66636.1	chr7	45526214	45526234	-	1	NA	promoter-TSS (NM_148927)	promoter-TSS (NM_148927)	44	NM_008654	17872	Mm.4048	NM_008654	ENSMUSG00000040435	Ppp1r15a	9630030H21|Gadd34|Myd116	protein phosphatase 1, regulatory (inhibitor) subunit 15A	protein-coding
mm_42137.1	chr5	111289204	111289214	+	1	NA	3' UTR (NM_001267622, exon 23 of 23)	3' UTR (NM_001267622, exon 23 of 23)	-41488	NM_001301644	56305	Mm.200516	NM_019640	ENSMUSG00000050017	Pitpnb	PI-TP-beta	phosphatidylinositol transfer protein, beta	protein-coding
mm_92114.1	chr10	63203900	63203920	-	1	NA	promoter-TSS (NM_182992)	promoter-TSS (NM_182992)	42	NM_182992	68802	Mm.259767	NM_182992	ENSMUSG00000020067	Mypn	1110056A04Rik|9830112J03|AI853556|mKIAA4170	myopalladin	protein-coding
mm_85856.1	chr9	110742578	110742591	-	1	NA	promoter-TSS (NM_001083936)	promoter-TSS (NM_001083936)	26	NM_001083936	19228	Mm.3542	NM_011199	ENSMUSG00000032492	Pth1r	PPR|Pthr|Pthr1	parathyroid hormone 1 receptor	protein-coding
mm_30106.1	chr3	138526968	138527002	-	1	NA	promoter-TSS (NM_001313980)	promoter-TSS (NM_001313980)	-283	NM_001313980	13684	Mm.3941	NM_007917	ENSMUSG00000028156	Eif4e	EG668879|Eif4e-ps|If4e|eIF-4E	eukaryotic translation initiation factor 4E	protein-coding
mm_126452.1	chr15	80820423	80820434	+	1	NA	intron (NM_177124, intron 1 of 21)	intron (NM_177124, intron 1 of 21)	21818	NM_177124	213988	Mm.131328	NM_144812	ENSMUSG00000047888	Tnrc6b	2700090M07Rik|A730065C02Rik|AI848765|D230019K20Rik	trinucleotide repeat containing 6b	protein-coding
mm_38937.1	chr4	150196143	150196155	-	1	NA	intron (NM_009802, intron 3 of 7)	intron (NM_009802, intron 3 of 7)	4986	NM_009802	12353	Mm.232523	NM_009802	ENSMUSG00000028972	Car6	Ca6|DOC1	carbonic anhydrase 6	protein-coding
mm_109458.1	chr12	111166350	111166397	+	1	NA	promoter-TSS (NM_011632)	promoter-TSS (NM_011632)	3	NM_011632	22031	Mm.27431	NM_011632	ENSMUSG00000021277	Traf3	AI528849|CAP-1|CD40bp|CRAF1|LAP1|T-BAM|amn	TNF receptor-associated factor 3	protein-coding
mm_121831.1	chr14	20496730	20496736	-	1	NA	5' UTR (NM_029104, exon 1 of 7)	5' UTR (NM_029104, exon 1 of 7)	168	NM_029104	74843	Mm.295241	NM_029104	ENSMUSG00000021815	Mss51	4833444M15Rik|Zmynd17	MSS51 mitochondrial translational activator	protein-coding
mm_157147.1	chrX	9461804	9461826	-	1	NA	intron (NM_007807, intron 3 of 12)	intron (NM_007807, intron 3 of 12)	7509	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_162208.1	chrX	135993878	135993878	+	1	NA	promoter-TSS (NM_029823)	promoter-TSS (NM_029823)	58	NM_029823	76976	Mm.328305	NM_029823	ENSMUSG00000048040	Arxes2	2900062L11Rik|Spc22/23|Spcs3	adipocyte-related X-chromosome expressed sequence 2	protein-coding
mm_81765.1	chr9	114401140	114401155	+	1	NA	promoter-TSS (NM_009752)	promoter-TSS (NM_009752)	52	NM_001200002	100504715	Mm.290516	NM_001200002	ENSMUSG00000079260	Tmppe	-	transmembrane protein with metallophosphoesterase domain	protein-coding
mm_172955.1	chr9	88482059	88482062	-	1	NA	5' UTR (NM_001284328, exon 1 of 12)	5' UTR (NM_001284328, exon 1 of 12)	337	NM_019666	56403	Mm.260545	NM_019666	ENSMUSG00000032423	Syncrip	2610109K23Rik|4632417O19Rik|GRY-RBP|Nsap1|Nsap1l|hnRNP Q|pp68	synaptotagmin binding, cytoplasmic RNA interacting protein	protein-coding
mm_117548.1	chr13	83987842	83987863	-	1	NA	Intergenic	Intergenic	76922	NR_131220	553095	Mm.39702	NR_131220	ENSMUSG00000098087	Gm17750	-	predicted gene, 17750	ncRNA
mm_129859.1	chr15	83313509	83313523	-	1	NA	exon (NM_025445, exon 11 of 16)	exon (NM_025445, exon 11 of 16)	36731	NM_025445	66251	Mm.258910	NM_025445	ENSMUSG00000054277	Arfgap3	0610009H19Rik|1810004P07Rik|1810035F16Rik|9130416J18Rik|Arfgap1	ADP-ribosylation factor GTPase activating protein 3	protein-coding
mm_94271.1	chr11	3649199	3649295	+	1	NA	promoter-TSS (NM_001159288)	promoter-TSS (NM_001159288)	-247	NM_001159288	74522	Mm.139127	NM_198162	ENSMUSG00000034543	Morc2a	8430403M08Rik|Zcwcc1	microrchidia 2A	protein-coding
mm_110790.1	chr12	72084714	72084745	-	1	NA	exon (NM_026038, exon 1 of 5)	exon (NM_026038, exon 1 of 5)	584	NM_026038	67217	Mm.286120	NM_026038	ENSMUSG00000019718	L3hypdh	2810055F11Rik	L-3-hydroxyproline dehydratase (trans-)	protein-coding
mm_64931.1	chr7	16286011	16286034	-	1	NA	intron (NM_001136471, intron 1 of 13)	intron (NM_001136471, intron 1 of 13)	773	NM_001136471	243846	Mm.482401	NM_172297	ENSMUSG00000041375	Ccdc9	2600011L02Rik	coiled-coil domain containing 9	protein-coding
mm_122734.1	chr14	52417307	52417307	-	1	NA	Intergenic	Intergenic	-6380	NM_146431	258423	Mm.377492	NM_146431	ENSMUSG00000063106	Olfr1510	MOR223-6	olfactory receptor 1510	protein-coding
mm_8445.1	chr1	152871187	152871230	-	1	NA	intron (NM_001005507, intron 1 of 21)	intron (NM_001005507, intron 1 of 21)	6960	NM_001160257	226517	Mm.270775	NM_001005507	ENSMUSG00000042772	Smg7	9430023P16Rik|mKIAA0250	Smg-7 homolog, nonsense mediated mRNA decay factor (C. elegans)	protein-coding
mm_4181.1	chr1	171159548	171159559	+	1	NA	exon (NM_008623, exon 6 of 8)	exon (NM_008623, exon 6 of 8)	4035	NM_001315500	17528	Mm.9986	NM_008623	ENSMUSG00000056569	Mpz	Mpp|P-zero|P0	myelin protein zero	protein-coding
mm_134486.1	chr16	18626694	18626702	-	1	NA	intron (NM_213614, intron 2 of 11)	CpG	3240	NM_213614	18951	Mm.20365	NM_213614	ENSMUSG00000072214	Sept5	Cdcrel-1|Cdcrel1|Pnutl1	septin 5	protein-coding
mm_129321.1	chr15	77766830	77766861	-	1	NA	exon (NM_022410, exon 34 of 41)	exon (NM_022410, exon 34 of 41)	-11616	NM_001081970	239552	Mm.125650	NM_001081970	ENSMUSG00000056656	Apol8	9830006J20Rik|APOL-II|Apol2	apolipoprotein L 8	protein-coding
mm_16138.1	chr2	170527601	170527619	+	1	NA	Intergenic	Intergenic	-15683	NR_040367	100502946	Mm.421284	NR_040367	ENSMUSG00000085495	Gm16796	-	predicted gene, 16796	ncRNA
mm_921.1	chr1	55131238	55131249	+	1	NA	promoter-TSS (NM_025283)	promoter-TSS (NM_025283)	-2	NM_001310585	19070	Mm.291037	NM_025283	ENSMUSG00000025979	Mob4	2610109B12Rik|Mobkl3|Phocn|Prei3	MOB family member 4, phocein	protein-coding
mm_155909.1	chrX	101794628	101794642	+	1	NA	Intergenic	CpG	-54750	NM_001163610	100042480	Mm.232	NM_001163610	ENSMUSG00000079481	Nhsl2	1110062M06Rik|6430511F03|AI225852|AW488865|EG621083|ENSMUSG00000073037|Gm10456	NHS-like 2	protein-coding
mm_97661.1	chr11	79591121	79591224	+	1	NA	promoter-TSS (NM_175543)	promoter-TSS (NM_175543)	-40	NM_175543	268451	Mm.130656	NM_175543	ENSMUSG00000017639	Rab11fip4	A730072L08Rik|RAB11-FIP4|mKIAA1821	RAB11 family interacting protein 4 (class II)	protein-coding
mm_69938.1	chr7	142095267	142095306	-	1	NA	promoter-TSS (NM_008748)	promoter-TSS (NM_008748)	-2	NM_008748	18218	Mm.39725	NM_008748	ENSMUSG00000037887	Dusp8	5530400B01Rik|AI593498|Nttp1	dual specificity phosphatase 8	protein-coding
mm_37313.1	chr4	119320497	119320516	-	1	NA	promoter-TSS (NM_001110130)	promoter-TSS (NM_001110130)	17	NM_001110129	66101	Mm.304080	NM_028677	ENSMUSG00000060288	Ppih	1100001J08Rik|2010111B15Rik|4833408F11Rik|AI464484|CYP-20|CYPH|D4Wsu43e	peptidyl prolyl isomerase H	protein-coding
mm_47663.1	chr5	125849898	125849904	-	1	NA	Intergenic	Intergenic	317483	NM_001190352	208151	Mm.40397	NM_001190352	ENSMUSG00000070498	Tmem132b	AK220418|mKIAA1786	transmembrane protein 132B	protein-coding
mm_172301.1	chr7	104288012	104288019	-	1	NA	promoter-TSS (NM_001310602)	promoter-TSS (NM_001310602)	91	NM_001310602	667823	Mm.482375	NM_001310602	ENSMUSG00000060441	Trim5	EG667823|Gm8833	tripartite motif-containing 5	protein-coding
mm_163430.1	chr12	84085053	84085055	+	1	NA	Intergenic	Intergenic	-15600	NM_172580	217700	Mm.49245	NM_172580	ENSMUSG00000043487	Acot6	4632408A20Rik|A330054B07|BE688602	acyl-CoA thioesterase 6	protein-coding
mm_18591.1	chr2	66674851	66674855	-	1	NA	3' UTR (NM_009135, exon 25 of 25)	3' UTR (NM_009135, exon 25 of 25)	-39891	NM_001290675	20274	Mm.440889	NM_018852	ENSMUSG00000075316	Scn9a	Nav1.7|PN1|mKIAA4197	sodium channel, voltage-gated, type IX, alpha	protein-coding
mm_171220.1	chr3	59767257	59767258	+	1	NA	Intergenic	L1Md_F3|LINE|L1	37471	NM_001101531	433597	Mm.297801	NM_001101531	ENSMUSG00000090527	Gm5538	-	predicted gene 5538	protein-coding
mm_143915.1	chr17	85615048	85615058	-	1	NA	intron (NR_038084, intron 2 of 3)	CpG	3343	NR_038084	100043902	Mm.150838	NR_015385	ENSMUSG00000093460	Six3os1	D17Mgi26|E130112H22Rik|Rncr1|Six3os	SIX homeobox 3, opposite strand 1	ncRNA
mm_8100.1	chr1	135848849	135848853	-	1	NA	exon (NM_001130176, exon 8 of 13)	exon (NM_001130176, exon 8 of 13)	7990	NM_001130176	21956	Mm.247470	NM_011619	ENSMUSG00000026414	Tnnt2	Tnt|cTnT	troponin T2, cardiac	protein-coding
mm_131101.1	chr16	5007284	5007293	+	1	NA	promoter-TSS (NM_001253803)	promoter-TSS (NM_001253803)	0	NM_001253803	432995	Mm.271618	NM_001253796	ENSMUSG00000096215	Smim22	EG432995|Gm5480	small integral membrane protein 22	protein-coding
mm_100282.1	chr11	117797727	117797748	+	1	NA	promoter-TSS (NM_029964)	promoter-TSS (NM_029964)	77	NM_029964	77727	Mm.159981	NM_029964	ENSMUSG00000025573	6030468B19Rik	-	RIKEN cDNA 6030468B19 gene	protein-coding
mm_17472.1	chr2	28559854	28559862	-	1	NA	exon (NM_009885, exon 5 of 11)	exon (NM_009885, exon 5 of 11)	3545	NM_009885	12613	Mm.236017	NM_009885	ENSMUSG00000026818	Cel	1810036E18Rik|BAL	carboxyl ester lipase	protein-coding
mm_151184.1	chr19	53390882	53390930	+	1	NA	promoter-TSS (NM_172429)	promoter-TSS (NM_172429)	-333	NM_172429	76479	Mm.313687	NM_172429	ENSMUSG00000025024	Smndc1	2410004J23Rik|4933440I19Rik	survival motor neuron domain containing 1	protein-coding
mm_108337.1	chr12	80168289	80168331	+	1	NA	3' UTR (NM_134156, exon 21 of 21)	3' UTR (NM_134156, exon 21 of 21)	-35466	NR_033514	69548	Mm.269712	NR_033514	ENSMUSG00000097729	2310015A10Rik	5330419I17Rik	RIKEN cDNA 2310015A10 gene	ncRNA
mm_91107.1	chr10	19122340	19122357	-	1	NA	Intergenic	Intergenic	-19401	NR_038021	100504265	Mm.383417	NR_038021		Gm20139	-	predicted gene, 20139	ncRNA
mm_45403.1	chr5	66173052	66173058	-	1	NA	intron (NR_040695, intron 2 of 2)	MTD|LTR|ERVL-MaLR	18280	NR_040695	73639	Mm.48851	NR_040695	ENSMUSG00000107014	1700126H18Rik	-	RIKEN cDNA 1700126H18 gene	ncRNA
mm_81542.1	chr9	110245422	110245491	+	1	NA	5' UTR (NM_013884, exon 1 of 5)	5' UTR (NM_013884, exon 1 of 5)	1673	NM_001166273	29873	Mm.38496	NM_013884	ENSMUSG00000032482	Cspg5	Caleb|Ngc	chondroitin sulfate proteoglycan 5	protein-coding
mm_66681.1	chr7	45814249	45814276	-	1	NA	promoter-TSS (NM_001112701)	promoter-TSS (NM_001112701)	54	NM_011181	19158	Mm.272130	NM_011181	ENSMUSG00000003269	Cyth2	ARNO|CLM2|Pscd2	cytohesin 2	protein-coding
mm_162590.1	chr1	181151006	181151016	+	1	NA	promoter-TSS (NM_030131)	promoter-TSS (NM_030131)	80	NM_030131	98417	Mm.38229	NM_030131	ENSMUSG00000062169	Cnih4	AI647760|AW050376|CNIH-4|D530030D03Rik|E430023H19Rik|HSPC163	cornichon family AMPA receptor auxiliary protein 4	protein-coding
mm_20240.1	chr2	126460637	126460642	-	1	NA	intron (NM_001080944, intron 4 of 27)	intron (NM_001080944, intron 4 of 27)	30914	NM_001080944	241633	Mm.222235	NM_001080944	ENSMUSG00000060131	Atp8b4	A530043E15|Im	ATPase, class I, type 8B, member 4	protein-coding
mm_87330.1	chr10	42901651	42901669	+	1	NA	intron (NM_172938, intron 1 of 8)	intron (NM_172938, intron 1 of 8)	41148	NM_172938	268297	Mm.98731	NM_172938	ENSMUSG00000044770	Scml4	9330161D17|mFLJ00197	sex comb on midleg-like 4 (Drosophila)	protein-coding
mm_73665.1	chr8	111043295	111043313	+	1	NA	exon (NM_146217, exon 8 of 21)	exon (NM_146217, exon 8 of 21)	9462	NM_146217	234734	Mm.24174	NM_146217	ENSMUSG00000031960	Aars	AI316495|C76919|sti	alanyl-tRNA synthetase	protein-coding
mm_148862.1	chr19	6401676	6401715	+	1	NA	intron (NM_011242, intron 1 of 16)	intron (NM_011242, intron 1 of 16)	1112	NM_011242	19395	Mm.77017	NM_011242	ENSMUSG00000032946	Rasgrp2	CDC25L|Caldaggef1	RAS, guanyl releasing protein 2	protein-coding
mm_165231.1	chr2	58239000	58239000	+	1	NA	Intergenic	IAPEY_LTR|LTR|ERVK	-37779	NR_040365	100502932	Mm.417207	NR_040365	ENSMUSG00000086995	Gm13544	OTTMUSG00000012672	predicted gene 13544	ncRNA
mm_96864.1	chr11	70130393	70130411	+	1	NA	promoter-TSS (NM_145137)	promoter-TSS (NM_145137)	45	NM_145137	216864	Mm.222465	NM_145137	ENSMUSG00000040950	Mgl2	CD301b	macrophage galactose N-acetyl-galactosamine specific lectin 2	protein-coding
mm_21667.1	chr2	164425443	164425465	-	1	NA	3' UTR (NM_011521, exon 5 of 5)	3' UTR (NM_011521, exon 5 of 5)	17734	NM_011521	20971	Mm.3815	NM_011521	ENSMUSG00000017009	Sdc4	AA959608|AW108331|S4|Synd4|ryudocan|syndecan-4	syndecan 4	protein-coding
mm_115859.1	chr13	21401858	21401863	-	1	NA	intron (NM_001145778, intron 1 of 5)	intron (NM_001145778, intron 1 of 5)	895	NM_001145778	72739	Mm.296071	NM_023685	ENSMUSG00000021327	Zkscan3	2810435N07Rik|AA408594|AI132359|Skz1|Zf47|Zfp-47|Zfp306|Zfp307|mszf35	zinc finger with KRAB and SCAN domains 3	protein-coding
mm_154617.1	chrX	7697165	7697187	+	1	NA	promoter-TSS (NM_173747)	promoter-TSS (NM_173747)	42	NM_173747	209416	Mm.148753	NM_173747	ENSMUSG00000031148	Gpkow	4432411B18|DXErtd697e|DXImx41e|T54	G patch domain and KOW motifs	protein-coding
mm_70718.1	chr8	15326792	15326793	+	1	NA	Intergenic	RMER17A2|LTR|ERVK	269139	NM_008664	17930	Mm.272115	NM_008664	ENSMUSG00000031461	Myom2	AW146149	myomesin 2	protein-coding
mm_96891.1	chr11	70437253	70437259	+	1	NA	promoter-TSS (NR_106064)	promoter-TSS (NR_106064)	-999	NR_106064	102465670		NR_106064	ENSMUSG00000099109	Mir7115	Gm27902|mmu-mir-7115	microRNA 7115	ncRNA
mm_129899.1	chr15	83724980	83725044	-	1	NA	promoter-TSS (NM_001271473)	promoter-TSS (NM_001271473)	27	NM_001271472	64706	Mm.40393	NM_022723	ENSMUSG00000016763	Scube1	7330410C13Rik|A630023E24Rik	signal peptide, CUB domain, EGF-like 1	protein-coding
mm_169820.1	chr16	21694616	21694616	-	1	NA	promoter-TSS (NM_001001881)	promoter-TSS (NM_001001881)	49	NM_001001881	72190	Mm.131606	NM_001001881	ENSMUSG00000043391	2510009E07Rik	AI194952	RIKEN cDNA 2510009E07 gene	protein-coding
mm_85397.1	chr9	103347721	103347724	-	1	NA	intron (NM_176979, intron 27 of 27)	B3A|SINE|B2	17257	NM_001134427	321022	Mm.261025	NM_175565	ENSMUSG00000032803	Cdv3	2510010F10Rik|C230084J24Rik|C79446|TPP36	carnitine deficiency-associated gene expressed in ventricle 3	protein-coding
mm_113733.1	chr13	44197058	44197062	+	1	NA	intron (NR_045088, intron 3 of 3)	intron (NR_045088, intron 3 of 3)	19427	NR_045088	100503592	Mm.184925	NR_045088		A330076C08Rik	-	RIKEN cDNA A330076C08 gene	ncRNA
mm_14497.1	chr2	132021285	132021297	+	1	NA	intron (NM_175445, intron 1 of 10)	intron (NM_175445, intron 1 of 10)	8697	NM_175445	215653	Mm.204737	NM_175445	ENSMUSG00000027339	Rassf2	3830431H01Rik|9030412M04Rik|AI852669|AW495050	Ras association (RalGDS/AF-6) domain family member 2	protein-coding
mm_4026.1	chr1	165767161	165767187	+	1	NA	intron (NM_011804, intron 1 of 3)	intron (NM_011804, intron 1 of 3)	3394	NM_011804	433375	Mm.294885	NM_011804	ENSMUSG00000040713	Creg1	AA755314|Creg	cellular repressor of E1A-stimulated genes 1	protein-coding
mm_127095.1	chr15	97788114	97788119	+	1	NA	intron (NM_026353, intron 1 of 2)	tRNA-Ala-GCY_|tRNA|tRNA	3751	NM_026353	67739	Mm.28955	NM_026353	ENSMUSG00000081534	Slc48a1	4930570C03Rik	solute carrier family 48 (heme transporter), member 1	protein-coding
mm_57301.1	chr6	124542282	124542307	-	1	NA	promoter-TSS (NM_144938)	promoter-TSS (NM_144938)	27	NM_144938	50908	Mm.219527	NM_144938	ENSMUSG00000038521	C1s1	AA959438|AI255193|AI327365|C1s|C1sa	complement component 1, s subcomponent 1	protein-coding
mm_151155.1	chr19	53185711	53185719	+	1	NA	intron (NM_013758, intron 1 of 15)	intron (NM_013758, intron 1 of 15)	41718	NM_013758	27360	Mm.426080	NM_013758	ENSMUSG00000025026	Add3	AI463285|R75380	adducin 3 (gamma)	protein-coding
mm_41878.1	chr5	105198388	105198410	+	1	NA	Intergenic	Intergenic	41134	NM_001039646	626578	Mm.275893	NM_001039646	ENSMUSG00000105096	Gbp10	-	guanylate-binding protein 10	protein-coding
mm_16926.1	chr2	13793032	13793036	-	1	NA	intron (NM_145838, intron 1 of 7)	intron (NM_145838, intron 1 of 7)	486	NM_145838	241230	Mm.330004	NM_145838	ENSMUSG00000003418	St8sia6	1700007J08Rik|AI314453|AI875066|ST8SiaVI|Siat8f	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 6	protein-coding
mm_79164.1	chr9	47832939	47832944	+	1	NA	intron (NM_207675, intron 9 of 10)	intron (NM_207675, intron 9 of 10)	-14733	NR_046048	100038460	Mm.447649	NR_046048		Gm10677	ENSMUSG00000074363	predicted gene 10677	ncRNA
mm_69527.1	chr7	135652149	135652173	-	1	NA	exon (NM_011212, exon 5 of 21)	exon (NM_011212, exon 5 of 21)	153	NR_015548	67765	Mm.445272	NR_015548	ENSMUSG00000097471	5830432E09Rik	-	RIKEN cDNA 5830432E09 gene	ncRNA
mm_121062.1	chr14	88636029	88636039	+	1	NA	Intergenic	L1_Mur3|LINE|L1	-164638	NM_178685	219257	Mm.128861	NM_178685	ENSMUSG00000050505	Pcdh20	C630015B17Rik|Pcdh13	protocadherin 20	protein-coding
mm_22719.1	chr3	19311482	19311495	+	1	NA	promoter-TSS (NM_001122759)	promoter-TSS (NM_001122759)	-166	NM_001122759	18583	Mm.355614	NM_008802	ENSMUSG00000069094	Pde7a	AU015378|AW047537	phosphodiesterase 7A	protein-coding
mm_170759.1	chr2	158468381	158468402	-	1	NA	intron (NM_001291137, intron 23 of 30)	Lx4B|LINE|L1	-34221	NM_145635	246747	Mm.28800	NM_145635	ENSMUSG00000044405	Adig	SMAF-1|Smaf1	adipogenin	protein-coding
mm_151973.1	chr19	5826672	5826746	-	1	NA	non-coding (NR_131212, exon 1 of 1)	non-coding (NR_131212, exon 1 of 1)	18769	NR_131212	66961	Mm.281895	NR_003513	ENSMUSG00000092274	Neat1	2310043N10Rik|VINC	nuclear paraspeckle assembly transcript 1 (non-protein coding)	ncRNA
mm_171139.1	chr3	150073611	150073620	-	1	NA	Intergenic	Intergenic	798878	NR_040591	381482	Mm.393866	NR_040591		Gm1653	-	predicted gene 1653	ncRNA
mm_16612.1	chr2	5306490	5306493	-	1	NA	intron (NM_001290374, intron 7 of 9)	intron (NM_001290374, intron 7 of 9)	-72899	NR_030601	100124465		NR_030601	ENSMUSG00000078031	Mir466d	Mirn466d	microRNA 466d	ncRNA
mm_126104.1	chr15	78246409	78246440	+	1	NA	intron (NM_008677, intron 1 of 9)	intron (NM_008677, intron 1 of 9)	1613	NM_008677	17972	Mm.2068	NM_008677	ENSMUSG00000071715	Ncf4	AI451400|p40phox	neutrophil cytosolic factor 4	protein-coding
mm_167064.1	chr7	96210251	96210259	+	1	NA	promoter-TSS (NM_011858)	promoter-TSS (NM_011858)	-382	NM_011858	23966	Mm.254610	NM_011858	ENSMUSG00000048078	Tenm4	Doc4|ELM2|Odz4|R75022|Ten-m4|l(7)-3Rn|l7Rn3|mKIAA1302	teneurin transmembrane protein 4	protein-coding
mm_65697.1	chr7	28377075	28377091	-	1	NA	3' UTR (NM_011756, exon 2 of 2)	3' UTR (NM_011756, exon 2 of 2)	2145	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_105710.1	chr11	108321585	108321588	-	1	NA	intron (NM_011101, intron 2 of 16)	intron (NM_011101, intron 2 of 16)	22302	NM_011101	18750	Mm.222178	NM_011101	ENSMUSG00000050965	Prkca	AI875142|Pkca	protein kinase C, alpha	protein-coding
mm_117277.1	chr13	65112905	65112962	-	1	NA	promoter-TSS (NM_001083901)	promoter-TSS (NM_001083901)	49	NM_001083901	66631	Mm.239196	NM_133680	ENSMUSG00000038212	Mfsd14b	5730414C17Rik|AU045608|AW539692|Hiatl1	major facilitator superfamily domain containing 14B	protein-coding
mm_120910.1	chr14	76251476	76251486	+	1	NA	Intergenic	Intergenic	140590	NM_013745	27275	Mm.21138	NM_013745	ENSMUSG00000022009	Nufip1	Nufip	nuclear fragile X mental retardation protein interacting protein 1	protein-coding
mm_116109.1	chr13	28950022	28950030	-	1	NA	TTS (NM_009238)	TTS (NM_009238)	3656	NM_009238	20677	Mm.240627	NM_009238	ENSMUSG00000076431	Sox4	AA682046|Sox-4	SRY (sex determining region Y)-box 4	protein-coding
mm_151764.1	chr19	5205805	5205813	-	1	NA	intron (NM_153129, intron 1 of 23)	intron (NM_153129, intron 1 of 23)	67310	NM_153129	107975	Mm.234923	NM_153129	ENSMUSG00000024855	Pacs1	AI325977	phosphofurin acidic cluster sorting protein 1	protein-coding
mm_86593.1	chr10	13129826	13129856	+	1	NA	3' UTR (NM_009538, exon 6 of 6)	3' UTR (NM_009538, exon 6 of 6)	38996	NR_131912	338438		NR_131912		Hymai	-	hydatidiform mole associated and imprinted transcript	ncRNA
mm_30867.1	chr4	32015544	32015552	+	1	NA	intron (NM_172688, intron 13 of 15)	intron (NM_172688, intron 13 of 15)	51441	NM_172688	26409	Mm.258589	NM_009316	ENSMUSG00000028284	Map3k7	B430101B05|C87327|Tak1	mitogen-activated protein kinase kinase kinase 7	protein-coding
mm_44494.1	chr5	23684584	23684586	-	1	NA	Intergenic	MLT1F1|LTR|ERVL-MaLR	28082	NR_038090	433855	Mm.205125	NR_015554	ENSMUSG00000105987	AI506816	-	expressed sequence AI506816	ncRNA
mm_145077.1	chr18	42275398	42275411	+	1	NA	promoter-TSS (NM_172626)	promoter-TSS (NM_172626)	51	NM_172626	225432	Mm.329400	NM_172626	ENSMUSG00000024491	Rbm27	A730010I06|AI043120|Psc1|mKIAA1311	RNA binding motif protein 27	protein-coding
mm_167055.1	chr7	89338419	89338422	+	1	NA	intron (NM_028343, intron 1 of 14)	intron (NM_028343, intron 1 of 14)	367	NM_028343	72759	Mm.208477	NM_028343	ENSMUSG00000039428	Tmem135	2810439K08Rik|AW319712|PMP52	transmembrane protein 135	protein-coding
mm_102257.1	chr11	55310705	55310712	-	1	NA	exon (NM_001029988, exon 1 of 23)	exon (NM_001029988, exon 1 of 23)	1549	NM_001029988	245827	Mm.339363	NM_001029988	ENSMUSG00000055333	Fat2	EMI2|Fath2|Gm523|mKIAA0811	FAT atypical cadherin 2	protein-coding
mm_71390.1	chr8	46152635	46152648	+	1	NA	Intergenic	Intergenic	-16915	NM_025747	66756	Mm.133623	NM_025747	ENSMUSG00000031631	Cfap97	1110068E21Rik|4933411K20Rik|AW049273|Kiaa1430|mKIAA1430	cilia and flagella associated protein 97	protein-coding
mm_122023.1	chr14	28909053	28909056	-	1	NA	intron (NM_009785, intron 35 of 37)	intron (NM_009785, intron 35 of 37)	-109154	NM_176920	319476	Mm.95780	NM_176920	ENSMUSG00000045776	Lrtm1	A930016D02Rik	leucine-rich repeats and transmembrane domains 1	protein-coding
mm_2999.1	chr1	133245889	133245905	+	1	NA	promoter-TSS (NM_001160268)	promoter-TSS (NM_001160268)	-200	NM_001160268	240753	Mm.253559	NM_182930	ENSMUSG00000041757	Plekha6	9530028L01Rik|AU042621|Pepp3	pleckstrin homology domain containing, family A member 6	protein-coding
mm_74295.1	chr8	125995376	125995404	+	1	NA	5' UTR (NM_008430, exon 1 of 3)	5' UTR (NM_008430, exon 1 of 3)	288	NM_008430	16525	Mm.10800	NM_008430	ENSMUSG00000033998	Kcnk1	AI788889|TWIK-1	potassium channel, subfamily K, member 1	protein-coding
mm_23470.1	chr3	60479879	60479885	+	1	NA	intron (NM_001253713, intron 2 of 9)	intron (NM_001253713, intron 2 of 9)	7052	NM_001253713	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_48770.1	chr5	148400014	148400038	-	1	NA	promoter-TSS (NM_007513)	promoter-TSS (NM_007513)	-122	NM_007513	11987	Mm.275489	NM_007513	ENSMUSG00000041313	Slc7a1	4831426K01Rik|AI447493|Atrc-1|Atrc1|Cat1|Rec-1|Rev-1|mCAT-1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 1	protein-coding
mm_83574.1	chr9	47530092	47530099	-	1	NA	promoter-TSS (NM_018770)	promoter-TSS (NM_018770)	-75	NM_001310841	54725	Mm.234832	NM_018770	ENSMUSG00000032076	Cadm1	2900073G06Rik|3100001I08Rik|AI987920|Bl2|Igsf4|Igsf4a|Necl2|RA175|RA175A|RA175B|RA175C|RA175N|ST17|SgIGSF|SynCam|Tslc1	cell adhesion molecule 1	protein-coding
mm_160039.1	chr6	135310339	135310339	-	1	NA	promoter-TSS (NM_029595)	promoter-TSS (NM_029595)	45	NM_029595	76400	Mm.293018	NM_029595	ENSMUSG00000047104	Pbp2	1700023A18Rik|AI326308|Pebp-2|Pebp2	phosphatidylethanolamine binding protein 2	protein-coding
mm_154778.1	chrX	12888210	12888256	+	1	NA	Intergenic	Intergenic	-48640	NM_001272033	245350	Mm.302695	NM_001272033		AA414768	OTTMUSG00000017000	expressed sequence AA414768	protein-coding
mm_128302.1	chr15	37474062	37474071	-	1	NA	intron (NM_001170866, intron 4 of 6)	intron (NM_001170866, intron 4 of 6)	-14684	NM_001170868	52589	Mm.283370	NM_134094	ENSMUSG00000051359	Ncald	AI848120|D030020D09Rik|D15Ertd412e	neurocalcin delta	protein-coding
mm_40789.1	chr5	67450514	67450550	+	1	NA	Intergenic	Intergenic	-13366	NR_110363	320479	Mm.387187	NR_015582	ENSMUSG00000107385	C330024D21Rik	-	RIKEN cDNA C330024D21 gene	ncRNA
mm_143870.1	chr17	84186914	84186932	-	1	NA	exon (NM_001001806, exon 2 of 2)	exon (NM_001001806, exon 2 of 2)	1024	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_125526.1	chr15	57839599	57839604	+	1	NA	3' UTR (NM_199449, exon 4 of 4)	3' UTR (NM_199449, exon 4 of 4)	52817	NM_024207	67819	Mm.289387	NM_024207	ENSMUSG00000022365	Derl1	1110021N07Rik|AI195141|AW551338|Derlin-1	Der1-like domain family, member 1	protein-coding
mm_93992.1	chr10	127525847	127525860	-	1	NA	3' UTR (NM_183297, exon 2 of 2)	3' UTR (NM_183297, exon 2 of 2)	-3409	NM_028230	108037	Mm.29890	NM_028230	ENSMUSG00000025403	Shmt2	2700043D08Rik|AA408223|AA986903	serine hydroxymethyltransferase 2 (mitochondrial)	protein-coding
mm_159782.1	chr5	106638261	106638261	-	1	NA	exon (NM_026856, exon 3 of 7)	exon (NM_026856, exon 3 of 7)	58569	NM_026856	52397	Mm.249474	NM_026856	ENSMUSG00000049606	Zfp644	1110068L01Rik|AA408882|BM-005|D5Ertd689e|Zep-2	zinc finger protein 644	protein-coding
mm_135355.1	chr16	43889502	43889507	-	1	NA	promoter-TSS (NM_027801)	promoter-TSS (NM_027801)	172	NM_029128	106248	Mm.275354	NM_029128	ENSMUSG00000022704	Qtrtd1	3110012M05Rik|4930470H18Rik|AI648807|Qtrt2	queuine tRNA-ribosyltransferase domain containing 1	protein-coding
mm_90980.1	chr10	13553112	13553126	-	1	NA	promoter-TSS (NM_019961)	promoter-TSS (NM_019961)	23	NM_019961	56535	Mm.282711	NM_019961	ENSMUSG00000019809	Pex3	1700014F15Rik|2810027F19Rik|2900010N04Rik	peroxisomal biogenesis factor 3	protein-coding
mm_119812.1	chr14	54222839	54222850	+	1	NA	Intergenic	Intergenic	31085	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_12371.1	chr2	69821997	69822007	+	1	NA	promoter-TSS (NM_177784)	promoter-TSS (NM_177784)	-368	NM_177784	277396	Mm.138073	NM_177784	ENSMUSG00000042155	Klhl23	C130068N17Rik	kelch-like 23	protein-coding
mm_132176.1	chr16	32385099	32385113	+	1	NA	3' UTR (NM_177633, exon 11 of 11)	3' UTR (NM_177633, exon 11 of 11)	-15400	NM_001160402	277203	Mm.484240	NM_001160402	ENSMUSG00000079625	Tm4sf19	EG277203	transmembrane 4 L six family member 19	protein-coding
mm_60790.1	chr7	45567160	45567191	+	1	NA	TTS (NR_038166)	TTS (NR_038166)	-2978	NM_009737	12036	Mm.24210	NM_009737	ENSMUSG00000030826	Bcat2	Bcat-2|Eca40	branched chain aminotransferase 2, mitochondrial	protein-coding
mm_161404.1	chr14	122935985	122935985	-	1	NA	intron (NM_028651, intron 11 of 17)	intron (NM_028651, intron 11 of 17)	-22820	NM_145466	223267	Mm.379358	NM_145466	ENSMUSG00000041625	Ggact	A2ld1	gamma-glutamylamine cyclotransferase	protein-coding
mm_122300.1	chr14	34620710	34620740	-	1	NA	Intergenic	Intergenic	-20583	NM_013887	30044	Mm.272060	NM_013887	ENSMUSG00000021799	Opn4	1110007J02Rik|Gm533	opsin 4 (melanopsin)	protein-coding
mm_97390.1	chr11	77801292	77801321	+	1	NA	promoter-TSS (NM_001291215)	promoter-TSS (NM_001291215)	8	NM_001291215	360013	Mm.341248	NM_011586	ENSMUSG00000000631	Myo18a	MAJN|MyoPDZ|MysPDZ|SP-R210	myosin XVIIIA	protein-coding
mm_139869.1	chr17	70534576	70534585	+	1	NA	intron (NM_001347414, intron 1 of 10)	L1M2|LINE|L1	12470	NM_001128180	224997	Mm.311840	NM_027712	ENSMUSG00000003279	Dlgap1	4933422O14Rik|9630002F18|AI845682|AI848168|BB075781|D17Bwg0511e|GKAP/SAPAP|GKPA/SAPAP|Gkap|Sapap1|mKIAA4162	discs, large (Drosophila) homolog-associated protein 1	protein-coding
mm_71264.1	chr8	40918582	40918604	+	1	NA	3' UTR (NM_001044740, exon 12 of 12)	3' UTR (NM_001044740, exon 12 of 12)	-7640	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_28846.1	chr3	96727437	96727452	-	1	NA	promoter-TSS (NM_026406)	promoter-TSS (NM_026406)	-5	NM_028925	74414	Mm.276043	NM_028925	ENSMUSG00000028099	Polr3c	4933407E01Rik|RPC3|RPC62	polymerase (RNA) III (DNA directed) polypeptide C	protein-coding
mm_157853.1	chrX	74428912	74428922	-	1	NA	promoter-TSS (NM_178590)	promoter-TSS (NM_178590)	244	NM_008062	14381	Mm.27210	NM_008062	ENSMUSG00000031400	G6pdx	G28A|G6pd|Gpdx	glucose-6-phosphate dehydrogenase X-linked	protein-coding
mm_49325.1	chr6	21214574	21214600	+	1	NA	Intergenic	CpG	-1522	NM_019697	16508	Mm.425316	NM_019697	ENSMUSG00000060882	Kcnd2	AI839615|AW555701|Kv4.2|R75121|mKIAA1044	potassium voltage-gated channel, Shal-related family, member 2	protein-coding
mm_159679.1	chr5	3571504	3571504	+	1	NA	promoter-TSS (NM_029843)	promoter-TSS (NM_029843)	-212	NM_029843	77036	Mm.389069	NM_029843	ENSMUSG00000008307	1700109H08Rik	-	RIKEN cDNA 1700109H08 gene	protein-coding
mm_16258.1	chr2	173275494	173275504	+	1	NA	intron (NM_022995, intron 1 of 3)	intron (NM_022995, intron 1 of 3)	1034	NM_022995	65112	Mm.73682	NM_022995	ENSMUSG00000038400	Pmepa1	2210418I02Rik|AW455466|Erg1.2|N4wbp4|Stag1|Tmepai	prostate transmembrane protein, androgen induced 1	protein-coding
mm_56280.1	chr6	91233913	91233964	-	1	NA	exon (NM_001081437, exon 2 of 17)	exon (NM_001081437, exon 2 of 17)	21174	NM_007992	14115	Mm.249146	NM_007992	ENSMUSG00000064080	Fbln2	5730577E14Rik|FIBL-2	fibulin 2	protein-coding
mm_172105.1	chr6	3183269	3183269	+	1	NA	Intergenic	Intergenic	-105250	NR_036696	667335	Mm.380219	NR_036696	ENSMUSG00000106779	Gm8579	EG667335	spermatogenesis associated glutamate (E)-rich protein 4a pseudogene	pseudo
mm_159122.1	chr2	70038928	70038928	+	1	NA	promoter-TSS (NM_177376)	promoter-TSS (NM_177376)	-198	NM_177376	329421	Mm.99648	NM_177376	ENSMUSG00000042064	Myo3b	A430065P19Rik	myosin IIIB	protein-coding
mm_153475.1	chr19	41273756	41273768	-	1	NA	TTS (NM_031376)	TTS (NM_031376)	-9758	NM_133352	107358	Mm.246440	NM_133352	ENSMUSG00000025016	Tm9sf3	1810073M23Rik|2810031D16Rik|AI115521|AI413748|AW146116|AW549777|Smbp|mKIAA4036	transmembrane 9 superfamily member 3	protein-coding
mm_82950.1	chr9	35558523	35558548	-	1	NA	promoter-TSS (NM_013932)	promoter-TSS (NM_013932)	-65	NM_013932	30959	Mm.291723	NM_013932	ENSMUSG00000032101	Ddx25	AW047046|GRTH	DEAD (Asp-Glu-Ala-Asp) box polypeptide 25	protein-coding
mm_114528.1	chr13	73502886	73502888	+	1	NA	intron (NM_145376, intron 7 of 13)	intron (NM_145376, intron 7 of 13)	-33860	NM_010020	13162	Mm.41993	NM_010020	ENSMUSG00000021609	Slc6a3	DAT|Dat1	solute carrier family 6 (neurotransmitter transporter, dopamine), member 3	protein-coding
mm_63580.1	chr7	128118067	128118087	+	1	NA	3' UTR (NM_008401, exon 30 of 30)	3' UTR (NM_008401, exon 30 of 30)	-11491	NM_021334	16411	Mm.22378	NM_021334	ENSMUSG00000030789	Itgax	AI449405|Cd11c|Cr4|N418	integrin alpha X	protein-coding
mm_121009.1	chr14	79530693	79530707	+	1	NA	intron (NM_001286411, intron 1 of 8)	intron (NM_001286411, intron 1 of 8)	15026	NM_001286411	13709	Mm.20938	NM_007920	ENSMUSG00000036461	Elf1	Elf-1|Sts1|mElf-1|p70	E74-like factor 1	protein-coding
mm_156473.1	chrX	143664358	143664362	+	1	NA	intron (NM_008778, intron 1 of 14)	intron (NM_008778, intron 1 of 14)	-1385	NM_001195049	18481	Mm.40035	NM_008778	ENSMUSG00000031284	Pak3	PAK-3|Pak65alpha|Pak65beta|Stk4	p21 protein (Cdc42/Rac)-activated kinase 3	protein-coding
mm_5283.1	chr1	20618093	20618097	-	1	NA	promoter-TSS (NM_153179)	promoter-TSS (NM_153179)	-38	NM_153179	241035	Mm.249253	NM_153179	ENSMUSG00000043760	Pkhd1	AI118496|AI182499|FPC|Tigm1	polycystic kidney and hepatic disease 1	protein-coding
mm_161510.1	chr15	98437418	98437418	+	1	NA	promoter-TSS (NM_146457)	promoter-TSS (NM_146457)	-52	NM_146457	258449	Mm.324601	NM_146457	ENSMUSG00000063780	Olfr282	MOR160-2	olfactory receptor 282	protein-coding
mm_83251.1	chr9	42401565	42401579	-	1	NA	Intergenic	Intergenic	-1643	NM_001324548	21683	Mm.42209	NM_009347	ENSMUSG00000037705	Tecta	Tctna	tectorin alpha	protein-coding
mm_69616.1	chr7	137304596	137304615	-	1	NA	intron (NM_001113415, intron 6 of 15)	intron (NM_001113415, intron 6 of 15)	9840	NM_001113415	13593	Mm.258708	NM_010096	ENSMUSG00000010476	Ebf3	3110018A08Rik|O/E-2|mKIAA4201	early B cell factor 3	protein-coding
mm_145299.1	chr18	53320977	53320978	+	1	NA	intron (NM_029394, intron 1 of 6)	ORR1A2|LTR|ERVL-MaLR	75315	NM_029394	69226	Mm.32414	NM_029394	ENSMUSG00000024535	Snx24	2810011K15Rik|5730433I16Rik|AI451341	sorting nexing 24	protein-coding
mm_109150.1	chr12	107379057	107379057	+	1	NA	Intergenic	MER89|LTR|ERV1	356431	NR_045973	74968	Mm.359821	NR_045973	ENSMUSG00000085641	4930465M20Rik	4930431H15Rik	RIKEN cDNA 4930465M20 gene	ncRNA
mm_84686.1	chr9	72111756	72111817	-	1	NA	promoter-TSS (NM_011544)	promoter-TSS (NM_011544)	33	NM_011544	21406	Mm.171615	NM_011544	ENSMUSG00000032228	Tcf12	A130037E08Rik|ALF1|HEB|HEBAlt|HTF-4|HTF4|ME1|REB|bHLHb20	transcription factor 12	protein-coding
mm_15959.1	chr2	166003305	166003325	+	1	NA	intron (NM_008679, intron 1 of 22)	B3|SINE|B2	10678	NM_008679	17979	Mm.469663	NM_008679	ENSMUSG00000027678	Ncoa3	2010305B15Rik|AW321064|Actr|Aib1|KAT13B|Rac3|Src3|Tram-1|Tram1|bHLHe42|p/Cip|pCip	nuclear receptor coactivator 3	protein-coding
mm_28818.1	chr3	96263326	96263340	-	1	NA	promoter-TSS (NM_033596)	promoter-TSS (NM_033596)	-16	NM_033596	97122	Mm.227295	NM_033596	ENSMUSG00000091405	Hist2h4	H4|X04652	histone cluster 2, H4	protein-coding
mm_23442.1	chr3	59432147	59432176	+	1	NA	Intergenic	Intergenic	-87905	NM_001162884	242050	Mm.228086	NM_001162884	ENSMUSG00000036334	Igsf10	6530405F15Rik|9030224D03|AA409708|AA536958|AI414626|Adlican2|CMF608	immunoglobulin superfamily, member 10	protein-coding
mm_35119.1	chr4	11007523	11007533	-	1	NA	promoter-TSS (NM_175175)	promoter-TSS (NM_175175)	91	NM_175175	71801	Mm.34351	NM_175175	ENSMUSG00000049969	Plekhf2	1110070J07Rik|AA673237|ZFYVE18	pleckstrin homology domain containing, family F (with FYVE domain) member 2	protein-coding
mm_129648.1	chr15	80697602	80697616	-	1	NA	promoter-TSS (NR_045309)	promoter-TSS (NR_045309)	1	NR_045309	106059	Mm.442457	NR_045309		A430088P11Rik	-	RIKEN cDNA A430088P11 gene	ncRNA
mm_62024.1	chr7	91608983	91608986	+	1	NA	intron (NM_011807, intron 2 of 22)	(T)n|Simple_repeat|Simple_repeat	-453410	NM_001243046	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_56524.1	chr6	99521154	99521167	-	1	NA	promoter-TSS (NM_001347345)	promoter-TSS (NM_001347345)	-167	NM_001347345	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_149552.1	chr19	12625426	12625426	+	1	NA	intron (NM_001013762, intron 5 of 5)	intron (NM_001013762, intron 5 of 5)	-7882	NM_145935	107146	Mm.39974	NM_145935	ENSMUSG00000063683	Glyat	A330009E03Rik|ACGNAT|AI195249|AI315345|CAT|GAT	glycine-N-acyltransferase	protein-coding
mm_158848.1	chrX	169979230	169979253	-	1	NA	promoter-TSS (NR_029457)	promoter-TSS (NR_029457)	-324	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_161041.1	chr12	33302529	33302529	+	1	NA	promoter-TSS (NM_001033436)	promoter-TSS (NM_001033436)	14	NM_001033436	380753	Mm.41540	NM_028139	ENSMUSG00000020564	Atxn7l1	2810423G08Rik|Atxn7l4	ataxin 7-like 1	protein-coding
mm_75946.1	chr8	71592002	71592022	-	1	NA	promoter-TSS (NM_025396)	promoter-TSS (NM_025396)	-172	NM_025396	66171	Mm.282284	NM_025396	ENSMUSG00000031807	Pgls	1110030K05Rik|AI447866|Plgs	6-phosphogluconolactonase	protein-coding
mm_139567.1	chr17	56997333	56997365	+	1	NA	promoter-TSS (NM_025538)	promoter-TSS (NM_025538)	10	NM_027372	66400	Mm.196150	NM_025538	ENSMUSG00000002661	Alkbh7	2310045B01Rik|2510008E23Rik|Abh7|Spata11	alkB homolog 7	protein-coding
mm_37068.1	chr4	116144513	116144528	-	1	NA	promoter-TSS (NM_026547)	promoter-TSS (NM_026547)	96	NM_026547	68075	Mm.132803	NM_026547	ENSMUSG00000028701	Lurap1	1520402A15Rik|Lrp35a	leucine rich adaptor protein 1	protein-coding
mm_140538.1	chr17	6778341	6778344	-	1	NA	intron (NM_009510, intron 1 of 12)	intron (NM_009510, intron 1 of 12)	4438	NM_009510	22350	Mm.277812	NM_009510	ENSMUSG00000052397	Ezr	AW146364|R75297|Vil2|p81	ezrin	protein-coding
mm_71811.1	chr8	68880724	68880730	+	1	NA	5' UTR (NM_008509, exon 1 of 10)	5' UTR (NM_008509, exon 1 of 10)	172	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_24258.1	chr3	89186777	89186787	+	1	NA	exon (NM_001014995, exon 8 of 12)	exon (NM_001014995, exon 8 of 12)	3557	NM_001014995	68521	Mm.274708	NM_001014995	ENSMUSG00000032657	Fam189b	1110013L07Rik	family with sequence similarity 189, member B	protein-coding
mm_106127.1	chr11	116429487	116429529	-	1	NA	Intergenic	Intergenic	-4586	NM_176902	319370	Mm.258466	NM_176902	ENSMUSG00000050628	Ubald2	1110014K08Rik|D030012E24Rik|Fam100b	UBA-like domain containing 2	protein-coding
mm_100775.1	chr11	4789835	4789842	-	1	NA	exon (NM_001252253, exon 12 of 15)	exon (NM_001252253, exon 12 of 15)	-43060	NM_138948	192650	Mm.207056	NM_138948	ENSMUSG00000009075	Cabp7	-	calcium binding protein 7	protein-coding
mm_169178.1	chr13	65813058	65813060	-	1	NA	Intergenic	Intergenic	-300394	NM_001177832	628709	Mm.390595	NM_001177832	ENSMUSG00000095909	Gm10324	ENSMUSG00000071302	predicted gene 10324	protein-coding
mm_36776.1	chr4	102921772	102921780	-	1	NA	intron (NM_001285852, intron 16 of 25)	intron (NM_001285852, intron 16 of 25)	-64603	NM_001163767	67344	Mm.111346	NM_026100	ENSMUSG00000028523	Tctex1d1	1700055O19Rik	Tctex1 domain containing 1	protein-coding
mm_159071.1	chr2	25243040	25243040	+	1	NA	5' UTR (NM_176834, exon 1 of 1)	5' UTR (NM_176834, exon 1 of 1)	111	NM_176834	68846	Mm.24777	NM_176834	ENSMUSG00000044628	Rnf208	1110061N23Rik	ring finger protein 208	protein-coding
mm_112674.1	chr13	16027595	16027610	+	1	NA	3' UTR (NM_008380, exon 5 of 5)	3' UTR (NM_008380, exon 5 of 5)	15751	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_35784.1	chr4	46452573	46452615	-	1	NA	intron (NM_130889, intron 1 of 6)	intron (NM_130889, intron 1 of 6)	1668	NM_130889	67628	Mm.263913	NM_130889	ENSMUSG00000028333	Anp32b	2410015B15Rik|PAL31|PHAPI2a|Ssp29	acidic (leucine-rich) nuclear phosphoprotein 32 family, member B	protein-coding
mm_158732.1	chrX	163958635	163958674	-	1	NA	promoter-TSS (NM_009453)	promoter-TSS (NM_009453)	12	NM_009453	22184	Mm.426178	NM_009453	ENSMUSG00000031370	Zrsr2	35kDa|5031411E02Rik|A230052C13Rik|C77286|U2af1-rs2|URP	zinc finger (CCCH type), RNA binding motif and serine/arginine rich 2	protein-coding
mm_167189.1	chr7	142511516	142511526	+	1	NA	exon (NM_001163669, exon 12 of 17)	exon (NM_001163669, exon 12 of 17)	-4750	NR_033261	677289	Mm.350054	NR_033261	ENSMUSG00000043795	Prr33	ENSMUSG00000043795|Gm14492|OTTMUSG00000016823	proline rich 33	ncRNA
mm_102842.1	chr11	69364931	69364983	-	1	NA	intron (NM_146019, intron 1 of 39)	intron (NM_146019, intron 1 of 39)	4469	NM_146019	216848	Mm.178246	NM_146019	ENSMUSG00000018474	Chd3	2600010P09Rik|AF020312|Chd7|Prp7|Prp9-1	chromodomain helicase DNA binding protein 3	protein-coding
mm_66975.1	chr7	63923415	63923418	-	1	NA	intron (NM_021366, intron 1 of 1)	intron (NM_021366, intron 1 of 1)	6559	NM_001256311	381994	Mm.425466	NM_001256311	ENSMUSG00000095061	E030018B13Rik	Gm1697	RIKEN cDNA E030018B13 gene	protein-coding
mm_170994.1	chr2	75191833	75191833	-	1	NA	Intergenic	Intergenic	252346	NR_040635	77269	Mm.389278	NR_040635		9430019J16Rik	-	RIKEN cDNA 9430019J16 gene	ncRNA
mm_101751.1	chr11	43381336	43381357	-	1	NA	Intergenic	Intergenic	-6885	NR_029558	387164		NR_029558	ENSMUSG00000065601	Mir146	Mirn146|miR-146a|mmu-mir-146	microRNA 146	ncRNA
mm_85177.1	chr9	96539885	96539888	-	1	NA	3' UTR (NM_053268, exon 24 of 24)	3' UTR (NM_053268, exon 24 of 24)	-61211	NM_001311135	19823	Mm.28235	NM_011279	ENSMUSG00000051234	Rnf7	Rbx2|SAG	ring finger protein 7	protein-coding
mm_113959.1	chr13	51166009	51166019	+	1	NA	Intergenic	Intergenic	-5011	NM_029173	75124	Mm.179243	NM_029173	ENSMUSG00000021396	Nxnl2	4930519N16Rik|Rdcvf2	nucleoredoxin-like 2	protein-coding
mm_161484.1	chr15	84123017	84123017	-	1	NA	exon (NM_029427, exon 1 of 10)	exon (NM_029427, exon 1 of 10)	158	NM_029427	75772	Mm.159565	NM_029427	ENSMUSG00000018868	Pnpla5	4833426H19Rik|GS2L	patatin-like phospholipase domain containing 5	protein-coding
mm_159210.1	chr2	121955847	121955847	-	1	NA	promoter-TSS (NM_001290992)	promoter-TSS (NM_001290992)	-154	NM_001290992	329506	Mm.249405	NM_212450	ENSMUSG00000033411	Ctdspl2	D2Ertd485e	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase like 2	protein-coding
mm_158068.1	chrX	101222427	101222561	-	1	NA	promoter-TSS (NM_001110310)	promoter-TSS (NM_001110310)	69	NM_001110311	55988	Mm.206949	NM_018875	ENSMUSG00000046032	Snx12	2610001F05Rik|AW045757|SDP8	sorting nexin 12	protein-coding
mm_116853.1	chr13	54759918	54759955	-	1	NA	exon (NM_033610, exon 5 of 6)	exon (NM_033610, exon 5 of 6)	6504	NM_033610	104069	Mm.200843	NM_033610	ENSMUSG00000034891	Sncb	AI838531|betaSYN	synuclein, beta	protein-coding
mm_45606.1	chr5	75044674	75044695	-	1	NA	promoter-TSS (NM_028850)	promoter-TSS (NM_028850)	-43	NM_028850	74277	Mm.239814	NM_028850	ENSMUSG00000029229	Chic2	1700081B18Rik|4930502K01Rik|BTL	cysteine-rich hydrophobic domain 2	protein-coding
mm_11478.1	chr2	32384838	32384856	+	1	NA	3' UTR (NM_008491, exon 6 of 6)	3' UTR (NM_008491, exon 6 of 6)	2892	NM_008491	16819	Mm.9537	NM_008491	ENSMUSG00000026822	Lcn2	24p3|AW212229|NRL|Sip24	lipocalin 2	protein-coding
mm_19934.1	chr2	116065692	116065705	-	1	NA	promoter-TSS (NM_010825)	promoter-TSS (NM_010825)	-640	NM_010825	17536	Mm.247566	NM_010825	ENSMUSG00000027210	Meis2	A430109D20Rik|Mrg1|Stra10	Meis homeobox 2	protein-coding
mm_54562.1	chr6	37441911	37441928	-	1	NA	5' UTR (NM_178661, exon 1 of 12)	5' UTR (NM_178661, exon 1 of 12)	229	NM_178661	208647	Mm.169929	NM_178661	ENSMUSG00000038648	Creb3l2	BBF2H7|C530025K05Rik|SCIRR69	cAMP responsive element binding protein 3-like 2	protein-coding
mm_132247.1	chr16	32751338	32751354	+	1	NA	exon (NM_080457, exon 2 of 27)	exon (NM_080457, exon 2 of 27)	15460	NM_080457	140474	Mm.214599	NM_080457	ENSMUSG00000079620	Muc4	4933405I11Rik|Asgp	mucin 4	protein-coding
mm_41056.1	chr5	86804340	86804344	+	1	NA	promoter-TSS (NM_177680)	promoter-TSS (NM_177680)	76	NM_001347376	231386	Mm.196325	NM_177680	ENSMUSG00000035851	Ythdc1	A730098D12Rik|C80342|mKIAA1966	YTH domain containing 1	protein-coding
mm_112315.1	chr12	114937593	114937598	-	1	NA	Intergenic	Intergenic	-423901	NR_106063	102465664		NR_106063	ENSMUSG00000098357	Mir7094-2	Gm27508|mmu-mir-7094-2	microRNA 7094-2	ncRNA
mm_77378.1	chr8	119840186	119840223	-	1	NA	exon (NM_028071, exon 2 of 4)	exon (NM_028071, exon 2 of 4)	375	NM_028071	72042	Mm.393405	NM_028071	ENSMUSG00000031827	Cotl1	1810074P22Rik|2010004C08Rik|Clp	coactosin-like 1 (Dictyostelium)	protein-coding
mm_47360.1	chr5	122821299	122821315	-	1	NA	promoter-TSS (NM_021505)	promoter-TSS (NM_021505)	35	NM_021505	59008	Mm.332667	NM_021505	ENSMUSG00000029472	Anapc5	2510006G12Rik|AA408751|AA536819|AA986414|APC5|Anpc5	anaphase-promoting complex subunit 5	protein-coding
mm_126935.1	chr15	91772275	91772283	+	1	NA	intron (NM_025730, intron 36 of 50)	intron (NM_025730, intron 36 of 50)	-66047	NM_207243	239611	Mm.486225	NM_207243		Muc19	MUC-19|sld	mucin 19	protein-coding
mm_67549.1	chr7	81497161	81497170	-	1	NA	intron (NM_001193274, intron 1 of 5)	intron (NM_001193274, intron 1 of 5)	1165	NM_183143	210321	Mm.99511	NM_183143	ENSMUSG00000061877	BC048679	-	cDNA sequence BC048679	protein-coding
mm_20909.1	chr2	150600342	150600352	-	1	NA	exon (NM_027977, exon 2 of 9)	exon (NM_027977, exon 2 of 9)	8176	NM_027977	71881	Mm.26599	NM_027977	ENSMUSG00000033096	Apmap	2310001A20Rik|AI314817	adipocyte plasma membrane associated protein	protein-coding
mm_123917.1	chr14	73362987	73363041	-	1	NA	3' UTR (NM_008410, exon 6 of 6)	3' UTR (NM_008410, exon 6 of 6)	22257	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_28137.1	chr3	87208009	87208033	-	1	NA	Intergenic	MTEa|LTR|ERVL-MaLR	-33274	NM_130867	170643	Mm.89552	NM_130867	ENSMUSG00000041734	Kirrel	6720469N11Rik|Kirrel1|Neph1	kin of IRRE like (Drosophila)	protein-coding
mm_115764.1	chr13	19193679	19193682	-	1	NA	Intergenic	Intergenic	202133	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_60957.1	chr7	47054580	47054618	+	1	NA	3' UTR (NM_026436, exon 3 of 3)	3' UTR (NM_026436, exon 3 of 3)	3959	NM_026436	67893	Mm.27338	NM_026436	ENSMUSG00000010307	Tmem86a	1810054O13Rik|AI414959|AW742698	transmembrane protein 86A	protein-coding
mm_101713.1	chr11	42133685	42133711	-	1	NA	exon (NM_010250, exon 10 of 10)	exon (NM_010250, exon 10 of 10)	49232	NM_010250	14394	Mm.439668	NM_010250	ENSMUSG00000010803	Gabra1	Gabra-1	gamma-aminobutyric acid (GABA) A receptor, subunit alpha 1	protein-coding
mm_116172.1	chr13	30817494	30817504	-	1	NA	intron (NM_025588, intron 27 of 27)	intron (NM_025588, intron 27 of 27)	68266	NM_013674	16364	Mm.4677	NM_013674	ENSMUSG00000021356	Irf4	AI385587|IRF-4|LSIRF|NF-EM5|Spip	interferon regulatory factor 4	protein-coding
mm_69117.1	chr7	127025946	127025954	-	1	NA	exon (NM_010772, exon 2 of 5)	exon (NM_010772, exon 2 of 5)	529	NM_010772	17188	Mm.378964	NM_010772	ENSMUSG00000030678	Maz	MAZI|PUR1|Pur-1|SAF-1|SAF-2	MYC-associated zinc finger protein (purine-binding transcription factor)	protein-coding
mm_106752.1	chr12	4133048	4133126	+	1	NA	promoter-TSS (NM_001159536)	promoter-TSS (NM_001159536)	-310	NM_001159537	104111	Mm.489807	NM_138305	ENSMUSG00000020654	Adcy3	AC3|mKIAA0511	adenylate cyclase 3	protein-coding
mm_133260.1	chr16	77329630	77329656	+	1	NA	non-coding (NR_015543, exon 1 of 5)	non-coding (NR_015543, exon 1 of 5)	315	NR_015543	77994	Mm.394688	NR_015543	ENSMUSG00000090386	Mir99ahg	2810055G20Rik|D730043B02Rik	Mir99a and Mirlet7c-1 host gene (non-protein coding)	ncRNA
mm_43224.1	chr5	129791801	129791812	+	1	NA	exon (NM_009838, exon 7 of 13)	exon (NM_009838, exon 7 of 13)	-2755	NR_003681	100113364	Mm.449738	NR_003681	ENSMUSG00000093413	Snora15	MBI-79	small nucleolar RNA, H/ACA box 15	snoRNA
mm_107692.1	chr12	55377161	55377211	+	1	NA	exon (NM_025373, exon 5 of 7)	exon (NM_025373, exon 5 of 7)	6491	NR_035430	100316807		NR_035430	ENSMUSG00000080645	Mir1198	Mirn1198|mmu-mir-1198	microRNA 1198	ncRNA
mm_164068.1	chr14	118662740	118662753	-	1	NA	intron (NM_001033336, intron 3 of 30)	MTE2b|LTR|ERVL-MaLR	14185	NM_001163675	239273	Mm.40537	NM_001033336	ENSMUSG00000032849	Abcc4	ABCC4-N1|D630049P08Rik|MOATB|MRP4	ATP-binding cassette, sub-family C (CFTR/MRP), member 4	protein-coding
mm_118209.1	chr13	110060512	110060527	-	1	NA	3' UTR (NM_023852, exon 5 of 5)	3' UTR (NM_023852, exon 5 of 5)	156710	NR_035442	100316683		NR_035442	ENSMUSG00000084651	Mir1904	Mirn1904|mmu-mir-1904	microRNA 1904	ncRNA
mm_157544.1	chrX	51205903	51205931	-	1	NA	promoter-TSS (NM_134163)	promoter-TSS (NM_134163)	73	NM_001310515	171170	Mm.295324	NM_134163	ENSMUSG00000036109	Mbnl3	A530038J18Rik|AI661274|CHCR|E430034C16Rik|MBLX|MBLX39|MBXL	muscleblind-like 3 (Drosophila)	protein-coding
mm_169577.1	chr15	22714197	22714205	-	1	NA	exon (NM_001165971, exon 1 of 1)	exon (NM_001165971, exon 1 of 1)	783	NM_001165971	545091	Mm.475598	NM_001165971		Gm5803	EG545091	predicted gene 5803	protein-coding
mm_85319.1	chr9	101251743	101251756	-	1	NA	promoter-TSS (NM_001161362)	promoter-TSS (NM_001161362)	83	NM_001161362	235542	Mm.335386	NM_172144	ENSMUSG00000043154	Ppp2r3a	3222402P14Rik|A730042E07	protein phosphatase 2, regulatory subunit B'', alpha	protein-coding
mm_110945.1	chr12	76612709	76612728	-	1	NA	exon (NM_013675, exon 16 of 36)	exon (NM_013675, exon 16 of 36)	-64793	NR_046044	100504549	Mm.440349	NR_046044		AI463170	-	expressed sequence AI463170	ncRNA
mm_154753.1	chrX	10715037	10715057	+	1	NA	Intergenic	Intergenic	-2318	NM_026524	68041	Mm.29429	NM_026524	ENSMUSG00000008035	Mid1ip1	3110038L01Rik|Mig12|S14R	Mid1 interacting protein 1 (gastrulation specific G12-like (zebrafish))	protein-coding
mm_61251.1	chr7	65804062	65804062	+	1	NA	promoter-TSS (NR_045301)	promoter-TSS (NR_045301)	10	NR_045301	100503969	Mm.383527	NR_045301		1810008I18Rik	-	RIKEN cDNA 1810008I18 gene	ncRNA
mm_87296.1	chr10	42533203	42533216	+	1	NA	exon (NM_017472, exon 3 of 4)	exon (NM_017472, exon 3 of 4)	31155	NM_017472	54198	Mm.277870	NM_017472	ENSMUSG00000019804	Snx3	SDP3	sorting nexin 3	protein-coding
mm_83409.1	chr9	44802840	44802880	-	1	NA	promoter-TSS (NM_138951)	promoter-TSS (NM_138951)	91	NM_138951	192653	Mm.325487	NM_138951	ENSMUSG00000039438	Ttc36	-	tetratricopeptide repeat domain 36	protein-coding
mm_138205.1	chr17	34300861	34300876	+	1	NA	Intergenic	Intergenic	-4999	NM_010382	14969	Mm.22564	NM_010382	ENSMUSG00000060586	H2-Eb1	Eb|H-2Eb|H2Eb|Ia-4|Ia4	histocompatibility 2, class II antigen E beta	protein-coding
mm_69429.1	chr7	132813652	132813667	-	1	NA	promoter-TSS (NM_212473)	promoter-TSS (NM_212473)	-463	NM_212473	77938	Mm.225649	NM_175268	ENSMUSG00000030956	Fam53b	A930008G19Rik|mKIAA0140	family with sequence similarity 53, member B	protein-coding
mm_14935.1	chr2	151542820	151542823	+	1	NA	exon (NM_008019, exon 2 of 5)	exon (NM_008019, exon 2 of 5)	338	NM_001302078	14225	Mm.278458	NM_008019	ENSMUSG00000032966	Fkbp1a	FKBP12|Fkbp|Fkbp1	FK506 binding protein 1a	protein-coding
mm_88708.1	chr10	80150813	80150825	+	1	NA	intron (NM_001347117, intron 2 of 7)	CpG-1261	1137	NM_001305799	59090	Mm.143813	NM_021565	ENSMUSG00000035621	Midn	3000003C15Rik	midnolin	protein-coding
mm_115760.1	chr13	19193554	19193570	-	1	NA	Intergenic	Intergenic	202251	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_63796.1	chr7	132931148	132931155	+	1	NA	Intergenic	CpG	-18471	NM_207302	360216	Mm.389984	NM_207302	ENSMUSG00000030967	Zranb1	9330160G10Rik|D7Wsu87e|Gm1956|Trabid	zinc finger, RAN-binding domain containing 1	protein-coding
mm_142077.1	chr17	35702023	35702037	-	1	NA	promoter-TSS (NM_001198831)	promoter-TSS (NM_001198831)	14	NM_001198831	12305	Mm.5021	NM_007584	ENSMUSG00000003534	Ddr1	6030432F18|AI323681|CD167a|Cak|Nep|PTK3A	discoidin domain receptor family, member 1	protein-coding
mm_36356.1	chr4	75278247	75278338	-	1	NA	promoter-TSS (NM_025849)	promoter-TSS (NM_025849)	-6	NM_025849	66928	Mm.24332	NM_025849	ENSMUSG00000028398	Tmem261	1700027K24Rik|3110001D03Rik	transmembrane protein 261	protein-coding
mm_168478.1	chr11	48992243	48992254	-	1	NA	promoter-TSS (NM_011579)	promoter-TSS (NM_011579)	-2	NM_011579	21822	Mm.15793	NM_011579	ENSMUSG00000078922	Tgtp1	Gtp2|Irgb6|Mg21|Tgtp	T cell specific GTPase 1	protein-coding
mm_140887.1	chr17	23955269	23955302	-	1	NA	promoter-TSS (NM_001077421)	promoter-TSS (NM_001077421)	-12	NM_001077421	638345	Mm.46428	NM_001077421	ENSMUSG00000024125	Sbpl	2310068J22Rik	spermine binding protein-like	protein-coding
mm_94232.1	chr11	3290809	3290839	+	1	NA	exon (NM_001253691, exon 1 of 5)	exon (NM_001253691, exon 1 of 5)	367	NM_019574	56218	Mm.275563	NM_019574	ENSMUSG00000020453	Patz1	8430401L15Rik|AI447519|Mazr|Patz|Zfp278	POZ (BTB) and AT hook containing zinc finger 1	protein-coding
mm_22120.1	chr2	170158421	170158442	-	1	NA	Intergenic	Intergenic	-15756	NM_001159683	228913	Mm.22858	NM_001033299	ENSMUSG00000052056	Zfp217	4933431C08Rik|AW987152|Gm562|ZABC1|Znf217	zinc finger protein 217	protein-coding
mm_91972.1	chr10	61433216	61433249	-	1	NA	3' UTR (NM_010124, exon 3 of 3)	3' UTR (NM_010124, exon 3 of 3)	15260	NM_013611	18119	Mm.57195	NM_013611	ENSMUSG00000037171	Nodal	Tg.413d	nodal	protein-coding
mm_10822.1	chr2	24353358	24353362	+	1	NA	Intergenic	Intergenic	7989	NM_001039701	16181	Mm.882	NM_031167	ENSMUSG00000026981	Il1rn	F630041P17Rik|IL-1ra	interleukin 1 receptor antagonist	protein-coding
mm_26157.1	chr3	138217790	138217803	+	1	NA	promoter-TSS (NM_009626)	promoter-TSS (NM_009626)	23	NM_009626	11529	Mm.8473	NM_009626	ENSMUSG00000055301	Adh7	AI325182|Adh-3|Adh-3e|Adh-3t|Adh3|Adh3-e|Adh3-t|Adh4|Adt-1	alcohol dehydrogenase 7 (class IV), mu or sigma polypeptide	protein-coding
mm_121044.1	chr14	80022232	80022240	+	1	NA	TTS (NM_001030294)	TTS (NM_001030294)	21934	NM_001030294	380924	Mm.26456	NM_001030294	ENSMUSG00000022026	Olfm4	GC1|GW112|Gm296|Gm913|OlfD|pPD4	olfactomedin 4	protein-coding
mm_79112.1	chr9	46270265	46270278	+	1	NA	exon (NM_080434, exon 4 of 4)	exon (NM_080434, exon 4 of 4)	1663	NM_080434	66113	Mm.29738	NM_080434	ENSMUSG00000032079	Apoa5	1300007O05Rik|Apoav|RAP3	apolipoprotein A-V	protein-coding
mm_163975.1	chr14	55758439	55758445	-	1	NA	promoter-TSS (NM_009894)	promoter-TSS (NM_009894)	-18	NM_009894	12684	Mm.466766	NM_009894	ENSMUSG00000022219	Cideb	1110030C18Rik|AI790179|CIDE-B	cell death-inducing DNA fragmentation factor, alpha subunit-like effector B	protein-coding
mm_83886.1	chr9	55478873	55478878	-	1	NA	intron (NM_145615, intron 9 of 11)	intron (NM_145615, intron 9 of 11)	33368	NM_145615	110842	Mm.290853	NM_145615	ENSMUSG00000032314	Etfa	2010200I21Rik|D9Ertd394e	electron transferring flavoprotein, alpha polypeptide	protein-coding
mm_95579.1	chr11	52764652	52764693	+	1	NA	promoter-TSS (NM_177059)	promoter-TSS (NM_177059)	-34	NM_177059	320027	Mm.44518	NM_177059	ENSMUSG00000036264	Fstl4	B230374F23Rik|SPIG1|mKIAA1061	follistatin-like 4	protein-coding
mm_171973.1	chr5	88626704	88626722	+	1	NA	intron (NM_001289774, intron 5 of 17)	B1_Mus1|SINE|Alu	43200	NM_027530	52822	Mm.270469	NM_027530	ENSMUSG00000029291	Rufy3	2810428M05Rik|6330416M07Rik|AW455998|AW538594|D5Bwg0860e|Ripx|Rpipx	RUN and FYVE domain containing 3	protein-coding
mm_157405.1	chrX	38435428	38435450	-	1	NA	exon (NM_001017959, exon 4 of 9)	exon (NM_001017959, exon 4 of 9)	21021	NM_010685	16784	Mm.486	NM_010685	ENSMUSG00000016534	Lamp2	CD107b|LGP-B|Lamp II|Lamp-2|Lamp-2a|Lamp-2b|Lamp-2c|Mac3	lysosomal-associated membrane protein 2	protein-coding
mm_111698.1	chr12	103657124	103657134	-	1	NA	promoter-TSS (NM_007618)	promoter-TSS (NM_007618)	89	NM_007618	12401	Mm.290079	NM_007618	ENSMUSG00000060807	Serpina6	Cbg	serine (or cysteine) peptidase inhibitor, clade A, member 6	protein-coding
mm_129820.1	chr15	83033253	83033274	-	1	NA	5' UTR (NM_001271412, exon 1 of 6)	5' UTR (NM_001271412, exon 1 of 6)	134	NM_001271412	74039	Mm.32584	NM_028728	ENSMUSG00000058099	Nfam1	4921501M20Rik|Cnaip	Nfat activating molecule with ITAM motif 1	protein-coding
mm_169988.1	chr17	15041799	15041811	+	1	NA	promoter-TSS (NM_011560)	promoter-TSS (NM_011560)	193	NM_001039552	381062	Mm.393767	NM_183133	ENSMUSG00000036552	Ermard	2210404J11Rik|2410011O22Rik|AI448938	ER membrane associated RNA degradation	protein-coding
mm_82846.1	chr9	31170532	31170539	-	1	NA	exon (NM_009691, exon 5 of 16)	exon (NM_009691, exon 5 of 16)	-38736	NM_011176	19143	Mm.243926	NM_011176	ENSMUSG00000031995	St14	Epithin|MT-SP1|Prss14|Tmprss14|mCAP3|matriptase	suppression of tumorigenicity 14 (colon carcinoma)	protein-coding
mm_95915.1	chr11	58220482	58220510	+	1	NA	exon (NM_019440, exon 2 of 2)	exon (NM_019440, exon 2 of 2)	5519	NM_019440	54396	Mm.458517	NM_019440	ENSMUSG00000069874	Irgm2	AI481100|GTPI|Ifggd2|Iigp2	immunity-related GTPase family M member 2	protein-coding
mm_25810.1	chr3	127790104	127790125	+	1	NA	5' UTR (NM_145133, exon 1 of 3)	5' UTR (NM_145133, exon 1 of 3)	201	NM_145133	211550	Mm.31852	NM_145133	ENSMUSG00000046688	Tifa	T2bp	TRAF-interacting protein with forkhead-associated domain	protein-coding
mm_17723.1	chr2	32409219	32409237	-	1	NA	Intergenic	Intergenic	13338	NM_133783	96979	Mm.28048	NM_133783	ENSMUSG00000026820	Ptges2	0610038H10Rik|C79137|Gbf1|Mpges2|Pges2	prostaglandin E synthase 2	protein-coding
mm_141179.1	chr17	26841577	26841591	-	1	NA	promoter-TSS (NM_008700)	promoter-TSS (NM_008700)	-19	NM_008700	18091	Mm.41974	NM_008700	ENSMUSG00000015579	Nkx2-5	Csx|Nkx-2.5|Nkx2.5|tinman	NK2 homeobox 5	protein-coding
mm_110485.1	chr12	51939907	51939963	-	1	NA	intron (NM_177171, intron 11 of 35)	intron (NM_177171, intron 11 of 35)	31386	NM_177171	320487	Mm.131941	NM_177171	ENSMUSG00000035181	Heatr5a	C230081H03Rik|D930036F22Rik|mKIAA1316	HEAT repeat containing 5A	protein-coding
mm_126103.1	chr15	78245021	78245051	+	1	NA	5' UTR (NM_008677, exon 1 of 10)	5' UTR (NM_008677, exon 1 of 10)	225	NM_008677	17972	Mm.2068	NM_008677	ENSMUSG00000071715	Ncf4	AI451400|p40phox	neutrophil cytosolic factor 4	protein-coding
mm_100961.1	chr11	6637246	6637260	-	1	NA	exon (NM_011709, exon 2 of 4)	exon (NM_011709, exon 2 of 4)	1396	NM_011709	22373	Mm.268094	NM_011709	ENSMUSG00000000381	Wap	-	whey acidic protein	protein-coding
mm_122293.1	chr14	34567530	34567550	-	1	NA	exon (NM_001039071, exon 6 of 13)	exon (NM_001039071, exon 6 of 13)	21067	NM_001039074	24131	Mm.29733	NM_011918	ENSMUSG00000021798	Ldb3	AW742271|PDLIM6|ZASP	LIM domain binding 3	protein-coding
mm_55937.1	chr6	84771257	84771268	-	1	NA	intron (NM_177077, intron 19 of 21)	intron (NM_177077, intron 19 of 21)	-177354	NM_001177713	232174	Mm.255246	NM_175475	ENSMUSG00000063415	Cyp26b1	CP26|P450RAI-2	cytochrome P450, family 26, subfamily b, polypeptide 1	protein-coding
mm_9670.1	chr1	178318171	178318192	-	1	NA	promoter-TSS (NM_025511)	promoter-TSS (NM_025511)	-972	NM_025511	66359	Mm.489720	NM_025511	ENSMUSG00000026500	Cox20	2310005N03Rik|Fam36a	COX20 Cox2 chaperone	protein-coding
mm_29330.1	chr3	108085423	108085438	-	1	NA	promoter-TSS (NM_001289720)	promoter-TSS (NM_001289720)	-4	NM_001289720	109674	Mm.274335	NM_028779	ENSMUSG00000027889	Ampd2	1200014F01Rik|AI552571|Ampd-2|m4521Dajl	adenosine monophosphate deaminase 2	protein-coding
mm_151266.1	chr19	54045589	54045603	+	1	NA	5' UTR (NM_007417, exon 1 of 1)	5' UTR (NM_007417, exon 1 of 1)	414	NM_007417	11551	Mm.235195	NM_007417	ENSMUSG00000033717	Adra2a	AW122659|Adra-2|Adra-2a|alpha(2A)AR|alpha2-C10|alpha2A|alpha2A-AR	adrenergic receptor, alpha 2a	protein-coding
mm_85486.1	chr9	106096812	106096823	-	1	NA	promoter-TSS (NM_026763)	promoter-TSS (NM_026763)	-126	NM_026763	68553	Mm.28854	NM_026763	ENSMUSG00000032572	Col6a4	1110001D15Rik|AI413310|AU023415|Dvwa|EG235580|Vwa6	collagen, type VI, alpha 4	protein-coding
mm_110804.1	chr12	72212479	72212506	-	1	NA	non-coding (NR_104446, exon 7 of 7)	non-coding (NR_104446, exon 7 of 7)	23254	NR_104446	104001	Mm.221275	NM_153457	ENSMUSG00000021087	Rtn1	Nsp	reticulon 1	protein-coding
mm_158984.1	chr1	131599194	131599194	+	1	NA	promoter-TSS (NM_011924)	promoter-TSS (NM_011924)	80	NM_011924	26361	Mm.89986	NM_011924	ENSMUSG00000026432	Avpr1b	AVPR3|V3/V1b|VIBR|VPR3	arginine vasopressin receptor 1B	protein-coding
mm_118129.1	chr13	104621646	104621652	-	1	NA	Intergenic	RMER19B|LTR|ERVK	195304	NM_026072	67285	Mm.235398	NM_026072	ENSMUSG00000021715	Cwc27	3110009E13Rik|NY-CO-10|Sdccag10	CWC27 spliceosome-associated protein	protein-coding
mm_19258.1	chr2	84775389	84775411	-	1	NA	promoter-TSS (NM_009776)	promoter-TSS (NM_009776)	29	NM_009776	12258	Mm.38888	NM_009776	ENSMUSG00000023224	Serping1	C1INH|C1nh	serine (or cysteine) peptidase inhibitor, clade G, member 1	protein-coding
mm_2379.1	chr1	93373865	93373871	+	1	NA	promoter-TSS (NM_207031)	promoter-TSS (NM_207031)	-28	NM_207031	404545	Mm.297411	NM_207031	ENSMUSG00000034107	Ano7	Ngep|Ngep-L|Pcanap5|Tmem16g	anoctamin 7	protein-coding
mm_14422.1	chr2	130482383	130482398	+	1	NA	intron (NM_001163688, intron 1 of 20)	intron (NM_001163688, intron 1 of 20)	32112	NM_001163688	19262	Mm.224246	NM_008980	ENSMUSG00000027303	Ptpra	Ptpa|Ptpalpha|Rptpalpha|Rptra|Rptralpha	protein tyrosine phosphatase, receptor type, A	protein-coding
mm_20024.1	chr2	119442860	119442863	-	1	NA	intron (NM_026574, intron 11 of 35)	intron (NM_026574, intron 11 of 35)	34768	NM_026574	68142	Mm.330496	NM_026574	ENSMUSG00000034154	Ino80	2310079N15Rik|4632409L19Rik|Inoc1	INO80 complex subunit	protein-coding
mm_78750.1	chr9	42142140	42142150	+	1	NA	Intergenic	Intergenic	-17856	NM_011436	20660	Mm.121920	NM_011436	ENSMUSG00000049313	Sorl1	2900010L19Rik|AI596264|AW261561|LR11|SorLA|gp250|mSorLA	sortilin-related receptor, LDLR class A repeats-containing	protein-coding
mm_120753.1	chr14	73334108	73334121	+	1	NA	Intergenic	ERVL-E-int|LTR|ERVL	-8323	NM_009029	19645	Mm.273862	NM_009029	ENSMUSG00000022105	Rb1	Rb|Rb-1|pRb	retinoblastoma 1	protein-coding
mm_137032.1	chr17	17890099	17890112	+	1	NA	intron (NM_008039, intron 1 of 1)	intron (NM_008039, intron 1 of 1)	2281	NM_008039	14289	Mm.378918	NM_008039	ENSMUSG00000052270	Fpr2	E330010I07Rik|Fpr-rs2	formyl peptide receptor 2	protein-coding
mm_73775.1	chr8	116605948	116605955	+	1	NA	intron (NM_029441, intron 2 of 6)	intron (NM_029441, intron 2 of 6)	100936	NM_029297	75465	Mm.23114	NM_029297	ENSMUSG00000034467	Dynlrb2	1700009A04Rik|DNLC2B|Dncl2b	dynein light chain roadblock-type 2	protein-coding
mm_134047.1	chr16	5222258	5222299	-	1	NA	promoter-TSS (NM_001033220)	promoter-TSS (NM_001033220)	21	NM_001033220	239691	Mm.325639	NM_001033220	ENSMUSG00000051669	AU021092	-	expressed sequence AU021092	protein-coding
mm_26278.1	chr3	142505558	142505572	+	1	NA	exon (NM_153564, exon 7 of 11)	exon (NM_153564, exon 7 of 11)	8631	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_24998.1	chr3	97633159	97633169	+	1	NA	intron (NM_001161765, intron 1 of 7)	intron (NM_001161765, intron 1 of 7)	4326	NM_010232	14263	Mm.385180	NM_010232	ENSMUSG00000028088	Fmo5	5033418D19Rik|AI195026	flavin containing monooxygenase 5	protein-coding
mm_7777.1	chr1	131276686	131276720	-	1	NA	intron (NM_019777, intron 2 of 21)	intron (NM_019777, intron 2 of 21)	2860	NM_019777	56489	Mm.386783	NM_019777	ENSMUSG00000042349	Ikbke	AW558201|IKK-i|IKKepsilon|Ikki	inhibitor of kappaB kinase epsilon	protein-coding
mm_170322.1	chr18	4197109	4197112	-	1	NA	Intergenic	B3A|SINE|B2	31278	NM_026092	67328	Mm.158148	NM_026092	ENSMUSG00000024233	Lyzl1	1700038F02Rik|Lyc2|Lyzd1	lysozyme-like 1	protein-coding
mm_104697.1	chr11	97955269	97955310	-	1	NA	intron (NM_001163608, intron 5 of 13)	intron (NM_001163608, intron 5 of 13)	31157	NM_028199	72324	Mm.39617	NM_028199	ENSMUSG00000017417	Plxdc1	2410003I07Rik|AI848450|Tem7	plexin domain containing 1	protein-coding
mm_145073.1	chr18	42053728	42053738	+	1	NA	promoter-TSS (NM_001146299)	promoter-TSS (NM_001146299)	23	NM_001146299	269016	Mm.45472	NM_172966	ENSMUSG00000057719	Sh3rf2	2310046K19|9130023G24Rik|AI452083|Ppp1r39|RNF158	SH3 domain containing ring finger 2	protein-coding
mm_4089.1	chr1	167089118	167089120	+	1	NA	3' UTR (NM_175461, exon 3 of 3)	3' UTR (NM_175461, exon 3 of 3)	87702	NM_001160261	226610	Mm.389217	NM_175461	ENSMUSG00000060568	Fam78b	C030014K22Rik|C030020L09Rik	family with sequence similarity 78, member B	protein-coding
mm_28600.1	chr3	94580128	94580139	-	1	NA	intron (NM_001082484, intron 1 of 11)	intron (NM_001082484, intron 1 of 11)	2583	NM_001082484	76742	Mm.28160	NM_029721	ENSMUSG00000028136	Snx27	5730552M22Rik|ESTM45|ESTM47|R75405	sorting nexin family member 27	protein-coding
mm_105323.1	chr11	102893514	102893531	-	1	NA	exon (NM_010277, exon 5 of 9)	exon (NM_010277, exon 5 of 9)	3678	NM_001131020	14580	Mm.1239	NM_010277	ENSMUSG00000020932	Gfap	AI836096	glial fibrillary acidic protein	protein-coding
mm_42275.1	chr5	114146676	114146715	+	1	NA	Intergenic	Intergenic	15539	NM_011677	22256	Mm.1393	NM_011677	ENSMUSG00000029591	Ung	UNG1|UNG2	uracil DNA glycosylase	protein-coding
mm_165237.1	chr2	61804778	61804787	+	1	NA	exon (NM_009322, exon 1 of 6)	exon (NM_009322, exon 1 of 6)	329	NM_009322	21375	Mm.308525	NM_009322	ENSMUSG00000035033	Tbr1	-	T-box brain gene 1	protein-coding
mm_102207.1	chr11	54787718	54787720	-	1	NA	promoter-TSS (NM_178626)	promoter-TSS (NM_178626)	-16	NM_178626	72729	Mm.29476	NM_178626	ENSMUSG00000052298	Cdc42se2	2810404F18Rik|AA408783|AA536669|SPEC2	CDC42 small effector 2	protein-coding
mm_55119.1	chr6	50397069	50397077	-	1	NA	intron (NM_001347213, intron 2 of 23)	intron (NM_001347213, intron 2 of 23)	-14236	NM_027881	71720	Mm.44153	NM_027881	ENSMUSG00000029822	Osbpl3	1200014M06Rik|6720421I08Rik|A530055M08|ORP-3|ORP3|OSBP3	oxysterol binding protein-like 3	protein-coding
mm_33739.1	chr4	134121843	134121860	+	1	NA	intron (NR_045571, intron 8 of 13)	intron (NR_045571, intron 8 of 13)	6902	NM_080559	73723	Mm.22240	NM_080559	ENSMUSG00000028843	Sh3bgrl3	1110004L05Rik|AU022188	SH3 domain binding glutamic acid-rich protein-like 3	protein-coding
mm_11975.1	chr2	55105568	55105570	+	1	NA	intron (NM_173030, intron 12 of 12)	intron (NM_173030, intron 12 of 12)	-330401	NM_001304810	16519	Mm.5127	NM_008426	ENSMUSG00000026824	Kcnj3	GIRK-1|GIRK1|Kcnf3|Kir3.1	potassium inwardly-rectifying channel, subfamily J, member 3	protein-coding
mm_22321.1	chr2	180642280	180642288	-	1	NA	exon (NM_178254, exon 1 of 6)	exon (NM_178254, exon 1 of 6)	407	NM_178254	277353	Mm.473700	NM_178254	ENSMUSG00000038932	Tcfl5	AV260129|Figlb|Sosf1	transcription factor-like 5 (basic helix-loop-helix)	protein-coding
mm_91760.1	chr10	51485750	51485785	-	1	NA	3' UTR (NM_008147, exon 8 of 9)	3' UTR (NM_008147, exon 8 of 9)	-5131	NM_001291894	14728	Mm.34408	NM_013532	ENSMUSG00000062593	Lilrb4a	CD85K|Gp49b|HM18|ILT3|LIR-5|Lilrb4|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4A	protein-coding
mm_78899.1	chr9	44673186	44673188	+	1	NA	promoter-TSS (NM_001277851)	promoter-TSS (NM_001277851)	-46	NM_001277851	58866	Mm.45380	NM_021481	ENSMUSG00000032098	Treh	2210412M19Rik	trehalase (brush-border membrane glycoprotein)	protein-coding
mm_37912.1	chr4	132757249	132757259	-	1	NA	promoter-TSS (NM_133888)	promoter-TSS (NM_133888)	-83	NM_133888	100340	Mm.287187	NM_133888	ENSMUSG00000028885	Smpdl3b	1110054A24Rik|AU045240|Asml3b	sphingomyelin phosphodiesterase, acid-like 3B	protein-coding
mm_133706.1	chr16	93153055	93153070	+	1	NA	Intergenic	Intergenic	200127	NR_040486	69857	Mm.81192	NR_040486	ENSMUSG00000100277	1810053B23Rik	1810008L18Rik|1810056K14Rik	RIKEN cDNA 1810053B23 gene	ncRNA
mm_97458.1	chr11	78245094	78245115	+	1	NA	promoter-TSS (NM_009143)	promoter-TSS (NM_009143)	599	NM_009297	20926	Mm.20755	NM_009297	ENSMUSG00000002052	Supt6	5131400N11Rik|AI132449|SPT6|Supt6h|mKIAA0162	suppressor of Ty 6	protein-coding
mm_122.1	chr1	9807007	9807014	+	1	NA	intron (NM_177547, intron 1 of 16)	(CGGG)n|Simple_repeat|Simple_repeat	8880	NM_177547	170755	Mm.336410	NM_133220	ENSMUSG00000025915	Sgk3	2510015P22Rik|A330005P07Rik|Cisk|fy|fz	serum/glucocorticoid regulated kinase 3	protein-coding
mm_127651.1	chr15	102490693	102490752	+	1	NA	exon (NM_001174073, exon 12 of 13)	exon (NM_001174073, exon 12 of 13)	20090	NM_001174073	18521	Mm.236513	NM_011042	ENSMUSG00000056851	Pcbp2	AW412548|Hnrpx|alphaCP-2	poly(rC) binding protein 2	protein-coding
mm_93436.1	chr10	109010956	109010983	-	1	NA	promoter-TSS (NM_001252342)	promoter-TSS (NM_001252342)	6	NM_009306	20979	Mm.289702	NM_009306	ENSMUSG00000035864	Syt1	AW124717|G630098F17Rik|SytI	synaptotagmin I	protein-coding
mm_125005.1	chr15	25363488	25363499	+	1	NA	3' UTR (NM_027395, exon 2 of 2)	3' UTR (NM_027395, exon 2 of 2)	50271	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	brain abundant, membrane attached signal protein 1	protein-coding
mm_71341.1	chr8	45627710	45627754	+	1	NA	promoter-TSS (NM_001310707)	promoter-TSS (NM_001310707)	-19	NM_001310707	234214	Mm.211096	NM_172752	ENSMUSG00000031626	Sorbs2	2010203O03Rik|9430041O17Rik|A530071H08|Argbp2|mKIAA0777|nArgBP2	sorbin and SH3 domain containing 2	protein-coding
mm_1655.1	chr1	74713130	74713142	+	1	NA	promoter-TSS (NM_024264)	promoter-TSS (NM_024264)	-399	NM_024264	104086	Mm.85083	NM_024264	ENSMUSG00000026170	Cyp27a1	1300013A03Rik|Cyp27	cytochrome P450, family 27, subfamily a, polypeptide 1	protein-coding
mm_129353.1	chr15	77927864	77927895	-	1	NA	exon (NM_019913, exon 2 of 4)	exon (NM_019913, exon 2 of 4)	1115	NM_019913	56551	Mm.291917	NM_019913	ENSMUSG00000005354	Txn2	2510006J11Rik|AI788873|Trx2	thioredoxin 2	protein-coding
mm_128371.1	chr15	42676096	42676116	-	1	NA	intron (NM_009640, intron 1 of 8)	intron (NM_009640, intron 1 of 8)	871	NM_001286062	11600	Mm.309336	NM_009640	ENSMUSG00000022309	Angpt1	1110046O21Rik|Ang-1|Ang1	angiopoietin 1	protein-coding
mm_149924.1	chr19	26623420	26623471	+	1	NA	intron (NM_011416, intron 2 of 32)	intron (NM_011416, intron 2 of 32)	18285	NM_011416	67155	Mm.342988	NM_011416	ENSMUSG00000024921	Smarca2	2610209L14Rik|SNF2alpha|Snf2l2|brahma|brm	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	protein-coding
mm_13890.1	chr2	120404168	120404257	+	1	NA	promoter-TSS (NM_173734)	promoter-TSS (NM_173734)	-96	NM_001110496	211499	Mm.260712	NM_173734	ENSMUSG00000033808	Tmem87a	A930025J12Rik	transmembrane protein 87A	protein-coding
mm_27386.1	chr3	50628434	50628472	-	1	NA	Intergenic	Intergenic	-184840	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_165910.1	chr4	57578667	57578678	+	1	NA	intron (NM_001304544, intron 1 of 8)	RMER12C|LTR|ERVK	10424	NM_172868	242481	Mm.331630	NM_172868	ENSMUSG00000090053	Palm2	53-H12|B130066I24|R75368|pEN70	paralemmin 2	protein-coding
mm_129858.1	chr15	83265939	83265953	-	1	NA	Intergenic	RLTR19B|LTR|ERVK	-14172	NM_001004150	239559	Mm.323805	NM_001004150	ENSMUSG00000047878	A4galt	-	alpha 1,4-galactosyltransferase	protein-coding
mm_77748.1	chr8	127441176	127441187	-	1	NA	intron (NM_001309391, intron 20 of 24)	intron (NM_001309391, intron 20 of 24)	141529	NM_001013580	93742	Mm.299254	NM_033620	ENSMUSG00000025812	Pard3	AA960621|AI256638|Asip|D8Ertd580e|Par-3|Par3|Pard-3|Pard3a|Phip	par-3 family cell polarity regulator	protein-coding
mm_167554.1	chr9	35194144	35194155	-	1	NA	intron (NM_001177845, intron 2 of 6)	intron (NM_001177845, intron 2 of 6)	5756	NM_001177847	117149	Mm.23987	NM_054096	ENSMUSG00000032041	Tirap	AA407980|C130027E04Rik|Mal|Tlr4ap|Wyatt	toll-interleukin 1 receptor (TIR) domain-containing adaptor protein	protein-coding
mm_156239.1	chrX	136201667	136201727	+	1	NA	exon (NM_177919, exon 3 of 3)	exon (NM_177919, exon 3 of 3)	2154	NM_177919	331532	Mm.41605	NM_177919	ENSMUSG00000054034	Tceal5	6430401A05Rik	transcription elongation factor A (SII)-like 5	protein-coding
mm_223.1	chr1	17601843	17601859	+	1	NA	promoter-TSS (NM_053191)	promoter-TSS (NM_053191)	-50	NM_053191	94227	Mm.442452	NM_053191	ENSMUSG00000067780	Pi15	P24TI|P25TI|PI-15|SugarCrisp	peptidase inhibitor 15	protein-coding
mm_47956.1	chr5	135573003	135573029	-	1	NA	promoter-TSS (NM_019577)	promoter-TSS (NM_019577)	27	NM_019577	56221	Mm.31505	NM_019577	ENSMUSG00000004814	Ccl24	CKb-6|MPIF-2|Scya24	chemokine (C-C motif) ligand 24	protein-coding
mm_165153.1	chr2	21501864	21501871	+	1	NA	intron (NM_001004761, intron 2 of 10)	Lx8|LINE|L1	134300	NM_001004761	241263	Mm.166647	NM_175706	ENSMUSG00000045967	Gpr158	5330427M13Rik|mKIAA1136	G protein-coupled receptor 158	protein-coding
mm_124411.1	chr14	116065953	116065953	-	1	NA	intron (NM_175500, intron 7 of 7)	intron (NM_175500, intron 7 of 7)	-656401	NR_045761	75088	Mm.444706	NR_045761	ENSMUSG00000093551	4930505G20Rik	-	RIKEN cDNA 4930505G20 gene	ncRNA
mm_42378.1	chr5	114929949	114929970	+	1	NA	exon (NM_145209, exon 4 of 7)	exon (NM_145209, exon 4 of 7)	6719	NM_145209	231655	Mm.95479	NM_145209	ENSMUSG00000041827	Oasl1	7530414C13Rik|oasl9	2'-5' oligoadenylate synthetase-like 1	protein-coding
mm_125504.1	chr15	55307799	55307805	+	1	NA	promoter-TSS (NM_181277)	promoter-TSS (NM_181277)	52	NM_181277	12818	Mm.297859	NM_181277	ENSMUSG00000022371	Col14a1	5730412L22Rik|AW108078	collagen, type XIV, alpha 1	protein-coding
mm_120221.1	chr14	62837730	62837754	+	1	NA	promoter-TSS (NR_106174)	promoter-TSS (NR_106174)	21	NR_106174	102465889		NR_106174	ENSMUSG00000099245	Mir8098	Gm27462|mmu-mir-8098	microRNA 8098	ncRNA
mm_31017.1	chr4	40722913	40723001	+	1	NA	promoter-TSS (NM_001164672)	promoter-TSS (NM_001164672)	27	NM_001164672	15502	Mm.27897	NM_008298	ENSMUSG00000028410	Dnaja1	HSJ-2|Hsj2|Nedd7	DnaJ heat shock protein family (Hsp40) member A1	protein-coding
mm_102983.1	chr11	69681904	69681953	-	1	NA	promoter-TSS (NM_030702)	promoter-TSS (NM_030702)	42	NM_030702	80886	Mm.284592	NM_030702	ENSMUSG00000005204	Senp3	AA408656|Smt3ip|Smt3ip1	SUMO/sentrin specific peptidase 3	protein-coding
mm_10728.1	chr2	22895483	22895485	+	1	NA	promoter-TSS (NM_019501)	promoter-TSS (NM_019501)	-38	NM_019501	56075	Mm.249752	NM_019501	ENSMUSG00000026784	Pdss1	2610203G20Rik|2700031G06Rik|TPT|TPT 1|Tprt|mDLP1|mSPS1	prenyl (solanesyl) diphosphate synthase, subunit 1	protein-coding
mm_108107.1	chr12	75308388	75308408	+	1	NA	promoter-TSS (NM_023275)	promoter-TSS (NM_023275)	85	NM_023275	80837	Mm.27467	NM_023275	ENSMUSG00000046768	Rhoj	1110005O19Rik|AW210585|Arhj|TC10L|TCL	ras homolog family member J	protein-coding
mm_55907.1	chr6	83703542	83703554	-	1	NA	non-coding (NR_002873, exon 2 of 2)	non-coding (NR_002873, exon 2 of 2)	7258	NR_075094	574519	Mm.487605	NR_002871	ENSMUSG00000085794	Vax2os	Vas2os|Vax2os1|Vax2os2	ventral anterior homeobox 2, opposite strand	ncRNA
mm_10348.1	chr2	11689809	11689825	+	1	NA	3' UTR (NM_008367, exon 8 of 8)	3' UTR (NM_008367, exon 8 of 8)	-15476	NM_001271498	16169	Mm.200196	NM_008358	ENSMUSG00000023206	Il15ra	AA690181|IL-15RA	interleukin 15 receptor, alpha chain	protein-coding
mm_154127.1	chr19	57241713	57241715	-	1	NA	Intergenic	Intergenic	-25682	NM_178688	226251	Mm.217161	NM_178688	ENSMUSG00000025085	Ablim1	2210411C18Rik|2610209L21Rik|4833406P10Rik|9330196J19Rik|AV079770|AW060987|AW215784|Limab1|mKIAA0059	actin-binding LIM protein 1	protein-coding
mm_124098.1	chr14	79300316	79300318	-	1	NA	intron (NM_025427, intron 2 of 4)	ID_B1|SINE|B4	1318	NM_025427	66214	Mm.29811	NM_025427	ENSMUSG00000022018	Rgcc	1190002H23Rik|Rgc-32|Rgc32	regulator of cell cycle	protein-coding
mm_165296.1	chr2	91099074	91099085	+	1	NA	intron (NM_011355, intron 1 of 4)	intron (NM_011355, intron 1 of 4)	2401	NM_011355	20375	Mm.1302	NM_011355	ENSMUSG00000002111	Spi1	Dis-1|Dis1|PU.1|Sfpi-1|Sfpi1|Spi-1|Tcfpu1|Tfpu.1	spleen focus forming virus (SFFV) proviral integration oncogene	protein-coding
mm_57877.1	chr6	131243957	131243966	-	1	NA	exon (NM_001170851, exon 3 of 9)	exon (NM_001170851, exon 3 of 9)	3401	NM_001170851	16633	Mm.4783	NM_008462	ENSMUSG00000030187	Klra2	Klra30|Ly49b	killer cell lectin-like receptor, subfamily A, member 2	protein-coding
mm_64293.1	chr7	141858852	141858891	+	1	NA	exon (NM_028801, exon 31 of 49)	exon (NM_028801, exon 31 of 49)	19799	NM_028801	74180	Mm.200752	NM_028801	ENSMUSG00000066108	Muc5b	2300002I04Rik|A130042M24|AV085033|MUC5|MUC9|mucin 5b	mucin 5, subtype B, tracheobronchial	protein-coding
mm_124839.1	chr15	9370334	9370344	+	1	NA	exon (NM_144845, exon 7 of 7)	exon (NM_144845, exon 7 of 7)	34741	NM_144845	223337	Mm.422853	NM_144845	ENSMUSG00000049152	Ugt3a2	AI313915	UDP glycosyltransferases 3 family, polypeptide A2	protein-coding
mm_137040.1	chr17	17893811	17893859	+	1	NA	3' UTR (NM_008039, exon 2 of 2)	3' UTR (NM_008039, exon 2 of 2)	6011	NM_008039	14289	Mm.378918	NM_008039	ENSMUSG00000052270	Fpr2	E330010I07Rik|Fpr-rs2	formyl peptide receptor 2	protein-coding
mm_151955.1	chr19	5801349	5801349	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	1323	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_73902.1	chr8	119446746	119446766	+	1	NA	promoter-TSS (NM_054095)	promoter-TSS (NM_054095)	37	NM_054095	117148	Mm.356184	NM_054095	ENSMUSG00000031837	Necab2	Efcbp2	N-terminal EF-hand calcium binding protein 2	protein-coding
mm_17384.1	chr2	27027272	27027288	-	1	NA	exon (NM_172659, exon 2 of 10)	exon (NM_172659, exon 2 of 10)	718	NM_172659	227659	Mm.41203	NM_172659	ENSMUSG00000036067	Slc2a6	A330096C23|F630103L12Rik|Glut6|Glut9	solute carrier family 2 (facilitated glucose transporter), member 6	protein-coding
mm_38595.1	chr4	141825606	141825634	-	1	NA	exon (NM_007919, exon 2 of 8)	exon (NM_007919, exon 2 of 8)	385	NM_007919	13706	Mm.45316	NM_007919	ENSMUSG00000058579	Cela2a	Ela-2|Ela2|Ela2a	chymotrypsin-like elastase family, member 2A	protein-coding
mm_147588.1	chr18	56562216	56562254	-	1	NA	promoter-TSS (NM_138600)	promoter-TSS (NM_138600)	63	NM_138600	110695	Mm.30250	NM_138600	ENSMUSG00000053644	Aldh7a1	Atq1|D18Wsu181e	aldehyde dehydrogenase family 7, member A1	protein-coding
mm_7675.1	chr1	128589030	128589040	-	1	NA	exon (NM_009911, exon 2 of 2)	exon (NM_009911, exon 2 of 2)	3264	NM_009911	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding
mm_140027.1	chr17	73950360	73950377	+	1	NA	promoter-TSS (NM_011723)	promoter-TSS (NM_011723)	-172	NM_011723	22436	Mm.11223	NM_011723	ENSMUSG00000024066	Xdh	XO|Xor|Xox-1|Xox1	xanthine dehydrogenase	protein-coding
mm_101190.1	chr11	17953862	17953897	-	1	NA	promoter-TSS (NM_026576)	promoter-TSS (NM_026576)	-4	NM_026576	68145	Mm.178684	NM_026576	ENSMUSG00000016984	Etaa1	5730466H23Rik|AA672646	Ewing tumor-associated antigen 1	protein-coding
mm_169415.1	chr14	52948577	52948579	+	1	NA	Intergenic	Intergenic	-452883	NM_001170918	57269	Mm.88822	NM_020512	ENSMUSG00000059887	Olfr1507	MOR244-1|Mor28|Or28	olfactory receptor 1507	protein-coding
mm_10942.1	chr2	25501820	25501841	+	1	NA	promoter-TSS (NM_001271777)	promoter-TSS (NM_001271777)	-111	NM_001271777	69379	Mm.24596	NM_027062	ENSMUSG00000015083	C8g	-	complement component 8, gamma polypeptide	protein-coding
mm_128910.1	chr15	73487324	73487333	-	1	NA	Intergenic	Intergenic	-25232	NM_001081066	105841	Mm.322557	NM_001081066	ENSMUSG00000036661	Dennd3	AI447457|E030003N15Rik	DENN/MADD domain containing 3	protein-coding
mm_29169.1	chr3	106486334	106486336	-	1	NA	promoter-TSS (NR_033207)	promoter-TSS (NR_033207)	295	NM_028110	72121	Mm.14816	NM_028110	ENSMUSG00000027901	Dennd2d	2010308M01Rik|AI451421	DENN/MADD domain containing 2D	protein-coding
mm_12703.1	chr2	76537518	76537528	+	1	NA	intron (NM_001290733, intron 4 of 26)	intron (NM_001290733, intron 4 of 26)	38517	NM_001290735	99031	Mm.240435	NM_145525	ENSMUSG00000042359	Osbpl6	1110062M20Rik|AI596402|ORP-6|mKIAA4128	oxysterol binding protein-like 6	protein-coding
mm_63916.1	chr7	139248212	139248229	+	1	NA	promoter-TSS (NM_001098636)	promoter-TSS (NM_001098636)	-262	NM_001033206	101631	Mm.334300	NM_001033206	ENSMUSG00000060260	Pwwp2b	AI594893|D7Ertd517e|D930023J19Rik|Pwwp2	PWWP domain containing 2B	protein-coding
mm_17218.1	chr2	25493906	25493960	-	1	NA	promoter-TSS (NM_029958)	promoter-TSS (NM_029958)	-22	NM_029958	77701	Mm.99123	NM_029958	ENSMUSG00000026943	Lcn12	9230102M18Rik	lipocalin 12	protein-coding
mm_54688.1	chr6	39420499	39420505	-	1	NA	promoter-TSS (NM_018810)	promoter-TSS (NM_018810)	-133	NM_018810	54484	Mm.270484	NM_018810	ENSMUSG00000029922	Mkrn1	RFP	makorin, ring finger protein, 1	protein-coding
mm_25606.1	chr3	117575492	117575507	+	1	NA	5' UTR (NM_029425, exon 1 of 6)	5' UTR (NM_029425, exon 1 of 6)	272	NM_001305451	75769	Mm.72187	NM_029425	ENSMUSG00000033342	Plppr5	4833424O15Rik|Lppr5|PRG-5|Pap2d	phospholipid phosphatase related 5	protein-coding
mm_6114.1	chr1	64121238	64121252	-	1	NA	5' UTR (NM_033563, exon 1 of 4)	5' UTR (NM_033563, exon 1 of 4)	144	NM_033563	93691	Mm.29466	NM_033563	ENSMUSG00000025959	Klf7	9830124P08Rik	Kruppel-like factor 7 (ubiquitous)	protein-coding
mm_100121.1	chr11	115899944	115899954	+	1	NA	promoter-TSS (NM_183259)	promoter-TSS (NM_183259)	-190	NM_183259	66528	Mm.275740	NM_183259	ENSMUSG00000048442	Smim5	2210020M01Rik	small integral membrane protein 5	protein-coding
mm_110769.1	chr12	70269238	70269240	-	1	NA	intron (NM_053167, intron 6 of 13)	intron (NM_053167, intron 6 of 13)	-39266	NR_037248	100526482		NR_037248	ENSMUSG00000078026	Mir466o	Mir4660|mmu-mir-466o	microRNA 466o	ncRNA
mm_108240.1	chr12	78194226	78194238	+	1	NA	Intergenic	Intergenic	-32423	NM_172952	268566	Mm.341742	NM_145965	ENSMUSG00000047454	Gphn	5730552E08Rik|AI662856|BC027112|C230040D23|GPH|GPHRYN|geph	gephyrin	protein-coding
mm_38878.1	chr4	149697848	149697856	-	1	NA	intron (NM_008840, intron 1 of 24)	intron (NM_008840, intron 1 of 24)	856	NM_001164050	18707	Mm.229108	NM_008840	ENSMUSG00000039936	Pik3cd	2410099E07Rik|2610208K16Rik|AW545373|p110delta	phosphatidylinositol 3-kinase catalytic delta polypeptide	protein-coding
mm_136141.1	chr16	87440499	87440542	-	1	NA	promoter-TSS (NM_016924)	promoter-TSS (NM_016924)	72	NM_016924	53858	Mm.162406	NM_016924	ENSMUSG00000041079	Rwdd2b	ORF5	RWD domain containing 2B	protein-coding
mm_140992.1	chr17	24850321	24850344	-	1	NA	promoter-TSS (NM_024284)	promoter-TSS (NM_024284)	-30	NM_023480	68636	Mm.347964	NM_023480	ENSMUSG00000045316	Fahd1	1110025H10Rik|AV002085	fumarylacetoacetate hydrolase domain containing 1	protein-coding
mm_130677.1	chr15	100675417	100675436	-	1	NA	exon (NM_033612, exon 7 of 8)	exon (NM_033612, exon 7 of 8)	-5926	NM_001270537	668218	Mm.451225	NM_001270537	ENSMUSG00000098112	Bin2	-	bridging integrator 2	protein-coding
mm_87011.1	chr10	26881208	26881213	+	1	NA	intron (NM_176837, intron 10 of 14)	B3A|SINE|B2	108698	NM_176837	73910	Mm.356496	NM_176837	ENSMUSG00000039031	Arhgap18	4833419J07Rik|AI314906|AI843501	Rho GTPase activating protein 18	protein-coding
mm_76303.1	chr8	84257263	84257301	-	1	NA	promoter-TSS (NM_026423)	promoter-TSS (NM_026423)	42	NM_026423	67873	Mm.278085	NM_026423	ENSMUSG00000004996	Mri1	2410018C20Rik	methylthioribose-1-phosphate isomerase 1	protein-coding
mm_34889.1	chr4	155601415	155601443	+	1	NA	promoter-TSS (NM_177186)	promoter-TSS (NM_177186)	13	NM_177186	320541	Mm.306018	NM_177186	ENSMUSG00000042202	Slc35e2	A530082C11Rik|AI957035	solute carrier family 35, member E2	protein-coding
mm_4053.1	chr1	165809442	165809455	+	1	NA	intron (NM_001113391, intron 1 of 7)	MIRb|SINE|MIR	20767	NM_001113392	12503	Mm.217308	NM_031162	ENSMUSG00000005763	Cd247	4930549J05Rik|A430104F18Rik|AW552088|Cd3|Cd3-eta|Cd3-zeta|Cd3h|Cd3z|Cd3zeta|T3z|Tcrk|Tcrz	CD247 antigen	protein-coding
mm_60924.1	chr7	46847103	46847118	+	1	NA	promoter-TSS (NM_001136069)	promoter-TSS (NM_001136069)	28	NM_001136069	16828	Mm.29324	NM_010699	ENSMUSG00000063229	Ldha	Ldh1|Ldhm|l7R2	lactate dehydrogenase A	protein-coding
mm_92393.1	chr10	76599412	76599429	-	1	NA	3' UTR (NM_001347207, exon 28 of 28)	3' UTR (NM_001347207, exon 28 of 28)	23772	NM_080845	14317	Mm.36278	NM_080845	ENSMUSG00000001155	Ftcd	-	formiminotransferase cyclodeaminase	protein-coding
mm_24514.1	chr3	92689292	92689306	+	1	NA	Intergenic	Intergenic	-2089	NM_027137	69611	Mm.176243	NM_027137	ENSMUSG00000103243	Lce1d	2310037L11Rik|AI415320|Sprrl7	late cornified envelope 1D	protein-coding
mm_146463.1	chr18	86711639	86711650	+	1	NA	promoter-TSS (NM_172633)	promoter-TSS (NM_172633)	-421	NM_172633	12405	Mm.70775	NM_172633	ENSMUSG00000024647	Cbln2	6330593N19Rik|A730004O05	cerebellin 2 precursor protein	protein-coding
mm_10980.1	chr2	25823686	25823703	+	1	NA	exon (NM_029959, exon 2 of 7)	exon (NM_029959, exon 2 of 7)	541	NM_029959	77704	Mm.159974	NM_029959	ENSMUSG00000023210	Lcn9	9230102I19Rik	lipocalin 9	protein-coding
mm_116288.1	chr13	35027078	35027099	-	1	NA	Intergenic	Intergenic	-32944	NM_001110331	23986	Mm.491141	NM_011868	ENSMUSG00000021417	Eci2	Acbd2|Drs1|Hca88|Peci	enoyl-Coenzyme A delta isomerase 2	protein-coding
mm_117769.1	chr13	96542335	96542345	-	1	NA	promoter-TSS (NM_001164222)	promoter-TSS (NM_001164222)	239	NM_012048	27015	Mm.89926	NM_012048	ENSMUSG00000021668	Polk	DINP|Dinb1	polymerase (DNA directed), kappa	protein-coding
mm_91835.1	chr10	57516896	57516953	-	1	NA	3' UTR (NM_019760, exon 9 of 9)	3' UTR (NM_019760, exon 9 of 9)	15605	NM_019760	56442	Mm.29344	NM_019760	ENSMUSG00000019877	Serinc1	1500011D18Rik|AI315070|AIGP-2|TMS-2|Tde1l|Tde2|Tms2|mKIAA1253	serine incorporator 1	protein-coding
mm_137058.1	chr17	17937759	17937778	+	1	NA	Intergenic	L1_Mur2|LINE|L1	-32690	NM_008042	14294	Mm.378918	NM_008042	ENSMUSG00000079700	Fpr3	ALX|Fpr-rs1|Fpr-s1|Fprl1|LXA4-R|Lxa4r	formyl peptide receptor 3	protein-coding
mm_33254.1	chr4	127168628	127168652	+	1	NA	promoter-TSS (NM_198618)	promoter-TSS (NM_198618)	-564	NM_198618	242667	Mm.331885	NM_198618	ENSMUSG00000042388	Dlgap3	BC058433|DAP-3|DAP3|Prpl8|Sapap3	discs, large (Drosophila) homolog-associated protein 3	protein-coding
mm_24087.1	chr3	87975768	87975796	+	1	NA	exon (NM_016701, exon 4 of 4)	exon (NM_016701, exon 4 of 4)	4689	NM_016701	18008	Mm.331129	NM_016701	ENSMUSG00000004891	Nes	AA166324|C78523|ESTM46	nestin	protein-coding
mm_103169.1	chr11	70459631	70459652	-	1	NA	promoter-TSS (NM_001029929)	promoter-TSS (NM_001029929)	19	NM_001029929	574428	Mm.472771	NM_001029929	ENSMUSG00000040829	Zmynd15	-	zinc finger, MYND-type containing 15	protein-coding
mm_65958.1	chr7	30428724	30428748	-	1	NA	TTS (NM_172142)	TTS (NM_172142)	5432	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_128696.1	chr15	62547961	62547968	-	1	NA	Intergenic	MTE-int|LTR|ERVL-MaLR	-328513	NR_003523	67552	Mm.484027	NM_026230		H2afy3	4933432H23Rik	H2A histone family, member Y3	pseudo
mm_79949.1	chr9	66060099	66060109	+	1	NA	promoter-TSS (NM_011149)	promoter-TSS (NM_011149)	-65	NM_011149	19035	Mm.335249	NM_011149	ENSMUSG00000032383	Ppib	AA408962|AA553318|AI844835|Cphn-2|Cphn2|CyP-20b	peptidylprolyl isomerase B	protein-coding
mm_8524.1	chr1	154884347	154884357	-	1	NA	Intergenic	Intergenic	-158432	NM_009782	12290	Mm.267517	NM_009782	ENSMUSG00000004110	Cacna1e	A430040I15|BII|Cach6|Cacnl1a6|Cav2.3|Cchra1|alpha1E	calcium channel, voltage-dependent, R type, alpha 1E subunit	protein-coding
mm_44061.1	chr5	148303177	148303236	+	1	NA	intron (NM_029920, intron 12 of 14)	Lx9|LINE|L1	89609	NM_001301424	11987	Mm.275489	NM_007513	ENSMUSG00000041313	Slc7a1	4831426K01Rik|AI447493|Atrc-1|Atrc1|Cat1|Rec-1|Rev-1|mCAT-1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 1	protein-coding
mm_125987.1	chr15	76344432	76344452	+	1	NA	exon (NM_025567, exon 2 of 7)	exon (NM_025567, exon 2 of 7)	919	NM_025567	66445	Mm.29196	NM_025567	ENSMUSG00000022551	Cyc1	2610002H19Rik|AA408921|Cyct1	cytochrome c-1	protein-coding
mm_144280.1	chr18	11839417	11839475	+	1	NA	promoter-TSS (NR_045421)	promoter-TSS (NR_045421)	-69	NR_045421	621998	Mm.353277	NR_045421		Gm6277	-	predicted gene 6277	ncRNA
mm_139006.1	chr17	45570336	45570348	+	1	NA	exon (NM_008302, exon 6 of 11)	exon (NM_008302, exon 6 of 11)	2919	NM_008302	15516	Mm.2180	NM_008302	ENSMUSG00000023944	Hsp90ab1	90kDa|AL022974|C81438|Hsp84|Hsp84-1|Hsp90|Hspcb	heat shock protein 90 alpha (cytosolic), class B member 1	protein-coding
mm_136824.1	chr17	12584184	12584195	+	1	NA	promoter-TSS (NM_013667)	promoter-TSS (NM_013667)	0	NM_013667	20518	Mm.17322	NM_013667	ENSMUSG00000040966	Slc22a2	Oct2|Orct2	solute carrier family 22 (organic cation transporter), member 2	protein-coding
mm_99943.1	chr11	111066184	111066188	+	1	NA	promoter-TSS (NM_008425)	promoter-TSS (NM_008425)	22	NM_008425	16518	Mm.4951	NM_008425	ENSMUSG00000041695	Kcnj2	IRK1|Kcnf1|Kir2.1	potassium inwardly-rectifying channel, subfamily J, member 2	protein-coding
mm_157192.1	chrX	12079270	12079276	-	1	NA	intron (NM_001168321, intron 1 of 13)	CpG	1280	NM_175045	71458	Mm.196328	NM_029510	ENSMUSG00000040363	Bcor	2900008C10Rik|5830466J11Rik|8430401K06Rik|BcorR|D930024N20Rik|mKIAA1575	BCL6 interacting corepressor	protein-coding
mm_53346.1	chr6	129350204	129350210	+	1	NA	promoter-TSS (NM_177686)	promoter-TSS (NM_177686)	-37	NM_177686	232413	Mm.90241	NM_177686	ENSMUSG00000053063	Clec12a	CLL-1|D230024O04|KLRL1|Micl	C-type lectin domain family 12, member a	protein-coding
mm_121513.1	chr14	121998240	121998270	+	1	NA	intron (NM_026861, intron 7 of 8)	MER21C|LTR|ERVL	-33062	NM_183031	321019	Mm.265618	NM_183031	ENSMUSG00000051212	Gpr183	Ebi2	G protein-coupled receptor 183	protein-coding
mm_59922.1	chr7	30422390	30422431	+	1	NA	promoter-TSS (NM_172142)	promoter-TSS (NM_172142)	-894	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_54893.1	chr6	46530187	46530203	-	1	NA	intron (NM_001004357, intron 13 of 23)	intron (NM_001004357, intron 13 of 23)	-714201	NM_025771	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding
mm_8617.1	chr1	156036474	156036478	-	1	NA	promoter-TSS (NM_144791)	promoter-TSS (NM_144791)	4	NM_144791	208263	Mm.211654	NM_144791	ENSMUSG00000026466	Tor1aip1	LAP1|Lap1B	torsin A interacting protein 1	protein-coding
mm_4353.1	chr1	171907320	171907344	+	1	NA	Intergenic	RMER17A2|LTR|ERVK	-10130	NM_001347187	30925	Mm.486404	NM_030710	ENSMUSG00000015314	Slamf6	KAL1|KAL1b|Ly108|NTB-A|NTBA|SF2000	SLAM family member 6	protein-coding
mm_94958.1	chr11	30771746	30771792	+	1	NA	promoter-TSS (NM_134013)	promoter-TSS (NM_134013)	-6	NM_134013	103554	Mm.240066	NM_134013	ENSMUSG00000040850	Psme4	AA409398|AU041366|TEMO|mKIAA0077	proteasome (prosome, macropain) activator subunit 4	protein-coding
mm_132834.1	chr16	45535304	45535317	+	1	NA	promoter-TSS (NM_198106)	promoter-TSS (NM_198106)	44	NM_198106	208169	Mm.277437	NM_198106	ENSMUSG00000033210	Slc9c1	Gm610|NHE-10|Slc9a10|sNHE|spermNHE	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	protein-coding
mm_14869.1	chr2	148799555	148799563	+	1	NA	intron (NM_009978, intron 1 of 3)	intron (NM_009978, intron 1 of 3)	720	NM_009978	13012	Mm.20435	NM_009978	ENSMUSG00000027442	Cst8	Cres|Cst-rs1	cystatin 8 (cystatin-related epididymal spermatogenic)	protein-coding
mm_120538.1	chr14	67234621	67234645	+	1	NA	intron (NM_010095, intron 1 of 16)	CpG	1341	NM_001276387	13592	Mm.319947	NM_010095	ENSMUSG00000022053	Ebf2	D14Ggc1e|EBF-2|Mmot1|O/E-3|OE-3	early B cell factor 2	protein-coding
mm_142003.1	chr17	35199756	35199766	-	1	NA	3' UTR (NM_013693, exon 4 of 4)	3' UTR (NM_013693, exon 4 of 4)	2246	NM_013693	21926	Mm.1293	NM_013693	ENSMUSG00000024401	Tnf	DIF|TNF-a|TNF-alpha|TNFSF2|TNFalpha|Tnfa|Tnfsf1a|Tnlg1f	tumor necrosis factor	protein-coding
mm_26035.1	chr3	135511865	135511873	+	1	NA	exon (NM_027288, exon 4 of 17)	exon (NM_027288, exon 4 of 17)	26258	NM_027288	110173	Mm.280536	NM_027288	ENSMUSG00000028164	Manba	2410030O07Rik|B930014J03Rik|Bmn	mannosidase, beta A, lysosomal	protein-coding
mm_132587.1	chr16	38371974	38372006	+	1	NA	intron (NM_001081984, intron 2 of 3)	intron (NM_001081984, intron 2 of 3)	9800	NM_022318	64082	Mm.390856	NM_022318	ENSMUSG00000022803	Popdc2	AV006127|Pop2	popeye domain containing 2	protein-coding
mm_15284.1	chr2	155276597	155276614	+	1	NA	non-coding (NR_046364, exon 1 of 3)	non-coding (NR_046364, exon 1 of 3)	241	NR_046364	66734	Mm.196239	NM_025735	ENSMUSG00000027602	Map1lc3a	1010001H21Rik|4922501H04Rik|LC3|LC3a	microtubule-associated protein 1 light chain 3 alpha	protein-coding
mm_28020.1	chr3	83045971	83045973	-	1	NA	intron (NM_181849, intron 3 of 7)	intron (NM_181849, intron 3 of 7)	3891	NM_181849	110135	Mm.30063	NM_181849	ENSMUSG00000033831	Fgb	2510049G14Rik	fibrinogen beta chain	protein-coding
mm_166784.1	chr6	143085585	143085589	-	1	NA	intron (NM_001109688, intron 3 of 24)	ORR1C2-int|LTR|ERVL-MaLR	14565	NM_001286578	74741	Mm.130260	NM_029081	ENSMUSG00000030279	C2cd5	5730419I09Rik|C030008B15Rik|CDP138	C2 calcium-dependent domain containing 5	protein-coding
mm_38866.1	chr4	149485158	149485199	-	1	NA	promoter-TSS (NM_026963)	promoter-TSS (NM_026963)	-36	NM_133435	66454	Mm.76062	NM_133435	ENSMUSG00000028992	Nmnat1	2610529L11Rik|5730441G13Rik|D4Cole1e|nmnat	nicotinamide nucleotide adenylyltransferase 1	protein-coding
mm_98226.1	chr11	88067675	88067703	+	1	NA	promoter-TSS (NM_016686)	promoter-TSS (NM_016686)	-590	NM_016686	22344	Mm.46628	NM_016686	ENSMUSG00000018377	Vezf1	AI848691|AW046909|db1	vascular endothelial zinc finger 1	protein-coding
mm_119050.1	chr14	30635449	30635466	+	1	NA	Intergenic	Intergenic	-9249	NM_011103	18753	Mm.2314	NM_011103	ENSMUSG00000021948	Prkcd	AI385711|D14Ertd420e|PKC[d]|PKCdelta|Pkcd	protein kinase C, delta	protein-coding
mm_11018.1	chr2	26604505	26604506	+	1	NA	promoter-TSS (NM_026212)	promoter-TSS (NM_026212)	-88	NM_026212	67512	Mm.24244	NM_026212	ENSMUSG00000026922	Agpat2	2510002J07Rik|AV000834|BSCL|BSCL1|LPAAB|LPAAT-beta	1-acylglycerol-3-phosphate O-acyltransferase 2 (lysophosphatidic acid acyltransferase, beta)	protein-coding
mm_161569.1	chr16	20589536	20589536	+	1	NA	promoter-TSS (NM_182636)	promoter-TSS (NM_182636)	-46	NM_182636	328643	Mm.40539	NM_182636	ENSMUSG00000046613	Vwa5b2	BB182430|EG328644|Gm1738|Gm931	von Willebrand factor A domain containing 5B2	protein-coding
mm_60390.1	chr7	44474605	44474615	+	1	NA	Intergenic	Intergenic	4263	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_144584.1	chr18	31937271	31937288	+	1	NA	intron (NM_144862, intron 1 of 9)	intron (NM_144862, intron 1 of 9)	5772	NM_144862	225341	Mm.24551	NM_144862	ENSMUSG00000024395	Lims2	PINCH2	LIM and senescent cell antigen like domains 2	protein-coding
mm_76788.1	chr8	102717244	102717254	-	1	NA	intron (NM_009866, intron 2 of 12)	intron (NM_009866, intron 2 of 12)	67862	NM_009866	12552	Mm.1571	NM_009866	ENSMUSG00000031673	Cdh11	Cad11|OSF-4	cadherin 11	protein-coding
mm_3996.1	chr1	164473505	164473535	+	1	NA	Intergenic	Intergenic	-15165	NM_009721	11931	Mm.4550	NM_009721	ENSMUSG00000026576	Atp1b1	Atp4b|Atpb|Atpb-1|NKbeta1	ATPase, Na+/K+ transporting, beta 1 polypeptide	protein-coding
mm_108182.1	chr12	76533541	76533597	+	1	NA	promoter-TSS (NR_039597)	promoter-TSS (NR_039597)	9	NM_153804	263406	Mm.291854	NM_153804	ENSMUSG00000052609	Plekhg3	BC030417	pleckstrin homology domain containing, family G (with RhoGef domain) member 3	protein-coding
mm_17028.1	chr2	19553889	19553894	-	1	NA	promoter-TSS (NM_027600)	promoter-TSS (NM_027600)	19	NM_027600	70909	Mm.158488	NM_027600	ENSMUSG00000026734	4921504E06Rik	4921522E24Rik	RIKEN cDNA 4921504E06 gene	protein-coding
mm_96482.1	chr11	67684199	67684223	+	1	NA	3' UTR (NM_001277080, exon 13 of 13)	3' UTR (NM_001277080, exon 13 of 13)	-11115	NM_009038	19674	Mm.439726	NM_009038	ENSMUSG00000020907	Rcvrn	CAR|S-modulin	recoverin	protein-coding
mm_116698.1	chr13	49790242	49790244	-	1	NA	Intergenic	Intergenic	108113	NM_172015	105148	Mm.21118	NM_172015	ENSMUSG00000037851	Iars	2510016L12Rik|AI327140|AU044614|E430001P04Rik|ILRS	isoleucine-tRNA synthetase	protein-coding
mm_158471.1	chrX	141207593	141207608	-	1	NA	intron (NM_053185, intron 14 of 44)	intron (NM_053185, intron 14 of 44)	-250889	NM_001164177	53380	Mm.17640	NM_016883	ENSMUSG00000031429	Psmd10	AW554874	proteasome (prosome, macropain) 26S subunit, non-ATPase, 10	protein-coding
mm_104837.1	chr11	99168008	99168038	-	1	NA	Intergenic	Intergenic	-12946	NM_007719	12775	Mm.2932	NM_007719	ENSMUSG00000037944	Ccr7	CC-CKR-7|CCR-7|CD197|Cdw197|Cmkbr7|EBI1|Ebi1h	chemokine (C-C motif) receptor 7	protein-coding
mm_119834.1	chr14	54368362	54368379	+	1	NA	exon (NM_026936, exon 10 of 10)	exon (NM_026936, exon 10 of 10)	7529	NM_026936	69089	Mm.182340	NM_026936	ENSMUSG00000000959	Oxa1l	1810020M02Rik|AI894287	oxidase assembly 1-like	protein-coding
mm_148825.1	chr19	6306873	6306896	+	1	NA	intron (NM_001033342, intron 1 of 36)	intron (NM_001033342, intron 1 of 36)	427	NM_001033342	240505	Mm.329622	NM_001033342	ENSMUSG00000024769	Cdc42bpg	BC046418|MRCKgamma	CDC42 binding protein kinase gamma (DMPK-like)	protein-coding
mm_107237.1	chr12	26478391	26478402	+	1	NA	3' UTR (NM_020557, exon 5 of 5)	3' UTR (NM_020557, exon 5 of 5)	9181	NM_020557	22169	Mm.271839	NM_020557	ENSMUSG00000020638	Cmpk2	1200004E04Rik|TDKI|Tyki	cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial	protein-coding
mm_40193.1	chr5	36748598	36748620	+	1	NA	promoter-TSS (NM_133724)	promoter-TSS (NM_133724)	70	NM_133724	117197	Mm.46744	NM_133724	ENSMUSG00000060708	Bloc1s4	2610101N07Rik|Blos4|Cno	biogenesis of lysosomal organelles complex-1, subunit 4, cappuccino	protein-coding
mm_169068.1	chr1	32728077	32728078	+	1	NA	Intergenic	Intergenic	-180784	NM_001164286	408191	Mm.479439	NM_001164286	ENSMUSG00000091318	Gm5415	EG408191|Senp14	predicted gene 5415	protein-coding
mm_101168.1	chr11	16974109	16974132	-	1	NA	3' UTR (NM_019549, exon 10 of 10)	3' UTR (NM_019549, exon 10 of 10)	22710	NM_176982	319701	Mm.120672	NM_176982	ENSMUSG00000044966	Fbxo48	A630050E13Rik	F-box protein 48	protein-coding
mm_157601.1	chrX	53370471	53370501	-	1	NA	promoter-TSS (NM_027409)	promoter-TSS (NM_027409)	73	NM_027409	70380	Mm.491083	NM_027409	ENSMUSG00000023074	Mospd1	1810018L05Rik	motile sperm domain containing 1	protein-coding
mm_54556.1	chr6	37213001	37213011	-	1	NA	intron (NM_001347104, intron 1 of 32)	intron (NM_001347104, intron 1 of 32)	86970	NM_001081206	320127	Mm.119469	NM_001081206	ENSMUSG00000038665	Dgki	C130010K08Rik	diacylglycerol kinase, iota	protein-coding
mm_97977.1	chr11	83865622	83865631	+	1	NA	intron (NM_001291269, intron 4 of 8)	intron (NM_001291269, intron 4 of 8)	12666	NM_001291269	21410	Mm.7226	NM_009330	ENSMUSG00000020679	Hnf1b	HNF-1-beta|HNF-1B|HNF-1Beta|Hnf1beta|LFB3|Tcf-2|Tcf2|vHNF1	HNF1 homeobox B	protein-coding
mm_13326.1	chr2	102783159	102783174	+	1	NA	3' UTR (NM_001077514, exon 11 of 11)	3' UTR (NM_001077514, exon 11 of 11)	76728	NM_001077515	20511	Mm.267547	NM_011393	ENSMUSG00000005089	Slc1a2	1700091C19Rik|2900019G14Rik|AI159670|Eaat2|GLT-1|GLT1|MGLT1	solute carrier family 1 (glial high affinity glutamate transporter), member 2	protein-coding
mm_53792.1	chr6	146657211	146657218	+	1	NA	promoter-TSS (NR_046277)	promoter-TSS (NR_046277)	-4	NR_046277	74925	Mm.386304	NR_046277	ENSMUSG00000085238	4930479D17Rik	-	RIKEN cDNA 4930479D17 gene	ncRNA
mm_134340.1	chr16	16542190	16542209	-	1	NA	intron (NM_001301817, intron 1 of 16)	Lx7|LINE|L1	-14788	NM_001301818	224014	Mm.256131	NM_139232	ENSMUSG00000022788	Fgd4	9030023J02Rik|9330209B17Rik|Frabp|ZFYVE6	FYVE, RhoGEF and PH domain containing 4	protein-coding
mm_3393.1	chr1	142612233	142612233	+	1	NA	Intergenic	IAPEY_LTR|LTR|ERVK	-1028464	NM_020025	26878	Mm.285580	NM_020025	ENSMUSG00000033849	B3galt2	-	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 2	protein-coding
mm_72599.1	chr8	84415018	84415032	+	1	NA	promoter-TSS (NM_001252060)	promoter-TSS (NM_001252060)	-339	NM_001252060	12286	Mm.334658	NM_007578	ENSMUSG00000034656	Cacna1a	APCA|BI|Caca1a|Cacnl1a4|Cav2.1|Ccha1a|EA2|FHM|HPCA|MHP|MHP1|SCA6|alpha1A|la|nmf352|rkr|smrl|tg	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	protein-coding
mm_7020.1	chr1	86666690	86666694	-	1	NA	3' UTR (NM_010933, exon 3 of 3)	3' UTR (NM_010933, exon 3 of 3)	3881	NM_010933	18159	Mm.12802	NM_010933	ENSMUSG00000026241	Nppc	CNP|lbab	natriuretic peptide type C	protein-coding
mm_19369.1	chr2	91183018	91183060	-	1	NA	promoter-TSS (NM_145527)	promoter-TSS (NM_145527)	8	NM_001177719	228355	Mm.36410	NM_145527	ENSMUSG00000040687	Madd	9630059K23Rik|IG20	MAP-kinase activating death domain	protein-coding
mm_53788.1	chr6	146633835	146633878	+	1	NA	intron (NM_026281, intron 1 of 11)	intron (NM_026281, intron 1 of 11)	736	NM_026281	67623	Mm.278037	NM_026281	ENSMUSG00000040234	Tm7sf3	2010003B14Rik|NARP1	transmembrane 7 superfamily member 3	protein-coding
mm_152452.1	chr19	10832174	10832188	-	1	NA	Intergenic	Intergenic	-2123	NM_009852	12511	Mm.290897	NM_009852	ENSMUSG00000024670	Cd6	-	CD6 antigen	protein-coding
mm_5938.1	chr1	55764644	55764646	-	1	NA	Intergenic	L2b|LINE|L2	-166596	NR_045837	329159	Mm.98697	NR_045837	ENSMUSG00000099950	9130227L01Rik	-	RIKEN cDNA 9130227L01 gene	ncRNA
mm_102922.1	chr11	69600560	69600575	-	1	NA	3' UTR (NM_013415, exon 7 of 7)	3' UTR (NM_013415, exon 7 of 7)	5393	NM_013415	11932	Mm.235204	NM_013415	ENSMUSG00000041329	Atp1b2	Amog|Atpb-2	ATPase, Na+/K+ transporting, beta 2 polypeptide	protein-coding
mm_63725.1	chr7	130861815	130861827	+	1	NA	Intergenic	Intergenic	-3903	NM_001346515	101476	Mm.323554	NM_133942	ENSMUSG00000040268	Plekha1	AA960558|C920009D07Rik|TAPP1	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 1	protein-coding
mm_111769.1	chr12	104032871	104032893	-	1	NA	intron (NM_026535, intron 3 of 4)	intron (NM_026535, intron 3 of 4)	11561	NM_026535	68054	Mm.20286	NM_026535	ENSMUSG00000041567	Serpina12	4632419J12Rik	serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 12	protein-coding
mm_166551.1	chr6	41312278	41312297	+	1	NA	exon (NM_001003405, exon 3 of 5)	exon (NM_001003405, exon 3 of 5)	2423	NM_001003405	103964	Mm.333022	NM_001003405	ENSMUSG00000036938	Try5	1810049H19Rik|Tc|Tesp4	trypsin 5	protein-coding
mm_121621.1	chr14	8299630	8299665	-	1	NA	exon (NM_183187, exon 3 of 4)	exon (NM_183187, exon 3 of 4)	10129	NM_183187	268709	Mm.256058	NM_183187	ENSMUSG00000021750	Fam107a	DRR1	family with sequence similarity 107, member A	protein-coding
mm_52941.1	chr6	122952421	122952440	+	1	NA	promoter-TSS (NM_153197)	promoter-TSS (NM_153197)	-85	NM_001204241	73149	Mm.25684	NM_153197	ENSMUSG00000043832	Clec4a3	3110037K17Rik|Dcir3	C-type lectin domain family 4, member a3	protein-coding
mm_141458.1	chr17	30563816	30563819	-	1	NA	intron (NM_172618, intron 1 of 11)	L1MC4|LINE|L1	12470	NM_172618	224671	Mm.41220	NM_027060	ENSMUSG00000062202	Btbd9	1700023F20Rik|4930402L05|AI464421	BTB (POZ) domain containing 9	protein-coding
mm_138496.1	chr17	35200736	35200746	+	1	NA	intron (NM_001278601, intron 2 of 2)	intron (NM_001278601, intron 2 of 2)	1266	NM_013693	21926	Mm.1293	NM_013693	ENSMUSG00000024401	Tnf	DIF|TNF-a|TNF-alpha|TNFSF2|TNFalpha|Tnfa|Tnfsf1a|Tnlg1f	tumor necrosis factor	protein-coding
mm_42041.1	chr5	108406053	108406059	+	1	NA	intron (NM_008806, intron 3 of 21)	RSINE1|SINE|B4	17683	NM_008806	18587	Mm.1372	NM_008806	ENSMUSG00000029491	Pde6b	Pdeb|r|rd|rd-1|rd1|rd10	phosphodiesterase 6B, cGMP, rod receptor, beta polypeptide	protein-coding
mm_37245.1	chr4	118179629	118179682	-	1	NA	intron (NM_172382, intron 1 of 18)	intron (NM_172382, intron 1 of 18)	388	NM_172382	230674	Mm.234234	NM_172382	ENSMUSG00000033326	Kdm4a	D4Ertd222e|JHDM3A|Jmjd2|Jmjd2a|mKIAA0677	lysine (K)-specific demethylase 4A	protein-coding
mm_102177.1	chr11	54028097	54028111	-	1	NA	promoter-TSS (NM_001330304)	promoter-TSS (NM_001330304)	0	NM_019687	30805	Mm.274590	NM_019687	ENSMUSG00000020334	Slc22a4	Octn1	solute carrier family 22 (organic cation transporter), member 4	protein-coding
mm_128626.1	chr15	59044532	59044538	-	1	NA	intron (NM_001146180, intron 3 of 13)	intron (NM_001146180, intron 3 of 13)	37491	NM_001146180	211401	Mm.215481	NM_144800	ENSMUSG00000022353	Mtss1	2310003N14Rik|BC024131|D130001D01Rik|Mim|mKIAA0429	metastasis suppressor 1	protein-coding
mm_162231.1	chrX	150655464	150655464	-	1	NA	exon (NM_019548, exon 3 of 14)	exon (NM_019548, exon 3 of 14)	1972	NM_019548	56191	Mm.3597	NM_019548	ENSMUSG00000025272	Tro	AA409408|Maged3|Maged3l|Tnn|Trol|magphinin	trophinin	protein-coding
mm_157376.1	chrX	37878816	37878820	-	1	NA	exon (NM_001004193, exon 1 of 4)	exon (NM_001004193, exon 1 of 4)	126	NM_001004193	434768	Mm.336025	NM_001004193	ENSMUSG00000064137	Rhox8	Tox	reproductive homeobox 8	protein-coding
mm_95691.1	chr11	54314929	54314957	+	1	NA	promoter-TSS (NM_001033599)	promoter-TSS (NM_001033599)	40	NM_001033599	216739	Mm.267478	NM_144823	ENSMUSG00000020333	Acsl6	A330035H04Rik|AW050338|Facl6|LACS|Lacsl|mKIAA0837	acyl-CoA synthetase long-chain family member 6	protein-coding
mm_145705.1	chr18	62657369	62657370	+	1	NA	intron (NM_177829, intron 5 of 8)	intron (NM_177829, intron 5 of 8)	-61105	NM_001001803	408198	Mm.478742	NM_001001803	ENSMUSG00000060201	Spink7	EG408198|Ecg2	serine peptidase inhibitor, Kazal type 7 (putative)	protein-coding
mm_168783.1	chr12	18679094	18679095	-	1	NA	Intergenic	B1_Mm|SINE|Alu	164584	NM_001201330	236366	Mm.352227	NM_001033157	ENSMUSG00000073197	5730507C01Rik	-	RIKEN cDNA 5730507C01 gene	protein-coding
mm_2560.1	chr1	115684728	115684744	+	1	NA	promoter-TSS (NM_001077425)	promoter-TSS (NM_001077425)	-401	NM_001077425	636808	Mm.101576	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding
mm_81850.1	chr9	118606688	118606751	+	1	NA	promoter-TSS (NM_133721)	promoter-TSS (NM_133721)	10	NM_133721	104099	Mm.335520	NM_133721	ENSMUSG00000039115	Itga9	(alpha)9|2610002H11Rik|6720458D17Rik|AI461869|D130073C02|D9Ertd428e	integrin alpha 9	protein-coding
mm_70260.1	chr8	3516919	3516932	+	1	NA	intron (NM_001122818, intron 3 of 34)	CpG	1541	NM_015801	50767	Mm.23085	NM_015801	ENSMUSG00000004565	Pnpla6	AI661849|MSws|Nte	patatin-like phospholipase domain containing 6	protein-coding
mm_33062.1	chr4	123233814	123233822	+	1	NA	5' UTR (NM_013905, exon 1 of 5)	5' UTR (NM_013905, exon 1 of 5)	262	NM_013905	56198	Mm.103615	NM_013905	ENSMUSG00000032744	Heyl	Hey3|Hrt3|bHLHb33|hesr3	hairy/enhancer-of-split related with YRPW motif-like	protein-coding
mm_37261.1	chr4	118437332	118437354	-	1	NA	promoter-TSS (NM_023223)	promoter-TSS (NM_023223)	0	NM_023223	107995	Mm.261764	NM_023223	ENSMUSG00000006398	Cdc20	2310042N09Rik|C87100|p55CDC	cell division cycle 20	protein-coding
mm_112653.1	chr13	16026420	16026424	+	1	NA	exon (NM_008380, exon 5 of 5)	exon (NM_008380, exon 5 of 5)	14571	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_62041.1	chr7	92235080	92235123	+	1	NA	5' UTR (NM_001243047, exon 1 of 11)	5' UTR (NM_001243047, exon 1 of 11)	131	NM_001243047	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_9928.1	chr1	189883978	189883999	-	1	NA	exon (NM_026796, exon 10 of 12)	exon (NM_026796, exon 10 of 12)	38300	NM_026796	226830	Mm.156895	NM_026796	ENSMUSG00000026603	Smyd2	1110020E07Rik|4930402C15|KMT3C|Zmynd14	SET and MYND domain containing 2	protein-coding
mm_155575.1	chrX	77511242	77511250	+	1	NA	promoter-TSS (NM_020601)	promoter-TSS (NM_020601)	19	NM_020601	21372	Mm.258476	NM_020601	ENSMUSG00000025246	Tbl1x	5330429M20|Tbl1	transducin (beta)-like 1 X-linked	protein-coding
mm_39369.1	chr5	10233955	10233960	+	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	-508605	NM_181850	108069	Mm.318966	NM_181850	ENSMUSG00000003974	Grm3	0710001G23Rik|Gprc1c|mGlu3|mGluR3	glutamate receptor, metabotropic 3	protein-coding
mm_39664.1	chr5	25222845	25222855	+	1	NA	promoter-TSS (NM_144908)	promoter-TSS (NM_144908)	-43	NM_144908	231050	Mm.21814	NM_144908	ENSMUSG00000038072	Galnt11	A430075I06Rik|AI648252|E430002F06Rik	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 11	protein-coding
mm_35445.1	chr4	40239714	40239727	-	1	NA	5' UTR (NM_172689, exon 1 of 18)	5' UTR (NM_172689, exon 1 of 18)	105	NM_172689	230073	Mm.86382	NM_172689	ENSMUSG00000040296	Ddx58	6430573D20Rik|C330021E21|RIG-I|RLR-1	DEAD (Asp-Glu-Ala-Asp) box polypeptide 58	protein-coding
mm_45405.1	chr5	66299332	66299342	-	1	NA	3' UTR (NM_009686, exon 18 of 18)	3' UTR (NM_009686, exon 18 of 18)	38328	NM_001201416	11787	Mm.5159	NM_009686	ENSMUSG00000029207	Apbb2	2310007D03Rik|FE65L1|Rirl1|TR2L|Zfra	amyloid beta (A4) precursor protein-binding, family B, member 2	protein-coding
mm_82514.1	chr9	20521549	20521629	-	1	NA	promoter-TSS (NM_001135019)	promoter-TSS (NM_001135019)	-170	NM_001082485	77519	Mm.431849	NM_001082485	ENSMUSG00000060510	Zfp266	5330440G10Rik|5730601F06Rik|AW552317	zinc finger protein 266	protein-coding
mm_163233.1	chr11	103621414	103621416	-	1	NA	Intergenic	Intergenic	-6676	NM_001033434	380730	Mm.380214	NM_001033434	ENSMUSG00000034239	Gm884	LRRC37	predicted gene 884	protein-coding
mm_50325.1	chr6	48395653	48395688	+	1	NA	promoter-TSS (NM_133922)	promoter-TSS (NM_133922)	84	NM_001347153	77827	Mm.107646	NM_133922	ENSMUSG00000042810	Krba1	A930040G15Rik|AI448780	KRAB-A domain containing 1	protein-coding
mm_46554.1	chr5	106680319	106680321	-	1	NA	intron (NM_026856, intron 1 of 6)	B1_Mur3|SINE|Alu	16510	NM_026856	52397	Mm.249474	NM_026856	ENSMUSG00000049606	Zfp644	1110068L01Rik|AA408882|BM-005|D5Ertd689e|Zep-2	zinc finger protein 644	protein-coding
mm_153645.1	chr19	44246561	44246587	-	1	NA	Intergenic	Intergenic	43286	NM_024450	30049	Mm.480594	NM_024450	ENSMUSG00000025202	Scd3	4930513N16Rik	stearoyl-coenzyme A desaturase 3	protein-coding
mm_38269.1	chr4	136880763	136880773	-	1	NA	exon (NM_009777, exon 3 of 3)	exon (NM_009777, exon 3 of 3)	5409	NM_009777	12260	Mm.2570	NM_009777	ENSMUSG00000036905	C1qb	-	complement component 1, q subcomponent, beta polypeptide	protein-coding
mm_89353.1	chr10	88201088	88201116	+	1	NA	promoter-TSS (NM_001122960)	promoter-TSS (NM_001122960)	5	NM_027487	67282	Mm.208465	NM_026070	ENSMUSG00000020056	Washc3	2900091E11Rik|5730495F03Rik|Ccdc53	WASH complex subunit 3	protein-coding
mm_81327.1	chr9	108508051	108508076	+	1	NA	promoter-TSS (NM_133794)	promoter-TSS (NM_133794)	58	NM_133794	97541	Mm.272427	NM_133794	ENSMUSG00000032604	Qars	1110018N24Rik|1200016L19Rik|C80286|GLNRS	glutaminyl-tRNA synthetase	protein-coding
mm_128761.1	chr15	65912420	65912437	-	1	NA	promoter-TSS (NM_010953)	promoter-TSS (NM_010953)	-141	NM_010953	18256	Mm.41776	NM_010953	ENSMUSG00000015001	Oc90	Ocn-95|PLA2L|Pla2ll|oc95	otoconin 90	protein-coding
mm_103323.1	chr11	73326473	73326478	-	1	NA	Intergenic	Intergenic	-1838	NM_023113	11484	Mm.293574	NM_023113	ENSMUSG00000020774	Aspa	Acy-2|Acy2|nur7	aspartoacylase	protein-coding
mm_37977.1	chr4	133601478	133601515	-	1	NA	exon (NM_018754, exon 1 of 1)	exon (NM_018754, exon 1 of 1)	672	NM_018754	55948	Mm.44482	NM_018754	ENSMUSG00000047281	Sfn	Er|Mme1|Ywhas	stratifin	protein-coding
mm_4558.1	chr1	177445661	177445672	+	1	NA	promoter-TSS (NM_013915)	promoter-TSS (NM_013915)	-155	NM_013915	30928	Mm.330700	NM_013915	ENSMUSG00000063659	Zbtb18	RP58|Zfp238|Znf238	zinc finger and BTB domain containing 18	protein-coding
mm_118871.1	chr14	25855780	25855788	+	1	NA	intron (NM_013469, intron 1 of 14)	HAL1|LINE|L1	13629	NM_013469	11744	Mm.294083	NM_013469	ENSMUSG00000021866	Anxa11	A830099O17Rik|Anx11	annexin A11	protein-coding
mm_134255.1	chr16	13730488	13730503	-	1	NA	promoter-TSS (NM_011987)	promoter-TSS (NM_011987)	-11	NM_011987	26565	Mm.4214	NM_011987	ENSMUSG00000022683	Pla2g10	GX sPLA2|PLA2GX|sPLA2-X	phospholipase A2, group X	protein-coding
mm_12567.1	chr2	72979429	72979501	+	1	NA	promoter-TSS (NR_045269)	promoter-TSS (NR_045269)	33	NR_045269	100503849	Mm.389285	NM_183265		Sp3os	1700011J10Rik	trans-acting transcription factor 3, opposite strand	ncRNA
mm_16899.1	chr2	13283266	13283273	-	1	NA	intron (NM_001081084, intron 63 of 66)	intron (NM_001081084, intron 63 of 66)	-11854	NM_009105	20163	Mm.905	NM_009105	ENSMUSG00000026727	Rsu1	RsuI|rsp-1	Ras suppressor protein 1	protein-coding
mm_140618.1	chr17	11385374	11385382	-	1	NA	intron (NM_001317726, intron 4 of 6)	intron (NM_001317726, intron 4 of 6)	497811	NR_045808	52027	Mm.442257	NR_045808		D17Ertd648e	-	DNA segment, Chr 17, ERATO Doi 648, expressed	ncRNA
mm_137543.1	chr17	27556844	27556858	+	1	NA	5' UTR (NM_016660, exon 1 of 5)	intron (NM_001025427, intron 1 of 4)	198	NM_001166477	111241	Mm.426212	NM_001166476	ENSMUSG00000078249	Hmga1-rs1	ENSMUSG00000041059|Hmgi-rs1	high mobility group AT-hook I, related sequence 1	protein-coding
mm_156312.1	chrX	136927321	136927329	+	1	NA	promoter-TSS (NM_027067)	promoter-TSS (NM_027067)	0	NM_027067	69389	Mm.302721	NM_027067	ENSMUSG00000048155	H2bfm	1700014N06Rik|H2bfw|H2bl2	H2B histone family, member M	protein-coding
mm_134822.1	chr16	25965754	25965765	-	1	NA	exon (NM_173379, exon 14 of 15)	exon (NM_173379, exon 14 of 15)	140025	NM_173379	210530	Mm.326869	NM_173379	ENSMUSG00000038168	P3h2	4832416N06|AW553532|Leprel1|Mlat4	prolyl 3-hydroxylase 2	protein-coding
mm_43241.1	chr5	130079427	130079435	+	1	NA	promoter-TSS (NM_001130476)	promoter-TSS (NM_001130476)	61	NM_001130476	22021	Mm.332720	NM_013837	ENSMUSG00000034118	Tpst1	R75054|Tango13a	protein-tyrosine sulfotransferase 1	protein-coding
mm_18823.1	chr2	74659790	74659802	-	1	NA	promoter-TSS (NM_007967)	promoter-TSS (NM_007967)	-239	NM_007967	14029	Mm.25365	NM_007967	ENSMUSG00000001815	Evx2	Evx-2	even-skipped homeobox 2	protein-coding
mm_106564.1	chr11	120633595	120633605	-	1	NA	promoter-TSS (NM_010756)	promoter-TSS (NM_010756)	-53	NM_010756	17134	Mm.268010	NM_010756	ENSMUSG00000051510	Mafg	AA545192|C630022N07Rik	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein G (avian)	protein-coding
mm_56033.1	chr6	86649040	86649042	-	1	NA	3' UTR (NM_010751, exon 6 of 6)	3' UTR (NM_010751, exon 6 of 6)	20118	NM_010751	17119	Mm.279580	NM_010751	ENSMUSG00000001156	Mxd1	AW122478|Mad|Mad1	MAX dimerization protein 1	protein-coding
mm_164647.1	chr17	35534104	35534119	+	1	NA	exon (NM_020576, exon 2 of 2)	exon (NM_020576, exon 2 of 2)	910	NM_020576	57390	Mm.34201	NM_020576	ENSMUSG00000024409	Psors1c2	AI448740|Pcg|SPR1	psoriasis susceptibility 1 candidate 2 (human)	protein-coding
mm_64896.1	chr7	15950089	15950092	-	1	NA	3' UTR (NM_153068, exon 6 of 6)	3' UTR (NM_153068, exon 6 of 6)	-3982	NM_133831	68077	Mm.277634	NM_133831	ENSMUSG00000041560	Gltscr2	5330430H08Rik|9430097C02Rik|AU041936|AW536441|PICT-1|R74911	glioma tumor suppressor candidate region gene 2	protein-coding
mm_45522.1	chr5	72617383	72617391	-	1	NA	intron (NM_007723, intron 3 of 8)	intron (NM_007723, intron 3 of 8)	25365	NM_007723	12788	Mm.436652	NM_007723	ENSMUSG00000067220	Cnga1	Cncg	cyclic nucleotide gated channel alpha 1	protein-coding
mm_35586.1	chr4	42874181	42874187	-	1	NA	promoter-TSS (NM_177785)	promoter-TSS (NM_177785)	19	NM_177785	277773	Mm.212727	NM_177785	ENSMUSG00000050141	Fam205c	4931430D02|FAM205CP	family with sequence similarity 205, member C	protein-coding
mm_4236.1	chr1	171380145	171380166	+	1	NA	exon (NM_027893, exon 2 of 9)	exon (NM_027893, exon 2 of 9)	-8805	NM_001005508	226652	Mm.251048	NM_001005508	ENSMUSG00000048865	Arhgap30	6030405P05Rik|Gm102|mFLJ00267	Rho GTPase activating protein 30	protein-coding
mm_120461.1	chr14	65970662	65970669	+	1	NA	intron (NM_013492, intron 1 of 8)	intron (NM_013492, intron 1 of 8)	2182	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_147655.1	chr18	60526044	60526079	-	1	NA	promoter-TSS (NM_026302)	promoter-TSS (NM_026302)	-160	NM_026302	67665	Mm.272801	NM_026302	ENSMUSG00000024603	Dctn4	1110001K06Rik|4930547K17Rik|C130039E17Rik|p62	dynactin 4	protein-coding
mm_91170.1	chr10	20720012	20720046	-	1	NA	intron (NM_013875, intron 1 of 12)	intron (NM_013875, intron 1 of 12)	5049	NM_013875	29863	Mm.425617	NM_013875	ENSMUSG00000019990	Pde7b	-	phosphodiesterase 7B	protein-coding
mm_129420.1	chr15	78405357	78405381	-	1	NA	exon (NM_009437, exon 1 of 2)	exon (NM_009437, exon 1 of 2)	490	NM_009437	22117	Mm.15312	NM_009437	ENSMUSG00000044986	Tst	Rhodanese	thiosulfate sulfurtransferase, mitochondrial	protein-coding
mm_80879.1	chr9	98986433	98986468	+	1	NA	promoter-TSS (NM_001122851)	promoter-TSS (NM_001122851)	77	NM_011810	23873	Mm.74605	NM_011810	ENSMUSG00000032463	Faim	-	Fas apoptotic inhibitory molecule	protein-coding
mm_17116.1	chr2	24475120	24475122	-	1	NA	5' UTR (NM_011040, exon 2 of 12)	5' UTR (NM_011040, exon 2 of 12)	478	NM_011040	18510	Mm.2533	NM_011040	ENSMUSG00000026976	Pax8	Pax-8	paired box 8	protein-coding
mm_95824.1	chr11	55401946	55401956	+	1	NA	exon (NM_009242, exon 6 of 10)	exon (NM_009242, exon 6 of 10)	18129	NM_009242	20692	Mm.291442	NM_009242	ENSMUSG00000018593	Sparc	BM-40|ON	secreted acidic cysteine rich glycoprotein	protein-coding
mm_124203.1	chr14	98169812	98169840	-	1	NA	promoter-TSS (NM_001038610)	promoter-TSS (NM_001038610)	-61	NM_007826	13134	Mm.320593	NM_007826	ENSMUSG00000055639	Dach1	Dac|Dach	dachshund 1 (Drosophila)	protein-coding
mm_69668.1	chr7	139983375	139983394	-	1	NA	intron (NM_007403, intron 20 of 23)	intron (NM_007403, intron 20 of 23)	3490	NR_106029	102465643		NR_106029	ENSMUSG00000099092	Mir7062	Gm27339|mmu-mir-7062	microRNA 7062	ncRNA
mm_140373.1	chr17	86980934	86980939	+	1	NA	intron (NM_145491, intron 2 of 4)	intron (NM_145491, intron 2 of 4)	17825	NM_145491	104215	Mm.826	NM_145491	ENSMUSG00000024143	Rhoq	Arhq|TC10A|Tc10	ras homolog family member Q	protein-coding
mm_152120.1	chr19	6987522	6987534	-	1	NA	TTS (NM_020566)	TTS (NM_020566)	123	NM_001185164	22340	Mm.15607	NM_011697	ENSMUSG00000024962	Vegfb	VEGF-B|Vrf	vascular endothelial growth factor B	protein-coding
mm_7966.1	chr1	133930180	133930184	-	1	NA	Intergenic	MamGypLTR1c|LTR|Gypsy	-8781	NM_054077	116847	Mm.214514	NM_054077	ENSMUSG00000041577	Prelp	7330409J17Rik|SLRR2A	proline arginine-rich end leucine-rich repeat	protein-coding
mm_87126.1	chr10	33851001	33851004	+	1	NA	Intergenic	Intergenic	-6720	NM_020565	57430	Mm.6590	NM_020565	ENSMUSG00000069668	Sult3a1	ST3A1|Sult-x2|Sultx2	sulfotransferase family 3A, member 1	protein-coding
mm_64281.1	chr7	141818640	141818642	+	1	NA	exon (NM_010844, exon 50 of 50)	exon (NM_010844, exon 50 of 50)	-20431	NM_028801	74180	Mm.200752	NM_028801	ENSMUSG00000066108	Muc5b	2300002I04Rik|A130042M24|AV085033|MUC5|MUC9|mucin 5b	mucin 5, subtype B, tracheobronchial	protein-coding
mm_62858.1	chr7	114570964	114570987	+	1	NA	Intergenic	Intergenic	-8003	NM_177382	244209	Mm.108037	NM_177382	ENSMUSG00000030670	Cyp2r1	-	cytochrome P450, family 2, subfamily r, polypeptide 1	protein-coding
mm_139021.1	chr17	46122750	46122774	+	1	NA	exon (NM_026768, exon 3 of 6)	exon (NM_026768, exon 3 of 6)	11758	NM_026768	68565	Mm.287443	NM_026768	ENSMUSG00000023967	Mrps18a	1110004O20Rik|C79712	mitochondrial ribosomal protein S18A	protein-coding
mm_132697.1	chr16	43363014	43363024	+	1	NA	intron (NM_181058, intron 2 of 6)	LFSINE_Vert|SINE|tRNA	57177	NR_046026	626693	Mm.447083	NR_046026	ENSMUSG00000085499	Gm15713	OTTMUSG00000025617	predicted gene 15713	ncRNA
mm_9252.1	chr1	171531132	171531148	-	1	NA	exon (NM_010584, exon 5 of 8)	exon (NM_010584, exon 5 of 8)	4154	NM_010584	16429	Mm.247426	NM_010584	ENSMUSG00000038209	Itln1	IntL|Itln|Itln2|Itln3|Itln5|Itlna|Lfr	intelectin 1 (galactofuranose binding)	protein-coding
mm_12969.1	chr2	90738461	90738471	+	1	NA	Intergenic	B4|SINE|B4	-6904	NM_018828	55935	Mm.489638	NM_018828	ENSMUSG00000008200	Fnbp4	FBP30|Fnbp30|mKIAA1014	formin binding protein 4	protein-coding
mm_52589.1	chr6	116669386	116669398	+	1	NA	intron (NM_178045, intron 1 of 10)	MLTR14|LTR|ERV1	4444	NM_178045	213391	Mm.257931	NM_178045	ENSMUSG00000042129	Rassf4	3830411C14Rik|AD037|AI586137	Ras association (RalGDS/AF-6) domain family member 4	protein-coding
mm_86848.1	chr10	21593127	21593137	+	1	NA	promoter-TSS (NR_027968)	promoter-TSS (NR_027968)	-13	NR_027968	67692	Mm.54306	NM_183266	ENSMUSG00000050844	1700020N01Rik	-	RIKEN cDNA 1700020N01 gene	ncRNA
mm_135326.1	chr16	38800218	38800228	-	1	NA	promoter-TSS (NM_178924)	promoter-TSS (NM_178924)	-20	NM_178924	22268	Mm.130793	NM_178924	ENSMUSG00000049436	Upk1b	AI413235|Tspan20|UPIb|Upk1	uroplakin 1B	protein-coding
mm_129913.1	chr15	84132064	84132077	-	1	NA	Intergenic	Intergenic	-8895	NM_029427	75772	Mm.159565	NM_029427	ENSMUSG00000018868	Pnpla5	4833426H19Rik|GS2L	patatin-like phospholipase domain containing 5	protein-coding
mm_68283.1	chr7	105600104	105600123	-	1	NA	promoter-TSS (NM_017371)	promoter-TSS (NM_017371)	3	NM_017371	15458	Mm.3485	NM_017371	ENSMUSG00000030895	Hpx	Hpxn|hx	hemopexin	protein-coding
mm_60181.1	chr7	43078053	43078067	+	1	NA	Intergenic	Intergenic	59262	NM_001105061	668612	Mm.469896	NM_001105061	ENSMUSG00000091528	Gm9268	EG668612|Vmn2r64	predicted gene 9268	protein-coding
mm_91761.1	chr10	51486312	51486328	-	1	NA	TTS (NM_008147)	TTS (NM_008147)	-4578	NM_001291894	14728	Mm.34408	NM_013532	ENSMUSG00000062593	Lilrb4a	CD85K|Gp49b|HM18|ILT3|LIR-5|Lilrb4|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4A	protein-coding
mm_102830.1	chr11	69098589	69098629	-	1	NA	promoter-TSS (NM_011065)	promoter-TSS (NM_011065)	-347	NM_011065	18626	Mm.7373	NM_011065	ENSMUSG00000020893	Per1	Hftm|Per|m-rigui|mPer1	period circadian clock 1	protein-coding
mm_56714.1	chr6	115317106	115317114	-	1	NA	Intergenic	Intergenic	-43841	NM_001127330	19016	Mm.3020	NM_011146	ENSMUSG00000000440	Pparg	Nr1c3|PPAR-gamma|PPAR-gamma2|PPARgamma|PPARgamma2	peroxisome proliferator activated receptor gamma	protein-coding
mm_8633.1	chr1	156340952	156340961	-	1	NA	intron (NM_001346967, intron 21 of 25)	intron (NM_001346967, intron 21 of 25)	30237	NM_130456	170484	Mm.289099	NM_130456	ENSMUSG00000026602	Nphs2	PDCN|SRN1	nephrosis 2, podocin	protein-coding
mm_10581.1	chr2	18156193	18156219	+	1	NA	intron (NR_045539, intron 11 of 24)	RMER19B2|LTR|ERVK	91621	NM_001252561	17354	Mm.209175	NM_010804	ENSMUSG00000026743	Mllt10	Af10|B130021D15Rik|D630001B22Rik|mKIAA4140	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 10	protein-coding
mm_111385.1	chr12	87459449	87459486	-	1	NA	exon (NM_025507, exon 7 of 14)	exon (NM_025507, exon 7 of 14)	12832	NM_025507	66354	Mm.271174	NM_025507	ENSMUSG00000021039	Snw1	2310008B08Rik|AW048543|NCoA-62|SKIP|Skiip	SNW domain containing 1	protein-coding
mm_163550.1	chr13	23571112	23571112	-	1	NA	promoter-TSS (NM_178196)	promoter-TSS (NM_178196)	108	NM_178187	319166	Mm.261665	NM_178187	ENSMUSG00000069272	Hist1h2ae	1190022L06	histone cluster 1, H2ae	protein-coding
mm_170439.1	chr18	80025798	80025805	+	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	-21094	NM_053117	93737	Mm.24678	NM_053117	ENSMUSG00000056214	Pard6g	2410049N21Rik|Par6a	par-6 family cell polarity regulator gamma	protein-coding
mm_143999.1	chr17	88053668	88053688	-	1	NA	intron (NM_001081034, intron 1 of 22)	B2_Mm2|SINE|B2	11607	NM_001081034	225055	Mm.386857	NM_001081034	ENSMUSG00000005371	Fbxo11	C80048|Jf	F-box protein 11	protein-coding
mm_129338.1	chr15	77836289	77836316	-	1	NA	intron (NM_022410, intron 1 of 40)	intron (NM_022410, intron 1 of 40)	5873	NM_022410	17886	Mm.29677	NM_022410	ENSMUSG00000022443	Myh9	Fltn|Myhn-1|Myhn1|NMHCIIA|NMMHC-A|NMMHC-IIA|TU72.6	myosin, heavy polypeptide 9, non-muscle	protein-coding
mm_92427.1	chr10	77089463	77089477	-	1	NA	intron (NM_009929, intron 3 of 41)	ORR1E|LTR|ERVL-MaLR	24235	NM_001109991	12822	Mm.4352	NM_009929	ENSMUSG00000001435	Col18a1	-	collagen, type XVIII, alpha 1	protein-coding
mm_67035.1	chr7	66733479	66733488	-	1	NA	Intergenic	Intergenic	-10021	NM_001164201	545975	Mm.380104	NM_001164201	ENSMUSG00000030510	Cers3	4930550L11Rik|Gm488|Lass3|T3L	ceramide synthase 3	protein-coding
mm_7904.1	chr1	133660950	133660974	-	1	NA	promoter-TSS (NM_001166552)	promoter-TSS (NM_001166552)	-77	NM_001166552	667118	Mm.245357	NM_001166552	ENSMUSG00000094410	Zbed6	Gm8466|MGR	zinc finger, BED type containing 6	protein-coding
mm_101312.1	chr11	22779316	22779320	-	1	NA	Intergenic	Intergenic	80417	NM_016888	53625	Mm.395495	NM_016888	ENSMUSG00000051650	B3gnt2	AA408337|AA409404|AW260308|B3Galt6|B3gnt1|BGnT-1|BGnT-2|BGnT1|BGnT2|Beta3gnt	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 2	protein-coding
mm_57815.1	chr6	129462636	129462652	-	1	NA	non-coding (NR_132130, exon 6 of 6)	non-coding (NR_132130, exon 6 of 6)	10135	NM_001309637	56644	Mm.239516	NM_020008	ENSMUSG00000079293	Clec7a	BGR|Clecsf12|beta-GR	C-type lectin domain family 7, member a	protein-coding
mm_140219.1	chr17	83848022	83848056	+	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	-1249	NM_025325	107766	Mm.30100	NM_025325	ENSMUSG00000000673	Haao	0610007K21Rik|0610012J07Rik|3-HAO|3-HAOxase|3HAO	3-hydroxyanthranilate 3,4-dioxygenase	protein-coding
mm_149428.1	chr19	11469388	11469403	+	1	NA	promoter-TSS (NM_028595)	promoter-TSS (NM_028595)	27	NM_028595	73656	Mm.440719	NM_028595	ENSMUSG00000079419	Ms4a6c	2200009H22Rik|2210417N07Rik	membrane-spanning 4-domains, subfamily A, member 6C	protein-coding
mm_135606.1	chr16	52249566	52249578	-	1	NA	3' UTR (NM_001331110, exon 15 of 15)	3' UTR (NM_001331110, exon 15 of 15)	203509	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_130158.1	chr15	91191734	91191825	-	1	NA	promoter-TSS (NM_011994)	promoter-TSS (NM_011994)	28	NM_011994	26874	Mm.295456	NM_011994	ENSMUSG00000055782	Abcd2	ABC39|ALDL1|ALDR|ALDRP	ATP-binding cassette, sub-family D (ALD), member 2	protein-coding
mm_34641.1	chr4	150661934	150661937	+	1	NA	Intergenic	Intergenic	-9761	NM_173774	242773	Mm.29280	NM_173774	ENSMUSG00000039838	Slc45a1	C230078B22|Dnb5	solute carrier family 45, member 1	protein-coding
mm_157336.1	chrX	36645360	36645414	-	1	NA	promoter-TSS (NM_001081956)	promoter-TSS (NM_001081956)	27	NM_001081956	338351	Mm.116704	NM_001081956	ENSMUSG00000059708	Akap17b	AA407619|AKAP-17B|B230333C21Rik|C230056F04Rik|PRKA17B|Sfrs17b|Srsf17b|Talia	A kinase (PRKA) anchor protein 17B	protein-coding
mm_155267.1	chrX	58911473	58911488	+	1	NA	promoter-TSS (NM_023774)	promoter-TSS (NM_023774)	19	NM_023774	75352	Mm.60906	NM_023774	ENSMUSG00000046180	4930550L24Rik	mage-k1	RIKEN cDNA 4930550L24 gene	protein-coding
mm_84403.1	chr9	65555167	65555184	-	1	NA	3' UTR (NM_153119, exon 6 of 6)	3' UTR (NM_153119, exon 6 of 6)	24912	NM_153119	102595	Mm.247303	NM_153119	ENSMUSG00000050721	Plekho2	AI840980|Plekhq1	pleckstrin homology domain containing, family O member 2	protein-coding
mm_165285.1	chr2	84383980	84383982	-	1	NA	intron (NM_018782, intron 2 of 15)	Lx8b|LINE|L1	41285	NM_018782	54598	Mm.75467	NM_018782	ENSMUSG00000059588	Calcrl	AV071593|CRLR	calcitonin receptor-like	protein-coding
mm_4585.1	chr1	178319128	178319138	+	1	NA	promoter-TSS (NM_025511)	promoter-TSS (NM_025511)	-20	NM_025511	66359	Mm.489720	NM_025511	ENSMUSG00000026500	Cox20	2310005N03Rik|Fam36a	COX20 Cox2 chaperone	protein-coding
mm_152089.1	chr19	6907765	6907778	-	1	NA	intron (NM_012021, intron 2 of 5)	L4_A_Mam|LINE|RTE-X	1874	NM_012021	54683	Mm.279782	NM_012021	ENSMUSG00000024953	Prdx5	AOEB166|AOPP|Pmp20|Prdx6|PrxV	peroxiredoxin 5	protein-coding
mm_154692.1	chrX	8049230	8049241	+	1	NA	Intergenic	RMER19B|LTR|ERVK	25078	NM_001290716	20937	Mm.9244	NM_011514	ENSMUSG00000039231	Suv39h1	AI852103|AL022883|DXHXS7466e|H3-K9-HMTase 1|KMT1A|mIS6	suppressor of variegation 3-9 homolog 1 (Drosophila)	protein-coding
mm_116232.1	chr13	33559682	33559690	-	1	NA	Intergenic	RLTR48A|LTR|ERV1	9183	NR_131140	619715	Mm.390575	NR_131140		Gm6093	EG619715	predicted gene 6093	ncRNA
mm_115471.1	chr13	119466394	119466397	+	1	NA	intron (NM_001113550, intron 2 of 12)	B1_Mur4|SINE|Alu	3636	NM_026127	67392	Mm.390641	NM_026127	ENSMUSG00000062822	4833420G17Rik	2210017J06Rik|5730533D17Rik|AW107518|C85193	RIKEN cDNA 4833420G17 gene	protein-coding
mm_121903.1	chr14	21889815	21889819	-	1	NA	Intergenic	Intergenic	-40907	NM_026965	69156	Mm.11827	NM_026965	ENSMUSG00000021773	Comtd1	1810030M08Rik|MT773	catechol-O-methyltransferase domain containing 1	protein-coding
mm_69930.1	chr7	142029202	142029219	-	1	NA	intron (NM_028308, intron 1 of 4)	intron (NM_028308, intron 1 of 4)	31643	NM_001347560	101513	Mm.53259	NM_028308	ENSMUSG00000025147	Mob2	1110017M21Rik|2700078K21Rik|AI256456|Mmh	MOB kinase activator 2	protein-coding
mm_144590.1	chr18	32068884	32068887	+	1	NA	intron (NM_173441, intron 1 of 13)	B1_Mur1|SINE|Alu	1151	NM_173441	73473	Mm.66853	NM_173441	ENSMUSG00000024384	Iws1	1700069O15Rik|3000008H23|AL117927|AW214353	IWS1, SUPT6 interacting protein	protein-coding
mm_26104.1	chr3	137341077	137341095	+	1	NA	promoter-TSS (NM_016885)	promoter-TSS (NM_016885)	8	NM_016885	59308	Mm.27343	NM_016885	ENSMUSG00000054690	Emcn	0610012K22Rik|AI315669|Muc14	endomucin	protein-coding
mm_49370.1	chr6	23947774	23947774	+	1	NA	Intergenic	Intergenic	22286	NM_207022	387347	Mm.377909	NM_207022	ENSMUSG00000043865	Tas2r118	Gm465|T2R18|Tas2r16|Tas2r18|mGR18|mt2r40	taste receptor, type 2, member 118	protein-coding
mm_12945.1	chr2	87481486	87481523	+	1	NA	Intergenic	Intergenic	10914	NM_178250	347712	Mm.6018	NM_178250	ENSMUSG00000025839	Pramel7	AA675346|C81180	preferentially expressed antigen in melanoma like 7	protein-coding
mm_149891.1	chr19	25406937	25407002	+	1	NA	intron (NM_181404, intron 4 of 13)	intron (NM_181404, intron 4 of 13)	-98737	NM_015826	50796	Mm.391208	NM_015826	ENSMUSG00000024837	Dmrt1	-	doublesex and mab-3 related transcription factor 1	protein-coding
mm_110433.1	chr12	46819470	46819498	-	1	NA	promoter-TSS (NM_021361)	promoter-TSS (NM_021361)	-709	NM_021361	664883	Mm.247195	NM_021361	ENSMUSG00000021047	Nova1	9430099M15Rik|G630039L02|Nova-1	neuro-oncological ventral antigen 1	protein-coding
mm_33335.1	chr4	129189864	129189956	+	1	NA	promoter-TSS (NM_029036)	promoter-TSS (NM_029036)	115	NM_134151	107271	Mm.145488	NM_134151	ENSMUSG00000028811	Yars	AL024047|AU018965	tyrosyl-tRNA synthetase	protein-coding
mm_36717.1	chr4	98699117	98699129	-	1	NA	intron (NM_172696, intron 42 of 43)	intron (NM_172696, intron 42 of 43)	-27631	NM_001081202	381591	Mm.34340	NM_001081202	ENSMUSG00000087166	L1td1	AA546746|AB211064|D76865|ECAT11	LINE-1 type transposase domain containing 1	protein-coding
mm_106325.1	chr11	118310635	118310645	-	1	NA	exon (NM_011594, exon 4 of 5)	exon (NM_011594, exon 4 of 5)	-20396	NM_001033528	72344	Mm.232293	NM_001033528	ENSMUSG00000033909	Usp36	2700002L06Rik|mKIAA1453	ubiquitin specific peptidase 36	protein-coding
mm_140912.1	chr17	24168776	24168822	-	1	NA	intron (NR_037854, intron 1 of 2)	intron (NR_037854, intron 1 of 2)	596	NR_037854	100039636	Mm.30155	NR_037854		Atp6v0c-ps2	Atp6l-ps2|Gm15487	ATPase, H+ transporting, lysosomal V0 subunit C, pseudogene 2	pseudo
mm_100195.1	chr11	116752357	116752363	+	1	NA	non-coding (NR_003364, exon 1 of 4)	non-coding (NR_003364, exon 1 of 4)	193	NR_003364	193217	Mm.100084	NR_003364		BC018473	-	cDNA sequence BC018473	ncRNA
mm_164915.1	chr18	75360182	75360187	-	1	NA	Intergenic	Intergenic	-7181	NM_001042660	17131	Mm.34407	NM_008543	ENSMUSG00000025880	Smad7	Madh7	SMAD family member 7	protein-coding
mm_137581.1	chr17	28007472	28007502	+	1	NA	intron (NM_001286040, intron 11 of 24)	intron (NM_001286040, intron 11 of 24)	73097	NM_013687	21463	Mm.29758	NM_013687	ENSMUSG00000062859	Tcp11	D17Ken1|Tcp-11	t-complex protein 11	protein-coding
mm_161357.1	chr14	56042115	56042115	+	1	NA	promoter-TSS (NM_008571)	promoter-TSS (NM_008571)	-8	NM_008571	17225	Mm.4409	NM_008571	ENSMUSG00000022226	Mcpt2	MMCP-2|Mcp-2	mast cell protease 2	protein-coding
mm_144903.1	chr18	37333854	37333863	+	1	NA	promoter-TSS (NM_053131)	promoter-TSS (NM_053131)	-170	NM_053131	93877	Mm.59009	NM_053131	ENSMUSG00000051678	Pcdhb6	Pcdhb5B|PcdhbF	protocadherin beta 6	protein-coding
mm_94299.1	chr11	4121488	4121499	+	1	NA	Intergenic	Intergenic	-2764	NM_144520	67815	Mm.253922	NM_144520	ENSMUSG00000003585	Sec14l2	1300013M05Rik|Spf|TAP	SEC14-like lipid binding 2	protein-coding
mm_71392.1	chr8	46162266	46162274	+	1	NA	Intergenic	Intergenic	-7286	NM_025747	66756	Mm.133623	NM_025747	ENSMUSG00000031631	Cfap97	1110068E21Rik|4933411K20Rik|AW049273|Kiaa1430|mKIAA1430	cilia and flagella associated protein 97	protein-coding
mm_157122.1	chrX	9445688	9445722	-	1	NA	intron (NM_007807, intron 9 of 12)	intron (NM_007807, intron 9 of 12)	23619	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_66071.1	chr7	30878093	30878131	-	1	NA	intron (NR_102722, intron 3 of 15)	intron (NR_102722, intron 3 of 15)	916	NM_009845	12483	Mm.260994	NM_009845	ENSMUSG00000030577	Cd22	A530093D23|Lyb-8|Lyb8	CD22 antigen	protein-coding
mm_105541.1	chr11	106313708	106313738	-	1	NA	intron (NM_008339, intron 1 of 5)	intron (NM_008339, intron 1 of 5)	839	NM_008339	15985	Mm.2987	NM_008339	ENSMUSG00000040592	Cd79b	B29|Ig-beta|Igb|Igbeta	CD79B antigen	protein-coding
mm_152784.1	chr19	21440890	21440902	-	1	NA	intron (NM_010266, intron 1 of 13)	L1MC4|LINE|L1	31765	NM_010266	14544	Mm.45054	NM_010266	ENSMUSG00000058624	Gda	AU015411|AW047581|GAH	guanine deaminase	protein-coding
mm_60660.1	chr7	44943235	44943251	+	1	NA	promoter-TSS (NM_001077591)	promoter-TSS (NM_001077591)	3	NM_011651	22116	Mm.84502	NM_011651	ENSMUSG00000059891	Tsks	Stk22s1|Tssks1	testis-specific serine kinase substrate	protein-coding
mm_75388.1	chr8	45555733	45555735	-	1	NA	intron (NM_172752, intron 1 of 22)	ORR1B1|LTR|ERVL-MaLR	47946	NM_001205219	234214	Mm.211096	NM_172752	ENSMUSG00000031626	Sorbs2	2010203O03Rik|9430041O17Rik|A530071H08|Argbp2|mKIAA0777|nArgBP2	sorbin and SH3 domain containing 2	protein-coding
mm_38100.1	chr4	134287216	134287258	-	1	NA	promoter-TSS (NM_001163794)	promoter-TSS (NM_001163794)	16	NM_001163794	230809	Mm.22778	NM_146156	ENSMUSG00000050890	Pdik1l	BC027088|stk35l2	PDLIM1 interacting kinase 1 like	protein-coding
mm_142899.1	chr17	51956548	51956566	-	1	NA	intron (NR_045095, intron 2 of 2)	intron (NR_045095, intron 2 of 2)	73830	NR_045095	100504169	Mm.417731	NR_045095		Gm20098	-	predicted gene, 20098	ncRNA
mm_47247.1	chr5	121572115	121572125	-	1	NA	exon (NM_001308450, exon 10 of 11)	exon (NM_001308450, exon 10 of 11)	21704	NM_009656	11669	Mm.284446	NM_009656	ENSMUSG00000029455	Aldh2	AHD-M1|ALDH-E2|ALDHI|Ahd-5|Ahd5	aldehyde dehydrogenase 2, mitochondrial	protein-coding
mm_90305.1	chr10	126978904	126978914	+	1	NA	5' UTR (NM_001113470, exon 1 of 8)	5' UTR (NM_001113470, exon 1 of 8)	192	NM_001113470	52468	Mm.29490	NM_146012	ENSMUSG00000078429	Ctdsp2	AI586070|D10Ertd73e|OS-4|OS4|SCP2	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 2	protein-coding
mm_108866.1	chr12	99047160	99047167	+	1	NA	Intergenic	Intergenic	115645	NR_038130	67639	Mm.87374	NR_038130		4930474N09Rik	-	RIKEN cDNA 4930474N09 gene	ncRNA
mm_84973.1	chr9	85323740	85323771	-	1	NA	3' UTR (NM_001160378, exon 3 of 3)	3' UTR (NM_001160378, exon 3 of 3)	3369	NM_001160378	212943	Mm.74610	NM_001160378	ENSMUSG00000032265	Fam46a	BAP014|D930050G01Rik	family with sequence similarity 46, member A	protein-coding
mm_33292.1	chr4	128936000	128936012	+	1	NA	intron (NM_001301841, intron 7 of 8)	intron (NM_001301841, intron 7 of 8)	26449	NM_172875	242669	Mm.215814	NM_172875	ENSMUSG00000028789	Azin2	4933429I20Rik|Adc|Azi2|B930082O19|ODC-p|Odcp	antizyme inhibitor 2	protein-coding
mm_57898.1	chr6	131383765	131383809	-	1	NA	intron (NM_139117, intron 2 of 9)	intron (NM_139117, intron 2 of 9)	4663	NM_139117	56449	Mm.458000	NM_011733	ENSMUSG00000030189	Ybx3	Csda|Dpba|MSY3|MSY4|Yb2|dbpA|oxyR	Y box protein 3	protein-coding
mm_74010.1	chr8	121118326	121118332	+	1	NA	3' UTR (NM_013519, exon 1 of 1)	3' UTR (NM_013519, exon 1 of 1)	2158	NM_013519	14234	Mm.14092	NM_013519	ENSMUSG00000046714	Foxc2	Fkh14|Hfhbf3|MFH-1|Mfh1	forkhead box C2	protein-coding
mm_87249.1	chr10	41343212	41343222	+	1	NA	Intergenic	L1M4|LINE|L1	-39976	NM_133999	103199	Mm.277242	NM_133999	ENSMUSG00000038417	Fig4	A530089I17Rik|AI326867|Sac3	FIG4 phosphoinositide 5-phosphatase	protein-coding
mm_88050.1	chr10	67539975	67540001	+	1	NA	exon (NM_010118, exon 2 of 2)	exon (NM_010118, exon 2 of 2)	2058	NM_001347458	13654	Mm.290421	NM_010118	ENSMUSG00000037868	Egr2	Egr-2|Krox-20|Krox20|NGF1-B|Zfp-25|Zfp-6	early growth response 2	protein-coding
mm_90791.1	chr10	7064232	7064243	-	1	NA	Intergenic	Intergenic	-41052	NM_001033391	320495	Mm.331674	NM_001033391	ENSMUSG00000064065	Ipcef1	A130090K04Rik	interaction protein for cytohesin exchange factors 1	protein-coding
mm_21565.1	chr2	164190602	164190614	-	1	NA	promoter-TSS (NM_138684)	promoter-TSS (NM_138684)	-50	NM_138684	192200	Mm.6433	NM_138684	ENSMUSG00000042845	Wfdc12	Swam2|WAP2	WAP four-disulfide core domain 12	protein-coding
mm_110922.1	chr12	76369155	76369167	-	1	NA	intron (NM_028356, intron 1 of 2)	CpG	303	NM_001172104	109929	Mm.41880	NM_028356	ENSMUSG00000056459	Zbtb25	2810462M08Rik|2900064P18Rik|AI842128|Kup|Zfp-50|Zfp50	zinc finger and BTB domain containing 25	protein-coding
mm_34153.1	chr4	139380659	139380684	+	1	NA	promoter-TSS (NM_001160319)	promoter-TSS (NM_001160319)	12	NM_001160319	69116	Mm.271956	NM_001160319	ENSMUSG00000066036	Ubr4	1810009A16Rik|A930005E13Rik|D930005K06Rik|Gm1032|Gm1666|N28143|RBAF600|Zubr1|mKIAA0462|p600	ubiquitin protein ligase E3 component n-recognin 4	protein-coding
mm_68247.1	chr7	105565476	105565489	-	1	NA	intron (NM_001310600, intron 8 of 12)	intron (NM_001310600, intron 8 of 12)	3295	NM_001310600	11785	Mm.38469	NM_009685	ENSMUSG00000037032	Apbb1	Fe65|Rir	amyloid beta (A4) precursor protein-binding, family B, member 1	protein-coding
mm_48351.1	chr5	139325772	139325772	-	1	NA	promoter-TSS (NM_172723)	promoter-TSS (NM_172723)	-308	NM_172723	231821	Mm.297819	NM_172723	ENSMUSG00000056413	Adap1	4930431P11Rik|Centa1|GC1L|p42IP4	ArfGAP with dual PH domains 1	protein-coding
mm_30606.1	chr4	6394859	6394910	+	1	NA	3' UTR (NM_016807, exon 9 of 9)	3' UTR (NM_016807, exon 9 of 9)	29204	NM_001098227	53378	Mm.247473	NM_016807	ENSMUSG00000028249	Sdcbp	MDA-9|Sycl|syntenin-1	syndecan binding protein	protein-coding
mm_155477.1	chrX	73673130	73673135	+	1	NA	promoter-TSS (NM_001142809)	promoter-TSS (NM_001142809)	-1	NM_001142810	102857	Mm.274553	NM_133987	ENSMUSG00000019558	Slc6a8	AA589632|CRT|CRTR|CT1|CTR5|Creat	solute carrier family 6 (neurotransmitter transporter, creatine), member 8	protein-coding
mm_149681.1	chr19	20492664	20492670	+	1	NA	promoter-TSS (NR_015502)	promoter-TSS (NR_015502)	-48	NR_015502	320092	Mm.482524	NR_015502		E030003E18Rik	1700127G21Rik	RIKEN cDNA E030003E18 gene	ncRNA
mm_143719.1	chr17	81375435	81375446	-	1	NA	non-coding (NR_104580, exon 9 of 9)	non-coding (NR_104580, exon 9 of 9)	-310355	NM_028138	72167	Mm.273257	NM_028138	ENSMUSG00000024246	Thumpd2	2810025A12Rik	THUMP domain containing 2	protein-coding
mm_5725.1	chr1	44102471	44102475	-	1	NA	promoter-TSS (NM_029368)	promoter-TSS (NM_029368)	-85	NM_029368	75623	Mm.348017	NM_029368	ENSMUSG00000026049	Tex30	1700029F09Rik|3110030D08Rik	testis expressed 30	protein-coding
mm_49112.1	chr6	8504115	8504125	+	1	NA	Intergenic	Intergenic	5041	NR_040452	320312	Mm.374890	NR_040452	ENSMUSG00000087305	A430035B10Rik	2810488G03Rik	RIKEN cDNA A430035B10 gene	ncRNA
mm_122176.1	chr14	31545819	31545827	-	1	NA	intron (NM_009937, intron 6 of 16)	ID_B1|SINE|B4	31560	NM_009937	382864	Mm.239821	NM_009937	ENSMUSG00000057606	Colq	A130034K24Rik	collagen-like tail subunit (single strand of homotrimer) of asymmetric acetylcholinesterase	protein-coding
mm_31681.1	chr4	62298000	62298024	+	1	NA	3' UTR (NM_025286, exon 4 of 4)	3' UTR (NM_025286, exon 4 of 4)	6465	NM_001290518	20530	Mm.292539	NM_025286	ENSMUSG00000066152	Slc31a2	AI604396|CTR2	solute carrier family 31, member 2	protein-coding
mm_31370.1	chr4	47353232	47353265	+	1	NA	promoter-TSS (NM_009370)	promoter-TSS (NM_009370)	26	NM_009370	21812	Mm.197552	NM_009370	ENSMUSG00000007613	Tgfbr1	ALK5|AU017191|Alk-5|ESK2|TGFR-1|TbetaR-I|TbetaRI	transforming growth factor, beta receptor I	protein-coding
mm_59393.1	chr7	26764489	26764505	+	1	NA	intron (NM_007814, intron 6 of 8)	intron (NM_007814, intron 6 of 8)	7355	NM_007814	13090	Mm.14098	NM_007814	ENSMUSG00000066704	Cyp2b19	CYPIIB19	cytochrome P450, family 2, subfamily b, polypeptide 19	protein-coding
mm_140272.1	chr17	84683202	84683208	+	1	NA	promoter-TSS (NM_031884)	promoter-TSS (NM_031884)	84	NM_026180	67470	Mm.26581	NM_026180	ENSMUSG00000024254	Abcg8	1300003C16Rik|AI114946|sterolin-2	ATP-binding cassette, sub-family G (WHITE), member 8	protein-coding
mm_105766.1	chr11	109611338	109611349	-	1	NA	promoter-TSS (NM_145940)	promoter-TSS (NM_145940)	46	NM_145940	52639	Mm.35817	NM_145940	ENSMUSG00000041895	Wipi1	4930533H01Rik|AW411817|D11Ertd498e	WD repeat domain, phosphoinositide interacting 1	protein-coding
mm_133678.1	chr16	92292451	92292461	+	1	NA	promoter-TSS (NM_134110)	promoter-TSS (NM_134110)	67	NM_134110	246133	Mm.156736	NM_134110	ENSMUSG00000039672	Kcne2	2200002I16Rik|AW048273|MiRP1	potassium voltage-gated channel, Isk-related subfamily, gene 2	protein-coding
mm_73376.1	chr8	105636489	105636499	+	1	NA	promoter-TSS (NM_181322)	promoter-TSS (NM_181322)	-44	NM_181322	13018	Mm.269474	NM_181322	ENSMUSG00000005698	Ctcf	AW108038	CCCTC-binding factor	protein-coding
mm_11650.1	chr2	34961720	34961752	+	1	NA	promoter-TSS (NM_001326601)	promoter-TSS (NM_001326601)	36	NM_009421	22029	Mm.239514	NM_009421	ENSMUSG00000026875	Traf1	4732496E14Rik	TNF receptor-associated factor 1	protein-coding
mm_72330.1	chr8	79028179	79028237	+	1	NA	promoter-TSS (NM_178267)	promoter-TSS (NM_178267)	-229	NM_001294279	622675	Mm.48724	NM_178267	ENSMUSG00000071064	Zfp827	2810449M09Rik|D630040G17Rik|Znf827	zinc finger protein 827	protein-coding
mm_10584.1	chr2	18172706	18172710	+	1	NA	intron (NR_045539, intron 15 of 24)	intron (NR_045539, intron 15 of 24)	108123	NM_001252561	17354	Mm.209175	NM_010804	ENSMUSG00000026743	Mllt10	Af10|B130021D15Rik|D630001B22Rik|mKIAA4140	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 10	protein-coding
mm_49596.1	chr6	30670202	30670206	+	1	NA	intron (NR_130781, intron 3 of 11)	intron (NR_130781, intron 3 of 11)	23545	NM_031998	83922	Mm.65389	NM_031998	ENSMUSG00000029790	Cep41	1700017E11Rik|2810431D15Rik|Tsga14	centrosomal protein 41	protein-coding
mm_44641.1	chr5	28124052	28124064	-	1	NA	Intergenic	Intergenic	-41638	NM_010134	13799	Mm.4298	NM_010134	ENSMUSG00000039095	En2	BB131122|En-2	engrailed 2	protein-coding
mm_39756.1	chr5	29735968	29735989	+	1	NA	promoter-TSS (NM_001037941)	promoter-TSS (NM_001037941)	-42	NR_028426	332993	Mm.473746	NR_028426		Gm5129	EG332993|ENSMUSG00000053121	predicted gene 5129	ncRNA
mm_67969.1	chr7	100608294	100608308	-	1	NA	promoter-TSS (NR_003559)	promoter-TSS (NR_003559)	-305	NR_003559	52443	Mm.473730	NM_198831	ENSMUSG00000030706	Mrpl48	1810030E20Rik|2610028L11Rik|CGI-118|D4Ertd786e	mitochondrial ribosomal protein L48	protein-coding
mm_6852.1	chr1	84253587	84253590	-	1	NA	intron (NM_001003948, intron 1 of 2)	intron (NM_001003948, intron 1 of 2)	31057	NM_001003948	98496	Mm.187470	NM_001003948	ENSMUSG00000045658	Pid1	5033414K04Rik|NYGGF4	phosphotyrosine interaction domain containing 1	protein-coding
mm_17040.1	chr2	20671746	20671751	-	1	NA	intron (NM_029895, intron 4 of 18)	intron (NM_029895, intron 4 of 18)	152235	NM_001177631	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding
mm_70830.1	chr8	23143249	23143269	+	1	NA	promoter-TSS (NR_037293)	promoter-TSS (NR_037293)	-597	NR_037293	100526510		NR_037293	ENSMUSG00000106471	Mir3107	mir-486b|mmu-mir-3107|mmu-mir-486b	microRNA 3107	ncRNA
mm_64375.1	chr7	142442966	142442997	+	1	NA	intron (NM_009405, intron 1 of 5)	intron (NM_009405, intron 1 of 5)	513	NM_009405	21953	Mm.39469	NM_009405	ENSMUSG00000031097	Tnni2	-	troponin I, skeletal, fast 2	protein-coding
mm_89412.1	chr10	90829643	90829658	+	1	NA	promoter-TSS (NM_001347054)	promoter-TSS (NM_001347054)	-4	NM_001347054	77531	Mm.440605	NM_181398	ENSMUSG00000058589	Anks1b	AIDA-1b|C030032C09Rik|E530015N03Rik|ENSMUSG00000078431|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding
mm_124427.1	chr14	118236217	118236242	-	1	NA	promoter-TSS (NR_131969)	promoter-TSS (NR_131969)	-3	NR_131969	105245869	Mm.460408	NR_131969	ENSMUSG00000090534	LOC105245869	-	uncharacterized LOC105245869	ncRNA
mm_23955.1	chr3	84918268	84918273	+	1	NA	intron (NM_001177773, intron 4 of 13)	AT_rich|Low_complexity|Low_complexity	-33941	NM_080428	50754	Mm.196475	NM_080428	ENSMUSG00000028086	Fbxw7	1110001A17Rik|AGO|Cdc4|Fbw7|Fbwd6|Fbx30|Fbxo30|Fbxw6|SEL-10	F-box and WD-40 domain protein 7	protein-coding
mm_111939.1	chr12	108893500	108893518	-	1	NA	promoter-TSS (NM_177602)	promoter-TSS (NM_177602)	-298	NM_011710	22375	Mm.38433	NM_011710	ENSMUSG00000021266	Wars	TrpRS|WRS	tryptophanyl-tRNA synthetase	protein-coding
mm_55703.1	chr6	72957567	72957589	-	1	NA	3' UTR (NM_025284, exon 3 of 3)	3' UTR (NM_025284, exon 3 of 3)	654	NM_001039392	19240	Mm.3532	NM_025284	ENSMUSG00000079523	Tmsb10	Ptmb10|Tb10	thymosin, beta 10	protein-coding
mm_20233.1	chr2	125859199	125859221	-	1	NA	promoter-TSS (NM_001285513)	promoter-TSS (NM_001285513)	101	NM_175154	69976	Mm.20216	NM_175154	ENSMUSG00000027207	Galk2	2810017M24Rik|AI327030|Gk2	galactokinase 2	protein-coding
mm_164982.1	chr19	10001706	10001712	+	1	NA	promoter-TSS (NM_011913)	promoter-TSS (NM_011913)	40	NM_001347429	74760	Mm.281969	NM_144538	ENSMUSG00000024663	Rab3il1	1200014K04Rik|AI115013|C76746|Rab3ail1	RAB3A interacting protein (rabin3)-like 1	protein-coding
mm_38190.1	chr4	135338065	135338078	-	1	NA	exon (NM_001130477, exon 9 of 18)	exon (NM_001130477, exon 9 of 18)	15143	NM_016799	51796	Mm.1963	NM_016799	ENSMUSG00000028809	Srrm1	AA407769|POP101|Srm160	serine/arginine repetitive matrix 1	protein-coding
mm_108816.1	chr12	95695191	95695195	+	1	NA	intron (NM_201518, intron 1 of 1)	CpG	2967	NM_201518	399558	Mm.341948	NM_201518	ENSMUSG00000047414	Flrt2	-	fibronectin leucine rich transmembrane protein 2	protein-coding
mm_106953.1	chr12	8791888	8791936	+	1	NA	3' UTR (NM_011519, exon 5 of 5)	3' UTR (NM_011519, exon 5 of 5)	20516	NM_011519	20969	Mm.2580	NM_011519	ENSMUSG00000020592	Sdc1	AA408134|AA409076|CD138|Sstn|Synd|Synd1|syn-1	syndecan 1	protein-coding
mm_81752.1	chr9	113956044	113956048	+	1	NA	exon (NM_001083319, exon 5 of 17)	exon (NM_001083319, exon 5 of 17)	25112	NM_013699	22221	Mm.28052	NM_013699	ENSMUSG00000009741	Ubp1	Cp2b|LBP-1a|LBP-1b|NF2d9	upstream binding protein 1	protein-coding
mm_93756.1	chr10	120174335	120174365	-	1	NA	intron (NM_028679, intron 5 of 11)	intron (NM_028679, intron 5 of 11)	27187	NM_028679	73914	Mm.146194	NM_028679	ENSMUSG00000020227	Irak3	4833428C18Rik|AI563835|IRAK-M	interleukin-1 receptor-associated kinase 3	protein-coding
mm_27813.1	chr3	78594514	78594522	-	1	NA	Intergenic	Intergenic	550369	NM_001310536	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_118908.1	chr14	26656171	26656185	+	1	NA	3' UTR (NM_007479, exon 6 of 6)	3' UTR (NM_007479, exon 6 of 6)	13430	NR_106132	102465773		NR_106132	ENSMUSG00000098751	Mir7672	Gm27314|mmu-mir-7672	microRNA 7672	ncRNA
mm_8785.1	chr1	161251142	161251144	-	1	NA	promoter-TSS (NM_007453)	promoter-TSS (NM_007453)	67	NR_130150	11758	Mm.186185	NM_007453	ENSMUSG00000026701	Prdx6	1-Cys Prx|1-cysPrx|9430088D19Rik|AA690119|Aop2|Brp-12|CP-3|GPx|Ltw-4|Ltw4|Lvtw-4|NSGPx|ORF06|Prdx5|aiPLA2	peroxiredoxin 6	protein-coding
mm_108638.1	chr12	85759512	85759537	+	1	NA	intron (NM_145447, intron 1 of 9)	intron (NM_145447, intron 1 of 9)	12985	NM_145447	217721	Mm.301076	NM_145447	ENSMUSG00000034258	Mfsd7c	CCT|Flvcr2	major facilitator superfamily domain containing 7C	protein-coding
mm_68095.1	chr7	101933816	101933897	-	1	NA	promoter-TSS (NM_027053)	promoter-TSS (NM_027053)	1	NM_027053	69358	Mm.214841	NM_027053	ENSMUSG00000064307	Lrrc51	1700008D07Rik|Lrtomt	leucine rich repeat containing 51	protein-coding
mm_160707.1	chr10	56379062	56379062	+	1	NA	intron (NM_010288, intron 1 of 1)	intron (NM_010288, intron 1 of 1)	1762	NM_010288	14609	Mm.378921	NM_010288	ENSMUSG00000050953	Gja1	AU042049|AW546267|Cnx43|Cx43|Cx43alpha1|Gja-1|Npm1|connexin43	gap junction protein, alpha 1	protein-coding
mm_101014.1	chr11	8549220	8549244	-	1	NA	intron (NM_001083587, intron 5 of 30)	intron (NM_001083587, intron 5 of 30)	115303	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_110542.1	chr12	55302960	55302968	-	1	NA	promoter-TSS (NM_021529)	promoter-TSS (NM_021529)	36	NM_021529	59032	Mm.427307	NM_021529	ENSMUSG00000021022	Ppp2r3c	4930511A21Rik|5730412A08Rik|G4-1|G5pr	protein phosphatase 2, regulatory subunit B'', gamma	protein-coding
mm_9529.1	chr1	173798113	173798117	-	1	NA	Intergenic	Intergenic	-31196	NM_008329	15951	Mm.261270	NM_008329	ENSMUSG00000073489	Ifi204	Ifi16|p204	interferon activated gene 204	protein-coding
mm_93183.1	chr10	93844802	93844851	-	1	NA	intron (NM_001206851, intron 2 of 6)	B3|SINE|B2	13271	NM_001206851	327799	Mm.491598	NM_183199	ENSMUSG00000020020	Usp44	E430004F17Rik	ubiquitin specific peptidase 44	protein-coding
mm_143122.1	chr17	57210277	57210299	-	1	NA	exon (NM_009778, exon 30 of 41)	exon (NM_009778, exon 30 of 41)	6940	NR_105944	102465591		NR_105944	ENSMUSG00000099066	Mir6978	Gm27858|mmu-mir-6978	microRNA 6978	ncRNA
mm_13144.1	chr2	92185439	92185463	+	1	NA	promoter-TSS (NM_001109691)	promoter-TSS (NM_001109691)	-32	NM_001109691	192285	Mm.330408	NM_138755	ENSMUSG00000058318	Phf21a	80kDa|Bhc|Bhc80|D030065N23Rik|PFTF1	PHD finger protein 21A	protein-coding
mm_58004.1	chr6	136449312	136449330	-	1	NA	Intergenic	Intergenic	-33752	NM_001201390	100502936	Mm.21182	NM_001201390	ENSMUSG00000045291	E330021D16Rik	C85549	RIKEN cDNA E330021D16 gene	protein-coding
mm_152312.1	chr19	9899391	9899401	-	1	NA	5' UTR (NM_016692, exon 1 of 18)	5' UTR (NM_016692, exon 1 of 18)	137	NM_016692	16319	Mm.29755	NM_016692	ENSMUSG00000024660	Incenp	2700067E22Rik|AU019509|C130081E20|C77457	inner centromere protein	protein-coding
mm_149004.1	chr19	8712222	8712234	+	1	NA	intron (NM_001161413, intron 3 of 9)	ID_B1|SINE|B4	1669	NM_008577	17254	Mm.4114	NM_008577	ENSMUSG00000010095	Slc3a2	4F2|4F2HC|AI314110|Cd98|Ly-10|Ly-m10|Ly10|Mdu1|Mgp-2hc|NACAE	solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2	protein-coding
mm_61789.1	chr7	83883725	83883740	+	1	NA	5' UTR (NM_030705, exon 1 of 1)	5' UTR (NM_030705, exon 1 of 1)	609	NM_030705	80889	Mm.272998	NM_030705	ENSMUSG00000070462	Mesdc1	AW061151	mesoderm development candidate 1	protein-coding
mm_164589.1	chr17	26509526	26509532	-	1	NA	Intergenic	Intergenic	-1057	NM_013642	19252	Mm.239041	NM_013642	ENSMUSG00000024190	Dusp1	3CH134|MKP1|Ptpn16|U19515|erp|mkp-1	dual specificity phosphatase 1	protein-coding
mm_117861.1	chr13	98815585	98815606	-	1	NA	promoter-TSS (NM_172591)	promoter-TSS (NM_172591)	-146	NM_172591	218503	Mm.23928	NM_172591	ENSMUSG00000041685	Fcho2	5832424M12Rik|AA387320	FCH domain only 2	protein-coding
mm_126263.1	chr15	79109056	79109074	+	1	NA	promoter-TSS (NM_177461)	promoter-TSS (NM_177461)	82	NM_177461	27008	Mm.196480	NM_177461	ENSMUSG00000033039	Micall1	AI448246|D15Mit260|D15N2e|EST573322|EST820961|MIRab13|mKIAA1668	microtubule associated monooxygenase, calponin and LIM domain containing -like 1	protein-coding
mm_168135.1	chr10	29619634	29619653	+	1	NA	Intergenic	L1Md_T|LINE|L1	-83776	NM_028351	72780	Mm.45191	NM_028351	ENSMUSG00000019880	Rspo3	2810459H04Rik|AW742308|Cristin1|Thsd2	R-spondin 3	protein-coding
mm_105546.1	chr11	106345097	106345108	-	1	NA	intron (NM_133199, intron 6 of 23)	B4|SINE|B4	4288	NM_133199	110880	Mm.432528	NM_133199	ENSMUSG00000001027	Scn4a	Nav1.4|SkM1|mH2	sodium channel, voltage-gated, type IV, alpha	protein-coding
mm_163390.1	chr12	58268836	58268838	-	1	NA	5' UTR (NM_025809, exon 1 of 1)	5' UTR (NM_025809, exon 1 of 1)	421	NM_025809	66864	Mm.280563	NM_025809	ENSMUSG00000045930	Clec14a	1200003C23Rik|AI642649	C-type lectin domain family 14, member a	protein-coding
mm_43153.1	chr5	125532404	125532419	+	1	NA	promoter-TSS (NM_001190352)	promoter-TSS (NM_001190352)	-7	NM_001190352	208151	Mm.40397	NM_001190352	ENSMUSG00000070498	Tmem132b	AK220418|mKIAA1786	transmembrane protein 132B	protein-coding
mm_32355.1	chr4	105157416	105157426	+	1	NA	promoter-TSS (NM_080555)	promoter-TSS (NM_080555)	74	NM_080555	67916	Mm.348326	NM_080555	ENSMUSG00000028517	Plpp3	1110003O22Rik|2610002D05Rik|AV025606|D4Bwg0538e|D4Bwg1535e|Lpp3|Ppab2b|Ppap2b	phospholipid phosphatase 3	protein-coding
mm_155744.1	chrX	96166801	96166841	+	1	NA	3' UTR (NM_010833, exon 13 of 13)	3' UTR (NM_010833, exon 13 of 13)	70776	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_68574.1	chr7	115841621	115841624	-	1	NA	intron (NM_001025560, intron 2 of 15)	B1_Mur3|SINE|Alu	4518	NM_001277326	20679	Mm.323365	NM_011445	ENSMUSG00000051910	Sox6	AI987981|SOX-LZ	SRY (sex determining region Y)-box 6	protein-coding
mm_168904.1	chr12	55155340	55155340	+	1	NA	5' UTR (NM_001100109, exon 1 of 16).2	5' UTR (NM_001100109, exon 1 of 16).2	236	NM_001100109	665155	Mm.12848	NM_001100109	ENSMUSG00000079108	Srp54b	-	signal recognition particle 54B	protein-coding
mm_65349.1	chr7	24997223	24997233	-	1	NA	exon (NM_001290469, exon 8 of 23)	exon (NM_001290469, exon 8 of 23)	8709	NM_001290469	232975	Mm.44101	NM_144921	ENSMUSG00000040907	Atp1a3	Atpa-2	ATPase, Na+/K+ transporting, alpha 3 polypeptide	protein-coding
mm_161849.1	chr18	12305682	12305682	-	1	NA	promoter-TSS (NM_001190371)	promoter-TSS (NM_001190371)	38	NM_001190371	225187	Mm.53865	NM_001190371	ENSMUSG00000057766	Ankrd29	G630054C21|G630054C21Rik|Gm95	ankyrin repeat domain 29	protein-coding
mm_23583.1	chr3	63964790	63964830	+	1	NA	promoter-TSS (NM_001272035)	promoter-TSS (NM_001272035)	-77	NM_015728	11416	Mm.135619	NM_015728	ENSMUSG00000027822	Slc33a1	AI315656|AI788741|Acatn|D630022N01Rik	solute carrier family 33 (acetyl-CoA transporter), member 1	protein-coding
mm_168555.1	chr1	165526608	165526612	+	1	NA	intron (NM_173029, intron 13 of 33)	intron (NM_173029, intron 13 of 33)	41427	NM_173029	271639	Mm.66952	NM_173029	ENSMUSG00000026567	Adcy10	4930431D04Rik|4931412F17|Sacy|sAC	adenylate cyclase 10	protein-coding
mm_124075.1	chr14	78620958	78620959	-	1	NA	intron (NM_001081336, intron 7 of 28)	intron (NM_001081336, intron 7 of 28)	8332	NM_001253766	380921	Mm.89591	NM_001081336	ENSMUSG00000034731	Dgkh	5930402B05Rik|D130015C16|DGK	diacylglycerol kinase, eta	protein-coding
mm_61418.1	chr7	73617287	73617343	+	1	NA	Intergenic	Intergenic	-58920	NR_037569	69170	Mm.34539	NR_037569	ENSMUSG00000101970	1810026B05Rik	-	RIKEN cDNA 1810026B05 gene	ncRNA
mm_95451.1	chr11	50325901	50325949	+	1	NA	promoter-TSS (NM_001110500)	promoter-TSS (NM_001110500)	-252	NM_001110500	12330	Mm.248827	NM_007597	ENSMUSG00000020368	Canx	1110069N15Rik|AI988026|Cnx|D11Ertd153e	calnexin	protein-coding
mm_135130.1	chr16	35843992	35844014	-	1	NA	intron (NM_001039530, intron 12 of 16)	intron (NM_001039530, intron 12 of 16)	27379	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_29833.1	chr3	129755306	129755326	-	1	NA	promoter-TSS (NM_010113)	promoter-TSS (NM_010113)	6	NM_010113	13645	Mm.252481	NM_010113	ENSMUSG00000028017	Egf	AI790464	epidermal growth factor	protein-coding
mm_42191.1	chr5	112269509	112269545	+	1	NA	TTS (NM_001312894)	TTS (NM_001312894)	-7164	NM_001326590	22022	Mm.250631	NM_009419	ENSMUSG00000029344	Tpst2	AI448750|D5Ucla3|Tango13b|grm|grt	protein-tyrosine sulfotransferase 2	protein-coding
mm_49502.1	chr6	29768551	29768555	+	1	NA	exon (NM_021414, exon 1 of 17)	exon (NM_021414, exon 1 of 17)	110	NM_001171000	74340	Mm.210899	NM_021414	ENSMUSG00000029772	Ahcyl2	4631427C17Rik|AI227036|Adohcyase3|mKIAA0828	S-adenosylhomocysteine hydrolase-like 2	protein-coding
mm_26175.1	chr3	138288834	138288840	+	1	NA	exon (NM_007409, exon 7 of 9)	exon (NM_007409, exon 7 of 9)	11192	NM_007409	11522	Mm.2409	NM_007409	ENSMUSG00000074207	Adh1	ADH-AA|AI194826|Adh-1|Adh-1-t|Adh-1e|Adh-1t|Adh-3e|Adh1-e|Adh1-t|Adh1tl|Adh3-e	alcohol dehydrogenase 1 (class I)	protein-coding
mm_84911.1	chr9	79977783	79977809	-	1	NA	promoter-TSS (NM_001081243)	promoter-TSS (NM_001081243)	86	NM_001081243	70598	Mm.23049	NM_001081243	ENSMUSG00000034898	Filip1	5730485H21Rik|AI843021	filamin A interacting protein 1	protein-coding
mm_77873.1	chr9	6168571	6168595	+	1	NA	promoter-TSS (NM_027924)	promoter-TSS (NM_027924)	-29	NM_027924	71785	Mm.390122	NM_027924	ENSMUSG00000032006	Pdgfd	1110003I09Rik	platelet-derived growth factor, D polypeptide	protein-coding
mm_148463.1	chr19	4081566	4081583	+	1	NA	promoter-TSS (NM_001160253)	promoter-TSS (NM_001160253)	-914	NM_001160253	29866	Mm.46268	NM_013878	ENSMUSG00000024857	Cabp2	-	calcium binding protein 2	protein-coding
mm_93808.1	chr10	120979328	120979373	-	1	NA	promoter-TSS (NM_001081193)	promoter-TSS (NM_001081193)	-20	NM_001081193	380664	Mm.339371	NM_001081193	ENSMUSG00000048661	Lemd3	AI316861|Man1	LEM domain containing 3	protein-coding
mm_98919.1	chr11	98326303	98326312	+	1	NA	3' UTR (NM_010895, exon 2 of 2)	3' UTR (NM_010895, exon 2 of 2)	3338	NM_010895	18013	Mm.4814	NM_010895	ENSMUSG00000038255	Neurod2	Ndrf|bHLHa1	neurogenic differentiation 2	protein-coding
mm_127890.1	chr15	9155337	9155341	-	1	NA	promoter-TSS (NM_001285980)	promoter-TSS (NM_001285980)	86	NM_001285980	27401	Mm.35584	NM_013787	ENSMUSG00000054115	Skp2	4930500A04Rik|FBXL1|FWD1|p45	S-phase kinase-associated protein 2 (p45)	protein-coding
mm_37647.1	chr4	128745085	128745128	-	1	NA	exon (NM_018774, exon 11 of 15)	exon (NM_018774, exon 11 of 15)	-14152	NM_001009819	215493	Mm.300900	NM_001009819	ENSMUSG00000028794	A3galt2	Gm433|iGb3|iGb3S	alpha 1,3-galactosyltransferase 2 (isoglobotriaosylceramide synthase)	protein-coding
mm_31000.1	chr4	40155822	40155831	+	1	NA	intron (NM_007386, intron 1 of 20)	intron (NM_007386, intron 1 of 20)	12561	NM_007386	11428	Mm.331547	NM_007386	ENSMUSG00000028405	Aco1	Aco-1|Irebp|Irp1	aconitase 1	protein-coding
mm_11070.1	chr2	27676994	27677005	+	1	NA	promoter-TSS (NM_011305)	promoter-TSS (NM_011305)	-202	NM_011305	20181	Mm.24624	NM_011305	ENSMUSG00000015846	Rxra	9530071D11Rik|Nr2b1|RXRalpha1	retinoid X receptor alpha	protein-coding
mm_11818.1	chr2	44160885	44160894	+	1	NA	intron (NM_001301832, intron 11 of 14)	intron (NM_001301832, intron 11 of 14)	-95565	NR_040622	320872	Mm.445023	NR_040622	ENSMUSG00000085089	Arhgap15os	A430092G05Rik	Rho GTPase activating protein 15, opposite strand	ncRNA
mm_26164.1	chr3	138279785	138279808	+	1	NA	exon (NM_007409, exon 2 of 9)	exon (NM_007409, exon 2 of 9)	2151	NM_007409	11522	Mm.2409	NM_007409	ENSMUSG00000074207	Adh1	ADH-AA|AI194826|Adh-1|Adh-1-t|Adh-1e|Adh-1t|Adh-3e|Adh1-e|Adh1-t|Adh1tl|Adh3-e	alcohol dehydrogenase 1 (class I)	protein-coding
mm_104064.1	chr11	86585043	86585059	-	1	NA	promoter-TSS (NR_029738)	promoter-TSS (NR_029738)	-893	NR_029738	387140		NR_029738	ENSMUSG00000065455	Mir21a	Mir21|Mirn21|mmu-mir-21|mmu-mir-21a	microRNA 21a	ncRNA
mm_71083.1	chr8	34804924	34804938	+	1	NA	Intergenic	Intergenic	-2679	NM_176933	319520	Mm.170276	NM_176933	ENSMUSG00000031530	Dusp4	2700078F24Rik|AI844617|BB104621|E130306H24Rik|MKP2	dual specificity phosphatase 4	protein-coding
mm_65463.1	chr7	25471974	25471997	-	1	NA	exon (NM_001039186, exon 5 of 8)	exon (NM_001039186, exon 5 of 8)	5640	NM_001039185	26365	Mm.322502	NM_011926	ENSMUSG00000074272	Ceacam1	Bgp|Bgp1|C-CAM|CD66a|Cc1|Cea-1|Cea-7|Cea1|Cea7|Hv-2|Hv2|MHVR|MHVR1|Mhv-1|bb-1|mCEA1|mmCGM1|mmCGM1a|mmCGM2	carcinoembryonic antigen-related cell adhesion molecule 1	protein-coding
mm_69503.1	chr7	134232155	134232175	-	1	NA	Intergenic	Intergenic	-7068	NM_007400	11489	Mm.439714	NM_007400	ENSMUSG00000054555	Adam12	Mltna	a disintegrin and metallopeptidase domain 12 (meltrin alpha)	protein-coding
mm_52487.1	chr6	114643195	114643203	+	1	NA	intron (NM_028835, intron 1 of 18)	CpG	102	NM_001253717	74244	Mm.275332	NM_028835	ENSMUSG00000030314	Atg7	1810013K23Rik|Agp7|Apg7l|Atg7l|Gm21553	autophagy related 7	protein-coding
mm_164510.1	chr16	94760926	94760926	-	1	NA	TTS (NM_010606)	TTS (NM_010606)	95764	NM_001025590	16522	Mm.328720	NM_010606	ENSMUSG00000043301	Kcnj6	BIR1|GIRK2|KATP2|KCNJ7|Kir3.2|weaver|wv	potassium inwardly-rectifying channel, subfamily J, member 6	protein-coding
mm_60986.1	chr7	49160509	49160520	+	1	NA	intron (NM_001111016, intron 2 of 38)	intron (NM_001111016, intron 2 of 38)	-85675	NM_175272	78286	Mm.333881	NM_175272	ENSMUSG00000052512	Nav2	5330421F07Rik|AU067780|BQ960892|HELAD1|POMFIL2|RAINB1|RAINB2|Unc53H2|mKIAA3015	neuron navigator 2	protein-coding
mm_24674.1	chr3	94837381	94837419	+	1	NA	promoter-TSS (NM_172683)	promoter-TSS (NM_172683)	-167	NM_001165948	229584	Mm.274787	NM_172683	ENSMUSG00000038902	Pogz	9530006B08Rik	pogo transposable element with ZNF domain	protein-coding
mm_74159.1	chr8	123397855	123397874	+	1	NA	intron (NM_001286362, intron 12 of 16)	intron (NM_001286362, intron 12 of 16)	-9218	NM_008559	17199	Mm.324942	NM_008559	ENSMUSG00000074037	Mc1r	Mcr1|Mshra|Tob|e	melanocortin 1 receptor	protein-coding
mm_26311.1	chr3	142519322	142519333	+	1	NA	intron (NM_153564, intron 10 of 10)	intron (NM_153564, intron 10 of 10)	-11009	NM_001083312	229900	Mm.45740	NM_145545	ENSMUSG00000040253	Gbp7	9830147J24Rik	guanylate binding protein 7	protein-coding
mm_16244.1	chr2	173158360	173158375	+	1	NA	exon (NM_011044, exon 10 of 10)	exon (NM_011044, exon 10 of 10)	5294	NM_011044	18534	Mm.266867	NM_011044	ENSMUSG00000027513	Pck1	AI265463|PEPCK|Pck-1	phosphoenolpyruvate carboxykinase 1, cytosolic	protein-coding
mm_116169.1	chr13	30792265	30792271	-	1	NA	Intergenic	Intergenic	43035	NM_013674	16364	Mm.4677	NM_013674	ENSMUSG00000021356	Irf4	AI385587|IRF-4|LSIRF|NF-EM5|Spip	interferon regulatory factor 4	protein-coding
mm_64552.1	chr7	144424118	144424121	+	1	NA	intron (NR_037302, intron 1 of 5)	intron (NR_037302, intron 1 of 5)	19314	NR_037302	100499519		NR_037302	ENSMUSG00000093912	Mir3470b	mmu-mir-3470b	microRNA 3470b	ncRNA
mm_17077.1	chr2	22874981	22875004	-	1	NA	exon (NM_019456, exon 14 of 14)	exon (NM_019456, exon 14 of 14)	-20530	NM_019501	56075	Mm.249752	NM_019501	ENSMUSG00000026784	Pdss1	2610203G20Rik|2700031G06Rik|TPT|TPT 1|Tprt|mDLP1|mSPS1	prenyl (solanesyl) diphosphate synthase, subunit 1	protein-coding
mm_155522.1	chrX	74255264	74255277	+	1	NA	exon (NM_007927, exon 2 of 6)	exon (NM_007927, exon 2 of 6)	583	NM_007927	13726	Mm.18892	NM_007927	ENSMUSG00000001964	Emd	AW550900|Sta	emerin	protein-coding
mm_33416.1	chr4	129960761	129960781	+	1	NA	promoter-TSS (NR_040648)	promoter-TSS (NR_040648)	-77	NR_040648	72225	Mm.102193	NR_040647		1700003M07Rik	-	RIKEN cDNA 1700003M07 gene	ncRNA
mm_128855.1	chr15	72034203	72034224	-	1	NA	promoter-TSS (NM_027174)	promoter-TSS (NM_027174)	14	NM_027174	69700	Mm.322500	NM_027174	ENSMUSG00000079022	Col22a1	2310067L16Rik|C80743	collagen, type XXII, alpha 1	protein-coding
mm_171060.1	chr3	108571684	108571711	+	1	NA	promoter-TSS (NM_025444)	promoter-TSS (NM_025444)	-2	NM_025444	99730	Mm.24431	NM_025444	ENSMUSG00000048100	Taf13	1810004N01Rik|2010309N11Rik|AI847295|TAFII18	TATA-box binding protein associated factor 13	protein-coding
mm_135608.1	chr16	52249875	52249890	-	1	NA	3' UTR (NM_001331110, exon 15 of 15)	3' UTR (NM_001331110, exon 15 of 15)	203199	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_89700.1	chr10	97613256	97613257	+	1	NA	3' UTR (NM_008438, exon 3 of 3)	3' UTR (NM_008438, exon 3 of 3)	6051	NM_008438	16545	Mm.6228	NM_008438	ENSMUSG00000019932	Kera	CNA2|SLRR2B	keratocan	protein-coding
mm_97413.1	chr11	77982160	77982162	+	1	NA	promoter-TSS (NM_174852)	promoter-TSS (NM_174852)	-655	NM_174852	268448	Mm.274329	NM_174852	ENSMUSG00000037791	Phf12	2410142K10Rik|F630045O13|PF1|mKIAA1523	PHD finger protein 12	protein-coding
mm_114840.1	chr13	92611120	92611139	+	1	NA	promoter-TSS (NM_172588)	promoter-TSS (NM_172588)	-9	NM_172588	218442	Mm.297970	NM_172588	ENSMUSG00000021703	Serinc5	A130038L21Rik|AIGP3|C86123|TPO1	serine incorporator 5	protein-coding
mm_162086.1	chrX	36864159	36864159	-	1	NA	promoter-TSS (NM_029951)	promoter-TSS (NM_029951)	87	NM_029951	77644	Mm.290704	NM_029951	ENSMUSG00000006423	C330007P06Rik	-	RIKEN cDNA C330007P06 gene	protein-coding
mm_149750.1	chr19	22692574	22692595	+	1	NA	promoter-TSS (NM_001035246)	promoter-TSS (NM_001035246)	-35	NM_001035245	226025	Mm.131943	NM_177341	ENSMUSG00000052387	Trpm3	6330504P12Rik|9330180E14|AU018608|B930001P07Rik|LTRPC3|MLSN2	transient receptor potential cation channel, subfamily M, member 3	protein-coding
mm_7604.1	chr1	126322426	126322428	-	1	NA	intron (NM_001081756, intron 5 of 16)	intron (NM_001081756, intron 5 of 16)	170500	NM_172484	210356	Mm.377234	NM_172484	ENSMUSG00000049690	Nckap5	8430408F21|D130011D22Rik|E030049G20Rik|Erih1|Erih2|Gm1548|Nap5	NCK-associated protein 5	protein-coding
mm_135987.1	chr16	75092818	75092843	-	1	NA	Intergenic	Intergenic	493231	NM_001252513	320355	Mm.99517	NM_177142	ENSMUSG00000032948	Lipi	D930038D03Rik|lpd1	lipase, member I	protein-coding
mm_61250.1	chr7	65804043	65804050	+	1	NA	promoter-TSS (NR_045301)	promoter-TSS (NR_045301)	-6	NR_045301	100503969	Mm.383527	NR_045301		1810008I18Rik	-	RIKEN cDNA 1810008I18 gene	ncRNA
mm_147801.1	chr18	61658141	61658156	-	1	NA	intron (NR_045402, intron 1 of 4)	intron (NR_045402, intron 1 of 4)	7390	NR_045402	328968	Mm.392305	NR_045402		Carmn	Carmen|E330013P06|Gm16908|Mir143hg	cardiac mesoderm enhancer-associated non-coding RNA	ncRNA
mm_45556.1	chr5	73175165	73175170	-	1	NA	intron (NM_028194, intron 3 of 62)	intron (NM_028194, intron 3 of 62)	81451	NM_028194	72313	Mm.260594	NM_028194	ENSMUSG00000070733	Fryl	2010313D22Rik|2310004H21Rik|2510002A14Rik|9030227G01Rik|mKIAA0826	FRY like transcription coactivator	protein-coding
mm_27883.1	chr3	79173267	79173277	-	1	NA	Intergenic	Intergenic	-27397	NM_001099624	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_50052.1	chr6	41178163	41178166	+	1	NA	Intergenic	L1MC4|LINE|L1	-124108	NM_011646	22074	Mm.383263	NM_011646	ENSMUSG00000054106	Try4	0910001B19Rik|Td	trypsin 4	protein-coding
mm_157491.1	chrX	48419149	48419162	-	1	NA	exon (NM_019680, exon 5 of 9)	exon (NM_019680, exon 5 of 9)	43977	NM_019680	56501	Mm.36808	NM_019680	ENSMUSG00000031103	Elf4	AV314029|BC042423|ENSMUSG00000053512|Gm9907|Mef	E74-like factor 4 (ets domain transcription factor)	protein-coding
mm_36471.1	chr4	82705736	82705754	-	1	NA	Intergenic	Intergenic	153916	NM_026647	68268	Mm.32047	NM_026647	ENSMUSG00000028403	Zdhhc21	9130404H11Rik|AL024349|D130004H04Rik|dep	zinc finger, DHHC domain containing 21	protein-coding
mm_18532.1	chr2	64055383	64055398	-	1	NA	intron (NM_001267847, intron 1 of 3)	MER103C|DNA|hAT-Charlie	42648	NM_001267846	60344	Mm.130769	NM_021716	ENSMUSG00000075324	Fign	fi|fidget	fidgetin	protein-coding
mm_149489.1	chr19	11818076	11818104	+	1	NA	intron (NM_001025307, intron 1 of 10)	intron (NM_001025307, intron 1 of 10)	1313	NM_001286543	20908	Mm.272264	NM_011502	ENSMUSG00000041488	Stx3	Syn-3	syntaxin 3	protein-coding
mm_88785.1	chr10	80606571	80606601	+	1	NA	exon (NM_001100606, exon 2 of 2)	exon (NM_001100606, exon 2 of 2)	-2674	NR_105877	102465550		NR_105877	ENSMUSG00000099283	Mir6912	Gm27990|mmu-mir-6912	microRNA 6912	ncRNA
mm_106763.1	chr12	4592630	4592648	+	1	NA	promoter-TSS (NM_001198969)	promoter-TSS (NM_001198969)	-369	NM_001198969	20403	Mm.341204	NM_011365	ENSMUSG00000020640	Itsn2	AI327390|Ese2|Sh3d1B|Sh3p18|mKIAA1256	intersectin 2	protein-coding
mm_68946.1	chr7	126503659	126503677	-	1	NA	promoter-TSS (NM_183020)	promoter-TSS (NM_183020)	-366	NM_183020	233871	Mm.231450	NM_183020	ENSMUSG00000032637	Atxn2l	A2D|A2LG|A2RP|A2lp|Atxnl2	ataxin 2-like	protein-coding
mm_88556.1	chr10	78780471	78780541	+	1	NA	promoter-TSS (NM_009200)	promoter-TSS (NM_009200)	10	NM_009200	20513	Mm.6257	NM_009200	ENSMUSG00000005357	Slc1a6	EAAT4	solute carrier family 1 (high affinity aspartate/glutamate transporter), member 6	protein-coding
mm_5501.1	chr1	37334170	37334179	-	1	NA	intron (NM_001290797, intron 1 of 25)	intron (NM_001290797, intron 1 of 25)	34336	NM_001290797	269180	Mm.5294	NM_030266	ENSMUSG00000026113	Inpp4a	107kDa|9630012D15|D130048C09Rik|R74740	inositol polyphosphate-4-phosphatase, type I	protein-coding
mm_61870.1	chr7	89426271	89426277	+	1	NA	promoter-TSS (NR_102276)	promoter-TSS (NR_102276)	-32	NR_102276	101521	Mm.26902	NR_102276	ENSMUSG00000109311	AI314278	-	expressed sequence AI314278	ncRNA
mm_94259.1	chr11	3488209	3488232	+	1	NA	promoter-TSS (NM_172791)	promoter-TSS (NM_172791)	-7	NM_172791	237625	Mm.100476	NM_172791	ENSMUSG00000034579	Pla2g3	-	phospholipase A2, group III	protein-coding
mm_101443.1	chr11	30159688	30159699	-	1	NA	intron (NM_175836, intron 1 of 34)	tRNA-Lys-AAG|tRNA|tRNA	38564	NM_009260	20742	Mm.123110	NM_009260	ENSMUSG00000020315	Sptbn1	9930031C03Rik|AL033301|SPTB2|Spnb-2|Spnb2|elf1|elf3|mKIAA4049	spectrin beta, non-erythrocytic 1	protein-coding
mm_66334.1	chr7	42980863	42980866	-	1	NA	Intergenic	IAPLTR4|LTR|ERVK	-37934	NM_001105061	668612	Mm.469896	NM_001105061	ENSMUSG00000091528	Gm9268	EG668612|Vmn2r64	predicted gene 9268	protein-coding
mm_141608.1	chr17	32809001	32809042	-	1	NA	intron (NM_183177, intron 1 of 3)	intron (NM_183177, intron 1 of 3)	910	NM_001267583	240063	Mm.30675	NM_183177	ENSMUSG00000055202	Zfp811	BC052046	zinc finger protein 811	protein-coding
mm_74818.1	chr8	22805597	22805649	-	1	NA	promoter-TSS (NM_029505)	promoter-TSS (NM_029505)	31	NM_029505	64933	Mm.390023	NM_029505	ENSMUSG00000031539	Ap3m2	5830445E16Rik|AP-3B	adaptor-related protein complex 3, mu 2 subunit	protein-coding
mm_60610.1	chr7	44590887	44590905	+	1	NA	promoter-TSS (NM_001290682)	promoter-TSS (NM_001290682)	10	NM_001290682	16504	Mm.40312	NM_008422	ENSMUSG00000062785	Kcnc3	KShIIID|Kcr2-3|Kv3.3	potassium voltage gated channel, Shaw-related subfamily, member 3	protein-coding
mm_125687.1	chr15	66803980	66804001	+	1	NA	intron (NM_001029841, intron 1 of 7)	intron (NM_001029841, intron 1 of 7)	27839	NM_001029841	20491	Mm.7601	NM_009192	ENSMUSG00000022372	Sla	Slap|Slap-1	src-like adaptor	protein-coding
mm_78984.1	chr9	45390748	45390763	+	1	NA	intron (NM_022004, intron 3 of 7)	intron (NM_022004, intron 3 of 7)	-8954	NR_028499	11936	Mm.22742	NM_007503	ENSMUSG00000059412	Fxyd2	Atp1g1	FXYD domain-containing ion transport regulator 2	protein-coding
mm_9451.1	chr1	172602556	172602566	-	1	NA	promoter-TSS (NM_001164725)	promoter-TSS (NM_001164725)	-10	NM_001164725	677296	Mm.439612	NM_001164725	ENSMUSG00000070504	Fcrl6	ENSMUSG00000070504|FcRH6|mIFGP6|moFcRH6	Fc receptor-like 6	protein-coding
mm_98106.1	chr11	86860442	86860470	+	1	NA	intron (NR_106195, intron 4 of 8)	intron (NR_106195, intron 4 of 8)	-52796	NM_026191	67487	Mm.260627	NM_026191	ENSMUSG00000018425	Dhx40	2410016C14Rik|ARG147|DDX40|PAD	DEAH (Asp-Glu-Ala-His) box polypeptide 40	protein-coding
mm_48990.1	chr6	4756052	4756066	+	1	NA	exon (NM_130877, exon 2 of 2)	exon (NM_130877, exon 2 of 2)	8753	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_144997.1	chr18	38297248	38297266	+	1	NA	intron (NM_001164621, intron 1 of 9)	MIRc|SINE|MIR	452	NM_001164621	56736	Mm.228903	NM_020012	ENSMUSG00000060450	Rnf14	2310075C09Rik|2610005D23Rik|AA986456|AU041447|D18Ertd188e|D7Bwg0165e|Triad2	ring finger protein 14	protein-coding
mm_139989.1	chr17	72871695	72871711	+	1	NA	Intergenic	Intergenic	34999	NM_027166	383295	Mm.277533	NM_027166	ENSMUSG00000039770	Ypel5	2310076K21Rik|CGI-127	yippee-like 5 (Drosophila)	protein-coding
mm_122614.1	chr14	51093521	51093532	-	1	NA	intron (NM_021472, intron 1 of 1)	intron (NM_021472, intron 1 of 1)	2449	NM_021472	58809	Mm.202665	NM_021472	ENSMUSG00000021876	Rnase4	C730049F20Rik|Rab1	ribonuclease, RNase A family 4	protein-coding
mm_105299.1	chr11	102553030	102553033	-	1	NA	intron (NM_001159492, intron 1 of 7)	ID_B1|SINE|B4	3127	NM_001159492	237943	Mm.260282	NM_001159492	ENSMUSG00000034621	Gpatch8	5430405G24Rik|AU018890|ENSMUSG00000075516|Fbm1|Gpatc8|mKIAA0553	G patch domain containing 8	protein-coding
mm_96985.1	chr11	70656932	70656943	+	1	NA	promoter-TSS (NM_007933)	promoter-TSS (NM_007933)	-239	NM_001136062	13808	Mm.251322	NM_007933	ENSMUSG00000060600	Eno3	Eno-3|MSE	enolase 3, beta muscle	protein-coding
mm_19018.1	chr2	76928927	76928952	-	1	NA	intron (NM_028004, intron 42 of 191)	intron (NM_028004, intron 42 of 191)	53608	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_146074.1	chr18	70568427	70568506	+	1	NA	exon (NM_010773, exon 1 of 7)	exon (NM_010773, exon 1 of 7)	174	NM_010773	17191	Mm.322	NM_010773	ENSMUSG00000024513	Mbd2	MBD2a	methyl-CpG binding domain protein 2	protein-coding
mm_87777.1	chr10	60295067	60295081	+	1	NA	exon (NM_011179, exon 6 of 15)	exon (NM_011179, exon 6 of 15)	10613	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_116823.1	chr13	54593999	54594009	-	1	NA	exon (NM_028870, exon 5 of 5)	exon (NM_028870, exon 5 of 5)	3773	NM_025933	67044	Mm.29353	NM_025933	ENSMUSG00000025868	Higd2a	2010110M21Rik|AA690237	HIG1 domain family, member 2A	protein-coding
mm_139138.1	chr17	47509518	47509534	+	1	NA	intron (NM_001081635, intron 1 of 6)	intron (NM_001081635, intron 1 of 6)	4475	NM_001081635	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_149442.1	chr19	11481013	11481021	+	1	NA	intron (NM_028595, intron 6 of 6)	intron (NM_028595, intron 6 of 6)	-11021	NM_001164202	666926	Mm.486382	NM_001164202	ENSMUSG00000058470	Gm8369	EG666926	predicted gene 8369	protein-coding
mm_108601.1	chr12	85468945	85468965	+	1	NA	Intergenic	Intergenic	-4946	NM_010234	14281	Mm.246513	NM_010234	ENSMUSG00000021250	Fos	D12Rfj1|c-fos|cFos	FBJ osteosarcoma oncogene	protein-coding
mm_151192.1	chr19	53529138	53529151	+	1	NA	promoter-TSS (NM_001085390)	promoter-TSS (NM_001085390)	-174	NM_001085390	240672	Mm.482424	NM_001085390	ENSMUSG00000034765	Dusp5	Gm337	dual specificity phosphatase 5	protein-coding
mm_97487.1	chr11	78324892	78324930	+	1	NA	exon (NM_009657, exon 3 of 8)	exon (NM_009657, exon 3 of 8)	713	NM_009657	11676	Mm.7729	NM_009657	ENSMUSG00000017390	Aldoc	AI847350|AU040929|Aldo3|Scrg2	aldolase C, fructose-bisphosphate	protein-coding
mm_98028.1	chr11	85194358	85194370	+	1	NA	intron (NM_025825, intron 12 of 12)	intron (NM_025825, intron 12 of 12)	23268	NM_028589	73634	Mm.48850	NM_028589	ENSMUSG00000018479	1700125H20Rik	-	RIKEN cDNA 1700125H20 gene	protein-coding
mm_169369.1	chr14	33185252	33185262	-	1	NA	promoter-TSS (NM_001146022)	promoter-TSS (NM_001146022)	-191	NM_001146022	545030	Mm.318345	NM_001146022	ENSMUSG00000051506	Wdfy4	Gm18810	WD repeat and FYVE domain containing 4	protein-coding
mm_167682.1	chr9	80696365	80696367	+	1	NA	Intergenic	U4|snRNA|snRNA	-230928	NM_022016	63859	Mm.422780	NM_022016	ENSMUSG00000032343	Impg1	A930015H12Rik|IMP150|SPACR	interphotoreceptor matrix proteoglycan 1	protein-coding
mm_135711.1	chr16	55523732	55523746	-	1	NA	Intergenic	Intergenic	29008	NR_039578	100628589		NR_039578	ENSMUSG00000093292	Mir5118	mmu-mir-5118|mu-mir-5118	microRNA 5118	ncRNA
mm_99891.1	chr11	109543695	109543736	+	1	NA	promoter-TSS (NM_001166177)	promoter-TSS (NM_001166177)	4	NM_001166177	74008	Mm.482224	NM_028710	ENSMUSG00000020604	Arsg	6330406P08Rik|AI846872	arylsulfatase G	protein-coding
mm_128913.1	chr15	73643256	73643260	-	1	NA	Intergenic	AT_rich|Low_complexity|Low_complexity	-18514	NM_001033219	106068	Mm.212813	NM_001033219	ENSMUSG00000079020	Slc45a4	9330175B01Rik|AW552276	solute carrier family 45, member 4	protein-coding
mm_26895.1	chr3	19238878	19238898	-	1	NA	intron (NM_001122759, intron 5 of 12)	intron (NM_001122759, intron 5 of 12)	26120	NM_008802	18583	Mm.355614	NM_008802	ENSMUSG00000069094	Pde7a	AU015378|AW047537	phosphodiesterase 7A	protein-coding
mm_43320.1	chr5	134986192	134986270	+	1	NA	promoter-TSS (NM_009902)	promoter-TSS (NM_009902)	17	NM_009902	12739	Mm.158662	NM_009902	ENSMUSG00000070473	Cldn3	AI182374|Cpetr2|mRVP1	claudin 3	protein-coding
mm_83302.1	chr9	43736966	43736992	-	1	NA	Intergenic	Intergenic	-7597	NM_021424	58235	Mm.335096	NM_021424	ENSMUSG00000032012	Nectin1	AI835281|AW549174|Cd111|HIgR|HveC|PRR|PRR1|Pvrl1|nectin-1	nectin cell adhesion molecule 1	protein-coding
mm_104562.1	chr11	96829905	96829951	-	1	NA	promoter-TSS (NM_008686)	promoter-TSS (NM_008686)	40	NM_008686	18023	Mm.6743	NM_008686	ENSMUSG00000038615	Nfe2l1	AA408798|AW212678|LCR-F1|Lcrf1|NRF1|TCF-11|TCF11	nuclear factor, erythroid derived 2,-like 1	protein-coding
mm_33871.1	chr4	135997428	135997431	+	1	NA	Intergenic	MurERV4-int|LTR|ERVK	-10185	NM_025411	66193	Mm.29131	NM_025411	ENSMUSG00000028669	Pithd1	1110049F12Rik|AA408179|Trp26	PITH (C-terminal proteasome-interacting domain of thioredoxin-like) domain containing 1	protein-coding
mm_162971.1	chr11	11699548	11699563	-	1	NA	intron (NM_001301866, intron 1 of 5)	intron (NM_001301866, intron 1 of 5)	9378	NM_001301863	22778	Mm.103545	NM_009578	ENSMUSG00000018654	Ikzf1	5832432G11Rik|Ikaros|LyF-1|Zfpn1a1|Znfn1a1|hlk-1|mKIAA4227	IKAROS family zinc finger 1	protein-coding
mm_8105.1	chr1	135850806	135850808	-	1	NA	exon (NM_001130176, exon 10 of 13)	exon (NM_001130176, exon 10 of 13)	9946	NM_001130176	21956	Mm.247470	NM_011619	ENSMUSG00000026414	Tnnt2	Tnt|cTnT	troponin T2, cardiac	protein-coding
mm_171701.1	chr4	72028136	72028148	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	172751	NM_011599	21885	Mm.278444	NM_011599	ENSMUSG00000008305	Tle1	C230057C06Rik|Estm14|Grg-1|Grg1|Tle4l	transducin-like enhancer of split 1	protein-coding
mm_24172.1	chr3	88573248	88573253	+	1	NA	Intergenic	RLTR41|LTR|ERV1	-6421	NM_025448	66256	Mm.7091	NM_025448	ENSMUSG00000041355	Ssr2	1500032E05Rik|AI315033|AU020133|TLAP|TRAPB|TRAPbeta	signal sequence receptor, beta	protein-coding
mm_106616.1	chr11	120818586	120818597	-	1	NA	exon (NM_007988, exon 10 of 43)	exon (NM_007988, exon 10 of 43)	5956	NM_007988	14104	Mm.236443	NM_007988	ENSMUSG00000025153	Fasn	A630082H08Rik|FAS	fatty acid synthase	protein-coding
mm_85713.1	chr9	108208465	108208478	-	1	NA	exon (NM_001276486, exon 4 of 4)	exon (NM_001276486, exon 4 of 4)	-18088	NM_007567	12217	Mm.20425	NM_007567	ENSMUSG00000032589	Bsn	-	bassoon	protein-coding
mm_64001.1	chr7	140137596	140137668	+	1	NA	promoter-TSS (NM_199301)	promoter-TSS (NM_199301)	68	NM_199301	212508	Mm.296088	NM_199301	ENSMUSG00000039018	Mtg1	Gm169|Gtpbp7	mitochondrial ribosome-associated GTPase 1	protein-coding
mm_61967.1	chr7	90426556	90426577	+	1	NA	5' UTR (NM_027298, exon 1 of 1)	5' UTR (NM_027298, exon 1 of 1)	254	NM_027298	70054	Mm.307198	NM_027298	ENSMUSG00000044362	Ccdc89	1700019B01Rik|AU022100|BOIP	coiled-coil domain containing 89	protein-coding
mm_119448.1	chr14	46882995	46882999	+	1	NA	promoter-TSS (NM_028966)	promoter-TSS (NM_028966)	32	NM_001037221	74480	Mm.214454	NM_028966	ENSMUSG00000021838	Samd4	1700024G08Rik|1700111L17Rik|4933436G17Rik|Samd4a|Smaug|Smaug1|sunk	sterile alpha motif domain containing 4	protein-coding
mm_169954.1	chr16	8562814	8562820	-	1	NA	intron (NM_172961, intron 1 of 15)	RLTR9E|LTR|ERVK	49388	NM_172961	268860	Mm.259315	NM_172961	ENSMUSG00000057880	Abat	9630038C02Rik|AI255750|ENSMUSG00000051226|Gabaat|Gabat|Gm9851|I54|Laibat|X61497	4-aminobutyrate aminotransferase	protein-coding
mm_142616.1	chr17	46858657	46858684	-	1	NA	Intergenic	Intergenic	-27257	NM_001100452	210982	Mm.37642	NM_001100452	ENSMUSG00000036568	Gltscr1l	mKIAA0240	GLTSCR1-like	protein-coding
mm_65001.1	chr7	17027808	17027846	-	1	NA	promoter-TSS (NM_011155)	promoter-TSS (NM_011155)	87	NM_011155	19060	Mm.3294	NM_011155	ENSMUSG00000003099	Ppp5c	AU020526|PP5	protein phosphatase 5, catalytic subunit	protein-coding
mm_105105.1	chr11	100958900	100958906	-	1	NA	exon (NM_008986, exon 2 of 2)	exon (NM_008986, exon 2 of 2)	11714	NM_008986	19285	Mm.21864	NM_008986	ENSMUSG00000004044	Ptrf	2310075E07Rik|AW546441|Cav-p60|Cavin	polymerase I and transcript release factor	protein-coding
mm_50110.1	chr6	41533790	41533800	+	1	NA	Intergenic	Intergenic	12019	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_38212.1	chr4	135898483	135898496	-	1	NA	intron (NM_009924, intron 1 of 1)	MIRb|SINE|MIR	3300	NM_009924	12802	Mm.297251	NM_009924	ENSMUSG00000062585	Cnr2	CB-2|CB2|CB2-R	cannabinoid receptor 2 (macrophage)	protein-coding
mm_106757.1	chr12	4227567	4227574	+	1	NA	intron (NM_134046, intron 3 of 6)	intron (NM_134046, intron 3 of 6)	-6457	NM_001204912	69709	Mm.250552	NM_001204912	ENSMUSG00000096199	Ptrhd1	2410017P09Rik	peptidyl-tRNA hydrolase domain containing 1	protein-coding
mm_47712.1	chr5	129998120	129998134	-	1	NA	exon (NM_010368, exon 7 of 12)	exon (NM_010368, exon 7 of 12)	4701	NM_010368	110006	Mm.3317	NM_010368	ENSMUSG00000025534	Gusb	AI747421|Gur|Gus|Gus-r|Gus-s|Gus-t|Gus-u|Gut|asd|g	glucuronidase, beta	protein-coding
mm_154631.1	chrX	7762704	7762729	+	1	NA	promoter-TSS (NM_001271489)	promoter-TSS (NM_001271489)	55	NM_172472	209446	Mm.249142	NM_172472	ENSMUSG00000000134	Tfe3	F830016E06Rik|Tcfe3|Tfe-3|bHLHe33	transcription factor E3	protein-coding
mm_76590.1	chr8	89042761	89042774	-	1	NA	intron (NM_021390, intron 1 of 3)	CpG-14342	1395	NM_021390	58198	Mm.214361	NM_021390	ENSMUSG00000031665	Sall1	Msal-3	sal-like 1 (Drosophila)	protein-coding
mm_19401.1	chr2	91635909	91635935	-	1	NA	exon (NM_010168, exon 2 of 14)	exon (NM_010168, exon 2 of 14)	535	NM_010168	14061	Mm.89048	NM_010168	ENSMUSG00000027249	F2	Cf-2|Cf2|FII	coagulation factor II	protein-coding
mm_143125.1	chr17	57211713	57211725	-	1	NA	exon (NM_009778, exon 29 of 41)	exon (NM_009778, exon 29 of 41)	5509	NR_105944	102465591		NR_105944	ENSMUSG00000099066	Mir6978	Gm27858|mmu-mir-6978	microRNA 6978	ncRNA
mm_22579.1	chr3	10366993	10367001	+	1	NA	promoter-TSS (NM_025519)	promoter-TSS (NM_025519)	24	NM_025519	66371	Mm.366147	NM_025519	ENSMUSG00000027536	Chmp4c	2010012P02Rik|2210015K02Rik|2310010I16Rik|Shax3|Snf7-3	charged multivesicular body protein 4C	protein-coding
mm_167714.1	chr9	97234168	97234173	-	1	NA	Intergenic	Intergenic	-123129	NM_138756	192287	Mm.228067	NM_138756	ENSMUSG00000032449	Slc25a36	C330005L02Rik	solute carrier family 25, member 36	protein-coding
mm_84838.1	chr9	78368168	78368177	-	1	NA	promoter-TSS (NM_025274)	promoter-TSS (NM_025274)	27	NM_025274	434423	Mm.139314	NM_025274	ENSMUSG00000060461	Dppa5a	AA536857|Dppa5|Esg1|ecat2	developmental pluripotency associated 5A	protein-coding
mm_29122.1	chr3	105052949	105052987	-	1	NA	promoter-TSS (NM_001163333)	promoter-TSS (NM_001163333)	-15	NM_001163332	80281	Mm.200327	NM_030249	ENSMUSG00000062127	Cttnbp2nl	AA552995|AA589392|AU018624|BC003236|mKIAA1433	CTTNBP2 N-terminal like	protein-coding
mm_107470.1	chr12	37416688	37416690	+	1	NA	intron (NM_178767, intron 12 of 12)	RMER4B|LTR|ERVK	175050	NM_178767	319660	Mm.485540	NM_178767	ENSMUSG00000050103	Agmo	A530016O06Rik|AI790538|Tmem195	alkylglycerol monooxygenase	protein-coding
mm_85087.1	chr9	91381422	91381432	-	1	NA	intron (NM_009576, intron 3 of 4)	intron (NM_009576, intron 3 of 4)	12455	NM_009576	22774	Mm.8062	NM_009576	ENSMUSG00000036972	Zic4	-	zinc finger protein of the cerebellum 4	protein-coding
mm_131525.1	chr16	17619531	17619548	+	1	NA	intron (NM_001164609, intron 1 of 19)	CpG	185	NM_001164609	77626	Mm.34659	NM_029945	ENSMUSG00000005899	Smpd4	4122402O22Rik|mKIAA1418	sphingomyelin phosphodiesterase 4	protein-coding
mm_64396.1	chr7	142494871	142494878	+	1	NA	TTS (NM_001271509)	TTS (NM_001271509)	-3962	NM_001347549	21957	Mm.389992	NM_011620	ENSMUSG00000061723	Tnnt3	fTnT	troponin T3, skeletal, fast	protein-coding
mm_72458.1	chr8	83243102	83243112	+	1	NA	intron (NM_027758, intron 6 of 17)	RMER15|LTR|ERVL	-47241	NM_009463	22227	Mm.4177	NM_009463	ENSMUSG00000031710	Ucp1	AI385626|Slc25a7|Ucp	uncoupling protein 1 (mitochondrial, proton carrier)	protein-coding
mm_75849.1	chr8	70648374	70648377	-	1	NA	3' UTR (NM_023217, exon 5 of 5)	3' UTR (NM_023217, exon 5 of 5)	11363	NM_023217	66522	Mm.154906	NM_023217	ENSMUSG00000056204	Pgpep1	2810003H13Rik|Gm19458|PAP-I|PGP|PGP-I|PGPI|Pcp	pyroglutamyl-peptidase I	protein-coding
mm_93958.1	chr10	127282565	127282585	-	1	NA	TTS (NM_027151)	TTS (NM_027151)	6443	NM_001347171	110962	Mm.372826	NM_033072	ENSMUSG00000025409	Mbd6	D10Wsu93e	methyl-CpG binding domain protein 6	protein-coding
mm_128151.1	chr15	32244414	32244438	-	1	NA	promoter-TSS (NM_009154)	promoter-TSS (NM_009154)	236	NR_038186	100616095	Mm.391938	NR_038186	ENSMUSG00000096956	Snhg18	0610007N19Rik|Snord123	small nucleolar RNA host gene 18	ncRNA
mm_25348.1	chr3	106788262	106788268	+	1	NA	intron (NM_007651, intron 1 of 7)	intron (NM_007651, intron 1 of 7)	1884	NM_007651	12508	Mm.316861	NM_007651	ENSMUSG00000040747	Cd53	AI323659|Ox-44|Tspan25	CD53 antigen	protein-coding
mm_79097.1	chr9	46243032	46243040	+	1	NA	exon (NM_007468, exon 3 of 3)	exon (NM_007468, exon 3 of 3)	2192	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_68306.1	chr7	105746669	105746690	-	1	NA	exon (NM_009906, exon 13 of 13)	exon (NM_009906, exon 13 of 13)	-2341	NM_020024	24075	Mm.274846	NM_020024	ENSMUSG00000043866	Taf10	30kDa|AU041226|TAFII30|Taf2h	TATA-box binding protein associated factor 10	protein-coding
mm_76607.1	chr8	90817060	90817079	-	1	NA	Intergenic	Intergenic	-11766	NM_177224	109151	Mm.100615	NM_177224	ENSMUSG00000056608	Chd9	1810014J18Rik|9030205D12Rik|A330063D19Rik|AD013|PRIC320|mKIAA0308	chromodomain helicase DNA binding protein 9	protein-coding
mm_11451.1	chr2	32085493	32085502	+	1	NA	Intergenic	Intergenic	-1792	NM_175511	241303	Mm.250441	NM_175511	ENSMUSG00000050592	Fam78a	A130092J06Rik	family with sequence similarity 78, member A	protein-coding
mm_87151.1	chr10	35102620	35102620	+	1	NA	Intergenic	T-rich|Low_complexity|Low_complexity	619220	NM_010237	14302	Mm.332432	NM_010237	ENSMUSG00000019779	Frk	BSK|BSK/IYK|C85044|GTK|RAK	fyn-related kinase	protein-coding
mm_44531.1	chr5	24445255	24445275	-	1	NA	promoter-TSS (NM_023229)	promoter-TSS (NM_023229)	-30	NM_023229	66587	Mm.28123	NM_023229	ENSMUSG00000028959	Fastk	0610011K02Rik|610011K02Rik	Fas-activated serine/threonine kinase	protein-coding
mm_94018.1	chr10	127663471	127663481	-	1	NA	intron (NM_001122895, intron 3 of 5)	intron (NM_001122895, intron 3 of 5)	3227	NM_001122895	17937	Mm.336898	NM_008668	ENSMUSG00000025402	Nab2	AI451907	Ngfi-A binding protein 2	protein-coding
mm_13222.1	chr2	97466448	97466485	+	1	NA	intron (NM_001289743, intron 5 of 6)	intron (NM_001289743, intron 5 of 6)	-1191	NM_001289744	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_11834.1	chr2	45110473	45110495	+	1	NA	promoter-TSS (NM_001289521)	promoter-TSS (NM_001289521)	-207	NM_001289521	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_87749.1	chr10	60267186	60267195	+	1	NA	Intergenic	Intergenic	-10438	NM_001146123	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_90790.1	chr10	7064191	7064201	-	1	NA	Intergenic	Intergenic	-41011	NM_001033391	320495	Mm.331674	NM_001033391	ENSMUSG00000064065	Ipcef1	A130090K04Rik	interaction protein for cytohesin exchange factors 1	protein-coding
mm_27970.1	chr3	80797981	80797996	-	1	NA	intron (NM_001083806, intron 2 of 15)	A-rich|Low_complexity|Low_complexity	4803	NM_013540	14800	Mm.220224	NM_013540	ENSMUSG00000033981	Gria2	GluA2|GluR-B|Glur-2|Glur2	glutamate receptor, ionotropic, AMPA2 (alpha 2)	protein-coding
mm_142255.1	chr17	37995704	37995716	-	1	NA	Intergenic	Intergenic	-42688	NM_001011829	258094	Mm.377348	NM_001011829	ENSMUSG00000109376	Olfr761	MOR218-12|MOR218-5P|MOR218-6P|Olfr1552-ps1	olfactory receptor 761	protein-coding
mm_131445.1	chr16	16269682	16269689	+	1	NA	exon (NM_026163, exon 12 of 13)	exon (NM_026163, exon 12 of 13)	-33280	NR_038046	70120	Mm.37486	NM_198246	ENSMUSG00000022792	Yars2	2210023C10Rik|tyrRS	tyrosyl-tRNA synthetase 2 (mitochondrial)	protein-coding
mm_138389.1	chr17	35050246	35050272	+	1	NA	promoter-TSS (NM_033444)	promoter-TSS (NM_033444)	16	NM_033444	114584	Mm.29524	NM_033444	ENSMUSG00000007041	Clic1	Clcp|G6	chloride intracellular channel 1	protein-coding
mm_139740.1	chr17	61781610	61781611	+	1	NA	Intergenic	Intergenic	1099707	NM_207654	13640	Mm.7978	NM_010109	ENSMUSG00000048915	Efna5	AL-1|AV158822|EFL-5|Ephrin-A5|Epl7|LERK-7|RAGS	ephrin A5	protein-coding
mm_52085.1	chr6	97829321	97829346	+	1	NA	intron (NM_001113198, intron 1 of 9)	intron (NM_001113198, intron 1 of 9)	22275	NM_001113198	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_32624.1	chr4	114610607	114610610	+	1	NA	3' UTR (NM_001085549, exon 7 of 7)	3' UTR (NM_001085549, exon 7 of 7)	203884	NM_001085549	666048	Mm.331779	NM_001085549	ENSMUSG00000070867	Trabd2b	Gm12824|Hkat|OTTMUSG00000008561	TraB domain containing 2B	protein-coding
mm_132928.1	chr16	49843046	49843055	+	1	NA	Intergenic	MT2C_Mm|LTR|ERVL	-12604	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_86672.1	chr10	18055794	18055815	+	1	NA	promoter-TSS (NM_001111065)	promoter-TSS (NM_001111065)	-136	NM_009048	19707	Mm.4479	NM_009048	ENSMUSG00000019854	Reps1	BB161292	RalBP1 associated Eps domain containing protein	protein-coding
mm_74347.1	chr8	127521197	127521201	+	1	NA	intron (NM_001309391, intron 22 of 24)	intron (NM_001309391, intron 22 of 24)	221547	NM_001013580	93742	Mm.299254	NM_033620	ENSMUSG00000025812	Pard3	AA960621|AI256638|Asip|D8Ertd580e|Par-3|Par3|Pard-3|Pard3a|Phip	par-3 family cell polarity regulator	protein-coding
mm_24343.1	chr3	89782274	89782316	+	1	NA	3' UTR (NM_027315, exon 13 of 13)	3' UTR (NM_027315, exon 13 of 13)	8686	NM_027315	70093	Mm.41438	NM_027315	ENSMUSG00000042572	Ube2q1	1110002C01Rik|2310012M18Rik|AI854014|Gtap|NICE-5|PRO3094|Ube2q	ubiquitin-conjugating enzyme E2Q family member 1	protein-coding
mm_32970.1	chr4	120032767	120032866	+	1	NA	intron (NM_010657, intron 2 of 8)	(CCGAG)n|Simple_repeat|Simple_repeat	-128390	NM_007902	13615	Mm.284855	NM_007902	ENSMUSG00000028635	Edn2	ET-2|PPET2|VIC	endothelin 2	protein-coding
mm_159380.1	chr3	90213700	90213700	+	1	NA	promoter-TSS (NM_001293741)	promoter-TSS (NM_001293741)	-15	NM_001293741	68328	Mm.29355	NM_026677	ENSMUSG00000027935	Rab13	0610007N03Rik|B230212B15Rik	RAB13, member RAS oncogene family	protein-coding
mm_145187.1	chr18	49755767	49755785	+	1	NA	promoter-TSS (NM_001170960)	promoter-TSS (NM_001170960)	-175	NM_001170960	68857	Mm.96010	NM_026854	ENSMUSG00000024505	Dtwd2	1190002H09Rik|8030470C17Rik|AI414673|BB115449	DTW domain containing 2	protein-coding
mm_29050.1	chr3	103735714	103735724	-	1	NA	3' UTR (NM_133859, exon 3 of 3)	3' UTR (NM_133859, exon 3 of 3)	2282	NM_133859	99543	Mm.211535	NM_133859	ENSMUSG00000027848	Olfml3	2810002E22Rik|AI115209|AW550633|HNOEL-iso|ONT3|mONT3	olfactomedin-like 3	protein-coding
mm_36924.1	chr4	108218008	108218048	-	1	NA	promoter-TSS (NM_001167936)	promoter-TSS (NM_001167936)	-106	NM_001167936	230590	Mm.301798	NM_001167936	ENSMUSG00000034645	Zyg11a	BC022150	zyg-11 family member A, cell cycle regulator	protein-coding
mm_150268.1	chr19	34232610	34232614	+	1	NA	intron (NM_029682, intron 5 of 10)	RLTR11C_MM|LTR|ERVK	22761	NM_007392	11475	Mm.213025	NM_007392	ENSMUSG00000035783	Acta2	0610041G09Rik|Actvs|SMalphaA|a-SMA|alphaSMA	actin, alpha 2, smooth muscle, aorta	protein-coding
mm_58192.1	chr6	143075807	143075826	-	1	NA	intron (NM_001109688, intron 7 of 24)	intron (NM_001109688, intron 7 of 24)	24336	NM_001286578	74741	Mm.130260	NM_029081	ENSMUSG00000030279	C2cd5	5730419I09Rik|C030008B15Rik|CDP138	C2 calcium-dependent domain containing 5	protein-coding
mm_61188.1	chr7	63444827	63444871	+	1	NA	promoter-TSS (NM_130880)	promoter-TSS (NM_130880)	77	NM_130880	170711	Mm.156872	NM_130880	ENSMUSG00000033510	Otud7a	AJ430384|Otud7	OTU domain containing 7A	protein-coding
mm_41209.1	chr5	88554449	88554495	+	1	NA	promoter-TSS (NM_023054)	promoter-TSS (NM_023054)	-11	NM_023054	65961	Mm.490364	NM_023054	ENSMUSG00000070697	Utp3	2400011K09Rik|AW557551|C87704|Crl1|Crlz1|Sas10	UTP3 small subunit processome component	protein-coding
mm_15298.1	chr2	155384565	155384568	+	1	NA	intron (NM_178111, intron 1 of 3)	ID_B1|SINE|B4	2710	NM_178111	68728	Mm.293605	NM_178111	ENSMUSG00000038375	Trp53inp2	1110029F20Rik|Tp53inp2	transformation related protein 53 inducible nuclear protein 2	protein-coding
mm_18005.1	chr2	38229987	38229997	-	1	NA	intron (NM_146122, intron 2 of 21)	intron (NM_146122, intron 2 of 21)	57392	NM_146122	227801	Mm.314245	NM_146122	ENSMUSG00000035392	Dennd1a	6030446I19Rik|connecdenn	DENN/MADD domain containing 1A	protein-coding
mm_878.1	chr1	52155342	52155359	+	1	NA	intron (NM_001205313, intron 23 of 24)	intron (NM_001205313, intron 23 of 24)	35728	NM_001205313	20846	Mm.277406	NM_009283	ENSMUSG00000026104	Stat1	2010005J02Rik|AA408197	signal transducer and activator of transcription 1	protein-coding
mm_116759.1	chr13	52561929	52561932	-	1	NA	Intergenic	Intergenic	11295	NR_046069	100040572	Mm.278873	NR_046069		Gm2848	-	predicted gene 2848	ncRNA
mm_30797.1	chr4	19872222	19872232	+	1	NA	Intergenic	Intergenic	50339	NM_175406	242341	Mm.19298	NM_175406	ENSMUSG00000028238	Atp6v0d2	1620401A02Rik|AI324824|V-ATPase	ATPase, H+ transporting, lysosomal V0 subunit D2	protein-coding
mm_22683.1	chr3	16196517	16196535	+	1	NA	intron (NR_027375, intron 4 of 5)	intron (NR_027375, intron 4 of 5)	13343	NM_001145919	229096	Mm.23834	NM_172677	ENSMUSG00000047213	Ythdf3	9130022A11Rik	YTH domain family 3	protein-coding
mm_169166.1	chr13	65503683	65503702	-	1	NA	Intergenic	Intergenic	224838	NM_178364	170936	Mm.151546	NM_178364	ENSMUSG00000021514	Zfp369	B930030B22Rik|D230020H11Rik|NRIF2	zinc finger protein 369	protein-coding
mm_97996.1	chr11	84129738	84129755	+	1	NA	promoter-TSS (NM_172562)	promoter-TSS (NM_172562)	-178	NM_172562	217031	Mm.45159	NM_172562	ENSMUSG00000018651	Tada2a	AV319371|D030022J10Rik|Tada2l	transcriptional adaptor 2A	protein-coding
mm_139484.1	chr17	56074725	56074746	+	1	NA	intron (NM_024432, intron 1 of 10)	CpG	254	NM_024432	66530	Mm.28000	NM_024432	ENSMUSG00000019578	Ubxn6	1200008L11Rik|2210415J11Rik|AU040909|Ubxd1|Ubxdc2	UBX domain protein 6	protein-coding
mm_61326.1	chr7	68228110	68228122	+	1	NA	3' UTR (NM_010513, exon 21 of 21)	3' UTR (NM_010513, exon 21 of 21)	36117	NM_030101	78444	Mm.425468	NM_030101	ENSMUSG00000030553	Pgpep1l	C330024D12Rik	pyroglutamyl-peptidase I-like	protein-coding
mm_117909.1	chr13	99430459	99430469	-	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-17638	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_90201.1	chr10	120317041	120317053	+	1	NA	Intergenic	Intergenic	-72476	NR_040626	320626	Mm.446091	NR_040626	ENSMUSG00000090191	9230105E05Rik	-	RIKEN cDNA 9230105E05 gene	ncRNA
mm_3377.1	chr1	139268286	139268289	+	1	NA	intron (NM_133239, intron 5 of 11)	intron (NM_133239, intron 5 of 11)	108789	NM_133239	170788	Mm.95700	NM_133239	ENSMUSG00000063681	Crb1	7530426H14Rik|A930008G09Rik	crumbs family member 1, photoreceptor morphogenesis associated	protein-coding
mm_7107.1	chr1	89683870	89683904	-	1	NA	promoter-TSS (NR_015540)	promoter-TSS (NR_015540)	5	NR_015540	74403	Mm.444291	NR_015540		4933400F21Rik	1700091C04Rik|4930565K10Rik	RIKEN cDNA 4933400F21 gene	ncRNA
mm_90909.1	chr10	11492110	11492126	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-117106	NM_013898	30058	Mm.214504	NM_013898	ENSMUSG00000048007	Timm8a1	DXHXS1274E|Ddp1|Fci-12|Tim8a|Timm8a	translocase of inner mitochondrial membrane 8A1	protein-coding
mm_60485.1	chr7	44478500	44478527	+	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	-6004	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_10244.1	chr2	8947012	8947020	+	1	NA	Intergenic	Intergenic	-242499	NR_038180	73438	Mm.23558	NR_038180	ENSMUSG00000085580	1700061F12Rik	-	RIKEN cDNA 1700061F12 gene	ncRNA
mm_84810.1	chr9	77347817	77347887	-	1	NA	promoter-TSS (NM_027150)	promoter-TSS (NM_027150)	18	NM_027150	69642	Mm.35008	NM_027150	ENSMUSG00000032355	Mlip	2310046A06Rik|AI931782|CIP	muscular LMNA-interacting protein	protein-coding
mm_32877.1	chr4	118620814	118620899	+	1	NA	promoter-TSS (NM_026789)	promoter-TSS (NM_026789)	57	NM_026932	69072	Mm.29906	NM_026932	ENSMUSG00000028729	Ebna1bp2	1810014B19Rik|AA537058|B830003A16Rik|C81321|Ebp2|Nobp|p40	EBNA1 binding protein 2	protein-coding
mm_17328.1	chr2	26503790	26503800	-	1	NA	promoter-TSS (NM_008714)	promoter-TSS (NM_008714)	27	NM_008714	18128	Mm.290610	NM_008714	ENSMUSG00000026923	Notch1	9930111A19Rik|Mis6|N1|Tan1|lin-12	notch 1	protein-coding
mm_81597.1	chr9	110532439	110532467	+	1	NA	promoter-TSS (NM_001081340)	promoter-TSS (NM_001081340)	-144	NM_001081340	235626	Mm.288949	NM_001081340	ENSMUSG00000044791	Setd2	4921524K10Rik|BC031601|KMT3A	SET domain containing 2	protein-coding
mm_15618.1	chr2	160888157	160888199	+	1	NA	promoter-TSS (NM_001199118)	promoter-TSS (NM_001199118)	10	NM_001199118	64899	Mm.292111	NM_022883	ENSMUSG00000027412	Lpin3	9130206L11Rik|AA438110|AV236139|mKIAA4023	lipin 3	protein-coding
mm_24199.1	chr3	88615445	88615470	+	1	NA	promoter-TSS (NM_001198911)	promoter-TSS (NM_001198911)	-750	NM_001198911	16800	Mm.239329	NM_008487	ENSMUSG00000028059	Arhgef2	AA408978|GEF|GEF-H1|GEFH1|LFP40|Lbcl1|Lfc|P40|mKIAA0651	rho/rac guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_29459.1	chr3	113574218	113574225	-	1	NA	intron (NM_001110505, intron 1 of 10)	intron (NM_001110505, intron 1 of 10)	541	NM_007446	11722	Mm.439727	NM_007446	ENSMUSG00000074264	Amy1	Amy-1|Amy1a|C030014B17Rik	amylase 1, salivary	protein-coding
mm_149154.1	chr19	9015437	9015453	+	1	NA	exon (NM_009643, exon 5 of 5)	exon (NM_009643, exon 5 of 5)	-2459	NR_105786	102465190		NR_105786	ENSMUSG00000099308	Mir6367	Gm27467|mmu-mir-6367	microRNA 6367	ncRNA
mm_171687.1	chr4	60457887	60457896	-	1	NA	Intergenic	L1Md_T|LINE|L1	-35939	NM_001281979	100038948	Mm.482231	NM_001126319	ENSMUSG00000078686	Mup9	Gm14076|Mup2|Mup6|OTTMUSG00000015595	major urinary protein 9	protein-coding
mm_156199.1	chrX	134404544	134404589	+	1	NA	promoter-TSS (NM_010078)	promoter-TSS (NM_010078)	-214	NM_010078	13497	Mm.121662	NM_010078	ENSMUSG00000000223	Drp2	AW495265|DRP-2	dystrophin related protein 2	protein-coding
mm_158971.1	chr1	107161126	107161126	-	1	NA	promoter-TSS (NM_198680)	promoter-TSS (NM_198680)	-12	NM_198680	383548	Mm.483991	NM_198680	ENSMUSG00000073602	Serpinb3b	Scca2-rs|Scca2-rs1	serine (or cysteine) peptidase inhibitor, clade B (ovalbumin), member 3B	protein-coding
mm_47820.1	chr5	134232235	134232250	-	1	NA	Intergenic	Intergenic	-2617	NR_104383	17969	Mm.425296	NM_010876	ENSMUSG00000015950	Ncf1	NCF-47K|NOXO2|Ncf-1|p47-phox|p47<phox>|p47phox	neutrophil cytosolic factor 1	protein-coding
mm_32337.1	chr4	104463984	104464013	+	1	NA	intron (NM_010014, intron 1 of 6)	intron (NM_010014, intron 1 of 6)	96460	NM_177259	13131	Mm.289682	NM_010014	ENSMUSG00000028519	Dab1	AI956902|C630028C02Rik|scm|scr|scrambler|yot	disabled 1	protein-coding
mm_24348.1	chr3	89864396	89864411	+	1	NA	Intergenic	Intergenic	33033	NM_172530	214547	Mm.225	NM_172530	ENSMUSG00000046280	She	9430022A14	src homology 2 domain-containing transforming protein E	protein-coding
mm_118974.1	chr14	28008240	28008242	+	1	NA	intron (NM_177814, intron 7 of 15)	intron (NM_177814, intron 7 of 15)	385834	NM_177814	238988	Mm.318004	NM_177814	ENSMUSG00000040640	Erc2	6430531D06|CAST|CAST1/ERC2|D14Ertd171e|ELKS2alpha	ELKS/RAB6-interacting/CAST family member 2	protein-coding
mm_115717.1	chr13	15908856	15908882	-	1	NA	Intergenic	Lx9|LINE|L1	101626	NR_046131	328190	Mm.446957	NR_046131		A530046M15Rik	A530046M15	RIKEN cDNA A530046M15 gene	ncRNA
mm_34122.1	chr4	139249599	139249640	+	1	NA	intron (NM_001037761, intron 2 of 9)	intron (NM_001037761, intron 2 of 9)	55508	NM_001271405	12345	Mm.2945	NM_009798	ENSMUSG00000028745	Capzb	1700120C01Rik|AI325129|CPB1|CPB2|CPbeat2|CPbeta1|CPbeta2|Cappb1	capping protein (actin filament) muscle Z-line, beta	protein-coding
mm_154341.1	chrM	4751	4765	+	1	NA	NA	Intergenic	NA	NA								
mm_59082.1	chr7	19678180	19678210	+	1	NA	promoter-TSS (NM_001277944)	promoter-TSS (NM_001277944)	-254	NM_001277944	11813	Mm.28394	NM_001277944	ENSMUSG00000002992	Apoc2	apo-CII|apoC-II	apolipoprotein C-II	protein-coding
mm_35851.1	chr4	48473404	48473457	-	1	NA	promoter-TSS (NM_172304)	promoter-TSS (NM_172304)	-8	NM_172304	269536	Mm.272025	NM_172304	ENSMUSG00000028345	Tex10	2610206N19Rik|2810462N03Rik|BC006867	testis expressed gene 10	protein-coding
mm_77986.1	chr9	7873173	7873186	+	1	NA	promoter-TSS (NM_007464)	promoter-TSS (NM_007464)	-9	NM_007464	11796	Mm.2026	NM_007464	ENSMUSG00000032000	Birc3	AW107670|Api1|Api2|Birc2|C-IAP2|HIAP2|IAP1|IAP2|MIAP1|MIAP2|MIHB|MIHC|RNF49|cIAP-1|cIAP-2|cIAP1|cIAP2	baculoviral IAP repeat-containing 3	protein-coding
mm_159066.1	chr2	23321246	23321246	+	1	NA	promoter-TSS (NM_008752)	promoter-TSS (NM_008752)	0	NM_008752	18232	Mm.131616	NM_008752	ENSMUSG00000069132	Nxph2	-	neurexophilin 2	protein-coding
mm_113930.1	chr13	49609128	49609170	+	1	NA	5' UTR (NM_008760, exon 2 of 7)	5' UTR (NM_008760, exon 2 of 7)	1078	NM_008760	18295	Mm.4258	NM_008760	ENSMUSG00000021390	Ogn	3110079A16Rik|OG|OIF|SLRR3A|mimecan|mimican	osteoglycin	protein-coding
mm_154031.1	chr19	53451519	53451534	-	1	NA	intron (NR_028427, intron 3 of 9)	intron (NR_028427, intron 3 of 9)	13270	NR_028427	381232	Mm.248624	NR_028427	ENSMUSG00000097636	Mirt1	4833407H14Rik|5430437C04Rik|5830416P10Rik|ENSMUSG00000074788|Gm10758	myocardial infarction associated transcript 1	ncRNA
mm_148624.1	chr19	5425238	5425248	+	1	NA	promoter-TSS (NM_024176)	promoter-TSS (NM_024176)	99	NM_001256515	107242	Mm.329658	NM_134149	ENSMUSG00000047423	AI837181	Bles03|N28173	expressed sequence AI837181	protein-coding
mm_96688.1	chr11	69589664	69589683	+	1	NA	exon (NM_011640, exon 8 of 11)	exon (NM_011640, exon 8 of 11)	9314	NM_001127233	22059	Mm.222	NM_011640	ENSMUSG00000059552	Trp53	Tp53|bbl|bfy|bhy|p44|p53	transformation related protein 53	protein-coding
mm_118110.1	chr13	103921120	103921179	-	1	NA	promoter-TSS (NM_001289475)	promoter-TSS (NM_001289475)	-563	NM_001005868	59079	Mm.277354	NM_021563	ENSMUSG00000021709	Erbin	1700028E05Rik|Erbb2ip|mKIAA1225	Erbb2 interacting protein	protein-coding
mm_31452.1	chr4	48618745	48618769	+	1	NA	intron (NM_021436, intron 5 of 9)	B1_Mur4|SINE|Alu	33564	NM_021436	230157	Mm.422686	NM_021436	ENSMUSG00000028347	Tmeff1	A830033E11|M7365|Tr1	transmembrane protein with EGF-like and two follistatin-like domains 1	protein-coding
mm_25051.1	chr3	98310025	98310046	+	1	NA	3' UTR (NM_008256, exon 10 of 10)	3' UTR (NM_008256, exon 10 of 10)	29604	NM_008256	15360	Mm.289131	NM_008256	ENSMUSG00000027875	Hmgcs2	1300002P16|mHS	3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2	protein-coding
mm_14330.1	chr2	129371936	129371946	+	1	NA	promoter-TSS (NM_008361)	promoter-TSS (NM_008361)	-802	NM_008361	16176	Mm.222830	NM_008361	ENSMUSG00000027398	Il1b	IL-1beta|Il-1b	interleukin 1 beta	protein-coding
mm_10234.1	chr2	6472068	6472076	+	1	NA	Intergenic	MLT1B|LTR|ERVL-MaLR	119336	NM_181399	98910	Mm.40673	NM_181399	ENSMUSG00000039046	Usp6nl	AI316785|RNTRE|TRE2NL|mKIAA0019	USP6 N-terminal like	protein-coding
mm_99875.1	chr11	109425581	109425600	+	1	NA	promoter-TSS (NM_025275)	promoter-TSS (NM_025275)	-356	NM_025275	13929	Mm.211850	NM_025275	ENSMUSG00000020610	Amz2	AA408420|ESTM12|X83328	archaelysin family metallopeptidase 2	protein-coding
mm_62062.1	chr7	92447719	92447731	+	1	NA	3' UTR (NM_001243047, exon 11 of 11)	3' UTR (NM_001243047, exon 11 of 11)	-113424	NM_025515	66365	Mm.21173	NM_025515	ENSMUSG00000030613	Ccdc90b	2310015N07Rik|C86558	coiled-coil domain containing 90B	protein-coding
mm_65873.1	chr7	29505915	29505917	-	1	NA	promoter-TSS (NM_001081028)	promoter-TSS (NM_001081028)	-456	NM_001081028	74206	Mm.447042	NM_001081028	ENSMUSG00000030583	Sipa1l3	2610511M17Rik	signal-induced proliferation-associated 1 like 3	protein-coding
mm_13362.1	chr2	103439391	103439393	+	1	NA	exon (NM_010125, exon 3 of 7)	exon (NM_010125, exon 3 of 7)	15324	NM_010125	13711	Mm.20888	NM_010125	ENSMUSG00000027186	Elf5	ESE-2|ESE-5|ESE-5.	E74-like factor 5	protein-coding
mm_172589.1	chr8	125521392	125521398	-	1	NA	Intergenic	ID_B1|SINE|B4	-28685	NM_001081337	244668	Mm.271668	NM_001081337	ENSMUSG00000001995	Sipa1l2	BC058408|mKIAA1389	signal-induced proliferation-associated 1 like 2	protein-coding
mm_59873.1	chr7	30280088	30280142	+	1	NA	promoter-TSS (NR_144498)	promoter-TSS (NR_144498)	21	NR_144498	108167416	Mm.471845	NR_144498		LOC108167416	-	uncharacterized LOC108167416	ncRNA
mm_88955.1	chr10	81384458	81384507	+	1	NA	promoter-TSS (NM_133964)	promoter-TSS (NM_133964)	54	NM_133964	102115	Mm.294975	NM_133964	ENSMUSG00000078440	Dohh	1110033C18Rik|AI585913|AL022869|Hlrc1	deoxyhypusine hydroxylase/monooxygenase	protein-coding
mm_105865.1	chr11	114185648	114185654	-	1	NA	Intergenic	Intergenic	-12607	NR_045930	73536	Mm.54275	NR_045930	ENSMUSG00000078600	1700092K14Rik	-	RIKEN cDNA 1700092K14 gene	ncRNA
mm_152297.1	chr19	9083746	9083750	-	1	NA	3' UTR (NM_011681, exon 3 of 3)	3' UTR (NM_011681, exon 3 of 3)	4208	NM_011681	22287	Mm.2258	NM_011681	ENSMUSG00000024653	Scgb1a1	CC10|CC16|CCSP|PCB-BP|UG|UGB|Utg	secretoglobin, family 1A, member 1 (uteroglobin)	protein-coding
mm_350.1	chr1	31222809	31222821	+	1	NA	promoter-TSS (NM_029062)	promoter-TSS (NM_029062)	-24	NM_029062	74708	Mm.246796	NM_029062	ENSMUSG00000026063	Pih1d3	4930521A18Rik	PIH1 domain containing 3	protein-coding
mm_110959.1	chr12	76795472	76795478	-	1	NA	promoter-TSS (NM_030677)	promoter-TSS (NM_030677)	79	NM_030677	14776	Mm.441856	NM_030677	ENSMUSG00000042808	Gpx2	GI-GPx|GPx-GI|GSHPx-2|GSHPx-GI	glutathione peroxidase 2	protein-coding
mm_162860.1	chr10	93124060	93124084	-	1	NA	Intergenic	Intergenic	-36804	NM_146239	237459	Mm.217404	NM_146239	ENSMUSG00000020015	Cdk17	6430598J10Rik|Pctk2	cyclin-dependent kinase 17	protein-coding
mm_66235.1	chr7	35275547	35275560	-	1	NA	TTS (NM_026181)	TTS (NM_026181)	42887	NM_026181	67471	Mm.358705	NM_026181	ENSMUSG00000063808	Gpatch1	1300003A17Rik|ECGP|Gpatc1	G patch domain containing 1	protein-coding
mm_137066.1	chr17	20277298	20277298	+	1	NA	intron (NM_001104568, intron 4 of 5)	intron (NM_001104568, intron 4 of 5)	8132	NM_001104568	224576	Mm.469854	NM_001104568	ENSMUSG00000091656	Vmn2r106	EG224576	vomeronasal 2, receptor 106	protein-coding
mm_90097.1	chr10	116964748	116964760	+	1	NA	promoter-TSS (NR_027847)	promoter-TSS (NR_027847)	14	NR_027847	103175	Mm.27138	NR_027846	ENSMUSG00000031294	D630029K05Rik	AI314111|AI875589	RIKEN cDNA D630029K05 gene	ncRNA
mm_56594.1	chr6	108532788	108532806	-	1	NA	intron (NM_010585, intron 60 of 61)	intron (NM_010585, intron 60 of 61)	43054	NR_106121	102465766		NR_106121	ENSMUSG00000105697	Mir7661	mmu-mir-7661	microRNA 7661	ncRNA
mm_40388.1	chr5	52741629	52741651	+	1	NA	promoter-TSS (NM_025951)	promoter-TSS (NM_025951)	66	NM_025951	67073	Mm.248647	NM_025951	ENSMUSG00000029186	Pi4k2b	2610042N09Rik|4933409G22Rik	phosphatidylinositol 4-kinase type 2 beta	protein-coding
mm_23460.1	chr3	60472784	60472786	+	1	NA	promoter-TSS (NM_001253713)	promoter-TSS (NM_001253713)	-45	NM_001253713	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_89805.1	chr10	103028944	103028979	+	1	NA	promoter-TSS (NM_172553)	promoter-TSS (NM_172553)	-184	NM_172553	216285	Mm.19287	NM_172553	ENSMUSG00000036602	Alx1	AI314867|C130005I02|Cart1	ALX homeobox 1	protein-coding
mm_150436.1	chr19	37550398	37550468	+	1	NA	promoter-TSS (NM_175353)	promoter-TSS (NM_175353)	15	NM_175353	107371	Mm.24865	NM_175353	ENSMUSG00000053799	Exoc6	4833405E05Rik|AW413330|C430002C19|Sec15|Sec15l1|hbd|msec15	exocyst complex component 6	protein-coding
mm_87741.1	chr10	60266881	60266883	+	1	NA	Intergenic	Intergenic	-10746	NM_001146123	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_101119.1	chr11	12025850	12025883	-	1	NA	intron (NM_010345, intron 1 of 16)	CpG	2105	NM_001177629	14783	Mm.273117	NM_010345	ENSMUSG00000020176	Grb10	5730571D09Rik|AI325020|Meg1|mKIAA0207	growth factor receptor bound protein 10	protein-coding
mm_128244.1	chr15	36608827	36608840	-	1	NA	5' UTR (NM_008774, exon 1 of 15)	5' UTR (NM_008774, exon 1 of 15)	140	NM_008774	18458	Mm.371570	NM_008774	ENSMUSG00000022283	Pabpc1	PABP|Pabp1|PabpI|Pabpl1|ePAB	poly(A) binding protein, cytoplasmic 1	protein-coding
mm_116890.1	chr13	55329724	55329776	-	1	NA	promoter-TSS (NM_016662)	promoter-TSS (NM_016662)	-20	NM_016662	17121	Mm.20350	NM_016662	ENSMUSG00000021485	Mxd3	4631412E13Rik|Mad3|bHLHc13	Max dimerization protein 3	protein-coding
mm_90555.1	chr10	128110761	128110775	+	1	NA	exon (NM_054078, exon 4 of 30)	exon (NM_054078, exon 4 of 30)	17985	NM_054078	116848	Mm.252213	NM_054078	ENSMUSG00000040054	Baz2a	AA415431|C030005G16Rik|C78388|Tip5|Walp3|mKIAA0314	bromodomain adjacent to zinc finger domain, 2A	protein-coding
mm_26954.1	chr3	20506186	20506210	-	1	NA	Intergenic	Intergenic	-139021	NM_175086	11608	Mm.134863	NM_175086	ENSMUSG00000054988	Agtr1b	AT1B|AT2R1B|Agtr-1b|Angtr-1b	angiotensin II receptor, type 1b	protein-coding
mm_164472.1	chr16	67620761	67620795	-	1	NA	5' UTR (NM_178721, exon 1 of 10)	5' UTR (NM_178721, exon 1 of 10)	130	NM_001347247	239857	Mm.394300	NM_178721	ENSMUSG00000064115	Cadm2	2900078E11Rik|9330131D06|A830029E02Rik|Igdf4d|Igsf4d|NECL3|SynCAM 2|SynCAM2	cell adhesion molecule 2	protein-coding
mm_115021.1	chr13	98692305	98692322	+	1	NA	exon (NM_001025606, exon 2 of 4)	exon (NM_001025606, exon 2 of 4)	2518	NM_001025606	380863	Mm.28264	NM_001025606	ENSMUSG00000052485	Tmem171	Gm905	transmembrane protein 171	protein-coding
mm_27170.1	chr3	33844213	33844248	-	1	NA	promoter-TSS (NM_026222)	promoter-TSS (NM_026222)	80	NM_026222	51938	Mm.275710	NM_026222	ENSMUSG00000027676	Ccdc39	4921507O14Rik|AI447426|AI844750|D3Ertd789e|b2b1304Clo|b2b1735Clo|b2b2025.1Clo	coiled-coil domain containing 39	protein-coding
mm_144860.1	chr18	36709230	36709240	+	1	NA	Intergenic	Intergenic	-13310	NM_172831	240216	Mm.252323	NM_172831	ENSMUSG00000044719	E230025N22Rik	EG240216	Riken cDNA E230025N22 gene	protein-coding
mm_33843.1	chr4	135803088	135803096	+	1	NA	intron (NM_001085509, intron 28 of 36)	intron (NM_001085509, intron 28 of 36)	43377	NM_001085509	242702	Mm.318639	NM_001085509	ENSMUSG00000037139	Myom3	8430427K15Rik|Gm434	myomesin family, member 3	protein-coding
mm_77545.1	chr8	123212743	123212779	-	1	NA	promoter-TSS (NM_145606)	promoter-TSS (NM_145606)	27	NM_145606	234852	Mm.41596	NM_145606	ENSMUSG00000000743	Chmp1a	2900018H07Rik|Pcoln3	charged multivesicular body protein 1A	protein-coding
mm_166359.1	chr5	122622415	122622423	-	1	NA	Intergenic	RMER17C|LTR|ERVK	-7901	NM_009879	12589	Mm.10125	NM_009879	ENSMUSG00000029469	Ift81	AW060663|Cdv-1|Cdv-1r|Cdv1	intraflagellar transport 81	protein-coding
mm_18794.1	chr2	73886176	73886179	-	1	NA	intron (NM_001284374, intron 1 of 11)	intron (NM_001284374, intron 1 of 11)	6462	NM_001284371	11909	Mm.209903	NM_009715	ENSMUSG00000027104	Atf2	Atf-2|CRE-BP|Creb2|D130078H02Rik|D18875|Tg(Gzma-Klra1)7Wum|mXBP	activating transcription factor 2	protein-coding
mm_164336.1	chr16	10992336	10992354	+	1	NA	intron (NM_019980, intron 1 of 3)	intron (NM_019980, intron 1 of 3)	776	NM_019980	56722	Mm.294753	NM_019980	ENSMUSG00000022500	Litaf	3222402J11Rik|C85531|N4WBP3|TBX1	LPS-induced TN factor	protein-coding
mm_85700.1	chr9	108104862	108104872	-	1	NA	exon (NM_007567, exon 8 of 12)	exon (NM_007567, exon 8 of 12)	-10387	NM_146226	235606	Mm.219639	NM_146226	ENSMUSG00000032590	Apeh	-	acylpeptide hydrolase	protein-coding
mm_75845.1	chr8	70631632	70631640	-	1	NA	5' UTR (NM_011819, exon 1 of 2)	5' UTR (NM_011819, exon 1 of 2)	459	NM_011819	23886	Mm.31325	NM_011819	ENSMUSG00000038508	Gdf15	MIC-1|NAG-1|SBF	growth differentiation factor 15	protein-coding
mm_100214.1	chr11	116918845	116918888	+	1	NA	promoter-TSS (NM_172948)	promoter-TSS (NM_172948)	3	NM_172948	268510	Mm.35141	NM_172948	ENSMUSG00000043857	Mgat5b	C330018B01|GnT-IX|mGnTVB	mannoside acetylglucosaminyltransferase 5, isoenzyme B	protein-coding
mm_109498.1	chr12	111450514	111450523	+	1	NA	intron (NM_009396, intron 8 of 11)	intron (NM_009396, intron 8 of 11)	7857	NM_009396	21928	Mm.255332	NM_009396	ENSMUSG00000021281	Tnfaip2	B94|Exoc3l3|M-sec|Tnfip2|tnfb94	tumor necrosis factor, alpha-induced protein 2	protein-coding
mm_78135.1	chr9	20888242	20888283	+	1	NA	promoter-TSS (NM_145610)	promoter-TSS (NM_145610)	87	NM_145610	235036	Mm.2930	NM_145610	ENSMUSG00000004100	Ppan	A230087P06Rik|SSF1	peter pan homolog (Drosophila)	protein-coding
mm_88027.1	chr10	67224852	67224870	+	1	NA	exon (NM_001242396, exon 9 of 25)	exon (NM_001242396, exon 9 of 25)	39111	NM_001242396	108829	Mm.23846	NM_207221	ENSMUSG00000037876	Jmjd1c	5430433L24Rik|D630035I23Rik|Jmjdic|TRIP8	jumonji domain containing 1C	protein-coding
mm_61200.1	chr7	63939320	63939345	+	1	NA	promoter-TSS (NM_021366)	promoter-TSS (NM_021366)	-417	NM_021366	50794	Mm.240473	NM_021366	ENSMUSG00000052040	Klf13	0610043C13Rik|9430029L20Rik|Bteb3|FKLF-2|FKLF2|NSLP1|RFLAT-1|RFLAT1	Kruppel-like factor 13	protein-coding
mm_168662.1	chr11	88980705	88980705	+	1	NA	intron (NM_016706, intron 1 of 6)	intron (NM_016706, intron 1 of 6)	6770	NM_016706	12812	Mm.268004	NM_016706	ENSMUSG00000033983	Coil	C79982|Cln80|p80|p80-coilin	coilin	protein-coding
mm_29817.1	chr3	129105398	129105406	-	1	NA	Intergenic	Intergenic	-94476	NM_001286942	18741	Mm.246804	NM_011098	ENSMUSG00000028023	Pitx2	9430085M16Rik|Brx1|Brx1b|Munc30|Otlx2|Ptx2|Rieg	paired-like homeodomain transcription factor 2	protein-coding
mm_128054.1	chr15	25830548	25830560	-	1	NA	Intergenic	Intergenic	-12744	NM_001034851	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_41211.1	chr5	88565010	88565058	+	1	NA	promoter-TSS (NM_001289775)	promoter-TSS (NM_001289775)	-6	NM_001289774	52822	Mm.270469	NM_027530	ENSMUSG00000029291	Rufy3	2810428M05Rik|6330416M07Rik|AW455998|AW538594|D5Bwg0860e|Ripx|Rpipx	RUN and FYVE domain containing 3	protein-coding
mm_114003.1	chr13	52588198	52588209	+	1	NA	intron (NM_001198977, intron 1 of 13)	intron (NM_001198977, intron 1 of 13)	4766	NM_001198977	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_74248.1	chr8	124831708	124831744	+	1	NA	3' UTR (NM_198632, exon 10 of 10)	3' UTR (NM_198632, exon 10 of 10)	31303	NM_025615	66523	Mm.436864	NM_025615	ENSMUSG00000031984	2810004N23Rik	3110004G14Rik|Ayu21-55|Gt(pU21)55Imeg|GtAyu21-55	RIKEN cDNA 2810004N23 gene	protein-coding
mm_121335.1	chr14	115042753	115042756	+	1	NA	promoter-TSS (NR_029785)	promoter-TSS (NR_029785)	-917	NR_029785	723905		NR_029785	ENSMUSG00000065508	Mir17	Mirn17|mir-17|mmu-mir-17	microRNA 17	ncRNA
mm_155715.1	chrX	96097823	96097826	+	1	NA	intron (NM_010833, intron 1 of 12)	B1F|SINE|Alu	1779	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_74775.1	chr8	21885427	21885443	-	1	NA	promoter-TSS (NM_139219)	promoter-TSS (NM_139219)	-1	NM_139219	246079	Mm.171224	NM_139219	ENSMUSG00000047390	Defb9	BD-9	defensin beta 9	protein-coding
mm_117797.1	chr13	97202957	97202957	-	1	NA	Intergenic	Intergenic	-4600	NM_010422	15212	Mm.27816	NM_010422	ENSMUSG00000021665	Hexb	-	hexosaminidase B	protein-coding
mm_136146.1	chr16	87495808	87495820	-	1	NA	promoter-TSS (NM_009840)	promoter-TSS (NM_009840)	55	NM_009840	12469	Mm.328673	NM_009840	ENSMUSG00000025613	Cct8	AI132397|Cctq|Tcpq	chaperonin containing Tcp1, subunit 8 (theta)	protein-coding
mm_53240.1	chr6	127457357	127457371	+	1	NA	intron (NM_001346512, intron 1 of 5)	ORR1C2-int|LTR|ERVL-MaLR	3641	NM_181402	101187	Mm.110818	NM_181402	ENSMUSG00000037997	Parp11	5330431N24Rik|AI851877|ARTD11|HIN1L|PARP-11	poly (ADP-ribose) polymerase family, member 11	protein-coding
mm_139152.1	chr17	47540278	47540288	+	1	NA	intron (NM_001081635, intron 1 of 6)	MLT1C|LTR|ERVL-MaLR	35232	NM_001081635	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_76883.1	chr8	105629128	105629130	-	1	NA	Intergenic	B1_Mm|SINE|Alu	-7409	NM_181322	13018	Mm.269474	NM_181322	ENSMUSG00000005698	Ctcf	AW108038	CCCTC-binding factor	protein-coding
mm_37092.1	chr4	116557447	116557464	-	1	NA	promoter-TSS (NM_029868)	promoter-TSS (NM_029868)	-272	NM_029868	77110	Mm.41715	NM_029868	ENSMUSG00000034042	Gpbp1l1	5330440M15Rik|BC002292	GC-rich promoter binding protein 1-like 1	protein-coding
mm_125545.1	chr15	58415522	58415534	+	1	NA	promoter-TSS (NM_145959)	promoter-TSS (NM_145959)	60	NM_145959	210998	Mm.3224	NM_145959	ENSMUSG00000037119	Fam91a1	AV220772|BC033609|D15Ertd621e|SKIN|mKIAA0493	family with sequence similarity 91, member A1	protein-coding
mm_143133.1	chr17	57217148	57217170	-	1	NA	promoter-TSS (NR_105944)	promoter-TSS (NR_105944)	69	NR_105944	102465591		NR_105944	ENSMUSG00000099066	Mir6978	Gm27858|mmu-mir-6978	microRNA 6978	ncRNA
mm_32374.1	chr4	106313319	106313329	+	1	NA	Intergenic	Intergenic	-2889	NM_183225	329908	Mm.234544	NM_183225	ENSMUSG00000028514	Usp24	2700066K03Rik|2810030C21Rik|AI414051|B130021E18|C79851	ubiquitin specific peptidase 24	protein-coding
mm_16856.1	chr2	11637253	11637285	-	1	NA	Intergenic	Intergenic	-5523	NM_008367	16184	Mm.915	NM_008367	ENSMUSG00000026770	Il2ra	CD25|Il2r|Ly-43	interleukin 2 receptor, alpha chain	protein-coding
mm_77961.1	chr9	7695262	7695274	+	1	NA	exon (NM_010810, exon 2 of 6)	exon (NM_010810, exon 2 of 6)	363	NR_126562	102722	Mm.334941	NR_126562	ENSMUSG00000086381	AV064505	-	expressed sequence AV064505	ncRNA
mm_155048.1	chrX	42151029	42151068	+	1	NA	intron (NM_021465, intron 1 of 32)	intron (NM_021465, intron 1 of 32)	347	NM_021465	20843	Mm.290422	NM_021465	ENSMUSG00000025862	Stag2	9230105L23Rik|B230112I07Rik|SA-2|SAP2	stromal antigen 2	protein-coding
mm_8801.1	chr1	161834497	161834510	-	1	NA	exon (NM_172645, exon 18 of 24)	exon (NM_172645, exon 18 of 24)	42158	NM_172645	226551	Mm.170002	NM_172645	ENSMUSG00000040297	Suco	4732491B11|AI848100|AU016931|Opt	SUN domain containing ossification factor	protein-coding
mm_70049.1	chr7	142578087	142578091	-	1	NA	promoter-TSS (NR_130974)	promoter-TSS (NR_130974)	57	NR_130974	14955	Mm.14802	NR_001592	ENSMUSG00000000031	H19	AI747191	H19, imprinted maternally expressed transcript	ncRNA
mm_171079.1	chr3	121249952	121249952	-	1	NA	intron (NM_178936, intron 1 of 7)	LSU-rRNA_Hsa|rRNA|rRNA	13364	NM_178936	99887	Mm.26088	NM_178936	ENSMUSG00000028132	Tmem56	4930577M16Rik|AU018104|AW109744|C730036B01Rik	transmembrane protein 56	protein-coding
mm_160015.1	chr6	129593734	129593734	+	1	NA	exon (NM_010654, exon 3 of 6)	exon (NM_010654, exon 3 of 6)	1923	NM_010654	16643	Mm.391515	NM_010654	ENSMUSG00000030165	Klrd1	CD94	killer cell lectin-like receptor, subfamily D, member 1	protein-coding
mm_108250.1	chr12	78226686	78226710	+	1	NA	promoter-TSS (NM_172952)	promoter-TSS (NM_172952)	43	NM_145965	268566	Mm.341742	NM_145965	ENSMUSG00000047454	Gphn	5730552E08Rik|AI662856|BC027112|C230040D23|GPH|GPHRYN|geph	gephyrin	protein-coding
mm_114147.1	chr13	55335944	55335993	+	1	NA	Intergenic	ORR1D1|LTR|ERVL-MaLR	-6238	NM_016662	17121	Mm.20350	NM_016662	ENSMUSG00000021485	Mxd3	4631412E13Rik|Mad3|bHLHc13	Max dimerization protein 3	protein-coding
mm_29407.1	chr3	108908072	108908089	-	1	NA	exon (NM_025845, exon 3 of 6)	exon (NM_025845, exon 3 of 6)	3624	NM_025845	66921	Mm.51049	NM_025845	ENSMUSG00000027881	Prpf38b	1110021E09Rik|AU018955	PRP38 pre-mRNA processing factor 38 (yeast) domain containing B	protein-coding
mm_91894.1	chr10	59951825	59951840	-	1	NA	promoter-TSS (NM_029083)	promoter-TSS (NM_029083)	-62	NM_029083	74747	Mm.21697	NM_029083	ENSMUSG00000020108	Ddit4	5830413E08Rik|AA415483|REDD1|Rtp801|dig2	DNA-damage-inducible transcript 4	protein-coding
mm_127531.1	chr15	102100395	102100423	+	1	NA	Intergenic	CpG	-2579	NM_153533	209039	Mm.29389	NM_153533	ENSMUSG00000037003	Tns2	C1-ten|Tenc1|nep|nph	tensin 2	protein-coding
mm_156583.1	chrX	152036392	152036424	+	1	NA	exon (NM_019710, exon 13 of 25)	exon (NM_019710, exon 13 of 25)	19980	NM_019710	24061	Mm.482095	NM_019710	ENSMUSG00000041133	Smc1a	5830426I24Rik|SMC-1A|Sb1.8|Smc1|Smc1alpha|Smc1l1|Smcb|mKIAA0178	structural maintenance of chromosomes 1A	protein-coding
mm_143045.1	chr17	56874396	56874398	-	1	NA	promoter-TSS (NM_001039114)	promoter-TSS (NM_001039114)	50	NM_001039114	328845	Mm.179421	NM_001039114	ENSMUSG00000024207	Acsbg2	Bgr	acyl-CoA synthetase bubblegum family member 2	protein-coding
mm_110313.1	chr12	33316645	33316655	-	1	NA	intron (NM_001033436, intron 1 of 7)	intron (NM_001033436, intron 1 of 7)	14135	NM_001033436	380753	Mm.41540	NM_028139	ENSMUSG00000020564	Atxn7l1	2810423G08Rik|Atxn7l4	ataxin 7-like 1	protein-coding
mm_111741.1	chr12	103895126	103895167	-	1	NA	exon (NM_009245, exon 5 of 5)	exon (NM_009245, exon 5 of 5)	9804	NM_009245	20702	Mm.439692	NM_009245	ENSMUSG00000079015	Serpina1c	Pi3|Pi6|Skalp|Spi1-3|Spi1-6|Wap3	serine (or cysteine) peptidase inhibitor, clade A, member 1C	protein-coding
mm_23387.1	chr3	56575691	56575701	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	-391995	NM_030595	26422	Mm.384353	NM_030595	ENSMUSG00000027799	Nbea	Lyst2|mKIAA1544	neurobeachin	protein-coding
mm_130546.1	chr15	98953663	98953676	-	1	NA	promoter-TSS (NM_011653)	promoter-TSS (NM_011653)	-168	NM_011653	22142	Mm.405359	NM_011653	ENSMUSG00000072235	Tuba1a	Tuba-1|Tuba1	tubulin, alpha 1A	protein-coding
mm_21319.1	chr2	157099187	157099208	-	1	NA	3' UTR (NM_001139520, exon 17 of 17)	3' UTR (NM_001139520, exon 17 of 17)	12142	NM_001177439	383766	Mm.480305	NM_001177439	ENSMUSG00000074628	Tldc2	Gm1332	TBC/LysM associated domain containing 2	protein-coding
mm_135423.1	chr16	45224820	45224831	-	1	NA	intron (NM_177584, intron 1 of 5)	intron (NM_177584, intron 1 of 5)	488	NM_177584	208154	Mm.38199	NM_177584	ENSMUSG00000052013	Btla	A630002H24	B and T lymphocyte associated	protein-coding
mm_900.1	chr1	53750130	53750153	+	1	NA	Intergenic	MMERVK9C_I-int|LTR|ERVK	35074	NM_133810	98267	Mm.25559	NM_133810	ENSMUSG00000026094	Stk17b	3110009A03Rik|AI120141|Drak2	serine/threonine kinase 17b (apoptosis-inducing)	protein-coding
mm_34374.1	chr4	144893620	144893646	+	1	NA	exon (NM_001172424, exon 2 of 7)	exon (NM_001172424, exon 2 of 7)	496	NM_011303	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding
mm_132768.1	chr16	44765754	44765828	+	1	NA	promoter-TSS (NM_021325)	promoter-TSS (NM_021325)	55	NM_021325	57781	Mm.416152	NM_021325	ENSMUSG00000022667	Cd200r1	CD200R|Mox2r|OX2R	CD200 receptor 1	protein-coding
mm_41695.1	chr5	100798736	100798770	+	1	NA	promoter-TSS (NM_026826)	promoter-TSS (NM_026826)	-6	NM_026826	68735	Mm.25585	NM_026826	ENSMUSG00000016833	Mrps18c	1110037D14Rik	mitochondrial ribosomal protein S18C	protein-coding
mm_73927.1	chr8	119840726	119840749	+	1	NA	promoter-TSS (NM_028071)	promoter-TSS (NM_028071)	-158	NM_028071	72042	Mm.393405	NM_028071	ENSMUSG00000031827	Cotl1	1810074P22Rik|2010004C08Rik|Clp	coactosin-like 1 (Dictyostelium)	protein-coding
mm_54532.1	chr6	36715502	36715520	-	1	NA	TTS (NM_008973)	TTS (NM_008973)	95850	NM_008973	19242	Mm.279690	NM_008973	ENSMUSG00000029838	Ptn	HARP|HB-GAM|HBBN|HBGF-8|HBNF|OSF|Osf-1|Osf1	pleiotrophin	protein-coding
mm_20695.1	chr2	132793530	132793540	-	1	NA	exon (NM_007694, exon 4 of 5)	exon (NM_007694, exon 4 of 5)	12257	NM_007694	12653	Mm.255241	NM_007694	ENSMUSG00000027350	Chgb	Scg-1	chromogranin B	protein-coding
mm_45498.1	chr5	72168143	72168199	-	1	NA	promoter-TSS (NM_178599)	promoter-TSS (NM_178599)	12	NM_178599	27784	Mm.44223	NM_178599	ENSMUSG00000029213	Commd8	C77770|D5Buc26e	COMM domain containing 8	protein-coding
mm_145175.1	chr18	46959608	46959613	+	1	NA	intron (NM_178377, intron 1 of 6)	intron (NM_178377, intron 1 of 6)	734	NM_178377	69456	Mm.210734	NM_178377	ENSMUSG00000042705	Commd10	2310003A05Rik|AU019438|DRWMS2	COMM domain containing 10	protein-coding
mm_146753.1	chr18	16766283	16766285	-	1	NA	intron (NM_007664, intron 2 of 15)	intron (NM_007664, intron 2 of 15)	42962	NM_007664	12558	Mm.257437	NM_007664	ENSMUSG00000024304	Cdh2	CDHN|N-CAD|Ncad	cadherin 2	protein-coding
mm_36126.1	chr4	58987069	58987086	-	1	NA	promoter-TSS (NM_025968)	promoter-TSS (NM_025968)	1	NM_025968	67103	Mm.34497	NM_025968	ENSMUSG00000028378	Ptgr1	2510002C21Rik|Ltb4dh|Zadh3	prostaglandin reductase 1	protein-coding
mm_90105.1	chr10	117045347	117045363	+	1	NA	promoter-TSS (NM_146242)	promoter-TSS (NM_146242)	14	NM_146242	237560	Mm.37320	NM_146242	ENSMUSG00000060187	Lrrc10	D330003I11Rik|Hrlrrp|Serdin1	leucine rich repeat containing 10	protein-coding
mm_127528.1	chr15	102095307	102095321	+	1	NA	exon (NM_145625, exon 15 of 15)	exon (NM_145625, exon 15 of 15)	-7674	NM_153533	209039	Mm.29389	NM_153533	ENSMUSG00000037003	Tns2	C1-ten|Tenc1|nep|nph	tensin 2	protein-coding
mm_35566.1	chr4	41640243	41640273	-	1	NA	promoter-TSS (NM_027147)	promoter-TSS (NM_027147)	44	NM_027147	69638	Mm.372459	NM_027147	ENSMUSG00000028445	Enho	1110065P19Rik|2310040A07Rik	energy homeostasis associated	protein-coding
mm_78096.1	chr9	18478364	18478377	+	1	NA	promoter-TSS (NM_028557)	promoter-TSS (NM_028557)	-25	NM_028557	73503	Mm.160088	NM_028557	ENSMUSG00000038691	Mbd3l1	1700070G05Rik|1700095H13Rik|Mbd3l	methyl-CpG binding domain protein 3-like 1	protein-coding
mm_70280.1	chr8	3603365	3603406	+	1	NA	intron (NM_001347112, intron 10 of 17)	intron (NM_001347112, intron 10 of 17)	15935	NM_001347111	69697	Mm.390010	NM_027171	ENSMUSG00000044433	Camsap3	2310057J16Rik|Kiaa1543|Nezha	calmodulin regulated spectrin-associated protein family, member 3	protein-coding
mm_70661.1	chr8	14881569	14881575	+	1	NA	Intergenic	Intergenic	-6964	NM_012000	26889	Mm.254027	NM_012000	ENSMUSG00000026317	Cln8	mnd	ceroid-lipofuscinosis, neuronal 8	protein-coding
mm_132050.1	chr16	29210157	29210202	+	1	NA	intron (NM_013751, intron 1 of 3)	CpG	484	NM_013751	27281	Mm.103650	NM_013751	ENSMUSG00000022525	Hrasls	2810012B06Rik|A-C1|HRSL1|Hrasrs	HRAS-like suppressor	protein-coding
mm_29107.1	chr3	104818540	104818572	-	1	NA	promoter-TSS (NM_008619)	promoter-TSS (NM_008619)	7	NM_001163440	17454	Mm.1597	NM_008619	ENSMUSG00000002227	Mov10	C77703|Mov-10	Moloney leukemia virus 10	protein-coding
mm_147497.1	chr18	47415381	47415388	-	1	NA	Intergenic	Intergenic	-37284	NR_033453	77668	Mm.98433	NR_033453		9130209A04Rik	-	RIKEN cDNA 9130209A04 gene	ncRNA
mm_93852.1	chr10	122047294	122047322	-	1	NA	promoter-TSS (NM_001081037)	promoter-TSS (NM_001081037)	7	NM_001242411	117600	Mm.288698	NM_001081037	ENSMUSG00000020121	Srgap1	4930572H05Rik|Arhgap13	SLIT-ROBO Rho GTPase activating protein 1	protein-coding
mm_128507.1	chr15	53258159	53258161	-	1	NA	intron (NM_010162, intron 1 of 10)	intron (NM_010162, intron 1 of 10)	88023	NM_010162	14042	Mm.309395	NM_010162	ENSMUSG00000061731	Ext1	AA409028	exostoses (multiple) 1	protein-coding
mm_38961.1	chr4	150781419	150781422	-	1	NA	Intergenic	Intergenic	73529	NR_040649	73348	Mm.396218	NR_040649	ENSMUSG00000078492	1700045H11Rik	-	RIKEN cDNA 1700045H11 gene	ncRNA
mm_15461.1	chr2	157447708	157447738	+	1	NA	intron (NM_009271, intron 2 of 14)	intron (NM_009271, intron 2 of 14)	23430	NM_001025395	20779	Mm.22845	NM_009271	ENSMUSG00000027646	Src	AW259666|pp60c-src	Rous sarcoma oncogene	protein-coding
mm_91625.1	chr10	41754915	41754922	-	1	NA	intron (NM_001243074, intron 2 of 10)	intron (NM_001243074, intron 2 of 10)	54745	NM_001243075	103268	Mm.338605	NM_026643	ENSMUSG00000019813	Cep57l1	2410017P07Rik|4930484D11Rik|AI607327|cep57R	centrosomal protein 57-like 1	protein-coding
mm_70993.1	chr8	27447691	27447701	+	1	NA	promoter-TSS (NM_027618)	promoter-TSS (NM_027618)	26	NM_027618	70952	Mm.158160	NM_026256	ENSMUSG00000063932	Poteg	4921537P18Rik|4930456F22Rik|Gsarp1|Gsarp2	POTE ankyrin domain family, member G	protein-coding
mm_167151.1	chr7	131322351	131322359	-	1	NA	promoter-TSS (NM_008411)	promoter-TSS (NM_008411)	-63	NM_008411	16433	Mm.142717	NM_008411	ENSMUSG00000040205	Cuzd1	Erg-1|Itmap1|Uo-44|Usg|Utczp	CUB and zona pellucida-like domains 1	protein-coding
mm_36797.1	chr4	103120171	103120177	-	1	NA	intron (NM_001039081, intron 1 of 12)	ID4|SINE|ID	784	NM_001039081	71148	Mm.288721	NM_027696	ENSMUSG00000028522	Mier1	4933425I22Rik|5830411K19Rik|er1	MEIR1 treanscription regulator	protein-coding
mm_169025.1	chr13	113723786	113723808	+	1	NA	Intergenic	ERVB7_1-LTR_MM|LTR|ERVK	-60121	NM_019960	56534	Mm.41410	NM_019960	ENSMUSG00000051456	Hspb3	2310035K17Rik|AI844863|Hsbp3|spb3	heat shock protein 3	protein-coding
mm_85519.1	chr9	106447549	106447582	-	1	NA	5' UTR (NM_145919, exon 1 of 7)	5' UTR (NM_145919, exon 1 of 7)	113	NM_145919	68644	Mm.268925	NM_145919	ENSMUSG00000042210	Abhd14a	1110013B16Rik|AW558221|Dorz1	abhydrolase domain containing 14A	protein-coding
mm_23700.1	chr3	68698020	68698036	+	1	NA	exon (NM_008351, exon 7 of 7)	exon (NM_008351, exon 7 of 7)	6604	NM_008351	16159	Mm.103783	NM_008351	ENSMUSG00000027776	Il12a	IL-12p35|Il-12a|Ll12a|p35	interleukin 12a	protein-coding
mm_155731.1	chrX	96165369	96165405	+	1	NA	exon (NM_010833, exon 11 of 13)	exon (NM_010833, exon 11 of 13)	69342	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_24454.1	chr3	90613283	90613292	+	1	NA	intron (NM_011313, intron 1 of 2)	intron (NM_011313, intron 1 of 2)	393	NM_011313	20200	Mm.100144	NM_011313	ENSMUSG00000001025	S100a6	2A9|5B10|CALCYCLIN|Cacy|PRA	S100 calcium binding protein A6 (calcyclin)	protein-coding
mm_76564.1	chr8	88636060	88636116	-	1	NA	promoter-TSS (NM_027840)	promoter-TSS (NM_027840)	40	NM_027840	71607	Mm.270607	NM_027840	ENSMUSG00000031662	Snx20	9130017C17Rik	sorting nexin 20	protein-coding
mm_109619.1	chr12	112763999	112764050	+	1	NA	exon (NM_178911, exon 4 of 11)	exon (NM_178911, exon 4 of 11)	3369	NM_178911	104759	Mm.203915	NM_178911	ENSMUSG00000052160	Pld4	AI132321|thss	phospholipase D family, member 4	protein-coding
mm_98223.1	chr11	88049542	88049604	+	1	NA	exon (NM_173374, exon 4 of 4)	exon (NM_173374, exon 4 of 4)	2200	NM_173374	110809	Mm.391719	NM_173374	ENSMUSG00000018379	Srsf1	1110054N12Rik|5730507C05Rik|6330415C05Rik|AI482334|AW491331|Asf|Sf2|Sfrs1	serine/arginine-rich splicing factor 1	protein-coding
mm_25588.1	chr3	116886172	116886183	+	1	NA	intron (NM_009146, intron 7 of 16)	PB1D10|SINE|Alu	24497	NM_009146	20321	Mm.66293	NM_009146	ENSMUSG00000033386	Frrs1	AI131732|Sdfr2	ferric-chelate reductase 1	protein-coding
mm_67987.1	chr7	100855892	100855903	-	1	NA	intron (NM_177073, intron 1 of 10)	intron (NM_177073, intron 1 of 10)	7516	NM_177073	320100	Mm.40336	NM_177073	ENSMUSG00000008318	Relt	E430021K24Rik|Tnfrsf19l	RELT tumor necrosis factor receptor	protein-coding
mm_67749.1	chr7	92258693	92258701	-	1	NA	intron (NM_001243047, intron 1 of 10)	intron (NM_001243047, intron 1 of 10)	23727	NM_001243047	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_47266.1	chr5	121837603	121837606	-	1	NA	promoter-TSS (NM_001306128)	promoter-TSS (NM_001306128)	-745	NM_008507	16923	Mm.65493	NM_008507	ENSMUSG00000042594	Sh2b3	AI429800|Lnk	SH2B adaptor protein 3	protein-coding
mm_69743.1	chr7	140954943	140954976	-	1	NA	3' UTR (NM_030694, exon 2 of 2)	3' UTR (NM_030694, exon 2 of 2)	1002	NM_030694	80876	Mm.379266	NM_030694	ENSMUSG00000060591	Ifitm2	DSPA2c|Ifitm3l|fragilis3|mil-3	interferon induced transmembrane protein 2	protein-coding
mm_102869.1	chr11	69407638	69407649	-	1	NA	exon (NM_001017426, exon 6 of 23)	exon (NM_001017426, exon 6 of 23)	6032	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_167199.1	chr7	143068948	143068955	-	1	NA	promoter-TSS (NM_020285)	promoter-TSS (NM_020285)	-417	NM_020285	56844	Mm.139675	NM_020285	ENSMUSG00000045752	Tssc4	AA241958|ESTM671070	tumor-suppressing subchromosomal transferable fragment 4	protein-coding
mm_110376.1	chr12	40203438	40203456	-	1	NA	exon (NM_013562, exon 12 of 12)	exon (NM_013562, exon 12 of 12)	-4132	NM_001033437	380755	Mm.390463	NM_001033437	ENSMUSG00000071342	Lsmem1	Gm889	leucine-rich single-pass membrane protein 1	protein-coding
mm_84837.1	chr9	78368153	78368164	-	1	NA	promoter-TSS (NM_025274)	promoter-TSS (NM_025274)	41	NM_025274	434423	Mm.139314	NM_025274	ENSMUSG00000060461	Dppa5a	AA536857|Dppa5|Esg1|ecat2	developmental pluripotency associated 5A	protein-coding
mm_92969.1	chr10	86123247	86123280	-	1	NA	intron (NM_013722, intron 7 of 13)	intron (NM_013722, intron 7 of 13)	27409	NR_038024	78170	Mm.444790	NR_038024		4930486F22Rik	-	RIKEN cDNA 4930486F22 gene	ncRNA
mm_143637.1	chr17	79020703	79020710	-	1	NA	5' UTR (NM_029239, exon 1 of 19)	5' UTR (NM_029239, exon 1 of 19)	110	NM_001171004	75292	Mm.252776	NM_029239	ENSMUSG00000024070	Prkd3	4930557O20Rik|5730497N19Rik|PKD3|Pkcnu|Prkcn	protein kinase D3	protein-coding
mm_112552.1	chr13	12468721	12468737	+	1	NA	Intergenic	Intergenic	-6991	NM_001291057	56048	Mm.474138	NM_018886	ENSMUSG00000057554	Lgals8	1200015E08Rik|AI326142|D13Ertd524e|Lgals-8	lectin, galactose binding, soluble 8	protein-coding
mm_86242.1	chr9	121277161	121277217	-	1	NA	promoter-TSS (NM_177589)	promoter-TSS (NM_177589)	-17	NM_177589	209012	Mm.371804	NM_177589	ENSMUSG00000040936	Ulk4	4932415A06Rik|A730098P15	unc-51-like kinase 4	protein-coding
mm_64066.1	chr7	140881899	140881910	+	1	NA	promoter-TSS (NM_001127351)	promoter-TSS (NM_001127351)	-35	NM_001177804	64384	Mm.29760	NM_022433	ENSMUSG00000025486	Sirt3	2310003L23Rik|AI848213|Sir2l3	sirtuin 3	protein-coding
mm_43602.1	chr5	137857219	137857240	+	1	NA	exon (NM_133209, exon 2 of 5)	exon (NM_133209, exon 2 of 5)	820	NM_133209	170741	Mm.347593	NM_133209	ENSMUSG00000066684	Pilrb1	FDFACT|Fdact|Pilrb	paired immunoglobin-like type 2 receptor beta 1	protein-coding
mm_72461.1	chr8	83251309	83251324	+	1	NA	intron (NM_027758, intron 7 of 17)	intron (NM_027758, intron 7 of 17)	-39032	NM_009463	22227	Mm.4177	NM_009463	ENSMUSG00000031710	Ucp1	AI385626|Slc25a7|Ucp	uncoupling protein 1 (mitochondrial, proton carrier)	protein-coding
mm_100811.1	chr11	5099054	5099081	-	1	NA	promoter-TSS (NM_177370)	promoter-TSS (NM_177370)	21	NM_001283062	14030	Mm.142822	NM_007968	ENSMUSG00000009079	Ewsr1	Ews|Ewsh	Ewing sarcoma breakpoint region 1	protein-coding
mm_148566.1	chr19	4756832	4756869	+	1	NA	intron (NM_025717, intron 1 of 3)	intron (NM_025717, intron 1 of 3)	325	NM_025717	66704	Mm.396734	NM_025717	ENSMUSG00000033760	Rbm4b	4921506I22Rik|AI504630|AI506404|Lark2|Neosin	RNA binding motif protein 4B	protein-coding
mm_3230.1	chr1	135849457	135849466	+	1	NA	intron (NM_001130174, intron 10 of 13)	intron (NM_001130174, intron 10 of 13)	8600	NM_001130176	21956	Mm.247470	NM_011619	ENSMUSG00000026414	Tnnt2	Tnt|cTnT	troponin T2, cardiac	protein-coding
mm_106536.1	chr11	120578705	120578715	-	1	NA	3' UTR (NM_133796, exon 6 of 6)	3' UTR (NM_133796, exon 6 of 6)	2910	NM_133796	192662	Mm.30016	NM_133796	ENSMUSG00000025132	Arhgdia	5330430M07Rik|Gdi-1|Rho-GDI|RhoDGI|RhoGDI-1	Rho GDP dissociation inhibitor (GDI) alpha	protein-coding
mm_62362.1	chr7	100537171	100537179	+	1	NA	promoter-TSS (NM_183270)	promoter-TSS (NM_183270)	75	NM_183270	68185	Mm.228995	NM_183270	ENSMUSG00000044881	Coa4	5330414O08Rik|AI115477|AW047259|Chchd8|E2ig2	cytochrome c oxidase assembly factor 4	protein-coding
mm_55424.1	chr6	65144706	65144765	-	1	NA	promoter-TSS (NM_019455)	promoter-TSS (NM_019455)	-5	NM_019455	54486	Mm.410688	NM_019455	ENSMUSG00000029919	Hpgds	H-PGDS|Ptgds2	hematopoietic prostaglandin D synthase	protein-coding
mm_129851.1	chr15	83172167	83172207	-	1	NA	promoter-TSS (NM_029787)	promoter-TSS (NM_029787)	21	NM_029787	109754	Mm.22560	NM_029787	ENSMUSG00000018042	Cyb5r3	0610016L08Rik|2500002N19Rik|C85115|Dia-1|Dia1|WU:AL591952.1-001|WU:AL591952.1-002|WU:AL591952.1-003|WU:Cyb5r3	cytochrome b5 reductase 3	protein-coding
mm_169804.1	chr16	18360769	18360769	+	1	NA	intron (NM_033474, intron 2 of 18)	intron (NM_033474, intron 2 of 18)	12587	NM_001272029	11877	Mm.293599	NM_033474	ENSMUSG00000000325	Arvcf	-	armadillo repeat gene deleted in velo-cardio-facial syndrome	protein-coding
mm_43688.1	chr5	138995039	138995066	+	1	NA	promoter-TSS (NM_008808)	promoter-TSS (NM_008808)	-99	NM_008808	18590	Mm.2675	NM_008808	ENSMUSG00000025856	Pdgfa	-	platelet derived growth factor, alpha	protein-coding
mm_165263.1	chr2	73660421	73660425	-	1	NA	promoter-TSS (NM_175752)	promoter-TSS (NM_175752)	0	NM_175752	108699	Mm.257073	NM_029716	ENSMUSG00000056486	Chn1	0610007I19Rik|0710001E19Rik|1700112L09Rik|2900046J01Rik|AI413815|ARHGAP2	chimerin 1	protein-coding
mm_17946.1	chr2	36136554	36136560	-	1	NA	non-coding (NR_027515, exon 1 of 6)	non-coding (NR_027515, exon 1 of 6)	147	NM_026434	67889	Mm.205937	NM_026434	ENSMUSG00000026889	Rbm18	2010004P11Rik|AU015530	RNA binding motif protein 18	protein-coding
mm_69799.1	chr7	141172789	141172803	-	1	NA	promoter-TSS (NM_001172100)	promoter-TSS (NM_001172100)	55	NM_001172100	107702	Mm.197493	NM_145135	ENSMUSG00000038650	Rnh1	AW546468|C80305|RNH	ribonuclease/angiogenin inhibitor 1	protein-coding
mm_169246.1	chr13	74864814	74864832	+	1	NA	Intergenic	Intergenic	-56063	NM_001301153	12380	Mm.29163	NM_009817	ENSMUSG00000021585	Cast	-	calpastatin	protein-coding
mm_136654.1	chr17	5975748	5975759	+	1	NA	5' UTR (NM_001113351, exon 1 of 25)	5' UTR (NM_001113351, exon 1 of 25)	167	NM_011523	20975	Mm.236068	NM_011523	ENSMUSG00000023805	Synj2	AI481647|SJ2|mKIAA0348	synaptojanin 2	protein-coding
mm_123949.1	chr14	73385226	73385311	-	1	NA	promoter-TSS (NM_008410)	promoter-TSS (NM_008410)	3	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_50054.1	chr6	41178321	41178335	+	1	NA	Intergenic	Intergenic	-123944	NM_011646	22074	Mm.383263	NM_011646	ENSMUSG00000054106	Try4	0910001B19Rik|Td	trypsin 4	protein-coding
mm_161827.1	chr17	79614763	79614763	+	1	NA	promoter-TSS (NM_201361)	promoter-TSS (NM_201361)	-137	NM_201361	381110	Mm.209801	NM_201361	ENSMUSG00000036368	Rmdn2	AW061290|Fam82a1|RMD-2|mRMD-2	regulator of microtubule dynamics 2	protein-coding
mm_75681.1	chr8	68062247	68062344	-	1	NA	Intergenic	CpG	-87721	NM_177698	234353	Mm.32525	NM_027626	ENSMUSG00000030465	Psd3	4931420C21Rik|AI661273|BC003498|D430018P08|EFA6D	pleckstrin and Sec7 domain containing 3	protein-coding
mm_142677.1	chr17	47732447	47732460	-	1	NA	exon (NM_025973, exon 6 of 9)	exon (NM_025973, exon 6 of 9)	-4584	NM_001161722	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_81866.1	chr9	118959739	118959742	+	1	NA	intron (NM_133710, intron 1 of 7)	intron (NM_133710, intron 1 of 7)	33204	NM_133710	69274	Mm.439928	NM_133710	ENSMUSG00000047409	Ctdspl	2810418J22Rik|AI426263|HYA22|SCP3	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase-like	protein-coding
mm_96729.1	chr11	69684552	69684562	+	1	NA	intron (NM_001034097, intron 9 of 12)	intron (NM_001034097, intron 9 of 12)	997	NM_001159505	69583	Mm.8983	NM_023517	ENSMUSG00000089669	Tnfsf13	2310026N09Rik|April|Tall2|Tnlg7b|Trdl1	tumor necrosis factor (ligand) superfamily, member 13	protein-coding
mm_78990.1	chr9	45402616	45402626	+	1	NA	promoter-TSS (NM_052823)	promoter-TSS (NM_052823)	-517	NM_052823	11936	Mm.22742	NM_007503	ENSMUSG00000059412	Fxyd2	Atp1g1	FXYD domain-containing ion transport regulator 2	protein-coding
mm_34154.1	chr4	139390832	139390850	+	1	NA	exon (NM_001160319, exon 3 of 106)	exon (NM_001160319, exon 3 of 106)	10182	NM_001160319	69116	Mm.271956	NM_001160319	ENSMUSG00000066036	Ubr4	1810009A16Rik|A930005E13Rik|D930005K06Rik|Gm1032|Gm1666|N28143|RBAF600|Zubr1|mKIAA0462|p600	ubiquitin protein ligase E3 component n-recognin 4	protein-coding
mm_22888.1	chr3	30647959	30647977	+	1	NA	promoter-TSS (NM_001290510)	promoter-TSS (NM_001290510)	82	NM_001290510	68307	Mm.389425	NM_026668	ENSMUSG00000027703	Lrriq4	4930558O21Rik	leucine-rich repeats and IQ motif containing 4	protein-coding
mm_8891.1	chr1	162898331	162898342	-	1	NA	intron (NM_018881, intron 1 of 8)	intron (NM_018881, intron 1 of 8)	376	NM_018881	55990	Mm.10929	NM_018881	ENSMUSG00000040170	Fmo2	2310008D08Rik|2310042I22Rik|AW107733	flavin containing monooxygenase 2	protein-coding
mm_4490.1	chr1	173633677	173633683	+	1	NA	intron (NM_175026, intron 1 of 6)	Lx7|LINE|L1	2821	NM_175026	236312	Mm.447	NM_175026	ENSMUSG00000043263	Ifi209	4930422C14|AI447904|Ifix|Pyhin-1|Pyhin1	interferon activated gene 209	protein-coding
mm_60844.1	chr7	45785332	45785390	+	1	NA	promoter-TSS (NM_001290990)	promoter-TSS (NM_001290990)	-19	NM_001290990	381983	Mm.44928	NM_001005511	ENSMUSG00000062044	Lmtk3	BC059845|aatyk3	lemur tyrosine kinase 3	protein-coding
mm_46641.1	chr5	108548602	108548610	-	1	NA	5' UTR (NM_007756, exon 2 of 4)	5' UTR (NM_007756, exon 2 of 4)	1421	NM_007756	12889	Mm.5195	NM_007756	ENSMUSG00000033615	Cplx1	921-S	complexin 1	protein-coding
mm_159402.1	chr3	98510045	98510045	-	1	NA	intron (NM_008294, intron 1 of 3)	intron (NM_008294, intron 1 of 3)	427	NM_001111336	15495	Mm.14309	NM_008294	ENSMUSG00000095143	Hsd3b4	-	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 4	protein-coding
mm_5966.1	chr1	56978513	56978524	-	1	NA	Intergenic	Intergenic	7049	NR_024325	329160	Mm.419039	NR_024325	ENSMUSG00000087022	9130024F11Rik	B530002L08|EG329160	RIKEN cDNA 9130024F11 gene	ncRNA
mm_108057.1	chr12	73927364	73927375	+	1	NA	intron (NM_001313920, intron 2 of 14)	intron (NM_001313920, intron 2 of 14)	19502	NM_001313919	15251	Mm.3879	NM_010431	ENSMUSG00000021109	Hif1a	AA959795|HIF-1-alpha|HIF1-alpha|HIF1alpha|MOP1|bHLHe78	hypoxia inducible factor 1, alpha subunit	protein-coding
mm_154563.1	chrX	6400077	6400109	+	1	NA	promoter-TSS (NM_001040459)	promoter-TSS (NM_001040459)	61	NM_001040459	208431	Mm.23208	NM_001040459	ENSMUSG00000068270	Shroom4	D430043L16Rik|Gm724|Shrm4	shroom family member 4	protein-coding
mm_155600.1	chrX	82814887	82814920	+	1	NA	Intergenic	Intergenic	-133967	NM_007868	13405	Mm.275608	NM_007868	ENSMUSG00000045103	Dmd	DXSmh7|DXSmh9|Dp427|Dp71|dys|mdx|pke	dystrophin, muscular dystrophy	protein-coding
mm_159804.1	chr5	114131781	114131781	+	1	NA	intron (NM_001040691, intron 2 of 6)	intron (NM_001040691, intron 2 of 6)	625	NM_011677	22256	Mm.1393	NM_011677	ENSMUSG00000029591	Ung	UNG1|UNG2	uracil DNA glycosylase	protein-coding
mm_45886.1	chr5	88526497	88526506	-	1	NA	intron (NM_152839, intron 1 of 3)	ID_B1|SINE|B4	1396	NM_152839	16069	Mm.1192	NM_152839	ENSMUSG00000067149	Jchain	9530090F24Rik|AI323815|Igj|Jch	immunoglobulin joining chain	protein-coding
mm_120839.1	chr14	75180226	75180229	+	1	NA	intron (NM_008879, intron 2 of 16)	intron (NM_008879, intron 2 of 16)	43802	NM_008879	18826	Mm.153911	NM_008879	ENSMUSG00000021998	Lcp1	AW536232|D14Ertd310e|LCP-1|Pls2|pp65	lymphocyte cytosolic protein 1	protein-coding
mm_139380.1	chr17	51859597	51859597	+	1	NA	Intergenic	Intergenic	-23130	NR_045095	100504169	Mm.417731	NR_045095		Gm20098	-	predicted gene, 20098	ncRNA
mm_146492.1	chr18	90579772	90579845	+	1	NA	Intergenic	Intergenic	69654	NM_198295	67988	Mm.268041	NM_198295	ENSMUSG00000024614	Tmx3	6430411B10Rik|A730024F05Rik|AV259382|Txndc10|mKIAA1830	thioredoxin-related transmembrane protein 3	protein-coding
mm_25948.1	chr3	131564888	131564910	+	1	NA	5' UTR (NM_001289478, exon 1 of 13)	5' UTR (NM_001289478, exon 1 of 13)	131	NM_011863	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_59435.1	chr7	27131201	27131211	+	1	NA	exon (NM_007817, exon 8 of 10)	exon (NM_007817, exon 8 of 10)	11251	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_55276.1	chr6	54158600	54158615	-	1	NA	intron (NM_001163640, intron 1 of 12)	intron (NM_001163640, intron 1 of 12)	-106251	NM_001311133	69993	Mm.321147	NM_023543	ENSMUSG00000004633	Chn2	1700026N20Rik|4930557O16Rik|ARHGAP3|Bch	chimerin 2	protein-coding
mm_79865.1	chr9	65077883	65077887	+	1	NA	intron (NM_028906, intron 18 of 20)	intron (NM_028906, intron 18 of 20)	-23601	NM_001290315	56741	Mm.209041	NM_020043	ENSMUSG00000032816	Igdcc4	DDM36|Nope	immunoglobulin superfamily, DCC subclass, member 4	protein-coding
mm_40769.1	chr5	67054766	67054775	+	1	NA	3' UTR (NM_001001980, exon 26 of 26)	3' UTR (NM_001001980, exon 26 of 26)	44356	NM_008888	18935	Mm.62505	NM_008888	ENSMUSG00000012520	Phox2b	Dilp1|NBPhox|Pmx2b|Px2b	paired-like homeobox 2b	protein-coding
mm_158991.1	chr1	134332859	134332859	-	1	NA	promoter-TSS (NM_001144855)	promoter-TSS (NM_001144855)	69	NM_001144855	68507	Mm.295105	NM_001144855	ENSMUSG00000026458	Ppfia4	100042382|1110008G13Rik|AI448359|AI852265|C81506|Gm3812	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 4	protein-coding
mm_5032.1	chr1	193302000	193302029	+	1	NA	promoter-TSS (NM_001277928)	promoter-TSS (NM_001277928)	20	NM_008484	16780	Mm.435441	NM_008484	ENSMUSG00000026639	Lamb3	-	laminin, beta 3	protein-coding
mm_70796.1	chr8	22757727	22757729	+	1	NA	promoter-TSS (NM_008872)	promoter-TSS (NM_008872)	6	NM_008872	18791	Mm.154660	NM_008872	ENSMUSG00000031538	Plat	AU020998|AW212668|D8Ertd2e|tPA	plasminogen activator, tissue	protein-coding
mm_138658.1	chr17	35868518	35868521	+	1	NA	exon (NM_001146711, exon 2 of 4)	exon (NM_001146711, exon 2 of 4)	1904	NM_175242	76448	Mm.359982	NM_175242	ENSMUSG00000034595	Ppp1r18	2310014H01Rik|AA407849|AI450394	protein phosphatase 1, regulatory subunit 18	protein-coding
mm_120388.1	chr14	64590405	64590426	+	1	NA	promoter-TSS (NR_029813)	promoter-TSS (NR_029813)	-242	NR_029813	387233		NR_029813	ENSMUSG00000065597	Mir124a-1	Mirn124a|Mirn124a-1	microRNA 124a-1	ncRNA
mm_63805.1	chr7	133309754	133309755	+	1	NA	Intergenic	L1M4|LINE|L1	181503	NR_046279	74970	Mm.491044	NR_046279	ENSMUSG00000109816	4930483O08Rik	-	RIKEN cDNA 4930483O08 gene	ncRNA
mm_150220.1	chr19	33961158	33961162	+	1	NA	promoter-TSS (NM_026334)	promoter-TSS (NM_026334)	-88	NM_026334	67717	Mm.329816	NM_026334	ENSMUSG00000024768	Lipf	2310051B21Rik|AV082900	lipase, gastric	protein-coding
mm_165139.1	chr2	11522027	11522048	+	1	NA	intron (NM_001177758, intron 1 of 14)	intron (NM_001177758, intron 1 of 14)	-19947	NM_001177757	170768	Mm.19669	NM_133232	ENSMUSG00000026773	Pfkfb3	E330010H22Rik|iPFK-2|uPFK-2	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	protein-coding
mm_99135.1	chr11	100320038	100320057	+	1	NA	promoter-TSS (NM_011508)	promoter-TSS (NM_011508)	98	NM_011508	20918	Mm.13886	NM_011508	ENSMUSG00000035530	Eif1	Sui1-rs1	eukaryotic translation initiation factor 1	protein-coding
mm_428.1	chr1	34472782	34472792	+	1	NA	exon (NM_011206, exon 13 of 15)	exon (NM_011206, exon 13 of 15)	13041	NM_011206	19253	Mm.361	NM_011206	ENSMUSG00000026126	Ptpn18	FLP1|HSCF|PTP-HSCF|PTP-K1|Ptpk1	protein tyrosine phosphatase, non-receptor type 18	protein-coding
mm_60735.1	chr7	45438009	45438033	+	1	NA	intron (NM_030678, intron 2 of 15)	intron (NM_030678, intron 2 of 15)	3182	NM_030678	14936	Mm.275654	NM_030678	ENSMUSG00000003865	Gys1	Gys3|MGS	glycogen synthase 1, muscle	protein-coding
mm_70209.1	chr7	144857292	144857303	-	1	NA	Intergenic	L1MB3|LINE|L1	-4089	NM_010202	14175	Mm.4956	NM_010202	ENSMUSG00000050917	Fgf4	Fgf-4|Fgfk|HBGF-4|Hst1|Hstf-1|KS3|hst|hst-1|kFGF	fibroblast growth factor 4	protein-coding
mm_71844.1	chr8	68904984	68904998	+	1	NA	3' UTR (NM_008509, exon 10 of 10)	3' UTR (NM_008509, exon 10 of 10)	24436	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_16749.1	chr2	9857431	9857435	-	1	NA	3' UTR (NM_008091, exon 6 of 6)	3' UTR (NM_008091, exon 6 of 6)	21167	NM_008091	14462	Mm.313866	NM_008091	ENSMUSG00000015619	Gata3	Gata-3|jal	GATA binding protein 3	protein-coding
mm_117746.1	chr13	95891906	95891929	-	1	NA	promoter-TSS (NM_027711)	promoter-TSS (NM_027711)	5	NM_027711	544963	Mm.38878	NM_027711	ENSMUSG00000021676	Iqgap2	4933417J23Rik|A630053O10|AI788777	IQ motif containing GTPase activating protein 2	protein-coding
mm_38693.1	chr4	145213711	145213728	-	1	NA	3' UTR (NM_011610, exon 10 of 10)	3' UTR (NM_011610, exon 10 of 10)	-18714	NM_001276465	230895	Mm.240310	NM_001033190	ENSMUSG00000020220	Vps13d	-	vacuolar protein sorting 13D	protein-coding
mm_4606.1	chr1	178448659	178448701	+	1	NA	intron (NM_026626, intron 2 of 6)	intron (NM_026626, intron 2 of 6)	42799	NM_026626	68226	Mm.252132	NM_026626	ENSMUSG00000026495	Efcab2	1700073K01Rik|D830011E08Rik	EF-hand calcium binding domain 2	protein-coding
mm_73422.1	chr8	106107456	106107459	+	1	NA	intron (NM_010901, intron 8 of 9)	B1_Mur4|SINE|Alu	-27943	NR_040345	69771	Mm.393274	NR_040344		1810019D21Rik	-	RIKEN cDNA 1810019D21 gene	ncRNA
mm_32919.1	chr4	119136778	119136788	+	1	NA	3' UTR (NM_011400, exon 10 of 10)	3' UTR (NM_011400, exon 10 of 10)	28038	NM_011400	20525	Mm.21002	NM_011400	ENSMUSG00000028645	Slc2a1	Glut-1|Glut1	solute carrier family 2 (facilitated glucose transporter), member 1	protein-coding
mm_13111.1	chr2	91546306	91546329	+	1	NA	promoter-TSS (NM_001165989)	promoter-TSS (NM_001165989)	-5	NM_001165989	75786	Mm.168478	NM_029437	ENSMUSG00000040549	Ckap5	3110043H24Rik|4930432B04Rik|D730027C18Rik|T25636|mKIAA0097	cytoskeleton associated protein 5	protein-coding
mm_30620.1	chr4	8690400	8690453	+	1	NA	promoter-TSS (NM_001277149)	promoter-TSS (NM_001277149)	20	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_34258.1	chr4	141420228	141420237	+	1	NA	promoter-TSS (NM_013868)	promoter-TSS (NM_013868)	-547	NM_013868	29818	Mm.46181	NM_013868	ENSMUSG00000006221	Hspb7	27kDa|Hsp25-2|cvHsp	heat shock protein family, member 7 (cardiovascular)	protein-coding
mm_121088.1	chr14	99298946	99298989	+	1	NA	5' UTR (NM_009769, exon 1 of 4)	5' UTR (NM_009769, exon 1 of 4)	276	NM_009769	12224	Mm.30262	NM_009769	ENSMUSG00000005148	Klf5	4930520J07Rik|Bteb2|CKLF|IKLF	Kruppel-like factor 5	protein-coding
mm_151962.1	chr19	5801599	5801678	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	1034	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_7516.1	chr1	124045248	124045267	-	1	NA	intron (NM_199021, intron 1 of 25)	intron (NM_199021, intron 1 of 25)	302	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_309.1	chr1	24177690	24177711	+	1	NA	promoter-TSS (NM_007740)	promoter-TSS (NM_007740)	90	NM_007740	12839	Mm.154662	NM_007740	ENSMUSG00000026147	Col9a1	Col9a-1	collagen, type IX, alpha 1	protein-coding
mm_33108.1	chr4	124714810	124714879	+	1	NA	promoter-TSS (NM_029157)	promoter-TSS (NM_029157)	-17	NM_029157	75062	Mm.25779	NM_029157	ENSMUSG00000028902	Sf3a3	4930512K19Rik|60kDa	splicing factor 3a, subunit 3	protein-coding
mm_7551.1	chr1	124592293	124592294	-	1	NA	Intergenic	Intergenic	-546734	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_86018.1	chr9	112235453	112235502	-	1	NA	promoter-TSS (NM_001177619)	promoter-TSS (NM_001177619)	-636	NM_001177619	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_39230.1	chr4	156228796	156228809	-	1	NA	promoter-TSS (NM_001008233)	promoter-TSS (NM_001008233)	-260	NM_001008233	231002	Mm.423124	NM_001008233	ENSMUSG00000078485	Plekhn1	BC025458	pleckstrin homology domain containing, family N member 1	protein-coding
mm_47237.1	chr5	121452340	121452417	-	1	NA	promoter-TSS (NM_029912)	promoter-TSS (NM_029912)	96	NM_026129	67397	Mm.154570	NM_026129	ENSMUSG00000029616	Erp29	1200015M03Rik|2810446M09Rik|AW209030|Erp28|Erp31|PDI-Db	endoplasmic reticulum protein 29	protein-coding
mm_4115.1	chr1	167689526	167689534	+	1	NA	promoter-TSS (NM_033652)	promoter-TSS (NM_033652)	-28	NM_033652	110648	Mm.330081	NM_033652	ENSMUSG00000026686	Lmx1a	Lmx1.1|dr|dreher|sst	LIM homeobox transcription factor 1 alpha	protein-coding
mm_101095.1	chr11	11890369	11890379	-	1	NA	promoter-TSS (NM_016672)	promoter-TSS (NM_016672)	34	NM_016672	13195	Mm.12906	NM_016672	ENSMUSG00000020182	Ddc	Aadc	dopa decarboxylase	protein-coding
mm_112901.1	chr13	20899246	20899262	+	1	NA	intron (NM_012054, intron 4 of 20)	intron (NM_012054, intron 4 of 20)	105141	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_52631.1	chr6	117174353	117174363	+	1	NA	3' UTR (NM_021704, exon 3 of 3)	3' UTR (NM_021704, exon 3 of 3)	5823	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_164491.1	chr16	88758845	88758851	+	1	NA	promoter-TSS (NM_054100)	promoter-TSS (NM_054100)	1	NM_054100	117172	Mm.160339	NM_054100	ENSMUSG00000068078	2310034C09Rik	-	RIKEN cDNA 2310034C09 gene	protein-coding
mm_47118.1	chr5	119671361	119671369	-	1	NA	5' UTR (NM_011535, exon 1 of 8)	5' UTR (NM_011535, exon 1 of 8)	132	NM_011535	21386	Mm.219139	NM_011535	ENSMUSG00000018604	Tbx3	D5Ertd189e	T-box 3	protein-coding
mm_709.1	chr1	40805579	40805692	+	1	NA	promoter-TSS (NM_001081198)	promoter-TSS (NM_001081198)	34	NM_001081198	381339	Mm.334678	NM_001081198	ENSMUSG00000079588	Tmem182	2310079P10Rik|AI414494	transmembrane protein 182	protein-coding
mm_9339.1	chr1	172027252	172027268	-	1	NA	promoter-TSS (NM_033509)	promoter-TSS (NM_033509)	35	NM_033509	93840	Mm.36148	NM_033509	ENSMUSG00000026556	Vangl2	C530001F03Rik|Lootl|Lp|Lpp1|Ltap|Vang1l2|loop-tail|ska17|ska<m17Jus>|stbm|strabismus	vang-like 2 (van gogh, Drosophila)	protein-coding
mm_156181.1	chrX	130461846	130461849	+	1	NA	3' UTR (NM_172493, exon 27 of 27)	3' UTR (NM_172493, exon 27 of 27)	712105	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diaph2	Dia3|Diap2|Drf2|E430022I22Rik	diaphanous related formin 2	protein-coding
mm_172886.1	chr9	53690045	53690055	-	1	NA	intron (NM_175562, intron 1 of 1)	intron (NM_175562, intron 1 of 1)	16182	NM_175562	270160	Mm.290285	NM_175562	ENSMUSG00000055069	Rab39	C230094F14Rik|Rab39a	RAB39, member RAS oncogene family	protein-coding
mm_66804.1	chr7	47204932	47204976	-	1	NA	Intergenic	Intergenic	-15538	NR_131899	381886	Mm.377894	NM_205821		Mrgpra6	MrgA6	MAS-related GPR, member A6	protein-coding
mm_156313.1	chrX	136993148	136993216	+	1	NA	promoter-TSS (NM_025893)	promoter-TSS (NM_025893)	27	NM_001035509	66995	Mm.440155	NM_025893	ENSMUSG00000031428	Zcchc18	1500031H04Rik|Sizn2	zinc finger, CCHC domain containing 18	protein-coding
mm_4293.1	chr1	171767145	171767170	+	1	NA	promoter-TSS (NM_013730)	promoter-TSS (NM_013730)	25	NM_013730	27218	Mm.103648	NM_013730	ENSMUSG00000015316	Slamf1	4933415F16|AA177906|CD150|CDw150|ESTM51|IPO-3|Slam	signaling lymphocytic activation molecule family member 1	protein-coding
mm_143667.1	chr17	79891132	79891135	-	1	NA	intron (NM_019717, intron 1 of 12)	Lx3A|LINE|L1	4990	NM_178050	56298	Mm.175403	NM_019717	ENSMUSG00000059811	Atl2	2010110I21Rik|AA407293|AV334690|Aip-2|Arl6ip2	atlastin GTPase 2	protein-coding
mm_136738.1	chr17	8340456	8340480	+	1	NA	promoter-TSS (NM_178774)	promoter-TSS (NM_178774)	62	NR_028280	320111	Mm.442510	NM_178774	ENSMUSG00000055945	Prr18	9630019K15Rik	proline rich 18	protein-coding
mm_14123.1	chr2	125947852	125947854	+	1	NA	intron (NM_175154, intron 8 of 9)	ID4|SINE|ID	81630	NM_001291002	69976	Mm.20216	NM_175154	ENSMUSG00000027207	Galk2	2810017M24Rik|AI327030|Gk2	galactokinase 2	protein-coding
mm_143119.1	chr17	57209616	57209653	-	1	NA	exon (NM_009778, exon 31 of 41)	exon (NM_009778, exon 31 of 41)	7594	NR_105944	102465591		NR_105944	ENSMUSG00000099066	Mir6978	Gm27858|mmu-mir-6978	microRNA 6978	ncRNA
mm_30282.1	chr3	148948906	148948917	-	1	NA	intron (NM_001081298, intron 1 of 23)	(A)n|Simple_repeat|Simple_repeat	5724	NM_001081298	99633	Mm.9776	NM_001081298	ENSMUSG00000028184	Adgrl2	AI450192|CIRL-2|Gm619|Lec1|Lphh1|Lphn2|mKIAA0786	adhesion G protein-coupled receptor L2	protein-coding
mm_138515.1	chr17	35237811	35237822	+	1	NA	3' UTR (NM_023179, exon 3 of 3)	3' UTR (NM_023179, exon 3 of 3)	1220	NM_023179	66237	Mm.396107	NM_023179	ENSMUSG00000024403	Atp6v1g2	1500002D01Rik|Atp6g2|NG38|VAG2	ATPase, H+ transporting, lysosomal V1 subunit G2	protein-coding
mm_14329.1	chr2	129371481	129371491	+	1	NA	promoter-TSS (NM_008361)	promoter-TSS (NM_008361)	-347	NM_008361	16176	Mm.222830	NM_008361	ENSMUSG00000027398	Il1b	IL-1beta|Il-1b	interleukin 1 beta	protein-coding
mm_149374.1	chr19	11375489	11375528	+	1	NA	promoter-TSS (NM_001310331)	promoter-TSS (NM_001310331)	20	NM_001310331	666907		NM_001310331	ENSMUSG00000101389	Ms4a4a	EG666907	membrane-spanning 4-domains, subfamily A, member 4A	protein-coding
mm_60206.1	chr7	43437133	43437174	+	1	NA	promoter-TSS (NM_024253)	promoter-TSS (NM_024253)	15	NM_024253	72310	Mm.34613	NM_024253	ENSMUSG00000004612	Nkg7	2500004F03Rik	natural killer cell group 7 sequence	protein-coding
mm_72682.1	chr8	84949875	84949885	+	1	NA	intron (NM_144929, intron 1 of 5)	intron (NM_144929, intron 1 of 5)	2889	NM_144929	234542	Mm.461701	NM_144929	ENSMUSG00000048617	Rtbdn	A330096I21Rik|BC022744|Rtbnd	retbindin	protein-coding
mm_129535.1	chr15	79328155	79328191	-	1	NA	5' UTR (NM_001199024, exon 1 of 16)	5' UTR (NM_001199024, exon 1 of 16)	198	NM_016915	53357	Mm.155620	NM_016915	ENSMUSG00000042632	Pla2g6	BB112799|PNPLA9|iPLA(2)beta|iPLA2|iPLA2beta	phospholipase A2, group VI	protein-coding
mm_151001.1	chr19	46654106	46654134	+	1	NA	exon (NM_001177813, exon 4 of 4)	exon (NM_001177813, exon 4 of 4)	18880	NM_007809	13074	Mm.1262	NM_007809	ENSMUSG00000003555	Cyp17a1	Cyp17|p450c17	cytochrome P450, family 17, subfamily a, polypeptide 1	protein-coding
mm_30227.1	chr3	145649705	145649709	-	1	NA	intron (NM_010516, intron 1 of 4)	CpG	278	NM_010516	16007	Mm.1231	NM_010516	ENSMUSG00000028195	Cyr61	AI325051|CCN1|Igfbp10	cysteine rich protein 61	protein-coding
mm_22641.1	chr3	14864163	14864173	+	1	NA	intron (NM_007606, intron 1 of 6)	intron (NM_007606, intron 1 of 6)	630	NM_007606	12350	Mm.300	NM_007606	ENSMUSG00000027559	Car3	BB219044|Ca3|Car-3	carbonic anhydrase 3	protein-coding
mm_96880.1	chr11	70221225	70221240	+	1	NA	promoter-TSS (NM_172371)	promoter-TSS (NM_172371)	-238	NM_172371	69309	Mm.93266	NM_172371	ENSMUSG00000044367	Slc16a13	1700007D07Rik	solute carrier family 16 (monocarboxylic acid transporters), member 13	protein-coding
mm_148696.1	chr19	5741893	5741902	+	1	NA	5' UTR (NM_008520, exon 2 of 28)	5' UTR (NM_008520, exon 2 of 28)	993	NM_008520	16998	Mm.182396	NM_008520	ENSMUSG00000024940	Ltbp3	Ltbp2|mFLJ00070	latent transforming growth factor beta binding protein 3	protein-coding
mm_79960.1	chr9	66350067	66350085	+	1	NA	promoter-TSS (NM_145617)	promoter-TSS (NM_145617)	-374	NM_145617	235439	Mm.244179	NM_145617	ENSMUSG00000038664	Herc1	2810449H11Rik|B230218H07|D130015N03Rik|tbl	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	protein-coding
mm_156204.1	chrX	134427057	134427079	+	1	NA	intron (NM_010078, intron 2 of 22)	intron (NM_010078, intron 2 of 22)	22288	NM_010078	13497	Mm.121662	NM_010078	ENSMUSG00000000223	Drp2	AW495265|DRP-2	dystrophin related protein 2	protein-coding
mm_50418.1	chr6	48747925	48747957	+	1	NA	intron (NM_175035, intron 1 of 2)	intron (NM_175035, intron 1 of 2)	1744	NM_175035	317757	Mm.455917	NM_175035	ENSMUSG00000043505	Gimap5	D630024P16|E230026N22Rik	GTPase, IMAP family member 5	protein-coding
mm_21710.1	chr2	164593539	164593577	-	1	NA	promoter-TSS (NM_029325)	promoter-TSS (NM_029325)	13	NM_029325	75526	Mm.159533	NM_029325	ENSMUSG00000017733	Eppin	1700024E17Rik|Spinlw1	epididymal peptidase inhibitor	protein-coding
mm_38362.1	chr4	138138460	138138478	-	1	NA	promoter-TSS (NR_126429)	promoter-TSS (NR_126429)	49	NR_126429	73563	Mm.444294	NR_126429	ENSMUSG00000084804	1700095J12Rik	-	RIKEN cDNA 1700095J12 gene	ncRNA
mm_34055.1	chr4	138304783	138304833	+	1	NA	promoter-TSS (NM_007838)	promoter-TSS (NM_007838)	70	NM_007838	13200	Mm.7236	NM_007838	ENSMUSG00000028757	Ddost	-	dolichyl-di-phosphooligosaccharide-protein glycotransferase	protein-coding
mm_148686.1	chr19	5704438	5704468	+	1	NA	promoter-TSS (NM_010609)	promoter-TSS (NM_010609)	-18	NM_010609	16530	Mm.440033	NM_010609	ENSMUSG00000024936	Kcnk7	2310014G03Rik|Kcnk6|Kcnk8|Knot|Mlk3	potassium channel, subfamily K, member 7	protein-coding
mm_86745.1	chr10	19356559	19356565	+	1	NA	promoter-TSS (NM_053008)	promoter-TSS (NM_053008)	23	NM_053008	94222	Mm.156946	NM_053008	ENSMUSG00000045591	Olig3	Bhlhb7|bHLHe20|oligo3	oligodendrocyte transcription factor 3	protein-coding
mm_164733.1	chr17	66320488	66320500	+	1	NA	Intergenic	Intergenic	129256	NM_172963	68617	Mm.33421	NM_172963	ENSMUSG00000052105	Mtcl1	1110012J17Rik|Ccdc165|D130071O13|Kiaa0802|Soga2|mKIAA0802|t8219b25	microtubule crosslinking factor 1	protein-coding
mm_120713.1	chr14	72634352	72634359	+	1	NA	intron (NM_207636, intron 3 of 25)	MLT1E3|LTR|ERVL-MaLR	75648	NM_207636	319448	Mm.205421	NM_207636	ENSMUSG00000033487	Fndc3a	1700094E19Rik|D14Ertd453e|F730017H24Rik|Fndc3|sys	fibronectin type III domain containing 3A	protein-coding
mm_41312.1	chr5	90469496	90469567	+	1	NA	exon (NM_009654, exon 9 of 15)	exon (NM_009654, exon 9 of 15)	8661	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_63451.1	chr7	127512092	127512102	+	1	NA	non-coding (NR_024331, exon 1 of 1)	non-coding (NR_024331, exon 1 of 1)	114	NM_001304266	100043597	Mm.428042	NM_175144	ENSMUSG00000053877	Srcap	B930091H02Rik|D030022P06Rik|F630004O05Rik	Snf2-related CREBBP activator protein	protein-coding
mm_33343.1	chr4	129287723	129287738	+	1	NA	5' UTR (NM_023485, exon 1 of 5)	5' UTR (NM_023485, exon 1 of 5)	109	NM_023485	68828	Mm.132243	NM_023485	ENSMUSG00000001333	Sync	1110057H03Rik|SNIP4	syncoilin	protein-coding
mm_79413.1	chr9	55208941	55208989	+	1	NA	promoter-TSS (NM_028049)	promoter-TSS (NM_028049)	30	NM_028049	71999	Mm.276429	NM_028049	ENSMUSG00000032309	Fbxo22	0610033L19Rik|1600016C16Rik	F-box protein 22	protein-coding
mm_30769.1	chr4	17853247	17853282	+	1	NA	promoter-TSS (NM_019724)	promoter-TSS (NM_019724)	-194	NM_019724	17389	Mm.187315	NM_019724	ENSMUSG00000028226	Mmp16	MT-MMP 3|MT3-MMP|Mt3mmp	matrix metallopeptidase 16	protein-coding
mm_51361.1	chr6	72636227	72636237	+	1	NA	intron (NM_009332, intron 4 of 11)	intron (NM_009332, intron 4 of 11)	6401	NR_040421	100038714	Mm.321330	NR_040421		Gm15401	ENSMUSG00000072999|OTTMUSG00000021199	predicted gene 15401	ncRNA
mm_110185.1	chr12	27338336	27338340	-	1	NA	3' UTR (NM_009234, exon 1 of 1)	3' UTR (NM_009234, exon 1 of 1)	4380	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding
mm_3761.1	chr1	156052449	156052474	+	1	NA	3' UTR (NM_001160182, exon 3 of 3)	3' UTR (NM_001160182, exon 3 of 3)	11600	NM_022329	240832	Mm.253335	NM_022329	ENSMUSG00000050565	Tor1aip2	1110020D10Rik|15kDa|A130072J07|AA103493|AW060462|AW610675|C77739|Ifrg15|Lull1	torsin A interacting protein 2	protein-coding
mm_9964.1	chr1	191176710	191176731	-	1	NA	intron (NM_007498, intron 2 of 3)	B3|SINE|B2	6613	NM_007498	11910	Mm.2706	NM_007498	ENSMUSG00000026628	Atf3	LRG-21	activating transcription factor 3	protein-coding
mm_45932.1	chr5	89676899	89676902	-	1	NA	3' UTR (NM_177872, exon 22 of 22)	3' UTR (NM_177872, exon 22 of 22)	60464	NR_037571	631105	Mm.7732	NR_037571		Gm7056	Gm149	predicted gene 7056	ncRNA
mm_66003.1	chr7	30562913	30562933	-	1	NA	promoter-TSS (NM_170760)	promoter-TSS (NM_170760)	261	NM_025498	66340	Mm.86557	NM_025498	ENSMUSG00000036835	Psenen	1700023M09Rik|Pen-2	presenilin enhancer gamma secretase subunit	protein-coding
mm_42624.1	chr5	118245227	118245289	+	1	NA	promoter-TSS (NM_001081236)	promoter-TSS (NM_001081236)	31	NM_001081236	76792	Mm.103428	NM_001081236	ENSMUSG00000032840	2410131K14Rik	-	RIKEN cDNA 2410131K14 gene	protein-coding
mm_33138.1	chr4	125066724	125066732	+	1	NA	promoter-TSS (NM_175246)	promoter-TSS (NM_175246)	35	NM_175246	76793	Mm.22548	NM_175246	ENSMUSG00000050213	Snip1	2410133M08Rik	Smad nuclear interacting protein 1	protein-coding
mm_27640.1	chr3	63851252	63851290	-	1	NA	promoter-TSS (NM_183191)	promoter-TSS (NM_183191)	-280	NM_001177732	269437	Mm.316391	NM_183191	ENSMUSG00000036834	Plch1	BC042549|PLC-eta-1|PLCeta1|Plcl3	phospholipase C, eta 1	protein-coding
mm_122380.1	chr14	40893223	40893237	-	1	NA	promoter-TSS (NM_177816)	promoter-TSS (NM_177816)	-265	NM_177816	328381	Mm.235694	NM_177816	ENSMUSG00000037833	Sh2d4b	A430109M18Rik|D030001E08	SH2 domain containing 4B	protein-coding
mm_72331.1	chr8	79028254	79028309	+	1	NA	promoter-TSS (NM_178267)	promoter-TSS (NM_178267)	-156	NM_001294279	622675	Mm.48724	NM_178267	ENSMUSG00000071064	Zfp827	2810449M09Rik|D630040G17Rik|Znf827	zinc finger protein 827	protein-coding
mm_24712.1	chr3	95228311	95228368	+	1	NA	promoter-TSS (NM_172395)	promoter-TSS (NM_172395)	-85	NM_172395	57912	Mm.28189	NM_172395	ENSMUSG00000046722	Cdc42se1	1300002M12Rik|AW558204|Cdcse1|SCIP1|Spec1	CDC42 small effector 1	protein-coding
mm_135475.1	chr16	45937478	45937488	-	1	NA	Intergenic	RSINE1|SINE|B4	72930	NM_001134480	433022	Mm.380993	NM_001134480	ENSMUSG00000087141	Plcxd2	AW494639|EG433022	phosphatidylinositol-specific phospholipase C, X domain containing 2	protein-coding
mm_149483.1	chr19	11770442	11770463	+	1	NA	promoter-TSS (NM_025606)	promoter-TSS (NM_025606)	37	NM_025606	94063	Mm.203928	NM_025606	ENSMUSG00000024683	Mrpl16	2310039D06Rik	mitochondrial ribosomal protein L16	protein-coding
mm_105828.1	chr11	113172979	113173041	-	1	NA	intron (NR_015556, intron 1 of 2)	intron (NR_015556, intron 1 of 2)	28828	NR_015556	72386	Mm.266961	NR_015556	ENSMUSG00000087259	2610035D17Rik	-	RIKEN cDNA 2610035D17 gene	ncRNA
mm_92877.1	chr10	82492643	82492645	-	1	NA	promoter-TSS (NM_001255990)	promoter-TSS (NM_001255990)	-26	NM_001255990	432480	Mm.280394	NM_001255990	ENSMUSG00000094186	Gm1553	Lcrn	predicted gene 1553	protein-coding
mm_29115.1	chr3	104961669	104961686	-	1	NA	promoter-TSS (NM_009520)	promoter-TSS (NM_009520)	32	NM_009520	22414	Mm.10740	NM_009520	ENSMUSG00000027840	Wnt2b	Wnt13	wingless-type MMTV integration site family, member 2B	protein-coding
mm_16207.1	chr2	173062279	173062289	+	1	NA	Intergenic	Intergenic	40382	NM_019547	56190	Mm.485782	NM_019547	ENSMUSG00000027510	Rbm38	Rnpc1|Seb4|Seb4l	RNA binding motif protein 38	protein-coding
mm_67111.1	chr7	70359932	70359948	-	1	NA	exon (NM_009697, exon 1 of 3)	exon (NM_009697, exon 1 of 3)	653	NM_009697	11819	Mm.158143	NM_009697	ENSMUSG00000030551	Nr2f2	2700033K02Rik|9430015G03Rik|ARP-1|Aporp1|COUP-TF2|COUP-TFII|COUPTFB|EAR3|SVP40|Tcfcoup2	nuclear receptor subfamily 2, group F, member 2	protein-coding
mm_3919.1	chr1	162221296	162221299	+	1	NA	non-coding (NR_002870, exon 1 of 1)	non-coding (NR_002870, exon 1 of 1)	-2071	NR_029796	387210		NR_029796	ENSMUSG00000065516	Mir214	Mirn214|mir-214|mmu-mir-214	microRNA 214	ncRNA
mm_108437.1	chr12	82339708	82339716	+	1	NA	intron (NM_172579, intron 1 of 20)	intron (NM_172579, intron 1 of 20)	28363	NM_172579	217692	Mm.261333	NM_172579	ENSMUSG00000042700	Sipa1l1	4931426N11Rik|AW213287|Spar|mKIAA0440	signal-induced proliferation-associated 1 like 1	protein-coding
mm_88338.1	chr10	75589353	75589355	+	1	NA	promoter-TSS (NM_011820)	promoter-TSS (NM_011820)	-27	NM_011820	23887	Mm.257927	NM_011820	ENSMUSG00000006344	Ggt5	AI551243|GGL|GGT-REL|Ggtla1	gamma-glutamyltransferase 5	protein-coding
mm_98660.1	chr11	96271617	96271657	+	1	NA	exon (NM_008270, exon 1 of 2)	exon (NM_008270, exon 1 of 2)	307	NM_008270	15417	Mm.258271	NM_008270	ENSMUSG00000020875	Hoxb9	Hox-2.5	homeobox B9	protein-coding
mm_43876.1	chr5	143732586	143732616	+	1	NA	promoter-TSS (NM_029749)	promoter-TSS (NM_029749)	-321	NM_029749	76800	Mm.259620	NM_029749	ENSMUSG00000051306	Usp42	2410140K03Rik|3110031A07Rik|A630018G05Rik|D5Ertd591e	ubiquitin specific peptidase 42	protein-coding
mm_22141.1	chr2	171962815	171962828	-	1	NA	promoter-TSS (NR_040509)	promoter-TSS (NR_040509)	-22	NR_040509	75655	Mm.396203	NR_040509	ENSMUSG00000086823	1700028P15Rik	-	RIKEN cDNA 1700028P15 gene	ncRNA
mm_142132.1	chr17	35909225	35909246	-	1	NA	intron (NM_001347378, intron 3 of 11)	intron (NM_001347378, intron 3 of 11)	833	NM_001142745	73242	Mm.273155	NM_028476	ENSMUSG00000024426	Atat1	0610011P08Rik|2610008K08Rik|2610110G12Rik|3110080J08Rik|Mec17|TAT	alpha tubulin acetyltransferase 1	protein-coding
mm_37301.1	chr4	119232723	119232728	-	1	NA	promoter-TSS (NM_019782)	promoter-TSS (NM_019782)	-1	NM_001012400	230696	Mm.473722	NM_001012400	ENSMUSG00000078584	AU022252	AI450326	expressed sequence AU022252	protein-coding
mm_119127.1	chr14	31138326	31138348	+	1	NA	TTS (NM_138672)	TTS (NM_138672)	3484	NM_027289	70021	Mm.261681	NM_027289	ENSMUSG00000071547	Nt5dc2	2510015F01Rik	5'-nucleotidase domain containing 2	protein-coding
mm_42338.1	chr5	114903641	114903665	+	1	NA	intron (NM_011854, intron 3 of 5)	ID4_|SINE|ID	6719	NM_011854	23962	Mm.228363	NM_011854	ENSMUSG00000029561	Oasl2	M1204|Mmu-OASL|Oasl	2'-5' oligoadenylate synthetase-like 2	protein-coding
mm_140004.1	chr17	73107983	73108080	+	1	NA	promoter-TSS (NM_001081071)	promoter-TSS (NM_001081071)	46	NM_001177967	225010	Mm.329194	NM_001081071	ENSMUSG00000054469	Lclat1	AI181996|Agpat8|Alcat1|Gm91|Lycat	lysocardiolipin acyltransferase 1	protein-coding
mm_49707.1	chr6	34412191	34412202	+	1	NA	promoter-TSS (NM_009731)	promoter-TSS (NM_009731)	-166	NM_009731	11997	Mm.482073	NM_009731	ENSMUSG00000052131	Akr1b7	AR|Avdp|MVDP	aldo-keto reductase family 1, member B7	protein-coding
mm_58461.1	chr7	3366177	3366188	+	1	NA	intron (NM_133189, intron 4 of 4)	intron (NM_133189, intron 4 of 4)	-27860	NM_133190	81905	Mm.357990	NM_133190	ENSMUSG00000053395	Cacng8	-	calcium channel, voltage-dependent, gamma subunit 8	protein-coding
mm_15157.1	chr2	154009166	154009174	+	1	NA	exon (NM_008953, exon 2 of 9)	exon (NM_008953, exon 2 of 9)	894	NM_008953	19194	Mm.29197	NM_008953	ENSMUSG00000042459	Bpifa2	Bpifa2e|Psp	BPI fold containing family A, member 2	protein-coding
mm_79196.1	chr9	48495212	48495220	+	1	NA	promoter-TSS (NM_001004191)	promoter-TSS (NM_001004191)	114	NM_001326355	67010	Mm.76911	NM_144948	ENSMUSG00000042396	Rbm7	1200007M24Rik|1500011D06Rik|AU041934|AW554393	RNA binding motif protein 7	protein-coding
mm_81730.1	chr9	113726415	113726420	+	1	NA	Intergenic	RLTR53_Mm|LTR|ERVK	-15056	NM_001286599	76499	Mm.222272	NM_029633	ENSMUSG00000033392	Clasp2	1500004F14Rik|8030404L10Rik|C77448|CLASP2beta|mKIAA0627	CLIP associating protein 2	protein-coding
mm_11743.1	chr2	38351061	38351080	+	1	NA	promoter-TSS (NM_010710)	promoter-TSS (NM_010710)	-238	NM_010710	16870	Mm.142856	NM_010710	ENSMUSG00000000247	Lhx2	LH2A|Lh-2|Lim2|ap|apterous	LIM homeobox protein 2	protein-coding
mm_126621.1	chr15	83154203	83154221	+	1	NA	3' UTR (NM_029787, exon 9 of 9)	3' UTR (NM_029787, exon 9 of 9)	4567	NR_004432	104307	Mm.471434	NR_004432	ENSMUSG00000065176	Rnu12	-	RNA U12, small nuclear	snRNA
mm_76012.1	chr8	72998347	72998347	-	1	NA	intron (NM_001317391, intron 7 of 15)	intron (NM_001317391, intron 7 of 15)	-18165	NR_039551	100628574		NR_039551	ENSMUSG00000093140	Mir28b	mmu-mir-28b	microRNA 28b	ncRNA
mm_47982.1	chr5	135911474	135911484	-	1	NA	exon (NM_018871, exon 2 of 2)	exon (NM_018871, exon 2 of 2)	23162	NM_018871	22628	Mm.233813	NM_018871	ENSMUSG00000051391	Ywhag	14-3-3gamma|D7Bwg1348e	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, gamma polypeptide	protein-coding
mm_163882.1	chr14	21857031	21857031	+	1	NA	TTS (NM_176925)	TTS (NM_176925)	-8121	NM_026965	69156	Mm.11827	NM_026965	ENSMUSG00000021773	Comtd1	1810030M08Rik|MT773	catechol-O-methyltransferase domain containing 1	protein-coding
mm_127381.1	chr15	100870927	100870961	+	1	NA	intron (NM_001077499, intron 1 of 26)	CpG	299	NM_001077499	20273	Mm.385012	NM_011323	ENSMUSG00000023033	Scn8a	AI853486|C630029C19Rik|NaCh6|Nav1.6|dmu|med|mnd-2|mnd2|nmf2|nmf335|nmf58|nur14|seal	sodium channel, voltage-gated, type VIII, alpha	protein-coding
mm_72129.1	chr8	71789246	71789260	+	1	NA	Intergenic	Intergenic	-63572	NM_028715	74015	Mm.22025	NM_028715	ENSMUSG00000070000	Fcho1	3322402E17Rik|N28152	FCH domain only 1	protein-coding
mm_81738.1	chr9	113792982	113792992	+	1	NA	promoter-TSS (NM_001286603)	promoter-TSS (NM_001286603)	-343	NM_001286603	76499	Mm.222272	NM_029633	ENSMUSG00000033392	Clasp2	1500004F14Rik|8030404L10Rik|C77448|CLASP2beta|mKIAA0627	CLIP associating protein 2	protein-coding
mm_10928.1	chr2	25456831	25456850	+	1	NA	promoter-TSS (NM_027085)	promoter-TSS (NM_027085)	-3	NM_027085	69454	Mm.44194	NM_027085	ENSMUSG00000015093	Clic3	2300003G24Rik	chloride intracellular channel 3	protein-coding
mm_23051.1	chr3	35721258	35721266	+	1	NA	Intergenic	Intergenic	-32876	NM_029570	76295	Mm.239416	NM_029570	ENSMUSG00000037400	Atp11b	1110019I14Rik|ATPIF|ATPIR|mKIAA0956	ATPase, class VI, type 11B	protein-coding
mm_14739.1	chr2	144368867	144368884	+	1	NA	promoter-TSS (NM_001166640)	promoter-TSS (NM_001166640)	-108	NM_001164813	100048644	Mm.227925	NM_001164813	ENSMUSG00000098387	Pet117	Gm20571	PET117 homolog	protein-coding
mm_161009.1	chr11	118443404	118443404	+	1	NA	promoter-TSS (NM_001204130)	promoter-TSS (NM_001204130)	-130	NM_001204130	56745	Mm.23845	NM_019959	ENSMUSG00000017446	C1qtnf1	1600017K21Rik|CTRP1|Zsig37	C1q and tumor necrosis factor related protein 1	protein-coding
mm_122366.1	chr14	39388380	39388415	-	1	NA	intron (NM_001190187, intron 1 of 9)	intron (NM_001190187, intron 1 of 9)	-84032	NR_131973	432842	Mm.352566	NR_131973		LOC432842	-	uncharacterized LOC432842	ncRNA
mm_154691.1	chrX	8047189	8047205	+	1	NA	Intergenic	Intergenic	27116	NM_001290716	20937	Mm.9244	NM_011514	ENSMUSG00000039231	Suv39h1	AI852103|AL022883|DXHXS7466e|H3-K9-HMTase 1|KMT1A|mIS6	suppressor of variegation 3-9 homolog 1 (Drosophila)	protein-coding
mm_65710.1	chr7	28378172	28378182	-	1	NA	exon (NM_011756, exon 2 of 2)	exon (NM_011756, exon 2 of 2)	1051	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_171083.1	chr3	122276274	122276278	+	1	NA	exon (NM_153806, exon 2 of 7)	exon (NM_153806, exon 2 of 7)	1862	NM_153806	99480	Mm.398647	NM_153806	ENSMUSG00000039756	Dnttip2	4930588M11Rik|AA408582|AU014960|HSU15552	deoxynucleotidyltransferase, terminal, interacting protein 2	protein-coding
mm_154477.1	chrM	4278	4328	-	1	NA	NA	Intergenic	NA	NA								
mm_157207.1	chrX	12761784	12761842	-	1	NA	promoter-TSS (NR_045852)	promoter-TSS (NR_045852)	160	NM_012005	26896	Mm.17616	NM_012005	ENSMUSG00000064127	Med14	9930001L01Rik|AU041628|Crsp2|ENSMUSG00000073278|Gm641|ORF1|Trap170	mediator complex subunit 14	protein-coding
mm_29522.1	chr3	116594817	116594841	-	1	NA	promoter-TSS (NM_001289571)	promoter-TSS (NM_001289571)	-129	NM_001289568	72776	Mm.440836	NM_028349	ENSMUSG00000027959	Sass6	2810453L12Rik	SAS-6 centriolar assembly protein	protein-coding
mm_49792.1	chr6	35252671	35252681	+	1	NA	promoter-TSS (NR_015608)	promoter-TSS (NR_015608)	-23	NR_015608	67705	Mm.228046	NR_015608	ENSMUSG00000073155	1810058I24Rik	AI414869|AI848234	RIKEN cDNA 1810058I24 gene	ncRNA
mm_40683.1	chr5	65579005	65579021	+	1	NA	intron (NR_144566, intron 2 of 5)	AT_rich|Low_complexity|Low_complexity	41768	NM_001310619	53323	Mm.319512	NM_016786	ENSMUSG00000029203	Ube2k	AW492011|D5Ertd601e|E2-25k|HIP-2|Hip2|Hypg|Lig	ubiquitin-conjugating enzyme E2K	protein-coding
mm_46136.1	chr5	92675835	92675882	-	1	NA	promoter-TSS (NM_177230)	promoter-TSS (NM_177230)	-731	NM_177230	320696	Mm.209991	NM_177230	ENSMUSG00000050050	Ccdc158	4932413O14Rik	coiled-coil domain containing 158	protein-coding
mm_96919.1	chr11	70469002	70469013	+	1	NA	Intergenic	MER58B|DNA|hAT-Charlie	-9023	NM_023158	66102	Mm.425692	NM_023158	ENSMUSG00000018920	Cxcl16	0910001K24Rik|AV290116|BB024863|CXCL16v1|CXCL16v2|SR-PSOX|Zmynd15|b2b498Clo	chemokine (C-X-C motif) ligand 16	protein-coding
mm_143488.1	chr17	71310926	71310947	-	1	NA	promoter-TSS (NM_145158)	promoter-TSS (NM_145158)	29	NM_145158	246707	Mm.23462	NM_145158	ENSMUSG00000024053	Emilin2	FOAP-10	elastin microfibril interfacer 2	protein-coding
mm_32821.1	chr4	117496421	117496463	+	1	NA	intron (NM_025739, intron 1 of 14)	CpG	610	NM_025739	66743	Mm.318331	NM_025739	ENSMUSG00000028677	Rnf220	4732477A13|4931406I20Rik|5730503K05Rik|AV302541	ring finger protein 220	protein-coding
mm_19593.1	chr2	102137971	102137984	-	1	NA	intron (NM_001290784, intron 1 of 5)	intron (NM_001290784, intron 1 of 5)	48483	NM_178886	241576	Mm.489740	NM_178886	ENSMUSG00000048058	Ldlrad3	6430500P08|AI194318|Lrad3	low density lipoprotein receptor class A domain containing 3	protein-coding
mm_7206.1	chr1	93073092	93073104	-	1	NA	exon (NM_008440, exon 9 of 48)	exon (NM_008440, exon 9 of 48)	9382	NM_001294150	16560	Mm.276408	NM_008440	ENSMUSG00000014602	Kif1a	ATSV|C630002N23Rik|Gm1626|Kns1	kinesin family member 1A	protein-coding
mm_162235.1	chrX	152367997	152367997	-	1	NA	promoter-TSS (NR_045451)	promoter-TSS (NR_045451)	-575	NR_045451	75693	Mm.287381	NR_045451	ENSMUSG00000084885	3010001F23Rik	-	RIKEN cDNA 3010001F23 gene	ncRNA
mm_80095.1	chr9	70250576	70250589	+	1	NA	intron (NM_181072, intron 1 of 27)	intron (NM_181072, intron 1 of 27)	43232	NM_181072	71602	Mm.249311	NM_181072	ENSMUSG00000032220	Myo1e	2310020N23Rik|9130023P14Rik|AA407778|myosin-1e|myr 3	myosin IE	protein-coding
mm_29241.1	chr3	107216050	107216074	-	1	NA	exon (NM_001111143, exon 5 of 9)	exon (NM_001111143, exon 5 of 9)	5670	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_139481.1	chr17	56040332	56040349	+	1	NA	promoter-TSS (NM_013733)	promoter-TSS (NM_013733)	-76	NM_013733	27221	Mm.391010	NM_013733	ENSMUSG00000002835	Chaf1a	AL023013|AL024058|CAF-1|Cac1p	chromatin assembly factor 1, subunit A (p150)	protein-coding
mm_42383.1	chr5	114933661	114933683	+	1	NA	intron (NM_145209, intron 5 of 6)	intron (NM_145209, intron 5 of 6)	-8530	NM_028211	72357	Mm.292672	NM_028211	ENSMUSG00000029559	2210016L21Rik	-	RIKEN cDNA 2210016L21 gene	protein-coding
mm_111635.1	chr12	102591315	102591317	-	1	NA	intron (NM_172584, intron 4 of 9)	Lx8|LINE|L1	36375	NM_007693	12652	Mm.4137	NM_007693	ENSMUSG00000021194	Chga	ChrA|cgA	chromogranin A	protein-coding
mm_159059.1	chr2	4152872	4152872	+	1	NA	promoter-TSS (NM_172475)	promoter-TSS (NM_172475)	9	NM_172475	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding
mm_142933.1	chr17	56000163	56000173	-	1	NA	intron (NM_145934, intron 6 of 12)	intron (NM_145934, intron 6 of 12)	5438	NM_145934	106766	Mm.204991	NM_145934	ENSMUSG00000038781	Stap2	AW049765|STAP-2	signal transducing adaptor family member 2	protein-coding
mm_156087.1	chrX	110814423	110814449	+	1	NA	promoter-TSS (NM_008901)	promoter-TSS (NM_008901)	57	NM_008901	18994	Mm.56946	NM_008901	ENSMUSG00000056854	Pou3f4	Brn-4|Brn4|OTF-9|Otf9|Slf|oct-9	POU domain, class 3, transcription factor 4	protein-coding
mm_41399.1	chr5	90786101	90786105	+	1	NA	promoter-TSS (NM_203320)	promoter-TSS (NM_203320)	2	NM_203320	330122	Mm.244289	NM_203320	ENSMUSG00000029379	Cxcl3	Dcip1|Gm1960	chemokine (C-X-C motif) ligand 3	protein-coding
mm_46765.1	chr5	112267354	112267362	-	1	NA	exon (NM_001312894, exon 5 of 6)	exon (NM_001312894, exon 5 of 6)	-9333	NM_001326590	22022	Mm.250631	NM_009419	ENSMUSG00000029344	Tpst2	AI448750|D5Ucla3|Tango13b|grm|grt	protein-tyrosine sulfotransferase 2	protein-coding
mm_65225.1	chr7	19710240	19710243	-	1	NA	intron (NM_016871, intron 6 of 9)	intron (NM_016871, intron 6 of 9)	5188	NM_001109748	53333	Mm.61682	NM_016871	ENSMUSG00000002984	Tomm40	AW539759|Mom35|Tom40	translocase of outer mitochondrial membrane 40 homolog (yeast)	protein-coding
mm_47156.1	chr5	120634277	120634294	-	1	NA	promoter-TSS (NM_001195094)	promoter-TSS (NM_001195094)	-50	NM_001195094	546886	Mm.464847	NM_001195094	ENSMUSG00000094282	Cfap73	Ccdc42b|Gm5988	cilia and flagella associated protein 73	protein-coding
mm_12987.1	chr2	90885422	90885426	+	1	NA	promoter-TSS (NM_026161)	promoter-TSS (NM_026161)	-362	NM_026161	67445	Mm.258993	NM_026161	ENSMUSG00000040794	C1qtnf4	0710001E10Rik|9430004J15Rik|CTRP4	C1q and tumor necrosis factor related protein 4	protein-coding
mm_147175.1	chr18	36744452	36744460	-	1	NA	promoter-TSS (NM_011879)	promoter-TSS (NM_011879)	131	NM_010885	17991	Mm.29867	NM_010885	ENSMUSG00000014294	Ndufa2	AV000592|B8|C1-B8|CI-B8	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 2	protein-coding
mm_117297.1	chr13	67011527	67011533	-	1	NA	intron (NR_045851, intron 2 of 8)	intron (NR_045851, intron 2 of 8)	20875	NR_045851	71226	Mm.399574	NR_045851		4933433G19Rik	-	RIKEN cDNA 4933433G19 gene	ncRNA
mm_137020.1	chr17	17850020	17850051	+	1	NA	exon (NM_008215, exon 2 of 5)	exon (NM_008215, exon 2 of 5)	5153	NM_008215	15116	Mm.255701	NM_008215	ENSMUSG00000003665	Has1	HAS	hyaluronan synthase1	protein-coding
mm_40056.1	chr5	33996411	33996424	+	1	NA	5' UTR (NM_001001985, exon 1 of 3)	5' UTR (NM_001001985, exon 1 of 3)	433	NM_001001985	269642	Mm.274610	NM_001001985	ENSMUSG00000048142	Nat8l	1110038O08Rik|Shati	N-acetyltransferase 8-like	protein-coding
mm_7677.1	chr1	128589194	128589202	-	1	NA	exon (NM_009911, exon 2 of 2)	exon (NM_009911, exon 2 of 2)	3101	NM_009911	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding
mm_118299.1	chr13	113079192	113079198	-	1	NA	intron (NM_001281487, intron 7 of 11)	intron (NM_001281487, intron 7 of 11)	21786	NM_010370	14938	Mm.15510	NM_010370	ENSMUSG00000023132	Gzma	AW494114|Ctla-3|Ctla3|Hf|Hf1|SE1|TSP-1|TSP1	granzyme A	protein-coding
mm_68698.1	chr7	119620397	119620400	-	1	NA	intron (NM_054094, intron 1 of 13)	MIR|SINE|MIR	2570	NM_054094	117147	Mm.427560	NM_054094	ENSMUSG00000033533	Acsm1	Acas3|Bucs1|Macs	acyl-CoA synthetase medium-chain family member 1	protein-coding
mm_84597.1	chr9	70038044	70038052	-	1	NA	promoter-TSS (NM_028087)	promoter-TSS (NM_028087)	40	NM_028087	72077	Mm.195555	NM_028087	ENSMUSG00000032226	Gcnt3	2010013H22Rik|2210021I22Rik|2210401J11Rik	glucosaminyl (N-acetyl) transferase 3, mucin type	protein-coding
mm_63824.1	chr7	134735936	134735942	+	1	NA	intron (NM_001033420, intron 4 of 51)	(T)n|Simple_repeat|Simple_repeat	65252	NM_001033420	330662	Mm.436572	NM_001033420	ENSMUSG00000058325	Dock1	9130006G06Rik|AI854900|D630004B07Rik	dedicator of cytokinesis 1	protein-coding
mm_41957.1	chr5	105876221	105876222	+	1	NA	promoter-TSS (NM_018759)	promoter-TSS (NM_018759)	-347	NR_030777	54367	Mm.248876	NM_018759	ENSMUSG00000029290	Zfp326	5730470H14Rik|ZAN75|Znf326	zinc finger protein 326	protein-coding
mm_53936.1	chr6	4756603	4756612	-	1	NA	exon (NM_130877, exon 2 of 2)	exon (NM_130877, exon 2 of 2)	9301	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_86428.1	chr10	3859681	3859690	+	1	NA	intron (NM_001159942, intron 2 of 16)	intron (NM_001159942, intron 2 of 16)	-12982	NM_001033253	213783	Mm.150831	NM_001033253	ENSMUSG00000040624	Plekhg1	D10Ertd733e|Gm521|mKIAA1209	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	protein-coding
mm_136462.1	chr16	95349800	95349807	-	1	NA	Intergenic	Intergenic	92245	NM_001271690	16516	Mm.272239	NM_019664	ENSMUSG00000062609	Kcnj15	4930414N08Rik|AI182284|AI267127|IRKK|Kir4.2	potassium inwardly-rectifying channel, subfamily J, member 15	protein-coding
mm_14368.1	chr2	129629982	129629993	+	1	NA	exon (NM_001291022, exon 5 of 5)	exon (NM_001291022, exon 5 of 5)	36818	NM_001291022	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_118093.1	chr13	103845590	103845601	-	1	NA	exon (NM_001289475, exon 16 of 26)	exon (NM_001289475, exon 16 of 26)	74991	NM_001289473	59079	Mm.277354	NM_021563	ENSMUSG00000021709	Erbin	1700028E05Rik|Erbb2ip|mKIAA1225	Erbb2 interacting protein	protein-coding
mm_81251.1	chr9	107976904	107976914	+	1	NA	exon (NM_023738, exon 6 of 24)	exon (NM_023738, exon 6 of 24)	1342	NM_023738	74153	Mm.277125	NM_023738	ENSMUSG00000032596	Uba7	1300004C08Rik|Ube1l	ubiquitin-like modifier activating enzyme 7	protein-coding
mm_49662.1	chr6	31216903	31216936	+	1	NA	intron (NR_110469, intron 1 of 3)	CpG	1555	NR_110470	232685	Mm.443019	NM_144555	ENSMUSG00000044471	Lncpint	Lincpint|MNCb-1768|Pint|linc-Pint	long non-protein coding RNA, Trp53 induced transcript	ncRNA
mm_29803.1	chr3	127780462	127780529	-	1	NA	promoter-TSS (NM_027808)	promoter-TSS (NM_027808)	32	NM_027808	71481	Mm.158704	NM_027808	ENSMUSG00000028028	Alpk1	8430410J10Rik|LAK	alpha-kinase 1	protein-coding
mm_44907.1	chr5	35663457	35663551	-	1	NA	intron (NM_001042615, intron 6 of 6)	(TGGA)n|Simple_repeat|Simple_repeat	16276	NM_001042615	78558	Mm.274255	NM_030127	ENSMUSG00000029096	Htra3	2210021K23Rik|9530081K03Rik|Prsp|Tasp	HtrA serine peptidase 3	protein-coding
mm_36106.1	chr4	58839915	58839948	-	1	NA	intron (NM_172381, intron 19 of 48)	intron (NM_172381, intron 19 of 48)	-54211	NM_146920	258922	Mm.223327	NM_146920	ENSMUSG00000043385	Olfr267	MOR262-1	olfactory receptor 267	protein-coding
mm_94920.1	chr11	29503978	29503989	+	1	NA	exon (NM_176841, exon 30 of 32)	exon (NM_176841, exon 30 of 32)	11050	NM_026465	67939	Mm.251087	NM_026465	ENSMUSG00000032673	Prorsd1	2010316F05Rik|Ncrna00117|Prdxdd1	prolyl-tRNA synthetase domain containing 1	protein-coding
mm_71870.1	chr8	69209034	69209073	+	1	NA	promoter-TSS (NM_001013379)	promoter-TSS (NM_001013379)	7	NM_001013379	234358	Mm.334577	NM_001013379	ENSMUSG00000059897	Zfp930	-	zinc finger protein 930	protein-coding
mm_13332.1	chr2	102785933	102785943	+	1	NA	3' UTR (NM_001077514, exon 11 of 11)	3' UTR (NM_001077514, exon 11 of 11)	79500	NM_001077515	20511	Mm.267547	NM_011393	ENSMUSG00000005089	Slc1a2	1700091C19Rik|2900019G14Rik|AI159670|Eaat2|GLT-1|GLT1|MGLT1	solute carrier family 1 (glial high affinity glutamate transporter), member 2	protein-coding
mm_5583.1	chr1	39552291	39552303	-	1	NA	3' UTR (NM_001033135, exon 7 of 7)	3' UTR (NM_001033135, exon 7 of 7)	-3457	NR_028555	100217461		NR_028555	ENSMUSG00000077704	Snord89	MBII-289	small nucleolar RNA, C/D box 89	snoRNA
mm_45509.1	chr5	72504190	72504200	-	1	NA	promoter-TSS (NM_016869)	promoter-TSS (NM_016869)	13	NM_016869	53419	Mm.332425	NM_016869	ENSMUSG00000005220	Corin	AV273130|Lrp4	corin	protein-coding
mm_119700.1	chr14	53716681	53716706	+	1	NA	Intergenic	Intergenic	537236	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_135492.1	chr16	46120186	46120190	-	1	NA	promoter-TSS (NM_032465)	promoter-TSS (NM_032465)	60	NM_032465	84544	Mm.29204	NM_032465	ENSMUSG00000022657	Cd96	1700109I12Rik|Tactile	CD96 antigen	protein-coding
mm_140997.1	chr17	24885937	24885945	-	1	NA	promoter-TSS (NM_001163750)	promoter-TSS (NM_001163750)	409	NM_011956	26426	Mm.36718	NM_011956	ENSMUSG00000039183	Nubp2	D17Wsu11e	nucleotide binding protein 2	protein-coding
mm_63278.1	chr7	126763803	126763817	+	1	NA	exon (NM_011952, exon 5 of 9)	exon (NM_011952, exon 5 of 9)	-2604	NM_024228	68616	Mm.246881	NM_024228	ENSMUSG00000030703	Gdpd3	1110015E22Rik	glycerophosphodiester phosphodiesterase domain containing 3	protein-coding
mm_47672.1	chr5	127633261	127633263	-	1	NA	intron (NM_177005, intron 1 of 11)	intron (NM_177005, intron 1 of 11)	1000	NM_177005	319804	Mm.237888	NM_177005	ENSMUSG00000049971	Glt1d1	5730455A04Rik	glycosyltransferase 1 domain containing 1	protein-coding
mm_126547.1	chr15	82029204	82029213	+	1	NA	exon (NM_010247, exon 8 of 13)	exon (NM_010247, exon 8 of 13)	12839	NM_010247	14375	Mm.288809	NM_010247	ENSMUSG00000022471	Xrcc6	70kDa|G22p1|Ku70	X-ray repair complementing defective repair in Chinese hamster cells 6	protein-coding
mm_83775.1	chr9	52125472	52125483	-	1	NA	intron (NM_001162921, intron 3 of 5)	intron (NM_001162921, intron 3 of 5)	9854	NR_105750	102465150		NR_105750	ENSMUSG00000099311	Mir6244	Gm27368|mmu-mir-6244	microRNA 6244	ncRNA
mm_28539.1	chr3	92778896	92778903	-	1	NA	promoter-TSS (NM_029667)	promoter-TSS (NM_029667)	0	NM_029667	76585	Mm.291782	NM_029667	ENSMUSG00000068888	Lce1i	2310069N01Rik	late cornified envelope 1I	protein-coding
mm_9968.1	chr1	191181968	191181978	-	1	NA	intron (NM_007498, intron 1 of 3)	intron (NM_007498, intron 1 of 3)	1360	NM_007498	11910	Mm.2706	NM_007498	ENSMUSG00000026628	Atf3	LRG-21	activating transcription factor 3	protein-coding
mm_143581.1	chr17	74323884	74323886	-	1	NA	promoter-TSS (NM_024428)	promoter-TSS (NM_024428)	59	NM_024428	66310	Mm.28536	NM_024428	ENSMUSG00000024067	Dpy30	2810410M20Rik|C87842	dpy-30, histone methyltransferase complex regulatory subunit	protein-coding
mm_88352.1	chr10	75893444	75893452	+	1	NA	promoter-TSS (NM_024440)	promoter-TSS (NM_024440)	50	NM_024440	70377	Mm.275878	NM_024440	ENSMUSG00000009092	Derl3	1810006I20Rik|1810063P04Rik|IZP6|derlin-3	Der1-like domain family, member 3	protein-coding
mm_134153.1	chr16	10786470	10786499	-	1	NA	promoter-TSS (NM_001271603)	promoter-TSS (NM_001271603)	-948	NM_001271603	12703	Mm.130	NM_009896	ENSMUSG00000038037	Socs1	Cish1|Cish7|JAB|SOCS-1|SSI-1	suppressor of cytokine signaling 1	protein-coding
mm_95958.1	chr11	58790898	58790928	+	1	NA	Intergenic	L1MB3|LINE|L1	4774	NM_001011760	257917	Mm.377302	NM_001011760	ENSMUSG00000059504	Olfr314	MOR278-2	olfactory receptor 314	protein-coding
mm_33954.1	chr4	137454594	137454606	+	1	NA	exon (NM_027063, exon 2 of 2)	exon (NM_027063, exon 2 of 2)	1304	NM_027063	69380	Mm.272519	NM_027063	ENSMUSG00000041399	1700013G24Rik	AI507018	RIKEN cDNA 1700013G24 gene	protein-coding
mm_96120.1	chr11	60728482	60728502	+	1	NA	promoter-TSS (NM_001009927)	promoter-TSS (NM_001009927)	94	NM_001009927	237781	Mm.339760	NM_001009927	ENSMUSG00000018599	Mief2	AI482195|Gm11|Smcr7	mitochondrial elongation factor 2	protein-coding
mm_43170.1	chr5	127406660	127406661	+	1	NA	intron (NM_175432, intron 2 of 8)	intron (NM_175432, intron 2 of 8)	-125037	NR_038128	67351	Mm.320172	NR_038127	ENSMUSG00000087104	Tmem132cos	1700085B03Rik	transmembrane protein 132C, opposite strand	ncRNA
mm_139980.1	chr17	71800782	71800821	+	1	NA	exon (NM_001271484, exon 4 of 15)	exon (NM_001271484, exon 4 of 15)	18854	NM_030179	78785	Mm.196382	NM_030179	ENSMUSG00000024059	Clip4	1700024K14Rik|1700074B05Rik|4833417L20Rik|5830409B12Rik|Rsnl2	CAP-GLY domain containing linker protein family, member 4	protein-coding
mm_121956.1	chr14	24486967	24486976	-	1	NA	promoter-TSS (NM_001081247)	promoter-TSS (NM_001081247)	75	NM_001081247	218832	Mm.343610	NM_183157	ENSMUSG00000025280	Polr3a	9330175N20Rik|BC053071|RPC1|RPC155	polymerase (RNA) III (DNA directed) polypeptide A	protein-coding
mm_43572.1	chr5	137745752	137745797	+	1	NA	promoter-TSS (NM_023910)	promoter-TSS (NM_023910)	-195	NM_023910	78829	Mm.286399	NM_023910	ENSMUSG00000029723	Tsc22d4	0610009M14Rik|1700023B23Rik|AI415410|Thg-1pit|Tilz2	TSC22 domain family, member 4	protein-coding
mm_79367.1	chr9	54586451	54586512	+	1	NA	promoter-TSS (NM_029573)	promoter-TSS (NM_029573)	-30	NM_029573	67834	Mm.279195	NM_029573	ENSMUSG00000032279	Idh3a	1110003P10Rik|1500012E04Rik|AA407078|AI316514	isocitrate dehydrogenase 3 (NAD+) alpha	protein-coding
mm_98436.1	chr11	94938065	94938078	+	1	NA	exon (NM_007742, exon 2 of 51)	exon (NM_007742, exon 2 of 51)	1847	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_53207.1	chr6	125690616	125690624	+	1	NA	5' UTR (NM_153589, exon 1 of 26)	5' UTR (NM_153589, exon 1 of 26)	201	NM_153589	243634	Mm.333398	NM_153589	ENSMUSG00000038115	Ano2	BC033409|Tmem16b	anoctamin 2	protein-coding
mm_3741.1	chr1	155244612	155244622	+	1	NA	Intergenic	CpG	85914	NM_021433	58244	Mm.66264	NM_021433	ENSMUSG00000026470	Stx6	2310039E05Rik|2410005I16Rik|AA437559|AI415714|AI845861	syntaxin 6	protein-coding
mm_131214.1	chr16	8830094	8830104	+	1	NA	promoter-TSS (NM_001081400)	promoter-TSS (NM_001081400)	-1	NM_001081400	69053	Mm.390868	NM_001081400	ENSMUSG00000022507	1810013L24Rik	1110017P05Rik|3010002C02Rik|AA792997|AW124177|Gm19906|R74903	RIKEN cDNA 1810013L24 gene	protein-coding
mm_83891.1	chr9	55938175	55938202	-	1	NA	promoter-TSS (NM_001081341)	promoter-TSS (NM_001081341)	-73	NM_001081341	244891	Mm.86588	NM_175536	ENSMUSG00000034007	Scaper	C430017I08|D530014O03Rik|Zfp291	S phase cyclin A-associated protein in the ER	protein-coding
mm_71779.1	chr8	66472427	66472432	+	1	NA	TTS (NM_001293784)	TTS (NM_001293784)	14078	NM_025465	66282	Mm.294985	NM_025465	ENSMUSG00000025591	Tma16	1810029B16Rik	translation machinery associated 16	protein-coding
mm_10281.1	chr2	10080183	10080186	+	1	NA	promoter-TSS (NM_025280)	promoter-TSS (NM_025280)	326	NM_020615	11949	Mm.12677	NM_020615	ENSMUSG00000025781	Atp5c1	1700094F02Rik	ATP synthase, H+ transporting, mitochondrial F1 complex, gamma polypeptide 1	protein-coding
mm_11833.1	chr2	45110446	45110457	+	1	NA	promoter-TSS (NM_001289521)	promoter-TSS (NM_001289521)	-174	NM_001289521	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_2764.1	chr1	130508890	130508893	+	1	NA	Intergenic	Intergenic	-46147	NM_010016	13136	Mm.101591	NM_010016	ENSMUSG00000026399	Cd55	Daf|Daf-GPI|Daf1|GPI-DAF	CD55 molecule, decay accelerating factor for complement	protein-coding
mm_36389.1	chr4	77426987	77426988	-	1	NA	intron (NM_011211, intron 4 of 39)	intron (NM_011211, intron 4 of 39)	784908	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding
mm_133915.1	chr16	97557884	97557892	+	1	NA	intron (NM_013606, intron 12 of 13)	MTEb|LTR|ERVL-MaLR	21805	NM_013606	17858	Mm.14157	NM_013606	ENSMUSG00000023341	Mx2	AI528743|Mx-2	MX dynamin-like GTPase 2	protein-coding
mm_111001.1	chr12	78857350	78857352	-	1	NA	intron (NM_023721, intron 1 of 8)	intron (NM_023721, intron 1 of 8)	4287	NM_023721	73834	Mm.311549	NM_023721	ENSMUSG00000021114	Atp6v1d	1110004P10Rik|Atp6m|VATD|Vma8	ATPase, H+ transporting, lysosomal V1 subunit D	protein-coding
mm_140115.1	chr17	78916519	78916531	+	1	NA	promoter-TSS (NM_001177403)	promoter-TSS (NM_001177403)	26	NM_001177402	68554	Mm.391820	NM_001177402	ENSMUSG00000062691	Cebpzos	1110001A16Rik	CCAAT/enhancer binding protein (C/EBP), zeta, opposite strand	protein-coding
mm_154267.1	chr19	60771718	60771744	-	1	NA	exon (NM_010123, exon 14 of 22)	exon (NM_010123, exon 14 of 22)	2654	NR_034047	100217439		NR_034047		Snora19	MBI-51	small nucleolar RNA, H/ACA box 19	snoRNA
mm_33286.1	chr4	128808380	128808386	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-2271	NM_001081098	230761	Mm.22616	NM_001081098	ENSMUSG00000028799	Zfp362	-	zinc finger protein 362	protein-coding
mm_162555.1	chr1	171845579	171845583	-	1	NA	intron (NM_001289470, intron 2 of 8)	B4A|SINE|B4	5884	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_75285.1	chr8	41039569	41039581	-	1	NA	intron (NM_001005863, intron 5 of 13)	intron (NM_001005863, intron 5 of 13)	2356	NM_001005865	102103	Mm.149438	NM_001005863	ENSMUSG00000045636	Mtus1	AI481402|ATBP135|Atip1|B430010I23Rik|B430305I03Rik|C85752|Cctsg1-440|MD44|MTSG1|mKIAA1288	mitochondrial tumor suppressor 1	protein-coding
mm_33561.1	chr4	131873703	131873722	+	1	NA	promoter-TSS (NM_020587)	promoter-TSS (NM_020587)	73	NM_020587	57317	Mm.2478	NM_020587	ENSMUSG00000028911	Srsf4	5730499P16Rik|AW550192|MNCb-2616|SRp75|Sfrs4	serine/arginine-rich splicing factor 4	protein-coding
mm_11864.1	chr2	48949496	48949522	+	1	NA	promoter-TSS (NM_001177313)	promoter-TSS (NM_001177313)	1	NM_029924	109241	Mm.440436	NM_029924	ENSMUSG00000036792	Mbd5	9430004D19Rik|AA536666|AI426407|C030040A15Rik|Gm1630|OTTMUSG00000012483	methyl-CpG binding domain protein 5	protein-coding
mm_146776.1	chr18	20059499	20059519	-	1	NA	promoter-TSS (NM_013505)	promoter-TSS (NM_013505)	45	NM_013505	13506	Mm.280547	NM_013505	ENSMUSG00000024331	Dsc2	AW228162	desmocollin 2	protein-coding
mm_65166.1	chr7	19676825	19676866	-	1	NA	5' UTR (NM_001277944, exon 2 of 5)	5' UTR (NM_001277944, exon 2 of 5)	1096	NM_001277944	11813	Mm.28394	NM_001277944	ENSMUSG00000002992	Apoc2	apo-CII|apoC-II	apolipoprotein C-II	protein-coding
mm_17888.1	chr2	35013672	35013673	-	1	NA	exon (NM_010406, exon 24 of 41)	exon (NM_010406, exon 24 of 41)	47769	NM_010406	15139	Mm.2168	NM_010406	ENSMUSG00000026874	Hc	C5|C5a|He	hemolytic complement	protein-coding
mm_164116.1	chr15	33465150	33465150	+	1	NA	intron (NM_176073, intron 5 of 7)	intron (NM_176073, intron 5 of 7)	-59211	NR_033608	73486	Mm.483393	NM_028551	ENSMUSG00000058101	1700084J12Rik	-	ribosomal protein L7-like 1 pseudogene	pseudo
mm_138366.1	chr17	35000947	35000962	+	1	NA	promoter-TSS (NM_011690)	promoter-TSS (NM_011690)	47	NM_011690	22321	Mm.28420	NM_011690	ENSMUSG00000007029	Vars	Bat6|D17H6S56E|G7a|Vars2	valyl-tRNA synthetase	protein-coding
mm_173022.1	chrX	103037722	103037734	+	1	NA	Intergenic	Intergenic	-103505	NR_026596	331480	Mm.145294	NR_026596		Gm5126	EG331480	predicted pseudogene 5126	ncRNA
mm_33084.1	chr4	124377637	124377642	+	1	NA	Intergenic	Intergenic	108320	NR_040774	78460	Mm.452060	NR_040774		1700057H15Rik	-	RIKEN cDNA 1700057H15 gene	ncRNA
mm_35498.1	chr4	41047984	41047999	-	1	NA	5' UTR (NM_007473, exon 1 of 8)	5' UTR (NM_007473, exon 1 of 8)	145	NM_007473	11832	Mm.8728	NM_007473	ENSMUSG00000028427	Aqp7	AQP7L|AQPap	aquaporin 7	protein-coding
mm_163190.1	chr11	94991043	94991090	+	1	NA	promoter-TSS (NM_172261)	promoter-TSS (NM_172261)	-146	NM_172261	217124	Mm.229087	NM_172261	ENSMUSG00000038976	Ppp1r9b	SPL|Spn	protein phosphatase 1, regulatory subunit 9B	protein-coding
mm_68997.1	chr7	126676211	126676231	-	1	NA	intron (NM_133670, intron 1 of 6)	intron (NM_133670, intron 1 of 6)	136	NM_133670	20887	Mm.368982	NM_133670	ENSMUSG00000030711	Sult1a1	AI266890|PST|ST1A1|Stp|Stp1	sulfotransferase family 1A, phenol-preferring, member 1	protein-coding
mm_8675.1	chr1	156718947	156718973	-	1	NA	promoter-TSS (NM_145413)	promoter-TSS (NM_145413)	-50	NM_145413	215015	Mm.229107	NM_145413	ENSMUSG00000033557	Fam20b	C530043G21Rik|mKIAA0475	family with sequence similarity 20, member B	protein-coding
mm_16298.1	chr2	174289477	174289498	+	1	NA	intron (NR_002846, intron 1 of 4)	intron (NR_002846, intron 1 of 4)	5167	NM_022000	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_82690.1	chr9	22376178	22376192	-	1	NA	exon (NM_028390, exon 4 of 24)	exon (NM_028390, exon 4 of 24)	3038	NR_030448	751551		NR_030448	ENSMUSG00000076117	Mir680-2	Mirn680-2	microRNA 680-2	ncRNA
mm_133973.1	chr16	4420417	4420441	-	1	NA	promoter-TSS (NM_009624)	promoter-TSS (NM_009624)	69	NM_001291910	11515	Mm.439750	NM_009624	ENSMUSG00000005580	Adcy9	AC9|ACtp10|AW125421|D16Wsu65e|mKIAA0520	adenylate cyclase 9	protein-coding
mm_103725.1	chr11	79530550	79530565	-	1	NA	promoter-TSS (NM_010161)	promoter-TSS (NM_010161)	52	NM_146023	101488212	Mm.439665	NM_146023	ENSMUSG00000070354	Gm21975	Evi2a-evi2b	predicted gene 21975	protein-coding
mm_97574.1	chr11	78940264	78940276	+	1	NA	exon (NM_010927, exon 11 of 27)	exon (NM_010927, exon 11 of 27)	14979	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_126719.1	chr15	85336445	85336460	+	1	NA	promoter-TSS (NM_016843)	promoter-TSS (NM_016843)	71	NM_016843	54138	Mm.248906	NM_016843	ENSMUSG00000016541	Atxn10	AI325283|C77170|E46|Sca10|TEG-169|Tex169	ataxin 10	protein-coding
mm_157652.1	chrX	57326594	57326682	-	1	NA	intron (NM_152801, intron 2 of 21)	intron (NM_152801, intron 2 of 21)	12091	NM_152801	73341	Mm.261443	NM_152801	ENSMUSG00000031133	Arhgef6	1600028C08Rik|1700038J06Rik|4930592P22Rik|alpha-PIX	Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_55320.1	chr6	55173928	55173970	-	1	NA	intron (NM_009349, intron 1 of 2)	intron (NM_009349, intron 1 of 2)	1041	NM_009349	21743	Mm.299	NM_009349	ENSMUSG00000003477	Inmt	Temt	indolethylamine N-methyltransferase	protein-coding
mm_81328.1	chr9	108508296	108508327	+	1	NA	intron (NM_133794, intron 1 of 23)	intron (NM_133794, intron 1 of 23)	306	NM_133794	97541	Mm.272427	NM_133794	ENSMUSG00000032604	Qars	1110018N24Rik|1200016L19Rik|C80286|GLNRS	glutaminyl-tRNA synthetase	protein-coding
mm_97953.1	chr11	83704054	83704090	+	1	NA	promoter-TSS (NM_001081957)	promoter-TSS (NM_001081957)	16	NM_001081957	100034251	Mm.24097	NM_001081957	ENSMUSG00000069792	Wfdc17	Amwap|Gm11428|OTTMUSG00000000971	WAP four-disulfide core domain 17	protein-coding
mm_68037.1	chr7	101347985	101348014	-	1	NA	promoter-TSS (NM_001040111)	promoter-TSS (NM_001040111)	-70	NM_001040111	69710	Mm.277687	NM_027180	ENSMUSG00000032812	Arap1	2410002L19Rik|Centd2|mKIAA0782	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	protein-coding
mm_84288.1	chr9	63109310	63109338	-	1	NA	Intergenic	Intergenic	37656	NM_172446	207667	Mm.36349	NM_172446	ENSMUSG00000022245	Skor1	AV273001|C230094B15Rik|Corl1|Lbxcor1	SKI family transcriptional corepressor 1	protein-coding
mm_71432.1	chr8	46503658	46503666	+	1	NA	intron (NM_001302163, intron 2 of 20)	intron (NM_001302163, intron 2 of 20)	12696	NM_001302163	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_41648.1	chr5	98186713	98186727	+	1	NA	3' UTR (NM_029947, exon 4 of 4)	3' UTR (NM_029947, exon 4 of 4)	5851	NM_029947	77630	Mm.332511	NM_029947	ENSMUSG00000035456	Prdm8	4930565F05Rik|PFM5	PR domain containing 8	protein-coding
mm_160274.1	chr7	119690023	119690023	+	1	NA	promoter-TSS (NM_178414)	promoter-TSS (NM_178414)	-3	NM_178414	233801	Mm.240412	NM_178414	ENSMUSG00000047026	Acsm4	O-MACS|OMACS	acyl-CoA synthetase medium-chain family member 4	protein-coding
mm_107410.1	chr12	33957646	33957665	+	1	NA	promoter-TSS (NM_011658)	promoter-TSS (NM_011658)	-16	NM_011658	22160	Mm.3280	NM_011658	ENSMUSG00000035799	Twist1	M-Twist|Pde|Ska10|Ska<m10Jus>|Twist|bHLHa38|pdt	twist basic helix-loop-helix transcription factor 1	protein-coding
mm_171597.1	chr4	147702619	147702620	-	1	NA	promoter-TSS (NM_001127188)	promoter-TSS (NM_001127188)	12	NM_001127188	100503584	Mm.276881	NM_001127188	ENSMUSG00000062518	Zfp534	Gm13159|OTTMUSG00000010681	zinc finger protein 534	protein-coding
mm_104173.1	chr11	87591752	87591773	-	1	NA	promoter-TSS (NM_133215)	promoter-TSS (NM_133215)	-455	NM_133215	170749	Mm.399376	NM_133215	ENSMUSG00000018401	Mtmr4	AA596759|ESTM44|FYVE-DSP2|ZFYVE11|mKIAA0647	myotubularin related protein 4	protein-coding
mm_157802.1	chrX	73928041	73928057	-	1	NA	intron (NM_023132, intron 7 of 10)	intron (NM_023132, intron 7 of 10)	2801	NM_023132	19703	Mm.236969	NM_023132	ENSMUSG00000031387	Renbp	Age|Rnbp	renin binding protein	protein-coding
mm_83135.1	chr9	40437191	40437204	-	1	NA	intron (NM_172768, intron 1 of 19)	intron (NM_172768, intron 1 of 19)	18567	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_13038.1	chr2	91082154	91082189	+	1	NA	Intergenic	Intergenic	-11856	NM_001290765	68427	Mm.192375	NM_026721	ENSMUSG00000002105	Slc39a13	1100001L14Rik|AA387663|ZIP-13|ZIP13	solute carrier family 39 (metal ion transporter), member 13	protein-coding
mm_55520.1	chr6	70372628	70372635	-	1	NA	Intergenic	Intergenic	419544	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_167731.1	chr9	104727897	104727898	+	1	NA	intron (NM_028719, intron 2 of 15)	RMER15|LTR|ERVL	158109	NM_028719	74020	Mm.326240	NM_028719	ENSMUSG00000032564	Cpne4	3632411M23Rik|4933406O10Rik	copine IV	protein-coding
mm_34289.1	chr4	141566484	141566500	+	1	NA	Intergenic	Intergenic	20330	NR_030695	320456	Mm.32859	NM_177163		B330016D10Rik	-	RIKEN cDNA B330016D10 gene	ncRNA
mm_45369.1	chr5	66019423	66019434	-	1	NA	exon (NM_139065, exon 7 of 7)	exon (NM_139065, exon 7 of 7)	-15143	NR_027961	231253	Mm.436542	NM_177679	ENSMUSG00000054598	9130230L23Rik	-	RIKEN cDNA 9130230L23 gene	ncRNA
mm_165867.1	chr4	34730121	34730127	-	1	NA	promoter-TSS (NM_027041)	promoter-TSS (NM_027041)	82	NM_027041	69329	Mm.389548	NM_027041	ENSMUSG00000028294	Cfap206	1700003M02Rik|AU024269	cilia and flagella associated protein 206	protein-coding
mm_97325.1	chr11	76945720	76945791	+	1	NA	promoter-TSS (NM_178645)	promoter-TSS (NM_178645)	99	NM_178645	104184	Mm.399785	NM_178645	ENSMUSG00000020840	Blmh	AI035728|Bh|Bmh	bleomycin hydrolase	protein-coding
mm_76715.1	chr8	94678726	94678739	-	1	NA	intron (NM_026385, intron 2 of 3)	intron (NM_026385, intron 2 of 3)	11641	NM_024269	107566	Mm.393247	NM_024191	ENSMUSG00000031776	Arl2bp	1700010P10Rik|1700027H16Rik|6330544B05Rik|AI482273|AI849834|BART|Bart1	ADP-ribosylation factor-like 2 binding protein	protein-coding
mm_51106.1	chr6	67278218	67278220	+	1	NA	intron (NM_001113564, intron 6 of 7)	B2_Mm2|SINE|B2	11240	NM_025814	66870	Mm.240490	NM_025814	ENSMUSG00000036371	Serbp1	1200009K13Rik|9330147J08Rik|AL022786|Pairbp1	serpine1 mRNA binding protein 1	protein-coding
mm_55538.1	chr6	70777220	70777224	-	1	NA	intron (NM_009075, intron 4 of 8)	intron (NM_009075, intron 4 of 8)	14953	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_30186.1	chr3	144691393	144691423	-	1	NA	3' UTR (NM_019464, exon 9 of 9)	3' UTR (NM_019464, exon 9 of 9)	28927	NM_001282042	54673	Mm.271775	NM_019464	ENSMUSG00000037062	Sh3glb1	AA409932|AI314629|AU015566|Bif-1|mKIAA0491	SH3-domain GRB2-like B1 (endophilin)	protein-coding
mm_51384.1	chr6	77242630	77242640	+	1	NA	promoter-TSS (NM_028880)	promoter-TSS (NM_028880)	-82	NM_028880	74342	Mm.292568	NM_028880	ENSMUSG00000060780	Lrrtm1	4632401D06Rik|AW125451	leucine rich repeat transmembrane neuronal 1	protein-coding
mm_9739.1	chr1	180256295	180256305	-	1	NA	promoter-TSS (NM_001128605)	promoter-TSS (NM_001128605)	0	NM_001128605	19165	Mm.330850	NM_011183	ENSMUSG00000010609	Psen2	ALG-3|Ad4h|Alg3|PS-2|PS2|Psnl2|STM2	presenilin 2	protein-coding
mm_51135.1	chr6	68570734	68570739	+	1	NA	Intergenic	Intergenic	756438	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_42946.1	chr5	122990791	122990825	+	1	NA	intron (NR_045820, intron 1 of 2)	intron (NR_045820, intron 1 of 2)	1454	NR_045820	109202	Mm.30769	NM_175405	ENSMUSG00000056735	A930024E05Rik	-	RIKEN cDNA A930024E05 gene	ncRNA
mm_107794.1	chr12	62687770	62687772	+	1	NA	promoter-TSS (NR_131949)	promoter-TSS (NR_131949)	-16	NR_131949	73309	Mm.276558	NR_131949		Spanxn4	1700047L15Rik	SPANX family, member N4	ncRNA
mm_53653.1	chr6	141249985	141249998	+	1	NA	exon (NM_018779, exon 1 of 16)	exon (NM_018779, exon 1 of 16)	722	NM_018779	54611	Mm.103728	NM_018779	ENSMUSG00000041741	Pde3a	A930022O17Rik|C87899	phosphodiesterase 3A, cGMP inhibited	protein-coding
mm_40627.1	chr5	64821916	64821930	+	1	NA	exon (NM_008453, exon 3 of 6)	exon (NM_008453, exon 3 of 6)	18400	NM_008453	16599	Mm.392759	NM_008453	ENSMUSG00000029178	Klf3	9930027G08Rik|AL024007|Bklf|Tef-2	Kruppel-like factor 3 (basic)	protein-coding
mm_36568.1	chr4	87806297	87806325	-	1	NA	promoter-TSS (NM_029931)	promoter-TSS (NM_029931)	12	NM_001286158	70122	Mm.288898	NM_027326	ENSMUSG00000028496	Mllt3	2210011H10Rik|2610012I03Rik|3830408D16Rik|Af9|D4Ertd321e	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 3	protein-coding
mm_154273.1	chr19	60776653	60776713	-	1	NA	exon (NM_010123, exon 7 of 22)	exon (NM_010123, exon 7 of 22)	-2286	NR_037245	100526521		NR_037245	ENSMUSG00000104890	Mir3084-1	Mir3084|mmu-mir-3084|mmu-mir-3084-1	microRNA 3084-1	ncRNA
mm_172881.1	chr9	48975076	48975080	-	1	NA	Intergenic	RMER19B|LTR|ERVK	-10088	NM_020274	57014	Mm.117131	NM_020274	ENSMUSG00000008590	Htr3b	5-HT3B	5-hydroxytryptamine (serotonin) receptor 3B	protein-coding
mm_53723.1	chr6	144672877	144672889	+	1	NA	promoter-TSS (NR_040519)	promoter-TSS (NR_040519)	15	NR_040519	66760	Mm.233631	NR_040519	ENSMUSG00000085785	Sox5os3	4933425H06Rik	SRY (sex determining region Y)-box 5, opposite strand 3	ncRNA
mm_55548.1	chr6	71201669	71201691	-	1	NA	exon (NM_017399, exon 2 of 4)	exon (NM_017399, exon 2 of 4)	1792	NM_017399	14080	Mm.22126	NM_017399	ENSMUSG00000054422	Fabp1	Fabpl|L-FABP	fatty acid binding protein 1, liver	protein-coding
mm_116762.1	chr13	52572588	52572631	-	1	NA	intron (NR_046069, intron 1 of 3)	intron (NR_046069, intron 1 of 3)	616	NR_046069	100040572	Mm.278873	NR_046069		Gm2848	-	predicted gene 2848	ncRNA
mm_60825.1	chr7	45706192	45706220	+	1	NA	intron (NM_016974, intron 1 of 3)	intron (NM_016974, intron 1 of 3)	959	NM_016974	13170	Mm.24222	NM_016974	ENSMUSG00000059824	Dbp	-	D site albumin promoter binding protein	protein-coding
mm_27841.1	chr3	79154789	79154792	-	1	NA	Intergenic	Intergenic	-8915	NM_001099624	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_28021.1	chr3	83046076	83046081	-	1	NA	exon (NM_181849, exon 3 of 8)	exon (NM_181849, exon 3 of 8)	3785	NM_181849	110135	Mm.30063	NM_181849	ENSMUSG00000033831	Fgb	2510049G14Rik	fibrinogen beta chain	protein-coding
mm_127521.1	chr15	102029882	102029893	+	1	NA	exon (NM_010664, exon 3 of 7)	exon (NM_010664, exon 3 of 7)	1671	NM_010664	16668	Mm.22479	NM_010664	ENSMUSG00000023043	Krt18	CK18|K18|Krt1-18	keratin 18	protein-coding
mm_77073.1	chr8	110142720	110142762	-	1	NA	3' UTR (NM_007586, exon 11 of 11)	3' UTR (NM_007586, exon 11 of 11)	25465	NM_007586	12308	Mm.2755	NM_007586	ENSMUSG00000003657	Calb2	CR	calbindin 2	protein-coding
mm_19575.1	chr2	101643730	101643741	-	1	NA	exon (NM_009019, exon 2 of 2)	exon (NM_009019, exon 2 of 2)	5797	NM_009019	19373	Mm.828	NM_009019	ENSMUSG00000061311	Rag1	Rag-1	recombination activating gene 1	protein-coding
mm_92955.1	chr10	85539512	85539524	-	1	NA	intron (NM_028709, intron 1 of 16)	intron (NM_028709, intron 1 of 16)	-58893	NM_001017525	74007	Mm.36544	NM_028709	ENSMUSG00000020042	Btbd11	6330404E16Rik	BTB (POZ) domain containing 11	protein-coding
mm_114260.1	chr13	56747968	56747979	+	1	NA	Intergenic	L2c|LINE|L2	44305	NM_001164042	17129	Mm.272920	NM_008541	ENSMUSG00000021540	Smad5	1110051M15Rik|AI451355|Dwf-C|Madh5|MusMLP	SMAD family member 5	protein-coding
mm_32760.1	chr4	116687842	116687848	+	1	NA	intron (NM_011034, intron 2 of 5)	B2_Mm1a|SINE|B2	-1823	NR_040442	100502959	Mm.395400	NR_040442		AV051173	-	expressed sequence AV051173	ncRNA
mm_58494.1	chr7	3704026	3704051	+	1	NA	promoter-TSS (NM_029767)	promoter-TSS (NM_029767)	-3	NM_029767	76846	Mm.13944	NM_029767	ENSMUSG00000006333	Rps9	3010033P07Rik|AL022771|AL022885	ribosomal protein S9	protein-coding
mm_125682.1	chr15	66700957	66700961	+	1	NA	intron (NM_009375, intron 20 of 47)	MIRb|SINE|MIR	30189	NM_009375	21819	Mm.441333	NM_009375	ENSMUSG00000053469	Tg	Tgn|cog	thyroglobulin	protein-coding
mm_23886.1	chr3	83031194	83031212	+	1	NA	exon (NM_010196, exon 5 of 5)	exon (NM_010196, exon 5 of 5)	5050	NM_001111048	14161	Mm.88793	NM_010196	ENSMUSG00000028001	Fga	ENSMUSG00000059807|Fib	fibrinogen alpha chain	protein-coding
mm_113300.1	chr13	30748663	30748685	+	1	NA	promoter-TSS (NM_013674)	promoter-TSS (NM_013674)	-559	NM_001347508	16364	Mm.4677	NM_013674	ENSMUSG00000021356	Irf4	AI385587|IRF-4|LSIRF|NF-EM5|Spip	interferon regulatory factor 4	protein-coding
mm_143804.1	chr17	83514312	83514335	-	1	NA	promoter-TSS (NM_001159529)	promoter-TSS (NM_001159529)	10	NM_009187	20463	Mm.30072	NM_009187	ENSMUSG00000024248	Cox7a2l	COX7AR|COX7RP|EB1|SIG-81|SIG81|Silg81	cytochrome c oxidase subunit VIIa polypeptide 2-like	protein-coding
mm_1573.1	chr1	74263734	74263794	+	1	NA	exon (NM_029711, exon 8 of 10)	exon (NM_029711, exon 8 of 10)	-14836	NM_174985	227289	Mm.246587	NM_174985	ENSMUSG00000064272	Gpbar1	BG37|GPCR|GPR131|M-BAR|TGR5	G protein-coupled bile acid receptor 1	protein-coding
mm_103659.1	chr11	78984937	78984943	-	1	NA	promoter-TSS (NM_010708)	promoter-TSS (NM_010708)	-16	NM_010708	16859	Mm.341434	NM_010708	ENSMUSG00000001123	Lgals9	AA407335|AI194909|AI265545|LGALS35|Lgals5|gal-9|galectin-9	lectin, galactose binding, soluble 9	protein-coding
mm_127396.1	chr15	101128928	101128948	+	1	NA	5' UTR (NM_001277259, exon 2 of 12)	5' UTR (NM_001277259, exon 2 of 12)	416	NM_001277257	11482	Mm.279542	NM_009612	ENSMUSG00000000530	Acvrl1	AI115505|AI427544|Acvrlk1|Alk1	activin A receptor, type II-like 1	protein-coding
mm_47192.1	chr5	120756963	120756977	-	1	NA	exon (NM_145226, exon 13 of 16)	exon (NM_145226, exon 13 of 16)	-7122	NM_001347448	246728	Mm.260926	NM_145227	ENSMUSG00000032690	Oas2	Oasl11	2'-5' oligoadenylate synthetase 2	protein-coding
mm_125798.1	chr15	74835795	74835805	+	1	NA	exon (NM_001033229, exon 9 of 9)	exon (NM_001033229, exon 9 of 9)	5843	NM_001033229	110115	Mm.322606	NM_001033229	ENSMUSG00000075604	Cyp11b1	AA389061|CPN1|Cyp11b|Cyp11b-1|FHI	cytochrome P450, family 11, subfamily b, polypeptide 1	protein-coding
mm_44300.1	chr5	8995740	8995744	-	1	NA	intron (NM_023733, intron 2 of 17)	intron (NM_023733, intron 2 of 17)	1404	NM_023733	74114	Mm.28197	NM_023733	ENSMUSG00000003623	Crot	1200003H03Rik	carnitine O-octanoyltransferase	protein-coding
mm_79179.1	chr9	48314425	48314443	+	1	NA	Intergenic	L1MB2|LINE|L1	26464	NM_030069	78252	Mm.31626	NM_030069	ENSMUSG00000032028	Nxpe2	4432416J03Rik|AI323362|Fam55b	neurexophilin and PC-esterase domain family, member 2	protein-coding
mm_54462.1	chr6	34878007	34878078	-	1	NA	promoter-TSS (NM_001135611)	promoter-TSS (NM_001135611)	23	NM_199145	78412	Mm.248440	NM_199145	ENSMUSG00000046806	3110062M04Rik	AL023049|Mri	RIKEN cDNA 3110062M04 gene	protein-coding
mm_83160.1	chr9	40465742	40465764	-	1	NA	Intergenic	Intergenic	-9989	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_60126.1	chr7	36711898	36711902	+	1	NA	intron (NM_172298, intron 1 of 1)	intron (NM_172298, intron 1 of 1)	13782	NM_172298	243931	Mm.44141	NM_172298	ENSMUSG00000021217	Tshz3	A630038G13Rik|Tsh3|Zfp537|mKIAA1474|teashirt3	teashirt zinc finger family member 3	protein-coding
mm_172267.1	chr6	77763379	77763393	-	1	NA	intron (NM_001109764, intron 3 of 19)	B1_Mm|SINE|Alu	216281	NM_145732	12386	Mm.34637	NM_009819	ENSMUSG00000063063	Ctnna2	AI481747|Catna|Catna2|cdf|chp	catenin (cadherin associated protein), alpha 2	protein-coding
mm_86111.1	chr9	115310865	115310877	-	1	NA	promoter-TSS (NM_024222)	promoter-TSS (NM_024222)	-450	NM_024222	68292	Mm.296158	NM_024222	ENSMUSG00000032437	Stt3b	1300006C19Rik|Simp	STT3, subunit of the oligosaccharyltransferase complex, homolog B (S. cerevisiae)	protein-coding
mm_54817.1	chr6	42351292	42351300	-	1	NA	exon (NM_011777, exon 4 of 10)	exon (NM_011777, exon 4 of 10)	1468	NM_001289619	22793	Mm.282303	NM_011777	ENSMUSG00000029860	Zyx	9530098H06Rik|R75157	zyxin	protein-coding
mm_166541.1	chr6	34179190	34179200	+	1	NA	Intergenic	Intergenic	-2141	NM_021435	58246	Mm.245527	NM_021435	ENSMUSG00000018999	Slc35b4	4930474D06Rik|AB041549|AW494345	solute carrier family 35, member B4	protein-coding
mm_91715.1	chr10	44441224	44441257	-	1	NA	exon (NM_007548, exon 5 of 7)	exon (NM_007548, exon 5 of 7)	17508	NM_007548	12142	Mm.4800	NM_007548	ENSMUSG00000038151	Prdm1	Blimp-1|Blimp1|PRDI-BF1|ZNFPR1A1|b2b1765Clo	PR domain containing 1, with ZNF domain	protein-coding
mm_94498.1	chr11	7145058	7145088	+	1	NA	exon (NM_009622, exon 10 of 20)	exon (NM_009622, exon 10 of 20)	43496	NR_045101	100041347	Mm.300962	NR_045101	ENSMUSG00000087512	Gm11985	OTTMUSG00000005133	predicted gene 11985	ncRNA
mm_28712.1	chr3	95653719	95653725	-	1	NA	Intergenic	Intergenic	-4999	NM_008562	17210	Mm.1639	NM_008562	ENSMUSG00000038612	Mcl1	AW556805|Mcl-1	myeloid cell leukemia sequence 1	protein-coding
mm_55298.1	chr6	54760247	54760273	-	1	NA	Intergenic	Intergenic	-56656	NM_199143	387524	Mm.286149	NM_199143	ENSMUSG00000058446	Znrf2	1190002C14Rik|AU044205|D6Ertd365e	zinc and ring finger 2	protein-coding
mm_4835.1	chr1	186587480	186587492	+	1	NA	Intergenic	MIR|SINE|MIR	-28805	NR_131158	320449	Mm.404477	NR_131124	ENSMUSG00000103690	A730004F24Rik	-	RIKEN cDNA A730004F24 gene	ncRNA
mm_94319.1	chr11	4236824	4236837	+	1	NA	promoter-TSS (NM_001013365)	promoter-TSS (NM_001013365)	45	NM_001013365	18413	Mm.131422	NM_001013365	ENSMUSG00000058755	Osm	OncoM	oncostatin M	protein-coding
mm_7139.1	chr1	91063240	91063256	-	1	NA	intron (NM_001310732, intron 1 of 24)	intron (NM_001310732, intron 1 of 24)	9804	NM_008515	16978	Mm.45039	NM_008515	ENSMUSG00000026305	Lrrfip1	AU024550|Fliiap1	leucine rich repeat (in FLII) interacting protein 1	protein-coding
mm_44516.1	chr5	24351073	24351116	-	1	NA	intron (NM_013569, intron 1 of 14)	intron (NM_013569, intron 1 of 14)	510	NM_013569	16511	Mm.6539	NM_013569	ENSMUSG00000038319	Kcnh2	AI326795|ERG1|LQT|Lqt2|M-erg|Merg1|merg1a|merg1b	potassium voltage-gated channel, subfamily H (eag-related), member 2	protein-coding
mm_95001.1	chr11	31872935	31872987	+	1	NA	exon (NM_026252, exon 1 of 10)	exon (NM_026252, exon 1 of 10)	2021	NM_026252	67579	Mm.339792	NM_026252	ENSMUSG00000020300	Cpeb4	Cpe-bp4|Cpeb-4|mCPEB-4	cytoplasmic polyadenylation element binding protein 4	protein-coding
mm_115406.1	chr13	114113565	114113568	+	1	NA	intron (NM_172595, intron 4 of 4)	intron (NM_172595, intron 4 of 4)	38026	NR_045836	319803	Mm.386896	NM_177004		A430090L17Rik	-	RIKEN cDNA A430090L17 gene	ncRNA
mm_92866.1	chr10	81627517	81627527	-	1	NA	promoter-TSS (NM_001163430)	promoter-TSS (NM_001163430)	86	NM_181586	50721	Mm.25643	NM_181586	ENSMUSG00000034748	Sirt6	2810449N18Rik|AI043036|Sir2l6	sirtuin 6	protein-coding
mm_110142.1	chr12	26448376	26448389	-	1	NA	intron (NM_021384, intron 4 of 5)	intron (NM_021384, intron 4 of 5)	8070	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_154552.1	chrM	15076	15100	-	1	NA	NA	Intergenic	NA	NA								
mm_131414.1	chr16	14705576	14705590	+	1	NA	promoter-TSS (NM_011415)	promoter-TSS (NM_011415)	-276	NM_011415	20583	Mm.4272	NM_011415	ENSMUSG00000022676	Snai2	Slug|Slugh|Snail2	snail family zinc finger 2	protein-coding
mm_48285.1	chr5	138171845	138171887	-	1	NA	promoter-TSS (NM_008568)	promoter-TSS (NM_008568)	-4	NM_008568	17220	Mm.378965	NM_008568	ENSMUSG00000029730	Mcm7	AI747533|Mcmd7|mCDC47	minichromosome maintenance complex component 7	protein-coding
mm_2896.1	chr1	131932020	131932037	+	1	NA	3' UTR (NM_001145804, exon 7 of 7)	3' UTR (NM_001145804, exon 7 of 7)	21570	NM_001145804	98415	Mm.246869	NM_175294	ENSMUSG00000026434	Nucks1	2700010L10Rik|8430423A01Rik|AI647518|C78391|Nucks	nuclear casein kinase and cyclin-dependent kinase substrate 1	protein-coding
mm_46440.1	chr5	105078515	105078544	-	1	NA	3' UTR (NM_172777, exon 11 of 11)	3' UTR (NM_172777, exon 11 of 11)	-24968	NM_029509	76074	Mm.458519	NM_029509	ENSMUSG00000034438	Gbp8	5830443L24Rik|mGBP8	guanylate-binding protein 8	protein-coding
mm_100589.1	chr11	120955325	120955360	+	1	NA	exon (NM_001038654, exon 2 of 5)	exon (NM_001038654, exon 2 of 5)	6275	NM_001038654	80879	Mm.28632	NM_030696	ENSMUSG00000025161	Slc16a3	Mct3|Mct4	solute carrier family 16 (monocarboxylic acid transporters), member 3	protein-coding
mm_94937.1	chr11	29707284	29707295	+	1	NA	exon (NM_194051, exon 3 of 9)	exon (NM_194051, exon 3 of 9)	-11274	NM_024226	68585	Mm.192580	NM_024226	ENSMUSG00000020458	Rtn4	1110020G17Rik|AA407876|AA409940|AA960376|ASY|C130026I10Rik|NOGO|NSP-CL|NgA|Nogo-A|Nogo-B|Nogo-C|mKIAA0886|mKIAA4153	reticulon 4	protein-coding
mm_76978.1	chr8	106769264	106769269	-	1	NA	intron (NM_173037, intron 14 of 17)	intron (NM_173037, intron 14 of 17)	86198	NM_173037	272538	Mm.87151	NM_173037	ENSMUSG00000041949	Tango6	AW413431|E330010G16|Tmco7	transport and golgi organization 6	protein-coding
mm_64045.1	chr7	140835189	140835189	+	1	NA	promoter-TSS (NM_029821)	promoter-TSS (NM_029821)	51	NM_001347605	76974	Mm.272359	NM_029821	ENSMUSG00000025481	Urah	1190003J15Rik|2810420C16Rik	urate (5-hydroxyiso-) hydrolase	protein-coding
mm_51128.1	chr6	68302409	68302410	+	1	NA	Intergenic	Intergenic	-736710	NR_003100	75070	Mm.463364	NR_003100		4930515G16Rik	-	myc induced nuclear antigen pseudogene	pseudo
mm_73025.1	chr8	94152993	94153004	+	1	NA	intron (NM_013603, intron 1 of 2)	intron (NM_013603, intron 1 of 2)	391	NM_013603	17751	Mm.2064	NM_013603	ENSMUSG00000031760	Mt3	Mt-3	metallothionein 3	protein-coding
mm_66896.1	chr7	59922607	59922624	-	1	NA	Intergenic	Intergenic	51816	NR_015456	52480	Mm.482346	NR_015456	ENSMUSG00000100826	Snhg14	AU018661|D7Ertd715e|Lncat	small nucleolar RNA host gene 14	ncRNA
mm_19417.1	chr2	91929869	91929890	-	1	NA	TTS (NM_007699)	TTS (NM_007699)	1823	NM_001291481	17242	Mm.906	NM_010784	ENSMUSG00000027239	Mdk	MK|Mek	midkine	protein-coding
mm_34754.1	chr4	152330054	152330072	+	1	NA	exon (NM_001277114, exon 3 of 4)	exon (NM_001277114, exon 3 of 4)	4337	NR_102291	19934	Mm.307846	NM_009079	ENSMUSG00000028936	Rpl22	2700038K18Rik	ribosomal protein L22	protein-coding
mm_86697.1	chr10	18469959	18469974	+	1	NA	promoter-TSS (NM_001163592)	promoter-TSS (NM_001163592)	-15	NM_001163592	215819	Mm.297971	NM_173390	ENSMUSG00000039835	Nhsl1	5730409E15Rik|A630035H13Rik|A730096F01|BC013565|D10Bwg0940e|mKIAA1357	NHS-like 1	protein-coding
mm_123711.1	chr14	69815909	69815921	-	1	NA	Intergenic	Intergenic	-10370	NM_153514	246710	Mm.102367	NM_153514	ENSMUSG00000022075	Rhobtb2	Dbc2|E130206H14Rik|mKIAA0717	Rho-related BTB domain containing 2	protein-coding
mm_48316.1	chr5	138977004	138977055	-	1	NA	TTS (NM_008808)	TTS (NM_008808)	17924	NM_008808	18590	Mm.2675	NM_008808	ENSMUSG00000025856	Pdgfa	-	platelet derived growth factor, alpha	protein-coding
mm_47323.1	chr5	122471208	122471256	-	1	NA	exon (NM_009722, exon 7 of 21)	exon (NM_009722, exon 7 of 21)	30993	NM_001110140	11938	Mm.227583	NM_009722	ENSMUSG00000029467	Atp2a2	9530097L16Rik|D5Wsu150e|SERCA2|SERCA2B|Serca2a|mKIAA4195	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	protein-coding
mm_82310.1	chr9	7872887	7872909	-	1	NA	5' UTR (NM_007464, exon 1 of 9)	5' UTR (NM_007464, exon 1 of 9)	272	NM_007464	11796	Mm.2026	NM_007464	ENSMUSG00000032000	Birc3	AW107670|Api1|Api2|Birc2|C-IAP2|HIAP2|IAP1|IAP2|MIAP1|MIAP2|MIHB|MIHC|RNF49|cIAP-1|cIAP-2|cIAP1|cIAP2	baculoviral IAP repeat-containing 3	protein-coding
mm_36778.1	chr4	102959666	102959673	-	1	NA	intron (NM_001285852, intron 20 of 25)	RMER17C|LTR|ERVK	-26710	NM_001163767	67344	Mm.111346	NM_026100	ENSMUSG00000028523	Tctex1d1	1700055O19Rik	Tctex1 domain containing 1	protein-coding
mm_139468.1	chr17	55961598	55961610	+	1	NA	intron (NM_028381, intron 2 of 7)	ORR1C2|LTR|ERVL-MaLR	-2203	NR_108021	100504333	Mm.391908	NR_108021	ENSMUSG00000097077	Gm16712	-	predicted gene, 16712	ncRNA
mm_138710.1	chr17	36043824	36043839	+	1	NA	intron (NM_001034909, intron 1 of 2)	intron (NM_001034909, intron 1 of 2)	870	NM_001034909	547347	Mm.484641	NM_001034909	ENSMUSG00000073407	Gm6034	EG547347|H2-gs14-2	predicted gene 6034	protein-coding
mm_91584.1	chr10	40233371	40233383	-	1	NA	intron (NM_001042556, intron 6 of 9)	intron (NM_001042556, intron 6 of 9)	13602	NM_001042556	67239	Mm.11480	NM_023323	ENSMUSG00000038510	Rpf2	2810470K21Rik|AU040229|AU043242|Bxdc1	ribosome production factor 2 homolog	protein-coding
mm_163865.1	chr14	19418933	19418981	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	183630	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_76718.1	chr8	94802464	94802464	-	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	-7989	NM_011332	20295	Mm.41988	NM_011332	ENSMUSG00000031780	Ccl17	Abcd-2|Scya17|Scya17l|Tarc	chemokine (C-C motif) ligand 17	protein-coding
mm_36817.1	chr4	104853776	104853788	-	1	NA	exon (NM_146148, exon 6 of 11)	exon (NM_146148, exon 6 of 11)	22616	NM_001290645	230558	Mm.197638	NM_146148	ENSMUSG00000035031	C8a	-	complement component 8, alpha polypeptide	protein-coding
mm_54444.1	chr6	34423115	34423138	-	1	NA	TTS (NM_009731)	TTS (NM_009731)	10764	NM_009731	11997	Mm.482073	NM_009731	ENSMUSG00000052131	Akr1b7	AR|Avdp|MVDP	aldo-keto reductase family 1, member B7	protein-coding
mm_47708.1	chr5	129918371	129918380	-	1	NA	Intergenic	Intergenic	9835	NM_026916	69034	Mm.211372	NM_026916	ENSMUSG00000095789	Nupr1l	1810010E01Rik|4930579G22Rik|Nupr2	nuclear protein transcriptional regulator 1 like	protein-coding
mm_146985.1	chr18	33891995	33892029	-	1	NA	intron (NM_013512, intron 3 of 23)	intron (NM_013512, intron 3 of 23)	97120	NR_038151	69749	Mm.248787	NR_038151	ENSMUSG00000087590	Epb41l4aos	2410004N09Rik|Epb4.1l4aos	erythrocyte membrane protein band 4.1 like 4a, opposite strand	ncRNA
mm_117331.1	chr13	68999283	68999336	-	1	NA	5' UTR (NM_153534, exon 1 of 25)	5' UTR (NM_153534, exon 1 of 25)	232	NM_153534	210044	Mm.390617	NM_153534	ENSMUSG00000021536	Adcy2	mKIAA1060	adenylate cyclase 2	protein-coding
mm_114829.1	chr13	92355140	92355176	+	1	NA	promoter-TSS (NM_010829)	promoter-TSS (NM_010829)	-155	NM_010829	17686	Mm.343101	NM_010829	ENSMUSG00000014850	Msh3	D13Em1|Rep-3|Rep3	mutS homolog 3	protein-coding
mm_87790.1	chr10	60298207	60298216	+	1	NA	intron (NM_011179, intron 8 of 14)	intron (NM_011179, intron 8 of 14)	13750	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_163313.1	chr12	5892070	5892084	+	1	NA	Intergenic	Intergenic	515575	NR_015579	72669	Mm.10434	NM_028318		2810032G03Rik	AI461720	RIKEN cDNA 2810032G03 gene	ncRNA
mm_133513.1	chr16	90738509	90738519	+	1	NA	5' UTR (NM_029844, exon 1 of 3)	5' UTR (NM_029844, exon 1 of 3)	190	NM_029844	77037	Mm.22455	NM_029844	ENSMUSG00000039956	Mrap	1110025G12Rik|Falp|ORF61	melanocortin 2 receptor accessory protein	protein-coding
mm_171975.1	chr5	89203927	89203949	-	1	NA	intron (NM_001197147, intron 18 of 25)	RLTRETN_Mm|LTR|ERVK	253960	NM_008096	14473	Mm.196595	NM_008096	ENSMUSG00000035540	Gc	DBP|VDB	group specific component	protein-coding
mm_37729.1	chr4	129572376	129572385	-	1	NA	intron (NM_001162433, intron 1 of 12)	intron (NM_001162433, intron 1 of 12)	1261	NM_001162433	16818	Mm.293753	NM_010693	ENSMUSG00000000409	Lck	Hck-3|Lsk|Lskt|p56<lck>|p56Lck	lymphocyte protein tyrosine kinase	protein-coding
mm_42947.1	chr5	122990856	122990864	+	1	NA	intron (NR_045820, intron 1 of 2)	ID2|SINE|ID	1506	NR_045820	109202	Mm.30769	NM_175405	ENSMUSG00000056735	A930024E05Rik	-	RIKEN cDNA A930024E05 gene	ncRNA
mm_171069.1	chr3	115745286	115745295	+	1	NA	Intergenic	Intergenic	-30235	NM_007901	13609	Mm.982	NM_007901	ENSMUSG00000045092	S1pr1	AI849002|Edg1|Lpb1|S1p|S1p1	sphingosine-1-phosphate receptor 1	protein-coding
mm_109835.1	chr12	4233715	4233738	-	1	NA	promoter-TSS (NM_001204912)	promoter-TSS (NM_001204912)	-301	NM_001204912	69709	Mm.250552	NM_001204912	ENSMUSG00000096199	Ptrhd1	2410017P09Rik	peptidyl-tRNA hydrolase domain containing 1	protein-coding
mm_161423.1	chr15	39437004	39437004	+	1	NA	exon (NM_053271, exon 6 of 27)	exon (NM_053271, exon 6 of 27)	-222507	NM_001256384	116838	Mm.309296	NM_053271	ENSMUSG00000037386	Rims2	2810036I15Rik|AW048769|RIM2|Rab3ip2|Rim2(+40A)|Rim2(+44A)|Rim2(+4A)|Serg2|Syt3-rs|mKIAA0751	regulating synaptic membrane exocytosis 2	protein-coding
mm_29340.1	chr3	108217687	108217717	-	1	NA	exon (NM_008596, exon 4 of 6)	exon (NM_008596, exon 4 of 6)	-7175	NM_175183	72522	Mm.187326	NM_175183	ENSMUSG00000048997	Atxn7l2	2610528J18Rik	ataxin 7-like 2	protein-coding
mm_18856.1	chr2	75679393	75679405	-	1	NA	exon (NM_010902, exon 2 of 5)	exon (NM_010902, exon 2 of 5)	20109	NR_033513	627828	Mm.459502	NR_033513	ENSMUSG00000092086	Gm6793	EG627828	heterogeneous nuclear ribonucleoprotein A3 pseudogene	pseudo
mm_127688.1	chr15	102972230	102972235	+	1	NA	TTS (NM_010462)	TTS (NM_010462)	-1118	NR_029722	723958		NR_029722	ENSMUSG00000065488	Mir196a-2	Mirn196a-2|mir-196a-2	microRNA 196a-2	ncRNA
mm_116340.1	chr13	38503466	38503500	-	1	NA	exon (NM_145367, exon 9 of 10)	exon (NM_145367, exon 9 of 10)	24431	NM_001289599	105245	Mm.28622	NM_145367	ENSMUSG00000038991	Txndc5	AL022641|ERp46|PC-TRP	thioredoxin domain containing 5	protein-coding
mm_128475.1	chr15	50889217	50889259	-	1	NA	promoter-TSS (NR_035444)	promoter-TSS (NR_035444)	-124	NR_035444	100316685		NR_035444	ENSMUSG00000084458	Mir1907	Mirn1907|mmu-mir-1907	microRNA 1907	ncRNA
mm_5557.1	chr1	38665593	38665599	-	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	-38352	NM_001290814	16764	Mm.336679	NM_010678	ENSMUSG00000037138	Aff3	3222402O04Rik|A730046J16|LAF-4|Laf4	AF4/FMR2 family, member 3	protein-coding
mm_143115.1	chr17	57207364	57207374	-	1	NA	exon (NM_009778, exon 35 of 41)	exon (NM_009778, exon 35 of 41)	9859	NR_105944	102465591		NR_105944	ENSMUSG00000099066	Mir6978	Gm27858|mmu-mir-6978	microRNA 6978	ncRNA
mm_140091.1	chr17	75465601	75465625	+	1	NA	promoter-TSS (NM_207246)	promoter-TSS (NM_207246)	75	NM_207246	240168	Mm.329203	NM_207246	ENSMUSG00000071042	Rasgrp3	BC066069|Gm327	RAS, guanyl releasing protein 3	protein-coding
mm_149018.1	chr19	8741795	8741811	+	1	NA	promoter-TSS (NM_019829)	promoter-TSS (NM_019829)	0	NM_019829	56389	Mm.153061	NM_019829	ENSMUSG00000010110	Stx5a	0610031F24Rik|D19Ertd627e|Stx5	syntaxin 5A	protein-coding
mm_166814.1	chr7	16372229	16372246	-	1	NA	intron (NM_001285892, intron 2 of 8)	MTD-int|LTR|ERVL-MaLR	15659	NM_001285892	56459	Mm.258530	NM_019748	ENSMUSG00000052833	Sae1	2400010M20Rik|2610044L12Rik|AL033372|AOS1|AW743391|D7Ertd177e|HSPC140|Sua1|Uble1a	SUMO1 activating enzyme subunit 1	protein-coding
mm_101999.1	chr11	51262989	51263012	-	1	NA	promoter-TSS (NM_177567)	promoter-TSS (NM_177567)	-49	NM_177567	193286	Mm.80975	NM_177567	ENSMUSG00000045942	BC049762	4930503F14	cDNA sequence BC049762	protein-coding
mm_83284.1	chr9	43106156	43106168	-	1	NA	promoter-TSS (NM_027144)	promoter-TSS (NM_027144)	-444	NM_027144	69632	Mm.275266	NM_027144	ENSMUSG00000059495	Arhgef12	2310014B11Rik|AU019857|Larg|mKIAA0382	Rho guanine nucleotide exchange factor (GEF) 12	protein-coding
mm_39227.1	chr4	156200838	156200846	-	1	NA	promoter-TSS (NM_015783)	promoter-TSS (NM_015783)	-24	NM_015783	100038882	Mm.4950	NM_015783	ENSMUSG00000035692	Isg15	G1p2|IGI15|IP17|Irfp|UCRP	ISG15 ubiquitin-like modifier	protein-coding
mm_137801.1	chr17	29774586	29774590	+	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	-57571	NM_001163741	68597	Mm.390979	NM_026782	ENSMUSG00000024018	Ccdc167	1110021J02Rik	coiled-coil domain containing 167	protein-coding
mm_126283.1	chr15	79212757	79212766	+	1	NA	intron (NR_029470, intron 4 of 4)	intron (NR_029470, intron 4 of 4)	-16412	NM_008837	18693	Mm.259464	NM_008837	ENSMUSG00000068206	Pick1	Prkcabp	protein interacting with C kinase 1	protein-coding
mm_154813.1	chrX	13661355	13661366	+	1	NA	promoter-TSS (NM_175669)	promoter-TSS (NM_175669)	-3	NM_175669	319200	Mm.383294	NM_175669	ENSMUSG00000047678	Gpr82	-	G protein-coupled receptor 82	protein-coding
mm_113150.1	chr13	24761551	24761594	+	1	NA	intron (NM_020567, intron 1 of 6)	CpG	365	NM_020567	57441	Mm.12239	NM_020567	ENSMUSG00000006715	Gmnn	AW546347|Gem	geminin	protein-coding
mm_13799.1	chr2	118926556	118926575	+	1	NA	promoter-TSS (NM_028117)	promoter-TSS (NM_028117)	68	NM_028117	72136	Mm.486238	NM_028117	ENSMUSG00000074916	Chst14	2600016L03Rik|D4ST-1|D4st1	carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 14	protein-coding
mm_74287.1	chr8	125734530	125734553	+	1	NA	intron (NM_001310688, intron 1 of 3)	intron (NM_001310688, intron 1 of 3)	338	NM_001310688	66566	Mm.25296	NM_025636	ENSMUSG00000031851	Ntpcr	2310079N02Rik|AI449709	nucleoside-triphosphatase, cancer-related	protein-coding
mm_14435.1	chr2	130589471	130589483	+	1	NA	TTS (NM_001255994)	TTS (NM_001255994)	-6889	NM_009732	11998	Mm.6190	NM_009732	ENSMUSG00000037727	Avp	Vp|Vsp	arginine vasopressin	protein-coding
mm_7632.1	chr1	127732558	127732572	-	1	NA	intron (NM_001033041, intron 1 of 9)	RCHARR1|DNA|hAT-Charlie	3152	NM_001033041	266645	Mm.25735	NM_001033041	ENSMUSG00000026348	Acmsd	-	amino carboxymuconate semialdehyde decarboxylase	protein-coding
mm_164243.1	chr15	95185030	95185040	-	1	NA	Intergenic	Intergenic	-35717	NR_015482	100043315	Mm.159041	NR_015482	ENSMUSG00000100603	LOC100043315	-	uncharacterized LOC100043315	ncRNA
mm_109516.1	chr12	111454373	111454398	+	1	NA	3' UTR (NM_009396, exon 12 of 12)	3' UTR (NM_009396, exon 12 of 12)	11724	NM_009396	21928	Mm.255332	NM_009396	ENSMUSG00000021281	Tnfaip2	B94|Exoc3l3|M-sec|Tnfip2|tnfb94	tumor necrosis factor, alpha-induced protein 2	protein-coding
mm_80590.1	chr9	85842725	85842761	+	1	NA	promoter-TSS (NM_001164792)	promoter-TSS (NM_001164792)	-109	NM_001164792	21983	Mm.20864	NM_011627	ENSMUSG00000035274	Tpbg	5T4|AW495680|WAIF1	trophoblast glycoprotein	protein-coding
mm_152547.1	chr19	11372377	11372390	-	1	NA	Intergenic	Intergenic	-3105	NM_001310331	666907		NM_001310331	ENSMUSG00000101389	Ms4a4a	EG666907	membrane-spanning 4-domains, subfamily A, member 4A	protein-coding
mm_133291.1	chr16	77487808	77487815	+	1	NA	intron (NR_015543, intron 3 of 4)	(TAG)n|Simple_repeat|Simple_repeat	-111125	NR_029535	387229		NR_029535	ENSMUSG00000065530	Mir99a	Mirn99a|mir-99a|mmu-mir-99a	microRNA 99a	ncRNA
mm_112350.1	chr12	118301371	118301426	-	1	NA	promoter-TSS (NM_009239)	promoter-TSS (NM_009239)	42	NM_009239	20688	Mm.34699	NM_009239	ENSMUSG00000025323	Sp4	5730497N03Rik|HF-1b|HF1-b	trans-acting transcription factor 4	protein-coding
mm_125448.1	chr15	48782816	48782819	+	1	NA	intron (NM_001081391, intron 1 of 70)	intron (NM_001081391, intron 1 of 70)	9172	NM_001081391	239420	Mm.309363	NM_001081391	ENSMUSG00000022311	Csmd3	4930500N14Rik|mKIAA1894	CUB and Sushi multiple domains 3	protein-coding
mm_154904.1	chrX	20962096	20962135	+	1	NA	promoter-TSS (NM_013840)	promoter-TSS (NM_013840)	1	NR_027446	320742	Mm.391227	NR_027445		A230072C01Rik	-	RIKEN cDNA A230072C01 gene	ncRNA
mm_4571.1	chr1	177729881	177729893	+	1	NA	promoter-TSS (NM_027077)	promoter-TSS (NM_027077)	73	NM_027077	69428	Mm.84467	NM_027077	ENSMUSG00000015962	1700016C15Rik	-	RIKEN cDNA 1700016C15 gene	protein-coding
mm_11703.1	chr2	36136385	36136428	+	1	NA	promoter-TSS (NM_026422)	promoter-TSS (NM_026422)	8	NM_026422	67871	Mm.378232	NM_026422	ENSMUSG00000026887	Mrrf	2400002D02Rik|MRFF|MTRRF|RRF	mitochondrial ribosome recycling factor	protein-coding
mm_72932.1	chr8	91313302	91313306	+	1	NA	promoter-TSS (NM_173431)	promoter-TSS (NM_173431)	-82	NM_173431	244585	Mm.324592	NM_173431	ENSMUSG00000033282	Rpgrip1l	1700047E16Rik|4931437C01|Ftm|Nphp8	Rpgrip1-like	protein-coding
mm_125908.1	chr15	76009576	76009591	+	1	NA	promoter-TSS (NM_001168253)	promoter-TSS (NM_001168253)	-85	NM_001168253	105732	Mm.267178	NM_134087	ENSMUSG00000046761	Fam83h	AA409316	family with sequence similarity 83, member H	protein-coding
mm_121610.1	chr14	8258911	8258954	-	1	NA	promoter-TSS (NM_053115)	promoter-TSS (NM_053115)	87	NM_053115	93732	Mm.28700	NM_053115	ENSMUSG00000021751	Acox2	THCCox	acyl-Coenzyme A oxidase 2, branched chain	protein-coding
mm_59969.1	chr7	30435119	30435158	+	1	NA	3' UTR (NM_007467, exon 17 of 17)	3' UTR (NM_007467, exon 17 of 17)	10444	NM_007467	11803	Mm.2381	NM_007467	ENSMUSG00000006651	Aplp1	-	amyloid beta (A4) precursor-like protein 1	protein-coding
mm_100859.1	chr11	5876881	5876909	-	1	NA	exon (NM_008894, exon 2 of 11)	exon (NM_008894, exon 2 of 11)	1361	NM_008894	18972	Mm.35788	NM_008894	ENSMUSG00000020471	Pold2	50kDa|p50|po1D2	polymerase (DNA directed), delta 2, regulatory subunit	protein-coding
mm_73990.1	chr8	120669298	120669321	+	1	NA	exon (NM_009941, exon 2 of 5)	exon (NM_009941, exon 2 of 5)	989	NM_001293559	12857	Mm.386758	NM_009941	ENSMUSG00000031818	Cox4i1	AL024441|COX|COX IV-1|COXIV|Cox4|Cox4a|IV-1	cytochrome c oxidase subunit IV isoform 1	protein-coding
mm_163698.1	chr13	102762415	102762441	+	1	NA	TTS (NR_130171)	TTS (NR_130171)	2173	NR_130171	76624	Mm.426384	NR_130171	ENSMUSG00000091906	1700099I09Rik	-	RIKEN cDNA 1700099I09 gene	ncRNA
mm_81054.1	chr9	105658480	105658489	+	1	NA	exon (NM_001081309, exon 7 of 20)	exon (NM_001081309, exon 7 of 20)	15489	NM_001081309	75669	Mm.274830	NM_029380	ENSMUSG00000032571	Pik3r4	2210010O15Rik|C730038E05Rik|C85833|D9Ertd418e	phosphatidylinositol 3 kinase, regulatory subunit, polypeptide 4, p150	protein-coding
mm_81557.1	chr9	110344210	110344229	+	1	NA	intron (NM_001001144, intron 1 of 22)	RSINE1|SINE|B4	10863	NM_001001144	235623	Mm.288741	NM_001001144	ENSMUSG00000032485	Scap	9530044G19|mKIAA0199	SREBF chaperone	protein-coding
mm_166556.1	chr6	42593339	42593341	-	1	NA	exon (NM_203396, exon 2 of 7)	exon (NM_203396, exon 2 of 7)	4032	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_136831.1	chr17	12741361	12741384	+	1	NA	promoter-TSS (NR_027784)	promoter-TSS (NR_027784)	61	NR_027784	104103	Mm.26553	NR_002853	ENSMUSG00000078247	Airn	2810051F02Rik|2810434M15Rik|AI256653|AI597500|AW049873|Air|B930018I07Rik|D17Ertd663e|IGF2RAS	antisense Igf2r RNA	ncRNA
mm_130408.1	chr15	97976853	97976878	-	1	NA	exon (NM_001113515, exon 52 of 53)	exon (NM_001113515, exon 52 of 53)	12636	NM_001252153	380967	Mm.196630	NM_201359	ENSMUSG00000052369	Tmem106c	AI046681|BC046621|D15Ertd405e	transmembrane protein 106C	protein-coding
mm_106749.1	chr12	4082576	4082594	+	1	NA	promoter-TSS (NM_153082)	promoter-TSS (NM_153082)	11	NM_153082	217378	Mm.271656	NM_153082	ENSMUSG00000020657	Dnajc27	AI639580|C330021A05Rik|Rabj|Rbj	DnaJ heat shock protein family (Hsp40) member C27	protein-coding
mm_104618.1	chr11	97280627	97280650	-	1	NA	promoter-TSS (NM_008942)	promoter-TSS (NM_008942)	-62	NM_008942	19155	Mm.29824	NM_008942	ENSMUSG00000001441	Npepps	AAP-S|MP100|Psa|R74825|goku	aminopeptidase puromycin sensitive	protein-coding
mm_142196.1	chr17	36958176	36958198	-	1	NA	promoter-TSS (NM_029602)	promoter-TSS (NM_029602)	241	NM_023162	66136	Mm.486229	NM_023162	ENSMUSG00000036315	Znrd1	1110014N07Rik|Rpa12	zinc ribbon domain containing, 1	protein-coding
mm_66333.1	chr7	42954404	42954414	-	1	NA	Intergenic	Intergenic	-20620	NM_001105060	435975	Mm.469897	NM_001105060	ENSMUSG00000090751	Vmn2r63	EG435975	vomeronasal 2, receptor 63	protein-coding
mm_169277.1	chr13	93448410	93448429	+	1	NA	intron (NM_021310, intron 7 of 10)	intron (NM_021310, intron 7 of 10)	51389	NM_021310	57748	Mm.100273	NM_021310	ENSMUSG00000021690	Jmy	-	junction-mediating and regulatory protein	protein-coding
mm_170511.1	chr19	28560802	28560805	-	1	NA	intron (NM_175459, intron 2 of 10)	intron (NM_175459, intron 2 of 10)	-117421	NR_045330	320176	Mm.406716	NR_045330	ENSMUSG00000097735	D930032P07Rik	-	RIKEN cDNA D930032P07 gene	ncRNA
mm_113452.1	chr13	35833557	35833559	+	1	NA	intron (NM_001123386, intron 2 of 6)	L1M4|LINE|L1	72789	NM_145938	208366	Mm.35545	NM_145938	ENSMUSG00000021418	Rpp40	D8Bwg1265e|Rnasep1	ribonuclease P 40 subunit	protein-coding
mm_76294.1	chr8	84203484	84203495	-	1	NA	Intergenic	Intergenic	-5029	NR_029740	387216		NR_029740	ENSMUSG00000065611	Mir23a	Mirn23a|mir-23a|mmu-mir-23a	microRNA 23a	ncRNA
mm_70895.1	chr8	25601488	25601497	+	1	NA	promoter-TSS (NM_001308482)	promoter-TSS (NM_001308482)	-109	NM_001308481	234135	Mm.217337	NM_001001735	ENSMUSG00000054823	Whsc1l1	6720429E03|A530023P05|AI528490|NSD3|WHISTLE	Wolf-Hirschhorn syndrome candidate 1-like 1 (human)	protein-coding
mm_24979.1	chr3	96829494	96829501	+	1	NA	promoter-TSS (NM_001163497)	promoter-TSS (NM_001163497)	-146	NM_001163496	54215	Mm.34693	NM_018767	ENSMUSG00000038304	Cd160	AU045688|By55	CD160 antigen	protein-coding
mm_170370.1	chr18	54699225	54699228	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	87482	NR_045400	328957	Mm.402781	NR_045400		9330117O12Rik	9330117O12	RIKEN cDNA 9330117O12 gene	ncRNA
mm_96491.1	chr11	67798270	67798286	+	1	NA	promoter-TSS (NM_001013013)	promoter-TSS (NM_001013013)	7	NM_001013013	68460	Mm.22167	NM_001013013	ENSMUSG00000033044	Dhrs7c	1110001P11Rik|AI120487|SRP-35	dehydrogenase/reductase (SDR family) member 7C	protein-coding
mm_127641.1	chr15	102478647	102478670	+	1	NA	exon (NM_001174073, exon 6 of 13)	exon (NM_001174073, exon 6 of 13)	8026	NM_001174073	18521	Mm.236513	NM_011042	ENSMUSG00000056851	Pcbp2	AW412548|Hnrpx|alphaCP-2	poly(rC) binding protein 2	protein-coding
mm_172288.1	chr6	95216602	95216611	-	1	NA	Intergenic	Intergenic	98726	NM_001008785	243574	Mm.333275	NM_001008785	ENSMUSG00000030031	Kbtbd8	AU040152|SSEC-51|SSEC51|Takrp|mKIAA1842	kelch repeat and BTB (POZ) domain containing 8	protein-coding
mm_123519.1	chr14	66296910	66296954	-	1	NA	promoter-TSS (NM_029979)	promoter-TSS (NM_029979)	-93	NM_029979	66854	Mm.43871	NM_029979	ENSMUSG00000022043	Trim35	0710005M05Rik|A430106H13Rik|AW046487|HLS5|Mair|NC8|mKIAA1098	tripartite motif-containing 35	protein-coding
mm_126689.1	chr15	84987964	84987987	+	1	NA	promoter-TSS (NM_001033273)	promoter-TSS (NM_001033273)	-4	NM_001033273	223739	Mm.323925	NM_001033273	ENSMUSG00000036046	5031439G07Rik	AW554572|mKIAA0930	RIKEN cDNA 5031439G07 gene	protein-coding
mm_52245.1	chr6	105677812	105677831	+	1	NA	promoter-TSS (NM_173004)	promoter-TSS (NM_173004)	76	NM_173004	269784	Mm.321683	NM_173004	ENSMUSG00000064293	Cntn4	9630050B05|Axcam|BIG-2	contactin 4	protein-coding
mm_61815.1	chr7	87304270	87304287	+	1	NA	intron (NM_015760, intron 4 of 17)	intron (NM_015760, intron 4 of 17)	57629	NM_001285833	50490	Mm.31748	NM_015760	ENSMUSG00000030562	Nox4	AI648021	NADPH oxidase 4	protein-coding
mm_89232.1	chr10	87562566	87562569	+	1	NA	intron (NM_008777, intron 4 of 12)	intron (NM_008777, intron 4 of 12)	40772	NM_008777	18478	Mm.263539	NM_008777	ENSMUSG00000020051	Pah	AW106920	phenylalanine hydroxylase	protein-coding
mm_15199.1	chr2	154206466	154206497	+	1	NA	exon (NM_153418, exon 5 of 16)	exon (NM_153418, exon 5 of 16)	6101	NM_153418	228801	Mm.3783	NM_153418	ENSMUSG00000027485	Bpifb1	Lplunc1	BPI fold containing family B, member 1	protein-coding
mm_146413.1	chr18	84091815	84091827	+	1	NA	intron (NM_146090, intron 1 of 1)	intron (NM_146090, intron 1 of 1)	3663	NM_146090	225791	Mm.147052	NM_146090	ENSMUSG00000049090	Zadh2	C530046K17Rik|PTGR-3|Pthr3	zinc binding alcohol dehydrogenase, domain containing 2	protein-coding
mm_167069.1	chr7	99540428	99540434	+	1	NA	intron (NM_177231, intron 1 of 15)	(T)n|Simple_repeat|Simple_repeat	4945	NM_177231	109689	Mm.260193	NM_177231	ENSMUSG00000018909	Arrb1	1200006I17Rik|AW208571|G430100A01Rik	arrestin, beta 1	protein-coding
mm_58016.1	chr6	136659307	136659346	-	1	NA	intron (NM_025806, intron 1 of 10)	intron (NM_025806, intron 1 of 10)	2567	NM_025806	66857	Mm.3311	NM_025806	ENSMUSG00000030214	Plbd1	1100001H23Rik	phospholipase B domain containing 1	protein-coding
mm_57479.1	chr6	125236955	125236971	-	1	NA	promoter-TSS (NM_001042564)	promoter-TSS (NM_001042564)	64	NM_001033126	21940	Mm.367714	NM_001033126	ENSMUSG00000030336	Cd27	S152|Tnfrsf7|Tp55	CD27 antigen	protein-coding
mm_48650.1	chr5	145857766	145857786	-	1	NA	intron (NM_007818, intron 12 of 12)	B3|SINE|B2	22078	NM_007818	13112	Mm.332844	NM_007818	ENSMUSG00000056035	Cyp3a11	AI256190|Cyp3a|IIIAm1|Pcn	cytochrome P450, family 3, subfamily a, polypeptide 11	protein-coding
mm_118057.1	chr13	102666455	102666467	-	1	NA	Intergenic	Intergenic	-27097	NM_008533	17079	Mm.373974	NM_008533	ENSMUSG00000021624	Cd180	F630107B15|Ly78|RP105	CD180 antigen	protein-coding
mm_9486.1	chr1	173599244	173599277	-	1	NA	promoter-TSS (NM_001177350)	promoter-TSS (NM_001177350)	14	NM_001177349	623121	Mm.138449	NM_001033384	ENSMUSG00000073491	Ifi213	E030037K03Rik|E430029J22Rik|Pydc4|Pyr-A	interferon activated gene 213	protein-coding
mm_12099.1	chr2	60972394	60972405	+	1	NA	intron (NR_045335, intron 1 of 3)	intron (NR_045335, intron 1 of 3)	2752	NR_045335	100038493	Mm.388076	NR_045335	ENSMUSG00000075325	Gm13582	ENSMUSG00000075325|OTTMUSG00000012844	predicted gene 13582	ncRNA
mm_170244.1	chr17	92701842	92701843	-	1	NA	Intergenic	L1Md_T|LINE|L1	-497175	NM_001315503	11516	Mm.3407	NM_009625	ENSMUSG00000024256	Adcyap1	PACAP	adenylate cyclase activating polypeptide 1	protein-coding
mm_150280.1	chr19	34251805	34251819	+	1	NA	exon (NM_007392, exon 3 of 9)	exon (NM_007392, exon 3 of 9)	3561	NM_007392	11475	Mm.213025	NM_007392	ENSMUSG00000035783	Acta2	0610041G09Rik|Actvs|SMalphaA|a-SMA|alphaSMA	actin, alpha 2, smooth muscle, aorta	protein-coding
mm_44355.1	chr5	17795619	17795656	-	1	NA	exon (NM_001159558, exon 12 of 16)	exon (NM_001159558, exon 12 of 16)	40259	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_36423.1	chr4	81442757	81442836	-	1	NA	promoter-TSS (NM_001305286)	promoter-TSS (NM_001305286)	19	NM_010820	17475	Mm.153039	NM_010820	ENSMUSG00000028402	Mpdz	AI225843|B930003D11Rik|MUPP1	multiple PDZ domain protein	protein-coding
mm_21560.1	chr2	164182639	164182652	-	1	NA	promoter-TSS (NM_145369)	promoter-TSS (NM_145369)	97	NM_145369	209232	Mm.218273	NM_145369	ENSMUSG00000040154	Wfdc5	BC019734|Prg5|Wap1	WAP four-disulfide core domain 5	protein-coding
mm_8397.1	chr1	151475700	151475730	-	1	NA	intron (NM_011277, intron 4 of 6)	intron (NM_011277, intron 4 of 6)	25108	NM_011277	19821	Mm.474038	NM_011277	ENSMUSG00000026484	Rnf2	AI326319|AI450156|AU019207|Ring1B|dinG	ring finger protein 2	protein-coding
mm_104508.1	chr11	95982584	95982593	-	1	NA	intron (NM_009951, intron 2 of 14)	intron (NM_009951, intron 2 of 14)	-19205	NR_037223	100526468		NR_037223	ENSMUSG00000093358	Mir3063	mmu-mir-3063	microRNA 3063	ncRNA
mm_106197.1	chr11	116842849	116842869	-	1	NA	promoter-TSS (NM_028865)	promoter-TSS (NM_028865)	590	NM_033398	107817	Mm.481684	NM_033398	ENSMUSG00000056962	Jmjd6	5730436I23Rik|D11Ertd195e|PSR|PtdSerR|Ptdsr|mKIAA0585	jumonji domain containing 6	protein-coding
mm_106145.1	chr11	116543407	116543408	-	1	NA	intron (NM_173755, intron 12 of 17)	intron (NM_173755, intron 12 of 17)	8667	NM_011451	20698	Mm.20944	NM_011451	ENSMUSG00000061878	Sphk1	1110006G24Rik|Sk1|Spk1	sphingosine kinase 1	protein-coding
mm_79952.1	chr9	66126638	66126649	+	1	NA	promoter-TSS (NM_026635)	promoter-TSS (NM_026635)	32	NM_026635	68250	Mm.27107	NM_026635	ENSMUSG00000032381	Fam96a	5730536A07Rik	family with sequence similarity 96, member A	protein-coding
mm_15402.1	chr2	156730707	156730727	+	1	NA	intron (NM_001042487, intron 1 of 6)	intron (NM_001042487, intron 1 of 6)	9438	NM_001042487	228836	Mm.22094	NM_146128	ENSMUSG00000061689	Dlgap4	AI225853|BC024558|DAP-4|DAP4|SAPAP-4|Sapap4|WBP16	discs, large homolog-associated protein 4 (Drosophila)	protein-coding
mm_92384.1	chr10	76468812	76468868	-	1	NA	promoter-TSS (NM_019434)	promoter-TSS (NM_019434)	-131	NM_019434	54387	Mm.30098	NM_019434	ENSMUSG00000001150	Mcm3ap	GANP|mKIAA0572	minichromosome maintenance complex component 3 associated protein	protein-coding
mm_168464.1	chr1	147671259	147671261	+	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	1173573	NM_001145807	215378	Mm.441817	NM_153539	ENSMUSG00000035131	Brinp3	B830045N13Rik|Fam5c	bone morphogenetic protein/retinoic acid inducible neural specific 3	protein-coding
mm_116997.1	chr13	56626167	56626181	-	1	NA	exon (NM_009369, exon 6 of 17)	exon (NM_009369, exon 6 of 17)	16571	NM_009369	21810	Mm.14455	NM_009369	ENSMUSG00000035493	Tgfbi	68kDa|AI181842|AI747162|Beta-ig|big-h3	transforming growth factor, beta induced	protein-coding
mm_1344.1	chr1	66175287	66175348	+	1	NA	promoter-TSS (NM_008632)	promoter-TSS (NM_008632)	-12	NM_008632	17756	Mm.256966	NM_008632	ENSMUSG00000015222	Map2	G1-397-34|MAP-2|Mtap-2|Mtap2|repro4	microtubule-associated protein 2	protein-coding
mm_154677.1	chrX	7899389	7899432	+	1	NA	promoter-TSS (NM_001252528)	promoter-TSS (NM_001252528)	74	NR_132589	21855	Mm.27393	NM_011591	ENSMUSG00000031158	Timm17b	17kDa|Sfc3|mTim17b	translocase of inner mitochondrial membrane 17b	protein-coding
mm_152079.1	chr19	6857516	6857541	-	1	NA	intron (NM_001081291, intron 2 of 26)	intron (NM_001081291, intron 2 of 26)	683	NM_001081291	78317	Mm.329596	NM_198008	ENSMUSG00000047810	Ccdc88b	2610041P08Rik|Ccdc88	coiled-coil domain containing 88B	protein-coding
mm_69097.1	chr7	127019678	127019698	-	1	NA	exon (NM_001102563, exon 2 of 4)	exon (NM_001102563, exon 2 of 4)	1523	NM_001102563	69017	Mm.392047	NM_001102563	ENSMUSG00000045114	Prrt2	1500031I19Rik|AI195361|DSPB3	proline-rich transmembrane protein 2	protein-coding
mm_143100.1	chr17	57081243	57081254	-	1	NA	exon (NM_009451, exon 4 of 4)	exon (NM_009451, exon 4 of 4)	-2738	NM_153551	70785	Mm.284447	NM_153551	ENSMUSG00000002668	Dennd1c	4432409M07Rik	DENN/MADD domain containing 1C	protein-coding
mm_135001.1	chr16	32179580	32179586	-	1	NA	promoter-TSS (NM_001033539)	promoter-TSS (NM_001033539)	-217	NM_001033539	328660	Mm.441006	NM_001033539	ENSMUSG00000075269	Bex6	B020003O03Rik	brain expressed family member 6	protein-coding
mm_165568.1	chr3	18243215	18243252	-	1	NA	5' UTR (NM_007825, exon 1 of 6)	5' UTR (NM_007825, exon 1 of 6)	105	NM_007825	13123	Mm.316000	NM_007825	ENSMUSG00000039519	Cyp7b1	AW261589|D3Ertd552e|hct-1	cytochrome P450, family 7, subfamily b, polypeptide 1	protein-coding
mm_17966.1	chr2	37573614	37573617	-	1	NA	3' UTR (NM_009261, exon 17 of 17)	3' UTR (NM_009261, exon 17 of 17)	56989	NM_177383	338346	Mm.445325	NM_177383	ENSMUSG00000053164	Gpr21	C230004C13Rik	G protein-coupled receptor 21	protein-coding
mm_145700.1	chr18	62657240	62657245	+	1	NA	intron (NM_177829, intron 5 of 8)	intron (NM_177829, intron 5 of 8)	-60978	NM_001001803	408198	Mm.478742	NM_001001803	ENSMUSG00000060201	Spink7	EG408198|Ecg2	serine peptidase inhibitor, Kazal type 7 (putative)	protein-coding
mm_94295.1	chr11	4069927	4069968	+	1	NA	intron (NM_001029937, intron 6 of 11)	intron (NM_001029937, intron 6 of 11)	5094	NM_001029937	380683	Mm.296806	NM_001029937	ENSMUSG00000054986	Sec14l3	1110069O07Rik	SEC14-like lipid binding 3	protein-coding
mm_108674.1	chr12	86678532	86678548	+	1	NA	promoter-TSS (NM_177354)	promoter-TSS (NM_177354)	-160	NM_177354	238328	Mm.216101	NM_177354	ENSMUSG00000021256	Vash1	AI834978|D930046M13Rik|G630009D10Rik	vasohibin 1	protein-coding
mm_119719.1	chr14	53902984	53902986	+	1	NA	Intergenic	Intergenic	350944	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_37546.1	chr4	125127151	125127171	-	1	NA	intron (NM_153159, intron 1 of 5)	intron (NM_153159, intron 1 of 5)	720	NM_153159	230738	Mm.402	NM_153159	ENSMUSG00000042677	Zc3h12a	BC036563|MCPIP|MCPIP-1|Mcpip1|Reg1	zinc finger CCCH type containing 12A	protein-coding
mm_35193.1	chr4	16013888	16013890	-	1	NA	promoter-TSS (NM_145950)	promoter-TSS (NM_145950)	-12	NM_145950	209212	Mm.46455	NM_145950	ENSMUSG00000041153	Osgin2	BC010311|C230027H09Rik	oxidative stress induced growth inhibitor family member 2	protein-coding
mm_112311.1	chr12	114880371	114880375	-	1	NA	Intergenic	Intergenic	-366679	NR_106063	102465664		NR_106063	ENSMUSG00000098357	Mir7094-2	Gm27508|mmu-mir-7094-2	microRNA 7094-2	ncRNA
mm_19069.1	chr2	77703376	77703417	-	1	NA	promoter-TSS (NM_001113399)	promoter-TSS (NM_001113399)	-124	NM_001113399	241494	Mm.490320	NM_178723	ENSMUSG00000027016	Zfp385b	B830010L13Rik|C130013B13Rik|Zfp533|Znf385b	zinc finger protein 385B	protein-coding
mm_12105.1	chr2	61582040	61582050	+	1	NA	intron (NM_011529, intron 1 of 7)	intron (NM_011529, intron 1 of 7)	3459	NM_011529	21353	Mm.244393	NM_011529	ENSMUSG00000064289	Tank	C86182|E430026L09Rik|I-TRAF	TRAF family member-associated Nf-kappa B activator	protein-coding
mm_157881.1	chrX	75843017	75843025	-	1	NA	promoter-TSS (NM_001346520)	promoter-TSS (NM_001346520)	0	NM_001166454	102866	Mm.28777	NM_145629	ENSMUSG00000016382	Pls3	AI115446|AL024105	plastin 3 (T-isoform)	protein-coding
mm_148435.1	chr19	3943587	3943610	+	1	NA	exon (NM_019449, exon 8 of 11)	exon (NM_019449, exon 8 of 11)	8412	NM_001161428	54445	Mm.262094	NM_019449	ENSMUSG00000036908	Unc93b1	Unc-93B1|Unc93b	unc-93 homolog B1 (C. elegans)	protein-coding
mm_84330.1	chr9	64021996	64022008	-	1	NA	promoter-TSS (NM_008542)	promoter-TSS (NM_008542)	57	NM_008542	17130	Mm.325757	NM_008542	ENSMUSG00000036867	Smad6	Madh6|b2b390Clo	SMAD family member 6	protein-coding
mm_21158.1	chr2	154569789	154569799	-	1	NA	promoter-TSS (NM_001291105)	promoter-TSS (NM_001291105)	98	NM_007891	13555	Mm.18036	NM_007891	ENSMUSG00000027490	E2f1	E2F-1|mKIAA4009	E2F transcription factor 1	protein-coding
mm_3282.1	chr1	136624998	136625020	+	1	NA	5' UTR (NM_001160251, exon 1 of 2)	5' UTR (NM_001160251, exon 1 of 2)	108	NM_001160251	226442	Mm.62521	NM_177643	ENSMUSG00000041483	Zfp281	Znf281	zinc finger protein 281	protein-coding
mm_10589.1	chr2	18497488	18497491	+	1	NA	Intergenic	RLTR17|LTR|ERVK	-104659	NM_007869	13418	Mm.246674	NM_007869	ENSMUSG00000026740	Dnajc1	4733401K02Rik|AA960110|D230036H06Rik|Dnajl1|ERdj1|ERj1p|MTJ1	DnaJ heat shock protein family (Hsp40) member C1	protein-coding
mm_14370.1	chr2	129630063	129630077	+	1	NA	exon (NM_001291022, exon 5 of 5)	exon (NM_001291022, exon 5 of 5)	36901	NM_001291022	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_6672.1	chr1	80340603	80340613	-	1	NA	promoter-TSS (NM_016716)	promoter-TSS (NM_016716)	82	NM_001313728	26554	Mm.12665	NM_016716	ENSMUSG00000004364	Cul3	KIAA0617	cullin 3	protein-coding
mm_66742.1	chr7	46710643	46710687	-	1	NA	promoter-TSS (NM_030233)	promoter-TSS (NM_030233)	-14	NM_030233	78935	Mm.289866	NM_030233	ENSMUSG00000006763	Saal1	5031425D22Rik|SPACIA1	serum amyloid A-like 1	protein-coding
mm_118434.1	chr14	8016561	8016588	+	1	NA	intron (NM_001331064, intron 1 of 8)	intron (NM_001331064, intron 1 of 8)	13608	NM_001331064	66082	Mm.181473	NM_025341	ENSMUSG00000025277	Abhd6	0610041D24Rik|AA673485|AV065425	abhydrolase domain containing 6	protein-coding
mm_95866.1	chr11	58010020	58010047	+	1	NA	intron (NM_028451, intron 1 of 18)	CpG	969	NM_028451	73158	Mm.248843	NM_028451	ENSMUSG00000037331	Larp1	1810024J12Rik|3110040D16Rik|Larp|mKIAA0731	La ribonucleoprotein domain family, member 1	protein-coding
mm_148530.1	chr19	4558008	4558011	+	1	NA	intron (NM_001162946, intron 2 of 20)	intron (NM_001162946, intron 2 of 20)	-36310	NM_008797	18563	Mm.1845	NM_008797	ENSMUSG00000024892	Pcx	Pc|Pcb	pyruvate carboxylase	protein-coding
mm_128422.1	chr15	45632375	45632417	-	1	NA	Intergenic	RMER17B2|LTR|ERVK	-517462	NM_026200	67498	Mm.300079	NM_026200	ENSMUSG00000022342	Kcnv1	2700023A03Rik|vibe	potassium channel, subfamily V, member 1	protein-coding
mm_6032.1	chr1	59548791	59548802	-	1	NA	intron (NM_001013771, intron 4 of 19)	intron (NM_001013771, intron 4 of 19)	32532	NM_001013771	381260	Mm.486706	NM_001013771	ENSMUSG00000047361	Gm973	AW554518	predicted gene 973	protein-coding
mm_134492.1	chr16	18733223	18733246	-	1	NA	Intergenic	Intergenic	-43613	NM_013805	12741	Mm.22768	NM_013805	ENSMUSG00000041378	Cldn5	AI854493|MBEC1|Tmvcf	claudin 5	protein-coding
mm_158253.1	chrX	108748231	108748239	-	1	NA	intron (NM_001081477, intron 40 of 40)	intron (NM_001081477, intron 40 of 40)	86120	NM_001081477	382236	Mm.100112	NM_001081477	ENSMUSG00000063663	Brwd3	Brodl|D030064D06Rik|Gm596	bromodomain and WD repeat domain containing 3	protein-coding
mm_90931.1	chr10	12868291	12868304	-	1	NA	Intergenic	Intergenic	-6562	NM_011682	22288	Mm.331784	NM_011682	ENSMUSG00000019820	Utrn	AA589569|DRP|Dmdl	utrophin	protein-coding
mm_108761.1	chr12	89290592	89290592	+	1	NA	intron (NM_172544, intron 6 of 19)	intron (NM_172544, intron 6 of 19)	337202	NM_172544	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding
mm_30075.1	chr3	137981549	137981564	-	1	NA	promoter-TSS (NM_001310753)	promoter-TSS (NM_001310753)	-7	NM_001310753	26377	Mm.254835	NM_011932	ENSMUSG00000028159	Dapp1	Bam32	dual adaptor for phosphotyrosine and 3-phosphoinositides 1	protein-coding
mm_47239.1	chr5	121503398	121503440	-	1	NA	promoter-TSS (NM_172125)	promoter-TSS (NM_172125)	-439	NM_172125	280667	Mm.444773	NM_172125	ENSMUSG00000062438	Adam1b	Adam1|Ftna	a disintegrin and metallopeptidase domain 1b	protein-coding
mm_122843.1	chr14	54724795	54724808	-	1	NA	exon (NM_016972, exon 10 of 11)	exon (NM_016972, exon 10 of 11)	-12627	NM_207131	110794	Mm.236223	NM_207131	ENSMUSG00000052435	Cebpe	C/EBPe|CRP1|Gm294	CCAAT/enhancer binding protein (C/EBP), epsilon	protein-coding
mm_955.1	chr1	57774934	57774955	+	1	NA	promoter-TSS (NM_144882)	promoter-TSS (NM_144882)	83	NM_144882	67198	Mm.159989	NM_144882	ENSMUSG00000038305	Spats2l	2810022L02Rik|A230104H11Rik|AA987173|AI480531|AI842453|AW413586	spermatogenesis associated, serine-rich 2-like	protein-coding
mm_151790.1	chr19	5394336	5394383	-	1	NA	Intergenic	Intergenic	-5656	NM_016882	20227	Mm.34562	NM_016882	ENSMUSG00000039148	Sart1	U5-110K	squamous cell carcinoma antigen recognized by T cells 1	protein-coding
mm_115620.1	chr13	12082508	12082521	-	1	NA	intron (NM_023868, intron 1 of 104)	MTEb|LTR|ERVL-MaLR	24431	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding
mm_20029.1	chr2	119546884	119546888	-	1	NA	promoter-TSS (NM_019769)	promoter-TSS (NM_019769)	741	NM_172857	241624	Mm.212773	NM_172857	ENSMUSG00000048647	Exd1	4932702D22Rik|Exdl1|mExd1	exonuclease 3'-5' domain containing 1	protein-coding
mm_156497.1	chrX	144336695	144336697	+	1	NA	intron (NR_037145, intron 4 of 26)	intron (NR_037145, intron 4 of 26)	18730	NM_026247	67574	Mm.249084	NM_026247	ENSMUSG00000041718	Alg13	2810046O15Rik|4833435D08Rik|Glt28d1|MDS031|OTTMUSG00000018917	asparagine-linked glycosylation 13	protein-coding
mm_139798.1	chr17	66005742	66005754	+	1	NA	intron (NM_001025572, intron 8 of 12)	intron (NM_001025572, intron 8 of 12)	-54561	NM_023053	65960	Mm.10153	NM_023053	ENSMUSG00000024098	Twsg1	1810013J15Rik|9030422N06Rik|AW552143|D17Ertd403e|Tsg|Twg	twisted gastrulation BMP signaling modulator 1	protein-coding
mm_75201.1	chr8	39598361	39598399	-	1	NA	intron (NM_001113326, intron 8 of 9)	intron (NM_001113326, intron 8 of 9)	44298	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_169672.1	chr15	63613319	63613325	+	1	NA	Intergenic	Intergenic	-133714	NR_045279	432958	Mm.255105	NR_045279		Gm20740	-	predicted gene, 20740	ncRNA
mm_24098.1	chr3	88055124	88055134	+	1	NA	exon (NM_001110809, exon 8 of 8)	exon (NM_001110809, exon 8 of 8)	3366	NM_144897	246703	Mm.205996	NM_144897	ENSMUSG00000028070	Apoa1bp	AA087124|AI-BP|AIBP|Apoa1ip|ESTM37|Naxe	apolipoprotein A-I binding protein	protein-coding
mm_89818.1	chr10	104746953	104746956	+	1	NA	Intergenic	RMER15-int|LTR|ERVL	459685	NR_105838	102465222		NR_105838	ENSMUSG00000099264	Mir6411	Gm27767|mmu-mir-6411	microRNA 6411	ncRNA
mm_14728.1	chr2	144165500	144165514	+	1	NA	Intergenic	CpG	23783	NR_136884	433481	Mm.330630	NR_136884	ENSMUSG00000074758	Gm5535	EG433481	predicted gene 5535	ncRNA
mm_94140.1	chr10	128720714	128720716	-	1	NA	TTS (NM_021882)	TTS (NM_021882)	14457	NM_021882	20431	Mm.16756	NM_021882	ENSMUSG00000025359	Pmel	D10H12S53E|D12S53Eh|Pmel17|Si|Silv|gp100|gp87	premelanosome protein	protein-coding
mm_47365.1	chr5	122915036	122915041	-	1	NA	intron (NM_001003953, intron 12 of 22)	RMER15-int|LTR|ERVL	-14688	NM_013910	30841	Mm.86406	NM_013910	ENSMUSG00000029475	Kdm2b	Cxxc2|Fbl10|Fbxl10|Jhdm1b|PCCX2	lysine (K)-specific demethylase 2B	protein-coding
mm_2982.1	chr1	133131268	133131283	+	1	NA	5' UTR (NM_133819, exon 1 of 2)	5' UTR (NM_133819, exon 1 of 2)	109	NM_133819	108954	Mm.293628	NM_133819	ENSMUSG00000046062	Ppp1r15b	1810033K10Rik|AI606441|C530022L24Rik|CReP	protein phosphatase 1, regulatory (inhibitor) subunit 15b	protein-coding
mm_46918.1	chr5	114658365	114658379	-	1	NA	promoter-TSS (NM_022017)	promoter-TSS (NM_022017)	49	NM_022017	63873	Mm.266450	NM_022017	ENSMUSG00000014158	Trpv4	0610033B08Rik|OTRPC4|Trp12|VR-OAC|VRL-2|VROAC	transient receptor potential cation channel, subfamily V, member 4	protein-coding
mm_34842.1	chr4	155409202	155409266	+	1	NA	promoter-TSS (NM_001166029)	promoter-TSS (NM_001166029)	44	NM_001166029	544678	Mm.472798	NM_177674	ENSMUSG00000078490	Cfap74	2010015L04Rik|A530045M11	cilia and flagella associated protein 74	protein-coding
mm_26058.1	chr3	135826096	135826118	+	1	NA	intron (NM_001135150, intron 1 of 8)	intron (NM_001135150, intron 1 of 8)	317	NM_001135150	67547	Mm.30239	NM_026228	ENSMUSG00000053897	Slc39a8	4933419D20Rik|AA986696|BIGM103|ZIP-8|Zip8	solute carrier family 39 (metal ion transporter), member 8	protein-coding
mm_98235.1	chr11	88099204	88099254	+	1	NA	promoter-TSS (NM_198013)	promoter-TSS (NM_198013)	83	NM_198013	103841	Mm.374846	NM_198013	ENSMUSG00000018378	Cuedc1	AI841487|C330016O16Rik	CUE domain containing 1	protein-coding
mm_167687.1	chr9	85842710	85842721	+	1	NA	promoter-TSS (NM_001164792)	promoter-TSS (NM_001164792)	-137	NM_001164792	21983	Mm.20864	NM_011627	ENSMUSG00000035274	Tpbg	5T4|AW495680|WAIF1	trophoblast glycoprotein	protein-coding
mm_59186.1	chr7	24474199	24474201	+	1	NA	intron (NM_011113, intron 5 of 6)	intron (NM_011113, intron 5 of 6)	-7823	NM_153112	260299	Mm.178322	NM_153112	ENSMUSG00000054793	Cadm4	Igdf4c|Igsf4c|Tsll2	cell adhesion molecule 4	protein-coding
mm_167032.1	chr7	70990645	70990646	+	1	NA	Intergenic	Lx7|LINE|L1	-623899	NM_183261	11819	Mm.158143	NM_009697	ENSMUSG00000030551	Nr2f2	2700033K02Rik|9430015G03Rik|ARP-1|Aporp1|COUP-TF2|COUP-TFII|COUPTFB|EAR3|SVP40|Tcfcoup2	nuclear receptor subfamily 2, group F, member 2	protein-coding
mm_102457.1	chr11	59839276	59839296	-	1	NA	intron (NM_011991, intron 1 of 11)	CpG	481	NM_011991	26572	Mm.40	NM_011991	ENSMUSG00000019373	Cops3	Csn3|Sgn3	COP9 signalosome subunit 3	protein-coding
mm_119512.1	chr14	47385519	47385594	+	1	NA	exon (NM_010705, exon 6 of 6)	exon (NM_010705, exon 6 of 6)	11696	NM_001145953	16854	Mm.248615	NM_010705	ENSMUSG00000050335	Lgals3	GBP|L-34|Mac-2|gal3	lectin, galactose binding, soluble 3	protein-coding
mm_99927.1	chr11	110997055	110997062	+	1	NA	promoter-TSS (NM_001252209)	promoter-TSS (NM_001252209)	-429	NM_001252209	16517	Mm.30176	NM_010604	ENSMUSG00000051497	Kcnj16	6430410F18Rik|AI132396|Kir5.1	potassium inwardly-rectifying channel, subfamily J, member 16	protein-coding
mm_15950.1	chr2	165969100	165969112	+	1	NA	Intergenic	Intergenic	-23531	NM_008679	17979	Mm.469663	NM_008679	ENSMUSG00000027678	Ncoa3	2010305B15Rik|AW321064|Actr|Aib1|KAT13B|Rac3|Src3|Tram-1|Tram1|bHLHe42|p/Cip|pCip	nuclear receptor coactivator 3	protein-coding
mm_9775.1	chr1	181093783	181093795	-	1	NA	3' UTR (NM_026171, exon 23 of 23)	3' UTR (NM_026171, exon 23 of 23)	42552	NM_001033819	619326	Mm.355174	NM_001033819	ENSMUSG00000038768	9130409I23Rik	-	RIKEN cDNA 9130409I23 gene	protein-coding
mm_87643.1	chr10	58375147	58375165	+	1	NA	intron (NM_201242, intron 1 of 9)	intron (NM_201242, intron 1 of 9)	3702	NM_201242	110829	Mm.57734	NM_026148	ENSMUSG00000019920	Lims1	2310016J22Rik|4921524A02Rik|AI507642|AU021743|AW551584|C430041B13Rik|Lims1l|PINCH|PINCH1	LIM and senescent cell antigen-like domains 1	protein-coding
mm_173191.1	chrX	61874120	61874124	-	1	NA	Intergenic	Intergenic	164506	NM_001018087	434784	Mm.23468	NM_001018087	ENSMUSG00000057615	Ldoc1	Gm366|Mar7|Mart7|Sirh7	leucine zipper, down-regulated in cancer 1	protein-coding
mm_168949.1	chr12	76795388	76795402	-	1	NA	5' UTR (NM_030677, exon 1 of 2)	5' UTR (NM_030677, exon 1 of 2)	159	NM_030677	14776	Mm.441856	NM_030677	ENSMUSG00000042808	Gpx2	GI-GPx|GPx-GI|GSHPx-2|GSHPx-GI	glutathione peroxidase 2	protein-coding
mm_51811.1	chr6	88835208	88835210	+	1	NA	TTS (NM_030251)	TTS (NM_030251)	6726	NM_030251	80283	Mm.166858	NM_030251	ENSMUSG00000030083	Abtb1	AI847549|BC003234|BPOZ|EF1ABP	ankyrin repeat and BTB (POZ) domain containing 1	protein-coding
mm_16434.1	chr2	180394380	180394398	+	1	NA	intron (NR_045331, intron 3 of 3)	intron (NR_045331, intron 3 of 3)	-3990	NR_029901	723954		NR_029901	ENSMUSG00000065460	Mir133a-2	Mirn133a-2|mir-133a-2	microRNA 133a-2	ncRNA
mm_7467.1	chr1	120484805	120484818	-	1	NA	exon (NM_010766, exon 11 of 17)	exon (NM_010766, exon 11 of 17)	20273	NM_010766	17167	Mm.1856	NM_010766	ENSMUSG00000026390	Marco	AI323439|Ly112|Scara2	macrophage receptor with collagenous structure	protein-coding
mm_124338.1	chr14	103844247	103844267	-	1	NA	promoter-TSS (NM_001276296)	promoter-TSS (NM_001276296)	219	NM_001136061	13618	Mm.229532	NM_007904	ENSMUSG00000022122	Ednrb	ET-B|ET-BR|ETR-b|ETb|Sox10m1	endothelin receptor type B	protein-coding
mm_73574.1	chr8	109778567	109778577	+	1	NA	promoter-TSS (NM_009677)	promoter-TSS (NM_009677)	-11	NM_009677	11765	Mm.37210	NM_009677	ENSMUSG00000031731	Ap1g1	AA409002|AU041323|AW551707|Adtg|D8Ertd374e	adaptor protein complex AP-1, gamma 1 subunit	protein-coding
mm_159940.1	chr6	82402922	82402922	+	1	NA	5' UTR (NM_009313, exon 2 of 6)	5' UTR (NM_009313, exon 2 of 6)	447	NM_009313	21336	Mm.8055	NM_009313	ENSMUSG00000030043	Tacr1	Nk1r|Spr|Tac1r	tachykinin receptor 1	protein-coding
mm_24743.1	chr3	95314833	95314866	+	1	NA	promoter-TSS (NM_029789)	promoter-TSS (NM_029789)	-341	NM_029789	76893	Mm.181009	NM_029789	ENSMUSG00000015714	Cers2	0610013I17Rik|AI225939|Lass2|TRH3	ceramide synthase 2	protein-coding
mm_12509.1	chr2	71981061	71981071	+	1	NA	promoter-TSS (NM_001204167)	promoter-TSS (NM_001204167)	-149	NM_001204167	56508	Mm.196153	NM_019688	ENSMUSG00000049044	Rapgef4	1300003D15Rik|5730402K07Rik|6330581N18Rik|EPAC 2|Epac-2|Epac2|mKIAA4040	Rap guanine nucleotide exchange factor (GEF) 4	protein-coding
mm_24842.1	chr3	95661860	95661905	+	1	NA	3' UTR (NM_008562, exon 3 of 3)	3' UTR (NM_008562, exon 3 of 3)	3161	NM_008562	17210	Mm.1639	NM_008562	ENSMUSG00000038612	Mcl1	AW556805|Mcl-1	myeloid cell leukemia sequence 1	protein-coding
mm_18618.1	chr2	68471946	68471994	-	1	NA	promoter-TSS (NM_016866)	promoter-TSS (NM_016866)	11	NM_016866	53416	Mm.198414	NM_016866	ENSMUSG00000027030	Stk39	AW227544|AW556857|DCHT|RF005|Rnl5|SPAK	serine/threonine kinase 39	protein-coding
mm_81856.1	chr9	118703478	118703488	+	1	NA	intron (NM_133721, intron 15 of 27)	intron (NM_133721, intron 15 of 27)	-8209	NM_001113514	104099	Mm.335520	NM_133721	ENSMUSG00000039115	Itga9	(alpha)9|2610002H11Rik|6720458D17Rik|AI461869|D130073C02|D9Ertd428e	integrin alpha 9	protein-coding
mm_107340.1	chr12	32379222	32379234	+	1	NA	exon (NM_001162903, exon 1 of 1)	exon (NM_001162903, exon 1 of 1)	439	NM_001162903	72123	Mm.341352	NM_028111	ENSMUSG00000090946	Ccdc71l	2010109K11Rik|AV375874	coiled-coil domain containing 71 like	protein-coding
mm_38163.1	chr4	135216663	135216677	-	1	NA	3' UTR (NM_013885, exon 6 of 6)	3' UTR (NM_013885, exon 6 of 6)	56090	NM_013885	29876	Mm.257765	NM_013885	ENSMUSG00000037242	Clic4	D0Jmb3|TU-74|mc3s5|mtCLIC	chloride intracellular channel 4 (mitochondrial)	protein-coding
mm_54832.1	chr6	42585986	42585997	-	1	NA	Intergenic	Intergenic	11381	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_148297.1	chr18	82618871	82618888	-	1	NA	exon (NM_177832, exon 23 of 30)	exon (NM_177832, exon 23 of 30)	64371	NM_001025254	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_63002.1	chr7	120842825	120842836	+	1	NA	promoter-TSS (NM_001267710)	promoter-TSS (NM_001267710)	-1	NM_007908	13631	Mm.25997	NM_007908	ENSMUSG00000035064	Eef2k	C86191|eEF-2K	eukaryotic elongation factor-2 kinase	protein-coding
mm_104058.1	chr11	86580433	86580437	-	1	NA	Intergenic	Intergenic	3723	NR_029738	387140		NR_029738	ENSMUSG00000065455	Mir21a	Mir21|Mirn21|mmu-mir-21|mmu-mir-21a	microRNA 21a	ncRNA
mm_82567.1	chr9	21077187	21077189	-	1	NA	intron (NR_038081, intron 9 of 16)	ID_B1|SINE|B4	-1600	NR_106050	102465656		NR_106050	ENSMUSG00000098907	Mir7082	Gm27933|mmu-mir-7082	microRNA 7082	ncRNA
mm_151311.1	chr19	55804369	55804372	+	1	NA	intron (NM_001331150, intron 4 of 14)	intron (NM_001331150, intron 4 of 14)	62560	NM_001142923	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_165391.1	chr2	131855399	131855407	-	1	NA	3' UTR (NM_001166206, exon 2 of 2)	3' UTR (NM_001166206, exon 2 of 2)	4344	NM_001166206	71995	Mm.22	NM_028045	ENSMUSG00000037482	Erv3	1600014E20Rik|AA389086|AI426069|AI448024|D19349	endogenous retroviral sequence 3	protein-coding
mm_14357.1	chr2	129615569	129615581	+	1	NA	exon (NM_007547, exon 3 of 8)	exon (NM_007547, exon 3 of 8)	22406	NM_001291022	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_46088.1	chr5	92347001	92347005	-	1	NA	3' UTR (NM_021274, exon 4 of 4)	3' UTR (NM_021274, exon 4 of 4)	1886	NM_021274	15945	Mm.877	NM_021274	ENSMUSG00000034855	Cxcl10	C7|CRG-2|INP10|IP-10|IP10|Ifi10|Scyb10|gIP-10|mob-1	chemokine (C-X-C motif) ligand 10	protein-coding
mm_21401.1	chr2	157794235	157794257	-	1	NA	intron (NM_025680, intron 4 of 15)	intron (NM_025680, intron 4 of 15)	56845	NM_025680	66642	Mm.45193	NM_025680	ENSMUSG00000027649	Ctnnbl1	5730471K09Rik|NAP|NYD-SP19|P14L	catenin, beta like 1	protein-coding
mm_18465.1	chr2	62352133	62352177	-	1	NA	exon (NM_010074, exon 20 of 26)	exon (NM_010074, exon 20 of 26)	60076	NM_010074	13482	Mm.1151	NM_010074	ENSMUSG00000035000	Dpp4	Cd26|Dpp-4|THAM	dipeptidylpeptidase 4	protein-coding
mm_138137.1	chr17	34198180	34198206	+	1	NA	promoter-TSS (NM_010724)	promoter-TSS (NM_010724)	-2	NM_010724	16913	Mm.180191	NM_010724	ENSMUSG00000024338	Psmb8	Lmp-7|Lmp7	proteasome (prosome, macropain) subunit, beta type 8 (large multifunctional peptidase 7)	protein-coding
mm_85727.1	chr9	108340069	108340080	-	1	NA	exon (NM_008160, exon 2 of 2)	exon (NM_008160, exon 2 of 2)	994	NM_001329528	14775	Mm.1090	NM_008160	ENSMUSG00000063856	Gpx1	AI195024|AL033363|CGPx|GPx-1|GSHPx-1|Gpx	glutathione peroxidase 1	protein-coding
mm_150947.1	chr19	46310206	46310230	+	1	NA	exon (NM_001177370, exon 16 of 22)	exon (NM_001177370, exon 16 of 22)	4288	NM_001177370	18034	Mm.102365	NM_019408	ENSMUSG00000025225	Nfkb2	NF-kappaB2|lyt|p49|p49/p100|p50B|p52	nuclear factor of kappa light polypeptide gene enhancer in B cells 2, p49/p100	protein-coding
mm_99595.1	chr11	104328577	104328598	+	1	NA	3' UTR (NM_010838, exon 10 of 10)	3' UTR (NM_010838, exon 10 of 10)	97151	NM_001285454	17762	Mm.1287	NM_010838	ENSMUSG00000018411	Mapt	AI413597|AW045860|Mtapt|Tau	microtubule-associated protein tau	protein-coding
mm_108828.1	chr12	95748053	95748066	+	1	NA	intron (NM_201518, intron 1 of 1)	intron (NM_201518, intron 1 of 1)	55833	NM_201518	399558	Mm.341948	NM_201518	ENSMUSG00000047414	Flrt2	-	fibronectin leucine rich transmembrane protein 2	protein-coding
mm_141956.1	chr17	35115670	35115690	-	1	NA	promoter-TSS (NM_148939)	promoter-TSS (NM_148939)	-280	NM_148939	266614	Mm.104680	NM_148939	ENSMUSG00000043807	Ly6g5b	-	lymphocyte antigen 6 complex, locus G5B	protein-coding
mm_145230.1	chr18	50128270	50128333	+	1	NA	promoter-TSS (NM_008292)	promoter-TSS (NM_008292)	100	NM_008292	15488	Mm.277857	NM_008292	ENSMUSG00000024507	Hsd17b4	17-beta-HSD|17[b]-HSD|DBP|MFE-2|MFP2|MPF-2|Mfp-2|perMFE-2	hydroxysteroid (17-beta) dehydrogenase 4	protein-coding
mm_68719.1	chr7	120095684	120095711	-	1	NA	Intergenic	Intergenic	-6729	NM_145586	233806	Mm.257952	NM_145586	ENSMUSG00000030917	Tmem159	8430420C20Rik	transmembrane protein 159	protein-coding
mm_139618.1	chr17	57362554	57362564	+	1	NA	intron (NM_010130, intron 2 of 21)	RLTR22_Mur|LTR|ERVK	3873	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_22334.1	chr2	180709081	180709101	-	1	NA	intron (NM_177852, intron 1 of 14)	intron (NM_177852, intron 1 of 14)	908	NM_177852	23856	Mm.253836	NM_011805	ENSMUSG00000038914	Dido1	6720461J16Rik|D130048F08Rik|DATF-1|DIO-1|Datf1|dido	death inducer-obliterator 1	protein-coding
mm_158052.1	chrX	100594861	100594876	-	1	NA	promoter-TSS (NM_020621)	promoter-TSS (NM_020621)	1	NM_020621	57385	Mm.117118	NM_020621	ENSMUSG00000044359	P2ry4	P2Y4|P2Y4R	pyrimidinergic receptor P2Y, G-protein coupled, 4	protein-coding
mm_62016.1	chr7	91488693	91488694	+	1	NA	intron (NM_011807, intron 2 of 22)	MIR3|SINE|MIR	397907	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_109570.1	chr12	112106792	112106810	+	1	NA	5' UTR (NM_001081169, exon 1 of 15)	5' UTR (NM_001081169, exon 1 of 15)	118	NM_001081169	104816	Mm.77133	NM_001081169	ENSMUSG00000037686	Aspg	A530050D06Rik|AI429460|Gm690	asparaginase	protein-coding
mm_44083.1	chr5	149157399	149157415	+	1	NA	intron (NR_015478, intron 1 of 2)	intron (NR_015478, intron 1 of 2)	-1215	NR_028061	667410	Mm.441522	NR_028061		Gm8615	EG667410	glucosamine-6-phosphate deaminase 1 pseudogene	pseudo
mm_37585.1	chr4	126429406	126429416	-	1	NA	5' UTR (NM_153402, exon 1 of 19)	5' UTR (NM_153402, exon 1 of 19)	131	NM_153402	214150	Mm.440915	NM_153402	ENSMUSG00000028842	Ago3	AW048688|C130014L07Rik|Eif2c3	argonaute RISC catalytic subunit 3	protein-coding
mm_34011.1	chr4	137993446	137993474	+	1	NA	promoter-TSS (NM_001256198)	promoter-TSS (NM_001256198)	4	NM_172703	230861	Mm.268903	NM_172703	ENSMUSG00000028760	Eif4g3	1500002J22Rik|4930523M17Rik|G1-419-52|eIF4GII|repro8	eukaryotic translation initiation factor 4 gamma, 3	protein-coding
mm_27034.1	chr3	26321653	26321656	-	1	NA	intron (NM_138666, intron 1 of 7)	intron (NM_138666, intron 1 of 7)	10255	NM_138666	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_147842.1	chr18	63087477	63087480	-	1	NA	intron (NM_001039485, intron 20 of 53)	intron (NM_001039485, intron 20 of 53)	109562	NM_028017	108123	Mm.292687	NM_028017	ENSMUSG00000024581	Napg	2400003O04Rik|SNARE	N-ethylmaleimide sensitive fusion protein attachment protein gamma	protein-coding
mm_71457.1	chr8	46521886	46521896	+	1	NA	intron (NM_001302163, intron 11 of 20)	Lx7|LINE|L1	-30178	NM_027973	71876	Mm.22108	NM_027973	ENSMUSG00000031629	Cenpu	1700029A22Rik|Mlf1ip	centromere protein U	protein-coding
mm_103625.1	chr11	78697371	78697475	-	1	NA	promoter-TSS (NM_008702)	promoter-TSS (NM_008702)	2	NM_008702	18099	Mm.9001	NM_008702	ENSMUSG00000017376	Nlk	AI194375	nemo like kinase	protein-coding
mm_158058.1	chrX	101059656	101059664	-	1	NA	promoter-TSS (NM_001167997)	promoter-TSS (NM_001167997)	-21	NM_001167997	83558	Mm.134024	NM_031384	ENSMUSG00000009670	Tex11	4930565P14Rik|BB024231|ZIP4H	testis expressed gene 11	protein-coding
mm_104939.1	chr11	100112155	100112162	-	1	NA	Intergenic	Intergenic	-6532	NM_001174099	16673	Mm.306829	NM_008472	ENSMUSG00000020916	Krt36	HRa-1|K36|Krt1-22|Krt1-5|MHRa-1	keratin 36	protein-coding
mm_81455.1	chr9	109833060	109833073	+	1	NA	intron (NM_018757, intron 1 of 6)	intron (NM_018757, intron 1 of 6)	272	NM_018757	54369	Mm.12951	NM_018757	ENSMUSG00000032478	Nme6	nm23-M6	NME/NM23 nucleoside diphosphate kinase 6	protein-coding
mm_61093.1	chr7	51787443	51787444	+	1	NA	Intergenic	Intergenic	-74572	NM_001330608	14453	Mm.207360	NM_008087	ENSMUSG00000030498	Gas2	Gas-2	growth arrest specific 2	protein-coding
mm_81339.1	chr9	108524656	108524659	+	1	NA	intron (NM_001114119, intron 2 of 10)	B2_Mm2|SINE|B2	7570	NM_175143	69232	Mm.335449	NM_175143	ENSMUSG00000006673	Qrich1	2610028H07Rik	glutamine-rich 1	protein-coding
mm_148071.1	chr18	72350394	72350405	-	1	NA	exon (NM_007831, exon 1 of 29)	exon (NM_007831, exon 1 of 29)	670	NM_007831	13176	Mm.167882	NM_007831	ENSMUSG00000060534	Dcc	C030036D22Rik|Igdcc1	deleted in colorectal carcinoma	protein-coding
mm_86413.1	chr10	3366507	3366590	+	1	NA	5' UTR (NM_133485, exon 1 of 4)	5' UTR (NM_133485, exon 1 of 4)	398	NM_133485	76142	Mm.308126	NM_133485	ENSMUSG00000040653	Ppp1r14c	6330514J04Rik|KEPI	protein phosphatase 1, regulatory (inhibitor) subunit 14c	protein-coding
mm_73337.1	chr8	105304747	105304772	+	1	NA	promoter-TSS (NM_172760)	promoter-TSS (NM_172760)	-842	NM_172760	234683	Mm.237966	NM_172760	ENSMUSG00000014791	Elmo3	9930107J06|BC058752|CED-12|Ced12	engulfment and cell motility 3	protein-coding
mm_77391.1	chr8	120228105	120228145	-	1	NA	non-coding (NR_110496, exon 1 of 3)	non-coding (NR_110496, exon 1 of 3)	105	NR_110496	434353	Mm.411793	NR_110496	ENSMUSG00000097960	A330074K22Rik	-	RIKEN cDNA A330074K22 gene	ncRNA
mm_153347.1	chr19	39649047	39649061	-	1	NA	promoter-TSS (NM_001024719)	promoter-TSS (NM_001024719)	-12	NM_001024719	545288	Mm.297048	NM_001024719	ENSMUSG00000062624	Cyp2c67	C730004C24Rik	cytochrome P450, family 2, subfamily c, polypeptide 67	protein-coding
mm_40585.1	chr5	64160050	64160060	+	1	NA	promoter-TSS (NM_019636)	promoter-TSS (NM_019636)	-205	NM_019636	57915	Mm.286353	NM_019636	ENSMUSG00000029174	Tbc1d1	1110062G02Rik|AI385682|AW555803|Nob1|Nobq1|Tbc1|mKIAA1108	TBC1 domain family, member 1	protein-coding
mm_17547.1	chr2	29890335	29890370	-	1	NA	intron (NM_013615, intron 1 of 16)	CpG	289	NM_013615	18286	Mm.330116	NM_013615	ENSMUSG00000026790	Odf2	AI848335|MMTEST29	outer dense fiber of sperm tails 2	protein-coding
mm_96699.1	chr11	69633257	69633284	+	1	NA	5' UTR (NM_011814, exon 1 of 17)	5' UTR (NM_011814, exon 1 of 17)	299	NM_011814	23879	Mm.41930	NM_011814	ENSMUSG00000018765	Fxr2	Fxr2h	fragile X mental retardation, autosomal homolog 2	protein-coding
mm_162476.1	chr1	133350286	133350300	+	1	NA	promoter-TSS (NM_031193)	promoter-TSS (NM_031193)	-273	NM_031193	19702	Mm.220955	NM_031193		Ren2	Ren|Ren-2|Ren-B|Rn-2|Rnr	renin 2 tandem duplication of Ren1	protein-coding
mm_78415.1	chr9	31019077	31019087	+	1	NA	Intergenic	Intergenic	-11562	NM_001115130	235132	Mm.239355	NM_172765	ENSMUSG00000047412	Zbtb44	6030404E16Rik|Btbd15|E230011F09	zinc finger and BTB domain containing 44	protein-coding
mm_13660.1	chr2	114055299	114055312	+	1	NA	non-coding (NR_028422, exon 1 of 3)	non-coding (NR_028422, exon 1 of 3)	909	NR_028422	100303644	Mm.330469	NR_028422	ENSMUSG00000092397	C130080G10Rik	-	RIKEN cDNA C130080G10 gene	ncRNA
mm_148274.1	chr18	81927638	81927640	-	1	NA	Intergenic	Intergenic	64441	NR_039589	100628596		NR_039589	ENSMUSG00000093036	Mir5127	mmu-mir-5127|mu-mir-5127	microRNA 5127	ncRNA
mm_128608.1	chr15	58818129	58818133	-	1	NA	intron (NM_175212, intron 1 of 6)	MLT1D|LTR|ERVL-MaLR	5296	NM_175212	74868	Mm.293754	NM_175212	ENSMUSG00000062373	Tmem65	2610029O13Rik|4930438D12Rik	transmembrane protein 65	protein-coding
mm_143173.1	chr17	57228085	57228101	-	1	NA	promoter-TSS (NM_009778)	promoter-TSS (NM_009778)	43	NM_009778	12266	Mm.19131	NM_009778	ENSMUSG00000024164	C3	AI255234|ASP|HSE-MSF|Plp	complement component 3	protein-coding
mm_96177.1	chr11	61651135	61651161	+	1	NA	Intergenic	Intergenic	-2173	NM_027817	71520	Mm.202760	NM_027817	ENSMUSG00000004837	Grap	8430435N19Rik|BB233594	GRB2-related adaptor protein	protein-coding
mm_161602.1	chr16	37916370	37916370	+	1	NA	promoter-TSS (NM_153394)	promoter-TSS (NM_153394)	-126	NM_153394	239845	Mm.228018	NM_153394	ENSMUSG00000046961	Gpr156	Gababl	G protein-coupled receptor 156	protein-coding
mm_64044.1	chr7	140835109	140835181	+	1	NA	promoter-TSS (NM_029821)	promoter-TSS (NM_029821)	7	NM_001347605	76974	Mm.272359	NM_029821	ENSMUSG00000025481	Urah	1190003J15Rik|2810420C16Rik	urate (5-hydroxyiso-) hydrolase	protein-coding
mm_150205.1	chr19	32778162	32778165	+	1	NA	intron (NM_008960, intron 2 of 8)	B1_Mur1|SINE|Alu	20586	NM_008960	19211	Mm.245395	NM_008960	ENSMUSG00000013663	Pten	2310035O07Rik|A130070J02Rik|AI463227|B430203M17Rik|MMAC1|TEP1	phosphatase and tensin homolog	protein-coding
mm_7498.1	chr1	121430691	121430700	-	1	NA	promoter-TSS (NM_029955)	promoter-TSS (NM_029955)	-372	NM_029955	70829	Mm.25788	NM_027567	ENSMUSG00000026339	Ccdc93	4633402D15Rik|9230102M16Rik	coiled-coil domain containing 93	protein-coding
mm_131229.1	chr16	10411929	10411965	+	1	NA	promoter-TSS (NM_011955)	promoter-TSS (NM_011955)	9	NM_011955	26425	Mm.29037	NM_011955	ENSMUSG00000022503	Nubp1	-	nucleotide binding protein 1	protein-coding
mm_44618.1	chr5	25529623	25529639	-	1	NA	promoter-TSS (NR_027388)	promoter-TSS (NR_027388)	-387	NR_027388	73571	Mm.105263	NR_027388	ENSMUSG00000101856	1700096K18Rik	-	RIKEN cDNA 1700096K18 gene	ncRNA
mm_107560.1	chr12	41732419	41732421	+	1	NA	intron (NM_053122, intron 6 of 6)	B4A|SINE|B4	-246363	NM_010733	16981	Mm.404786	NM_010733	ENSMUSG00000036295	Lrrn3	NLRR-3	leucine rich repeat protein 3, neuronal	protein-coding
mm_112719.1	chr13	19190718	19190731	+	1	NA	Intergenic	Intergenic	205089	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_25464.1	chr3	108591468	108591489	+	1	NA	5' UTR (NM_181400, exon 1 of 15)	5' UTR (NM_181400, exon 1 of 15)	200	NM_181400	99512	Mm.285968	NM_181400	ENSMUSG00000040389	Wdr47	1810073M12Rik|AA552998|mKIAA0893	WD repeat domain 47	protein-coding
mm_47987.1	chr5	135934591	135934613	-	1	NA	promoter-TSS (NM_018871)	promoter-TSS (NM_018871)	39	NM_018871	22628	Mm.233813	NM_018871	ENSMUSG00000051391	Ywhag	14-3-3gamma|D7Bwg1348e	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, gamma polypeptide	protein-coding
mm_27161.1	chr3	33143026	33143086	-	1	NA	5' UTR (NM_001163516, exon 1 of 13)	5' UTR (NM_001163516, exon 1 of 13)	135	NM_001163516	58869	Mm.151332	NM_021483	ENSMUSG00000027674	Pex5l	1700016J08Rik|PXR2|Pex2|TRIP8b|pex5Rp	peroxisomal biogenesis factor 5-like	protein-coding
mm_29322.1	chr3	108017812	108017826	-	1	NA	5' UTR (NM_010358, exon 1 of 8)	5' UTR (NM_010358, exon 1 of 8)	154	NM_010358	14862	Mm.37199	NM_010358	ENSMUSG00000058135	Gstm1	Gstb-1|Gstb1	glutathione S-transferase, mu 1	protein-coding
mm_52889.1	chr6	122577872	122577898	+	1	NA	TTS (NM_031159)	TTS (NM_031159)	24076	NM_009645	11628	Mm.391503	NM_009645	ENSMUSG00000040627	Aicda	Aid|Arp2	activation-induced cytidine deaminase	protein-coding
mm_153886.1	chr19	46961917	46961930	-	1	NA	intron (NM_001164363, intron 1 of 17)	CpG	428	NM_029810	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_143770.1	chr17	81670146	81670158	-	1	NA	intron (NR_104580, intron 1 of 8)	CpG	68235	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_115029.1	chr13	99247683	99247693	+	1	NA	TTS (NM_001004149)	TTS (NM_001004149)	62865	NM_001004149	238803	Mm.343207	NM_001004149	ENSMUSG00000050919	Zfp366	DC-SCRIPT|Znf366	zinc finger protein 366	protein-coding
mm_159501.1	chr4	43770903	43770903	-	1	NA	exon (NM_019476, exon 1 of 1)	exon (NM_019476, exon 1 of 1)	106	NM_019476	29849	Mm.88845	NM_019476	ENSMUSG00000044801	Olfr159	MOR262-5|Olfr37e|mOR37e	olfactory receptor 159	protein-coding
mm_45330.1	chr5	65492985	65492991	-	1	NA	promoter-TSS (NM_133697)	promoter-TSS (NM_133697)	-153	NM_133697	68552	Mm.10709	NM_133697	ENSMUSG00000037822	Smim14	1110003E01Rik|1700127H04Rik|5430439C17Rik|MAd4	small integral membrane protein 14	protein-coding
mm_170187.1	chr17	63671747	63671755	-	1	NA	Intergenic	L1Md_T|LINE|L1	-171171	NM_015794	50758	Mm.136366	NM_015794	ENSMUSG00000023965	Fbxl17	6330576B01Rik|AI452053|BB073797|C130023C01Rik|Fbx13|Fbxo13	F-box and leucine-rich repeat protein 17	protein-coding
mm_22816.1	chr3	27192133	27192146	+	1	NA	intron (NM_178772, intron 1 of 4)	intron (NM_178772, intron 1 of 4)	9135	NM_178772	320024	Mm.24576	NM_178772	ENSMUSG00000027698	Nceh1	Aadacl1|B230106I24Rik|CPO-BP|Nceh	neutral cholesterol ester hydrolase 1	protein-coding
mm_88978.1	chr10	81559429	81559444	+	1	NA	promoter-TSS (NM_010347)	promoter-TSS (NM_010347)	-8	NR_074087	14797	Mm.180013	NM_010347	ENSMUSG00000054452	Aes	AL024115|Esp1|Grg|Grg-5|Grg5|Tle5	amino-terminal enhancer of split	protein-coding
mm_83415.1	chr9	44879092	44879095	-	1	NA	intron (NM_001081049, intron 1 of 35)	intron (NM_001081049, intron 1 of 35)	2181	NM_001081049	214162	Mm.2389	NM_001081049	ENSMUSG00000002028	Kmt2a	6430520K01|ALL-1|All1|Cxxc7|HRX|HTRX1|Mll|Mll1|mKIAA4050	lysine (K)-specific methyltransferase 2A	protein-coding
mm_148514.1	chr19	4231990	4232000	+	1	NA	promoter-TSS (NR_132280)	promoter-TSS (NR_132280)	102	NM_027196	69745	Mm.32518	NM_027196	ENSMUSG00000024854	Pold4	2410012M21Rik|AI463381|AW060307|Polds|p12	polymerase (DNA-directed), delta 4	protein-coding
mm_121225.1	chr14	103055493	103055503	+	1	NA	exon (NM_008392, exon 5 of 5)	exon (NM_008392, exon 5 of 5)	8486	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_136365.1	chr16	92797350	92797381	-	1	NA	intron (NM_001111022, intron 2 of 6)	ID_B1|SINE|B4	28709	NM_001111021	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_161186.1	chr13	49090949	49090949	-	1	NA	exon (NM_001290311, exon 7 of 29)	exon (NM_001290311, exon 7 of 29)	57379	NM_029361	75607	Mm.342723	NM_029361	ENSMUSG00000037989	Wnk2	1810073P09Rik|AW122246|ESTM15|X83337|mKIAA1760	WNK lysine deficient protein kinase 2	protein-coding
mm_137302.1	chr17	24850692	24850700	+	1	NA	promoter-TSS (NM_023480)	promoter-TSS (NM_023480)	29	NM_001159626	14651	Mm.43784	NM_024284	ENSMUSG00000024158	Hagh	BC019817|Glo-2|Glo2|Rsp29	hydroxyacyl glutathione hydrolase	protein-coding
mm_104398.1	chr11	94507289	94507299	-	1	NA	intron (NM_170671, intron 12 of 18)	intron (NM_170671, intron 12 of 18)	-7320	NM_027984	71889	Mm.248620	NM_027984	ENSMUSG00000010080	Epn3	2310022G12Rik	epsin 3	protein-coding
mm_84743.1	chr9	75387960	75387973	-	1	NA	3' UTR (NM_015806, exon 6 of 6)	3' UTR (NM_015806, exon 6 of 6)	21393	NM_027418	50772	Mm.480076	NM_015806	ENSMUSG00000042688	Mapk6	2610021I23Rik|D130053K17Rik|Erk3|Mapk4|Mapk63|Prkm4|Prkm6	mitogen-activated protein kinase 6	protein-coding
mm_148848.1	chr19	6384396	6384422	+	1	NA	promoter-TSS (NM_011224)	promoter-TSS (NM_011224)	1	NM_011224	19309	Mm.27806	NM_011224	ENSMUSG00000032648	Pygm	AI115133|PG	muscle glycogen phosphorylase	protein-coding
mm_7482.1	chr1	120531840	120531863	-	1	NA	Intergenic	Intergenic	-26767	NM_010766	17167	Mm.1856	NM_010766	ENSMUSG00000026390	Marco	AI323439|Ly112|Scara2	macrophage receptor with collagenous structure	protein-coding
mm_98313.1	chr11	90035966	90035976	+	1	NA	3' UTR (NM_026433, exon 3 of 3)	3' UTR (NM_026433, exon 3 of 3)	5623	NM_026433	67888	Mm.212428	NM_026433	ENSMUSG00000069763	Tmem100	1810057C19Rik|AV011897	transmembrane protein 100	protein-coding
mm_72507.1	chr8	83900089	83900093	+	1	NA	promoter-TSS (NM_181039)	promoter-TSS (NM_181039)	-7	NM_181039	330814	Mm.260733	NM_181039	ENSMUSG00000013033	Adgrl1	2900070I05Rik|AI182398|CLIBA|Lec2|Lphn1|mKIAA0821	adhesion G protein-coupled receptor L1	protein-coding
mm_162695.1	chr10	19939522	19939530	+	1	NA	intron (NM_008580, intron 1 of 29)	intron (NM_008580, intron 1 of 29)	5000	NM_008580	26408	Mm.6595	NM_008580	ENSMUSG00000071369	Map3k5	7420452D20Rik|ASK|ASK1|MAPKKK5|Mekk5	mitogen-activated protein kinase kinase kinase 5	protein-coding
mm_53370.1	chr6	129408917	129408927	+	1	NA	promoter-TSS (NM_001205364)	promoter-TSS (NM_001205364)	60	NM_172732	232414	Mm.391518	NM_172732	ENSMUSG00000046080	Clec9a	9830005G06Rik|DNGR-1	C-type lectin domain family 9, member a	protein-coding
mm_120412.1	chr14	65266681	65266692	+	1	NA	promoter-TSS (NM_015795)	promoter-TSS (NM_015795)	-15	NM_015795	50759	Mm.65308	NM_015795	ENSMUSG00000034532	Fbxo16	4932435C24Rik|Fbx16	F-box protein 16	protein-coding
mm_19010.1	chr2	76904870	76904873	-	1	NA	intron (NM_011652, intron 46 of 312)	Lx9|LINE|L1	77676	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_63212.1	chr7	126272476	126272492	+	1	NA	promoter-TSS (NM_145587)	promoter-TSS (NM_145587)	-135	NM_145587	104175	Mm.29660	NM_145587	ENSMUSG00000042978	Sbk1	Sbk	SH3-binding kinase 1	protein-coding
mm_49471.1	chr6	29471500	29471518	+	1	NA	promoter-TSS (NM_001145360)	promoter-TSS (NM_001145360)	72	NM_001145360	668210	Mm.420607	NM_001145360	ENSMUSG00000090685	Gm9047	EG668210	predicted gene 9047	protein-coding
mm_44043.1	chr5	147548071	147548074	+	1	NA	3' UTR (NM_028291, exon 19 of 19)	3' UTR (NM_028291, exon 19 of 19)	117492	NM_028291	72587	Mm.320469	NM_028291	ENSMUSG00000029647	Pan3	2700050F09Rik|A430027N15Rik|AU014670	PAN3 poly(A) specific ribonuclease subunit	protein-coding
mm_112406.1	chr13	3548887	3548926	+	1	NA	exon (NM_008112, exon 2 of 11)	exon (NM_008112, exon 2 of 11)	10831	NM_008112	14569	Mm.153226	NM_008112	ENSMUSG00000021218	Gdi2	GDI-B|GDIB|Gdi3	guanosine diphosphate (GDP) dissociation inhibitor 2	protein-coding
mm_34161.1	chr4	139574645	139574690	+	1	NA	promoter-TSS (NM_001205173)	promoter-TSS (NM_001205173)	-53	NM_001205173	212632	Mm.30464	NM_183148	ENSMUSG00000041025	Iffo2	C79267	intermediate filament family orphan 2	protein-coding
mm_32632.1	chr4	115000157	115000170	+	1	NA	promoter-TSS (NM_009185)	promoter-TSS (NM_009185)	45	NM_001304555	20460	Mm.3988	NM_009185	ENSMUSG00000028718	Stil	Sil	Scl/Tal1 interrupting locus	protein-coding
mm_96302.1	chr11	63157875	63157878	+	1	NA	intron (NM_001302261, intron 3 of 3)	intron (NM_001302261, intron 3 of 3)	25073	NM_001302260	18858	Mm.1237	NM_008885	ENSMUSG00000018217	Pmp22	22kDa|Gas-3|HNPP|Tr|trembler	peripheral myelin protein 22	protein-coding
mm_163680.1	chr13	92131548	92131561	-	1	NA	Intergenic	CpG	-143512	NM_009027	19418	Mm.248630	NM_009027	ENSMUSG00000021708	Rasgrf2	6330417G04Rik|AW048350|Grf2|Ras-GRF2	RAS protein-specific guanine nucleotide-releasing factor 2	protein-coding
mm_78662.1	chr9	40685955	40685976	+	1	NA	promoter-TSS (NM_133733)	promoter-TSS (NM_133733)	1	NM_133733	71566	Mm.280560	NM_133733	ENSMUSG00000032024	Clmp	9030425E11Rik|ACAM|ASP5|AW557819	CXADR-like membrane protein	protein-coding
mm_92828.1	chr10	81482094	81482113	-	1	NA	intron (NM_001311124, intron 1 of 11)	G-rich|Low_complexity|Low_complexity	606	NM_176954	319586	Mm.152689	NM_176954	ENSMUSG00000034818	Celf5	4930565A21Rik|Brunol5	CUGBP, Elav-like family member 5	protein-coding
mm_120200.1	chr14	61648436	61648445	+	1	NA	intron (NR_028264, intron 1 of 6)	CpG	-16330	NR_029733	387174		NR_029733	ENSMUSG00000093007	Mir15a	Mirn15a|mir-15a|mmu-mir-15a	microRNA 15a	ncRNA
mm_48411.1	chr5	140262526	140262534	-	1	NA	intron (NM_010752, intron 9 of 17)	intron (NM_010752, intron 9 of 17)	59022	NM_010752	17120	Mm.27250	NM_010752	ENSMUSG00000029554	Mad1l1	AI173502|AW550425|Mad1	MAD1 mitotic arrest deficient 1-like 1	protein-coding
mm_105263.1	chr11	102357162	102357172	-	1	NA	exon (NM_011403, exon 10 of 20)	exon (NM_011403, exon 10 of 20)	8114	NM_011403	20533	Mm.7248	NM_011403	ENSMUSG00000006574	Slc4a1	Ae1|CD233|Empb3|l11Jus51	solute carrier family 4 (anion exchanger), member 1	protein-coding
mm_160814.1	chr11	22512278	22512278	+	1	NA	promoter-TSS (NM_153596)	promoter-TSS (NM_153596)	-5	NM_153596	103765	Mm.221274	NM_153596	ENSMUSG00000049904	Tmem17	AI503894|AW049890	transmembrane protein 17	protein-coding
mm_83205.1	chr9	41876214	41876218	-	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	248073	NM_011436	20660	Mm.121920	NM_011436	ENSMUSG00000049313	Sorl1	2900010L19Rik|AI596264|AW261561|LR11|SorLA|gp250|mSorLA	sortilin-related receptor, LDLR class A repeats-containing	protein-coding
mm_49008.1	chr6	4758348	4758350	+	1	NA	3' UTR (NM_130877, exon 2 of 2)	3' UTR (NM_130877, exon 2 of 2)	11043	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_79632.1	chr9	59539644	59539717	+	1	NA	5' UTR (NM_010421, exon 1 of 14)	5' UTR (NM_010421, exon 1 of 14)	140	NM_010421	15211	Mm.2284	NM_010421	ENSMUSG00000025232	Hexa	Hex-1	hexosaminidase A	protein-coding
mm_107313.1	chr12	31265242	31265267	+	1	NA	promoter-TSS (NM_008482)	promoter-TSS (NM_008482)	-40	NM_008482	16777	Mm.172674	NM_008482	ENSMUSG00000002900	Lamb1	C77966|C80098|C81607|D130003D08Rik|Lamb-1|Lamb1-1	laminin B1	protein-coding
mm_110853.1	chr12	73284999	73285028	-	1	NA	exon (NM_029580, exon 2 of 5)	exon (NM_029580, exon 2 of 5)	1698	NM_029580	76357	Mm.311344	NM_029580	ENSMUSG00000034442	Trmt5	2610027O18Rik|mKIAA1393	TRM5 tRNA methyltransferase 5	protein-coding
mm_149934.1	chr19	27019766	27019769	+	1	NA	Intergenic	Intergenic	133842	NM_001033407	329047	Mm.293289	NM_001033407	ENSMUSG00000074913	Gm815	-	predicted gene 815	protein-coding
mm_3951.1	chr1	164062071	164062098	+	1	NA	promoter-TSS (NM_001164059)	promoter-TSS (NM_001164059)	8	NM_001164059	20343	Mm.1461	NM_011346	ENSMUSG00000026581	Sell	AI528707|CD62L|L-selectin|LECAM-1|Lnhr|Ly-22|Ly-m22|Lyam-1|Lyam1	selectin, lymphocyte	protein-coding
mm_97512.1	chr11	78499247	78499272	+	1	NA	5' UTR (NM_011707, exon 1 of 8)	5' UTR (NM_011707, exon 1 of 8)	139	NM_011707	22370	Mm.3667	NM_011707	ENSMUSG00000017344	Vtn	AI256434|Vn	vitronectin	protein-coding
mm_66500.1	chr7	45062394	45062436	-	1	NA	promoter-TSS (NM_025533)	promoter-TSS (NM_025533)	-14	NM_001163684	66394	Mm.272139	NM_025533	ENSMUSG00000003421	Nosip	2310061K06Rik|CGI-25	nitric oxide synthase interacting protein	protein-coding
mm_34603.1	chr4	150237304	150237342	+	1	NA	promoter-TSS (NM_001025388).2	promoter-TSS (NM_001025388).2	-1	NM_001025388	433182	Mm.70666	NM_001025388	ENSMUSG00000059040	Eno1b	EG433182|Eno1|Gm5506	enolase 1B, retrotransposed	protein-coding
mm_145716.1	chr18	62977935	62977952	+	1	NA	promoter-TSS (NM_028017)	promoter-TSS (NM_028017)	27	NM_028017	108123	Mm.292687	NM_028017	ENSMUSG00000024581	Napg	2400003O04Rik|SNARE	N-ethylmaleimide sensitive fusion protein attachment protein gamma	protein-coding
mm_34938.1	chr4	155841169	155841175	+	1	NA	exon (NM_024263, exon 3 of 10)	exon (NM_024263, exon 3 of 10)	1492	NM_024263	74761	Mm.159028	NM_024263	ENSMUSG00000029070	Mxra8	1200013A08Rik|1700095D18Rik|AI131686|Asp3|Dicam	matrix-remodelling associated 8	protein-coding
mm_98521.1	chr11	94955410	94955419	+	1	NA	Intergenic	Intergenic	-12179	NM_018792	54388	Mm.30482	NM_018792	ENSMUSG00000038994	Hils1	H1.9|TISP64	histone H1-like protein in spermatids 1	protein-coding
mm_148318.1	chr18	83826782	83826807	-	1	NA	Intergenic	Intergenic	259768	NM_001081300	110796	Mm.102136	NM_001081300	ENSMUSG00000046982	Tshz1	5730407I04Rik|D18Bwg1409e|Mtsh1|NY-CO-33|Sdccag33|Tsh1|mKIAA4206|teashirt1	teashirt zinc finger family member 1	protein-coding
mm_18743.1	chr2	73214324	73214332	-	1	NA	5' UTR (NM_025942, exon 1 of 11)	5' UTR (NM_025942, exon 1 of 11)	119	NM_030091	67059	Mm.22661	NM_025942	ENSMUSG00000027108	Ola1	2510025G09Rik|2810405J23Rik|2810409H07Rik|Gtpbp9|PTD004	Obg-like ATPase 1	protein-coding
mm_124083.1	chr14	78692213	78692230	-	1	NA	intron (NM_001081336, intron 1 of 28)	intron (NM_001081336, intron 1 of 28)	32868	NM_001081336	380921	Mm.89591	NM_001081336	ENSMUSG00000034731	Dgkh	5930402B05Rik|D130015C16|DGK	diacylglycerol kinase, eta	protein-coding
mm_173322.1	chrY	90737000	90737007	+	1	NA	Intergenic	IMPB_01|Satellite|Satellite	18047	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_82443.1	chr9	15301450	15301549	-	1	NA	5' UTR (NM_001199485, exon 2 of 9)	5' UTR (NM_001199485, exon 2 of 9)	108	NM_133732	70984	Mm.261842	NM_133732	ENSMUSG00000031938	4931406C07Rik	-	RIKEN cDNA 4931406C07 gene	protein-coding
mm_6687.1	chr1	80665253	80665305	-	1	NA	promoter-TSS (NM_001285927)	promoter-TSS (NM_001285927)	73	NM_001285927	210293	Mm.133473	NM_175291	ENSMUSG00000038608	Dock10	9330153B10Rik|A630054M16Rik|Jr4|Jr5|R75174|ZIZ3|Zizimin3|mKIAA0694	dedicator of cytokinesis 10	protein-coding
mm_53989.1	chr6	6871589	6871589	-	1	NA	Intergenic	Intergenic	-2056	NR_015388	320038	Mm.94021	NR_015388		Dlx6os1	A230055N17Rik|Dlx6as1|Evf-1|Evf-2|Evf1|Evf1/2|Evf2|Shhrs|mEvf-1	distal-less homeobox 6, opposite strand 1	ncRNA
mm_29900.1	chr3	131470863	131470866	-	1	NA	Intergenic	Intergenic	-93904	NM_001289479	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_168051.1	chrY	90812015	90812133	+	1	NA	intron (NM_133362, intron 2 of 3)	IMPB_01|Satellite|Satellite	26632	NM_133362	170942	Mm.76062	NM_133362	ENSMUSG00000096768	Erdr1	edr	erythroid differentiation regulator 1	protein-coding
mm_132872.1	chr16	48611845	48611853	+	1	NA	intron (NM_010816, intron 20 of 26)	B1_Mur3|SINE|Alu	160107	NM_198297	77647	Mm.167298	NM_198297	ENSMUSG00000030775	Trat1	C030046M14Rik|Tcrim|Trim	T cell receptor associated transmembrane adaptor 1	protein-coding
mm_52151.1	chr6	97994377	97994402	+	1	NA	exon (NM_001178049, exon 4 of 10)	exon (NM_001178049, exon 4 of 10)	2606	NM_008601	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_160146.1	chr7	39413365	39413365	-	1	NA	promoter-TSS (NM_177890)	promoter-TSS (NM_177890)	-205	NM_177890	330513	Mm.67238	NM_177890	ENSMUSG00000053742	Gm5114	4921507A12|EG330513	predicted gene 5114	protein-coding
mm_50391.1	chr6	48707940	48707987	+	1	NA	exon (NM_153175, exon 1 of 3)	exon (NM_153175, exon 1 of 3)	281	NM_153175	231931	Mm.321047	NM_153175	ENSMUSG00000047867	Gimap6	4833419H03Rik|Ian6|mFLJ00102	GTPase, IMAP family member 6	protein-coding
mm_153246.1	chr19	36120095	36120106	-	1	NA	promoter-TSS (NM_013468)	promoter-TSS (NM_013468)	-256	NM_013468	107765	Mm.10279	NM_013468	ENSMUSG00000024803	Ankrd1	Alrp|CARP|Crap|MARP1	ankyrin repeat domain 1 (cardiac muscle)	protein-coding
mm_45697.1	chr5	82124692	82124697	-	1	NA	promoter-TSS (NR_138557)	promoter-TSS (NR_138557)	19	NR_138557	67327	Mm.87058	NR_138557		1700031L13Rik	-	RIKEN cDNA 1700031L13 gene	ncRNA
mm_108810.1	chr12	95162839	95162839	+	1	NA	Intergenic	L1MA4|LINE|L1	-529387	NM_201518	399558	Mm.341948	NM_201518	ENSMUSG00000047414	Flrt2	-	fibronectin leucine rich transmembrane protein 2	protein-coding
mm_70910.1	chr8	25687685	25687705	+	1	NA	intron (NM_001081269, intron 13 of 22)	(T)n|Simple_repeat|Simple_repeat	-32353	NR_121642	71910	Mm.385055	NM_028000	ENSMUSG00000031570	Plpp5	1810019D05Rik|2310022A04Rik|AW045471|Ppapdc1|Ppapdc1b	phospholipid phosphatase 5	protein-coding
mm_13901.1	chr2	120476902	120476904	+	1	NA	promoter-TSS (NM_001109761)	promoter-TSS (NM_001109761)	-6	NM_001109761	12335	Mm.458021	NM_007601	ENSMUSG00000079110	Capn3	AI323605|Capa-3|Capa3|Lp82|p94	calpain 3	protein-coding
mm_106142.1	chr11	116529563	116529566	-	1	NA	Intergenic	ORR1B1-int|LTR|ERVL-MaLR	-2347	NM_001172475	20698	Mm.20944	NM_011451	ENSMUSG00000061878	Sphk1	1110006G24Rik|Sk1|Spk1	sphingosine kinase 1	protein-coding
mm_120704.1	chr14	70978479	70978505	+	1	NA	exon (NM_008115, exon 9 of 9)	exon (NM_008115, exon 9 of 9)	88385	NM_001302094	14586	Mm.32619	NM_008115	ENSMUSG00000022103	Gfra2	-	glial cell line derived neurotrophic factor family receptor alpha 2	protein-coding
mm_49001.1	chr6	4756825	4756844	+	1	NA	exon (NM_130877, exon 2 of 2)	exon (NM_130877, exon 2 of 2)	9528	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_44392.1	chr5	17829486	17829548	-	1	NA	5' UTR (NM_001159558, exon 3 of 16)	5' UTR (NM_001159558, exon 3 of 16)	6379	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_57045.1	chr6	122342111	122342114	-	1	NA	Intergenic	Intergenic	-1885	NM_001271579	13619	Mm.6822	NM_007905	ENSMUSG00000040669	Phc1	AW557034|Edr|Edr1|Mph1|Rae-28|rae28	polyhomeotic-like 1 (Drosophila)	protein-coding
mm_151439.1	chr19	57361029	57361113	+	1	NA	promoter-TSS (NM_145505)	promoter-TSS (NM_145505)	62	NM_145505	226252	Mm.358870	NM_145505	ENSMUSG00000033478	Fam160b1	AI450540|mKIAA1600	family with sequence similarity 160, member B1	protein-coding
mm_142268.1	chr17	39846524	39846541	-	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	3535	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_20693.1	chr2	132792888	132792894	-	1	NA	exon (NM_007694, exon 4 of 5)	exon (NM_007694, exon 4 of 5)	11613	NM_007694	12653	Mm.255241	NM_007694	ENSMUSG00000027350	Chgb	Scg-1	chromogranin B	protein-coding
mm_54259.1	chr6	28397939	28397951	-	1	NA	Intergenic	CpG	23779	NM_028900	74375	Mm.332950	NM_028900	ENSMUSG00000029708	Gcc1	4932417P04Rik	golgi coiled coil 1	protein-coding
mm_161886.1	chr18	37751595	37751595	+	1	NA	promoter-TSS (NM_033579)	promoter-TSS (NM_033579)	-184	NM_033579	93704	Mm.247203	NM_033579	ENSMUSG00000104063	Pcdhgb7	-	protocadherin gamma subfamily B, 7	protein-coding
mm_96877.1	chr11	70215013	70215019	+	1	NA	exon (NM_153081, exon 3 of 5)	exon (NM_153081, exon 3 of 5)	1106	NM_153081	216867	Mm.289238	NM_153081	ENSMUSG00000040938	Slc16a11	AB041591|MCT 11|MNCb-2717	solute carrier family 16 (monocarboxylic acid transporters), member 11	protein-coding
mm_98160.1	chr11	87662686	87662699	+	1	NA	promoter-TSS (NM_172448)	promoter-TSS (NM_172448)	-395	NM_172448	207742	Mm.440230	NM_172448	ENSMUSG00000034177	Rnf43	4732452J19Rik	ring finger protein 43	protein-coding
mm_120856.1	chr14	75228066	75228079	+	1	NA	intron (NM_008879, intron 16 of 16)	B4|SINE|B4	-14215	NM_019775	56373	Mm.24242	NM_019775	ENSMUSG00000021999	Cpb2	1110032P04Rik|4930405E17Rik|AI255929|CPR|Cpu|TAFI	carboxypeptidase B2 (plasma)	protein-coding
mm_160490.1	chr8	126593613	126593613	-	1	NA	promoter-TSS (NM_001164598)	promoter-TSS (NM_001164598)	-177	NM_001164598	270110	Mm.334918	NM_001164598	ENSMUSG00000051495	Irf2bp2	E130305N23Rik|IRF-2BP2	interferon regulatory factor 2 binding protein 2	protein-coding
mm_23193.1	chr3	41024370	41024384	+	1	NA	Intergenic	Intergenic	58669	NM_027558	70804	Mm.40321	NM_027558	ENSMUSG00000049940	Pgrmc2	4631434O19Rik|5730409G06Rik|DG6|PMBP	progesterone receptor membrane component 2	protein-coding
mm_62108.1	chr7	96512616	96512629	+	1	NA	intron (NM_001310762, intron 4 of 32)	intron (NM_001310762, intron 4 of 32)	-170658	NR_046043	670727	Mm.421352	NR_046043	ENSMUSG00000085751	Gm15412	OTTMUSG00000021245	predicted gene 15412	ncRNA
mm_72602.1	chr8	84415489	84415498	+	1	NA	5' UTR (NM_001252060, exon 1 of 48)	5' UTR (NM_001252060, exon 1 of 48)	129	NM_001252061	12286	Mm.334658	NM_007578	ENSMUSG00000034656	Cacna1a	APCA|BI|Caca1a|Cacnl1a4|Cav2.1|Ccha1a|EA2|FHM|HPCA|MHP|MHP1|SCA6|alpha1A|la|nmf352|rkr|smrl|tg	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	protein-coding
mm_109862.1	chr12	4907230	4907257	-	1	NA	intron (NM_145441, intron 1 of 6)	CpG	277	NM_145441	217379	Mm.259170	NM_145441	ENSMUSG00000020634	Ubxn2a	6330407P03Rik|Ubxd4	UBX domain protein 2A	protein-coding
mm_73948.1	chr8	120145248	120145263	+	1	NA	5' UTR (NM_001163762, exon 2 of 8)	5' UTR (NM_001163762, exon 2 of 8)	326	NM_001163760	234797	Mm.101958	NM_172286	ENSMUSG00000031824	6430548M08Rik	AW049007|Kiaa0513|mKIAA0513	RIKEN cDNA 6430548M08 gene	protein-coding
mm_51855.1	chr6	90462615	90462636	+	1	NA	promoter-TSS (NM_023184)	promoter-TSS (NM_023184)	-1	NM_023184	66277	Mm.38343	NM_023184	ENSMUSG00000030087	Klf15	1810013I09Rik|AV048136|AW494632|CKLF|KKLF	Kruppel-like factor 15	protein-coding
mm_162228.1	chrX	148882559	148882559	+	1	NA	promoter-TSS (NM_001114383)	promoter-TSS (NM_001114383)	-17	NM_001114383	434865	Mm.473681	NM_001114383	ENSMUSG00000079387	Luzp4	ENSMUSG00000072927	leucine zipper protein 4	protein-coding
mm_136809.1	chr17	12390242	12390252	+	1	NA	exon (NM_008877, exon 5 of 19)	exon (NM_008877, exon 5 of 19)	11638	NM_008877	18815	Mm.971	NM_008877	ENSMUSG00000059481	Plg	AI649309|Pg	plasminogen	protein-coding
mm_42734.1	chr5	120630067	120630077	+	1	NA	exon (NM_001195094, exon 5 of 7)	exon (NM_001195094, exon 5 of 7)	4163	NM_001195094	546886	Mm.464847	NM_001195094	ENSMUSG00000094282	Cfap73	Ccdc42b|Gm5988	cilia and flagella associated protein 73	protein-coding
mm_35035.1	chr4	4133843	4133856	-	1	NA	exon (NM_001002927, exon 2 of 2)	exon (NM_001002927, exon 2 of 2)	4596	NM_001002927	18619	Mm.475097	NM_001002927	ENSMUSG00000045573	Penk	AI326464|ENK|PPA|Penk1	preproenkephalin	protein-coding
mm_115633.1	chr13	12200406	12200417	-	1	NA	intron (NM_001081128, intron 24 of 32)	intron (NM_001081128, intron 24 of 32)	-13923	NR_045170	328186	Mm.188154	NM_183202		Gm10336	B330003H21|ENSMUSG00000071543	predicted gene 10336	ncRNA
mm_16497.1	chr2	181187637	181187652	+	1	NA	5' UTR (NM_025598, exon 2 of 5)	5' UTR (NM_025598, exon 2 of 5)	301	NM_025598	66496	Mm.213943	NM_025598	ENSMUSG00000016344	Ppdpf	0610012G23Rik|2610317A05Rik|2700038C09Rik|3110053G12Rik	pancreatic progenitor cell differentiation and proliferation factor	protein-coding
mm_88217.1	chr10	70246416	70246433	+	1	NA	intron (NM_025807, intron 1 of 5)	intron (NM_025807, intron 1 of 5)	1148	NM_025807	66859	Mm.19325	NM_025807	ENSMUSG00000037762	Slc16a9	1200003C15Rik|4930425B13Rik|AI552636	solute carrier family 16 (monocarboxylic acid transporters), member 9	protein-coding
mm_52270.1	chr6	108473116	108473128	+	1	NA	intron (NM_010585, intron 45 of 61)	intron (NM_010585, intron 45 of 61)	-16621	NR_106121	102465766		NR_106121	ENSMUSG00000105697	Mir7661	mmu-mir-7661	microRNA 7661	ncRNA
mm_172991.1	chrM	1320	1320	+	1	NA	NA	Intergenic	NA	NA								
mm_158296.1	chrX	113185486	113185522	-	1	NA	promoter-TSS (NM_018818)	promoter-TSS (NM_018818)	11	NM_018818	12662	Mm.257316	NM_018818	ENSMUSG00000025531	Chm	Rep-1	choroidermia (RAB escort protein 1)	protein-coding
mm_90326.1	chr10	127075330	127075398	+	1	NA	Intergenic	Intergenic	-3543	NM_001301014	216439	Mm.336761	NM_001033263	ENSMUSG00000025422	Agap2	AGAP-2|Centg1|PIKE|cnt-g1|mKIAA0167	ArfGAP with GTPase domain, ankyrin repeat and PH domain 2	protein-coding
mm_27250.1	chr3	36690119	36690172	-	1	NA	promoter-TSS (NM_019510)	promoter-TSS (NM_019510)	22	NM_019510	22065	Mm.74363	NM_019510	ENSMUSG00000027716	Trpc3	Mwk|Trcp3|Trp3|Trrp3	transient receptor potential cation channel, subfamily C, member 3	protein-coding
mm_157857.1	chrX	75084900	75084946	-	1	NA	promoter-TSS (NM_181584)	promoter-TSS (NM_181584)	-18	NM_181584	210710	Mm.267056	NM_181584	ENSMUSG00000032750	Gab3	5930433H21Rik	growth factor receptor bound protein 2-associated protein 3	protein-coding
mm_58156.1	chr6	142472799	142472805	-	1	NA	5' UTR (NM_145572, exon 1 of 17)	5' UTR (NM_145572, exon 1 of 17)	307	NM_145572	232493	Mm.275975	NM_145572	ENSMUSG00000030244	Gys2	BC021322|LGS	glycogen synthase 2	protein-coding
mm_70722.1	chr8	16433162	16433180	+	1	NA	intron (NM_053171, intron 7 of 69)	intron (NM_053171, intron 7 of 69)	-264333	NR_037214	100526464		NR_037214	ENSMUSG00000093142	Mir3106	mir-3106|mmu-mir-3106	microRNA 3106	ncRNA
mm_168447.1	chr11	40721643	40721650	-	1	NA	exon (NM_013552, exon 7 of 18)	exon (NM_013552, exon 7 of 18)	11791	NM_013552	15366	Mm.116997	NM_013552	ENSMUSG00000020330	Hmmr	AA386826|CD168|Rhamm	hyaluronan mediated motility receptor (RHAMM)	protein-coding
mm_151256.1	chr19	53944841	53944867	+	1	NA	promoter-TSS (NM_019658)	promoter-TSS (NM_019658)	-22	NM_019658	56392	Mm.228669	NM_019658	ENSMUSG00000024976	Shoc2	AU017287|Sur8|mKIAA0862	soc-2 (suppressor of clear) homolog (C. elegans)	protein-coding
mm_14825.1	chr2	147013859	147013867	+	1	NA	intron (NM_011917, intron 1 of 29)	intron (NM_011917, intron 1 of 29)	803	NM_011917	24128	Mm.3065	NM_011917	ENSMUSG00000027433	Xrn2	-	5'-3' exoribonuclease 2	protein-coding
mm_143815.1	chr17	83831855	83831901	-	1	NA	exon (NM_025325, exon 9 of 10)	exon (NM_025325, exon 9 of 10)	14912	NM_025325	107766	Mm.30100	NM_025325	ENSMUSG00000000673	Haao	0610007K21Rik|0610012J07Rik|3-HAO|3-HAOxase|3HAO	3-hydroxyanthranilate 3,4-dioxygenase	protein-coding
mm_110792.1	chr12	72085335	72085361	-	1	NA	promoter-TSS (NM_024205)	promoter-TSS (NM_024205)	-35	NM_026038	67217	Mm.286120	NM_026038	ENSMUSG00000019718	L3hypdh	2810055F11Rik	L-3-hydroxyproline dehydratase (trans-)	protein-coding
mm_29741.1	chr3	126922927	126922949	-	1	NA	3' UTR (NM_178655, exon 25 of 25)	3' UTR (NM_178655, exon 25 of 25)	20448	NM_001034168	109676	Mm.220242	NM_178655	ENSMUSG00000032826	Ank2	100043364|AI835472|AW491075|Ank-2|Gm4392	ankyrin 2, brain	protein-coding
mm_114513.1	chr13	72628832	72628848	+	1	NA	promoter-TSS (NR_030701)	promoter-TSS (NR_030701)	43	NM_010574	16372	Mm.28888	NM_010574	ENSMUSG00000001504	Irx2	-	Iroquois related homeobox 2 (Drosophila)	protein-coding
mm_25548.1	chr3	115888209	115888233	+	1	NA	promoter-TSS (NR_027895)	promoter-TSS (NR_027895)	38	NM_027193	69740	Mm.5915	NM_027193	ENSMUSG00000033554	Dph5	2410012M04Rik|AU045680|C80186	diphthamide biosynthesis 5	protein-coding
mm_48025.1	chr5	136244932	136244949	-	1	NA	promoter-TSS (NM_018825)	promoter-TSS (NM_018825)	0	NM_001302939	23921	Mm.425294	NM_018825	ENSMUSG00000005057	Sh2b2	Aps	SH2B adaptor protein 2	protein-coding
mm_117303.1	chr13	67332526	67332553	-	1	NA	promoter-TSS (NM_177622)	promoter-TSS (NM_177622)	21	NM_177622	218314	Mm.289695	NM_177622	ENSMUSG00000057842	Zfp595	A230042K10Rik|Rslcan23	zinc finger protein 595	protein-coding
mm_27993.1	chr3	82274700	82274709	-	1	NA	Intergenic	Intergenic	-83368	NM_001081230	213582	Mm.271269	NM_001081230	ENSMUSG00000033900	Map9	5033421J10Rik|5330427D05Rik|ASAP|Mtap9	microtubule-associated protein 9	protein-coding
mm_135115.1	chr16	35837928	35837936	-	1	NA	intron (NM_001039530, intron 15 of 16)	RSINE1|SINE|B4	33450	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_143716.1	chr17	80933480	80933497	-	1	NA	TTS (NR_131127)	TTS (NR_131127)	-11144	NM_026516	68027	Mm.357108	NM_026516	ENSMUSG00000024245	Tmem178	2810417M05Rik|Tmem178a	transmembrane protein 178	protein-coding
mm_143708.1	chr17	80680046	80680054	-	1	NA	intron (NM_001290345, intron 2 of 33)	intron (NM_001290345, intron 2 of 33)	47975	NM_001290345	225028	Mm.311948	NM_001081357	ENSMUSG00000024242	Map4k3	4833416M01Rik|4833416M07Rik|9530052P13Rik|Glk|MAPKKKK3|MEKKK 3|MEKKK3|RAB8IPL1	mitogen-activated protein kinase kinase kinase kinase 3	protein-coding
mm_17714.1	chr2	32386057	32386068	-	1	NA	intron (NM_008491, intron 2 of 5)	intron (NM_008491, intron 2 of 5)	1677	NM_008491	16819	Mm.9537	NM_008491	ENSMUSG00000026822	Lcn2	24p3|AW212229|NRL|Sip24	lipocalin 2	protein-coding
mm_144661.1	chr18	34315151	34315160	+	1	NA	exon (NM_007462, exon 16 of 16)	exon (NM_007462, exon 16 of 16)	-15990	NM_025527	66384	Mm.29452	NM_025527	ENSMUSG00000014504	Srp19	2310020D23Rik	signal recognition particle 19	protein-coding
mm_134642.1	chr16	21762982	21763015	-	1	NA	exon (NM_023737, exon 7 of 7)	exon (NM_023737, exon 7 of 7)	24836	NM_023737	74147	Mm.28100	NM_023737	ENSMUSG00000022853	Ehhadh	1300002P22Rik|HD|L-PBE|LBFP|LBP|MFP|MFP1|PBFE	enoyl-Coenzyme A, hydratase/3-hydroxyacyl Coenzyme A dehydrogenase	protein-coding
mm_159188.1	chr2	116879278	116879278	+	1	NA	5' UTR (NM_026104, exon 2 of 12)	5' UTR (NM_026104, exon 2 of 12)	587	NM_026104	67356	Mm.131623	NM_026104	ENSMUSG00000027355	Tmco5	1700095F04Rik|Tmco5a	transmembrane and coiled-coil domains 5	protein-coding
mm_162473.1	chr1	133098645	133098655	+	1	NA	exon (NM_001099276, exon 24 of 33)	exon (NM_001099276, exon 24 of 33)	-32516	NM_133819	108954	Mm.293628	NM_133819	ENSMUSG00000046062	Ppp1r15b	1810033K10Rik|AI606441|C530022L24Rik|CReP	protein phosphatase 1, regulatory (inhibitor) subunit 15b	protein-coding
mm_6466.1	chr1	74035325	74035352	-	1	NA	intron (NM_027884, intron 3 of 34)	intron (NM_027884, intron 3 of 34)	89109	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_22929.1	chr3	31149772	31149787	+	1	NA	promoter-TSS (NM_008770)	promoter-TSS (NM_008770)	-141	NM_008770	18417	Mm.4425	NM_008770	ENSMUSG00000037625	Cldn11	Claudin-11|Claudin11|Osp|Otm	claudin 11	protein-coding
mm_98348.1	chr11	93341509	93341515	+	1	NA	intron (NM_028296, intron 3 of 8)	intron (NM_028296, intron 3 of 8)	242222	NM_028296	72605	Mm.342160	NM_028296	ENSMUSG00000056158	Car10	2700029L05Rik|BB085816|Ca10	carbonic anhydrase 10	protein-coding
mm_92099.1	chr10	62892845	62892872	-	1	NA	Intergenic	Intergenic	-12844	NM_001253857	52463	Mm.17774	NM_027384	ENSMUSG00000047146	Tet1	2510010B09Rik|AA517754|BB001228|Cxxc6|D10Ertd17e|LCX|mKIAA1676	tet methylcytosine dioxygenase 1	protein-coding
mm_29026.1	chr3	102165895	102165909	-	1	NA	intron (NM_177545, intron 5 of 7)	intron (NM_177545, intron 5 of 7)	38791	NM_177545	229658	Mm.118004	NM_177545	ENSMUSG00000027860	Vangl1	Kitenin|Lpp2|Stb2|Stbm	vang-like 1 (van gogh, Drosophila)	protein-coding
mm_146361.1	chr18	82584289	82584308	+	1	NA	3' UTR (NM_010777, exon 7 of 7)	3' UTR (NM_010777, exon 7 of 7)	29790	NM_001025254	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_137965.1	chr17	33432303	33432308	+	1	NA	promoter-TSS (NM_183282)	promoter-TSS (NM_183282)	-594	NM_183282	69481	Mm.154333	NM_183282	ENSMUSG00000092519	Actl9	1700029I08Rik|AV259599	actin-like 9	protein-coding
mm_78376.1	chr9	27397239	27397256	+	1	NA	promoter-TSS (NM_001305058)	promoter-TSS (NM_001305058)	35	NM_001305058	75469	Mm.45824	NM_029299	ENSMUSG00000031991	Spata19	1700001L23Rik|AV047838|spergen-1	spermatogenesis associated 19	protein-coding
mm_111044.1	chr12	79642827	79642857	-	1	NA	intron (NM_009014, intron 7 of 10)	intron (NM_009014, intron 7 of 10)	281891	NR_131075	77290	Mm.395042	NR_131073		9430078K24Rik	-	RIKEN cDNA 9430078K24 gene	ncRNA
mm_69098.1	chr7	127019790	127019803	-	1	NA	exon (NM_001102563, exon 2 of 4)	exon (NM_001102563, exon 2 of 4)	1415	NM_001102563	69017	Mm.392047	NM_001102563	ENSMUSG00000045114	Prrt2	1500031I19Rik|AI195361|DSPB3	proline-rich transmembrane protein 2	protein-coding
mm_28678.1	chr3	95315153	95315217	-	1	NA	promoter-TSS (NM_029789)	promoter-TSS (NM_029789)	-5	NM_029789	76893	Mm.181009	NM_029789	ENSMUSG00000015714	Cers2	0610013I17Rik|AI225939|Lass2|TRH3	ceramide synthase 2	protein-coding
mm_139105.1	chr17	47267369	47267377	+	1	NA	intron (NM_001097623, intron 4 of 19)	intron (NM_001097623, intron 4 of 19)	37143	NM_172622	224829	Mm.260989	NM_172622		Trerf1	9430096I18Rik|AI429294|B830015H24|RAPA|Trep-132|Trep132	transcriptional regulating factor 1	protein-coding
mm_84674.1	chr9	72047076	72047081	-	1	NA	intron (NM_001253862, intron 3 of 19)	intron (NM_001253862, intron 3 of 19)	64123	NM_001253862	21406	Mm.171615	NM_011544	ENSMUSG00000032228	Tcf12	A130037E08Rik|ALF1|HEB|HEBAlt|HTF-4|HTF4|ME1|REB|bHLHb20	transcription factor 12	protein-coding
mm_49681.1	chr6	32511180	32511190	+	1	NA	promoter-TSS (NR_040277)	promoter-TSS (NR_040277)	44	NR_040277	319849	Mm.440860	NR_040277	ENSMUSG00000086763	Plxna4os1	B230378P21Rik	plexin A4, opposite strand 1	ncRNA
mm_3746.1	chr1	155558498	155558552	+	1	NA	5' UTR (NM_026683, exon 1 of 4)	5' UTR (NM_026683, exon 1 of 4)	405	NM_026683	72482	Mm.288249	NM_026683	ENSMUSG00000033701	Acbd6	0610010G04Rik|2610100E10Rik	acyl-Coenzyme A binding domain containing 6	protein-coding
mm_27512.1	chr3	56059294	56059306	-	1	NA	intron (NM_030595, intron 8 of 57)	B1_Mus2|SINE|Alu	124401	NM_030595	26422	Mm.384353	NM_030595	ENSMUSG00000027799	Nbea	Lyst2|mKIAA1544	neurobeachin	protein-coding
mm_86332.1	chr9	123085280	123085286	-	1	NA	intron (NM_026917, intron 3 of 6)	intron (NM_026917, intron 3 of 6)	27922	NM_026917	69035	Mm.28300	NM_026917	ENSMUSG00000025786	Zdhhc3	1110020O22Rik|1810006O10Rik|2210017C02Rik|DHHC-3|GODZ|Gramp1|Zfp373	zinc finger, DHHC domain containing 3	protein-coding
mm_19739.1	chr2	104712640	104712650	-	1	NA	promoter-TSS (NM_177190)	promoter-TSS (NM_177190)	-483	NM_177190	320554	Mm.249065	NM_177190	ENSMUSG00000027175	Tcp11l1	C130096D04Rik	t-complex 11 like 1	protein-coding
mm_46585.1	chr5	107687991	107688025	-	1	NA	Intergenic	CpG	15472	NR_045871	654809	Mm.399159	NR_045871	ENSMUSG00000106333	4930428O21Rik	-	RIKEN cDNA 4930428O21 gene	ncRNA
mm_36191.1	chr4	62313920	62313941	-	1	NA	intron (NM_001045528, intron 20 of 27)	intron (NM_001045528, intron 20 of 27)	22383	NM_001290518	20530	Mm.292539	NM_025286	ENSMUSG00000066152	Slc31a2	AI604396|CTR2	solute carrier family 31, member 2	protein-coding
mm_113489.1	chr13	37378577	37378588	+	1	NA	intron (NM_010745, intron 3 of 4)	MER2|DNA|TcMar-Tigger	33237	NM_010745	17084	Mm.2639	NM_010745	ENSMUSG00000021423	Ly86	MD-1|MD1|ly86_tv2	lymphocyte antigen 86	protein-coding
mm_89815.1	chr10	104267540	104267546	+	1	NA	Intergenic	Lx5|LINE|L1	-19726	NR_105838	102465222		NR_105838	ENSMUSG00000099264	Mir6411	Gm27767|mmu-mir-6411	microRNA 6411	ncRNA
mm_7629.1	chr1	127677883	127677897	-	1	NA	5' UTR (NM_028135, exon 1 of 8)	5' UTR (NM_028135, exon 1 of 8)	131	NM_028135	72160	Mm.281287	NM_028135	ENSMUSG00000026347	Tmem163	2610024A01Rik|SV31	transmembrane protein 163	protein-coding
mm_47172.1	chr5	120744298	120744313	-	1	NA	intron (NM_001347448, intron 3 of 11)	L1M5|LINE|L1	5543	NM_145227	246728	Mm.260926	NM_145227	ENSMUSG00000032690	Oas2	Oasl11	2'-5' oligoadenylate synthetase 2	protein-coding
mm_48746.1	chr5	147894778	147894786	-	1	NA	promoter-TSS (NM_027872)	promoter-TSS (NM_027872)	20	NM_027872	71706	Mm.153218	NM_027872	ENSMUSG00000029650	Slc46a3	1200006F02Rik	solute carrier family 46, member 3	protein-coding
mm_111560.1	chr12	101083654	101083717	-	1	NA	promoter-TSS (NM_001160214)	promoter-TSS (NM_001160214)	17	NM_211355	68734	Mm.87077	NM_211355	ENSMUSG00000041846	Smek1	1110034C04Rik|BC064465|Ppp4r3a|mKIAA2010	SMEK homolog 1, suppressor of mek1 (Dictyostelium)	protein-coding
mm_123481.1	chr14	65981420	65981444	-	1	NA	3' UTR (NM_013492, exon 9 of 9)	3' UTR (NM_013492, exon 9 of 9)	12949	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_70144.1	chr7	143458773	143458794	-	1	NA	3' UTR (NM_001161624, exon 4 of 4)	3' UTR (NM_001161624, exon 4 of 4)	2267	NM_009876	12577	Mm.168789	NM_009876	ENSMUSG00000037664	Cdkn1c	AL024410|CDKI|Kip2|p57(kip2)|p57Kip2	cyclin-dependent kinase inhibitor 1C (P57)	protein-coding
mm_19881.1	chr2	114049601	114049631	-	1	NA	exon (NM_009608, exon 4 of 7)	exon (NM_009608, exon 4 of 7)	3259	NM_009608	11464	Mm.686	NM_009608	ENSMUSG00000068614	Actc1	Actc-1	actin, alpha, cardiac muscle 1	protein-coding
mm_88941.1	chr10	81319503	81319540	+	1	NA	3' UTR (NM_001146687, exon 17 of 17)	3' UTR (NM_001146687, exon 17 of 17)	-1582	NM_027381	70312	Mm.87628	NM_027381	ENSMUSG00000034889	Cactin	2510012J08Rik	cactin, spliceosome C complex subunit	protein-coding
mm_132347.1	chr16	33887360	33887363	+	1	NA	intron (NM_010580, intron 5 of 14)	intron (NM_010580, intron 5 of 14)	57696	NM_001145884	16419	Mm.6424	NM_010580	ENSMUSG00000022817	Itgb5	AA475909|AI874634|ESTM23|[b]-5|[b]5|[b]5A|[b]5B|beta-5|beta5	integrin beta 5	protein-coding
mm_68169.1	chr7	103813742	103813755	-	1	NA	intron (NM_008220, intron 1 of 2)	intron (NM_008220, intron 1 of 2)	175	NM_016956	15130	Mm.288567	NM_016956		Hbb-b2	AI036344|Hbb2|Hbbt2|beta2	hemoglobin, beta adult minor chain	protein-coding
mm_132712.1	chr16	43503482	43503521	+	1	NA	intron (NM_181058, intron 3 of 6)	intron (NM_181058, intron 3 of 6)	-83305	NR_046026	626693	Mm.447083	NR_046026	ENSMUSG00000085499	Gm15713	OTTMUSG00000025617	predicted gene 15713	ncRNA
mm_30674.1	chr4	11159317	11159321	+	1	NA	intron (NM_021897, intron 1 of 3)	intron (NM_021897, intron 1 of 3)	2878	NM_021897	60599	Mm.393018	NM_021897	ENSMUSG00000028211	Trp53inp1	2700057G22Rik|SIP|SIP18|SIP27|Stinp|Teap	transformation related protein 53 inducible nuclear protein 1	protein-coding
mm_172044.1	chr6	128313328	128313347	+	1	NA	Intergenic	Intergenic	-12524	NM_011567	21679	Mm.14774	NM_011567	ENSMUSG00000030353	Tead4	ETFR-2|Etfr2|FR-19|Rtef1|TEAD-4|TEF-3|Tcf13r1|Tef3|Tefr|Tefr1|Tefr1a	TEA domain family member 4	protein-coding
mm_32669.1	chr4	115652320	115652320	+	1	NA	Intergenic	Intergenic	-4615	NM_007823	13120	Mm.1840	NM_007823	ENSMUSG00000028713	Cyp4b1	-	cytochrome P450, family 4, subfamily b, polypeptide 1	protein-coding
mm_73014.1	chr8	93966864	93966877	+	1	NA	exon (NM_010308, exon 8 of 9)	exon (NM_010308, exon 8 of 9)	45770	NM_011787	23802	Mm.34641	NM_011787	ENSMUSG00000031751	Amfr	gp78	autocrine motility factor receptor	protein-coding
mm_155115.1	chrX	48623738	48623790	+	1	NA	promoter-TSS (NM_001290705)	promoter-TSS (NM_001290705)	90	NM_001166450	20523	Mm.34953	NM_011398	ENSMUSG00000031105	Slc25a14	BMCP1|UCP5|UCP5L|UCP5S	solute carrier family 25 (mitochondrial carrier, brain), member 14	protein-coding
mm_44449.1	chr5	21701333	21701404	-	1	NA	promoter-TSS (NM_178728)	promoter-TSS (NM_178728)	-23	NM_178728	242864	Mm.153292	NM_178728	ENSMUSG00000044968	Napepld	A530089G06|Mbldc1|NAPE-PLD	N-acyl phosphatidylethanolamine phospholipase D	protein-coding
mm_23004.1	chr3	34104438	34104447	+	1	NA	Intergenic	Intergenic	-23088	NM_026332	67713	Mm.274266	NM_026332	ENSMUSG00000027679	Dnajc19	1810055D05Rik|AA959924|Tim14	DnaJ heat shock protein family (Hsp40) member C19	protein-coding
mm_77304.1	chr8	117461249	117461266	-	1	NA	3' UTR (NM_001163262, exon 21 of 21)	3' UTR (NM_001163262, exon 21 of 21)	1992	NR_106046	102465653		NR_106046	ENSMUSG00000098483	Mir7078	Gm27386|mmu-mir-7078	microRNA 7078	ncRNA
mm_81602.1	chr9	110547672	110547708	+	1	NA	exon (NM_001081340, exon 3 of 21)	exon (NM_001081340, exon 3 of 21)	15093	NM_001081340	235626	Mm.288949	NM_001081340	ENSMUSG00000044791	Setd2	4921524K10Rik|BC031601|KMT3A	SET domain containing 2	protein-coding
mm_141632.1	chr17	32947373	32947387	-	1	NA	promoter-TSS (NM_130882)	promoter-TSS (NM_130882)	-19	NM_130882	170716	Mm.254838	NM_130882	ENSMUSG00000024055	Cyp4f13	0610030I10Rik|Cypf13	cytochrome P450, family 4, subfamily f, polypeptide 13	protein-coding
mm_125345.1	chr15	39112952	39112960	+	1	NA	promoter-TSS (NM_198606)	promoter-TSS (NM_198606)	82	NM_198606	223499	Mm.321937	NM_198606	ENSMUSG00000022300	Dcaf13	Gm83|Wdsof1	DDB1 and CUL4 associated factor 13	protein-coding
mm_117754.1	chr13	95961486	95961494	-	1	NA	intron (NM_029210, intron 12 of 12)	intron (NM_029210, intron 12 of 12)	-69568	NM_027711	544963	Mm.38878	NM_027711	ENSMUSG00000021676	Iqgap2	4933417J23Rik|A630053O10|AI788777	IQ motif containing GTPase activating protein 2	protein-coding
mm_172734.1	chr8	78146902	78146907	-	1	NA	Intergenic	ETnERV-int|LTR|ERVK	-66438	NM_183096	73301	Mm.61243	NM_183096	ENSMUSG00000037101	Ttc29	1700031F13Rik	tetratricopeptide repeat domain 29	protein-coding
mm_49328.1	chr6	21215332	21215353	+	1	NA	promoter-TSS (NM_019697)	promoter-TSS (NM_019697)	-767	NM_019697	16508	Mm.425316	NM_019697	ENSMUSG00000060882	Kcnd2	AI839615|AW555701|Kv4.2|R75121|mKIAA1044	potassium voltage-gated channel, Shal-related family, member 2	protein-coding
mm_43942.1	chr5	145127920	145127938	+	1	NA	TTS (NM_001033313)	TTS (NM_001033313)	12160	NM_001033313	231887	Mm.188851	NM_001033313	ENSMUSG00000029623	Pdap1	HASPP28|PAP|PAP1	PDGFA associated protein 1	protein-coding
mm_116120.1	chr13	28950558	28950572	-	1	NA	TTS (NM_009238)	TTS (NM_009238)	3117	NM_009238	20677	Mm.240627	NM_009238	ENSMUSG00000076431	Sox4	AA682046|Sox-4	SRY (sex determining region Y)-box 4	protein-coding
mm_76412.1	chr8	84893909	84893948	-	1	NA	promoter-TSS (NM_001044744)	promoter-TSS (NM_001044744)	-7	NM_008097	270076	Mm.2475	NM_008097	ENSMUSG00000003809	Gcdh	9030411L18|AI266902|D17825|GCD	glutaryl-Coenzyme A dehydrogenase	protein-coding
mm_31422.1	chr4	48051524	48051535	+	1	NA	exon (NM_015743, exon 3 of 8)	exon (NM_015743, exon 3 of 8)	283	NM_001307989	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_101917.1	chr11	50200521	50200541	-	1	NA	TTS (NM_026543)	TTS (NM_026543)	10289	NM_001290769	18412	Mm.40828	NM_011018	ENSMUSG00000015837	Sqstm1	A170|OSF-6|Osi|STAP|STONE14|p62	sequestosome 1	protein-coding
mm_140358.1	chr17	86831474	86831492	+	1	NA	3' UTR (NM_010137, exon 16 of 16)	3' UTR (NM_010137, exon 16 of 16)	77619	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_95175.1	chr11	40755477	40755501	+	1	NA	promoter-TSS (NM_009831)	promoter-TSS (NM_009831)	-203	NM_009831	12450	Mm.2103	NM_009831	ENSMUSG00000020326	Ccng1	AI314029	cyclin G1	protein-coding
mm_7272.1	chr1	96997591	96997595	-	1	NA	promoter-TSS (NR_120500)	promoter-TSS (NR_120500)	-33	NR_120500	67854	Mm.263706	NM_026413	ENSMUSG00000045463	Slco6b1	1700022M03Rik	solute carrier organic anion transporter family, member 6b1	ncRNA
mm_125494.1	chr15	55112361	55112403	+	1	NA	promoter-TSS (NM_145470)	promoter-TSS (NM_145470)	65	NM_145470	97998	Mm.295397	NM_145470	ENSMUSG00000022419	Deptor	Depdc6	DEP domain containing MTOR-interacting protein	protein-coding
mm_70634.1	chr8	13792138	13792160	+	1	NA	exon (NM_025924, exon 5 of 9)	exon (NM_025924, exon 5 of 9)	6534	NM_025924	67031	Mm.44858	NM_025924	ENSMUSG00000038398	Upf3a	2600001C03Rik|4930546M19Rik|RENT3A|UPF3	UPF3 regulator of nonsense transcripts homolog A (yeast)	protein-coding
mm_39984.1	chr5	32459298	32459355	+	1	NA	5' UTR (NM_172707, exon 1 of 8)	5' UTR (NM_172707, exon 1 of 8)	356	NM_172707	19046	Mm.241931	NM_172707	ENSMUSG00000014956	Ppp1cb	1200010B19	protein phosphatase 1, catalytic subunit, beta isoform	protein-coding
mm_57522.1	chr6	125573319	125573345	-	1	NA	intron (NM_011708, intron 6 of 51)	intron (NM_011708, intron 6 of 51)	20384	NM_011708	22371	Mm.22339	NM_011708	ENSMUSG00000001930	Vwf	6820430P06Rik|AI551257|B130011O06Rik|C630030D09|F8VWF|VWD	Von Willebrand factor	protein-coding
mm_44156.1	chr5	150496984	150496989	+	1	NA	3' UTR (NM_172887, exon 61 of 61)	3' UTR (NM_172887, exon 61 of 61)	5233	NR_024513	194292	Mm.300184	NR_024513		Gm5	Gm1812	predicted gene 5	ncRNA
mm_168233.1	chr10	81649050	81649064	+	1	NA	promoter-TSS (NM_001142963)	promoter-TSS (NM_001142963)	-12	NM_001142963	100233208	Mm.327168	NM_001142963	ENSMUSG00000096856	Gm10778	ENSMUSG00000074860	predicted gene 10778	protein-coding
mm_159699.1	chr5	26121374	26121374	-	1	NA	promoter-TSS (NM_001134299)	promoter-TSS (NM_001134299)	51	NM_001134299	434689	Mm.484129	NM_001134299	ENSMUSG00000067698	Gm10220	ENSMUSG00000067698	predicted gene 10220	protein-coding
mm_121318.1	chr14	111674861	111674924	+	1	NA	promoter-TSS (NM_198865)	promoter-TSS (NM_198865)	-223	NM_198865	75409	Mm.235097	NM_029273	ENSMUSG00000033214	Slitrk5	2610019D03Rik	SLIT and NTRK-like family, member 5	protein-coding
mm_106422.1	chr11	119252489	119252508	-	1	NA	intron (NM_175430, intron 13 of 18)	intron (NM_175430, intron 13 of 18)	-15465	NM_001159324	14387	Mm.4793	NM_008064	ENSMUSG00000025579	Gaa	E430018M07Rik	glucosidase, alpha, acid	protein-coding
mm_81169.1	chr9	107299972	107299982	+	1	NA	exon (NM_009895, exon 2 of 3)	exon (NM_009895, exon 2 of 3)	3318	NM_009895	12700	Mm.4592	NM_009895	ENSMUSG00000032578	Cish	CIS-1|CIS1|Cis|F17|F23|SOCS	cytokine inducible SH2-containing protein	protein-coding
mm_106606.1	chr11	120784184	120784209	-	1	NA	promoter-TSS (NM_145370)	promoter-TSS (NM_145370)	8	NM_009053	19719	Mm.871	NM_009053	ENSMUSG00000025158	Rfng	-	RFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	protein-coding
mm_49275.1	chr6	17637006	17637014	+	1	NA	promoter-TSS (NM_007604)	promoter-TSS (NM_007604)	-88	NM_007604	12343	Mm.392504	NM_007604	ENSMUSG00000015733	Capza2	1110053K06Rik|AW208808|Cappa2	capping protein (actin filament) muscle Z-line, alpha 2	protein-coding
mm_16814.1	chr2	11332572	11332587	-	1	NA	Intergenic	Intergenic	-6910	NR_040369	100503147	Mm.91961	NR_040369	ENSMUSG00000086006	Gm13293	OTTMUSG00000011311	predicted gene 13293	ncRNA
mm_10096.1	chr2	3424124	3424207	+	1	NA	promoter-TSS (NM_175683)	promoter-TSS (NM_175683)	34	NM_001302684	227525	Mm.23483	NM_146114	ENSMUSG00000026648	Dclre1c	9930121L06Rik|AI661365|Art|Snm1l	DNA cross-link repair 1C	protein-coding
mm_88115.1	chr10	69212653	69212667	+	1	NA	promoter-TSS (NM_001081347)	promoter-TSS (NM_001081347)	3	NM_001081347	69288	Mm.26659	NM_001081347	ENSMUSG00000019944	Rhobtb1	1700008H16Rik|3110048G13Rik|AI173445|AI573858|AV350930	Rho-related BTB domain containing 1	protein-coding
mm_44388.1	chr5	17828983	17828996	-	1	NA	intron (NM_007643, intron 2 of 14)	intron (NM_007643, intron 2 of 14)	6907	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_141543.1	chr17	31871029	31871037	-	1	NA	Intergenic	Intergenic	-15241	NM_010831	17691	Mm.290941	NM_010831	ENSMUSG00000024042	Sik1	Msk|Sik|Snf1lk	salt inducible kinase 1	protein-coding
mm_26768.1	chr3	8913986	8913990	-	1	NA	intron (NM_025434, intron 1 of 2)	intron (NM_025434, intron 1 of 2)	9869	NM_025434	66230	Mm.38460	NM_025434	ENSMUSG00000040269	Mrps28	1500012D08Rik|AW061224	mitochondrial ribosomal protein S28	protein-coding
mm_48856.1	chr5	149636332	149636339	-	1	NA	promoter-TSS (NM_013559)	promoter-TSS (NM_013559)	1	NM_001347534	15505	Mm.270681	NM_013559	ENSMUSG00000029657	Hsph1	105kDa|AI790491|Hsp105|Hsp110|hsp-E7I|hsp110/105	heat shock 105kDa/110kDa protein 1	protein-coding
mm_28676.1	chr3	95307450	95307459	-	1	NA	promoter-TSS (NM_023628)	promoter-TSS (NM_023628)	-278	NM_023628	71790	Mm.218844	NM_023628	ENSMUSG00000015702	Anxa9	1110003P15Rik|2310069F17Rik	annexin A9	protein-coding
mm_2751.1	chr1	128713190	128713198	+	1	NA	Intergenic	Intergenic	-120895	NM_009911	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding
mm_66734.1	chr7	46667376	46667378	-	1	NA	promoter-TSS (NM_001276372)	promoter-TSS (NM_001276372)	0	NM_001136084	21990	Mm.248684	NM_009414	ENSMUSG00000040046	Tph1	Tph	tryptophan hydroxylase 1	protein-coding
mm_9061.1	chr1	167393776	167393824	-	1	NA	promoter-TSS (NM_025569)	promoter-TSS (NM_025569)	-3	NM_025569	66447	Mm.218286	NM_025569	ENSMUSG00000026688	Mgst3	2010012L10Rik|2010306B17Rik|2700004G04Rik|AA516734|GST-III	microsomal glutathione S-transferase 3	protein-coding
mm_88567.1	chr10	79665531	79665534	+	1	NA	exon (NM_013591, exon 3 of 5)	exon (NM_013591, exon 3 of 5)	958	NM_013591	17123	Mm.391556	NM_013591	ENSMUSG00000020310	Madcam1	AV211525	mucosal vascular addressin cell adhesion molecule 1	protein-coding
mm_26251.1	chr3	141634562	141634602	+	1	NA	intron (NM_001293561, intron 1 of 16)	intron (NM_001293561, intron 1 of 16)	169018	NM_001293561	22253	Mm.24430	NM_009472	ENSMUSG00000059921	Unc5c	B130051O18Rik|Unc5h3|rcm	unc-5 netrin receptor C	protein-coding
mm_83483.1	chr9	45930389	45930410	-	1	NA	TTS (NM_008794)	TTS (NM_008794)	5659	NM_011526	21345	Mm.283283	NM_011526	ENSMUSG00000032085	Tagln	Sm22|Sm22a|Ws310	transgelin	protein-coding
mm_146347.1	chr18	82539701	82539703	+	1	NA	intron (NM_001025245, intron 3 of 3)	L1MA5A|LINE|L1	-14761	NM_001025256	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_159536.1	chr4	86811272	86811272	+	1	NA	intron (NM_184088, intron 16 of 31)	intron (NM_184088, intron 16 of 31)	46095	NM_009096	20104	Mm.379007	NM_009096	ENSMUSG00000028495	Rps6	S6R	ribosomal protein S6	protein-coding
mm_105568.1	chr11	106579094	106579105	-	1	NA	intron (NM_198292, intron 1 of 11)	intron (NM_198292, intron 1 of 11)	33831	NM_198292	21763	Mm.102407	NM_198292	ENSMUSG00000040548	Tex2	4930568E07Rik|AI553404|Def-5|Taz4	testis expressed gene 2	protein-coding
mm_63233.1	chr7	126487256	126487266	+	1	NA	promoter-TSS (NM_001163713)	promoter-TSS (NM_001163713)	-94	NM_172745	233870	Mm.197829	NM_172745	ENSMUSG00000073838	Tufm	2300002G02Rik|C76308|C76389|EF-TuMT|EFTU	Tu translation elongation factor, mitochondrial	protein-coding
mm_24658.1	chr3	94478355	94478366	+	1	NA	promoter-TSS (NM_001289613)	promoter-TSS (NM_001289613)	65	NM_001289620	78784	Mm.44292	NM_172434	ENSMUSG00000028137	Celf3	4930415M08Rik|BRUNOL1|CAGH4|ERDA4|Tnrc4	CUGBP, Elav-like family member 3	protein-coding
mm_81934.1	chr9	120180040	120180052	+	1	NA	Intergenic	Intergenic	30304	NM_001039364	17433	Mm.486167	NM_008614	ENSMUSG00000032517	Mobp	AI835053|AI839848|MOBP155|MOBP170|MOBP69|MOBP73|MOBP81|R74645	myelin-associated oligodendrocytic basic protein	protein-coding
mm_33196.1	chr4	126274016	126274027	+	1	NA	exon (NM_013718, exon 4 of 5)	exon (NM_013718, exon 4 of 5)	11616	NM_013718	27096	Mm.8392	NM_013718	ENSMUSG00000028847	Trappc3	1110058K12Rik|AI835942|AU019197|Bet3	trafficking protein particle complex 3	protein-coding
mm_167044.1	chr7	80501209	80501215	+	1	NA	intron (NM_001042527, intron 7 of 21)	intron (NM_001042527, intron 7 of 21)	33786	NM_007550	12144	Mm.12932	NM_007550	ENSMUSG00000030528	Blm	-	Bloom syndrome, RecQ helicase-like	protein-coding
mm_129357.1	chr15	77945766	77945780	-	1	NA	intron (NM_001168260, intron 7 of 8)	intron (NM_001168260, intron 7 of 8)	10949	NM_001168260	239554	Mm.295605	NM_001017983	ENSMUSG00000016552	Foxred2	A430097D04Rik|D15Bwg0759e|Gm304	FAD-dependent oxidoreductase domain containing 2	protein-coding
mm_124355.1	chr14	105115311	105115324	-	1	NA	promoter-TSS (NR_040628)	promoter-TSS (NR_040628)	-641	NR_040628	100502987	Mm.124957	NR_040628		Gm17066	-	predicted gene 17066	ncRNA
mm_73857.1	chr8	118283624	118283633	+	1	NA	promoter-TSS (NM_019707)	promoter-TSS (NM_019707)	17	NM_019707	12554	Mm.334841	NM_019707	ENSMUSG00000031841	Cdh13	4932416G01Rik|Cdht|Tcad	cadherin 13	protein-coding
mm_127687.1	chr15	102971437	102971474	+	1	NA	3' UTR (NM_010462, exon 2 of 2)	3' UTR (NM_010462, exon 2 of 2)	-1895	NR_029722	723958		NR_029722	ENSMUSG00000065488	Mir196a-2	Mirn196a-2|mir-196a-2	microRNA 196a-2	ncRNA
mm_5692.1	chr1	43186175	43186188	-	1	NA	intron (NM_001289533, intron 1 of 5)	B4|SINE|B4	10580	NM_001289533	14200	Mm.6799	NM_010212	ENSMUSG00000008136	Fhl2	FHL-2|SLIM-3|SLIM3	four and a half LIM domains 2	protein-coding
mm_9576.1	chr1	173982843	173982848	-	1	NA	promoter-TSS (NM_011940)	promoter-TSS (NM_011940)	-1	NM_011940	26388	Mm.218770	NM_008327	ENSMUSG00000026535	Ifi202b	Ifbip-1|Ifi202|Ifi202a|p202	interferon activated gene 202B	protein-coding
mm_125524.1	chr15	57695691	57695702	+	1	NA	intron (NM_199449, intron 1 of 3)	CpG	1029	NM_199449	387609	Mm.36557	NM_199449	ENSMUSG00000071757	Zhx2	Afr-1|Afr1|Raf|mKIAA0854	zinc fingers and homeoboxes 2	protein-coding
mm_143297.1	chr17	65951128	65951154	-	1	NA	promoter-TSS (NM_023053)	promoter-TSS (NM_023053)	46	NM_023053	65960	Mm.10153	NM_023053	ENSMUSG00000024098	Twsg1	1810013J15Rik|9030422N06Rik|AW552143|D17Ertd403e|Tsg|Twg	twisted gastrulation BMP signaling modulator 1	protein-coding
mm_3440.1	chr1	150102647	150102674	+	1	NA	exon (NM_011198, exon 5 of 10)	exon (NM_011198, exon 5 of 10)	2629	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_120521.1	chr14	66784524	66784537	+	1	NA	Intergenic	Intergenic	84070	NM_009955	12934	Mm.352648	NM_009955	ENSMUSG00000022048	Dpysl2	AI851130|Crmp2|DRP2|Musunc33|TOAD-64|Ulip2	dihydropyrimidinase-like 2	protein-coding
mm_85126.1	chr9	95511898	95511908	-	1	NA	promoter-TSS (NM_001114977)	promoter-TSS (NM_001114977)	93	NM_026476	67958	Mm.292742	NM_026476	ENSMUSG00000032407	U2surp	2610101N10Rik|AU023006|Sr140	U2 snRNP-associated SURP domain containing	protein-coding
mm_11729.1	chr2	37443343	37443359	+	1	NA	promoter-TSS (NM_146121)	promoter-TSS (NM_146121)	66	NM_146121	227800	Mm.383192	NM_146121	ENSMUSG00000035437	Rabgap1	Gapcena|mKIAA4104	RAB GTPase activating protein 1	protein-coding
mm_143572.1	chr17	74295475	74295535	-	1	NA	promoter-TSS (NM_133771)	promoter-TSS (NM_133771)	-642	NM_133771	76890	Mm.311874	NM_133771	ENSMUSG00000058704	Memo1	0610016J10Rik|D930048L02Rik	mediator of cell motility 1	protein-coding
mm_103102.1	chr11	69940635	69940646	-	1	NA	exon (NM_016875, exon 7 of 9)	exon (NM_016875, exon 7 of 9)	4312	NM_001347634	53422	Mm.29286	NM_016875	ENSMUSG00000018554	Ybx2	Msy2	Y box protein 2	protein-coding
mm_119880.1	chr14	54891521	54891524	+	1	NA	Intergenic	ID_B1|SINE|B4	-2621	NM_019402	54196	Mm.7723	NM_019402	ENSMUSG00000022194	Pabpn1	PAB2|Pabp3|mPABII	poly(A) binding protein, nuclear 1	protein-coding
mm_3111.1	chr1	134560191	134560213	+	1	NA	promoter-TSS (NM_152895)	promoter-TSS (NM_152895)	24	NM_152895	75605	Mm.28995	NM_152895	ENSMUSG00000042207	Kdm5b	2010009J12Rik|2210016I17Rik|AW556288|D1Ertd202e|Jarid1b|PLU-1|PUT1|Plu1|RBBP2H1A|Rb-Bp2|mKIAA4034	lysine (K)-specific demethylase 5B	protein-coding
mm_166926.1	chr7	32542951	32542951	+	1	NA	Intergenic	L1Md_F|LINE|L1	101410	NM_001256066	384589	Mm.454021	NM_001256066	ENSMUSG00000078757	Scgb1b29	Abpa29|Abpa29_a7|EG384589|Gm5326	secretoglobin, family 1B, member 29	protein-coding
mm_69726.1	chr7	140770220	140770233	-	1	NA	exon (NM_021282, exon 5 of 9)	exon (NM_021282, exon 5 of 9)	6394	NM_021282	13106	Mm.21758	NM_021282	ENSMUSG00000025479	Cyp2e1	Cyp2e	cytochrome P450, family 2, subfamily e, polypeptide 1	protein-coding
mm_89240.1	chr10	87853578	87853592	+	1	NA	Intergenic	Intergenic	-4680	NM_001314010	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_50774.1	chr6	53644389	53644394	+	1	NA	intron (NM_001327821, intron 7 of 10)	intron (NM_001327821, intron 7 of 10)	71017	NM_172728	231991	Mm.227444	NM_172728	ENSMUSG00000053007	Creb5	9430076C15Rik|CRE-BPa|Crebpa|D430026C09Rik	cAMP responsive element binding protein 5	protein-coding
mm_49111.1	chr6	8397073	8397075	+	1	NA	intron (NM_001302354, intron 3 of 3)	AT_rich|Low_complexity|Low_complexity	112087	NR_040452	320312	Mm.374890	NR_040452	ENSMUSG00000087305	A430035B10Rik	2810488G03Rik	RIKEN cDNA A430035B10 gene	ncRNA
mm_172551.1	chr8	102784922	102784926	-	1	NA	5' UTR (NM_009866, exon 1 of 13)	5' UTR (NM_009866, exon 1 of 13)	187	NM_009866	12552	Mm.1571	NM_009866	ENSMUSG00000031673	Cdh11	Cad11|OSF-4	cadherin 11	protein-coding
mm_172081.1	chr6	145932928	145932928	-	1	NA	intron (NM_001310837, intron 1 of 2)	LSU-rRNA_Hsa|rRNA|rRNA	1055	NM_001310837	16651	Mm.49689	NM_010656	ENSMUSG00000030255	Sspn	Krag	sarcospan	protein-coding
mm_83471.1	chr9	45779610	45779636	-	1	NA	intron (NM_001081373, intron 13 of 29)	intron (NM_001081373, intron 13 of 29)	49015	NM_001081373	214552	Mm.260103	NM_172531	ENSMUSG00000043987	Cep164	AI450905|BC027092|D030051D21|mKIAA1052	centrosomal protein 164	protein-coding
mm_166493.1	chr5	150409132	150409181	+	1	NA	intron (NM_172887, intron 31 of 60)	intron (NM_172887, intron 31 of 60)	93063	NR_024513	194292	Mm.300184	NR_024513		Gm5	Gm1812	predicted gene 5	ncRNA
mm_55860.1	chr6	83456407	83456421	-	1	NA	promoter-TSS (NM_001347313)	promoter-TSS (NM_001347313)	-22	NM_001347313	194388	Mm.211030	NM_183138	ENSMUSG00000034832	Tet3	B430006D22Rik|BC037432|D230004J03Rik	tet methylcytosine dioxygenase 3	protein-coding
mm_27094.1	chr3	30190096	30190114	-	1	NA	Intergenic	RLTR17B_Mm|LTR|ERVK	-176901	NM_007963	14013	Mm.56965	NM_007963	ENSMUSG00000027684	Mecom	D630039M04Rik|Evi-1|Evi1|Jbo|Mds|Mds1|Mds1-Evi1|Prdm3|Znfpr1b1	MDS1 and EVI1 complex locus	protein-coding
mm_143808.1	chr17	83631893	83631934	-	1	NA	promoter-TSS (NM_153512)	promoter-TSS (NM_153512)	-18	NM_153512	225030	Mm.223506	NM_153512	ENSMUSG00000045053	Kcng3	KV6.3|Kv10.1a|Kv10.1b	potassium voltage-gated channel, subfamily G, member 3	protein-coding
mm_35263.1	chr4	19892383	19892411	-	1	NA	intron (NM_175406, intron 2 of 7)	intron (NM_175406, intron 2 of 7)	30169	NM_175406	242341	Mm.19298	NM_175406	ENSMUSG00000028238	Atp6v0d2	1620401A02Rik|AI324824|V-ATPase	ATPase, H+ transporting, lysosomal V0 subunit D2	protein-coding
mm_106344.1	chr11	118393321	118393345	-	1	NA	exon (NM_011150, exon 6 of 6)	exon (NM_011150, exon 6 of 6)	8598	NM_011150	19039	Mm.3152	NM_011150	ENSMUSG00000033880	Lgals3bp	90K|CyCAP|MAC-2BP|Ppicap|Tango10b	lectin, galactoside-binding, soluble, 3 binding protein	protein-coding
mm_144524.1	chr18	25037073	25037074	+	1	NA	intron (NM_175276, intron 13 of 26)	intron (NM_175276, intron 13 of 26)	128892	NM_001142697	66648	Mm.263189	NM_001004361	ENSMUSG00000024269	Tpgs2	5730437P09Rik|5730494M16Rik|AI666318|Pgs2	tubulin polyglutamylase complex subunit 2	protein-coding
mm_162505.1	chr1	148978896	148978896	+	1	NA	Intergenic	Intergenic	943543	NM_001305632	18783	Mm.4186	NM_008869	ENSMUSG00000056220	Pla2g4a	Pla2g4|cPLA2|cPLA2-alpha|cPLA2alpha	phospholipase A2, group IVA (cytosolic, calcium-dependent)	protein-coding
mm_116238.1	chr13	33905154	33905164	-	1	NA	intron (NM_148942, intron 1 of 6)	intron (NM_148942, intron 1 of 6)	549	NM_148942	97848	Mm.272188	NM_148942	ENSMUSG00000052180	Serpinb6c	C76171|C76174|SPI3C|SPIC|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 6c	protein-coding
mm_83826.1	chr9	53975247	53975348	-	1	NA	promoter-TSS (NM_177769)	promoter-TSS (NM_177769)	4	NM_177769	270162	Mm.259791	NM_177769	ENSMUSG00000041986	Elmod1	4831417L10|AI428506|AI834991	ELMO/CED-12 domain containing 1	protein-coding
mm_171137.1	chr3	150072748	150072760	-	1	NA	Intergenic	Intergenic	798017	NR_040591	381482	Mm.393866	NR_040591		Gm1653	-	predicted gene 1653	ncRNA
mm_33632.1	chr4	132884528	132884552	+	1	NA	promoter-TSS (NM_133887)	promoter-TSS (NM_133887)	-82	NM_133887	100226	Mm.28237	NM_133887	ENSMUSG00000028879	Stx12	AI850350|AU041521|Stx13	syntaxin 12	protein-coding
mm_128415.1	chr15	44752249	44752265	-	1	NA	5' UTR (NM_178765, exon 1 of 8)	5' UTR (NM_178765, exon 1 of 8)	201	NM_178765	319613	Mm.207715	NM_176998	ENSMUSG00000022340	Sybu	Golsyn	syntabulin (syntaxin-interacting)	protein-coding
mm_20965.1	chr2	151970957	151970977	-	1	NA	intron (NM_146127, intron 1 of 1)	intron (NM_146127, intron 1 of 1)	2427	NM_001289151	73847	Mm.272444	NM_028666	ENSMUSG00000027459	Fam110a	1700008J10Rik|5430432M24Rik|AI747080	family with sequence similarity 110, member A	protein-coding
mm_44663.1	chr5	28467094	28467109	-	1	NA	promoter-TSS (NM_009170)	promoter-TSS (NM_009170)	0	NM_009170	20423	Mm.57202	NM_009170	ENSMUSG00000002633	Shh	9530036O11Rik|Dsh|Hhg1|Hx|Hxl3|M100081	sonic hedgehog	protein-coding
mm_23213.1	chr3	41742638	41742669	+	1	NA	promoter-TSS (NM_001081411)	promoter-TSS (NM_001081411)	35	NM_027271	73852	Mm.29006	NM_027271	ENSMUSG00000025766	D3Ertd751e	2810009O15Rik|4930415G15Rik	DNA segment, Chr 3, ERATO Doi 751, expressed	protein-coding
mm_40792.1	chr5	67463887	67463937	+	1	NA	promoter-TSS (NR_015582)	promoter-TSS (NR_015582)	14	NR_015582	320479	Mm.387187	NR_015582	ENSMUSG00000107385	C330024D21Rik	-	RIKEN cDNA C330024D21 gene	ncRNA
mm_33450.1	chr4	130670203	130670206	+	1	NA	intron (NM_001159606, intron 2 of 17)	intron (NM_001159606, intron 2 of 17)	6845	NM_001159605	80912	Mm.440206	NM_030722	ENSMUSG00000028580	Pum1	AA517475|Pumm|mKIAA0099	pumilio RNA-binding family member 1	protein-coding
mm_162315.1	chr1	37998256	37998273	+	1	NA	5' UTR (NM_198303, exon 1 of 24)	5' UTR (NM_198303, exon 1 of 24)	254	NM_198303	226982	Mm.260943	NM_198303	ENSMUSG00000026083	Eif5b	A030003E17Rik|BC018347|IF2	eukaryotic translation initiation factor 5B	protein-coding
mm_106167.1	chr11	116671555	116671573	-	1	NA	promoter-TSS (NR_027821)	promoter-TSS (NR_027821)	-96	NR_027821	66293	Mm.432051	NM_025472	ENSMUSG00000020812	1810032O08Rik	-	RIKEN cDNA 1810032O08 gene	ncRNA
mm_54324.1	chr6	30502556	30502558	-	1	NA	intron (NM_001347087, intron 4 of 13)	intron (NM_001347087, intron 4 of 13)	7216	NM_001347087	72649	Mm.45418	NM_178625	ENSMUSG00000029782	Tmem209	2700094F01Rik|AI428435	transmembrane protein 209	protein-coding
mm_95186.1	chr11	42421234	42421240	+	1	NA	promoter-TSS (NM_001347314)	promoter-TSS (NM_001347314)	-113	NM_001347314	14401	Mm.338723	NM_008070	ENSMUSG00000007653	Gabrb2	AI834970|C030002O17Rik|C030021G16Rik|Gabrab2|Gabrb-2	gamma-aminobutyric acid (GABA) A receptor, subunit beta 2	protein-coding
mm_126505.1	chr15	81802571	81802577	+	1	NA	promoter-TSS (NM_153484)	promoter-TSS (NM_153484)	-99	NM_153484	21685	Mm.270278	NM_017376	ENSMUSG00000022389	Tef	2310028D20Rik	thyrotroph embryonic factor	protein-coding
mm_13728.1	chr2	117886399	117886401	+	1	NA	intron (NR_040631, intron 3 of 5)	intron (NR_040631, intron 3 of 5)	64472	NR_040631	73938	Mm.399107	NR_040631	ENSMUSG00000086221	4930412B13Rik	-	RIKEN cDNA 4930412B13 gene	ncRNA
mm_11054.1	chr2	27229542	27229542	+	1	NA	intron (NM_138665, intron 10 of 20)	intron (NM_138665, intron 10 of 20)	17761	NM_138665	192166	Mm.278467	NM_138665	ENSMUSG00000009614	Sardh	-	sarcosine dehydrogenase	protein-coding
mm_150470.1	chr19	38481058	38481120	+	1	NA	Intergenic	CpG	-43108	NM_019588	74055	Mm.34031	NM_019588	ENSMUSG00000024998	Plce1	4933403A21Rik|PLCepsilon|Plce|mKIAA1516	phospholipase C, epsilon 1	protein-coding
mm_87446.1	chr10	51481724	51481742	+	1	NA	exon (NM_008147, exon 4 of 9)	exon (NM_008147, exon 4 of 9)	1121	NM_001291892	14727	Mm.439661	NM_008147	ENSMUSG00000062593	Lilr4b	Gp49a|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4B	protein-coding
mm_163193.1	chr11	94997861	94997879	+	1	NA	intron (NM_172261, intron 2 of 9)	intron (NM_172261, intron 2 of 9)	6658	NM_172261	217124	Mm.229087	NM_172261	ENSMUSG00000038976	Ppp1r9b	SPL|Spn	protein phosphatase 1, regulatory subunit 9B	protein-coding
mm_138453.1	chr17	35135876	35135918	+	1	NA	intron (NM_001252469, intron 1 of 23)	intron (NM_001252469, intron 1 of 23)	183	NM_001252469	224727	Mm.203962	NM_057171	ENSMUSG00000024392	Bag6	2410045D21Rik|AA408914|BAG-6|Bat3|D17H6S52E|G3|Scythe	BCL2-associated athanogene 6	protein-coding
mm_161471.1	chr15	79254712	79254712	-	1	NA	promoter-TSS (NM_020516)	promoter-TSS (NM_020516)	36	NM_020516	57274	Mm.441697	NM_020516	ENSMUSG00000032988	Slc16a8	Mct3	solute carrier family 16 (monocarboxylic acid transporters), member 8	protein-coding
mm_74469.1	chr8	4258177	4258220	-	1	NA	3' UTR (NM_183315, exon 2 of 2)	3' UTR (NM_183315, exon 2 of 2)	1076	NM_183315	330695	Mm.34210	NM_183315	ENSMUSG00000048644	Ctxn1	BC028881|Ctxn	cortexin 1	protein-coding
mm_30217.1	chr3	145018730	145018744	-	1	NA	exon (NM_017474, exon 5 of 14)	exon (NM_017474, exon 5 of 14)	14039	NM_017474	23844	Mm.33483	NM_017474	ENSMUSG00000028255	Clca1	Clca2|Clca3|gob-5|gob5	chloride channel accessory 1	protein-coding
mm_25607.1	chr3	117575520	117575534	+	1	NA	5' UTR (NM_029425, exon 1 of 6)	5' UTR (NM_029425, exon 1 of 6)	300	NM_001305451	75769	Mm.72187	NM_029425	ENSMUSG00000033342	Plppr5	4833424O15Rik|Lppr5|PRG-5|Pap2d	phospholipid phosphatase related 5	protein-coding
mm_32670.1	chr4	115737739	115737752	+	1	NA	promoter-TSS (NM_172698)	promoter-TSS (NM_172698)	-328	NM_172698	230648	Mm.283565	NM_172698	ENSMUSG00000034210	Efcab14	4732418C07Rik	EF-hand calcium binding domain 14	protein-coding
mm_170976.1	chr2	6840418	6840434	+	1	NA	intron (NM_001110229, intron 2 of 14)	L1Md_T|LINE|L1	31609	NM_001347094	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_7509.1	chr1	123623762	123623769	-	1	NA	intron (NM_199021, intron 5 of 25)	intron (NM_199021, intron 5 of 25)	421794	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_172192.1	chr6	51465223	51465226	-	1	NA	exon (NM_182650, exon 7 of 10)	exon (NM_182650, exon 7 of 10)	4670	NM_182650	53379	Mm.155896	NM_016806	ENSMUSG00000004980	Hnrnpa2b1	9130414A06Rik|Hnrpa2|Hnrpa2b1|hnrnp-A	heterogeneous nuclear ribonucleoprotein A2/B1	protein-coding
mm_5800.1	chr1	52164714	52164724	-	1	NA	3' UTR (NM_001081081, exon 18 of 18)	3' UTR (NM_001081081, exon 18 of 18)	45097	NM_001205313	20846	Mm.277406	NM_009283	ENSMUSG00000026104	Stat1	2010005J02Rik|AA408197	signal transducer and activator of transcription 1	protein-coding
mm_96048.1	chr11	59559265	59559280	+	1	NA	intron (NM_145827, intron 7 of 9)	ID_B1|SINE|B4	12466	NM_001011789	257962	Mm.377316	NM_001011789	ENSMUSG00000059610	Olfr222	MOR256-45P	olfactory receptor 222	protein-coding
mm_80425.1	chr9	77920179	77920187	+	1	NA	intron (NM_134255, intron 1 of 7)	intron (NM_134255, intron 1 of 7)	2818	NM_134255	68801	Mm.430736	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	ELOVL family member 5, elongation of long chain fatty acids (yeast)	protein-coding
mm_115843.1	chr13	21287354	21287366	-	1	NA	3' UTR (NM_010343, exon 5 of 5)	3' UTR (NM_010343, exon 5 of 5)	5326	NM_010343	14780	Mm.1332	NM_010343	ENSMUSG00000004344	Gpx5	AV379049|Arep	glutathione peroxidase 5	protein-coding
mm_104994.1	chr11	100354126	100354143	-	1	NA	exon (NM_177981, exon 4 of 13)	exon (NM_177981, exon 4 of 13)	2007	NM_177981	15114	Mm.281700	NM_010404	ENSMUSG00000006930	Hap1	HAP-1	huntingtin-associated protein 1	protein-coding
mm_145016.1	chr18	38714316	38714334	+	1	NA	Intergenic	Intergenic	-113057	NM_011898	24066	Mm.42038	NM_011898	ENSMUSG00000024427	Spry4	A030006O18Rik|sprouty4	sprouty homolog 4 (Drosophila)	protein-coding
mm_91436.1	chr10	33786716	33786737	-	1	NA	Intergenic	Intergenic	-4611	NM_001101452	215895	Mm.473684	NM_001101452	ENSMUSG00000090298	Sult3a2	EG215895|Gm4794	sulfotransferase family 3A, member 2	protein-coding
mm_108044.1	chr12	73907960	73907970	+	1	NA	promoter-TSS (NM_010431)	promoter-TSS (NM_010431)	98	NM_001313919	15251	Mm.3879	NM_010431	ENSMUSG00000021109	Hif1a	AA959795|HIF-1-alpha|HIF1-alpha|HIF1alpha|MOP1|bHLHe78	hypoxia inducible factor 1, alpha subunit	protein-coding
mm_107700.1	chr12	55446927	55446932	+	1	NA	intron (NR_035430, intron 1 of 3)	intron (NR_035430, intron 1 of 3)	45718	NM_010907	18035	Mm.170515	NM_010907	ENSMUSG00000021025	Nfkbia	AI462015|Nfkbi	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, alpha	protein-coding
mm_154792.1	chrX	13072807	13072826	+	1	NA	intron (NM_009481, intron 1 of 44)	CpG	1318	NM_009481	22284	Mm.242646	NM_009481	ENSMUSG00000031010	Usp9x	5730589N07Rik|AA407302|AA407699|AL022658|AL022749|Dffrx|FAF-X|Fafl	ubiquitin specific peptidase 9, X chromosome	protein-coding
mm_20060.1	chr2	120352973	120352983	-	1	NA	exon (NM_178851, exon 1 of 25)	exon (NM_178851, exon 1 of 25)	155	NM_178851	269338	Mm.246131	NM_147153	ENSMUSG00000027291	Vps39	A230065P22Rik|AW743070|Vam6|Vam6P|mVam6	VPS39 HOPS complex subunit	protein-coding
mm_1794.1	chr1	79776097	79776132	+	1	NA	promoter-TSS (NM_001081210)	promoter-TSS (NM_001081210)	96	NM_001081210	69163	Mm.238455	NM_001081210	ENSMUSG00000026248	Mrpl44	1810030E18Rik|5730593H20Rik|AI463302	mitochondrial ribosomal protein L44	protein-coding
mm_152655.1	chr19	12795015	12795050	-	1	NA	exon (NM_053009, exon 1 of 11)	exon (NM_053009, exon 1 of 11)	1091	NR_024093	664779	Mm.290924	NM_001039718	ENSMUSG00000024695	Gm44505	Zfp91-Cntf|Zfp91Cntf	predicted readthrough transcript (NMD candidate), 44505	ncRNA
mm_129713.1	chr15	81858787	81858803	-	1	NA	promoter-TSS (NM_020507)	promoter-TSS (NM_020507)	-469	NM_020507	57259	Mm.323595	NM_020507	ENSMUSG00000048546	Tob2	2900090N22Rik|4930545K18Rik|AV071822|mKIAA1663	transducer of ERBB2, 2	protein-coding
mm_23088.1	chr3	36942382	36942411	+	1	NA	exon (NM_172679, exon 26 of 86)	exon (NM_172679, exon 26 of 86)	79290	NM_172679	229227	Mm.207907	NM_172679	ENSMUSG00000037270	4932438A13Rik	4732443H21|B830039D19Rik|D630029K19Rik|FSA|Kiaa1109|Tweek	RIKEN cDNA 4932438A13 gene	protein-coding
mm_42002.1	chr5	107904554	107904556	+	1	NA	intron (NM_016980, intron 5 of 7)	intron (NM_016980, intron 5 of 7)	4027	NM_016980	100503670	Mm.277897	NM_016980	ENSMUSG00000058558	Rpl5	U21RNA	ribosomal protein L5	protein-coding
mm_101820.1	chr11	46690307	46690320	-	1	NA	promoter-TSS (NM_001161356)	promoter-TSS (NM_001161356)	44	NM_001161356	171284	Mm.234654	NM_134249	ENSMUSG00000040413	Timd2	AA816106|AU019358|AU019662|C78111|G9D3|TIM-2|Tim2	T cell immunoglobulin and mucin domain containing 2	protein-coding
mm_125422.1	chr15	41848964	41848966	+	1	NA	intron (NM_001130166, intron 12 of 16)	intron (NM_001130166, intron 12 of 16)	18007	NM_001130164	170719	Mm.254267	NM_130885	ENSMUSG00000022307	Oxr1	2210416C20Rik|C7|C7B	oxidation resistance 1	protein-coding
mm_9004.1	chr1	165848956	165848987	-	1	NA	intron (NM_001113391, intron 1 of 7)	intron (NM_001113391, intron 1 of 7)	60290	NM_001113392	12503	Mm.217308	NM_031162	ENSMUSG00000005763	Cd247	4930549J05Rik|A430104F18Rik|AW552088|Cd3|Cd3-eta|Cd3-zeta|Cd3h|Cd3z|Cd3zeta|T3z|Tcrk|Tcrz	CD247 antigen	protein-coding
mm_75210.1	chr8	39605372	39605384	-	1	NA	3' UTR (NM_031195, exon 9 of 9)	3' UTR (NM_031195, exon 9 of 9)	37300	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_119577.1	chr14	50834739	50834784	+	1	NA	intron (NM_009351, intron 41 of 54)	RLTR12B|LTR|ERVK	26815	NM_009632	11546	Mm.281482	NM_009632	ENSMUSG00000036023	Parp2	ARTD2|Adprt2|Adprtl2|Aspartl2|C78626|PARP-2	poly (ADP-ribose) polymerase family, member 2	protein-coding
mm_73758.1	chr8	115110933	115110936	+	1	NA	intron (NM_019573, intron 8 of 8)	intron (NM_019573, intron 8 of 8)	595960	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_75271.1	chr8	40855554	40855557	-	1	NA	Intergenic	Intergenic	-6812	NM_007514	11988	Mm.4676	NM_007514	ENSMUSG00000031596	Slc7a2	20.5|AI158848|Atrc2|CAT-2|Cat2|Tea	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	protein-coding
mm_93810.1	chr10	121310990	121311003	-	1	NA	5' UTR (NM_029057, exon 1 of 12)	5' UTR (NM_029057, exon 1 of 12)	193	NM_029057	74694	Mm.233833	NM_029057	ENSMUSG00000052302	Tbc1d30	4930505D03Rik	TBC1 domain family, member 30	protein-coding
mm_98042.1	chr11	85492738	85492751	+	1	NA	intron (NM_138681, intron 14 of 25)	intron (NM_138681, intron 14 of 25)	139580	NM_001166643	192197	Mm.209989	NM_138681	ENSMUSG00000059439	Bcas3	1500019F07Rik|2610028P08Rik|AU021018|BC028339|K20D4|rudhira	breast carcinoma amplified sequence 3	protein-coding
mm_131784.1	chr16	22896494	22896576	+	1	NA	exon (NM_001276450, exon 5 of 7)	exon (NM_001276450, exon 5 of 7)	-2149	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_15798.1	chr2	164456937	164456988	+	1	NA	Intergenic	Intergenic	-4009	NM_025575	66460	Mm.44218	NM_025575	ENSMUSG00000045503	Sys1	2610042O14Rik|AI266964|C87389	SYS1 Golgi-localized integral membrane protein homolog (S. cerevisiae)	protein-coding
mm_44417.1	chr5	18006999	18007018	-	1	NA	intron (NM_001081143, intron 5 of 7)	MER63A|DNA|hAT-Blackjack	44438	NM_001081143	242851	Mm.332230	NM_001081143	ENSMUSG00000028777	Gnat3	Ggust|Gtn	guanine nucleotide binding protein, alpha transducing 3	protein-coding
mm_58353.1	chr6	147531291	147531299	-	1	NA	intron (NM_025911, intron 3 of 12)	intron (NM_025911, intron 3 of 12)	55424	NM_025911	67015	Mm.209774	NM_025911	ENSMUSG00000030301	Ccdc91	1700086G08Rik|1810060J02Rik|AU045683|AW555238|p56	coiled-coil domain containing 91	protein-coding
mm_45120.1	chr5	45832145	45832161	-	1	NA	intron (NM_001163073, intron 1 of 6)	Charlie7|DNA|hAT-Charlie	24399	NM_172153	209707	Mm.71498	NM_172153	ENSMUSG00000015882	Lcorl	Mlr1	ligand dependent nuclear receptor corepressor-like	protein-coding
mm_91963.1	chr10	61273382	61273404	-	1	NA	promoter-TSS (NM_001081127)	promoter-TSS (NM_001081127)	45	NM_001081127	237360	Mm.333252	NM_001081127	ENSMUSG00000059901	Adamts14	Adamts-14|TS14	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 14	protein-coding
mm_100421.1	chr11	119440901	119440916	+	1	NA	Intergenic	Intergenic	50436	NR_035453	100316690		NR_035453	ENSMUSG00000088015	Mir1932	mir-1932|mmu-mir-1932	microRNA 1932	ncRNA
mm_52181.1	chr6	99340547	99340557	+	1	NA	intron (NM_001347345, intron 2 of 19)	intron (NM_001347345, intron 2 of 19)	-74037	NM_001197321	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_140286.1	chr17	85190064	85190068	+	1	NA	intron (NM_028576, intron 3 of 10)	intron (NM_028576, intron 3 of 10)	99366	NM_028576	73582	Mm.260753	NM_028576	ENSMUSG00000071037	Camkmt	1700106N22Rik|AI480743|AV099781|CLNMT|CaM KMT	calmodulin-lysine N-methyltransferase	protein-coding
mm_27396.1	chr3	51211490	51211494	-	1	NA	Intergenic	Intergenic	-12955	NM_009834	12457	Mm.86541	NM_009834	ENSMUSG00000023087	Noct	AU043840|Ccr4|Ccrn4l	nocturnin	protein-coding
mm_14649.1	chr2	136911010	136911029	+	1	NA	intron (NM_001038641, intron 2 of 7)	intron (NM_001038641, intron 2 of 7)	11668	NM_001038641	74243	Mm.330612	NM_028201	ENSMUSG00000027281	Slx4ip	2210009G21Rik|2410004I22Rik|C85661|Slxip	SLX4 interacting protein	protein-coding
mm_110457.1	chr12	51692005	51692009	-	1	NA	promoter-TSS (NM_001172098)	promoter-TSS (NM_001172098)	-93	NM_052973	94186	Mm.65979	NM_052973	ENSMUSG00000020954	Strn3	Gs2na|SG2NA	striatin, calmodulin binding protein 3	protein-coding
mm_57303.1	chr6	124636935	124636952	-	1	NA	promoter-TSS (NM_173864)	promoter-TSS (NM_173864)	-858	NM_173864	317677	Mm.483270	NM_173864	ENSMUSG00000079343	C1s2	C1sb|EG317677|Gm5077	complement component 1, s subcomponent 2	protein-coding
mm_159153.1	chr2	88930239	88930239	-	1	NA	promoter-TSS (NM_001011804)	promoter-TSS (NM_001011804)	74	NM_001011804	258025	Mm.377332	NM_001011804	ENSMUSG00000075112	Olfr1211	MOR233-16P|MOR233-21	olfactory receptor 1211	protein-coding
mm_149215.1	chr19	9984904	9984929	+	1	NA	TTS (NM_011913)	TTS (NM_011913)	2270	NM_010239	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
mm_2997.1	chr1	133241184	133241213	+	1	NA	Intergenic	Intergenic	-4899	NM_001160268	240753	Mm.253559	NM_182930	ENSMUSG00000041757	Plekha6	9530028L01Rik|AU042621|Pepp3	pleckstrin homology domain containing, family A member 6	protein-coding
mm_1097.1	chr1	59709001	59709040	+	1	NA	exon (NM_018868, exon 13 of 15)	exon (NM_018868, exon 13 of 15)	4212	NR_028521	100217421		NR_028521		Snord11	MBII-95	small nucleolar RNA, C/D box 11	snoRNA
mm_119293.1	chr14	34674055	34674065	+	1	NA	5' UTR (NM_001301330, exon 1 of 19)	5' UTR (NM_001301330, exon 1 of 19)	132	NM_001301330	218914	Mm.27957	NM_001004436	ENSMUSG00000041408	Wapl	A530089A20Rik|BC037674|DIF-2|FOE|Wapal	WAPL cohesin release factor	protein-coding
mm_63271.1	chr7	126760699	126760744	+	1	NA	intron (NM_011952, intron 1 of 8)	intron (NM_011952, intron 1 of 8)	1095	NM_011952	26417	Mm.8385	NM_011952	ENSMUSG00000063065	Mapk3	Erk-1|Erk1|Ert2|Esrk1|Mnk1|Mtap2k|Prkm3|p44|p44erk1|p44mapk	mitogen-activated protein kinase 3	protein-coding
mm_89792.1	chr10	102225702	102225705	+	1	NA	intron (NM_001162369, intron 1 of 5)	intron (NM_001162369, intron 1 of 5)	66624	NM_001162369	67569	Mm.25252	NM_026243	ENSMUSG00000019888	Mgat4c	9130411I17Rik|GntIVh	MGAT4 family, member C	protein-coding
mm_157001.1	chrX	7572322	7572324	-	1	NA	intron (NM_138605, intron 1 of 3)	intron (NM_138605, intron 1 of 3)	-1277	NR_029473	78185	Mm.160055	NR_029473	ENSMUSG00000039545	Ppp1r3fos	4930524L23Rik	protein phosphatase 1, regulatory subunit 3F, opposite strand	ncRNA
mm_49925.1	chr6	39380022	39380047	+	1	NA	Intergenic	Intergenic	-1394	NM_011226	19331	Mm.123866	NM_011226	ENSMUSG00000029923	Rab19	-	RAB19, member RAS oncogene family	protein-coding
mm_31870.1	chr4	80004512	80004519	+	1	NA	Intergenic	Intergenic	-829698	NM_031202	22178	Mm.30438	NM_031202	ENSMUSG00000005994	Tyrp1	Oca3|TRP-1|TRP1|Tyrp|b|brown|isa	tyrosinase-related protein 1	protein-coding
mm_23152.1	chr3	40531008	40531029	+	1	NA	Intergenic	Intergenic	-8106	NR_040445	100040882	Mm.272869	NR_040445	ENSMUSG00000037884	1700017G19Rik	-	RIKEN cDNA 1700017G19 gene	ncRNA
mm_79581.1	chr9	58135081	58135102	+	1	NA	exon (NM_001162479, exon 2 of 19)	exon (NM_001162479, exon 2 of 19)	426	NM_001162479	20897	Mm.10801	NM_009291	ENSMUSG00000032327	Stra6	AI891933	stimulated by retinoic acid gene 6	protein-coding
mm_52579.1	chr6	116629077	116629120	+	1	NA	promoter-TSS (NM_026057)	promoter-TSS (NM_026057)	-99	NM_026057	67255	Mm.18810	NM_026057	ENSMUSG00000059878	Zfp422	2900028O21Rik|AU041373|KOX15|Krox-25-2|Krox-26|Krox25|Krox26|Znf22	zinc finger protein 422	protein-coding
mm_100950.1	chr11	6605572	6605642	-	1	NA	exon (NM_001081652, exon 1 of 8)	exon (NM_001081652, exon 1 of 8)	447	NM_001081652	192950	Mm.337771	NM_001081652	ENSMUSG00000041073	Nacad	D230024G13Rik|mKIAA0363	NAC alpha domain containing	protein-coding
mm_160909.1	chr11	82870777	82870777	-	1	NA	promoter-TSS (NM_001164570)	promoter-TSS (NM_001164570)	-33	NM_001164570	67338	Mm.341608	NM_026097	ENSMUSG00000020696	Rffl	1700051E09Rik|4930516L10Rik|BG080975|Carp2	ring finger and FYVE like domain containing protein	protein-coding
mm_116933.1	chr13	55831264	55831280	-	1	NA	5' UTR (NM_011097, exon 1 of 3)	5' UTR (NM_011097, exon 1 of 3)	153	NM_011097	18740	Mm.135195	NM_011097	ENSMUSG00000021506	Pitx1	Bft|P-OTX|Potx|Ptx1	paired-like homeodomain transcription factor 1	protein-coding
mm_109082.1	chr12	104413640	104413657	+	1	NA	3' UTR (NM_009252, exon 5 of 5)	3' UTR (NM_009252, exon 5 of 5)	6940	NM_009252	20716	Mm.482074	NM_009252	ENSMUSG00000021091	Serpina3n	Spi2-2|Spi2.2|Spi2/eb.4	serine (or cysteine) peptidase inhibitor, clade A, member 3N	protein-coding
mm_120714.1	chr14	72709513	72709516	+	1	NA	intron (NM_207636, intron 1 of 25)	CpG	489	NM_207636	319448	Mm.205421	NM_207636	ENSMUSG00000033487	Fndc3a	1700094E19Rik|D14Ertd453e|F730017H24Rik|Fndc3|sys	fibronectin type III domain containing 3A	protein-coding
mm_50104.1	chr6	41533247	41533257	+	1	NA	Intergenic	Intergenic	11476	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_134398.1	chr16	17531020	17531071	-	1	NA	promoter-TSS (NM_026909)	promoter-TSS (NM_026909)	7	NM_026909	69009	Mm.10174	NM_026909	ENSMUSG00000022760	Thap7	1810004B07Rik	THAP domain containing 7	protein-coding
mm_32409.1	chr4	106953514	106953517	+	1	NA	intron (NM_023672, intron 4 of 17)	intron (NM_023672, intron 4 of 17)	42045	NM_023672	72475	Mm.195635	NM_023672	ENSMUSG00000061887	Ssbp3	2610021L12Rik|2610200M23Rik|5730488C10Rik|AI854733|AW551939|LAST|SSDP1	single-stranded DNA binding protein 3	protein-coding
mm_93054.1	chr10	88605018	88605033	-	1	NA	5' UTR (NM_001252372, exon 1 of 29)	5' UTR (NM_001252372, exon 1 of 29)	127	NM_001252372	109272	Mm.147208	NM_175418	ENSMUSG00000020061	Mybpc1	8030451F13Rik	myosin binding protein C, slow-type	protein-coding
mm_91518.1	chr10	37138648	37138660	-	1	NA	5' UTR (NM_008538, exon 1 of 2)	5' UTR (NM_008538, exon 1 of 2)	272	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_25531.1	chr3	114904469	114904480	+	1	NA	promoter-TSS (NM_001286750)	promoter-TSS (NM_001286750)	-161	NM_001286750	229759	Mm.54183	NM_153157	ENSMUSG00000027965	Olfm3	B230206G02Rik	olfactomedin 3	protein-coding
mm_146168.1	chr18	75278924	75278961	+	1	NA	intron (NM_027727, intron 16 of 16)	intron (NM_027727, intron 16 of 16)	18375	NR_045394	100503117	Mm.250517	NR_045393	ENSMUSG00000102047	2010010A06Rik	5033420E22Rik	RIKEN cDNA 2010010A06 gene	ncRNA
mm_117506.1	chr13	78200407	78200423	-	1	NA	intron (NR_045195, intron 1 of 2)	intron (NR_045195, intron 1 of 2)	-1542	NM_010151	13865	Mm.439653	NM_010151	ENSMUSG00000069171	Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR-3|EAR3|Erbal3|SVP44|Tcfcoup1	nuclear receptor subfamily 2, group F, member 1	protein-coding
mm_135860.1	chr16	59639383	59639445	-	1	NA	promoter-TSS (NM_019665)	promoter-TSS (NM_019665)	-5	NM_001347244	56297	Mm.392505	NM_019665	ENSMUSG00000022722	Arl6	1110018H24Rik|2210411E14Rik|BBS3	ADP-ribosylation factor-like 6	protein-coding
mm_100837.1	chr11	5542227	5542243	-	1	NA	promoter-TSS (NM_134033)	promoter-TSS (NM_134033)	-18	NM_134033	104479	Mm.210403	NM_134033	ENSMUSG00000020482	Ccdc117	1110004K02Rik|1700026O03Rik|AU018638|AU042822|AV173073|BC018601	coiled-coil domain containing 117	protein-coding
mm_54388.1	chr6	31218471	31218485	-	1	NA	promoter-TSS (NR_110471)	promoter-TSS (NR_110471)	-4	NR_110469	232685	Mm.443019	NM_144555	ENSMUSG00000044471	Lncpint	Lincpint|MNCb-1768|Pint|linc-Pint	long non-protein coding RNA, Trp53 induced transcript	ncRNA
mm_97042.1	chr11	72308609	72308629	+	1	NA	exon (NM_001291153, exon 3 of 4)	exon (NM_001291153, exon 3 of 4)	-5825	NM_001099688	628100	Mm.390365	NM_001099688	ENSMUSG00000070388	Fbxo39	1700010H23Rik	F-box protein 39	protein-coding
mm_73167.1	chr8	95020707	95020719	+	1	NA	intron (NM_173036, intron 1 of 11)	intron (NM_173036, intron 1 of 11)	3021	NM_173036	54672	Mm.27995	NM_173036	ENSMUSG00000060470	Adgrg3	A030001G24Rik|AW214383|Gpr97|Pb1|Pb99	adhesion G protein-coupled receptor G3	protein-coding
mm_17891.1	chr2	35061404	35061419	-	1	NA	promoter-TSS (NM_010406)	promoter-TSS (NM_010406)	30	NM_010406	15139	Mm.2168	NM_010406	ENSMUSG00000026874	Hc	C5|C5a|He	hemolytic complement	protein-coding
mm_153657.1	chr19	44394943	44394951	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	12762	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_19832.1	chr2	112259282	112259312	-	1	NA	promoter-TSS (NM_172521)	promoter-TSS (NM_172521)	-6	NM_172521	213765	Mm.78965	NM_172521	ENSMUSG00000041358	Nutm1	4932438M10|Nut	NUT midline carcinoma, family member 1	protein-coding
mm_27762.1	chr3	69673573	69673580	-	1	NA	Intergenic	Intergenic	-48479	NM_133787	97112	Mm.21062	NM_133787	ENSMUSG00000027787	Nmd3	C87860	NMD3 ribosome export adaptor	protein-coding
mm_101150.1	chr11	16742245	16742280	-	1	NA	Intergenic	Intergenic	-9941	NM_207655	13649	Mm.8534	NM_007912	ENSMUSG00000020122	Egfr	9030024J15Rik|AI552599|Erbb|Errb1|Errp|Wa5|wa-2|wa2	epidermal growth factor receptor	protein-coding
mm_159353.1	chr3	79144979	79144979	-	1	NA	promoter-TSS (NM_001310536)	promoter-TSS (NM_001310536)	-92	NM_001310536	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_100561.1	chr11	120730262	120730296	+	1	NA	exon (NM_007621, exon 6 of 8)	exon (NM_007621, exon 6 of 8)	1742	NM_007621	12409	Mm.21454	NM_007621	ENSMUSG00000025150	Cbr2	MLCR	carbonyl reductase 2	protein-coding
mm_65381.1	chr7	25090803	25090816	-	1	NA	TTS (NM_001163556)	TTS (NM_001163556)	6366	NR_105855	102465968		NR_105855	ENSMUSG00000098441	Mir6537	Gm27808|mmu-mir-6537	microRNA 6537	ncRNA
mm_51141.1	chr6	70371433	70371446	+	1	NA	Intergenic	Intergenic	420736	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_72154.1	chr8	72152625	72152636	+	1	NA	3' UTR (NM_001001491, exon 8 of 8)	3' UTR (NM_001001491, exon 8 of 8)	-8570	NM_023126	17274	Mm.162811	NM_023126	ENSMUSG00000003037	Rab8a	AA409338|Mel	RAB8A, member RAS oncogene family	protein-coding
mm_72022.1	chr8	70743109	70743114	+	1	NA	intron (NM_001310465, intron 3 of 16)	intron (NM_001310465, intron 3 of 16)	-11568	NM_001328047	19339	Mm.5083	NM_009001	ENSMUSG00000031840	Rab3a	-	RAB3A, member RAS oncogene family	protein-coding
mm_34799.1	chr4	154637570	154637587	+	1	NA	promoter-TSS (NM_027504)	promoter-TSS (NM_027504)	-705	NM_027504	70673	Mm.257785	NM_027504	ENSMUSG00000039410	Prdm16	5730557K01Rik|csp1|mel1	PR domain containing 16	protein-coding
mm_103965.1	chr11	84491521	84491526	-	1	NA	intron (NM_019816, intron 5 of 12)	intron (NM_019816, intron 5 of 12)	21978	NM_019816	56321	Mm.257482	NM_019816	ENSMUSG00000018697	Aatf	4933415H02Rik|5830465M17Rik|Che-1|Trb	apoptosis antagonizing transcription factor	protein-coding
mm_69465.1	chr7	133602203	133602206	-	1	NA	promoter-TSS (NM_028654)	promoter-TSS (NM_028654)	-89	NM_028654	73808	Mm.159067	NM_028654	ENSMUSG00000030976	Tex36	4930404H21Rik	testis expressed 36	protein-coding
mm_92363.1	chr10	75940041	75940047	-	1	NA	intron (NM_001277132, intron 2 of 6)	intron (NM_001277132, intron 2 of 6)	628	NM_001277132	333670	Mm.291320	NM_001037714	ENSMUSG00000050157	Gm867	Gm736	predicted gene 867	protein-coding
mm_10444.1	chr2	14263395	14263409	+	1	NA	intron (NM_008625, intron 6 of 29)	intron (NM_008625, intron 6 of 29)	2399	NR_030609	100124488		NR_030609	ENSMUSG00000077897	Mir511	Mirn511|mir-511|mmu-mir-511	microRNA 511	ncRNA
mm_88159.1	chr10	69706071	69706090	+	1	NA	intron (NM_170730, intron 1 of 17)	intron (NM_170730, intron 1 of 17)	172372	NM_146005	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_74816.1	chr8	22783445	22783447	-	1	NA	TTS (NM_008872)	TTS (NM_008872)	22208	NM_029505	64933	Mm.390023	NM_029505	ENSMUSG00000031539	Ap3m2	5830445E16Rik|AP-3B	adaptor-related protein complex 3, mu 2 subunit	protein-coding
mm_144347.1	chr18	15195205	15195249	+	1	NA	Intergenic	Intergenic	-43781	NM_134112	106931	Mm.329299	NM_134112	ENSMUSG00000036225	Kctd1	4933402K10Rik|AI661543|AW553000	potassium channel tetramerisation domain containing 1	protein-coding
mm_84984.1	chr9	85749309	85749356	-	1	NA	promoter-TSS (NM_001081282)	promoter-TSS (NM_001081282)	2	NM_001081282	108837	Mm.22315	NM_175371	ENSMUSG00000035941	Ibtk	5430411K16Rik|AA409502|BTKI|mKIAA1417	inhibitor of Bruton agammaglobulinemia tyrosine kinase	protein-coding
mm_75398.1	chr8	46207554	46207573	-	1	NA	exon (NM_007450, exon 4 of 4)	exon (NM_007450, exon 4 of 4)	3446	NM_007450	11739	Mm.16228	NM_007450	ENSMUSG00000031633	Slc25a4	AU019225|Ant1	solute carrier family 25 (mitochondrial carrier, adenine nucleotide translocator), member 4	protein-coding
mm_95150.1	chr11	35769375	35769404	+	1	NA	promoter-TSS (NM_145962)	promoter-TSS (NM_145962)	-106	NM_145962	211347	Mm.255044	NM_145962	ENSMUSG00000018846	Pank3	-	pantothenate kinase 3	protein-coding
mm_116298.1	chr13	36620932	36620936	-	1	NA	Intergenic	LTRIS_Mus|LTR|ERV1	113543	NM_153529	68404	Mm.232930	NM_153529	ENSMUSG00000039114	Nrn1	0710008J23Rik|Cpg15|Nrn	neuritin 1	protein-coding
mm_67981.1	chr7	100662332	100662362	-	1	NA	promoter-TSS (NM_001163182)	promoter-TSS (NM_001163182)	47	NM_013746	27276	Mm.491216	NM_013746	ENSMUSG00000030701	Plekhb1	AI315628|PHR1|Phret1|evt-1	pleckstrin homology domain containing, family B (evectins) member 1	protein-coding
mm_11108.1	chr2	28193044	28193050	+	1	NA	promoter-TSS (NM_001038613)	promoter-TSS (NM_001038613)	-46	NM_001038613	56177	Mm.43278	NM_019498	ENSMUSG00000026833	Olfm1	AMY|AW742568|Noe1|OlfA|Pancortin|Pancortin3	olfactomedin 1	protein-coding
mm_89567.1	chr10	95417353	95417385	+	1	NA	promoter-TSS (NM_007706)	promoter-TSS (NM_007706)	-6	NR_045339	70523	Mm.158398	NR_045338	ENSMUSG00000097766	5730420D15Rik	-	RIKEN cDNA 5730420D15 gene	ncRNA
mm_75590.1	chr8	61591214	61591231	-	1	NA	promoter-TSS (NM_001293774)	promoter-TSS (NM_001293774)	-53	NM_001293774	72333	Mm.29933	NM_001081390	ENSMUSG00000058056	Palld	2410003B16Rik|6030492A02	palladin, cytoskeletal associated protein	protein-coding
mm_106241.1	chr11	117780614	117780629	-	1	NA	promoter-TSS (NM_181321)	promoter-TSS (NM_181321)	0	NM_181321	217353	Mm.286963	NM_145439	ENSMUSG00000025572	Tmc6	D11Ertd204e|EVER1	transmembrane channel-like gene family 6	protein-coding
mm_147090.1	chr18	35648467	35648482	-	1	NA	intron (NM_027222, intron 1 of 3)	intron (NM_027222, intron 1 of 3)	893	NM_027222	69816	Mm.27252	NM_027222	ENSMUSG00000024353	Mzb1	2010001M09Rik|AV064572|PACAP|pERp1	marginal zone B and B1 cell-specific protein 1	protein-coding
mm_50629.1	chr6	50566721	50566750	+	1	NA	promoter-TSS (NM_007808)	promoter-TSS (NM_007808)	92	NR_027892	73183	Mm.430720	NR_015581	ENSMUSG00000085776	5430402O13Rik	3110047M22Rik	RIKEN cDNA 5430402O13 gene	ncRNA
mm_47418.1	chr5	123140136	123140149	-	1	NA	Intergenic	Intergenic	-2051	NM_001040398	208043	Mm.250391	NM_177581	ENSMUSG00000038384	Setd1b	AA516740|BC035291|KMT2G|mKIAA1076	SET domain containing 1B	protein-coding
mm_119118.1	chr14	31072160	31072163	+	1	NA	intron (NM_001081251, intron 19 of 32)	intron (NM_001081251, intron 19 of 32)	53023	NM_001081251	66923	Mm.27913	NM_025847	ENSMUSG00000042323	Pbrm1	2610016F04Rik|AI507524|BAF180|Pb1	polybromo 1	protein-coding
mm_107678.1	chr12	54343735	54343745	+	1	NA	Intergenic	L1MA5|LINE|L1	47578	NR_033689	665239	Mm.26856	NR_033689		Gm7550	EG665239|Gm666	predicted gene 7550	ncRNA
mm_75383.1	chr8	45409896	45409900	-	1	NA	5' UTR (NM_126166, exon 2 of 7)	5' UTR (NM_126166, exon 2 of 7)	641	NM_126166	142980	Mm.33874	NM_126166	ENSMUSG00000031639	Tlr3	AI957183	toll-like receptor 3	protein-coding
mm_105632.1	chr11	106973098	106973117	-	1	NA	Intergenic	Intergenic	26418	NM_010655	16647	Mm.12508	NM_010655	ENSMUSG00000018362	Kpna2	2410044B12Rik|IPOA1|PTAC58|Rch1	karyopherin (importin) alpha 2	protein-coding
mm_135286.1	chr16	38452613	38452675	-	1	NA	promoter-TSS (NM_007414)	promoter-TSS (NM_007414)	45	NM_007414	11544	Mm.20047	NM_007414	ENSMUSG00000002844	Adprh	Arh1	ADP-ribosylarginine hydrolase	protein-coding
mm_83033.1	chr9	37255624	37255635	-	1	NA	5' UTR (NM_001145960, exon 1 of 19)	5' UTR (NM_001145960, exon 1 of 19)	109	NM_020258	56857	Mm.440037	NM_020258	ENSMUSG00000032122	Slc37a2	G3PP|Slc37a1|cI-2|ci2	solute carrier family 37 (glycerol-3-phosphate transporter), member 2	protein-coding
mm_67767.1	chr7	92878755	92878761	-	1	NA	intron (NM_028243, intron 1 of 8)	intron (NM_028243, intron 1 of 8)	3505	NM_028243	72461	Mm.389969	NM_028243	ENSMUSG00000061119	Prcp	2510048K03Rik|2610104A14Rik|AI451719|HUMPCP|PCP	prolylcarboxypeptidase (angiotensinase C)	protein-coding
mm_47968.1	chr5	135778341	135778391	-	1	NA	promoter-TSS (NM_029659)	promoter-TSS (NM_029659)	19	NM_029659	76571	Mm.247666	NM_029659	ENSMUSG00000019178	Styxl1	1700011C14Rik|Dusp24|Mkstyx	serine/threonine/tyrosine interacting-like 1	protein-coding
mm_65694.1	chr7	28372658	28372666	-	1	NA	promoter-TSS (NM_001083912)	promoter-TSS (NM_001083912)	0	NM_138752	101497	Mm.235700	NM_138752	ENSMUSG00000037552	Plekhg2	AI194308|Clg|Cslg	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	protein-coding
mm_151217.1	chr19	53676374	53676416	+	1	NA	promoter-TSS (NM_001170847)	promoter-TSS (NM_001170847)	-911	NM_001170847	73713	Mm.313695	NM_001170847	ENSMUSG00000043639	Rbm20	1110018J23Rik|2010003H22Rik|AI646761	RNA binding motif protein 20	protein-coding
mm_283.1	chr1	21262892	21262903	+	1	NA	exon (NM_010356, exon 6 of 7)	exon (NM_010356, exon 6 of 7)	22312	NM_010356	14859	Mm.394593	NM_010356	ENSMUSG00000025934	Gsta3	Gst2-3	glutathione S-transferase, alpha 3	protein-coding
mm_107180.1	chr12	24982270	24982286	+	1	NA	exon (NM_001081378, exon 2 of 32)	exon (NM_001081378, exon 2 of 32)	7346	NM_001081378	77480	Mm.250641	NM_001081378	ENSMUSG00000036333	Kidins220	3110039L19Rik|AI194387|AI316525|C330002I19Rik|mKIAA1250	kinase D-interacting substrate 220	protein-coding
mm_108339.1	chr12	80174454	80174480	+	1	NA	exon (NM_134156, exon 15 of 21)	exon (NM_134156, exon 15 of 21)	-41623	NR_033514	69548	Mm.269712	NR_033514	ENSMUSG00000097729	2310015A10Rik	5330419I17Rik	RIKEN cDNA 2310015A10 gene	ncRNA
mm_152691.1	chr19	16780904	16780967	-	1	NA	promoter-TSS (NM_173028)	promoter-TSS (NM_173028)	-2	NM_173028	271564	Mm.211963	NM_173028	ENSMUSG00000046230	Vps13a	4930425F11|4930516E05Rik|4930543C13Rik|9930023P20|Chac|Chorein|D330038K10Rik|mKIAA0986	vacuolar protein sorting 13A	protein-coding
mm_144728.1	chr18	35536540	35536546	+	1	NA	Intergenic	Intergenic	-16867	NR_038073	100503380	Mm.482118	NR_038073	ENSMUSG00000097769	Snhg4	Gm17457	small nucleolar RNA host gene 4	ncRNA
mm_102792.1	chr11	68691727	68691754	-	1	NA	promoter-TSS (NM_175260)	promoter-TSS (NM_175260)	-175	NM_175260	77579	Mm.218233	NM_175260	ENSMUSG00000020900	Myh10	5730504C04Rik|9330167F11Rik|Fltn|Myhn-2|Myhn2|NMHC II-B|NMHC-B|NMHCII-B|NMMHC II-b|NMMHC-B|NMMHC-IIB|SMemb|mKIAA3005	myosin, heavy polypeptide 10, non-muscle	protein-coding
mm_48455.1	chr5	140760470	140760496	-	1	NA	3' UTR (NM_010302, exon 4 of 4)	3' UTR (NM_010302, exon 4 of 4)	36356	NM_173405	231842	Mm.491298	NM_173405	ENSMUSG00000050022	Amz1	5330426I05|6530401C20Rik	archaelysin family metallopeptidase 1	protein-coding
mm_12457.1	chr2	71262872	71262926	+	1	NA	3' UTR (NM_001198877, exon 19 of 19)	3' UTR (NM_001198877, exon 19 of 19)	50953	NM_010064	13427	Mm.249479	NM_010064	ENSMUSG00000027012	Dync1i2	3110079H08Rik|AW554389|Dncic2	dynein cytoplasmic 1 intermediate chain 2	protein-coding
mm_69666.1	chr7	139982817	139982832	-	1	NA	exon (NM_001291066, exon 22 of 24)	exon (NM_001291066, exon 22 of 24)	4050	NR_106029	102465643		NR_106029	ENSMUSG00000099092	Mir7062	Gm27339|mmu-mir-7062	microRNA 7062	ncRNA
mm_137745.1	chr17	29376260	29376274	+	1	NA	intron (NM_001159538, intron 13 of 15)	intron (NM_001159538, intron 13 of 15)	15353	NM_001159538	26382	Mm.279187	NM_013710	ENSMUSG00000024013	Fgd2	Tcd-2|Tcd2|ZFYVE4|tcs-2|tcs2	FYVE, RhoGEF and PH domain containing 2	protein-coding
mm_6689.1	chr1	80709376	80709401	-	1	NA	intron (NM_175291, intron 1 of 55)	intron (NM_175291, intron 1 of 55)	-44036	NM_001285927	210293	Mm.133473	NM_175291	ENSMUSG00000038608	Dock10	9330153B10Rik|A630054M16Rik|Jr4|Jr5|R75174|ZIZ3|Zizimin3|mKIAA0694	dedicator of cytokinesis 10	protein-coding
mm_31086.1	chr4	41631661	41631672	+	1	NA	intron (NM_175138, intron 16 of 19)	intron (NM_175138, intron 16 of 19)	8636	NM_027147	69638	Mm.372459	NM_027147	ENSMUSG00000028445	Enho	1110065P19Rik|2310040A07Rik	energy homeostasis associated	protein-coding
mm_157830.1	chrX	74245738	74245769	-	1	NA	intron (NM_010227, intron 1 of 45)	intron (NM_010227, intron 1 of 45)	781	NM_010227	192176	Mm.295533	NM_010227	ENSMUSG00000031328	Flna	ABP-280|Dilp2|F730004A14Rik|Fln1|GENA 379|filamin-1	filamin, alpha	protein-coding
mm_129173.1	chr15	76249902	76249914	-	1	NA	TTS (NM_023168)	TTS (NM_023168)	1717	NR_105918	102465575		NR_105918	ENSMUSG00000098625	Mir6953	Gm27738|mmu-mir-6953	microRNA 6953	ncRNA
mm_131432.1	chr16	15887279	15887292	+	1	NA	promoter-TSS (NM_007679)	promoter-TSS (NM_007679)	-1	NM_007679	12609	Mm.347407	NM_007679	ENSMUSG00000071637	Cebpd	c/EBPdelta	CCAAT/enhancer binding protein (C/EBP), delta	protein-coding
mm_11930.1	chr2	52313824	52313850	+	1	NA	exon (NM_010889, exon 11 of 157)	exon (NM_010889, exon 11 of 157)	22835	NR_040620	78049	Mm.243883	NR_040620		4930573O16Rik	-	RIKEN cDNA 4930573O16 gene	ncRNA
mm_108587.1	chr12	85288671	85288712	+	1	NA	promoter-TSS (NM_172414)	promoter-TSS (NM_172414)	100	NM_172414	72350	Mm.158810	NM_172414	ENSMUSG00000045064	Zc2hc1c	2810002I04Rik|AV046379|Fam164c	zinc finger, C2HC-type containing 1C	protein-coding
mm_47827.1	chr5	134266585	134266618	-	1	NA	exon (NM_010365, exon 12 of 34)	exon (NM_010365, exon 12 of 34)	-36976	NR_104383	17969	Mm.425296	NM_010876	ENSMUSG00000015950	Ncf1	NCF-47K|NOXO2|Ncf-1|p47-phox|p47<phox>|p47phox	neutrophil cytosolic factor 1	protein-coding
mm_28271.1	chr3	88762245	88762255	-	1	NA	exon (NM_018804, exon 2 of 4)	exon (NM_018804, exon 2 of 4)	10349	NM_018804	229521	Mm.379376	NM_018804	ENSMUSG00000068923	Syt11	1500004A13Rik|3632445O20Rik|5430404N14Rik|6530420C11Rik|AI851970	synaptotagmin XI	protein-coding
mm_13359.1	chr2	103424121	103424135	+	1	NA	promoter-TSS (NM_010125)	promoter-TSS (NM_010125)	60	NM_010125	13711	Mm.20888	NM_010125	ENSMUSG00000027186	Elf5	ESE-2|ESE-5|ESE-5.	E74-like factor 5	protein-coding
mm_141621.1	chr17	32891550	32891565	-	1	NA	promoter-TSS (NM_207245)	promoter-TSS (NM_207245)	46	NM_207245	240066	Mm.26636	NM_207245	ENSMUSG00000095325	Zfp870	AI173952	zinc finger protein 870	protein-coding
mm_61633.1	chr7	80246530	80246579	+	1	NA	5' UTR (NM_177765, exon 1 of 15)	5' UTR (NM_177765, exon 1 of 15)	178	NM_177765	269954	Mm.276780	NM_177765	ENSMUSG00000045467	Ttll13	1700111A04Rik|4921538O11|BC024578	tubulin tyrosine ligase-like family, member 13	protein-coding
mm_53115.1	chr6	125096745	125096773	+	1	NA	promoter-TSS (NR_106012)	promoter-TSS (NR_106012)	-265	NR_106012	102466272		NR_106012	ENSMUSG00000098762	Mir7045	Gm27758|mmu-mir-7045	microRNA 7045	ncRNA
mm_59146.1	chr7	24349211	24349227	+	1	NA	promoter-TSS (NM_029806)	promoter-TSS (NM_029806)	-5	NM_029806	76942	Mm.261468	NM_029806	ENSMUSG00000030484	Lypd5	2210003I03Rik	Ly6/Plaur domain containing 5	protein-coding
mm_41438.1	chr5	90904350	90904360	+	1	NA	intron (NM_009140, intron 2 of 3)	intron (NM_009140, intron 2 of 3)	456	NM_009140	20310	Mm.4979	NM_009140	ENSMUSG00000058427	Cxcl2	CINC-2a|GROb|Gro2|MIP-2|MIP-2a|Mgsa-b|Mip2|Scyb|Scyb2	chemokine (C-X-C motif) ligand 2	protein-coding
mm_30583.1	chr4	5632332	5632340	+	1	NA	promoter-TSS (NR_038183)	promoter-TSS (NR_038183)	8	NR_038183	73872	Mm.427301	NR_038183	ENSMUSG00000086066	4930423M02Rik	-	RIKEN cDNA 4930423M02 gene	ncRNA
mm_172735.1	chr8	78147038	78147040	-	1	NA	Intergenic	ERVB7_1-LTR_MM|LTR|ERVK	-66303	NM_183096	73301	Mm.61243	NM_183096	ENSMUSG00000037101	Ttc29	1700031F13Rik	tetratricopeptide repeat domain 29	protein-coding
mm_146034.1	chr18	69521830	69521860	+	1	NA	intron (NM_013685, intron 6 of 19)	intron (NM_013685, intron 6 of 19)	176124	NM_001083967	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding
mm_62981.1	chr7	120184509	120184519	+	1	NA	TTS (NM_028085)	TTS (NM_028085)	10656	NM_028085	72074	Mm.23165	NM_028085	ENSMUSG00000030909	Anks4b	2010013E14Rik|AI956809|Harp	ankyrin repeat and sterile alpha motif domain containing 4B	protein-coding
mm_21819.1	chr2	165286544	165286560	-	1	NA	intron (NM_144893, intron 1 of 9)	intron (NM_144893, intron 1 of 9)	1235	NM_001252574	228875	Mm.21184	NM_144893	ENSMUSG00000017664	Slc35c2	C85957|CGI-15|D2Wsu58e|Ovcov1	solute carrier family 35, member C2	protein-coding
mm_173181.1	chrX	56903077	56903084	+	1	NA	Intergenic	(T)n|Simple_repeat|Simple_repeat	-80755	NM_177293	320923	Mm.186745	NM_177293	ENSMUSG00000067878	Mtap7d3	4933424A10Rik|Map7d3	MAP7 domain containing 3	protein-coding
mm_95086.1	chr11	33513063	33513083	+	1	NA	intron (NM_023146, intron 1 of 27)	CpG	673	NR_110973	66011	Mm.383775	NM_023146	ENSMUSG00000040594	Ranbp17	-	RAN binding protein 17	protein-coding
mm_35866.1	chr4	49506491	49506513	-	1	NA	promoter-TSS (NM_007519)	promoter-TSS (NM_007519)	56	NM_007519	12012	Mm.2859	NM_007519	ENSMUSG00000039653	Baat	AI118337|AI158864|BAT	bile acid-Coenzyme A: amino acid N-acyltransferase	protein-coding
mm_4977.1	chr1	191332096	191332120	+	1	NA	intron (NM_025864, intron 2 of 7)	L1M2|LINE|L1	6143	NM_025864	66950	Mm.236300	NM_025864	ENSMUSG00000026627	Tmem206	2310028N02Rik|AI118576	transmembrane protein 206	protein-coding
mm_36149.1	chr4	59476276	59476289	-	1	NA	3' UTR (NM_144904, exon 15 of 15)	3' UTR (NM_144904, exon 15 of 15)	-37649	NM_001163288	634731	Mm.483589	NM_001163288	ENSMUSG00000038578	Susd1	A530080P10|Gm12528|OTTMUSG00000007332	sushi domain containing 1	protein-coding
mm_10044.1	chr1	193130202	193130257	-	1	NA	promoter-TSS (NM_145415)	promoter-TSS (NM_145415)	22	NM_145415	215193	Mm.173758	NM_145415	ENSMUSG00000016181	Diexf	AA408296|AW045375|Def	digestive organ expansion factor homolog (zebrafish)	protein-coding
mm_123277.1	chr14	61370896	61370925	-	1	NA	exon (NM_008466, exon 13 of 17)	exon (NM_008466, exon 13 of 17)	-10465	NM_026598	68177	Mm.22758	NM_026598	ENSMUSG00000021928	Ebpl	5730442K12Rik|EBRP	emopamil binding protein-like	protein-coding
mm_123737.1	chr14	70177730	70177747	-	1	NA	promoter-TSS (NM_001253736)	promoter-TSS (NM_001253736)	-66	NM_145978	213019	Mm.283968	NM_145978	ENSMUSG00000022090	Pdlim2	4732462F18Rik|Slim	PDZ and LIM domain 2	protein-coding
mm_124619.1	chr15	3279975	3279977	+	1	NA	TTS (NM_001166063)	TTS (NM_001166063)	8999	NM_009155	20363	Mm.392203	NM_009155	ENSMUSG00000064373	Selenop	AU018766|D15Ucla1|Se-P|Sepp1|selp	selenoprotein P	protein-coding
mm_130511.1	chr15	98846175	98846199	-	1	NA	exon (NM_001033276, exon 40 of 55)	exon (NM_001033276, exon 40 of 55)	-14679	NM_016781	19082	Mm.6670	NM_016781	ENSMUSG00000067713	Prkag1	AA571379|BB036179|Prkaac	protein kinase, AMP-activated, gamma 1 non-catalytic subunit	protein-coding
mm_146017.1	chr18	69438034	69438037	+	1	NA	intron (NM_013685, intron 3 of 19)	intron (NM_013685, intron 3 of 19)	92314	NM_001083967	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding
mm_71898.1	chr8	70001424	70001458	+	1	NA	Intergenic	Intergenic	-5057	NM_145596	234366	Mm.270044	NM_145596	ENSMUSG00000036180	Gatad2a	1110066C11Rik|BC031407|C80248	GATA zinc finger domain containing 2A	protein-coding
mm_55690.1	chr6	72789041	72789061	-	1	NA	promoter-TSS (NM_009332)	promoter-TSS (NM_009332)	-6	NM_009332	21415	Mm.440067	NM_009332	ENSMUSG00000055799	Tcf7l1	Tcf-3|Tcf3|bHLHb21	transcription factor 7 like 1 (T cell specific, HMG box)	protein-coding
mm_95503.1	chr11	51915662	51915664	+	1	NA	Intergenic	Intergenic	-51968	NM_029976	52626	Mm.289456	NM_029976	ENSMUSG00000020392	Cdkn2aipnl	A430101B06Rik|AA409260|D11Ertd497e|MNCb-1520	CDKN2A interacting protein N-terminal like	protein-coding
mm_171984.1	chr5	93019751	93019757	-	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	25268	NM_175270	78088	Mm.245085	NM_175270	ENSMUSG00000045314	Sowahb	5730467H21Rik|Ankrd56	sosondowah ankyrin repeat domain family member B	protein-coding
mm_127062.1	chr15	97361181	97361225	+	1	NA	5' UTR (NM_172293, exon 4 of 6)	5' UTR (NM_172293, exon 4 of 6)	-113916	NM_001164602	105827	Mm.24005	NM_178114	ENSMUSG00000048218	Amigo2	AI415330|AMIGO-2|AW208913|Ali1	adhesion molecule with Ig like domain 2	protein-coding
mm_35931.1	chr4	53032402	53032426	-	1	NA	3' UTR (NM_013454, exon 50 of 50)	3' UTR (NM_013454, exon 50 of 50)	20534	NM_025623	66536	Mm.38244	NM_025623	ENSMUSG00000015247	Nipsnap3b	2700063N13Rik|Nipsnap3a	nipsnap homolog 3B (C. elegans)	protein-coding
mm_35624.1	chr4	43454601	43454635	-	1	NA	promoter-TSS (NM_001110320)	promoter-TSS (NM_001110320)	8	NM_001110320	12517	Mm.188157	NM_007654	ENSMUSG00000028459	Cd72	CD72c|Ly-19|Ly-32|Ly-m19|Lyb-2	CD72 antigen	protein-coding
mm_37780.1	chr4	130175114	130175138	-	1	NA	promoter-TSS (NM_001168333)	promoter-TSS (NM_001168333)	-4	NM_023476	94242	Mm.15801	NM_023476	ENSMUSG00000028776	Tinagl1	1110021J17Rik|AZ-1|AZ1|Arg1|Lcn7|TARP|Tinagl	tubulointerstitial nephritis antigen-like 1	protein-coding
mm_35162.1	chr4	14516368	14516378	-	1	NA	intron (NM_145947, intron 14 of 18)	intron (NM_145947, intron 14 of 18)	105405	NM_145947	208890	Mm.483839	NM_145947	ENSMUSG00000040569	Slc26a7	-	solute carrier family 26, member 7	protein-coding
mm_150903.1	chr19	45575141	45575162	+	1	NA	intron (NM_172639, intron 4 of 5)	intron (NM_172639, intron 4 of 5)	14536	NM_172639	226162	Mm.21978	NM_172639	ENSMUSG00000041035	Dpcd	5330431N19Rik|Ndac	deleted in primary ciliary dyskinesia	protein-coding
mm_72902.1	chr8	90876638	90876669	+	1	NA	intron (NM_177224, intron 2 of 39)	intron (NM_177224, intron 2 of 39)	47818	NM_177224	109151	Mm.100615	NM_177224	ENSMUSG00000056608	Chd9	1810014J18Rik|9030205D12Rik|A330063D19Rik|AD013|PRIC320|mKIAA0308	chromodomain helicase DNA binding protein 9	protein-coding
mm_55943.1	chr6	85126042	85126054	-	1	NA	promoter-TSS (NM_001034902)	promoter-TSS (NM_001034902)	46	NM_001034902	545861	Mm.321419	NM_001034902	ENSMUSG00000072952	Gm5878	EG545861	predicted gene 5878	protein-coding
mm_46833.1	chr5	113280548	113280569	-	1	NA	promoter-TSS (NM_001309528)	promoter-TSS (NM_001309528)	43	NM_001309528	52850	Mm.200203	NM_172718	ENSMUSG00000042216	Sgsm1	2410098H20Rik|AA408781|D5Bwg1524e|E130107M15|NuIP|Rutbc2	small G protein signaling modulator 1	protein-coding
mm_20222.1	chr2	125780564	125780586	-	1	NA	intron (NM_177608, intron 1 of 17)	B4A|SINE|B4	2295	NM_177608	70354	Mm.138091	NM_133725	ENSMUSG00000035093	Secisbp2l	3110001I20Rik|AI504340|C630011I23	SECIS binding protein 2-like	protein-coding
mm_41465.1	chr5	91074298	91074308	+	1	NA	promoter-TSS (NM_007950)	promoter-TSS (NM_007950)	-314	NM_007950	13874	Mm.4791	NM_007950	ENSMUSG00000029377	Ereg	EPR	epiregulin	protein-coding
mm_126201.1	chr15	78877250	78877264	+	1	NA	promoter-TSS (NM_145929)	promoter-TSS (NM_145929)	67	NM_145929	106039	Mm.251331	NM_145929	ENSMUSG00000033128	Gga1	4930406E12Rik|AU016030|AW209092	golgi associated, gamma adaptin ear containing, ARF binding protein 1	protein-coding
mm_171375.1	chr4	119282807	119282807	-	1	NA	exon (NM_011732, exon 4 of 8)	exon (NM_011732, exon 4 of 8)	11706	NM_011732	22608	Mm.258204	NM_011732	ENSMUSG00000028639	Ybx1	1700102N10Rik|C79409|EF1A|MSY1|Nsep1|YB-1|dbpB|mYB-1a	Y box protein 1	protein-coding
mm_83724.1	chr9	50775134	50775157	-	1	NA	promoter-TSS (NM_133981)	promoter-TSS (NM_133981)	-80	NM_133981	102580	Mm.160035	NM_133981	ENSMUSG00000032059	Alg9	8230402H15Rik|AI747665|B430313H07Rik|Dibd1	asparagine-linked glycosylation 9 (alpha 1,2 mannosyltransferase)	protein-coding
mm_16061.1	chr2	167932024	167932064	+	1	NA	promoter-TSS (NM_011201)	promoter-TSS (NM_011201)	-283	NM_011201	19246	Mm.277916	NM_011201	ENSMUSG00000027540	Ptpn1	PTP-1B|PTP-HA2|PTP1B	protein tyrosine phosphatase, non-receptor type 1	protein-coding
mm_94228.1	chr11	3289681	3289741	+	1	NA	promoter-TSS (NM_001253691)	promoter-TSS (NM_001253691)	580	NR_045109	56218	Mm.275563	NM_019574	ENSMUSG00000020453	Patz1	8430401L15Rik|AI447519|Mazr|Patz|Zfp278	POZ (BTB) and AT hook containing zinc finger 1	protein-coding
mm_49828.1	chr6	37806463	37806498	+	1	NA	Intergenic	Intergenic	-64331	NM_001272064	21848	Mm.41063	NM_145076	ENSMUSG00000029833	Trim24	A130082H20Rik|AI447469|D430004I05Rik|TIF1|TIF1-alpha|TIF1alpha|Tif1a	tripartite motif-containing 24	protein-coding
mm_97053.1	chr11	72458156	72458171	+	1	NA	intron (NM_153060, intron 5 of 12)	intron (NM_153060, intron 5 of 12)	16785	NM_016776	18432	Mm.147946	NM_016776	ENSMUSG00000040463	Mybbp1a	AL024407|AU019902|P160|p160MBP|p67MBP	MYB binding protein (P160) 1a	protein-coding
mm_91461.1	chr10	34096481	34096497	-	1	NA	promoter-TSS (NM_178908)	promoter-TSS (NM_178908)	30	NM_178908	103511	Mm.66334	NM_178908	ENSMUSG00000049872	Fam26e	BB146404	family with sequence similarity 26, member E	protein-coding
mm_101895.1	chr11	49096966	49096977	-	1	NA	TTS (NM_001271677)	TTS (NM_001271677)	9954	NM_008330	15953	Mm.24769	NM_008330	ENSMUSG00000078920	Ifi47	47kDa|IRG-47|Ifggc1|Igrd|Iigp4|Iipg4|Irgd	interferon gamma inducible protein 47	protein-coding
mm_80190.1	chr9	72394137	72394148	+	1	NA	Intergenic	Intergenic	-44387	NM_008613	17427	Mm.387671	NM_008613	ENSMUSG00000032221	Mns1	AW546487	meiosis-specific nuclear structural protein 1	protein-coding
mm_122650.1	chr14	51908653	51908661	-	1	NA	intron (NM_013864, intron 7 of 15)	intron (NM_013864, intron 7 of 15)	4831	NM_001145959	29811	Mm.26722	NM_013864	ENSMUSG00000004558	Ndrg2	AI182517|AU040374|Ndr2|SYLD	N-myc downstream regulated gene 2	protein-coding
mm_120039.1	chr14	56402657	56402700	+	1	NA	promoter-TSS (NM_001033043)	promoter-TSS (NM_001033043)	-19	NM_001033043	30054	Mm.287783	NM_001033043	ENSMUSG00000000365	Rnf17	MMIP-2|Mmip2|TDRD4	ring finger protein 17	protein-coding
mm_51533.1	chr6	83189062	83189080	+	1	NA	intron (NM_001347310, intron 2 of 26)	intron (NM_001347310, intron 2 of 26)	3125	NM_001347310	13191	Mm.6919	NM_007835	ENSMUSG00000031865	Dctn1	AL022633|DAP-150|DP-150|Glued|p150|p150-glued|p150<glued>	dynactin 1	protein-coding
mm_24328.1	chr3	89459187	89459214	+	1	NA	promoter-TSS (NM_026784)	promoter-TSS (NM_026784)	82	NM_026784	68603	Mm.34242	NM_026784	ENSMUSG00000027952	Pmvk	1110011E12Rik|2900002L22Rik|AV001327|PMK|PMKA|PMKASE	phosphomevalonate kinase	protein-coding
mm_158920.1	chr1	58447622	58447622	+	1	NA	intron (NM_022988, intron 1 of 6)	intron (NM_022988, intron 1 of 6)	-2136	NM_001285827	70225	Mm.340195	NM_027351	ENSMUSG00000026035	Ppil3	2310076N22Rik|2510026K04Rik|Cyp10l	peptidylprolyl isomerase (cyclophilin)-like 3	protein-coding
mm_119982.1	chr14	55575806	55575852	+	1	NA	exon (NM_026808, exon 1 of 2)	exon (NM_026808, exon 1 of 2)	155	NM_026808	68680	Mm.36758	NM_026808	ENSMUSG00000022215	Fitm1	1110028A07Rik|AV010547|Cg10671|Fit1	fat storage-inducing transmembrane protein 1	protein-coding
mm_141005.1	chr17	24943235	24943247	-	1	NA	3' UTR (NM_198937, exon 5 of 5)	3' UTR (NM_198937, exon 5 of 5)	-6264	NM_013931	30957	Mm.43081	NM_013931	ENSMUSG00000024163	Mapk8ip3	BB120594|D17Wsu15e|JIP-3|JSAP1|JSAP1a|JSAP1b|JSAP1c|JSAP1d|Jip3|Syd2|mKIAA1066	mitogen-activated protein kinase 8 interacting protein 3	protein-coding
mm_1343.1	chr1	66175273	66175283	+	1	NA	promoter-TSS (NM_008632)	promoter-TSS (NM_008632)	-51	NM_008632	17756	Mm.256966	NM_008632	ENSMUSG00000015222	Map2	G1-397-34|MAP-2|Mtap-2|Mtap2|repro4	microtubule-associated protein 2	protein-coding
mm_24276.1	chr3	89213927	89213944	+	1	NA	exon (NM_013604, exon 1 of 8)	exon (NM_013604, exon 1 of 8)	400	NM_001161824	17827	Mm.280943	NM_013604	ENSMUSG00000064068	Mtx1	Gcap6|Mtx	metaxin 1	protein-coding
mm_72053.1	chr8	71367554	71367632	+	1	NA	intron (NM_001145780, intron 2 of 8)	intron (NM_001145780, intron 2 of 8)	376	NM_025917	67023	Mm.41890	NM_025917	ENSMUSG00000002395	Use1	2010315L10Rik|5730403H22Rik|AV002165|D12|Ed2|Q-snare|p31	unconventional SNARE in the ER 1 homolog (S. cerevisiae)	protein-coding
mm_24400.1	chr3	90357989	90358011	+	1	NA	exon (NM_139304, exon 10 of 10)	exon (NM_139304, exon 10 of 10)	16346	NM_139304	229542	Mm.270999	NM_139304	ENSMUSG00000042390	Gatad2b	AL118180|C430014D17Rik|P66beta|mKIAA1150	GATA zinc finger domain containing 2B	protein-coding
mm_78483.1	chr9	32696987	32697011	+	1	NA	intron (NM_011808, intron 1 of 7)	intron (NM_011808, intron 1 of 7)	957	NM_001038642	23871	Mm.292415	NM_011808	ENSMUSG00000032035	Ets1	AI196000|AI448617|D230050P06|Ets-1|Tpl1|vs	E26 avian leukemia oncogene 1, 5' domain	protein-coding
mm_65459.1	chr7	25466358	25466383	-	1	NA	exon (NM_001039186, exon 6 of 8)	exon (NM_001039186, exon 6 of 8)	11255	NM_001039185	26365	Mm.322502	NM_011926	ENSMUSG00000074272	Ceacam1	Bgp|Bgp1|C-CAM|CD66a|Cc1|Cea-1|Cea-7|Cea1|Cea7|Hv-2|Hv2|MHVR|MHVR1|Mhv-1|bb-1|mCEA1|mmCGM1|mmCGM1a|mmCGM2	carcinoembryonic antigen-related cell adhesion molecule 1	protein-coding
mm_26473.1	chr3	144570410	144570490	+	1	NA	promoter-TSS (NM_053102)	promoter-TSS (NM_053102)	23	NM_053102	93684	Mm.29812	NM_053102	ENSMUSG00000037072	Selenof	9430015P09Rik|Sep15	selenoprotein F	protein-coding
mm_10199.1	chr2	4930737	4930766	+	1	NA	exon (NM_010726, exon 6 of 9)	exon (NM_010726, exon 6 of 9)	11755	NM_010726	16922	Mm.391704	NM_010726	ENSMUSG00000026664	Phyh	AI256161|AI265699|Lnap1|PAHX	phytanoyl-CoA hydroxylase	protein-coding
mm_80678.1	chr9	90315910	90315925	+	1	NA	Intergenic	Intergenic	-45148	NM_194334	67016	Mm.335347	NM_194334	ENSMUSG00000037410	Tbc1d2b	1810061M12Rik|AI480956|AV021536|AV023399|AW491493|mKIAA1055	TBC1 domain family, member 2B	protein-coding
mm_60278.1	chr7	43953927	43953972	+	1	NA	exon (NM_008457, exon 3 of 5)	exon (NM_008457, exon 3 of 5)	3283	NM_008457	16624	Mm.435488	NM_008457	ENSMUSG00000063089	Klk1b8	Klk8|Nrpn|TADG14|kallikrein|mGK-8	kallikrein 1-related peptidase b8	protein-coding
mm_49164.1	chr6	13871518	13871562	+	1	NA	promoter-TSS (NR_024619)	promoter-TSS (NR_024619)	-29	NR_045995	76311	Mm.367129	NR_045995	ENSMUSG00000097616	1110019D14Rik	-	RIKEN cDNA 1110019D14 gene	ncRNA
mm_161283.1	chr14	24014700	24014700	-	1	NA	Intergenic	Intergenic	9709	NR_131107	78019	Mm.243845	NR_131107		4930519K11Rik	-	RIKEN cDNA 4930519K11 gene	ncRNA
mm_27219.1	chr3	36000618	36000647	-	1	NA	promoter-TSS (NM_023644)	promoter-TSS (NM_023644)	46	NM_023644	72039	Mm.249016	NM_023644	ENSMUSG00000027709	Mccc1	1810045E08Rik|2310058B18Rik|MCCalpha|Mcca|R75106	methylcrotonoyl-Coenzyme A carboxylase 1 (alpha)	protein-coding
mm_65601.1	chr7	27360113	27360136	-	1	NA	intron (NM_001199235, intron 15 of 17)	intron (NM_001199235, intron 15 of 17)	-4116	NM_138676	192192	Mm.21297	NM_138676	ENSMUSG00000089832	Shkbp1	B930062H15Rik|Sb1	Sh3kbp1 binding protein 1	protein-coding
mm_155727.1	chrX	96160084	96160137	+	1	NA	exon (NM_010833, exon 8 of 13)	exon (NM_010833, exon 8 of 13)	64065	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_159849.1	chr5	137287587	137287587	+	1	NA	promoter-TSS (NM_009599)	promoter-TSS (NM_009599)	-667	NM_009599	11423	Mm.255464	NM_009599	ENSMUSG00000023328	Ache	-	acetylcholinesterase	protein-coding
mm_100801.1	chr11	4986736	4986747	-	1	NA	promoter-TSS (NM_001243044)	promoter-TSS (NM_001243044)	-83	NM_001243044	11764	Mm.274816	NM_007454	ENSMUSG00000009090	Ap1b1	Adtb1|b2b1660Clo	adaptor protein complex AP-1, beta 1 subunit	protein-coding
mm_72997.1	chr8	93810466	93810486	+	1	NA	promoter-TSS (NM_010308)	promoter-TSS (NM_010308)	-362	NM_010308	14681	Mm.251445	NM_010308	ENSMUSG00000031748	Gnao1	AW050213|Galphao|Gnao|alphaO	guanine nucleotide binding protein, alpha O	protein-coding
mm_75581.1	chr8	61516077	61516102	-	1	NA	intron (NM_001081390, intron 17 of 19)	intron (NM_001081390, intron 17 of 19)	28355	NM_145595	234309	Mm.29059	NM_145595	ENSMUSG00000031641	Cbr4	A730083J17Rik|BC009118	carbonyl reductase 4	protein-coding
mm_5757.1	chr1	46888086	46888100	-	1	NA	Intergenic	Intergenic	-34584	NM_172653	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|mKIAA1265	solute carrier family 39 (zinc transporter), member 10	protein-coding
mm_48203.1	chr5	137533298	137533311	-	1	NA	promoter-TSS (NM_010312)	promoter-TSS (NM_010312)	-75	NM_010312	14693	Mm.30141	NM_010312	ENSMUSG00000029713	Gnb2	Gnb-2	guanine nucleotide binding protein (G protein), beta 2	protein-coding
mm_24772.1	chr3	95526879	95526889	+	1	NA	promoter-TSS (NM_021281)	promoter-TSS (NM_021281)	98	NM_001267695	13040	Mm.3619	NM_021281	ENSMUSG00000038642	Ctss	Cats	cathepsin S	protein-coding
mm_84756.1	chr9	75567489	75567502	-	1	NA	3' UTR (NM_001038710, exon 10 of 10)	3' UTR (NM_001038710, exon 10 of 10)	-7838	NM_016963	50875	Mm.38445	NM_016963	ENSMUSG00000058587	Tmod3	U-Tmod|UTMOD	tropomodulin 3	protein-coding
mm_34274.1	chr4	141424301	141424310	+	1	NA	3' UTR (NM_013868, exon 3 of 3)	3' UTR (NM_013868, exon 3 of 3)	3526	NM_013868	29818	Mm.46181	NM_013868	ENSMUSG00000006221	Hspb7	27kDa|Hsp25-2|cvHsp	heat shock protein family, member 7 (cardiovascular)	protein-coding
mm_24301.1	chr3	89367617	89367622	+	1	NA	Intergenic	Intergenic	-2366	NM_029974	77772	Mm.164013	NM_029974	ENSMUSG00000042672	Dcst1	A330106H01Rik	DC-STAMP domain containing 1	protein-coding
mm_55400.1	chr6	60828084	60828096	-	1	NA	intron (NM_009221, intron 1 of 5)	intron (NM_009221, intron 1 of 5)	914	NM_001042451	20617	Mm.17484	NM_009221	ENSMUSG00000025889	Snca	NACP|alphaSYN	synuclein, alpha	protein-coding
mm_81425.1	chr9	109056939	109056953	+	1	NA	TTS (NM_011637)	TTS (NM_011637)	2080	NM_026381	66940	Mm.196533	NM_025858	ENSMUSG00000025647	Shisa5	2310008D10Rik|6430628I05Rik|Scotin|mShisa5	shisa family member 5	protein-coding
mm_25693.1	chr3	122261496	122261505	+	1	NA	intron (NM_008129, intron 3 of 6)	B2_Mm2|SINE|B2	-12914	NM_153806	99480	Mm.398647	NM_153806	ENSMUSG00000039756	Dnttip2	4930588M11Rik|AA408582|AU014960|HSU15552	deoxynucleotidyltransferase, terminal, interacting protein 2	protein-coding
mm_40269.1	chr5	38561896	38561925	+	1	NA	promoter-TSS (NM_011715)	promoter-TSS (NM_011715)	-315	NM_011715	22388	Mm.2654	NM_011715	ENSMUSG00000005103	Wdr1	Aip1|D5Wsu185e|rede	WD repeat domain 1	protein-coding
mm_18909.1	chr2	76730456	76730464	-	1	NA	exon (NM_011652, exon 284 of 313)	exon (NM_011652, exon 284 of 313)	55145	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_63856.1	chr7	135668258	135668268	+	1	NA	intron (NM_001316681, intron 8 of 17)	intron (NM_001316681, intron 8 of 17)	-15949	NR_015548	67765	Mm.445272	NR_015548	ENSMUSG00000097471	5830432E09Rik	-	RIKEN cDNA 5830432E09 gene	ncRNA
mm_143007.1	chr17	56436101	56436127	-	1	NA	exon (NM_001252453, exon 8 of 29)	exon (NM_001252453, exon 8 of 29)	-17205	NR_105943	102465590		NR_105943	ENSMUSG00000098339	Mir6977	Gm27922|mmu-mir-6977	microRNA 6977	ncRNA
mm_121304.1	chr14	105897391	105897449	+	1	NA	promoter-TSS (NM_011897)	promoter-TSS (NM_011897)	-601	NM_011897	24064	Mm.89982	NM_011897	ENSMUSG00000022114	Spry2	sprouty2	sprouty homolog 2 (Drosophila)	protein-coding
mm_117102.1	chr13	60174988	60174997	-	1	NA	3' UTR (NM_008086, exon 1 of 1)	3' UTR (NM_008086, exon 1 of 1)	2543	NM_008086	14451	Mm.22701	NM_008086	ENSMUSG00000052957	Gas1	AW554192|Gas-1	growth arrest specific 1	protein-coding
mm_112034.1	chr12	111537918	111537956	-	1	NA	promoter-TSS (NM_178041)	promoter-TSS (NM_178041)	-164	NM_178041	217869	Mm.271222	NM_173363	ENSMUSG00000021282	Eif5	2810011H21Rik|D12Ertd549e	eukaryotic translation initiation factor 5	protein-coding
mm_77703.1	chr8	126590990	126591001	-	1	NA	3' UTR (NM_001164598, exon 2 of 2)	3' UTR (NM_001164598, exon 2 of 2)	2441	NM_001164598	270110	Mm.334918	NM_001164598	ENSMUSG00000051495	Irf2bp2	E130305N23Rik|IRF-2BP2	interferon regulatory factor 2 binding protein 2	protein-coding
mm_44038.1	chr5	147506171	147506173	+	1	NA	intron (NM_028291, intron 5 of 18)	intron (NM_028291, intron 5 of 18)	75592	NM_028291	72587	Mm.320469	NM_028291	ENSMUSG00000029647	Pan3	2700050F09Rik|A430027N15Rik|AU014670	PAN3 poly(A) specific ribonuclease subunit	protein-coding
mm_28777.1	chr3	95977118	95977167	-	1	NA	Intergenic	Intergenic	-8368	NR_045872	668224	Mm.357766	NR_045872		Gm9054	EG668224	predicted gene 9054	ncRNA
mm_131652.1	chr16	20537594	20537618	+	1	NA	intron (NM_001302970, intron 1 of 10)	intron (NM_001302970, intron 1 of 10)	2126	NM_009679	11773	Mm.18946	NM_009679	ENSMUSG00000022841	Ap2m1	-	adaptor-related protein complex 2, mu 1 subunit	protein-coding
mm_78537.1	chr9	35211290	35211301	+	1	NA	promoter-TSS (NM_172291)	promoter-TSS (NM_172291)	92	NM_026130	67398	Mm.284688	NM_026130	ENSMUSG00000032042	Srpr	1300011P19Rik|D11Mgi27|Srpra	signal recognition particle receptor ('docking protein')	protein-coding
mm_38670.1	chr4	144721454	144721467	-	1	NA	promoter-TSS (NM_001085536)	promoter-TSS (NM_001085536)	-56	NM_001085536	546849	Mm.457885	NM_001085536	ENSMUSG00000041735	Gm13178	Gm437|OTTMUSG00000010750	predicted gene 13178	protein-coding
mm_15477.1	chr2	157560766	157560789	+	1	NA	intron (NM_001291128, intron 2 of 2)	intron (NM_001291128, intron 2 of 2)	699	NM_180960	18111	Mm.34330	NM_010923	ENSMUSG00000067786	Nnat	5730414I02Rik|AW107673|Peg5	neuronatin	protein-coding
mm_73305.1	chr8	105170669	105170686	+	1	NA	promoter-TSS (NM_001161458)	promoter-TSS (NM_001161458)	3	NM_001161458	12400	Mm.2018	NM_022309	ENSMUSG00000031885	Cbfb	AI893578|PEA2|PEBP2b|Pebp2|Pebpb2	core binding factor beta	protein-coding
mm_155948.1	chrX	105079736	105079754	+	1	NA	promoter-TSS (NM_001281871)	promoter-TSS (NM_001281871)	-11	NM_001281871	67683	Mm.273405	NM_026312	ENSMUSG00000031226	Pbdc1	2610029G23Rik	polysaccharide biosynthesis domain containing 1	protein-coding
mm_37689.1	chr4	129231651	129231661	-	1	NA	intron (NM_001285867, intron 1 of 6)	intron (NM_001285867, intron 1 of 6)	-3745	NM_001285866	97130	Mm.331907	NM_001033189	ENSMUSG00000050390	C77080	Kiaa1522|mKIAA1522	expressed sequence C77080	protein-coding
mm_73083.1	chr8	94480682	94480692	+	1	NA	intron (NM_001033207, intron 6 of 48)	intron (NM_001033207, intron 6 of 48)	7924	NM_001033207	434341	Mm.334720	NM_001033207	ENSMUSG00000074151	Nlrc5	AI451557|AK220210|NOD27	NLR family, CARD domain containing 5	protein-coding
mm_134380.1	chr16	17166933	17166936	-	1	NA	intron (NM_009456, intron 2 of 3)	intron (NM_009456, intron 2 of 3)	-19705	NM_001306169	76872	Mm.101656	NM_029779	ENSMUSG00000022768	Ccdc116	4930432J16Rik	coiled-coil domain containing 116	protein-coding
mm_113060.1	chr13	23738805	23738809	+	1	NA	promoter-TSS (NM_015786)	promoter-TSS (NM_015786)	0	NM_015786	50708	Mm.193539	NM_015786	ENSMUSG00000036181	Hist1h1c	0610008C09Rik|H1.2|H1c|H1f2|H1var1|His1a	histone cluster 1, H1c	protein-coding
mm_169329.1	chr14	117546774	117546775	+	1	NA	intron (NM_001079844, intron 3 of 9)	L1Md_A|LINE|L1	407073	NR_105747	102465148		NR_105747	ENSMUSG00000098648	Mir6239	Gm28025|mmu-mir-6239	microRNA 6239	ncRNA
mm_106374.1	chr11	118415835	118415841	-	1	NA	promoter-TSS (NM_001267591)	promoter-TSS (NM_001267591)	-38	NM_001267591	76025	Mm.177551	NM_029502	ENSMUSG00000025575	Cant1	5830420C20Rik|Apy1h|D11Bwg0554e|Entpd8|SCAN-1|Shapy	calcium activated nucleotidase 1	protein-coding
mm_22444.1	chr2	181693900	181693987	-	1	NA	promoter-TSS (NM_026446)	promoter-TSS (NM_026446)	34	NM_001291207	56470	Mm.274366	NM_026446	ENSMUSG00000002458	Rgs19	2610042F04Rik|AI324841|AW547781|GAIP	regulator of G-protein signaling 19	protein-coding
mm_63138.1	chr7	123124143	123124171	+	1	NA	5' UTR (NM_144925, exon 1 of 24)	5' UTR (NM_144925, exon 1 of 24)	272	NM_144925	233833	Mm.102305	NM_144925	ENSMUSG00000052707	Tnrc6a	2010321I05Rik|3110054G10Rik|AW557223|CAGH26|D130023A07Rik|GW182|Tnrc6	trinucleotide repeat containing 6a	protein-coding
mm_129387.1	chr15	78200678	78200681	-	1	NA	intron (NM_013645, intron 4 of 4)	intron (NM_013645, intron 4 of 4)	3558	NM_001330686	19293	Mm.2766	NM_013645	ENSMUSG00000005716	Pvalb	PV|Parv|Pva	parvalbumin	protein-coding
mm_34934.1	chr4	155839828	155839840	+	1	NA	5' UTR (NM_024263, exon 1 of 10)	5' UTR (NM_024263, exon 1 of 10)	154	NM_024263	74761	Mm.159028	NM_024263	ENSMUSG00000029070	Mxra8	1200013A08Rik|1700095D18Rik|AI131686|Asp3|Dicam	matrix-remodelling associated 8	protein-coding
mm_96312.1	chr11	63158817	63158831	+	1	NA	3' UTR (NM_008885, exon 5 of 5)	3' UTR (NM_008885, exon 5 of 5)	26021	NM_001302260	18858	Mm.1237	NM_008885	ENSMUSG00000018217	Pmp22	22kDa|Gas-3|HNPP|Tr|trembler	peripheral myelin protein 22	protein-coding
mm_121965.1	chr14	25467753	25467766	-	1	NA	intron (NM_001310666, intron 1 of 23)	intron (NM_001310666, intron 1 of 23)	8574	NM_183208	328365	Mm.227484	NM_183208	ENSMUSG00000007817	Zmiz1	BC065120|E330020C23|ENSMUSG00000072684|Gm10397|I920194n01|Rai17|Zimp10	zinc finger, MIZ-type containing 1	protein-coding
mm_8201.1	chr1	138122872	138122923	-	1	NA	intron (NM_001111316, intron 2 of 31)	(CATATA)n|Simple_repeat|Simple_repeat	52229	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_8401.1	chr1	151500865	151500875	-	1	NA	promoter-TSS (NM_011277)	promoter-TSS (NM_011277)	-47	NM_011277	19821	Mm.474038	NM_011277	ENSMUSG00000026484	Rnf2	AI326319|AI450156|AU019207|Ring1B|dinG	ring finger protein 2	protein-coding
mm_43390.1	chr5	135733865	135733879	+	1	NA	exon (NM_008898, exon 12 of 16)	exon (NM_008898, exon 12 of 16)	2017	NR_106001	102466791		NR_106001	ENSMUSG00000099197	Mir7034	Gm27372|mmu-mir-7034	microRNA 7034	ncRNA
mm_17469.1	chr2	28559397	28559437	-	1	NA	exon (NM_009885, exon 7 of 11)	exon (NM_009885, exon 7 of 11)	3986	NM_009885	12613	Mm.236017	NM_009885	ENSMUSG00000026818	Cel	1810036E18Rik|BAL	carboxyl ester lipase	protein-coding
mm_148982.1	chr19	7612520	7612618	+	1	NA	promoter-TSS (NM_025731)	promoter-TSS (NM_025731)	0	NM_025731	66727	Mm.116803	NM_025731	ENSMUSG00000024973	Hrasls5	1700055A14Rik|1700086E08Rik|4921526K24Rik|HRSL5|iNAT	HRAS-like suppressor family, member 5	protein-coding
mm_169813.1	chr16	20177070	20177070	-	1	NA	promoter-TSS (NR_030454).5	promoter-TSS (NR_030454).5	-836	NR_030454	735274		NR_030454	ENSMUSG00000106252	Mir684-1	Mirn684-1	microRNA 684-1	ncRNA
mm_167050.1	chr7	83567898	83567901	+	1	NA	Intergenic	RLTR27|LTR|ERVK	-17032	NM_177695	233424	Mm.486619	NM_177695	ENSMUSG00000038540	Tmc3	9030203A06	transmembrane channel-like gene family 3	protein-coding
mm_46434.1	chr5	104460363	104460383	-	1	NA	intron (NM_008861, intron 1 of 14)	CpG	916	NM_008861	18764	Mm.6442	NM_008861	ENSMUSG00000034462	Pkd2	C030034P18Rik|PC2|TRPP2	polycystic kidney disease 2	protein-coding
mm_154793.1	chrX	13159832	13159860	+	1	NA	exon (NM_009481, exon 38 of 45)	exon (NM_009481, exon 38 of 45)	76437	NR_045430	72122	Mm.75434	NR_045429	ENSMUSG00000100714	2010308F09Rik	-	RIKEN cDNA 2010308F09 gene	ncRNA
mm_5010.1	chr1	192759418	192759432	+	1	NA	intron (NM_144881, intron 2 of 11)	(CAG)n|Simple_repeat|Simple_repeat	11794	NM_144881	226861	Mm.145857	NM_144881	ENSMUSG00000037375	Hhat	2810432O22Rik|AI462858|AP-2CRE|Skn|Tg(TFAP2A-cre)1Will	hedgehog acyltransferase	protein-coding
mm_159791.1	chr5	109330375	109330375	+	1	NA	promoter-TSS (NM_001104627)	promoter-TSS (NM_001104627)	-6	NM_001104627	384220	Mm.469880	NM_001104627	ENSMUSG00000092080	Vmn2r16	EG384220	vomeronasal 2, receptor 16	protein-coding
mm_8478.1	chr1	153487685	153487690	-	1	NA	promoter-TSS (NM_007842)	promoter-TSS (NM_007842)	-27	NM_007842	13211	Mm.20000	NM_007842	ENSMUSG00000042699	Dhx9	AI326842|Ddx9|HEL-5|NDHII|RHA|mHEL-5	DEAH (Asp-Glu-Ala-His) box polypeptide 9	protein-coding
mm_106053.1	chr11	116110186	116110206	-	1	NA	promoter-TSS (NM_001205081)	promoter-TSS (NM_001205081)	39	NM_001205081	217333	Mm.347770	NM_172570	ENSMUSG00000020773	Trim47	2210023F24Rik	tripartite motif-containing 47	protein-coding
mm_80845.1	chr9	98287471	98287484	+	1	NA	Intergenic	ERV3-16A3_LTR|LTR|ERVL	-9106	NM_144533	74080	Mm.294082	NM_144533	ENSMUSG00000032456	Nmnat3	4933408N02Rik|PNAT3	nicotinamide nucleotide adenylyltransferase 3	protein-coding
mm_75292.1	chr8	41053478	41053487	-	1	NA	intron (NM_001005863, intron 3 of 13)	intron (NM_001005863, intron 3 of 13)	1314	NM_001005864	102103	Mm.149438	NM_001005863	ENSMUSG00000045636	Mtus1	AI481402|ATBP135|Atip1|B430010I23Rik|B430305I03Rik|C85752|Cctsg1-440|MD44|MTSG1|mKIAA1288	mitochondrial tumor suppressor 1	protein-coding
mm_161534.1	chr15	102473269	102473269	+	1	NA	5' UTR (NM_011042, exon 2 of 14)	5' UTR (NM_011042, exon 2 of 14)	2637	NM_001174073	18521	Mm.236513	NM_011042	ENSMUSG00000056851	Pcbp2	AW412548|Hnrpx|alphaCP-2	poly(rC) binding protein 2	protein-coding
mm_136028.1	chr16	76373855	76373871	-	1	NA	promoter-TSS (NM_173440)	promoter-TSS (NM_173440)	-814	NM_173440	268903	Mm.74711	NM_173440	ENSMUSG00000048490	Nrip1	6030458L20Rik|8430438I05Rik|9630050P12|AA959574|AW456757|RIP140	nuclear receptor interacting protein 1	protein-coding
mm_22020.1	chr2	167997665	167997697	-	1	NA	intron (NM_001080708, intron 3 of 21)	intron (NM_001080708, intron 3 of 21)	12912	NM_001080708	69553	Mm.68454	NM_001080708	ENSMUSG00000074577	Fam65c	2310033K02Rik|Gm124	family with sequence similarity 65, member C	protein-coding
mm_98138.1	chr11	87578385	87578470	+	1	NA	promoter-TSS (NM_001284398)	promoter-TSS (NM_001284398)	38	NM_001284398	18952	Mm.2214	NM_011129	ENSMUSG00000020486	Sept4	ARTS|Bh5|OTTMUSG00000001265|Pnutl2	septin 4	protein-coding
mm_58539.1	chr7	4500922	4500929	+	1	NA	intron (NM_029834, intron 1 of 21)	intron (NM_029834, intron 1 of 21)	755	NM_029834	232807	Mm.360391	NM_029834	ENSMUSG00000019254	Ppp1r12c	2410197A17Rik|AI839747|B430101M08|Mbs85	protein phosphatase 1, regulatory (inhibitor) subunit 12C	protein-coding
mm_4063.1	chr1	166125555	166125571	+	1	NA	intron (NM_001033344, intron 2 of 5)	ORR1C1|LTR|ERVL-MaLR	2335	NM_001033344	240892	Mm.35315	NM_001033344	ENSMUSG00000026564	Dusp27	C130085G02Rik|Gm209	dual specificity phosphatase 27 (putative)	protein-coding
mm_128940.1	chr15	74728012	74728030	-	1	NA	promoter-TSS (NM_020519)	promoter-TSS (NM_020519)	5	NM_020519	57277	Mm.27630	NM_020519	ENSMUSG00000022596	Slurp1	1110021N19Rik|AI415082|ARS|ArsB|Slurp-1	secreted Ly6/Plaur domain containing 1	protein-coding
mm_31519.1	chr4	54945039	54945082	+	1	NA	Intergenic	CpG	-2885	NM_172867	242466	Mm.102904	NM_172867	ENSMUSG00000060206	Zfp462	6030417H05|9430078C22Rik|Gt4-2|Zfpip	zinc finger protein 462	protein-coding
mm_69808.1	chr7	141221707	141221728	-	1	NA	promoter-TSS (NR_029793)	promoter-TSS (NR_029793)	-224	NR_029793	387206		NR_029793	ENSMUSG00000065551	Mir210	Mirn210|mir-210|mmu-mir-210	microRNA 210	ncRNA
mm_5677.1	chr1	43159187	43159192	-	1	NA	intron (NM_001289533, intron 1 of 5)	intron (NM_001289533, intron 1 of 5)	4772	NM_010212	14200	Mm.6799	NM_010212	ENSMUSG00000008136	Fhl2	FHL-2|SLIM-3|SLIM3	four and a half LIM domains 2	protein-coding
mm_106302.1	chr11	118268045	118268050	-	1	NA	intron (NM_001033528, intron 14 of 20)	intron (NM_001033528, intron 14 of 20)	-19455	NM_011180	19157	Mm.86413	NM_011180	ENSMUSG00000017132	Cyth1	CLM1|CTH-1|CYTIP|Pscd1	cytohesin 1	protein-coding
mm_119143.1	chr14	31251455	31251530	+	1	NA	promoter-TSS (NM_027088)	promoter-TSS (NM_027088)	3	NM_027088	104416	Mm.3779	NM_027088	ENSMUSG00000021901	Bap1	2300006C11Rik|AA989761|AW553466|mKIAA0272|uch-x4	Brca1 associated protein 1	protein-coding
mm_162481.1	chr1	134405966	134405970	+	1	NA	promoter-TSS (NM_028057)	promoter-TSS (NM_028057)	-22	NM_028057	72017	Mm.280230	NM_028057	ENSMUSG00000026456	Cyb5r1	1500005G05Rik|B5R.1|C80155|Nqo3a2	cytochrome b5 reductase 1	protein-coding
mm_645.1	chr1	40422062	40422063	+	1	NA	Intergenic	B1_Mus2|SINE|Alu	-7508	NM_001294171	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_114416.1	chr13	64367027	64367073	+	1	NA	exon (NM_009984, exon 5 of 8)	exon (NM_009984, exon 5 of 8)	3470	NM_009984	13039	Mm.930	NM_009984	ENSMUSG00000021477	Ctsl	1190035F06Rik|CatL|Ctsl1|MEP|fs|nkt	cathepsin L	protein-coding
mm_36809.1	chr4	103214792	103214818	-	1	NA	promoter-TSS (NM_177732)	promoter-TSS (NM_177732)	79	NM_177732	242585	Mm.281800	NM_177732	ENSMUSG00000028521	Slc35d1	AI834976|C330011J09|UGTREL7|mKIAA0260	solute carrier family 35 (UDP-glucuronic acid/UDP-N-acetylgalactosamine dual transporter), member D1	protein-coding
mm_156563.1	chrX	151803643	151803673	+	1	NA	intron (NM_021523, intron 1 of 82)	CpG	376	NM_021523	59026	Mm.27372	NM_021523	ENSMUSG00000025261	Huwe1	5430439H10Rik|AU041296|Arf-bp1|C430014N20Rik|C80292|Gm1718|Ib772|LASU1|Mule|Ureb1	HECT, UBA and WWE domain containing 1	protein-coding
mm_69873.1	chr7	141476248	141476267	-	1	NA	promoter-TSS (NM_001252588)	promoter-TSS (NM_001252588)	-123	NM_001252588	64540	Mm.489619	NM_053082	ENSMUSG00000025511	Tspan4	AI325509|AI746565|D130042I01Rik|NAG-2|Tm4sf7|Tspan-4	tetraspanin 4	protein-coding
mm_11647.1	chr2	34961402	34961417	+	1	NA	intron (NM_009421, intron 1 of 10)	intron (NM_009421, intron 1 of 10)	363	NM_009421	22029	Mm.239514	NM_009421	ENSMUSG00000026875	Traf1	4732496E14Rik	TNF receptor-associated factor 1	protein-coding
mm_42521.1	chr5	115559506	115559519	+	1	NA	promoter-TSS (NM_007475)	promoter-TSS (NM_007475)	45	NM_007475	11837	Mm.5286	NM_007475	ENSMUSG00000067274	Rplp0	36B4|Arbp|L10E	ribosomal protein, large, P0	protein-coding
mm_31629.1	chr4	59287379	59287393	+	1	NA	Intergenic	Intergenic	27335	NR_105031	101055769	Mm.421401	NR_105031		Gm12596	OTTMUSG00000007649	predicted gene 12596	ncRNA
mm_27342.1	chr3	50414773	50414782	-	1	NA	intron (NM_011990, intron 6 of 11)	intron (NM_011990, intron 6 of 11)	28836	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_84965.1	chr9	83806242	83806260	-	1	NA	promoter-TSS (NM_148941)	promoter-TSS (NM_148941)	54	NM_148941	83603	Mm.83949	NM_148941	ENSMUSG00000032262	Elovl4	-	elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 4	protein-coding
mm_53747.1	chr6	145211230	145211240	+	1	NA	promoter-TSS (NM_133688)	promoter-TSS (NM_133688)	88	NM_133688	67636	Mm.486359	NM_133688	ENSMUSG00000040370	Lyrm5	4930469P12Rik|AL022899|Etfrf1|Ghiso	LYR motif containing 5	protein-coding
mm_90264.1	chr10	122678727	122678755	+	1	NA	promoter-TSS (NR_106182)	promoter-TSS (NR_106182)	-21	NM_176919	319468	Mm.489703	NM_176919	ENSMUSG00000034613	Ppm1h	A430075L18Rik|ARHCL1|C030002B11Rik	protein phosphatase 1H (PP2C domain containing)	protein-coding
mm_162246.1	chrX	159446053	159446053	+	1	NA	exon (NM_001081124, exon 3 of 17)	exon (NM_001081124, exon 3 of 17)	-13072	NM_001313752	78283	Mm.160079	NM_001081124	ENSMUSG00000041020	Map7d2	1600028E09Rik|2900002G04Rik|5330432J06Rik|C030036K04Rik|Mtap7d2	MAP7 domain containing 2	protein-coding
mm_17945.1	chr2	36136260	36136280	-	1	NA	promoter-TSS (NM_026422)	promoter-TSS (NM_026422)	-128	NM_026422	67871	Mm.378232	NM_026422	ENSMUSG00000026887	Mrrf	2400002D02Rik|MRFF|MTRRF|RRF	mitochondrial ribosome recycling factor	protein-coding
mm_25547.1	chr3	115888140	115888200	+	1	NA	promoter-TSS (NR_027895)	promoter-TSS (NR_027895)	-13	NM_027193	69740	Mm.5915	NM_027193	ENSMUSG00000033554	Dph5	2410012M04Rik|AU045680|C80186	diphthamide biosynthesis 5	protein-coding
mm_111546.1	chr12	100908191	100908220	-	1	NA	promoter-TSS (NM_175493)	promoter-TSS (NM_175493)	-7	NM_001177673	238377	Mm.32160	NM_175493	ENSMUSG00000047415	Gpr68	BB131428|Ogr1	G protein-coupled receptor 68	protein-coding
mm_59018.1	chr7	19266297	19266312	+	1	NA	intron (NR_104069, intron 1 of 10)	intron (NR_104069, intron 1 of 10)	5550	NM_001282021	22323	Mm.9684	NM_009499	ENSMUSG00000030403	Vasp	-	vasodilator-stimulated phosphoprotein	protein-coding
mm_127135.1	chr15	98167938	98167992	+	1	NA	5' UTR (NM_177716, exon 1 of 1)	5' UTR (NM_177716, exon 1 of 1)	159	NM_177716	239650	Mm.54140	NM_177716	ENSMUSG00000029875	Ccdc184	5630400A08|AI836003	coiled-coil domain containing 184	protein-coding
mm_68321.1	chr7	106502912	106502923	-	1	NA	Intergenic	RMER12B|LTR|ERVK	-61844	NR_003967	209380	Mm.461779	NM_001001318		Gm4759	EG209380	GTPase, very large interferon inducible 1 pseudogene	pseudo
mm_52061.1	chr6	97312099	97312146	+	1	NA	intron (NM_001346639, intron 11 of 22)	intron (NM_001346639, intron 11 of 22)	-59342	NM_001081157	320502	Mm.68163	NM_001081157	ENSMUSG00000044086	Lmod3	5430424A14Rik	leiomodin 3 (fetal)	protein-coding
mm_94180.1	chr10	128919260	128919305	-	1	NA	promoter-TSS (NM_134006)	promoter-TSS (NM_134006)	15	NM_134006	19682	Mm.439856	NM_134006	ENSMUSG00000025350	Rdh5	9-cis|AI987873|RDH4|cRDH	retinol dehydrogenase 5	protein-coding
mm_95993.1	chr11	59202481	59202529	+	1	NA	promoter-TSS (NM_026035)	promoter-TSS (NM_026035)	19	NM_001302336	67212	Mm.282694	NM_026035	ENSMUSG00000036860	Mrpl55	2810038N09Rik|L55mt|MRP-L55	mitochondrial ribosomal protein L55	protein-coding
mm_157894.1	chrX	76664612	76664613	-	1	NA	Intergenic	MurERV4_19-int|LTR|ERVK	-61688	NM_001201395	74987	Mm.107996	NM_001201395	ENSMUSG00000079525	Cldn34d	4930468A15Rik	claudin 34D	protein-coding
mm_77605.1	chr8	123893204	123893229	-	1	NA	exon (NM_009606, exon 3 of 7)	exon (NM_009606, exon 3 of 7)	1559	NM_001272041	11459	Mm.214950	NM_009606	ENSMUSG00000031972	Acta1	AA959943|Acta-2|Acts|Actsk-1	actin, alpha 1, skeletal muscle	protein-coding
mm_34237.1	chr4	141150477	141150483	+	1	NA	intron (NM_172518, intron 1 of 9)	B1_Mus1|SINE|Alu	2558	NM_172518	213499	Mm.28865	NM_172518	ENSMUSG00000028920	Fbxo42	6720460I06Rik|mKIAA1332	F-box protein 42	protein-coding
mm_69583.1	chr7	135704435	135704447	-	1	NA	exon (NM_001081117, exon 9 of 14)	exon (NM_001081117, exon 9 of 14)	11938	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_171773.1	chr5	109547001	109547007	-	1	NA	Intergenic	B3|SINE|B2	11989	NM_016715	57914	Mm.35771	NM_016715	ENSMUSG00000033467	Crlf2	CRLM2|Ly114|Tpte2|Tslpr	cytokine receptor-like factor 2	protein-coding
mm_22201.1	chr2	173578172	173578180	-	1	NA	exon (NM_001199955, exon 1 of 2)	exon (NM_001199955, exon 1 of 2)	165	NM_001199955	70065	Mm.425115	NM_027303	ENSMUSG00000027517	Ankrd60	1700019A24Rik|1700030G11Rik	ankyrin repeat domain 60	protein-coding
mm_49130.1	chr6	8594280	8594288	+	1	NA	3' UTR (NM_001286729, exon 8 of 8)	3' UTR (NM_001286729, exon 8 of 8)	74226	NM_001286729	170772	Mm.210787	NM_133236	ENSMUSG00000029638	Glcci1	2310047L21Rik|A130036A18Rik|Fam117c|Gig18|Tssn1	glucocorticoid induced transcript 1	protein-coding
mm_44713.1	chr5	30945507	30945587	-	1	NA	promoter-TSS (NM_026770)	promoter-TSS (NM_026770)	-67	NM_026770	68567	Mm.45127	NM_026770	ENSMUSG00000029161	Cgref1	1110004G24Rik|AW045201|Cgr11	cell growth regulator with EF hand domain 1	protein-coding
mm_139373.1	chr17	51832779	51832800	+	1	NA	promoter-TSS (NM_009122)	promoter-TSS (NM_009122)	-142	NM_009122	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_156273.1	chrX	136835098	136835143	+	1	NA	exon (NM_011123, exon 6 of 7)	exon (NM_011123, exon 6 of 7)	12374	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_108381.1	chr12	80877470	80877490	+	1	NA	3' UTR (NM_178682, exon 6 of 6)	3' UTR (NM_178682, exon 6 of 6)	46967	NR_033786	67340	Mm.386790	NR_033786	ENSMUSG00000101912	1700052I22Rik	-	RIKEN cDNA 1700052I22 gene	ncRNA
mm_102354.1	chr11	58214777	58214798	-	1	NA	promoter-TSS (NM_019440)	promoter-TSS (NM_019440)	-190	NM_019440	54396	Mm.458517	NM_019440	ENSMUSG00000069874	Irgm2	AI481100|GTPI|Ifggd2|Iigp2	immunity-related GTPase family M member 2	protein-coding
mm_75496.1	chr8	50916209	50916224	-	1	NA	Intergenic	CpG	548104	NR_046067	100039954	Mm.400419	NR_046067	ENSMUSG00000110281	Gm2516	-	predicted gene 2516	ncRNA
mm_41437.1	chr5	90904185	90904213	+	1	NA	exon (NM_009140, exon 2 of 4)	exon (NM_009140, exon 2 of 4)	300	NM_009140	20310	Mm.4979	NM_009140	ENSMUSG00000058427	Cxcl2	CINC-2a|GROb|Gro2|MIP-2|MIP-2a|Mgsa-b|Mip2|Scyb|Scyb2	chemokine (C-X-C motif) ligand 2	protein-coding
mm_69466.1	chr7	133702474	133702475	-	1	NA	promoter-TSS (NM_001302087)	promoter-TSS (NM_001302087)	26	NM_001302087	22276	Mm.3160	NM_009479	ENSMUSG00000030979	Uros	AI415298|UROIIIS|Uros3	uroporphyrinogen III synthase	protein-coding
mm_61148.1	chr7	57734360	57734364	+	1	NA	intron (NM_008071, intron 3 of 8)	intron (NM_008071, intron 3 of 8)	143189	NM_008071	14402	Mm.8004	NM_008071	ENSMUSG00000033676	Gabrb3	A230092K12Rik|AW049585|Cp1|Gabrb-3|beta3	gamma-aminobutyric acid (GABA) A receptor, subunit beta 3	protein-coding
mm_67947.1	chr7	100467218	100467244	-	1	NA	intron (NM_001017985, intron 32 of 32)	intron (NM_001017985, intron 32 of 32)	-5760	NM_009464	22229	Mm.6254	NM_009464	ENSMUSG00000032942	Ucp3	AI645527|Slc25a9|UCP-3	uncoupling protein 3 (mitochondrial, proton carrier)	protein-coding
mm_154954.1	chrX	36743703	36743721	+	1	NA	promoter-TSS (NM_001085497)	promoter-TSS (NM_001085497)	80	NR_075096	194744	Mm.336014	NM_001085497	ENSMUSG00000037636	Slc25a43	Gm8	solute carrier family 25, member 43	protein-coding
mm_55611.1	chr6	72042518	72042533	-	1	NA	promoter-TSS (NR_046180)	promoter-TSS (NR_046180)	3	NR_046180	330350	Mm.246787	NR_046180	ENSMUSG00000108356	9130221F21Rik	9130221F21	RIKEN cDNA 9130221F21 gene	ncRNA
mm_120674.1	chr14	70554543	70554560	+	1	NA	5' UTR (NM_021877, exon 2 of 20)	5' UTR (NM_021877, exon 2 of 20)	495	NM_021877	15460	Mm.7598	NM_021877	ENSMUSG00000022096	Hr	ALUNC|AU|N|ba|bldy|hr|rh|rh-bmh|rhino	hairless	protein-coding
mm_32052.1	chr4	97630316	97630320	+	1	NA	intron (NM_001122952, intron 1 of 10)	intron (NM_001122952, intron 1 of 10)	-45727	NR_015513	319865	Mm.373807	NM_177023		E130114P18Rik	-	RIKEN cDNA E130114P18 gene	ncRNA
mm_144270.1	chr18	11059043	11059053	+	1	NA	intron (NM_010258, intron 2 of 6)	intron (NM_010258, intron 2 of 6)	-6481	NR_105023	68434	Mm.57626	NR_105022	ENSMUSG00000097222	1010001N08Rik	Gata6as	RIKEN cDNA 1010001N08 gene	ncRNA
mm_11375.1	chr2	31140281	31140286	+	1	NA	intron (NM_001038700, intron 1 of 14)	intron (NM_001038700, intron 1 of 14)	1725	NM_001177649	14269	Mm.52297	NM_019406	ENSMUSG00000075415	Fnbp1	1110057E06Rik|2210010H06Rik|FBP1|Fbp17	formin binding protein 1	protein-coding
mm_75202.1	chr8	39604538	39604582	-	1	NA	3' UTR (NM_031195, exon 9 of 9)	3' UTR (NM_031195, exon 9 of 9)	38118	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_66223.1	chr7	34812678	34812693	-	1	NA	promoter-TSS (NM_175140)	promoter-TSS (NM_175140)	26	NM_175140	68947	Mm.29380	NM_175140	ENSMUSG00000060402	Chst8	1500011J21Rik|AI426009	carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 8	protein-coding
mm_46705.1	chr5	110286011	110286028	-	1	NA	promoter-TSS (NM_011132)	promoter-TSS (NM_011132)	149	NM_008993	19301	Mm.21853	NM_008993	ENSMUSG00000029499	Pxmp2	22kDa|PMP22	peroxisomal membrane protein 2	protein-coding
mm_156806.1	chrX	163911426	163911439	+	1	NA	exon (NM_026887, exon 2 of 5)	exon (NM_026887, exon 2 of 5)	2415	NM_001290379	108012	Mm.426783	NM_026887	ENSMUSG00000031367	Ap1s2	1500012A13Rik|AI853648|EST1	adaptor-related protein complex 1, sigma 2 subunit	protein-coding
mm_90585.1	chr10	128269202	128269213	+	1	NA	exon (NM_133997, exon 2 of 2)	exon (NM_133997, exon 2 of 2)	1210	NM_133997	103161	Mm.26513	NM_133997	ENSMUSG00000047631	Apof	AI255964	apolipoprotein F	protein-coding
mm_122550.1	chr14	48667478	48667478	-	1	NA	5' UTR (NM_001286482, exon 1 of 5)	5' UTR (NM_001286482, exon 1 of 5)	166	NM_001286482	18424	Mm.134516	NM_144841	ENSMUSG00000021848	Otx2	E130306E05Rik	orthodenticle homeobox 2	protein-coding
mm_5595.1	chr1	39558363	39558380	-	1	NA	exon (NM_001033135, exon 5 of 7)	exon (NM_001033135, exon 5 of 7)	-9531	NR_028555	100217461		NR_028555	ENSMUSG00000077704	Snord89	MBII-289	small nucleolar RNA, C/D box 89	snoRNA
mm_25257.1	chr3	104781049	104781128	+	1	NA	promoter-TSS (NM_027982)	promoter-TSS (NM_027982)	32	NM_027982	71887	Mm.379204	NM_027982	ENSMUSG00000002228	Ppm1j	2310008J22Rik|PP2Czeta|Ppp2cz	protein phosphatase 1J	protein-coding
mm_127009.1	chr15	95830126	95830142	+	1	NA	intron (NM_175344, intron 1 of 19)	MER5B|DNA|hAT-Charlie	39291	NM_001253813	105722	Mm.38087	NM_175344	ENSMUSG00000064210	Ano6	2900059G15Rik|AA407480|AW554778|F730003B03Rik|Tmem16f	anoctamin 6	protein-coding
mm_135715.1	chr16	55811943	55811958	-	1	NA	3' UTR (NM_030612, exon 14 of 14)	3' UTR (NM_030612, exon 14 of 14)	10188	NM_001159394	80859	Mm.247272	NM_030612	ENSMUSG00000035356	Nfkbiz	AA408868|INAP|Mail	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, zeta	protein-coding
mm_13490.1	chr2	106693446	106693499	+	1	NA	promoter-TSS (NM_001143683)	promoter-TSS (NM_001143683)	13	NM_001143683	77015	Mm.45628	NM_029837	ENSMUSG00000016386	Mpped2	239Fb|2700082O15Rik|AV354767|AW060960	metallophosphoesterase domain containing 2	protein-coding
mm_75579.1	chr8	61450521	61450524	-	1	NA	Intergenic	PB1D7|SINE|Alu	-37212	NM_145595	234309	Mm.29059	NM_145595	ENSMUSG00000031641	Cbr4	A730083J17Rik|BC009118	carbonyl reductase 4	protein-coding
mm_38314.1	chr4	137166824	137166841	-	1	NA	Intergenic	Intergenic	-1766	NR_040443	100503595	Mm.421314	NR_040443	ENSMUSG00000085833	Gm13003	OTTMUSG00000009822	predicted gene 13003	ncRNA
mm_120968.1	chr14	77904893	77904902	+	1	NA	intron (NM_178825, intron 1 of 6)	intron (NM_178825, intron 1 of 6)	658	NM_029495	108670	Mm.68134	NM_029495	ENSMUSG00000022014	Epsti1	2310046K10Rik|5033415K03Rik|BRESI1	epithelial stromal interaction 1 (breast)	protein-coding
mm_121596.1	chr14	7994192	7994217	-	1	NA	promoter-TSS (NM_007870)	promoter-TSS (NM_007870)	-22	NM_007870	13421	Mm.272258	NM_007870	ENSMUSG00000025279	Dnase1l3	DNasegamma|Dhp2|Lsd	deoxyribonuclease 1-like 3	protein-coding
mm_51604.1	chr6	84019347	84019351	+	1	NA	promoter-TSS (NM_021469)	promoter-TSS (NM_021469)	-37	NM_001310152	26903	Mm.220982	NM_021469	ENSMUSG00000033788	Dysf	2310004N10Rik|AI604795|D6Pas3	dysferlin	protein-coding
mm_68543.1	chr7	114117736	114117750	-	1	NA	promoter-TSS (NM_025846)	promoter-TSS (NM_025846)	38	NM_025846	66922	Mm.276572	NM_025846	ENSMUSG00000055723	Rras2	2610016H24Rik|C86394|TC21	related RAS viral (r-ras) oncogene 2	protein-coding
mm_82437.1	chr9	15279362	15279366	-	1	NA	intron (NM_144933, intron 1 of 11)	intron (NM_144933, intron 1 of 11)	503	NM_144933	234959	Mm.44151	NM_144933	ENSMUSG00000031935	Med17	77kDa|C330002H14Rik|Crsp6|Trap80	mediator complex subunit 17	protein-coding
mm_57030.1	chr6	122294475	122294488	-	1	NA	Intergenic	L1_Mus3|LINE|L1	-11648	NM_016970	50928	Mm.20434	NM_016970	ENSMUSG00000030114	Klrg1	2F1-Ag|MAFA|MAFA-L	killer cell lectin-like receptor subfamily G, member 1	protein-coding
mm_25129.1	chr3	102167843	102167853	+	1	NA	intron (NM_177545, intron 4 of 7)	intron (NM_177545, intron 4 of 7)	36845	NM_177545	229658	Mm.118004	NM_177545	ENSMUSG00000027860	Vangl1	Kitenin|Lpp2|Stb2|Stbm	vang-like 1 (van gogh, Drosophila)	protein-coding
mm_113133.1	chr13	24616860	24616865	+	1	NA	intron (NM_178658, intron 1 of 13)	intron (NM_178658, intron 1 of 13)	2256	NM_178658	193385	Mm.217319	NM_029679	ENSMUSG00000036006	Fam65b	-	family with sequence similarity 65, member B	protein-coding
mm_165446.1	chr2	155826435	155826445	-	1	NA	5' UTR (NM_010579, exon 1 of 6)	5' UTR (NM_010579, exon 1 of 6)	485	NM_010579	16418	Mm.271674	NM_010579	ENSMUSG00000027613	Eif6	1110004P11|AA408895|CAB|Itgb4bp|eIF-6|imc-415|p27(BBP)|p27BBP	eukaryotic translation initiation factor 6	protein-coding
mm_107930.1	chr12	71137226	71137242	+	1	NA	promoter-TSS (NM_001286203)	promoter-TSS (NM_001286203)	386	NM_001163378	76967	Mm.87290	NM_029818	ENSMUSG00000034601	2700049A03Rik	Ta3|Talpid3|mKIAA0586	RIKEN cDNA 2700049A03 gene	protein-coding
mm_71186.1	chr8	40863168	40863184	+	1	NA	intron (NM_007514, intron 1 of 11)	intron (NM_007514, intron 1 of 11)	809	NM_001044740	11988	Mm.4676	NM_007514	ENSMUSG00000031596	Slc7a2	20.5|AI158848|Atrc2|CAT-2|Cat2|Tea	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	protein-coding
mm_64589.1	chr7	3169062	3169080	-	1	NA	exon (NM_001004153, exon 1 of 12)	exon (NM_001004153, exon 1 of 12)	132	NM_001004153	245128	Mm.268551	NM_001004153	ENSMUSG00000054753	AU018091	-	expressed sequence AU018091	protein-coding
mm_114024.1	chr13	52633328	52633337	+	1	NA	intron (NM_001198977, intron 9 of 13)	RSINE1|SINE|B4	36450	NM_011518	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_16595.1	chr2	4938383	4938406	-	1	NA	3' UTR (NM_010726, exon 9 of 9)	3' UTR (NM_010726, exon 9 of 9)	19398	NM_010726	16922	Mm.391704	NM_010726	ENSMUSG00000026664	Phyh	AI256161|AI265699|Lnap1|PAHX	phytanoyl-CoA hydroxylase	protein-coding
mm_126145.1	chr15	78349096	78349119	+	1	NA	TTS (NR_106138)	TTS (NR_106138)	508	NR_106138	102466845		NR_106138	ENSMUSG00000099059	Mir7676-2	Gm27790|mmu-mir-7676-2	microRNA 7676-2	ncRNA
mm_112179.1	chr12	113422035	113422043	-	1	NA	Intergenic	Intergenic	-67526	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_118248.1	chr13	111984050	111984060	-	1	NA	Intergenic	Intergenic	116119	NR_130345	102636620	Mm.402328	NR_130345	ENSMUSG00000086111	Gm15326	OTTMUSG00000020187	predicted gene 15326	ncRNA
mm_155988.1	chrX	106143244	106143302	+	1	NA	promoter-TSS (NM_205820)	promoter-TSS (NM_205820)	-2	NM_205820	279572	Mm.336203	NM_205820	ENSMUSG00000033777	Tlr13	AI666735|Gm713	toll-like receptor 13	protein-coding
mm_38473.1	chr4	140665855	140665867	-	1	NA	promoter-TSS (NM_001112722)	promoter-TSS (NM_001112722)	26	NM_001290803	72754	Mm.29329	NM_172415	ENSMUSG00000040964	Arhgef10l	2810441C07Rik	Rho guanine nucleotide exchange factor (GEF) 10-like	protein-coding
mm_92476.1	chr10	78185103	78185155	-	1	NA	promoter-TSS (NM_029546)	promoter-TSS (NM_029546)	20	NM_029546	110816	Mm.103522	NM_029546	ENSMUSG00000032834	Pwp2	6530411D08Rik|Pwp2h|wdp103	PWP2 periodic tryptophan protein homolog (yeast)	protein-coding
mm_136050.1	chr16	78576623	78576645	-	1	NA	promoter-TSS (NM_001252440)	promoter-TSS (NM_001252440)	54	NM_001252438	67102	Mm.37332	NM_025967	ENSMUSG00000022864	D16Ertd472e	1700010I10Rik|2310009O17Rik|E330003K22Rik|Eurl	DNA segment, Chr 16, ERATO Doi 472, expressed	protein-coding
mm_93127.1	chr10	91189070	91189082	-	1	NA	Intergenic	RLTR41|LTR|ERV1	-17457	NM_001080130	21917	Mm.159684	NM_011605	ENSMUSG00000019961	Tmpo	5630400D24Rik|AI195756|AI606875|AW214352|AW547477|LAP2|TP	thymopoietin	protein-coding
mm_56889.1	chr6	119036988	119036991	-	1	NA	intron (NM_001256002, intron 3 of 47)	intron (NM_001256002, intron 3 of 47)	71506	NM_001159534	12288	Mm.41628	NM_009781	ENSMUSG00000051331	Cacna1c	Cav1.2|Cchl1a1|D930026N18Rik|MBC|MELC-CC	calcium channel, voltage-dependent, L type, alpha 1C subunit	protein-coding
mm_152081.1	chr19	6858180	6858218	-	1	NA	promoter-TSS (NM_001081291)	promoter-TSS (NM_001081291)	12	NM_001081291	78317	Mm.329596	NM_198008	ENSMUSG00000047810	Ccdc88b	2610041P08Rik|Ccdc88	coiled-coil domain containing 88B	protein-coding
mm_108784.1	chr12	90430463	90430472	+	1	NA	Intergenic	MLT-int|LTR|ERVL-MaLR	308570	NM_010050	13371	Mm.21389	NM_010050	ENSMUSG00000007682	Dio2	5DII|AI324267|DIOII	deiodinase, iodothyronine, type II	protein-coding
mm_150729.1	chr19	43689799	43689868	+	1	NA	5' UTR (NM_053103, exon 1 of 13)	5' UTR (NM_053103, exon 1 of 13)	144	NM_053103	93685	Mm.248237	NM_053103	ENSMUSG00000025192	Entpd7	1810012B13Rik|1810020C02Rik|2810003F23Rik|LALP1|Lysal2	ectonucleoside triphosphate diphosphohydrolase 7	protein-coding
mm_22014.1	chr2	167777921	167777934	-	1	NA	Intergenic	Intergenic	86750	NR_015500	329562	Mm.123101	NM_177851	ENSMUSG00000006462	A530013C23Rik	-	RIKEN cDNA A530013C23 gene	ncRNA
mm_117384.1	chr13	73346917	73346925	-	1	NA	non-coding (NR_045293, exon 2 of 3)	non-coding (NR_045293, exon 2 of 3)	463	NR_045293	432777	Mm.415319	NR_045293		D630045M09Rik	AU019512	RIKEN cDNA D630045M09 gene	ncRNA
mm_40307.1	chr5	43818900	43818928	+	1	NA	promoter-TSS (NM_009763)	promoter-TSS (NM_009763)	21	NM_009763	12182	Mm.246332	NM_009763	ENSMUSG00000029082	Bst1	114/A10|A530073F09|BP-3|Bp3|Bsta1|CD157|Ly65	bone marrow stromal cell antigen 1	protein-coding
mm_93305.1	chr10	97644048	97644057	-	1	NA	promoter-TSS (NM_007884)	promoter-TSS (NM_007884)	-16	NM_007884	13516	Mm.148886	NM_007884	ENSMUSG00000019936	Epyc	Dspg3|PG-Lb|SLRR3B	epiphycan	protein-coding
mm_168804.1	chr12	20615001	20615012	+	1	NA	Intergenic	CpG	200773	NR_015521	69513	Mm.273972	NR_015521	ENSMUSG00000099759	1700030C10Rik	-	RIKEN cDNA 1700030C10 gene	ncRNA
mm_28120.1	chr3	86920364	86920390	-	1	NA	5' UTR (NM_001195500, exon 1 of 12)	5' UTR (NM_001195500, exon 1 of 12)	507	NM_001195496	70762	Mm.44490	NM_027539	ENSMUSG00000028078	Dclk2	6330415M09Rik|AU044875|CL2|CLICK2|Click-II|Dcamkl2	doublecortin-like kinase 2	protein-coding
mm_101677.1	chr11	39794270	39794285	-	1	NA	Intergenic	Intergenic	-404052	NR_126439	75315	Mm.461295	NR_126439		4930553C11Rik	-	RIKEN cDNA 4930553C11 gene	ncRNA
mm_74939.1	chr8	25812971	25813003	-	1	NA	3' UTR (NM_011485, exon 7 of 7)	3' UTR (NM_011485, exon 7 of 7)	4513	NM_011485	20845	Mm.293314	NM_011485	ENSMUSG00000031574	Star	AV363654|D8Ertd419e|stARD1	steroidogenic acute regulatory protein	protein-coding
mm_17471.1	chr2	28559674	28559681	-	1	NA	exon (NM_009885, exon 6 of 11)	exon (NM_009885, exon 6 of 11)	3726	NM_009885	12613	Mm.236017	NM_009885	ENSMUSG00000026818	Cel	1810036E18Rik|BAL	carboxyl ester lipase	protein-coding
mm_122892.1	chr14	54949510	54949542	-	1	NA	promoter-TSS (NR_029724)	promoter-TSS (NR_029724)	-384	NR_029724	387204		NR_029724	ENSMUSG00000065432	Mir208a	Mirn208|Mirn208a|mir-208|mir-208a|mmu-mir-208	microRNA 208a	ncRNA
mm_76193.1	chr8	82403015	82403034	-	1	NA	promoter-TSS (NM_001254747)	promoter-TSS (NM_001254747)	-438	NM_008357	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_68342.1	chr7	106506419	106506429	-	1	NA	Intergenic	Intergenic	-65351	NR_003967	209380	Mm.461779	NM_001001318		Gm4759	EG209380	GTPase, very large interferon inducible 1 pseudogene	pseudo
mm_160049.1	chr6	148946439	148946439	-	1	NA	promoter-TSS (NM_019643)	promoter-TSS (NM_019643)	-7	NM_019643	56306	Mm.18637	NM_019643	ENSMUSG00000039985	Fam60a	Ppcs1|Pptcs1|Tera	family with sequence similarity 60, member A	protein-coding
mm_84457.1	chr9	66576029	66576048	-	1	NA	intron (NM_001302116, intron 1 of 13)	intron (NM_001302116, intron 1 of 13)	17077	NM_144937	235441	Mm.32465	NM_144937	ENSMUSG00000032376	Usp3	AA409661|BC017156	ubiquitin specific peptidase 3	protein-coding
mm_41817.1	chr5	103814978	103815007	+	1	NA	exon (NM_133919, exon 5 of 20)	exon (NM_133919, exon 5 of 20)	60419	NM_001080798	17355	Mm.6949	NM_133919	ENSMUSG00000029313	Aff1	9630032B01Rik|AW319193|Af4|Mllt2h|Rob	AF4/FMR2 family, member 1	protein-coding
mm_26230.1	chr3	139205659	139205684	+	1	NA	promoter-TSS (NM_198659)	promoter-TSS (NM_198659)	-222	NM_198659	381476	Mm.188334	NM_198659	ENSMUSG00000047940	Stpg2	B930007M17Rik|Gm1017	sperm tail PG rich repeat containing 2	protein-coding
mm_130094.1	chr15	89425310	89425314	-	1	NA	non-coding (NR_004843, exon 11 of 27)	non-coding (NR_004843, exon 11 of 27)	550	NM_009948	12895	Mm.227738	NM_009948	ENSMUSG00000078937	Cpt1b	Cpt1|Cpt1-m|Cpti|Cpti-m|M-cpti	carnitine palmitoyltransferase 1b, muscle	protein-coding
mm_168177.1	chr10	56497456	56497461	+	1	NA	Intergenic	Intergenic	120158	NM_010288	14609	Mm.378921	NM_010288	ENSMUSG00000050953	Gja1	AU042049|AW546267|Cnx43|Cx43|Cx43alpha1|Gja-1|Npm1|connexin43	gap junction protein, alpha 1	protein-coding
mm_70206.1	chr7	144751969	144752007	-	1	NA	Intergenic	Intergenic	-13396	NM_001242349	101772	Mm.26700	NM_178642	ENSMUSG00000031075	Ano1	Tmem16a	anoctamin 1, calcium activated chloride channel	protein-coding
mm_25940.1	chr3	131476242	131476243	+	1	NA	Intergenic	Intergenic	-88526	NM_001289479	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_85605.1	chr9	107594470	107594477	-	1	NA	Intergenic	Intergenic	6755	NM_025903	15983	Mm.215335	NM_025903	ENSMUSG00000010048	Ifrd2	1810034A24Rik|AA470234|AI838527|SKMc15	interferon-related developmental regulator 2	protein-coding
mm_84329.1	chr9	64021945	64021960	-	1	NA	5' UTR (NM_008542, exon 1 of 4)	5' UTR (NM_008542, exon 1 of 4)	107	NM_008542	17130	Mm.325757	NM_008542	ENSMUSG00000036867	Smad6	Madh6|b2b390Clo	SMAD family member 6	protein-coding
mm_87362.1	chr10	43901783	43901845	+	1	NA	promoter-TSS (NM_130892)	promoter-TSS (NM_130892)	7	NM_130892	170728	Mm.390253	NM_130892	ENSMUSG00000019864	Rtn4ip1	D10Ertd690e|NIMP	reticulon 4 interacting protein 1	protein-coding
mm_77131.1	chr8	111338442	111338461	-	1	NA	promoter-TSS (NM_001310613)	promoter-TSS (NM_001310613)	-246	NM_029005	74568	Mm.207971	NM_029005	ENSMUSG00000012519	Mlkl	9130019I15Rik	mixed lineage kinase domain-like	protein-coding
mm_91215.1	chr10	21844624	21844640	-	1	NA	Intergenic	Intergenic	-37552	NM_001161845	20393	Mm.28405	NM_011361	ENSMUSG00000019970	Sgk1	Sgk	serum/glucocorticoid regulated kinase 1	protein-coding
mm_79013.1	chr9	45742574	45742585	+	1	NA	intron (NM_001081270, intron 22 of 32)	intron (NM_001081270, intron 22 of 32)	86059	NM_001081373	214552	Mm.260103	NM_172531	ENSMUSG00000043987	Cep164	AI450905|BC027092|D030051D21|mKIAA1052	centrosomal protein 164	protein-coding
mm_84120.1	chr9	58555188	58555217	-	1	NA	Intergenic	CpG	-14262	NM_133983	102657	Mm.5356	NM_133983	ENSMUSG00000035914	Cd276	6030411F23Rik|AU016588|B7RP-2|B7h3	CD276 antigen	protein-coding
mm_2055.1	chr1	87443014	87443015	+	1	NA	intron (NM_146112, intron 26 of 28)	MIRb|SINE|MIR	-27250	NM_028473	73234	Mm.7310	NM_028473	ENSMUSG00000026258	3110079O15Rik	Snorc	RIKEN cDNA 3110079O15 gene	protein-coding
mm_6719.1	chr1	82478165	82478176	-	1	NA	intron (NM_007735, intron 37 of 47)	intron (NM_007735, intron 37 of 47)	108679	NM_007735	12829	Mm.40253	NM_007735	ENSMUSG00000067158	Col4a4	E130010M05Rik|[a]4(IV)	collagen, type IV, alpha 4	protein-coding
mm_34178.1	chr4	140699965	140699975	+	1	NA	Intergenic	Intergenic	-1503	NM_173867	108911	Mm.253	NM_173867	ENSMUSG00000040945	Rcc2	2610510H01Rik|2610529N02Rik|AA536646|AA675016|Td60|mKIAA1470	regulator of chromosome condensation 2	protein-coding
mm_42949.1	chr5	123015011	123015118	+	1	NA	promoter-TSS (NM_175423)	promoter-TSS (NM_175423)	-10	NM_175423	109305	Mm.218582	NM_175423	ENSMUSG00000049686	Orai1	D730049H07Rik|Tmem142a|orai-1	ORAI calcium release-activated calcium modulator 1	protein-coding
mm_59340.1	chr7	25471981	25471987	+	1	NA	exon (NM_001039186, exon 5 of 8)	exon (NM_001039186, exon 5 of 8)	5641	NM_001039185	26365	Mm.322502	NM_011926	ENSMUSG00000074272	Ceacam1	Bgp|Bgp1|C-CAM|CD66a|Cc1|Cea-1|Cea-7|Cea1|Cea7|Hv-2|Hv2|MHVR|MHVR1|Mhv-1|bb-1|mCEA1|mmCGM1|mmCGM1a|mmCGM2	carcinoembryonic antigen-related cell adhesion molecule 1	protein-coding
mm_160790.1	chr10	129723602	129723602	-	1	NA	promoter-TSS (NM_146555)	promoter-TSS (NM_146555)	-60	NM_146555	258548	Mm.391456	NM_146555	ENSMUSG00000096858	Olfr805	MOR110-4	olfactory receptor 805	protein-coding
mm_84935.1	chr9	82938142	82938146	-	1	NA	intron (NM_001081216, intron 7 of 39)	A-rich|Low_complexity|Low_complexity	37345	NM_001081216	83946	Mm.221688	NM_031879	ENSMUSG00000032253	Phip	2810004D21Rik|4632404O06Rik|Ndrp|Wdr11	pleckstrin homology domain interacting protein	protein-coding
mm_107405.1	chr12	33394859	33394868	+	1	NA	promoter-TSS (NM_029152)	promoter-TSS (NM_029152)	9	NM_029152	75040	Mm.156068	NM_029152	ENSMUSG00000020562	Efcab10	4930504H06Rik	EF-hand calcium binding domain 10	protein-coding
mm_172056.1	chr6	128974925	128974925	-	1	NA	promoter-TSS (NR_106107).2	promoter-TSS (NR_106107).2	-30	NR_106107	102465757		NR_106107	ENSMUSG00000098359	Mir7649	mmu-mir-7649	microRNA 7649	ncRNA
mm_125641.1	chr15	62169964	62169967	+	1	NA	intron (NR_003368, intron 4 of 8)	intron (NR_003368, intron 4 of 8)	49486	NR_003523	67552	Mm.484027	NM_026230		H2afy3	4933432H23Rik	H2A histone family, member Y3	pseudo
mm_164609.1	chr17	31143255	31143271	-	1	NA	exon (NM_009363, exon 2 of 4)	exon (NM_009363, exon 2 of 4)	1019	NM_009363	21785	Mm.1825	NM_009363	ENSMUSG00000024028	Tff2	SP|mSP	trefoil factor 2 (spasmolytic protein 1)	protein-coding
mm_496.1	chr1	36903990	36903999	+	1	NA	intron (NM_018872, intron 1 of 40)	intron (NM_018872, intron 1 of 40)	35533	NM_018872	56030	Mm.186943	NM_018872	ENSMUSG00000026116	Tmem131	2610524E03Rik|CC28|D1Bwg0491e|Neg|RW1|YR-23|mKIAA0257	transmembrane protein 131	protein-coding
mm_69123.1	chr7	127026414	127026425	-	1	NA	promoter-TSS (NM_010772)	promoter-TSS (NM_010772)	60	NM_010772	17188	Mm.378964	NM_010772	ENSMUSG00000030678	Maz	MAZI|PUR1|Pur-1|SAF-1|SAF-2	MYC-associated zinc finger protein (purine-binding transcription factor)	protein-coding
mm_33634.1	chr4	132959677	132959682	+	1	NA	Intergenic	Intergenic	-14416	NM_010208	14191	Mm.271665	NM_010208	ENSMUSG00000028874	Fgr	-	FGR proto-oncogene, Src family tyrosine kinase	protein-coding
mm_146540.1	chr18	5593796	5593814	-	1	NA	intron (NM_011546, intron 1 of 7)	intron (NM_011546, intron 1 of 7)	-1368	NR_033552	791318	Mm.84339	NR_033552	ENSMUSG00000063087	Gm10125	ENSMUSG00000063087|Zeb1os	predicted gene 10125	ncRNA
mm_97619.1	chr11	78955402	78955411	+	1	NA	exon (NM_010927, exon 24 of 27)	exon (NM_010927, exon 24 of 27)	29518	NM_001159301	16859	Mm.341434	NM_010708	ENSMUSG00000001123	Lgals9	AA407335|AI194909|AI265545|LGALS35|Lgals5|gal-9|galectin-9	lectin, galactose binding, soluble 9	protein-coding
mm_72225.1	chr8	72741801	72741808	+	1	NA	intron (NM_009188, intron 7 of 18)	intron (NM_009188, intron 7 of 18)	18534	NM_009188	20467	Mm.2137	NM_009188	ENSMUSG00000031622	Sin3b	2810430C10Rik	transcriptional regulator, SIN3B (yeast)	protein-coding
mm_36637.1	chr4	93335511	93335548	-	1	NA	promoter-TSS (NM_026954)	promoter-TSS (NM_026954)	-18	NM_026954	69136	Mm.171558	NM_026954	ENSMUSG00000054000	Tusc1	2200001D17Rik|TSG-9	tumor suppressor candidate 1	protein-coding
mm_168613.1	chr11	76862494	76862499	-	1	NA	Intergenic	MT2_Mm|LTR|ERVL	-15488	NM_007754	12874	Mm.276736	NM_007754	ENSMUSG00000020841	Cpd	AA960140|AW322530|D830034L15Rik	carboxypeptidase D	protein-coding
mm_143786.1	chr17	81731276	81731284	-	1	NA	intron (NR_104580, intron 1 of 8)	intron (NR_104580, intron 1 of 8)	7107	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_42520.1	chr5	115559489	115559499	+	1	NA	promoter-TSS (NM_007475)	promoter-TSS (NM_007475)	27	NM_007475	11837	Mm.5286	NM_007475	ENSMUSG00000067274	Rplp0	36B4|Arbp|L10E	ribosomal protein, large, P0	protein-coding
mm_59571.1	chr7	28104774	28104780	+	1	NA	exon (NM_001122603, exon 14 of 20)	exon (NM_001122603, exon 14 of 20)	-24689	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_36972.1	chr4	109476483	109476496	-	1	NA	promoter-TSS (NM_013876)	promoter-TSS (NM_013876)	16	NM_013876	29864	Mm.392580	NM_013876	ENSMUSG00000028557	Rnf11	-	ring finger protein 11	protein-coding
mm_1126.1	chr1	60181582	60181591	+	1	NA	5' UTR (NM_173444, exon 2 of 55)	5' UTR (NM_173444, exon 2 of 55)	987	NM_173444	269198	Mm.205224	NM_173444	ENSMUSG00000073664	Nbeal1	2310076G13Rik|A530050O19Rik|A530083I02Rik|AI662228|ALS2CR17	neurobeachin like 1	protein-coding
mm_98959.1	chr11	98551174	98551178	+	1	NA	promoter-TSS (NM_001166494)	promoter-TSS (NM_001166494)	79	NM_001166494	69376	Mm.55996	NM_027061	ENSMUSG00000017195	Zpbp2	1700017D11Rik|2610022C02Rik|ZPBPL	zona pellucida binding protein 2	protein-coding
mm_159898.1	chr6	38197050	38197050	-	1	NA	exon (NM_194061, exon 2 of 20)	exon (NM_194061, exon 2 of 20)	56959	NM_194061	330286	Mm.277163	NM_194061	ENSMUSG00000063455	D630045J12Rik	Kiaa1549|mKIAA1549	RIKEN cDNA D630045J12 gene	protein-coding
mm_103566.1	chr11	77882190	77882237	-	1	NA	exon (NM_008952, exon 6 of 8)	exon (NM_008952, exon 6 of 8)	11659	NM_008952	19193	Mm.8543	NM_008952	ENSMUSG00000017453	Pipox	LPIPOX|Pso	pipecolic acid oxidase	protein-coding
mm_100897.1	chr11	6066355	6066365	-	1	NA	promoter-TSS (NM_001174054)	promoter-TSS (NM_001174054)	-612	NM_007595	12323	Mm.439733	NM_007595	ENSMUSG00000057897	Camk2b	CaMKII	calcium/calmodulin-dependent protein kinase II, beta	protein-coding
mm_130884.1	chr15	102257307	102257370	-	1	NA	5' UTR (NM_011244, exon 1 of 10)	5' UTR (NM_011244, exon 1 of 10)	184	NM_011244	19411	Mm.1273	NM_011244	ENSMUSG00000001288	Rarg	Nr1b3|RAR-gamma|RARD|RARgamma2	retinoic acid receptor, gamma	protein-coding
mm_6943.1	chr1	85727483	85727504	-	1	NA	intron (NM_177055, intron 1 of 5)	Lx8|LINE|L1	9113	NM_177055	319997	Mm.116691	NM_177055	ENSMUSG00000052760	A630001G21Rik	-	RIKEN cDNA A630001G21 gene	protein-coding
mm_101034.1	chr11	8600719	8600747	-	1	NA	intron (NM_001083587, intron 2 of 30)	intron (NM_001083587, intron 2 of 30)	63802	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_36777.1	chr4	102921784	102921790	-	1	NA	intron (NM_001285852, intron 16 of 25)	intron (NM_001285852, intron 16 of 25)	-64592	NM_001163767	67344	Mm.111346	NM_026100	ENSMUSG00000028523	Tctex1d1	1700055O19Rik	Tctex1 domain containing 1	protein-coding
mm_56573.1	chr6	106748013	106748019	-	1	NA	intron (NM_008370, intron 1 of 12)	intron (NM_008370, intron 1 of 12)	1021	NM_008370	16192	Mm.3448	NM_008370	ENSMUSG00000005364	Il5ra	CD125|CDw125|Il5r	interleukin 5 receptor, alpha	protein-coding
mm_22111.1	chr2	170132038	170132051	-	1	NA	promoter-TSS (NM_001033299)	promoter-TSS (NM_001033299)	-824	NM_001033299	228913	Mm.22858	NM_001033299	ENSMUSG00000052056	Zfp217	4933431C08Rik|AW987152|Gm562|ZABC1|Znf217	zinc finger protein 217	protein-coding
mm_14335.1	chr2	129592819	129592885	+	1	NA	promoter-TSS (NM_001291022)	promoter-TSS (NM_001291022)	13	NM_001291020	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_36336.1	chr4	72199031	72199063	-	1	NA	intron (NM_001285530, intron 2 of 17)	intron (NM_001285530, intron 2 of 17)	1846	NM_011599	21885	Mm.278444	NM_011599	ENSMUSG00000008305	Tle1	C230057C06Rik|Estm14|Grg-1|Grg1|Tle4l	transducin-like enhancer of split 1	protein-coding
mm_32860.1	chr4	118409332	118409374	+	1	NA	promoter-TSS (NM_198170)	promoter-TSS (NM_198170)	16	NM_020000	80509	Mm.259567	NM_020000	ENSMUSG00000006392	Med8	2210021A15Rik|AB041805|ARC32	mediator complex subunit 8	protein-coding
mm_105159.1	chr11	101551838	101551893	-	1	NA	promoter-TSS (NM_001252222)	promoter-TSS (NM_001252222)	90	NM_009764	12189	Mm.244975	NM_009764	ENSMUSG00000017146	Brca1	-	breast cancer 1, early onset	protein-coding
mm_128185.1	chr15	34678829	34678851	-	1	NA	promoter-TSS (NM_145469)	promoter-TSS (NM_145469)	-134	NM_145469	223473	Mm.258402	NM_145469	ENSMUSG00000038879	Nipal2	9330161F08Rik|Npal2	NIPA-like domain containing 2	protein-coding
mm_61457.1	chr7	75596294	75596322	+	1	NA	intron (NM_029332, intron 5 of 36)	intron (NM_029332, intron 5 of 36)	140774	NM_029332	75547	Mm.216107	NM_029332	ENSMUSG00000066406	Akap13	1700026G02Rik|5730522G15Rik|5830460E08Rik|AKAP-13|AKAP-Lbc|BRX|Ht31|LBC|PROTO-LB|PROTO-LBC	A kinase (PRKA) anchor protein 13	protein-coding
mm_65960.1	chr7	30435149	30435171	-	1	NA	3' UTR (NM_007467, exon 17 of 17)	3' UTR (NM_007467, exon 17 of 17)	10422	NM_007467	11803	Mm.2381	NM_007467	ENSMUSG00000006651	Aplp1	-	amyloid beta (A4) precursor-like protein 1	protein-coding
mm_107619.1	chr12	51348371	51348406	+	1	NA	5' UTR (NM_001015099, exon 1 of 15)	5' UTR (NM_001015099, exon 1 of 15)	158	NM_001015099	217558	Mm.253264	NM_001015099	ENSMUSG00000035293	G2e3	6030408C04Rik|9030416F18|AW046379|D930034K21Rik|mKIAA1333	G2/M-phase specific E3 ubiquitin ligase	protein-coding
mm_172739.1	chr8	7856427	7856428	-	1	NA	Intergenic	ERVB7_1-LTR_MM|LTR|ERVK	804346	NM_010111	13642	Mm.209813	NM_010111	ENSMUSG00000001300	Efnb2	ELF-2|Epl5|Eplg5|Htk-L|LERK-5|Lerk5|NLERK-1	ephrin B2	protein-coding
mm_92796.1	chr10	81350306	81350369	-	1	NA	promoter-TSS (NM_010440)	promoter-TSS (NM_010440)	89	NM_001163165	15353	Mm.38474	NM_010440	ENSMUSG00000020232	Hmg20b	AW610687|BRAF35|Hmgx2|Hmgxb2|Smarce1r	high mobility group 20B	protein-coding
mm_123400.1	chr14	63438069	63438082	-	1	NA	intron (NM_177628, intron 1 of 3)	intron (NM_177628, intron 1 of 3)	1681	NM_177628	219148	Mm.37882	NM_177628	ENSMUSG00000035095	Fam167a	A030013D21	family with sequence similarity 167, member A	protein-coding
mm_44272.1	chr5	5694437	5694447	-	1	NA	promoter-TSS (NM_001103156)	promoter-TSS (NM_001103156)	-116	NM_001285469	74051	Mm.274956	NM_028734	ENSMUSG00000015653	Steap2	4921538B17Rik|AI930049|AW045895|IPCA-1|IPCA1|PCANAP1|STAMP1|STMP	six transmembrane epithelial antigen of prostate 2	protein-coding
mm_49699.1	chr6	34179227	34179246	+	1	NA	Intergenic	Intergenic	-2182	NM_021435	58246	Mm.245527	NM_021435	ENSMUSG00000018999	Slc35b4	4930474D06Rik|AB041549|AW494345	solute carrier family 35, member B4	protein-coding
mm_21740.1	chr2	164778077	164778087	-	1	NA	exon (NM_009394, exon 3 of 6)	exon (NM_009394, exon 3 of 6)	1652	NM_009394	21925	Mm.1716	NM_009394	ENSMUSG00000017300	Tnnc2	Tncs	troponin C2, fast	protein-coding
mm_128288.1	chr15	37135752	37135769	-	1	NA	Intergenic	CpG	-97276	NM_026496	252973	Mm.244612	NM_026496	ENSMUSG00000022286	Grhl2	0610015A08Rik|BOM|Tcfcp2l3|clft3	grainyhead-like 2 (Drosophila)	protein-coding
mm_92865.1	chr10	81622248	81622251	-	1	NA	3' UTR (NM_181586, exon 8 of 8)	3' UTR (NM_181586, exon 8 of 8)	5073	NM_001163430	50721	Mm.25643	NM_181586	ENSMUSG00000034748	Sirt6	2810449N18Rik|AI043036|Sir2l6	sirtuin 6	protein-coding
mm_50216.1	chr6	42286710	42286718	+	1	NA	promoter-TSS (NM_013491)	promoter-TSS (NM_013491)	29	NM_013491	12723	Mm.386757	NM_013491	ENSMUSG00000029862	Clcn1	Clc-1|Clc1|SMCC1|adr|mto|myotonia|nmf355	chloride channel, voltage-sensitive 1	protein-coding
mm_61986.1	chr7	91090729	91090751	+	1	NA	promoter-TSS (NM_011807)	promoter-TSS (NM_011807)	-46	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_110785.1	chr12	71136612	71136701	-	1	NA	promoter-TSS (NM_001163378)	promoter-TSS (NM_001163378)	19	NM_001024853	30056	Mm.207767	NM_013896	ENSMUSG00000021079	Timm9	2810011L15Rik|Tim10a|Timm10	translocase of inner mitochondrial membrane 9	protein-coding
mm_25368.1	chr3	107101661	107101669	+	1	NA	promoter-TSS (NM_008417)	promoter-TSS (NM_008417)	98	NM_008417	16490	Mm.39285	NM_008417	ENSMUSG00000040724	Kcna2	Akr6a4|ENSMUSG00000074335|Gm10672|Kca1-2|Kv1.2|Mk-2	potassium voltage-gated channel, shaker-related subfamily, member 2	protein-coding
mm_77590.1	chr8	123891841	123891859	-	1	NA	TTS (NM_009606)	TTS (NM_009606)	2925	NM_001272041	11459	Mm.214950	NM_009606	ENSMUSG00000031972	Acta1	AA959943|Acta-2|Acts|Actsk-1	actin, alpha 1, skeletal muscle	protein-coding
mm_72470.1	chr8	83389847	83389872	+	1	NA	promoter-TSS (NM_001329627)	promoter-TSS (NM_001329627)	17	NM_001329680	12745	Mm.358581	NM_009904	ENSMUSG00000002190	Clgn	4930459O04Rik|A2/6|AI528775|Cln	calmegin	protein-coding
mm_90504.1	chr10	128036219	128036239	+	1	NA	intron (NM_001113199, intron 1 of 8)	CpG	883	NM_001113199	17938	Mm.3746	NM_013608	ENSMUSG00000061315	Naca	AL022831|AL024382|Gm1878|mKIAA0363|skNAC	nascent polypeptide-associated complex alpha polypeptide	protein-coding
mm_56130.1	chr6	87672122	87672138	-	1	NA	promoter-TSS (NM_001170489)	promoter-TSS (NM_001170489)	38	NM_024251	72103	Mm.31770	NM_024251	ENSMUSG00000030051	Aplf	2010301N04Rik|AI452191	aprataxin and PNKP like factor	protein-coding
mm_11497.1	chr2	32525014	32525037	+	1	NA	Intergenic	Intergenic	-10334	NM_153560	98952	Mm.4065	NM_153560	ENSMUSG00000039157	Fam102a	AI426465|C230093N12Rik|Eeig1	family with sequence similarity 102, member A	protein-coding
mm_8081.1	chr1	135585732	135585817	-	1	NA	promoter-TSS (NM_173437)	promoter-TSS (NM_173437)	-419	NM_173437	215690	Mm.34977	NM_173437	ENSMUSG00000009418	Nav1	9530089B19|9930003A20Rik|C230080M11Rik|Pomfil3|Unc53h1|mKIAA1151|steerin-1	neuron navigator 1	protein-coding
mm_40257.1	chr5	38230554	38230582	+	1	NA	exon (NM_025281, exon 6 of 9)	exon (NM_025281, exon 6 of 9)	10086	NM_025281	17089	Mm.28560	NM_025281	ENSMUSG00000067367	Lyar	MLZ-264	Ly1 antibody reactive clone	protein-coding
mm_99346.1	chr11	101553809	101553824	+	1	NA	intron (NM_001252223, intron 1 of 22)	intron (NM_001252223, intron 1 of 22)	1162	NM_001252223	17966	Mm.784	NM_008676	ENSMUSG00000017119	Nbr1	mKIAA0049	neighbor of Brca1 gene 1	protein-coding
mm_93563.1	chr10	116522100	116522103	-	1	NA	intron (NM_028082, intron 2 of 14)	intron (NM_028082, intron 2 of 14)	-48578	NM_021452	58802	Mm.440652	NM_021452	ENSMUSG00000054934	Kcnmb4	1700058G18Rik|2900045G12Rik	potassium large conductance calcium-activated channel, subfamily M, beta member 4	protein-coding
mm_111051.1	chr12	80109728	80109748	-	1	NA	exon (NM_007564, exon 2 of 2)	exon (NM_007564, exon 2 of 2)	3275	NM_007564	12192	Mm.235132	NM_007564	ENSMUSG00000021127	Zfp36l1	AW742437|AW743212|Berg36|Brf1|D530020L18Rik|ERF1|TIS11b|cMG1	zinc finger protein 36, C3H type-like 1	protein-coding
mm_160708.1	chr10	58232753	58232753	-	1	NA	promoter-TSS (NM_001081954)	promoter-TSS (NM_001081954)	-78	NM_001081954	664783	Mm.482575	NM_001081954		Dux	AW822073|Dux4|Duxbl|EG664783	double homeobox	protein-coding
mm_99645.1	chr11	105304386	105304389	+	1	NA	intron (NM_008626, intron 1 of 29)	intron (NM_008626, intron 1 of 29)	11741	NM_008626	17534	Mm.235616	NM_008626	ENSMUSG00000020695	Mrc2	Endo180|mKIAA0709|uPARAP	mannose receptor, C type 2	protein-coding
mm_145040.1	chr18	39496750	39496763	+	1	NA	Intergenic	Intergenic	-9511	NM_008173	14815	Mm.129481	NM_008173	ENSMUSG00000024431	Nr3c1	GR|Grl-1|Grl1	nuclear receptor subfamily 3, group C, member 1	protein-coding
mm_105938.1	chr11	115187291	115187318	-	1	NA	promoter-TSS (NM_025400)	promoter-TSS (NM_025400)	12	NM_025400	66176	Mm.86823	NM_025400	ENSMUSG00000015542	Nat9	1110028N05Rik	N-acetyltransferase 9 (GCN5-related, putative)	protein-coding
mm_124608.1	chr15	3279368	3279368	+	1	NA	exon (NM_009155, exon 5 of 5)	exon (NM_009155, exon 5 of 5)	8391	NM_009155	20363	Mm.392203	NM_009155	ENSMUSG00000064373	Selenop	AU018766|D15Ucla1|Se-P|Sepp1|selp	selenoprotein P	protein-coding
mm_119626.1	chr14	51145337	51145347	+	1	NA	3' UTR (NM_011271, exon 2 of 2)	3' UTR (NM_011271, exon 2 of 2)	1425	NM_011271	19752	Mm.235538	NM_011271	ENSMUSG00000035896	Rnase1	AI574248|Rib-1|Rib1	ribonuclease, RNase A family, 1 (pancreatic)	protein-coding
mm_136142.1	chr16	87440552	87440612	-	1	NA	promoter-TSS (NM_016924)	promoter-TSS (NM_016924)	10	NM_016924	53858	Mm.162406	NM_016924	ENSMUSG00000041079	Rwdd2b	ORF5	RWD domain containing 2B	protein-coding
mm_119151.1	chr14	31495098	31495181	+	1	NA	promoter-TSS (NM_025907)	promoter-TSS (NM_025907)	60	NM_028932	74427	Mm.491208	NM_028932	ENSMUSG00000021890	Eaf1	4933403C17Rik|AI666536	ELL associated factor 1	protein-coding
mm_37741.1	chr4	129595110	129595113	-	1	NA	exon (NM_018799, exon 6 of 11)	exon (NM_018799, exon 6 of 11)	5537	NM_018799	54709	Mm.250874	NM_018799	ENSMUSG00000028798	Eif3i	36kDa|D4Ertd632e|Eif3s2|Trip1	eukaryotic translation initiation factor 3, subunit I	protein-coding
mm_20162.1	chr2	122150988	122150998	-	1	NA	exon (NM_009735, exon 2 of 4)	exon (NM_009735, exon 2 of 4)	3306	NM_009735	12010	Mm.163	NM_009735	ENSMUSG00000060802	B2m	Ly-m11|beta2-m|beta2m	beta-2 microglobulin	protein-coding
mm_80438.1	chr9	77941235	77941244	+	1	NA	intron (NM_134255, intron 1 of 7)	intron (NM_134255, intron 1 of 7)	23874	NM_134255	68801	Mm.430736	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	ELOVL family member 5, elongation of long chain fatty acids (yeast)	protein-coding
mm_117817.1	chr13	98013378	98013382	-	1	NA	intron (NM_012026, intron 9 of 35)	B1_Mur1|SINE|Alu	192785	NM_012026	110596	Mm.252718	NM_012026	ENSMUSG00000021662	Arhgef28	9230110L08Rik|AI323540|D13Bwg1089e|RIP2|Rgnef|RhoGEF|Rhoip2|p190RhoGEF	Rho guanine nucleotide exchange factor (GEF) 28	protein-coding
mm_114817.1	chr13	91624298	91624304	+	1	NA	intron (NM_024186, intron 4 of 15)	Lx6|LINE|L1	-117220	NM_028790	74156	Mm.275963	NM_028790	ENSMUSG00000021620	Acot12	1300004O04Rik|4930449F15Rik|AV027244|Cach|mCACH-1	acyl-CoA thioesterase 12	protein-coding
mm_64383.1	chr7	142474991	142475001	+	1	NA	intron (NM_001271508, intron 1 of 10)	intron (NM_001271508, intron 1 of 10)	-2017	NM_001271523	16985	Mm.234003	NM_019391	ENSMUSG00000018819	Lsp1	Lsp-1|WP34|p50|pp52	lymphocyte specific 1	protein-coding
mm_99512.1	chr11	103103052	103103115	+	1	NA	5' UTR (NM_025988, exon 2 of 10)	5' UTR (NM_025988, exon 2 of 10)	1395	NM_025988	67131	Mm.390367	NM_025988	ENSMUSG00000056938	Acbd4	2010009P05Rik|2010015A21Rik|AI849317	acyl-Coenzyme A binding domain containing 4	protein-coding
mm_76798.1	chr8	103347532	103347546	-	1	NA	promoter-TSS (NR_036588)	promoter-TSS (NR_036588)	-5	NR_036588	69794	Mm.396139	NR_036588	ENSMUSG00000110340	1600027J07Rik	-	RIKEN cDNA 1600027J07 gene	ncRNA
mm_18666.1	chr2	70825404	70825455	-	1	NA	promoter-TSS (NM_172664)	promoter-TSS (NM_172664)	51	NM_172664	228012	Mm.136511	NM_172664	ENSMUSG00000041997	Tlk1	4930545J15Rik	tousled-like kinase 1	protein-coding
mm_63266.1	chr7	126759683	126759710	+	1	NA	promoter-TSS (NM_011952)	promoter-TSS (NM_011952)	70	NM_011952	26417	Mm.8385	NM_011952	ENSMUSG00000063065	Mapk3	Erk-1|Erk1|Ert2|Esrk1|Mnk1|Mtap2k|Prkm3|p44|p44erk1|p44mapk	mitogen-activated protein kinase 3	protein-coding
mm_137002.1	chr17	17491486	17491496	+	1	NA	Intergenic	Intergenic	88805	NM_025681	66643	Mm.268018	NM_025681	ENSMUSG00000047786	Lix1	5730466L18Rik	limb and CNS expressed 1	protein-coding
mm_5259.1	chr1	16688144	16688156	-	1	NA	promoter-TSS (NM_001159711)	promoter-TSS (NM_001159711)	-306	NM_001159711	17087	Mm.116844	NM_016923	ENSMUSG00000025779	Ly96	ESOP-1|MD-2|MD2	lymphocyte antigen 96	protein-coding
mm_82769.1	chr9	26923093	26923095	-	1	NA	promoter-TSS (NM_001281475)	promoter-TSS (NM_001281475)	-13	NM_001281475	382064	Mm.335028	NM_001177509	ENSMUSG00000079644	Gm1110	-	predicted gene 1110	protein-coding
mm_163051.1	chr11	58421081	58421087	+	1	NA	promoter-TSS (NM_027239)	promoter-TSS (NM_027239)	-27	NM_027239	69864	Mm.45641	NM_027239	ENSMUSG00000013653	1810065E05Rik	AV047390	RIKEN cDNA 1810065E05 gene	protein-coding
mm_135931.1	chr16	73958358	73958368	-	1	NA	exon (NM_175549, exon 15 of 28)	exon (NM_175549, exon 15 of 28)	383704	NR_030464	751561		NR_030464	ENSMUSG00000104758	Mir691	Mirn691|mir-691|mmu-mir-691	microRNA 691	ncRNA
mm_70246.1	chr8	3392998	3393015	+	1	NA	promoter-TSS (NM_133962)	promoter-TSS (NM_133962)	-2	NM_133962	102098	Mm.170461	NM_133962	ENSMUSG00000004568	Arhgef18	AI467246|D030053O22Rik	rho/rac guanine nucleotide exchange factor (GEF) 18	protein-coding
mm_112327.1	chr12	115604412	115604432	-	1	NA	Intergenic	Intergenic	91372	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
mm_92541.1	chr10	79645750	79645762	-	1	NA	promoter-TSS (NM_001033473)	promoter-TSS (NM_001033473)	-18	NM_001033473	382384	Mm.244510	NM_001033473	ENSMUSG00000035963	Odf3l2	Gm1157	outer dense fiber of sperm tails 3-like 2	protein-coding
mm_110972.1	chr12	76962071	76962083	-	1	NA	5' UTR (NM_001146176, exon 1 of 4)	5' UTR (NM_001146176, exon 1 of 4)	171	NM_008558	17187	Mm.268548	NM_008558	ENSMUSG00000059436	Max	AA960152|AI875693|bHLHd4|bHLHd5|bHLHd6|bHLHd7|bHLHd8	Max protein	protein-coding
mm_2700.1	chr1	127868772	127868780	+	1	NA	promoter-TSS (NM_178690)	promoter-TSS (NM_178690)	3	NM_178690	226407	Mm.489713	NM_178690	ENSMUSG00000036104	Rab3gap1	1700003B17Rik|4732493F09Rik|AL117896|Rab3gap|p130	RAB3 GTPase activating protein subunit 1	protein-coding
mm_49820.1	chr6	37530158	37530158	+	1	NA	promoter-TSS (NM_145364)	promoter-TSS (NM_145364)	-15	NM_145364	208665	Mm.262635	NM_145364	ENSMUSG00000038641	Akr1d1	-	aldo-keto reductase family 1, member D1	protein-coding
mm_44746.1	chr5	31219265	31219267	-	1	NA	intron (NM_008014, intron 1 of 9)	intron (NM_008014, intron 1 of 9)	1279	NM_008014	14208	Mm.14501	NM_008014	ENSMUSG00000029147	Ppm1g	AI385652|Fin13	protein phosphatase 1G (formerly 2C), magnesium-dependent, gamma isoform	protein-coding
mm_171766.1	chr5	107900600	107900601	+	1	NA	promoter-TSS (NM_016980)	promoter-TSS (NM_016980)	72	NM_016980	100503670	Mm.277897	NM_016980	ENSMUSG00000058558	Rpl5	U21RNA	ribosomal protein L5	protein-coding
mm_152840.1	chr19	23448290	23448300	-	1	NA	promoter-TSS (NM_174857)	promoter-TSS (NM_174857)	27	NM_174857	71738	Mm.50841	NM_174857	ENSMUSG00000033207	Mamdc2	1200015L10Rik|AI591564|mamcan	MAM domain containing 2	protein-coding
mm_104686.1	chr11	97744660	97744774	-	1	NA	promoter-TSS (NR_106180)	promoter-TSS (NR_106180)	-13	NM_054051	108083	Mm.39700	NM_054051	ENSMUSG00000018547	Pip4k2b	AI848124|PI5P4Kbeta|Pip5k2b|c11	phosphatidylinositol-5-phosphate 4-kinase, type II, beta	protein-coding
mm_65808.1	chr7	29006145	29006193	-	1	NA	intron (NM_009109, intron 101 of 105)	RLTR15|LTR|ERVK	23315	NM_008279	26411	Mm.148278	NM_008279	ENSMUSG00000037337	Map4k1	Hpk1|mHPK1	mitogen-activated protein kinase kinase kinase kinase 1	protein-coding
mm_140446.1	chr17	88581960	88581974	+	1	NA	intron (NM_028658, intron 19 of 21)	intron (NM_028658, intron 19 of 21)	-44588	NM_029858	77057	Mm.482203	NM_029858	ENSMUSG00000033855	Ston1	4921524J06Rik|C86231|Salf|Sblf	stonin 1	protein-coding
mm_40000.1	chr5	32746120	32746124	+	1	NA	intron (NM_001347332, intron 1 of 8)	intron (NM_001347332, intron 1 of 8)	220	NM_001347332	320951	Mm.273765	NM_177298	ENSMUSG00000023452	Pisd	9030221M09Rik	phosphatidylserine decarboxylase	protein-coding
mm_171437.1	chr4	141060465	141060465	-	1	NA	promoter-TSS (NM_001145958)	promoter-TSS (NM_001145958)	80	NM_001145958	230872	Mm.80685	NM_172122	ENSMUSG00000040860	Crocc	-	ciliary rootlet coiled-coil, rootletin	protein-coding
mm_124157.1	chr14	93371749	93371752	-	1	NA	intron (NM_001271798, intron 2 of 3)	intron (NM_001271798, intron 2 of 3)	517138	NM_001271800	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding
mm_102807.1	chr11	68871884	68871927	-	1	NA	Intergenic	Intergenic	-16648	NM_177060	320040	Mm.305696	NM_177060	ENSMUSG00000046490	Rnf222	9930039A11Rik	ring finger protein 222	protein-coding
mm_16718.1	chr2	7147782	7147785	-	1	NA	intron (NM_001110231, intron 3 of 15)	B4A|SINE|B4	-66481	NM_001160292	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_26018.1	chr3	135438380	135438390	+	1	NA	promoter-TSS (NM_025356)	promoter-TSS (NM_025356)	280	NR_030689	319587	Mm.358971	NR_030689	ENSMUSG00000097032	4930539J05Rik	8030475D13Rik	RIKEN cDNA 4930539J05 gene	ncRNA
mm_3010.1	chr1	133360255	133360265	+	1	NA	TTS (NM_031193)	TTS (NM_031193)	-3312	NM_175443	214253	Mm.52111	NM_175443	ENSMUSG00000070644	Etnk2	4933417N20Rik|AI197444|EKI 2|Eki2|Tuc1	ethanolamine kinase 2	protein-coding
mm_147850.1	chr18	63692280	63692290	-	1	NA	promoter-TSS (NM_016792)	promoter-TSS (NM_016792)	74	NM_016792	53382	Mm.19169	NM_016792	ENSMUSG00000024583	Txnl1	32kDa|TRP32|Txnl	thioredoxin-like 1	protein-coding
mm_33521.1	chr4	130930785	130930802	+	1	NA	exon (NM_010686, exon 6 of 8)	exon (NM_010686, exon 6 of 8)	-13592	NM_010769	17180	Mm.271796	NM_010769	ENSMUSG00000040533	Matn1	CMP|Crtm|Mat1|matrilin-1	matrilin 1, cartilage matrix protein	protein-coding
mm_135568.1	chr16	50192891	50192899	-	1	NA	3' UTR (NM_027444, exon 17 of 17)	3' UTR (NM_027444, exon 17 of 17)	-120043	NR_045935	224180	Mm.146439	NM_175010		Gm4827	B130050K08|EG224180	predicted gene 4827	ncRNA
mm_102986.1	chr11	69682071	69682079	-	1	NA	promoter-TSS (NM_001163571)	promoter-TSS (NM_001163571)	9	NM_001163571	80886	Mm.284592	NM_030702	ENSMUSG00000005204	Senp3	AA408656|Smt3ip|Smt3ip1	SUMO/sentrin specific peptidase 3	protein-coding
mm_138164.1	chr17	34261854	34261858	+	1	NA	Intergenic	Intergenic	-1371	NM_207105	14961	Mm.254067	NM_207105	ENSMUSG00000073421	H2-Ab1	AI845868|Abeta|H-2Ab|H2-Ab|I-Abeta|IAb|Ia-2|Ia2|Rmcs1	histocompatibility 2, class II antigen A, beta 1	protein-coding
mm_84726.1	chr9	74863396	74863436	-	1	NA	intron (NM_008262, intron 1 of 1)	CpG	1495	NM_008262	15379	Mm.303355	NM_008262	ENSMUSG00000043013	Onecut1	D9Ertd423e|HNF-6|Hfh12|Hnf6|Hnf6b|OC-1|Oc1	one cut domain, family member 1	protein-coding
mm_5167.1	chr1	10162225	10162247	-	1	NA	intron (NM_001102430, intron 22 of 37)	intron (NM_001102430, intron 22 of 37)	70434	NM_001102430	211673	Mm.229141	NM_001102430	ENSMUSG00000067851	Arfgef1	ARFGEP1|BIG1|D130059B05Rik|D730028O18Rik|P200	ADP-ribosylation factor guanine nucleotide-exchange factor 1(brefeldin A-inhibited)	protein-coding
mm_106835.1	chr12	8006246	8006252	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	28572	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_144957.1	chr18	37813370	37813385	+	1	NA	intron (NM_033581, intron 1 of 3)	(CA)n|Simple_repeat|Simple_repeat	-1702	NM_033582	93707	Mm.247203	NM_033582	ENSMUSG00000023036	Pcdhgc4	-	protocadherin gamma subfamily C, 4	protein-coding
mm_160340.1	chr8	15046020	15046020	-	1	NA	promoter-TSS (NR_037972)	promoter-TSS (NR_037972)	58	NR_037972	434285	Mm.334425	NM_001007591	ENSMUSG00000049008	BB014433	-	expressed sequence BB014433	ncRNA
mm_138845.1	chr17	40561481	40561487	+	1	NA	promoter-TSS (NM_001287195)	promoter-TSS (NM_001287195)	-23	NM_001177529	433107	Mm.353122	NM_001177529	ENSMUSG00000092043	Esp6	EG433107|Esp5|Gm5494	exocrine gland secreted peptide 6	protein-coding
mm_118018.1	chr13	100786539	100786556	-	1	NA	promoter-TSS (NM_172301)	promoter-TSS (NM_172301)	-61	NM_172301	268697	Mm.260114	NM_172301	ENSMUSG00000041431	Ccnb1	Ccnb1-rs1|Ccnb1-rs13|CycB1|Cycb-4|Cycb-5|Cycb1-rs1	cyclin B1	protein-coding
mm_73604.1	chr8	109999248	109999261	+	1	NA	3' UTR (NM_146214, exon 12 of 12)	3' UTR (NM_146214, exon 12 of 12)	8818	NM_146214	234724	Mm.28110	NM_146214	ENSMUSG00000001670	Tat	-	tyrosine aminotransferase	protein-coding
mm_107493.1	chr12	38783504	38783527	+	1	NA	promoter-TSS (NM_001163154)	promoter-TSS (NM_001163154)	-196	NM_001163154	14009	Mm.4866	NM_007960	ENSMUSG00000004151	Etv1	ER81|Etsrp81	ets variant 1	protein-coding
mm_22946.1	chr3	32074096	32074101	+	1	NA	intron (NM_028231, intron 2 of 5)	intron (NM_028231, intron 2 of 5)	171395	NM_028231	72413	Mm.64790	NM_028231	ENSMUSG00000037610	Kcnmb2	2700049B16Rik|3110031N04Rik	potassium large conductance calcium-activated channel, subfamily M, beta member 2	protein-coding
mm_74867.1	chr8	25007962	25007965	-	1	NA	intron (NM_001270996, intron 1 of 21)	intron (NM_001270996, intron 1 of 21)	8959	NM_001270996	11502	Mm.28908	NM_007404	ENSMUSG00000031555	Adam9	AU020942|MDC9|Mltng|mKIAA0021	a disintegrin and metallopeptidase domain 9 (meltrin gamma)	protein-coding
mm_17329.1	chr2	26503815	26503836	-	1	NA	promoter-TSS (NM_008714)	promoter-TSS (NM_008714)	-3	NM_008714	18128	Mm.290610	NM_008714	ENSMUSG00000026923	Notch1	9930111A19Rik|Mis6|N1|Tan1|lin-12	notch 1	protein-coding
mm_104197.1	chr11	87980471	87980492	-	1	NA	3' UTR (NM_001168471, exon 3 of 3)	3' UTR (NM_001168471, exon 3 of 3)	6104	NM_001168472	68097	Mm.246436	NM_026556	ENSMUSG00000020483	Dynll2	1700064A15Rik|6720463E02Rik|C87222|DLC8|DLC8b|Dlc2	dynein light chain LC8-type 2	protein-coding
mm_142440.1	chr17	45572442	45572477	-	1	NA	intron (NM_008302, intron 1 of 10)	intron (NM_008302, intron 1 of 10)	802	NM_008302	15516	Mm.2180	NM_008302	ENSMUSG00000023944	Hsp90ab1	90kDa|AL022974|C81438|Hsp84|Hsp84-1|Hsp90|Hspcb	heat shock protein 90 alpha (cytosolic), class B member 1	protein-coding
mm_149440.1	chr19	11480290	11480316	+	1	NA	exon (NM_028595, exon 6 of 7)	exon (NM_028595, exon 6 of 7)	10935	NM_028595	73656	Mm.440719	NM_028595	ENSMUSG00000079419	Ms4a6c	2200009H22Rik|2210417N07Rik	membrane-spanning 4-domains, subfamily A, member 6C	protein-coding
mm_33646.1	chr4	133039392	133039405	+	1	NA	intron (NM_146155, intron 2 of 6)	CpG	27892	NM_146155	230793	Mm.31816	NM_146155	ENSMUSG00000037692	Ahdc1	D030015G18Rik	AT hook, DNA binding motif, containing 1	protein-coding
mm_92071.1	chr10	62599515	62599518	-	1	NA	intron (NM_019553, intron 1 of 14)	intron (NM_019553, intron 1 of 14)	2782	NM_019553	56200	Mm.413275	NM_019553	ENSMUSG00000020075	Ddx21	AI255159|AL022742|D10Ertd645e|D10Wsu42e	DEAD (Asp-Glu-Ala-Asp) box polypeptide 21	protein-coding
mm_41466.1	chr5	91074612	91074629	+	1	NA	promoter-TSS (NM_007950)	promoter-TSS (NM_007950)	3	NM_007950	13874	Mm.4791	NM_007950	ENSMUSG00000029377	Ereg	EPR	epiregulin	protein-coding
mm_138986.1	chr17	45487453	45487463	+	1	NA	Intergenic	Intergenic	-12520	NM_027649	71020	Mm.44257	NM_027649	ENSMUSG00000023935	Spats1	1700011H05Rik|4933400B06Rik|Daip2|Ddip|Srsp1	spermatogenesis associated, serine-rich 1	protein-coding
mm_139545.1	chr17	56764739	56764763	+	1	NA	promoter-TSS (NM_144858)	promoter-TSS (NM_144858)	0	NM_144858	224907	Mm.293973	NM_144858	ENSMUSG00000007603	Dus3l	AI662135|AW557805	dihydrouridine synthase 3-like (S. cerevisiae)	protein-coding
mm_52173.1	chr6	99189083	99189106	+	1	NA	intron (NM_001347345, intron 4 of 19)	intron (NM_001347345, intron 4 of 19)	77421	NM_001197321	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_128282.1	chr15	37007275	37007353	-	1	NA	promoter-TSS (NM_026521)	promoter-TSS (NM_026521)	88	NM_026521	68036	Mm.371631	NM_026521	ENSMUSG00000062397	Zfp706	3110006P09Rik|AA793007|AW536850|C77232|Znf706	zinc finger protein 706	protein-coding
mm_173302.1	chrY	67624431	67624431	-	1	NA	Intergenic	Intergenic	-284384	NM_001160135	100039574	Mm.458579	NM_001160135	ENSMUSG00000094739	Gm20806	-	predicted gene, 20806	protein-coding
mm_146035.1	chr18	69521922	69521925	+	1	NA	intron (NM_013685, intron 6 of 19)	intron (NM_013685, intron 6 of 19)	176202	NM_001083967	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding
mm_22901.1	chr3	30855731	30855758	+	1	NA	promoter-TSS (NM_027965)	promoter-TSS (NM_027965)	-206	NM_001134385	71862	Mm.272019	NM_027965	ENSMUSG00000037661	Gpr160	1700025D19Rik|GPCR150	G protein-coupled receptor 160	protein-coding
mm_90217.1	chr10	121033986	121034012	+	1	NA	promoter-TSS (NM_011915)	promoter-TSS (NM_011915)	-5	NM_011915	24117	Mm.32831	NM_011915	ENSMUSG00000020218	Wif1	AW107799|WIF-1	Wnt inhibitory factor 1	protein-coding
mm_53642.1	chr6	140623477	140623615	+	1	NA	promoter-TSS (NM_009637)	promoter-TSS (NM_009637)	44	NM_001005605	11569	Mm.86453	NM_009637	ENSMUSG00000030232	Aebp2	AU023766|B230313N05Rik	AE binding protein 2	protein-coding
mm_24863.1	chr3	95929333	95929343	+	1	NA	promoter-TSS (NM_001253757)	promoter-TSS (NM_001253757)	81	NM_023210	66471	Mm.218657	NM_023210	ENSMUSG00000015749	Anp32e	2810018A15Rik|AI047746|AI326868|CPD1|LANP-L|LANPL|mLANP-L	acidic (leucine-rich) nuclear phosphoprotein 32 family, member E	protein-coding
mm_148212.1	chr18	80200577	80200583	-	1	NA	promoter-TSS (NM_199197)	promoter-TSS (NM_199197)	39	NM_199197	68731	Mm.186936	NM_199197	ENSMUSG00000024570	Rbfa	1110032A13Rik|AI595940	ribosome binding factor A	protein-coding
mm_11156.1	chr2	28542437	28542447	+	1	NA	exon (NM_009058, exon 3 of 18)	exon (NM_009058, exon 3 of 18)	8978	NM_001145836	19730	Mm.5236	NM_009058	ENSMUSG00000026821	Ralgds	Gnds|Rgds|mKIAA1308	ral guanine nucleotide dissociation stimulator	protein-coding
mm_164378.1	chr16	30436129	30436129	-	1	NA	Intergenic	Intergenic	-47599	NM_001128096	224088	Mm.8924	NM_001128094	ENSMUSG00000022533	Atp13a3	AU022875|Gm1745|Gm541|Gm542	ATPase type 13A3	protein-coding
mm_67722.1	chr7	90067985	90067999	-	1	NA	Intergenic	Intergenic	38833	NR_110364	319711	Mm.31753	NR_015614	ENSMUSG00000097585	E230029C05Rik	AI452102|B230337J15	RIKEN cDNA E230029C05 gene	ncRNA
mm_920.1	chr1	55131096	55131108	+	1	NA	promoter-TSS (NM_025283)	promoter-TSS (NM_025283)	-143	NM_001310585	19070	Mm.291037	NM_025283	ENSMUSG00000025979	Mob4	2610109B12Rik|Mobkl3|Phocn|Prei3	MOB family member 4, phocein	protein-coding
mm_155949.1	chrX	105079765	105079803	+	1	NA	promoter-TSS (NM_001281871)	promoter-TSS (NM_001281871)	28	NM_026312	67683	Mm.273405	NM_026312	ENSMUSG00000031226	Pbdc1	2610029G23Rik	polysaccharide biosynthesis domain containing 1	protein-coding
mm_88760.1	chr10	80330128	80330211	+	1	NA	promoter-TSS (NM_139292)	promoter-TSS (NM_139292)	24	NM_139292	70335	Mm.28147	NM_139292	ENSMUSG00000035504	Reep6	0610011M24Rik|Dp1l1	receptor accessory protein 6	protein-coding
mm_28006.1	chr3	83031103	83031123	-	1	NA	exon (NM_010196, exon 5 of 5)	exon (NM_010196, exon 5 of 5)	4960	NM_001111048	14161	Mm.88793	NM_010196	ENSMUSG00000028001	Fga	ENSMUSG00000059807|Fib	fibrinogen alpha chain	protein-coding
mm_125270.1	chr15	36139700	36139702	+	1	NA	intron (NM_001195748, intron 2 of 27)	intron (NM_001195748, intron 2 of 27)	699	NM_001195748	626596	Mm.321798	NM_001195748	ENSMUSG00000037627	Rgs22	-	regulator of G-protein signalling 22	protein-coding
mm_106661.1	chr11	121325599	121325602	-	1	NA	Intergenic	ID_B1|SINE|B4	28847	NM_025793	66840	Mm.103986	NM_025793	ENSMUSG00000025173	Wdr45b	0610008N23Rik|AA408735|D16Bwg0193e|WIPI-3|Wdr45l	WD repeat domain 45B	protein-coding
mm_136559.1	chr17	3115280	3115291	+	1	NA	5' UTR (NM_134123, exon 1 of 20)	5' UTR (NM_134123, exon 1 of 20)	313	NM_134123	106583	Mm.124373	NM_134123	ENSMUSG00000046201	Scaf8	A630086M08Rik|A930036P18Rik|AA408306|AI447644|AI448652|AU015035|Rbm16|mKIAA1116	SR-related CTD-associated factor 8	protein-coding
mm_6572.1	chr1	75192632	75192682	-	1	NA	promoter-TSS (NM_001288613)	promoter-TSS (NM_001288613)	497	NR_051999	52231	Mm.259326	NM_026187	ENSMUSG00000026199	Ankzf1	1300008P06Rik|2810025E10Rik|D1Ertd161e	ankyrin repeat and zinc finger domain containing 1	protein-coding
mm_23836.1	chr3	82358101	82358111	+	1	NA	promoter-TSS (NM_001081230)	promoter-TSS (NM_001081230)	34	NM_001081230	213582	Mm.271269	NM_001081230	ENSMUSG00000033900	Map9	5033421J10Rik|5330427D05Rik|ASAP|Mtap9	microtubule-associated protein 9	protein-coding
mm_25180.1	chr3	103279850	103279873	+	1	NA	5' UTR (NM_053170, exon 1 of 20)	5' UTR (NM_053170, exon 1 of 20)	568	NM_001079830	94093	Mm.195036	NM_053170	ENSMUSG00000033014	Trim33	8030451N04Rik|AI413936|Ecto|Tif1g	tripartite motif-containing 33	protein-coding
mm_61944.1	chr7	90183151	90183154	+	1	NA	intron (NM_001252520, intron 13 of 20)	intron (NM_001252520, intron 13 of 20)	52920	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_3736.1	chr1	155122419	155122425	+	1	NA	Intergenic	Intergenic	-22786	NM_010500	15939	Mm.12246	NM_010500	ENSMUSG00000056708	Ier5	-	immediate early response 5	protein-coding
mm_139399.1	chr17	52307575	52307622	+	1	NA	Intergenic	Intergenic	-295111	NM_001031811	211468	Mm.399068	NM_001031811	ENSMUSG00000035580	Kcnh8	C130090D05Rik|ELK|ELK1|ELK3|Kv12.1	potassium voltage-gated channel, subfamily H (eag-related), member 8	protein-coding
mm_136172.1	chr16	88647787	88647799	-	1	NA	promoter-TSS (NM_027105)	promoter-TSS (NM_027105)	3	NM_027105	69533	Mm.30967	NM_027105	ENSMUSG00000071471	Krtap26-1	2310002B14Rik|AI507462	keratin associated protein 26-1	protein-coding
mm_125288.1	chr15	36726668	36726696	+	1	NA	Intergenic	RMER17C|LTR|ERVK	64250	NM_001253807	22631	Mm.3360	NM_011740	ENSMUSG00000022285	Ywhaz	1110013I11Rik|14-3-3zeta|AI596267|AL022924|AU020854	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide	protein-coding
mm_132871.1	chr16	48611810	48611820	+	1	NA	intron (NM_010816, intron 20 of 26)	B1_Mur3|SINE|Alu	160141	NM_198297	77647	Mm.167298	NM_198297	ENSMUSG00000030775	Trat1	C030046M14Rik|Tcrim|Trim	T cell receptor associated transmembrane adaptor 1	protein-coding
mm_155740.1	chrX	96166590	96166600	+	1	NA	exon (NM_010833, exon 13 of 13)	exon (NM_010833, exon 13 of 13)	70550	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_14280.1	chr2	128796942	128796972	+	1	NA	intron (NM_008587, intron 18 of 18)	intron (NM_008587, intron 18 of 18)	-21346	NM_028248	72477	Mm.259688	NM_028248	ENSMUSG00000014353	Tmem87b	2610301K12Rik|2810431I02Rik|AU014804	transmembrane protein 87B	protein-coding
mm_113961.1	chr13	51171296	51171305	+	1	NA	5' UTR (NM_029173, exon 1 of 2)	5' UTR (NM_029173, exon 1 of 2)	275	NM_029173	75124	Mm.179243	NM_029173	ENSMUSG00000021396	Nxnl2	4930519N16Rik|Rdcvf2	nucleoredoxin-like 2	protein-coding
mm_86176.1	chr9	119190266	119190266	-	1	NA	intron (NM_001037749, intron 1 of 11)	intron (NM_001037749, intron 1 of 11)	127	NM_001037749	382113	Mm.335525	NM_001037749	ENSMUSG00000070280	Slc22a14	Gm1128	solute carrier family 22 (organic cation transporter), member 14	protein-coding
mm_43536.1	chr5	137350102	137350117	+	1	NA	promoter-TSS (NM_010144)	promoter-TSS (NM_010144)	0	NM_001159571	13846	Mm.34533	NM_010144	ENSMUSG00000029710	Ephb4	AI042935|Htk|MDK2|Myk1|Tyro11	Eph receptor B4	protein-coding
mm_114758.1	chr13	85189434	85189487	+	1	NA	promoter-TSS (NM_001347588)	promoter-TSS (NM_001347588)	75	NM_023243	66671	Mm.18474	NM_023243	ENSMUSG00000021548	Ccnh	6330408H09Rik|AI661354|AV102684|AW538719	cyclin H	protein-coding
mm_90823.1	chr10	7936059	7936062	-	1	NA	intron (NM_138667, intron 1 of 6)	intron (NM_138667, intron 1 of 6)	20063	NM_138667	68652	Mm.193041	NM_138667	ENSMUSG00000015755	Tab2	1110030N06Rik|A530078N03Rik|Map3k7ip2|mKIAA0733	TGF-beta activated kinase 1/MAP3K7 binding protein 2	protein-coding
mm_50481.1	chr6	48988274	48988286	+	1	NA	exon (NM_172888, exon 1 of 5)	exon (NM_172888, exon 1 of 5)	1419	NM_172888	243377	Mm.446302	NM_172888	ENSMUSG00000039215	Svs1	9530003A11	seminal vesicle secretory protein 1	protein-coding
mm_9162.1	chr1	170965796	170965811	-	1	NA	exon (NM_001077189, exon 5 of 8)	exon (NM_001077189, exon 5 of 8)	10268	NM_001077189	14130	Mm.425062	NM_010187	ENSMUSG00000026656	Fcgr2b	AI528646|CD32|F630109E10Rik|Fc[g]RII|FcgRII|Fcgr2|Fcgr2a|Fcr-2|Fcr-3|Ly-17|Ly-m20|LyM-1|Lym-1|fcRII	Fc receptor, IgG, low affinity IIb	protein-coding
mm_117110.1	chr13	60177358	60177373	-	1	NA	5' UTR (NM_008086, exon 1 of 1)	5' UTR (NM_008086, exon 1 of 1)	170	NM_008086	14451	Mm.22701	NM_008086	ENSMUSG00000052957	Gas1	AW554192|Gas-1	growth arrest specific 1	protein-coding
mm_47592.1	chr5	124862217	124862227	-	1	NA	promoter-TSS (NM_001081750)	promoter-TSS (NM_001081750)	-1	NM_144819	215707	Mm.389693	NM_144819	ENSMUSG00000037979	Ccdc92	AW050178|D5Bwg0834e	coiled-coil domain containing 92	protein-coding
mm_164914.1	chr18	74531256	74531260	+	1	NA	promoter-TSS (NR_045368)	promoter-TSS (NR_045368)	-134	NR_045368	73606	Mm.444734	NR_045368		1700120E14Rik	-	RIKEN cDNA 1700120E14 gene	ncRNA
mm_108954.1	chr12	102368249	102368258	+	1	NA	intron (NM_177620, intron 5 of 9)	intron (NM_177620, intron 5 of 9)	71560	NM_011175	19141	Mm.17185	NM_011175	ENSMUSG00000021190	Lgmn	AEP|AI746452|AU022324|Prsc1	legumain	protein-coding
mm_172628.1	chr8	20410361	20410362	-	1	NA	non-coding (NR_028428, exon 2 of 6)	non-coding (NR_028428, exon 2 of 6)	14453	NR_028428	381598	Mm.359054	NM_001024708	ENSMUSG00000071793	2610005L07Rik	2810038F24Rik|6720476A01Rik	cadherin 11 pseudogene	pseudo
mm_79790.1	chr9	63731621	63731639	+	1	NA	intron (NM_016769, intron 1 of 8)	intron (NM_016769, intron 1 of 8)	26364	NM_016769	17127	Mm.7320	NM_016769	ENSMUSG00000032402	Smad3	AU022421|Madh3	SMAD family member 3	protein-coding
mm_122107.1	chr14	30921978	30921992	-	1	NA	exon (NM_008407, exon 3 of 21)	exon (NM_008407, exon 3 of 21)	1602	NM_008407	16426	Mm.4517	NM_008407	ENSMUSG00000006522	Itih3	AW108094|ITI-HC3|Intin3|Itih-3	inter-alpha trypsin inhibitor, heavy chain 3	protein-coding
mm_107539.1	chr12	40572832	40572845	+	1	NA	intron (NM_172803, intron 1 of 52)	intron (NM_172803, intron 1 of 52)	126785	NM_172803	238130	Mm.341423	NM_172803	ENSMUSG00000035954	Dock4	5330406C03|6330411N01Rik|AF263288|C030023J22|mKIAA0716	dedicator of cytokinesis 4	protein-coding
mm_19159.1	chr2	83722989	83722990	-	1	NA	Intergenic	Intergenic	-1408	NM_008402	16410	Mm.227	NM_008402	ENSMUSG00000027087	Itgav	1110004F14Rik|2610028E01Rik|CD51|D430040G12Rik	integrin alpha V	protein-coding
mm_122252.1	chr14	34102664	34102668	-	1	NA	promoter-TSS (NM_001251843)	promoter-TSS (NM_001251843)	88	NM_001251843	105518	Mm.246608	NM_001251843	ENSMUSG00000095493	A630023A22Rik	AI461879	RIKEN cDNA A630023A22 gene	protein-coding
mm_107808.1	chr12	65039733	65039742	+	1	NA	intron (NM_177806, intron 1 of 13)	intron (NM_177806, intron 1 of 13)	3403	NM_177806	328110	Mm.283339	NM_177806	ENSMUSG00000035597	Prpf39	Srcs1	pre-mRNA processing factor 39	protein-coding
mm_164307.1	chr15	103897457	103897463	-	1	NA	exon (NM_009267, exon 3 of 4)	exon (NM_009267, exon 3 of 4)	1840	NM_009268	20771	Mm.30276	NM_009268		Mucl1	Spt-2|Spt2	mucin-like 1	protein-coding
mm_69852.1	chr7	141428000	141428008	-	1	NA	intron (NM_021316, intron 1 of 1)	intron (NM_021316, intron 1 of 1)	1416	NM_021316	57754	Mm.87027	NM_021316	ENSMUSG00000060240	Cend1	1500001H12Rik|AI415214|BM88	cell cycle exit and neuronal differentiation 1	protein-coding
mm_39747.1	chr5	29569821	29569830	+	1	NA	intron (NM_133907, intron 1 of 22)	intron (NM_133907, intron 1 of 22)	583	NM_133907	100763	Mm.137746	NM_133907	ENSMUSG00000039000	Ube3c	AI853514|mKIAA0010	ubiquitin protein ligase E3C	protein-coding
mm_76203.1	chr8	83106096	83106130	-	1	NA	Intergenic	MTE2a|LTR|ERVL-MaLR	-59239	NM_001111304	71310	Mm.24031	NM_027758	ENSMUSG00000031709	Tbc1d9	4933431N12Rik|AI847101|AW490653|C76116	TBC1 domain family, member 9	protein-coding
mm_118831.1	chr14	25607595	25607605	+	1	NA	intron (NM_001310666, intron 6 of 23)	CpG	4087	NM_001309430	100188919	Mm.473810	NM_001309430		Israa	-	immune system released activating agent	protein-coding
mm_61847.1	chr7	88297092	88297102	+	1	NA	exon (NM_009982, exon 3 of 7)	exon (NM_009982, exon 3 of 7)	19012	NM_001311790	13032	Mm.89295	NM_009982	ENSMUSG00000030560	Ctsc	AI047818|CatC|DPP1|DPPI	cathepsin C	protein-coding
mm_56426.1	chr6	97311055	97311068	-	1	NA	intron (NM_001346639, intron 11 of 22)	intron (NM_001346639, intron 11 of 22)	-58281	NM_001081157	320502	Mm.68163	NM_001081157	ENSMUSG00000044086	Lmod3	5430424A14Rik	leiomodin 3 (fetal)	protein-coding
mm_129394.1	chr15	78244840	78244850	-	1	NA	promoter-TSS (NM_008677)	promoter-TSS (NM_008677)	34	NM_008677	17972	Mm.2068	NM_008677	ENSMUSG00000071715	Ncf4	AI451400|p40phox	neutrophil cytosolic factor 4	protein-coding
mm_99326.1	chr11	101459725	101459766	+	1	NA	3' UTR (NM_012037, exon 6 of 6)	3' UTR (NM_012037, exon 6 of 6)	6454	NM_012037	26949	Mm.29210	NM_012037	ENSMUSG00000034993	Vat1	VAT-1	vesicle amine transport 1	protein-coding
mm_8598.1	chr1	156034766	156034779	-	1	NA	promoter-TSS (NM_001160180)	promoter-TSS (NM_001160180)	45	NM_001160019	208263	Mm.211654	NM_144791	ENSMUSG00000026466	Tor1aip1	LAP1|Lap1B	torsin A interacting protein 1	protein-coding
mm_70554.1	chr8	13060910	13060918	+	1	NA	promoter-TSS (NM_025834)	promoter-TSS (NM_025834)	6	NM_025834	66901	Mm.441140	NM_025834	ENSMUSG00000031445	Proz	1300015B06Rik	protein Z, vitamin K-dependent plasma glycoprotein	protein-coding
mm_28081.1	chr3	84582617	84582699	-	1	NA	promoter-TSS (NM_001293801)	promoter-TSS (NM_001293801)	-33	NM_001293801	99889	Mm.316536	NM_001081093	ENSMUSG00000074513	Arfip1	2310030I10Rik|Arfaptin|D3Ertd598e	ADP-ribosylation factor interacting protein 1	protein-coding
mm_13586.1	chr2	112383849	112383852	+	1	NA	intron (NM_024254, intron 1 of 9)	B1_Mus1|SINE|Alu	4639	NM_024254	72425	Mm.425091	NM_024254	ENSMUSG00000027132	Katnbl1	2410042D21Rik|AA166487|AA473307|AI467442	katanin p80 subunit B like 1	protein-coding
mm_151423.1	chr19	56826269	56826288	+	1	NA	promoter-TSS (NM_031387)	promoter-TSS (NM_031387)	3	NM_001002240	83561	Mm.247541	NM_031387	ENSMUSG00000025081	Tdrd1	MTR-1	tudor domain containing 1	protein-coding
mm_122576.1	chr14	50826920	50826941	-	1	NA	intron (NM_009351, intron 50 of 54)	intron (NM_009351, intron 50 of 54)	18984	NM_009632	11546	Mm.281482	NM_009632	ENSMUSG00000036023	Parp2	ARTD2|Adprt2|Adprtl2|Aspartl2|C78626|PARP-2	poly (ADP-ribose) polymerase family, member 2	protein-coding
mm_106111.1	chr11	116334148	116334179	-	1	NA	exon (NM_008240, exon 2 of 3)	exon (NM_008240, exon 2 of 3)	1191	NM_008240	15223	Mm.378938	NM_008240	ENSMUSG00000034227	Foxj1	FKHL-13|HFH-4|Hfh4	forkhead box J1	protein-coding
mm_3970.1	chr1	164181706	164181715	+	1	NA	exon (NM_007976, exon 7 of 25)	exon (NM_007976, exon 7 of 25)	-29493	NR_037987	100503816	Mm.398579	NR_037987	ENSMUSG00000086593	Gm16548	-	predicted gene 16548	ncRNA
mm_88514.1	chr10	78049861	78049867	+	1	NA	promoter-TSS (NM_019448)	promoter-TSS (NM_019448)	22	NM_019448	54427	Mm.13433	NM_019448	ENSMUSG00000000730	Dnmt3l	D6Ertd14e|ecat7	DNA (cytosine-5-)-methyltransferase 3-like	protein-coding
mm_32335.1	chr4	104389880	104389882	+	1	NA	intron (NM_010014, intron 1 of 6)	intron (NM_010014, intron 1 of 6)	22343	NM_177259	13131	Mm.289682	NM_010014	ENSMUSG00000028519	Dab1	AI956902|C630028C02Rik|scm|scr|scrambler|yot	disabled 1	protein-coding
mm_66926.1	chr7	61528841	61528847	-	1	NA	TTS (NR_045727)	TTS (NR_045727)	86483	NR_045727	319752	Mm.294476	NR_045727		B230209E15Rik	-	RIKEN cDNA B230209E15 gene	ncRNA
mm_86604.1	chr10	13502705	13502718	+	1	NA	intron (NM_025799, intron 1 of 6)	intron (NM_025799, intron 1 of 6)	1683	NM_025799	66848	Mm.26625	NM_025799	ENSMUSG00000019810	Fuca2	0610025O11Rik|5530401P20Rik	fucosidase, alpha-L- 2, plasma	protein-coding
mm_143793.1	chr17	81838415	81838442	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-100041	NM_011406	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_109042.1	chr12	104236240	104236245	+	1	NA	intron (NM_009251, intron 2 of 5)	intron (NM_009251, intron 2 of 5)	-11654	NR_033450	546546	Mm.390522	NM_001034870		Serpina3h	6C28|Spi2	serine (or cysteine) peptidase inhibitor, clade A, member 3H	pseudo
mm_85247.1	chr9	99136104	99136106	-	1	NA	intron (NM_029094, intron 1 of 23)	PB1D7|SINE|Alu	4106	NM_029094	74769	Mm.213128	NM_029094	ENSMUSG00000032462	Pik3cb	1110001J02Rik|AI447572|p110beta	phosphatidylinositol 3-kinase, catalytic, beta polypeptide	protein-coding
mm_60777.1	chr7	45559387	45559391	+	1	NA	exon (NM_025330, exon 5 of 9)	exon (NM_025330, exon 5 of 9)	4461	NM_025330	66065	Mm.285710	NM_025330	ENSMUSG00000030825	Hsd17b14	0610039E24Rik|Dhrs10|retSDR3	hydroxysteroid (17-beta) dehydrogenase 14	protein-coding
mm_80906.1	chr9	100643526	100643542	+	1	NA	promoter-TSS (NM_009282)	promoter-TSS (NM_009282)	-89	NM_009282	20842	Mm.42135	NM_009282	ENSMUSG00000037286	Stag1	AU045003|SA-1|Scc3	stromal antigen 1	protein-coding
mm_12506.1	chr2	71873366	71873374	+	1	NA	exon (NM_172665, exon 1 of 11)	exon (NM_172665, exon 1 of 11)	146	NM_172665	228026	Mm.34411	NM_172665	ENSMUSG00000006494	Pdk1	B830012B01|D530020C15Rik	pyruvate dehydrogenase kinase, isoenzyme 1	protein-coding
mm_100880.1	chr11	5976320	5976329	-	1	NA	intron (NM_007595, intron 17 of 20)	intron (NM_007595, intron 17 of 20)	20566	NM_019661	56418	Mm.294821	NM_019661	ENSMUSG00000002741	Ykt6	0610042I15Rik|1810013M05Rik|AW105923	YKT6 v-SNARE homolog (S. cerevisiae)	protein-coding
mm_82667.1	chr9	22130054	22130072	-	1	NA	exon (NM_001102404, exon 2 of 5)	exon (NM_001102404, exon 2 of 5)	535	NM_007388	11433	Mm.46354	NM_007388	ENSMUSG00000001348	Acp5	TRACP|TRAP	acid phosphatase 5, tartrate resistant	protein-coding
mm_14010.1	chr2	122147476	122147494	+	1	NA	promoter-TSS (NM_009735)	promoter-TSS (NM_009735)	-202	NM_009735	12010	Mm.163	NM_009735	ENSMUSG00000060802	B2m	Ly-m11|beta2-m|beta2m	beta-2 microglobulin	protein-coding
mm_100620.1	chr11	121592594	121592613	+	1	NA	intron (NM_029878, intron 25 of 38)	intron (NM_029878, intron 25 of 38)	-73261	NM_178763	319530	Mm.11395	NM_178763	ENSMUSG00000039238	Zfp750	A030007D23Rik|Znf750	zinc finger protein 750	protein-coding
mm_45749.1	chr5	86676329	86676335	-	1	NA	promoter-TSS (NM_177024)	promoter-TSS (NM_177024)	-34	NM_177024	319875	Mm.253994	NM_177024	ENSMUSG00000035861	Tmprss11b	9930019B18Rik|Tmprss11bnl	transmembrane protease, serine 11B	protein-coding
mm_121746.1	chr14	18893377	18893420	-	1	NA	intron (NM_144839, intron 1 of 5)	CpG	229	NM_144839	218793	Mm.23551	NM_144839	ENSMUSG00000058317	Ube2e2	BC016265	ubiquitin-conjugating enzyme E2E 2	protein-coding
mm_111380.1	chr12	87388190	87388247	-	1	NA	5' UTR (NM_011479, exon 1 of 12)	5' UTR (NM_011479, exon 1 of 12)	137	NM_011479	20773	Mm.565	NM_011479	ENSMUSG00000021036	Sptlc2	LCB2|LCB2a|Spt2	serine palmitoyltransferase, long chain base subunit 2	protein-coding
mm_67110.1	chr7	70359018	70359043	-	1	NA	intron (NM_183261, intron 1 of 2)	intron (NM_183261, intron 1 of 2)	1563	NM_009697	11819	Mm.158143	NM_009697	ENSMUSG00000030551	Nr2f2	2700033K02Rik|9430015G03Rik|ARP-1|Aporp1|COUP-TF2|COUP-TFII|COUPTFB|EAR3|SVP40|Tcfcoup2	nuclear receptor subfamily 2, group F, member 2	protein-coding
mm_111022.1	chr12	79089624	79089660	-	1	NA	promoter-TSS (NM_029988)	promoter-TSS (NM_029988)	28	NM_029988	110417	Mm.268317	NM_029988	ENSMUSG00000021120	Pigh	2210416H01Rik|A930028P05Rik	phosphatidylinositol glycan anchor biosynthesis, class H	protein-coding
mm_115031.1	chr13	99247777	99247792	+	1	NA	TTS (NM_001004149)	TTS (NM_001004149)	62961	NM_001004149	238803	Mm.343207	NM_001004149	ENSMUSG00000050919	Zfp366	DC-SCRIPT|Znf366	zinc finger protein 366	protein-coding
mm_63216.1	chr7	126272785	126272795	+	1	NA	5' UTR (NM_145587, exon 1 of 4)	5' UTR (NM_145587, exon 1 of 4)	171	NM_145587	104175	Mm.29660	NM_145587	ENSMUSG00000042978	Sbk1	Sbk	SH3-binding kinase 1	protein-coding
mm_60125.1	chr7	36700637	36700642	+	1	NA	intron (NM_172298, intron 1 of 1)	intron (NM_172298, intron 1 of 1)	2521	NM_172298	243931	Mm.44141	NM_172298	ENSMUSG00000021217	Tshz3	A630038G13Rik|Tsh3|Zfp537|mKIAA1474|teashirt3	teashirt zinc finger family member 3	protein-coding
mm_143994.1	chr17	87974874	87974911	-	1	NA	promoter-TSS (NM_010830)	promoter-TSS (NM_010830)	-158	NM_010830	17688	Mm.18210	NM_010830	ENSMUSG00000005370	Msh6	AU044881|AW550279|GTBP|Gtmbp	mutS homolog 6	protein-coding
mm_141092.1	chr17	25985624	25985634	-	1	NA	5' UTR (NM_001347334, exon 1 of 12)	5' UTR (NM_001347334, exon 1 of 12)	245	NM_001347334	50817	Mm.216072	NM_015830	ENSMUSG00000037326	Capn15	Solh	calpain 15	protein-coding
mm_46891.1	chr5	113989740	113989744	-	1	NA	intron (NM_198109, intron 1 of 14)	intron (NM_198109, intron 1 of 14)	4015	NM_198109	231637	Mm.389682	NM_198109	ENSMUSG00000042121	Ssh1	AW551225|Gm1394|Gm1395|SSH-1|SSH-1L	slingshot homolog 1 (Drosophila)	protein-coding
mm_143193.1	chr17	62606680	62606682	-	1	NA	3' UTR (NM_207654, exon 5 of 5)	3' UTR (NM_207654, exon 5 of 5)	274636	NM_207654	13640	Mm.7978	NM_010109	ENSMUSG00000048915	Efna5	AL-1|AV158822|EFL-5|Ephrin-A5|Epl7|LERK-7|RAGS	ephrin A5	protein-coding
mm_152219.1	chr19	8263191	8263199	-	1	NA	Intergenic	Intergenic	-44295	NM_001347426	236293	Mm.440581	NM_172776	ENSMUSG00000075044	Slc22a29	D630002G06Rik	solute carrier family 22. member 29	protein-coding
mm_109170.1	chr12	108370986	108371025	+	1	NA	promoter-TSS (NM_001286346)	promoter-TSS (NM_001286346)	-148	NM_001286346	68519	Mm.236645	NM_001043335	ENSMUSG00000058070	Eml1	1110008N23Rik|A930030P13Rik|AA171013|AI847476|AI853955|ELP79|EMAP|EMAPL|heco	echinoderm microtubule associated protein like 1	protein-coding
mm_75511.1	chr8	54529350	54529363	-	1	NA	intron (NM_029701, intron 1 of 4)	intron (NM_029701, intron 1 of 4)	642	NM_029701	76687	Mm.86437	NM_029701	ENSMUSG00000054408	Spcs3	1810011E08Rik|SPC22/23	signal peptidase complex subunit 3 homolog (S. cerevisiae)	protein-coding
mm_60388.1	chr7	44474032	44474045	+	1	NA	Intergenic	Intergenic	3691	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_92731.1	chr10	80855188	80855220	-	1	NA	promoter-TSS (NM_025349)	promoter-TSS (NM_025349)	5	NM_025349	66094	Mm.379101	NM_025349	ENSMUSG00000035215	Lsm7	0910001B06Rik|1110033F18Rik	LSM7 homolog, U6 small nuclear RNA and mRNA degradation associated	protein-coding
mm_159056.1	chr1	191098324	191098324	+	1	NA	promoter-TSS (NM_030060)	promoter-TSS (NM_030060)	-90	NM_030060	381319	Mm.6922	NM_030060	ENSMUSG00000026630	Batf3	9130211I03Rik|Snft	basic leucine zipper transcription factor, ATF-like 3	protein-coding
mm_67278.1	chr7	78451706	78451707	-	1	NA	intron (NM_008746, intron 10 of 16)	intron (NM_008746, intron 10 of 16)	126132	NM_008746	18213	Mm.33496	NM_008746	ENSMUSG00000059146	Ntrk3	AW125844|Ntrk3_tv3|TrkC	neurotrophic tyrosine kinase, receptor, type 3	protein-coding
mm_20638.1	chr2	132021110	132021120	-	1	NA	intron (NM_175445, intron 1 of 10)	intron (NM_175445, intron 1 of 10)	8873	NM_175445	215653	Mm.204737	NM_175445	ENSMUSG00000027339	Rassf2	3830431H01Rik|9030412M04Rik|AI852669|AW495050	Ras association (RalGDS/AF-6) domain family member 2	protein-coding
mm_127680.1	chr15	102928087	102928092	+	1	NA	3' UTR (NM_010464, exon 2 of 2)	3' UTR (NM_010464, exon 2 of 2)	6958	NM_010464	15422	Mm.207062	NM_010464	ENSMUSG00000001655	Hoxc13	-	homeobox C13	protein-coding
mm_132475.1	chr16	36709784	36709797	+	1	NA	intron (NM_001285791, intron 3 of 6)	intron (NM_001285791, intron 3 of 6)	15812	NM_001285791	106347	Mm.17807	NM_134109	ENSMUSG00000022900	Ildr1	AU041483|AU044638	immunoglobulin-like domain containing receptor 1	protein-coding
mm_141880.1	chr17	34858114	34858124	-	1	NA	promoter-TSS (NR_105938)	promoter-TSS (NR_105938)	-487	NR_105938	102465587		NR_105938	ENSMUSG00000098445	Mir6972	Gm27810|mmu-mir-6972	microRNA 6972	ncRNA
mm_68384.1	chr7	109438999	109439017	-	1	NA	promoter-TSS (NM_054103)	promoter-TSS (NM_054103)	45	NM_054103	117229	Mm.389950	NM_054103	ENSMUSG00000031027	Stk33	4921505G21Rik|AW061264	serine/threonine kinase 33	protein-coding
mm_121577.1	chr14	122913070	122913082	+	1	NA	promoter-TSS (NM_145466)	promoter-TSS (NM_145466)	89	NM_145466	223267	Mm.379358	NM_145466	ENSMUSG00000041625	Ggact	A2ld1	gamma-glutamylamine cyclotransferase	protein-coding
mm_55534.1	chr6	70726959	70726965	-	1	NA	Intergenic	Intergenic	65213	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_39080.1	chr4	154359743	154359759	-	1	NA	intron (NM_001177995, intron 4 of 15)	intron (NM_001177995, intron 4 of 15)	-59856	NM_001112744	230972	Mm.38481	NM_001112744	ENSMUSG00000029032	Arhgef16	-	Rho guanine nucleotide exchange factor (GEF) 16	protein-coding
mm_136392.1	chr16	93142264	93142275	-	1	NA	Intergenic	Intergenic	210920	NR_040486	69857	Mm.81192	NR_040486	ENSMUSG00000100277	1810053B23Rik	1810008L18Rik|1810056K14Rik	RIKEN cDNA 1810053B23 gene	ncRNA
mm_115544.1	chr13	8815996	8816010	-	1	NA	intron (NM_001039388, intron 13 of 13)	L1_Mur2|LINE|L1	55041	NM_001039389	207615	Mm.284654	NM_172445	ENSMUSG00000021147	Wdr37	-	WD repeat domain 37	protein-coding
mm_85871.1	chr9	110909665	110909692	-	1	NA	Intergenic	Intergenic	7183	NM_001195437	235634	Mm.31788	NM_001195437	ENSMUSG00000096393	Gm590	-	predicted gene 590	protein-coding
mm_128382.1	chr15	42676968	42676978	-	1	NA	promoter-TSS (NM_001286062)	promoter-TSS (NM_001286062)	4	NM_001286062	11600	Mm.309336	NM_009640	ENSMUSG00000022309	Angpt1	1110046O21Rik|Ang-1|Ang1	angiopoietin 1	protein-coding
mm_125732.1	chr15	73176184	73176218	+	1	NA	intron (NM_153178, intron 1 of 18)	RMER4B|LTR|ERVK	8746	NM_153178	239528	Mm.23095	NM_153178	ENSMUSG00000036698	Ago2	1110029L17Rik|2310051F07Rik|AI225898|AL022874|AW546247|ENSMUSG00000072493|Eif2c2|Gerp95|Gm10365|mKIAA4215	argonaute RISC catalytic subunit 2	protein-coding
mm_19631.1	chr2	102813872	102813882	-	1	NA	3' UTR (NM_009851, exon 19 of 19)	3' UTR (NM_009851, exon 19 of 19)	87788	NM_001177785	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_142831.1	chr17	51779049	51779051	-	1	NA	intron (NM_009122, intron 7 of 10)	intron (NM_009122, intron 7 of 10)	33004	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_138828.1	chr17	39848015	39848025	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	5023	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_32917.1	chr4	119136686	119136696	+	1	NA	3' UTR (NM_011400, exon 10 of 10)	3' UTR (NM_011400, exon 10 of 10)	27946	NM_011400	20525	Mm.21002	NM_011400	ENSMUSG00000028645	Slc2a1	Glut-1|Glut1	solute carrier family 2 (facilitated glucose transporter), member 1	protein-coding
mm_137855.1	chr17	31108404	31108414	+	1	NA	exon (NM_009593, exon 9 of 15)	exon (NM_009593, exon 9 of 15)	21202	NM_011575	21786	Mm.4641	NM_011575	ENSMUSG00000024029	Tff3	ITF|mITF	trefoil factor 3, intestinal	protein-coding
mm_160986.1	chr11	104467767	104467767	-	1	NA	Intergenic	Intergenic	-25476	NM_001081045	76719	Mm.136418	NM_001081045	ENSMUSG00000018412	Kansl1	1700081L11Rik|9430041J06Rik|mKIAA1267	KAT8 regulatory NSL complex subunit 1	protein-coding
mm_150968.1	chr19	46500757	46500770	+	1	NA	promoter-TSS (NM_053100)	promoter-TSS (NM_053100)	-885	NM_053100	93679	Mm.392177	NM_053100	ENSMUSG00000025034	Trim8	AA408830|BB006755|GERP|Rnf27	tripartite motif-containing 8	protein-coding
mm_113492.1	chr13	37401003	37401005	+	1	NA	intron (NM_010745, intron 3 of 4)	MLT1A1|LTR|ERVL-MaLR	55659	NM_010745	17084	Mm.2639	NM_010745	ENSMUSG00000021423	Ly86	MD-1|MD1|ly86_tv2	lymphocyte antigen 86	protein-coding
mm_84912.1	chr9	79977811	79977836	-	1	NA	promoter-TSS (NM_001081243)	promoter-TSS (NM_001081243)	59	NM_001081243	70598	Mm.23049	NM_001081243	ENSMUSG00000034898	Filip1	5730485H21Rik|AI843021	filamin A interacting protein 1	protein-coding
mm_169037.1	chr13	13437659	13437670	+	1	NA	promoter-TSS (NM_010917)	promoter-TSS (NM_010917)	62	NM_010917	18073	Mm.4691	NM_010917	ENSMUSG00000005397	Nid1	A630025O17|Nid|entactin|entactin-1|nidogen-1	nidogen 1	protein-coding
mm_134066.1	chr16	8637515	8637553	-	1	NA	promoter-TSS (NM_016881)	promoter-TSS (NM_016881)	167	NM_025708	66690	Mm.10068	NM_025708	ENSMUSG00000043140	Tmem186	2810440M13Rik|4432406C05Rik|AI648175|AW210586	transmembrane protein 186	protein-coding
mm_4074.1	chr1	166254051	166254090	+	1	NA	promoter-TSS (NM_001164528)	promoter-TSS (NM_001164528)	-69	NM_001164528	100039795	Mm.101743	NM_001164528	ENSMUSG00000040612	Ildr2	2810478N18Rik|3110063L10Rik|AI852300|D1Ertd471e|Dbsm1|ENSMUSG00000040612|Ll	immunoglobulin-like domain containing receptor 2	protein-coding
mm_46191.1	chr5	97996038	97996054	-	1	NA	intron (NM_133738, intron 7 of 16)	intron (NM_133738, intron 7 of 16)	34916	NM_133738	71914	Mm.24842	NM_133738	ENSMUSG00000029338	Antxr2	2310046B19Rik|AW561899|CMG-2|CMG2|cI-35	anthrax toxin receptor 2	protein-coding
mm_44726.1	chr5	31047859	31047867	-	1	NA	promoter-TSS (NM_027855)	promoter-TSS (NM_027855)	216	NM_177870	330064	Mm.205463	NM_177870	ENSMUSG00000006641	Slc5a6	E430023I20	solute carrier family 5 (sodium-dependent vitamin transporter), member 6	protein-coding
mm_100740.1	chr11	4104814	4104824	-	1	NA	intron (NM_144520, intron 8 of 11)	intron (NM_144520, intron 8 of 11)	-9388	NM_026443	67900	Mm.41719	NM_026443	ENSMUSG00000004748	Mtfp1	1700020C11Rik|2610507A21Rik|AV005788|Mtp18	mitochondrial fission process 1	protein-coding
mm_141648.1	chr17	33660268	33660294	-	1	NA	exon (NM_001109913, exon 11 of 17)	exon (NM_001109913, exon 11 of 17)	22186	NR_028279	378460	Mm.272606	NM_001002842	ENSMUSG00000032739	Pram1	AY665714	PML-RAR alpha-regulated adaptor molecule 1	protein-coding
mm_27954.1	chr3	79842643	79842684	-	1	NA	promoter-TSS (NM_027495)	promoter-TSS (NM_027495)	-1	NM_027495	70652	Mm.46635	NM_027495	ENSMUSG00000027956	Tmem144	1110057I03Rik|5730537D05Rik	transmembrane protein 144	protein-coding
mm_97362.1	chr11	77506923	77506952	+	1	NA	3' UTR (NM_001004144, exon 20 of 20)	3' UTR (NM_001004144, exon 20 of 20)	6336	NM_001024920	216964	Mm.341211	NM_001024920	ENSMUSG00000044328	Trp53i13	2410019G02Rik|Tp53i13	transformation related protein 53 inducible protein 13	protein-coding
mm_8117.1	chr1	135984288	135984303	-	1	NA	exon (NM_177642, exon 4 of 27)	exon (NM_177642, exon 4 of 27)	22047	NM_177642	226438	Mm.119675	NM_177642	ENSMUSG00000051985	Igfn1	9830123M21Rik	immunoglobulin-like and fibronectin type III domain containing 1	protein-coding
mm_86712.1	chr10	18855788	18855816	+	1	NA	exon (NM_022032, exon 3 of 3)	exon (NM_022032, exon 3 of 3)	10731	NM_022032	64058	Mm.28209	NM_022032	ENSMUSG00000019851	Perp	1110017A08Rik|KCP1|KRTCAP1|PIGPC1|THW	PERP, TP53 apoptosis effector	protein-coding
mm_88077.1	chr10	67979710	67979720	+	1	NA	5' UTR (NM_001081346, exon 1 of 13)	5' UTR (NM_001081346, exon 1 of 13)	117	NM_001081346	170799	Mm.209844	NM_133244	ENSMUSG00000037846	Rtkn2	B130039D23Rik|Mbf|Plekhk1	rhotekin 2	protein-coding
mm_42479.1	chr5	115468477	115468489	+	1	NA	intron (NM_011107, intron 1 of 3)	intron (NM_011107, intron 1 of 3)	2217	NM_011107	18778	Mm.20190	NM_011107	ENSMUSG00000029522	Pla2g1b	Pla2a|sPLA2IB	phospholipase A2, group IB, pancreas	protein-coding
mm_165328.1	chr2	112265805	112265807	+	1	NA	promoter-TSS (NM_133649)	promoter-TSS (NM_133649)	-508	NM_133649	107723	Mm.491155	NM_133648	ENSMUSG00000027130	Slc12a6	9530023I19Rik|KCC3|gaxp	solute carrier family 12, member 6	protein-coding
mm_124776.1	chr15	7193516	7193518	+	1	NA	3' UTR (NM_013584, exon 20 of 20)	3' UTR (NM_013584, exon 20 of 20)	52975	NM_013584	16880	Mm.149720	NM_013584	ENSMUSG00000054263	Lifr	A230075M04Rik|AW061234|LIF	leukemia inhibitory factor receptor	protein-coding
mm_164859.1	chr18	53147826	53147836	+	1	NA	Intergenic	Intergenic	-28534	NM_026386	67804	Mm.252171	NM_026386	ENSMUSG00000034484	Snx2	0610030A03Rik	sorting nexin 2	protein-coding
mm_161833.1	chr17	84368684	84368684	-	1	NA	intron (NM_183021, intron 26 of 37)	L2|LINE|L2	97524	NM_183021	240174	Mm.246767	NM_177826	ENSMUSG00000024251	Thada	6530405K19|A930021O22|AU019899|BC052885|GITA	thyroid adenoma associated	protein-coding
mm_67623.1	chr7	84086495	84086509	-	1	NA	promoter-TSS (NM_030728)	promoter-TSS (NM_030728)	3	NM_030728	80982	Mm.160389	NM_030728	ENSMUSG00000052353	Cemip	12H19.01.T7|6330404C01Rik|9930013L23Rik|AY007814|Kiaa1199	cell migration inducing protein, hyaluronan binding	protein-coding
mm_45613.1	chr5	75835642	75835652	-	1	NA	Intergenic	Intergenic	142781	NM_010612	16542	Mm.285	NM_010612	ENSMUSG00000062960	Kdr	6130401C07|Flk-1|Flk1|Krd-1|Ly73|VEGFR-2|VEGFR2|sVEGFR-2	kinase insert domain protein receptor	protein-coding
mm_128138.1	chr15	31467972	31467980	-	1	NA	intron (NM_172606, intron 22 of 25)	MTB|LTR|ERVL-MaLR	-14287	NM_145852	252967	Mm.436668	NM_145852	ENSMUSG00000022236	Ropn1l	ASP|AV047578|Akapasp	ropporin 1-like	protein-coding
mm_74669.1	chr8	13686558	13686562	-	1	NA	Intergenic	Intergenic	-8973	NM_009025	19414	Mm.18517	NM_009025	ENSMUSG00000031453	Rasa3	AI326412|C86362|E130011G04|GAPIII|hlb381|scat	RAS p21 protein activator 3	protein-coding
mm_21081.1	chr2	152933203	152933218	-	1	NA	promoter-TSS (NM_010226)	promoter-TSS (NM_010226)	-2	NM_010226	14239	Mm.205798	NM_010226	ENSMUSG00000074676	Foxs1	FREAC10|Fkh3|Fkhl18	forkhead box S1	protein-coding
mm_89689.1	chr10	97565637	97565671	+	1	NA	5' UTR (NM_008524, exon 1 of 3)	5' UTR (NM_008524, exon 1 of 3)	153	NM_008524	17022	Mm.18888	NM_008524	ENSMUSG00000036446	Lum	Ldc|SLRR2D	lumican	protein-coding
mm_148254.1	chr18	80743011	80743026	-	1	NA	intron (NM_001201569, intron 26 of 29)	intron (NM_001201569, intron 26 of 29)	-29947	NM_001164109	18018	Mm.329560	NM_016791	ENSMUSG00000033016	Nfatc1	2210017P03Rik|AI449492|AV076380|NF-ATc|NFAT2|NFATc|Nfatcb	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 1	protein-coding
mm_36297.1	chr4	66404459	66404509	-	1	NA	promoter-TSS (NM_207109)	promoter-TSS (NM_207109)	-1	NM_207109	56079	Mm.445312	NM_019514	ENSMUSG00000028373	Astn2	1d8|Astnl|bM452J22.1	astrotactin 2	protein-coding
mm_19037.1	chr2	76975101	76975122	-	1	NA	exon (NM_011652, exon 4 of 313)	exon (NM_011652, exon 4 of 313)	7436	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_130978.1	chr15	103344559	103344574	-	1	NA	3' UTR (NM_010577, exon 30 of 30)	3' UTR (NM_010577, exon 30 of 30)	-4480	NM_013866	29813	Mm.14099	NM_013866	ENSMUSG00000000552	Zfp385a	Hzf|Zfp385|Znf385a	zinc finger protein 385A	protein-coding
mm_113069.1	chr13	23752342	23752351	+	1	NA	promoter-TSS (NM_178203)	promoter-TSS (NM_178203)	-34	NM_178203	319150		NM_178203	ENSMUSG00000069267	Hist1h3b	H3-53	histone cluster 1, H3b	protein-coding
mm_125380.1	chr15	40655070	40655082	+	1	NA	promoter-TSS (NM_011766)	promoter-TSS (NM_011766)	34	NM_011766	22762	Mm.39496	NM_011766	ENSMUSG00000022306	Zfpm2	B330005D23Rik|FOG-2|FOG2	zinc finger protein, multitype 2	protein-coding
mm_99308.1	chr11	101376658	101376670	+	1	NA	exon (NM_008061, exon 5 of 5)	exon (NM_008061, exon 5 of 5)	8948	NM_008061	14377	Mm.18064	NM_008061	ENSMUSG00000078650	G6pc	AW107337|G6Pase|G6pt|Glc-6-Pase	glucose-6-phosphatase, catalytic	protein-coding
mm_9687.1	chr1	178336069	178336093	-	1	NA	exon (NM_016805, exon 2 of 14)	exon (NM_016805, exon 2 of 14)	1703	NM_016805	51810	Mm.86589	NM_016805	ENSMUSG00000039630	Hnrnpu	AA408410|AI256620|AL024194|AL024437|AW557595|C86794|Hnrpu|SAFA|Sp120|hnRNP U	heterogeneous nuclear ribonucleoprotein U	protein-coding
mm_79837.1	chr9	64806103	64806158	+	1	NA	Intergenic	Intergenic	-4881	NM_001162917	102442	Mm.222473	NM_176935	ENSMUSG00000053641	Dennd4a	AI115600|AI851943|F730015K02Rik	DENN/MADD domain containing 4A	protein-coding
mm_133433.1	chr16	87692463	87692463	+	1	NA	Intergenic	Intergenic	-6491	NM_007520	12013	Mm.26147	NM_007520	ENSMUSG00000025612	Bach1	6230421P05Rik|AI323795	BTB and CNC homology 1, basic leucine zipper transcription factor 1	protein-coding
mm_74324.1	chr8	126868044	126868060	+	1	NA	Intergenic	Intergenic	77869	NM_024214	67952	Mm.6932	NM_024214	ENSMUSG00000093904	Tomm20	1810060K07Rik|BB284719|Gm19268|MAS20|MOM19|TOM20|mKIAA0016	translocase of outer mitochondrial membrane 20 homolog (yeast)	protein-coding
mm_76071.1	chr8	78810283	78810295	-	1	NA	intron (NM_001191004, intron 3 of 4)	intron (NM_001191004, intron 3 of 4)	10863	NM_001191004	78651	Mm.28694	NM_030145	ENSMUSG00000031683	Lsm6	1500031N17Rik|2410088K19Rik|AI747288	LSM6 homolog, U6 small nuclear RNA and mRNA degradation associated	protein-coding
mm_44259.1	chr5	5514809	5514830	-	1	NA	promoter-TSS (NM_001193660)	promoter-TSS (NM_001193660)	-30	NM_001193660	64945	Mm.40132	NM_022890	ENSMUSG00000046798	Cldn12	-	claudin 12	protein-coding
mm_76426.1	chr8	84978069	84978080	-	1	NA	exon (NM_008416, exon 1 of 1)	exon (NM_008416, exon 1 of 1)	674	NM_008416	16477	Mm.1167	NM_008416	ENSMUSG00000052837	Junb	-	jun B proto-oncogene	protein-coding
mm_101257.1	chr11	20831311	20831332	-	1	NA	promoter-TSS (NM_173752)	promoter-TSS (NM_173752)	-213	NM_173752	216551	Mm.76694	NM_173752	ENSMUSG00000042363	Lgalsl	1110067D22Rik|A530071M23|Grpa|Hspc159|Lgalsla	lectin, galactoside binding-like	protein-coding
mm_128857.1	chr15	72547689	72547707	-	1	NA	Intergenic	CpG-4938	-1419	NM_001033876	223604	Mm.386856	NM_001033876	ENSMUSG00000036760	Kcnk9	Task3	potassium channel, subfamily K, member 9	protein-coding
mm_63722.1	chr7	130834500	130834533	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-31208	NM_001346515	101476	Mm.323554	NM_133942	ENSMUSG00000040268	Plekha1	AA960558|C920009D07Rik|TAPP1	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 1	protein-coding
mm_52271.1	chr6	108512430	108512431	+	1	NA	intron (NM_010585, intron 55 of 61)	intron (NM_010585, intron 55 of 61)	22687	NR_106121	102465766		NR_106121	ENSMUSG00000105697	Mir7661	mmu-mir-7661	microRNA 7661	ncRNA
mm_43583.1	chr5	137746953	137746975	+	1	NA	5' UTR (NM_023910, exon 2 of 5)	5' UTR (NM_023910, exon 2 of 5)	995	NM_029805	78829	Mm.286399	NM_023910	ENSMUSG00000029723	Tsc22d4	0610009M14Rik|1700023B23Rik|AI415410|Thg-1pit|Tilz2	TSC22 domain family, member 4	protein-coding
mm_13184.1	chr2	93186800	93186808	+	1	NA	promoter-TSS (NM_001025246)	promoter-TSS (NM_001025246)	-780	NM_001025246	277414	Mm.41033	NM_001025246	ENSMUSG00000068735	Trp53i11	Tp53i11	transformation related protein 53 inducible protein 11	protein-coding
mm_171262.1	chr3	84155723	84155723	-	1	NA	promoter-TSS (NM_029797)	promoter-TSS (NM_029797)	63	NM_029797	76915	Mm.274829	NM_029797	ENSMUSG00000033752	Mnd1	2610034E18Rik|AI591601|Gaj	meiotic nuclear divisions 1	protein-coding
mm_39943.1	chr5	31849474	31849477	+	1	NA	intron (NM_144541, intron 6 of 11)	B1_Mur1|SINE|Alu	151425	NM_144541	107976	Mm.482126	NM_144541	ENSMUSG00000052139	Bre	6030405P19Rik|AI429776|B830038C02Rik	brain and reproductive organ-expressed protein	protein-coding
mm_28493.1	chr3	92484389	92484394	-	1	NA	exon (NM_009264, exon 2 of 2)	exon (NM_009264, exon 2 of 2)	1490	NM_009264	20753	Mm.331191	NM_009264	ENSMUSG00000050359	Sprr1a	AI528815|SPR1a|mSPRR1A	small proline-rich protein 1A	protein-coding
mm_30009.1	chr3	135657363	135657379	-	1	NA	intron (NM_008689, intron 5 of 24)	(CA)n|Simple_repeat|Simple_repeat	34176	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_128305.1	chr15	37764539	37764556	-	1	NA	intron (NM_134094, intron 1 of 6)	RSINE1|SINE|B4	27453	NM_001170866	52589	Mm.283370	NM_134094	ENSMUSG00000051359	Ncald	AI848120|D030020D09Rik|D15Ertd412e	neurocalcin delta	protein-coding
mm_31792.1	chr4	63935641	63935652	+	1	NA	Intergenic	Intergenic	-74362	NM_009403	21949	Mm.4664	NM_009403	ENSMUSG00000028362	Tnfsf8	CD153|CD30LG|Cd30l|Tnlg3a	tumor necrosis factor (ligand) superfamily, member 8	protein-coding
mm_16824.1	chr2	11474037	11474044	-	1	NA	3' UTR (NM_001177754, exon 16 of 16)	3' UTR (NM_001177754, exon 16 of 16)	28050	NM_001177754	170768	Mm.19669	NM_133232	ENSMUSG00000026773	Pfkfb3	E330010H22Rik|iPFK-2|uPFK-2	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	protein-coding
mm_154826.1	chrX	17609655	17609689	+	1	NA	Intergenic	MLT1E1-int|LTR|ERVL-MaLR	-37347	NM_028058	72018	Mm.41558	NM_028058	ENSMUSG00000025040	Fundc1	1500005J14Rik|1810033P05Rik	FUN14 domain containing 1	protein-coding
mm_68934.1	chr7	126501953	126501960	-	1	NA	intron (NM_183020, intron 1 of 22)	intron (NM_183020, intron 1 of 22)	469	NM_001347658	233871	Mm.231450	NM_183020	ENSMUSG00000032637	Atxn2l	A2D|A2LG|A2RP|A2lp|Atxnl2	ataxin 2-like	protein-coding
mm_140467.1	chr17	93199118	93199146	+	1	NA	promoter-TSS (NM_009625)	promoter-TSS (NM_009625)	-36	NM_001315504	11516	Mm.3407	NM_009625	ENSMUSG00000024256	Adcyap1	PACAP	adenylate cyclase activating polypeptide 1	protein-coding
mm_170310.1	chr18	35495256	35495258	+	1	NA	intron (NM_030749, intron 1 of 9)	intron (NM_030749, intron 1 of 9)	3668	NM_030749	81500	Mm.291482	NM_030749	ENSMUSG00000024357	Sil1	1810057E01Rik|AI042831|wz	endoplasmic reticulum chaperone SIL1 homolog (S. cerevisiae)	protein-coding
mm_68083.1	chr7	101870712	101870756	-	1	NA	promoter-TSS (NM_008034)	promoter-TSS (NM_008034)	54	NM_001252554	14275	Mm.2135	NM_008034	ENSMUSG00000001827	Folr1	FBP1|Folbp-1|Folbp1	folate receptor 1 (adult)	protein-coding
mm_65221.1	chr7	19699720	19699737	-	1	NA	promoter-TSS (NM_009696)	promoter-TSS (NM_009696)	-540	NM_009696	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_8544.1	chr1	155099534	155099544	-	1	NA	promoter-TSS (NM_010500)	promoter-TSS (NM_010500)	97	NM_010500	15939	Mm.12246	NM_010500	ENSMUSG00000056708	Ier5	-	immediate early response 5	protein-coding
mm_162168.1	chrX	100774532	100774532	+	1	NA	promoter-TSS (NM_001177779)	promoter-TSS (NM_001177779)	37	NM_001177779	53310	Mm.4615	NM_016747	ENSMUSG00000000881	Dlg3	Dlgh3|SAP102|mKIAA1232	discs, large homolog 3 (Drosophila)	protein-coding
mm_88388.1	chr10	76469077	76469086	+	1	NA	promoter-TSS (NM_172550)	promoter-TSS (NM_172550)	33	NM_172550	216119	Mm.344778	NM_172550	ENSMUSG00000033126	Ybey	1110068N23Rik|A130042E20Rik|C21orf57|ORF57|ORF66	ybeY metallopeptidase	protein-coding
mm_89163.1	chr10	86139185	86139205	+	1	NA	intron (NM_013722, intron 6 of 13)	intron (NM_013722, intron 6 of 13)	43341	NR_038024	78170	Mm.444790	NR_038024		4930486F22Rik	-	RIKEN cDNA 4930486F22 gene	ncRNA
mm_85044.1	chr9	89703176	89703220	-	1	NA	intron (NM_025360, intron 1 of 2)	intron (NM_025360, intron 1 of 2)	1845	NM_025360	66111	Mm.27606	NM_025360	ENSMUSG00000032353	Tmed3	1200002G13Rik|AW546672|P24b	transmembrane p24 trafficking protein 3	protein-coding
mm_63357.1	chr7	127014654	127014663	+	1	NA	promoter-TSS (NM_080638)	promoter-TSS (NM_080638)	-64	NM_080638	78388	Mm.228797	NM_080638	ENSMUSG00000030681	Mvp	2310009M24Rik|LRP|VAULT1	major vault protein	protein-coding
mm_151299.1	chr19	55552809	55552815	+	1	NA	intron (NM_001293686, intron 7 of 7)	MIRb|SINE|MIR	149392	NR_045318	77594	Mm.329924	NR_045318	ENSMUSG00000097632	4930552P12Rik	-	RIKEN cDNA 4930552P12 gene	ncRNA
mm_47466.1	chr5	123671098	123671109	-	1	NA	intron (NM_001347468, intron 1 of 24)	intron (NM_001347468, intron 1 of 24)	13258	NM_019765	56430	Mm.241109	NM_019765	ENSMUSG00000049550	Clip1	1110007I12Rik|4631429H07Rik|AV017631|C81039|CLIP-170|CLIP170|CYLN1|Clip50|Rsn|mKIAA4046|restin	CAP-GLY domain containing linker protein 1	protein-coding
mm_2335.1	chr1	92831793	92831814	+	1	NA	5' UTR (NM_016696, exon 1 of 9)	5' UTR (NM_016696, exon 1 of 9)	117	NM_016696	14733	Mm.297976	NM_016696	ENSMUSG00000034220	Gpc1	AI462976	glypican 1	protein-coding
mm_66547.1	chr7	45211487	45211516	-	1	NA	exon (NM_015789, exon 2 of 5)	exon (NM_015789, exon 2 of 5)	382	NM_015789	50722	Mm.27287	NM_015789	ENSMUSG00000030792	Dkkl1	AI414495|SGY|SGY-1|SGY1|Soggy|mSgy	dickkopf-like 1	protein-coding
mm_89532.1	chr10	94499318	94499328	+	1	NA	Intergenic	B3A|SINE|B2	-15534	NM_172051	319880	Mm.23047	NM_172051	ENSMUSG00000020023	Tmcc3	AW488095|C630016B22Rik|C88213|Tmcc1	transmembrane and coiled coil domains 3	protein-coding
mm_89659.1	chr10	97483365	97483377	+	1	NA	exon (NM_007833, exon 2 of 8)	exon (NM_007833, exon 2 of 8)	1040	NM_007833	13179	Mm.56769	NM_007833	ENSMUSG00000019929	Dcn	DC|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding
mm_137780.1	chr17	29493133	29493143	+	1	NA	intron (NM_008842, intron 4 of 5)	intron (NM_008842, intron 4 of 5)	2093	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_95569.1	chr11	52396452	52396473	+	1	NA	promoter-TSS (NM_153117)	promoter-TSS (NM_153117)	34	NM_153117	213673	Mm.291979	NM_153117	ENSMUSG00000036275	9530068E07Rik	C85061|Kct2	RIKEN cDNA 9530068E07 gene	protein-coding
mm_23641.1	chr3	67159156	67159160	+	1	NA	intron (NM_025822, intron 4 of 9)	intron (NM_025822, intron 4 of 9)	173486	NM_025822	66880	Mm.316418	NM_025822	ENSMUSG00000034544	Rsrc1	1200013F24Rik|SRrp53	arginine/serine-rich coiled-coil 1	protein-coding
mm_145888.1	chr18	65582258	65582275	+	1	NA	intron (NM_207255, intron 1 of 5)	intron (NM_207255, intron 1 of 5)	2036	NM_207255	328977	Mm.286232	NM_207255	ENSMUSG00000042439	Zfp532	C530030I18Rik|Znf532|mKIAA1629	zinc finger protein 532	protein-coding
mm_27518.1	chr3	57294789	57294799	-	1	NA	5' UTR (NM_008536, exon 3 of 7)	5' UTR (NM_008536, exon 3 of 7)	7125	NM_008536	17112	Mm.856	NM_008536	ENSMUSG00000027800	Tm4sf1	L6|M3s1	transmembrane 4 superfamily member 1	protein-coding
mm_129690.1	chr15	81522922	81522933	-	1	NA	Intergenic	Intergenic	56611	NM_019712	56438	Mm.29405	NM_019712	ENSMUSG00000022400	Rbx1	1500002P15Rik|AA517855|ROC1	ring-box 1	protein-coding
mm_109766.1	chr12	118316589	118316589	+	1	NA	Intergenic	Intergenic	-15149	NM_001166385	20688	Mm.34699	NM_009239	ENSMUSG00000025323	Sp4	5730497N03Rik|HF-1b|HF1-b	trans-acting transcription factor 4	protein-coding
mm_130056.1	chr15	89180682	89180701	-	1	NA	promoter-TSS (NM_001284506)	promoter-TSS (NM_001284506)	97	NM_001284506	140570	Mm.267514	NM_138749	ENSMUSG00000036606	Plxnb2	Debt|plexin-B2	plexin B2	protein-coding
mm_102654.1	chr11	63464080	63464114	-	1	NA	Intergenic	Intergenic	-78028	NR_105772	102466632		NR_105772	ENSMUSG00000098829	Mir6354	Gm27282|mmu-mir-6354	microRNA 6354	ncRNA
mm_42246.1	chr5	113873146	113873152	+	1	NA	intron (NM_011779, intron 2 of 10)	intron (NM_011779, intron 2 of 10)	35557	NM_011779	23790	Mm.260158	NM_011779	ENSMUSG00000004530	Coro1c	AL022675|AW455561|AW548837	coronin, actin binding protein 1C	protein-coding
mm_784.1	chr1	45321590	45321641	+	1	NA	exon (NM_009930, exon 2 of 51)	exon (NM_009930, exon 2 of 51)	10077	NM_009930	12825	Mm.249555	NM_009930	ENSMUSG00000026043	Col3a1	AW550625|Col3a-1|Tsk-2|Tsk2	collagen, type III, alpha 1	protein-coding
mm_60787.1	chr7	45566962	45566973	+	1	NA	TTS (NR_038166)	TTS (NR_038166)	-3186	NM_009737	12036	Mm.24210	NM_009737	ENSMUSG00000030826	Bcat2	Bcat-2|Eca40	branched chain aminotransferase 2, mitochondrial	protein-coding
mm_22388.1	chr2	181157789	181157807	-	1	NA	promoter-TSS (NM_007906)	promoter-TSS (NM_007906)	-783	NM_007906	13628	Mm.2645	NM_007906	ENSMUSG00000016349	Eef1a2	Eef1a|S1|wasted|wst	eukaryotic translation elongation factor 1 alpha 2	protein-coding
mm_155759.1	chrX	96167809	96167896	+	1	NA	3' UTR (NM_010833, exon 13 of 13)	3' UTR (NM_010833, exon 13 of 13)	71807	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_157320.1	chrX	21714903	21714938	-	1	NA	promoter-TSS (NM_020049)	promoter-TSS (NM_020049)	20	NM_020049	56774	Mm.253984	NM_020049	ENSMUSG00000031089	Slc6a14	1110007A17Rik|9030613J17Rik|ATB0plus|CATB0plus	solute carrier family 6 (neurotransmitter transporter), member 14	protein-coding
mm_72918.1	chr8	91074073	91074080	+	1	NA	intron (NM_011250, intron 1 of 21)	intron (NM_011250, intron 1 of 21)	4019	NM_001282000	19651	Mm.235580	NM_011250	ENSMUSG00000031666	Rbl2	PRB2|RBR-2|Rb2|p130	retinoblastoma-like 2	protein-coding
mm_170482.1	chr19	13899469	13899470	+	1	NA	Intergenic	Intergenic	-11261	NM_146634	258627	Mm.453527	NM_146634	ENSMUSG00000059105	Olfr1504	MOR212-2	olfactory receptor 1504	protein-coding
mm_133329.1	chr16	78309553	78309564	+	1	NA	intron (NM_001276263, intron 1 of 2)	intron (NM_001276263, intron 1 of 2)	7887	NM_001276263	13052	Mm.66222	NM_009988	ENSMUSG00000022865	Cxadr	2610206D03Rik|AU016810|AW553441|CAR|MCAR|MCVADR	coxsackie virus and adenovirus receptor	protein-coding
mm_139035.1	chr17	46163233	46163252	+	1	NA	intron (NM_019581, intron 1 of 11)	intron (NM_019581, intron 1 of 11)	2210	NM_001145979	56055	Mm.22147	NM_019581	ENSMUSG00000023952	Gtpbp2	nmf205	GTP binding protein 2	protein-coding
mm_11102.1	chr2	28095449	28095486	+	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-10589	NM_010190	14134	Mm.182935	NM_010190	ENSMUSG00000026835	Fcnb	Fcn2	ficolin B	protein-coding
mm_8943.1	chr1	164438041	164438059	-	1	NA	TTS (NM_001293313)	TTS (NM_001293313)	20305	NM_009721	11931	Mm.4550	NM_009721	ENSMUSG00000026576	Atp1b1	Atp4b|Atpb|Atpb-1|NKbeta1	ATPase, Na+/K+ transporting, beta 1 polypeptide	protein-coding
mm_123501.1	chr14	66213809	66213836	-	1	NA	promoter-TSS (NM_001162366)	promoter-TSS (NM_001162366)	-270	NM_001162366	19229	Mm.21613	NM_172498	ENSMUSG00000059456	Ptk2b	CADTK|CAKB|CAKbeta|E430023O05Rik|FADK2|FAK2|PYK2|Raftk	PTK2 protein tyrosine kinase 2 beta	protein-coding
mm_167537.1	chr9	21962310	21962324	-	1	NA	exon (NM_010149, exon 2 of 8)	exon (NM_010149, exon 2 of 8)	1259	NM_010149	13857	Mm.2653	NM_010149	ENSMUSG00000006235	Epor	-	erythropoietin receptor	protein-coding
mm_63549.1	chr7	128070157	128070160	+	1	NA	intron (NM_001082960, intron 3 of 29)	B1_Mur1|SINE|Alu	7518	NM_008401	16409	Mm.262106	NM_008401	ENSMUSG00000030786	Itgam	CD11b/CD18|CR3|CR3A|Cd11b|F730045J24Rik|Ly-40|MAC1|Mac-1|Mac-1a	integrin alpha M	protein-coding
mm_169073.1	chr13	30370352	30370365	+	1	NA	intron (NM_177322, intron 2 of 2)	IAPLTR1a_Mm|LTR|ERVK	34002	NM_177322	11607	Mm.35062	NM_177322	ENSMUSG00000049115	Agtr1a	1810074K20Rik|AG2S|AI551199|AT1|AT1a|AT2R1|AT2R1A|Agtr-1a|Agtr1|Angtr-1a	angiotensin II receptor, type 1a	protein-coding
mm_170837.1	chr2	177085805	177085822	-	1	NA	Intergenic	Intergenic	-158000	NM_001305133	102639598	Mm.379980	NM_029813	ENSMUSG00000074527	Gm14296	-	predicted gene 14296	protein-coding
mm_136467.1	chr16	95585569	95585588	-	1	NA	intron (NM_001302152, intron 1 of 10)	CpG	1015	NM_001302152	13876	Mm.164531	NM_133659	ENSMUSG00000040732	Erg	D030036I24Rik	avian erythroblastosis virus E-26 (v-ets) oncogene related	protein-coding
mm_51942.1	chr6	91709442	91709451	+	1	NA	intron (NM_009320, intron 2 of 14)	intron (NM_009320, intron 2 of 14)	25379	NM_009320	21366	Mm.395650	NM_009320	ENSMUSG00000030096	Slc6a6	AA589629|C80501|Taut	solute carrier family 6 (neurotransmitter transporter, taurine), member 6	protein-coding
mm_148355.1	chr18	84720774	84720783	-	1	NA	intron (NM_173770, intron 1 of 4)	intron (NM_173770, intron 1 of 4)	536	NM_173770	240479	Mm.472378	NM_173770	ENSMUSG00000047992	Fam69c	B230399E16Rik	family with sequence similarity 69, member C	protein-coding
mm_169101.1	chr13	43355598	43355598	-	1	NA	Intergenic	(CTG)n|Simple_repeat|Simple_repeat	-15118	NM_178848	68346	Mm.35325	NM_178848	ENSMUSG00000054021	Sirt5	0610012J09Rik|1500032M05Rik|AV001953	sirtuin 5	protein-coding
mm_60173.1	chr7	41335436	41335451	+	1	NA	Intergenic	Intergenic	51116	NM_001033782	434172	Mm.247214	NM_001033782	ENSMUSG00000072259	Gm5592	EG434172	predicted gene 5592	protein-coding
mm_147831.1	chr18	62191459	62191469	-	1	NA	Intergenic	Intergenic	-11483	NM_007420	11555	Mm.5598	NM_007420	ENSMUSG00000045730	Adrb2	Adrb-2|Badm|Gpcr7	adrenergic receptor, beta 2	protein-coding
mm_2898.1	chr1	131932072	131932085	+	1	NA	3' UTR (NM_001145804, exon 7 of 7)	3' UTR (NM_001145804, exon 7 of 7)	21620	NM_001145804	98415	Mm.246869	NM_175294	ENSMUSG00000026434	Nucks1	2700010L10Rik|8430423A01Rik|AI647518|C78391|Nucks	nuclear casein kinase and cyclin-dependent kinase substrate 1	protein-coding
mm_106636.1	chr11	120991021	120991037	-	1	NA	5' UTR (NM_139059, exon 1 of 9)	5' UTR (NM_139059, exon 1 of 9)	304	NM_139059	104318	Mm.216227	NM_027874	ENSMUSG00000025162	Csnk1d	1200006A05Rik|AA409348|D930010H05Rik	casein kinase 1, delta	protein-coding
mm_172370.1	chr7	123852665	123852675	+	1	NA	Intergenic	RLTR17|LTR|ERVK	-130511	NM_001252072	628779	Mm.40210	NM_001252072	ENSMUSG00000078591	Hs3st4	EG628779|Gm6915	heparan sulfate (glucosamine) 3-O-sulfotransferase 4	protein-coding
mm_10002.1	chr1	191541071	191541083	-	1	NA	exon (NM_001305233, exon 15 of 16)	exon (NM_001305233, exon 15 of 16)	34467	NM_001305233	76843	Mm.189102	NM_029766	ENSMUSG00000037474	Dtl	2810047L02Rik|5730564G15Rik|L2dtl|Ramp	denticleless E3 ubiquitin protein ligase	protein-coding
mm_169289.1	chr13	9834375	9834375	-	1	NA	Intergenic	L1Md_T|LINE|L1	-69054	NM_144516	66505	Mm.397307	NM_144516	ENSMUSG00000021156	Zmynd11	2210402G22Rik|BS69	zinc finger, MYND domain containing 11	protein-coding
mm_24105.1	chr3	88141768	88141771	+	1	NA	promoter-TSS (NM_001310593)	promoter-TSS (NM_001310593)	-603	NM_001310587	17261	Mm.28184	NM_133665	ENSMUSG00000001419	Mef2d	C80750	myocyte enhancer factor 2D	protein-coding
mm_100133.1	chr11	115974779	115974781	+	1	NA	promoter-TSS (NM_133663)	promoter-TSS (NM_133663)	55	NM_133663	192897	Mm.213873	NM_133663	ENSMUSG00000020758	Itgb4	AA407042|C230078O20|CD104	integrin beta 4	protein-coding
mm_2993.1	chr1	133181341	133181404	+	1	NA	Intergenic	Intergenic	50206	NM_133819	108954	Mm.293628	NM_133819	ENSMUSG00000046062	Ppp1r15b	1810033K10Rik|AI606441|C530022L24Rik|CReP	protein phosphatase 1, regulatory (inhibitor) subunit 15b	protein-coding
mm_45406.1	chr5	66299368	66299382	-	1	NA	3' UTR (NM_009686, exon 18 of 18)	3' UTR (NM_009686, exon 18 of 18)	38290	NM_001201416	11787	Mm.5159	NM_009686	ENSMUSG00000029207	Apbb2	2310007D03Rik|FE65L1|Rirl1|TR2L|Zfra	amyloid beta (A4) precursor protein-binding, family B, member 2	protein-coding
mm_98729.1	chr11	96351975	96352018	+	1	NA	exon (NM_134032, exon 1 of 2)	exon (NM_134032, exon 1 of 2)	364	NM_134032	103889	Mm.281153	NM_134032	ENSMUSG00000075588	Hoxb2	AI894218|Hox-2.8|Hoxbes2	homeobox B2	protein-coding
mm_135764.1	chr16	56717447	56717457	-	1	NA	promoter-TSS (NM_001252443)	promoter-TSS (NM_001252443)	-2	NM_019678	21787	Mm.425970	NM_019678	ENSMUSG00000022757	Tfg	AI173908	Trk-fused gene	protein-coding
mm_136303.1	chr16	91597387	91597415	-	1	NA	intron (NM_030018, intron 1 of 6)	CpG	279	NM_030018	77975	Mm.290341	NM_030018	ENSMUSG00000022964	Tmem50b	AU015466|AU019872|B230114J08Rik	transmembrane protein 50B	protein-coding
mm_60497.1	chr7	44478871	44478892	+	1	NA	Intergenic	L1M4c|LINE|L1	-5636	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_50162.1	chr6	41547495	41547508	+	1	NA	Intergenic	Intergenic	25725	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_135736.1	chr16	55838631	55838641	-	1	NA	promoter-TSS (NM_030612)	promoter-TSS (NM_030612)	5	NM_030612	80859	Mm.247272	NM_030612	ENSMUSG00000035356	Nfkbiz	AA408868|INAP|Mail	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, zeta	protein-coding
mm_36419.1	chr4	80003465	80003497	-	1	NA	Intergenic	Intergenic	-830732	NM_031202	22178	Mm.30438	NM_031202	ENSMUSG00000005994	Tyrp1	Oca3|TRP-1|TRP1|Tyrp|b|brown|isa	tyrosinase-related protein 1	protein-coding
mm_98631.1	chr11	96081179	96081216	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-5503	NM_007506	11951	Mm.258	NM_007506	ENSMUSG00000006057	Atp5g1	-	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit C1 (subunit 9)	protein-coding
mm_171956.1	chr5	80540192	80540200	-	1	NA	Intergenic	(A)n|Simple_repeat|Simple_repeat	-480375	NM_001347367	319387	Mm.273631	NM_198702	ENSMUSG00000037605	Adgrl3	5430402I23Rik|CIRL-3|D130075K09Rik|Gm1379|LEC3|Lphn3|mKIAA0768	adhesion G protein-coupled receptor L3	protein-coding
mm_114996.1	chr13	97600257	97600289	+	1	NA	Intergenic	Intergenic	40273	NR_046157	328314	Mm.138047	NR_046157	ENSMUSG00000110235	Gm5086	B230311A21|EG328314	predicted gene 5086	ncRNA
mm_62118.1	chr7	96648091	96648111	+	1	NA	intron (NM_001310760, intron 6 of 32)	intron (NM_001310760, intron 6 of 32)	153448	NR_045874	791381	Mm.402112	NR_045874	ENSMUSG00000053049	Gm15413	ENSMUSG00000053049|OTTMUSG00000021246	predicted gene 15413	ncRNA
mm_120724.1	chr14	73138780	73138799	+	1	NA	Intergenic	Intergenic	-3721	NM_001170694	105670	Mm.280068	NM_134083	ENSMUSG00000022106	Rcbtb2	2610028E02Rik|2810420M18Rik|AI448345|AW240694|Chc1l|RC/BTB2	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 2	protein-coding
mm_128300.1	chr15	37459382	37459405	-	1	NA	promoter-TSS (NM_001170868)	promoter-TSS (NM_001170868)	-11	NM_001170868	52589	Mm.283370	NM_134094	ENSMUSG00000051359	Ncald	AI848120|D030020D09Rik|D15Ertd412e	neurocalcin delta	protein-coding
mm_61730.1	chr7	81862579	81862587	+	1	NA	promoter-TSS (NM_001291282)	promoter-TSS (NM_001291282)	-104	NM_001291282	107769	Mm.221412	NM_145375	ENSMUSG00000038623	Tm6sf1	AI428514|BC023123|C630016D09Rik	transmembrane 6 superfamily member 1	protein-coding
mm_88364.1	chr10	75937298	75937333	+	1	NA	TTS (NM_001277132)	TTS (NM_001277132)	1742	NM_175329	103172	Mm.333849	NM_175329	ENSMUSG00000049422	Chchd10	1620401E04Rik|AI267078|Ndg2	coiled-coil-helix-coiled-coil-helix domain containing 10	protein-coding
mm_35984.1	chr4	55399050	55399067	-	1	NA	Intergenic	Intergenic	19784	NR_040674	100415914	Mm.261765	NR_040674	ENSMUSG00000087070	Gm12505	OTTMUSG00000007226	predicted gene 12505	ncRNA
mm_124125.1	chr14	79662120	79662145	-	1	NA	promoter-TSS (NM_001310655)	promoter-TSS (NM_001310655)	51	NM_001310655	16840	Mm.46561	NM_010701	ENSMUSG00000022025	Cnmd	Bricd3|ChM-I|Chmd|Lect1	chondromodulin	protein-coding
mm_100533.1	chr11	120608493	120608502	+	1	NA	promoter-TSS (NM_153288)	promoter-TSS (NM_153288)	20	NM_001347616	208990	Mm.29444	NM_153288	ENSMUSG00000044034	Npb	-	neuropeptide B	protein-coding
mm_115119.1	chr13	104228995	104229005	+	1	NA	promoter-TSS (NM_021790)	promoter-TSS (NM_021790)	-156	NM_172807	238831	Mm.98910	NM_172807	ENSMUSG00000021713	Ppwd1	4632422M10Rik|A330090G21Rik	peptidylprolyl isomerase domain and WD repeat containing 1	protein-coding
mm_135881.1	chr16	63864115	63864182	-	1	NA	promoter-TSS (NM_010140)	promoter-TSS (NM_010140)	9	NM_010140	13837	Mm.1977	NM_010140	ENSMUSG00000052504	Epha3	AW492086|Cek4|ETK1|End3|Hek|Hek4|Mek4|Tyro4	Eph receptor A3	protein-coding
mm_83185.1	chr9	40994574	40994589	-	1	NA	exon (NM_019465, exon 2 of 10)	exon (NM_019465, exon 2 of 10)	10047	NM_001281954	54698	Mm.42791	NM_019465	ENSMUSG00000032021	Crtam	-	cytotoxic and regulatory T cell molecule	protein-coding
mm_41990.1	chr5	107726058	107726067	+	1	NA	promoter-TSS (NM_001267621)	promoter-TSS (NM_001267621)	-257	NM_001267621	14581	Mm.2078	NM_010278	ENSMUSG00000029275	Gfi1	AW495828|Gfi-1|Pal-1|Pal1	growth factor independent 1	protein-coding
mm_18402.1	chr2	60284210	60284218	-	1	NA	5' UTR (NM_025422, exon 1 of 5)	5' UTR (NM_025422, exon 1 of 5)	270	NM_025422	66205	Mm.227281	NM_025422	ENSMUSG00000060703	Cd302	1110055L24Rik|AI159627	CD302 antigen	protein-coding
mm_123819.1	chr14	70599802	70599812	-	1	NA	promoter-TSS (NM_194345)	promoter-TSS (NM_194345)	28	NM_194345	239170	Mm.247582	NM_194345	ENSMUSG00000022095	Fam160b2	G430067P06Rik|Rai16	family with sequence similarity 160, member B2	protein-coding
mm_35447.1	chr4	40239780	40239831	-	1	NA	promoter-TSS (NM_172689)	promoter-TSS (NM_172689)	20	NM_172689	230073	Mm.86382	NM_172689	ENSMUSG00000040296	Ddx58	6430573D20Rik|C330021E21|RIG-I|RLR-1	DEAD (Asp-Glu-Ala-Asp) box polypeptide 58	protein-coding
mm_151711.1	chr19	4615648	4615700	-	1	NA	promoter-TSS (NM_153388)	promoter-TSS (NM_153388)	-7	NM_153388	225875	Mm.329675	NM_153388	ENSMUSG00000045045	Lrfn4	BC023156|Salm3	leucine rich repeat and fibronectin type III domain containing 4	protein-coding
mm_64932.1	chr7	16286745	16286788	-	1	NA	promoter-TSS (NM_001136471)	promoter-TSS (NM_001136471)	29	NM_001136471	243846	Mm.482401	NM_172297	ENSMUSG00000041375	Ccdc9	2600011L02Rik	coiled-coil domain containing 9	protein-coding
mm_79409.1	chr9	55149604	55149606	+	1	NA	promoter-TSS (NM_001346658)	promoter-TSS (NM_001346658)	236	NM_001346657	109161	Mm.207894	NM_180600	ENSMUSG00000032307	Ube2q2	3010021M21Rik	ubiquitin-conjugating enzyme E2Q family member 2	protein-coding
mm_67898.1	chr7	99626795	99626833	-	1	NA	5' UTR (NM_001195529, exon 1 of 1)	5' UTR (NM_001195529, exon 1 of 1)	289	NM_001195529	100503386	Mm.180719	NM_001195529	ENSMUSG00000096606	Tpbgl	EG245190|Gm4980	trophoblast glycoprotein-like	protein-coding
mm_33595.1	chr4	132565361	132565368	+	1	NA	intron (NM_001081211, intron 1 of 1)	intron (NM_001081211, intron 1 of 1)	1297	NM_001081211	19204	Mm.89389	NM_001081211	ENSMUSG00000056529	Ptafr	PAFR	platelet-activating factor receptor	protein-coding
mm_30709.1	chr4	12113357	12113365	+	1	NA	Intergenic	Intergenic	23991	NM_198957	77604	Mm.474129	NM_198957	ENSMUSG00000052137	Rbm12b2	AV299215|C430048L16Rik|Rbm12bb	RNA binding motif protein 12 B2	protein-coding
mm_51701.1	chr6	86612618	86612629	+	1	NA	Intergenic	L1MD3|LINE|L1	-15551	NM_026414	67855	Mm.183043	NM_026414	ENSMUSG00000033508	Asprv1	2300003P22Rik|AA986851|SASP|SASPase|Taps	aspartic peptidase, retroviral-like 1	protein-coding
mm_31156.1	chr4	43442321	43442339	+	1	NA	promoter-TSS (NM_011571)	promoter-TSS (NM_011571)	53	NM_011571	21754	Mm.485441	NM_011571	ENSMUSG00000028458	Tesk1	AI326901	testis specific protein kinase 1	protein-coding
mm_148372.1	chr18	88952788	88952805	-	1	NA	Intergenic	RMER19C|LTR|ERVK	-18994	NM_175542	246102	Mm.772	NM_175542	ENSMUSG00000023066	Rttn	4921538A15Rik|AI666264|C530033I08Rik|D230040K24	rotatin	protein-coding
mm_95110.1	chr11	34073536	34073558	+	1	NA	exon (NM_010696, exon 8 of 21)	exon (NM_010696, exon 8 of 21)	26346	NM_010696	16822	Mm.265350	NM_010696	ENSMUSG00000002699	Lcp2	AI323664|BB161688|SLP-76|SLP76|m1Khoe|twm	lymphocyte cytosolic protein 2	protein-coding
mm_169811.1	chr16	19160982	19161001	-	1	NA	Intergenic	ERVB7_1-LTR_MM|LTR|ERVK	125750	NM_146451	258443	Mm.377506	NM_146451	ENSMUSG00000050742	Olfr164	MOR279-2	olfactory receptor 164	protein-coding
mm_158708.1	chrX	162415247	162415261	-	1	NA	3' UTR (NM_001290633, exon 18 of 18)	3' UTR (NM_001290633, exon 18 of 18)	228404	NM_001290633	194590	Mm.442441	NM_178256	ENSMUSG00000040855	Reps2	POB1	RALBP1 associated Eps domain containing protein 2	protein-coding
mm_133527.1	chr16	90935032	90935051	+	1	NA	promoter-TSS (NM_026502)	promoter-TSS (NM_026502)	-192	NM_026502	68001	Mm.45374	NM_026502	ENSMUSG00000022972	1110004E09Rik	-	RIKEN cDNA 1110004E09 gene	protein-coding
mm_153922.1	chr19	47314746	47314761	-	1	NA	intron (NM_001164717, intron 7 of 13)	intron (NM_001164717, intron 7 of 13)	-41164	NR_105961	102466782		NR_105961	ENSMUSG00000098786	Mir6995	Gm27576|mmu-mir-6995	microRNA 6995	ncRNA
mm_90886.1	chr10	9996304	9996307	-	1	NA	Intergenic	Intergenic	-95265	NM_001081344	78808	Mm.331751	NM_030191	ENSMUSG00000019790	Stxbp5	0710001E20Rik|4930565N16Rik|AW742610|LGL3|mKIAA1006	syntaxin binding protein 5 (tomosyn)	protein-coding
mm_128714.1	chr15	63990619	63990621	-	1	NA	intron (NM_144846, intron 1 of 11)	ORR1D1|LTR|ERVL-MaLR	69828	NM_144846	223601	Mm.246108	NM_144846	ENSMUSG00000022378	Fam49b	0910001A06Rik|AW122079	family with sequence similarity 49, member B	protein-coding
mm_156198.1	chrX	134308140	134308209	+	1	NA	promoter-TSS (NM_145924)	promoter-TSS (NM_145924)	90	NM_001305631	102920	Mm.34903	NM_145924	ENSMUSG00000031262	Cenpi	CENP-I|Fshprh1	centromere protein I	protein-coding
mm_90214.1	chr10	120899898	120899901	+	1	NA	promoter-TSS (NM_177092)	promoter-TSS (NM_177092)	-928	NM_177092	320183	Mm.169755	NM_177092	ENSMUSG00000051236	Msrb3	D430026P16Rik|I-8-23|MsrB2	methionine sulfoxide reductase B3	protein-coding
mm_117601.1	chr13	90089061	90089092	-	1	NA	promoter-TSS (NM_025335)	promoter-TSS (NM_025335)	532	NM_028012	108138	Mm.37531	NM_028012	ENSMUSG00000021615	Xrcc4	2310057B22Rik|AW413319|AW545101	X-ray repair complementing defective repair in Chinese hamster cells 4	protein-coding
mm_25696.1	chr3	122268274	122268321	+	1	NA	Intergenic	B3|SINE|B2	-6117	NM_153806	99480	Mm.398647	NM_153806	ENSMUSG00000039756	Dnttip2	4930588M11Rik|AA408582|AU014960|HSU15552	deoxynucleotidyltransferase, terminal, interacting protein 2	protein-coding
mm_42186.1	chr5	112269311	112269318	+	1	NA	intron (NM_023695, intron 5 of 5)	intron (NM_023695, intron 5 of 5)	-7377	NM_001326590	22022	Mm.250631	NM_009419	ENSMUSG00000029344	Tpst2	AI448750|D5Ucla3|Tango13b|grm|grt	protein-tyrosine sulfotransferase 2	protein-coding
mm_24855.1	chr3	95877054	95877059	+	1	NA	intron (NR_040446, intron 1 of 3)	intron (NR_040446, intron 1 of 3)	5172	NM_001033302	229599	Mm.331218	NM_001033302	ENSMUSG00000038550	Ciart	Chrono|Gm129	circadian associated repressor of transcription	protein-coding
mm_110522.1	chr12	54863072	54863101	-	1	NA	promoter-TSS (NM_007688)	promoter-TSS (NM_007688)	-209	NM_007688	12632	Mm.276826	NM_007688	ENSMUSG00000062929	Cfl2	-	cofilin 2, muscle	protein-coding
mm_94829.1	chr11	23306885	23306906	+	1	NA	promoter-TSS (NM_001190401)	promoter-TSS (NM_001190401)	0	NM_001190401	17847	Mm.119155	NM_001190401	ENSMUSG00000056342	Usp34	A530081C03Rik|Murr2	ubiquitin specific peptidase 34	protein-coding
mm_36315.1	chr4	70243663	70243691	-	1	NA	intron (NM_145990, intron 29 of 36)	intron (NM_145990, intron 29 of 36)	166758	NM_001313762	214444	Mm.370777	NM_145990	ENSMUSG00000039298	Cdk5rap2	2900018K03Rik|an|mKIAA1633	CDK5 regulatory subunit associated protein 2	protein-coding
mm_40469.1	chr5	53809614	53809629	+	1	NA	promoter-TSS (NM_144517)	promoter-TSS (NM_144517)	-6	NM_144517	67249	Mm.28823	NM_144517	ENSMUSG00000039178	Tbc1d19	2810453K03Rik	TBC1 domain family, member 19	protein-coding
mm_125075.1	chr15	25984384	25984391	+	1	NA	promoter-TSS (NM_144523)	promoter-TSS (NM_144523)	21	NM_144523	52521	Mm.29145	NM_144523	ENSMUSG00000052253	Zfp622	1110033B05Rik|D15Ertd806e|ZPR9|Znf622	zinc finger protein 622	protein-coding
mm_66823.1	chr7	48691760	48691774	-	1	NA	Intergenic	Intergenic	-47966	NM_207537	404238	Mm.377926	NM_207537	ENSMUSG00000070546	Mrgprb3	MrgB3	MAS-related GPR, member B3	protein-coding
mm_23905.1	chr3	83032080	83032089	+	1	NA	3' UTR (NM_010196, exon 5 of 5)	3' UTR (NM_010196, exon 5 of 5)	5931	NM_001111048	14161	Mm.88793	NM_010196	ENSMUSG00000028001	Fga	ENSMUSG00000059807|Fib	fibrinogen alpha chain	protein-coding
mm_59359.1	chr7	25687126	25687136	+	1	NA	TTS (NM_172148)	TTS (NM_172148)	129	NM_011577	21803	Mm.248380	NM_011577	ENSMUSG00000002603	Tgfb1	TGF-beta1|TGFbeta1|Tgfb|Tgfb-1	transforming growth factor, beta 1	protein-coding
mm_78748.1	chr9	42142105	42142115	+	1	NA	Intergenic	Intergenic	-17821	NM_011436	20660	Mm.121920	NM_011436	ENSMUSG00000049313	Sorl1	2900010L19Rik|AI596264|AW261561|LR11|SorLA|gp250|mSorLA	sortilin-related receptor, LDLR class A repeats-containing	protein-coding
mm_157783.1	chrX	73824354	73824367	-	1	NA	5' UTR (NM_001290540, exon 1 of 6)	5' UTR (NM_001290540, exon 1 of 6)	609	NM_001029868	245469	Mm.103782	NM_001029868	ENSMUSG00000002006	Pdzd4	B230341P03|D130075J17Rik|Kiaa1444-hp|LU1|PDZRN4L|Pdzk4|Pdzrnk4l|Xlu	PDZ domain containing 4	protein-coding
mm_79023.1	chr9	45930357	45930367	+	1	NA	TTS (NM_008794)	TTS (NM_008794)	5696	NM_011526	21345	Mm.283283	NM_011526	ENSMUSG00000032085	Tagln	Sm22|Sm22a|Ws310	transgelin	protein-coding
mm_135544.1	chr16	49792516	49792528	-	1	NA	Intergenic	Intergenic	-63132	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_111575.1	chr12	101818944	101818952	-	1	NA	5' UTR (NM_011812, exon 1 of 11)	5' UTR (NM_011812, exon 1 of 11)	171	NM_011812	23876	Mm.288381	NM_011812	ENSMUSG00000021186	Fbln5	A55|DANCE|EVEC	fibulin 5	protein-coding
mm_73409.1	chr8	106011492	106011526	+	1	NA	promoter-TSS (NM_025518)	promoter-TSS (NM_025518)	-23	NM_028038	71986	Mm.307515	NM_028038	ENSMUSG00000045538	Ddx28	2410004K13Rik|AI449652|Mddx28	DEAD (Asp-Glu-Ala-Asp) box polypeptide 28	protein-coding
mm_108320.1	chr12	79750487	79750528	+	1	NA	intron (NM_009014, intron 8 of 10)	MIRc|SINE|MIR	174226	NR_131075	77290	Mm.395042	NR_131073		9430078K24Rik	-	RIKEN cDNA 9430078K24 gene	ncRNA
mm_101905.1	chr11	49204258	49204283	-	1	NA	intron (NM_009562, intron 1 of 3)	(TG)n|Simple_repeat|Simple_repeat	770	NM_009562	22720	Mm.16650	NM_009562	ENSMUSG00000046311	Zfp62	-	zinc finger protein 62	protein-coding
mm_69211.1	chr7	127470863	127470899	-	1	NA	promoter-TSS (NM_145589)	promoter-TSS (NM_145589)	-733	NM_145589	233895	Mm.44183	NM_145589	ENSMUSG00000030822	Prr14	BC006909	proline rich 14	protein-coding
mm_103692.1	chr11	79515570	79515581	-	1	NA	exon (NM_001077496, exon 2 of 2)	exon (NM_001077496, exon 2 of 2)	8187	NM_001077496	216984	Mm.439665	NM_001077496	ENSMUSG00000093938	Evi2b	Evi-2|Evi2	ecotropic viral integration site 2b	protein-coding
mm_162318.1	chr1	38704066	38704072	+	1	NA	Intergenic	Intergenic	-76825	NM_001290814	16764	Mm.336679	NM_010678	ENSMUSG00000037138	Aff3	3222402O04Rik|A730046J16|LAF-4|Laf4	AF4/FMR2 family, member 3	protein-coding
mm_39849.1	chr5	30913455	30913487	+	1	NA	promoter-TSS (NM_133918)	promoter-TSS (NM_133918)	-315	NM_133918	100952	Mm.286375	NM_133918	ENSMUSG00000029163	Emilin1	5830419M17Rik|AW229038|BB105748|EMILIN-1|gp115	elastin microfibril interfacer 1	protein-coding
mm_47988.1	chr5	135934620	135934633	-	1	NA	promoter-TSS (NM_018871)	promoter-TSS (NM_018871)	15	NM_018871	22628	Mm.233813	NM_018871	ENSMUSG00000051391	Ywhag	14-3-3gamma|D7Bwg1348e	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, gamma polypeptide	protein-coding
mm_27915.1	chr3	79531738	79531746	-	1	NA	intron (NM_001162999, intron 1 of 16)	intron (NM_001162999, intron 1 of 16)	35937	NM_001162999	329679	Mm.244005	NM_001162999	ENSMUSG00000061175	Fnip2	D630023B12Rik|mKIAA1450	folliculin interacting protein 2	protein-coding
mm_102116.1	chr11	53300200	53300221	-	1	NA	5' UTR (NM_008300, exon 1 of 19)	5' UTR (NM_008300, exon 1 of 19)	269	NM_008300	15525	Mm.239865	NM_008300	ENSMUSG00000020361	Hspa4	70kDa|AI317151|APG-2|Hsp110|Hsp70RY|mKIAA4025	heat shock protein 4	protein-coding
mm_113115.1	chr13	24487273	24487322	+	1	NA	Intergenic	Intergenic	72175	NM_001284520	12763	Mm.8396	NM_007717	ENSMUSG00000016756	Cmah	-	cytidine monophospho-N-acetylneuraminic acid hydroxylase	protein-coding
mm_82119.1	chr9	123462141	123462166	+	1	NA	3' UTR (NM_153168, exon 21 of 21)	3' UTR (NM_153168, exon 21 of 21)	-16548	NM_013860	29806	Mm.10987	NM_013860	ENSMUSG00000025239	Limd1	AW822033|D9Ertd192e	LIM domains containing 1	protein-coding
mm_56325.1	chr6	92481344	92481405	-	1	NA	promoter-TSS (NM_001134460)	promoter-TSS (NM_001134460)	18	NM_001134460	243548	Mm.248820	NM_001081146	ENSMUSG00000030020	Prickle2	6230400G14Rik|6720451F06Rik|mpk2	prickle planar cell polarity protein 2	protein-coding
mm_74514.1	chr8	8690042	8690116	-	1	NA	promoter-TSS (NR_106114)	promoter-TSS (NR_106114)	83	NR_106114	102465762		NR_106114	ENSMUSG00000098917	Mir7654	Gm27748|mmu-mir-7654	microRNA 7654	ncRNA
mm_33881.1	chr4	136172667	136172753	+	1	NA	5' UTR (NM_177733, exon 1 of 7)	5' UTR (NM_177733, exon 1 of 7)	436	NM_177733	242705	Mm.307932	NM_177733	ENSMUSG00000018983	E2f2	E2F-2	E2F transcription factor 2	protein-coding
mm_82609.1	chr9	21592806	21592846	-	1	NA	promoter-TSS (NM_138303)	promoter-TSS (NM_138303)	5	NM_001205158	74766	Mm.475712	NM_138303	ENSMUSG00000032182	Yipf2	1300010K09Rik	Yip1 domain family, member 2	protein-coding
mm_25343.1	chr3	106721899	106721954	+	1	NA	5' UTR (NM_001039488, exon 1 of 4)	5' UTR (NM_001039488, exon 1 of 4)	244	NM_001286685	321000	Mm.259638	NM_028081	ENSMUSG00000056260	Lrif1	2010012G17Rik|4933421E11Rik|AI450568	ligand dependent nuclear receptor interacting factor 1	protein-coding
mm_89968.1	chr10	111473963	111473966	+	1	NA	intron (NM_015781, intron 1 of 15)	intron (NM_015781, intron 1 of 15)	772	NM_015781	53605	Mm.290407	NM_015781	ENSMUSG00000058799	Nap1l1	AA407126|AI256722|D10Ertd68e|NAP-1	nucleosome assembly protein 1-like 1	protein-coding
mm_47700.1	chr5	129873269	129873273	-	1	NA	intron (NM_011079, intron 3 of 9)	intron (NM_011079, intron 3 of 9)	5812	NM_011079	18682	Mm.3159	NM_011079	ENSMUSG00000025537	Phkg1	Phkg	phosphorylase kinase gamma 1	protein-coding
mm_1115.1	chr1	59875097	59875120	+	1	NA	3' UTR (NM_007561, exon 13 of 13)	3' UTR (NM_007561, exon 13 of 13)	-37898	NM_001037725	72750	Mm.258250	NM_001037725	ENSMUSG00000041040	Fam117b	2810425F24Rik|6330416D14Rik|Als2cr13	family with sequence similarity 117, member B	protein-coding
mm_28414.1	chr3	90389885	90389924	-	1	NA	promoter-TSS (NM_001316688)	promoter-TSS (NM_001316688)	34	NM_001316688	26568	Mm.45519	NM_011988	ENSMUSG00000027932	Slc27a3	Acsvl3|FATP-3|FATP3|Vlcs-3	solute carrier family 27 (fatty acid transporter), member 3	protein-coding
mm_78407.1	chr9	29442398	29442403	+	1	NA	intron (NM_172290, intron 1 of 7)	MLT2D|LTR|ERVL	520729	NM_172290	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding
mm_142043.1	chr17	35425351	35425380	-	1	NA	exon (NM_207648, exon 2 of 5)	exon (NM_207648, exon 2 of 5)	488	NM_207648	110557	Mm.439827	NM_207648	ENSMUSG00000073409	H2-Q6	0610037M15Rik|H-2Q6|Qa-6|Qa6	histocompatibility 2, Q region locus 6	protein-coding
mm_32914.1	chr4	119136254	119136265	+	1	NA	exon (NM_011400, exon 10 of 10)	exon (NM_011400, exon 10 of 10)	27514	NM_011400	20525	Mm.21002	NM_011400	ENSMUSG00000028645	Slc2a1	Glut-1|Glut1	solute carrier family 2 (facilitated glucose transporter), member 1	protein-coding
mm_89061.1	chr10	82887723	82887731	+	1	NA	intron (NM_001042513, intron 13 of 14)	Charlie9|DNA|hAT-Charlie	21101	NM_025499	66341	Mm.443284	NM_025499	ENSMUSG00000109864	Eid3	1700027M21Rik|NS4EB	EP300 interacting inhibitor of differentiation 3	protein-coding
mm_7930.1	chr1	133907054	133907062	-	1	NA	5' UTR (NM_001160422, exon 1 of 5)	5' UTR (NM_001160422, exon 1 of 5)	115	NM_054076	269120	Mm.59985	NM_054076	ENSMUSG00000010311	Optc	-	opticin	protein-coding
mm_117979.1	chr13	100104084	100104094	-	1	NA	promoter-TSS (NM_001081061)	promoter-TSS (NM_001081061)	-19	NM_001081061	544971	Mm.288546	NM_001081061	ENSMUSG00000049658	Bdp1	AI662220|AW049390|AW456745|B130055N23Rik|G630013P12Rik|TAF3B1|TFC5|TFIIIB150|TFIIIB90|Tfnr|mKIAA1241	B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB	protein-coding
mm_71231.1	chr8	40905861	40905871	+	1	NA	intron (NM_007514, intron 6 of 11)	intron (NM_007514, intron 6 of 11)	-20367	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_70691.1	chr8	15018466	15018474	+	1	NA	intron (NM_029116, intron 1 of 1)	intron (NM_029116, intron 1 of 1)	7445	NM_029116	74901	Mm.46675	NM_029116	ENSMUSG00000055675	Kbtbd11	2900016B01Rik|4930465M17Rik|mKIAA0711	kelch repeat and BTB (POZ) domain containing 11	protein-coding
mm_50169.1	chr6	41554811	41554831	+	1	NA	Intergenic	Intergenic	33045	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_36603.1	chr4	88938424	88938433	-	1	NA	intron (NR_132735, intron 1 of 2)	L1M4b|LINE|L1	3614	NR_132734	106557447	Mm.484668	NR_132734		LOC106557447	-	uncharacterized LOC106557447	ncRNA
mm_170461.1	chr1	89216629	89216633	+	1	NA	Intergenic	Intergenic	146169	NM_133816	98402	Mm.170983	NM_133816	ENSMUSG00000036206	Sh3bp4	AI594717|AW227605|BOG25	SH3-domain binding protein 4	protein-coding
mm_167170.1	chr7	137789769	137789774	+	1	NA	Intergenic	Intergenic	352097	NR_033611	620016	Mm.388932	NR_033611	ENSMUSG00000100863	Gm12669	OTTMUSG00000007920	glutaredoxin 3 pseudogene	pseudo
mm_56371.1	chr6	93913679	93913719	-	1	NA	promoter-TSS (NR_104594)	promoter-TSS (NR_104594)	-9	NM_001083320	14924	Mm.217216	NM_010367	ENSMUSG00000045095	Magi1	AIP3|BAP1|Baiap1|Gukmi1|MAGI1c|Magi-1|TNRC19|WWP3|mKIAA4129	membrane associated guanylate kinase, WW and PDZ domain containing 1	protein-coding
mm_42763.1	chr5	121204824	121204850	+	1	NA	intron (NM_011290, intron 1 of 6)	CpG	336	NM_011290	19988	Mm.262021	NM_011290	ENSMUSG00000029614	Rpl6	Taxreb107	ribosomal protein L6	protein-coding
mm_35969.1	chr4	53149530	53149540	-	1	NA	intron (NM_013454, intron 1 of 49)	B1_Mur4|SINE|Alu	10360	NM_013454	11303	Mm.277376	NM_013454	ENSMUSG00000015243	Abca1	ABC-1|Abc1	ATP-binding cassette, sub-family A (ABC1), member 1	protein-coding
mm_95400.1	chr11	49722859	49722870	+	1	NA	Intergenic	L1MDb|LINE|L1	-10142	NM_212484	104625	Mm.247113	NM_212484	ENSMUSG00000020362	Cnot6	CCR4	CCR4-NOT transcription complex, subunit 6	protein-coding
mm_26009.1	chr3	135298934	135298940	+	1	NA	intron (NM_001172055, intron 7 of 9)	intron (NM_001172055, intron 7 of 9)	-8763	NM_178877	97086	Mm.441764	NM_178877	ENSMUSG00000037994	Slc9b2	C80638|NHA2|NHE10|Nhedc2|nha-oc|nhaoc	solute carrier family 9, subfamily B (NHA2, cation proton antiporter 2), member 2	protein-coding
mm_38443.1	chr4	139967116	139967133	-	1	NA	TTS (NR_035519)	TTS (NR_035519)	496	NR_035519	100316727		NR_035519	ENSMUSG00000089294	Mir2139	mmu-mir-2139	microRNA 2139	ncRNA
mm_106227.1	chr11	117265987	117266000	-	1	NA	promoter-TSS (NM_001113487)	promoter-TSS (NM_001113487)	-253	NM_001113487	53860	Mm.38450	NM_017380	ENSMUSG00000059248	Sept9	MSF1|Msf|PNUTL4|Sint1	septin 9	protein-coding
mm_120482.1	chr14	65975739	65975798	+	1	NA	exon (NM_013492, exon 5 of 9)	exon (NM_013492, exon 5 of 9)	7285	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_54687.1	chr6	39420419	39420481	-	1	NA	promoter-TSS (NM_018810)	promoter-TSS (NM_018810)	-81	NM_018810	54484	Mm.270484	NM_018810	ENSMUSG00000029922	Mkrn1	RFP	makorin, ring finger protein, 1	protein-coding
mm_85210.1	chr9	96787915	96787955	-	1	NA	Intergenic	Intergenic	22373	NR_102296	319707	Mm.392191	NR_102293	ENSMUSG00000101581	C430002N11Rik	-	RIKEN cDNA C430002N11 gene	ncRNA
mm_74235.1	chr8	124357233	124357244	+	1	NA	Intergenic	U4|snRNA|snRNA	76698	NM_171824	209966	Mm.234233	NM_171824	ENSMUSG00000050751	Pgbd5	2900019M05Rik|AI854313	piggyBac transposable element derived 5	protein-coding
mm_40660.1	chr5	65199692	65199735	+	1	NA	promoter-TSS (NM_153391)	promoter-TSS (NM_153391)	17	NM_153391	213081	Mm.127550	NM_153391	ENSMUSG00000037890	Wdr19	C330027H04Rik|D330023L08Rik|DYF2|Ift144|PWDMP|mKIAA1638	WD repeat domain 19	protein-coding
mm_25071.1	chr3	99352675	99352689	+	1	NA	3' UTR (NM_009323, exon 8 of 8)	3' UTR (NM_009323, exon 8 of 8)	98922	NM_009323	21384	Mm.88761	NM_009323	ENSMUSG00000027868	Tbx15	Tbx14|Tbx8|de	T-box 15	protein-coding
mm_73822.1	chr8	117456877	117456938	+	1	NA	exon (NM_001163262, exon 20 of 21)	exon (NM_001163262, exon 20 of 21)	-2358	NR_106046	102465653		NR_106046	ENSMUSG00000098483	Mir7078	Gm27386|mmu-mir-7078	microRNA 7078	ncRNA
mm_52118.1	chr6	97925663	97925666	+	1	NA	intron (NM_001113198, intron 1 of 9)	intron (NM_001113198, intron 1 of 9)	-4153	NM_001178049	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_141935.1	chr17	35046540	35046559	-	1	NA	promoter-TSS (NR_130641)	promoter-TSS (NR_130641)	73	NM_013600	17687	Mm.24192	NM_013600	ENSMUSG00000007035	Msh5	Mut5	mutS homolog 5	protein-coding
mm_62395.1	chr7	101108465	101108503	+	1	NA	promoter-TSS (NM_001146010)	promoter-TSS (NM_001146010)	-291	NM_001146010	207278	Mm.263041	NM_199012	ENSMUSG00000030691	Fchsd2	BC034086|R74866|Sh3md3|mKIAA0769	FCH and double SH3 domains 2	protein-coding
mm_94011.1	chr10	127621243	127621258	-	1	NA	promoter-TSS (NM_008512)	promoter-TSS (NM_008512)	-102	NM_008512	16971	Mm.271854	NM_008512	ENSMUSG00000040249	Lrp1	A2mr|AI316852|CD91|Lrp|b2b1554Clo	low density lipoprotein receptor-related protein 1	protein-coding
mm_52970.1	chr6	123229848	123229863	+	1	NA	promoter-TSS (NM_001190321)	promoter-TSS (NM_001190321)	12	NM_001190321	56620	Mm.271782	NM_020001	ENSMUSG00000023349	Clec4n	Clec6a|Clecsf10|Nkcl	C-type lectin domain family 4, member n	protein-coding
mm_48914.1	chr6	4003945	4004028	+	1	NA	promoter-TSS (NM_025331)	promoter-TSS (NM_025331)	-1	NM_025331	66066	Mm.25547	NM_025331	ENSMUSG00000032766	Gng11	0610037B21Rik	guanine nucleotide binding protein (G protein), gamma 11	protein-coding
mm_37023.1	chr4	114908893	114908914	-	1	NA	promoter-TSS (NM_008593)	promoter-TSS (NM_008593)	-5	NM_008593	17301	Mm.7997	NM_008593	ENSMUSG00000055210	Foxd2	AI426778|Mf2	forkhead box D2	protein-coding
mm_88309.1	chr10	75407006	75407022	+	1	NA	5' UTR (NM_133995, exon 1 of 10)	5' UTR (NM_133995, exon 1 of 10)	103	NM_133995	103149	Mm.441195	NM_133995	ENSMUSG00000033427	Upb1	AI195023	ureidopropionase, beta	protein-coding
mm_72229.1	chr8	74872693	74872740	+	1	NA	promoter-TSS (NM_027837)	promoter-TSS (NM_027837)	-458	NM_027837	71597	Mm.158735	NM_027837	ENSMUSG00000031621	Isx	9130012O13Rik|Pix-1	intestine specific homeobox	protein-coding
mm_129592.1	chr15	79804226	79804241	-	1	NA	exon (NM_030689, exon 1 of 5)	exon (NM_030689, exon 1 of 5)	476	NM_030689	73340	Mm.38438	NM_030689	ENSMUSG00000022421	Nptxr	1200009K17Rik|1700036C17Rik|5730406O18Rik|AI452369|AI785356|D15Bwg0580e|NPR|Npcd	neuronal pentraxin receptor	protein-coding
mm_121739.1	chr14	18332046	18332064	-	1	NA	promoter-TSS (NM_009455)	promoter-TSS (NM_009455)	-211	NM_009455	22194	Mm.4429	NM_009455	ENSMUSG00000021774	Ube2e1	UbcM3|Ubce5|ubcM2	ubiquitin-conjugating enzyme E2E 1	protein-coding
mm_73431.1	chr8	106135943	106135953	+	1	NA	intron (NR_040344, intron 1 of 4)	CpG	548	NR_040346	69771	Mm.393274	NR_040344		1810019D21Rik	-	RIKEN cDNA 1810019D21 gene	ncRNA
mm_93287.1	chr10	96263698	96263732	-	1	NA	Intergenic	Intergenic	37508	NR_110448	74881	Mm.410819	NR_110448		4930459C07Rik	-	RIKEN cDNA 4930459C07 gene	ncRNA
mm_79653.1	chr9	59617303	59617378	+	1	NA	promoter-TSS (NM_029922)	promoter-TSS (NM_029922)	56	NR_038074	67287	Mm.439943	NM_029922	ENSMUSG00000025237	Parp6	1700119G14Rik|2310028P13Rik|3110038K10Rik|ARTD17|C030013N01Rik|PARP-6	poly (ADP-ribose) polymerase family, member 6	protein-coding
mm_138689.1	chr17	35970057	35970068	+	1	NA	promoter-TSS (NM_013854)	promoter-TSS (NM_013854)	-312	NM_013854	224742	Mm.329022	NM_013854	ENSMUSG00000038762	Abcf1	AU041969|Abc50|D17Wsu166e|GCN20	ATP-binding cassette, sub-family F (GCN20), member 1	protein-coding
mm_111773.1	chr12	104044351	104044366	-	1	NA	promoter-TSS (NM_026535)	promoter-TSS (NM_026535)	85	NM_026535	68054	Mm.20286	NM_026535	ENSMUSG00000041567	Serpina12	4632419J12Rik	serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 12	protein-coding
mm_137021.1	chr17	17865452	17865471	+	1	NA	Intergenic	Intergenic	-10273	NM_008215	15116	Mm.255701	NM_008215	ENSMUSG00000003665	Has1	HAS	hyaluronan synthase1	protein-coding
mm_61153.1	chr7	58658356	58658376	+	1	NA	5' UTR (NM_009728, exon 1 of 21)	5' UTR (NM_009728, exon 1 of 21)	164	NM_009728	11982	Mm.135129	NM_009728	ENSMUSG00000025324	Atp10a	Atp10c|pfatp	ATPase, class V, type 10A	protein-coding
mm_141189.1	chr17	26939465	26939525	-	1	NA	promoter-TSS (NM_026307)	promoter-TSS (NM_026307)	-37	NR_104458	67675	Mm.439919	NM_026307	ENSMUSG00000024194	Cuta	0610039D01Rik|1810022E02Rik|1810060C03Rik|2700094G22Rik|AI326454	cutA divalent cation tolerance homolog	protein-coding
mm_96316.1	chr11	63989692	63989700	+	1	NA	intron (NM_178379, intron 5 of 6)	intron (NM_178379, intron 5 of 6)	25470	NR_131111	78883	Mm.410764	NR_131111	ENSMUSG00000086359	9630013K17Rik	-	RIKEN cDNA 9630013K17 gene	ncRNA
mm_47155.1	chr5	120630008	120630019	-	1	NA	exon (NM_001195094, exon 5 of 7)	exon (NM_001195094, exon 5 of 7)	4222	NM_001195094	546886	Mm.464847	NM_001195094	ENSMUSG00000094282	Cfap73	Ccdc42b|Gm5988	cilia and flagella associated protein 73	protein-coding
mm_15032.1	chr2	152736245	152736261	+	1	NA	promoter-TSS (NM_010495)	promoter-TSS (NM_010495)	2	NM_010495	15901	Mm.444	NM_010495	ENSMUSG00000042745	Id1	AI323524|D2Wsu140e|Idb1|bHLHb24	inhibitor of DNA binding 1	protein-coding
mm_20998.1	chr2	152332559	152332569	-	1	NA	promoter-TSS (NM_019705)	promoter-TSS (NM_019705)	75	NM_019705	24105	Mm.182145	NM_019705	ENSMUSG00000027466	Rbck1	AL033326|HOIL-1|HOIL-1L|UIP28|Ubce7ip3	RanBP-type and C3HC4-type zinc finger containing 1	protein-coding
mm_45456.1	chr5	67776125	67776129	-	1	NA	intron (NM_001284345, intron 8 of 36)	intron (NM_001284345, intron 8 of 36)	71304	NM_009727	11980	Mm.153230	NM_009727	ENSMUSG00000037685	Atp8a1	AI481521|AI853962|APLT|AW743152|AW822227|Atp3a2|B230107D19Rik|ClassI	ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1	protein-coding
mm_24747.1	chr3	95318802	95318819	+	1	NA	promoter-TSS (NM_001320492)	promoter-TSS (NM_001320492)	-20	NM_001320492	76893	Mm.181009	NM_029789	ENSMUSG00000015714	Cers2	0610013I17Rik|AI225939|Lass2|TRH3	ceramide synthase 2	protein-coding
mm_71004.1	chr8	31111790	31111799	+	1	NA	promoter-TSS (NM_175136)	promoter-TSS (NM_175136)	-52	NM_175136	68867	Mm.29532	NM_175136	ENSMUSG00000039328	Rnf122	1110063C11Rik	ring finger protein 122	protein-coding
mm_85892.1	chr9	111055254	111055265	-	1	NA	3' UTR (NM_017466, exon 2 of 2)	3' UTR (NM_017466, exon 2 of 2)	1985	NM_001302377	54199	Mm.7336	NM_017466	ENSMUSG00000043953	Ccrl2	1810047I05Rik|Ackr5|CCR11|Cmkbr1l2|E01|L-CCR	chemokine (C-C motif) receptor-like 2	protein-coding
mm_19560.1	chr2	98667265	98667282	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	1199616	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_150918.1	chr19	46076000	46076020	+	1	NA	5' UTR (NM_001039352, exon 1 of 13)	5' UTR (NM_001039352, exon 1 of 13)	163	NM_001039351	70769	Mm.402190	NM_053086	ENSMUSG00000015176	Nolc1	NOPP130|NOPP140|P130	nucleolar and coiled-body phosphoprotein 1	protein-coding
mm_119859.1	chr14	54467486	54467519	+	1	NA	exon (NM_022993, exon 4 of 7)	exon (NM_022993, exon 4 of 7)	3355	NM_022993	65107	Mm.472719	NM_022993	ENSMUSG00000022175	Lrp10	Lrp9	low-density lipoprotein receptor-related protein 10	protein-coding
mm_136873.1	chr17	12918085	12918101	+	1	NA	exon (NM_013686, exon 3 of 12)	exon (NM_013686, exon 3 of 12)	1764	NM_013686	21454	Mm.229342	NM_013686	ENSMUSG00000068039	Tcp1	AI528772|CCT|Cct1|Ccta|TRic|Tcp-1|Tp63|c-cpn|p63	t-complex protein 1	protein-coding
mm_86124.1	chr9	116175177	116175185	-	1	NA	5' UTR (NM_029575, exon 1 of 7)	5' UTR (NM_029575, exon 1 of 7)	182	NM_029575	21813	Mm.172346	NM_009371	ENSMUSG00000032440	Tgfbr2	1110020H15Rik|AU042018|DNIIR|RIIDN|TBR-II|TbetaR-II|TbetaRII	transforming growth factor, beta receptor II	protein-coding
mm_125643.1	chr15	62181746	62181761	+	1	NA	intron (NR_132746, intron 3 of 6)	intron (NR_132746, intron 3 of 6)	37698	NR_003523	67552	Mm.484027	NM_026230		H2afy3	4933432H23Rik	H2A histone family, member Y3	pseudo
mm_111740.1	chr12	103865775	103865783	-	1	NA	Intergenic	Intergenic	-2160	NM_009243	20700	Mm.439692	NM_009243	ENSMUSG00000066366	Serpina1a	Aat-2|Aat2|Dom1|PI1|Spi1-1|Spi1-3	serine (or cysteine) peptidase inhibitor, clade A, member 1A	protein-coding
mm_26665.1	chr3	154711098	154711107	+	1	NA	promoter-TSS (NM_175176)	promoter-TSS (NM_175176)	-31	NM_175176	209601	Mm.331454	NM_175176	ENSMUSG00000078161	Erich3	1700013E18Rik|4922501L14Rik|5031409G23Rik|AI596448|Gm133	glutamate rich 3	protein-coding
mm_21862.1	chr2	165885516	165885531	-	1	NA	promoter-TSS (NM_001252584)	promoter-TSS (NM_001252584)	-685	NM_001252587	228880	Mm.227598	NM_027230	ENSMUSG00000039671	Zmynd8	1110013E22Rik|2010005I16Rik|3632413B07Rik|AI316811|AL024039|Prkcbp1|RACK7	zinc finger, MYND-type containing 8	protein-coding
mm_16463.1	chr2	180604100	180604145	+	1	NA	intron (NM_009936, intron 9 of 31)	intron (NM_009936, intron 9 of 31)	5900	NM_009936	12841	Mm.141312	NM_009936	ENSMUSG00000027570	Col9a3	AV006866	collagen, type IX, alpha 3	protein-coding
mm_119060.1	chr14	30716879	30716882	+	1	NA	intron (NM_001166532, intron 1 of 20)	intron (NM_001166532, intron 1 of 20)	1265	NM_001166532	54650	Mm.294662	NM_019460	ENSMUSG00000006527	Sfmbt1	4930442N21Rik|9330180L21Rik|AA536974|Sfmbt|Smr	Scm-like with four mbt domains 1	protein-coding
mm_22782.1	chr3	21962716	21962761	+	1	NA	Intergenic	B4|SINE|B4	-113914	NM_030732	81004	Mm.202966	NM_030732	ENSMUSG00000027630	Tbl1xr1	8030499H02Rik|A630076E03Rik|AW539987|C21|C230089I12Rik|DC42|Ira1|TBLR1	transducin (beta)-like 1X-linked receptor 1	protein-coding
mm_95197.1	chr11	43155782	43155784	+	1	NA	intron (NM_176999, intron 3 of 22)	intron (NM_176999, intron 3 of 22)	5906	NM_176999	319767	Mm.252339	NM_176999	ENSMUSG00000055415	Atp10b	5930426O13Rik|9030605H24Rik	ATPase, class V, type 10B	protein-coding
mm_81688.1	chr9	111125342	111125344	+	1	NA	intron (NM_027742, intron 2 of 13)	L1MB3|LINE|L1	7232	NM_001164838	71268	Mm.302287	NM_027742	ENSMUSG00000032497	Lrrfip2	5133400F20Rik|AI850587	leucine rich repeat (in FLII) interacting protein 2	protein-coding
mm_82059.1	chr9	122686766	122686769	+	1	NA	Intergenic	Intergenic	3891	NR_029819	387156		NR_029819	ENSMUSG00000065414	Mir138-1	Mirn138|Mirn138-1|mir-138-1	microRNA 138-1	ncRNA
mm_65834.1	chr7	29180652	29180689	-	1	NA	promoter-TSS (NM_026545)	promoter-TSS (NM_026545)	3	NM_026545	57296	Mm.273152	NM_026545	ENSMUSG00000030591	Psmd8	6720456J22Rik|AA407360|AL033291|AL033322|AL033323|C76433	proteasome (prosome, macropain) 26S subunit, non-ATPase, 8	protein-coding
mm_34479.1	chr4	148448553	148448563	+	1	NA	promoter-TSS (NM_020009)	promoter-TSS (NM_020009)	-24	NM_020009	56717	Mm.21158	NM_020009	ENSMUSG00000028991	Mtor	2610315D21Rik|AI327068|FRAP|FRAP2|Frap1|RAFT1|RAPT1|flat	mechanistic target of rapamycin (serine/threonine kinase)	protein-coding
mm_13982.1	chr2	121506716	121506733	+	1	NA	promoter-TSS (NM_030234)	promoter-TSS (NM_030234)	1	NM_001290986	241627	Mm.293284	NM_030234	ENSMUSG00000027242	Wdr76	5830411K18Rik|6030457D09|AA517836	WD repeat domain 76	protein-coding
mm_39501.1	chr5	21186376	21186390	+	1	NA	exon (NM_175437, exon 1 of 31)	exon (NM_175437, exon 1 of 31)	116	NM_175437	212167	Mm.121705	NM_175437	ENSMUSG00000039934	Gsap	A530088I07Rik|Pion	gamma-secretase activating protein	protein-coding
mm_55342.1	chr6	56569109	56569122	-	1	NA	Intergenic	Intergenic	135584	NM_025520	66373	Mm.25642	NM_025520	ENSMUSG00000091625	Lsm5	2010208O10Rik|2310034K10Rik	LSM5 homolog, U6 small nuclear RNA and mRNA degradation associated	protein-coding
mm_171614.1	chr4	150281540	150281544	+	1	NA	promoter-TSS (NM_001085492)	promoter-TSS (NM_001085492)	-374	NM_001085492	68703	Mm.291274	NM_001085492	ENSMUSG00000039852	Rere	1110033A15Rik|AI414665|ARG|ARP|ATN1L|AW742570|Atr2|DNB1|eye<m03Jus>|eyes3|mKIAA0458	arginine glutamic acid dipeptide (RE) repeats	protein-coding
mm_98407.1	chr11	94339845	94339855	+	1	NA	TTS (NM_146024)	TTS (NM_146024)	11849	NM_146024	71452	Mm.141054	NM_027799	ENSMUSG00000020864	Ankrd40	1110011C06Rik|5530600A18Rik|Gcap15	ankyrin repeat domain 40	protein-coding
mm_111808.1	chr12	105222713	105222722	-	1	NA	promoter-TSS (NR_110339)	promoter-TSS (NR_110339)	20	NM_001309485	21432	Mm.18154	NM_009337	ENSMUSG00000041359	Tcl1	Tcl1a	T cell lymphoma breakpoint 1	protein-coding
mm_65128.1	chr7	19458802	19458856	-	1	NA	promoter-TSS (NM_172279)	promoter-TSS (NM_172279)	-335	NM_172279	232944	Mm.260504	NM_172279	ENSMUSG00000030397	Mark4	2410090P21Rik|C79806|Markl1	MAP/microtubule affinity regulating kinase 4	protein-coding
mm_125776.1	chr15	74636852	74636863	+	1	NA	promoter-TSS (NM_001177437)	promoter-TSS (NM_001177437)	-539	NM_001177437	69439	Mm.263708	NM_001177437	ENSMUSG00000022603	Mroh4	1700016M24Rik	maestro heat-like repeat family member 4	protein-coding
mm_171029.1	chr2	88513524	88513537	+	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	-11971	NM_146530	258523	Mm.377551	NM_146530	ENSMUSG00000082882	Olfr1186	MOR230-5	olfactory receptor 1186	protein-coding
mm_6027.1	chr1	59316107	59316128	-	1	NA	intron (NM_001033373, intron 10 of 13)	intron (NM_001033373, intron 10 of 13)	59210	NM_001033373	271697	Mm.297713	NM_001033373	ENSMUSG00000026023	Cdk15	Als2cr7|Pftk2	cyclin-dependent kinase 15	protein-coding
mm_55316.1	chr6	55132959	55132973	-	1	NA	promoter-TSS (NM_001288618)	promoter-TSS (NM_001288618)	50	NM_009953	12922	Mm.236081	NM_009953	ENSMUSG00000003476	Crhr2	CRF-R2|CRFR2alpha|CRFR2beta|Crfr2	corticotropin releasing hormone receptor 2	protein-coding
mm_24725.1	chr3	95282499	95282555	+	1	NA	promoter-TSS (NM_133858)	promoter-TSS (NM_133858)	-408	NM_133858	75007	Mm.279287	NM_133858	ENSMUSG00000038712	Fam63a	1810005H09Rik|4930504E06Rik|AA562754|AA960384|AW561904|cI-40|mKIAA1390|ni	family with sequence similarity 63, member A	protein-coding
mm_131296.1	chr16	11399621	11399639	+	1	NA	intron (NM_028964, intron 5 of 20)	intron (NM_028964, intron 5 of 20)	-6018	NM_001290148	74478	Mm.325831	NM_028964	ENSMUSG00000071669	Snx29	4933437K13Rik|ENSMUSG00000079738|Gm11170|Gm1737|Gm930|Rundc2a	sorting nexin 29	protein-coding
mm_46254.1	chr5	99252840	99252854	-	1	NA	promoter-TSS (NM_181318)	promoter-TSS (NM_181318)	80	NM_181318	320292	Mm.259074	NM_145839	ENSMUSG00000089809	Rasgef1b	4732452O09Rik|GPIgamma4|Gpig4	RasGEF domain family, member 1B	protein-coding
mm_146499.1	chr18	3281728	3281742	-	1	NA	promoter-TSS (NM_001110855)	promoter-TSS (NM_001110855)	12	NM_001110854	12916	Mm.5244	NM_013498	ENSMUSG00000063889	Crem	ICER|ICERI	cAMP responsive element modulator	protein-coding
mm_94903.1	chr11	29197658	29197664	+	1	NA	intron (NM_134034, intron 7 of 15)	intron (NM_134034, intron 7 of 15)	24754	NM_134034	104570	Mm.276386	NM_134034	ENSMUSG00000020463	Smek2	AW011752|AW557776|Ppp4r3b|mKIAA1387	SMEK homolog 2, suppressor of mek1 (Dictyostelium)	protein-coding
mm_76789.1	chr8	102739221	102739251	-	1	NA	intron (NM_009866, intron 1 of 12)	intron (NM_009866, intron 1 of 12)	45875	NM_009866	12552	Mm.1571	NM_009866	ENSMUSG00000031673	Cdh11	Cad11|OSF-4	cadherin 11	protein-coding
mm_83318.1	chr9	44144528	44144548	-	1	NA	Intergenic	Intergenic	9880	NM_023061	84004	Mm.275003	NM_023061	ENSMUSG00000032135	Mcam	1-gicerin|AV025631|CD146|CD149|Muc18|s-endo|s-gicerin	melanoma cell adhesion molecule	protein-coding
mm_10994.1	chr2	26330427	26330441	+	1	NA	intron (NM_153410, intron 9 of 13)	intron (NM_153410, intron 9 of 13)	10664	NM_001199147	67839	Mm.266611	NM_153410	ENSMUSG00000026930	Gpsm1	1810037C22Rik|AW107933|Ags3	G-protein signalling modulator 1 (AGS3-like, C. elegans)	protein-coding
mm_103578.1	chr11	78160911	78160929	-	1	NA	exon (NM_009423, exon 6 of 7)	exon (NM_009423, exon 6 of 7)	4630	NM_009423	22032	Mm.390418	NM_009423	ENSMUSG00000017386	Traf4	A530032M13Rik|CART1|msp2	TNF receptor associated factor 4	protein-coding
mm_103763.1	chr11	81153706	81153719	-	1	NA	promoter-TSS (NM_007384)	promoter-TSS (NM_007384)	-809	NM_007384	11418	Mm.234998	NM_007384	ENSMUSG00000020704	Asic2	ACIC2|Accn1|BNC1|BNaC1|BNaC1a|Mdeg	acid-sensing (proton-gated) ion channel 2	protein-coding
mm_62055.1	chr7	92447509	92447525	+	1	NA	3' UTR (NM_001243047, exon 11 of 11)	3' UTR (NM_001243047, exon 11 of 11)	-113632	NM_025515	66365	Mm.21173	NM_025515	ENSMUSG00000030613	Ccdc90b	2310015N07Rik|C86558	coiled-coil domain containing 90B	protein-coding
mm_55246.1	chr6	52640304	52640386	-	1	NA	promoter-TSS (NM_145567)	promoter-TSS (NM_145567)	-45	NM_145567	58875	Mm.286458	NM_145567	ENSMUSG00000029776	Hibadh	6430402H10Rik|AI265272	3-hydroxyisobutyrate dehydrogenase	protein-coding
mm_49918.1	chr6	39126620	39126644	+	1	NA	intron (NR_045813, intron 1 of 3)	MTEb|LTR|ERVL-MaLR	8159	NR_045813	75379	Mm.348014	NR_045813	ENSMUSG00000073144	4930599N23Rik	-	RIKEN cDNA 4930599N23 gene	ncRNA
mm_148056.1	chr18	72144839	72144848	-	1	NA	intron (NM_007831, intron 1 of 28)	Lx2B2|LINE|L1	206226	NM_007831	13176	Mm.167882	NM_007831	ENSMUSG00000060534	Dcc	C030036D22Rik|Igdcc1	deleted in colorectal carcinoma	protein-coding
mm_107596.1	chr12	49382058	49382078	+	1	NA	promoter-TSS (NM_008241)	promoter-TSS (NM_008241)	-815	NM_001160112	15228	Mm.4704	NM_008241	ENSMUSG00000020950	Foxg1	2900064B05Rik|BF-1|Bf1|Hfh9|Hfhbf1	forkhead box G1	protein-coding
mm_50782.1	chr6	53698067	53698069	+	1	NA	3' UTR (NM_001327821, exon 11 of 11)	3' UTR (NM_001327821, exon 11 of 11)	122757	NM_025817	66873	Mm.422727	NM_025817	ENSMUSG00000043496	Tril	1200009O22Rik|AI316813|mKIAA0644	TLR4 interactor with leucine-rich repeats	protein-coding
mm_36655.1	chr4	94650135	94650149	-	1	NA	promoter-TSS (NM_175305)	promoter-TSS (NM_175305)	2	NM_175305	100061	Mm.26760	NM_175305	ENSMUSG00000049799	Lrrc19	9130022A01Rik|AI314124|AL022954|AW261791	leucine rich repeat containing 19	protein-coding
mm_98932.1	chr11	98356713	98356726	+	1	NA	intron (NM_144828, intron 5 of 6)	intron (NM_144828, intron 5 of 6)	1564	NR_045477	69338	Mm.398308	NR_045477	ENSMUSG00000085944	1700003D09Rik	-	RIKEN cDNA 1700003D09 gene	ncRNA
mm_73939.1	chr8	120101355	120101395	+	1	NA	promoter-TSS (NM_133967)	promoter-TSS (NM_133967)	97	NM_133967	102193	Mm.240076	NM_133967	ENSMUSG00000031823	Zdhhc7	AL024087|Gramp2	zinc finger, DHHC domain containing 7	protein-coding
mm_75299.1	chr8	41061202	41061205	-	1	NA	intron (NM_001005863, intron 3 of 13)	intron (NM_001005863, intron 3 of 13)	-6407	NM_001005864	102103	Mm.149438	NM_001005863	ENSMUSG00000045636	Mtus1	AI481402|ATBP135|Atip1|B430010I23Rik|B430305I03Rik|C85752|Cctsg1-440|MD44|MTSG1|mKIAA1288	mitochondrial tumor suppressor 1	protein-coding
mm_172079.1	chr6	145932835	145932840	-	1	NA	intron (NM_001310837, intron 1 of 2)	LSU-rRNA_Hsa|rRNA|rRNA	964	NM_001310837	16651	Mm.49689	NM_010656	ENSMUSG00000030255	Sspn	Krag	sarcospan	protein-coding
mm_171208.1	chr3	5860394	5860406	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-284152	NM_001163305	19302	Mm.132336	NM_008994	ENSMUSG00000040374	Pex2	D3Ertd138e|PAF-1|PMP35|Pxmp3	peroxisomal biogenesis factor 2	protein-coding
mm_35627.1	chr4	43478766	43478811	-	1	NA	Intergenic	Intergenic	4921	NM_019436	54390	Mm.31775	NM_019436	ENSMUSG00000028460	Sit1	Sit	suppression inducing transmembrane adaptor 1	protein-coding
mm_513.1	chr1	37400369	37400372	+	1	NA	intron (NM_001290797, intron 25 of 25)	(T)n|Simple_repeat|Simple_repeat	29733	NM_198006	76178	Mm.28085	NM_198006	ENSMUSG00000026112	Coa5	1700001A24Rik|6330578E17Rik|Pet191	cytochrome C oxidase assembly factor 5	protein-coding
mm_59792.1	chr7	28984730	28984730	+	1	NA	intron (NM_008279, intron 4 of 31)	BC1_Mm|scRNA|scRNA	1876	NM_008279	26411	Mm.148278	NM_008279	ENSMUSG00000037337	Map4k1	Hpk1|mHPK1	mitogen-activated protein kinase kinase kinase kinase 1	protein-coding
mm_85431.1	chr9	103692786	103692812	-	1	NA	intron (NM_178638, intron 2 of 5)	intron (NM_178638, intron 2 of 5)	69038	NM_178638	81907	Mm.384704	NM_178638	ENSMUSG00000042757	Tmem108	AI462967|B130017P16Rik|R74726	transmembrane protein 108	protein-coding
mm_133137.1	chr16	66852634	66852635	+	1	NA	intron (NM_001347247, intron 2 of 9)	RLTR16|LTR|ERVK	195516	NR_040512	75501	Mm.394300	NR_040512	ENSMUSG00000092599	1700010K23Rik	-	RIKEN cDNA 1700010K23 gene	ncRNA
mm_166748.1	chr6	125191675	125191678	-	1	NA	promoter-TSS (NM_025595)	promoter-TSS (NM_025595)	-90	NM_146171	68298	Mm.257590	NM_146171	ENSMUSG00000038252	Ncapd2	2810406C15Rik|2810465G24Rik|CAP-D2|CNAP1|mKIAA0159	non-SMC condensin I complex, subunit D2	protein-coding
mm_18052.1	chr2	39196553	39196573	-	1	NA	TTS (NM_024209)	TTS (NM_024209)	-5833	NM_178778	320271	Mm.204836	NM_178778	ENSMUSG00000035236	Scai	9330112M16|A930041I02Rik|AI662729	suppressor of cancer cell invasion	protein-coding
mm_53990.1	chr6	6871622	6871635	-	1	NA	Intergenic	Intergenic	-2095	NR_015388	320038	Mm.94021	NR_015388		Dlx6os1	A230055N17Rik|Dlx6as1|Evf-1|Evf-2|Evf1|Evf1/2|Evf2|Shhrs|mEvf-1	distal-less homeobox 6, opposite strand 1	ncRNA
mm_21154.1	chr2	154548759	154548780	-	1	NA	promoter-TSS (NM_029305)	promoter-TSS (NM_029305)	-135	NM_029305	75480	Mm.440434	NM_029305	ENSMUSG00000038523	1700003F12Rik	-	RIKEN cDNA 1700003F12 gene	protein-coding
mm_19451.1	chr2	92001893	92001904	-	1	NA	exon (NM_011957, exon 2 of 12)	exon (NM_011957, exon 2 of 12)	22272	NM_011957	26427	Mm.10353	NM_011957	ENSMUSG00000027230	Creb3l1	Oasis	cAMP responsive element binding protein 3-like 1	protein-coding
mm_150542.1	chr19	39310674	39310684	+	1	NA	intron (NM_007815, intron 5 of 8)	intron (NM_007815, intron 5 of 8)	23594	NM_007815	13095	Mm.20764	NM_007815	ENSMUSG00000003053	Cyp2c29	AHOH|AHOHase|AI159681|AI196010|Ah-2|Ahh-1|Cyp2c|P450-2C	cytochrome P450, family 2, subfamily c, polypeptide 29	protein-coding
mm_54214.1	chr6	25689872	25689898	-	1	NA	promoter-TSS (NM_010338)	promoter-TSS (NM_010338)	95	NM_010338	14763	Mm.409670	NM_010338	ENSMUSG00000039904	Gpr37	AI848630|Pael-R	G protein-coupled receptor 37	protein-coding
mm_15710.1	chr2	164017667	164017684	+	1	NA	3' UTR (NM_018753, exon 6 of 6)	3' UTR (NM_018753, exon 6 of 6)	-7549	NM_001114079	381404	Mm.82301	NM_001114079	ENSMUSG00000054582	Pabpc1l	1810053B01Rik|Epab	poly(A) binding protein, cytoplasmic 1-like	protein-coding
mm_107165.1	chr12	24681926	24681936	+	1	NA	promoter-TSS (NM_001161807)	promoter-TSS (NM_001161807)	-136	NM_001161807	12879	Mm.52265	NM_138686	ENSMUSG00000062563	Cys1	2900006B19Rik|AV218859|Ccap|ck|cpk	cystin 1	protein-coding
mm_132144.1	chr16	32078226	32078234	+	1	NA	intron (NM_177326, intron 1 of 14)	intron (NM_177326, intron 1 of 14)	1112	NM_177326	224105	Mm.234204	NM_177326	ENSMUSG00000022781	Pak2	5330420P17Rik|A130002K10Rik|AI836325|D16Ertd269e|PAK-2|mKIAA4182	p21 protein (Cdc42/Rac)-activated kinase 2	protein-coding
mm_14256.1	chr2	128159286	128159295	+	1	NA	3' UTR (NM_009754, exon 4 of 4)	3' UTR (NM_009754, exon 4 of 4)	31715	NM_001284410	12125	Mm.141083	NM_009754	ENSMUSG00000027381	Bcl2l11	1500006F24Rik|Bim|Bod|bcl2-L-11	BCL2-like 11 (apoptosis facilitator)	protein-coding
mm_89915.1	chr10	111178429	111178442	+	1	NA	intron (NM_175489, intron 1 of 23)	intron (NM_175489, intron 1 of 23)	13633	NM_175489	237542	Mm.220204	NM_175489	ENSMUSG00000020189	Osbpl8	AA536976|AA536995|C730029P18Rik|D330025H14Rik|ORP-8	oxysterol binding protein-like 8	protein-coding
mm_69100.1	chr7	127020083	127020110	-	1	NA	exon (NM_001102563, exon 2 of 4)	exon (NM_001102563, exon 2 of 4)	1115	NM_001102563	69017	Mm.392047	NM_001102563	ENSMUSG00000045114	Prrt2	1500031I19Rik|AI195361|DSPB3	proline-rich transmembrane protein 2	protein-coding
mm_149538.1	chr19	12465859	12465876	+	1	NA	TTS (NM_010821)	TTS (NM_010821)	5088	NM_010821	17476	Mm.3999	NM_010821	ENSMUSG00000046805	Mpeg1	MPS1|Mpg-1	macrophage expressed gene 1	protein-coding
mm_88768.1	chr10	80335922	80335939	+	1	NA	3' UTR (NM_139292, exon 6 of 6)	3' UTR (NM_139292, exon 6 of 6)	5785	NM_139292	70335	Mm.28147	NM_139292	ENSMUSG00000035504	Reep6	0610011M24Rik|Dp1l1	receptor accessory protein 6	protein-coding
mm_167217.1	chr8	9506266	9506275	+	1	NA	intron (NM_001347127, intron 1 of 3)	LTR40a|LTR|ERVL	264753	NM_173446	270028	Mm.268163	NM_173446	ENSMUSG00000079157	Fam155a	6430500D16|AW121567|Tmem28	family with sequence similarity 155, member A	protein-coding
mm_20670.1	chr2	132247624	132247644	-	1	NA	5' UTR (NM_027478, exon 1 of 4)	5' UTR (NM_027478, exon 1 of 4)	154	NM_027478	70612	Mm.30116	NM_027478	ENSMUSG00000027341	Tmem230	5730494N06Rik|AA407821	transmembrane protein 230	protein-coding
mm_52247.1	chr6	106332445	106332446	+	1	NA	intron (NM_001109751, intron 4 of 18)	intron (NM_001109751, intron 4 of 18)	213680	NM_001109751	269784	Mm.321683	NM_173004	ENSMUSG00000064293	Cntn4	9630050B05|Axcam|BIG-2	contactin 4	protein-coding
mm_163457.1	chr12	98385696	98385699	-	1	NA	Intergenic	Intergenic	117062	NM_008152	14744	Mm.378924	NM_008152	ENSMUSG00000021886	Gpr65	Dig1|Gpcr25|TDAG8	G-protein coupled receptor 65	protein-coding
mm_44785.1	chr5	32135625	32135642	-	1	NA	promoter-TSS (NM_008037)	promoter-TSS (NM_008037)	-839	NM_008037	14284	Mm.24684	NM_008037	ENSMUSG00000029135	Fosl2	Fra-2	fos-like antigen 2	protein-coding
mm_44865.1	chr5	34336819	34336832	-	1	NA	promoter-TSS (NM_001304270)	promoter-TSS (NM_001304270)	-107	NM_001304270	19822	Mm.21281	NM_011278	ENSMUSG00000029110	Rnf4	AU018689|Gtrgeo8|SNURF	ring finger protein 4	protein-coding
mm_150148.1	chr19	31914330	31914335	+	1	NA	intron (NM_001081074, intron 4 of 11)	intron (NM_001081074, intron 4 of 11)	45571	NM_001081074	69865	Mm.87538	NM_001081074	ENSMUSG00000052595	A1cf	1810073H04Rik|ACF64|ACF65|ASP|Acf|MCM|MerCreMer|Tg(Myh6-cre/Esr1*)1Jmk|mer	APOBEC1 complementation factor	protein-coding
mm_113065.1	chr13	23746746	23746763	+	1	NA	promoter-TSS (NM_175664)	promoter-TSS (NM_175664)	20	NM_175664	319178	Mm.390567	NM_175664	ENSMUSG00000075031	Hist1h2bb	H2b-143	histone cluster 1, H2bb	protein-coding
mm_57987.1	chr6	136171514	136171524	-	1	NA	5' UTR (NM_008171, exon 3 of 15)	5' UTR (NM_008171, exon 3 of 15)	1992	NM_008171	14812	Mm.436649	NM_008171	ENSMUSG00000030209	Grin2b	AW490526|GluN2B|NR2B|Nmdar2b	glutamate receptor, ionotropic, NMDA2B (epsilon 2)	protein-coding
mm_125860.1	chr15	75216355	75216392	+	1	NA	Intergenic	Intergenic	-52048	NM_008530	17071	Mm.377095	NM_008530	ENSMUSG00000022583	Ly6f	-	lymphocyte antigen 6 complex, locus F	protein-coding
mm_50300.1	chr6	47545697	47545716	+	1	NA	exon (NM_001146689, exon 10 of 20)	exon (NM_001146689, exon 10 of 20)	49324	NM_007971	14056	Mm.246688	NM_007971	ENSMUSG00000029687	Ezh2	Enx-1|Enx1h|KMT6|mKIAA4065	enhancer of zeste 2 polycomb repressive complex 2 subunit	protein-coding
mm_170007.1	chr17	16676775	16676788	-	1	NA	Intergenic	Intergenic	-387322	NM_001005358	449000	Mm.483718	NM_001005358	ENSMUSG00000096696	Zfp960	-	zinc finger protein 960	protein-coding
mm_7830.1	chr1	132116940	132116951	-	1	NA	exon (NM_008795, exon 11 of 16)	exon (NM_008795, exon 11 of 16)	22740	NM_008795	18557	Mm.28130	NM_008795	ENSMUSG00000026437	Cdk18	AA682070|Ctk18|Pctk3	cyclin-dependent kinase 18	protein-coding
mm_83277.1	chr9	43071284	43071334	-	1	NA	intron (NM_027144, intron 1 of 40)	intron (NM_027144, intron 1 of 40)	34409	NM_027144	69632	Mm.275266	NM_027144	ENSMUSG00000059495	Arhgef12	2310014B11Rik|AU019857|Larg|mKIAA0382	Rho guanine nucleotide exchange factor (GEF) 12	protein-coding
mm_113936.1	chr13	49653298	49653367	+	1	NA	promoter-TSS (NM_025495)	promoter-TSS (NM_025495)	254	NR_073167	70930	Mm.258915	NM_001081350	ENSMUSG00000021392	Nol8	4921532D18Rik|5730412B09Rik	nucleolar protein 8	protein-coding
mm_53888.1	chr6	3376933	3376943	-	1	NA	exon (NM_010156, exon 2 of 2)	exon (NM_010156, exon 2 of 2)	22633	NM_010156	209086	Mm.196013	NM_010156	ENSMUSG00000047735	Samd9l	AA175286|ESTM25|mKIAA2005	sterile alpha motif domain containing 9-like	protein-coding
mm_134459.1	chr16	18413453	18413467	-	1	NA	promoter-TSS (NM_001111063)	promoter-TSS (NM_001111063)	34	NM_001111063	12846	Mm.100940	NM_007744	ENSMUSG00000000326	Comt	Comt1|D16Wsu103e|D330014B15Rik	catechol-O-methyltransferase	protein-coding
mm_163158.1	chr11	83850884	83850886	+	1	NA	promoter-TSS (NM_001291268)	promoter-TSS (NM_001291268)	16	NM_009330	21410	Mm.7226	NM_009330	ENSMUSG00000020679	Hnf1b	HNF-1-beta|HNF-1B|HNF-1Beta|Hnf1beta|LFB3|Tcf-2|Tcf2|vHNF1	HNF1 homeobox B	protein-coding
mm_137536.1	chr17	27556602	27556612	+	1	NA	promoter-TSS (NM_001166545)	promoter-TSS (NM_001166545)	3	NM_001166537	15361	Mm.4438	NM_016660	ENSMUSG00000046711	Hmga1	AL023995|Hmga1a|Hmga1b|Hmgi|Hmgiy|Hmgy	high mobility group AT-hook 1	protein-coding
mm_831.1	chr1	51289362	51289370	+	1	NA	5' UTR (NM_138741, exon 1 of 2)	5' UTR (NM_138741, exon 1 of 2)	240	NM_138741	20324	Mm.398690	NM_138741	ENSMUSG00000045954	Sdpr	-	serum deprivation response	protein-coding
mm_19319.1	chr2	90563190	90563203	-	1	NA	intron (NM_008982, intron 1 of 23)	intron (NM_008982, intron 1 of 23)	17451	NM_008982	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_110688.1	chr12	69159110	69159133	-	1	NA	promoter-TSS (NM_009093)	promoter-TSS (NM_009093)	65	NM_009093	20090	Mm.379006	NM_009093	ENSMUSG00000034892	Rps29	-	ribosomal protein S29	protein-coding
mm_111500.1	chr12	99393011	99393090	-	1	NA	intron (NM_183186, intron 1 of 5)	CpG	57024	NM_183186	71375	Mm.341972	NM_183186	ENSMUSG00000033713	Foxn3	5430426H20Rik|AA589593|AW556347|Ches1|Ches1l|HTLFL1	forkhead box N3	protein-coding
mm_28110.1	chr3	86548583	86548598	-	1	NA	promoter-TSS (NM_011839)	promoter-TSS (NM_011839)	-307	NM_011839	23937	Mm.389466	NM_011839	ENSMUSG00000057777	Mab21l2	-	mab-21-like 2 (C. elegans)	protein-coding
mm_110069.1	chr12	21417139	21417163	-	1	NA	5' UTR (NM_011739, exon 1 of 5)	5' UTR (NM_011739, exon 1 of 5)	285	NM_011739	22630	Mm.289630	NM_011739	ENSMUSG00000076432	Ywhaq	2700028P07Rik|AA409740|AU021156|R74690	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide	protein-coding
mm_131619.1	chr16	19760826	19760836	+	1	NA	intron (NM_054052, intron 2 of 3)	intron (NM_054052, intron 2 of 3)	597	NM_001159407	108105	Mm.33935	NM_054052	ENSMUSG00000022686	B3gnt5	beta3GnT5	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5	protein-coding
mm_131027.1	chr16	3723594	3723595	+	1	NA	Intergenic	Intergenic	-5470	NM_001161791	54483	Mm.143718	NM_019453	ENSMUSG00000022534	Mefv	FMF|TRIM20|pyrin	Mediterranean fever	protein-coding
mm_93946.1	chr10	127230739	127230771	-	1	NA	intron (NM_008447, intron 25 of 27)	intron (NM_008447, intron 25 of 27)	-19133	NM_054097	117150	Mm.22682	NM_054097	ENSMUSG00000025417	Pip4k2c	Pip5k2c	phosphatidylinositol-5-phosphate 4-kinase, type II, gamma	protein-coding
mm_18258.1	chr2	52277513	52277531	-	1	NA	exon (NM_010889, exon 46 of 157)	exon (NM_010889, exon 46 of 157)	-13480	NR_040620	78049	Mm.243883	NR_040620		4930573O16Rik	-	RIKEN cDNA 4930573O16 gene	ncRNA
mm_148879.1	chr19	6498167	6498173	+	1	NA	intron (NM_001205234, intron 17 of 22)	CpG	44900	NM_009203	20521	Mm.391146	NM_009203	ENSMUSG00000061742	Slc22a12	AI987855|OAT4L|Rst|Slc22al2|URAT1	solute carrier family 22 (organic anion/cation transporter), member 12	protein-coding
mm_27297.1	chr3	46445644	46445646	-	1	NA	3' UTR (NM_001101479, exon 2 of 2)	3' UTR (NM_001101479, exon 2 of 2)	2296	NM_001101479	241989	Mm.119234	NM_001101479	ENSMUSG00000090919	Pabpc4l	C330050A14Rik|EG241989	poly(A) binding protein, cytoplasmic 4-like	protein-coding
mm_67230.1	chr7	74555183	74555196	-	1	NA	promoter-TSS (NM_023908)	promoter-TSS (NM_023908)	-409	NM_001038643	108116	Mm.425467	NM_023908	ENSMUSG00000025790	Slco3a1	5830414C08Rik|Anr1|MJAM|OATP-D|R75096|Slc21a11	solute carrier organic anion transporter family, member 3a1	protein-coding
mm_39827.1	chr5	30798574	30798623	+	1	NA	3' UTR (NM_023047, exon 13 of 13)	3' UTR (NM_023047, exon 13 of 13)	-16043	NM_133350	100732	Mm.332295	NM_133350	ENSMUSG00000029166	Mapre3	AI790651|EB2|EB3|EBF3|RP3	microtubule-associated protein, RP/EB family, member 3	protein-coding
mm_87537.1	chr10	53580426	53580430	+	1	NA	intron (NM_027830, intron 8 of 13)	RMER17B|LTR|ERVK	-16533	NM_025541	66403	Mm.272989	NM_025541	ENSMUSG00000019857	Asf1a	2310079C17Rik|C79052	anti-silencing function 1A histone chaperone	protein-coding
mm_87765.1	chr10	60292847	60292850	+	1	NA	intron (NM_001146120, intron 3 of 13)	PB1D9|SINE|Alu	8387	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_106668.1	chr11	121519774	121519794	-	1	NA	promoter-TSS (NM_178763)	promoter-TSS (NM_178763)	-442	NM_178763	319530	Mm.11395	NM_178763	ENSMUSG00000039238	Zfp750	A030007D23Rik|Znf750	zinc finger protein 750	protein-coding
mm_127691.1	chr15	102982098	102982118	+	1	NA	exon (NM_008272, exon 2 of 3)	exon (NM_008272, exon 2 of 3)	5076	NM_008272	15427	Mm.4765	NM_008272	ENSMUSG00000036139	Hoxc9	Hox-3.2	homeobox C9	protein-coding
mm_44182.1	chr5	151368684	151368723	+	1	NA	promoter-TSS (NR_045700)	promoter-TSS (NR_045700)	28	NR_045699	625175	Mm.443286	NR_045699	ENSMUSG00000097321	1700028E10Rik	A630054D14|Gm6561	RIKEN cDNA 1700028E10 gene	ncRNA
mm_11629.1	chr2	34775582	34775593	+	1	NA	exon (NM_001163434, exon 9 of 9)	exon (NM_001163434, exon 9 of 9)	3497	NM_022310	14828	Mm.330160	NM_022310	ENSMUSG00000026864	Hspa5	AL022860|AU019543|Bip|D2Wsu141e|D2Wsu17e|Grp78|Hsce70|SEZ-7|Sez7|baffled|mBiP	heat shock protein 5	protein-coding
mm_75934.1	chr8	71535472	71535489	-	1	NA	intron (NM_198095, intron 3 of 4)	B4A|SINE|B4	1957	NM_198095	69550	Mm.260325	NM_198095	ENSMUSG00000046718	Bst2	2310015I10Rik|Bst-2|C87040|CD317|DAMP-1|GREG	bone marrow stromal cell antigen 2	protein-coding
mm_142760.1	chr17	49113467	49113469	-	1	NA	promoter-TSS (NR_038142)	promoter-TSS (NR_038142)	65	NR_038141	69311	Mm.46140	NR_038141	ENSMUSG00000101012	1700008K24Rik	-	RIKEN cDNA 1700008K24 gene	ncRNA
mm_115955.1	chr13	23761168	23761188	-	1	NA	promoter-TSS (NM_178192)	promoter-TSS (NM_178192)	71	NM_178192	326619	Mm.228709	NM_178192	ENSMUSG00000060093	Hist1h4a	-	histone cluster 1, H4a	protein-coding
mm_72669.1	chr8	84908614	84908673	+	1	NA	promoter-TSS (NM_010062)	promoter-TSS (NM_010062)	19	NM_010062	13423	Mm.350831	NM_010062	ENSMUSG00000003812	Dnase2a	Dnase2	deoxyribonuclease II alpha	protein-coding
mm_63004.1	chr7	120842917	120842925	+	1	NA	promoter-TSS (NM_001267710)	promoter-TSS (NM_001267710)	90	NM_007908	13631	Mm.25997	NM_007908	ENSMUSG00000035064	Eef2k	C86191|eEF-2K	eukaryotic elongation factor-2 kinase	protein-coding
mm_117162.1	chr13	62653193	62653232	-	1	NA	Intergenic	Intergenic	-29030	NM_173381	211378	Mm.247448	NM_173381	ENSMUSG00000072066	6720489N17Rik	9330128I06	RIKEN cDNA 6720489N17 gene	protein-coding
mm_147440.1	chr18	46525078	46525086	-	1	NA	intron (NM_173423, intron 1 of 2)	intron (NM_173423, intron 1 of 2)	889	NM_173423	240263	Mm.38249	NM_173423	ENSMUSG00000033319	Fem1c	2610312A07Rik|3632443A22Rik|AI646567	fem-1 homolog c (C.elegans)	protein-coding
mm_127796.1	chr15	3583429	3583441	-	1	NA	promoter-TSS (NM_010284)	promoter-TSS (NM_010284)	-83	NM_010284	14600	Mm.3986	NM_010284	ENSMUSG00000055737	Ghr	GHBP|GHR/BP	growth hormone receptor	protein-coding
mm_144336.1	chr18	14424822	14424823	+	1	NA	Intergenic	Intergenic	192516	NR_045373	74529	Mm.400519	NR_045373		8430422H06Rik	-	RIKEN cDNA 8430422H06 gene	ncRNA
mm_1680.1	chr1	74854955	74854965	+	1	NA	promoter-TSS (NM_009872)	promoter-TSS (NM_009872)	-69	NM_009872	12570	Mm.153833	NM_009872	ENSMUSG00000090071	Cdk5r2	B230310J22Rik|p39	cyclin-dependent kinase 5, regulatory subunit 2 (p39)	protein-coding
mm_83612.1	chr9	48652474	48652490	-	1	NA	Intergenic	(A)n|Simple_repeat|Simple_repeat	-47359	NM_010924	18113	Mm.8362	NM_010924	ENSMUSG00000032271	Nnmt	-	nicotinamide N-methyltransferase	protein-coding
mm_171193.1	chr3	46140925	46140942	+	1	NA	Intergenic	L1_Mus3|LINE|L1	307008	NM_001101479	241989	Mm.119234	NM_001101479	ENSMUSG00000090919	Pabpc4l	C330050A14Rik|EG241989	poly(A) binding protein, cytoplasmic 4-like	protein-coding
mm_96091.1	chr11	60417129	60417133	+	1	NA	promoter-TSS (NM_145427)	promoter-TSS (NM_145427)	-14	NM_025757	66771	Mm.29950	NM_025757	ENSMUSG00000018415	Gid4	4933439F18Rik	GID complex subunit 4, VID24 homolog	protein-coding
mm_108661.1	chr12	86421783	86421797	+	1	NA	5' UTR (NM_011934, exon 1 of 7)	5' UTR (NM_011934, exon 1 of 7)	146	NM_011934	26380	Mm.235550	NM_011934	ENSMUSG00000021255	Esrrb	Err2|Errb|Estrrb|Nr3b2	estrogen related receptor, beta	protein-coding
mm_32274.1	chr4	102741288	102741298	+	1	NA	Intergenic	Intergenic	-18842	NM_001285860	73094	Mm.54201	NM_144906	ENSMUSG00000028524	Sgip1	3110007P09Rik|SGIP1alpha|gag	SH3-domain GRB2-like (endophilin) interacting protein 1	protein-coding
mm_144687.1	chr18	34777848	34777863	+	1	NA	intron (NM_001081256, intron 1 of 23)	intron (NM_001081256, intron 1 of 23)	847	NM_001081256	277250	Mm.277906	NM_029518	ENSMUSG00000038773	Kdm3b	5830462I21Rik|JHDM2B|Jmjd1b|mKIAA1082	KDM3B lysine (K)-specific demethylase 3B	protein-coding
mm_136874.1	chr17	12991000	12991012	+	1	NA	intron (NM_175394, intron 1 of 5)	B3|SINE|B2	1253	NM_001113533	60532	Mm.275521	NM_175394	ENSMUSG00000060475	Wtap	2810408K05Rik|9430038B09Rik	Wilms tumour 1-associating protein	protein-coding
mm_14802.1	chr2	145886877	145886899	+	1	NA	3' UTR (NM_028724, exon 13 of 13)	3' UTR (NM_028724, exon 13 of 13)	-16353	NM_026425	67877	Mm.151168	NM_026425	ENSMUSG00000002728	Naa20	1500004D14Rik|2900026I01Rik|AU041458|D2Ertd186e|Nat5	N(alpha)-acetyltransferase 20, NatB catalytic subunit	protein-coding
mm_167428.1	chr8	117074884	117074895	+	1	NA	intron (NM_029686, intron 4 of 42)	L1ME3Cz|LINE|L1	7560	NM_029686	76645	Mm.159753	NM_029686	ENSMUSG00000034416	Pkd1l2	1700126L06Rik	polycystic kidney disease 1 like 2	protein-coding
mm_26435.1	chr3	142620687	142620704	+	1	NA	promoter-TSS (NM_010260)	promoter-TSS (NM_010260)	32	NM_010260	14469	Mm.24038	NM_010260	ENSMUSG00000028270	Gbp2	-	guanylate binding protein 2	protein-coding
mm_23210.1	chr3	41564873	41564906	+	1	NA	promoter-TSS (NM_001130186)	promoter-TSS (NM_001130186)	9	NM_001130186	269424	Mm.286285	NM_172303	ENSMUSG00000025764	Jade1	AU041499|D530048A03Rik|Phf17|mKIAA1807	jade family PHD finger 1	protein-coding
mm_168786.1	chr12	19044390	19044402	+	1	NA	Intergenic	CpG	529886	NM_001201330	236366	Mm.352227	NM_001033157	ENSMUSG00000073197	5730507C01Rik	-	RIKEN cDNA 5730507C01 gene	protein-coding
mm_107514.1	chr12	40223572	40223616	+	1	NA	promoter-TSS (NM_013562)	promoter-TSS (NM_013562)	230	NR_045157	629820	Mm.435540	NR_045157	ENSMUSG00000035983	Gm7008	EG629820	predicted gene 7008	ncRNA
mm_72744.1	chr8	85087213	85087225	+	1	NA	exon (NM_010764, exon 6 of 24)	exon (NM_010764, exon 6 of 24)	3950	NM_010764	17159	Mm.4219	NM_010764	ENSMUSG00000005142	Man2b1	AW107687|LAMAN	mannosidase 2, alpha B1	protein-coding
mm_168773.1	chr12	17464081	17464089	-	1	NA	Intergenic	MMERVK9E_I-int|LTR|ERVK	-80788	NM_013614	18263	Mm.34102	NM_013614	ENSMUSG00000011179	Odc1	ODC	ornithine decarboxylase, structural 1	protein-coding
mm_11880.1	chr2	49527332	49527333	+	1	NA	intron (NM_172663, intron 4 of 13)	intron (NM_172663, intron 4 of 13)	75846	NM_172663	227867	Mm.29167	NM_172663	ENSMUSG00000069495	Epc2	5830499L14|D2Ertd694e	enhancer of polycomb homolog 2 (Drosophila)	protein-coding
mm_130375.1	chr15	97824787	97824791	-	1	NA	intron (NM_001204275, intron 1 of 24)	MIRb|SINE|MIR	6978	NM_019572	56233	Mm.384027	NM_019572	ENSMUSG00000022475	Hdac7	5830434K02Rik|HD7|HD7a|Hdac7a|mFLJ00062	histone deacetylase 7	protein-coding
mm_6779.1	chr1	84137487	84137500	-	1	NA	intron (NM_001003948, intron 2 of 2)	Lx7|LINE|L1	81468	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_117627.1	chr13	92030898	92030908	-	1	NA	Intergenic	Intergenic	-42861	NM_009027	19418	Mm.248630	NM_009027	ENSMUSG00000021708	Rasgrf2	6330417G04Rik|AW048350|Grf2|Ras-GRF2	RAS protein-specific guanine nucleotide-releasing factor 2	protein-coding
mm_10148.1	chr2	4300624	4300635	+	1	NA	intron (NM_172475, intron 1 of 22)	intron (NM_172475, intron 1 of 22)	-100347	NM_001177843	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding
mm_140583.1	chr17	10212422	10212447	-	1	NA	3' UTR (NM_001159516, exon 7 of 7)	3' UTR (NM_001159516, exon 7 of 7)	106927	NM_021881	19317	Mm.130694	NM_021881	ENSMUSG00000062078	Qk	1110003F05Rik|1500005P18|QkI|l(17)-1Wis|l17Wis1	quaking	protein-coding
mm_35217.1	chr4	19650425	19650445	-	1	NA	exon (NM_177327, exon 9 of 25)	exon (NM_177327, exon 9 of 25)	58569	NM_177327	107568	Mm.78312	NM_177327	ENSMUSG00000041058	Wwp1	8030445B08Rik|AIP5|SDRP1|Tiul1	WW domain containing E3 ubiquitin protein ligase 1	protein-coding
mm_103343.1	chr11	74724133	74724160	-	1	NA	promoter-TSS (NR_037610)	promoter-TSS (NR_037610)	238	NM_013625	18472	Mm.397111	NM_013625	ENSMUSG00000020745	Pafah1b1	LIS-1|Lis1|MMS10-U|Mdsh|Ms10u|Pafaha	platelet-activating factor acetylhydrolase, isoform 1b, subunit 1	protein-coding
mm_16728.1	chr2	7396142	7396152	-	1	NA	promoter-TSS (NM_001110232)	promoter-TSS (NM_001110232)	51	NM_001110231	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_104836.1	chr11	99155068	99155085	-	1	NA	promoter-TSS (NM_007719)	promoter-TSS (NM_007719)	1	NM_001301713	12775	Mm.2932	NM_007719	ENSMUSG00000037944	Ccr7	CC-CKR-7|CCR-7|CD197|Cdw197|Cmkbr7|EBI1|Ebi1h	chemokine (C-C motif) receptor 7	protein-coding
mm_45738.1	chr5	86469135	86469141	-	1	NA	promoter-TSS (NM_001033233)	promoter-TSS (NM_001033233)	-148	NM_001033233	194597	Mm.249106	NM_001033233	ENSMUSG00000072845	Tmprss11a	Gm7	transmembrane protease, serine 11a	protein-coding
mm_73732.1	chr8	113638729	113638741	+	1	NA	exon (NM_001048143, exon 4 of 6)	exon (NM_001048143, exon 4 of 6)	2936	NM_173015	270096	Mm.74689	NM_173015	ENSMUSG00000078908	Mon1b	5031407H10|5033413H12Rik	MON1 homolog B, secretory traffciking associated	protein-coding
mm_94950.1	chr11	29742084	29742143	+	1	NA	TTS (NM_146016)	TTS (NM_146016)	23550	NM_024226	68585	Mm.192580	NM_024226	ENSMUSG00000020458	Rtn4	1110020G17Rik|AA407876|AA409940|AA960376|ASY|C130026I10Rik|NOGO|NSP-CL|NgA|Nogo-A|Nogo-B|Nogo-C|mKIAA0886|mKIAA4153	reticulon 4	protein-coding
mm_115885.1	chr13	21832195	21832198	-	1	NA	promoter-TSS (NM_175657).2	promoter-TSS (NM_175657).2	-38	NM_175657	319161	Mm.261664	NM_175657	ENSMUSG00000069305	Hist1h4n	-	histone cluster 1, H4n	protein-coding
mm_164173.1	chr15	75704265	75704291	+	1	NA	promoter-TSS (NM_001163465)	promoter-TSS (NM_001163465)	-10	NM_001163465	14787	Mm.57052	NM_008164	ENSMUSG00000022580	Rhpn1	BB023497|Grbp|Rhophilin|mKIAA1929	rhophilin, Rho GTPase binding protein 1	protein-coding
mm_102262.1	chr11	55336545	55336553	-	1	NA	Intergenic	Intergenic	-24292	NM_001029988	245827	Mm.339363	NM_001029988	ENSMUSG00000055333	Fat2	EMI2|Fath2|Gm523|mKIAA0811	FAT atypical cadherin 2	protein-coding
mm_36307.1	chr4	68954741	68954758	-	1	NA	promoter-TSS (NM_019967)	promoter-TSS (NM_019967)	-352	NM_019967	56710	Mm.248788	NM_019967	ENSMUSG00000028351	Brinp1	BRINP|Dbc1|Dbccr1|Fam5a	bone morphogenic protein/retinoic acid inducible neural specific 1	protein-coding
mm_117186.1	chr13	63540324	63540329	-	1	NA	intron (NM_001328514, intron 10 of 23)	intron (NM_001328514, intron 10 of 23)	25409	NM_008957	19206	Mm.228798	NM_008957	ENSMUSG00000021466	Ptch1	A230106A15Rik|Ptc|Ptc1|Ptch|mes	patched 1	protein-coding
mm_133714.1	chr16	93607832	93607896	+	1	NA	promoter-TSS (NM_007620)	promoter-TSS (NM_007620)	27	NM_007620	12408	Mm.26940	NM_007620	ENSMUSG00000051483	Cbr1	AW261796|CR|Cbr	carbonyl reductase 1	protein-coding
mm_14343.1	chr2	129593206	129593221	+	1	NA	promoter-TSS (NM_001291022)	promoter-TSS (NM_001291022)	44	NM_001291022	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_77520.1	chr8	122895913	122895933	-	1	NA	non-coding (NR_037865, exon 10 of 14)	non-coding (NR_037865, exon 10 of 14)	47549	NM_007662	12555	Mm.1976	NM_007662	ENSMUSG00000031962	Cdh15	AI323380|Cdh14|Mcad	cadherin 15	protein-coding
mm_99424.1	chr11	102393522	102393542	+	1	NA	5' UTR (NM_001252347, exon 1 of 11)	5' UTR (NM_001252347, exon 1 of 11)	129	NM_001252347	51799	Mm.2560	NM_016759	ENSMUSG00000006575	Rundc3a	RPIP-8|Rap2ip|Rpip8	RUN domain containing 3A	protein-coding
mm_117804.1	chr13	97482509	97482521	-	1	NA	promoter-TSS (NR_110431)	promoter-TSS (NR_110431)	-186	NR_110430	100039691	Mm.219358	NR_110430	ENSMUSG00000078952	Lncenc1	ENSMUSG00000078952|Gm11019|Gm2373|Lincenc1|Platr18|linc-Enc1	long non-coding RNA, embryonic stem cells expressed 1	ncRNA
mm_46724.1	chr5	110770133	110770173	-	1	NA	intron (NM_173066, intron 1 of 50)	CpG	564	NM_029337	75560	Mm.270487	NM_029337	ENSMUSG00000029505	Ep400	1700020J09Rik|AU023439|mDomino|mKIAA1498|p400	E1A binding protein p400	protein-coding
mm_108900.1	chr12	100199520	100199538	+	1	NA	promoter-TSS (NM_009790)	promoter-TSS (NM_009790)	94	NM_009790	12313	Mm.285993	NM_009790	ENSMUSG00000001175	Calm1	AI256814|AI327027|AI461935|AL024000|CaM|Calm	calmodulin 1	protein-coding
mm_67532.1	chr7	81345101	81345111	-	1	NA	intron (NM_009092, intron 1 of 4)	CpG-13305	128	NM_009092	20068	Mm.42767	NM_009092	ENSMUSG00000061787	Rps17	-	ribosomal protein S17	protein-coding
mm_62634.1	chr7	107653056	107653072	+	1	NA	exon (NM_008905, exon 3 of 25)	exon (NM_008905, exon 3 of 25)	46220	NM_001163557	19024	Mm.2817	NM_008905	ENSMUSG00000036528	Ppfibp2	Cclp1	PTPRF interacting protein, binding protein 2 (liprin beta 2)	protein-coding
mm_32921.1	chr4	119136874	119136889	+	1	NA	3' UTR (NM_011400, exon 10 of 10)	3' UTR (NM_011400, exon 10 of 10)	28136	NM_011400	20525	Mm.21002	NM_011400	ENSMUSG00000028645	Slc2a1	Glut-1|Glut1	solute carrier family 2 (facilitated glucose transporter), member 1	protein-coding
mm_96008.1	chr11	59542628	59542644	+	1	NA	promoter-TSS (NM_145827)	promoter-TSS (NM_145827)	-50	NM_145827	216799	Mm.54174	NM_145827	ENSMUSG00000032691	Nlrp3	AGTAVPRL|AII/AVP|Cias1|FCAS|FCU|MWS|Mmig1|NALP3|Pypaf1	NLR family, pyrin domain containing 3	protein-coding
mm_166604.1	chr6	67534773	67534781	-	1	NA	exon (NM_020047, exon 1 of 1)	exon (NM_020047, exon 1 of 1)	1045	NM_020047	56753	Mm.439913	NM_020047	ENSMUSG00000051397	Tacstd2	C80403|EGP-1|GA733-1|Ly97|TROP2	tumor-associated calcium signal transducer 2	protein-coding
mm_27542.1	chr3	57651668	57651727	-	1	NA	promoter-TSS (NM_175095)	promoter-TSS (NM_175095)	-13	NM_175095	52245	Mm.21901	NM_175095	ENSMUSG00000036513	Commd2	1190017G07Rik|AI047739|D3Ertd176e|HSPC042	COMM domain containing 2	protein-coding
mm_129438.1	chr15	78512457	78512476	-	1	NA	Intergenic	Intergenic	17185	NM_001204153	72709	Mm.34776	NM_028331	ENSMUSG00000022440	C1qtnf6	2810036M19Rik|CTRP6	C1q and tumor necrosis factor related protein 6	protein-coding
mm_133725.1	chr16	93777209	93777219	+	1	NA	intron (NM_027293, intron 22 of 36)	(CA)n|Simple_repeat|Simple_repeat	-54907	NM_001045529	338467	Mm.287329	NM_001045529	ENSMUSG00000039456	Morc3	1110051N18Rik|AI452146|BF318192|D16Jhu32e|NXP2|Zcwcc3	microrchidia 3	protein-coding
mm_66418.1	chr7	44531368	44531381	-	1	NA	intron (NM_019866, intron 1 of 5)	intron (NM_019866, intron 1 of 5)	697	NM_019866	272382	Mm.8012	NM_019866	ENSMUSG00000008193	Spib	Spi-B	Spi-B transcription factor (Spi-1/PU.1 related)	protein-coding
mm_5340.1	chr1	24100307	24100355	-	1	NA	promoter-TSS (NM_026604)	promoter-TSS (NM_026604)	10	NM_026604	68187	Mm.87130	NM_026604	ENSMUSG00000026153	Fam135a	4921533L14Rik|AI256732|AI835491	family with sequence similarity 135, member A	protein-coding
mm_80939.1	chr9	102717693	102717697	+	1	NA	promoter-TSS (NM_019764)	promoter-TSS (NM_019764)	-109	NM_019764	56332	Mm.21145	NM_019764	ENSMUSG00000032531	Amotl2	AW549739|C79691|Lccp|MASCOT|mKIAA0989	angiomotin-like 2	protein-coding
mm_146039.1	chr18	69592802	69592849	+	1	NA	intron (NM_013685, intron 8 of 19)	intron (NM_013685, intron 8 of 19)	247104	NM_001083967	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding
mm_22510.1	chr3	7613872	7613889	+	1	NA	promoter-TSS (NM_001313889)	promoter-TSS (NM_001313889)	-120	NM_001313888	16196	Mm.3825	NM_008371	ENSMUSG00000040329	Il7	A630026I06Rik|Il-7|hlb368	interleukin 7	protein-coding
mm_19818.1	chr2	110452754	110452754	-	1	NA	Intergenic	ORR1D2|LTR|ERVL-MaLR	-89761	NM_026271	67606	Mm.291809	NM_026271	ENSMUSG00000074971	Fibin	1110018M03Rik	fin bud initiation factor homolog (zebrafish)	protein-coding
mm_124108.1	chr14	79390667	79390743	-	1	NA	promoter-TSS (NM_025832)	promoter-TSS (NM_025832)	-37	NM_025832	66897	Mm.24425	NM_025832	ENSMUSG00000022020	Naa16	1300019C06Rik|Narg1l	N(alpha)-acetyltransferase 16, NatA auxiliary subunit	protein-coding
mm_69977.1	chr7	142377363	142377394	-	1	NA	exon (NM_009983, exon 6 of 9)	exon (NM_009983, exon 6 of 9)	-3632	NM_001347541	320802	Mm.154486	NM_177265	ENSMUSG00000045777	Ifitm10	6330512M04Rik|AI848576|DSPA3	interferon induced transmembrane protein 10	protein-coding
mm_63716.1	chr7	130730071	130730074	+	1	NA	intron (NM_001347637, intron 3 of 14)	intron (NM_001347637, intron 3 of 14)	37516	NM_021314	57752	Mm.86322	NM_021314	ENSMUSG00000030852	Tacc2	mKIAA4180	transforming, acidic coiled-coil containing protein 2	protein-coding
mm_54317.1	chr6	30175734	30175736	-	1	NA	promoter-TSS (NR_038124)	promoter-TSS (NR_038124)	-888	NR_038124	100463519	Mm.361139	NR_038124		BB283400	BF465573|Rncr4	expressed sequence BB283400	ncRNA
mm_40130.1	chr5	35041623	35041653	+	1	NA	exon (NM_019447, exon 1 of 14)	exon (NM_019447, exon 1 of 14)	129	NM_019447	54426	Mm.27369	NM_019447	ENSMUSG00000029102	Hgfac	HGFA	hepatocyte growth factor activator	protein-coding
mm_109912.1	chr12	8480213	8480229	-	1	NA	Intergenic	Intergenic	19764	NM_007483	11852	Mm.687	NM_007483	ENSMUSG00000054364	Rhob	AA017882|Arh6|Arhb	ras homolog family member B	protein-coding
mm_64448.1	chr7	142658597	142658629	+	1	NA	5' UTR (NM_010514, exon 1 of 4)	5' UTR (NM_010514, exon 1 of 4)	191	NM_010514	16002	Mm.3862	NM_010514	ENSMUSG00000048583	Igf2	AL033362|Igf-2|Igf-II|M6pr|Mpr|Peg2	insulin-like growth factor 2	protein-coding
mm_4384.1	chr1	172198655	172198671	+	1	NA	exon (NM_001329871, exon 4 of 4)	exon (NM_001329871, exon 4 of 4)	8141	NM_001329871	18611	Mm.544	NM_011063	ENSMUSG00000013698	Pea15a	Mat1|PEA-15|Pea15|Pkcs15	phosphoprotein enriched in astrocytes 15A	protein-coding
mm_113558.1	chr13	38151412	38151422	+	1	NA	5' UTR (NM_023842, exon 1 of 24)	5' UTR (NM_023842, exon 1 of 24)	123	NM_023842	109620	Mm.355327	NM_023842	ENSMUSG00000054889	Dsp	2300002E22Rik|5730453H04Rik|AA407887|AA407888|AW109828|DP|rul	desmoplakin	protein-coding
mm_134489.1	chr16	18629961	18629971	-	1	NA	promoter-TSS (NM_213614)	promoter-TSS (NM_213614)	-28	NM_213614	18951	Mm.20365	NM_213614	ENSMUSG00000072214	Sept5	Cdcrel-1|Cdcrel1|Pnutl1	septin 5	protein-coding
mm_54634.1	chr6	38716072	38716080	-	1	NA	exon (NM_010433, exon 12 of 15)	exon (NM_010433, exon 12 of 15)	53007	NM_001101507	665180	Mm.349066	NM_001101507	ENSMUSG00000079598	Clec2l	AI414054|AW122724|Gm1064	C-type lectin domain family 2, member L	protein-coding
mm_129542.1	chr15	79378599	79378645	-	1	NA	exon (NM_001253819, exon 2 of 10)	exon (NM_001253819, exon 2 of 10)	-3322	NR_035464	100316695		NR_035464	ENSMUSG00000088901	Mir1943	mir-1943|mmu-mir-1943	microRNA 1943	ncRNA
mm_155384.1	chrX	71816235	71816289	+	1	NA	promoter-TSS (NM_001081356)	promoter-TSS (NM_001081356)	182	NM_001290781	67048	Mm.41102	NM_001081356	ENSMUSG00000073131	Vma21	2610030H06Rik|AI840175	VMA21 vacuolar H+-ATPase homolog (S. cerevisiae)	protein-coding
mm_145266.1	chr18	52693683	52693713	+	1	NA	promoter-TSS (NM_010293)	promoter-TSS (NM_010293)	19	NM_010293	14625	Mm.32242	NM_010293	ENSMUSG00000053624	Gykl1	AI449806|Gk-rs1	glycerol kinase-like 1	protein-coding
mm_51884.1	chr6	90601957	90601965	+	1	NA	Intergenic	Intergenic	-2919	NM_027868	71699	Mm.272633	NM_027868	ENSMUSG00000030089	Slc41a3	1010001P06Rik|AI480742|SLC41A1-L2	solute carrier family 41, member 3	protein-coding
mm_41267.1	chr5	89083765	89083771	+	1	NA	intron (NM_018760, intron 6 of 25)	intron (NM_018760, intron 6 of 25)	196508	NM_018760	54403	Mm.41044	NM_018760	ENSMUSG00000060961	Slc4a4	AI835705|NBC|NBC1	solute carrier family 4 (anion exchanger), member 4	protein-coding
mm_117515.1	chr13	80885598	80885617	-	1	NA	intron (NM_001042591, intron 1 of 7)	CpG	2185	NM_001042591	105171	Mm.423137	NM_001042591	ENSMUSG00000074794	Arrdc3	AI450344|mKIAA1376	arrestin domain containing 3	protein-coding
mm_62139.1	chr7	97091889	97091895	+	1	NA	intron (NM_001162477, intron 1 of 9)	MIRb|SINE|MIR	10141	NM_010248	14389	Mm.42033	NM_010248	ENSMUSG00000004508	Gab2	AI463667|D130058I17Rik|p97	growth factor receptor bound protein 2-associated protein 2	protein-coding
mm_50091.1	chr6	41525024	41525043	+	1	NA	TTS (NM_009430)	TTS (NM_009430)	3257	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_41403.1	chr5	90786413	90786441	+	1	NA	exon (NM_203320, exon 2 of 4)	exon (NM_203320, exon 2 of 4)	326	NM_203320	330122	Mm.244289	NM_203320	ENSMUSG00000029379	Cxcl3	Dcip1|Gm1960	chemokine (C-X-C motif) ligand 3	protein-coding
mm_32092.1	chr4	98541618	98541619	+	1	NA	intron (NM_172696, intron 27 of 43)	intron (NM_172696, intron 27 of 43)	-5016	NM_007704	12695	Mm.90218	NM_007704	ENSMUSG00000061859	Patj	Cipp|Inadl	PATJ, crumbs cell polarity complex component	protein-coding
mm_59848.1	chr7	29816062	29816153	+	1	NA	promoter-TSS (NM_001145880)	promoter-TSS (NM_001145880)	35	NM_001145880	233056	Mm.224766	NM_146185	ENSMUSG00000011427	Zfp790	6330581L23Rik	zinc finger protein 790	protein-coding
mm_126032.1	chr15	76818281	76818294	+	1	NA	promoter-TSS (NM_001168288)	promoter-TSS (NM_001168288)	-117	NM_198420	223666	Mm.322931	NM_198420	ENSMUSG00000033697	Arhgap39	9530053N22|AI843066|D15Wsu169e|Kiaa1688|Porf-2	Rho GTPase activating protein 39	protein-coding
mm_112664.1	chr13	16027105	16027131	+	1	NA	exon (NM_008380, exon 5 of 5)	exon (NM_008380, exon 5 of 5)	15267	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_167924.1	chrX	102908900	102908910	+	1	NA	promoter-TSS (NM_027591)	promoter-TSS (NM_027591)	0	NR_073044	75443	Mm.46161	NR_073044	ENSMUSG00000079476	1700011M02Rik	-	RIKEN cDNA 1700011M02 gene	ncRNA
mm_103472.1	chr11	76479732	76479771	-	1	NA	intron (NM_001346670, intron 2 of 21)	PB1D7|SINE|Alu	-11286	NM_001291186	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_31883.1	chr4	82065881	82065891	+	1	NA	non-coding (NR_040659, exon 1 of 3)	non-coding (NR_040659, exon 1 of 3)	506	NR_040659	545641	Mm.216028	NR_040659	ENSMUSG00000085022	Gm5860	EG545641	predicted gene 5860	ncRNA
mm_125473.1	chr15	54410756	54410797	+	1	NA	promoter-TSS (NM_173422)	promoter-TSS (NM_173422)	2	NM_173422	239447	Mm.82400	NM_173422	ENSMUSG00000038591	Colec10	CL-L1	collectin sub-family member 10	protein-coding
mm_2811.1	chr1	130874227	130874237	+	1	NA	exon (NM_026976, exon 2 of 8)	exon (NM_026976, exon 2 of 8)	8455	NM_026976	69169	Mm.46042	NM_026976	ENSMUSG00000042474	Fcmr	1810037B05Rik|Faim3|FcmuR|Toso	Fc fragment of IgM receptor	protein-coding
mm_15915.1	chr2	165064195	165064205	+	1	NA	intron (NM_170703, intron 5 of 7)	B4|SINE|B4	8564	NM_011611	21939	Mm.271833	NM_011611	ENSMUSG00000017652	Cd40	AI326936|Bp50|GP39|HIGM1|IGM|IMD3|T-BAM|TRAP|Tnfrsf5|p50	CD40 antigen	protein-coding
mm_123198.1	chr14	59178777	59178781	-	1	NA	promoter-TSS (NM_001004158)	promoter-TSS (NM_001004158)	-30	NM_001004158	380907	Mm.81009	NM_001004158	ENSMUSG00000053868	Gm5142	EG380907	predicted gene 5142	protein-coding
mm_43105.1	chr5	124483554	124483592	+	1	NA	intron (NM_029532, intron 1 of 1)	CpG	418	NM_029532	76167	Mm.156035	NM_029532	ENSMUSG00000029402	Snrnp35	6330548G22Rik	small nuclear ribonucleoprotein 35 (U11/U12)	protein-coding
mm_44680.1	chr5	30073555	30073609	-	1	NA	promoter-TSS (NM_021288)	promoter-TSS (NM_021288)	43	NR_033402	22171	Mm.268395	NM_021288	ENSMUSG00000025747	Tyms	Ts	thymidylate synthase	protein-coding
mm_4815.1	chr1	185411496	185411502	+	1	NA	intron (NM_029735, intron 22 of 31)	intron (NM_029735, intron 22 of 31)	30320	NR_038006	319562	Mm.184335	NM_176943	ENSMUSG00000051295	9630028B13Rik	-	RIKEN cDNA 9630028B13 gene	ncRNA
mm_111484.1	chr12	98737594	98737616	-	1	NA	promoter-TSS (NM_001146199)	promoter-TSS (NM_001146199)	-200	NM_001146199	24000	Mm.4420	NM_011877	ENSMUSG00000021009	Ptpn21	PTPD1|PTPRL10	protein tyrosine phosphatase, non-receptor type 21	protein-coding
mm_3306.1	chr1	137898626	137898628	+	1	NA	Intergenic	Intergenic	-67828	NR_029795	735252		NR_029795	ENSMUSG00000065565	Mir181a-1	Mirn181a-1|Mirn213|miR-213|mir-181a-1|mmu-mir-213	microRNA 181a-1	ncRNA
mm_19800.1	chr2	110305583	110305592	-	1	NA	exon (NM_130452, exon 1 of 7)	exon (NM_130452, exon 1 of 7)	138	NM_130452	170442	Mm.27335	NM_130452	ENSMUSG00000041660	Bbox1	AI874739	butyrobetaine (gamma), 2-oxoglutarate dioxygenase 1 (gamma-butyrobetaine hydroxylase)	protein-coding
mm_118091.1	chr13	103774576	103774644	-	1	NA	Intergenic	CpG	-10028	NM_172592	218543	Mm.458176	NM_172592	ENSMUSG00000032621	Srek1	8430401B01|AI450757|AI462342|SRrp508|SRrp86|Sfrs12|Srsf12	splicing regulatory glutamine/lysine-rich protein 1	protein-coding
mm_78303.1	chr9	22475873	22475889	+	1	NA	5' UTR (NM_181316, exon 1 of 22)	5' UTR (NM_181316, exon 1 of 22)	166	NM_178415	319845	Mm.176725	NM_178415	ENSMUSG00000035919	Bbs9	E130103I17Rik	Bardet-Biedl syndrome 9 (human)	protein-coding
mm_81734.1	chr9	113756725	113756751	+	1	NA	intron (NM_001286599, intron 1 of 10)	SSU-rRNA_Hsa|rRNA|rRNA	15265	NM_001114347	76499	Mm.222272	NM_029633	ENSMUSG00000033392	Clasp2	1500004F14Rik|8030404L10Rik|C77448|CLASP2beta|mKIAA0627	CLIP associating protein 2	protein-coding
mm_97730.1	chr11	80391930	80391948	+	1	NA	non-coding (NR_045038, exon 8 of 17)	non-coding (NR_045038, exon 8 of 17)	8660	NM_001130171	22680	Mm.401332	NM_011751	ENSMUSG00000017421	Zfp207	8430401D15Rik|BuGZ|Zep|Znf207	zinc finger protein 207	protein-coding
mm_163443.1	chr12	86242738	86242747	-	1	NA	intron (NM_001324488, intron 1 of 8)	intron (NM_001324488, intron 1 of 8)	884	NM_001324488	70373	Mm.252967	NM_027405	ENSMUSG00000021254	Gpatch2l	1700020O03Rik|4732487G21Rik|A630090I05Rik|Kiaa1152	G patch domain containing 2 like	protein-coding
mm_30934.1	chr4	32983360	32983400	+	1	NA	5' UTR (NM_027491, exon 1 of 7)	5' UTR (NM_027491, exon 1 of 7)	382	NM_027491	52187	Mm.300814	NM_027491	ENSMUSG00000028278	Rragd	5730543C08Rik|AI467523|C030003H22Rik|D4Ertd174e	Ras-related GTP binding D	protein-coding
mm_128565.1	chr15	56694510	56694523	-	1	NA	promoter-TSS (NM_008216)	promoter-TSS (NM_008216)	30	NM_008216	15117	Mm.5148	NM_008216	ENSMUSG00000022367	Has2	-	hyaluronan synthase 2	protein-coding
mm_95619.1	chr11	53543713	53543736	+	1	NA	3' UTR (NM_001252332, exon 10 of 10)	3' UTR (NM_001252332, exon 10 of 10)	-23645	NM_008443	16568	Mm.88694	NM_008443	ENSMUSG00000018395	Kif3a	Kif3|Kifl|Kns3	kinesin family member 3A	protein-coding
mm_170255.1	chr18	11898570	11898571	+	1	NA	intron (NM_022021, intron 3 of 8)	intron (NM_022021, intron 3 of 8)	-58132	NR_035447	100316686		NR_035447	ENSMUSG00000084565	Mir1901	Mirn1901|mmu-mir-1901	microRNA 1901	ncRNA
mm_108416.1	chr12	81959187	81959194	+	1	NA	intron (NM_018814, intron 14 of 35)	intron (NM_018814, intron 14 of 35)	99160	NM_018814	54604	Mm.86584	NM_018814	ENSMUSG00000021140	Pcnx	2900024E21Rik|3526401J03Rik|AF096286|AI327143|AI413187|Pcnx1|Pcnxl1	pecanex homolog (Drosophila)	protein-coding
mm_18568.1	chr2	65363941	65363950	-	1	NA	promoter-TSS (NM_177074)	promoter-TSS (NM_177074)	81	NM_177074	320106	Mm.227703	NM_177074	ENSMUSG00000061171	Slc38a11	9330158F14Rik	solute carrier family 38, member 11	protein-coding
mm_65912.1	chr7	30195021	30195031	-	1	NA	promoter-TSS (NM_009795)	promoter-TSS (NM_009795)	22	NM_009795	12336	Mm.439782	NM_009795	ENSMUSG00000001794	Capns1	Capa-4|Capa4|Capn4|D7Ertd146e	calpain, small subunit 1	protein-coding
mm_18596.1	chr2	66784904	66784920	-	1	NA	promoter-TSS (NM_009135)	promoter-TSS (NM_009135)	-2	NM_009135	20272	Mm.38127	NM_009135	ENSMUSG00000034810	Scn7a	1110034K09Rik|AI642000|NaG|Nav2|Nav2.3|Nax|Scn6a	sodium channel, voltage-gated, type VII, alpha	protein-coding
mm_149331.1	chr19	10843315	10843323	+	1	NA	exon (NM_023044, exon 1 of 8)	exon (NM_023044, exon 1 of 8)	775	NM_023044	65221	Mm.27387	NM_023044	ENSMUSG00000024737	Slc15a3	Ci1|cI-1	solute carrier family 15, member 3	protein-coding
mm_22077.1	chr2	168749993	168750018	-	1	NA	3' UTR (NM_201396, exon 3 of 3)	3' UTR (NM_201396, exon 3 of 3)	-7869	NM_001289446	11981	Mm.330819	NM_015731	ENSMUSG00000027546	Atp9a	IIa	ATPase, class II, type 9A	protein-coding
mm_130557.1	chr15	99248935	99248947	-	1	NA	intron (NM_001164156, intron 3 of 13)	intron (NM_001164156, intron 3 of 13)	-2847	NR_045627	73600	Mm.475134	NR_045627	ENSMUSG00000100599	1700120C14Rik	-	RIKEN cDNA 1700120C14 gene	ncRNA
mm_102506.1	chr11	60727253	60727255	-	1	NA	promoter-TSS (NM_022009)	promoter-TSS (NM_022009)	9	NM_022009	14248	Mm.339755	NM_022009	ENSMUSG00000002812	Flii	3632430F08Rik|Fliih	flightless I actin binding protein	protein-coding
mm_153744.1	chr19	44749618	44749621	-	1	NA	Intergenic	Intergenic	-7775	NM_011037	18504	Mm.192158	NM_011037	ENSMUSG00000004231	Pax2	Opdc|Pax-2	paired box 2	protein-coding
mm_128768.1	chr15	66453843	66453846	-	1	NA	intron (NM_019457, intron 5 of 11)	intron (NM_019457, intron 5 of 11)	47066	NM_019457	54562	Mm.244890	NM_019457	ENSMUSG00000022375	Lrrc6	LRTP	leucine rich repeat containing 6 (testis)	protein-coding
mm_36226.1	chr4	62524845	62524850	-	1	NA	promoter-TSS (NM_177607)	promoter-TSS (NM_177607)	167	NM_021498	59001	Mm.27444	NM_021498	ENSMUSG00000028394	Pole3	1810034K18Rik|YBL1	polymerase (DNA directed), epsilon 3 (p17 subunit)	protein-coding
mm_86728.1	chr10	19063773	19063780	+	1	NA	Intergenic	L1M5|LINE|L1	-48366	NM_009397	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_136592.1	chr17	5000551	5000553	+	1	NA	intron (NM_001085355, intron 1 of 19)	intron (NM_001085355, intron 1 of 19)	5478	NM_001085355	239985	Mm.133401	NM_001085355	ENSMUSG00000069729	Arid1b	8030481M12|9330189K18Rik|AI836955|Ardi1b|B230217J03Rik|mKIAA1235	AT rich interactive domain 1B (SWI-like)	protein-coding
mm_136548.1	chr16	97996973	97996990	-	1	NA	promoter-TSS (NR_130962)	promoter-TSS (NR_130962)	-366	NR_130962	245305	Mm.148033	NR_130962		B230307C23Rik	EG245305|OTTMUSG00000028475	RIKEN cDNA B230307C23 gene	ncRNA
mm_44148.1	chr5	150259960	150260010	+	1	NA	promoter-TSS (NM_172887)	promoter-TSS (NM_172887)	55	NM_172887	320365	Mm.216590	NM_172887	ENSMUSG00000056602	Fry	13CDNA73|9330186A19Rik|AF346502|AI462658|C87180|D930046M03|cg003|mKIAA4143	FRY microtubule binding protein	protein-coding
mm_40927.1	chr5	76183916	76183970	+	1	NA	promoter-TSS (NM_011626)	promoter-TSS (NM_011626)	63	NM_011626	21982	Mm.790	NM_011626	ENSMUSG00000029234	Tmem165	AV026557|Tpardl|Tparl|pFT27	transmembrane protein 165	protein-coding
mm_48974.1	chr6	4754232	4754242	+	1	NA	exon (NM_130877, exon 2 of 2)	exon (NM_130877, exon 2 of 2)	6931	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_22340.1	chr2	180726762	180726766	-	1	NA	intron (NM_183161, intron 1 of 12)	intron (NM_183161, intron 1 of 12)	1425	NM_183161	228993	Mm.87189	NM_183161	ENSMUSG00000023393	Slc17a9	1700019H03Rik|BC019537|Vnut	solute carrier family 17, member 9	protein-coding
mm_96564.1	chr11	69026067	69026085	+	1	NA	exon (NM_001281465, exon 6 of 23)	exon (NM_001281465, exon 6 of 23)	10165	NM_001013256	68964	Mm.285785	NM_001013256	ENSMUSG00000020898	Ctc1	1500010J02Rik|AAF-132|AAF132	CTS telomere maintenance complex component 1	protein-coding
mm_143481.1	chr17	71268568	71268588	-	1	NA	intron (NM_145158, intron 4 of 7)	intron (NM_145158, intron 4 of 7)	42387	NM_145158	246707	Mm.23462	NM_145158	ENSMUSG00000024053	Emilin2	FOAP-10	elastin microfibril interfacer 2	protein-coding
mm_169885.1	chr16	43906806	43906816	+	1	NA	exon (NM_027801, exon 4 of 16)	exon (NM_027801, exon 4 of 16)	16909	NM_027801	212153	Mm.209835	NM_027801	ENSMUSG00000022701	Ccdc191	2610015P09Rik|8430422M09Rik|AU040712	coiled-coil domain containing 191	protein-coding
mm_82905.1	chr9	32915656	32915668	-	1	NA	intron (NR_131058, intron 1 of 3)	intron (NR_131058, intron 1 of 3)	13304	NR_131058	330917	Mm.488283	NR_131058		Gm27162	A430016B06	predicted gene 27162	ncRNA
mm_71662.1	chr8	60632857	60632905	+	1	NA	promoter-TSS (NM_027756)	promoter-TSS (NM_027756)	56	NM_001293769	71306	Mm.23242	NM_027756	ENSMUSG00000031647	Mfap3l	4933428A15Rik|5430405D20Rik|AI461995|AW125052|NYD-sp9|mKIAA0626	microfibrillar-associated protein 3-like	protein-coding
mm_162517.1	chr1	156671362	156671377	-	1	NA	intron (NM_023141, intron 2 of 5)	B4|SINE|B4	2970	NM_023141	30935	Mm.206737	NM_023141	ENSMUSG00000060519	Tor3a	Adir	torsin family 3, member A	protein-coding
mm_33216.1	chr4	126609946	126609952	+	1	NA	promoter-TSS (NM_001145950)	promoter-TSS (NM_001145950)	95	NM_001145950	230757	Mm.296838	NM_001013755	ENSMUSG00000073755	5730409E04Rik	7530403E16Rik|AI849033	RIKEN cDNA 5730409E04Rik gene	protein-coding
mm_81717.1	chr9	111439064	111439097	+	1	NA	promoter-TSS (NM_172928)	promoter-TSS (NM_172928)	-1	NM_172928	245038	Mm.26361	NM_172928	ENSMUSG00000032500	Dclk3	BC056929|C730036H08|Dcamkl3	doublecortin-like kinase 3	protein-coding
mm_24432.1	chr3	90541190	90541213	+	1	NA	promoter-TSS (NM_026416)	promoter-TSS (NM_026416)	-22	NM_026416	67860	Mm.331185	NM_026416	ENSMUSG00000074457	S100a16	2300002L21Rik|AI325039|AI663996|DT1P1A7|S100F	S100 calcium binding protein A16	protein-coding
mm_78065.1	chr9	15239067	15239155	+	1	NA	promoter-TSS (NM_026955)	promoter-TSS (NM_026955)	66	NM_026955	69137	Mm.41396	NM_026955	ENSMUSG00000031937	Vstm5	2200002K05Rik	V-set and transmembrane domain containing 5	protein-coding
mm_12693.1	chr2	76370054	76370060	+	1	NA	promoter-TSS (NM_153405)	promoter-TSS (NM_153405)	73	NM_153405	241490	Mm.33310	NM_153405	ENSMUSG00000042369	Rbm45	Drb1|Drbp1|G430095G15Rik	RNA binding motif protein 45	protein-coding
mm_9248.1	chr1	171388755	171388763	-	1	NA	promoter-TSS (NM_001005508)	promoter-TSS (NM_001005508)	-201	NM_001005508	226652	Mm.251048	NM_001005508	ENSMUSG00000048865	Arhgap30	6030405P05Rik|Gm102|mFLJ00267	Rho GTPase activating protein 30	protein-coding
mm_125218.1	chr15	34083030	34083038	+	1	NA	5' UTR (NM_026002, exon 1 of 12)	5' UTR (NM_026002, exon 1 of 12)	315	NM_026002	67154	Mm.130883	NM_026002	ENSMUSG00000022255	Mtdh	2610103J23Rik|3D3|3D3/Lyric|AEG-1|AV353288|D8Bwg1112e|Lyric	metadherin	protein-coding
mm_156020.1	chrX	107148970	107148980	+	1	NA	promoter-TSS (NM_175442)	promoter-TSS (NM_175442)	48	NM_001122596	213438	Mm.265244	NM_175442	ENSMUSG00000054293	A630033H20Rik	AI662791|P2ry10	RIKEN cDNA A630033H20 gene	protein-coding
mm_17330.1	chr2	26505337	26505340	-	1	NA	TTS (NR_132655)	TTS (NR_132655)	1411	NR_132655	102639736		NR_132655		Gm35978	-	predicted gene, 35978	ncRNA
mm_155193.1	chrX	56454872	56454887	+	1	NA	promoter-TSS (NM_172779)	promoter-TSS (NM_172779)	40	NM_172779	236790	Mm.474772	NM_172779	ENSMUSG00000035967	Ints6l	4930535D10Rik|6330505F04Rik|D130066O12|Ddx26b	integrator complex subunit 6 like	protein-coding
mm_109405.1	chr12	110447089	110447123	+	1	NA	promoter-TSS (NM_001135001)	promoter-TSS (NM_001135001)	-73	NM_001135001	26931	Mm.240396	NM_012023	ENSMUSG00000017843	Ppp2r5c	2610043M05Rik|2700063L20Rik|AI060890|AW545884|C85228|D12Bwg0916e|mKIAA0044	protein phosphatase 2, regulatory subunit B', gamma	protein-coding
mm_101465.1	chr11	30471875	30471886	-	1	NA	promoter-TSS (NM_001100394)	promoter-TSS (NM_001100394)	-51	NM_001100394	75087	Mm.159422	NM_001100394	ENSMUSG00000040919	4930505A04Rik	-	RIKEN cDNA 4930505A04 gene	protein-coding
mm_107568.1	chr12	44328542	44328548	+	1	NA	promoter-TSS (NM_176930)	promoter-TSS (NM_176930)	-340	NM_176930	319504	Mm.208439	NM_176930	ENSMUSG00000020598	Nrcam	Bravo|C030017F07Rik|C130076O07Rik|mKIAA0343	neuronal cell adhesion molecule	protein-coding
mm_27009.1	chr3	25869833	25869846	-	1	NA	intron (NM_001163387, intron 3 of 5)	ID_B1|SINE|B4	283468	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_30004.1	chr3	135608362	135608379	-	1	NA	intron (NM_008689, intron 12 of 24)	intron (NM_008689, intron 12 of 24)	83177	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_95878.1	chr11	58092789	58092817	+	1	NA	Intergenic	Intergenic	-11350	NM_026949	69125	Mm.28910	NM_026949	ENSMUSG00000020515	Cnot8	1500015I04Rik|1810022F04Rik|AA536816|AU015770|AU043059	CCR4-NOT transcription complex, subunit 8	protein-coding
mm_7380.1	chr1	107163231	107163239	-	1	NA	Intergenic	Lx2|LINE|L1	-2121	NM_198680	383548	Mm.483991	NM_198680	ENSMUSG00000073602	Serpinb3b	Scca2-rs|Scca2-rs1	serine (or cysteine) peptidase inhibitor, clade B (ovalbumin), member 3B	protein-coding
mm_25922.1	chr3	131170421	131170436	+	1	NA	intron (NM_001276403, intron 3 of 11)	intron (NM_001276403, intron 3 of 11)	57637	NM_001276403	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_77044.1	chr8	109575761	109575770	-	1	NA	exon (NM_017370, exon 5 of 5)	exon (NM_017370, exon 5 of 5)	3407	NM_017370	15439	Mm.26730	NM_017370	ENSMUSG00000031722	Hp	HP-1|preHP2	haptoglobin	protein-coding
mm_122089.1	chr14	30625144	30625158	-	1	NA	intron (NM_011103, intron 1 of 17)	intron (NM_011103, intron 1 of 17)	1057	NM_011103	18753	Mm.2314	NM_011103	ENSMUSG00000021948	Prkcd	AI385711|D14Ertd420e|PKC[d]|PKCdelta|Pkcd	protein kinase C, delta	protein-coding
mm_99021.1	chr11	98927786	98927810	+	1	NA	Intergenic	Intergenic	-9898	NM_009024	19401	Mm.439744	NM_009024	ENSMUSG00000037992	Rara	Nr1b1|RAR|RARalpha1	retinoic acid receptor, alpha	protein-coding
mm_50041.1	chr6	41150318	41150322	+	1	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	-114811	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_27259.1	chr3	37600238	37600244	-	1	NA	Intergenic	Intergenic	-9650	NR_130162	75947	Mm.109620	NR_130161	ENSMUSG00000085677	4930594O21Rik	-	RIKEN cDNA 4930594O21 gene	ncRNA
mm_105297.1	chr11	102481063	102481073	-	1	NA	exon (NM_001159492, exon 8 of 8)	exon (NM_001159492, exon 8 of 8)	-11185	NM_010575	16399	Mm.26646	NM_010575	ENSMUSG00000034664	Itga2b	AI172977|CD41|CD41B|GpIIb|alphaIIb	integrin alpha 2b	protein-coding
mm_134335.1	chr16	16496140	16496153	-	1	NA	intron (NM_001301817, intron 2 of 16)	Lx|LINE|L1	31265	NM_001301818	224014	Mm.256131	NM_139232	ENSMUSG00000022788	Fgd4	9030023J02Rik|9330209B17Rik|Frabp|ZFYVE6	FYVE, RhoGEF and PH domain containing 4	protein-coding
mm_84598.1	chr9	70038055	70038057	-	1	NA	promoter-TSS (NM_028087)	promoter-TSS (NM_028087)	32	NM_028087	72077	Mm.195555	NM_028087	ENSMUSG00000032226	Gcnt3	2010013H22Rik|2210021I22Rik|2210401J11Rik	glucosaminyl (N-acetyl) transferase 3, mucin type	protein-coding
mm_41958.1	chr5	105876533	105876585	+	1	NA	promoter-TSS (NM_018759)	promoter-TSS (NM_018759)	-9	NR_030777	54367	Mm.248876	NM_018759	ENSMUSG00000029290	Zfp326	5730470H14Rik|ZAN75|Znf326	zinc finger protein 326	protein-coding
mm_139157.1	chr17	47540743	47540755	+	1	NA	intron (NM_001081635, intron 1 of 6)	PB1D10|SINE|Alu	35698	NM_001081635	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_98040.1	chr11	85353157	85353219	+	1	NA	promoter-TSS (NM_001166643)	promoter-TSS (NM_001166643)	24	NM_001166643	192197	Mm.209989	NM_138681	ENSMUSG00000059439	Bcas3	1500019F07Rik|2610028P08Rik|AU021018|BC028339|K20D4|rudhira	breast carcinoma amplified sequence 3	protein-coding
mm_117430.1	chr13	74562090	74562092	-	1	NA	Intergenic	B1_Mus1|SINE|Alu	-68141	NM_146231	235956	Mm.296909	NM_146231	ENSMUSG00000069208	Zfp825	-	zinc finger protein 825	protein-coding
mm_145628.1	chr18	61109762	61109770	+	1	NA	exon (NM_001037859, exon 3 of 22)	exon (NM_001037859, exon 3 of 22)	4194	NM_001037859	12978	Mm.22574	NM_007779	ENSMUSG00000024621	Csf1r	AI323359|CD115|CSF-1R|Csfmr|Fim-2|Fim2|Fms|M-CSF-R|M-CSFR	colony stimulating factor 1 receptor	protein-coding
mm_25367.1	chr3	107101597	107101649	+	1	NA	promoter-TSS (NM_008417)	promoter-TSS (NM_008417)	56	NM_008417	16490	Mm.39285	NM_008417	ENSMUSG00000040724	Kcna2	Akr6a4|ENSMUSG00000074335|Gm10672|Kca1-2|Kv1.2|Mk-2	potassium voltage-gated channel, shaker-related subfamily, member 2	protein-coding
mm_91756.1	chr10	50592549	50592558	-	1	NA	promoter-TSS (NM_198007)	promoter-TSS (NM_198007)	-116	NM_198007	77987	Mm.222497	NM_198007	ENSMUSG00000038774	Ascc3	ASC1p200|B630009I04Rik|BC023451|D430001L07Rik|D630041L21|Helic1|RNAH	activating signal cointegrator 1 complex subunit 3	protein-coding
mm_132056.1	chr16	29579442	29579459	+	1	NA	5' UTR (NM_133752, exon 1 of 29)	5' UTR (NM_133752, exon 1 of 29)	116	NM_001199177	74143	Mm.274285	NM_133752	ENSMUSG00000038084	Opa1	1200011N24Rik|AI225888|AI847218|lilr3|mKIAA0567	OPA1, mitochondrial dynamin like GTPase	protein-coding
mm_164469.1	chr16	62190455	62190458	+	1	NA	Intergenic	MIR|SINE|MIR	596260	NM_178925	106338	Mm.26321	NM_178925	ENSMUSG00000050312	Nsun3	6720484A09Rik|AU022521	NOL1/NOP2/Sun domain family member 3	protein-coding
mm_6434.1	chr1	73984474	73984497	-	1	NA	intron (NM_027884, intron 16 of 34)	intron (NM_027884, intron 16 of 34)	-120019	NR_045311	109198	Mm.359721	NR_045311	ENSMUSG00000100301	6030407O03Rik	-	RIKEN cDNA 6030407O03 gene	ncRNA
mm_115637.1	chr13	12258044	12258062	-	1	NA	promoter-TSS (NM_001081128)	promoter-TSS (NM_001081128)	60	NM_001081128	238505	Mm.40335	NM_001081128	ENSMUSG00000021311	Mtr	AI894170|D830038K18Rik|MS	5-methyltetrahydrofolate-homocysteine methyltransferase	protein-coding
mm_36996.1	chr4	110287480	110287534	-	1	NA	promoter-TSS (NM_010488)	promoter-TSS (NM_010488)	4	NM_001038698	15572	Mm.3970	NM_010488	ENSMUSG00000028546	Elavl4	Elav|Hud|PNEM	ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4 (Hu antigen D)	protein-coding
mm_109080.1	chr12	104413471	104413483	+	1	NA	exon (NM_009252, exon 5 of 5)	exon (NM_009252, exon 5 of 5)	6769	NM_009252	20716	Mm.482074	NM_009252	ENSMUSG00000021091	Serpina3n	Spi2-2|Spi2.2|Spi2/eb.4	serine (or cysteine) peptidase inhibitor, clade A, member 3N	protein-coding
mm_147859.1	chr18	64191745	64191747	-	1	NA	intron (NR_045366, intron 2 of 5)	intron (NR_045366, intron 2 of 5)	-62613	NM_009182	20451	Mm.252110	NM_009182	ENSMUSG00000056812	St8sia3	AI847333|ST8SiaIII|Siat8c	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3	protein-coding
mm_137380.1	chr17	25748614	25748622	+	1	NA	TTS (NM_177822)	TTS (NM_177822)	5709	NM_018857	56047	Mm.17510	NM_018857	ENSMUSG00000063011	Msln	MPF	mesothelin	protein-coding
mm_77271.1	chr8	116529415	116529422	-	1	NA	Intergenic	Intergenic	24403	NM_029297	75465	Mm.23114	NM_029297	ENSMUSG00000034467	Dynlrb2	1700009A04Rik|DNLC2B|Dncl2b	dynein light chain roadblock-type 2	protein-coding
mm_5115.1	chr1	6443558	6443567	-	1	NA	Intergenic	Lx8b|LINE|L1	-43669	NM_001244693	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding
mm_125800.1	chr15	74896680	74896711	+	1	NA	Intergenic	Intergenic	-14991	NM_025929	67038	Mm.154566	NM_025929	ENSMUSG00000063522	2010109I03Rik	Ly6m	RIKEN cDNA 2010109I03 gene	protein-coding
mm_116720.1	chr13	51701724	51701742	-	1	NA	3' UTR (NM_001281880, exon 17 of 17)	3' UTR (NM_001281880, exon 17 of 17)	50025	NM_029279	75420	Mm.275981	NM_029279	ENSMUSG00000035139	Secisbp2	2210413N07Rik|2810012K13Rik|SBP2	SECIS binding protein 2	protein-coding
mm_93292.1	chr10	96370828	96370840	-	1	NA	Intergenic	Intergenic	144627	NR_110448	74881	Mm.410819	NR_110448		4930459C07Rik	-	RIKEN cDNA 4930459C07 gene	ncRNA
mm_43072.1	chr5	124446728	124446747	+	1	NA	promoter-TSS (NM_001310727)	promoter-TSS (NM_001310727)	33	NM_001310727	67956	Mm.137966	NM_030241	ENSMUSG00000049327	Kmt5a	2410195B05Rik|AA617402|AW536475|PR-SET7|PR/SET07|Setd8	lysine methyltransferase 5A	protein-coding
mm_67584.1	chr7	83531729	83531731	-	1	NA	Intergenic	MT2B1|LTR|ERVL	-53201	NM_177695	233424	Mm.486619	NM_177695	ENSMUSG00000038540	Tmc3	9030203A06	transmembrane channel-like gene family 3	protein-coding
mm_20944.1	chr2	151542395	151542487	-	1	NA	promoter-TSS (NM_008019)	promoter-TSS (NM_008019)	-42	NR_126058	14225	Mm.278458	NM_008019	ENSMUSG00000032966	Fkbp1a	FKBP12|Fkbp|Fkbp1	FK506 binding protein 1a	protein-coding
mm_79693.1	chr9	60713106	60713159	+	1	NA	promoter-TSS (NM_026235)	promoter-TSS (NM_026235)	11	NM_026235	67557	Mm.44546	NM_026235	ENSMUSG00000034839	Larp6	5430431G03Rik|AI552438|Achn	La ribonucleoprotein domain family, member 6	protein-coding
mm_138921.1	chr17	43611878	43611950	+	1	NA	exon (NM_013737, exon 12 of 12)	exon (NM_013737, exon 12 of 12)	18385	NM_001161366	210510	Mm.329058	NM_198418	ENSMUSG00000040140	Tdrd6	AB097085|Tdr2	tudor domain containing 6	protein-coding
mm_136251.1	chr16	90946661	90946692	-	1	NA	intron (NM_001164483, intron 29 of 31)	MIR3|SINE|MIR	-11827	NM_026502	68001	Mm.45374	NM_026502	ENSMUSG00000022972	1110004E09Rik	-	RIKEN cDNA 1110004E09 gene	protein-coding
mm_68466.1	chr7	110611660	110611662	-	1	NA	intron (NM_177324, intron 1 of 40)	L1ME1|LINE|L1	3259	NM_177324	319934	Mm.102970	NM_177324	ENSMUSG00000038371	Sbf2	4833411B01Rik|AA414977|AI317167|B430219L04Rik|Mtmr13|mMTMH1	SET binding factor 2	protein-coding
mm_42263.1	chr5	114130389	114130444	+	1	NA	promoter-TSS (NM_011677)	promoter-TSS (NM_011677)	-19	NM_001040691	22256	Mm.1393	NM_011677	ENSMUSG00000029591	Ung	UNG1|UNG2	uracil DNA glycosylase	protein-coding
mm_93196.1	chr10	94298651	94298659	-	1	NA	promoter-TSS (NR_033209)	promoter-TSS (NR_033209)	48	NR_033209	215472	Mm.255656	NM_174999	ENSMUSG00000053420	Gm4792	E130012K09|EG215472	predicted gene 4792	ncRNA
mm_54232.1	chr6	28235110	28235118	-	1	NA	Intergenic	Intergenic	26487	NM_001081678	627049	Mm.84441	NM_001081678	ENSMUSG00000039841	Zfp800	AA407452|Znf800	zinc finger protein 800	protein-coding
mm_7095.1	chr1	88700782	88700802	-	1	NA	3' UTR (NM_177305, exon 1 of 1)	3' UTR (NM_177305, exon 1 of 1)	1399	NM_177305	320982	Mm.27968	NM_177305	ENSMUSG00000049866	Arl4c	A630084M22Rik|Arl7|LAK	ADP-ribosylation factor-like 4C	protein-coding
mm_5941.1	chr1	56637431	56637449	-	1	NA	promoter-TSS (NM_027661)	promoter-TSS (NM_027661)	11	NM_027661	71066	Mm.152656	NM_027661	ENSMUSG00000045336	Hsfy2	4933413G11Rik|Hspy2l	heat shock transcription factor, Y-linked 2	protein-coding
mm_76083.1	chr8	79374538	79374548	-	1	NA	intron (NM_008539, intron 1 of 6)	intron (NM_008539, intron 1 of 6)	24925	NM_008539	17125	Mm.223717	NM_008539	ENSMUSG00000031681	Smad1	AI528653|Madh1|Madr1|Mlp1|MusMLP	SMAD family member 1	protein-coding
mm_138946.1	chr17	44105911	44105933	+	1	NA	promoter-TSS (NM_199016)	promoter-TSS (NM_199016)	-114	NM_199016	224794	Mm.255971	NM_199016	ENSMUSG00000023961	Enpp4	4933413N07Rik|AA986363|AI195364|E-NPP 4|Gm90|mKIAA0879	ectonucleotide pyrophosphatase/phosphodiesterase 4	protein-coding
mm_100768.1	chr11	4704304	4704330	-	1	NA	promoter-TSS (NM_026015)	promoter-TSS (NM_026015)	27	NM_197979	66152	Mm.269736	NM_197979	ENSMUSG00000059534	Uqcr10	1110020P15Rik|AA960494|Ucrc	ubiquinol-cytochrome c reductase, complex III subunit X	protein-coding
mm_163208.1	chr11	99566364	99566368	-	1	NA	exon (NM_023511, exon 1 of 1)	exon (NM_023511, exon 1 of 1)	264	NM_023511	69473	Mm.158281	NM_023511	ENSMUSG00000047564	Krtap3-1	2310003K17Rik|KAP3.1|KRTAP3.1	keratin associated protein 3-1	protein-coding
mm_20869.1	chr2	148443510	148443520	-	1	NA	promoter-TSS (NM_010740)	promoter-TSS (NM_010740)	20	NM_010740	17064	Mm.681	NM_010740	ENSMUSG00000027435	Cd93	6030404G09Rik|AA145088|AA4.1|AW555904|C1qr1|C1qrp|Ly68	CD93 antigen	protein-coding
mm_22522.1	chr3	7646797	7646815	+	1	NA	Intergenic	Intergenic	-33046	NM_001313888	16196	Mm.3825	NM_008371	ENSMUSG00000040329	Il7	A630026I06Rik|Il-7|hlb368	interleukin 7	protein-coding
mm_9231.1	chr1	171280919	171280955	-	1	NA	5' UTR (NM_008911, exon 1 of 13)	5' UTR (NM_008911, exon 1 of 13)	249	NM_008911	19044	Mm.266888	NM_008911	ENSMUSG00000062729	Ppox	Ppo	protoporphyrinogen oxidase	protein-coding
mm_67495.1	chr7	80752019	80752039	-	1	NA	exon (NM_016721, exon 13 of 38)	exon (NM_016721, exon 13 of 38)	51302	NM_016721	29875	Mm.207619	NM_016721	ENSMUSG00000030536	Iqgap1	AA682088|D7Ertd237e|D7Ertd257e|mKIAA0051	IQ motif containing GTPase activating protein 1	protein-coding
mm_20855.1	chr2	148405505	148405507	-	1	NA	3' UTR (NM_009378, exon 1 of 1)	3' UTR (NM_009378, exon 1 of 1)	2682	NM_009378	21824	Mm.24096	NM_009378	ENSMUSG00000074743	Thbd	AI385582|CD141|TM	thrombomodulin	protein-coding
mm_128706.1	chr15	63718247	63718292	-	1	NA	Intergenic	Intergenic	90470	NM_031378	83492	Mm.335619	NM_031378	ENSMUSG00000079025	Gsdmc	Gsdmc1|Mlze	gasdermin C	protein-coding
mm_158961.1	chr1	92491991	92491991	-	1	NA	promoter-TSS (NM_001011525)	promoter-TSS (NM_001011525)	-238	NM_001011525	258228	Mm.377386	NM_001011525	ENSMUSG00000057464	Olfr1415	MOR103-12	olfactory receptor 1415	protein-coding
mm_59023.1	chr7	19282614	19282702	+	1	NA	promoter-TSS (NM_013648)	promoter-TSS (NM_013648)	34	NM_013648	20167	Mm.24142	NM_013648	ENSMUSG00000030401	Rtn2	MMS10-P|Ms10p|NSPLI|Nspl1	reticulon 2 (Z-band associated protein)	protein-coding
mm_9906.1	chr1	187215245	187215279	-	1	NA	promoter-TSS (NM_026367)	promoter-TSS (NM_026367)	184	NM_029067	74717	Mm.250430	NM_028848	ENSMUSG00000026611	Spata17	1700065F16Rik|4930504I07Rik|4930513F16Rik|MSRG-11	spermatogenesis associated 17	protein-coding
mm_141970.1	chr17	35131791	35131807	-	1	NA	promoter-TSS (NM_018816)	promoter-TSS (NM_018816)	-47	NM_018816	55938	Mm.2161	NM_018816	ENSMUSG00000024391	Apom	1190010O19Rik|G3a|NG20	apolipoprotein M	protein-coding
mm_128215.1	chr15	36164873	36164877	-	1	NA	promoter-TSS (NM_001081253)	promoter-TSS (NM_001081253)	9	NM_001081253	78803	Mm.26393	NM_175281	ENSMUSG00000048230	Fbxo43	4930533G20Rik|Emi2	F-box protein 43	protein-coding
mm_33859.1	chr4	135911676	135911687	+	1	NA	promoter-TSS (NM_001305278)	promoter-TSS (NM_001305278)	1	NM_001305278	12802	Mm.297251	NM_009924	ENSMUSG00000062585	Cnr2	CB-2|CB2|CB2-R	cannabinoid receptor 2 (macrophage)	protein-coding
mm_53105.1	chr6	125071268	125071289	+	1	NA	promoter-TSS (NM_001163268)	promoter-TSS (NM_001163268)	1	NM_001163268	381810	Mm.333386	NM_001163268	ENSMUSG00000067714	Lpar5	GPR93|Gm1072|Gpr92|LPA5	lysophosphatidic acid receptor 5	protein-coding
mm_76102.1	chr8	80395103	80395109	-	1	NA	Intergenic	Intergenic	-98939	NM_010369	14934	Mm.13123	NM_010369	ENSMUSG00000051839	Gypa	AI853584|CD235a|GPA	glycophorin A	protein-coding
mm_52060.1	chr6	97262554	97262569	+	1	NA	Intergenic	RLTR30|LTR|ERV1	-9781	NM_001081157	320502	Mm.68163	NM_001081157	ENSMUSG00000044086	Lmod3	5430424A14Rik	leiomodin 3 (fetal)	protein-coding
mm_63364.1	chr7	127051712	127051723	+	1	NA	exon (NM_026918, exon 2 of 3)	exon (NM_026918, exon 2 of 3)	260	NM_026918	69036	Mm.21835	NM_026918	ENSMUSG00000049350	Zg16	1810010M01Rik|AI593689|ZG16p	zymogen granule protein 16	protein-coding
mm_101950.1	chr11	50252855	50252864	-	1	NA	Intergenic	Intergenic	-14327	NR_132733	17001	Mm.245151	NM_008521	ENSMUSG00000020377	Ltc4s	-	leukotriene C4 synthase	protein-coding
mm_76199.1	chr8	82774107	82774163	-	1	NA	promoter-TSS (NM_145600)	promoter-TSS (NM_145600)	-9	NM_145600	30932	Mm.269248	NM_145600	ENSMUSG00000031711	Zfp330	BC008086|Noa36|Znf330	zinc finger protein 330	protein-coding
mm_133270.1	chr16	77371583	77371612	+	1	NA	intron (NR_015543, intron 2 of 4)	intron (NR_015543, intron 2 of 4)	42269	NR_015543	77994	Mm.394688	NR_015543	ENSMUSG00000090386	Mir99ahg	2810055G20Rik|D730043B02Rik	Mir99a and Mirlet7c-1 host gene (non-protein coding)	ncRNA
mm_167062.1	chr7	94475984	94475989	+	1	NA	Intergenic	Intergenic	1396107	NM_021427	58238	Mm.113787	NM_021427	ENSMUSG00000051515	Fam181b	A830059I20Rik|AB041569	family with sequence similarity 181, member B	protein-coding
mm_62815.1	chr7	113289714	113289717	+	1	NA	intron (NM_001243048, intron 6 of 16)	intron (NM_001243048, intron 6 of 16)	79624	NM_133700	68815	Mm.238034	NM_133700	ENSMUSG00000038187	Btbd10	1110056N09Rik|Gmrp1	BTB (POZ) domain containing 10	protein-coding
mm_14217.1	chr2	127337902	127337920	+	1	NA	promoter-TSS (NM_172539)	promoter-TSS (NM_172539)	-728	NM_172539	215095	Mm.31313	NM_172539	ENSMUSG00000050468	Astl	7420700F21|C87576|Sas1b	astacin-like metalloendopeptidase (M12 family)	protein-coding
mm_105398.1	chr11	103403952	103403958	-	1	NA	intron (NM_183034, intron 1 of 11)	intron (NM_183034, intron 1 of 11)	8709	NM_183034	353047	Mm.18556	NM_183034	ENSMUSG00000034247	Plekhm1	AP162|B2|BC038943|D330036J23Rik	pleckstrin homology domain containing, family M (with RUN domain) member 1	protein-coding
mm_100083.1	chr11	115468297	115468300	+	1	NA	intron (NM_001080934, intron 2 of 3)	intron (NM_001080934, intron 2 of 3)	5825	NM_001080934	217316	Mm.25773	NM_001080934	ENSMUSG00000045775	Slc16a5	A130015N09Rik|MCT 5|MCT 6|MCT5	solute carrier family 16 (monocarboxylic acid transporters), member 5	protein-coding
mm_114637.1	chr13	76443671	76443675	+	1	NA	intron (NM_030174, intron 1 of 20)	intron (NM_030174, intron 1 of 20)	58712	NM_030174	78771	Mm.316249	NM_030174	ENSMUSG00000021596	Mctp1	2810465F10Rik	multiple C2 domains, transmembrane 1	protein-coding
mm_9560.1	chr1	173974854	173974930	-	1	NA	exon (NM_011940, exon 3 of 7)	exon (NM_011940, exon 3 of 7)	7952	NM_008327	26388	Mm.218770	NM_008327	ENSMUSG00000026535	Ifi202b	Ifbip-1|Ifi202|Ifi202a|p202	interferon activated gene 202B	protein-coding
mm_77824.1	chr9	3416967	3416997	+	1	NA	intron (NM_027545, intron 3 of 17)	B3A|SINE|B2	12897	NM_027545	244672	Mm.245482	NM_027545	ENSMUSG00000025898	Cwf19l2	3230401L03Rik|9030209E10	CWF19-like 2, cell cycle control (S. pombe)	protein-coding
mm_9358.1	chr1	172198048	172198061	-	1	NA	3' UTR (NM_001329871, exon 4 of 4)	3' UTR (NM_001329871, exon 4 of 4)	8750	NM_001329871	18611	Mm.544	NM_011063	ENSMUSG00000013698	Pea15a	Mat1|PEA-15|Pea15|Pkcs15	phosphoprotein enriched in astrocytes 15A	protein-coding
mm_86043.1	chr9	114496572	114496581	-	1	NA	promoter-TSS (NM_009916)	promoter-TSS (NM_009916)	-32	NM_009916	12773	Mm.1337	NM_009916	ENSMUSG00000047898	Ccr4	C-C CKR-4|CHEMR1|Cmkbr4|LESTR|Sdf1r	chemokine (C-C motif) receptor 4	protein-coding
mm_43403.1	chr5	135862855	135862859	+	1	NA	intron (NM_021403, intron 11 of 14)	intron (NM_021403, intron 11 of 14)	-25062	NM_013560	15507	Mm.13849	NM_013560	ENSMUSG00000004951	Hspb1	27kDa|Hsp25	heat shock protein 1	protein-coding
mm_10496.1	chr2	14948108	14948116	+	1	NA	intron (NM_023116, intron 3 of 13)	L1_Mus1|LINE|L1	74456	NM_001309519	12296	Mm.313930	NM_023116	ENSMUSG00000057914	Cacnb2	AW060387|CAB2|Cavbeta2|Cchb2	calcium channel, voltage-dependent, beta 2 subunit	protein-coding
mm_117082.1	chr13	59672010	59672013	-	1	NA	intron (NM_001035122, intron 1 of 9)	intron (NM_001035122, intron 1 of 9)	3773	NM_001035122	105348	Mm.171335	NM_027307	ENSMUSG00000021556	Golm1	2310001L02Rik|AW125446|D030064E01Rik|GP73|Golph2|PSEC0257	golgi membrane protein 1	protein-coding
mm_81917.1	chr9	120114963	120114978	+	1	NA	intron (NM_144793, intron 1 of 6)	intron (NM_144793, intron 1 of 6)	4571	NM_144793	208638	Mm.236656	NM_144793	ENSMUSG00000032519	Slc25a38	AV019094|BC010801|appoptosin	solute carrier family 25, member 38	protein-coding
mm_128926.1	chr15	74487637	74487682	-	1	NA	promoter-TSS (NR_144499)	promoter-TSS (NR_144499)	-13	NR_144499	102634630		NR_144499		Gm32168	-	predicted gene, 32168	ncRNA
mm_62371.1	chr7	100639305	100639313	+	1	NA	exon (NM_024287, exon 8 of 8)	exon (NM_024287, exon 8 of 8)	17656	NM_001163187	27276	Mm.491216	NM_013746	ENSMUSG00000030701	Plekhb1	AI315628|PHR1|Phret1|evt-1	pleckstrin homology domain containing, family B (evectins) member 1	protein-coding
mm_104511.1	chr11	96001404	96001409	-	1	NA	intron (NM_009951, intron 2 of 14)	intron (NM_009951, intron 2 of 14)	4538	NM_009951	140486	Mm.294769	NM_009951	ENSMUSG00000013415	Igf2bp1	AL024068|AW549074|CRD-BP|Crdbp|D030026A21Rik|D11Moh40e|D11Moh45|IMP-1|IMP1|Neilsen|ZBP-1|Zbp1|mir-3063	insulin-like growth factor 2 mRNA binding protein 1	protein-coding
mm_13895.1	chr2	120411486	120411490	+	1	NA	exon (NM_172672, exon 3 of 24)	exon (NM_172672, exon 3 of 24)	-7372	NM_001110496	211499	Mm.260712	NM_173734	ENSMUSG00000033808	Tmem87a	A930025J12Rik	transmembrane protein 87A	protein-coding
mm_160452.1	chr8	105699631	105699631	-	1	NA	exon (NM_001012638, exon 7 of 11)	exon (NM_001012638, exon 7 of 11)	1464	NM_001012638	497652	Mm.12964	NM_001012638	ENSMUSG00000038000	Acd	-	adrenocortical dysplasia	protein-coding
mm_3659.1	chr1	153305018	153305029	+	1	NA	intron (NM_010683, intron 1 of 27)	intron (NM_010683, intron 1 of 27)	27763	NM_010683	226519	Mm.1249	NM_010683	ENSMUSG00000026478	Lamc1	Lamb2	laminin, gamma 1	protein-coding
mm_137702.1	chr17	29091119	29091125	+	1	NA	intron (NM_001111099, intron 1 of 2)	intron (NM_001111099, intron 1 of 2)	143	NM_001111099	12575	Mm.195663	NM_007669	ENSMUSG00000023067	Cdkn1a	CAP20|CDKI|CIP1|Cdkn1|P21|SDI1|Waf1|mda6|p21Cip1|p21WAF	cyclin-dependent kinase inhibitor 1A (P21)	protein-coding
mm_109108.1	chr12	105337196	105337225	+	1	NA	intron (NR_125773, intron 1 of 3)	CpG	217	NR_125773	69952	Mm.158311	NR_045047	ENSMUSG00000097929	Tunar	2810011L19Rik|Tuna	Tcl1 upstream neural differentiation associated RNA	ncRNA
mm_44021.1	chr5	147418589	147418629	+	1	NA	promoter-TSS (NR_033625)	promoter-TSS (NR_033625)	-11	NR_033625	100039805	Mm.394705	NR_033625	ENSMUSG00000106820	D5Ertd605e	Gm2433	DNA segment, Chr 5, ERATO Doi 605, expressed	ncRNA
mm_89041.1	chr10	82833967	82833975	+	1	NA	promoter-TSS (NM_001042523)	promoter-TSS (NM_001042523)	20	NM_001042523	50493	Mm.210155	NM_015762	ENSMUSG00000020250	Txnrd1	TR|TR1|TrxR1	thioredoxin reductase 1	protein-coding
mm_6936.1	chr1	85604508	85604539	-	1	NA	promoter-TSS (NM_175397)	promoter-TSS (NM_175397)	-632	NM_175397	109032	Mm.335802	NM_030194	ENSMUSG00000070034	Sp110	5031415C07Rik|52kDa|5830484A20Rik|ENSMUSG00000075603|Ifi75|Ipr1	Sp110 nuclear body protein	protein-coding
mm_91648.1	chr10	42475102	42475119	-	1	NA	intron (NM_145743, intron 1 of 12)	intron (NM_145743, intron 1 of 12)	3455	NM_145743	215951	Mm.89646	NM_145743	ENSMUSG00000038302	Lace1	CG8520	lactation elevated 1	protein-coding
mm_31698.1	chr4	62480026	62480098	+	1	NA	promoter-TSS (NM_138653)	promoter-TSS (NM_138653)	-5	NM_138653	192120	Mm.29808	NM_138653	ENSMUSG00000028392	Bspry	-	B-box and SPRY domain containing	protein-coding
mm_47598.1	chr5	124862486	124862501	-	1	NA	promoter-TSS (NM_001081750)	promoter-TSS (NM_001081750)	-212	NM_001081750	269704	Mm.138617	NM_001081750	ENSMUSG00000079215	Zfp664	AW060232|D930038J03Rik|ZFOC1|Znf664	zinc finger protein 664	protein-coding
mm_88206.1	chr10	70189207	70189234	+	1	NA	exon (NM_001111121, exon 9 of 9)	exon (NM_001111121, exon 9 of 9)	-15444	NM_001304739	69563	Mm.64672	NM_001304739	ENSMUSG00000019933	Mrln	2310015B20Rik|Mln	myoregulin	protein-coding
mm_42632.1	chr5	118437511	118437518	+	1	NA	Intergenic	Intergenic	-123205	NM_001347445	76199	Mm.206238	NM_172424	ENSMUSG00000018076	Med13l	2210413I17Rik|6330591G05Rik|9030618F05Rik|Thrap2|Trap240L|mKIAA1025	mediator complex subunit 13-like	protein-coding
mm_141785.1	chr17	34304810	34304825	-	1	NA	Intergenic	Intergenic	-1050	NM_010382	14969	Mm.22564	NM_010382	ENSMUSG00000060586	H2-Eb1	Eb|H-2Eb|H2Eb|Ia-4|Ia4	histocompatibility 2, class II antigen E beta	protein-coding
mm_107413.1	chr12	33965062	33965065	+	1	NA	Intergenic	Intergenic	7392	NM_011658	22160	Mm.3280	NM_011658	ENSMUSG00000035799	Twist1	M-Twist|Pde|Ska10|Ska<m10Jus>|Twist|bHLHa38|pdt	twist basic helix-loop-helix transcription factor 1	protein-coding
mm_87089.1	chr10	31391349	31391349	+	1	NA	intron (NM_009413, intron 1 of 6)	(CA)n|Simple_repeat|Simple_repeat	23086	NM_011509	100041294	Mm.7821	NM_011509		Supt4b	Gm3258|Supt4h1b|Supt4h2	suppressor of Ty 4B	protein-coding
mm_121240.1	chr14	103056257	103056267	+	1	NA	3' UTR (NM_008392, exon 5 of 5)	3' UTR (NM_008392, exon 5 of 5)	9250	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_72238.1	chr8	74993660	74993698	+	1	NA	promoter-TSS (NM_001316753)	promoter-TSS (NM_001316753)	29	NM_178017	70823	Mm.261739	NM_178017	ENSMUSG00000034518	Hmgxb4	4733401K04Rik|AI316803|Hmgb2l1	HMG box domain containing 4	protein-coding
mm_169768.1	chr15	99820159	99820159	-	1	NA	promoter-TSS (NM_023063)	promoter-TSS (NM_023063)	-10	NM_023063	65970	Mm.33207	NM_023063	ENSMUSG00000023022	Lima1	Eplin	LIM domain and actin binding 1	protein-coding
mm_120198.1	chr14	61648361	61648365	+	1	NA	intron (NR_028264, intron 1 of 6)	CpG	-16253	NR_029733	387174		NR_029733	ENSMUSG00000093007	Mir15a	Mirn15a|mir-15a|mmu-mir-15a	microRNA 15a	ncRNA
mm_68511.1	chr7	111593846	111593871	-	1	NA	intron (NM_173739, intron 3 of 10)	intron (NM_173739, intron 3 of 10)	186119	NM_173739	233733	Mm.323322	NM_173739	ENSMUSG00000038296	Galnt18	2900011G21Rik|BC024988|Galntl4	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 18	protein-coding
mm_109694.1	chr12	113148692	113148704	+	1	NA	Intergenic	Intergenic	-3314	NM_007763	12925	Mm.272368	NM_007763	ENSMUSG00000006360	Crip1	CRHP|CRP1|Crip	cysteine-rich protein 1 (intestinal)	protein-coding
mm_133392.1	chr16	84774264	84774294	+	1	NA	5' UTR (NM_023844, exon 1 of 10)	5' UTR (NM_023844, exon 1 of 10)	156	NM_023844	67374	Mm.41758	NM_023844	ENSMUSG00000053062	Jam2	1110002N23Rik|2410030G21Rik|2410167M24Rik|JAM-2|JAM-B|Jcam2|VE-JAM	junction adhesion molecule 2	protein-coding
mm_127698.1	chr15	102990909	102990909	+	1	NA	exon (NM_010466, exon 1 of 2)	exon (NM_010466, exon 1 of 2)	370	NM_010466	15426	Mm.6167	NM_010466	ENSMUSG00000001657	Hoxc8	D130011F21Rik|Hox-3.1	homeobox C8	protein-coding
mm_105913.1	chr11	114984029	114984052	-	1	NA	3' UTR (NM_145437, exon 4 of 4)	3' UTR (NM_145437, exon 4 of 4)	5846	NM_145437	217305	Mm.275986	NM_145437	ENSMUSG00000034641	Cd300ld	4732429D16Rik|CLM5|Cd300ld1|LMIR4|MAIR-IV|clm-5	CD300 molecule like family member d	protein-coding
mm_110223.1	chr12	28635868	28635887	-	1	NA	promoter-TSS (NM_011300)	promoter-TSS (NM_011300)	76	NM_011300	20115	Mm.279839	NM_011300	ENSMUSG00000061477	Rps7	Mtu|Rps7A|S7	ribosomal protein S7	protein-coding
mm_101528.1	chr11	33159963	33159980	-	1	NA	exon (NM_001252261, exon 6 of 10)	exon (NM_001252261, exon 6 of 10)	3235	NM_001252261	18148	Mm.485384	NM_008722	ENSMUSG00000057113	Npm1	B23|NO38|Npm	nucleophosmin 1	protein-coding
mm_521.1	chr1	37541210	37541212	+	1	NA	promoter-TSS (NM_173870)	promoter-TSS (NM_173870)	-195	NM_173870	269181	Mm.25861	NM_173870	ENSMUSG00000026110	Mgat4a	9530018I07Rik|GnT-IVa|glcNAc-T-IVa	mannoside acetylglucosaminyltransferase 4, isoenzyme A	protein-coding
mm_155503.1	chrX	73787109	73787115	+	1	NA	promoter-TSS (NM_008323)	promoter-TSS (NM_008323)	-31	NM_009279	20832	Mm.831	NM_009279	ENSMUSG00000002014	Ssr4	AW743063|C78062|Trap	signal sequence receptor, delta	protein-coding
mm_47905.1	chr5	134945252	134945258	-	1	NA	3' UTR (NM_009903, exon 1 of 1)	3' UTR (NM_009903, exon 1 of 1)	1679	NM_009903	12740	Mm.7339	NM_009903	ENSMUSG00000047501	Cldn4	Cep-r|Cpetr|Cpetr1	claudin 4	protein-coding
mm_122623.1	chr14	51145590	51145622	-	1	NA	exon (NM_011271, exon 2 of 2)	exon (NM_011271, exon 2 of 2)	1161	NM_011271	19752	Mm.235538	NM_011271	ENSMUSG00000035896	Rnase1	AI574248|Rib-1|Rib1	ribonuclease, RNase A family, 1 (pancreatic)	protein-coding
mm_124612.1	chr15	3279491	3279501	+	1	NA	exon (NM_009155, exon 5 of 5)	exon (NM_009155, exon 5 of 5)	8519	NM_009155	20363	Mm.392203	NM_009155	ENSMUSG00000064373	Selenop	AU018766|D15Ucla1|Se-P|Sepp1|selp	selenoprotein P	protein-coding
mm_6940.1	chr1	85727158	85727179	-	1	NA	intron (NM_177055, intron 1 of 5)	intron (NM_177055, intron 1 of 5)	9438	NM_177055	319997	Mm.116691	NM_177055	ENSMUSG00000052760	A630001G21Rik	-	RIKEN cDNA A630001G21 gene	protein-coding
mm_164909.1	chr18	70753492	70753494	-	1	NA	Intergenic	Intergenic	185201	NM_010773	17191	Mm.322	NM_010773	ENSMUSG00000024513	Mbd2	MBD2a	methyl-CpG binding domain protein 2	protein-coding
mm_140211.1	chr17	83795396	83795402	+	1	NA	intron (NM_054082, intron 14 of 16)	intron (NM_054082, intron 14 of 16)	51391	NM_025325	107766	Mm.30100	NM_025325	ENSMUSG00000000673	Haao	0610007K21Rik|0610012J07Rik|3-HAO|3-HAOxase|3HAO	3-hydroxyanthranilate 3,4-dioxygenase	protein-coding
mm_115688.1	chr13	13862906	13862912	-	1	NA	Intergenic	RMER17B|LTR|ERVK	78602	NM_010317	14706	Mm.215394	NM_010317	ENSMUSG00000021303	Gng4	-	guanine nucleotide binding protein (G protein), gamma 4	protein-coding
mm_164474.1	chr16	68129712	68129713	+	1	NA	Intergenic	Intergenic	-508804	NM_178721	239857	Mm.394300	NM_178721	ENSMUSG00000064115	Cadm2	2900078E11Rik|9330131D06|A830029E02Rik|Igdf4d|Igsf4d|NECL3|SynCAM 2|SynCAM2	cell adhesion molecule 2	protein-coding
mm_158554.1	chrX	147554052	147554087	-	1	NA	promoter-TSS (NM_001081173)	promoter-TSS (NM_001081173)	12	NM_001081173	210297	Mm.30506	NM_001081173	ENSMUSG00000031290	Lrch2	AI316885|mKIAA1495	leucine-rich repeats and calponin homology (CH) domain containing 2	protein-coding
mm_45480.1	chr5	70842293	70842338	-	1	NA	5' UTR (NM_010252, exon 1 of 9)	5' UTR (NM_010252, exon 1 of 9)	302	NM_010252	14405	Mm.255292	NM_010252	ENSMUSG00000001260	Gabrg1	GabaA|GabaA/BZ	gamma-aminobutyric acid (GABA) A receptor, subunit gamma 1	protein-coding
mm_137001.1	chr17	17491376	17491400	+	1	NA	Intergenic	Intergenic	88702	NM_025681	66643	Mm.268018	NM_025681	ENSMUSG00000047786	Lix1	5730466L18Rik	limb and CNS expressed 1	protein-coding
mm_134000.1	chr16	4789866	4789885	-	1	NA	promoter-TSS (NM_025670)	promoter-TSS (NM_025670)	60	NM_025670	66626	Mm.157648	NM_025670	ENSMUSG00000004071	Cdip1	2700048O17Rik|5730403B10Rik|AU018521|AW742692|CDIP	cell death inducing Trp53 target 1	protein-coding
mm_10488.1	chr2	14824045	14824047	+	1	NA	promoter-TSS (NM_001252533)	promoter-TSS (NM_001252533)	-46	NM_001252533	12296	Mm.313930	NM_023116	ENSMUSG00000057914	Cacnb2	AW060387|CAB2|Cavbeta2|Cchb2	calcium channel, voltage-dependent, beta 2 subunit	protein-coding
mm_168380.1	chr1	12312748	12312750	-	1	NA	Intergenic	RLTR9D|LTR|ERVK	-113237	NR_105759	102465961		NR_105759	ENSMUSG00000098555	Mir6341	Gm27262|mmu-mir-6341	microRNA 6341	ncRNA
mm_89376.1	chr10	88885904	88885917	+	1	NA	promoter-TSS (NM_145423)	promoter-TSS (NM_145423)	-82	NM_145423	216225	Mm.77381	NM_145423	ENSMUSG00000020062	Slc5a8	Ait|SMCT	solute carrier family 5 (iodide transporter), member 8	protein-coding
mm_32681.1	chr4	115784997	115785052	+	1	NA	exon (NM_181040, exon 1 of 9)	exon (NM_181040, exon 1 of 9)	210	NM_181040	230649	Mm.109600	NM_181040	ENSMUSG00000028710	Atpaf1	6330547J17Rik|AI593252|ATP11|ATP11p	ATP synthase mitochondrial F1 complex assembly factor 1	protein-coding
mm_138408.1	chr17	35067125	35067136	+	1	NA	promoter-TSS (NM_023463)	promoter-TSS (NM_023463)	-195	NM_023463	68468	Mm.215096	NM_023463	ENSMUSG00000092586	Ly6g6c	1110003M04Rik|AU016360|G6c|NG24	lymphocyte antigen 6 complex, locus G6C	protein-coding
mm_122665.1	chr14	51913946	51914012	-	1	NA	promoter-TSS (NM_001145959)	promoter-TSS (NM_001145959)	-491	NM_013864	29811	Mm.26722	NM_013864	ENSMUSG00000004558	Ndrg2	AI182517|AU040374|Ndr2|SYLD	N-myc downstream regulated gene 2	protein-coding
mm_132405.1	chr16	35001761	35001800	+	1	NA	3' UTR (NM_139300, exon 32 of 32)	3' UTR (NM_139300, exon 32 of 32)	-20641	NM_023587	70757	Mm.27286	NM_023587	ENSMUSG00000035376	Hacd2	6330408J20Rik|AI255777|AI481689|Hcad2|Ptplb	3-hydroxyacyl-CoA dehydratase 2	protein-coding
mm_86015.1	chr9	112234885	112234903	-	1	NA	promoter-TSS (NM_001177619)	promoter-TSS (NM_001177619)	-53	NM_001177619	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_95585.1	chr11	53299856	53299872	+	1	NA	intron (NM_008300, intron 1 of 18)	CpG	615	NM_008300	15525	Mm.239865	NM_008300	ENSMUSG00000020361	Hspa4	70kDa|AI317151|APG-2|Hsp110|Hsp70RY|mKIAA4025	heat shock protein 4	protein-coding
mm_166516.1	chr6	17306141	17306188	+	1	NA	promoter-TSS (NM_007616)	promoter-TSS (NM_007616)	-171	NM_007616	12389	Mm.28278	NM_007616	ENSMUSG00000007655	Cav1	Cav|Cav-1	caveolin 1, caveolae protein	protein-coding
mm_139579.1	chr17	57080595	57080605	+	1	NA	3' UTR (NM_009451, exon 4 of 4)	3' UTR (NM_009451, exon 4 of 4)	-2090	NM_153551	70785	Mm.284447	NM_153551	ENSMUSG00000002668	Dennd1c	4432409M07Rik	DENN/MADD domain containing 1C	protein-coding
mm_100218.1	chr11	117076842	117076852	+	1	NA	promoter-TSS (NR_105853)	promoter-TSS (NR_105853)	64	NR_027059	76972	Mm.309167	NR_027059	ENSMUSG00000086859	Snhg20	2810008D09Rik	small nucleolar RNA host gene 20	ncRNA
mm_83012.1	chr9	36779998	36780012	-	1	NA	3' UTR (NM_001199494, exon 11 of 11)	3' UTR (NM_001199494, exon 11 of 11)	-12427	NM_008408	16430	Mm.2863	NM_008408	ENSMUSG00000032116	Stt3a	AA408947|BB081708|Itm1	STT3, subunit of the oligosaccharyltransferase complex, homolog A (S. cerevisiae)	protein-coding
mm_5006.1	chr1	191978248	191978259	+	1	NA	promoter-TSS (NM_001303132)	promoter-TSS (NM_001303132)	-1	NM_001303132	74023	Mm.274393	NM_023727	ENSMUSG00000049353	Rd3	3322402L07Rik|rd-3|rd3	retinal degeneration 3	protein-coding
mm_161180.1	chr13	46609538	46609538	+	1	NA	intron (NM_026056, intron 4 of 12)	intron (NM_026056, intron 4 of 12)	-59984	NM_001033192	97863	Mm.275934	NM_001033192	ENSMUSG00000069237	Fam8a1	C78339	family with sequence similarity 8, member A1	protein-coding
mm_169625.1	chr15	4026497	4026499	+	1	NA	promoter-TSS (NM_024188)	promoter-TSS (NM_024188)	70	NM_024188	67041	Mm.13445	NM_024188	ENSMUSG00000022186	Oxct1	2610008O03Rik|Oxct|Oxct2a|Scot-s	3-oxoacid CoA transferase 1	protein-coding
mm_69575.1	chr7	135700974	135700984	-	1	NA	exon (NM_001081117, exon 12 of 14)	exon (NM_001081117, exon 12 of 14)	15400	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_25842.1	chr3	129217563	129217579	+	1	NA	intron (NM_011098, intron 4 of 4)	intron (NM_011098, intron 4 of 4)	3639	NM_001287048	18741	Mm.246804	NM_011098	ENSMUSG00000028023	Pitx2	9430085M16Rik|Brx1|Brx1b|Munc30|Otlx2|Ptx2|Rieg	paired-like homeodomain transcription factor 2	protein-coding
mm_21861.1	chr2	165885067	165885071	-	1	NA	promoter-TSS (NM_001252584)	promoter-TSS (NM_001252584)	-231	NM_001252587	228880	Mm.227598	NM_027230	ENSMUSG00000039671	Zmynd8	1110013E22Rik|2010005I16Rik|3632413B07Rik|AI316811|AL024039|Prkcbp1|RACK7	zinc finger, MYND-type containing 8	protein-coding
mm_95068.1	chr11	32554907	32554915	+	1	NA	intron (NM_009288, intron 1 of 18)	intron (NM_009288, intron 1 of 18)	21645	NM_009288	20868	Mm.8235	NM_009288	ENSMUSG00000020272	Stk10	Gek1|Lok|mKIAA4026	serine/threonine kinase 10	protein-coding
mm_128286.1	chr15	37007800	37007804	-	1	NA	promoter-TSS (NM_026521)	promoter-TSS (NM_026521)	-400	NM_026521	68036	Mm.371631	NM_026521	ENSMUSG00000062397	Zfp706	3110006P09Rik|AA793007|AW536850|C77232|Znf706	zinc finger protein 706	protein-coding
mm_160126.1	chr7	28451876	28451876	+	1	NA	promoter-TSS (NM_001141921)	promoter-TSS (NM_001141921)	-109	NM_030562	80749	Mm.483073	NM_030562	ENSMUSG00000030600	Lrfn1	BC004018|SALM2|Semo1	leucine rich repeat and fibronectin type III domain containing 1	protein-coding
mm_159304.1	chr2	178430561	178430561	+	1	NA	promoter-TSS (NM_198656)	promoter-TSS (NM_198656)	46	NM_198656	381409	Mm.330860	NM_198656	ENSMUSG00000039155	Cdh26	Gm1010	cadherin-like 26	protein-coding
mm_122728.1	chr14	52316308	52316324	-	1	NA	promoter-TSS (NM_001244916)	promoter-TSS (NM_001244916)	7	NM_001244916	50524	Mm.39487	NM_015772	ENSMUSG00000049532	Sall2	AI225809|AW559097|Msal-2|Sal-2|mKIAA0360|p150(Sal2)	sal-like 2 (Drosophila)	protein-coding
mm_173165.1	chrX	41483073	41483081	+	1	NA	intron (NR_104053, intron 3 of 16)	L1Md_T|LINE|L1	81548	NM_001290451	53623	Mm.327681	NM_016886	ENSMUSG00000001986	Gria3	2900064I19Rik|GluA3|GluR-C|GluR-K3|Glur-3|Glur3|Gluralpha3	glutamate receptor, ionotropic, AMPA3 (alpha 3)	protein-coding
mm_120251.1	chr14	63011650	63011656	+	1	NA	promoter-TSS (NM_001039121)	promoter-TSS (NM_001039121)	-118	NM_001039121	654458	Mm.390737	NM_001039121	ENSMUSG00000075572	Defb43	BD-43|EG654458|mBD-43	defensin beta 43	protein-coding
mm_85314.1	chr9	101198977	101198997	-	1	NA	promoter-TSS (NM_172144)	promoter-TSS (NM_172144)	86	NM_172144	235542	Mm.335386	NM_172144	ENSMUSG00000043154	Ppp2r3a	3222402P14Rik|A730042E07	protein phosphatase 2, regulatory subunit B'', alpha	protein-coding
mm_48881.1	chr5	151137962	151137966	-	1	NA	intron (NM_146258, intron 1 of 13)	intron (NM_146258, intron 1 of 13)	52229	NM_001163493	243362	Mm.209272	NM_146258	ENSMUSG00000016128	Stard13	DLC2|GT650	StAR-related lipid transfer (START) domain containing 13	protein-coding
mm_132541.1	chr16	37881346	37881361	+	1	NA	exon (NM_177093, exon 4 of 4)	exon (NM_177093, exon 4 of 4)	12953	NM_177093	320184	Mm.390882	NM_177093	ENSMUSG00000034158	Lrrc58	1810012N18Rik|C330018J07Rik	leucine rich repeat containing 58	protein-coding
mm_122313.1	chr14	36919315	36919352	-	1	NA	5' UTR (NM_001347503, exon 1 of 8)	5' UTR (NM_001347503, exon 1 of 8)	202	NM_001347503	72972	Mm.27621	NM_027045	ENSMUSG00000058690	Ccser2	1700012P13Rik|2900054P12Rik|AI035535|AW108503|Fam190b|Gcap14	coiled-coil serine rich 2	protein-coding
mm_109496.1	chr12	111449839	111449853	+	1	NA	exon (NM_009396, exon 8 of 12)	exon (NM_009396, exon 8 of 12)	7185	NM_009396	21928	Mm.255332	NM_009396	ENSMUSG00000021281	Tnfaip2	B94|Exoc3l3|M-sec|Tnfip2|tnfb94	tumor necrosis factor, alpha-induced protein 2	protein-coding
mm_65035.1	chr7	18560561	18560569	-	1	NA	exon (NM_001037168, exon 4 of 5)	exon (NM_001037168, exon 4 of 5)	6740	NM_001037168	545925	Mm.440302	NM_001037168	ENSMUSG00000070797	Psg27	EG545925|cea15	pregnancy-specific glycoprotein 27	protein-coding
mm_15203.1	chr2	154211522	154211537	+	1	NA	exon (NM_153418, exon 8 of 16)	exon (NM_153418, exon 8 of 16)	11149	NM_153418	228801	Mm.3783	NM_153418	ENSMUSG00000027485	Bpifb1	Lplunc1	BPI fold containing family B, member 1	protein-coding
mm_94164.1	chr10	128747629	128747645	-	1	NA	promoter-TSS (NM_001170869)	promoter-TSS (NM_001170869)	-242	NM_030100	78428	Mm.27358	NM_030100	ENSMUSG00000064030	Pym1	A030010B05Rik|Pym|Wibg	PYM homolog 1, exon junction complex associated factor	protein-coding
mm_43350.1	chr5	135168444	135168502	+	1	NA	5' UTR (NM_009745, exon 1 of 6)	5' UTR (NM_009745, exon 1 of 6)	101	NM_009745	12054	Mm.405834	NM_009745	ENSMUSG00000029681	Bcl7b	-	B cell CLL/lymphoma 7B	protein-coding
mm_77938.1	chr9	7355360	7355391	+	1	NA	exon (NM_008605, exon 8 of 10)	exon (NM_008605, exon 8 of 10)	8001	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_97533.1	chr11	78536394	78536492	+	1	NA	promoter-TSS (NM_018854)	promoter-TSS (NM_018854)	7	NM_018854	55978	Mm.358671	NM_018854	ENSMUSG00000001105	Ift20	0610009H04Rik|AU015496	intraflagellar transport 20	protein-coding
mm_128264.1	chr15	36787865	36787890	-	1	NA	intron (NM_001253806, intron 2 of 5)	intron (NM_001253806, intron 2 of 5)	3055	NM_001253807	22631	Mm.3360	NM_011740	ENSMUSG00000022285	Ywhaz	1110013I11Rik|14-3-3zeta|AI596267|AL022924|AU020854	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide	protein-coding
mm_131107.1	chr16	5050013	5050122	+	1	NA	promoter-TSS (NM_028720)	promoter-TSS (NM_028720)	-1	NM_026666	170644	Mm.66356	NM_026666	ENSMUSG00000039473	Ubn1	1110029L11Rik|2610108L02Rik|AA673476|AW124741	ubinuclein 1	protein-coding
mm_158156.1	chrX	103480564	103480645	-	1	NA	non-coding (NR_001570, exon 1 of 8)	non-coding (NR_001570, exon 1 of 8)	2629	NR_001570	213742	Mm.274770	NR_001463	ENSMUSG00000086503	Xist	A430022B11|AI314753	inactive X specific transcripts	ncRNA
mm_160248.1	chr7	105368081	105368081	+	1	NA	promoter-TSS (NM_146355)	promoter-TSS (NM_146355)	-247	NM_146355	258352	Mm.377449	NM_146355	ENSMUSG00000073906	Olfr692	MOR36-1	olfactory receptor 692	protein-coding
mm_1237.1	chr1	62795987	62796000	+	1	NA	3' UTR (NM_001077407, exon 16 of 16)	3' UTR (NM_001077407, exon 16 of 16)	-1261	NR_040601	74992	Mm.401979	NR_040601		4930487H11Rik	-	RIKEN cDNA 4930487H11 gene	ncRNA
mm_150540.1	chr19	39309695	39309699	+	1	NA	exon (NM_007815, exon 5 of 9)	exon (NM_007815, exon 5 of 9)	22612	NM_007815	13095	Mm.20764	NM_007815	ENSMUSG00000003053	Cyp2c29	AHOH|AHOHase|AI159681|AI196010|Ah-2|Ahh-1|Cyp2c|P450-2C	cytochrome P450, family 2, subfamily c, polypeptide 29	protein-coding
mm_79593.1	chr9	58370550	58370565	+	1	NA	promoter-TSS (NR_040727)	promoter-TSS (NR_040727)	53	NR_040727	73529	Mm.490924	NR_040727	ENSMUSG00000100487	1700072B07Rik	-	RIKEN cDNA 1700072B07 gene	ncRNA
mm_39866.1	chr5	31054767	31054809	+	1	NA	promoter-TSS (NM_001289522)	promoter-TSS (NM_001289522)	8	NM_001289522	69719	Mm.305535	NM_023525	ENSMUSG00000013629	Cad	2410008J01Rik|AU018859|Cpad	carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase	protein-coding
mm_113657.1	chr13	42680830	42680859	+	1	NA	promoter-TSS (NM_001302635)	promoter-TSS (NM_001302635)	45	NM_001302635	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding
mm_115296.1	chr13	111984279	111984288	+	1	NA	Intergenic	Intergenic	116347	NR_130345	102636620	Mm.402328	NR_130345	ENSMUSG00000086111	Gm15326	OTTMUSG00000020187	predicted gene 15326	ncRNA
mm_56147.1	chr6	87811811	87811842	-	1	NA	promoter-TSS (NM_001039394)	promoter-TSS (NM_001039394)	-47	NM_001039394	69834	Mm.37380	NM_133717	ENSMUSG00000030055	Rab43	1810048P08Rik|2500004H21Rik|AW490415	RAB43, member RAS oncogene family	protein-coding
mm_100749.1	chr11	4160287	4160305	-	1	NA	promoter-TSS (NM_177616)	promoter-TSS (NM_177616)	-3	NM_001164620	216516	Mm.386854	NM_177616	ENSMUSG00000051427	Ccdc157	4930562D19Rik|mKIAA1656	coiled-coil domain containing 157	protein-coding
mm_23278.1	chr3	51661068	51661070	+	1	NA	promoter-TSS (NM_174995)	promoter-TSS (NM_174995)	-110	NM_174995	211666	Mm.24679	NM_174995	ENSMUSG00000074604	Mgst2	GST2|MGST-II	microsomal glutathione S-transferase 2	protein-coding
mm_9429.1	chr1	172500158	172500162	-	1	NA	promoter-TSS (NM_178598)	promoter-TSS (NM_178598)	-86	NM_178598	21346	Mm.271711	NM_178598	ENSMUSG00000026547	Tagln2	2700094C18Rik|SM22beta|Sm22B|Sm22a	transgelin 2	protein-coding
mm_42611.1	chr5	117949569	117949592	+	1	NA	intron (NM_008712, intron 25 of 27)	intron (NM_008712, intron 25 of 27)	-27190	NM_145564	231670	Mm.21912	NM_145564	ENSMUSG00000032898	Fbxo21	2810425J22Rik|AU016673	F-box protein 21	protein-coding
mm_23654.1	chr3	67582879	67582898	+	1	NA	exon (NM_025813, exon 1 of 16)	exon (NM_025813, exon 1 of 16)	120	NM_025813	66868	Mm.491153	NM_025813	ENSMUSG00000027775	Mfsd1	1200003O06Rik	major facilitator superfamily domain containing 1	protein-coding
mm_115854.1	chr13	21289273	21289286	-	1	NA	exon (NM_010343, exon 3 of 5)	exon (NM_010343, exon 3 of 5)	3407	NM_010343	14780	Mm.1332	NM_010343	ENSMUSG00000004344	Gpx5	AV379049|Arep	glutathione peroxidase 5	protein-coding
mm_100874.1	chr11	5950019	5950063	-	1	NA	promoter-TSS (NM_010292)	promoter-TSS (NM_010292)	40	NM_010292	103988	Mm.220358	NM_010292	ENSMUSG00000041798	Gck	GLK|Gk|Gls006|HK4|HKIV|HXKP|Hlb62|MODY2	glucokinase	protein-coding
mm_149399.1	chr19	11390262	11390270	+	1	NA	exon (NM_001310331, exon 6 of 7)	exon (NM_001310331, exon 6 of 7)	14778	NM_001310331	666907		NM_001310331	ENSMUSG00000101389	Ms4a4a	EG666907	membrane-spanning 4-domains, subfamily A, member 4A	protein-coding
mm_109646.1	chr12	112829661	112829685	+	1	NA	promoter-TSS (NM_028023)	promoter-TSS (NM_028023)	-284	NM_028023	71963	Mm.313185	NM_028023	ENSMUSG00000047832	Cdca4	2410018C03Rik|HEPP|SEI-3	cell division cycle associated 4	protein-coding
mm_163862.1	chr14	19418795	19418819	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	183780	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_19917.1	chr2	115859118	115859162	-	1	NA	Intergenic	Intergenic	205479	NM_001346044	17536	Mm.247566	NM_010825	ENSMUSG00000027210	Meis2	A430109D20Rik|Mrg1|Stra10	Meis homeobox 2	protein-coding
mm_43802.1	chr5	142822585	142822598	+	1	NA	Intergenic	Intergenic	-5204	NM_001122730	231861	Mm.354649	NM_178242	ENSMUSG00000039477	Tnrc18	BC025631|EG381742|Zfp469	trinucleotide repeat containing 18	protein-coding
mm_93889.1	chr10	125328548	125328556	-	1	NA	promoter-TSS (NM_011391)	promoter-TSS (NM_011391)	-17	NM_011391	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|Mct2	solute carrier family 16 (monocarboxylic acid transporters), member 7	protein-coding
mm_154955.1	chrX	36792964	36792969	+	1	NA	Intergenic	BC1_Mm|scRNA|scRNA	-2631	NM_007451	11740	Mm.371544	NM_007451	ENSMUSG00000016319	Slc25a5	Ant2	solute carrier family 25 (mitochondrial carrier, adenine nucleotide translocator), member 5	protein-coding
mm_67608.1	chr7	83883455	83883470	-	1	NA	5' UTR (NM_030705, exon 1 of 1)	5' UTR (NM_030705, exon 1 of 1)	879	NM_030705	80889	Mm.272998	NM_030705	ENSMUSG00000070462	Mesdc1	AW061151	mesoderm development candidate 1	protein-coding
mm_138810.1	chr17	39846511	39846525	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	3521	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_58762.1	chr7	14518557	14518567	+	1	NA	Intergenic	Intergenic	-25636	NM_001184981	638251	Mm.482063	NM_001184981	ENSMUSG00000094156	Sult2a7	EG638251|Gm7231	sulfotransferase family 2A, dehydroepiandrosterone (DHEA)-preferring, member 7	protein-coding
mm_12311.1	chr2	69135784	69135797	+	1	NA	promoter-TSS (NM_181547)	promoter-TSS (NM_181547)	-10	NM_181547	329416	Mm.90047	NM_181547	ENSMUSG00000034738	Nostrin	Daip2|mDaIP2	nitric oxide synthase trafficker	protein-coding
mm_94088.1	chr10	128498677	128498709	-	1	NA	promoter-TSS (NM_172259)	promoter-TSS (NM_172259)	-8	NM_172259	216459	Mm.291688	NM_172259	ENSMUSG00000039824	Myl6b	5730437E04Rik|BC037527|MLC1SA	myosin, light polypeptide 6B	protein-coding
mm_81634.1	chr9	110880193	110880207	+	1	NA	promoter-TSS (NM_001146059)	promoter-TSS (NM_001146059)	26	NM_001146059	235633	Mm.86338	NM_146228	ENSMUSG00000044037	Als2cl	79H19D|79H19E|BC022645|D930044G19Rik|mRn.49018	ALS2 C-terminal like	protein-coding
mm_23149.1	chr3	40160355	40160385	+	1	NA	Intergenic	(T)n|Simple_repeat|Simple_repeat	362542	NR_040445	100040882	Mm.272869	NR_040445	ENSMUSG00000037884	1700017G19Rik	-	RIKEN cDNA 1700017G19 gene	ncRNA
mm_72689.1	chr8	84969638	84969653	+	1	NA	promoter-TSS (NM_011563)	promoter-TSS (NM_011563)	23	NM_011563	21672	Mm.347009	NM_011563	ENSMUSG00000005161	Prdx2	AL022839|Band-8|NkefB|PRP|PrxII|TDX1|TPx|TPx-B|TR|TSA|Tdpx1|Torin	peroxiredoxin 2	protein-coding
mm_57135.1	chr6	122608495	122608523	-	1	NA	intron (NM_008108, intron 1 of 1)	B1F|SINE|Alu	1578	NM_008108	14562	Mm.299742	NM_008108	ENSMUSG00000030117	Gdf3	C78318|Gdf-3|Vgr-2|Vgr2|ecat9	growth differentiation factor 3	protein-coding
mm_79723.1	chr9	61595401	61595423	+	1	NA	Intergenic	Intergenic	223046	NM_001083927	21887	Mm.24255	NM_009389	ENSMUSG00000032280	Tle3	2610103N05Rik|ESG|Grg3a|Grg3b|mKIAA1547	transducin-like enhancer of split 3	protein-coding
mm_21232.1	chr2	156052951	156052964	-	1	NA	promoter-TSS (NM_001136556)	promoter-TSS (NM_001136556)	-10	NM_001136556	74562	Mm.159241	NM_001136556	ENSMUSG00000013338	Fer1l4	9130402C12Rik	fer-1-like 4 (C. elegans)	protein-coding
mm_143564.1	chr17	74265825	74265825	-	1	NA	intron (NM_133771, intron 1 of 8)	intron (NM_133771, intron 1 of 8)	29038	NM_133771	76890	Mm.311874	NM_133771	ENSMUSG00000058704	Memo1	0610016J10Rik|D930048L02Rik	mediator of cell motility 1	protein-coding
mm_4669.1	chr1	180382374	180382400	+	1	NA	intron (NM_001081175, intron 2 of 7)	intron (NM_001081175, intron 2 of 7)	-51838	NR_003623	277333	Mm.389223	NM_199472		Gm5069	EG277333	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_122675.1	chr14	52008966	52008986	-	1	NA	exon (NM_001253694, exon 4 of 6)	exon (NM_001253694, exon 4 of 6)	5582	NM_001253695	69890	Mm.475652	NM_027248	ENSMUSG00000049295	Zfp219	2010302A17Rik	zinc finger protein 219	protein-coding
mm_88890.1	chr10	81137721	81137744	+	1	NA	intron (NM_010731, intron 1 of 2)	CpG	1461	NM_010731	16969	Mm.20920	NM_010731	ENSMUSG00000035011	Zbtb7a	9030619K07Rik|9130006G12Rik|AI452336|FBI-1|Lrf|Pokemon|Zbtb7	zinc finger and BTB domain containing 7a	protein-coding
mm_147208.1	chr18	37935404	37935428	-	1	NA	promoter-TSS (NM_001305981)	promoter-TSS (NM_001305981)	60	NM_001305980	13367	Mm.195916	NM_007858	ENSMUSG00000024456	Diaph1	D18Wsu154e|Dia1|Diap1|Drf1|p140mDia	diaphanous related formin 1	protein-coding
mm_107336.1	chr12	32378873	32378895	+	1	NA	promoter-TSS (NM_001162903)	promoter-TSS (NM_001162903)	95	NM_001162903	72123	Mm.341352	NM_028111	ENSMUSG00000090946	Ccdc71l	2010109K11Rik|AV375874	coiled-coil domain containing 71 like	protein-coding
mm_129141.1	chr15	76200568	76200576	-	1	NA	promoter-TSS (NM_201391)	promoter-TSS (NM_201391)	35	NM_201390	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
mm_102713.1	chr11	67052641	67052651	-	1	NA	promoter-TSS (NM_025510)	promoter-TSS (NM_025510)	-24	NM_001040026	52892	Mm.129731	NM_001040026	ENSMUSG00000069844	Sco1	2610001C07Rik|D11Bwg1310e	SCO1 cytochrome c oxidase assembly protein	protein-coding
mm_26487.1	chr3	145096844	145096857	+	1	NA	intron (NM_178697, intron 2 of 13)	intron (NM_178697, intron 2 of 13)	2256	NM_178697	229933	Mm.331420	NM_178697	ENSMUSG00000036960	Clca2	4732440A06|AI586120|Clca5	chloride channel accessory 2	protein-coding
mm_168435.1	chr11	3539281	3539284	-	1	NA	promoter-TSS (NM_001284429)	promoter-TSS (NM_001284429)	10	NM_013870	29856	Mm.188516	NM_013870	ENSMUSG00000020439	Smtn	smsmo	smoothelin	protein-coding
mm_110090.1	chr12	25095722	25095793	-	1	NA	exon (NM_010496, exon 1 of 3)	exon (NM_010496, exon 1 of 3)	335	NM_010496	15902	Mm.34871	NM_010496	ENSMUSG00000020644	Id2	AI255428|C78922|Idb2|bHLHb26	inhibitor of DNA binding 2	protein-coding
mm_84427.1	chr9	65827708	65827740	-	1	NA	promoter-TSS (NM_172536)	promoter-TSS (NM_172536)	-160	NM_172536	214812	Mm.139231	NM_172536	ENSMUSG00000040524	Zfp609	9830165N24|BC016271|Znf609|mKIAA0295	zinc finger protein 609	protein-coding
mm_10142.1	chr2	4218168	4218170	+	1	NA	intron (NM_172475, intron 1 of 22)	intron (NM_172475, intron 1 of 22)	65306	NM_172475	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding
mm_102303.1	chr11	55607918	55608004	-	1	NA	5' UTR (NM_020492, exon 1 of 9)	5' UTR (NM_020492, exon 1 of 9)	237	NM_001290821	14654	Mm.89320	NM_020492	ENSMUSG00000000263	Glra1	nmf11|oscillator|ot|spasmodic|spd	glycine receptor, alpha 1 subunit	protein-coding
mm_117564.1	chr13	85284629	85284636	-	1	NA	intron (NM_145452, intron 1 of 24)	intron (NM_145452, intron 1 of 24)	4854	NM_145452	218397	Mm.259653	NM_145452	ENSMUSG00000021549	Rasa1	Gap|RasGAP|Rasa	RAS p21 protein activator 1	protein-coding
mm_51475.1	chr6	83006261	83006281	+	1	NA	intron (NM_033079, intron 6 of 9)	intron (NM_033079, intron 6 of 9)	27200	NM_010070	13448	Mm.156	NM_010070	ENSMUSG00000068335	Dok1	AW557123|p62DOK	docking protein 1	protein-coding
mm_88591.1	chr10	79728751	79728772	+	1	NA	intron (NM_008226, intron 3 of 7)	intron (NM_008226, intron 3 of 7)	12127	NM_008226	15166	Mm.12956	NM_008226	ENSMUSG00000020331	Hcn2	BCNG2|HAC1|trls	hyperpolarization-activated, cyclic nucleotide-gated K+ 2	protein-coding
mm_29832.1	chr3	129755255	129755265	-	1	NA	promoter-TSS (NM_010113)	promoter-TSS (NM_010113)	62	NM_010113	13645	Mm.252481	NM_010113	ENSMUSG00000028017	Egf	AI790464	epidermal growth factor	protein-coding
mm_170736.1	chr2	153196998	153197013	-	1	NA	intron (NM_133847, intron 12 of 17)	intron (NM_133847, intron 12 of 17)	28436	NM_198617	241732	Mm.277243	NM_198617	ENSMUSG00000074671	Tspyl3	AW212607|Gm36	TSPY-like 3	protein-coding
mm_173175.1	chrX	50181430	50181431	+	1	NA	Intergenic	L1Md_A|LINE|L1	-171195	NM_146390	258385	Mm.377470	NM_146390	ENSMUSG00000050504	Olfr1323	MOR216-1	olfactory receptor 1323	protein-coding
mm_78011.1	chr9	13466641	13466649	+	1	NA	Intergenic	Intergenic	35284	NR_028271	18689	Mm.41972	NM_008835	ENSMUSG00000031802	Phxr4	Sp5	per-hexamer repeat gene 4	ncRNA
mm_119514.1	chr14	47385726	47385732	+	1	NA	3' UTR (NM_010705, exon 6 of 6)	3' UTR (NM_010705, exon 6 of 6)	11869	NM_001145953	16854	Mm.248615	NM_010705	ENSMUSG00000050335	Lgals3	GBP|L-34|Mac-2|gal3	lectin, galactose binding, soluble 3	protein-coding
mm_68232.1	chr7	104465142	104465175	-	1	NA	promoter-TSS (NM_009099)	promoter-TSS (NM_009099)	35	NM_009099	20128	Mm.295578	NM_009099	ENSMUSG00000030921	Trim30a	Rpt-1|Rpt1|Trim30	tripartite motif-containing 30A	protein-coding
mm_90510.1	chr10	128042510	128042519	+	1	NA	exon (NM_001113199, exon 3 of 9)	exon (NM_001113199, exon 3 of 9)	7168	NM_001113199	17938	Mm.3746	NM_013608	ENSMUSG00000061315	Naca	AL022831|AL024382|Gm1878|mKIAA0363|skNAC	nascent polypeptide-associated complex alpha polypeptide	protein-coding
mm_166724.1	chr6	120473508	120473520	-	1	NA	intron (NM_008359, intron 3 of 12)	intron (NM_008359, intron 3 of 12)	10317	NM_008359	16172	Mm.4481	NM_008359	ENSMUSG00000002897	Il17ra	AW538159|Cdw217|Il17r|VDw217	interleukin 17 receptor A	protein-coding
mm_127777.1	chr15	3463853	3463858	-	1	NA	intron (NM_001048178, intron 1 of 8)	intron (NM_001048178, intron 1 of 8)	117987	NM_001286370	14600	Mm.3986	NM_010284	ENSMUSG00000055737	Ghr	GHBP|GHR/BP	growth hormone receptor	protein-coding
mm_125603.1	chr15	60141904	60141908	+	1	NA	Intergenic	Intergenic	-125288	NM_027668	71088	Mm.425950	NM_027668	ENSMUSG00000071749	4933412E24Rik	-	RIKEN cDNA 4933412E24 gene	protein-coding
mm_91012.1	chr10	15263218	15263223	-	1	NA	Intergenic	RLTR13D6|LTR|ERVK	502931	NM_008703	18101	Mm.487342	NM_008703	ENSMUSG00000019865	Nmbr	BB182387	neuromedin B receptor	protein-coding
mm_76146.1	chr8	82332477	82332505	-	1	NA	intron (NM_008357, intron 7 of 7)	intron (NM_008357, intron 7 of 7)	70095	NM_001254747	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_76582.1	chr8	89015651	89015664	-	1	NA	Intergenic	Intergenic	-9078	NR_106190	102465899		NR_106190	ENSMUSG00000099078	Mir8110	Gm27571|mmu-mir-8110	microRNA 8110	ncRNA
mm_169235.1	chr13	70422678	70422695	-	1	NA	Intergenic	Intergenic	-150555	NR_045934	73584	Mm.442491	NR_045934	ENSMUSG00000101051	1700100L14Rik	-	RIKEN cDNA 1700100L14 gene	ncRNA
mm_121281.1	chr14	103899480	103899488	+	1	NA	Intergenic	Intergenic	-55008	NM_001136061	13618	Mm.229532	NM_007904	ENSMUSG00000022122	Ednrb	ET-B|ET-BR|ETR-b|ETb|Sox10m1	endothelin receptor type B	protein-coding
mm_33975.1	chr4	137640325	137640327	+	1	NA	intron (NM_001347227, intron 22 of 26)	B1_Mur4|SINE|Alu	-24400	NM_029563	110351	Mm.180763	NM_029563	ENSMUSG00000041351	Rap1gap	1300019I11Rik|2310004O14Rik|AI427470|ARPP-90|Gap|Rap1GAP1|Rap1ga1	Rap1 GTPase-activating protein	protein-coding
mm_34459.1	chr4	148130884	148130895	+	1	NA	promoter-TSS (NM_027426)	promoter-TSS (NM_027426)	-31	NM_001305420	71890	Mm.9648	NM_027985	ENSMUSG00000029003	Mad2l2	2310033C13Rik|G1-453-4|MAD2B|REV7|repro22	MAD2 mitotic arrest deficient-like 2	protein-coding
mm_152974.1	chr19	29387016	29387025	-	1	NA	3' UTR (NM_021893, exon 7 of 7)	3' UTR (NM_021893, exon 7 of 7)	19582	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_134144.1	chr16	10784732	10784742	-	1	NA	exon (NM_001271603, exon 2 of 2)	exon (NM_001271603, exon 2 of 2)	799	NM_009896	12703	Mm.130	NM_009896	ENSMUSG00000038037	Socs1	Cish1|Cish7|JAB|SOCS-1|SSI-1	suppressor of cytokine signaling 1	protein-coding
mm_157933.1	chrX	81822767	81822815	-	1	NA	Intergenic	Intergenic	-364669	NM_173435	245492	Mm.109633	NM_173435	ENSMUSG00000060673	4930595M18Rik	-	RIKEN cDNA 4930595M18 gene	protein-coding
mm_34355.1	chr4	144613698	144613704	+	1	NA	promoter-TSS (NM_001081248)	promoter-TSS (NM_001081248)	-6	NM_001081248	435815	Mm.439623	NM_001081248	ENSMUSG00000070609	Gm13177	OTTMUSG00000010747	predicted gene 13177	protein-coding
mm_71611.1	chr8	56551146	56551161	+	1	NA	promoter-TSS (NM_015791)	promoter-TSS (NM_015791)	19	NM_015791	50753	Mm.251174	NM_015791	ENSMUSG00000038206	Fbxo8	Fbx8	F-box protein 8	protein-coding
mm_103849.1	chr11	83079885	83079897	-	1	NA	Intergenic	RLTR8|LTR|ERVK	14779	NM_011408	20556	Mm.278689	NM_011408	ENSMUSG00000072620	Slfn2	Shlf2	schlafen 2	protein-coding
mm_121828.1	chr14	20480107	20480114	-	1	NA	promoter-TSS (NM_001110794)	promoter-TSS (NM_001110794)	23	NM_001110794	11750	Mm.280231	NM_009674	ENSMUSG00000021814	Anxa7	AI265384|AI316497|Anx7|synexin	annexin A7	protein-coding
mm_101042.1	chr11	8622553	8622585	-	1	NA	intron (NM_001083587, intron 1 of 30)	intron (NM_001083587, intron 1 of 30)	41966	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_35575.1	chr4	41731225	41731263	-	1	NA	promoter-TSS (NM_001017362)	promoter-TSS (NM_001017362)	-102	NM_001252622	550619	Mm.425179	NM_001017362	ENSMUSG00000066224	Arid3c	OTTMUSG00000006683	AT rich interactive domain 3C (BRIGHT-like)	protein-coding
mm_157241.1	chrX	17572242	17572279	-	1	NA	promoter-TSS (NM_028058)	promoter-TSS (NM_028058)	65	NM_001313745	72018	Mm.41558	NM_028058	ENSMUSG00000025040	Fundc1	1500005J14Rik|1810033P05Rik	FUN14 domain containing 1	protein-coding
mm_88866.1	chr10	80940240	80940243	+	1	NA	Intergenic	Intergenic	10150	NM_008655	17873	Mm.1360	NM_008655	ENSMUSG00000015312	Gadd45b	AI323528|Myd118	growth arrest and DNA-damage-inducible 45 beta	protein-coding
mm_152306.1	chr19	9135557	9135602	-	1	NA	promoter-TSS (NM_025610)	promoter-TSS (NM_025610)	-13	NM_025610	66514	Mm.272847	NM_025610	ENSMUSG00000024654	Asrgl1	2410004D18Rik|ALP|ALP1|AU040643|AW060375	asparaginase like 1	protein-coding
mm_167590.1	chr9	46241026	46241042	+	1	NA	5' UTR (NM_007468, exon 1 of 3)	5' UTR (NM_007468, exon 1 of 3)	190	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_2713.1	chr1	128141941	128141968	+	1	NA	intron (NM_181750, intron 1 of 26)	intron (NM_181750, intron 1 of 26)	38648	NM_181750	226412	Mm.221041	NM_181750	ENSMUSG00000056211	R3hdm1	R3hdm	R3H domain containing 1	protein-coding
mm_71588.1	chr8	54954892	54954927	+	1	NA	5' UTR (NM_153581, exon 1 of 7)	5' UTR (NM_153581, exon 1 of 7)	181	NM_001253756	234267	Mm.241700	NM_153581	ENSMUSG00000031517	Gpm6a	Gpm6|M6A	glycoprotein m6a	protein-coding
mm_163953.1	chr14	54464031	54464050	-	1	NA	promoter-TSS (NM_022993)	promoter-TSS (NM_022993)	-107	NM_022993	65107	Mm.472719	NM_022993	ENSMUSG00000022175	Lrp10	Lrp9	low-density lipoprotein receptor-related protein 10	protein-coding
mm_133630.1	chr16	91647860	91647905	+	1	NA	promoter-TSS (NM_019973)	promoter-TSS (NM_019973)	58	NM_178880	20658	Mm.46401	NM_019973	ENSMUSG00000022961	Son	2900011L12Rik|AA409051|AU067731|C81487|mKIAA1019|nrebp	Son DNA binding protein	protein-coding
mm_165795.1	chr3	139274119	139274120	+	1	NA	intron (NM_198659, intron 6 of 13)	L1MA8|LINE|L1	68226	NM_198659	381476	Mm.188334	NM_198659	ENSMUSG00000047940	Stpg2	B930007M17Rik|Gm1017	sperm tail PG rich repeat containing 2	protein-coding
mm_81941.1	chr9	120470342	120470354	+	1	NA	intron (NM_144557, intron 16 of 16)	(CA)n|Simple_repeat|Simple_repeat	-22258	NM_026892	68969	Mm.28753	NM_026892	ENSMUSG00000006941	Eif1b	1500010M16Rik|3110001N14Rik|Gc20	eukaryotic translation initiation factor 1B	protein-coding
mm_94902.1	chr11	29194212	29194217	+	1	NA	intron (NM_134034, intron 4 of 15)	intron (NM_134034, intron 4 of 15)	21307	NM_134034	104570	Mm.276386	NM_134034	ENSMUSG00000020463	Smek2	AW011752|AW557776|Ppp4r3b|mKIAA1387	SMEK homolog 2, suppressor of mek1 (Dictyostelium)	protein-coding
mm_18279.1	chr2	52424812	52424822	-	1	NA	promoter-TSS (NM_182994)	promoter-TSS (NM_182994)	57	NM_182994	75423	Mm.314378	NM_182994	ENSMUSG00000036093	Arl5a	2410015N24Rik|2810410P22Rik|AA408731|AW610751|Arl5|T25534	ADP-ribosylation factor-like 5A	protein-coding
mm_16812.1	chr2	11259516	11259521	-	1	NA	intron (NM_008859, intron 11 of 17)	ORR1A4|LTR|ERVL-MaLR	-79971	NR_040369	100503147	Mm.91961	NR_040369	ENSMUSG00000086006	Gm13293	OTTMUSG00000011311	predicted gene 13293	ncRNA
mm_103974.1	chr11	84819391	84819415	-	1	NA	5' UTR (NM_145433, exon 1 of 5)	5' UTR (NM_145433, exon 1 of 5)	112	NM_145433	217038	Mm.280825	NM_145433	ENSMUSG00000018405	Mrm1	A530065E19Rik|ENSMUSG00000054212	mitochondrial rRNA methyltransferase 1	protein-coding
mm_116231.1	chr13	33159738	33159755	-	1	NA	promoter-TSS (NM_001164524)	promoter-TSS (NM_001164524)	8	NM_001164524	20707	Mm.219429	NM_011453	ENSMUSG00000021404	Serpinb9c	3830421J05Rik|Nk9|Spi11	serine (or cysteine) peptidase inhibitor, clade B, member 9c	protein-coding
mm_50633.1	chr6	51282890	51282892	+	1	NA	Intergenic	Intergenic	-12981	NR_029719	387166		NR_029719	ENSMUSG00000065505	Mir148a	Mirn148|Mirn148a|mir-148a	microRNA 148a	ncRNA
mm_141600.1	chr17	32635140	32635157	-	1	NA	exon (NM_001100187, exon 13 of 13)	exon (NM_001100187, exon 13 of 13)	13829	NM_001100187	677156	Mm.484117	NM_001100187	ENSMUSG00000062464	Cyp4f37	Gm9705	cytochrome P450, family 4, subfamily f, polypeptide 37	protein-coding
mm_114605.1	chr13	75789851	75789853	+	1	NA	Intergenic	Intergenic	-50034	NM_053108	93692	Mm.25844	NM_053108	ENSMUSG00000021591	Glrx	C86710|D13Wsu156e|Glrx1|Grx1|TTase	glutaredoxin	protein-coding
mm_56156.1	chr6	87850973	87850983	-	1	NA	5' UTR (NM_013493, exon 1 of 5)	5' UTR (NM_013493, exon 1 of 5)	128	NM_001109746	12785	Mm.290251	NM_013493	ENSMUSG00000030057	Cnbp	AA408710|Cnbp1|Znf9	cellular nucleic acid binding protein	protein-coding
mm_56493.1	chr6	99204463	99204470	-	1	NA	intron (NM_001347345, intron 4 of 19)	intron (NM_001347345, intron 4 of 19)	62049	NM_001197321	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_2932.1	chr1	132298607	132298631	+	1	NA	promoter-TSS (NM_144810)	promoter-TSS (NM_144810)	-7	NM_144810	213417	Mm.39723	NM_144810	ENSMUSG00000042115	Klhdc8a	A630065K24Rik	kelch domain containing 8A	protein-coding
mm_166879.1	chr7	25413027	25413032	-	1	NA	promoter-TSS (NM_153576)	promoter-TSS (NM_153576)	-143	NM_153576	232983	Mm.10545	NM_153576	ENSMUSG00000060188	Cxcl17	VCC-1|Vcc1	chemokine (C-X-C motif) ligand 17	protein-coding
mm_144160.1	chr18	5625969	5625972	+	1	NA	intron (NM_011546, intron 1 of 7)	B2_Mm1t|SINE|B2	-33533	NR_033552	791318	Mm.84339	NR_033552	ENSMUSG00000063087	Gm10125	ENSMUSG00000063087|Zeb1os	predicted gene 10125	ncRNA
mm_134802.1	chr16	24382344	24382352	-	1	NA	Intergenic	RMER4B|LTR|ERVK	-11002	NM_178665	210126	Mm.209385	NM_178665	ENSMUSG00000033306	Lpp	9430020K16Rik|AA959454|AU024130|B130055L10Rik|C79715|D630048H16	LIM domain containing preferred translocation partner in lipoma	protein-coding
mm_98808.1	chr11	97066839	97066858	+	1	NA	intron (NM_001310509, intron 18 of 22)	intron (NM_001310509, intron 18 of 22)	3080	NR_106181	102465893		NR_106181	ENSMUSG00000098769	Mir8103	Gm27841|mmu-mir-8103	microRNA 8103	ncRNA
mm_164041.1	chr14	88437780	88437781	+	1	NA	Intergenic	(TATATG)n|Simple_repeat|Simple_repeat	33616	NM_178685	219257	Mm.128861	NM_178685	ENSMUSG00000050505	Pcdh20	C630015B17Rik|Pcdh13	protocadherin 20	protein-coding
mm_146971.1	chr18	33463764	33463802	-	1	NA	promoter-TSS (NM_001267717)	promoter-TSS (NM_001267717)	-84	NM_001109989	27528	Mm.407415	NM_053078	ENSMUSG00000042834	Nrep	AI325076|D0H4S114|Harp|P311|PTZ17|SEZ17	neuronal regeneration related protein	protein-coding
mm_163301.1	chr11	120660601	120660612	-	1	NA	intron (NM_175263, intron 1 of 11)	CpG-2953	231	NM_175263	77583	Mm.32839	NM_175263	ENSMUSG00000042988	Notum	5730593N15Rik	notum pectinacetylesterase homolog (Drosophila)	protein-coding
mm_1243.1	chr1	62798098	62798151	+	1	NA	intron (NM_010939, intron 15 of 15)	intron (NM_010939, intron 15 of 15)	-3392	NR_040601	74992	Mm.401979	NR_040601		4930487H11Rik	-	RIKEN cDNA 4930487H11 gene	ncRNA
mm_93894.1	chr10	125388850	125388855	-	1	NA	Intergenic	Intergenic	-60317	NM_011391	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|Mct2	solute carrier family 16 (monocarboxylic acid transporters), member 7	protein-coding
mm_165338.1	chr2	117962172	117962205	+	1	NA	intron (NR_126479, intron 8 of 9)	intron (NR_126479, intron 8 of 9)	140260	NR_040631	73938	Mm.399107	NR_040631	ENSMUSG00000086221	4930412B13Rik	-	RIKEN cDNA 4930412B13 gene	ncRNA
mm_156158.1	chrX	129979657	129979660	+	1	NA	intron (NM_172493, intron 17 of 26)	intron (NM_172493, intron 17 of 26)	229916	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diaph2	Dia3|Diap2|Drf2|E430022I22Rik	diaphanous related formin 2	protein-coding
mm_72108.1	chr8	71611231	71611249	+	1	NA	exon (NM_146211, exon 1 of 12)	exon (NM_146211, exon 1 of 12)	216	NM_146211	234407	Mm.240885	NM_146211	ENSMUSG00000034807	Colgalt1	2810024B22Rik|Glt25d1	collagen beta(1-O)galactosyltransferase 1	protein-coding
mm_168761.1	chr12	119772876	119772882	+	1	NA	Intergenic	RLTR10A|LTR|ERVK	-173083	NM_001294154	217951	Mm.387395	NM_001160385	ENSMUSG00000048004	Tmem196	Gm528	transmembrane protein 196	protein-coding
mm_70859.1	chr8	24419600	24419600	+	1	NA	Intergenic	Intergenic	19346	NM_026931	69068	Mm.25775	NM_026931	ENSMUSG00000056313	1810011O10Rik	1110065B09Rik|AW121743|AW321058	RIKEN cDNA 1810011O10 gene	protein-coding
mm_22246.1	chr2	174614346	174614370	-	1	NA	Intergenic	Intergenic	-29176	NM_001099328	100043757	Mm.48711	NM_001099328	ENSMUSG00000050600	Zfp831	ENSMUSG00000050600|OTTMUSG00000017459	zinc finger protein 831	protein-coding
mm_76614.1	chr8	91135688	91135699	-	1	NA	promoter-TSS (NM_010241)	promoter-TSS (NM_010241)	-199	NM_010241	14339	Mm.324588	NM_010241	ENSMUSG00000031667	Aktip	AL023020|Fif|Ft|Ft1|Fts	thymoma viral proto-oncogene 1 interacting protein	protein-coding
mm_166165.1	chr5	20779296	20779342	+	1	NA	intron (NM_172992, intron 10 of 17)	intron (NM_172992, intron 10 of 17)	102805	NM_172992	68770	Mm.86410	NM_172992	ENSMUSG00000039987	Phtf2	1110054G21Rik|9530062N20Rik|AI447096|C77923	putative homeodomain transcription factor 2	protein-coding
mm_127732.1	chr15	103282048	103282051	+	1	NA	intron (NM_019817, intron 1 of 8)	ID_B1|SINE|B4	-3076	NR_029766	724064		NR_029766	ENSMUSG00000065560	Mir148b	Mirn148b|mir-148b	microRNA 148b	ncRNA
mm_111855.1	chr12	107939233	107939249	-	1	NA	intron (NM_001286343, intron 1 of 1)	intron (NM_001286343, intron 1 of 1)	64173	NM_001079883	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_99380.1	chr11	102041521	102041531	+	1	NA	promoter-TSS (NM_001160713)	promoter-TSS (NM_001160713)	15	NM_001160713	52685	Mm.266885	NM_027987	ENSMUSG00000017309	Cd300lg	2310016B05Rik|Clm9|D11Ertd736e	CD300 molecule like family member G	protein-coding
mm_72495.1	chr8	83738405	83738421	+	1	NA	intron (NM_001163031, intron 1 of 17)	intron (NM_001163031, intron 1 of 17)	2898	NM_001163029	26364	Mm.334648	NM_011925	ENSMUSG00000002885	Adgre5	AA409984|Cd97|TM7LN1	adhesion G protein-coupled receptor E5	protein-coding
mm_18000.1	chr2	38212442	38212454	-	1	NA	intron (NM_146122, intron 2 of 21)	intron (NM_146122, intron 2 of 21)	74936	NM_146122	227801	Mm.314245	NM_146122	ENSMUSG00000035392	Dennd1a	6030446I19Rik|connecdenn	DENN/MADD domain containing 1A	protein-coding
mm_34810.1	chr4	154935946	154935992	+	1	NA	Intergenic	Intergenic	-7892	NM_178931	230979	Mm.215147	NM_178931	ENSMUSG00000042333	Tnfrsf14	Atar|HveA|Hvem|Tnfrs14	tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)	protein-coding
mm_55780.1	chr6	81910481	81910515	-	1	NA	intron (NR_046040, intron 1 of 5)	intron (NR_046040, intron 1 of 5)	302	NR_046040	74220	Mm.490521	NR_046040	ENSMUSG00000101404	1700009C05Rik	-	RIKEN cDNA 1700009C05 gene	ncRNA
mm_4320.1	chr1	171851902	171851912	+	1	NA	exon (NM_013489, exon 3 of 9)	exon (NM_013489, exon 3 of 9)	12210	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_68914.1	chr7	126459743	126459749	-	1	NA	intron (NM_007504, intron 4 of 22)	intron (NM_007504, intron 4 of 22)	3327	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_80693.1	chr9	91403466	91403474	+	1	NA	Intergenic	Intergenic	34498	NM_009576	22774	Mm.8062	NM_009576	ENSMUSG00000036972	Zic4	-	zinc finger protein of the cerebellum 4	protein-coding
mm_137423.1	chr17	26204318	26204330	+	1	NA	intron (NM_001081069, intron 4 of 16)	intron (NM_001081069, intron 4 of 16)	1362	NM_001081069	50782	Mm.109840	NM_001081069	ENSMUSG00000024186	Rgs11	C78048	regulator of G-protein signaling 11	protein-coding
mm_113574.1	chr13	40545564	40545564	+	1	NA	Intergenic	MTE2a|LTR|ERVL-MaLR	-182244	NR_125899	102633805		NR_125899	ENSMUSG00000097752	Gm26688	Tfap2a-as1	predicted gene, 26688	ncRNA
mm_150876.1	chr19	45076088	45076090	+	1	NA	promoter-TSS (NM_178929)	promoter-TSS (NM_178929)	-50	NM_178929	107250	Mm.24417	NM_178929	ENSMUSG00000025213	Kazald1	AI842353|Bono1|IGFBP-rP10	Kazal-type serine peptidase inhibitor domain 1	protein-coding
mm_161624.1	chr16	59202226	59202226	-	1	NA	exon (NM_001011808, exon 1 of 1)	exon (NM_001011808, exon 1 of 1)	198	NM_001011808	258036	Mm.390851	NM_001011808	ENSMUSG00000052537	Olfr198	MOR182-8	olfactory receptor 198	protein-coding
mm_47164.1	chr5	120735920	120735924	-	1	NA	intron (NM_001347448, intron 8 of 11)	intron (NM_001347448, intron 8 of 11)	13926	NM_145227	246728	Mm.260926	NM_145227	ENSMUSG00000032690	Oas2	Oasl11	2'-5' oligoadenylate synthetase 2	protein-coding
mm_45246.1	chr5	59886222	59886224	-	1	NA	Intergenic	Lx8b|LINE|L1	99779	NR_040683	71057	Mm.50817	NR_040682	ENSMUSG00000106013	4933402J10Rik	-	RIKEN cDNA 4933402J10 gene	ncRNA
mm_27426.1	chr3	51521336	51521342	-	1	NA	exon (NM_080793, exon 8 of 8)	exon (NM_080793, exon 8 of 8)	37373	NM_016858	19338	Mm.1664	NM_016858	ENSMUSG00000027739	Rab33b	-	RAB33B, member RAS oncogene family	protein-coding
mm_170311.1	chr18	35554270	35554272	+	1	NA	promoter-TSS (NR_035472)	promoter-TSS (NR_035472)	-296	NR_035472	100316700		NR_035472	ENSMUSG00000105743	Mir1949	mir-1949|mmu-mir-1949	microRNA 1949	ncRNA
mm_37816.1	chr4	131807940	131807943	-	1	NA	intron (NM_001083119, intron 8 of 30)	B4A|SINE|B4	30337	NM_011214	19273	Mm.4860	NM_011214	ENSMUSG00000028909	Ptpru	Ftp-1|PCP-2|PTP|PTP-lambda|PTPlambda|Pcp2|Ptpf|Ptprl|R-PTP-U|R-PTP-psi|RPTPlambda	protein tyrosine phosphatase, receptor type, U	protein-coding
mm_113073.1	chr13	23779283	23779294	+	1	NA	Intergenic	Intergenic	-3253	NM_001029935	214158	Mm.314151	NM_001029935	ENSMUSG00000064140	Trim38	Gm23	tripartite motif-containing 38	protein-coding
mm_17729.1	chr2	32451397	32451470	-	1	NA	promoter-TSS (NM_001164357)	promoter-TSS (NM_001164357)	37	NM_001164357	227731	Mm.37395	NM_146118	ENSMUSG00000026819	Slc25a25	1110030N17Rik|MCSC|mKIAA1896	solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 25	protein-coding
mm_72414.1	chr8	81856325	81856376	+	1	NA	intron (NM_001297591, intron 7 of 24)	intron (NM_001297591, intron 7 of 24)	513788	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_23179.1	chr3	40800058	40800068	+	1	NA	non-coding (NR_045576, exon 1 of 16)	non-coding (NR_045576, exon 1 of 16)	112	NR_045576	20873	Mm.3794	NM_011495	ENSMUSG00000025758	Plk4	1700028H20|AI385771|Sak|Stk18	polo-like kinase 4	protein-coding
mm_23037.1	chr3	34757444	34757456	+	1	NA	Intergenic	PB1D7|SINE|Alu	-14625	NR_110488	102638436	Mm.261793	NR_110488	ENSMUSG00000106519	Gm38509	Peril	predicted gene, 38509	ncRNA
mm_36387.1	chr4	77168749	77168783	-	1	NA	intron (NM_011211, intron 7 of 39)	RLTR16C_MM|LTR|ERVK	1043129	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding
mm_63497.1	chr7	127784030	127784050	+	1	NA	exon (NM_178029, exon 6 of 19)	exon (NM_178029, exon 6 of 19)	6651	NM_178029	233904	Mm.435494	NM_010940	ENSMUSG00000042308	Setd1a	BC010250|KMT2F|Nsccn1|mKIAA0339|mNSC1	SET domain containing 1A	protein-coding
mm_57668.1	chr6	128488020	128488031	-	1	NA	exon (NM_007376, exon 30 of 36)	exon (NM_007376, exon 30 of 36)	38695	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_42522.1	chr5	115565257	115565281	+	1	NA	promoter-TSS (NM_172719)	promoter-TSS (NM_172719)	6	NM_172719	231659	Mm.153014	NM_172719	ENSMUSG00000041638	Gcn1l1	4932409G22|AL022764|G431004K08Rik|GCN1L|Gcn1|mKIAA0219	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	protein-coding
mm_49494.1	chr6	29735612	29735629	+	1	NA	5' UTR (NM_176996, exon 1 of 12)	5' UTR (NM_176996, exon 1 of 12)	123	NM_176996	319757	Mm.29279	NM_176996	ENSMUSG00000001761	Smo	E130215L21Rik|Smoh|bnb|smoothened	smoothened, frizzled class receptor	protein-coding
mm_22520.1	chr3	7635801	7635804	+	1	NA	Intergenic	L1_Mus2|LINE|L1	-22042	NM_001313888	16196	Mm.3825	NM_008371	ENSMUSG00000040329	Il7	A630026I06Rik|Il-7|hlb368	interleukin 7	protein-coding
mm_116045.1	chr13	27249466	27249487	-	1	NA	exon (NM_008865, exon 5 of 5)	exon (NM_008865, exon 5 of 5)	7046	NM_008865	18776	Mm.37203	NM_008865	ENSMUSG00000038891	Prl3b1	Csh2|Ghd8|PL|Pl-2|Pl2|mPL-II|mplII	prolactin family 3, subfamily b, member 1	protein-coding
mm_54368.1	chr6	31126704	31126730	-	1	NA	intron (NR_110471, intron 3 of 3)	intron (NR_110471, intron 3 of 3)	-63624	NR_029532	387223		NR_029532	ENSMUSG00000065604	Mir29b-1	Mirn29b|Mirn29b-1|mir-29b-1	microRNA 29b-1	ncRNA
mm_165850.1	chr4	8939229	8939239	+	1	NA	Intergenic	Intergenic	248828	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_64473.1	chr7	143026617	143026617	+	1	NA	intron (NR_110354, intron 4 of 4)	MTEa|LTR|ERVL-MaLR	20958	NM_001128081	27027	Mm.28172	NM_020286	ENSMUSG00000000244	Tspan32	AW208513|Art-1|BB235973|D7Wsu37e|Phemx|Tssc6	tetraspanin 32	protein-coding
mm_50177.1	chr6	41572178	41572185	+	1	NA	Intergenic	Intergenic	-33301	NM_001146351	13848	Mm.271976	NM_007680	ENSMUSG00000029869	Ephb6	Cekl|Mep	Eph receptor B6	protein-coding
mm_146019.1	chr18	69500902	69500972	+	1	NA	intron (NM_013685, intron 5 of 19)	intron (NM_013685, intron 5 of 19)	155216	NM_001083967	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding
mm_91585.1	chr10	40234894	40234896	-	1	NA	exon (NM_023323, exon 6 of 10)	exon (NM_023323, exon 6 of 10)	12084	NM_001042556	67239	Mm.11480	NM_023323	ENSMUSG00000038510	Rpf2	2810470K21Rik|AU040229|AU043242|Bxdc1	ribosome production factor 2 homolog	protein-coding
mm_117776.1	chr13	96670816	96670829	-	1	NA	5' UTR (NM_008255, exon 1 of 20)	5' UTR (NM_008255, exon 1 of 20)	114	NM_008255	15357	Mm.316652	NM_008255	ENSMUSG00000021670	Hmgcr	HMG-CoAR|Red	3-hydroxy-3-methylglutaryl-Coenzyme A reductase	protein-coding
mm_97100.1	chr11	73326577	73326621	+	1	NA	Intergenic	Intergenic	-1962	NM_023113	11484	Mm.293574	NM_023113	ENSMUSG00000020774	Aspa	Acy-2|Acy2|nur7	aspartoacylase	protein-coding
mm_169628.1	chr15	44017126	44017126	-	1	NA	Intergenic	Intergenic	-147097	NM_175502	239408	Mm.41219	NM_175502	ENSMUSG00000054409	Tmem74	AA549547|B230382K22Rik	transmembrane protein 74	protein-coding
mm_102790.1	chr11	68451364	68451369	-	1	NA	intron (NM_177320, intron 1 of 18)	intron (NM_177320, intron 1 of 18)	19241	NM_177320	320207	Mm.244960	NM_177320	ENSMUSG00000020901	Pik3r5	AV230647|F730038I15Rik	phosphoinositide-3-kinase, regulatory subunit 5, p101	protein-coding
mm_46515.1	chr5	105288075	105288093	-	1	NA	intron (NM_194336, intron 3 of 10)	L1MA6|LINE|L1	5615	NM_194336	100702	Mm.491210	NM_194336	ENSMUSG00000079362	Gbp6	AI595338|Mpa2l	guanylate binding protein 6	protein-coding
mm_6056.1	chr1	60180358	60180368	-	1	NA	promoter-TSS (NM_173444)	promoter-TSS (NM_173444)	-236	NM_173444	269198	Mm.205224	NM_173444	ENSMUSG00000073664	Nbeal1	2310076G13Rik|A530050O19Rik|A530083I02Rik|AI662228|ALS2CR17	neurobeachin like 1	protein-coding
mm_17858.1	chr2	34799768	34799826	-	1	NA	5' UTR (NM_145522, exon 1 of 8)	5' UTR (NM_145522, exon 1 of 8)	115	NM_145522	227746	Mm.158705	NM_145522	ENSMUSG00000070953	Rabepk	8430412M01Rik|9530020D24Rik|AV073337|C87311|Rab9p40	Rab9 effector protein with kelch motifs	protein-coding
mm_93891.1	chr10	125328642	125328655	-	1	NA	promoter-TSS (NM_011391)	promoter-TSS (NM_011391)	-113	NM_011391	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|Mct2	solute carrier family 16 (monocarboxylic acid transporters), member 7	protein-coding
mm_127160.1	chr15	98634731	98634735	+	1	NA	promoter-TSS (NM_007581)	promoter-TSS (NM_007581)	-34	NM_007581	12297	Mm.3544	NM_007581	ENSMUSG00000003352	Cacnb3	Beta3|CAB3|Ca(v)beta3|Cchb3	calcium channel, voltage-dependent, beta 3 subunit	protein-coding
mm_46192.1	chr5	98016903	98016916	-	1	NA	intron (NM_133738, intron 3 of 16)	intron (NM_133738, intron 3 of 16)	14053	NM_133738	71914	Mm.24842	NM_133738	ENSMUSG00000029338	Antxr2	2310046B19Rik|AW561899|CMG-2|CMG2|cI-35	anthrax toxin receptor 2	protein-coding
mm_146106.1	chr18	74216198	74216237	+	1	NA	promoter-TSS (NM_028868)	promoter-TSS (NM_028868)	5	NM_028868	74322	Mm.17537	NM_028868	ENSMUSG00000024560	Cxxc1	2410002I16Rik|5830420C16Rik|AI426635|Cfp1|Cgbp|PHF18	CXXC finger 1 (PHD domain)	protein-coding
mm_130658.1	chr15	100641460	100641482	-	1	NA	3' UTR (NM_001270537, exon 11 of 11)	3' UTR (NM_001270537, exon 11 of 11)	-4531	NM_001033872	207818	Mm.26282	NM_174992	ENSMUSG00000053559	Smagp	-	small cell adhesion glycoprotein	protein-coding
mm_57223.1	chr6	123263348	123263352	-	1	NA	intron (NM_001163161, intron 1 of 5)	intron (NM_001163161, intron 1 of 5)	1243	NM_010819	17474	Mm.441101	NM_010819	ENSMUSG00000030144	Clec4d	Clecsf8|Mpcl|mcl	C-type lectin domain family 4, member d	protein-coding
mm_55699.1	chr6	72899815	72899843	-	1	NA	promoter-TSS (NM_001347231)	promoter-TSS (NM_001347231)	150	NM_019715	74287	Mm.29194	NM_019715	ENSMUSG00000055239	Kcmf1	1700094M07Rik|Debt91|Pmcf	potassium channel modulatory factor 1	protein-coding
mm_133977.1	chr16	4523057	4523075	-	1	NA	promoter-TSS (NM_175347)	promoter-TSS (NM_175347)	9	NM_001347162	106393	Mm.35811	NM_175347	ENSMUSG00000022519	Srl	9830004M20Rik|AW108387|sar	sarcalumenin	protein-coding
mm_121471.1	chr14	120911214	120911253	+	1	NA	promoter-TSS (NM_023579)	promoter-TSS (NM_023579)	39	NM_023579	70572	Mm.221452	NM_023579	ENSMUSG00000030662	Ipo5	1110011C18Rik|5730478E03Rik|AA409333|C76941|IMB3|Kpnb3|Ranbp5	importin 5	protein-coding
mm_23109.1	chr3	37481354	37481372	+	1	NA	intron (NM_001310473, intron 14 of 16)	LSU-rRNA_Hsa|rRNA|rRNA	61413	NM_021343	57815	Mm.172679	NM_021343	ENSMUSG00000027722	Spata5	2510048F20Rik|C78064|Spaf	spermatogenesis associated 5	protein-coding
mm_163345.1	chr12	16672276	16672303	+	1	NA	3' UTR (NM_015764, exon 35 of 35)	3' UTR (NM_015764, exon 35 of 35)	18819	NM_008747	18217	Mm.281715	NM_008747	ENSMUSG00000020591	Ntsr2	NT2R|NTRL	neurotensin receptor 2	protein-coding
mm_169949.1	chr16	74206247	74206266	+	1	NA	intron (NM_175549, intron 2 of 27)	L1Md_T|LINE|L1	135811	NR_030464	751561		NR_030464	ENSMUSG00000104758	Mir691	Mirn691|mir-691|mmu-mir-691	microRNA 691	ncRNA
mm_45673.1	chr5	77216247	77216251	-	1	NA	Intergenic	Lx8|LINE|L1	-4778	NM_001289768	69982	Mm.46106	NM_183284	ENSMUSG00000053030	Spink2	1700007F22Rik|AV038945|HUSI-II	serine peptidase inhibitor, Kazal type 2	protein-coding
mm_72477.1	chr8	83608290	83608308	+	1	NA	promoter-TSS (NM_001308227)	promoter-TSS (NM_001308227)	124	NM_018808	81489	Mm.282092	NM_018808	ENSMUSG00000005483	Dnajb1	0610007I11Rik|DjB1|HSPF1|Hdj1|Hsp40	DnaJ heat shock protein family (Hsp40) member B1	protein-coding
mm_120596.1	chr14	70077207	70077222	+	1	NA	promoter-TSS (NM_001289927)	promoter-TSS (NM_001289927)	-231	NM_018781	13655	Mm.103737	NM_018781	ENSMUSG00000033730	Egr3	Pilot	early growth response 3	protein-coding
mm_82100.1	chr9	123061739	123061748	+	1	NA	exon (NM_177911, exon 11 of 14)	exon (NM_177911, exon 11 of 14)	27002	NM_177911	331046	Mm.195309	NM_177911	ENSMUSG00000025787	Tgm4	9530008N10Rik|Eapa1|TGP	transglutaminase 4 (prostate)	protein-coding
mm_126559.1	chr15	82149125	82149129	+	1	NA	intron (NM_033218, intron 1 of 18)	intron (NM_033218, intron 1 of 18)	1858	NM_033218	20788	Mm.9002	NM_033218	ENSMUSG00000022463	Srebf2	AI608257|SREBP-2|SREBP2|SREBP2gc|bHLHd2|lop13|nuc	sterol regulatory element binding factor 2	protein-coding
mm_50622.1	chr6	50133298	50133321	+	1	NA	intron (NM_019939, intron 1 of 12)	intron (NM_019939, intron 1 of 12)	23068	NM_001164733	56524	Mm.41288	NM_008016	ENSMUSG00000038388	Mpp6	P55t|Pals2	membrane protein, palmitoylated 6 (MAGUK p55 subfamily member 6)	protein-coding
mm_99360.1	chr11	101640047	101640051	+	1	NA	Intergenic	RMER15|LTR|ERVL	12100	NM_025654	66599	Mm.41449	NM_025654	ENSMUSG00000010362	Rdm1	2410008M22Rik|AW212028|Rad52b	RAD52 motif 1	protein-coding
mm_141329.1	chr17	28484870	28484872	-	1	NA	intron (NM_010220, intron 1 of 10)	A-rich|Low_complexity|Low_complexity	1278	NM_010220	14229	Mm.276405	NM_010220	ENSMUSG00000024222	Fkbp5	D17Ertd592e|Dit1|FKBP-5|FKBP51	FK506 binding protein 5	protein-coding
mm_130732.1	chr15	101248142	101248144	-	1	NA	Intergenic	Intergenic	-18703	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_30396.1	chr3	152248430	152248435	-	1	NA	intron (NM_199465, intron 5 of 12)	intron (NM_199465, intron 5 of 12)	17888	NM_199465	68810	Mm.200188	NM_199465	ENSMUSG00000039103	Nexn	1110046H09Rik|AA553326|NELIN	nexilin	protein-coding
mm_169291.1	chr13	98926310	98926310	-	1	NA	promoter-TSS (NM_178716)	promoter-TSS (NM_178716)	74	NM_178716	238799	Mm.173286	NM_178716	ENSMUSG00000009470	Tnpo1	AU021749|D13Ertd688e|IPO2|Kpnb2|MIP|MIP1|TRN	transportin 1	protein-coding
mm_55383.1	chr6	58965500	58965523	-	1	NA	intron (NM_153574, intron 7 of 17)	intron (NM_153574, intron 7 of 17)	-58385	NM_021432	58243	Mm.389747	NM_021432	ENSMUSG00000055430	Nap1l5	1110020M21Rik	nucleosome assembly protein 1-like 5	protein-coding
mm_44234.1	chr5	5265697	5265697	-	1	NA	5' UTR (NM_001310448, exon 1 of 14)	5' UTR (NM_001310448, exon 1 of 14)	371	NM_001310448	18647	Mm.389061	NM_011074	ENSMUSG00000028926	Cdk14	Pftk1|mKIAA0834	cyclin-dependent kinase 14	protein-coding
mm_64825.1	chr7	11988545	11988555	-	1	NA	Intergenic	Intergenic	-52749	NM_001166731	628946	Mm.484974	NM_001166731	ENSMUSG00000095864	Vmn1r77	Gm6935	vomeronasal 1 receptor 77	protein-coding
mm_133462.1	chr16	89157951	89157952	+	1	NA	Intergenic	Intergenic	-47910	NM_001163615	622935	Mm.459837	NM_001163615	ENSMUSG00000091039	Krtap20-2	1190004K03Rik|EG622935|Gm6371	keratin associated protein 20-2	protein-coding
mm_72730.1	chr8	85080940	85080977	+	1	NA	promoter-TSS (NM_026399)	promoter-TSS (NM_026399)	-5	NM_001001493	414077	Mm.35790	NM_001001493	ENSMUSG00000059355	Wdr83os	-	WD repeat domain 83 opposite strand	protein-coding
mm_170099.1	chr17	39843239	39843239	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	242	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_35983.1	chr4	55134832	55134837	-	1	NA	Intergenic	Intergenic	186889	NM_172867	242466	Mm.102904	NM_172867	ENSMUSG00000060206	Zfp462	6030417H05|9430078C22Rik|Gt4-2|Zfpip	zinc finger protein 462	protein-coding
mm_87935.1	chr10	62678476	62678478	+	1	NA	intron (NM_001033260, intron 1 of 3)	B1F1|SINE|Alu	-4031	NR_106074	102465987		NR_106074	ENSMUSG00000105329	Mir7215	mmu-mir-7215	microRNA 7215	ncRNA
mm_55491.1	chr6	69544941	69544945	-	1	NA	Intergenic	Intergenic	-217769	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_21756.1	chr2	164839722	164839752	-	1	NA	exon (NM_011125, exon 16 of 16)	exon (NM_011125, exon 16 of 16)	5964	NM_008906	19025	Mm.359633	NM_008906	ENSMUSG00000017760	Ctsa	AU019505|PPCA|Ppgb	cathepsin A	protein-coding
mm_36400.1	chr4	77823565	77823567	-	1	NA	intron (NM_011211, intron 2 of 39)	intron (NM_011211, intron 2 of 39)	388329	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding
mm_56391.1	chr6	94826882	94826889	-	1	NA	Intergenic	Intergenic	44029	NR_035483	100316707		NR_035483	ENSMUSG00000088552	Mir1957a	Mir1957|mmu-mir-1957|mmu-mir-1957a	microRNA 1957a	ncRNA
mm_76233.1	chr8	83574678	83574707	-	1	NA	intron (NM_134118, intron 1 of 12)	intron (NM_134118, intron 1 of 12)	7934	NM_025843	66916	Mm.29683	NM_025843	ENSMUSG00000033938	Ndufb7	1110002H15Rik	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 7	protein-coding
mm_130736.1	chr15	101253698	101253705	-	1	NA	Intergenic	Intergenic	-13145	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_29680.1	chr3	122984379	122984396	-	1	NA	promoter-TSS (NM_133857)	promoter-TSS (NM_133857)	60	NM_133857	99526	Mm.491248	NM_133857	ENSMUSG00000039701	Usp53	AA939927|Phxr3|Sp6|mKIAA1350|mbo	ubiquitin specific peptidase 53	protein-coding
mm_100665.1	chr11	3331181	3331201	-	1	NA	intron (NM_178149, intron 1 of 5)	intron (NM_178149, intron 1 of 5)	460	NM_178149	216505	Mm.390323	NM_178149	ENSMUSG00000034614	Pik3ip1	1500004A08Rik|5830455E04Rik|Crkd|Hgfl	phosphoinositide-3-kinase interacting protein 1	protein-coding
mm_79435.1	chr9	56052902	56052904	+	1	NA	intron (NM_011992, intron 3 of 6)	intron (NM_011992, intron 3 of 6)	11058	NM_011992	26611	Mm.1782	NM_011992	ENSMUSG00000032320	Rcn2	AA408742|Tcbp49	reticulocalbin 2	protein-coding
mm_165972.1	chr4	100861412	100861418	+	1	NA	intron (NM_198037, intron 1 of 26)	intron (NM_198037, intron 1 of 26)	84736	NM_198037	320508	Mm.151962	NM_198037	ENSMUSG00000028532	Cachd1	1190007F10Rik|AI852726|B430218L07Rik|Vwcd1|mKIAA1573	cache domain containing 1	protein-coding
mm_10965.1	chr2	25702403	25702412	+	1	NA	intron (NM_153558, intron 5 of 6)	intron (NM_153558, intron 5 of 6)	2333	NM_153558	227627	Mm.44630	NM_153558	ENSMUSG00000062061	Obp2a	BC027556|Lcn13	odorant binding protein 2A	protein-coding
mm_70723.1	chr8	17590517	17590544	+	1	NA	Intergenic	L2a|LINE|L2	-55145	NM_053171	94109	Mm.436988	NM_053171	ENSMUSG00000060924	Csmd1	B930082H09|mKIAA1890	CUB and Sushi multiple domains 1	protein-coding
mm_16662.1	chr2	6721028	6721074	-	1	NA	intron (NM_001347094, intron 2 of 12)	intron (NM_001347094, intron 2 of 12)	611	NM_001310447	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_65513.1	chr7	25754802	25754810	-	1	NA	promoter-TSS (NM_178089)	promoter-TSS (NM_178089)	-86	NM_144922	232989	Mm.254223	NM_144922	ENSMUSG00000040725	Hnrnpul1	E130317O14Rik|E1B-AP5|E1BAP5|Hnrnpul|Hnrpul1	heterogeneous nuclear ribonucleoprotein U-like 1	protein-coding
mm_1184.1	chr1	61880330	61880333	+	1	NA	intron (NM_001081050, intron 2 of 22)	intron (NM_001081050, intron 2 of 22)	241507	NM_001081050	72823	Mm.35153	NM_001081050	ENSMUSG00000052062	Pard3b	1810008K04Rik|2010002N16Rik|2810455B10Rik|Als2cr19|PAR3B|PAR3L|PAR3beta	par-3 family cell polarity regulator beta	protein-coding
mm_98120.1	chr11	87127165	87127171	+	1	NA	promoter-TSS (NM_197987)	promoter-TSS (NM_197987)	93	NM_197987	68729	Mm.17436	NM_197987	ENSMUSG00000018548	Trim37	1110032A10Rik|2810004E07Rik|AI848587|AU043018|MUL|TEF3|mKIAA0898	tripartite motif-containing 37	protein-coding
mm_14169.1	chr2	126674643	126674646	+	1	NA	intron (NM_001271470, intron 1 of 8)	CpG	948	NM_001271469	14391	Mm.293266	NM_010249	ENSMUSG00000027361	Gabpb1	BABPB2|E4TF1|E4TF1-47|E4TF1-53|E4Tf1B|GABPB|GABPB-1|GABPB-2|GABPB1-1|GABPB1-2|NRF2B1|NRF2B2	GA repeat binding protein, beta 1	protein-coding
mm_145246.1	chr18	51189205	51189229	+	1	NA	intron (NM_001081224, intron 1 of 1)	Lx8|LINE|L1	71319	NM_001081224	71373	Mm.63546	NM_001081224	ENSMUSG00000073565	Prr16	5430406M13Rik|AI607429	proline rich 16	protein-coding
mm_31739.1	chr4	63214089	63214101	+	1	NA	Intergenic	CpG	-1317	NM_025685	373864	Mm.194116	NM_025685	ENSMUSG00000045672	Col27a1	5730512J02Rik|AI449266	collagen, type XXVII, alpha 1	protein-coding
mm_92612.1	chr10	80137377	80137443	-	1	NA	promoter-TSS (NM_001195268)	promoter-TSS (NM_001195268)	-23	NM_001195268	100503659	Mm.485395	NM_015761	ENSMUSG00000035640	Cbarp	9630008F14|Dos|R29144/1	calcium channel, voltage-dependent, beta subunit associated regulatory protein	protein-coding
mm_57740.1	chr6	129038544	129038553	-	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-7353	NR_024262	232408	Mm.259262	NM_153094	ENSMUSG00000030154	Klrb1f	A630024B12Rik|Nkr-p1f|Nkrp1-f|Nkrp1f	killer cell lectin-like receptor subfamily B member 1F	protein-coding
mm_124221.1	chr14	100284694	100284728	-	1	NA	Intergenic	Intergenic	-134915	NM_010636	16597	Mm.396499	NM_010636	ENSMUSG00000072294	Klf12	2700063E05Rik|AI225908|AI315654|AP-2rep|B130052C06Rik|D530033K05Rik	Kruppel-like factor 12	protein-coding
mm_79670.1	chr9	59676907	59676929	+	1	NA	intron (NM_011099, intron 9 of 10)	intron (NM_011099, intron 9 of 10)	20550	NM_001253883	18746	Mm.326167	NM_011099	ENSMUSG00000032294	Pkm	AA414905|AL024370|AL024424|Pk-2|Pk-3|Pk3|Pkm2	pyruvate kinase, muscle	protein-coding
mm_135940.1	chr16	74279738	74279741	-	1	NA	intron (NM_175549, intron 2 of 27)	intron (NM_175549, intron 2 of 27)	62328	NR_030464	751561		NR_030464	ENSMUSG00000104758	Mir691	Mirn691|mir-691|mmu-mir-691	microRNA 691	ncRNA
mm_36107.1	chr4	58839985	58839997	-	1	NA	intron (NM_172381, intron 19 of 48)	intron (NM_172381, intron 19 of 48)	-54271	NM_146920	258922	Mm.223327	NM_146920	ENSMUSG00000043385	Olfr267	MOR262-1	olfactory receptor 267	protein-coding
mm_162349.1	chr1	53851615	53851630	+	1	NA	exon (NM_001001883, exon 21 of 29)	exon (NM_001001883, exon 21 of 29)	2198	NR_106149	102465783		NR_106149	ENSMUSG00000098443	Mir7681	Gm27806|mmu-mir-7681	microRNA 7681	ncRNA
mm_167783.1	chr9	119691369	119691387	+	1	NA	intron (NM_009134, intron 3 of 27)	intron (NM_009134, intron 3 of 27)	27654	NM_009134	20264	Mm.247042	NM_009134	ENSMUSG00000034533	Scn10a	Nav1.8|PN3|SNS	sodium channel, voltage-gated, type X, alpha	protein-coding
mm_150207.1	chr19	32792204	32792209	+	1	NA	intron (NM_008960, intron 2 of 8)	intron (NM_008960, intron 2 of 8)	34629	NM_008960	19211	Mm.245395	NM_008960	ENSMUSG00000013663	Pten	2310035O07Rik|A130070J02Rik|AI463227|B430203M17Rik|MMAC1|TEP1	phosphatase and tensin homolog	protein-coding
mm_142244.1	chr17	37482749	37482756	-	1	NA	exon (NM_008204, exon 3 of 4)	exon (NM_008204, exon 3 of 4)	777	NM_008204	14990	Mm.329041	NM_008204	ENSMUSG00000016283	H2-M2	H-2M2|Thy19.4	histocompatibility 2, M region locus 2	protein-coding
mm_143796.1	chr17	82941033	82941037	-	1	NA	Intergenic	AT_rich|Low_complexity|Low_complexity	137190	NR_045094	100503434	Mm.187281	NR_045094		Gm19689	-	predicted gene, 19689	ncRNA
mm_53135.1	chr6	125192178	125192210	+	1	NA	promoter-TSS (NM_025595)	promoter-TSS (NM_025595)	-6	NM_025595	66493	Mm.138749	NM_025595	ENSMUSG00000030335	Mrpl51	2610511M02Rik|CDA09|HSPC241|Mrp64	mitochondrial ribosomal protein L51	protein-coding
mm_13451.1	chr2	105425961	105425963	+	1	NA	Intergenic	Intergenic	-26643	NM_009037	19672	Mm.4876	NM_009037	ENSMUSG00000005973	Rcn1	Rcn	reticulocalbin 1	protein-coding
mm_151508.1	chr19	58732101	58732121	+	1	NA	exon (NM_018874, exon 5 of 13)	exon (NM_018874, exon 5 of 13)	3224	NM_018874	18946	Mm.10753	NM_018874	ENSMUSG00000042179	Pnliprp1	Plrp1	pancreatic lipase related protein 1	protein-coding
mm_2722.1	chr1	128171789	128171820	+	1	NA	intron (NM_181750, intron 7 of 26)	intron (NM_181750, intron 7 of 26)	-30557	NR_029543	387147		NR_029543	ENSMUSG00000065520	Mir128-1	Mirn128|Mirn128-1|Mirn128a|mir-128-1	microRNA 128-1	ncRNA
mm_94615.1	chr11	16752246	16752265	+	1	NA	promoter-TSS (NM_007912)	promoter-TSS (NM_007912)	52	NM_007912	13649	Mm.8534	NM_007912	ENSMUSG00000020122	Egfr	9030024J15Rik|AI552599|Erbb|Errb1|Errp|Wa5|wa-2|wa2	epidermal growth factor receptor	protein-coding
mm_129069.1	chr15	75664145	75664166	-	1	NA	intron (NM_028404, intron 10 of 13)	intron (NM_028404, intron 10 of 13)	14635	NM_028404	72960	Mm.182401	NM_028404	ENSMUSG00000000934	Top1mt	2900052H09Rik	DNA topoisomerase 1, mitochondrial	protein-coding
mm_49685.1	chr6	33368640	33368654	+	1	NA	intron (NM_001347089, intron 7 of 9)	intron (NM_001347089, intron 7 of 9)	119497	NM_009148	20336	Mm.265512	NM_009148	ENSMUSG00000029763	Exoc4	C78892|Sec8|Sec8l1	exocyst complex component 4	protein-coding
mm_49204.1	chr6	15720488	15720511	+	1	NA	promoter-TSS (NM_175088)	promoter-TSS (NM_175088)	-162	NM_175088	16543	Mm.1314	NM_175088	ENSMUSG00000041390	Mdfic	Kdt1|Mdfid	MyoD family inhibitor domain containing	protein-coding
mm_99883.1	chr11	109432712	109432730	+	1	NA	intron (NM_001252193, intron 5 of 7)	intron (NM_001252193, intron 5 of 7)	6501	NM_001252193	13929	Mm.211850	NM_025275	ENSMUSG00000020610	Amz2	AA408420|ESTM12|X83328	archaelysin family metallopeptidase 2	protein-coding
mm_121424.1	chr14	120286954	120286957	+	1	NA	intron (NM_175341, intron 1 of 8)	intron (NM_175341, intron 1 of 8)	11286	NM_175341	105559	Mm.238266	NM_175341	ENSMUSG00000022139	Mbnl2	1110002M11Rik|AI047808|AI837313|AI849185|AL118326|MBLL|R75232|mKIAA4072	muscleblind-like 2	protein-coding
mm_55951.1	chr6	85333479	85333489	-	1	NA	promoter-TSS (NM_178639)	promoter-TSS (NM_178639)	-62	NM_178639	94282	Mm.121485	NM_178639	ENSMUSG00000033720	Sfxn5	C230001H08Rik	sideroflexin 5	protein-coding
mm_25082.1	chr3	100436978	100436981	+	1	NA	intron (NR_040543, intron 2 of 2)	intron (NR_040543, intron 2 of 2)	10574	NR_040543	73806	Mm.396549	NR_040543	ENSMUSG00000086923	4930406D18Rik	-	RIKEN cDNA 4930406D18 gene	ncRNA
mm_10604.1	chr2	18699053	18699057	+	1	NA	promoter-TSS (NM_001001334)	promoter-TSS (NM_001001334)	33	NM_001001334	381350	Mm.330024	NM_001001334	ENSMUSG00000037708	Spag6	Spag6l	sperm associated antigen 6	protein-coding
mm_102176.1	chr11	54027740	54027746	-	1	NA	exon (NM_019687, exon 1 of 10)	exon (NM_019687, exon 1 of 10)	361	NM_019687	30805	Mm.274590	NM_019687	ENSMUSG00000020334	Slc22a4	Octn1	solute carrier family 22 (organic cation transporter), member 4	protein-coding
mm_39555.1	chr5	22550392	22550442	+	1	NA	promoter-TSS (NM_011959)	promoter-TSS (NM_011959)	4	NR_102315	320719	Mm.459265	NR_102315	ENSMUSG00000097207	6030443J06Rik	1700030G06Rik	RIKEN cDNA 6030443J06 gene	ncRNA
mm_7132.1	chr1	91052855	91052872	-	1	NA	promoter-TSS (NM_008515)	promoter-TSS (NM_008515)	-581	NM_001310732	16978	Mm.45039	NM_008515	ENSMUSG00000026305	Lrrfip1	AU024550|Fliiap1	leucine rich repeat (in FLII) interacting protein 1	protein-coding
mm_146923.1	chr18	31911251	31911278	-	1	NA	5' UTR (NM_026006, exon 1 of 1)	5' UTR (NM_026006, exon 1 of 1)	639	NM_026006	67158	Mm.31537	NM_026006	ENSMUSG00000044982	Sft2d3	2610206C24Rik|AI847965|AW046173	SFT2 domain containing 3	protein-coding
mm_28643.1	chr3	95228148	95228164	-	1	NA	promoter-TSS (NM_172395)	promoter-TSS (NM_172395)	-268	NM_172395	57912	Mm.28189	NM_172395	ENSMUSG00000046722	Cdc42se1	1300002M12Rik|AW558204|Cdcse1|SCIP1|Spec1	CDC42 small effector 1	protein-coding
mm_103834.1	chr11	83020728	83020738	-	1	NA	promoter-TSS (NM_001167743)	promoter-TSS (NM_001167743)	-11	NM_001167743	276950	Mm.491599	NM_181545	ENSMUSG00000035208	Slfn8	-	schlafen 8	protein-coding
mm_120155.1	chr14	60702947	60702971	+	1	NA	intron (NM_001033272, intron 2 of 12)	intron (NM_001033272, intron 2 of 12)	-29945	NM_001310594	219140	Mm.149776	NM_001033272	ENSMUSG00000021990	Spata13	C79050|ESTM11|X83327|mFLJ00298	spermatogenesis associated 13	protein-coding
mm_130013.1	chr15	88124431	88124431	-	1	NA	Intergenic	Intergenic	-190443	NR_045281	328579	Mm.146839	NR_045281		B230214G05Rik	B230214G05	RIKEN cDNA B230214G05 gene	ncRNA
mm_35516.1	chr4	41124293	41124316	-	1	NA	promoter-TSS (NM_139236)	promoter-TSS (NM_139236)	35	NM_139236	230082	Mm.285797	NM_139236	ENSMUSG00000028430	Nol6	AA410091|Nrap	nucleolar protein family 6 (RNA-associated)	protein-coding
mm_61897.1	chr7	90060142	90060183	+	1	NA	Intergenic	Intergenic	31003	NR_110364	319711	Mm.31753	NR_015614	ENSMUSG00000097585	E230029C05Rik	AI452102|B230337J15	RIKEN cDNA E230029C05 gene	ncRNA
mm_103528.1	chr11	77200818	77200821	-	1	NA	Intergenic	Intergenic	-11851	NM_176965	319634	Mm.108786	NM_176965	ENSMUSG00000050944	Efcab5	4930563A03Rik	EF-hand calcium binding domain 5	protein-coding
mm_41977.1	chr5	107484767	107484768	+	1	NA	intron (NM_001255991, intron 5 of 8)	B1_Mur1|SINE|Alu	-12978	NM_001007574	231570	Mm.261891	NM_001007574	ENSMUSG00000044060	A830010M20Rik	AI849226|Kiaa1107|mKIAA1107	RIKEN cDNA A830010M20 gene	protein-coding
mm_22855.1	chr3	28263568	28263577	+	1	NA	5' UTR (NM_001163009, exon 1 of 31)	5' UTR (NM_001163009, exon 1 of 31)	358	NM_001163009	665113	Mm.126193	NM_026910	ENSMUSG00000027692	Tnik	1500031A17Rik|4831440I19Rik|AI451411|C530008O15Rik|C630040K21Rik	TRAF2 and NCK interacting kinase	protein-coding
mm_128982.1	chr15	74833699	74833708	-	1	NA	Intergenic	Intergenic	7940	NM_001033229	110115	Mm.322606	NM_001033229	ENSMUSG00000075604	Cyp11b1	AA389061|CPN1|Cyp11b|Cyp11b-1|FHI	cytochrome P450, family 11, subfamily b, polypeptide 1	protein-coding
mm_164807.1	chr18	29785898	29785898	-	1	NA	Intergenic	Intergenic	-289482	NR_045391	78058	Mm.416952	NR_045391		4930578E11Rik	-	RIKEN cDNA 4930578E11 gene	ncRNA
mm_90841.1	chr10	8723529	8723542	-	1	NA	3' UTR (NM_175155, exon 20 of 20)	3' UTR (NM_175155, exon 20 of 20)	162535	NM_175155	70097	Mm.338275	NM_175155	ENSMUSG00000015305	Sash1	1100001C18Rik|2500002E12Rik|A330076K04Rik|mKIAA0790	SAM and SH3 domain containing 1	protein-coding
mm_36193.1	chr4	62329391	62329399	-	1	NA	exon (NM_001045528, exon 13 of 28)	exon (NM_001045528, exon 13 of 28)	31153	NM_001045528	338355	Mm.357792	NM_001045528	ENSMUSG00000066151	Fkbp15	BB131447|C430014M02Rik|FKBO133|FKBP-133|FKBP-15|FKBP133|mKIAA0674	FK506 binding protein 15	protein-coding
mm_39405.1	chr5	14514996	14514996	+	1	NA	promoter-TSS (NM_011995)	promoter-TSS (NM_011995)	78	NM_001110796	26875	Mm.146275	NM_011995	ENSMUSG00000061601	Pclo	Acz|Pico	piccolo (presynaptic cytomatrix protein)	protein-coding
mm_18918.1	chr2	76739090	76739103	-	1	NA	exon (NM_011652, exon 275 of 313)	exon (NM_011652, exon 275 of 313)	63781	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_169282.1	chr13	96693904	96693916	-	1	NA	Intergenic	BGLII|LTR|ERVK	-22974	NM_008255	15357	Mm.316652	NM_008255	ENSMUSG00000021670	Hmgcr	HMG-CoAR|Red	3-hydroxy-3-methylglutaryl-Coenzyme A reductase	protein-coding
mm_22370.1	chr2	181147867	181147885	-	1	NA	3' UTR (NM_007906, exon 8 of 8)	3' UTR (NM_007906, exon 8 of 8)	9139	NM_007906	13628	Mm.2645	NM_007906	ENSMUSG00000016349	Eef1a2	Eef1a|S1|wasted|wst	eukaryotic translation elongation factor 1 alpha 2	protein-coding
mm_167621.1	chr9	58026995	58026999	+	1	NA	TTS (NM_001346787)	TTS (NM_001346787)	-5277	NM_001243265	330951	Mm.406992	NM_001243265		Gm16130	E330033L03|OTTMUSG00000030814	predicted gene 16130	protein-coding
mm_168449.1	chr11	41111521	41111521	-	1	NA	Intergenic	L1Md_T|LINE|L1	-356235	NM_009831	12450	Mm.2103	NM_009831	ENSMUSG00000020326	Ccng1	AI314029	cyclin G1	protein-coding
mm_8202.1	chr1	138123483	138123522	-	1	NA	intron (NM_001111316, intron 2 of 31)	PB1D11|SINE|Alu	51624	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_101398.1	chr11	26593608	26593663	-	1	NA	5' UTR (NM_027260, exon 1 of 13)	5' UTR (NM_027260, exon 1 of 13)	285	NM_027260	69922	Mm.285351	NM_027260	ENSMUSG00000064090	Vrk2	2810003O05Rik|AI447698	vaccinia related kinase 2	protein-coding
mm_162995.1	chr11	29130780	29130788	+	1	NA	promoter-TSS (NM_027869)	promoter-TSS (NM_027869)	33	NM_027869	71701	Mm.211131	NM_027869	ENSMUSG00000020464	Pnpt1	1200003F12Rik|Old35|PNPase|Pnptl1	polyribonucleotide nucleotidyltransferase 1	protein-coding
mm_34458.1	chr4	148130776	148130830	+	1	NA	promoter-TSS (NM_027426)	promoter-TSS (NM_027426)	-105	NM_027426	70433	Mm.275288	NM_027426	ENSMUSG00000029005	Draxin	2610109H07Rik|neucrin	dorsal inhibitory axon guidance protein	protein-coding
mm_58543.1	chr7	4521814	4521845	+	1	NA	exon (NM_009406, exon 3 of 8)	exon (NM_009406, exon 3 of 8)	614	NM_009406	21954	Mm.27674	NM_009406	ENSMUSG00000035458	Tnni3	Tn1|cTnI	troponin I, cardiac 3	protein-coding
mm_51055.1	chr6	65631522	65631549	+	1	NA	3' UTR (NM_001001495, exon 8 of 8)	3' UTR (NM_001001495, exon 8 of 8)	-40076	NM_172399	68169	Mm.52392	NM_172399	ENSMUSG00000049001	Ndnf	A930038C07Rik|epidermacan	neuron-derived neurotrophic factor	protein-coding
mm_144389.1	chr18	20669976	20670045	+	1	NA	exon (NM_013697, exon 3 of 4)	exon (NM_013697, exon 3 of 4)	4760	NM_013697	22139	Mm.2108	NM_013697	ENSMUSG00000061808	Ttr	AA408768|AI787086|D17860|prealbumin	transthyretin	protein-coding
mm_79506.1	chr9	57428167	57428177	+	1	NA	intron (NM_176831, intron 3 of 6)	intron (NM_176831, intron 3 of 6)	11942	NM_176831	66812	Mm.250508	NM_176831	ENSMUSG00000063849	Ppcdc	1810057I13Rik|8430432M10Rik	phosphopantothenoylcysteine decarboxylase	protein-coding
mm_70018.1	chr7	142558591	142558605	-	1	NA	promoter-TSS (NR_002452)	promoter-TSS (NR_002452)	0	NR_002452	330677	Mm.265130	NR_002452	ENSMUSG00000087090	Nctc1	9530074L01|Rhit1	non-coding transcript 1	ncRNA
mm_86254.1	chr9	121495652	121495672	-	1	NA	promoter-TSS (NM_001284508)	promoter-TSS (NM_001284508)	32	NM_001284508	12424	Mm.2619	NM_031161	ENSMUSG00000032532	Cck	-	cholecystokinin	protein-coding
mm_50213.1	chr6	42282216	42282218	+	1	NA	3' UTR (NM_007610, exon 11 of 11)	3' UTR (NM_007610, exon 11 of 11)	-4468	NM_013491	12723	Mm.386757	NM_013491	ENSMUSG00000029862	Clcn1	Clc-1|Clc1|SMCC1|adr|mto|myotonia|nmf355	chloride channel, voltage-sensitive 1	protein-coding
mm_43614.1	chr5	138085084	138085147	+	1	NA	promoter-TSS (NM_029869)	promoter-TSS (NM_029869)	31	NM_029869	74570	Mm.213114	NM_029869	ENSMUSG00000029729	Zkscan1	5930429A01Rik|9130423L19Rik|9230118B16Rik|AI646829|AI788588|C87323|KOX18|PHZ-37|ZNF139	zinc finger with KRAB and SCAN domains 1	protein-coding
mm_95749.1	chr11	54891508	54891516	+	1	NA	Intergenic	ID_B1|SINE|B4	-11342	NM_001329860	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_80444.1	chr9	77960973	77960985	+	1	NA	exon (NM_134255, exon 3 of 8)	exon (NM_134255, exon 3 of 8)	43614	NM_134255	68801	Mm.430736	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	ELOVL family member 5, elongation of long chain fatty acids (yeast)	protein-coding
mm_118000.1	chr13	100552443	100552479	-	1	NA	promoter-TSS (NM_008756)	promoter-TSS (NM_008756)	37	NM_008756	18260	Mm.4807	NM_008756	ENSMUSG00000021638	Ocln	AI503564|Ocl	occludin	protein-coding
mm_117628.1	chr13	92030920	92030954	-	1	NA	Intergenic	Intergenic	-42895	NM_009027	19418	Mm.248630	NM_009027	ENSMUSG00000021708	Rasgrf2	6330417G04Rik|AW048350|Grf2|Ras-GRF2	RAS protein-specific guanine nucleotide-releasing factor 2	protein-coding
mm_6142.1	chr1	64816676	64816690	-	1	NA	intron (NM_001039493, intron 7 of 7)	L1M4|LINE|L1	-78933	NM_022721	14367	Mm.150813	NM_022721	ENSMUSG00000045005	Fzd5	5330434N09Rik|AI427138|Fz-5|Fz5|mFz5	frizzled class receptor 5	protein-coding
mm_70956.1	chr8	26978151	26978190	+	1	NA	intron (NM_001101502, intron 1 of 1)	CpG	834	NM_001110508	353310	Mm.212469	NM_001101502	ENSMUSG00000085795	Zfp703	1110032O19Rik|AI430822|AL022941|Csmn1|End2|Zeppo1|Znf703|Zpo1	zinc finger protein 703	protein-coding
mm_119332.1	chr14	39655362	39655373	+	1	NA	promoter-TSS (NR_045936)	promoter-TSS (NR_045936)	-296	NR_045936	73591	Mm.65499	NR_045936	ENSMUSG00000101261	1700109I08Rik	-	RIKEN cDNA 1700109I08 gene	ncRNA
mm_82191.1	chr9	123942284	123942298	+	1	NA	Intergenic	Intergenic	26401	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_43194.1	chr5	128814350	128814350	+	1	NA	intron (NM_001310733, intron 4 of 20)	intron (NM_001310733, intron 4 of 20)	78104	NM_021311	57749	Mm.272720	NM_021311	ENSMUSG00000029423	Piwil1	MIWI	piwi-like RNA-mediated gene silencing 1	protein-coding
mm_22545.1	chr3	9028361	9028371	+	1	NA	Intergenic	Intergenic	-23851	NM_001025264	21985	Mm.371590	NM_009412	ENSMUSG00000027506	Tpd52	AI043038|mD52	tumor protein D52	protein-coding
mm_70982.1	chr8	27260322	27260332	+	1	NA	promoter-TSS (NM_007918)	promoter-TSS (NM_007918)	0	NM_007918	13685	Mm.6700	NM_007918	ENSMUSG00000031490	Eif4ebp1	4e-bp1|AA959816|PHAS-I	eukaryotic translation initiation factor 4E binding protein 1	protein-coding
mm_73821.1	chr8	117411306	117411322	+	1	NA	exon (NM_001163262, exon 4 of 21)	exon (NM_001163262, exon 4 of 21)	-41709	NR_106045	102466801		NR_106045	ENSMUSG00000099062	Mir7077	Gm27774|mmu-mir-7077	microRNA 7077	ncRNA
mm_131875.1	chr16	23192095	23192141	+	1	NA	Intergenic	Lx8|LINE|L1	-32622	NM_145933	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_81174.1	chr9	107301839	107301843	+	1	NA	3' UTR (NM_009895, exon 3 of 3)	3' UTR (NM_009895, exon 3 of 3)	5182	NM_009895	12700	Mm.4592	NM_009895	ENSMUSG00000032578	Cish	CIS-1|CIS1|Cis|F17|F23|SOCS	cytokine inducible SH2-containing protein	protein-coding
mm_111614.1	chr12	102401646	102401662	-	1	NA	intron (NM_011175, intron 8 of 13)	B3A|SINE|B2	38159	NM_011175	19141	Mm.17185	NM_011175	ENSMUSG00000021190	Lgmn	AEP|AI746452|AU022324|Prsc1	legumain	protein-coding
mm_51536.1	chr6	83195839	83195849	+	1	NA	intron (NM_001347310, intron 20 of 26)	intron (NM_001347310, intron 20 of 26)	9898	NM_001347310	13191	Mm.6919	NM_007835	ENSMUSG00000031865	Dctn1	AL022633|DAP-150|DP-150|Glued|p150|p150-glued|p150<glued>	dynactin 1	protein-coding
mm_148770.1	chr19	6095774	6095777	+	1	NA	Intergenic	Intergenic	-10023	NM_001009546	381204	Mm.359041	NM_001009546	ENSMUSG00000054999	Naaladl1	Gm964|Naaladasel	N-acetylated alpha-linked acidic dipeptidase-like 1	protein-coding
mm_80586.1	chr9	85327411	85327440	+	1	NA	promoter-TSS (NM_001160378)	promoter-TSS (NM_001160378)	-275	NM_001160379	212943	Mm.74610	NM_001160378	ENSMUSG00000032265	Fam46a	BAP014|D930050G01Rik	family with sequence similarity 46, member A	protein-coding
mm_60382.1	chr7	44473634	44473642	+	1	NA	Intergenic	Intergenic	3291	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_109165.1	chr12	108305992	108306003	+	1	NA	promoter-TSS (NM_001044380)	promoter-TSS (NM_001044380)	-273	NM_001044380	214305	Mm.36423	NM_001044380	ENSMUSG00000021260	Hhipl1	1600002O04Rik|AK129450|mKIAA1822	hedgehog interacting protein-like 1	protein-coding
mm_166104.1	chr4	146514982	146514989	+	1	NA	promoter-TSS (NM_001243139)	promoter-TSS (NM_001243139)	65	NM_001243139	100041433	Mm.441741	NM_001243138	ENSMUSG00000056300	Zfp981	Gm13247|OTTMUSG00000011075	zinc finger protein 981	protein-coding
mm_65072.1	chr7	19023543	19023546	-	1	NA	promoter-TSS (NM_026605)	promoter-TSS (NM_026605)	-5	NM_008260	15377	Mm.42260	NM_008260	ENSMUSG00000040891	Foxa3	Hnf-3g|Hnf3g|Tcf-3g|Tcf3g	forkhead box A3	protein-coding
mm_139534.1	chr17	56708859	56708868	+	1	NA	intron (NR_045519, intron 13 of 16)	intron (NR_045519, intron 13 of 16)	8058	NM_178926	106639	Mm.37290	NM_178926	ENSMUSG00000054723	Vmac	AI662250	vimentin-type intermediate filament associated coiled-coil protein	protein-coding
mm_23567.1	chr3	63295613	63295623	+	1	NA	promoter-TSS (NM_008604)	promoter-TSS (NM_008604)	183	NM_001289462	17380	Mm.296022	NM_008604	ENSMUSG00000027820	Mme	6030454K05Rik|C85356|CALLA|CD10|NEP|SFE	membrane metallo endopeptidase	protein-coding
mm_42554.1	chr5	116802719	116802723	+	1	NA	Intergenic	Intergenic	-210904	NM_026886	68955	Mm.146779	NM_026886	ENSMUSG00000063919	Srrm4	1500001A10Rik|B230202K19Rik|bv|mKIAA1853|nSR100	serine/arginine repetitive matrix 4	protein-coding
mm_15030.1	chr2	152695459	152695476	+	1	NA	intron (NM_010376, intron 9 of 11)	intron (NM_010376, intron 9 of 11)	8319	NM_025543	66405	Mm.440291	NM_025543	ENSMUSG00000042814	Mcts2	2400002F11Rik|MCT-2	malignant T cell amplified sequence 2	protein-coding
mm_136801.1	chr17	12318070	12318074	+	1	NA	promoter-TSS (NR_045290)	promoter-TSS (NR_045290)	588	NM_011948	26407	Mm.28587	NM_011948	ENSMUSG00000014426	Map3k4	D17Rp17|D17Rp17e|MAPKKK4|MEKK 4|MTK1|Mek4b|Mekk4|RP17|Rp17a|Tas|mKIAA0213	mitogen-activated protein kinase kinase kinase 4	protein-coding
mm_142197.1	chr17	36958207	36958234	-	1	NA	promoter-TSS (NM_029602)	promoter-TSS (NM_029602)	208	NM_023162	66136	Mm.486229	NM_023162	ENSMUSG00000036315	Znrd1	1110014N07Rik|Rpa12	zinc ribbon domain containing, 1	protein-coding
mm_110021.1	chr12	16753280	16753290	-	1	NA	intron (NM_001252071, intron 1 of 32)	intron (NM_001252071, intron 1 of 32)	3954	NM_001252071	268527	Mm.428062	NM_015764	ENSMUSG00000036523	Greb1	5730583K22Rik|9130004E13|AF180470|AU023194|mKIAA0575	gene regulated by estrogen in breast cancer protein	protein-coding
mm_107790.1	chr12	61631736	61631741	+	1	NA	intron (NM_178714, intron 1 of 3)	(CTTTG)n|Simple_repeat|Simple_repeat	108571	NM_001310586	238205	Mm.28802	NM_178714	ENSMUSG00000035653	Lrfn5	AI427653|AI604817|C130061B21|mKIAA4208	leucine rich repeat and fibronectin type III domain containing 5	protein-coding
mm_167058.1	chr7	90059956	90059963	-	1	NA	Intergenic	Intergenic	30800	NR_110364	319711	Mm.31753	NR_015614	ENSMUSG00000097585	E230029C05Rik	AI452102|B230337J15	RIKEN cDNA E230029C05 gene	ncRNA
mm_112841.1	chr13	20829535	20829555	+	1	NA	intron (NM_012054, intron 2 of 20)	RMER17B2|LTR|ERVK	35432	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_23558.1	chr3	62339574	62339610	+	1	NA	exon (NM_001081295, exon 1 of 14)	exon (NM_001081295, exon 1 of 14)	815	NM_001081295	622434	Mm.153974	NM_001081295	ENSMUSG00000036885	Arhgef26	4631416L12Rik|8430436L14Rik|AI303572|AW491953|SGEF	Rho guanine nucleotide exchange factor (GEF) 26	protein-coding
mm_362.1	chr1	33907865	33907949	+	1	NA	promoter-TSS (NM_001310484)	promoter-TSS (NM_001310484)	-140	NM_001310484	320705	Mm.336619	NM_177235	ENSMUSG00000042182	Bend6	B230209C24Rik	BEN domain containing 6	protein-coding
mm_53355.1	chr6	129350455	129350463	+	1	NA	exon (NM_177686, exon 1 of 6)	exon (NM_177686, exon 1 of 6)	215	NM_177686	232413	Mm.90241	NM_177686	ENSMUSG00000053063	Clec12a	CLL-1|D230024O04|KLRL1|Micl	C-type lectin domain family 12, member a	protein-coding
mm_46348.1	chr5	102480016	102480029	-	1	NA	Intergenic	Intergenic	-1369	NM_146161	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding
mm_25879.1	chr3	130617646	130617675	+	1	NA	promoter-TSS (NM_027907)	promoter-TSS (NM_027907)	85	NM_027907	71760	Mm.29125	NM_027907	ENSMUSG00000019232	Etnppl	1300019H02Rik|AI195447|Agxt2l1	ethanolamine phosphate phospholyase	protein-coding
mm_170020.1	chr1	7190316	7190320	+	1	NA	Intergenic	Intergenic	101398	NM_183028	319263	Mm.21539	NM_183028	ENSMUSG00000051285	Pcmtd1	8430411F12Rik|A030012M09Rik	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding
mm_148269.1	chr18	81924112	81924150	-	1	NA	Intergenic	Intergenic	67949	NR_039589	100628596		NR_039589	ENSMUSG00000093036	Mir5127	mmu-mir-5127|mu-mir-5127	microRNA 5127	ncRNA
mm_101276.1	chr11	21371265	21371276	-	1	NA	promoter-TSS (NM_139297)	promoter-TSS (NM_139297)	-3	NM_001290634	216558	Mm.28877	NM_139297	ENSMUSG00000001891	Ugp2	UDPGP|UGPase	UDP-glucose pyrophosphorylase 2	protein-coding
mm_137462.1	chr17	26607832	26607845	+	1	NA	intron (NM_026170, intron 1 of 9)	intron (NM_026170, intron 1 of 9)	46326	NM_026170	67458	Mm.30496	NM_026170	ENSMUSG00000001576	Ergic1	1200007D18Rik|maa-136	endoplasmic reticulum-golgi intermediate compartment (ERGIC) 1	protein-coding
mm_98805.1	chr11	97050595	97050630	+	1	NA	promoter-TSS (NM_001081434)	promoter-TSS (NM_001081434)	-16	NM_001310509	71240	Mm.190450	NM_001081434	ENSMUSG00000038534	Osbpl7	4933437E18Rik	oxysterol binding protein-like 7	protein-coding
mm_123381.1	chr14	63271709	63271723	-	1	NA	Intergenic	Intergenic	-26445	NM_001310610	14463	Mm.247669	NM_008092	ENSMUSG00000021944	Gata4	Gata-4	GATA binding protein 4	protein-coding
mm_5728.1	chr1	44218906	44218951	-	1	NA	promoter-TSS (NM_207281)	promoter-TSS (NM_207281)	3	NM_207281	403183	Mm.336176	NM_207281	ENSMUSG00000046828	Mettl21e	4832428D23Rik|Gm991	methyltransferase like 21E	protein-coding
mm_123809.1	chr14	70522653	70522675	-	1	NA	exon (NM_011359, exon 2 of 6)	exon (NM_011359, exon 2 of 6)	1417	NM_011359	20389	Mm.24040	NM_011359	ENSMUSG00000022097	Sftpc	Bricd6|SP-C|SP5|SPC|Sftp-2|Sftp2|pro-SpC	surfactant associated protein C	protein-coding
mm_43038.1	chr5	124004989	124005008	+	1	NA	3' UTR (NM_177876, exon 4 of 4)	3' UTR (NM_177876, exon 4 of 4)	8146	NR_105999	102465625		NR_105999	ENSMUSG00000098454	Mir7032	Gm27309|mmu-mir-7032	microRNA 7032	ncRNA
mm_13340.1	chr2	102787527	102787541	+	1	NA	3' UTR (NM_001077514, exon 11 of 11)	3' UTR (NM_001077514, exon 11 of 11)	81096	NM_001077515	20511	Mm.267547	NM_011393	ENSMUSG00000005089	Slc1a2	1700091C19Rik|2900019G14Rik|AI159670|Eaat2|GLT-1|GLT1|MGLT1	solute carrier family 1 (glial high affinity glutamate transporter), member 2	protein-coding
mm_118118.1	chr13	104037626	104037641	-	1	NA	intron (NM_029447, intron 9 of 12)	intron (NM_029447, intron 9 of 12)	71981	NM_029447	75805	Mm.127692	NM_029447	ENSMUSG00000021710	Nln	4930472G13Rik|C79345	neurolysin (metallopeptidase M3 family)	protein-coding
mm_63548.1	chr7	128068593	128068633	+	1	NA	exon (NM_008401, exon 3 of 30)	exon (NM_008401, exon 3 of 30)	5973	NM_008401	16409	Mm.262106	NM_008401	ENSMUSG00000030786	Itgam	CD11b/CD18|CR3|CR3A|Cd11b|F730045J24Rik|Ly-40|MAC1|Mac-1|Mac-1a	integrin alpha M	protein-coding
mm_102498.1	chr11	60417929	60417970	-	1	NA	promoter-TSS (NM_145427)	promoter-TSS (NM_145427)	804	NM_025757	66771	Mm.29950	NM_025757	ENSMUSG00000018415	Gid4	4933439F18Rik	GID complex subunit 4, VID24 homolog	protein-coding
mm_57497.1	chr6	125313845	125313878	-	1	NA	promoter-TSS (NM_010736)	promoter-TSS (NM_010736)	9	NM_010736	17000	Mm.3122	NM_010736	ENSMUSG00000030339	Ltbr	AI256028|CD18|LTbetaR|Ltar|TNF-R-III|TNFCR|TNFR-RP|TNFR2-RP|TNFRrp|Tnfbr|Tnfrsf3	lymphotoxin B receptor	protein-coding
mm_68027.1	chr7	101007798	101007807	-	1	NA	intron (NM_001302346, intron 1 of 2)	intron (NM_001302346, intron 1 of 2)	4196	NM_001302347	18442	Mm.3000	NM_008773	ENSMUSG00000032860	P2ry2	P2U1|P2Y2	purinergic receptor P2Y, G-protein coupled 2	protein-coding
mm_42331.1	chr5	114902730	114902747	+	1	NA	intron (NM_011854, intron 3 of 5)	intron (NM_011854, intron 3 of 5)	5804	NM_011854	23962	Mm.228363	NM_011854	ENSMUSG00000029561	Oasl2	M1204|Mmu-OASL|Oasl	2'-5' oligoadenylate synthetase-like 2	protein-coding
mm_30898.1	chr4	32335945	32335960	+	1	NA	Intergenic	Intergenic	-81483	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_142068.1	chr17	35690385	35690421	-	1	NA	intron (NM_001198831, intron 6 of 17)	intron (NM_001198831, intron 6 of 17)	10187	NM_001198833	12305	Mm.5021	NM_007584	ENSMUSG00000003534	Ddr1	6030432F18|AI323681|CD167a|Cak|Nep|PTK3A	discoidin domain receptor family, member 1	protein-coding
mm_163734.1	chr13	119689929	119689956	-	1	NA	promoter-TSS (NM_001291439)	promoter-TSS (NM_001291439)	-409	NM_145942	208715	Mm.61526	NM_145942	ENSMUSG00000093930	Hmgcs1	B130032C06Rik	3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1	protein-coding
mm_144645.1	chr18	33193289	33193335	+	1	NA	3' UTR (NM_009793, exon 11 of 11)	3' UTR (NM_009793, exon 11 of 11)	20550	NM_001347624	170459	Mm.127058	NM_133774	ENSMUSG00000024378	Stard4	4632419C16Rik|9030213J02Rik	StAR-related lipid transfer (START) domain containing 4	protein-coding
mm_128715.1	chr15	63998044	63998054	-	1	NA	intron (NM_144846, intron 1 of 11)	CpG	62399	NM_144846	223601	Mm.246108	NM_144846	ENSMUSG00000022378	Fam49b	0910001A06Rik|AW122079	family with sequence similarity 49, member B	protein-coding
mm_121155.1	chr14	102980109	102980127	+	1	NA	3' UTR (NM_177715, exon 1 of 1)	3' UTR (NM_177715, exon 1 of 1)	2514	NR_039592	100628599		NR_039592	ENSMUSG00000092901	Mir5130	mir-5130|mmu-mir-5130|mu-mir-5130	microRNA 5130	ncRNA
mm_172304.1	chr7	104315433	104315445	-	1	NA	promoter-TSS (NM_023835)	promoter-TSS (NM_023835)	56	NM_023835	76681	Mm.458309	NM_023835	ENSMUSG00000066258	Trim12a	2310043C01Rik|Trim12	tripartite motif-containing 12A	protein-coding
mm_147124.1	chr18	35830126	35830137	-	1	NA	intron (NM_133687, intron 1 of 2)	CpG	313	NM_133687	67393	Mm.94560	NM_133687	ENSMUSG00000046668	Cxxc5	4930415K17Rik	CXXC finger 5	protein-coding
mm_89038.1	chr10	82833892	82833897	+	1	NA	promoter-TSS (NM_001042523)	promoter-TSS (NM_001042523)	-57	NM_001042523	50493	Mm.210155	NM_015762	ENSMUSG00000020250	Txnrd1	TR|TR1|TrxR1	thioredoxin reductase 1	protein-coding
mm_123797.1	chr14	70505478	70505481	-	1	NA	intron (NR_033241, intron 6 of 19)	intron (NR_033241, intron 6 of 19)	14781	NM_009755	12153	Mm.27757	NM_009755	ENSMUSG00000022098	Bmp1	Pcp|Tld	bone morphogenetic protein 1	protein-coding
mm_158587.1	chrX	150814266	150814320	-	1	NA	promoter-TSS (NM_030700)	promoter-TSS (NM_030700)	46	NM_030700	80884	Mm.22575	NM_030700	ENSMUSG00000025268	Maged2	4833439A22Rik|Mage-d2|ORF1	melanoma antigen, family D, 2	protein-coding
mm_64714.1	chr7	4632087	4632100	-	1	NA	3' UTR (NM_172894, exon 24 of 24)	3' UTR (NM_172894, exon 24 of 24)	-1611	NM_023440	68255	Mm.389784	NM_023440	ENSMUSG00000045282	Tmem86b	C330014O21Rik	transmembrane protein 86B	protein-coding
mm_30604.1	chr4	6394625	6394649	+	1	NA	3' UTR (NM_016807, exon 9 of 9)	3' UTR (NM_016807, exon 9 of 9)	28957	NM_001098227	53378	Mm.247473	NM_016807	ENSMUSG00000028249	Sdcbp	MDA-9|Sycl|syntenin-1	syndecan binding protein	protein-coding
mm_7895.1	chr1	133424386	133424404	-	1	NA	promoter-TSS (NM_011439)	promoter-TSS (NM_011439)	-183	NM_011439	20668	Mm.8575	NM_011439	ENSMUSG00000070643	Sox13	AA407916|AW259412|AW540933|Sox-13	SRY (sex determining region Y)-box 13	protein-coding
mm_1218.1	chr1	62730307	62730321	+	1	NA	intron (NM_001077405, intron 2 of 15)	intron (NM_001077405, intron 2 of 15)	26997	NM_001077405	18187	Mm.266341	NM_010939	ENSMUSG00000025969	Nrp2	1110048P06Rik|Np-2|Np2|Npn-2|Npn2	neuropilin 2	protein-coding
mm_64346.1	chr7	142380881	142380892	+	1	NA	exon (NM_009983, exon 5 of 9)	exon (NM_009983, exon 5 of 9)	6984	NM_009983	13033	Mm.231395	NM_009983	ENSMUSG00000007891	Ctsd	CD|CatD	cathepsin D	protein-coding
mm_85313.1	chr9	101198941	101198954	-	1	NA	5' UTR (NM_172144, exon 1 of 13)	5' UTR (NM_172144, exon 1 of 13)	126	NM_172144	235542	Mm.335386	NM_172144	ENSMUSG00000043154	Ppp2r3a	3222402P14Rik|A730042E07	protein phosphatase 2, regulatory subunit B'', alpha	protein-coding
mm_148596.1	chr19	5088581	5088591	+	1	NA	promoter-TSS (NM_026553)	promoter-TSS (NM_026553)	48	NM_026553	68090	Mm.44202	NM_026553	ENSMUSG00000024875	Yif1a	5330422J23Rik|54TM|Yif1|Yif1p	Yip1 interacting factor homolog A (S. cerevisiae)	protein-coding
mm_122569.1	chr14	50807581	50807587	-	1	NA	promoter-TSS (NM_009632)	promoter-TSS (NM_009632)	187	NR_002142	85029		NR_002142	ENSMUSG00000092837	Rpph1	Gm24821|H1RNA|Rmrp5|Rpr	ribonuclease P RNA component H1	ncRNA
mm_49581.1	chr6	30642348	30642359	+	1	NA	exon (NM_025350, exon 7 of 10)	exon (NM_025350, exon 7 of 10)	3135	NM_025350	109697	Mm.25377	NM_025350	ENSMUSG00000054446	Cpa1	0910001L12Rik|Cpa	carboxypeptidase A1, pancreatic	protein-coding
mm_31407.1	chr4	48047739	48047753	+	1	NA	intron (NM_015743, intron 1 of 7)	intron (NM_015743, intron 1 of 7)	2441	NM_015743	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_147177.1	chr18	36744519	36744553	-	1	NA	promoter-TSS (NM_011879)	promoter-TSS (NM_011879)	51	NM_010885	17991	Mm.29867	NM_010885	ENSMUSG00000014294	Ndufa2	AV000592|B8|C1-B8|CI-B8	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 2	protein-coding
mm_124365.1	chr14	105643691	105643712	-	1	NA	Intergenic	Intergenic	-19931	NR_105814	102465207		NR_105814	ENSMUSG00000098780	Mir6390	Gm27562|mmu-mir-6390	microRNA 6390	ncRNA
mm_96595.1	chr11	69090877	69090897	+	1	NA	3' UTR (NM_009497, exon 5 of 5)	3' UTR (NM_009497, exon 5 of 5)	2359	NM_009497	22318	Mm.28643	NM_009497	ENSMUSG00000020894	Vamp2	Syb-2|Syb2|sybII	vesicle-associated membrane protein 2	protein-coding
mm_31159.1	chr4	43442469	43442483	+	1	NA	5' UTR (NM_011571, exon 1 of 10)	5' UTR (NM_011571, exon 1 of 10)	199	NM_011571	21754	Mm.485441	NM_011571	ENSMUSG00000028458	Tesk1	AI326901	testis specific protein kinase 1	protein-coding
mm_125620.1	chr15	61987792	61987800	+	1	NA	exon (NM_001177354, exon 2 of 3)	exon (NM_001177354, exon 2 of 3)	2455	NM_001177352	17869	Mm.2444	NM_010849	ENSMUSG00000022346	Myc	AU016757|Myc2|Niard|Nird|bHLHe39	myelocytomatosis oncogene	protein-coding
mm_95659.1	chr11	53770978	53770980	+	1	NA	intron (NM_001159396, intron 1 of 9)	intron (NM_001159396, intron 1 of 9)	506	NM_001159396	16362	Mm.105218	NM_008390	ENSMUSG00000018899	Irf1	AU020929|Irf-1	interferon regulatory factor 1	protein-coding
mm_164460.1	chr16	57888060	57888062	+	1	NA	Intergenic	Intergenic	-133324	NM_007739	12837	Mm.130388	NM_007739	ENSMUSG00000068196	Col8a1	Col8a-1	collagen, type VIII, alpha 1	protein-coding
mm_157529.1	chrX	51018012	51018032	-	1	NA	promoter-TSS (NM_172413)	promoter-TSS (NM_172413)	-4	NM_172413	72065	Mm.43152	NM_172413	ENSMUSG00000050029	Rap2c	2010200P20Rik|AI194294|AL022976	RAP2C, member of RAS oncogene family	protein-coding
mm_128612.1	chr15	58823567	58823581	-	1	NA	promoter-TSS (NM_175212)	promoter-TSS (NM_175212)	-147	NM_175212	74868	Mm.293754	NM_175212	ENSMUSG00000062373	Tmem65	2610029O13Rik|4930438D12Rik	transmembrane protein 65	protein-coding
mm_68327.1	chr7	106504013	106504051	-	1	NA	Intergenic	Intergenic	-62959	NR_003967	209380	Mm.461779	NM_001001318		Gm4759	EG209380	GTPase, very large interferon inducible 1 pseudogene	pseudo
mm_109703.1	chr12	113260177	113260197	+	1	NA	Intergenic	Intergenic	74284	NM_153776	69195	Mm.313244	NM_153776	ENSMUSG00000049036	Tmem121	2410008J05Rik|Hole	transmembrane protein 121	protein-coding
mm_63457.1	chr7	127541304	127541325	+	1	NA	exon (NM_001304266, exon 25 of 34)	exon (NM_001304266, exon 25 of 34)	13417	NR_034045	100217442	Mm.451113	NR_034045	ENSMUSG00000065259	Snora30	MBI-26	small nucleolar RNA, H/ACA box 30	snoRNA
mm_7835.1	chr1	132139667	132139692	-	1	NA	promoter-TSS (NM_008795)	promoter-TSS (NM_008795)	6	NM_008795	18557	Mm.28130	NM_008795	ENSMUSG00000026437	Cdk18	AA682070|Ctk18|Pctk3	cyclin-dependent kinase 18	protein-coding
mm_164652.1	chr17	35835834	35835855	-	1	NA	exon (NM_011655, exon 4 of 4)	exon (NM_011655, exon 4 of 4)	2457	NM_011655	22154	Mm.273538	NM_011655	ENSMUSG00000001525	Tubb5	AA408537|AI596182|B130022C14Rik|M(beta)5	tubulin, beta 5 class I	protein-coding
mm_55387.1	chr6	59024430	59024450	-	1	NA	promoter-TSS (NM_153574)	promoter-TSS (NM_153574)	62	NM_153574	58909	Mm.28813	NM_153574	ENSMUSG00000037709	Fam13a	AI462012|D430015B01Rik|FAM13A1|Precm1	family with sequence similarity 13, member A	protein-coding
mm_146322.1	chr18	80678785	80678788	+	1	NA	intron (NM_198429, intron 3 of 9)	intron (NM_198429, intron 3 of 9)	29387	NM_001164111	18018	Mm.329560	NM_016791	ENSMUSG00000033016	Nfatc1	2210017P03Rik|AI449492|AV076380|NF-ATc|NFAT2|NFATc|Nfatcb	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 1	protein-coding
mm_107919.1	chr12	71048373	71048419	+	1	NA	intron (NM_001081195, intron 11 of 23)	intron (NM_001081195, intron 11 of 23)	32429	NM_001081195	238247	Mm.241601	NM_001081195	ENSMUSG00000048118	Arid4a	A630009N03|A630067N03Rik|MmRBBP1|Rbbp1	AT rich interactive domain 4A (RBP1-like)	protein-coding
mm_23745.1	chr3	69344000	69344016	+	1	NA	intron (NM_178726, intron 1 of 3)	intron (NM_178726, intron 1 of 3)	27090	NM_178726	242083	Mm.40577	NM_178726	ENSMUSG00000027784	Ppm1l	3222401G13|5930404J21Rik|AI481720|AW045850|PP2C|PP2Cepsilon|Pp2ce|Ppp2ce|mKIAA4175	protein phosphatase 1 (formerly 2C)-like	protein-coding
mm_55421.1	chr6	65130008	65130034	-	1	NA	intron (NM_019455, intron 4 of 5)	ORR1A1|LTR|ERVL-MaLR	14709	NM_019455	54486	Mm.410688	NM_019455	ENSMUSG00000029919	Hpgds	H-PGDS|Ptgds2	hematopoietic prostaglandin D synthase	protein-coding
mm_71026.1	chr8	33599575	33599591	+	1	NA	promoter-TSS (NM_017374)	promoter-TSS (NM_017374)	-38	NM_017374	19053	Mm.29301	NM_017374	ENSMUSG00000009630	Ppp2cb	AI115466|D8Ertd766e|PP2Ac	protein phosphatase 2 (formerly 2A), catalytic subunit, beta isoform	protein-coding
mm_49997.1	chr6	41048140	41048153	+	1	NA	Intergenic	Intergenic	-12637	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_50121.1	chr6	41535492	41535498	+	1	NA	Intergenic	Intergenic	13719	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_13220.1	chr2	96834779	96834780	+	1	NA	intron (NM_001289743, intron 3 of 6)	intron (NM_001289743, intron 3 of 6)	516610	NM_001289743	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_158021.1	chrX	95970084	95970092	-	1	NA	Intergenic	Intergenic	-13114	NM_152822	76130	Mm.274318	NM_152822	ENSMUSG00000057421	Las1l	1810030A06Rik|5830482G23Rik	LAS1-like (S. cerevisiae)	protein-coding
mm_128182.1	chr15	34678695	34678746	-	1	NA	promoter-TSS (NM_145469)	promoter-TSS (NM_145469)	-14	NM_145469	223473	Mm.258402	NM_145469	ENSMUSG00000038879	Nipal2	9330161F08Rik|Npal2	NIPA-like domain containing 2	protein-coding
mm_51812.1	chr6	88835270	88835273	+	1	NA	TTS (NM_030251)	TTS (NM_030251)	6664	NM_030251	80283	Mm.166858	NM_030251	ENSMUSG00000030083	Abtb1	AI847549|BC003234|BPOZ|EF1ABP	ankyrin repeat and BTB (POZ) domain containing 1	protein-coding
mm_146509.1	chr18	3337402	3337424	-	1	NA	5' UTR (NM_001110852, exon 1 of 4)	5' UTR (NM_001110852, exon 1 of 4)	176	NM_001110851	12916	Mm.5244	NM_013498	ENSMUSG00000063889	Crem	ICER|ICERI	cAMP responsive element modulator	protein-coding
mm_131684.1	chr16	20677654	20677672	+	1	NA	intron (NM_001304432, intron 5 of 31)	intron (NM_001304432, intron 5 of 31)	4936	NM_001304432	208643	Mm.260256	NM_145941	ENSMUSG00000045983	Eif4g1	E030015G23Rik|eIF-4-gamma 1|eIF-4G 1|eIF-4G1|eIF4GI	eukaryotic translation initiation factor 4, gamma 1	protein-coding
mm_146888.1	chr18	25753666	25753734	-	1	NA	5' UTR (NM_001146295, exon 1 of 2)	5' UTR (NM_001146295, exon 1 of 2)	283	NM_133195	108013	Mm.266435	NM_133195	ENSMUSG00000024268	Celf4	A230070D14Rik|BRUNOL-4|Brul4|Brunol4|C130060B05Rik	CUGBP, Elav-like family member 4	protein-coding
mm_11522.1	chr2	32616172	32616174	+	1	NA	intron (NM_001289547, intron 5 of 6)	B3|SINE|B2	-5585	NM_001198790	11636	Mm.29189	NM_021515	ENSMUSG00000026817	Ak1	Ak-1|B430205N08Rik	adenylate kinase 1	protein-coding
mm_73641.1	chr8	110741187	110741205	+	1	NA	TTS (NM_001135100)	TTS (NM_001135100)	15470	NM_001310591	244654	Mm.490385	NM_198625	ENSMUSG00000033763	Mtss1l	ABBA	metastasis suppressor 1-like	protein-coding
mm_81034.1	chr9	104588052	104588075	+	1	NA	intron (NM_028719, intron 1 of 15)	intron (NM_028719, intron 1 of 15)	18275	NM_028719	74020	Mm.326240	NM_028719	ENSMUSG00000032564	Cpne4	3632411M23Rik|4933406O10Rik	copine IV	protein-coding
mm_11407.1	chr2	31515730	31515764	+	1	NA	intron (NR_002687, intron 14 of 15)	ID2|SINE|ID	45439	NR_002687	432466	Mm.333323	NR_002687	ENSMUSG00000046687	Gm5424	EG432466	argininosuccinate synthase pseudogene	pseudo
mm_50019.1	chr6	41116001	41116025	+	1	NA	Intergenic	Intergenic	-80504	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_137592.1	chr17	28079881	28079897	+	1	NA	intron (NM_001085555, intron 2 of 9)	CpG	695	NM_013687	21463	Mm.29758	NM_013687	ENSMUSG00000062859	Tcp11	D17Ken1|Tcp-11	t-complex protein 11	protein-coding
mm_29968.1	chr3	133506658	133506686	-	1	NA	intron (NM_001040400, intron 2 of 10)	MER21B|LTR|ERVL	37718	NM_001346736	214133	Mm.347816	NM_145989	ENSMUSG00000040943	Tet2	Ayu17-449|E130014J05Rik|mKIAA1546	tet methylcytosine dioxygenase 2	protein-coding
mm_136561.1	chr17	3188638	3188651	+	1	NA	intron (NM_134123, intron 15 of 19)	intron (NM_134123, intron 15 of 19)	73672	NM_134123	106583	Mm.124373	NM_134123	ENSMUSG00000046201	Scaf8	A630086M08Rik|A930036P18Rik|AA408306|AI447644|AI448652|AU015035|Rbm16|mKIAA1116	SR-related CTD-associated factor 8	protein-coding
mm_157129.1	chrX	9446853	9446868	-	1	NA	exon (NM_007807, exon 9 of 13)	exon (NM_007807, exon 9 of 13)	22464	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_45865.1	chr5	87929985	87929989	-	1	NA	exon (NM_007786, exon 4 of 5)	exon (NM_007786, exon 4 of 5)	4354	NM_007786	12994	Mm.296303	NM_007786	ENSMUSG00000001622	Csn3	AW208918|CSN10|Csnk	casein kappa	protein-coding
mm_138018.1	chr17	33909623	33909643	+	1	NA	promoter-TSS (NM_001199733)	promoter-TSS (NM_001199733)	32	NM_001199733	13163	Mm.271809	NM_007829	ENSMUSG00000002307	Daxx	-	Fas death domain-associated protein	protein-coding
mm_107957.1	chr12	72536343	72536396	+	1	NA	promoter-TSS (NM_026327)	promoter-TSS (NM_026327)	12	NM_026327	67708	Mm.11233	NM_026327	ENSMUSG00000034501	Pcnx4	1810048J11Rik|4932413O10|AU017192|Pcnxl4	pecanex homolog 4	protein-coding
mm_132425.1	chr16	35585339	35585343	+	1	NA	intron (NM_013661, intron 1 of 21)	(T)n|Simple_repeat|Simple_repeat	43979	NM_013661	20357	Mm.42015	NM_013661	ENSMUSG00000052133	Sema5b	AI893641|SemG|Semag|mKIAA1445	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B	protein-coding
mm_37997.1	chr4	133672602	133672652	-	1	NA	promoter-TSS (NM_178698)	promoter-TSS (NM_178698)	20	NM_001145955	230801	Mm.217004	NM_178698	ENSMUSG00000043257	Pigv	B330013B03|D430024F16Rik	phosphatidylinositol glycan anchor biosynthesis, class V	protein-coding
mm_142684.1	chr17	47733799	47733810	-	1	NA	exon (NM_025973, exon 8 of 9)	exon (NM_025973, exon 8 of 9)	-3233	NM_001161722	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_82952.1	chr9	35569752	35569761	-	1	NA	intron (NM_029762, intron 1 of 3)	CpG	313	NM_029762	76832	Mm.482285	NM_029762	ENSMUSG00000050555	Hyls1	3010015K02Rik	hydrolethalus syndrome 1	protein-coding
mm_9234.1	chr1	171281182	171281192	-	1	NA	promoter-TSS (NM_008911)	promoter-TSS (NM_008911)	-1	NM_008911	19044	Mm.266888	NM_008911	ENSMUSG00000062729	Ppox	Ppo	protoporphyrinogen oxidase	protein-coding
mm_2186.1	chr1	89016107	89016133	+	1	NA	promoter-TSS (NR_040471)	promoter-TSS (NR_040471)	7	NR_040471	73475	Mm.491040	NR_040471	ENSMUSG00000099378	1700067G17Rik	-	RIKEN cDNA 1700067G17 gene	ncRNA
mm_88010.1	chr10	67119500	67119513	+	1	NA	Intergenic	Intergenic	-7752	NM_207221	108829	Mm.23846	NM_207221	ENSMUSG00000037876	Jmjd1c	5430433L24Rik|D630035I23Rik|Jmjdic|TRIP8	jumonji domain containing 1C	protein-coding
mm_110729.1	chr12	69758648	69758673	-	1	NA	intron (NM_183294, intron 4 of 9)	intron (NM_183294, intron 4 of 9)	5284	NR_030450	751538		NR_030450	ENSMUSG00000076065	Mir681	Mirn681|mmu-mir-681	microRNA 681	ncRNA
mm_13164.1	chr2	92608337	92608352	+	1	NA	intron (NM_023850, intron 1 of 2)	intron (NM_023850, intron 1 of 2)	8637	NM_023850	76969	Mm.38021	NM_023850	ENSMUSG00000027221	Chst1	2610008E20Rik|AW125896|C6ST|GST-1|Gst1|KSGAL6ST	carbohydrate (keratan sulfate Gal-6) sulfotransferase 1	protein-coding
mm_94384.1	chr11	5520653	5520656	+	1	NA	promoter-TSS (NM_001271730)	promoter-TSS (NM_001271730)	13	NM_001271730	22433	Mm.469937	NM_013842	ENSMUSG00000020484	Xbp1	D11Ertd39e|TREB-5|TREB5|XBP-1	X-box binding protein 1	protein-coding
mm_92956.1	chr10	85540442	85540447	-	1	NA	intron (NM_028709, intron 1 of 16)	intron (NM_028709, intron 1 of 16)	-57967	NM_001017525	74007	Mm.36544	NM_028709	ENSMUSG00000020042	Btbd11	6330404E16Rik	BTB (POZ) domain containing 11	protein-coding
mm_42526.1	chr5	115611842	115611853	+	1	NA	intron (NM_172719, intron 44 of 57)	intron (NM_172719, intron 44 of 57)	19969	NR_027810	66123	Mm.133063	NM_021417	ENSMUSG00000107121	1110006O24Rik	-	RIKEN cDNA 1110006O24 gene	ncRNA
mm_152636.1	chr19	12501850	12501871	-	1	NA	5' UTR (NM_172442, exon 1 of 9)	5' UTR (NM_172442, exon 1 of 9)	136	NM_172442	207521	Mm.247695	NM_172442	ENSMUSG00000039982	Dtx4	AI449438|BC044798|D930042H13|RNF155	deltex 4, E3 ubiquitin ligase	protein-coding
mm_77015.1	chr8	107682229	107682251	-	1	NA	Intergenic	RLTR17|LTR|ERVK	-93758	NM_010817	17463	Mm.18347	NM_010817	ENSMUSG00000039067	Psmd7	AW107203|Mov-34|Mov34	proteasome (prosome, macropain) 26S subunit, non-ATPase, 7	protein-coding
mm_142470.1	chr17	45610126	45610174	-	1	NA	Intergenic	Intergenic	-8048	NM_001177469	653016	Mm.45676	NM_001177468	ENSMUSG00000079471	Gm7325	EG653016|Esgp	predicted gene 7325	protein-coding
mm_378.1	chr1	34011565	34011602	+	1	NA	promoter-TSS (NM_134448)	promoter-TSS (NM_134448)	-242	NM_133833	13518	Mm.336625	NM_010081	ENSMUSG00000026131	Dst	2310001O04Rik|A830042E19Rik|AW554249|BP230|BPAG1-n|Bpag|Bpag1|Macf2|ah|athetoid|dt|mKIAA0728|nmf203|nmf339	dystonin	protein-coding
mm_14886.1	chr2	148871960	148871994	+	1	NA	exon (NM_009976, exon 3 of 3)	exon (NM_009976, exon 3 of 3)	3535	NM_009976	13010	Mm.4263	NM_009976	ENSMUSG00000027447	Cst3	CysC	cystatin C	protein-coding
mm_146067.1	chr18	70472458	70472471	+	1	NA	promoter-TSS (NM_001289649)	promoter-TSS (NM_001289649)	10	NM_029019	170461	Mm.83623	NM_029019	ENSMUSG00000079608	Stard6	1700011K09Rik|4833424I06Rik|4933429L05Rik|AI644424	StAR-related lipid transfer (START) domain containing 6	protein-coding
mm_4922.1	chr1	190928574	190928652	+	1	NA	non-coding (NR_037579, exon 1 of 8)	non-coding (NR_037579, exon 1 of 8)	108	NR_037579	52477	Mm.289914	NM_021421	ENSMUSG00000026634	Angel2	2610307I21Rik|5730410O10Rik|AI845692|D1Ertd396e|D1Ertd654e	angel homolog 2	protein-coding
mm_51817.1	chr6	88902546	88902559	+	1	NA	intron (NM_011906, intron 1 of 11)	CpG	301	NM_011906	24100	Mm.284480	NM_011906	ENSMUSG00000002871	Tpra1	40kDa|Gpr175|Tpra40	transmembrane protein, adipocyte asscociated 1	protein-coding
mm_17375.1	chr2	26933404	26933467	-	1	NA	promoter-TSS (NM_011512)	promoter-TSS (NM_011512)	76	NM_011512	20932	Mm.300594	NM_011512	ENSMUSG00000014867	Surf4	AL033340|AL033373|Surf-4	surfeit gene 4	protein-coding
mm_147260.1	chr18	38671747	38671748	-	1	NA	Intergenic	L2b|LINE|L2	-70479	NM_011898	24066	Mm.42038	NM_011898	ENSMUSG00000024427	Spry4	A030006O18Rik|sprouty4	sprouty homolog 4 (Drosophila)	protein-coding
mm_44172.1	chr5	150952698	150952714	+	1	NA	promoter-TSS (NM_013823)	promoter-TSS (NM_013823)	99	NM_013823	16591	Mm.6500	NM_013823	ENSMUSG00000058488	Kl	alpha-kl	klotho	protein-coding
mm_35860.1	chr4	49481035	49481044	-	1	NA	Intergenic	RLTR9C|LTR|ERVK	25519	NM_007519	12012	Mm.2859	NM_007519	ENSMUSG00000039653	Baat	AI118337|AI158864|BAT	bile acid-Coenzyme A: amino acid N-acyltransferase	protein-coding
mm_58417.1	chr7	3291494	3291504	+	1	NA	intron (NM_001093765, intron 1 of 2)	intron (NM_001093765, intron 1 of 2)	943	NM_001093765	50918	Mm.29874	NM_016969	ENSMUSG00000068566	Myadm	D7Wsu62e	myeloid-associated differentiation marker	protein-coding
mm_24707.1	chr3	95164266	95164281	+	1	NA	promoter-TSS (NM_011351)	promoter-TSS (NM_011351)	-66	NM_011351	20360	Mm.23662	NM_011351	ENSMUSG00000038777	Sema6c	Semay|mKIAA1869	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C	protein-coding
mm_7142.1	chr1	91183477	91183485	-	1	NA	intron (NM_178401, intron 1 of 2)	intron (NM_178401, intron 1 of 2)	3659	NM_001168392	51801	Mm.3272	NM_016894	ENSMUSG00000034353	Ramp1	9130218E19Rik	receptor (calcitonin) activity modifying protein 1	protein-coding
mm_105947.1	chr11	115276974	115276984	-	1	NA	promoter-TSS (NM_007997)	promoter-TSS (NM_007997)	-10	NM_007997	14149	Mm.4719	NM_007997	ENSMUSG00000018861	Fdxr	-	ferredoxin reductase	protein-coding
mm_23879.1	chr3	83030962	83030985	+	1	NA	exon (NM_010196, exon 5 of 5)	exon (NM_010196, exon 5 of 5)	4820	NM_001111048	14161	Mm.88793	NM_010196	ENSMUSG00000028001	Fga	ENSMUSG00000059807|Fib	fibrinogen alpha chain	protein-coding
mm_103394.1	chr11	75431354	75431374	-	1	NA	TTS (NM_008878)	TTS (NM_008878)	8137	NM_008878	18816	Mm.279733	NM_008878	ENSMUSG00000038224	Serpinf2	AI747498|Pli|Serpimf2	serine (or cysteine) peptidase inhibitor, clade F, member 2	protein-coding
mm_100165.1	chr11	116436973	116437020	+	1	NA	intron (NM_176902, intron 2 of 2)	intron (NM_176902, intron 2 of 2)	2783	NR_003376	664849	Mm.258466	NR_003376		Gm7367	EG664849	1110014K08Rik pseudogene	pseudo
mm_38945.1	chr4	150220702	150220721	-	1	NA	Intergenic	Intergenic	-16486	NM_023119	13806	Mm.70666	NM_023119	ENSMUSG00000063524	Eno1	0610008I15|AL022784|Eno-1|MBP-1	enolase 1, alpha non-neuron	protein-coding
mm_150225.1	chr19	33964846	33964855	+	1	NA	exon (NM_026334, exon 3 of 10)	exon (NM_026334, exon 3 of 10)	3602	NM_026334	67717	Mm.329816	NM_026334	ENSMUSG00000024768	Lipf	2310051B21Rik|AV082900	lipase, gastric	protein-coding
mm_103875.1	chr11	83526504	83526515	-	1	NA	intron (NM_013653, intron 2 of 2)	intron (NM_013653, intron 2 of 2)	4009	NM_013653	20304	Mm.284248	NM_013653	ENSMUSG00000035042	Ccl5	MuRantes|RANTES|SISd|Scya5|TCP228	chemokine (C-C motif) ligand 5	protein-coding
mm_142904.1	chr17	52306622	52306623	-	1	NA	Intergenic	Intergenic	-296087	NM_001031811	211468	Mm.399068	NM_001031811	ENSMUSG00000035580	Kcnh8	C130090D05Rik|ELK|ELK1|ELK3|Kv12.1	potassium voltage-gated channel, subfamily H (eag-related), member 8	protein-coding
mm_93823.1	chr10	121476280	121476294	-	1	NA	promoter-TSS (NM_138956)	promoter-TSS (NM_138956)	-37	NM_138956	192678	Mm.41265	NM_138956	ENSMUSG00000025795	Rassf3	AW212023|AW322379	Ras association (RalGDS/AF-6) domain family member 3	protein-coding
mm_75948.1	chr8	71592442	71592455	-	1	NA	exon (NM_025396, exon 1 of 5)	exon (NM_025396, exon 1 of 5)	264	NM_001294269	66171	Mm.282284	NM_025396	ENSMUSG00000031807	Pgls	1110030K05Rik|AI447866|Plgs	6-phosphogluconolactonase	protein-coding
mm_113828.1	chr13	47066393	47066401	+	1	NA	intron (NM_172262, intron 11 of 20)	intron (NM_172262, intron 11 of 20)	22898	NM_172262	218214	Mm.31259	NM_172262	ENSMUSG00000038080	Kdm1b	4632428N09Rik|AI482520|Aof1	lysine (K)-specific demethylase 1B	protein-coding
mm_108978.1	chr12	102743713	102743747	+	1	NA	promoter-TSS (NM_177140)	promoter-TSS (NM_177140)	18	NM_001324515	320351	Mm.86546	NM_177140	ENSMUSG00000046675	Tmem251	D230037D09Rik	transmembrane protein 251	protein-coding
mm_130903.1	chr15	102405689	102405702	-	1	NA	promoter-TSS (NM_013672)	promoter-TSS (NM_013672)	-621	NM_013672	20683	Mm.4618	NM_013672	ENSMUSG00000001280	Sp1	1110003E12Rik|AA450830|AI845540|Sp1-1	trans-acting transcription factor 1	protein-coding
mm_23462.1	chr3	60472808	60472816	+	1	NA	promoter-TSS (NM_001253713)	promoter-TSS (NM_001253713)	-18	NM_001253713	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_107960.1	chr12	72665049	72665053	+	1	NA	promoter-TSS (NM_025522)	promoter-TSS (NM_025522)	-223	NM_025522	66375	Mm.289653	NM_025522	ENSMUSG00000021094	Dhrs7	2310016E22Rik|5730564L20Rik|AW061210|Retdsr4|Retsdr4	dehydrogenase/reductase (SDR family) member 7	protein-coding
mm_171260.1	chr3	83880809	83880817	+	1	NA	Intergenic	RLTR10D|LTR|ERVK	-39205	NM_011905	24088	Mm.87596	NM_011905	ENSMUSG00000027995	Tlr2	Ly105	toll-like receptor 2	protein-coding
mm_134953.1	chr16	31303510	31303540	-	1	NA	exon (NM_007470, exon 4 of 6)	exon (NM_007470, exon 4 of 6)	11283	NM_001301353	11815	Mm.2082	NM_007470	ENSMUSG00000022548	Apod	-	apolipoprotein D	protein-coding
mm_78374.1	chr9	27397203	27397221	+	1	NA	promoter-TSS (NM_001305058)	promoter-TSS (NM_001305058)	0	NM_001305058	75469	Mm.45824	NM_029299	ENSMUSG00000031991	Spata19	1700001L23Rik|AV047838|spergen-1	spermatogenesis associated 19	protein-coding
mm_96010.1	chr11	59542702	59542726	+	1	NA	promoter-TSS (NM_145827)	promoter-TSS (NM_145827)	28	NM_145827	216799	Mm.54174	NM_145827	ENSMUSG00000032691	Nlrp3	AGTAVPRL|AII/AVP|Cias1|FCAS|FCU|MWS|Mmig1|NALP3|Pypaf1	NLR family, pyrin domain containing 3	protein-coding
mm_113465.1	chr13	36117912	36117933	+	1	NA	promoter-TSS (NM_201358)	promoter-TSS (NM_201358)	279	NM_001039189	69955	Mm.70690	NM_024274	ENSMUSG00000021420	Fars2	Fars1|pheRS	phenylalanine-tRNA synthetase 2 (mitochondrial)	protein-coding
mm_170107.1	chr17	39844754	39844755	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	1757	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_86594.1	chr10	13130024	13130059	+	1	NA	3' UTR (NM_009538, exon 6 of 6)	3' UTR (NM_009538, exon 6 of 6)	39196	NR_131912	338438		NR_131912		Hymai	-	hydatidiform mole associated and imprinted transcript	ncRNA
mm_169129.1	chr13	58218681	58218691	+	1	NA	Intergenic	Intergenic	-3033	NM_026842	56085	Mm.182053	NM_026842	ENSMUSG00000005312	Ubqln1	1110046H03Rik|1810030E05Rik|AU019746|C77538|D13Ertd372e|Da41|Dsk2|Plic-1|Plic1|Xdrp1	ubiquilin 1	protein-coding
mm_129998.1	chr15	86186033	86186057	-	1	NA	promoter-TSS (NM_145475)	promoter-TSS (NM_145475)	96	NM_145475	223753	Mm.222685	NM_145475	ENSMUSG00000035891	Cerk	AI848610|D330016D08Rik|mKIAA1646	ceramide kinase	protein-coding
mm_67737.1	chr7	90131216	90131243	-	1	NA	intron (NM_001252520, intron 1 of 20)	intron (NM_001252520, intron 1 of 20)	997	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_172359.1	chr7	116598553	116598567	-	1	NA	Intergenic	Intergenic	94191	NM_001130479	53322	Mm.9901	NM_016773	ENSMUSG00000030659	Nucb2	AI607786|Calnuc|Nefa|Nesfatin-1	nucleobindin 2	protein-coding
mm_165735.1	chr3	106788533	106788548	+	1	NA	intron (NM_007651, intron 1 of 7)	intron (NM_007651, intron 1 of 7)	1609	NM_007651	12508	Mm.316861	NM_007651	ENSMUSG00000040747	Cd53	AI323659|Ox-44|Tspan25	CD53 antigen	protein-coding
mm_127147.1	chr15	98534500	98534537	+	1	NA	promoter-TSS (NM_001289439)	promoter-TSS (NM_001289439)	-249	NM_001289440	69612	Mm.229107	NM_133714	ENSMUSG00000022992	Kansl2	2310037I24Rik|B930009D17	KAT8 regulatory NSL complex subunit 2	protein-coding
mm_58597.1	chr7	5020611	5020631	+	1	NA	5' UTR (NM_001290426, exon 1 of 3)	5' UTR (NM_001290426, exon 1 of 3)	245	NM_001033383	319748	Mm.86607	NM_001033383	ENSMUSG00000074405	Zfp865	6430526N21Rik|Znf865	zinc finger protein 865	protein-coding
mm_140307.1	chr17	85691172	85691195	+	1	NA	Intergenic	Intergenic	-2929	NM_011380	20472	Mm.5039	NM_011380	ENSMUSG00000024134	Six2	-	sine oculis-related homeobox 2	protein-coding
mm_115315.1	chr13	112363447	112363468	+	1	NA	exon (NM_029898, exon 8 of 11)	exon (NM_029898, exon 8 of 11)	74939	NM_001168404	77318	Mm.159895	NM_029898	ENSMUSG00000049985	Ankrd55	C030011J08Rik	ankyrin repeat domain 55	protein-coding
mm_16407.1	chr2	180041712	180041738	+	1	NA	promoter-TSS (NM_178750)	promoter-TSS (NM_178750)	739	NM_001289476	26444	Mm.21728	NM_011969	ENSMUSG00000027566	Psma7	C6-I	proteasome (prosome, macropain) subunit, alpha type 7	protein-coding
mm_152587.1	chr19	11604734	11604748	-	1	NA	promoter-TSS (NM_026835)	promoter-TSS (NM_026835)	63	NM_026835	68774	Mm.290390	NM_026835	ENSMUSG00000024679	Ms4a6d	1110058E16Rik|AI447446|Ms4a11	membrane-spanning 4-domains, subfamily A, member 6D	protein-coding
mm_127371.1	chr15	100780244	100780247	+	1	NA	intron (NM_021530, intron 2 of 24)	intron (NM_021530, intron 2 of 24)	-1009	NM_001347102	59033	Mm.209856	NM_021530	ENSMUSG00000023032	Slc4a8	AW493845|C230026C11|NDCBE|kNBC-3	solute carrier family 4 (anion exchanger), member 8	protein-coding
mm_74238.1	chr8	124576106	124576126	+	1	NA	promoter-TSS (NM_023709)	promoter-TSS (NM_023709)	5	NM_023709	73647	Mm.6209	NM_023709	ENSMUSG00000031981	Capn9	2200003B16Rik|GC36|nCL-4|nCL4	calpain 9	protein-coding
mm_101755.1	chr11	43385142	43385158	-	1	NA	Intergenic	Intergenic	-10689	NR_029558	387164		NR_029558	ENSMUSG00000065601	Mir146	Mirn146|miR-146a|mmu-mir-146	microRNA 146	ncRNA
mm_69314.1	chr7	128440674	128440677	-	1	NA	3' UTR (NM_009383, exon 12 of 12)	3' UTR (NM_009383, exon 12 of 12)	20838	NM_009383	21843	Mm.242072	NM_009383	ENSMUSG00000030846	Tial1	5330433G13Rik|AL033329|TIAR|mTIAR	Tia1 cytotoxic granule-associated RNA binding protein-like 1	protein-coding
mm_59736.1	chr7	28813909	28813935	+	1	NA	exon (NM_177301, exon 3 of 13)	exon (NM_177301, exon 3 of 13)	3032	NM_177301	15388	Mm.9043	NM_177301	ENSMUSG00000015165	Hnrnpl	C79783|D830027H13Rik|Hnrpl	heterogeneous nuclear ribonucleoprotein L	protein-coding
mm_118745.1	chr14	22320675	22320684	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	222119	NR_046307	74896	Mm.444661	NR_046307		4930405A10Rik	4930456G20Rik	RIKEN cDNA 4930405A10 gene	ncRNA
mm_133643.1	chr16	91739272	91739285	+	1	NA	intron (NM_001110275, intron 1 of 28)	B4A|SINE|B4	9907	NM_010587	16443	Mm.40546	NM_010587	ENSMUSG00000022957	Itsn1	AA517634|AA545208|AI316805|AI839402|AI848451|Ehsh1|Ese1|Itsn|Sh3p17	intersectin 1 (SH3 domain protein 1A)	protein-coding
mm_58332.1	chr6	146577826	146577839	-	1	NA	promoter-TSS (NM_026218)	promoter-TSS (NM_026218)	3	NM_138757	71177	Mm.271774	NM_138757	ENSMUSG00000040250	Asun	4933424B01Rik|Spata30	asunder, spermatogenesis regulator	protein-coding
mm_47670.1	chr5	127617373	127617426	-	1	NA	promoter-TSS (NM_133895)	promoter-TSS (NM_133895)	-7	NM_133895	100561	Mm.28506	NM_133895	ENSMUSG00000029416	Slc15a4	AA987064|AW742963|C130069N12Rik|PHT1|PTR4	solute carrier family 15, member 4	protein-coding
mm_120881.1	chr14	75323847	75323851	+	1	NA	exon (NM_026083, exon 10 of 19)	exon (NM_026083, exon 10 of 19)	39476	NM_026083	67302	Mm.74704	NM_026083	ENSMUSG00000022000	Zc3h13	2600010B19Rik|3110050K21Rik|4930570G11Rik|C87618	zinc finger CCCH type containing 13	protein-coding
mm_126993.1	chr15	94629149	94629159	+	1	NA	promoter-TSS (NM_178789)	promoter-TSS (NM_178789)	-31	NM_178789	320709	Mm.74873	NM_178789	ENSMUSG00000063296	Tmem117	B930062P21Rik	transmembrane protein 117	protein-coding
mm_134711.1	chr16	22894424	22894441	-	1	NA	promoter-TSS (NR_110508)	promoter-TSS (NR_110508)	-46	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_37193.1	chr4	117496910	117496918	-	1	NA	5' UTR (NM_025739, exon 1 of 15)	5' UTR (NM_025739, exon 1 of 15)	138	NM_025739	66743	Mm.318331	NM_025739	ENSMUSG00000028677	Rnf220	4732477A13|4931406I20Rik|5730503K05Rik|AV302541	ring finger protein 220	protein-coding
mm_40669.1	chr5	65392643	65392647	+	1	NA	intron (NM_001310612, intron 2 of 10)	intron (NM_001310612, intron 2 of 10)	1148	NM_001310612	79464	Mm.195776	NM_024471	ENSMUSG00000029199	Lias	2900022L22Rik|4933425M12Rik|7a5ex|C77512|LS|lip-syn	lipoic acid synthetase	protein-coding
mm_773.1	chr1	44211722	44211731	+	1	NA	intron (NM_207281, intron 2 of 4)	intron (NM_207281, intron 2 of 4)	7205	NM_207281	403183	Mm.336176	NM_207281	ENSMUSG00000046828	Mettl21e	4832428D23Rik|Gm991	methyltransferase like 21E	protein-coding
mm_159878.1	chr6	5383287	5383287	+	1	NA	promoter-TSS (NM_023048)	promoter-TSS (NM_023048)	-99	NM_023048	65255	Mm.51340	NM_023048	ENSMUSG00000042607	Asb4	8430401O13Rik|AV117194|AW060255	ankyrin repeat and SOCS box-containing 4	protein-coding
mm_168440.1	chr11	37752433	37752439	+	1	NA	Intergenic	Intergenic	93447	NR_131154	100039148	Mm.120467	NR_131154	ENSMUSG00000087388	Gm12128	OTTMUSG00000005422	predicted gene 12128	ncRNA
mm_58739.1	chr7	13030955	13030966	+	1	NA	TTS (NM_011588)	TTS (NM_011588)	3817	NM_026885	68953	Mm.295670	NM_026885	ENSMUSG00000033916	Chmp2a	1500016L11Rik	charged multivesicular body protein 2A	protein-coding
mm_28557.1	chr3	93433941	93433962	-	1	NA	Intergenic	Intergenic	5460	NR_039585	100628630		NR_039585	ENSMUSG00000093269	Mir5124a	Mir5124|mmu-mir-5124|mmu-mir-5124a|mu-mir-5124	microRNA 5124a	ncRNA
mm_1612.1	chr1	74391417	74391477	+	1	NA	promoter-TSS (NM_153088)	promoter-TSS (NM_153088)	-162	NM_153088	227292	Mm.165042	NM_153088	ENSMUSG00000026176	Ctdsp1	GIP|NLIIF|Nif3|SCP1	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 1	protein-coding
mm_75114.1	chr8	34260529	34260573	-	1	NA	Intergenic	L1MA8|LINE|L1	-93839	NR_105820	102465211		NR_105820	ENSMUSG00000098785	Mir6395	Gm27561|mmu-mir-6395	microRNA 6395	ncRNA
mm_170824.1	chr2	176708307	176708326	+	1	NA	promoter-TSS (NM_001099327)	promoter-TSS (NM_001099327)	-37	NM_001099327	100043387	Mm.444048	NM_001099327	ENSMUSG00000078878	Gm14305	OTTMUSG00000016251	predicted gene 14305	protein-coding
mm_144410.1	chr18	20961424	20961467	+	1	NA	intron (NM_026301, intron 1 of 5)	CpG	16820	NM_026301	67664	Mm.45980	NM_026301	ENSMUSG00000033107	Rnf125	4930553F04Rik	ring finger protein 125	protein-coding
mm_1735.1	chr1	75400175	75400185	+	1	NA	promoter-TSS (NM_001173477)	promoter-TSS (NM_001173477)	95	NM_001173477	11790	Mm.275397	NM_007463	ENSMUSG00000026207	Speg	AW125581|Apeg1|BPEG|D1Bwg1450e|SPEGalpha|SPEGbeta|mKIAA1297	SPEG complex locus	protein-coding
mm_107978.1	chr12	72945679	72945688	+	1	NA	TTS (NM_011384)	TTS (NM_011384)	5801	NM_011384	20476	Mm.57138	NM_011384	ENSMUSG00000021099	Six6	Optx2|Six9	sine oculis-related homeobox 6	protein-coding
mm_119281.1	chr14	34319877	34319888	+	1	NA	exon (NM_008133, exon 2 of 13)	exon (NM_008133, exon 2 of 13)	9155	NM_008133	14661	Mm.10600	NM_008133	ENSMUSG00000021794	Glud1	AI118167|Gdh-X|Glud|Gludl	glutamate dehydrogenase 1	protein-coding
mm_8400.1	chr1	151500795	151500841	-	1	NA	promoter-TSS (NM_011277)	promoter-TSS (NM_011277)	5	NM_011277	19821	Mm.474038	NM_011277	ENSMUSG00000026484	Rnf2	AI326319|AI450156|AU019207|Ring1B|dinG	ring finger protein 2	protein-coding
mm_99597.1	chr11	104329958	104329969	+	1	NA	3' UTR (NM_010838, exon 10 of 10)	3' UTR (NM_010838, exon 10 of 10)	98527	NM_001285454	17762	Mm.1287	NM_010838	ENSMUSG00000018411	Mapt	AI413597|AW045860|Mtapt|Tau	microtubule-associated protein tau	protein-coding
mm_92240.1	chr10	69556452	69556461	-	1	NA	intron (NM_170730, intron 1 of 17)	intron (NM_170730, intron 1 of 17)	22748	NM_146005	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_100246.1	chr11	117277390	117277402	+	1	NA	intron (NM_001113487, intron 1 of 10)	intron (NM_001113487, intron 1 of 10)	11150	NM_001113487	53860	Mm.38450	NM_017380	ENSMUSG00000059248	Sept9	MSF1|Msf|PNUTL4|Sint1	septin 9	protein-coding
mm_100129.1	chr11	115971233	115971276	+	1	NA	Intergenic	Intergenic	-3471	NM_001005608	192897	Mm.213873	NM_133663	ENSMUSG00000020758	Itgb4	AA407042|C230078O20|CD104	integrin beta 4	protein-coding
mm_145180.1	chr18	47331461	47331469	+	1	NA	intron (NM_001311097, intron 1 of 17)	intron (NM_001311097, intron 1 of 17)	37403	NM_018744	20358	Mm.40909	NM_018744	ENSMUSG00000019647	Sema6a	A730020P05Rik|AI851735|Sema6A-1|Semaq|VIa	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A	protein-coding
mm_31525.1	chr4	54947999	54948054	+	1	NA	promoter-TSS (NM_172867)	promoter-TSS (NM_172867)	81	NM_172867	242466	Mm.102904	NM_172867	ENSMUSG00000060206	Zfp462	6030417H05|9430078C22Rik|Gt4-2|Zfpip	zinc finger protein 462	protein-coding
mm_63173.1	chr7	125368951	125368961	+	1	NA	promoter-TSS (NM_001145759)	promoter-TSS (NM_001145759)	95	NM_001145759	75861	Mm.349600	NM_001145759		4930571K23Rik	AI428146	RIKEN cDNA 4930571K23 gene	protein-coding
mm_39081.1	chr4	154361345	154361347	-	1	NA	intron (NM_001177995, intron 4 of 15)	intron (NM_001177995, intron 4 of 15)	-61451	NM_001112744	230972	Mm.38481	NM_001112744	ENSMUSG00000029032	Arhgef16	-	Rho guanine nucleotide exchange factor (GEF) 16	protein-coding
mm_35339.1	chr4	31998739	31998742	-	1	NA	intron (NM_009316, intron 12 of 16)	U4|snRNA|snRNA	34633	NM_172688	26409	Mm.258589	NM_009316	ENSMUSG00000028284	Map3k7	B430101B05|C87327|Tak1	mitogen-activated protein kinase kinase kinase 7	protein-coding
mm_111165.1	chr12	83590908	83590912	-	1	NA	intron (NM_183154, intron 2 of 11)	ID_B1|SINE|B4	6237	NM_183154	217695	Mm.59257	NM_183154	ENSMUSG00000042628	Zfyve1	DFCP1|G630053K23|TAFF1|ZNFN2A1|mKIAA1589	zinc finger, FYVE domain containing 1	protein-coding
mm_22451.1	chr2	181864199	181864233	-	1	NA	promoter-TSS (NM_025901)	promoter-TSS (NM_025901)	-144	NM_025901	67005	Mm.271986	NM_025901	ENSMUSG00000038628	Polr3k	12.3kDa|1500004O14Rik|AI196849|AU014893|C11|RPC10|RPC11	polymerase (RNA) III (DNA directed) polypeptide K	protein-coding
mm_531.1	chr1	37886361	37886364	+	1	NA	intron (NM_026913, intron 1 of 6)	intron (NM_026913, intron 1 of 6)	4049	NM_026913	69028	Mm.63984	NM_026913	ENSMUSG00000026088	Mitd1	1500032H18Rik	MIT, microtubule interacting and transport, domain containing 1	protein-coding
mm_178.1	chr1	13669002	13669040	+	1	NA	intron (NM_001011873, intron 1 of 3)	intron (NM_001011873, intron 1 of 3)	250	NM_001011873	381246	Mm.311142	NM_001011873	ENSMUSG00000067813	Xkr9	Gm1620|XRG9	X-linked Kx blood group related 9	protein-coding
mm_61898.1	chr7	90129499	90129527	+	1	NA	promoter-TSS (NM_001252521)	promoter-TSS (NM_001252521)	-39	NR_046006	78329	Mm.389940	NR_046006	ENSMUSG00000097162	2310010J17Rik	-	RIKEN cDNA 2310010J17 gene	ncRNA
mm_162131.1	chrX	73148779	73148779	+	1	NA	promoter-TSS (NM_001111293)	promoter-TSS (NM_001111293)	-62	NM_001111293	627081	Mm.255790	NM_001111293	ENSMUSG00000072479	Xlr5b	OTTMUSG00000017646	X-linked lymphocyte-regulated 5B	protein-coding
mm_17949.1	chr2	36136815	36136845	-	1	NA	promoter-TSS (NM_026434)	promoter-TSS (NM_026434)	-126	NR_027515	67889	Mm.205937	NM_026434	ENSMUSG00000026889	Rbm18	2010004P11Rik|AU015530	RNA binding motif protein 18	protein-coding
mm_126710.1	chr15	85239320	85239330	+	1	NA	exon (NM_010180, exon 11 of 17)	exon (NM_010180, exon 11 of 17)	33317	NM_010180	14114	Mm.297992	NM_010180	ENSMUSG00000006369	Fbln1	-	fibulin 1	protein-coding
mm_41141.1	chr5	87887492	87887520	+	1	NA	exon (NM_027128, exon 4 of 10)	exon (NM_027128, exon 4 of 10)	1811	NM_027128	69592	Mm.389652	NM_027128	ENSMUSG00000009580	Odam	2310011G06Rik|APIN	odontogenic, ameloblast asssociated	protein-coding
mm_28259.1	chr3	88570528	88570532	-	1	NA	TTS (NM_033526)	TTS (NM_033526)	-9141	NM_025448	66256	Mm.7091	NM_025448	ENSMUSG00000041355	Ssr2	1500032E05Rik|AI315033|AU020133|TLAP|TRAPB|TRAPbeta	signal sequence receptor, beta	protein-coding
mm_28111.1	chr3	86548608	86548620	-	1	NA	promoter-TSS (NM_011839)	promoter-TSS (NM_011839)	-331	NM_011839	23937	Mm.389466	NM_011839	ENSMUSG00000057777	Mab21l2	-	mab-21-like 2 (C. elegans)	protein-coding
mm_50316.1	chr6	47877644	47877708	+	1	NA	exon (NM_146175, exon 1 of 8)	exon (NM_146175, exon 1 of 8)	121	NM_146175	101095	Mm.440186	NM_146175	ENSMUSG00000025821	Zfp282	AI449432|C81429|E430019K09Rik|HUB1	zinc finger protein 282	protein-coding
mm_46843.1	chr5	113413070	113413079	-	1	NA	Intergenic	Intergenic	55780	NM_001012726	503692	Mm.348794	NM_001012726	ENSMUSG00000053873	Aym1	-	activator of yeast meiotic promoters 1	protein-coding
mm_38258.1	chr4	136835968	136835982	-	1	NA	promoter-TSS (NM_010142)	promoter-TSS (NM_010142)	37	NM_001290753	13844	Mm.250981	NM_010142	ENSMUSG00000028664	Ephb2	Cek5|Drt|ETECK|Erk|Hek5|Nuk|Prkm5|Qek5|Sek3|Tyro5	Eph receptor B2	protein-coding
mm_10664.1	chr2	20765845	20765851	+	1	NA	intron (NM_029895, intron 8 of 18)	(T)n|Simple_repeat|Simple_repeat	201873	NM_001081364	71435	Mm.28507	NM_001081364	ENSMUSG00000036591	Arhgap21	5530401C11Rik|AA416458|ARHGAP10	Rho GTPase activating protein 21	protein-coding
mm_111534.1	chr12	100744964	100744965	-	1	NA	Intergenic	Intergenic	-19844	NM_153587	73086	Mm.220417	NM_153587	ENSMUSG00000021180	Rps6ka5	3110005L17Rik|6330404E13Rik|AI854034|MSK1|MSPK1|RLPK|RLSK|S6K-alpha-5	ribosomal protein S6 kinase, polypeptide 5	protein-coding
mm_140117.1	chr17	78916642	78916677	+	1	NA	5' UTR (NM_001177403, exon 1 of 5)	5' UTR (NM_001177403, exon 1 of 5)	160	NM_001177402	68554	Mm.391820	NM_001177402	ENSMUSG00000062691	Cebpzos	1110001A16Rik	CCAAT/enhancer binding protein (C/EBP), zeta, opposite strand	protein-coding
mm_40203.1	chr5	37028330	37028376	+	1	NA	Intergenic	CpG	-22504	NM_178394	76071	Mm.85280	NM_178394	ENSMUSG00000063646	Jakmip1	5830437M04Rik|C330021K24Rik|Gababrbp|Marlin-1	janus kinase and microtubule interacting protein 1	protein-coding
mm_137670.1	chr17	28769328	28769376	+	1	NA	promoter-TSS (NM_011950)	promoter-TSS (NM_011950)	35	NM_011950	26415	Mm.27970	NM_011950	ENSMUSG00000004864	Mapk13	SAPK4|Serk4	mitogen-activated protein kinase 13	protein-coding
mm_97808.1	chr11	82961701	82961743	+	1	NA	3' UTR (NM_183201, exon 6 of 6)	3' UTR (NM_183201, exon 6 of 6)	-1041	NR_045932	76392	Mm.295205	NR_045932	ENSMUSG00000086327	Slfn5os	1700003F17Rik	schlafen 5, opposite strand	ncRNA
mm_21381.1	chr2	157447946	157447950	-	1	NA	intron (NM_009271, intron 2 of 14)	L1M4|LINE|L1	23655	NM_001025395	20779	Mm.22845	NM_009271	ENSMUSG00000027646	Src	AW259666|pp60c-src	Rous sarcoma oncogene	protein-coding
mm_101944.1	chr11	50210789	50210793	-	1	NA	promoter-TSS (NM_011018)	promoter-TSS (NM_011018)	29	NM_001290769	18412	Mm.40828	NM_011018	ENSMUSG00000015837	Sqstm1	A170|OSF-6|Osi|STAP|STONE14|p62	sequestosome 1	protein-coding
mm_28655.1	chr3	95232162	95232165	-	1	NA	intron (NM_001038708, intron 2 of 4)	intron (NM_001038708, intron 2 of 4)	3220	NM_001038708	57912	Mm.28189	NM_172395	ENSMUSG00000046722	Cdc42se1	1300002M12Rik|AW558204|Cdcse1|SCIP1|Spec1	CDC42 small effector 1	protein-coding
mm_24858.1	chr3	95882754	95882777	+	1	NA	promoter-TSS (NM_001033302)	promoter-TSS (NM_001033302)	-537	NM_001033302	229599	Mm.331218	NM_001033302	ENSMUSG00000038550	Ciart	Chrono|Gm129	circadian associated repressor of transcription	protein-coding
mm_78152.1	chr9	21017847	21017857	+	1	NA	intron (NM_010493, intron 1 of 6)	intron (NM_010493, intron 1 of 6)	1912	NM_010493	15894	Mm.435508	NM_010493	ENSMUSG00000037405	Icam1	CD54|Icam-1|Ly-47|MALA-2	intercellular adhesion molecule 1	protein-coding
mm_71225.1	chr8	40902495	40902523	+	1	NA	exon (NM_001044740, exon 4 of 12)	exon (NM_001044740, exon 4 of 12)	-23724	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_27995.1	chr3	82548037	82548054	-	1	NA	promoter-TSS (NM_001205099)	promoter-TSS (NM_001205099)	40	NM_008731	18167	Mm.1433	NM_008731	ENSMUSG00000028004	Npy2r	NPY2-R	neuropeptide Y receptor Y2	protein-coding
mm_59769.1	chr7	28834055	28834060	+	1	NA	promoter-TSS (NM_010707)	promoter-TSS (NM_010707)	-113	NM_010707	16857	Mm.210336	NM_010707		Lgals6	galectin-6	lectin, galactose binding, soluble 6	protein-coding
mm_20982.1	chr2	151974204	151974217	-	1	NA	promoter-TSS (NM_001289151)	promoter-TSS (NM_001289151)	-229	NM_028666	73847	Mm.272444	NM_028666	ENSMUSG00000027459	Fam110a	1700008J10Rik|5430432M24Rik|AI747080	family with sequence similarity 110, member A	protein-coding
mm_45750.1	chr5	86676347	86676369	-	1	NA	promoter-TSS (NM_177024)	promoter-TSS (NM_177024)	-60	NM_177024	319875	Mm.253994	NM_177024	ENSMUSG00000035861	Tmprss11b	9930019B18Rik|Tmprss11bnl	transmembrane protease, serine 11B	protein-coding
mm_21428.1	chr2	158258946	158258963	-	1	NA	intron (NM_177850, intron 1 of 14)	intron (NM_177850, intron 1 of 14)	713	NM_177850	329547	Mm.260883	NM_177850	ENSMUSG00000052922	Bpi	9230105K17Rik|Bpifd1	bactericidal permeablility increasing protein	protein-coding
mm_90116.1	chr10	117277852	117277912	+	1	NA	3' UTR (NM_017372, exon 4 of 4)	3' UTR (NM_017372, exon 4 of 4)	4390	NM_017372	17105	Mm.45436	NM_017372	ENSMUSG00000069516	Lyz2	AI326280|Lys|Lysm|Lyzf2|Lyzs|Lzm|Lzm-s1|Lzp	lysozyme 2	protein-coding
mm_54077.1	chr6	14755301	14755317	-	1	NA	promoter-TSS (NM_080464)	promoter-TSS (NM_080464)	-35	NM_080464	140491	Mm.209429	NM_080464	ENSMUSG00000042717	Ppp1r3a	GM|RG1|RGL	protein phosphatase 1, regulatory (inhibitor) subunit 3A	protein-coding
mm_968.1	chr1	58183499	58183499	+	1	NA	exon (NM_023617, exon 31 of 35)	exon (NM_023617, exon 31 of 35)	-26898	NM_023631	71872	Mm.244525	NM_023631	ENSMUSG00000038242	Aox4	2310003G12Rik|Aoh2	aldehyde oxidase 4	protein-coding
mm_157257.1	chrX	19153870	19153906	-	1	NA	Intergenic	Intergenic	-6917	NR_029807	723828		NR_029807	ENSMUSG00000065471	Mir222	Mirn222|mir-222|mmu-mir-222	microRNA 222	ncRNA
mm_44497.1	chr5	23684648	23684652	-	1	NA	Intergenic	MLT1F1|LTR|ERVL-MaLR	28017	NR_038090	433855	Mm.205125	NR_015554	ENSMUSG00000105987	AI506816	-	expressed sequence AI506816	ncRNA
mm_141450.1	chr17	30135366	30135396	-	1	NA	exon (NM_148926, exon 3 of 5)	exon (NM_148926, exon 3 of 5)	121154	NR_105839	102465223		NR_105839	ENSMUSG00000098522	Mir6412	Gm27364|mmu-mir-6412	microRNA 6412	ncRNA
mm_7868.1	chr1	132634691	132634693	-	1	NA	exon (NM_001160317, exon 5 of 28)	exon (NM_001160317, exon 5 of 28)	8166	NM_001160316	269116	Mm.326702	NM_182716	ENSMUSG00000026442	Nfasc	AA387016|D430023G06Rik|NF|mKIAA0756	neurofascin	protein-coding
mm_92630.1	chr10	80323122	80323133	-	1	NA	exon (NM_008793, exon 12 of 15)	exon (NM_008793, exon 12 of 15)	-2579	NM_025521	66374	Mm.383824	NM_025521	ENSMUSG00000020133	2310011J03Rik	AI452186|AW545358	RIKEN cDNA 2310011J03 gene	protein-coding
mm_115409.1	chr13	114803273	114803314	+	1	NA	Intergenic	ORR1C1-int|LTR|ERVL-MaLR	-14944	NM_013826	17434	Mm.19027	NM_013826	ENSMUSG00000015536	Mocs2	AI415403	molybdenum cofactor synthesis 2	protein-coding
mm_35006.1	chr4	3089569	3089587	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	-82505	NM_001167534	100312470	Mm.480297	NM_001167534	ENSMUSG00000094798	Vmn1r2	Gm11776|OTTMUSG00000004179	vomeronasal 1 receptor 2	protein-coding
mm_2703.1	chr1	127978366	127978382	+	1	NA	intron (NM_027678, intron 12 of 20)	intron (NM_027678, intron 12 of 20)	109601	NM_178690	226407	Mm.489713	NM_178690	ENSMUSG00000036104	Rab3gap1	1700003B17Rik|4732493F09Rik|AL117896|Rab3gap|p130	RAB3 GTPase activating protein subunit 1	protein-coding
mm_108326.1	chr12	79770440	79770442	+	1	NA	intron (NM_009014, intron 9 of 10)	intron (NM_009014, intron 9 of 10)	154292	NR_131075	77290	Mm.395042	NR_131073		9430078K24Rik	-	RIKEN cDNA 9430078K24 gene	ncRNA
mm_160198.1	chr7	79702830	79702830	-	1	NA	exon (NM_010626, exon 11 of 18)	exon (NM_010626, exon 11 of 18)	11356	NM_010626	16576	Mm.101633	NM_010626	ENSMUSG00000050382	Kif7	-	kinesin family member 7	protein-coding
mm_152957.1	chr19	29325314	29325371	-	1	NA	promoter-TSS (NM_013754)	promoter-TSS (NM_013754)	-24	NM_013754	27356	Mm.306511	NM_013754	ENSMUSG00000050957	Insl6	RIF1	insulin-like 6	protein-coding
mm_86855.1	chr10	21827245	21827255	+	1	NA	Intergenic	(T)n|Simple_repeat|Simple_repeat	-54934	NM_001161845	20393	Mm.28405	NM_011361	ENSMUSG00000019970	Sgk1	Sgk	serum/glucocorticoid regulated kinase 1	protein-coding
mm_102153.1	chr11	53683299	53683337	-	1	NA	exon (NM_009012, exon 13 of 25)	exon (NM_009012, exon 13 of 25)	24001	NM_009012	19360	Mm.4888	NM_009012	ENSMUSG00000020380	Rad50	Mrell|Rad50l	RAD50 double strand break repair protein	protein-coding
mm_97830.1	chr11	83064445	83064455	+	1	NA	promoter-TSS (NM_011408)	promoter-TSS (NM_011408)	-662	NM_011408	20556	Mm.278689	NM_011408	ENSMUSG00000072620	Slfn2	Shlf2	schlafen 2	protein-coding
mm_69536.1	chr7	135695091	135695101	-	1	NA	exon (NM_001081117, exon 12 of 14)	exon (NM_001081117, exon 12 of 14)	21283	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_23712.1	chr3	69004712	69004731	+	1	NA	promoter-TSS (NM_133786)	promoter-TSS (NM_133786)	-151	NM_026641	68259	Mm.389451	NM_026641	ENSMUSG00000027778	Ift80	4921524P20Rik|Wdr56|mKIAA1374	intraflagellar transport 80	protein-coding
mm_13898.1	chr2	120461015	120461025	+	1	NA	TTS (NM_172672)	TTS (NM_172672)	-2573	NM_001177799	12335	Mm.458021	NM_007601	ENSMUSG00000079110	Capn3	AI323605|Capa-3|Capa3|Lp82|p94	calpain 3	protein-coding
mm_6929.1	chr1	84891887	84891925	-	1	NA	intron (NM_025386, intron 2 of 3)	G-rich|Low_complexity|Low_complexity	43177	NM_027921	71781	Mm.158754	NM_027921	ENSMUSG00000026220	Slc16a14	1110004H10Rik	solute carrier family 16 (monocarboxylic acid transporters), member 14	protein-coding
mm_115488.1	chr13	3611018	3611034	-	1	NA	promoter-TSS (NM_134063)	promoter-TSS (NM_134063)	82	NM_134063	105203	Mm.221609	NM_134063	ENSMUSG00000033799	Fam208b	AI645998|Pap20|mKIAA2006	family with sequence similarity 208, member B	protein-coding
mm_51220.1	chr6	71369731	71369754	+	1	NA	Intergenic	Intergenic	-3685	NM_009857	12525	Mm.1858	NM_009857	ENSMUSG00000053977	Cd8a	BB154331|Ly-2|Ly-35|Ly-B|Lyt-2	CD8 antigen, alpha chain	protein-coding
mm_40430.1	chr5	53588753	53588767	+	1	NA	intron (NM_001080928, intron 1 of 10)	intron (NM_001080928, intron 1 of 10)	-1586	NM_009035	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_24225.1	chr3	88716885	88716905	+	1	NA	promoter-TSS (NM_001163310)	promoter-TSS (NM_001163310)	41	NM_001163310	19769	Mm.4009	NM_009069	ENSMUSG00000028057	Rit1	RIBB|ROC1|Rit	Ras-like without CAAX 1	protein-coding
mm_34146.1	chr4	139352590	139352621	+	1	NA	promoter-TSS (NM_146157)	promoter-TSS (NM_146157)	18	NM_146157	230866	Mm.394288	NM_146157	ENSMUSG00000078517	Emc1	2700016F22Rik	ER membrane protein complex subunit 1	protein-coding
mm_96074.1	chr11	59848153	59848180	+	1	NA	promoter-TSS (NM_134029)	promoter-TSS (NM_134029)	93	NM_134029	103850	Mm.41761	NM_134029	ENSMUSG00000032615	Nt5m	2010013E09Rik|AI846937|dNT-2	5',3'-nucleotidase, mitochondrial	protein-coding
mm_22090.1	chr2	168767191	168767206	-	1	NA	promoter-TSS (NM_201396)	promoter-TSS (NM_201396)	3	NM_201395	99377	Mm.434054	NM_175303	ENSMUSG00000027547	Sall4	5730441M18Rik|AA407717|AL022809|AW536104|C330011P20Rik|C78083|C78563|Tex20	sal-like 4 (Drosophila)	protein-coding
mm_89946.1	chr10	111282150	111282174	+	1	NA	exon (NM_001003717, exon 16 of 23)	exon (NM_001003717, exon 16 of 23)	-16517	NM_027914	71769	Mm.45256	NM_027914	ENSMUSG00000035759	Bbs10	1300007O09Rik|AI452285	Bardet-Biedl syndrome 10 (human)	protein-coding
mm_155540.1	chrX	74305093	74305106	+	1	NA	promoter-TSS (NM_010273)	promoter-TSS (NM_010273)	87	NM_010273	14567	Mm.205830	NM_010273	ENSMUSG00000015291	Gdi1	GDIA|GDIalpha	guanosine diphosphate (GDP) dissociation inhibitor 1	protein-coding
mm_127583.1	chr15	102326370	102326387	+	1	NA	intron (NM_027044, intron 1 of 5)	intron (NM_027044, intron 1 of 5)	262	NM_027044	56612	Mm.158264	NM_020031	ENSMUSG00000001289	Pfdn5	1190001O17Rik|1700010A06Rik|D15Ertd697e|Eig1|MM-1	prefoldin 5	protein-coding
mm_57387.1	chr6	124829399	124829452	-	1	NA	promoter-TSS (NM_013538)	promoter-TSS (NM_013538)	59	NM_001326594	22225	Mm.3571	NM_013700	ENSMUSG00000038429	Usp5	AA407472|ISOT|ISOT-1|Ucht	ubiquitin specific peptidase 5 (isopeptidase T)	protein-coding
mm_24535.1	chr3	93279527	93279534	+	1	NA	Intergenic	Intergenic	-40219	NM_133698	68723	Mm.208047	NM_133698	ENSMUSG00000041991	Hrnr	1110033K19Rik|A530063N20Rik|S100a18	hornerin	protein-coding
mm_85364.1	chr9	103219824	103219895	-	1	NA	exon (NM_133977, exon 10 of 17)	exon (NM_133977, exon 10 of 17)	10427	NM_133977	22041	Mm.37214	NM_133977	ENSMUSG00000032554	Trf	AI266983|Cd176|HP|Tf|Tfn|hpx	transferrin	protein-coding
mm_160481.1	chr8	123350081	123350081	+	1	NA	intron (NM_172287, intron 2 of 14)	PB1D7|SINE|Alu	17368	NM_172287	234857	Mm.150200	NM_172287	ENSMUSG00000010154	Spire2	BC026502|Spir-2|Spir2	spire homolog 2 (Drosophila)	protein-coding
mm_32776.1	chr4	116700033	116700037	+	1	NA	TTS (NM_011034)	TTS (NM_011034)	8350	NM_025962	67096	Mm.252785	NM_025962	ENSMUSG00000028690	Mmachc	1810037K07Rik|CblC	methylmalonic aciduria cblC type, with homocystinuria	protein-coding
mm_27014.1	chr3	26027130	26027140	-	1	NA	intron (NM_138666, intron 3 of 7)	(TG)n|Simple_repeat|Simple_repeat	126172	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_172627.1	chr8	20398069	20398072	-	1	NA	intron (NR_028428, intron 5 of 5)	B3|SINE|B2	26744	NR_028428	381598	Mm.359054	NM_001024708	ENSMUSG00000071793	2610005L07Rik	2810038F24Rik|6720476A01Rik	cadherin 11 pseudogene	pseudo
mm_8088.1	chr1	135679235	135679264	-	1	NA	Intergenic	Intergenic	-49948	NM_007791	13007	Mm.196484	NM_007791	ENSMUSG00000026421	Csrp1	AA408841|AA959891|AW545626|CRP1|Csrp	cysteine and glycine-rich protein 1	protein-coding
mm_69327.1	chr7	128717461	128717466	-	1	NA	intron (NM_145955, intron 5 of 15)	intron (NM_145955, intron 5 of 15)	22966	NM_145955	210711	Mm.58882	NM_145955	ENSMUSG00000048170	Mcmbp	1110007A13Rik|AU017382|BC025641|MCM-BP	minichromosome maintenance complex binding protein	protein-coding
mm_60499.1	chr7	44478927	44478946	+	1	NA	Intergenic	L1M4c|LINE|L1	-5581	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_18061.1	chr2	41081944	41081946	-	1	NA	intron (NM_053011, intron 41 of 90)	L1_Mur2|LINE|L1	1365623	NR_105754	102465171		NR_105754	ENSMUSG00000098660	Mir6336	Gm27584|mmu-mir-6336	microRNA 6336	ncRNA
mm_125234.1	chr15	34143062	34143104	+	1	NA	TTS (NM_026002)	TTS (NM_026002)	60364	NM_026002	67154	Mm.130883	NM_026002	ENSMUSG00000022255	Mtdh	2610103J23Rik|3D3|3D3/Lyric|AEG-1|AV353288|D8Bwg1112e|Lyric	metadherin	protein-coding
mm_113433.1	chr13	34875489	34875515	+	1	NA	promoter-TSS (NM_013830)	promoter-TSS (NM_013830)	8	NM_013830	19134	Mm.10027	NM_013830	ENSMUSG00000021413	Prpf4b	2610037H07|Prp4|Prp4k|Prpk|cbp143	pre-mRNA processing factor 4B	protein-coding
mm_84249.1	chr9	62377576	62377626	-	1	NA	exon (NM_009672, exon 7 of 7)	exon (NM_009672, exon 7 of 7)	36258	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	protein-coding
mm_41609.1	chr5	96657125	96657126	+	1	NA	intron (NM_175473, intron 28 of 73)	intron (NM_175473, intron 28 of 73)	-136260	NM_013470	11745	Mm.7214	NM_013470	ENSMUSG00000029484	Anxa3	Anx3	annexin A3	protein-coding
mm_83758.1	chr9	51945844	51945846	-	1	NA	3' UTR (NM_001301728, exon 4 of 4)	3' UTR (NM_001301728, exon 4 of 4)	17757	NM_007996	14148	Mm.1061	NM_007996	ENSMUSG00000032051	Fdx1	-	ferredoxin 1	protein-coding
mm_20582.1	chr2	131148407	131148449	-	1	NA	intron (NM_001311138, intron 3 of 5)	intron (NM_001311138, intron 3 of 5)	11592	NM_026091	67326	Mm.27711	NM_026091	ENSMUSG00000027327	1700037H04Rik	-	RIKEN cDNA 1700037H04 gene	protein-coding
mm_120350.1	chr14	63943667	63943687	+	1	NA	promoter-TSS (NM_011446)	promoter-TSS (NM_011446)	-29	NM_011446	20680	Mm.42162	NM_011446	ENSMUSG00000063060	Sox7	-	SRY (sex determining region Y)-box 7	protein-coding
mm_159063.1	chr2	18055613	18055613	+	1	NA	intron (NM_010804, intron 1 of 22)	intron (NM_010804, intron 1 of 22)	376	NM_010804	17354	Mm.209175	NM_010804	ENSMUSG00000026743	Mllt10	Af10|B130021D15Rik|D630001B22Rik|mKIAA4140	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 10	protein-coding
mm_160222.1	chr7	101450577	101450577	+	1	NA	promoter-TSS (NM_001143849)	promoter-TSS (NM_001143849)	57	NM_001243758	207728	Mm.247564	NM_001008548	ENSMUSG00000030653	Pde2a	CGS-PDE|cGSPDE	phosphodiesterase 2A, cGMP-stimulated	protein-coding
mm_120169.1	chr14	60768121	60768137	+	1	NA	promoter-TSS (NM_183175)	promoter-TSS (NM_183175)	-5	NM_183175	239126	Mm.319636	NM_183175	ENSMUSG00000071347	C1qtnf9	9130217G22Rik|CTRP9|Ciqtnf9	C1q and tumor necrosis factor related protein 9	protein-coding
mm_67829.1	chr7	98350939	98350944	-	1	NA	3' UTR (NM_001168539, exon 2 of 2)	3' UTR (NM_001168539, exon 2 of 2)	10347	NM_001168540	244152	Mm.25317	NM_001024619	ENSMUSG00000049580	Tsku	9530051K01Rik|E2ig4|Lrrc54|Tsk	tsukushi, small leucine rich proteoglycan	protein-coding
mm_46890.1	chr5	113988744	113988748	-	1	NA	intron (NM_198109, intron 2 of 14)	B1_Mus2|SINE|Alu	5011	NM_198109	231637	Mm.389682	NM_198109	ENSMUSG00000042121	Ssh1	AW551225|Gm1394|Gm1395|SSH-1|SSH-1L	slingshot homolog 1 (Drosophila)	protein-coding
mm_94224.1	chr11	3223380	3223382	+	1	NA	intron (NM_023743, intron 6 of 18)	PB1D10|SINE|Alu	20362	NM_001166549	74203	Mm.255649	NM_023743	ENSMUSG00000020454	Eif4enif1	2610509L04Rik|A930019J01Rik|AA410001|AU021239|Clast4|D11Ertd166e	eukaryotic translation initiation factor 4E nuclear import factor 1	protein-coding
mm_89352.1	chr10	88162185	88162185	+	1	NA	intron (NM_028334, intron 5 of 9)	intron (NM_028334, intron 5 of 9)	15114	NM_028334	69736	Mm.222184	NM_027191	ENSMUSG00000035351	Nup37	2410003L22Rik|2810039M17Rik	nucleoporin 37	protein-coding
mm_129770.1	chr15	82764177	82764192	-	1	NA	promoter-TSS (NM_023623)	promoter-TSS (NM_023623)	-62	NM_023623	71754	Mm.443024	NM_023623	ENSMUSG00000068083	Cyp2d40	1300013D18Rik|CYPIID3|P450-DB3	cytochrome P450, family 2, subfamily d, polypeptide 40	protein-coding
mm_127609.1	chr15	102459194	102459220	+	1	NA	promoter-TSS (NM_025385)	promoter-TSS (NM_025385)	37	NM_025385	66151	Mm.393955	NM_025385	ENSMUSG00000023048	Prr13	1110020C13Rik|2010324E22Rik	proline rich 13	protein-coding
mm_56374.1	chr6	94159790	94159792	-	1	NA	intron (NR_130996, intron 1 of 1)	intron (NR_130996, intron 1 of 1)	77651	NR_130996	78178	Mm.452749	NR_130996	ENSMUSG00000045095	4930511A08Rik	-	RIKEN cDNA 4930511A08 gene	ncRNA
mm_158606.1	chrX	152342405	152342410	-	1	NA	promoter-TSS (NM_029836)	promoter-TSS (NM_029836)	77	NM_029836	52808	Mm.9997	NM_029836	ENSMUSG00000041096	Tspyl2	CDA1|CINAP|DENTT|DXBwg1396e|DXHXS1008E|E130307F10Rik	TSPY-like 2	protein-coding
mm_46475.1	chr5	105131435	105131461	-	1	NA	intron (NM_008620, intron 3 of 10)	GA-rich|Low_complexity|Low_complexity	8104	NM_008620	17472	Mm.440525	NM_008620	ENSMUSG00000079363	Gbp4	AW228052|Mag-2|Mpa-2|Mpa2	guanylate binding protein 4	protein-coding
mm_120019.1	chr14	55761386	55761401	+	1	NA	promoter-TSS (NM_020490)	promoter-TSS (NM_020490)	-35	NM_020490	57260	Mm.159670	NM_020490	ENSMUSG00000040432	Ltb4r2	5830462O07Rik|BLT2|LTB4-R 2|LTB4-R-2|LTB4-R2	leukotriene B4 receptor 2	protein-coding
mm_83438.1	chr9	44999284	44999298	-	1	NA	3' UTR (NM_007648, exon 8 of 8)	3' UTR (NM_007648, exon 8 of 8)	10299	NM_007648	12501	Mm.210361	NM_007648	ENSMUSG00000032093	Cd3e	AI504783|CD3|CD3epsilon|T3e	CD3 antigen, epsilon polypeptide	protein-coding
mm_158129.1	chrX	102934179	102934207	-	1	NA	promoter-TSS (NR_026596)	promoter-TSS (NR_026596)	30	NR_026596	331480	Mm.145294	NR_026596		Gm5126	EG331480	predicted pseudogene 5126	ncRNA
mm_66761.1	chr7	46728689	46728716	-	1	NA	3' UTR (NM_011316, exon 4 of 4)	3' UTR (NM_011316, exon 4 of 4)	3901	NM_011316	20211	Mm.3489	NM_011316	ENSMUSG00000040017	Saa4	Saa-4|Saa-5	serum amyloid A 4	protein-coding
mm_36250.1	chr4	63403331	63403350	-	1	NA	5' UTR (NM_001045514, exon 1 of 22)	5' UTR (NM_001045514, exon 1 of 22)	105	NM_001045514	100182	Mm.387725	NM_001045514	ENSMUSG00000039158	Akna	AI597013	AT-hook transcription factor	protein-coding
mm_140309.1	chr17	86167598	86167617	+	1	NA	promoter-TSS (NM_011104)	promoter-TSS (NM_011104)	-178	NM_011104	18754	Mm.24614	NM_011104	ENSMUSG00000045038	Prkce	5830406C15Rik|PKC[e]|PKCepsilon|Pkce|R75156	protein kinase C, epsilon	protein-coding
mm_6325.1	chr1	71609504	71609548	-	1	NA	exon (NM_001276413, exon 27 of 44)	exon (NM_001276413, exon 27 of 44)	43708	NM_010233	14268	Mm.193099	NM_010233	ENSMUSG00000026193	Fn1	E330027I09|Fn|Fn-1	fibronectin 1	protein-coding
mm_135791.1	chr16	57175640	57175646	-	1	NA	intron (NM_026254, intron 15 of 17)	RSINE1|SINE|B4	-8311	NM_023175	52633	Mm.383203	NM_023175	ENSMUSG00000022751	Nit2	1190017B19Rik|D16Ertd502e	nitrilase family, member 2	protein-coding
mm_40465.1	chr5	53647140	53647152	+	1	NA	intron (NM_001080928, intron 5 of 10)	B1_Mus2|SINE|Alu	51442	NR_024201	19866		NR_024201	ENSMUSG00000089083	Rnu7	-	U7 small nuclear RNA	snRNA
mm_135587.1	chr16	50591065	50591067	-	1	NA	promoter-TSS (NM_027046)	promoter-TSS (NM_027046)	88	NM_027046	69339	Mm.422869	NM_027046	ENSMUSG00000050685	Ccdc54	1700007N18Rik|AI644412|BB013989|NYD-SP17	coiled-coil domain containing 54	protein-coding
mm_69442.1	chr7	132984157	132984160	-	1	NA	TTS (NM_207302)	TTS (NM_207302)	31089	NM_001170744	13017	Mm.246240	NM_009980	ENSMUSG00000030970	Ctbp2	AA407280|D7Ertd45e|Gtrgeo6|Ribeye	C-terminal binding protein 2	protein-coding
mm_61990.1	chr7	91090913	91090927	+	1	NA	5' UTR (NM_011807, exon 1 of 23)	5' UTR (NM_011807, exon 1 of 23)	134	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_168575.1	chr1	17135542	17135542	+	1	NA	Intergenic	RLTR10A|LTR|ERVK	-9831	NM_010267	14545	Mm.18218	NM_010267	ENSMUSG00000025777	Gdap1	-	ganglioside-induced differentiation-associated-protein 1	protein-coding
mm_49770.1	chr6	34866350	34866386	+	1	NA	intron (NM_197986, intron 1 of 1)	intron (NM_197986, intron 1 of 1)	3222	NM_197986	68487	Mm.248440	NM_197986	ENSMUSG00000057137	Tmem140	1110007F12Rik	transmembrane protein 140	protein-coding
mm_8540.1	chr1	155084153	155084161	-	1	NA	Intergenic	Intergenic	15479	NM_010500	15939	Mm.12246	NM_010500	ENSMUSG00000056708	Ier5	-	immediate early response 5	protein-coding
mm_121892.1	chr14	21742910	21742918	-	1	NA	promoter-TSS (NM_013849)	promoter-TSS (NM_013849)	-35	NM_013849	27389	Mm.390674	NM_013849	ENSMUSG00000021768	Dusp13	DUSP13A|DUSP13B|Gm1203|LMW-DSP6|MDSP|TMDP|TS-DSP6	dual specificity phosphatase 13	protein-coding
mm_81447.1	chr9	109816539	109816549	+	1	NA	promoter-TSS (NM_183136)	promoter-TSS (NM_183136)	-83	NM_183136	78709	Mm.99613	NM_183136	ENSMUSG00000050074	Spink8	C630041L24Rik	serine peptidase inhibitor, Kazal type 8	protein-coding
mm_113894.1	chr13	49193862	49193917	+	1	NA	exon (NM_013610, exon 2 of 4)	exon (NM_013610, exon 2 of 4)	6342	NM_013610	18081	Mm.18503	NM_013610	ENSMUSG00000037966	Ninj1	AU024536	ninjurin 1	protein-coding
mm_163416.1	chr12	79253288	79253297	-	1	NA	intron (NM_001008550, intron 29 of 41)	intron (NM_001008550, intron 29 of 41)	42990	NM_001008550	211978	Mm.297919	NM_001008550	ENSMUSG00000066440	Zfyve26	4930465A13|9330197E15Rik|A630028O16Rik|Gm893|mKIAA0321	zinc finger, FYVE domain containing 26	protein-coding
mm_59436.1	chr7	27131221	27131252	+	1	NA	exon (NM_007817, exon 8 of 10)	exon (NM_007817, exon 8 of 10)	11281	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_86876.1	chr10	21997069	21997079	+	1	NA	exon (NM_001161847, exon 8 of 12)	exon (NM_001161847, exon 8 of 12)	2408	NM_011361	20393	Mm.28405	NM_011361	ENSMUSG00000019970	Sgk1	Sgk	serum/glucocorticoid regulated kinase 1	protein-coding
mm_94216.1	chr11	3163955	3164001	+	1	NA	intron (NM_030207, intron 9 of 32)	RLTR51B_Mm|LTR|ERVK?	29485	NM_030207	78887	Mm.394071	NM_030207	ENSMUSG00000023764	Sfi1	-	Sfi1 homolog, spindle assembly associated (yeast)	protein-coding
mm_10230.1	chr2	6342665	6342668	+	1	NA	intron (NM_001080548, intron 2 of 14)	intron (NM_001080548, intron 2 of 14)	-10070	NM_181399	98910	Mm.40673	NM_181399	ENSMUSG00000039046	Usp6nl	AI316785|RNTRE|TRE2NL|mKIAA0019	USP6 N-terminal like	protein-coding
mm_22309.1	chr2	180386794	180386797	-	1	NA	promoter-TSS (NR_040745)	promoter-TSS (NR_040745)	-910	NR_040745	320485	Mm.405172	NR_040745		B230312C02Rik	-	RIKEN cDNA B230312C02 gene	ncRNA
mm_109861.1	chr12	4874342	4874367	-	1	NA	promoter-TSS (NM_001033488)	promoter-TSS (NM_001033488)	5	NM_001033488	432628	Mm.154078	NM_001033488	ENSMUSG00000037336	Mfsd2b	Gm1964	major facilitator superfamily domain containing 2B	protein-coding
mm_123665.1	chr14	69244617	69244630	-	1	NA	3' UTR (NM_026331, exon 4 of 4)	3' UTR (NM_026331, exon 4 of 4)	40480	NM_026331	67712	Mm.293635	NM_026331	ENSMUSG00000034248	Slc25a37	1700020E22Rik|4930513O14Rik|4930526G11Rik|AI848481|C330015G08Rik|Mfrn|Mfrn1|Mscp|frascati|mitoferrin	solute carrier family 25, member 37	protein-coding
mm_163425.1	chr12	82073382	82073395	+	1	NA	Intergenic	Intergenic	-96628	NM_001167983	217692	Mm.261333	NM_172579	ENSMUSG00000042700	Sipa1l1	4931426N11Rik|AW213287|Spar|mKIAA0440	signal-induced proliferation-associated 1 like 1	protein-coding
mm_172290.1	chr6	95658061	95658062	+	1	NA	intron (NM_011507, intron 1 of 10)	intron (NM_011507, intron 1 of 10)	34821	NM_001326558	20917	Mm.371585	NM_011507	ENSMUSG00000061838	Suclg2	AF171077|AW556404|D6Wsu120e|G-SCS|GTPSCS|SCS-betaG	succinate-Coenzyme A ligase, GDP-forming, beta subunit	protein-coding
mm_63578.1	chr7	128117988	128117996	+	1	NA	3' UTR (NM_008401, exon 30 of 30)	3' UTR (NM_008401, exon 30 of 30)	-11576	NM_021334	16411	Mm.22378	NM_021334	ENSMUSG00000030789	Itgax	AI449405|Cd11c|Cr4|N418	integrin alpha X	protein-coding
mm_8769.1	chr1	160842648	160842650	-	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	-49711	NM_013862	29809	Mm.25833	NM_013862	ENSMUSG00000026721	Rabgap1l	5830411O09Rik|8430421H08Rik|9630005B12Rik|AW049894|HHL|Hh1|mKIAA0471	RAB GTPase activating protein 1-like	protein-coding
mm_165908.1	chr4	56419756	56419794	+	1	NA	Intergenic	Intergenic	321650	NM_025271	11471	Mm.251434	NM_025271	ENSMUSG00000070980	Actl7b	Tact1	actin-like 7b	protein-coding
mm_93545.1	chr10	116098641	116098648	-	1	NA	intron (NM_011217, intron 2 of 13)	intron (NM_011217, intron 2 of 13)	15273	NM_001161855	619332	Mm.391427	NM_001033821	ENSMUSG00000074734	4933416C03Rik	-	RIKEN cDNA 4933416C03 gene	protein-coding
mm_151085.1	chr19	47625369	47625389	+	1	NA	exon (NM_001164639, exon 12 of 18)	exon (NM_001164639, exon 12 of 18)	45360	NM_001164639	20874	Mm.281011	NM_009289	ENSMUSG00000025060	Slk	9A2|AV021402|AW411554|Etk4|SMAK|Stk2|mKIAA0204|mSLK	STE20-like kinase	protein-coding
mm_92863.1	chr10	81597602	81597629	-	1	NA	intron (NM_001346695, intron 4 of 13)	intron (NM_001346695, intron 4 of 13)	3285	NM_053254	114606	Mm.206764	NM_053254	ENSMUSG00000034758	Tle6	1810057E06Rik|Grg6	transducin-like enhancer of split 6	protein-coding
mm_53689.1	chr6	142413377	142413391	+	1	NA	promoter-TSS (NM_001242345)	promoter-TSS (NM_001242345)	-47	NM_001242345	319552	Mm.39649	NM_001242345	ENSMUSG00000071112	Spx	B230216G23Rik|Npq	spexin hormone	protein-coding
mm_133008.1	chr16	55973882	55973892	+	1	NA	promoter-TSS (NM_173026)	promoter-TSS (NM_173026)	83	NM_173026	271377	Mm.282814	NM_173026	ENSMUSG00000022601	Zbtb11	9230110G02Rik|ZNF-U69274	zinc finger and BTB domain containing 11	protein-coding
mm_61178.1	chr7	60145439	60145446	+	1	NA	Intergenic	Intergenic	-5223	NM_001082962	20646	Mm.274995	NM_013670	ENSMUSG00000102252	Snrpn	2410045I01Rik|HCERN3|Peg4|Pwcr1|SMN	small nuclear ribonucleoprotein N	protein-coding
mm_66406.1	chr7	44478430	44478441	-	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-6082	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_38027.1	chr4	133865317	133865337	-	1	NA	intron (NM_001285505, intron 10 of 21)	intron (NM_001285505, intron 10 of 21)	9404	NM_001285506	20111	Mm.301827	NM_009097	ENSMUSG00000003644	Rps6ka1	Mapkapk-1a|Rsk|Rsk-1|Rsk1|S6K-alpha-1|p90-Rsk1|p90Rsk1|p90S6K|p90rsk	ribosomal protein S6 kinase polypeptide 1	protein-coding
mm_84139.1	chr9	59284200	59284207	-	1	NA	Intergenic	Intergenic	-7369	NM_028121	72141	Mm.22456	NM_028121	ENSMUSG00000025236	Adpgk	2610017G09Rik|Adp-gk|C77577	ADP-dependent glucokinase	protein-coding
mm_61466.1	chr7	75610640	75610672	+	1	NA	exon (NM_029332, exon 7 of 37)	exon (NM_029332, exon 7 of 37)	155122	NM_029332	75547	Mm.216107	NM_029332	ENSMUSG00000066406	Akap13	1700026G02Rik|5730522G15Rik|5830460E08Rik|AKAP-13|AKAP-Lbc|BRX|Ht31|LBC|PROTO-LB|PROTO-LBC	A kinase (PRKA) anchor protein 13	protein-coding
mm_12674.1	chr2	75777176	75777193	+	1	NA	Intergenic	Intergenic	-54993	NM_172666	228061	Mm.31227	NM_172666	ENSMUSG00000042410	Agps	5832437L22|9930035G10Rik|AW123847|Adaps|Adas|Adhaps|Adps|Aldhpsy|bs2	alkylglycerone phosphate synthase	protein-coding
mm_49284.1	chr6	17648510	17648551	+	1	NA	exon (NM_007604, exon 2 of 10)	exon (NM_007604, exon 2 of 10)	11432	NM_007604	12343	Mm.392504	NM_007604	ENSMUSG00000015733	Capza2	1110053K06Rik|AW208808|Cappa2	capping protein (actin filament) muscle Z-line, alpha 2	protein-coding
mm_49162.1	chr6	13838680	13838701	+	1	NA	5' UTR (NM_001330667, exon 2 of 3)	5' UTR (NM_001330667, exon 2 of 3)	1252	NM_001330666	64450	Mm.167625	NM_145066	ENSMUSG00000048216	Gpr85	2900026B03Rik	G protein-coupled receptor 85	protein-coding
mm_154299.1	chr19	61224839	61224849	-	1	NA	3' UTR (NM_009970, exon 12 of 12)	3' UTR (NM_009970, exon 12 of 12)	3574	NM_009970	12982	Mm.287228	NM_009970	ENSMUSG00000059326	Csf2ra	CD116|Csfgmra|GM-CSF-Ra|GM-CSFR	colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)	protein-coding
mm_58828.1	chr7	16749093	16749104	+	1	NA	3' UTR (NM_198613, exon 5 of 5)	3' UTR (NM_198613, exon 5 of 5)	10654	NM_198613	232910	Mm.333597	NM_198613	ENSMUSG00000008036	Ap2s1	AI043088	adaptor-related protein complex 2, sigma 1 subunit	protein-coding
mm_171134.1	chr3	148901522	148901522	+	1	NA	intron (NM_001081298, intron 1 of 23)	intron (NM_001081298, intron 1 of 23)	53113	NM_001081298	99633	Mm.9776	NM_001081298	ENSMUSG00000028184	Adgrl2	AI450192|CIRL-2|Gm619|Lec1|Lphh1|Lphn2|mKIAA0786	adhesion G protein-coupled receptor L2	protein-coding
mm_128317.1	chr15	37968447	37968464	-	1	NA	exon (NM_001081359, exon 59 of 59)	exon (NM_001081359, exon 59 of 59)	-7400	NM_199476	382985	Mm.24738	NM_199476	ENSMUSG00000022292	Rrm2b	p53R2	ribonucleotide reductase M2 B (TP53 inducible)	protein-coding
mm_44869.1	chr5	34504461	34504464	-	1	NA	intron (NM_139064, intron 1 of 5)	B1_Mus1|SINE|Alu	9517	NM_139064	231130	Mm.28615	NM_139064	ENSMUSG00000059866	Tnip2	1810020H16Rik|ABIN-2|AI428870	TNFAIP3 interacting protein 2	protein-coding
mm_102479.1	chr11	60100000	60100019	-	1	NA	Intergenic	Intergenic	-5004	NM_009021	19377	Mm.296366	NM_009021	ENSMUSG00000062115	Rai1	Gt1	retinoic acid induced 1	protein-coding
mm_94410.1	chr11	5800148	5800184	+	1	NA	3' UTR (NM_001146309, exon 13 of 13)	3' UTR (NM_001146309, exon 13 of 13)	3630	NM_018870	56012	Mm.219627	NM_018870	ENSMUSG00000020475	Pgam2	-	phosphoglycerate mutase 2	protein-coding
mm_64227.1	chr7	141690334	141690348	+	1	NA	promoter-TSS (NM_023566)	promoter-TSS (NM_023566)	1	NM_023566	17831	Mm.2041	NM_023566		Muc2	2010015E03Rik|MCM|wnn	mucin 2	protein-coding
mm_101763.1	chr11	43601552	43601567	-	1	NA	promoter-TSS (NM_008375)	promoter-TSS (NM_008375)	3	NM_008375	16204	Mm.142716	NM_008375	ENSMUSG00000020405	Fabp6	GT|I-15P|I-BABP|ILBP|ILBP3|Illbp	fatty acid binding protein 6, ileal (gastrotropin)	protein-coding
mm_118170.1	chr13	105299749	105299775	-	1	NA	Intergenic	Intergenic	-6748	NM_027934	71816	Mm.317015	NM_027934	ENSMUSG00000021720	Rnf180	3110001E11Rik|Rines	ring finger protein 180	protein-coding
mm_3619.1	chr1	152682993	152683003	+	1	NA	intron (NM_001346117, intron 1 of 18)	intron (NM_001346117, intron 1 of 18)	-57781	NM_016846	19731	Mm.245270	NM_016846	ENSMUSG00000026482	Rgl1	Rgl|mKIAA0959	ral guanine nucleotide dissociation stimulator,-like 1	protein-coding
mm_137295.1	chr17	24779785	24779799	+	1	NA	Intergenic	Intergenic	-24590	NM_029197	75178	Mm.52592	NM_029197	ENSMUSG00000024155	Meiob	4930528F23Rik|MLZ-675	meiosis specific with OB domains	protein-coding
mm_164557.1	chr17	14943060	14943086	-	1	NA	promoter-TSS (NM_001083881)	promoter-TSS (NM_001083881)	51	NM_175173	71682	Mm.122698	NM_175173	ENSMUSG00000046991	Wdr27	0610012K18Rik	WD repeat domain 27	protein-coding
mm_29231.1	chr3	107213474	107213477	-	1	NA	exon (NM_001111143, exon 7 of 9)	exon (NM_001111143, exon 7 of 9)	8257	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_131308.1	chr16	11461846	11461862	+	1	NA	intron (NM_001290148, intron 6 of 13)	intron (NM_001290148, intron 6 of 13)	56206	NM_001290148	74478	Mm.325831	NM_028964	ENSMUSG00000071669	Snx29	4933437K13Rik|ENSMUSG00000079738|Gm11170|Gm1737|Gm930|Rundc2a	sorting nexin 29	protein-coding
mm_57506.1	chr6	125460657	125460668	-	1	NA	exon (NM_007657, exon 8 of 8)	exon (NM_007657, exon 8 of 8)	34093	NM_007657	12527	Mm.210676	NM_007657	ENSMUSG00000030342	Cd9	Tspan29	CD9 antigen	protein-coding
mm_115172.1	chr13	108046412	108046419	+	1	NA	intron (NM_001048250, intron 1 of 2)	intron (NM_001048250, intron 1 of 2)	1941	NM_001048250	75616	Mm.491164	NM_001048250	ENSMUSG00000071180	Smim15	2810008M24Rik	small integral membrane protein 15	protein-coding
mm_42194.1	chr5	112276760	112276770	+	1	NA	promoter-TSS (NM_009419)	promoter-TSS (NM_009419)	74	NM_009419	22022	Mm.250631	NM_009419	ENSMUSG00000029344	Tpst2	AI448750|D5Ucla3|Tango13b|grm|grt	protein-tyrosine sulfotransferase 2	protein-coding
mm_63057.1	chr7	121981737	121981771	+	1	NA	promoter-TSS (NM_001033318)	promoter-TSS (NM_001033318)	-61	NM_001033318	233824	Mm.442015	NM_001033318	ENSMUSG00000034951	Cog7	5630400E24Rik|Gm167	component of oligomeric golgi complex 7	protein-coding
mm_126233.1	chr15	78959943	78959962	+	1	NA	exon (NM_001039155, exon 6 of 8)	exon (NM_001039155, exon 6 of 8)	12228	NM_001039155	110253	Mm.123714	NM_138579	ENSMUSG00000033088	Triobp	AI428493|EST478828|Tara|mKIAA1662	TRIO and F-actin binding protein	protein-coding
mm_155391.1	chrX	71962972	71963013	+	1	NA	promoter-TSS (NM_001081135)	promoter-TSS (NM_001081135)	10	NM_001081135	208748	Mm.25626	NM_001081135	ENSMUSG00000033361	Prrg3	Gm368	proline rich Gla (G-carboxyglutamic acid) 3 (transmembrane)	protein-coding
mm_142856.1	chr17	51812338	51812345	-	1	NA	promoter-TSS (NM_001163630)	promoter-TSS (NM_001163630)	-287	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_23724.1	chr3	69016088	69016108	+	1	NA	exon (NM_133786, exon 6 of 24)	exon (NM_133786, exon 6 of 24)	6196	NR_029735	723949		NR_029735	ENSMUSG00000065606	Mir16-2	Mirn16-2|mir-16-2	microRNA 16-2	ncRNA
mm_130058.1	chr15	89180817	89180821	-	1	NA	promoter-TSS (NM_001284506)	promoter-TSS (NM_001284506)	-31	NM_138749	140570	Mm.267514	NM_138749	ENSMUSG00000036606	Plxnb2	Debt|plexin-B2	plexin B2	protein-coding
mm_115090.1	chr13	102706543	102706553	+	1	NA	TTS (NM_008533)	TTS (NM_008533)	12990	NM_008533	17079	Mm.373974	NM_008533	ENSMUSG00000021624	Cd180	F630107B15|Ly78|RP105	CD180 antigen	protein-coding
mm_23585.1	chr3	63976110	63976135	+	1	NA	promoter-TSS (NM_001033300)	promoter-TSS (NM_001033300)	-21	NM_001033300	229363	Mm.331051	NM_001033300	ENSMUSG00000027823	Gmps	670032|AA591640|AI047208|Gm9479	guanine monophosphate synthetase	protein-coding
mm_50219.1	chr6	42349792	42349800	+	1	NA	promoter-TSS (NM_001289618)	promoter-TSS (NM_001289618)	-32	NM_011777	22793	Mm.282303	NM_011777	ENSMUSG00000029860	Zyx	9530098H06Rik|R75157	zyxin	protein-coding
mm_116891.1	chr13	55349940	55349943	-	1	NA	intron (NM_025828, intron 6 of 7)	intron (NM_025828, intron 6 of 7)	12842	NM_025828	66890	Mm.38868	NM_025828	ENSMUSG00000021484	Lman2	1110003H06Rik|1300009F09Rik|AA408240|AL023023|AU040819|GP36B|VIP36	lectin, mannose-binding 2	protein-coding
mm_147632.1	chr18	58210732	58210744	-	1	NA	promoter-TSS (NM_010181)	promoter-TSS (NM_010181)	-812	NM_010181	14119	Mm.20271	NM_010181	ENSMUSG00000024598	Fbn2	BC063774|Fib-2|mKIAA4226|sne|sy	fibrillin 2	protein-coding
mm_165283.1	chr2	83812847	83812855	+	1	NA	exon (NM_175514, exon 1 of 8)	exon (NM_175514, exon 1 of 8)	123	NM_175514	241520	Mm.330351	NM_175514	ENSMUSG00000048388	Fam171b	D430039N05Rik	family with sequence similarity 171, member B	protein-coding
mm_70052.1	chr7	142650802	142650812	-	1	NA	TTS (NM_010514)	TTS (NM_010514)	4189	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_156628.1	chrX	155262512	155262522	+	1	NA	promoter-TSS (NM_019736)	promoter-TSS (NM_019736)	74	NM_019736	56360	Mm.268710	NM_019736	ENSMUSG00000025287	Acot9	0610041P13Rik|Acate2|C76421|MT-ACT48|MTE-2|U8|p48	acyl-CoA thioesterase 9	protein-coding
mm_154346.1	chrM	5401	5413	+	1	NA	NA	Intergenic	NA	NA								
mm_163665.1	chr13	78273990	78273992	-	1	NA	Intergenic	Intergenic	-75118	NM_010151	13865	Mm.439653	NM_010151	ENSMUSG00000069171	Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR-3|EAR3|Erbal3|SVP44|Tcfcoup1	nuclear receptor subfamily 2, group F, member 1	protein-coding
mm_128220.1	chr15	36367103	36367111	-	1	NA	Intergenic	Intergenic	-83960	NM_013923	30945	Mm.5181	NM_013923	ENSMUSG00000022280	Rnf19a	AA032313|Dorfin|Rnf19|UIP117|Ubce7ip2|XYbp	ring finger protein 19A	protein-coding
mm_158672.1	chrX	157598625	157598637	-	1	NA	promoter-TSS (NM_172307)	promoter-TSS (NM_172307)	84	NM_172307	270669	Mm.37577	NM_172307	ENSMUSG00000046873	Mbtps2	9630032G22Rik|AI662535	membrane-bound transcription factor peptidase, site 2	protein-coding
mm_121095.1	chr14	99310947	99310949	+	1	NA	intron (NM_009769, intron 3 of 3)	intron (NM_009769, intron 3 of 3)	12257	NM_009769	12224	Mm.30262	NM_009769	ENSMUSG00000005148	Klf5	4930520J07Rik|Bteb2|CKLF|IKLF	Kruppel-like factor 5	protein-coding
mm_104295.1	chr11	90390539	90390541	-	1	NA	5' UTR (NM_172563, exon 1 of 4)	5' UTR (NM_172563, exon 1 of 4)	377	NM_172563	217082	Mm.158903	NM_172563	ENSMUSG00000003949	Hlf	E230015K02Rik	hepatic leukemia factor	protein-coding
mm_12912.1	chr2	84840678	84840688	+	1	NA	promoter-TSS (NM_001083809)	promoter-TSS (NM_001083809)	57	NM_001083809	72401	Mm.22716	NM_024497	ENSMUSG00000027075	Slc43a1	2610016F07Rik|AA986141|Lat3|PB39|Pov1|R00504	solute carrier family 43, member 1	protein-coding
mm_49912.1	chr6	39033384	39033401	+	1	NA	intron (NM_011539, intron 9 of 12)	G-rich|Low_complexity|Low_complexity	34194	NR_040523	69986	Mm.490941	NR_040523	ENSMUSG00000100121	1700025N23Rik	-	RIKEN cDNA 1700025N23 gene	ncRNA
mm_16941.1	chr2	14987538	14987543	-	1	NA	3' UTR (NM_001309519, exon 13 of 13)	3' UTR (NM_001309519, exon 13 of 13)	61772	NM_001165942	74455	Mm.478923	NM_028950	ENSMUSG00000026707	Nsun6	4933403D21Rik|4933414E04Rik|NOPD1	NOL1/NOP2/Sun domain family member 6	protein-coding
mm_145257.1	chr18	52529189	52529199	+	1	NA	exon (NM_010728, exon 1 of 7)	exon (NM_010728, exon 1 of 7)	527	NM_001286181	16948	Mm.172	NM_010728	ENSMUSG00000024529	Lox	AI893619|TSC-160|rrg	lysyl oxidase	protein-coding
mm_44391.1	chr5	17829292	17829297	-	1	NA	intron (NM_007643, intron 2 of 14)	intron (NM_007643, intron 2 of 14)	6602	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_61042.1	chr7	49759540	49759563	+	1	NA	promoter-TSS (NM_001146052)	promoter-TSS (NM_001146052)	39	NM_001146052	53415	Mm.20801	NM_016865	ENSMUSG00000039745	Htatip2	AW111545|Cc3|Tip30	HIV-1 Tat interactive protein 2	protein-coding
mm_28511.1	chr3	92584000	92584014	-	1	NA	3' UTR (NM_008574, exon 2 of 2)	3' UTR (NM_008574, exon 2 of 2)	5017	NM_008574	17235	Mm.331192	NM_008574		Smcp	Mcs|Mcsp	sperm mitochondria-associated cysteine-rich protein	protein-coding
mm_156519.1	chrX	150589908	150589996	+	1	NA	promoter-TSS (NM_008824)	promoter-TSS (NM_008824)	31	NM_008824	18639	Mm.249131	NM_008824	ENSMUSG00000025271	Pfkfb1	PFK/FBPase 1	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1	protein-coding
mm_118244.1	chr13	111808751	111808766	-	1	NA	exon (NM_011945, exon 1 of 20)	exon (NM_011945, exon 1 of 20)	225	NM_011945	26401	Mm.15918	NM_011945	ENSMUSG00000021754	Map3k1	MAPKKK1|MEKK1|Mekk	mitogen-activated protein kinase kinase kinase 1	protein-coding
mm_1754.1	chr1	75509748	75509769	+	1	NA	exon (NM_010564, exon 2 of 2)	exon (NM_010564, exon 2 of 2)	2149	NM_001329843	16322	Mm.1100	NM_010564	ENSMUSG00000032968	Inha	AW555078	inhibin alpha	protein-coding
mm_140555.1	chr17	7827290	7827310	-	1	NA	Intergenic	CpG	-22326	NM_001081416	68655	Mm.379161	NM_001081416	ENSMUSG00000071984	Fndc1	1110027O12Rik|1110051A18Rik|mKIAA1866	fibronectin type III domain containing 1	protein-coding
mm_114326.1	chr13	60610556	60610559	+	1	NA	intron (NM_029653, intron 2 of 25)	intron (NM_029653, intron 2 of 25)	8346	NM_134062	69635	Mm.24103	NM_029653	ENSMUSG00000021559	Dapk1	D13Ucla1|DAP-Kinase	death associated protein kinase 1	protein-coding
mm_71664.1	chr8	60640854	60640873	+	1	NA	intron (NM_001293769, intron 1 of 1)	intron (NM_001293769, intron 1 of 1)	8038	NM_001293769	71306	Mm.23242	NM_027756	ENSMUSG00000031647	Mfap3l	4933428A15Rik|5430405D20Rik|AI461995|AW125052|NYD-sp9|mKIAA0626	microfibrillar-associated protein 3-like	protein-coding
mm_38145.1	chr4	134853854	134853879	-	1	NA	promoter-TSS (NM_025382)	promoter-TSS (NM_025382)	-521	NM_025382	66146	Mm.99793	NM_025382	ENSMUSG00000028826	Tmem57	1110007C24Rik|9230118A01Rik|AI317300|AI606104|C61	transmembrane protein 57	protein-coding
mm_124644.1	chr15	4898206	4898224	+	1	NA	promoter-TSS (NM_001166066)	promoter-TSS (NM_001166066)	-522	NM_001166066	223825	Mm.159281	NM_001166066	ENSMUSG00000022155	Mroh2b	4930455B06Rik|Heatr7b2|SPIF	maestro heat-like repeat family member 2B	protein-coding
mm_127501.1	chr15	101427611	101427621	+	1	NA	exon (NM_033073, exon 9 of 9)	exon (NM_033073, exon 9 of 9)	11188	NM_001003668	406219	Mm.347934	NM_001003668	ENSMUSG00000047641	Krt87	K83|K87|Krt2-25|Krt83	keratin 87	protein-coding
mm_94033.1	chr10	127888689	127888750	-	1	NA	promoter-TSS (NM_001150749)	promoter-TSS (NM_001150749)	14	NM_001150749	54150	Mm.6696	NM_017473	ENSMUSG00000040134	Rdh7	AI194929|CRAD2	retinol dehydrogenase 7	protein-coding
mm_79254.1	chr9	50751340	50751367	+	1	NA	promoter-TSS (NM_001289782)	promoter-TSS (NM_001289782)	28	NM_001289782	12955	Mm.178	NM_009964	ENSMUSG00000032060	Cryab	Crya-2|Crya2|HspB5|P23	crystallin, alpha B	protein-coding
mm_125614.1	chr15	61987305	61987318	+	1	NA	intron (NM_001177353, intron 1 of 2)	CpG	1970	NM_001177352	17869	Mm.2444	NM_010849	ENSMUSG00000022346	Myc	AU016757|Myc2|Niard|Nird|bHLHe39	myelocytomatosis oncogene	protein-coding
mm_131.1	chr1	10039798	10039819	+	1	NA	intron (NM_026493, intron 1 of 29)	CpG	1590	NM_026493	211660	Mm.244046	NM_026493	ENSMUSG00000056763	Cspp1	2310020J12Rik|4930413O22Rik|AA387550|BC055915|Cspp2|Cspp3	centrosome and spindle pole associated protein 1	protein-coding
mm_124439.1	chr14	118706181	118706234	-	1	NA	promoter-TSS (NM_001163676)	promoter-TSS (NM_001163676)	12	NM_001163676	239273	Mm.40537	NM_001033336	ENSMUSG00000032849	Abcc4	ABCC4-N1|D630049P08Rik|MOATB|MRP4	ATP-binding cassette, sub-family C (CFTR/MRP), member 4	protein-coding
mm_54037.1	chr6	12749194	12749209	-	1	NA	promoter-TSS (NM_001164805)	promoter-TSS (NM_001164805)	52	NM_001164805	330267	Mm.11989	NM_001164805	ENSMUSG00000032625	Thsd7a	Gm837	thrombospondin, type I, domain containing 7A	protein-coding
mm_43673.1	chr5	138780506	138780512	+	1	NA	intron (NM_030565, intron 3 of 9)	intron (NM_030565, intron 3 of 9)	25428	NM_030565	80752	Mm.320355	NM_030565	ENSMUSG00000025854	Fam20c	C76981|DMP-4|DMP4|GEF-CK|mKIAA4081	family with sequence similarity 20, member C	protein-coding
mm_169582.1	chr15	24162034	24162036	-	1	NA	Intergenic	RLTR10D2|LTR|ERVK	1125572	NM_001081299	320865	Mm.241965	NM_001081299	ENSMUSG00000040420	Cdh18	B230220E17Rik|Cdh14l	cadherin 18	protein-coding
mm_58162.1	chr6	142473076	142473115	-	1	NA	promoter-TSS (NM_145572)	promoter-TSS (NM_145572)	14	NM_145572	232493	Mm.275975	NM_145572	ENSMUSG00000030244	Gys2	BC021322|LGS	glycogen synthase 2	protein-coding
mm_35700.1	chr4	44167430	44167440	-	1	NA	5' UTR (NM_175201, exon 1 of 11)	5' UTR (NM_175201, exon 1 of 11)	103	NM_175201	73469	Mm.262859	NM_175201	ENSMUSG00000035696	Rnf38	1700065B19Rik|2610202O07Rik|AA673263|Oip1	ring finger protein 38	protein-coding
mm_85960.1	chr9	112126806	112126808	-	1	NA	intron (NM_001177618, intron 14 of 18)	intron (NM_001177618, intron 14 of 18)	-8096	NR_029823	723815		NR_029823	ENSMUSG00000065441	Mir128-2	Mirn128-2|Mirn128b|mir-128-2|mir-128b	microRNA 128-2	ncRNA
mm_34281.1	chr4	141424648	141424669	+	1	NA	3' UTR (NM_013868, exon 3 of 3)	3' UTR (NM_013868, exon 3 of 3)	3879	NM_013868	29818	Mm.46181	NM_013868	ENSMUSG00000006221	Hspb7	27kDa|Hsp25-2|cvHsp	heat shock protein family, member 7 (cardiovascular)	protein-coding
mm_117217.1	chr13	64107147	64107179	-	1	NA	intron (NM_001001321, intron 7 of 11)	intron (NM_001001321, intron 7 of 11)	-17962	NM_008291	15487	Mm.5109	NM_008291	ENSMUSG00000033122	Hsd17b3	-	hydroxysteroid (17-beta) dehydrogenase 3	protein-coding
mm_75079.1	chr8	33902582	33902586	-	1	NA	intron (NM_001042674, intron 1 of 7)	intron (NM_001042674, intron 1 of 7)	27279	NM_019733	19663	Mm.323997	NM_019733	ENSMUSG00000031586	Rbpms	2010300K22Rik|2700019M19Rik|AU017537|RBP-MS|hermes	RNA binding protein gene with multiple splicing	protein-coding
mm_71507.1	chr8	46837565	46837577	+	1	NA	intron (NM_008391, intron 6 of 8)	intron (NM_008391, intron 6 of 8)	97826	NM_008391	16363	Mm.1149	NM_008391	ENSMUSG00000031627	Irf2	9830146E22Rik|AI646973|Irf-2	interferon regulatory factor 2	protein-coding
mm_156038.1	chrX	107676838	107676857	+	1	NA	intron (NM_145224, intron 1 of 8)	intron (NM_145224, intron 1 of 8)	335	NM_145224	245572	Mm.137011	NM_145224	ENSMUSG00000031241	Tbx22	D230020M15Rik	T-box 22	protein-coding
mm_242.1	chr1	19209095	19209101	+	1	NA	5' UTR (NM_009334, exon 1 of 7)	5' UTR (NM_009334, exon 1 of 7)	184	NM_001286340	21419	Mm.137021	NM_009334	ENSMUSG00000025927	Tfap2b	AI606113|AP-2(beta)|E130018K07Rik|Tcfap2b	transcription factor AP-2 beta	protein-coding
mm_40924.1	chr5	76016386	76016393	+	1	NA	Intergenic	Intergenic	-37961	NM_010612	16542	Mm.285	NM_010612	ENSMUSG00000062960	Kdr	6130401C07|Flk-1|Flk1|Krd-1|Ly73|VEGFR-2|VEGFR2|sVEGFR-2	kinase insert domain protein receptor	protein-coding
mm_146617.1	chr18	10093944	10093967	-	1	NA	exon (NM_009071, exon 21 of 33)	exon (NM_009071, exon 21 of 33)	-63806	NM_001038589	59025	Mm.329277	NM_021522	ENSMUSG00000047879	Usp14	2610005K12Rik|2610037B11Rik|AW107924|C78769|ax|nmf375	ubiquitin specific peptidase 14	protein-coding
mm_94392.1	chr11	5541897	5541929	+	1	NA	exon (NM_134033, exon 1 of 5)	exon (NM_134033, exon 1 of 5)	304	NM_134033	104479	Mm.210403	NM_134033	ENSMUSG00000020482	Ccdc117	1110004K02Rik|1700026O03Rik|AU018638|AU042822|AV173073|BC018601	coiled-coil domain containing 117	protein-coding
mm_32514.1	chr4	108620010	108620027	+	1	NA	promoter-TSS (NM_177045)	promoter-TSS (NM_177045)	62	NM_177045	319965	Mm.151129	NM_177045	ENSMUSG00000028582	Cc2d1b	A830039B04Rik|Freud2	coiled-coil and C2 domain containing 1B	protein-coding
mm_158301.1	chrX	119853572	119853589	-	1	NA	Intergenic	RMER17D|LTR|ERVK	-73616	NM_053114	93728	Mm.125979	NM_053114	ENSMUSG00000034732	Pabpc5	C820015E17	poly(A) binding protein, cytoplasmic 5	protein-coding
mm_42831.1	chr5	122101778	122101799	+	1	NA	exon (NM_010861, exon 2 of 7)	exon (NM_010861, exon 2 of 7)	808	NM_010861	17906	Mm.1529	NM_010861	ENSMUSG00000013936	Myl2	MLC-2|MLC-2s/v|MLC-2v|Mlc2v|Mylpc	myosin, light polypeptide 2, regulatory, cardiac, slow	protein-coding
mm_52026.1	chr6	94745552	94745558	+	1	NA	Intergenic	Intergenic	-37301	NR_035483	100316707		NR_035483	ENSMUSG00000088552	Mir1957a	Mir1957|mmu-mir-1957|mmu-mir-1957a	microRNA 1957a	ncRNA
mm_103331.1	chr11	74572693	74572728	-	1	NA	intron (NM_001015046, intron 1 of 24)	intron (NM_001015046, intron 1 of 24)	17448	NM_001015046	380711	Mm.425690	NM_001015046	ENSMUSG00000038807	Rap1gap2	AU067654|Garnl4|Gm1561|mKIAA1039	RAP1 GTPase activating protein 2	protein-coding
mm_28283.1	chr3	88951091	88951115	-	1	NA	promoter-TSS (NM_022994)	promoter-TSS (NM_022994)	-821	NM_001164533	65111	Mm.29028	NM_022994	ENSMUSG00000068921	Dap3	4921514D13Rik|DAP-3|MRP-S29|S29mt	death associated protein 3	protein-coding
mm_59223.1	chr7	24636480	24636520	+	1	NA	promoter-TSS (NM_133743)	promoter-TSS (NM_133743)	-70	NM_133743	72434	Mm.281093	NM_133743	ENSMUSG00000057454	Lypd3	2310061G07Rik|C4.4a	Ly6/Plaur domain containing 3	protein-coding
mm_127334.1	chr15	100468976	100468993	+	1	NA	promoter-TSS (NM_134093)	promoter-TSS (NM_134093)	-50	NM_134093	68614	Mm.275272	NM_134093	ENSMUSG00000037353	Letmd1	1110019O13Rik|AI593524|BB130465|BB235638|HCCR-2|HCCR1|MCC-32|Mccr	LETM1 domain containing 1	protein-coding
mm_12690.1	chr2	76369928	76369951	+	1	NA	promoter-TSS (NM_153405)	promoter-TSS (NM_153405)	-45	NM_153405	241490	Mm.33310	NM_153405	ENSMUSG00000042369	Rbm45	Drb1|Drbp1|G430095G15Rik	RNA binding motif protein 45	protein-coding
mm_54984.1	chr6	48742011	48742030	-	1	NA	intron (NM_175860, intron 2 of 2)	intron (NM_175860, intron 2 of 2)	2973	NM_008376	16205	Mm.252599	NM_008376	ENSMUSG00000090019	Gimap1	IAP38|Imap38|imap	GTPase, IMAP family member 1	protein-coding
mm_136830.1	chr17	12741340	12741350	+	1	NA	promoter-TSS (NR_027784)	promoter-TSS (NR_027784)	34	NR_027784	104103	Mm.26553	NR_002853	ENSMUSG00000078247	Airn	2810051F02Rik|2810434M15Rik|AI256653|AI597500|AW049873|Air|B930018I07Rik|D17Ertd663e|IGF2RAS	antisense Igf2r RNA	ncRNA
mm_110816.1	chr12	72408292	72408323	-	1	NA	intron (NM_153457, intron 1 of 8)	CpG	747	NM_001286448	104001	Mm.221275	NM_153457	ENSMUSG00000021087	Rtn1	Nsp	reticulon 1	protein-coding
mm_33833.1	chr4	135626813	135626832	+	1	NA	non-coding (NR_027909, exon 1 of 2)	non-coding (NR_027909, exon 1 of 2)	167	NR_027909	73937	Mm.292326	NM_028688	ENSMUSG00000086788	1700029M20Rik	4930406E24Rik	RIKEN cDNA 1700029M20 gene	ncRNA
mm_143721.1	chr17	81375522	81375534	-	1	NA	non-coding (NR_104580, exon 9 of 9)	non-coding (NR_104580, exon 9 of 9)	-310443	NM_028138	72167	Mm.273257	NM_028138	ENSMUSG00000024246	Thumpd2	2810025A12Rik	THUMP domain containing 2	protein-coding
mm_33812.1	chr4	135226074	135226085	+	1	NA	exon (NM_013885, exon 3 of 6)	exon (NM_013885, exon 3 of 6)	46681	NM_013885	29876	Mm.257765	NM_013885	ENSMUSG00000037242	Clic4	D0Jmb3|TU-74|mc3s5|mtCLIC	chloride intracellular channel 4 (mitochondrial)	protein-coding
mm_979.1	chr1	58406528	58406536	+	1	NA	TTS (NM_025824)	TTS (NM_025824)	13396	NM_025824	66882	Mm.21848	NM_025824	ENSMUSG00000051223	Bzw1	1200015E15Rik|mKIAA0005	basic leucine zipper and W2 domains 1	protein-coding
mm_56007.1	chr6	86493945	86493951	-	1	NA	Intergenic	Intergenic	-5721	NR_040292	381792	Mm.333223	NR_040292	ENSMUSG00000101655	2310040G24Rik	-	RIKEN cDNA 2310040G24 gene	ncRNA
mm_26788.1	chr3	9623520	9623528	-	1	NA	Intergenic	Intergenic	-13439	NM_133218	170753	Mm.212908	NM_133218	ENSMUSG00000040209	Zfp704	C030026M03|C030034L19Rik|Gig1|Znf704	zinc finger protein 704	protein-coding
mm_93133.1	chr10	92124209	92124219	-	1	NA	intron (NR_028262, intron 9 of 12)	intron (NR_028262, intron 9 of 12)	13009	NR_037219	100526517		NR_037219	ENSMUSG00000093227	Mir1251	mir-1251|mmu-mir-1251	microRNA 1251	ncRNA
mm_150566.1	chr19	40089627	40089636	+	1	NA	promoter-TSS (NM_001167877)	promoter-TSS (NM_001167877)	-48	NM_134144	107141	Mm.474575	NM_134144	ENSMUSG00000054827	Cyp2c50	AI266900	cytochrome P450, family 2, subfamily c, polypeptide 50	protein-coding
mm_92091.1	chr10	62865280	62865290	-	1	NA	intron (NM_027384, intron 1 of 10)	intron (NM_027384, intron 1 of 10)	14729	NM_027384	52463	Mm.17774	NM_027384	ENSMUSG00000047146	Tet1	2510010B09Rik|AA517754|BB001228|Cxxc6|D10Ertd17e|LCX|mKIAA1676	tet methylcytosine dioxygenase 1	protein-coding
mm_68243.1	chr7	105481854	105481904	-	1	NA	exon (NM_028444, exon 1 of 2)	exon (NM_028444, exon 1 of 2)	318	NM_028444	109042	Mm.3124	NM_028444	ENSMUSG00000037060	Prkcdbp	3110015B12Rik|6330514M23Rik|SRBC	protein kinase C, delta binding protein	protein-coding
mm_89394.1	chr10	89873498	89873516	+	1	NA	promoter-TSS (NM_001128086)	promoter-TSS (NM_001128086)	-2	NM_001128086	77531	Mm.440605	NM_181398	ENSMUSG00000058589	Anks1b	AIDA-1b|C030032C09Rik|E530015N03Rik|ENSMUSG00000078431|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding
mm_96730.1	chr11	69685938	69685950	+	1	NA	promoter-TSS (NM_001159505)	promoter-TSS (NM_001159505)	-390	NM_023517	69583	Mm.8983	NM_023517	ENSMUSG00000089669	Tnfsf13	2310026N09Rik|April|Tall2|Tnlg7b|Trdl1	tumor necrosis factor (ligand) superfamily, member 13	protein-coding
mm_71191.1	chr8	40871287	40871318	+	1	NA	intron (NM_007514, intron 1 of 11)	intron (NM_007514, intron 1 of 11)	8935	NM_001044740	11988	Mm.4676	NM_007514	ENSMUSG00000031596	Slc7a2	20.5|AI158848|Atrc2|CAT-2|Cat2|Tea	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	protein-coding
mm_88732.1	chr10	80249107	80249124	+	1	NA	promoter-TSS (NM_029272)	promoter-TSS (NM_029272)	-337	NM_029272	75406	Mm.28712	NM_029272	ENSMUSG00000020153	Ndufs7	1010001M04Rik	NADH dehydrogenase (ubiquinone) Fe-S protein 7	protein-coding
mm_75564.1	chr8	58913273	58913286	-	1	NA	3' UTR (NM_173411, exon 3 of 3)	3' UTR (NM_173411, exon 3 of 3)	1524	NM_173411	234290	Mm.39244	NM_173411	ENSMUSG00000049946	BC030500	-	cDNA sequence BC030500	protein-coding
mm_43761.1	chr5	140616991	140617009	+	1	NA	Intergenic	Intergenic	9659	NM_008494	16848	Mm.12834	NM_008494	ENSMUSG00000029570	Lfng	AW061165	LFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	protein-coding
mm_161257.1	chr13	112594300	112594300	-	1	NA	Intergenic	Intergenic	-13638	NM_139299	218624	Mm.380801	NM_139299	ENSMUSG00000050377	Il31ra	CRL3|GLM-R|GPL|Glmr|NR10	interleukin 31 receptor A	protein-coding
mm_23739.1	chr3	69222376	69222384	+	1	NA	promoter-TSS (NM_027843)	promoter-TSS (NM_027843)	-39	NM_027843	71619	Mm.98122	NM_027843	ENSMUSG00000098207	Arl14	9130014L17Rik|Arf7	ADP-ribosylation factor-like 14	protein-coding
mm_142737.1	chr17	48388394	48388404	-	1	NA	3' UTR (NM_010913, exon 9 of 9)	3' UTR (NM_010913, exon 9 of 9)	12181	NM_001347402	18044	Mm.4929	NM_010913	ENSMUSG00000023994	Nfya	AA407810|Cbf-b|SEZ-10|SEZ10	nuclear transcription factor-Y alpha	protein-coding
mm_109663.1	chr12	113022437	113022440	+	1	NA	intron (NM_001291444, intron 1 of 23)	ID_B1|SINE|B4	7930	NM_001291444	217893	Mm.35754	NM_198165	ENSMUSG00000021143	Pacs2	6720425G15Rik|AW208651|AW489976|E230011J22|Pacs1l|mKIAA0602	phosphofurin acidic cluster sorting protein 2	protein-coding
mm_64813.1	chr7	6730413	6730431	-	1	NA	promoter-TSS (NM_001290994)	promoter-TSS (NM_001290994)	-3	NM_008817	18616	Mm.389800	NM_008817	ENSMUSG00000002265	Peg3	AL022617|ASF-1|End4|Gcap4|Pw1|Zfp102|mKIAA0287	paternally expressed 3	protein-coding
mm_128311.1	chr15	37792392	37792415	-	1	NA	promoter-TSS (NM_134094)	promoter-TSS (NM_134094)	25	NM_134094	52589	Mm.283370	NM_134094	ENSMUSG00000051359	Ncald	AI848120|D030020D09Rik|D15Ertd412e	neurocalcin delta	protein-coding
mm_93291.1	chr10	96370767	96370805	-	1	NA	Intergenic	Intergenic	144579	NR_110448	74881	Mm.410819	NR_110448		4930459C07Rik	-	RIKEN cDNA 4930459C07 gene	ncRNA
mm_125094.1	chr15	27571373	27571394	+	1	NA	promoter-TSS (NR_106065)	promoter-TSS (NR_106065)	-111	NR_106065	102466808		NR_106065	ENSMUSG00000098416	Mir7117	Gm27729|mmu-mir-7117	microRNA 7117	ncRNA
mm_145212.1	chr18	50031071	50031088	+	1	NA	intron (NM_001177759, intron 1 of 1)	intron (NM_001177759, intron 1 of 1)	-22203	NM_134131	106869	Mm.27740	NM_134131	ENSMUSG00000062210	Tnfaip8	AA987150|E130304C20Rik|ENSMUSG00000073567|Gg2-1|Gm10539|Nded|Ssc-2|Tipe	tumor necrosis factor, alpha-induced protein 8	protein-coding
mm_112004.1	chr12	110845185	110845216	-	1	NA	Intergenic	Intergenic	-4261	NM_011973	26448	Mm.140948	NM_011973	ENSMUSG00000056458	Mok	RAGE1|Rage|Stk30	MOK protein kinase	protein-coding
mm_136487.1	chr16	96082696	96082709	-	1	NA	promoter-TSS (NM_145125)	promoter-TSS (NM_145125)	-274	NM_145125	93871	Mm.240871	NM_145125	ENSMUSG00000022914	Brwd1	5330419I02Rik|D530019K20Rik|G1-403-16|Wdr9|repro5	bromodomain and WD repeat domain containing 1	protein-coding
mm_106387.1	chr11	118513355	118513375	-	1	NA	exon (NM_001039167, exon 5 of 15)	exon (NM_001039167, exon 5 of 15)	36405	NM_172573	217364	Mm.473963	NM_172573	ENSMUSG00000033857	Engase	C130099A03|D230014K01Rik	endo-beta-N-acetylglucosaminidase	protein-coding
mm_60697.1	chr7	45175318	45175328	+	1	NA	3' UTR (NM_182993, exon 12 of 12)	3' UTR (NM_182993, exon 12 of 12)	2020	NR_106022	102465638		NR_106022	ENSMUSG00000106470	Mir7055	mmu-mir-7055	microRNA 7055	ncRNA
mm_147347.1	chr18	43323857	43323871	-	1	NA	3' UTR (NM_001291455, exon 14 of 14)	3' UTR (NM_001291455, exon 14 of 14)	49408	NM_001136086	22240	Mm.8180	NM_009468	ENSMUSG00000024501	Dpysl3	CRMP-4|DRP-3|TUC4|ULIP-1|Ulip|Ulip1	dihydropyrimidinase-like 3	protein-coding
mm_25066.1	chr3	99253347	99253383	+	1	NA	promoter-TSS (NM_009323)	promoter-TSS (NM_009323)	-395	NM_009323	21384	Mm.88761	NM_009323	ENSMUSG00000027868	Tbx15	Tbx14|Tbx8|de	T-box 15	protein-coding
mm_149282.1	chr19	10621869	10621896	+	1	NA	exon (NM_015735, exon 14 of 27)	exon (NM_015735, exon 14 of 27)	-12351	NM_027913	71768	Mm.169261	NM_027913	ENSMUSG00000043789	Vwce	1300015B04Rik	von Willebrand factor C and EGF domains	protein-coding
mm_132263.1	chr16	32776300	32776313	+	1	NA	intron (NM_080457, intron 21 of 26)	intron (NM_080457, intron 21 of 26)	21129	NM_146071	224116	Mm.153301	NM_146071	ENSMUSG00000035638	Muc20	BC026367	mucin 20	protein-coding
mm_48977.1	chr6	4754571	4754581	+	1	NA	exon (NM_130877, exon 2 of 2)	exon (NM_130877, exon 2 of 2)	7270	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_13930.1	chr2	120977249	120977308	+	1	NA	5' UTR (NM_175285, exon 1 of 14)	5' UTR (NM_175285, exon 1 of 14)	216	NM_175285	96957	Mm.315212	NM_175285	ENSMUSG00000054484	Tmem62	B830009D23Rik|C77355	transmembrane protein 62	protein-coding
mm_129455.1	chr15	78565964	78565981	-	1	NA	exon (NM_009008, exon 3 of 7)	exon (NM_009008, exon 3 of 7)	6811	NM_009008	19354	Mm.1972	NM_009008	ENSMUSG00000033220	Rac2	AI323801|AI452260	RAS-related C3 botulinum substrate 2	protein-coding
mm_32071.1	chr4	97860115	97860176	+	1	NA	intron (NM_010905, intron 2 of 10)	ID2|SINE|ID	82519	NM_010905	18027	Mm.31274	NM_010905	ENSMUSG00000028565	Nfia	1110047K16Rik|9430022M17Rik|CTF|NF1-A|NF1A	nuclear factor I/A	protein-coding
mm_67381.1	chr7	79842230	79842245	-	1	NA	exon (NM_008486, exon 1 of 20)	exon (NM_008486, exon 1 of 20)	115	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_20741.1	chr2	138081525	138081526	-	1	NA	Intergenic	Intergenic	-175059	NM_001025431	228662	Mm.153405	NM_145534	ENSMUSG00000062098	Btbd3	mKIAA0952	BTB (POZ) domain containing 3	protein-coding
mm_121297.1	chr14	105589507	105589531	+	1	NA	promoter-TSS (NR_102319)	promoter-TSS (NR_102319)	-30	NR_102319	380930	Mm.427836	NR_102319		9330188P03Rik	Gm1589|mgt-6	RIKEN cDNA 9330188P03 gene	ncRNA
mm_158926.1	chr1	60098666	60098666	-	1	NA	promoter-TSS (NM_001199060)	promoter-TSS (NM_001199060)	-166	NM_001199060	57750	Mm.281079	NM_021312	ENSMUSG00000026019	Wdr12	4933402C23Rik|Ytm1|Ytm1p	WD repeat domain 12	protein-coding
mm_73938.1	chr8	120050228	120050262	+	1	NA	intron (NM_030209, intron 14 of 14)	intron (NM_030209, intron 14 of 14)	51227	NM_133967	102193	Mm.240076	NM_133967	ENSMUSG00000031823	Zdhhc7	AL024087|Gramp2	zinc finger, DHHC domain containing 7	protein-coding
mm_72073.1	chr8	71543158	71543173	+	1	NA	exon (NM_028617, exon 2 of 9)	exon (NM_028617, exon 2 of 9)	235	NM_028617	73711	Mm.307770	NM_028617	ENSMUSG00000031813	Mvb12a	1110012M11Rik|Fam125a	multivesicular body subunit 12A	protein-coding
mm_69914.1	chr7	141693996	141694007	-	1	NA	exon (NM_023566, exon 7 of 46)	exon (NM_023566, exon 7 of 46)	3661	NM_023566	17831	Mm.2041	NM_023566		Muc2	2010015E03Rik|MCM|wnn	mucin 2	protein-coding
mm_12667.1	chr2	75704130	75704140	+	1	NA	intron (NR_132727, intron 1 of 1)	CpG	528	NR_132727	18024	Mm.1025	NM_010902	ENSMUSG00000015839	Nfe2l2	Nrf2	nuclear factor, erythroid derived 2, like 2	protein-coding
mm_130522.1	chr15	98881256	98881316	-	1	NA	5' UTR (NM_026967, exon 1 of 8)	5' UTR (NM_026967, exon 1 of 8)	128	NM_026967	69159	Mm.259708	NM_026967	ENSMUSG00000023755	Rhebl1	1810036J22Rik|Rheb2	Ras homolog enriched in brain like 1	protein-coding
mm_33180.1	chr4	126058652	126058660	+	1	NA	promoter-TSS (NM_172701)	promoter-TSS (NM_172701)	91	NM_172701	230751	Mm.38907	NM_172701	ENSMUSG00000042616	Oscp1	1810007P19Rik|5730415O04|6030436A01Rik	organic solute carrier partner 1	protein-coding
mm_35028.1	chr4	4019509	4019562	-	1	NA	5' UTR (NM_181989, exon 1 of 7)	5' UTR (NM_181989, exon 1 of 7)	128	NM_181989	242285	Mm.98096	NM_181989	ENSMUSG00000028236	Sdr16c5	Rdhe2|Scdr9	short chain dehydrogenase/reductase family 16C, member 5	protein-coding
mm_116448.1	chr13	43171352	43171368	-	1	NA	5' UTR (NM_025935, exon 1 of 8)	5' UTR (NM_025935, exon 1 of 8)	141	NM_001252639	67046	Mm.269213	NM_025935	ENSMUSG00000021368	Tbc1d7	2610009C09Rik	TBC1 domain family, member 7	protein-coding
mm_137614.1	chr17	28271958	28271968	+	1	NA	intron (NR_045427, intron 1 of 2)	intron (NR_045427, intron 1 of 2)	255	NR_045427	69050	Mm.486938	NR_045427	ENSMUSG00000002250	1810013A23Rik	-	RIKEN cDNA 1810013A23 gene	ncRNA
mm_97092.1	chr11	73160404	73160420	+	1	NA	promoter-TSS (NM_033321)	promoter-TSS (NM_033321)	-118	NM_033321	94045	Mm.156893	NM_033321	ENSMUSG00000005950	P2rx5	P2X5	purinergic receptor P2X, ligand-gated ion channel, 5	protein-coding
mm_163201.1	chr11	96773403	96773413	-	1	NA	intron (NM_001163389, intron 3 of 7)	B1F2|SINE|Alu	4147	NM_028965	74479	Mm.270781	NM_028965	ENSMUSG00000020876	Snx11	4933439F10Rik|A930041K09Rik|AI117694	sorting nexin 11	protein-coding
mm_124213.1	chr14	100109803	100109811	-	1	NA	exon (NM_010636, exon 2 of 7)	exon (NM_010636, exon 2 of 7)	39989	NM_010636	16597	Mm.396499	NM_010636	ENSMUSG00000072294	Klf12	2700063E05Rik|AI225908|AI315654|AP-2rep|B130052C06Rik|D530033K05Rik	Kruppel-like factor 12	protein-coding
mm_115577.1	chr13	11573757	11573764	-	1	NA	intron (NM_023868, intron 97 of 104)	B4A|SINE|B4	51708	NR_027813	664793	Mm.410565	NR_027813		Zp4-ps	EG664793|Zp4|Zpb	zona pellucida glycoprotein 4, pseudogene	pseudo
mm_161952.1	chr19	5672613	5672613	-	1	NA	exon (NM_144868, exon 26 of 35)	exon (NM_144868, exon 26 of 35)	6463	NR_105953	102465596		NR_105953	ENSMUSG00000098568	Mir6987	Gm27891|mmu-mir-6987	microRNA 6987	ncRNA
mm_14147.1	chr2	126552837	126552893	+	1	NA	promoter-TSS (NM_011978)	promoter-TSS (NM_011978)	-159	NM_011978	26458	Mm.290044	NM_011978	ENSMUSG00000027359	Slc27a2	ACSVL1|FATP2|VLCS|Vlac|Vlacs	solute carrier family 27 (fatty acid transporter), member 2	protein-coding
mm_111777.1	chr12	104153816	104153833	-	1	NA	promoter-TSS (NM_008458)	promoter-TSS (NM_008458)	48	NM_008458	16625	Mm.422814	NM_008458	ENSMUSG00000066361	Serpina3c	1A1|Kalbp|Klkbp|spi2	serine (or cysteine) peptidase inhibitor, clade A, member 3C	protein-coding
mm_61879.1	chr7	89632418	89632450	+	1	NA	promoter-TSS (NM_181407)	promoter-TSS (NM_181407)	-384	NM_181407	109264	Mm.334011	NM_181407	ENSMUSG00000030621	Me3	1700020C08Rik|B230207H15Rik	malic enzyme 3, NADP(+)-dependent, mitochondrial	protein-coding
mm_16383.1	chr2	178327664	178327683	+	1	NA	intron (NM_001177790, intron 8 of 12)	intron (NM_001177790, intron 8 of 12)	79985	NM_177191	320558	Mm.70781	NM_177191	ENSMUSG00000060445	Sycp2	3830402K23Rik|4930518F03Rik	synaptonemal complex protein 2	protein-coding
mm_23979.1	chr3	86011591	86011614	+	1	NA	Intergenic	MLT1F1|LTR|ERVL-MaLR	-9111	NM_001001650	368202	Mm.253822	NM_001001650	ENSMUSG00000049013	Prss48	Esspl|Gm1019	protease, serine 48	protein-coding
mm_94710.1	chr11	20469532	20469546	+	1	NA	Intergenic	Intergenic	-73714	NM_021372	58172	Mm.339676	NM_021372	ENSMUSG00000049800	Sertad2	AB041541|AU021878|Kiaa0127|MNCb-1504|SEI-2|Sei2|TRIP-Br2|mKIAA0127	SERTA domain containing 2	protein-coding
mm_139886.1	chr17	70834621	70834674	+	1	NA	Intergenic	CpG	12130	NM_001164077	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_47928.1	chr5	135013132	135013158	-	1	NA	promoter-TSS (NR_026688)	promoter-TSS (NR_026688)	12	NR_026688	69812	Mm.18422	NR_026688	ENSMUSG00000085042	Abhd11os	2010001M06Rik|AI462243|Wbscr26|Wnscr26	abhydrolase domain containing 11, opposite strand	ncRNA
mm_42325.1	chr5	114901299	114901325	+	1	NA	exon (NM_011854, exon 3 of 6)	exon (NM_011854, exon 3 of 6)	4378	NM_011854	23962	Mm.228363	NM_011854	ENSMUSG00000029561	Oasl2	M1204|Mmu-OASL|Oasl	2'-5' oligoadenylate synthetase-like 2	protein-coding
mm_5418.1	chr1	33907722	33907809	-	1	NA	promoter-TSS (NM_001310484)	promoter-TSS (NM_001310484)	2	NM_001310484	320705	Mm.336619	NM_177235	ENSMUSG00000042182	Bend6	B230209C24Rik	BEN domain containing 6	protein-coding
mm_77611.1	chr8	123893597	123893628	-	1	NA	exon (NM_009606, exon 2 of 7)	exon (NM_009606, exon 2 of 7)	1163	NM_001272041	11459	Mm.214950	NM_009606	ENSMUSG00000031972	Acta1	AA959943|Acta-2|Acts|Actsk-1	actin, alpha 1, skeletal muscle	protein-coding
mm_1997.1	chr1	87126934	87126945	+	1	NA	exon (NM_007432, exon 9 of 11)	exon (NM_007432, exon 9 of 11)	1931	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_99303.1	chr11	101373995	101374012	+	1	NA	intron (NM_008061, intron 3 of 4)	ORR1D2|LTR|ERVL-MaLR	6287	NM_008061	14377	Mm.18064	NM_008061	ENSMUSG00000078650	G6pc	AW107337|G6Pase|G6pt|Glc-6-Pase	glucose-6-phosphatase, catalytic	protein-coding
mm_30973.1	chr4	34550678	34550688	+	1	NA	promoter-TSS (NM_001007589)	promoter-TSS (NM_001007589)	68	NM_001007589	433693	Mm.389532	NM_026019	ENSMUSG00000028291	Akirin2	2700059D21Rik|AA114675|AA522011|AU019887|Akirin-2	akirin 2	protein-coding
mm_29983.1	chr3	135423382	135423453	-	1	NA	promoter-TSS (NM_025902)	promoter-TSS (NM_025902)	16	NM_025902	67006	Mm.269993	NM_025902	ENSMUSG00000028165	Cisd2	1500009M05Rik|1500026J14Rik|1500031D15Rik|AI848398|B630006A20Rik|Miner1|Naf-1|Noxp70|Zcd2	CDGSH iron sulfur domain 2	protein-coding
mm_143587.1	chr17	74438655	74438667	-	1	NA	intron (NM_001033367, intron 5 of 8)	intron (NM_001033367, intron 5 of 8)	20447	NM_001033367	268973	Mm.311884	NM_001033367	ENSMUSG00000039193	Nlrc4	9530011P19Rik|CLAN|CLAN1|CLANA|CLANB|CLANC|CLAND|Card12|IPAF	NLR family, CARD domain containing 4	protein-coding
mm_10103.1	chr2	3475173	3475186	+	1	NA	promoter-TSS (NM_022724)	promoter-TSS (NM_022724)	-193	NR_027509	64707	Mm.23483	NM_022724	ENSMUSG00000026646	Suv39h2	4930507K23Rik|AA536750|D030054H19Rik|D2Ertd544e|KMT1B	suppressor of variegation 3-9 homolog 2 (Drosophila)	protein-coding
mm_4200.1	chr1	171229598	171229611	+	1	NA	TTS (NM_010185)	TTS (NM_010185)	4550	NM_013474	11807	Mm.389209	NM_013474	ENSMUSG00000005681	Apoa2	Alp-2|Apo-AII|ApoA-II|ApoAII|Apoa-2|Hdl-1	apolipoprotein A-II	protein-coding
mm_67649.1	chr7	84679347	84679401	-	1	NA	promoter-TSS (NM_022985)	promoter-TSS (NM_022985)	-23	NM_022985	65098	Mm.209349	NM_022985	ENSMUSG00000030629	Zfand6	3110005P07Rik|Awp1|Za20d3	zinc finger, AN1-type domain 6	protein-coding
mm_105248.1	chr11	102350109	102350128	-	1	NA	3' UTR (NM_011403, exon 20 of 20)	3' UTR (NM_011403, exon 20 of 20)	15163	NM_011403	20533	Mm.7248	NM_011403	ENSMUSG00000006574	Slc4a1	Ae1|CD233|Empb3|l11Jus51	solute carrier family 4 (anion exchanger), member 1	protein-coding
mm_79568.1	chr9	58134243	58134258	+	1	NA	promoter-TSS (NM_001162479)	promoter-TSS (NM_001162479)	175	NM_001162476	20897	Mm.10801	NM_009291	ENSMUSG00000032327	Stra6	AI891933	stimulated by retinoic acid gene 6	protein-coding
mm_45835.1	chr5	87694832	87694924	-	1	NA	exon (NM_001286023, exon 5 of 7)	exon (NM_001286023, exon 5 of 7)	4547	NM_001286020	12991	Mm.268737	NM_009972	ENSMUSG00000063157	Csn2	Csnb	casein beta	protein-coding
mm_127854.1	chr15	8099183	8099215	-	1	NA	promoter-TSS (NM_001081402)	promoter-TSS (NM_001081402)	10	NM_001081402	545085	Mm.321312	NM_198413	ENSMUSG00000039828	Wdr70	4833422F06Rik	WD repeat domain 70	protein-coding
mm_39024.1	chr4	152131814	152131829	-	1	NA	intron (NM_207688, intron 3 of 10)	CpG-10714	-2896	NM_019585	56226	Mm.264215	NM_019585	ENSMUSG00000028943	Espn	je	espin	protein-coding
mm_61689.1	chr7	81031566	81031569	+	1	NA	intron (NM_178707, intron 4 of 9)	B1F1|SINE|Alu	-26033	NM_054085	116904	Mm.475768	NM_054085	ENSMUSG00000038763	Alpk3	AW319487|D330016D04|MAK|Midori|mKIAA1330	alpha-kinase 3	protein-coding
mm_172172.1	chr6	45460711	45460711	+	1	NA	intron (NM_001004357, intron 1 of 23)	(TAG)n|Simple_repeat|Simple_repeat	400650	NM_001004357	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding
mm_102466.1	chr11	59964912	59964922	-	1	NA	promoter-TSS (NM_009026)	promoter-TSS (NM_009026)	27	NM_009026	19416	Mm.3903	NM_009026	ENSMUSG00000049892	Rasd1	Dexras1	RAS, dexamethasone-induced 1	protein-coding
mm_122502.1	chr14	46822123	46822135	-	1	NA	5' UTR (NM_022023, exon 1 of 7)	5' UTR (NM_022023, exon 1 of 7)	113	NM_022023	63985	Mm.87312	NM_022023	ENSMUSG00000062014	Gmfb	3110001H22Rik|3110001O16Rik|AI851627|C79176|D14Ertd630e	glia maturation factor, beta	protein-coding
mm_81842.1	chr9	118512913	118512934	+	1	NA	intron (NM_018748, intron 1 of 23)	intron (NM_018748, intron 1 of 23)	6605	NM_018748	54214	Mm.10409	NM_018748	ENSMUSG00000038708	Golga4	AI225887|AU019508|Olp-1	golgi autoantigen, golgin subfamily a, 4	protein-coding
mm_898.1	chr1	53313693	53313701	+	1	NA	promoter-TSS (NM_001285839)	promoter-TSS (NM_001285839)	73	NR_104360	72085	Mm.482256	NM_028091	ENSMUSG00000026096	Osgepl1	2610001M19Rik|AA416452	O-sialoglycoprotein endopeptidase-like 1	protein-coding
mm_31246.1	chr4	44924169	44924171	+	1	NA	intron (NM_138590, intron 6 of 8)	ID_B1|SINE|B4	-57224	NM_080289	76238	Mm.196574	NM_080289	ENSMUSG00000035637	Grhpr	1110059D05Rik|6430629L09Rik|Glxr	glyoxylate reductase/hydroxypyruvate reductase	protein-coding
mm_30814.1	chr4	21747712	21747734	+	1	NA	3' UTR (NM_001122982, exon 12 of 12)	3' UTR (NM_001122982, exon 12 of 12)	19488	NM_029840	77032	Mm.87238	NM_029840	ENSMUSG00000028251	Tstd3	2610029I01Rik	thiosulfate sulfurtransferase (rhodanese)-like domain containing 3	protein-coding
mm_123286.1	chr14	61439832	61439869	-	1	NA	promoter-TSS (NM_008466)	promoter-TSS (NM_008466)	97	NM_008466	16648	Mm.25548	NM_008466	ENSMUSG00000021929	Kpna3	IPOA4	karyopherin (importin) alpha 3	protein-coding
mm_127659.1	chr15	102518308	102518331	+	1	NA	5' UTR (NM_009319, exon 1 of 9)	5' UTR (NM_009319, exon 1 of 9)	127	NM_009319	21357	Mm.291485	NM_009319	ENSMUSG00000023051	Tarbp2	Prbp|TRBP	TARBP2, RISC loading complex RNA binding subunit	protein-coding
mm_61762.1	chr7	82771875	82771904	+	1	NA	intron (NM_175317, intron 18 of 19)	intron (NM_175317, intron 18 of 19)	-16245	NR_046004	77800	Mm.444811	NR_046004	ENSMUSG00000086690	4933406J10Rik	A930009F24Rik	RIKEN cDNA 4933406J10 gene	ncRNA
mm_70950.1	chr8	26976020	26976022	+	1	NA	Intergenic	Intergenic	-1315	NM_001101502	353310	Mm.212469	NM_001101502	ENSMUSG00000085795	Zfp703	1110032O19Rik|AI430822|AL022941|Csmn1|End2|Zeppo1|Znf703|Zpo1	zinc finger protein 703	protein-coding
mm_154706.1	chrX	8276133	8276144	+	1	NA	exon (NM_172479, exon 8 of 16)	exon (NM_172479, exon 8 of 16)	4757	NM_172479	209837	Mm.6055	NM_172479	ENSMUSG00000031170	Slc38a5	C81234|E330031E14|JM24|SN2	solute carrier family 38, member 5	protein-coding
mm_31030.1	chr4	40888997	40888999	+	1	NA	Intergenic	Intergenic	-31058	NM_011463	20731	Mm.25246	NM_011463	ENSMUSG00000028415	Spink4	MPGC60	serine peptidase inhibitor, Kazal type 4	protein-coding
mm_96636.1	chr11	69326253	69326275	+	1	NA	promoter-TSS (NM_010599)	promoter-TSS (NM_010599)	6	NM_010599	16499	Mm.232472	NM_010599	ENSMUSG00000018470	Kcnab3	C330022D06Rik|Kcnab4|mKv(beta)4	potassium voltage-gated channel, shaker-related subfamily, beta member 3	protein-coding
mm_65795.1	chr7	28907295	28907299	-	1	NA	intron (NM_021895, intron 8 of 20)	intron (NM_021895, intron 8 of 20)	25641	NM_001110807	60594	Mm.476990	NM_021894	ENSMUSG00000054083	Capn12	CANP 12	calpain 12	protein-coding
mm_15061.1	chr2	152962522	152962528	+	1	NA	promoter-TSS (NM_029064)	promoter-TSS (NM_029064)	40	NM_001083618	74711	Mm.44746	NM_029064	ENSMUSG00000074673	Ttll9	1700016F23Rik|4930509O20Rik|AW046572	tubulin tyrosine ligase-like family, member 9	protein-coding
mm_10158.1	chr2	4400799	4400828	+	1	NA	promoter-TSS (NM_001177843)	promoter-TSS (NM_001177843)	-163	NM_001177843	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding
mm_136672.1	chr17	6106909	6106922	+	1	NA	promoter-TSS (NM_001103181)	promoter-TSS (NM_001103181)	85	NM_001103181	68842	Mm.449307	NM_054040	ENSMUSG00000034377	Tulp4	1110057P05Rik|2210038L17Rik|Tusp	tubby like protein 4	protein-coding
mm_123382.1	chr14	63271824	63271850	-	1	NA	Intergenic	Intergenic	-26566	NM_001310610	14463	Mm.247669	NM_008092	ENSMUSG00000021944	Gata4	Gata-4	GATA binding protein 4	protein-coding
mm_171096.1	chr3	130068417	130068421	+	1	NA	Intergenic	CpG	-7512	NM_207209	99683	Mm.192303	NM_207209	ENSMUSG00000001052	Sec24b	AI605202|SEC24	Sec24 related gene family, member B (S. cerevisiae)	protein-coding
mm_136924.1	chr17	13846192	13846196	+	1	NA	intron (NM_010806, intron 13 of 32)	intron (NM_010806, intron 13 of 32)	-84800	NM_022311	21646	Mm.486358	NM_022311	ENSMUSG00000038347	Tcte2	AI429268|Tcte-2	t-complex-associated testis expressed 2	protein-coding
mm_93923.1	chr10	127136615	127136634	-	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-15464	NM_001171026	216440	Mm.295246	NM_177614	ENSMUSG00000040462	Os9	4632413K17Rik|AU022351	amplified in osteosarcoma	protein-coding
mm_53825.1	chr6	147475866	147475922	+	1	NA	promoter-TSS (NM_025911)	promoter-TSS (NM_025911)	23	NM_025911	67015	Mm.209774	NM_025911	ENSMUSG00000030301	Ccdc91	1700086G08Rik|1810060J02Rik|AU045683|AW555238|p56	coiled-coil domain containing 91	protein-coding
mm_116547.1	chr13	45966280	45966325	-	1	NA	Intergenic	Intergenic	-1311	NM_009124	20238	Mm.342683	NM_009124	ENSMUSG00000046876	Atxn1	2900016G23Rik|Atx1|C85907|ENSMUSG00000074917|Gm10786|Sca1	ataxin 1	protein-coding
mm_59934.1	chr7	30423921	30423922	+	1	NA	intron (NM_172142, intron 2 of 10)	B1F2|SINE|Alu	617	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_157758.1	chrX	73495068	73495098	-	1	NA	3' UTR (NM_007542, exon 8 of 8)	3' UTR (NM_007542, exon 8 of 8)	-8003	NM_001310537	320707	Mm.210095	NM_177236	ENSMUSG00000031376	Atp2b3	6430519O13Rik|Pmca3	ATPase, Ca++ transporting, plasma membrane 3	protein-coding
mm_130502.1	chr15	98831453	98831488	-	1	NA	promoter-TSS (NM_016781)	promoter-TSS (NM_016781)	38	NM_016781	19082	Mm.6670	NM_016781	ENSMUSG00000067713	Prkag1	AA571379|BB036179|Prkaac	protein kinase, AMP-activated, gamma 1 non-catalytic subunit	protein-coding
mm_22129.1	chr2	170387972	170388017	-	1	NA	intron (NM_029815, intron 4 of 12)	intron (NM_029815, intron 4 of 12)	31633	NR_040610	73303	Mm.443297	NR_040610	ENSMUSG00000086999	Bcas1os2	1700040N02Rik	breast carcinoma amplified sequence 1, opposite strand 2	ncRNA
mm_110380.1	chr12	40210546	40210563	-	1	NA	intron (NM_013562, intron 8 of 11)	intron (NM_013562, intron 8 of 11)	-11239	NM_001033437	380755	Mm.390463	NM_001033437	ENSMUSG00000071342	Lsmem1	Gm889	leucine-rich single-pass membrane protein 1	protein-coding
mm_162239.1	chrX	154890168	154890168	-	1	NA	promoter-TSS (NM_001097980)	promoter-TSS (NM_001097980)	99	NM_001097980	100040937	Mm.359511	NM_001097980	ENSMUSG00000072100	Cldn34b1	EG546400|Gm16390	claudin 34B1	protein-coding
mm_81662.1	chr9	111019285	111019298	+	1	NA	promoter-TSS (NM_008522)	promoter-TSS (NM_008522)	-1	NM_008522	17002	Mm.282359	NM_008522	ENSMUSG00000032496	Ltf	Csp82|Lf|MMS10R|Ms10r	lactotransferrin	protein-coding
mm_161450.1	chr15	74799941	74799941	-	1	NA	promoter-TSS (NM_029627)	promoter-TSS (NM_029627)	27	NM_029627	76486	Mm.273319	NM_029627	ENSMUSG00000044678	Ly6k	2410015A16Rik|3110035B01Rik|mLy-6K	lymphocyte antigen 6 complex, locus K	protein-coding
mm_166082.1	chr4	137796286	137796296	-	1	NA	promoter-TSS (NM_007431)	promoter-TSS (NM_007431)	93	NM_007431	11647	Mm.288186	NM_007431	ENSMUSG00000028766	Alpl	ALP|APTNAP|Akp-2|Akp2|TNAP|TNSALP	alkaline phosphatase, liver/bone/kidney	protein-coding
mm_114683.1	chr13	80963064	80963082	+	1	NA	Intergenic	CpG	-1001	NR_015587	319983	Mm.343027	NR_015587	ENSMUSG00000097098	9330111N05Rik	-	RIKEN cDNA 9330111N05 gene	ncRNA
mm_169550.1	chr15	103242416	103242420	+	1	NA	exon (NM_010447, exon 6 of 10)	exon (NM_010447, exon 6 of 10)	1964	NR_002883	434858	Mm.391346	NR_002883		Gm5643	EG434858	heterogeneous nuclear ribonucleoprotein A1 pseudogene	pseudo
mm_134073.1	chr16	8667411	8667415	-	1	NA	intron (NM_025821, intron 1 of 3)	L2b|LINE|L2	4740	NM_025821	52502	Mm.142095	NM_025821	ENSMUSG00000008393	Carhsp1	1200011K09Rik|Crhsp-24|D16Ertd465e	calcium regulated heat stable protein 1	protein-coding
mm_157362.1	chrX	37110258	37110346	-	1	NA	promoter-TSS (NM_026573)	promoter-TSS (NM_026573)	20	NM_026573	68134	Mm.271160	NM_026573	ENSMUSG00000036572	Upf3b	5730594O13Rik|AI317193|AW541158|RENT3B|UPF3X	UPF3 regulator of nonsense transcripts homolog B (yeast)	protein-coding
mm_14894.1	chr2	149405306	149405312	+	1	NA	promoter-TSS (NM_021405)	promoter-TSS (NM_021405)	60	NM_021405	58214	Mm.117117	NM_021405	ENSMUSG00000033156	Cst10	DD72	cystatin 10 (chondrocytes)	protein-coding
mm_105498.1	chr11	106160102	106160168	-	1	NA	promoter-TSS (NM_172397)	promoter-TSS (NM_172397)	7	NM_172397	67803	Mm.21687	NM_172397	ENSMUSG00000040699	Limd2	0610025L06Rik|AI413966	LIM domain containing 2	protein-coding
mm_62993.1	chr7	120624235	120624246	+	1	NA	Intergenic	Intergenic	-10949	NM_025899	67003	Mm.334206	NM_025899	ENSMUSG00000030884	Uqcrc2	1500004O06Rik	ubiquinol cytochrome c reductase core protein 2	protein-coding
mm_60520.1	chr7	44479932	44479947	+	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	-4578	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_54076.1	chr6	14755251	14755286	-	1	NA	promoter-TSS (NM_080464)	promoter-TSS (NM_080464)	6	NM_080464	140491	Mm.209429	NM_080464	ENSMUSG00000042717	Ppp1r3a	GM|RG1|RGL	protein phosphatase 1, regulatory (inhibitor) subunit 3A	protein-coding
mm_92859.1	chr10	81545176	81545192	-	1	NA	promoter-TSS (NM_010301)	promoter-TSS (NM_010301)	-138	NM_010301	14672	Mm.260925	NM_010301	ENSMUSG00000034781	Gna11	Dsk7|E430025L19	guanine nucleotide binding protein, alpha 11	protein-coding
mm_165787.1	chr3	131489713	131489729	+	1	NA	Intergenic	Intergenic	-75047	NM_001289479	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_161223.1	chr13	68999495	68999495	-	1	NA	promoter-TSS (NM_153534)	promoter-TSS (NM_153534)	46	NM_153534	210044	Mm.390617	NM_153534	ENSMUSG00000021536	Adcy2	mKIAA1060	adenylate cyclase 2	protein-coding
mm_149433.1	chr19	11470786	11470802	+	1	NA	intron (NM_001166376, intron 1 of 2)	intron (NM_001166376, intron 1 of 2)	1426	NM_028595	73656	Mm.440719	NM_028595	ENSMUSG00000079419	Ms4a6c	2200009H22Rik|2210417N07Rik	membrane-spanning 4-domains, subfamily A, member 6C	protein-coding
mm_47823.1	chr5	134244175	134244233	-	1	NA	intron (NM_001080746, intron 26 of 34)	intron (NM_001080746, intron 26 of 34)	-14579	NR_104383	17969	Mm.425296	NM_010876	ENSMUSG00000015950	Ncf1	NCF-47K|NOXO2|Ncf-1|p47-phox|p47<phox>|p47phox	neutrophil cytosolic factor 1	protein-coding
mm_148558.1	chr19	4721216	4721225	+	1	NA	intron (NM_021287, intron 2 of 36)	intron (NM_021287, intron 2 of 36)	9997	NM_021287	20743	Mm.329668	NM_021287	ENSMUSG00000067889	Sptbn2	Spnb3|mKIAA0302	spectrin beta, non-erythrocytic 2	protein-coding
mm_60365.1	chr7	44442024	44442038	+	1	NA	promoter-TSS (NM_198250)	promoter-TSS (NM_198250)	-456	NM_198250	272381	Mm.44173	NM_198250	ENSMUSG00000047085	Lrrc4b	A830007M12|Lrig4	leucine rich repeat containing 4B	protein-coding
mm_44858.1	chr5	34243532	34243553	-	1	NA	intron (NM_001015039, intron 1 of 12)	intron (NM_001015039, intron 1 of 12)	44782	NM_001015039	231125	Mm.113388	NM_001015039	ENSMUSG00000037224	Zfyve28	9630058O20Rik|Gm146|mKIAA1643	zinc finger, FYVE domain containing 28	protein-coding
mm_15892.1	chr2	164911428	164911455	+	1	NA	intron (NM_199027, intron 1 of 27)	CpG	309	NM_199027	329559	Mm.330776	NM_199027	ENSMUSG00000039834	Zfp335	1810045J01Rik|NIF-1|Nif1|Znf335	zinc finger protein 335	protein-coding
mm_95552.1	chr11	52307927	52307937	+	1	NA	Intergenic	Intergenic	-24918	NM_001313981	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_106761.1	chr12	4234439	4234452	+	1	NA	promoter-TSS (NM_134046)	promoter-TSS (NM_134046)	-151	NM_134046	52504	Mm.70546	NM_134046	ENSMUSG00000020652	Cenpo	2810429O05Rik|8430427C03Rik|D12Ertd482e	centromere protein O	protein-coding
mm_41475.1	chr5	91962426	91962428	+	1	NA	promoter-TSS (NR_028429)	promoter-TSS (NR_028429)	129	NR_073442	68098	Mm.159453	NM_026557	ENSMUSG00000029397	Rchy1	ARNIP|CHIMP|Pirh2|Zfp363|Znf363	ring finger and CHY zinc finger domain containing 1	protein-coding
mm_2422.1	chr1	95314088	95314100	+	1	NA	exon (NM_026321, exon 1 of 3)	exon (NM_026321, exon 1 of 3)	466	NM_026321	67698	Mm.272705	NM_026321	ENSMUSG00000051185	Fam174a	2310044D20Rik|Fam174|Naa6|Tmem157	family with sequence similarity 174, member A	protein-coding
mm_122579.1	chr14	50834034	50834058	-	1	NA	exon (NM_009351, exon 42 of 55)	exon (NM_009351, exon 42 of 55)	26100	NM_009632	11546	Mm.281482	NM_009632	ENSMUSG00000036023	Parp2	ARTD2|Adprt2|Adprtl2|Aspartl2|C78626|PARP-2	poly (ADP-ribose) polymerase family, member 2	protein-coding
mm_15067.1	chr2	153065989	153065999	+	1	NA	promoter-TSS (NM_145536)	promoter-TSS (NM_145536)	39	NM_145536	228788	Mm.299979	NM_145536	ENSMUSG00000027474	Ccm2l	-	cerebral cavernous malformation 2-like	protein-coding
mm_63980.1	chr7	139983303	139983342	+	1	NA	exon (NM_001291066, exon 21 of 24)	exon (NM_001291066, exon 21 of 24)	3552	NR_106029	102465643		NR_106029	ENSMUSG00000099092	Mir7062	Gm27339|mmu-mir-7062	microRNA 7062	ncRNA
mm_57926.1	chr6	134539519	134539522	-	1	NA	intron (NM_008514, intron 2 of 22)	intron (NM_008514, intron 2 of 22)	27393	NM_008514	16974	Mm.321990	NM_008514	ENSMUSG00000030201	Lrp6	C030016K15Rik|Cd|Gw|ska26|ska<m26Jus>|skax26	low density lipoprotein receptor-related protein 6	protein-coding
mm_2493.1	chr1	105993962	105993983	+	1	NA	intron (NM_001122676, intron 1 of 13)	CpG	3566	NM_001122675	227449	Mm.210188	NM_001122675	ENSMUSG00000038866	Zcchc2	9930114B20Rik|AW212015	zinc finger, CCHC domain containing 2	protein-coding
mm_100251.1	chr11	117326406	117326477	+	1	NA	intron (NM_001113487, intron 2 of 10)	intron (NM_001113487, intron 2 of 10)	-5274	NM_017380	53860	Mm.38450	NM_017380	ENSMUSG00000059248	Sept9	MSF1|Msf|PNUTL4|Sint1	septin 9	protein-coding
mm_131004.1	chr15	103562797	103562809	-	1	NA	TTS (NM_008134)	TTS (NM_008134)	2278	NM_001289587	14663	Mm.219621	NM_008134	ENSMUSG00000022491	Glycam1	MC26|Sgp50|glyCAM-1	glycosylation dependent cell adhesion molecule 1	protein-coding
mm_132830.1	chr16	45372818	45372826	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	36231	NM_010818	17470	Mm.245851	NM_010818	ENSMUSG00000022661	Cd200	Mox2|OX2	CD200 antigen	protein-coding
mm_80266.1	chr9	72925623	72925671	+	1	NA	promoter-TSS (NM_028116)	promoter-TSS (NM_028116)	-3	NM_028116	72135	Mm.273605	NM_028116	ENSMUSG00000034910	Pygo1	2600014C22Rik	pygopus 1	protein-coding
mm_108836.1	chr12	95782608	95782610	+	1	NA	3' UTR (NM_201518, exon 2 of 2)	3' UTR (NM_201518, exon 2 of 2)	90383	NM_201518	399558	Mm.341948	NM_201518	ENSMUSG00000047414	Flrt2	-	fibronectin leucine rich transmembrane protein 2	protein-coding
mm_157330.1	chrX	23365009	23365043	-	1	NA	promoter-TSS (NM_026167)	promoter-TSS (NM_026167)	56	NM_026167	67455	Mm.224306	NM_026167	ENSMUSG00000036782	Klhl13	1200009K10Rik|AI451128|Bklhd2|D130072F20Rik	kelch-like 13	protein-coding
mm_7390.1	chr1	111864710	111864722	-	1	NA	5' UTR (NM_001081316, exon 1 of 2)	5' UTR (NM_001081316, exon 1 of 2)	202	NM_001081316	319901	Mm.103468	NM_001081316	ENSMUSG00000038702	Dsel	9330132E09Rik|DS-epi2	dermatan sulfate epimerase-like	protein-coding
mm_41320.1	chr5	90472077	90472108	+	1	NA	exon (NM_009654, exon 11 of 15)	exon (NM_009654, exon 11 of 15)	11222	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_34357.1	chr4	144891437	144891447	+	1	NA	Intergenic	MER5A|DNA|hAT-Charlie	-1385	NM_001172424	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding
mm_88180.1	chr10	69925830	69925853	+	1	NA	5' UTR (NM_009670, exon 1 of 20)	5' UTR (NM_009670, exon 1 of 20)	309	NM_009670	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_119250.1	chr14	33923583	33923602	+	1	NA	promoter-TSS (NM_145741)	promoter-TSS (NM_145741)	5	NM_145741	14560	Mm.432071	NM_145741	ENSMUSG00000021943	Gdf10	Bmp3b	growth differentiation factor 10	protein-coding
mm_152092.1	chr19	6908290	6908310	-	1	NA	intron (NM_012021, intron 1 of 5)	intron (NM_012021, intron 1 of 5)	1345	NM_012021	54683	Mm.279782	NM_012021	ENSMUSG00000024953	Prdx5	AOEB166|AOPP|Pmp20|Prdx6|PrxV	peroxiredoxin 5	protein-coding
mm_148877.1	chr19	6498025	6498037	+	1	NA	intron (NM_001205234, intron 17 of 22)	CpG	45039	NM_009203	20521	Mm.391146	NM_009203	ENSMUSG00000061742	Slc22a12	AI987855|OAT4L|Rst|Slc22al2|URAT1	solute carrier family 22 (organic anion/cation transporter), member 12	protein-coding
mm_138944.1	chr17	44078826	44078910	+	1	NA	promoter-TSS (NM_001168620)	promoter-TSS (NM_001168620)	66	NM_001329619	83965	Mm.30145	NM_032003	ENSMUSG00000023960	Enpp5	AW061004|D17Abb1e|E-NPP 5	ectonucleotide pyrophosphatase/phosphodiesterase 5	protein-coding
mm_70303.1	chr8	4087695	4087717	+	1	NA	Intergenic	CpG	18058	NM_026956	69142	Mm.171061	NM_026956	ENSMUSG00000051906	Cd209f	1810029C22Rik|AI647041|SIGNR8	CD209f antigen	protein-coding
mm_102797.1	chr11	68853020	68853101	-	1	NA	promoter-TSS (NM_023668)	promoter-TSS (NM_023668)	71	NM_023668	83431	Mm.31979	NM_023668	ENSMUSG00000018736	Ndel1	2600006O07Rik|MITAP1|NUDEL|mNudel	nudE neurodevelopment protein 1 like 1	protein-coding
mm_3213.1	chr1	135838908	135838911	+	1	NA	intron (NM_001130181, intron 1 of 13)	intron (NM_001130181, intron 1 of 13)	-1952	NM_001130176	21956	Mm.247470	NM_011619	ENSMUSG00000026414	Tnnt2	Tnt|cTnT	troponin T2, cardiac	protein-coding
mm_77264.1	chr8	115707779	115707792	-	1	NA	promoter-TSS (NM_001025577)	promoter-TSS (NM_001025577)	-891	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_173194.1	chrX	62617038	62617038	+	1	NA	Intergenic	Intergenic	-90027	NR_045442	75545	Mm.391270	NR_045442	ENSMUSG00000085757	1700019B21Rik	-	RIKEN cDNA 1700019B21 gene	ncRNA
mm_152469.1	chr19	10968722	10968738	-	1	NA	exon (NM_023529, exon 2 of 9)	exon (NM_023529, exon 2 of 9)	5940	NM_023529	69826	Mm.273404	NM_023529	ENSMUSG00000024731	Ms4a10	2010001N17Rik	membrane-spanning 4-domains, subfamily A, member 10	protein-coding
mm_21479.1	chr2	162661076	162661090	-	1	NA	promoter-TSS (NM_021464)	promoter-TSS (NM_021464)	64	NM_001291151	19281	Mm.235807	NM_021464	ENSMUSG00000053141	Ptprt	R-PTP-T|RPTP-rfo|RPTP-rho|RPTPmam4|RPTPrho|mKIAA0283|mRPTPrho	protein tyrosine phosphatase, receptor type, T	protein-coding
mm_7792.1	chr1	131511424	131511433	-	1	NA	intron (NM_001081011, intron 2 of 22)	CT-rich|Low_complexity|Low_complexity	15933	NM_001081011	14270	Mm.276259	NM_019520	ENSMUSG00000026425	Srgap2	9930124L22Rik|AI448945|FBP2|Fnbp2|srGAP3	SLIT-ROBO Rho GTPase activating protein 2	protein-coding
mm_98590.1	chr11	95777980	95778017	+	1	NA	Intergenic	MLT1F1|LTR|ERVL-MaLR	28931	NM_201609	268469	Mm.389038	NM_201609	ENSMUSG00000075595	Zfp652	9530033F24Rik|ZNF652	zinc finger protein 652	protein-coding
mm_95029.1	chr11	32024869	32024886	+	1	NA	intron (NM_001290680, intron 3 of 4)	intron (NM_001290680, intron 3 of 4)	23600	NM_001290681	18197	Mm.3304	NM_008741	ENSMUSG00000020297	Nsg2	-	neuron specific gene family member 2	protein-coding
mm_123107.1	chr14	55884198	55884216	-	1	NA	promoter-TSS (NM_019820)	promoter-TSS (NM_019820)	49	NM_019820	56410	Mm.97163	NM_019820	ENSMUSG00000040380	Cbln3	-	cerebellin 3 precursor protein	protein-coding
mm_30616.1	chr4	8535605	8535717	+	1	NA	promoter-TSS (NM_021518)	promoter-TSS (NM_021518)	17	NM_021518	59021	Mm.397471	NM_021518	ENSMUSG00000047187	Rab2a	9330148M11Rik|C80220|Rab2	RAB2A, member RAS oncogene family	protein-coding
mm_44788.1	chr5	32184996	32185036	-	1	NA	Intergenic	Intergenic	-47692	NM_030072	665270	Mm.160067	NM_030072	ENSMUSG00000029134	Plb1	4632413E21Rik|4930433E17Rik|4930539A06Rik|BC033606	phospholipase B1	protein-coding
mm_70688.1	chr8	15011418	15011426	+	1	NA	intron (NM_029116, intron 1 of 1)	CpG	397	NM_029116	74901	Mm.46675	NM_029116	ENSMUSG00000055675	Kbtbd11	2900016B01Rik|4930465M17Rik|mKIAA0711	kelch repeat and BTB (POZ) domain containing 11	protein-coding
mm_66019.1	chr7	30603560	30603565	-	1	NA	3' UTR (NM_026815, exon 8 of 8)	3' UTR (NM_026815, exon 8 of 8)	9172	NM_026815	109637	Mm.25471	NM_026815	ENSMUSG00000006313	Upk1a	1110031P12Rik|AU019298|C87192|Tspan21|Upk1	uroplakin 1A	protein-coding
mm_32900.1	chr4	119072079	119072089	+	1	NA	Intergenic	Intergenic	-2973	NR_131914	433751	Mm.224312	NR_131914	ENSMUSG00000066060	Gm12866	OTTMUSG00000008833	predicted gene 12866	ncRNA
mm_51335.1	chr6	72390005	72390014	+	1	NA	intron (NM_016794, intron 1 of 2)	intron (NM_016794, intron 1 of 2)	658	NM_016794	22320	Mm.1838	NM_016794	ENSMUSG00000050732	Vamp8	AU041171|Edb|endobrevin	vesicle-associated membrane protein 8	protein-coding
mm_70301.1	chr8	4087529	4087551	+	1	NA	Intergenic	CpG	18224	NM_026956	69142	Mm.171061	NM_026956	ENSMUSG00000051906	Cd209f	1810029C22Rik|AI647041|SIGNR8	CD209f antigen	protein-coding
mm_115820.1	chr13	20016503	20016506	-	1	NA	Intergenic	RLTR27|LTR|ERVK	-74003	NM_080288	140580	Mm.342392	NM_080288	ENSMUSG00000041112	Elmo1	6330578D22Rik|C230095H21Rik|CED-12	engulfment and cell motility 1	protein-coding
mm_120631.1	chr14	70466567	70466597	+	1	NA	intron (NM_145981, intron 4 of 4)	intron (NM_145981, intron 4 of 4)	9065	NM_145981	105653	Mm.192598	NM_145981	ENSMUSG00000003469	Phyhip	AW049870|C630010D02Rik|Lnap1ip|PAHX-AP#1|PAHX-AP1	phytanoyl-CoA hydroxylase interacting protein	protein-coding
mm_89991.1	chr10	112060184	112060207	+	1	NA	promoter-TSS (NM_027018)	promoter-TSS (NM_027018)	6	NM_027018	69286	Mm.47058	NM_027018	ENSMUSG00000020213	Glipr1l1	1700011E04Rik	GLI pathogenesis-related 1 like 1	protein-coding
mm_68603.1	chr7	116238385	116238392	-	1	NA	promoter-TSS (NM_001305186)	promoter-TSS (NM_001305186)	-612	NM_001305186	233765	Mm.3741	NM_172743	ENSMUSG00000045659	Plekha7	A430081P20Rik|AI414265	pleckstrin homology domain containing, family A member 7	protein-coding
mm_95262.1	chr11	44699027	44699029	+	1	NA	intron (NM_007897, intron 6 of 15)	intron (NM_007897, intron 6 of 15)	80928	NM_001290710	13591	Mm.439662	NM_007897	ENSMUSG00000057098	Ebf1	Ebf|O/E-1|OE-1|Olf-1|Olf1	early B cell factor 1	protein-coding
mm_18007.1	chr2	38263159	38263162	-	1	NA	intron (NM_146122, intron 1 of 21)	intron (NM_146122, intron 1 of 21)	24224	NM_146122	227801	Mm.314245	NM_146122	ENSMUSG00000035392	Dennd1a	6030446I19Rik|connecdenn	DENN/MADD domain containing 1A	protein-coding
mm_137133.1	chr17	23600845	23600883	+	1	NA	promoter-TSS (NM_001033425)	promoter-TSS (NM_001033425)	38	NM_001289482	332221	Mm.270315	NM_001033425	ENSMUSG00000023902	Zscan10	BC068284|Zfp206|Zkscan10|Znf206	zinc finger and SCAN domain containing 10	protein-coding
mm_86992.1	chr10	25993621	25993628	+	1	NA	exon (NM_029881, exon 2 of 2)	exon (NM_029881, exon 2 of 2)	-84631	NR_028030	100040851	Mm.478630	NR_028030	ENSMUSG00000039098	Gm9767	ENSMUSG00000039098	predicted gene 9767	ncRNA
mm_51530.1	chr6	83188892	83188894	+	1	NA	intron (NM_001347310, intron 2 of 26)	intron (NM_001347310, intron 2 of 26)	2947	NM_001347310	13191	Mm.6919	NM_007835	ENSMUSG00000031865	Dctn1	AL022633|DAP-150|DP-150|Glued|p150|p150-glued|p150<glued>	dynactin 1	protein-coding
mm_153459.1	chr19	41217416	41217428	-	1	NA	exon (NM_133352, exon 13 of 15)	exon (NM_133352, exon 13 of 15)	-10648	NM_011904	24087	Mm.89983	NM_011904	ENSMUSG00000025013	Tll2	-	tolloid-like 2	protein-coding
mm_9708.1	chr1	179517993	179518026	-	1	NA	promoter-TSS (NM_027188)	promoter-TSS (NM_027188)	-6	NM_027188	69726	Mm.222338	NM_027188	ENSMUSG00000055067	Smyd3	2410008A19Rik|Zmynd1	SET and MYND domain containing 3	protein-coding
mm_70325.1	chr8	4325206	4325263	+	1	NA	promoter-TSS (NM_010485)	promoter-TSS (NM_010485)	24	NR_033527	20300	Mm.7275	NM_009138	ENSMUSG00000023235	Ccl25	A130072A22Rik|AI852536|CKb15|Scya25|TECK	chemokine (C-C motif) ligand 25	protein-coding
mm_45077.1	chr5	43881923	43881928	-	1	NA	intron (NM_007646, intron 1 of 7)	intron (NM_007646, intron 1 of 7)	13116	NM_007646	12494	Mm.249873	NM_007646	ENSMUSG00000029084	Cd38	ADPRC 1|Cd38-rs1|I-19	CD38 antigen	protein-coding
mm_98277.1	chr11	89019480	89019501	+	1	NA	3' UTR (NM_009546, exon 9 of 9)	3' UTR (NM_009546, exon 9 of 9)	20087	NM_009546	217069	Mm.248445	NM_009546	ENSMUSG00000000275	Trim25	AA960166|AL022677|EFP|Zfp147	tripartite motif-containing 25	protein-coding
mm_136105.1	chr16	85163696	85163718	-	1	NA	intron (NM_007471, intron 1 of 15)	intron (NM_007471, intron 1 of 15)	10000	NM_001198825	11820	Mm.277585	NM_007471	ENSMUSG00000022892	App	Abeta|Abpp|Adap|Ag|Cvap|E030013M08Rik|betaApp	amyloid beta (A4) precursor protein	protein-coding
mm_56262.1	chr6	90887112	90887114	-	1	NA	Intergenic	MIR|SINE|MIR	-76990	NM_001134384	232227	Mm.196943	NM_182784	ENSMUSG00000034312	Iqsec1	AW561907|BC026481|BRAG2|D6Ertd349e|cI-43	IQ motif and Sec7 domain 1	protein-coding
mm_17057.1	chr2	21205376	21205384	-	1	NA	promoter-TSS (NM_027728)	promoter-TSS (NM_027728)	-15	NM_027728	71233	Mm.27658	NM_027728	ENSMUSG00000026679	Enkur	4933434I06Rik|AU016229	enkurin, TRPC channel interacting protein	protein-coding
mm_128950.1	chr15	74753032	74753034	-	1	NA	promoter-TSS (NM_011838)	promoter-TSS (NM_011838)	-54	NM_011838	23936	Mm.257067	NM_011838	ENSMUSG00000022594	Lynx1	AI838844|SLURP-2	Ly6/neurotoxin 1	protein-coding
mm_172601.1	chr8	15519852	15519857	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	462201	NM_008664	17930	Mm.272115	NM_008664	ENSMUSG00000031461	Myom2	AW146149	myomesin 2	protein-coding
mm_162944.1	chr10	128961013	128961013	-	1	NA	promoter-TSS (NM_027853)	promoter-TSS (NM_027853)	-25	NM_027853	71664	Mm.337232	NM_027853	ENSMUSG00000025347	Mettl7b	0610006F02Rik|AI266817	methyltransferase like 7B	protein-coding
mm_86064.1	chr9	114688634	114688663	-	1	NA	promoter-TSS (NM_146229)	promoter-TSS (NM_146229)	-183	NM_146229	235661	Mm.128627	NM_146229	ENSMUSG00000032435	Dync1li1	1110053F02Rik|Dnclic1|LIC-1	dynein cytoplasmic 1 light intermediate chain 1	protein-coding
mm_43424.1	chr5	136057139	136057143	+	1	NA	promoter-TSS (NM_027158)	promoter-TSS (NM_027158)	-126	NM_027158	69665	Mm.75713	NM_027158	ENSMUSG00000006143	Upk3bl	2310043J07Rik	uroplakin 3B-like	protein-coding
mm_136854.1	chr17	12798596	12798609	+	1	NA	intron (NR_027784, intron 2 of 2)	B1F|SINE|Alu	-28896	NM_010515	16004	Mm.26553	NM_010515	ENSMUSG00000023830	Igf2r	AI661837|CD222|CI-MPR|M6P/IGF2R|Mpr300	insulin-like growth factor 2 receptor	protein-coding
mm_81414.1	chr9	109054882	109054901	+	1	NA	promoter-TSS (NM_026381)	promoter-TSS (NM_026381)	25	NM_026381	66940	Mm.196533	NM_025858	ENSMUSG00000025647	Shisa5	2310008D10Rik|6430628I05Rik|Scotin|mShisa5	shisa family member 5	protein-coding
mm_39838.1	chr5	30873067	30873100	+	1	NA	exon (NM_144525, exon 8 of 17)	exon (NM_144525, exon 8 of 17)	3436	NM_144525	68796	Mm.205169	NM_144525	ENSMUSG00000038828	Tmem214	1110039B18Rik|4921530J21Rik|AI841294|AU018742|C76280	transmembrane protein 214	protein-coding
mm_108745.1	chr12	88725658	88725686	+	1	NA	Intergenic	Intergenic	-68832	NM_001198587	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding
mm_122670.1	chr14	51923054	51923080	-	1	NA	promoter-TSS (NM_001011687)	promoter-TSS (NM_001011687)	-294	NM_001011687	497071	Mm.378602	NM_001011687	ENSMUSG00000068392	Rnase13	-	ribonuclease, RNase A family, 13 (non-active)	protein-coding
mm_48695.1	chr5	146832804	146832816	-	1	NA	promoter-TSS (NM_019647)	promoter-TSS (NM_019647)	-80	NM_019647	19933	Mm.316592	NM_019647	ENSMUSG00000041453	Rpl21	8430440E03Rik|L21	ribosomal protein L21	protein-coding
mm_32790.1	chr4	116807729	116807751	+	1	NA	promoter-TSS (NM_026654)	promoter-TSS (NM_026654)	6	NM_001159581	70603	Mm.180333	NM_133250	ENSMUSG00000028687	Mutyh	5730495A01Rik|Mutyha|Mutyhalpha|Mutyhb|Mutyhbeta|Mutyhc|Myh	mutY DNA glycosylase	protein-coding
mm_95167.1	chr11	40733623	40733631	+	1	NA	promoter-TSS (NM_013552)	promoter-TSS (NM_013552)	-34	NM_026023	52653	Mm.276504	NM_026023	ENSMUSG00000020328	Nudcd2	-	NudC domain containing 2	protein-coding
mm_80542.1	chr9	81264622	81264622	+	1	NA	Intergenic	Lx9|LINE|L1	-367308	NR_040394	319405	Mm.246494	NR_040393	ENSMUSG00000097466	D430036J16Rik	-	RIKEN cDNA D430036J16 gene	ncRNA
mm_127059.1	chr15	97247012	97247052	+	1	NA	promoter-TSS (NM_172293)	promoter-TSS (NM_172293)	-75	NM_172293	239647	Mm.130036	NM_172293	ENSMUSG00000044250	Pced1b	Fam113b	PC-esterase domain containing 1B	protein-coding
mm_82129.1	chr9	123515504	123515517	+	1	NA	intron (NM_013860, intron 4 of 7)	MER5A|DNA|hAT-Charlie	-14372	NM_030692	83493	Mm.273671	NM_030692	ENSMUSG00000025240	Sacm1l	SAC1|Sac1p|mKIAA0851	SAC1 suppressor of actin mutations 1-like (yeast)	protein-coding
mm_43073.1	chr5	124446749	124446776	+	1	NA	promoter-TSS (NM_001310727)	promoter-TSS (NM_001310727)	58	NM_001310727	67956	Mm.137966	NM_030241	ENSMUSG00000049327	Kmt5a	2410195B05Rik|AA617402|AW536475|PR-SET7|PR/SET07|Setd8	lysine methyltransferase 5A	protein-coding
mm_171288.1	chr3	90079711	90079711	+	1	NA	5' UTR (NM_001253740, exon 1 of 8)	5' UTR (NM_001253740, exon 1 of 8)	190	NM_001293749	59069	Mm.240839	NM_022314	ENSMUSG00000027940	Tpm3	TM30nm|TMnm|Tm5NM|Tpm-5|Tpm5|Trop-5|gamma-TM|hTM30nm|hTMnm	tropomyosin 3, gamma	protein-coding
mm_1200.1	chr1	62711684	62711690	+	1	NA	intron (NM_001077405, intron 1 of 15)	intron (NM_001077405, intron 1 of 15)	8370	NM_001077405	18187	Mm.266341	NM_010939	ENSMUSG00000025969	Nrp2	1110048P06Rik|Np-2|Np2|Npn-2|Npn2	neuropilin 2	protein-coding
mm_23361.1	chr3	55242562	55242579	+	1	NA	promoter-TSS (NM_001195538)	promoter-TSS (NM_001195538)	44	NM_001195538	13175	Mm.393242	NM_019978	ENSMUSG00000027797	Dclk1	1700113D08Rik|2810480F11Rik|AI836758|Click-I|Cpg16|Dcamkl1|Dcl|Dclk|mKIAA0369	doublecortin-like kinase 1	protein-coding
mm_50676.1	chr6	51544692	51544706	+	1	NA	5' UTR (NM_028035, exon 1 of 7)	5' UTR (NM_028035, exon 1 of 7)	176	NM_001127348	71982	Mm.294166	NM_028035	ENSMUSG00000038301	Snx10	2410004M09Rik	sorting nexin 10	protein-coding
mm_7499.1	chr1	121430967	121430984	-	1	NA	promoter-TSS (NM_029955)	promoter-TSS (NM_029955)	-92	NM_029955	70829	Mm.25788	NM_027567	ENSMUSG00000026339	Ccdc93	4633402D15Rik|9230102M16Rik	coiled-coil domain containing 93	protein-coding
mm_104752.1	chr11	98463631	98463683	-	1	NA	Intergenic	Intergenic	16823	NM_010346	14786	Mm.276702	NM_010346	ENSMUSG00000019312	Grb7	mKIAA4028	growth factor receptor bound protein 7	protein-coding
mm_33400.1	chr4	129821446	129821459	+	1	NA	intron (NM_001164745, intron 1 of 5)	intron (NM_001164745, intron 1 of 5)	744	NM_001164745	19244	Mm.193688	NM_008974	ENSMUSG00000028788	Ptp4a2	Prl-2	protein tyrosine phosphatase 4a2	protein-coding
mm_146107.1	chr18	74216347	74216407	+	1	NA	5' UTR (NM_028868, exon 1 of 15)	5' UTR (NM_028868, exon 1 of 15)	165	NM_028868	74322	Mm.17537	NM_028868	ENSMUSG00000024560	Cxxc1	2410002I16Rik|5830420C16Rik|AI426635|Cfp1|Cgbp|PHF18	CXXC finger 1 (PHD domain)	protein-coding
mm_163506.1	chr12	113140604	113140608	+	1	NA	promoter-TSS (NM_001347443)	promoter-TSS (NM_001347443)	1	NM_001347443	68337	Mm.133825	NM_024223	ENSMUSG00000006356	Crip2	0610010I23Rik|AW743261|C77570|CRP2|CRP4|Crp|ESP1|Hlp	cysteine rich protein 2	protein-coding
mm_119330.1	chr14	39220110	39220125	+	1	NA	intron (NM_001190187, intron 1 of 9)	MTB_Mm-int|LTR|ERVL-MaLR	-252312	NR_131973	432842	Mm.352566	NR_131973		LOC432842	-	uncharacterized LOC432842	ncRNA
mm_133308.1	chr16	77599740	77599744	+	1	NA	promoter-TSS (NR_029728)	promoter-TSS (NR_029728)	85	NR_029728	387246		NR_029728	ENSMUSG00000065557	Mirlet7c-1	Mirnlet7c|Mirnlet7c-1|let-7c-1	microRNA let7c-1	ncRNA
mm_47366.1	chr5	122922089	122922103	-	1	NA	intron (NM_001003953, intron 11 of 22)	B4A|SINE|B4	-21746	NM_013910	30841	Mm.86406	NM_013910	ENSMUSG00000029475	Kdm2b	Cxxc2|Fbl10|Fbxl10|Jhdm1b|PCCX2	lysine (K)-specific demethylase 2B	protein-coding
mm_33456.1	chr4	130792106	130792132	+	1	NA	promoter-TSS (NM_011520)	promoter-TSS (NM_011520)	-418	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_74587.1	chr8	11454925	11454934	-	1	NA	intron (NM_011227, intron 1 of 1)	PB1D9|SINE|Alu	-23000	NR_126558	102132	Mm.37632	NR_126558	ENSMUSG00000096957	E230013L22Rik	AI645545	RIKEN cDNA E230013L22 gene	ncRNA
mm_161061.1	chr12	70347370	70347370	-	1	NA	5' UTR (NM_001110203, exon 1 of 9)	5' UTR (NM_001110203, exon 1 of 9)	244	NM_001286386	94090	Mm.184012	NM_053167	ENSMUSG00000021071	Trim9	-	tripartite motif-containing 9	protein-coding
mm_7630.1	chr1	127677924	127677956	-	1	NA	promoter-TSS (NM_028135)	promoter-TSS (NM_028135)	81	NM_028135	72160	Mm.281287	NM_028135	ENSMUSG00000026347	Tmem163	2610024A01Rik|SV31	transmembrane protein 163	protein-coding
mm_99992.1	chr11	114741723	114741734	+	1	NA	intron (NM_001034878, intron 6 of 12)	intron (NM_001034878, intron 6 of 12)	8021	NR_037269	100526524		NR_037269	ENSMUSG00000077991	Mir466n	mmu-mir-466n	microRNA 466n	ncRNA
mm_6096.1	chr1	63273113	63273136	-	1	NA	promoter-TSS (NM_028673)	promoter-TSS (NM_028673)	-145	NM_028673	73884	Mm.86986	NM_028673	ENSMUSG00000027520	Zdbf2	4930431J08Rik|9330107J05Rik	zinc finger, DBF-type containing 2	protein-coding
mm_30293.1	chr3	148989987	148990044	-	1	NA	Intergenic	CpG	-35380	NM_001081298	99633	Mm.9776	NM_001081298	ENSMUSG00000028184	Adgrl2	AI450192|CIRL-2|Gm619|Lec1|Lphh1|Lphn2|mKIAA0786	adhesion G protein-coupled receptor L2	protein-coding
mm_74273.1	chr8	125013034	125013095	+	1	NA	promoter-TSS (NM_016909)	promoter-TSS (NM_016909)	67	NM_016909	53424	Mm.5248	NM_016909	ENSMUSG00000056820	Tsnax	R74833|Trax	translin-associated factor X	protein-coding
mm_48719.1	chr5	147322381	147322383	-	1	NA	promoter-TSS (NM_001039678)	promoter-TSS (NM_001039678)	58	NM_001039678	231903	Mm.291286	NM_001039678	ENSMUSG00000075543	Urad	EG231903|Prhoxnb	ureidoimidazoline (2-oxo-4-hydroxy-4-carboxy-5) decarboxylase	protein-coding
mm_15902.1	chr2	164968167	164968180	+	1	NA	5' UTR (NM_020333, exon 1 of 26)	5' UTR (NM_020333, exon 1 of 26)	185	NM_020333	57138	Mm.252987	NM_020333	ENSMUSG00000017740	Slc12a5	KCC2|mKIAA1176	solute carrier family 12, member 5	protein-coding
mm_172308.1	chr7	104507846	104507856	-	1	NA	promoter-TSS (NM_001167828)	promoter-TSS (NM_001167828)	-2	NM_001167828	209387	Mm.277377	NM_199146	ENSMUSG00000057596	Trim30d	AI451617|TRIM30-3|Trim79	tripartite motif-containing 30D	protein-coding
mm_153143.1	chr19	34248455	34248543	-	1	NA	exon (NM_007392, exon 4 of 9)	exon (NM_007392, exon 4 of 9)	6874	NM_007392	11475	Mm.213025	NM_007392	ENSMUSG00000035783	Acta2	0610041G09Rik|Actvs|SMalphaA|a-SMA|alphaSMA	actin, alpha 2, smooth muscle, aorta	protein-coding
mm_104036.1	chr11	86268549	86268565	-	1	NA	3' UTR (NM_001080931, exon 30 of 30)	3' UTR (NM_001080931, exon 30 of 30)	-10989	NM_027421	70422	Mm.171304	NM_027421	ENSMUSG00000018068	Ints2	2810417D08Rik|AA408260|AI987735|mKIAA1287	integrator complex subunit 2	protein-coding
mm_152792.1	chr19	21471189	21471205	-	1	NA	intron (NM_010266, intron 1 of 13)	intron (NM_010266, intron 1 of 13)	1464	NM_010266	14544	Mm.45054	NM_010266	ENSMUSG00000058624	Gda	AU015411|AW047581|GAH	guanine deaminase	protein-coding
mm_32637.1	chr4	115000248	115000268	+	1	NA	5' UTR (NM_009185, exon 1 of 17)	5' UTR (NM_009185, exon 1 of 17)	140	NM_001304555	20460	Mm.3988	NM_009185	ENSMUSG00000028718	Stil	Sil	Scl/Tal1 interrupting locus	protein-coding
mm_125047.1	chr15	25843140	25843188	+	1	NA	promoter-TSS (NM_001034851)	promoter-TSS (NM_001034851)	-134	NM_001034851	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_129984.1	chr15	86034178	86034208	-	1	NA	promoter-TSS (NM_009886)	promoter-TSS (NM_009886)	-416	NM_009886	12614	Mm.22680	NM_009886	ENSMUSG00000016028	Celsr1	Adgrc1|Crsh|Scy|crash	cadherin, EGF LAG seven-pass G-type receptor 1	protein-coding
mm_41145.1	chr5	87925625	87925639	+	1	NA	promoter-TSS (NM_007786)	promoter-TSS (NM_007786)	-1	NM_007786	12994	Mm.296303	NM_007786	ENSMUSG00000001622	Csn3	AW208918|CSN10|Csnk	casein kappa	protein-coding
mm_127120.1	chr15	98093419	98093514	+	1	NA	5' UTR (NM_144851, exon 1 of 18)	5' UTR (NM_144851, exon 1 of 18)	103	NM_144851	223870	Mm.384023	NM_144851	ENSMUSG00000033075	Senp1	2310046A20Rik|D15Ertd528e|E330036L07Rik|suPr-2	SUMO1/sentrin specific peptidase 1	protein-coding
mm_156625.1	chrX	155172523	155172554	+	1	NA	Intergenic	Intergenic	-24689	NM_001081671	73347	Mm.63848	NM_001081671	ENSMUSG00000057402	Cldn34b2	1700042B14Rik	claudin 34B2	protein-coding
mm_95241.1	chr11	44617552	44617558	+	1	NA	promoter-TSS (NM_001290711)	promoter-TSS (NM_001290711)	-545	NM_001290711	13591	Mm.439662	NM_007897	ENSMUSG00000057098	Ebf1	Ebf|O/E-1|OE-1|Olf-1|Olf1	early B cell factor 1	protein-coding
mm_128604.1	chr15	58324162	58324178	-	1	NA	promoter-TSS (NM_177755)	promoter-TSS (NM_177755)	-1	NM_177755	268807	Mm.124498	NM_177755	ENSMUSG00000022357	Klhl38	8230402K04Rik	kelch-like 38	protein-coding
mm_25221.1	chr3	103851334	103851344	+	1	NA	intron (NM_001142960, intron 3 of 3)	intron (NM_001142960, intron 3 of 3)	-8456	NR_104070	19260	Mm.395	NM_008979	ENSMUSG00000027843	Ptpn22	70zpep|PEP|Ptpn8	protein tyrosine phosphatase, non-receptor type 22 (lymphoid)	protein-coding
mm_123278.1	chr14	61374323	61374340	-	1	NA	exon (NM_008466, exon 11 of 17)	exon (NM_008466, exon 11 of 17)	-13886	NM_026598	68177	Mm.22758	NM_026598	ENSMUSG00000021928	Ebpl	5730442K12Rik|EBRP	emopamil binding protein-like	protein-coding
mm_120597.1	chr14	70077307	70077366	+	1	NA	promoter-TSS (NM_001289927)	promoter-TSS (NM_001289927)	-109	NM_018781	13655	Mm.103737	NM_018781	ENSMUSG00000033730	Egr3	Pilot	early growth response 3	protein-coding
mm_72186.1	chr8	72443875	72443953	+	1	NA	promoter-TSS (NM_028500)	promoter-TSS (NM_028500)	34	NM_028170	72254	Mm.30136	NM_028170	ENSMUSG00000052794	1700030K09Rik	-	RIKEN cDNA 1700030K09 gene	protein-coding
mm_133509.1	chr16	90738327	90738340	+	1	NA	promoter-TSS (NM_029844)	promoter-TSS (NM_029844)	9	NM_029844	77037	Mm.22455	NM_029844	ENSMUSG00000039956	Mrap	1110025G12Rik|Falp|ORF61	melanocortin 2 receptor accessory protein	protein-coding
mm_122558.1	chr14	49241179	49241181	-	1	NA	intron (NM_025956, intron 3 of 6)	L2a|LINE|L2	4248	NM_025956	67082	Mm.87439	NM_025956	ENSMUSG00000021850	1700011H14Rik	-	RIKEN cDNA 1700011H14 gene	protein-coding
mm_155837.1	chrX	100777307	100777313	+	1	NA	promoter-TSS (NM_001177780)	promoter-TSS (NM_001177780)	39	NM_001177780	53310	Mm.4615	NM_016747	ENSMUSG00000000881	Dlg3	Dlgh3|SAP102|mKIAA1232	discs, large homolog 3 (Drosophila)	protein-coding
mm_158676.1	chrX	158043267	158043286	-	1	NA	promoter-TSS (NM_177751)	promoter-TSS (NM_177751)	-79	NM_177751	245684	Mm.197074	NM_177751	ENSMUSG00000025658	Cnksr2	Cnk2|Ksr2	connector enhancer of kinase suppressor of Ras 2	protein-coding
mm_35992.1	chr4	55532180	55532238	-	1	NA	5' UTR (NM_010637, exon 1 of 5)	5' UTR (NM_010637, exon 1 of 5)	266	NM_010637	16600	Mm.4325	NM_010637	ENSMUSG00000003032	Klf4	EZF|Gklf|Zie	Kruppel-like factor 4 (gut)	protein-coding
mm_51573.1	chr6	83758633	83758644	+	1	NA	3' UTR (NM_134157, exon 14 of 14)	3' UTR (NM_134157, exon 14 of 14)	3870	NR_105027	67934	Mm.126190	NR_105027	ENSMUSG00000099354	1700124L16Rik	-	RIKEN cDNA 1700124L16 gene	ncRNA
mm_127270.1	chr15	99723704	99723754	+	1	NA	3' UTR (NM_010271, exon 8 of 8)	3' UTR (NM_010271, exon 8 of 8)	-1889	NM_183256	66379	Mm.5265	NM_183256	ENSMUSG00000023020	Cox14	2310016M24Rik|AA959804	cytochrome c oxidase assembly protein 14	protein-coding
mm_48573.1	chr5	143320279	143320282	-	1	NA	exon (NM_028379, exon 7 of 8)	exon (NM_028379, exon 7 of 8)	-4920	NM_172726	231868	Mm.440105	NM_172726	ENSMUSG00000039244	E130309D02Rik	A630028N22	RIKEN cDNA E130309D02 gene	protein-coding
mm_43931.1	chr5	145084101	145084109	+	1	NA	intron (NM_019767, intron 1 of 9)	intron (NM_019767, intron 1 of 9)	236	NM_019767	56443	Mm.371610	NM_019767	ENSMUSG00000029621	Arpc1a	0610010H08Rik|1110030K07Rik|41kDa|AA407347|Sid32|Sid329	actin related protein 2/3 complex, subunit 1A	protein-coding
mm_168091.1	chr10	128059158	128059161	+	1	NA	5' UTR (NM_019766, exon 1 of 8)	5' UTR (NM_019766, exon 1 of 8)	177	NM_019766	56351	Mm.305816	NM_019766	ENSMUSG00000071072	Ptges3	5730442A20Rik|Ptges|Tebp|cPGES|p23|sid3177	prostaglandin E synthase 3 (cytosolic)	protein-coding
mm_63816.1	chr7	133776858	133776902	+	1	NA	promoter-TSS (NM_025850)	promoter-TSS (NM_025850)	-11	NM_025850	66930	Mm.87448	NM_025850	ENSMUSG00000053111	Fank1	1700007B22Rik|AI850911	fibronectin type 3 and ankyrin repeat domains 1	protein-coding
mm_42042.1	chr5	108434448	108434458	+	1	NA	promoter-TSS (NM_007507)	promoter-TSS (NM_007507)	-75	NM_007507	11958	Mm.136093	NM_007507	ENSMUSG00000050856	Atp5k	2610008D24Rik|Atp5i|Lfm1	ATP synthase, H+ transporting, mitochondrial F1F0 complex, subunit E	protein-coding
mm_100379.1	chr11	119270228	119270242	+	1	NA	exon (NM_008064, exon 2 of 20)	exon (NM_008064, exon 2 of 20)	2272	NM_008064	14387	Mm.4793	NM_008064	ENSMUSG00000025579	Gaa	E430018M07Rik	glucosidase, alpha, acid	protein-coding
mm_150136.1	chr19	30232922	30232940	+	1	NA	promoter-TSS (NM_010776)	promoter-TSS (NM_010776)	-26	NM_010776	17195	Mm.30045	NM_010776	ENSMUSG00000024863	Mbl2	L-MBP|MBL|MBL-C|MBP-C	mannose-binding lectin (protein C) 2	protein-coding
mm_132730.1	chr16	43630313	43630334	+	1	NA	Intergenic	Intergenic	-10332	NR_030576	100124467		NR_030576	ENSMUSG00000076372	Mir568	Mirn568|mmu-mir-568	microRNA 568	ncRNA
mm_167762.1	chr9	110422724	110422728	-	1	NA	3' UTR (NM_008694, exon 4 of 4)	3' UTR (NM_008694, exon 4 of 4)	2918	NM_008694	18054	Mm.236225	NM_008694	ENSMUSG00000032484	Ngp	bectenecin	neutrophilic granule protein	protein-coding
mm_168237.1	chr10	81704842	81704844	+	1	NA	promoter-TSS (NM_001243067)	promoter-TSS (NM_001243067)	18	NM_001243067	73610	Mm.490466	NM_001243067	ENSMUSG00000096795	Zfp433	1700123A16Rik	zinc finger protein 433	protein-coding
mm_75346.1	chr8	43308413	43308423	-	1	NA	Intergenic	Intergenic	-1409	NM_009556	22702	Mm.285848	NM_009556	ENSMUSG00000051176	Zfp42	Rex-1|Rex1|Zfp-42	zinc finger protein 42	protein-coding
mm_146213.1	chr18	76944393	76944444	+	1	NA	promoter-TSS (NM_001039201)	promoter-TSS (NM_001039201)	0	NM_001039201	76987	Mm.236127	NM_029826	ENSMUSG00000025421	Hdhd2	0610039H12Rik|3110052N05Rik	haloacid dehalogenase-like hydrolase domain containing 2	protein-coding
mm_104597.1	chr11	97126951	97126995	-	1	NA	Intergenic	Intergenic	-11642	NM_019507	57765	Mm.94519	NM_019507	ENSMUSG00000001444	Tbx21	TBT1|Tbet|Tblym	T-box 21	protein-coding
mm_46280.1	chr5	100039893	100039903	-	1	NA	promoter-TSS (NM_016690)	promoter-TSS (NM_016690)	-96	NM_026421	67870	Mm.11311	NM_026421	ENSMUSG00000029326	Enoph1	2310057D15Rik|BB183658|C81437	enolase-phosphatase 1	protein-coding
mm_106974.1	chr12	9029983	9030012	+	1	NA	promoter-TSS (NM_029321)	promoter-TSS (NM_029321)	0	NM_029321	75516	Mm.37581	NM_029321	ENSMUSG00000066637	Ttc32	1700013G20Rik	tetratricopeptide repeat domain 32	protein-coding
mm_127256.1	chr15	99702631	99702656	+	1	NA	intron (NM_031842, intron 1 of 12)	intron (NM_031842, intron 1 of 12)	356	NM_031842	83797	Mm.273756	NM_031842	ENSMUSG00000023018	Smarcd1	AA407987|Baf60a|D15Kz1	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1	protein-coding
mm_83772.1	chr9	52048842	52048850	-	1	NA	promoter-TSS (NR_023357)	promoter-TSS (NR_023357)	-141	NR_023357	629557	Mm.422775	NR_023357		Gm6981	EG629557	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_65273.1	chr7	24299321	24299368	-	1	NA	5' UTR (NM_009561, exon 1 of 7)	5' UTR (NM_009561, exon 1 of 7)	205	NM_009561	22719	Mm.12832	NM_009561	ENSMUSG00000050605	Zfp61	-	zinc finger protein 61	protein-coding
mm_4339.1	chr1	171856515	171856530	+	1	NA	intron (NM_001289470, intron 3 of 8)	L1_Mur3|LINE|L1	16825	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_8213.1	chr1	138137125	138137131	-	1	NA	intron (NM_001111316, intron 1 of 31)	intron (NM_001111316, intron 1 of 31)	37998	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_82423.1	chr9	14903891	14903897	-	1	NA	promoter-TSS (NM_176807)	promoter-TSS (NM_176807)	57	NM_176807	64931	Mm.86738	NM_022888	ENSMUSG00000031933	Izumo1r	0910001L11Rik|C86255|Folbp3|Folr4|Juno	IZUMO1 receptor, JUNO	protein-coding
mm_5729.1	chr1	44218953	44218961	-	1	NA	promoter-TSS (NM_207281)	promoter-TSS (NM_207281)	-26	NM_207281	403183	Mm.336176	NM_207281	ENSMUSG00000046828	Mettl21e	4832428D23Rik|Gm991	methyltransferase like 21E	protein-coding
mm_106465.1	chr11	120070564	120070574	-	1	NA	exon (NM_009734, exon 15 of 26)	exon (NM_009734, exon 15 of 26)	16258	NM_009734	12009	Mm.2556	NM_009734	ENSMUSG00000039781	Cep131	AZ1|Azi|Azi1	centrosomal protein 131	protein-coding
mm_58501.1	chr7	3712582	3712585	+	1	NA	TTS (NM_011095)	TTS (NM_011095)	7799	NM_011095	18733	Mm.326531	NM_011095	ENSMUSG00000058818	Pirb	Gp91|LIR-3|Lilrb3|PIR-B	paired Ig-like receptor B	protein-coding
mm_24375.1	chr3	90220882	90220897	+	1	NA	5' UTR (NM_026677, exon 1 of 8)	5' UTR (NM_026677, exon 1 of 8)	105	NM_026677	68328	Mm.29355	NM_026677	ENSMUSG00000027935	Rab13	0610007N03Rik|B230212B15Rik	RAB13, member RAS oncogene family	protein-coding
mm_10746.1	chr2	23155955	23155980	+	1	NA	promoter-TSS (NM_013771)	promoter-TSS (NM_013771)	57	NM_025979	67121	Mm.253721	NM_025979	ENSMUSG00000026779	Mastl	2700091H24Rik|C88295|GW|GWL|MAST-L|THC2	microtubule associated serine/threonine kinase-like	protein-coding
mm_63664.1	chr7	129591980	129591986	+	1	NA	exon (NM_172255, exon 1 of 29)	exon (NM_172255, exon 1 of 29)	120	NM_172255	207425	Mm.229323	NM_172255	ENSMUSG00000042055	Wdr11	2900055P10Rik|AW489876|Brwd2|mKIAA1351	WD repeat domain 11	protein-coding
mm_162936.1	chr10	127676725	127676761	-	1	NA	promoter-TSS (NM_001113211)	promoter-TSS (NM_001113211)	-322	NM_173732	210035	Mm.251075	NM_173732	ENSMUSG00000040195	Nemp1	Tmem194|Tmem194a	nuclear envelope integral membrane protein 1	protein-coding
mm_70626.1	chr8	13686678	13686683	+	1	NA	Intergenic	Intergenic	-9093	NM_009025	19414	Mm.18517	NM_009025	ENSMUSG00000031453	Rasa3	AI326412|C86362|E130011G04|GAPIII|hlb381|scat	RAS p21 protein activator 3	protein-coding
mm_75324.1	chr8	43141477	43141483	-	1	NA	promoter-TSS (NM_177742)	promoter-TSS (NM_177742)	6	NM_177742	244448	Mm.64542	NM_177742	ENSMUSG00000031651	Triml1	4933403D14|BC050188	tripartite motif family-like 1	protein-coding
mm_31215.1	chr4	43977805	43977813	+	1	NA	3' UTR (NM_027450, exon 5 of 5)	3' UTR (NM_027450, exon 5 of 5)	-5695	NM_001002787	442829	Mm.348215	NM_001002787	ENSMUSG00000070999	Ccin	4933417A14Rik	calicin	protein-coding
mm_33921.1	chr4	136610432	136610451	+	1	NA	promoter-TSS (NM_026300)	promoter-TSS (NM_026300)	4	NM_026300	67663	Mm.158168	NM_026300	ENSMUSG00000036921	4930549C01Rik	-	RIKEN cDNA 4930549C01 gene	protein-coding
mm_134813.1	chr16	25045224	25045253	-	1	NA	Intergenic	Intergenic	-14401	NR_040374	319487	Mm.137341	NR_040374	ENSMUSG00000096960	A230028O05Rik	-	RIKEN cDNA A230028O05 gene	ncRNA
mm_81468.1	chr9	109896438	109896441	+	1	NA	Intergenic	Intergenic	6796	NR_106057	102465660		NR_106057	ENSMUSG00000098490	Mir7089	Gm27418|mmu-mir-7089	microRNA 7089	ncRNA
mm_130338.1	chr15	97731296	97731307	-	1	NA	5' UTR (NM_001168693, exon 1 of 10)	5' UTR (NM_001168693, exon 1 of 10)	104	NM_001168693	19011	Mm.1001	NM_008902	ENSMUSG00000022468	Endou	Pp11r|Tcl-30	endonuclease, polyU-specific	protein-coding
mm_34292.1	chr4	141573482	141573526	+	1	NA	Intergenic	Intergenic	26420	NM_001163256	74202	Mm.490327	NM_133754	ENSMUSG00000006219	Fblim1	2410043F08Rik|Cal|Fblp1|Gt10|migfilin|migfilin(s)	filamin binding LIM protein 1	protein-coding
mm_104611.1	chr11	97237878	97237881	-	1	NA	intron (NM_008942, intron 10 of 22)	intron (NM_008942, intron 10 of 22)	42697	NM_008942	19155	Mm.29824	NM_008942	ENSMUSG00000001441	Npepps	AAP-S|MP100|Psa|R74825|goku	aminopeptidase puromycin sensitive	protein-coding
mm_94214.1	chr11	3148818	3148819	+	1	NA	intron (NM_030207, intron 14 of 32)	intron (NM_030207, intron 14 of 32)	24797	NR_003517	236604	Mm.247625	NM_001004146		Pisd-ps1	-	phosphatidylserine decarboxylase, pseudogene 1	pseudo
mm_65421.1	chr7	25278754	25278763	-	1	NA	intron (NM_001302811, intron 2 of 20)	CpG	-3421	NM_027882	71722	Mm.28833	NM_027882	ENSMUSG00000005442	Cic	1200010B10Rik|mKIAA0306	capicua transcriptional repressor	protein-coding
mm_141483.1	chr17	31208798	31208805	-	1	NA	intron (NM_177823, intron 1 of 13)	intron (NM_177823, intron 1 of 13)	735	NM_177823	328795	Mm.387930	NM_177823	ENSMUSG00000042345	Ubash3a	5830413C03Rik|C330001M22|Sts-2|TULA|TULA-1	ubiquitin associated and SH3 domain containing, A	protein-coding
mm_55853.1	chr6	83441613	83441664	-	1	NA	promoter-TSS (NM_183138)	promoter-TSS (NM_183138)	40	NM_183138	194388	Mm.211030	NM_183138	ENSMUSG00000034832	Tet3	B430006D22Rik|BC037432|D230004J03Rik	tet methylcytosine dioxygenase 3	protein-coding
mm_161845.1	chr18	7608982	7608982	-	1	NA	intron (NM_001081287, intron 1 of 16)	SUBTEL_sa|Satellite|Satellite	17881	NM_001081287	75739	Mm.133293	NM_001081287	ENSMUSG00000057440	Mpp7	1110068J02Rik|2810038M04Rik|5430426E14Rik|AI415104|Gm955	membrane protein, palmitoylated 7 (MAGUK p55 subfamily member 7)	protein-coding
mm_107841.1	chr12	69296973	69296990	+	1	NA	5' UTR (NM_027117, exon 1 of 13)	5' UTR (NM_027117, exon 1 of 13)	300	NM_027117	69554	Mm.234368	NM_027117	ENSMUSG00000020978	Klhdc2	2310022K15Rik|D12Ertd522e|HCLP-1|LCP	kelch domain containing 2	protein-coding
mm_150705.1	chr19	42518771	42518794	+	1	NA	promoter-TSS (NM_177464)	promoter-TSS (NM_177464)	-23	NM_177464	52013	Mm.254169	NM_177464	ENSMUSG00000025184	R3hcc1l	1700036B12Rik|AI450607|C10orf28|D19Ertd386e|GIDRP86|Gidrp88	R3H domain and coiled-coil containing 1 like	protein-coding
mm_134755.1	chr16	23225226	23225240	-	1	NA	promoter-TSS (NM_001252505)	promoter-TSS (NM_001252505)	493	NM_145933	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_18206.1	chr2	48457258	48457269	-	1	NA	Intergenic	Intergenic	-356846	NM_007396	11480	Mm.314338	NM_007396	ENSMUSG00000052155	Acvr2a	ActrIIa|Acvr2|TactrII	activin receptor IIA	protein-coding
mm_140131.1	chr17	79615517	79615542	+	1	NA	intron (NM_201361, intron 1 of 10)	CpG	629	NM_201361	381110	Mm.209801	NM_201361	ENSMUSG00000036368	Rmdn2	AW061290|Fam82a1|RMD-2|mRMD-2	regulator of microtubule dynamics 2	protein-coding
mm_88286.1	chr10	75194725	75194737	+	1	NA	Intergenic	RLTR31_Mm|LTR|ERVK	-17342	NM_153406	74392	Mm.27716	NM_153406	ENSMUSG00000033444	Specc1l	4930470P14Rik|4932439K10Rik|9530057A13Rik|AI317249|Cytsa|mKIAA0376	sperm antigen with calponin homology and coiled-coil domains 1-like	protein-coding
mm_31541.1	chr4	55477873	55477883	+	1	NA	Intergenic	Intergenic	54597	NM_010637	16600	Mm.4325	NM_010637	ENSMUSG00000003032	Klf4	EZF|Gklf|Zie	Kruppel-like factor 4 (gut)	protein-coding
mm_15997.1	chr2	167129482	167129493	+	1	NA	intron (NM_008420, intron 1 of 1)	intron (NM_008420, intron 1 of 1)	59331	NM_008420	16500	Mm.205341	NM_008420	ENSMUSG00000050556	Kcnb1	Kcr1-1|Kv2.1|Shab	potassium voltage gated channel, Shab-related subfamily, member 1	protein-coding
mm_129062.1	chr15	75567280	75567280	-	1	NA	promoter-TSS (NM_011837)	promoter-TSS (NM_011837)	-98	NM_011837	23934	Mm.22154	NM_011837	ENSMUSG00000022577	Ly6h	-	lymphocyte antigen 6 complex, locus H	protein-coding
mm_38766.1	chr4	147904681	147904710	-	1	NA	promoter-TSS (NM_001285923)	promoter-TSS (NM_001285923)	3	NM_001285923	170731	Mm.154312	NM_133201	ENSMUSG00000029020	Mfn2	D630023P19Rik|Fzo	mitofusin 2	protein-coding
mm_57084.1	chr6	122583585	122583602	-	1	NA	intron (NM_001134391, intron 5 of 7)	intron (NM_001134391, intron 5 of 7)	18851	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_154970.1	chrX	37143965	37143981	+	1	NA	intron (NM_025937, intron 8 of 8)	intron (NM_025937, intron 8 of 8)	17210	NM_025937	67050	Mm.55422	NM_025937	ENSMUSG00000016409	Nkap	2610020O08Rik|AA987160|AI849147|AL024236	NFKB activating protein	protein-coding
mm_32081.1	chr4	98395769	98395796	+	1	NA	promoter-TSS (NM_172696)	promoter-TSS (NM_172696)	-44	NM_001005784	12695	Mm.90218	NM_007704	ENSMUSG00000061859	Patj	Cipp|Inadl	PATJ, crumbs cell polarity complex component	protein-coding
mm_168374.1	chr11	21259176	21259176	+	1	NA	intron (NM_139061, intron 1 of 22)	B1_Mm|SINE|Alu	20144	NM_001290628	245944	Mm.170103	NM_139061	ENSMUSG00000020128	Vps54	Hcc8|Vps54l|mSLP8|wr	VPS54 GARP complex subunit	protein-coding
mm_166597.1	chr6	67035510	67035520	-	1	NA	3' UTR (NM_007836, exon 4 of 4)	3' UTR (NM_007836, exon 4 of 4)	-1084	NR_040278	320172	Mm.449039	NR_040278	ENSMUSG00000087231	E230016M11Rik	-	RIKEN cDNA E230016M11 gene	ncRNA
mm_136756.1	chr17	8663835	8663848	+	1	NA	intron (NM_001290707, intron 1 of 22)	intron (NM_001290707, intron 1 of 22)	137040	NM_001290707	23984	Mm.87161	NM_011866	ENSMUSG00000023868	Pde10a	-	phosphodiesterase 10A	protein-coding
mm_115124.1	chr13	104287137	104287147	+	1	NA	promoter-TSS (NM_001081020)	promoter-TSS (NM_001081020)	-693	NR_136938	108154	Mm.208125	NM_175496	ENSMUSG00000046169	Adamts6	A930019D11Rik|ADAM-TS6|b2b1879.1Clo|b2b2029Clo|b2b2182Clo|b2b2187.1Clo|b2b2228Clo	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 6	protein-coding
mm_25251.1	chr3	104638659	104638675	+	1	NA	promoter-TSS (NM_009196)	promoter-TSS (NM_009196)	3	NM_009196	20501	Mm.9086	NM_009196	ENSMUSG00000032902	Slc16a1	AL022710|Mct1	solute carrier family 16 (monocarboxylic acid transporters), member 1	protein-coding
mm_137175.1	chr17	23816056	23816067	+	1	NA	exon (NM_175229, exon 10 of 14)	exon (NM_175229, exon 10 of 14)	12874	NM_175229	75956	Mm.5222	NM_175229	ENSMUSG00000039218	Srrm2	5033413A03Rik|AA410130|SRm300|mKIAA0324	serine/arginine repetitive matrix 2	protein-coding
mm_164716.1	chr17	56120195	56120215	+	1	NA	exon (NM_029796, exon 2 of 2)	exon (NM_029796, exon 2 of 2)	1741	NM_029796	76905	Mm.348025	NM_029796	ENSMUSG00000037095	Lrg1	1300008B03Rik|2310031E04Rik|Lrg|Lrhg	leucine-rich alpha-2-glycoprotein 1	protein-coding
mm_132147.1	chr16	32100041	32100055	+	1	NA	promoter-TSS (NM_001111025)	promoter-TSS (NM_001111025)	246	NM_025892	66994	Mm.22990	NM_025892	ENSMUSG00000035790	Cep19	1500031L02Rik|AI428934|AL022620	centrosomal protein 19	protein-coding
mm_11605.1	chr2	33825099	33825108	+	1	NA	exon (NM_175184, exon 6 of 10)	exon (NM_175184, exon 6 of 10)	19287	NR_045729	320482	Mm.442057	NR_045729	ENSMUSG00000086484	Nron	A630071L07Rik|Gm24353	non-protein coding RNA, repressor of NFAT	ncRNA
mm_144375.1	chr18	20558093	20558201	+	1	NA	promoter-TSS (NM_007883)	promoter-TSS (NM_007883)	73	NM_007883	13511	Mm.345891	NM_007883	ENSMUSG00000044393	Dsg2	AA408168|D18Ertd293e	desmoglein 2	protein-coding
mm_55558.1	chr6	71322550	71322570	-	1	NA	promoter-TSS (NM_009858)	promoter-TSS (NM_009858)	-252	NM_009858	12526	Mm.333148	NM_009858	ENSMUSG00000053044	Cd8b1	Cd8b|Ly-3|Ly-C|Lyt-3	CD8 antigen, beta chain 1	protein-coding
mm_19074.1	chr2	77816737	77816748	-	1	NA	promoter-TSS (NM_178723)	promoter-TSS (NM_178723)	74	NM_178723	241494	Mm.490320	NM_178723	ENSMUSG00000027016	Zfp385b	B830010L13Rik|C130013B13Rik|Zfp533|Znf385b	zinc finger protein 385B	protein-coding
mm_146216.1	chr18	77006733	77006735	+	1	NA	intron (NM_027721, intron 8 of 13)	intron (NM_027721, intron 8 of 13)	40562	NM_027721	71206	Mm.35803	NM_027721	ENSMUSG00000025420	Katnal2	3110023G01Rik|4933439B08Rik	katanin p60 subunit A-like 2	protein-coding
mm_117215.1	chr13	64089423	64089429	-	1	NA	promoter-TSS (NM_008291)	promoter-TSS (NM_008291)	-225	NM_008291	15487	Mm.5109	NM_008291	ENSMUSG00000033122	Hsd17b3	-	hydroxysteroid (17-beta) dehydrogenase 3	protein-coding
mm_71995.1	chr8	70618092	70618107	+	1	NA	exon (NM_153074, exon 2 of 3)	exon (NM_153074, exon 2 of 3)	1255	NM_153074	211228	Mm.132939	NM_153074	ENSMUSG00000049988	Lrrc25	Mapa	leucine rich repeat containing 25	protein-coding
mm_121542.1	chr14	122474440	122474464	+	1	NA	promoter-TSS (NM_009574)	promoter-TSS (NM_009574)	747	NR_045046	69248	Mm.235369	NR_045046	ENSMUSG00000085555	2610035F20Rik	-	RIKEN cDNA 2610035F20 gene	ncRNA
mm_86715.1	chr10	19008881	19008892	+	1	NA	intron (NM_001166402, intron 1 of 7)	intron (NM_001166402, intron 1 of 7)	3077	NM_001166402	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_161308.1	chr14	34819914	34819914	+	1	NA	promoter-TSS (NM_008166)	promoter-TSS (NM_008166)	-222	NM_008166	14803	Mm.121569	NM_008166	ENSMUSG00000041078	Grid1	GluD1|GluRdelta1	glutamate receptor, ionotropic, delta 1	protein-coding
mm_64167.1	chr7	141447646	141447655	+	1	NA	promoter-TSS (NM_026020)	promoter-TSS (NM_026020)	0	NM_026020	67186	Mm.380435	NM_026020	ENSMUSG00000025508	Rplp2	2700049I22Rik	ribosomal protein, large P2	protein-coding
mm_135883.1	chr16	64602324	64602363	-	1	NA	Intergenic	Intergenic	-123209	NM_173861	224291	Mm.246580	NM_173861	ENSMUSG00000068167	Csnka2ip	Ckt2	casein kinase 2, alpha prime interacting protein	protein-coding
mm_70920.1	chr8	25785539	25785587	+	1	NA	promoter-TSS (NM_026032)	promoter-TSS (NM_026032)	-28	NM_026032	67207	Mm.30198	NM_026032	ENSMUSG00000037296	Lsm1	2810025O06Rik|CASM	LSM1 homolog, mRNA degradation associated	protein-coding
mm_36994.1	chr4	110286620	110286641	-	1	NA	5' UTR (NM_010488, exon 1 of 7)	5' UTR (NM_010488, exon 1 of 7)	204	NM_010488	15572	Mm.3970	NM_010488	ENSMUSG00000028546	Elavl4	Elav|Hud|PNEM	ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4 (Hu antigen D)	protein-coding
mm_152140.1	chr19	7090750	7090752	-	1	NA	intron (NM_134147, intron 3 of 10)	intron (NM_134147, intron 3 of 10)	14978	NM_201411	396184	Mm.386930	NM_201411	ENSMUSG00000047787	Flrt1	AW742165|D630040I23Rik	fibronectin leucine rich transmembrane protein 1	protein-coding
mm_105460.1	chr11	104550617	104550623	-	1	NA	promoter-TSS (NM_010858)	promoter-TSS (NM_010858)	0	NM_001285990	217232	Mm.89845	NM_145436	ENSMUSG00000020687	Cdc27	AI452358|APC3|BC023187	cell division cycle 27	protein-coding
mm_157593.1	chrX	53209775	53209800	-	1	NA	Intergenic	Intergenic	60018	NM_030167	78755	Mm.28559	NM_030167	ENSMUSG00000036022	Fam122b	4632404H22Rik|AI256344|SPACIA2	family with sequence similarity 122, member B	protein-coding
mm_30026.1	chr3	135667815	135667821	-	1	NA	intron (NM_008689, intron 2 of 24)	intron (NM_008689, intron 2 of 24)	23729	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_102021.1	chr11	51644368	51644391	-	1	NA	exon (NM_145974, exon 4 of 5)	exon (NM_145974, exon 4 of 5)	-6575	NR_027958	97775	Mm.220299	NM_175289	ENSMUSG00000052563	D930048N14Rik	AI315703|R75254	RIKEN cDNA D930048N14 gene	ncRNA
mm_124220.1	chr14	100284666	100284689	-	1	NA	Intergenic	Intergenic	-134881	NM_010636	16597	Mm.396499	NM_010636	ENSMUSG00000072294	Klf12	2700063E05Rik|AI225908|AI315654|AP-2rep|B130052C06Rik|D530033K05Rik	Kruppel-like factor 12	protein-coding
mm_164005.1	chr14	66978441	66978445	-	1	NA	Intergenic	Intergenic	30434	NM_009761	12177	Mm.29820	NM_009761	ENSMUSG00000022051	Bnip3l	C86132|D14Ertd719e|Nip3L|Nix	BCL2/adenovirus E1B interacting protein 3-like	protein-coding
mm_164120.1	chr15	37024716	37024716	+	1	NA	Intergenic	MTC|LTR|ERVL-MaLR	-17314	NM_026521	68036	Mm.371631	NM_026521	ENSMUSG00000062397	Zfp706	3110006P09Rik|AA793007|AW536850|C77232|Znf706	zinc finger protein 706	protein-coding
mm_58992.1	chr7	19131687	19131709	+	1	NA	intron (NM_175530, intron 1 of 1)	CpG	11839	NM_175530	243867	Mm.230830	NM_175530	ENSMUSG00000050428	Fbxo46	20D7-FC4|4932704E22Rik|Fbxo34l	F-box protein 46	protein-coding
mm_124882.1	chr15	10249571	10249577	+	1	NA	intron (NM_001253781, intron 1 of 9)	intron (NM_001253781, intron 1 of 9)	25668	NM_001253781	19116	Mm.10516	NM_011169	ENSMUSG00000005268	Prlr	AI987712|Pr-1|Pr-3|Prlr-rs1	prolactin receptor	protein-coding
mm_44254.1	chr5	5420245	5420262	-	1	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	-40002	NM_011074	18647	Mm.389061	NM_011074	ENSMUSG00000028926	Cdk14	Pftk1|mKIAA0834	cyclin-dependent kinase 14	protein-coding
mm_27892.1	chr3	79287245	79287255	-	1	NA	Intergenic	CpG	-58126	NM_001142953	100233207	Mm.373801	NM_001142953	ENSMUSG00000091685	Gm17359	-	predicted gene, 17359	protein-coding
mm_92643.1	chr10	80348618	80348663	-	1	NA	promoter-TSS (NM_001285435)	promoter-TSS (NM_001285435)	-192	NR_104340	66548	Mm.71891	NM_025629	ENSMUSG00000043822	Adamtsl5	2010109H09Rik|Thsd6	ADAMTS-like 5	protein-coding
mm_36523.1	chr4	84675377	84675394	-	1	NA	promoter-TSS (NM_172870)	promoter-TSS (NM_172870)	-299	NM_172870	242509	Mm.190774	NM_172870	ENSMUSG00000028487	Bnc2	5031434M05Rik|8430420F16Rik	basonuclin 2	protein-coding
mm_169493.1	chr14	75372470	75372474	-	1	NA	intron (NR_030568, intron 2 of 3)	RLTR9E|LTR|ERVK	15674	NR_030568	100124475		NR_030568	ENSMUSG00000077981	Mir466f-3	Mirn466f-3	microRNA 466f-3	ncRNA
mm_104095.1	chr11	86683976	86683986	-	1	NA	promoter-TSS (NM_001098810)	promoter-TSS (NM_001098810)	-2	NM_175004	217057	Mm.24868	NM_175004	ENSMUSG00000072582	Ptrh2	A230072I16Rik|Bit1|CGI-147	peptidyl-tRNA hydrolase 2	protein-coding
mm_166239.1	chr5	73021999	73021999	+	1	NA	3' UTR (NM_028194, exon 63 of 63)	3' UTR (NM_028194, exon 63 of 63)	15095	NM_173403	231290	Mm.491387	NM_173403	ENSMUSG00000029219	Slc10a4	E130304D01	solute carrier family 10 (sodium/bile acid cotransporter family), member 4	protein-coding
mm_3483.1	chr1	150105641	150105656	+	1	NA	exon (NM_011198, exon 10 of 10)	exon (NM_011198, exon 10 of 10)	5617	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_65650.1	chr7	28115349	28115362	-	1	NA	intron (NM_001122603, intron 17 of 19)	intron (NM_001122603, intron 17 of 19)	-14111	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_22982.1	chr3	32820199	32820200	+	1	NA	intron (NM_001013024, intron 1 of 20)	intron (NM_001013024, intron 1 of 20)	2573	NM_001013024	72607	Mm.316153	NM_001013024	ENSMUSG00000056900	Usp13	2700071E21Rik|AI848077|ISOT3|IsoT-3	ubiquitin specific peptidase 13 (isopeptidase T-3)	protein-coding
mm_2648.1	chr1	125561011	125561095	+	1	NA	promoter-TSS (NM_028787)	promoter-TSS (NM_028787)	37	NM_028787	74150	Mm.28654	NM_028787	ENSMUSG00000026342	Slc35f5	1300003P13Rik|AI646727	solute carrier family 35, member F5	protein-coding
mm_74299.1	chr8	126029317	126029342	+	1	NA	intron (NM_008430, intron 2 of 2)	intron (NM_008430, intron 2 of 2)	34227	NM_008430	16525	Mm.10800	NM_008430	ENSMUSG00000033998	Kcnk1	AI788889|TWIK-1	potassium channel, subfamily K, member 1	protein-coding
mm_134716.1	chr16	22895292	22895332	-	1	NA	promoter-TSS (NR_110508)	promoter-TSS (NR_110508)	-926	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_97103.1	chr11	73390100	73390101	+	1	NA	Intergenic	Intergenic	9395	NM_146921	258923	Mm.246523	NM_146921	ENSMUSG00000069823	Olfr1	I54|MOR135-13	olfactory receptor 1	protein-coding
mm_167859.1	chrX	13358266	13358274	+	1	NA	Intergenic	MLT1E3|LTR|ERVL-MaLR	77248	NM_010028	13205	Mm.289662	NM_010028	ENSMUSG00000000787	Ddx3x	D1Pas1-rs2|Ddx3|Fin14	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 3, X-linked	protein-coding
mm_160586.1	chr9	64341005	64341005	-	1	NA	promoter-TSS (NM_001177784)	promoter-TSS (NM_001177784)	-232	NM_001177784	213550	Mm.268341	NM_172519	ENSMUSG00000032396	Dis3l	AV340375	DIS3 like exosome 3'-5' exoribonuclease	protein-coding
mm_26376.1	chr3	142566334	142566350	+	1	NA	intron (NM_001289493, intron 5 of 10)	(T)n|Simple_repeat|Simple_repeat	5846	NM_001289493	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_139645.1	chr17	57385045	57385056	+	1	NA	intron (NM_010130, intron 2 of 21)	B1_Mm|SINE|Alu	26364	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_147527.1	chr18	52529894	52529904	-	1	NA	promoter-TSS (NM_010728)	promoter-TSS (NM_010728)	-32	NM_001286182	16948	Mm.172	NM_010728	ENSMUSG00000024529	Lox	AI893619|TSC-160|rrg	lysyl oxidase	protein-coding
mm_56652.1	chr6	113431986	113431991	-	1	NA	intron (NM_001301295, intron 3 of 5)	intron (NM_001301295, intron 3 of 5)	3767	NM_178373	14311	Mm.10026	NM_178373	ENSMUSG00000030278	Cidec	CIDE-3|Fsp27	cell death-inducing DFFA-like effector c	protein-coding
mm_99499.1	chr11	102896761	102896769	+	1	NA	exon (NM_010277, exon 1 of 9)	exon (NM_010277, exon 1 of 9)	435	NM_001131020	14580	Mm.1239	NM_010277	ENSMUSG00000020932	Gfap	AI836096	glial fibrillary acidic protein	protein-coding
mm_151316.1	chr19	55868192	55868194	+	1	NA	intron (NR_138565, intron 4 of 15)	intron (NR_138565, intron 4 of 15)	-27128	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_143620.1	chr17	78853200	78853213	-	1	NA	promoter-TSS (NR_003363)	promoter-TSS (NR_003363)	-662	NR_003363	625054	Mm.311918	NR_003363		Gm6548	EG625054	eukaryotic translation elongation factor 1 alpha 1 pseudogene	pseudo
mm_72864.1	chr8	88583197	88583204	+	1	NA	intron (NM_001163660, intron 2 of 7)	intron (NM_001163660, intron 2 of 7)	52928	NM_027840	71607	Mm.270607	NM_027840	ENSMUSG00000031662	Snx20	9130017C17Rik	sorting nexin 20	protein-coding
mm_172102.1	chr6	31142712	31142726	-	1	NA	intron (NR_110471, intron 2 of 3)	intron (NR_110471, intron 2 of 3)	75755	NR_110470	232685	Mm.443019	NM_144555	ENSMUSG00000044471	Lncpint	Lincpint|MNCb-1768|Pint|linc-Pint	long non-protein coding RNA, Trp53 induced transcript	ncRNA
mm_35185.1	chr4	15958416	15958447	-	1	NA	intron (NM_013752, intron 1 of 15)	CpG	464	NM_013752	27354	Mm.20866	NM_013752	ENSMUSG00000028224	Nbn	Nbs1	nibrin	protein-coding
mm_70162.1	chr7	143569173	143569204	-	1	NA	intron (NM_013742, intron 15 of 22)	intron (NM_013742, intron 15 of 22)	1571	NR_106031	102465644		NR_106031	ENSMUSG00000098593	Mir7064	Gm27632|mmu-mir-7064	microRNA 7064	ncRNA
mm_42860.1	chr5	122219829	122219855	+	1	NA	intron (NM_028752, intron 2 of 6)	intron (NM_028752, intron 2 of 6)	9555	NM_028752	74096	Mm.28804	NM_028752	ENSMUSG00000064267	Hvcn1	0610039P13Rik|AI450555|BTS|HV1|Vsop.|mVSOP	hydrogen voltage-gated channel 1	protein-coding
mm_80756.1	chr9	95554510	95554522	+	1	NA	Intergenic	Intergenic	-5301	NM_198414	75552	Mm.151485	NM_198414	ENSMUSG00000064225	Paqr9	1700020G04Rik	progestin and adipoQ receptor family member IX	protein-coding
mm_67426.1	chr7	80368848	80368857	-	1	NA	exon (NM_172903, exon 4 of 24)	exon (NM_172903, exon 4 of 24)	2523	NM_172903	140481	Mm.269245	NM_172903	ENSMUSG00000038886	Man2a2	1700052O22Rik|4931438M07Rik|AI480988|MX|Man IIx	mannosidase 2, alpha 2	protein-coding
mm_25716.1	chr3	122729005	122729015	+	1	NA	promoter-TSS (NM_153422)	promoter-TSS (NM_153422)	-148	NM_153422	242202	Mm.134911	NM_153422	ENSMUSG00000053965	Pde5a	Cgbpde|Cn5n|PDE5a2|Pde5|Pde5a1	phosphodiesterase 5A, cGMP-specific	protein-coding
mm_109936.1	chr12	11204306	11204325	-	1	NA	non-coding (NR_131085, exon 1 of 3)	non-coding (NR_131085, exon 1 of 3)	187	NR_131084	77442	Mm.159922	NR_131083		9530020I12Rik	-	RIKEN cDNA 9530020I12 gene	ncRNA
mm_79071.1	chr9	46240911	46240920	+	1	NA	promoter-TSS (NM_007468)	promoter-TSS (NM_007468)	71	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_1431.1	chr1	67186898	67186900	+	1	NA	intron (NM_001080809, intron 21 of 37)	intron (NM_001080809, intron 21 of 37)	63872	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_114408.1	chr13	64183887	64183899	+	1	NA	intron (NM_019986, intron 6 of 7)	intron (NM_019986, intron 6 of 7)	22027	NM_019986	56541	Mm.40989	NM_019986	ENSMUSG00000021476	Habp4	4933413D03Rik|4933428J01Rik	hyaluronic acid binding protein 4	protein-coding
mm_98743.1	chr11	96464588	96464637	+	1	NA	promoter-TSS (NM_001177899)	promoter-TSS (NM_001177899)	21	NM_001177898	78473	Mm.395840	NM_001033186	ENSMUSG00000057058	Skap1	1700091G21Rik|Scap1|Skap-55	src family associated phosphoprotein 1	protein-coding
mm_170726.1	chr2	150786805	150786805	+	1	NA	promoter-TSS (NM_153781)	promoter-TSS (NM_153781)	9	NM_153781	110078	Mm.222584	NM_153781	ENSMUSG00000033059	Pygb	-	brain glycogen phosphorylase	protein-coding
mm_72097.1	chr8	71591867	71591884	+	1	NA	promoter-TSS (NM_025396)	promoter-TSS (NM_025396)	-309	NM_025396	66171	Mm.282284	NM_025396	ENSMUSG00000031807	Pgls	1110030K05Rik|AI447866|Plgs	6-phosphogluconolactonase	protein-coding
mm_63470.1	chr7	127588740	127588791	+	1	NA	promoter-TSS (NM_001033040)	promoter-TSS (NM_001033040)	67	NM_172281	233900	Mm.41122	NM_172281	ENSMUSG00000030816	Rnf40	AI848422|mKIAA0661	ring finger protein 40	protein-coding
mm_39520.1	chr5	21257939	21257949	+	1	NA	intron (NM_175437, intron 19 of 30)	intron (NM_175437, intron 19 of 30)	71677	NM_175437	212167	Mm.121705	NM_175437	ENSMUSG00000039934	Gsap	A530088I07Rik|Pion	gamma-secretase activating protein	protein-coding
mm_48064.1	chr5	136567530	136567536	-	1	NA	promoter-TSS (NM_009986)	promoter-TSS (NM_009986)	-43	NM_001291238	13047	Mm.320317	NM_009986	ENSMUSG00000029705	Cux1	CDP|Cutl1|Cux|Cux-1	cut-like homeobox 1	protein-coding
mm_8767.1	chr1	160793199	160793211	-	1	NA	promoter-TSS (NM_013862)	promoter-TSS (NM_013862)	-267	NM_013862	29809	Mm.25833	NM_013862	ENSMUSG00000026721	Rabgap1l	5830411O09Rik|8430421H08Rik|9630005B12Rik|AW049894|HHL|Hh1|mKIAA0471	RAB GTPase activating protein 1-like	protein-coding
mm_131410.1	chr16	14472037	14472051	+	1	NA	exon (NM_008576, exon 29 of 31)	exon (NM_008576, exon 29 of 31)	-90273	NR_033556	545280	Mm.123679	NR_033556	ENSMUSG00000075395	A630010A05Rik	-	RIKEN cDNA A630010A05 gene	ncRNA
mm_96484.1	chr11	67684676	67684687	+	1	NA	3' UTR (NM_001277080, exon 13 of 13)	3' UTR (NM_001277080, exon 13 of 13)	-10645	NM_009038	19674	Mm.439726	NM_009038	ENSMUSG00000020907	Rcvrn	CAR|S-modulin	recoverin	protein-coding
mm_128420.1	chr15	45114897	45114908	-	1	NA	promoter-TSS (NM_026200)	promoter-TSS (NM_026200)	32	NM_026200	67498	Mm.300079	NM_026200	ENSMUSG00000022342	Kcnv1	2700023A03Rik|vibe	potassium channel, subfamily V, member 1	protein-coding
mm_150026.1	chr19	29373634	29373651	+	1	NA	exon (NM_021893, exon 3 of 7)	exon (NM_021893, exon 3 of 7)	6204	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_157813.1	chrX	73966751	73966753	-	1	NA	promoter-TSS (NM_008224)	promoter-TSS (NM_008224)	-395	NM_008224	15161	Mm.491126	NM_008224	ENSMUSG00000031386	Hcfc1	AW060991|HCF|HCF1	host cell factor C1	protein-coding
mm_7772.1	chr1	131233661	131233679	-	1	NA	intron (NM_001313731, intron 1 of 5)	intron (NM_001313731, intron 1 of 5)	11508	NM_018750	54354	Mm.248291	NM_018750	ENSMUSG00000026430	Rassf5	1300019G20Rik|Maxp1|Nore1|Nore1A|Nore1B|Rapl	Ras association (RalGDS/AF-6) domain family member 5	protein-coding
mm_70479.1	chr8	12395630	12395644	+	1	NA	5' UTR (NM_009233, exon 1 of 1)	5' UTR (NM_009233, exon 1 of 1)	118	NM_009233	20664	Mm.39088	NM_009233	ENSMUSG00000096014	Sox1	BB176347|Sox-1	SRY (sex determining region Y)-box 1	protein-coding
mm_110490.1	chr12	52395286	52395321	-	1	NA	Intergenic	Intergenic	85306	NR_136881	102638611	Mm.363799	NR_136881		Gm35135	-	predicted gene, 35135	ncRNA
mm_142729.1	chr17	48300910	48300923	-	1	NA	intron (NM_001033405, intron 1 of 4)	intron (NM_001033405, intron 1 of 4)	878	NM_001033405	328833	Mm.329104	NM_001033405	ENSMUSG00000071068	Treml2	AW049306|Gm750|Tlt2	triggering receptor expressed on myeloid cells-like 2	protein-coding
mm_21112.1	chr2	153444442	153444492	-	1	NA	promoter-TSS (NM_001001986)	promoter-TSS (NM_001001986)	12	NM_001001986	329540	Mm.50600	NM_001001986	ENSMUSG00000061411	Nol4l	4931410H15|8430427H17Rik|AI429157|Gm1636	nucleolar protein 4-like	protein-coding
mm_65975.1	chr7	30442282	30442303	-	1	NA	exon (NM_007467, exon 6 of 17)	exon (NM_007467, exon 6 of 17)	3290	NM_007467	11803	Mm.2381	NM_007467	ENSMUSG00000006651	Aplp1	-	amyloid beta (A4) precursor-like protein 1	protein-coding
mm_84687.1	chr9	72111828	72111895	-	1	NA	promoter-TSS (NM_011544)	promoter-TSS (NM_011544)	-42	NM_001253865	21406	Mm.171615	NM_011544	ENSMUSG00000032228	Tcf12	A130037E08Rik|ALF1|HEB|HEBAlt|HTF-4|HTF4|ME1|REB|bHLHb20	transcription factor 12	protein-coding
mm_166825.1	chr7	18484088	18484095	-	1	NA	promoter-TSS (NM_001029893)	promoter-TSS (NM_001029893)	58	NM_001029893	574429	Mm.296754	NM_001029893	ENSMUSG00000070799	Psg26	EG574429|cea14	pregnancy-specific glycoprotein 26	protein-coding
mm_157794.1	chrX	73869832	73869846	-	1	NA	5' UTR (NM_008478, exon 2 of 29)	5' UTR (NM_008478, exon 2 of 29)	10995	NM_008478	16728	Mm.260568	NM_008478	ENSMUSG00000031391	L1cam	CD171|L1|N-CAM-L1|NCAM-L1	L1 cell adhesion molecule	protein-coding
mm_49981.1	chr6	40964761	40964781	+	1	NA	promoter-TSS (NM_023707)	promoter-TSS (NM_023707)	-1	NM_023707	73626	Mm.425319	NM_023707	ENSMUSG00000094808	1810009J06Rik	-	RIKEN cDNA 1810009J06 gene	protein-coding
mm_135733.1	chr16	55831321	55831331	-	1	NA	intron (NM_030612, intron 2 of 13)	B4|SINE|B4	7315	NM_030612	80859	Mm.247272	NM_030612	ENSMUSG00000035356	Nfkbiz	AA408868|INAP|Mail	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, zeta	protein-coding
mm_55641.1	chr6	72345135	72345143	-	1	NA	promoter-TSS (NM_138592)	promoter-TSS (NM_138592)	36	NM_138592	28035	Mm.281900	NM_138592	ENSMUSG00000056305	Usp39	AA408960|AI894154|CGI-21|D6Wsu157e|SAD1	ubiquitin specific peptidase 39	protein-coding
mm_101496.1	chr11	31824464	31824480	-	1	NA	promoter-TSS (NR_102314)	promoter-TSS (NR_102314)	75	NR_102310	414116	Mm.150222	NR_102310	ENSMUSG00000085772	D630024D03Rik	-	RIKEN cDNA D630024D03 gene	ncRNA
mm_83449.1	chr9	45011446	45011454	-	1	NA	Intergenic	Intergenic	-1860	NM_007648	12501	Mm.210361	NM_007648	ENSMUSG00000032093	Cd3e	AI504783|CD3|CD3epsilon|T3e	CD3 antigen, epsilon polypeptide	protein-coding
mm_6068.1	chr1	60898637	60898673	-	1	NA	Intergenic	Intergenic	-10370	NM_009843	12477	Mm.390	NM_009843	ENSMUSG00000026011	Ctla4	Cd152|Ctla-4|Ly-56	cytotoxic T-lymphocyte-associated protein 4	protein-coding
mm_103183.1	chr11	70514609	70514616	-	1	NA	promoter-TSS (NM_001013607)	promoter-TSS (NM_001013607)	4	NM_001013607	327956	Mm.244514	NM_001013607	ENSMUSG00000020830	Vmo1	Gm741	vitelline membrane outer layer 1 homolog (chicken)	protein-coding
mm_93578.1	chr10	116896909	116896956	-	1	NA	promoter-TSS (NM_001033333)	promoter-TSS (NM_001033333)	-53	NM_001033333	237558	Mm.336386	NM_001033333	ENSMUSG00000034057	Myrfl	Gm239	myelin regulatory factor-like	protein-coding
mm_119620.1	chr14	51128981	51128993	+	1	NA	promoter-TSS (NM_030098)	promoter-TSS (NM_030098)	-81	NM_030098	78416	Mm.103835	NM_030098	ENSMUSG00000021880	Rnase6	9530043P15Rik|BB119466	ribonuclease, RNase A family, 6	protein-coding
mm_25658.1	chr3	121571817	121571839	+	1	NA	Intergenic	MIR3|SINE|MIR	-39484	NM_145394	213603	Mm.33062	NM_145394	ENSMUSG00000039865	Slc44a3	BC010552	solute carrier family 44, member 3	protein-coding
mm_19500.1	chr2	93462364	93462384	-	1	NA	promoter-TSS (NM_001271461)	promoter-TSS (NM_001271461)	128	NM_001271430	12521	Mm.4261	NM_007656	ENSMUSG00000027215	Cd82	AA682076|AL023070|C33|IA4|Kai1|Tspan27	CD82 antigen	protein-coding
mm_81819.1	chr9	118041159	118041162	+	1	NA	intron (NM_001286507, intron 1 of 6)	CpG	638	NM_013727	27215	Mm.92705	NM_013727	ENSMUSG00000039285	Azi2	AA410145|AZ2	5-azacytidine induced gene 2	protein-coding
mm_114813.1	chr13	91564321	91564334	+	1	NA	intron (NM_024272, intron 3 of 16)	intron (NM_024272, intron 3 of 16)	103230	NM_024186	66970	Mm.343095	NM_024186	ENSMUSG00000003992	Ssbp2	1500004K09Rik|2310079I02Rik|9330163K02Rik|A830008M03Rik|AU067692|AW558684|Hspc116|SSDP2	single-stranded DNA binding protein 2	protein-coding
mm_21935.1	chr2	167056814	167056827	-	1	NA	exon (NM_001033196, exon 3 of 14)	exon (NM_001033196, exon 3 of 14)	-6114	NR_138563	68949	Mm.391959	NM_001081005		Zfas1	1500012F01Rik|Zfos1	zinc finger, NFX1-type containing 1, antisense RNA 1	ncRNA
mm_15117.1	chr2	153686621	153686635	+	1	NA	3' UTR (NM_010068, exon 21 of 21)	3' UTR (NM_010068, exon 21 of 21)	37179	NM_001271747	13436	Mm.89772	NM_010068	ENSMUSG00000027478	Dnmt3b	MmuIIIB	DNA methyltransferase 3B	protein-coding
mm_87684.1	chr10	59268316	59268333	+	1	NA	Intergenic	MT2A|LTR|ERVL	46402	NM_172939	268301	Mm.3036	NM_172939	ENSMUSG00000098188	Sowahc	4921515A04Rik|9430099J10Rik|Ankrd57|C820004L04Rik	sosondowah ankyrin repeat domain family member C	protein-coding
mm_31172.1	chr4	43466156	43466169	+	1	NA	Intergenic	Intergenic	-11536	NM_007654	12517	Mm.188157	NM_007654	ENSMUSG00000028459	Cd72	CD72c|Ly-19|Ly-32|Ly-m19|Lyb-2	CD72 antigen	protein-coding
mm_160310.1	chr7	141064458	141064458	+	1	NA	intron (NM_177897, intron 3 of 19)	intron (NM_177897, intron 3 of 19)	3184	NM_177897	330671	Mm.133741	NM_177897	ENSMUSG00000055629	B4galnt4	BC038881|Gm1095|beta4GalNAcT4	beta-1,4-N-acetyl-galactosaminyl transferase 4	protein-coding
mm_23606.1	chr3	65449535	65449539	+	1	NA	Intergenic	Intergenic	-56984	NM_026155	67437	Mm.232728	NM_026155	ENSMUSG00000027828	Ssr3	0610038P07Rik|AL022999|AU022074|AW553833|TRAPG	signal sequence receptor, gamma	protein-coding
mm_1491.1	chr1	71887917	71887928	+	1	NA	promoter-TSS (NR_027659)	promoter-TSS (NR_027659)	-190	NR_027658	667931	Mm.214128	NR_027658	ENSMUSG00000099707	Gm8883	EG667931|Gm554	predicted gene 8883	ncRNA
mm_128912.1	chr15	73622047	73622050	-	1	NA	intron (NM_001033219, intron 1 of 7)	intron (NM_001033219, intron 1 of 7)	2696	NM_001033219	106068	Mm.212813	NM_001033219	ENSMUSG00000079020	Slc45a4	9330175B01Rik|AW552276	solute carrier family 45, member 4	protein-coding
mm_115341.1	chr13	112507367	112507391	+	1	NA	TTS (NM_010560)	TTS (NM_010560)	43309	NM_010560	16195	Mm.4364	NM_010560	ENSMUSG00000021756	Il6st	5133400A03Rik|AA389424|BB405851|CD130|D13Ertd699e|gp130	interleukin 6 signal transducer	protein-coding
mm_170886.1	chr2	22410726	22410730	-	1	NA	intron (NM_148413, intron 19 of 19)	intron (NM_148413, intron 19 of 19)	183225	NM_148413	667663	Mm.330033	NM_148413	ENSMUSG00000025716	Myo3a	9030416P08Rik	myosin IIIA	protein-coding
mm_151151.1	chr19	53140630	53140645	+	1	NA	5' UTR (NM_001164099, exon 1 of 15)	5' UTR (NM_001164099, exon 1 of 15)	194	NM_001164101	27360	Mm.426080	NM_013758	ENSMUSG00000025026	Add3	AI463285|R75380	adducin 3 (gamma)	protein-coding
mm_55219.1	chr6	52230081	52230095	-	1	NA	promoter-TSS (NR_029912)	promoter-TSS (NR_029912)	77	NR_029912	723820		NR_029912	ENSMUSG00000065443	Mir196b	Mirn196b|mir-196b	microRNA 196b	ncRNA
mm_154426.1	chrM	419	446	-	1	NA	NA	Intergenic	NA	NA								
mm_127294.1	chr15	100156975	100156979	+	1	NA	intron (NM_001159361, intron 7 of 37)	intron (NM_001159361, intron 7 of 37)	2581	NM_172819	239667	Mm.243658	NM_172819	ENSMUSG00000023026	Dip2b	4932422C22|AI317237|AI854602|mKIAA1463	disco interacting protein 2 homolog B	protein-coding
mm_168241.1	chr10	81853274	81853291	-	1	NA	Intergenic	Intergenic	-10652	NM_001243067	73610	Mm.490466	NM_001243067	ENSMUSG00000096795	Zfp433	1700123A16Rik	zinc finger protein 433	protein-coding
mm_11351.1	chr2	30845484	30845508	+	1	NA	exon (NM_009116, exon 1 of 4)	exon (NM_009116, exon 1 of 4)	129	NM_009116	20204	Mm.1802	NM_009116	ENSMUSG00000039476	Prrx2	Prx2|S8	paired related homeobox 2	protein-coding
mm_161411.1	chr15	11037965	11037965	-	1	NA	promoter-TSS (NM_178717)	promoter-TSS (NM_178717)	3	NM_178717	239336	Mm.209312	NM_178717	ENSMUSG00000060735	Rxfp3	BC053073|GPCR135|Rln3r1|Salpr	relaxin family peptide receptor 3	protein-coding
mm_88670.1	chr10	80017693	80017709	+	1	NA	intron (NM_001347074, intron 1 of 22)	intron (NM_001347074, intron 1 of 22)	786	NM_001347074	70719	Mm.243954	NM_027521	ENSMUSG00000035697	Hmha1	6330406L22Rik|AW539505|Ha-1	histocompatibility (minor) HA-1	protein-coding
mm_128212.1	chr15	36164371	36164372	-	1	NA	intron (NM_001081253, intron 1 of 4)	intron (NM_001081253, intron 1 of 4)	513	NM_001081253	78803	Mm.26393	NM_175281	ENSMUSG00000048230	Fbxo43	4930533G20Rik|Emi2	F-box protein 43	protein-coding
mm_84536.1	chr9	67262088	67262106	-	1	NA	intron (NM_001081242, intron 46 of 57)	intron (NM_001081242, intron 46 of 57)	-25371	NR_029576	387185		NR_029576	ENSMUSG00000076379	Mir190a	Mir190|Mirn190|mir-190|mir-190a|mmu-mir-190|mmu-mir-190a	microRNA 190a	ncRNA
mm_68768.1	chr7	121947139	121947142	-	1	NA	intron (NM_001033318, intron 9 of 16)	intron (NM_001033318, intron 9 of 16)	34553	NM_001033318	233824	Mm.442015	NM_001033318	ENSMUSG00000034951	Cog7	5630400E24Rik|Gm167	component of oligomeric golgi complex 7	protein-coding
mm_72485.1	chr8	83666635	83666659	+	1	NA	promoter-TSS (NM_013641)	promoter-TSS (NM_013641)	7	NM_013641	19216	Mm.213000	NM_013641	ENSMUSG00000019464	Ptger1	42kDa|EP1|Ptgerep1	prostaglandin E receptor 1 (subtype EP1)	protein-coding
mm_91820.1	chr10	55992378	55992380	-	1	NA	Intergenic	Intergenic	-114538	NM_001163833	73390	Mm.181475	NM_133751	ENSMUSG00000047669	Msl3l2	1700060H10Rik	male-specific lethal 3-like 2 (Drosophila)	protein-coding
mm_172639.1	chr8	23411464	23411467	+	1	NA	promoter-TSS (NM_013834)	promoter-TSS (NM_013834)	-37	NM_013834	20377	Mm.281691	NM_013834	ENSMUSG00000031548	Sfrp1	2210415K03Rik|AW011917|AW107218|AW742929|sFRP-1	secreted frizzled-related protein 1	protein-coding
mm_129626.1	chr15	80134038	80134060	-	1	NA	intron (NM_025609, intron 1 of 10)	intron (NM_025609, intron 1 of 10)	895	NM_025609	66513	Mm.288245	NM_025609	ENSMUSG00000022414	Tab1	2310012M03Rik|Map3k7ip1|b2b449Clo	TGF-beta activated kinase 1/MAP3K7 binding protein 1	protein-coding
mm_59148.1	chr7	24369961	24369978	+	1	NA	promoter-TSS (NM_001163510)	promoter-TSS (NM_001163510)	-294	NM_001163510	16534	Mm.9911	NM_008433	ENSMUSG00000054342	Kcnn4	IK1|IKCA1|KCA4|KCa3.1|SK4|SKCas|mIKCa1	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4	protein-coding
mm_37629.1	chr4	127354075	127354086	-	1	NA	promoter-TSS (NM_008127)	promoter-TSS (NM_008127)	1	NM_008127	14621	Mm.56906	NM_008127	ENSMUSG00000046623	Gjb4	Cnx30.3|Cx30.3|Gjb-4	gap junction protein, beta 4	protein-coding
mm_107278.1	chr12	29535182	29535205	+	1	NA	5' UTR (NM_001093776, exon 1 of 25)	5' UTR (NM_001093776, exon 1 of 25)	288	NM_001093776	17933	Mm.253067	NM_008666	ENSMUSG00000061911	Myt1l	2900046C06Rik|2900093J19Rik|C630034G21Rik|Nztf1|Pmng1|Png-1|mKIAA1106	myelin transcription factor 1-like	protein-coding
mm_75816.1	chr8	70353244	70353336	-	1	NA	promoter-TSS (NM_001122829)	promoter-TSS (NM_001122829)	-11	NM_001122829	19704	Mm.258280	NM_030680	ENSMUSG00000058301	Upf1	B430202H16Rik|NORF1|PNORF-1|Rent1|Upflp	UPF1 regulator of nonsense transcripts homolog (yeast)	protein-coding
mm_75803.1	chr8	70139200	70139261	-	1	NA	promoter-TSS (NM_001145552)	promoter-TSS (NM_001145552)	-33	NM_001025589	19727	Mm.161167	NM_011266	ENSMUSG00000036120	Rfxank	Tvl1	regulatory factor X-associated ankyrin-containing protein	protein-coding
mm_97735.1	chr11	80428599	80428656	+	1	NA	promoter-TSS (NM_178616)	promoter-TSS (NM_178616)	12	NM_178616	69077	Mm.260539	NM_178616	ENSMUSG00000017428	Psmd11	1700089D09Rik|1810019E17Rik|2610024G20Rik|2810055C24Rik|C78232|P44.5|S9	proteasome (prosome, macropain) 26S subunit, non-ATPase, 11	protein-coding
mm_73484.1	chr8	107031219	107031229	+	1	NA	promoter-TSS (NM_126165)	promoter-TSS (NM_126165)	-102	NM_126165	116733	Mm.236004	NM_126165	ENSMUSG00000031913	Vps4a	4930589C15Rik|AI325971|AW553189	vacuolar protein sorting 4A	protein-coding
mm_24147.1	chr3	88326414	88326444	+	1	NA	exon (NM_020003, exon 4 of 6)	exon (NM_020003, exon 4 of 6)	1406	NM_020003	56700	Mm.439922	NM_020003	ENSMUSG00000001418	Glmp	0610031J06Rik|AB027141|NCU-G1	glycosylated lysosomal membrane protein	protein-coding
mm_146934.1	chr18	32134660	32134690	-	1	NA	intron (NM_001042767, intron 3 of 8)	intron (NM_001042767, intron 3 of 8)	3530	NM_008934	19123	Mm.2786	NM_008934	ENSMUSG00000024386	Proc	PC	protein C	protein-coding
mm_143585.1	chr17	74402658	74402667	-	1	NA	intron (NM_001252478, intron 2 of 13)	L2a|LINE|L2	7054	NM_144798	210148	Mm.243943	NM_144798	ENSMUSG00000024069	Slc30a6	9530029F08Rik|ZnT6	solute carrier family 30 (zinc transporter), member 6	protein-coding
mm_148027.1	chr18	69593293	69593342	-	1	NA	intron (NM_013685, intron 8 of 19)	intron (NM_013685, intron 8 of 19)	247596	NM_001083967	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding
mm_45593.1	chr5	74702855	74702886	-	1	NA	promoter-TSS (NM_001159577)	promoter-TSS (NM_001159577)	33	NM_001159577	16924	Mm.440403	NM_010727	ENSMUSG00000029228	Lnx1	Lnx	ligand of numb-protein X 1	protein-coding
mm_66460.1	chr7	44892675	44892692	-	1	NA	promoter-TSS (NM_001331208)	promoter-TSS (NM_001331208)	-259	NM_001331206	75613	Mm.157778	NM_029365	ENSMUSG00000002968	Med25	2610034E13Rik|2610529E18Rik|ESTM2	mediator complex subunit 25	protein-coding
mm_2421.1	chr1	95313679	95313704	+	1	NA	promoter-TSS (NM_026321)	promoter-TSS (NM_026321)	63	NM_026321	67698	Mm.272705	NM_026321	ENSMUSG00000051185	Fam174a	2310044D20Rik|Fam174|Naa6|Tmem157	family with sequence similarity 174, member A	protein-coding
mm_103078.1	chr11	69895524	69895560	-	1	NA	promoter-TSS (NM_153788)	promoter-TSS (NM_153788)	-3	NM_153788	216859	Mm.288671	NM_153788	ENSMUSG00000001588	Acap1	Centb1	ArfGAP with coiled-coil, ankyrin repeat and PH domains 1	protein-coding
mm_108002.1	chr12	73525994	73525994	+	1	NA	Intergenic	Intergenic	20401	NM_178715	238257	Mm.251196	NM_178715	ENSMUSG00000034435	Tmem30b	9130011B11Rik	transmembrane protein 30B	protein-coding
mm_97011.1	chr11	70971152	70971162	+	1	NA	intron (NM_001252413, intron 1 of 5)	MER20|DNA|hAT-Charlie	957	NM_001252415	69723	Mm.275691	NM_027186	ENSMUSG00000018449	Rpain	2400006N03Rik|Rip	RPA interacting protein	protein-coding
mm_4507.1	chr1	174172739	174172782	+	1	NA	promoter-TSS (NM_011465)	promoter-TSS (NM_011465)	-16	NM_011465	20739	Mm.200611	NM_011465	ENSMUSG00000026532	Spta1	AF093576|AI451697|Spna-1|Spna1|ha|ihj|nmf4|sph	spectrin alpha, erythrocytic 1	protein-coding
mm_53424.1	chr6	134035954	134035973	+	1	NA	5' UTR (NM_007961, exon 1 of 8)	5' UTR (NM_007961, exon 1 of 8)	263	NM_007961	14011	Mm.269995	NM_007961	ENSMUSG00000030199	Etv6	AW123102|AW557856|Tel	ets variant 6	protein-coding
mm_6871.1	chr1	84284479	84284489	-	1	NA	5' UTR (NM_001003948, exon 1 of 3)	5' UTR (NM_001003948, exon 1 of 3)	161	NM_001003948	98496	Mm.187470	NM_001003948	ENSMUSG00000045658	Pid1	5033414K04Rik|NYGGF4	phosphotyrosine interaction domain containing 1	protein-coding
mm_111180.1	chr12	83921900	83921912	-	1	NA	promoter-TSS (NR_073564)	promoter-TSS (NR_073564)	28	NR_073563	18222	Mm.4390	NM_010949	ENSMUSG00000021224	Numb	Nb	numb homolog (Drosophila)	protein-coding
mm_44325.1	chr5	9725473	9725483	-	1	NA	promoter-TSS (NM_181850)	promoter-TSS (NM_181850)	-126	NM_181850	108069	Mm.318966	NM_181850	ENSMUSG00000003974	Grm3	0710001G23Rik|Gprc1c|mGlu3|mGluR3	glutamate receptor, metabotropic 3	protein-coding
mm_82549.1	chr9	20941788	20941798	-	1	NA	exon (NM_001199431, exon 3 of 39)	exon (NM_001199431, exon 3 of 39)	10830	NM_001199433	13433	Mm.128580	NM_010066	ENSMUSG00000004099	Dnmt1	Cxxc9|Dnmt|Dnmt1o|MCMT|MTase|Met-1|Met1|MommeD2|m.MmuI	DNA methyltransferase (cytosine-5) 1	protein-coding
mm_132029.1	chr16	27388973	27388998	+	1	NA	promoter-TSS (NM_001289436)	promoter-TSS (NM_001289436)	29	NM_001289436	67501	Mm.258985	NM_026202	ENSMUSG00000038127	Ccdc50	C3orf6	coiled-coil domain containing 50	protein-coding
mm_2653.1	chr1	125676970	125677015	+	1	NA	promoter-TSS (NM_027677)	promoter-TSS (NM_027677)	-4	NM_027677	71111	Mm.32727	NM_027677	ENSMUSG00000026343	Gpr39	4933415E13Rik	G protein-coupled receptor 39	protein-coding
mm_108830.1	chr12	95750326	95750336	+	1	NA	intron (NM_201518, intron 1 of 1)	intron (NM_201518, intron 1 of 1)	58105	NM_201518	399558	Mm.341948	NM_201518	ENSMUSG00000047414	Flrt2	-	fibronectin leucine rich transmembrane protein 2	protein-coding
mm_113047.1	chr13	23581564	23581569	+	1	NA	promoter-TSS (NM_175654)	promoter-TSS (NM_175654)	-36	NM_175654	319156	Mm.260530	NM_175654	ENSMUSG00000061482	Hist1h4d	-	histone cluster 1, H4d	protein-coding
mm_120897.1	chr14	75845962	75845970	+	1	NA	intron (NM_009429, intron 2 of 5)	CpG	710	NM_009429	22070	Mm.297482	NM_009429	ENSMUSG00000060126	Tpt1	TCTP|Trt|p21|p23	tumor protein, translationally-controlled 1	protein-coding
mm_59459.1	chr7	27196399	27196459	+	1	NA	promoter-TSS (NM_015782)	promoter-TSS (NM_015782)	-158	NM_001285825	53607	Mm.386890	NM_015782	ENSMUSG00000061479	Snrpa	C430021M15Rik|Rnu1a-1|Rnu1a1|U1-A|U1A	small nuclear ribonucleoprotein polypeptide A	protein-coding
mm_37331.1	chr4	119540386	119540416	-	1	NA	intron (NM_172699, intron 1 of 12)	intron (NM_172699, intron 1 of 12)	740	NM_172699	230700	Mm.259227	NM_172699	ENSMUSG00000032998	Foxj3	C330039G02Rik|Fhd6	forkhead box J3	protein-coding
mm_116673.1	chr13	49215859	49215903	-	1	NA	intron (NM_026738, intron 1 of 5)	CpG	145	NM_026738	68480	Mm.3336	NM_026738	ENSMUSG00000037960	Card19	1110007C09Rik|AI851695|Bincard	caspase recruitment domain family, member 19	protein-coding
mm_125980.1	chr15	76331245	76331255	+	1	NA	promoter-TSS (NM_010331)	promoter-TSS (NM_010331)	-44	NM_010331	14731	Mm.5903	NM_010331	ENSMUSG00000022561	Gpaa1	C80044|mGAA1	GPI anchor attachment protein 1	protein-coding
mm_20767.1	chr2	142838211	142838235	-	1	NA	intron (NM_001081133, intron 10 of 25)	intron (NM_001081133, intron 10 of 25)	63241	NM_001081133	16558	Mm.251934	NM_001081133	ENSMUSG00000038844	Kif16b	8430434E15Rik|AA623607|AI789011|C80253|C80902|mKIAA1590	kinesin family member 16B	protein-coding
mm_84414.1	chr9	65567704	65567734	-	1	NA	intron (NM_153119, intron 2 of 5)	intron (NM_153119, intron 2 of 5)	12368	NM_153119	102595	Mm.247303	NM_153119	ENSMUSG00000050721	Plekho2	AI840980|Plekhq1	pleckstrin homology domain containing, family O member 2	protein-coding
mm_85610.1	chr9	107605264	107605283	-	1	NA	5' UTR (NM_009153, exon 1 of 18)	5' UTR (NM_009153, exon 1 of 18)	129	NM_009153	20347	Mm.4083	NM_009153	ENSMUSG00000057969	Sema3b	SemA|Semaa|sema5|semaV	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B	protein-coding
mm_84190.1	chr9	60449697	60449705	-	1	NA	intron (NM_001040426, intron 3 of 17)	intron (NM_001040426, intron 3 of 17)	61334	NM_001040426	207596	Mm.28791	NM_172444	ENSMUSG00000032289	Thsd4	ADAMTSL-6|ADAMTSL6|AI585901|Adamtsl4|B230114P05Rik	thrombospondin, type I, domain containing 4	protein-coding
mm_36954.1	chr4	109131508	109131532	-	1	NA	intron (NM_001346502, intron 4 of 23)	intron (NM_001346502, intron 4 of 23)	-13484	NM_001134791	100273	Mm.366315	NM_133885	ENSMUSG00000028559	Osbpl9	2600011I06Rik|AU015843|Orp-9	oxysterol binding protein-like 9	protein-coding
mm_164538.1	chr17	6827979	6827984	+	1	NA	Intergenic	CpG	-45201	NM_009510	22350	Mm.277812	NM_009510	ENSMUSG00000052397	Ezr	AW146364|R75297|Vil2|p81	ezrin	protein-coding
mm_161565.1	chr16	18590588	18590588	-	1	NA	promoter-TSS (NM_001285472)	promoter-TSS (NM_001285472)	83	NM_001285472	21380	Mm.295194	NM_011532	ENSMUSG00000009097	Tbx1	-	T-box 1	protein-coding
mm_81375.1	chr9	108854712	108854738	+	1	NA	5' UTR (NM_134420, exon 1 of 18)	5' UTR (NM_134420, exon 1 of 18)	682	NM_134420	171429	Mm.45201	NM_134420	ENSMUSG00000023259	Slc26a6	B930010B04Rik|CFEX|Pat-1|Pat1	solute carrier family 26, member 6	protein-coding
mm_116280.1	chr13	34963826	34963836	-	1	NA	promoter-TSS (NM_026947)	promoter-TSS (NM_026947)	-22	NM_026947	69123	Mm.482475	NM_026947	ENSMUSG00000021416	Eci3	1810022C23Rik|Kseg2	enoyl-Coenzyme A delta isomerase 3	protein-coding
mm_6598.1	chr1	75316999	75317025	-	1	NA	promoter-TSS (NM_016878)	promoter-TSS (NM_016878)	5	NM_016878	13437	Mm.24680	NM_016878	ENSMUSG00000026209	Dnpep	AA407814	aspartyl aminopeptidase	protein-coding
mm_162535.1	chr1	167284842	167284850	-	1	NA	exon (NM_030724, exon 1 of 7)	exon (NM_030724, exon 1 of 7)	281	NM_030724	80914	Mm.280895	NM_030724	ENSMUSG00000026558	Uck2	AA407809|AI481316|AU018180|AU020720|TSA903|UK|UMK|Umpk	uridine-cytidine kinase 2	protein-coding
mm_162847.1	chr10	86348436	86348444	+	1	NA	3' UTR (NM_011595, exon 5 of 5)	3' UTR (NM_011595, exon 5 of 5)	48028	NM_011595	21859	Mm.4871	NM_011595	ENSMUSG00000020044	Timp3	Timp-3	tissue inhibitor of metalloproteinase 3	protein-coding
mm_41122.1	chr5	87784540	87784540	+	1	NA	intron (NM_001304769, intron 9 of 12)	intron (NM_001304769, intron 9 of 12)	10090	NM_007785	12993	Mm.4908	NM_007785	ENSMUSG00000061937	Csn1s2a	Csng|PP22	casein alpha s2-like A	protein-coding
mm_134479.1	chr16	18621623	18621637	-	1	NA	TTS (NM_213614)	TTS (NM_213614)	773	NM_001001999	14724	Mm.475622	NM_010327	ENSMUSG00000050761	Gp1bb	-	glycoprotein Ib, beta polypeptide	protein-coding
mm_92414.1	chr10	76816718	76816734	-	1	NA	intron (NM_001347216, intron 3 of 15)	intron (NM_001347216, intron 3 of 15)	-90682	NM_009933	12833	Mm.2509	NM_009933	ENSMUSG00000001119	Col6a1	AI747156|Col6a-1	collagen, type VI, alpha 1	protein-coding
mm_15221.1	chr2	154436438	154436497	+	1	NA	promoter-TSS (NM_001285446)	promoter-TSS (NM_001285446)	-17	NM_172860	12396	Mm.29914	NM_009823	ENSMUSG00000038533	Cbfa2t2	A430091M07|C330013D05Rik|Cbfa2t2h|MTGR1	core-binding factor, runt domain, alpha subunit 2, translocated to, 2 (human)	protein-coding
mm_56867.1	chr6	118455476	118455518	-	1	NA	promoter-TSS (NM_028335)	promoter-TSS (NM_028335)	9	NM_028335	72720	Mm.212572	NM_028335	ENSMUSG00000030145	Zfp248	2810037F07Rik|E130106N01Rik	zinc finger protein 248	protein-coding
mm_97309.1	chr11	76679906	76679922	+	1	NA	promoter-TSS (NM_177709)	promoter-TSS (NM_177709)	41	NM_177709	237858	Mm.127006	NM_177709	ENSMUSG00000046275	Tusc5	C130069F04Rik|DSPB1|Lost1	tumor suppressor candidate 5	protein-coding
mm_153582.1	chr19	43500480	43500490	-	1	NA	exon (NM_010324, exon 9 of 9)	exon (NM_010324, exon 9 of 9)	24120	NM_010324	14718	Mm.19039	NM_010324	ENSMUSG00000025190	Got1	AI789014|Got-1|cAspAT|cCAT	glutamic-oxaloacetic transaminase 1, soluble	protein-coding
mm_158240.1	chrX	106603601	106603617	-	1	NA	promoter-TSS (NM_001281859)	promoter-TSS (NM_001281859)	70	NM_001281862	58861	Mm.287166	NM_021476	ENSMUSG00000052821	Cysltr1	BB147369|CysLT1R|Cyslt1	cysteinyl leukotriene receptor 1	protein-coding
mm_161054.1	chr12	55599130	55599130	+	1	NA	5' UTR (NM_020287, exon 1 of 1)	5' UTR (NM_020287, exon 1 of 1)	213	NM_020287	56856	Mm.114886	NM_020287	ENSMUSG00000045440	Insm2	Mlt1	insulinoma-associated 2	protein-coding
mm_19257.1	chr2	84774864	84774876	-	1	NA	intron (NM_009776, intron 1 of 7)	intron (NM_009776, intron 1 of 7)	559	NM_009776	12258	Mm.38888	NM_009776	ENSMUSG00000023224	Serping1	C1INH|C1nh	serine (or cysteine) peptidase inhibitor, clade G, member 1	protein-coding
mm_38104.1	chr4	134402060	134402070	-	1	NA	promoter-TSS (NM_001285877)	promoter-TSS (NM_001285877)	-847	NM_001285874	100163	Mm.22116	NM_133880	ENSMUSG00000037366	Pafah2	2310074E22Rik|AI507170	platelet-activating factor acetylhydrolase 2	protein-coding
mm_134877.1	chr16	28929951	28929961	-	1	NA	promoter-TSS (NM_177718)	promoter-TSS (NM_177718)	-258	NM_177718	239796	Mm.155887	NM_177718	ENSMUSG00000051065	Mb21d2	1600021P15Rik|A430031N04|C87006	Mab-21 domain containing 2	protein-coding
mm_172487.1	chr7	52815806	52815806	+	1	NA	Intergenic	L1Md_T|LINE|L1	-800090	NM_001195601	100503036	Mm.279725	NM_001195601	ENSMUSG00000094445	1700015G11Rik	Ccdc179	RIKEN cDNA 1700015G11 gene	protein-coding
mm_15045.1	chr2	152830819	152830822	+	1	NA	promoter-TSS (NM_001289716)	promoter-TSS (NM_001289716)	-103	NM_001289739	12048	Mm.238213	NM_009743	ENSMUSG00000007659	Bcl2l1	Bcl(X)L|Bcl-XL|Bcl2l|BclX|bcl-x|bcl2-L-1	BCL2-like 1	protein-coding
mm_89067.1	chr10	82897473	82897514	+	1	NA	3' UTR (NM_001042523, exon 15 of 15)	3' UTR (NM_001042523, exon 15 of 15)	30867	NM_025499	66341	Mm.443284	NM_025499	ENSMUSG00000109864	Eid3	1700027M21Rik|NS4EB	EP300 interacting inhibitor of differentiation 3	protein-coding
mm_172569.1	chr8	111854274	111854275	-	1	NA	promoter-TSS (NM_011801)	promoter-TSS (NM_011801)	36	NM_011801	23837	Mm.279437	NM_011801	ENSMUSG00000031954	Cfdp1	AA408409|Bcnt|Bucentaur|Cfdp|cp27	craniofacial development protein 1	protein-coding
mm_110630.1	chr12	57542341	57542350	-	1	NA	exon (NM_008259, exon 2 of 2)	exon (NM_008259, exon 2 of 2)	3776	NM_008259	15375	Mm.4578	NM_008259	ENSMUSG00000035451	Foxa1	Hnf-3a|Hnf3a|Tcf-3a|Tcf3a	forkhead box A1	protein-coding
mm_32134.1	chr4	99194253	99194266	+	1	NA	5' UTR (NM_001145967, exon 1 of 11)	5' UTR (NM_001145967, exon 1 of 11)	112	NM_001145967	242557	Mm.241663	NM_175029	ENSMUSG00000028550	Atg4c	Apg4-C|Apg4c|Atg4cl|Autl1	autophagy related 4C, cysteine peptidase	protein-coding
mm_24164.1	chr3	88532713	88532765	+	1	NA	exon (NM_001029890, exon 1 of 2)	exon (NM_001029890, exon 1 of 2)	344	NM_001029890	72640	Mm.275154	NM_001029890	ENSMUSG00000074480	Mex3a	2700083E18Rik|Gm411|Rkhd4	mex3 RNA binding family member A	protein-coding
mm_83479.1	chr9	45906370	45906437	-	1	NA	promoter-TSS (NM_008794)	promoter-TSS (NM_008794)	-166	NM_008794	18554	Mm.3255	NM_008794	ENSMUSG00000035382	Pcsk7	AA959856|PC7|SPC7	proprotein convertase subtilisin/kexin type 7	protein-coding
mm_166379.1	chr5	130213743	130213746	+	1	NA	3' UTR (NM_019983, exon 8 of 8)	3' UTR (NM_019983, exon 8 of 8)	-6000	NM_001081394	71667	Mm.258508	NM_027854	ENSMUSG00000053094	Tmem248	0610007L01Rik|A930023A16Rik|AW557951|G430067H08Rik	transmembrane protein 248	protein-coding
mm_124560.1	chr14	123283957	123283966	-	1	NA	intron (NM_177393, intron 41 of 43)	intron (NM_177393, intron 41 of 43)	114775	NR_045144	380934	Mm.393838	NR_045143		AA536875	Gm1591	expressed sequence AA536875	ncRNA
mm_35880.1	chr4	49538251	49538266	-	1	NA	exon (NM_144903, exon 8 of 9)	exon (NM_144903, exon 8 of 9)	11288	NM_144903	230163	Mm.482116	NM_144903	ENSMUSG00000028307	Aldob	Aldo-2|Aldo2|BC016435	aldolase B, fructose-bisphosphate	protein-coding
mm_28086.1	chr3	85037955	85037956	-	1	NA	Intergenic	Intergenic	85744	NM_080428	50754	Mm.196475	NM_080428	ENSMUSG00000028086	Fbxw7	1110001A17Rik|AGO|Cdc4|Fbw7|Fbwd6|Fbx30|Fbxo30|Fbxw6|SEL-10	F-box and WD-40 domain protein 7	protein-coding
mm_96364.1	chr11	67171060	67171071	+	1	NA	promoter-TSS (NM_001039545)	promoter-TSS (NM_001039545)	38	NM_001039545	17882	Mm.422801	NM_144961	ENSMUSG00000033196	Myh2	MHC2A|MyHC-IIa|Myh2a|Myhs-f|Myhs-f1|Myhsf1	myosin, heavy polypeptide 2, skeletal muscle, adult	protein-coding
mm_41469.1	chr5	91141053	91141058	+	1	NA	exon (NM_009704, exon 2 of 6)	exon (NM_009704, exon 2 of 6)	1456	NM_009704	11839	Mm.8039	NM_009704	ENSMUSG00000029378	Areg	AR|Mcub|Sdgf	amphiregulin	protein-coding
mm_165835.1	chr3	154711424	154711428	+	1	NA	intron (NM_175176, intron 1 of 6)	intron (NM_175176, intron 1 of 6)	293	NM_175176	209601	Mm.331454	NM_175176	ENSMUSG00000078161	Erich3	1700013E18Rik|4922501L14Rik|5031409G23Rik|AI596448|Gm133	glutamate rich 3	protein-coding
mm_160143.1	chr7	35449229	35449229	+	1	NA	promoter-TSS (NM_021291)	promoter-TSS (NM_021291)	50	NM_021291	30962	Mm.45874	NM_021291	ENSMUSG00000030492	Slc7a9	CSNU3	solute carrier family 7 (cationic amino acid transporter, y+ system), member 9	protein-coding
mm_140102.1	chr17	78508115	78508133	+	1	NA	promoter-TSS (NM_001197028)	promoter-TSS (NM_001197028)	61	NM_028813	74199	Mm.292983	NM_028813	ENSMUSG00000024076	Vit	1700052E02Rik|1700110E08Rik|2810429K11Rik	vitrin	protein-coding
mm_83448.1	chr9	45009864	45009876	-	1	NA	promoter-TSS (NM_007648)	promoter-TSS (NM_007648)	-280	NM_007648	12501	Mm.210361	NM_007648	ENSMUSG00000032093	Cd3e	AI504783|CD3|CD3epsilon|T3e	CD3 antigen, epsilon polypeptide	protein-coding
mm_26938.1	chr3	20263769	20263793	-	1	NA	exon (NM_029706, exon 7 of 11)	exon (NM_029706, exon 7 of 11)	11952	NM_029706	76703	Mm.34692	NM_029706	ENSMUSG00000011463	Cpb1	0910001A18Rik|1810063F02Rik|2210008M23Rik|AI504870	carboxypeptidase B1 (tissue)	protein-coding
mm_127607.1	chr15	102446669	102446695	+	1	NA	intron (NM_144547, intron 3 of 10)	intron (NM_144547, intron 3 of 10)	1315	NM_144547	110542	Mm.60331	NM_144547	ENSMUSG00000023047	Amhr2	Misiir|Misrii|Mrii	anti-Mullerian hormone type 2 receptor	protein-coding
mm_150130.1	chr19	30030664	30030672	+	1	NA	5' UTR (NM_144873, exon 1 of 16)	5' UTR (NM_144873, exon 1 of 16)	155	NM_144873	109113	Mm.313364	NM_144873	ENSMUSG00000024817	Uhrf2	2310065A22Rik|AI426270|AW214556|D130071B19Rik|Nirf	ubiquitin-like, containing PHD and RING finger domains 2	protein-coding
mm_155117.1	chrX	48624557	48624560	+	1	NA	intron (NM_001166450, intron 2 of 10)	intron (NM_001166450, intron 2 of 10)	884	NM_001166450	20523	Mm.34953	NM_011398	ENSMUSG00000031105	Slc25a14	BMCP1|UCP5|UCP5L|UCP5S	solute carrier family 25 (mitochondrial carrier, brain), member 14	protein-coding
mm_52816.1	chr6	121346649	121346671	+	1	NA	promoter-TSS (NM_133661)	promoter-TSS (NM_133661)	-37	NM_133661	14411	Mm.274506	NM_133661	ENSMUSG00000030109	Slc6a12	BGT1|GAT-2|GAT2|Gabt2	solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12	protein-coding
mm_15071.1	chr2	153108475	153108484	+	1	NA	promoter-TSS (NM_010407)	promoter-TSS (NM_010407)	11	NM_010407	15162	Mm.715	NM_010407	ENSMUSG00000003283	Hck	AI849071|Bmk	hemopoietic cell kinase	protein-coding
mm_115326.1	chr13	112464085	112464162	+	1	NA	promoter-TSS (NM_010560)	promoter-TSS (NM_010560)	53	NM_010560	16195	Mm.4364	NM_010560	ENSMUSG00000021756	Il6st	5133400A03Rik|AA389424|BB405851|CD130|D13Ertd699e|gp130	interleukin 6 signal transducer	protein-coding
mm_86988.1	chr10	25489635	25489653	+	1	NA	intron (NM_001199265, intron 12 of 19)	intron (NM_001199265, intron 12 of 19)	46628	NM_001195596	100504474	Mm.46323	NM_001195596	ENSMUSG00000096546	Smlr1	2010003K15Rik	small leucine-rich protein 1	protein-coding
mm_2570.1	chr1	118459588	118459621	+	1	NA	promoter-TSS (NR_027901)	promoter-TSS (NR_027901)	-339	NR_027901	68204	Mm.443536	NR_027901	ENSMUSG00000107722	2900060B14Rik	-	RIKEN cDNA 2900060B14 gene	ncRNA
mm_131928.1	chr16	23609896	23609961	+	1	NA	promoter-TSS (NM_023386)	promoter-TSS (NM_023386)	9	NM_023386	67775	Mm.475107	NM_023386	ENSMUSG00000033355	Rtp4	5830458K16Rik|Ifrg28	receptor transporter protein 4	protein-coding
mm_37933.1	chr4	132922488	132922544	-	1	NA	promoter-TSS (NM_145553)	promoter-TSS (NM_145553)	35	NM_145553	230789	Mm.11473	NM_145553	ENSMUSG00000028878	Fam76a	-	family with sequence similarity 76, member A	protein-coding
mm_64543.1	chr7	144284389	144284399	+	1	NA	promoter-TSS (NM_001081370)	promoter-TSS (NM_001081370)	9	NM_001081370	210274	Mm.483624	NM_001081370	ENSMUSG00000037541	Shank2	ProSAP1|mKIAA1022	SH3/ankyrin domain gene 2	protein-coding
mm_109884.1	chr12	5246841	5246870	-	1	NA	intron (NM_001164493, intron 2 of 13)	intron (NM_001164493, intron 2 of 13)	128827	NM_001164493	208439	Mm.388281	NM_001164493	ENSMUSG00000020627	Klhl29	A230106N14Rik|Gm68|Kbtbd9|mKIAA1921	kelch-like 29	protein-coding
mm_18025.1	chr2	38619366	38619371	-	1	NA	intron (NM_011187, intron 5 of 7)	intron (NM_011187, intron 5 of 7)	24538	NM_011187	19177	Mm.389251	NM_011187	ENSMUSG00000026750	Psmb7	AU020723|MC14	proteasome (prosome, macropain) subunit, beta type 7	protein-coding
mm_113171.1	chr13	24813534	24813544	+	1	NA	TTS (NM_024473)	TTS (NM_024473)	11882	NM_024473	79555	Mm.266668	NM_024473	ENSMUSG00000019132	BC005537	8030460C05Rik|C78201	cDNA sequence BC005537	protein-coding
mm_133847.1	chr16	96205842	96205858	+	1	NA	intron (NM_015825, intron 1 of 7)	intron (NM_015825, intron 1 of 7)	5380	NM_015825	50795	Mm.28638	NM_015825	ENSMUSG00000040666	Sh3bgr	5430437A18Rik	SH3-binding domain glutamic acid-rich protein	protein-coding
mm_27158.1	chr3	33138237	33138240	-	1	NA	intron (NM_001163516, intron 1 of 12)	intron (NM_001163516, intron 1 of 12)	4953	NM_001163516	58869	Mm.151332	NM_021483	ENSMUSG00000027674	Pex5l	1700016J08Rik|PXR2|Pex2|TRIP8b|pex5Rp	peroxisomal biogenesis factor 5-like	protein-coding
mm_55670.1	chr6	72522459	72522480	-	1	NA	Intergenic	Intergenic	-21922	NM_007599	12332	Mm.18626	NM_007599	ENSMUSG00000056737	Capg	gCap39|mbh1	capping protein (actin filament), gelsolin-like	protein-coding
mm_125064.1	chr15	25941004	25941014	+	1	NA	5' UTR (NM_001277315, exon 1 of 7)	5' UTR (NM_001277315, exon 1 of 7)	183	NM_025459	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_64374.1	chr7	142442892	142442902	+	1	NA	intron (NM_009405, intron 1 of 5)	intron (NM_009405, intron 1 of 5)	429	NM_009405	21953	Mm.39469	NM_009405	ENSMUSG00000031097	Tnni2	-	troponin I, skeletal, fast 2	protein-coding
mm_11415.1	chr2	31639718	31639723	+	1	NA	promoter-TSS (NM_001123362)	promoter-TSS (NM_001123362)	-317	NM_001123362	381359	Mm.379512	NM_001123362	ENSMUSG00000079466	Prdm12	Gm998	PR domain containing 12	protein-coding
mm_37589.1	chr4	126468581	126468653	-	1	NA	promoter-TSS (NM_001317173)	promoter-TSS (NM_001317173)	-34	NM_153403	236511	Mm.30800	NM_153403	ENSMUSG00000041530	Ago1	Eif2c1	argonaute RISC catalytic subunit 1	protein-coding
mm_167912.1	chrX	93832085	93832094	-	1	NA	promoter-TSS (NM_145630)	promoter-TSS (NM_145630)	6	NM_145630	236900	Mm.12775	NM_145630	ENSMUSG00000035232	Pdk3	2610001M10Rik|AI035637	pyruvate dehydrogenase kinase, isoenzyme 3	protein-coding
mm_111108.1	chr12	80958084	80958102	-	1	NA	exon (NM_001177561, exon 3 of 5)	exon (NM_001177561, exon 3 of 5)	9986	NM_011387	20493	Mm.486361	NM_011387	ENSMUSG00000021135	Slc10a1	Ntcp	solute carrier family 10 (sodium/bile acid cotransporter family), member 1	protein-coding
mm_129976.1	chr15	85821788	85821801	-	1	NA	promoter-TSS (NM_011105)	promoter-TSS (NM_011105)	-61	NM_011105	18766	Mm.89965	NM_011105	ENSMUSG00000052496	Pkdrej	-	polycystin (PKD) family receptor for egg jelly	protein-coding
mm_130373.1	chr15	97823660	97823671	-	1	NA	intron (NM_001204275, intron 1 of 24)	intron (NM_001204275, intron 1 of 24)	8102	NM_019572	56233	Mm.384027	NM_019572	ENSMUSG00000022475	Hdac7	5830434K02Rik|HD7|HD7a|Hdac7a|mFLJ00062	histone deacetylase 7	protein-coding
mm_48744.1	chr5	147875549	147875563	-	1	NA	3' UTR (NM_025624, exon 6 of 6)	3' UTR (NM_025624, exon 6 of 6)	14928	NM_025624	66537	Mm.332855	NM_025624	ENSMUSG00000029649	Pomp	2510048O06Rik|Ump1	proteasome maturation protein	protein-coding
mm_82361.1	chr9	14500395	14500427	-	1	NA	promoter-TSS (NM_023153)	promoter-TSS (NM_023153)	71	NM_173433	244694	Mm.240457	NM_173433	ENSMUSG00000053914	Kdm4d	4932416A15|Jmjd2d	lysine (K)-specific demethylase 4D	protein-coding
mm_108835.1	chr12	95780781	95780794	+	1	NA	exon (NM_201518, exon 2 of 2)	exon (NM_201518, exon 2 of 2)	88561	NM_201518	399558	Mm.341948	NM_201518	ENSMUSG00000047414	Flrt2	-	fibronectin leucine rich transmembrane protein 2	protein-coding
mm_8527.1	chr1	154884478	154884485	-	1	NA	Intergenic	Intergenic	-158561	NM_009782	12290	Mm.267517	NM_009782	ENSMUSG00000004110	Cacna1e	A430040I15|BII|Cach6|Cacnl1a6|Cav2.3|Cchra1|alpha1E	calcium channel, voltage-dependent, R type, alpha 1E subunit	protein-coding
mm_161179.1	chr13	43480928	43480928	-	1	NA	promoter-TSS (NM_019930)	promoter-TSS (NM_019930)	45	NM_019930	56705	Mm.148781	NM_019930	ENSMUSG00000038546	Ranbp9	IBAP-1|Ibap1|RanBPM	RAN binding protein 9	protein-coding
mm_168274.1	chr1	102628246	102628264	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	1472487	NR_037989	100504525	Mm.87065	NR_037989	ENSMUSG00000100684	Gm20268	-	predicted gene, 20268	ncRNA
mm_20899.1	chr2	149092385	149092394	-	1	NA	Intergenic	Intergenic	-216877	NM_009976	13010	Mm.4263	NM_009976	ENSMUSG00000027447	Cst3	CysC	cystatin C	protein-coding
mm_144426.1	chr18	21001354	21001358	+	1	NA	promoter-TSS (NM_207623)	promoter-TSS (NM_207623)	56	NM_001303005	56515	Mm.253542	NM_019706	ENSMUSG00000024317	Rnf138	2410015A17Rik|2810480D20Rik|STRIN|Trif|Trif-d	ring finger protein 138	protein-coding
mm_116635.1	chr13	48968757	48968759	-	1	NA	promoter-TSS (NM_001033268)	promoter-TSS (NM_001033268)	646	NR_015601	68128	Mm.426304	NR_015601		Fam120aos	C030044B11Rik	family with sequence similarity 120A, opposite strand	ncRNA
mm_131011.1	chr15	103562995	103563004	-	1	NA	exon (NM_008134, exon 4 of 4)	exon (NM_008134, exon 4 of 4)	2082	NM_001289587	14663	Mm.219621	NM_008134	ENSMUSG00000022491	Glycam1	MC26|Sgp50|glyCAM-1	glycosylation dependent cell adhesion molecule 1	protein-coding
mm_77339.1	chr8	119563724	119563727	-	1	NA	3' UTR (NM_175185, exon 5 of 5)	3' UTR (NM_175185, exon 5 of 5)	-4964	NM_019709	56453	Mm.206934	NM_019709	ENSMUSG00000031835	Mbtps1	0610038M03Rik|AV003995|S1P|SKI-1|Ski1|mKIAA0091	membrane-bound transcription factor peptidase, site 1	protein-coding
mm_156529.1	chrX	151046913	151046933	+	1	NA	promoter-TSS (NM_008001)	promoter-TSS (NM_008001)	-247	NM_008001	14163	Mm.8142	NM_008001	ENSMUSG00000025265	Fgd1	ZFYVE3	FYVE, RhoGEF and PH domain containing 1	protein-coding
mm_117301.1	chr13	67269094	67269131	-	1	NA	promoter-TSS (NM_001001152)	promoter-TSS (NM_001001152)	-44	NM_001001152	238690	Mm.306358	NM_001001152	ENSMUSG00000055480	Zfp458	BC062958|Rslcan-7|Znf728|mszf59-2	zinc finger protein 458	protein-coding
mm_72636.1	chr8	84689270	84689303	+	1	NA	promoter-TSS (NM_198020)	promoter-TSS (NM_198020)	39	NM_198020	212528	Mm.275720	NM_198020	ENSMUSG00000001909	Trmt1	6720406L13Rik|6720477L24|D8Ertd812e	tRNA methyltransferase 1	protein-coding
mm_72373.1	chr8	81342502	81342510	+	1	NA	promoter-TSS (NM_001297596)	promoter-TSS (NM_001297596)	-56	NM_001024617	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_100512.1	chr11	120530521	120530534	+	1	NA	promoter-TSS (NM_008101)	promoter-TSS (NM_008101)	-200	NM_008101	14527	Mm.22329	NM_008101	ENSMUSG00000025127	Gcgr	GR	glucagon receptor	protein-coding
mm_136709.1	chr17	7926100	7926113	+	1	NA	5' UTR (NM_145968, exon 1 of 10)	5' UTR (NM_145968, exon 1 of 10)	106	NM_145968	72536	Mm.119680	NM_145968	ENSMUSG00000033450	Tagap	2610315E15Rik	T cell activation Rho GTPase activating protein	protein-coding
mm_124459.1	chr14	120422918	120422943	-	1	NA	intron (NM_175341, intron 8 of 8)	intron (NM_175341, intron 8 of 8)	-55531	NM_029519	76108	Mm.261448	NM_029519	ENSMUSG00000051615	Rap2a	5830461H18Rik	RAS related protein 2a	protein-coding
mm_171953.1	chr5	78128707	78128710	+	1	NA	Intergenic	L1Md_A|LINE|L1	663220	NR_131050	69370	Mm.426881	NR_131050	ENSMUSG00000107232	1700017L05Rik	-	RIKEN cDNA 1700017L05 gene	ncRNA
mm_96856.1	chr11	70056069	70056084	+	1	NA	exon (NM_009714, exon 3 of 9)	exon (NM_009714, exon 3 of 9)	1721	NM_001291132	11889	Mm.6559	NM_009714	ENSMUSG00000020884	Asgr1	ASGPR1|Asgr|Asgr-1|HL-1	asialoglycoprotein receptor 1	protein-coding
mm_117555.1	chr13	85126631	85126639	-	1	NA	Intergenic	Intergenic	-62750	NM_001347587	66671	Mm.18474	NM_023243	ENSMUSG00000021548	Ccnh	6330408H09Rik|AI661354|AV102684|AW538719	cyclin H	protein-coding
mm_115055.1	chr13	100651611	100651631	+	1	NA	promoter-TSS (NM_001015889)	promoter-TSS (NM_001015889)	14	NM_001015889	108143	Mm.301148	NM_027139	ENSMUSG00000052293	Taf9	2310012M09Rik|AA673500|AU045423|TAFII31|TAFII32|Taf2g	TATA-box binding protein associated factor 9	protein-coding
mm_101945.1	chr11	50212048	50212058	-	1	NA	Intergenic	ID_B1|SINE|B4	-1233	NM_011018	18412	Mm.40828	NM_011018	ENSMUSG00000015837	Sqstm1	A170|OSF-6|Osi|STAP|STONE14|p62	sequestosome 1	protein-coding
mm_118964.1	chr14	27622327	27622368	+	1	NA	promoter-TSS (NM_001347497)	promoter-TSS (NM_001347497)	-60	NM_001347497	238988	Mm.318004	NM_177814	ENSMUSG00000040640	Erc2	6430531D06|CAST|CAST1/ERC2|D14Ertd171e|ELKS2alpha	ELKS/RAB6-interacting/CAST family member 2	protein-coding
mm_10671.1	chr2	20970255	20970257	+	1	NA	TTS (NR_033225)	TTS (NR_033225)	1382	NR_033225	433408	Mm.386941	NR_033225		Gm13375	OTTMUSG00000011664	predicted gene 13375	ncRNA
mm_155493.1	chrX	73734565	73734575	+	1	NA	exon (NM_007435, exon 7 of 10)	exon (NM_007435, exon 7 of 10)	-16755	NM_001313698	27061	Mm.17	NM_012060	ENSMUSG00000002015	Bcap31	Bap31	B cell receptor associated protein 31	protein-coding
mm_99393.1	chr11	102145474	102145501	+	1	NA	promoter-TSS (NM_145829)	promoter-TSS (NM_145829)	-26	NM_145829	217214	Mm.31686	NM_145829	ENSMUSG00000048217	Nags	1700120E20Rik|argA	N-acetylglutamate synthase	protein-coding
mm_108868.1	chr12	99514774	99514774	+	1	NA	Intergenic	Intergenic	-49067	NR_136760	102639404	Mm.396324	NR_136760	ENSMUSG00000097917	Gm26839	-	predicted gene, 26839	ncRNA
mm_162865.1	chr10	93309905	93309924	+	1	NA	intron (NM_013508, intron 1 of 4)	intron (NM_013508, intron 1 of 4)	1245	NM_001322268	13713	Mm.4454	NM_013508	ENSMUSG00000008398	Elk3	D430049E23Rik|Erp|Etrp|Net|Sap-2	ELK3, member of ETS oncogene family	protein-coding
mm_107894.1	chr12	70649995	70650002	+	1	NA	intron (NR_037248, intron 4 of 4)	intron (NR_037248, intron 4 of 4)	-175516	NM_028127	319710	Mm.2962	NM_028127	ENSMUSG00000048285	Frmd6	2610019M19Rik|4930488L10Rik|AW212977|Willin	FERM domain containing 6	protein-coding
mm_95631.1	chr11	53631981	53631989	+	1	NA	3' UTR (NM_008355, exon 4 of 4)	3' UTR (NM_008355, exon 4 of 4)	2717	NM_008355	16163	Mm.1284	NM_008355	ENSMUSG00000020383	Il13	Il-13	interleukin 13	protein-coding
mm_12451.1	chr2	71211829	71211839	+	1	NA	promoter-TSS (NM_001198877)	promoter-TSS (NM_001198877)	-112	NM_001198878	13427	Mm.249479	NM_010064	ENSMUSG00000027012	Dync1i2	3110079H08Rik|AW554389|Dncic2	dynein cytoplasmic 1 intermediate chain 2	protein-coding
mm_77307.1	chr8	117671261	117671271	-	1	NA	5' UTR (NM_028725, exon 1 of 3)	5' UTR (NM_028725, exon 1 of 3)	249	NM_028725	74032	Mm.296302	NM_028725	ENSMUSG00000034308	Sdr42e1	4632417N05Rik|AI117603	short chain dehydrogenase/reductase family 42E, member 1	protein-coding
mm_73383.1	chr8	105686028	105686056	+	1	NA	Intergenic	Intergenic	-4864	NM_001033320	234695	Mm.471640	NM_001033320	ENSMUSG00000050357	Carmil2	CG1399-PB|D130029J02Rik|Gm585|Rltpr	capping protein regulator and myosin 1 linker 2	protein-coding
mm_16765.1	chr2	9878361	9878369	-	1	NA	intron (NM_008091, intron 1 of 5)	intron (NM_008091, intron 1 of 5)	235	NM_008091	14462	Mm.313866	NM_008091	ENSMUSG00000015619	Gata3	Gata-3|jal	GATA binding protein 3	protein-coding
mm_34958.1	chr4	155993449	155993455	+	1	NA	promoter-TSS (NM_080445)	promoter-TSS (NM_080445)	115	NM_001302468	20318	Mm.293517	NM_011341	ENSMUSG00000029076	Sdf4	Cab45	stromal cell derived factor 4	protein-coding
mm_76451.1	chr8	85087218	85087240	-	1	NA	exon (NM_010764, exon 6 of 24)	exon (NM_010764, exon 6 of 24)	3960	NM_010764	17159	Mm.4219	NM_010764	ENSMUSG00000005142	Man2b1	AW107687|LAMAN	mannosidase 2, alpha B1	protein-coding
mm_51653.1	chr6	86048358	86048360	+	1	NA	intron (NM_001271858, intron 1 of 15)	intron (NM_001271858, intron 1 of 15)	19678	NM_001271860	11519	Mm.104155	NM_013458	ENSMUSG00000030000	Add2	2900072M03Rik|add97	adducin 2 (beta)	protein-coding
mm_103757.1	chr11	80858278	80858287	-	1	NA	promoter-TSS (NM_029367)	promoter-TSS (NM_029367)	18	NR_110449	75043	Mm.410815	NR_110449	ENSMUSG00000086703	4930507D10Rik	-	RIKEN cDNA 4930507D10 gene	ncRNA
mm_112580.1	chr13	13699197	13699211	+	1	NA	intron (NM_010748, intron 31 of 52)	intron (NM_010748, intron 31 of 52)	-84855	NM_001302997	14706	Mm.215394	NM_010317	ENSMUSG00000021303	Gng4	-	guanine nucleotide binding protein (G protein), gamma 4	protein-coding
mm_131917.1	chr16	23308137	23308150	+	1	NA	intron (NM_001252506, intron 1 of 6)	intron (NM_001252506, intron 1 of 6)	17673	NM_001252506	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_106585.1	chr11	120729666	120729671	-	1	NA	3' UTR (NM_007621, exon 8 of 8)	3' UTR (NM_007621, exon 8 of 8)	2353	NM_007621	12409	Mm.21454	NM_007621	ENSMUSG00000025150	Cbr2	MLCR	carbonyl reductase 2	protein-coding
mm_128007.1	chr15	13132924	13132929	-	1	NA	intron (NM_007666, intron 1 of 11)	MTE2b|LTR|ERVL-MaLR	40749	NM_007666	12563	Mm.57048	NM_007666	ENSMUSG00000039385	Cdh6	cad6	cadherin 6	protein-coding
mm_148752.1	chr19	6057926	6057958	+	1	NA	promoter-TSS (NM_001190436)	promoter-TSS (NM_001190436)	-25	NM_001190436	14109	Mm.329631	NM_007990	ENSMUSG00000038274	Fau	MNSFbeta	Finkel-Biskis-Reilly murine sarcoma virus (FBR-MuSV) ubiquitously expressed (fox derived)	protein-coding
mm_141747.1	chr17	34201438	34201453	-	1	NA	TTS (NM_010724)	TTS (NM_010724)	-3034	NM_011530	21355	Mm.14814	NM_011530	ENSMUSG00000024339	Tap2	ABC18|AI462429|APT2|Abcb3|Ham-2|Ham2|MTP2|PSF2|RING11|Tap-2|Y1|jas	transporter 2, ATP-binding cassette, sub-family B (MDR/TAP)	protein-coding
mm_92235.1	chr10	69212997	69213014	-	1	NA	promoter-TSS (NM_001252638)	promoter-TSS (NM_001252638)	93	NM_001331193	320700	Mm.396529	NM_001331193	ENSMUSG00000090622	A930033H14Rik	-	RIKEN cDNA A930033H14 gene	protein-coding
mm_26142.1	chr3	138061916	138061920	+	1	NA	intron (NR_037975, intron 1 of 3)	intron (NR_037975, intron 1 of 3)	5470	NR_037975	329763	Mm.169710	NM_177860	ENSMUSG00000049349	Gm5105	D830013H12|EG329763	predicted gene 5105	ncRNA
mm_71450.1	chr8	46521627	46521652	+	1	NA	intron (NM_001302163, intron 11 of 20)	intron (NM_001302163, intron 11 of 20)	-30430	NM_027973	71876	Mm.22108	NM_027973	ENSMUSG00000031629	Cenpu	1700029A22Rik|Mlf1ip	centromere protein U	protein-coding
mm_151553.1	chr19	59458732	59458781	+	1	NA	promoter-TSS (NM_010132)	promoter-TSS (NM_010132)	66	NM_010132	13797	Mm.245394	NM_010132	ENSMUSG00000043969	Emx2	Pdo	empty spiracles homeobox 2	protein-coding
mm_91346.1	chr10	26741563	26741579	-	1	NA	Intergenic	Intergenic	-30941	NM_176837	73910	Mm.356496	NM_176837	ENSMUSG00000039031	Arhgap18	4833419J07Rik|AI314906|AI843501	Rho GTPase activating protein 18	protein-coding
mm_126431.1	chr15	80572802	80572825	+	1	NA	intron (NM_001289442, intron 1 of 7)	intron (NM_001289442, intron 1 of 7)	216	NM_001289442	17444	Mm.12947	NM_010815	ENSMUSG00000042351	Grap2	GRAP-2|GRB2L|GRBLG|GRID|Gads|GrbX|Grf40|GrpL|Mona|P38	GRB2-related adaptor protein 2	protein-coding
mm_62783.1	chr7	112427886	112427952	+	1	NA	5' UTR (NM_020606, exon 1 of 13)	5' UTR (NM_020606, exon 1 of 13)	213	NM_020606	57342	Mm.143763	NM_020606	ENSMUSG00000030770	Parva	2010012A22Rik|5430400F08Rik|AI225929|AU042898|Actp|CH-ILKBP|Parvin	parvin, alpha	protein-coding
mm_51033.1	chr6	65590383	65590412	+	1	NA	promoter-TSS (NM_001001495)	promoter-TSS (NM_001001495)	-1	NM_001001495	414084	Mm.117558	NM_001001495	ENSMUSG00000044162	Tnip3	9030611K07Rik|ABIN-3|LIND	TNFAIP3 interacting protein 3	protein-coding
mm_39294.1	chr5	5421720	5421722	+	1	NA	Intergenic	Intergenic	-41470	NM_011074	18647	Mm.389061	NM_011074	ENSMUSG00000028926	Cdk14	Pftk1|mKIAA0834	cyclin-dependent kinase 14	protein-coding
mm_6161.1	chr1	65051149	65051150	-	1	NA	promoter-TSS (NM_007777)	promoter-TSS (NM_007777)	14	NM_007777	12968	Mm.258170	NM_007777	ENSMUSG00000070870	Cryge	Cryg-2|Cryg-6|DGcry-2|Elo	crystallin, gamma E	protein-coding
mm_92962.1	chr10	85957776	85957818	-	1	NA	promoter-TSS (NM_145422)	promoter-TSS (NM_145422)	-4	NM_145422	28088	Mm.9257	NM_145422	ENSMUSG00000001783	Rtcb	AI255213|AI463255|D10Wsu52e|FAAP|HSPC117	RNA 2',3'-cyclic phosphate and 5'-OH ligase	protein-coding
mm_114999.1	chr13	97919855	97919863	+	1	NA	intron (NM_012026, intron 35 of 35)	intron (NM_012026, intron 35 of 35)	286306	NM_012026	110596	Mm.252718	NM_012026	ENSMUSG00000021662	Arhgef28	9230110L08Rik|AI323540|D13Bwg1089e|RIP2|Rgnef|RhoGEF|Rhoip2|p190RhoGEF	Rho guanine nucleotide exchange factor (GEF) 28	protein-coding
mm_29795.1	chr3	127692547	127692548	-	1	NA	intron (NM_027808, intron 4 of 13)	URR1B|DNA|hAT-Charlie	59402	NM_009718	11924	Mm.42017	NM_009718	ENSMUSG00000027967	Neurog2	Atoh4|Math4A|bHLHa8|ngn-2|ngn2	neurogenin 2	protein-coding
mm_155901.1	chrX	101667345	101667362	+	1	NA	exon (NM_001290535, exon 10 of 22)	exon (NM_001290535, exon 10 of 22)	27135	NM_001290535	108155	Mm.487332	NM_139144	ENSMUSG00000034160	Ogt	1110038P24Rik|4831420N21Rik|AI115525|Ogtl	O-linked N-acetylglucosamine (GlcNAc) transferase (UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase)	protein-coding
mm_55852.1	chr6	83441591	83441601	-	1	NA	promoter-TSS (NM_183138)	promoter-TSS (NM_183138)	82	NM_183138	194388	Mm.211030	NM_183138	ENSMUSG00000034832	Tet3	B430006D22Rik|BC037432|D230004J03Rik	tet methylcytosine dioxygenase 3	protein-coding
mm_2495.1	chr1	106022138	106022146	+	1	NA	intron (NM_001122676, intron 9 of 13)	intron (NM_001122676, intron 9 of 13)	31736	NM_001122675	227449	Mm.210188	NM_001122675	ENSMUSG00000038866	Zcchc2	9930114B20Rik|AW212015	zinc finger, CCHC domain containing 2	protein-coding
mm_46722.1	chr5	110729877	110729905	-	1	NA	exon (NM_029337, exon 8 of 52)	exon (NM_029337, exon 8 of 52)	40826	NM_029337	75560	Mm.270487	NM_029337	ENSMUSG00000029505	Ep400	1700020J09Rik|AU023439|mDomino|mKIAA1498|p400	E1A binding protein p400	protein-coding
mm_138721.1	chr17	36869568	36869581	+	1	NA	promoter-TSS (NM_011280)	promoter-TSS (NM_011280)	0	NM_011280	19824	Mm.299155	NM_011280	ENSMUSG00000073400	Trim10	AI324236|BB139825|Herf1|Rnf9	tripartite motif-containing 10	protein-coding
mm_54530.1	chr6	36715466	36715474	-	1	NA	TTS (NM_008973)	TTS (NM_008973)	95891	NM_008973	19242	Mm.279690	NM_008973	ENSMUSG00000029838	Ptn	HARP|HB-GAM|HBBN|HBGF-8|HBNF|OSF|Osf-1|Osf1	pleiotrophin	protein-coding
mm_63705.1	chr7	130646267	130646277	+	1	NA	intron (NM_001004468, intron 3 of 21)	CpG	-46284	NM_001347637	57752	Mm.86322	NM_021314	ENSMUSG00000030852	Tacc2	mKIAA4180	transforming, acidic coiled-coil containing protein 2	protein-coding
mm_95602.1	chr11	53351055	53351065	+	1	NA	5' UTR (NM_033565, exon 1 of 21)	5' UTR (NM_033565, exon 1 of 21)	293	NM_033565	93736	Mm.395281	NM_033565	ENSMUSG00000049470	Aff4	AF5Q31|Alf4|Laf4l|MCEF	AF4/FMR2 family, member 4	protein-coding
mm_36498.1	chr4	83324136	83324205	-	1	NA	promoter-TSS (NM_027238)	promoter-TSS (NM_027238)	19	NM_027238	69863	Mm.5540	NM_025782	ENSMUSG00000038172	Ttc39b	1810054D07Rik|9130422G05Rik|AI450603|AV103077|AW215585	tetratricopeptide repeat domain 39B	protein-coding
mm_147438.1	chr18	46522197	46522200	-	1	NA	intron (NM_173423, intron 2 of 2)	intron (NM_173423, intron 2 of 2)	3773	NM_173423	240263	Mm.38249	NM_173423	ENSMUSG00000033319	Fem1c	2610312A07Rik|3632443A22Rik|AI646567	fem-1 homolog c (C.elegans)	protein-coding
mm_33729.1	chr4	134097531	134097549	+	1	NA	Intergenic	Intergenic	-2467	NM_013706	23833	Mm.24130	NM_013706	ENSMUSG00000000682	Cd52	AI463198|B7|B7-Ag|CAMPATH-1|CLS1|MB7	CD52 antigen	protein-coding
mm_105889.1	chr11	114933769	114933779	-	1	NA	intron (NM_199221, intron 1 of 3)	intron (NM_199221, intron 1 of 3)	612	NM_001347651	217304	Mm.185355	NM_199221	ENSMUSG00000063193	Cd300lb	CLM-7|Clm7|Gm253|LMIR5	CD300 molecule like family member B	protein-coding
mm_37610.1	chr4	126753747	126753782	-	1	NA	promoter-TSS (NM_001035526)	promoter-TSS (NM_001035526)	-6	NM_133886	100317	Mm.206206	NM_133886	ENSMUSG00000028830	AU040320	A730047D20Rik|AAVR|Kiaa0319l	expressed sequence AU040320	protein-coding
mm_143421.1	chr17	70845031	70845061	-	1	NA	exon (NM_001164077, exon 2 of 2)	exon (NM_001164077, exon 2 of 2)	1731	NM_001164077	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_129095.1	chr15	75929734	75929772	-	1	NA	promoter-TSS (NM_031201)	promoter-TSS (NM_031201)	-23	NM_031201	22122	Mm.22596	NM_031201	ENSMUSG00000022570	Tsta3	AI256181|FX|Tstap35b	tissue specific transplantation antigen P35B	protein-coding
mm_81213.1	chr9	107581301	107581312	+	1	NA	promoter-TSS (NM_178020)	promoter-TSS (NM_178020)	10	NM_178020	109685	Mm.447916	NM_178020	ENSMUSG00000036091	Hyal3	Hyl3	hyaluronoglucosaminidase 3	protein-coding
mm_24255.1	chr3	89186713	89186721	+	1	NA	intron (NM_001014995, intron 7 of 11)	intron (NM_001014995, intron 7 of 11)	3492	NM_001014995	68521	Mm.274708	NM_001014995	ENSMUSG00000032657	Fam189b	1110013L07Rik	family with sequence similarity 189, member B	protein-coding
mm_68919.1	chr7	126462157	126462175	-	1	NA	exon (NM_007504, exon 3 of 23)	exon (NM_007504, exon 3 of 23)	907	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_127835.1	chr15	6831865	6831868	-	1	NA	intron (NM_001310469, intron 9 of 17)	intron (NM_001310469, intron 9 of 17)	42447	NM_011019	18414	Mm.10760	NM_011019	ENSMUSG00000022146	Osmr	OSMRB	oncostatin M receptor	protein-coding
mm_86465.1	chr10	4429288	4429302	+	1	NA	promoter-TSS (NR_002891)	promoter-TSS (NR_002891)	-129	NR_002891	433224	Mm.153111	NR_002891		Gm5512	EG433224	required for meiotic nuclear division 1 pseudogene	pseudo
mm_117731.1	chr13	95618420	95618435	-	1	NA	promoter-TSS (NM_010169)	promoter-TSS (NM_010169)	6	NM_010169	14062	Mm.24816	NM_010169	ENSMUSG00000048376	F2r	AI482343|Cf2r|Par1|ThrR	coagulation factor II (thrombin) receptor	protein-coding
mm_6663.1	chr1	80277440	80277451	-	1	NA	exon (NM_016716, exon 12 of 16)	exon (NM_016716, exon 12 of 16)	63245	NM_001313728	26554	Mm.12665	NM_016716	ENSMUSG00000004364	Cul3	KIAA0617	cullin 3	protein-coding
mm_113015.1	chr13	21981191	21981204	+	1	NA	promoter-TSS (NM_001162929)	promoter-TSS (NM_001162929)	3	NM_001162929	195236	Mm.204664	NM_001162928	ENSMUSG00000016982	Pom121l2	Gm24	POM121 membrane glycoprotein-like 2 (rat)	protein-coding
mm_97093.1	chr11	73176479	73176501	+	1	NA	promoter-TSS (NM_029564)	promoter-TSS (NM_029564)	518	NM_001168470	66048	Mm.73608	NM_025318	ENSMUSG00000047260	Emc6	0610009E20Rik|0610025L18Rik|Tmem93	ER membrane protein complex subunit 6	protein-coding
mm_30933.1	chr4	32983312	32983339	+	1	NA	5' UTR (NM_027491, exon 1 of 7)	5' UTR (NM_027491, exon 1 of 7)	327	NM_027491	52187	Mm.300814	NM_027491	ENSMUSG00000028278	Rragd	5730543C08Rik|AI467523|C030003H22Rik|D4Ertd174e	Ras-related GTP binding D	protein-coding
mm_160928.1	chr11	87986355	87986355	-	1	NA	5' UTR (NM_001168472, exon 1 of 3)	5' UTR (NM_001168472, exon 1 of 3)	230	NM_001168472	68097	Mm.246436	NM_026556	ENSMUSG00000020483	Dynll2	1700064A15Rik|6720463E02Rik|C87222|DLC8|DLC8b|Dlc2	dynein light chain LC8-type 2	protein-coding
mm_15578.1	chr2	158667192	158667194	+	1	NA	promoter-TSS (NM_001159662)	promoter-TSS (NM_001159662)	58	NM_001159662	228852	Mm.150540	NM_153089	ENSMUSG00000037754	Ppp1r16b	ANKRD4|C130078N17Rik|TIMAP|Wdt4	protein phosphatase 1, regulatory (inhibitor) subunit 16B	protein-coding
mm_115776.1	chr13	19311309	19311326	-	1	NA	Intergenic	Intergenic	84496	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_36963.1	chr4	109189056	109189062	-	1	NA	intron (NM_001346502, intron 1 of 23)	Lx8b|LINE|L1	13213	NM_133885	100273	Mm.366315	NM_133885	ENSMUSG00000028559	Osbpl9	2600011I06Rik|AU015843|Orp-9	oxysterol binding protein-like 9	protein-coding
mm_148163.1	chr18	77714447	77714501	-	1	NA	promoter-TSS (NM_178670)	promoter-TSS (NM_178670)	290	NR_027978	67640	Mm.482903	NM_026289		4930465K10Rik	-	RIKEN cDNA 4930465K10 gene	ncRNA
mm_91392.1	chr10	30700057	30700061	-	1	NA	intron (NM_172495, intron 5 of 15)	intron (NM_172495, intron 5 of 15)	-44192	NM_001111267	211329	Mm.297903	NM_172495	ENSMUSG00000039697	Ncoa7	9030406N13Rik	nuclear receptor coactivator 7	protein-coding
mm_35692.1	chr4	44084168	44084187	-	1	NA	promoter-TSS (NM_015828)	promoter-TSS (NM_015828)	0	NM_015828	50798	Mm.256718	NM_015828	ENSMUSG00000028479	Gne	2310066H07Rik|DMRV|GLCNE|IBM2|NM|Uae1	glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase	protein-coding
mm_158588.1	chrX	150815645	150815688	-	1	NA	Intergenic	Intergenic	-1327	NM_030700	80884	Mm.22575	NM_030700	ENSMUSG00000025268	Maged2	4833439A22Rik|Mage-d2|ORF1	melanoma antigen, family D, 2	protein-coding
mm_105620.1	chr11	106789084	106789109	-	1	NA	promoter-TSS (NM_177088)	promoter-TSS (NM_177088)	-156	NM_177088	320162	Mm.30524	NM_177088	ENSMUSG00000018372	Cep95	4732496G21Rik|AI118346|AI448335|Ccdc45|D330027A14Rik|F630025I20Rik	centrosomal protein 95	protein-coding
mm_45434.1	chr5	67099209	67099219	-	1	NA	promoter-TSS (NM_008888)	promoter-TSS (NM_008888)	-88	NM_008888	18935	Mm.62505	NM_008888	ENSMUSG00000012520	Phox2b	Dilp1|NBPhox|Pmx2b|Px2b	paired-like homeobox 2b	protein-coding
mm_30494.1	chr3	156920752	156920785	-	1	NA	intron (NM_177274, intron 2 of 6)	intron (NM_177274, intron 2 of 6)	358974	NM_001039094	320840	Mm.317293	NM_177274	ENSMUSG00000040037	Negr1	5330422G01Rik|KILON|Ntra	neuronal growth regulator 1	protein-coding
mm_74531.1	chr8	9625133	9625150	-	1	NA	intron (NM_001347127, intron 1 of 3)	intron (NM_001347127, intron 1 of 3)	145882	NM_173446	270028	Mm.268163	NM_173446	ENSMUSG00000079157	Fam155a	6430500D16|AW121567|Tmem28	family with sequence similarity 155, member A	protein-coding
mm_154320.1	chrM	2251	2259	+	1	NA	NA	Intergenic	NA	NA								
mm_115233.1	chr13	109903124	109903133	+	1	NA	promoter-TSS (NR_035442)	promoter-TSS (NR_035442)	-681	NR_035442	100316683		NR_035442	ENSMUSG00000084651	Mir1904	Mirn1904|mmu-mir-1904	microRNA 1904	ncRNA
mm_53143.1	chr6	125231955	125231976	+	1	NA	promoter-TSS (NM_145391)	promoter-TSS (NM_145391)	-105	NM_145391	213233	Mm.296902	NM_145391	ENSMUSG00000038213	Tapbpl	BC017613|TAPBPL-R|Tapbplr	TAP binding protein-like	protein-coding
mm_54251.1	chr6	28261957	28261967	-	1	NA	promoter-TSS (NM_001081678)	promoter-TSS (NM_001081678)	-361	NM_001081678	627049	Mm.84441	NM_001081678	ENSMUSG00000039841	Zfp800	AA407452|Znf800	zinc finger protein 800	protein-coding
mm_133775.1	chr16	94724487	94724505	+	1	NA	Intergenic	Intergenic	113077	NM_001347731	13548	Mm.310973	NM_007890	ENSMUSG00000022897	Dyrk1a	2310043O08Rik|D16Ertd272e|D16Ertd493e|Dyrk|ENSMUSG00000074897|Gm10783|Mnbh|Mp86|mmb	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1a	protein-coding
mm_39906.1	chr5	31291229	31291242	+	1	NA	promoter-TSS (NM_026298)	promoter-TSS (NM_026298)	-121	NM_026298	67661	Mm.293023	NM_026298	ENSMUSG00000038564	Ift172	4930553F24Rik|Slb|avc1|wim	intraflagellar transport 172	protein-coding
mm_74289.1	chr8	125910340	125910350	+	1	NA	promoter-TSS (NM_145608)	promoter-TSS (NM_145608)	-105	NM_145608	234878	Mm.216458	NM_145608	ENSMUSG00000031853	Map3k21	Mlk4|mKIAA1804	mitogen-activated protein kinase kinase kinase 21	protein-coding
mm_154823.1	chrX	16619825	16619842	+	1	NA	5' UTR (NM_173740, exon 1 of 15)	5' UTR (NM_173740, exon 1 of 15)	135	NM_173740	17161	Mm.21108	NM_173740	ENSMUSG00000025037	Maoa	1110061B18Rik|AA407771	monoamine oxidase A	protein-coding
mm_28475.1	chr3	92081644	92081659	-	1	NA	exon (NM_008508, exon 2 of 2)	exon (NM_008508, exon 2 of 2)	1491	NM_008508	16939	Mm.1121	NM_008508	ENSMUSG00000043165	Lor	AI036317|S77319	loricrin	protein-coding
mm_166451.1	chr5	137517460	137517479	+	1	NA	Intergenic	Intergenic	-1411	NM_031408	57330	Mm.268344	NM_031408	ENSMUSG00000029714	Gigyf1	Perq1|mKIAA4110	GRB10 interacting GYF protein 1	protein-coding
mm_58476.1	chr7	3411473	3411515	+	1	NA	intron (NM_133190, intron 2 of 3)	intron (NM_133190, intron 2 of 3)	-3572	NR_128566	104795667		NR_128566	ENSMUSG00000094210	Gm23450	Mir935|mmu-mir-935	predicted gene, 23450	ncRNA
mm_146276.1	chr18	77882467	77882477	+	1	NA	3' UTR (NM_013831, exon 15 of 15)	3' UTR (NM_013831, exon 15 of 15)	-55995	NM_001195633	100502841	Mm.297782	NM_001195633	ENSMUSG00000039840	Epg5	4732475F16|5430411K18Rik|AI661957|AW456499|mKIAA1632	ectopic P-granules autophagy protein 5 homolog (C. elegans)	protein-coding
mm_47802.1	chr5	132542376	132542386	-	1	NA	promoter-TSS (NM_177047)	promoter-TSS (NM_177047)	-38	NM_177047	319974	Mm.409595	NM_177047	ENSMUSG00000029673	Auts2	2700063G02Rik|A730011F23Rik|D830032G16Rik	autism susceptibility candidate 2	protein-coding
mm_122607.1	chr14	51057467	51057473	-	1	NA	promoter-TSS (NM_001011875)	promoter-TSS (NM_001011875)	-228	NM_001011875	497106	Mm.379740	NM_001011875	ENSMUSG00000068407	Rnase12	Rai1	ribonuclease, RNase A family, 12 (non-active)	protein-coding
mm_75550.1	chr8	57652555	57652586	-	1	NA	intron (NR_040698, intron 1 of 3)	CpG	485	NM_001167981	108150	Mm.62886	NM_144731	ENSMUSG00000031608	Galnt7	AI225872	UDP-N-acetyl-alpha-D-galactosamine: polypeptide N-acetylgalactosaminyltransferase 7	protein-coding
mm_30646.1	chr4	8837826	8837836	+	1	NA	intron (NM_001277149, intron 15 of 37)	intron (NM_001277149, intron 15 of 37)	147425	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_21281.1	chr2	156953355	156953361	-	1	NA	intron (NM_013865, intron 3 of 15)	intron (NM_013865, intron 3 of 15)	38753	NM_013865	29812	Mm.279256	NM_013865	ENSMUSG00000027634	Ndrg3	4833415O14Rik|AI747193|Ndr3	N-myc downstream regulated gene 3	protein-coding
mm_154162.1	chr19	58670597	58670598	-	1	NA	intron (NM_026925, intron 2 of 12)	intron (NM_026925, intron 2 of 12)	232	NM_026925	69060	Mm.20407	NM_026925	ENSMUSG00000046008	Pnlip	1810007A24Rik|PL|PTL	pancreatic lipase	protein-coding
mm_106792.1	chr12	4782137	4782154	+	1	NA	Intergenic	Intergenic	12850	NM_028376	382562	Mm.251575	NM_028376	ENSMUSG00000020639	Pfn4	2900024P18Rik	profilin family, member 4	protein-coding
mm_20373.1	chr2	128429237	128429259	-	1	NA	non-coding (NR_028591, exon 1 of 2)	non-coding (NR_028591, exon 1 of 2)	103	NR_028591	100043424	Mm.297222	NR_028589		Gm14005	OTTMUSG00000015351	predicted gene 14005	ncRNA
mm_56506.1	chr6	99339399	99339417	-	1	NA	intron (NM_001347345, intron 2 of 19)	intron (NM_001347345, intron 2 of 19)	-72893	NM_001197321	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_1233.1	chr1	62778058	62778095	+	1	NA	intron (NM_001077405, intron 12 of 15)	intron (NM_001077405, intron 12 of 15)	16656	NR_040601	74992	Mm.401979	NR_040601		4930487H11Rik	-	RIKEN cDNA 4930487H11 gene	ncRNA
mm_86318.1	chr9	122950909	122950915	-	1	NA	promoter-TSS (NM_025419)	promoter-TSS (NM_025419)	88	NM_025419	66202	Mm.268307	NM_025419	ENSMUSG00000032551	1110059G10Rik	-	RIKEN cDNA 1110059G10 gene	protein-coding
mm_106540.1	chr11	120578959	120578959	-	1	NA	3' UTR (NM_133796, exon 6 of 6)	3' UTR (NM_133796, exon 6 of 6)	2661	NM_133796	192662	Mm.30016	NM_133796	ENSMUSG00000025132	Arhgdia	5330430M07Rik|Gdi-1|Rho-GDI|RhoDGI|RhoGDI-1	Rho GDP dissociation inhibitor (GDI) alpha	protein-coding
mm_126293.1	chr15	79347600	79347614	+	1	NA	promoter-TSS (NM_010755)	promoter-TSS (NM_010755)	87	NM_010755	17133	Mm.86646	NM_010755	ENSMUSG00000042622	Maff	-	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein F (avian)	protein-coding
mm_121634.1	chr14	8368121	8368136	-	1	NA	intron (NM_146050, intron 1 of 9)	intron (NM_146050, intron 1 of 9)	10635	NM_146050	18300	Mm.25351	NM_146050	ENSMUSG00000021749	Oit1	2310076N21Rik|AV067083|EF-7|Fam3d	oncoprotein induced transcript 1	protein-coding
mm_96240.1	chr11	62551775	62551821	+	1	NA	promoter-TSS (NM_001313984)	promoter-TSS (NM_001313984)	67	NM_001313984	22187	Mm.371592	NM_011664	ENSMUSG00000019505	Ubb	AL033289|Rps27a|Uba52|Ubb2|Ubc	ubiquitin B	protein-coding
mm_84781.1	chr9	76323560	76323586	-	1	NA	promoter-TSS (NM_198962)	promoter-TSS (NM_198962)	5	NM_198962	387285	Mm.335300	NM_198962	ENSMUSG00000032360	Hcrtr2	OX2R|mOX2aR|mOX2bR|mOXR2	hypocretin (orexin) receptor 2	protein-coding
mm_148574.1	chr19	4869400	4869414	+	1	NA	exon (NM_013456, exon 8 of 21)	exon (NM_013456, exon 8 of 21)	8502	NM_013456	11474	Mm.5316	NM_013456	ENSMUSG00000006457	Actn3	-	actinin alpha 3	protein-coding
mm_111602.1	chr12	102356858	102356871	-	1	NA	intron (NM_177620, intron 4 of 9)	intron (NM_177620, intron 4 of 9)	73223	NM_001161365	217835	Mm.24145	NM_177620	ENSMUSG00000044456	Rin3	6430500K07|C86933	Ras and Rab interactor 3	protein-coding
mm_15843.1	chr2	164769893	164769903	+	1	NA	promoter-TSS (NM_026785)	promoter-TSS (NM_026785)	-31	NM_026785	68612	Mm.89830	NM_026785	ENSMUSG00000001403	Ube2c	1110015A16Rik|D2Ertd695e	ubiquitin-conjugating enzyme E2C	protein-coding
mm_115276.1	chr13	111686304	111686346	+	1	NA	5' UTR (NM_172593, exon 1 of 13)	5' UTR (NM_172593, exon 1 of 13)	147	NM_172593	218613	Mm.31012	NM_172593	ENSMUSG00000032727	Mier3	5730509D14|AU015422|D130064H19Rik	MIER family member 3	protein-coding
mm_101.1	chr1	9545398	9545479	+	1	NA	promoter-TSS (NM_021511)	promoter-TSS (NM_021511)	30	NM_021511	59014	Mm.29061	NM_021511	ENSMUSG00000061024	Rrs1	5730466A07Rik|AA415037|D1Ertd701e|Rrr	ribosome biogenesis regulator 1	protein-coding
mm_123420.1	chr14	64417042	64417047	-	1	NA	promoter-TSS (NM_001253716)	promoter-TSS (NM_001253716)	-88	NM_001253716	110265	Mm.26713	NM_026322	ENSMUSG00000054733	Msra	2310045J23Rik|6530413P12Rik|MSR-A	methionine sulfoxide reductase A	protein-coding
mm_130358.1	chr15	97767681	97767703	-	1	NA	promoter-TSS (NM_001177811)	promoter-TSS (NM_001177811)	-26	NM_001177811	223864	Mm.24028	NM_144850	ENSMUSG00000022469	Rapgef3	2310016P22Rik|9330170P05Rik|Epac|Epac1	Rap guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_158135.1	chrX	103186536	103186546	-	1	NA	5' UTR (NM_008671, exon 1 of 1)	5' UTR (NM_008671, exon 1 of 1)	123	NM_008671	17954	Mm.388694	NM_008671	ENSMUSG00000082229	Nap1l2	Bpx	nucleosome assembly protein 1-like 2	protein-coding
mm_1514.1	chr1	72583294	72583300	+	1	NA	promoter-TSS (NM_018817)	promoter-TSS (NM_018817)	46	NM_018817	54380	Mm.274232	NM_018817	ENSMUSG00000039354	Smarcal1	6030401P21Rik|AI851716|Mharp	SWI/SNF related matrix associated, actin dependent regulator of chromatin, subfamily a-like 1	protein-coding
mm_111408.1	chr12	91266057	91266059	-	1	NA	intron (NM_181815, intron 15 of 25)	intron (NM_181815, intron 15 of 25)	118351	NM_181815	75216	Mm.312204	NM_181815	ENSMUSG00000061533	Cep128	4930534B04Rik|5430424K18Rik|AI449708|AI480494|E230024F20	centrosomal protein 128	protein-coding
mm_146947.1	chr18	32462506	32462512	-	1	NA	Intergenic	Intergenic	-84225	NR_045403	402767	Mm.385109	NR_045403	ENSMUSG00000097413	A830052D11Rik	-	RIKEN cDNA A830052D11 gene	ncRNA
mm_5767.1	chr1	49400788	49400799	-	1	NA	Intergenic	RMER12|LTR|ERVK	-1526730	NM_019790	56363	Mm.245154	NM_019790	ENSMUSG00000026109	Tmeff2	4832418D20Rik|7630402F16Rik|TR-2	transmembrane protein with EGF-like and two follistatin-like domains 2	protein-coding
mm_168149.1	chr10	37707778	37707778	-	1	NA	Intergenic	L1Md_T|LINE|L1	-467996	NR_131035	75877	Mm.402094	NR_131035	ENSMUSG00000111234	4930591E09Rik	-	RIKEN cDNA 4930591E09 gene	ncRNA
mm_29511.1	chr3	116422224	116422237	-	1	NA	intron (NM_001080818, intron 2 of 15)	intron (NM_001080818, intron 2 of 15)	1802	NM_001080818	229776	Mm.17647	NM_001080818	ENSMUSG00000033502	Cdc14a	A830059A17Rik|CDC14A2|CDC14a1|Cdc14	CDC14 cell division cycle 14A	protein-coding
mm_160173.1	chr7	45361694	45361694	-	1	NA	exon (NM_029741, exon 2 of 30)	exon (NM_029741, exon 2 of 30)	-4469	NR_015480	50994	Mm.389897	NM_016664	ENSMUSG00000091510	Mtag2	MAG	metastasis associated gene 2	ncRNA
mm_119189.1	chr14	32342139	32342142	+	1	NA	exon (NM_001081130, exon 16 of 24)	exon (NM_001081130, exon 16 of 24)	20121	NM_001081130	239017	Mm.318302	NM_001081130	ENSMUSG00000021913	Ogdhl	-	oxoglutarate dehydrogenase-like	protein-coding
mm_53854.1	chr6	149189696	149189699	+	1	NA	promoter-TSS (NM_001113424)	promoter-TSS (NM_001113424)	-985	NM_001113424	232566	Mm.209147	NM_001113424	ENSMUSG00000068250	Amn1	5830467E07Rik|A230083D09|C730024G19Rik	antagonist of mitotic exit network 1	protein-coding
mm_55300.1	chr6	54816932	54816974	-	1	NA	promoter-TSS (NM_199143)	promoter-TSS (NM_199143)	37	NM_199143	387524	Mm.286149	NM_199143	ENSMUSG00000058446	Znrf2	1190002C14Rik|AU044205|D6Ertd365e	zinc and ring finger 2	protein-coding
mm_39509.1	chr5	21246789	21246799	+	1	NA	intron (NM_175437, intron 13 of 30)	intron (NM_175437, intron 13 of 30)	60527	NM_175437	212167	Mm.121705	NM_175437	ENSMUSG00000039934	Gsap	A530088I07Rik|Pion	gamma-secretase activating protein	protein-coding
mm_81137.1	chr9	106626600	106626613	+	1	NA	promoter-TSS (NM_001101628)	promoter-TSS (NM_001101628)	24	NM_001101628	100041096	Mm.477435	NM_001101628	ENSMUSG00000091129	Iqcf6	-	IQ motif containing F6	protein-coding
mm_58046.1	chr6	136828052	136828062	-	1	NA	promoter-TSS (NM_178776)	promoter-TSS (NM_178776)	159	NM_021714	60321	Mm.141197	NM_021714	ENSMUSG00000030216	Wbp11	2510026P17Rik|D6Wsu113e|Npwbp|SIPP1	WW domain binding protein 11	protein-coding
mm_50002.1	chr6	41055864	41055893	+	1	NA	Intergenic	Intergenic	-20369	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_92410.1	chr10	76721967	76721981	-	1	NA	exon (NM_009933, exon 4 of 35)	exon (NM_009933, exon 4 of 35)	4070	NM_009933	12833	Mm.2509	NM_009933	ENSMUSG00000001119	Col6a1	AI747156|Col6a-1	collagen, type VI, alpha 1	protein-coding
mm_131897.1	chr16	23237404	23237409	+	1	NA	intron (NM_001252505, intron 1 of 7)	intron (NM_001252505, intron 1 of 7)	11385	NM_001252505	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_85588.1	chr9	107313311	107313348	-	1	NA	Intergenic	Intergenic	16670	NM_009895	12700	Mm.4592	NM_009895	ENSMUSG00000032578	Cish	CIS-1|CIS1|Cis|F17|F23|SOCS	cytokine inducible SH2-containing protein	protein-coding
mm_56882.1	chr6	119030864	119030874	-	1	NA	intron (NM_001256002, intron 3 of 47)	IMPB_01|Satellite|Satellite	77626	NM_001159534	12288	Mm.41628	NM_009781	ENSMUSG00000051331	Cacna1c	Cav1.2|Cchl1a1|D930026N18Rik|MBC|MELC-CC	calcium channel, voltage-dependent, L type, alpha 1C subunit	protein-coding
mm_17958.1	chr2	37373446	37373482	-	1	NA	3' UTR (NM_001100591, exon 22 of 22)	3' UTR (NM_001100591, exon 22 of 22)	-14132	NM_026176	67466	Mm.30709	NM_026176	ENSMUSG00000009030	Pdcl	1200011E13Rik|AW108059|PhLP1	phosducin-like	protein-coding
mm_168337.1	chr11	11906253	11906261	+	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	-8113	NM_001190448	13195	Mm.12906	NM_016672	ENSMUSG00000020182	Ddc	Aadc	dopa decarboxylase	protein-coding
mm_157937.1	chrX	85080403	85080414	-	1	NA	intron (NM_001314038, intron 2 of 8)	intron (NM_001314038, intron 2 of 8)	32113	NM_001314034	13405	Mm.275608	NM_007868	ENSMUSG00000045103	Dmd	DXSmh7|DXSmh9|Dp427|Dp71|dys|mdx|pke	dystrophin, muscular dystrophy	protein-coding
mm_109808.1	chr12	3356962	3356980	-	1	NA	Intergenic	Intergenic	-8161	NM_008445	16570	Mm.7688	NM_008445	ENSMUSG00000020668	Kif3c	mKIAA4058	kinesin family member 3C	protein-coding
mm_67076.1	chr7	68264202	68264232	-	1	NA	promoter-TSS (NM_030101)	promoter-TSS (NM_030101)	16	NM_030101	78444	Mm.425468	NM_030101	ENSMUSG00000030553	Pgpep1l	C330024D12Rik	pyroglutamyl-peptidase I-like	protein-coding
mm_3576.1	chr1	151086296	151086297	+	1	NA	Intergenic	Intergenic	-51738	NR_038011	402734	Mm.337666	NR_038011		C730036E19Rik	lncLSTR	RIKEN cDNA C730036E19 gene	ncRNA
mm_42025.1	chr5	108279132	108279143	+	1	NA	3' UTR (NM_026106, exon 3 of 3)	3' UTR (NM_026106, exon 3 of 3)	10240	NM_026106	13486	Mm.303534	NM_026106	ENSMUSG00000029265	Dr1	1700121L09Rik|Dr1l|NC2|NC2beta	down-regulator of transcription 1	protein-coding
mm_61606.1	chr7	80029911	80029927	+	1	NA	intron (NM_175433, intron 1 of 4)	intron (NM_175433, intron 1 of 4)	3691	NM_175433	209225	Mm.290925	NM_175433	ENSMUSG00000048897	Zfp710	5430400N05Rik|9830165K13|AI324798|Znf710	zinc finger protein 710	protein-coding
mm_600.1	chr1	39852442	39852469	+	1	NA	Intergenic	Intergenic	-5125	NR_040465	73426	Mm.396239	NR_040465	ENSMUSG00000101634	1700066B17Rik	-	RIKEN cDNA 1700066B17 gene	ncRNA
mm_172816.1	chr9	123690246	123690260	-	1	NA	Intergenic	Intergenic	-11421	NM_139142	102680	Mm.440867	NM_139142	ENSMUSG00000036814	Slc6a20a	A730081N20Rik|AU022428|Xt3s1|Xtrp3s1	solute carrier family 6 (neurotransmitter transporter), member 20A	protein-coding
mm_106798.1	chr12	4917333	4917343	+	1	NA	promoter-TSS (NM_001099628)	promoter-TSS (NM_001099628)	-15	NM_001099628	320817	Mm.210966	NM_001099628	ENSMUSG00000052812	Atad2b	1110014E10Rik|BC032887|C79189|D530031C13Rik	ATPase family, AAA domain containing 2B	protein-coding
mm_147829.1	chr18	62179949	62179986	-	1	NA	promoter-TSS (NM_007420)	promoter-TSS (NM_007420)	14	NM_007420	11555	Mm.5598	NM_007420	ENSMUSG00000045730	Adrb2	Adrb-2|Badm|Gpcr7	adrenergic receptor, beta 2	protein-coding
mm_47851.1	chr5	134549957	134549964	-	1	NA	intron (NM_009990, intron 1 of 16)	intron (NM_009990, intron 1 of 16)	2474	NM_001039162	269713	Mm.255138	NM_009990	ENSMUSG00000063146	Clip2	B230327O20|CLIP-115|Clip1|Cyln2|WSCR4|mKIAA0291|wbscr4	CAP-GLY domain containing linker protein 2	protein-coding
mm_85262.1	chr9	99420248	99420257	-	1	NA	intron (NM_008624, intron 1 of 5)	intron (NM_008624, intron 1 of 5)	16460	NM_008624	17532	Mm.2045	NM_008624	ENSMUSG00000032470	Mras	2900078C09Rik|AI326250	muscle and microspikes RAS	protein-coding
mm_168411.1	chr1	131573813	131573832	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-25292	NM_011924	26361	Mm.89986	NM_011924	ENSMUSG00000026432	Avpr1b	AVPR3|V3/V1b|VIBR|VPR3	arginine vasopressin receptor 1B	protein-coding
mm_18150.1	chr2	45067162	45067174	-	1	NA	intron (NM_001289521, intron 1 of 8)	intron (NM_001289521, intron 1 of 8)	43109	NM_001289521	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_46601.1	chr5	107868179	107868183	-	1	NA	intron (NM_007964, intron 1 of 17)	intron (NM_007964, intron 1 of 17)	6926	NM_007964	14020	Mm.35796	NM_007964	ENSMUSG00000011831	Evi5	NB4S	ecotropic viral integration site 5	protein-coding
mm_46311.1	chr5	100572082	100572114	-	1	NA	intron (NM_139198, intron 1 of 4)	intron (NM_139198, intron 1 of 4)	107	NM_139198	231507	Mm.34609	NM_139198	ENSMUSG00000029322	Plac8	C15|D5Wsu111e	placenta-specific 8	protein-coding
mm_117201.1	chr13	64066128	64066138	-	1	NA	intron (NM_008291, intron 6 of 10)	B4A|SINE|B4	23068	NM_008291	15487	Mm.5109	NM_008291	ENSMUSG00000033122	Hsd17b3	-	hydroxysteroid (17-beta) dehydrogenase 3	protein-coding
mm_81490.1	chr9	110003811	110003824	+	1	NA	3' UTR (NM_001205331, exon 4 of 4)	3' UTR (NM_001205331, exon 4 of 4)	-48204	NM_001311163	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_59851.1	chr7	29908493	29908573	+	1	NA	promoter-TSS (NM_001243908)	promoter-TSS (NM_001243908)	16	NM_001243908	73729	Mm.333743	NM_001243908	ENSMUSG00000099689	Zfp383	1110003H10Rik	zinc finger protein 383	protein-coding
mm_146538.1	chr18	5593378	5593388	-	1	NA	promoter-TSS (NR_033552)	promoter-TSS (NR_033552)	-946	NR_033552	791318	Mm.84339	NR_033552	ENSMUSG00000063087	Gm10125	ENSMUSG00000063087|Zeb1os	predicted gene 10125	ncRNA
mm_143137.1	chr17	57218507	57218525	-	1	NA	exon (NM_009778, exon 21 of 41)	exon (NM_009778, exon 21 of 41)	-1288	NR_105944	102465591		NR_105944	ENSMUSG00000099066	Mir6978	Gm27858|mmu-mir-6978	microRNA 6978	ncRNA
mm_155756.1	chrX	96167552	96167563	+	1	NA	3' UTR (NM_010833, exon 13 of 13)	3' UTR (NM_010833, exon 13 of 13)	71512	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_57389.1	chr6	124839968	124840016	-	1	NA	5' UTR (NM_013530, exon 1 of 10)	5' UTR (NM_013530, exon 1 of 10)	283	NM_013530	14695	Mm.68889	NM_013530	ENSMUSG00000023439	Gnb3	Gnb-3	guanine nucleotide binding protein (G protein), beta 3	protein-coding
mm_150014.1	chr19	29367193	29367199	+	1	NA	promoter-TSS (NM_021893)	promoter-TSS (NM_021893)	-242	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_33481.1	chr4	130818907	130818917	+	1	NA	exon (NM_011520, exon 3 of 5)	exon (NM_011520, exon 3 of 5)	26375	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_129323.1	chr15	77767644	77767656	-	1	NA	exon (NM_022410, exon 32 of 41)	exon (NM_022410, exon 32 of 41)	-12421	NM_001081970	239552	Mm.125650	NM_001081970	ENSMUSG00000056656	Apol8	9830006J20Rik|APOL-II|Apol2	apolipoprotein L 8	protein-coding
mm_119847.1	chr14	54440742	54440756	+	1	NA	3' UTR (NM_008608, exon 10 of 10)	3' UTR (NM_008608, exon 10 of 10)	9151	NM_008608	17387	Mm.280175	NM_008608	ENSMUSG00000000957	Mmp14	AI325305|MMP-X1|MT-MMP-1|MT1-MMP|sabe	matrix metallopeptidase 14 (membrane-inserted)	protein-coding
mm_30833.1	chr4	21931684	21931728	+	1	NA	exon (NM_175234, exon 1 of 6)	exon (NM_175234, exon 1 of 6)	380	NM_175234	76132	Mm.159689	NM_175234	ENSMUSG00000028246	Faxc	6230409E13Rik|AW742931	failed axon connections homolog	protein-coding
mm_12194.1	chr2	65620963	65620974	+	1	NA	5' UTR (NM_001346679, exon 1 of 27)	5' UTR (NM_001346679, exon 1 of 27)	199	NM_001346679	110876	Mm.220329	NM_001099298	ENSMUSG00000075318	Scn2a	6430408L10|A230052E19Rik|Nav1.2|Scn2a1	sodium channel, voltage-gated, type II, alpha	protein-coding
mm_150704.1	chr19	42306466	42306497	+	1	NA	intron (NM_145123, intron 6 of 14)	intron (NM_145123, intron 6 of 14)	-26311	NR_037246	100526549		NR_037246	ENSMUSG00000093234	Mir3085	mir-3085|mmu-mir-3085	microRNA 3085	ncRNA
mm_30158.1	chr3	142882035	142882042	-	1	NA	promoter-TSS (NM_178654)	promoter-TSS (NM_178654)	-34	NM_178654	109333	Mm.244236	NM_178654	ENSMUSG00000004591	Pkn2	6030436C20Rik|AI507382|PRK2|Prkcl2|Stk7	protein kinase N2	protein-coding
mm_25695.1	chr3	122266553	122266576	+	1	NA	3' UTR (NM_008129, exon 7 of 7)	3' UTR (NM_008129, exon 7 of 7)	-7850	NM_153806	99480	Mm.398647	NM_153806	ENSMUSG00000039756	Dnttip2	4930588M11Rik|AA408582|AU014960|HSU15552	deoxynucleotidyltransferase, terminal, interacting protein 2	protein-coding
mm_21991.1	chr2	167643572	167643583	-	1	NA	3' UTR (NM_145538, exon 6 of 6)	3' UTR (NM_145538, exon 6 of 6)	-11572	NM_023230	66589	Mm.278783	NM_023230	ENSMUSG00000078923	Ube2v1	0610011J09Rik|AI256840|CROC-1|CROC1|D7Bwg1382e|UEV-1	ubiquitin-conjugating enzyme E2 variant 1	protein-coding
mm_142221.1	chr17	37185525	37185536	-	1	NA	Intergenic	Intergenic	-8362	NM_023137	24108	Mm.140210	NM_023137	ENSMUSG00000035186	Ubd	FAT10	ubiquitin D	protein-coding
mm_4259.1	chr1	171419061	171419092	+	1	NA	promoter-TSS (NM_001164525)	promoter-TSS (NM_001164525)	43	NM_001164525	226654	Mm.46366	NM_001164525	ENSMUSG00000103711	Tstd1	AV065366|EG226654|Gm4848|KAT	thiosulfate sulfurtransferase (rhodanese)-like domain containing 1	protein-coding
mm_116420.1	chr13	41800670	41800680	-	1	NA	intron (NM_175417, intron 4 of 6)	MLT1A1|LTR|ERVL-MaLR	46813	NM_175417	109254	Mm.25195	NM_175417	ENSMUSG00000058022	Adtrp	9530008L14Rik	androgen dependent TFPI regulating protein	protein-coding
mm_17320.1	chr2	26463754	26463766	-	1	NA	exon (NM_008714, exon 31 of 34)	exon (NM_008714, exon 31 of 34)	6359	NR_105962	102465602		NR_105962	ENSMUSG00000098548	Mir6996	Gm27531|mmu-mir-6996	microRNA 6996	ncRNA
mm_118382.1	chr13	117025835	117025854	-	1	NA	promoter-TSS (NM_001081009)	promoter-TSS (NM_001081009)	-328	NM_001081009	52552	Mm.274466	NM_027272	ENSMUSG00000021725	Parp8	2810430O08Rik|ARTD16|D13Ertd275e	poly (ADP-ribose) polymerase family, member 8	protein-coding
mm_163389.1	chr12	56529492	56529498	-	1	NA	promoter-TSS (NR_045082)	promoter-TSS (NR_045082)	-75	NR_045082	104798	Mm.310950	NR_045082		E030019B13Rik	AI413669	RIKEN cDNA E030019B13 gene	ncRNA
mm_122277.1	chr14	34417288	34417293	-	1	NA	intron (NM_009758, intron 10 of 12)	MTEa|LTR|ERVL-MaLR	41786	NM_153127	105450	Mm.272673	NM_153127	ENSMUSG00000041445	Mmrn2	AA986839|ENDOGLYX1|Emilin3|EndoGlyx-1	multimerin 2	protein-coding
mm_141941.1	chr17	35051267	35051296	-	1	NA	intron (NM_033444, intron 1 of 5)	intron (NM_033444, intron 1 of 5)	1038	NM_033444	114584	Mm.29524	NM_033444	ENSMUSG00000007041	Clic1	Clcp|G6	chloride intracellular channel 1	protein-coding
mm_119967.1	chr14	55491063	55491136	+	1	NA	promoter-TSS (NM_001024645)	promoter-TSS (NM_001024645)	6	NM_001024645	268747	Mm.151577	NM_001024645	ENSMUSG00000022211	Carmil3	Lrrc16b|mFLJ00240	capping protein regulator and myosin 1 linker 3	protein-coding
mm_150044.1	chr19	29379105	29379123	+	1	NA	intron (NM_021893, intron 3 of 6)	ID_B1|SINE|B4	11676	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_89908.1	chr10	111167196	111167210	+	1	NA	intron (NM_175489, intron 1 of 23)	intron (NM_175489, intron 1 of 23)	2401	NM_175489	237542	Mm.220204	NM_175489	ENSMUSG00000020189	Osbpl8	AA536976|AA536995|C730029P18Rik|D330025H14Rik|ORP-8	oxysterol binding protein-like 8	protein-coding
mm_28800.1	chr3	96198461	96198484	-	1	NA	promoter-TSS (NM_026975)	promoter-TSS (NM_026975)	-886	NM_026975	69168	Mm.104531	NM_026975	ENSMUSG00000015943	Bola1	1810037G04Rik	bolA-like 1 (E. coli)	protein-coding
mm_64642.1	chr7	4008352	4008372	-	1	NA	3' UTR (NM_178611, exon 7 of 7)	3' UTR (NM_178611, exon 7 of 7)	54842	NM_001302677	52855	Mm.290880	NM_178611	ENSMUSG00000055541	Lair1	5133400O11Rik|BB115266|D7Bwg0421e|Lair-1	leukocyte-associated Ig-like receptor 1	protein-coding
mm_21002.1	chr2	152343965	152343971	-	1	NA	promoter-TSS (NM_175093)	promoter-TSS (NM_175093)	92	NM_175093	228775	Mm.276018	NM_144554	ENSMUSG00000032715	Trib3	Ifld2|Nipk|SINK|SKIP3|TRB-3|Trb3	tribbles pseudokinase 3	protein-coding
mm_119288.1	chr14	34501944	34501962	+	1	NA	intron (NM_009758, intron 1 of 12)	intron (NM_009758, intron 1 of 12)	593	NM_009758	12166	Mm.237825	NM_009758	ENSMUSG00000021796	Bmpr1a	1110037I22Rik|ALK3|AU045487|BMPR-IA|Bmpr	bone morphogenetic protein receptor, type 1A	protein-coding
mm_143012.1	chr17	56461826	56461869	-	1	NA	intron (NM_001252455, intron 1 of 27)	CpG	374	NM_001252456	19280	Mm.258771	NM_011218	ENSMUSG00000013236	Ptprs	AL022616|PTP|PTP-NU3|PTPNU-3|PTPsigma|Ptpt9|R-PTP-S|RPTPsigma	protein tyrosine phosphatase, receptor type, S	protein-coding
mm_156049.1	chrX	109095400	109095412	+	1	NA	promoter-TSS (NM_019989)	promoter-TSS (NM_019989)	-1	NM_019989	56726	Mm.260760	NM_019989	ENSMUSG00000031246	Sh3bgrl	1190008F14Rik	SH3-binding domain glutamic acid-rich protein like	protein-coding
mm_137117.1	chr17	22497396	22497405	+	1	NA	Intergenic	MLT1K|LTR|ERVL-MaLR	73198	NM_001331198	74149	Mm.30767	NM_198003	ENSMUSG00000071266	Zfp946	1300003B13Rik	zinc finger protein 946	protein-coding
mm_55033.1	chr6	48976600	48976623	-	1	NA	exon (NM_001029987, exon 1 of 4)	exon (NM_001029987, exon 1 of 4)	1468	NM_001029987	243376	Mm.244112	NM_001029987	ENSMUSG00000068536	Doxl2	-	diamine oxidase-like protein 2	protein-coding
mm_117040.1	chr13	58291707	58291711	-	1	NA	intron (NM_175214, intron 15 of 16)	intron (NM_175214, intron 15 of 16)	-17521	NM_019832	56278	Mm.296625	NM_019832	ENSMUSG00000021552	Gkap1	42kDa|4933400B15Rik|D13Ertd340e|Gkap42	G kinase anchoring protein 1	protein-coding
mm_19572.1	chr2	101641268	101641278	-	1	NA	3' UTR (NM_009019, exon 2 of 2)	3' UTR (NM_009019, exon 2 of 2)	8259	NM_009019	19373	Mm.828	NM_009019	ENSMUSG00000061311	Rag1	Rag-1	recombination activating gene 1	protein-coding
mm_49695.1	chr6	33941300	33941304	+	1	NA	intron (NM_009148, intron 17 of 17)	intron (NM_009148, intron 17 of 17)	-88146	NM_028886	74354	Mm.127952	NM_028886	ENSMUSG00000056215	Lrguk	4921528H16Rik	leucine-rich repeats and guanylate kinase domain containing	protein-coding
mm_51664.1	chr6	86195443	86195459	+	1	NA	5' UTR (NM_031199, exon 1 of 6)	5' UTR (NM_031199, exon 1 of 6)	224	NM_031199	21802	Mm.137222	NM_031199	ENSMUSG00000029999	Tgfa	wa-1|wa1	transforming growth factor alpha	protein-coding
mm_28218.1	chr3	88410366	88410370	-	1	NA	promoter-TSS (NM_025928)	promoter-TSS (NM_025928)	29	NM_001310605	67037	Mm.36715	NM_025928	ENSMUSG00000028066	Pmf1	2600009M07Rik|AL033286|AW060657	polyamine-modulated factor 1	protein-coding
mm_137352.1	chr17	25228177	25228186	+	1	NA	intron (NM_028789, intron 1 of 4)	PB1D9|SINE|Alu	5599	NM_028789	74154	Mm.267353	NM_028789	ENSMUSG00000015127	Unkl	1300004G08Rik	unkempt family like zinc finger	protein-coding
mm_140655.1	chr17	12740579	12740608	-	1	NA	promoter-TSS (NR_027784)	promoter-TSS (NR_027784)	-718	NR_002853	104103	Mm.26553	NR_002853	ENSMUSG00000078247	Airn	2810051F02Rik|2810434M15Rik|AI256653|AI597500|AW049873|Air|B930018I07Rik|D17Ertd663e|IGF2RAS	antisense Igf2r RNA	ncRNA
mm_132892.1	chr16	48842844	48842855	+	1	NA	exon (NM_020509, exon 2 of 4)	exon (NM_020509, exon 2 of 4)	297	NM_020509	57262	Mm.441868	NM_020509	ENSMUSG00000061100	Retnla	1810019L16Rik|Fizz-1|Fizz1|HIMF|RELM-alpha|RELMa|RELMalpha|Xcp2	resistin like alpha	protein-coding
mm_78481.1	chr9	32696006	32696095	+	1	NA	promoter-TSS (NM_001038642)	promoter-TSS (NM_001038642)	8	NM_001038642	23871	Mm.292415	NM_011808	ENSMUSG00000032035	Ets1	AI196000|AI448617|D230050P06|Ets-1|Tpl1|vs	E26 avian leukemia oncogene 1, 5' domain	protein-coding
mm_139256.1	chr17	47737126	47737149	+	1	NA	promoter-TSS (NM_001161723)	promoter-TSS (NM_001161723)	100	NM_001161722	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_123757.1	chr14	70203456	70203466	-	1	NA	intron (NM_011366, intron 1 of 20)	intron (NM_011366, intron 1 of 20)	1162	NM_001271408	20410	Mm.5068	NM_011366	ENSMUSG00000022091	Sorbs3	SCAM-1|SH3P3|Sh3d4|vinexin-g	sorbin and SH3 domain containing 3	protein-coding
mm_142057.1	chr17	35667485	35667496	-	1	NA	TTS (NM_010364)	TTS (NM_010364)	102	NM_175137	68915	Mm.32002	NM_175137	ENSMUSG00000038838	Vars2	1190004I24Rik|Vars2l|mKIAA1885	valyl-tRNA synthetase 2, mitochondrial	protein-coding
mm_126051.1	chr15	76948729	76948778	+	1	NA	exon (NM_001347540, exon 2 of 5)	exon (NM_001347540, exon 2 of 5)	209	NM_054099	117171	Mm.322968	NM_054099	ENSMUSG00000063236	1110038F14Rik	-	RIKEN cDNA 1110038F14 gene	protein-coding
mm_103627.1	chr11	78751657	78751711	-	1	NA	promoter-TSS (NM_197989)	promoter-TSS (NM_197989)	45	NM_197989	69109	Mm.341420	NM_197989	ENSMUSG00000049489	Fam58b	1810009O10Rik|Fam58a	family with sequence similarity 58, member B	protein-coding
mm_33662.1	chr4	133174472	133174475	+	1	NA	intron (NM_153423, intron 1 of 8)	intron (NM_153423, intron 1 of 8)	-21182	NR_105984	102466215		NR_105984	ENSMUSG00000099202	Mir7017	Gm27945|mmu-mir-7017	microRNA 7017	ncRNA
mm_52558.1	chr6	116173629	116173635	+	1	NA	intron (NM_177412, intron 1 of 5)	intron (NM_177412, intron 1 of 5)	19742	NM_177412	330401	Mm.425352	NM_177412	ENSMUSG00000030126	Tmcc1	3632431M01Rik|mKIAA0779	transmembrane and coiled coil domains 1	protein-coding
mm_39295.1	chr5	5479178	5479189	+	1	NA	promoter-TSS (NM_001200025)	promoter-TSS (NM_001200025)	-40	NM_001200025	381716	Mm.276086	NM_001200025	ENSMUSG00000079666	1700015F17Rik	Gm1686	RIKEN cDNA 1700015F17 gene	protein-coding
mm_748.1	chr1	43544885	43544908	+	1	NA	intron (NM_010879, intron 3 of 4)	URR1A|DNA|hAT-Charlie	99145	NM_010879	17974	Mm.389903	NM_010879	ENSMUSG00000066877	Nck2	4833426I10Rik|Grb4|NCKbeta|Nck-2	non-catalytic region of tyrosine kinase adaptor protein 2	protein-coding
mm_118505.1	chr14	13961258	13961286	+	1	NA	promoter-TSS (NM_025435)	promoter-TSS (NM_025435)	41	NM_001285780	66231	Mm.295875	NM_025435	ENSMUSG00000053453	Thoc7	Nif3l1bp1	THO complex 7	protein-coding
mm_51439.1	chr6	80019069	80019079	+	1	NA	promoter-TSS (NM_178731)	promoter-TSS (NM_178731)	197	NM_001134743	243499	Mm.483425	NM_178731	ENSMUSG00000052581	Lrrtm4	7530419J18Rik|A230052N11	leucine rich repeat transmembrane neuronal 4	protein-coding
mm_156906.1	chrX	169037673	169037677	+	1	NA	intron (NR_109847, intron 1 of 14)	intron (NR_109847, intron 1 of 14)	1064	NR_109847	11856	Mm.441810	NM_009707	ENSMUSG00000031355	Arhgap6	AI504284|RhoGAPX-1	Rho GTPase activating protein 6	protein-coding
mm_35127.1	chr4	11209271	11209282	-	1	NA	exon (NM_001159595, exon 25 of 27)	exon (NM_001159595, exon 25 of 27)	17567	NM_001282943	12448	Mm.35867	NM_009830	ENSMUSG00000028212	Ccne2	-	cyclin E2	protein-coding
mm_31342.1	chr4	46489275	46489356	+	1	NA	promoter-TSS (NM_053179)	promoter-TSS (NM_053179)	-14	NM_053179	94181	Mm.249349	NM_053179	ENSMUSG00000028334	Nans	4632418E04Rik|BB056474|Sas	N-acetylneuraminic acid synthase (sialic acid synthase)	protein-coding
mm_13355.1	chr2	103411761	103411770	+	1	NA	promoter-TSS (NM_001145813)	promoter-TSS (NM_001145813)	-333	NM_001145813	13711	Mm.20888	NM_010125	ENSMUSG00000027186	Elf5	ESE-2|ESE-5|ESE-5.	E74-like factor 5	protein-coding
mm_19480.1	chr2	93014602	93014636	-	1	NA	intron (NM_001177536, intron 1 of 6)	intron (NM_001177536, intron 1 of 6)	-14729	NR_110333	433456	Mm.235231	NM_001002794	ENSMUSG00000075027	4631405J19Rik	-	RIKEN cDNA 4631405J19 gene	ncRNA
mm_98683.1	chr11	96287057	96287079	+	1	NA	exon (NM_010460, exon 1 of 2)	exon (NM_010460, exon 1 of 2)	422	NM_010460	15415	Mm.390366	NM_010460	ENSMUSG00000038721	Hoxb7	AI325018|Hox-2.3	homeobox B7	protein-coding
mm_132874.1	chr16	48629919	48629922	+	1	NA	intron (NM_010816, intron 26 of 26)	RLTR23|LTR|ERV1	142036	NM_198297	77647	Mm.167298	NM_198297	ENSMUSG00000030775	Trat1	C030046M14Rik|Tcrim|Trim	T cell receptor associated transmembrane adaptor 1	protein-coding
mm_107827.1	chr12	69184160	69184170	+	1	NA	promoter-TSS (NM_025589)	promoter-TSS (NM_025589)	7	NM_146035	217664	Mm.206642	NM_146035	ENSMUSG00000043998	Mgat2	AA407964|CDGS2|GLCNACTII|GNT-II|GNT2	mannoside acetylglucosaminyltransferase 2	protein-coding
mm_73384.1	chr8	105686147	105686228	+	1	NA	Intergenic	Intergenic	-4719	NM_001033320	234695	Mm.471640	NM_001033320	ENSMUSG00000050357	Carmil2	CG1399-PB|D130029J02Rik|Gm585|Rltpr	capping protein regulator and myosin 1 linker 2	protein-coding
mm_138258.1	chr17	34590852	34590896	+	1	NA	exon (NM_134116, exon 3 of 4)	exon (NM_134116, exon 3 of 4)	1068	NM_134116	106512	Mm.26584	NM_134116	ENSMUSG00000034786	Gpsm3	AA960287|AGS4	G-protein signalling modulator 3 (AGS3-like, C. elegans)	protein-coding
mm_172498.1	chr7	65784808	65784822	+	1	NA	Intergenic	Intergenic	-19237	NR_045301	100503969	Mm.383527	NR_045301		1810008I18Rik	-	RIKEN cDNA 1810008I18 gene	ncRNA
mm_148474.1	chr19	4097801	4097809	+	1	NA	intron (NM_026373, intron 1 of 3)	intron (NM_026373, intron 1 of 3)	454	NM_026373	52004	Mm.29609	NM_026373	ENSMUSG00000024856	Cdk2ap2	5830466O21Rik|D19Ertd144e|Doc-1r	CDK2-associated protein 2	protein-coding
mm_54729.1	chr6	40585818	40585828	-	1	NA	promoter-TSS (NM_021364)	promoter-TSS (NM_021364)	-18	NM_001038604	23845	Mm.103765	NM_021364	ENSMUSG00000029915	Clec5a	Clecsf5|Ly100|MDL-1|Mdl1	C-type lectin domain family 5, member a	protein-coding
mm_162357.1	chr1	58586629	58586641	+	1	NA	promoter-TSS (NM_172513)	promoter-TSS (NM_172513)	238	NM_025597	66495	Mm.2033	NM_025597	ENSMUSG00000026032	Ndufb3	2700033I16Rik|CI-B12	NADH dehydrogenase (ubiquinone) 1 beta subcomplex 3	protein-coding
mm_78436.1	chr9	32036930	32036930	+	1	NA	Intergenic	Intergenic	-79206	NM_001195632	330914	Mm.46683	NM_177379	ENSMUSG00000041444	Arhgap32	3426406O18Rik|Gc-gap|Grit|Px-rics|Rics|mKIAA0712|p200Rhogap|p250Gap	Rho GTPase activating protein 32	protein-coding
mm_50895.1	chr6	56868842	56868854	+	1	NA	exon (NM_012056, exon 7 of 10)	exon (NM_012056, exon 7 of 10)	33038	NM_001252374	107569	Mm.158936	NM_026004	ENSMUSG00000029780	Nt5c3	1600024P05Rik|2610206B05Rik|3110004A18Rik|AI842776|Nt5c3a|Nt5y|PN-1|PN-I|PSN1|UMPH|Umph-1|Umph1|cN-III|lupin|p36	5'-nucleotidase, cytosolic III	protein-coding
mm_41121.1	chr5	87781828	87781863	+	1	NA	exon (NM_001304768, exon 8 of 13)	exon (NM_001304768, exon 8 of 13)	7395	NM_007785	12993	Mm.4908	NM_007785	ENSMUSG00000061937	Csn1s2a	Csng|PP22	casein alpha s2-like A	protein-coding
mm_28707.1	chr3	95624723	95624749	-	1	NA	promoter-TSS (NM_019561)	promoter-TSS (NM_019561)	-244	NM_019561	56205	Mm.241365	NM_019561	ENSMUSG00000038619	Ensa	1700020C18Rik|2610007F17Rik|AI451924	endosulfine alpha	protein-coding
mm_81643.1	chr9	110907737	110907740	+	1	NA	Intergenic	ERVB5_1-LTR_MM|LTR|ERVK	9123	NM_001195437	235634	Mm.31788	NM_001195437	ENSMUSG00000096393	Gm590	-	predicted gene 590	protein-coding
mm_68235.1	chr7	104842582	104842585	-	1	NA	promoter-TSS (NM_201409)	promoter-TSS (NM_201409)	-79	NM_201409	381944	Mm.334094	NM_201409	ENSMUSG00000062369	Usp17lb	DUB-1A|Dub1a|USP17-B	ubiquitin specific peptidase 17-like B	protein-coding
mm_78344.1	chr9	25297876	25297883	+	1	NA	exon (NM_001205367, exon 8 of 13)	exon (NM_001205367, exon 8 of 13)	45440	NM_001205367	235072	Mm.270259	NM_009859	ENSMUSG00000001833	Sept7	Cdc10|E430034N22	septin 7	protein-coding
mm_129039.1	chr15	75048808	75048844	-	1	NA	promoter-TSS (NM_001252055)	promoter-TSS (NM_001252055)	11	NM_001252057	17067	Mm.1583	NM_010741	ENSMUSG00000079018	Ly6c1	AA682074|AA959465|Ly-6C|Ly-6C1|Ly6c	lymphocyte antigen 6 complex, locus C1	protein-coding
mm_131951.1	chr16	24418296	24418296	+	1	NA	intron (NM_178665, intron 1 of 12)	intron (NM_178665, intron 1 of 12)	-24641	NR_037954	68841	Mm.361995	NR_037954		Lppos	1110054M08Rik|AI481106	LIM domain containing preferred translocation partner in lipoma, opposite strand	ncRNA
mm_65672.1	chr7	28294610	28294670	-	1	NA	exon (NM_007866, exon 7 of 9)	exon (NM_007866, exon 7 of 9)	-3506	NM_175033	280621	Mm.212777	NM_175033	ENSMUSG00000046750	Selenov	Selv	selenoprotein V	protein-coding
mm_31943.1	chr4	86658607	86658635	+	1	NA	exon (NM_007408, exon 7 of 8)	exon (NM_007408, exon 7 of 8)	11438	NM_007408	11520	Mm.381	NM_007408	ENSMUSG00000028494	Plin2	AA407157|ADPH|Adfp|Adrp	perilipin 2	protein-coding
mm_26130.1	chr3	137868078	137868117	+	1	NA	intron (NM_001033155, intron 1 of 7)	GC_rich|Low_complexity|Low_complexity	422	NM_001033155	70604	Mm.256488	NM_001033155	ENSMUSG00000074212	Dnajb14	5730496F10Rik	DnaJ heat shock protein family (Hsp40) member B14	protein-coding
mm_87543.1	chr10	53596924	53596934	+	1	NA	promoter-TSS (NM_025541)	promoter-TSS (NM_025541)	-32	NM_025541	66403	Mm.272989	NM_025541	ENSMUSG00000019857	Asf1a	2310079C17Rik|C79052	anti-silencing function 1A histone chaperone	protein-coding
mm_35904.1	chr4	49597861	49597892	-	1	NA	promoter-TSS (NM_025944)	promoter-TSS (NM_025944)	-6	NM_025944	67063	Mm.490285	NM_025944	ENSMUSG00000039611	Tmem246	2810432L12Rik|9330170P15Rik|AI835809	transmembrane protein 246	protein-coding
mm_35955.1	chr4	53130853	53130869	-	1	NA	intron (NM_013454, intron 3 of 49)	intron (NM_013454, intron 3 of 49)	29034	NM_013454	11303	Mm.277376	NM_013454	ENSMUSG00000015243	Abca1	ABC-1|Abc1	ATP-binding cassette, sub-family A (ABC1), member 1	protein-coding
mm_168855.1	chr12	24252474	24252481	-	1	NA	Intergenic	CpG	-155208	NM_001256489	66808	Mm.379124	NM_001256489	ENSMUSG00000073158	9030624G23Rik	-	RIKEN cDNA 9030624G23 gene	protein-coding
mm_144399.1	chr18	20749993	20749997	+	1	NA	Intergenic	Intergenic	-3591	NM_019737	56386	Mm.393827	NM_019737	ENSMUSG00000056124	B4galt6	AA536803|AU022389	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 6	protein-coding
mm_82577.1	chr9	21131252	21131288	-	1	NA	promoter-TSS (NM_018793)	promoter-TSS (NM_018793)	5	NM_018793	54721	Mm.20249	NM_018793	ENSMUSG00000032175	Tyk2	JTK1	tyrosine kinase 2	protein-coding
mm_118928.1	chr14	27039015	27039050	+	1	NA	promoter-TSS (NM_134437)	promoter-TSS (NM_134437)	31	NM_134437	171463	Mm.206726	NM_027265	ENSMUSG00000040717	Il17rd	2810004A10Rik|AI428510|Sef|Sef-S	interleukin 17 receptor D	protein-coding
mm_74566.1	chr8	11008914	11008936	-	1	NA	promoter-TSS (NM_001081212)	promoter-TSS (NM_001081212)	-495	NM_001081212	384783	Mm.407207	NM_001081212	ENSMUSG00000038894	Irs2	Irs-2	insulin receptor substrate 2	protein-coding
mm_140674.1	chr17	12960730	12960738	-	1	NA	promoter-TSS (NM_009338)	promoter-TSS (NM_009338)	-9	NM_009338	110460	Mm.439711	NM_009338	ENSMUSG00000023832	Acat2	AW742799|Tcp-1x|Tcp1-rs1	acetyl-Coenzyme A acetyltransferase 2	protein-coding
mm_100359.1	chr11	118475827	118475836	+	1	NA	Intergenic	Intergenic	-1129	NM_172573	217364	Mm.473963	NM_172573	ENSMUSG00000033857	Engase	C130099A03|D230014K01Rik	endo-beta-N-acetylglucosaminidase	protein-coding
mm_65879.1	chr7	29555639	29555647	-	1	NA	Intergenic	Intergenic	-50183	NM_001081028	74206	Mm.447042	NM_001081028	ENSMUSG00000030583	Sipa1l3	2610511M17Rik	signal-induced proliferation-associated 1 like 3	protein-coding
mm_56076.1	chr6	87182654	87182665	-	1	NA	intron (NM_054041, intron 16 of 17)	intron (NM_054041, intron 16 of 17)	77913	NM_001167937	52372	Mm.282851	NM_001167937	ENSMUSG00000090891	D6Ertd527e	AU043841	DNA segment, Chr 6, ERATO Doi 527, expressed	protein-coding
mm_111023.1	chr12	79089662	79089687	-	1	NA	promoter-TSS (NM_029988)	promoter-TSS (NM_029988)	-4	NM_029988	110417	Mm.268317	NM_029988	ENSMUSG00000021120	Pigh	2210416H01Rik|A930028P05Rik	phosphatidylinositol glycan anchor biosynthesis, class H	protein-coding
mm_155008.1	chrX	41400903	41400907	+	1	NA	promoter-TSS (NM_001290451)	promoter-TSS (NM_001290451)	-396	NM_016886	53623	Mm.327681	NM_016886	ENSMUSG00000001986	Gria3	2900064I19Rik|GluA3|GluR-C|GluR-K3|Glur-3|Glur3|Gluralpha3	glutamate receptor, ionotropic, AMPA3 (alpha 3)	protein-coding
mm_68214.1	chr7	104409529	104409539	-	1	NA	3' UTR (NM_009099, exon 8 of 8)	3' UTR (NM_009099, exon 8 of 8)	-50888	NM_175648	244183	Mm.347647	NM_175648	ENSMUSG00000052749	Trim30b	A530023O14Rik|Trim30-1	tripartite motif-containing 30B	protein-coding
mm_111569.1	chr12	101818478	101818488	-	1	NA	intron (NM_011812, intron 1 of 10)	intron (NM_011812, intron 1 of 10)	636	NM_011812	23876	Mm.288381	NM_011812	ENSMUSG00000021186	Fbln5	A55|DANCE|EVEC	fibulin 5	protein-coding
mm_135947.1	chr16	74411719	74411731	-	1	NA	promoter-TSS (NM_175549)	promoter-TSS (NM_175549)	-813	NM_175549	268902	Mm.171736	NM_175549	ENSMUSG00000052516	Robo2	2600013A04Rik|9430089E08Rik|BB097918|D230004I22Rik|mKIAA1568	roundabout guidance receptor 2	protein-coding
mm_83117.1	chr9	40392424	40392433	-	1	NA	intron (NM_172768, intron 2 of 19)	intron (NM_172768, intron 2 of 19)	58956	NR_040728	73558	Mm.398307	NR_040728		1700110K17Rik	-	RIKEN cDNA 1700110K17 gene	ncRNA
mm_83555.1	chr9	46242664	46242711	-	1	NA	exon (NM_007468, exon 3 of 3)	exon (NM_007468, exon 3 of 3)	1843	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_99055.1	chr11	99051797	99051818	+	1	NA	3' UTR (NM_010517, exon 4 of 4)	3' UTR (NM_010517, exon 4 of 4)	10547	NM_010517	16010	Mm.233799	NM_010517	ENSMUSG00000017493	Igfbp4	AI875747|Deb2|IGFBP-4	insulin-like growth factor binding protein 4	protein-coding
mm_155352.1	chrX	68761876	68761887	+	1	NA	promoter-TSS (NM_001166620)	promoter-TSS (NM_001166620)	42	NM_001166619	207854	Mm.284945	NM_174993	ENSMUSG00000062170	Fmr1nb	3830422N12Rik|NY-SAR-35|NYSAR35	fragile X mental retardation 1 neighbor	protein-coding
mm_171917.1	chr5	5782425	5782444	-	1	NA	Intergenic	Intergenic	-33117	NM_027399	70358	Mm.85429	NM_027399	ENSMUSG00000015652	Steap1	2410007B19Rik|Prss24|Steap	six transmembrane epithelial antigen of the prostate 1	protein-coding
mm_28268.1	chr3	88752846	88752849	-	1	NA	intron (NM_018804, intron 2 of 3)	intron (NM_018804, intron 2 of 3)	19752	NM_018804	229521	Mm.379376	NM_018804	ENSMUSG00000068923	Syt11	1500004A13Rik|3632445O20Rik|5430404N14Rik|6530420C11Rik|AI851970	synaptotagmin XI	protein-coding
mm_156523.1	chrX	150594339	150594358	+	1	NA	intron (NM_008824, intron 1 of 13)	intron (NM_008824, intron 1 of 13)	4427	NM_008824	18639	Mm.249131	NM_008824	ENSMUSG00000025271	Pfkfb1	PFK/FBPase 1	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1	protein-coding
mm_109848.1	chr12	4593793	4593812	-	1	NA	intron (NM_011365, intron 1 of 38)	intron (NM_011365, intron 1 of 38)	794	NM_001198968	20403	Mm.341204	NM_011365	ENSMUSG00000020640	Itsn2	AI327390|Ese2|Sh3d1B|Sh3p18|mKIAA1256	intersectin 2	protein-coding
mm_119916.1	chr14	54953384	54953412	+	1	NA	exon (NM_010856, exon 22 of 39)	exon (NM_010856, exon 22 of 39)	-4256	NR_029724	387204		NR_029724	ENSMUSG00000065432	Mir208a	Mirn208|Mirn208a|mir-208|mir-208a|mmu-mir-208	microRNA 208a	ncRNA
mm_123239.1	chr14	60177568	60177618	-	1	NA	Intergenic	GC_rich|Low_complexity|Low_complexity	51322	NR_030458	751526		NR_030458	ENSMUSG00000076270	Mir719	Mirn719|mmu-mir-719	microRNA 719	ncRNA
mm_43936.1	chr5	145114250	145114275	+	1	NA	promoter-TSS (NM_023142)	promoter-TSS (NM_023142)	6	NM_023142	11867	Mm.30010	NM_023142	ENSMUSG00000029622	Arpc1b	41kDa|AA408064|AA408534|AA571392|AF007010|AW208418|L72|SOP2Hs|p41-ARC	actin related protein 2/3 complex, subunit 1B	protein-coding
mm_90806.1	chr10	7664120	7664128	-	1	NA	promoter-TSS (NM_008786)	promoter-TSS (NM_008786)	-516	NM_001347228	18537	Mm.258431	NM_008786	ENSMUSG00000019795	Pcmt1	C79501|PIMT	protein-L-isoaspartate (D-aspartate) O-methyltransferase 1	protein-coding
mm_126881.1	chr15	89453791	89453835	+	1	NA	promoter-TSS (NM_021921)	promoter-TSS (NM_021921)	-98	NM_021921	60597	Mm.173337	NM_021921	ENSMUSG00000022619	Mapk8ip2	3230402N03Rik|AI847694|AW049958|IB2|Jip2|R75148	mitogen-activated protein kinase 8 interacting protein 2	protein-coding
mm_26612.1	chr3	152346466	152346531	+	1	NA	promoter-TSS (NM_133247)	promoter-TSS (NM_133247)	20	NM_001076676	170822	Mm.258320	NM_133247	ENSMUSG00000025437	Usp33	9830169D19Rik|AA409780|Vdu1	ubiquitin specific peptidase 33	protein-coding
mm_160297.1	chr7	132802528	132802528	-	1	NA	intron (NM_212473, intron 1 of 4)	intron (NM_212473, intron 1 of 4)	10668	NM_212473	77938	Mm.225649	NM_175268	ENSMUSG00000030956	Fam53b	A930008G19Rik|mKIAA0140	family with sequence similarity 53, member B	protein-coding
mm_82161.1	chr9	123781457	123781472	+	1	NA	3' UTR (NM_001166625, exon 4 of 4)	3' UTR (NM_001166625, exon 4 of 4)	14253	NM_001166625	12769	Mm.440604	NM_009913	ENSMUSG00000029530	Ccr9	A130091K22Rik|Cmkbr10|GPR-9-6	chemokine (C-C motif) receptor 9	protein-coding
mm_32425.1	chr4	107127028	107127030	+	1	NA	Intergenic	Intergenic	30138	NM_172873	242603	Mm.257231	NM_172873	ENSMUSG00000047636	Cdcp2	D030010E02Rik	CUB domain containing protein 2	protein-coding
mm_109436.1	chr12	110695905	110695914	+	1	NA	intron (NM_010480, intron 1 of 10)	CpG	486	NM_010480	15519	Mm.1843	NM_010480	ENSMUSG00000021270	Hsp90aa1	86kDa|89kDa|AL024080|AL024147|Hsp86-1|Hsp89|Hsp90|Hspca|hsp4	heat shock protein 90, alpha (cytosolic), class A member 1	protein-coding
mm_27093.1	chr3	30140408	30140433	-	1	NA	Intergenic	Intergenic	-127216	NM_007963	14013	Mm.56965	NM_007963	ENSMUSG00000027684	Mecom	D630039M04Rik|Evi-1|Evi1|Jbo|Mds|Mds1|Mds1-Evi1|Prdm3|Znfpr1b1	MDS1 and EVI1 complex locus	protein-coding
mm_128161.1	chr15	33687805	33687835	-	1	NA	promoter-TSS (NM_001085421)	promoter-TSS (NM_001085421)	63	NM_001085421	239364	Mm.60794	NM_001085421	ENSMUSG00000038984	Tspyl5	6330530B20|E130308C19Rik	testis-specific protein, Y-encoded-like 5	protein-coding
mm_32620.1	chr4	114406668	114406710	+	1	NA	promoter-TSS (NM_001085549)	promoter-TSS (NM_001085549)	-35	NM_001085549	666048	Mm.331779	NM_001085549	ENSMUSG00000070867	Trabd2b	Gm12824|Hkat|OTTMUSG00000008561	TraB domain containing 2B	protein-coding
mm_164882.1	chr18	59062313	59062338	+	1	NA	promoter-TSS (NR_033765)	promoter-TSS (NR_033765)	-56	NR_033764	225583	Mm.209711	NM_173759	ENSMUSG00000050875	A730017C20Rik	-	RIKEN cDNA A730017C20 gene	protein-coding
mm_100310.1	chr11	117977998	117978010	+	1	NA	Intergenic	Intergenic	-8638	NM_007707	12702	Mm.3468	NM_007707	ENSMUSG00000053113	Socs3	Cis3|Cish3|EF-10|Ef10|SSI-3|Ssi3	suppressor of cytokine signaling 3	protein-coding
mm_151313.1	chr19	55832875	55832888	+	1	NA	intron (NR_138565, intron 4 of 15)	B3A|SINE|B2	-62440	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_138904.1	chr17	43576761	43576784	+	1	NA	intron (NM_013737, intron 1 of 11)	intron (NM_013737, intron 1 of 11)	8321	NM_013737	27226	Mm.9277	NM_013737	ENSMUSG00000023913	Pla2g7	PAF-AH|R75400	phospholipase A2, group VII (platelet-activating factor acetylhydrolase, plasma)	protein-coding
mm_139209.1	chr17	47726835	47726848	+	1	NA	promoter-TSS (NM_025973)	promoter-TSS (NM_025973)	-1	NM_025973	109820	Mm.22957	NM_025973	ENSMUSG00000023987	Pgc	2210410L06Rik|Upg-1|Upg1	progastricsin (pepsinogen C)	protein-coding
mm_122066.1	chr14	30469900	30469911	-	1	NA	intron (NM_028981, intron 1 of 46)	intron (NM_028981, intron 1 of 46)	-9660	NM_133761	75901	Mm.28733	NM_133761	ENSMUSG00000021962	Dcp1a	1110066A22Rik|4930568L04Rik|AU019772|D14Ertd817e|Mitc1|SMIF	decapping mRNA 1A	protein-coding
mm_50759.1	chr6	53573339	53573349	+	1	NA	promoter-TSS (NM_172728)	promoter-TSS (NM_172728)	-30	NM_172728	231991	Mm.227444	NM_172728	ENSMUSG00000053007	Creb5	9430076C15Rik|CRE-BPa|Crebpa|D430026C09Rik	cAMP responsive element binding protein 5	protein-coding
mm_44778.1	chr5	32122527	32122531	-	1	NA	Intergenic	Intergenic	-13943	NM_008037	14284	Mm.24684	NM_008037	ENSMUSG00000029135	Fosl2	Fra-2	fos-like antigen 2	protein-coding
mm_61660.1	chr7	80766297	80766309	+	1	NA	intron (NM_016721, intron 4 of 37)	intron (NM_016721, intron 4 of 37)	37028	NM_016721	29875	Mm.207619	NM_016721	ENSMUSG00000030536	Iqgap1	AA682088|D7Ertd237e|D7Ertd257e|mKIAA0051	IQ motif containing GTPase activating protein 1	protein-coding
mm_15878.1	chr2	164837202	164837221	+	1	NA	exon (NM_008906, exon 10 of 15)	exon (NM_008906, exon 10 of 15)	3438	NM_008906	19025	Mm.359633	NM_008906	ENSMUSG00000017760	Ctsa	AU019505|PPCA|Ppgb	cathepsin A	protein-coding
mm_67803.1	chr7	98111453	98111461	-	1	NA	intron (NM_001256081, intron 2 of 48)	CpG	-2209	NM_001256083	17921	Mm.1403	NM_008663	ENSMUSG00000030761	Myo7a	Hdb|Myo7|USH1B|nmf371|polka|sh-1|sh1	myosin VIIA	protein-coding
mm_134379.1	chr16	17153761	17153806	-	1	NA	3' UTR (NM_009456, exon 4 of 4)	3' UTR (NM_009456, exon 4 of 4)	-6554	NM_001306169	76872	Mm.101656	NM_029779	ENSMUSG00000022768	Ccdc116	4930432J16Rik	coiled-coil domain containing 116	protein-coding
mm_16004.1	chr2	167358971	167358983	+	1	NA	Intergenic	Intergenic	-9799	NM_019835	56336	Mm.200886	NM_019835	ENSMUSG00000017929	B4galt5	9430078I07Rik|AW049941|AW539721	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 5	protein-coding
mm_65598.1	chr7	27355700	27355729	-	1	NA	TTS (NM_032610)	TTS (NM_032610)	294	NM_138676	192192	Mm.21297	NM_138676	ENSMUSG00000089832	Shkbp1	B930062H15Rik|Sb1	Sh3kbp1 binding protein 1	protein-coding
mm_51547.1	chr6	83237650	83237661	+	1	NA	5' UTR (NM_001166067, exon 1 of 25)	5' UTR (NM_001166067, exon 1 of 25)	280	NM_001166067	232156	Mm.333189	NM_001166067	ENSMUSG00000068323	Slc4a5	C330006M16|C330016K18Rik	solute carrier family 4, sodium bicarbonate cotransporter, member 5	protein-coding
mm_162359.1	chr1	61638913	61638923	+	1	NA	promoter-TSS (NM_001081050)	promoter-TSS (NM_001081050)	94	NM_001081050	72823	Mm.35153	NM_001081050	ENSMUSG00000052062	Pard3b	1810008K04Rik|2010002N16Rik|2810455B10Rik|Als2cr19|PAR3B|PAR3L|PAR3beta	par-3 family cell polarity regulator beta	protein-coding
mm_95507.1	chr11	51967650	51967709	+	1	NA	promoter-TSS (NM_029976)	promoter-TSS (NM_029976)	48	NM_029976	52626	Mm.289456	NM_029976	ENSMUSG00000020392	Cdkn2aipnl	A430101B06Rik|AA409260|D11Ertd497e|MNCb-1520	CDKN2A interacting protein N-terminal like	protein-coding
mm_10484.1	chr2	14763147	14763158	+	1	NA	intron (NM_023116, intron 2 of 13)	intron (NM_023116, intron 2 of 13)	42510	NR_028497	625342	Mm.484784	NR_028497		Gm13315	OTTMUSG00000011384	lactate dehydrogenase A pseudogene	pseudo
mm_22280.1	chr2	179976670	179976728	-	1	NA	promoter-TSS (NM_001081092)	promoter-TSS (NM_001081092)	-53	NM_001081092	228980	Mm.235542	NM_001081092	ENSMUSG00000039117	Taf4	135kDa|AI450312|TAFII130|TAFII135|Taf2c1|Taf4a	TATA-box binding protein associated factor 4	protein-coding
mm_123783.1	chr14	70331490	70331508	-	1	NA	intron (NM_001135151, intron 1 of 9)	intron (NM_001135151, intron 1 of 9)	16934	NM_001135152	213053	Mm.270647	NM_144808	ENSMUSG00000022094	Slc39a14	FAD-123|ZIP-14|Zip14|fad123	solute carrier family 39 (zinc transporter), member 14	protein-coding
mm_48916.1	chr6	4004074	4004078	+	1	NA	promoter-TSS (NM_025331)	promoter-TSS (NM_025331)	89	NM_025331	66066	Mm.25547	NM_025331	ENSMUSG00000032766	Gng11	0610037B21Rik	guanine nucleotide binding protein (G protein), gamma 11	protein-coding
mm_97902.1	chr11	83418962	83418977	+	1	NA	3' UTR (NM_001013386, exon 4 of 4)	3' UTR (NM_001013386, exon 4 of 4)	8897	NM_001013386	276952	Mm.66275	NM_001013386	ENSMUSG00000020684	Rasl10b	B230331P10Rik|Gm729|VTS58635	RAS-like, family 10, member B	protein-coding
mm_127987.1	chr15	12549301	12549305	-	1	NA	intron (NM_001081064, intron 1 of 23)	intron (NM_001081064, intron 1 of 23)	43253	NM_001081064	68070	Mm.423205	NM_001081064	ENSMUSG00000022197	Pdzd2	4930537L06Rik|A930022H17Rik|Gm21706|Gm82|Pdzk3|mKIAA0300	PDZ domain containing 2	protein-coding
mm_135142.1	chr16	35855003	35855048	-	1	NA	intron (NM_001039530, intron 6 of 16)	B1_Mus1|SINE|Alu	16357	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_34881.1	chr4	155582522	155582547	+	1	NA	intron (NM_138671, intron 3 of 11)	intron (NM_138671, intron 3 of 11)	18719	NM_001159637	192185	Mm.28347	NM_138671	ENSMUSG00000029063	Nadk	4432404C02Rik|BC004012	NAD kinase	protein-coding
mm_90914.1	chr10	12445283	12445285	-	1	NA	intron (NM_011682, intron 61 of 73)	intron (NM_011682, intron 61 of 73)	416451	NM_011682	22288	Mm.331784	NM_011682	ENSMUSG00000019820	Utrn	AA589569|DRP|Dmdl	utrophin	protein-coding
mm_74489.1	chr8	4779473	4779487	-	1	NA	promoter-TSS (NM_011369)	promoter-TSS (NM_011369)	54	NM_011369	20419	Mm.37801	NM_011369	ENSMUSG00000022322	Shcbp1	mPAL	Shc SH2-domain binding protein 1	protein-coding
mm_58205.1	chr6	143757270	143757271	-	1	NA	Intergenic	MER58A|DNA|hAT-Charlie	-105982	NR_045732	73425	Mm.417844	NR_045732	ENSMUSG00000086887	1700060C16Rik	-	RIKEN cDNA 1700060C16 gene	ncRNA
mm_78305.1	chr9	22643272	22643288	+	1	NA	intron (NM_178415, intron 13 of 22)	Lx8|LINE|L1	167565	NM_178415	319845	Mm.176725	NM_178415	ENSMUSG00000035919	Bbs9	E130103I17Rik	Bardet-Biedl syndrome 9 (human)	protein-coding
mm_168936.1	chr12	69159084	69159101	-	1	NA	promoter-TSS (NM_009093)	promoter-TSS (NM_009093)	94	NM_009093	20090	Mm.379006	NM_009093	ENSMUSG00000034892	Rps29	-	ribosomal protein S29	protein-coding
mm_124592.1	chr15	3274800	3274845	+	1	NA	exon (NM_009155, exon 2 of 5)	exon (NM_009155, exon 2 of 5)	3845	NM_009155	20363	Mm.392203	NM_009155	ENSMUSG00000064373	Selenop	AU018766|D15Ucla1|Se-P|Sepp1|selp	selenoprotein P	protein-coding
mm_70716.1	chr8	15086118	15086125	+	1	NA	intron (NM_008664, intron 13 of 36)	intron (NM_008664, intron 13 of 36)	28468	NM_008664	17930	Mm.272115	NM_008664	ENSMUSG00000031461	Myom2	AW146149	myomesin 2	protein-coding
mm_135944.1	chr16	74411445	74411451	-	1	NA	promoter-TSS (NM_175549)	promoter-TSS (NM_175549)	-536	NM_175549	268902	Mm.171736	NM_175549	ENSMUSG00000052516	Robo2	2600013A04Rik|9430089E08Rik|BB097918|D230004I22Rik|mKIAA1568	roundabout guidance receptor 2	protein-coding
mm_160094.1	chr7	17150331	17150331	+	1	NA	promoter-TSS (NM_054059)	promoter-TSS (NM_054059)	-69	NM_054059	384557	Mm.486145	NM_054059	ENSMUSG00000053228	Ceacam3	EG384557|Psg24|cea12	carcinoembryonic antigen-related cell adhesion molecule 3	protein-coding
mm_137934.1	chr17	32659010	32659020	+	1	NA	promoter-TSS (NM_001101588)	promoter-TSS (NM_001101588)	-468	NM_001101588	631304	Mm.328950	NM_001101588	ENSMUSG00000090700	Cyp4f40	EG631304	cytochrome P450, family 4, subfamily f, polypeptide 40	protein-coding
mm_164595.1	chr17	27534944	27534944	+	1	NA	Intergenic	Intergenic	-21630	NM_001166536	15361	Mm.4438	NM_016660	ENSMUSG00000046711	Hmga1	AL023995|Hmga1a|Hmga1b|Hmgi|Hmgiy|Hmgy	high mobility group AT-hook 1	protein-coding
mm_9081.1	chr1	168431696	168431713	-	1	NA	5' UTR (NM_001291509, exon 1 of 7)	5' UTR (NM_001291509, exon 1 of 7)	465	NM_001291508	18514	Mm.43358	NM_008783	ENSMUSG00000052534	Pbx1	2310056B04Rik|D230003C07Rik|Pbx-1	pre B cell leukemia homeobox 1	protein-coding
mm_46655.1	chr5	108670640	108670651	-	1	NA	3' UTR (NM_001310692, exon 3 of 3)	3' UTR (NM_001310692, exon 3 of 3)	4151	NM_001310692	231583	Mm.440571	NM_174870	ENSMUSG00000046959	Slc26a1	Sat1	solute carrier family 26 (sulfate transporter), member 1	protein-coding
mm_76777.1	chr8	96403859	96403872	-	1	NA	Intergenic	Intergenic	142108	NR_039538	100628567		NR_039538	ENSMUSG00000104794	Mir28c	mmu-mir-28c	microRNA 28c	ncRNA
mm_129839.1	chr15	83154476	83154495	-	1	NA	3' UTR (NM_029787, exon 9 of 9)	3' UTR (NM_029787, exon 9 of 9)	4840	NR_004432	104307	Mm.471434	NR_004432	ENSMUSG00000065176	Rnu12	-	RNA U12, small nuclear	snRNA
mm_161124.1	chr12	111039689	111039689	+	1	NA	promoter-TSS (NM_198023)	promoter-TSS (NM_198023)	-109	NM_198023	217864	Mm.23808	NM_198023	ENSMUSG00000037896	Rcor1	5730409O11|6720480E22Rik|AU042633|D12Wsu95e|Rocr1|mKIAA0071	REST corepressor 1	protein-coding
mm_136860.1	chr17	12810543	12810564	+	1	NA	intron (NR_027784, intron 2 of 2)	intron (NR_027784, intron 2 of 2)	-40847	NM_010515	16004	Mm.26553	NM_010515	ENSMUSG00000023830	Igf2r	AI661837|CD222|CI-MPR|M6P/IGF2R|Mpr300	insulin-like growth factor 2 receptor	protein-coding
mm_8044.1	chr1	135284076	135284086	-	1	NA	promoter-TSS (NM_145417)	promoter-TSS (NM_145417)	3	NM_145417	215615	Mm.291048	NM_145417	ENSMUSG00000041926	Rnpep	-	arginyl aminopeptidase (aminopeptidase B)	protein-coding
mm_68424.1	chr7	109759342	109759348	-	1	NA	3' UTR (NM_020610, exon 7 of 7)	3' UTR (NM_020610, exon 7 of 7)	-7082	NM_020050	56786	Mm.240668	NM_020050	ENSMUSG00000031021	Tmem9b	2310004K06Rik|AW539847|D7H11orf15|ICRFP703B1614Q5.3	TMEM9 domain family, member B	protein-coding
mm_58552.1	chr7	4740138	4740175	+	1	NA	promoter-TSS (NM_001115018)	promoter-TSS (NM_001115018)	29	NM_001115018	232811	Mm.247844	NM_146177	ENSMUSG00000059851	Kmt5c	BC024816|Suv4-20h2|Suv420h2	lysine methyltransferase 5C	protein-coding
mm_42667.1	chr5	119671161	119671162	+	1	NA	promoter-TSS (NM_011535)	promoter-TSS (NM_011535)	-72	NM_011535	21386	Mm.219139	NM_011535	ENSMUSG00000018604	Tbx3	D5Ertd189e	T-box 3	protein-coding
mm_29690.1	chr3	123105283	123105285	-	1	NA	intron (NM_080451, intron 4 of 4)	MTC|LTR|ERVL-MaLR	-70297	NM_021503	59006	Mm.141157	NM_021503	ENSMUSG00000028116	Myoz2	1110012I24Rik|Fatz-2|Myozl2	myozenin 2	protein-coding
mm_144706.1	chr18	34864351	34864361	+	1	NA	3' UTR (NM_007913, exon 2 of 2)	3' UTR (NM_007913, exon 2 of 2)	3149	NM_007913	13653	Mm.181959	NM_007913	ENSMUSG00000038418	Egr1	A530045N19Rik|ETR103|Egr-1|Krox-1|Krox-24|Krox24|NGF1-A|NGFI-A|NGFIA|TIS8|Zenk|Zfp-6|Zif268|egr	early growth response 1	protein-coding
mm_72775.1	chr8	86388038	86388041	+	1	NA	Intergenic	Intergenic	178551	NM_172912	244562	Mm.67485	NM_172912	ENSMUSG00000036872	Abcc12	4930467B22Rik|MRP9	ATP-binding cassette, sub-family C (CFTR/MRP), member 12	protein-coding
mm_41575.1	chr5	93172793	93172815	+	1	NA	3' UTR (NM_001009818, exon 10 of 10)	3' UTR (NM_001009818, exon 10 of 10)	33691	NM_017367	12453	Mm.250419	NM_017367	ENSMUSG00000063015	Ccni	-	cyclin I	protein-coding
mm_123137.1	chr14	56575462	56575482	-	1	NA	promoter-TSS (NM_001145978)	promoter-TSS (NM_001145978)	-147	NM_001145978	328417	Mm.379357	NM_001145978	ENSMUSG00000054509	Parp4	Adprtl1|C030027K23Rik|E230037B21Rik|Gm743|PARPL|PH5P|VAULT3|VPARP|p193	poly (ADP-ribose) polymerase family, member 4	protein-coding
mm_27335.1	chr3	50401472	50401485	-	1	NA	intron (NM_011990, intron 6 of 11)	intron (NM_011990, intron 6 of 11)	42135	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_158442.1	chrX	140505849	140505874	-	1	NA	Intergenic	Intergenic	36807	NR_122039	14605	Mm.22216	NM_010286	ENSMUSG00000031431	Tsc22d3	DIP|Dsip1|Gilz|TSC-22R|Tilz3	TSC22 domain family, member 3	protein-coding
mm_127096.1	chr15	97789229	97789261	+	1	NA	intron (NM_026353, intron 1 of 2)	intron (NM_026353, intron 1 of 2)	4880	NM_026353	67739	Mm.28955	NM_026353	ENSMUSG00000081534	Slc48a1	4930570C03Rik	solute carrier family 48 (heme transporter), member 1	protein-coding
mm_169658.1	chr15	58134810	58134812	-	1	NA	exon (NM_027435, exon 1 of 28)	exon (NM_027435, exon 1 of 28)	271	NM_027435	70472	Mm.221758	NM_027435	ENSMUSG00000022360	Atad2	2610509G12Rik	ATPase family, AAA domain containing 2	protein-coding
mm_149461.1	chr19	11519927	11519960	+	1	NA	intron (NM_027209, intron 1 of 6)	intron (NM_027209, intron 1 of 6)	1384	NM_027209	69774	Mm.436639	NM_027209	ENSMUSG00000024677	Ms4a6b	1810027D10Rik	membrane-spanning 4-domains, subfamily A, member 6B	protein-coding
mm_28684.1	chr3	95402776	95402780	-	1	NA	promoter-TSS (NR_015490)	promoter-TSS (NR_015490)	63	NR_015490	67654	Mm.75066	NR_015490	ENSMUSG00000105734	4930558C23Rik	-	RIKEN cDNA 4930558C23 gene	ncRNA
mm_123661.1	chr14	69244265	69244282	-	1	NA	3' UTR (NM_026331, exon 4 of 4)	3' UTR (NM_026331, exon 4 of 4)	40830	NM_026331	67712	Mm.293635	NM_026331	ENSMUSG00000034248	Slc25a37	1700020E22Rik|4930513O14Rik|4930526G11Rik|AI848481|C330015G08Rik|Mfrn|Mfrn1|Mscp|frascati|mitoferrin	solute carrier family 25, member 37	protein-coding
mm_80356.1	chr9	75193298	75193311	+	1	NA	intron (NM_010864, intron 30 of 40)	intron (NM_010864, intron 30 of 40)	-38710	NM_001081322	208943	Mm.41339	NM_001081322	ENSMUSG00000033590	Myo5c	9130003O20Rik|BB085560|C330029I24	myosin VC	protein-coding
mm_72480.1	chr8	83608549	83608575	+	1	NA	promoter-TSS (NM_001308227)	promoter-TSS (NM_001308227)	14	NM_001308227	81489	Mm.282092	NM_018808	ENSMUSG00000005483	Dnajb1	0610007I11Rik|DjB1|HSPF1|Hdj1|Hsp40	DnaJ heat shock protein family (Hsp40) member B1	protein-coding
mm_159751.1	chr5	86289276	86289276	-	1	NA	promoter-TSS (NM_001030297)	promoter-TSS (NM_001030297)	32	NM_001030297	435845	Mm.359654	NM_001030297	ENSMUSG00000061184	Tmprss11c	Tmprss13	transmembrane protease, serine 11c	protein-coding
mm_7815.1	chr1	131910851	131910867	-	1	NA	intron (NM_175294, intron 1 of 6)	CpG	401	NM_001145804	98415	Mm.246869	NM_175294	ENSMUSG00000026434	Nucks1	2700010L10Rik|8430423A01Rik|AI647518|C78391|Nucks	nuclear casein kinase and cyclin-dependent kinase substrate 1	protein-coding
mm_38806.1	chr4	148160032	148160072	-	1	NA	promoter-TSS (NM_001161852)	promoter-TSS (NM_001161852)	42	NM_173401	230903	Mm.220327	NM_173401	ENSMUSG00000029001	Fbxo44	5730411K09|AV001623|FBG3|FBX30|Fbx6a|Fbxo6a	F-box protein 44	protein-coding
mm_94001.1	chr10	127594560	127594591	-	1	NA	intron (NM_008512, intron 8 of 88)	MIRc|SINE|MIR	26573	NM_008512	16971	Mm.271854	NM_008512	ENSMUSG00000040249	Lrp1	A2mr|AI316852|CD91|Lrp|b2b1554Clo	low density lipoprotein receptor-related protein 1	protein-coding
mm_149746.1	chr19	22448243	22448247	+	1	NA	promoter-TSS (NM_177341)	promoter-TSS (NM_177341)	37	NM_177341	226025	Mm.131943	NM_177341	ENSMUSG00000052387	Trpm3	6330504P12Rik|9330180E14|AU018608|B930001P07Rik|LTRPC3|MLSN2	transient receptor potential cation channel, subfamily M, member 3	protein-coding
mm_81069.1	chr9	106203109	106203171	+	1	NA	promoter-TSS (NM_011876)	promoter-TSS (NM_011876)	32	NM_011876	23999	Mm.274346	NM_011876	ENSMUSG00000023277	Twf2	A6-related|AU014993|Ptk9l|Ptk9r	twinfilin actin binding protein 2	protein-coding
mm_14711.1	chr2	143546145	143546215	+	1	NA	promoter-TSS (NM_008792)	promoter-TSS (NM_008792)	47	NM_008792	18549	Mm.294493	NM_008792	ENSMUSG00000027419	Pcsk2	6330411F23Rik|AI839700|Nec-2|Nec2|PC2|Phpp-2|SPC2	proprotein convertase subtilisin/kexin type 2	protein-coding
mm_152753.1	chr19	20123868	20123874	-	1	NA	Intergenic	Intergenic	266800	NM_010730	16952	Mm.248360	NM_010730	ENSMUSG00000024659	Anxa1	Anx-1|Anx-A1|C430014K04Rik|Lpc-1|Lpc1	annexin A1	protein-coding
mm_105352.1	chr11	103017168	103017179	-	1	NA	promoter-TSS (NM_026551)	promoter-TSS (NM_026551)	-26	NM_026551	68087	Mm.277449	NM_026551	ENSMUSG00000020935	Dcakd	3010024O21Rik|6720485C15Rik|AI849483	dephospho-CoA kinase domain containing	protein-coding
mm_131133.1	chr16	6042363	6042371	+	1	NA	intron (NM_021477, intron 1 of 16)	intron (NM_021477, intron 1 of 16)	66780	NR_045799	68238	Mm.434605	NR_045799	ENSMUSG00000101481	1700123O21Rik	-	RIKEN cDNA 1700123O21 gene	ncRNA
mm_56470.1	chr6	99028196	99028204	-	1	NA	promoter-TSS (NM_001197322)	promoter-TSS (NM_001197322)	98	NM_001197322	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_16413.1	chr2	180070577	180070611	+	1	NA	promoter-TSS (NM_001083329)	promoter-TSS (NM_001083329)	1	NM_001083329	52856	Mm.219658	NM_028422	ENSMUSG00000039069	Mtg2	1810011P19Rik|2900056P18Rik|D2Bwg0647e|Gtpbp5	mitochondrial ribosome associated GTPase 2	protein-coding
mm_77910.1	chr9	7349753	7349765	+	1	NA	exon (NM_008605, exon 3 of 10)	exon (NM_008605, exon 3 of 10)	2385	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_6600.1	chr1	75317300	75317342	-	1	NA	promoter-TSS (NM_016878)	promoter-TSS (NM_016878)	-304	NM_016878	13437	Mm.24680	NM_016878	ENSMUSG00000026209	Dnpep	AA407814	aspartyl aminopeptidase	protein-coding
mm_165585.1	chr3	31813207	31813209	+	1	NA	Intergenic	Lx5b|LINE|L1	-89495	NM_028231	72413	Mm.64790	NM_028231	ENSMUSG00000037610	Kcnmb2	2700049B16Rik|3110031N04Rik	potassium large conductance calcium-activated channel, subfamily M, beta member 2	protein-coding
mm_140759.1	chr17	17599744	17599785	-	1	NA	intron (NM_172827, intron 1 of 17)	intron (NM_172827, intron 1 of 17)	24725	NM_172827	240028	Mm.328807	NM_172827	ENSMUSG00000023845	Lnpep	2010309L07Rik|4732490P18Rik|CAP|IRAP|PLAP|gp160|vp165	leucyl/cystinyl aminopeptidase	protein-coding
mm_67824.1	chr7	98282393	98282404	-	1	NA	intron (NM_025408, intron 1 of 10)	Charlie1a|DNA|hAT-Charlie	27129	NM_025408	66190	Mm.334041	NM_025408	ENSMUSG00000030760	Acer3	1110057L18Rik|5430429L08Rik|AV015045|Phca	alkaline ceramidase 3	protein-coding
mm_125128.1	chr15	30184752	30184755	+	1	NA	intron (NM_008729, intron 1 of 22)	RMER15|LTR|ERVL	12160	NM_008729	18163	Mm.321648	NM_008729	ENSMUSG00000022240	Ctnnd2	Catnd2|Nprap|neurojugin	catenin (cadherin associated protein), delta 2	protein-coding
mm_21695.1	chr2	164478373	164478396	-	1	NA	Intergenic	L1MC1|LINE|L1	-4660	NM_001271575	73603	Mm.472883	NM_001271575	ENSMUSG00000017720	Trp53tg5	1700126L10Rik	transformation related protein 53 target 5	protein-coding
mm_140711.1	chr17	14943115	14943151	-	1	NA	promoter-TSS (NM_001083881)	promoter-TSS (NM_001083881)	-9	NM_175173	71682	Mm.122698	NM_175173	ENSMUSG00000046991	Wdr27	0610012K18Rik	WD repeat domain 27	protein-coding
mm_52515.1	chr6	115399235	115399264	+	1	NA	intron (NM_001308352, intron 2 of 7)	L1MB4|LINE|L1	-22817	NM_011146	19016	Mm.3020	NM_011146	ENSMUSG00000000440	Pparg	Nr1c3|PPAR-gamma|PPAR-gamma2|PPARgamma|PPARgamma2	peroxisome proliferator activated receptor gamma	protein-coding
mm_170258.1	chr18	14570107	14570107	+	1	NA	Intergenic	Intergenic	112807	NM_001161369	268996	Mm.31761	NM_009280	ENSMUSG00000037013	Ss18	D130059H17|Ssxt|Syt	SS18, nBAF chromatin remodeling complex subunit	protein-coding
mm_147391.1	chr18	44175063	44175076	-	1	NA	promoter-TSS (NM_183123)	promoter-TSS (NM_183123)	4	NM_183123	77424	Mm.99224	NM_183123	ENSMUSG00000053729	Spinkl	9530002K18Rik	serine protease inhibitor, Kazal type-like	protein-coding
mm_93098.1	chr10	89741215	89741236	-	1	NA	Intergenic	Intergenic	-3766	NM_029166	75089	Mm.268922	NM_029166	ENSMUSG00000019951	Uhrf1bp1l	2010319N22Rik|4930506D01Rik|AA589495|C80672|E030041M21Rik|mKIAA0701	UHRF1 (ICBP90) binding protein 1-like	protein-coding
mm_96192.1	chr11	61976086	61976096	+	1	NA	intron (NM_001310526, intron 1 of 7)	ORR1A2|LTR|ERVL-MaLR	19328	NM_001310526	432572	Mm.438022	NM_001029936	ENSMUSG00000042331	Specc1	2810012G08Rik|B230396K10Rik|Cytsb	sperm antigen with calponin homology and coiled-coil domains 1	protein-coding
mm_160898.1	chr11	73984796	73984796	-	1	NA	promoter-TSS (NM_146710)	promoter-TSS (NM_146710)	-190	NM_146710	258705	Mm.377645	NM_146710	ENSMUSG00000049041	Olfr398	MOR157-1	olfactory receptor 398	protein-coding
mm_123049.1	chr14	55603970	55604002	-	1	NA	promoter-TSS (NM_001159417)	promoter-TSS (NM_001159417)	1	NM_001159417	16391	Mm.2032	NM_008394	ENSMUSG00000002325	Irf9	Irf-9|Isgf3g|p48	interferon regulatory factor 9	protein-coding
mm_42461.1	chr5	115436966	115436978	+	1	NA	intron (NM_008629, intron 6 of 14)	intron (NM_008629, intron 6 of 14)	7287	NM_008629	17690	Mm.5077	NM_008629	ENSMUSG00000054256	Msi1	Msi1h|Musahi1|m-Msi-1	musashi RNA-binding protein 1	protein-coding
mm_56817.1	chr6	116716720	116716734	-	1	NA	promoter-TSS (NM_178768)	promoter-TSS (NM_178768)	31	NM_178768	319776	Mm.133120	NM_178768	ENSMUSG00000048108	Tmem72	C230095G01Rik	transmembrane protein 72	protein-coding
mm_48894.1	chr5	151645571	151645585	-	1	NA	exon (NM_027009, exon 5 of 9)	exon (NM_027009, exon 5 of 9)	5630	NM_027009	69263	Mm.12553	NM_027009	ENSMUSG00000033970	Rfc3	2810416I22Rik|38kDa|AU022547|Recc3	replication factor C (activator 1) 3	protein-coding
mm_12273.1	chr2	68991376	68991389	+	1	NA	intron (NM_172856, intron 3 of 9)	intron (NM_172856, intron 3 of 9)	129941	NM_001347161	241447	Mm.222222	NM_172856	ENSMUSG00000027035	Cers6	4732462C07Rik|AW544719|Lass6|T1L	ceramide synthase 6	protein-coding
mm_74570.1	chr8	11183700	11183703	-	1	NA	Intergenic	Intergenic	-129104	NM_009932	12827	Mm.181021	NM_009932	ENSMUSG00000031503	Col4a2	Col4a-2	collagen, type IV, alpha 2	protein-coding
mm_52569.1	chr6	116337872	116337898	+	1	NA	promoter-TSS (NM_027920)	promoter-TSS (NM_027920)	-137	NM_001302385	71779	Mm.27064	NM_027920	ENSMUSG00000025702	March8	1300017E09Rik|MARCH-VIII|Mir	membrane-associated ring finger (C3HC4) 8	protein-coding
mm_34361.1	chr4	144892751	144892782	+	1	NA	promoter-TSS (NM_001172424)	promoter-TSS (NM_001172424)	-61	NM_001172424	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding
mm_6882.1	chr1	84669418	84669421	-	1	NA	intron (NM_152915, intron 1 of 12)	intron (NM_152915, intron 1 of 12)	-26420	NR_039588	100628595		NR_039588	ENSMUSG00000093254	Mir5126	mir-5126|mmu-mir-5126|mu-mir-5126	microRNA 5126	ncRNA
mm_15419.1	chr2	156840961	156840986	+	1	NA	intron (NM_173396, intron 1 of 2)	CpG	966	NM_173396	228839	Mm.315625	NM_173396	ENSMUSG00000062175	Tgif2	4921501K24|5730599O09Rik|C80753|C81206	TGFB-induced factor homeobox 2	protein-coding
mm_66095.1	chr7	30973895	30973915	-	1	NA	promoter-TSS (NM_017405)	promoter-TSS (NM_017405)	101	NR_038860	76415	Mm.259739	NM_175240	ENSMUSG00000046826	Fam187b	1700020B09Rik|Tmem162	family with sequence similarity 187, member B	protein-coding
mm_65915.1	chr7	30195222	30195225	-	1	NA	promoter-TSS (NM_009795)	promoter-TSS (NM_009795)	-175	NM_009795	12336	Mm.439782	NM_009795	ENSMUSG00000001794	Capns1	Capa-4|Capa4|Capn4|D7Ertd146e	calpain, small subunit 1	protein-coding
mm_1460.1	chr1	67233421	67233428	+	1	NA	Intergenic	L1_Mur3|LINE|L1	110397	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_147359.1	chr18	43393052	43393137	-	1	NA	5' UTR (NM_009468, exon 1 of 14)	5' UTR (NM_009468, exon 1 of 14)	283	NM_009468	22240	Mm.8180	NM_009468	ENSMUSG00000024501	Dpysl3	CRMP-4|DRP-3|TUC4|ULIP-1|Ulip|Ulip1	dihydropyrimidinase-like 3	protein-coding
mm_133959.1	chr16	4086127	4086140	-	1	NA	exon (NM_001025432, exon 31 of 31)	exon (NM_001025432, exon 31 of 31)	-8323	NM_026508	68015	Mm.123366	NM_026508	ENSMUSG00000005981	Trap1	2410002K23Rik|HSP75	TNF receptor-associated protein 1	protein-coding
mm_59068.1	chr7	19489084	19489094	+	1	NA	Intergenic	Intergenic	19242	NM_177692	232946	Mm.64557	NM_177692	ENSMUSG00000057667	Bloc1s3	BC043666|Blos3|E230011O18|rp	biogenesis of lysosomal organelles complex-1, subunit 3	protein-coding
mm_68614.1	chr7	116443440	116443462	-	1	NA	promoter-TSS (NM_011083)	promoter-TSS (NM_011083)	7	NM_011083	18704	Mm.3810	NM_011083	ENSMUSG00000030660	Pik3c2a	Cpk-m|PI3KC2	phosphatidylinositol 3-kinase, C2 domain containing, alpha polypeptide	protein-coding
mm_106165.1	chr11	116654076	116654082	-	1	NA	5' UTR (NM_030206, exon 1 of 4)	5' UTR (NM_030206, exon 1 of 4)	234	NM_030206	114886	Mm.34598	NM_030206	ENSMUSG00000020810	Cygb	3110001K20Rik|HGb|Staap	cytoglobin	protein-coding
mm_16429.1	chr2	180389120	180389122	+	1	NA	promoter-TSS (NR_029528)	promoter-TSS (NR_029528)	73	NR_029528	387136		NR_029528	ENSMUSG00000070144	Mir1a-1	Mir1-1|Mirn1-1|Mirn1b|Mirn1c|Mirn1d|mir-1a-1|mmu-mir-1-1|mmu-mir-1a-1	microRNA 1a-1	ncRNA
mm_154894.1	chrX	20870216	20870226	+	1	NA	promoter-TSS (NM_011593)	promoter-TSS (NM_011593)	55	NM_001294280	21857	Mm.8245	NM_011593	ENSMUSG00000001131	Timp1	Clgi|EPA|TIMP-1|TPA-S1|Timp	tissue inhibitor of metalloproteinase 1	protein-coding
mm_80799.1	chr9	96258807	96258830	+	1	NA	promoter-TSS (NM_001184710)	promoter-TSS (NM_001184710)	113	NM_001184709	211586	Mm.17977	NM_178667	ENSMUSG00000032411	Tfdp2	1110029I05Rik|A330080J22Rik|DP-3|DP3	transcription factor Dp 2	protein-coding
mm_79068.1	chr9	46234413	46234437	+	1	NA	exon (NM_001289755, exon 3 of 4)	exon (NM_001289755, exon 3 of 4)	874	NM_001289833	11814	Mm.390161	NM_023114	ENSMUSG00000032081	Apoc3	apo-CIII|apoC-III	apolipoprotein C-III	protein-coding
mm_143097.1	chr17	57080937	57080950	-	1	NA	exon (NM_009451, exon 4 of 4)	exon (NM_009451, exon 4 of 4)	-2433	NM_153551	70785	Mm.284447	NM_153551	ENSMUSG00000002668	Dennd1c	4432409M07Rik	DENN/MADD domain containing 1C	protein-coding
mm_166058.1	chr4	133172690	133172693	+	1	NA	intron (NM_153423, intron 1 of 8)	B4A|SINE|B4	-22964	NR_105984	102466215		NR_105984	ENSMUSG00000099202	Mir7017	Gm27945|mmu-mir-7017	microRNA 7017	ncRNA
mm_28026.1	chr3	83046723	83046739	-	1	NA	exon (NM_181849, exon 2 of 8)	exon (NM_181849, exon 2 of 8)	3132	NM_181849	110135	Mm.30063	NM_181849	ENSMUSG00000033831	Fgb	2510049G14Rik	fibrinogen beta chain	protein-coding
mm_7202.1	chr1	93023072	93023120	-	1	NA	intron (NM_001294150, intron 39 of 46)	intron (NM_001294150, intron 39 of 46)	16762	NM_001159658	208760	Mm.235537	NM_177587	ENSMUSG00000045091	Aqp12	AB084104|mAQP12	aquaporin 12	protein-coding
mm_6769.1	chr1	84130917	84130921	-	1	NA	intron (NM_001003948, intron 2 of 2)	intron (NM_001003948, intron 2 of 2)	88042	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_55077.1	chr6	49210284	49210287	-	1	NA	intron (NM_023670, intron 2 of 14)	intron (NM_023670, intron 2 of 14)	4669	NM_023670	140488	Mm.281018	NM_023670	ENSMUSG00000029814	Igf2bp3	2610101N11Rik|AA522010|AL022933|AU045931|IMP-3|IMP3|Koc13|Neilsen|mimp3	insulin-like growth factor 2 mRNA binding protein 3	protein-coding
mm_145906.1	chr18	65801444	65801469	+	1	NA	intron (NM_025468, intron 1 of 5)	intron (NM_025468, intron 1 of 5)	878	NM_025468	66286	Mm.27800	NM_025468	ENSMUSG00000024516	Sec11c	1810029G24Rik|Sec11l3	SEC11 homolog C, signal peptidase complex subunit	protein-coding
mm_5928.1	chr1	55237038	55237045	-	1	NA	promoter-TSS (NM_175439)	promoter-TSS (NM_175439)	-136	NM_175439	212679	Mm.19223	NM_175439	ENSMUSG00000046994	Mars2	C730026E21Rik|MetRS	methionine-tRNA synthetase 2 (mitochondrial)	protein-coding
mm_166806.1	chr7	5742024	5742027	-	1	NA	Intergenic	RLTR9C|LTR|ERVK	61606	NM_001167568	100039499	Mm.160382	NM_001167568	ENSMUSG00000096244	Vmn1r187	-	vomeronasal 1 receptor Vmn1r187	protein-coding
mm_105597.1	chr11	106750473	106750486	-	1	NA	promoter-TSS (NM_001271373)	promoter-TSS (NM_001271373)	-747	NM_001271375	380732	Mm.343952	NM_001033435	ENSMUSG00000040528	Milr1	Allergin-1|Gm885|Mca32	mast cell immunoglobulin like receptor 1	protein-coding
mm_56830.1	chr6	117174409	117174458	-	1	NA	3' UTR (NM_021704, exon 3 of 3)	3' UTR (NM_021704, exon 3 of 3)	5898	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_45926.1	chr5	89443560	89443583	-	1	NA	exon (NM_008096, exon 4 of 13)	exon (NM_008096, exon 4 of 13)	14327	NM_008096	14473	Mm.196595	NM_008096	ENSMUSG00000035540	Gc	DBP|VDB	group specific component	protein-coding
mm_93450.1	chr10	110000903	110000913	-	1	NA	promoter-TSS (NM_001081035)	promoter-TSS (NM_001081035)	-689	NM_001081035	260315	Mm.225050	NM_177797	ENSMUSG00000020181	Nav3	4732483H20Rik|9630020C08Rik|POMFIL1|Pomfil1p|mKIAA0938|unc53H3	neuron navigator 3	protein-coding
mm_69035.1	chr7	126798593	126798607	-	1	NA	intron (NM_001177307, intron 1 of 9)	intron (NM_001177307, intron 1 of 9)	578	NM_001177307	11674	Mm.275831	NM_007438	ENSMUSG00000030695	Aldoa	Aldo-1|Aldo1	aldolase A, fructose-bisphosphate	protein-coding
mm_154105.1	chr19	57118808	57118814	-	1	NA	5' UTR (NM_001103178, exon 1 of 20)	5' UTR (NM_001103178, exon 1 of 20)	213	NM_001347459	226251	Mm.217161	NM_178688	ENSMUSG00000025085	Ablim1	2210411C18Rik|2610209L21Rik|4833406P10Rik|9330196J19Rik|AV079770|AW060987|AW215784|Limab1|mKIAA0059	actin-binding LIM protein 1	protein-coding
mm_16542.1	chr2	181680285	181680332	+	1	NA	promoter-TSS (NM_009326)	promoter-TSS (NM_009326)	-2	NM_009326	21400	Mm.24245	NM_009326	ENSMUSG00000059540	Tcea2	AI326274|S-II-T1|SII-T1|Tceat	transcription elongation factor A (SII), 2	protein-coding
mm_132233.1	chr16	32750333	32750343	+	1	NA	exon (NM_080457, exon 2 of 27)	exon (NM_080457, exon 2 of 27)	14452	NM_080457	140474	Mm.214599	NM_080457	ENSMUSG00000079620	Muc4	4933405I11Rik|Asgp	mucin 4	protein-coding
mm_119533.1	chr14	47667311	47667322	+	1	NA	exon (NM_001293636, exon 4 of 40)	exon (NM_001293636, exon 4 of 40)	3560	NM_001347522	16709	Mm.3110	NM_008477	ENSMUSG00000021843	Ktn1	-	kinectin 1	protein-coding
mm_73747.1	chr8	114439713	114439736	+	1	NA	promoter-TSS (NM_019573)	promoter-TSS (NM_019573)	72	NM_019573	80707	Mm.440420	NM_019573	ENSMUSG00000004637	Wwox	5330426P09Rik|9030416C10Rik|WOX1	WW domain-containing oxidoreductase	protein-coding
mm_51253.1	chr6	71909037	71909043	+	1	NA	promoter-TSS (NM_009088)	promoter-TSS (NM_009088)	-13	NM_009088	20019	Mm.135581	NM_009088	ENSMUSG00000049553	Polr1a	194kDa|3010014K16Rik|RPA194|Rpo1-4|mRPA1	polymerase (RNA) I polypeptide A	protein-coding
mm_112019.1	chr12	111377706	111377719	-	1	NA	promoter-TSS (NM_183016)	promoter-TSS (NM_183016)	6	NM_183016	217866	Mm.27397	NM_183016	ENSMUSG00000021279	Cdc42bpb	MRCKb	CDC42 binding protein kinase beta	protein-coding
mm_172008.1	chr6	109505311	109505311	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	676670	NM_138677	192193	Mm.21596	NM_138677	ENSMUSG00000030104	Edem1	A130059K23Rik|EDEM|mKIAA0212	ER degradation enhancer, mannosidase alpha-like 1	protein-coding
mm_125000.1	chr15	23474455	23474458	+	1	NA	TTS (NM_001081299)	TTS (NM_001081299)	437993	NM_001081299	320865	Mm.241965	NM_001081299	ENSMUSG00000040420	Cdh18	B230220E17Rik|Cdh14l	cadherin 18	protein-coding
mm_87535.1	chr10	53488271	53488278	+	1	NA	Intergenic	MTEa|LTR|ERVL-MaLR	30715	NR_037973	100502868	Mm.297722	NR_037973		Gm20597	B230314j19	predicted gene, 20597	ncRNA
mm_137539.1	chr17	27556678	27556690	+	1	NA	promoter-TSS (NM_001166477)	promoter-TSS (NM_001166477)	31	NM_001166477	111241	Mm.426212	NM_001166476	ENSMUSG00000078249	Hmga1-rs1	ENSMUSG00000041059|Hmgi-rs1	high mobility group AT-hook I, related sequence 1	protein-coding
mm_3850.1	chr1	160792195	160792243	+	1	NA	intron (NM_013862, intron 1 of 20)	CpG	719	NM_013862	29809	Mm.25833	NM_013862	ENSMUSG00000026721	Rabgap1l	5830411O09Rik|8430421H08Rik|9630005B12Rik|AW049894|HHL|Hh1|mKIAA0471	RAB GTPase activating protein 1-like	protein-coding
mm_2546.1	chr1	107529019	107529058	+	1	NA	promoter-TSS (NM_001160307)	promoter-TSS (NM_001160307)	35	NM_198028	241197	Mm.123919	NM_198028	ENSMUSG00000092572	Serpinb10	9830131G07|BB233602|Serpinb10-ps	serine (or cysteine) peptidase inhibitor, clade B (ovalbumin), member 10	protein-coding
mm_52345.1	chr6	110940433	110940443	+	1	NA	intron (NM_001346640, intron 2 of 10)	intron (NM_001346640, intron 2 of 10)	294840	NM_177328	108073	Mm.240881	NM_177328	ENSMUSG00000056755	Grm7	6330570A01Rik|BB176677|C030018L03|E130018M02Rik|Gpr1g|Gprc1g|SMN2|Tg(SMN2)89Ahmb|mGluR7	glutamate receptor, metabotropic 7	protein-coding
mm_44380.1	chr5	17821431	17821441	-	1	NA	intron (NM_007643, intron 3 of 14)	intron (NM_007643, intron 3 of 14)	14460	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_39848.1	chr5	30913419	30913439	+	1	NA	promoter-TSS (NM_133918)	promoter-TSS (NM_133918)	-357	NM_133918	100952	Mm.286375	NM_133918	ENSMUSG00000029163	Emilin1	5830419M17Rik|AW229038|BB105748|EMILIN-1|gp115	elastin microfibril interfacer 1	protein-coding
mm_107620.1	chr12	51377547	51377557	+	1	NA	promoter-TSS (NM_001306178)	promoter-TSS (NM_001306178)	39	NM_029825	76983	Mm.216511	NM_029825	ENSMUSG00000020952	Scfd1	3110021P21Rik|RA410|STXBP1L2	Sec1 family domain containing 1	protein-coding
mm_8799.1	chr1	161794565	161794600	-	1	NA	Intergenic	Intergenic	-6087	NM_010177	14103	Mm.3355	NM_010177	ENSMUSG00000000817	Fasl	APT1LG1|CD178|CD95-L|CD95L|Fas-L|Faslg|Tnfsf6|Tnlg1a|gld	Fas ligand (TNF superfamily, member 6)	protein-coding
mm_8329.1	chr1	149961231	149961300	-	1	NA	promoter-TSS (NM_008869)	promoter-TSS (NM_008869)	25	NM_008869	18783	Mm.4186	NM_008869	ENSMUSG00000056220	Pla2g4a	Pla2g4|cPLA2|cPLA2-alpha|cPLA2alpha	phospholipase A2, group IVA (cytosolic, calcium-dependent)	protein-coding
mm_98269.1	chr11	88999443	88999479	+	1	NA	promoter-TSS (NM_009546)	promoter-TSS (NM_009546)	58	NM_009546	217069	Mm.248445	NM_009546	ENSMUSG00000000275	Trim25	AA960166|AL022677|EFP|Zfp147	tripartite motif-containing 25	protein-coding
mm_64159.1	chr7	141356143	141356154	+	1	NA	exon (NM_133191, exon 8 of 21)	exon (NM_133191, exon 8 of 21)	8962	NR_033532	320871	Mm.475463	NM_177280	ENSMUSG00000086844	B230206H07Rik	-	RIKEN cDNA B230206H07 gene	ncRNA
mm_164876.1	chr18	58009105	58009108	-	1	NA	3' UTR (NM_010181, exon 65 of 65)	3' UTR (NM_010181, exon 65 of 65)	130428	NM_009194	20496	Mm.399997	NM_009194	ENSMUSG00000024597	Slc12a2	9330166H04Rik|Nkcc1|mBSC2|sy-ns	solute carrier family 12, member 2	protein-coding
mm_87229.1	chr10	40570358	40570362	+	1	NA	promoter-TSS (NM_027572)	promoter-TSS (NM_027572)	-2	NM_027572	70840	Mm.332570	NM_027572	ENSMUSG00000019834	Slc22a16	4921504E14Rik|CT2|FLIPT2|OCT6|OKB1	solute carrier family 22 (organic cation transporter), member 16	protein-coding
mm_37961.1	chr4	133352888	133352897	-	1	NA	Intergenic	Intergenic	-13577	NM_199306	230796	Mm.226576	NM_199306	ENSMUSG00000037622	Wdtc1	Gm695|adipose|adp	WD and tetratricopeptide repeats 1	protein-coding
mm_12557.1	chr2	72475997	72476000	+	1	NA	promoter-TSS (NM_025866)	promoter-TSS (NM_025866)	-221	NM_025866	66953	Mm.270676	NM_025866	ENSMUSG00000055612	Cdca7	2310021G01Rik|AU044109|JPO1	cell division cycle associated 7	protein-coding
mm_89787.1	chr10	102158981	102158997	+	1	NA	promoter-TSS (NM_001162369)	promoter-TSS (NM_001162369)	-90	NM_001162369	67569	Mm.25252	NM_026243	ENSMUSG00000019888	Mgat4c	9130411I17Rik|GntIVh	MGAT4 family, member C	protein-coding
mm_61366.1	chr7	69579703	69579713	+	1	NA	Intergenic	Intergenic	83614	NR_045940	73796	Mm.410832	NR_045940	ENSMUSG00000108885	4930402F11Rik	-	RIKEN cDNA 4930402F11 gene	ncRNA
mm_76763.1	chr8	95740727	95740730	-	1	NA	intron (NM_001205226, intron 33 of 48)	intron (NM_001205226, intron 33 of 48)	12486	NR_106041	102465650		NR_106041	ENSMUSG00000106145	Mir7073	mmu-mir-7073	microRNA 7073	ncRNA
mm_17905.1	chr2	35315223	35315248	-	1	NA	3' UTR (NM_013515, exon 7 of 7)	3' UTR (NM_013515, exon 7 of 7)	21774	NM_013515	13830	Mm.295284	NM_013515	ENSMUSG00000026880	Stom	Epb7.2	stomatin	protein-coding
mm_2661.1	chr1	125677677	125677687	+	1	NA	exon (NM_027677, exon 1 of 2)	exon (NM_027677, exon 1 of 2)	686	NM_027677	71111	Mm.32727	NM_027677	ENSMUSG00000026343	Gpr39	4933415E13Rik	G protein-coupled receptor 39	protein-coding
mm_14467.1	chr2	131280352	131280367	+	1	NA	exon (NM_153501, exon 3 of 7)	exon (NM_153501, exon 3 of 7)	-7693	NR_029755	723825		NR_029755	ENSMUSG00000065563	Mir103-2	Mirn103-2|mir-103-2	microRNA 103-2	ncRNA
mm_105518.1	chr11	106272831	106272860	-	1	NA	5' UTR (NM_001130187, exon 1 of 13)	5' UTR (NM_001130187, exon 1 of 13)	127	NM_001130187	83796	Mm.21772	NM_031878	ENSMUSG00000078619	Smarcd2	AW322457|Baf60b	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2	protein-coding
mm_122103.1	chr14	30917357	30917367	-	1	NA	exon (NM_008407, exon 11 of 21)	exon (NM_008407, exon 11 of 21)	6225	NM_008407	16426	Mm.4517	NM_008407	ENSMUSG00000006522	Itih3	AW108094|ITI-HC3|Intin3|Itih-3	inter-alpha trypsin inhibitor, heavy chain 3	protein-coding
mm_134446.1	chr16	18289187	18289196	-	1	NA	promoter-TSS (NM_033324)	promoter-TSS (NM_033324)	-23	NM_033324	94223	Mm.447352	NM_033324	ENSMUSG00000022718	Dgcr8	D16H22S1742E|D16H22S788E|D16Wis2|Gy1|N41|Vo59c07|mir-1306	DiGeorge syndrome critical region gene 8	protein-coding
mm_159271.1	chr2	164171119	164171119	-	1	NA	promoter-TSS (NM_008435)	promoter-TSS (NM_008435)	-6	NM_008435	16538	Mm.6217	NM_008435	ENSMUSG00000040164	Kcns1	Kv9.1	K+ voltage-gated channel, subfamily S, 1	protein-coding
mm_134940.1	chr16	31179041	31179044	-	1	NA	intron (NM_030138, intron 1 of 22)	intron (NM_030138, intron 1 of 22)	22196	NM_030138	78618	Mm.274646	NM_030138	ENSMUSG00000049076	Acap2	4832442G16|9530039J15Rik|CNT-B2|Centb2|mKIAA0041	ArfGAP with coiled-coil, ankyrin repeat and PH domains 2	protein-coding
mm_61204.1	chr7	64153863	64153865	+	1	NA	promoter-TSS (NM_001039104)	promoter-TSS (NM_001039104)	29	NM_001039104	17364	Mm.38875	NM_018752	ENSMUSG00000030523	Trpm1	4732499L03Rik|AI606771|Ltrpc1|Mlsn1	transient receptor potential cation channel, subfamily M, member 1	protein-coding
mm_50923.1	chr6	57608114	57608156	+	1	NA	intron (NM_025992, intron 8 of 22)	intron (NM_025992, intron 8 of 22)	27143	NM_025992	67138	Mm.297393	NM_025992	ENSMUSG00000029798	Herc6	1700121D12Rik|2510038N07Rik|4930427L17Rik|AI451296|CEB1|Herc5	hect domain and RLD 6	protein-coding
mm_141901.1	chr17	34951898	34951929	-	1	NA	promoter-TSS (NR_028527)	promoter-TSS (NR_028527)	555	NR_027943	68763	Mm.28895	NR_015536	ENSMUSG00000092203	1110038B12Rik	0610009C20Rik|0910001G04Rik	RIKEN cDNA 1110038B12 gene	ncRNA
mm_29451.1	chr3	113195083	113195105	-	1	NA	Intergenic	LTRIS_Mm|LTR|ERV1	-38367	NM_001190403	545562	Mm.462977	NM_001190403		Amy2b	Amy-X|Amy2-2|OTTMUSG00000022462|mAmy2-1	amylase 2b	protein-coding
mm_16174.1	chr2	172550762	172550767	+	1	NA	promoter-TSS (NM_001159696)	promoter-TSS (NM_001159696)	-227	NM_001159696	21420	Mm.3629	NM_009335	ENSMUSG00000028640	Tfap2c	AA409384|AP2gamma|Ap-2.2|Stra2|Tcfap2c	transcription factor AP-2, gamma	protein-coding
mm_68457.1	chr7	110122920	110122944	-	1	NA	intron (NM_009516, intron 1 of 10)	CpG	873	NM_009516	22390	Mm.287173	NM_009516	ENSMUSG00000031016	Wee1	Wee1A	WEE 1 homolog 1 (S. pombe)	protein-coding
mm_62893.1	chr7	116031997	116032009	+	1	NA	promoter-TSS (NM_001025560)	promoter-TSS (NM_001025560)	-956	NM_001025560	20679	Mm.323365	NM_011445	ENSMUSG00000051910	Sox6	AI987981|SOX-LZ	SRY (sex determining region Y)-box 6	protein-coding
mm_97151.1	chr11	75461667	75461686	+	1	NA	non-coding (NR_030711, exon 1 of 3)	non-coding (NR_030711, exon 1 of 3)	137	NR_030711	100042498	Mm.482242	NR_030711	ENSMUSG00000085148	Mir22hg	2210403K04Rik|mir-22	Mir22 host gene (non-protein coding)	ncRNA
mm_158874.1	chrY	1286564	1286615	-	1	NA	promoter-TSS (NM_012008)	promoter-TSS (NM_012008)	24	NM_012008	26900	Mm.302938	NM_012008	ENSMUSG00000069045	Ddx3y	8030469F12Rik|D1Pas1-rs1|Dby	DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, Y-linked	protein-coding
mm_3469.1	chr1	150104490	150104498	+	1	NA	exon (NM_011198, exon 8 of 10)	exon (NM_011198, exon 8 of 10)	4463	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_88509.1	chr10	77978621	77978671	+	1	NA	promoter-TSS (NM_026431)	promoter-TSS (NM_026431)	-4	NM_026431	67884	Mm.297512	NM_026431	ENSMUSG00000020284	1810043G02Rik	AV026620|D10Jhu13e	RIKEN cDNA 1810043G02 gene	protein-coding
mm_152074.1	chr19	6840591	6840644	-	1	NA	promoter-TSS (NM_019924)	promoter-TSS (NM_019924)	10	NM_019924	56613	Mm.20914	NM_019924	ENSMUSG00000024952	Rps6ka4	1110069D02Rik|90kDa|AI848992|Msk2|mMSK2	ribosomal protein S6 kinase, polypeptide 4	protein-coding
mm_99928.1	chr11	110997086	110997097	+	1	NA	promoter-TSS (NM_001252209)	promoter-TSS (NM_001252209)	-396	NM_001252209	16517	Mm.30176	NM_010604	ENSMUSG00000051497	Kcnj16	6430410F18Rik|AI132396|Kir5.1	potassium inwardly-rectifying channel, subfamily J, member 16	protein-coding
mm_126106.1	chr15	78247932	78247953	+	1	NA	intron (NM_008677, intron 1 of 9)	intron (NM_008677, intron 1 of 9)	3131	NM_008677	17972	Mm.2068	NM_008677	ENSMUSG00000071715	Ncf4	AI451400|p40phox	neutrophil cytosolic factor 4	protein-coding
mm_71046.1	chr8	33674367	33674379	+	1	NA	intron (NM_010344, intron 5 of 12)	intron (NM_010344, intron 5 of 12)	21135	NM_010344	14782	Mm.283573	NM_010344	ENSMUSG00000031584	Gsr	AI325518|D8Ertd238e|Gr-1|Gr1	glutathione reductase	protein-coding
mm_141705.1	chr17	33999793	33999802	-	1	NA	exon (NM_001001892, exon 2 of 8)	exon (NM_001001892, exon 2 of 8)	536	NM_001001892	14972	Mm.422886	NM_001001892	ENSMUSG00000061232	H2-K1	H-2K|H-2K(d)|H2-K|K-f	histocompatibility 2, K1, K region	protein-coding
mm_54489.1	chr6	35326074	35326089	-	1	NA	promoter-TSS (NM_173375)	promoter-TSS (NM_173375)	60	NM_173375	208164	Mm.257766	NM_173375	ENSMUSG00000047420	Fam180a	B230314O19	family with sequence similarity 180, member A	protein-coding
mm_60429.1	chr7	44476751	44476790	+	1	NA	Intergenic	L1MEd|LINE|L1	6423	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_150845.1	chr19	44988925	44988942	+	1	NA	promoter-TSS (NM_011976)	promoter-TSS (NM_011976)	-411	NM_011976	26456	Mm.34404	NM_011976	ENSMUSG00000025207	Sema4g	AI507908|AW554132	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4G	protein-coding
mm_140532.1	chr17	6754719	6754744	-	1	NA	exon (NM_009510, exon 4 of 13)	exon (NM_009510, exon 4 of 13)	28049	NM_009510	22350	Mm.277812	NM_009510	ENSMUSG00000052397	Ezr	AW146364|R75297|Vil2|p81	ezrin	protein-coding
mm_139887.1	chr17	70834743	70834749	+	1	NA	Intergenic	CpG	12031	NM_001164077	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_148554.1	chr19	4712119	4712173	+	1	NA	intron (NM_021287, intron 1 of 36)	CpG	923	NM_021287	20743	Mm.329668	NM_021287	ENSMUSG00000067889	Sptbn2	Spnb3|mKIAA0302	spectrin beta, non-erythrocytic 2	protein-coding
mm_2652.1	chr1	125676886	125676895	+	1	NA	promoter-TSS (NM_027677)	promoter-TSS (NM_027677)	-106	NM_027677	71111	Mm.32727	NM_027677	ENSMUSG00000026343	Gpr39	4933415E13Rik	G protein-coupled receptor 39	protein-coding
mm_152142.1	chr19	7165992	7166099	-	1	NA	intron (NM_134147, intron 3 of 10)	CpG	40239	NM_134150	107260	Mm.203921	NM_134150	ENSMUSG00000024767	Otub1	AI850305	OTU domain, ubiquitin aldehyde binding 1	protein-coding
mm_25466.1	chr3	108592435	108592438	+	1	NA	intron (NM_181400, intron 1 of 14)	intron (NM_181400, intron 1 of 14)	1158	NM_181400	99512	Mm.285968	NM_181400	ENSMUSG00000040389	Wdr47	1810073M12Rik|AA552998|mKIAA0893	WD repeat domain 47	protein-coding
mm_29022.1	chr3	101924509	101924520	-	1	NA	promoter-TSS (NM_001039371)	promoter-TSS (NM_001039371)	-61	NM_001039371	242126	Mm.90204	NM_001039371	ENSMUSG00000033147	Slc22a15	2610034P21Rik|4930477M19|A530052I06Rik|BB219042	solute carrier family 22 (organic anion/cation transporter), member 15	protein-coding
mm_28772.1	chr3	95928824	95928834	-	1	NA	promoter-TSS (NM_001253757)	promoter-TSS (NM_001253757)	-428	NM_001253758	66471	Mm.218657	NM_023210	ENSMUSG00000015749	Anp32e	2810018A15Rik|AI047746|AI326868|CPD1|LANP-L|LANPL|mLANP-L	acidic (leucine-rich) nuclear phosphoprotein 32 family, member E	protein-coding
mm_34944.1	chr4	155891826	155891892	+	1	NA	promoter-TSS (NM_207223)	promoter-TSS (NM_207223)	-16	NM_207223	140500	Mm.219591	NM_207223	ENSMUSG00000029033	Acap3	Centb5|Kiaa1716-hp|mKIAA1716	ArfGAP with coiled-coil, ankyrin repeat and PH domains 3	protein-coding
mm_153133.1	chr19	34243344	34243361	-	1	NA	exon (NM_007392, exon 8 of 9)	exon (NM_007392, exon 8 of 9)	12021	NM_007392	11475	Mm.213025	NM_007392	ENSMUSG00000035783	Acta2	0610041G09Rik|Actvs|SMalphaA|a-SMA|alphaSMA	actin, alpha 2, smooth muscle, aorta	protein-coding
mm_94537.1	chr11	9125115	9125143	+	1	NA	intron (NM_001159401, intron 2 of 8)	intron (NM_001159401, intron 2 of 8)	6622	NM_001159402	22271	Mm.4610	NM_009477	ENSMUSG00000020407	Upp1	AI325217|UPase|UdRPase|Up|Upp	uridine phosphorylase 1	protein-coding
mm_161460.1	chr15	77411080	77411080	-	1	NA	promoter-TSS (NM_001162883)	promoter-TSS (NM_001162883)	0	NM_001162883	223672	Mm.243758	NM_173786	ENSMUSG00000057346	Apol9a	-	apolipoprotein L 9a	protein-coding
mm_34496.1	chr4	148593915	148593934	+	1	NA	exon (NM_009272, exon 5 of 7)	exon (NM_009272, exon 5 of 7)	2411	NM_009272	20810	Mm.10	NM_009272	ENSMUSG00000006442	Srm	AA407669|SpdST|SpdSy	spermidine synthase	protein-coding
mm_131935.1	chr16	23613142	23613178	+	1	NA	exon (NM_023386, exon 2 of 2)	exon (NM_023386, exon 2 of 2)	3241	NM_023386	67775	Mm.475107	NM_023386	ENSMUSG00000033355	Rtp4	5830458K16Rik|Ifrg28	receptor transporter protein 4	protein-coding
mm_5486.1	chr1	36891652	36891676	-	1	NA	intron (NM_018872, intron 1 of 40)	intron (NM_018872, intron 1 of 40)	47863	NM_018872	56030	Mm.186943	NM_018872	ENSMUSG00000026116	Tmem131	2610524E03Rik|CC28|D1Bwg0491e|Neg|RW1|YR-23|mKIAA0257	transmembrane protein 131	protein-coding
mm_27425.1	chr3	51518795	51518810	-	1	NA	3' UTR (NM_080793, exon 8 of 8)	3' UTR (NM_080793, exon 8 of 8)	34836	NM_016858	19338	Mm.1664	NM_016858	ENSMUSG00000027739	Rab33b	-	RAB33B, member RAS oncogene family	protein-coding
mm_151057.1	chr19	47179117	47179176	+	1	NA	5' UTR (NM_021360, exon 1 of 6)	5' UTR (NM_021360, exon 1 of 6)	326	NM_021360	18011	Mm.313651	NM_021360	ENSMUSG00000006435	Neurl1a	2410129E16Rik|AI450910|AI481072|Neu1|Neur1|Neurl|Neurl1|Nlz|Rnf67	neuralized E3 ubiquitin protein ligase 1A	protein-coding
mm_160256.1	chr7	108256158	108256158	-	1	NA	promoter-TSS (NM_146732)	promoter-TSS (NM_146732)	-22	NM_146732	258727	Mm.377660	NM_146732	ENSMUSG00000096465	Olfr488	MOR204-15	olfactory receptor 488	protein-coding
mm_114529.1	chr13	73536782	73536810	+	1	NA	promoter-TSS (NM_010020)	promoter-TSS (NM_010020)	49	NM_010020	13162	Mm.41993	NM_010020	ENSMUSG00000021609	Slc6a3	DAT|Dat1	solute carrier family 6 (neurotransmitter transporter, dopamine), member 3	protein-coding
mm_9049.1	chr1	167285080	167285103	-	1	NA	promoter-TSS (NM_030724)	promoter-TSS (NM_030724)	36	NM_030724	80914	Mm.280895	NM_030724	ENSMUSG00000026558	Uck2	AA407809|AI481316|AU018180|AU020720|TSA903|UK|UMK|Umpk	uridine-cytidine kinase 2	protein-coding
mm_26549.1	chr3	146325281	146325282	+	1	NA	Intergenic	Intergenic	53663	NR_033542	100038607	Mm.365888	NR_033542	ENSMUSG00000105602	Gm10636	ENSMUSG00000074175	predicted gene 10636	ncRNA
mm_59675.1	chr7	28383101	28383129	+	1	NA	Intergenic	Intergenic	-3887	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_97333.1	chr11	77235478	77235481	+	1	NA	intron (NM_177710, intron 1 of 14)	intron (NM_177710, intron 1 of 14)	19054	NM_177710	237860	Mm.440381	NM_177710	ENSMUSG00000037926	Ssh2	SSH-2|SSH-2L|mSSH-2L	slingshot homolog 2 (Drosophila)	protein-coding
mm_152621.1	chr19	12463837	12463854	-	1	NA	3' UTR (NM_010821, exon 2 of 2)	3' UTR (NM_010821, exon 2 of 2)	3066	NM_010821	17476	Mm.3999	NM_010821	ENSMUSG00000046805	Mpeg1	MPS1|Mpg-1	macrophage expressed gene 1	protein-coding
mm_68651.1	chr7	118491913	118491965	-	1	NA	promoter-TSS (NM_001033380)	promoter-TSS (NM_001033380)	36	NM_001033380	319622	Mm.323386	NM_001033380	ENSMUSG00000095115	Itpripl2	C130081G24|E030018N11Rik	inositol 1,4,5-triphosphate receptor interacting protein-like 2	protein-coding
mm_171930.1	chr5	63518188	63518191	-	1	NA	Intergenic	RLTR9E|LTR|ERVK	-130914	NM_177006	319807	Mm.319487	NM_028470	ENSMUSG00000090061	Nwd2	3110047P20Rik|B830017A01Rik|Hn1-ps2|mKIAA1239	NACHT and WD repeat domain containing 2	protein-coding
mm_45774.1	chr5	87092035	87092041	-	1	NA	exon (NM_001029867, exon 1 of 6)	exon (NM_001029867, exon 1 of 6)	517	NM_001029867	231396	Mm.439851	NM_001029867	ENSMUSG00000070704	Ugt2b36	-	UDP glucuronosyltransferase 2 family, polypeptide B36	protein-coding
mm_101781.1	chr11	45852617	45852629	-	1	NA	intron (NM_001346760, intron 1 of 11)	intron (NM_001346760, intron 1 of 11)	659	NM_001045520	216705	Mm.169673	NM_001045520	ENSMUSG00000006169	Clint1	AI642036|AW537616|C530049I24Rik|Enth|Epn4|F630206G17Rik|mKIAA0171	clathrin interactor 1	protein-coding
mm_117393.1	chr13	73678006	73678026	-	1	NA	promoter-TSS (NM_001168646)	promoter-TSS (NM_001168646)	7	NM_001168646	22598	Mm.30370	NM_011730	ENSMUSG00000021612	Slc6a18	B0AT3|D630001K16Rik|Xt2|Xtrp2	solute carrier family 6 (neurotransmitter transporter), member 18	protein-coding
mm_37819.1	chr4	131838295	131838305	-	1	NA	promoter-TSS (NM_011214)	promoter-TSS (NM_011214)	-22	NM_001083119	19273	Mm.4860	NM_011214	ENSMUSG00000028909	Ptpru	Ftp-1|PCP-2|PTP|PTP-lambda|PTPlambda|Pcp2|Ptpf|Ptprl|R-PTP-U|R-PTP-psi|RPTPlambda	protein tyrosine phosphatase, receptor type, U	protein-coding
mm_75876.1	chr8	70765005	70765021	-	1	NA	exon (NM_023065, exon 2 of 8)	exon (NM_023065, exon 2 of 8)	1650	NM_023065	65972	Mm.30241	NM_023065	ENSMUSG00000031838	Ifi30	GILT|IP30	interferon gamma inducible protein 30	protein-coding
mm_10930.1	chr2	25461202	25461221	+	1	NA	promoter-TSS (NM_153557)	promoter-TSS (NM_153557)	-117	NM_153557	227622	Mm.261780	NM_153557	ENSMUSG00000047617	BC029214	D930050G13Rik|Paxx	cDNA sequence BC029214	protein-coding
mm_143704.1	chr17	80577769	80577783	-	1	NA	Intergenic	Intergenic	-13942	NM_001033443	381113	Mm.329216	NM_001033443	ENSMUSG00000033966	Cdkl4	AU067824|Gm942	cyclin-dependent kinase-like 4	protein-coding
mm_12859.1	chr2	83762584	83762587	+	1	NA	intron (NM_008402, intron 5 of 29)	intron (NM_008402, intron 5 of 29)	38188	NM_008402	16410	Mm.227	NM_008402	ENSMUSG00000027087	Itgav	1110004F14Rik|2610028E01Rik|CD51|D430040G12Rik	integrin alpha V	protein-coding
mm_54158.1	chr6	23085161	23085175	-	1	NA	intron (NM_013930, intron 18 of 23)	intron (NM_013930, intron 18 of 23)	47818	NM_013930	30956	Mm.18651	NM_013930	ENSMUSG00000029695	Aass	LKR|LKR/SDH|LOR|LOR/SDH|Lorsdh|SDH	aminoadipate-semialdehyde synthase	protein-coding
mm_86845.1	chr10	21571748	21571754	+	1	NA	Intergenic	Intergenic	-21394	NR_027968	67692	Mm.54306	NM_183266	ENSMUSG00000050844	1700020N01Rik	-	RIKEN cDNA 1700020N01 gene	ncRNA
mm_10872.1	chr2	25225044	25225071	+	1	NA	promoter-TSS (NM_146116)	promoter-TSS (NM_146116)	-355	NM_146116	227613	Mm.227260	NM_146116	ENSMUSG00000036752	Tubb4b	4930542G03Rik|Tubb2c|Tubb2c1	tubulin, beta 4B class IVB	protein-coding
mm_27884.1	chr3	79173290	79173309	-	1	NA	Intergenic	Intergenic	-27424	NM_001099624	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_53234.1	chr6	127446820	127446872	+	1	NA	promoter-TSS (NM_001346513)	promoter-TSS (NM_001346513)	6	NM_001346513	101187	Mm.110818	NM_181402	ENSMUSG00000037997	Parp11	5330431N24Rik|AI851877|ARTD11|HIN1L|PARP-11	poly (ADP-ribose) polymerase family, member 11	protein-coding
mm_127573.1	chr15	102279554	102279572	+	1	NA	5' UTR (NM_134100, exon 1 of 2)	5' UTR (NM_134100, exon 1 of 2)	107	NM_134100	106073	Mm.287740	NM_134100	ENSMUSG00000045665	Mfsd5	AA409375|AW556797|D15Mgi27	major facilitator superfamily domain containing 5	protein-coding
mm_84448.1	chr9	66512454	66512488	-	1	NA	intron (NM_175206, intron 1 of 1)	intron (NM_175206, intron 1 of 1)	2122	NM_175206	74165	Mm.297998	NM_175206	ENSMUSG00000050503	Fbxl22	1110004B15Rik	F-box and leucine-rich repeat protein 22	protein-coding
mm_41808.1	chr5	103754561	103754581	+	1	NA	promoter-TSS (NM_001080798)	promoter-TSS (NM_001080798)	-2	NM_001080798	17355	Mm.6949	NM_133919	ENSMUSG00000029313	Aff1	9630032B01Rik|AW319193|Af4|Mllt2h|Rob	AF4/FMR2 family, member 1	protein-coding
mm_23769.1	chr3	75557511	75557521	+	1	NA	promoter-TSS (NM_009250)	promoter-TSS (NM_009250)	-17	NM_009250	20713	Mm.41560	NM_009250	ENSMUSG00000027834	Serpini1	AI837402|Ns|PI-12|PI12|Spi17	serine (or cysteine) peptidase inhibitor, clade I, member 1	protein-coding
mm_8722.1	chr1	160046970	160046971	-	1	NA	intron (NM_001162896, intron 1 of 2)	intron (NM_001162896, intron 1 of 2)	2590	NM_001162896	67647	Mm.171518	NM_001024470	ENSMUSG00000090394	4930523C07Rik	-	RIKEN cDNA 4930523C07 gene	protein-coding
mm_71098.1	chr8	35216528	35216533	+	1	NA	Intergenic	MER101B|LTR|ERV1	-159211	NM_177741	244416	Mm.247126	NM_177741	ENSMUSG00000046794	Ppp1r3b	6430576E21|AW821953|GL|PTG	protein phosphatase 1, regulatory (inhibitor) subunit 3B	protein-coding
mm_34369.1	chr4	144893183	144893193	+	1	NA	promoter-TSS (NM_011303)	promoter-TSS (NM_011303)	51	NM_011303	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding
mm_47715.1	chr5	130000859	130000877	-	1	NA	exon (NM_010368, exon 2 of 12)	exon (NM_010368, exon 2 of 12)	1960	NM_010368	110006	Mm.3317	NM_010368	ENSMUSG00000025534	Gusb	AI747421|Gur|Gus|Gus-r|Gus-s|Gus-t|Gus-u|Gut|asd|g	glucuronidase, beta	protein-coding
mm_112441.1	chr13	5841720	5841720	+	1	NA	Intergenic	Intergenic	16372	NR_045891	71867	Mm.179181	NR_045891	ENSMUSG00000100625	1700016G22Rik	-	RIKEN cDNA 1700016G22 gene	ncRNA
mm_76180.1	chr8	82401794	82401807	-	1	NA	intron (NM_001254747, intron 1 of 7)	intron (NM_001254747, intron 1 of 7)	786	NM_001254747	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_36903.1	chr4	107889769	107889801	-	1	NA	promoter-TSS (NM_028754)	promoter-TSS (NM_028754)	-41	NM_001347160	74098	Mm.274853	NM_028754	ENSMUSG00000028608	0610037L13Rik	1110008H16Rik	RIKEN cDNA 0610037L13 gene	protein-coding
mm_109558.1	chr12	111791110	111791174	+	1	NA	intron (NM_001081959, intron 13 of 15)	BC1_Mm|scRNA|scRNA	22737	NM_028875	74335	Mm.19082	NM_028875	ENSMUSG00000021287	Xrcc3	-	X-ray repair complementing defective repair in Chinese hamster cells 3	protein-coding
mm_71869.1	chr8	69157778	69157801	+	1	NA	Intergenic	Intergenic	-16836	NM_199364	211134	Mm.409446	NM_199364	ENSMUSG00000036306	Lzts1	F37|FEZ1|PSD-Zip70	leucine zipper, putative tumor suppressor 1	protein-coding
mm_108233.1	chr12	77239129	77239142	+	1	NA	non-coding (NR_045554, exon 1 of 12)	non-coding (NR_045554, exon 1 of 12)	396	NR_045554	53618	Mm.35628	NM_016893	ENSMUSG00000021065	Fut8	-	fucosyltransferase 8	protein-coding
mm_64124.1	chr7	141132434	141132450	+	1	NA	intron (NM_013782, intron 1 of 11)	intron (NM_013782, intron 1 of 11)	1156	NM_013782	27388	Mm.293591	NM_013782	ENSMUSG00000025495	Ptdss2	AI481134|AI988017|PSS2	phosphatidylserine synthase 2	protein-coding
mm_84887.1	chr9	79759850	79759856	-	1	NA	promoter-TSS (NM_009945)	promoter-TSS (NM_009945)	0	NM_009945	12866	Mm.152627	NM_009945	ENSMUSG00000032330	Cox7a2	COX7AL|Cox7a3|CoxVIIa-L	cytochrome c oxidase subunit VIIa 2	protein-coding
mm_63383.1	chr7	127213193	127213203	+	1	NA	exon (NM_016754, exon 3 of 7)	exon (NM_016754, exon 3 of 7)	1590	NM_016754	17907	Mm.14526	NM_016754	ENSMUSG00000030672	Mylpf	2410014J02Rik|MLC-2|Mlc2	myosin light chain, phosphorylatable, fast skeletal muscle	protein-coding
mm_87031.1	chr10	28668389	28668404	+	1	NA	promoter-TSS (NM_178666)	promoter-TSS (NM_178666)	36	NM_178666	210757	Mm.123021	NM_178666	ENSMUSG00000049109	Themis	E430004N04Rik|Gasp|Spot|Tsepa|thylex	thymocyte selection associated	protein-coding
mm_23209.1	chr3	41563394	41563466	+	1	NA	promoter-TSS (NM_001130185)	promoter-TSS (NM_001130185)	47	NM_172303	269424	Mm.286285	NM_172303	ENSMUSG00000025764	Jade1	AU041499|D530048A03Rik|Phf17|mKIAA1807	jade family PHD finger 1	protein-coding
mm_48959.1	chr6	4540930	4540946	+	1	NA	3' UTR (NM_007743, exon 52 of 52)	3' UTR (NM_007743, exon 52 of 52)	35320	NM_007743	12843	Mm.277792	NM_007743	ENSMUSG00000029661	Col1a2	AA960264|AI325291|Col1a-2|Cola-2|Cola2|oim	collagen, type I, alpha 2	protein-coding
mm_171004.1	chr2	79332320	79332330	-	1	NA	TTS (NM_001048176)	TTS (NM_001048176)	76899	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D|Itga4B	integrin alpha 4	protein-coding
mm_171966.1	chr5	86997436	86997445	-	1	NA	Intergenic	Intergenic	-3420	NM_172881	243085	Mm.312095	NM_172881	ENSMUSG00000035811	Ugt2b35	C730031G17	UDP glucuronosyltransferase 2 family, polypeptide B35	protein-coding
mm_86485.1	chr10	4981519	4981534	+	1	NA	intron (NM_001302531, intron 7 of 8)	intron (NM_001302531, intron 7 of 8)	87537	NM_022027	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_84130.1	chr9	59036236	59036244	-	1	NA	5' UTR (NM_008684, exon 1 of 29)	5' UTR (NM_008684, exon 1 of 29)	201	NM_008684	18007	Mm.42249	NM_008684	ENSMUSG00000032340	Neo1	2610028H22Rik|AI327052|D930014N22Rik|Igdcc2	neogenin	protein-coding
mm_102004.1	chr11	51601270	51601314	-	1	NA	3' UTR (NM_010448, exon 7 of 7)	3' UTR (NM_010448, exon 7 of 7)	5589	NM_001048061	15384	Mm.256875	NM_010448	ENSMUSG00000020358	Hnrnpab	3010025C11Rik|CBF-A|Cgbfa|Hnrpab	heterogeneous nuclear ribonucleoprotein A/B	protein-coding
mm_22604.1	chr3	14506291	14506301	+	1	NA	TTS (NM_080852)	TTS (NM_080852)	25597	NM_080852	140918	Mm.215250	NM_080852	ENSMUSG00000039710	Slc7a12	Asc-2|XAT1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 12	protein-coding
mm_111217.1	chr12	84436473	84436512	-	1	NA	exon (NM_134042, exon 9 of 12)	exon (NM_134042, exon 9 of 12)	11825	NM_001313967	104776	Mm.247510	NM_134042	ENSMUSG00000021238	Aldh6a1	1110038I05Rik|Mmsdh	aldehyde dehydrogenase family 6, subfamily A1	protein-coding
mm_30820.1	chr4	21865888	21865900	+	1	NA	exon (NM_025669, exon 7 of 12)	exon (NM_025669, exon 7 of 12)	-13781	NM_172687	230027	Mm.5662	NM_172687	ENSMUSG00000028247	Coq3	4732433J24|C77934	coenzyme Q3 methyltransferase	protein-coding
mm_139389.1	chr17	52217657	52217667	+	1	NA	Intergenic	MT2A|LTR|ERVL	334935	NR_045095	100504169	Mm.417731	NR_045095		Gm20098	-	predicted gene, 20098	ncRNA
mm_54609.1	chr6	38345927	38345938	-	1	NA	intron (NM_001347122, intron 1 of 12)	intron (NM_001347122, intron 1 of 12)	8671	NM_028864	78781	Mm.25243	NM_028421	ENSMUSG00000029826	Zc3hav1	1200014N16Rik|2900058M19Rik|9130009D18Rik|9830115L13Rik|ARTD13|D6Bwg1452e|ZAP	zinc finger CCCH type, antiviral 1	protein-coding
mm_172812.1	chr9	123689568	123689572	-	1	NA	Intergenic	(CCA)n|Simple_repeat|Simple_repeat	-10738	NM_139142	102680	Mm.440867	NM_139142	ENSMUSG00000036814	Slc6a20a	A730081N20Rik|AU022428|Xt3s1|Xtrp3s1	solute carrier family 6 (neurotransmitter transporter), member 20A	protein-coding
mm_5059.1	chr1	194986595	194986611	+	1	NA	Intergenic	Intergenic	-9644	NR_033564	320400	Mm.417608	NR_033564	ENSMUSG00000097325	Gm16897	C030002c11rik	predicted gene, 16897	ncRNA
mm_80827.1	chr9	96800626	96800635	+	1	NA	Intergenic	RLTR23|LTR|ERV1	35068	NR_102296	319707	Mm.392191	NR_102293	ENSMUSG00000101581	C430002N11Rik	-	RIKEN cDNA C430002N11 gene	ncRNA
mm_38218.1	chr4	135972575	135972618	-	1	NA	promoter-TSS (NM_011942)	promoter-TSS (NM_011942)	-2	NM_011942	26394	Mm.34302	NM_011942	ENSMUSG00000028670	Lypla2	LysoII	lysophospholipase 2	protein-coding
mm_75623.1	chr8	64619484	64619508	-	1	NA	exon (NM_013494, exon 2 of 9)	exon (NM_013494, exon 2 of 9)	73613	NM_013494	12876	Mm.31395	NM_013494	ENSMUSG00000037852	Cpe	CPH|Cph-1|Cph1|R74677|fat	carboxypeptidase E	protein-coding
mm_118074.1	chr13	103006322	103006326	-	1	NA	intron (NM_175171, intron 4 of 28)	B1_Mur1|SINE|Alu	246069	NR_130171	76624	Mm.426384	NR_130171	ENSMUSG00000091906	1700099I09Rik	-	RIKEN cDNA 1700099I09 gene	ncRNA
mm_167751.1	chr9	110415605	110415609	+	1	NA	Intergenic	Intergenic	-4201	NM_008694	18054	Mm.236225	NM_008694	ENSMUSG00000032484	Ngp	bectenecin	neutrophilic granule protein	protein-coding
mm_143544.1	chr17	74017071	74017077	-	1	NA	TTS (NM_053188)	TTS (NM_053188)	30842	NM_053188	94224	Mm.38933	NM_053188	ENSMUSG00000038541	Srd5a2	5ART2|S5AR 2	steroid 5 alpha-reductase 2	protein-coding
mm_3243.1	chr1	136052755	136052761	+	1	NA	promoter-TSS (NM_014193)	promoter-TSS (NM_014193)	-143	NM_001081023	12292	Mm.4418	NM_014193	ENSMUSG00000026407	Cacna1s	AW493108|Cav1.1|Cchl1a3|fmd|mdg|sj	calcium channel, voltage-dependent, L type, alpha 1S subunit	protein-coding
mm_12596.1	chr2	74668208	74668229	+	1	NA	promoter-TSS (NM_008275)	promoter-TSS (NM_008275)	-92	NM_008275	15433	Mm.57227	NM_008275	ENSMUSG00000001819	Hoxd13	Hox-4.8|spdh	homeobox D13	protein-coding
mm_77132.1	chr8	111346379	111346408	-	1	NA	3' UTR (NM_178086, exon 7 of 7)	3' UTR (NM_178086, exon 7 of 7)	-8188	NM_029005	74568	Mm.207971	NM_029005	ENSMUSG00000012519	Mlkl	9130019I15Rik	mixed lineage kinase domain-like	protein-coding
mm_13421.1	chr2	104493799	104493814	+	1	NA	intron (NM_010434, intron 1 of 15)	CpG	683	NM_010434	15259	Mm.257925	NM_010434	ENSMUSG00000027177	Hipk3	DYRK6|FIST3|PKY|mir-1902	homeodomain interacting protein kinase 3	protein-coding
mm_74949.1	chr8	25976731	25976735	-	1	NA	promoter-TSS (NM_029884)	promoter-TSS (NM_029884)	11	NM_029884	52120	Mm.28326	NM_029884	ENSMUSG00000037260	Hgsnat	9430010M12Rik|AW208455|D8Ertd354e|Tmem76	heparan-alpha-glucosaminide N-acetyltransferase	protein-coding
mm_102890.1	chr11	69414107	69414112	-	1	NA	promoter-TSS (NM_001017426)	promoter-TSS (NM_001017426)	-434	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_104348.1	chr11	94295091	94295094	-	1	NA	intron (NM_026313, intron 9 of 10)	intron (NM_026313, intron 9 of 10)	26819	NM_026313	67684	Mm.30927	NM_026313	ENSMUSG00000020863	Luc7l3	3300001P08Rik|Luc7a	LUC7-like 3 (S. cerevisiae)	protein-coding
mm_71924.1	chr8	70234533	70234608	+	1	NA	promoter-TSS (NM_133972)	promoter-TSS (NM_133972)	-148	NM_133972	76813	Mm.383251	NM_133972	ENSMUSG00000002343	Armc6	2410153K17Rik|AW554412	armadillo repeat containing 6	protein-coding
mm_11652.1	chr2	34963171	34963202	+	1	NA	Intergenic	Intergenic	-1414	NM_001326601	22029	Mm.239514	NM_009421	ENSMUSG00000026875	Traf1	4732496E14Rik	TNF receptor-associated factor 1	protein-coding
mm_79418.1	chr9	55216406	55216416	+	1	NA	intron (NM_028049, intron 4 of 6)	ORR1C2|LTR|ERVL-MaLR	7476	NM_028049	71999	Mm.276429	NM_028049	ENSMUSG00000032309	Fbxo22	0610033L19Rik|1600016C16Rik	F-box protein 22	protein-coding
mm_45600.1	chr5	75025024	75025026	-	1	NA	intron (NM_028850, intron 3 of 5)	intron (NM_028850, intron 3 of 5)	19616	NM_028850	74277	Mm.239814	NM_028850	ENSMUSG00000029229	Chic2	1700081B18Rik|4930502K01Rik|BTL	cysteine-rich hydrophobic domain 2	protein-coding
mm_70155.1	chr7	143502516	143502532	-	1	NA	promoter-TSS (NM_009434)	promoter-TSS (NM_009434)	0	NM_009434	22113	Mm.334344	NM_009434	ENSMUSG00000010760	Phlda2	Ipl|Tssc3	pleckstrin homology like domain, family A, member 2	protein-coding
mm_1926.1	chr1	86064626	86064648	+	1	NA	promoter-TSS (NM_027357)	promoter-TSS (NM_027357)	18	NM_027357	70247	Mm.280013	NM_027357	ENSMUSG00000026229	Psmd1	2410026J11Rik|P112|S1	proteasome (prosome, macropain) 26S subunit, non-ATPase, 1	protein-coding
mm_162775.1	chr10	68240457	68240460	-	1	NA	intron (NM_023598, intron 3 of 9)	intron (NM_023598, intron 3 of 9)	38268	NM_023598	71371	Mm.440357	NM_023598	ENSMUSG00000019947	Arid5b	4930580B11|5430435G07Rik|AI467247|Desrt|Mrf2|Mrf2alpha|Mrf2beta	AT rich interactive domain 5B (MRF1-like)	protein-coding
mm_34985.1	chr4	156026305	156026371	+	1	NA	promoter-TSS (NM_009400)	promoter-TSS (NM_009400)	-4	NM_009400	21936	Mm.3180	NM_009400	ENSMUSG00000041954	Tnfrsf18	AITR|Gitr	tumor necrosis factor receptor superfamily, member 18	protein-coding
mm_8711.1	chr1	158969508	158969517	-	1	NA	Intergenic	Intergenic	-12074	NM_001085376	23850	Mm.458621	NM_001085376	ENSMUSG00000073530	Pappa2	PAPP-A2|PLAC3|Pappe	pappalysin 2	protein-coding
mm_72091.1	chr8	71580484	71580506	+	1	NA	intron (NM_011977, intron 6 of 13)	intron (NM_011977, intron 6 of 13)	11568	NM_011977	26457	Mm.38165	NM_011977	ENSMUSG00000031808	Slc27a1	FATP1|Fatp	solute carrier family 27 (fatty acid transporter), member 1	protein-coding
mm_110514.1	chr12	54795699	54795714	-	1	NA	promoter-TSS (NM_026998)	promoter-TSS (NM_026998)	-44	NM_026998	72183	Mm.28240	NM_026998	ENSMUSG00000005656	Snx6	2010006G21Rik|2610032J07Rik|2810425K19Rik|AU018928|C85963	sorting nexin 6	protein-coding
mm_47277.1	chr5	122049823	122049882	-	1	NA	promoter-TSS (NM_001312908)	promoter-TSS (NM_001312908)	-1	NM_001312908	13048	Mm.156172	NM_007804	ENSMUSG00000042589	Cux2	1700051K22Rik|Cutl2|Cux-2|ENSMUSG00000072641	cut-like homeobox 2	protein-coding
mm_159660.1	chr4	150237241	150237241	+	1	NA	promoter-TSS (NM_001025388).2	promoter-TSS (NM_001025388).2	44	NM_023119	13806	Mm.70666	NM_023119	ENSMUSG00000063524	Eno1	0610008I15|AL022784|Eno-1|MBP-1	enolase 1, alpha non-neuron	protein-coding
mm_66534.1	chr7	45137660	45137707	-	1	NA	Intergenic	Intergenic	-1251	NR_102725	14256	Mm.1658	NM_013520	ENSMUSG00000110206	Flt3l	Flt3lg|Ly72L	FMS-like tyrosine kinase 3 ligand	protein-coding
mm_58224.1	chr6	144209664	144209690	-	1	NA	promoter-TSS (NM_011444)	promoter-TSS (NM_011444)	-109	NM_001243163	20678	Mm.1752	NM_011444	ENSMUSG00000041540	Sox5	A730017D01Rik|AI528773	SRY (sex determining region Y)-box 5	protein-coding
mm_136800.1	chr17	12195367	12195371	+	1	NA	intron (NM_026644, intron 2 of 8)	intron (NM_026644, intron 2 of 8)	76085	NM_026644	68262	Mm.258300	NM_026644	ENSMUSG00000023827	Agpat4	1500003P24Rik	1-acylglycerol-3-phosphate O-acyltransferase 4 (lysophosphatidic acid acyltransferase, delta)	protein-coding
mm_46427.1	chr5	104358733	104358742	-	1	NA	Intergenic	Intergenic	33408	NM_053172	94111	Mm.196672	NM_053172	ENSMUSG00000053863	Mepe	Of45	matrix extracellular phosphoglycoprotein with ASARM motif (bone)	protein-coding
mm_167248.1	chr8	23080243	23080251	+	1	NA	intron (NR_102385, intron 2 of 45)	intron (NR_102385, intron 2 of 45)	21988	NR_102385	11733	Mm.334444	NM_031158	ENSMUSG00000031543	Ank1	Ank-1|nb|pale	ankyrin 1, erythroid	protein-coding
mm_148813.1	chr19	6296823	6296847	+	1	NA	intron (NM_010119, intron 3 of 4)	intron (NM_010119, intron 3 of 4)	-9622	NM_001033342	240505	Mm.329622	NM_001033342	ENSMUSG00000024769	Cdc42bpg	BC046418|MRCKgamma	CDC42 binding protein kinase gamma (DMPK-like)	protein-coding
mm_81714.1	chr9	111351873	111351897	+	1	NA	intron (NM_001164659, intron 7 of 21)	intron (NM_001164659, intron 7 of 21)	40146	NM_001164659	320429	Mm.270754	NM_001164659	ENSMUSG00000062296	Trank1	A230061D21Rik|C030048J01Rik|Gm187|Lba1	tetratricopeptide repeat and ankyrin repeat containing 1	protein-coding
mm_34263.1	chr4	141421751	141421771	+	1	NA	5' UTR (NM_013868, exon 1 of 3)	5' UTR (NM_013868, exon 1 of 3)	982	NM_013868	29818	Mm.46181	NM_013868	ENSMUSG00000006221	Hspb7	27kDa|Hsp25-2|cvHsp	heat shock protein family, member 7 (cardiovascular)	protein-coding
mm_138013.1	chr17	33908393	33908410	+	1	NA	non-coding (NR_045146, exon 2 of 2)	non-coding (NR_045146, exon 2 of 2)	777	NR_045146	407803	Mm.250393	NR_045146	ENSMUSG00000092564	BC051226	-	cDNA sequence BC051226	ncRNA
mm_117323.1	chr13	67755193	67755211	-	1	NA	promoter-TSS (NM_001001130)	promoter-TSS (NM_001001130)	-68	NM_001001130	22746	Mm.288396	NM_001001130	ENSMUSG00000058331	Zfp85	KRAB19|Rslcan2|Zfp71|Zfp85-rs1	zinc finger protein 85	protein-coding
mm_35744.1	chr4	45408879	45408907	-	1	NA	promoter-TSS (NM_001009949)	promoter-TSS (NM_001009949)	-127	NM_001009949	230125	Mm.260210	NM_001009949	ENSMUSG00000045973	Slc25a51	9130208E07Rik|D130005A03Rik|Gm138|Mcart1	solute carrier family 25, member 51	protein-coding
mm_12460.1	chr2	71334631	71334635	+	1	NA	intron (NM_172436, intron 3 of 17)	intron (NM_172436, intron 3 of 17)	32921	NM_172436	78830	Mm.30928	NM_172436	ENSMUSG00000027010	Slc25a12	2610002D09Rik|AI839531|B230107K20Rik|BB129864	solute carrier family 25 (mitochondrial carrier, Aralar), member 12	protein-coding
mm_4273.1	chr1	171559218	171559234	+	1	NA	promoter-TSS (NM_018729)	promoter-TSS (NM_018729)	33	NM_018729	18106	Mm.2299	NM_018729	ENSMUSG00000004709	Cd244	2B4|C9.1|F730046O15Rik|Ly90|NAIL|NKR2B4|Nmrk|SLAMF4	CD244 natural killer cell receptor 2B4	protein-coding
mm_76906.1	chr8	105833841	105833886	-	1	NA	intron (NM_024445, intron 2 of 15)	intron (NM_024445, intron 2 of 15)	6119	NM_024445	72236	Mm.386810	NM_024445	ENSMUSG00000031893	Tsnaxip1	1700016K08Rik|TXI1	translin-associated factor X (Tsnax) interacting protein 1	protein-coding
mm_58698.1	chr7	12925747	12925770	+	1	NA	exon (NM_009095, exon 4 of 6)	exon (NM_009095, exon 4 of 6)	-1658	NM_029809	381845	Mm.439896	NM_029809	ENSMUSG00000033967	Rnf225	2310014L17Rik|AV237412|C77118	ring finger protein 225	protein-coding
mm_42130.1	chr5	110990683	110990685	+	1	NA	intron (NM_001267622, intron 2 of 22)	B1_Mur3|SINE|Alu	-13460	NR_030482	735278		NR_030482	ENSMUSG00000076163	Mir701	Mirn701|mir-701|mmu-mir-701	microRNA 701	ncRNA
mm_68645.1	chr7	118487537	118487566	-	1	NA	3' UTR (NM_001033380, exon 1 of 1)	3' UTR (NM_001033380, exon 1 of 1)	4424	NM_001033380	319622	Mm.323386	NM_001033380	ENSMUSG00000095115	Itpripl2	C130081G24|E030018N11Rik	inositol 1,4,5-triphosphate receptor interacting protein-like 2	protein-coding
mm_151523.1	chr19	58740515	58740528	+	1	NA	exon (NM_018874, exon 11 of 13)	exon (NM_018874, exon 11 of 13)	11634	NM_018874	18946	Mm.10753	NM_018874	ENSMUSG00000042179	Pnliprp1	Plrp1	pancreatic lipase related protein 1	protein-coding
mm_101541.1	chr11	33527397	33527424	-	1	NA	Intergenic	Intergenic	-13664	NM_023146	66011	Mm.383775	NM_023146	ENSMUSG00000040594	Ranbp17	-	RAN binding protein 17	protein-coding
mm_63477.1	chr7	127744300	127744321	+	1	NA	Intergenic	Intergenic	-2465	NM_172748	233902	Mm.259353	NM_172748	ENSMUSG00000030811	Fbxl19	6030430O11|BC059812|Fbl19	F-box and leucine-rich repeat protein 19	protein-coding
mm_152601.1	chr19	11759008	11759046	-	1	NA	exon (NM_008118, exon 7 of 9)	exon (NM_008118, exon 7 of 9)	-11388	NM_025606	94063	Mm.203928	NM_025606	ENSMUSG00000024683	Mrpl16	2310039D06Rik	mitochondrial ribosomal protein L16	protein-coding
mm_29418.1	chr3	108973282	108973300	-	1	NA	3' UTR (NM_001163567, exon 11 of 11)	3' UTR (NM_001163567, exon 11 of 11)	32734	NM_001078646	66715	Mm.158124	NM_025723	ENSMUSG00000045662	Henmt1	4921515J06Rik|Hen1|mHEN1	HEN1 methyltransferase homolog 1 (Arabidopsis)	protein-coding
mm_113231.1	chr13	27243741	27243753	+	1	NA	exon (NM_008865, exon 2 of 5)	exon (NM_008865, exon 2 of 5)	1317	NM_008865	18776	Mm.37203	NM_008865	ENSMUSG00000038891	Prl3b1	Csh2|Ghd8|PL|Pl-2|Pl2|mPL-II|mplII	prolactin family 3, subfamily b, member 1	protein-coding
mm_27619.1	chr3	59344014	59344046	-	1	NA	5' UTR (NM_001162884, exon 1 of 7)	5' UTR (NM_001162884, exon 1 of 7)	226	NM_001162884	242050	Mm.228086	NM_001162884	ENSMUSG00000036334	Igsf10	6530405F15Rik|9030224D03|AA409708|AA536958|AI414626|Adlican2|CMF608	immunoglobulin superfamily, member 10	protein-coding
mm_1347.1	chr1	66302114	66302127	+	1	NA	intron (NM_001039934, intron 3 of 14)	intron (NM_001039934, intron 3 of 14)	-19604	NM_001310634	17756	Mm.256966	NM_008632	ENSMUSG00000015222	Map2	G1-397-34|MAP-2|Mtap-2|Mtap2|repro4	microtubule-associated protein 2	protein-coding
mm_79876.1	chr9	65195375	65195381	+	1	NA	Intergenic	Intergenic	-19312	NM_177460	214424	Mm.31129	NM_177460	ENSMUSG00000032392	Parp16	ARTD15|BC055447|C79952|PARP-16	poly (ADP-ribose) polymerase family, member 16	protein-coding
mm_157091.1	chrX	9437128	9437155	-	1	NA	3' UTR (NM_007807, exon 13 of 13)	3' UTR (NM_007807, exon 13 of 13)	32183	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_2268.1	chr1	91214232	91214258	+	1	NA	intron (NM_016894, intron 2 of 2)	B1_Mus1|SINE|Alu	34423	NM_001168392	51801	Mm.3272	NM_016894	ENSMUSG00000034353	Ramp1	9130218E19Rik	receptor (calcitonin) activity modifying protein 1	protein-coding
mm_169371.1	chr14	34258791	34258810	+	1	NA	intron (NM_029389, intron 5 of 10)	BGLII|LTR|ERVK	38754	NM_181529	319508	Mm.228006	NM_176931	ENSMUSG00000041479	Syt15	CHR10SYT|E230025K04Rik|sytXV	synaptotagmin XV	protein-coding
mm_26882.1	chr3	17786308	17786318	-	1	NA	Intergenic	CpG	-3608	NR_033490	70441	Mm.458192	NR_033490	ENSMUSG00000100252	Mir124-2hg	100040120|2610100L16Rik|6430547I21Rik|A930005K07Rik|AW125202|Gm2612	Mir124-2 host gene (non-protein coding)	ncRNA
mm_87324.1	chr10	42860749	42860759	+	1	NA	5' UTR (NM_172938, exon 1 of 9)	5' UTR (NM_172938, exon 1 of 9)	242	NM_172938	268297	Mm.98731	NM_172938	ENSMUSG00000044770	Scml4	9330161D17|mFLJ00197	sex comb on midleg-like 4 (Drosophila)	protein-coding
mm_125662.1	chr15	64220504	64220508	+	1	NA	intron (NM_010026, intron 3 of 30)	intron (NM_010026, intron 3 of 30)	92167	NM_001276462	13196	Mm.277236	NM_010026	ENSMUSG00000022377	Asap1	AV239055|DEF-1|Ddef1|PAP|mKIAA1249|s19	ArfGAP with SH3 domain, ankyrin repeat and PH domain1	protein-coding
mm_72236.1	chr8	74876349	74876352	+	1	NA	intron (NM_001294278, intron 1 of 3)	intron (NM_001294278, intron 1 of 3)	3176	NM_001294278	71597	Mm.158735	NM_027837	ENSMUSG00000031621	Isx	9130012O13Rik|Pix-1	intestine specific homeobox	protein-coding
mm_90426.1	chr10	127501673	127501706	+	1	NA	promoter-TSS (NM_177707)	promoter-TSS (NM_177707)	-28	NM_177707	237611	Mm.32087	NM_177707	ENSMUSG00000040287	Stac3	9830125E18	SH3 and cysteine rich domain 3	protein-coding
mm_170633.1	chr19	8319103	8319118	+	1	NA	Intergenic	IAPLTR4|LTR|ERVK	85995	NM_177002	319800	Mm.426083	NM_177002	ENSMUSG00000052562	Slc22a30	AA986766|C730048C13Rik|UST1R	solute carrier family 22, member 30	protein-coding
mm_85324.1	chr9	101862412	101862426	-	1	NA	Intergenic	Intergenic	442556	NR_106163	102466241		NR_106163	ENSMUSG00000098521	Mir7243	Gm27363|mmu-mir-7243	microRNA 7243	ncRNA
mm_60130.1	chr7	37215665	37215665	+	1	NA	Intergenic	Intergenic	517547	NM_172298	243931	Mm.44141	NM_172298	ENSMUSG00000021217	Tshz3	A630038G13Rik|Tsh3|Zfp537|mKIAA1474|teashirt3	teashirt zinc finger family member 3	protein-coding
mm_124307.1	chr14	103099488	103099497	-	1	NA	promoter-TSS (NM_015822)	promoter-TSS (NM_015822)	17	NM_015822	50789	Mm.214746	NM_015822	ENSMUSG00000022124	Fbxl3	AU041772|AW212966|FBK|Fbl3a|Fbxl3a|Ovtm|Play68	F-box and leucine-rich repeat protein 3	protein-coding
mm_138163.1	chr17	34261848	34261851	+	1	NA	Intergenic	Intergenic	-1378	NM_207105	14961	Mm.254067	NM_207105	ENSMUSG00000073421	H2-Ab1	AI845868|Abeta|H-2Ab|H2-Ab|I-Abeta|IAb|Ia-2|Ia2|Rmcs1	histocompatibility 2, class II antigen A, beta 1	protein-coding
mm_2307.1	chr1	91540688	91540761	+	1	NA	promoter-TSS (NM_023046)	promoter-TSS (NM_023046)	159	NM_001039126	65247	Mm.234152	NM_023046	ENSMUSG00000026311	Asb1	1700029O08Rik|1700054C17Rik|AI426616|AI851378|mKIAA1146	ankyrin repeat and SOCS box-containing 1	protein-coding
mm_162381.1	chr1	73928496	73928496	-	1	NA	intron (NM_001289895, intron 22 of 32)	intron (NM_001289895, intron 22 of 32)	-64030	NR_045311	109198	Mm.359721	NR_045311	ENSMUSG00000100301	6030407O03Rik	-	RIKEN cDNA 6030407O03 gene	ncRNA
mm_41264.1	chr5	89028098	89028104	+	1	NA	intron (NM_001197147, intron 3 of 25)	intron (NM_001197147, intron 3 of 25)	140841	NM_018760	54403	Mm.41044	NM_018760	ENSMUSG00000060961	Slc4a4	AI835705|NBC|NBC1	solute carrier family 4 (anion exchanger), member 4	protein-coding
mm_150413.1	chr19	36930030	36930032	+	1	NA	intron (NM_001080706, intron 1 of 37)	intron (NM_001080706, intron 1 of 37)	3952	NM_001080706	107182	Mm.295062	NM_001080706	ENSMUSG00000040565	Btaf1	AI414500|AI447930|E430027O22Rik|TAF170	B-TFIID TATA-box binding protein associated factor 1	protein-coding
mm_167365.1	chr8	85520691	85520693	+	1	NA	intron (NM_173866, intron 9 of 11)	L1MB3|LINE|L1	28075	NM_173866	108682	Mm.200423	NM_173866	ENSMUSG00000031700	Gpt2	4631422C05Rik|ALT2|AU014768|AU041193|C87201	glutamic pyruvate transaminase (alanine aminotransferase) 2	protein-coding
mm_159703.1	chr5	27781450	27781450	-	1	NA	exon (NM_018878, exon 4 of 21)	exon (NM_018878, exon 4 of 21)	10100	NM_018878	55982	Mm.277190	NM_018878	ENSMUSG00000002221	Paxip1	D5Ertd149e|PTIP	PAX interacting (with transcription-activation domain) protein 1	protein-coding
mm_160424.1	chr8	85519372	85519372	+	1	NA	intron (NM_173866, intron 8 of 11)	intron (NM_173866, intron 8 of 11)	26755	NM_173866	108682	Mm.200423	NM_173866	ENSMUSG00000031700	Gpt2	4631422C05Rik|ALT2|AU014768|AU041193|C87201	glutamic pyruvate transaminase (alanine aminotransferase) 2	protein-coding
mm_130136.1	chr15	90898422	90898424	-	1	NA	promoter-TSS (NR_033583)	promoter-TSS (NR_033583)	53	NR_033583	20738	Mm.431547	NR_033583		Spn-ps	Cd43-ps	sialophorin, pseudogene	pseudo
mm_66974.1	chr7	63918972	63918978	-	1	NA	intron (NM_001256311, intron 1 of 2)	intron (NM_001256311, intron 1 of 2)	2118	NM_001256311	381994	Mm.425466	NM_001256311	ENSMUSG00000095061	E030018B13Rik	Gm1697	RIKEN cDNA E030018B13 gene	protein-coding
mm_125968.1	chr15	76274359	76274375	+	1	NA	intron (NM_028852, intron 1 of 4)	B1_Mur4|SINE|Alu	-4528	NR_045747	100038659	Mm.448549	NR_045747		Mirt2	ENSMUSG00000075583|Gm10872|Gm24562	myocardial infraction associated transcript 2	ncRNA
mm_103236.1	chr11	70683691	70683701	-	1	NA	intron (NM_178116, intron 5 of 22)	intron (NM_178116, intron 5 of 22)	4409	NM_001190376	216874	Mm.473726	NM_178116	ENSMUSG00000040712	Camta2	Kiaa0909-hp|mKIAA0909	calmodulin binding transcription activator 2	protein-coding
mm_74735.1	chr8	18741488	18741500	-	1	NA	promoter-TSS (NM_007426)	promoter-TSS (NM_007426)	68	NM_007426	11601	Mm.439874	NM_007426	ENSMUSG00000031465	Angpt2	Agpt2|Ang-2|Ang2	angiopoietin 2	protein-coding
mm_46654.1	chr5	108670586	108670606	-	1	NA	3' UTR (NM_001310692, exon 3 of 3)	3' UTR (NM_001310692, exon 3 of 3)	4200	NM_001310692	231583	Mm.440571	NM_174870	ENSMUSG00000046959	Slc26a1	Sat1	solute carrier family 26 (sulfate transporter), member 1	protein-coding
mm_22695.1	chr3	17795744	17795746	+	1	NA	promoter-TSS (NR_029814)	promoter-TSS (NR_029814)	83	NR_029814	723950		NR_029814	ENSMUSG00000093073	Mir124a-2	Mirn124a-2|mir-124-2|mir-124a-2	microRNA 124a-2	ncRNA
mm_2848.1	chr1	131661904	131661939	+	1	NA	5' UTR (NM_007799, exon 2 of 10)	5' UTR (NM_007799, exon 2 of 10)	23607	NM_007799	13034	Mm.230249	NM_007799	ENSMUSG00000004552	Ctse	A430072O03Rik|C920004C08Rik|CE|CatE	cathepsin E	protein-coding
mm_62474.1	chr7	101837839	101837897	+	1	NA	promoter-TSS (NM_001122739)	promoter-TSS (NM_001122739)	-44	NM_001122739	16332	Mm.476000	NM_010567	ENSMUSG00000032737	Inppl1	51C|SHIP2	inositol polyphosphate phosphatase-like 1	protein-coding
mm_79322.1	chr9	52679849	52679859	+	1	NA	promoter-TSS (NM_178906)	promoter-TSS (NM_178906)	-9	NR_045333	382139	Mm.335162	NR_045333	ENSMUSG00000111020	Gm1715	-	predicted gene 1715	ncRNA
mm_46656.1	chr5	108674777	108674785	-	1	NA	promoter-TSS (NM_001310692)	promoter-TSS (NM_001310692)	15	NM_001310692	231583	Mm.440571	NM_174870	ENSMUSG00000046959	Slc26a1	Sat1	solute carrier family 26 (sulfate transporter), member 1	protein-coding
mm_138329.1	chr17	34856373	34856384	+	1	NA	TTS (NM_138580)	TTS (NM_138580)	1254	NR_105938	102465587		NR_105938	ENSMUSG00000098445	Mir6972	Gm27810|mmu-mir-6972	microRNA 6972	ncRNA
mm_44487.1	chr5	23616529	23616597	-	1	NA	promoter-TSS (NM_009274)	promoter-TSS (NM_009274)	8	NM_009274	20817	Mm.288728	NM_009274	ENSMUSG00000062604	Srpk2	AW226533|AW492537|AW547358|Wbp6|mSRPK2	serine/arginine-rich protein specific kinase 2	protein-coding
mm_39234.1	chr4	156254710	156254720	-	1	NA	intron (NM_001110516, intron 1 of 10)	intron (NM_001110516, intron 1 of 10)	623	NM_001110516	231004	Mm.406833	NM_173736	ENSMUSG00000096351	Samd11	BC026991|mr-s	sterile alpha motif domain containing 11	protein-coding
mm_2574.1	chr1	118481505	118481515	+	1	NA	intron (NM_001293300, intron 8 of 40)	intron (NM_001293300, intron 8 of 40)	-22245	NR_027901	68204	Mm.443536	NR_027901	ENSMUSG00000107722	2900060B14Rik	-	RIKEN cDNA 2900060B14 gene	ncRNA
mm_6485.1	chr1	74108315	74108340	-	1	NA	intron (NM_027884, intron 1 of 34)	intron (NM_027884, intron 1 of 34)	16120	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_26544.1	chr3	146182965	146182977	+	1	NA	intron (NM_001005846, intron 9 of 13)	intron (NM_001005846, intron 9 of 13)	32797	NM_001005846	68279	Mm.116862	NM_026656	ENSMUSG00000011008	Mcoln2	3300002C04Rik|AI549968|C86638|TRPML2	mucolipin 2	protein-coding
mm_93010.1	chr10	87058365	87058374	-	1	NA	intron (NM_029685, intron 1 of 5)	intron (NM_029685, intron 1 of 5)	323	NM_029685	76640	Mm.78423	NM_029685	ENSMUSG00000047129	1700113H08Rik	-	RIKEN cDNA 1700113H08 gene	protein-coding
mm_63863.1	chr7	135684125	135684135	+	1	NA	3' UTR (NM_011212, exon 21 of 21)	3' UTR (NM_011212, exon 21 of 21)	-31816	NR_015548	67765	Mm.445272	NR_015548	ENSMUSG00000097471	5830432E09Rik	-	RIKEN cDNA 5830432E09 gene	ncRNA
mm_146008.1	chr18	69344576	69344586	+	1	NA	promoter-TSS (NM_013685)	promoter-TSS (NM_013685)	89	NM_013685	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding
mm_82270.1	chr9	7348691	7348729	-	1	NA	exon (NM_008605, exon 2 of 10)	exon (NM_008605, exon 2 of 10)	1336	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_41672.1	chr5	99649757	99649769	+	1	NA	intron (NR_030692, intron 1 of 3)	intron (NR_030692, intron 1 of 3)	79297	NR_030692	319818	Mm.295233	NR_030692	ENSMUSG00000089809	A930011G23Rik	-	RIKEN cDNA A930011G23 gene	ncRNA
mm_114645.1	chr13	76825199	76825208	+	1	NA	intron (NM_030174, intron 12 of 20)	intron (NM_030174, intron 12 of 20)	310265	NM_134071	105377	Mm.209730	NM_134071	ENSMUSG00000021597	Slf1	2700017A04Rik|AW545819|Ankrd32|Brctd1|Brctx|C730024G01Rik	SMC5-SMC6 complex localization factor 1	protein-coding
mm_30467.1	chr3	154328644	154328663	-	1	NA	intron (NM_010713, intron 1 of 8)	CpG-9681	1907	NM_010713	16875	Mm.15530	NM_010713	ENSMUSG00000096225	Lhx8	L3|Lhx7	LIM homeobox protein 8	protein-coding
mm_106460.1	chr11	120041775	120041790	-	1	NA	promoter-TSS (NM_001198787)	promoter-TSS (NM_001198787)	-1	NM_001198787	11302	Mm.6826	NM_007377	ENSMUSG00000025375	Aatk	AATYK|aatyk1|mKIAA0641	apoptosis-associated tyrosine kinase	protein-coding
mm_109593.1	chr12	112644637	112644684	+	1	NA	promoter-TSS (NM_001161737)	promoter-TSS (NM_001161737)	-168	NM_001161737	30954	Mm.289812	NM_013929	ENSMUSG00000064326	Siva1	CD27bp|Siva	SIVA1, apoptosis-inducing factor	protein-coding
mm_159519.1	chr4	61228348	61228348	-	1	NA	promoter-TSS (NM_001134674)	promoter-TSS (NM_001134674)	-62	NM_001134674	100039089	Mm.443549	NM_001134674	ENSMUSG00000089873	Mup13	Gm13513|Mup11|OTTMUSG00000012492	major urinary protein 13	protein-coding
mm_84557.1	chr9	67713493	67713496	-	1	NA	Intergenic	Intergenic	14286	NR_106100	102466824		NR_106100	ENSMUSG00000098937	Mir7241	Gm27918|mmu-mir-7241	microRNA 7241	ncRNA
mm_41917.1	chr5	105599617	105599621	+	1	NA	intron (NM_133897, intron 3 of 3)	intron (NM_133897, intron 3 of 3)	80148	NM_133897	100604	Mm.319847	NM_133897	ENSMUSG00000054720	Lrrc8c	AD158|AI326115|E430036I04Rik|fad158	leucine rich repeat containing 8 family, member C	protein-coding
mm_117954.1	chr13	99444444	99444488	-	1	NA	intron (NM_008634, intron 2 of 6)	intron (NM_008634, intron 2 of 6)	-31640	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_73179.1	chr8	95058387	95058392	+	1	NA	intron (NM_001042715, intron 3 of 17)	intron (NM_001042715, intron 3 of 17)	3286	NM_001042715	330830	Mm.277112	NM_001042715	ENSMUSG00000031786	Drc7	Ccdc135|Gm770|SRG-L|SRG-S	dynein regulatory complex subunit 7	protein-coding
mm_118842.1	chr14	25650512	25650520	+	1	NA	intron (NM_001310666, intron 12 of 23)	intron (NM_001310666, intron 12 of 23)	-43654	NM_134084	105675	Mm.41656	NM_134084	ENSMUSG00000021868	Ppif	AW457192|CyP-D|CyP-F|CypD|PPIase	peptidylprolyl isomerase F (cyclophilin F)	protein-coding
mm_110453.1	chr12	51637312	51637315	-	1	NA	intron (NM_052973, intron 8 of 17)	intron (NM_052973, intron 8 of 17)	43972	NM_001198835	12810	Mm.21325	NM_007728	ENSMUSG00000020953	Coch	AW122937|Coch-5B2|D12H14S564E	cochlin	protein-coding
mm_79440.1	chr9	56090016	56090060	+	1	NA	promoter-TSS (NM_011193)	promoter-TSS (NM_011193)	62	NM_011193	19200	Mm.2534	NM_011193	ENSMUSG00000032322	Pstpip1	CD2BP1|def-2	proline-serine-threonine phosphatase-interacting protein 1	protein-coding
mm_165737.1	chr3	107211425	107211431	-	1	NA	exon (NM_001111143, exon 9 of 9)	exon (NM_001111143, exon 9 of 9)	10304	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_140330.1	chr17	86754123	86754133	+	1	NA	5' UTR (NM_010137, exon 1 of 16)	5' UTR (NM_010137, exon 1 of 16)	264	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_129229.1	chr15	76614358	76614367	-	1	NA	intron (NM_028064, intron 5 of 11)	intron (NM_028064, intron 5 of 11)	2490	NM_028064	72027	Mm.276829	NM_028064	ENSMUSG00000063354	Slc39a4	1600025H15Rik|AU041686|AWMS2|ZIP4	solute carrier family 39 (zinc transporter), member 4	protein-coding
mm_24456.1	chr3	90613729	90613769	+	1	NA	5' UTR (NM_011313, exon 2 of 3)	5' UTR (NM_011313, exon 2 of 3)	855	NM_011313	20200	Mm.100144	NM_011313	ENSMUSG00000001025	S100a6	2A9|5B10|CALCYCLIN|Cacy|PRA	S100 calcium binding protein A6 (calcyclin)	protein-coding
mm_138702.1	chr17	36000663	36000681	+	1	NA	intron (NR_015618, intron 1 of 1)	intron (NR_015618, intron 1 of 1)	6168	NR_015618	77810	Mm.483143	NR_015618		A930015D03Rik	-	RIKEN cDNA A930015D03 gene	ncRNA
mm_148210.1	chr18	80172915	80172950	-	1	NA	Intergenic	RLTR33|LTR|ERVK	-13307	NR_131039	105246506	Mm.392326	NR_131039		LOC105246506	-	uncharacterized LOC105246506	ncRNA
mm_91931.1	chr10	60454948	60454948	-	1	NA	intron (NR_045556, intron 14 of 68)	intron (NR_045556, intron 14 of 68)	55222	NM_001164374	100302688	Mm.444135	NM_001164374	ENSMUSG00000090439	Gm17455	-	predicted gene, 17455	protein-coding
mm_46266.1	chr5	99964743	99964761	-	1	NA	exon (NM_007516, exon 5 of 8)	exon (NM_007516, exon 5 of 8)	14186	NM_001077266	11991	Mm.150231	NM_007516	ENSMUSG00000000568	Hnrnpd	Auf1|Hnrpd	heterogeneous nuclear ribonucleoprotein D	protein-coding
mm_165490.1	chr2	164613694	164613703	+	1	NA	promoter-TSS (NM_001080550)	promoter-TSS (NM_001080550)	-2	NM_001012725	433502	Mm.376157	NM_001012725	ENSMUSG00000070531	Wfdc6b	WAP6b|Wfdc6	WAP four-disulfide core domain 6B	protein-coding
mm_124910.1	chr15	11000749	11000763	+	1	NA	promoter-TSS (NM_053077)	promoter-TSS (NM_053077)	35	NM_053077	22293	Mm.138278	NM_053077	ENSMUSG00000022243	Slc45a2	Aim-1|Aim1|Dbr|Matp|Oca4|blanc-sale|bls|uw	solute carrier family 45, member 2	protein-coding
mm_61206.1	chr7	64153943	64153949	+	1	NA	5' UTR (NM_001039104, exon 1 of 27)	5' UTR (NM_001039104, exon 1 of 27)	111	NM_001039104	17364	Mm.38875	NM_018752	ENSMUSG00000030523	Trpm1	4732499L03Rik|AI606771|Ltrpc1|Mlsn1	transient receptor potential cation channel, subfamily M, member 1	protein-coding
mm_170659.1	chr2	109109703	109109711	+	1	NA	intron (NM_029790, intron 5 of 5)	intron (NM_029790, intron 5 of 5)	168583	NM_029790	76894	Mm.330451	NM_029790	ENSMUSG00000057234	Mettl15	0610027B03Rik|AI303697|AW049952|Mett5d1	methyltransferase like 15	protein-coding
mm_105023.1	chr11	100461668	100461671	-	1	NA	TTS (NM_172565)	TTS (NM_172565)	11113	NM_172565	217194	Mm.183320	NM_172565	ENSMUSG00000048732	Klhl11	BC011167	kelch-like 11	protein-coding
mm_136241.1	chr16	90934749	90934760	-	1	NA	promoter-TSS (NM_026502)	promoter-TSS (NM_026502)	95	NM_026502	68001	Mm.45374	NM_026502	ENSMUSG00000022972	1110004E09Rik	-	RIKEN cDNA 1110004E09 gene	protein-coding
mm_160548.1	chr9	45195734	45195734	+	1	NA	promoter-TSS (NM_001198971)	promoter-TSS (NM_001198971)	-32	NM_001198971	408059	Mm.249297	NM_001198971	ENSMUSG00000091996	BC049352	-	cDNA sequence BC049352	protein-coding
mm_81881.1	chr9	119341367	119341409	+	1	NA	promoter-TSS (NM_130864)	promoter-TSS (NM_130864)	94	NM_130864	113868	Mm.205266	NM_130864	ENSMUSG00000036138	Acaa1a	Acaa|Acaa1|D9Ertd25e|PTL	acetyl-Coenzyme A acyltransferase 1A	protein-coding
mm_117382.1	chr13	73344246	73344251	-	1	NA	TTS (NR_045293)	TTS (NR_045293)	3136	NR_045293	432777	Mm.415319	NR_045293		D630045M09Rik	AU019512	RIKEN cDNA D630045M09 gene	ncRNA
mm_128972.1	chr15	74832376	74832380	-	1	NA	Intergenic	Intergenic	9265	NM_001033229	110115	Mm.322606	NM_001033229	ENSMUSG00000075604	Cyp11b1	AA389061|CPN1|Cyp11b|Cyp11b-1|FHI	cytochrome P450, family 11, subfamily b, polypeptide 1	protein-coding
mm_140411.1	chr17	87647513	87647516	+	1	NA	intron (NM_008532, intron 8 of 9)	intron (NM_008532, intron 8 of 9)	11535	NM_008532	17075	Mm.4259	NM_008532	ENSMUSG00000045394	Epcam	CD326|EGP|EGP-2|Egp314|Ep-CAM|EpCAM1|GA733-2|Ly74|TROP1|Tacsd1|Tacstd1|gp40	epithelial cell adhesion molecule	protein-coding
mm_75896.1	chr8	70897438	70897448	-	1	NA	promoter-TSS (NM_029751)	promoter-TSS (NM_029751)	0	NM_029751	76808	Mm.379251	NM_029751	ENSMUSG00000045128	Rpl18a	2510019J09Rik	ribosomal protein L18A	protein-coding
mm_59694.1	chr7	28540864	28540886	+	1	NA	promoter-TSS (NM_026716)	promoter-TSS (NM_026716)	-10	NM_026716	68416	Mm.25210	NM_026716	ENSMUSG00000084174	Sycn	0910001K16Rik|1810038B08Rik|SYL	syncollin	protein-coding
mm_60285.1	chr7	43979102	43979118	+	1	NA	intron (NM_010116, intron 2 of 4)	intron (NM_010116, intron 2 of 4)	3049	NM_010116	13648	Mm.440884	NM_010116	ENSMUSG00000059042	Klk1b9	EGF-BP C|Egfbp-3|Egfbp3|KAL|Klk9|kallikrein|mGk-9	kallikrein 1-related peptidase b9	protein-coding
mm_87826.1	chr10	60351055	60351077	+	1	NA	intron (NM_028732, intron 1 of 6)	intron (NM_028732, intron 1 of 6)	4215	NM_028732	74048	Mm.273584	NM_028732	ENSMUSG00000020101	Vsir	4632428N05Rik|Dies1|PD-1H|VISTA	V-set immunoregulatory receptor	protein-coding
mm_77677.1	chr8	125054597	125054685	-	1	NA	intron (NM_174853, intron 1 of 11)	CpG	446	NM_174854	244667	Mm.233504	NM_170596	ENSMUSG00000043051	Disc1	-	disrupted in schizophrenia 1	protein-coding
mm_27904.1	chr3	79509322	79509338	-	1	NA	intron (NM_001162999, intron 5 of 16)	PB1D10|SINE|Alu	58349	NM_001162999	329679	Mm.244005	NM_001162999	ENSMUSG00000061175	Fnip2	D630023B12Rik|mKIAA1450	folliculin interacting protein 2	protein-coding
mm_58469.1	chr7	3390470	3390479	+	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	-3568	NM_133190	81905	Mm.357990	NM_133190	ENSMUSG00000053395	Cacng8	-	calcium channel, voltage-dependent, gamma subunit 8	protein-coding
mm_83968.1	chr9	57158244	57158252	-	1	NA	promoter-TSS (NM_025417)	promoter-TSS (NM_025417)	51	NM_025417	66199	Mm.41687	NM_025417	ENSMUSG00000032299	Commd4	1110039H05Rik	COMM domain containing 4	protein-coding
mm_22142.1	chr2	172043047	172043061	-	1	NA	5' UTR (NM_175631, exon 1 of 3)	5' UTR (NM_175631, exon 1 of 3)	412	NM_175631	228942	Mm.40555	NM_175631	ENSMUSG00000067578	Cbln4	AI848962	cerebellin 4 precursor protein	protein-coding
mm_94762.1	chr11	21219535	21219575	+	1	NA	Intergenic	Intergenic	-19477	NM_139061	245944	Mm.170103	NM_139061	ENSMUSG00000020128	Vps54	Hcc8|Vps54l|mSLP8|wr	VPS54 GARP complex subunit	protein-coding
mm_27744.1	chr3	69127037	69127060	-	1	NA	promoter-TSS (NM_008467)	promoter-TSS (NM_008467)	44	NM_008467	16649	Mm.30601	NM_008467	ENSMUSG00000027782	Kpna4	1110058D08Rik|IPOA3	karyopherin (importin) alpha 4	protein-coding
mm_11994.1	chr2	55597318	55597343	+	1	NA	3' UTR (NM_001304810, exon 3 of 3)	3' UTR (NM_001304810, exon 3 of 3)	161360	NM_008426	16519	Mm.5127	NM_008426	ENSMUSG00000026824	Kcnj3	GIRK-1|GIRK1|Kcnf3|Kir3.1	potassium inwardly-rectifying channel, subfamily J, member 3	protein-coding
mm_119628.1	chr14	51145470	51145525	+	1	NA	exon (NM_011271, exon 2 of 2)	exon (NM_011271, exon 2 of 2)	1270	NM_011271	19752	Mm.235538	NM_011271	ENSMUSG00000035896	Rnase1	AI574248|Rib-1|Rib1	ribonuclease, RNase A family, 1 (pancreatic)	protein-coding
mm_2104.1	chr1	87803934	87803945	+	1	NA	5' UTR (NM_009118, exon 1 of 16)	5' UTR (NM_009118, exon 1 of 16)	259	NM_009118	20215	Mm.1276	NM_009118	ENSMUSG00000056055	Sag	A930001K18Rik|Arr1|Irbp|arrestin	S-antigen, retina and pineal gland (arrestin)	protein-coding
mm_6006.1	chr1	58973387	58973397	-	1	NA	promoter-TSS (NM_172406)	promoter-TSS (NM_172406)	90	NM_172406	70827	Mm.222887	NM_172406	ENSMUSG00000026028	Trak2	2900022D04Rik|4733401O11Rik|AI480836|AW046271|Als2cr3|CALS-C|GRIF-1|GRIF1|OIP98|mKIAA0549	trafficking protein, kinesin binding 2	protein-coding
mm_107071.1	chr12	16904963	16904987	+	1	NA	intron (NM_009072, intron 1 of 32)	PB1D10|SINE|Alu	9997	NM_009072	19878	Mm.276024	NM_009072	ENSMUSG00000020580	Rock2	B230113H15Rik|ROKalpha|Rho-kinase|Rock-II|Rock2m|mKIAA0619	Rho-associated coiled-coil containing protein kinase 2	protein-coding
mm_42787.1	chr5	121463212	121463222	+	1	NA	promoter-TSS (NM_001161627)	promoter-TSS (NM_001161627)	36	NM_001161627	77462	Mm.358781	NM_029912	ENSMUSG00000029452	Tmem116	4930406A18Rik|4930513P12Rik|C030022K24Rik	transmembrane protein 116	protein-coding
mm_59942.1	chr7	30425238	30425245	+	1	NA	exon (NM_172142, exon 4 of 11)	exon (NM_172142, exon 4 of 11)	1937	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_19728.1	chr2	104493743	104493753	-	1	NA	intron (NM_010434, intron 1 of 15)	CpG	741	NM_010434	15259	Mm.257925	NM_010434	ENSMUSG00000027177	Hipk3	DYRK6|FIST3|PKY|mir-1902	homeodomain interacting protein kinase 3	protein-coding
mm_92104.1	chr10	63023763	63023765	-	1	NA	promoter-TSS (NM_001079824)	promoter-TSS (NM_001079824)	85	NM_001079824	432467	Mm.274784	NM_001079824	ENSMUSG00000020069	Hnrnph3	AA693301|AI666703|Hnrph3	heterogeneous nuclear ribonucleoprotein H3	protein-coding
mm_94482.1	chr11	6588228	6588231	+	1	NA	intron (NM_146014, intron 4 of 9)	ID_B1|SINE|B4	17825	NM_001081652	192950	Mm.337771	NM_001081652	ENSMUSG00000041073	Nacad	D230024G13Rik|mKIAA0363	NAC alpha domain containing	protein-coding
mm_104063.1	chr11	86585022	86585041	-	1	NA	promoter-TSS (NR_029738)	promoter-TSS (NR_029738)	-873	NR_029738	387140		NR_029738	ENSMUSG00000065455	Mir21a	Mir21|Mirn21|mmu-mir-21|mmu-mir-21a	microRNA 21a	ncRNA
mm_89563.1	chr10	95412027	95412048	+	1	NA	3' UTR (NM_007706, exon 3 of 3)	3' UTR (NM_007706, exon 3 of 3)	3246	NM_001168657	216233	Mm.474283	NM_007706	ENSMUSG00000020027	Socs2	8030460M17|AI527257|AW108012|CIS2|Cish2|D130043N08Rik|JAB|SOCS-2|SSI-2|hg	suppressor of cytokine signaling 2	protein-coding
mm_86196.1	chr9	119937515	119937558	-	1	NA	promoter-TSS (NM_028735)	promoter-TSS (NM_028735)	22	NM_028976	74498	Mm.104789	NM_028976	ENSMUSG00000032513	Gorasp1	5430411C10Rik|GOLPH5|GRASP65|P65	golgi reassembly stacking protein 1	protein-coding
mm_43556.1	chr5	137610388	137610406	+	1	NA	exon (NM_008788, exon 2 of 9)	exon (NM_008788, exon 2 of 9)	1007	NM_008788	18542	Mm.262345	NM_008788	ENSMUSG00000029718	Pcolce	Astt-2|Astt2|P14|PCPE-1	procollagen C-endopeptidase enhancer protein	protein-coding
mm_145120.1	chr18	44380480	44380554	+	1	NA	promoter-TSS (NM_027490)	promoter-TSS (NM_027490)	17	NM_027490	70640	Mm.87629	NM_027490	ENSMUSG00000024472	Dcp2	2410015D23Rik|5730537H01Rik|AL118268	decapping mRNA 2	protein-coding
mm_28494.1	chr3	92484413	92484419	-	1	NA	exon (NM_009264, exon 2 of 2)	exon (NM_009264, exon 2 of 2)	1465	NM_009264	20753	Mm.331191	NM_009264	ENSMUSG00000050359	Sprr1a	AI528815|SPR1a|mSPRR1A	small proline-rich protein 1A	protein-coding
mm_23039.1	chr3	34760467	34760486	+	1	NA	Intergenic	Intergenic	-11599	NR_110488	102638436	Mm.261793	NR_110488	ENSMUSG00000106519	Gm38509	Peril	predicted gene, 38509	ncRNA
mm_152669.1	chr19	14597758	14597795	-	1	NA	promoter-TSS (NM_001302951)	promoter-TSS (NM_001302951)	407	NM_001302950	21888	Mm.103638	NM_011600	ENSMUSG00000024642	Tle4	5730411M05Rik|AA792082|Bce-1|Bce1|ESTM13|ESTM14|Grg4|X83332|X83333|grg-4	transducin-like enhancer of split 4	protein-coding
mm_69716.1	chr7	140164130	140164174	-	1	NA	Intergenic	Intergenic	-1204	NM_146952	258954	Mm.377769	NM_146952	ENSMUSG00000051180	Olfr522	MOR103-5	olfactory receptor 522	protein-coding
mm_59337.1	chr7	25463653	25463666	+	1	NA	3' UTR (NM_001039186, exon 8 of 8)	3' UTR (NM_001039186, exon 8 of 8)	13966	NM_001039185	26365	Mm.322502	NM_011926	ENSMUSG00000074272	Ceacam1	Bgp|Bgp1|C-CAM|CD66a|Cc1|Cea-1|Cea-7|Cea1|Cea7|Hv-2|Hv2|MHVR|MHVR1|Mhv-1|bb-1|mCEA1|mmCGM1|mmCGM1a|mmCGM2	carcinoembryonic antigen-related cell adhesion molecule 1	protein-coding
mm_46260.1	chr5	99721983	99721986	-	1	NA	intron (NR_030692, intron 1 of 3)	intron (NR_030692, intron 1 of 3)	7076	NR_030692	319818	Mm.295233	NR_030692	ENSMUSG00000089809	A930011G23Rik	-	RIKEN cDNA A930011G23 gene	ncRNA
mm_83829.1	chr9	54068470	54068512	-	1	NA	promoter-TSS (NM_001033535)	promoter-TSS (NM_001033535)	-80	NM_001033535	244882	Mm.325589	NM_001033535	ENSMUSG00000074345	Tnfaip8l3	9930029P06Rik|Gm517	tumor necrosis factor, alpha-induced protein 8-like 3	protein-coding
mm_11012.1	chr2	26581078	26581093	+	1	NA	promoter-TSS (NM_178444)	promoter-TSS (NM_178444)	29	NM_178444	353156	Mm.268933	NM_178444	ENSMUSG00000026921	Egfl7	VE-statin|Zneu1	EGF-like domain 7	protein-coding
mm_152382.1	chr19	10272931	10272933	-	1	NA	intron (NM_198114, intron 1 of 19)	intron (NM_198114, intron 1 of 19)	31945	NM_198114	269060	Mm.329718	NM_198114	ENSMUSG00000035735	Dagla	Nsddr	diacylglycerol lipase, alpha	protein-coding
mm_5847.1	chr1	52963279	52963292	-	1	NA	Intergenic	Intergenic	-10445	NM_144953	67080	Mm.236287	NM_144953	ENSMUSG00000043629	1700019D03Rik	2410136C24Rik|AA410151|smAKAP	RIKEN cDNA 1700019D03 gene	protein-coding
mm_146450.1	chr18	86394811	86394863	+	1	NA	promoter-TSS (NM_144946)	promoter-TSS (NM_144946)	-115	NM_144946	246317	Mm.329578	NM_144946	ENSMUSG00000050321	Neto1	AI851453|Btcl1|C130005O10Rik	neuropilin (NRP) and tolloid (TLL)-like 1	protein-coding
mm_112054.1	chr12	111809941	111809974	-	1	NA	exon (NM_028875, exon 4 of 8)	exon (NM_028875, exon 4 of 8)	3922	NM_028875	74335	Mm.19082	NM_028875	ENSMUSG00000021287	Xrcc3	-	X-ray repair complementing defective repair in Chinese hamster cells 3	protein-coding
mm_68754.1	chr7	121069599	121069610	-	1	NA	intron (NM_030691, intron 2 of 5)	intron (NM_030691, intron 2 of 5)	4926	NM_030691	80719	Mm.160384	NM_030691	ENSMUSG00000035004	Igsf6	-	immunoglobulin superfamily, member 6	protein-coding
mm_73379.1	chr8	105636927	105636979	+	1	NA	intron (NM_181322, intron 1 of 11)	CpG	415	NM_181322	13018	Mm.269474	NM_181322	ENSMUSG00000005698	Ctcf	AW108038	CCCTC-binding factor	protein-coding
mm_85935.1	chr9	112097970	112097978	-	1	NA	intron (NM_001177618, intron 17 of 18)	B4A|SINE|B4	20737	NR_029823	723815		NR_029823	ENSMUSG00000065441	Mir128-2	Mirn128-2|Mirn128b|mir-128-2|mir-128b	microRNA 128-2	ncRNA
mm_128258.1	chr15	36771278	36771291	-	1	NA	3' UTR (NM_001253807, exon 5 of 5)	3' UTR (NM_001253807, exon 5 of 5)	19648	NM_001253807	22631	Mm.3360	NM_011740	ENSMUSG00000022285	Ywhaz	1110013I11Rik|14-3-3zeta|AI596267|AL022924|AU020854	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide	protein-coding
mm_165500.1	chr2	167382004	167382004	+	1	NA	Intergenic	Intergenic	-32826	NM_019835	56336	Mm.200886	NM_019835	ENSMUSG00000017929	B4galt5	9430078I07Rik|AW049941|AW539721	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 5	protein-coding
mm_114496.1	chr13	69959870	69959870	+	1	NA	promoter-TSS (NR_138559)	promoter-TSS (NR_138559)	37	NR_138559	67550	Mm.158159	NR_138559		4933416O17Rik	-	RIKEN cDNA 4933416O17 gene	ncRNA
mm_92445.1	chr10	77607114	77607119	-	1	NA	intron (NM_001301671, intron 1 of 3)	intron (NM_001301671, intron 1 of 3)	518	NM_001301671	20610	Mm.24433	NM_019929	ENSMUSG00000020265	Sumo3	2810014B19Rik|D10Ertd345e|SMT3A|SUMO-3|Smt3h1	small ubiquitin-like modifier 3	protein-coding
mm_64889.1	chr7	15922336	15922357	-	1	NA	promoter-TSS (NM_009156)	promoter-TSS (NM_009156)	25	NM_009156	20364	Mm.42829	NM_009156	ENSMUSG00000041571	Selenow	Sepw1|selW	selenoprotein W	protein-coding
mm_8003.1	chr1	134549664	134549687	-	1	NA	promoter-TSS (NM_001145300)	promoter-TSS (NM_001145300)	7	NM_001145300	71001	Mm.158529	NM_183292	ENSMUSG00000046367	Mgat4e	4931440L10Rik	MGAT4 family, member E	protein-coding
mm_130839.1	chr15	101851981	101851984	-	1	NA	Intergenic	Intergenic	-1196	NM_008473	16678	Mm.183137	NM_008473	ENSMUSG00000046834	Krt1	Krt-2.1|Krt2-1|Krt86	keratin 1	protein-coding
mm_79340.1	chr9	53367735	53367756	+	1	NA	intron (NM_176846, intron 5 of 5)	intron (NM_176846, intron 5 of 5)	-16278	NM_212445	68304	Mm.427519	NM_212445	ENSMUSG00000034487	Kdelc2	2010004J24Rik|4833410J10Rik|AW549401	KDEL (Lys-Asp-Glu-Leu) containing 2	protein-coding
mm_78174.1	chr9	21165721	21165762	+	1	NA	promoter-TSS (NM_183408)	promoter-TSS (NM_183408)	27	NM_183408	18577	Mm.191749	NM_019798	ENSMUSG00000032177	Pde4a	D9Ertd60e|Dpde2	phosphodiesterase 4A, cAMP specific	protein-coding
mm_9903.1	chr1	187143073	187143104	-	1	NA	intron (NM_028848, intron 5 of 9)	intron (NM_028848, intron 5 of 9)	17950	NR_040554	69308	Mm.490882	NR_040554	ENSMUSG00000089730	1700007P06Rik	-	RIKEN cDNA 1700007P06 gene	ncRNA
mm_10940.1	chr2	25500773	25500783	+	1	NA	promoter-TSS (NM_027062)	promoter-TSS (NM_027062)	0	NM_013908	30839	Mm.29170	NM_013908	ENSMUSG00000015095	Fbxw5	AI159739|Fbw5	F-box and WD-40 domain protein 5	protein-coding
mm_118879.1	chr14	25869611	25869621	+	1	NA	intron (NM_013469, intron 2 of 14)	intron (NM_013469, intron 2 of 14)	27461	NM_013469	11744	Mm.294083	NM_013469	ENSMUSG00000021866	Anxa11	A830099O17Rik|Anx11	annexin A11	protein-coding
mm_53184.1	chr6	125432732	125432752	+	1	NA	Intergenic	Intergenic	-52238	NM_198604	213522	Mm.333396	NM_198604	ENSMUSG00000038167	Plekhg6	BC026778|Gm155	pleckstrin homology domain containing, family G (with RhoGef domain) member 6	protein-coding
mm_16968.1	chr2	17707024	17707026	-	1	NA	intron (NM_028757, intron 2 of 6)	intron (NM_028757, intron 2 of 6)	24043	NM_028757	74103	Mm.120298	NM_028757	ENSMUSG00000053702	Nebl	1200007O21Rik|A630080F05Rik|BB140644|D830029A09Rik|Lnebl	nebulette	protein-coding
mm_152797.1	chr19	21630763	21630783	-	1	NA	intron (NM_025423, intron 1 of 3)	intron (NM_025423, intron 1 of 3)	22018	NM_025423	66206	Mm.272430	NM_025423	ENSMUSG00000035171	1110059E24Rik	-	RIKEN cDNA 1110059E24 gene	protein-coding
mm_17552.1	chr2	30093608	30093641	-	1	NA	promoter-TSS (NM_025428)	promoter-TSS (NM_025428)	11	NM_025428	66220	Mm.22538	NM_025428	ENSMUSG00000015335	Zdhhc12	1190004A01Rik	zinc finger, DHHC domain containing 12	protein-coding
mm_52341.1	chr6	110736265	110736275	+	1	NA	intron (NM_001346640, intron 1 of 10)	B1_Mus1|SINE|Alu	90672	NM_177328	108073	Mm.240881	NM_177328	ENSMUSG00000056755	Grm7	6330570A01Rik|BB176677|C030018L03|E130018M02Rik|Gpr1g|Gprc1g|SMN2|Tg(SMN2)89Ahmb|mGluR7	glutamate receptor, metabotropic 7	protein-coding
mm_92342.1	chr10	75835542	75835597	-	1	NA	promoter-TSS (NM_010361)	promoter-TSS (NM_010361)	-688	NM_010361	14872	Mm.24118	NM_010361	ENSMUSG00000033318	Gstt2	AI266894|Yrs|mGSTT2	glutathione S-transferase, theta 2	protein-coding
mm_144199.1	chr18	9212155	9212171	+	1	NA	promoter-TSS (NM_008058)	promoter-TSS (NM_008058)	-693	NM_008058	14370	Mm.184289	NM_008058	ENSMUSG00000036904	Fzd8	Fz8	frizzled class receptor 8	protein-coding
mm_129849.1	chr15	83170169	83170186	-	1	NA	intron (NM_029787, intron 1 of 8)	intron (NM_029787, intron 1 of 8)	2031	NM_029787	109754	Mm.22560	NM_029787	ENSMUSG00000018042	Cyb5r3	0610016L08Rik|2500002N19Rik|C85115|Dia-1|Dia1|WU:AL591952.1-001|WU:AL591952.1-002|WU:AL591952.1-003|WU:Cyb5r3	cytochrome b5 reductase 3	protein-coding
mm_117232.1	chr13	64274923	64274947	-	1	NA	promoter-TSS (NM_172587)	promoter-TSS (NM_172587)	53	NM_172587	218294	Mm.25335	NM_172587	ENSMUSG00000033102	Cdc14b	2810432N10Rik|A530086E13Rik|AA472821|CDC14B3|Cdc14B1	CDC14 cell division cycle 14B	protein-coding
mm_119612.1	chr14	51105413	51105485	+	1	NA	3' UTR (NM_201239, exon 2 of 2)	3' UTR (NM_201239, exon 2 of 2)	9449	NM_201239	58809	Mm.202665	NM_021472	ENSMUSG00000021876	Rnase4	C730049F20Rik|Rab1	ribonuclease, RNase A family 4	protein-coding
mm_120533.1	chr14	67233183	67233208	+	1	NA	promoter-TSS (NM_001276387)	promoter-TSS (NM_001276387)	-97	NM_010095	13592	Mm.319947	NM_010095	ENSMUSG00000022053	Ebf2	D14Ggc1e|EBF-2|Mmot1|O/E-3|OE-3	early B cell factor 2	protein-coding
mm_98508.1	chr11	94952278	94952286	+	1	NA	3' UTR (NM_007742, exon 51 of 51)	3' UTR (NM_007742, exon 51 of 51)	-15311	NM_018792	54388	Mm.30482	NM_018792	ENSMUSG00000038994	Hils1	H1.9|TISP64	histone H1-like protein in spermatids 1	protein-coding
mm_68002.1	chr7	100938211	100938226	-	1	NA	exon (NM_183168, exon 3 of 3)	exon (NM_183168, exon 3 of 3)	-6057	NM_001081116	207212	Mm.29954	NM_001081116	ENSMUSG00000032875	Arhgef17	8030463K16|AI428794|AW558066|BC035332|mKIAA0337	Rho guanine nucleotide exchange factor (GEF) 17	protein-coding
mm_164927.1	chr18	80253294	80253305	+	1	NA	Intergenic	RLTR35B_MM|LTR|ERVL	-1946	NM_001164420	66943	Mm.29247	NM_025861	ENSMUSG00000034006	Pqlc1	2310009N05Rik|4933425L21Rik|5730564E11Rik|C78974	PQ loop repeat containing 1	protein-coding
mm_130828.1	chr15	101846275	101846285	-	1	NA	intron (NM_008473, intron 8 of 8)	intron (NM_008473, intron 8 of 8)	4506	NM_008473	16678	Mm.183137	NM_008473	ENSMUSG00000046834	Krt1	Krt-2.1|Krt2-1|Krt86	keratin 1	protein-coding
mm_136066.1	chr16	84735217	84735266	-	1	NA	promoter-TSS (NM_017404)	promoter-TSS (NM_017404)	61	NM_017404	27393	Mm.103655	NM_017404	ENSMUSG00000022889	Mrpl39	C21orf8|MRP-L5|ORF22|Rpml5	mitochondrial ribosomal protein L39	protein-coding
mm_156441.1	chrX	142228285	142228306	+	1	NA	promoter-TSS (NM_001290533)	promoter-TSS (NM_001290533)	118	NM_172782	237082	Mm.41899	NM_172782	ENSMUSG00000042271	Nxt2	6330587F24Rik|AI787442|P15-2	nuclear transport factor 2-like export factor 2	protein-coding
mm_63646.1	chr7	128688451	128688472	+	1	NA	promoter-TSS (NM_001346517)	promoter-TSS (NM_001346517)	-409	NM_001346517	101490	Mm.490344	NM_178641	ENSMUSG00000042105	Inpp5f	5830435P03Rik|AI115354|AW561896|SAC2|cI-27|hSAC2|mKIAA0966	inositol polyphosphate-5-phosphatase F	protein-coding
mm_42351.1	chr5	114911492	114911513	+	1	NA	3' UTR (NM_011854, exon 6 of 6)	3' UTR (NM_011854, exon 6 of 6)	-11738	NM_145209	231655	Mm.95479	NM_145209	ENSMUSG00000041827	Oasl1	7530414C13Rik|oasl9	2'-5' oligoadenylate synthetase-like 1	protein-coding
mm_92010.1	chr10	62340158	62340181	-	1	NA	promoter-TSS (NR_038038)	promoter-TSS (NR_038038)	252	NM_001146100	15275	Mm.196605	NM_010438	ENSMUSG00000037012	Hk1	BB404130|Hk-1|Hk1-s|dea|mHk1-s	hexokinase 1	protein-coding
mm_95434.1	chr11	50210945	50210958	+	1	NA	promoter-TSS (NM_011018)	promoter-TSS (NM_011018)	-131	NM_011018	18412	Mm.40828	NM_011018	ENSMUSG00000015837	Sqstm1	A170|OSF-6|Osi|STAP|STONE14|p62	sequestosome 1	protein-coding
mm_87144.1	chr10	34483547	34483599	+	1	NA	5' UTR (NM_001159544, exon 1 of 8)	5' UTR (NM_001159544, exon 1 of 8)	173	NM_010237	14302	Mm.332432	NM_010237	ENSMUSG00000019779	Frk	BSK|BSK/IYK|C85044|GTK|RAK	fyn-related kinase	protein-coding
mm_30944.1	chr4	33063279	33063297	+	1	NA	exon (NM_008076, exon 1 of 9)	exon (NM_008076, exon 1 of 9)	176	NM_008076	14409	Mm.6227	NM_008076	ENSMUSG00000023267	Gabrr2	-	gamma-aminobutyric acid (GABA) C receptor, subunit rho 2	protein-coding
mm_170993.1	chr2	75191758	75191772	-	1	NA	Intergenic	Intergenic	252414	NR_040635	77269	Mm.389278	NR_040635		9430019J16Rik	-	RIKEN cDNA 9430019J16 gene	ncRNA
mm_89749.1	chr10	99261870	99261891	+	1	NA	Intergenic	CpG	-1351	NM_026268	67603	Mm.1791	NM_026268	ENSMUSG00000019960	Dusp6	1300019I03Rik|MKP-3|MKP3|PYST1	dual specificity phosphatase 6	protein-coding
mm_82480.1	chr9	17556317	17556327	-	1	NA	Intergenic	RLTR16|LTR|ERVK	-735945	NM_025844	66917	Mm.103534	NM_025844	ENSMUSG00000001774	Chordc1	1110001O09Rik|AA409036|Chp-1|morgana	cysteine and histidine-rich domain (CHORD)-containing, zinc-binding protein 1	protein-coding
mm_128006.1	chr15	12962272	12962283	-	1	NA	Intergenic	RLTR17|LTR|ERVK	137462	NM_001130149	14000	Mm.293142	NM_026799	ENSMUSG00000022191	Drosha	1110013A17Rik|AI874853|Etohi2|Rn3|Rnasen	drosha, ribonuclease type III	protein-coding
mm_152939.1	chr19	28742579	28742588	-	1	NA	Intergenic	Intergenic	-62506	NM_175459	226075	Mm.223508	NM_175459	ENSMUSG00000052942	Glis3	4833409N03Rik|E330013K21Rik	GLIS family zinc finger 3	protein-coding
mm_90837.1	chr10	8518476	8518491	-	1	NA	5' UTR (NM_177387, exon 1 of 8)	5' UTR (NM_177387, exon 1 of 8)	342	NM_177387	338362	Mm.41163	NM_177387	ENSMUSG00000047712	Ust	D930010O20Rik|UA2OST	uronyl-2-sulfotransferase	protein-coding
mm_126138.1	chr15	78348068	78348079	+	1	NA	promoter-TSS (NR_106138)	promoter-TSS (NR_106138)	-526	NR_106137	102465776		NR_106137	ENSMUSG00000098996	Mir7676-1	Gm27600|mmu-mir-7676-1	microRNA 7676-1	ncRNA
mm_110767.1	chr12	70232344	70232348	-	1	NA	intron (NR_045174, intron 2 of 4)	intron (NR_045174, intron 2 of 4)	4505	NR_045174	414124	Mm.416164	NR_045174	ENSMUSG00000085298	F730035M05Rik	-	RIKEN cDNA F730035M05 gene	ncRNA
mm_82768.1	chr9	26923061	26923086	-	1	NA	promoter-TSS (NM_001281475)	promoter-TSS (NM_001281475)	8	NM_001281475	382064	Mm.335028	NM_001177509	ENSMUSG00000079644	Gm1110	-	predicted gene 1110	protein-coding
mm_82835.1	chr9	31150581	31150591	-	1	NA	3' UTR (NM_009691, exon 16 of 16)	3' UTR (NM_009691, exon 16 of 16)	-18787	NM_011176	19143	Mm.243926	NM_011176	ENSMUSG00000031995	St14	Epithin|MT-SP1|Prss14|Tmprss14|mCAP3|matriptase	suppression of tumorigenicity 14 (colon carcinoma)	protein-coding
mm_30960.1	chr4	33924637	33924651	+	1	NA	promoter-TSS (NM_007726)	promoter-TSS (NM_007726)	12	NM_007726	12801	Mm.7992	NM_007726	ENSMUSG00000044288	Cnr1	CB-R|CB1|CB1R	cannabinoid receptor 1 (brain)	protein-coding
mm_110417.1	chr12	46785270	46785272	-	1	NA	intron (NM_021361, intron 2 of 4)	L1_Mur3|LINE|L1	33504	NM_021361	664883	Mm.247195	NM_021361	ENSMUSG00000021047	Nova1	9430099M15Rik|G630039L02|Nova-1	neuro-oncological ventral antigen 1	protein-coding
mm_142832.1	chr17	51782604	51782615	-	1	NA	intron (NM_009122, intron 7 of 10)	intron (NM_009122, intron 7 of 10)	29445	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_64525.1	chr7	143978098	143978140	+	1	NA	intron (NR_037302, intron 5 of 5)	CpG	-31135	NR_037292	100526562		NR_037292	ENSMUSG00000093221	Mir3105	mmu-mir-3105	microRNA 3105	ncRNA
mm_66313.1	chr7	39910945	39910952	-	1	NA	Intergenic	Intergenic	393182	NM_001004139	70227	Mm.333800	NM_001004139	ENSMUSG00000068959	Zfp619	3000002G13Rik	zinc finger protein 619	protein-coding
mm_20337.1	chr2	127584669	127584703	-	1	NA	promoter-TSS (NM_028141)	promoter-TSS (NM_028141)	-9	NM_028141	72180	Mm.46715	NM_028141	ENSMUSG00000034800	Zfp661	2810405K07Rik|A1-5|Znf2	zinc finger protein 661	protein-coding
mm_69994.1	chr7	142385594	142385611	-	1	NA	exon (NM_009983, exon 2 of 9)	exon (NM_009983, exon 2 of 9)	2268	NM_009983	13033	Mm.231395	NM_009983	ENSMUSG00000007891	Ctsd	CD|CatD	cathepsin D	protein-coding
mm_23031.1	chr3	34650223	34650233	+	1	NA	5' UTR (NM_011443, exon 1 of 1)	5' UTR (NM_011443, exon 1 of 1)	233	NM_011443	20674	Mm.65396	NM_011443	ENSMUSG00000074637	Sox2	Sox-2|lcc|ysb	SRY (sex determining region Y)-box 2	protein-coding
mm_95743.1	chr11	54702087	54702090	+	1	NA	Intergenic	Intergenic	85615	NM_178626	72729	Mm.29476	NM_178626	ENSMUSG00000052298	Cdc42se2	2810404F18Rik|AA408783|AA536669|SPEC2	CDC42 small effector 2	protein-coding
mm_17524.1	chr2	29252923	29252949	-	1	NA	promoter-TSS (NR_029460)	promoter-TSS (NR_029460)	57	NR_029460	76220	Mm.330108	NR_029460	ENSMUSG00000079499	6530402F18Rik	mKIAA1857	RIKEN cDNA 6530402F18 gene	ncRNA
mm_97681.1	chr11	79993193	79993232	+	1	NA	5' UTR (NM_001163018, exon 1 of 15)	5' UTR (NM_001163018, exon 1 of 15)	106	NM_199196	52615	Mm.283410	NM_199196	ENSMUSG00000017548	Suz12	2610028O16Rik|AI195385|AU016842|AW536442|D11Ertd530e|mKIAA0160	suppressor of zeste 12 homolog (Drosophila)	protein-coding
mm_13200.1	chr2	93453470	93453505	+	1	NA	promoter-TSS (NM_001271462)	promoter-TSS (NM_001271462)	668	NR_040533	100038525	Mm.440596	NR_040532	ENSMUSG00000075025	Gm10804	ENSMUSG00000075025	predicted gene 10804	ncRNA
mm_168500.1	chr1	152902115	152902116	-	1	NA	intron (NM_001005507, intron 1 of 21)	CpG	531	NM_001160256	226517	Mm.270775	NM_001005507	ENSMUSG00000042772	Smg7	9430023P16Rik|mKIAA0250	Smg-7 homolog, nonsense mediated mRNA decay factor (C. elegans)	protein-coding
mm_37239.1	chr4	118134674	118134687	-	1	NA	5' UTR (NM_001285520, exon 1 of 12)	5' UTR (NM_001285520, exon 1 of 12)	266	NM_001285520	20441	Mm.251002	NM_009176	ENSMUSG00000028538	St3gal3	ST3GalIII|ST3N|Siat3|Siat6	ST3 beta-galactoside alpha-2,3-sialyltransferase 3	protein-coding
mm_15858.1	chr2	164805238	164805270	+	1	NA	promoter-TSS (NM_133240)	promoter-TSS (NM_133240)	140	NM_178375	67538	Mm.33184	NM_178375	ENSMUSG00000045822	Zswim3	4921517A06Rik|C86566	zinc finger SWIM-type containing 3	protein-coding
mm_79021.1	chr9	45906514	45906552	+	1	NA	promoter-TSS (NM_008794)	promoter-TSS (NM_008794)	-36	NM_008794	18554	Mm.3255	NM_008794	ENSMUSG00000035382	Pcsk7	AA959856|PC7|SPC7	proprotein convertase subtilisin/kexin type 7	protein-coding
mm_75258.1	chr8	40591835	40591842	-	1	NA	intron (NM_001040699, intron 4 of 13)	intron (NM_001040699, intron 4 of 13)	42954	NM_001040699	54384	Mm.294871	NM_019433	ENSMUSG00000039431	Mtmr7	-	myotubularin related protein 7	protein-coding
mm_169865.1	chr16	33844671	33844679	+	1	NA	intron (NM_010580, intron 1 of 14)	intron (NM_010580, intron 1 of 14)	15010	NM_001145884	16419	Mm.6424	NM_010580	ENSMUSG00000022817	Itgb5	AA475909|AI874634|ESTM23|[b]-5|[b]5|[b]5A|[b]5B|beta-5|beta5	integrin beta 5	protein-coding
mm_117634.1	chr13	92173868	92173873	-	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	-180913	NM_010049	13361	Mm.23695	NM_010049	ENSMUSG00000021707	Dhfr	8430436I03Rik|AA607882|AI662710|AW555094	dihydrofolate reductase	protein-coding
mm_108481.1	chr12	83660591	83660645	+	1	NA	exon (NM_027349, exon 9 of 19)	exon (NM_027349, exon 9 of 19)	-27945	NM_008943	19164	Mm.998	NM_008943	ENSMUSG00000019969	Psen1	Ad3h|PS-1|PS1|S182	presenilin 1	protein-coding
mm_80713.1	chr9	92275691	92275702	+	1	NA	promoter-TSS (NM_001195084)	promoter-TSS (NM_001195084)	94	NM_001195084	18828	Mm.10306	NM_008880	ENSMUSG00000032372	Plscr2	-	phospholipid scramblase 2	protein-coding
mm_25255.1	chr3	104771735	104771742	+	1	NA	intron (NM_183224, intron 6 of 6)	intron (NM_183224, intron 6 of 6)	5809	NM_183224	329731	Mm.389494	NM_183224	ENSMUSG00000055865	Fam19a3	7530404M11Rik|TAFA3|Tafa-3	family with sequence similarity 19, member A3	protein-coding
mm_68597.1	chr7	116198488	116198517	-	1	NA	promoter-TSS (NM_001305189)	promoter-TSS (NM_001305189)	59	NM_001305189	233765	Mm.3741	NM_172743	ENSMUSG00000045659	Plekha7	A430081P20Rik|AI414265	pleckstrin homology domain containing, family A member 7	protein-coding
mm_110936.1	chr12	76474086	76474091	-	1	NA	Intergenic	Intergenic	29591	NR_028520	100041694	Mm.259350	NR_028520		Gm10451	ENSMUSG00000073000	predicted gene 10451	ncRNA
mm_122337.1	chr14	37135127	37135141	-	1	NA	promoter-TSS (NM_001199122)	promoter-TSS (NM_001199122)	5	NM_001199122	66092	Mm.182912	NM_078478	ENSMUSG00000041028	Ghitm	1010001P14Rik|C77840|MICS1|PTD010|Tmbim5	growth hormone inducible transmembrane protein	protein-coding
mm_92027.1	chr10	62455681	62455692	-	1	NA	3' UTR (NM_001113355, exon 9 of 9)	3' UTR (NM_001113355, exon 9 of 9)	-5993	NM_181423	338359	Mm.235898	NM_181423	ENSMUSG00000020079	Supv3l1	6330443E10Rik	suppressor of var1, 3-like 1 (S. cerevisiae)	protein-coding
mm_3593.1	chr1	151428726	151428736	+	1	NA	promoter-TSS (NM_025819)	promoter-TSS (NM_025819)	83	NM_026876	98685	Mm.289373	NM_026876	ENSMUSG00000053286	Trmt1l	1190005F20Rik|AW226554|C1orf25|Trm1-like|Trm1l	tRNA methyltransferase 1 like	protein-coding
mm_2468.1	chr1	105663870	105663920	+	1	NA	promoter-TSS (NM_013784)	promoter-TSS (NM_013784)	34	NM_173187	227446	Mm.337339	NM_029349	ENSMUSG00000026319	2310035C23Rik	6430401N10|Kiaa1468|mKIAA1468	RIKEN cDNA 2310035C23 gene	protein-coding
mm_46689.1	chr5	110058013	110058053	-	1	NA	Intergenic	Intergenic	-41936	NM_207279	403178	Mm.297057	NM_207279	ENSMUSG00000064247	Plcxd1	A330045H12Rik|Gm576	phosphatidylinositol-specific phospholipase C, X domain containing 1	protein-coding
mm_16300.1	chr2	174289525	174289535	+	1	NA	intron (NR_002846, intron 1 of 4)	intron (NR_002846, intron 1 of 4)	5210	NM_022000	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_125195.1	chr15	32778901	32778932	+	1	NA	Intergenic	Intergenic	-141807	NM_008304	15529	Mm.234266	NM_008304	ENSMUSG00000022261	Sdc2	4833414L08Rik|AA960457|Hspg1|Synd2|syndecan-2	syndecan 2	protein-coding
mm_36431.1	chr4	82294431	82294458	-	1	NA	3' UTR (NM_001113209, exon 12 of 12)	3' UTR (NM_001113209, exon 12 of 12)	211335	NM_001286127	18028	Mm.317947	NM_008687	ENSMUSG00000008575	Nfib	6720429L07Rik|CTF|E030026I10Rik|NF-I/B|NF1-B|NFI-B	nuclear factor I/B	protein-coding
mm_99388.1	chr11	102097503	102097506	+	1	NA	Intergenic	Intergenic	3796	NM_008918	19064	Mm.1269	NM_008918	ENSMUSG00000017316	Ppy	AV061413|IGSPP|PP	pancreatic polypeptide	protein-coding
mm_65906.1	chr7	30193121	30193143	-	1	NA	intron (NM_009795, intron 2 of 10)	intron (NM_009795, intron 2 of 10)	1916	NM_009795	12336	Mm.439782	NM_009795	ENSMUSG00000001794	Capns1	Capa-4|Capa4|Capn4|D7Ertd146e	calpain, small subunit 1	protein-coding
mm_88111.1	chr10	69151428	69151449	+	1	NA	Intergenic	Intergenic	-57114	NM_001252636	69288	Mm.26659	NM_001081347	ENSMUSG00000019944	Rhobtb1	1700008H16Rik|3110048G13Rik|AI173445|AI573858|AV350930	Rho-related BTB domain containing 1	protein-coding
mm_159787.1	chr5	107507384	107507384	+	1	NA	exon (NM_001007574, exon 6 of 6)	exon (NM_001007574, exon 6 of 6)	9605	NM_001168557	231570	Mm.261891	NM_001007574	ENSMUSG00000044060	A830010M20Rik	AI849226|Kiaa1107|mKIAA1107	RIKEN cDNA A830010M20 gene	protein-coding
mm_137357.1	chr17	25308643	25308647	+	1	NA	promoter-TSS (NM_053259)	promoter-TSS (NM_053259)	-1	NM_053259	114661	Mm.207081	NM_053259	ENSMUSG00000024171	Prss28	Isp1|mIsp-1	protease, serine 28	protein-coding
mm_86460.1	chr10	4355681	4355685	+	1	NA	exon (NM_031185, exon 3 of 4)	exon (NM_031185, exon 3 of 4)	32425	NM_001033466	381990	Mm.262466	NM_001033466	ENSMUSG00000075327	Zbtb2	Gm1103	zinc finger and BTB domain containing 2	protein-coding
mm_75475.1	chr8	48555201	48555244	-	1	NA	intron (NM_011857, intron 2 of 28)	CpG	119468	NM_001145937	23965	Mm.42191	NM_011857	ENSMUSG00000031561	Tenm3	2610100B16Rik|Odz1|Odz3|Ten-m3|mKIAA1455	teneurin transmembrane protein 3	protein-coding
mm_173095.1	chrX	151801088	151801099	+	1	NA	Intergenic	Intergenic	-2189	NM_021523	59026	Mm.27372	NM_021523	ENSMUSG00000025261	Huwe1	5430439H10Rik|AU041296|Arf-bp1|C430014N20Rik|C80292|Gm1718|Ib772|LASU1|Mule|Ureb1	HECT, UBA and WWE domain containing 1	protein-coding
mm_170239.1	chr17	89751853	89751858	+	1	NA	Intergenic	L1Md_F3|LINE|L1	336513	NM_001346962	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_172718.1	chr8	70896289	70896291	-	1	NA	promoter-TSS (NR_002901)	promoter-TSS (NR_002901)	-434	NR_002901	104370		NR_002901		Snora68	MBI-30|Rnu68	small nucleolar RNA, H/ACA box 68	snoRNA
mm_86416.1	chr10	3452535	3452550	+	1	NA	intron (NM_133485, intron 3 of 3)	B4A|SINE|B4	86392	NM_133485	76142	Mm.308126	NM_133485	ENSMUSG00000040653	Ppp1r14c	6330514J04Rik|KEPI	protein phosphatase 1, regulatory (inhibitor) subunit 14c	protein-coding
mm_110835.1	chr12	72846213	72846224	-	1	NA	Intergenic	Intergenic	71547	NM_029444	75801	Mm.242892	NM_029444	ENSMUSG00000021098	4930447C04Rik	4921504I02Rik|A930035O15Rik|Six6OS|Six6as|Six6os1	RIKEN cDNA 4930447C04 gene	protein-coding
mm_157355.1	chrX	37048693	37048703	-	1	NA	promoter-TSS (NM_173779)	promoter-TSS (NM_173779)	-147	NM_173779	245381	Mm.123697	NM_173779	ENSMUSG00000044400	Sowahd	A630014H24Rik|Ankrd58	sosondowah ankyrin repeat domain family member D	protein-coding
mm_159552.1	chr4	102870549	102870549	+	1	NA	exon (NM_144906, exon 7 of 24)	exon (NM_144906, exon 7 of 24)	110414	NM_001285859	73094	Mm.54201	NM_144906	ENSMUSG00000028524	Sgip1	3110007P09Rik|SGIP1alpha|gag	SH3-domain GRB2-like (endophilin) interacting protein 1	protein-coding
mm_92808.1	chr10	81378829	81378844	-	1	NA	promoter-TSS (NM_019757)	promoter-TSS (NM_019757)	-466	NM_019757	56371	Mm.24202	NM_019757	ENSMUSG00000020235	Fzr1	AW108046|Cdh1|FZR|FZR2|Fyr|HCDH|HCDH1	fizzy/cell division cycle 20 related 1 (Drosophila)	protein-coding
mm_6543.1	chr1	75125229	75125255	-	1	NA	TTS (NM_194333)	TTS (NM_194333)	8648	NM_194333	22626	Mm.68157	NM_194333	ENSMUSG00000026205	Slc23a3	SVCT3|Yspl1	solute carrier family 23 (nucleobase transporters), member 3	protein-coding
mm_97183.1	chr11	75563654	75563666	+	1	NA	exon (NM_001199283, exon 9 of 14)	exon (NM_001199283, exon 9 of 14)	12231	NR_039553	100628624		NR_039553	ENSMUSG00000093100	Mir3971	mmu-mir-3971|mu-mir-3971	microRNA 3971	ncRNA
mm_113426.1	chr13	34130585	34130606	+	1	NA	promoter-TSS (NM_023716)	promoter-TSS (NM_023716)	-241	NM_023716	73710	Mm.379227	NM_023716	ENSMUSG00000045136	Tubb2b	2410129E14Rik|brdp	tubulin, beta 2B class IIB	protein-coding
mm_106153.1	chr11	116617601	116617624	-	1	NA	intron (NM_172572, intron 1 of 18)	intron (NM_172572, intron 1 of 18)	6640	NM_001167680	217344	Mm.89695	NM_172572	ENSMUSG00000020806	Rhbdf2	4732465I17Rik|Rhbdl6|cub	rhomboid 5 homolog 2	protein-coding
mm_116369.1	chr13	40731593	40731632	-	1	NA	intron (NM_001301674, intron 2 of 7)	CpG	-1155	NM_001122948	21418	Mm.85544	NM_011547	ENSMUSG00000021359	Tfap2a	AP-2|AP2alpha|Ap-2 (a)|Ap2|Ap2tf|Tcfap2a	transcription factor AP-2, alpha	protein-coding
mm_28735.1	chr3	95736597	95736650	-	1	NA	exon (NM_007899, exon 7 of 11)	exon (NM_007899, exon 7 of 11)	-1650	NR_105981	102466787		NR_105981	ENSMUSG00000098737	Mir7014	Gm27837|mmu-mir-7014	microRNA 7014	ncRNA
mm_111696.1	chr12	103656366	103656403	-	1	NA	intron (NM_007618, intron 1 of 4)	intron (NM_007618, intron 1 of 4)	834	NM_007618	12401	Mm.290079	NM_007618	ENSMUSG00000060807	Serpina6	Cbg	serine (or cysteine) peptidase inhibitor, clade A, member 6	protein-coding
mm_162202.1	chrX	135177603	135177603	-	1	NA	promoter-TSS (NM_001099321)	promoter-TSS (NM_001099321)	11	NM_001099321	100040635	Mm.336240	NM_001099321	ENSMUSG00000079432	Gm15023	OTTMUSG00000018782	predicted gene 15023	protein-coding
mm_154759.1	chrX	10911558	10911565	+	1	NA	Intergenic	Intergenic	194196	NM_001166635	68041	Mm.29429	NM_026524	ENSMUSG00000008035	Mid1ip1	3110038L01Rik|Mig12|S14R	Mid1 interacting protein 1 (gastrulation specific G12-like (zebrafish))	protein-coding
mm_77582.1	chr8	123754139	123754160	-	1	NA	Intergenic	L2|LINE|L2	20191	NR_040702	234863	Mm.246601	NR_040702	ENSMUSG00000110599	6030466F02Rik	-	RIKEN cDNA 6030466F02 gene	ncRNA
mm_36330.1	chr4	70534905	70534987	-	1	NA	promoter-TSS (NM_172694)	promoter-TSS (NM_172694)	-18	NM_172694	230316	Mm.251188	NM_172694	ENSMUSG00000039270	Megf9	4933405H16Rik|9630025C07|Egfl5|mKIAA0818	multiple EGF-like-domains 9	protein-coding
mm_163079.1	chr11	68872046	68872068	+	1	NA	Intergenic	Intergenic	-16496	NM_177060	320040	Mm.305696	NM_177060	ENSMUSG00000046490	Rnf222	9930039A11Rik	ring finger protein 222	protein-coding
mm_88527.1	chr10	78078875	78078899	+	1	NA	3' UTR (NM_015790, exon 7 of 7)	3' UTR (NM_015790, exon 7 of 7)	9519	NM_015790	50723	Mm.17819	NM_015790	ENSMUSG00000000732	Icosl	AU044799|B7-H2|B7RP-1|B7h|BG071784|GI50|GL50|GL50-B|ICOS-L|Icoslg|LICOS|Ly115l|mKIAA0653	icos ligand	protein-coding
mm_72253.1	chr8	75094555	75094564	+	1	NA	intron (NM_010442, intron 1 of 4)	AT_rich|Low_complexity|Low_complexity	941	NM_010442	15368	Mm.276389	NM_010442	ENSMUSG00000005413	Hmox1	D8Wsu38e|HO-1|HO1|Hemox|Hmox|Hsp32	heme oxygenase 1	protein-coding
mm_15361.1	chr2	156418676	156418708	+	1	NA	Intergenic	L3|LINE|CR1	-2217	NM_001291122	13821	Mm.20852	NM_013510	ENSMUSG00000027624	Epb41l1	4.1N|Epb4.1l1|NBL1|mKIAA0338	erythrocyte membrane protein band 4.1 like 1	protein-coding
mm_68806.1	chr7	125491525	125491539	-	1	NA	promoter-TSS (NM_026330)	promoter-TSS (NM_026330)	10	NM_026330	67711	Mm.4467	NM_026330	ENSMUSG00000030750	Nsmce1	2510027N19Rik	NSE1 homolog, SMC5-SMC6 complex component	protein-coding
mm_143397.1	chr17	70746884	70746890	-	1	NA	intron (NM_001347411, intron 9 of 14)	intron (NM_001347411, intron 9 of 14)	99890	NM_001164077	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_9623.1	chr1	176756316	176756337	-	1	NA	exon (NM_001099637, exon 13 of 20)	exon (NM_001099637, exon 13 of 20)	16097	NR_029775	723921		NR_029775	ENSMUSG00000065573	Mir350	Mirn350|mir-350|mmu-mir-350	microRNA 350	ncRNA
mm_75580.1	chr8	61480496	61480522	-	1	NA	Intergenic	Intergenic	-7225	NM_145595	234309	Mm.29059	NM_145595	ENSMUSG00000031641	Cbr4	A730083J17Rik|BC009118	carbonyl reductase 4	protein-coding
mm_108206.1	chr12	76909484	76909496	+	1	NA	intron (NM_145927, intron 8 of 11)	intron (NM_145927, intron 8 of 11)	52758	NM_008558	17187	Mm.268548	NM_008558	ENSMUSG00000059436	Max	AA960152|AI875693|bHLHd4|bHLHd5|bHLHd6|bHLHd7|bHLHd8	Max protein	protein-coding
mm_48381.1	chr5	139771608	139771614	-	1	NA	exon (NM_026748, exon 7 of 47)	exon (NM_026748, exon 7 of 47)	-3668	NR_106004	102465628		NR_106004	ENSMUSG00000098574	Mir7037	Gm27447|mmu-mir-7037	microRNA 7037	ncRNA
mm_84625.1	chr9	70656135	70656138	-	1	NA	intron (NM_172772, intron 1 of 8)	PB1D10|SINE|Alu	1038	NM_172772	235461	Mm.170855	NM_172772	ENSMUSG00000042444	Fam63b	AI465301|B230380D07Rik|mKIAA1164	family with sequence similarity 63, member B	protein-coding
mm_158425.1	chrX	139782360	139782368	-	1	NA	promoter-TSS (NM_001037915)	promoter-TSS (NM_001037915)	-11	NM_001037915	622473	Mm.391312	NM_001037915	ENSMUSG00000072945	Ripply1	-	ripply transcriptional repressor 1	protein-coding
mm_90977.1	chr10	13552856	13552870	-	1	NA	promoter-TSS (NM_025748)	promoter-TSS (NM_025748)	-44	NM_025748	66757	Mm.331841	NM_025748	ENSMUSG00000019808	Adat2	4933426M09Rik|Deadc1	adenosine deaminase, tRNA-specific 2	protein-coding
mm_114871.1	chr13	94083427	94083431	+	1	NA	intron (NM_172589, intron 1 of 3)	intron (NM_172589, intron 1 of 3)	25633	NM_172589	218454	Mm.316553	NM_172589	ENSMUSG00000045312	Lhfpl2	6030465B15|AI447312|AW050335|mKIAA0206|vgim	lipoma HMGIC fusion partner-like 2	protein-coding
mm_168801.1	chr12	20312207	20312208	+	1	NA	Intergenic	CpG	503572	NR_015521	69513	Mm.273972	NR_015521	ENSMUSG00000099759	1700030C10Rik	-	RIKEN cDNA 1700030C10 gene	ncRNA
mm_112928.1	chr13	20959579	20959593	+	1	NA	intron (NM_012054, intron 12 of 20)	intron (NM_012054, intron 12 of 20)	113713	NM_146535	258528	Mm.377554	NM_146535	ENSMUSG00000042869	Olfr1370	MOR256-14	olfactory receptor 1370	protein-coding
mm_149218.1	chr19	10001693	10001703	+	1	NA	promoter-TSS (NM_011913)	promoter-TSS (NM_011913)	29	NM_001347429	74760	Mm.281969	NM_144538	ENSMUSG00000024663	Rab3il1	1200014K04Rik|AI115013|C76746|Rab3ail1	RAB3A interacting protein (rabin3)-like 1	protein-coding
mm_45582.1	chr5	74029239	74029262	-	1	NA	exon (NM_177561, exon 4 of 9)	exon (NM_177561, exon 4 of 9)	39161	NM_177561	69727	Mm.48795	NM_177561	ENSMUSG00000054814	Usp46	1190009E20Rik|2410018I08Rik|AI451644	ubiquitin specific peptidase 46	protein-coding
mm_138609.1	chr17	35667662	35667677	+	1	NA	promoter-TSS (NM_175137)	promoter-TSS (NM_175137)	-77	NM_175137	68915	Mm.32002	NM_175137	ENSMUSG00000038838	Vars2	1190004I24Rik|Vars2l|mKIAA1885	valyl-tRNA synthetase 2, mitochondrial	protein-coding
mm_169077.1	chr13	3231479	3231481	+	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	82005	NR_001581	73266	Mm.335891	NR_001581		Speer6-ps1	1700039A02Rik|SPEER-6	spermatogenesis associated glutamate (E)-rich protein 6, pseudogene 1	pseudo
mm_122126.1	chr14	31155725	31155729	-	1	NA	intron (NM_138672, intron 22 of 68)	intron (NM_138672, intron 22 of 68)	12914	NM_138672	192187	Mm.220821	NM_138672	ENSMUSG00000042286	Stab1	FEEL-1|FELE-1|MFEEL-1|MS-1|STAB-1|mKIAA0246	stabilin 1	protein-coding
mm_38726.1	chr4	145235831	145235866	-	1	NA	intron (NM_011610, intron 1 of 9)	B4|SINE|B4	11022	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_134986.1	chr16	32136038	32136040	-	1	NA	Intergenic	RLTR17|LTR|ERVK	29437	NM_146069	224109	Mm.33498	NM_146069	ENSMUSG00000052384	Nrros	E430025L02Rik|Lrcc33|Lrrc33	negative regulator of reactive oxygen species	protein-coding
mm_103373.1	chr11	75336790	75336810	-	1	NA	intron (NM_026653, intron 4 of 16)	MTEa|LTR|ERVL-MaLR	11583	NM_001164223	68275	Mm.102574	NM_026653	ENSMUSG00000000751	Rpa1	5031405K23Rik|70kDa|AA589576|AW557552|RF-A|RP-A|Rpa	replication protein A1	protein-coding
mm_97156.1	chr11	75464047	75464116	+	1	NA	TTS (NR_029739)	TTS (NR_029739)	365	NR_029739	387141		NR_029739	ENSMUSG00000065529	Mir22	Mirn22|mmu-mir-22	microRNA 22	ncRNA
mm_161480.1	chr15	82340927	82340927	+	1	NA	promoter-TSS (NM_177391)	promoter-TSS (NM_177391)	-252	NM_177391	338368	Mm.444916	NM_177391	ENSMUSG00000049687	Fam109b	C920005C14Rik|IPIP27B|Ses2	family with sequence similarity 109, member B	protein-coding
mm_154590.1	chrX	7579702	7579712	+	1	NA	promoter-TSS (NM_054039)	promoter-TSS (NM_054039)	31	NM_054039	20371	Mm.182291	NM_054039	ENSMUSG00000039521	Foxp3	JM2|scurfin|sf	forkhead box P3	protein-coding
mm_102415.1	chr11	59202170	59202209	-	1	NA	promoter-TSS (NM_026035)	promoter-TSS (NM_026035)	242	NR_037964	72203	Mm.339566	NR_037964		2610507I01Rik	5033414D05Rik	RIKEN cDNA 2610507I01 gene	ncRNA
mm_22918.1	chr3	31094962	31094976	+	1	NA	promoter-TSS (NM_001039090)	promoter-TSS (NM_001039090)	-89	NM_011386	20482	Mm.15406	NM_011386	ENSMUSG00000027660	Skil	Skir|SnoN|sno	SKI-like	protein-coding
mm_124121.1	chr14	79535676	79535678	-	1	NA	intron (NM_001286411, intron 1 of 8)	intron (NM_001286411, intron 1 of 8)	20003	NM_001286411	13709	Mm.20938	NM_007920	ENSMUSG00000036461	Elf1	Elf-1|Sts1|mElf-1|p70	E74-like factor 1	protein-coding
mm_102010.1	chr11	51605623	51605636	-	1	NA	exon (NM_010448, exon 3 of 7)	exon (NM_010448, exon 3 of 7)	1252	NM_001048061	15384	Mm.256875	NM_010448	ENSMUSG00000020358	Hnrnpab	3010025C11Rik|CBF-A|Cgbfa|Hnrpab	heterogeneous nuclear ribonucleoprotein A/B	protein-coding
mm_18900.1	chr2	76715764	76715780	-	1	NA	exon (NM_011652, exon 304 of 313)	exon (NM_011652, exon 304 of 313)	40457	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_87807.1	chr10	60301720	60301730	+	1	NA	exon (NM_011179, exon 15 of 15)	exon (NM_011179, exon 15 of 15)	17264	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_120988.1	chr14	79180680	79180685	+	1	NA	intron (NM_027906, intron 40 of 44)	intron (NM_027906, intron 40 of 44)	66685	NM_001033215	105590	Mm.486536	NM_001033215	ENSMUSG00000071262	Zfp957	AU017455	zinc finger protein 957	protein-coding
mm_114584.1	chr13	75707577	75707587	+	1	NA	promoter-TSS (NM_138953)	promoter-TSS (NM_138953)	98	NM_138953	192657	Mm.21288	NM_138953	ENSMUSG00000001542	Ell2	-	elongation factor RNA polymerase II 2	protein-coding
mm_78591.1	chr9	37385906	37385920	+	1	NA	3' UTR (NM_175189, exon 7 of 7)	3' UTR (NM_175189, exon 7 of 7)	-15984	NM_028783	74144	Mm.485070	NM_028783	ENSMUSG00000032125	Robo4	1200012D01Rik|AI593217	roundabout guidance receptor 4	protein-coding
mm_86171.1	chr9	119157015	119157029	-	1	NA	promoter-TSS (NM_146230)	promoter-TSS (NM_146230)	71	NM_146230	235674	Mm.379402	NM_146230	ENSMUSG00000010651	Acaa1b	-	acetyl-Coenzyme A acyltransferase 1B	protein-coding
mm_43531.1	chr5	137293534	137293564	+	1	NA	promoter-TSS (NR_106196)	promoter-TSS (NR_106196)	-231	NR_106196	102466887		NR_106196	ENSMUSG00000099145	Mir8116	Gm27485|mmu-mir-8116	microRNA 8116	ncRNA
mm_172938.1	chr9	78809569	78809569	-	1	NA	Intergenic	RLTR10E|LTR|ERVK	194023	NM_153098	235505	Mm.32955	NM_153098	ENSMUSG00000046186	Cd109	9930012E15Rik|AI480638|GARP	CD109 antigen	protein-coding
mm_93807.1	chr10	120979314	120979322	-	1	NA	promoter-TSS (NM_001081193)	promoter-TSS (NM_001081193)	12	NM_001081193	380664	Mm.339371	NM_001081193	ENSMUSG00000048661	Lemd3	AI316861|Man1	LEM domain containing 3	protein-coding
mm_13199.1	chr2	93453430	93453442	+	1	NA	promoter-TSS (NM_001271462)	promoter-TSS (NM_001271462)	617	NR_040533	100038525	Mm.440596	NR_040532	ENSMUSG00000075025	Gm10804	ENSMUSG00000075025	predicted gene 10804	ncRNA
mm_96260.1	chr11	62605729	62605778	+	1	NA	TTS (NR_030738)	TTS (NR_030738)	1223	NR_028541	100217444		NR_028541		Snord65	MBII-135|snoRNA135	small nucleolar RNA, C/D box 65	snoRNA
mm_171166.1	chr3	26229716	26229716	+	1	NA	intron (NM_138666, intron 1 of 7)	B1_Mur4|SINE|Alu	-76409	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_74631.1	chr8	13192289	13192336	-	1	NA	intron (NM_025768, intron 2 of 7)	intron (NM_025768, intron 2 of 7)	-3214	NR_035494	100316713		NR_035494	ENSMUSG00000088054	Mir1968	mir-1968|mmu-mir-1968	microRNA 1968	ncRNA
mm_127718.1	chr15	103034701	103034720	+	1	NA	5' UTR (NM_013553, exon 1 of 2)	5' UTR (NM_013553, exon 1 of 2)	315	NM_013553	15423	Mm.1351	NM_013553	ENSMUSG00000075394	Hoxc4	Hox-3.5	homeobox C4	protein-coding
mm_42539.1	chr5	115908696	115908734	+	1	NA	exon (NM_007708, exon 9 of 47)	exon (NM_007708, exon 9 of 47)	63059	NM_007708	12704	Mm.8321	NM_007708	ENSMUSG00000029516	Cit	C030025P15Rik|CRIK|CRIK-SK|Cit-k	citron	protein-coding
mm_161883.1	chr18	37638711	37638711	-	1	NA	promoter-TSS (NM_001159275)	promoter-TSS (NM_001159275)	12	NM_001159275	83885	Mm.193029	NM_001159275	ENSMUSG00000050304	Slc25a2	Ornt2	solute carrier family 25 (mitochondrial carrier, ornithine transporter) member 2	protein-coding
mm_109328.1	chr12	109564895	109564911	+	1	NA	non-coding (NR_003633, exon 5 of 5)	non-coding (NR_003633, exon 5 of 5)	1211	NR_030427	791079		NR_030427	ENSMUSG00000076451	Mir770	Mirn770|mir-770|mmu-mir-770	microRNA 770	ncRNA
mm_149106.1	chr19	8952071	8952085	+	1	NA	3' UTR (NM_011842, exon 18 of 18)	3' UTR (NM_011842, exon 18 of 18)	-1754	NM_197993	70044	Mm.165979	NM_197993	ENSMUSG00000071645	Tut1	2700038E08Rik|PAPD2|Rbm21|TUTase6|U6-TUTase|star-PAP	terminal uridylyl transferase 1, U6 snRNA-specific	protein-coding
mm_9530.1	chr1	173802712	173802730	-	1	NA	Intergenic	Intergenic	-35802	NM_008329	15951	Mm.261270	NM_008329	ENSMUSG00000073489	Ifi204	Ifi16|p204	interferon activated gene 204	protein-coding
mm_42744.1	chr5	120753763	120753779	+	1	NA	3' UTR (NM_145226, exon 16 of 16)	3' UTR (NM_145226, exon 16 of 16)	-3923	NM_001347448	246728	Mm.260926	NM_145227	ENSMUSG00000032690	Oas2	Oasl11	2'-5' oligoadenylate synthetase 2	protein-coding
mm_161282.1	chr14	21751494	21751494	+	1	NA	intron (NM_026283, intron 1 of 5)	intron (NM_026283, intron 1 of 5)	963	NM_026283	67630	Mm.102765	NM_026283	ENSMUSG00000021770	Samd8	1110053F04Rik|1700010P07Rik|SMSr	sterile alpha motif domain containing 8	protein-coding
mm_40905.1	chr5	75203723	75203726	+	1	NA	Intergenic	L1M5|LINE|L1	26893	NR_105992	102465620		NR_105992	ENSMUSG00000099060	Mir7025	Gm27860|mmu-mir-7025	microRNA 7025	ncRNA
mm_144829.1	chr18	36348936	36348957	+	1	NA	intron (NM_001081365, intron 1 of 2)	CpG	322	NM_001081365	66060	Mm.272527	NM_001081365	ENSMUSG00000046727	Cystm1	0610010O12Rik	cysteine-rich transmembrane module containing 1	protein-coding
mm_57253.1	chr6	123283556	123283560	-	1	NA	exon (NM_019948, exon 6 of 6)	exon (NM_019948, exon 6 of 6)	6313	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_140712.1	chr17	15041458	15041469	-	1	NA	promoter-TSS (NM_001039552)	promoter-TSS (NM_001039552)	96	NM_001123368	100041586	Mm.440445	NM_001123368	ENSMUSG00000079710	Gm3417	-	predicted gene 3417	protein-coding
mm_136183.1	chr16	88924267	88924271	-	1	NA	Intergenic	Intergenic	7995	NM_133359	170939	Mm.188445	NM_133359	ENSMUSG00000057174	Krtap19-9b	Krtap16-10b|Krtap16.10L	keratin associated protein 19-9B	protein-coding
mm_169165.1	chr13	65503568	65503584	+	1	NA	Intergenic	Intergenic	224722	NM_178364	170936	Mm.151546	NM_178364	ENSMUSG00000021514	Zfp369	B930030B22Rik|D230020H11Rik|NRIF2	zinc finger protein 369	protein-coding
mm_113924.1	chr13	49582746	49582778	+	1	NA	promoter-TSS (NM_012050)	promoter-TSS (NM_012050)	15	NM_012050	27047	Mm.390589	NM_012050	ENSMUSG00000048368	Omd	OSAD|SLRR2C	osteomodulin	protein-coding
mm_47624.1	chr5	125277738	125277753	-	1	NA	3' UTR (NM_001205082, exon 12 of 12)	3' UTR (NM_001205082, exon 12 of 12)	63349	NM_016741	20778	Mm.282242	NM_016741	ENSMUSG00000037936	Scarb1	AI120173|CD36|Cd36l1|Chohd1|Cla-1|Cla1|D5Ertd460e|Hdlq1|Hlb398|SR-B1|SR-BI|SRBI|Srb1|mSR-BI	scavenger receptor class B, member 1	protein-coding
mm_33816.1	chr4	135337785	135337793	+	1	NA	intron (NM_016799, intron 9 of 17)	intron (NM_016799, intron 9 of 17)	15425	NM_016799	51796	Mm.1963	NM_016799	ENSMUSG00000028809	Srrm1	AA407769|POP101|Srm160	serine/arginine repetitive matrix 1	protein-coding
mm_100890.1	chr11	6065672	6065688	-	1	NA	promoter-TSS (NM_001174054)	promoter-TSS (NM_001174054)	68	NM_001174054	12323	Mm.439733	NM_007595	ENSMUSG00000057897	Camk2b	CaMKII	calcium/calmodulin-dependent protein kinase II, beta	protein-coding
mm_166473.1	chr5	142909983	142909992	+	1	NA	Intergenic	Intergenic	-3233	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_4715.1	chr1	180952678	180952685	+	1	NA	intron (NM_144794, intron 4 of 22)	intron (NM_144794, intron 4 of 22)	10163	NM_144794	208795	Mm.185518	NM_144794	ENSMUSG00000026519	Tmem63a	BC014795|Tmem64a	transmembrane protein 63a	protein-coding
mm_18652.1	chr2	69737827	69737830	-	1	NA	intron (NM_001081086, intron 9 of 13)	intron (NM_001081086, intron 9 of 13)	14740	NM_001081086	228005	Mm.11815	NM_001081086	ENSMUSG00000042133	Ppig	AU019516|AU022200|B230312B02Rik|CYP|SRCyp	peptidyl-prolyl isomerase G (cyclophilin G)	protein-coding
mm_25609.1	chr3	117786660	117786667	+	1	NA	intron (NM_001190156, intron 7 of 7)	intron (NM_001190156, intron 7 of 7)	82273	NM_001190156	76561	Mm.33824	NM_029655	ENSMUSG00000028007	Snx7	2510028H01Rik	sorting nexin 7	protein-coding
mm_139057.1	chr17	46383799	46383822	+	1	NA	promoter-TSS (NM_021346)	promoter-TSS (NM_021346)	44	NM_021346	57908	Mm.439916	NM_021346	ENSMUSG00000015597	Zfp318	2610034E08Rik|D530032D06Rik|TZF|Znf318	zinc finger protein 318	protein-coding
mm_95930.1	chr11	58379037	58379052	+	1	NA	promoter-TSS (NM_001083884)	promoter-TSS (NM_001083884)	12	NM_001083884	70163	Mm.24119	NM_027339	ENSMUSG00000013643	Lypd8	2210415F13Rik	LY6/PLAUR domain containing 8	protein-coding
mm_88856.1	chr10	80930766	80930779	+	1	NA	intron (NM_008655, intron 2 of 3)	intron (NM_008655, intron 2 of 3)	681	NM_008655	17873	Mm.1360	NM_008655	ENSMUSG00000015312	Gadd45b	AI323528|Myd118	growth arrest and DNA-damage-inducible 45 beta	protein-coding
mm_8124.1	chr1	136135181	136135198	-	1	NA	intron (NM_001039472, intron 1 of 34)	intron (NM_001039472, intron 1 of 34)	3788	NM_001039472	16565	Mm.276135	NM_019962	ENSMUSG00000041642	Kif21b	2610511N21Rik|mKIAA0449	kinesin family member 21B	protein-coding
mm_160621.1	chr9	96731649	96731649	-	1	NA	promoter-TSS (NM_175537)	promoter-TSS (NM_175537)	26	NM_175537	245007	Mm.485954	NM_175537	ENSMUSG00000040433	Zbtb38	A930014K01Rik|CIBZ	zinc finger and BTB domain containing 38	protein-coding
mm_4005.1	chr1	164796736	164796746	+	1	NA	promoter-TSS (NM_019759)	promoter-TSS (NM_019759)	9	NM_019759	56429	Mm.28935	NM_019759	ENSMUSG00000026574	Dpt	1810032B19Rik|5033416F05Rik|EQ-1|Eq1	dermatopontin	protein-coding
mm_172023.1	chr6	116926674	116926678	+	1	NA	Intergenic	B4A|SINE|B4	-209918	NM_178768	319776	Mm.133120	NM_178768	ENSMUSG00000048108	Tmem72	C230095G01Rik	transmembrane protein 72	protein-coding
mm_12277.1	chr2	68999980	68999991	+	1	NA	intron (NM_172856, intron 3 of 9)	intron (NM_172856, intron 3 of 9)	-135815	NM_181547	329416	Mm.90047	NM_181547	ENSMUSG00000034738	Nostrin	Daip2|mDaIP2	nitric oxide synthase trafficker	protein-coding
mm_162236.1	chrX	153118802	153118802	+	1	NA	promoter-TSS (NM_001034894)	promoter-TSS (NM_001034894)	14	NM_001034894	436240	Mm.373353	NM_001034894	ENSMUSG00000071665	Foxr2	EG436240|Foxn6	forkhead box R2	protein-coding
mm_77861.1	chr9	5321298	5321311	+	1	NA	exon (NM_007609, exon 2 of 9)	exon (NM_007609, exon 2 of 9)	12455	NM_007609	12363	Mm.1569	NM_007609	ENSMUSG00000033538	Casp4	CASP-11|CASP-4|Casp11|Caspl|ich-3	caspase 4, apoptosis-related cysteine peptidase	protein-coding
mm_145508.1	chr18	60391611	60391619	+	1	NA	3' UTR (NM_001146275, exon 3 of 3)	3' UTR (NM_001146275, exon 3 of 3)	15586	NM_001146275	60440	Mm.261140	NM_021792	ENSMUSG00000054072	Iigp1	2900074L10Rik|AI046432|AW111922|Ifgga1|Iigp|Irga6	interferon inducible GTPase 1	protein-coding
mm_86458.1	chr10	4353435	4353455	+	1	NA	exon (NM_031185, exon 3 of 4)	exon (NM_031185, exon 3 of 4)	34663	NM_001033466	381990	Mm.262466	NM_001033466	ENSMUSG00000075327	Zbtb2	Gm1103	zinc finger and BTB domain containing 2	protein-coding
mm_142288.1	chr17	40242380	40242384	-	1	NA	promoter-TSS (NM_009639)	promoter-TSS (NM_009639)	-124	NM_009639	11572	Mm.14138	NM_009639	ENSMUSG00000025433	Crisp3	Aeg2|CRISP-3|CRS3|SGP28	cysteine-rich secretory protein 3	protein-coding
mm_140342.1	chr17	86823756	86823777	+	1	NA	exon (NM_010137, exon 8 of 16)	exon (NM_010137, exon 8 of 16)	69902	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_44019.1	chr5	147400418	147400426	+	1	NA	promoter-TSS (NM_010229)	promoter-TSS (NM_010229)	67	NM_010229	14255	Mm.194	NM_010229	ENSMUSG00000042817	Flt3	B230315G04|CD135|Flk-2|Flk2|Flt-3|Ly72|wmfl	FMS-like tyrosine kinase 3	protein-coding
mm_54740.1	chr6	41030697	41030709	-	1	NA	3' UTR (NM_023333, exon 5 of 5)	3' UTR (NM_023333, exon 5 of 5)	4806	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_137056.1	chr17	17931998	17932008	+	1	NA	Intergenic	Intergenic	-38455	NM_008042	14294	Mm.378918	NM_008042	ENSMUSG00000079700	Fpr3	ALX|Fpr-rs1|Fpr-s1|Fprl1|LXA4-R|Lxa4r	formyl peptide receptor 3	protein-coding
mm_130727.1	chr15	101217271	101217278	-	1	NA	Intergenic	AT_rich|Low_complexity|Low_complexity	-3973	NR_045996	105968	Mm.120798	NR_045996		AU021063	-	expressed sequence AU021063	ncRNA
mm_101382.1	chr11	23818888	23818907	-	1	NA	Intergenic	L4_C_Mam|LINE|RTE-X	-47927	NM_009044	19696	Mm.4869	NM_009044	ENSMUSG00000020275	Rel	c-Rel	reticuloendotheliosis oncogene	protein-coding
mm_154303.1	chr19	61225600	61225642	-	1	NA	exon (NM_009970, exon 9 of 12)	exon (NM_009970, exon 9 of 12)	2797	NM_009970	12982	Mm.287228	NM_009970	ENSMUSG00000059326	Csf2ra	CD116|Csfgmra|GM-CSF-Ra|GM-CSFR	colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)	protein-coding
mm_11812.1	chr2	43973085	43973103	+	1	NA	intron (NM_001301832, intron 7 of 14)	RSINE1|SINE|B4	92230	NR_040622	320872	Mm.445023	NR_040622	ENSMUSG00000085089	Arhgap15os	A430092G05Rik	Rho GTPase activating protein 15, opposite strand	ncRNA
mm_96618.1	chr11	69103366	69103383	+	1	NA	exon (NM_001159367, exon 12 of 23)	exon (NM_001159367, exon 12 of 23)	3216	NM_001159367	18626	Mm.7373	NM_011065	ENSMUSG00000020893	Per1	Hftm|Per|m-rigui|mPer1	period circadian clock 1	protein-coding
mm_44405.1	chr5	17847806	17847831	-	1	NA	intron (NM_001159558, intron 1 of 15)	intron (NM_001159558, intron 1 of 15)	1974	NM_001159557	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_145250.1	chr18	52465677	52465710	+	1	NA	promoter-TSS (NM_026040)	promoter-TSS (NM_026040)	0	NM_026040	67222	Mm.100617	NM_026040	ENSMUSG00000024528	Srfbp1	2810036K01Rik|p49/STRAP	serum response factor binding protein 1	protein-coding
mm_44195.1	chr5	3596541	3596579	-	1	NA	promoter-TSS (NM_172991)	promoter-TSS (NM_172991)	-13	NM_172991	269623	Mm.38014	NM_172991	ENSMUSG00000040302	Rbm48	AW548102|C030048B08Rik	RNA binding motif protein 48	protein-coding
mm_635.1	chr1	40380569	40380586	+	1	NA	Intergenic	Intergenic	-48993	NM_001294171	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_657.1	chr1	40434529	40434532	+	1	NA	intron (NM_001294171, intron 1 of 7)	L1ME2|LINE|L1	4960	NM_001294171	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_27676.1	chr3	65925910	65925948	-	1	NA	Intergenic	Intergenic	32296	NM_019937	56706	Mm.175612	NM_019937	ENSMUSG00000027829	Ccnl1	2610030E23Rik|AU018493|Ccnl|ania-6a	cyclin L1	protein-coding
mm_8811.1	chr1	161896171	161896174	-	1	NA	Intergenic	Intergenic	-19511	NM_172645	226551	Mm.170002	NM_172645	ENSMUSG00000040297	Suco	4732491B11|AI848100|AU016931|Opt	SUN domain containing ossification factor	protein-coding
mm_117723.1	chr13	95525181	95525191	-	1	NA	promoter-TSS (NM_007974)	promoter-TSS (NM_007974)	54	NM_007974	14063	Mm.1614	NM_007974	ENSMUSG00000021678	F2rl1	Gpcr11|PAR-2|Par2	coagulation factor II (thrombin) receptor-like 1	protein-coding
mm_66296.1	chr7	38023491	38023502	-	1	NA	Intergenic	Intergenic	-3944	NM_011274	19777	Mm.387220	NM_011274	ENSMUSG00000030421	Uri1	C80913|NNX3|Rmp	URI1, prefoldin-like chaperone	protein-coding
mm_7806.1	chr1	131526726	131526745	-	1	NA	intron (NM_001081011, intron 1 of 22)	CpG	626	NM_001081011	14270	Mm.276259	NM_019520	ENSMUSG00000026425	Srgap2	9930124L22Rik|AI448945|FBP2|Fnbp2|srGAP3	SLIT-ROBO Rho GTPase activating protein 2	protein-coding
mm_123133.1	chr14	56366822	56366835	-	1	NA	intron (NM_138652, intron 2 of 22)	intron (NM_138652, intron 2 of 22)	1760	NM_138652	192113	Mm.273271	NM_138652	ENSMUSG00000022229	Atp12a	Atp1al1|HKalpha2|cHKA	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	protein-coding
mm_144646.1	chr18	33794883	33794902	+	1	NA	promoter-TSS (NR_038152)	promoter-TSS (NR_038152)	0	NR_038152	69749	Mm.248787	NR_038151	ENSMUSG00000087590	Epb41l4aos	2410004N09Rik|Epb4.1l4aos	erythrocyte membrane protein band 4.1 like 4a, opposite strand	ncRNA
mm_147983.1	chr18	67601415	67601421	-	1	NA	Intergenic	Intergenic	39918	NM_001081073	225659	Mm.111928	NM_001081073	ENSMUSG00000073542	Cep76	6230425F05Rik|9630013E05	centrosomal protein 76	protein-coding
mm_168556.1	chr11	6559531	6559536	-	1	NA	promoter-TSS (NM_001190344)	promoter-TSS (NM_001190344)	-650	NM_001190344	216527	Mm.221271	NM_146014	ENSMUSG00000000378	Ccm2	BC029157	cerebral cavernous malformation 2	protein-coding
mm_127990.1	chr15	12550051	12550067	-	1	NA	intron (NM_001081064, intron 1 of 23)	intron (NM_001081064, intron 1 of 23)	42497	NM_001081064	68070	Mm.423205	NM_001081064	ENSMUSG00000022197	Pdzd2	4930537L06Rik|A930022H17Rik|Gm21706|Gm82|Pdzk3|mKIAA0300	PDZ domain containing 2	protein-coding
mm_20343.1	chr2	127705486	127705515	-	1	NA	3' UTR (NM_145532, exon 4 of 4)	3' UTR (NM_145532, exon 4 of 4)	24397	NM_145532	228576	Mm.133036	NM_145532	ENSMUSG00000027377	Mall	BC012256|BENE	mal, T cell differentiation protein-like	protein-coding
mm_98944.1	chr11	98412377	98412388	+	1	NA	promoter-TSS (NM_001003817)	promoter-TSS (NM_001003817)	-102	NM_001003817	13866	Mm.290822	NM_001003817	ENSMUSG00000062312	Erbb2	Erbb-2|HER-2|HER2|Neu|c-erbB2|c-neu|l11Jus8|mKIAA3023	erb-b2 receptor tyrosine kinase 2	protein-coding
mm_40423.1	chr5	53466117	53466131	+	1	NA	Intergenic	Intergenic	-89655	NM_001080928	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_101568.1	chr11	34208086	34208092	-	1	NA	promoter-TSS (NM_023907)	promoter-TSS (NM_023907)	0	NM_023907	14233	Mm.32926	NM_023907	ENSMUSG00000047861	Foxi1	5830401E05Rik|FREAC6|Fkh10|HFH-3|Hfh3	forkhead box I1	protein-coding
mm_28812.1	chr3	96259752	96259764	-	1	NA	Intergenic	Intergenic	3559	NM_033596	97122	Mm.227295	NM_033596	ENSMUSG00000091405	Hist2h4	H4|X04652	histone cluster 2, H4	protein-coding
mm_24462.1	chr3	90654104	90654106	+	1	NA	promoter-TSS (NM_199422)	promoter-TSS (NM_199422)	-197	NM_199422	381493	Mm.291525	NM_199422	ENSMUSG00000063767	S100a7a	AY465109|Gm1020|S100A7L1|S100A7f|S100a15|S100a15a|S100a17l1	S100 calcium binding protein A7A	protein-coding
mm_4844.1	chr1	186967088	186967108	+	1	NA	promoter-TSS (NM_033077)	promoter-TSS (NM_033077)	-318	NM_033077	110957	Mm.108054	NM_033077	ENSMUSG00000039224	D1Pas1	Pl10	DNA segment, Chr 1, Pasteur Institute 1	protein-coding
mm_69907.1	chr7	141639993	141640015	-	1	NA	intron (NM_001330001, intron 31 of 33)	intron (NM_001330001, intron 31 of 33)	15315	NM_001330001	353328	Mm.246621	NM_181729	ENSMUSG00000048191	Muc6	-	mucin 6, gastric	protein-coding
mm_32832.1	chr4	117610824	117610828	+	1	NA	intron (NM_001285901, intron 5 of 7)	intron (NM_001285901, intron 5 of 7)	60461	NM_080469	140546	Mm.235891	NM_080469	ENSMUSG00000033423	Eri3	PINT1|Prnpip1	exoribonuclease 3	protein-coding
mm_11198.1	chr2	29125202	29125212	+	1	NA	5' UTR (NM_198033, exon 1 of 26)	5' UTR (NM_198033, exon 1 of 26)	215	NM_198033	269254	Mm.41867	NM_198033	ENSMUSG00000043535	Setx	A130090N03|A930037J23Rik|AOA2|AW060766|Als4|SCAR1|Sen1|mKIAA0625	senataxin	protein-coding
mm_149159.1	chr19	9017733	9017759	+	1	NA	promoter-TSS (NR_105786)	promoter-TSS (NR_105786)	-158	NR_105786	102465190		NR_105786	ENSMUSG00000099308	Mir6367	Gm27467|mmu-mir-6367	microRNA 6367	ncRNA
mm_65838.1	chr7	29232479	29232527	-	1	NA	promoter-TSS (NM_001033525)	promoter-TSS (NM_001033525)	19	NM_001033525	52150	Mm.24877	NM_001033525	ENSMUSG00000046410	Kcnk6	D7Ertd764e|Toss|Twik2	potassium inwardly-rectifying channel, subfamily K, member 6	protein-coding
mm_37800.1	chr4	130531657	130531669	-	1	NA	3' UTR (NM_025998, exon 7 of 7)	3' UTR (NM_025998, exon 7 of 7)	42373	NM_025998	67149	Mm.423029	NM_025998	ENSMUSG00000078532	Nkain1	2610200G18Rik|2810426C15Rik	Na+/K+ transporting ATPase interacting 1	protein-coding
mm_109303.1	chr12	109560634	109560653	+	1	NA	non-coding (NR_003633, exon 5 of 5)	non-coding (NR_003633, exon 5 of 5)	-3049	NR_030427	791079		NR_030427	ENSMUSG00000076451	Mir770	Mirn770|mir-770|mmu-mir-770	microRNA 770	ncRNA
mm_73287.1	chr8	104926238	104926291	+	1	NA	promoter-TSS (NM_001163756)	promoter-TSS (NM_001163756)	4	NM_172759	234673	Mm.441134	NM_172759	ENSMUSG00000031886	Ces2e	9030624L02Rik|Ces5	carboxylesterase 2E	protein-coding
mm_449.1	chr1	36063300	36063314	+	1	NA	Intergenic	Intergenic	-5093	NM_015818	50785	Mm.213566	NM_015818	ENSMUSG00000045216	Hs6st1	6Ost1	heparan sulfate 6-O-sulfotransferase 1	protein-coding
mm_161451.1	chr15	74955119	74955119	+	1	NA	promoter-TSS (NM_001164036)	promoter-TSS (NM_001164036)	13	NM_001164040	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_150933.1	chr19	46305857	46305870	+	1	NA	promoter-TSS (NM_001177370)	promoter-TSS (NM_001177370)	-67	NM_001177370	18034	Mm.102365	NM_019408	ENSMUSG00000025225	Nfkb2	NF-kappaB2|lyt|p49|p49/p100|p50B|p52	nuclear factor of kappa light polypeptide gene enhancer in B cells 2, p49/p100	protein-coding
mm_110127.1	chr12	26444534	26444616	-	1	NA	3' UTR (NM_021384, exon 6 of 6)	3' UTR (NM_021384, exon 6 of 6)	11877	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_131551.1	chr16	17898649	17898673	+	1	NA	promoter-TSS (NM_009436)	promoter-TSS (NM_009436)	24	NM_009436	22115	Mm.310201	NM_009436	ENSMUSG00000045521	Tssk2	DGS-G|SPOGA2|Stk22b|Tsk2	testis-specific serine kinase 2	protein-coding
mm_42675.1	chr5	119680267	119680287	+	1	NA	intron (NM_198052, intron 6 of 7)	intron (NM_198052, intron 6 of 7)	9044	NM_011535	21386	Mm.219139	NM_011535	ENSMUSG00000018604	Tbx3	D5Ertd189e	T-box 3	protein-coding
mm_37483.1	chr4	123572940	123572959	-	1	NA	intron (NM_001199136, intron 1 of 97)	intron (NM_001199136, intron 1 of 97)	-43471	NR_105824	102465214		NR_105824	ENSMUSG00000099005	Mir6398	Gm27657|mmu-mir-6398	microRNA 6398	ncRNA
mm_3557.1	chr1	150423792	150423806	+	1	NA	exon (NM_133780, exon 27 of 52)	exon (NM_133780, exon 27 of 52)	-30744	NM_145511	226499	Mm.222093	NM_145511	ENSMUSG00000006010	BC003331	1810053E15Rik|Odr4|odr-4	cDNA sequence BC003331	protein-coding
mm_98770.1	chr11	96693604	96693614	+	1	NA	intron (NM_001033186, intron 4 of 12)	ORR1B1|LTR|ERVL-MaLR	83946	NM_028965	74479	Mm.270781	NM_028965	ENSMUSG00000020876	Snx11	4933439F10Rik|A930041K09Rik|AI117694	sorting nexin 11	protein-coding
mm_118676.1	chr14	22064051	22064074	+	1	NA	intron (NM_028275, intron 2 of 6)	B4A|SINE|B4	44350	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_131096.1	chr16	4927732	4927756	+	1	NA	exon (NM_029657, exon 12 of 17)	exon (NM_029657, exon 12 of 17)	-11367	NM_001316715	66911	Mm.428698	NM_025839	ENSMUSG00000022516	Nudt16l1	1110001K21Rik|5330437I08Rik|Sdos	nudix (nucleoside diphosphate linked moiety X)-type motif 16-like 1	protein-coding
mm_41453.1	chr5	90905560	90905581	+	1	NA	3' UTR (NM_009140, exon 4 of 4)	3' UTR (NM_009140, exon 4 of 4)	1671	NM_009140	20310	Mm.4979	NM_009140	ENSMUSG00000058427	Cxcl2	CINC-2a|GROb|Gro2|MIP-2|MIP-2a|Mgsa-b|Mip2|Scyb|Scyb2	chemokine (C-X-C motif) ligand 2	protein-coding
mm_22329.1	chr2	180692855	180692873	-	1	NA	promoter-TSS (NR_111965)	promoter-TSS (NR_111965)	-816	NR_111965	23856	Mm.253836	NM_011805	ENSMUSG00000038914	Dido1	6720461J16Rik|D130048F08Rik|DATF-1|DIO-1|Datf1|dido	death inducer-obliterator 1	protein-coding
mm_21470.1	chr2	160982719	160982730	-	1	NA	intron (NR_126509, intron 22 of 35)	intron (NR_126509, intron 22 of 35)	-70385	NM_182840	280635	Mm.330747	NM_182840	ENSMUSG00000050700	Emilin3	1110013O17Rik|EMILIN-3|EMILIN-5|EMILIN-T|Emilin5	elastin microfibril interfacer 3	protein-coding
mm_17956.1	chr2	37359275	37359290	-	1	NA	promoter-TSS (NM_026176)	promoter-TSS (NM_026176)	50	NM_026176	67466	Mm.30709	NM_026176	ENSMUSG00000009030	Pdcl	1200011E13Rik|AW108059|PhLP1	phosducin-like	protein-coding
mm_2837.1	chr1	131527981	131528002	+	1	NA	promoter-TSS (NM_001081011)	promoter-TSS (NM_001081011)	88	NM_175382	108900	Mm.31278	NM_175382	ENSMUSG00000055184	Fam72a	2700049P18Rik|P17	family with sequence similarity 72, member A	protein-coding
mm_47442.1	chr5	123310350	123310360	-	1	NA	Intergenic	Intergenic	-34093	NM_029850	77045	Mm.151960	NM_029850	ENSMUSG00000029438	Bcl7a	4432415N06Rik|AI448316	B cell CLL/lymphoma 7A	protein-coding
mm_69689.1	chr7	139991372	139991395	-	1	NA	exon (NM_001291066, exon 2 of 24)	exon (NM_001291066, exon 2 of 24)	1179	NM_007403	11501	Mm.15969	NM_007403	ENSMUSG00000025473	Adam8	ADAM 8|CD156|CD156a|E430039A18Rik|MS2	a disintegrin and metallopeptidase domain 8	protein-coding
mm_66679.1	chr7	45808226	45808231	-	1	NA	exon (NM_001112701, exon 10 of 12)	exon (NM_001112701, exon 10 of 12)	6088	NM_011181	19158	Mm.272130	NM_011181	ENSMUSG00000003269	Cyth2	ARNO|CLM2|Pscd2	cytohesin 2	protein-coding
mm_162363.1	chr1	65048849	65048858	+	1	NA	exon (NM_007777, exon 3 of 3)	exon (NM_007777, exon 3 of 3)	2310	NM_007777	12968	Mm.258170	NM_007777	ENSMUSG00000070870	Cryge	Cryg-2|Cryg-6|DGcry-2|Elo	crystallin, gamma E	protein-coding
mm_80937.1	chr9	102716693	102716704	+	1	NA	Intergenic	Intergenic	-1106	NM_019764	56332	Mm.21145	NM_019764	ENSMUSG00000032531	Amotl2	AW549739|C79691|Lccp|MASCOT|mKIAA0989	angiomotin-like 2	protein-coding
mm_33017.1	chr4	121016071	121016102	+	1	NA	intron (NM_133716, intron 1 of 9)	intron (NM_133716, intron 1 of 9)	1161	NM_133716	69780	Mm.271819	NM_133716	ENSMUSG00000032870	Smap2	1810031K02Rik|AA408614|Smap1l	small ArfGAP 2	protein-coding
mm_165059.1	chr19	41981788	41981798	+	1	NA	promoter-TSS (NM_028152)	promoter-TSS (NM_028152)	30	NM_145500	226122	Mm.22948	NM_145500	ENSMUSG00000025171	Ubtd1	BC016129	ubiquitin domain containing 1	protein-coding
mm_40301.1	chr5	43672305	43672326	+	1	NA	intron (NM_172274, intron 4 of 39)	intron (NM_172274, intron 4 of 39)	9936	NM_172274	231214	Mm.44434	NM_172274	ENSMUSG00000039765	Cc2d2a	5730509K17Rik|b2b1035Clo	coiled-coil and C2 domain containing 2A	protein-coding
mm_164230.1	chr15	89336854	89336862	+	1	NA	3' UTR (NM_019977, exon 10 of 10)	3' UTR (NM_019977, exon 10 of 10)	2385	NM_019977	56727	Mm.158200	NM_019977	ENSMUSG00000022613	Miox	0610009I10Rik|AI314022|Aldrl6|C85427|RSOR	myo-inositol oxygenase	protein-coding
mm_29665.1	chr3	122619443	122619463	-	1	NA	intron (NM_153118, intron 1 of 13)	CpG	261	NM_001114665	214459	Mm.209491	NM_153118	ENSMUSG00000039735	Fnbp1l	2610318I01Rik|AW548221|TOCA1|toca-1	formin binding protein 1-like	protein-coding
mm_131859.1	chr16	23079954	23079975	+	1	NA	TTS (NM_001102411)	TTS (NM_001102411)	21664	NM_001102412	16644	Mm.2160	NM_023125	ENSMUSG00000022875	Kng1	Kng	kininogen 1	protein-coding
mm_1107.1	chr1	59763937	59763991	+	1	NA	promoter-TSS (NM_007561)	promoter-TSS (NM_007561)	-315	NM_007561	12168	Mm.7106	NM_007561	ENSMUSG00000067336	Bmpr2	2610024H22Rik|AL117858|AW546137|BB189135|BMP-2|BMPR-2|BMPR-II|BMPRII|BRK-3|Gm20272	bone morphogenetic protein receptor, type II (serine/threonine kinase)	protein-coding
mm_77522.1	chr8	122939588	122939592	-	1	NA	intron (NM_001081379, intron 2 of 12)	intron (NM_001081379, intron 2 of 12)	91216	NM_007662	12555	Mm.1976	NM_007662	ENSMUSG00000031962	Cdh15	AI323380|Cdh14|Mcad	cadherin 15	protein-coding
mm_76534.1	chr8	87959561	87959576	-	1	NA	promoter-TSS (NM_033327)	promoter-TSS (NM_033327)	27	NM_033327	94187	Mm.23452	NM_033327	ENSMUSG00000045333	Zfp423	Ebfaz|Roaz|Zfp104|Znf423|ataxia1|mKIAA0760|nur12	zinc finger protein 423	protein-coding
mm_157925.1	chrX	79635548	79635558	-	1	NA	promoter-TSS (NM_001113734)	promoter-TSS (NM_001113734)	29	NM_001113734	71967	Mm.379207	NM_028025	ENSMUSG00000046942	Mageb16	2410003J06Rik	melanoma antigen family B, 16	protein-coding
mm_71996.1	chr8	70618138	70618170	+	1	NA	exon (NM_153074, exon 2 of 3)	exon (NM_153074, exon 2 of 3)	1310	NM_153074	211228	Mm.132939	NM_153074	ENSMUSG00000049988	Lrrc25	Mapa	leucine rich repeat containing 25	protein-coding
mm_67910.1	chr7	99706637	99706652	-	1	NA	5' UTR (NM_001252530, exon 1 of 14)	5' UTR (NM_001252530, exon 1 of 14)	198	NM_001252530	101488	Mm.11249	NM_175316	ENSMUSG00000030737	Slco2b1	AI060904|AI852653|OATP-B|Slc21a9	solute carrier organic anion transporter family, member 2b1	protein-coding
mm_156373.1	chrX	139665421	139665432	+	1	NA	exon (NM_023270, exon 6 of 7)	exon (NM_023270, exon 6 of 7)	-19570	NM_001081499	245638	Mm.275869	NM_001081499	ENSMUSG00000042473	Tbc1d8b	4921505D17Rik|9030605E16Rik	TBC1 domain family, member 8B	protein-coding
mm_165779.1	chr3	130420629	130420629	+	1	NA	intron (NM_029838, intron 5 of 37)	intron (NM_029838, intron 5 of 37)	-196819	NM_001163587	71760	Mm.29125	NM_027907	ENSMUSG00000019232	Etnppl	1300019H02Rik|AI195447|Agxt2l1	ethanolamine phosphate phospholyase	protein-coding
mm_161215.1	chr13	66905414	66905414	+	1	NA	promoter-TSS (NM_026219)	promoter-TSS (NM_026219)	-1	NM_001177750	100038538	Mm.405005	NM_001177750	ENSMUSG00000074826	Gm10767	ENSMUSG00000074826	predicted gene 10767	protein-coding
mm_33667.1	chr4	133185042	133185074	+	1	NA	exon (NM_153423, exon 3 of 9)	exon (NM_153423, exon 3 of 9)	-10597	NR_105984	102466215		NR_105984	ENSMUSG00000099202	Mir7017	Gm27945|mmu-mir-7017	microRNA 7017	ncRNA
mm_105047.1	chr11	100619594	100619596	-	1	NA	exon (NM_019795, exon 1 of 14)	exon (NM_019795, exon 1 of 14)	573	NM_019795	56354	Mm.402409	NM_019795	ENSMUSG00000014195	Dnajc7	2010003F24Rik|2010004G07Rik|CCRP|Ttc2|mDj11|mTpr2	DnaJ heat shock protein family (Hsp40) member C7	protein-coding
mm_62585.1	chr7	105554500	105554514	+	1	NA	5' UTR (NM_011421, exon 1 of 6)	5' UTR (NM_011421, exon 1 of 6)	147	NM_011421	20597	Mm.4628	NM_011421	ENSMUSG00000037049	Smpd1	A-SMase|ASM|Zn-SMase|aSMase	sphingomyelin phosphodiesterase 1, acid lysosomal	protein-coding
mm_53935.1	chr6	4754236	4754257	-	1	NA	exon (NM_130877, exon 2 of 2)	exon (NM_130877, exon 2 of 2)	6940	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_160431.1	chr8	90932405	90932405	+	1	NA	5' UTR (NM_177224, exon 3 of 40)	5' UTR (NM_177224, exon 3 of 40)	156	NM_001310530	109151	Mm.100615	NM_177224	ENSMUSG00000056608	Chd9	1810014J18Rik|9030205D12Rik|A330063D19Rik|AD013|PRIC320|mKIAA0308	chromodomain helicase DNA binding protein 9	protein-coding
mm_65701.1	chr7	28377267	28377284	-	1	NA	3' UTR (NM_011756, exon 2 of 2)	3' UTR (NM_011756, exon 2 of 2)	1953	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_69634.1	chr7	137564607	137564620	-	1	NA	Intergenic	Intergenic	126939	NR_033611	620016	Mm.388932	NR_033611	ENSMUSG00000100863	Gm12669	OTTMUSG00000007920	glutaredoxin 3 pseudogene	pseudo
mm_93770.1	chr10	120362667	120362669	-	1	NA	3' UTR (NM_010441, exon 5 of 5)	3' UTR (NM_010441, exon 5 of 5)	-26855	NR_040626	320626	Mm.446091	NR_040626	ENSMUSG00000090191	9230105E05Rik	-	RIKEN cDNA 9230105E05 gene	ncRNA
mm_104999.1	chr11	100356138	100356144	-	1	NA	promoter-TSS (NM_177981)	promoter-TSS (NM_177981)	0	NM_177981	15114	Mm.281700	NM_010404	ENSMUSG00000006930	Hap1	HAP-1	huntingtin-associated protein 1	protein-coding
mm_79928.1	chr9	65630811	65630820	+	1	NA	5' UTR (NM_028030, exon 1 of 8)	5' UTR (NM_028030, exon 1 of 8)	233	NM_028030	71973	Mm.29148	NM_028030	ENSMUSG00000032387	Rbpms2	2400008B06Rik|AI316523	RNA binding protein with multiple splicing 2	protein-coding
mm_1980.1	chr1	86587126	86587156	+	1	NA	promoter-TSS (NM_172974)	promoter-TSS (NM_172974)	41	NM_172974	26895	Mm.12973	NM_172974	ENSMUSG00000026240	Cops7b	D1Wsu66e|E130114M23	COP9 signalosome subunit 7B	protein-coding
mm_112490.1	chr13	6548177	6548190	+	1	NA	promoter-TSS (NM_145131)	promoter-TSS (NM_145131)	26	NM_145131	69617	Mm.41933	NM_145131	ENSMUSG00000021193	Pitrm1	2310012C15Rik|AA410010|MP-1|MP1|Ntup1|PreP|mKIAA1104	pitrilysin metallepetidase 1	protein-coding
mm_77725.1	chr8	126847779	126847794	-	1	NA	Intergenic	Intergenic	98135	NM_024214	67952	Mm.6932	NM_024214	ENSMUSG00000093904	Tomm20	1810060K07Rik|BB284719|Gm19268|MAS20|MOM19|TOM20|mKIAA0016	translocase of outer mitochondrial membrane 20 homolog (yeast)	protein-coding
mm_107879.1	chr12	69986440	69986462	+	1	NA	intron (NM_022028, intron 1 of 4)	intron (NM_022028, intron 1 of 4)	551	NM_022028	64010	Mm.390480	NM_022028	ENSMUSG00000021067	Sav1	1700040G09Rik|Salv|Sav|WW45|Wwp3|Wwp4	salvador family WW domain containing 1	protein-coding
mm_66499.1	chr7	45061922	45061958	-	1	NA	promoter-TSS (NM_025533)	promoter-TSS (NM_025533)	-288	NM_022999	65116	Mm.379098	NM_022999	ENSMUSG00000007837	Prrg2	1600014G02Rik|2510041M06Rik|N4WBP1	proline-rich Gla (G-carboxyglutamic acid) polypeptide 2	protein-coding
mm_168370.1	chr1	119054770	119054781	-	1	NA	Intergenic	Intergenic	-1156	NM_001081125	14633	Mm.273292	NM_001081125	ENSMUSG00000048402	Gli2	-	GLI-Kruppel family member GLI2	protein-coding
mm_161592.1	chr16	35658321	35658321	+	1	NA	intron (NM_013661, intron 12 of 21)	intron (NM_013661, intron 12 of 21)	111035	NM_153550	224132	Mm.24094	NM_153550	ENSMUSG00000022848	Dirc2	RCC4	disrupted in renal carcinoma 2 (human)	protein-coding
mm_34135.1	chr4	139291077	139291135	+	1	NA	3' UTR (NM_001271405, exon 9 of 9)	3' UTR (NM_001271405, exon 9 of 9)	19594	NM_145384	212555	Mm.45131	NM_145384	ENSMUSG00000028744	Pqlc2	BC019216	PQ loop repeat containing 2	protein-coding
mm_78420.1	chr9	31030807	31030815	+	1	NA	5' UTR (NM_001115130, exon 1 of 6)	5' UTR (NM_001115130, exon 1 of 6)	167	NM_172765	235132	Mm.239355	NM_172765	ENSMUSG00000047412	Zbtb44	6030404E16Rik|Btbd15|E230011F09	zinc finger and BTB domain containing 44	protein-coding
mm_166263.1	chr5	87786642	87786647	-	1	NA	exon (NM_001304768, exon 11 of 13)	exon (NM_001304768, exon 11 of 13)	12194	NM_007785	12993	Mm.4908	NM_007785	ENSMUSG00000061937	Csn1s2a	Csng|PP22	casein alpha s2-like A	protein-coding
mm_74334.1	chr8	127064090	127064105	+	1	NA	promoter-TSS (NM_033620)	promoter-TSS (NM_033620)	41	NM_001309391	93742	Mm.299254	NM_033620	ENSMUSG00000025812	Pard3	AA960621|AI256638|Asip|D8Ertd580e|Par-3|Par3|Pard-3|Pard3a|Phip	par-3 family cell polarity regulator	protein-coding
mm_151109.1	chr19	47864317	47864325	+	1	NA	exon (NM_010362, exon 6 of 6)	exon (NM_010362, exon 6 of 6)	-1224	NM_030051	68214	Mm.63791	NM_026619	ENSMUSG00000025069	Gsto2	1700020F09Rik|4930425C18Rik|GSTO 2-2	glutathione S-transferase omega 2	protein-coding
mm_61643.1	chr7	80370320	80370359	+	1	NA	intron (NM_172903, intron 2 of 23)	intron (NM_172903, intron 2 of 23)	1036	NM_172903	140481	Mm.269245	NM_172903	ENSMUSG00000038886	Man2a2	1700052O22Rik|4931438M07Rik|AI480988|MX|Man IIx	mannosidase 2, alpha 2	protein-coding
mm_2670.1	chr1	127205348	127205405	+	1	NA	5' UTR (NM_145128, exon 1 of 18)	5' UTR (NM_145128, exon 1 of 18)	390	NM_145128	107895	Mm.214682	NM_145128	ENSMUSG00000036155	Mgat5	4930471A21Rik|5330407H02Rik|AI480971|GlcNAc-TV	mannoside acetylglucosaminyltransferase 5	protein-coding
mm_71866.1	chr8	69103645	69103703	+	1	NA	exon (NM_007509, exon 9 of 14)	exon (NM_007509, exon 9 of 14)	-14452	NM_153054	110877	Mm.19301	NM_153054	ENSMUSG00000036330	Slc18a1	4832416I10Rik|Vat1|Vmat1	solute carrier family 18 (vesicular monoamine), member 1	protein-coding
mm_141276.1	chr17	27820535	27820572	-	1	NA	promoter-TSS (NM_001271511)	promoter-TSS (NM_001271511)	-11	NM_001271511	224647	Mm.196577	NM_001033279	ENSMUSG00000056692	D17Wsu92e	AU020189|C030010A15|C80239	DNA segment, Chr 17, Wayne State University 92, expressed	protein-coding
mm_40651.1	chr5	65107619	65107655	+	1	NA	promoter-TSS (NM_001347355)	promoter-TSS (NM_001347355)	69	NM_001347355	71778	Mm.10281	NM_175174	ENSMUSG00000054920	Klhl5	1300013C10Rik	kelch-like 5	protein-coding
mm_123499.1	chr14	66213572	66213589	-	1	NA	promoter-TSS (NM_001162366)	promoter-TSS (NM_001162366)	-28	NM_001162366	19229	Mm.21613	NM_172498	ENSMUSG00000059456	Ptk2b	CADTK|CAKB|CAKbeta|E430023O05Rik|FADK2|FAK2|PYK2|Raftk	PTK2 protein tyrosine kinase 2 beta	protein-coding
mm_152016.1	chr19	5991579	5991627	-	1	NA	exon (NM_007600, exon 19 of 22)	exon (NM_007600, exon 19 of 22)	-5460	NM_198650	381203	Mm.329638	NM_198650	ENSMUSG00000037451	Slc22a20	Gm963|OAT1-L|mOAT6	solute carrier family 22 (organic anion transporter), member 20	protein-coding
mm_135461.1	chr16	45742889	45742947	-	1	NA	promoter-TSS (NM_001272070)	promoter-TSS (NM_001272070)	37	NM_001272070	213012	Mm.247453	NM_172511	ENSMUSG00000033157	Abhd10	-	abhydrolase domain containing 10	protein-coding
mm_60376.1	chr7	44468052	44468070	+	1	NA	promoter-TSS (NM_001205073)	promoter-TSS (NM_001205073)	81	NM_001205070	66124	Mm.358691	NM_025368	ENSMUSG00000038695	Josd2	1110007C05Rik	Josephin domain containing 2	protein-coding
mm_113664.1	chr13	42682079	42682093	+	1	NA	intron (NM_001302635, intron 1 of 13)	intron (NM_001302635, intron 1 of 13)	1287	NM_001302635	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding
mm_21838.1	chr2	165793337	165793362	-	1	NA	intron (NM_027230, intron 20 of 23)	intron (NM_027230, intron 20 of 23)	64824	NM_001252585	228880	Mm.227598	NM_027230	ENSMUSG00000039671	Zmynd8	1110013E22Rik|2010005I16Rik|3632413B07Rik|AI316811|AL024039|Prkcbp1|RACK7	zinc finger, MYND-type containing 8	protein-coding
mm_171649.1	chr4	38919654	38919673	+	1	NA	Intergenic	RLTR10C|LTR|ERVK	-530630	NM_001081095	75471	Mm.23522	NM_001081095	ENSMUSG00000028287	1700009N14Rik	AI429145	RIKEN cDNA 1700009N14 gene	protein-coding
mm_14801.1	chr2	145886644	145886654	+	1	NA	3' UTR (NM_028724, exon 13 of 13)	3' UTR (NM_028724, exon 13 of 13)	-16592	NM_026425	67877	Mm.151168	NM_026425	ENSMUSG00000002728	Naa20	1500004D14Rik|2900026I01Rik|AU041458|D2Ertd186e|Nat5	N(alpha)-acetyltransferase 20, NatB catalytic subunit	protein-coding
mm_45235.1	chr5	53594344	53594354	-	1	NA	intron (NM_001080927, intron 1 of 10)	intron (NM_001080927, intron 1 of 10)	3863	NM_001080927	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_65404.1	chr7	25229561	25229575	-	1	NA	non-coding (NR_046001, exon 1 of 1)	non-coding (NR_046001, exon 1 of 1)	845	NR_046001	77124	Mm.294664	NM_178400	ENSMUSG00000090330	9130221H12Rik	AU016887	RIKEN cDNA 9130221H12 gene	ncRNA
mm_124030.1	chr14	77024475	77024491	-	1	NA	3' UTR (NM_172488, exon 8 of 8)	3' UTR (NM_172488, exon 8 of 8)	12134	NM_172488	210808	Mm.89278	NM_172488	ENSMUSG00000044350	Lacc1	9030625A04Rik	laccase (multicopper oxidoreductase) domain containing 1	protein-coding
mm_133550.1	chr16	91372866	91372878	+	1	NA	promoter-TSS (NM_010509)	promoter-TSS (NM_010509)	89	NM_001110498	15976	Mm.6834	NM_010509	ENSMUSG00000022971	Ifnar2	AI747302|Ifnar-2	interferon (alpha and beta) receptor 2	protein-coding
mm_54295.1	chr6	29380427	29380435	-	1	NA	promoter-TSS (NM_007538)	promoter-TSS (NM_007538)	82	NM_007538	12057	Mm.56987	NM_007538	ENSMUSG00000058831	Opn1sw	AW551857|Bcp	opsin 1 (cone pigments), short-wave-sensitive (color blindness, tritan)	protein-coding
mm_45501.1	chr5	72264611	72264624	-	1	NA	intron (NM_153389, intron 12 of 22)	intron (NM_153389, intron 12 of 22)	61274	NM_153389	231287	Mm.32775	NM_153389	ENSMUSG00000046808	Atp10d	9830145H18Rik|ATPVD|D5Buc24e	ATPase, class V, type 10D	protein-coding
mm_44421.1	chr5	19226672	19226696	-	1	NA	promoter-TSS (NR_102342)	promoter-TSS (NR_102342)	-129	NR_102342	70832	Mm.398993	NR_102341	ENSMUSG00000097626	4921504A21Rik	-	RIKEN cDNA 4921504A21 gene	ncRNA
mm_137376.1	chr17	25717215	25717236	+	1	NA	promoter-TSS (NM_022422)	promoter-TSS (NM_022422)	53	NM_022422	64337	Mm.171123	NM_022422	ENSMUSG00000025739	Gng13	1500031D04Rik|AB030194|Ggamma13	guanine nucleotide binding protein (G protein), gamma 13	protein-coding
mm_13233.1	chr2	97630828	97630836	+	1	NA	exon (NM_178725, exon 3 of 3)	exon (NM_178725, exon 3 of 3)	163175	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_93528.1	chr10	115315618	115315624	-	1	NA	promoter-TSS (NM_024454)	promoter-TSS (NM_024454)	-30	NM_024454	216344	Mm.21936	NM_024454	ENSMUSG00000020132	Rab21	9630024B22	RAB21, member RAS oncogene family	protein-coding
mm_133710.1	chr16	93532409	93532427	+	1	NA	Intergenic	Intergenic	71397	NM_145482	224440	Mm.10628	NM_145482	ENSMUSG00000022948	Setd4	AY037804|C21orf18|ORF21	SET domain containing 4	protein-coding
mm_82201.1	chr9	124101945	124101959	+	1	NA	promoter-TSS (NM_009915)	promoter-TSS (NM_009915)	-231	NM_009915	12772	Mm.6272	NM_009915	ENSMUSG00000049103	Ccr2	Cc-ckr-2|Ccr2a|Ccr2b|Ckr2|Ckr2a|Ckr2b|Cmkbr2|mJe-r	chemokine (C-C motif) receptor 2	protein-coding
mm_154156.1	chr19	58455596	58455604	-	1	NA	promoter-TSS (NM_010279)	promoter-TSS (NM_010279)	-202	NM_010279	14585	Mm.88367	NM_010279	ENSMUSG00000025089	Gfra1	AU042498	glial cell line derived neurotrophic factor family receptor alpha 1	protein-coding
mm_169819.1	chr16	21409320	21409322	-	1	NA	Intergenic	(TTTC)n|Simple_repeat|Simple_repeat	-13797	NM_001285893	209018	Mm.235683	NM_145948	ENSMUSG00000033653	Vps8	AI315068|AU040738|mKIAA0804	VPS8 CORVET complex subunit	protein-coding
mm_37492.1	chr4	123613802	123613813	-	1	NA	intron (NM_001199136, intron 1 of 97)	intron (NM_001199136, intron 1 of 97)	-2613	NR_105824	102465214		NR_105824	ENSMUSG00000099005	Mir6398	Gm27657|mmu-mir-6398	microRNA 6398	ncRNA
mm_84796.1	chr9	77229429	77229440	-	1	NA	intron (NM_027150, intron 2 of 7)	intron (NM_027150, intron 2 of 7)	118436	NM_027150	69642	Mm.35008	NM_027150	ENSMUSG00000032355	Mlip	2310046A06Rik|AI931782|CIP	muscular LMNA-interacting protein	protein-coding
mm_8855.1	chr1	162713342	162713360	-	1	NA	exon (NM_001081290, exon 11 of 35)	exon (NM_001081290, exon 11 of 35)	27205	NM_001081290	226562	Mm.245446	NM_001081290	ENSMUSG00000040225	Prrc2c	1810043M20Rik|9630039I18Rik|A630006J20|Bat2d|Bat2d1|Bat2l2|E130112L15Rik|Prrc3|mKIAA1096	proline-rich coiled-coil 2C	protein-coding
mm_43903.1	chr5	144255224	144255242	+	1	NA	promoter-TSS (NM_018772)	promoter-TSS (NM_018772)	8	NM_018772	55950	Mm.38011	NM_018772	ENSMUSG00000047843	Bri3	I3	brain protein I3	protein-coding
mm_140568.1	chr17	8565693	8565705	-	1	NA	intron (NM_001290707, intron 1 of 22)	(CAAAA)n|Simple_repeat|Simple_repeat	38898	NM_001290707	23984	Mm.87161	NM_011866	ENSMUSG00000023868	Pde10a	-	phosphodiesterase 10A	protein-coding
mm_71592.1	chr8	54955024	54955024	+	1	NA	5' UTR (NM_153581, exon 1 of 7)	5' UTR (NM_153581, exon 1 of 7)	296	NM_001253756	234267	Mm.241700	NM_153581	ENSMUSG00000031517	Gpm6a	Gpm6|M6A	glycoprotein m6a	protein-coding
mm_170810.1	chr2	176121701	176121714	-	1	NA	Intergenic	Intergenic	-104858	NM_001305137	100504263	Mm.379980	NM_001305136	ENSMUSG00000078894	2210418O10Rik	Gm6182	predicted gene 2210418O10Rik	protein-coding
mm_145438.1	chr18	59062380	59062389	+	1	NA	promoter-TSS (NR_033765)	promoter-TSS (NR_033765)	3	NR_033765	225583	Mm.209711	NM_173759	ENSMUSG00000050875	A730017C20Rik	-	RIKEN cDNA A730017C20 gene	protein-coding
mm_88824.1	chr10	80804038	80804063	+	1	NA	exon (NM_013651, exon 9 of 9)	exon (NM_013651, exon 9 of 9)	-1198	NM_007445	11705	Mm.376094	NM_007445	ENSMUSG00000035262	Amh	MIS	anti-Mullerian hormone	protein-coding
mm_167327.1	chr8	70278074	70278086	+	1	NA	Intergenic	Intergenic	-4919	NM_011984	26558	Mm.388127	NM_011984	ENSMUSG00000003573	Homer3	AW146114	homer scaffolding protein 3	protein-coding
mm_93853.1	chr10	122047468	122047503	-	1	NA	promoter-TSS (NM_001081037)	promoter-TSS (NM_001081037)	-170	NM_001081037	117600	Mm.288698	NM_001081037	ENSMUSG00000020121	Srgap1	4930572H05Rik|Arhgap13	SLIT-ROBO Rho GTPase activating protein 1	protein-coding
mm_115534.1	chr13	6598379	6598382	-	1	NA	intron (NM_019703, intron 15 of 21)	intron (NM_019703, intron 15 of 21)	50223	NM_145131	69617	Mm.41933	NM_145131	ENSMUSG00000021193	Pitrm1	2310012C15Rik|AA410010|MP-1|MP1|Ntup1|PreP|mKIAA1104	pitrilysin metallepetidase 1	protein-coding
mm_48920.1	chr6	4004242	4004274	+	1	NA	5' UTR (NM_025331, exon 1 of 2)	5' UTR (NM_025331, exon 1 of 2)	271	NM_025331	66066	Mm.25547	NM_025331	ENSMUSG00000032766	Gng11	0610037B21Rik	guanine nucleotide binding protein (G protein), gamma 11	protein-coding
mm_161.1	chr1	12718674	12718753	+	1	NA	5' UTR (NM_172294, exon 1 of 22)	5' UTR (NM_172294, exon 1 of 22)	168	NM_172294	240725	Mm.45563	NM_172294	ENSMUSG00000016918	Sulf1	AI467640|AW121680|mKIAA1077	sulfatase 1	protein-coding
mm_92585.1	chr10	80039646	80039672	-	1	NA	promoter-TSS (NM_025554)	promoter-TSS (NM_025554)	0	NM_025554	66420	Mm.18579	NM_025554	ENSMUSG00000004667	Polr2e	2410021N14Rik|25kDa|AW208866|RPB5|XAP4	polymerase (RNA) II (DNA directed) polypeptide E	protein-coding
mm_15253.1	chr2	154859693	154859710	+	1	NA	exon (NM_001139513, exon 3 of 9)	exon (NM_001139513, exon 3 of 9)	33205	NM_026030	67204	Mm.377134	NM_026030	ENSMUSG00000074656	Eif2s2	2810026E11Rik|38kDa|AA408636|AA571381|AA986487|AW822225|D2Ertd303e|EIF2|EIF2B	eukaryotic translation initiation factor 2, subunit 2 (beta)	protein-coding
mm_139440.1	chr17	54138785	54138791	+	1	NA	Intergenic	MTB_Mm|LTR|ERVL-MaLR	-148157	NM_018751	20888	Mm.10108	NM_018751	ENSMUSG00000023943	Sult1c1	(PST)G|P-SULT|ST1C1|Stp2|Sult1a2|mOLFST	sulfotransferase family, cytosolic, 1C, member 1	protein-coding
mm_163600.1	chr13	44870072	44870101	-	1	NA	intron (NM_001205044, intron 4 of 18)	LSU-rRNA_Hsa|rRNA|rRNA	132010	NM_025772	94245	Mm.352311	NM_025772	ENSMUSG00000057531	Dtnbp1	5430437B18Rik|AW048963|Bloc1s8|dysbindin|sdy	dystrobrevin binding protein 1	protein-coding
mm_31947.1	chr4	86711139	86711151	+	1	NA	Intergenic	MLTR25A|LTR|ERVK	-37410	NM_184088	329877	Mm.273718	NM_184088	ENSMUSG00000038024	Dennd4c	1700065A05Rik|AA420392	DENN/MADD domain containing 4C	protein-coding
mm_132981.1	chr16	52144087	52144087	+	1	NA	intron (NM_001033238, intron 9 of 17)	intron (NM_001033238, intron 9 of 17)	112538	NM_001033238	208650	Mm.328206	NM_001033238	ENSMUSG00000022637	Cblb	AI429560|AI851073|Cbl-b	Casitas B-lineage lymphoma b	protein-coding
mm_6031.1	chr1	59548780	59548784	-	1	NA	intron (NM_001013771, intron 4 of 19)	intron (NM_001013771, intron 4 of 19)	32518	NM_001013771	381260	Mm.486706	NM_001013771	ENSMUSG00000047361	Gm973	AW554518	predicted gene 973	protein-coding
mm_72048.1	chr8	71337418	71337431	+	1	NA	intron (NM_015742, intron 14 of 39)	RSINE1|SINE|B4	-29424	NM_001145780	67023	Mm.41890	NM_025917	ENSMUSG00000002395	Use1	2010315L10Rik|5730403H22Rik|AV002165|D12|Ed2|Q-snare|p31	unconventional SNARE in the ER 1 homolog (S. cerevisiae)	protein-coding
mm_56047.1	chr6	86737734	86737744	-	1	NA	3' UTR (NM_001331120, exon 13 of 13)	3' UTR (NM_001331120, exon 13 of 13)	-4361	NM_011818	23885	Mm.321452	NM_011818	ENSMUSG00000001157	Gmcl1	2810049L19Rik|Btbd13|DIP|Gcl|Gcl-1|glc-1|mglc-1	germ cell-less, spermatogenesis associated 1	protein-coding
mm_50814.1	chr6	54329839	54329843	+	1	NA	3' UTR (NM_030024, exon 2 of 2)	3' UTR (NM_030024, exon 2 of 2)	2829	NM_030024	78004	Mm.41984	NM_030024	ENSMUSG00000045725	Prr15	E130201N16Rik|G90	proline rich 15	protein-coding
mm_13655.1	chr2	114055150	114055161	+	1	NA	non-coding (NR_028422, exon 1 of 3)	non-coding (NR_028422, exon 1 of 3)	759	NR_028422	100303644	Mm.330469	NR_028422	ENSMUSG00000092397	C130080G10Rik	-	RIKEN cDNA C130080G10 gene	ncRNA
mm_168245.1	chr10	81986397	81986414	-	1	NA	Intergenic	Intergenic	-55893	NM_001346707	100040944		NM_001346707		Gm3055	-	predicted gene 3055	protein-coding
mm_5376.1	chr1	30948676	30948678	-	1	NA	intron (NM_011200, intron 1 of 5)	intron (NM_011200, intron 1 of 5)	1033	NR_002688	433406	Mm.389003	NR_002688		Gm13363	OTTMUSG00000011595	predicted gene 13363	pseudo
mm_132684.1	chr16	43072167	43072172	+	1	NA	intron (NM_001285805, intron 2 of 10)	intron (NM_001285805, intron 2 of 10)	116589	NR_002445	170658	Mm.375824	NR_002445		BC002163	-	NADH dehydrogenase Fe-S protein 5 pseudogene	pseudo
mm_100534.1	chr11	120617307	120617314	+	1	NA	intron (NM_001347615, intron 1 of 12)	ID2|SINE|ID	580	NM_024229	68671	Mm.21439	NM_024229	ENSMUSG00000025137	Pcyt2	1110033E03Rik|ET	phosphate cytidylyltransferase 2, ethanolamine	protein-coding
mm_63157.1	chr7	123421511	123421521	+	1	NA	intron (NM_025304, intron 7 of 10)	intron (NM_025304, intron 7 of 10)	-40778	NM_007474	11833	Mm.273175	NM_007474	ENSMUSG00000030762	Aqp8	AI255744|AQP-8	aquaporin 8	protein-coding
mm_61512.1	chr7	78885620	78885651	+	1	NA	Intergenic	Intergenic	-2642	NR_029826	723884		NR_029826	ENSMUSG00000065609	Mir7-2	Mir7a2|Mirn7-2|mir-7a-2|mir-7a2|mmu-mir-7-2|mmu-mir-7a2	microRNA 7-2	ncRNA
mm_14896.1	chr2	149830790	149830807	+	1	NA	promoter-TSS (NM_001085521)	promoter-TSS (NM_001085521)	15	NM_001085521	433485	Mm.330649	NM_001085521	ENSMUSG00000074736	Syndig1	AW123113|DSPC2|Gm14134|H2C20orf39|OTTMUSG00000015750|Tmem90b	synapse differentiation inducing 1	protein-coding
mm_36027.1	chr4	57120008	57120014	-	1	NA	intron (NM_019427, intron 1 of 15)	intron (NM_019427, intron 1 of 15)	23145	NM_019427	54357	Mm.28217	NM_019427	ENSMUSG00000028434	Epb41l4b	6430543G08Rik|AA589614|AU021054|BB007528|D4Ertd346e|Ehm2|Epb4.1l4b|Lulu2	erythrocyte membrane protein band 4.1 like 4b	protein-coding
mm_145737.1	chr18	64265226	64265234	+	1	NA	5' UTR (NM_009182, exon 3 of 6)	5' UTR (NM_009182, exon 3 of 6)	10871	NM_009182	20451	Mm.252110	NM_009182	ENSMUSG00000056812	St8sia3	AI847333|ST8SiaIII|Siat8c	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3	protein-coding
mm_3298.1	chr1	136696199	136696213	+	1	NA	promoter-TSS (NR_037986)	promoter-TSS (NR_037986)	-5	NR_037986	100503474	Mm.428276	NR_037986		Platr22	Gm16880	pluripotency associated transcript 22	ncRNA
mm_857.1	chr1	52127732	52127744	+	1	NA	intron (NM_001205313, intron 5 of 24)	intron (NM_001205313, intron 5 of 24)	8116	NM_001205313	20846	Mm.277406	NM_009283	ENSMUSG00000026104	Stat1	2010005J02Rik|AA408197	signal transducer and activator of transcription 1	protein-coding
mm_115827.1	chr13	21286481	21286486	-	1	NA	TTS (NM_010343)	TTS (NM_010343)	6203	NM_010343	14780	Mm.1332	NM_010343	ENSMUSG00000004344	Gpx5	AV379049|Arep	glutathione peroxidase 5	protein-coding
mm_116753.1	chr13	52507631	52507640	-	1	NA	3' UTR (NM_001024474, exon 2 of 2)	3' UTR (NM_001024474, exon 2 of 2)	23201	NM_001024474	68203	Mm.29362	NM_001024474	ENSMUSG00000047842	Diras2	2900052J15Rik|AI414999	DIRAS family, GTP-binding RAS-like 2	protein-coding
mm_52948.1	chr6	122952811	122952832	+	1	NA	5' UTR (NM_153197, exon 1 of 6)	5' UTR (NM_153197, exon 1 of 6)	177	NM_153197	73149	Mm.25684	NM_153197	ENSMUSG00000043832	Clec4a3	3110037K17Rik|Dcir3	C-type lectin domain family 4, member a3	protein-coding
mm_116225.1	chr13	32964053	32964062	-	1	NA	Intergenic	Intergenic	-1456	NM_011454	20708	Mm.36526	NM_011454	ENSMUSG00000042842	Serpinb6b	NK13|Spi12|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 6b	protein-coding
mm_63268.1	chr7	126759781	126759789	+	1	NA	exon (NM_011952, exon 1 of 9)	exon (NM_011952, exon 1 of 9)	159	NM_011952	26417	Mm.8385	NM_011952	ENSMUSG00000063065	Mapk3	Erk-1|Erk1|Ert2|Esrk1|Mnk1|Mtap2k|Prkm3|p44|p44erk1|p44mapk	mitogen-activated protein kinase 3	protein-coding
mm_56295.1	chr6	91515879	91515889	-	1	NA	promoter-TSS (NM_009531)	promoter-TSS (NM_009531)	4	NM_009531	22591	Mm.2806	NM_009531	ENSMUSG00000030094	Xpc	-	xeroderma pigmentosum, complementation group C	protein-coding
mm_17216.1	chr2	25493883	25493889	-	1	NA	promoter-TSS (NM_029958)	promoter-TSS (NM_029958)	25	NM_029958	77701	Mm.99123	NM_029958	ENSMUSG00000026943	Lcn12	9230102M18Rik	lipocalin 12	protein-coding
mm_94209.1	chr11	3105665	3105681	+	1	NA	Intergenic	IAPLTR3-int|LTR|ERVK	-18348	NR_003517	236604	Mm.247625	NM_001004146		Pisd-ps1	-	phosphatidylserine decarboxylase, pseudogene 1	pseudo
mm_44941.1	chr5	36509372	36509380	-	1	NA	intron (NM_133910, intron 9 of 13)	intron (NM_133910, intron 9 of 13)	21247	NM_001113364	100855	Mm.486203	NM_133910	ENSMUSG00000029192	Tbc1d14	2810413P16Rik|AU043625|C86258|D5Ertd110e|mKIAA1322	TBC1 domain family, member 14	protein-coding
mm_137705.1	chr17	29098600	29098645	+	1	NA	exon (NM_007669, exon 2 of 3)	exon (NM_007669, exon 2 of 3)	4853	NM_007669	12575	Mm.195663	NM_007669	ENSMUSG00000023067	Cdkn1a	CAP20|CDKI|CIP1|Cdkn1|P21|SDI1|Waf1|mda6|p21Cip1|p21WAF	cyclin-dependent kinase inhibitor 1A (P21)	protein-coding
mm_83898.1	chr9	56139385	56139385	-	1	NA	intron (NM_019793, intron 6 of 6)	L1_Mur3|LINE|L1	21685	NM_019793	56434	Mm.28484	NM_019793	ENSMUSG00000032324	Tspan3	1700055K04Rik|TM4-A|Tm4sf8	tetraspanin 3	protein-coding
mm_61499.1	chr7	75848352	75848401	+	1	NA	promoter-TSS (NM_001122780)	promoter-TSS (NM_001122780)	38	NM_029652	207952	Mm.206223	NM_029652	ENSMUSG00000055652	Klhl25	2810402K13Rik|BC027373|Enc-1	kelch-like 25	protein-coding
mm_54117.1	chr6	18030394	18030403	-	1	NA	promoter-TSS (NM_023653)	promoter-TSS (NM_023653)	47	NM_023653	22413	Mm.33653	NM_023653	ENSMUSG00000010797	Wnt2	2610510E18Rik|Int1l1|Irp|Mirp|Wnt-2|Wnt2a	wingless-type MMTV integration site family, member 2	protein-coding
mm_171503.1	chr4	146270337	146270344	+	1	NA	promoter-TSS (NM_001083918).2	promoter-TSS (NM_001083918).2	-45	NM_001083918	666532	Mm.392861	NM_001083918	ENSMUSG00000067916	Zfp991	Gm13139|OTTMUSG00000010657	zinc finger protein 991	protein-coding
mm_144602.1	chr18	32395912	32395951	+	1	NA	intron (NM_001083334, intron 1 of 14)	MTD|LTR|ERVL-MaLR	-17647	NR_045403	402767	Mm.385109	NR_045403	ENSMUSG00000097413	A830052D11Rik	-	RIKEN cDNA A830052D11 gene	ncRNA
mm_167424.1	chr8	111689319	111689333	+	1	NA	TTS (NR_106044)	TTS (NR_106044)	348	NR_106044	102466993		NR_106044	ENSMUSG00000099129	Mir7076	Gm27318|mmu-mir-7076	microRNA 7076	ncRNA
mm_95844.1	chr11	57518658	57518722	+	1	NA	promoter-TSS (NM_145426)	promoter-TSS (NM_145426)	25	NM_145426	216760	Mm.30501	NM_145426	ENSMUSG00000020522	Mfap3	2610509F16Rik|2700079M14Rik|AW536327	microfibrillar-associated protein 3	protein-coding
mm_107477.1	chr12	37880701	37880728	+	1	NA	promoter-TSS (NM_178681)	promoter-TSS (NM_178681)	9	NM_178681	217480	Mm.126525	NM_178681	ENSMUSG00000036095	Dgkb	6430574F24|90kda|C630029D13Rik|DAGK2|DGK|DGK-beta|mKIAA0718	diacylglycerol kinase, beta	protein-coding
mm_173141.1	chrX	21680615	21680625	-	1	NA	Intergenic	L1_Mur3|LINE|L1	-34280	NM_020049	56774	Mm.253984	NM_020049	ENSMUSG00000031089	Slc6a14	1110007A17Rik|9030613J17Rik|ATB0plus|CATB0plus	solute carrier family 6 (neurotransmitter transporter), member 14	protein-coding
mm_90689.1	chr10	128940684	128940694	+	1	NA	exon (NM_008398, exon 4 of 25)	exon (NM_008398, exon 4 of 25)	6876	NM_001330160	16404	Mm.179747	NM_008398	ENSMUSG00000025348	Itga7	[a]7|alpha7	integrin alpha 7	protein-coding
mm_66176.1	chr7	34013883	34013888	-	1	NA	promoter-TSS (NM_001276475)	promoter-TSS (NM_001276475)	57	NM_001276475	233099	Mm.110829	NM_001100464	ENSMUSG00000066584	Scgb2b27	Abpbg27|Abpbg5|Scgb2b5	secretoglobin, family 2B, member 27	protein-coding
mm_53382.1	chr6	129514453	129514456	+	1	NA	intron (NM_001081186, intron 2 of 4)	intron (NM_001081186, intron 2 of 4)	1897	NM_001081186	330428	Mm.44237	NM_001081186	ENSMUSG00000030160	Tmem52b	D630042F21Rik	transmembrane protein 52B	protein-coding
mm_109289.1	chr12	109559300	109559315	+	1	NA	non-coding (NR_003633, exon 5 of 5)	non-coding (NR_003633, exon 5 of 5)	-4385	NR_030427	791079		NR_030427	ENSMUSG00000076451	Mir770	Mirn770|mir-770|mmu-mir-770	microRNA 770	ncRNA
mm_71571.1	chr8	54077495	54077524	+	1	NA	promoter-TSS (NM_009506)	promoter-TSS (NM_009506)	-23	NM_009506	22341	Mm.1402	NM_009506	ENSMUSG00000031520	Vegfc	AW228853|VEGF-C	vascular endothelial growth factor C	protein-coding
mm_126382.1	chr15	80173305	80173410	+	1	NA	promoter-TSS (NM_010795)	promoter-TSS (NM_010795)	-364	NM_010795	17309	Mm.299693	NM_010795	ENSMUSG00000042428	Mgat3	1110038J12Rik|AI848272|GnT-III	mannoside acetylglucosaminyltransferase 3	protein-coding
mm_23241.1	chr3	51221190	51221200	+	1	NA	Intergenic	Intergenic	-3252	NM_009834	12457	Mm.86541	NM_009834	ENSMUSG00000023087	Noct	AU043840|Ccr4|Ccrn4l	nocturnin	protein-coding
mm_128385.1	chr15	43078156	43078182	-	1	NA	exon (NM_172815, exon 4 of 6)	exon (NM_172815, exon 4 of 6)	92649	NM_172815	239405	Mm.193274	NM_172815	ENSMUSG00000051920	Rspo2	2610028F08Rik|AA673245|D430027K22|ftls	R-spondin 2	protein-coding
mm_62072.1	chr7	92741633	92741715	+	1	NA	promoter-TSS (NM_029494)	promoter-TSS (NM_029494)	-40	NM_029494	75985	Mm.323004	NM_029494	ENSMUSG00000030643	Rab30	5033421K01Rik|AI323892|Rsb30	RAB30, member RAS oncogene family	protein-coding
mm_158433.1	chrX	139997849	139997864	-	1	NA	intron (NM_001172147, intron 1 of 7)	intron (NM_001172147, intron 1 of 7)	739	NM_153586	237073	Mm.256670	NM_153586	ENSMUSG00000031433	Rbm41	BB131279|D330023I21Rik	RNA binding motif protein 41	protein-coding
mm_155965.1	chrX	106027593	106027596	+	1	NA	intron (NM_001109757, intron 1 of 22)	intron (NM_001109757, intron 1 of 22)	370	NM_009726	11977	Mm.254297	NM_009726	ENSMUSG00000033792	Atp7a	MNK	ATPase, Cu++ transporting, alpha polypeptide	protein-coding
mm_13713.1	chr2	117178621	117178633	+	1	NA	3' UTR (NM_033524, exon 7 of 7)	3' UTR (NM_033524, exon 7 of 7)	-6500	NR_030440	732489		NR_030440	ENSMUSG00000076376	Mir674	Mirn674|mir-674|mmu-mir-674	microRNA 674	ncRNA
mm_99821.1	chr11	108682644	108682652	+	1	NA	promoter-TSS (NM_029586)	promoter-TSS (NM_029586)	30	NM_029586	76380	Mm.344071	NM_029586	ENSMUSG00000020728	Cep112	1700001M19Rik|1700029K01Rik|8430407H02Rik|AV043680|AV207351|Ccdc46|Macoco	centrosomal protein 112	protein-coding
mm_106545.1	chr11	120579229	120579244	-	1	NA	exon (NM_133796, exon 6 of 6)	exon (NM_133796, exon 6 of 6)	2384	NM_133796	192662	Mm.30016	NM_133796	ENSMUSG00000025132	Arhgdia	5330430M07Rik|Gdi-1|Rho-GDI|RhoDGI|RhoGDI-1	Rho GDP dissociation inhibitor (GDI) alpha	protein-coding
mm_68628.1	chr7	118129568	118129584	-	1	NA	promoter-TSS (NM_019419)	promoter-TSS (NM_019419)	49	NM_019419	54208	Mm.29924	NM_019419	ENSMUSG00000030654	Arl6ip1	AIP-6|AL022945|ARMER|AU042858|Aip-1|Arl6ip|C85138|mKIAA0069	ADP-ribosylation factor-like 6 interacting protein 1	protein-coding
mm_169800.1	chr16	17222402	17222402	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-11185	NM_178922	58180	Mm.261602	NM_178922	ENSMUSG00000050240	Hic2	AA409108|HRG22|mKIAA1020	hypermethylated in cancer 2	protein-coding
mm_50539.1	chr6	49046151	49046161	+	1	NA	intron (NM_053110, intron 4 of 10)	intron (NM_053110, intron 4 of 10)	9638	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_128609.1	chr15	58823408	58823459	-	1	NA	promoter-TSS (NM_175212)	promoter-TSS (NM_175212)	-6	NM_175212	74868	Mm.293754	NM_175212	ENSMUSG00000062373	Tmem65	2610029O13Rik|4930438D12Rik	transmembrane protein 65	protein-coding
mm_126618.1	chr15	83122214	83122261	+	1	NA	intron (NM_029101, intron 1 of 6)	intron (NM_029101, intron 1 of 6)	564	NM_029101	74778	Mm.30056	NM_029101	ENSMUSG00000018040	Rrp7a	1110014J01Rik|AA408146|Kheg1	ribosomal RNA processing 7 homolog A (S. cerevisiae)	protein-coding
mm_8693.1	chr1	157256820	157256841	-	1	NA	intron (NM_177644, intron 3 of 17)	intron (NM_177644, intron 3 of 17)	-148150	NM_001305063	73435	Mm.116705	NM_028540	ENSMUSG00000026592	Tex35	1700057K13Rik	testis expressed 35	protein-coding
mm_74761.1	chr8	19600935	19600935	-	1	NA	Intergenic	Intergenic	105838	NM_139220	246080	Mm.207067	NM_139220	ENSMUSG00000037790	Defb7	BD-7|Defb15	defensin beta 7	protein-coding
mm_36012.1	chr4	56846061	56846093	-	1	NA	intron (NM_018761, intron 2 of 18)	intron (NM_018761, intron 2 of 18)	19134	NM_018761	54366	Mm.218891	NM_018761	ENSMUSG00000038816	Ctnnal1	ACRP|AI616177|AW545119|C86009|Catnal1	catenin (cadherin associated protein), alpha-like 1	protein-coding
mm_53040.1	chr6	124663086	124663086	+	1	NA	promoter-TSS (NM_145130)	promoter-TSS (NM_145130)	-18	NM_145130	14792	Mm.273915	NM_145130	ENSMUSG00000004270	Lpcat3	C3f|Grcc3f|Lpcat|Lpeat|Lplat5|Lpsat|Mboat5|Moact5|Oact5|PTG	lysophosphatidylcholine acyltransferase 3	protein-coding
mm_60083.1	chr7	34168660	34168676	+	1	NA	promoter-TSS (NM_016682)	promoter-TSS (NM_016682)	-139	NM_016682	50995	Mm.27560	NM_016682	ENSMUSG00000052997	Uba2	AA986091|Arx|Sae2|UBA1|Ubl1a2|Uble1b	ubiquitin-like modifier activating enzyme 2	protein-coding
mm_144401.1	chr18	20762682	20762694	+	1	NA	Intergenic	MTC-int|LTR|ERVL-MaLR	-16284	NM_019737	56386	Mm.393827	NM_019737	ENSMUSG00000056124	B4galt6	AA536803|AU022389	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 6	protein-coding
mm_135225.1	chr16	36784827	36784848	-	1	NA	5' UTR (NM_021301, exon 1 of 22)	5' UTR (NM_021301, exon 1 of 22)	125	NM_001145899	57738	Mm.281804	NM_021301	ENSMUSG00000022899	Slc15a2	8430408C16Rik|C78862|Pept2	solute carrier family 15 (H+/peptide transporter), member 2	protein-coding
mm_139480.1	chr17	56009500	56009523	+	1	NA	exon (NM_026530, exon 2 of 13)	exon (NM_026530, exon 2 of 13)	310	NM_026530	68047	Mm.358710	NM_026530	ENSMUSG00000003199	Mpnd	E130307M08Rik	MPN domain containing	protein-coding
mm_73151.1	chr8	94994366	94994390	+	1	NA	intron (NM_018882, intron 1 of 13)	intron (NM_018882, intron 1 of 13)	9979	NM_018882	14766	Mm.290834	NM_018882	ENSMUSG00000031785	Adgrg1	Cyt28|Gpr56|TM7LN4|TM7XN1	adhesion G protein-coupled receptor G1	protein-coding
mm_164376.1	chr16	27302883	27302883	+	1	NA	Intergenic	L1M4|LINE|L1	-4758	NM_198112	239790	Mm.390880	NM_198112	ENSMUSG00000052276	Ostn	Ostc	osteocrin	protein-coding
mm_74858.1	chr8	24814119	24814126	-	1	NA	intron (NM_001272059, intron 5 of 18)	MTD|LTR|ERVL-MaLR	10247	NM_001272058	11499	Mm.143889	NM_007401	ENSMUSG00000031554	Adam5	tMDC II|tMDCII	a disintegrin and metallopeptidase domain 5	protein-coding
mm_60991.1	chr7	49246132	49246202	+	1	NA	promoter-TSS (NM_175272)	promoter-TSS (NM_175272)	-22	NM_175272	78286	Mm.333881	NM_175272	ENSMUSG00000052512	Nav2	5330421F07Rik|AU067780|BQ960892|HELAD1|POMFIL2|RAINB1|RAINB2|Unc53H2|mKIAA3015	neuron navigator 2	protein-coding
mm_111141.1	chr12	81781044	81781066	-	1	NA	5' UTR (NM_177395, exon 1 of 8)	5' UTR (NM_177395, exon 1 of 8)	115	NM_177395	338372	Mm.35284	NM_177395	ENSMUSG00000042724	Map3k9	E130314H24Rik|Mlk1|Prke1	mitogen-activated protein kinase kinase kinase 9	protein-coding
mm_106068.1	chr11	116138851	116138859	-	1	NA	promoter-TSS (NM_024177)	promoter-TSS (NM_024177)	13	NM_024177	60441	Mm.29974	NM_024177	ENSMUSG00000020775	Mrpl38	1110036N21Rik|4733401F03Rik|MRP-L3|R75240|Rpml3	mitochondrial ribosomal protein L38	protein-coding
mm_26866.1	chr3	16006382	16006400	-	1	NA	promoter-TSS (NM_001081687)	promoter-TSS (NM_001081687)	-59	NM_001081687	381484	Mm.217376	NM_001081687	ENSMUSG00000078780	Gm5150	-	predicted gene 5150	protein-coding
mm_143713.1	chr17	80728027	80728061	-	1	NA	promoter-TSS (NM_001290345)	promoter-TSS (NM_001290345)	-19	NM_001290345	225028	Mm.311948	NM_001081357	ENSMUSG00000024242	Map4k3	4833416M01Rik|4833416M07Rik|9530052P13Rik|Glk|MAPKKKK3|MEKKK 3|MEKKK3|RAB8IPL1	mitogen-activated protein kinase kinase kinase kinase 3	protein-coding
mm_78299.1	chr9	22448707	22448778	+	1	NA	exon (NM_018739, exon 6 of 6)	exon (NM_018739, exon 6 of 6)	19614	NM_018739	55934	Mm.38235	NM_018739	ENSMUSG00000032239	Rp9	PAP-1|Rp9h	retinitis pigmentosa 9 (human)	protein-coding
mm_70686.1	chr8	15011268	15011301	+	1	NA	5' UTR (NM_029116, exon 1 of 2)	5' UTR (NM_029116, exon 1 of 2)	259	NM_029116	74901	Mm.46675	NM_029116	ENSMUSG00000055675	Kbtbd11	2900016B01Rik|4930465M17Rik|mKIAA0711	kelch repeat and BTB (POZ) domain containing 11	protein-coding
mm_163841.1	chr14	19417974	19417984	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	184608	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_57757.1	chr6	129230263	129230293	-	1	NA	Intergenic	Intergenic	7767	NR_040265	76432	Mm.261738	NR_040265	ENSMUSG00000097354	2310001H17Rik	AI646108	RIKEN cDNA 2310001H17 gene	ncRNA
mm_47768.1	chr5	131538674	131538684	-	1	NA	intron (NM_177047, intron 5 of 18)	CpG	-231157	NM_145218	212996	Mm.299204	NM_145218	ENSMUSG00000034040	Wbscr17	AA388321|E330012B09Rik	Williams-Beuren syndrome chromosome region 17 homolog (human)	protein-coding
mm_132314.1	chr16	33726672	33726688	+	1	NA	exon (NM_175256, exon 4 of 15)	exon (NM_175256, exon 4 of 15)	42214	NM_175256	77446	Mm.245741	NM_172934	ENSMUSG00000075254	Heg1	4632417D23Rik|5530401I02Rik|9530025L16Rik|BC038614|Gm629|OTTMUSG00000027315	heart development protein with EGF-like domains 1	protein-coding
mm_11792.1	chr2	43183908	43183909	+	1	NA	Intergenic	Intergenic	-371417	NM_001289593	70789	Mm.105278	NM_027552	ENSMUSG00000026866	Kynu	4432411A05Rik	kynureninase (L-kynurenine hydrolase)	protein-coding
mm_10657.1	chr2	20722371	20722386	+	1	NA	intron (NM_029895, intron 6 of 18)	intron (NM_029895, intron 6 of 18)	202865	NM_001177631	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding
mm_5478.1	chr1	36699775	36699778	-	1	NA	3' UTR (NM_146107, exon 11 of 11)	3' UTR (NM_146107, exon 11 of 11)	8289	NM_009942	12859	Mm.180182	NM_009942	ENSMUSG00000061518	Cox5b	-	cytochrome c oxidase subunit Vb	protein-coding
mm_165396.1	chr2	134845568	134845574	+	1	NA	intron (NM_019677, intron 2 of 32)	intron (NM_019677, intron 2 of 32)	59407	NM_001145830	18795	Mm.330607	NM_019677	ENSMUSG00000051177	Plcb1	3110043I21Rik|AI132408|Plcb|mKIAA0581	phospholipase C, beta 1	protein-coding
mm_9102.1	chr1	169975026	169975038	-	1	NA	3' UTR (NM_022563, exon 17 of 17)	3' UTR (NM_022563, exon 17 of 17)	5623	NR_040438	67303	Mm.396611	NR_040438	ENSMUSG00000097503	3110045C21Rik	AI838577	RIKEN cDNA 3110045C21 gene	ncRNA
mm_65807.1	chr7	28981788	28981821	-	1	NA	promoter-TSS (NM_028659)	promoter-TSS (NM_028659)	84	NM_001285943	73830	Mm.29714	NM_028659	ENSMUSG00000053565	Eif3k	1200009C21Rik|Eif3s12	eukaryotic translation initiation factor 3, subunit K	protein-coding
mm_9296.1	chr1	171637324	171637337	-	1	NA	exon (NM_144539, exon 6 of 8)	exon (NM_144539, exon 6 of 8)	4570	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_135446.1	chr16	45531983	45532042	-	1	NA	Intergenic	Intergenic	-3254	NM_198106	208169	Mm.277437	NM_198106	ENSMUSG00000033210	Slc9c1	Gm610|NHE-10|Slc9a10|sNHE|spermNHE	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	protein-coding
mm_169991.1	chr17	15498312	15498314	-	1	NA	promoter-TSS (NM_011185)	promoter-TSS (NM_011185)	-37	NM_011185	19170	Mm.32912	NM_011185	ENSMUSG00000014769	Psmb1	AA409053|C81484|Lmpc5	proteasome (prosome, macropain) subunit, beta type 1	protein-coding
mm_141023.1	chr17	25140323	25140330	-	1	NA	intron (NM_001317404, intron 1 of 24)	intron (NM_001317404, intron 1 of 24)	3695	NM_001317404	26373	Mm.270587	NM_011930	ENSMUSG00000036636	Clcn7	ClC-7|D17Wsu51e	chloride channel, voltage-sensitive 7	protein-coding
mm_98011.1	chr11	84525648	84525658	+	1	NA	promoter-TSS (NM_008498)	promoter-TSS (NM_008498)	-7	NR_038057	78365	Mm.260345	NR_038057	ENSMUSG00000087211	Lhx1os	1500016L03Rik|Lhx1as	LIM homeobox 1, opposite strand	ncRNA
mm_153554.1	chr19	42128970	42128980	-	1	NA	promoter-TSS (NM_027106)	promoter-TSS (NM_027106)	18	NM_027106	69534	Mm.30060	NM_027106	ENSMUSG00000018821	Avpi1	2310008N12Rik|AA410041|VIT32|esu|mVIT32	arginine vasopressin-induced 1	protein-coding
mm_87085.1	chr10	30010895	30010925	+	1	NA	Intergenic	Intergenic	189630	NM_001109747	66311	Mm.251779	NM_001109747	ENSMUSG00000075266	Cenpw	2610036L11Rik|Cug2	centromere protein W	protein-coding
mm_66559.1	chr7	45239042	45239066	-	1	NA	promoter-TSS (NM_007645)	promoter-TSS (NM_007645)	61	NM_001290802	12493	Mm.3689	NM_007645	ENSMUSG00000030798	Cd37	Tspan26	CD37 antigen	protein-coding
mm_151588.1	chr19	3282802	3282853	-	1	NA	promoter-TSS (NM_001347420)	promoter-TSS (NM_001347420)	-74	NM_001347420	353242	Mm.74084	NM_172252	ENSMUSG00000024829	Mrpl21	BC028768	mitochondrial ribosomal protein L21	protein-coding
mm_160968.1	chr11	99804446	99804446	-	1	NA	promoter-TSS (NM_001099312)	promoter-TSS (NM_001099312)	0	NM_001099312	670472	Mm.425705	NM_001099312	ENSMUSG00000078260	Gm11569	OTTMUSG00000002208	predicted gene 11569	protein-coding
mm_36746.1	chr4	100568005	100568037	-	1	NA	Intergenic	Intergenic	89154	NM_001033773	381534	Mm.318133	NM_001033773	ENSMUSG00000069733	Ube2u	-	ubiquitin-conjugating enzyme E2U (putative)	protein-coding
mm_152764.1	chr19	20385632	20385635	-	1	NA	intron (NM_010730, intron 1 of 12)	intron (NM_010730, intron 1 of 12)	5038	NM_010730	16952	Mm.248360	NM_010730	ENSMUSG00000024659	Anxa1	Anx-1|Anx-A1|C430014K04Rik|Lpc-1|Lpc1	annexin A1	protein-coding
mm_144496.1	chr18	24206016	24206038	+	1	NA	promoter-TSS (NM_001160404)	promoter-TSS (NM_001160404)	33	NM_001160404	14423	Mm.30249	NM_013814	ENSMUSG00000000420	Galnt1	-	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 1	protein-coding
mm_10543.1	chr2	16548738	16548755	+	1	NA	intron (NM_026162, intron 3 of 13)	intron (NM_026162, intron 3 of 13)	192442	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding
mm_110320.1	chr12	34714338	34714349	-	1	NA	intron (NM_001271386, intron 3 of 27)	intron (NM_001271386, intron 3 of 27)	-185454	NM_024124	79221	Mm.310551	NM_024124	ENSMUSG00000004698	Hdac9	AV022454|D030072B18Rik|HD7B|HD9|HDRP|Hdac7b|Mitr|mKIAA0744	histone deacetylase 9	protein-coding
mm_84054.1	chr9	58159013	58159032	-	1	NA	promoter-TSS (NM_001195431)	promoter-TSS (NM_001195431)	199	NM_012043	26968	Mm.367887	NM_012043	ENSMUSG00000037206	Islr	AW553146|Meflin	immunoglobulin superfamily containing leucine-rich repeat	protein-coding
mm_29647.1	chr3	122195085	122195087	-	1	NA	Intergenic	Intergenic	-50471	NM_008129	14630	Mm.292676	NM_008129	ENSMUSG00000028124	Gclm	AI649393|Gcmc|Glclr	glutamate-cysteine ligase, modifier subunit	protein-coding
mm_162107.1	chrX	48674478	48674478	-	1	NA	promoter-TSS (NM_181751)	promoter-TSS (NM_181751)	0	NM_181751	236781	Mm.269129	NM_181751	ENSMUSG00000051209	Gpr119	-	G-protein coupled receptor 119	protein-coding
mm_100160.1	chr11	116382706	116382717	+	1	NA	intron (NM_027258, intron 2 of 18)	intron (NM_027258, intron 2 of 18)	30321	NM_027258	217340	Mm.426344	NM_027258	ENSMUSG00000052949	Rnf157	2610036E23Rik|A130073L17Rik|mKIAA1917	ring finger protein 157	protein-coding
mm_114449.1	chr13	66933347	66933357	+	1	NA	promoter-TSS (NM_025547)	promoter-TSS (NM_025547)	-280	NM_025547	66410	Mm.347939	NM_025547	ENSMUSG00000021519	Mterf3	2410017I18Rik|Mterfd1	mitochondrial transcription termination factor 3	protein-coding
mm_162798.1	chr10	76726248	76726286	-	1	NA	promoter-TSS (NM_009933)	promoter-TSS (NM_009933)	-223	NM_009933	12833	Mm.2509	NM_009933	ENSMUSG00000001119	Col6a1	AI747156|Col6a-1	collagen, type VI, alpha 1	protein-coding
mm_147815.1	chr18	61726348	61726358	-	1	NA	promoter-TSS (NM_021296)	promoter-TSS (NM_021296)	-22	NM_021296	17714	Mm.269657	NM_021296	ENSMUSG00000024580	Grpel2	mt-GrpE#2|mt-Grpel2	GrpE-like 2, mitochondrial	protein-coding
mm_67387.1	chr7	79842558	79842575	-	1	NA	promoter-TSS (NM_008486)	promoter-TSS (NM_008486)	-214	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_20747.1	chr2	140060216	140060222	-	1	NA	intron (NR_110351, intron 1 of 13)	RLTR31C_MM|LTR|ERVK	6586	NM_001159640	75812	Mm.293449	NM_175225	ENSMUSG00000039033	Tasp1	4930485D02Rik|AW986064	taspase, threonine aspartase 1	protein-coding
mm_93143.1	chr10	92165194	92165209	-	1	NA	promoter-TSS (NR_028262)	promoter-TSS (NR_028262)	-23	NR_028262	110333	Mm.429764	NR_028262		Rmst	100041799|AI853140|C230053E11Rik|D930049J19Rik|Dmt2|Gm3515|M2|Ncrms	rhabdomyosarcoma 2 associated transcript (non-coding RNA)	ncRNA
mm_169286.1	chr13	97190620	97190631	-	1	NA	intron (NM_010422, intron 3 of 13)	LSU-rRNA_Hsa|rRNA|rRNA	7732	NM_010422	15212	Mm.27816	NM_010422	ENSMUSG00000021665	Hexb	-	hexosaminidase B	protein-coding
mm_34242.1	chr4	141213949	141213998	+	1	NA	promoter-TSS (NM_001081174)	promoter-TSS (NM_001081174)	17	NM_001081174	76166	Mm.271064	NM_001081174	ENSMUSG00000073733	Rsg1	6330545A04Rik|Gm723	REM2 and RAB-like small GTPase 1	protein-coding
mm_29577.1	chr3	116969515	116969523	-	1	NA	promoter-TSS (NM_023245)	promoter-TSS (NM_023245)	-567	NM_023245	114301	Mm.253736	NM_023245	ENSMUSG00000033377	Palmd	4631423C22Rik|PALML	palmdelphin	protein-coding
mm_65374.1	chr7	25073224	25073242	-	1	NA	promoter-TSS (NM_008168)	promoter-TSS (NM_008168)	-864	NM_008168	14809	Mm.2879	NM_008168	ENSMUSG00000003378	Grik5	GluK5|GluRgamma2|KA2	glutamate receptor, ionotropic, kainate 5 (gamma 2)	protein-coding
mm_156124.1	chrX	116448959	116448969	+	1	NA	promoter-TSS (NM_001033471)	promoter-TSS (NM_001033471)	20	NM_001033471	382239	Mm.336224	NM_001033471	ENSMUSG00000072995	Cpxcr1	Gm1143	CPX chromosome region, candidate 1	protein-coding
mm_39096.1	chr4	154899078	154899097	-	1	NA	promoter-TSS (NM_025582)	promoter-TSS (NM_025582)	-44	NM_025582	66469	Mm.41868	NM_025582	ENSMUSG00000029059	Fam213b	2810405K02Rik|AI836168|PM/PGFS	family with sequence similarity 213, member B	protein-coding
mm_58852.1	chr7	16875407	16875447	+	1	NA	exon (NM_001081655, exon 1 of 4)	exon (NM_001081655, exon 1 of 4)	110	NM_001081655	629378	Mm.491123	NM_001081655	ENSMUSG00000078794	Dact3	EG666671|naa-3	dishevelled-binding antagonist of beta-catenin 3	protein-coding
mm_17797.1	chr2	33131677	33131695	-	1	NA	Intergenic	Intergenic	-44482	NM_178888	99326	Mm.41290	NM_178888	ENSMUSG00000038860	Garnl3	AW120551	GTPase activating RANGAP domain-like 3	protein-coding
mm_108558.1	chr12	84640931	84640942	+	1	NA	promoter-TSS (NM_001168589)	promoter-TSS (NM_001168589)	-83	NM_001168589	432677	Mm.311913	NM_001033776	ENSMUSG00000071235	Vrtn	7420416P09Rik	vertebrae development associated	protein-coding
mm_42171.1	chr5	112261683	112261690	+	1	NA	intron (NM_023695, intron 3 of 5)	intron (NM_023695, intron 3 of 5)	5866	NM_001312893	12960	Mm.29488	NM_023695	ENSMUSG00000029343	Crybb1	3110006K12Rik|BB1CRY	crystallin, beta B1	protein-coding
mm_132225.1	chr16	32650525	32650528	+	1	NA	intron (NM_016788, intron 1 of 15)	intron (NM_016788, intron 1 of 15)	5883	NM_016788	51789	Mm.251115	NM_016788	ENSMUSG00000022791	Tnk2	Ack|Ack-1|Ack1|Cdgip|Pyk1	tyrosine kinase, non-receptor, 2	protein-coding
mm_74307.1	chr8	126589943	126589958	+	1	NA	3' UTR (NM_001164598, exon 2 of 2)	3' UTR (NM_001164598, exon 2 of 2)	3486	NM_001164598	270110	Mm.334918	NM_001164598	ENSMUSG00000051495	Irf2bp2	E130305N23Rik|IRF-2BP2	interferon regulatory factor 2 binding protein 2	protein-coding
mm_107445.1	chr12	36532791	36532799	+	1	NA	intron (NM_178629, intron 8 of 9)	intron (NM_178629, intron 8 of 9)	117179	NR_037309	100499526		NR_037309	ENSMUSG00000092917	Mir3472	mmu-mir-3472	microRNA 3472	ncRNA
mm_127340.1	chr15	100599723	100599747	+	1	NA	intron (NM_001304965, intron 1 of 10)	CpG	249	NM_001304965	19009	Mm.28825	NM_010127	ENSMUSG00000009739	Pou6f1	2310038G18Rik|C79593|Emb|cns-1	POU domain, class 6, transcription factor 1	protein-coding
mm_122980.1	chr14	54983376	54983404	-	1	NA	exon (NM_080728, exon 25 of 41)	exon (NM_080728, exon 25 of 41)	-7614	NR_030607	100124433		NR_030607	ENSMUSG00000077928	Mir208b	Mirn208b|mir-208b	microRNA 208b	ncRNA
mm_140511.1	chr17	5573190	5573193	-	1	NA	intron (NM_146073, intron 1 of 8)	intron (NM_146073, intron 1 of 8)	80591	NM_146073	224454	Mm.487663	NM_146073	ENSMUSG00000034265	Zdhhc14	B530001K09Rik|New1cp	zinc finger, DHHC domain containing 14	protein-coding
mm_11131.1	chr2	28382325	28382330	+	1	NA	Intergenic	L1MC4a|LINE|L1	-65614	NM_001005420	241289	Mm.330095	NM_001005420	ENSMUSG00000035829	Ppp1r26	Gm347|Kiaa0649|mKIAA0649	protein phosphatase 1, regulatory subunit 26	protein-coding
mm_29971.1	chr3	133544269	133544313	-	1	NA	promoter-TSS (NM_001346736)	promoter-TSS (NM_001346736)	99	NM_001346736	214133	Mm.347816	NM_145989	ENSMUSG00000040943	Tet2	Ayu17-449|E130014J05Rik|mKIAA1546	tet methylcytosine dioxygenase 2	protein-coding
mm_97300.1	chr11	76498000	76498014	+	1	NA	intron (NM_198895, intron 2 of 22)	intron (NM_198895, intron 2 of 22)	-3512	NM_001346670	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_101217.1	chr11	20112877	20112925	-	1	NA	promoter-TSS (NM_146243)	promoter-TSS (NM_146243)	50	NM_146243	66713	Mm.259045	NM_146243	ENSMUSG00000020152	Actr2	4921510D23Rik|AA409782|Arp2|D6Ertd746e	ARP2 actin-related protein 2	protein-coding
mm_33101.1	chr4	124703602	124703640	+	1	NA	intron (NM_010213, intron 1 of 5)	intron (NM_010213, intron 1 of 5)	2922	NM_010213	14201	Mm.331856	NM_010213	ENSMUSG00000032643	Fhl3	SLIM2	four and a half LIM domains 3	protein-coding
mm_58471.1	chr7	3390786	3390861	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-3219	NM_133190	81905	Mm.357990	NM_133190	ENSMUSG00000053395	Cacng8	-	calcium channel, voltage-dependent, gamma subunit 8	protein-coding
mm_11734.1	chr2	37516619	37516634	+	1	NA	promoter-TSS (NM_177383)	promoter-TSS (NM_177383)	0	NM_177383	338346	Mm.445325	NM_177383	ENSMUSG00000053164	Gpr21	C230004C13Rik	G protein-coupled receptor 21	protein-coding
mm_58738.1	chr7	13030509	13030537	+	1	NA	exon (NM_011588, exon 16 of 17)	exon (NM_011588, exon 16 of 17)	4254	NM_026885	68953	Mm.295670	NM_026885	ENSMUSG00000033916	Chmp2a	1500016L11Rik	charged multivesicular body protein 2A	protein-coding
mm_136778.1	chr17	10324595	10324611	+	1	NA	promoter-TSS (NR_045461)	promoter-TSS (NR_045461)	1	NR_045461	76634	Mm.491052	NR_045461	ENSMUSG00000099384	1700110C19Rik	-	RIKEN cDNA 1700110C19 gene	ncRNA
mm_28129.1	chr3	87012245	87012253	-	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	-12909	NM_007639	12479	Mm.1894	NM_007639	ENSMUSG00000028076	Cd1d1	AI747460|CD1.1|Cd1a|Cd1d|Ly-38	CD1d1 antigen	protein-coding
mm_203.1	chr1	16106365	16106377	+	1	NA	intron (NM_133832, intron 1 of 5)	intron (NM_133832, intron 1 of 5)	489	NM_133832	98711	Mm.274376	NM_133832	ENSMUSG00000025921	Rdh10	3110069K09Rik|4921506A21Rik|AI875664|AW549993|D1Ertd762e|m366Asp	retinol dehydrogenase 10 (all-trans)	protein-coding
mm_168331.1	chr11	118222841	118222856	-	1	NA	intron (NM_001112699, intron 1 of 12)	intron (NM_001112699, intron 1 of 12)	-10106	NM_001112700	19157	Mm.86413	NM_011180	ENSMUSG00000017132	Cyth1	CLM1|CTH-1|CYTIP|Pscd1	cytohesin 1	protein-coding
mm_41868.1	chr5	104459590	104459610	+	1	NA	5' UTR (NM_008861, exon 1 of 15)	5' UTR (NM_008861, exon 1 of 15)	143	NM_008861	18764	Mm.6442	NM_008861	ENSMUSG00000034462	Pkd2	C030034P18Rik|PC2|TRPP2	polycystic kidney disease 2	protein-coding
mm_83197.1	chr9	41157477	41157526	-	1	NA	promoter-TSS (NM_176860)	promoter-TSS (NM_176860)	-7	NM_176860	72828	Mm.133615	NM_176860	ENSMUSG00000032020	Ubash3b	2810457I06Rik|BB125008|TULA-2|p70	ubiquitin associated and SH3 domain containing, B	protein-coding
mm_162087.1	chrX	37265396	37265396	+	1	NA	promoter-TSS (NM_001039688).2	promoter-TSS (NM_001039688).2	21	NM_001039688	664609	Mm.296330	NM_001039688	ENSMUSG00000079639	Rhox4a	Rhox4|Rhox4.1	reproductive homeobox 4A	protein-coding
mm_8861.1	chr1	162724825	162724857	-	1	NA	5' UTR (NM_001081290, exon 2 of 35)	5' UTR (NM_001081290, exon 2 of 35)	15715	NM_001081290	226562	Mm.245446	NM_001081290	ENSMUSG00000040225	Prrc2c	1810043M20Rik|9630039I18Rik|A630006J20|Bat2d|Bat2d1|Bat2l2|E130112L15Rik|Prrc3|mKIAA1096	proline-rich coiled-coil 2C	protein-coding
mm_168324.1	chr11	115724836	115724842	-	1	NA	Intergenic	B1_Mus1|SINE|Alu	-16242	NM_008163	14784	Mm.439649	NM_008163	ENSMUSG00000059923	Grb2	AA408164|Ash	growth factor receptor bound protein 2	protein-coding
mm_6532.1	chr1	74851107	74851114	-	1	NA	Intergenic	Intergenic	-3919	NM_009872	12570	Mm.153833	NM_009872	ENSMUSG00000090071	Cdk5r2	B230310J22Rik|p39	cyclin-dependent kinase 5, regulatory subunit 2 (p39)	protein-coding
mm_160212.1	chr7	98109309	98109309	-	1	NA	promoter-TSS (NM_001256082)	promoter-TSS (NM_001256082)	-61	NM_001256083	17921	Mm.1403	NM_008663	ENSMUSG00000030761	Myo7a	Hdb|Myo7|USH1B|nmf371|polka|sh-1|sh1	myosin VIIA	protein-coding
mm_43292.1	chr5	134313647	134313664	+	1	NA	intron (NM_001080746, intron 1 of 34)	CpG	1105	NM_001080746	14886	Mm.261570	NM_010365	ENSMUSG00000060261	Gtf2i	6030441I21Rik|BAP-135|Diws1t|GtfII-I|Spin|TFII-I|WBSCR6	general transcription factor II I	protein-coding
mm_121862.1	chr14	20702992	20703034	-	1	NA	promoter-TSS (NR_029446)	promoter-TSS (NR_029446)	-14	NM_025366	66121	Mm.246996	NM_025366	ENSMUSG00000063787	Chchd1	1110001O19Rik|2400010G13Rik|MRP-S37	coiled-coil-helix-coiled-coil-helix domain containing 1	protein-coding
mm_22610.1	chr3	14533805	14533815	+	1	NA	promoter-TSS (NM_028915)	promoter-TSS (NM_028915)	22	NM_028915	71710	Mm.257449	NM_028915	ENSMUSG00000027550	Lrrcc1	1200008A14Rik|4932441F23Rik|AI195358|AI447421	leucine rich repeat and coiled-coil domain containing 1	protein-coding
mm_60371.1	chr7	44465392	44465419	+	1	NA	promoter-TSS (NM_026690)	promoter-TSS (NM_026690)	-30	NM_026690	68352	Mm.88478	NM_026690	ENSMUSG00000038704	Aspdh	0610012D14Rik	aspartate dehydrogenase domain containing	protein-coding
mm_93144.1	chr10	92165214	92165239	-	1	NA	promoter-TSS (NR_028262)	promoter-TSS (NR_028262)	-48	NR_028262	110333	Mm.429764	NR_028262		Rmst	100041799|AI853140|C230053E11Rik|D930049J19Rik|Dmt2|Gm3515|M2|Ncrms	rhabdomyosarcoma 2 associated transcript (non-coding RNA)	ncRNA
mm_171514.1	chr4	146501962	146501966	+	1	NA	promoter-TSS (NM_001243138)	promoter-TSS (NM_001243138)	-36	NM_001243138	100041433	Mm.441741	NM_001243138	ENSMUSG00000056300	Zfp981	Gm13247|OTTMUSG00000011075	zinc finger protein 981	protein-coding
mm_35446.1	chr4	40239747	40239766	-	1	NA	promoter-TSS (NM_172689)	promoter-TSS (NM_172689)	69	NM_172689	230073	Mm.86382	NM_172689	ENSMUSG00000040296	Ddx58	6430573D20Rik|C330021E21|RIG-I|RLR-1	DEAD (Asp-Glu-Ala-Asp) box polypeptide 58	protein-coding
mm_137674.1	chr17	28800754	28800785	+	1	NA	promoter-TSS (NM_001081315)	promoter-TSS (NM_001081315)	-357	NM_001081315	268936	Mm.291877	NM_199061	ENSMUSG00000063952	Brpf3	AI413466|AW493400|mKIAA1286	bromodomain and PHD finger containing, 3	protein-coding
mm_4167.1	chr1	171051247	171051267	+	1	NA	TTS (NM_010188)	TTS (NM_010188)	8146	NM_010188	14131	Mm.22119	NM_010188	ENSMUSG00000059498	Fcgr3	CD16	Fc receptor, IgG, low affinity III	protein-coding
mm_72406.1	chr8	81773106	81773120	+	1	NA	intron (NM_001024617, intron 7 of 24)	intron (NM_001024617, intron 7 of 24)	430551	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_57972.1	chr6	135349746	135349767	-	1	NA	Intergenic	Intergenic	-13175	NM_010128	13730	Mm.182785	NM_010128	ENSMUSG00000030208	Emp1	I-8-09|TMP	epithelial membrane protein 1	protein-coding
mm_120323.1	chr14	63143000	63143007	+	1	NA	3' UTR (NM_007798, exon 10 of 10)	3' UTR (NM_007798, exon 10 of 10)	20541	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_48317.1	chr5	138977077	138977092	-	1	NA	3' UTR (NM_008808, exon 6 of 6)	3' UTR (NM_008808, exon 6 of 6)	17869	NM_008808	18590	Mm.2675	NM_008808	ENSMUSG00000025856	Pdgfa	-	platelet derived growth factor, alpha	protein-coding
mm_60776.1	chr7	45559374	45559385	+	1	NA	intron (NM_025330, intron 4 of 8)	intron (NM_025330, intron 4 of 8)	4451	NM_025330	66065	Mm.285710	NM_025330	ENSMUSG00000030825	Hsd17b14	0610039E24Rik|Dhrs10|retSDR3	hydroxysteroid (17-beta) dehydrogenase 14	protein-coding
mm_44922.1	chr5	35729291	35729312	-	1	NA	promoter-TSS (NM_194344)	promoter-TSS (NM_194344)	-25	NM_194344	231147	Mm.290429	NM_194344	ENSMUSG00000036553	Sh3tc1	4631428G15|BC024909	SH3 domain and tetratricopeptide repeats 1	protein-coding
mm_67275.1	chr7	78192531	78192550	-	1	NA	3' UTR (NM_008746, exon 17 of 17)	3' UTR (NM_008746, exon 17 of 17)	385298	NM_008746	18213	Mm.33496	NM_008746	ENSMUSG00000059146	Ntrk3	AW125844|Ntrk3_tv3|TrkC	neurotrophic tyrosine kinase, receptor, type 3	protein-coding
mm_20635.1	chr2	132019415	132019456	-	1	NA	intron (NM_175445, intron 1 of 10)	intron (NM_175445, intron 1 of 10)	10553	NM_175445	215653	Mm.204737	NM_175445	ENSMUSG00000027339	Rassf2	3830431H01Rik|9030412M04Rik|AI852669|AW495050	Ras association (RalGDS/AF-6) domain family member 2	protein-coding
mm_91860.1	chr10	59441749	59441782	-	1	NA	promoter-TSS (NM_010959)	promoter-TSS (NM_010959)	14	NM_010959	18302	Mm.123013	NM_010959	ENSMUSG00000009654	Oit3	EF-9|LZP	oncoprotein induced transcript 3	protein-coding
mm_126645.1	chr15	83788945	83788981	+	1	NA	intron (NM_172610, intron 1 of 6)	intron (NM_172610, intron 1 of 6)	8940	NM_172610	223726	Mm.36395	NM_172610	ENSMUSG00000041708	Mpped1	6230403M19|AW456965|D15Bwg0669e	metallophosphoesterase domain containing 1	protein-coding
mm_102008.1	chr11	51605122	51605125	-	1	NA	intron (NM_001048061, intron 3 of 7)	intron (NM_001048061, intron 3 of 7)	1758	NM_001048061	15384	Mm.256875	NM_010448	ENSMUSG00000020358	Hnrnpab	3010025C11Rik|CBF-A|Cgbfa|Hnrpab	heterogeneous nuclear ribonucleoprotein A/B	protein-coding
mm_19911.1	chr2	114654862	114654915	-	1	NA	promoter-TSS (NM_025675)	promoter-TSS (NM_025675)	40	NM_025675	66632	Mm.117809	NM_025675	ENSMUSG00000057147	Dph6	5730421E18Rik|Atpbd4	diphthamine biosynthesis 6	protein-coding
mm_102091.1	chr11	52283231	52283239	-	1	NA	promoter-TSS (NM_009331)	promoter-TSS (NM_009331)	-221	NM_001313981	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_109556.1	chr12	111758924	111758939	+	1	NA	promoter-TSS (NM_001025363)	promoter-TSS (NM_001025363)	63	NM_001025361	16593	Mm.278357	NM_008450	ENSMUSG00000021288	Klc1	AI874768|Kns2	kinesin light chain 1	protein-coding
mm_26586.1	chr3	151294142	151294178	+	1	NA	Intergenic	Intergenic	-143722	NM_133222	170757	Mm.317261	NM_133222	ENSMUSG00000039167	Adgrl4	1110033N21Rik|ETL1|Eltd1|Etl	adhesion G protein-coupled receptor L4	protein-coding
mm_81193.1	chr9	107554578	107554591	+	1	NA	promoter-TSS (NM_019713)	promoter-TSS (NM_019713)	1	NM_019713	56289	Mm.12091	NM_019713	ENSMUSG00000010067	Rassf1	123F2|AA536941|AU044980|NORE2A|RDA32|REH3P21|Rassf1A|Rassf1B|Rassf1C	Ras association (RalGDS/AF-6) domain family member 1	protein-coding
mm_166279.1	chr5	92326803	92326803	-	1	NA	exon (NM_008599, exon 2 of 4)	exon (NM_008599, exon 2 of 4)	1276	NM_008599	17329	Mm.766	NM_008599	ENSMUSG00000029417	Cxcl9	BB139920|CMK|Mig|MuMIG|Scyb9|crg-10	chemokine (C-X-C motif) ligand 9	protein-coding
mm_92238.1	chr10	69352869	69352881	-	1	NA	promoter-TSS (NM_007659)	promoter-TSS (NM_007659)	37	NM_007659	12534	Mm.281367	NM_007659	ENSMUSG00000019942	Cdk1	Cdc2|Cdc2a|p34<CDC2>	cyclin-dependent kinase 1	protein-coding
mm_160893.1	chr11	72215591	72215591	-	1	NA	promoter-TSS (NM_026068)	promoter-TSS (NM_026068)	1	NM_026068	67279	Mm.159496	NM_026068	ENSMUSG00000020801	Med31	3110004H13Rik|CGI-125|l11Jus15	mediator complex subunit 31	protein-coding
mm_169227.1	chr1	36691556	36691570	+	1	NA	promoter-TSS (NM_009942)	promoter-TSS (NM_009942)	76	NM_009942	12859	Mm.180182	NM_009942	ENSMUSG00000061518	Cox5b	-	cytochrome c oxidase subunit Vb	protein-coding
mm_168423.1	chr11	33161550	33161569	-	1	NA	exon (NM_001252261, exon 2 of 10)	exon (NM_001252261, exon 2 of 10)	1647	NM_001252261	18148	Mm.485384	NM_008722	ENSMUSG00000057113	Npm1	B23|NO38|Npm	nucleophosmin 1	protein-coding
mm_127423.1	chr15	101267246	101267246	+	1	NA	intron (NM_010444, intron 1 of 6)	intron (NM_010444, intron 1 of 6)	400	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_84450.1	chr9	66514534	66514536	-	1	NA	promoter-TSS (NM_175206)	promoter-TSS (NM_175206)	58	NM_175206	74165	Mm.297998	NM_175206	ENSMUSG00000050503	Fbxl22	1110004B15Rik	F-box and leucine-rich repeat protein 22	protein-coding
mm_64475.1	chr7	143052777	143052797	+	1	NA	promoter-TSS (NM_133655)	promoter-TSS (NM_133655)	37	NM_133655	12520	Mm.806	NM_133655	ENSMUSG00000037706	Cd81	Tapa-1|Tapa1|Tspan28	CD81 antigen	protein-coding
mm_41810.1	chr5	103780244	103780245	+	1	NA	intron (NM_001080798, intron 1 of 19)	intron (NM_001080798, intron 1 of 19)	25671	NM_001080798	17355	Mm.6949	NM_133919	ENSMUSG00000029313	Aff1	9630032B01Rik|AW319193|Af4|Mllt2h|Rob	AF4/FMR2 family, member 1	protein-coding
mm_92030.1	chr10	62477759	62477763	-	1	NA	intron (NM_133672, intron 2 of 8)	B2_Mm2|SINE|B2	8837	NM_001113355	30930	Mm.260703	NM_133672	ENSMUSG00000020078	Vps26a	AA407240|HB58|Vps26	VPS26 retromer complex component A	protein-coding
mm_51912.1	chr6	91233211	91233219	+	1	NA	exon (NM_001081437, exon 2 of 17)	exon (NM_001081437, exon 2 of 17)	20451	NM_007992	14115	Mm.249146	NM_007992	ENSMUSG00000064080	Fbln2	5730577E14Rik|FIBL-2	fibulin 2	protein-coding
mm_96924.1	chr11	70509962	70509990	+	1	NA	intron (NM_029360, intron 2 of 4)	intron (NM_029360, intron 2 of 4)	4640	NM_001013607	327956	Mm.244514	NM_001013607	ENSMUSG00000020830	Vmo1	Gm741	vitelline membrane outer layer 1 homolog (chicken)	protein-coding
mm_82645.1	chr9	22016433	22016451	-	1	NA	3' UTR (NM_010487, exon 7 of 7)	3' UTR (NM_010487, exon 7 of 7)	13454	NM_008925	19089	Mm.214593	NM_008925	ENSMUSG00000003402	Prkcsh	80K-H|PKCSH	protein kinase C substrate 80K-H	protein-coding
mm_146809.1	chr18	20746268	20746333	-	1	NA	5' UTR (NM_019737, exon 1 of 9)	5' UTR (NM_019737, exon 1 of 9)	104	NM_019737	56386	Mm.393827	NM_019737	ENSMUSG00000056124	B4galt6	AA536803|AU022389	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 6	protein-coding
mm_45911.1	chr5	89435023	89435057	-	1	NA	exon (NM_008096, exon 10 of 13)	exon (NM_008096, exon 10 of 13)	22858	NM_008096	14473	Mm.196595	NM_008096	ENSMUSG00000035540	Gc	DBP|VDB	group specific component	protein-coding
mm_36081.1	chr4	58206579	58206587	-	1	NA	promoter-TSS (NM_022814)	promoter-TSS (NM_022814)	13	NM_022814	64817	Mm.261024	NM_022814	ENSMUSG00000028369	Svep1	1110021D17Rik|4833413O10Rik|AA387071|D430029O09Rik|Polydom	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	protein-coding
mm_11563.1	chr2	32875856	32875875	+	1	NA	promoter-TSS (NM_146119)	promoter-TSS (NM_146119)	-269	NM_146119	227737	Mm.301646	NM_146119	ENSMUSG00000026796	Fam129b	9130404D14Rik	family with sequence similarity 129, member B	protein-coding
mm_8282.1	chr1	140097836	140097838	-	1	NA	intron (NM_009888, intron 20 of 21)	intron (NM_009888, intron 20 of 21)	85574	NM_009888	12628	Mm.8655	NM_009888	ENSMUSG00000026365	Cfh	Mud-1|NOM|Sas-1|Sas1	complement component factor h	protein-coding
mm_13645.1	chr2	114050434	114050453	+	1	NA	exon (NM_009608, exon 3 of 7)	exon (NM_009608, exon 3 of 7)	2432	NM_009608	11464	Mm.686	NM_009608	ENSMUSG00000068614	Actc1	Actc-1	actin, alpha, cardiac muscle 1	protein-coding
mm_171381.1	chr4	119294216	119294224	-	1	NA	exon (NM_011732, exon 1 of 8)	exon (NM_011732, exon 1 of 8)	293	NM_011732	22608	Mm.258204	NM_011732	ENSMUSG00000028639	Ybx1	1700102N10Rik|C79409|EF1A|MSY1|Nsep1|YB-1|dbpB|mYB-1a	Y box protein 1	protein-coding
mm_159716.1	chr5	33661212	33661212	+	1	NA	intron (NM_001310541, intron 1 of 14)	intron (NM_001310541, intron 1 of 14)	3084	NM_001040435	21335	Mm.379024	NM_011524	ENSMUSG00000037313	Tacc3	Aint|C86661|Eric1	transforming, acidic coiled-coil containing protein 3	protein-coding
mm_160499.1	chr9	14782978	14782978	-	1	NA	promoter-TSS (NM_019683)	promoter-TSS (NM_019683)	-14	NM_019683	56503	Mm.395005	NM_019683	ENSMUSG00000031931	Ankrd49	AW060934|C86108|Gbif	ankyrin repeat domain 49	protein-coding
mm_115270.1	chr13	111580599	111580604	+	1	NA	Intergenic	Intergenic	-90560	NM_001122963	73274	Mm.57286	NM_028487	ENSMUSG00000032745	Gpbp1	1700034P14Rik|AU019836|D230035M11Rik|Gpbp|mGPBP	GC-rich promoter binding protein 1	protein-coding
mm_49774.1	chr6	34873393	34873404	+	1	NA	3' UTR (NM_197986, exon 2 of 2)	3' UTR (NM_197986, exon 2 of 2)	4667	NM_199145	78412	Mm.248440	NM_199145	ENSMUSG00000046806	3110062M04Rik	AL023049|Mri	RIKEN cDNA 3110062M04 gene	protein-coding
mm_57313.1	chr6	124727114	124727124	-	1	NA	intron (NM_001077705, intron 9 of 15)	intron (NM_001077705, intron 9 of 15)	6035	NM_013545	15170	Mm.271799	NM_013545	ENSMUSG00000004266	Ptpn6	70Z-SHP|Hcph|PTPTY-42|Ptp1C|SH-PTP1|SHP-1|hcp|me	protein tyrosine phosphatase, non-receptor type 6	protein-coding
mm_117958.1	chr13	99447524	99447530	-	1	NA	intron (NM_008634, intron 2 of 6)	intron (NM_008634, intron 2 of 6)	-34701	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_51523.1	chr6	83179569	83179630	+	1	NA	promoter-TSS (NM_007835)	promoter-TSS (NM_007835)	10	NM_007835	13191	Mm.6919	NM_007835	ENSMUSG00000031865	Dctn1	AL022633|DAP-150|DP-150|Glued|p150|p150-glued|p150<glued>	dynactin 1	protein-coding
mm_23222.1	chr3	49062356	49062370	+	1	NA	Intergenic	RLTR20C2_MM|LTR|ERVK	-453263	NR_003617	66332	Mm.46124	NM_025493		1700018B24Rik	-	enhancer of rudimentary homolog pseudogene	pseudo
mm_112738.1	chr13	19305124	19305173	+	1	NA	Intergenic	Intergenic	90665	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_117480.1	chr13	77101724	77101729	-	1	NA	intron (NM_134071, intron 8 of 20)	intron (NM_134071, intron 8 of 20)	33742	NM_134071	105377	Mm.209730	NM_134071	ENSMUSG00000021597	Slf1	2700017A04Rik|AW545819|Ankrd32|Brctd1|Brctx|C730024G01Rik	SMC5-SMC6 complex localization factor 1	protein-coding
mm_117774.1	chr13	96658673	96658700	-	1	NA	exon (NM_008255, exon 11 of 20)	exon (NM_008255, exon 11 of 20)	12250	NM_008255	15357	Mm.316652	NM_008255	ENSMUSG00000021670	Hmgcr	HMG-CoAR|Red	3-hydroxy-3-methylglutaryl-Coenzyme A reductase	protein-coding
mm_81236.1	chr9	107914976	107915008	+	1	NA	promoter-TSS (NM_001287261)	promoter-TSS (NM_001287261)	-11	NM_001287261	19882	Mm.3901	NM_009074	ENSMUSG00000032584	Mst1r	CD136|CDw136|Fv-2|Fv2|PTK8|Ron|STK	macrophage stimulating 1 receptor (c-met-related tyrosine kinase)	protein-coding
mm_170002.1	chr1	71652848	71652853	-	1	NA	promoter-TSS (NR_040308)	promoter-TSS (NR_040308)	384	NM_010233	14268	Mm.193099	NM_010233	ENSMUSG00000026193	Fn1	E330027I09|Fn|Fn-1	fibronectin 1	protein-coding
mm_125223.1	chr15	34099509	34099531	+	1	NA	exon (NM_026002, exon 2 of 12)	exon (NM_026002, exon 2 of 12)	16801	NM_026002	67154	Mm.130883	NM_026002	ENSMUSG00000022255	Mtdh	2610103J23Rik|3D3|3D3/Lyric|AEG-1|AV353288|D8Bwg1112e|Lyric	metadherin	protein-coding
mm_67687.1	chr7	89404192	89404204	-	1	NA	promoter-TSS (NM_008055)	promoter-TSS (NM_008055)	-168	NM_008055	14366	Mm.86755	NM_008055	ENSMUSG00000049791	Fzd4	Fz4	frizzled class receptor 4	protein-coding
mm_65300.1	chr7	24611189	24611206	-	1	NA	promoter-TSS (NM_001102613)	promoter-TSS (NM_001102613)	-131	NM_001102613	232970	Mm.333663	NM_001102613	ENSMUSG00000074277	Phldb3	EG232970|ENSMUSG00000061511|Gm10102	pleckstrin homology like domain, family B, member 3	protein-coding
mm_27072.1	chr3	28265231	28265247	-	1	NA	intron (NM_026910, intron 1 of 32)	intron (NM_026910, intron 1 of 32)	2025	NM_001163009	665113	Mm.126193	NM_026910	ENSMUSG00000027692	Tnik	1500031A17Rik|4831440I19Rik|AI451411|C530008O15Rik|C630040K21Rik	TRAF2 and NCK interacting kinase	protein-coding
mm_157294.1	chrX	20862354	20862358	-	1	NA	TTS (NR_049190)	TTS (NR_049190)	826	NR_049190	100885829		NR_049190	ENSMUSG00000093408	Mir5617	Gm25192|mir-5617|mmu-mir-5617	microRNA 5617	ncRNA
mm_115921.1	chr13	23551663	23551672	-	1	NA	promoter-TSS (NM_175655)	promoter-TSS (NM_175655)	-24	NM_175655	319157	Mm.442307	NM_175655	ENSMUSG00000069274	Hist1h4f	-	histone cluster 1, H4f	protein-coding
mm_115976.1	chr13	24206238	24206254	-	1	NA	intron (NM_001311122, intron 2 of 37)	intron (NM_001311122, intron 2 of 37)	74544	NM_001311122	68732	Mm.211047	NM_026825	ENSMUSG00000021338	Carmil1	1110037D04Rik|AI425970|CARMIL|CARML1|D130057M20|Lrrc16|Lrrc16a	capping protein regulator and myosin 1 linker 1	protein-coding
mm_65923.1	chr7	30242864	30242871	-	1	NA	exon (NM_146186, exon 27 of 33)	exon (NM_146186, exon 27 of 33)	-6102	NM_001289817	381867	Mm.483986	NM_001289817	ENSMUSG00000100512	Ovol3	Gm1903|movo3	ovo like zinc finger 3	protein-coding
mm_150444.1	chr19	38016462	38016494	+	1	NA	intron (NM_001302140, intron 3 of 53)	MTC|LTR|ERVL-MaLR	27099	NM_001099634	226101	Mm.34674	NM_177035	ENSMUSG00000048612	Myof	2310004N10Rik|2310051D19Rik|E030042N20Rik|Fer1l3	myoferlin	protein-coding
mm_74671.1	chr8	13838558	13838565	-	1	NA	promoter-TSS (NM_153093)	promoter-TSS (NM_153093)	-472	NM_153093	231201	Mm.423959	NM_153093	ENSMUSG00000057116	AF366264	Susp4	cDNA sequence AF366264	protein-coding
mm_170731.1	chr2	152226867	152226873	+	1	NA	promoter-TSS (NM_007788)	promoter-TSS (NM_007788)	30	NM_007788	12995	Mm.23692	NM_007788	ENSMUSG00000074698	Csnk2a1	Csnk2a1-rs4	casein kinase 2, alpha 1 polypeptide	protein-coding
mm_147635.1	chr18	60211552	60211562	-	1	NA	promoter-TSS (NM_001033767)	promoter-TSS (NM_001033767)	-520	NM_001033767	240327	Mm.357104	NM_001033767	ENSMUSG00000073555	Gm4951	EG240327|Ifgga2	predicted gene 4951	protein-coding
mm_123270.1	chr14	61365514	61365532	-	1	NA	3' UTR (NM_008466, exon 17 of 17)	3' UTR (NM_008466, exon 17 of 17)	-5078	NM_026598	68177	Mm.22758	NM_026598	ENSMUSG00000021928	Ebpl	5730442K12Rik|EBRP	emopamil binding protein-like	protein-coding
mm_94620.1	chr11	16759614	16759639	+	1	NA	intron (NM_207655, intron 1 of 27)	intron (NM_207655, intron 1 of 27)	7423	NM_007912	13649	Mm.8534	NM_007912	ENSMUSG00000020122	Egfr	9030024J15Rik|AI552599|Erbb|Errb1|Errp|Wa5|wa-2|wa2	epidermal growth factor receptor	protein-coding
mm_100722.1	chr11	3913770	3913792	-	1	NA	5' UTR (NM_153142, exon 1 of 2)	5' UTR (NM_153142, exon 1 of 2)	883	NM_153142	103710	Mm.171514	NM_153142	ENSMUSG00000048807	Slc35e4	A330108F03Rik|AI414849|AI536442	solute carrier family 35, member E4	protein-coding
mm_140406.1	chr17	87644875	87644889	+	1	NA	intron (NM_008532, intron 7 of 9)	ID_B1|SINE|B4	8903	NM_008532	17075	Mm.4259	NM_008532	ENSMUSG00000045394	Epcam	CD326|EGP|EGP-2|Egp314|Ep-CAM|EpCAM1|GA733-2|Ly74|TROP1|Tacsd1|Tacstd1|gp40	epithelial cell adhesion molecule	protein-coding
mm_63254.1	chr7	126649298	126649344	+	1	NA	promoter-TSS (NM_029339)	promoter-TSS (NM_029339)	12	NM_029339	75565	Mm.45686	NM_029339	ENSMUSG00000030714	Sgf29	1700023O11Rik|9530025I05Rik|Ccdc101	SAGA complex associated factor 29	protein-coding
mm_41225.1	chr5	88650703	88650713	+	1	NA	3' UTR (NM_001289774, exon 18 of 18)	3' UTR (NM_001289774, exon 18 of 18)	24872	NM_001098476	231413	Mm.332474	NM_178700	ENSMUSG00000044221	Grsf1	BB232551|C80280|D5Wsu31e	G-rich RNA sequence binding factor 1	protein-coding
mm_147445.1	chr18	46526003	46526009	-	1	NA	promoter-TSS (NM_173423)	promoter-TSS (NM_173423)	-35	NM_173423	240263	Mm.38249	NM_173423	ENSMUSG00000033319	Fem1c	2610312A07Rik|3632443A22Rik|AI646567	fem-1 homolog c (C.elegans)	protein-coding
mm_17485.1	chr2	28582717	28582724	-	1	NA	intron (NM_148928, intron 1 of 11)	intron (NM_148928, intron 1 of 11)	559	NM_148928	70239	Mm.274120	NM_148928	ENSMUSG00000026816	Gtf3c5	2700084A09Rik|TFIIIC63|TFiiiC2-63	general transcription factor IIIC, polypeptide 5	protein-coding
mm_142827.1	chr17	51767499	51767501	-	1	NA	intron (NM_009122, intron 9 of 10)	intron (NM_009122, intron 9 of 10)	44554	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_123955.1	chr14	74784204	74784204	-	1	NA	intron (NM_001252132, intron 17 of 18)	intron (NM_001252132, intron 17 of 18)	51907	NM_016903	13885	Mm.38055	NM_016903	ENSMUSG00000021996	Esd	Es-10|Es10|FGH|sid478	esterase D/formylglutathione hydrolase	protein-coding
mm_141390.1	chr17	29148976	29148989	-	1	NA	TTS (NM_001002786)	TTS (NM_001002786)	13926	NM_001002786	442827	Mm.440341	NM_001002786	ENSMUSG00000064147	Rab44	9830134C10Rik	RAB44, member RAS oncogene family	protein-coding
mm_78105.1	chr9	20492758	20492800	+	1	NA	promoter-TSS (NM_001110309)	promoter-TSS (NM_001110309)	-33	NM_001110309	235028	Mm.297660	NM_146221	ENSMUSG00000059475	Zfp426	2900057C04Rik|KRAB1|Zfo61|Zfp68-rs1|Znf426|mKIAA4237	zinc finger protein 426	protein-coding
mm_53506.1	chr6	135368884	135368903	+	1	NA	intron (NM_001288627, intron 1 of 4)	B4|SINE|B4	1400	NM_001288627	13730	Mm.182785	NM_010128	ENSMUSG00000030208	Emp1	I-8-09|TMP	epithelial membrane protein 1	protein-coding
mm_128729.1	chr15	64110989	64111003	-	1	NA	exon (NM_001276463, exon 23 of 28)	exon (NM_001276463, exon 23 of 28)	-50548	NM_144846	223601	Mm.246108	NM_144846	ENSMUSG00000022378	Fam49b	0910001A06Rik|AW122079	family with sequence similarity 49, member B	protein-coding
mm_4390.1	chr1	172341198	172341217	+	1	NA	promoter-TSS (NM_001039484)	promoter-TSS (NM_001039484)	-3	NM_001039484	16513	Mm.254563	NM_020269	ENSMUSG00000044708	Kcnj10	BIR10|BIRK-1|Kir1.2|Kir4.1	potassium inwardly-rectifying channel, subfamily J, member 10	protein-coding
mm_78539.1	chr9	35267858	35267894	+	1	NA	promoter-TSS (NM_001286604)	promoter-TSS (NM_001286604)	-5	NM_028040	71989	Mm.273515	NM_028040	ENSMUSG00000032044	Rpusd4	2410001E19Rik	RNA pseudouridylate synthase domain containing 4	protein-coding
mm_23716.1	chr3	69005338	69005354	+	1	NA	promoter-TSS (NM_026641)	promoter-TSS (NM_026641)	374	NM_133786	70099	Mm.206841	NM_133786	ENSMUSG00000034349	Smc4	2500002A22Rik|C79747|SMC-4|Smc4l1	structural maintenance of chromosomes 4	protein-coding
mm_133862.1	chr16	96330066	96330068	+	1	NA	Intergenic	Intergenic	-31690	NM_001177887	72058	Mm.119714	NM_028078	ENSMUSG00000000159	Igsf5	2010003D20Rik|JCAM|Jam4	immunoglobulin superfamily, member 5	protein-coding
mm_117887.1	chr13	99422198	99422209	-	1	NA	3' UTR (NM_008634, exon 7 of 7)	3' UTR (NM_008634, exon 7 of 7)	-9377	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_41381.1	chr5	90723567	90723585	+	1	NA	Intergenic	Intergenic	-35722	NM_009141	20311	Mm.4660	NM_009141	ENSMUSG00000029371	Cxcl5	AMCF-II|Cxcl6|ENA-78|GCP-2|LIX|Scyb5|Scyb6	chemokine (C-X-C motif) ligand 5	protein-coding
mm_6790.1	chr1	84141064	84141076	-	1	NA	intron (NM_001003948, intron 2 of 2)	L1_Mur3|LINE|L1	77891	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_77770.1	chr9	3005918	3005928	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	32820	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_71614.1	chr8	56877238	56877239	+	1	NA	Intergenic	Intergenic	326104	NM_015791	50753	Mm.251174	NM_015791	ENSMUSG00000038206	Fbxo8	Fbx8	F-box protein 8	protein-coding
mm_46988.1	chr5	115326985	115327016	-	1	NA	promoter-TSS (NM_025573)	promoter-TSS (NM_025573)	-177	NM_025573	108014	Mm.287826	NM_025573	ENSMUSG00000029538	Srsf9	25kDa|2610029M16Rik|SRp30c|Sfrs9	serine/arginine-rich splicing factor 9	protein-coding
mm_96833.1	chr11	70000805	70000831	+	1	NA	TTS (NM_030064)	TTS (NM_030064)	192	NM_007888	13543	Mm.5114	NM_007888	ENSMUSG00000020888	Dvl2	-	dishevelled segment polarity protein 2	protein-coding
mm_165808.1	chr3	144760757	144760767	-	1	NA	non-coding (NR_130895, exon 1 of 13)	non-coding (NR_130895, exon 1 of 13)	215	NR_130895	12722	Mm.454553	NM_009899	ENSMUSG00000056025	Clca3a1	Cacc|Clca1	chloride channel accessory 3A1	protein-coding
mm_152356.1	chr19	10064147	10064200	-	1	NA	TTS (NM_019699)	TTS (NM_019699)	22625	NM_021890	60527	Mm.253875	NM_021890	ENSMUSG00000024664	Fads3	AI464531	fatty acid desaturase 3	protein-coding
mm_80524.1	chr9	80111378	80111415	+	1	NA	exon (NM_146003, exon 7 of 23)	exon (NM_146003, exon 7 of 23)	44493	NM_146003	215351	Mm.28232	NM_146003	ENSMUSG00000034252	Senp6	2810017C20Rik|E130319N12Rik|Susp1|mKIAA0797	SUMO/sentrin specific peptidase 6	protein-coding
mm_35126.1	chr4	11191215	11191233	-	1	NA	promoter-TSS (NM_009830)	promoter-TSS (NM_009830)	-127	NM_001037134	12448	Mm.35867	NM_009830	ENSMUSG00000028212	Ccne2	-	cyclin E2	protein-coding
mm_72379.1	chr8	81364225	81364225	+	1	NA	intron (NM_001024617, intron 1 of 24)	Lx7|LINE|L1	21663	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_67963.1	chr7	100550746	100550754	-	1	NA	intron (NM_198831, intron 6 of 7)	intron (NM_198831, intron 6 of 7)	13650	NM_183270	68185	Mm.228995	NM_183270	ENSMUSG00000044881	Coa4	5330414O08Rik|AI115477|AW047259|Chchd8|E2ig2	cytochrome c oxidase assembly factor 4	protein-coding
mm_163788.1	chr14	8258836	8258840	-	1	NA	promoter-TSS (NM_001161667)	promoter-TSS (NM_001161667)	1	NM_001161667	93732	Mm.28700	NM_053115	ENSMUSG00000021751	Acox2	THCCox	acyl-Coenzyme A oxidase 2, branched chain	protein-coding
mm_61150.1	chr7	57825677	57825691	+	1	NA	3' UTR (NM_001038701, exon 9 of 9)	3' UTR (NM_001038701, exon 9 of 9)	234511	NM_008071	14402	Mm.8004	NM_008071	ENSMUSG00000033676	Gabrb3	A230092K12Rik|AW049585|Cp1|Gabrb-3|beta3	gamma-aminobutyric acid (GABA) A receptor, subunit beta 3	protein-coding
mm_44074.1	chr5	148959320	148959340	+	1	NA	Intergenic	Intergenic	9080	NR_040686	71473	Mm.90306	NR_040686	ENSMUSG00000079069	8430423G03Rik	-	RIKEN cDNA 8430423G03 gene	ncRNA
mm_169256.1	chr1	37890551	37890554	+	1	NA	promoter-TSS (NM_027098)	promoter-TSS (NM_027098)	-1	NM_027098	107734	Mm.26614	NM_027098	ENSMUSG00000026087	Mrpl30	2310001L22Rik|MRP-L28|Rpml28	mitochondrial ribosomal protein L30	protein-coding
mm_89361.1	chr10	88414064	88414069	+	1	NA	intron (NM_001004164, intron 4 of 20)	PB1D11|SINE|Alu	34654	NM_001004164	432486	Mm.335190	NM_001004164	ENSMUSG00000035311	Gnptab	EG432486|mKIAA1208	N-acetylglucosamine-1-phosphate transferase, alpha and beta subunits	protein-coding
mm_134574.1	chr16	20401779	20401794	-	1	NA	intron (NM_176839, intron 6 of 6)	intron (NM_176839, intron 6 of 6)	24608	NM_013790	27416	Mm.20845	NM_013790	ENSMUSG00000022822	Abcc5	2900011L11Rik|AI132311|Abcc5a|Abcc5b|Mrp5	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	protein-coding
mm_71705.1	chr8	61931100	61931119	+	1	NA	intron (NM_001293783, intron 1 of 37)	intron (NM_001293783, intron 1 of 37)	3022	NM_001293783	234311	Mm.275233	NM_144928	ENSMUSG00000037921	Ddx60	9830118M07	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	protein-coding
mm_6951.1	chr1	85895455	85895462	-	1	NA	intron (NM_022417, intron 1 of 5)	intron (NM_022417, intron 1 of 5)	948	NM_022417	64294	Mm.29870	NM_022417	ENSMUSG00000026223	Itm2c	3110038L02Rik|BRI3|Bricd2c|E25|E25C|ITM3	integral membrane protein 2C	protein-coding
mm_88372.1	chr10	76032666	76032699	+	1	NA	promoter-TSS (NM_177475)	promoter-TSS (NM_177475)	70	NM_177475	64453	Mm.80609	NM_177475	ENSMUSG00000049764	Zfp280b	D10Jhu82e|Suhw2	zinc finger protein 280B	protein-coding
mm_101194.1	chr11	18890986	18891002	-	1	NA	intron (NM_001193271, intron 9 of 12)	intron (NM_001193271, intron 9 of 12)	127975	NM_001193271	17268	Mm.356578	NM_010789	ENSMUSG00000020160	Meis1	C530044H18Rik|Evi8	Meis homeobox 1	protein-coding
mm_114007.1	chr13	52596921	52596939	+	1	NA	promoter-TSS (NM_011518)	promoter-TSS (NM_011518)	48	NM_011518	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_61088.1	chr7	51622617	51622627	+	1	NA	5' UTR (NM_080853, exon 1 of 12)	5' UTR (NM_080853, exon 1 of 12)	792	NM_080853	140919	Mm.256618	NM_080853	ENSMUSG00000030500	Slc17a6	2900073D12Rik|DNPI|VGLUT2	solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 6	protein-coding
mm_84019.1	chr9	57677200	57677208	-	1	NA	3' UTR (NM_009993, exon 7 of 7)	3' UTR (NM_009993, exon 7 of 7)	6451	NM_009993	13077	Mm.15537	NM_009993	ENSMUSG00000032310	Cyp1a2	CP12|Cyp1a1|P450-3	cytochrome P450, family 1, subfamily a, polypeptide 2	protein-coding
mm_37150.1	chr4	117120332	117120342	-	1	NA	non-coding (NR_024078, exon 7 of 7)	non-coding (NR_024078, exon 7 of 7)	5388	NR_024078	78611	Mm.446227	NM_001033187		Btbd19	9530048O09Rik|BB115071	BTB (POZ) domain containing 19	ncRNA
mm_165333.1	chr2	114047573	114047580	-	1	NA	exon (NM_009608, exon 7 of 7)	exon (NM_009608, exon 7 of 7)	5299	NM_009608	11464	Mm.686	NM_009608	ENSMUSG00000068614	Actc1	Actc-1	actin, alpha, cardiac muscle 1	protein-coding
mm_112546.1	chr13	12276418	12276436	+	1	NA	exon (NM_033268, exon 17 of 21)	exon (NM_033268, exon 17 of 21)	-18314	NM_001081128	238505	Mm.40335	NM_001081128	ENSMUSG00000021311	Mtr	AI894170|D830038K18Rik|MS	5-methyltetrahydrofolate-homocysteine methyltransferase	protein-coding
mm_128152.1	chr15	32244444	32244454	-	1	NA	promoter-TSS (NM_009154)	promoter-TSS (NM_009154)	213	NR_038186	100616095	Mm.391938	NR_038186	ENSMUSG00000096956	Snhg18	0610007N19Rik|Snord123	small nucleolar RNA host gene 18	ncRNA
mm_122469.1	chr14	45530189	45530219	-	1	NA	promoter-TSS (NM_146054)	promoter-TSS (NM_146054)	-139	NM_146054	218952	Mm.210018	NM_146054	ENSMUSG00000037712	Fermt2	AA960555|Kindlin-2|Mig2|Plekhc1	fermitin family member 2	protein-coding
mm_71986.1	chr8	70616115	70616140	+	1	NA	promoter-TSS (NM_153074)	promoter-TSS (NM_153074)	-717	NM_153074	211228	Mm.132939	NM_153074	ENSMUSG00000049988	Lrrc25	Mapa	leucine rich repeat containing 25	protein-coding
mm_155805.1	chrX	99136074	99136084	+	1	NA	promoter-TSS (NM_010110)	promoter-TSS (NM_010110)	18	NM_010110	13641	Mm.3374	NM_010110	ENSMUSG00000031217	Efnb1	Cek5-L|EFL-3|Elk-L|Epl2|Eplg2|LERK-2|Lerk2|Stra1	ephrin B1	protein-coding
mm_141000.1	chr17	24895048	24895077	-	1	NA	promoter-TSS (NM_001163102)	promoter-TSS (NM_001163102)	25	NM_001163102	193838	Mm.440199	NM_001163102	ENSMUSG00000073436	Eme2	2810013J18Rik	essential meiotic structure-specific endonuclease subunit 2	protein-coding
mm_47898.1	chr5	134747439	134747468	-	1	NA	promoter-TSS (NM_007925)	promoter-TSS (NM_007925)	-130	NM_007925	13717	Mm.275320	NM_007925	ENSMUSG00000029675	Eln	AI385707|AI480567|E030024M20Rik	elastin	protein-coding
mm_94225.1	chr11	3233985	3233988	+	1	NA	intron (NM_001166548, intron 10 of 17)	intron (NM_001166548, intron 10 of 17)	30967	NM_001166549	74203	Mm.255649	NM_023743	ENSMUSG00000020454	Eif4enif1	2610509L04Rik|A930019J01Rik|AA410001|AU021239|Clast4|D11Ertd166e	eukaryotic translation initiation factor 4E nuclear import factor 1	protein-coding
mm_87455.1	chr10	51483823	51483855	+	1	NA	exon (NM_008147, exon 6 of 9)	exon (NM_008147, exon 6 of 9)	3227	NM_001291892	14727	Mm.439661	NM_008147	ENSMUSG00000062593	Lilr4b	Gp49a|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4B	protein-coding
mm_148053.1	chr18	71913845	71913849	-	1	NA	intron (NM_007831, intron 2 of 28)	intron (NM_007831, intron 2 of 28)	437222	NM_007831	13176	Mm.167882	NM_007831	ENSMUSG00000060534	Dcc	C030036D22Rik|Igdcc1	deleted in colorectal carcinoma	protein-coding
mm_44232.1	chr5	5265225	5265234	-	1	NA	intron (NM_011074, intron 2 of 14)	intron (NM_011074, intron 2 of 14)	839	NM_001310448	18647	Mm.389061	NM_011074	ENSMUSG00000028926	Cdk14	Pftk1|mKIAA0834	cyclin-dependent kinase 14	protein-coding
mm_109466.1	chr12	111408519	111408557	+	1	NA	5' UTR (NM_001101503, exon 2 of 4)	5' UTR (NM_001101503, exon 2 of 4)	1729	NM_001101503	380787	Mm.125602	NM_001101503	ENSMUSG00000087075	A230065H16Rik	Gm898|Lbh2	RIKEN cDNA A230065H16 gene	protein-coding
mm_31443.1	chr4	48585199	48585215	+	1	NA	promoter-TSS (NM_021436)	promoter-TSS (NM_021436)	14	NM_021436	230157	Mm.422686	NM_021436	ENSMUSG00000028347	Tmeff1	A830033E11|M7365|Tr1	transmembrane protein with EGF-like and two follistatin-like domains 1	protein-coding
mm_148337.1	chr18	84412390	84412398	-	1	NA	intron (NM_001033341, intron 4 of 8)	intron (NM_001033341, intron 4 of 8)	177110	NM_001033341	240476	Mm.329575	NM_001033341	ENSMUSG00000048410	Zfp407	6430585N13Rik|Gm333|Gm334|Gm948|ZNF407	zinc finger protein 407	protein-coding
mm_122131.1	chr14	31160562	31160620	-	1	NA	exon (NM_138672, exon 12 of 69)	exon (NM_138672, exon 12 of 69)	8050	NM_138672	192187	Mm.220821	NM_138672	ENSMUSG00000042286	Stab1	FEEL-1|FELE-1|MFEEL-1|MS-1|STAB-1|mKIAA0246	stabilin 1	protein-coding
mm_122864.1	chr14	54912318	54912331	-	1	NA	5' UTR (NM_021551, exon 2 of 9)	5' UTR (NM_021551, exon 2 of 9)	808	NM_021551	59049	Mm.27435	NM_021551	ENSMUSG00000022199	Slc22a17	1700094C23Rik|24p3R|AU041908|AW555662|BOIT|Boct	solute carrier family 22 (organic cation transporter), member 17	protein-coding
mm_10684.1	chr2	22621850	22621874	+	1	NA	promoter-TSS (NM_008078)	promoter-TSS (NM_008078)	-465	NM_008078	14417	Mm.4784	NM_008078	ENSMUSG00000026787	Gad2	6330404F12Rik|GAD(65)|GAD65|Gad-2	glutamic acid decarboxylase 2	protein-coding
mm_111102.1	chr12	80792993	80793036	-	1	NA	intron (NM_001242419, intron 1 of 6)	intron (NM_001242419, intron 1 of 6)	2482	NM_001242419	217684	Mm.341776	NM_178682	ENSMUSG00000021133	Susd6	4933426M11Rik|mKIAA0247	sushi domain containing 6	protein-coding
mm_15025.1	chr2	152687022	152687041	+	1	NA	promoter-TSS (NM_025543)	promoter-TSS (NM_025543)	-117	NM_025543	66405	Mm.440291	NM_025543	ENSMUSG00000042814	Mcts2	2400002F11Rik|MCT-2	malignant T cell amplified sequence 2	protein-coding
mm_164933.1	chr18	82997083	82997087	+	1	NA	intron (NM_183033, intron 5 of 5)	intron (NM_183033, intron 5 of 5)	-76525	NR_033307	75853	Mm.420737	NR_033307		4930592I03Rik	-	RIKEN cDNA 4930592I03 gene	ncRNA
mm_115093.1	chr13	102706926	102706938	+	1	NA	TTS (NM_008533)	TTS (NM_008533)	13374	NM_008533	17079	Mm.373974	NM_008533	ENSMUSG00000021624	Cd180	F630107B15|Ly78|RP105	CD180 antigen	protein-coding
mm_119012.1	chr14	29978347	29978357	+	1	NA	promoter-TSS (NM_027493)	promoter-TSS (NM_027493)	15	NM_027493	56249	Mm.215110	NM_027493	ENSMUSG00000015971	Actr8	5730542K05Rik|ARP8	ARP8 actin-related protein 8	protein-coding
mm_87507.1	chr10	52391607	52391610	+	1	NA	promoter-TSS (NM_025684)	promoter-TSS (NM_025684)	0	NM_025684	66650	Mm.90950	NM_025684	ENSMUSG00000038624	Nepn	5730521E12Rik|Npn|periolin	nephrocan	protein-coding
mm_83921.1	chr9	56620604	56620612	-	1	NA	exon (NM_181074, exon 4 of 4)	exon (NM_181074, exon 4 of 4)	15040	NM_001311076	235402	Mm.246605	NM_181074	ENSMUSG00000049556	Lingo1	4930471K13Rik|AV148400|LERN1|LINGO-1|Lrrn6a|UNQ201	leucine rich repeat and Ig domain containing 1	protein-coding
mm_102517.1	chr11	60811229	60811241	-	1	NA	promoter-TSS (NM_009171)	promoter-TSS (NM_009171)	30	NM_009171	20425	Mm.364956	NM_009171	ENSMUSG00000020534	Shmt1	AI324848|AI385541|C81125|Shmt|mshmt|mshmt1|mshmt2	serine hydroxymethyltransferase 1 (soluble)	protein-coding
mm_161666.1	chr17	12876218	12876218	+	1	NA	5' UTR (NM_030726, exon 1 of 1)	5' UTR (NM_030726, exon 1 of 1)	184	NM_030726	80978	Mm.160368	NM_030726	ENSMUSG00000059408	Mrgprh	Gpr90|Mgrb|MrgH	MAS-related GPR, member H	protein-coding
mm_50770.1	chr6	53621200	53621206	+	1	NA	intron (NM_001327821, intron 7 of 10)	intron (NM_001327821, intron 7 of 10)	47829	NM_172728	231991	Mm.227444	NM_172728	ENSMUSG00000053007	Creb5	9430076C15Rik|CRE-BPa|Crebpa|D430026C09Rik	cAMP responsive element binding protein 5	protein-coding
mm_82679.1	chr9	22132325	22132334	-	1	NA	promoter-TSS (NM_001102404)	promoter-TSS (NM_001102404)	-464	NM_001102404	11433	Mm.46354	NM_007388	ENSMUSG00000001348	Acp5	TRACP|TRAP	acid phosphatase 5, tartrate resistant	protein-coding
mm_153289.1	chr19	37317553	37317568	-	1	NA	intron (NM_031156, intron 4 of 23)	intron (NM_031156, intron 4 of 23)	13053	NM_031156	15925	Mm.28366	NM_031156	ENSMUSG00000056999	Ide	1300012G03Rik|4833415K22Rik|AA675336|AI507533	insulin degrading enzyme	protein-coding
mm_4210.1	chr1	171270322	171270360	+	1	NA	promoter-TSS (NM_020579)	promoter-TSS (NM_020579)	13	NM_020579	57370	Mm.274011	NM_020579	ENSMUSG00000052423	B4galt3	9530061M23Rik|AA104562|AW125175|ESTM26|ESTM6|R74981	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 3	protein-coding
mm_138293.1	chr17	34629535	34629620	+	1	NA	promoter-TSS (NM_030890)	promoter-TSS (NM_030890)	-109	NM_030890	260297	Mm.390965	NM_030890	ENSMUSG00000015476	Prrt1	Bat-4|Bat4|D17H6S54E|DSPD1|G5b|NG5|ORF31	proline-rich transmembrane protein 1	protein-coding
mm_156370.1	chrX	139618525	139618532	+	1	NA	intron (NM_023270, intron 1 of 6)	Lx4B|LINE|L1	7908	NM_023270	66889	Mm.27764	NM_023270	ENSMUSG00000031438	Rnf128	1300002C13Rik|AI987883|GRAIL|Greul1	ring finger protein 128	protein-coding
mm_85584.1	chr9	107300663	107300685	-	1	NA	exon (NM_009895, exon 3 of 3)	exon (NM_009895, exon 3 of 3)	4015	NM_009895	12700	Mm.4592	NM_009895	ENSMUSG00000032578	Cish	CIS-1|CIS1|Cis|F17|F23|SOCS	cytokine inducible SH2-containing protein	protein-coding
mm_60535.1	chr7	44480371	44480387	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-4138	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_172898.1	chr9	57110863	57110877	+	1	NA	exon (NM_011378, exon 16 of 22)	exon (NM_011378, exon 16 of 22)	-19907	NM_028636	73744	Mm.30110	NM_028636	ENSMUSG00000032295	Man2c1	1110025H24Rik	mannosidase, alpha, class 2C, member 1	protein-coding
mm_106574.1	chr11	120711114	120711163	-	1	NA	3' UTR (NM_016665, exon 5 of 5)	3' UTR (NM_016665, exon 5 of 5)	2629	NM_016665	20892	Mm.259716	NM_016665	ENSMUSG00000025144	Cenpx	Stra13	centromere protein X	protein-coding
mm_50122.1	chr6	41535514	41535529	+	1	NA	Intergenic	Intergenic	13745	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_38769.1	chr4	147904868	147904923	-	1	NA	promoter-TSS (NM_001285923)	promoter-TSS (NM_001285923)	14	NM_001285922	170731	Mm.154312	NM_133201	ENSMUSG00000029020	Mfn2	D630023P19Rik|Fzo	mitofusin 2	protein-coding
mm_43575.1	chr5	137746114	137746178	+	1	NA	5' UTR (NM_023910, exon 1 of 5)	5' UTR (NM_023910, exon 1 of 5)	177	NM_029805	78829	Mm.286399	NM_023910	ENSMUSG00000029723	Tsc22d4	0610009M14Rik|1700023B23Rik|AI415410|Thg-1pit|Tilz2	TSC22 domain family, member 4	protein-coding
mm_167004.1	chr7	50313839	50313840	+	1	NA	intron (NM_001037906, intron 12 of 19)	intron (NM_001037906, intron 12 of 19)	262045	NR_045928	73515	Mm.437440	NR_045928	ENSMUSG00000085265	Nell1os	1700081H22Rik	NEL-like 1, opposite strand	ncRNA
mm_107613.1	chr12	49385445	49385463	+	1	NA	exon (NM_008241, exon 2 of 2)	exon (NM_008241, exon 2 of 2)	2447	NM_008241	15228	Mm.4704	NM_008241	ENSMUSG00000020950	Foxg1	2900064B05Rik|BF-1|Bf1|Hfh9|Hfhbf1	forkhead box G1	protein-coding
mm_139810.1	chr17	66471956	66471963	+	1	NA	Intergenic	Intergenic	-22209	NM_001114098	68617	Mm.33421	NM_172963	ENSMUSG00000052105	Mtcl1	1110012J17Rik|Ccdc165|D130071O13|Kiaa0802|Soga2|mKIAA0802|t8219b25	microtubule crosslinking factor 1	protein-coding
mm_152545.1	chr19	11372243	11372261	-	1	NA	Intergenic	Intergenic	-3236	NM_001310331	666907		NM_001310331	ENSMUSG00000101389	Ms4a4a	EG666907	membrane-spanning 4-domains, subfamily A, member 4A	protein-coding
mm_60222.1	chr7	43562329	43562340	+	1	NA	promoter-TSS (NM_001008549)	promoter-TSS (NM_001008549)	-36	NM_001008549	210104	Mm.333821	NM_001008549	ENSMUSG00000056592	Zfp658	-	zinc finger protein 658	protein-coding
mm_7728.1	chr1	130729250	130729260	-	1	NA	promoter-TSS (NM_001162415)	promoter-TSS (NM_001162415)	-2	NM_001162415	18640	Mm.249861	NM_008825	ENSMUSG00000026409	Pfkfb2	4930568D07Rik	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2	protein-coding
mm_53029.1	chr6	124493102	124493170	+	1	NA	promoter-TSS (NM_181344)	promoter-TSS (NM_181344)	23	NM_181344	232371	Mm.132974	NM_181344	ENSMUSG00000038527	C1rl	C1r-LP|C1rl1|C1rlp	complement component 1, r subcomponent-like	protein-coding
mm_44134.1	chr5	150018784	150018799	+	1	NA	5' UTR (NM_001289564, exon 1 of 17)	5' UTR (NM_001289564, exon 1 of 17)	116	NM_001289566	140498	Mm.444643	NM_080468	ENSMUSG00000053368	Rxfp2	Gpr106|Great|Lgr8	relaxin/insulin-like family peptide receptor 2	protein-coding
mm_157370.1	chrX	37218331	37218337	-	1	NA	intron (NM_001025084, intron 1 of 4)	intron (NM_001025084, intron 1 of 4)	3924	NM_001025084	385343	Mm.379566	NM_001025084	ENSMUSG00000071773	Rhox1	-	reproductive homeobox 1	protein-coding
mm_99411.1	chr11	102268780	102268788	+	1	NA	promoter-TSS (NM_148953)	promoter-TSS (NM_148953)	-39	NM_148953	217217	Mm.216432	NM_148953	ENSMUSG00000034768	Asb16	-	ankyrin repeat and SOCS box-containing 16	protein-coding
mm_71760.1	chr8	66386810	66386820	+	1	NA	intron (NM_175188, intron 5 of 7)	intron (NM_175188, intron 5 of 7)	514	NM_001166375	72925	Mm.380457	NM_175188	ENSMUSG00000036469	March1	2900024D24Rik|BB085186	membrane-associated ring finger (C3HC4) 1	protein-coding
mm_58548.1	chr7	4690625	4690672	+	1	NA	promoter-TSS (NM_001003920)	promoter-TSS (NM_001003920)	-280	NM_001003920	381979	Mm.297064	NM_001003920	ENSMUSG00000035390	Brsk1	Gm1100|SAD-B|SADB	BR serine/threonine kinase 1	protein-coding
mm_152416.1	chr19	10669451	10669459	-	1	NA	intron (NM_021453, intron 7 of 8)	intron (NM_021453, intron 7 of 8)	8616	NM_021453	58803	Mm.34037	NM_021453	ENSMUSG00000024738	Pga5	1110035E17Rik|Pepf	pepsinogen 5, group I	protein-coding
mm_105977.1	chr11	115564118	115564130	-	1	NA	promoter-TSS (NM_001002929)	promoter-TSS (NM_001002929)	-320	NM_001002929	445007	Mm.4379	NM_001002929	ENSMUSG00000020739	Nup85	Pcnt1|frount	nucleoporin 85	protein-coding
mm_21365.1	chr2	157134139	157134143	-	1	NA	intron (NM_018851, intron 1 of 15)	(A)n|Simple_repeat|Simple_repeat	1081	NM_001139520	56045	Mm.248478	NM_018851	ENSMUSG00000027639	Samhd1	E330031J07Rik|Mg11	SAM domain and HD domain, 1	protein-coding
mm_69782.1	chr7	141090370	141090408	-	1	NA	TTS (NM_023059)	TTS (NM_023059)	10157	NM_023059	24058	Mm.38017	NM_023059	ENSMUSG00000025494	Sigirr	AI256711|TIR8	single immunoglobulin and toll-interleukin 1 receptor (TIR) domain	protein-coding
mm_152147.1	chr19	7206262	7206301	-	1	NA	promoter-TSS (NM_134150)	promoter-TSS (NM_134150)	3	NM_134150	107260	Mm.203921	NM_134150	ENSMUSG00000024767	Otub1	AI850305	OTU domain, ubiquitin aldehyde binding 1	protein-coding
mm_22794.1	chr3	22211354	22211362	+	1	NA	3' UTR (NM_030732, exon 16 of 16)	3' UTR (NM_030732, exon 16 of 16)	-40012	NR_004439	19784		NR_004439		Rprl2	RPRH3|Rmrp3	ribonuclease P RNA-like 2	ncRNA
mm_45078.1	chr5	43909863	43909881	-	1	NA	intron (NM_007646, intron 7 of 7)	intron (NM_007646, intron 7 of 7)	41063	NM_007646	12494	Mm.249873	NM_007646	ENSMUSG00000029084	Cd38	ADPRC 1|Cd38-rs1|I-19	CD38 antigen	protein-coding
mm_68299.1	chr7	105744313	105744358	-	1	NA	promoter-TSS (NM_020024)	promoter-TSS (NM_020024)	3	NM_020024	24075	Mm.274846	NM_020024	ENSMUSG00000043866	Taf10	30kDa|AU041226|TAFII30|Taf2h	TATA-box binding protein associated factor 10	protein-coding
mm_10903.1	chr2	25332223	25332247	+	1	NA	promoter-TSS (NM_001029983)	promoter-TSS (NM_001029983)	336	NR_027448	100272219	Mm.382103	NR_027448	ENSMUSG00000097345	AA543186	-	expressed sequence AA543186	ncRNA
mm_64419.1	chr7	142575990	142576071	+	1	NA	non-coding (NR_130974, exon 5 of 5)	non-coding (NR_130974, exon 5 of 5)	1117	NR_030416	735280		NR_030416	ENSMUSG00000076275	Mir675	Mirn675|mir-675|mmu-mir-675	microRNA 675	ncRNA
mm_159566.1	chr4	111919491	111919491	+	1	NA	promoter-TSS (NM_001100466)	promoter-TSS (NM_001100466)	-64	NM_001100466	639774	Mm.248185	NM_001100466	ENSMUSG00000078599	Skint8	OTTMUSG00000009475	selection and upkeep of intraepithelial T cells 8	protein-coding
mm_81223.1	chr9	107614541	107614645	+	1	NA	3' UTR (NM_008138, exon 9 of 9)	3' UTR (NM_008138, exon 9 of 9)	-5352	NM_001291539	20347	Mm.4083	NM_009153	ENSMUSG00000057969	Sema3b	SemA|Semaa|sema5|semaV	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B	protein-coding
mm_61273.1	chr7	66733559	66733585	+	1	NA	Intergenic	Intergenic	-9932	NM_001164201	545975	Mm.380104	NM_001164201	ENSMUSG00000030510	Cers3	4930550L11Rik|Gm488|Lass3|T3L	ceramide synthase 3	protein-coding
mm_93673.1	chr10	117710645	117710661	-	1	NA	5' UTR (NM_010786, exon 1 of 12)	5' UTR (NM_010786, exon 1 of 12)	105	NM_010786	17246	Mm.22670	NM_010786	ENSMUSG00000020184	Mdm2	1700007J15Rik|AA415488|Mdm-2	transformed mouse 3T3 cell double minute 2	protein-coding
mm_151669.1	chr19	4186112	4186123	-	1	NA	intron (NM_178650, intron 8 of 9)	RSINE1|SINE|B4	4930	NM_178650	108995	Mm.288312	NM_178650	ENSMUSG00000040247	Tbc1d10c	1810062O14Rik|AI428527	TBC1 domain family, member 10c	protein-coding
mm_169394.1	chr1	44374987	44374990	-	1	NA	Intergenic	L1Md_A|LINE|L1	-156057	NM_207281	403183	Mm.336176	NM_207281	ENSMUSG00000046828	Mettl21e	4832428D23Rik|Gm991	methyltransferase like 21E	protein-coding
mm_116551.1	chr13	46726608	46726615	-	1	NA	intron (NM_175749, intron 1 of 21)	intron (NM_175749, intron 1 of 21)	1238	NM_175749	218210	Mm.255398	NM_175749	ENSMUSG00000021374	Nup153	B130015D15Rik|C88147	nucleoporin 153	protein-coding
mm_1770.1	chr1	77848022	77848028	+	1	NA	Intergenic	Intergenic	-332937	NM_007936	13838	Mm.400747	NM_007936	ENSMUSG00000026235	Epha4	2900005C20Rik|AI385584|Cek8|Hek8|Sek|Sek1|Tyro1|rb	Eph receptor A4	protein-coding
mm_135366.1	chr16	44027984	44027996	-	1	NA	promoter-TSS (NM_001172107)	promoter-TSS (NM_001172107)	-45	NM_001172107	207798	Mm.19316	NM_153528	ENSMUSG00000036292	Gramd1c	4921521N14Rik	GRAM domain containing 1C	protein-coding
mm_85629.1	chr9	107616270	107616317	-	1	NA	exon (NM_008138, exon 7 of 9)	exon (NM_008138, exon 7 of 9)	-7052	NM_001291539	20347	Mm.4083	NM_009153	ENSMUSG00000057969	Sema3b	SemA|Semaa|sema5|semaV	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B	protein-coding
mm_38583.1	chr4	141819985	141819992	-	1	NA	intron (NM_007919, intron 5 of 7)	URR1A|DNA|hAT-Charlie	6017	NM_007919	13706	Mm.45316	NM_007919	ENSMUSG00000058579	Cela2a	Ela-2|Ela2|Ela2a	chymotrypsin-like elastase family, member 2A	protein-coding
mm_28410.1	chr3	90292777	90292782	-	1	NA	Intergenic	CpG	22630	NR_105979	102465612		NR_105979	ENSMUSG00000099199	Mir7012	Gm27370|mmu-mir-7012	microRNA 7012	ncRNA
mm_152500.1	chr19	11130820	11130859	-	1	NA	promoter-TSS (NM_027058)	promoter-TSS (NM_027058)	39	NM_027058	69369	Mm.391200	NM_027058	ENSMUSG00000024729	1700017D01Rik	-	RIKEN cDNA 1700017D01 gene	protein-coding
mm_32036.1	chr4	95738373	95738400	+	1	NA	intron (NM_001113412, intron 6 of 15)	intron (NM_001113412, intron 6 of 15)	158965	NM_029347	75578	Mm.276098	NM_029347	ENSMUSG00000028573	Fggy	2310009E04Rik	FGGY carbohydrate kinase domain containing	protein-coding
mm_144523.1	chr18	25019186	25019189	+	1	NA	intron (NM_001289654, intron 10 of 24)	intron (NM_001289654, intron 10 of 24)	146778	NM_001142697	66648	Mm.263189	NM_001004361	ENSMUSG00000024269	Tpgs2	5730437P09Rik|5730494M16Rik|AI666318|Pgs2	tubulin polyglutamylase complex subunit 2	protein-coding
mm_44111.1	chr5	149411792	149411811	+	1	NA	promoter-TSS (NM_027519)	promoter-TSS (NM_027519)	-5	NM_027519	70717	Mm.252139	NM_027519	ENSMUSG00000029659	Medag	6330406I15Rik|Awms3|MEDA-4|Meda4|mAWMS3	mesenteric estrogen dependent adipogenesis	protein-coding
mm_68188.1	chr7	104150541	104150561	-	1	NA	promoter-TSS (NM_198624)	promoter-TSS (NM_198624)	5	NM_198624	244179	Mm.189668	NM_198624	ENSMUSG00000051437	Ubqlnl	4922504M18Rik|Gm490	ubiquilin-like	protein-coding
mm_143198.1	chr17	62734077	62734080	-	1	NA	intron (NM_010109, intron 1 of 3)	intron (NM_010109, intron 1 of 3)	147239	NM_207654	13640	Mm.7978	NM_010109	ENSMUSG00000048915	Efna5	AL-1|AV158822|EFL-5|Ephrin-A5|Epl7|LERK-7|RAGS	ephrin A5	protein-coding
mm_36904.1	chr4	107923480	107923495	-	1	NA	5' UTR (NM_009949, exon 1 of 5)	5' UTR (NM_009949, exon 1 of 5)	102	NM_009949	12896	Mm.307620	NM_009949	ENSMUSG00000028607	Cpt2	AI323697|CPTII	carnitine palmitoyltransferase 2	protein-coding
mm_56818.1	chr6	116716738	116716770	-	1	NA	promoter-TSS (NM_178768)	promoter-TSS (NM_178768)	4	NM_178768	319776	Mm.133120	NM_178768	ENSMUSG00000048108	Tmem72	C230095G01Rik	transmembrane protein 72	protein-coding
mm_22669.1	chr3	14872294	14872298	+	1	NA	TTS (NM_007606)	TTS (NM_007606)	8758	NM_007606	12350	Mm.300	NM_007606	ENSMUSG00000027559	Car3	BB219044|Ca3|Car-3	carbonic anhydrase 3	protein-coding
mm_104023.1	chr11	85832295	85832310	-	1	NA	promoter-TSS (NM_009324)	promoter-TSS (NM_009324)	86	NR_077059	69909	Mm.440214	NR_077059	ENSMUSG00000087013	2610027K06Rik	-	RIKEN cDNA 2610027K06 gene	ncRNA
mm_116464.1	chr13	43478893	43478907	-	1	NA	intron (NM_019930, intron 1 of 13)	intron (NM_019930, intron 1 of 13)	2073	NM_019930	56705	Mm.148781	NM_019930	ENSMUSG00000038546	Ranbp9	IBAP-1|Ibap1|RanBPM	RAN binding protein 9	protein-coding
mm_106539.1	chr11	120578888	120578903	-	1	NA	3' UTR (NM_133796, exon 6 of 6)	3' UTR (NM_133796, exon 6 of 6)	2725	NM_133796	192662	Mm.30016	NM_133796	ENSMUSG00000025132	Arhgdia	5330430M07Rik|Gdi-1|Rho-GDI|RhoDGI|RhoGDI-1	Rho GDP dissociation inhibitor (GDI) alpha	protein-coding
mm_6152.1	chr1	64956732	64956782	-	1	NA	promoter-TSS (NM_001039493)	promoter-TSS (NM_001039493)	67	NM_001039493	241075	Mm.239534	NM_175509	ENSMUSG00000051344	Plekhm3	9430067K14Rik|A230102O09Rik|AI449570|DAPR|Plekhm1l	pleckstrin homology domain containing, family M, member 3	protein-coding
mm_105081.1	chr11	100822526	100822576	-	1	NA	promoter-TSS (NM_011489)	promoter-TSS (NM_011489)	19	NM_011489	20851	Mm.34064	NM_011489	ENSMUSG00000020919	Stat5b	-	signal transducer and activator of transcription 5B	protein-coding
mm_150331.1	chr19	34575025	34575037	+	1	NA	3' UTR (NM_008332, exon 3 of 3)	3' UTR (NM_008332, exon 3 of 3)	-8498	NM_010501	15959	Mm.426079	NM_010501	ENSMUSG00000074896	Ifit3	Ifi49|P49	interferon-induced protein with tetratricopeptide repeats 3	protein-coding
mm_4396.1	chr1	172370474	172370485	+	1	NA	3' UTR (NM_001039484, exon 2 of 2)	3' UTR (NM_001039484, exon 2 of 2)	-6052	NM_026234	67556	Mm.26612	NM_026234	ENSMUSG00000050229	Pigm	4933437L05Rik|AI644422|AV302080|C920011G20Rik	phosphatidylinositol glycan anchor biosynthesis, class M	protein-coding
mm_24201.1	chr3	88616195	88616248	+	1	NA	promoter-TSS (NM_001198911)	promoter-TSS (NM_001198911)	14	NM_001198911	16800	Mm.239329	NM_008487	ENSMUSG00000028059	Arhgef2	AA408978|GEF|GEF-H1|GEFH1|LFP40|Lbcl1|Lfc|P40|mKIAA0651	rho/rac guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_117714.1	chr13	95255123	95255138	-	1	NA	Intergenic	ORR1G|LTR|ERVL-MaLR	-4794	NM_001346782	218461	Mm.100167	NM_172263	ENSMUSG00000021684	Pde8b	B230331L10Rik|C030047E14Rik	phosphodiesterase 8B	protein-coding
mm_106168.1	chr11	116677443	116677448	-	1	NA	3' UTR (NM_009180, exon 9 of 9)	3' UTR (NM_009180, exon 9 of 9)	2848	NR_028570	100216538		NR_028570	ENSMUSG00000065094	Snord1a	snR38	small nucleolar RNA, C/D box 1A	snoRNA
mm_82502.1	chr9	20451860	20451862	-	1	NA	intron (NM_011753, intron 2 of 9)	L1_Mur3|LINE|L1	8299	NM_011753	22688	Mm.107441	NM_011753	ENSMUSG00000063108	Zfp26	5033428C05Rik|KRAB15|Zfp-26|Zfp70|Zfp81-rs1|mKIAA4196|mkr-3|mszf14|mszf52	zinc finger protein 26	protein-coding
mm_165291.1	chr2	90816313	90816314	+	1	NA	TTS (NM_178755)	TTS (NM_178755)	-30842	NM_001317241	56428	Mm.28023	NM_019758	ENSMUSG00000027282	Mtch2	2310034D24Rik|4930539J07Rik|HSPC032	mitochondrial carrier 2	protein-coding
mm_105873.1	chr11	114909106	114909145	-	1	NA	Intergenic	Intergenic	19084	NM_170758	217303	Mm.294439	NM_170758	ENSMUSG00000034652	Cd300a	B230315M08Rik|Clm8|LMIR1|MAIR-I|MAIR-Ia|MMAC8|Pigr4|mcpir1	CD300A molecule	protein-coding
mm_134195.1	chr16	10993101	10993111	-	1	NA	promoter-TSS (NM_019980)	promoter-TSS (NM_019980)	15	NM_019980	56722	Mm.294753	NM_019980	ENSMUSG00000022500	Litaf	3222402J11Rik|C85531|N4WBP3|TBX1	LPS-induced TN factor	protein-coding
mm_52238.1	chr6	104593163	104593166	+	1	NA	intron (NM_017383, intron 2 of 22)	(T)n|Simple_repeat|Simple_repeat	100120	NM_017383	53870	Mm.321671	NM_017383	ENSMUSG00000030092	Cntn6	NB-3	contactin 6	protein-coding
mm_162881.1	chr10	100590438	100590445	-	1	NA	Intergenic	Intergenic	-1182	NM_175128	68281	Mm.268474	NM_175128	ENSMUSG00000046567	4930430F08Rik	4930571E09Rik|A730088G13Rik|AW551239|C430008C19Rik	RIKEN cDNA 4930430F08 gene	protein-coding
mm_130672.1	chr15	100674707	100674717	-	1	NA	exon (NM_033612, exon 8 of 8)	exon (NM_033612, exon 8 of 8)	-5212	NM_001270537	668218	Mm.451225	NM_001270537	ENSMUSG00000098112	Bin2	-	bridging integrator 2	protein-coding
mm_153788.1	chr19	45816379	45816397	-	1	NA	promoter-TSS (NM_030716)	promoter-TSS (NM_030716)	-325	NM_145703	80906	Mm.213204	NM_030716	ENSMUSG00000025221	Kcnip2	KChIP2	Kv channel-interacting protein 2	protein-coding
mm_149016.1	chr19	8741416	8741461	+	1	NA	promoter-TSS (NM_001167799)	promoter-TSS (NM_001167799)	14	NM_001167799	56389	Mm.153061	NM_019829	ENSMUSG00000010110	Stx5a	0610031F24Rik|D19Ertd627e|Stx5	syntaxin 5A	protein-coding
mm_112170.1	chr12	113416306	113416314	-	1	NA	Intergenic	Intergenic	-73255	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_123945.1	chr14	73376931	73376944	-	1	NA	intron (NM_008410, intron 1 of 5)	intron (NM_008410, intron 1 of 5)	8334	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_143078.1	chr17	57044502	57044521	-	1	NA	3' UTR (NM_025877, exon 10 of 10)	3' UTR (NM_025877, exon 10 of 10)	-2857	NM_175333	103775	Mm.33647	NM_175333	ENSMUSG00000011486	Slc25a41	4933406J04Rik|AI507137	solute carrier family 25, member 41	protein-coding
mm_95761.1	chr11	54906828	54906835	+	1	NA	intron (NM_001329860, intron 1 of 5)	intron (NM_001329860, intron 1 of 5)	3977	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_35768.1	chr4	46196274	46196284	-	1	NA	promoter-TSS (NM_011728)	promoter-TSS (NM_011728)	32	NM_011728	22590	Mm.247036	NM_011728	ENSMUSG00000028329	Xpa	AI573865|Xpac	xeroderma pigmentosum, complementation group A	protein-coding
mm_10269.1	chr2	9880454	9880483	+	1	NA	promoter-TSS (NR_024257)	promoter-TSS (NR_024257)	-778	NR_024257	381347	Mm.441450	NR_024257		4930412O13Rik	ENSMUSG00000075535|Gm10853	RIKEN cDNA 4930412O13 gene	ncRNA
mm_63280.1	chr7	126766398	126766425	+	1	NA	promoter-TSS (NM_024228)	promoter-TSS (NM_024228)	-3	NM_024228	68616	Mm.246881	NM_024228	ENSMUSG00000030703	Gdpd3	1110015E22Rik	glycerophosphodiester phosphodiesterase domain containing 3	protein-coding
mm_13836.1	chr2	119351283	119351299	+	1	NA	promoter-TSS (NM_026929)	promoter-TSS (NM_026929)	49	NM_026929	69065	Mm.35083	NM_026929	ENSMUSG00000027313	Chac1	1810008K03Rik	ChaC, cation transport regulator 1	protein-coding
mm_4995.1	chr1	191821477	191821489	+	1	NA	promoter-TSS (NM_010892)	promoter-TSS (NM_010892)	10	NM_010892	18005	Mm.33773	NM_010892	ENSMUSG00000026622	Nek2	AA617254|C77054	NIMA (never in mitosis gene a)-related expressed kinase 2	protein-coding
mm_161578.1	chr16	26968152	26968152	-	1	NA	promoter-TSS (NM_001285916)	promoter-TSS (NM_001285916)	93	NM_001285916	239789	Mm.326909	NM_001013761	ENSMUSG00000068428	Gmnc	Gemc1|Gm1778|Gm606	geminin coiled-coil domain containing	protein-coding
mm_18231.1	chr2	51934691	51934710	-	1	NA	promoter-TSS (NM_001141982)	promoter-TSS (NM_001141982)	-56	NM_001141982	71684	Mm.28309	NM_030243	ENSMUSG00000036249	Rbm43	0610033I05Rik	RNA binding motif protein 43	protein-coding
mm_32680.1	chr4	115784950	115784991	+	1	NA	5' UTR (NM_181040, exon 1 of 9)	5' UTR (NM_181040, exon 1 of 9)	156	NM_181040	230649	Mm.109600	NM_181040	ENSMUSG00000028710	Atpaf1	6330547J17Rik|AI593252|ATP11|ATP11p	ATP synthase mitochondrial F1 complex assembly factor 1	protein-coding
mm_129110.1	chr15	76069682	76069759	-	1	NA	promoter-TSS (NM_134089)	promoter-TSS (NM_134089)	64	NM_134089	105782	Mm.25568	NM_134089	ENSMUSG00000022568	Scrib	AI118201|CRIB|Crc|SCRIB1|Scrb1|mKIAA0147|vartul	scribbled planar cell polarity	protein-coding
mm_126879.1	chr15	89430060	89430064	+	1	NA	promoter-TSS (NR_004843)	promoter-TSS (NR_004843)	-135	NR_037153	12651	Mm.485045	NM_007692	ENSMUSG00000022617	Chkb	Chetk|Chkl|Ck|Ck/Ek|Ck/Ek-beta|Ckb|Ckekb|Ek	choline kinase beta	protein-coding
mm_35063.1	chr4	6453748	6453759	-	1	NA	intron (NM_010945, intron 1 of 30)	CpG	518	NM_010945	18201	Mm.3059	NM_010945	ENSMUSG00000028245	Nsmaf	AA959567|C630007J05|Fan	neutral sphingomyelinase (N-SMase) activation associated factor	protein-coding
mm_118876.1	chr14	25862070	25862074	+	1	NA	intron (NM_013469, intron 1 of 14)	intron (NM_013469, intron 1 of 14)	19917	NM_013469	11744	Mm.294083	NM_013469	ENSMUSG00000021866	Anxa11	A830099O17Rik|Anx11	annexin A11	protein-coding
mm_55646.1	chr6	72361426	72361439	-	1	NA	exon (NM_001331167, exon 3 of 6)	exon (NM_001331167, exon 3 of 6)	1000	NR_138581	66510	Mm.170023	NM_025607	ENSMUSG00000055850	Rnf181	1700047F16Rik|2500002L14Rik|6230415N01Rik|C77350	ring finger protein 181	protein-coding
mm_16180.1	chr2	172643940	172643953	+	1	NA	Intergenic	Intergenic	92955	NM_001159696	21420	Mm.3629	NM_009335	ENSMUSG00000028640	Tfap2c	AA409384|AP2gamma|Ap-2.2|Stra2|Tcfap2c	transcription factor AP-2, gamma	protein-coding
mm_127911.1	chr15	9529814	9529846	-	1	NA	promoter-TSS (NM_008372)	promoter-TSS (NM_008372)	46	NM_008372	16197	Mm.389	NM_008372	ENSMUSG00000003882	Il7r	CD127|IL-7Ralpha	interleukin 7 receptor	protein-coding
mm_133901.1	chr16	97548605	97548619	+	1	NA	intron (NM_013606, intron 7 of 13)	L1_Mur3|LINE|L1	12529	NM_013606	17858	Mm.14157	NM_013606	ENSMUSG00000023341	Mx2	AI528743|Mx-2	MX dynamin-like GTPase 2	protein-coding
mm_32925.1	chr4	119195336	119195344	+	1	NA	promoter-TSS (NM_024462)	promoter-TSS (NM_024462)	30	NM_024462	69216	Mm.36697	NM_024462	ENSMUSG00000028643	Svbp	2410005K17Rik|AI851162|Ccdc23	small vasohibin binding protein	protein-coding
mm_91226.1	chr10	22068539	22068546	-	1	NA	promoter-TSS (NM_053264)	promoter-TSS (NM_053264)	-463	NM_053264	114671	Mm.288194	NM_053264	ENSMUSG00000069712	4930444G20Rik	-	RIKEN cDNA 4930444G20 gene	protein-coding
mm_106228.1	chr11	117266035	117266054	-	1	NA	promoter-TSS (NM_001113487)	promoter-TSS (NM_001113487)	-202	NM_001113487	53860	Mm.38450	NM_017380	ENSMUSG00000059248	Sept9	MSF1|Msf|PNUTL4|Sint1	septin 9	protein-coding
mm_41338.1	chr5	90497210	90497245	+	1	NA	exon (NM_007423, exon 5 of 15)	exon (NM_007423, exon 5 of 15)	6513	NM_007423	11576	Mm.358570	NM_007423	ENSMUSG00000054932	Afp	-	alpha fetoprotein	protein-coding
mm_6867.1	chr1	84279932	84279942	-	1	NA	intron (NM_001003948, intron 1 of 2)	intron (NM_001003948, intron 1 of 2)	4708	NM_001003948	98496	Mm.187470	NM_001003948	ENSMUSG00000045658	Pid1	5033414K04Rik|NYGGF4	phosphotyrosine interaction domain containing 1	protein-coding
mm_30868.1	chr4	32051711	32051731	+	1	NA	Intergenic	Intergenic	87614	NM_172688	26409	Mm.258589	NM_009316	ENSMUSG00000028284	Map3k7	B430101B05|C87327|Tak1	mitogen-activated protein kinase kinase kinase 7	protein-coding
mm_16879.1	chr2	12877782	12877786	-	1	NA	Intergenic	Intergenic	-46257	NM_008961	19212	Mm.229322	NM_008961	ENSMUSG00000026730	Pter	AI790318|Mpr56-1	phosphotriesterase related	protein-coding
mm_77318.1	chr8	117801963	117801973	-	1	NA	promoter-TSS (NM_026758)	promoter-TSS (NM_026758)	-39	NM_026758	68533	Mm.181836	NM_026758	ENSMUSG00000031843	Mphosph6	1110001M01Rik|AA536809|C86426	M phase phosphoprotein 6	protein-coding
mm_150574.1	chr19	40191023	40191032	+	1	NA	Intergenic	Intergenic	-3741	NM_145499	226105	Mm.29119	NM_145499	ENSMUSG00000060613	Cyp2c70	-	cytochrome P450, family 2, subfamily c, polypeptide 70	protein-coding
mm_84768.1	chr9	75611309	75611334	-	1	NA	promoter-TSS (NM_016711)	promoter-TSS (NM_016711)	4	NM_016711	50876	Mm.291880	NM_016711	ENSMUSG00000032186	Tmod2	N-Tmod|NTMOD	tropomodulin 2	protein-coding
mm_41103.1	chr5	87774553	87774573	+	1	NA	5' UTR (NM_001304768, exon 1 of 13)	5' UTR (NM_001304768, exon 1 of 13)	113	NM_007785	12993	Mm.4908	NM_007785	ENSMUSG00000061937	Csn1s2a	Csng|PP22	casein alpha s2-like A	protein-coding
mm_162649.1	chr1	195176688	195176694	-	1	NA	promoter-TSS (NM_007758)	promoter-TSS (NM_007758)	24	NM_007758	12902	Mm.235387	NM_007758	ENSMUSG00000026616	Cr2	C3DR|CD21|CD35|Cr-1|Cr-2|Cr1	complement receptor 2	protein-coding
mm_89674.1	chr10	97513594	97513619	+	1	NA	exon (NM_007833, exon 7 of 8)	exon (NM_007833, exon 7 of 8)	31275	NM_007833	13179	Mm.56769	NM_007833	ENSMUSG00000019929	Dcn	DC|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding
mm_70563.1	chr8	13105648	13105676	+	1	NA	promoter-TSS (NM_178708)	promoter-TSS (NM_178708)	-59	NM_146207	99375	Mm.212861	NM_146207	ENSMUSG00000031446	Cul4a	2810470J21Rik|AW495282	cullin 4A	protein-coding
mm_95205.1	chr11	43528806	43528820	+	1	NA	promoter-TSS (NM_001045530)	promoter-TSS (NM_001045530)	64	NM_001045530	380694	Mm.247595	NM_001045530	ENSMUSG00000044707	Ccnjl	Gm877	cyclin J-like	protein-coding
mm_87992.1	chr10	65643852	65643857	+	1	NA	Intergenic	IAPEz-int|LTR|ERVK	480210	NR_038039	69433	Mm.23366	NR_038039	ENSMUSG00000100000	1700023F02Rik	AV205046	RIKEN cDNA 1700023F02 gene	ncRNA
mm_60357.1	chr7	44428599	44428629	+	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	-13873	NM_198250	272381	Mm.44173	NM_198250	ENSMUSG00000047085	Lrrc4b	A830007M12|Lrig4	leucine rich repeat containing 4B	protein-coding
mm_72252.1	chr8	75094463	75094473	+	1	NA	intron (NM_010442, intron 1 of 4)	B1_Mus2|SINE|Alu	850	NM_010442	15368	Mm.276389	NM_010442	ENSMUSG00000005413	Hmox1	D8Wsu38e|HO-1|HO1|Hemox|Hmox|Hsp32	heme oxygenase 1	protein-coding
mm_119919.1	chr14	54957378	54957408	+	1	NA	exon (NM_010856, exon 17 of 39)	exon (NM_010856, exon 17 of 39)	-8251	NR_029724	387204		NR_029724	ENSMUSG00000065432	Mir208a	Mirn208|Mirn208a|mir-208|mir-208a|mmu-mir-208	microRNA 208a	ncRNA
mm_86133.1	chr9	116384281	116384316	-	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	-208935	NM_009371	21813	Mm.172346	NM_009371	ENSMUSG00000032440	Tgfbr2	1110020H15Rik|AU042018|DNIIR|RIIDN|TBR-II|TbetaR-II|TbetaRII	transforming growth factor, beta receptor II	protein-coding
mm_157288.1	chrX	20861420	20861430	-	1	NA	TTS (NM_009703)	TTS (NM_009703)	1757	NR_049190	100885829		NR_049190	ENSMUSG00000093408	Mir5617	Gm25192|mir-5617|mmu-mir-5617	microRNA 5617	ncRNA
mm_80482.1	chr9	78230645	78230664	+	1	NA	promoter-TSS (NM_008181)	promoter-TSS (NM_008181)	-15	NM_008181	14857	Mm.467426	NM_008181	ENSMUSG00000074183	Gsta1	Gst2-1|OTTMUSG00000031890	glutathione S-transferase, alpha 1 (Ya)	protein-coding
mm_19587.1	chr2	101883025	101883042	-	1	NA	Intergenic	Intergenic	-3229	NM_029635	76501	Mm.330424	NM_029635	ENSMUSG00000027163	Commd9	1810029F08Rik|AA409293	COMM domain containing 9	protein-coding
mm_134792.1	chr16	24090107	24090118	-	1	NA	Intergenic	Intergenic	-101500	NM_009744	12053	Mm.347398	NM_009744	ENSMUSG00000022508	Bcl6	Bcl5	B cell leukemia/lymphoma 6	protein-coding
mm_130350.1	chr15	97750000	97750015	-	1	NA	exon (NM_001177811, exon 21 of 27)	exon (NM_001177811, exon 21 of 27)	17659	NM_001177810	223864	Mm.24028	NM_144850	ENSMUSG00000022469	Rapgef3	2310016P22Rik|9330170P05Rik|Epac|Epac1	Rap guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_154402.1	chrM	14118	14129	+	1	NA	NA	Intergenic	NA	NA								
mm_101452.1	chr11	30212937	30212940	-	1	NA	intron (NM_175836, intron 1 of 34)	intron (NM_175836, intron 1 of 34)	6834	NM_175836	20742	Mm.123110	NM_009260	ENSMUSG00000020315	Sptbn1	9930031C03Rik|AL033301|SPTB2|Spnb-2|Spnb2|elf1|elf3|mKIAA4049	spectrin beta, non-erythrocytic 1	protein-coding
mm_95560.1	chr11	52336259	52336267	+	1	NA	Intergenic	Intergenic	-24599	NM_011694	22333	Mm.3555	NM_011694	ENSMUSG00000020402	Vdac1	AL033343|Vdac5|mVDAC1|mVDAC5	voltage-dependent anion channel 1	protein-coding
mm_72452.1	chr8	83166137	83166152	+	1	NA	exon (NM_001111304, exon 1 of 21)	exon (NM_001111304, exon 1 of 21)	792	NM_027758	71310	Mm.24031	NM_027758	ENSMUSG00000031709	Tbc1d9	4933431N12Rik|AI847101|AW490653|C76116	TBC1 domain family, member 9	protein-coding
mm_24767.1	chr3	95499892	95499896	+	1	NA	intron (NM_007802, intron 1 of 7)	intron (NM_007802, intron 1 of 7)	684	NM_007802	13038	Mm.272085	NM_007802	ENSMUSG00000028111	Ctsk	AI323530|MMS10-Q|Ms10q|catK	cathepsin K	protein-coding
mm_137874.1	chr17	31442939	31442953	+	1	NA	intron (NM_008804, intron 4 of 18)	intron (NM_008804, intron 4 of 18)	56712	NM_001163748	18585	Mm.10812	NM_008804	ENSMUSG00000041119	Pde9a	PDE9A1	phosphodiesterase 9A	protein-coding
mm_82985.1	chr9	36529447	36529464	-	1	NA	Intergenic	RMER17D2|LTR|ERVK	12508	NM_001033783	434396	Mm.118836	NM_001033783	ENSMUSG00000074448	Gm5615	EG434396|Pate-H|Pate9	predicted gene 5615	protein-coding
mm_35908.1	chr4	49747260	49747271	-	1	NA	intron (NM_001033351, intron 3 of 8)	intron (NM_001033351, intron 3 of 8)	-65282	NM_001004025	19059	Mm.46125	NM_001004025	ENSMUSG00000028310	Ppp3r2	CaNB2|CnB2	protein phosphatase 3, regulatory subunit B, alpha isoform (calcineurin B, type II)	protein-coding
mm_38174.1	chr4	135260353	135260377	-	1	NA	intron (NM_013885, intron 1 of 5)	B3|SINE|B2	12395	NM_013885	29876	Mm.257765	NM_013885	ENSMUSG00000037242	Clic4	D0Jmb3|TU-74|mc3s5|mtCLIC	chloride intracellular channel 4 (mitochondrial)	protein-coding
mm_120999.1	chr14	79451940	79451951	+	1	NA	5' UTR (NM_001034882, exon 1 of 1)	5' UTR (NM_001034882, exon 1 of 1)	110	NM_001034882	432879	Mm.308666	NM_001034882	ENSMUSG00000075502	Kbtbd6	EG432879|Gm5465|Zbtbd6	kelch repeat and BTB (POZ) domain containing 6	protein-coding
mm_44831.1	chr5	33996537	33996548	-	1	NA	5' UTR (NM_001001985, exon 1 of 3)	5' UTR (NM_001001985, exon 1 of 3)	558	NM_001001985	269642	Mm.274610	NM_001001985	ENSMUSG00000048142	Nat8l	1110038O08Rik|Shati	N-acetyltransferase 8-like	protein-coding
mm_36941.1	chr4	108780641	108780760	-	1	NA	intron (NM_001347163, intron 1 of 18)	CpG	388	NM_001347163	230597	Mm.196776	NM_183300	ENSMUSG00000034557	Zfyve9	Madhip|NSP|SARA|SMADIP	zinc finger, FYVE domain containing 9	protein-coding
mm_113285.1	chr13	30146014	30146014	+	1	NA	intron (NM_153546, intron 1 of 12)	intron (NM_153546, intron 1 of 12)	9524	NM_153546	218121	Mm.89682	NM_153546	ENSMUSG00000038732	Mboat1	9130215M02Rik|BC023845|LPEAT1|Moact1|Oact1	membrane bound O-acyltransferase domain containing 1	protein-coding
mm_62807.1	chr7	112933862	112933878	+	1	NA	Intergenic	Intergenic	-20092	NM_175279	78748	Mm.349943	NM_175279	ENSMUSG00000098132	Rassf10	4632411J06Rik	Ras association (RalGDS/AF-6) domain family (N-terminal) member 10	protein-coding
mm_97396.1	chr11	77838006	77838009	+	1	NA	intron (NM_001291214, intron 19 of 38)	intron (NM_001291214, intron 19 of 38)	36709	NM_001291215	360013	Mm.341248	NM_011586	ENSMUSG00000000631	Myo18a	MAJN|MyoPDZ|MysPDZ|SP-R210	myosin XVIIIA	protein-coding
mm_75453.1	chr8	47711657	47711677	-	1	NA	exon (NM_172407, exon 3 of 3)	exon (NM_172407, exon 3 of 3)	2264	NM_172407	70925	Mm.393807	NM_172407	ENSMUSG00000038069	Cdkn2aip	4921511I16Rik|AW208986|CARF	CDKN2A interacting protein	protein-coding
mm_65877.1	chr7	29555589	29555598	-	1	NA	Intergenic	Intergenic	-50133	NM_001081028	74206	Mm.447042	NM_001081028	ENSMUSG00000030583	Sipa1l3	2610511M17Rik	signal-induced proliferation-associated 1 like 3	protein-coding
mm_138876.1	chr17	43270341	43270366	+	1	NA	promoter-TSS (NM_133776)	promoter-TSS (NM_133776)	6	NM_133776	77596	Mm.159950	NM_133776	ENSMUSG00000041293	Adgrf1	5031409J19Rik|Gpr110|KPG_009	adhesion G protein-coupled receptor F1	protein-coding
mm_133792.1	chr16	95258340	95258371	+	1	NA	non-coding (NR_073406, exon 2 of 6)	non-coding (NR_073406, exon 2 of 6)	797	NM_001271690	16516	Mm.272239	NM_019664	ENSMUSG00000062609	Kcnj15	4930414N08Rik|AI182284|AI267127|IRKK|Kir4.2	potassium inwardly-rectifying channel, subfamily J, member 15	protein-coding
mm_99519.1	chr11	103133334	103133359	+	1	NA	promoter-TSS (NM_027658)	promoter-TSS (NM_027658)	7	NM_001130516	71059	Mm.273871	NM_027658	ENSMUSG00000043372	Hexim2	4933402L21Rik	hexamethylene bis-acetamide inducible 2	protein-coding
mm_138764.1	chr17	37053718	37053722	+	1	NA	intron (NM_019439, intron 6 of 22)	intron (NM_019439, intron 6 of 22)	7754	NM_019439	54393	Mm.32191	NM_019439	ENSMUSG00000024462	Gabbr1	GABAB1|GABAbR1|bM573K1.1	gamma-aminobutyric acid (GABA) B receptor, 1	protein-coding
mm_76276.1	chr8	84182161	84182164	-	1	NA	Intergenic	Intergenic	-3201	NR_029821	723819		NR_029821	ENSMUSG00000065483	Mir181c	Mirn181c|mir-181c	microRNA 181c	ncRNA
mm_137979.1	chr17	33584323	33584362	+	1	NA	intron (NM_053214, intron 12 of 27)	intron (NM_053214, intron 12 of 27)	28635	NM_053214	17916	Mm.42019	NM_053214	ENSMUSG00000024300	Myo1f	C330006B10Rik	myosin IF	protein-coding
mm_58860.1	chr7	16906489	16906539	+	1	NA	promoter-TSS (NM_008967)	promoter-TSS (NM_008967)	24	NM_008967	19222	Mm.287572	NM_008967	ENSMUSG00000043017	Ptgir	IP|PGI2	prostaglandin I receptor (IP)	protein-coding
mm_29260.1	chr3	107238658	107238707	-	1	NA	intron (NM_001044382, intron 1 of 2)	intron (NM_001044382, intron 1 of 2)	1025	NM_001044382	246691	Mm.490697	NM_001044382	ENSMUSG00000070368	Prok1	EG-VEGF	prokineticin 1	protein-coding
mm_31234.1	chr4	44664424	44664435	+	1	NA	intron (NM_008782, intron 5 of 9)	CpG	-38371	NR_073462	70602	Mm.491142	NR_073462	ENSMUSG00000103995	5730488B01Rik	-	RIKEN cDNA 5730488B01 gene	ncRNA
mm_21924.1	chr2	166996099	166996109	-	1	NA	5' UTR (NM_011490, exon 1 of 12)	5' UTR (NM_011490, exon 1 of 12)	195	NM_011490	20853	Mm.73276	NM_011490	ENSMUSG00000039536	Stau1	5830401L18Rik|AW549911|C85792|Stau	staufen (RNA binding protein) homolog 1 (Drosophila)	protein-coding
mm_26945.1	chr3	20266491	20266500	-	1	NA	exon (NM_029706, exon 4 of 11)	exon (NM_029706, exon 4 of 11)	9238	NM_029706	76703	Mm.34692	NM_029706	ENSMUSG00000011463	Cpb1	0910001A18Rik|1810063F02Rik|2210008M23Rik|AI504870	carboxypeptidase B1 (tissue)	protein-coding
mm_103787.1	chr11	82829025	82829042	-	1	NA	promoter-TSS (NM_026097)	promoter-TSS (NM_026097)	10	NM_026097	67338	Mm.341608	NM_026097	ENSMUSG00000020696	Rffl	1700051E09Rik|4930516L10Rik|BG080975|Carp2	ring finger and FYVE like domain containing protein	protein-coding
mm_75038.1	chr8	32610678	32610713	-	1	NA	Intergenic	Intergenic	339331	NM_001177589	100042715	Mm.291093	NM_001177589		Gm3985	-	predicted gene 3985	protein-coding
mm_117846.1	chr13	98694807	98694819	-	1	NA	promoter-TSS (NM_001025606)	promoter-TSS (NM_001025606)	18	NM_001025606	380863	Mm.28264	NM_001025606	ENSMUSG00000052485	Tmem171	Gm905	transmembrane protein 171	protein-coding
mm_30117.1	chr3	139886015	139886027	-	1	NA	Intergenic	Intergenic	-142228	NR_105798	102465198		NR_105798	ENSMUSG00000099169	Mir7j	Gm27716|Mirlet7j|mmu-let-7j	microRNA 7j	ncRNA
mm_141629.1	chr17	32917221	32917227	-	1	NA	promoter-TSS (NM_022434)	promoter-TSS (NM_022434)	105	NM_001204334	64385	Mm.486449	NM_022434	ENSMUSG00000024292	Cyp4f14	1300014O15Rik|cyp4f-14	cytochrome P450, family 4, subfamily f, polypeptide 14	protein-coding
mm_72953.1	chr8	92357974	92357988	+	1	NA	5' UTR (NM_018826, exon 1 of 3)	5' UTR (NM_018826, exon 1 of 3)	185	NM_018826	54352	Mm.101153	NM_018826	ENSMUSG00000031737	Irx5	-	Iroquois related homeobox 5 (Drosophila)	protein-coding
mm_82687.1	chr9	22298837	22298843	-	1	NA	intron (NM_145612, intron 2 of 7)	intron (NM_145612, intron 2 of 7)	8798	NM_145612	235050	Mm.306038	NM_145612	ENSMUSG00000066829	Zfp810	BC005471	zinc finger protein 810	protein-coding
mm_21617.1	chr2	164276039	164276051	-	1	NA	TTS (NM_009300)	TTS (NM_009300)	2262	NM_009300	20941	Mm.1286	NM_009300	ENSMUSG00000016998	Svs4	SVS-IV|Svp-2|Svp-4|Svp2|Svp4	seminal vesicle secretory protein 4	protein-coding
mm_9712.1	chr1	179802500	179802521	-	1	NA	intron (NM_026375, intron 1 of 35)	intron (NM_026375, intron 1 of 35)	1505	NM_026375	226747	Mm.128165	NM_026375	ENSMUSG00000026491	Ahctf1	6230412P20Rik|AV011447|Elys	AT hook containing transcription factor 1	protein-coding
mm_35781.1	chr4	46413470	46413483	-	1	NA	Intergenic	Intergenic	-9293	NM_053149	93966	Mm.25793	NM_053149	ENSMUSG00000028332	Hemgn	4921524M03Rik|AI317176|EDAG|Hgn|mNDR	hemogen	protein-coding
mm_84214.1	chr9	61694459	61694461	-	1	NA	Intergenic	Intergenic	220050	NM_018853	56040	Mm.3158	NM_018853	ENSMUSG00000007892	Rplp1	2410042H16Rik|Arpp1|C430017H15Rik	ribosomal protein, large, P1	protein-coding
mm_64372.1	chr7	142442371	142442373	+	1	NA	promoter-TSS (NM_009405)	promoter-TSS (NM_009405)	-96	NM_009405	21953	Mm.39469	NM_009405	ENSMUSG00000031097	Tnni2	-	troponin I, skeletal, fast 2	protein-coding
mm_26171.1	chr3	138286855	138286872	+	1	NA	exon (NM_007409, exon 6 of 9)	exon (NM_007409, exon 6 of 9)	9218	NM_007409	11522	Mm.2409	NM_007409	ENSMUSG00000074207	Adh1	ADH-AA|AI194826|Adh-1|Adh-1-t|Adh-1e|Adh-1t|Adh-3e|Adh1-e|Adh1-t|Adh1tl|Adh3-e	alcohol dehydrogenase 1 (class I)	protein-coding
mm_117915.1	chr13	99431602	99431615	-	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-18782	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_129166.1	chr15	76247613	76247661	-	1	NA	promoter-TSS (NR_105918)	promoter-TSS (NR_105918)	-554	NR_105918	102465575		NR_105918	ENSMUSG00000098625	Mir6953	Gm27738|mmu-mir-6953	microRNA 6953	ncRNA
mm_40175.1	chr5	35958880	35958885	+	1	NA	intron (NM_027373, intron 6 of 16)	B1_Mur3|SINE|Alu	65563	NM_027373	70292	Mm.125167	NM_027373	ENSMUSG00000029094	Afap1	2600003E23Rik|9630044L16Rik|AI848729|Afap|mKIAA3018	actin filament associated protein 1	protein-coding
mm_24519.1	chr3	92932976	92932983	+	1	NA	promoter-TSS (NM_025501)	promoter-TSS (NM_025501)	0	NM_025501	66344	Mm.443421	NM_025501	ENSMUSG00000042031	Lce3b	2310007F04Rik|Sprrl6A	late cornified envelope 3B	protein-coding
mm_33088.1	chr4	124659674	124659689	+	1	NA	3' UTR (NM_011141, exon 1 of 1)	3' UTR (NM_011141, exon 1 of 1)	2035	NM_011141	18991	Mm.297371	NM_011141	ENSMUSG00000090125	Pou3f1	Oct-6|Oct6|Otf-6|Otf6|Scip|Test1|Tst-1|Tst1	POU domain, class 3, transcription factor 1	protein-coding
mm_96737.1	chr11	69766496	69766559	+	1	NA	intron (NM_029348, intron 1 of 3)	CpG	615	NM_029348	75580	Mm.426361	NM_029348	ENSMUSG00000018750	Zbtb4	2310026P19Rik|9230111I22Rik|mKIAA1538	zinc finger and BTB domain containing 4	protein-coding
mm_132357.1	chr16	34651203	34651219	+	1	NA	promoter-TSS (NM_030744)	promoter-TSS (NM_030744)	0	NM_030744	76378	Mm.23515	NM_030744	ENSMUSG00000022832	Ropn1	1700008N21Rik|ODF6|RHPNAP1|Rppn|ropporin	ropporin, rhophilin associated protein 1	protein-coding
mm_138499.1	chr17	35202682	35202696	+	1	NA	promoter-TSS (NM_013693)	promoter-TSS (NM_013693)	-682	NM_001278601	21926	Mm.1293	NM_013693	ENSMUSG00000024401	Tnf	DIF|TNF-a|TNF-alpha|TNFSF2|TNFalpha|Tnfa|Tnfsf1a|Tnlg1f	tumor necrosis factor	protein-coding
mm_97440.1	chr11	78178704	78178772	+	1	NA	promoter-TSS (NM_001291236)	promoter-TSS (NM_001291236)	80	NM_026708	68385	Mm.390375	NM_026708	ENSMUSG00000019437	Tlcd1	-	TLC domain containing 1	protein-coding
mm_75200.1	chr8	39119002	39119013	-	1	NA	intron (NM_030254, intron 6 of 7)	intron (NM_030254, intron 6 of 7)	113140	NM_030254	80286	Mm.272722	NM_030254	ENSMUSG00000039530	Tusc3	AU022242|BC003311|N33	tumor suppressor candidate 3	protein-coding
mm_74871.1	chr8	25016902	25016924	-	1	NA	promoter-TSS (NM_007404)	promoter-TSS (NM_007404)	9	NM_001270996	11502	Mm.28908	NM_007404	ENSMUSG00000031555	Adam9	AU020942|MDC9|Mltng|mKIAA0021	a disintegrin and metallopeptidase domain 9 (meltrin gamma)	protein-coding
mm_166877.1	chr7	25412966	25412974	-	1	NA	promoter-TSS (NM_153576)	promoter-TSS (NM_153576)	-84	NM_153576	232983	Mm.10545	NM_153576	ENSMUSG00000060188	Cxcl17	VCC-1|Vcc1	chemokine (C-X-C motif) ligand 17	protein-coding
mm_95105.1	chr11	34048972	34048984	+	1	NA	intron (NM_010696, intron 1 of 20)	intron (NM_010696, intron 1 of 20)	1777	NM_010696	16822	Mm.265350	NM_010696	ENSMUSG00000002699	Lcp2	AI323664|BB161688|SLP-76|SLP76|m1Khoe|twm	lymphocyte cytosolic protein 2	protein-coding
mm_54461.1	chr6	34875645	34875674	-	1	NA	TTS (NM_197986)	TTS (NM_197986)	2406	NM_199145	78412	Mm.248440	NM_199145	ENSMUSG00000046806	3110062M04Rik	AL023049|Mri	RIKEN cDNA 3110062M04 gene	protein-coding
mm_143065.1	chr17	57021310	57021327	-	1	NA	3' UTR (NM_010613, exon 18 of 18)	3' UTR (NM_010613, exon 18 of 18)	-10030	NM_133801	98053	Mm.24632	NM_133801	ENSMUSG00000002658	Gtf2f1	2810405L04Rik|C76800|RAP74	general transcription factor IIF, polypeptide 1	protein-coding
mm_130697.1	chr15	100683303	100683306	-	1	NA	intron (NM_033612, intron 4 of 7)	AT_rich|Low_complexity|Low_complexity	4616	NM_033612	109901	Mm.2131	NM_033612	ENSMUSG00000023031	Cela1	1810009A17Rik|1810062B19Rik|Ela-1|Ela1|PC-TsF	chymotrypsin-like elastase family, member 1	protein-coding
mm_21103.1	chr2	153241403	153241411	-	1	NA	promoter-TSS (NM_080463)	promoter-TSS (NM_080463)	-49	NM_018807	54711	Mm.103199	NM_018807	ENSMUSG00000051413	Plagl2	AU018672|AW552839|mKIAA0198	pleiomorphic adenoma gene-like 2	protein-coding
mm_137798.1	chr17	29691259	29691279	+	1	NA	exon (NM_028791, exon 13 of 24)	exon (NM_028791, exon 13 of 24)	25748	NM_026782	68597	Mm.390979	NM_026782	ENSMUSG00000024018	Ccdc167	1110021J02Rik	coiled-coil domain containing 167	protein-coding
mm_129164.1	chr15	76243402	76243448	-	1	NA	promoter-TSS (NM_001163575)	promoter-TSS (NM_001163575)	15	NM_001163576	671535	Mm.373750	NM_001163575	ENSMUSG00000063268	Parp10	-	poly (ADP-ribose) polymerase family, member 10	protein-coding
mm_135546.1	chr16	49799786	49799806	-	1	NA	Intergenic	Intergenic	-55858	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_13242.1	chr2	98662740	98662754	+	1	NA	Intergenic	SYNREP_MM|Satellite|Satellite	1195090	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_16577.1	chr2	3498104	3498108	-	1	NA	exon (NM_015765, exon 8 of 14)	exon (NM_015765, exon 8 of 14)	14708	NR_103465	50497	Mm.89341	NM_015765	ENSMUSG00000051396	Hspa14	70kDa|HSP70L1|Hsp70-4|NST-1|hsr.1	heat shock protein 14	protein-coding
mm_129521.1	chr15	79156534	79156546	-	1	NA	exon (NM_011437, exon 4 of 4)	exon (NM_011437, exon 4 of 4)	7950	NM_011437	20665	Mm.276739	NM_011437	ENSMUSG00000033006	Sox10	Dom|Sox21|gt	SRY (sex determining region Y)-box 10	protein-coding
mm_164235.1	chr15	91633382	91633396	+	1	NA	Intergenic	B1_Mur1|SINE|Alu	-39835	NM_025730	66725	Mm.37558	NM_025730	ENSMUSG00000036273	Lrrk2	4921513O20Rik|9330188B09Rik|AW561911|D630001M17Rik|Gm927|cI-46	leucine-rich repeat kinase 2	protein-coding
mm_21872.1	chr2	165983085	165983115	-	1	NA	Intergenic	MLT1M|LTR|ERVL-MaLR	-9537	NM_008679	17979	Mm.469663	NM_008679	ENSMUSG00000027678	Ncoa3	2010305B15Rik|AW321064|Actr|Aib1|KAT13B|Rac3|Src3|Tram-1|Tram1|bHLHe42|p/Cip|pCip	nuclear receptor coactivator 3	protein-coding
mm_35703.1	chr4	44167770	44167779	-	1	NA	promoter-TSS (NM_175201)	promoter-TSS (NM_175201)	-236	NM_175201	73469	Mm.262859	NM_175201	ENSMUSG00000035696	Rnf38	1700065B19Rik|2610202O07Rik|AA673263|Oip1	ring finger protein 38	protein-coding
mm_12724.1	chr2	78369987	78369990	+	1	NA	Intergenic	Intergenic	132441	NM_177843	329436	Mm.235448	NM_177843		Gm14461	A830093M07|OTTMUSG00000016703	predicted gene 14461	protein-coding
mm_27926.1	chr3	79551065	79551088	-	1	NA	intron (NM_001162999, intron 1 of 16)	intron (NM_001162999, intron 1 of 16)	16603	NM_001162999	329679	Mm.244005	NM_001162999	ENSMUSG00000061175	Fnip2	D630023B12Rik|mKIAA1450	folliculin interacting protein 2	protein-coding
mm_53245.1	chr6	127577938	127577938	+	1	NA	promoter-TSS (NM_001033464)	promoter-TSS (NM_001033464)	-37	NM_001033464	381812	Mm.296093	NM_001033464	ENSMUSG00000061414	Cracr2a	Efcab4b|Gm1073|Gm462	calcium release activated channel regulator 2A	protein-coding
mm_60454.1	chr7	44477555	44477576	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-6952	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_1944.1	chr1	86303490	86303503	+	1	NA	5' UTR (NM_145222, exon 1 of 2)	5' UTR (NM_145222, exon 1 of 2)	275	NM_145222	227327	Mm.86467	NM_145222	ENSMUSG00000079445	B3gnt7	C330001H22Rik|beta-3GnT7	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 7	protein-coding
mm_170815.1	chr2	176282686	176282699	-	1	NA	Intergenic	Intergenic	-7251	NR_040256	626877	Mm.490744	NR_040256		Gm14405	OTTMUSG00000016573	predicted gene 14405	pseudo
mm_31731.1	chr4	62979685	62979708	+	1	NA	intron (NM_028326, intron 1 of 14)	ORR1A3-int|LTR|ERVL-MaLR	14122	NM_028326	72701	Mm.26479	NM_028326	ENSMUSG00000028358	Zfp618	2810031P15Rik|2810040O04Rik|AI415580|AI505139|D430033D05Rik|Nedd10|Znf618|bM257P7.1	zinc finger protein 618	protein-coding
mm_10082.1	chr1	195176708	195176725	-	1	NA	promoter-TSS (NM_007758)	promoter-TSS (NM_007758)	-1	NM_007758	12902	Mm.235387	NM_007758	ENSMUSG00000026616	Cr2	C3DR|CD21|CD35|Cr-1|Cr-2|Cr1	complement receptor 2	protein-coding
mm_120807.1	chr14	74946944	74946986	+	1	NA	intron (NM_001252132, intron 1 of 18)	CpG	912	NM_001252132	380916	Mm.288868	NM_001033439	ENSMUSG00000068015	Lrch1	4832412D13Rik|AI552548|AW215503|Chdc1|mKIAA1016	leucine-rich repeats and calponin homology (CH) domain containing 1	protein-coding
mm_161669.1	chr17	13131808	13131808	-	1	NA	promoter-TSS (NM_199252)	promoter-TSS (NM_199252)	-17	NM_199252	381058	Mm.390935	NM_199252	ENSMUSG00000067049	Unc93a	Unc93l|unc-93A	unc-93 homolog A (C. elegans)	protein-coding
mm_65856.1	chr7	29288260	29288305	-	1	NA	Intergenic	RMER17C|LTR|ERVK	-1038	NM_026731	68458	Mm.2343	NM_026731	ENSMUSG00000037166	Ppp1r14a	1110001M11Rik|Cpi17	protein phosphatase 1, regulatory (inhibitor) subunit 14A	protein-coding
mm_38172.1	chr4	135226093	135226153	-	1	NA	exon (NM_013885, exon 3 of 6)	exon (NM_013885, exon 3 of 6)	46637	NM_013885	29876	Mm.257765	NM_013885	ENSMUSG00000037242	Clic4	D0Jmb3|TU-74|mc3s5|mtCLIC	chloride intracellular channel 4 (mitochondrial)	protein-coding
mm_153889.1	chr19	46962326	46962333	-	1	NA	promoter-TSS (NM_029810)	promoter-TSS (NM_029810)	22	NM_029810	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_98502.1	chr11	94952023	94952041	+	1	NA	3' UTR (NM_007742, exon 51 of 51)	3' UTR (NM_007742, exon 51 of 51)	-15561	NM_018792	54388	Mm.30482	NM_018792	ENSMUSG00000038994	Hils1	H1.9|TISP64	histone H1-like protein in spermatids 1	protein-coding
mm_153236.1	chr19	36112057	36112095	-	1	NA	3' UTR (NM_013468, exon 9 of 9)	3' UTR (NM_013468, exon 9 of 9)	7768	NM_013468	107765	Mm.10279	NM_013468	ENSMUSG00000024803	Ankrd1	Alrp|CARP|Crap|MARP1	ankyrin repeat domain 1 (cardiac muscle)	protein-coding
mm_90787.1	chr10	7054942	7054956	-	1	NA	Intergenic	Intergenic	-31764	NM_001033391	320495	Mm.331674	NM_001033391	ENSMUSG00000064065	Ipcef1	A130090K04Rik	interaction protein for cytohesin exchange factors 1	protein-coding
mm_69264.1	chr7	127894679	127894687	-	1	NA	intron (NM_178600, intron 1 of 2)	intron (NM_178600, intron 1 of 2)	934	NM_178600	27973	Mm.29703	NM_178600	ENSMUSG00000096145	Vkorc1	D7Wsu86e	vitamin K epoxide reductase complex, subunit 1	protein-coding
mm_136982.1	chr17	16951557	16951589	+	1	NA	Intergenic	Intergenic	-112530	NM_001005358	449000	Mm.483718	NM_001005358	ENSMUSG00000096696	Zfp960	-	zinc finger protein 960	protein-coding
mm_30920.1	chr4	32672548	32672559	+	1	NA	intron (NM_001081392, intron 9 of 101)	intron (NM_001081392, intron 9 of 101)	15434	NM_001081392	100019	Mm.24627	NM_133874	ENSMUSG00000058006	Mdn1	4833432B22Rik|A130070M06|AA958993|D4Abb1e|Gm135	midasin AAA ATPase 1	protein-coding
mm_17759.1	chr2	32775596	32775619	-	1	NA	promoter-TSS (NM_001290563)	promoter-TSS (NM_001290563)	26	NM_177384	338348	Mm.475130	NM_177384	ENSMUSG00000039021	Ttc16	1200002K10Rik	tetratricopeptide repeat domain 16	protein-coding
mm_53887.1	chr6	3376884	3376907	-	1	NA	exon (NM_010156, exon 2 of 2)	exon (NM_010156, exon 2 of 2)	22676	NM_010156	209086	Mm.196013	NM_010156	ENSMUSG00000047735	Samd9l	AA175286|ESTM25|mKIAA2005	sterile alpha motif domain containing 9-like	protein-coding
mm_52435.1	chr6	113600759	113600764	+	1	NA	promoter-TSS (NM_027633)	promoter-TSS (NM_027633)	-46	NM_027633	70979	Mm.72959	NM_027633	ENSMUSG00000033963	Fancd2os	4931417G12Rik	Fancd2 opposite strand	protein-coding
mm_116961.1	chr13	56142677	56142690	-	1	NA	Intergenic	Charlie1a|DNA|hAT-Charlie	-7133	NM_001159513	26914	Mm.283802	NM_012015	ENSMUSG00000015937	H2afy	H2AF12M|mH2a1|macroH2A1	H2A histone family, member Y	protein-coding
mm_7076.1	chr1	88264819	88264865	-	1	NA	TTS (NM_172505)	TTS (NM_172505)	4566	NR_040291	78605	Mm.384762	NR_040291		6430706D22Rik	-	RIKEN cDNA 6430706D22 gene	ncRNA
mm_107786.1	chr12	61571442	61571444	+	1	NA	intron (NM_178714, intron 1 of 3)	Lx3_Mus|LINE|L1	48276	NM_001310586	238205	Mm.28802	NM_178714	ENSMUSG00000035653	Lrfn5	AI427653|AI604817|C130061B21|mKIAA4208	leucine rich repeat and fibronectin type III domain containing 5	protein-coding
mm_23120.1	chr3	37643725	37643745	+	1	NA	3' UTR (NM_011896, exon 3 of 3)	3' UTR (NM_011896, exon 3 of 3)	3788	NM_001305442	24063	Mm.330986	NM_011896	ENSMUSG00000037211	Spry1	sprouty1|spry-1	sprouty homolog 1 (Drosophila)	protein-coding
mm_139959.1	chr17	71569827	71569831	+	1	NA	non-coding (NR_015549, exon 4 of 7)	non-coding (NR_015549, exon 4 of 7)	17768	NM_029254	70891	Mm.477599	NM_029254	ENSMUSG00000052525	Spdya	4921517J08Rik|4930548B21Rik|GS4|MLZ-465|Spdy1	speedy/RINGO cell cycle regulator family, member A	protein-coding
mm_77945.1	chr9	7358379	7358409	+	1	NA	3' UTR (NM_008605, exon 10 of 10)	3' UTR (NM_008605, exon 10 of 10)	11020	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_81500.1	chr9	110034432	110034526	+	1	NA	exon (NM_008633, exon 7 of 19)	exon (NM_008633, exon 7 of 19)	-17542	NM_001311163	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_137087.1	chr17	21489078	21489088	+	1	NA	promoter-TSS (NM_013843)	promoter-TSS (NM_013843)	95	NM_013843	24132	Mm.42140	NM_013843	ENSMUSG00000057409	Zfp53	D030067O06Rik|KRAZ1|Zfp-53|Zfp118|zfas8	zinc finger protein 53	protein-coding
mm_162215.1	chrX	136779839	136779839	-	1	NA	promoter-TSS (NM_010297)	promoter-TSS (NM_010297)	-118	NM_010297	14657	Mm.215168	NM_010297	ENSMUSG00000018595	Glra4	-	glycine receptor, alpha 4 subunit	protein-coding
mm_81949.1	chr9	120521782	120521786	+	1	NA	Intergenic	Intergenic	-18034	NM_178676	215446	Mm.76648	NM_178676	ENSMUSG00000041608	Entpd3	Cd39l3|HB6|NTPDase-3	ectonucleoside triphosphate diphosphohydrolase 3	protein-coding
mm_41343.1	chr5	90499643	90499703	+	1	NA	exon (NM_007423, exon 7 of 15)	exon (NM_007423, exon 7 of 15)	8959	NM_007423	11576	Mm.358570	NM_007423	ENSMUSG00000054932	Afp	-	alpha fetoprotein	protein-coding
mm_161930.1	chr18	80974601	80974601	-	1	NA	exon (NM_178280, exon 2 of 4)	exon (NM_178280, exon 2 of 4)	11977	NM_178280	20689	Mm.215917	NM_178280	ENSMUSG00000024565	Sall3	B130022O04Rik|Msal|Msal-1|Sal|Salt|Spalt	sal-like 3 (Drosophila)	protein-coding
mm_94990.1	chr11	31871412	31871420	+	1	NA	5' UTR (NM_026252, exon 1 of 10)	5' UTR (NM_026252, exon 1 of 10)	476	NM_026252	67579	Mm.339792	NM_026252	ENSMUSG00000020300	Cpeb4	Cpe-bp4|Cpeb-4|mCPEB-4	cytoplasmic polyadenylation element binding protein 4	protein-coding
mm_759.1	chr1	43934758	43934761	+	1	NA	intron (NM_001310540, intron 1 of 28)	intron (NM_001310540, intron 1 of 28)	765	NM_009418	22019	Mm.401675	NM_009418	ENSMUSG00000041763	Tpp2	TPP-2|TppII	tripeptidyl peptidase II	protein-coding
mm_68860.1	chr7	126412207	126412229	-	1	NA	intron (NM_009844, intron 4 of 14)	intron (NM_009844, intron 4 of 14)	2652	NM_009844	12478	Mm.4360	NM_009844	ENSMUSG00000030724	Cd19	AW495831	CD19 antigen	protein-coding
mm_105069.1	chr11	100738115	100738140	-	1	NA	promoter-TSS (NM_001305003)	promoter-TSS (NM_001305003)	88	NM_024456	19345	Mm.29829	NM_024456	ENSMUSG00000019173	Rab5c	AI326010|Rabl	RAB5C, member RAS oncogene family	protein-coding
mm_105624.1	chr11	106789437	106789454	-	1	NA	promoter-TSS (NM_007840)	promoter-TSS (NM_007840)	193	NM_001166685	320162	Mm.30524	NM_177088	ENSMUSG00000018372	Cep95	4732496G21Rik|AI118346|AI448335|Ccdc45|D330027A14Rik|F630025I20Rik	centrosomal protein 95	protein-coding
mm_61181.1	chr7	61732754	61732762	+	1	NA	intron (NR_015533, intron 6 of 8)	Lx|LINE|L1	2844	NR_037284	100526541		NR_037284	ENSMUSG00000077869	Mir344e	mir-344e|mmu-mir-344e	microRNA 344e	ncRNA
mm_162586.1	chr1	180848696	180848711	-	1	NA	Intergenic	Intergenic	-2448	NM_145943	208768	Mm.272625	NM_145943	ENSMUSG00000038806	Sde2	-	SDE2 telomere maintenance homolog (S. pombe)	protein-coding
mm_145091.1	chr18	42553406	42553415	+	1	NA	exon (NM_001289526, exon 14 of 22)	exon (NM_001289526, exon 14 of 22)	26242	NM_181543	240239	Mm.186779	NM_181543	ENSMUSG00000042816	Gpr151	C130082O03Rik|GalRL|PGR7|nGPCR-2037	G protein-coupled receptor 151	protein-coding
mm_147574.1	chr18	55939504	55939536	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	-492612	NM_026240	107022	Mm.24356	NM_026240	ENSMUSG00000001700	Gramd3	9030613F08Rik|9130427A09Rik|AW061306|NS3TP2	GRAM domain containing 3	protein-coding
mm_29096.1	chr3	104792046	104792062	-	1	NA	intron (NM_001291859, intron 2 of 4)	intron (NM_001291859, intron 2 of 4)	3020	NM_007484	11853	Mm.262	NM_007484	ENSMUSG00000002233	Rhoc	AI324259|Arh9|Arhc	ras homolog family member C	protein-coding
mm_140864.1	chr17	23771491	23771499	-	1	NA	promoter-TSS (NM_153791)	promoter-TSS (NM_153791)	96	NM_153791	224613	Mm.328835	NM_153791	ENSMUSG00000040097	Flywch1	E030034P13Rik|mKIAA1552	FLYWCH-type zinc finger 1	protein-coding
mm_137308.1	chr17	24878226	24878264	+	1	NA	promoter-TSS (NM_008340)	promoter-TSS (NM_008340)	-525	NM_008340	16005	Mm.3135	NM_008340	ENSMUSG00000046070	Igfals	ALS|Albs|mKIAA4111	insulin-like growth factor binding protein, acid labile subunit	protein-coding
mm_101482.1	chr11	30986327	30986372	-	1	NA	promoter-TSS (NM_026527)	promoter-TSS (NM_026527)	16	NM_026527	68044	Mm.32656	NM_026527	ENSMUSG00000020309	Chac2	-	ChaC, cation transport regulator 2	protein-coding
mm_110134.1	chr12	26447173	26447196	-	1	NA	exon (NM_021384, exon 5 of 6)	exon (NM_021384, exon 5 of 6)	9268	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_108239.1	chr12	77467323	77467326	+	1	NA	intron (NR_045554, intron 11 of 11)	RMER6A|LTR|ERVK	57183	NM_001252616	53618	Mm.35628	NM_016893	ENSMUSG00000021065	Fut8	-	fucosyltransferase 8	protein-coding
mm_141917.1	chr17	34999437	34999449	-	1	NA	exon (NM_033075, exon 2 of 2)	exon (NM_033075, exon 2 of 2)	1303	NM_033075	110956	Mm.22506	NM_033075		D17H6S56E-5	G7e	DNA segment, Chr 17, human D6S56E 5	protein-coding
mm_12502.1	chr2	71873259	71873263	+	1	NA	promoter-TSS (NM_172665)	promoter-TSS (NM_172665)	37	NM_172665	228026	Mm.34411	NM_172665	ENSMUSG00000006494	Pdk1	B830012B01|D530020C15Rik	pyruvate dehydrogenase kinase, isoenzyme 1	protein-coding
mm_100610.1	chr11	121434949	121434987	+	1	NA	promoter-TSS (NM_022014)	promoter-TSS (NM_022014)	15	NM_022014	63828	Mm.266448	NM_022014	ENSMUSG00000025175	Fn3k	2310074G21Rik	fructosamine 3 kinase	protein-coding
mm_111954.1	chr12	109545899	109545906	-	1	NA	non-coding (NR_003633, exon 1 of 5)	non-coding (NR_003633, exon 1 of 5)	504	NR_003633	17263	Mm.289645	NM_144513	ENSMUSG00000021268	Meg3	2900016C05Rik|3110050O07Rik|6330408G06Rik|AI425946|AW108224|D12Bwg1266e|Gtl2|R74756|R75394	maternally expressed 3	ncRNA
mm_126408.1	chr15	80255491	80255511	+	1	NA	5' UTR (NM_009716, exon 1 of 3)	5' UTR (NM_009716, exon 1 of 3)	317	NM_009716	11911	Mm.641	NM_009716	ENSMUSG00000042406	Atf4	Atf-4|C/ATF|CREB2|TAXREB67	activating transcription factor 4	protein-coding
mm_12095.1	chr2	60842372	60842422	+	1	NA	exon (NM_001141932, exon 2 of 15)	exon (NM_001141932, exon 2 of 15)	39041	NM_001141932	56878	Mm.259667	NM_020296	ENSMUSG00000026970	Rbms1	2600014B10Rik|AI255215|MSSP-1|MSSP-2|MSSP-3|YC1	RNA binding motif, single stranded interacting protein 1	protein-coding
mm_107347.1	chr12	32820305	32820362	+	1	NA	promoter-TSS (NM_021524)	promoter-TSS (NM_021524)	-2	NM_021524	59027	Mm.202727	NM_021524	ENSMUSG00000020572	Nampt	1110035O14Rik|AI314458|AI480535|NAmPRTase|Pbef|Pbef1|Visfatin	nicotinamide phosphoribosyltransferase	protein-coding
mm_124732.1	chr15	6580676	6580680	+	1	NA	exon (NM_001278269, exon 1 of 17)	exon (NM_001278269, exon 1 of 17)	831	NM_011815	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_146595.1	chr18	9449594	9449600	-	1	NA	exon (NM_026484, exon 1 of 10)	exon (NM_026484, exon 1 of 10)	553	NM_026484	67974	Mm.86523	NM_026484	ENSMUSG00000024286	Ccny	1700025H17Rik|3110050L10Rik|4631402G10Rik|5730405I09Rik	cyclin Y	protein-coding
mm_66330.1	chr7	42735648	42735652	-	1	NA	Intergenic	L1_Mus4|LINE|L1	-42932	NM_001008427	434179	Mm.284947	NM_001008427	ENSMUSG00000069727	Zfp975	EG434179|Gm5595|mszf88	zinc finger protein 975	protein-coding
mm_108981.1	chr12	102743976	102743985	+	1	NA	promoter-TSS (NM_001142937)	promoter-TSS (NM_001142937)	220	NM_177140	320351	Mm.86546	NM_177140	ENSMUSG00000046675	Tmem251	D230037D09Rik	transmembrane protein 251	protein-coding
mm_112661.1	chr13	16027031	16027045	+	1	NA	exon (NM_008380, exon 5 of 5)	exon (NM_008380, exon 5 of 5)	15187	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_164925.1	chr18	77948840	77948864	+	1	NA	exon (NM_001195633, exon 2 of 44)	exon (NM_001195633, exon 2 of 44)	10385	NM_001195633	100502841	Mm.297782	NM_001195633	ENSMUSG00000039840	Epg5	4732475F16|5430411K18Rik|AI661957|AW456499|mKIAA1632	ectopic P-granules autophagy protein 5 homolog (C. elegans)	protein-coding
mm_100552.1	chr11	120721982	120722031	+	1	NA	TTS (NM_153545)	TTS (NM_153545)	538	NM_133223	170758	Mm.34008	NM_133223	ENSMUSG00000018012	Rac3	Rac1B	RAS-related C3 botulinum substrate 3	protein-coding
mm_90019.1	chr10	115383918	115383950	+	1	NA	intron (NM_025780, intron 1 of 2)	intron (NM_025780, intron 1 of 2)	501	NM_025780	66816	Mm.32314	NM_025780	ENSMUSG00000020137	Thap2	2900040O07Rik|9030625G08Rik|AI450385|AI649097	THAP domain containing, apoptosis associated protein 2	protein-coding
mm_39481.1	chr5	20882095	20882102	+	1	NA	promoter-TSS (NM_177601)	promoter-TSS (NM_177601)	26	NM_172992	68770	Mm.86410	NM_172992	ENSMUSG00000039987	Phtf2	1110054G21Rik|9530062N20Rik|AI447096|C77923	putative homeodomain transcription factor 2	protein-coding
mm_30377.1	chr3	152241049	152241050	-	1	NA	intron (NM_199465, intron 10 of 12)	B1_Mus2|SINE|Alu	25271	NM_199465	68810	Mm.200188	NM_199465	ENSMUSG00000039103	Nexn	1110046H09Rik|AA553326|NELIN	nexilin	protein-coding
mm_71070.1	chr8	34146376	34146384	+	1	NA	intron (NM_026609, intron 1 of 3)	intron (NM_026609, intron 1 of 3)	359	NM_026609	68192	Mm.34212	NM_026609	ENSMUSG00000031513	Leprotl1	1110067H13Rik|1520402O14Rik|AI854296	leptin receptor overlapping transcript-like 1	protein-coding
mm_147636.1	chr18	60238718	60238739	-	1	NA	intron (NM_001033767, intron 2 of 2)	intron (NM_001033767, intron 2 of 2)	26651	NM_001033767	240327	Mm.357104	NM_001033767	ENSMUSG00000073555	Gm4951	EG240327|Ifgga2	predicted gene 4951	protein-coding
mm_110101.1	chr12	25396860	25396860	-	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	267686	NR_045844	432641	Mm.112955	NR_045844		Gm17746	-	predicted gene, 17746	ncRNA
mm_53027.1	chr6	124477229	124477235	+	1	NA	Intergenic	Intergenic	-12448	NM_153508	232370	Mm.193701	NM_153508	ENSMUSG00000008153	Clstn3	CSTN3|Cs3|Cst-3|alc-beta	calsyntenin 3	protein-coding
mm_148622.1	chr19	5425024	5425037	+	1	NA	promoter-TSS (NM_024176)	promoter-TSS (NM_024176)	-51	NM_001291080	66556	Mm.275446	NM_024176	ENSMUSG00000024914	Drap1	2310074H19Rik|NC2-alpha	Dr1 associated protein 1 (negative cofactor 2 alpha)	protein-coding
mm_81913.1	chr9	120094927	120094937	+	1	NA	TTS (NM_007720)	TTS (NM_007720)	2799	NM_007720	12776	Mm.442098	NM_007720	ENSMUSG00000042262	Ccr8	C-C|C-C CKR-8|CC-CKR-8|CCR-8|CKR-8|Cmkbr8|mCCR8	chemokine (C-C motif) receptor 8	protein-coding
mm_162150.1	chrX	76264440	76264440	+	1	NA	5' UTR (NM_001013760, exon 1 of 2)	5' UTR (NM_001013760, exon 1 of 2)	134	NM_001013760	238829	Mm.292319	NM_001013760	ENSMUSG00000071738	Cldn34b3	EG238829|Gm4937	claudin 34B3	protein-coding
mm_12613.1	chr2	74691886	74691896	+	1	NA	promoter-TSS (NM_013554)	promoter-TSS (NM_013554)	0	NM_013554	15430	Mm.24420	NM_013554	ENSMUSG00000050368	Hoxd10	AI385591|AI874987|Hox-4.5|Hox-5.3	homeobox D10	protein-coding
mm_126371.1	chr15	80133512	80133527	+	1	NA	intron (NM_025609, intron 1 of 10)	CpG	365	NM_025609	66513	Mm.288245	NM_025609	ENSMUSG00000022414	Tab1	2310012M03Rik|Map3k7ip1|b2b449Clo	TGF-beta activated kinase 1/MAP3K7 binding protein 1	protein-coding
mm_72281.1	chr8	75100378	75100385	+	1	NA	3' UTR (NM_010442, exon 5 of 5)	3' UTR (NM_010442, exon 5 of 5)	6763	NM_010442	15368	Mm.276389	NM_010442	ENSMUSG00000005413	Hmox1	D8Wsu38e|HO-1|HO1|Hemox|Hmox|Hsp32	heme oxygenase 1	protein-coding
mm_20201.1	chr2	125088672	125088678	-	1	NA	TTS (NM_175034)	TTS (NM_175034)	20548	NM_175034	317750	Mm.330538	NM_175034	ENSMUSG00000035183	Slc24a5	F630045L20Rik|JSX|NCKX5|NCX5|Oca6	solute carrier family 24, member 5	protein-coding
mm_122444.1	chr14	45285973	45285994	-	1	NA	3' UTR (NM_015774, exon 16 of 16)	3' UTR (NM_015774, exon 16 of 16)	32589	NM_015774	50527	Mm.387108	NM_015774	ENSMUSG00000021831	Ero1l	ERO1-L|Ero1a	ERO1-like (S. cerevisiae)	protein-coding
mm_48721.1	chr5	147322436	147322449	-	1	NA	promoter-TSS (NM_001039678)	promoter-TSS (NM_001039678)	-2	NM_001039678	231903	Mm.291286	NM_001039678	ENSMUSG00000075543	Urad	EG231903|Prhoxnb	ureidoimidazoline (2-oxo-4-hydroxy-4-carboxy-5) decarboxylase	protein-coding
mm_42572.1	chr5	117240450	117240464	+	1	NA	intron (NM_001081308, intron 12 of 19)	intron (NM_001081308, intron 12 of 19)	47107	NM_018858	23980	Mm.195898	NM_018858	ENSMUSG00000032959	Pebp1	HCNP|Pbp|Pbp1|Pbpr|Rkip	phosphatidylethanolamine binding protein 1	protein-coding
mm_64962.1	chr7	16614779	16614788	-	1	NA	5' UTR (NM_172739, exon 1 of 7)	5' UTR (NM_172739, exon 1 of 7)	210	NM_172739	232906	Mm.28646	NM_172739	ENSMUSG00000058230	Arhgap35	6430596G11Rik|AI841135|Grlf1|mKIAA1722|p190A|p190RhoGAP	Rho GTPase activating protein 35	protein-coding
mm_47813.1	chr5	134184399	134184424	-	1	NA	intron (NM_053266, intron 1 of 15)	CpG	373	NM_053266	114674	Mm.218744	NM_053266	ENSMUSG00000015942	Gtf2ird2	1700012P16Rik	GTF2I repeat domain containing 2	protein-coding
mm_111649.1	chr12	102743626	102743688	-	1	NA	promoter-TSS (NM_177140)	promoter-TSS (NM_177140)	4	NM_001142937	64113	Mm.291222	NM_022323	ENSMUSG00000096458	Moap1	AA987038|Map-1|Pnma4	modulator of apoptosis 1	protein-coding
mm_85969.1	chr9	112156214	112156231	-	1	NA	intron (NM_001177619, intron 10 of 10)	intron (NM_001177619, intron 10 of 10)	29727	NM_001177618	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_163135.1	chr11	79057607	79057617	-	1	NA	intron (NM_013571, intron 2 of 17)	intron (NM_013571, intron 2 of 17)	34015	NR_045873	790910	Mm.440410	NR_045873		Gm11201	ENSMUSG00000072637|OTTMUSG00000000169	predicted gene 11201	ncRNA
mm_27946.1	chr3	79737902	79737912	-	1	NA	promoter-TSS (NM_212452)	promoter-TSS (NM_212452)	-113	NM_212452	381489	Mm.331086	NM_212452	ENSMUSG00000034009	Rxfp1	Gm1018|Lgr7	relaxin/insulin-like family peptide receptor 1	protein-coding
mm_32942.1	chr4	119422843	119422881	+	1	NA	promoter-TSS (NM_026494)	promoter-TSS (NM_026494)	178	NM_001014900	332934	Mm.388911	NM_001014900	ENSMUSG00000070806	Zmynd12	AI414736	zinc finger, MYND domain containing 12	protein-coding
mm_165819.1	chr3	146651335	146651339	-	1	NA	promoter-TSS (NM_029144)	promoter-TSS (NM_029144)	-20	NM_029144	75015	Mm.250432	NM_029144	ENSMUSG00000048652	4930503B20Rik	1700013A07Rik|1700095G21Rik|4930483N21Rik|Gm1652|Samd13	RIKEN cDNA 4930503B20 gene	protein-coding
mm_113129.1	chr13	24614219	24614244	+	1	NA	promoter-TSS (NM_001286101)	promoter-TSS (NM_001286101)	-375	NM_001286101	193385	Mm.217319	NM_029679	ENSMUSG00000036006	Fam65b	-	family with sequence similarity 65, member B	protein-coding
mm_156438.1	chrX	142226766	142226806	+	1	NA	promoter-TSS (NM_001290532)	promoter-TSS (NM_001290532)	16	NM_001290532	237082	Mm.41899	NM_172782	ENSMUSG00000042271	Nxt2	6330587F24Rik|AI787442|P15-2	nuclear transport factor 2-like export factor 2	protein-coding
mm_13539.1	chr2	110721504	110721514	+	1	NA	promoter-TSS (NM_001290786)	promoter-TSS (NM_001290786)	15	NM_172979	269328	Mm.32566	NM_172979	ENSMUSG00000050808	Muc15	4732460E09|D730046L02Rik|MUC-15	mucin 15	protein-coding
mm_132641.1	chr16	40019363	40019364	+	1	NA	Intergenic	Intergenic	1117018	NM_170599	207683	Mm.245564	NM_170599	ENSMUSG00000022790	Igsf11	1700025L02Rik|BT-IgSF|Igsf13	immunoglobulin superfamily, member 11	protein-coding
mm_139454.1	chr17	55952717	55952725	+	1	NA	promoter-TSS (NM_015766)	promoter-TSS (NM_015766)	98	NM_015766	50498	Mm.256798	NM_015766	ENSMUSG00000003206	Ebi3	EBI-3|IL-27	Epstein-Barr virus induced gene 3	protein-coding
mm_101538.1	chr11	33513737	33513771	-	1	NA	promoter-TSS (NR_110973)	promoter-TSS (NR_110973)	-8	NM_023146	66011	Mm.383775	NM_023146	ENSMUSG00000040594	Ranbp17	-	RAN binding protein 17	protein-coding
mm_95902.1	chr11	58202575	58202584	+	1	NA	intron (NM_018738, intron 2 of 2)	intron (NM_018738, intron 2 of 2)	3023	NM_018738	16145	Mm.33902	NM_018738	ENSMUSG00000078853	Igtp	AW558444|Irgm3	interferon gamma induced GTPase	protein-coding
mm_131808.1	chr16	22918271	22918277	+	1	NA	promoter-TSS (NM_001083905)	promoter-TSS (NM_001083905)	-108	NM_001083905	59083	Mm.28461	NM_021564	ENSMUSG00000022871	Fetub	2310011O17Rik|AI255764|D17980|Gugu	fetuin beta	protein-coding
mm_163366.1	chr12	33845520	33845521	+	1	NA	Intergenic	Intergenic	-82905	NM_033522	114712	Mm.204643	NM_033522	ENSMUSG00000046518	Ferd3l	Mnato3|N-twist|Nato|Nato3|Ntwist|Ptfb|bHLHa31|fer3	Fer3-like (Drosophila)	protein-coding
mm_128153.1	chr15	32244568	32244615	-	1	NA	promoter-TSS (NM_009154)	promoter-TSS (NM_009154)	71	NR_038186	100616095	Mm.391938	NR_038186	ENSMUSG00000096956	Snhg18	0610007N19Rik|Snord123	small nucleolar RNA host gene 18	ncRNA
mm_47178.1	chr5	120749688	120749700	-	1	NA	exon (NM_145227, exon 1 of 11)	exon (NM_145227, exon 1 of 11)	154	NM_145227	246728	Mm.260926	NM_145227	ENSMUSG00000032690	Oas2	Oasl11	2'-5' oligoadenylate synthetase 2	protein-coding
mm_85204.1	chr9	96766860	96766898	-	1	NA	intron (NR_102294, intron 1 of 2)	MT2B1|LTR|ERVL	1317	NR_102296	319707	Mm.392191	NR_102293	ENSMUSG00000101581	C430002N11Rik	-	RIKEN cDNA C430002N11 gene	ncRNA
mm_67833.1	chr7	98361311	98361320	-	1	NA	promoter-TSS (NM_001168539)	promoter-TSS (NM_001168539)	13	NM_001168539	244152	Mm.25317	NM_001024619	ENSMUSG00000049580	Tsku	9530051K01Rik|E2ig4|Lrrc54|Tsk	tsukushi, small leucine rich proteoglycan	protein-coding
mm_21489.1	chr2	163331306	163331308	-	1	NA	Intergenic	Intergenic	66666	NM_021566	59091	Mm.34459	NM_021566	ENSMUSG00000017817	Jph2	1110002E14Rik|JP-2|Jp2	junctophilin 2	protein-coding
mm_152023.1	chr19	6046949	6047031	-	1	NA	promoter-TSS (NM_001164709)	promoter-TSS (NM_001164709)	-155	NM_001164709	74126	Mm.149870	NM_028769	ENSMUSG00000024807	Syvn1	1200010C09Rik|AW211966|C85322|D530017H19Rik|Hrd1	synovial apoptosis inhibitor 1, synoviolin	protein-coding
mm_166621.1	chr6	72430431	72430447	+	1	NA	3' UTR (NM_019802, exon 15 of 15)	3' UTR (NM_019802, exon 15 of 15)	-8244	NR_046011	78108	Mm.440743	NR_046011	ENSMUSG00000108591	Particl	4930414L22Rik|AI449819	promoter of Mat2a antisense radiation induced circulating long non-coding RNA	ncRNA
mm_71160.1	chr8	40431897	40431910	+	1	NA	intron (NM_178395, intron 1 of 12)	intron (NM_178395, intron 1 of 12)	8088	NM_178395	70546	Mm.34326	NM_178395	ENSMUSG00000039470	Zdhhc2	5730415P04Rik|6430583A19Rik	zinc finger, DHHC domain containing 2	protein-coding
mm_2663.1	chr1	125839961	125839972	+	1	NA	intron (NM_027677, intron 1 of 1)	intron (NM_027677, intron 1 of 1)	71421	NM_001311090	72585	Mm.490405	NM_145100	ENSMUSG00000026344	Lypd1	2700050C12Rik|AI853408|C530008O16Rik|Lynx2|Lypdc1	Ly6/Plaur domain containing 1	protein-coding
mm_142523.1	chr17	46327950	46327987	-	1	NA	promoter-TSS (NM_170680)	promoter-TSS (NM_170680)	55	NM_001347396	224814	Mm.76543	NM_145140	ENSMUSG00000032842	Abcc10	Mrp7|mFLJ00002	ATP-binding cassette, sub-family C (CFTR/MRP), member 10	protein-coding
mm_128572.1	chr15	57695545	57695560	-	1	NA	intron (NM_199449, intron 1 of 3)	CpG	885	NM_199449	387609	Mm.36557	NM_199449	ENSMUSG00000071757	Zhx2	Afr-1|Afr1|Raf|mKIAA0854	zinc fingers and homeoboxes 2	protein-coding
mm_15293.1	chr2	155382187	155382274	+	1	NA	intron (NM_178111, intron 1 of 3)	CpG	374	NM_178111	68728	Mm.293605	NM_178111	ENSMUSG00000038375	Trp53inp2	1110029F20Rik|Tp53inp2	transformation related protein 53 inducible nuclear protein 2	protein-coding
mm_167052.1	chr7	83882219	83882220	+	1	NA	exon (NM_030705, exon 1 of 1)	exon (NM_030705, exon 1 of 1)	2122	NM_030705	80889	Mm.272998	NM_030705	ENSMUSG00000070462	Mesdc1	AW061151	mesoderm development candidate 1	protein-coding
mm_117938.1	chr13	99434572	99434603	-	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-21761	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_95614.1	chr11	53515315	53515316	+	1	NA	Intergenic	RSINE1|SINE|B4	-4421	NM_033144	20362	Mm.274399	NM_033144	ENSMUSG00000018398	Sept8	AW046166|Sepl	septin 8	protein-coding
mm_65680.1	chr7	28338428	28338461	-	1	NA	intron (NM_013676, intron 1 of 29)	CpG-12904	275	NM_013676	20924	Mm.285906	NM_013676	ENSMUSG00000003435	Supt5	AL033283|AL033321|AU019549|Spt5|Supt5h	suppressor of Ty 5	protein-coding
mm_141292.1	chr17	28074693	28074712	-	1	NA	exon (NM_013687, exon 4 of 10)	exon (NM_013687, exon 4 of 10)	5882	NM_013687	21463	Mm.29758	NM_013687	ENSMUSG00000062859	Tcp11	D17Ken1|Tcp-11	t-complex protein 11	protein-coding
mm_125253.1	chr15	35296091	35296112	+	1	NA	promoter-TSS (NM_054049)	promoter-TSS (NM_054049)	-11	NM_054049	107587	Mm.46336	NM_054049	ENSMUSG00000022330	Osr2	5430409I15Rik|Osr2A|Osr2B	odd-skipped related 2	protein-coding
mm_75049.1	chr8	32884289	32884300	-	1	NA	Intergenic	CpG	65732	NM_001177589	100042715	Mm.291093	NM_001177589		Gm3985	-	predicted gene 3985	protein-coding
mm_26401.1	chr3	142603635	142603655	+	1	NA	exon (NM_010259, exon 5 of 11)	exon (NM_010259, exon 5 of 11)	8798	NM_010259	14468	Mm.457978	NM_010259	ENSMUSG00000040264	Gbp2b	Gbp-1|Gbp1|Mag-1|Mpa-1|Mpa1	guanylate binding protein 2b	protein-coding
mm_151381.1	chr19	56287912	56287936	+	1	NA	promoter-TSS (NM_001329936)	promoter-TSS (NM_001329936)	12	NM_146101	226243	Mm.25791	NM_146101	ENSMUSG00000025075	Habp2	AI035669|FSAP|HABP|HGFAL|PHBP	hyaluronic acid binding protein 2	protein-coding
mm_127046.1	chr15	96642562	96642571	+	1	NA	promoter-TSS (NM_001166456)	promoter-TSS (NM_001166456)	-223	NM_001166456	105727	Mm.103568	NM_134086	ENSMUSG00000023169	Slc38a1	AA408026|AA409865|AL022800|AU015942|NAT2	solute carrier family 38, member 1	protein-coding
mm_73871.1	chr8	118970390	118970393	+	1	NA	intron (NM_019707, intron 6 of 13)	B4A|SINE|B4	-374147	NM_024219	68196	Mm.358714	NM_024219	ENSMUSG00000031839	Hsbp1	0610007A03Rik|AA408769|Hsp25	heat shock factor binding protein 1	protein-coding
mm_71775.1	chr8	66470952	66470966	+	1	NA	3' UTR (NM_001293784, exon 9 of 9)	3' UTR (NM_001293784, exon 9 of 9)	15548	NM_025465	66282	Mm.294985	NM_025465	ENSMUSG00000025591	Tma16	1810029B16Rik	translation machinery associated 16	protein-coding
mm_27786.1	chr3	75165013	75165055	-	1	NA	Intergenic	Intergenic	-21262	NM_172515	213234	Mm.80075	NM_172515	ENSMUSG00000034151	Zbbx	4931432L23	zinc finger, B-box domain containing	protein-coding
mm_90183.1	chr10	119992963	119992972	+	1	NA	promoter-TSS (NM_001277295)	promoter-TSS (NM_001277295)	45	NR_102387	74053	Mm.196692	NM_028736	ENSMUSG00000034813	Grip1	4931400F03Rik|GRIP|eb	glutamate receptor interacting protein 1	protein-coding
mm_135752.1	chr16	55974514	55974525	-	1	NA	promoter-TSS (NR_027965)	promoter-TSS (NR_027965)	98	NR_027965	66391	Mm.472722	NM_133677	ENSMUSG00000102101	Zbtb11os1	2310061J03Rik	zinc finger and BTB domain containing 11, opposite strand 1	ncRNA
mm_58656.1	chr7	6410219	6410229	+	1	NA	Intergenic	Intergenic	-4951	NM_001134752	100042450	Mm.416919	NM_001134752	ENSMUSG00000093536	Smim17	Gm16532	small integral membrane protein 17	protein-coding
mm_171946.1	chr5	76103851	76103852	-	1	NA	Intergenic	RLTR9D|LTR|ERVK	-36422	NM_020611	57357	Mm.289446	NM_020611	ENSMUSG00000029233	Srd5a3	1110025P14Rik|A430076C09|AV364670|AW987574|D730040M03Rik|H5ar|S5AR 3|Srd5a2l	steroid 5 alpha-reductase 3	protein-coding
mm_115918.1	chr13	23533657	23533661	-	1	NA	promoter-TSS (NM_175661)	promoter-TSS (NM_175661)	-252	NM_175661	319173	Mm.377878	NM_175661	ENSMUSG00000061991	Hist1h2af	H2a-221	histone cluster 1, H2af	protein-coding
mm_53429.1	chr6	134043832	134043865	+	1	NA	intron (NM_007961, intron 1 of 7)	intron (NM_007961, intron 1 of 7)	8148	NM_007961	14011	Mm.269995	NM_007961	ENSMUSG00000030199	Etv6	AW123102|AW557856|Tel	ets variant 6	protein-coding
mm_143361.1	chr17	67315640	67315652	-	1	NA	intron (NM_008984, intron 1 of 30)	intron (NM_008984, intron 1 of 30)	38813	NM_008984	19274	Mm.311809	NM_008984	ENSMUSG00000033278	Ptprm	RPTPmu|mKIAA4044	protein tyrosine phosphatase, receptor type, M	protein-coding
mm_114774.1	chr13	88821680	88821684	+	1	NA	5' UTR (NM_001037987, exon 1 of 11)	5' UTR (NM_001037987, exon 1 of 11)	210	NM_001037987	13612	Mm.125580	NM_010103	ENSMUSG00000034488	Edil3	Del-1|Del1	EGF-like repeats and discoidin I-like domains 3	protein-coding
mm_128657.1	chr15	59795767	59795777	-	1	NA	promoter-TSS (NR_045076)	promoter-TSS (NR_045076)	-813	NR_045076	100503021	Mm.402924	NR_045076		Gm19510	-	predicted gene, 19510	ncRNA
mm_102122.1	chr11	53307655	53307658	-	1	NA	Intergenic	Intergenic	-7177	NM_008300	15525	Mm.239865	NM_008300	ENSMUSG00000020361	Hspa4	70kDa|AI317151|APG-2|Hsp110|Hsp70RY|mKIAA4025	heat shock protein 4	protein-coding
mm_21543.1	chr2	163918963	163918979	-	1	NA	promoter-TSS (NM_183023)	promoter-TSS (NM_183023)	-288	NM_183023	241770	Mm.330760	NM_183023	ENSMUSG00000035226	Rims4	6530406L02|Rim4	regulating synaptic membrane exocytosis 4	protein-coding
mm_154110.1	chr19	57131355	57131359	-	1	NA	intron (NM_001290813, intron 6 of 20)	L1MB5|LINE|L1	-12333	NM_001103178	226251	Mm.217161	NM_178688	ENSMUSG00000025085	Ablim1	2210411C18Rik|2610209L21Rik|4833406P10Rik|9330196J19Rik|AV079770|AW060987|AW215784|Limab1|mKIAA0059	actin-binding LIM protein 1	protein-coding
mm_120325.1	chr14	63143175	63143189	+	1	NA	3' UTR (NM_007798, exon 10 of 10)	3' UTR (NM_007798, exon 10 of 10)	20720	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_165930.1	chr4	63979852	63979856	+	1	NA	intron (NM_011607, intron 15 of 25)	intron (NM_011607, intron 15 of 25)	67161	NM_011607	21923	Mm.980	NM_011607	ENSMUSG00000028364	Tnc	AI528729|C130033P17Rik|Hxb|TN|TN-C|Ten|cytotactin|tenascin-C	tenascin C	protein-coding
mm_66447.1	chr7	44866291	44866299	-	1	NA	intron (NM_133949, intron 5 of 11)	intron (NM_133949, intron 5 of 11)	3493	NM_133949	84113	Mm.42855	NM_133949	ENSMUSG00000038502	Ptov1	1110030G05Rik|AU041779|Gcap3	prostate tumor over expressed gene 1	protein-coding
mm_47639.1	chr5	125327692	125327740	-	1	NA	intron (NM_001205083, intron 1 of 10)	intron (NM_001205083, intron 1 of 10)	13378	NM_016741	20778	Mm.282242	NM_016741	ENSMUSG00000037936	Scarb1	AI120173|CD36|Cd36l1|Chohd1|Cla-1|Cla1|D5Ertd460e|Hdlq1|Hlb398|SR-B1|SR-BI|SRBI|Srb1|mSR-BI	scavenger receptor class B, member 1	protein-coding
mm_46467.1	chr5	105121843	105121866	-	1	NA	exon (NM_001256005, exon 7 of 11)	exon (NM_001256005, exon 7 of 11)	-11562	NM_172777	236573	Mm.425261	NM_172777	ENSMUSG00000029298	Gbp9	-	guanylate-binding protein 9	protein-coding
mm_151616.1	chr19	3902078	3902097	-	1	NA	intron (NM_001167784, intron 9 of 19)	intron (NM_001167784, intron 9 of 19)	3143	NM_016921	27060	Mm.271689	NM_016921	ENSMUSG00000001750	Tcirg1	ATP6N1C|ATP6a3|Atp6i|OC-116|OPTB1|Stv1|TIRC7|Vph1|oc	T cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 protein A3	protein-coding
mm_168192.1	chr10	62879586	62879587	-	1	NA	exon (NM_001253857, exon 1 of 12)	exon (NM_001253857, exon 1 of 12)	428	NM_027384	52463	Mm.17774	NM_027384	ENSMUSG00000047146	Tet1	2510010B09Rik|AA517754|BB001228|Cxxc6|D10Ertd17e|LCX|mKIAA1676	tet methylcytosine dioxygenase 1	protein-coding
mm_126779.1	chr15	86194737	86194773	+	1	NA	Intergenic	Intergenic	-8614	NM_145475	223753	Mm.222685	NM_145475	ENSMUSG00000035891	Cerk	AI848610|D330016D08Rik|mKIAA1646	ceramide kinase	protein-coding
mm_170626.1	chr19	7399092	7399100	-	1	NA	Intergenic	Intergenic	-16070	NM_001167831	68229	Mm.34766	NM_001033139	ENSMUSG00000024970	AI846148	1700105P06Rik	expressed sequence AI846148	protein-coding
mm_124482.1	chr14	121698240	121698250	-	1	NA	exon (NM_001081039, exon 1 of 54)	exon (NM_001081039, exon 1 of 54)	172	NM_001347596	105445	Mm.378591	NM_134074	ENSMUSG00000025558	Dock9	AA959601|AW538057|B230309H04Rik|D14Wsu89e|Zizimin1|mKIAA1058	dedicator of cytokinesis 9	protein-coding
mm_50525.1	chr6	49045309	49045317	+	1	NA	exon (NM_053110, exon 4 of 11)	exon (NM_053110, exon 4 of 11)	8795	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_104945.1	chr11	100120431	100120440	-	1	NA	intron (NM_010662, intron 1 of 7)	intron (NM_010662, intron 1 of 7)	142	NM_001313949	16663	Mm.4646	NM_010662	ENSMUSG00000044041	Krt13	CK13|K13|Krt-1.13|Krt1-13	keratin 13	protein-coding
mm_126688.1	chr15	84923441	84923451	+	1	NA	promoter-TSS (NM_016714)	promoter-TSS (NM_016714)	18	NM_016714	18141	Mm.28379	NM_016714	ENSMUSG00000016619	Nup50	1700030K07Rik|AI413123|Npap60	nucleoporin 50	protein-coding
mm_76928.1	chr8	105936973	105936983	-	1	NA	exon (NM_013640, exon 5 of 8)	exon (NM_013640, exon 5 of 8)	1414	NM_013640	19171	Mm.787	NM_013640	ENSMUSG00000031897	Psmb10	Mecl-1|Mecl1	proteasome (prosome, macropain) subunit, beta type 10	protein-coding
mm_113281.1	chr13	30136530	30136594	+	1	NA	promoter-TSS (NM_153546)	promoter-TSS (NM_153546)	72	NM_153546	218121	Mm.89682	NM_153546	ENSMUSG00000038732	Mboat1	9130215M02Rik|BC023845|LPEAT1|Moact1|Oact1	membrane bound O-acyltransferase domain containing 1	protein-coding
mm_38800.1	chr4	148152108	148152146	-	1	NA	promoter-TSS (NM_001163707)	promoter-TSS (NM_001163707)	8	NM_001163707	50762	Mm.27445	NM_015797	ENSMUSG00000055401	Fbxo6	AA408845|FBG2|Fbs2|Fbx6b|Fbxo6b	F-box protein 6	protein-coding
mm_160302.1	chr7	139212958	139212958	+	1	NA	promoter-TSS (NM_027164)	promoter-TSS (NM_027164)	-30	NM_027164	76612	Mm.17757	NM_027164	ENSMUSG00000015980	Lrrc27	1700071K18Rik|2310044E02Rik	leucine rich repeat containing 27	protein-coding
mm_109163.1	chr12	108195695	108195713	+	1	NA	exon (NM_009832, exon 9 of 12)	exon (NM_009832, exon 9 of 12)	15966	NM_009832	12454	Mm.474441	NM_009832	ENSMUSG00000021258	Ccnk	AW123198|AW413594|CPR4|CycK	cyclin K	protein-coding
mm_158192.1	chrX	104670985	104671013	-	1	NA	promoter-TSS (NM_175358)	promoter-TSS (NM_175358)	65	NM_175358	108672	Mm.30574	NM_175358	ENSMUSG00000033906	Zdhhc15	6030457O13Rik	zinc finger, DHHC domain containing 15	protein-coding
mm_137068.1	chr17	20661982	20662008	+	1	NA	Intergenic	Intergenic	-25513	NM_134191	171225	Mm.377184	NM_134191	ENSMUSG00000042848	Vmn1r226	V1re2	vomeronasal 1 receptor 226	protein-coding
mm_99146.1	chr11	100545673	100545678	+	1	NA	promoter-TSS (NM_028918)	promoter-TSS (NM_028918)	43	NM_028918	74407	Mm.31590	NM_028918	ENSMUSG00000006784	Ttc25	4933404O19Rik	tetratricopeptide repeat domain 25	protein-coding
mm_82353.1	chr9	14354745	14354752	-	1	NA	3' UTR (NM_028013, exon 2 of 2)	3' UTR (NM_028013, exon 2 of 2)	26494	NM_028013	71946	Mm.41423	NM_028013	ENSMUSG00000037419	Endod1	2210414F18Rik|2310067E08Rik|C85344	endonuclease domain containing 1	protein-coding
mm_11728.1	chr2	37443274	37443339	+	1	NA	promoter-TSS (NM_146121)	promoter-TSS (NM_146121)	21	NM_146121	227800	Mm.383192	NM_146121	ENSMUSG00000035437	Rabgap1	Gapcena|mKIAA4104	RAB GTPase activating protein 1	protein-coding
mm_142951.1	chr17	56109801	56109806	-	1	NA	promoter-TSS (NM_020568)	promoter-TSS (NM_020568)	-1	NM_020568	57435	Mm.12966	NM_020568	ENSMUSG00000002831	Plin4	S3-12|mKIAA1881	perilipin 4	protein-coding
mm_27500.1	chr3	55055479	55055491	-	1	NA	promoter-TSS (NM_007628)	promoter-TSS (NM_007628)	243	NR_040593	70970	Mm.251485	NR_040593	ENSMUSG00000106589	4931419H13Rik	-	RIKEN cDNA 4931419H13 gene	ncRNA
mm_161633.1	chr16	89031660	89031660	+	1	NA	promoter-TSS (NM_010672)	promoter-TSS (NM_010672)	-39	NM_010672	16700	Mm.6973	NM_010672	ENSMUSG00000058172	Krtap6-1	HGTpII.1|HGTpII.2	keratin associated protein 6-1	protein-coding
mm_127061.1	chr15	97361135	97361155	+	1	NA	intron (NM_172293, intron 3 of 5)	intron (NM_172293, intron 3 of 5)	-113858	NM_001164602	105827	Mm.24005	NM_178114	ENSMUSG00000048218	Amigo2	AI415330|AMIGO-2|AW208913|Ali1	adhesion molecule with Ig like domain 2	protein-coding
mm_91504.1	chr10	37136228	37136289	-	1	NA	exon (NM_008538, exon 2 of 2)	exon (NM_008538, exon 2 of 2)	2668	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_135685.1	chr16	52424705	52424720	-	1	NA	intron (NM_009655, intron 1 of 15)	intron (NM_009655, intron 1 of 15)	28369	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_138558.1	chr17	35267140	35267193	+	1	NA	TTS (NM_001267808)	TTS (NM_001267808)	4043	NM_001267808	14980	Mm.439675	NM_001267808		H2-L	H-2L	histocompatibility 2, D region locus L	protein-coding
mm_20300.1	chr2	127133910	127133952	-	1	NA	promoter-TSS (NM_144818)	promoter-TSS (NM_144818)	23	NM_144818	215387	Mm.29786	NM_144818	ENSMUSG00000034906	Ncaph	A730011O11Rik|Brrn1|HCAP-H|mKIAA0074	non-SMC condensin I complex, subunit H	protein-coding
mm_112062.1	chr12	111966729	111966775	-	1	NA	intron (NM_027360, intron 1 of 3)	CpG	225	NM_027360	70257	Mm.318	NM_027360	ENSMUSG00000021290	2010107E04Rik	9430003J03Rik|AU043134|AV124504|Mp68	RIKEN cDNA 2010107E04 gene	protein-coding
mm_131290.1	chr16	11361079	11361096	+	1	NA	intron (NM_028964, intron 3 of 20)	intron (NM_028964, intron 3 of 20)	38183	NM_028964	74478	Mm.325831	NM_028964	ENSMUSG00000071669	Snx29	4933437K13Rik|ENSMUSG00000079738|Gm11170|Gm1737|Gm930|Rundc2a	sorting nexin 29	protein-coding
mm_37462.1	chr4	123472521	123472532	-	1	NA	exon (NM_001199136, exon 36 of 98)	exon (NM_001199136, exon 36 of 98)	-60615	NM_001167918	442834	Mm.483803	NM_001167918		D830031N03Rik	Kiaa0754|mKIAA0754	RIKEN cDNA D830031N03 gene	protein-coding
mm_6968.1	chr1	86215413	86215423	-	1	NA	intron (NM_030184, intron 19 of 24)	MTD|LTR|ERVL-MaLR	60638	NM_001310702	78795	Mm.379264	NM_027456	ENSMUSG00000062590	Armc9	3830422A13Rik|4831423D23Rik|4930438O05Rik|5730415N24Rik	armadillo repeat containing 9	protein-coding
mm_160350.1	chr8	21096093	21096093	-	1	NA	promoter-TSS (NM_001177482)	promoter-TSS (NM_001177482)	-43	NM_001177482	634825	Mm.429748	NM_001177482	ENSMUSG00000061958	Gm14851	CRS1C-2|OTTMUSG00000018260	predicted gene 14851	protein-coding
mm_152581.1	chr19	11603035	11603048	-	1	NA	intron (NM_026835, intron 2 of 6)	intron (NM_026835, intron 2 of 6)	1763	NM_026835	68774	Mm.290390	NM_026835	ENSMUSG00000024679	Ms4a6d	1110058E16Rik|AI447446|Ms4a11	membrane-spanning 4-domains, subfamily A, member 6D	protein-coding
mm_154071.1	chr19	56378267	56378270	-	1	NA	intron (NM_001286552, intron 9 of 39)	intron (NM_001286552, intron 9 of 39)	11770	NM_198059	18175	Mm.386769	NM_008733	ENSMUSG00000049134	Nrap	-	nebulin-related anchoring protein	protein-coding
mm_95636.1	chr11	53707414	53707433	+	1	NA	promoter-TSS (NM_009012)	promoter-TSS (NM_009012)	-104	NM_009012	19360	Mm.4888	NM_009012	ENSMUSG00000020380	Rad50	Mrell|Rad50l	RAD50 double strand break repair protein	protein-coding
mm_28647.1	chr3	95228292	95228304	-	1	NA	promoter-TSS (NM_172395)	promoter-TSS (NM_172395)	-126	NM_172395	57912	Mm.28189	NM_172395	ENSMUSG00000046722	Cdc42se1	1300002M12Rik|AW558204|Cdcse1|SCIP1|Spec1	CDC42 small effector 1	protein-coding
mm_103223.1	chr11	70656773	70656793	-	1	NA	promoter-TSS (NM_007933)	promoter-TSS (NM_007933)	-393	NM_001136062	13808	Mm.251322	NM_007933	ENSMUSG00000060600	Eno3	Eno-3|MSE	enolase 3, beta muscle	protein-coding
mm_40548.1	chr5	58059479	58059504	+	1	NA	intron (NM_001310608, intron 3 of 3)	intron (NM_001310608, intron 3 of 3)	341410	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_2184.1	chr1	89015724	89015728	+	1	NA	promoter-TSS (NR_040471)	promoter-TSS (NR_040471)	-387	NR_040471	73475	Mm.491040	NR_040471	ENSMUSG00000099378	1700067G17Rik	-	RIKEN cDNA 1700067G17 gene	ncRNA
mm_36788.1	chr4	103077650	103077667	-	1	NA	intron (NM_146254, intron 7 of 16)	intron (NM_146254, intron 7 of 16)	36641	NM_146254	242584	Mm.374877	NM_146254	ENSMUSG00000035126	Wdr78	BC028975	WD repeat domain 78	protein-coding
mm_133006.1	chr16	55973812	55973830	+	1	NA	promoter-TSS (NM_173026)	promoter-TSS (NM_173026)	17	NM_173026	271377	Mm.282814	NM_173026	ENSMUSG00000022601	Zbtb11	9230110G02Rik|ZNF-U69274	zinc finger and BTB domain containing 11	protein-coding
mm_100993.1	chr11	8446234	8446236	-	1	NA	intron (NM_001083587, intron 24 of 30)	intron (NM_001083587, intron 24 of 30)	218300	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_51202.1	chr6	71322776	71322844	+	1	NA	promoter-TSS (NM_009858)	promoter-TSS (NM_009858)	-2	NM_009858	12526	Mm.333148	NM_009858	ENSMUSG00000053044	Cd8b1	Cd8b|Ly-3|Ly-C|Lyt-3	CD8 antigen, beta chain 1	protein-coding
mm_16376.1	chr2	178141921	178141939	+	1	NA	promoter-TSS (NM_028806)	promoter-TSS (NM_028806)	-3	NM_028806	74189	Mm.44413	NM_028806	ENSMUSG00000027525	Phactr3	1500003N10Rik|4930415A02Rik|H17739|Scapin1|Scapinin|mKIAA4224	phosphatase and actin regulator 3	protein-coding
mm_16931.1	chr2	13794014	13794025	-	1	NA	promoter-TSS (NM_145838)	promoter-TSS (NM_145838)	-499	NM_145838	241230	Mm.330004	NM_145838	ENSMUSG00000003418	St8sia6	1700007J08Rik|AI314453|AI875066|ST8SiaVI|Siat8f	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 6	protein-coding
mm_58440.1	chr7	3298130	3298138	+	1	NA	3' UTR (NM_016969, exon 3 of 3)	3' UTR (NM_016969, exon 3 of 3)	5106	NM_001093766	50918	Mm.29874	NM_016969	ENSMUSG00000068566	Myadm	D7Wsu62e	myeloid-associated differentiation marker	protein-coding
mm_86174.1	chr9	119190234	119190236	-	1	NA	intron (NM_001037749, intron 1 of 11)	intron (NM_001037749, intron 1 of 11)	158	NM_001037749	382113	Mm.335525	NM_001037749	ENSMUSG00000070280	Slc22a14	Gm1128	solute carrier family 22 (organic cation transporter), member 14	protein-coding
mm_43534.1	chr5	137307749	137307803	+	1	NA	promoter-TSS (NM_031405)	promoter-TSS (NM_031405)	-102	NM_001109909	83701	Mm.387734	NM_031405	ENSMUSG00000037364	Srrt	2810019G02Rik|ASR2A|ASR2B|ASR2C|ASR2D|Ars2|Asr2	serrate RNA effector molecule homolog (Arabidopsis)	protein-coding
mm_19357.1	chr2	91082265	91082292	-	1	NA	Intergenic	Intergenic	-11963	NM_001290765	68427	Mm.192375	NM_026721	ENSMUSG00000002105	Slc39a13	1100001L14Rik|AA387663|ZIP-13|ZIP13	solute carrier family 39 (metal ion transporter), member 13	protein-coding
mm_88138.1	chr10	69398981	69398993	+	1	NA	Intergenic	CpG	-46075	NM_007659	12534	Mm.281367	NM_007659	ENSMUSG00000019942	Cdk1	Cdc2|Cdc2a|p34<CDC2>	cyclin-dependent kinase 1	protein-coding
mm_13266.1	chr2	98666799	98666821	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	1199153	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_139977.1	chr17	71781316	71781332	+	1	NA	promoter-TSS (NM_030179)	promoter-TSS (NM_030179)	25	NM_001271483	78785	Mm.196382	NM_030179	ENSMUSG00000024059	Clip4	1700024K14Rik|1700074B05Rik|4833417L20Rik|5830409B12Rik|Rsnl2	CAP-GLY domain containing linker protein family, member 4	protein-coding
mm_88220.1	chr10	70359718	70359764	+	1	NA	Intergenic	URR1A|DNA|hAT-Charlie	-80927	NM_001143777	71721	Mm.477813	NM_024244	ENSMUSG00000043259	Fam13c	1200015N20Rik|C030038O19Rik|mKIAA1796	family with sequence similarity 13, member C	protein-coding
mm_51492.1	chr6	83057054	83057068	+	1	NA	promoter-TSS (NM_033606)	promoter-TSS (NM_033606)	-783	NM_033606	93838	Mm.140332	NM_033606	ENSMUSG00000009145	Dqx1	2310066E11Rik	DEAQ RNA-dependent ATPase	protein-coding
mm_99541.1	chr11	103208653	103208663	+	1	NA	promoter-TSS (NM_001254724)	promoter-TSS (NM_001254724)	-110	NM_001254724	69441	Mm.380648	NM_027082	ENSMUSG00000020940	1700023F06Rik	-	RIKEN cDNA 1700023F06 gene	protein-coding
mm_168474.1	chr11	48800327	48800328	+	1	NA	promoter-TSS (NM_008143)	promoter-TSS (NM_008143)	-33	NM_008143	14694	Mm.5305	NM_008143	ENSMUSG00000020372	Rack1	AL033335|GB-like|Gnb2-rs1|Gnb2l1|p205	receptor for activated C kinase 1	protein-coding
mm_117131.1	chr13	60936551	60936569	-	1	NA	promoter-TSS (NM_001145799)	promoter-TSS (NM_001145799)	6	NM_001145799	13024	Mm.482089	NM_007796	ENSMUSG00000044258	Ctla2a	Ctla-2a	cytotoxic T lymphocyte-associated protein 2 alpha	protein-coding
mm_64873.1	chr7	14427852	14427900	-	1	NA	exon (NM_001199306, exon 2 of 7)	exon (NM_001199306, exon 2 of 7)	10675	NM_001199306	76971	Mm.290727	NM_175250	ENSMUSG00000030378	Sult2a8	2810007J24Rik	sulfotransferase family 2A, dehydroepiandrosterone (DHEA)-preferring, member 8	protein-coding
mm_152867.1	chr19	24225044	24225051	-	1	NA	promoter-TSS (NM_011597)	promoter-TSS (NM_011597)	-21	NM_011597	21873	Mm.104744	NM_011597	ENSMUSG00000024812	Tjp2	ZO-2	tight junction protein 2	protein-coding
mm_83594.1	chr9	48480690	48480710	-	1	NA	promoter-TSS (NM_024233)	promoter-TSS (NM_024233)	-89	NM_024233	104444	Mm.21911	NM_024233	ENSMUSG00000032026	Rexo2	1810038D15Rik|AW107347|Rex2|Sfn|Smfn	RNA exonuclease 2	protein-coding
mm_9881.1	chr1	186117252	186117294	-	1	NA	promoter-TSS (NM_146106)	promoter-TSS (NM_146106)	37	NM_146106	226791	Mm.257116	NM_146106	ENSMUSG00000039246	Lyplal1	BC027340|Q96AVO	lysophospholipase-like 1	protein-coding
mm_135244.1	chr16	37384916	37384931	-	1	NA	promoter-TSS (NM_172440)	promoter-TSS (NM_172440)	35	NM_001114613	207227	Mm.80170	NM_172440	ENSMUSG00000022829	Stxbp5l	9430094L02|A830015P08Rik|LLGL4|T2dm1|t2md1|tomosyn-2	syntaxin binding protein 5-like	protein-coding
mm_58104.1	chr6	137571039	137571054	-	1	NA	promoter-TSS (NM_001271587)	promoter-TSS (NM_001271587)	-37	NM_001271587	13860	Mm.235346	NM_007945	ENSMUSG00000015766	Eps8	AW261790	epidermal growth factor receptor pathway substrate 8	protein-coding
mm_71468.1	chr8	46534725	46534736	+	1	NA	3' UTR (NM_007981, exon 21 of 21)	3' UTR (NM_007981, exon 21 of 21)	-17339	NM_027973	71876	Mm.22108	NM_027973	ENSMUSG00000031629	Cenpu	1700029A22Rik|Mlf1ip	centromere protein U	protein-coding
mm_28234.1	chr3	88455693	88455707	-	1	NA	promoter-TSS (NM_013658)	promoter-TSS (NM_013658)	61	NM_013658	20351	Mm.439752	NM_013658	ENSMUSG00000028064	Sema4a	AI132332|SemB|Semab	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A	protein-coding
mm_126769.1	chr15	86058747	86058793	+	1	NA	promoter-TSS (NM_001205353)	promoter-TSS (NM_001205353)	43	NM_001205353	223752	Mm.24442	NM_172611	ENSMUSG00000035900	Gramd4	9930016O13	GRAM domain containing 4	protein-coding
mm_158697.1	chrX	162018856	162018887	-	1	NA	intron (NM_001081052, intron 1 of 7)	L2a|LINE|L2	140570	NM_001081052	195727	Mm.336313	NM_001081052	ENSMUSG00000059493	Nhs	Gm389|Gm48|Nhs1|Xcat	Nance-Horan syndrome (human)	protein-coding
mm_61892.1	chr7	90007737	90007745	+	1	NA	Intergenic	Intergenic	-21418	NR_110365	319711	Mm.31753	NR_015614	ENSMUSG00000097585	E230029C05Rik	AI452102|B230337J15	RIKEN cDNA E230029C05 gene	ncRNA
mm_167744.1	chr9	108648314	108648334	+	1	NA	intron (NM_011790, intron 1 of 15)	B1_Mm|SINE|Alu	1056	NM_011790	23807	Mm.290447	NM_011790	ENSMUSG00000064145	Arih2	AI843547|ARI2|TRIAD1|UIP48	ariadne RBR E3 ubiquitin protein ligase 2	protein-coding
mm_132527.1	chr16	37834472	37834521	+	1	NA	3' UTR (NM_008047, exon 11 of 11)	3' UTR (NM_008047, exon 11 of 11)	-33904	NM_177093	320184	Mm.390882	NM_177093	ENSMUSG00000034158	Lrrc58	1810012N18Rik|C330018J07Rik	leucine rich repeat containing 58	protein-coding
mm_84118.1	chr9	58555082	58555127	-	1	NA	Intergenic	CpG	-14164	NM_133983	102657	Mm.5356	NM_133983	ENSMUSG00000035914	Cd276	6030411F23Rik|AU016588|B7RP-2|B7h3	CD276 antigen	protein-coding
mm_51142.1	chr6	70518202	70518209	+	1	NA	Intergenic	Intergenic	273970	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_13869.1	chr2	119799765	119799785	+	1	NA	5' UTR (NM_019392, exon 1 of 19)	5' UTR (NM_019392, exon 1 of 19)	261	NM_019392	22174	Mm.2901	NM_019392	ENSMUSG00000027298	Tyro3	AI323366|Brt|Dtk|Etk-2|Rse|Sky|TK19-2|Tif|etk2/tyro3|tk19-1	TYRO3 protein tyrosine kinase 3	protein-coding
mm_116389.1	chr13	41184790	41184801	-	1	NA	3' UTR (NM_019423, exon 8 of 8)	3' UTR (NM_019423, exon 8 of 8)	35367	NM_001311121	54326	Mm.2567	NM_019423	ENSMUSG00000021364	Elovl2	AI317360|Ssc2	elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 2	protein-coding
mm_45585.1	chr5	74068337	74068350	-	1	NA	promoter-TSS (NM_177561)	promoter-TSS (NM_177561)	68	NM_177561	69727	Mm.48795	NM_177561	ENSMUSG00000054814	Usp46	1190009E20Rik|2410018I08Rik|AI451644	ubiquitin specific peptidase 46	protein-coding
mm_71581.1	chr8	54600775	54600804	+	1	NA	promoter-TSS (NM_133711)	promoter-TSS (NM_133711)	8	NM_133711	69281	Mm.45833	NM_133711	ENSMUSG00000031518	Spata4	1700001N01Rik|Srg2|TSARG2	spermatogenesis associated 4	protein-coding
mm_14423.1	chr2	130490558	130490561	+	1	NA	intron (NM_001163688, intron 1 of 20)	intron (NM_001163688, intron 1 of 20)	40281	NM_001163688	19262	Mm.224246	NM_008980	ENSMUSG00000027303	Ptpra	Ptpa|Ptpalpha|Rptpalpha|Rptra|Rptralpha	protein tyrosine phosphatase, receptor type, A	protein-coding
mm_90659.1	chr10	128805530	128805590	+	1	NA	promoter-TSS (NM_028873)	promoter-TSS (NM_028873)	-116	NM_028873	74330	Mm.296915	NM_028873	ENSMUSG00000025354	Dnajc14	5730551F12Rik|DNAJ|DRIP78|HDJ3|LIP6	DnaJ heat shock protein family (Hsp40) member C14	protein-coding
mm_77272.1	chr8	116529443	116529449	-	1	NA	Intergenic	Intergenic	24431	NM_029297	75465	Mm.23114	NM_029297	ENSMUSG00000034467	Dynlrb2	1700009A04Rik|DNLC2B|Dncl2b	dynein light chain roadblock-type 2	protein-coding
mm_55296.1	chr6	54751899	54751902	-	1	NA	Intergenic	Intergenic	-65016	NM_199143	387524	Mm.286149	NM_199143	ENSMUSG00000058446	Znrf2	1190002C14Rik|AU044205|D6Ertd365e	zinc and ring finger 2	protein-coding
mm_42468.1	chr5	115454050	115454075	+	1	NA	3' UTR (NM_008629, exon 15 of 15)	3' UTR (NM_008629, exon 15 of 15)	-12204	NM_011107	18778	Mm.20190	NM_011107	ENSMUSG00000029522	Pla2g1b	Pla2a|sPLA2IB	phospholipase A2, group IB, pancreas	protein-coding
mm_10876.1	chr2	25241904	25241926	+	1	NA	Intergenic	Intergenic	-1014	NM_176834	68846	Mm.24777	NM_176834	ENSMUSG00000044628	Rnf208	1110061N23Rik	ring finger protein 208	protein-coding
mm_94365.1	chr11	5012635	5012647	+	1	NA	intron (NM_007454, intron 2 of 20)	intron (NM_007454, intron 2 of 20)	25817	NM_007454	11764	Mm.274816	NM_007454	ENSMUSG00000009090	Ap1b1	Adtb1|b2b1660Clo	adaptor protein complex AP-1, beta 1 subunit	protein-coding
mm_171780.1	chr5	109996532	109996532	+	1	NA	promoter-TSS (NM_145563)	promoter-TSS (NM_145563)	5	NM_145563	69504	Mm.441438	NM_145563	ENSMUSG00000066613	Zfp932	2310001H12Rik|Znf431	zinc finger protein 932	protein-coding
mm_19740.1	chr2	104742803	104742820	-	1	NA	promoter-TSS (NM_144804)	promoter-TSS (NM_144804)	-10	NM_144804	211896	Mm.288805	NM_144804	ENSMUSG00000027173	Depdc7	AV216087	DEP domain containing 7	protein-coding
mm_7264.1	chr1	95314056	95314072	-	1	NA	exon (NM_026321, exon 1 of 3)	exon (NM_026321, exon 1 of 3)	436	NM_026321	67698	Mm.272705	NM_026321	ENSMUSG00000051185	Fam174a	2310044D20Rik|Fam174|Naa6|Tmem157	family with sequence similarity 174, member A	protein-coding
mm_74237.1	chr8	124576076	124576090	+	1	NA	promoter-TSS (NM_023709)	promoter-TSS (NM_023709)	-28	NM_023709	73647	Mm.6209	NM_023709	ENSMUSG00000031981	Capn9	2200003B16Rik|GC36|nCL-4|nCL4	calpain 9	protein-coding
mm_71250.1	chr8	40915839	40915858	+	1	NA	intron (NM_007514, intron 11 of 11)	intron (NM_007514, intron 11 of 11)	-10385	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_69628.1	chr7	137322761	137322785	-	1	NA	Intergenic	CpG	-8328	NM_010096	13593	Mm.258708	NM_010096	ENSMUSG00000010476	Ebf3	3110018A08Rik|O/E-2|mKIAA4201	early B cell factor 3	protein-coding
mm_109168.1	chr12	108334240	108334260	+	1	NA	promoter-TSS (NM_010010)	promoter-TSS (NM_010010)	-131	NM_010010	13116	Mm.41911	NM_010010	ENSMUSG00000021259	Cyp46a1	Cyp46	cytochrome P450, family 46, subfamily a, polypeptide 1	protein-coding
mm_127978.1	chr15	12419593	12419603	-	1	NA	intron (NM_001081064, intron 5 of 23)	intron (NM_001081064, intron 5 of 23)	98102	NM_025673	66629	Mm.157655	NM_025673	ENSMUSG00000022200	Golph3	4733401N08Rik|5730410D03Rik|AW413496	golgi phosphoprotein 3	protein-coding
mm_127630.1	chr15	102469556	102469561	+	1	NA	Intergenic	Intergenic	-1074	NM_011042	18521	Mm.236513	NM_011042	ENSMUSG00000056851	Pcbp2	AW412548|Hnrpx|alphaCP-2	poly(rC) binding protein 2	protein-coding
mm_162146.1	chrX	74645493	74645493	-	1	NA	intron (NM_001099302, intron 1 of 3)	intron (NM_001099302, intron 1 of 3)	142	NM_001099302	434797	Mm.391298	NM_001099302	ENSMUSG00000079534	Gm5640	EG434797	predicted gene 5640	protein-coding
mm_27650.1	chr3	63964535	63964549	-	1	NA	5' UTR (NM_001272035, exon 1 of 7)	5' UTR (NM_001272035, exon 1 of 7)	191	NM_001331067	11416	Mm.135619	NM_015728	ENSMUSG00000027822	Slc33a1	AI315656|AI788741|Acatn|D630022N01Rik	solute carrier family 33 (acetyl-CoA transporter), member 1	protein-coding
mm_80817.1	chr9	96630994	96631030	+	1	NA	intron (NM_053268, intron 1 of 23)	CpG	491	NM_053268	114713	Mm.124502	NM_053268	ENSMUSG00000032413	Rasa2	5430433H21Rik|AA517451|AU023900|GAP1m	RAS p21 protein activator 2	protein-coding
mm_116826.1	chr13	54611275	54611297	-	1	NA	promoter-TSS (NM_028870)	promoter-TSS (NM_028870)	87	NM_028870	74325	Mm.290026	NM_028870	ENSMUSG00000047547	Cltb	2310046E19Rik|lcb	clathrin, light polypeptide (Lcb)	protein-coding
mm_71195.1	chr8	40880104	40880125	+	1	NA	intron (NM_007514, intron 1 of 11)	L1_Mus3|LINE|L1	17747	NM_001044740	11988	Mm.4676	NM_007514	ENSMUSG00000031596	Slc7a2	20.5|AI158848|Atrc2|CAT-2|Cat2|Tea	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	protein-coding
mm_12743.1	chr2	79122726	79122753	+	1	NA	Intergenic	Intergenic	-132687	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D|Itga4B	integrin alpha 4	protein-coding
mm_157029.1	chrX	7922392	7922402	-	1	NA	exon (NM_013892, exon 2 of 3)	exon (NM_013892, exon 2 of 3)	2575	NM_013892	30052	Mm.4881	NM_013892	ENSMUSG00000039278	Pcsk1n	AI848336|KEP|PEN|PEN19|PEN20|Pan3|SAAS|SAASCT|bLEN|lLEN|proSAAS	proprotein convertase subtilisin/kexin type 1 inhibitor	protein-coding
mm_93836.1	chr10	121586870	121586880	-	1	NA	promoter-TSS (NM_019786)	promoter-TSS (NM_019786)	-81	NM_019786	56480	Mm.34580	NM_019786	ENSMUSG00000020115	Tbk1	1200008B05Rik|AI462036|AW048562	TANK-binding kinase 1	protein-coding
mm_101288.1	chr11	22001585	22001601	-	1	NA	promoter-TSS (NM_011023)	promoter-TSS (NM_011023)	58	NM_011023	18423	Mm.129663	NM_011023	ENSMUSG00000005917	Otx1	A730044F23Rik|jv	orthodenticle homeobox 1	protein-coding
mm_95291.1	chr11	45980354	45980362	+	1	NA	promoter-TSS (NM_173384)	promoter-TSS (NM_173384)	48	NM_173384	214105	Mm.66708	NM_173384	ENSMUSG00000040489	Sox30	-	SRY (sex determining region Y)-box 30	protein-coding
mm_12037.1	chr2	58767272	58767291	+	1	NA	intron (NM_029692, intron 2 of 6)	MLT1J1|LTR|ERVL-MaLR	12097	NM_029692	76654	Mm.200370	NM_029692	ENSMUSG00000026839	Upp2	1700124F02Rik|AI266885|UDRPASE2|UP2|UPASE2	uridine phosphorylase 2	protein-coding
mm_51600.1	chr6	84008635	84008645	+	1	NA	promoter-TSS (NM_001077694)	promoter-TSS (NM_001077694)	42	NM_001077694	26903	Mm.220982	NM_021469	ENSMUSG00000033788	Dysf	2310004N10Rik|AI604795|D6Pas3	dysferlin	protein-coding
mm_28894.1	chr3	97888912	97888929	-	1	NA	promoter-TSS (NM_001289701)	promoter-TSS (NM_001289701)	-213	NM_001289701	83679	Mm.129840	NM_031401	ENSMUSG00000038170	Pde4dip	4732458A06Rik|9430063L05Rik|C87016|D130016K21Rik|D3Bwg1078e|Usmg4|mKIAA0454	phosphodiesterase 4D interacting protein (myomegalin)	protein-coding
mm_159726.1	chr5	38319399	38319399	+	1	NA	promoter-TSS (NM_013503)	promoter-TSS (NM_013503)	-110	NM_013503	13492	Mm.167154	NM_013503	ENSMUSG00000039358	Drd5	D5R|Drd-5|Drd1b|Gpcr1	dopamine receptor D5	protein-coding
mm_133842.1	chr16	96200596	96200608	+	1	NA	5' UTR (NM_015825, exon 1 of 8)	5' UTR (NM_015825, exon 1 of 8)	132	NM_015825	50795	Mm.28638	NM_015825	ENSMUSG00000040666	Sh3bgr	5430437A18Rik	SH3-binding domain glutamic acid-rich protein	protein-coding
mm_144011.1	chr17	88403476	88403489	-	1	NA	Intergenic	Intergenic	-37230	NM_180974	14236	Mm.112824	NM_180974	ENSMUSG00000034998	Foxn2	3230402J05Rik|6030465J18Rik|Fkh19|Foxn1|HTLF	forkhead box N2	protein-coding
mm_344.1	chr1	30949890	30949909	+	1	NA	promoter-TSS (NR_002688)	promoter-TSS (NR_002688)	-144	NM_011200	19243	Mm.491181	NM_011200	ENSMUSG00000026064	Ptp4a1	AA415290|AU019864|C130021B01|Prl-1	protein tyrosine phosphatase 4a1	protein-coding
mm_37911.1	chr4	132757230	132757240	-	1	NA	promoter-TSS (NM_133888)	promoter-TSS (NM_133888)	-64	NM_133888	100340	Mm.287187	NM_133888	ENSMUSG00000028885	Smpdl3b	1110054A24Rik|AU045240|Asml3b	sphingomyelin phosphodiesterase, acid-like 3B	protein-coding
mm_44673.1	chr5	29735903	29735925	-	1	NA	promoter-TSS (NM_001037941)	promoter-TSS (NM_001037941)	16	NM_001127367	23950	Mm.290110	NM_011847	ENSMUSG00000029131	Dnajb6	Mrj|mDj4	DnaJ heat shock protein family (Hsp40) member B6	protein-coding
mm_4012.1	chr1	165461191	165461239	+	1	NA	promoter-TSS (NM_028759)	promoter-TSS (NM_028759)	7	NM_027430	70456	Mm.195625	NM_027430	ENSMUSG00000026568	Mpc2	0610006C01Rik|2010002I07Rik|2610205H19Rik|AA108335|Brp44|ESTM43	mitochondrial pyruvate carrier 2	protein-coding
mm_34164.1	chr4	139622843	139622902	+	1	NA	promoter-TSS (NM_175438)	promoter-TSS (NM_175438)	-22	NM_175438	212647	Mm.273571	NM_175438	ENSMUSG00000028737	Aldh4a1	A930035F14Rik|Ahd-1|Ahd1|Aldh4|Aldh5a1|E330022C09|P5cd|P5cdh|P5cdhl|P5cdhs|Ssdh1	aldehyde dehydrogenase 4 family, member A1	protein-coding
mm_116327.1	chr13	38031901	38031935	-	1	NA	intron (NM_027724, intron 2 of 12)	intron (NM_027724, intron 2 of 12)	5019	NM_027724	71213	Mm.314688	NM_027724	ENSMUSG00000044566	Cage1	4933427I01Rik|Ctag3	cancer antigen 1	protein-coding
mm_160730.1	chr10	77042409	77042409	+	1	NA	exon (NM_031196, exon 3 of 6)	exon (NM_031196, exon 3 of 6)	9197	NM_031196	20509	Mm.265060	NM_031196	ENSMUSG00000001436	Slc19a1	AI323572|RFC|RFC-1|RFC1	solute carrier family 19 (folate transporter), member 1	protein-coding
mm_156841.1	chrX	164373731	164373780	+	1	NA	TTS (NM_027153)	TTS (NM_027153)	233	NM_010216	14205	Mm.297978	NM_010216	ENSMUSG00000031380	Vegfd	AI325264|Figf|VEGF-D	vascular endothelial growth factor D	protein-coding
mm_71689.1	chr8	61280943	61280947	+	1	NA	TTS (NR_045475)	TTS (NR_045475)	7927	NR_045475	69279	Mm.417857	NR_045475	ENSMUSG00000099419	1700001D01Rik	-	RIKEN cDNA 1700001D01 gene	ncRNA
mm_39624.1	chr5	24425251	24425291	+	1	NA	promoter-TSS (NM_009207)	promoter-TSS (NM_009207)	39	NM_009207	20535	Mm.4580	NM_009207	ENSMUSG00000028962	Slc4a2	Ae2|B3RP	solute carrier family 4 (anion exchanger), member 2	protein-coding
mm_120986.1	chr14	79077283	79077289	+	1	NA	intron (NM_027906, intron 26 of 44)	intron (NM_027906, intron 26 of 44)	170081	NM_001033215	105590	Mm.486536	NM_001033215	ENSMUSG00000071262	Zfp957	AU017455	zinc finger protein 957	protein-coding
mm_34793.1	chr4	154506934	154506951	+	1	NA	intron (NM_001177995, intron 2 of 15)	intron (NM_001177995, intron 2 of 15)	129425	NR_045643	320939	Mm.436738	NR_045643		5930403L14Rik	-	RIKEN cDNA 5930403L14 gene	ncRNA
mm_117422.1	chr13	74363921	74363927	-	1	NA	promoter-TSS (NM_001033042)	promoter-TSS (NM_001033042)	76	NM_001033042	432779	Mm.324679	NM_001033042	ENSMUSG00000021579	Lrrc14b	AI595366	leucine rich repeat containing 14B	protein-coding
mm_22576.1	chr3	10366904	10366922	+	1	NA	promoter-TSS (NM_025519)	promoter-TSS (NM_025519)	-60	NM_025519	66371	Mm.366147	NM_025519	ENSMUSG00000027536	Chmp4c	2010012P02Rik|2210015K02Rik|2310010I16Rik|Shax3|Snf7-3	charged multivesicular body protein 4C	protein-coding
mm_111308.1	chr12	85815778	85815812	-	1	NA	3' UTR (NM_021446, exon 5 of 5)	3' UTR (NM_021446, exon 5 of 5)	8750	NM_021446	58520	Mm.143795	NM_021446	ENSMUSG00000021252	0610007P14Rik	1190004E09Rik|AU019315|C77855|ORF11	RIKEN cDNA 0610007P14 gene	protein-coding
mm_104404.1	chr11	94521325	94521349	-	1	NA	intron (NM_170671, intron 1 of 18)	CpG	165	NM_170671	104601	Mm.84725	NM_170671	ENSMUSG00000039110	Mycbpap	4932408B01Rik|AMAP-1|AW125474	MYCBP associated protein	protein-coding
mm_90902.1	chr10	11045586	11045596	-	1	NA	intron (NM_016976, intron 2 of 8)	intron (NM_016976, intron 2 of 8)	36740	NM_001114333	14816	Mm.391904	NM_016976	ENSMUSG00000019828	Grm1	4930455H15Rik|ENSMUSG00000075319|Gm10828|Gprc1a|mGluR1|nmf373|rcw|wobl	glutamate receptor, metabotropic 1	protein-coding
mm_70044.1	chr7	142577986	142577990	-	1	NA	promoter-TSS (NR_030416)	promoter-TSS (NR_030416)	158	NR_130974	14955	Mm.14802	NR_001592	ENSMUSG00000000031	H19	AI747191	H19, imprinted maternally expressed transcript	ncRNA
mm_80018.1	chr9	67891808	67891814	+	1	NA	intron (NM_177184, intron 18 of 84)	intron (NM_177184, intron 18 of 84)	51415	NM_177184	320528	Mm.241454	NM_177184	ENSMUSG00000035284	Vps13c	AI552542|AV026040|C230055H22Rik|W51662|chorein	vacuolar protein sorting 13C	protein-coding
mm_82721.1	chr9	24773179	24773182	-	1	NA	intron (NM_194263, intron 1 of 7)	intron (NM_194263, intron 1 of 7)	1123	NM_020496	57246	Mm.31452	NM_020496	ENSMUSG00000031965	Tbx20	9430010M06Rik|AL022859|Tbx12	T-box 20	protein-coding
mm_158478.1	chrX	141870495	141870503	-	1	NA	Intergenic	Intergenic	-145282	NM_010572	16370	Mm.261591	NM_010572	ENSMUSG00000054667	Irs4	IRS-4	insulin receptor substrate 4	protein-coding
mm_105942.1	chr11	115188765	115188774	-	1	NA	intron (NM_001033393, intron 2 of 9)	intron (NM_001033393, intron 2 of 9)	1282	NM_001033393	320534	Mm.260587	NM_001033393	ENSMUSG00000045980	Tmem104	C630005D06Rik|mFLJ00021	transmembrane protein 104	protein-coding
mm_139624.1	chr17	57362888	57362898	+	1	NA	intron (NM_010130, intron 2 of 21)	RLTR22_Mur|LTR|ERVK	4207	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_116236.1	chr13	33843377	33843380	-	1	NA	promoter-TSS (NM_001045535)	promoter-TSS (NM_001045535)	30	NM_001045535	435350	Mm.263418	NM_001045535	ENSMUSG00000069248	Serpinb6e	Gm11396|OTTMUSG00000000720|SPI3B|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 6e	protein-coding
mm_44472.1	chr5	23432710	23432727	-	1	NA	non-coding (NR_040469, exon 1 of 1)	non-coding (NR_040469, exon 1 of 1)	1635	NR_040469	269630	Mm.425231	NR_040469	ENSMUSG00000073147	5031425E22Rik	-	RIKEN cDNA 5031425E22 gene	ncRNA
mm_99341.1	chr11	101469377	101469382	+	1	NA	intron (NM_009708, intron 2 of 4)	(T)n|Simple_repeat|Simple_repeat	1041	NM_009708	11858	Mm.378883	NM_009708	ENSMUSG00000001313	Rnd2	Arhn|Rohn	Rho family GTPase 2	protein-coding
mm_53860.1	chr6	149309734	149309755	+	1	NA	5' UTR (NM_001289662, exon 1 of 5)	5' UTR (NM_001289662, exon 1 of 5)	330	NM_001289662	67246	Mm.333515	NM_026054	ENSMUSG00000032712	2810474O19Rik	6720435I21Rik|AA536804|AU020969|GET|Kiaa1551	RIKEN cDNA 2810474O19 gene	protein-coding
mm_34837.1	chr4	155361668	155361678	+	1	NA	promoter-TSS (NM_008860)	promoter-TSS (NM_008860)	-245	NM_008860	18762	Mm.28561	NM_008860	ENSMUSG00000029053	Prkcz	AI098070|C80388|Pkcz|R74924|aPKCzeta|nPKC-zeta|zetaPKC	protein kinase C, zeta	protein-coding
mm_35481.1	chr4	40853951	40854021	-	1	NA	5' UTR (NM_022305, exon 1 of 6)	5' UTR (NM_022305, exon 1 of 6)	551	NM_022305	14595	Mm.15622	NM_022305	ENSMUSG00000028413	B4galt1	B-1,4-GalT|B-1,4-GalT1|GalT|Ggtb|Ggtb2|b4Gal-T1|beta-1,4-GalT|beta-1,4-GalT1|beta4Gal-T1	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1	protein-coding
mm_161815.1	chr17	69207849	69207849	+	1	NA	intron (NM_013813, intron 1 of 21)	intron (NM_013813, intron 1 of 21)	51039	NM_013813	13823	Mm.131135	NM_013813	ENSMUSG00000024044	Epb41l3	4.1B|DAL1P|Dal1|Epb4.1l3|NBL3	erythrocyte membrane protein band 4.1 like 3	protein-coding
mm_139840.1	chr17	69262108	69262116	+	1	NA	intron (NM_013813, intron 11 of 21)	intron (NM_013813, intron 11 of 21)	15094	NR_045428	69750	Mm.439063	NR_045428	ENSMUSG00000100572	2410021H03Rik	-	RIKEN cDNA 2410021H03 gene	ncRNA
mm_44102.1	chr5	149364314	149364325	+	1	NA	Intergenic	L2a|LINE|L2	-47487	NM_027519	70717	Mm.252139	NM_027519	ENSMUSG00000029659	Medag	6330406I15Rik|Awms3|MEDA-4|Meda4|mAWMS3	mesenteric estrogen dependent adipogenesis	protein-coding
mm_30785.1	chr4	19575140	19575216	+	1	NA	5' UTR (NM_025476, exon 1 of 10)	5' UTR (NM_025476, exon 1 of 10)	112	NM_025476	66302	Mm.440686	NM_025476	ENSMUSG00000028229	Rmdn1	Fam82b|RMD-1	regulator of microtubule dynamics 1	protein-coding
mm_152003.1	chr19	5912835	5912852	-	1	NA	promoter-TSS (NM_001291078)	promoter-TSS (NM_001291078)	28	NM_011262	19708	Mm.2651	NM_011262	ENSMUSG00000024826	Dpf2	2210010M07Rik|BAF45D|Req|ubi-d4	D4, zinc and double PHD fingers family 2	protein-coding
mm_61397.1	chr7	73375495	73375549	+	1	NA	promoter-TSS (NM_177740)	promoter-TSS (NM_177740)	2	NM_177740	244058	Mm.333943	NM_177740	ENSMUSG00000070509	Rgma	BC059072|C230063O06	repulsive guidance molecule family member A	protein-coding
mm_89860.1	chr10	108162114	108162125	+	1	NA	promoter-TSS (NM_027892)	promoter-TSS (NM_027892)	-281	NM_027892	17931	Mm.422959	NM_027892	ENSMUSG00000019907	Ppp1r12a	1200015F06Rik|5730577I22Rik|AA792106|AV099298|D10Ertd625e|Mypt1	protein phosphatase 1, regulatory (inhibitor) subunit 12A	protein-coding
mm_19272.1	chr2	85086512	85086516	-	1	NA	promoter-TSS (NR_040504)	promoter-TSS (NR_040504)	-53	NR_040504	74687	Mm.66996	NR_040504	ENSMUSG00000086969	4930443O20Rik	-	RIKEN cDNA 4930443O20 gene	ncRNA
mm_105070.1	chr11	100738154	100738212	-	1	NA	promoter-TSS (NM_001305003)	promoter-TSS (NM_001305003)	32	NM_024456	19345	Mm.29829	NM_024456	ENSMUSG00000019173	Rab5c	AI326010|Rabl	RAB5C, member RAS oncogene family	protein-coding
mm_116632.1	chr13	48968210	48968220	-	1	NA	promoter-TSS (NM_001033268)	promoter-TSS (NM_001033268)	103	NR_015601	68128	Mm.426304	NR_015601		Fam120aos	C030044B11Rik	family with sequence similarity 120A, opposite strand	ncRNA
mm_83607.1	chr9	48605086	48605100	-	1	NA	promoter-TSS (NM_001311062)	promoter-TSS (NM_001311062)	30	NM_001311062	18113	Mm.8362	NM_010924	ENSMUSG00000032271	Nnmt	-	nicotinamide N-methyltransferase	protein-coding
mm_97677.1	chr11	79973673	79973687	+	1	NA	Intergenic	Intergenic	-11293	NM_144826	216987	Mm.274961	NM_144826	ENSMUSG00000035575	Utp6	4732497O03Rik|HCA66	UTP6 small subunit processome component	protein-coding
mm_154344.1	chrM	5320	5333	+	1	NA	NA	Intergenic	NA	NA								
mm_1002.1	chr1	58714645	58714657	+	1	NA	intron (NM_009805, intron 1 of 4)	intron (NM_009805, intron 1 of 4)	1365	NM_207653	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_11000.1	chr2	26445895	26445951	+	1	NA	promoter-TSS (NM_153125)	promoter-TSS (NM_153125)	-707	NM_153125	227648	Mm.206371	NM_153125	ENSMUSG00000026924	Sec16a	AU024582|C230052J16Rik	SEC16 homolog A, endoplasmic reticulum export factor	protein-coding
mm_48135.1	chr5	137150179	137150186	-	1	NA	Intergenic	(TGG)n|Simple_repeat|Simple_repeat	-33975	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_100856.1	chr11	5862295	5862301	-	1	NA	exon (NM_009636, exon 1 of 21)	exon (NM_009636, exon 1 of 21)	432	NM_001291857	11568	Mm.3317	NM_009636	ENSMUSG00000020473	Aebp1	ACLP	AE binding protein 1	protein-coding
mm_67139.1	chr7	73105215	73105228	-	1	NA	Intergenic	Intergenic	-3153	NR_046024	625243	Mm.261798	NR_046024	ENSMUSG00000108383	Gm6567	-	predicted gene 6567	ncRNA
mm_15370.1	chr2	156421163	156421174	+	1	NA	5' UTR (NM_001291121, exon 1 of 22)	5' UTR (NM_001291121, exon 1 of 22)	259	NM_001291123	13821	Mm.20852	NM_013510	ENSMUSG00000027624	Epb41l1	4.1N|Epb4.1l1|NBL1|mKIAA0338	erythrocyte membrane protein band 4.1 like 1	protein-coding
mm_148218.1	chr18	80236817	80236843	-	1	NA	5' UTR (NM_001136181, exon 2 of 5)	5' UTR (NM_001136181, exon 2 of 5)	10272	NM_001136181	66255	Mm.272341	NM_001136181	ENSMUSG00000078963	Hsbp1l1	1810005K13Rik	heat shock factor binding protein 1-like 1	protein-coding
mm_98530.1	chr11	94997900	94997924	+	1	NA	intron (NM_172261, intron 2 of 9)	intron (NM_172261, intron 2 of 9)	6700	NM_172261	217124	Mm.229087	NM_172261	ENSMUSG00000038976	Ppp1r9b	SPL|Spn	protein phosphatase 1, regulatory subunit 9B	protein-coding
mm_7707.1	chr1	130449217	130449228	-	1	NA	intron (NM_010016, intron 7 of 9)	intron (NM_010016, intron 7 of 9)	13522	NM_010016	13136	Mm.101591	NM_010016	ENSMUSG00000026399	Cd55	Daf|Daf-GPI|Daf1|GPI-DAF	CD55 molecule, decay accelerating factor for complement	protein-coding
mm_114723.1	chr13	83715257	83715267	+	1	NA	Intergenic	Intergenic	-12844	NR_015561	320203	Mm.245636	NM_177100	ENSMUSG00000050334	C130071C03Rik	2810449C10Rik	RIKEN cDNA C130071C03 gene	ncRNA
mm_158063.1	chrX	101212820	101212840	-	1	NA	3' UTR (NM_001110310, exon 4 of 4)	3' UTR (NM_001110310, exon 4 of 4)	9733	NM_001110311	55988	Mm.206949	NM_018875	ENSMUSG00000046032	Snx12	2610001F05Rik|AW045757|SDP8	sorting nexin 12	protein-coding
mm_53893.1	chr6	3377274	3377282	-	1	NA	5' UTR (NM_010156, exon 2 of 2)	5' UTR (NM_010156, exon 2 of 2)	22293	NM_010156	209086	Mm.196013	NM_010156	ENSMUSG00000047735	Samd9l	AA175286|ESTM25|mKIAA2005	sterile alpha motif domain containing 9-like	protein-coding
mm_47144.1	chr5	120560353	120560372	-	1	NA	intron (NM_145853, intron 2 of 27)	intron (NM_145853, intron 2 of 27)	28251	NM_145853	252972	Mm.114054	NM_145853	ENSMUSG00000032741	Tpcn1	5730403B01Rik|Tpc1|mKIAA1169	two pore channel 1	protein-coding
mm_38856.1	chr4	149426230	149426242	-	1	NA	5' UTR (NM_022022, exon 1 of 27)	5' UTR (NM_022022, exon 1 of 27)	395	NM_022022	63958	Mm.415260	NM_022022	ENSMUSG00000028960	Ube4b	4930551I19Rik|4933406G05Rik|AU014668|D4Bwg0973e|UFD2|UFD2a|Ufd2p|mKIAA0684	ubiquitination factor E4B	protein-coding
mm_28933.1	chr3	98882039	98882071	-	1	NA	exon (NM_019545, exon 5 of 9)	exon (NM_019545, exon 5 of 9)	11175	NM_019545	56185	Mm.281874	NM_019545	ENSMUSG00000027870	Hao2	AI325478|Hao-2|Hao3|Haox3	hydroxyacid oxidase 2	protein-coding
mm_45336.1	chr5	65697897	65697963	-	1	NA	promoter-TSS (NM_001081321)	promoter-TSS (NM_001081321)	-74	NM_001081321	71521	Mm.278974	NM_027818	ENSMUSG00000029202	Pds5a	9030416H16Rik|E230024D05Rik|mKIAA0648	PDS5 cohesin associated factor A	protein-coding
mm_147170.1	chr18	36726669	36726691	-	1	NA	5' UTR (NM_009841, exon 1 of 2)	5' UTR (NM_009841, exon 1 of 2)	135	NM_009841	12475	Mm.3460	NM_009841	ENSMUSG00000051439	Cd14	-	CD14 antigen	protein-coding
mm_31324.1	chr4	46389462	46389501	+	1	NA	promoter-TSS (NM_029086)	promoter-TSS (NM_029086)	-44	NM_001347095	74753	Mm.45973	NM_029086	ENSMUSG00000028331	Trmo	5830415F09Rik|AV014846|Nap1	tRNA methyltransferase O	protein-coding
mm_157642.1	chrX	57281592	57281596	-	1	NA	intron (NM_152801, intron 6 of 21)	intron (NM_152801, intron 6 of 21)	57135	NM_152801	73341	Mm.261443	NM_152801	ENSMUSG00000031133	Arhgef6	1600028C08Rik|1700038J06Rik|4930592P22Rik|alpha-PIX	Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_14079.1	chr2	124610423	124610436	+	1	NA	5' UTR (NM_199238, exon 1 of 17)	5' UTR (NM_199238, exon 1 of 17)	133	NM_172537	214968	Mm.330536	NM_172537	ENSMUSG00000027200	Sema6d	1110067B02Rik|AA409156|D330011G23|mKIAA1479	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	protein-coding
mm_89761.1	chr10	100027061	100027077	+	1	NA	intron (NM_001347156, intron 1 of 8)	intron (NM_001347156, intron 1 of 8)	11248	NM_013598	17311	Mm.45124	NM_013598	ENSMUSG00000019966	Kitl	Clo|Con|Gb|Kitlg|Mgf|SCF|SF|SLF|Sl|blz|contrasted	kit ligand	protein-coding
mm_82486.1	chr9	18468193	18468203	-	1	NA	intron (NM_028935, intron 4 of 7)	intron (NM_028935, intron 4 of 7)	5361	NM_028935	72230	Mm.289689	NM_028935	ENSMUSG00000074500	Zfp558	1700007A21Rik|4932704I17Rik|Zfp558-ps	zinc finger protein 558	protein-coding
mm_154069.1	chr19	55910610	55910652	-	1	NA	exon (NM_001142918, exon 6 of 15)	exon (NM_001142918, exon 6 of 15)	15310	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_50478.1	chr6	48988115	48988123	+	1	NA	exon (NM_172888, exon 1 of 5)	exon (NM_172888, exon 1 of 5)	1258	NM_172888	243377	Mm.446302	NM_172888	ENSMUSG00000039215	Svs1	9530003A11	seminal vesicle secretory protein 1	protein-coding
mm_163749.1	chr13	119755969	119756035	-	1	NA	promoter-TSS (NM_175538)	promoter-TSS (NM_175538)	-120	NM_175538	245269	Mm.403943	NM_175538	ENSMUSG00000095930	Nim1k	E130304F04Rik|Nim1	NIM1 serine/threonine protein kinase	protein-coding
mm_36783.1	chr4	103011958	103011970	-	1	NA	promoter-TSS (NR_028391)	promoter-TSS (NR_028391)	1	NR_028391	100473	Mm.393171	NR_028391	ENSMUSG00000085041	BB031773	-	expressed sequence BB031773	ncRNA
mm_84697.1	chr9	72409773	72409822	-	1	NA	Intergenic	Intergenic	-28732	NM_008613	17427	Mm.387671	NM_008613	ENSMUSG00000032221	Mns1	AW546487	meiosis-specific nuclear structural protein 1	protein-coding
mm_31911.1	chr4	85205121	85205131	+	1	NA	promoter-TSS (NM_019535)	promoter-TSS (NM_019535)	-330	NM_019535	20404	Mm.143603	NM_019535	ENSMUSG00000028488	Sh3gl2	9530001L19Rik|AI120490|AW555077|B930049H17Rik|EEN-B1|SH3PA|Sh3d2a	SH3-domain GRB2-like 2	protein-coding
mm_75011.1	chr8	27413938	27413946	-	1	NA	promoter-TSS (NM_021369)	promoter-TSS (NM_021369)	2	NM_021369	11440	Mm.283137	NM_021369	ENSMUSG00000031491	Chrna6	Acra6|Nica6	cholinergic receptor, nicotinic, alpha polypeptide 6	protein-coding
mm_33006.1	chr4	120666563	120666579	+	1	NA	promoter-TSS (NM_019563)	promoter-TSS (NM_019563)	8	NM_019563	56222	Mm.272646	NM_019563	ENSMUSG00000070803	Cited4	MRG-2|Mrg2	Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 4	protein-coding
mm_5962.1	chr1	56972233	56972254	-	1	NA	promoter-TSS (NM_139146)	promoter-TSS (NM_139146)	774	NR_024325	329160	Mm.419039	NR_024325	ENSMUSG00000087022	9130024F11Rik	B530002L08|EG329160	RIKEN cDNA 9130024F11 gene	ncRNA
mm_106476.1	chr11	120139450	120139451	-	1	NA	intron (NM_024249, intron 4 of 16)	intron (NM_024249, intron 4 of 16)	11901	NM_001164799	72055	Mm.253403	NM_024249	ENSMUSG00000061306	Slc38a10	1810073N04Rik	solute carrier family 38, member 10	protein-coding
mm_111279.1	chr12	85350554	85350554	-	1	NA	intron (NM_026775, intron 3 of 4)	intron (NM_026775, intron 3 of 4)	-11192	NM_145138	217718	Mm.29071	NM_145138	ENSMUSG00000034290	Nek9	C130021H08Rik	NIMA (never in mitosis gene a)-related expressed kinase 9	protein-coding
mm_18073.1	chr2	42652974	42652996	-	1	NA	5' UTR (NM_053011, exon 1 of 91)	5' UTR (NM_053011, exon 1 of 91)	613	NM_053011	94217	Mm.441398	NM_053011	ENSMUSG00000049252	Lrp1b	9630004P12Rik|LRP-DIT	low density lipoprotein-related protein 1B (deleted in tumors)	protein-coding
mm_123680.1	chr14	69503317	69503323	-	1	NA	Intergenic	CpG	9229	NM_173420	239167	Mm.259889	NM_173420	ENSMUSG00000047977	Synb	D930020E02Rik|syncytin-B	syncytin b	protein-coding
mm_126056.1	chr15	76949575	76949584	+	1	NA	exon (NM_054099, exon 3 of 4)	exon (NM_054099, exon 3 of 4)	1035	NM_054099	117171	Mm.322968	NM_054099	ENSMUSG00000063236	1110038F14Rik	-	RIKEN cDNA 1110038F14 gene	protein-coding
mm_84397.1	chr9	65552101	65552118	-	1	NA	TTS (NM_153119)	TTS (NM_153119)	27978	NM_153119	102595	Mm.247303	NM_153119	ENSMUSG00000050721	Plekho2	AI840980|Plekhq1	pleckstrin homology domain containing, family O member 2	protein-coding
mm_41757.1	chr5	102846009	102846042	+	1	NA	5' UTR (NM_001346585, exon 1 of 7)	5' UTR (NM_001346585, exon 1 of 7)	1018	NM_001346585	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding
mm_53481.1	chr6	134981921	134981953	+	1	NA	promoter-TSS (NM_001109914)	promoter-TSS (NM_001109914)	-64	NM_001109914	381823	Mm.296104	NM_001109914	ENSMUSG00000090698	Apold1	Gm1075	apolipoprotein L domain containing 1	protein-coding
mm_136807.1	chr17	12382827	12382844	+	1	NA	intron (NM_008877, intron 2 of 18)	B4A|SINE|B4	4226	NM_008877	18815	Mm.971	NM_008877	ENSMUSG00000059481	Plg	AI649309|Pg	plasminogen	protein-coding
mm_78050.1	chr9	14704526	14704551	+	1	NA	intron (NM_177905, intron 17 of 18)	intron (NM_177905, intron 17 of 18)	36195	NM_177905	330890	Mm.334969	NM_177905	ENSMUSG00000036912	Piwil4	9230101H05Rik|Miwi2	piwi-like RNA-mediated gene silencing 4	protein-coding
mm_68271.1	chr7	105595673	105595682	-	1	NA	intron (NM_017371, intron 5 of 9)	intron (NM_017371, intron 5 of 9)	4439	NM_017371	15458	Mm.3485	NM_017371	ENSMUSG00000030895	Hpx	Hpxn|hx	hemopexin	protein-coding
mm_93132.1	chr10	92116499	92116503	-	1	NA	intron (NR_028262, intron 9 of 12)	intron (NR_028262, intron 9 of 12)	20722	NR_037219	100526517		NR_037219	ENSMUSG00000093227	Mir1251	mir-1251|mmu-mir-1251	microRNA 1251	ncRNA
mm_102746.1	chr11	67254827	67254841	-	1	NA	exon (NM_010855, exon 30 of 40)	exon (NM_010855, exon 30 of 40)	17022	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_145945.1	chr18	67390667	67390691	+	1	NA	promoter-TSS (NM_026473)	promoter-TSS (NM_026473)	-52	NM_026473	67951	Mm.181860	NM_026473	ENSMUSG00000001473	Tubb6	2310057H16Rik|BB220206	tubulin, beta 6 class V	protein-coding
mm_11263.1	chr2	29966366	29966389	+	1	NA	intron (NM_001309460, intron 1 of 57)	intron (NM_001309460, intron 1 of 57)	817	NM_001309460	20740	Mm.204969	NM_001076554	ENSMUSG00000057738	Sptan1	2610027H02Rik|Spna-2|Spna2	spectrin alpha, non-erythrocytic 1	protein-coding
mm_2717.1	chr1	128151233	128151279	+	1	NA	intron (NM_181750, intron 1 of 26)	intron (NM_181750, intron 1 of 26)	47950	NM_181750	226412	Mm.221041	NM_181750	ENSMUSG00000056211	R3hdm1	R3hdm	R3H domain containing 1	protein-coding
mm_156518.1	chrX	150589887	150589899	+	1	NA	promoter-TSS (NM_008824)	promoter-TSS (NM_008824)	-28	NM_008824	18639	Mm.249131	NM_008824	ENSMUSG00000025271	Pfkfb1	PFK/FBPase 1	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1	protein-coding
mm_101407.1	chr11	27507125	27507128	-	1	NA	Intergenic	Intergenic	722018	NR_002890	654472	Mm.347777	NR_002890		Gm12070	OTTMUSG00000005300	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_102757.1	chr11	67379774	67379786	-	1	NA	Intergenic	MLT1K|LTR|ERVL-MaLR	52677	NM_001081250	544791	Mm.461064	NM_001081250	ENSMUSG00000060180	Myh13	MyHC-eo	myosin, heavy polypeptide 13, skeletal muscle	protein-coding
mm_60966.1	chr7	47772668	47772705	+	1	NA	Intergenic	Intergenic	-171314	NM_153067	233222	Mm.240142	NM_153067	ENSMUSG00000078698	Mrgpra3	Mrga3	MAS-related GPR, member A3	protein-coding
mm_44307.1	chr5	8997139	8997161	-	1	NA	promoter-TSS (NM_023733)	promoter-TSS (NM_023733)	-4	NM_023733	74114	Mm.28197	NM_023733	ENSMUSG00000003623	Crot	1200003H03Rik	carnitine O-octanoyltransferase	protein-coding
mm_34077.1	chr4	138457985	138458002	+	1	NA	3' UTR (NM_025451, exon 2 of 2)	3' UTR (NM_025451, exon 2 of 2)	2845	NM_025451	66259	Mm.41603	NM_025451	ENSMUSG00000046447	Camk2n1	1810006K23Rik|AI848599|AI891706	calcium/calmodulin-dependent protein kinase II inhibitor 1	protein-coding
mm_54460.1	chr6	34875609	34875628	-	1	NA	TTS (NM_197986)	TTS (NM_197986)	2447	NM_199145	78412	Mm.248440	NM_199145	ENSMUSG00000046806	3110062M04Rik	AL023049|Mri	RIKEN cDNA 3110062M04 gene	protein-coding
mm_172064.1	chr6	135362962	135362962	+	1	NA	promoter-TSS (NM_001288628)	promoter-TSS (NM_001288628)	31	NM_001288628	13730	Mm.182785	NM_010128	ENSMUSG00000030208	Emp1	I-8-09|TMP	epithelial membrane protein 1	protein-coding
mm_29834.1	chr3	129804090	129804097	-	1	NA	promoter-TSS (NM_001287224)	promoter-TSS (NM_001287224)	-63	NM_001287224	242235	Mm.302549	NM_001205102	ENSMUSG00000093865	Lrit3	Gm421	leucine-rich repeat, immunoglobulin-like and transmembrane domains 3	protein-coding
mm_163215.1	chr11	100938750	100938767	+	1	NA	intron (NM_213660, intron 1 of 23)	intron (NM_213660, intron 1 of 23)	782	NM_213660	20848	Mm.249934	NM_011486	ENSMUSG00000004040	Stat3	1110034C02Rik|AW109958|Aprf	signal transducer and activator of transcription 3	protein-coding
mm_93369.1	chr10	105314044	105314047	-	1	NA	intron (NM_177368, intron 7 of 11)	intron (NM_177368, intron 7 of 11)	260434	NM_177368	278279	Mm.25225	NM_177368	ENSMUSG00000036019	Tmtc2	8430438D04Rik|D330034A10Rik	transmembrane and tetratricopeptide repeat containing 2	protein-coding
mm_13072.1	chr2	91119859	91119863	+	1	NA	intron (NM_008653, intron 2 of 31)	intron (NM_008653, intron 2 of 31)	1717	NM_008653	17868	Mm.10728	NM_008653	ENSMUSG00000002100	Mybpc3	-	myosin binding protein C, cardiac	protein-coding
mm_1897.1	chr1	85709420	85709433	+	1	NA	3' UTR (NM_013673, exon 20 of 20)	3' UTR (NM_013673, exon 20 of 20)	27180	NM_177055	319997	Mm.116691	NM_177055	ENSMUSG00000052760	A630001G21Rik	-	RIKEN cDNA A630001G21 gene	protein-coding
mm_144299.1	chr18	12333929	12333946	+	1	NA	promoter-TSS (NM_010680)	promoter-TSS (NM_010680)	-87	NM_010680	16774	Mm.42012	NM_010680	ENSMUSG00000024421	Lama3	Lama3B|[a]3B	laminin, alpha 3	protein-coding
mm_151557.1	chr19	59459563	59459593	+	1	NA	promoter-TSS (NR_002863)	promoter-TSS (NR_002863)	888	NM_010132	13797	Mm.245394	NM_010132	ENSMUSG00000043969	Emx2	Pdo	empty spiracles homeobox 2	protein-coding
mm_168347.1	chr11	12241734	12241741	+	1	NA	intron (NM_172496, intron 14 of 14)	MTC|LTR|ERVL-MaLR	170403	NM_001282994	12808	Mm.22847	NM_172496	ENSMUSG00000020173	Cobl	-	cordon-bleu WH2 repeat	protein-coding
mm_154817.1	chrX	14714728	14714733	+	1	NA	Intergenic	AT_rich|Low_complexity|Low_complexity	396759	NR_033171	67395	Mm.50369	NM_026128	ENSMUSG00000045217	Ppp1r2-ps9	4930403L05Rik	protein phosphatase 1, regulatory (inhibitor) subunit 2, pseudogene 9	pseudo
mm_37217.1	chr4	117914941	117914957	-	1	NA	promoter-TSS (NM_146152)	promoter-TSS (NM_146152)	50	NM_146152	230673	Mm.287810	NM_146152	ENSMUSG00000033365	Ipo13	Imp13|Kap13|Ranbp13	importin 13	protein-coding
mm_48256.1	chr5	137831239	137831245	-	1	NA	exon (NM_153510, exon 3 of 7)	exon (NM_153510, exon 3 of 7)	5036	NM_153510	231805	Mm.379385	NM_153510	ENSMUSG00000046245	Pilra	AV021745|FDF03	paired immunoglobin-like type 2 receptor alpha	protein-coding
mm_110920.1	chr12	76274216	76274245	-	1	NA	intron (NM_138745, intron 2 of 27)	intron (NM_138745, intron 2 of 27)	18998	NM_138745	108156	Mm.29584	NM_138745	ENSMUSG00000021048	Mthfd1	Dcs|E430024A07Rik|Mthfd	methylenetetrahydrofolate dehydrogenase (NADP+ dependent), methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthase	protein-coding
mm_131965.1	chr16	24670518	24670548	+	1	NA	intron (NM_001145952, intron 5 of 11)	intron (NM_001145952, intron 5 of 11)	-51322	NM_001145954	210126	Mm.209385	NM_178665	ENSMUSG00000033306	Lpp	9430020K16Rik|AA959454|AU024130|B130055L10Rik|C79715|D630048H16	LIM domain containing preferred translocation partner in lipoma	protein-coding
mm_52280.1	chr6	108660520	108660534	+	1	NA	promoter-TSS (NM_011498)	promoter-TSS (NM_011498)	-102	NM_011498	20893	Mm.2436	NM_011498	ENSMUSG00000030103	Bhlhe40	Bhlhb2|C130042M06Rik|CR8|Clast5|Dec1|Sharp2|Stra13|Stra14	basic helix-loop-helix family, member e40	protein-coding
mm_10800.1	chr2	24349640	24349648	+	1	NA	3' UTR (NM_031167, exon 5 of 5)	3' UTR (NM_031167, exon 5 of 5)	4273	NM_001039701	16181	Mm.882	NM_031167	ENSMUSG00000026981	Il1rn	F630041P17Rik|IL-1ra	interleukin 1 receptor antagonist	protein-coding
mm_24089.1	chr3	87976024	87976045	+	1	NA	exon (NM_016701, exon 4 of 4)	exon (NM_016701, exon 4 of 4)	4941	NM_016701	18008	Mm.331129	NM_016701	ENSMUSG00000004891	Nes	AA166324|C78523|ESTM46	nestin	protein-coding
mm_156230.1	chrX	135839080	135839086	+	1	NA	promoter-TSS (NM_001163017)	promoter-TSS (NM_001163017)	49	NM_001163017	245607	Mm.489763	NM_001163015	ENSMUSG00000072966	Gprasp2	5330440H13Rik|GASP-2|GASP2|Prpl5	G protein-coupled receptor associated sorting protein 2	protein-coding
mm_128550.1	chr15	55636805	55636808	-	1	NA	Intergenic	Intergenic	79398	NM_001168250	105837	Mm.390829	NM_134092	ENSMUSG00000022369	Mtbp	AI429604|MDM2BP	Mdm2, transformed 3T3 cell double minute p53 binding protein	protein-coding
mm_18412.1	chr2	60599909	60599913	-	1	NA	3' UTR (NM_001159564, exon 18 of 18)	3' UTR (NM_001159564, exon 18 of 18)	-46603	NM_008867	18779	Mm.5092	NM_008867	ENSMUSG00000054580	Pla2r1	Pla2-r|Pla2g1br|Pla2r	phospholipase A2 receptor 1	protein-coding
mm_17882.1	chr2	34961803	34961818	-	1	NA	promoter-TSS (NM_001326601)	promoter-TSS (NM_001326601)	-38	NM_001326601	22029	Mm.239514	NM_009421	ENSMUSG00000026875	Traf1	4732496E14Rik	TNF receptor-associated factor 1	protein-coding
mm_126982.1	chr15	93473484	93473487	+	1	NA	intron (NM_175363, intron 8 of 8)	intron (NM_175363, intron 8 of 8)	75021	NM_001285863	223828	Mm.74208	NM_146062	ENSMUSG00000036167	Pphln1	CR|HSPC206|HSPC232	periphilin 1	protein-coding
mm_131600.1	chr16	19051333	19051369	+	1	NA	Intergenic	Intergenic	174601	NM_010435	15260	Mm.15694	NM_010435	ENSMUSG00000022702	Hira	AA138857|D16Ertd95e|Gm15797|N28177|OTTMUSG00000026264|Tuple1	histone cell cycle regulator	protein-coding
mm_18480.1	chr2	62573814	62573818	-	1	NA	intron (NM_007986, intron 1 of 25)	intron (NM_007986, intron 1 of 25)	205	NM_007986	14089	Mm.41816	NM_007986	ENSMUSG00000000392	Fap	SIMP	fibroblast activation protein	protein-coding
mm_140457.1	chr17	89718098	89718098	+	1	NA	Intergenic	Intergenic	338857	NR_045952	100043904	Mm.396198	NR_045952		Gm4719	-	predicted gene 4719	ncRNA
mm_97610.1	chr11	78951140	78951179	+	1	NA	exon (NM_010927, exon 21 of 27)	exon (NM_010927, exon 21 of 27)	25868	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_37061.1	chr4	116053777	116053822	-	1	NA	promoter-TSS (NM_028142)	promoter-TSS (NM_028142)	77	NM_028142	72181	Mm.282560	NM_028142	ENSMUSG00000028706	Nsun4	2310010O12Rik|2810405F18Rik|AI507900|Shtap	NOL1/NOP2/Sun domain family, member 4	protein-coding
mm_78554.1	chr9	35424920	35424940	+	1	NA	Intergenic	Intergenic	-27146	NM_021339	57810	Mm.80509	NM_021339	ENSMUSG00000038119	Cdon	CDO|Cd0|Orcam	cell adhesion molecule-related/down-regulated by oncogenes	protein-coding
mm_24516.1	chr3	92689371	92689406	+	1	NA	Intergenic	Intergenic	-2178	NM_027137	69611	Mm.176243	NM_027137	ENSMUSG00000103243	Lce1d	2310037L11Rik|AI415320|Sprrl7	late cornified envelope 1D	protein-coding
mm_148127.1	chr18	75666138	75666157	-	1	NA	intron (NM_201354, intron 1 of 11)	intron (NM_201354, intron 1 of 11)	31549	NM_201354	269037	Mm.36745	NM_201354	ENSMUSG00000052928	Ctif	Gm672	CBP80/20-dependent translation initiation factor	protein-coding
mm_108423.1	chr12	82170248	82170304	+	1	NA	intron (NM_001167983, intron 1 of 23)	CpG	260	NM_001167983	217692	Mm.261333	NM_172579	ENSMUSG00000042700	Sipa1l1	4931426N11Rik|AW213287|Spar|mKIAA0440	signal-induced proliferation-associated 1 like 1	protein-coding
mm_48280.1	chr5	138170993	138171033	-	1	NA	intron (NM_008568, intron 1 of 14)	CpG	849	NM_008568	17220	Mm.378965	NM_008568	ENSMUSG00000029730	Mcm7	AI747533|Mcmd7|mCDC47	minichromosome maintenance complex component 7	protein-coding
mm_26292.1	chr3	142506878	142506889	+	1	NA	exon (NM_153564, exon 8 of 11)	exon (NM_153564, exon 8 of 11)	9949	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_29114.1	chr3	104916195	104916196	-	1	NA	intron (NM_001253702, intron 11 of 13)	intron (NM_001253702, intron 11 of 13)	45514	NM_009520	22414	Mm.10740	NM_009520	ENSMUSG00000027840	Wnt2b	Wnt13	wingless-type MMTV integration site family, member 2B	protein-coding
mm_26081.1	chr3	136670816	136670824	+	1	NA	5' UTR (NM_001293622, exon 1 of 13)	5' UTR (NM_001293622, exon 1 of 13)	754	NM_001293622	19055	Mm.331389	NM_008913	ENSMUSG00000028161	Ppp3ca	2900074D19Rik|CN|Caln|Calna|CnA	protein phosphatase 3, catalytic subunit, alpha isoform	protein-coding
mm_82292.1	chr9	7764756	7764789	-	1	NA	intron (NM_133739, intron 1 of 4)	intron (NM_133739, intron 1 of 4)	695	NM_133739	71929	Mm.283293	NM_133739	ENSMUSG00000050912	Tmem123	2310075C12Rik	transmembrane protein 123	protein-coding
mm_27725.1	chr3	69004504	69004545	-	1	NA	promoter-TSS (NM_133786)	promoter-TSS (NM_133786)	46	NM_026641	68259	Mm.389451	NM_026641	ENSMUSG00000027778	Ift80	4921524P20Rik|Wdr56|mKIAA1374	intraflagellar transport 80	protein-coding
mm_40412.1	chr5	53063915	53063924	+	1	NA	exon (NM_011402, exon 7 of 13)	exon (NM_011402, exon 7 of 13)	14566	NM_011402	20531	Mm.284891	NM_011402	ENSMUSG00000029188	Slc34a2	AA536683|D5Ertd227e|NaPi-2b|Npt2b	solute carrier family 34 (sodium phosphate), member 2	protein-coding
mm_52475.1	chr6	114302151	114302156	+	1	NA	exon (NM_178703, exon 3 of 16)	exon (NM_178703, exon 3 of 16)	19518	NM_178703	232333	Mm.5260	NM_178703	ENSMUSG00000030310	Slc6a1	A730043E01|GABATHG|GABATR|GAT-1|Gabt|Gabt1|Gat1|XT-1|Xtrp1	solute carrier family 6 (neurotransmitter transporter, GABA), member 1	protein-coding
mm_163937.1	chr14	50943260	50943261	+	1	NA	Intergenic	Intergenic	-1043	NM_013632	18950	Mm.17932	NM_013632	ENSMUSG00000021871	Pnp	AL024301|AU015798|Np|Np-1|Np-2|Pnp1	purine-nucleoside phosphorylase	protein-coding
mm_87598.1	chr10	57645862	57645886	+	1	NA	promoter-TSS (NM_001039053)	promoter-TSS (NM_001039053)	5	NM_001039053	18768	Mm.262135	NM_008863	ENSMUSG00000019876	Pkib	Pkibeta|Prkacn2	protein kinase inhibitor beta, cAMP dependent, testis specific	protein-coding
mm_28013.1	chr3	83043796	83043805	-	1	NA	exon (NM_181849, exon 6 of 8)	exon (NM_181849, exon 6 of 8)	6063	NM_181849	110135	Mm.30063	NM_181849	ENSMUSG00000033831	Fgb	2510049G14Rik	fibrinogen beta chain	protein-coding
mm_82580.1	chr9	21149874	21149887	-	1	NA	promoter-TSS (NM_016742)	promoter-TSS (NM_016742)	26	NM_016742	12539	Mm.32331	NM_016742	ENSMUSG00000019471	Cdc37	p50|p50Cdc37	cell division cycle 37	protein-coding
mm_65069.1	chr7	19001161	19001174	-	1	NA	3' UTR (NM_145579, exon 3 of 3)	3' UTR (NM_145579, exon 3 of 3)	-2898	NM_178757	272359	Mm.274237	NM_178757	ENSMUSG00000044030	Irf2bp1	6330414O09Rik|C530033F24	interferon regulatory factor 2 binding protein 1	protein-coding
mm_155173.1	chrX	53607893	53607916	+	1	NA	promoter-TSS (NM_028375)	promoter-TSS (NM_028375)	-18	NM_028375	72865	Mm.158897	NM_028375	ENSMUSG00000051851	Cxx1c	2900027G03Rik|Mar8.1|Mart8a	CAAX box 1C	protein-coding
mm_19393.1	chr2	91526465	91526469	-	1	NA	Intergenic	Intergenic	-19855	NM_001165989	75786	Mm.168478	NM_029437	ENSMUSG00000040549	Ckap5	3110043H24Rik|4930432B04Rik|D730027C18Rik|T25636|mKIAA0097	cytoskeleton associated protein 5	protein-coding
mm_137262.1	chr17	24640760	24640789	+	1	NA	intron (NM_023449, intron 4 of 5)	intron (NM_023449, intron 4 of 5)	4183	NM_023449	65962	Mm.21587	NM_023055	ENSMUSG00000002504	Slc9a3r2	0610011L07Rik|1200011K07Rik|2010007A20Rik|E3karp|NHERF-2|Nherf2|Octs2|Sip-1|Sip1|Sryip1|Tka-1	solute carrier family 9 (sodium/hydrogen exchanger), member 3 regulator 2	protein-coding
mm_109510.1	chr12	111453749	111453758	+	1	NA	3' UTR (NM_009396, exon 12 of 12)	3' UTR (NM_009396, exon 12 of 12)	11092	NM_009396	21928	Mm.255332	NM_009396	ENSMUSG00000021281	Tnfaip2	B94|Exoc3l3|M-sec|Tnfip2|tnfb94	tumor necrosis factor, alpha-induced protein 2	protein-coding
mm_62425.1	chr7	101332858	101332859	+	1	NA	intron (NM_019990, intron 2 of 6)	BC1_Mm|scRNA|scRNA	11539	NM_019990	56018	Mm.28896	NM_019990	ENSMUSG00000030688	Stard10	AV048538|CGI-52|NY-C0-28|PC-TP2|PCTP2|Pctpl|Sdccag28|SdccagG28|TISP-81	START domain containing 10	protein-coding
mm_149277.1	chr19	10605685	10605695	+	1	NA	promoter-TSS (NM_015735)	promoter-TSS (NM_015735)	65	NM_015735	13194	Mm.289915	NM_015735	ENSMUSG00000024740	Ddb1	127kDa|AA408517|p127-Ddb1	damage specific DNA binding protein 1	protein-coding
mm_122281.1	chr14	34502635	34502657	-	1	NA	promoter-TSS (NM_009758)	promoter-TSS (NM_009758)	-100	NM_009758	12166	Mm.237825	NM_009758	ENSMUSG00000021796	Bmpr1a	1110037I22Rik|ALK3|AU045487|BMPR-IA|Bmpr	bone morphogenetic protein receptor, type 1A	protein-coding
mm_46435.1	chr5	104859792	104859805	-	1	NA	5' UTR (NM_001039231, exon 1 of 5)	5' UTR (NM_001039231, exon 1 of 5)	270	NM_001039231	626391	Mm.385405	NM_001039231	ENSMUSG00000072774	Zfp951	C230055K05Rik	zinc finger protein 951	protein-coding
mm_27378.1	chr3	50443540	50443549	-	1	NA	promoter-TSS (NM_011990)	promoter-TSS (NM_011990)	69	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_132515.1	chr16	37580138	37580151	+	1	NA	promoter-TSS (NR_027778)	promoter-TSS (NR_027778)	-9	NR_027778	15233	Mm.157442	NM_013547	ENSMUSG00000022821	Hgd	Hgo|aku	homogentisate 1, 2-dioxygenase	protein-coding
mm_171002.1	chr2	78505001	78505003	+	1	NA	Intergenic	L1Md_T|LINE|L1	267455	NM_177843	329436	Mm.235448	NM_177843		Gm14461	A830093M07|OTTMUSG00000016703	predicted gene 14461	protein-coding
mm_90277.1	chr10	122805551	122805552	+	1	NA	intron (NM_176919, intron 3 of 8)	intron (NM_176919, intron 3 of 8)	126236	NR_106182	102466884		NR_106182	ENSMUSG00000099225	Mir8104	Gm27380|mmu-mir-8104	microRNA 8104	ncRNA
mm_152135.1	chr19	7032549	7032577	-	1	NA	exon (NM_016737, exon 5 of 14)	exon (NM_016737, exon 5 of 14)	7463	NM_016737	20867	Mm.258633	NM_016737	ENSMUSG00000024966	Stip1	Hop|Sti1|p60	stress-induced phosphoprotein 1	protein-coding
mm_88756.1	chr10	80329503	80329508	+	1	NA	promoter-TSS (NM_139292)	promoter-TSS (NM_139292)	-32	NM_008793	18551	Mm.299916	NM_008793	ENSMUSG00000020131	Pcsk4	AI647044|L21221|NEC 3|NEC3|PC4|SPC5	proprotein convertase subtilisin/kexin type 4	protein-coding
mm_27232.1	chr3	36461972	36462001	-	1	NA	exon (NM_009673, exon 5 of 13)	exon (NM_009673, exon 5 of 13)	13538	NR_105976	102466786		NR_105976	ENSMUSG00000098808	Mir7009	Gm27472|mmu-mir-7009	microRNA 7009	ncRNA
mm_116261.1	chr13	34246632	34246642	-	1	NA	intron (NM_001033167, intron 3 of 10)	intron (NM_001033167, intron 3 of 10)	83673	NM_001110515	69666	Mm.24788	NM_001101430	ENSMUSG00000071451	Psmg4	PAC-4|mPAC4	proteasome (prosome, macropain) assembly chaperone 4	protein-coding
mm_88774.1	chr10	80356481	80356494	+	1	NA	promoter-TSS (NM_001347124)	promoter-TSS (NM_001347124)	28	NM_001347124	216166	Mm.17613	NM_183152	ENSMUSG00000035486	Plk5	6330514A18Rik	polo-like kinase 5	protein-coding
mm_71579.1	chr8	54571431	54571469	+	1	NA	intron (NM_029569, intron 1 of 6)	intron (NM_029569, intron 1 of 6)	21119	NM_029569	76294	Mm.33171	NM_029569	ENSMUSG00000031519	Asb5	1110018D09Rik	ankyrin repeat and SOCs box-containing 5	protein-coding
mm_161293.1	chr14	26460199	26460199	-	1	NA	exon (NM_032008, exon 10 of 23)	exon (NM_032008, exon 10 of 23)	74425	NM_032008	83997	Mm.36769	NM_032008	ENSMUSG00000021870	Slmap	D330001L02Rik|Miranda|Slap|mKIAA1601	sarcolemma associated protein	protein-coding
mm_122824.1	chr14	54686133	54686167	-	1	NA	promoter-TSS (NM_021437)	promoter-TSS (NM_021437)	-21	NM_021437	58248	Mm.197509	NM_021437	ENSMUSG00000040822	1700123O20Rik	MNCb-2990	RIKEN cDNA 1700123O20 gene	protein-coding
mm_12015.1	chr2	57369307	57369318	+	1	NA	3' UTR (NM_010274, exon 17 of 17)	3' UTR (NM_010274, exon 17 of 17)	130930	NM_010274	14571	Mm.3711	NM_010274	ENSMUSG00000026827	Gpd2	AA408484|AI448216|AU021455|AW494132|GPDH|Gdm1|Gpd-m|Gpdh-m|TISP38	glycerol phosphate dehydrogenase 2, mitochondrial	protein-coding
mm_70638.1	chr8	13907737	13907745	+	1	NA	promoter-TSS (NM_025785)	promoter-TSS (NM_025785)	2	NM_001347316	66822	Mm.37950	NM_025785	ENSMUSG00000038365	Fbxo25	9130015I06Rik|AI649137|Fbx25	F-box protein 25	protein-coding
mm_59961.1	chr7	30427621	30427628	+	1	NA	intron (NM_172142, intron 10 of 10)	intron (NM_172142, intron 10 of 10)	4320	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_131742.1	chr16	22059008	22059016	+	1	NA	TTS (NM_183029)	TTS (NM_183029)	49528	NR_027488	75826	Mm.297431	NM_029457	ENSMUSG00000022855	Senp2	2310007L05Rik|4930538C18Rik|AI646780|AW554757|Smt3ip2|SuPr-1|mKIAA1331	SUMO/sentrin specific peptidase 2	protein-coding
mm_19938.1	chr2	116065945	116065965	-	1	NA	promoter-TSS (NM_010825)	promoter-TSS (NM_010825)	-897	NM_010825	17536	Mm.247566	NM_010825	ENSMUSG00000027210	Meis2	A430109D20Rik|Mrg1|Stra10	Meis homeobox 2	protein-coding
mm_18369.1	chr2	59882557	59882612	-	1	NA	promoter-TSS (NM_028118)	promoter-TSS (NM_028118)	22	NM_001159636	72137	Mm.288734	NM_028118	ENSMUSG00000026988	Wdsub1	1700048E19Rik|2610014F08Rik	WD repeat, SAM and U-box domain containing 1	protein-coding
mm_90554.1	chr10	128108958	128109004	+	1	NA	exon (NM_054078, exon 3 of 30)	exon (NM_054078, exon 3 of 30)	16198	NM_054078	116848	Mm.252213	NM_054078	ENSMUSG00000040054	Baz2a	AA415431|C030005G16Rik|C78388|Tip5|Walp3|mKIAA0314	bromodomain adjacent to zinc finger domain, 2A	protein-coding
mm_29079.1	chr3	104089534	104089563	-	1	NA	exon (NM_133853, exon 4 of 22)	exon (NM_133853, exon 4 of 22)	-121232	NR_030676	100125931	Mm.400392	NR_030676	ENSMUSG00000089998	Phtf1os	A130049A11Rik	putative homeodomain transcription factor 1, opposite strand	ncRNA
mm_6683.1	chr1	80631396	80631422	-	1	NA	intron (NM_175291, intron 3 of 55)	intron (NM_175291, intron 3 of 55)	33943	NM_001285927	210293	Mm.133473	NM_175291	ENSMUSG00000038608	Dock10	9330153B10Rik|A630054M16Rik|Jr4|Jr5|R75174|ZIZ3|Zizimin3|mKIAA0694	dedicator of cytokinesis 10	protein-coding
mm_59911.1	chr7	30414493	30414586	+	1	NA	exon (NM_011662, exon 3 of 5)	exon (NM_011662, exon 3 of 5)	751	NM_011662	22177	Mm.46301	NM_011662	ENSMUSG00000030579	Tyrobp	DAP12|KARAP|Ly83	TYRO protein tyrosine kinase binding protein	protein-coding
mm_47497.1	chr5	124032215	124032290	-	1	NA	promoter-TSS (NM_177876)	promoter-TSS (NM_177876)	8	NM_177876	330192	Mm.4079	NM_177876	ENSMUSG00000066278	Vps37b	2300007F24Rik|AI415429|BC026744	vacuolar protein sorting 37B	protein-coding
mm_23589.1	chr3	64039300	64039300	+	1	NA	Intergenic	ERVB4_1-I_MM-int|LTR|ERVK	-42342	NM_019918	56544	Mm.57069	NM_019918	ENSMUSG00000027824	Vmn2r1	Casrl1|EG56544|V2r83	vomeronasal 2, receptor 1	protein-coding
mm_66486.1	chr7	45019299	45019341	-	1	NA	intron (NM_009101, intron 1 of 5)	intron (NM_009101, intron 1 of 5)	1313	NM_009101	20130	Mm.389894	NM_009101	ENSMUSG00000038387	Rras	AI573426	related RAS viral (r-ras) oncogene	protein-coding
mm_95582.1	chr11	52860425	52860426	+	1	NA	intron (NM_177059, intron 3 of 15)	intron (NM_177059, intron 3 of 15)	95719	NM_177059	320027	Mm.44518	NM_177059	ENSMUSG00000036264	Fstl4	B230374F23Rik|SPIG1|mKIAA1061	follistatin-like 4	protein-coding
mm_35420.1	chr4	35130758	35130761	-	1	NA	intron (NM_178061, intron 1 of 3)	intron (NM_178061, intron 1 of 3)	-21296	NM_199157	387510	Mm.386929	NM_199157	ENSMUSG00000042993	Ifnk	-	interferon kappa	protein-coding
mm_91591.1	chr10	40302187	40302206	-	1	NA	promoter-TSS (NM_009665)	promoter-TSS (NM_009665)	-8	NM_009665	11702	Mm.253533	NM_009665	ENSMUSG00000075232	Amd1	AdoMetDC|Amd-1|SAMDC|SAMDC 1|adoMetDC1	S-adenosylmethionine decarboxylase 1	protein-coding
mm_55158.1	chr6	51592289	51592314	-	1	NA	Intergenic	Intergenic	47778	NM_001127348	71982	Mm.294166	NM_028035	ENSMUSG00000038301	Snx10	2410004M09Rik	sorting nexin 10	protein-coding
mm_119096.1	chr14	30895431	30895448	+	1	NA	exon (NM_001289633, exon 13 of 22)	exon (NM_001289633, exon 13 of 22)	8963	NM_001289632	16427	Mm.34819	NM_018746	ENSMUSG00000021922	Itih4	ITI-HC4|Itih-4|PK-120	inter alpha-trypsin inhibitor, heavy chain 4	protein-coding
mm_24324.1	chr3	89436737	89436761	+	1	NA	promoter-TSS (NM_146131)	promoter-TSS (NM_146131)	45	NM_146131	229534	Mm.65906	NM_146131	ENSMUSG00000042613	Pbxip1	4732463H20Rik	pre B cell leukemia transcription factor interacting protein 1	protein-coding
mm_98846.1	chr11	97658985	97658997	+	1	NA	Intergenic	Intergenic	-4421	NM_139311	246198	Mm.23685	NM_139311	ENSMUSG00000038437	Mllt6	AI315037|Af17	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 6	protein-coding
mm_4174.1	chr1	171121702	171121708	+	1	NA	promoter-TSS (NM_001081275)	promoter-TSS (NM_001081275)	44	NM_001081275	75472	Mm.32760	NM_029301	ENSMUSG00000026649	Cfap126	1700009P17Rik|AV282292|Flattop|Fltp	cilia and flagella associated protein 126	protein-coding
mm_8438.1	chr1	152766324	152766352	-	1	NA	promoter-TSS (NM_026369)	promoter-TSS (NM_026369)	-33	NM_001346117	19731	Mm.245270	NM_016846	ENSMUSG00000026482	Rgl1	Rgl|mKIAA0959	ral guanine nucleotide dissociation stimulator,-like 1	protein-coding
mm_168726.1	chr12	110695359	110695363	-	1	NA	exon (NM_010480, exon 3 of 11)	exon (NM_010480, exon 3 of 11)	1034	NM_010480	15519	Mm.1843	NM_010480	ENSMUSG00000021270	Hsp90aa1	86kDa|89kDa|AL024080|AL024147|Hsp86-1|Hsp89|Hsp90|Hspca|hsp4	heat shock protein 90, alpha (cytosolic), class A member 1	protein-coding
mm_8229.1	chr1	138175284	138175311	-	1	NA	promoter-TSS (NM_001268286)	promoter-TSS (NM_001268286)	8	NM_011210	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_52192.1	chr6	99774940	99774952	+	1	NA	Intergenic	Intergenic	-48554	NM_001170419	50501	Mm.87365	NM_015768	ENSMUSG00000030069	Prok2	Bv8|PK2|Prok1	prokineticin 2	protein-coding
mm_139641.1	chr17	57377572	57377588	+	1	NA	intron (NM_010130, intron 2 of 21)	Lx5b|LINE|L1	18894	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_4408.1	chr1	172481801	172481819	+	1	NA	promoter-TSS (NM_001145800)	promoter-TSS (NM_001145800)	-403	NM_001145800	93842	Mm.214530	NM_033608	ENSMUSG00000037995	Igsf9	644ETD8|Dasm1|Kiaa1355-hp|NRT1|Ncaml|mKIAA1355	immunoglobulin superfamily, member 9	protein-coding
mm_68828.1	chr7	126200330	126200335	-	1	NA	promoter-TSS (NM_028816)	promoter-TSS (NM_028816)	76	NM_028816	74204	Mm.235663	NM_028816	ENSMUSG00000000131	Xpo6	2610005L19Rik|AL022631|C230091E20Rik|R75304|Ranbp20|mKIAA0370	exportin 6	protein-coding
mm_61608.1	chr7	80030759	80030774	+	1	NA	intron (NM_175433, intron 1 of 4)	MT2B|LTR|ERVL	4538	NM_175433	209225	Mm.290925	NM_175433	ENSMUSG00000048897	Zfp710	5430400N05Rik|9830165K13|AI324798|Znf710	zinc finger protein 710	protein-coding
mm_104540.1	chr11	96713350	96713405	-	1	NA	intron (NM_001177898, intron 9 of 10)	intron (NM_001177898, intron 9 of 10)	64178	NM_028965	74479	Mm.270781	NM_028965	ENSMUSG00000020876	Snx11	4933439F10Rik|A930041K09Rik|AI117694	sorting nexin 11	protein-coding
mm_107101.1	chr12	17728257	17728264	+	1	NA	intron (NM_016677, intron 1 of 3)	intron (NM_016677, intron 1 of 3)	37446	NM_016677	53602	Mm.313619	NM_016677	ENSMUSG00000071379	Hpcal1	NVP-3|Nvp3|VILIP3|Vnsl3|Vsnl3	hippocalcin-like 1	protein-coding
mm_70914.1	chr8	25720136	25720148	+	1	NA	promoter-TSS (NM_001293703)	promoter-TSS (NM_001293703)	94	NR_121643	71910	Mm.385055	NM_028000	ENSMUSG00000031570	Plpp5	1810019D05Rik|2310022A04Rik|AW045471|Ppapdc1|Ppapdc1b	phospholipid phosphatase 5	protein-coding
mm_90500.1	chr10	128035588	128035594	+	1	NA	5' UTR (NM_013608, exon 1 of 8)	5' UTR (NM_013608, exon 1 of 8)	245	NM_001113199	17938	Mm.3746	NM_013608	ENSMUSG00000061315	Naca	AL022831|AL024382|Gm1878|mKIAA0363|skNAC	nascent polypeptide-associated complex alpha polypeptide	protein-coding
mm_112468.1	chr13	5868382	5868394	+	1	NA	3' UTR (NM_011803, exon 4 of 4)	3' UTR (NM_011803, exon 4 of 4)	6899	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_119991.1	chr14	55591162	55591175	+	1	NA	promoter-TSS (NM_011190)	promoter-TSS (NM_011190)	-67	NM_001029855	19188	Mm.371573	NM_011190	ENSMUSG00000079197	Psme2	AA589371|AI788882|PA28b	proteasome (prosome, macropain) activator subunit 2 (PA28 beta)	protein-coding
mm_32500.1	chr4	108459782	108459795	+	1	NA	intron (NM_175472, intron 1 of 30)	CpG	362	NM_175472	230594	Mm.25181	NM_175472	ENSMUSG00000034610	Zcchc11	6030404K05Rik|9230115F04Rik|PPAPD3|mKIAA0191	zinc finger, CCHC domain containing 11	protein-coding
mm_86309.1	chr9	122805460	122805475	-	1	NA	promoter-TSS (NM_001013405)	promoter-TSS (NM_001013405)	-80	NM_001013405	382117	Mm.215892	NM_001013405	ENSMUSG00000046603	Tcaim	D9Ertd402e|Gm1129|TOAG-1	T cell activation inhibitor, mitochondrial	protein-coding
mm_156627.1	chrX	155262461	155262481	+	1	NA	promoter-TSS (NM_019736)	promoter-TSS (NM_019736)	28	NM_019736	56360	Mm.268710	NM_019736	ENSMUSG00000025287	Acot9	0610041P13Rik|Acate2|C76421|MT-ACT48|MTE-2|U8|p48	acyl-CoA thioesterase 9	protein-coding
mm_56927.1	chr6	119467211	119467223	-	1	NA	promoter-TSS (NM_001271758)	promoter-TSS (NM_001271758)	-6	NM_001271758	22419	Mm.321818	NM_009525	ENSMUSG00000030170	Wnt5b	AW545702|Wnt-5b	wingless-type MMTV integration site family, member 5B	protein-coding
mm_28570.1	chr3	93445067	93445073	-	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	2740	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_18679.1	chr2	71338444	71338481	-	1	NA	intron (NM_172436, intron 3 of 17)	intron (NM_172436, intron 3 of 17)	29092	NM_172436	78830	Mm.30928	NM_172436	ENSMUSG00000027010	Slc25a12	2610002D09Rik|AI839531|B230107K20Rik|BB129864	solute carrier family 25 (mitochondrial carrier, Aralar), member 12	protein-coding
mm_100312.1	chr11	117978103	117978176	+	1	NA	Intergenic	Intergenic	-8718	NM_133757	74451	Mm.28864	NM_133757	ENSMUSG00000017715	Pgs1	2610019F11Rik|4933424M23Rik|SAF	phosphatidylglycerophosphate synthase 1	protein-coding
mm_127263.1	chr15	99712668	99712690	+	1	NA	3' UTR (NM_031842, exon 13 of 13)	3' UTR (NM_031842, exon 13 of 13)	-4914	NM_010271	14555	Mm.252391	NM_010271	ENSMUSG00000023019	Gpd1	AI747587|Gdc-1|Gdc1|mKIAA4010	glycerol-3-phosphate dehydrogenase 1 (soluble)	protein-coding
mm_8773.1	chr1	161038531	161038537	-	1	NA	TTS (NR_028543)	TTS (NR_028543)	442	NR_028543	100217446		NR_028543	ENSMUSG00000064968	Snord47	MBII-96	small nucleolar RNA, C/D box 47	snoRNA
mm_66958.1	chr7	62423310	62423319	-	1	NA	Intergenic	Intergenic	-3175	NM_011746	22652	Mm.146	NM_011746	ENSMUSG00000070527	Mkrn3	D7H15S9-1|Zfp127	makorin, ring finger protein, 3	protein-coding
mm_39360.1	chr5	9113246	9113262	+	1	NA	intron (NM_001081029, intron 2 of 4)	intron (NM_001081029, intron 2 of 4)	12517	NM_001081029	652925	Mm.439954	NM_001081029	ENSMUSG00000079659	Tmem243	4930420K17Rik|E030031F02Rik	transmembrane protein 243, mitochondrial	protein-coding
mm_7351.1	chr1	106594440	106594453	-	1	NA	intron (NM_009741, intron 1 of 1)	intron (NM_009741, intron 1 of 1)	-47815	NR_106164	102466254		NR_106164	ENSMUSG00000098344	Mir3473f	Gm27846|mmu-mir-3473f	microRNA 3473f	ncRNA
mm_142537.1	chr17	46552841	46552859	-	1	NA	TTS (NR_105942)	TTS (NR_105942)	1039	NR_105942	102466778		NR_105942	ENSMUSG00000106514	Mir6976	mmu-mir-6976	microRNA 6976	ncRNA
mm_72274.1	chr8	75100076	75100087	+	1	NA	3' UTR (NM_010442, exon 5 of 5)	3' UTR (NM_010442, exon 5 of 5)	6463	NM_010442	15368	Mm.276389	NM_010442	ENSMUSG00000005413	Hmox1	D8Wsu38e|HO-1|HO1|Hemox|Hmox|Hsp32	heme oxygenase 1	protein-coding
mm_63527.1	chr7	127913012	127913014	+	1	NA	intron (NM_026370, intron 1 of 10)	intron (NM_026370, intron 1 of 10)	496	NM_026370	67773	Mm.425492	NM_026370	ENSMUSG00000030801	Kat8	2010203C02Rik|5830450F21Rik|D7Ertd629e|MOF|Myst1	K(lysine) acetyltransferase 8	protein-coding
mm_93691.1	chr10	117820530	117820566	-	1	NA	exon (NM_024457, exon 5 of 8)	exon (NM_024457, exon 5 of 8)	25426	NM_024457	215449	Mm.233009	NM_024457	ENSMUSG00000052681	Rap1b	2810443E11Rik	RAS related protein 1b	protein-coding
mm_62269.1	chr7	99535513	99535591	+	1	NA	promoter-TSS (NM_178220)	promoter-TSS (NM_178220)	66	NM_177231	109689	Mm.260193	NM_177231	ENSMUSG00000018909	Arrb1	1200006I17Rik|AW208571|G430100A01Rik	arrestin, beta 1	protein-coding
mm_80595.1	chr9	85845502	85845505	+	1	NA	3' UTR (NM_001164792, exon 2 of 2)	3' UTR (NM_001164792, exon 2 of 2)	2651	NM_001164792	21983	Mm.20864	NM_011627	ENSMUSG00000035274	Tpbg	5T4|AW495680|WAIF1	trophoblast glycoprotein	protein-coding
mm_138448.1	chr17	35135550	35135560	+	1	NA	promoter-TSS (NM_001252469)	promoter-TSS (NM_001252469)	-159	NM_001252469	224727	Mm.203962	NM_057171	ENSMUSG00000024392	Bag6	2410045D21Rik|AA408914|BAG-6|Bat3|D17H6S52E|G3|Scythe	BCL2-associated athanogene 6	protein-coding
mm_84749.1	chr9	75409952	75410039	-	1	NA	promoter-TSS (NR_040719)	promoter-TSS (NR_040719)	21	NM_015806	50772	Mm.480076	NM_015806	ENSMUSG00000042688	Mapk6	2610021I23Rik|D130053K17Rik|Erk3|Mapk4|Mapk63|Prkm4|Prkm6	mitogen-activated protein kinase 6	protein-coding
mm_68898.1	chr7	126450153	126450176	-	1	NA	exon (NM_007504, exon 14 of 23)	exon (NM_007504, exon 14 of 23)	12909	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_94322.1	chr11	4238108	4238116	+	1	NA	intron (NM_001013365, intron 1 of 2)	intron (NM_001013365, intron 1 of 2)	1327	NM_001013365	18413	Mm.131422	NM_001013365	ENSMUSG00000058755	Osm	OncoM	oncostatin M	protein-coding
mm_92889.1	chr10	82771130	82771130	-	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	-6989	NM_010914	18045	Mm.245998	NM_010914	ENSMUSG00000020248	Nfyb	AA985999|Cbf-A	nuclear transcription factor-Y beta	protein-coding
mm_32938.1	chr4	119262265	119262266	+	1	NA	3' UTR (NM_153105, exon 4 of 4)	3' UTR (NM_153105, exon 4 of 4)	6796	NM_001038590	242653	Mm.130701	NM_153105	ENSMUSG00000066058	Cldn19	-	claudin 19	protein-coding
mm_154424.1	chrM	381	394	-	1	NA	NA	Intergenic	NA	NA								
mm_134400.1	chr16	17554807	17554814	-	1	NA	intron (NM_029053, intron 4 of 8)	RMER17A2|LTR|ERVK	6437	NM_029053	74685	Mm.38634	NM_029053	ENSMUSG00000022759	Lrrc74b	4930451C15Rik|mCG12354|mCP17390	leucine rich repeat containing 74B	protein-coding
mm_143995.1	chr17	88002527	88002539	-	1	NA	intron (NM_001081034, intron 12 of 22)	B3|SINE|B2	27483	NM_010830	17688	Mm.18210	NM_010830	ENSMUSG00000005370	Msh6	AU044881|AW550279|GTBP|Gtmbp	mutS homolog 6	protein-coding
mm_81428.1	chr9	109057296	109057309	+	1	NA	TTS (NM_011637)	TTS (NM_011637)	1949	NM_001012236	22040	Mm.439964	NM_011637	ENSMUSG00000049734	Trex1	AU041952	three prime repair exonuclease 1	protein-coding
mm_161413.1	chr15	18820485	18820485	+	1	NA	5' UTR (NM_009865, exon 1 of 12)	5' UTR (NM_009865, exon 1 of 12)	156	NM_009865	320873	Mm.117794	NM_009865	ENSMUSG00000022321	Cdh10	A830016G23Rik|C030003B10Rik|C030011H18Rik	cadherin 10	protein-coding
mm_89284.1	chr10	87871937	87871949	+	1	NA	intron (NM_001314010, intron 3 of 4)	intron (NM_001314010, intron 3 of 4)	10832	NM_001111276	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_90436.1	chr10	127642976	127643034	+	1	NA	promoter-TSS (NM_009284)	promoter-TSS (NM_009284)	19	NM_009284	20852	Mm.121721	NM_009284	ENSMUSG00000002147	Stat6	-	signal transducer and activator of transcription 6	protein-coding
mm_36001.1	chr4	56741404	56741417	-	1	NA	promoter-TSS (NM_025271)	promoter-TSS (NM_025271)	15	NM_025271	11471	Mm.251434	NM_025271	ENSMUSG00000070980	Actl7b	Tact1	actin-like 7b	protein-coding
mm_126961.1	chr15	92340333	92340352	+	1	NA	3' UTR (NM_001159647, exon 24 of 24)	3' UTR (NM_001159647, exon 24 of 24)	-56468	NM_001164593	239618	Mm.309826	NM_001164593	ENSMUSG00000036218	Pdzrn4	1110017D07Rik|LNX4|SAMCAP3L|mKIAA3027	PDZ domain containing RING finger 4	protein-coding
mm_14324.1	chr2	129366000	129366008	+	1	NA	exon (NM_008361, exon 6 of 7)	exon (NM_008361, exon 6 of 7)	-3898	NR_015474	329514	Mm.207315	NM_177848	ENSMUSG00000074805	Il1bos	9430083I22|Gm14047|OTTMUSG00000015529	interleukin 1 beta, opposite strand	ncRNA
mm_168065.1	chr10	103214153	103214155	-	1	NA	TTS (NM_029134)	TTS (NM_029134)	22168	NM_001163559	74978	Mm.483817	NM_029134	ENSMUSG00000019892	Lrriq1	4930503E15Rik|Gm1557	leucine-rich repeats and IQ motif containing 1	protein-coding
mm_92204.1	chr10	68136780	68136782	-	1	NA	intron (NM_023598, intron 4 of 9)	intron (NM_023598, intron 4 of 9)	141945	NM_023598	71371	Mm.440357	NM_023598	ENSMUSG00000019947	Arid5b	4930580B11|5430435G07Rik|AI467247|Desrt|Mrf2|Mrf2alpha|Mrf2beta	AT rich interactive domain 5B (MRF1-like)	protein-coding
mm_77048.1	chr8	109576743	109576761	-	1	NA	exon (NM_017370, exon 4 of 5)	exon (NM_017370, exon 4 of 5)	2420	NM_017370	15439	Mm.26730	NM_017370	ENSMUSG00000031722	Hp	HP-1|preHP2	haptoglobin	protein-coding
mm_89699.1	chr10	97607292	97607338	+	1	NA	5' UTR (NM_008438, exon 1 of 3)	5' UTR (NM_008438, exon 1 of 3)	110	NM_008438	16545	Mm.6228	NM_008438	ENSMUSG00000019932	Kera	CNA2|SLRR2B	keratocan	protein-coding
mm_1873.1	chr1	85600869	85600879	+	1	NA	5' UTR (NM_001013817, exon 1 of 17)	5' UTR (NM_001013817, exon 1 of 17)	171	NM_001013817	434484	Mm.445821	NM_001013817	ENSMUSG00000070031	Sp140	-	Sp140 nuclear body protein	protein-coding
mm_166369.1	chr5	125304233	125304249	+	1	NA	exon (NM_001205082, exon 2 of 12)	exon (NM_001205082, exon 2 of 12)	36853	NM_016741	20778	Mm.282242	NM_016741	ENSMUSG00000037936	Scarb1	AI120173|CD36|Cd36l1|Chohd1|Cla-1|Cla1|D5Ertd460e|Hdlq1|Hlb398|SR-B1|SR-BI|SRBI|Srb1|mSR-BI	scavenger receptor class B, member 1	protein-coding
mm_100306.1	chr11	117976218	117976228	+	1	NA	Intergenic	Intergenic	-6857	NM_007707	12702	Mm.3468	NM_007707	ENSMUSG00000053113	Socs3	Cis3|Cish3|EF-10|Ef10|SSI-3|Ssi3	suppressor of cytokine signaling 3	protein-coding
mm_150429.1	chr19	37465249	37465265	+	1	NA	promoter-TSS (NR_131009)	promoter-TSS (NR_131009)	3	NR_131009	78640	Mm.234265	NR_131008		1700122C19Rik	-	RIKEN cDNA 1700122C19 gene	ncRNA
mm_144680.1	chr18	34759101	34759112	+	1	NA	5' UTR (NM_175104, exon 1 of 5)	5' UTR (NM_175104, exon 1 of 5)	200	NM_175104	66306	Mm.29424	NM_175104	ENSMUSG00000034300	Fam53c	2810012G03Rik|Gm21179	family with sequence similarity 53, member C	protein-coding
mm_51083.1	chr6	67017640	67017652	+	1	NA	3' UTR (NM_001177559, exon 5 of 5)	3' UTR (NM_001177559, exon 5 of 5)	-18953	NR_040278	320172	Mm.449039	NR_040278	ENSMUSG00000087231	E230016M11Rik	-	RIKEN cDNA E230016M11 gene	ncRNA
mm_113054.1	chr13	23692092	23692118	+	1	NA	intron (NM_023422, intron 1 of 1)	intron (NM_023422, intron 1 of 1)	-3706	NM_010377	107970	Mm.8048	NM_010377	ENSMUSG00000036211	Hist1h1t	H1.6|H1ft|H1t	histone cluster 1, H1t	protein-coding
mm_126194.1	chr15	78772658	78772662	+	1	NA	intron (NM_008595, intron 1 of 7)	intron (NM_008595, intron 1 of 7)	785	NM_008595	17305	Mm.149235	NM_008595	ENSMUSG00000018169	Mfng	AW546563	MFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	protein-coding
mm_82212.1	chr9	124143945	124143967	+	1	NA	Intergenic	Intergenic	22413	NM_009917	12774	Mm.14302	NM_009917	ENSMUSG00000079227	Ccr5	AM4-7|CD195|Cmkbr5	chemokine (C-C motif) receptor 5	protein-coding
mm_79117.1	chr9	46282998	46283024	+	1	NA	promoter-TSS (NM_146000)	promoter-TSS (NM_146000)	-1	NM_146000	215051	Mm.32648	NM_146000	ENSMUSG00000032077	Bud13	AV305342|D030060M11Rik	BUD13 homolog	protein-coding
mm_28890.1	chr3	97869690	97869693	-	1	NA	intron (NM_001039376, intron 1 of 46)	intron (NM_001039376, intron 1 of 46)	19016	NM_001289702	83679	Mm.129840	NM_031401	ENSMUSG00000038170	Pde4dip	4732458A06Rik|9430063L05Rik|C87016|D130016K21Rik|D3Bwg1078e|Usmg4|mKIAA0454	phosphodiesterase 4D interacting protein (myomegalin)	protein-coding
mm_129100.1	chr15	76013173	76013183	-	1	NA	intron (NM_134087, intron 1 of 4)	intron (NM_134087, intron 1 of 4)	1158	NM_134087	105732	Mm.267178	NM_134087	ENSMUSG00000046761	Fam83h	AA409316	family with sequence similarity 83, member H	protein-coding
mm_56193.1	chr6	88825845	88825848	-	1	NA	3' UTR (NM_001166251, exon 8 of 8)	3' UTR (NM_001166251, exon 8 of 8)	16089	NM_030251	80283	Mm.166858	NM_030251	ENSMUSG00000030083	Abtb1	AI847549|BC003234|BPOZ|EF1ABP	ankyrin repeat and BTB (POZ) domain containing 1	protein-coding
mm_42919.1	chr5	122719926	122719937	+	1	NA	intron (NM_001310720, intron 5 of 10)	Lx3_Mus|LINE|L1	12387	NM_001310718	18438	Mm.290884	NM_011026	ENSMUSG00000029470	P2rx4	AI504491|AW555605|D5Ertd444e|P2X4	purinergic receptor P2X, ligand-gated ion channel 4	protein-coding
mm_80277.1	chr9	73010350	73010372	+	1	NA	exon (NM_001286546, exon 7 of 8)	exon (NM_001286546, exon 7 of 8)	24857	NM_028181	72278	Mm.268475	NM_028181	ENSMUSG00000034563	Ccpg1	1700030B06Rik|1810073J13Rik|9430028F23Rik|AI426686|AI875170|CPR8|D9Ertd392e	cell cycle progression 1	protein-coding
mm_132082.1	chr16	30198115	30198137	+	1	NA	Intergenic	RMER17B|LTR|ERVK	69406	NM_027904	71756	Mm.290614	NM_027904	ENSMUSG00000023176	Cpn2	1300018K11Rik	carboxypeptidase N, polypeptide 2	protein-coding
mm_36782.1	chr4	102989631	102989667	-	1	NA	non-coding (NR_040444, exon 1 of 4)	non-coding (NR_040444, exon 1 of 4)	106	NR_040444	100504717	Mm.394445	NR_040444	ENSMUSG00000085181	Gm12709	OTTMUSG00000008056	predicted gene 12709	ncRNA
mm_46575.1	chr5	107289531	107289551	-	1	NA	promoter-TSS (NM_011578)	promoter-TSS (NM_011578)	54	NM_011578	21814	Mm.200775	NM_011578	ENSMUSG00000029287	Tgfbr3	1110036H20Rik|AU015626|AW215636|TBRIII	transforming growth factor, beta receptor III	protein-coding
mm_35820.1	chr4	46992039	46992042	-	1	NA	promoter-TSS (NM_001081141)	promoter-TSS (NM_001081141)	-326	NM_001081141	242425	Mm.101909	NM_001081141	ENSMUSG00000039809	Gabbr2	GABABR2|Gb2|Gm425|Gpr51	gamma-aminobutyric acid (GABA) B receptor, 2	protein-coding
mm_141399.1	chr17	29263907	29263913	-	1	NA	promoter-TSS (NM_026845)	promoter-TSS (NM_026845)	61	NM_026845	68816	Mm.328928	NM_026845	ENSMUSG00000024007	Ppil1	1110060O10Rik|AI327391|Cypl1	peptidylprolyl isomerase (cyclophilin)-like 1	protein-coding
mm_63187.1	chr7	125552314	125552323	+	1	NA	promoter-TSS (NM_001008700)	promoter-TSS (NM_001008700)	36	NM_001008700	16190	Mm.233802	NM_010557	ENSMUSG00000030748	Il4ra	CD124|Il4r	interleukin 4 receptor, alpha	protein-coding
mm_43773.1	chr5	141241594	141241605	+	1	NA	promoter-TSS (NM_177879)	promoter-TSS (NM_177879)	65	NM_177879	330222	Mm.151931	NM_177879	ENSMUSG00000039683	Sdk1	5330440E10|6720466O15Rik	sidekick cell adhesion molecule 1	protein-coding
mm_140833.1	chr17	23669922	23669938	-	1	NA	exon (NM_001008425, exon 8 of 13)	exon (NM_001008425, exon 8 of 13)	-3678	NM_181821	353502	Mm.359030	NM_181821	ENSMUSG00000023904	Hcfc1r1	HPIP	host cell factor C1 regulator 1 (XPO1-dependent)	protein-coding
mm_89993.1	chr10	112083335	112083341	+	1	NA	promoter-TSS (NM_026223)	promoter-TSS (NM_026223)	-16	NM_001347157	67537	Mm.292351	NM_026223	ENSMUSG00000020214	Glipr1l2	4921508O11Rik	GLI pathogenesis-related 1 like 2	protein-coding
mm_128520.1	chr15	54278296	54278312	-	1	NA	5' UTR (NM_008764, exon 1 of 5)	5' UTR (NM_008764, exon 1 of 5)	180	NM_008764	18383	Mm.15383	NM_008764	ENSMUSG00000063727	Tnfrsf11b	OCIF|Opg|TR1	tumor necrosis factor receptor superfamily, member 11b (osteoprotegerin)	protein-coding
mm_65831.1	chr7	29179408	29179437	-	1	NA	intron (NM_026545, intron 1 of 6)	intron (NM_026545, intron 1 of 6)	1251	NM_026545	57296	Mm.273152	NM_026545	ENSMUSG00000030591	Psmd8	6720456J22Rik|AA407360|AL033291|AL033322|AL033323|C76433	proteasome (prosome, macropain) 26S subunit, non-ATPase, 8	protein-coding
mm_12699.1	chr2	76499109	76499128	+	1	NA	intron (NM_001290735, intron 1 of 4)	intron (NM_001290735, intron 1 of 4)	112	NM_001290735	99031	Mm.240435	NM_145525	ENSMUSG00000042359	Osbpl6	1110062M20Rik|AI596402|ORP-6|mKIAA4128	oxysterol binding protein-like 6	protein-coding
mm_154157.1	chr19	58455609	58455622	-	1	NA	promoter-TSS (NM_010279)	promoter-TSS (NM_010279)	-217	NM_010279	14585	Mm.88367	NM_010279	ENSMUSG00000025089	Gfra1	AU042498	glial cell line derived neurotrophic factor family receptor alpha 1	protein-coding
mm_32856.1	chr4	118359983	118360032	+	1	NA	promoter-TSS (NM_026601)	promoter-TSS (NM_026601)	8	NR_003946	68180	Mm.193212	NM_026601	ENSMUSG00000006395	Hyi	2700033B16Rik|6430559E15Rik|HT036	hydroxypyruvate isomerase (putative)	protein-coding
mm_53862.1	chr6	149310329	149310335	+	1	NA	5' UTR (NM_001289662, exon 2 of 5)	5' UTR (NM_001289662, exon 2 of 5)	918	NM_001289662	67246	Mm.333515	NM_026054	ENSMUSG00000032712	2810474O19Rik	6720435I21Rik|AA536804|AU020969|GET|Kiaa1551	RIKEN cDNA 2810474O19 gene	protein-coding
mm_1362.1	chr1	66364666	66364680	+	1	NA	intron (NM_001310634, intron 3 of 14)	intron (NM_001310634, intron 3 of 14)	42949	NM_001310634	17756	Mm.256966	NM_008632	ENSMUSG00000015222	Map2	G1-397-34|MAP-2|Mtap-2|Mtap2|repro4	microtubule-associated protein 2	protein-coding
mm_119389.1	chr14	41137392	41137403	+	1	NA	Intergenic	Lx9|LINE|L1	5609	NM_023134	20387	Mm.46062	NM_023134	ENSMUSG00000021789	Sftpa1	SP-A|Sftp-1|Sftp1	surfactant associated protein A1	protein-coding
mm_64670.1	chr7	4445638	4445662	-	1	NA	promoter-TSS (NM_001290411)	promoter-TSS (NM_001290411)	7	NM_175372	108841	Mm.413106	NM_175372	ENSMUSG00000008435	Rdh13	8430425D21Rik	retinol dehydrogenase 13 (all-trans and 9-cis)	protein-coding
mm_160904.1	chr11	77188898	77188898	-	1	NA	promoter-TSS (NM_176965)	promoter-TSS (NM_176965)	70	NM_176965	319634	Mm.108786	NM_176965	ENSMUSG00000050944	Efcab5	4930563A03Rik	EF-hand calcium binding domain 5	protein-coding
mm_130155.1	chr15	91191441	91191455	-	1	NA	exon (NM_011994, exon 1 of 10)	exon (NM_011994, exon 1 of 10)	359	NM_011994	26874	Mm.295456	NM_011994	ENSMUSG00000055782	Abcd2	ABC39|ALDL1|ALDR|ALDRP	ATP-binding cassette, sub-family D (ALD), member 2	protein-coding
mm_121707.1	chr14	15438959	15438963	-	1	NA	promoter-TSS (NM_146052)	promoter-TSS (NM_146052)	26	NM_146052	218763	Mm.138039	NM_146052	ENSMUSG00000045201	Lrrc3b	BC019794|LRP15	leucine rich repeat containing 3B	protein-coding
mm_61737.1	chr7	82174827	82174854	+	1	NA	Intergenic	CpG	-85068	NM_001277955	20408	Mm.736	NM_017400	ENSMUSG00000030638	Sh3gl3	EEN-B2|SH3P13|Sh3d2c|Sh3d2c2	SH3-domain GRB2-like 3	protein-coding
mm_41210.1	chr5	88564983	88565005	+	1	NA	promoter-TSS (NM_001289775)	promoter-TSS (NM_001289775)	-46	NM_001289774	52822	Mm.270469	NM_027530	ENSMUSG00000029291	Rufy3	2810428M05Rik|6330416M07Rik|AW455998|AW538594|D5Bwg0860e|Ripx|Rpipx	RUN and FYVE domain containing 3	protein-coding
mm_86703.1	chr10	18532705	18532708	+	1	NA	3' UTR (NM_001163592, exon 8 of 8)	3' UTR (NM_001163592, exon 8 of 8)	13370	NM_019487	56016	Mm.35551	NM_019487	ENSMUSG00000019853	Hebp2	SOUL	heme binding protein 2	protein-coding
mm_5523.1	chr1	37865041	37865116	-	1	NA	promoter-TSS (NM_207228)	promoter-TSS (NM_207228)	4	NM_207228	211484	Mm.332756	NM_207228	ENSMUSG00000060771	Tsga10	4933432N21Rik|AI843383|Gm217|Mtsga10	testis specific 10	protein-coding
mm_88368.1	chr10	75948336	75948353	+	1	NA	promoter-TSS (NM_009514)	promoter-TSS (NM_009514)	32	NM_009514	22364	Mm.333851	NM_009514	ENSMUSG00000000903	Vpreb3	8HS-20|AI528709|Vpreb-3	pre-B lymphocyte gene 3	protein-coding
mm_25220.1	chr3	103851309	103851323	+	1	NA	intron (NM_001142960, intron 3 of 3)	intron (NM_001142960, intron 3 of 3)	-8479	NR_104070	19260	Mm.395	NM_008979	ENSMUSG00000027843	Ptpn22	70zpep|PEP|Ptpn8	protein tyrosine phosphatase, non-receptor type 22 (lymphoid)	protein-coding
mm_7584.1	chr1	125421990	125421997	-	1	NA	intron (NM_001205385, intron 2 of 12)	(A)n|Simple_repeat|Simple_repeat	13734	NM_023735	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding
mm_63912.1	chr7	139220575	139220619	+	1	NA	intron (NM_001143755, intron 4 of 8)	intron (NM_001143755, intron 4 of 8)	-7290	NM_001162540	57740	Mm.65336	NM_021302	ENSMUSG00000015981	Stk32c	PKE|Pkek|YANK3	serine/threonine kinase 32C	protein-coding
mm_34511.1	chr4	148889346	148889363	+	1	NA	intron (NM_027195, intron 2 of 15)	intron (NM_027195, intron 2 of 15)	84962	NM_027195	69743	Mm.233879	NM_027195	ENSMUSG00000028977	Casz1	2410019P08Rik|AV096627|BC040081|Cst|D4Ertd432e	castor zinc finger 1	protein-coding
mm_141584.1	chr17	32403485	32403495	-	1	NA	promoter-TSS (NM_178785)	promoter-TSS (NM_178785)	91	NM_178785	320484	Mm.122284	NM_178785	ENSMUSG00000052142	Rasal3	A430107D22Rik	RAS protein activator like 3	protein-coding
mm_81513.1	chr9	110035230	110035241	+	1	NA	exon (NM_008633, exon 7 of 19)	exon (NM_008633, exon 7 of 19)	-16786	NM_001311163	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_164810.1	chr18	32147744	32147756	+	1	NA	Intergenic	Intergenic	-8180	NM_001042767	19123	Mm.2786	NM_008934	ENSMUSG00000024386	Proc	PC	protein C	protein-coding
mm_103770.1	chr11	82006828	82006840	-	1	NA	Intergenic	Intergenic	-28743	NM_011333	20296	Mm.290320	NM_011333	ENSMUSG00000035385	Ccl2	AI323594|HC11|JE|MCAF|MCP-1|MCP1|SMC-CF|Scya2|Sigje	chemokine (C-C motif) ligand 2	protein-coding
mm_85801.1	chr9	110117449	110117469	-	1	NA	5' UTR (NM_001252682, exon 1 of 23)	5' UTR (NM_001252682, exon 1 of 23)	157	NM_001252682	72831	Mm.276305	NM_133347	ENSMUSG00000032480	Dhx30	2810477H02Rik|C130058C04Rik|Ddx30|HELG|Ret-CoR	DEAH (Asp-Glu-Ala-His) box polypeptide 30	protein-coding
mm_65158.1	chr7	19665006	19665028	-	1	NA	promoter-TSS (NM_019649)	promoter-TSS (NM_019649)	13	NM_019649	56457	Mm.290960	NM_019649	ENSMUSG00000002981	Clptm1	HS9|N14	cleft lip and palate associated transmembrane protein 1	protein-coding
mm_6723.1	chr1	82586761	82586779	-	1	NA	promoter-TSS (NM_007735)	promoter-TSS (NM_007735)	79	NM_007735	12829	Mm.40253	NM_007735	ENSMUSG00000067158	Col4a4	E130010M05Rik|[a]4(IV)	collagen, type IV, alpha 4	protein-coding
mm_52594.1	chr6	116857958	116857967	+	1	NA	Intergenic	Intergenic	-141204	NM_178768	319776	Mm.133120	NM_178768	ENSMUSG00000048108	Tmem72	C230095G01Rik	transmembrane protein 72	protein-coding
mm_138451.1	chr17	35135821	35135856	+	1	NA	intron (NM_001252469, intron 1 of 23)	intron (NM_001252469, intron 1 of 23)	124	NM_001252469	224727	Mm.203962	NM_057171	ENSMUSG00000024392	Bag6	2410045D21Rik|AA408914|BAG-6|Bat3|D17H6S52E|G3|Scythe	BCL2-associated athanogene 6	protein-coding
mm_161804.1	chr17	56393701	56393701	+	1	NA	intron (NM_172132, intron 11 of 22)	intron (NM_172132, intron 11 of 22)	25208	NR_105943	102465590		NR_105943	ENSMUSG00000098339	Mir6977	Gm27922|mmu-mir-6977	microRNA 6977	ncRNA
mm_48997.1	chr6	4756673	4756693	+	1	NA	exon (NM_130877, exon 2 of 2)	exon (NM_130877, exon 2 of 2)	9377	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_45506.1	chr5	72503408	72503417	-	1	NA	intron (NM_001122756, intron 1 of 21)	intron (NM_001122756, intron 1 of 21)	796	NM_016869	53419	Mm.332425	NM_016869	ENSMUSG00000005220	Corin	AV273130|Lrp4	corin	protein-coding
mm_55048.1	chr6	49042825	49042835	-	1	NA	exon (NM_053110, exon 2 of 11)	exon (NM_053110, exon 2 of 11)	6312	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_115149.1	chr13	105291622	105291626	+	1	NA	intron (NM_027934, intron 1 of 7)	intron (NM_027934, intron 1 of 7)	1390	NM_027934	71816	Mm.317015	NM_027934	ENSMUSG00000021720	Rnf180	3110001E11Rik|Rines	ring finger protein 180	protein-coding
mm_100438.1	chr11	119486244	119486285	+	1	NA	Intergenic	Intergenic	-5083	NM_001164636	338371	Mm.271946	NM_177394	ENSMUSG00000039850	Endov	A730011L01Rik	endonuclease V	protein-coding
mm_128451.1	chr15	50772589	50772638	-	1	NA	intron (NM_001310485, intron 5 of 7)	intron (NM_001310485, intron 5 of 7)	116436	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_10959.1	chr2	25682753	25682772	+	1	NA	promoter-TSS (NM_178036)	promoter-TSS (NM_178036)	36	NM_178036	332578	Mm.246797	NM_178036	ENSMUSG00000047356	Lcn10	9230112J07Rik	lipocalin 10	protein-coding
mm_98813.1	chr11	97279740	97279758	+	1	NA	intron (NM_008942, intron 1 of 22)	intron (NM_008942, intron 1 of 22)	827	NM_008942	19155	Mm.29824	NM_008942	ENSMUSG00000001441	Npepps	AAP-S|MP100|Psa|R74825|goku	aminopeptidase puromycin sensitive	protein-coding
mm_126117.1	chr15	78261470	78261498	+	1	NA	intron (NM_008677, intron 9 of 9)	(CA)n|Simple_repeat|Simple_repeat	16673	NM_008677	17972	Mm.2068	NM_008677	ENSMUSG00000071715	Ncf4	AI451400|p40phox	neutrophil cytosolic factor 4	protein-coding
mm_104016.1	chr11	85352626	85352640	-	1	NA	promoter-TSS (NM_001166643)	promoter-TSS (NM_001166643)	-531	NM_001166642	192197	Mm.209989	NM_138681	ENSMUSG00000059439	Bcas3	1500019F07Rik|2610028P08Rik|AU021018|BC028339|K20D4|rudhira	breast carcinoma amplified sequence 3	protein-coding
mm_63648.1	chr7	128688886	128688899	+	1	NA	promoter-TSS (NM_001346517)	promoter-TSS (NM_001346517)	22	NM_001346517	101490	Mm.490344	NM_178641	ENSMUSG00000042105	Inpp5f	5830435P03Rik|AI115354|AW561896|SAC2|cI-27|hSAC2|mKIAA0966	inositol polyphosphate-5-phosphatase F	protein-coding
mm_10292.1	chr2	10371610	10371614	+	1	NA	promoter-TSS (NM_177386)	promoter-TSS (NM_177386)	-824	NM_001198809	353282	Mm.329991	NM_177386	ENSMUSG00000061186	Sfmbt2	D2Wsu23e|D330030P06Rik	Scm-like with four mbt domains 2	protein-coding
mm_144930.1	chr18	37714713	37714729	+	1	NA	promoter-TSS (NM_033590)	promoter-TSS (NM_033590)	-113	NM_033590	93715	Mm.247203	NM_033590	ENSMUSG00000103472	Pcdhga7	-	protocadherin gamma subfamily A, 7	protein-coding
mm_50383.1	chr6	48687681	48687693	+	1	NA	intron (NM_174990, intron 2 of 2)	intron (NM_174990, intron 2 of 2)	3109	NM_174990	107526	Mm.333048	NM_174990	ENSMUSG00000054435	Gimap4	AU019574|E430007K16Rik|Ian-1|Ian1|Imap4	GTPase, IMAP family member 4	protein-coding
mm_42788.1	chr5	121483785	121483796	+	1	NA	intron (NM_001161627, intron 5 of 10)	T-rich|Low_complexity|Low_complexity	19190	NM_172125	280667	Mm.444773	NM_172125	ENSMUSG00000062438	Adam1b	Adam1|Ftna	a disintegrin and metallopeptidase domain 1b	protein-coding
mm_129003.1	chr15	74856240	74856244	-	1	NA	promoter-TSS (NM_009991)	promoter-TSS (NM_009991)	76	NM_009991	13072	Mm.377079	NM_009991	ENSMUSG00000022589	Cyp11b2	Cpn2|Cyp11b|Cyp11b-2	cytochrome P450, family 11, subfamily b, polypeptide 2	protein-coding
mm_67704.1	chr7	89903579	89903633	-	1	NA	promoter-TSS (NM_001162979)	promoter-TSS (NM_001162979)	23	NM_001162979	70884	Mm.252823	NM_001162979	ENSMUSG00000039391	Ccdc81	4921513D09Rik	coiled-coil domain containing 81	protein-coding
mm_79909.1	chr9	65460927	65460983	+	1	NA	promoter-TSS (NM_138584)	promoter-TSS (NM_138584)	18	NM_138584	27965	Mm.272475	NM_138584	ENSMUSG00000032388	Spg21	ACP33|BM-019|C78576|D9Wsu18e|GL010|MAST	spastic paraplegia 21 homolog (human)	protein-coding
mm_166172.1	chr5	27537848	27537881	+	1	NA	intron (NM_010075, intron 5 of 25)	intron (NM_010075, intron 5 of 25)	-36472	NM_028561	73526	Mm.389608	NM_028561	ENSMUSG00000048703	Speer4b	1700081O22Rik|SPEER-4B	spermatogenesis associated glutamate (E)-rich protein 4B	protein-coding
mm_126987.1	chr15	94543667	94543681	+	1	NA	promoter-TSS (NM_029926)	promoter-TSS (NM_029926)	14	NM_029926	266632	Mm.422858	NM_029926	ENSMUSG00000059883	Irak4	8430405M07Rik|9330209D03Rik|IRAK-4|NY-REN-64	interleukin-1 receptor-associated kinase 4	protein-coding
mm_149887.1	chr19	25383600	25383622	+	1	NA	intron (NM_181404, intron 4 of 13)	intron (NM_181404, intron 4 of 13)	-122095	NM_015826	50796	Mm.391208	NM_015826	ENSMUSG00000024837	Dmrt1	-	doublesex and mab-3 related transcription factor 1	protein-coding
mm_130333.1	chr15	97721112	97721170	-	1	NA	promoter-TSS (NM_008902)	promoter-TSS (NM_008902)	9	NM_008902	19011	Mm.1001	NM_008902	ENSMUSG00000022468	Endou	Pp11r|Tcl-30	endonuclease, polyU-specific	protein-coding
mm_64923.1	chr7	16257861	16257894	-	1	NA	intron (NM_007577, intron 2 of 2)	intron (NM_007577, intron 2 of 2)	1461	NM_001173550	12273	Mm.247623	NM_007577	ENSMUSG00000049130	C5ar1	C5aR|C5r1|Cd88|D7Msu1	complement component 5a receptor 1	protein-coding
mm_5664.1	chr1	42693148	42693158	-	1	NA	intron (NR_027826, intron 1 of 3)	intron (NR_027826, intron 1 of 3)	1672	NR_027826	66297	Mm.45203	NM_183252	ENSMUSG00000060424	Pantr1	2610017I09Rik|Pou3f3os|linc-Brn1a	POU domain, class 3, transcription factor 3 adjacent noncoding transcript 1	ncRNA
mm_97909.1	chr11	83473080	83473123	+	1	NA	promoter-TSS (NM_027427)	promoter-TSS (NM_027427)	-7	NM_027427	70439	Mm.181050	NM_027427	ENSMUSG00000020680	Taf15	2610111C21Rik|68kDa|TAFII68|Taf2n	TATA-box binding protein associated factor 15	protein-coding
mm_104434.1	chr11	94951594	94951650	-	1	NA	3' UTR (NM_007742, exon 51 of 51)	3' UTR (NM_007742, exon 51 of 51)	15398	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_148657.1	chr19	5510909	5510922	+	1	NA	promoter-TSS (NM_001024560)	promoter-TSS (NM_001024560)	-426	NM_001024560	225861	Mm.20071	NM_001024560	ENSMUSG00000056185	Snx32	B930037P14Rik|Snx6b	sorting nexin 32	protein-coding
mm_100327.1	chr11	118209933	118209938	+	1	NA	intron (NM_001112699, intron 1 of 12)	intron (NM_001112699, intron 1 of 12)	2807	NM_001112700	19157	Mm.86413	NM_011180	ENSMUSG00000017132	Cyth1	CLM1|CTH-1|CYTIP|Pscd1	cytohesin 1	protein-coding
mm_95277.1	chr11	45852835	45852837	+	1	NA	intron (NM_001346760, intron 1 of 11)	intron (NM_001346760, intron 1 of 11)	872	NM_001045520	216705	Mm.169673	NM_001045520	ENSMUSG00000006169	Clint1	AI642036|AW537616|C530049I24Rik|Enth|Epn4|F630206G17Rik|mKIAA0171	clathrin interactor 1	protein-coding
mm_114773.1	chr13	88821670	88821676	+	1	NA	5' UTR (NM_001037987, exon 1 of 11)	5' UTR (NM_001037987, exon 1 of 11)	201	NM_001037987	13612	Mm.125580	NM_010103	ENSMUSG00000034488	Edil3	Del-1|Del1	EGF-like repeats and discoidin I-like domains 3	protein-coding
mm_169852.1	chr16	32332220	32332221	+	1	NA	promoter-TSS (NM_177633)	promoter-TSS (NM_177633)	-32	NM_177633	224111	Mm.31275	NM_177633	ENSMUSG00000053774	Ubxn7	A630090P18|AI196514|Ubxd7|mKIAA0794	UBX domain protein 7	protein-coding
mm_54749.1	chr6	41033046	41033184	-	1	NA	exon (NM_023333, exon 3 of 5)	exon (NM_023333, exon 3 of 5)	2394	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_162308.1	chr1	37089659	37089660	+	1	NA	Intergenic	Intergenic	-128619	NM_001282010	12790	Mm.214224	NM_009918	ENSMUSG00000026114	Cnga3	CNG3	cyclic nucleotide gated channel alpha 3	protein-coding
mm_113916.1	chr13	49504944	49504958	+	1	NA	5' UTR (NM_001012324, exon 1 of 10)	5' UTR (NM_001012324, exon 1 of 10)	141	NM_001012324	407800	Mm.386931	NM_001012324	ENSMUSG00000043631	Ecm2	9030618O22Rik|BC065151|tenonectin	extracellular matrix protein 2, female organ and adipocyte specific	protein-coding
mm_64532.1	chr7	144175256	144175272	+	1	NA	promoter-TSS (NM_001113373)	promoter-TSS (NM_001113373)	-256	NM_001113373	210274	Mm.483624	NM_001081370	ENSMUSG00000037541	Shank2	ProSAP1|mKIAA1022	SH3/ankyrin domain gene 2	protein-coding
mm_120158.1	chr14	60709396	60709483	+	1	NA	exon (NM_001033272, exon 4 of 13)	exon (NM_001033272, exon 4 of 13)	-23465	NM_001310594	219140	Mm.149776	NM_001033272	ENSMUSG00000021990	Spata13	C79050|ESTM11|X83327|mFLJ00298	spermatogenesis associated 13	protein-coding
mm_1850.1	chr1	83159734	83159773	+	1	NA	promoter-TSS (NM_027725)	promoter-TSS (NM_027725)	-9	NR_027636	71227	Mm.256482	NM_027725	ENSMUSG00000053161	Daw1	4930563E19Rik|4933429D11Rik|Wdr69|b2b1116Clo|b2b1584Clo	dynein assembly factor with WDR repeat domains 1	protein-coding
mm_156931.1	chrX	169685150	169685159	+	1	NA	promoter-TSS (NM_010797)	promoter-TSS (NM_010797)	-45	NM_010797	17318	Mm.34441	NM_010797	ENSMUSG00000035299	Mid1	61B3-R|DXHXS1141|Fxy|Trim18	midline 1	protein-coding
mm_67420.1	chr7	80324419	80324458	-	1	NA	promoter-TSS (NM_173445)	promoter-TSS (NM_173445)	16	NM_173445	269955	Mm.474502	NM_173445	ENSMUSG00000038930	Rccd1	5830436H09|E430018M08Rik	RCC1 domain containing 1	protein-coding
mm_9518.1	chr1	173748878	173748888	-	1	NA	intron (NM_008329, intron 8 of 8)	intron (NM_008329, intron 8 of 8)	-7074	NM_001204910	226691	Mm.440876	NM_001204910	ENSMUSG00000073490	Ifi207	AI607873|Pyhin-A	interferon activated gene 207	protein-coding
mm_148806.1	chr19	6276169	6276172	+	1	NA	promoter-TSS (NM_010119)	promoter-TSS (NM_010119)	-726	NM_010119	13660	Mm.30169	NM_010119	ENSMUSG00000024772	Ehd1	AA409636|Past1|RME-1	EH-domain containing 1	protein-coding
mm_71144.1	chr8	39130742	39130745	+	1	NA	TTS (NM_030254)	TTS (NM_030254)	124876	NM_030254	80286	Mm.272722	NM_030254	ENSMUSG00000039530	Tusc3	AU022242|BC003311|N33	tumor suppressor candidate 3	protein-coding
mm_26259.1	chr3	142500598	142500606	+	1	NA	exon (NM_153564, exon 2 of 11)	exon (NM_153564, exon 2 of 11)	3668	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_148934.1	chr19	7018785	7018797	+	1	NA	exon (NM_153795, exon 2 of 15)	exon (NM_153795, exon 2 of 15)	678	NM_153795	108101	Mm.157591	NM_153795	ENSMUSG00000024965	Fermt3	C79673|Kindlin3	fermitin family member 3	protein-coding
mm_90704.1	chr10	130368075	130368078	+	1	NA	Intergenic	MurSatRep1|Unknown|Unknown	26165	NM_001081448	625068	Mm.359168	NM_001081448	ENSMUSG00000070601	Vmn2r84	EG625068	vomeronasal 2, receptor 84	protein-coding
mm_67455.1	chr7	80402231	80402262	-	1	NA	intron (NM_001081454, intron 1 of 15)	CpG	566	NM_011046	18550	Mm.5241	NM_011046	ENSMUSG00000030530	Furin	9130404I01Rik|Fur|PACE|Pcsk3|SPC1	furin (paired basic amino acid cleaving enzyme)	protein-coding
mm_20815.1	chr2	144527440	144527450	-	1	NA	promoter-TSS (NM_029763)	promoter-TSS (NM_029763)	-47	NM_172859	241688	Mm.442156	NM_172859	ENSMUSG00000037259	Dzank1	2810039F03Rik|6330439K17Rik|6430408C01|AI851115|Ankrd64	double zinc ribbon and ankyrin repeat domains 1	protein-coding
mm_92965.1	chr10	86057619	86057631	-	1	NA	exon (NM_013722, exon 13 of 14)	exon (NM_013722, exon 13 of 14)	35471	NM_001347151	69754	Mm.44236	NM_153195	ENSMUSG00000001786	Fbxo7	2410015K21Rik|A230052G17Rik|AI117679|AW260462|C85118	F-box protein 7	protein-coding
mm_141277.1	chr17	27820614	27820683	-	1	NA	promoter-TSS (NM_001271511)	promoter-TSS (NM_001271511)	-106	NM_001271511	224647	Mm.196577	NM_001033279	ENSMUSG00000056692	D17Wsu92e	AU020189|C030010A15|C80239	DNA segment, Chr 17, Wayne State University 92, expressed	protein-coding
mm_114963.1	chr13	97073564	97073570	+	1	NA	intron (NM_001100458, intron 1 of 12)	(T)n|Simple_repeat|Simple_repeat	1924	NM_001100458	320557	Mm.458280	NM_001100458	ENSMUSG00000041817	Fam169a	B230112C05Rik|SLAP75	family with sequence similarity 169, member A	protein-coding
mm_5793.1	chr1	51915969	51915978	-	1	NA	promoter-TSS (NM_010863)	promoter-TSS (NM_010863)	5	NM_001290982	17912	Mm.3390	NM_010863	ENSMUSG00000018417	Myo1b	AA406997|MIH-L|MMIa	myosin IB	protein-coding
mm_117288.1	chr13	66441126	66441146	-	1	NA	promoter-TSS (NM_001290196)	promoter-TSS (NM_001290196)	-18	NM_001290196	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
mm_2341.1	chr1	92858554	92858576	+	1	NA	3' UTR (NM_016696, exon 9 of 9)	3' UTR (NM_016696, exon 9 of 9)	8187	NR_029559	387167		NR_029559	ENSMUSG00000065470	Mir149	Mirn149|mir-149|mmu-mir-149	microRNA 149	ncRNA
mm_15942.1	chr2	165810301	165810309	+	1	NA	intron (NM_027230, intron 15 of 23)	intron (NM_027230, intron 15 of 23)	47868	NM_001252585	228880	Mm.227598	NM_027230	ENSMUSG00000039671	Zmynd8	1110013E22Rik|2010005I16Rik|3632413B07Rik|AI316811|AL024039|Prkcbp1|RACK7	zinc finger, MYND-type containing 8	protein-coding
mm_91662.1	chr10	42888460	42888471	-	1	NA	intron (NM_172938, intron 1 of 8)	intron (NM_172938, intron 1 of 8)	27953	NM_172938	268297	Mm.98731	NM_172938	ENSMUSG00000044770	Scml4	9330161D17|mFLJ00197	sex comb on midleg-like 4 (Drosophila)	protein-coding
mm_169271.1	chr1	38620951	38620960	-	1	NA	intron (NM_001290814, intron 1 of 21)	intron (NM_001290814, intron 1 of 21)	6289	NM_001290814	16764	Mm.336679	NM_010678	ENSMUSG00000037138	Aff3	3222402O04Rik|A730046J16|LAF-4|Laf4	AF4/FMR2 family, member 3	protein-coding
mm_128618.1	chr15	58933662	58933675	-	1	NA	promoter-TSS (NM_023172)	promoter-TSS (NM_023172)	62	NM_175151	69694	Mm.383230	NM_175151	ENSMUSG00000050891	Tatdn1	2310079P03Rik|CDA11	TatD DNase domain containing 1	protein-coding
mm_131111.1	chr16	5146961	5146981	+	1	NA	promoter-TSS (NM_001127725)	promoter-TSS (NM_001127725)	-138	NM_001127725	665119	Mm.102072	NM_001127725	ENSMUSG00000091712	Sec14l5	-	SEC14-like lipid binding 5	protein-coding
mm_125369.1	chr15	39736616	39736616	+	1	NA	Intergenic	Intergenic	-9314	NM_001289506	75766	Mm.159563	NM_029422	ENSMUSG00000022303	Dcstamp	4833414I07Rik|DC-STAMP|FIND|Tm7sf4|mDC-STAMP	dendrocyte expressed seven transmembrane protein	protein-coding
mm_135457.1	chr16	45724696	45724698	-	1	NA	promoter-TSS (NM_019754)	promoter-TSS (NM_019754)	-166	NM_019754	56370	Mm.24183	NM_019754	ENSMUSG00000022658	Tagln3	2700038H05Rik|2900005O10Rik|AI426007|Np25	transgelin 3	protein-coding
mm_31474.1	chr4	50485293	50485294	+	1	NA	Intergenic	Intergenic	-639524	NM_001276355	242443	Mm.440095	NM_001033351	ENSMUSG00000039579	Grin3a	6430537F04|A830097C19Rik|NMDAR-L|NR3A|mKIAA1973	glutamate receptor ionotropic, NMDA3A	protein-coding
mm_13618.1	chr2	113440053	113440055	+	1	NA	intron (NM_010230, intron 3 of 19)	intron (NM_010230, intron 3 of 19)	-1010	NM_001285459	14260	Mm.4938	NM_010230	ENSMUSG00000044042	Fmn1	Fmn|formin-1|ld	formin 1	protein-coding
mm_64205.1	chr7	141475246	141475256	+	1	NA	promoter-TSS (NM_025593)	promoter-TSS (NM_025593)	15	NM_053082	64540	Mm.489619	NM_053082	ENSMUSG00000025511	Tspan4	AI325509|AI746565|D130042I01Rik|NAG-2|Tm4sf7|Tspan-4	tetraspanin 4	protein-coding
mm_33405.1	chr4	129839240	129839269	+	1	NA	5' UTR (NM_001164745, exon 2 of 6)	5' UTR (NM_001164745, exon 2 of 6)	18546	NM_001164745	19244	Mm.193688	NM_008974	ENSMUSG00000028788	Ptp4a2	Prl-2	protein tyrosine phosphatase 4a2	protein-coding
mm_20062.1	chr2	120353000	120353021	-	1	NA	non-coding (NR_027618, exon 1 of 26)	non-coding (NR_027618, exon 1 of 26)	123	NM_178851	269338	Mm.246131	NM_147153	ENSMUSG00000027291	Vps39	A230065P22Rik|AW743070|Vam6|Vam6P|mVam6	VPS39 HOPS complex subunit	protein-coding
mm_120360.1	chr14	64323981	64323985	+	1	NA	intron (NM_001253712, intron 1 of 5)	intron (NM_001253712, intron 1 of 5)	92973	NM_001253716	110265	Mm.26713	NM_026322	ENSMUSG00000054733	Msra	2310045J23Rik|6530413P12Rik|MSR-A	methionine sulfoxide reductase A	protein-coding
mm_158724.1	chrX	162964558	162964576	-	1	NA	promoter-TSS (NM_009789)	promoter-TSS (NM_009789)	32	NM_009789	12309	Mm.6891	NM_009789	ENSMUSG00000040808	S100g	AU042539|CABP1|CaBP-D9K|Cabp9k|Calb3	S100 calcium binding protein G	protein-coding
mm_168183.1	chr10	59386914	59386918	+	1	NA	Intergenic	IAPLTR1_Mm|LTR|ERVK	-16769	NM_023530	69836	Mm.30268	NM_023530	ENSMUSG00000009646	Pla2g12b	2010002E04Rik|Fksg71|Pla2g13|hlb218	phospholipase A2, group XIIB	protein-coding
mm_146516.1	chr18	4198516	4198541	-	1	NA	Intergenic	Intergenic	32696	NM_026092	67328	Mm.158148	NM_026092	ENSMUSG00000024233	Lyzl1	1700038F02Rik|Lyc2|Lyzd1	lysozyme-like 1	protein-coding
mm_24237.1	chr3	88970718	88970721	+	1	NA	intron (NM_138679, intron 1 of 26)	U6|snRNA|snRNA	4907	NM_138679	192195	Mm.130752	NM_138679	ENSMUSG00000028053	Ash1l	8030453L17Rik|Ash1|E430018P19Rik|Kmt2h	ash1 (absent, small, or homeotic)-like (Drosophila)	protein-coding
mm_89862.1	chr10	108162175	108162177	+	1	NA	promoter-TSS (NM_027892)	promoter-TSS (NM_027892)	-224	NM_027892	17931	Mm.422959	NM_027892	ENSMUSG00000019907	Ppp1r12a	1200015F06Rik|5730577I22Rik|AA792106|AV099298|D10Ertd625e|Mypt1	protein phosphatase 1, regulatory (inhibitor) subunit 12A	protein-coding
mm_94989.1	chr11	31871374	31871399	+	1	NA	5' UTR (NM_026252, exon 1 of 10)	5' UTR (NM_026252, exon 1 of 10)	446	NM_026252	67579	Mm.339792	NM_026252	ENSMUSG00000020300	Cpeb4	Cpe-bp4|Cpeb-4|mCPEB-4	cytoplasmic polyadenylation element binding protein 4	protein-coding
mm_18708.1	chr2	72054914	72054918	-	1	NA	5' UTR (NM_001204166, exon 1 of 28)	5' UTR (NM_001204166, exon 1 of 28)	299	NM_001204166	56508	Mm.196153	NM_019688	ENSMUSG00000049044	Rapgef4	1300003D15Rik|5730402K07Rik|6330581N18Rik|EPAC 2|Epac-2|Epac2|mKIAA4040	Rap guanine nucleotide exchange factor (GEF) 4	protein-coding
mm_97024.1	chr11	72042462	72042481	+	1	NA	promoter-TSS (NM_144526)	promoter-TSS (NM_144526)	-31	NM_144526	109212	Mm.33118	NM_144526	ENSMUSG00000020808	Fam64a	2610008F03Rik|6720460F02Rik|AI115087|CATS	family with sequence similarity 64, member A	protein-coding
mm_35580.1	chr4	41740976	41741002	-	1	NA	intron (NM_011014, intron 1 of 3)	CpG-9828	370	NM_001286540	18391	Mm.425181	NM_011014	ENSMUSG00000036078	Sigmar1	Oprs1|Sig1R|sigma1R	sigma non-opioid intracellular receptor 1	protein-coding
mm_2958.1	chr1	132865829	132865839	+	1	NA	Intergenic	MIR|SINE|MIR	-14521	NM_010732	16980	Mm.39640	NM_010732	ENSMUSG00000026443	Lrrn2	5730406J09Rik|NLRR-2	leucine rich repeat protein 2, neuronal	protein-coding
mm_58641.1	chr7	6172497	6172531	+	1	NA	promoter-TSS (NM_001146024)	promoter-TSS (NM_001146024)	1	NM_001146024	72667	Mm.274089	NM_028316	ENSMUSG00000044876	Zfp444	2810031J10Rik|6230401O10Rik|mFLJ00134	zinc finger protein 444	protein-coding
mm_166917.1	chr7	30445598	30445606	-	1	NA	promoter-TSS (NM_007467)	promoter-TSS (NM_007467)	-20	NM_007467	11803	Mm.2381	NM_007467	ENSMUSG00000006651	Aplp1	-	amyloid beta (A4) precursor-like protein 1	protein-coding
mm_38278.1	chr4	136890000	136890042	-	1	NA	3' UTR (NM_007574, exon 3 of 3)	3' UTR (NM_007574, exon 3 of 3)	2893	NM_007574	12262	Mm.439732	NM_007574	ENSMUSG00000036896	C1qc	AI385742|C1qg|Ciqc	complement component 1, q subcomponent, C chain	protein-coding
mm_72798.1	chr8	87218573	87218591	+	1	NA	Intergenic	Intergenic	-18732	NR_040697	100038706	Mm.334690	NR_040697	ENSMUSG00000099207	Gm10637	ENSMUSG00000074176	predicted gene 10637	ncRNA
mm_99134.1	chr11	100319974	100319988	+	1	NA	promoter-TSS (NM_011508)	promoter-TSS (NM_011508)	32	NM_011508	20918	Mm.13886	NM_011508	ENSMUSG00000035530	Eif1	Sui1-rs1	eukaryotic translation initiation factor 1	protein-coding
mm_77693.1	chr8	126589452	126589467	-	1	NA	3' UTR (NM_001164598, exon 2 of 2)	3' UTR (NM_001164598, exon 2 of 2)	3977	NM_001164598	270110	Mm.334918	NM_001164598	ENSMUSG00000051495	Irf2bp2	E130305N23Rik|IRF-2BP2	interferon regulatory factor 2 binding protein 2	protein-coding
mm_109524.1	chr12	111536074	111536111	+	1	NA	Intergenic	Intergenic	-2009	NM_178041	217869	Mm.271222	NM_173363	ENSMUSG00000021282	Eif5	2810011H21Rik|D12Ertd549e	eukaryotic translation initiation factor 5	protein-coding
mm_166821.1	chr7	18065939	18065947	+	1	NA	promoter-TSS (NM_001162524)	promoter-TSS (NM_001162524)	14	NM_001162523	67315	Mm.46089	NM_026087	ENSMUSG00000030366	Ceacam12	1600031J20Rik|Ceacam12-C1|Ceacam12-C3|Ceacam12C1|Ceacam12C3	carcinoembryonic antigen-related cell adhesion molecule 12	protein-coding
mm_19072.1	chr2	77816681	77816691	-	1	NA	5' UTR (NM_178723, exon 1 of 10)	5' UTR (NM_178723, exon 1 of 10)	130	NM_178723	241494	Mm.490320	NM_178723	ENSMUSG00000027016	Zfp385b	B830010L13Rik|C130013B13Rik|Zfp533|Znf385b	zinc finger protein 385B	protein-coding
mm_112628.1	chr13	15852538	15852539	+	1	NA	Intergenic	Intergenic	45295	NR_046131	328190	Mm.446957	NR_046131		A530046M15Rik	A530046M15	RIKEN cDNA A530046M15 gene	ncRNA
mm_136393.1	chr16	93147700	93147710	-	1	NA	Intergenic	Intergenic	205484	NR_040486	69857	Mm.81192	NR_040486	ENSMUSG00000100277	1810053B23Rik	1810008L18Rik|1810056K14Rik	RIKEN cDNA 1810053B23 gene	ncRNA
mm_47392.1	chr5	123015970	123015980	-	1	NA	intron (NM_175423, intron 1 of 1)	intron (NM_175423, intron 1 of 1)	901	NM_175423	109305	Mm.218582	NM_175423	ENSMUSG00000049686	Orai1	D730049H07Rik|Tmem142a|orai-1	ORAI calcium release-activated calcium modulator 1	protein-coding
mm_47386.1	chr5	122990534	122990573	-	1	NA	intron (NR_045820, intron 1 of 2)	intron (NR_045820, intron 1 of 2)	1199	NR_045820	109202	Mm.30769	NM_175405	ENSMUSG00000056735	A930024E05Rik	-	RIKEN cDNA A930024E05 gene	ncRNA
mm_130919.1	chr15	102671817	102671840	-	1	NA	promoter-TSS (NR_030460)	promoter-TSS (NR_030460)	38	NR_030460	751542		NR_030460	ENSMUSG00000076009	Mir688	Mirn688|mmu-mir-688	microRNA 688	ncRNA
mm_70752.1	chr8	19681872	19681877	+	1	NA	Intergenic	Intergenic	-47702	NM_001270553	100861668	Mm.491087	NM_001270553	ENSMUSG00000095294	Gm21119	-	predicted gene, 21119	protein-coding
mm_52708.1	chr6	119479481	119479502	+	1	NA	promoter-TSS (NM_133940)	promoter-TSS (NM_133940)	-177	NM_133940	101358	Mm.125477	NM_133940	ENSMUSG00000030019	Fbxl14	AW322056|Fbx14l	F-box and leucine-rich repeat protein 14	protein-coding
mm_859.1	chr1	52132589	52132599	+	1	NA	exon (NM_001205314, exon 6 of 25)	exon (NM_001205314, exon 6 of 25)	12972	NM_001205313	20846	Mm.277406	NM_009283	ENSMUSG00000026104	Stat1	2010005J02Rik|AA408197	signal transducer and activator of transcription 1	protein-coding
mm_159249.1	chr2	151974129	151974129	-	1	NA	promoter-TSS (NM_001289151)	promoter-TSS (NM_001289151)	-148	NM_028666	73847	Mm.272444	NM_028666	ENSMUSG00000027459	Fam110a	1700008J10Rik|5430432M24Rik|AI747080	family with sequence similarity 110, member A	protein-coding
mm_89973.1	chr10	111506940	111506962	+	1	NA	exon (NM_009344, exon 1 of 2)	exon (NM_009344, exon 1 of 2)	665	NM_009344	21664	Mm.3117	NM_009344	ENSMUSG00000020205	Phlda1	DT1P1B11|TDAG51|Tdag	pleckstrin homology like domain, family A, member 1	protein-coding
mm_133859.1	chr16	96280983	96280994	+	1	NA	promoter-TSS (NM_033149)	promoter-TSS (NM_033149)	-44	NM_033149	93961	Mm.154783	NM_033149	ENSMUSG00000074892	B3galt5	1190002B21Rik|AU045265|b3Galt-V	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 5	protein-coding
mm_22218.1	chr2	174341679	174341705	-	1	NA	non-coding (NR_003258, exon 5 of 13)	non-coding (NR_003258, exon 5 of 13)	11603	NM_001077510	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_140223.1	chr17	83976142	83976150	+	1	NA	Intergenic	Intergenic	-22406	NR_130994	78148	Mm.243918	NR_130994		8430430B14Rik	-	RIKEN cDNA 8430430B14 gene	ncRNA
mm_42821.1	chr5	122093517	122093523	+	1	NA	Intergenic	Intergenic	-7460	NM_010861	17906	Mm.1529	NM_010861	ENSMUSG00000013936	Myl2	MLC-2|MLC-2s/v|MLC-2v|Mlc2v|Mylpc	myosin, light polypeptide 2, regulatory, cardiac, slow	protein-coding
mm_93878.1	chr10	125291593	125291623	-	1	NA	intron (NM_011391, intron 4 of 6)	B1_Mur4|SINE|Alu	36927	NM_011391	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|Mct2	solute carrier family 16 (monocarboxylic acid transporters), member 7	protein-coding
mm_53441.1	chr6	134262422	134262423	+	1	NA	intron (NM_001303102, intron 7 of 8)	intron (NM_001303102, intron 7 of 8)	-133907	NM_025778	66813	Mm.474472	NM_025778	ENSMUSG00000030200	Bcl2l14	4930452K23Rik|4933405K19Rik|9030625M01Rik|AI429211|Bclg	BCL2-like 14 (apoptosis facilitator)	protein-coding
mm_34692.1	chr4	152009013	152009023	+	1	NA	exon (NM_001033352, exon 1 of 4)	exon (NM_001033352, exon 1 of 4)	127	NM_001033352	242785	Mm.22306	NM_001033352	ENSMUSG00000073700	Klhl21	1810045K06Rik|D330008A20|mKIAA0469	kelch-like 21	protein-coding
mm_12819.1	chr2	80316844	80316873	+	1	NA	intron (NM_024181, intron 1 of 22)	intron (NM_024181, intron 1 of 22)	1392	NM_024181	66861	Mm.21762	NM_024181	ENSMUSG00000027006	Dnajc10	1200006L06Rik|D2Ertd706e|ERdj5|JPDI	DnaJ heat shock protein family (Hsp40) member C10	protein-coding
mm_113188.1	chr13	24942691	24942711	+	1	NA	promoter-TSS (NM_008156)	promoter-TSS (NM_008156)	-451	NM_008156	14756	Mm.291831	NM_008156	ENSMUSG00000021340	Gpld1	6330541J12Rik|AW546131	glycosylphosphatidylinositol specific phospholipase D1	protein-coding
mm_152732.1	chr19	18936497	18936499	-	1	NA	3' UTR (NM_001289921, exon 11 of 11)	3' UTR (NM_001289921, exon 11 of 11)	64619	NM_146095	225998	Mm.234641	NM_146095	ENSMUSG00000036192	Rorb	Nr1f2|RZR-beta|RZRB|Rorbeta|hstp	RAR-related orphan receptor beta	protein-coding
mm_35920.1	chr4	53031717	53031723	-	1	NA	3' UTR (NM_013454, exon 50 of 50)	3' UTR (NM_013454, exon 50 of 50)	19840	NM_025623	66536	Mm.38244	NM_025623	ENSMUSG00000015247	Nipsnap3b	2700063N13Rik|Nipsnap3a	nipsnap homolog 3B (C. elegans)	protein-coding
mm_99942.1	chr11	111066155	111066174	+	1	NA	promoter-TSS (NM_008425)	promoter-TSS (NM_008425)	0	NM_008425	16518	Mm.4951	NM_008425	ENSMUSG00000041695	Kcnj2	IRK1|Kcnf1|Kir2.1	potassium inwardly-rectifying channel, subfamily J, member 2	protein-coding
mm_84707.1	chr9	72985284	72985297	-	1	NA	promoter-TSS (NM_001286546)	promoter-TSS (NM_001286546)	86	NM_001198789	546143	Mm.260946	NM_001198789	ENSMUSG00000086158	Ccpg1os	EG546143|Gm5918	cell cycle progression 1, opposite strand	protein-coding
mm_12115.1	chr2	61595100	61595110	+	1	NA	intron (NM_001164071, intron 2 of 8)	RSINE1|SINE|B4	2008	NM_001164071	21353	Mm.244393	NM_011529	ENSMUSG00000064289	Tank	C86182|E430026L09Rik|I-TRAF	TRAF family member-associated Nf-kappa B activator	protein-coding
mm_39696.1	chr5	27072650	27072673	+	1	NA	intron (NM_207282, intron 1 of 25)	intron (NM_207282, intron 1 of 25)	23462	NM_207282	13483	Mm.42078	NM_010075	ENSMUSG00000061576	Dpp6	B930011P16Rik|D5Buc3|D5Buc4|D5Buc5|DPP VI|Dpp-6|Gm1377|In(5)6H-p|Peplb|Rw	dipeptidylpeptidase 6	protein-coding
mm_42606.1	chr5	117841840	117841857	+	1	NA	Intergenic	CpG	-24991	NM_008712	18125	Mm.44249	NM_008712	ENSMUSG00000029361	Nos1	2310005C01Rik|N-NOS|NC-NOS|NO|NOS|NOS-I|Nos-1|bNOS|nNOS	nitric oxide synthase 1, neuronal	protein-coding
mm_30720.1	chr4	13743295	13743316	+	1	NA	promoter-TSS (NM_001111026)	promoter-TSS (NM_001111026)	3	NM_001111026	12395	Mm.4909	NM_009822	ENSMUSG00000006586	Runx1t1	Cbfa2t1h|ETO|MTG8	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	protein-coding
mm_68394.1	chr7	109525743	109525757	-	1	NA	non-coding (NR_037617, exon 18 of 20)	non-coding (NR_037617, exon 18 of 20)	5618	NR_028079	100302499	Mm.482651	NR_028079	ENSMUSG00000065016	Snora3	MBI-28	small nucleolar RNA, H/ACA box 3	snoRNA
mm_144971.1	chr18	37830602	37830605	+	1	NA	intron (NM_001301259, intron 2 of 3)	intron (NM_001301259, intron 2 of 3)	11057	NM_033583	93708	Mm.247203	NM_033583	ENSMUSG00000102543	Pcdhgc5	-	protocadherin gamma subfamily C, 5	protein-coding
mm_67639.1	chr7	84410062	84410068	-	1	NA	promoter-TSS (NM_007488)	promoter-TSS (NM_007488)	-27	NM_007488	11864	Mm.38594	NM_007488	ENSMUSG00000015709	Arnt2	Hif-2b|bHLHe1|mKIAA0307	aryl hydrocarbon receptor nuclear translocator 2	protein-coding
mm_157186.1	chrX	10595719	10595752	-	1	NA	3' UTR (NM_019634, exon 8 of 8)	3' UTR (NM_019634, exon 8 of 8)	110619	NM_019634	21912	Mm.18590	NM_019634	ENSMUSG00000058254	Tspan7	1200014P11Rik|A15|AI323365|Cd231|Mxs1|PE31|R74651|TALLA|Tm4sf2	tetraspanin 7	protein-coding
mm_81289.1	chr9	108306861	108306915	+	1	NA	promoter-TSS (NM_133986)	promoter-TSS (NM_133986)	91	NM_001313962	11848	Mm.757	NM_016802	ENSMUSG00000007815	Rhoa	Arha|Arha1|Arha2	ras homolog family member A	protein-coding
mm_139737.1	chr17	59071377	59071378	+	1	NA	Intergenic	Intergenic	-58055	NM_026497	67993	Mm.36507	NM_026497	ENSMUSG00000024228	Nudt12	0610016O18Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 12	protein-coding
mm_80741.1	chr9	94743290	94743299	+	1	NA	intron (NM_177909, intron 4 of 15)	intron (NM_177909, intron 4 of 15)	-8535	NR_106116	102465763		NR_106116	ENSMUSG00000098251	Mir7656	Gm27614|mmu-mir-7656	microRNA 7656	ncRNA
mm_77360.1	chr8	119661302	119661334	-	1	NA	Intergenic	Intergenic	-5047	NM_023395	67866	Mm.87599	NM_023395	ENSMUSG00000023336	Wfdc1	2310058A03Rik|ps20	WAP four-disulfide core domain 1	protein-coding
mm_74020.1	chr8	121581735	121581736	+	1	NA	Intergenic	Intergenic	-2929	NM_133765	76454	Mm.24829	NM_133765	ENSMUSG00000052934	Fbxo31	1110003O08Rik|2310046N15Rik|Fbx14|Fbxo14	F-box protein 31	protein-coding
mm_62068.1	chr7	92637226	92637235	+	1	NA	promoter-TSS (NM_028665)	promoter-TSS (NM_028665)	-88	NM_028665	73845	Mm.73248	NM_028665	ENSMUSG00000041343	Ankrd42	4931426M20|4933417L02Rik|Ikbn	ankyrin repeat domain 42	protein-coding
mm_89199.1	chr10	86348206	86348223	+	1	NA	3' UTR (NM_011595, exon 5 of 5)	3' UTR (NM_011595, exon 5 of 5)	47802	NM_011595	21859	Mm.4871	NM_011595	ENSMUSG00000020044	Timp3	Timp-3	tissue inhibitor of metalloproteinase 3	protein-coding
mm_117695.1	chr13	94295049	94295059	-	1	NA	Intergenic	MTC|LTR|ERVL-MaLR	-9223	NM_001346609	107767	Mm.201455	NM_029153	ENSMUSG00000021687	Scamp1	4930505M11Rik|AI415563|AW122395	secretory carrier membrane protein 1	protein-coding
mm_149824.1	chr19	24476734	24476752	+	1	NA	exon (NM_026520, exon 1 of 1)	exon (NM_026520, exon 1 of 1)	731	NM_026520	68034	Mm.440181	NM_026520	ENSMUSG00000074922	Fam122a	2410124L17Rik|2900009I07Rik|ENSMUSG00000051082|Gm9849	family with sequence similarity 122, member A	protein-coding
mm_51741.1	chr6	87347067	87347071	+	1	NA	exon (NM_025466, exon 5 of 6)	exon (NM_025466, exon 5 of 6)	3846	NM_025466	66283	Mm.46414	NM_025466	ENSMUSG00000030050	Gkn1	2200002K21Rik|AMP-18|BRICD1|Fov	gastrokine 1	protein-coding
mm_89027.1	chr10	82699098	82699149	+	1	NA	5' UTR (NM_001081218, exon 1 of 15)	5' UTR (NM_001081218, exon 1 of 15)	116	NM_001081218	67933	Mm.127405	NM_026462	ENSMUSG00000020246	Hcfc2	1700129L13Rik|AU019838	host cell factor C2	protein-coding
mm_158538.1	chrX	143933090	143933142	-	1	NA	promoter-TSS (NM_001110222)	promoter-TSS (NM_001110222)	8	NM_001110222	13193	Mm.12871	NM_010025	ENSMUSG00000031285	Dcx	Dbct	doublecortin	protein-coding
mm_14974.1	chr2	152104915	152104935	+	1	NA	promoter-TSS (NM_029688)	promoter-TSS (NM_029688)	-599	NM_029688	76650	Mm.218639	NM_029688	ENSMUSG00000032802	Srxn1	1700127B04Rik|AI854065|AW488194|Npn3|Srx|Srx1|TX01	sulfiredoxin 1 homolog (S. cerevisiae)	protein-coding
mm_13416.1	chr2	104122796	104122813	+	1	NA	promoter-TSS (NM_026634)	promoter-TSS (NM_026634)	35	NM_026634	68243	Mm.158191	NM_026634	ENSMUSG00000032671	A930018P22Rik	-	RIKEN cDNA A930018P22 gene	protein-coding
mm_108041.1	chr12	73901403	73901419	+	1	NA	promoter-TSS (NM_001313920)	promoter-TSS (NM_001313920)	87	NM_001313920	15251	Mm.3879	NM_010431	ENSMUSG00000021109	Hif1a	AA959795|HIF-1-alpha|HIF1-alpha|HIF1alpha|MOP1|bHLHe78	hypoxia inducible factor 1, alpha subunit	protein-coding
mm_158499.1	chrX	142390335	142390345	-	1	NA	5' UTR (NM_207625, exon 1 of 16)	5' UTR (NM_207625, exon 1 of 16)	195	NM_001033600	50790	Mm.391337	NM_019477	ENSMUSG00000031278	Acsl4	9430020A05Rik|ACS4|AU018108|Facl4|Lacs4	acyl-CoA synthetase long-chain family member 4	protein-coding
mm_52929.1	chr6	122928987	122929012	+	1	NA	intron (NM_199311, intron 3 of 5)	L1MDa|LINE|L1	7151	NM_199311	269799	Mm.297275	NM_199311	ENSMUSG00000049037	Clec4a1	BC049354|Dcir4	C-type lectin domain family 4, member a1	protein-coding
mm_32773.1	chr4	116699162	116699182	+	1	NA	exon (NM_011034, exon 6 of 6)	exon (NM_011034, exon 6 of 6)	9213	NM_025962	67096	Mm.252785	NM_025962	ENSMUSG00000028690	Mmachc	1810037K07Rik|CblC	methylmalonic aciduria cblC type, with homocystinuria	protein-coding
mm_153086.1	chr19	32388463	32388483	-	1	NA	promoter-TSS (NM_144792)	promoter-TSS (NM_144792)	-19	NM_144792	208449	Mm.329810	NM_144792	ENSMUSG00000040451	Sgms1	9530058O11Rik|AI841905|C80702|Mob|Sms1|Sor1|Tmem23	sphingomyelin synthase 1	protein-coding
mm_130003.1	chr15	86214287	86214297	-	1	NA	promoter-TSS (NM_145476)	promoter-TSS (NM_145476)	-167	NM_145476	223754	Mm.28904	NM_145476	ENSMUSG00000051864	Tbc1d22a	BC023106|D15Ertd781e	TBC1 domain family, member 22a	protein-coding
mm_171031.1	chr2	89707171	89707182	-	1	NA	Intergenic	RLTR9F|LTR|ERVK	14933	NM_207568	404331	Mm.377275	NM_207568	ENSMUSG00000110819	Olfr1252	GA_x5J8B7W62NC-992588-991951	olfactory receptor 1252	protein-coding
mm_88446.1	chr10	77548547	77548567	+	1	NA	exon (NM_008404, exon 6 of 16)	exon (NM_008404, exon 6 of 16)	18209	NM_008404	16414	Mm.1137	NM_008404	ENSMUSG00000000290	Itgb2	2E6|AI528527|Cd18|LAD|LCAMB|Lfa1|MF17	integrin beta 2	protein-coding
mm_98922.1	chr11	98348639	98348641	+	1	NA	5' UTR (NM_144828, exon 1 of 7)	5' UTR (NM_144828, exon 1 of 7)	234	NM_144828	19049	Mm.45372	NM_144828	ENSMUSG00000061718	Ppp1r1b	AU040756|DARPP-32|Darpp32	protein phosphatase 1, regulatory (inhibitor) subunit 1B	protein-coding
mm_107473.1	chr12	37880183	37880213	+	1	NA	promoter-TSS (NM_178681)	promoter-TSS (NM_178681)	-507	NM_178681	217480	Mm.126525	NM_178681	ENSMUSG00000036095	Dgkb	6430574F24|90kda|C630029D13Rik|DAGK2|DGK|DGK-beta|mKIAA0718	diacylglycerol kinase, beta	protein-coding
mm_132795.1	chr16	45093904	45093952	+	1	NA	promoter-TSS (NM_026439)	promoter-TSS (NM_026439)	-125	NM_026439	67896	Mm.181074	NM_026439	ENSMUSG00000022665	Ccdc80	2610001E17Rik|DRO1|Ssg1|Urb	coiled-coil domain containing 80	protein-coding
mm_105267.1	chr11	102363693	102363704	-	1	NA	intron (NM_011403, intron 1 of 19)	intron (NM_011403, intron 1 of 19)	1583	NM_011403	20533	Mm.7248	NM_011403	ENSMUSG00000006574	Slc4a1	Ae1|CD233|Empb3|l11Jus51	solute carrier family 4 (anion exchanger), member 1	protein-coding
mm_22109.1	chr2	170122078	170122084	-	1	NA	intron (NM_001159683, intron 2 of 6)	intron (NM_001159683, intron 2 of 6)	9139	NM_001033299	228913	Mm.22858	NM_001033299	ENSMUSG00000052056	Zfp217	4933431C08Rik|AW987152|Gm562|ZABC1|Znf217	zinc finger protein 217	protein-coding
mm_87964.1	chr10	63386595	63386641	+	1	NA	promoter-TSS (NM_013888)	promoter-TSS (NM_013888)	55	NM_013888	30045	Mm.32550	NM_013888	ENSMUSG00000036764	Dnajc12	Jdp1|mJDP1	DnaJ heat shock protein family (Hsp40) member C12	protein-coding
mm_129137.1	chr15	76199836	76199859	-	1	NA	promoter-TSS (NM_201392)	promoter-TSS (NM_201392)	-12	NM_001163549	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
mm_55936.1	chr6	84593917	84593922	-	1	NA	promoter-TSS (NM_175475)	promoter-TSS (NM_175475)	-11	NM_001177713	232174	Mm.255246	NM_175475	ENSMUSG00000063415	Cyp26b1	CP26|P450RAI-2	cytochrome P450, family 26, subfamily b, polypeptide 1	protein-coding
mm_131774.1	chr16	22894797	22894816	+	1	NA	promoter-TSS (NR_110508)	promoter-TSS (NR_110508)	-420	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_25433.1	chr3	107896266	107896314	+	1	NA	promoter-TSS (NR_015459)	promoter-TSS (NR_015459)	-77	NR_015459	329735	Mm.270500	NM_177858	ENSMUSG00000086968	4933431E20Rik	-	RIKEN cDNA 4933431E20 gene	ncRNA
mm_139537.1	chr17	56709982	56709992	+	1	NA	intron (NR_045519, intron 14 of 16)	intron (NR_045519, intron 14 of 16)	6934	NM_178926	106639	Mm.37290	NM_178926	ENSMUSG00000054723	Vmac	AI662250	vimentin-type intermediate filament associated coiled-coil protein	protein-coding
mm_3647.1	chr1	153009681	153009687	+	1	NA	intron (NM_175460, intron 1 of 10)	RLTR41|LTR|ERV1	54583	NM_175460	226518	Mm.40548	NM_175460	ENSMUSG00000042751	Nmnat2	AI843915|D030041I09Rik|PNAT1|PNAT2	nicotinamide nucleotide adenylyltransferase 2	protein-coding
mm_131367.1	chr16	13818856	13818883	+	1	NA	promoter-TSS (NM_001346106)	promoter-TSS (NM_001346106)	-382	NM_010946	18203	Mm.380410	NM_010946	ENSMUSG00000022681	Ntan1	PNAA|PNAD	N-terminal Asn amidase	protein-coding
mm_88920.1	chr10	81183285	81183329	+	1	NA	promoter-TSS (NM_001190473)	promoter-TSS (NM_001190473)	44	NM_001190473	13144	Mm.10294	NM_007828	ENSMUSG00000034974	Dapk3	ZIPK|dlk	death-associated protein kinase 3	protein-coding
mm_113131.1	chr13	24614589	24614603	+	1	NA	promoter-TSS (NM_001286101)	promoter-TSS (NM_001286101)	-10	NM_001286101	193385	Mm.217319	NM_029679	ENSMUSG00000036006	Fam65b	-	family with sequence similarity 65, member B	protein-coding
mm_24799.1	chr3	95550075	95550086	+	1	NA	exon (NM_021281, exon 7 of 8)	exon (NM_021281, exon 7 of 8)	-9597	NM_026489	67981	Mm.179050	NM_026489	ENSMUSG00000028109	Hormad1	4921522K05Rik|Nohma	HORMA domain containing 1	protein-coding
mm_158940.1	chr1	78511144	78511144	+	1	NA	promoter-TSS (NM_026713)	promoter-TSS (NM_026713)	84	NM_026713	68393	Mm.41325	NM_026713	ENSMUSG00000012187	Mogat1	0610030A14Rik|1110064N14Rik|Dgat2l|Dgat2l1|MGAT1|WI1-2612I11.1|mDC2	monoacylglycerol O-acyltransferase 1	protein-coding
mm_162979.1	chr11	19996946	19996960	-	1	NA	intron (NM_033523, intron 1 of 5)	intron (NM_033523, intron 1 of 5)	72511	NM_033523	114716	Mm.266627	NM_033523	ENSMUSG00000045671	Spred2	C79158	sprouty-related, EVH1 domain containing 2	protein-coding
mm_55688.1	chr6	72731039	72731042	-	1	NA	intron (NM_001079822, intron 3 of 12)	intron (NM_001079822, intron 3 of 12)	58005	NM_001079822	21415	Mm.440067	NM_009332	ENSMUSG00000055799	Tcf7l1	Tcf-3|Tcf3|bHLHb21	transcription factor 7 like 1 (T cell specific, HMG box)	protein-coding
mm_45692.1	chr5	81801014	81801023	-	1	NA	Intergenic	Intergenic	323695	NR_138557	67327	Mm.87058	NR_138557		1700031L13Rik	-	RIKEN cDNA 1700031L13 gene	ncRNA
mm_10385.1	chr2	12301304	12301313	+	1	NA	promoter-TSS (NR_040353)	promoter-TSS (NR_040353)	62	NR_040353	338535	Mm.483275	NR_040353	ENSMUSG00000086843	E030013I19Rik	-	RIKEN cDNA E030013I19 gene	ncRNA
mm_145314.1	chr18	53937346	53937346	+	1	NA	intron (NM_152809, intron 10 of 12)	intron (NM_152809, intron 10 of 12)	75233	NM_152809	70425	Mm.368668	NM_152809	ENSMUSG00000073563	Csnk1g3	3300002K07Rik|C330049O21Rik	casein kinase 1, gamma 3	protein-coding
mm_58964.1	chr7	18959025	18959027	+	1	NA	3' UTR (NM_001029877, exon 4 of 4)	3' UTR (NM_001029877, exon 4 of 4)	-28498	NM_194064	378430	Mm.277153	NM_194064	ENSMUSG00000051965	Nanos2	nos2	nanos homolog 2 (Drosophila)	protein-coding
mm_66120.1	chr7	31051495	31051505	-	1	NA	promoter-TSS (NM_022007)	promoter-TSS (NM_022007)	-46	NM_022007	57780	Mm.41770	NM_022007	ENSMUSG00000036578	Fxyd7	1110035I01Rik	FXYD domain-containing ion transport regulator 7	protein-coding
mm_49782.1	chr6	35177611	35177627	+	1	NA	promoter-TSS (NM_027513)	promoter-TSS (NM_027513)	3	NM_027513	70699	Mm.261208	NM_027513	ENSMUSG00000038759	Nup205	3830404O05Rik|AV248391|mKIAA0225	nucleoporin 205	protein-coding
mm_132174.1	chr16	32375965	32375995	+	1	NA	exon (NM_177633, exon 8 of 11)	exon (NM_177633, exon 8 of 11)	-24526	NM_001160402	277203	Mm.484240	NM_001160402	ENSMUSG00000079625	Tm4sf19	EG277203	transmembrane 4 L six family member 19	protein-coding
mm_141046.1	chr17	25433555	25433574	-	1	NA	5' UTR (NM_021415, exon 1 of 35)	5' UTR (NM_021415, exon 1 of 35)	219	NM_021415	58226	Mm.268378	NM_021415	ENSMUSG00000024112	Cacna1h	Cav3.2|MNCb-1209|alpha13.2	calcium channel, voltage-dependent, T type, alpha 1H subunit	protein-coding
mm_54994.1	chr6	48770834	48770884	-	1	NA	promoter-TSS (NM_031247)	promoter-TSS (NM_031247)	-8	NM_031247	83408	Mm.333050	NM_031247	ENSMUSG00000039264	Gimap3	2010110D23Rik|Gimap5|Ian4	GTPase, IMAP family member 3	protein-coding
mm_165053.1	chr19	41263408	41263423	+	1	NA	intron (NM_133352, intron 1 of 14)	CpG	589	NM_133352	107358	Mm.246440	NM_133352	ENSMUSG00000025016	Tm9sf3	1810073M23Rik|2810031D16Rik|AI115521|AI413748|AW146116|AW549777|Smbp|mKIAA4036	transmembrane 9 superfamily member 3	protein-coding
mm_159886.1	chr6	28134550	28134550	-	1	NA	promoter-TSS (NM_008174)	promoter-TSS (NM_008174)	-181	NM_008174	14823	Mm.320732	NM_008174	ENSMUSG00000024211	Grm8	A230002O04|Gprc1h|mGluR8	glutamate receptor, metabotropic 8	protein-coding
mm_104130.1	chr11	86807566	86807622	-	1	NA	promoter-TSS (NM_026191)	promoter-TSS (NM_026191)	66	NM_026191	67487	Mm.260627	NM_026191	ENSMUSG00000018425	Dhx40	2410016C14Rik|ARG147|DDX40|PAD	DEAH (Asp-Glu-Ala-His) box polypeptide 40	protein-coding
mm_110205.1	chr12	27341649	27341659	-	1	NA	exon (NM_009234, exon 1 of 1)	exon (NM_009234, exon 1 of 1)	1064	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding
mm_160138.1	chr7	30879254	30879254	-	1	NA	promoter-TSS (NM_009845)	promoter-TSS (NM_009845)	-226	NM_009845	12483	Mm.260994	NM_009845	ENSMUSG00000030577	Cd22	A530093D23|Lyb-8|Lyb8	CD22 antigen	protein-coding
mm_11363.1	chr2	30963100	30963149	+	1	NA	intron (NM_144884, intron 4 of 4)	intron (NM_144884, intron 4 of 4)	4794	NM_144884	30931	Mm.154994	NM_144884	ENSMUSG00000026849	Tor1a	DQ2|Dyt1|torsinA	torsin family 1, member A (torsin A)	protein-coding
mm_46084.1	chr5	92346848	92346858	-	1	NA	3' UTR (NM_021274, exon 4 of 4)	3' UTR (NM_021274, exon 4 of 4)	2036	NM_021274	15945	Mm.877	NM_021274	ENSMUSG00000034855	Cxcl10	C7|CRG-2|INP10|IP-10|IP10|Ifi10|Scyb10|gIP-10|mob-1	chemokine (C-X-C motif) ligand 10	protein-coding
mm_114590.1	chr13	75756332	75756347	+	1	NA	exon (NM_138953, exon 5 of 12)	exon (NM_138953, exon 5 of 12)	48855	NM_138953	192657	Mm.21288	NM_138953	ENSMUSG00000001542	Ell2	-	elongation factor RNA polymerase II 2	protein-coding
mm_128387.1	chr15	43136047	43136048	-	1	NA	intron (NM_172815, intron 2 of 5)	intron (NM_172815, intron 2 of 5)	34771	NM_172815	239405	Mm.193274	NM_172815	ENSMUSG00000051920	Rspo2	2610028F08Rik|AA673245|D430027K22|ftls	R-spondin 2	protein-coding
mm_14305.1	chr2	129122885	129122886	+	1	NA	intron (NM_009086, intron 12 of 14)	intron (NM_009086, intron 12 of 14)	-6815	NM_025395	66170	Mm.40621	NM_025395	ENSMUSG00000037938	Chchd5	1110027L01Rik|AW045710	coiled-coil-helix-coiled-coil-helix domain containing 5	protein-coding
mm_130399.1	chr15	97976061	97976068	-	1	NA	exon (NM_001113515, exon 53 of 53)	exon (NM_001113515, exon 53 of 53)	11835	NM_001252153	380967	Mm.196630	NM_201359	ENSMUSG00000052369	Tmem106c	AI046681|BC046621|D15Ertd405e	transmembrane protein 106C	protein-coding
mm_113839.1	chr13	47193872	47193882	+	1	NA	promoter-TSS (NM_001170643)	promoter-TSS (NM_001170643)	-126	NM_001170643	218215	Mm.287609	NM_146042	ENSMUSG00000038068	Rnf144b	BC025007|E130105P19Rik|Ibrdc2|Pir2	ring finger protein 144B	protein-coding
mm_82078.1	chr9	122999195	122999221	+	1	NA	exon (NM_010620, exon 21 of 35)	exon (NM_010620, exon 21 of 35)	-22118	NM_025339	66079	Mm.482265	NM_025339	ENSMUSG00000066233	Tmem42	0610027O18Rik|4933429E06Rik|AV003444|D9Ertd662e	transmembrane protein 42	protein-coding
mm_60864.1	chr7	45897470	45897534	+	1	NA	promoter-TSS (NM_001291064)	promoter-TSS (NM_001291064)	433	NM_144801	70209	Mm.163766	NM_144801	ENSMUSG00000002781	Tmem143	2310076O21Rik|AI481604	transmembrane protein 143	protein-coding
mm_127097.1	chr15	97790879	97790957	+	1	NA	3' UTR (NM_026353, exon 3 of 3)	3' UTR (NM_026353, exon 3 of 3)	6553	NM_026353	67739	Mm.28955	NM_026353	ENSMUSG00000081534	Slc48a1	4930570C03Rik	solute carrier family 48 (heme transporter), member 1	protein-coding
mm_144079.1	chr17	91092985	91092995	-	1	NA	promoter-TSS (NM_020252)	promoter-TSS (NM_020252)	-188	NM_020252	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_167168.1	chr7	136465511	136465512	+	1	NA	Intergenic	Intergenic	-116096	NR_040459	330664	Mm.127762	NR_040459	ENSMUSG00000109633	C230079O03Rik	C230079O03	RIKEN cDNA C230079O03 gene	ncRNA
mm_35940.1	chr4	53065790	53065791	-	1	NA	intron (NM_013454, intron 30 of 49)	intron (NM_013454, intron 30 of 49)	53910	NM_025623	66536	Mm.38244	NM_025623	ENSMUSG00000015247	Nipsnap3b	2700063N13Rik|Nipsnap3a	nipsnap homolog 3B (C. elegans)	protein-coding
mm_946.1	chr1	56974033	56974036	+	1	NA	non-coding (NR_024325, exon 1 of 1)	non-coding (NR_024325, exon 1 of 1)	2565	NR_024325	329160	Mm.419039	NR_024325	ENSMUSG00000087022	9130024F11Rik	B530002L08|EG329160	RIKEN cDNA 9130024F11 gene	ncRNA
mm_11922.1	chr2	52072824	52072854	+	1	NA	promoter-TSS (NM_175238)	promoter-TSS (NM_175238)	2	NM_175238	51869	Mm.254530	NM_175238	ENSMUSG00000036202	Rif1	5730435J01Rik|6530403D07Rik|AU016181|AW549474|D2Ertd145e	replication timing regulatory factor 1	protein-coding
mm_14451.1	chr2	131170946	131170953	+	1	NA	3' UTR (NM_027641, exon 7 of 7)	3' UTR (NM_027641, exon 7 of 7)	3861	NM_027641	70997	Mm.252722	NM_027641	ENSMUSG00000027329	Spef1	4931426K16Rik|Clamp	sperm flagellar 1	protein-coding
mm_54767.1	chr6	41377605	41377618	-	1	NA	promoter-TSS (NM_011645)	promoter-TSS (NM_011645)	2	NM_011645	22073	Mm.425318	NM_011645	ENSMUSG00000071519	Prss3	MTG|TRY4|Tb|Try3	protease, serine 3	protein-coding
mm_63467.1	chr7	127573865	127573873	+	1	NA	5' UTR (NM_026888, exon 2 of 10)	5' UTR (NM_026888, exon 2 of 10)	521	NM_026888	68961	Mm.274473	NM_026888	ENSMUSG00000030815	Phkg2	1500017I02Rik	phosphorylase kinase, gamma 2 (testis)	protein-coding
mm_159437.1	chr3	121993661	121993661	+	1	NA	exon (NM_172525, exon 12 of 23)	exon (NM_172525, exon 12 of 23)	40335	NM_172525	214137	Mm.229287	NM_172525	ENSMUSG00000039831	Arhgap29	6720461J18Rik|A830014I19|AU040217|B130017I01Rik|C76601|Parg1	Rho GTPase activating protein 29	protein-coding
mm_166461.1	chr5	139924254	139924254	-	1	NA	intron (NM_175522, intron 1 of 1)	L1ME1|LINE|L1	16311	NM_175522	243312	Mm.237102	NM_175522	ENSMUSG00000048988	Elfn1	A930017N06Rik|AI197272|Ppp1r28	leucine rich repeat and fibronectin type III, extracellular 1	protein-coding
mm_29776.1	chr3	127282446	127282475	-	1	NA	intron (NM_001327938, intron 1 of 47)	intron (NM_001327938, intron 1 of 47)	121155	NR_105029	100862268	Mm.444603	NR_105029	ENSMUSG00000097456	LOC100862268	-	uncharacterized LOC100862268	ncRNA
mm_65945.1	chr7	30417464	30417498	-	1	NA	TTS (NM_011827)	TTS (NM_011827)	2373	NM_011827	23900	Mm.379050	NM_011827	ENSMUSG00000064109	Hcst	DAP10|KAP10	hematopoietic cell signal transducer	protein-coding
mm_2531.1	chr1	106934531	106934540	+	1	NA	promoter-TSS (NM_027971)	promoter-TSS (NM_027971)	86	NM_027971	71869	Mm.321740	NM_027971	ENSMUSG00000059956	Serpinb12	2300003F07Rik|4833409F13Rik	serine (or cysteine) peptidase inhibitor, clade B (ovalbumin), member 12	protein-coding
mm_68588.1	chr7	116034310	116034338	-	1	NA	intron (NM_001025559, intron 1 of 15)	intron (NM_001025559, intron 1 of 15)	-3277	NM_001025560	20679	Mm.323365	NM_011445	ENSMUSG00000051910	Sox6	AI987981|SOX-LZ	SRY (sex determining region Y)-box 6	protein-coding
mm_126716.1	chr15	85336338	85336344	+	1	NA	promoter-TSS (NM_016843)	promoter-TSS (NM_016843)	-40	NM_016843	54138	Mm.248906	NM_016843	ENSMUSG00000016541	Atxn10	AI325283|C77170|E46|Sca10|TEG-169|Tex169	ataxin 10	protein-coding
mm_91806.1	chr10	53913673	53913677	-	1	NA	intron (NM_008548, intron 11 of 12)	intron (NM_008548, intron 11 of 12)	162121	NM_008548	17155	Mm.117294	NM_008548	ENSMUSG00000003746	Man1a	Man1a1|PCR1	mannosidase 1, alpha	protein-coding
mm_165517.1	chr2	173291121	173291133	-	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-14594	NM_022995	65112	Mm.73682	NM_022995	ENSMUSG00000038400	Pmepa1	2210418I02Rik|AW455466|Erg1.2|N4wbp4|Stag1|Tmepai	prostate transmembrane protein, androgen induced 1	protein-coding
mm_135447.1	chr16	45654051	45654061	-	1	NA	promoter-TSS (NM_145389)	promoter-TSS (NM_145389)	62	NM_145389	212998	Mm.97511	NM_145389	ENSMUSG00000033187	BC016579	-	cDNA sequence, BC016579	protein-coding
mm_15998.1	chr2	167189661	167189676	+	1	NA	promoter-TSS (NM_008420)	promoter-TSS (NM_008420)	-850	NM_008420	16500	Mm.205341	NM_008420	ENSMUSG00000050556	Kcnb1	Kcr1-1|Kv2.1|Shab	potassium voltage gated channel, Shab-related subfamily, member 1	protein-coding
mm_13123.1	chr2	91664453	91664495	+	1	NA	intron (NR_027371, intron 5 of 13)	(CA)n|Simple_repeat|Simple_repeat	11266	NM_146124	228359	Mm.22413	NM_146124	ENSMUSG00000027247	Arhgap1	B230365D05Rik|C76222|Cdc42GAP|p50rhoGAP	Rho GTPase activating protein 1	protein-coding
mm_55956.1	chr6	85374607	85374664	-	1	NA	promoter-TSS (NM_177466)	promoter-TSS (NM_177466)	-1	NM_001003955	52055	Mm.220334	NM_177466	ENSMUSG00000051343	Rab11fip5	9130206P09Rik|C75969|D6Ertd32e|GAF1|RIP11	RAB11 family interacting protein 5 (class I)	protein-coding
mm_157245.1	chrX	18461286	18461323	-	1	NA	promoter-TSS (NM_175228)	promoter-TSS (NM_175228)	93	NR_132634	75905	Mm.159617	NM_175228	ENSMUSG00000037358	4930578C19Rik	-	RIKEN cDNA 4930578C19 gene	protein-coding
mm_58096.1	chr6	137537660	137537678	-	1	NA	exon (NM_001271587, exon 3 of 21)	exon (NM_001271587, exon 3 of 21)	-17774	NM_001271589	13860	Mm.235346	NM_007945	ENSMUSG00000015766	Eps8	AW261790	epidermal growth factor receptor pathway substrate 8	protein-coding
mm_2620.1	chr1	120602379	120602391	+	1	NA	promoter-TSS (NM_010133)	promoter-TSS (NM_010133)	-102	NM_010133	13798	Mm.2657	NM_010133	ENSMUSG00000058665	En1	En-1|Mo-en.1|engrailed-1	engrailed 1	protein-coding
mm_59821.1	chr7	29238479	29238507	+	1	NA	intron (NM_029887, intron 1 of 7)	CpG	170	NM_029887	77254	Mm.36699	NM_029887	ENSMUSG00000030588	Yif1b	9430029K10Rik|Yip1b	Yip1 interacting factor homolog B (S. cerevisiae)	protein-coding
mm_19016.1	chr2	76906704	76906706	-	1	NA	intron (NM_011652, intron 45 of 312)	intron (NM_011652, intron 45 of 312)	75842	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_150904.1	chr19	45749200	45749228	+	1	NA	intron (NM_008723, intron 1 of 5)	CpG-7591	349	NM_008723	18150	Mm.1406	NM_008723	ENSMUSG00000056209	Npm3	Nub1	nucleoplasmin 3	protein-coding
mm_104617.1	chr11	97280471	97280606	-	1	NA	promoter-TSS (NM_008942)	promoter-TSS (NM_008942)	38	NM_008942	19155	Mm.29824	NM_008942	ENSMUSG00000001441	Npepps	AAP-S|MP100|Psa|R74825|goku	aminopeptidase puromycin sensitive	protein-coding
mm_154141.1	chr19	57668090	57668108	-	1	NA	intron (NM_181415, intron 9 of 28)	RLTR20B4_MM|LTR|ERVK	57065	NM_181415	226255	Mm.245340	NM_181415	ENSMUSG00000054843	Atrnl1	AI504415|AW555641|Alp|Atrnl|Atrnlp	attractin like 1	protein-coding
mm_81831.1	chr9	118079272	118079275	+	1	NA	intron (NM_026442, intron 2 of 3)	intron (NM_026442, intron 2 of 3)	38751	NM_013727	27215	Mm.92705	NM_013727	ENSMUSG00000039285	Azi2	AA410145|AZ2	5-azacytidine induced gene 2	protein-coding
mm_66563.1	chr7	45239289	45239295	-	1	NA	promoter-TSS (NM_007645)	promoter-TSS (NM_007645)	-177	NM_001290804	12493	Mm.3689	NM_007645	ENSMUSG00000030798	Cd37	Tspan26	CD37 antigen	protein-coding
mm_37394.1	chr4	121098158	121098171	-	1	NA	promoter-TSS (NM_172700)	promoter-TSS (NM_172700)	79	NM_172700	230709	Mm.34399	NM_172700	ENSMUSG00000043207	Zmpste24	A530043O15Rik|D030046F19|FACE1|Face-1|MADB|STE24|Ste24p	zinc metallopeptidase, STE24	protein-coding
mm_22779.1	chr3	20980293	20980294	+	1	NA	Intergenic	B4A|SINE|B4	-613116	NM_175086	11608	Mm.134863	NM_175086	ENSMUSG00000054988	Agtr1b	AT1B|AT2R1B|Agtr-1b|Angtr-1b	angiotensin II receptor, type 1b	protein-coding
mm_14639.1	chr2	136781936	136781942	+	1	NA	3' UTR (NM_001291056, exon 8 of 8)	3' UTR (NM_001291056, exon 8 of 8)	68489	NM_001291056	20614	Mm.45953	NM_011428	ENSMUSG00000027273	Snap25	Bdr|GENA70|SNAP-25|SUP|sp	synaptosomal-associated protein 25	protein-coding
mm_110844.1	chr12	73046458	73046476	-	1	NA	5' UTR (NM_009189, exon 1 of 2)	5' UTR (NM_009189, exon 1 of 2)	245	NM_009189	20471	Mm.4645	NM_009189	ENSMUSG00000051367	Six1	BB138287	sine oculis-related homeobox 1	protein-coding
mm_158595.1	chrX	151017252	151017296	-	1	NA	promoter-TSS (NM_198110)	promoter-TSS (NM_198110)	19	NM_001168600	237107	Mm.45987	NM_198110	ENSMUSG00000025266	Gnl3l	BC020354	guanine nucleotide binding protein-like 3 (nucleolar)-like	protein-coding
mm_59141.1	chr7	24254745	24254812	+	1	NA	promoter-TSS (NM_018791)	promoter-TSS (NM_018791)	-16	NM_018791	54678	Mm.468052	NM_018791	ENSMUSG00000030486	Zfp108	-	zinc finger protein 108	protein-coding
mm_142317.1	chr17	43017548	43017558	-	1	NA	intron (NM_178589, intron 1 of 5)	CpG	998	NM_178589	94185	Mm.200792	NM_178589	ENSMUSG00000023915	Tnfrsf21	AA959878|DR6|R74815|TR7	tumor necrosis factor receptor superfamily, member 21	protein-coding
mm_108946.1	chr12	102283117	102283194	+	1	NA	promoter-TSS (NM_001161365)	promoter-TSS (NM_001161365)	81	NM_177620	217835	Mm.24145	NM_177620	ENSMUSG00000044456	Rin3	6430500K07|C86933	Ras and Rab interactor 3	protein-coding
mm_39444.1	chr5	17574221	17574240	+	1	NA	promoter-TSS (NM_013657)	promoter-TSS (NM_013657)	-586	NM_013657	20348	Mm.5071	NM_013657	ENSMUSG00000028780	Sema3c	1110036B02Rik|SemE|Semae	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	protein-coding
mm_103215.1	chr11	70654915	70654935	-	1	NA	promoter-TSS (NM_011072)	promoter-TSS (NM_011072)	-275	NM_011072	18643	Mm.2647	NM_011072	ENSMUSG00000018293	Pfn1	Pfn	profilin 1	protein-coding
mm_4291.1	chr1	171766926	171766941	+	1	NA	promoter-TSS (NM_013730)	promoter-TSS (NM_013730)	-199	NM_013730	27218	Mm.103648	NM_013730	ENSMUSG00000015316	Slamf1	4933415F16|AA177906|CD150|CDw150|ESTM51|IPO-3|Slam	signaling lymphocytic activation molecule family member 1	protein-coding
mm_133173.1	chr16	72027650	72027670	+	1	NA	Intergenic	Intergenic	206667	NR_131116	319533	Mm.373754	NR_131115		8030451O07Rik	-	RIKEN cDNA 8030451O07 gene	ncRNA
mm_142628.1	chr17	47395743	47395775	-	1	NA	intron (NM_008189, intron 1 of 3)	intron (NM_008189, intron 1 of 3)	4847	NM_008189	14913	Mm.16224	NM_008189	ENSMUSG00000023982	Guca1a	GC-A|Gcap1|Guca1|mGCAP1	guanylate cyclase activator 1a (retina)	protein-coding
mm_76985.1	chr8	107048161	107048172	-	1	NA	TTS (NM_139229)	TTS (NM_139229)	448	NM_026513	68023	Mm.482335	NM_026513	ENSMUSG00000078931	Pdf	2610019N19Rik	peptide deformylase (mitochondrial)	protein-coding
mm_46760.1	chr5	112251187	112251205	-	1	NA	intron (NM_001312884, intron 1 of 4)	intron (NM_001312884, intron 1 of 4)	1322	NM_001312884	12959	Mm.40324	NM_021351	ENSMUSG00000066975	Cryba4	-	crystallin, beta A4	protein-coding
mm_157145.1	chrX	9460986	9461016	-	1	NA	intron (NM_007807, intron 3 of 12)	intron (NM_007807, intron 3 of 12)	8323	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_47222.1	chr5	121191366	121191400	-	1	NA	promoter-TSS (NM_001109992)	promoter-TSS (NM_001109992)	14	NM_001109992	19247	Mm.8681	NM_011202	ENSMUSG00000043733	Ptpn11	2700084A17Rik|AW536184|PTP1D|PTP2C|SAP-2|SH-PTP2|SH-PTP3|SHP-2|Shp2|Syp	protein tyrosine phosphatase, non-receptor type 11	protein-coding
mm_145890.1	chr18	65582349	65582365	+	1	NA	intron (NM_207255, intron 1 of 5)	intron (NM_207255, intron 1 of 5)	2127	NM_207255	328977	Mm.286232	NM_207255	ENSMUSG00000042439	Zfp532	C530030I18Rik|Znf532|mKIAA1629	zinc finger protein 532	protein-coding
mm_142391.1	chr17	44880834	44880838	-	1	NA	promoter-TSS (NM_029257)	promoter-TSS (NM_029257)	49	NM_029257	75341	Mm.386821	NM_029257		4930564C03Rik	-	RIKEN cDNA 4930564C03 gene	protein-coding
mm_150517.1	chr19	39035316	39035324	+	1	NA	intron (NM_028089, intron 6 of 8)	intron (NM_028089, intron 6 of 8)	-25686	NM_028191	72303	Mm.482578	NM_028191	ENSMUSG00000067231	Cyp2c65	2210009K14Rik	cytochrome P450, family 2, subfamily c, polypeptide 65	protein-coding
mm_138212.1	chr17	34306587	34306601	+	1	NA	intron (NM_010382, intron 1 of 5)	intron (NM_010382, intron 1 of 5)	727	NM_010382	14969	Mm.22564	NM_010382	ENSMUSG00000060586	H2-Eb1	Eb|H-2Eb|H2Eb|Ia-4|Ia4	histocompatibility 2, class II antigen E beta	protein-coding
mm_5257.1	chr1	16656909	16656922	-	1	NA	promoter-TSS (NM_026456)	promoter-TSS (NM_026456)	-50	NM_026456	67923	Mm.289248	NM_026456	ENSMUSG00000079658	Eloc	2610043E24Rik|2610301I15Rik|AA407206|AI987979|AW049146|Tceb1	elongin C	protein-coding
mm_35632.1	chr4	43508715	43508734	-	1	NA	exon (NM_139305, exon 3 of 11)	exon (NM_139305, exon 3 of 11)	1698	NM_139305	230099	Mm.283682	NM_139305	ENSMUSG00000028463	Car9	CAIX|Ca9|MN/CA9	carbonic anhydrase 9	protein-coding
mm_121962.1	chr14	25460062	25460077	-	1	NA	intron (NM_001310666, intron 1 of 23)	CpG	884	NM_183208	328365	Mm.227484	NM_183208	ENSMUSG00000007817	Zmiz1	BC065120|E330020C23|ENSMUSG00000072684|Gm10397|I920194n01|Rai17|Zimp10	zinc finger, MIZ-type containing 1	protein-coding
mm_10160.1	chr2	4401097	4401120	+	1	NA	5' UTR (NM_001177843, exon 1 of 24)	5' UTR (NM_001177843, exon 1 of 24)	132	NM_001177843	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding
mm_71535.1	chr8	46986899	46986910	+	1	NA	promoter-TSS (NM_177304)	promoter-TSS (NM_177304)	17	NM_177304	320981	Mm.211429	NM_177304	ENSMUSG00000038173	Enpp6	4833421B01Rik|B830047L21Rik|D8Ertd514e|E-NPP 6|GPC-Cpde|Npp6	ectonucleotide pyrophosphatase/phosphodiesterase 6	protein-coding
mm_25849.1	chr3	129532454	129532510	+	1	NA	promoter-TSS (NM_130450)	promoter-TSS (NM_130450)	96	NM_130450	170439	Mm.314113	NM_130450	ENSMUSG00000041220	Elovl6	C77826|FAE|LCE	ELOVL family member 6, elongation of long chain fatty acids (yeast)	protein-coding
mm_159770.1	chr5	100159774	100159774	-	1	NA	promoter-TSS (NM_182841)	promoter-TSS (NM_182841)	34	NM_182841	231503	Mm.99790	NM_182841	ENSMUSG00000050640	Tmem150c	-	transmembrane protein 150C	protein-coding
mm_118627.1	chr14	21194575	21194586	+	1	NA	intron (NM_001243041, intron 4 of 10)	intron (NM_001243041, intron 4 of 10)	118428	NM_001243041	11534	Mm.188734	NM_134079	ENSMUSG00000039197	Adk	2310026J05Rik|5033405D03Rik|AI255373|AI987814|Ak	adenosine kinase	protein-coding
mm_31799.1	chr4	63982641	63982651	+	1	NA	intron (NM_011607, intron 15 of 25)	intron (NM_011607, intron 15 of 25)	64369	NM_011607	21923	Mm.980	NM_011607	ENSMUSG00000028364	Tnc	AI528729|C130033P17Rik|Hxb|TN|TN-C|Ten|cytotactin|tenascin-C	tenascin C	protein-coding
mm_20441.1	chr2	129309108	129309132	-	1	NA	intron (NM_010554, intron 1 of 6)	intron (NM_010554, intron 1 of 6)	852	NM_010554	16175	Mm.15534	NM_010554	ENSMUSG00000027399	Il1a	Il-1a	interleukin 1 alpha	protein-coding
mm_75215.1	chr8	39605621	39605643	-	1	NA	3' UTR (NM_031195, exon 9 of 9)	3' UTR (NM_031195, exon 9 of 9)	37046	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_167851.1	chrX	8145245	8145286	-	1	NA	promoter-TSS (NR_033561)	promoter-TSS (NR_033561)	-162	NR_033561	70226	Mm.391639	NR_033561	ENSMUSG00000055188	Rbm3os	2900002K06Rik	RNA binding motif protein 3, opposite strand	ncRNA
mm_112460.1	chr13	5866438	5866458	+	1	NA	intron (NM_011803, intron 2 of 3)	intron (NM_011803, intron 2 of 3)	4959	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_86894.1	chr10	22302978	22302983	+	1	NA	intron (NM_009018, intron 5 of 5)	intron (NM_009018, intron 5 of 5)	-3740	NR_015465	606736	Mm.387042	NR_015465	ENSMUSG00000097352	C920009B18Rik	-	RIKEN cDNA C920009B18 gene	ncRNA
mm_143653.1	chr17	79615447	79615487	-	1	NA	intron (NM_201361, intron 1 of 10)	CpG	567	NM_201361	381110	Mm.209801	NM_201361	ENSMUSG00000036368	Rmdn2	AW061290|Fam82a1|RMD-2|mRMD-2	regulator of microtubule dynamics 2	protein-coding
mm_137991.1	chr17	33637801	33637812	+	1	NA	promoter-TSS (NR_028279)	promoter-TSS (NR_028279)	-250	NM_001002842	378460	Mm.272606	NM_001002842	ENSMUSG00000032739	Pram1	AY665714	PML-RAR alpha-regulated adaptor molecule 1	protein-coding
mm_127619.1	chr15	102460532	102460578	+	1	NA	exon (NM_025385, exon 4 of 5)	exon (NM_025385, exon 4 of 5)	1385	NM_025385	66151	Mm.393955	NM_025385	ENSMUSG00000023048	Prr13	1110020C13Rik|2010324E22Rik	proline rich 13	protein-coding
mm_21714.1	chr2	164608672	164608695	-	1	NA	exon (NM_001080550, exon 3 of 8)	exon (NM_001080550, exon 3 of 8)	4703	NM_001276432	277343	Mm.383292	NM_001080550	ENSMUSG00000070533	Wfdc8	Gm706	WAP four-disulfide core domain 8	protein-coding
mm_31529.1	chr4	55044893	55044897	+	1	NA	intron (NM_172867, intron 7 of 12)	intron (NM_172867, intron 7 of 12)	96950	NM_172867	242466	Mm.102904	NM_172867	ENSMUSG00000060206	Zfp462	6030417H05|9430078C22Rik|Gt4-2|Zfpip	zinc finger protein 462	protein-coding
mm_131099.1	chr16	4964565	4964605	+	1	NA	promoter-TSS (NM_028301)	promoter-TSS (NM_028301)	296	NR_073370	74684	Mm.374835	NM_001271586		4930451G09Rik	-	RIKEN cDNA 4930451G09 gene	protein-coding
mm_102703.1	chr11	66339590	66339593	-	1	NA	intron (NM_001034874, intron 2 of 4)	intron (NM_001034874, intron 2 of 4)	-171040	NM_001099633	237806	Mm.264210	NM_001099633	ENSMUSG00000056752	Dnah9	9030022M04|A230091C01|C230051G16|D11Ertd686e|Dnahc9|mKIAA0357	dynein, axonemal, heavy chain 9	protein-coding
mm_119322.1	chr14	37068043	37068054	+	1	NA	promoter-TSS (NM_173418)	promoter-TSS (NM_173418)	-1	NM_173418	239038	Mm.134302	NM_173418	ENSMUSG00000043418	Lrit2	A930010E21Rik|Lrrc22	leucine-rich repeat, immunoglobulin-like and transmembrane domains 2	protein-coding
mm_94484.1	chr11	6626121	6626191	+	1	NA	promoter-TSS (NM_134011)	promoter-TSS (NM_134011)	-89	NM_134011	21379	Mm.247761	NM_134011	ENSMUSG00000000384	Tbrg4	2310042P22Rik|AA120735|AA408001|AI527316|Cpr2|R74877|Tb-12|mKIAA0948	transforming growth factor beta regulated gene 4	protein-coding
mm_130062.1	chr15	89187420	89187432	-	1	NA	exon (NM_027081, exon 10 of 20)	exon (NM_027081, exon 10 of 20)	-1889	NR_105923	102465578		NR_105923	ENSMUSG00000098663	Mir6958	Gm27581|mmu-mir-6958	microRNA 6958	ncRNA
mm_156390.1	chrX	139800944	139800963	+	1	NA	5' UTR (NM_016675, exon 1 of 2)	5' UTR (NM_016675, exon 1 of 2)	145	NM_016675	12738	Mm.117068	NM_016675	ENSMUSG00000047230	Cldn2	AL022813	claudin 2	protein-coding
mm_148974.1	chr19	7557501	7557513	+	1	NA	promoter-TSS (NM_139269)	promoter-TSS (NM_139269)	48	NM_139269	225845	Mm.274810	NM_139269	ENSMUSG00000060675	Pla2g16	C78643|HRSL3|Hrasls3|Hrev107|MLP-3	phospholipase A2, group XVI	protein-coding
mm_96404.1	chr11	67250972	67250981	+	1	NA	exon (NM_010855, exon 22 of 40)	exon (NM_010855, exon 22 of 40)	13164	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_132737.1	chr16	43889882	43889892	+	1	NA	promoter-TSS (NM_029128)	promoter-TSS (NM_029128)	-15	NM_027801	212153	Mm.209835	NM_027801	ENSMUSG00000022701	Ccdc191	2610015P09Rik|8430422M09Rik|AU040712	coiled-coil domain containing 191	protein-coding
mm_87315.1	chr10	42812432	42812460	+	1	NA	exon (NM_153055, exon 15 of 21)	exon (NM_153055, exon 15 of 21)	-48066	NM_172938	268297	Mm.98731	NM_172938	ENSMUSG00000044770	Scml4	9330161D17|mFLJ00197	sex comb on midleg-like 4 (Drosophila)	protein-coding
mm_131926.1	chr16	23387521	23387552	+	1	NA	Intergenic	L1_Mur3|LINE|L1	-41597	NM_001004151	239766	Mm.208751	NM_001004151	ENSMUSG00000033383	Rtp1	Gm1766|Gm604	receptor transporter protein 1	protein-coding
mm_87591.1	chr10	57486539	57486545	+	1	NA	promoter-TSS (NR_045353)	promoter-TSS (NR_045353)	157	NM_008297	15500	Mm.261395	NM_008297	ENSMUSG00000019878	Hsf2	AI661205	heat shock factor 2	protein-coding
mm_17287.1	chr2	26140533	26140554	-	1	NA	promoter-TSS (NM_001256522)	promoter-TSS (NM_001256522)	-37	NM_001256521	109299	Mm.389259	NM_001256521		C330006A16Rik	AI551216	RIKEN cDNA C330006A16 gene	protein-coding
mm_164615.1	chr17	31161514	31161525	-	1	NA	3' UTR (NM_009362, exon 3 of 3)	3' UTR (NM_009362, exon 3 of 3)	3534	NM_009362	21784	Mm.2854	NM_009362	ENSMUSG00000024032	Tff1	Bcei|PS2	trefoil factor 1	protein-coding
mm_133851.1	chr16	96219481	96219495	+	1	NA	intron (NM_015825, intron 3 of 7)	intron (NM_015825, intron 3 of 7)	-16313	NM_001122993	93961	Mm.154783	NM_033149	ENSMUSG00000074892	B3galt5	1190002B21Rik|AU045265|b3Galt-V	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 5	protein-coding
mm_64852.1	chr7	13034605	13034673	-	1	NA	TTS (NM_145578)	TTS (NM_145578)	138	NM_026885	68953	Mm.295670	NM_026885	ENSMUSG00000033916	Chmp2a	1500016L11Rik	charged multivesicular body protein 2A	protein-coding
mm_133877.1	chr16	96441227	96441240	+	1	NA	intron (NM_008405, intron 1 of 15)	intron (NM_008405, intron 1 of 15)	2381	NM_008405	16415	Mm.12872	NM_008405	ENSMUSG00000000157	Itgb2l	5033406G21Rik|pactolus	integrin beta 2-like	protein-coding
mm_120182.1	chr14	61309820	61309855	+	1	NA	promoter-TSS (NM_177337)	promoter-TSS (NM_177337)	84	NM_177337	219144	Mm.206566	NM_177337	ENSMUSG00000043157	Arl11	ARLTS1|C730007L20Rik	ADP-ribosylation factor-like 11	protein-coding
mm_75268.1	chr8	40659911	40659915	-	1	NA	Intergenic	Intergenic	-15164	NM_010086	13526	Mm.67403	NM_010086	ENSMUSG00000046723	Adam24	Dtgn5	a disintegrin and metallopeptidase domain 24 (testase 1)	protein-coding
mm_90289.1	chr10	123432566	123432570	+	1	NA	intron (NM_182807, intron 2 of 5)	U2|snRNA|snRNA	168492	NM_001252387	268354	Mm.51939	NM_182807	ENSMUSG00000044071	Fam19a2	6330575M02|FAM19A2 TAFA-2|TAFA2|Tafa-2	family with sequence similarity 19, member A2	protein-coding
mm_138552.1	chr17	35264837	35264850	+	1	NA	intron (NM_010380, intron 3 of 7)	B1_Mm|SINE|Alu	1720	NM_001267808	14980	Mm.439675	NM_001267808		H2-L	H-2L	histocompatibility 2, D region locus L	protein-coding
mm_173261.1	chrX	9487954	9487955	-	1	NA	Intergenic	RLTR9E|LTR|ERVK	-18630	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_142259.1	chr17	39843629	39843649	-	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	642	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_102394.1	chr11	58999363	58999407	-	1	NA	exon (NM_001171512, exon 93 of 104)	exon (NM_001171512, exon 93 of 104)	21292	NM_053168	94091	Mm.248049	NM_053168	ENSMUSG00000020455	Trim11	-	tripartite motif-containing 11	protein-coding
mm_131046.1	chr16	3909033	3909089	+	1	NA	promoter-TSS (NM_029738)	promoter-TSS (NM_029738)	52	NM_029738	76779	Mm.458921	NM_029738	ENSMUSG00000014232	Cluap1	2310030D15Rik|2610111M03Rik	clusterin associated protein 1	protein-coding
mm_78164.1	chr9	21028258	21028285	+	1	NA	3' UTR (NM_010493, exon 7 of 7)	3' UTR (NM_010493, exon 7 of 7)	-1102	NM_023892	78369	Mm.30220	NM_023892	ENSMUSG00000001014	Icam4	1810015M19Rik|Cd242|ICAM-4	intercellular adhesion molecule 4, Landsteiner-Wiener blood group	protein-coding
mm_52984.1	chr6	123263871	123263890	+	1	NA	intron (NM_001163161, intron 1 of 5)	B1F|SINE|Alu	1773	NM_010819	17474	Mm.441101	NM_010819	ENSMUSG00000030144	Clec4d	Clecsf8|Mpcl|mcl	C-type lectin domain family 4, member d	protein-coding
mm_130981.1	chr15	103344731	103344767	-	1	NA	3' UTR (NM_010577, exon 30 of 30)	3' UTR (NM_010577, exon 30 of 30)	-4663	NM_013866	29813	Mm.14099	NM_013866	ENSMUSG00000000552	Zfp385a	Hzf|Zfp385|Znf385a	zinc finger protein 385A	protein-coding
mm_10978.1	chr2	25823145	25823160	+	1	NA	promoter-TSS (NM_029959)	promoter-TSS (NM_029959)	-1	NM_029959	77704	Mm.159974	NM_029959	ENSMUSG00000023210	Lcn9	9230102I19Rik	lipocalin 9	protein-coding
mm_3216.1	chr1	135845402	135845412	+	1	NA	intron (NM_001130174, intron 3 of 13)	intron (NM_001130174, intron 3 of 13)	4546	NM_001130176	21956	Mm.247470	NM_011619	ENSMUSG00000026414	Tnnt2	Tnt|cTnT	troponin T2, cardiac	protein-coding
mm_88044.1	chr10	67538464	67538499	+	1	NA	intron (NM_001347458, intron 2 of 2)	CpG	551	NM_001347458	13654	Mm.290421	NM_010118	ENSMUSG00000037868	Egr2	Egr-2|Krox-20|Krox20|NGF1-B|Zfp-25|Zfp-6	early growth response 2	protein-coding
mm_47150.1	chr5	120588616	120588651	-	1	NA	promoter-TSS (NM_145853)	promoter-TSS (NM_145853)	-20	NM_145853	252972	Mm.114054	NM_145853	ENSMUSG00000032741	Tpcn1	5730403B01Rik|Tpc1|mKIAA1169	two pore channel 1	protein-coding
mm_124630.1	chr15	4026557	4026567	+	1	NA	non-coding (NR_028266, exon 1 of 2)	non-coding (NR_028266, exon 1 of 2)	134	NM_024188	67041	Mm.13445	NM_024188	ENSMUSG00000022186	Oxct1	2610008O03Rik|Oxct|Oxct2a|Scot-s	3-oxoacid CoA transferase 1	protein-coding
mm_158659.1	chrX	157414773	157414792	-	1	NA	5' UTR (NM_011077, exon 1 of 22)	5' UTR (NM_011077, exon 1 of 22)	504	NM_011077	18675	Mm.2529	NM_011077	ENSMUSG00000057457	Phex	Gy|HPDR|HPDR1|Hyp|PEX	phosphate regulating endopeptidase homolog, X-linked	protein-coding
mm_35249.1	chr4	19877659	19877669	-	1	NA	3' UTR (NM_175406, exon 8 of 8)	3' UTR (NM_175406, exon 8 of 8)	44902	NM_175406	242341	Mm.19298	NM_175406	ENSMUSG00000028238	Atp6v0d2	1620401A02Rik|AI324824|V-ATPase	ATPase, H+ transporting, lysosomal V0 subunit D2	protein-coding
mm_130341.1	chr15	97731411	97731435	-	1	NA	promoter-TSS (NM_001168693)	promoter-TSS (NM_001168693)	-18	NM_001168693	19011	Mm.1001	NM_008902	ENSMUSG00000022468	Endou	Pp11r|Tcl-30	endonuclease, polyU-specific	protein-coding
mm_141070.1	chr17	25832891	25832966	-	1	NA	5' UTR (NM_019719, exon 1 of 7)	5' UTR (NM_019719, exon 1 of 7)	433	NM_019719	56424	Mm.277599	NM_019719	ENSMUSG00000039615	Stub1	0610033N24Rik|2210017D18Rik|2310040B03Rik|AW046544|Chip	STIP1 homology and U-Box containing protein 1	protein-coding
mm_91093.1	chr10	19062129	19062137	-	1	NA	Intergenic	Intergenic	-46723	NM_009397	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_94786.1	chr11	22184516	22184518	+	1	NA	intron (NM_001252515, intron 5 of 24)	Lx7|LINE|L1	102278	NM_153078	216565	Mm.491265	NM_153078	ENSMUSG00000042302	Ehbp1	AF424697|Flj21950|NACSIN	EH domain binding protein 1	protein-coding
mm_71912.1	chr8	70089432	70089456	+	1	NA	3' UTR (NM_177900, exon 5 of 5)	3' UTR (NM_177900, exon 5 of 5)	5915	NM_177900	330790	Mm.152048	NM_177900	ENSMUSG00000007594	Hapln4	9330174O11|Bral2|Lpr4	hyaluronan and proteoglycan link protein 4	protein-coding
mm_42484.1	chr5	115470871	115470880	+	1	NA	exon (NM_011107, exon 2 of 4)	exon (NM_011107, exon 2 of 4)	4609	NM_011107	18778	Mm.20190	NM_011107	ENSMUSG00000029522	Pla2g1b	Pla2a|sPLA2IB	phospholipase A2, group IB, pancreas	protein-coding
mm_44595.1	chr5	24995885	24995919	-	1	NA	promoter-TSS (NM_001310480)	promoter-TSS (NM_001310480)	-149	NM_001310480	108099	Mm.33649	NM_145401	ENSMUSG00000028944	Prkag2	2410051C13Rik|AAKG|AAKG2|AI854673|H91620p|WPWS	protein kinase, AMP-activated, gamma 2 non-catalytic subunit	protein-coding
mm_59507.1	chr7	27560528	27560555	+	1	NA	promoter-TSS (NM_001122767)	promoter-TSS (NM_001122767)	65	NM_001122767	66367	Mm.29831	NM_175107	ENSMUSG00000049643	2310022A10Rik	-	RIKEN cDNA 2310022A10 gene	protein-coding
mm_165423.1	chr2	151459148	151459167	+	1	NA	Intergenic	Intergenic	16994	NM_198655	381393	Mm.280614	NM_198655	ENSMUSG00000061525	4921509C19Rik	Gm1005	RIKEN cDNA 4921509C19 gene	protein-coding
mm_170631.1	chr19	8034016	8034031	+	1	NA	Intergenic	IAPLTR4|LTR|ERVK	-67996	NM_134256	171405	Mm.326517	NM_134256	ENSMUSG00000067656	Slc22a27	Oat9|mOAT6-L|mOAT6-S	solute carrier family 22, member 27	protein-coding
mm_171115.1	chr3	138396118	138396119	+	1	NA	Intergenic	Intergenic	-19379	NM_011996	26876	Mm.158750	NM_011996	ENSMUSG00000037797	Adh4	Adh2	alcohol dehydrogenase 4 (class II), pi polypeptide	protein-coding
mm_135615.1	chr16	52271267	52271280	-	1	NA	intron (NM_009655, intron 11 of 15)	intron (NM_009655, intron 11 of 15)	181808	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_116085.1	chr13	28538413	28538414	-	1	NA	intron (NR_045053, intron 7 of 8)	Lx7|LINE|L1	172460	NR_105787	102466635		NR_105787	ENSMUSG00000099158	Mir6368	Gm27800|mmu-mir-6368	microRNA 6368	ncRNA
mm_91458.1	chr10	34044303	34044317	-	1	NA	promoter-TSS (NM_001081165)	promoter-TSS (NM_001081165)	3	NM_001081165	270711	Mm.303077	NM_001081165	ENSMUSG00000039508	Fam26d	4732454E20Rik|AI586164|Gm643	family with sequence similarity 26, member D	protein-coding
mm_157009.1	chrX	7605321	7605368	-	1	NA	promoter-TSS (NM_138603)	promoter-TSS (NM_138603)	76	NM_138603	54638	Mm.288192	NM_138603	ENSMUSG00000031143	Ccdc22	AI481216|DXImx40e|Ppp1r3f|Sfc22	coiled-coil domain containing 22	protein-coding
mm_8380.1	chr1	151250808	151250837	-	1	NA	Intergenic	MLT1H|LTR|ERVL-MaLR	-93676	NM_001039512	117198	Mm.33764	NM_028582	ENSMUSG00000023150	Ivns1abp	1190004M08Rik|1700126I16Rik|AA960440|HSPC068|ND1|NS-1|NS1-BP|Nd1-L|Nd1-S|mKIAA0850	influenza virus NS1A binding protein	protein-coding
mm_147745.1	chr18	61131125	61131141	-	1	NA	TTS (NM_178277)	TTS (NM_178277)	13665	NR_105949	102466212		NR_105949	ENSMUSG00000098389	Mir6983	Gm27496|mmu-mir-6983	microRNA 6983	ncRNA
mm_92032.1	chr10	62486556	62486566	-	1	NA	promoter-TSS (NM_001113355)	promoter-TSS (NM_001113355)	37	NM_001113355	30930	Mm.260703	NM_133672	ENSMUSG00000020078	Vps26a	AA407240|HB58|Vps26	VPS26 retromer complex component A	protein-coding
mm_52221.1	chr6	103510961	103511008	+	1	NA	5' UTR (NM_007697, exon 1 of 27)	5' UTR (NM_007697, exon 1 of 27)	108	NM_007697	12661	Mm.251288	NM_007697	ENSMUSG00000030077	Chl1	A530023M13Rik|AI465420|CALL|LICAM2	cell adhesion molecule L1-like	protein-coding
mm_6365.1	chr1	72216868	72216877	-	1	NA	Intergenic	RLTR34D_MM|LTR|ERVK	-4565	NM_001005423	381269	Mm.422636	NM_001005423	ENSMUSG00000039395	Mreg	Gm974|Wdt2|dsu	melanoregulin	protein-coding
mm_80659.1	chr9	90054581	90054590	+	1	NA	exon (NM_007801, exon 1 of 12)	exon (NM_007801, exon 1 of 12)	318	NM_001312649	13036	Mm.2277	NM_007801	ENSMUSG00000032359	Ctsh	AL022844	cathepsin H	protein-coding
mm_59857.1	chr7	29983918	29983942	+	1	NA	promoter-TSS (NM_001167873)	promoter-TSS (NM_001167873)	-25	NM_001167873	243905	Mm.322432	NM_001033355	ENSMUSG00000074221	Zfp568	C80731|Gm1691|Znf568|chato	zinc finger protein 568	protein-coding
mm_101412.1	chr11	28584220	28584229	-	1	NA	promoter-TSS (NM_181577)	promoter-TSS (NM_181577)	100	NM_001166661	216613	Mm.93759	NM_181577	ENSMUSG00000032878	Ccdc85a	-	coiled-coil domain containing 85A	protein-coding
mm_101923.1	chr11	50200914	50200951	-	1	NA	TTS (NM_026543)	TTS (NM_026543)	9888	NM_001290769	18412	Mm.40828	NM_011018	ENSMUSG00000015837	Sqstm1	A170|OSF-6|Osi|STAP|STONE14|p62	sequestosome 1	protein-coding
mm_47738.1	chr5	130248049	130248052	-	1	NA	intron (NM_023248, intron 4 of 4)	intron (NM_023248, intron 4 of 4)	7480	NM_023248	66711	Mm.280484	NM_023248	ENSMUSG00000025337	Sbds	4733401P19Rik|AI836084|CGI-97|SDS	Shwachman-Bodian-Diamond syndrome homolog (human)	protein-coding
mm_38102.1	chr4	134372530	134372561	-	1	NA	promoter-TSS (NM_019578)	promoter-TSS (NM_019578)	2	NM_019578	56219	Mm.30978	NM_019578	ENSMUSG00000028838	Extl1	D430033M16Rik	exostoses (multiple)-like 1	protein-coding
mm_3710.1	chr1	153907931	153907944	+	1	NA	exon (NM_008131, exon 7 of 7)	exon (NM_008131, exon 7 of 7)	8008	NM_008131	14645	Mm.210745	NM_008131	ENSMUSG00000026473	Glul	GS|Glns	glutamate-ammonia ligase (glutamine synthetase)	protein-coding
mm_155839.1	chrX	100798416	100798431	+	1	NA	intron (NM_001177778, intron 11 of 19)	intron (NM_001177778, intron 11 of 19)	21152	NM_001177780	53310	Mm.4615	NM_016747	ENSMUSG00000000881	Dlg3	Dlgh3|SAP102|mKIAA1232	discs, large homolog 3 (Drosophila)	protein-coding
mm_87424.1	chr10	50777204	50777226	+	1	NA	intron (NM_198007, intron 36 of 41)	L1MA8|LINE|L1	-118436	NM_011376	20464	Mm.4774	NM_011376	ENSMUSG00000019913	Sim1	bHLHe14|mSIM1	single-minded homolog 1 (Drosophila)	protein-coding
mm_25775.1	chr3	126596814	126596854	+	1	NA	promoter-TSS (NM_001293663)	promoter-TSS (NM_001293663)	-117	NM_001293663	108058	Mm.255822	NM_023813	ENSMUSG00000053819	Camk2d	2810011D23Rik|8030469K03Rik|CaMK II|[d]-CaMKII	calcium/calmodulin-dependent protein kinase II, delta	protein-coding
mm_41008.1	chr5	81020747	81020761	+	1	NA	promoter-TSS (NM_198702)	promoter-TSS (NM_198702)	183	NM_001347369	319387	Mm.273631	NM_198702	ENSMUSG00000037605	Adgrl3	5430402I23Rik|CIRL-3|D130075K09Rik|Gm1379|LEC3|Lphn3|mKIAA0768	adhesion G protein-coupled receptor L3	protein-coding
mm_167099.1	chr7	110164882	110164926	-	1	NA	Intergenic	Intergenic	42845	NM_009516	22390	Mm.287173	NM_009516	ENSMUSG00000031016	Wee1	Wee1A	WEE 1 homolog 1 (S. pombe)	protein-coding
mm_94354.1	chr11	4941273	4941285	+	1	NA	exon (NM_010904, exon 4 of 4)	exon (NM_010904, exon 4 of 4)	-6242	NM_001243043	11764	Mm.274816	NM_007454	ENSMUSG00000009090	Ap1b1	Adtb1|b2b1660Clo	adaptor protein complex AP-1, beta 1 subunit	protein-coding
mm_104085.1	chr11	86602362	86602372	-	1	NA	intron (NM_029478, intron 9 of 11)	intron (NM_029478, intron 9 of 11)	-18209	NR_029738	387140		NR_029738	ENSMUSG00000065455	Mir21a	Mir21|Mirn21|mmu-mir-21|mmu-mir-21a	microRNA 21a	ncRNA
mm_26220.1	chr3	138860490	138860506	+	1	NA	intron (NM_019571, intron 1 of 7)	intron (NM_019571, intron 1 of 7)	118290	NM_019571	56224	Mm.31927	NM_019571	ENSMUSG00000028152	Tspan5	2810455A09Rik|4930505M03Rik|NET-4|Tm4sf9	tetraspanin 5	protein-coding
mm_9089.1	chr1	168432307	168432347	-	1	NA	promoter-TSS (NM_001291509)	promoter-TSS (NM_001291509)	-158	NM_008783	18514	Mm.43358	NM_008783	ENSMUSG00000052534	Pbx1	2310056B04Rik|D230003C07Rik|Pbx-1	pre B cell leukemia homeobox 1	protein-coding
mm_123966.1	chr14	74947866	74947883	-	1	NA	promoter-TSS (NM_001033439)	promoter-TSS (NM_001033439)	3	NM_001252132	380916	Mm.288868	NM_001033439	ENSMUSG00000068015	Lrch1	4832412D13Rik|AI552548|AW215503|Chdc1|mKIAA1016	leucine-rich repeats and calponin homology (CH) domain containing 1	protein-coding
mm_164338.1	chr16	11456611	11456626	+	1	NA	intron (NM_001290148, intron 6 of 13)	intron (NM_001290148, intron 6 of 13)	50970	NM_001290148	74478	Mm.325831	NM_028964	ENSMUSG00000071669	Snx29	4933437K13Rik|ENSMUSG00000079738|Gm11170|Gm1737|Gm930|Rundc2a	sorting nexin 29	protein-coding
mm_85248.1	chr9	99140066	99140080	-	1	NA	5' UTR (NM_029094, exon 1 of 24)	5' UTR (NM_029094, exon 1 of 24)	138	NM_029094	74769	Mm.213128	NM_029094	ENSMUSG00000032462	Pik3cb	1110001J02Rik|AI447572|p110beta	phosphatidylinositol 3-kinase, catalytic, beta polypeptide	protein-coding
mm_154171.1	chr19	58730083	58730087	-	1	NA	exon (NM_018874, exon 3 of 13)	exon (NM_018874, exon 3 of 13)	1198	NM_018874	18946	Mm.10753	NM_018874	ENSMUSG00000042179	Pnliprp1	Plrp1	pancreatic lipase related protein 1	protein-coding
mm_116027.1	chr13	25269167	25269213	-	1	NA	intron (NM_009513, intron 1 of 3)	intron (NM_009513, intron 1 of 3)	806	NM_009513	22360	Mm.4766	NM_009513	ENSMUSG00000048978	Nrsn1	Neurensin-1|Neuro-p24|Vmp	neurensin 1	protein-coding
mm_104682.1	chr11	97700328	97700349	-	1	NA	promoter-TSS (NM_001163308)	promoter-TSS (NM_001163308)	159	NM_009545	22658	Mm.2418	NM_009545	ENSMUSG00000018537	Pcgf2	Mel18|Rnf110|Zfp144|mel-18	polycomb group ring finger 2	protein-coding
mm_118872.1	chr14	25857564	25857567	+	1	NA	intron (NM_013469, intron 1 of 14)	intron (NM_013469, intron 1 of 14)	15410	NM_013469	11744	Mm.294083	NM_013469	ENSMUSG00000021866	Anxa11	A830099O17Rik|Anx11	annexin A11	protein-coding
mm_149526.1	chr19	12460786	12460796	+	1	NA	promoter-TSS (NM_010821)	promoter-TSS (NM_010821)	12	NM_010821	17476	Mm.3999	NM_010821	ENSMUSG00000046805	Mpeg1	MPS1|Mpg-1	macrophage expressed gene 1	protein-coding
mm_108938.1	chr12	101976007	101976017	+	1	NA	promoter-TSS (NM_016856)	promoter-TSS (NM_016856)	38	NM_016856	51786	Mm.716	NM_016856	ENSMUSG00000041781	Cpsf2	100kDa|2610024B04Rik|AI662483|Cpsf|MCPSF|mKIAA1367	cleavage and polyadenylation specific factor 2	protein-coding
mm_10990.1	chr2	26315460	26315466	+	1	NA	promoter-TSS (NM_001199146)	promoter-TSS (NM_001199146)	-70	NM_001199146	67839	Mm.266611	NM_153410	ENSMUSG00000026930	Gpsm1	1810037C22Rik|AW107933|Ags3	G-protein signalling modulator 1 (AGS3-like, C. elegans)	protein-coding
mm_58716.1	chr7	13014745	13014757	+	1	NA	Intergenic	Intergenic	-4951	NM_001024699	232879	Mm.279272	NM_001024699	ENSMUSG00000049600	Zbtb45	BB161562|Gm157|Zfp499	zinc finger and BTB domain containing 45	protein-coding
mm_85742.1	chr9	108567315	108567333	-	1	NA	promoter-TSS (NR_029577)	promoter-TSS (NR_029577)	18	NM_023247	66706	Mm.29471	NM_023247	ENSMUSG00000070283	Ndufaf3	4733401H18Rik	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, assembly factor 3	protein-coding
mm_29631.1	chr3	121616079	121616086	-	1	NA	Intergenic	RLTR12E|LTR|ERVK	27403	NR_036456	100503044	Mm.65320	NM_176992	ENSMUSG00000044522	A730020M07Rik	-	RIKEN cDNA A730020M07 gene	ncRNA
mm_98293.1	chr11	89073922	89073934	+	1	NA	promoter-TSS (NM_001033266)	promoter-TSS (NM_001033266)	87	NM_001033266	217071	Mm.342127	NM_001033266	ENSMUSG00000072553	Gm525	-	predicted gene 525	protein-coding
mm_49851.1	chr6	38381485	38381528	+	1	NA	promoter-TSS (NM_153600)	promoter-TSS (NM_153600)	-18	NM_153600	264134	Mm.253446	NM_153600	ENSMUSG00000056832	Ttc26	9330141E21Rik|9430097H08Rik|hop|hpy	tetratricopeptide repeat domain 26	protein-coding
mm_56771.1	chr6	116461121	116461140	-	1	NA	promoter-TSS (NM_009662)	promoter-TSS (NM_009662)	48	NM_009662	11689	Mm.41072	NM_009662	ENSMUSG00000025701	Alox5	5-LO|5-LOX|5LO|5LX|AI850497|F730011J02	arachidonate 5-lipoxygenase	protein-coding
mm_139669.1	chr17	57412038	57412049	+	1	NA	intron (NM_010130, intron 9 of 21)	intron (NM_010130, intron 9 of 21)	53357	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_26022.1	chr3	135438544	135438584	+	1	NA	promoter-TSS (NM_025356)	promoter-TSS (NM_025356)	101	NR_030689	319587	Mm.358971	NR_030689	ENSMUSG00000097032	4930539J05Rik	8030475D13Rik	RIKEN cDNA 4930539J05 gene	ncRNA
mm_157527.1	chrX	51017925	51017939	-	1	NA	promoter-TSS (NM_172413)	promoter-TSS (NM_172413)	86	NM_172413	72065	Mm.43152	NM_172413	ENSMUSG00000050029	Rap2c	2010200P20Rik|AI194294|AL022976	RAP2C, member of RAS oncogene family	protein-coding
mm_44974.1	chr5	36821871	36821880	-	1	NA	exon (NM_008550, exon 6 of 19)	exon (NM_008550, exon 6 of 19)	8774	NM_008550	17160	Mm.761	NM_008550	ENSMUSG00000029119	Man2b2	mKIAA0935	mannosidase 2, alpha B2	protein-coding
mm_168271.1	chr10	96077867	96077883	-	1	NA	Intergenic	Intergenic	137212	NM_001001932	216238	Mm.210035	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding
mm_34690.1	chr4	152008895	152008928	+	1	NA	promoter-TSS (NM_001033352)	promoter-TSS (NM_001033352)	20	NM_001033352	242785	Mm.22306	NM_001033352	ENSMUSG00000073700	Klhl21	1810045K06Rik|D330008A20|mKIAA0469	kelch-like 21	protein-coding
mm_56035.1	chr6	86649930	86649982	-	1	NA	3' UTR (NM_010751, exon 6 of 6)	3' UTR (NM_010751, exon 6 of 6)	19203	NM_010751	17119	Mm.279580	NM_010751	ENSMUSG00000001156	Mxd1	AW122478|Mad|Mad1	MAX dimerization protein 1	protein-coding
mm_119987.1	chr14	55578445	55578539	+	1	NA	promoter-TSS (NM_011189)	promoter-TSS (NM_011189)	-2	NM_011189	19186	Mm.830	NM_011189	ENSMUSG00000022216	Psme1	AW413925|PA28a	proteasome (prosome, macropain) activator subunit 1 (PA28 alpha)	protein-coding
mm_130360.1	chr15	97767882	97767930	-	1	NA	promoter-TSS (NM_001177811)	promoter-TSS (NM_001177811)	-240	NM_001177811	223864	Mm.24028	NM_144850	ENSMUSG00000022469	Rapgef3	2310016P22Rik|9330170P05Rik|Epac|Epac1	Rap guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_108175.1	chr12	76406103	76406116	+	1	NA	exon (NM_001002012, exon 2 of 2)	exon (NM_001002012, exon 2 of 2)	1739	NM_008301	15512	Mm.296181	NM_008301	ENSMUSG00000059970	Hspa2	70kDa|HSP70.2|HSP70A2|Hsp70-2	heat shock protein 2	protein-coding
mm_161637.1	chr16	93730067	93730067	+	1	NA	intron (NM_027293, intron 2 of 36)	intron (NM_027293, intron 2 of 36)	18160	NM_027293	70028	Mm.23230	NM_026700	ENSMUSG00000022946	Dopey2	0610038M01Rik|2610510B01Rik|AI503246|C21orf5|mKIAA0933	dopey family member 2	protein-coding
mm_130080.1	chr15	89374084	89374145	-	1	NA	promoter-TSS (NM_001111288)	promoter-TSS (NM_001111288)	-296	NM_001111288	100126824	Mm.287977	NM_001111288	ENSMUSG00000091780	Sco2	-	SCO2 cytochrome c oxidase assembly protein	protein-coding
mm_43844.1	chr5	143181007	143181009	+	1	NA	promoter-TSS (NM_177880)	promoter-TSS (NM_177880)	-9	NM_177880	330228	Mm.255752	NM_177880	ENSMUSG00000029586	Spdye4b	4933411G11Rik	speedy/RINGO cell cycle regulator family, member E4B	protein-coding
mm_107146.1	chr12	21543285	21543315	+	1	NA	Intergenic	CpG	-125864	NM_011739	22630	Mm.289630	NM_011739	ENSMUSG00000076432	Ywhaq	2700028P07Rik|AA409740|AU021156|R74690	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide	protein-coding
mm_106969.1	chr12	8938451	8938465	+	1	NA	3' UTR (NM_008640, exon 7 of 7)	3' UTR (NM_008640, exon 7 of 7)	-9471	NM_010770	17182	Mm.42226	NM_010770	ENSMUSG00000020583	Matn3	AV009181	matrilin 3	protein-coding
mm_140645.1	chr17	12682816	12682820	-	1	NA	3' UTR (NM_010515, exon 48 of 48)	3' UTR (NM_010515, exon 48 of 48)	-6980	NM_009202	20517	Mm.594	NM_009202	ENSMUSG00000023829	Slc22a1	Lx1|Oct1|Orct|Orct1	solute carrier family 22 (organic cation transporter), member 1	protein-coding
mm_38855.1	chr4	149408471	149408480	-	1	NA	intron (NM_022022, intron 1 of 26)	intron (NM_022022, intron 1 of 26)	18156	NM_022022	63958	Mm.415260	NM_022022	ENSMUSG00000028960	Ube4b	4930551I19Rik|4933406G05Rik|AU014668|D4Bwg0973e|UFD2|UFD2a|Ufd2p|mKIAA0684	ubiquitination factor E4B	protein-coding
mm_24490.1	chr3	92352142	92352144	+	1	NA	promoter-TSS (NM_011471)	promoter-TSS (NM_011471)	0	NM_011471	20759	Mm.261596	NM_011471	ENSMUSG00000055030	Sprr2e	-	small proline-rich protein 2E	protein-coding
mm_105945.1	chr11	115276917	115276943	-	1	NA	promoter-TSS (NM_007997)	promoter-TSS (NM_007997)	39	NM_007997	14149	Mm.4719	NM_007997	ENSMUSG00000018861	Fdxr	-	ferredoxin reductase	protein-coding
mm_18194.1	chr2	45116965	45116998	-	1	NA	Intergenic	Intergenic	-3702	NM_015753	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_33967.1	chr4	137594313	137594319	+	1	NA	5' UTR (NM_130879, exon 1 of 28)	5' UTR (NM_130879, exon 1 of 28)	127	NM_130879	170707	Mm.218478	NM_130879	ENSMUSG00000043411	Usp48	2810449C13Rik|AI115503|BC021769|D330022K21Rik|Usp31	ubiquitin specific peptidase 48	protein-coding
mm_139467.1	chr17	55959766	55959784	+	1	NA	promoter-TSS (NR_108021)	promoter-TSS (NR_108021)	-374	NR_108021	100504333	Mm.391908	NR_108021	ENSMUSG00000097077	Gm16712	-	predicted gene, 16712	ncRNA
mm_135702.1	chr16	52453162	52453188	-	1	NA	promoter-TSS (NM_001331110)	promoter-TSS (NM_001331110)	-94	NM_001331110	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_114273.1	chr13	58157643	58157689	+	1	NA	promoter-TSS (NM_001048060)	promoter-TSS (NM_001048060)	17	NM_198004	75731	Mm.293919	NM_198004	ENSMUSG00000050002	Idnk	5133401N09Rik	idnK gluconokinase homolog (E. coli)	protein-coding
mm_154755.1	chrX	10717452	10717491	+	1	NA	5' UTR (NM_001166635, exon 1 of 2)	5' UTR (NM_001166635, exon 1 of 2)	106	NM_001166635	68041	Mm.29429	NM_026524	ENSMUSG00000008035	Mid1ip1	3110038L01Rik|Mig12|S14R	Mid1 interacting protein 1 (gastrulation specific G12-like (zebrafish))	protein-coding
mm_69899.1	chr7	141638795	141638808	-	1	NA	intron (NM_001330001, intron 31 of 33)	intron (NM_001330001, intron 31 of 33)	16518	NM_001330001	353328	Mm.246621	NM_181729	ENSMUSG00000048191	Muc6	-	mucin 6, gastric	protein-coding
mm_142039.1	chr17	35264069	35264104	-	1	NA	exon (NM_001267808, exon 7 of 11)	exon (NM_001267808, exon 7 of 11)	963	NM_001267808	14980	Mm.439675	NM_001267808		H2-L	H-2L	histocompatibility 2, D region locus L	protein-coding
mm_20433.1	chr2	129306539	129306552	-	1	NA	exon (NM_010554, exon 4 of 7)	exon (NM_010554, exon 4 of 7)	3427	NM_010554	16175	Mm.15534	NM_010554	ENSMUSG00000027399	Il1a	Il-1a	interleukin 1 alpha	protein-coding
mm_73640.1	chr8	110741058	110741071	+	1	NA	TTS (NM_001135100)	TTS (NM_001135100)	15338	NM_001310591	244654	Mm.490385	NM_198625	ENSMUSG00000033763	Mtss1l	ABBA	metastasis suppressor 1-like	protein-coding
mm_505.1	chr1	37153841	37153857	+	1	NA	Intergenic	Intergenic	-64429	NM_001282010	12790	Mm.214224	NM_009918	ENSMUSG00000026114	Cnga3	CNG3	cyclic nucleotide gated channel alpha 3	protein-coding
mm_112450.1	chr13	5862600	5862621	+	1	NA	intron (NM_011803, intron 1 of 3)	intron (NM_011803, intron 1 of 3)	1121	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_118674.1	chr14	22031964	22031974	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	12257	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_18355.1	chr2	58195475	58195491	-	1	NA	Intergenic	Intergenic	31509	NR_045895	100042926	Mm.446515	NR_045895	ENSMUSG00000086862	Gm13546	OTTMUSG00000012675	predicted gene 13546	ncRNA
mm_71325.1	chr8	44950656	44950669	+	1	NA	exon (NM_001081286, exon 1 of 26)	exon (NM_001081286, exon 1 of 26)	454	NM_001081286	14107	Mm.27365	NM_001081286	ENSMUSG00000070047	Fat1	2310038E12Rik|AU023433|Fath|mFat1	FAT atypical cadherin 1	protein-coding
mm_36668.1	chr4	95487382	95487398	-	1	NA	Intergenic	Intergenic	-70117	NM_001113412	75578	Mm.276098	NM_029347	ENSMUSG00000028573	Fggy	2310009E04Rik	FGGY carbohydrate kinase domain containing	protein-coding
mm_68939.1	chr7	126502381	126502419	-	1	NA	promoter-TSS (NM_001347658)	promoter-TSS (NM_001347658)	25	NM_001347658	233871	Mm.231450	NM_183020	ENSMUSG00000032637	Atxn2l	A2D|A2LG|A2RP|A2lp|Atxnl2	ataxin 2-like	protein-coding
mm_54386.1	chr6	31218422	31218440	-	1	NA	promoter-TSS (NR_110471)	promoter-TSS (NR_110471)	43	NR_110470	232685	Mm.443019	NM_144555	ENSMUSG00000044471	Lncpint	Lincpint|MNCb-1768|Pint|linc-Pint	long non-protein coding RNA, Trp53 induced transcript	ncRNA
mm_168572.1	chr11	70983026	70983031	-	1	NA	promoter-TSS (NM_007573)	promoter-TSS (NM_007573)	-2	NM_007573	12261	Mm.30049	NM_007573	ENSMUSG00000018446	C1qbp	AA407365|AA986492|D11Wsu182e|HABP1|P32|gC1qBP	complement component 1, q subcomponent binding protein	protein-coding
mm_169211.1	chr13	66563789	66563802	-	1	NA	Intergenic	Intergenic	-122677	NM_001290196	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
mm_150631.1	chr19	41382984	41382995	+	1	NA	intron (NM_031376, intron 1 of 16)	intron (NM_031376, intron 1 of 16)	2081	NM_031376	83490	Mm.222266	NM_031376	ENSMUSG00000025017	Pik3ap1	1810044J04Rik|BCAP	phosphoinositide-3-kinase adaptor protein 1	protein-coding
mm_25228.1	chr3	103860295	103860307	+	1	NA	promoter-TSS (NM_008979)	promoter-TSS (NM_008979)	24	NM_008979	19260	Mm.395	NM_008979	ENSMUSG00000027843	Ptpn22	70zpep|PEP|Ptpn8	protein tyrosine phosphatase, non-receptor type 22 (lymphoid)	protein-coding
mm_141012.1	chr17	25015709	25015718	-	1	NA	promoter-TSS (NM_020608)	promoter-TSS (NM_020608)	-373	NM_134126	106633	Mm.32802	NM_134126	ENSMUSG00000024169	Ift140	AI661311|Tce5|Wdtc2|mKIAA0590	intraflagellar transport 140	protein-coding
mm_103624.1	chr11	78697284	78697290	-	1	NA	5' UTR (NM_008702, exon 1 of 11)	5' UTR (NM_008702, exon 1 of 11)	138	NM_008702	18099	Mm.9001	NM_008702	ENSMUSG00000017376	Nlk	AI194375	nemo like kinase	protein-coding
mm_128068.1	chr15	26895950	26895967	-	1	NA	promoter-TSS (NM_176959)	promoter-TSS (NM_176959)	-394	NM_176959	448987	Mm.253378	NM_176959	ENSMUSG00000043556	Fbxl7	AL023057|D230018M15Rik|FBL7|Fbl6	F-box and leucine-rich repeat protein 7	protein-coding
mm_125482.1	chr15	54600861	54600867	+	1	NA	3' UTR (NM_178920, exon 4 of 4)	3' UTR (NM_178920, exon 4 of 4)	29498	NM_178920	105853	Mm.410994	NM_178920	ENSMUSG00000024479	Mal2	AI461653	mal, T cell differentiation protein 2	protein-coding
mm_114118.1	chr13	55105265	55105275	+	1	NA	promoter-TSS (NM_012017)	promoter-TSS (NM_012017)	-39	NM_012017	26919	Mm.22795	NM_012017	ENSMUSG00000021481	Zfp346	Jaz|Znf346	zinc finger protein 346	protein-coding
mm_110690.1	chr12	69184057	69184065	-	1	NA	promoter-TSS (NM_025589)	promoter-TSS (NM_025589)	6	NM_025589	66483	Mm.379115	NM_025589	ENSMUSG00000049751	Rpl36al	2410038A03Rik|RPL36A	ribosomal protein L36A-like	protein-coding
mm_112402.1	chr13	3538440	3538461	+	1	NA	intron (NM_008112, intron 1 of 10)	CpG	375	NM_008112	14569	Mm.153226	NM_008112	ENSMUSG00000021218	Gdi2	GDI-B|GDIB|Gdi3	guanosine diphosphate (GDP) dissociation inhibitor 2	protein-coding
mm_91133.1	chr10	19609203	19609214	-	1	NA	exon (NM_010511, exon 7 of 7)	exon (NM_010511, exon 7 of 7)	-12820	NM_178258	237310	Mm.331979	NM_178258	ENSMUSG00000039760	Il22ra2	CRF2-10|CRF2-s1|CRF2X|Il-22bp	interleukin 22 receptor, alpha 2	protein-coding
mm_126614.1	chr15	83100202	83100210	+	1	NA	promoter-TSS (NM_023475)	promoter-TSS (NM_023475)	1	NM_023475	68607	Mm.30056	NM_023475	ENSMUSG00000058586	Serhl	0610008B10Rik|1110019M09Rik|AU019786	serine hydrolase-like	protein-coding
mm_103622.1	chr11	78696205	78696224	-	1	NA	exon (NM_008702, exon 1 of 11)	exon (NM_008702, exon 1 of 11)	1211	NM_008702	18099	Mm.9001	NM_008702	ENSMUSG00000017376	Nlk	AI194375	nemo like kinase	protein-coding
mm_76890.1	chr8	105698808	105698846	-	1	NA	TTS (NM_001033320)	TTS (NM_001033320)	2268	NM_001012638	497652	Mm.12964	NM_001012638	ENSMUSG00000038000	Acd	-	adrenocortical dysplasia	protein-coding
mm_51502.1	chr6	83115496	83115574	+	1	NA	promoter-TSS (NM_020619)	promoter-TSS (NM_020619)	29	NM_020619	57377	Mm.28188	NM_020619	ENSMUSG00000030036	Mogs	1810017N02Rik|AI181835|Gcs1	mannosyl-oligosaccharide glucosidase	protein-coding
mm_147664.1	chr18	60613422	60613426	-	1	NA	intron (NM_177340, intron 1 of 2)	intron (NM_177340, intron 1 of 2)	-3320	NM_001109975	104027	Mm.252321	NM_177340	ENSMUSG00000043079	Synpo	9030217H17Rik|9130229N11|9330140I15Rik|AW046661	synaptopodin	protein-coding
mm_76545.1	chr8	88118603	88118611	-	1	NA	promoter-TSS (NM_029074)	promoter-TSS (NM_029074)	-152	NM_029074	382030	Mm.216574	NM_029074	ENSMUSG00000036810	Cnep1r1	5033428A16Rik|NEP1-R1|Tmem188	CTD nuclear envelope phosphatase 1 regulatory subunit 1	protein-coding
mm_4790.1	chr1	184478263	184478271	+	1	NA	Intergenic	Intergenic	79424	NR_040472	73590	Mm.82792	NR_040472	ENSMUSG00000101574	1700112H15Rik	-	RIKEN cDNA 1700112H15 gene	ncRNA
mm_147171.1	chr18	36726717	36726724	-	1	NA	promoter-TSS (NM_009841)	promoter-TSS (NM_009841)	95	NM_009841	12475	Mm.3460	NM_009841	ENSMUSG00000051439	Cd14	-	CD14 antigen	protein-coding
mm_60778.1	chr7	45563026	45563057	+	1	NA	intron (NM_025330, intron 6 of 8)	intron (NM_025330, intron 6 of 8)	-7112	NM_009737	12036	Mm.24210	NM_009737	ENSMUSG00000030826	Bcat2	Bcat-2|Eca40	branched chain aminotransferase 2, mitochondrial	protein-coding
mm_86657.1	chr10	17724684	17724695	+	1	NA	exon (NM_010828, exon 2 of 2)	exon (NM_010828, exon 2 of 2)	1461	NM_010828	17684	Mm.272321	NM_010828	ENSMUSG00000039910	Cited2	AI835299|ER154-like|Mrg1|Msg2|p35srj	Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 2	protein-coding
mm_19704.1	chr2	103779367	103779401	-	1	NA	exon (NM_016739, exon 5 of 19)	exon (NM_016739, exon 5 of 19)	17694	NM_001111290	53872	Mm.427589	NM_016739	ENSMUSG00000027184	Caprin1	AL022980|Caprin-1|Gpiap|Gpiap1|Mmgpip137|P137|rng105	cell cycle associated protein 1	protein-coding
mm_152959.1	chr19	29356439	29356441	-	1	NA	intron (NM_026362, intron 3 of 5)	intron (NM_026362, intron 3 of 5)	5431	NM_026362	67759	Mm.275511	NM_026362	ENSMUSG00000016495	Plgrkt	1110007H22Rik|5033414D02Rik|AI852040|Plg-R(KT)|Plg-RKT	plasminogen receptor, C-terminal lysine transmembrane protein	protein-coding
mm_140807.1	chr17	22225617	22225639	-	1	NA	promoter-TSS (NM_001205095)	promoter-TSS (NM_001205095)	-14	NM_001205095	240038	Mm.227945	NM_001205095	ENSMUSG00000096433	Zfp994	EG240038|Gm4944	zinc finger protein 994	protein-coding
mm_154638.1	chrX	7764277	7764287	+	1	NA	intron (NM_001271491, intron 1 of 8)	intron (NM_001271491, intron 1 of 8)	241	NM_001271491	209446	Mm.249142	NM_172472	ENSMUSG00000000134	Tfe3	F830016E06Rik|Tcfe3|Tfe-3|bHLHe33	transcription factor E3	protein-coding
mm_167575.1	chr9	44498252	44498285	+	1	NA	promoter-TSS (NM_030256)	promoter-TSS (NM_030256)	-868	NM_030256	80288	Mm.370270	NM_030256	ENSMUSG00000063382	Bcl9l	B9L|BC003321|BCL9-2|DLNB11	B cell CLL/lymphoma 9-like	protein-coding
mm_67652.1	chr7	84689846	84689899	-	1	NA	intron (NR_038175, intron 1 of 4)	CpG	232	NR_038175	72495	Mm.382914	NR_038175	ENSMUSG00000085236	2610206C17Rik	-	RIKEN cDNA 2610206C17 gene	ncRNA
mm_10727.1	chr2	22874841	22874852	+	1	NA	exon (NM_019456, exon 14 of 14)	exon (NM_019456, exon 14 of 14)	-20676	NM_019501	56075	Mm.249752	NM_019501	ENSMUSG00000026784	Pdss1	2610203G20Rik|2700031G06Rik|TPT|TPT 1|Tprt|mDLP1|mSPS1	prenyl (solanesyl) diphosphate synthase, subunit 1	protein-coding
mm_131541.1	chr16	17797218	17797228	+	1	NA	promoter-TSS (NM_153790)	promoter-TSS (NM_153790)	-59	NM_153790	224024	Mm.194950	NM_153790	ENSMUSG00000012017	Scarf2	NSR1|SREC-II|SRECRP-1|Scatf1|Srec2|SrecII	scavenger receptor class F, member 2	protein-coding
mm_147817.1	chr18	61737341	61737376	-	1	NA	intron (NM_178928, intron 15 of 18)	RLTR51B_Mm|LTR|ERVK?	10968	NR_029432	68982	Mm.441992	NR_029432	ENSMUSG00000098702	1500015A07Rik	-	RIKEN cDNA 1500015A07 gene	ncRNA
mm_99894.1	chr11	109616125	109616151	+	1	NA	Intergenic	ID_B1|SINE|B4	-4749	NM_145940	52639	Mm.35817	NM_145940	ENSMUSG00000041895	Wipi1	4930533H01Rik|AW411817|D11Ertd498e	WD repeat domain, phosphoinositide interacting 1	protein-coding
mm_86118.1	chr9	116041066	116041099	-	1	NA	intron (NM_028638, intron 14 of 14)	intron (NM_028638, intron 14 of 14)	131627	NM_028638	73748	Mm.485018	NM_028638	ENSMUSG00000056880	Gadl1	1110027M19Rik|ADC|CSADC	glutamate decarboxylase-like 1	protein-coding
mm_27398.1	chr3	51222351	51222388	-	1	NA	Intergenic	Lx8|LINE|L1	-2078	NM_009834	12457	Mm.86541	NM_009834	ENSMUSG00000023087	Noct	AU043840|Ccr4|Ccrn4l	nocturnin	protein-coding
mm_81827.1	chr9	118052450	118052458	+	1	NA	intron (NM_001286507, intron 4 of 6)	intron (NM_001286507, intron 4 of 6)	11932	NM_013727	27215	Mm.92705	NM_013727	ENSMUSG00000039285	Azi2	AA410145|AZ2	5-azacytidine induced gene 2	protein-coding
mm_17550.1	chr2	30093534	30093544	-	1	NA	promoter-TSS (NM_025428)	promoter-TSS (NM_025428)	96	NM_025428	66220	Mm.22538	NM_025428	ENSMUSG00000015335	Zdhhc12	1190004A01Rik	zinc finger, DHHC domain containing 12	protein-coding
mm_13202.1	chr2	93459872	93459883	+	1	NA	intron (NR_040532, intron 2 of 4)	intron (NR_040532, intron 2 of 4)	1974	NM_001271461	12521	Mm.4261	NM_007656	ENSMUSG00000027215	Cd82	AA682076|AL023070|C33|IA4|Kai1|Tspan27	CD82 antigen	protein-coding
mm_78154.1	chr9	21025468	21025476	+	1	NA	intron (NM_010493, intron 2 of 6)	intron (NM_010493, intron 2 of 6)	-3901	NM_023892	78369	Mm.30220	NM_023892	ENSMUSG00000001014	Icam4	1810015M19Rik|Cd242|ICAM-4	intercellular adhesion molecule 4, Landsteiner-Wiener blood group	protein-coding
mm_38822.1	chr4	148744229	148744242	-	1	NA	Intergenic	Intergenic	-60157	NM_001159344	69743	Mm.233879	NM_027195	ENSMUSG00000028977	Casz1	2410019P08Rik|AV096627|BC040081|Cst|D4Ertd432e	castor zinc finger 1	protein-coding
mm_137316.1	chr17	24886690	24886765	+	1	NA	promoter-TSS (NM_001163750)	promoter-TSS (NM_001163750)	53	NM_001163751	79043	Mm.274794	NM_027141	ENSMUSG00000024160	Spsb3	2310012N15Rik|3300001M01Rik|SSB3|Tce1|mKIAA4204	splA/ryanodine receptor domain and SOCS box containing 3	protein-coding
mm_168426.1	chr11	33538048	33538058	+	1	NA	Intergenic	Intergenic	-24307	NM_023146	66011	Mm.383775	NM_023146	ENSMUSG00000040594	Ranbp17	-	RAN binding protein 17	protein-coding
mm_79737.1	chr9	62345358	62345367	+	1	NA	intron (NM_009672, intron 1 of 6)	intron (NM_009672, intron 1 of 6)	4019	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	protein-coding
mm_129567.1	chr15	79620762	79620780	-	1	NA	exon (NM_029407, exon 15 of 18)	exon (NM_029407, exon 15 of 18)	-15662	NM_010059	13404	Mm.2524	NM_010059	ENSMUSG00000022429	Dmc1	Dmc1h|Lim15|Mei11|sgdp	DNA meiotic recombinase 1	protein-coding
mm_97697.1	chr11	80171484	80171488	+	1	NA	intron (NM_172133, intron 7 of 10)	B1_Mur1|SINE|Alu	-12386	NM_028019	71956	Mm.22985	NM_028019	ENSMUSG00000020707	Rnf135	0610037N03Rik|2410006N06Rik	ring finger protein 135	protein-coding
mm_121645.1	chr14	8800518	8800519	-	1	NA	Intergenic	Intergenic	134128	NR_045968	74859	Mm.84041	NR_045968	ENSMUSG00000097898	4930455B14Rik	1700027C12Rik	RIKEN cDNA 4930455B14 gene	ncRNA
mm_32169.1	chr4	100336859	100336861	+	1	NA	intron (NM_013845, intron 4 of 8)	intron (NM_013845, intron 4 of 8)	-142007	NM_001033773	381534	Mm.318133	NM_001033773	ENSMUSG00000069733	Ube2u	-	ubiquitin-conjugating enzyme E2U (putative)	protein-coding
mm_55511.1	chr6	69963882	69963897	-	1	NA	Intergenic	Intergenic	-636715	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_16998.1	chr2	18392663	18392665	-	1	NA	5' UTR (NM_001190817, exon 1 of 13)	5' UTR (NM_001190817, exon 1 of 13)	166	NM_001190817	13418	Mm.246674	NM_007869	ENSMUSG00000026740	Dnajc1	4733401K02Rik|AA960110|D230036H06Rik|Dnajl1|ERdj1|ERj1p|MTJ1	DnaJ heat shock protein family (Hsp40) member C1	protein-coding
mm_894.1	chr1	53297097	53297124	+	1	NA	promoter-TSS (NM_145517)	promoter-TSS (NM_145517)	15	NM_145517	227102	Mm.212846	NM_145517	ENSMUSG00000026097	Ormdl1	C730042F17Rik	ORM1-like 1 (S. cerevisiae)	protein-coding
mm_37675.1	chr4	129122053	129122063	-	1	NA	promoter-TSS (NM_010471)	promoter-TSS (NM_010471)	-133	NM_001286081	15444	Mm.384452	NM_010471	ENSMUSG00000028785	Hpca	-	hippocalcin	protein-coding
mm_25115.1	chr3	101634773	101634774	+	1	NA	Intergenic	MIR|SINE|MIR	-30066	NM_144900	11928	Mm.193670	NM_144900	ENSMUSG00000033161	Atp1a1	Atpa-1|BC010319	ATPase, Na+/K+ transporting, alpha 1 polypeptide	protein-coding
mm_41125.1	chr5	87786583	87786603	+	1	NA	exon (NM_001304768, exon 11 of 13)	exon (NM_001304768, exon 11 of 13)	12143	NM_007785	12993	Mm.4908	NM_007785	ENSMUSG00000061937	Csn1s2a	Csng|PP22	casein alpha s2-like A	protein-coding
mm_109858.1	chr12	4829436	4829485	-	1	NA	Intergenic	B1_Mus1|SINE|Alu	11852	NM_025323	66055	Mm.102627	NM_025323	ENSMUSG00000037361	Sf3b6	0610009D07Rik|6030419K15Rik|AV001342|Sf3b14	splicing factor 3B, subunit 6	protein-coding
mm_126571.1	chr15	82256099	82256130	+	1	NA	promoter-TSS (NR_037698)	promoter-TSS (NR_037698)	91	NR_037698	76505	Mm.23023	NR_037697	ENSMUSG00000068099	1500009C09Rik	-	RIKEN cDNA 1500009C09 gene	ncRNA
mm_27906.1	chr3	79511610	79511656	-	1	NA	intron (NM_001162999, intron 5 of 16)	intron (NM_001162999, intron 5 of 16)	56046	NM_001162999	329679	Mm.244005	NM_001162999	ENSMUSG00000061175	Fnip2	D630023B12Rik|mKIAA1450	folliculin interacting protein 2	protein-coding
mm_3709.1	chr1	153904617	153904629	+	1	NA	exon (NM_008131, exon 3 of 7)	exon (NM_008131, exon 3 of 7)	4694	NM_008131	14645	Mm.210745	NM_008131	ENSMUSG00000026473	Glul	GS|Glns	glutamate-ammonia ligase (glutamine synthetase)	protein-coding
mm_14283.1	chr2	128801864	128801872	+	1	NA	3' UTR (NM_008587, exon 19 of 19)	3' UTR (NM_008587, exon 19 of 19)	-16435	NM_028248	72477	Mm.259688	NM_028248	ENSMUSG00000014353	Tmem87b	2610301K12Rik|2810431I02Rik|AU014804	transmembrane protein 87B	protein-coding
mm_91274.1	chr10	24595798	24595809	-	1	NA	intron (NM_010217, intron 1 of 4)	CpG	361	NM_010217	14219	Mm.390287	NM_010217	ENSMUSG00000019997	Ctgf	Ccn2|Fisp12|Hcs24|fisp-12	connective tissue growth factor	protein-coding
mm_76212.1	chr8	83442609	83442630	-	1	NA	promoter-TSS (NM_019708)	promoter-TSS (NM_019708)	43	NM_001285992	56367	Mm.246911	NM_019708	ENSMUSG00000063253	Scoc	0610011C06Rik|2810002J11Rik|AA415030|SCOCO	short coiled-coil protein	protein-coding
mm_150839.1	chr19	44931155	44931172	+	1	NA	promoter-TSS (NM_001081225)	promoter-TSS (NM_001081225)	44	NM_001081225	226151	Mm.212609	NM_172638	ENSMUSG00000036097	Fam178a	3632432H19|6030443O07Rik|AU014917|Slf2	family with sequence similarity 178, member A	protein-coding
mm_79220.1	chr9	49505265	49505275	+	1	NA	3' UTR (NM_001311065, exon 18 of 18)	3' UTR (NM_001311065, exon 18 of 18)	-13018	NR_029465	100036537	Mm.437541	NR_029465	ENSMUSG00000079564	Gm11149	ENSMUSG00000060603|ENSMUSG00000079564	predicted gene 11149	ncRNA
mm_131342.1	chr16	13447715	13447719	+	1	NA	Intergenic	(CCCA)n|Simple_repeat|Simple_repeat	-1806	NR_030549	100124432		NR_030549	ENSMUSG00000076972	Mir193b	Mir193|Mirn193b|mir-193b	microRNA 193b	ncRNA
mm_49304.1	chr6	17749569	17749572	+	1	NA	5' UTR (NM_001083315, exon 1 of 15)	5' UTR (NM_001083315, exon 1 of 15)	400	NM_022332	64213	Mm.12051	NM_022332	ENSMUSG00000029534	St7	9430001H04Rik|Fam4a2|HELG|RAY1|SEN4|TSG7	suppression of tumorigenicity 7	protein-coding
mm_110336.1	chr12	35686256	35686269	-	1	NA	promoter-TSS (NR_045051)	promoter-TSS (NR_045051)	42	NR_045051	71581	Mm.100110	NR_045050		9130015A21Rik	100043575|Gm4527	RIKEN cDNA 9130015A21 gene	ncRNA
mm_72459.1	chr8	83245849	83245860	+	1	NA	intron (NM_027758, intron 6 of 17)	Lx8|LINE|L1	-44494	NM_009463	22227	Mm.4177	NM_009463	ENSMUSG00000031710	Ucp1	AI385626|Slc25a7|Ucp	uncoupling protein 1 (mitochondrial, proton carrier)	protein-coding
mm_48924.1	chr6	4505696	4505709	+	1	NA	promoter-TSS (NM_007743)	promoter-TSS (NM_007743)	84	NM_007743	12843	Mm.277792	NM_007743	ENSMUSG00000029661	Col1a2	AA960264|AI325291|Col1a-2|Cola-2|Cola2|oim	collagen, type I, alpha 2	protein-coding
mm_102402.1	chr11	59120926	59120962	-	1	NA	intron (NM_199152, intron 10 of 89)	L1MEg|LINE|L1	15431	NM_001171512	380698	Mm.339542	NM_199152	ENSMUSG00000061462	Obscn	BC046431|Gm878|OTTMUSG00000005786|UNC89	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	protein-coding
mm_48214.1	chr5	137610610	137610620	-	1	NA	intron (NM_008788, intron 1 of 8)	intron (NM_008788, intron 1 of 8)	789	NM_008788	18542	Mm.262345	NM_008788	ENSMUSG00000029718	Pcolce	Astt-2|Astt2|P14|PCPE-1	procollagen C-endopeptidase enhancer protein	protein-coding
mm_78901.1	chr9	44720792	44720835	+	1	NA	intron (NM_153537, intron 4 of 21)	intron (NM_153537, intron 4 of 21)	14385	NM_153537	102693	Mm.28639	NM_153537	ENSMUSG00000048537	Phldb1	AU041016|D330037A14Rik|Ll5a	pleckstrin homology like domain, family B, member 1	protein-coding
mm_82479.1	chr9	17556294	17556307	-	1	NA	Intergenic	RLTR16|LTR|ERVK	-735967	NM_025844	66917	Mm.103534	NM_025844	ENSMUSG00000001774	Chordc1	1110001O09Rik|AA409036|Chp-1|morgana	cysteine and histidine-rich domain (CHORD)-containing, zinc-binding protein 1	protein-coding
mm_87097.1	chr10	33083477	33083567	+	1	NA	promoter-TSS (NM_029726)	promoter-TSS (NM_029726)	39	NM_029726	76757	Mm.338508	NM_029726	ENSMUSG00000019787	Trdn	2310045H21Rik|EG432451|TDN	triadin	protein-coding
mm_115391.1	chr13	113293207	113293223	+	1	NA	Intergenic	CpG	83556	NM_023612	71690	Mm.38929	NM_023612	ENSMUSG00000042379	Esm1	0610042H23Rik|AV004503|ESM-1	endothelial cell-specific molecule 1	protein-coding
mm_130844.1	chr15	101918580	101918590	-	1	NA	TTS (NM_008475)	TTS (NM_008475)	6150	NM_008475	16682	Mm.46425	NM_008475	ENSMUSG00000059668	Krt4	AW108092|K4|Krt-2.4|Krt2-4	keratin 4	protein-coding
mm_77875.1	chr9	6168639	6168671	+	1	NA	promoter-TSS (NM_027924)	promoter-TSS (NM_027924)	43	NM_027924	71785	Mm.390122	NM_027924	ENSMUSG00000032006	Pdgfd	1110003I09Rik	platelet-derived growth factor, D polypeptide	protein-coding
mm_161700.1	chr17	23941996	23941996	+	1	NA	promoter-TSS (NM_011321)	promoter-TSS (NM_011321)	0	NM_011321	20234	Mm.390958	NM_011321	ENSMUSG00000024128	Sbp	AV082137|AV082259|p25	spermine binding protein	protein-coding
mm_104046.1	chr11	86357347	86357385	-	1	NA	intron (NM_001080931, intron 1 of 29)	CpG	159	NM_001080931	327987	Mm.341886	NM_001080931	ENSMUSG00000034297	Med13	1110067M05Rik|D030023K18|Thrap1|Trap240	mediator complex subunit 13	protein-coding
mm_100937.1	chr11	6520895	6520969	-	1	NA	promoter-TSS (NM_178440)	promoter-TSS (NM_178440)	26	NM_178440	246177	Mm.239554	NM_178440	ENSMUSG00000020437	Myo1g	E430002D17Rik	myosin IG	protein-coding
mm_132883.1	chr16	48790302	48790307	+	1	NA	Intergenic	Intergenic	-18348	NM_198297	77647	Mm.167298	NM_198297	ENSMUSG00000030775	Trat1	C030046M14Rik|Tcrim|Trim	T cell receptor associated transmembrane adaptor 1	protein-coding
mm_155413.1	chrX	73483689	73483693	+	1	NA	promoter-TSS (NM_007542)	promoter-TSS (NM_007542)	90	NM_007542	12111	Mm.2608	NM_007542	ENSMUSG00000031375	Bgn	BG|DSPG1|PG-S1|PGI|SLRR1A	biglycan	protein-coding
mm_18329.1	chr2	57238311	57238346	-	1	NA	promoter-TSS (NM_010274)	promoter-TSS (NM_010274)	-54	NM_010274	14571	Mm.3711	NM_010274	ENSMUSG00000026827	Gpd2	AA408484|AI448216|AU021455|AW494132|GPDH|Gdm1|Gpd-m|Gpdh-m|TISP38	glycerol phosphate dehydrogenase 2, mitochondrial	protein-coding
mm_12951.1	chr2	87845345	87845345	+	1	NA	Intergenic	U2|snRNA|snRNA	-11832	NM_146638	258631	Mm.377602	NM_146638	ENSMUSG00000047039	Olfr1151	MOR177-9	olfactory receptor 1151	protein-coding
mm_160264.1	chr7	110366048	110366048	-	1	NA	intron (NM_177324, intron 23 of 40)	intron (NM_177324, intron 23 of 40)	144345	NM_009302	20947	Mm.334144	NM_009302	ENSMUSG00000031015	Swap70	70kDa|AV235546	SWA-70 protein	protein-coding
mm_93415.1	chr10	108500529	108500539	-	1	NA	3' UTR (NM_001252342, exon 11 of 11)	3' UTR (NM_001252342, exon 11 of 11)	168345	NM_054056	114774	Mm.391419	NM_054056	ENSMUSG00000035873	Pawr	2310001G03Rik|PAR4|Par-4	PRKC, apoptosis, WT1, regulator	protein-coding
mm_133787.1	chr16	95257774	95257782	+	1	NA	intron (NM_001039056, intron 1 of 3)	intron (NM_001039056, intron 1 of 3)	220	NM_001271690	16516	Mm.272239	NM_019664	ENSMUSG00000062609	Kcnj15	4930414N08Rik|AI182284|AI267127|IRKK|Kir4.2	potassium inwardly-rectifying channel, subfamily J, member 15	protein-coding
mm_69787.1	chr7	141096684	141096696	-	1	NA	intron (NM_023059, intron 1 of 9)	intron (NM_023059, intron 1 of 9)	3856	NM_023059	24058	Mm.38017	NM_023059	ENSMUSG00000025494	Sigirr	AI256711|TIR8	single immunoglobulin and toll-interleukin 1 receptor (TIR) domain	protein-coding
mm_48459.1	chr5	140808523	140808527	-	1	NA	intron (NM_010302, intron 1 of 3)	B1F1|SINE|Alu	21906	NM_010302	14673	Mm.370185	NM_010302	ENSMUSG00000000149	Gna12	AI414047|AI504261|Galpha12	guanine nucleotide binding protein, alpha 12	protein-coding
mm_64122.1	chr7	141131269	141131333	+	1	NA	promoter-TSS (NM_013782)	promoter-TSS (NM_013782)	15	NM_013782	27388	Mm.293591	NM_013782	ENSMUSG00000025495	Ptdss2	AI481134|AI988017|PSS2	phosphatidylserine synthase 2	protein-coding
mm_141330.1	chr17	28486083	28486099	-	1	NA	promoter-TSS (NM_010220)	promoter-TSS (NM_010220)	58	NM_010220	14229	Mm.276405	NM_010220	ENSMUSG00000024222	Fkbp5	D17Ertd592e|Dit1|FKBP-5|FKBP51	FK506 binding protein 5	protein-coding
mm_90244.1	chr10	121488870	121488879	+	1	NA	Intergenic	Intergenic	-12624	NM_138956	192678	Mm.41265	NM_138956	ENSMUSG00000025795	Rassf3	AW212023|AW322379	Ras association (RalGDS/AF-6) domain family member 3	protein-coding
mm_157021.1	chrX	7763742	7763788	-	1	NA	promoter-TSS (NM_001271491)	promoter-TSS (NM_001271491)	-178	NM_001105197	209446	Mm.249142	NM_172472	ENSMUSG00000000134	Tfe3	F830016E06Rik|Tcfe3|Tfe-3|bHLHe33	transcription factor E3	protein-coding
mm_35991.1	chr4	55532137	55532167	-	1	NA	5' UTR (NM_010637, exon 1 of 5)	5' UTR (NM_010637, exon 1 of 5)	323	NM_010637	16600	Mm.4325	NM_010637	ENSMUSG00000003032	Klf4	EZF|Gklf|Zie	Kruppel-like factor 4 (gut)	protein-coding
mm_22216.1	chr2	174327349	174327362	-	1	NA	promoter-TSS (NR_003258)	promoter-TSS (NR_003258)	-413	NM_001310083	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_7183.1	chr1	92726398	92726418	-	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	-77567	NM_153114	260301	Mm.219545	NM_153114	ENSMUSG00000044055	Otos	OTOSP	otospiralin	protein-coding
mm_93960.1	chr10	127286425	127286431	-	1	NA	exon (NM_001347171, exon 6 of 13)	exon (NM_001347171, exon 6 of 13)	2590	NM_001347171	110962	Mm.372826	NM_033072	ENSMUSG00000025409	Mbd6	D10Wsu93e	methyl-CpG binding domain protein 6	protein-coding
mm_168875.1	chr12	40884055	40884057	-	1	NA	Intergenic	Intergenic	-140034	NM_053122	93757	Mm.363813	NM_053122	ENSMUSG00000056899	Immp2l	AI853880|IMP2	IMP2 inner mitochondrial membrane peptidase-like (S. cerevisiae)	protein-coding
mm_111516.1	chr12	99642715	99642723	-	1	NA	Intergenic	Lx9|LINE|L1	-14745	NR_045288	73457	Mm.383439	NR_045288	ENSMUSG00000100211	1700064M15Rik	-	RIKEN cDNA 1700064M15 gene	ncRNA
mm_170088.1	chr17	35689820	35689827	-	1	NA	exon (NM_001198833, exon 8 of 18)	exon (NM_001198833, exon 8 of 18)	10767	NM_001198833	12305	Mm.5021	NM_007584	ENSMUSG00000003534	Ddr1	6030432F18|AI323681|CD167a|Cak|Nep|PTK3A	discoidin domain receptor family, member 1	protein-coding
mm_89156.1	chr10	86033039	86033043	+	1	NA	intron (NM_001347151, intron 4 of 8)	intron (NM_001347151, intron 4 of 8)	10887	NM_001347151	69754	Mm.44236	NM_153195	ENSMUSG00000001786	Fbxo7	2410015K21Rik|A230052G17Rik|AI117679|AW260462|C85118	F-box protein 7	protein-coding
mm_19396.1	chr2	91630564	91630574	-	1	NA	exon (NM_010168, exon 7 of 14)	exon (NM_010168, exon 7 of 14)	5888	NM_010168	14061	Mm.89048	NM_010168	ENSMUSG00000027249	F2	Cf-2|Cf2|FII	coagulation factor II	protein-coding
mm_40470.1	chr5	53809633	53809683	+	1	NA	promoter-TSS (NM_144517)	promoter-TSS (NM_144517)	31	NM_144517	67249	Mm.28823	NM_144517	ENSMUSG00000039178	Tbc1d19	2810453K03Rik	TBC1 domain family, member 19	protein-coding
mm_26533.1	chr3	146117702	146117718	+	1	NA	Intergenic	Intergenic	-4081	NM_134160	171166	Mm.114683	NM_134160	ENSMUSG00000036853	Mcoln3	6720490O21Rik|TRPML3|Va	mucolipin 3	protein-coding
mm_35156.1	chr4	12171782	12171796	-	1	NA	exon (NM_001310743, exon 1 of 8)	exon (NM_001310743, exon 1 of 8)	226	NM_001310743	68099	Mm.25340	NM_026558	ENSMUSG00000028218	Fam92a	6720467C03Rik|Fam92a1	family with sequence similarity 92, member A	protein-coding
mm_4485.1	chr1	173630895	173630897	+	1	NA	promoter-TSS (NM_175026)	promoter-TSS (NM_175026)	37	NM_175026	236312	Mm.447	NM_175026	ENSMUSG00000043263	Ifi209	4930422C14|AI447904|Ifix|Pyhin-1|Pyhin1	interferon activated gene 209	protein-coding
mm_108115.1	chr12	75591358	75591363	+	1	NA	intron (NM_012024, intron 2 of 13)	intron (NM_012024, intron 2 of 13)	4840	NM_012024	26932	Mm.259626	NM_012024	ENSMUSG00000021051	Ppp2r5e	4633401M22Rik|AI449017|B56beta	protein phosphatase 2, regulatory subunit B', epsilon	protein-coding
mm_45680.1	chr5	77349485	77349495	-	1	NA	TTS (NM_153798)	TTS (NM_153798)	39006	NM_153798	231329	Mm.273217	NM_153798	ENSMUSG00000029250	Polr2b	Pol2rb|Rpb140|Rpb2	polymerase (RNA) II (DNA directed) polypeptide B	protein-coding
mm_128345.1	chr15	39784795	39784805	-	1	NA	intron (NM_022722, intron 8 of 9)	intron (NM_022722, intron 8 of 9)	-12245	NR_045788	100503072	Mm.446661	NR_045788	ENSMUSG00000087695	Gm16291	OTTMUSG00000033244	predicted gene 16291	ncRNA
mm_157989.1	chrX	94366853	94366862	-	1	NA	promoter-TSS (NM_026673)	promoter-TSS (NM_026673)	-253	NM_026673	68316	Mm.379156	NM_026673	ENSMUSG00000079508	Apoo	0610008C08Rik|1110019O03Rik	apolipoprotein O	protein-coding
mm_37972.1	chr4	133536770	133536784	-	1	NA	intron (NM_010948, intron 2 of 7)	intron (NM_010948, intron 2 of 7)	9250	NM_010948	18221	Mm.69	NM_010948	ENSMUSG00000028851	Nudc	SIG-92|Silg92	nudC nuclear distribution protein	protein-coding
mm_146085.1	chr18	73551663	73551678	+	1	NA	Intergenic	Tigger16b|DNA|TcMar-Tigger	-21035	NM_001039214	240396	Mm.24131	NM_001039214	ENSMUSG00000037253	Mex3c	A130001D14Rik|BC035207|BM-013|Rkhd2	mex3 RNA binding family member C	protein-coding
mm_165702.1	chr3	95550092	95550097	+	1	NA	exon (NM_021281, exon 7 of 8)	exon (NM_021281, exon 7 of 8)	-9583	NM_026489	67981	Mm.179050	NM_026489	ENSMUSG00000028109	Hormad1	4921522K05Rik|Nohma	HORMA domain containing 1	protein-coding
mm_4007.1	chr1	164823839	164823844	+	1	NA	3' UTR (NM_019759, exon 4 of 4)	3' UTR (NM_019759, exon 4 of 4)	27109	NM_019759	56429	Mm.28935	NM_019759	ENSMUSG00000026574	Dpt	1810032B19Rik|5033416F05Rik|EQ-1|Eq1	dermatopontin	protein-coding
mm_88725.1	chr10	80179432	80179464	+	1	NA	promoter-TSS (NM_007909)	promoter-TSS (NM_007909)	-34	NM_007909	13637	Mm.1478	NM_007909	ENSMUSG00000003070	Efna2	CEK7L|Elf1|Epl6|Eplg6|Lerk6	ephrin A2	protein-coding
mm_100716.1	chr11	3863896	3863910	-	1	NA	promoter-TSS (NM_152818)	promoter-TSS (NM_152818)	0	NM_152818	74309	Mm.61022	NM_152818	ENSMUSG00000020435	Osbp2	1700095P05Rik|C630001G20Rik|Gm244|ORP-4|OSBPL1	oxysterol binding protein 2	protein-coding
mm_127784.1	chr15	3542438	3542455	-	1	NA	intron (NM_001048178, intron 1 of 8)	Tigger7|DNA|TcMar-Tigger	39396	NM_001286370	14600	Mm.3986	NM_010284	ENSMUSG00000055737	Ghr	GHBP|GHR/BP	growth hormone receptor	protein-coding
mm_164037.1	chr14	84445268	84445295	+	1	NA	5' UTR (NM_001013753, exon 1 of 4)	5' UTR (NM_001013753, exon 1 of 4)	1718	NM_001013753	219228	Mm.153643	NM_001013753	ENSMUSG00000035566	Pcdh17	C030033F14Rik|Gm78	protocadherin 17	protein-coding
mm_49978.1	chr6	40891404	40891427	+	1	NA	intron (NR_035473, intron 2 of 3)	intron (NR_035473, intron 2 of 3)	-3921	NM_139296	194357	Mm.207087	NM_139296	ENSMUSG00000029885	Moxd2	Dbhl1	monooxygenase, DBH-like 2	protein-coding
mm_54681.1	chr6	39419821	39419827	-	1	NA	promoter-TSS (NM_001311109)	promoter-TSS (NM_001311109)	-48	NM_001311109	54484	Mm.270484	NM_018810	ENSMUSG00000029922	Mkrn1	RFP	makorin, ring finger protein, 1	protein-coding
mm_95349.1	chr11	48802267	48802296	+	1	NA	promoter-TSS (NR_028564)	promoter-TSS (NR_028564)	248	NR_028563	100216534		NR_028563	ENSMUSG00000064725	Snord96a	U96	small nucleolar RNA, C/D box 96A	snoRNA
mm_139646.1	chr17	57386612	57386625	+	1	NA	intron (NM_010130, intron 2 of 21)	L1_Mur1|LINE|L1	27932	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_69439.1	chr7	132910983	132910983	-	1	NA	Intergenic	Intergenic	-38639	NM_207302	360216	Mm.389984	NM_207302	ENSMUSG00000030967	Zranb1	9330160G10Rik|D7Wsu87e|Gm1956|Trabid	zinc finger, RAN-binding domain containing 1	protein-coding
mm_9415.1	chr1	172313992	172314035	-	1	NA	intron (NM_080419, intron 1 of 6)	intron (NM_080419, intron 1 of 6)	1646	NM_080419	140559	Mm.271717	NM_080419	ENSMUSG00000038034	Igsf8	ESTM34|EWI-2|KCT-4|PGRL	immunoglobulin superfamily, member 8	protein-coding
mm_126900.1	chr15	89532817	89532870	+	1	NA	intron (NM_021423, intron 16 of 21)	intron (NM_021423, intron 16 of 21)	32986	NM_021423	58234	Mm.146855	NM_021423	ENSMUSG00000022623	Shank3	AI841104|SHANK3c-3|SHANK3c-4|Shank3b	SH3/ankyrin domain gene 3	protein-coding
mm_31442.1	chr4	48585136	48585187	+	1	NA	promoter-TSS (NM_021436)	promoter-TSS (NM_021436)	-32	NM_021436	230157	Mm.422686	NM_021436	ENSMUSG00000028347	Tmeff1	A830033E11|M7365|Tr1	transmembrane protein with EGF-like and two follistatin-like domains 1	protein-coding
mm_149174.1	chr19	9102514	9102534	+	1	NA	Intergenic	Intergenic	-14568	NM_011681	22287	Mm.2258	NM_011681	ENSMUSG00000024653	Scgb1a1	CC10|CC16|CCSP|PCB-BP|UG|UGB|Utg	secretoglobin, family 1A, member 1 (uteroglobin)	protein-coding
mm_60198.1	chr7	43409264	43409273	+	1	NA	exon (NM_172900, exon 4 of 12)	exon (NM_172900, exon 4 of 12)	988	NM_172900	243958	Mm.24444	NM_172900	ENSMUSG00000030468	Siglecg	9830164H23|A630096C01Rik|Siglec-G|Siglec10|mSiglec-G	sialic acid binding Ig-like lectin G	protein-coding
mm_153930.1	chr19	47416148	47416162	-	1	NA	intron (NM_001164717, intron 2 of 13)	intron (NM_001164717, intron 2 of 13)	48256	NM_001164717	14218	Mm.127560	NM_008018	ENSMUSG00000053617	Sh3pxd2a	2310014D11Rik|AA589508|AI256723|AI413738|C230050L11|EG329070|Fish|Gm5098|Sh3md1|TSK5|Tks5	SH3 and PX domains 2A	protein-coding
mm_63543.1	chr7	128062695	128062697	+	1	NA	promoter-TSS (NM_008401)	promoter-TSS (NM_008401)	56	NM_008401	16409	Mm.262106	NM_008401	ENSMUSG00000030786	Itgam	CD11b/CD18|CR3|CR3A|Cd11b|F730045J24Rik|Ly-40|MAC1|Mac-1|Mac-1a	integrin alpha M	protein-coding
mm_101211.1	chr11	20064234	20064265	-	1	NA	3' UTR (NM_146243, exon 9 of 9)	3' UTR (NM_146243, exon 9 of 9)	48702	NM_146243	66713	Mm.259045	NM_146243	ENSMUSG00000020152	Actr2	4921510D23Rik|AA409782|Arp2|D6Ertd746e	ARP2 actin-related protein 2	protein-coding
mm_96376.1	chr11	67240558	67240605	+	1	NA	intron (NM_010855, intron 2 of 39)	intron (NM_010855, intron 2 of 39)	2769	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_95130.1	chr11	34299737	34299755	+	1	NA	intron (NM_033374, intron 30 of 51)	intron (NM_033374, intron 30 of 51)	-15076	NM_001025382	574403	Mm.444796	NM_001025382	ENSMUSG00000069911	Fam196b	EG574403|Gm6041	family with sequence similarity 196, member B	protein-coding
mm_47844.1	chr5	134314679	134314721	-	1	NA	promoter-TSS (NM_010365)	promoter-TSS (NM_010365)	60	NM_001080746	14886	Mm.261570	NM_010365	ENSMUSG00000060261	Gtf2i	6030441I21Rik|BAP-135|Diws1t|GtfII-I|Spin|TFII-I|WBSCR6	general transcription factor II I	protein-coding
mm_149667.1	chr19	18758608	18758645	+	1	NA	intron (NM_153417, intron 1 of 38)	intron (NM_153417, intron 1 of 38)	8643	NM_153417	225997	Mm.215171	NM_153417	ENSMUSG00000024727	Trpm6	CHAK2|TRPM6/CHAK2	transient receptor potential cation channel, subfamily M, member 6	protein-coding
mm_92876.1	chr10	82492613	82492625	-	1	NA	promoter-TSS (NM_001255990)	promoter-TSS (NM_001255990)	-1	NM_001255990	432480	Mm.280394	NM_001255990	ENSMUSG00000094186	Gm1553	Lcrn	predicted gene 1553	protein-coding
mm_162099.1	chrX	37661695	37661695	-	1	NA	exon (NM_001114157, exon 3 of 6)	exon (NM_001114157, exon 3 of 6)	7069	NM_001114157	434758	Mm.357753	NM_001114157	ENSMUSG00000071769	Rhox3h	EG434758|Rhox3.8|Rhox3g	reproductive homeobox 3H	protein-coding
mm_25419.1	chr3	107753781	107753801	+	1	NA	exon (NM_007778, exon 4 of 9)	exon (NM_007778, exon 4 of 9)	6678	NM_001113530	12977	Mm.795	NM_007778	ENSMUSG00000014599	Csf1	C87615|Csfm|MCSF|op	colony stimulating factor 1 (macrophage)	protein-coding
mm_121637.1	chr14	8378728	8378751	-	1	NA	promoter-TSS (NM_146050)	promoter-TSS (NM_146050)	24	NM_146050	18300	Mm.25351	NM_146050	ENSMUSG00000021749	Oit1	2310076N21Rik|AV067083|EF-7|Fam3d	oncoprotein induced transcript 1	protein-coding
mm_125978.1	chr15	76327430	76327491	+	1	NA	promoter-TSS (NM_175399)	promoter-TSS (NM_175399)	63	NM_175399	109075	Mm.322752	NM_175399	ENSMUSG00000034259	Exosc4	1110039I09Rik|1500001N04Rik|Rrp41	exosome component 4	protein-coding
mm_130583.1	chr15	99535914	99535917	-	1	NA	Intergenic	Intergenic	-7750	NM_001038658	72393	Mm.39760	NM_028224	ENSMUSG00000023011	Faim2	2900002L20Rik|Lfg|Lfg2|NMP25|Nmp35|Tmbim2	Fas apoptotic inhibitory molecule 2	protein-coding
mm_160667.1	chr9	121791347	121791347	-	1	NA	promoter-TSS (NR_027967)	promoter-TSS (NR_027967)	-227	NR_027967	74770	Mm.44195	NM_029095	ENSMUSG00000032523	Hhatl	1110011D13Rik|Gup1|Mg56	hedgehog acyltransferase-like	protein-coding
mm_5484.1	chr1	36891594	36891602	-	1	NA	intron (NM_018872, intron 1 of 40)	intron (NM_018872, intron 1 of 40)	47929	NM_018872	56030	Mm.186943	NM_018872	ENSMUSG00000026116	Tmem131	2610524E03Rik|CC28|D1Bwg0491e|Neg|RW1|YR-23|mKIAA0257	transmembrane protein 131	protein-coding
mm_69796.1	chr7	141168658	141168666	-	1	NA	promoter-TSS (NM_001172101)	promoter-TSS (NM_001172101)	24	NM_001172101	107702	Mm.197493	NM_145135	ENSMUSG00000038650	Rnh1	AW546468|C80305|RNH	ribonuclease/angiogenin inhibitor 1	protein-coding
mm_173101.1	chrX	152909635	152909640	-	1	NA	Intergenic	Lx3B|LINE|L1	-96832	NM_001137547	635253	Mm.426169	NM_001137547	ENSMUSG00000067215	Usp51	AV136873	ubiquitin specific protease 51	protein-coding
mm_78316.1	chr9	23799148	23799155	+	1	NA	Intergenic	Lx10|LINE|L1	-298867	NM_175678	319239	Mm.130824	NM_175678	ENSMUSG00000043659	Npsr1	9330128H10Rik|GPRA|Gpr154|MVTR|PGR14|VRR1	neuropeptide S receptor 1	protein-coding
mm_94429.1	chr11	6291965	6291997	+	1	NA	promoter-TSS (NM_001252288)	promoter-TSS (NM_001252288)	384	NM_001252283	18293	Mm.276348	NM_010956	ENSMUSG00000020456	Ogdh	2210403E04Rik|2210412K19Rik|AA409584|d1401|mKIAA4192	oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)	protein-coding
mm_168616.1	chr11	77293853	77293867	+	1	NA	intron (NM_177710, intron 1 of 14)	intron (NM_177710, intron 1 of 14)	-54420	NM_001291190	237860	Mm.440381	NM_177710	ENSMUSG00000037926	Ssh2	SSH-2|SSH-2L|mSSH-2L	slingshot homolog 2 (Drosophila)	protein-coding
mm_138583.1	chr17	35471645	35471683	+	1	NA	intron (NM_010391, intron 3 of 6)	intron (NM_010391, intron 3 of 6)	1575	NM_010391	15007	Mm.88795	NM_010391	ENSMUSG00000067235	H2-Q10	H-2Q10|Q10|Qa10	histocompatibility 2, Q region locus 10	protein-coding
mm_14994.1	chr2	152333874	152333876	+	1	NA	Intergenic	Intergenic	-1236	NM_019705	24105	Mm.182145	NM_019705	ENSMUSG00000027466	Rbck1	AL033326|HOIL-1|HOIL-1L|UIP28|Ubce7ip3	RanBP-type and C3HC4-type zinc finger containing 1	protein-coding
mm_66213.1	chr7	34360623	34360623	-	1	NA	intron (NM_025948, intron 4 of 10)	intron (NM_025948, intron 4 of 10)	28917	NM_025948	67070	Mm.276503	NM_025948	ENSMUSG00000066568	Lsm14a	2700023B17Rik|AA407828|AU017544|Tral	LSM14A mRNA processing body assembly factor	protein-coding
mm_83653.1	chr9	49508626	49508641	-	1	NA	exon (NM_001311065, exon 17 of 18)	exon (NM_001311065, exon 17 of 18)	-9655	NR_029465	100036537	Mm.437541	NR_029465	ENSMUSG00000079564	Gm11149	ENSMUSG00000060603|ENSMUSG00000079564	predicted gene 11149	ncRNA
mm_5041.1	chr1	193655636	193655668	+	1	NA	Intergenic	Intergenic	-148122	NR_029592	387201		NR_029592	ENSMUSG00000065533	Mir205	Mirn205|mir-205|mmu-mir-205	microRNA 205	ncRNA
mm_64802.1	chr7	6691163	6691176	-	1	NA	intron (NM_011769, intron 2 of 7)	B4A|SINE|B4	5263	NM_011769	22776	Mm.89976	NM_011769	ENSMUSG00000002266	Zim1	-	zinc finger, imprinted 1	protein-coding
mm_147116.1	chr18	35740025	35740035	-	1	NA	intron (NM_028261, intron 1 of 7)	intron (NM_028261, intron 1 of 7)	524	NM_001289592	72512	Mm.45995	NM_028261	ENSMUSG00000024349	Tmem173	2610307O08Rik|ERIS|MPYS|Mita|STING	transmembrane protein 173	protein-coding
mm_43244.1	chr5	130079479	130079492	+	1	NA	5' UTR (NM_001130476, exon 1 of 6)	5' UTR (NM_001130476, exon 1 of 6)	115	NM_001130476	22021	Mm.332720	NM_013837	ENSMUSG00000034118	Tpst1	R75054|Tango13a	protein-tyrosine sulfotransferase 1	protein-coding
mm_114188.1	chr13	55714663	55714756	+	1	NA	promoter-TSS (NM_175150)	promoter-TSS (NM_175150)	59	NM_175150	69672	Mm.294457	NM_175150	ENSMUSG00000021497	Txndc15	2310047H23Rik|AI854086|C5orf14|UNQ335	thioredoxin domain containing 15	protein-coding
mm_78349.1	chr9	25307792	25307800	+	1	NA	3' UTR (NM_001205367, exon 13 of 13)	3' UTR (NM_001205367, exon 13 of 13)	55357	NM_001205367	235072	Mm.270259	NM_009859	ENSMUSG00000001833	Sept7	Cdc10|E430034N22	septin 7	protein-coding
mm_35406.1	chr4	34756196	34756201	-	1	NA	promoter-TSS (NM_001033255)	promoter-TSS (NM_001033255)	61	NM_001033255	214568	Mm.297405	NM_001033255	ENSMUSG00000071015	Gm136	-	predicted gene 136	protein-coding
mm_158072.1	chrX	101264741	101264749	-	1	NA	promoter-TSS (NM_001317221)	promoter-TSS (NM_001317221)	-753	NM_001317221	245536	Mm.212463	NM_001033362	ENSMUSG00000090141	Gm614	-	predicted gene 614	protein-coding
mm_107221.1	chr12	26470350	26470360	+	1	NA	intron (NM_020557, intron 1 of 4)	intron (NM_020557, intron 1 of 4)	1140	NM_020557	22169	Mm.271839	NM_020557	ENSMUSG00000020638	Cmpk2	1200004E04Rik|TDKI|Tyki	cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial	protein-coding
mm_114907.1	chr13	94875626	94875643	+	1	NA	promoter-TSS (NM_011021)	promoter-TSS (NM_011021)	7	NM_011021	18420	Mm.42051	NM_011021	ENSMUSG00000021685	Otp	-	orthopedia homeobox	protein-coding
mm_12419.1	chr2	70562113	70562123	+	1	NA	promoter-TSS (NM_008077)	promoter-TSS (NM_008077)	-11	NM_001312900	14415	Mm.272120	NM_008077	ENSMUSG00000070880	Gad1	EP10|Gad-1	glutamate decarboxylase 1	protein-coding
mm_94624.1	chr11	16778654	16778692	+	1	NA	intron (NM_207655, intron 1 of 27)	intron (NM_207655, intron 1 of 27)	26470	NM_007912	13649	Mm.8534	NM_007912	ENSMUSG00000020122	Egfr	9030024J15Rik|AI552599|Erbb|Errb1|Errp|Wa5|wa-2|wa2	epidermal growth factor receptor	protein-coding
mm_87465.1	chr10	51485753	51485762	+	1	NA	exon (NM_008147, exon 8 of 9)	exon (NM_008147, exon 8 of 9)	-5141	NM_001291894	14728	Mm.34408	NM_013532	ENSMUSG00000062593	Lilrb4a	CD85K|Gp49b|HM18|ILT3|LIR-5|Lilrb4|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4A	protein-coding
mm_108809.1	chr12	94055312	94055316	+	1	NA	Intergenic	RMER19B|LTR|ERVK	127976	NR_106201	102466888		NR_106201	ENSMUSG00000098931	Mir8099-2	Gm27692|mmu-mir-8099-2	microRNA 8099-2	ncRNA
mm_67078.1	chr7	68264601	68264622	-	1	NA	promoter-TSS (NM_030101)	promoter-TSS (NM_030101)	-378	NM_030101	78444	Mm.425468	NM_030101	ENSMUSG00000030553	Pgpep1l	C330024D12Rik	pyroglutamyl-peptidase I-like	protein-coding
mm_70418.1	chr8	11461213	11461223	+	1	NA	intron (NM_011227, intron 1 of 1)	intron (NM_011227, intron 1 of 1)	-16711	NR_126558	102132	Mm.37632	NR_126558	ENSMUSG00000096957	E230013L22Rik	AI645545	RIKEN cDNA E230013L22 gene	ncRNA
mm_33139.1	chr4	125085112	125085122	+	1	NA	promoter-TSS (NM_001290701)	promoter-TSS (NM_001290701)	-17	NM_027310	70088	Mm.291214	NM_027310	ENSMUSG00000028863	Meaf6	2310005N01Rik|2810036M01Rik	MYST/Esa1-associated factor 6	protein-coding
mm_137760.1	chr17	29489339	29489348	+	1	NA	Intergenic	Intergenic	-1702	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_87454.1	chr10	51483678	51483689	+	1	NA	intron (NM_001291892, intron 5 of 8)	intron (NM_001291892, intron 5 of 8)	3071	NM_001291892	14727	Mm.439661	NM_008147	ENSMUSG00000062593	Lilr4b	Gp49a|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4B	protein-coding
mm_106101.1	chr11	116262892	116262923	-	1	NA	exon (NM_146032, exon 6 of 16)	exon (NM_146032, exon 6 of 16)	11310	NM_146032	217337	Mm.29655	NM_146032	ENSMUSG00000020780	Srp68	2610024I03Rik	signal recognition particle 68	protein-coding
mm_73343.1	chr8	105348093	105348099	+	1	NA	promoter-TSS (NM_001081332)	promoter-TSS (NM_001081332)	-126	NM_177699	234686	Mm.87724	NM_177699	ENSMUSG00000014778	Fhod1	BC017144|FHOS|FHOS1	formin homology 2 domain containing 1	protein-coding
mm_111431.1	chr12	91779130	91779144	-	1	NA	intron (NM_175367, intron 1 of 6)	CpG	7299	NM_175367	108800	Mm.23125	NM_175367	ENSMUSG00000020961	Ston2	4933401N24Rik|AI425999|AW544599	stonin 2	protein-coding
mm_35090.1	chr4	8238092	8238102	-	1	NA	exon (NM_007592, exon 2 of 9)	exon (NM_007592, exon 2 of 9)	944	NM_007592	12319	Mm.119320	NM_007592	ENSMUSG00000041261	Car8	AW546993|Ca8|Cals|Cals1|Carp|wdl	carbonic anhydrase 8	protein-coding
mm_80648.1	chr9	89869852	89869873	+	1	NA	Intergenic	Intergenic	-39913	NM_011245	19417	Mm.44561	NM_011245	ENSMUSG00000032356	Rasgrf1	AI844718|CDC25|CDC25Mm|Gnrp|Grf1|Grfbeta|P190-A|Ras-GRF1|p190|p190RhoGEF	RAS protein-specific guanine nucleotide-releasing factor 1	protein-coding
mm_82517.1	chr9	20640398	20640401	-	1	NA	intron (NM_001002846, intron 2 of 2)	B1_Mur4|SINE|Alu	2407	NM_013911	30843	Mm.24608	NM_013911	ENSMUSG00000066892	Fbxl12	3110048D16Rik|Fbl12	F-box and leucine-rich repeat protein 12	protein-coding
mm_160497.1	chr9	7835292	7835292	-	1	NA	5' UTR (NM_007465, exon 2 of 8)	5' UTR (NM_007465, exon 2 of 8)	1514	NM_001291503	11797	Mm.335659	NM_007465	ENSMUSG00000057367	Birc2	AW146227|Api1|Api2|Birc3|C-IAP1|C330006D17Rik|HIAP1|HIAP2|IAP1|IAP2|MIAP1|MIAP2|MIHB|MIHC|RNF48|cIAP1|cIAP2|mcIAP1	baculoviral IAP repeat-containing 2	protein-coding
mm_55787.1	chr6	82688384	82688403	-	1	NA	Intergenic	Intergenic	-35528	NM_025882	66979	Mm.195753	NM_025882	ENSMUSG00000030042	Pole4	2400007P05Rik|5830430F06Rik	polymerase (DNA-directed), epsilon 4 (p12 subunit)	protein-coding
mm_171820.1	chr5	139844927	139844932	+	1	NA	Intergenic	Intergenic	-18086	NM_025604	66506	Mm.29070	NM_025604	ENSMUSG00000029551	Psmg3	1810042K04Rik|4930403H09Rik|AI303239	proteasome (prosome, macropain) assembly chaperone 3	protein-coding
mm_37418.1	chr4	122864663	122864713	-	1	NA	exon (NM_007598, exon 8 of 13)	exon (NM_007598, exon 8 of 13)	21369	NM_007598	12331	Mm.8687	NM_007598	ENSMUSG00000028656	Cap1	-	CAP, adenylate cyclase-associated protein 1 (yeast)	protein-coding
mm_120602.1	chr14	70080149	70080163	+	1	NA	3' UTR (NM_001289927, exon 2 of 2)	3' UTR (NM_001289927, exon 2 of 2)	2361	NM_001289927	13655	Mm.103737	NM_018781	ENSMUSG00000033730	Egr3	Pilot	early growth response 3	protein-coding
mm_168189.1	chr10	62602191	62602196	-	1	NA	exon (NM_019553, exon 1 of 15)	exon (NM_019553, exon 1 of 15)	105	NM_019553	56200	Mm.413275	NM_019553	ENSMUSG00000020075	Ddx21	AI255159|AL022742|D10Ertd645e|D10Wsu42e	DEAD (Asp-Glu-Ala-Asp) box polypeptide 21	protein-coding
mm_134973.1	chr16	32019588	32019600	-	1	NA	3' UTR (NM_177326, exon 15 of 15)	3' UTR (NM_177326, exon 15 of 15)	-16307	NM_177103	320213	Mm.152890	NM_023801	ENSMUSG00000022772	Senp5	6230429P13Rik|A730063F07Rik|AI851888|BB189556|SMT3IP3	SUMO/sentrin specific peptidase 5	protein-coding
mm_16103.1	chr2	169632853	169632897	+	1	NA	promoter-TSS (NM_080455)	promoter-TSS (NM_080455)	-771	NM_080455	228911	Mm.315789	NM_080455	ENSMUSG00000047907	Tshz2	2900073F20Rik|B830045G17|Mtsh2|Sdccag33l|Tsh2|Zfp218|mKIAA4248|teashirt2	teashirt zinc finger family member 2	protein-coding
mm_23808.1	chr3	79885950	79886002	+	1	NA	promoter-TSS (NM_133187)	promoter-TSS (NM_133187)	46	NM_133187	68659	Mm.427274	NM_133187	ENSMUSG00000027955	Fam198b	1110032E23Rik|2210419I08Rik|AV011458|Ened	family with sequence similarity 198, member B	protein-coding
mm_117445.1	chr13	74770583	74770595	-	1	NA	5' UTR (NM_001301157, exon 1 of 28)	5' UTR (NM_001301157, exon 1 of 28)	147	NM_001301156	12380	Mm.29163	NM_009817	ENSMUSG00000021585	Cast	-	calpastatin	protein-coding
mm_136057.1	chr16	79091066	79091074	-	1	NA	promoter-TSS (NM_178855)	promoter-TSS (NM_178855)	27	NM_008941	19146	Mm.5184	NM_008941	ENSMUSG00000022857	Tmprss15	Entk|Prss7	transmembrane protease, serine 15	protein-coding
mm_57402.1	chr6	124864152	124864165	-	1	NA	promoter-TSS (NM_013533)	promoter-TSS (NM_013533)	-241	NM_013533	14788	Mm.2514	NM_013533	ENSMUSG00000038390	Gpr162	A-2|BC031437|Grca	G protein-coupled receptor 162	protein-coding
mm_84405.1	chr9	65555303	65555321	-	1	NA	3' UTR (NM_153119, exon 6 of 6)	3' UTR (NM_153119, exon 6 of 6)	24775	NM_153119	102595	Mm.247303	NM_153119	ENSMUSG00000050721	Plekho2	AI840980|Plekhq1	pleckstrin homology domain containing, family O member 2	protein-coding
mm_71740.1	chr8	62958973	62958977	+	1	NA	intron (NM_023689, intron 3 of 11)	Lx3_Mus|LINE|L1	7630	NM_023689	72902	Mm.334552	NM_023689	ENSMUSG00000054162	Spock3	2900045C01Rik|AI428471|mKIAA4039	sparc/osteonectin, cwcv and kazal-like domains proteoglycan 3	protein-coding
mm_125956.1	chr15	76249475	76249489	+	1	NA	3' UTR (NM_023168, exon 7 of 7)	3' UTR (NM_023168, exon 7 of 7)	1291	NR_105918	102465575		NR_105918	ENSMUSG00000098625	Mir6953	Gm27738|mmu-mir-6953	microRNA 6953	ncRNA
mm_62431.1	chr7	101361968	101361978	+	1	NA	intron (NM_001040111, intron 1 of 33)	intron (NM_001040111, intron 1 of 33)	13904	NM_001040111	69710	Mm.277687	NM_027180	ENSMUSG00000032812	Arap1	2410002L19Rik|Centd2|mKIAA0782	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	protein-coding
mm_159187.1	chr2	113363658	113363658	+	1	NA	intron (NM_001285458, intron 1 of 16)	intron (NM_001285458, intron 1 of 16)	35922	NM_010230	14260	Mm.4938	NM_010230	ENSMUSG00000044042	Fmn1	Fmn|formin-1|ld	formin 1	protein-coding
mm_105001.1	chr11	100371245	100371279	-	1	NA	3' UTR (NM_010593, exon 14 of 14)	3' UTR (NM_010593, exon 14 of 14)	-15121	NM_010404	15114	Mm.281700	NM_010404	ENSMUSG00000006930	Hap1	HAP-1	huntingtin-associated protein 1	protein-coding
mm_14342.1	chr2	129593137	129593147	+	1	NA	promoter-TSS (NM_001291022)	promoter-TSS (NM_001291022)	-27	NM_001291019	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_98892.1	chr11	97841283	97841359	+	1	NA	exon (NM_001080935, exon 2 of 3)	exon (NM_001080935, exon 2 of 3)	541	NM_001080935	68127	Mm.110270	NM_001080935	ENSMUSG00000050538	B230217C12Rik	AI840637	RIKEN cDNA B230217C12 gene	protein-coding
mm_75075.1	chr8	33853694	33853702	-	1	NA	intron (NM_001042674, intron 4 of 7)	intron (NM_001042674, intron 4 of 7)	76165	NM_019733	19663	Mm.323997	NM_019733	ENSMUSG00000031586	Rbpms	2010300K22Rik|2700019M19Rik|AU017537|RBP-MS|hermes	RNA binding protein gene with multiple splicing	protein-coding
mm_32212.1	chr4	101550378	101550398	+	1	NA	promoter-TSS (NM_001164583)	promoter-TSS (NM_001164583)	-206	NM_001164583	72685	Mm.76494	NM_198412	ENSMUSG00000028528	Dnajc6	2810027M23Rik|mKIAA0473	DnaJ heat shock protein family (Hsp40) member C6	protein-coding
mm_102094.1	chr11	52284393	52284417	-	1	NA	Intergenic	Intergenic	-1391	NM_001313981	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_36166.1	chr4	61674095	61674097	-	1	NA	promoter-TSS (NM_001199333)	promoter-TSS (NM_001199333)	-2	NM_001199333	100048884	Mm.335875	NM_001199333	ENSMUSG00000078674	Mup18	100039228|Gm12561|Mup16|Mup6|Mup9|OTTMUSG00000007486	major urinary protein 18	protein-coding
mm_101814.1	chr11	46389455	46389467	-	1	NA	promoter-TSS (NM_001281968)	promoter-TSS (NM_001281968)	54	NM_001281968	16428	Mm.339927	NM_010583	ENSMUSG00000020395	Itk	Emt|Tcsk|Tsk	IL2 inducible T cell kinase	protein-coding
mm_39170.1	chr4	155697003	155697018	-	1	NA	TTS (NM_178699)	TTS (NM_178699)	2668	NM_178699	230991	Mm.29083	NM_178699	ENSMUSG00000074738	Fndc10	B930041F14Rik|MNCb-3966	fibronectin type III domain containing 10	protein-coding
mm_113795.1	chr13	46418213	46418238	+	1	NA	promoter-TSS (NM_001081425)	promoter-TSS (NM_001081425)	-75	NM_001081425	666794	Mm.38269	NM_001081425	ENSMUSG00000038132	Rbm24	6330546B05Rik|AI606861	RNA binding motif protein 24	protein-coding
mm_47918.1	chr5	135001281	135001285	-	1	NA	promoter-TSS (NR_026907)	promoter-TSS (NR_026907)	67	NR_026907	71304	Mm.482317	NR_026907	ENSMUSG00000054909	Wbscr25	4933433J03Rik|4933439O14Rik	Williams Beuren syndrome chromosome region 25 (human)	ncRNA
mm_10250.1	chr2	9189559	9189563	+	1	NA	promoter-TSS (NR_038180)	promoter-TSS (NR_038180)	46	NR_038180	73438	Mm.23558	NR_038180	ENSMUSG00000085580	1700061F12Rik	-	RIKEN cDNA 1700061F12 gene	ncRNA
mm_87748.1	chr10	60267113	60267124	+	1	NA	Intergenic	Intergenic	-10510	NM_001146123	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_87452.1	chr10	51483584	51483605	+	1	NA	intron (NM_001291892, intron 5 of 8)	MIR3|SINE|MIR	2982	NM_001291892	14727	Mm.439661	NM_008147	ENSMUSG00000062593	Lilr4b	Gp49a|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4B	protein-coding
mm_93692.1	chr10	117835329	117835335	-	1	NA	intron (NM_024457, intron 1 of 7)	intron (NM_024457, intron 1 of 7)	10642	NM_024457	215449	Mm.233009	NM_024457	ENSMUSG00000052681	Rap1b	2810443E11Rik	RAS related protein 1b	protein-coding
mm_148018.1	chr18	68429264	68429268	-	1	NA	promoter-TSS (NM_001271716)	promoter-TSS (NM_001271716)	54	NM_001301372	17200	Mm.426053	NM_008560	ENSMUSG00000045569	Mc2r	ACTH-R|ACTHR|MC2-R	melanocortin 2 receptor	protein-coding
mm_169502.1	chr14	78725721	78725724	-	1	NA	promoter-TSS (NM_001081336)	promoter-TSS (NM_001081336)	-633	NM_001081336	380921	Mm.89591	NM_001081336	ENSMUSG00000034731	Dgkh	5930402B05Rik|D130015C16|DGK	diacylglycerol kinase, eta	protein-coding
mm_9233.1	chr1	171281114	171281152	-	1	NA	promoter-TSS (NM_008911)	promoter-TSS (NM_008911)	53	NM_008911	19044	Mm.266888	NM_008911	ENSMUSG00000062729	Ppox	Ppo	protoporphyrinogen oxidase	protein-coding
mm_166747.1	chr6	125096011	125096036	+	1	NA	promoter-TSS (NM_145979)	promoter-TSS (NM_145979)	42	NM_001346610	107932	Mm.333388	NM_145979	ENSMUSG00000063870	Chd4	9530019N15Rik|AA617397|BC005710|D6Ertd380e|Mi-2beta|mKIAA4075	chromodomain helicase DNA binding protein 4	protein-coding
mm_29425.1	chr3	109017759	109017771	-	1	NA	intron (NM_001163567, intron 1 of 10)	intron (NM_001163567, intron 1 of 10)	9842	NM_001163567	329739	Mm.69013	NM_001163567	ENSMUSG00000040339	Fam102b	1600010D10Rik|B430201A12Rik	family with sequence similarity 102, member B	protein-coding
mm_13857.1	chr2	119705588	119705603	+	1	NA	exon (NM_030112, exon 4 of 18)	exon (NM_030112, exon 4 of 18)	30527	NM_030112	76246	Mm.33437	NM_030112	ENSMUSG00000027304	Rtf1	2900005O08Rik|6530416A09Rik|AI853581|AU043144|AW553985|Gtl7|cbp82	RTF1, Paf1/RNA polymerase II complex component	protein-coding
mm_83838.1	chr9	54392747	54392752	-	1	NA	intron (NM_172771, intron 28 of 43)	intron (NM_172771, intron 28 of 43)	-91179	NR_045805	73567	Mm.211290	NM_001033169	ENSMUSG00000074343	Gldnos	1700104A03Rik	gliomedin, opposite strand	ncRNA
mm_132555.1	chr16	37884462	37884479	+	1	NA	3' UTR (NM_177093, exon 4 of 4)	3' UTR (NM_177093, exon 4 of 4)	16070	NM_177093	320184	Mm.390882	NM_177093	ENSMUSG00000034158	Lrrc58	1810012N18Rik|C330018J07Rik	leucine rich repeat containing 58	protein-coding
mm_153757.1	chr19	45352813	45352817	-	1	NA	Intergenic	RLTR1B|LTR|ERV1	-10919	NM_001286466	12234	Mm.119717	NM_009771	ENSMUSG00000025217	Btrc	Beta-Trcp1|E3RS-IkappaB|E3RSIkappaB|FWD1|Fbw1a|HOS|Slimb|b-TrCP|beta-TrCP	beta-transducin repeat containing protein	protein-coding
mm_18835.1	chr2	74753431	74753444	-	1	NA	non-coding (NR_110447, exon 2 of 2)	non-coding (NR_110447, exon 2 of 2)	753	NR_110447	102634401	Mm.235021	NR_110447	ENSMUSG00000085015	LOC102634401	-	uncharacterized LOC102634401	ncRNA
mm_43061.1	chr5	124233003	124233025	+	1	NA	intron (NR_045369, intron 2 of 5)	L1MB8|LINE|L1	3289	NR_045369	75927	Mm.410803	NR_045369	ENSMUSG00000090220	Pitpnm2os1	4930568K20Rik	phosphatidylinositol transfer protein, membrane-associated 2, opposite strand 1	ncRNA
mm_116116.1	chr13	28950313	28950326	-	1	NA	TTS (NM_009238)	TTS (NM_009238)	3363	NM_009238	20677	Mm.240627	NM_009238	ENSMUSG00000076431	Sox4	AA682046|Sox-4	SRY (sex determining region Y)-box 4	protein-coding
mm_152872.1	chr19	24477449	24477490	-	1	NA	promoter-TSS (NM_026520)	promoter-TSS (NM_026520)	5	NM_026520	68034	Mm.440181	NM_026520	ENSMUSG00000074922	Fam122a	2410124L17Rik|2900009I07Rik|ENSMUSG00000051082|Gm9849	family with sequence similarity 122, member A	protein-coding
mm_144700.1	chr18	34862930	34862965	+	1	NA	exon (NM_007913, exon 2 of 2)	exon (NM_007913, exon 2 of 2)	1740	NM_007913	13653	Mm.181959	NM_007913	ENSMUSG00000038418	Egr1	A530045N19Rik|ETR103|Egr-1|Krox-1|Krox-24|Krox24|NGF1-A|NGFI-A|NGFIA|TIS8|Zenk|Zfp-6|Zif268|egr	early growth response 1	protein-coding
mm_80403.1	chr9	77636576	77636610	+	1	NA	promoter-TSS (NM_172925)	promoter-TSS (NM_172925)	-139	NM_172925	244923	Mm.138238	NM_172925	ENSMUSG00000044938	Klhl31	9830147P19Rik|D930047P17Rik|Kbtbd1	kelch-like 31	protein-coding
mm_76837.1	chr8	105281491	105281508	-	1	NA	3' UTR (NM_028888, exon 8 of 8)	3' UTR (NM_028888, exon 8 of 8)	5052	NM_030152	78688	Mm.475715	NM_030152	ENSMUSG00000014776	Nol3	ARC|B430311C09Rik|MYC|NOP|Nop30	nucleolar protein 3 (apoptosis repressor with CARD domain)	protein-coding
mm_15542.1	chr2	158385028	158385029	+	1	NA	3' UTR (NM_175692, exon 5 of 5)	3' UTR (NM_175692, exon 5 of 5)	9390	NM_175692	319317	Mm.294494	NM_175692	ENSMUSG00000044349	Snhg11	A930034L06Rik|AI854265|AL022637|AW319638|E130013N09Rik	small nucleolar RNA host gene 11	protein-coding
mm_10910.1	chr2	25372316	25372368	+	1	NA	5' UTR (NM_001290407, exon 1 of 6)	5' UTR (NM_001290407, exon 1 of 6)	307	NM_001081085	72080	Mm.250293	NM_001081085	ENSMUSG00000026955	Sapcd2	2010317E24Rik|6030458L21Rik|AL033337|ang	suppressor APC domain containing 2	protein-coding
mm_76661.1	chr8	93270348	93270355	-	1	NA	intron (NM_144930, intron 4 of 13)	intron (NM_144930, intron 4 of 13)	9385	NM_144930	234564	Mm.29110	NM_144930	ENSMUSG00000031725	Ces1f	AU018778|CesML1|TGH-2	carboxylesterase 1F	protein-coding
mm_25875.1	chr3	130185222	130185225	+	1	NA	intron (NM_029838, intron 2 of 37)	intron (NM_029838, intron 2 of 37)	4378	NM_001244952	77018	Mm.91728	NM_029838	ENSMUSG00000058897	Col25a1	2700062B08Rik|CLAC-P	collagen, type XXV, alpha 1	protein-coding
mm_67904.1	chr7	99695573	99695622	-	1	NA	5' UTR (NM_001252531, exon 1 of 14)	5' UTR (NM_001252531, exon 1 of 14)	212	NM_001252531	101488	Mm.11249	NM_175316	ENSMUSG00000030737	Slco2b1	AI060904|AI852653|OATP-B|Slc21a9	solute carrier organic anion transporter family, member 2b1	protein-coding
mm_66432.1	chr7	44669309	44669331	-	1	NA	intron (NM_001271540, intron 1 of 41)	CpG	1523	NM_001271540	71960	Mm.158289	NM_028021	ENSMUSG00000030739	Myh14	2400004E04Rik|II-C|NHMCII|NMHC II-C	myosin, heavy polypeptide 14	protein-coding
mm_146079.1	chr18	70607202	70607222	+	1	NA	intron (NM_010773, intron 3 of 6)	intron (NM_010773, intron 3 of 6)	38920	NM_010773	17191	Mm.322	NM_010773	ENSMUSG00000024513	Mbd2	MBD2a	methyl-CpG binding domain protein 2	protein-coding
mm_161710.1	chr17	25025620	25025620	+	1	NA	exon (NM_134126, exon 4 of 30)	exon (NM_134126, exon 4 of 30)	9534	NM_134126	106633	Mm.32802	NM_134126	ENSMUSG00000024169	Ift140	AI661311|Tce5|Wdtc2|mKIAA0590	intraflagellar transport 140	protein-coding
mm_89099.1	chr10	84550079	84550086	+	1	NA	intron (NR_040658, intron 2 of 3)	RSINE1|SINE|B4	3256	NR_040658	442847	Mm.128292	NR_040658	ENSMUSG00000097076	Platr7	C330046G13Rik	pluripotency associated transcript 7	ncRNA
mm_151755.1	chr19	5099506	5099525	-	1	NA	promoter-TSS (NM_009920)	promoter-TSS (NM_009920)	-994	NM_009920	12794	Mm.299737	NM_009920	ENSMUSG00000024873	Cnih2	CNIH-2|Cnil	cornichon family AMPA receptor auxiliary protein 2	protein-coding
mm_2902.1	chr1	131962988	131963001	+	1	NA	promoter-TSS (NM_001177628)	promoter-TSS (NM_001177628)	79	NM_001177628	212980	Mm.200307	NM_145977	ENSMUSG00000026435	Slc45a3	2210413P12Rik|AU023994|AU043764|IPCA-6|PRST|Pcanap6	solute carrier family 45, member 3	protein-coding
mm_162184.1	chrX	102908687	102908687	-	1	NA	promoter-TSS (NM_027591)	promoter-TSS (NM_027591)	0	NM_027591	70887	Mm.29672	NM_027591	ENSMUSG00000031323	Dmrtc1a	1700030H14Rik|4921520P21Rik|DMRTC1|Dmrt8.1	DMRT-like family C1a	protein-coding
mm_52096.1	chr6	97850918	97850943	+	1	NA	intron (NM_001113198, intron 1 of 9)	intron (NM_001113198, intron 1 of 9)	43872	NM_001113198	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_169975.1	chr1	71494203	71494219	-	1	NA	Intergenic	Intergenic	-62945	NM_026195	108147	Mm.38010	NM_026195	ENSMUSG00000026192	Atic	2610509C24Rik|AA536954|AW212393	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	protein-coding
mm_143936.1	chr17	86230256	86230266	-	1	NA	intron (NM_011104, intron 1 of 14)	intron (NM_011104, intron 1 of 14)	56917	NR_045435	72104	Mm.443401	NR_045435	ENSMUSG00000100738	2010106C02Rik	-	RIKEN cDNA 2010106C02 gene	ncRNA
mm_85889.1	chr9	111053935	111053957	-	1	NA	TTS (NM_017466)	TTS (NM_017466)	3298	NM_001302377	54199	Mm.7336	NM_017466	ENSMUSG00000043953	Ccrl2	1810047I05Rik|Ackr5|CCR11|Cmkbr1l2|E01|L-CCR	chemokine (C-C motif) receptor-like 2	protein-coding
mm_80061.1	chr9	69397976	69397987	+	1	NA	promoter-TSS (NM_145618)	promoter-TSS (NM_145618)	-17	NM_145618	93697	Mm.35911	NM_145618	ENSMUSG00000032235	Ice2	B230343B06Rik|Narg2	interactor of little elongation complex ELL subunit 2	protein-coding
mm_159619.1	chr4	134287847	134287847	-	1	NA	promoter-TSS (NM_001163794)	promoter-TSS (NM_001163794)	-1	NM_146156	230809	Mm.22778	NM_146156	ENSMUSG00000050890	Pdik1l	BC027088|stk35l2	PDLIM1 interacting kinase 1 like	protein-coding
mm_6962.1	chr1	86111910	86111927	-	1	NA	promoter-TSS (NM_008311)	promoter-TSS (NM_008311)	52	NM_008311	15559	Mm.439747	NM_008311	ENSMUSG00000026228	Htr2b	5-HT2B|AJ012488|AV377389	5-hydroxytryptamine (serotonin) receptor 2B	protein-coding
mm_133306.1	chr16	77598162	77598179	+	1	NA	promoter-TSS (NR_029535)	promoter-TSS (NR_029535)	-766	NR_029535	387229		NR_029535	ENSMUSG00000065530	Mir99a	Mirn99a|mir-99a|mmu-mir-99a	microRNA 99a	ncRNA
mm_70375.1	chr8	10006632	10006653	+	1	NA	promoter-TSS (NM_033622)	promoter-TSS (NM_033622)	9	NM_033622	24099	Mm.28835	NM_033622	ENSMUSG00000031497	Tnfsf13b	BAFF|BLyS|D8Ertd387e|TALL-1|TALL1|THANK|TNFSF20|Tnlg7a|zTNF4	tumor necrosis factor (ligand) superfamily, member 13b	protein-coding
mm_36625.1	chr4	91376316	91376330	-	1	NA	5' UTR (NM_001177883, exon 1 of 7)	5' UTR (NM_001177883, exon 1 of 7)	168	NM_001347149	15569	Mm.318042	NM_010486	ENSMUSG00000008489	Elavl2	Hub|mel-N1	ELAV (embryonic lethal, abnormal vision, Drosophila)-like 2 (Hu antigen B)	protein-coding
mm_153106.1	chr19	32757370	32757383	-	1	NA	promoter-TSS (NM_008960)	promoter-TSS (NM_008960)	-201	NM_008960	19211	Mm.245395	NM_008960	ENSMUSG00000013663	Pten	2310035O07Rik|A130070J02Rik|AI463227|B430203M17Rik|MMAC1|TEP1	phosphatase and tensin homolog	protein-coding
mm_16172.1	chr2	172549582	172549605	+	1	NA	promoter-TSS (NM_009335)	promoter-TSS (NM_009335)	0	NM_009335	21420	Mm.3629	NM_009335	ENSMUSG00000028640	Tfap2c	AA409384|AP2gamma|Ap-2.2|Stra2|Tcfap2c	transcription factor AP-2, gamma	protein-coding
mm_66562.1	chr7	45239279	45239287	-	1	NA	promoter-TSS (NM_007645)	promoter-TSS (NM_007645)	-168	NM_001290804	12493	Mm.3689	NM_007645	ENSMUSG00000030798	Cd37	Tspan26	CD37 antigen	protein-coding
mm_21087.1	chr2	153090641	153090661	-	1	NA	Intergenic	Intergenic	-17817	NM_001172117	15162	Mm.715	NM_010407	ENSMUSG00000003283	Hck	AI849071|Bmk	hemopoietic cell kinase	protein-coding
mm_111185.1	chr12	84148214	84148227	-	1	NA	TTS (NM_001163501)	TTS (NM_001163501)	269	NM_027438	70481	Mm.444348	NM_027438	ENSMUSG00000054383	Pnma1	5730402C15Rik	paraneoplastic antigen MA1	protein-coding
mm_108464.1	chr12	83520529	83520598	+	1	NA	promoter-TSS (NM_030246)	promoter-TSS (NM_030246)	97	NM_030246	73828	Mm.38238	NM_030246	ENSMUSG00000021222	Dcaf4	1110018E21Rik|Wdr21	DDB1 and CUL4 associated factor 4	protein-coding
mm_98221.1	chr11	88047789	88047832	+	1	NA	5' UTR (NM_001078167, exon 1 of 3)	5' UTR (NM_001078167, exon 1 of 3)	437	NM_173374	110809	Mm.391719	NM_173374	ENSMUSG00000018379	Srsf1	1110054N12Rik|5730507C05Rik|6330415C05Rik|AI482334|AW491331|Asf|Sf2|Sfrs1	serine/arginine-rich splicing factor 1	protein-coding
mm_173074.1	chrX	136215448	136215459	-	1	NA	promoter-TSS (NM_009052)	promoter-TSS (NM_009052)	60	NM_009052	19716	Mm.422943	NM_009052	ENSMUSG00000050071	Bex1	AA407839|AU018692|Bex4|Rex3	brain expressed X-linked 1	protein-coding
mm_36195.1	chr4	62329447	62329467	-	1	NA	intron (NM_001045528, intron 12 of 27)	intron (NM_001045528, intron 12 of 27)	31091	NM_001045528	338355	Mm.357792	NM_001045528	ENSMUSG00000066151	Fkbp15	BB131447|C430014M02Rik|FKBO133|FKBP-133|FKBP-15|FKBP133|mKIAA0674	FK506 binding protein 15	protein-coding
mm_29616.1	chr3	121283052	121283058	-	1	NA	Intergenic	Intergenic	-8762	NM_024178	66789	Mm.269881	NM_024178	ENSMUSG00000039887	Alg14	5430428G01Rik|AI854024	asparagine-linked glycosylation 14	protein-coding
mm_14617.1	chr2	136758305	136758330	+	1	NA	exon (NM_001291056, exon 3 of 8)	exon (NM_001291056, exon 3 of 8)	44867	NM_001291056	20614	Mm.45953	NM_011428	ENSMUSG00000027273	Snap25	Bdr|GENA70|SNAP-25|SUP|sp	synaptosomal-associated protein 25	protein-coding
mm_104108.1	chr11	86711887	86711903	-	1	NA	exon (NM_001003908, exon 16 of 32)	exon (NM_001003908, exon 16 of 32)	27814	NM_001098810	217057	Mm.24868	NM_175004	ENSMUSG00000072582	Ptrh2	A230072I16Rik|Bit1|CGI-147	peptidyl-tRNA hydrolase 2	protein-coding
mm_133880.1	chr16	96499242	96499251	+	1	NA	intron (NM_008791, intron 2 of 2)	intron (NM_008791, intron 2 of 2)	31640	NM_008791	18546	Mm.5023	NM_008791	ENSMUSG00000090223	Pcp4	P16Rimb19|Pcp-4|Pep19	Purkinje cell protein 4	protein-coding
mm_1742.1	chr1	75450583	75450614	+	1	NA	promoter-TSS (NM_183022)	promoter-TSS (NM_183022)	88	NM_183022	241118	Mm.110790	NM_183022	ENSMUSG00000033007	Asic4	Accn4|BNAC4	acid-sensing (proton-gated) ion channel family member 4	protein-coding
mm_122344.1	chr14	37136007	37136015	-	1	NA	promoter-TSS (NM_001199122)	promoter-TSS (NM_001199122)	-689	NM_078478	66092	Mm.182912	NM_078478	ENSMUSG00000041028	Ghitm	1010001P14Rik|C77840|MICS1|PTD010|Tmbim5	growth hormone inducible transmembrane protein	protein-coding
mm_14833.1	chr2	147364990	147365011	+	1	NA	promoter-TSS (NM_008780)	promoter-TSS (NM_008780)	6	NM_008780	18503	Mm.315502	NM_008780	ENSMUSG00000037034	Pax1	Pax-1|hbs|hunchback|un|undulated|wt	paired box 1	protein-coding
mm_163897.1	chr14	27555376	27555381	-	1	NA	Intergenic	MERV1_LTR|LTR|ERV1	-46918	NM_177111	320234	Mm.247767	NM_177111	ENSMUSG00000046753	Ccdc66	E230015L20Rik	coiled-coil domain containing 66	protein-coding
mm_78565.1	chr9	35908303	35908304	+	1	NA	Intergenic	Intergenic	-58423	NR_030730	100041605	Mm.99350	NR_030730	ENSMUSG00000098705	Gm3428	-	predicted gene 3428	ncRNA
mm_41778.1	chr5	103715317	103715336	+	1	NA	Intergenic	Intergenic	-38836	NM_133919	17355	Mm.6949	NM_133919	ENSMUSG00000029313	Aff1	9630032B01Rik|AW319193|Af4|Mllt2h|Rob	AF4/FMR2 family, member 1	protein-coding
mm_10034.1	chr1	192771200	192771245	-	1	NA	promoter-TSS (NM_144881)	promoter-TSS (NM_144881)	-3	NM_144881	226861	Mm.145857	NM_144881	ENSMUSG00000037375	Hhat	2810432O22Rik|AI462858|AP-2CRE|Skn|Tg(TFAP2A-cre)1Will	hedgehog acyltransferase	protein-coding
mm_126198.1	chr15	78850962	78850989	+	1	NA	TTS (NM_027219)	TTS (NM_027219)	4554	NM_025622	107753	Mm.390793	NM_025622	ENSMUSG00000043501	Lgals2	2200008F12Rik|AI324147	lectin, galactose-binding, soluble 2	protein-coding
mm_12748.1	chr2	79231277	79231287	+	1	NA	Intergenic	Intergenic	-24144	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D|Itga4B	integrin alpha 4	protein-coding
mm_31863.1	chr4	80002703	80002752	+	1	NA	Intergenic	Intergenic	-831486	NM_031202	22178	Mm.30438	NM_031202	ENSMUSG00000005994	Tyrp1	Oca3|TRP-1|TRP1|Tyrp|b|brown|isa	tyrosinase-related protein 1	protein-coding
mm_53785.1	chr6	146577953	146577970	+	1	NA	promoter-TSS (NM_026218)	promoter-TSS (NM_026218)	50	NM_026218	67529	Mm.333499	NM_026218	ENSMUSG00000040242	Fgfr1op2	1500031J01Rik	FGFR1 oncogene partner 2	protein-coding
mm_92058.1	chr10	62508138	62508170	-	1	NA	promoter-TSS (NM_011157)	promoter-TSS (NM_011157)	-399	NM_011157	19073	Mm.338790	NM_011157	ENSMUSG00000020077	Srgn	Prg|Prg1|Sgc	serglycin	protein-coding
mm_8063.1	chr1	135430428	135430488	-	1	NA	promoter-TSS (NM_153774)	promoter-TSS (NM_153774)	33	NM_153774	226432	Mm.271642	NM_153774	ENSMUSG00000041879	Ipo9	0710008K06Rik|AI845704|C78347|Imp9|Ranbp9|mKIAA1192	importin 9	protein-coding
mm_108343.1	chr12	80435084	80435146	+	1	NA	intron (NM_177267, intron 1 of 8)	CpG	1486	NM_177267	320808	Mm.220310	NM_177267	ENSMUSG00000049106	Dcaf5	9430020B07Rik|AI325023|AI430035|AI848110|AW124614|BCRG2|BCRP2|Wdr22	DDB1 and CUL4 associated factor 5	protein-coding
mm_45212.1	chr5	52994136	52994153	-	1	NA	Intergenic	Intergenic	-1852	NR_040413	75954	Mm.258937	NR_040413	ENSMUSG00000106352	5033403H07Rik	-	RIKEN cDNA 5033403H07 gene	ncRNA
mm_164448.1	chr16	49913293	49913297	+	1	NA	Intergenic	Intergenic	57641	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_89446.1	chr10	93123003	93123017	+	1	NA	Intergenic	Intergenic	-37866	NM_146239	237459	Mm.217404	NM_146239	ENSMUSG00000020015	Cdk17	6430598J10Rik|Pctk2	cyclin-dependent kinase 17	protein-coding
mm_154470.1	chrM	3756	3776	-	1	NA	NA	Intergenic	NA	NA								
mm_72704.1	chr8	84978973	84978987	+	1	NA	promoter-TSS (NM_008416)	promoter-TSS (NM_008416)	-232	NM_008416	16477	Mm.1167	NM_008416	ENSMUSG00000052837	Junb	-	jun B proto-oncogene	protein-coding
mm_163424.1	chr12	81764463	81764508	-	1	NA	intron (NM_001174107, intron 2 of 10)	intron (NM_001174107, intron 2 of 10)	16685	NM_177395	338372	Mm.35284	NM_177395	ENSMUSG00000042724	Map3k9	E130314H24Rik|Mlk1|Prke1	mitogen-activated protein kinase kinase kinase 9	protein-coding
mm_21493.1	chr2	163397888	163397899	-	1	NA	promoter-TSS (NM_001205076)	promoter-TSS (NM_001205076)	80	NM_021566	59091	Mm.34459	NM_021566	ENSMUSG00000017817	Jph2	1110002E14Rik|JP-2|Jp2	junctophilin 2	protein-coding
mm_104326.1	chr11	93968024	93968053	-	1	NA	intron (NM_008704, intron 1 of 4)	intron (NM_008704, intron 1 of 4)	483	NM_008704	18102	Mm.439702	NM_008704	ENSMUSG00000037601	Nme1	AL024257|NDPK-A|NM23-M1|NM23A	NME/NM23 nucleoside diphosphate kinase 1	protein-coding
mm_75081.1	chr8	33914588	33914590	-	1	NA	intron (NM_001042674, intron 1 of 7)	intron (NM_001042674, intron 1 of 7)	15274	NM_019733	19663	Mm.323997	NM_019733	ENSMUSG00000031586	Rbpms	2010300K22Rik|2700019M19Rik|AU017537|RBP-MS|hermes	RNA binding protein gene with multiple splicing	protein-coding
mm_166844.1	chr7	19696452	19696461	+	1	NA	exon (NM_009696, exon 4 of 4)	exon (NM_009696, exon 4 of 4)	1942	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_136102.1	chr16	85123835	85123839	-	1	NA	intron (NM_007471, intron 1 of 15)	intron (NM_007471, intron 1 of 15)	49870	NM_001198825	11820	Mm.277585	NM_007471	ENSMUSG00000022892	App	Abeta|Abpp|Adap|Ag|Cvap|E030013M08Rik|betaApp	amyloid beta (A4) precursor protein	protein-coding
mm_95070.1	chr11	32563066	32563074	+	1	NA	intron (NM_009288, intron 2 of 18)	intron (NM_009288, intron 2 of 18)	29804	NM_009288	20868	Mm.8235	NM_009288	ENSMUSG00000020272	Stk10	Gek1|Lok|mKIAA4026	serine/threonine kinase 10	protein-coding
mm_110273.1	chr12	31996978	31996982	-	1	NA	intron (NM_011158, intron 2 of 10)	MamRep605|LTR?|LTR?	-46445	NM_153198	73389	Mm.390461	NM_153198	ENSMUSG00000002996	Hbp1	1700058O05Rik|BE629963|C330012F01Rik|C86454	high mobility group box transcription factor 1	protein-coding
mm_31084.1	chr4	41630563	41630579	+	1	NA	intron (NM_175138, intron 15 of 19)	intron (NM_175138, intron 15 of 19)	9731	NM_027147	69638	Mm.372459	NM_027147	ENSMUSG00000028445	Enho	1110065P19Rik|2310040A07Rik	energy homeostasis associated	protein-coding
mm_129496.1	chr15	78844873	78844874	-	1	NA	intron (NM_027219, intron 1 of 2)	intron (NM_027219, intron 1 of 2)	2226	NM_027219	104445	Mm.307488	NM_027219	ENSMUSG00000049521	Cdc42ep1	1810058K22Rik|AA980734|Borg5|CEP1|MSE55	CDC42 effector protein (Rho GTPase binding) 1	protein-coding
mm_82653.1	chr9	22046434	22046437	-	1	NA	intron (NM_010487, intron 1 of 6)	PB1D11|SINE|Alu	5588	NM_010487	15571	Mm.390167	NM_010487	ENSMUSG00000003410	Elavl3	2600009P04Rik|Huc|PLE21|mHuC	ELAV (embryonic lethal, abnormal vision, Drosophila)-like 3 (Hu antigen C)	protein-coding
mm_24883.1	chr3	96086691	96086735	+	1	NA	intron (NR_035496, intron 1 of 1)	intron (NR_035496, intron 1 of 1)	6117	NR_035496	100316714		NR_035496	ENSMUSG00000088478	Mir1946b	mmu-mir-1946b	microRNA 1946b	ncRNA
mm_5230.1	chr1	14310043	14310074	-	1	NA	5' UTR (NM_001252192, exon 1 of 17)	5' UTR (NM_001252192, exon 1 of 17)	141	NM_001310459	14048	Mm.250185	NM_010164	ENSMUSG00000025932	Eya1	bor	EYA transcriptional coactivator and phosphatase 1	protein-coding
mm_58264.1	chr6	145306652	145306653	-	1	NA	Intergenic	Intergenic	56100	NR_045598	100039495	Mm.121014	NR_045598	ENSMUSG00000086013	Gm15706	OTTMUSG00000025463	predicted gene 15706	ncRNA
mm_153667.1	chr19	44395999	44396010	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	11705	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_16472.1	chr2	180710343	180710358	+	1	NA	promoter-TSS (NM_001291432)	promoter-TSS (NM_001291432)	22	NM_001289651	76425	Mm.41464	NM_029607	ENSMUSG00000027573	Gid8	2310003C23Rik|4833420G11Rik|AI451474|Twa1	GID complex subunit 8	protein-coding
mm_146406.1	chr18	83813004	83813009	+	1	NA	Intergenic	Intergenic	273556	NM_001081300	110796	Mm.102136	NM_001081300	ENSMUSG00000046982	Tshz1	5730407I04Rik|D18Bwg1409e|Mtsh1|NY-CO-33|Sdccag33|Tsh1|mKIAA4206|teashirt1	teashirt zinc finger family member 1	protein-coding
mm_167457.1	chr8	123280959	123280967	+	1	NA	intron (NM_016925, intron 30 of 42)	PB1D7|SINE|Alu	-26741	NM_028200	72325	Mm.276193	NM_028200	ENSMUSG00000001062	Vps9d1	1300018I17Rik|2410004N05Rik|5DOS1|Vsp9d1	VPS9 domain containing 1	protein-coding
mm_34828.1	chr4	155217533	155217562	+	1	NA	intron (NM_011385, intron 1 of 6)	intron (NM_011385, intron 1 of 6)	4988	NM_011385	20481	Mm.28520	NM_011385	ENSMUSG00000029050	Ski	2310012I02Rik|2610001A11Rik|AA062172|AA589460|BC004088	ski sarcoma viral oncogene homolog (avian)	protein-coding
mm_54047.1	chr6	13829018	13829020	-	1	NA	Intergenic	Intergenic	10923	NM_001330666	64450	Mm.167625	NM_145066	ENSMUSG00000048216	Gpr85	2900026B03Rik	G protein-coupled receptor 85	protein-coding
mm_20964.1	chr2	151970802	151970829	-	1	NA	exon (NM_146127, exon 2 of 2)	exon (NM_146127, exon 2 of 2)	2579	NM_001289151	73847	Mm.272444	NM_028666	ENSMUSG00000027459	Fam110a	1700008J10Rik|5430432M24Rik|AI747080	family with sequence similarity 110, member A	protein-coding
mm_76211.1	chr8	83442584	83442594	-	1	NA	promoter-TSS (NM_019708)	promoter-TSS (NM_019708)	73	NM_001285992	56367	Mm.246911	NM_019708	ENSMUSG00000063253	Scoc	0610011C06Rik|2810002J11Rik|AA415030|SCOCO	short coiled-coil protein	protein-coding
mm_145054.1	chr18	40270541	40270549	+	1	NA	intron (NM_026135, intron 1 of 1)	intron (NM_026135, intron 1 of 1)	12184	NM_026135	383348	Mm.76366	NM_026135	ENSMUSG00000051401	Kctd16	4930434H12Rik|Gm1267	potassium channel tetramerisation domain containing 16	protein-coding
mm_33038.1	chr4	122858568	122858570	+	1	NA	TTS (NM_007598)	TTS (NM_007598)	22342	NM_008917	19063	Mm.277719	NM_008917	ENSMUSG00000028657	Ppt1	9530043G02Rik|AA960502|C77813|CLN1|D4Ertd184e|INCL|PPT	palmitoyl-protein thioesterase 1	protein-coding
mm_30124.1	chr3	141931405	141931439	-	1	NA	5' UTR (NM_001277220, exon 1 of 12)	5' UTR (NM_001277220, exon 1 of 12)	166	NM_001277218	12167	Mm.39089	NM_007560	ENSMUSG00000052430	Bmpr1b	AI385617|ALK-6|AV355320|Acvrlk6|Alk6|BMPR-1B|BMPR-IB|CFK-43a|SKR6	bone morphogenetic protein receptor, type 1B	protein-coding
mm_136632.1	chr17	5688089	5688132	+	1	NA	intron (NM_146073, intron 3 of 8)	intron (NM_146073, intron 3 of 8)	-110547	NR_045081	78512	Mm.23696	NR_045079	ENSMUSG00000096965	3300005D01Rik	-	RIKEN cDNA 3300005D01 gene	ncRNA
mm_96871.1	chr11	70207213	70207219	+	1	NA	Intergenic	RMER15-int|LTR|ERVL	-6694	NM_153081	216867	Mm.289238	NM_153081	ENSMUSG00000040938	Slc16a11	AB041591|MCT 11|MNCb-2717	solute carrier family 16 (monocarboxylic acid transporters), member 11	protein-coding
mm_62669.1	chr7	108950698	108950703	+	1	NA	Intergenic	CpG	16285	NM_025344	66085	Mm.182962	NM_025344	ENSMUSG00000031029	Eif3f	0610037M02Rik|AA409853|Eif3s5	eukaryotic translation initiation factor 3, subunit F	protein-coding
mm_96987.1	chr11	70657197	70657210	+	1	NA	promoter-TSS (NM_007933)	promoter-TSS (NM_007933)	27	NM_007933	13808	Mm.251322	NM_007933	ENSMUSG00000060600	Eno3	Eno-3|MSE	enolase 3, beta muscle	protein-coding
mm_155816.1	chrX	100524832	100524844	+	1	NA	promoter-TSS (NM_001114084)	promoter-TSS (NM_001114084)	0	NM_001114084	668257	Mm.95646	NM_001114084	ENSMUSG00000067597	Dgat2l6	9930021F22Rik	diacylglycerol O-acyltransferase 2-like 6	protein-coding
mm_87690.1	chr10	59403645	59403669	+	1	NA	promoter-TSS (NM_023530)	promoter-TSS (NM_023530)	-28	NM_023530	69836	Mm.30268	NM_023530	ENSMUSG00000009646	Pla2g12b	2010002E04Rik|Fksg71|Pla2g13|hlb218	phospholipase A2, group XIIB	protein-coding
mm_5411.1	chr1	33814475	33814488	-	1	NA	5' UTR (NM_001290700, exon 1 of 4)	5' UTR (NM_001290700, exon 1 of 4)	114	NM_133817	98403	Mm.289103	NM_133817	ENSMUSG00000042197	Zfp451	4930515K21Rik|4933435G09Rik|AI596398|COASTER|Kiaa0576-hp|Znf451|mKIAA1702	zinc finger protein 451	protein-coding
mm_51677.1	chr6	86438715	86438727	+	1	NA	promoter-TSS (NM_001243742)	promoter-TSS (NM_001243742)	75	NM_001243741	232196	Mm.404040	NM_146170	ENSMUSG00000046679	C87436	-	expressed sequence C87436	protein-coding
mm_106200.1	chr11	116843152	116843162	-	1	NA	promoter-TSS (NM_028865)	promoter-TSS (NM_028865)	292	NM_033398	107817	Mm.481684	NM_033398	ENSMUSG00000056962	Jmjd6	5730436I23Rik|D11Ertd195e|PSR|PtdSerR|Ptdsr|mKIAA0585	jumonji domain containing 6	protein-coding
mm_9825.1	chr1	182517420	182517424	-	1	NA	promoter-TSS (NM_009794)	promoter-TSS (NM_009794)	61	NM_009794	12334	Mm.19306	NM_009794	ENSMUSG00000026509	Capn2	AI326419|Capa-2|Capa2|m-calpain|m-calpin	calpain 2	protein-coding
mm_156480.1	chrX	144317800	144317801	+	1	NA	promoter-TSS (NM_026247)	promoter-TSS (NM_026247)	-166	NR_037145	67574	Mm.249084	NM_026247	ENSMUSG00000041718	Alg13	2810046O15Rik|4833435D08Rik|Glt28d1|MDS031|OTTMUSG00000018917	asparagine-linked glycosylation 13	protein-coding
mm_2695.1	chr1	127774184	127774238	+	1	NA	promoter-TSS (NM_028399)	promoter-TSS (NM_028399)	47	NM_028399	72949	Mm.268672	NM_028399	ENSMUSG00000026349	Ccnt2	2900041I18Rik|C81304|CycT2|CycT2a|CycT2b	cyclin T2	protein-coding
mm_13579.1	chr2	112376984	112377006	+	1	NA	Intergenic	RLTR12D|LTR|ERVK	-2216	NM_024254	72425	Mm.425091	NM_024254	ENSMUSG00000027132	Katnbl1	2410042D21Rik|AA166487|AA473307|AI467442	katanin p80 subunit B like 1	protein-coding
mm_67255.1	chr7	75613245	75613260	-	1	NA	intron (NM_029332, intron 7 of 36)	intron (NM_029332, intron 7 of 36)	157718	NM_029332	75547	Mm.216107	NM_029332	ENSMUSG00000066406	Akap13	1700026G02Rik|5730522G15Rik|5830460E08Rik|AKAP-13|AKAP-Lbc|BRX|Ht31|LBC|PROTO-LB|PROTO-LBC	A kinase (PRKA) anchor protein 13	protein-coding
mm_20615.1	chr2	131855390	131855398	-	1	NA	3' UTR (NM_001166206, exon 2 of 2)	3' UTR (NM_001166206, exon 2 of 2)	4353	NM_001166206	71995	Mm.22	NM_028045	ENSMUSG00000037482	Erv3	1600014E20Rik|AA389086|AI426069|AI448024|D19349	endogenous retroviral sequence 3	protein-coding
mm_126085.1	chr15	77849779	77849819	+	1	NA	Intergenic	Intergenic	-7624	NM_022410	17886	Mm.29677	NM_022410	ENSMUSG00000022443	Myh9	Fltn|Myhn-1|Myhn1|NMHCIIA|NMMHC-A|NMMHC-IIA|TU72.6	myosin, heavy polypeptide 9, non-muscle	protein-coding
mm_160335.1	chr8	13287870	13287870	+	1	NA	promoter-TSS (NM_172282)	promoter-TSS (NM_172282)	-143	NM_172282	234076	Mm.219813	NM_172282	ENSMUSG00000038497	Tmco3	B230339H12Rik|C87304	transmembrane and coiled-coil domains 3	protein-coding
mm_13598.1	chr2	112618412	112618436	+	1	NA	intron (NM_001165935, intron 1 of 4)	intron (NM_001165935, intron 1 of 4)	58742	NM_001165935	74268	Mm.315125	NM_028844	ENSMUSG00000003604	Aven	1700013A01Rik|1700056A21Rik|mAven-L|mAven-S	apoptosis, caspase activation inhibitor	protein-coding
mm_14403.1	chr2	130123276	130123293	+	1	NA	promoter-TSS (NM_177726)	promoter-TSS (NM_177726)	9	NM_177726	241636	Mm.83437	NM_177726	ENSMUSG00000027403	Tgm6	TGM3L|TGY	transglutaminase 6	protein-coding
mm_32155.1	chr4	99955698	99955702	+	1	NA	intron (NM_028132, intron 1 of 10)	intron (NM_028132, intron 1 of 10)	26249	NM_028132	72157	Mm.217764	NM_028132	ENSMUSG00000025791	Pgm2	2610020G18Rik|AA407108|AI098105|Pgm-2|Pgm1	phosphoglucomutase 2	protein-coding
mm_101970.1	chr11	50310821	50310842	-	1	NA	exon (NM_001110500, exon 3 of 15)	exon (NM_001110500, exon 3 of 15)	14842	NM_001110499	12330	Mm.248827	NM_007597	ENSMUSG00000020368	Canx	1110069N15Rik|AI988026|Cnx|D11Ertd153e	calnexin	protein-coding
mm_53522.1	chr6	136518821	136518851	+	1	NA	promoter-TSS (NM_019426)	promoter-TSS (NM_019426)	-15	NM_019426	54343	Mm.173271	NM_019426	ENSMUSG00000030213	Atf7ip	2610204M12Rik|AM|Mcaf1	activating transcription factor 7 interacting protein	protein-coding
mm_79181.1	chr9	48362035	48362056	+	1	NA	promoter-TSS (NM_172921)	promoter-TSS (NM_172921)	4	NM_172921	244853	Mm.325522	NM_172921	ENSMUSG00000044229	Nxpe4	C130036J11|D930028F11Rik|Fam55d	neurexophilin and PC-esterase domain family, member 4	protein-coding
mm_133242.1	chr16	77085476	77085479	+	1	NA	intron (NM_013918, intron 17 of 23)	intron (NM_013918, intron 17 of 23)	71408	NM_013918	30940	Mm.40986	NM_013918	ENSMUSG00000022867	Usp25	-	ubiquitin specific peptidase 25	protein-coding
mm_19253.1	chr2	84773515	84773553	-	1	NA	exon (NM_009776, exon 3 of 8)	exon (NM_009776, exon 3 of 8)	1895	NM_009776	12258	Mm.38888	NM_009776	ENSMUSG00000023224	Serping1	C1INH|C1nh	serine (or cysteine) peptidase inhibitor, clade G, member 1	protein-coding
mm_138488.1	chr17	35200324	35200329	+	1	NA	exon (NM_013693, exon 4 of 4)	exon (NM_013693, exon 4 of 4)	1681	NM_013693	21926	Mm.1293	NM_013693	ENSMUSG00000024401	Tnf	DIF|TNF-a|TNF-alpha|TNFSF2|TNFalpha|Tnfa|Tnfsf1a|Tnlg1f	tumor necrosis factor	protein-coding
mm_158917.1	chr1	54250766	54250766	+	1	NA	promoter-TSS (NM_030025)	promoter-TSS (NM_030025)	83	NM_030025	78016	Mm.67455	NM_030025	ENSMUSG00000025983	Ccdc150	4930511H11Rik	coiled-coil domain containing 150	protein-coding
mm_142842.1	chr17	51796139	51796166	-	1	NA	intron (NM_009122, intron 5 of 10)	B1_Mus1|SINE|Alu	15902	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_39622.1	chr5	24423852	24423865	+	1	NA	promoter-TSS (NM_007668)	promoter-TSS (NM_007668)	-328	NM_007668	12568	Mm.298798	NM_007668	ENSMUSG00000028969	Cdk5	AW048668|Crk6	cyclin-dependent kinase 5	protein-coding
mm_144240.1	chr18	10725531	10725564	+	1	NA	promoter-TSS (NM_144860)	promoter-TSS (NM_144860)	-78	NM_144860	225164	Mm.21500	NM_144860	ENSMUSG00000024294	Mib1	DIP-1|E430019M12Rik|Mib|mKIAA1323	mindbomb E3 ubiquitin protein ligase 1	protein-coding
mm_61052.1	chr7	49910207	49910223	+	1	NA	promoter-TSS (NM_001146013)	promoter-TSS (NM_001146013)	-84	NM_001146013	104245	Mm.207053	NM_148931	ENSMUSG00000039728	Slc6a5	Glyt2|prestin	solute carrier family 6 (neurotransmitter transporter, glycine), member 5	protein-coding
mm_131168.1	chr16	7039703	7039734	+	1	NA	intron (NM_021477, intron 5 of 16)	GA-rich|Low_complexity|Low_complexity	-30117	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_60216.1	chr7	43466009	43466021	+	1	NA	intron (NM_001290316, intron 4 of 9)	intron (NM_001290316, intron 4 of 9)	2782	NM_001290316	75690	Mm.30200	NM_001290316	ENSMUSG00000070604	Vsig10l	-	V-set and immunoglobulin domain containing 10 like	protein-coding
mm_82848.1	chr9	31170569	31170582	-	1	NA	exon (NM_009691, exon 5 of 16)	exon (NM_009691, exon 5 of 16)	-38776	NM_011176	19143	Mm.243926	NM_011176	ENSMUSG00000031995	St14	Epithin|MT-SP1|Prss14|Tmprss14|mCAP3|matriptase	suppression of tumorigenicity 14 (colon carcinoma)	protein-coding
mm_92655.1	chr10	80406793	80406809	-	1	NA	promoter-TSS (NM_025650)	promoter-TSS (NM_025650)	20	NM_025650	66594	Mm.379119	NM_025650	ENSMUSG00000020163	Uqcr11	0710008D09Rik|AL022707|Uqcr	ubiquinol-cytochrome c reductase, complex III subunit XI	protein-coding
mm_35534.1	chr4	41314779	41314787	-	1	NA	5' UTR (NM_026893, exon 1 of 9)	5' UTR (NM_026893, exon 1 of 9)	118	NM_026893	68970	Mm.28891	NM_026893	ENSMUSG00000028436	Dcaf12	1500001L20Rik|5830424K06Rik|AA420338|AI851081|Wdr40a	DDB1 and CUL4 associated factor 12	protein-coding
mm_158196.1	chrX	104857229	104857282	-	1	NA	promoter-TSS (NM_053206)	promoter-TSS (NM_053206)	12	NM_053206	272790	Mm.165776	NM_053206	ENSMUSG00000031224	Magee2	9630059J11Rik|BB131182|Mage-e2	melanoma antigen, family E, 2	protein-coding
mm_85836.1	chr9	110532351	110532362	-	1	NA	promoter-TSS (NM_001081340)	promoter-TSS (NM_001081340)	-241	NM_001081340	235626	Mm.288949	NM_001081340	ENSMUSG00000044791	Setd2	4921524K10Rik|BC031601|KMT3A	SET domain containing 2	protein-coding
mm_163189.1	chr11	94951982	94951984	+	1	NA	3' UTR (NM_007742, exon 51 of 51)	3' UTR (NM_007742, exon 51 of 51)	-15610	NM_018792	54388	Mm.30482	NM_018792	ENSMUSG00000038994	Hils1	H1.9|TISP64	histone H1-like protein in spermatids 1	protein-coding
mm_160901.1	chr11	75449821	75449821	-	1	NA	exon (NM_138950, exon 2 of 10)	exon (NM_138950, exon 2 of 10)	4896	NM_138950	192652	Mm.340378	NM_138950	ENSMUSG00000045374	Wdr81	BC054822|Gm883|mFLJ00182|nur5	WD repeat domain 81	protein-coding
mm_86248.1	chr9	121452470	121452475	-	1	NA	intron (NM_175114, intron 11 of 15)	ORR1A2|LTR|ERVL-MaLR	43222	NM_001284508	12424	Mm.2619	NM_031161	ENSMUSG00000032532	Cck	-	cholecystokinin	protein-coding
mm_43608.1	chr5	137928671	137928684	+	1	NA	Intergenic	Intergenic	-7058	NM_007819	13113	Mm.289886	NM_007819	ENSMUSG00000029727	Cyp3a13	IIIAm2	cytochrome P450, family 3, subfamily a, polypeptide 13	protein-coding
mm_129955.1	chr15	85106967	85107013	-	1	NA	exon (NM_080470, exon 12 of 25)	exon (NM_080470, exon 12 of 25)	24967	NM_080470	140557	Mm.182737	NM_080470	ENSMUSG00000022432	Smc1b	SMC-1B|SMC1beta|Smc1l2	structural maintenance of chromosomes 1B	protein-coding
mm_123378.1	chr14	63271623	63271647	-	1	NA	Intergenic	Intergenic	-26364	NM_001310610	14463	Mm.247669	NM_008092	ENSMUSG00000021944	Gata4	Gata-4	GATA binding protein 4	protein-coding
mm_142495.1	chr17	46024503	46024516	-	1	NA	exon (NM_001025250, exon 4 of 8)	exon (NM_001025250, exon 4 of 8)	654	NM_001110267	22339	Mm.282184	NM_009505	ENSMUSG00000023951	Vegfa	Vegf|Vpf	vascular endothelial growth factor A	protein-coding
mm_53567.1	chr6	137252430	137252474	+	1	NA	5' UTR (NM_011216, exon 1 of 27)	5' UTR (NM_011216, exon 1 of 27)	153	NM_011216	19277	Mm.186361	NM_011216	ENSMUSG00000030223	Ptpro	D28|GLEPP1|PTPBK|PTPROt|PTPU2|PTPoc|PTPphi|Ptpn15|R-PTP-O	protein tyrosine phosphatase, receptor type, O	protein-coding
mm_153676.1	chr19	44396529	44396538	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	11176	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_61833.1	chr7	88280609	88280621	+	1	NA	intron (NM_001311790, intron 1 of 3)	intron (NM_001311790, intron 1 of 3)	2530	NM_001311790	13032	Mm.89295	NM_009982	ENSMUSG00000030560	Ctsc	AI047818|CatC|DPP1|DPPI	cathepsin C	protein-coding
mm_109918.1	chr12	8496797	8496800	-	1	NA	TTS (NM_007483)	TTS (NM_007483)	3187	NM_007483	11852	Mm.687	NM_007483	ENSMUSG00000054364	Rhob	AA017882|Arh6|Arhb	ras homolog family member B	protein-coding
mm_155981.1	chrX	106126999	106127010	+	1	NA	3' UTR (NM_009726, exon 23 of 23)	3' UTR (NM_009726, exon 23 of 23)	-16271	NM_205820	279572	Mm.336203	NM_205820	ENSMUSG00000033777	Tlr13	AI666735|Gm713	toll-like receptor 13	protein-coding
mm_111181.1	chr12	83951554	83951568	-	1	NA	exon (NM_023633, exon 1 of 1)	exon (NM_023633, exon 1 of 1)	953	NM_023633	71952	Mm.251483	NM_023633	ENSMUSG00000046791	2410016O06Rik	MAPJD|NO66	RIKEN cDNA 2410016O06 gene	protein-coding
mm_91073.1	chr10	19009431	19009442	-	1	NA	intron (NM_001166402, intron 1 of 7)	intron (NM_001166402, intron 1 of 7)	2527	NM_001166402	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_23856.1	chr3	83010460	83010470	+	1	NA	exon (NM_133862, exon 6 of 10)	exon (NM_133862, exon 6 of 10)	2741	NM_001317105	99571	Mm.16422	NM_133862	ENSMUSG00000033860	Fgg	3010002H13Rik|AI256424	fibrinogen gamma chain	protein-coding
mm_167142.1	chr7	127946520	127946526	-	1	NA	5' UTR (NM_001319147, exon 1 of 15)	5' UTR (NM_001319147, exon 1 of 15)	202	NM_001319147	77613	Mm.334253	NM_001081374	ENSMUSG00000070371	Prss36	C330007D15Rik	protease, serine 36	protein-coding
mm_37039.1	chr4	115496130	115496147	-	1	NA	promoter-TSS (NM_007822)	promoter-TSS (NM_007822)	3	NM_007822	13119	Mm.250901	NM_007822	ENSMUSG00000028715	Cyp4a14	AI314743	cytochrome P450, family 4, subfamily a, polypeptide 14	protein-coding
mm_1882.1	chr1	85663547	85663572	+	1	NA	exon (NM_013673, exon 4 of 20)	exon (NM_013673, exon 4 of 20)	13571	NM_001313714	20684	Mm.290906	NM_013673	ENSMUSG00000026222	Sp100	A430075G10Rik	nuclear antigen Sp100	protein-coding
mm_23778.1	chr3	77760160	77760164	+	1	NA	Intergenic	Intergenic	1384725	NM_001310536	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_105442.1	chr11	104403596	104403597	-	1	NA	intron (NM_001081045, intron 2 of 13)	intron (NM_001081045, intron 2 of 13)	38695	NM_001081045	76719	Mm.136418	NM_001081045	ENSMUSG00000018412	Kansl1	1700081L11Rik|9430041J06Rik|mKIAA1267	KAT8 regulatory NSL complex subunit 1	protein-coding
mm_80894.1	chr9	99629824	99629853	+	1	NA	5' UTR (NM_001311142, exon 1 of 16)	5' UTR (NM_001311142, exon 1 of 16)	260	NM_001311142	72507	Mm.221455	NM_028258	ENSMUSG00000037784	Dzip1l	2610524A10Rik|AI663976	DAZ interacting protein 1-like	protein-coding
mm_84599.1	chr9	70038076	70038093	-	1	NA	promoter-TSS (NM_028087)	promoter-TSS (NM_028087)	4	NM_028087	72077	Mm.195555	NM_028087	ENSMUSG00000032226	Gcnt3	2010013H22Rik|2210021I22Rik|2210401J11Rik	glucosaminyl (N-acetyl) transferase 3, mucin type	protein-coding
mm_41959.1	chr5	106294153	106294159	+	1	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	-27184	NR_136913	102635633	Mm.383511	NR_136913	ENSMUSG00000105508	Gm32921	-	predicted gene, 32921	ncRNA
mm_4943.1	chr1	191185880	191185922	+	1	NA	Intergenic	Intergenic	-2568	NM_007498	11910	Mm.2706	NM_007498	ENSMUSG00000026628	Atf3	LRG-21	activating transcription factor 3	protein-coding
mm_539.1	chr1	37998153	37998165	+	1	NA	promoter-TSS (NM_172054)	promoter-TSS (NM_172054)	149	NM_198303	226982	Mm.260943	NM_198303	ENSMUSG00000026083	Eif5b	A030003E17Rik|BC018347|IF2	eukaryotic translation initiation factor 5B	protein-coding
mm_36175.1	chr4	62150811	62150826	-	1	NA	promoter-TSS (NM_001009550)	promoter-TSS (NM_001009550)	23	NM_001009550	381531	Mm.472122	NM_001009550	ENSMUSG00000066153	Mup21	Gm11208|Mup|Mup26|OTTMUSG00000000231|bM64F17.1|bM64F17.4	major urinary protein 21	protein-coding
mm_3205.1	chr1	135818872	135818900	+	1	NA	5' UTR (NM_133664, exon 1 of 10)	5' UTR (NM_133664, exon 1 of 10)	288	NM_133664	16763	Mm.36726	NM_133664	ENSMUSG00000041782	Lad1	-	ladinin	protein-coding
mm_68600.1	chr7	116237644	116237661	-	1	NA	5' UTR (NM_001305186, exon 1 of 25)	5' UTR (NM_001305186, exon 1 of 25)	124	NM_001305186	233765	Mm.3741	NM_172743	ENSMUSG00000045659	Plekha7	A430081P20Rik|AI414265	pleckstrin homology domain containing, family A member 7	protein-coding
mm_42340.1	chr5	114903760	114903770	+	1	NA	intron (NM_011854, intron 3 of 5)	RSINE1|SINE|B4	6831	NM_011854	23962	Mm.228363	NM_011854	ENSMUSG00000029561	Oasl2	M1204|Mmu-OASL|Oasl	2'-5' oligoadenylate synthetase-like 2	protein-coding
mm_139604.1	chr17	57285359	57285368	+	1	NA	intron (NM_001163816, intron 1 of 25)	intron (NM_001163816, intron 1 of 25)	6263	NM_001163815	22324	Mm.248172	NM_011691	ENSMUSG00000034116	Vav1	Vav|vav-T	vav 1 oncogene	protein-coding
mm_161919.1	chr18	70472589	70472589	+	1	NA	promoter-TSS (NM_001289649)	promoter-TSS (NM_001289649)	17	NM_001289648	170461	Mm.83623	NM_029019	ENSMUSG00000079608	Stard6	1700011K09Rik|4833424I06Rik|4933429L05Rik|AI644424	StAR-related lipid transfer (START) domain containing 6	protein-coding
mm_89260.1	chr10	87859373	87859387	+	1	NA	exon (NM_010512, exon 1 of 5)	exon (NM_010512, exon 1 of 5)	328	NM_010512	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_46882.1	chr5	113908686	113908720	-	1	NA	promoter-TSS (NM_011779)	promoter-TSS (NM_011779)	3	NM_011779	23790	Mm.260158	NM_011779	ENSMUSG00000004530	Coro1c	AL022675|AW455561|AW548837	coronin, actin binding protein 1C	protein-coding
mm_72178.1	chr8	72319584	72319607	+	1	NA	exon (NM_008452, exon 2 of 3)	exon (NM_008452, exon 2 of 3)	533	NM_008452	16598	Mm.26938	NM_008452	ENSMUSG00000055148	Klf2	Lklf	Kruppel-like factor 2 (lung)	protein-coding
mm_95330.1	chr11	46750563	46750577	+	1	NA	promoter-TSS (NM_001166631)	promoter-TSS (NM_001166631)	59	NM_001166631	171283	Mm.17771	NM_134248	ENSMUSG00000040405	Havcr1	AI503787|KIM-1|TIM-1|Tim1|Timd1	hepatitis A virus cellular receptor 1	protein-coding
mm_131946.1	chr16	24393380	24393428	+	1	NA	promoter-TSS (NM_178665)	promoter-TSS (NM_178665)	54	NM_178665	210126	Mm.209385	NM_178665	ENSMUSG00000033306	Lpp	9430020K16Rik|AA959454|AU024130|B130055L10Rik|C79715|D630048H16	LIM domain containing preferred translocation partner in lipoma	protein-coding
mm_123518.1	chr14	66296856	66296877	-	1	NA	promoter-TSS (NM_029979)	promoter-TSS (NM_029979)	-159	NM_029979	66854	Mm.43871	NM_029979	ENSMUSG00000022043	Trim35	0710005M05Rik|A430106H13Rik|AW046487|HLS5|Mair|NC8|mKIAA1098	tripartite motif-containing 35	protein-coding
mm_101458.1	chr11	30267617	30267628	-	1	NA	Intergenic	CpG	-47850	NM_175836	20742	Mm.123110	NM_009260	ENSMUSG00000020315	Sptbn1	9930031C03Rik|AL033301|SPTB2|Spnb-2|Spnb2|elf1|elf3|mKIAA4049	spectrin beta, non-erythrocytic 1	protein-coding
mm_2267.1	chr1	91180059	91180067	+	1	NA	5' UTR (NM_001168392, exon 1 of 4)	5' UTR (NM_001168392, exon 1 of 4)	241	NM_001168392	51801	Mm.3272	NM_016894	ENSMUSG00000034353	Ramp1	9130218E19Rik	receptor (calcitonin) activity modifying protein 1	protein-coding
mm_62094.1	chr7	94055378	94055379	+	1	NA	Intergenic	Intergenic	975499	NM_021427	58238	Mm.113787	NM_021427	ENSMUSG00000051515	Fam181b	A830059I20Rik|AB041569	family with sequence similarity 181, member B	protein-coding
mm_129351.1	chr15	77915676	77915697	-	1	NA	3' UTR (NM_019913, exon 4 of 4)	3' UTR (NM_019913, exon 4 of 4)	13308	NM_019913	56551	Mm.291917	NM_019913	ENSMUSG00000005354	Txn2	2510006J11Rik|AI788873|Trx2	thioredoxin 2	protein-coding
mm_109116.1	chr12	105563124	105563142	+	1	NA	promoter-TSS (NM_009747)	promoter-TSS (NM_009747)	-39	NM_009747	12062	Mm.390475	NM_009747	ENSMUSG00000021070	Bdkrb2	B(2)|B2|B2R|BK-2|BK2|BK2R|BKR2|BRB2	bradykinin receptor, beta 2	protein-coding
mm_168244.1	chr10	81978658	81978672	+	1	NA	Intergenic	CpG	-48153	NM_001346707	100040944		NM_001346707		Gm3055	-	predicted gene 3055	protein-coding
mm_103453.1	chr11	76243688	76243704	-	1	NA	promoter-TSS (NM_183263)	promoter-TSS (NM_183263)	3	NM_026029	67201	Mm.482113	NM_026029	ENSMUSG00000017286	Glod4	1700082G03Rik|2700085E05Rik|C81254	glyoxalase domain containing 4	protein-coding
mm_137491.1	chr17	26948922	26948978	+	1	NA	promoter-TSS (NR_037244)	promoter-TSS (NR_037244)	-831	NR_037244	100526534		NR_037244	ENSMUSG00000093118	Mir3083	mir-3083|mmu-mir-3083	microRNA 3083	ncRNA
mm_47216.1	chr5	121009634	121009644	-	1	NA	promoter-TSS (NM_011286)	promoter-TSS (NM_011286)	-101	NM_011286	19894	Mm.181166	NM_011286	ENSMUSG00000029608	Rph3a	2900002P20Rik|AU022689|AW108370	rabphilin 3A	protein-coding
mm_83264.1	chr9	42461415	42461436	-	1	NA	intron (NM_173038, intron 1 of 7)	intron (NM_173038, intron 1 of 7)	10801	NM_173038	272589	Mm.34483	NM_173038	ENSMUSG00000037287	Tbcel	D330014K23|E130107N23Rik|Lrrc35	tubulin folding cofactor E-like	protein-coding
mm_21443.1	chr2	160334112	160334122	-	1	NA	Intergenic	Intergenic	-6623	NM_001033411	329554	Mm.291144	NM_001033411	ENSMUSG00000074623	Gm826	-	predicted gene 826	protein-coding
mm_81858.1	chr9	118703773	118703789	+	1	NA	intron (NM_133721, intron 15 of 27)	(CA)n|Simple_repeat|Simple_repeat	-7911	NM_001113514	104099	Mm.335520	NM_133721	ENSMUSG00000039115	Itga9	(alpha)9|2610002H11Rik|6720458D17Rik|AI461869|D130073C02|D9Ertd428e	integrin alpha 9	protein-coding
mm_100110.1	chr11	115780766	115780786	+	1	NA	intron (NM_028014, intron 2 of 31)	intron (NM_028014, intron 2 of 31)	-15048	NR_049194	100885833		NR_049194	ENSMUSG00000093539	Mir5621	Gm22564|mir-5621|mmu-mir-5621	microRNA 5621	ncRNA
mm_80086.1	chr9	70207399	70207414	+	1	NA	promoter-TSS (NM_181072)	promoter-TSS (NM_181072)	56	NM_181072	71602	Mm.249311	NM_181072	ENSMUSG00000032220	Myo1e	2310020N23Rik|9130023P14Rik|AA407778|myosin-1e|myr 3	myosin IE	protein-coding
mm_10754.1	chr2	23197813	23197829	+	1	NA	3' UTR (NM_013771, exon 19 of 19)	3' UTR (NM_013771, exon 19 of 19)	-9655	NM_027635	70981	Mm.314026	NM_027635	ENSMUSG00000026774	4931423N10Rik	-	RIKEN cDNA 4931423N10 gene	protein-coding
mm_151795.1	chr19	5408433	5408468	-	1	NA	intron (NR_027938, intron 1 of 3)	B1_Mur4|SINE|Alu	1635	NR_027938	74931	Mm.388511	NR_015545	ENSMUSG00000086938	4930481A15Rik	-	RIKEN cDNA 4930481A15 gene	ncRNA
mm_172904.1	chr9	58582945	58582947	+	1	NA	intron (NM_001293673, intron 1 of 7)	intron (NM_001293673, intron 1 of 7)	706	NM_009145	20320	Mm.15125	NM_009145	ENSMUSG00000032336	Nptn	AW554172|SDR-1|Sdfr1	neuroplastin	protein-coding
mm_81441.1	chr9	109105285	109105327	+	1	NA	exon (NM_172775, exon 11 of 38)	exon (NM_172775, exon 11 of 38)	9870	NM_172775	235611	Mm.53862	NM_172775	ENSMUSG00000053646	Plxnb1	2900002G15Rik|AU042020|mKIAA0407	plexin B1	protein-coding
mm_117560.1	chr13	85245119	85245124	-	1	NA	intron (NM_145452, intron 7 of 24)	intron (NM_145452, intron 7 of 24)	44365	NM_145452	218397	Mm.259653	NM_145452	ENSMUSG00000021549	Rasa1	Gap|RasGAP|Rasa	RAS p21 protein activator 1	protein-coding
mm_165720.1	chr3	101428847	101428850	+	1	NA	intron (NM_207205, intron 4 of 10)	intron (NM_207205, intron 4 of 10)	51723	NM_207205	78908	Mm.257997	NM_207205	ENSMUSG00000042035	Igsf3	1700016K10Rik|2810035F16Rik|4833439O17Rik|mKIAA0466	immunoglobulin superfamily, member 3	protein-coding
mm_88583.1	chr10	79704500	79704512	+	1	NA	5' UTR (NM_001077184, exon 1 of 7)	5' UTR (NM_001077184, exon 1 of 7)	148	NM_009768	12215	Mm.726	NM_009768	ENSMUSG00000023175	Bsg	AI115436|AI325119|CD147|EMMPRIN|HT-7	basigin	protein-coding
mm_138011.1	chr17	33893193	33893220	+	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	-2573	NM_001195298	100502766	Mm.335713	NM_001195298	ENSMUSG00000079553	Kifc1	100042970|Gm4137|HSET|KNSL2|Kifc5a|Knsl2a|Tctex-7|Tctex-7A|Tctex7|Tctex7a	kinesin family member C1	protein-coding
mm_156602.1	chrX	153006462	153006504	+	1	NA	promoter-TSS (NM_001137547)	promoter-TSS (NM_001137547)	14	NM_001137547	635253	Mm.426169	NM_001137547	ENSMUSG00000067215	Usp51	AV136873	ubiquitin specific protease 51	protein-coding
mm_55655.1	chr6	72381681	72381705	-	1	NA	Intergenic	Intergenic	-1225	NM_001080742	53620	Mm.440321	NM_016872	ENSMUSG00000073002	Vamp5	AF119384|Camp	vesicle-associated membrane protein 5	protein-coding
mm_166281.1	chr5	96162171	96162216	-	1	NA	promoter-TSS (NM_178854)	promoter-TSS (NM_178854)	-203	NM_144910	231464	Mm.28374	NM_144910	ENSMUSG00000034724	Cnot6l	4932442K20Rik	CCR4-NOT transcription complex, subunit 6-like	protein-coding
mm_32106.1	chr4	98733950	98733952	+	1	NA	exon (NM_001081202, exon 3 of 5)	exon (NM_001081202, exon 3 of 5)	7197	NM_001081202	381591	Mm.34340	NM_001081202	ENSMUSG00000087166	L1td1	AA546746|AB211064|D76865|ECAT11	LINE-1 type transposase domain containing 1	protein-coding
mm_22773.1	chr3	20266416	20266446	+	1	NA	exon (NM_029706, exon 4 of 11)	exon (NM_029706, exon 4 of 11)	9302	NM_029706	76703	Mm.34692	NM_029706	ENSMUSG00000011463	Cpb1	0910001A18Rik|1810063F02Rik|2210008M23Rik|AI504870	carboxypeptidase B1 (tissue)	protein-coding
mm_81227.1	chr9	107655935	107655945	+	1	NA	exon (NM_001199218, exon 11 of 16)	exon (NM_001199218, exon 11 of 16)	11459	NM_023805	76257	Mm.296560	NM_023805	ENSMUSG00000010064	Slc38a3	0610012J02Rik|D9Ucla2|Nat1|Slc38-3|Sn1|Snat3|mNAT	solute carrier family 38, member 3	protein-coding
mm_71954.1	chr8	70510449	70510520	+	1	NA	promoter-TSS (NM_019883)	promoter-TSS (NM_019883)	-117	NM_019883	22186	Mm.297372	NM_019883	ENSMUSG00000090137	Uba52	D8Ertd21e|Gm1863|Rps27a|Ubb|Ubc	ubiquitin A-52 residue ribosomal protein fusion product 1	protein-coding
mm_62730.1	chr7	110803089	110803101	+	1	NA	exon (NM_009667, exon 9 of 15)	exon (NM_009667, exon 9 of 15)	30491	NM_009667	11717	Mm.3238	NM_009667	ENSMUSG00000005686	Ampd3	-	adenosine monophosphate deaminase 3	protein-coding
mm_64706.1	chr7	4603106	4603160	-	1	NA	5' UTR (NM_207270, exon 2 of 20)	5' UTR (NM_207270, exon 2 of 20)	908	NM_207270	545902	Mm.188925	NM_207270	ENSMUSG00000035429	Ptprh	R-PTP-H|sap-1	protein tyrosine phosphatase, receptor type, H	protein-coding
mm_153679.1	chr19	44396601	44396616	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	11101	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_79782.1	chr9	62868653	62868703	+	1	NA	exon (NM_138304, exon 3 of 5)	exon (NM_138304, exon 3 of 5)	-6654	NR_003965	677044	Mm.422004	NR_003965	ENSMUSG00000074250	Gm10653	ENSMUSG00000074250	ribsomal protein S2 pseudogene	pseudo
mm_115732.1	chr13	17772694	17772744	-	1	NA	exon (NM_001081058, exon 2 of 14)	exon (NM_001081058, exon 2 of 14)	25246	NR_035412	100316665		NR_035412	ENSMUSG00000080574	Mir466i	Mirn466i|mmu-mir-466i	microRNA 466i	ncRNA
mm_72016.1	chr8	70718510	70718520	+	1	NA	promoter-TSS (NM_001195253)	promoter-TSS (NM_001195253)	-28	NM_001195253	100502950	Mm.52981	NM_001195253	ENSMUSG00000095026	Gm3336	100041434|2410018E23Rik	predicted gene 3336	protein-coding
mm_86494.1	chr10	5594773	5594775	+	1	NA	intron (NM_026793, intron 1 of 1)	intron (NM_026793, intron 1 of 1)	1046	NM_026793	68632	Mm.338242	NM_026793	ENSMUSG00000046916	Myct1	1110020B04Rik|AI225941|AI642973|Mtmc1	myc target 1	protein-coding
mm_6376.1	chr1	72537273	72537319	-	1	NA	promoter-TSS (NM_001045533)	promoter-TSS (NM_001045533)	-732	NM_001045533	381270	Mm.337023	NM_001045533	ENSMUSG00000039372	March4	BC056494|mKIAA1399	membrane-associated ring finger (C3HC4) 4	protein-coding
mm_77954.1	chr9	7566198	7566198	+	1	NA	exon (NM_008611, exon 8 of 10)	exon (NM_008611, exon 8 of 10)	-5198	NM_001310717	234911	Mm.334940	NM_001030289	ENSMUSG00000070323	Mmp27	Gm180	matrix metallopeptidase 27	protein-coding
mm_121937.1	chr14	24004285	24004300	-	1	NA	promoter-TSS (NM_001253365)	promoter-TSS (NM_001253365)	-87	NM_001253374	16531	Mm.343607	NM_010610	ENSMUSG00000063142	Kcnma1	5730414M22Rik|BKCa|MaxiK|Slo|Slo1|mSlo|mSlo1	potassium large conductance calcium-activated channel, subfamily M, alpha member 1	protein-coding
mm_37272.1	chr4	118548257	118548288	-	1	NA	Intergenic	Intergenic	-4546	NM_172383	230678	Mm.23639	NM_172383	ENSMUSG00000050854	Tmem125	6330530A05Rik|AV223516	transmembrane protein 125	protein-coding
mm_51482.1	chr6	83039277	83039283	+	1	NA	intron (NM_013586, intron 4 of 13)	(T)n|Simple_repeat|Simple_repeat	5056	NM_013586	16950	Mm.380433	NM_013586	ENSMUSG00000000693	Loxl3	Lor2|Loxl2	lysyl oxidase-like 3	protein-coding
mm_52781.1	chr6	121252567	121252578	+	1	NA	intron (NM_011909, intron 2 of 10)	intron (NM_011909, intron 2 of 10)	6666	NM_011909	24110	Mm.326911	NM_011909	ENSMUSG00000030107	Usp18	1110058H21Rik|AW047653|UBP43|Ubp15	ubiquitin specific peptidase 18	protein-coding
mm_56644.1	chr6	113343976	113343989	-	1	NA	promoter-TSS (NM_133926)	promoter-TSS (NM_133926)	-60	NM_133926	52163	Mm.277373	NM_133926	ENSMUSG00000030272	Camk1	AI505105|CaMKIalpha|D6Ertd263e	calcium/calmodulin-dependent protein kinase I	protein-coding
mm_168458.1	chr1	143683198	143683198	+	1	NA	intron (NM_145991, intron 6 of 16)	intron (NM_145991, intron 6 of 16)	19695	NM_145991	214498	Mm.156727	NM_145991	ENSMUSG00000026361	Cdc73	8430414L16Rik|C130030P16Rik|C81219|Hrpt2	cell division cycle 73, Paf1/RNA polymerase II complex component	protein-coding
mm_115714.1	chr13	15902507	15902523	-	1	NA	Intergenic	(A)n|Simple_repeat|Simple_repeat	95272	NR_046131	328190	Mm.446957	NR_046131		A530046M15Rik	A530046M15	RIKEN cDNA A530046M15 gene	ncRNA
mm_16361.1	chr2	174598654	174598674	+	1	NA	Intergenic	Intergenic	-44870	NM_001099328	100043757	Mm.48711	NM_001099328	ENSMUSG00000050600	Zfp831	ENSMUSG00000050600|OTTMUSG00000017459	zinc finger protein 831	protein-coding
mm_91703.1	chr10	44004499	44004510	-	1	NA	5' UTR (NM_172393, exon 1 of 20)	5' UTR (NM_172393, exon 1 of 20)	342	NM_172393	11630	Mm.292082	NM_172393	ENSMUSG00000019866	Aim1	AI462491|AI463325	absent in melanoma 1	protein-coding
mm_81834.1	chr9	118478448	118478451	+	1	NA	5' UTR (NM_010136, exon 1 of 6)	5' UTR (NM_010136, exon 1 of 6)	260	NM_010136	13813	Mm.200692	NM_010136	ENSMUSG00000032446	Eomes	C77258|TBR-2|Tbr2	eomesodermin	protein-coding
mm_31233.1	chr4	44664392	44664417	+	1	NA	intron (NM_008782, intron 5 of 9)	CpG	-38396	NR_073462	70602	Mm.491142	NR_073462	ENSMUSG00000103995	5730488B01Rik	-	RIKEN cDNA 5730488B01 gene	ncRNA
mm_52585.1	chr6	116651780	116651796	+	1	NA	exon (NM_001166580, exon 2 of 2)	exon (NM_001166580, exon 2 of 2)	1104	NM_001166580	213393	Mm.38231	NM_145980	ENSMUSG00000048489	8430408G22Rik	Depp|Fseg	RIKEN cDNA 8430408G22 gene	protein-coding
mm_144200.1	chr18	9212198	9212200	+	1	NA	promoter-TSS (NM_008058)	promoter-TSS (NM_008058)	-657	NM_008058	14370	Mm.184289	NM_008058	ENSMUSG00000036904	Fzd8	Fz8	frizzled class receptor 8	protein-coding
mm_91607.1	chr10	41477203	41477234	-	1	NA	intron (NM_138315, intron 1 of 23)	intron (NM_138315, intron 1 of 23)	904	NM_138315	171580	Mm.290431	NM_138315	ENSMUSG00000019823	Mical1	MICAL|MICAL-1|Nical	microtubule associated monooxygenase, calponin and LIM domain containing 1	protein-coding
mm_10763.1	chr2	24186436	24186451	+	1	NA	promoter-TSS (NM_153511)	promoter-TSS (NM_153511)	-33	NM_153511	215257	Mm.249379	NM_153511	ENSMUSG00000044103	Il1f9	Il36g	interleukin 1 family, member 9	protein-coding
mm_108759.1	chr12	89081381	89081383	+	1	NA	intron (NM_172544, intron 2 of 19)	intron (NM_172544, intron 2 of 19)	127992	NM_172544	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding
mm_50189.1	chr6	41684415	41684441	+	1	NA	promoter-TSS (NM_029671)	promoter-TSS (NM_029671)	-3	NM_029671	76606	Mm.272520	NM_029671	ENSMUSG00000029867	1700034O15Rik	-	RIKEN cDNA 1700034O15 gene	protein-coding
mm_19607.1	chr2	102568939	102568949	-	1	NA	intron (NM_173749, intron 1 of 10)	intron (NM_173749, intron 1 of 10)	18923	NM_173749	210622	Mm.28649	NM_173749	ENSMUSG00000027188	Pamr1	5930437L24|E430002G05Rik|Ramp	peptidase domain containing associated with muscle regeneration 1	protein-coding
mm_58437.1	chr7	3297890	3297903	+	1	NA	3' UTR (NM_016969, exon 3 of 3)	3' UTR (NM_016969, exon 3 of 3)	4868	NM_001093766	50918	Mm.29874	NM_016969	ENSMUSG00000068566	Myadm	D7Wsu62e	myeloid-associated differentiation marker	protein-coding
mm_150271.1	chr19	34241766	34241791	+	1	NA	exon (NM_007392, exon 9 of 9)	exon (NM_007392, exon 9 of 9)	13595	NM_007392	11475	Mm.213025	NM_007392	ENSMUSG00000035783	Acta2	0610041G09Rik|Actvs|SMalphaA|a-SMA|alphaSMA	actin, alpha 2, smooth muscle, aorta	protein-coding
mm_1556.1	chr1	73024586	73024590	+	1	NA	promoter-TSS (NR_038002)	promoter-TSS (NR_038002)	2	NR_038002	69449	Mm.250447	NR_038001	ENSMUSG00000101968	1700027A15Rik	-	RIKEN cDNA 1700027A15 gene	ncRNA
mm_85335.1	chr9	102618891	102618904	-	1	NA	exon (NM_001081122, exon 5 of 17)	exon (NM_001081122, exon 5 of 17)	7227	NM_001301689	28135	Mm.38910	NM_001081122	ENSMUSG00000032534	Cep63	4921501M07|AL450317.13gm1|AW107703|CD20R|D9Mgc41|D9Mgc48e|ET2	centrosomal protein 63	protein-coding
mm_92201.1	chr10	68136685	68136696	-	1	NA	intron (NM_023598, intron 4 of 9)	intron (NM_023598, intron 4 of 9)	142036	NM_023598	71371	Mm.440357	NM_023598	ENSMUSG00000019947	Arid5b	4930580B11|5430435G07Rik|AI467247|Desrt|Mrf2|Mrf2alpha|Mrf2beta	AT rich interactive domain 5B (MRF1-like)	protein-coding
mm_167755.1	chr9	110422369	110422382	-	1	NA	exon (NM_008694, exon 4 of 4)	exon (NM_008694, exon 4 of 4)	2567	NM_008694	18054	Mm.236225	NM_008694	ENSMUSG00000032484	Ngp	bectenecin	neutrophilic granule protein	protein-coding
mm_117863.1	chr13	98840292	98840302	-	1	NA	Intergenic	Intergenic	-24848	NM_172591	218503	Mm.23928	NM_172591	ENSMUSG00000041685	Fcho2	5832424M12Rik|AA387320	FCH domain only 2	protein-coding
mm_64109.1	chr7	141061098	141061109	+	1	NA	promoter-TSS (NM_177897)	promoter-TSS (NM_177897)	-171	NM_177897	330671	Mm.133741	NM_177897	ENSMUSG00000055629	B4galnt4	BC038881|Gm1095|beta4GalNAcT4	beta-1,4-N-acetyl-galactosaminyl transferase 4	protein-coding
mm_6996.1	chr1	86359359	86359381	-	1	NA	promoter-TSS (NM_010880)	promoter-TSS (NM_010880)	85	NM_010880	17975	Mm.154378	NM_010880	ENSMUSG00000026234	Ncl	B530004O11Rik|C23|D0Nds28|D1Nds28|Nucl	nucleolin	protein-coding
mm_90139.1	chr10	118052913	118052918	+	1	NA	Intergenic	Intergenic	-88872	NM_001162904	17245	Mm.101191	NM_010785	ENSMUSG00000020212	Mdm1	Arrd2|Mdm-1	transformed mouse 3T3 cell double minute 1	protein-coding
mm_118304.1	chr13	113100972	113100988	-	1	NA	promoter-TSS (NM_010370)	promoter-TSS (NM_010370)	1	NM_010370	14938	Mm.15510	NM_010370	ENSMUSG00000023132	Gzma	AW494114|Ctla-3|Ctla3|Hf|Hf1|SE1|TSP-1|TSP1	granzyme A	protein-coding
mm_138941.1	chr17	44026674	44026693	+	1	NA	intron (NM_001286653, intron 4 of 4)	intron (NM_001286653, intron 4 of 4)	-52119	NM_001168620	83965	Mm.30145	NM_032003	ENSMUSG00000023960	Enpp5	AW061004|D17Abb1e|E-NPP 5	ectonucleotide pyrophosphatase/phosphodiesterase 5	protein-coding
mm_142045.1	chr17	35505913	35505934	-	1	NA	promoter-TSS (NM_013633)	promoter-TSS (NM_013633)	-109	NM_013633	18999	Mm.17031	NM_013633	ENSMUSG00000024406	Pou5f1	NF-A3|Oct-3|Oct-3/4|Oct-4|Oct3|Oct3/4|Oct4|Otf-3|Otf-4|Otf3|Otf3-rs7|Otf3g|Otf4	POU domain, class 5, transcription factor 1	protein-coding
mm_12808.1	chr2	80302312	80302318	+	1	NA	Intergenic	Intergenic	9845	NM_177256	320769	Mm.60992	NM_177256	ENSMUSG00000050114	Prdx6b	1-cysPrx-P1|4930414C22Rik|Aop2-rs1|Prdx5-rs1|Prdx6-ps1|Prdx6-rs1|Prdx6-rs1-ps	peroxiredoxin 6B	protein-coding
mm_148013.1	chr18	68300195	68300228	-	1	NA	promoter-TSS (NM_026440)	promoter-TSS (NM_026440)	122	NM_153794	108654	Mm.125857	NM_153794	ENSMUSG00000038121	Fam210a	4933403F05Rik|AA987140|AV134576|AW491926	family with sequence similarity 210, member A	protein-coding
mm_172697.1	chr8	63816046	63816046	+	1	NA	Intergenic	L1Md_F2|LINE|L1	136124	NM_001195687	244495	Mm.485331	NM_001195687	ENSMUSG00000094443	Sgol2b	EG244495|Gm4975|Sgo2B	shugoshin like 2b (S. pombe)	protein-coding
mm_129257.1	chr15	76710524	76710556	-	1	NA	promoter-TSS (NM_058214)	promoter-TSS (NM_058214)	19	NM_058214	79456	Mm.18373	NM_058214	ENSMUSG00000033762	Recql4	RecQ4	RecQ protein-like 4	protein-coding
mm_45937.1	chr5	90223924	90224020	-	1	NA	promoter-TSS (NM_001033310)	promoter-TSS (NM_001033310)	24	NR_028088	231430	Mm.319697	NM_001033310	ENSMUSG00000035505	Cox18	BC038311	cytochrome c oxidase assembly protein 18	protein-coding
mm_37960.1	chr4	133352853	133352876	-	1	NA	Intergenic	Intergenic	-13549	NM_199306	230796	Mm.226576	NM_199306	ENSMUSG00000037622	Wdtc1	Gm695|adipose|adp	WD and tetratricopeptide repeats 1	protein-coding
mm_82388.1	chr9	14663099	14663117	-	1	NA	Intergenic	Intergenic	-48108	NM_001081395	75723	Mm.159552	NM_001081395	ENSMUSG00000013076	Amotl1	2310010G08Rik|2310067L22Rik|4932416D09Rik|JEAP|mFLJ00155	angiomotin-like 1	protein-coding
mm_96096.1	chr11	60417543	60417600	+	1	NA	promoter-TSS (NM_145427)	promoter-TSS (NM_145427)	426	NM_025757	66771	Mm.29950	NM_025757	ENSMUSG00000018415	Gid4	4933439F18Rik	GID complex subunit 4, VID24 homolog	protein-coding
mm_91240.1	chr10	22306395	22306418	-	1	NA	promoter-TSS (NR_015465)	promoter-TSS (NR_015465)	-314	NR_015465	606736	Mm.387042	NR_015465	ENSMUSG00000097352	C920009B18Rik	-	RIKEN cDNA C920009B18 gene	ncRNA
mm_53238.1	chr6	127453706	127453716	+	1	NA	promoter-TSS (NM_181402)	promoter-TSS (NM_181402)	-12	NM_181402	101187	Mm.110818	NM_181402	ENSMUSG00000037997	Parp11	5330431N24Rik|AI851877|ARTD11|HIN1L|PARP-11	poly (ADP-ribose) polymerase family, member 11	protein-coding
mm_156711.1	chrX	159627501	159627514	+	1	NA	5' UTR (NM_001135727, exon 1 of 18)	5' UTR (NM_001135727, exon 1 of 18)	235	NM_001135727	58194	Mm.286495	NM_021389	ENSMUSG00000040990	Sh3kbp1	1200007H22Rik|1700125L08Rik|5830464D22Rik|AI447724|Cin85|IN85|Ruk|Seta	SH3-domain kinase binding protein 1	protein-coding
mm_93002.1	chr10	86885814	86885832	-	1	NA	intron (NM_138673, intron 42 of 68)	intron (NM_138673, intron 42 of 68)	106818	NM_175331	103466	Mm.200446	NM_175331	ENSMUSG00000054027	Nt5dc3	AU040402|AW540062|C630002B14Rik|TU12B1-TY	5'-nucleotidase domain containing 3	protein-coding
mm_96840.1	chr11	70023923	70023958	+	1	NA	intron (NM_001109752, intron 1 of 19)	C-rich|Low_complexity|Low_complexity	5335	NM_007864	13385	Mm.27256	NM_007864	ENSMUSG00000020886	Dlg4	Dlgh4|PSD-95|PSD95|SAP90|SAP90A	discs, large homolog 4 (Drosophila)	protein-coding
mm_97246.1	chr11	75742247	75742262	+	1	NA	intron (NM_009536, intron 1 of 5)	ID_B1|SINE|B4	9367	NM_009536	22627	Mm.234700	NM_009536	ENSMUSG00000020849	Ywhae	AU019196	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide	protein-coding
mm_1151.1	chr1	60778744	60778748	+	1	NA	Intergenic	Intergenic	32358	NM_007642	12487	Mm.255003	NM_007642	ENSMUSG00000026012	Cd28	-	CD28 antigen	protein-coding
mm_128055.1	chr15	25843595	25843635	-	1	NA	intron (NM_001034851, intron 1 of 8)	intron (NM_001034851, intron 1 of 8)	317	NM_001034851	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_153085.1	chr19	32388429	32388461	-	1	NA	promoter-TSS (NM_144792)	promoter-TSS (NM_144792)	9	NM_144792	208449	Mm.329810	NM_144792	ENSMUSG00000040451	Sgms1	9530058O11Rik|AI841905|C80702|Mob|Sms1|Sor1|Tmem23	sphingomyelin synthase 1	protein-coding
mm_116199.1	chr13	31984824	31984827	-	1	NA	intron (NM_146041, intron 7 of 10)	intron (NM_146041, intron 7 of 10)	178179	NM_008592	17300	Mm.12949	NM_008592	ENSMUSG00000050295	Foxc1	FREAC3|Fkh1|Mf1|Mf4|ch|fkh-1|frkhda	forkhead box C1	protein-coding
mm_74025.1	chr8	121730334	121730358	+	1	NA	promoter-TSS (NM_020605)	promoter-TSS (NM_020605)	-213	NM_020605	57340	Mm.306870	NM_020605	ENSMUSG00000025318	Jph3	JP-3|Jp3	junctophilin 3	protein-coding
mm_72736.1	chr8	85084416	85084456	+	1	NA	exon (NM_010764, exon 2 of 24)	exon (NM_010764, exon 2 of 24)	1167	NM_010764	17159	Mm.4219	NM_010764	ENSMUSG00000005142	Man2b1	AW107687|LAMAN	mannosidase 2, alpha B1	protein-coding
mm_56281.1	chr6	91321041	91321049	-	1	NA	Intergenic	Intergenic	90324	NM_009527	22421	Mm.56964	NM_009527	ENSMUSG00000030093	Wnt7a	AI849442|Wnt-7a|px|tw	wingless-type MMTV integration site family, member 7A	protein-coding
mm_121702.1	chr14	14781326	14781351	-	1	NA	intron (NM_001033270, intron 20 of 24)	ORR1B2|LTR|ERVL-MaLR	-39477	NM_001195229	674895	Mm.317563	NM_001034865	ENSMUSG00000042567	Nek10	Gm282	NIMA (never in mitosis gene a)- related kinase 10	protein-coding
mm_139715.1	chr17	57463368	57463391	+	1	NA	intron (NM_010130, intron 18 of 21)	intron (NM_010130, intron 18 of 21)	81935	NM_001104591	224916	Mm.469889	NM_001104591	ENSMUSG00000090655	Vmn2r120	EG224916	vomeronasal 2, receptor 120	protein-coding
mm_22067.1	chr2	168734061	168734135	-	1	NA	5' UTR (NM_001289445, exon 1 of 28)	5' UTR (NM_001289445, exon 1 of 28)	241	NM_001289445	11981	Mm.330819	NM_015731	ENSMUSG00000027546	Atp9a	IIa	ATPase, class II, type 9A	protein-coding
mm_90660.1	chr10	128805593	128805651	+	1	NA	promoter-TSS (NM_028873)	promoter-TSS (NM_028873)	-54	NM_028873	74330	Mm.296915	NM_028873	ENSMUSG00000025354	Dnajc14	5730551F12Rik|DNAJ|DRIP78|HDJ3|LIP6	DnaJ heat shock protein family (Hsp40) member C14	protein-coding
mm_135161.1	chr16	35866178	35866228	-	1	NA	exon (NM_001039530, exon 2 of 17)	exon (NM_001039530, exon 2 of 17)	5179	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_87801.1	chr10	60300199	60300233	+	1	NA	exon (NM_011179, exon 12 of 15)	exon (NM_011179, exon 12 of 15)	15755	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_23449.1	chr3	60006863	60006879	+	1	NA	5' UTR (NM_001128091, exon 1 of 5)	5' UTR (NM_001128091, exon 1 of 5)	128	NM_001128091	639634	Mm.475611	NM_001128091	ENSMUSG00000091376	Aadacl2	EG639634	arylacetamide deacetylase-like 2	protein-coding
mm_7159.1	chr1	91540376	91540393	-	1	NA	promoter-TSS (NM_001039126)	promoter-TSS (NM_001039126)	-181	NM_001039126	65247	Mm.234152	NM_023046	ENSMUSG00000026311	Asb1	1700029O08Rik|1700054C17Rik|AI426616|AI851378|mKIAA1146	ankyrin repeat and SOCS box-containing 1	protein-coding
mm_28781.1	chr3	95990864	95990894	-	1	NA	exon (NM_023320, exon 5 of 6)	exon (NM_023320, exon 5 of 6)	4960	NM_023320	67220	Mm.458147	NM_023320	ENSMUSG00000015745	Plekho1	2810052M02Rik|CKIP-1|Ckip1|JZA-20|Jza2	pleckstrin homology domain containing, family O member 1	protein-coding
mm_27588.1	chr3	59130575	59130603	-	1	NA	5' UTR (NM_001287124, exon 1 of 2)	5' UTR (NM_001287124, exon 1 of 2)	173	NM_001008497	140795	Mm.439021	NM_133200	ENSMUSG00000036381	P2ry14	A330108O13Rik|Gpr105|P2Y14	purinergic receptor P2Y, G-protein coupled, 14	protein-coding
mm_117224.1	chr13	64152707	64152748	-	1	NA	exon (NM_175494, exon 1 of 5)	exon (NM_175494, exon 1 of 5)	472	NM_175494	238673	Mm.300065	NM_175494	ENSMUSG00000044934	Zfp367	8030486J21Rik|ZFF29a|ZFF29b|Znf367	zinc finger protein 367	protein-coding
mm_13455.1	chr2	105660801	105660812	+	1	NA	non-coding (NR_117095, exon 1 of 1)	non-coding (NR_117095, exon 1 of 1)	537	NR_117095	103164605	Mm.444995	NR_117095	ENSMUSG00000102424	Paupar	-	Pax6 upstream antisense RNA	ncRNA
mm_48725.1	chr5	147400301	147400332	-	1	NA	5' UTR (NM_010229, exon 1 of 24)	5' UTR (NM_010229, exon 1 of 24)	173	NM_010229	14255	Mm.194	NM_010229	ENSMUSG00000042817	Flt3	B230315G04|CD135|Flk-2|Flk2|Flt-3|Ly72|wmfl	FMS-like tyrosine kinase 3	protein-coding
mm_56402.1	chr6	97148858	97148904	-	1	NA	promoter-TSS (NM_175313)	promoter-TSS (NM_175313)	2	NM_175313	101351	Mm.116802	NM_175313	ENSMUSG00000035245	Eogt	A130022J15Rik|AI447490|AW214473|AW259391|Aer61	EGF domain-specific O-linked N-acetylglucosamine (GlcNAc) transferase	protein-coding
mm_120916.1	chr14	76414930	76414974	+	1	NA	promoter-TSS (NM_207652)	promoter-TSS (NM_207652)	-9	NM_001310646	21807	Mm.153272	NM_009366	ENSMUSG00000022010	Tsc22d1	AA589566|AW105905|Egr5|TSC-22|Tgfb1i4|Tsc|Tsc22	TSC22 domain family, member 1	protein-coding
mm_15230.1	chr2	154551772	154551786	+	1	NA	promoter-TSS (NM_001171640)	promoter-TSS (NM_001171640)	3	NM_001171640	70362	Mm.479620	NM_001171640	ENSMUSG00000078129	Actl10	1700007I08Rik	actin-like 10	protein-coding
mm_40373.1	chr5	52190720	52190728	+	1	NA	promoter-TSS (NM_001042620)	promoter-TSS (NM_001042620)	43	NR_015537	414108	Mm.383512	NR_015537	ENSMUSG00000097145	9230114K14Rik	-	RIKEN cDNA 9230114K14 gene	ncRNA
mm_32802.1	chr4	117113024	117113026	+	1	NA	intron (NM_001312903, intron 19 of 21)	B3|SINE|B2	12700	NR_024078	78611	Mm.446227	NM_001033187		Btbd19	9530048O09Rik|BB115071	BTB (POZ) domain containing 19	ncRNA
mm_168433.1	chr1	135232045	135232063	+	1	NA	Intergenic	Intergenic	26418	NM_001163131	13710	Mm.441439	NM_007921	ENSMUSG00000003051	Elf3	ESE-1|ESX|jen	E74-like factor 3	protein-coding
mm_46580.1	chr5	107431935	107431940	-	1	NA	5' UTR (NM_027599, exon 1 of 2)	5' UTR (NM_027599, exon 1 of 2)	388	NM_027599	70902	Mm.55870	NM_027599	ENSMUSG00000033794	Lpcat2b	4921521K07Rik|Aytl1b	lysophosphatidylcholine acyltransferase 2B	protein-coding
mm_148319.1	chr18	83827604	83827608	-	1	NA	Intergenic	Intergenic	258956	NM_001081300	110796	Mm.102136	NM_001081300	ENSMUSG00000046982	Tshz1	5730407I04Rik|D18Bwg1409e|Mtsh1|NY-CO-33|Sdccag33|Tsh1|mKIAA4206|teashirt1	teashirt zinc finger family member 1	protein-coding
mm_98281.1	chr11	89060626	89060639	+	1	NA	promoter-TSS (NR_110336)	promoter-TSS (NR_110336)	116	NM_019505	56077	Mm.153695	NM_019505	ENSMUSG00000000276	Dgke	C87606|DAGK6|DGK	diacylglycerol kinase, epsilon	protein-coding
mm_112510.1	chr13	8885938	8885980	+	1	NA	exon (NM_145360, exon 1 of 5)	exon (NM_145360, exon 1 of 5)	353	NM_145360	319554	Mm.29847	NM_145360	ENSMUSG00000058258	Idi1	4832416K17Rik	isopentenyl-diphosphate delta isomerase	protein-coding
mm_109721.1	chr12	116140969	116140979	+	1	NA	intron (NM_009511, intron 10 of 12)	MTC|LTR|ERVL-MaLR	63248	NM_009511	22355	Mm.395245	NM_009511	ENSMUSG00000011171	Vipr2	VPAC2|VPAC2R|Vip2	vasoactive intestinal peptide receptor 2	protein-coding
mm_27358.1	chr3	50418019	50418039	-	1	NA	exon (NM_011990, exon 6 of 12)	exon (NM_011990, exon 6 of 12)	25584	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_68691.1	chr7	119479250	119479260	-	1	NA	promoter-TSS (NM_001278605)	promoter-TSS (NM_001278605)	7	NM_009470	22242	Mm.10826	NM_009470	ENSMUSG00000030963	Umod	THP|Urehd1|urehr4	uromodulin	protein-coding
mm_114666.1	chr13	78202365	78202388	+	1	NA	intron (NR_045195, intron 1 of 2)	intron (NR_045195, intron 1 of 2)	-3503	NM_010151	13865	Mm.439653	NM_010151	ENSMUSG00000069171	Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR-3|EAR3|Erbal3|SVP44|Tcfcoup1	nuclear receptor subfamily 2, group F, member 1	protein-coding
mm_108450.1	chr12	82543598	82543606	+	1	NA	Intergenic	Intergenic	-73323	NM_001310478	50779	Mm.126176	NM_015812	ENSMUSG00000021219	Rgs6	-	regulator of G-protein signaling 6	protein-coding
mm_99192.1	chr11	100969865	100969894	+	1	NA	intron (NM_008986, intron 1 of 1)	CpG	738	NM_008986	19285	Mm.21864	NM_008986	ENSMUSG00000004044	Ptrf	2310075E07Rik|AW546441|Cav-p60|Cavin	polymerase I and transcript release factor	protein-coding
mm_153538.1	chr19	41933277	41933319	-	1	NA	promoter-TSS (NM_001320233)	promoter-TSS (NM_001320233)	16	NM_001164561	66583	Mm.289086	NM_025644	ENSMUSG00000034321	Exosc1	2610035C18Rik|2610104C07Rik|2610312F07Rik|AI447561	exosome component 1	protein-coding
mm_124579.1	chr14	124625790	124625807	-	1	NA	intron (NM_207667, intron 1 of 4)	B1F|SINE|Alu	51329	NM_207667	14169	Mm.206362	NM_010201	ENSMUSG00000025551	Fgf14	FHF-4|Fhf4|mFHF-4(1B)	fibroblast growth factor 14	protein-coding
mm_37033.1	chr4	115134105	115134121	-	1	NA	promoter-TSS (NM_001003947)	promoter-TSS (NM_001003947)	-136	NM_001003947	81906	Mm.215544	NM_001003947	ENSMUSG00000047155	Cyp4x1	A230025G20|CYPIVX1|CYP_a|Cyp4a28-ps	cytochrome P450, family 4, subfamily x, polypeptide 1	protein-coding
mm_60620.1	chr7	44602591	44602601	+	1	NA	3' UTR (NM_001290682, exon 5 of 5)	3' UTR (NM_001290682, exon 5 of 5)	11710	NM_001290682	16504	Mm.40312	NM_008422	ENSMUSG00000062785	Kcnc3	KShIIID|Kcr2-3|Kv3.3	potassium voltage gated channel, Shaw-related subfamily, member 3	protein-coding
mm_165927.1	chr4	63344475	63344482	+	1	NA	promoter-TSS (NM_008768)	promoter-TSS (NM_008768)	-78	NM_008768	18405	Mm.4777	NM_008768	ENSMUSG00000039196	Orm1	Agp-1|Agp-2|Orm-1	orosomucoid 1	protein-coding
mm_168093.1	chr10	128565755	128565758	-	1	NA	exon (NM_011119, exon 1 of 12)	exon (NM_011119, exon 1 of 12)	178	NM_011119	18813	Mm.4742	NM_011119	ENSMUSG00000025364	Pa2g4	38kDa|AA672939|Ebp1|Plfap	proliferation-associated 2G4	protein-coding
mm_149451.1	chr19	11492023	11492053	+	1	NA	promoter-TSS (NM_001164202)	promoter-TSS (NM_001164202)	0	NM_001164202	666926	Mm.486382	NM_001164202	ENSMUSG00000058470	Gm8369	EG666926	predicted gene 8369	protein-coding
mm_126024.1	chr15	76695766	76695787	+	1	NA	promoter-TSS (NM_182805)	promoter-TSS (NM_182805)	-950	NM_182805	76282	Mm.30130	NM_182805	ENSMUSG00000022546	Gpt	1300007J06Rik|2310022B03Rik|ALT|ALT1|Gpt-1|Gpt1	glutamic pyruvic transaminase, soluble	protein-coding
mm_43973.1	chr5	146109204	146109214	+	1	NA	intron (NM_001105160, intron 12 of 12)	intron (NM_001105160, intron 12 of 12)	29951	NM_001105160	100041449	Mm.301900	NM_001105160	ENSMUSG00000061292	Cyp3a59	ENSMUSG00000061292	cytochrome P450, family 3, subfamily a, polypeptide 59	protein-coding
mm_102740.1	chr11	67252597	67252604	-	1	NA	exon (NM_010855, exon 25 of 40)	exon (NM_010855, exon 25 of 40)	14788	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_4027.1	chr1	165767273	165767293	+	1	NA	intron (NM_011804, intron 1 of 3)	intron (NM_011804, intron 1 of 3)	3503	NM_011804	433375	Mm.294885	NM_011804	ENSMUSG00000040713	Creg1	AA755314|Creg	cellular repressor of E1A-stimulated genes 1	protein-coding
mm_29811.1	chr3	127876722	127876730	-	1	NA	intron (NM_027482, intron 1 of 1)	intron (NM_027482, intron 1 of 1)	19597	NM_027482	70617	Mm.317049	NM_027482	ENSMUSG00000050549	5730508B09Rik	2700063A17Rik|C80506	RIKEN cDNA 5730508B09 gene	protein-coding
mm_4361.1	chr1	171919481	171919495	+	1	NA	intron (NM_001347187, intron 1 of 7)	intron (NM_001347187, intron 1 of 7)	1951	NM_030710	30925	Mm.486404	NM_030710	ENSMUSG00000015314	Slamf6	KAL1|KAL1b|Ly108|NTB-A|NTBA|SF2000	SLAM family member 6	protein-coding
mm_8625.1	chr1	156270765	156270767	-	1	NA	intron (NM_001134741, intron 12 of 17)	intron (NM_001134741, intron 12 of 17)	32582	NM_001134741	214575	Mm.252800	NM_001134741	ENSMUSG00000060985	Tdrd5	Gm103	tudor domain containing 5	protein-coding
mm_157168.1	chrX	9467991	9467996	-	1	NA	intron (NM_007807, intron 1 of 12)	intron (NM_007807, intron 1 of 12)	1331	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_100958.1	chr11	6635546	6635555	-	1	NA	TTS (NM_011709)	TTS (NM_011709)	3099	NM_011709	22373	Mm.268094	NM_011709	ENSMUSG00000000381	Wap	-	whey acidic protein	protein-coding
mm_107057.1	chr12	16653769	16653775	+	1	NA	exon (NM_008747, exon 1 of 4)	exon (NM_008747, exon 1 of 4)	302	NM_008747	18217	Mm.281715	NM_008747	ENSMUSG00000020591	Ntsr2	NT2R|NTRL	neurotensin receptor 2	protein-coding
mm_70878.1	chr8	25118241	25118282	+	1	NA	Intergenic	Intergenic	-16450	NM_031257	83436	Mm.261122	NM_031257	ENSMUSG00000031557	Plekha2	6430512N22Rik|AI851530|AU041791|TAPP2|W91773	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 2	protein-coding
mm_62374.1	chr7	100706624	100706668	+	1	NA	promoter-TSS (NM_178764)	promoter-TSS (NM_178764)	-56	NM_178764	319604	Mm.260362	NM_178764	ENSMUSG00000029461	Fam168a	2610030B18Rik|B930006L02Rik|mKIAA0280	family with sequence similarity 168, member A	protein-coding
mm_141466.1	chr17	30597875	30597885	-	1	NA	intron (NM_025374, intron 3 of 5)	intron (NM_025374, intron 3 of 5)	14779	NM_025374	109801	Mm.261984	NM_025374	ENSMUSG00000024026	Glo1	0610009E22Rik|1110008E19Rik|2510049H23Rik|AW550643|GLY1|Glo-1|Glo-1r|Glo-1s|Glo1-r|Glo1-s|Qglo	glyoxalase 1	protein-coding
mm_113637.1	chr13	42052113	42052128	+	1	NA	promoter-TSS (NM_007772)	promoter-TSS (NM_007772)	99	NM_007772	110521	Mm.4808	NM_007772	ENSMUSG00000021366	Hivep1	Cryabp1	human immunodeficiency virus type I enhancer binding protein 1	protein-coding
mm_27654.1	chr3	63964660	63964666	-	1	NA	promoter-TSS (NM_001272035)	promoter-TSS (NM_001272035)	70	NM_001331067	11416	Mm.135619	NM_015728	ENSMUSG00000027822	Slc33a1	AI315656|AI788741|Acatn|D630022N01Rik	solute carrier family 33 (acetyl-CoA transporter), member 1	protein-coding
mm_64455.1	chr7	142660335	142660343	+	1	NA	non-coding (NR_002855, exon 1 of 4)	non-coding (NR_002855, exon 1 of 4)	659	NR_002855	111975	Mm.440180	NR_002855	ENSMUSG00000086266	Igf2os	Igf2as|Peg8	insulin-like growth factor 2, opposite strand	ncRNA
mm_150092.1	chr19	29454409	29454416	+	1	NA	intron (NM_021396, intron 4 of 5)	intron (NM_021396, intron 4 of 5)	43493	NM_021396	58205	Mm.116737	NM_021396	ENSMUSG00000016498	Pdcd1lg2	B7-DC|Btdc|F730015O22Rik|PD-L2	programmed cell death 1 ligand 2	protein-coding
mm_106814.1	chr12	7977751	7977755	+	1	NA	promoter-TSS (NM_009693)	promoter-TSS (NM_009693)	76	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_59874.1	chr7	30280187	30280188	+	1	NA	promoter-TSS (NR_144498)	promoter-TSS (NR_144498)	93	NR_144498	108167416	Mm.471845	NR_144498		LOC108167416	-	uncharacterized LOC108167416	ncRNA
mm_158427.1	chrX	139822415	139822419	-	1	NA	3' UTR (NM_001193309, exon 17 of 17)	3' UTR (NM_001193309, exon 17 of 17)	21609	NM_016675	12738	Mm.117068	NM_016675	ENSMUSG00000047230	Cldn2	AL022813	claudin 2	protein-coding
mm_103146.1	chr11	70255330	70255347	-	1	NA	promoter-TSS (NM_001331118)	promoter-TSS (NM_001331118)	32	NM_001331118	11684	Mm.12286	NM_007440	ENSMUSG00000000320	Alox12	9930022G08Rik|Alox12p|P-12LO	arachidonate 12-lipoxygenase	protein-coding
mm_41769.1	chr5	103501451	103501476	+	1	NA	exon (NM_011204, exon 7 of 48)	exon (NM_011204, exon 7 of 48)	76271	NM_011204	19249	Mm.3414	NM_011204	ENSMUSG00000034573	Ptpn13	AI324989|PTP-BL|PTPL1|Ptpri|RIP	protein tyrosine phosphatase, non-receptor type 13	protein-coding
mm_73110.1	chr8	94667083	94667128	+	1	NA	promoter-TSS (NM_024269)	promoter-TSS (NM_024269)	14	NM_024269	107566	Mm.393247	NM_024191	ENSMUSG00000031776	Arl2bp	1700010P10Rik|1700027H16Rik|6330544B05Rik|AI482273|AI849834|BART|Bart1	ADP-ribosylation factor-like 2 binding protein	protein-coding
mm_142201.1	chr17	36958539	36958554	-	1	NA	promoter-TSS (NM_029602)	promoter-TSS (NM_029602)	-46	NM_029602	76416	Mm.26684	NM_029602	ENSMUSG00000036214	Znrd1as	1700022C21Rik|AI746295|Znrd1-as	zinc ribbon domain containing 1, antisense	protein-coding
mm_73428.1	chr8	106135498	106135512	+	1	NA	non-coding (NR_040346, exon 1 of 4)	non-coding (NR_040346, exon 1 of 4)	105	NR_040346	69771	Mm.393274	NR_040344		1810019D21Rik	-	RIKEN cDNA 1810019D21 gene	ncRNA
mm_6527.1	chr1	74600584	74600622	-	1	NA	promoter-TSS (NM_175031)	promoter-TSS (NM_175031)	794	NM_021313	57751	Mm.280920	NM_021313	ENSMUSG00000026171	Rnf25	0610009H16Rik|AO7	ring finger protein 25	protein-coding
mm_35681.1	chr4	43668834	43668863	-	1	NA	promoter-TSS (NM_175517)	promoter-TSS (NM_175517)	11	NM_175517	242408	Mm.440423	NM_175517	ENSMUSG00000043633	Fam221b	4930412F15Rik	family with sequence similarity 221, member B	protein-coding
mm_160327.1	chr8	3690876	3690876	-	1	NA	promoter-TSS (NM_001253745)	promoter-TSS (NM_001253745)	-15	NM_001253746	14128	Mm.1233	NM_013517	ENSMUSG00000005540	Fcer2a	CD23|Fce2|Fcer2|Ly-42	Fc receptor, IgE, low affinity II, alpha polypeptide	protein-coding
mm_114541.1	chr13	73763681	73763763	+	1	NA	promoter-TSS (NM_011390)	promoter-TSS (NM_011390)	25	NM_011390	20499	Mm.275800	NM_011390	ENSMUSG00000017756	Slc12a7	AA408796|D13Ertd261e|Kcc4	solute carrier family 12, member 7	protein-coding
mm_55257.1	chr6	53068707	53068765	-	1	NA	promoter-TSS (NM_173406)	promoter-TSS (NM_173406)	-112	NM_173406	231986	Mm.386865	NM_173406	ENSMUSG00000063568	Jazf1	AI591476|C820002C15|Jaz1|Tip27	JAZF zinc finger 1	protein-coding
mm_1763.1	chr1	75546523	75546541	+	1	NA	intron (NM_009208, intron 1 of 22)	CpG	266	NM_009208	20536	Mm.5053	NM_009208	ENSMUSG00000006576	Slc4a3	A930038D23Rik|Ae3	solute carrier family 4 (anion exchanger), member 3	protein-coding
mm_2770.1	chr1	130717503	130717561	+	1	NA	exon (NM_178691, exon 1 of 2)	exon (NM_178691, exon 1 of 2)	205	NM_178691	226418	Mm.106553	NM_178691	ENSMUSG00000046404	Yod1	6330564D18Rik|9930028C20Rik|Hshin7	YOD1 deubiquitinase	protein-coding
mm_105331.1	chr11	102946012	102946056	-	1	NA	exon (NM_011795, exon 1 of 2)	exon (NM_011795, exon 1 of 2)	427	NM_011795	23829	Mm.57154	NM_011795	ENSMUSG00000045532	C1ql1	C1qrf|CRF|CTRP14|gliacolin	complement component 1, q subcomponent-like 1	protein-coding
mm_89506.1	chr10	94083862	94083862	+	1	NA	intron (NM_053072, intron 3 of 20)	intron (NM_053072, intron 3 of 20)	47861	NM_053072	13998	Mm.269596	NM_053072	ENSMUSG00000020021	Fgd6	AA123052|Etohd4|ZFYVE24	FYVE, RhoGEF and PH domain containing 6	protein-coding
mm_28406.1	chr3	90248765	90248776	-	1	NA	intron (NM_013901, intron 1 of 3)	intron (NM_013901, intron 1 of 3)	578	NM_013901	30791	Mm.294709	NM_013901	ENSMUSG00000052310	Slc39a1	Zip1|Zirtl	solute carrier family 39 (zinc transporter), member 1	protein-coding
mm_91689.1	chr10	43996338	43996362	-	1	NA	intron (NM_172393, intron 2 of 19)	intron (NM_172393, intron 2 of 19)	8496	NM_172393	11630	Mm.292082	NM_172393	ENSMUSG00000019866	Aim1	AI462491|AI463325	absent in melanoma 1	protein-coding
mm_165062.1	chr19	42202106	42202110	-	1	NA	5' UTR (NM_018780, exon 1 of 3)	5' UTR (NM_018780, exon 1 of 3)	144	NM_018780	54612	Mm.470071	NM_018780	ENSMUSG00000018822	Sfrp5	AI605071|SARP3	secreted frizzled-related sequence protein 5	protein-coding
mm_23337.1	chr3	54692776	54692800	+	1	NA	promoter-TSS (NM_019995)	promoter-TSS (NM_019995)	-317	NM_019995	56790	Mm.486375	NM_019995	ENSMUSG00000027751	Supt20	AA667204|AI450544|D3Ertd300e|Fam48a|Supt20h|p38IP	suppressor of Ty 20	protein-coding
mm_60708.1	chr7	45225653	45225706	+	1	NA	exon (NM_001285498, exon 8 of 12)	exon (NM_001285498, exon 8 of 12)	9926	NM_001285498	21677	Mm.3019	NM_011565	ENSMUSG00000030796	Tead2	ETF|Etdf|TEAD-2|TEF-4|TEF4	TEA domain family member 2	protein-coding
mm_144734.1	chr18	35562201	35562260	+	1	NA	promoter-TSS (NM_010771)	promoter-TSS (NM_010771)	72	NM_010771	17184	Mm.215034	NM_010771	ENSMUSG00000037236	Matr3	1110061A14Rik|2810017I02Rik|AI841759|AW555618|D030046F20Rik|mKIAA0723	matrin 3	protein-coding
mm_42909.1	chr5	122525437	122525469	+	1	NA	Intergenic	Intergenic	-23228	NR_027838	11938	Mm.227583	NM_009722	ENSMUSG00000029467	Atp2a2	9530097L16Rik|D5Wsu150e|SERCA2|SERCA2B|Serca2a|mKIAA4195	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	protein-coding
mm_18733.1	chr2	72980896	72980912	-	1	NA	promoter-TSS (NM_001018042)	promoter-TSS (NM_001018042)	-458	NM_001018042	20687	Mm.124328	NM_011450	ENSMUSG00000027109	Sp3	D130027J01Rik	trans-acting transcription factor 3	protein-coding
mm_95693.1	chr11	54315030	54315038	+	1	NA	5' UTR (NM_001033599, exon 1 of 21)	5' UTR (NM_001033599, exon 1 of 21)	131	NM_001033599	216739	Mm.267478	NM_144823	ENSMUSG00000020333	Acsl6	A330035H04Rik|AW050338|Facl6|LACS|Lacsl|mKIAA0837	acyl-CoA synthetase long-chain family member 6	protein-coding
mm_45792.1	chr5	87535154	87535179	-	1	NA	intron (NM_019878, intron 1 of 7)	intron (NM_019878, intron 1 of 7)	3029	NM_019878	56362	Mm.23502	NM_019878	ENSMUSG00000029269	Sult1b1	ST1B1|St2b2	sulfotransferase family 1B, member 1	protein-coding
mm_107228.1	chr12	26477052	26477064	+	1	NA	exon (NM_020557, exon 4 of 5)	exon (NM_020557, exon 4 of 5)	7843	NM_020557	22169	Mm.271839	NM_020557	ENSMUSG00000020638	Cmpk2	1200004E04Rik|TDKI|Tyki	cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial	protein-coding
mm_32049.1	chr4	97581783	97581805	+	1	NA	promoter-TSS (NM_001122952)	promoter-TSS (NM_001122952)	-149	NM_001122952	18027	Mm.31274	NM_010905	ENSMUSG00000028565	Nfia	1110047K16Rik|9430022M17Rik|CTF|NF1-A|NF1A	nuclear factor I/A	protein-coding
mm_81496.1	chr9	110032144	110032169	+	1	NA	exon (NM_008633, exon 6 of 19)	exon (NM_008633, exon 6 of 19)	-19865	NM_001311163	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_167437.1	chr8	119975194	119975196	+	1	NA	Intergenic	Intergenic	-17243	NM_030209	78892	Mm.264680	NM_030209	ENSMUSG00000031825	Crispld2	1810049K24Rik|Lcrisp2|Lgl1|coffeecrisp	cysteine-rich secretory protein LCCL domain containing 2	protein-coding
mm_17097.1	chr2	23069272	23069283	-	1	NA	exon (NM_001102438, exon 1 of 13)	exon (NM_001102438, exon 1 of 13)	205	NM_001102438	74159	Mm.181973	NM_028793	ENSMUSG00000026781	Acbd5	1300014E15Rik	acyl-Coenzyme A binding domain containing 5	protein-coding
mm_51231.1	chr6	71374519	71374542	+	1	NA	exon (NM_009857, exon 2 of 4)	exon (NM_009857, exon 2 of 4)	1103	NM_001081110	12525	Mm.1858	NM_009857	ENSMUSG00000053977	Cd8a	BB154331|Ly-2|Ly-35|Ly-B|Lyt-2	CD8 antigen, alpha chain	protein-coding
mm_104896.1	chr11	99598142	99598147	-	1	NA	promoter-TSS (NM_029351)	promoter-TSS (NM_029351)	-38	NM_029351	75586	Mm.75707	NM_029351	ENSMUSG00000049809	Krtap9-3	2310040M23Rik	keratin associated protein 9-3	protein-coding
mm_127406.1	chr15	101246573	101246587	+	1	NA	Intergenic	CpG	-20266	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_25488.1	chr3	109340340	109340368	+	1	NA	promoter-TSS (NM_020505)	promoter-TSS (NM_020505)	-329	NM_020505	57257	Mm.282257	NM_020505	ENSMUSG00000033721	Vav3	A530094I06Rik|AA986410|Idd18.1	vav 3 oncogene	protein-coding
mm_79501.1	chr9	57175258	57175266	+	1	NA	promoter-TSS (NR_033784)	promoter-TSS (NR_033784)	-13	NR_033784	67319	Mm.234187	NR_033784	ENSMUSG00000100282	1700041C23Rik	-	RIKEN cDNA 1700041C23 gene	ncRNA
mm_24968.1	chr3	96727660	96727726	+	1	NA	promoter-TSS (NM_026406)	promoter-TSS (NM_026406)	82	NM_026406	67845	Mm.386792	NM_026406	ENSMUSG00000028098	Rnf115	2610028E05Rik|AU042696|Zfp364	ring finger protein 115	protein-coding
mm_83232.1	chr9	42398663	42398691	-	1	NA	intron (NM_009347, intron 1 of 23)	intron (NM_009347, intron 1 of 23)	1252	NM_009347	21683	Mm.42209	NM_009347	ENSMUSG00000037705	Tecta	Tctna	tectorin alpha	protein-coding
mm_75161.1	chr8	36568728	36568732	-	1	NA	3' UTR (NM_015802, exon 14 of 14)	3' UTR (NM_015802, exon 14 of 14)	45213	NM_015802	50768	Mm.125155	NM_015802	ENSMUSG00000031523	Dlc1	A730069N07Rik|Arhgap7|HP|STARD12|dlc-1	deleted in liver cancer 1	protein-coding
mm_92963.1	chr10	85993510	85993527	-	1	NA	intron (NM_177772, intron 3 of 15)	intron (NM_177772, intron 3 of 15)	18342	NM_177772	270757	Mm.107214	NM_177772	ENSMUSG00000050108	Bpifc	4732454E24|Bpil2	BPI fold containing family C	protein-coding
mm_133309.1	chr16	77601600	77601617	+	1	NA	Intergenic	B3A|SINE|B2	1951	NR_029728	387246		NR_029728	ENSMUSG00000065557	Mirlet7c-1	Mirnlet7c|Mirnlet7c-1|let-7c-1	microRNA let7c-1	ncRNA
mm_158136.1	chrX	103186556	103186616	-	1	NA	promoter-TSS (NM_008671)	promoter-TSS (NM_008671)	78	NM_008671	17954	Mm.388694	NM_008671	ENSMUSG00000082229	Nap1l2	Bpx	nucleosome assembly protein 1-like 2	protein-coding
mm_163646.1	chr13	63256764	63256773	+	1	NA	intron (NR_110520, intron 2 of 5)	B1_Mm|SINE|Alu	16739	NR_110521	72061	Mm.188105	NM_028079	ENSMUSG00000021458	2010111I01Rik	2300006M17Rik|AP-O|AW742919|Aopep|ApO|mir-23b|mir-24-1|mir-27b	RIKEN cDNA 2010111I01 gene	protein-coding
mm_43265.1	chr5	130369408	130369417	+	1	NA	promoter-TSS (NM_181045)	promoter-TSS (NM_181045)	-46	NM_181045	140904	Mm.40875	NM_021371	ENSMUSG00000060371	Caln1	9630012C17Rik|Cabp8|MNCb-0849	calneuron 1	protein-coding
mm_160591.1	chr9	70453755	70453755	-	1	NA	exon (NM_033604, exon 7 of 15)	exon (NM_033604, exon 7 of 15)	-32201	NM_007630	12442	Mm.22592	NM_007630	ENSMUSG00000032218	Ccnb2	CycB2	cyclin B2	protein-coding
mm_133113.1	chr16	65533984	65533995	+	1	NA	TTS (NM_008849)	TTS (NM_008849)	13360	NM_008849	18736	Mm.355440	NM_008849	ENSMUSG00000004842	Pou1f1	GHF-1|Hmp1|Pit-1|Pit1|Pit1-rs1|dw|dwarf	POU domain, class 1, transcription factor 1	protein-coding
mm_165196.1	chr2	32387068	32387085	+	1	NA	exon (NM_008491, exon 2 of 6)	exon (NM_008491, exon 2 of 6)	663	NM_008491	16819	Mm.9537	NM_008491	ENSMUSG00000026822	Lcn2	24p3|AW212229|NRL|Sip24	lipocalin 2	protein-coding
mm_104512.1	chr11	96005873	96005952	-	1	NA	promoter-TSS (NM_009951)	promoter-TSS (NM_009951)	32	NM_009951	140486	Mm.294769	NM_009951	ENSMUSG00000013415	Igf2bp1	AL024068|AW549074|CRD-BP|Crdbp|D030026A21Rik|D11Moh40e|D11Moh45|IMP-1|IMP1|Neilsen|ZBP-1|Zbp1|mir-3063	insulin-like growth factor 2 mRNA binding protein 1	protein-coding
mm_98085.1	chr11	86579153	86579178	+	1	NA	Intergenic	MIR|SINE|MIR	4993	NR_029738	387140		NR_029738	ENSMUSG00000065455	Mir21a	Mir21|Mirn21|mmu-mir-21|mmu-mir-21a	microRNA 21a	ncRNA
mm_13804.1	chr2	119039201	119039207	+	1	NA	3' UTR (NM_173450, exon 3 of 3)	3' UTR (NM_173450, exon 3 of 3)	4414	NM_173450	271842	Mm.33617	NM_173450	ENSMUSG00000027324	Rpusd2	4921503C21Rik|9630001E10|BB231107	RNA pseudouridylate synthase domain containing 2	protein-coding
mm_347.1	chr1	31095099	31095110	+	1	NA	intron (NR_136907, intron 1 of 3)	LTR88c|LTR|Gypsy?	1350	NR_136907	102634473	Mm.484482	NR_136907	ENSMUSG00000100371	Gm29669	-	predicted gene 29669	ncRNA
mm_82086.1	chr9	123040464	123040468	+	1	NA	exon (NM_177911, exon 2 of 14)	exon (NM_177911, exon 2 of 14)	5725	NM_177911	331046	Mm.195309	NM_177911	ENSMUSG00000025787	Tgm4	9530008N10Rik|Eapa1|TGP	transglutaminase 4 (prostate)	protein-coding
mm_65562.1	chr7	27168686	27168720	-	1	NA	3' UTR (NM_029391, exon 8 of 8)	3' UTR (NM_029391, exon 8 of 8)	-1901	NM_053208	112406	Mm.29978	NM_053208	ENSMUSG00000058709	Egln2	0610011A13Rik|C85656|Hif-p4h-1|Ier4|Phd1|SM-20	egl-9 family hypoxia-inducible factor 2	protein-coding
mm_81347.1	chr9	108567485	108567497	+	1	NA	promoter-TSS (NR_029577)	promoter-TSS (NR_029577)	-149	NM_023247	66706	Mm.29471	NM_023247	ENSMUSG00000070283	Ndufaf3	4733401H18Rik	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, assembly factor 3	protein-coding
mm_1567.1	chr1	74236480	74236598	+	1	NA	promoter-TSS (NM_029711)	promoter-TSS (NM_029711)	-11	NM_029711	76709	Mm.337038	NM_029711	ENSMUSG00000006304	Arpc2	2210023N03Rik|34kDa|p34-Arc	actin related protein 2/3 complex, subunit 2	protein-coding
mm_25191.1	chr3	103575239	103575255	+	1	NA	promoter-TSS (NM_018800)	promoter-TSS (NM_018800)	-35	NM_001276679	54524	Mm.88818	NM_018800	ENSMUSG00000027849	Syt6	3110037A08Rik|AW048930|sytVI	synaptotagmin VI	protein-coding
mm_124691.1	chr15	6435510	6435537	+	1	NA	exon (NM_001102400, exon 10 of 13)	exon (NM_001102400, exon 10 of 13)	-9810	NM_013485	12279	Mm.29095	NM_013485	ENSMUSG00000022149	C9	-	complement component 9	protein-coding
mm_66331.1	chr7	42738988	42738993	-	1	NA	Intergenic	Intergenic	-46272	NM_001008427	434179	Mm.284947	NM_001008427	ENSMUSG00000069727	Zfp975	EG434179|Gm5595|mszf88	zinc finger protein 975	protein-coding
mm_31571.1	chr4	57594901	57594919	+	1	NA	intron (NM_001304544, intron 1 of 8)	intron (NM_001304544, intron 1 of 8)	26662	NM_172868	242481	Mm.331630	NM_172868	ENSMUSG00000090053	Palm2	53-H12|B130066I24|R75368|pEN70	paralemmin 2	protein-coding
mm_81210.1	chr9	107580722	107580732	+	1	NA	promoter-TSS (NM_178020)	promoter-TSS (NM_178020)	58	NM_019750	56441	Mm.10305	NM_019750	ENSMUSG00000079334	Nat6	AI225910|Fus2	N-acetyltransferase 6	protein-coding
mm_18335.1	chr2	57367639	57367672	-	1	NA	3' UTR (NM_010274, exon 17 of 17)	3' UTR (NM_010274, exon 17 of 17)	129273	NM_010274	14571	Mm.3711	NM_010274	ENSMUSG00000026827	Gpd2	AA408484|AI448216|AU021455|AW494132|GPDH|Gdm1|Gpd-m|Gpdh-m|TISP38	glycerol phosphate dehydrogenase 2, mitochondrial	protein-coding
mm_77041.1	chr8	109575485	109575496	-	1	NA	exon (NM_017370, exon 5 of 5)	exon (NM_017370, exon 5 of 5)	3682	NM_017370	15439	Mm.26730	NM_017370	ENSMUSG00000031722	Hp	HP-1|preHP2	haptoglobin	protein-coding
mm_74709.1	chr8	17186908	17186917	-	1	NA	intron (NM_053171, intron 2 of 69)	Lx|LINE|L1	348473	NM_053171	94109	Mm.436988	NM_053171	ENSMUSG00000060924	Csmd1	B930082H09|mKIAA1890	CUB and Sushi multiple domains 1	protein-coding
mm_141221.1	chr17	27242626	27242680	-	1	NA	intron (NR_131118, intron 1 of 2)	intron (NR_131118, intron 1 of 2)	5413	NR_131118	319720	Mm.394996	NR_131118		9630028I04Rik	-	RIKEN cDNA 9630028I04 gene	ncRNA
mm_35831.1	chr4	48039745	48039753	-	1	NA	Intergenic	Intergenic	-5556	NM_015743	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_13166.1	chr2	92609501	92609516	+	1	NA	intron (NM_023850, intron 1 of 2)	intron (NM_023850, intron 1 of 2)	9801	NM_023850	76969	Mm.38021	NM_023850	ENSMUSG00000027221	Chst1	2610008E20Rik|AW125896|C6ST|GST-1|Gst1|KSGAL6ST	carbohydrate (keratan sulfate Gal-6) sulfotransferase 1	protein-coding
mm_172996.1	chrM	1495	1498	+	1	NA	NA	Intergenic	NA	NA								
mm_67394.1	chr7	79848192	79848224	-	1	NA	Intergenic	Intergenic	-5856	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_16105.1	chr2	169633020	169633055	+	1	NA	promoter-TSS (NM_080455)	promoter-TSS (NM_080455)	-609	NM_080455	228911	Mm.315789	NM_080455	ENSMUSG00000047907	Tshz2	2900073F20Rik|B830045G17|Mtsh2|Sdccag33l|Tsh2|Zfp218|mKIAA4248|teashirt2	teashirt zinc finger family member 2	protein-coding
mm_20754.1	chr2	140659689	140659715	-	1	NA	3' UTR (NM_178382, exon 3 of 3)	3' UTR (NM_178382, exon 3 of 3)	11774	NM_001172160	71436	Mm.426781	NM_178382	ENSMUSG00000051379	Flrt3	5530600M07Rik|C430047I10Rik|mKIAA1469	fibronectin leucine rich transmembrane protein 3	protein-coding
mm_108920.1	chr12	100779089	100779101	+	1	NA	promoter-TSS (NM_145448)	promoter-TSS (NM_145448)	-28	NM_145448	217830	Mm.218590	NM_145448	ENSMUSG00000021185	9030617O03Rik	-	RIKEN cDNA 9030617O03 gene	protein-coding
mm_67307.1	chr7	79386944	79386981	-	1	NA	promoter-TSS (NM_020599)	promoter-TSS (NM_020599)	65	NM_020599	19771	Mm.41653	NM_020599	ENSMUSG00000039194	Rlbp1	3110056M11Rik|CRALBP	retinaldehyde binding protein 1	protein-coding
mm_46351.1	chr5	102911256	102911282	-	1	NA	3' UTR (NM_001081567, exon 14 of 14)	3' UTR (NM_001081567, exon 14 of 14)	66262	NM_001346585	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding
mm_80077.1	chr9	69995416	69995429	+	1	NA	5' UTR (NM_016787, exon 2 of 11)	5' UTR (NM_016787, exon 2 of 11)	5956	NM_001008238	12175	Mm.159777	NM_016787	ENSMUSG00000011958	Bnip2	5730523P12Rik|BNIP2beta|Nip21	BCL2/adenovirus E1B interacting protein 2	protein-coding
mm_166599.1	chr6	67532534	67532541	-	1	NA	Intergenic	Intergenic	3285	NM_020047	56753	Mm.439913	NM_020047	ENSMUSG00000051397	Tacstd2	C80403|EGP-1|GA733-1|Ly97|TROP2	tumor-associated calcium signal transducer 2	protein-coding
mm_94369.1	chr11	5058112	5058147	+	1	NA	promoter-TSS (NM_145216)	promoter-TSS (NM_145216)	1	NM_145216	75668	Mm.374836	NM_145216	ENSMUSG00000034209	Rasl10a	2210403B10Rik|AI852688	RAS-like, family 10, member A	protein-coding
mm_109877.1	chr12	4918140	4918150	-	1	NA	intron (NM_001099628, intron 1 of 30)	intron (NM_001099628, intron 1 of 30)	792	NM_001099628	320817	Mm.210966	NM_001099628	ENSMUSG00000052812	Atad2b	1110014E10Rik|BC032887|C79189|D530031C13Rik	ATPase family, AAA domain containing 2B	protein-coding
mm_86917.1	chr10	23851428	23851453	+	1	NA	promoter-TSS (NM_011979)	promoter-TSS (NM_011979)	-22	NM_011979	26464	Mm.27334	NM_011979	ENSMUSG00000020010	Vnn3	-	vanin 3	protein-coding
mm_113952.1	chr13	51100495	51100515	+	1	NA	promoter-TSS (NM_001283028)	promoter-TSS (NM_001283028)	222	NR_029463	77428	Mm.405630	NR_029463		9430083A17Rik	-	RIKEN cDNA 9430083A17 gene	ncRNA
mm_100143.1	chr11	115993010	115993021	+	1	NA	intron (NM_001005608, intron 23 of 39)	intron (NM_001005608, intron 23 of 39)	18290	NM_133663	192897	Mm.213873	NM_133663	ENSMUSG00000020758	Itgb4	AA407042|C230078O20|CD104	integrin beta 4	protein-coding
mm_43780.1	chr5	142365729	142365738	+	1	NA	Intergenic	Intergenic	-35764	NM_199068	17425	Mm.24214	NM_010812	ENSMUSG00000056493	Foxk1	A630048H08Rik|AI463295|ENSMUSG00000075577|Gm10868|Mnf	forkhead box K1	protein-coding
mm_36808.1	chr4	103173622	103173634	-	1	NA	3' UTR (NM_177732, exon 10 of 10)	3' UTR (NM_177732, exon 10 of 10)	41256	NM_177732	242585	Mm.281800	NM_177732	ENSMUSG00000028521	Slc35d1	AI834976|C330011J09|UGTREL7|mKIAA0260	solute carrier family 35 (UDP-glucuronic acid/UDP-N-acetylgalactosamine dual transporter), member D1	protein-coding
mm_96243.1	chr11	62560492	62560496	+	1	NA	Intergenic	FordPrefect|DNA|hAT-Tip100	8763	NM_001313984	22187	Mm.371592	NM_011664	ENSMUSG00000019505	Ubb	AL033289|Rps27a|Uba52|Ubb2|Ubc	ubiquitin B	protein-coding
mm_87620.1	chr10	57794684	57794717	+	1	NA	exon (NM_020561, exon 1 of 8)	exon (NM_020561, exon 1 of 8)	156	NM_020561	57319	Mm.2379	NM_020561	ENSMUSG00000019872	Smpdl3a	0610010C24Rik|AI529588|ASM3A|ASML3|ASML3A	sphingomyelin phosphodiesterase, acid-like 3A	protein-coding
mm_142532.1	chr17	46442213	46442214	-	1	NA	TTS (NM_001162864)	TTS (NM_001162864)	-3736	NM_144856	108114	Mm.387538	NM_144856	ENSMUSG00000067144	Slc22a7	NLT|OAT2	solute carrier family 22 (organic anion transporter), member 7	protein-coding
mm_126176.1	chr15	78597113	78597121	+	1	NA	promoter-TSS (NM_028195)	promoter-TSS (NM_028195)	70	NM_028195	72318	Mm.32911	NM_028195	ENSMUSG00000018008	Cyth4	2510004M07Rik|5830469K17Rik|AI467541|Pscd4|mFLJ00017	cytohesin 4	protein-coding
mm_91751.1	chr10	49788744	49788769	-	1	NA	promoter-TSS (NM_010349)	promoter-TSS (NM_010349)	-2	NM_001111268	14806	Mm.332838	NM_010349	ENSMUSG00000056073	Grik2	AW124492|GluK2|Glur-6|Glur6|Glurbeta2	glutamate receptor, ionotropic, kainate 2 (beta 2)	protein-coding
mm_120249.1	chr14	62998064	62998081	+	1	NA	promoter-TSS (NM_001039125)	promoter-TSS (NM_001039125)	-5	NM_001039125	654465	Mm.424929	NM_001039125	ENSMUSG00000075573	Defb47	Defb41|EG654465	defensin beta 47	protein-coding
mm_157883.1	chrX	75843162	75843175	-	1	NA	promoter-TSS (NM_001346520)	promoter-TSS (NM_001346520)	-105	NM_001346520	102866	Mm.28777	NM_145629	ENSMUSG00000016382	Pls3	AI115446|AL024105	plastin 3 (T-isoform)	protein-coding
mm_136113.1	chr16	85550154	85550177	-	1	NA	5' UTR (NM_144853, exon 1 of 4)	5' UTR (NM_144853, exon 1 of 4)	208	NM_144853	224405	Mm.213203	NM_144853	ENSMUSG00000041134	Cyyr1	-	cysteine and tyrosine-rich protein 1	protein-coding
mm_139070.1	chr17	46650329	46650340	+	1	NA	promoter-TSS (NM_025611)	promoter-TSS (NM_025611)	-4	NM_025611	66515	Mm.329078	NM_025611	ENSMUSG00000038545	Cul7	2510004L20Rik|AA409809|C230011P08Rik|p185|p193	cullin 7	protein-coding
mm_89404.1	chr10	90576778	90576784	+	1	NA	promoter-TSS (NM_181398)	promoter-TSS (NM_181398)	90	NM_181398	77531	Mm.440605	NM_181398	ENSMUSG00000058589	Anks1b	AIDA-1b|C030032C09Rik|E530015N03Rik|ENSMUSG00000078431|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding
mm_2068.1	chr1	87620432	87620438	+	1	NA	non-coding (NR_122078, exon 1 of 28)	non-coding (NR_122078, exon 1 of 28)	123	NM_001110193	16331	Mm.15105	NM_010566	ENSMUSG00000026288	Inpp5d	SHIP|SHIP-1|SHIP1|SIP-145|p150Ship|s-SHIP	inositol polyphosphate-5-phosphatase D	protein-coding
mm_5571.1	chr1	39450265	39450275	-	1	NA	intron (NM_018775, intron 1 of 19)	intron (NM_018775, intron 1 of 19)	28477	NM_018775	54610	Mm.387293	NM_018775	ENSMUSG00000003134	Tbc1d8	AD3|HBLP1|VRP	TBC1 domain family, member 8	protein-coding
mm_53726.1	chr6	145075340	145075342	+	1	NA	intron (NM_007532, intron 1 of 10)	intron (NM_007532, intron 1 of 10)	816	NM_007532	12035	Mm.4606	NM_007532	ENSMUSG00000030268	Bcat1	BCATc|Eca39	branched chain aminotransferase 1, cytosolic	protein-coding
mm_22933.1	chr3	31163353	31163363	+	1	NA	3' UTR (NM_008770, exon 3 of 3)	3' UTR (NM_008770, exon 3 of 3)	13438	NM_008770	18417	Mm.4425	NM_008770	ENSMUSG00000037625	Cldn11	Claudin-11|Claudin11|Osp|Otm	claudin 11	protein-coding
mm_134667.1	chr16	22261078	22261081	-	1	NA	intron (NM_001330555, intron 1 of 9)	intron (NM_001330555, intron 1 of 9)	4926	NM_001330554	20462	Mm.210352	NM_009186	ENSMUSG00000022858	Tra2b	5730405G21Rik|D16Ertd266e|SIG-41|Sfrs10|Silg41|TRA2beta	transformer 2 beta homolog (Drosophila)	protein-coding
mm_166532.1	chr6	29914704	29914707	+	1	NA	Intergenic	BC1_Mm|scRNA|scRNA	-2308	NM_001037740	320609	Mm.56097	NM_177204	ENSMUSG00000039629	Strip2	D330017J20Rik|Fam40b	striatin interacting protein 2	protein-coding
mm_129183.1	chr15	76307218	76307230	-	1	NA	promoter-TSS (NM_153122)	promoter-TSS (NM_153122)	21	NM_153122	75475	Mm.322738	NM_153122	ENSMUSG00000022562	Oplah	1700010G02Rik	5-oxoprolinase (ATP-hydrolysing)	protein-coding
mm_157549.1	chrX	51681334	51681365	-	1	NA	promoter-TSS (NM_015819)	promoter-TSS (NM_015819)	253	NM_001077202	50786	Mm.252561	NM_015819	ENSMUSG00000062184	Hs6st2	6OST2	heparan sulfate 6-O-sulfotransferase 2	protein-coding
mm_67265.1	chr7	75780328	75780409	-	1	NA	Intergenic	Intergenic	-67970	NM_001122780	207952	Mm.206223	NM_029652	ENSMUSG00000055652	Klhl25	2810402K13Rik|BC027373|Enc-1	kelch-like 25	protein-coding
mm_55941.1	chr6	85069437	85069445	-	1	NA	promoter-TSS (NM_177077)	promoter-TSS (NM_177077)	72	NM_177077	75914	Mm.159621	NM_177077	ENSMUSG00000033769	Exoc6b	4930569O18Rik|G430127E12Rik|Sec15b|Sec15l2|mKIAA0919	exocyst complex component 6B	protein-coding
mm_20625.1	chr2	131910699	131910701	-	1	NA	intron (NM_001278258, intron 1 of 3)	intron (NM_001278258, intron 1 of 3)	772	NM_001278256	19122	Mm.648	NM_011170	ENSMUSG00000079037	Prnp	AA960666|AI325101|CD230|PrP|PrP<C>|PrPC|PrPSc|Prn-i|Prn-p|Sinc|prP27-30|prP33-35C	prion protein	protein-coding
mm_148091.1	chr18	73815431	73815453	-	1	NA	promoter-TSS (NM_145494)	promoter-TSS (NM_145494)	-50	NM_145494	107029	Mm.36817	NM_145494	ENSMUSG00000024556	Me2	AW120568|D030040L20Rik|NAD-ME	malic enzyme 2, NAD(+)-dependent, mitochondrial	protein-coding
mm_167048.1	chr7	82335735	82335759	+	1	NA	promoter-TSS (NM_001190374)	promoter-TSS (NM_001190374)	53	NM_001190374	269959	Mm.65306	NM_001190374	ENSMUSG00000070469	Adamtsl3	9230119C12Rik|C130057K09|mKIAA1233	ADAMTS-like 3	protein-coding
mm_54125.1	chr6	18443854	18443856	-	1	NA	intron (NM_080285, intron 3 of 22)	intron (NM_080285, intron 3 of 22)	70970	NM_080285	30785	Mm.224189	NM_080285	ENSMUSG00000000416	Cttnbp2	3010022N24Rik|4732477G22Rik|6430526E05|9130022E09Rik|AU040881|Cortbp2|ORF4|mKIAA1758	cortactin binding protein 2	protein-coding
mm_93438.1	chr10	109780081	109780083	-	1	NA	intron (NM_001081035, intron 12 of 38)	B1_Mus2|SINE|Alu	220137	NM_001081035	260315	Mm.225050	NM_177797	ENSMUSG00000020181	Nav3	4732483H20Rik|9630020C08Rik|POMFIL1|Pomfil1p|mKIAA0938|unc53H3	neuron navigator 3	protein-coding
mm_71964.1	chr8	70529540	70529562	+	1	NA	exon (NM_001199631, exon 2 of 9)	exon (NM_001199631, exon 2 of 9)	1705	NM_001199631	14232	Mm.141864	NM_010223	ENSMUSG00000019428	Fkbp8	38kDa|FKBP-38|FKBP-8|Fkbp38	FK506 binding protein 8	protein-coding
mm_74612.1	chr8	12573280	12573290	-	1	NA	intron (NM_024279, intron 1 of 6)	intron (NM_024279, intron 1 of 6)	236	NM_024279	78634	Mm.116871	NM_024279	ENSMUSG00000010435	Spaca7	1700094C09Rik	sperm acrosome associated 7	protein-coding
mm_34759.1	chr4	152338975	152338998	+	1	NA	exon (NM_001081376, exon 1 of 42)	exon (NM_001081376, exon 1 of 42)	335	NM_001081376	269610	Mm.40192	NM_029216	ENSMUSG00000005045	Chd5	4930532L22Rik|AW060752|B230399N07Rik|CHD-5	chromodomain helicase DNA binding protein 5	protein-coding
mm_160306.1	chr7	140667445	140667445	+	1	NA	exon (NM_146961, exon 1 of 1)	exon (NM_146961, exon 1 of 1)	156	NM_146961	258963	Mm.377773	NM_146961	ENSMUSG00000059136	Olfr539	MOR253-4	olfactory receptor 539	protein-coding
mm_173093.1	chrX	151215682	151215692	-	1	NA	intron (NM_001271678, intron 4 of 21)	intron (NM_001271678, intron 4 of 21)	17609	NM_001271678	279561	Mm.441474	NM_001271678	ENSMUSG00000041245	Wnk3	Prkwnk3|Wnk3-ps	WNK lysine deficient protein kinase 3	protein-coding
mm_66449.1	chr7	44869551	44869562	-	1	NA	5' UTR (NM_133949, exon 1 of 12)	5' UTR (NM_133949, exon 1 of 12)	232	NM_133949	84113	Mm.42855	NM_133949	ENSMUSG00000038502	Ptov1	1110030G05Rik|AU041779|Gcap3	prostate tumor over expressed gene 1	protein-coding
mm_46108.1	chr5	92348207	92348224	-	1	NA	exon (NM_021274, exon 2 of 4)	exon (NM_021274, exon 2 of 4)	674	NM_021274	15945	Mm.877	NM_021274	ENSMUSG00000034855	Cxcl10	C7|CRG-2|INP10|IP-10|IP10|Ifi10|Scyb10|gIP-10|mob-1	chemokine (C-X-C motif) ligand 10	protein-coding
mm_32438.1	chr4	107253256	107253280	+	1	NA	promoter-TSS (NM_028394)	promoter-TSS (NM_028394)	265	NM_029985	77809	Mm.29681	NM_029985	ENSMUSG00000028617	Lrrc42	A930011F22Rik|AA536996	leucine rich repeat containing 42	protein-coding
mm_138988.1	chr17	45506826	45506857	+	1	NA	promoter-TSS (NM_198608)	promoter-TSS (NM_198608)	0	NM_198608	224805	Mm.329063	NM_198608	ENSMUSG00000023938	Aars2	Aarsl|AlaRS|Gm89	alanyl-tRNA synthetase 2, mitochondrial	protein-coding
mm_167602.1	chr9	50905553	50905577	+	1	NA	intron (NM_178710, intron 9 of 15)	intron (NM_178710, intron 9 of 15)	48641	NM_001286553	73699	Mm.7726	NM_028614	ENSMUSG00000032058	Ppp2r1b	2410091N08Rik|AI790395	protein phosphatase 2, regulatory subunit A, beta	protein-coding
mm_22177.1	chr2	173215765	173215805	-	1	NA	exon (NM_021394, exon 3 of 8)	exon (NM_021394, exon 3 of 8)	3137	NM_021394	58203	Mm.116687	NM_021394	ENSMUSG00000027514	Zbp1	2010010H03Rik|Dai|Dlm1|mZaDLM	Z-DNA binding protein 1	protein-coding
mm_163920.1	chr14	44256189	44256191	+	1	NA	Intergenic	BC1_Mm|scRNA|scRNA	-42953	NR_073363	74328	Mm.439150	NR_073363		1700047E10Rik	-	RIKEN cDNA 1700047E10 gene	ncRNA
mm_122794.1	chr14	54438730	54438745	-	1	NA	exon (NM_008608, exon 6 of 10)	exon (NM_008608, exon 6 of 10)	7139	NM_008608	17387	Mm.280175	NM_008608	ENSMUSG00000000957	Mmp14	AI325305|MMP-X1|MT-MMP-1|MT1-MMP|sabe	matrix metallopeptidase 14 (membrane-inserted)	protein-coding
mm_114877.1	chr13	94173996	94174027	+	1	NA	intron (NM_172589, intron 2 of 3)	intron (NM_172589, intron 2 of 3)	111270	NM_029153	107767	Mm.201455	NM_029153	ENSMUSG00000021687	Scamp1	4930505M11Rik|AI415563|AW122395	secretory carrier membrane protein 1	protein-coding
mm_100431.1	chr11	119465116	119465148	+	1	NA	Intergenic	Intergenic	-26215	NM_001164636	338371	Mm.271946	NM_177394	ENSMUSG00000039850	Endov	A730011L01Rik	endonuclease V	protein-coding
mm_40978.1	chr5	77037077	77037087	+	1	NA	intron (NM_027970, intron 1 of 8)	intron (NM_027970, intron 1 of 8)	-18219	NR_077218	68246	Mm.319633	NR_077218	ENSMUSG00000086632	1700112J05Rik	1700110A09Rik	RIKEN cDNA 1700112J05 gene	ncRNA
mm_73806.1	chr8	117330397	117330481	+	1	NA	intron (NM_001163262, intron 1 of 20)	intron (NM_001163262, intron 1 of 20)	-18731	NM_028941	74440	Mm.233181	NM_028941	ENSMUSG00000034390	Cmip	4933407C03Rik|5830471E12Rik|AI314065|AI464126	c-Maf inducing protein	protein-coding
mm_82230.1	chr9	3031912	3031924	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	6825	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_172933.1	chr9	7751695	7751700	+	1	NA	Intergenic	Intergenic	-12380	NM_133739	71929	Mm.283293	NM_133739	ENSMUSG00000050912	Tmem123	2310075C12Rik	transmembrane protein 123	protein-coding
mm_40834.1	chr5	72914555	72914565	+	1	NA	5' UTR (NM_001113423, exon 1 of 8)	5' UTR (NM_001113423, exon 1 of 8)	198	NM_153567	75991	Mm.121285	NM_153567	ENSMUSG00000036087	Slain2	5033405K12Rik|8030444K12Rik|AI596370	SLAIN motif family, member 2	protein-coding
mm_134193.1	chr16	10992645	10992665	-	1	NA	intron (NM_019980, intron 1 of 3)	CpG	466	NM_019980	56722	Mm.294753	NM_019980	ENSMUSG00000022500	Litaf	3222402J11Rik|C85531|N4WBP3|TBX1	LPS-induced TN factor	protein-coding
mm_63174.1	chr7	125368973	125368983	+	1	NA	5' UTR (NM_001145759, exon 1 of 1)	5' UTR (NM_001145759, exon 1 of 1)	117	NM_001145759	75861	Mm.349600	NM_001145759		4930571K23Rik	AI428146	RIKEN cDNA 4930571K23 gene	protein-coding
mm_136687.1	chr17	6828067	6828084	+	1	NA	Intergenic	CpG	-45295	NM_009510	22350	Mm.277812	NM_009510	ENSMUSG00000052397	Ezr	AW146364|R75297|Vil2|p81	ezrin	protein-coding
mm_39568.1	chr5	23418610	23418650	+	1	NA	Intergenic	Intergenic	15723	NR_040469	269630	Mm.425231	NR_040469	ENSMUSG00000073147	5031425E22Rik	-	RIKEN cDNA 5031425E22 gene	ncRNA
mm_40692.1	chr5	65764074	65764158	+	1	NA	intron (NM_001024917, intron 1 of 19)	CpG	595	NM_001024917	333789	Mm.332398	NM_001024917	ENSMUSG00000037795	N4bp2	B3bp|E430014I16|Gm1791|Gm868	NEDD4 binding protein 2	protein-coding
mm_37915.1	chr4	132783474	132783501	-	1	NA	exon (NM_001033308, exon 5 of 6)	exon (NM_001033308, exon 5 of 6)	12877	NM_001033308	230787	Mm.290912	NM_001033308	ENSMUSG00000037731	Themis2	ICB-1	thymocyte selection associated family member 2	protein-coding
mm_14703.1	chr2	142631996	142632007	+	1	NA	intron (NM_001081133, intron 25 of 25)	intron (NM_001081133, intron 25 of 25)	269463	NM_001081133	16558	Mm.251934	NM_001081133	ENSMUSG00000038844	Kif16b	8430434E15Rik|AA623607|AI789011|C80253|C80902|mKIAA1590	kinesin family member 16B	protein-coding
mm_18981.1	chr2	76851675	76851699	-	1	NA	exon (NM_011652, exon 132 of 313)	exon (NM_011652, exon 132 of 313)	130860	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_118100.1	chr13	103920310	103920314	-	1	NA	5' UTR (NM_001289475, exon 1 of 26)	5' UTR (NM_001289475, exon 1 of 26)	274	NM_001289473	59079	Mm.277354	NM_021563	ENSMUSG00000021709	Erbin	1700028E05Rik|Erbb2ip|mKIAA1225	Erbb2 interacting protein	protein-coding
mm_119713.1	chr14	53875960	53875989	+	1	NA	Intergenic	Intergenic	377955	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_129413.1	chr15	78336385	78336406	-	1	NA	exon (NM_007780, exon 3 of 14)	exon (NM_007780, exon 3 of 14)	10405	NM_007780	12983	Mm.235324	NM_007780	ENSMUSG00000071713	Csf2rb	AI848964|AIC2B|Bc|CDw131|Csf2rb1|Csfgmrb|Il3r|Il3rb|Il3rb1|Il5rb	colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage)	protein-coding
mm_71584.1	chr8	54779591	54779610	+	1	NA	5' UTR (NM_001253754, exon 1 of 7)	5' UTR (NM_001253754, exon 1 of 7)	166	NM_001253754	234267	Mm.241700	NM_153581	ENSMUSG00000031517	Gpm6a	Gpm6|M6A	glycoprotein m6a	protein-coding
mm_165078.1	chr19	46349044	46349103	+	1	NA	promoter-TSS (NR_040418)	promoter-TSS (NR_040418)	-85	NR_040418	75579	Mm.436708	NR_040418		2310034G01Rik	-	RIKEN cDNA 2310034G01 gene	ncRNA
mm_35124.1	chr4	11156210	11156224	-	1	NA	promoter-TSS (NM_001199105)	promoter-TSS (NM_001199105)	-224	NM_001199105	60599	Mm.393018	NM_021897	ENSMUSG00000028211	Trp53inp1	2700057G22Rik|SIP|SIP18|SIP27|Stinp|Teap	transformation related protein 53 inducible nuclear protein 1	protein-coding
mm_32675.1	chr4	115775597	115775609	+	1	NA	3' UTR (NM_172698, exon 12 of 12)	3' UTR (NM_172698, exon 12 of 12)	5431	NM_029196	75173	Mm.331798	NM_029196	ENSMUSG00000044556	Tex38	4930544O15Rik|Theg4	testis expressed 38	protein-coding
mm_64815.1	chr7	7121482	7121485	-	1	NA	promoter-TSS (NM_172738)	promoter-TSS (NM_172738)	-7	NM_172738	232853	Mm.23838	NM_172738	ENSMUSG00000062116	Zfp954	5730403M16Rik|8030437F07|AA123315	zinc finger protein 954	protein-coding
mm_117931.1	chr13	99434339	99434400	-	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-21543	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_149050.1	chr19	8837562	8837597	+	1	NA	5' UTR (NM_001136064, exon 1 of 12)	5' UTR (NM_001136064, exon 1 of 12)	112	NM_001136064	14705	Mm.345134	NM_008144	ENSMUSG00000071657	Bscl2	2900097C17Rik|AI046355|Gng3lg	Berardinelli-Seip congenital lipodystrophy 2 (seipin)	protein-coding
mm_98889.1	chr11	97838107	97838119	+	1	NA	3' UTR (NM_010688, exon 7 of 7)	3' UTR (NM_010688, exon 7 of 7)	-2667	NM_001080935	68127	Mm.110270	NM_001080935	ENSMUSG00000050538	B230217C12Rik	AI840637	RIKEN cDNA B230217C12 gene	protein-coding
mm_93572.1	chr10	116581479	116581507	-	1	NA	promoter-TSS (NM_028082)	promoter-TSS (NM_028082)	18	NM_001037848	72068	Mm.351553	NM_028082	ENSMUSG00000020166	Cnot2	2600016M12Rik|2810470K03Rik|AA537049|AA959607|AW557563|C79650	CCR4-NOT transcription complex, subunit 2	protein-coding
mm_9367.1	chr1	172200485	172200502	-	1	NA	exon (NM_001329871, exon 2 of 4)	exon (NM_001329871, exon 2 of 4)	6311	NM_001329871	18611	Mm.544	NM_011063	ENSMUSG00000013698	Pea15a	Mat1|PEA-15|Pea15|Pkcs15	phosphoprotein enriched in astrocytes 15A	protein-coding
mm_32828.1	chr4	117564604	117564642	+	1	NA	exon (NM_080469, exon 3 of 9)	exon (NM_080469, exon 3 of 9)	14258	NM_080469	140546	Mm.235891	NM_080469	ENSMUSG00000033423	Eri3	PINT1|Prnpip1	exoribonuclease 3	protein-coding
mm_66735.1	chr7	46667428	46667435	-	1	NA	promoter-TSS (NM_001276372)	promoter-TSS (NM_001276372)	-54	NM_001276372	21990	Mm.248684	NM_009414	ENSMUSG00000040046	Tph1	Tph	tryptophan hydroxylase 1	protein-coding
mm_34818.1	chr4	154960916	154960930	+	1	NA	promoter-TSS (NM_010419)	promoter-TSS (NM_010419)	0	NM_010419	15208	Mm.137268	NM_010419	ENSMUSG00000048001	Hes5	bHLHb38	hairy and enhancer of split 5 (Drosophila)	protein-coding
mm_12887.1	chr2	84743881	84743909	+	1	NA	Intergenic	Intergenic	-2717	NR_029544	387149		NR_029544	ENSMUSG00000065484	Mir130a	Mirn130|Mirn130a|mir-130a	microRNA 130a	ncRNA
mm_152678.1	chr19	15924929	15925015	-	1	NA	promoter-TSS (NM_001205339)	promoter-TSS (NM_001205339)	87	NM_177420	107272	Mm.289936	NM_177420	ENSMUSG00000024640	Psat1	D8Ertd814e|EPIP|PSA|Psat	phosphoserine aminotransferase 1	protein-coding
mm_135946.1	chr16	74411568	74411628	-	1	NA	promoter-TSS (NM_175549)	promoter-TSS (NM_175549)	-686	NM_175549	268902	Mm.171736	NM_175549	ENSMUSG00000052516	Robo2	2600013A04Rik|9430089E08Rik|BB097918|D230004I22Rik|mKIAA1568	roundabout guidance receptor 2	protein-coding
mm_63042.1	chr7	121089941	121089943	+	1	NA	intron (NM_139310, intron 1 of 28)	L1MEc|LINE|L1	6504	NM_139310	246190	Mm.221073	NM_139310	ENSMUSG00000034990	Otoa	-	otoancorin	protein-coding
mm_19556.1	chr2	98666867	98666889	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	1199221	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_30566.1	chr4	3790309	3790329	+	1	NA	3' UTR (NM_001111096, exon 13 of 13)	3' UTR (NM_001111096, exon 13 of 13)	45336	NM_026147	67427	Mm.21938	NM_026147	ENSMUSG00000028234	Rps20	4632426K06Rik|Dsk4	ribosomal protein S20	protein-coding
mm_134522.1	chr16	19236219	19236251	-	1	NA	Intergenic	L1_Mur2|LINE|L1	50506	NM_146451	258443	Mm.377506	NM_146451	ENSMUSG00000050742	Olfr164	MOR279-2	olfactory receptor 164	protein-coding
mm_121013.1	chr14	79535641	79535654	+	1	NA	intron (NM_001286411, intron 1 of 8)	intron (NM_001286411, intron 1 of 8)	19973	NM_001286411	13709	Mm.20938	NM_007920	ENSMUSG00000036461	Elf1	Elf-1|Sts1|mElf-1|p70	E74-like factor 1	protein-coding
mm_88812.1	chr10	80797954	80797967	+	1	NA	promoter-TSS (NM_013651)	promoter-TSS (NM_013651)	666	NM_023900	78670	Mm.41479	NM_023900	ENSMUSG00000035278	Plekhj1	9530063M10Rik	pleckstrin homology domain containing, family J member 1	protein-coding
mm_115402.1	chr13	113981482	113981495	+	1	NA	intron (NM_172595, intron 4 of 4)	(T)n|Simple_repeat|Simple_repeat	170104	NR_045836	319803	Mm.386896	NM_177004		A430090L17Rik	-	RIKEN cDNA A430090L17 gene	ncRNA
mm_80745.1	chr9	94946062	94946065	+	1	NA	intron (NM_177909, intron 8 of 15)	intron (NM_177909, intron 8 of 15)	194234	NR_106116	102465763		NR_106116	ENSMUSG00000098251	Mir7656	Gm27614|mmu-mir-7656	microRNA 7656	ncRNA
mm_58200.1	chr6	143167078	143167088	-	1	NA	promoter-TSS (NM_029250)	promoter-TSS (NM_029250)	-147	NM_029250	75320	Mm.272548	NM_029250	ENSMUSG00000030275	Etnk1	1110061E11Rik|4930555L11Rik|AI195356|AI841245|C80956|D6Ertd3e|EKI1	ethanolamine kinase 1	protein-coding
mm_72450.1	chr8	83165682	83165695	+	1	NA	5' UTR (NM_001111304, exon 1 of 21)	5' UTR (NM_001111304, exon 1 of 21)	336	NM_027758	71310	Mm.24031	NM_027758	ENSMUSG00000031709	Tbc1d9	4933431N12Rik|AI847101|AW490653|C76116	TBC1 domain family, member 9	protein-coding
mm_158705.1	chrX	162159718	162159732	-	1	NA	promoter-TSS (NM_001290526)	promoter-TSS (NM_001290526)	-284	NM_001290526	195727	Mm.336313	NM_001081052	ENSMUSG00000059493	Nhs	Gm389|Gm48|Nhs1|Xcat	Nance-Horan syndrome (human)	protein-coding
mm_97370.1	chr11	77685754	77685782	+	1	NA	promoter-TSS (NM_001024205)	promoter-TSS (NM_001024205)	-371	NM_001024205	68564	Mm.428996	NM_001024205	ENSMUSG00000037857	Nufip2	1110001M19Rik|9530056D24Rik|AI256692|AI461731|PIG1|mKIAA1321	nuclear fragile X mental retardation protein interacting protein 2	protein-coding
mm_31495.1	chr4	53227339	53227378	+	1	NA	Intergenic	Intergenic	-18838	NR_040665	78180	Mm.243847	NR_040665	ENSMUSG00000086947	4930522O17Rik	-	RIKEN cDNA 4930522O17 gene	ncRNA
mm_81197.1	chr9	107554686	107554763	+	1	NA	5' UTR (NM_019713, exon 1 of 5)	5' UTR (NM_019713, exon 1 of 5)	141	NM_019713	56289	Mm.12091	NM_019713	ENSMUSG00000010067	Rassf1	123F2|AA536941|AU044980|NORE2A|RDA32|REH3P21|Rassf1A|Rassf1B|Rassf1C	Ras association (RalGDS/AF-6) domain family member 1	protein-coding
mm_108136.1	chr12	76104840	76104864	+	1	NA	intron (NM_001005510, intron 109 of 115)	intron (NM_001005510, intron 109 of 115)	72407	NM_010157	13983	Mm.2561	NM_010157	ENSMUSG00000021055	Esr2	ER[b]|ERbeta|Estrb	estrogen receptor 2 (beta)	protein-coding
mm_164265.1	chr15	100819562	100819603	+	1	NA	3' UTR (NM_021530, exon 25 of 25)	3' UTR (NM_021530, exon 25 of 25)	38328	NM_001347102	59033	Mm.209856	NM_021530	ENSMUSG00000023032	Slc4a8	AW493845|C230026C11|NDCBE|kNBC-3	solute carrier family 4 (anion exchanger), member 8	protein-coding
mm_1943.1	chr1	86303454	86303482	+	1	NA	5' UTR (NM_145222, exon 1 of 2)	5' UTR (NM_145222, exon 1 of 2)	247	NM_145222	227327	Mm.86467	NM_145222	ENSMUSG00000079445	B3gnt7	C330001H22Rik|beta-3GnT7	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 7	protein-coding
mm_6851.1	chr1	84251306	84251343	-	1	NA	intron (NM_001003948, intron 1 of 2)	Lx8|LINE|L1	-32363	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_11875.1	chr2	49451489	49451559	+	1	NA	promoter-TSS (NM_172663)	promoter-TSS (NM_172663)	38	NM_172663	227867	Mm.29167	NM_172663	ENSMUSG00000069495	Epc2	5830499L14|D2Ertd694e	enhancer of polycomb homolog 2 (Drosophila)	protein-coding
mm_160082.1	chr7	13329322	13329322	+	1	NA	promoter-TSS (NM_001004762)	promoter-TSS (NM_001004762)	0	NM_001004762	232889	Mm.223639	NM_001004762	ENSMUSG00000033847	Pla2g4c	D7Ertd445e	phospholipase A2, group IVC (cytosolic, calcium-independent)	protein-coding
mm_137230.1	chr17	24352038	24352149	+	1	NA	promoter-TSS (NM_001039581)	promoter-TSS (NM_001039581)	70	NM_001039581	27410	Mm.239470	NM_013855	ENSMUSG00000024130	Abca3	1810036E22Rik|ABC-C|Abc3	ATP-binding cassette, sub-family A (ABC1), member 3	protein-coding
mm_105257.1	chr11	102356211	102356240	-	1	NA	exon (NM_011403, exon 13 of 20)	exon (NM_011403, exon 13 of 20)	9056	NM_011403	20533	Mm.7248	NM_011403	ENSMUSG00000006574	Slc4a1	Ae1|CD233|Empb3|l11Jus51	solute carrier family 4 (anion exchanger), member 1	protein-coding
mm_55468.1	chr6	68736785	68736800	-	1	NA	Intergenic	Intergenic	590382	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_42176.1	chr5	112261803	112261853	+	1	NA	intron (NM_023695, intron 3 of 5)	(TCCA)n|Simple_repeat|Simple_repeat	6008	NM_001312893	12960	Mm.29488	NM_023695	ENSMUSG00000029343	Crybb1	3110006K12Rik|BB1CRY	crystallin, beta B1	protein-coding
mm_102934.1	chr11	69601020	69601030	-	1	NA	3' UTR (NM_013415, exon 7 of 7)	3' UTR (NM_013415, exon 7 of 7)	4935	NM_013415	11932	Mm.235204	NM_013415	ENSMUSG00000041329	Atp1b2	Amog|Atpb-2	ATPase, Na+/K+ transporting, beta 2 polypeptide	protein-coding
mm_21836.1	chr2	165792844	165792855	-	1	NA	exon (NM_001281926, exon 20 of 23)	exon (NM_001281926, exon 20 of 23)	65324	NM_001252585	228880	Mm.227598	NM_027230	ENSMUSG00000039671	Zmynd8	1110013E22Rik|2010005I16Rik|3632413B07Rik|AI316811|AL024039|Prkcbp1|RACK7	zinc finger, MYND-type containing 8	protein-coding
mm_15820.1	chr2	164563317	164563340	+	1	NA	exon (NM_026323, exon 2 of 5)	exon (NM_026323, exon 2 of 5)	612	NM_026323	67701	Mm.27289	NM_026323	ENSMUSG00000017723	Wfdc2	1600023A02Rik|HE4|WAP5	WAP four-disulfide core domain 2	protein-coding
mm_62659.1	chr7	107722910	107722928	+	1	NA	intron (NM_001163557, intron 13 of 25)	intron (NM_001163557, intron 13 of 25)	35113	NM_001205227	320635	Mm.132828	NM_177216	ENSMUSG00000048065	Cyb5r2	D630003K02Rik|b5R.2	cytochrome b5 reductase 2	protein-coding
mm_29478.1	chr3	115711265	115711281	-	1	NA	3' UTR (NM_007901, exon 2 of 2)	3' UTR (NM_007901, exon 2 of 2)	3782	NM_007901	13609	Mm.982	NM_007901	ENSMUSG00000045092	S1pr1	AI849002|Edg1|Lpb1|S1p|S1p1	sphingosine-1-phosphate receptor 1	protein-coding
mm_78600.1	chr9	37489024	37489050	+	1	NA	promoter-TSS (NM_146222)	promoter-TSS (NM_146222)	-284	NM_146222	235184	Mm.127892	NM_146222	ENSMUSG00000042138	Msantd2	2810450G17Rik|9530092B10Rik	Myb/SANT-like DNA-binding domain containing 2	protein-coding
mm_32174.1	chr4	100479177	100479181	+	1	NA	5' UTR (NM_001033773, exon 1 of 10)	5' UTR (NM_001033773, exon 1 of 10)	312	NM_001033773	381534	Mm.318133	NM_001033773	ENSMUSG00000069733	Ube2u	-	ubiquitin-conjugating enzyme E2U (putative)	protein-coding
mm_42752.1	chr5	120812674	120812684	+	1	NA	promoter-TSS (NR_003507)	promoter-TSS (NR_003507)	41	NM_001083925	23961	Mm.233471	NM_001083925	ENSMUSG00000029605	Oas1b	Flv|L1|Mmu-L1|Oas1|Oias-2|Oias2|Wnv	2'-5' oligoadenylate synthetase 1B	protein-coding
mm_1413.1	chr1	67156895	67156903	+	1	NA	exon (NM_001080809, exon 9 of 38)	exon (NM_001080809, exon 9 of 38)	33872	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_170884.1	chr2	22164894	22164897	-	1	NA	Intergenic	L1Md_T|LINE|L1	-62608	NM_148413	667663	Mm.330033	NM_148413	ENSMUSG00000025716	Myo3a	9030416P08Rik	myosin IIIA	protein-coding
mm_108912.1	chr12	100206602	100206636	+	1	NA	3' UTR (NM_009790, exon 6 of 6)	3' UTR (NM_009790, exon 6 of 6)	6475	NM_001313934	12313	Mm.285993	NM_009790	ENSMUSG00000001175	Calm1	AI256814|AI327027|AI461935|AL024000|CaM|Calm	calmodulin 1	protein-coding
mm_150715.1	chr19	43440405	43440447	+	1	NA	promoter-TSS (NM_031396)	promoter-TSS (NM_031396)	-10	NM_031396	83674	Mm.329864	NM_031396	ENSMUSG00000025189	Cnnm1	AI846314|Acdp1|CLP-1	cyclin M1	protein-coding
mm_89952.1	chr10	111293271	111293281	+	1	NA	3' UTR (NM_001003717, exon 23 of 23)	3' UTR (NM_001003717, exon 23 of 23)	-5403	NM_027914	71769	Mm.45256	NM_027914	ENSMUSG00000035759	Bbs10	1300007O09Rik|AI452285	Bardet-Biedl syndrome 10 (human)	protein-coding
mm_153697.1	chr19	44397467	44397487	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	10232	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_155692.1	chrX	94234922	94234972	+	1	NA	promoter-TSS (NM_153165)	promoter-TSS (NM_153165)	17	NM_001039061	236904	Mm.115533	NM_153165	ENSMUSG00000043929	Klhl15	6330500C13Rik	kelch-like 15	protein-coding
mm_128236.1	chr15	36608485	36608513	-	1	NA	exon (NM_008774, exon 1 of 15)	exon (NM_008774, exon 1 of 15)	474	NM_008774	18458	Mm.371570	NM_008774	ENSMUSG00000022283	Pabpc1	PABP|Pabp1|PabpI|Pabpl1|ePAB	poly(A) binding protein, cytoplasmic 1	protein-coding
mm_133180.1	chr16	72563509	72563540	+	1	NA	Intergenic	Intergenic	-99625	NM_019413	19876	Mm.310772	NM_019413	ENSMUSG00000022883	Robo1	AW494633|AW742721|DUTT1|Gm310	roundabout guidance receptor 1	protein-coding
mm_75642.1	chr8	65018580	65018588	-	1	NA	5' UTR (NM_001177551, exon 1 of 2)	5' UTR (NM_001177551, exon 1 of 2)	104	NM_153097	234329	Mm.28010	NM_153097	ENSMUSG00000053490	Trim60	2czf45|Rnf33	tripartite motif-containing 60	protein-coding
mm_136753.1	chr17	8565488	8565494	+	1	NA	intron (NM_001290707, intron 1 of 22)	intron (NM_001290707, intron 1 of 22)	38690	NM_001290707	23984	Mm.87161	NM_011866	ENSMUSG00000023868	Pde10a	-	phosphodiesterase 10A	protein-coding
mm_147880.1	chr18	64660824	64660915	-	1	NA	5' UTR (NM_001001488, exon 1 of 28)	5' UTR (NM_001001488, exon 1 of 28)	131	NM_001001488	54670	Mm.270043	NM_001001488	ENSMUSG00000039529	Atp8b1	AI451886|FIC1|Ic	ATPase, class I, type 8B, member 1	protein-coding
mm_87279.1	chr10	41910888	41910890	+	1	NA	Intergenic	L1MB3|LINE|L1	23450	NM_001013370	140742	Mm.139418	NM_001013370	ENSMUSG00000038332	Sesn1	1110002G11Rik|AU044290|Pa26|Sest1	sestrin 1	protein-coding
mm_5114.1	chr1	6383048	6383058	-	1	NA	intron (NM_001195732, intron 1 of 4)	CpG	23722	NM_001195732	620393	Mm.388992	NM_001195732	ENSMUSG00000087247	Fam150a	EG620393	family with sequence similarity 150, member A	protein-coding
mm_148946.1	chr19	7265172	7265182	+	1	NA	Intergenic	Intergenic	-2217	NM_054048	104383	Mm.283859	NM_054048	ENSMUSG00000024968	Rcor2	1A13|AW122124|CoREST|Rcor|Rcor1	REST corepressor 2	protein-coding
mm_147650.1	chr18	60501668	60501677	-	1	NA	5' UTR (NM_134133, exon 1 of 2)	5' UTR (NM_134133, exon 1 of 2)	311	NM_134133	106878	Mm.273197	NM_134133	ENSMUSG00000038059	Smim3	2010002N04Rik|AI195350|AW561905|Nid67|cI-41	small integral membrane protein 3	protein-coding
mm_164149.1	chr15	62339523	62339524	-	1	NA	Intergenic	Intergenic	-120072	NR_003523	67552	Mm.484027	NM_026230		H2afy3	4933432H23Rik	H2A histone family, member Y3	pseudo
mm_159476.1	chr4	32923493	32923493	-	1	NA	promoter-TSS (NM_080471)	promoter-TSS (NM_080471)	12	NM_080471	140577	Mm.214766	NM_080471	ENSMUSG00000040183	Ankrd6	-	ankyrin repeat domain 6	protein-coding
mm_8750.1	chr1	160307401	160307419	-	1	NA	intron (NM_001038621, intron 2 of 8)	intron (NM_001038621, intron 2 of 8)	-11438	NR_035448	100316784		NR_035448	ENSMUSG00000089204	Mir1927	mmu-mir-1927	microRNA 1927	ncRNA
mm_134555.1	chr16	20241265	20241274	-	1	NA	promoter-TSS (NM_198599)	promoter-TSS (NM_198599)	89	NM_198599	208158	Mm.326383	NM_198599	ENSMUSG00000041205	Map6d1	A330066I15Rik	MAP6 domain containing 1	protein-coding
mm_93769.1	chr10	120201559	120201575	-	1	NA	promoter-TSS (NM_028679)	promoter-TSS (NM_028679)	-30	NM_028679	73914	Mm.146194	NM_028679	ENSMUSG00000020227	Irak3	4833428C18Rik|AI563835|IRAK-M	interleukin-1 receptor-associated kinase 3	protein-coding
mm_90274.1	chr10	122782698	122782713	+	1	NA	intron (NM_176919, intron 2 of 8)	(T)n|Simple_repeat|Simple_repeat	103390	NR_106182	102466884		NR_106182	ENSMUSG00000099225	Mir8104	Gm27380|mmu-mir-8104	microRNA 8104	ncRNA
mm_166923.1	chr7	31035461	31035485	-	1	NA	intron (NM_008761, intron 6 of 8)	intron (NM_008761, intron 6 of 8)	4844	NR_106017	102465635		NR_106017	ENSMUSG00000098783	Mir7050	Gm27578|mmu-mir-7050	microRNA 7050	ncRNA
mm_55386.1	chr6	59017071	59017108	-	1	NA	intron (NM_153574, intron 1 of 17)	intron (NM_153574, intron 1 of 17)	7413	NM_153574	58909	Mm.28813	NM_153574	ENSMUSG00000037709	Fam13a	AI462012|D430015B01Rik|FAM13A1|Precm1	family with sequence similarity 13, member A	protein-coding
mm_173120.1	chrX	162703290	162703291	-	1	NA	intron (NR_038088, intron 4 of 5)	(CTG)n|Simple_repeat|Simple_repeat	-57082	NM_009031	245688	Mm.270186	NM_009031	ENSMUSG00000031353	Rbbp7	AA409861|AI173248|AU019541|BB114024|mRbAp46	retinoblastoma binding protein 7	protein-coding
mm_109407.1	chr12	110447203	110447207	+	1	NA	promoter-TSS (NM_001135001)	promoter-TSS (NM_001135001)	26	NM_001135001	26931	Mm.240396	NM_012023	ENSMUSG00000017843	Ppp2r5c	2610043M05Rik|2700063L20Rik|AI060890|AW545884|C85228|D12Bwg0916e|mKIAA0044	protein phosphatase 2, regulatory subunit B', gamma	protein-coding
mm_164902.1	chr18	67470465	67470466	+	1	NA	intron (NM_144867, intron 1 of 6)	intron (NM_144867, intron 1 of 6)	5616	NM_144867	225655	Mm.221420	NM_144867	ENSMUSG00000024530	Slmo1	A230074A19Rik|BC019561|Prelid3a	slowmo homolog 1 (Drosophila)	protein-coding
mm_91323.1	chr10	25200111	25200178	-	1	NA	promoter-TSS (NM_001347460)	promoter-TSS (NM_001347460)	26	NM_001347460	432442	Mm.485937	NM_018747	ENSMUSG00000039166	Akap7	6430401D08|AI662165|AKAP15|Akap18|BB170514	A kinase (PRKA) anchor protein 7	protein-coding
mm_75707.1	chr8	68896664	68896725	-	1	NA	exon (NM_008509, exon 6 of 10)	exon (NM_008509, exon 6 of 10)	16139	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_28072.1	chr3	84304679	84304692	-	1	NA	promoter-TSS (NM_001271726)	promoter-TSS (NM_001271726)	90	NM_001271726	80890	Mm.44876	NM_030706	ENSMUSG00000027993	Trim2	mKIAA0517|narf	tripartite motif-containing 2	protein-coding
mm_61047.1	chr7	49778455	49778471	+	1	NA	5' UTR (NM_133740, exon 1 of 16)	5' UTR (NM_133740, exon 1 of 16)	105	NM_133740	71974	Mm.33202	NM_133740	ENSMUSG00000030505	Prmt3	2010005E20Rik|2410018A17Rik|AL033309|Hrmt1l3	protein arginine N-methyltransferase 3	protein-coding
mm_78363.1	chr9	26879678	26879682	+	1	NA	3' UTR (NM_001281475, exon 21 of 21)	3' UTR (NM_001281475, exon 21 of 21)	-18857	NM_001113323	70893	Mm.78118	NM_001113323	ENSMUSG00000031966	Glb1l3	4921509F24Rik	galactosidase, beta 1 like 3	protein-coding
mm_26789.1	chr3	9705001	9705004	-	1	NA	intron (NM_001195031, intron 4 of 8)	intron (NM_001195031, intron 4 of 8)	-94917	NM_133218	170753	Mm.212908	NM_133218	ENSMUSG00000040209	Zfp704	C030026M03|C030034L19Rik|Gig1|Znf704	zinc finger protein 704	protein-coding
mm_95045.1	chr11	32284305	32284343	+	1	NA	exon (NM_008218, exon 3 of 3)	exon (NM_008218, exon 3 of 3)	649	NM_001083955	110257	Mm.196110	NM_001083955	ENSMUSG00000069917	Hba-a2	-	hemoglobin alpha, adult chain 2	protein-coding
mm_97775.1	chr11	82101837	82101849	+	1	NA	promoter-TSS (NM_011331)	promoter-TSS (NM_011331)	-2	NM_011331	20293	Mm.867	NM_011331	ENSMUSG00000035352	Ccl12	MCP-5|Scya12	chemokine (C-C motif) ligand 12	protein-coding
mm_106542.1	chr11	120579106	120579143	-	1	NA	3' UTR (NM_133796, exon 6 of 6)	3' UTR (NM_133796, exon 6 of 6)	2496	NM_133796	192662	Mm.30016	NM_133796	ENSMUSG00000025132	Arhgdia	5330430M07Rik|Gdi-1|Rho-GDI|RhoDGI|RhoGDI-1	Rho GDP dissociation inhibitor (GDI) alpha	protein-coding
mm_88325.1	chr10	75566258	75566302	+	1	NA	Intergenic	Intergenic	-2382	NM_001305992	14598	Mm.4559	NM_008116	ENSMUSG00000006345	Ggt1	CD224|GGT|GGT 1|GGT-1|Ggtp|dwg	gamma-glutamyltransferase 1	protein-coding
mm_122696.1	chr14	52080194	52080198	-	1	NA	intron (NM_016884, intron 5 of 8)	B1_Mus2|SINE|Alu	10881	NR_028552	100217457		NR_028552	ENSMUSG00000064871	Snord58b	MBII-199	small nucleolar RNA, C/D box 58B	snoRNA
mm_118986.1	chr14	28504679	28504689	+	1	NA	promoter-TSS (NM_009524)	promoter-TSS (NM_009524)	-789	NM_009524	22418	Mm.287544	NM_009524	ENSMUSG00000021994	Wnt5a	8030457G12Rik|Wnt-5a	wingless-type MMTV integration site family, member 5A	protein-coding
mm_53455.1	chr6	134791481	134791500	+	1	NA	intron (NM_001048054, intron 1 of 6)	intron (NM_001048054, intron 1 of 6)	1138	NM_130447	70686	Mm.491182	NM_130447	ENSMUSG00000030203	Dusp16	3830417M17Rik|AW558566|D6Ertd213e|MKP-7|MKP7|Mkpm	dual specificity phosphatase 16	protein-coding
mm_19984.1	chr2	118545311	118545344	-	1	NA	promoter-TSS (NR_138603)	promoter-TSS (NR_138603)	-740	NR_138603	171543	Mm.210125	NM_138313	ENSMUSG00000040093	Bmf	AW260063|AW411872	BCL2 modifying factor	protein-coding
mm_19506.1	chr2	93822538	93822581	-	1	NA	promoter-TSS (NM_010163)	promoter-TSS (NM_010163)	9	NM_010163	14043	Mm.4336	NM_010163	ENSMUSG00000027198	Ext2	AI893565	exostoses (multiple) 2	protein-coding
mm_89628.1	chr10	96371263	96371270	+	1	NA	Intergenic	Intergenic	145059	NR_110448	74881	Mm.410819	NR_110448		4930459C07Rik	-	RIKEN cDNA 4930459C07 gene	ncRNA
mm_16972.1	chr2	17731416	17731449	-	1	NA	promoter-TSS (NM_028757)	promoter-TSS (NM_028757)	-364	NM_028757	74103	Mm.120298	NM_028757	ENSMUSG00000053702	Nebl	1200007O21Rik|A630080F05Rik|BB140644|D830029A09Rik|Lnebl	nebulette	protein-coding
mm_63608.1	chr7	128188556	128188557	+	1	NA	intron (NM_001029872, intron 11 of 30)	intron (NM_001029872, intron 11 of 30)	14610	NM_001029872	381924	Mm.334257	NM_001029872	ENSMUSG00000070369	Itgad	Cd11d	integrin, alpha D	protein-coding
mm_94880.1	chr11	24319967	24319970	+	1	NA	Intergenic	MER20|DNA|hAT-Charlie	-161941	NR_045857	71316	Mm.79162	NR_045857	ENSMUSG00000086892	4933430M04Rik	-	RIKEN cDNA 4933430M04 gene	ncRNA
mm_45021.1	chr5	38561626	38561640	-	1	NA	promoter-TSS (NM_011715)	promoter-TSS (NM_011715)	-38	NM_011715	22388	Mm.2654	NM_011715	ENSMUSG00000005103	Wdr1	Aip1|D5Wsu185e|rede	WD repeat domain 1	protein-coding
mm_52974.1	chr6	123253133	123253142	+	1	NA	Intergenic	Intergenic	-8970	NM_001163161	17474	Mm.441101	NM_010819	ENSMUSG00000030144	Clec4d	Clecsf8|Mpcl|mcl	C-type lectin domain family 4, member d	protein-coding
mm_34809.1	chr4	154928229	154928274	+	1	NA	promoter-TSS (NM_178931)	promoter-TSS (NM_178931)	-174	NM_178931	230979	Mm.215147	NM_178931	ENSMUSG00000042333	Tnfrsf14	Atar|HveA|Hvem|Tnfrs14	tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)	protein-coding
mm_163651.1	chr13	65052381	65052386	-	1	NA	Intergenic	Intergenic	19325	NM_001083890	238683	Mm.295543	NM_001083890	ENSMUSG00000074849	Spata31d1c	4932441B19Rik|Fam75d1c	spermatogenesis associated 31 subfamily D, member 1C	protein-coding
mm_156549.1	chrX	151521147	151521206	+	1	NA	5' UTR (NM_001113354, exon 1 of 22)	5' UTR (NM_001113354, exon 1 of 22)	504	NM_001113354	320595	Mm.17156	NM_177201	ENSMUSG00000041229	Phf8	9830141C09Rik|mKIAA1111	PHD finger protein 8	protein-coding
mm_23885.1	chr3	83031171	83031188	+	1	NA	exon (NM_010196, exon 5 of 5)	exon (NM_010196, exon 5 of 5)	5026	NM_001111048	14161	Mm.88793	NM_010196	ENSMUSG00000028001	Fga	ENSMUSG00000059807|Fib	fibrinogen alpha chain	protein-coding
mm_144360.1	chr18	20310739	20310757	+	1	NA	promoter-TSS (NM_010079)	promoter-TSS (NM_010079)	-125	NM_010079	13510	Mm.37953	NM_010079	ENSMUSG00000069441	Dsg1a	DG1|DGI|Dsg1|dsg1-alpha	desmoglein 1 alpha	protein-coding
mm_99080.1	chr11	99389048	99389062	+	1	NA	exon (NM_010660, exon 1 of 8)	exon (NM_010660, exon 1 of 8)	309	NM_010660	16661	Mm.22662	NM_010660	ENSMUSG00000019761	Krt10	D130054E02Rik|K10|K1C1|Krt-1.10|Krt1-10	keratin 10	protein-coding
mm_157478.1	chrX	48147907	48147946	-	1	NA	intron (NM_001313749, intron 1 of 7)	intron (NM_001313749, intron 1 of 7)	1490	NM_028773	74131	Mm.276131	NM_028773	ENSMUSG00000031101	Sash3	1200013B08Rik|AW413946|SLY1	SAM and SH3 domain containing 3	protein-coding
mm_41770.1	chr5	103501557	103501570	+	1	NA	exon (NM_011204, exon 7 of 48)	exon (NM_011204, exon 7 of 48)	76371	NM_011204	19249	Mm.3414	NM_011204	ENSMUSG00000034573	Ptpn13	AI324989|PTP-BL|PTPL1|Ptpri|RIP	protein tyrosine phosphatase, non-receptor type 13	protein-coding
mm_130840.1	chr15	101869696	101869712	-	1	NA	promoter-TSS (NM_001003667)	promoter-TSS (NM_001003667)	-86	NM_001003667	406220	Mm.292992	NM_001003667	ENSMUSG00000067594	Krt77	4732484G22Rik|K1emb|Krt239|mK1b	keratin 77	protein-coding
mm_51180.1	chr6	70726826	70726832	+	1	NA	Intergenic	Intergenic	65346	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_48739.1	chr5	147637493	147637503	-	1	NA	intron (NM_010228, intron 13 of 29)	intron (NM_010228, intron 13 of 29)	88490	NM_010228	14254	Mm.389712	NM_010228	ENSMUSG00000029648	Flt1	AI323757|Flt-1|VEGFR-1|VEGFR1|sFlt1	FMS-like tyrosine kinase 1	protein-coding
mm_90885.1	chr10	9901161	9901250	-	1	NA	promoter-TSS (NM_001081344)	promoter-TSS (NM_001081344)	-165	NM_001081344	78808	Mm.331751	NM_030191	ENSMUSG00000019790	Stxbp5	0710001E20Rik|4930565N16Rik|AW742610|LGL3|mKIAA1006	syntaxin binding protein 5 (tomosyn)	protein-coding
mm_96808.1	chr11	69991584	69991630	+	1	NA	5' UTR (NM_019749, exon 1 of 4)	5' UTR (NM_019749, exon 1 of 4)	237	NM_019749	56486	Mm.272460	NM_019749	ENSMUSG00000018567	Gabarap	-	gamma-aminobutyric acid receptor associated protein	protein-coding
mm_141437.1	chr17	29549632	29549643	-	1	NA	promoter-TSS (NM_001162901)	promoter-TSS (NM_001162901)	-44	NM_001162902	71138	Mm.158581	NM_001162901	ENSMUSG00000079580	Tmem217	4933413N12Rik|EG622644	transmembrane protein 217	protein-coding
mm_57474.1	chr6	125233056	125233065	-	1	NA	3' UTR (NM_001042564, exon 4 of 4)	3' UTR (NM_001042564, exon 4 of 4)	-1200	NM_145391	213233	Mm.296902	NM_145391	ENSMUSG00000038213	Tapbpl	BC017613|TAPBPL-R|Tapbplr	TAP binding protein-like	protein-coding
mm_12835.1	chr2	80638845	80638856	+	1	NA	promoter-TSS (NM_027091)	promoter-TSS (NM_027091)	38	NM_027091	69482	Mm.29200	NM_027091	ENSMUSG00000026999	Nup35	2310006I24Rik|35kDa|5330402E05Rik|MP44|NO44	nucleoporin 35	protein-coding
mm_44428.1	chr5	20945535	20945546	-	1	NA	intron (NM_001080977, intron 1 of 7)	MLT1B|LTR|ERVL-MaLR	-5449	NR_030699	320770	Mm.491217	NR_030699	ENSMUSG00000101013	A630072M18Rik	Aptr	RIKEN cDNA A630072M18 gene	ncRNA
mm_170546.1	chr19	40125620	40125627	+	1	NA	Intergenic	MMERVK9C_I-int|LTR|ERVK	35944	NM_001167875	107141	Mm.474575	NM_134144	ENSMUSG00000054827	Cyp2c50	AI266900	cytochrome P450, family 2, subfamily c, polypeptide 50	protein-coding
mm_32117.1	chr4	99030947	99030961	+	1	NA	promoter-TSS (NM_013913)	promoter-TSS (NM_013913)	0	NM_013913	30924	Mm.28341	NM_013913	ENSMUSG00000028553	Angptl3	hypl	angiopoietin-like 3	protein-coding
mm_108972.1	chr12	102561828	102561840	+	1	NA	exon (NM_007693, exon 6 of 8)	exon (NM_007693, exon 6 of 8)	6893	NM_007693	12652	Mm.4137	NM_007693	ENSMUSG00000021194	Chga	ChrA|cgA	chromogranin A	protein-coding
mm_109002.1	chr12	103314858	103314892	+	1	NA	promoter-TSS (NM_001195726)	promoter-TSS (NM_001195726)	-84	NM_001195726	100504156	Mm.425749	NM_001195726	ENSMUSG00000096753	Fam181a	EG544888	family with sequence similarity 181, member A	protein-coding
mm_121649.1	chr14	10176659	10176660	-	1	NA	intron (NM_001308286, intron 2 of 6)	ORR1E-int|LTR|ERVL-MaLR	276799	NM_001308286	14198	Mm.397619	NM_010210	ENSMUSG00000060579	Fhit	AW045638|Fra14A2	fragile histidine triad gene	protein-coding
mm_140874.1	chr17	23804015	23804027	-	1	NA	intron (NM_175229, intron 1 of 13)	intron (NM_175229, intron 1 of 13)	834	NM_175229	75956	Mm.5222	NM_175229	ENSMUSG00000039218	Srrm2	5033413A03Rik|AA410130|SRm300|mKIAA0324	serine/arginine repetitive matrix 2	protein-coding
mm_95688.1	chr11	54304140	54304157	+	1	NA	promoter-TSS (NM_144823)	promoter-TSS (NM_144823)	-56	NM_144823	216739	Mm.267478	NM_144823	ENSMUSG00000020333	Acsl6	A330035H04Rik|AW050338|Facl6|LACS|Lacsl|mKIAA0837	acyl-CoA synthetase long-chain family member 6	protein-coding
mm_144804.1	chr18	36281349	36281386	+	1	NA	5' UTR (NM_008989, exon 1 of 2)	5' UTR (NM_008989, exon 1 of 2)	205	NM_008989	19290	Mm.231802	NM_008989	ENSMUSG00000043991	Pura	CAGER-1|Pur-alpha|ssCRE-BP	purine rich element binding protein A	protein-coding
mm_7565.1	chr1	124759920	124759930	-	1	NA	Intergenic	Intergenic	675802	NM_023735	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding
mm_169779.1	chr16	11144013	11144015	+	1	NA	intron (NR_027502, intron 19 of 22)	LSU-rRNA_Hsa|rRNA|rRNA	-9482	NM_029582	106200	Mm.291015	NM_029582	ENSMUSG00000022498	Txndc11	2810408E11Rik|AI427833|EFP1|Txdc11	thioredoxin domain containing 11	protein-coding
mm_112871.1	chr13	20852790	20852800	+	1	NA	TTS (NM_001281854)	TTS (NM_001281854)	58682	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_131115.1	chr16	5375083	5375095	+	1	NA	Intergenic	Intergenic	-119133	NM_027446	70511	Mm.45780	NM_027446	ENSMUSG00000022544	Eef2kmt	5730409G15Rik|Fam86|Fam86a|eEF2-KMT	eukaryotic elongation factor 2 lysine methyltransferase	protein-coding
mm_41255.1	chr5	88825181	88825184	+	1	NA	Intergenic	Intergenic	60169	NM_007832	13178	Mm.298892	NM_007832	ENSMUSG00000029366	Dck	-	deoxycytidine kinase	protein-coding
mm_99243.1	chr11	101078438	101078446	+	1	NA	promoter-TSS (NM_010475)	promoter-TSS (NM_010475)	31	NM_010475	15485	Mm.188939	NM_010475	ENSMUSG00000019301	Hsd17b1	17HSDB1|17beta-HSD|E2DH|Hsd17ba	hydroxysteroid (17-beta) dehydrogenase 1	protein-coding
mm_111837.1	chr12	107913500	107913510	-	1	NA	3' UTR (NM_021399, exon 3 of 3)	3' UTR (NM_021399, exon 3 of 3)	89909	NM_001079883	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_155339.1	chrX	67458188	67458198	+	1	NA	Intergenic	LTR101_Mam|LTR|ERVL	235369	NM_001126317	382217	Mm.422933	NM_001126317	ENSMUSG00000079578	Gm1140	-	predicted gene 1140	protein-coding
mm_51260.1	chr6	72097404	72097418	+	1	NA	promoter-TSS (NM_011375)	promoter-TSS (NM_011375)	-197	NM_001035228	20454	Mm.38248	NM_011375	ENSMUSG00000056091	St3gal5	3S-T|Siat9|[a]2	ST3 beta-galactoside alpha-2,3-sialyltransferase 5	protein-coding
mm_40252.1	chr5	38220578	38220588	+	1	NA	promoter-TSS (NM_029162)	promoter-TSS (NM_029162)	101	NM_025281	17089	Mm.28560	NM_025281	ENSMUSG00000067367	Lyar	MLZ-264	Ly1 antibody reactive clone	protein-coding
mm_133332.1	chr16	78694986	78694991	+	1	NA	Intergenic	Lx8|LINE|L1	-118300	NM_025967	67102	Mm.37332	NM_025967	ENSMUSG00000022864	D16Ertd472e	1700010I10Rik|2310009O17Rik|E330003K22Rik|Eurl	DNA segment, Chr 16, ERATO Doi 472, expressed	protein-coding
mm_70064.1	chr7	142652297	142652318	-	1	NA	3' UTR (NM_010514, exon 4 of 4)	3' UTR (NM_010514, exon 4 of 4)	2689	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_58275.1	chr6	145434933	145434953	-	1	NA	promoter-TSS (NM_028742)	promoter-TSS (NM_028742)	-18	NM_028742	74071	Mm.441497	NM_028742	ENSMUSG00000054966	Lmntd1	4933403M22Rik|AI482300|Ifltd1|Lmna-rs1|Lmna1|OTTMUSG00000022798	lamin tail domain containing 1	protein-coding
mm_4643.1	chr1	180072459	180072482	+	1	NA	exon (NM_001033285, exon 10 of 37)	exon (NM_001033285, exon 10 of 37)	111381	NM_001033285	226751	Mm.259655	NM_001033285	ENSMUSG00000026490	Cdc42bpa	A930014J19Rik|DMPK-like	CDC42 binding protein kinase alpha	protein-coding
mm_77113.1	chr8	111081899	111081916	-	1	NA	promoter-TSS (NM_181549)	promoter-TSS (NM_181549)	-199	NM_181549	353287	Mm.135495	NM_181549	ENSMUSG00000033633	Clec18a	Mrcl	C-type lectin domain family 18, member A	protein-coding
mm_37925.1	chr4	132843112	132843184	-	1	NA	promoter-TSS (NM_001290725)	promoter-TSS (NM_001290725)	21	NM_001290725	100336	Mm.105230	NM_146154	ENSMUSG00000028882	Ppp1r8	6330548N22Rik|AU044684|NIPP1	protein phosphatase 1, regulatory (inhibitor) subunit 8	protein-coding
mm_138251.1	chr17	34590116	34590142	+	1	NA	5' UTR (NM_134116, exon 1 of 4)	5' UTR (NM_134116, exon 1 of 4)	323	NM_134116	106512	Mm.26584	NM_134116	ENSMUSG00000034786	Gpsm3	AA960287|AGS4	G-protein signalling modulator 3 (AGS3-like, C. elegans)	protein-coding
mm_152641.1	chr19	12526424	12526441	-	1	NA	Intergenic	L1MC3|LINE|L1	-24436	NM_172442	207521	Mm.247695	NM_172442	ENSMUSG00000039982	Dtx4	AI449438|BC044798|D930042H13|RNF155	deltex 4, E3 ubiquitin ligase	protein-coding
mm_6820.1	chr1	84194237	84194247	-	1	NA	intron (NM_001003948, intron 1 of 2)	B4|SINE|B4	24719	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_16373.1	chr2	178119167	178119183	+	1	NA	5' UTR (NM_001177790, exon 1 of 13)	5' UTR (NM_001177790, exon 1 of 13)	200	NM_001177790	74189	Mm.44413	NM_028806	ENSMUSG00000027525	Phactr3	1500003N10Rik|4930415A02Rik|H17739|Scapin1|Scapinin|mKIAA4224	phosphatase and actin regulator 3	protein-coding
mm_92793.1	chr10	81349228	81349240	-	1	NA	intron (NM_001163165, intron 3 of 9)	intron (NM_001163165, intron 3 of 9)	1192	NM_001163165	15353	Mm.38474	NM_010440	ENSMUSG00000020232	Hmg20b	AW610687|BRAF35|Hmgx2|Hmgxb2|Smarce1r	high mobility group 20B	protein-coding
mm_61727.1	chr7	81859289	81859297	+	1	NA	non-coding (NR_111910, exon 1 of 8)	non-coding (NR_111910, exon 1 of 8)	292	NM_145375	107769	Mm.221412	NM_145375	ENSMUSG00000038623	Tm6sf1	AI428514|BC023123|C630016D09Rik	transmembrane 6 superfamily member 1	protein-coding
mm_157337.1	chrX	36692531	36692563	-	1	NA	Intergenic	MTE2b|LTR|ERVL-MaLR	-47133	NM_001081956	338351	Mm.116704	NM_001081956	ENSMUSG00000059708	Akap17b	AA407619|AKAP-17B|B230333C21Rik|C230056F04Rik|PRKA17B|Sfrs17b|Srsf17b|Talia	A kinase (PRKA) anchor protein 17B	protein-coding
mm_34663.1	chr4	150867090	150867101	+	1	NA	exon (NM_133753, exon 4 of 4)	exon (NM_133753, exon 4 of 4)	12004	NM_133753	74155	Mm.318841	NM_133753	ENSMUSG00000028967	Errfi1	1300002F13Rik|AI788755|Mig-6|Mig6|RALT	ERBB receptor feedback inhibitor 1	protein-coding
mm_104776.1	chr11	98545992	98546007	-	1	NA	promoter-TSS (NM_011771)	promoter-TSS (NM_011771)	32	NM_011771	22780	Mm.133367	NM_011771	ENSMUSG00000018168	Ikzf3	5830411O07Rik|Aiolos|Zfpn1a3|Znfn1a3	IKAROS family zinc finger 3	protein-coding
mm_64078.1	chr7	140941522	140941534	+	1	NA	promoter-TSS (NM_145387)	promoter-TSS (NM_145387)	-53	NM_145387	212974	Mm.260139	NM_145387	ENSMUSG00000062031	Pgghg	5730511L01Rik|Athl1|BC023151	protein glucosylgalactosylhydroxylysine glucosidase	protein-coding
mm_171616.1	chr4	150315496	150315499	-	1	NA	intron (NM_001085492, intron 1 of 22)	intron (NM_001085492, intron 1 of 22)	33581	NM_001085492	68703	Mm.291274	NM_001085492	ENSMUSG00000039852	Rere	1110033A15Rik|AI414665|ARG|ARP|ATN1L|AW742570|Atr2|DNB1|eye<m03Jus>|eyes3|mKIAA0458	arginine glutamic acid dipeptide (RE) repeats	protein-coding
mm_154718.1	chrX	9200025	9200039	+	1	NA	promoter-TSS (NM_173414)	promoter-TSS (NM_173414)	59	NM_173414	236285	Mm.245119	NM_173414	ENSMUSG00000047344	Lancl3	6030463G20Rik	LanC lantibiotic synthetase component C-like 3 (bacterial)	protein-coding
mm_147005.1	chr18	34481399	34481444	-	1	NA	intron (NM_146084, intron 7 of 20)	MYSERV6-int|LTR|ERVK	25402	NM_146084	225358	Mm.226899	NM_146084	ENSMUSG00000036501	Fam13b	2610024E20Rik|AW060714|AW546153	family with sequence similarity 13, member B	protein-coding
mm_15264.1	chr2	155047646	155047658	+	1	NA	intron (NM_015770, intron 2 of 3)	intron (NM_015770, intron 2 of 3)	26845	NM_016661	269378	Mm.330692	NM_016661	ENSMUSG00000027597	Ahcy	AA987153|AL024110|CuBP|SAHH	S-adenosylhomocysteine hydrolase	protein-coding
mm_143824.1	chr17	83874684	83874707	-	1	NA	Intergenic	Intergenic	-27905	NM_025325	107766	Mm.30100	NM_025325	ENSMUSG00000000673	Haao	0610007K21Rik|0610012J07Rik|3-HAO|3-HAOxase|3HAO	3-hydroxyanthranilate 3,4-dioxygenase	protein-coding
mm_29402.1	chr3	108905357	108905369	-	1	NA	intron (NM_025845, intron 4 of 5)	intron (NM_025845, intron 4 of 5)	6341	NM_025845	66921	Mm.51049	NM_025845	ENSMUSG00000027881	Prpf38b	1110021E09Rik|AU018955	PRP38 pre-mRNA processing factor 38 (yeast) domain containing B	protein-coding
mm_101290.1	chr11	22007186	22007206	-	1	NA	exon (NM_153078, exon 24 of 25)	exon (NM_153078, exon 24 of 25)	-5545	NM_011023	18423	Mm.129663	NM_011023	ENSMUSG00000005917	Otx1	A730044F23Rik|jv	orthodenticle homeobox 1	protein-coding
mm_156131.1	chrX	120431747	120431748	+	1	NA	intron (NR_073451, intron 3 of 7)	intron (NR_073451, intron 3 of 7)	-118521	NM_001281531	624957		NM_001281531	ENSMUSG00000083616	H2afb3	EG624957|H2A.Bbd3|H2afb3-ps	H2A histone family, member B3	protein-coding
mm_66740.1	chr7	46672528	46672541	-	1	NA	promoter-TSS (NM_009414)	promoter-TSS (NM_009414)	3	NM_009414	21990	Mm.248684	NM_009414	ENSMUSG00000040046	Tph1	Tph	tryptophan hydroxylase 1	protein-coding
mm_98954.1	chr11	98470491	98470506	+	1	NA	intron (NM_011771, intron 7 of 7)	intron (NM_011771, intron 7 of 7)	23664	NM_010346	14786	Mm.276702	NM_010346	ENSMUSG00000019312	Grb7	mKIAA4028	growth factor receptor bound protein 7	protein-coding
mm_110815.1	chr12	72375129	72375138	-	1	NA	intron (NM_153457, intron 1 of 8)	intron (NM_153457, intron 1 of 8)	33921	NM_001286448	104001	Mm.221275	NM_153457	ENSMUSG00000021087	Rtn1	Nsp	reticulon 1	protein-coding
mm_80596.1	chr9	85845599	85845601	+	1	NA	3' UTR (NM_001164792, exon 2 of 2)	3' UTR (NM_001164792, exon 2 of 2)	2748	NM_001164792	21983	Mm.20864	NM_011627	ENSMUSG00000035274	Tpbg	5T4|AW495680|WAIF1	trophoblast glycoprotein	protein-coding
mm_69025.1	chr7	126792470	126792478	-	1	NA	promoter-TSS (NM_019674)	promoter-TSS (NM_019674)	-3	NM_019674	56420	Mm.41998	NM_019674	ENSMUSG00000030697	Ppp4c	1110002D08Rik|AU016079|Ppx	protein phosphatase 4, catalytic subunit	protein-coding
mm_110535.1	chr12	55053473	55053506	-	1	NA	intron (NR_030764, intron 5 of 7)	intron (NR_030764, intron 5 of 7)	26621	NR_030764	72658	Mm.434380	NM_028314	ENSMUSG00000062198	2700097O09Rik	AW552125	RIKEN cDNA 2700097O09 gene	protein-coding
mm_101611.1	chr11	35828249	35828256	-	1	NA	intron (NM_025936, intron 3 of 14)	intron (NM_025936, intron 3 of 14)	6276	NM_025936	104458	Mm.284906	NM_025936	ENSMUSG00000018848	Rars	2610011N19Rik|2610037E21Rik|AL033339|AW985894	arginyl-tRNA synthetase	protein-coding
mm_12186.1	chr2	65277342	65277342	+	1	NA	Intergenic	Intergenic	-38716	NM_027225	319876	Mm.34159	NM_027225	ENSMUSG00000034903	Cobll1	1810047P18Rik|Coblr1|D430044D16Rik	Cobl-like 1	protein-coding
mm_125774.1	chr15	74636356	74636368	+	1	NA	promoter-TSS (NM_001177437)	promoter-TSS (NM_001177437)	-44	NM_001177437	69439	Mm.263708	NM_001177437	ENSMUSG00000022603	Mroh4	1700016M24Rik	maestro heat-like repeat family member 4	protein-coding
mm_89940.1	chr10	111273887	111273912	+	1	NA	intron (NM_175489, intron 12 of 23)	intron (NM_175489, intron 12 of 23)	-24780	NM_027914	71769	Mm.45256	NM_027914	ENSMUSG00000035759	Bbs10	1300007O09Rik|AI452285	Bardet-Biedl syndrome 10 (human)	protein-coding
mm_79665.1	chr9	59659604	59659609	+	1	NA	intron (NM_001253883, intron 1 of 10)	intron (NM_001253883, intron 1 of 10)	3238	NM_001253883	18746	Mm.326167	NM_011099	ENSMUSG00000032294	Pkm	AA414905|AL024370|AL024424|Pk-2|Pk-3|Pk3|Pkm2	pyruvate kinase, muscle	protein-coding
mm_86726.1	chr10	19062758	19062787	+	1	NA	Intergenic	Intergenic	-47362	NM_009397	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_7988.1	chr1	134234904	134234912	-	1	NA	promoter-TSS (NM_001291928)	promoter-TSS (NM_001291928)	-52	NM_001291928	11539	Mm.298908	NM_009629	ENSMUSG00000042429	Adora1	A1-AR|A1AR|A1R|AA1R|AI848715|BB176431|Ri	adenosine A1 receptor	protein-coding
mm_47848.1	chr5	134456228	134456263	-	1	NA	promoter-TSS (NM_001081465)	promoter-TSS (NM_001081465)	17	NM_001081465	57080	Mm.332735	NM_020331	ENSMUSG00000023079	Gtf2ird1	1700012P16Rik|BEN|Cream1|ESTM9|GTF3|Gtf2il|MusTRD1|Tg(Alb1-Myc)166.8Sst|WBSCR11|X83320	general transcription factor II I repeat domain-containing 1	protein-coding
mm_9017.1	chr1	166127877	166127904	-	1	NA	promoter-TSS (NM_001160049)	promoter-TSS (NM_001160049)	8	NM_001033344	240892	Mm.35315	NM_001033344	ENSMUSG00000026564	Dusp27	C130085G02Rik|Gm209	dual specificity phosphatase 27 (putative)	protein-coding
mm_145985.1	chr18	68228036	68228048	+	1	NA	intron (NM_172631, intron 3 of 5)	intron (NM_172631, intron 3 of 5)	32931	NR_106078	102465702		NR_106078	ENSMUSG00000098253	Mir7219	Gm27613|mmu-mir-7219	microRNA 7219	ncRNA
mm_59180.1	chr7	24461484	24461494	+	1	NA	promoter-TSS (NM_011113)	promoter-TSS (NM_011113)	-994	NM_011113	18793	Mm.1359	NM_011113	ENSMUSG00000046223	Plaur	Cd87|u-PAR|uPAR	plasminogen activator, urokinase receptor	protein-coding
mm_88925.1	chr10	81207052	81207064	+	1	NA	intron (NM_178662, intron 12 of 12)	intron (NM_178662, intron 12 of 12)	-5021	NM_027120	69564	Mm.437211	NM_027120	ENSMUSG00000004939	Nmrk2	2310015C21Rik|Itgb1bp3|Mibp	nicotinamide riboside kinase 2	protein-coding
mm_173339.1	chrY	90811837	90811837	+	1	NA	intron (NM_133362, intron 2 of 3)	(CAGA)n|Simple_repeat|Simple_repeat	26395	NM_133362	170942	Mm.76062	NM_133362	ENSMUSG00000096768	Erdr1	edr	erythroid differentiation regulator 1	protein-coding
mm_78887.1	chr9	44603777	44603790	+	1	NA	Intergenic	Intergenic	-1109	NM_001110826	13209	Mm.267061	NM_007841	ENSMUSG00000032097	Ddx6	1110001P04Rik|E230023J21Rik|HLR2|mRCK/P54|p54|rck	DEAD (Asp-Glu-Ala-Asp) box polypeptide 6	protein-coding
mm_51660.1	chr6	86195262	86195298	+	1	NA	promoter-TSS (NM_031199)	promoter-TSS (NM_031199)	53	NM_031199	21802	Mm.137222	NM_031199	ENSMUSG00000029999	Tgfa	wa-1|wa1	transforming growth factor alpha	protein-coding
mm_52513.1	chr6	115362312	115362322	+	1	NA	promoter-TSS (NM_001308354)	promoter-TSS (NM_001308354)	-32	NM_001308354	19016	Mm.3020	NM_011146	ENSMUSG00000000440	Pparg	Nr1c3|PPAR-gamma|PPAR-gamma2|PPARgamma|PPARgamma2	peroxisome proliferator activated receptor gamma	protein-coding
mm_114749.1	chr13	84280756	84280758	+	1	NA	intron (NR_029418, intron 4 of 10)	intron (NR_029418, intron 4 of 10)	58461	NM_175187	72745	Mm.295063	NM_175187	ENSMUSG00000035762	Tmem161b	2810446P07Rik|AI843389	transmembrane protein 161B	protein-coding
mm_149921.1	chr19	26607440	26607497	+	1	NA	intron (NM_011416, intron 1 of 32)	CpG	2308	NM_011416	67155	Mm.342988	NM_011416	ENSMUSG00000024921	Smarca2	2610209L14Rik|SNF2alpha|Snf2l2|brahma|brm	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	protein-coding
mm_3188.1	chr1	135799491	135799499	+	1	NA	promoter-TSS (NM_021467)	promoter-TSS (NM_021467)	-16	NM_001112702	21952	Mm.44379	NM_021467	ENSMUSG00000026418	Tnni1	2700018B22Rik|AI747285|ssTnI	troponin I, skeletal, slow 1	protein-coding
mm_31061.1	chr4	41314902	41314914	+	1	NA	promoter-TSS (NM_026893)	promoter-TSS (NM_026893)	-7	NM_026893	68970	Mm.28891	NM_026893	ENSMUSG00000028436	Dcaf12	1500001L20Rik|5830424K06Rik|AA420338|AI851081|Wdr40a	DDB1 and CUL4 associated factor 12	protein-coding
mm_129617.1	chr15	80014279	80014290	-	1	NA	5' UTR (NM_011057, exon 1 of 7)	5' UTR (NM_011057, exon 1 of 7)	524	NM_011057	18591	Mm.144089	NM_011057	ENSMUSG00000000489	Pdgfb	PDGF-B|Sis	platelet derived growth factor, B polypeptide	protein-coding
mm_155597.1	chrX	82327260	82327261	+	1	NA	Intergenic	Intergenic	-621610	NM_007868	13405	Mm.275608	NM_007868	ENSMUSG00000045103	Dmd	DXSmh7|DXSmh9|Dp427|Dp71|dys|mdx|pke	dystrophin, muscular dystrophy	protein-coding
mm_73799.1	chr8	117275084	117275097	+	1	NA	intron (NM_001163262, intron 1 of 20)	intron (NM_001163262, intron 1 of 20)	18071	NM_001163262	74440	Mm.233181	NM_028941	ENSMUSG00000034390	Cmip	4933407C03Rik|5830471E12Rik|AI314065|AI464126	c-Maf inducing protein	protein-coding
mm_63238.1	chr7	126584938	126584947	+	1	NA	promoter-TSS (NM_138310)	promoter-TSS (NM_138310)	-66	NM_138310	171504	Mm.170665	NM_138310	ENSMUSG00000042759	Apobr	Apob-48r|Apob48r	apolipoprotein B receptor	protein-coding
mm_145349.1	chr18	56483366	56483370	+	1	NA	intron (NM_026240, intron 6 of 13)	intron (NM_026240, intron 6 of 13)	51236	NM_026240	107022	Mm.24356	NM_026240	ENSMUSG00000001700	Gramd3	9030613F08Rik|9130427A09Rik|AW061306|NS3TP2	GRAM domain containing 3	protein-coding
mm_96849.1	chr11	70043097	70043107	+	1	NA	intron (NM_001109752, intron 17 of 19)	intron (NM_001109752, intron 17 of 19)	-11022	NM_001291131	11889	Mm.6559	NM_009714	ENSMUSG00000020884	Asgr1	ASGPR1|Asgr|Asgr-1|HL-1	asialoglycoprotein receptor 1	protein-coding
mm_100211.1	chr11	116868343	116868437	+	1	NA	intron (NM_178620, intron 9 of 12)	intron (NM_178620, intron 9 of 12)	14375	NM_178620	69900	Mm.348004	NM_178620	ENSMUSG00000020818	Mfsd11	2600014M03Rik	major facilitator superfamily domain containing 11	protein-coding
mm_7731.1	chr1	130741287	130741296	-	1	NA	intron (NM_177604, intron 3 of 3)	intron (NM_177604, intron 3 of 3)	9315	NM_177604	212439	Mm.268547	NM_177604	ENSMUSG00000042510	AA986860	E030025M07|Sarg	expressed sequence AA986860	protein-coding
mm_99711.1	chr11	106217052	106217058	+	1	NA	promoter-TSS (NM_026009)	promoter-TSS (NM_026009)	129	NM_028074	72047	Mm.41367	NM_028074	ENSMUSG00000020705	Ddx42	1810047H21Rik|AW319508|AW556242|B430002H05Rik|RHELP|RNAHP|SF3b125	DEAD (Asp-Glu-Ala-Asp) box polypeptide 42	protein-coding
mm_110344.1	chr12	36156782	36156815	-	1	NA	promoter-TSS (NM_025840)	promoter-TSS (NM_025840)	27	NM_025840	66912	Mm.288669	NM_025840	ENSMUSG00000020547	Bzw2	1110001I24Rik|Bdm2|HSPC028	basic leucine zipper and W2 domains 2	protein-coding
mm_31624.1	chr4	59197561	59197564	+	1	NA	intron (NM_011673, intron 1 of 8)	intron (NM_011673, intron 1 of 8)	8012	NM_011673	22234	Mm.198803	NM_011673	ENSMUSG00000028381	Ugcg	AU043821|C80537|Epcs21|GlcT-1|Ugcgl	UDP-glucose ceramide glucosyltransferase	protein-coding
mm_9684.1	chr1	178333641	178333651	-	1	NA	exon (NM_016805, exon 5 of 14)	exon (NM_016805, exon 5 of 14)	4138	NM_016805	51810	Mm.86589	NM_016805	ENSMUSG00000039630	Hnrnpu	AA408410|AI256620|AL024194|AL024437|AW557595|C86794|Hnrpu|SAFA|Sp120|hnRNP U	heterogeneous nuclear ribonucleoprotein U	protein-coding
mm_83977.1	chr9	57262592	57262609	-	1	NA	promoter-TSS (NM_028820)	promoter-TSS (NM_028820)	-1	NM_028820	74211	Mm.428905	NM_028820	ENSMUSG00000032300	1700017B05Rik	AA682102|D9Ertd278e	RIKEN cDNA 1700017B05 gene	protein-coding
mm_84067.1	chr9	58201396	58201406	-	1	NA	exon (NM_001161535, exon 1 of 2)	exon (NM_001161535, exon 1 of 2)	314	NM_001161535	320563	Mm.186499	NM_177193	ENSMUSG00000051243	Islr2	B930052A04Rik|Linx|Mbu-3|mKIAA1465	immunoglobulin superfamily containing leucine-rich repeat 2	protein-coding
mm_94168.1	chr10	128804354	128804374	-	1	NA	promoter-TSS (NM_178066)	promoter-TSS (NM_178066)	6	NM_178066	73827	Mm.24630	NM_178066	ENSMUSG00000047090	Tmem198b	1110012D08Rik	transmembrane protein 198b	protein-coding
mm_117670.1	chr13	93637565	93637576	-	1	NA	5' UTR (NM_016668, exon 1 of 8)	5' UTR (NM_016668, exon 1 of 8)	188	NM_016668	12116	Mm.329582	NM_016668	ENSMUSG00000074768	Bhmt	-	betaine-homocysteine methyltransferase	protein-coding
mm_73765.1	chr8	115707982	115707987	+	1	NA	Intergenic	Intergenic	-1090	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_100104.1	chr11	115766781	115766796	+	1	NA	intron (NM_028014, intron 1 of 31)	intron (NM_028014, intron 1 of 31)	1355	NM_028014	71947	Mm.23168	NM_028014	ENSMUSG00000020747	Tmem94	2310067B10Rik|Kiaa0195|mKIAA0195	transmembrane protein 94	protein-coding
mm_17161.1	chr2	25239851	25239870	-	1	NA	promoter-TSS (NM_026415)	promoter-TSS (NM_026415)	37	NM_026415	67859	Mm.46431	NM_026415	ENSMUSG00000036731	Cysrt1	2310002J15Rik|AV023762	cysteine rich tail 1	protein-coding
mm_150831.1	chr19	44746719	44746727	+	1	NA	Intergenic	CpG	-10671	NM_011037	18504	Mm.192158	NM_011037	ENSMUSG00000004231	Pax2	Opdc|Pax-2	paired box 2	protein-coding
mm_137227.1	chr17	24351938	24351948	+	1	NA	promoter-TSS (NM_001039581)	promoter-TSS (NM_001039581)	-80	NM_013855	27410	Mm.239470	NM_013855	ENSMUSG00000024130	Abca3	1810036E22Rik|ABC-C|Abc3	ATP-binding cassette, sub-family A (ABC1), member 3	protein-coding
mm_125499.1	chr15	55252434	55252452	+	1	NA	3' UTR (NM_145470, exon 9 of 9)	3' UTR (NM_145470, exon 9 of 9)	-55307	NM_181277	12818	Mm.297859	NM_181277	ENSMUSG00000022371	Col14a1	5730412L22Rik|AW108078	collagen, type XIV, alpha 1	protein-coding
mm_33321.1	chr4	129083882	129083905	+	1	NA	exon (NM_029219, exon 9 of 9)	exon (NM_029219, exon 9 of 9)	-21637	NM_025452	66260	Mm.25295	NM_025452	ENSMUSG00000028786	Tmem54	1810017F10Rik|AI507302	transmembrane protein 54	protein-coding
mm_70549.1	chr8	13056028	13056036	+	1	NA	3' UTR (NM_007972, exon 9 of 9)	3' UTR (NM_007972, exon 9 of 9)	-4876	NM_025834	66901	Mm.441140	NM_025834	ENSMUSG00000031445	Proz	1300015B06Rik	protein Z, vitamin K-dependent plasma glycoprotein	protein-coding
mm_88800.1	chr10	80702283	80702313	+	1	NA	promoter-TSS (NM_027829)	promoter-TSS (NM_027829)	-395	NM_027829	71564	Mm.35802	NM_027829	ENSMUSG00000055862	Izumo4	9030607L17Rik|AI550407	IZUMO family member 4	protein-coding
mm_113242.1	chr13	27345685	27345685	+	1	NA	promoter-TSS (NM_010088)	promoter-TSS (NM_010088)	12	NM_001289919	13529	Mm.291450	NM_010088	ENSMUSG00000018259	Prl8a2	D/tPRP|DPRP|Dtprp|Ghd11|mdPRP	prolactin family 8, subfamily a, member 2	protein-coding
mm_14700.1	chr2	142374059	142374075	+	1	NA	intron (NM_001013802, intron 16 of 18)	intron (NM_001013802, intron 16 of 18)	527397	NM_001081133	16558	Mm.251934	NM_001081133	ENSMUSG00000038844	Kif16b	8430434E15Rik|AA623607|AI789011|C80253|C80902|mKIAA1590	kinesin family member 16B	protein-coding
mm_15046.1	chr2	152847962	152847972	+	1	NA	promoter-TSS (NM_001141978)	promoter-TSS (NM_001141978)	3	NM_028109	72119	Mm.407737	NM_028109	ENSMUSG00000027469	Tpx2	2610005B21Rik|DIL2|REPP86|p100	TPX2, microtubule-associated	protein-coding
mm_171311.1	chr3	95036714	95036721	-	1	NA	exon (NM_008951, exon 2 of 10)	exon (NM_008951, exon 2 of 10)	5897	NM_001282017	19185	Mm.2261	NM_008951	ENSMUSG00000005625	Psmd4	Af1|Mcb1|angiocidin	proteasome (prosome, macropain) 26S subunit, non-ATPase, 4	protein-coding
mm_78023.1	chr9	13751419	13751420	+	1	NA	intron (NR_024025, intron 1 of 15)	intron (NR_024025, intron 1 of 15)	2238	NR_024025	77116	Mm.210405	NM_023858	ENSMUSG00000031918	Mtmr2	6030445P13Rik	myotubularin related protein 2	protein-coding
mm_62213.1	chr7	97919950	97919966	+	1	NA	promoter-TSS (NM_177696)	promoter-TSS (NM_177696)	0	NM_177696	233537	Mm.375772	NM_177696	ENSMUSG00000035582	Gdpd4	4921513O04	glycerophosphodiester phosphodiesterase domain containing 4	protein-coding
mm_9043.1	chr1	167273517	167273534	-	1	NA	intron (NM_030724, intron 1 of 6)	intron (NM_030724, intron 1 of 6)	11602	NM_030724	80914	Mm.280895	NM_030724	ENSMUSG00000026558	Uck2	AA407809|AI481316|AU018180|AU020720|TSA903|UK|UMK|Umpk	uridine-cytidine kinase 2	protein-coding
mm_97201.1	chr11	75596151	75596162	+	1	NA	intron (NM_008850, intron 2 of 11)	intron (NM_008850, intron 2 of 11)	4075	NR_110477	654359	Mm.439961	NR_110477		Gm12338	OTTMUSG00000006216	cytochrome c oxidase, subunit VIIc pseudogene	pseudo
mm_108268.1	chr12	78748997	78749019	+	1	NA	promoter-TSS (NM_019579)	promoter-TSS (NM_019579)	61	NM_019579	56217	Mm.425777	NM_019579	ENSMUSG00000021112	Mpp5	3830420B02Rik|AI255216|AI644496|Pals1	membrane protein, palmitoylated 5 (MAGUK p55 subfamily member 5)	protein-coding
mm_11005.1	chr2	26501874	26501876	+	1	NA	intron (NM_008714, intron 2 of 33)	intron (NM_008714, intron 2 of 33)	1947	NM_008714	18128	Mm.290610	NM_008714	ENSMUSG00000026923	Notch1	9930111A19Rik|Mis6|N1|Tan1|lin-12	notch 1	protein-coding
mm_149507.1	chr19	11965789	11965811	+	1	NA	promoter-TSS (NM_001033174)	promoter-TSS (NM_001033174)	-44	NM_001033174	76303	Mm.291279	NM_001033174	ENSMUSG00000024687	Osbp	1110018F06Rik|AW559088|mKIAA4220	oxysterol binding protein	protein-coding
mm_125317.1	chr15	38219327	38219346	+	1	NA	5' UTR (NM_008757, exon 1 of 2)	5' UTR (NM_008757, exon 1 of 2)	133	NM_008757	18285	Mm.252830	NM_008757	ENSMUSG00000061923	Odf1	-	outer dense fiber of sperm tails 1	protein-coding
mm_137062.1	chr17	19031813	19031817	+	1	NA	Intergenic	ERVB4_3-LTR_MM|LTR|ERVK	-21678	NM_001104550	224552	Mm.469860	NM_001104550	ENSMUSG00000096717	Vmn2r98	EG224552	vomeronasal 2, receptor 98	protein-coding
mm_30548.1	chr4	3684852	3684865	+	1	NA	intron (NM_010747, intron 1 of 12)	Lx9|LINE|L1	6737	NM_010747	17096	Mm.317331	NM_010747	ENSMUSG00000042228	Lyn	AA407514|Hck-2|p53Lyn|p56Lyn	LYN proto-oncogene, Src family tyrosine kinase	protein-coding
mm_22705.1	chr3	18695667	18695674	+	1	NA	Intergenic	Intergenic	-215193	NR_040544	73959	Mm.60616	NR_040544	ENSMUSG00000102699	4930433B08Rik	-	RIKEN cDNA 4930433B08 gene	ncRNA
mm_67701.1	chr7	89527087	89527120	-	1	NA	Intergenic	Intergenic	-9517	NM_029614	76453	Mm.250438	NM_029614	ENSMUSG00000039405	Prss23	2310046G15Rik|4930479H08Rik|AI790574|Spuve	protease, serine 23	protein-coding
mm_12348.1	chr2	69749027	69749037	+	1	NA	exon (NM_001081086, exon 13 of 14)	exon (NM_001081086, exon 13 of 14)	25944	NM_001081086	228005	Mm.11815	NM_001081086	ENSMUSG00000042133	Ppig	AU019516|AU022200|B230312B02Rik|CYP|SRCyp	peptidyl-prolyl isomerase G (cyclophilin G)	protein-coding
mm_98704.1	chr11	96304056	96304074	+	1	NA	exon (NM_008268, exon 1 of 2)	exon (NM_008268, exon 1 of 2)	553	NM_008268	15413	Mm.207	NM_008268	ENSMUSG00000038700	Hoxb5	AI385717|Hox-2.1	homeobox B5	protein-coding
mm_99139.1	chr11	100334408	100334414	+	1	NA	promoter-TSS (NM_010257)	promoter-TSS (NM_010257)	4	NM_010257	14459	Mm.4767	NM_010257	ENSMUSG00000017165	Gast	GAS	gastrin	protein-coding
mm_98865.1	chr11	97775384	97775394	+	1	NA	intron (NM_028156, intron 1 of 2)	intron (NM_028156, intron 1 of 2)	529	NM_028156	72215	Mm.269049	NM_028156	ENSMUSG00000018543	1700001P01Rik	-	RIKEN cDNA 1700001P01 gene	protein-coding
mm_66098.1	chr7	31037019	31037094	-	1	NA	intron (NM_008761, intron 5 of 8)	intron (NM_008761, intron 5 of 8)	3261	NR_106017	102465635		NR_106017	ENSMUSG00000098783	Mir7050	Gm27578|mmu-mir-7050	microRNA 7050	ncRNA
mm_9315.1	chr1	171646412	171646423	-	1	NA	intron (NM_001347184, intron 1 of 5)	intron (NM_001347184, intron 1 of 5)	2582	NM_001347184	75345	Mm.164642	NM_144539	ENSMUSG00000038179	Slamf7	19A|19A24|4930560D03Rik|CRACC|CS1	SLAM family member 7	protein-coding
mm_34777.1	chr4	154011772	154011818	+	1	NA	promoter-TSS (NM_201226)	promoter-TSS (NM_201226)	-8	NM_201226	72946	Mm.260690	NM_201226	ENSMUSG00000029028	Lrrc47	2900010D03Rik|AA960559|mKIAA1185	leucine rich repeat containing 47	protein-coding
mm_25262.1	chr3	104788573	104788595	+	1	NA	promoter-TSS (NM_007484)	promoter-TSS (NM_007484)	-450	NM_001291859	11853	Mm.262	NM_007484	ENSMUSG00000002233	Rhoc	AI324259|Arh9|Arhc	ras homolog family member C	protein-coding
mm_87631.1	chr10	58323541	58323607	+	1	NA	5' UTR (NM_026148, exon 1 of 10)	5' UTR (NM_026148, exon 1 of 10)	108	NM_026148	110829	Mm.57734	NM_026148	ENSMUSG00000019920	Lims1	2310016J22Rik|4921524A02Rik|AI507642|AU021743|AW551584|C430041B13Rik|Lims1l|PINCH|PINCH1	LIM and senescent cell antigen-like domains 1	protein-coding
mm_89878.1	chr10	108332164	108332170	+	1	NA	promoter-TSS (NM_054056)	promoter-TSS (NM_054056)	-22	NM_054056	114774	Mm.391419	NM_054056	ENSMUSG00000035873	Pawr	2310001G03Rik|PAR4|Par-4	PRKC, apoptosis, WT1, regulator	protein-coding
mm_160974.1	chr11	100620285	100620285	+	1	NA	promoter-TSS (NM_019795)	promoter-TSS (NM_019795)	-117	NM_019795	56354	Mm.402409	NM_019795	ENSMUSG00000014195	Dnajc7	2010003F24Rik|2010004G07Rik|CCRP|Ttc2|mDj11|mTpr2	DnaJ heat shock protein family (Hsp40) member C7	protein-coding
mm_80740.1	chr9	94713560	94713573	+	1	NA	intron (NM_177909, intron 4 of 15)	RMER12|LTR|ERVK	-38263	NR_106116	102465763		NR_106116	ENSMUSG00000098251	Mir7656	Gm27614|mmu-mir-7656	microRNA 7656	ncRNA
mm_104787.1	chr11	98707571	98707582	-	1	NA	exon (NM_011869, exon 20 of 26)	exon (NM_011869, exon 20 of 26)	6263	NM_009971	12985	Mm.1238	NM_009971	ENSMUSG00000038067	Csf3	Csfg|G-CSF|MGI-IG	colony stimulating factor 3 (granulocyte)	protein-coding
mm_31997.1	chr4	91940015	91940030	+	1	NA	Intergenic	Intergenic	207199	NM_027034	69314	Mm.55891	NM_027034	ENSMUSG00000028533	Izumo3	1700011H22Rik	IZUMO family member 3	protein-coding
mm_147802.1	chr18	61658170	61658184	-	1	NA	intron (NR_045402, intron 1 of 4)	intron (NR_045402, intron 1 of 4)	7361	NR_045402	328968	Mm.392305	NR_045402		Carmn	Carmen|E330013P06|Gm16908|Mir143hg	cardiac mesoderm enhancer-associated non-coding RNA	ncRNA
mm_131175.1	chr16	7069850	7069870	+	1	NA	promoter-TSS (NM_183188)	promoter-TSS (NM_183188)	25	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_131698.1	chr16	20696180	20696211	+	1	NA	intron (NM_133778, intron 2 of 5)	CpG	1138	NM_133778	78408	Mm.196512	NM_133778	ENSMUSG00000050821	Fam131a	2900046G09Rik	family with sequence similarity 131, member A	protein-coding
mm_77976.1	chr9	7870430	7870432	+	1	NA	intron (NM_007464, intron 1 of 8)	ORR1A2|LTR|ERVL-MaLR	2739	NM_007464	11796	Mm.2026	NM_007464	ENSMUSG00000032000	Birc3	AW107670|Api1|Api2|Birc2|C-IAP2|HIAP2|IAP1|IAP2|MIAP1|MIAP2|MIHB|MIHC|RNF49|cIAP-1|cIAP-2|cIAP1|cIAP2	baculoviral IAP repeat-containing 3	protein-coding
mm_124128.1	chr14	79771306	79771318	-	1	NA	promoter-TSS (NM_021543)	promoter-TSS (NM_021543)	0	NM_001042726	18530	Mm.390715	NM_021543	ENSMUSG00000036422	Pcdh8	1700080P15Rik|Papc	protocadherin 8	protein-coding
mm_56174.1	chr6	88020856	88020871	-	1	NA	intron (NM_001293652, intron 1 of 7)	intron (NM_001293652, intron 1 of 7)	-1068	NM_001293655	19349	Mm.333233	NM_009005	ENSMUSG00000079477	Rab7	Rab7a	RAB7, member RAS oncogene family	protein-coding
mm_140994.1	chr17	24885860	24885870	-	1	NA	promoter-TSS (NM_001163750)	promoter-TSS (NM_001163750)	485	NM_011956	26426	Mm.36718	NM_011956	ENSMUSG00000039183	Nubp2	D17Wsu11e	nucleotide binding protein 2	protein-coding
mm_39393.1	chr5	14025268	14025291	+	1	NA	promoter-TSS (NM_011348)	promoter-TSS (NM_011348)	3	NM_011348	20349	Mm.134093	NM_011348	ENSMUSG00000063531	Sema3e	6430702L12|AA408817|Semah|mKIAA0331	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	protein-coding
mm_65306.1	chr7	24750832	24750842	-	1	NA	intron (NM_026862, intron 11 of 16)	intron (NM_026862, intron 11 of 16)	9474	NM_026862	68891	Mm.292848	NM_026862	ENSMUSG00000052212	Cd177	1190003K14Rik|Pdp3	CD177 antigen	protein-coding
mm_92151.1	chr10	67185571	67185581	-	1	NA	promoter-TSS (NM_001242396)	promoter-TSS (NM_001242396)	-174	NM_001242396	108829	Mm.23846	NM_207221	ENSMUSG00000037876	Jmjd1c	5430433L24Rik|D630035I23Rik|Jmjdic|TRIP8	jumonji domain containing 1C	protein-coding
mm_103012.1	chr11	69734761	69734768	-	1	NA	exon (NM_001291068, exon 29 of 29)	exon (NM_001291068, exon 29 of 29)	23869	NM_001291068	20020	Mm.16533	NM_009089	ENSMUSG00000005198	Polr2a	220kDa|Rpb1|Rpo2-1	polymerase (RNA) II (DNA directed) polypeptide A	protein-coding
mm_123479.1	chr14	65980905	65980913	-	1	NA	exon (NM_013492, exon 8 of 9)	exon (NM_013492, exon 8 of 9)	12426	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_67156.1	chr7	73541086	73541121	-	1	NA	non-coding (NR_037569, exon 5 of 5)	non-coding (NR_037569, exon 5 of 5)	643	NM_001081345	244059	Mm.34539	NM_001081345	ENSMUSG00000078671	Chd2	2810013C04Rik|2810040A01Rik|5630401D06Rik|AI851092|BC029703|CHD-2	chromodomain helicase DNA binding protein 2	protein-coding
mm_20516.1	chr2	130664566	130664636	-	1	NA	promoter-TSS (NM_029832)	promoter-TSS (NM_029832)	44	NM_029832	77006	Mm.440063	NM_029832	ENSMUSG00000068290	Ddrgk1	1110001I20Rik|2600009E05Rik|AI326138|Ufbp1	DDRGK domain containing 1	protein-coding
mm_131651.1	chr16	20537502	20537511	+	1	NA	intron (NM_001302970, intron 1 of 10)	intron (NM_001302970, intron 1 of 10)	2026	NM_009679	11773	Mm.18946	NM_009679	ENSMUSG00000022841	Ap2m1	-	adaptor-related protein complex 2, mu 1 subunit	protein-coding
mm_164800.1	chr18	23805748	23805767	-	1	NA	intron (NM_153058, intron 1 of 6)	intron (NM_153058, intron 1 of 6)	1787	NM_153058	212307	Mm.132237	NM_153058	ENSMUSG00000024277	Mapre2	AI314113|C820009F03Rik|D18Abb1e|EB1|EB2|RP1	microtubule-associated protein, RP/EB family, member 2	protein-coding
mm_155401.1	chrX	72997280	72997286	+	1	NA	exon (NM_001109043, exon 3 of 19)	exon (NM_001109043, exon 3 of 19)	5204	NR_035517	100316779		NR_035517	ENSMUSG00000089357	Mir2137	mmu-mir-2137	microRNA 2137	ncRNA
mm_94172.1	chr10	128805360	128805391	-	1	NA	promoter-TSS (NM_028873)	promoter-TSS (NM_028873)	-301	NM_028873	74330	Mm.296915	NM_028873	ENSMUSG00000025354	Dnajc14	5730551F12Rik|DNAJ|DRIP78|HDJ3|LIP6	DnaJ heat shock protein family (Hsp40) member C14	protein-coding
mm_144825.1	chr18	36348654	36348728	+	1	NA	promoter-TSS (NM_001081365)	promoter-TSS (NM_001081365)	67	NM_001081365	66060	Mm.272527	NM_001081365	ENSMUSG00000046727	Cystm1	0610010O12Rik	cysteine-rich transmembrane module containing 1	protein-coding
mm_141106.1	chr17	26021837	26021845	-	1	NA	promoter-TSS (NM_153140)	promoter-TSS (NM_153140)	19	NM_153140	215445	Mm.41191	NM_153140	ENSMUSG00000037098	Rab11fip3	Cart1|D030060O14Rik|Rab11-FIP3|mKIAA0665	RAB11 family interacting protein 3 (class II)	protein-coding
mm_42092.1	chr5	110308802	110308806	+	1	NA	intron (NM_011132, intron 25 of 48)	intron (NM_011132, intron 25 of 48)	22485	NM_011132	18973	Mm.35061	NM_011132	ENSMUSG00000007080	Pole	-	polymerase (DNA directed), epsilon	protein-coding
mm_80876.1	chr9	98955526	98955552	+	1	NA	promoter-TSS (NR_003248)	promoter-TSS (NR_003248)	-68	NM_012020	26927	Mm.151239	NM_012020	ENSMUSG00000050397	Foxl2	AU045128|BPES|PINTO|Pfrk	forkhead box L2	protein-coding
mm_45351.1	chr5	65911854	65911862	-	1	NA	Intergenic	Intergenic	48289	NM_001081105	74734	Mm.20323	NM_001081105	ENSMUSG00000029204	Rhoh	5830400A04Rik|AU019774|Arhh	ras homolog family member H	protein-coding
mm_52871.1	chr6	122341322	122341323	+	1	NA	Intergenic	Intergenic	-1095	NM_001271579	13619	Mm.6822	NM_007905	ENSMUSG00000040669	Phc1	AW557034|Edr|Edr1|Mph1|Rae-28|rae28	polyhomeotic-like 1 (Drosophila)	protein-coding
mm_136721.1	chr17	8195949	8195957	+	1	NA	3' UTR (NM_201230, exon 12 of 12)	3' UTR (NM_201230, exon 12 of 12)	30435	NM_201230	75296	Mm.227250	NM_201230	ENSMUSG00000069135	Fgfr1op	4930553O10Rik|FOP	Fgfr1 oncogene partner	protein-coding
mm_56654.1	chr6	113434530	113434546	-	1	NA	intron (NM_178373, intron 1 of 5)	intron (NM_178373, intron 1 of 5)	1217	NM_178373	14311	Mm.10026	NM_178373	ENSMUSG00000030278	Cidec	CIDE-3|Fsp27	cell death-inducing DFFA-like effector c	protein-coding
mm_96336.1	chr11	66135489	66135489	+	1	NA	intron (NM_001099633, intron 6 of 68)	L1MA5|LINE|L1	33062	NM_001099633	237806	Mm.264210	NM_001099633	ENSMUSG00000056752	Dnah9	9030022M04|A230091C01|C230051G16|D11Ertd686e|Dnahc9|mKIAA0357	dynein, axonemal, heavy chain 9	protein-coding
mm_152388.1	chr19	10462278	10462287	-	1	NA	Intergenic	Intergenic	-4835	NM_001111140	278795	Mm.490638	NM_001111140	ENSMUSG00000090291	Lrrc10b	Gm705|SerdinR	leucine rich repeat containing 10B	protein-coding
mm_97942.1	chr11	83663446	83663473	+	1	NA	exon (NM_013652, exon 2 of 3)	exon (NM_013652, exon 2 of 3)	875	NM_013652	20303	Mm.244263	NM_013652	ENSMUSG00000018930	Ccl4	AT744.1|Act-2|MIP-1B|Mip1b|Scya4	chemokine (C-C motif) ligand 4	protein-coding
mm_12167.1	chr2	62409080	62409085	+	1	NA	intron (NM_001159543, intron 2 of 24)	intron (NM_001159543, intron 2 of 24)	3149	NM_010074	13482	Mm.1151	NM_010074	ENSMUSG00000035000	Dpp4	Cd26|Dpp-4|THAM	dipeptidylpeptidase 4	protein-coding
mm_165745.1	chr3	107696270	107696280	-	1	NA	exon (NM_145542, exon 1 of 17)	exon (NM_145542, exon 1 of 17)	273	NM_145542	229709	Mm.220328	NM_145542	ENSMUSG00000027893	Ahcyl1	1110034F20Rik|AA409031|AA414901|Ahcy-rs3|DCAL|Irbit	S-adenosylhomocysteine hydrolase-like 1	protein-coding
mm_37086.1	chr4	116406135	116406238	-	1	NA	intron (NM_008641, intron 3 of 28)	intron (NM_008641, intron 3 of 28)	57995	NM_001042743	17776	Mm.9287	NM_008641	ENSMUSG00000003810	Mast2	MAST205|Mtssk	microtubule associated serine/threonine kinase 2	protein-coding
mm_29935.1	chr3	131613751	131613766	-	1	NA	intron (NM_001289477, intron 10 of 12)	intron (NM_001289477, intron 10 of 12)	47726	NM_001289477	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_126058.1	chr15	76974616	76974631	+	1	NA	Intergenic	Intergenic	26079	NM_054099	117171	Mm.322968	NM_054099	ENSMUSG00000063236	1110038F14Rik	-	RIKEN cDNA 1110038F14 gene	protein-coding
mm_131715.1	chr16	21299897	21299901	+	1	NA	Intergenic	L1MB3|LINE|L1	-3027	NR_046162	328646	Mm.404748	NR_046162	ENSMUSG00000096918	Gm16863	A830060N17	predicted gene, 16863	ncRNA
mm_166648.1	chr6	85832270	85832281	-	1	NA	promoter-TSS (NM_023455)	promoter-TSS (NM_023455)	-385	NM_023455	68396	Mm.154782	NM_023455	ENSMUSG00000030004	Nat8	0610037O16Rik|CCNAT|Cml4	N-acetyltransferase 8 (GCN5-related)	protein-coding
mm_13299.1	chr2	102400209	102400360	+	1	NA	exon (NM_020267, exon 1 of 5)	exon (NM_020267, exon 1 of 5)	616	NM_020267	80985	Mm.315002	NM_020267	ENSMUSG00000027189	Trim44	Dipb|Mc7	tripartite motif-containing 44	protein-coding
mm_114950.1	chr13	96748308	96748314	+	1	NA	Intergenic	CpG	-77375	NM_008255	15357	Mm.316652	NM_008255	ENSMUSG00000021670	Hmgcr	HMG-CoAR|Red	3-hydroxy-3-methylglutaryl-Coenzyme A reductase	protein-coding
mm_92709.1	chr10	80756994	80757006	-	1	NA	intron (NM_199322, intron 1 of 27)	intron (NM_199322, intron 1 of 27)	1794	NM_199322	208266	Mm.152371	NM_199322	ENSMUSG00000061589	Dot1l	A630076O07|AW907654|Dot1|KMT4|mDot1	DOT1-like, histone H3 methyltransferase (S. cerevisiae)	protein-coding
mm_144242.1	chr18	10725615	10725636	+	1	NA	promoter-TSS (NM_144860)	promoter-TSS (NM_144860)	0	NM_144860	225164	Mm.21500	NM_144860	ENSMUSG00000024294	Mib1	DIP-1|E430019M12Rik|Mib|mKIAA1323	mindbomb E3 ubiquitin protein ligase 1	protein-coding
mm_26607.1	chr3	152226144	152226162	+	1	NA	exon (NM_057172, exon 17 of 20)	exon (NM_057172, exon 17 of 20)	15695	NM_057172	51886	Mm.278922	NM_057172	ENSMUSG00000028034	Fubp1	9530027K12Rik|D3Ertd330e|FBP|Fubp|Fubp4	far upstream element (FUSE) binding protein 1	protein-coding
mm_140682.1	chr17	12994168	12994171	-	1	NA	Intergenic	MT2C_Mm|LTR|ERVL	-1630	NM_175394	60532	Mm.275521	NM_175394	ENSMUSG00000060475	Wtap	2810408K05Rik|9430038B09Rik	Wilms tumour 1-associating protein	protein-coding
mm_146821.1	chr18	21299947	21299958	-	1	NA	5' UTR (NM_001033445, exon 1 of 6)	5' UTR (NM_001033445, exon 1 of 6)	187	NM_001033445	381126	Mm.312276	NM_001033445	ENSMUSG00000042680	Garem1	C86169|Fam59a|Garem|Gm944|mKIAA4238	GRB2 associated regulator of MAPK1 subtype 1	protein-coding
mm_103358.1	chr11	74869256	74869296	-	1	NA	intron (NM_197943, intron 2 of 22)	intron (NM_197943, intron 2 of 22)	-1082	NR_105891	102465558		NR_105891	ENSMUSG00000098317	Mir6926	Gm27949|mmu-mir-6926	microRNA 6926	ncRNA
mm_146014.1	chr18	69365370	69365374	+	1	NA	intron (NM_013685, intron 3 of 19)	intron (NM_013685, intron 3 of 19)	19651	NM_001083967	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding
mm_21343.1	chr2	157109485	157109518	-	1	NA	exon (NM_001139520, exon 11 of 17)	exon (NM_001139520, exon 11 of 17)	22446	NM_001177439	383766	Mm.480305	NM_001177439	ENSMUSG00000074628	Tldc2	Gm1332	TBC/LysM associated domain containing 2	protein-coding
mm_171720.1	chr4	84915869	84915880	+	1	NA	intron (NM_175275, intron 2 of 25)	intron (NM_175275, intron 2 of 25)	31565	NM_177385	338349	Mm.440562	NM_175275	ENSMUSG00000038070	Cntln	AI448092|B430108F07Rik|D530005L17Rik	centlein, centrosomal protein	protein-coding
mm_31393.1	chr4	48045116	48045124	+	1	NA	promoter-TSS (NM_015743)	promoter-TSS (NM_015743)	-185	NM_015743	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_154963.1	chrX	36981105	36981113	+	1	NA	intron (NM_001177323, intron 1 of 9)	intron (NM_001177323, intron 1 of 9)	8586	NM_001177324	56526	Mm.260036	NM_019942	ENSMUSG00000050379	Sept6	2810035H17Rik|C920001C06Rik|Sep6|mKIAA0128	septin 6	protein-coding
mm_125133.1	chr15	30338456	30338458	+	1	NA	intron (NM_008729, intron 2 of 22)	intron (NM_008729, intron 2 of 22)	165864	NM_008729	18163	Mm.321648	NM_008729	ENSMUSG00000022240	Ctnnd2	Catnd2|Nprap|neurojugin	catenin (cadherin associated protein), delta 2	protein-coding
mm_82433.1	chr9	15045379	15045502	-	1	NA	promoter-TSS (NM_019482)	promoter-TSS (NM_019482)	38	NM_019482	55991	Mm.142253	NM_019482	ENSMUSG00000031934	Panx1	AI847747	pannexin 1	protein-coding
mm_143755.1	chr17	81598273	81598280	-	1	NA	intron (NR_104580, intron 2 of 8)	intron (NR_104580, intron 2 of 8)	140111	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_134378.1	chr16	17148216	17148227	-	1	NA	promoter-TSS (NM_001306169)	promoter-TSS (NM_001306169)	-992	NM_001306169	76872	Mm.101656	NM_029779	ENSMUSG00000022768	Ccdc116	4930432J16Rik	coiled-coil domain containing 116	protein-coding
mm_113647.1	chr13	42301613	42301626	+	1	NA	5' UTR (NM_010104, exon 1 of 5)	5' UTR (NM_010104, exon 1 of 5)	143	NM_010104	13614	Mm.14543	NM_010104	ENSMUSG00000021367	Edn1	ET-1|PPET1|preproET	endothelin 1	protein-coding
mm_65999.1	chr7	30559499	30559531	-	1	NA	5' UTR (NM_001290569, exon 1 of 9)	5' UTR (NM_001290569, exon 1 of 9)	131	NM_029377	75660	Mm.379242	NM_029377	ENSMUSG00000036845	Lin37	1810054G18Rik	lin-37 homolog (C. elegans)	protein-coding
mm_38392.1	chr4	138819252	138819258	-	1	NA	promoter-TSS (NM_011110)	promoter-TSS (NM_011110)	2	NM_011110	18784	Mm.486532	NM_011110	ENSMUSG00000041193	Pla2g5	PLA2|sPLA2	phospholipase A2, group V	protein-coding
mm_97931.1	chr11	83648218	83648222	+	1	NA	3' UTR (NM_011337, exon 3 of 3)	3' UTR (NM_011337, exon 3 of 3)	1158	NM_011337	20302	Mm.1282	NM_011337	ENSMUSG00000000982	Ccl3	AI323804|G0S19-1|LD78alpha|MIP-1alpha|MIP1-(a)|MIP1-alpha|Mip1a|Scya3	chemokine (C-C motif) ligand 3	protein-coding
mm_151029.1	chr19	47014661	47014671	+	1	NA	promoter-TSS (NM_146100)	promoter-TSS (NM_146100)	-32	NM_146100	226180	Mm.276251	NM_146100	ENSMUSG00000034336	Ina	AV028420|NF-66|NF66	internexin neuronal intermediate filament protein, alpha	protein-coding
mm_100800.1	chr11	4984796	4984802	-	1	NA	intron (NM_001243043, intron 1 of 22)	intron (NM_001243043, intron 1 of 22)	-2025	NM_001243044	11764	Mm.274816	NM_007454	ENSMUSG00000009090	Ap1b1	Adtb1|b2b1660Clo	adaptor protein complex AP-1, beta 1 subunit	protein-coding
mm_109274.1	chr12	109546073	109546091	+	1	NA	non-coding (NR_003633, exon 1 of 5)	non-coding (NR_003633, exon 1 of 5)	684	NR_003633	17263	Mm.289645	NM_144513	ENSMUSG00000021268	Meg3	2900016C05Rik|3110050O07Rik|6330408G06Rik|AI425946|AW108224|D12Bwg1266e|Gtl2|R74756|R75394	maternally expressed 3	ncRNA
mm_58248.1	chr6	145048731	145048747	-	1	NA	promoter-TSS (NM_001024468)	promoter-TSS (NM_001024468)	73	NM_001024468	12035	Mm.4606	NM_007532	ENSMUSG00000030268	Bcat1	BCATc|Eca39	branched chain aminotransferase 1, cytosolic	protein-coding
mm_39134.1	chr4	155154880	155154953	-	1	NA	3' UTR (NM_011385, exon 7 of 7)	3' UTR (NM_011385, exon 7 of 7)	67619	NM_011385	20481	Mm.28520	NM_011385	ENSMUSG00000029050	Ski	2310012I02Rik|2610001A11Rik|AA062172|AA589460|BC004088	ski sarcoma viral oncogene homolog (avian)	protein-coding
mm_129195.1	chr15	76477274	76477284	-	1	NA	promoter-TSS (NM_013481)	promoter-TSS (NM_013481)	-10	NM_013481	12181	Mm.4283	NM_013481	ENSMUSG00000022557	Bop1	AU020183|AW146150|D18861|Erb1p|Kiaa0124|mKIAA0124	block of proliferation 1	protein-coding
mm_42408.1	chr5	115025529	115025533	+	1	NA	intron (NM_029012, intron 1 of 10)	RMER17C2|LTR|ERVK	14007	NM_029012	74585	Mm.355894	NM_029012	ENSMUSG00000029550	Sppl3	4833416I09Rik|Psl4|Usmg3	signal peptide peptidase 3	protein-coding
mm_18126.1	chr2	45004438	45004484	-	1	NA	intron (NM_001289521, intron 3 of 8)	intron (NM_001289521, intron 3 of 8)	18716	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_155629.1	chrX	84109303	84109306	+	1	NA	intron (NM_007868, intron 44 of 78)	intron (NM_007868, intron 44 of 78)	-621380	NM_021898	100502723	Mm.383210	NM_021898	ENSMUSG00000035522	Tsga8	Halap-X|Halapx	testis specific gene A8	protein-coding
mm_141298.1	chr17	28080188	28080195	-	1	NA	exon (NM_013687, exon 2 of 10)	exon (NM_013687, exon 2 of 10)	393	NM_013687	21463	Mm.29758	NM_013687	ENSMUSG00000062859	Tcp11	D17Ken1|Tcp-11	t-complex protein 11	protein-coding
mm_111082.1	chr12	80260143	80260209	-	1	NA	5' UTR (NM_134156, exon 1 of 21)	5' UTR (NM_134156, exon 1 of 21)	195	NM_134156	109711	Mm.253564	NM_134156	ENSMUSG00000015143	Actn1	3110023F10Rik|Actn1a	actinin, alpha 1	protein-coding
mm_103428.1	chr11	75630799	75630807	-	1	NA	promoter-TSS (NM_008916)	promoter-TSS (NM_008916)	-217	NM_008916	19062	Mm.1458	NM_008916	ENSMUSG00000006127	Inpp5k	C62|Pps|SKIP	inositol polyphosphate 5-phosphatase K	protein-coding
mm_16205.1	chr2	173061696	173061730	+	1	NA	Intergenic	Intergenic	39811	NM_019547	56190	Mm.485782	NM_019547	ENSMUSG00000027510	Rbm38	Rnpc1|Seb4|Seb4l	RNA binding motif protein 38	protein-coding
mm_33630.1	chr4	132795280	132795299	+	1	NA	intron (NM_001033308, intron 1 of 5)	intron (NM_001033308, intron 1 of 5)	1075	NM_001033308	230787	Mm.290912	NM_001033308	ENSMUSG00000037731	Themis2	ICB-1	thymocyte selection associated family member 2	protein-coding
mm_74356.1	chr8	128357500	128357513	+	1	NA	Intergenic	CpG	-1567	NM_008737	18186	Mm.271745	NM_008737	ENSMUSG00000025810	Nrp1	C530029I03|NP-1|NPN-1|Npn1|Nrp	neuropilin 1	protein-coding
mm_59643.1	chr7	28159481	28159494	+	1	NA	exon (NM_001164655, exon 17 of 20)	exon (NM_001164655, exon 17 of 20)	-10261	NM_007991	14113	Mm.4595	NM_007991	ENSMUSG00000046865	Fbl	AL022665|FIB|FLRN|RNU3IP1	fibrillarin	protein-coding
mm_141431.1	chr17	29489074	29489085	-	1	NA	Intergenic	Intergenic	-1966	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_58069.1	chr6	136924008	136924023	-	1	NA	3' UTR (NM_007486, exon 6 of 6)	3' UTR (NM_007486, exon 6 of 6)	-1835	NM_026983	69187	Mm.33692	NM_026983	ENSMUSG00000030219	Erp27	1810033M07Rik|1810047B09Rik	endoplasmic reticulum protein 27	protein-coding
mm_54344.1	chr6	30693678	30693737	-	1	NA	promoter-TSS (NM_031998)	promoter-TSS (NM_031998)	42	NM_031998	83922	Mm.65389	NM_031998	ENSMUSG00000029790	Cep41	1700017E11Rik|2810431D15Rik|Tsga14	centrosomal protein 41	protein-coding
mm_20102.1	chr2	121085734	121085744	-	1	NA	promoter-TSS (NM_028799)	promoter-TSS (NM_028799)	20	NM_028799	74176	Mm.20187	NM_028799	ENSMUSG00000053675	Tgm5	2310007C07Rik|TGMX|TGx	transglutaminase 5	protein-coding
mm_72512.1	chr8	83900621	83900645	+	1	NA	5' UTR (NM_181039, exon 1 of 23)	5' UTR (NM_181039, exon 1 of 23)	535	NM_181039	330814	Mm.260733	NM_181039	ENSMUSG00000013033	Adgrl1	2900070I05Rik|AI182398|CLIBA|Lec2|Lphn1|mKIAA0821	adhesion G protein-coupled receptor L1	protein-coding
mm_172761.1	chr8	89146933	89146948	-	1	NA	Intergenic	Intergenic	-102778	NM_021390	58198	Mm.214361	NM_021390	ENSMUSG00000031665	Sall1	Msal-3	sal-like 1 (Drosophila)	protein-coding
mm_46093.1	chr5	92347187	92347197	-	1	NA	3' UTR (NM_021274, exon 4 of 4)	3' UTR (NM_021274, exon 4 of 4)	1697	NM_021274	15945	Mm.877	NM_021274	ENSMUSG00000034855	Cxcl10	C7|CRG-2|INP10|IP-10|IP10|Ifi10|Scyb10|gIP-10|mob-1	chemokine (C-X-C motif) ligand 10	protein-coding
mm_90332.1	chr10	127079035	127079035	+	1	NA	5' UTR (NM_001301014, exon 1 of 18)	5' UTR (NM_001301014, exon 1 of 18)	128	NM_001033263	216439	Mm.336761	NM_001033263	ENSMUSG00000025422	Agap2	AGAP-2|Centg1|PIKE|cnt-g1|mKIAA0167	ArfGAP with GTPase domain, ankyrin repeat and PH domain 2	protein-coding
mm_70130.1	chr7	143238091	143238103	-	1	NA	non-coding (NR_001461, exon 1 of 1)	non-coding (NR_001461, exon 1 of 1)	58450	NR_001461	63830	Mm.356096	NR_001461	ENSMUSG00000101609	Kcnq1ot1	Kvlqt1-as|Lit1|Tssc8	KCNQ1 overlapping transcript 1	ncRNA
mm_51901.1	chr6	90764424	90764454	+	1	NA	intron (NM_001134384, intron 1 of 13)	intron (NM_001134384, intron 1 of 13)	45684	NM_001134384	232227	Mm.196943	NM_182784	ENSMUSG00000034312	Iqsec1	AW561907|BC026481|BRAG2|D6Ertd349e|cI-43	IQ motif and Sec7 domain 1	protein-coding
mm_48021.1	chr5	136198915	136198970	-	1	NA	promoter-TSS (NM_025774)	promoter-TSS (NM_025774)	12	NM_025774	66801	Mm.425295	NM_025774	ENSMUSG00000039737	Prkrip1	8430424D23Rik|C114	Prkr interacting protein 1 (IL11 inducible)	protein-coding
mm_29311.1	chr3	107984630	107984640	-	1	NA	intron (NM_008183, intron 5 of 7)	intron (NM_008183, intron 5 of 7)	1801	NM_008183	14863	Mm.440086	NM_008183	ENSMUSG00000040562	Gstm2	Gstb-2|Gstb2	glutathione S-transferase, mu 2	protein-coding
mm_15433.1	chr2	157204277	157204316	+	1	NA	intron (NM_011249, intron 1 of 21)	CpG	238	NM_011249	19650	Mm.244671	NM_011249	ENSMUSG00000027641	Rbl1	AW547426|PRB1|p107	retinoblastoma-like 1 (p107)	protein-coding
mm_150792.1	chr19	44303302	44303310	+	1	NA	TTS (NR_039574)	TTS (NR_039574)	135	NR_039574	100628619		NR_039574	ENSMUSG00000093315	Mir5114	mmu-mir-5114|mu-mir-5114	microRNA 5114	ncRNA
mm_37347.1	chr4	119966829	119966843	-	1	NA	intron (NM_010657, intron 1 of 8)	intron (NM_010657, intron 1 of 8)	152158	NM_010657	16656	Mm.302758	NM_010657	ENSMUSG00000028634	Hivep3	2900056N03Rik|A130075N07|AI848000|E030045D18Rik|KBP-1|KBP1|Krc|Rc|Schnurri-3|Shn3|Zas3	human immunodeficiency virus type I enhancer binding protein 3	protein-coding
mm_41537.1	chr5	92856432	92856443	+	1	NA	intron (NM_001077595, intron 1 of 9)	intron (NM_001077595, intron 1 of 9)	-41556	NM_001077596	27428	Mm.46014	NM_015756	ENSMUSG00000029381	Shroom3	AL022960|D5Ertd287e|Shrm|Shrm3	shroom family member 3	protein-coding
mm_61678.1	chr7	80993647	80993657	+	1	NA	promoter-TSS (NM_178707)	promoter-TSS (NM_178707)	-32	NM_178707	233410	Mm.29525	NM_178707	ENSMUSG00000005621	Zfp592	8430405N24|A730014M16Rik|Znf592|mKIAA0211	zinc finger protein 592	protein-coding
mm_53714.1	chr6	143285967	143285984	+	1	NA	intron (NR_027803, intron 3 of 3)	intron (NR_027803, intron 3 of 3)	40087	NR_027803	52285	Mm.354898	NM_001033129		D6Ertd474e	1700001I24Rik|AU023129	DNA segment, Chr 6, ERATO Doi 474, expressed	ncRNA
mm_94604.1	chr11	14186130	14186133	+	1	NA	Intergenic	Intergenic	-7090	NR_131011	75280	Mm.108492	NR_131011	ENSMUSG00000085452	4930554G24Rik	-	RIKEN cDNA 4930554G24 gene	ncRNA
mm_100192.1	chr11	116752229	116752235	+	1	NA	promoter-TSS (NR_003364)	promoter-TSS (NR_003364)	65	NR_003364	193217	Mm.100084	NR_003364		BC018473	-	cDNA sequence BC018473	ncRNA
mm_97555.1	chr11	78931594	78931601	+	1	NA	exon (NM_010927, exon 5 of 27)	exon (NM_010927, exon 5 of 27)	6306	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_92671.1	chr10	80539083	80539103	-	1	NA	promoter-TSS (NM_026094)	promoter-TSS (NM_026094)	31	NM_026094	67331	Mm.52511	NM_026094	ENSMUSG00000003341	Atp8b3	1700042F02Rik|1700056N23Rik|ATPIK|SAPLT	ATPase, class I, type 8B, member 3	protein-coding
mm_116616.1	chr13	48871713	48871725	-	1	NA	promoter-TSS (NM_011078)	promoter-TSS (NM_011078)	-834	NM_011078	18676	Mm.486213	NM_011078	ENSMUSG00000038025	Phf2	GRC5	PHD finger protein 2	protein-coding
mm_87974.1	chr10	63480322	63480348	+	1	NA	intron (NM_001164376, intron 1 of 17)	intron (NM_001164376, intron 1 of 17)	22824	NM_001164376	216033	Mm.444692	NM_177612	ENSMUSG00000060843	Ctnna3	4930429L08Rik|4933408A16|Catna3|Vr22	catenin (cadherin associated protein), alpha 3	protein-coding
mm_89858.1	chr10	108162045	108162053	+	1	NA	promoter-TSS (NM_027892)	promoter-TSS (NM_027892)	-351	NM_027892	17931	Mm.422959	NM_027892	ENSMUSG00000019907	Ppp1r12a	1200015F06Rik|5730577I22Rik|AA792106|AV099298|D10Ertd625e|Mypt1	protein phosphatase 1, regulatory (inhibitor) subunit 12A	protein-coding
mm_93593.1	chr10	117072088	117072088	-	1	NA	3' UTR (NM_177798, exon 10 of 10)	3' UTR (NM_177798, exon 10 of 10)	-8274	NM_007636	12461	Mm.247788	NM_007636	ENSMUSG00000034024	Cct2	Cctb	chaperonin containing Tcp1, subunit 2 (beta)	protein-coding
mm_122465.1	chr14	45529776	45529841	-	1	NA	intron (NM_146054, intron 1 of 14)	CpG	257	NM_146054	218952	Mm.210018	NM_146054	ENSMUSG00000037712	Fermt2	AA960555|Kindlin-2|Mig2|Plekhc1	fermitin family member 2	protein-coding
mm_66513.1	chr7	45103171	45103189	-	1	NA	5' UTR (NM_010189, exon 2 of 7)	5' UTR (NM_010189, exon 2 of 7)	642	NM_010189	14132	Mm.3303	NM_010189	ENSMUSG00000003420	Fcgrt	FcRn	Fc receptor, IgG, alpha chain transporter	protein-coding
mm_116029.1	chr13	25269914	25269914	-	1	NA	promoter-TSS (NM_009513)	promoter-TSS (NM_009513)	82	NM_009513	22360	Mm.4766	NM_009513	ENSMUSG00000048978	Nrsn1	Neurensin-1|Neuro-p24|Vmp	neurensin 1	protein-coding
mm_64306.1	chr7	141862059	141862063	+	1	NA	exon (NM_028801, exon 31 of 49)	exon (NM_028801, exon 31 of 49)	22989	NM_028801	74180	Mm.200752	NM_028801	ENSMUSG00000066108	Muc5b	2300002I04Rik|A130042M24|AV085033|MUC5|MUC9|mucin 5b	mucin 5, subtype B, tracheobronchial	protein-coding
mm_6352.1	chr1	71650591	71650616	-	1	NA	exon (NM_001276413, exon 3 of 44)	exon (NM_001276413, exon 3 of 44)	2631	NM_010233	14268	Mm.193099	NM_010233	ENSMUSG00000026193	Fn1	E330027I09|Fn|Fn-1	fibronectin 1	protein-coding
mm_170288.1	chr18	3000029	3000037	+	1	NA	Intergenic	Intergenic	123379	NM_001167539	100312476	Mm.480293	NM_001167539	ENSMUSG00000091539	Vmn1r238	-	vomeronasal 1 receptor, 238	protein-coding
mm_102375.1	chr11	58801905	58801943	-	1	NA	promoter-TSS (NM_001162878)	promoter-TSS (NM_001162878)	36	NM_001162878	75429	Mm.296819	NM_029283	ENSMUSG00000049154	Fam183b	3100002J23Rik|Theg6	family with sequence similarity 183, member B	protein-coding
mm_14348.1	chr2	129593529	129593600	+	1	NA	5' UTR (NM_001291022, exon 1 of 5)	5' UTR (NM_001291022, exon 1 of 5)	395	NM_001291022	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_140677.1	chr17	12992189	12992226	-	1	NA	promoter-TSS (NM_001113533)	promoter-TSS (NM_001113533)	52	NM_001113533	60532	Mm.275521	NM_175394	ENSMUSG00000060475	Wtap	2810408K05Rik|9430038B09Rik	Wilms tumour 1-associating protein	protein-coding
mm_137065.1	chr17	20049001	20049037	+	1	NA	promoter-TSS (NM_001104566)	promoter-TSS (NM_001104566)	-814	NM_001104566	22313	Mm.379039	NM_001104566	ENSMUSG00000090315	Vmn2r104	V2r7	vomeronasal 2, receptor 104	protein-coding
mm_56485.1	chr6	99167760	99167763	-	1	NA	intron (NM_001347345, intron 4 of 19)	intron (NM_001347345, intron 4 of 19)	98754	NM_001197321	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_134602.1	chr16	20621431	20621447	-	1	NA	promoter-TSS (NM_028420)	promoter-TSS (NM_028420)	-161	NM_028420	73047	Mm.425977	NM_028420	ENSMUSG00000051146	Camk2n2	2900075A18Rik	calcium/calmodulin-dependent protein kinase II inhibitor 2	protein-coding
mm_88901.1	chr10	81176644	81176648	+	1	NA	promoter-TSS (NM_007907)	promoter-TSS (NM_007907)	15	NM_007907	13629	Mm.2903	NM_007907	ENSMUSG00000034994	Eef2	Ef-2	eukaryotic translation elongation factor 2	protein-coding
mm_46867.1	chr5	113825419	113825433	-	1	NA	intron (NM_009151, intron 1 of 1)	intron (NM_009151, intron 1 of 1)	5075	NM_009151	20345	Mm.332590	NM_009151	ENSMUSG00000048163	Selplg	CD162|Psgl-1|Psgl1|Selp1|Selpl	selectin, platelet (p-selectin) ligand	protein-coding
mm_77326.1	chr8	119424970	119425002	-	1	NA	Intergenic	Intergenic	-12176	NM_027950	71839	Mm.272357	NM_027950	ENSMUSG00000074063	Osgin1	1700012B18Rik|Okl38	oxidative stress induced growth inhibitor 1	protein-coding
mm_62605.1	chr7	105742523	105742538	+	1	NA	TTS (NM_020024)	TTS (NM_020024)	1808	NM_020024	24075	Mm.274846	NM_020024	ENSMUSG00000043866	Taf10	30kDa|AU041226|TAFII30|Taf2h	TATA-box binding protein associated factor 10	protein-coding
mm_1322.1	chr1	65100596	65100604	+	1	NA	exon (NM_007774, exon 3 of 3)	exon (NM_007774, exon 3 of 3)	2763	NM_007774	12964	Mm.26904	NM_007774	ENSMUSG00000044429	Cryga	Cryg-4|DGcry-4	crystallin, gamma A	protein-coding
mm_1698.1	chr1	75142829	75142837	+	1	NA	promoter-TSS (NM_026977)	promoter-TSS (NM_026977)	47	NM_001305231	227298	Mm.273062	NM_170755	ENSMUSG00000049339	Fam134a	-	family with sequence similarity 134, member A	protein-coding
mm_134429.1	chr16	17925762	17925799	-	1	NA	3' UTR (NM_153150, exon 9 of 9)	3' UTR (NM_153150, exon 9 of 9)	2439	NM_153150	13358	Mm.229291	NM_153150	ENSMUSG00000003528	Slc25a1	1300019P08Rik|2610100G11Rik|AI194714|Ctp|Dgsj|Slc20a3	solute carrier family 25 (mitochondrial carrier, citrate transporter), member 1	protein-coding
mm_88834.1	chr10	80807676	80807699	+	1	NA	TTS (NM_007445)	TTS (NM_007445)	2439	NM_007445	11705	Mm.376094	NM_007445	ENSMUSG00000035262	Amh	MIS	anti-Mullerian hormone	protein-coding
mm_119927.1	chr14	54968802	54968812	+	1	NA	promoter-TSS (NR_033497)	promoter-TSS (NR_033497)	20	NR_033497	791403	Mm.319176	NR_033497	ENSMUSG00000097652	Mhrt	D830015G02Rik|ENSMUSG00000053118|Myheart	myosin heavy chain associated RNA transcript	ncRNA
mm_72725.1	chr8	85060064	85060135	+	1	NA	promoter-TSS (NM_026791)	promoter-TSS (NM_026791)	-20	NM_026791	68628	Mm.374815	NM_026791	ENSMUSG00000008167	Fbxw9	1110017H11Rik|Fbw9	F-box and WD-40 domain protein 9	protein-coding
mm_125510.1	chr15	55557625	55557635	+	1	NA	promoter-TSS (NM_026759)	promoter-TSS (NM_026759)	222	NM_001168250	105837	Mm.390829	NM_134092	ENSMUSG00000022369	Mtbp	AI429604|MDM2BP	Mdm2, transformed 3T3 cell double minute p53 binding protein	protein-coding
mm_29569.1	chr3	116968677	116968692	-	1	NA	5' UTR (NM_023245, exon 1 of 8)	5' UTR (NM_023245, exon 1 of 8)	268	NM_023245	114301	Mm.253736	NM_023245	ENSMUSG00000033377	Palmd	4631423C22Rik|PALML	palmdelphin	protein-coding
mm_123364.1	chr14	63164669	63164685	-	1	NA	intron (NM_010191, intron 3 of 9)	intron (NM_010191, intron 3 of 9)	14901	NM_010191	14137	Mm.474432	NM_010191	ENSMUSG00000021273	Fdft1	SQS|SS	farnesyl diphosphate farnesyl transferase 1	protein-coding
mm_91098.1	chr10	19065165	19065171	-	1	NA	Intergenic	Intergenic	-49758	NM_009397	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_157171.1	chrX	9469437	9469446	-	1	NA	promoter-TSS (NM_007807)	promoter-TSS (NM_007807)	-117	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_10607.1	chr2	18998333	18998378	+	1	NA	promoter-TSS (NR_024323)	promoter-TSS (NR_024323)	36	NR_024323	74629	Mm.117687	NR_024323	ENSMUSG00000026736	4930426L09Rik	-	RIKEN cDNA 4930426L09 gene	ncRNA
mm_111390.1	chr12	88252866	88252872	-	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	21628	NM_001013824	435337	Mm.441366	NM_001013824	ENSMUSG00000079029	Gm5662	EG435337	predicted gene 5662	protein-coding
mm_116532.1	chr13	45852455	45852470	-	1	NA	intron (NM_001199304, intron 2 of 6)	intron (NM_001199304, intron 2 of 6)	112529	NM_001199304	20238	Mm.342683	NM_009124	ENSMUSG00000046876	Atxn1	2900016G23Rik|Atx1|C85907|ENSMUSG00000074917|Gm10786|Sca1	ataxin 1	protein-coding
mm_3881.1	chr1	161035524	161035542	+	1	NA	non-coding (NR_002840, exon 1 of 4)	non-coding (NR_002840, exon 1 of 4)	367	NR_002840	14455	Mm.270065	NR_002840	ENSMUSG00000053332	Gas5	Gas-5|Mir5117|Snhg2	growth arrest specific 5	ncRNA
mm_126949.1	chr15	92161165	92161221	+	1	NA	promoter-TSS (NM_001159647)	promoter-TSS (NM_001159647)	-164	NM_001159647	12805	Mm.4911	NM_007727	ENSMUSG00000055022	Cntn1	AW495098|CNTN|F3cam|usl	contactin 1	protein-coding
mm_4829.1	chr1	186137940	186137971	+	1	NA	Intergenic	Intergenic	-20645	NM_146106	226791	Mm.257116	NM_146106	ENSMUSG00000039246	Lyplal1	BC027340|Q96AVO	lysophospholipase-like 1	protein-coding
mm_111813.1	chr12	105614659	105614662	-	1	NA	3' UTR (NM_029654, exon 42 of 42)	3' UTR (NM_029654, exon 42 of 42)	10569	NM_007539	12061	Mm.377078	NM_007539	ENSMUSG00000041347	Bdkrb1	B1BKR|B1R|BKR1|BRADYB1|Bdkrb	bradykinin receptor, beta 1	protein-coding
mm_59164.1	chr7	24389668	24389703	+	1	NA	Intergenic	Intergenic	-9943	NM_028047	71997	Mm.150977	NM_028047	ENSMUSG00000002210	Smg9	1500002O20Rik|AI429693|N28092	smg-9 homolog, nonsense mediated mRNA decay factor (C. elegans)	protein-coding
mm_143596.1	chr17	74950288	74950316	-	1	NA	Intergenic	RMER1A|Other|Other	-55227	NM_019919	268977	Mm.269747	NM_019919	ENSMUSG00000001870	Ltbp1	9430031G15Rik|9830146M04|Ltbp-1|Ltbp1L|TGF-beta1-BP-1|Tgfb|b2b1000Clo	latent transforming growth factor beta binding protein 1	protein-coding
mm_145427.1	chr18	58667760	58667764	+	1	NA	intron (NM_025478, intron 1 of 4)	intron (NM_025478, intron 1 of 4)	8280	NM_025478	66307	Mm.182574	NM_025478	ENSMUSG00000024601	Isoc1	2610034N03Rik	isochorismatase domain containing 1	protein-coding
mm_82249.1	chr9	4795952	4795964	-	1	NA	5' UTR (NM_001113181, exon 1 of 11)	5' UTR (NM_001113181, exon 1 of 11)	276	NM_001113180	14802	Mm.209263	NM_019691	ENSMUSG00000025892	Gria4	GluA4|GluR-D|Glur-4|Glur4|Gluralpha4|spkw1	glutamate receptor, ionotropic, AMPA4 (alpha 4)	protein-coding
mm_63950.1	chr7	139894858	139894866	+	1	NA	5' UTR (NM_177261, exon 1 of 31)	5' UTR (NM_177261, exon 1 of 31)	166	NM_177261	76484	Mm.44442	NM_177261	ENSMUSG00000066129	Kndc1	2410012C07Rik|B830014K08Rik|VKIND|very-kind	kinase non-catalytic C-lobe domain (KIND) containing 1	protein-coding
mm_35283.1	chr4	20778886	20778907	-	1	NA	promoter-TSS (NM_172987)	promoter-TSS (NM_172987)	-228	NM_172987	269513	Mm.317473	NM_172987	ENSMUSG00000055761	Nkain3	C530048M05|E130310K16Rik	Na+/K+ transporting ATPase interacting 3	protein-coding
mm_137110.1	chr17	22080999	22081001	+	1	NA	Intergenic	Intergenic	84977	NM_177596	210853	Mm.441622	NM_177596	ENSMUSG00000063383	Zfp947	6720451E15|EG210853|Gm4769	zinc finger protein 947	protein-coding
mm_114848.1	chr13	92844751	92844790	+	1	NA	promoter-TSS (NM_001162945)	promoter-TSS (NM_001162945)	-17	NM_001162945	382793	Mm.296770	NM_001162945	ENSMUSG00000021704	Mtx3	4930470O13Rik|AA409304|AI853833|AU067765|EG624619|Gm1194|Gm6514	metaxin 3	protein-coding
mm_2966.1	chr1	133045985	133046082	+	1	NA	promoter-TSS (NM_001099276)	promoter-TSS (NM_001099276)	21	NM_001099276	240752	Mm.387308	NM_001099276	ENSMUSG00000026447	Pik3c2b	C330011J12Rik|Gm199|PI3K-C2beta|PI3KC2beta	phosphoinositide-3-kinase, class 2, beta polypeptide	protein-coding
mm_93566.1	chr10	116549102	116549128	-	1	NA	non-coding (NR_024327, exon 2 of 14)	non-coding (NR_024327, exon 2 of 14)	32396	NM_001037848	72068	Mm.351553	NM_028082	ENSMUSG00000020166	Cnot2	2600016M12Rik|2810470K03Rik|AA537049|AA959607|AW557563|C79650	CCR4-NOT transcription complex, subunit 2	protein-coding
mm_158259.1	chrX	109009844	109009848	-	1	NA	intron (NM_016710, intron 4 of 5)	U1|snRNA|snRNA	3534	NM_016710	50887	Mm.298443	NM_016710	ENSMUSG00000031245	Hmgn5	GARP45|NBP-45|Nsbp1	high-mobility group nucleosome binding domain 5	protein-coding
mm_117222.1	chr13	64150107	64150117	-	1	NA	intron (NM_175494, intron 1 of 4)	intron (NM_175494, intron 1 of 4)	3087	NM_175494	238673	Mm.300065	NM_175494	ENSMUSG00000044934	Zfp367	8030486J21Rik|ZFF29a|ZFF29b|Znf367	zinc finger protein 367	protein-coding
mm_163685.1	chr13	95374887	95374898	-	1	NA	exon (NM_025630, exon 1 of 14)	exon (NM_025630, exon 1 of 14)	465	NM_025630	66549	Mm.36785	NM_025630	ENSMUSG00000021681	Aggf1	2010009L17Rik|2310029P06Rik|AW112072|Peg3|VG5Q	angiogenic factor with G patch and FHA domains 1	protein-coding
mm_25663.1	chr3	121724812	121724826	+	1	NA	intron (NM_010171, intron 1 of 5)	(CA)n|Simple_repeat|Simple_repeat	1282	NM_010171	14066	Mm.273188	NM_010171	ENSMUSG00000028128	F3	AA409063|CD142|Cf-3|Cf3|TF	coagulation factor III	protein-coding
mm_126224.1	chr15	78929177	78929208	+	1	NA	intron (NM_008495, intron 2 of 3)	B1_Mm|SINE|Alu	2467	NM_008495	16852	Mm.43831	NM_008495	ENSMUSG00000068220	Lgals1	AA410090|Gal-1|Galbp|L-14.5|L14|Lect14|galectin-1	lectin, galactose binding, soluble 1	protein-coding
mm_166479.1	chr5	145042987	145042998	+	1	NA	promoter-TSS (NM_027069)	promoter-TSS (NM_027069)	2	NM_027069	69396	Mm.45463	NM_027069	ENSMUSG00000029620	1700018F24Rik	AV045857	RIKEN cDNA 1700018F24 gene	protein-coding
mm_152504.1	chr19	11165564	11165570	-	1	NA	promoter-TSS (NM_027074)	promoter-TSS (NM_027074)	-247	NM_027074	69416	Mm.72491	NM_027074	ENSMUSG00000024728	1700025F22Rik	-	RIKEN cDNA 1700025F22 gene	protein-coding
mm_79170.1	chr9	47852450	47852495	+	1	NA	3' UTR (NM_018770, exon 10 of 10)	3' UTR (NM_018770, exon 10 of 10)	-34264	NR_046048	100038460	Mm.447649	NR_046048		Gm10677	ENSMUSG00000074363	predicted gene 10677	ncRNA
mm_19191.1	chr2	84424424	84424432	-	1	NA	intron (NM_018782, intron 1 of 15)	intron (NM_018782, intron 1 of 15)	838	NM_018782	54598	Mm.75467	NM_018782	ENSMUSG00000059588	Calcrl	AV071593|CRLR	calcitonin receptor-like	protein-coding
mm_124444.1	chr14	118854843	118854856	-	1	NA	promoter-TSS (NM_001160099)	promoter-TSS (NM_001160099)	-101	NM_021386	58187	Mm.390755	NM_021386	ENSMUSG00000022132	Cldn10	6720456I16Rik|Cldn10a|Cldn10b|D14Ertd728e	claudin 10	protein-coding
mm_92790.1	chr10	81343276	81343286	-	1	NA	promoter-TSS (NM_148951)	promoter-TSS (NM_148951)	-15	NM_148951	209047	Mm.218755	NM_148951	ENSMUSG00000034872	Gipc3	Ahl5|Rgs19ip3	GIPC PDZ domain containing family, member 3	protein-coding
mm_156010.1	chrX	106920757	106920786	+	1	NA	5' UTR (NM_175271, exon 1 of 3)	5' UTR (NM_175271, exon 1 of 3)	146	NM_175271	78134	Mm.90147	NM_175271	ENSMUSG00000049929	Lpar4	5730485F04Rik|Gpr23|LPA4|p2y9	lysophosphatidic acid receptor 4	protein-coding
mm_65039.1	chr7	18562014	18562036	-	1	NA	exon (NM_001037168, exon 3 of 5)	exon (NM_001037168, exon 3 of 5)	5280	NM_001037168	545925	Mm.440302	NM_001037168	ENSMUSG00000070797	Psg27	EG545925|cea15	pregnancy-specific glycoprotein 27	protein-coding
mm_66453.1	chr7	44869745	44869755	-	1	NA	promoter-TSS (NM_133949)	promoter-TSS (NM_133949)	38	NM_133949	84113	Mm.42855	NM_133949	ENSMUSG00000038502	Ptov1	1110030G05Rik|AU041779|Gcap3	prostate tumor over expressed gene 1	protein-coding
mm_115514.1	chr13	5724440	5724458	-	1	NA	Intergenic	Intergenic	133643	NR_045891	71867	Mm.179181	NR_045891	ENSMUSG00000100625	1700016G22Rik	-	RIKEN cDNA 1700016G22 gene	ncRNA
mm_6010.1	chr1	58982619	58982623	-	1	NA	intron (NM_172656, intron 3 of 11)	RMER19B|LTR|ERVK	9050	NM_172656	227154	Mm.286006	NM_172656	ENSMUSG00000026027	Stradb	AA792893|Als2cr2|B830008M19|D1Ucla2|ILPIP|ILPIPA|PRO1038|Papk|Syradb	STE20-related kinase adaptor beta	protein-coding
mm_35719.1	chr4	44561511	44561513	-	1	NA	intron (NM_008782, intron 8 of 9)	intron (NM_008782, intron 8 of 9)	-141288	NR_073462	70602	Mm.491142	NR_073462	ENSMUSG00000103995	5730488B01Rik	-	RIKEN cDNA 5730488B01 gene	ncRNA
mm_57750.1	chr6	129100939	129100947	-	1	NA	promoter-TSS (NM_153506)	promoter-TSS (NM_153506)	-40	NM_153506	232409	Mm.30870	NM_153506	ENSMUSG00000030155	Clec2e	Clra|clr-a	C-type lectin domain family 2, member e	protein-coding
mm_37578.1	chr4	126301105	126301113	-	1	NA	intron (NM_199473, intron 2 of 3)	CpG	14315	NM_199473	329941	Mm.296327	NM_199473	ENSMUSG00000056174	Col8a2	AI429819	collagen, type VIII, alpha 2	protein-coding
mm_143485.1	chr17	71300923	71300937	-	1	NA	intron (NM_145158, intron 2 of 7)	MT2B|LTR|ERVL	10035	NM_145158	246707	Mm.23462	NM_145158	ENSMUSG00000024053	Emilin2	FOAP-10	elastin microfibril interfacer 2	protein-coding
mm_122523.1	chr14	47361522	47361566	-	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-12316	NM_010705	16854	Mm.248615	NM_010705	ENSMUSG00000050335	Lgals3	GBP|L-34|Mac-2|gal3	lectin, galactose binding, soluble 3	protein-coding
mm_59850.1	chr7	29860100	29860121	+	1	NA	intron (NM_172740, intron 1 of 3)	CpG	131	NM_172740	233058	Mm.297657	NM_172740	ENSMUSG00000058402	Zfp420	B230119D13|B230312I18Rik|mszf59-1|mszf70	zinc finger protein 420	protein-coding
mm_116922.1	chr13	55529381	55529385	-	1	NA	promoter-TSS (NM_013739)	promoter-TSS (NM_013739)	-845	NM_013739	27261	Mm.33910	NM_013739	ENSMUSG00000035711	Dok3	AI450713|Dokl	docking protein 3	protein-coding
mm_88093.1	chr10	68723793	68723822	+	1	NA	promoter-TSS (NM_177794)	promoter-TSS (NM_177794)	61	NM_177794	327766	Mm.2479	NM_177794	ENSMUSG00000060044	Tmem26	3230401A06|AI195372	transmembrane protein 26	protein-coding
mm_103363.1	chr11	74927520	74927528	-	1	NA	intron (NM_001002764, intron 1 of 18)	ID_B1|SINE|B4	1652	NM_001002764	103677	Mm.288460	NM_001002764	ENSMUSG00000038290	Smg6	AI317223|AU041178	Smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans)	protein-coding
mm_100236.1	chr11	117231947	117231979	+	1	NA	intron (NM_001113486, intron 2 of 11)	intron (NM_001113486, intron 2 of 11)	32302	NM_001113486	53860	Mm.38450	NM_017380	ENSMUSG00000059248	Sept9	MSF1|Msf|PNUTL4|Sint1	septin 9	protein-coding
mm_16134.1	chr2	170375621	170375631	+	1	NA	non-coding (NR_040610, exon 5 of 8)	non-coding (NR_040610, exon 5 of 8)	19265	NR_040610	73303	Mm.443297	NR_040610	ENSMUSG00000086999	Bcas1os2	1700040N02Rik	breast carcinoma amplified sequence 1, opposite strand 2	ncRNA
mm_77086.1	chr8	110755607	110755664	-	1	NA	5' UTR (NM_001135100, exon 2 of 7)	5' UTR (NM_001135100, exon 2 of 7)	29909	NM_001310591	244654	Mm.490385	NM_198625	ENSMUSG00000033763	Mtss1l	ABBA	metastasis suppressor 1-like	protein-coding
mm_48342.1	chr5	139216315	139216358	-	1	NA	intron (NM_001256115, intron 2 of 21)	intron (NM_001256115, intron 2 of 21)	1178	NM_001256116	77053	Mm.210845	NM_024451	ENSMUSG00000036817	Sun1	4632417G13Rik|5730434D03Rik|Unc84a|mKIAA0810	Sad1 and UNC84 domain containing 1	protein-coding
mm_44398.1	chr5	17835858	17835878	-	1	NA	promoter-TSS (NM_001159555)	promoter-TSS (NM_001159555)	28	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_88109.1	chr10	69151314	69151327	+	1	NA	Intergenic	Intergenic	-57232	NM_001252636	69288	Mm.26659	NM_001081347	ENSMUSG00000019944	Rhobtb1	1700008H16Rik|3110048G13Rik|AI173445|AI573858|AV350930	Rho-related BTB domain containing 1	protein-coding
mm_66112.1	chr7	31042077	31042085	-	1	NA	promoter-TSS (NM_001111073)	promoter-TSS (NM_001111073)	-242	NM_001111073	18301	Mm.1870	NM_008761	ENSMUSG00000009687	Fxyd5	EF-8|Oit2|RIC	FXYD domain-containing ion transport regulator 5	protein-coding
mm_36165.1	chr4	60741276	60741284	-	1	NA	promoter-TSS (NM_001199995)	promoter-TSS (NM_001199995)	1	NM_001199995	100039054	Mm.482236	NM_001199995	ENSMUSG00000094793	Mup12	Gm2024	major urinary protein 12	protein-coding
mm_86395.1	chr9	123968575	123968593	-	1	NA	5' UTR (NM_009912, exon 1 of 2)	5' UTR (NM_009912, exon 1 of 2)	108	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_43755.1	chr5	140441068	140441083	+	1	NA	exon (NM_133916, exon 15 of 19)	exon (NM_133916, exon 15 of 19)	13736	NR_106005	102466792		NR_106005	ENSMUSG00000098319	Mir7038	Gm27955|mmu-mir-7038	microRNA 7038	ncRNA
mm_135349.1	chr16	43664146	43664158	-	1	NA	promoter-TSS (NM_001146325)	promoter-TSS (NM_001146325)	32	NM_001146325	100043314	Mm.390896	NM_001146325	ENSMUSG00000071552	Tigit	ENSMUSG00000071552|Vstm3	T cell immunoreceptor with Ig and ITIM domains	protein-coding
mm_137969.1	chr17	33555728	33555796	+	1	NA	promoter-TSS (NM_053214)	promoter-TSS (NM_053214)	55	NM_053214	17916	Mm.42019	NM_053214	ENSMUSG00000024300	Myo1f	C330006B10Rik	myosin IF	protein-coding
mm_118465.1	chr14	11553500	11553514	+	1	NA	promoter-TSS (NM_008981)	promoter-TSS (NM_008981)	-46	NM_008981	19270	Mm.431266	NM_008981	ENSMUSG00000021745	Ptprg	5430405N12Rik|AW046354|AW549872|RPTPgamma	protein tyrosine phosphatase, receptor type, G	protein-coding
mm_24117.1	chr3	88163044	88163053	+	1	NA	exon (NM_001310593, exon 8 of 11)	exon (NM_001310593, exon 8 of 11)	14737	NR_045997	76642	Mm.424420	NR_045997	ENSMUSG00000096935	1700113A16Rik	2210408E11Rik|AA408983	RIKEN cDNA 1700113A16 gene	ncRNA
mm_154231.1	chr19	60226639	60226649	-	1	NA	promoter-TSS (NM_029648)	promoter-TSS (NM_029648)	53	NM_029648	76539	Mm.290183	NM_029648	ENSMUSG00000057858	Fam204a	2310065H12Rik|2610015K05Rik|D19Ertd737e	family with sequence similarity 204, member A	protein-coding
mm_166874.1	chr7	25390126	25390128	-	1	NA	promoter-TSS (NM_001039507)	promoter-TSS (NM_001039507)	-15	NM_001039507	16890	Mm.158548	NM_010719	ENSMUSG00000003123	Lipe	4933403G17Rik|HSL	lipase, hormone sensitive	protein-coding
mm_22498.1	chr3	7366590	7366594	+	1	NA	promoter-TSS (NM_008862)	promoter-TSS (NM_008862)	-12	NM_008862	18767	Mm.3193	NM_008862	ENSMUSG00000027499	Pkia	AI415001|PKIalpha	protein kinase inhibitor, alpha	protein-coding
mm_69920.1	chr7	141823030	141823069	-	1	NA	Intergenic	Intergenic	-16023	NM_028801	74180	Mm.200752	NM_028801	ENSMUSG00000066108	Muc5b	2300002I04Rik|A130042M24|AV085033|MUC5|MUC9|mucin 5b	mucin 5, subtype B, tracheobronchial	protein-coding
mm_124552.1	chr14	122913018	122913026	-	1	NA	intron (NM_145466, intron 1 of 2)	CpG	143	NM_145466	223267	Mm.379358	NM_145466	ENSMUSG00000041625	Ggact	A2ld1	gamma-glutamylamine cyclotransferase	protein-coding
mm_132106.1	chr16	31428894	31428902	+	1	NA	5' UTR (NM_001122683, exon 1 of 7)	5' UTR (NM_001122683, exon 1 of 7)	145	NM_001122683	71911	Mm.293470	NM_175177	ENSMUSG00000046598	Bdh1	2310032J20Rik|AI327223|Bdh	3-hydroxybutyrate dehydrogenase, type 1	protein-coding
mm_74002.1	chr8	121079480	121079485	+	1	NA	intron (NR_130109, intron 1 of 6)	intron (NR_130109, intron 1 of 6)	3628	NR_045471	68790	Mm.246916	NR_045471	ENSMUSG00000097336	Fendrr	1110050K14Rik|LL66|linc-Foxf1a|lincFoxf1	Foxf1 adjacent non-coding developmental regulatory RNA	ncRNA
mm_81569.1	chr9	110420806	110420833	+	1	NA	exon (NM_008694, exon 2 of 4)	exon (NM_008694, exon 2 of 4)	1011	NM_008694	18054	Mm.236225	NM_008694	ENSMUSG00000032484	Ngp	bectenecin	neutrophilic granule protein	protein-coding
mm_14870.1	chr2	148799628	148799654	+	1	NA	intron (NM_009978, intron 1 of 3)	intron (NM_009978, intron 1 of 3)	802	NM_009978	13012	Mm.20435	NM_009978	ENSMUSG00000027442	Cst8	Cres|Cst-rs1	cystatin 8 (cystatin-related epididymal spermatogenic)	protein-coding
mm_68747.1	chr7	121064636	121064647	-	1	NA	3' UTR (NM_030691, exon 6 of 6)	3' UTR (NM_030691, exon 6 of 6)	9889	NM_030691	80719	Mm.160384	NM_030691	ENSMUSG00000035004	Igsf6	-	immunoglobulin superfamily, member 6	protein-coding
mm_30577.1	chr4	3940748	3940751	+	1	NA	intron (NR_104354, intron 2 of 5)	intron (NR_104354, intron 2 of 5)	1325	NR_104356	66433	Mm.27406	NM_181391	ENSMUSG00000042198	Chchd7	1810049H20Rik	coiled-coil-helix-coiled-coil-helix domain containing 7	protein-coding
mm_73959.1	chr8	120487149	120487165	+	1	NA	Intergenic	Intergenic	-1709	NM_198671	382034	Mm.334856	NM_198671	ENSMUSG00000031822	Gse1	2210013I18Rik|mKIAA0182	genetic suppressor element 1, coiled-coil protein	protein-coding
mm_108940.1	chr12	102128719	102128739	+	1	NA	promoter-TSS (NM_172152)	promoter-TSS (NM_172152)	-690	NM_172152	238384	Mm.312448	NM_172152	ENSMUSG00000041771	Slc24a4	A930002M03Rik|AW492432|NCKX4	solute carrier family 24 (sodium/potassium/calcium exchanger), member 4	protein-coding
mm_12079.1	chr2	59806155	59806158	+	1	NA	intron (NM_198294, intron 14 of 26)	intron (NM_198294, intron 14 of 26)	76450	NM_001159636	72137	Mm.288734	NM_028118	ENSMUSG00000026988	Wdsub1	1700048E19Rik|2610014F08Rik	WD repeat, SAM and U-box domain containing 1	protein-coding
mm_81755.1	chr9	113958698	113958712	+	1	NA	exon (NM_001083319, exon 7 of 17)	exon (NM_001083319, exon 7 of 17)	27771	NM_013699	22221	Mm.28052	NM_013699	ENSMUSG00000009741	Ubp1	Cp2b|LBP-1a|LBP-1b|NF2d9	upstream binding protein 1	protein-coding
mm_70098.1	chr7	142660990	142661040	-	1	NA	non-coding (NR_002855, exon 1 of 4)	non-coding (NR_002855, exon 1 of 4)	256	NM_001122736	16002	Mm.3862	NM_010514	ENSMUSG00000048583	Igf2	AL033362|Igf-2|Igf-II|M6pr|Mpr|Peg2	insulin-like growth factor 2	protein-coding
mm_39735.1	chr5	29196102	29196123	+	1	NA	non-coding (NR_110371, exon 1 of 8)	non-coding (NR_110371, exon 1 of 8)	119	NR_110371	56874	Mm.87352	NM_021470	ENSMUSG00000029130	Rnf32	1700009J01Rik|2700025B22Rik|4930542N22Rik|Lmbr2	ring finger protein 32	protein-coding
mm_49188.1	chr6	15185583	15185595	+	1	NA	promoter-TSS (NM_001286607)	promoter-TSS (NM_001286607)	83	NM_001286607	114142	Mm.332919	NM_053242	ENSMUSG00000029563	Foxp2	2810043D05Rik|AI449000|CAG-16|D0Kist7	forkhead box P2	protein-coding
mm_134914.1	chr16	30310774	30310789	-	1	NA	promoter-TSS (NM_008148)	promoter-TSS (NM_008148)	0	NM_008148	14729	Mm.3519	NM_008148	ENSMUSG00000047953	Gp5	GPV	glycoprotein 5 (platelet)	protein-coding
mm_16807.1	chr2	10130639	10130689	-	1	NA	promoter-TSS (NM_010582)	promoter-TSS (NM_010582)	19	NM_010582	16425	Mm.182043	NM_010582	ENSMUSG00000037254	Itih2	AI747202|Intin2|Itih-2	inter-alpha trypsin inhibitor, heavy chain 2	protein-coding
mm_45129.1	chr5	48754522	48754536	-	1	NA	intron (NM_001199244, intron 1 of 7)	RLTR10B|LTR|ERVK	135028	NM_030265	80334	Mm.160172	NM_030265	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding
mm_8180.1	chr1	138080251	138080265	-	1	NA	exon (NM_001268286, exon 21 of 29)	exon (NM_001268286, exon 21 of 29)	94868	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_18577.1	chr2	66124715	66124764	-	1	NA	promoter-TSS (NM_015736)	promoter-TSS (NM_015736)	54	NM_015736	14425	Mm.439760	NM_015736	ENSMUSG00000026994	Galnt3	-	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 3	protein-coding
mm_37362.1	chr4	120797823	120797826	-	1	NA	intron (NM_001048168, intron 1 of 9)	intron (NM_001048168, intron 1 of 9)	-25127	NR_029602	723836		NR_029602	ENSMUSG00000065409	Mir30e	Mirn30e|mir-30e|mmu-mir-30e	microRNA 30e	ncRNA
mm_12327.1	chr2	69394210	69394257	+	1	NA	intron (NM_175512, intron 2 of 4)	intron (NM_175512, intron 2 of 4)	13771	NM_175512	241452	Mm.211655	NM_175512	ENSMUSG00000027068	Dhrs9	C730025I08Rik|Rdh15	dehydrogenase/reductase (SDR family) member 9	protein-coding
mm_26629.1	chr3	152908343	152908350	+	1	NA	intron (NM_012028, intron 2 of 4)	intron (NM_012028, intron 2 of 4)	73861	NM_012028	26938	Mm.40915	NM_012028	ENSMUSG00000039037	St6galnac5	AI851940|Siat7e	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 5	protein-coding
mm_119682.1	chr14	53345890	53345893	+	1	NA	Intergenic	Intergenic	-850196	NM_001170918	57269	Mm.88822	NM_020512	ENSMUSG00000059887	Olfr1507	MOR244-1|Mor28|Or28	olfactory receptor 1507	protein-coding
mm_46249.1	chr5	99249680	99249690	-	1	NA	intron (NM_145839, intron 1 of 13)	intron (NM_145839, intron 1 of 13)	3242	NM_181318	320292	Mm.259074	NM_145839	ENSMUSG00000089809	Rasgef1b	4732452O09Rik|GPIgamma4|Gpig4	RasGEF domain family, member 1B	protein-coding
mm_2382.1	chr1	93478982	93479054	+	1	NA	promoter-TSS (NM_010891)	promoter-TSS (NM_010891)	25	NM_001159717	18000	Mm.428652	NM_010891	ENSMUSG00000026276	Sept2	AW208991|Nedd-5|Nedd5|mKIAA0158	septin 2	protein-coding
mm_14672.1	chr2	139494039	139494050	+	1	NA	intron (NM_175467, intron 1 of 12)	intron (NM_175467, intron 1 of 12)	124	NM_175467	228677	Mm.100450	NM_175467	ENSMUSG00000039092	Sptlc3	C130053K05Rik	serine palmitoyltransferase, long chain base subunit 3	protein-coding
mm_155020.1	chrX	42060389	42060399	+	1	NA	Intergenic	ORR1A3|LTR|ERVL-MaLR	-7442	NM_009688	11798	Mm.259879	NM_009688	ENSMUSG00000025860	Xiap	1110015C02Rik|Aipa|Api3|Birc4|IAP3|ILP-1|MIHA	X-linked inhibitor of apoptosis	protein-coding
mm_153646.1	chr19	44248127	44248173	-	1	NA	Intergenic	Intergenic	44862	NM_024450	30049	Mm.480594	NM_024450	ENSMUSG00000025202	Scd3	4930513N16Rik	stearoyl-coenzyme A desaturase 3	protein-coding
mm_75789.1	chr8	70095279	70095296	-	1	NA	3' UTR (NM_007789, exon 15 of 15)	3' UTR (NM_007789, exon 15 of 15)	7299	NR_106033	102465646		NR_106033	ENSMUSG00000099042	Mir7066	Gm27290|mmu-mir-7066	microRNA 7066	ncRNA
mm_74153.1	chr8	123381437	123381460	+	1	NA	exon (NM_001037877, exon 2 of 18)	exon (NM_001037877, exon 2 of 18)	7737	NM_001286363	66855	Mm.178818	NM_025804	ENSMUSG00000001472	Tcf25	1100001J13Rik|1810041K11Rik|D8Ertd325e|Nulp1|mKIAA1049	transcription factor 25 (basic helix-loop-helix)	protein-coding
mm_143497.1	chr17	71475516	71475526	-	1	NA	promoter-TSS (NM_028887)	promoter-TSS (NM_028887)	-178	NM_028887	74355	Mm.194450	NM_028887	ENSMUSG00000024054	Smchd1	4931400A14Rik|AW554188|MommeD1|mKIAA0650	SMC hinge domain containing 1	protein-coding
mm_164146.1	chr15	59739280	59739305	-	1	NA	Intergenic	Intergenic	55667	NR_045076	100503021	Mm.402924	NR_045076		Gm19510	-	predicted gene, 19510	ncRNA
mm_160276.1	chr7	119896139	119896139	+	1	NA	promoter-TSS (NM_001163703)	promoter-TSS (NM_001163703)	-153	NM_029610	73919	Mm.46381	NM_029610	ENSMUSG00000030922	Lyrm1	1110065L10Rik|2310004B22Rik|4930404J24Rik	LYR motif containing 1	protein-coding
mm_33594.1	chr4	132564184	132564210	+	1	NA	5' UTR (NM_001081211, exon 1 of 2)	5' UTR (NM_001081211, exon 1 of 2)	130	NM_001081211	19204	Mm.89389	NM_001081211	ENSMUSG00000056529	Ptafr	PAFR	platelet-activating factor receptor	protein-coding
mm_93774.1	chr10	120476211	120476221	-	1	NA	5' UTR (NM_010441, exon 1 of 5)	5' UTR (NM_010441, exon 1 of 5)	253	NM_001347170	15364	Mm.157190	NM_010441	ENSMUSG00000056758	Hmga2	9430083A20Rik|HMGI-C|Hmgic|pg|pygmy	high mobility group AT-hook 2	protein-coding
mm_80216.1	chr9	72532185	72532207	+	1	NA	promoter-TSS (NM_001033536)	promoter-TSS (NM_001033536)	-44	NM_001033536	319758	Mm.32081	NM_001033536	ENSMUSG00000037674	Rfx7	2510005N23Rik|9930116O05Rik|D130086K05Rik|Rfxdc2	regulatory factor X, 7	protein-coding
mm_166457.1	chr5	138231044	138231076	+	1	NA	intron (NM_001013773, intron 2 of 5)	B1_Mus1|SINE|Alu	5156	NM_001013773	381680	Mm.156846	NM_001013773	ENSMUSG00000047592	Nxpe5	-	neurexophilin and PC-esterase domain family, member 5	protein-coding
mm_66045.1	chr7	30671572	30671594	-	1	NA	promoter-TSS (NR_027849)	promoter-TSS (NR_027849)	22	NR_027849	74927	Mm.87326	NM_183108	ENSMUSG00000049761	Pmis2	1700071L20Rik|4930479M11Rik	Pmis2, sperm specific protein	ncRNA
mm_89030.1	chr10	82699210	82699218	+	1	NA	exon (NM_001081218, exon 1 of 15)	exon (NM_001081218, exon 1 of 15)	207	NM_001081218	67933	Mm.127405	NM_026462	ENSMUSG00000020246	Hcfc2	1700129L13Rik|AU019838	host cell factor C2	protein-coding
mm_169825.1	chr16	23108498	23108500	+	1	NA	promoter-TSS (NR_030705)	promoter-TSS (NR_030705)	-454	NR_030705	100216532		NR_030705	ENSMUSG00000088524	Snord2	-	small nucleolar RNA, C/D box 2	snoRNA
mm_20358.1	chr2	128179149	128179172	-	1	NA	Intergenic	Intergenic	51585	NM_001284410	12125	Mm.141083	NM_009754	ENSMUSG00000027381	Bcl2l11	1500006F24Rik|Bim|Bod|bcl2-L-11	BCL2-like 11 (apoptosis facilitator)	protein-coding
mm_78545.1	chr9	35305429	35305468	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	24343	NR_040715	71133	Mm.158577	NR_040715	ENSMUSG00000111746	4933422A05Rik	-	RIKEN cDNA 4933422A05 gene	ncRNA
mm_150997.1	chr19	46624371	46624386	+	1	NA	intron (NM_001177813, intron 1 of 3)	intron (NM_001177813, intron 1 of 3)	977	NM_001177813	226178	Mm.329895	NM_146099	ENSMUSG00000047731	Wbp1l	D19Wsu162e|Opal1	WW domain binding protein 1 like	protein-coding
mm_61746.1	chr7	82648596	82648653	+	1	NA	promoter-TSS (NM_001159672)	promoter-TSS (NM_001159672)	10	NM_175317	101592	Mm.238020	NM_175317	ENSMUSG00000038563	Efl1	4932434J20Rik|6030468D11Rik|AI451340|AU019507|AU022896|D7Ertd791e|Eftud1	elongation factor like GPTase 1	protein-coding
mm_113467.1	chr13	36255480	36255484	+	1	NA	intron (NM_001039189, intron 3 of 5)	intron (NM_001039189, intron 3 of 5)	137839	NM_001039189	69955	Mm.70690	NM_024274	ENSMUSG00000021420	Fars2	Fars1|pheRS	phenylalanine-tRNA synthetase 2 (mitochondrial)	protein-coding
mm_121303.1	chr14	105896123	105896134	+	1	NA	intron (NM_011897, intron 1 of 1)	CpG	691	NM_011897	24064	Mm.89982	NM_011897	ENSMUSG00000022114	Spry2	sprouty2	sprouty homolog 2 (Drosophila)	protein-coding
mm_97066.1	chr11	72946587	72946601	+	1	NA	Intergenic	Intergenic	-14575	NM_016745	53313	Mm.6306	NM_016745	ENSMUSG00000020788	Atp2a3	SERCA3b|Serca3	ATPase, Ca++ transporting, ubiquitous	protein-coding
mm_66138.1	chr7	31114701	31114716	-	1	NA	5' UTR (NM_008281, exon 2 of 13)	5' UTR (NM_008281, exon 2 of 13)	618	NM_008281	15451	Mm.19182	NM_008281	ENSMUSG00000001249	Hpn	Hlb320	hepsin	protein-coding
mm_152734.1	chr19	18936614	18936625	-	1	NA	3' UTR (NM_001289921, exon 11 of 11)	3' UTR (NM_001289921, exon 11 of 11)	64498	NM_146095	225998	Mm.234641	NM_146095	ENSMUSG00000036192	Rorb	Nr1f2|RZR-beta|RZRB|Rorbeta|hstp	RAR-related orphan receptor beta	protein-coding
mm_63272.1	chr7	126762218	126762221	+	1	NA	intron (NM_011952, intron 2 of 8)	B1F2|SINE|Alu	2593	NM_011952	26417	Mm.8385	NM_011952	ENSMUSG00000063065	Mapk3	Erk-1|Erk1|Ert2|Esrk1|Mnk1|Mtap2k|Prkm3|p44|p44erk1|p44mapk	mitogen-activated protein kinase 3	protein-coding
mm_51281.1	chr6	72162807	72162837	+	1	NA	Intergenic	Intergenic	-39625	NR_045165	71265	Mm.442035	NR_045163	ENSMUSG00000108709	4933431G14Rik	4930565C19Rik	RIKEN cDNA 4933431G14 gene	ncRNA
mm_22407.1	chr2	181294836	181294836	-	1	NA	Intergenic	B1_Mur2|SINE|Alu	-6870	NM_198169	229004	Mm.220423	NM_198169	ENSMUSG00000038705	Gmeb2	AI839884	glucocorticoid modulatory element binding protein 2	protein-coding
mm_128234.1	chr15	36608356	36608360	-	1	NA	exon (NM_008774, exon 1 of 15)	exon (NM_008774, exon 1 of 15)	615	NM_008774	18458	Mm.371570	NM_008774	ENSMUSG00000022283	Pabpc1	PABP|Pabp1|PabpI|Pabpl1|ePAB	poly(A) binding protein, cytoplasmic 1	protein-coding
mm_93477.1	chr10	111799859	111799881	-	1	NA	Intergenic	Intergenic	74506	NR_046029	629206	Mm.391444	NR_046029		Gm20758	-	predicted gene, 20758	ncRNA
mm_115207.1	chr13	109260307	109260342	+	1	NA	intron (NM_011056, intron 3 of 16)	intron (NM_011056, intron 3 of 16)	-64420	NR_030644	100124489		NR_030644	ENSMUSG00000076946	Mir582	Mirn582|mir-582|mmu-mir-582	microRNA 582	ncRNA
mm_66536.1	chr7	45154235	45154289	-	1	NA	promoter-TSS (NM_029406)	promoter-TSS (NM_029406)	-41	NM_029406	68845	Mm.181689	NM_029406	ENSMUSG00000003423	Pih1d1	1110061L23Rik|4933413A04Rik|Nop17	PIH1 domain containing 1	protein-coding
mm_136995.1	chr17	17402866	17402910	+	1	NA	5' UTR (NM_025681, exon 1 of 6)	5' UTR (NM_025681, exon 1 of 6)	202	NM_025681	66643	Mm.268018	NM_025681	ENSMUSG00000047786	Lix1	5730466L18Rik	limb and CNS expressed 1	protein-coding
mm_170863.1	chr2	181932167	181932181	+	1	NA	Intergenic	Intergenic	-59052	NM_001205282	672125	Mm.489571	NM_001205282	ENSMUSG00000098505	Gm14496	OTTMUSG00000016837	predicted gene 14496	protein-coding
mm_94407.1	chr11	5797541	5797554	+	1	NA	intron (NM_013810, intron 8 of 12)	intron (NM_013810, intron 8 of 12)	6249	NM_018870	56012	Mm.219627	NM_018870	ENSMUSG00000020475	Pgam2	-	phosphoglycerate mutase 2	protein-coding
mm_74057.1	chr8	122335961	122335972	+	1	NA	exon (NM_009569, exon 10 of 10)	exon (NM_009569, exon 10 of 10)	24780	NM_133202	170732	Mm.154808	NM_133202	ENSMUSG00000039079	Trhr2	TRH-R2	thyrotropin releasing hormone receptor 2	protein-coding
mm_141573.1	chr17	32320656	32320682	-	1	NA	TTS (NM_017476)	TTS (NM_017476)	569	NM_019774	56399	Mm.328945	NM_019774	ENSMUSG00000024045	Akap8	1200016A02Rik|AA673585|AKAP-8|AKAP95|AU015639	A kinase (PRKA) anchor protein 8	protein-coding
mm_49593.1	chr6	30645292	30645323	+	1	NA	TTS (NM_025350)	TTS (NM_025350)	6089	NM_025350	109697	Mm.25377	NM_025350	ENSMUSG00000054446	Cpa1	0910001L12Rik|Cpa	carboxypeptidase A1, pancreatic	protein-coding
mm_158449.1	chrX	140543115	140543130	-	1	NA	promoter-TSS (NM_010286)	promoter-TSS (NM_010286)	65	NM_010286	14605	Mm.22216	NM_010286	ENSMUSG00000031431	Tsc22d3	DIP|Dsip1|Gilz|TSC-22R|Tilz3	TSC22 domain family, member 3	protein-coding
mm_32041.1	chr4	95967206	95967320	+	1	NA	promoter-TSS (NR_045777)	promoter-TSS (NR_045777)	-116	NM_030014	77963	Mm.49994	NM_030014	ENSMUSG00000028572	Hook1	A930033L17Rik|azh	hook microtubule tethering protein 1	protein-coding
mm_76049.1	chr8	77670926	77670929	-	1	NA	intron (NM_010332, intron 5 of 7)	intron (NM_010332, intron 5 of 7)	46755	NR_045467	67357	Mm.71129	NR_045467	ENSMUSG00000086781	1700092C02Rik	-	RIKEN cDNA 1700092C02 gene	ncRNA
mm_172729.1	chr8	76411859	76411859	+	1	NA	Intergenic	Intergenic	488314	NR_028579	100039211	Mm.367571	NR_028579	ENSMUSG00000074235	Gm10649	ENSMUSG00000074235	predicted gene 10649	ncRNA
mm_39349.1	chr5	8912760	8912763	+	1	NA	intron (NM_008830, intron 8 of 27)	intron (NM_008830, intron 8 of 27)	19040	NM_008830	18670	Mm.297825	NM_008830	ENSMUSG00000042476	Abcb4	Mdr2|Pgy-2|Pgy2|mdr-2	ATP-binding cassette, sub-family B (MDR/TAP), member 4	protein-coding
mm_88789.1	chr10	80615392	80615435	+	1	NA	3' UTR (NM_019575, exon 7 of 7)	3' UTR (NM_019575, exon 7 of 7)	6153	NR_105877	102465550		NR_105877	ENSMUSG00000099283	Mir6912	Gm27990|mmu-mir-6912	microRNA 6912	ncRNA
mm_17703.1	chr2	32381910	32381920	-	1	NA	promoter-TSS (NM_198001)	promoter-TSS (NM_198001)	0	NM_198001	73737	Mm.27608	NM_198001	ENSMUSG00000039195	1110008P14Rik	C79326	RIKEN cDNA 1110008P14 gene	protein-coding
mm_40568.1	chr5	62880032	62880034	+	1	NA	intron (NM_001170705, intron 7 of 8)	Lx9|LINE|L1	66210	NM_001170705	100322896	Mm.479821	NM_001170705	ENSMUSG00000090326	Dthd1	Gm17384	death domain containing 1	protein-coding
mm_22101.1	chr2	169403368	169403369	-	1	NA	Intergenic	MTA_Mm|LTR|ERVL-MaLR	-230278	NM_080455	228911	Mm.315789	NM_080455	ENSMUSG00000047907	Tshz2	2900073F20Rik|B830045G17|Mtsh2|Sdccag33l|Tsh2|Zfp218|mKIAA4248|teashirt2	teashirt zinc finger family member 2	protein-coding
mm_33259.1	chr4	127172867	127172898	+	1	NA	promoter-TSS (NM_001302081)	promoter-TSS (NM_001302081)	2	NM_001302081	242667	Mm.331885	NM_198618	ENSMUSG00000042388	Dlgap3	BC058433|DAP-3|DAP3|Prpl8|Sapap3	discs, large (Drosophila) homolog-associated protein 3	protein-coding
mm_656.1	chr1	40433898	40433905	+	1	NA	intron (NM_001294171, intron 1 of 7)	intron (NM_001294171, intron 1 of 7)	4331	NM_001294171	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_120239.1	chr14	62926445	62926456	+	1	NA	intron (NM_175546, intron 4 of 11)	MLT1F2|LTR|ERVL-MaLR	58060	NM_001037751	432867	Mm.99387	NM_001037751	ENSMUSG00000075574	Defb48	Defb42|EG432867	defensin beta 48	protein-coding
mm_96664.1	chr11	69409675	69409689	+	1	NA	intron (NM_001017426, intron 1 of 22)	intron (NM_001017426, intron 1 of 22)	3993	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_171240.1	chr3	74242591	74242614	+	1	NA	Intergenic	Intergenic	-225325	NR_040450	100504692	Mm.394454	NR_040450	ENSMUSG00000104096	Gm20356	-	predicted gene, 20356	ncRNA
mm_57783.1	chr6	129268068	129268077	-	1	NA	3' UTR (NM_001033122, exon 5 of 5)	3' UTR (NM_001033122, exon 5 of 5)	7297	NM_001033122	12515	Mm.74745	NM_001033122	ENSMUSG00000030156	Cd69	5830438K24Rik|AI452015|AIM|VEA	CD69 antigen	protein-coding
mm_119223.1	chr14	33247691	33247719	+	1	NA	intron (NM_153800, intron 2 of 10)	intron (NM_153800, intron 2 of 10)	30882	NM_153800	239027	Mm.318350	NM_153800	ENSMUSG00000063506	Arhgap22	B230341L19Rik|RHOGAP2|p68RacGAP	Rho GTPase activating protein 22	protein-coding
mm_126735.1	chr15	85670994	85671019	+	1	NA	Intergenic	CpG	-32767	NR_110483	102800312	Mm.33117	NR_110483		Lncppara	Lincppara|Mirlet7bhg|linc-Ppara	long noncoding RNA near Ppara	ncRNA
mm_11042.1	chr2	27034658	27034668	+	1	NA	Intergenic	Intergenic	-6665	NM_001177627	227659	Mm.41203	NM_172659	ENSMUSG00000036067	Slc2a6	A330096C23|F630103L12Rik|Glut6|Glut9	solute carrier family 2 (facilitated glucose transporter), member 6	protein-coding
mm_153721.1	chr19	44406632	44406652	-	1	NA	exon (NM_009127, exon 2 of 6)	exon (NM_009127, exon 2 of 6)	1067	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_47342.1	chr5	122502628	122502654	-	1	NA	promoter-TSS (NM_009722)	promoter-TSS (NM_009722)	-416	NR_027838	11938	Mm.227583	NM_009722	ENSMUSG00000029467	Atp2a2	9530097L16Rik|D5Wsu150e|SERCA2|SERCA2B|Serca2a|mKIAA4195	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	protein-coding
mm_4269.1	chr1	171559097	171559120	+	1	NA	promoter-TSS (NM_018729)	promoter-TSS (NM_018729)	-85	NM_018729	18106	Mm.2299	NM_018729	ENSMUSG00000004709	Cd244	2B4|C9.1|F730046O15Rik|Ly90|NAIL|NKR2B4|Nmrk|SLAMF4	CD244 natural killer cell receptor 2B4	protein-coding
mm_168609.1	chr11	75733001	75733002	+	1	NA	5' UTR (NM_009536, exon 1 of 6)	5' UTR (NM_009536, exon 1 of 6)	114	NM_009536	22627	Mm.234700	NM_009536	ENSMUSG00000020849	Ywhae	AU019196	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide	protein-coding
mm_105817.1	chr11	112157331	112157361	-	1	NA	Intergenic	B3A|SINE|B2	554010	NR_024085	217294	Mm.297761	NM_146031	ENSMUSG00000041674	BC006965	-	cDNA sequence BC006965	ncRNA
mm_128238.1	chr15	36608622	36608622	-	1	NA	5' UTR (NM_008774, exon 1 of 15)	5' UTR (NM_008774, exon 1 of 15)	351	NM_008774	18458	Mm.371570	NM_008774	ENSMUSG00000022283	Pabpc1	PABP|Pabp1|PabpI|Pabpl1|ePAB	poly(A) binding protein, cytoplasmic 1	protein-coding
mm_39638.1	chr5	24483905	24483921	+	1	NA	TTS (NM_001256431)	TTS (NM_001256431)	31736	NM_139153	213990	Mm.250703	NM_139153	ENSMUSG00000023353	Agap3	AGAP-3|AV028425|Centg3|Crag|Crag.|MRIP-1|cnt-g3	ArfGAP with GTPase domain, ankyrin repeat and PH domain 3	protein-coding
mm_78171.1	chr9	21091729	21091767	+	1	NA	intron (NR_038081, intron 1 of 16)	CpG	240	NM_027911	71766	Mm.196137	NM_027911	ENSMUSG00000010205	Raver1	1300006N24Rik|AA050359|mKIAA1978	ribonucleoprotein, PTB-binding 1	protein-coding
mm_92053.1	chr10	62506283	62506295	-	1	NA	intron (NM_011157, intron 1 of 2)	intron (NM_011157, intron 1 of 2)	1466	NM_011157	19073	Mm.338790	NM_011157	ENSMUSG00000020077	Srgn	Prg|Prg1|Sgc	serglycin	protein-coding
mm_80082.1	chr9	70067919	70067933	+	1	NA	Intergenic	RSINE1|SINE|B4	-29838	NM_028087	72077	Mm.195555	NM_028087	ENSMUSG00000032226	Gcnt3	2010013H22Rik|2210021I22Rik|2210401J11Rik	glucosaminyl (N-acetyl) transferase 3, mucin type	protein-coding
mm_38969.1	chr4	150902156	150902180	-	1	NA	intron (NM_020569, intron 5 of 6)	intron (NM_020569, intron 5 of 6)	7753	NM_020569	57320	Mm.277349	NM_020569	ENSMUSG00000028964	Park7	DJ-1|Dj1	Parkinson disease (autosomal recessive, early onset) 7	protein-coding
mm_33504.1	chr4	130905236	130905270	+	1	NA	Intergenic	MIRc|SINE|MIR	-8081	NM_010686	16792	Mm.271868	NM_010686	ENSMUSG00000028581	Laptm5	E3	lysosomal-associated protein transmembrane 5	protein-coding
mm_128373.1	chr15	42676305	42676344	-	1	NA	exon (NM_001286062, exon 1 of 9)	exon (NM_001286062, exon 1 of 9)	653	NM_001286062	11600	Mm.309336	NM_009640	ENSMUSG00000022309	Angpt1	1110046O21Rik|Ang-1|Ang1	angiopoietin 1	protein-coding
mm_150482.1	chr19	38931035	38931039	+	1	NA	promoter-TSS (NM_008234)	promoter-TSS (NM_008234)	47	NM_008234	15201	Mm.57223	NM_008234	ENSMUSG00000025001	Hells	AI323785|E130115I21Rik|LSH|Lysh|PASG|YFK8	helicase, lymphoid specific	protein-coding
mm_137552.1	chr17	27561353	27561359	+	1	NA	intron (NM_001166546, intron 3 of 4)	intron (NM_001166546, intron 3 of 4)	4371	NM_001002895	106672	Mm.61488	NM_001002895	ENSMUSG00000062753	AI413582	AI854251	expressed sequence AI413582	protein-coding
mm_31545.1	chr4	55532712	55532764	+	1	NA	promoter-TSS (NM_010637)	promoter-TSS (NM_010637)	-263	NM_010637	16600	Mm.4325	NM_010637	ENSMUSG00000003032	Klf4	EZF|Gklf|Zie	Kruppel-like factor 4 (gut)	protein-coding
mm_14337.1	chr2	129592967	129592986	+	1	NA	promoter-TSS (NM_001291022)	promoter-TSS (NM_001291022)	137	NM_001291020	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_154184.1	chr19	58793301	58793307	-	1	NA	intron (NM_026208, intron 1 of 5)	intron (NM_026208, intron 1 of 5)	1110	NM_026208	67507	Mm.27027	NM_026208	ENSMUSG00000026931	1700019N19Rik	-	RIKEN cDNA 1700019N19 gene	protein-coding
mm_5785.1	chr1	51797030	51797071	-	1	NA	exon (NM_010863, exon 11 of 30)	exon (NM_010863, exon 11 of 30)	118928	NM_001290982	17912	Mm.3390	NM_010863	ENSMUSG00000018417	Myo1b	AA406997|MIH-L|MMIa	myosin IB	protein-coding
mm_114660.1	chr13	78118258	78118261	+	1	NA	intron (NM_001163420, intron 8 of 8)	intron (NM_001163420, intron 8 of 8)	78190	NM_001347538	13865	Mm.439653	NM_010151	ENSMUSG00000069171	Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR-3|EAR3|Erbal3|SVP44|Tcfcoup1	nuclear receptor subfamily 2, group F, member 1	protein-coding
mm_59993.1	chr7	30555036	30555047	+	1	NA	TTS (NM_001290569)	TTS (NM_001290569)	1739	NM_001012401	243912	Mm.34885	NM_001012401	ENSMUSG00000036854	Hspb6	AA387366|Gm479|Hsp20	heat shock protein, alpha-crystallin-related, B6	protein-coding
mm_90050.1	chr10	116143882	116143902	+	1	NA	promoter-TSS (NM_001161837)	promoter-TSS (NM_001161837)	-6	NM_001161837	19279	Mm.336316	NM_011217	ENSMUSG00000020151	Ptprr	Gmcp1|PTP-SL|PTPBR7|RPTPRR|mPTP213	protein tyrosine phosphatase, receptor type, R	protein-coding
mm_126948.1	chr15	92160686	92160696	+	1	NA	promoter-TSS (NM_001159647)	promoter-TSS (NM_001159647)	-666	NM_001159647	12805	Mm.4911	NM_007727	ENSMUSG00000055022	Cntn1	AW495098|CNTN|F3cam|usl	contactin 1	protein-coding
mm_39952.1	chr5	32133540	32133564	+	1	NA	Intergenic	CpG	-2920	NM_008037	14284	Mm.24684	NM_008037	ENSMUSG00000029135	Fosl2	Fra-2	fos-like antigen 2	protein-coding
mm_170173.1	chr1	75713842	75713842	-	1	NA	Intergenic	L1Md_T|LINE|L1	167576	NM_009208	20536	Mm.5053	NM_009208	ENSMUSG00000006576	Slc4a3	A930038D23Rik|Ae3	solute carrier family 4 (anion exchanger), member 3	protein-coding
mm_71158.1	chr8	40423787	40423848	+	1	NA	promoter-TSS (NM_178395)	promoter-TSS (NM_178395)	2	NM_178395	70546	Mm.34326	NM_178395	ENSMUSG00000039470	Zdhhc2	5730415P04Rik|6430583A19Rik	zinc finger, DHHC domain containing 2	protein-coding
mm_48294.1	chr5	138207303	138207317	-	1	NA	Intergenic	Intergenic	12996	NM_177878	330216	Mm.19719	NM_177878	ENSMUSG00000049285	Mblac1	-	metallo-beta-lactamase domain containing 1	protein-coding
mm_117122.1	chr13	60897426	60897430	-	1	NA	promoter-TSS (NM_007797)	promoter-TSS (NM_007797)	19	NM_007797	13025	Mm.30144	NM_007797	ENSMUSG00000074874	Ctla2b	AW545568|Ctla-2b	cytotoxic T lymphocyte-associated protein 2 beta	protein-coding
mm_48617.1	chr5	144761579	144761631	-	1	NA	promoter-TSS (NM_177735)	promoter-TSS (NM_177735)	-27	NM_177735	243339	Mm.126793	NM_177735	ENSMUSG00000043388	Tmem130	BC067004|C130036G08	transmembrane protein 130	protein-coding
mm_23174.1	chr3	40784097	40784099	+	1	NA	intron (NM_011020, intron 14 of 18)	L1MB4|LINE|L1	-15853	NM_173169	20873	Mm.3794	NM_011495	ENSMUSG00000025758	Plk4	1700028H20|AI385771|Sak|Stk18	polo-like kinase 4	protein-coding
mm_105369.1	chr11	103208532	103208534	-	1	NA	promoter-TSS (NM_001254724)	promoter-TSS (NM_001254724)	15	NM_001254724	69441	Mm.380648	NM_027082	ENSMUSG00000020940	1700023F06Rik	-	RIKEN cDNA 1700023F06 gene	protein-coding
mm_45361.1	chr5	66001328	66001347	-	1	NA	non-coding (NR_027961, exon 2 of 7)	non-coding (NR_027961, exon 2 of 7)	2948	NR_027961	231253	Mm.436542	NM_177679	ENSMUSG00000054598	9130230L23Rik	-	RIKEN cDNA 9130230L23 gene	ncRNA
mm_163511.1	chr12	113259121	113259141	-	1	NA	Intergenic	Intergenic	73228	NM_153776	69195	Mm.313244	NM_153776	ENSMUSG00000049036	Tmem121	2410008J05Rik|Hole	transmembrane protein 121	protein-coding
mm_161516.1	chr15	99126179	99126179	+	1	NA	promoter-TSS (NM_139140)	promoter-TSS (NM_139140)	-666	NM_139140	72572	Mm.276650	NM_139140	ENSMUSG00000051934	Spats2	2700012F11Rik|59kDa|Scr59|p59	spermatogenesis associated, serine-rich 2	protein-coding
mm_155554.1	chrX	74449702	74449712	+	1	NA	3' UTR (NM_178590, exon 10 of 10)	3' UTR (NM_178590, exon 10 of 10)	20026	NM_010547	16151	Mm.12967	NM_010547	ENSMUSG00000004221	Ikbkg	1110037D23Rik|AI848108|AI851264|AW124339|IKK[g]|NEMO	inhibitor of kappaB kinase gamma	protein-coding
mm_59038.1	chr7	19333068	19333098	+	1	NA	Intergenic	CpG	-11988	NM_001127324	13870	Mm.280913	NM_007948	ENSMUSG00000003549	Ercc1	Ercc-1	excision repair cross-complementing rodent repair deficiency, complementation group 1	protein-coding
mm_106534.1	chr11	120573705	120573715	-	1	NA	promoter-TSS (NM_011032)	promoter-TSS (NM_011032)	-774	NM_011032	18453	Mm.16660	NM_011032	ENSMUSG00000025130	P4hb	ERp59|PDI|Pdia1|Thbp	prolyl 4-hydroxylase, beta polypeptide	protein-coding
mm_43326.1	chr5	135009308	135009317	+	1	NA	promoter-TSS (NM_145215)	promoter-TSS (NM_145215)	13	NM_145215	68758	Mm.389700	NM_145215	ENSMUSG00000040532	Abhd11	1110054D16Rik|A630008N09Rik|Wbscr21	abhydrolase domain containing 11	protein-coding
mm_145818.1	chr18	65431050	65431078	+	1	NA	promoter-TSS (NM_172833)	promoter-TSS (NM_172833)	67	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_98750.1	chr11	96545374	96545395	+	1	NA	intron (NM_001033186, intron 4 of 12)	intron (NM_001033186, intron 4 of 12)	80793	NM_001177898	78473	Mm.395840	NM_001033186	ENSMUSG00000057058	Skap1	1700091G21Rik|Scap1|Skap-55	src family associated phosphoprotein 1	protein-coding
mm_161643.1	chr16	96235605	96235605	+	1	NA	promoter-TSS (NM_001122993)	promoter-TSS (NM_001122993)	-196	NM_001122993	93961	Mm.154783	NM_033149	ENSMUSG00000074892	B3galt5	1190002B21Rik|AU045265|b3Galt-V	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 5	protein-coding
mm_172745.1	chr8	80739294	80739298	-	1	NA	5' UTR (NM_053124, exon 1 of 24)	5' UTR (NM_053124, exon 1 of 24)	163	NM_053124	93762	Mm.246803	NM_053124	ENSMUSG00000031715	Smarca5	4933427E24Rik|D030040M08Rik|D330027N15Rik|MommeD4|Snf2h	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5	protein-coding
mm_81296.1	chr9	108339049	108339070	+	1	NA	promoter-TSS (NM_008160)	promoter-TSS (NM_008160)	-21	NM_008160	14775	Mm.1090	NM_008160	ENSMUSG00000063856	Gpx1	AI195024|AL033363|CGPx|GPx-1|GSHPx-1|Gpx	glutathione peroxidase 1	protein-coding
mm_171389.1	chr4	122141696	122141696	+	1	NA	Intergenic	RLTR10C|LTR|ERVK	-519571	NM_001099309	666927	Mm.465133	NM_001099309	ENSMUSG00000078575	Gm12887	OTTMUSG00000008910	predicted gene 12887	protein-coding
mm_11998.1	chr2	57116897	57116905	+	1	NA	intron (NM_001139509, intron 1 of 7)	intron (NM_001139509, intron 1 of 7)	-1863	NM_013613	18227	Mm.3507	NM_013613	ENSMUSG00000026826	Nr4a2	HZF-3|NOT|Nurr1|RNR-1|TINOR|TINUR	nuclear receptor subfamily 4, group A, member 2	protein-coding
mm_100755.1	chr11	4346899	4346908	-	1	NA	intron (NM_029458, intron 10 of 10)	intron (NM_029458, intron 10 of 10)	80107	NM_001039537	16878	Mm.4964	NM_008501	ENSMUSG00000034394	Lif	-	leukemia inhibitory factor	protein-coding
mm_150034.1	chr19	29376657	29376670	+	1	NA	intron (NM_021893, intron 3 of 6)	intron (NM_021893, intron 3 of 6)	9225	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_116683.1	chr13	49248714	49248725	-	1	NA	promoter-TSS (NM_028340)	promoter-TSS (NM_028340)	-13	NM_028340	66329	Mm.34308	NM_025491	ENSMUSG00000021384	Susd3	1700017I11Rik|2810440J20Rik	sushi domain containing 3	protein-coding
mm_56957.1	chr6	120037861	120037880	-	1	NA	5' UTR (NM_001185020, exon 1 of 26)	5' UTR (NM_001185020, exon 1 of 26)	785	NM_001199083	232341	Mm.333349	NM_198703	ENSMUSG00000045962	Wnk1	6430573H23Rik|EG406236|Hsn2|Prkwnk1|mKIAA0344	WNK lysine deficient protein kinase 1	protein-coding
mm_79866.1	chr9	65077924	65077940	+	1	NA	intron (NM_028906, intron 18 of 20)	intron (NM_028906, intron 18 of 20)	-23554	NM_001290315	56741	Mm.209041	NM_020043	ENSMUSG00000032816	Igdcc4	DDM36|Nope	immunoglobulin superfamily, DCC subclass, member 4	protein-coding
mm_48566.1	chr5	143247628	143247633	-	1	NA	3' UTR (NM_001289590, exon 5 of 5)	3' UTR (NM_001289590, exon 5 of 5)	12467	NM_177681	231866	Mm.55211	NM_177681	ENSMUSG00000029587	Zfp12	C530015C18|Krox-7|Zfp-12|Znf12	zinc finger protein 12	protein-coding
mm_57818.1	chr6	129462729	129462737	-	1	NA	non-coding (NR_132130, exon 6 of 6)	non-coding (NR_132130, exon 6 of 6)	10046	NM_001309637	56644	Mm.239516	NM_020008	ENSMUSG00000079293	Clec7a	BGR|Clecsf12|beta-GR	C-type lectin domain family 7, member a	protein-coding
mm_75932.1	chr8	71525720	71525730	-	1	NA	Intergenic	CpG	11712	NM_198095	69550	Mm.260325	NM_198095	ENSMUSG00000046718	Bst2	2310015I10Rik|Bst-2|C87040|CD317|DAMP-1|GREG	bone marrow stromal cell antigen 2	protein-coding
mm_173185.1	chrX	60058098	60058099	-	1	NA	intron (NM_001289730, intron 25 of 25)	L1Md_F2|LINE|L1	58634	NM_001305797	14071	Mm.391283	NM_007979	ENSMUSG00000031138	F9	AW111646|Cf-9|Cf9	coagulation factor IX	protein-coding
mm_63375.1	chr7	127211698	127211711	+	1	NA	promoter-TSS (NM_016754)	promoter-TSS (NM_016754)	96	NM_016754	17907	Mm.14526	NM_016754	ENSMUSG00000030672	Mylpf	2410014J02Rik|MLC-2|Mlc2	myosin light chain, phosphorylatable, fast skeletal muscle	protein-coding
mm_64257.1	chr7	141744725	141744754	+	1	NA	exon (NM_023566, exon 28 of 46)	exon (NM_023566, exon 28 of 46)	-44272	NM_010844	17833	Mm.334332	NM_010844	ENSMUSG00000037974	Muc5ac	2210005L13Rik|MGM	mucin 5, subtypes A and C, tracheobronchial/gastric	protein-coding
mm_22481.1	chr3	5221190	5221203	+	1	NA	promoter-TSS (NR_045905)	promoter-TSS (NR_045905)	-373	NR_045905	72608	Mm.384359	NR_045905		2700069I18Rik	-	RIKEN cDNA 2700069I18 gene	ncRNA
mm_140933.1	chr17	24414398	24414451	-	1	NA	promoter-TSS (NM_001080128)	promoter-TSS (NM_001080128)	89	NR_033554	654822	Mm.489806	NM_001039561	ENSMUSG00000073437	D330041H03Rik	-	RIKEN cDNA D330041H03 gene	ncRNA
mm_79972.1	chr9	66593230	66593240	+	1	NA	promoter-TSS (NM_144937)	promoter-TSS (NM_144937)	-120	NM_001302122	235441	Mm.32465	NM_144937	ENSMUSG00000032376	Usp3	AA409661|BC017156	ubiquitin specific peptidase 3	protein-coding
mm_99373.1	chr11	101984271	101984289	+	1	NA	intron (NM_028207, intron 1 of 2)	intron (NM_028207, intron 1 of 2)	511	NM_028207	72349	Mm.196295	NM_028207	ENSMUSG00000003518	Dusp3	2210015O03Rik|5031436O03Rik|T-DSP11|VHR	dual specificity phosphatase 3 (vaccinia virus phosphatase VH1-related)	protein-coding
mm_46022.1	chr5	90905276	90905297	-	1	NA	3' UTR (NM_009140, exon 4 of 4)	3' UTR (NM_009140, exon 4 of 4)	1387	NM_009140	20310	Mm.4979	NM_009140	ENSMUSG00000058427	Cxcl2	CINC-2a|GROb|Gro2|MIP-2|MIP-2a|Mgsa-b|Mip2|Scyb|Scyb2	chemokine (C-X-C motif) ligand 2	protein-coding
mm_19308.1	chr2	90525033	90525045	-	1	NA	intron (NM_008982, intron 1 of 23)	intron (NM_008982, intron 1 of 23)	-45865	NM_001135657	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_74308.1	chr8	126592180	126592202	+	1	NA	intron (NM_001164598, intron 1 of 1)	intron (NM_001164598, intron 1 of 1)	1245	NM_001164598	270110	Mm.334918	NM_001164598	ENSMUSG00000051495	Irf2bp2	E130305N23Rik|IRF-2BP2	interferon regulatory factor 2 binding protein 2	protein-coding
mm_54799.1	chr6	41687557	41687584	-	1	NA	exon (NM_032540, exon 18 of 19)	exon (NM_032540, exon 18 of 19)	3139	NM_029671	76606	Mm.272520	NM_029671	ENSMUSG00000029867	1700034O15Rik	-	RIKEN cDNA 1700034O15 gene	protein-coding
mm_16754.1	chr2	9868835	9868845	-	1	NA	exon (NM_008091, exon 4 of 6)	exon (NM_008091, exon 4 of 6)	9760	NM_008091	14462	Mm.313866	NM_008091	ENSMUSG00000015619	Gata3	Gata-3|jal	GATA binding protein 3	protein-coding
mm_133446.1	chr16	87787541	87787551	+	1	NA	Intergenic	Intergenic	88592	NM_007520	12013	Mm.26147	NM_007520	ENSMUSG00000025612	Bach1	6230421P05Rik|AI323795	BTB and CNC homology 1, basic leucine zipper transcription factor 1	protein-coding
mm_105552.1	chr11	106388107	106388117	-	1	NA	Intergenic	Intergenic	-5331	NM_010494	15896	Mm.394	NM_010494	ENSMUSG00000001029	Icam2	CD102|Icam-2|Ly-60	intercellular adhesion molecule 2	protein-coding
mm_156968.1	chrX	169997221	169997276	+	1	NA	Intergenic	CpG	-18331	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_131377.1	chr16	13940631	13940722	+	1	NA	promoter-TSS (NM_033564)	promoter-TSS (NM_033564)	11	NM_033564	93734	Mm.76554	NM_033564	ENSMUSG00000022679	Mpv17l	M-LP	Mpv17 transgene, kidney disease mutant-like	protein-coding
mm_81667.1	chr9	111025036	111025048	+	1	NA	exon (NM_008522, exon 8 of 17)	exon (NM_008522, exon 8 of 17)	5750	NM_008522	17002	Mm.282359	NM_008522	ENSMUSG00000032496	Ltf	Csp82|Lf|MMS10R|Ms10r	lactotransferrin	protein-coding
mm_6645.1	chr1	79666818	79666820	-	1	NA	intron (NM_183027, intron 1 of 4)	RMER10A|LTR|ERVL	5153	NM_183027	252903	Mm.32409	NM_183027	ENSMUSG00000054702	Ap1s3	1190009B22|Jr2|[s]3A	adaptor-related protein complex AP-1, sigma 3	protein-coding
mm_129434.1	chr15	78495060	78495073	-	1	NA	promoter-TSS (NM_008368)	promoter-TSS (NM_008368)	0	NM_008368	16185	Mm.35287	NM_008368	ENSMUSG00000068227	Il2rb	CD122|IL-15Rbeta|IL15Rbeta|Il-2/15Rbeta|Il-2Rbeta|p70	interleukin 2 receptor, beta chain	protein-coding
mm_139786.1	chr17	65800037	65800046	+	1	NA	intron (NM_001114131, intron 2 of 19)	intron (NM_001114131, intron 2 of 19)	16686	NR_104465	70351	Mm.48686	NM_146081	ENSMUSG00000061950	Ppp4r1	3110001J10Rik|Pp4r1	protein phosphatase 4, regulatory subunit 1	protein-coding
mm_67706.1	chr7	89941068	89941070	-	1	NA	non-coding (NR_111916, exon 1 of 1)	non-coding (NR_111916, exon 1 of 1)	135	NM_001291289	67669	Mm.28679	NM_026304	ENSMUSG00000062797	Hikeshi	0610007P06Rik|1110002N09Rik|l(7)6Rn|l7Rn6	heat shock protein nuclear import factor	protein-coding
mm_118322.1	chr13	113600761	113600769	-	1	NA	intron (NM_130796, intron 1 of 1)	intron (NM_130796, intron 1 of 1)	17799	NM_130796	170625	Mm.33721	NM_130796	ENSMUSG00000042364	Snx18	Snag1	sorting nexin 18	protein-coding
mm_66817.1	chr7	48393517	48393519	-	1	NA	Intergenic	Lx3B|LINE|L1	4992	NM_207539	404240	Mm.357942	NM_207539	ENSMUSG00000050870	Mrgprb8	MrgB8	MAS-related GPR, member B8	protein-coding
mm_103247.1	chr11	70812511	70812532	-	1	NA	promoter-TSS (NM_001045526)	promoter-TSS (NM_001045526)	40	NM_001045526	327957	Mm.164325	NM_001045526	ENSMUSG00000057135	Scimp	A430084P05Rik	SLP adaptor and CSK interacting membrane protein	protein-coding
mm_51181.1	chr6	70726859	70726869	+	1	NA	Intergenic	Intergenic	65311	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_141640.1	chr17	33139673	33139675	-	1	NA	promoter-TSS (NM_177719)	promoter-TSS (NM_177719)	9	NM_177719	240069	Mm.157765	NM_177719	ENSMUSG00000048602	Morc2b	4932411A10Rik|Tce6	microrchidia 2B	protein-coding
mm_2040.1	chr1	87264346	87264370	+	1	NA	promoter-TSS (NM_028889)	promoter-TSS (NM_028889)	-6	NM_028889	98363	Mm.247951	NM_028889	ENSMUSG00000026255	Efhd1	4931430I01Rik|AI452351|PP3051|mitocalcin	EF hand domain containing 1	protein-coding
mm_94793.1	chr11	22971992	22972070	+	1	NA	promoter-TSS (NM_011663)	promoter-TSS (NM_011663)	26	NM_011663	22183	Mm.29542	NM_011663	ENSMUSG00000044068	Zrsr1	D11Ncvs75|Irlgs2|SP2|U2af1-rs1|U2afbp-rs	zinc finger (CCCH type), RNA binding motif and serine/arginine rich 1	protein-coding
mm_83398.1	chr9	44734013	44734024	-	1	NA	intron (NM_153537, intron 1 of 21)	CpG	1180	NM_153537	102693	Mm.28639	NM_153537	ENSMUSG00000048537	Phldb1	AU041016|D330037A14Rik|Ll5a	pleckstrin homology like domain, family B, member 1	protein-coding
mm_77192.1	chr8	111992259	111992295	-	1	NA	promoter-TSS (NM_013925)	promoter-TSS (NM_013925)	25	NM_013925	30947	Mm.282162	NM_013925	ENSMUSG00000031949	Adat1	MMADAT1|mADAT1	adenosine deaminase, tRNA-specific 1	protein-coding
mm_7476.1	chr1	120504750	120504768	-	1	NA	exon (NM_010766, exon 1 of 17)	exon (NM_010766, exon 1 of 17)	325	NM_010766	17167	Mm.1856	NM_010766	ENSMUSG00000026390	Marco	AI323439|Ly112|Scara2	macrophage receptor with collagenous structure	protein-coding
mm_140209.1	chr17	83775657	83775667	+	1	NA	exon (NM_001171052, exon 9 of 16)	exon (NM_001171052, exon 9 of 16)	69499	NM_001171052	116871	Mm.277668	NM_054082	ENSMUSG00000055817	Mta3	1110002J22Rik|mKIAA1266	metastasis associated 3	protein-coding
mm_96473.1	chr11	67652599	67652637	+	1	NA	intron (NM_001109657, intron 4 of 13)	intron (NM_001109657, intron 4 of 13)	-42708	NM_009038	19674	Mm.439726	NM_009038	ENSMUSG00000020907	Rcvrn	CAR|S-modulin	recoverin	protein-coding
mm_86302.1	chr9	122349229	122349255	-	1	NA	Intergenic	Intergenic	-2374	NM_026179	67469	Mm.280254	NM_026179	ENSMUSG00000032540	Abhd5	1300003D03Rik|2010002J10Rik|CDS|CGI-58|IECN5|NCIE2	abhydrolase domain containing 5	protein-coding
mm_83508.1	chr9	45984529	45984561	-	1	NA	intron (NM_008775, intron 1 of 5)	CpG	326	NM_008775	18475	Mm.200859	NM_008775	ENSMUSG00000003131	Pafah1b2	AI747451|AU021353|Pafahb|mus[b]	platelet-activating factor acetylhydrolase, isoform 1b, subunit 2	protein-coding
mm_73477.1	chr8	106917621	106917640	+	1	NA	exon (NM_011574, exon 14 of 17)	exon (NM_011574, exon 14 of 17)	-18120	NM_009229	20650	Mm.30228	NM_009229	ENSMUSG00000041308	Sntb2	Snt2	syntrophin, basic 2	protein-coding
mm_84757.1	chr9	75572801	75572804	-	1	NA	3' UTR (NM_001038710, exon 10 of 10)	3' UTR (NM_001038710, exon 10 of 10)	-13145	NM_016963	50875	Mm.38445	NM_016963	ENSMUSG00000058587	Tmod3	U-Tmod|UTMOD	tropomodulin 3	protein-coding
mm_148315.1	chr18	83768126	83768147	-	1	NA	Intergenic	Intergenic	318426	NM_001081300	110796	Mm.102136	NM_001081300	ENSMUSG00000046982	Tshz1	5730407I04Rik|D18Bwg1409e|Mtsh1|NY-CO-33|Sdccag33|Tsh1|mKIAA4206|teashirt1	teashirt zinc finger family member 1	protein-coding
mm_76982.1	chr8	106893582	106893609	-	1	NA	promoter-TSS (NM_011574)	promoter-TSS (NM_011574)	-2	NM_145412	214987	Mm.490308	NM_145412	ENSMUSG00000046691	Chtf8	5830457O10Rik|Ctf8|Derpc	CTF8, chromosome transmission fidelity factor 8	protein-coding
mm_48784.1	chr5	148553857	148553881	-	1	NA	Intergenic	Intergenic	-1081	NM_011908	24109	Mm.21846	NM_011908	ENSMUSG00000001687	Ubl3	AW108023|HCG	ubiquitin-like 3	protein-coding
mm_104129.1	chr11	86807542	86807553	-	1	NA	exon (NM_026191, exon 1 of 18)	exon (NM_026191, exon 1 of 18)	113	NM_026191	67487	Mm.260627	NM_026191	ENSMUSG00000018425	Dhx40	2410016C14Rik|ARG147|DDX40|PAD	DEAH (Asp-Glu-Ala-His) box polypeptide 40	protein-coding
mm_67330.1	chr7	79733338	79733345	-	1	NA	promoter-TSS (NM_175640)	promoter-TSS (NM_175640)	-565	NM_001113471	103968	Mm.254917	NM_175640	ENSMUSG00000030546	Plin1	6030432J05Rik|Peri|Plin	perilipin 1	protein-coding
mm_104237.1	chr11	88718049	88718059	-	1	NA	promoter-TSS (NR_038058)	promoter-TSS (NR_038058)	175	NM_054043	76626	Mm.400451	NM_054043	ENSMUSG00000069769	Msi2	1700105C15Rik|AI451722|AI563628|AW489193|Msi2h	musashi RNA-binding protein 2	protein-coding
mm_122961.1	chr14	54970716	54970727	-	1	NA	TTS (NM_080728)	TTS (NM_080728)	1934	NR_033497	791403	Mm.319176	NR_033497	ENSMUSG00000097652	Mhrt	D830015G02Rik|ENSMUSG00000053118|Myheart	myosin heavy chain associated RNA transcript	ncRNA
mm_97685.1	chr11	80089427	80089469	+	1	NA	promoter-TSS (NM_001029856)	promoter-TSS (NM_001029856)	48	NM_001029856	237877	Mm.89551	NM_001029856	ENSMUSG00000017550	Atad5	C130052G03Rik|FRAG1|Gm17	ATPase family, AAA domain containing 5	protein-coding
mm_66515.1	chr7	45103727	45103733	-	1	NA	promoter-TSS (NM_010189)	promoter-TSS (NM_010189)	92	NM_010189	14132	Mm.3303	NM_010189	ENSMUSG00000003420	Fcgrt	FcRn	Fc receptor, IgG, alpha chain transporter	protein-coding
mm_141364.1	chr17	28915315	28915330	-	1	NA	promoter-TSS (NM_172450)	promoter-TSS (NM_172450)	2	NM_172450	207819	Mm.248931	NM_172450	ENSMUSG00000048905	4930539E08Rik	9130014G02	RIKEN cDNA 4930539E08 gene	protein-coding
mm_91808.1	chr10	53957372	53957380	-	1	NA	intron (NM_008548, intron 6 of 12)	intron (NM_008548, intron 6 of 12)	118420	NM_008548	17155	Mm.117294	NM_008548	ENSMUSG00000003746	Man1a	Man1a1|PCR1	mannosidase 1, alpha	protein-coding
mm_97393.1	chr11	77802407	77802422	+	1	NA	intron (NM_001291214, intron 1 of 38)	intron (NM_001291214, intron 1 of 38)	1116	NM_001291215	360013	Mm.341248	NM_011586	ENSMUSG00000000631	Myo18a	MAJN|MyoPDZ|MysPDZ|SP-R210	myosin XVIIIA	protein-coding
mm_117010.1	chr13	58020946	58020950	-	1	NA	intron (NM_001195075, intron 10 of 16)	intron (NM_001195075, intron 10 of 16)	2252	NR_030544	100124491		NR_030544	ENSMUSG00000077962	Mir874	Mirn874|mir-874|mmu-mir-874	microRNA 874	ncRNA
mm_94933.1	chr11	29693160	29693168	+	1	NA	promoter-TSS (NM_194051)	promoter-TSS (NM_194051)	266	NM_194052	68585	Mm.192580	NM_024226	ENSMUSG00000020458	Rtn4	1110020G17Rik|AA407876|AA409940|AA960376|ASY|C130026I10Rik|NOGO|NSP-CL|NgA|Nogo-A|Nogo-B|Nogo-C|mKIAA0886|mKIAA4153	reticulon 4	protein-coding
mm_33222.1	chr4	126677697	126677702	+	1	NA	promoter-TSS (NM_011970)	promoter-TSS (NM_011970)	56	NM_011970	26445	Mm.22233	NM_011970	ENSMUSG00000028837	Psmb2	AU045357|AW108089|C7-I|D4Wsu33e|HC7-I	proteasome (prosome, macropain) subunit, beta type 2	protein-coding
mm_147833.1	chr18	62548722	62548765	-	1	NA	promoter-TSS (NM_177829)	promoter-TSS (NM_177829)	0	NM_134136	107035	Mm.21295	NM_134136	ENSMUSG00000042211	Fbxo38	6030410I24Rik|AU044865|AW214031|Moka|SP329	F-box protein 38	protein-coding
mm_53290.1	chr6	129008790	129008800	+	1	NA	Intergenic	RLTR34B_MM|LTR|ERVK	-5317	NM_001277202	435921	Mm.489572	NM_001277202		Clec2f	Clec2f-ps|Clr-c|Clrc|Clrz	C-type lectin domain family 2, member f	protein-coding
mm_26074.1	chr3	136670421	136670426	+	1	NA	5' UTR (NM_001293622, exon 1 of 13)	5' UTR (NM_001293622, exon 1 of 13)	357	NM_001293622	19055	Mm.331389	NM_008913	ENSMUSG00000028161	Ppp3ca	2900074D19Rik|CN|Caln|Calna|CnA	protein phosphatase 3, catalytic subunit, alpha isoform	protein-coding
mm_37587.1	chr4	126429502	126429513	-	1	NA	promoter-TSS (NM_153402)	promoter-TSS (NM_153402)	35	NM_153402	214150	Mm.440915	NM_153402	ENSMUSG00000028842	Ago3	AW048688|C130014L07Rik|Eif2c3	argonaute RISC catalytic subunit 3	protein-coding
mm_145868.1	chr18	65463275	65463312	+	1	NA	intron (NM_172833, intron 10 of 15)	intron (NM_172833, intron 10 of 15)	32296	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_40262.1	chr5	38277398	38277423	+	1	NA	promoter-TSS (NM_172709)	promoter-TSS (NM_172709)	6	NM_172709	21906	Mm.204765	NM_172709	ENSMUSG00000051596	Otop1	A530025J20Rik|Otp1|tlt	otopetrin 1	protein-coding
mm_20786.1	chr2	143989880	143989903	-	1	NA	exon (NM_133626, exon 2 of 3)	exon (NM_133626, exon 2 of 3)	21372	NM_133626	81910	Mm.13705	NM_024281	ENSMUSG00000027422	Rrbp1	1700087N07Rik|5730465C04Rik|ES/130|mKIAA1398|mRRp0|mRRp1.8|mRRp10|mRRp15a|mRRp15b|mRRp16.8|mRRp2|mRRp41|mRRp47|mRRp5.4|p180	ribosome binding protein 1	protein-coding
mm_81185.1	chr9	107534001	107534024	+	1	NA	promoter-TSS (NM_019704)	promoter-TSS (NM_019704)	67	NM_019704	56395	Mm.260153	NM_019704	ENSMUSG00000010045	Tmem115	C78915|Pl6|Pp6	transmembrane protein 115	protein-coding
mm_16579.1	chr2	3512747	3512782	-	1	NA	promoter-TSS (NR_103465)	promoter-TSS (NR_103465)	50	NR_103465	50497	Mm.89341	NM_015765	ENSMUSG00000051396	Hspa14	70kDa|HSP70L1|Hsp70-4|NST-1|hsr.1	heat shock protein 14	protein-coding
mm_156152.1	chrX	129943853	129943868	+	1	NA	exon (NM_172493, exon 9 of 27)	exon (NM_172493, exon 9 of 27)	194118	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diaph2	Dia3|Diap2|Drf2|E430022I22Rik	diaphanous related formin 2	protein-coding
mm_157583.1	chrX	53055377	53055391	-	1	NA	non-coding (NR_038185, exon 4 of 4)	non-coding (NR_038185, exon 4 of 4)	-1035	NR_029756	723907		NR_029756	ENSMUSG00000065418	Mir322	Mirn322|mmu-mir-322	microRNA 322	ncRNA
mm_100763.1	chr11	4579974	4579989	-	1	NA	intron (NM_028860, intron 1 of 17)	intron (NM_028860, intron 1 of 17)	14834	NM_028860	74302	Mm.425669	NM_028860	ENSMUSG00000034354	Mtmr3	1700092A20Rik|AI255150|AW557713|FYVE-DSP1|ZFYVE10|mKIAA0371	myotubularin related protein 3	protein-coding
mm_107182.1	chr12	25038356	25038380	+	1	NA	exon (NM_001081378, exon 24 of 32)	exon (NM_001081378, exon 24 of 32)	57724	NM_010496	15902	Mm.34871	NM_010496	ENSMUSG00000020644	Id2	AI255428|C78922|Idb2|bHLHb26	inhibitor of DNA binding 2	protein-coding
mm_57734.1	chr6	128970330	128970343	-	1	NA	promoter-TSS (NM_001316752)	promoter-TSS (NM_001316752)	-824	NM_001168224	70809	Mm.439891	NM_027562	ENSMUSG00000000248	Clec2g	4632413B12Rik|Clr-c|Clr-d|Clrc|Clrd|Clrx|Ddv10|Ocilrp1	C-type lectin domain family 2, member g	protein-coding
mm_57280.1	chr6	124321661	124321670	-	1	NA	intron (NM_053094, intron 11 of 16)	RLTR19-int|LTR|ERVK	17014	NM_053094	93671	Mm.37426	NM_053094	ENSMUSG00000008845	Cd163	CD163v2|CD163v3	CD163 antigen	protein-coding
mm_114040.1	chr13	53441908	53441912	+	1	NA	intron (NR_037991, intron 6 of 7)	intron (NR_037991, intron 6 of 7)	30870	NM_013601	17702	Mm.1763	NM_013601	ENSMUSG00000021469	Msx2	BB122635|Hox-8|Hox8|Hox8.1	msh homeobox 2	protein-coding
mm_21413.1	chr2	158123934	158123937	-	1	NA	intron (NM_009373, intron 10 of 12)	B4|SINE|B4	22457	NM_009373	21817	Mm.330731	NM_009373	ENSMUSG00000037820	Tgm2	G[a]h|TG2|TGase2|tTG|tTGas	transglutaminase 2, C polypeptide	protein-coding
mm_129058.1	chr15	75566912	75566919	-	1	NA	promoter-TSS (NM_001135689)	promoter-TSS (NM_001135689)	-59	NM_001135688	23934	Mm.22154	NM_011837	ENSMUSG00000022577	Ly6h	-	lymphocyte antigen 6 complex, locus H	protein-coding
mm_42979.1	chr5	123177523	123177559	+	1	NA	exon (NM_008277, exon 9 of 14)	exon (NM_008277, exon 9 of 14)	5145	NM_008277	15445	Mm.439709	NM_008277	ENSMUSG00000029445	Hpd	Fla|Flp|Hppd|Laf	4-hydroxyphenylpyruvic acid dioxygenase	protein-coding
mm_117930.1	chr13	99434318	99434334	-	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-21500	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_128489.1	chr15	51652547	51652575	-	1	NA	Intergenic	Intergenic	212900	NM_080635	68135	Mm.289800	NM_080635	ENSMUSG00000022312	Eif3h	1110008A16Rik|40kD|9430017H16Rik|EIF3-P40|EIF3-gamma|Eif3s3	eukaryotic translation initiation factor 3, subunit H	protein-coding
mm_155568.1	chrX	76393362	76393372	+	1	NA	promoter-TSS (NM_001033799)	promoter-TSS (NM_001033799)	17	NM_001033799	619294	Mm.423961	NM_001033799	ENSMUSG00000073085	Cldn34b4	4930428D18Rik	claudin 34B4	protein-coding
mm_154404.1	chrM	14291	14302	+	1	NA	NA	Intergenic	NA	NA								
mm_163163.1	chr11	85177999	85178011	+	1	NA	intron (NM_028589, intron 4 of 5)	intron (NM_028589, intron 4 of 5)	6909	NM_028589	73634	Mm.48850	NM_028589	ENSMUSG00000018479	1700125H20Rik	-	RIKEN cDNA 1700125H20 gene	protein-coding
mm_49120.1	chr6	8509909	8509929	+	1	NA	promoter-TSS (NR_040452)	promoter-TSS (NR_040452)	319	NM_133236	170772	Mm.210787	NM_133236	ENSMUSG00000029638	Glcci1	2310047L21Rik|A130036A18Rik|Fam117c|Gig18|Tssn1	glucocorticoid induced transcript 1	protein-coding
mm_56538.1	chr6	99667431	99667448	-	1	NA	promoter-TSS (NM_025829)	promoter-TSS (NM_025829)	-668	NM_025829	66892	Mm.32889	NM_025829	ENSMUSG00000093661	Eif4e3	1300018P11Rik|AI451927|eIF4E-3	eukaryotic translation initiation factor 4E member 3	protein-coding
mm_50000.1	chr6	41048328	41048347	+	1	NA	Intergenic	Intergenic	-12828	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_115128.1	chr13	104287509	104287524	+	1	NA	promoter-TSS (NM_001081020)	promoter-TSS (NM_001081020)	-319	NR_136938	108154	Mm.208125	NM_175496	ENSMUSG00000046169	Adamts6	A930019D11Rik|ADAM-TS6|b2b1879.1Clo|b2b2029Clo|b2b2182Clo|b2b2187.1Clo|b2b2228Clo	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 6	protein-coding
mm_90710.1	chr10	3755188	3755234	-	1	NA	intron (NM_001159942, intron 1 of 16)	intron (NM_001159942, intron 1 of 16)	14834	NM_001159942	213783	Mm.150831	NM_001033253	ENSMUSG00000040624	Plekhg1	D10Ertd733e|Gm521|mKIAA1209	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	protein-coding
mm_90946.1	chr10	12974683	12974709	-	1	NA	Intergenic	Intergenic	-10437	NM_001163591	74732	Mm.248648	NM_029075	ENSMUSG00000039232	Stx11	5830405C08Rik	syntaxin 11	protein-coding
mm_84946.1	chr9	83112573	83112594	-	1	NA	intron (NM_175074, intron 3 of 5)	intron (NM_175074, intron 3 of 5)	34024	NM_175074	94353	Mm.244426	NM_026122	ENSMUSG00000066456	Hmgn3	1110002A15Rik|6330514M13Rik|BB071015|TRIP7	high mobility group nucleosomal binding domain 3	protein-coding
mm_142539.1	chr17	46552875	46552891	-	1	NA	TTS (NR_105942)	TTS (NR_105942)	1006	NR_105942	102466778		NR_105942	ENSMUSG00000106514	Mir6976	mmu-mir-6976	microRNA 6976	ncRNA
mm_70288.1	chr8	3655803	3655813	+	1	NA	promoter-TSS (NM_001204959)	promoter-TSS (NM_001204959)	38	NM_022984	57264	Mm.1181	NM_022984	ENSMUSG00000012705	Retn	ADSF|Fizz3|Rstn|Xcp4	resistin	protein-coding
mm_51067.1	chr6	66267706	66267709	+	1	NA	Intergenic	Intergenic	-4798	NR_136927	102633773	Mm.272086	NR_136927	ENSMUSG00000107653	Gm31520	-	sterol-C5-desaturase pseudogene	pseudo
mm_93034.1	chr10	88336165	88336189	-	1	NA	intron (NM_027878, intron 4 of 6)	intron (NM_027878, intron 4 of 6)	20898	NM_027878	71712	Mm.35450	NM_027878	ENSMUSG00000020057	Dram1	1200002N14Rik|Dram	DNA-damage regulated autophagy modulator 1	protein-coding
mm_170373.1	chr18	54699354	54699368	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	87617	NR_045400	328957	Mm.402781	NR_045400		9330117O12Rik	9330117O12	RIKEN cDNA 9330117O12 gene	ncRNA
mm_4274.1	chr1	171559244	171559274	+	1	NA	promoter-TSS (NM_018729)	promoter-TSS (NM_018729)	66	NM_018729	18106	Mm.2299	NM_018729	ENSMUSG00000004709	Cd244	2B4|C9.1|F730046O15Rik|Ly90|NAIL|NKR2B4|Nmrk|SLAMF4	CD244 natural killer cell receptor 2B4	protein-coding
mm_5277.1	chr1	20167086	20167090	-	1	NA	intron (NM_153179, intron 60 of 66)	intron (NM_153179, intron 60 of 66)	-189366	NR_045734	75028	Mm.417820	NR_045734	ENSMUSG00000089914	4930486I03Rik	-	RIKEN cDNA 4930486I03 gene	ncRNA
mm_112090.1	chr12	112674827	112674837	-	1	NA	promoter-TSS (NM_001165894)	promoter-TSS (NM_001165894)	52	NM_001331107	11651	Mm.6645	NM_009652	ENSMUSG00000001729	Akt1	Akt|LTR-akt|PKB|PKB/Akt|PKBalpha|Rac	thymoma viral proto-oncogene 1	protein-coding
mm_163529.1	chr13	8952861	8952867	+	1	NA	promoter-TSS (NM_177197)	promoter-TSS (NM_177197)	1	NM_177197	320581	Mm.313743	NM_177197	ENSMUSG00000033520	Idi2	4833405L16Rik|IPPI2	isopentenyl-diphosphate delta isomerase 2	protein-coding
mm_114447.1	chr13	66932787	66932794	+	1	NA	promoter-TSS (NM_008959)	promoter-TSS (NM_008959)	-40	NM_008959	19210	Mm.281464	NM_008959	ENSMUSG00000021518	Ptdss1	AU044268|AW539008|PSS-1|mKIAA0024	phosphatidylserine synthase 1	protein-coding
mm_34789.1	chr4	154237550	154237571	+	1	NA	intron (NM_001162977, intron 4 of 36)	intron (NM_001162977, intron 4 of 36)	62335	NM_001112744	230972	Mm.38481	NM_001112744	ENSMUSG00000029032	Arhgef16	-	Rho guanine nucleotide exchange factor (GEF) 16	protein-coding
mm_147743.1	chr18	61109817	61109839	-	1	NA	exon (NM_001037859, exon 3 of 22)	exon (NM_001037859, exon 3 of 22)	4256	NM_001037859	12978	Mm.22574	NM_007779	ENSMUSG00000024621	Csf1r	AI323359|CD115|CSF-1R|Csfmr|Fim-2|Fim2|Fms|M-CSF-R|M-CSFR	colony stimulating factor 1 receptor	protein-coding
mm_142788.1	chr17	50164145	50164146	-	1	NA	intron (NM_181397, intron 2 of 9)	RLTR17B_Mm|LTR|ERVK	26352	NM_181397	76438	Mm.41854	NM_181397	ENSMUSG00000039316	Rftn1	2310015N21Rik|AI853526	raftlin lipid raft linker 1	protein-coding
mm_133570.1	chr16	91406196	91406208	+	1	NA	promoter-TSS (NM_008349)	promoter-TSS (NM_008349)	-33	NM_008349	16155	Mm.4154	NM_008349	ENSMUSG00000022969	Il10rb	6620401D04Rik|AI528744|CRF2-4|Crfb4|D16H21S58|D21S58h|IL-10R2|Il10r2	interleukin 10 receptor, beta	protein-coding
mm_124293.1	chr14	103054908	103054953	-	1	NA	exon (NM_008392, exon 5 of 5)	exon (NM_008392, exon 5 of 5)	7918	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_163785.1	chr13	120300326	120300334	+	1	NA	promoter-TSS (NM_001037925)	promoter-TSS (NM_001037925)	-62	NM_001037925	625360	Mm.327506	NM_001037925	ENSMUSG00000094796	BC147527	-	cDNA sequence BC147527	protein-coding
mm_50447.1	chr6	48895244	48895264	+	1	NA	promoter-TSS (NM_029638)	promoter-TSS (NM_029638)	-1	NM_029638	76507	Mm.213898	NM_029638	ENSMUSG00000029811	Aoc1	1600012D06Rik|Abp1|DAO	amine oxidase, copper-containing 1	protein-coding
mm_156098.1	chrX	112512419	112512441	+	1	NA	exon (NM_026333, exon 3 of 7)	exon (NM_026333, exon 3 of 7)	17156	NM_001168590	67715	Mm.45323	NM_026333	ENSMUSG00000025528	2010106E10Rik	-	RIKEN cDNA 2010106E10 gene	protein-coding
mm_71615.1	chr8	57320976	57320992	+	1	NA	promoter-TSS (NM_010402)	promoter-TSS (NM_010402)	1	NM_010402	15111	Mm.430844	NM_010402	ENSMUSG00000038193	Hand2	AI225906|AI661148|Ehand2|Hed|Th2|Thing2|bHLHa26|dHAND	heart and neural crest derivatives expressed transcript 2	protein-coding
mm_68207.1	chr7	104400728	104400739	-	1	NA	Intergenic	Intergenic	-42087	NM_175648	244183	Mm.347647	NM_175648	ENSMUSG00000052749	Trim30b	A530023O14Rik|Trim30-1	tripartite motif-containing 30B	protein-coding
mm_30345.1	chr3	151742315	151742333	-	1	NA	intron (NM_133871, intron 5 of 7)	RMER20B|LTR|ERVK	7635	NM_133871	99899	Mm.30756	NM_133871	ENSMUSG00000028037	Ifi44	A430056A10Rik|AW261460|MTAP44|p44	interferon-induced protein 44	protein-coding
mm_125592.1	chr15	59648423	59648431	+	1	NA	promoter-TSS (NM_144549)	promoter-TSS (NM_144549)	-227	NM_144549	211770	Mm.40298	NM_144549	ENSMUSG00000032501	Trib1	A530090O15Rik|TRB-1|Trb1	tribbles pseudokinase 1	protein-coding
mm_20561.1	chr2	131075017	131075032	-	1	NA	exon (NM_011426, exon 13 of 21)	exon (NM_011426, exon 13 of 21)	-11210	NM_001163529	110751	Mm.108550	NM_033615	ENSMUSG00000027318	Adam33	Adaml	a disintegrin and metallopeptidase domain 33	protein-coding
mm_77371.1	chr8	119822736	119822752	-	1	NA	exon (NM_028071, exon 3 of 4)	exon (NM_028071, exon 3 of 4)	17835	NM_028071	72042	Mm.393405	NM_028071	ENSMUSG00000031827	Cotl1	1810074P22Rik|2010004C08Rik|Clp	coactosin-like 1 (Dictyostelium)	protein-coding
mm_82535.1	chr9	20746319	20746339	-	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	-18115	NM_173777	244723	Mm.293552	NM_173777	ENSMUSG00000032172	Olfm2	A030009A06Rik	olfactomedin 2	protein-coding
mm_26967.1	chr3	24138129	24138129	-	1	NA	intron (NM_001326288, intron 9 of 13)	Lx7|LINE|L1	645877	NM_001326288	635702	Mm.448351	NM_001326288	ENSMUSG00000102758	Naaladl2	2810043G22Rik|EG635702|Gm1021	N-acetylated alpha-linked acidic dipeptidase-like 2	protein-coding
mm_8028.1	chr1	135131748	135131755	-	1	NA	promoter-TSS (NM_177081)	promoter-TSS (NM_177081)	824	NM_007955	13924	Mm.4450	NM_007955		Ptprv	Esp|OST|OST-PTP|mOST-PTP	protein tyrosine phosphatase, receptor type, V	protein-coding
mm_167688.1	chr9	86467960	86467964	+	1	NA	intron (NM_177208, intron 1 of 38)	intron (NM_177208, intron 1 of 38)	808	NM_177208	320615	Mm.245500	NM_177208	ENSMUSG00000034973	Dopey1	B130005I07Rik|BC035275|C130028L17|D9Ertd809e	dopey family member 1	protein-coding
mm_99745.1	chr11	106530376	106530380	+	1	NA	intron (NM_198292, intron 6 of 11)	B1_Mur3|SINE|Alu	29387	NR_030703	100216537		NR_030703	ENSMUSG00000065126	Snord104	-	small nucleolar RNA, C/D box 104	snoRNA
mm_142309.1	chr17	42823420	42823429	-	1	NA	intron (NM_009847, intron 9 of 17)	AT_rich|Low_complexity|Low_complexity	53000	NM_009847	12488	Mm.218637	NM_009847	ENSMUSG00000061665	Cd2ap	AL024079|C78928|METS-1|Mets1	CD2-associated protein	protein-coding
mm_92884.1	chr10	82763905	82763949	-	1	NA	intron (NM_010914, intron 1 of 7)	CpG	214	NM_010914	18045	Mm.245998	NM_010914	ENSMUSG00000020248	Nfyb	AA985999|Cbf-A	nuclear transcription factor-Y beta	protein-coding
mm_163398.1	chr12	70808950	70808956	+	1	NA	Intergenic	Intergenic	-16561	NM_028127	319710	Mm.2962	NM_028127	ENSMUSG00000048285	Frmd6	2610019M19Rik|4930488L10Rik|AW212977|Willin	FERM domain containing 6	protein-coding
mm_66862.1	chr7	56019473	56019512	-	1	NA	promoter-TSS (NM_153578)	promoter-TSS (NM_153578)	81	NM_153578	233280	Mm.389901	NM_153578	ENSMUSG00000047037	Nipa1	1110027G09Rik|A830014A18Rik|FSP3|Spg6	non imprinted in Prader-Willi/Angelman syndrome 1 homolog (human)	protein-coding
mm_768.1	chr1	44119953	44119985	+	1	NA	promoter-TSS (NM_144558)	promoter-TSS (NM_144558)	1	NM_144558	246229	Mm.386883	NM_144558	ENSMUSG00000041684	Bivm	AI854267	basic, immunoglobulin-like variable motif containing	protein-coding
mm_21707.1	chr2	164589569	164589583	-	1	NA	intron (NM_029325, intron 2 of 3)	intron (NM_029325, intron 2 of 3)	3995	NM_029325	75526	Mm.159533	NM_029325	ENSMUSG00000017733	Eppin	1700024E17Rik|Spinlw1	epididymal peptidase inhibitor	protein-coding
mm_67783.1	chr7	97413597	97413601	-	1	NA	intron (NM_009381, intron 1 of 1)	intron (NM_009381, intron 1 of 1)	3951	NM_009381	21835	Mm.28585	NM_009381	ENSMUSG00000035686	Thrsp	S14|SPOT14	thyroid hormone responsive	protein-coding
mm_111709.1	chr12	103695440	103695454	-	1	NA	promoter-TSS (NM_001164742)	promoter-TSS (NM_001164742)	82	NM_026687	68348	Mm.20149	NM_026687	ENSMUSG00000021081	Serpina1f	0610012A11Rik|AI327419|Serpina2|epserin	serine (or cysteine) peptidase inhibitor, clade A, member 1F	protein-coding
mm_119567.1	chr14	49172203	49172254	+	1	NA	promoter-TSS (NM_027492)	promoter-TSS (NM_027492)	-18	NM_027492	70646	Mm.275688	NM_027492	ENSMUSG00000036282	Naa30	4930487N19Rik|5730533P17Rik|AI447922|AW322455|Nat12	N(alpha)-acetyltransferase 30, NatC catalytic subunit	protein-coding
mm_160954.1	chr11	98150048	98150048	-	1	NA	promoter-TSS (NM_028149)	promoter-TSS (NM_028149)	-432	NM_028149	72194	Mm.218350	NM_028149	ENSMUSG00000020883	Fbxl20	2610511F20Rik|4632423N09Rik|AI849362|AL117906|C86145|Fbl2|Scr|mKIAA4147	F-box and leucine-rich repeat protein 20	protein-coding
mm_162037.1	chr19	55917566	55917566	+	1	NA	intron (NM_001142924, intron 5 of 11)	intron (NM_001142924, intron 5 of 11)	22245	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_151825.1	chr19	5638876	5638885	-	1	NA	exon (NM_009045, exon 4 of 11)	exon (NM_009045, exon 4 of 11)	1390	NM_009045	19697	Mm.249966	NM_009045	ENSMUSG00000024927	Rela	p65	v-rel reticuloendotheliosis viral oncogene homolog A (avian)	protein-coding
mm_49388.1	chr6	24858004	24858017	+	1	NA	promoter-TSS (NM_028957)	promoter-TSS (NM_028957)	13	NM_028957	74468	Mm.251601	NM_028957	ENSMUSG00000029678	Hyal5	4933439A12Rik	hyaluronoglucosaminidase 5	protein-coding
mm_37968.1	chr4	133497773	133497788	-	1	NA	3' UTR (NM_001081156, exon 1 of 2)	3' UTR (NM_001081156, exon 1 of 2)	770	NM_001081156	69539	Mm.151594	NM_001081156	ENSMUSG00000056596	Trnp1	2300002D11Rik|Trnp	TMF1-regulated nuclear protein 1	protein-coding
mm_94773.1	chr11	21244302	21244307	+	1	NA	intron (NM_139061, intron 1 of 22)	intron (NM_139061, intron 1 of 22)	5272	NM_001290628	245944	Mm.170103	NM_139061	ENSMUSG00000020128	Vps54	Hcc8|Vps54l|mSLP8|wr	VPS54 GARP complex subunit	protein-coding
mm_118479.1	chr14	11814526	11814528	+	1	NA	intron (NM_008981, intron 2 of 29)	intron (NM_008981, intron 2 of 29)	260974	NM_008981	19270	Mm.431266	NM_008981	ENSMUSG00000021745	Ptprg	5430405N12Rik|AW046354|AW549872|RPTPgamma	protein tyrosine phosphatase, receptor type, G	protein-coding
mm_88524.1	chr10	78057299	78057303	+	1	NA	exon (NM_019448, exon 11 of 13)	exon (NM_019448, exon 11 of 13)	1966	NM_001284200	54427	Mm.13433	NM_019448	ENSMUSG00000000730	Dnmt3l	D6Ertd14e|ecat7	DNA (cytosine-5-)-methyltransferase 3-like	protein-coding
mm_99036.1	chr11	98960545	98960593	+	1	NA	promoter-TSS (NM_001176528)	promoter-TSS (NM_001176528)	98	NM_001176528	19401	Mm.439744	NM_009024	ENSMUSG00000037992	Rara	Nr1b1|RAR|RARalpha1	retinoic acid receptor, alpha	protein-coding
mm_88350.1	chr10	75853601	75853603	+	1	NA	Intergenic	Intergenic	6648	NM_010798	17319	Mm.2326	NM_010798	ENSMUSG00000033307	Mif	GIF|Glif	macrophage migration inhibitory factor	protein-coding
mm_90416.1	chr10	127471776	127471795	+	1	NA	exon (NM_001168293, exon 12 of 24)	exon (NM_001168293, exon 12 of 24)	-29932	NM_177707	237611	Mm.32087	NM_177707	ENSMUSG00000040287	Stac3	9830125E18	SH3 and cysteine rich domain 3	protein-coding
mm_122372.1	chr14	39473457	39473508	-	1	NA	promoter-TSS (NM_008734)	promoter-TSS (NM_008734)	-394	NM_008734	18183	Mm.258705	NM_008734	ENSMUSG00000041014	Nrg3	ska	neuregulin 3	protein-coding
mm_110875.1	chr12	73949780	73949828	-	1	NA	Intergenic	CpG	-14726	NM_178392	75627	Mm.25937	NM_178392	ENSMUSG00000021113	Snapc1	2700033G17Rik|AU015787	small nuclear RNA activating complex, polypeptide 1	protein-coding
mm_135920.1	chr16	67620924	67620932	-	1	NA	promoter-TSS (NM_178721)	promoter-TSS (NM_178721)	-20	NM_178721	239857	Mm.394300	NM_178721	ENSMUSG00000064115	Cadm2	2900078E11Rik|9330131D06|A830029E02Rik|Igdf4d|Igsf4d|NECL3|SynCAM 2|SynCAM2	cell adhesion molecule 2	protein-coding
mm_173326.1	chrY	90768401	90768414	-	1	NA	Intergenic	Intergenic	-13357	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_98195.1	chr11	87794780	87794815	+	1	NA	exon (NM_010824, exon 3 of 14)	exon (NM_010824, exon 3 of 14)	1013	NM_010824	17523	Mm.4668	NM_010824	ENSMUSG00000009350	Mpo	mKIAA4033	myeloperoxidase	protein-coding
mm_163634.1	chr13	59510321	59510326	+	1	NA	intron (NM_001048008, intron 11 of 17)	intron (NM_001048008, intron 11 of 17)	34128	NM_001284221	67269	Mm.153008	NM_023328	ENSMUSG00000021557	Agtpbp1	1700020N17Rik|2310001G17Rik|2900054O13Rik|4930445M19Rik|5730402G09Rik|CCP1|Nna1|nmf243|pcd	ATP/GTP binding protein 1	protein-coding
mm_54731.1	chr6	40900369	40900394	-	1	NA	promoter-TSS (NM_175020)	promoter-TSS (NM_175020)	6	NM_175020	232717	Mm.56997	NM_175020	ENSMUSG00000051936	Prss58	1700020H15|Tryx3	protease, serine 58	protein-coding
mm_132211.1	chr16	32613537	32613549	+	1	NA	intron (NM_011638, intron 2 of 18)	intron (NM_011638, intron 2 of 18)	4647	NM_011638	22042	Mm.28683	NM_011638	ENSMUSG00000022797	Tfrc	2610028K12Rik|CD71|E430033M20Rik|Mtvr1|TFR|TFR1|TR|Trfr|p90	transferrin receptor	protein-coding
mm_39595.1	chr5	23501954	23501968	+	1	NA	exon (NM_026984, exon 26 of 26)	exon (NM_026984, exon 26 of 26)	67532	NM_026984	69188	Mm.205190	NM_026984	ENSMUSG00000029004	Kmt2e	1810033J14Rik|9530077A04Rik|D230038D11Rik|Mll5|NKp44L	lysine (K)-specific methyltransferase 2E	protein-coding
mm_36035.1	chr4	57240994	57241004	-	1	NA	intron (NM_011207, intron 10 of 25)	intron (NM_011207, intron 10 of 25)	60838	NM_011207	545622	Mm.246552	NM_011207	ENSMUSG00000038764	Ptpn3	9530011I20Rik|PTP-H1|PTPCL	protein tyrosine phosphatase, non-receptor type 3	protein-coding
mm_136708.1	chr17	7925991	7926006	+	1	NA	promoter-TSS (NM_145968)	promoter-TSS (NM_145968)	-2	NM_145968	72536	Mm.119680	NM_145968	ENSMUSG00000033450	Tagap	2610315E15Rik	T cell activation Rho GTPase activating protein	protein-coding
mm_139883.1	chr17	70756086	70756090	+	1	NA	intron (NM_001347411, intron 9 of 14)	intron (NM_001347411, intron 9 of 14)	90689	NM_001164077	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_18354.1	chr2	58163741	58163776	-	1	NA	promoter-TSS (NR_045895)	promoter-TSS (NR_045895)	-216	NR_045896	100042926	Mm.446515	NR_045895	ENSMUSG00000086862	Gm13546	OTTMUSG00000012675	predicted gene 13546	ncRNA
mm_38431.1	chr4	139345996	139346020	-	1	NA	Intergenic	Intergenic	6568	NM_001290810	69902	Mm.27871	NM_023536	ENSMUSG00000028741	Mrto4	2610012O22Rik|Mg684|Mrt4	mRNA turnover 4, ribosome maturation factor	protein-coding
mm_57705.1	chr6	128543338	128543376	-	1	NA	intron (NM_001001179, intron 31 of 35)	intron (NM_001001179, intron 31 of 35)	-16637	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_117688.1	chr13	94285282	94285342	-	1	NA	promoter-TSS (NM_029153)	promoter-TSS (NM_029153)	-31	NM_029153	107767	Mm.201455	NM_029153	ENSMUSG00000021687	Scamp1	4930505M11Rik|AI415563|AW122395	secretory carrier membrane protein 1	protein-coding
mm_118338.1	chr13	114388058	114388089	-	1	NA	promoter-TSS (NM_010887)	promoter-TSS (NM_010887)	21	NM_010887	17993	Mm.253142	NM_010887	ENSMUSG00000021764	Ndufs4	6720411N02Rik|C1-18k	NADH dehydrogenase (ubiquinone) Fe-S protein 4	protein-coding
mm_45924.1	chr5	89443474	89443493	-	1	NA	exon (NM_008096, exon 4 of 13)	exon (NM_008096, exon 4 of 13)	14415	NM_008096	14473	Mm.196595	NM_008096	ENSMUSG00000035540	Gc	DBP|VDB	group specific component	protein-coding
mm_44627.1	chr5	26493278	26493282	-	1	NA	promoter-TSS (NR_029445)	promoter-TSS (NR_029445)	34	NR_029445	75942	Mm.50087	NR_029445	ENSMUSG00000029044	4930584F24Rik	1700001J09Rik|4930522C06Rik	RIKEN cDNA 4930584F24 gene	ncRNA
mm_67573.1	chr7	81992278	81992314	-	1	NA	promoter-TSS (NM_007562)	promoter-TSS (NM_007562)	3	NM_007562	12173	Mm.243802	NM_007562	ENSMUSG00000025105	Bnc1	AI047752|AW546376|Bnc	basonuclin 1	protein-coding
mm_20933.1	chr2	150856146	150856161	-	1	NA	intron (NM_024465, intron 2 of 12)	B1_Mur1|SINE|Alu	48578	NM_024465	76192	Mm.112632	NM_024465	ENSMUSG00000032046	Abhd12	1500011G07Rik|6330583M11Rik|AI431047|AW547313	abhydrolase domain containing 12	protein-coding
mm_9082.1	chr1	168431861	168431884	-	1	NA	5' UTR (NM_001291509, exon 1 of 7)	5' UTR (NM_001291509, exon 1 of 7)	297	NM_001291508	18514	Mm.43358	NM_008783	ENSMUSG00000052534	Pbx1	2310056B04Rik|D230003C07Rik|Pbx-1	pre B cell leukemia homeobox 1	protein-coding
mm_64042.1	chr7	140773665	140773681	+	1	NA	exon (NM_021282, exon 8 of 9)	exon (NM_021282, exon 8 of 9)	9841	NM_021282	13106	Mm.21758	NM_021282	ENSMUSG00000025479	Cyp2e1	Cyp2e	cytochrome P450, family 2, subfamily e, polypeptide 1	protein-coding
mm_22763.1	chr3	20057803	20057857	+	1	NA	promoter-TSS (NR_105046)	promoter-TSS (NR_105046)	19	NM_009210	20585	Mm.209650	NM_009210	ENSMUSG00000002428	Hltf	AF010600|BC057116|P113|Smarca3|Snf2l3	helicase-like transcription factor	protein-coding
mm_56089.1	chr6	87335759	87335769	-	1	NA	promoter-TSS (NM_054041)	promoter-TSS (NM_054041)	11	NM_054041	69538	Mm.232525	NM_054041	ENSMUSG00000033420	Antxr1	2310008J16Rik|2810405N18Rik|Antrx1|Tem8	anthrax toxin receptor 1	protein-coding
mm_81735.1	chr9	113756826	113756844	+	1	NA	intron (NM_001286599, intron 1 of 10)	SSU-rRNA_Hsa|rRNA|rRNA	15362	NM_001114347	76499	Mm.222272	NM_029633	ENSMUSG00000033392	Clasp2	1500004F14Rik|8030404L10Rik|C77448|CLASP2beta|mKIAA0627	CLIP associating protein 2	protein-coding
mm_139940.1	chr17	71182590	71182596	+	1	NA	Intergenic	Intergenic	-1385	NM_022882	64898	Mm.227924	NM_022882	ENSMUSG00000024052	Lpin2	2610511G02Rik|AI481352|AW742896	lipin 2	protein-coding
mm_136878.1	chr17	13007956	13007988	+	1	NA	5' UTR (NM_013671, exon 1 of 5)	5' UTR (NM_013671, exon 1 of 5)	133	NM_013671	20656	Mm.290876	NM_013671	ENSMUSG00000006818	Sod2	MnSOD|Sod-2	superoxide dismutase 2, mitochondrial	protein-coding
mm_90236.1	chr10	121392802	121392814	+	1	NA	exon (NM_029364, exon 13 of 14)	exon (NM_029364, exon 13 of 14)	27718	NM_029364	75612	Mm.207683	NM_029364	ENSMUSG00000034707	Gns	2610016K11Rik|AU042285|C87209|G6S|N28088	glucosamine (N-acetyl)-6-sulfatase	protein-coding
mm_124133.1	chr14	84476410	84476429	-	1	NA	promoter-TSS (NR_015539)	promoter-TSS (NR_015539)	5	NR_015539	319903	Mm.440481	NR_015539		9630013A20Rik	-	RIKEN cDNA 9630013A20 gene	ncRNA
mm_116787.1	chr13	53373779	53373785	-	1	NA	intron (NM_009269, intron 2 of 14)	intron (NM_009269, intron 2 of 14)	3579	NM_009269	268656	Mm.240336	NM_009269	ENSMUSG00000021468	Sptlc1	AW552086|C77762|E030036H05|Lcb1	serine palmitoyltransferase, long chain base subunit 1	protein-coding
mm_48406.1	chr5	140261518	140261547	-	1	NA	exon (NM_010752, exon 10 of 18)	exon (NM_010752, exon 10 of 18)	60020	NM_010752	17120	Mm.27250	NM_010752	ENSMUSG00000029554	Mad1l1	AI173502|AW550425|Mad1	MAD1 mitotic arrest deficient 1-like 1	protein-coding
mm_20898.1	chr2	149003303	149003324	-	1	NA	Intergenic	Intergenic	-127801	NM_009976	13010	Mm.4263	NM_009976	ENSMUSG00000027447	Cst3	CysC	cystatin C	protein-coding
mm_135941.1	chr16	74301392	74301396	-	1	NA	intron (NM_175549, intron 2 of 27)	intron (NM_175549, intron 2 of 27)	40673	NR_030464	751561		NR_030464	ENSMUSG00000104758	Mir691	Mirn691|mir-691|mmu-mir-691	microRNA 691	ncRNA
mm_145129.1	chr18	44571155	44571156	+	1	NA	intron (NM_001085373, intron 3 of 18)	intron (NM_001085373, intron 3 of 18)	-90510	NR_026853	626275	Mm.427116	NR_026853	ENSMUSG00000097610	A930012L18Rik	-	RIKEN cDNA A930012L18 gene	ncRNA
mm_92661.1	chr10	80419552	80419562	-	1	NA	exon (NM_011548, exon 7 of 19)	exon (NM_011548, exon 7 of 19)	-12736	NM_025650	66594	Mm.379119	NM_025650	ENSMUSG00000020163	Uqcr11	0710008D09Rik|AL022707|Uqcr	ubiquinol-cytochrome c reductase, complex III subunit XI	protein-coding
mm_114836.1	chr13	92530934	92530961	+	1	NA	promoter-TSS (NM_173392)	promoter-TSS (NM_173392)	-137	NM_173392	218441	Mm.259585	NM_173392	ENSMUSG00000021706	Zfyve16	AI035632|B130024H06Rik|B130031L15|mKIAA0305	zinc finger, FYVE domain containing 16	protein-coding
mm_125159.1	chr15	31224407	31224530	+	1	NA	promoter-TSS (NM_146057)	promoter-TSS (NM_146057)	83	NM_146057	223453	Mm.222867	NM_146057	ENSMUSG00000039168	Dap	4921531N22Rik|AI789753|AU040360	death-associated protein	protein-coding
mm_24937.1	chr3	96560298	96560318	+	1	NA	exon (NM_023719, exon 7 of 8)	exon (NM_023719, exon 7 of 8)	2351	NM_023719	56338	Mm.410189	NM_023719	ENSMUSG00000038393	Txnip	1200008J08Rik|AA682105|Hyplip1|THIF|Tbp-2|VDUP1	thioredoxin interacting protein	protein-coding
mm_128619.1	chr15	58933689	58933745	-	1	NA	promoter-TSS (NM_023172)	promoter-TSS (NM_023172)	13	NM_175151	69694	Mm.383230	NM_175151	ENSMUSG00000050891	Tatdn1	2310079P03Rik|CDA11	TatD DNase domain containing 1	protein-coding
mm_89965.1	chr10	111473187	111473201	+	1	NA	promoter-TSS (NM_015781)	promoter-TSS (NM_015781)	2	NM_015781	53605	Mm.290407	NM_015781	ENSMUSG00000058799	Nap1l1	AA407126|AI256722|D10Ertd68e|NAP-1	nucleosome assembly protein 1-like 1	protein-coding
mm_52553.1	chr6	115995098	115995113	+	1	NA	promoter-TSS (NM_026376)	promoter-TSS (NM_026376)	-100	NM_026376	67784	Mm.3085	NM_026376	ENSMUSG00000030123	Plxnd1	6230425C21Rik|b2b1863Clo|b2b553Clo	plexin D1	protein-coding
mm_158947.1	chr1	85270549	85270549	-	1	NA	promoter-TSS (NM_001037909)	promoter-TSS (NM_001037909)	17	NM_175219	620078	Mm.386456	NM_175219	ENSMUSG00000052477	C130026I21Rik	4930565N07Rik|OTTMUSG00000029174	RIKEN cDNA C130026I21 gene	protein-coding
mm_66591.1	chr7	45422437	45422472	-	1	NA	TTS (NM_008497)	TTS (NM_008497)	1508	NM_008497	16866	Mm.57061	NM_008497	ENSMUSG00000100916	Lhb	Gm29035|LH|LH-B|LSH-B|LSH-beta	luteinizing hormone beta	protein-coding
mm_21497.1	chr2	163419115	163419166	-	1	NA	intron (NM_025699, intron 1 of 3)	CpG	330	NM_025699	66680	Mm.25119	NM_025699	ENSMUSG00000035399	Oser1	3230401D17Rik|AI256769|Perit1	oxidative stress responsive serine rich 1	protein-coding
mm_164899.1	chr18	66059548	66059558	-	1	NA	3' UTR (NM_178793, exon 11 of 11)	3' UTR (NM_178793, exon 11 of 11)	-56918	NM_001172062	70361	Mm.290857	NM_027400	ENSMUSG00000041891	Lman1	2610020P13Rik|AI326273|AU043785|C730041J05|ERGIC53|F5F8D|MCFD1|MR60|P58|gp58	lectin, mannose-binding, 1	protein-coding
mm_28716.1	chr3	95658631	95658660	-	1	NA	promoter-TSS (NM_008562)	promoter-TSS (NM_008562)	-76	NM_008562	17210	Mm.1639	NM_008562	ENSMUSG00000038612	Mcl1	AW556805|Mcl-1	myeloid cell leukemia sequence 1	protein-coding
mm_91889.1	chr10	59951482	59951497	-	1	NA	exon (NM_029083, exon 2 of 3)	exon (NM_029083, exon 2 of 3)	281	NM_029083	74747	Mm.21697	NM_029083	ENSMUSG00000020108	Ddit4	5830413E08Rik|AA415483|REDD1|Rtp801|dig2	DNA-damage-inducible transcript 4	protein-coding
mm_110249.1	chr12	31499880	31499892	-	1	NA	promoter-TSS (NM_001253847)	promoter-TSS (NM_001253847)	-270	NM_001253848	104836	Mm.273270	NM_134048	ENSMUSG00000020659	Cbll1	AI467391|Hakai|c-Cbl-like	Casitas B-lineage lymphoma-like 1	protein-coding
mm_96579.1	chr11	69070791	69070856	+	1	NA	promoter-TSS (NM_025838)	promoter-TSS (NM_025838)	14	NM_028336	66910	Mm.33964	NM_025838	ENSMUSG00000020895	Tmem107	1110004B13Rik|2810049P21Rik	transmembrane protein 107	protein-coding
mm_97709.1	chr11	80178710	80178724	+	1	NA	3' UTR (NM_172133, exon 11 of 11)	3' UTR (NM_172133, exon 11 of 11)	-5155	NM_028019	71956	Mm.22985	NM_028019	ENSMUSG00000020707	Rnf135	0610037N03Rik|2410006N06Rik	ring finger protein 135	protein-coding
mm_135719.1	chr16	55818455	55818475	-	1	NA	exon (NM_030612, exon 7 of 14)	exon (NM_030612, exon 7 of 14)	3673	NM_001159394	80859	Mm.247272	NM_030612	ENSMUSG00000035356	Nfkbiz	AA408868|INAP|Mail	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, zeta	protein-coding
mm_96952.1	chr11	70564336	70564338	+	1	NA	intron (NM_016713, intron 1 of 30)	intron (NM_016713, intron 1 of 30)	1456	NM_016713	50932	Mm.42967	NM_016713	ENSMUSG00000020827	Mink1	B55|MINK|Map4k6|Ysk2	misshapen-like kinase 1 (zebrafish)	protein-coding
mm_22097.1	chr2	168970112	168970130	-	1	NA	Intergenic	Intergenic	-8148	NR_040326	75508	Mm.271256	NR_040326	ENSMUSG00000086348	1700017J07Rik	-	RIKEN cDNA 1700017J07 gene	ncRNA
mm_47769.1	chr5	131538689	131538717	-	1	NA	intron (NM_177047, intron 5 of 18)	CpG	-231181	NM_145218	212996	Mm.299204	NM_145218	ENSMUSG00000034040	Wbscr17	AA388321|E330012B09Rik	Williams-Beuren syndrome chromosome region 17 homolog (human)	protein-coding
mm_108690.1	chr12	86895257	86895272	+	1	NA	Intergenic	Intergenic	-10450	NM_145836	238330	Mm.248358	NM_145836	ENSMUSG00000034168	Irf2bpl	6430527G18Rik|Eap1	interferon regulatory factor 2 binding protein-like	protein-coding
mm_160906.1	chr11	77842438	77842438	+	1	NA	intron (NM_001291214, intron 23 of 38)	intron (NM_001291214, intron 23 of 38)	41140	NM_001291215	360013	Mm.341248	NM_011586	ENSMUSG00000000631	Myo18a	MAJN|MyoPDZ|MysPDZ|SP-R210	myosin XVIIIA	protein-coding
mm_134348.1	chr16	16571449	16571471	-	1	NA	intron (NM_001301817, intron 1 of 16)	intron (NM_001301817, intron 1 of 16)	-11241	NM_139232	224014	Mm.256131	NM_139232	ENSMUSG00000022788	Fgd4	9030023J02Rik|9330209B17Rik|Frabp|ZFYVE6	FYVE, RhoGEF and PH domain containing 4	protein-coding
mm_92784.1	chr10	81291208	81291221	-	1	NA	promoter-TSS (NM_013769)	promoter-TSS (NM_013769)	53	NM_013769	27375	Mm.27984	NM_013769	ENSMUSG00000034917	Tjp3	-	tight junction protein 3	protein-coding
mm_109154.1	chr12	108178484	108178497	+	1	NA	intron (NM_028262, intron 1 of 12)	CpG	794	NM_028262	52690	Mm.159185	NM_028262	ENSMUSG00000056770	Setd3	2610102I01Rik|2610305M23Rik|6030490B17Rik|D12Ertd771e	SET domain containing 3	protein-coding
mm_60525.1	chr7	44480091	44480104	+	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	-4420	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_28884.1	chr3	97868147	97868157	-	1	NA	intron (NM_001039376, intron 1 of 46)	CpG	20555	NM_001289702	83679	Mm.129840	NM_031401	ENSMUSG00000038170	Pde4dip	4732458A06Rik|9430063L05Rik|C87016|D130016K21Rik|D3Bwg1078e|Usmg4|mKIAA0454	phosphodiesterase 4D interacting protein (myomegalin)	protein-coding
mm_152584.1	chr19	11603427	11603437	-	1	NA	intron (NM_026835, intron 1 of 6)	intron (NM_026835, intron 1 of 6)	1372	NM_026835	68774	Mm.290390	NM_026835	ENSMUSG00000024679	Ms4a6d	1110058E16Rik|AI447446|Ms4a11	membrane-spanning 4-domains, subfamily A, member 6D	protein-coding
mm_50689.1	chr6	51588207	51588216	+	1	NA	intron (NM_028035, intron 5 of 6)	intron (NM_028035, intron 5 of 6)	43688	NM_001127348	71982	Mm.294166	NM_028035	ENSMUSG00000038301	Snx10	2410004M09Rik	sorting nexin 10	protein-coding
mm_171185.1	chr3	39189832	39189832	-	1	NA	Intergenic	Intergenic	302892	NM_183221	329628	Mm.316210	NM_183221	ENSMUSG00000046743	Fat4	6030410K14Rik|9430004M15	FAT atypical cadherin 4	protein-coding
mm_141776.1	chr17	34287993	34288021	-	1	NA	promoter-TSS (NM_010378)	promoter-TSS (NM_010378)	-236	NM_010378	14960	Mm.235338	NM_010378	ENSMUSG00000036594	H2-Aa	Aalpha|H-2Aa|H2Aa|I-Aalpha|IAalpha|Ia-1|Ia1	histocompatibility 2, class II antigen A, alpha	protein-coding
mm_32440.1	chr4	107253913	107253918	+	1	NA	promoter-TSS (NM_029985)	promoter-TSS (NM_029985)	-19	NM_028394	72938	Mm.21787	NM_028394	ENSMUSG00000063172	Hspb11	2900042B11Rik|IFT25	heat shock protein family B (small), member 11	protein-coding
mm_31723.1	chr4	62674329	62674355	+	1	NA	intron (NM_001310706, intron 1 of 6)	intron (NM_001310706, intron 1 of 6)	368	NM_001310706	50780	Mm.286753	NM_019492	ENSMUSG00000059810	Rgs3	4930506N09Rik|C2PA-RGS3|C2pa|PDZ-RGS3|RGS3S	regulator of G-protein signaling 3	protein-coding
mm_12060.1	chr2	59351899	59351905	+	1	NA	intron (NM_026361, intron 20 of 21)	intron (NM_026361, intron 20 of 21)	34780	NR_040510	76676	Mm.110038	NR_040510	ENSMUSG00000087455	5330411J11Rik	-	RIKEN cDNA 5330411J11 gene	ncRNA
mm_162888.1	chr10	107719976	107719978	-	1	NA	promoter-TSS (NM_001081432)	promoter-TSS (NM_001081432)	50	NM_001081432	237523	Mm.391418	NM_001081432	ENSMUSG00000035916	Ptprq	-	protein tyrosine phosphatase, receptor type, Q	protein-coding
mm_100546.1	chr11	120708073	120708090	+	1	NA	intron (NM_198223, intron 11 of 14)	intron (NM_198223, intron 11 of 14)	5686	NM_016665	20892	Mm.259716	NM_016665	ENSMUSG00000025144	Cenpx	Stra13	centromere protein X	protein-coding
mm_67474.1	chr7	80503348	80503365	-	1	NA	exon (NM_007550, exon 6 of 22)	exon (NM_007550, exon 6 of 22)	31642	NM_007550	12144	Mm.12932	NM_007550	ENSMUSG00000030528	Blm	-	Bloom syndrome, RecQ helicase-like	protein-coding
mm_20834.1	chr2	147186366	147186382	-	1	NA	promoter-TSS (NM_001077632)	promoter-TSS (NM_001077632)	28	NM_001077632	18088	Mm.330639	NM_010919	ENSMUSG00000027434	Nkx2-2	Nkx-2.2|Nkx2.2|tinman	NK2 homeobox 2	protein-coding
mm_101245.1	chr11	20741448	20741524	-	1	NA	promoter-TSS (NM_001252503)	promoter-TSS (NM_001252503)	70	NM_001290545	216549	Mm.356580	NM_181411	ENSMUSG00000049659	Aftph	-	aftiphilin	protein-coding
mm_109489.1	chr12	111442654	111442669	+	1	NA	promoter-TSS (NM_009396)	promoter-TSS (NM_009396)	0	NM_009396	21928	Mm.255332	NM_009396	ENSMUSG00000021281	Tnfaip2	B94|Exoc3l3|M-sec|Tnfip2|tnfb94	tumor necrosis factor, alpha-induced protein 2	protein-coding
mm_38302.1	chr4	136896376	136896387	-	1	NA	exon (NM_007572, exon 3 of 3)	exon (NM_007572, exon 3 of 3)	2463	NM_007572	12259	Mm.439957	NM_007572	ENSMUSG00000036887	C1qa	AI255395|C1q	complement component 1, q subcomponent, alpha polypeptide	protein-coding
mm_52870.1	chr6	122340762	122340770	+	1	NA	promoter-TSS (NM_001271579)	promoter-TSS (NM_001271579)	-539	NM_001271579	13619	Mm.6822	NM_007905	ENSMUSG00000040669	Phc1	AW557034|Edr|Edr1|Mph1|Rae-28|rae28	polyhomeotic-like 1 (Drosophila)	protein-coding
mm_116156.1	chr13	30545255	30545346	-	1	NA	promoter-TSS (NM_025710)	promoter-TSS (NM_025710)	16	NM_025710	66694	Mm.181933	NM_025710	ENSMUSG00000038462	Uqcrfs1	4430402G14Rik|AI875505	ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1	protein-coding
mm_116230.1	chr13	33158395	33158417	-	1	NA	promoter-TSS (NM_011453)	promoter-TSS (NM_011453)	-55	NM_011453	20707	Mm.219429	NM_011453	ENSMUSG00000021404	Serpinb9c	3830421J05Rik|Nk9|Spi11	serine (or cysteine) peptidase inhibitor, clade B, member 9c	protein-coding
mm_114334.1	chr13	60672992	60673004	+	1	NA	intron (NM_029653, intron 2 of 25)	intron (NM_029653, intron 2 of 25)	70787	NM_134062	69635	Mm.24103	NM_029653	ENSMUSG00000021559	Dapk1	D13Ucla1|DAP-Kinase	death associated protein kinase 1	protein-coding
mm_105306.1	chr11	102697711	102697757	-	1	NA	promoter-TSS (NM_025918)	promoter-TSS (NM_025918)	-9	NM_025918	52715	Mm.277638	NM_025918	ENSMUSG00000020925	Ccdc43	2610001E01Rik|D11Ertd707e	coiled-coil domain containing 43	protein-coding
mm_130545.1	chr15	98953638	98953659	-	1	NA	promoter-TSS (NM_011653)	promoter-TSS (NM_011653)	-147	NM_011653	22142	Mm.405359	NM_011653	ENSMUSG00000072235	Tuba1a	Tuba-1|Tuba1	tubulin, alpha 1A	protein-coding
mm_157178.1	chrX	9655945	9655965	-	1	NA	3' UTR (NM_025975, exon 5 of 5)	3' UTR (NM_025975, exon 5 of 5)	7028	NM_025975	67117	Mm.29150	NM_025975	ENSMUSG00000031176	Dynlt3	2310075M16Rik|AU042796|Tcte1l	dynein light chain Tctex-type 3	protein-coding
mm_58310.1	chr6	146254548	146254552	-	1	NA	intron (NM_010586, intron 36 of 55)	intron (NM_010586, intron 36 of 55)	247673	NM_010586	16439	Mm.7800	NM_010586	ENSMUSG00000030287	Itpr2	AI649341|InsP3R-2|InsP3R-5|Ip3r2|Itpr5|insP3R2	inositol 1,4,5-triphosphate receptor 2	protein-coding
mm_38675.1	chr4	144903971	144903977	-	1	NA	intron (NM_011303, intron 1 of 5)	intron (NM_011303, intron 1 of 5)	10837	NM_011303	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding
mm_30429.1	chr3	152982241	152982251	-	1	NA	promoter-TSS (NM_012028)	promoter-TSS (NM_012028)	-39	NM_012028	26938	Mm.40915	NM_012028	ENSMUSG00000039037	St6galnac5	AI851940|Siat7e	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 5	protein-coding
mm_17235.1	chr2	25581617	25581625	-	1	NA	Intergenic	Intergenic	-1522	NM_001005424	381353	Mm.379511	NM_001005424	ENSMUSG00000029419	Gm996	-	predicted gene 996	protein-coding
mm_131701.1	chr16	20717796	20717817	+	1	NA	promoter-TSS (NM_145632)	promoter-TSS (NM_145632)	-20	NM_145632	245841	Mm.288730	NM_145632	ENSMUSG00000021018	Polr2h	-	polymerase (RNA) II (DNA directed) polypeptide H	protein-coding
mm_111474.1	chr12	98606814	98606818	-	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	-21326	NM_001289573	104871	Mm.210053	NM_178914	ENSMUSG00000021007	Spata7	AI661438|B230306G18Rik|HSD3	spermatogenesis associated 7	protein-coding
mm_46041.1	chr5	91963107	91963137	-	1	NA	promoter-TSS (NM_001271797)	promoter-TSS (NM_001271797)	-54	NM_001271797	68098	Mm.159453	NM_026557	ENSMUSG00000029397	Rchy1	ARNIP|CHIMP|Pirh2|Zfp363|Znf363	ring finger and CHY zinc finger domain containing 1	protein-coding
mm_154479.1	chrM	4357	4385	-	1	NA	NA	Intergenic	NA	NA								
mm_80933.1	chr9	102626619	102626686	+	1	NA	promoter-TSS (NM_001081122)	promoter-TSS (NM_001081122)	356	NM_181394	69010	Mm.2000	NM_181394	ENSMUSG00000035048	Anapc13	1810004D07Rik|APC13|SWM1	anaphase promoting complex subunit 13	protein-coding
mm_103586.1	chr11	78189380	78189402	-	1	NA	intron (NM_033475, intron 1 of 9)	CpG	643	NM_033475	19376	Mm.275864	NM_033475	ENSMUSG00000002059	Rab34	AI326479|Narr|Rah|Rah1	RAB34, member RAS oncogene family	protein-coding
mm_157950.1	chrX	87172889	87172898	-	1	NA	intron (NM_001160403, intron 5 of 10)	RMER17C2|LTR|ERVK	-817899	NR_036689	245502	Mm.490821	NR_036689		Gm41	-	melanoma antigen, family B, 4 pseudogene	pseudo
mm_53691.1	chr6	142677541	142677542	+	1	NA	intron (NM_001310143, intron 11 of 38)	intron (NM_001310143, intron 11 of 38)	24733	NM_021041	20928	Mm.35670	NM_011511	ENSMUSG00000030249	Abcc9	AI414027|AI449286|SUR2A|SUR2B|Sur2	ATP-binding cassette, sub-family C (CFTR/MRP), member 9	protein-coding
mm_7586.1	chr1	125434527	125434537	-	1	NA	intron (NM_001205385, intron 2 of 12)	intron (NM_001205385, intron 2 of 12)	1195	NM_023735	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding
mm_117925.1	chr13	99434196	99434204	-	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-21374	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_164090.1	chr15	9155344	9155350	-	1	NA	promoter-TSS (NM_001285980)	promoter-TSS (NM_001285980)	78	NM_001285980	27401	Mm.35584	NM_013787	ENSMUSG00000054115	Skp2	4930500A04Rik|FBXL1|FWD1|p45	S-phase kinase-associated protein 2 (p45)	protein-coding
mm_100931.1	chr11	6519498	6519513	-	1	NA	intron (NM_178440, intron 1 of 21)	intron (NM_178440, intron 1 of 21)	1453	NM_178440	246177	Mm.239554	NM_178440	ENSMUSG00000020437	Myo1g	E430002D17Rik	myosin IG	protein-coding
mm_50385.1	chr6	48690680	48690691	+	1	NA	exon (NM_001243199, exon 3 of 4)	exon (NM_001243199, exon 3 of 4)	6107	NM_174990	107526	Mm.333048	NM_174990	ENSMUSG00000054435	Gimap4	AU019574|E430007K16Rik|Ian-1|Ian1|Imap4	GTPase, IMAP family member 4	protein-coding
mm_133893.1	chr16	97511958	97511959	+	1	NA	Intergenic	Intergenic	-7022	NM_020622	52793	Mm.327932	NM_020622	ENSMUSG00000022938	Fam3b	2-21|9030624C24Rik|D16Jhu19e|ORF9|Pander	family with sequence similarity 3, member B	protein-coding
mm_160027.1	chr6	130380982	130380982	-	1	NA	promoter-TSS (NM_013793)	promoter-TSS (NM_013793)	-174	NM_053152	93969	Mm.333431	NM_053152		Klra22	Ly49v	killer cell lectin-like receptor subfamily A, member 22	protein-coding
mm_127530.1	chr15	102100366	102100384	+	1	NA	Intergenic	CpG	-2613	NM_153533	209039	Mm.29389	NM_153533	ENSMUSG00000037003	Tns2	C1-ten|Tenc1|nep|nph	tensin 2	protein-coding
mm_59625.1	chr7	28154694	28154714	+	1	NA	exon (NM_001164655, exon 13 of 20)	exon (NM_001164655, exon 13 of 20)	-15044	NM_007991	14113	Mm.4595	NM_007991	ENSMUSG00000046865	Fbl	AL022665|FIB|FLRN|RNU3IP1	fibrillarin	protein-coding
mm_54858.1	chr6	42594114	42594124	-	1	NA	exon (NM_203396, exon 2 of 7)	exon (NM_203396, exon 2 of 7)	3253	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_19410.1	chr2	91696210	91696227	-	1	NA	intron (NM_145528, intron 1 of 15)	intron (NM_145528, intron 1 of 15)	14374	NM_145528	51897	Mm.28492	NM_145528	ENSMUSG00000027244	Atg13	1110053A20Rik|D2Ertd391e|Harbi1	autophagy related 13	protein-coding
mm_20862.1	chr2	148438397	148438414	-	1	NA	3' UTR (NM_010740, exon 2 of 2)	3' UTR (NM_010740, exon 2 of 2)	5130	NM_010740	17064	Mm.681	NM_010740	ENSMUSG00000027435	Cd93	6030404G09Rik|AA145088|AA4.1|AW555904|C1qr1|C1qrp|Ly68	CD93 antigen	protein-coding
mm_124091.1	chr14	79151783	79151790	-	1	NA	intron (NM_027906, intron 37 of 44)	intron (NM_027906, intron 37 of 44)	95581	NM_001033215	105590	Mm.486536	NM_001033215	ENSMUSG00000071262	Zfp957	AU017455	zinc finger protein 957	protein-coding
mm_125170.1	chr15	31338943	31338980	+	1	NA	intron (NM_027496, intron 1 of 3)	L1MB4|LINE|L1	28798	NM_001164441	67434	Mm.102470	NM_026153	ENSMUSG00000022237	Ankrd33b	0610012A05Rik|3021401C12Rik|5730557B15Rik	ankyrin repeat domain 33B	protein-coding
mm_37351.1	chr4	120033371	120033376	-	1	NA	intron (NM_010657, intron 2 of 8)	intron (NM_010657, intron 2 of 8)	-127833	NM_007902	13615	Mm.284855	NM_007902	ENSMUSG00000028635	Edn2	ET-2|PPET2|VIC	endothelin 2	protein-coding
mm_147766.1	chr18	61375391	61375406	-	1	NA	intron (NM_133249, intron 1 of 11)	intron (NM_133249, intron 1 of 11)	25033	NM_133249	170826	Mm.415302	NM_133249	ENSMUSG00000033871	Ppargc1b	4631412G21Rik|Perc	peroxisome proliferative activated receptor, gamma, coactivator 1 beta	protein-coding
mm_65970.1	chr7	30438212	30438233	-	1	NA	exon (NM_007467, exon 11 of 17)	exon (NM_007467, exon 11 of 17)	7360	NM_007467	11803	Mm.2381	NM_007467	ENSMUSG00000006651	Aplp1	-	amyloid beta (A4) precursor-like protein 1	protein-coding
mm_51545.1	chr6	83237522	83237561	+	1	NA	5' UTR (NM_001166067, exon 1 of 25)	5' UTR (NM_001166067, exon 1 of 25)	166	NM_001166067	232156	Mm.333189	NM_001166067	ENSMUSG00000068323	Slc4a5	C330006M16|C330016K18Rik	solute carrier family 4, sodium bicarbonate cotransporter, member 5	protein-coding
mm_10193.1	chr2	4922611	4922631	+	1	NA	intron (NM_010726, intron 1 of 8)	intron (NM_010726, intron 1 of 8)	3625	NM_010726	16922	Mm.391704	NM_010726	ENSMUSG00000026664	Phyh	AI256161|AI265699|Lnap1|PAHX	phytanoyl-CoA hydroxylase	protein-coding
mm_119546.1	chr14	48446266	48446276	+	1	NA	promoter-TSS (NM_172600)	promoter-TSS (NM_172600)	-81	NM_172600	218989	Mm.85211	NM_172600	ENSMUSG00000036339	Tmem260	5930435P15|6720456H20Rik	transmembrane protein 260	protein-coding
mm_65965.1	chr7	30435383	30435399	-	1	NA	exon (NM_007467, exon 17 of 17)	exon (NM_007467, exon 17 of 17)	10191	NM_007467	11803	Mm.2381	NM_007467	ENSMUSG00000006651	Aplp1	-	amyloid beta (A4) precursor-like protein 1	protein-coding
mm_147061.1	chr18	34954277	34954287	-	1	NA	promoter-TSS (NM_010481)	promoter-TSS (NM_010481)	69	NM_010481	15526	Mm.209419	NM_010481	ENSMUSG00000024359	Hspa9	74kDa|Csa|Grp75|Hsc74|Hsp74|Hsp74a|Hspa9a|Mortalin|Mot-2|Mot2|Mthsp70|Pbp74	heat shock protein 9	protein-coding
mm_60720.1	chr7	45335300	45335310	+	1	NA	promoter-TSS (NM_010473)	promoter-TSS (NM_010473)	36	NM_010473	15464	Mm.39968	NM_010473	ENSMUSG00000038239	Hrc	-	histidine rich calcium binding protein	protein-coding
mm_148295.1	chr18	82585435	82585455	-	1	NA	3' UTR (NM_010777, exon 7 of 7)	3' UTR (NM_010777, exon 7 of 7)	30937	NM_001025254	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_100822.1	chr11	5261570	5261637	-	1	NA	promoter-TSS (NM_032396)	promoter-TSS (NM_032396)	7	NM_032396	84035	Mm.209989	NM_032396	ENSMUSG00000020393	Kremen1	AV002070|Kremen|Krm1	kringle containing transmembrane protein 1	protein-coding
mm_37634.1	chr4	127358196	127358208	-	1	NA	promoter-TSS (NM_010291)	promoter-TSS (NM_010291)	-38	NM_010291	14622	Mm.26859	NM_010291	ENSMUSG00000042357	Gjb5	Cnx31.1|Cx31.1|Gjb-5	gap junction protein, beta 5	protein-coding
mm_76512.1	chr8	86911269	86911278	-	1	NA	Intergenic	RMER19C|LTR|ERVK	-26015	NM_030563	80750	Mm.25117	NM_030563	ENSMUSG00000031652	N4bp1	AI481586|C81621	NEDD4 binding protein 1	protein-coding
mm_60471.1	chr7	44478094	44478130	+	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	-6405	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_35974.1	chr4	53339818	53339844	-	1	NA	Intergenic	Intergenic	-69599	NR_033139	381524	Mm.23351	NM_001033454	ENSMUSG00000086712	AI427809	Gm1659	expressed sequence AI427809	ncRNA
mm_20897.1	chr2	148875624	148875641	-	1	NA	promoter-TSS (NM_009976)	promoter-TSS (NM_009976)	-120	NM_009976	13010	Mm.4263	NM_009976	ENSMUSG00000027447	Cst3	CysC	cystatin C	protein-coding
mm_169895.1	chr16	48283796	48283796	+	1	NA	promoter-TSS (NM_028610)	promoter-TSS (NM_028610)	61	NM_001018002	73693	Mm.35597	NM_028610	ENSMUSG00000058550	Dppa4	2410091M23Rik|C76608|ECAT15-1	developmental pluripotency associated 4	protein-coding
mm_64946.1	chr7	16368693	16368702	-	1	NA	intron (NM_001285892, intron 3 of 8)	intron (NM_001285892, intron 3 of 8)	19199	NM_001285892	56459	Mm.258530	NM_019748	ENSMUSG00000052833	Sae1	2400010M20Rik|2610044L12Rik|AL033372|AOS1|AW743391|D7Ertd177e|HSPC140|Sua1|Uble1a	SUMO1 activating enzyme subunit 1	protein-coding
mm_83851.1	chr9	54501915	54501925	-	1	NA	promoter-TSS (NM_172771)	promoter-TSS (NM_172771)	-294	NM_172771	235380	Mm.93636	NM_172771	ENSMUSG00000041268	Dmxl2	6330586A12|6430411K14Rik|E130119P06Rik|mKIAA0856	Dmx-like 2	protein-coding
mm_145393.1	chr18	57142715	57142735	+	1	NA	intron (NM_001001979, intron 1 of 24)	intron (NM_001001979, intron 1 of 24)	9635	NM_001001979	70417	Mm.297863	NM_001001979	ENSMUSG00000024593	Megf10	3000002B06Rik|Gm331	multiple EGF-like-domains 10	protein-coding
mm_12988.1	chr2	90885451	90885459	+	1	NA	promoter-TSS (NM_026161)	promoter-TSS (NM_026161)	-331	NM_026161	67445	Mm.258993	NM_026161	ENSMUSG00000040794	C1qtnf4	0710001E10Rik|9430004J15Rik|CTRP4	C1q and tumor necrosis factor related protein 4	protein-coding
mm_75097.1	chr8	34108444	34108488	-	1	NA	promoter-TSS (NM_001293758)	promoter-TSS (NM_001293758)	246	NM_001293759	22428	Mm.150373	NM_011722	ENSMUSG00000031516	Dctn6	AU044699|WS-3|p27	dynactin 6	protein-coding
mm_52677.1	chr6	117917013	117917021	+	1	NA	promoter-TSS (NM_001166427)	promoter-TSS (NM_001166427)	-277	NM_001166427	98758	Mm.422979	NM_133834	ENSMUSG00000042079	Hnrnpf	4833420I20Rik|AA407306|Hnrpf	heterogeneous nuclear ribonucleoprotein F	protein-coding
mm_130928.1	chr15	103101965	103101970	-	1	NA	Intergenic	Intergenic	44861	NR_045743	432989	Mm.383979	NR_045743	ENSMUSG00000097003	D930007P13Rik	-	Riken cDNA D930007P13 gene	ncRNA
mm_106061.1	chr11	116131074	116131100	-	1	NA	promoter-TSS (NM_178802)	promoter-TSS (NM_178802)	41	NM_178802	338364	Mm.439976	NM_178802	ENSMUSG00000054517	Trim65	4732463G12Rik	tripartite motif-containing 65	protein-coding
mm_156039.1	chrX	107792584	107792609	+	1	NA	promoter-TSS (NM_001271008)	promoter-TSS (NM_001271008)	6	NM_001271008	213449	Mm.444635	NM_001163104	ENSMUSG00000073007	Fam46d	Gm377	family with sequence similarity 46, member D	protein-coding
mm_55116.1	chr6	50394072	50394096	-	1	NA	intron (NM_001347213, intron 2 of 23)	intron (NM_001347213, intron 2 of 23)	-11247	NM_027881	71720	Mm.44153	NM_027881	ENSMUSG00000029822	Osbpl3	1200014M06Rik|6720421I08Rik|A530055M08|ORP-3|ORP3|OSBP3	oxysterol binding protein-like 3	protein-coding
mm_157303.1	chrX	20929703	20929716	-	1	NA	exon (NM_008823, exon 3 of 9)	exon (NM_008823, exon 3 of 9)	1846	NM_008823	18636	Mm.3064	NM_008823	ENSMUSG00000001128	Cfp	BCFG|Pfc	complement factor properdin	protein-coding
mm_28226.1	chr3	88453420	88453426	-	1	NA	intron (NM_001163491, intron 2 of 14)	intron (NM_001163491, intron 2 of 14)	2338	NM_013658	20351	Mm.439752	NM_013658	ENSMUSG00000028064	Sema4a	AI132332|SemB|Semab	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A	protein-coding
mm_127181.1	chr15	98983735	98983747	+	1	NA	Intergenic	Intergenic	-2224	NR_045991	75951	Mm.441657	NR_045991	ENSMUSG00000097587	4930578M01Rik	3010001K12Rik	RIKEN cDNA 4930578M01 gene	ncRNA
mm_52537.1	chr6	115931856	115931858	+	1	NA	promoter-TSS (NM_145383)	promoter-TSS (NM_145383)	-70	NM_145383	212541	Mm.2965	NM_145383	ENSMUSG00000030324	Rho	Noerg1|Opn2|Ops|RP4	rhodopsin	protein-coding
mm_28260.1	chr3	88571857	88571863	-	1	NA	Intergenic	RLTR12E|LTR|ERVK	-7811	NM_025448	66256	Mm.7091	NM_025448	ENSMUSG00000041355	Ssr2	1500032E05Rik|AI315033|AU020133|TLAP|TRAPB|TRAPbeta	signal sequence receptor, beta	protein-coding
mm_147130.1	chr18	36103188	36103189	-	1	NA	intron (NM_001167891, intron 1 of 9)	intron (NM_001167891, intron 1 of 9)	-3015	NR_015571	74966	Mm.379238	NM_030089		4930471G03Rik	1700007N01Rik	RIKEN cDNA 4930471G03 gene	ncRNA
mm_95152.1	chr11	35769575	35769616	+	1	NA	promoter-TSS (NM_145962)	promoter-TSS (NM_145962)	100	NM_145962	211347	Mm.255044	NM_145962	ENSMUSG00000018846	Pank3	-	pantothenate kinase 3	protein-coding
mm_99675.1	chr11	105975205	105975215	+	1	NA	promoter-TSS (NM_009598)	promoter-TSS (NM_009598)	2	NM_009598	11421	Mm.754	NM_009598	ENSMUSG00000020681	Ace	AW208573|CD143	angiotensin I converting enzyme (peptidyl-dipeptidase A) 1	protein-coding
mm_161042.1	chr12	33928416	33928416	+	1	NA	promoter-TSS (NM_033522)	promoter-TSS (NM_033522)	-9	NM_033522	114712	Mm.204643	NM_033522	ENSMUSG00000046518	Ferd3l	Mnato3|N-twist|Nato|Nato3|Ntwist|Ptfb|bHLHa31|fer3	Fer3-like (Drosophila)	protein-coding
mm_118315.1	chr13	113136023	113136048	-	1	NA	promoter-TSS (NR_131045)	promoter-TSS (NR_131045)	-41	NR_131045	76720	Mm.54263	NR_131045		1700084D21Rik	-	RIKEN cDNA 1700084D21 gene	ncRNA
mm_129679.1	chr15	81399751	81399759	-	1	NA	promoter-TSS (NM_133726)	promoter-TSS (NM_133726)	-61	NM_133726	70356	Mm.180337	NM_133726	ENSMUSG00000022403	St13	1110007I03Rik|3110002K08Rik|AW555194|HIP|HOP|HSPABP|HSPABP1|PRO0786|SNC6|p48	suppression of tumorigenicity 13	protein-coding
mm_39251.1	chr5	3502046	3502053	+	1	NA	intron (NM_009873, intron 5 of 7)	intron (NM_009873, intron 5 of 7)	-41784	NM_001042501	68152	Mm.240265	NM_026583	ENSMUSG00000058503	Fam133b	2900022K02Rik|5830415L20Rik	family with sequence similarity 133, member B	protein-coding
mm_30427.1	chr3	152973629	152973640	-	1	NA	intron (NM_012028, intron 2 of 4)	B4A|SINE|B4	8573	NM_012028	26938	Mm.40915	NM_012028	ENSMUSG00000039037	St6galnac5	AI851940|Siat7e	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 5	protein-coding
mm_69569.1	chr7	135700793	135700807	-	1	NA	exon (NM_001081117, exon 12 of 14)	exon (NM_001081117, exon 12 of 14)	15579	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_35918.1	chr4	53031560	53031570	-	1	NA	3' UTR (NM_013454, exon 50 of 50)	3' UTR (NM_013454, exon 50 of 50)	19685	NM_025623	66536	Mm.38244	NM_025623	ENSMUSG00000015247	Nipsnap3b	2700063N13Rik|Nipsnap3a	nipsnap homolog 3B (C. elegans)	protein-coding
mm_81958.1	chr9	120821110	120821115	+	1	NA	Intergenic	Intergenic	94138	NR_040742	76402	Mm.436588	NR_040742	ENSMUSG00000100146	1700020M21Rik	-	RIKEN cDNA 1700020M21 gene	ncRNA
mm_75514.1	chr8	54529952	54530007	-	1	NA	promoter-TSS (NM_029701)	promoter-TSS (NM_029701)	19	NM_029701	76687	Mm.86437	NM_029701	ENSMUSG00000054408	Spcs3	1810011E08Rik|SPC22/23	signal peptidase complex subunit 3 homolog (S. cerevisiae)	protein-coding
mm_54328.1	chr6	30610903	30610912	-	1	NA	promoter-TSS (NM_144537)	promoter-TSS (NM_144537)	-103	NM_144537	74649	Mm.159276	NM_144537	ENSMUSG00000029788	Cpa5	4930430M09Rik	carboxypeptidase A5	protein-coding
mm_39857.1	chr5	30921868	30921896	+	1	NA	TTS (NM_133918)	TTS (NM_133918)	323	NM_001310524	16548	Mm.22451	NM_008439	ENSMUSG00000029162	Khk	-	ketohexokinase	protein-coding
mm_139754.1	chr17	63937952	63937972	+	1	NA	promoter-TSS (NM_008000)	promoter-TSS (NM_008000)	-10	NM_008000	14158	Mm.23039	NM_008000	ENSMUSG00000000127	Fer	AV082135|C330004K01Rik|Fert|Fert2	fer (fms/fps related) protein kinase	protein-coding
mm_93107.1	chr10	91082654	91082661	-	1	NA	promoter-TSS (NM_026166)	promoter-TSS (NM_026166)	86	NM_001042558	11783	Mm.220289	NM_009684	ENSMUSG00000019979	Apaf1	6230400I06Rik|Apaf-1|Apaf1l|fog|mKIAA0413	apoptotic peptidase activating factor 1	protein-coding
mm_149049.1	chr19	8837446	8837558	+	1	NA	promoter-TSS (NM_001136064)	promoter-TSS (NM_001136064)	35	NM_001136064	14705	Mm.345134	NM_008144	ENSMUSG00000071657	Bscl2	2900097C17Rik|AI046355|Gng3lg	Berardinelli-Seip congenital lipodystrophy 2 (seipin)	protein-coding
mm_103324.1	chr11	73326813	73326851	-	1	NA	Intergenic	Intergenic	-2195	NM_023113	11484	Mm.293574	NM_023113	ENSMUSG00000020774	Aspa	Acy-2|Acy2|nur7	aspartoacylase	protein-coding
mm_147772.1	chr18	61484573	61484575	-	1	NA	promoter-TSS (NR_045419)	promoter-TSS (NR_045419)	33	NR_045419	442846	Mm.417648	NR_045419		A530050N04Rik	-	RIKEN cDNA A530050N04 gene	ncRNA
mm_120749.1	chr14	73239057	73239069	+	1	NA	exon (NM_175116, exon 1 of 1)	exon (NM_175116, exon 1 of 1)	1172	NM_175116	67168	Mm.390681	NM_175116	ENSMUSG00000033446	Lpar6	2610302I02Rik|P2ry5|P2y5	lysophosphatidic acid receptor 6	protein-coding
mm_111691.1	chr12	103631405	103631444	-	1	NA	promoter-TSS (NM_001301404)	promoter-TSS (NM_001301404)	20	NM_001301404	217847	Mm.29094	NM_144834	ENSMUSG00000061947	Serpina10	PZI|ZPI	serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 10	protein-coding
mm_143766.1	chr17	81629353	81629357	-	1	NA	intron (NR_104580, intron 2 of 8)	intron (NR_104580, intron 2 of 8)	109032	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_864.1	chr1	52150611	52150645	+	1	NA	exon (NM_001205314, exon 19 of 25)	exon (NM_001205314, exon 19 of 25)	31006	NM_001205313	20846	Mm.277406	NM_009283	ENSMUSG00000026104	Stat1	2010005J02Rik|AA408197	signal transducer and activator of transcription 1	protein-coding
mm_25341.1	chr3	106721854	106721864	+	1	NA	5' UTR (NM_001039488, exon 1 of 4)	5' UTR (NM_001039488, exon 1 of 4)	177	NM_001286685	321000	Mm.259638	NM_028081	ENSMUSG00000056260	Lrif1	2010012G17Rik|4933421E11Rik|AI450568	ligand dependent nuclear receptor interacting factor 1	protein-coding
mm_94919.1	chr11	29499542	29499545	+	1	NA	intron (NM_176841, intron 27 of 31)	intron (NM_176841, intron 27 of 31)	15490	NM_026465	67939	Mm.251087	NM_026465	ENSMUSG00000032673	Prorsd1	2010316F05Rik|Ncrna00117|Prdxdd1	prolyl-tRNA synthetase domain containing 1	protein-coding
mm_37774.1	chr4	129821173	129821210	-	1	NA	intron (NM_001164745, intron 1 of 5)	intron (NM_001164745, intron 1 of 5)	483	NM_001164745	19244	Mm.193688	NM_008974	ENSMUSG00000028788	Ptp4a2	Prl-2	protein tyrosine phosphatase 4a2	protein-coding
mm_86789.1	chr10	20204860	20204900	+	1	NA	intron (NM_001198635, intron 1 of 17)	intron (NM_001198635, intron 1 of 17)	-3026	NR_045350	73811	Mm.55644	NR_045350	ENSMUSG00000110754	4930405J17Rik	-	RIKEN cDNA 4930405J17 gene	ncRNA
mm_161692.1	chr17	22361462	22361462	+	1	NA	promoter-TSS (NM_176962)	promoter-TSS (NM_176962)	9	NM_145484	224598	Mm.390945	NM_145484	ENSMUSG00000044501	Zfp758	BC021442	zinc finger protein 758	protein-coding
mm_146.1	chr1	11089739	11089753	+	1	NA	exon (NM_029525, exon 6 of 40)	exon (NM_029525, exon 6 of 40)	96281	NM_029525	109294	Mm.123247	NM_029525	ENSMUSG00000048960	Prex2	6230420N16Rik|AI316880|AI553603|C030045D06Rik|D430013K02|Depdc2|P-Rex2	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	protein-coding
mm_90565.1	chr10	128231387	128231397	+	1	NA	promoter-TSS (NM_001136082)	promoter-TSS (NM_001136082)	-671	NM_001164080	21853	Mm.6458	NM_011589	ENSMUSG00000039994	Timeless	C77407|Debt69|tim	timeless circadian clock 1	protein-coding
mm_126828.1	chr15	88862241	88862245	+	1	NA	promoter-TSS (NM_145478)	promoter-TSS (NM_145478)	49	NM_145478	223775	Mm.400129	NM_145478	ENSMUSG00000035828	Pim3	BC026639|Kid1	proviral integration site 3	protein-coding
mm_73436.1	chr8	106150424	106150438	+	1	NA	promoter-TSS (NM_133792)	promoter-TSS (NM_133792)	32	NM_133792	192654	Mm.284770	NM_133792	ENSMUSG00000031903	Pla2g15	ACS|C87498|LLPL|Lpla2|Lypla3	phospholipase A2, group XV	protein-coding
mm_88532.1	chr10	78393299	78393308	+	1	NA	Intergenic	Intergenic	15242	NR_105872	102465547		NR_105872	ENSMUSG00000098376	Mir6907	Gm27351|mmu-mir-6907	microRNA 6907	ncRNA
mm_56465.1	chr6	98930070	98930084	-	1	NA	3' UTR (NM_053202, exon 19 of 19)	3' UTR (NM_053202, exon 19 of 19)	98221	NM_001197322	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_1170.1	chr1	60913921	60913934	+	1	NA	intron (NM_009843, intron 3 of 3)	intron (NM_009843, intron 3 of 3)	4902	NM_001281976	12477	Mm.390	NM_009843	ENSMUSG00000026011	Ctla4	Cd152|Ctla-4|Ly-56	cytotoxic T-lymphocyte-associated protein 4	protein-coding
mm_151199.1	chr19	53537516	53537531	+	1	NA	exon (NM_001085390, exon 3 of 4)	exon (NM_001085390, exon 3 of 4)	8205	NM_001085390	240672	Mm.482424	NM_001085390	ENSMUSG00000034765	Dusp5	Gm337	dual specificity phosphatase 5	protein-coding
mm_155254.1	chrX	57224040	57224046	+	1	NA	TTS (NM_011616)	TTS (NM_011616)	11900	NM_011616	21947	Mm.4861	NM_011616	ENSMUSG00000031132	Cd40lg	CD154|CD40-L|Cd40l|HIGM1|IGM|IMD3|Ly-62|Ly62|T-BAM|TRAP|Tnfsf5|Tnlg8b|gp39	CD40 ligand	protein-coding
mm_105056.1	chr11	100704218	100704276	-	1	NA	promoter-TSS (NM_030150)	promoter-TSS (NM_030150)	24	NM_030150	80861	Mm.271830	NM_030150	ENSMUSG00000017830	Dhx58	B430001I08Rik|D11Lgp2e|LPG2|Lgp2|RLR-3	DEXH (Asp-Glu-X-His) box polypeptide 58	protein-coding
mm_99808.1	chr11	108381196	108381202	+	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	-14098	NM_013475	11818	Mm.2266	NM_013475	ENSMUSG00000000049	Apoh	B2GPI|beta-2-GPI|beta2-GPI	apolipoprotein H	protein-coding
mm_83161.1	chr9	40465803	40465811	-	1	NA	Intergenic	Intergenic	-10043	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_108871.1	chr12	99643095	99643097	+	1	NA	Intergenic	RLTR50A|LTR|ERVK	-15122	NR_045288	73457	Mm.383439	NR_045288	ENSMUSG00000100211	1700064M15Rik	-	RIKEN cDNA 1700064M15 gene	ncRNA
mm_155843.1	chrX	101254467	101254495	+	1	NA	promoter-TSS (NM_018789)	promoter-TSS (NM_018789)	-47	NM_018789	54601	Mm.240299	NM_018789	ENSMUSG00000042903	Foxo4	Afxh|Mllt7|afx	forkhead box O4	protein-coding
mm_65670.1	chr7	28291131	28291164	-	1	NA	promoter-TSS (NM_175033)	promoter-TSS (NM_175033)	-13	NM_175033	280621	Mm.212777	NM_175033	ENSMUSG00000046750	Selenov	Selv	selenoprotein V	protein-coding
mm_113940.1	chr13	49731474	49731492	+	1	NA	exon (NM_172015, exon 32 of 34)	exon (NM_172015, exon 32 of 34)	49353	NM_172015	105148	Mm.21118	NM_172015	ENSMUSG00000037851	Iars	2510016L12Rik|AI327140|AU044614|E430001P04Rik|ILRS	isoleucine-tRNA synthetase	protein-coding
mm_147804.1	chr18	61658313	61658333	-	1	NA	intron (NR_045402, intron 1 of 4)	intron (NR_045402, intron 1 of 4)	7215	NR_045402	328968	Mm.392305	NR_045402		Carmn	Carmen|E330013P06|Gm16908|Mir143hg	cardiac mesoderm enhancer-associated non-coding RNA	ncRNA
mm_157097.1	chrX	9437379	9437383	-	1	NA	3' UTR (NM_007807, exon 13 of 13)	3' UTR (NM_007807, exon 13 of 13)	31943	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_172112.1	chr6	3200950	3200950	+	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	-87569	NR_036696	667335	Mm.380219	NR_036696	ENSMUSG00000106779	Gm8579	EG667335	spermatogenesis associated glutamate (E)-rich protein 4a pseudogene	pseudo
mm_60985.1	chr7	49160423	49160434	+	1	NA	intron (NM_001111016, intron 2 of 38)	L3|LINE|CR1	-85761	NM_175272	78286	Mm.333881	NM_175272	ENSMUSG00000052512	Nav2	5330421F07Rik|AU067780|BQ960892|HELAD1|POMFIL2|RAINB1|RAINB2|Unc53H2|mKIAA3015	neuron navigator 2	protein-coding
mm_103065.1	chr11	69837782	69837787	-	1	NA	promoter-TSS (NM_026982)	promoter-TSS (NM_026982)	-741	NM_026982	69186	Mm.248772	NM_026982	ENSMUSG00000070394	Tmem256	1810027O10Rik|3110009M16Rik	transmembrane protein 256	protein-coding
mm_36632.1	chr4	92147186	92147227	-	1	NA	promoter-TSS (NM_027034)	promoter-TSS (NM_027034)	15	NM_027034	69314	Mm.55891	NM_027034	ENSMUSG00000028533	Izumo3	1700011H22Rik	IZUMO family member 3	protein-coding
mm_74443.1	chr8	3926808	3926838	-	1	NA	promoter-TSS (NM_001037800)	promoter-TSS (NM_001037800)	18	NM_001037800	69165	Mm.175163	NM_026972	ENSMUSG00000065987	Cd209b	1810030I22Rik|DC-SIGNR1|OtB7|SIGNR1|mSIGNR1	CD209b antigen	protein-coding
mm_74046.1	chr8	122025792	122025810	+	1	NA	3' UTR (NM_001110100, exon 14 of 14)	3' UTR (NM_001110100, exon 14 of 14)	47777	NR_106096	102466915		NR_106096	ENSMUSG00000099140	Mir7237	Gm27482|mmu-mir-7237	microRNA 7237	ncRNA
mm_37236.1	chr4	118076778	118076818	-	1	NA	intron (NM_009176, intron 2 of 11)	MTD|LTR|ERVL-MaLR	58148	NM_001285520	20441	Mm.251002	NM_009176	ENSMUSG00000028538	St3gal3	ST3GalIII|ST3N|Siat3|Siat6	ST3 beta-galactoside alpha-2,3-sialyltransferase 3	protein-coding
mm_67437.1	chr7	80387172	80387205	-	1	NA	exon (NM_010194, exon 2 of 19)	exon (NM_010194, exon 2 of 19)	758	NM_010194	14159	Mm.48757	NM_010194	ENSMUSG00000053158	Fes	AI586313|BB137047|FPS|c-fes	feline sarcoma oncogene	protein-coding
mm_161957.1	chr19	7105796	7105796	-	1	NA	promoter-TSS (NM_201411)	promoter-TSS (NM_201411)	-67	NM_201411	396184	Mm.386930	NM_201411	ENSMUSG00000047787	Flrt1	AW742165|D630040I23Rik	fibronectin leucine rich transmembrane protein 1	protein-coding
mm_78453.1	chr9	32313057	32313059	+	1	NA	Intergenic	Intergenic	31179	NM_010605	16521	Mm.69472	NM_010605	ENSMUSG00000032034	Kcnj5	GIRK4|Kir3.4	potassium inwardly-rectifying channel, subfamily J, member 5	protein-coding
mm_29306.1	chr3	107943364	107943379	-	1	NA	intron (NM_008184, intron 1 of 7)	intron (NM_008184, intron 1 of 7)	378	NM_008184	14867	Mm.458154	NM_008184	ENSMUSG00000068762	Gstm6	-	glutathione S-transferase, mu 6	protein-coding
mm_143850.1	chr17	84145917	84145938	-	1	NA	Intergenic	Intergenic	42020	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_45009.1	chr5	38502091	38502101	-	1	NA	promoter-TSS (NM_145559)	promoter-TSS (NM_145559)	56	NM_145559	117591	Mm.260137	NM_145559	ENSMUSG00000005107	Slc2a9	Glut9|SLC2A9B|SLC2a9A	solute carrier family 2 (facilitated glucose transporter), member 9	protein-coding
mm_116121.1	chr13	28950609	28950615	-	1	NA	TTS (NM_009238)	TTS (NM_009238)	3070	NM_009238	20677	Mm.240627	NM_009238	ENSMUSG00000076431	Sox4	AA682046|Sox-4	SRY (sex determining region Y)-box 4	protein-coding
mm_53871.1	chr6	149362756	149362780	+	1	NA	Intergenic	Intergenic	-46216	NM_001112796	12121	Mm.177181	NM_009753	ENSMUSG00000003452	Bicd1	B830009D06Rik|bic-D 1	bicaudal D homolog 1 (Drosophila)	protein-coding
mm_50897.1	chr6	57580972	57580985	+	1	NA	promoter-TSS (NM_025992)	promoter-TSS (NM_025992)	-14	NM_025992	67138	Mm.297393	NM_025992	ENSMUSG00000029798	Herc6	1700121D12Rik|2510038N07Rik|4930427L17Rik|AI451296|CEB1|Herc5	hect domain and RLD 6	protein-coding
mm_32519.1	chr4	108834611	108834617	+	1	NA	promoter-TSS (NM_025334)	promoter-TSS (NM_025334)	-64	NM_025334	66073	Mm.159965	NM_025334	ENSMUSG00000028567	Txndc12	0610040B21Rik|ERp16|ERp19	thioredoxin domain containing 12 (endoplasmic reticulum)	protein-coding
mm_72335.1	chr8	79225830	79225865	+	1	NA	intron (NM_026315, intron 2 of 5)	MTEa|LTR|ERVL-MaLR	22736	NM_026315	67687	Mm.178707	NM_026315	ENSMUSG00000031682	1700011L22Rik	-	RIKEN cDNA 1700011L22 gene	protein-coding
mm_58380.1	chr6	149188623	149188636	-	1	NA	promoter-TSS (NM_001113424)	promoter-TSS (NM_001113424)	83	NM_001113424	232566	Mm.209147	NM_001113424	ENSMUSG00000068250	Amn1	5830467E07Rik|A230083D09|C730024G19Rik	antagonist of mitotic exit network 1	protein-coding
mm_139065.1	chr17	46555243	46555256	+	1	NA	intron (NM_020493, intron 1 of 6)	CpG	913	NM_020493	20807	Mm.45044	NM_020493	ENSMUSG00000015605	Srf	AW049942|AW240594	serum response factor	protein-coding
mm_30434.1	chr3	153322813	153322833	-	1	NA	intron (NM_011372, intron 3 of 4)	intron (NM_011372, intron 3 of 4)	-24174	NR_126464	75489	Mm.443252	NR_126464	ENSMUSG00000105023	1700012D16Rik	-	RIKEN cDNA 1700012D16 gene	ncRNA
mm_130960.1	chr15	103314877	103314899	-	1	NA	3' UTR (NM_013866, exon 8 of 8)	3' UTR (NM_013866, exon 8 of 8)	-4450	NM_030720	80910	Mm.160369	NM_030720	ENSMUSG00000063234	Gpr84	EX33	G protein-coupled receptor 84	protein-coding
mm_32356.1	chr4	105157429	105157463	+	1	NA	promoter-TSS (NM_080555)	promoter-TSS (NM_080555)	99	NM_080555	67916	Mm.348326	NM_080555	ENSMUSG00000028517	Plpp3	1110003O22Rik|2610002D05Rik|AV025606|D4Bwg0538e|D4Bwg1535e|Lpp3|Ppab2b|Ppap2b	phospholipid phosphatase 3	protein-coding
mm_19271.1	chr2	85086470	85086498	-	1	NA	promoter-TSS (NR_040504)	promoter-TSS (NR_040504)	-23	NR_040504	74687	Mm.66996	NR_040504	ENSMUSG00000086969	4930443O20Rik	-	RIKEN cDNA 4930443O20 gene	ncRNA
mm_40652.1	chr5	65107659	65107665	+	1	NA	promoter-TSS (NM_001347355)	promoter-TSS (NM_001347355)	94	NM_001347355	71778	Mm.10281	NM_175174	ENSMUSG00000054920	Klhl5	1300013C10Rik	kelch-like 5	protein-coding
mm_19426.1	chr2	91931956	91931989	-	1	NA	promoter-TSS (NM_001291481)	promoter-TSS (NM_001291481)	-113	NM_001291482	17242	Mm.906	NM_010784	ENSMUSG00000027239	Mdk	MK|Mek	midkine	protein-coding
mm_59562.1	chr7	28086347	28086361	+	1	NA	exon (NM_001122603, exon 5 of 20)	exon (NM_001122603, exon 5 of 20)	15118	NM_001122603	215384	Mm.292276	NM_175444	ENSMUSG00000047730	Fcgbp	A430096B05Rik	Fc fragment of IgG binding protein	protein-coding
mm_34920.1	chr4	155761203	155761235	+	1	NA	promoter-TSS (NM_179203)	promoter-TSS (NM_179203)	27	NR_027972	70448	Mm.70636	NM_175157	ENSMUSG00000054514	Atad3aos	2610204G22Rik	ATPase family, AAA domain containing 3A, opposite strand	ncRNA
mm_43253.1	chr5	130219535	130219549	+	1	NA	promoter-TSS (NM_001081394)	promoter-TSS (NM_001081394)	-202	NM_001081394	71667	Mm.258508	NM_027854	ENSMUSG00000053094	Tmem248	0610007L01Rik|A930023A16Rik|AW557951|G430067H08Rik	transmembrane protein 248	protein-coding
mm_36058.1	chr4	57364260	57364303	-	1	NA	promoter-TSS (NR_038178)	promoter-TSS (NR_038178)	11	NR_038179	73349	Mm.393774	NR_038178		1700042G15Rik	-	RIKEN cDNA 1700042G15 gene	ncRNA
mm_154524.1	chrM	13446	13452	-	1	NA	NA	Intergenic	NA	NA								
mm_49440.1	chr6	29319192	29319194	+	1	NA	promoter-TSS (NM_001289664)	promoter-TSS (NM_001289664)	53	NM_001289664	330277	Mm.87624	NM_207258	ENSMUSG00000039742	Fam71f1	GARI-L1|Gm764|NYD-SP18	family with sequence similarity 71, member F1	protein-coding
mm_16262.1	chr2	173522576	173522581	+	1	NA	promoter-TSS (NM_028158)	promoter-TSS (NM_028158)	-14	NM_028158	72221	Mm.46132	NM_028158	ENSMUSG00000027518	1700021F07Rik	-	RIKEN cDNA 1700021F07 gene	protein-coding
mm_117091.1	chr13	59770290	59770304	-	1	NA	promoter-TSS (NM_026921)	promoter-TSS (NM_026921)	331	NR_015349	13996	Mm.490435	NR_015349	ENSMUSG00000089875	Etohd2	AW491659	ethanol decreased 2	ncRNA
mm_153508.1	chr19	41363919	41363935	-	1	NA	intron (NM_031376, intron 2 of 16)	intron (NM_031376, intron 2 of 16)	21143	NM_031376	83490	Mm.222266	NM_031376	ENSMUSG00000025017	Pik3ap1	1810044J04Rik|BCAP	phosphoinositide-3-kinase adaptor protein 1	protein-coding
mm_135633.1	chr16	52333153	52333159	-	1	NA	intron (NM_009655, intron 1 of 15)	intron (NM_009655, intron 1 of 15)	119925	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_114247.1	chr13	56630565	56630591	+	1	NA	exon (NM_009369, exon 9 of 17)	exon (NM_009369, exon 9 of 17)	20975	NM_009369	21810	Mm.14455	NM_009369	ENSMUSG00000035493	Tgfbi	68kDa|AI181842|AI747162|Beta-ig|big-h3	transforming growth factor, beta induced	protein-coding
mm_132909.1	chr16	48872856	48872865	+	1	NA	5' UTR (NM_181596, exon 2 of 4)	5' UTR (NM_181596, exon 2 of 4)	252	NM_181596	245195	Mm.231288	NM_181596	ENSMUSG00000022651	Retnlg	Fizz3|Relmg|Xcp1	resistin like gamma	protein-coding
mm_39746.1	chr5	29569491	29569499	+	1	NA	5' UTR (NM_133907, exon 1 of 23)	5' UTR (NM_133907, exon 1 of 23)	253	NM_133907	100763	Mm.137746	NM_133907	ENSMUSG00000039000	Ube3c	AI853514|mKIAA0010	ubiquitin protein ligase E3C	protein-coding
mm_142806.1	chr17	50668974	50668976	-	1	NA	intron (NM_013880, intron 5 of 5)	ORR1D2-int|LTR|ERVL-MaLR	-29706	NM_001297747	12228	Mm.392910	NM_009770	ENSMUSG00000022863	Btg3	ANA|tob5	B cell translocation gene 3	protein-coding
mm_93094.1	chr10	89686198	89686214	-	1	NA	promoter-TSS (NM_001310704)	promoter-TSS (NM_001310704)	79	NM_198021	213326	Mm.27651	NM_198021	ENSMUSG00000069539	Scyl2	AU015688|AW536445|BC030932|CVAK104|D10Ertd802e	SCY1-like 2 (S. cerevisiae)	protein-coding
mm_113319.1	chr13	30764853	30764860	+	1	NA	3' UTR (NM_013674, exon 9 of 9)	3' UTR (NM_013674, exon 9 of 9)	15623	NM_013674	16364	Mm.4677	NM_013674	ENSMUSG00000021356	Irf4	AI385587|IRF-4|LSIRF|NF-EM5|Spip	interferon regulatory factor 4	protein-coding
mm_53646.1	chr6	140639984	140639987	+	1	NA	intron (NM_001005605, intron 3 of 7)	intron (NM_001005605, intron 3 of 7)	13100	NM_001309436	11569	Mm.86453	NM_009637	ENSMUSG00000030232	Aebp2	AU023766|B230313N05Rik	AE binding protein 2	protein-coding
mm_27919.1	chr3	79531875	79531886	-	1	NA	intron (NM_001162999, intron 1 of 16)	intron (NM_001162999, intron 1 of 16)	35799	NM_001162999	329679	Mm.244005	NM_001162999	ENSMUSG00000061175	Fnip2	D630023B12Rik|mKIAA1450	folliculin interacting protein 2	protein-coding
mm_17192.1	chr2	25466806	25466820	-	1	NA	3' UTR (NM_008963, exon 7 of 7)	3' UTR (NM_008963, exon 7 of 7)	2936	NM_008963	19215	Mm.1008	NM_008963	ENSMUSG00000015090	Ptgds	21kDa|L-PGDS|PGD2|PGDS|PGDS2|Ptgs3	prostaglandin D2 synthase (brain)	protein-coding
mm_6869.1	chr1	84281987	84282000	-	1	NA	intron (NM_001003948, intron 1 of 2)	intron (NM_001003948, intron 1 of 2)	2652	NM_001003948	98496	Mm.187470	NM_001003948	ENSMUSG00000045658	Pid1	5033414K04Rik|NYGGF4	phosphotyrosine interaction domain containing 1	protein-coding
mm_81956.1	chr9	120571499	120571522	+	1	NA	promoter-TSS (NM_025974)	promoter-TSS (NM_025974)	-7	NM_025974	67115	Mm.289810	NM_025974	ENSMUSG00000025794	Rpl14	3100001N19Rik|AA407502|AL022816|CAG-ISL-7|CTG-B33|L14	ribosomal protein L14	protein-coding
mm_77322.1	chr8	119416919	119416928	-	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	-20239	NM_027950	71839	Mm.272357	NM_027950	ENSMUSG00000074063	Osgin1	1700012B18Rik|Okl38	oxidative stress induced growth inhibitor 1	protein-coding
mm_70362.1	chr8	8661808	8661817	+	1	NA	Intergenic	CpG-13817	-1039	NM_010111	13642	Mm.209813	NM_010111	ENSMUSG00000001300	Efnb2	ELF-2|Epl5|Eplg5|Htk-L|LERK-5|Lerk5|NLERK-1	ephrin B2	protein-coding
mm_60883.1	chr7	46376468	46376480	+	1	NA	promoter-TSS (NM_010866)	promoter-TSS (NM_010866)	0	NM_010866	17927	Mm.1526	NM_010866	ENSMUSG00000009471	Myod1	AI503393|MYF3|MyoD|Myod-1|bHLHc1	myogenic differentiation 1	protein-coding
mm_103113.1	chr11	69982631	69982669	-	1	NA	intron (NM_026017, intron 1 of 7)	intron (NM_026017, intron 1 of 7)	-1415	NM_018740	54351	Mm.13430	NM_018740	ENSMUSG00000018565	Elp5	Derp6|Rai12	elongator acetyltransferase complex subunit 5	protein-coding
mm_122230.1	chr14	33185081	33185100	-	1	NA	promoter-TSS (NM_001146022)	promoter-TSS (NM_001146022)	-24	NM_001146022	545030	Mm.318345	NM_001146022	ENSMUSG00000051506	Wdfy4	Gm18810	WD repeat and FYVE domain containing 4	protein-coding
mm_139598.1	chr17	57253948	57253956	+	1	NA	intron (NM_134125, intron 5 of 13)	PB1D10|SINE|Alu	4501	NM_001242389	106628	Mm.37368	NM_134125	ENSMUSG00000019487	Trip10	AI646975|Cip4	thyroid hormone receptor interactor 10	protein-coding
mm_156896.1	chrX	167207094	167207096	+	1	NA	TTS (NM_021278)	TTS (NM_021278)	2123	NM_021278	19241	Mm.142729	NM_021278	ENSMUSG00000049775	Tmsb4x	Ptmb4|Tb4	thymosin, beta 4, X chromosome	protein-coding
mm_80877.1	chr9	98986366	98986412	+	1	NA	promoter-TSS (NM_001122851)	promoter-TSS (NM_001122851)	16	NM_011810	23873	Mm.74605	NM_011810	ENSMUSG00000032463	Faim	-	Fas apoptotic inhibitory molecule	protein-coding
mm_75738.1	chr8	69716438	69716492	-	1	NA	promoter-TSS (NM_181274)	promoter-TSS (NM_181274)	21	NM_181274	66869	Mm.334581	NM_181274	ENSMUSG00000054648	Zfp869	1200003I07Rik	zinc finger protein 869	protein-coding
mm_158284.1	chrX	111697070	111697127	-	1	NA	promoter-TSS (NM_001290459)	promoter-TSS (NM_001290459)	-19	NM_001290459	245596	Mm.246623	NM_001080549	ENSMUSG00000034551	Hdx	D030011N01Rik|Gm380	highly divergent homeobox	protein-coding
mm_172849.1	chr9	36568668	36568668	-	1	NA	Intergenic	L1Md_T|LINE|L1	13967	NM_001167584	100312948	Mm.475849	NM_001167584	ENSMUSG00000091248	Gm17689	Pate-g|Pate8	predicted gene, 17689	protein-coding
mm_114264.1	chr13	58071484	58071489	+	1	NA	intron (NM_001195075, intron 6 of 16)	intron (NM_001195075, intron 6 of 16)	30942	NM_001195075	100503085	Mm.379256	NM_001195075	ENSMUSG00000014164	Klhl3	7530408C15Rik|AI430941|EG627648	kelch-like 3	protein-coding
mm_1530.1	chr1	72849201	72849214	+	1	NA	exon (NM_008342, exon 2 of 4)	exon (NM_008342, exon 2 of 4)	23820	NM_001310659	16008	Mm.141936	NM_008342	ENSMUSG00000039323	Igfbp2	AI255832|IBP-2|Igfbp-2|mIGFBP-2	insulin-like growth factor binding protein 2	protein-coding
mm_22899.1	chr3	30801112	30801128	+	1	NA	exon (NM_027016, exon 3 of 8)	exon (NM_027016, exon 3 of 8)	8244	NM_027016	69276	Mm.26017	NM_027016	ENSMUSG00000027706	Sec62	3100002M17Rik|AI844545|AW545092|Dtrp1|HTP1|Tloc1	SEC62 homolog (S. cerevisiae)	protein-coding
mm_19137.1	chr2	80447059	80447072	-	1	NA	5' UTR (NM_011356, exon 1 of 6)	5' UTR (NM_011356, exon 1 of 6)	331	NM_011356	20378	Mm.427436	NM_011356	ENSMUSG00000027004	Frzb	Frp|Sfrp3|frezzled|fritz|frzb-1	frizzled-related protein	protein-coding
mm_95819.1	chr11	55213784	55213814	+	1	NA	intron (NM_153139, intron 1 of 10)	intron (NM_153139, intron 1 of 10)	9459	NM_153139	215335	Mm.35732	NM_153139	ENSMUSG00000020261	Slc36a1	5830411H19Rik|AI839897|Pat1	solute carrier family 36 (proton/amino acid symporter), member 1	protein-coding
mm_102390.1	chr11	58978011	58978065	-	1	NA	promoter-TSS (NM_053168)	promoter-TSS (NM_053168)	-55	NM_001290988	94091	Mm.248049	NM_053168	ENSMUSG00000020455	Trim11	-	tripartite motif-containing 11	protein-coding
mm_108222.1	chr12	77177747	77177749	+	1	NA	Intergenic	Intergenic	-60356	NM_001252614	53618	Mm.35628	NM_016893	ENSMUSG00000021065	Fut8	-	fucosyltransferase 8	protein-coding
mm_22944.1	chr3	31984213	31984230	+	1	NA	intron (NM_028231, intron 2 of 5)	intron (NM_028231, intron 2 of 5)	81518	NM_028231	72413	Mm.64790	NM_028231	ENSMUSG00000037610	Kcnmb2	2700049B16Rik|3110031N04Rik	potassium large conductance calcium-activated channel, subfamily M, beta member 2	protein-coding
mm_127997.1	chr15	12737162	12737166	-	1	NA	Intergenic	Intergenic	87493	NM_029998	77877	Mm.207311	NM_029998	ENSMUSG00000022195	6030458C11Rik	-	RIKEN cDNA 6030458C11 gene	protein-coding
mm_56691.1	chr6	114165481	114165488	-	1	NA	intron (NM_172890, intron 5 of 13)	RMER13B|LTR|ERVK	34243	NM_172890	243616	Mm.44683	NM_172890	ENSMUSG00000030307	Slc6a11	D930045G19Rik|E130202I16Rik|GAT4|Gabt4|Gat3	solute carrier family 6 (neurotransmitter transporter, GABA), member 11	protein-coding
mm_47307.1	chr5	122397014	122397025	-	1	NA	intron (NM_019824, intron 2 of 6)	intron (NM_019824, intron 2 of 6)	5141	NM_019824	56378	Mm.275942	NM_019824	ENSMUSG00000029465	Arpc3	1110006A04Rik|p21-ARC|p21-Ar|p21Arc	actin related protein 2/3 complex, subunit 3	protein-coding
mm_64288.1	chr7	141856785	141856795	+	1	NA	exon (NM_028801, exon 30 of 49)	exon (NM_028801, exon 30 of 49)	17718	NM_028801	74180	Mm.200752	NM_028801	ENSMUSG00000066108	Muc5b	2300002I04Rik|A130042M24|AV085033|MUC5|MUC9|mucin 5b	mucin 5, subtype B, tracheobronchial	protein-coding
mm_47357.1	chr5	122779450	122779463	-	1	NA	promoter-TSS (NM_001199676)	promoter-TSS (NM_001199676)	-46	NM_145358	207565	Mm.289237	NM_145358	ENSMUSG00000029471	Camkk2	6330570N16Rik|AW061083|mKIAA0787	calcium/calmodulin-dependent protein kinase kinase 2, beta	protein-coding
mm_130211.1	chr15	95587052	95587084	-	1	NA	Intergenic	Intergenic	-58816	NM_001289653	54003	Mm.3959	NM_016743	ENSMUSG00000022454	Nell2	A330108N19Rik|R75516|mel91	NEL-like 2	protein-coding
mm_114256.1	chr13	56703505	56703537	+	1	NA	promoter-TSS (NM_001164042)	promoter-TSS (NM_001164042)	-147	NM_001164042	17129	Mm.272920	NM_008541	ENSMUSG00000021540	Smad5	1110051M15Rik|AI451355|Dwf-C|Madh5|MusMLP	SMAD family member 5	protein-coding
mm_55023.1	chr6	48841417	48841421	-	1	NA	promoter-TSS (NM_001164209)	promoter-TSS (NM_001164209)	-45	NM_001164208	65963	Mm.28385	NM_023056	ENSMUSG00000029810	Tmem176b	1810009M01Rik|Clast1|Lr8	transmembrane protein 176B	protein-coding
mm_156321.1	chrX	137358730	137358738	+	1	NA	Intergenic	Intergenic	-212020	NM_030688	60367	Mm.328321	NM_030688	ENSMUSG00000059203	Il1rapl2	-	interleukin 1 receptor accessory protein-like 2	protein-coding
mm_34847.1	chr4	155415012	155415018	+	1	NA	intron (NR_102283, intron 1 of 4)	RSINE1|SINE|B4	5825	NM_001166029	544678	Mm.472798	NM_177674	ENSMUSG00000078490	Cfap74	2010015L04Rik|A530045M11	cilia and flagella associated protein 74	protein-coding
mm_51777.1	chr6	88152376	88152390	+	1	NA	Intergenic	Intergenic	-46281	NM_008090	14461	Mm.491156	NM_008090	ENSMUSG00000015053	Gata2	Gata-2	GATA binding protein 2	protein-coding
mm_148243.1	chr18	80611710	80611715	-	1	NA	intron (NM_198429, intron 9 of 9)	intron (NM_198429, intron 9 of 9)	-67166	NR_028424	100039348	Mm.254722	NR_028424		Gm2176	A430076E10Rik	glucosamine-6-phosphate deaminase 1 pseudogene	pseudo
mm_148265.1	chr18	80987017	80987022	-	1	NA	promoter-TSS (NM_178280)	promoter-TSS (NM_178280)	-441	NM_178280	20689	Mm.215917	NM_178280	ENSMUSG00000024565	Sall3	B130022O04Rik|Msal|Msal-1|Sal|Salt|Spalt	sal-like 3 (Drosophila)	protein-coding
mm_171589.1	chr4	147642419	147642423	-	1	NA	promoter-TSS (NM_145078)	promoter-TSS (NM_145078)	87	NM_145078	112422	Mm.327194	NM_145078	ENSMUSG00000066000	Zfp979	2610305D13Rik|Ssm1b	zinc finger protein 979	protein-coding
mm_30309.1	chr3	149445352	149445369	-	1	NA	Intergenic	Intergenic	170623	NR_040591	381482	Mm.393866	NR_040591		Gm1653	-	predicted gene 1653	ncRNA
mm_11732.1	chr2	37505397	37505400	+	1	NA	intron (NM_001033960, intron 12 of 18)	B1_Mur3|SINE|Alu	-11228	NM_177383	338346	Mm.445325	NM_177383	ENSMUSG00000053164	Gpr21	C230004C13Rik	G protein-coupled receptor 21	protein-coding
mm_78915.1	chr9	44985436	44985454	+	1	NA	intron (NM_013487, intron 2 of 4)	intron (NM_013487, intron 2 of 4)	3659	NM_013487	12500	Mm.4527	NM_013487	ENSMUSG00000032094	Cd3d	T3d	CD3 antigen, delta polypeptide	protein-coding
mm_148090.1	chr18	73770508	73770510	-	1	NA	3' UTR (NM_145494, exon 16 of 16)	3' UTR (NM_145494, exon 16 of 16)	-16030	NM_053255	114615	Mm.50642	NM_053255	ENSMUSG00000036941	Elac1	2610018O07Rik|8430417G19Rik	elaC ribonuclease Z 1	protein-coding
mm_28176.1	chr3	88000351	88000359	-	1	NA	promoter-TSS (NM_001109758)	promoter-TSS (NM_001109758)	1	NM_007529	12032	Mm.4598	NM_007529	ENSMUSG00000004892	Bcan	Cspg7	brevican	protein-coding
mm_113040.1	chr13	23562586	23562641	+	1	NA	promoter-TSS (NM_178205)	promoter-TSS (NM_178205)	-248	NM_178205	319151	Mm.261658	NM_178205	ENSMUSG00000069273	Hist1h3e	H3-f|H3.1	histone cluster 1, H3e	protein-coding
mm_65322.1	chr7	24954662	24954674	-	1	NA	Intergenic	Intergenic	15407	NR_106013	102465633		NR_106013	ENSMUSG00000098802	Mir7046	Gm27469|mmu-mir-7046	microRNA 7046	ncRNA
mm_6893.1	chr1	84696149	84696159	-	1	NA	promoter-TSS (NM_152915)	promoter-TSS (NM_152915)	67	NM_152915	227325	Mm.292560	NM_152915	ENSMUSG00000036766	Dner	A930026D19Rik|BET|Bret	delta/notch-like EGF repeat containing	protein-coding
mm_52548.1	chr6	115935137	115935148	+	1	NA	exon (NM_145383, exon 3 of 5)	exon (NM_145383, exon 3 of 5)	3215	NM_145383	212541	Mm.2965	NM_145383	ENSMUSG00000030324	Rho	Noerg1|Opn2|Ops|RP4	rhodopsin	protein-coding
mm_5961.1	chr1	56972184	56972212	-	1	NA	promoter-TSS (NM_139146)	promoter-TSS (NM_139146)	729	NR_024325	329160	Mm.419039	NR_024325	ENSMUSG00000087022	9130024F11Rik	B530002L08|EG329160	RIKEN cDNA 9130024F11 gene	ncRNA
mm_9618.1	chr1	176614762	176614770	-	1	NA	Intergenic	Intergenic	157657	NR_029775	723921		NR_029775	ENSMUSG00000065573	Mir350	Mirn350|mir-350|mmu-mir-350	microRNA 350	ncRNA
mm_5476.1	chr1	36683098	36683108	-	1	NA	promoter-TSS (NM_201365)	promoter-TSS (NM_201365)	80	NM_001126046	381337	Mm.17413	NM_027957	ENSMUSG00000046337	Fam178b	1700024G10Rik|Gm990	family with sequence similarity 178, member B	protein-coding
mm_87534.1	chr10	53471524	53471529	+	1	NA	Intergenic	LTRIS4|LTR|ERV1	47463	NR_037973	100502868	Mm.297722	NR_037973		Gm20597	B230314j19	predicted gene, 20597	ncRNA
mm_90489.1	chr10	128015187	128015231	+	1	NA	promoter-TSS (NM_008921)	promoter-TSS (NM_008921)	-6	NM_008921	19075	Mm.2903	NM_008921	ENSMUSG00000025395	Prim1	AI324982	DNA primase, p49 subunit	protein-coding
mm_116788.1	chr13	53374308	53374319	-	1	NA	intron (NM_009269, intron 1 of 14)	intron (NM_009269, intron 1 of 14)	3048	NM_009269	268656	Mm.240336	NM_009269	ENSMUSG00000021468	Sptlc1	AW552086|C77762|E030036H05|Lcb1	serine palmitoyltransferase, long chain base subunit 1	protein-coding
mm_121788.1	chr14	19977152	19977204	-	1	NA	promoter-TSS (NM_001285911)	promoter-TSS (NM_001285911)	71	NM_001038637	14702	Mm.41737	NM_010315	ENSMUSG00000043004	Gng2	-	guanine nucleotide binding protein (G protein), gamma 2	protein-coding
mm_157031.1	chrX	7928508	7928526	-	1	NA	promoter-TSS (NM_181548)	promoter-TSS (NM_181548)	90	NM_181548	353283	Mm.250895	NM_181548	ENSMUSG00000031160	Eras	HRAS2|HRasp|Ha-Ras2|ecat5	ES cell-expressed Ras	protein-coding
mm_15599.1	chr2	160667876	160667881	+	1	NA	intron (NM_009408, intron 2 of 20)	intron (NM_009408, intron 2 of 20)	21981	NM_009408	21969	Mm.217233	NM_009408	ENSMUSG00000070544	Top1	AI467334|D130064I21Rik|Top-1	topoisomerase (DNA) I	protein-coding
mm_139972.1	chr17	71769730	71769749	+	1	NA	promoter-TSS (NM_001271484)	promoter-TSS (NM_001271484)	48	NM_001271484	78785	Mm.196382	NM_030179	ENSMUSG00000024059	Clip4	1700024K14Rik|1700074B05Rik|4833417L20Rik|5830409B12Rik|Rsnl2	CAP-GLY domain containing linker protein family, member 4	protein-coding
mm_100709.1	chr11	3722190	3722222	-	1	NA	promoter-TSS (NM_001302630)	promoter-TSS (NM_001302630)	21	NM_001302631	74309	Mm.61022	NM_152818	ENSMUSG00000020435	Osbp2	1700095P05Rik|C630001G20Rik|Gm244|ORP-4|OSBPL1	oxysterol binding protein 2	protein-coding
mm_37435.1	chr4	122950224	122950229	-	1	NA	exon (NM_029662, exon 9 of 14)	exon (NM_029662, exon 9 of 14)	10962	NM_029662	76574	Mm.331842	NM_029662	ENSMUSG00000028655	Mfsd2a	1700018O18Rik|Mfsd2|NLS1	major facilitator superfamily domain containing 2A	protein-coding
mm_61667.1	chr7	80779729	80779734	+	1	NA	intron (NM_016721, intron 2 of 37)	intron (NM_016721, intron 2 of 37)	23600	NM_016721	29875	Mm.207619	NM_016721	ENSMUSG00000030536	Iqgap1	AA682088|D7Ertd237e|D7Ertd257e|mKIAA0051	IQ motif containing GTPase activating protein 1	protein-coding
mm_50092.1	chr6	41532922	41532934	+	1	NA	Intergenic	Intergenic	11152	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_71943.1	chr8	70374962	70374974	+	1	NA	exon (NM_016685, exon 4 of 19)	exon (NM_016685, exon 4 of 19)	1420	NM_016685	12845	Mm.45071	NM_016685	ENSMUSG00000031849	Comp	TSP5	cartilage oligomeric matrix protein	protein-coding
mm_62934.1	chr7	118712668	118712679	+	1	NA	promoter-TSS (NM_182995)	promoter-TSS (NM_182995)	62	NM_182995	101565	Mm.23279	NM_182995	ENSMUSG00000033904	Ccp110	6330503K22Rik|AA415922|AI427129|AW557948|CP110	centriolar coiled coil protein 110	protein-coding
mm_45679.1	chr5	77349338	77349437	-	1	NA	TTS (NM_153798)	TTS (NM_153798)	38903	NM_153798	231329	Mm.273217	NM_153798	ENSMUSG00000029250	Polr2b	Pol2rb|Rpb140|Rpb2	polymerase (RNA) II (DNA directed) polypeptide B	protein-coding
mm_117617.1	chr13	91807613	91807619	-	1	NA	promoter-TSS (NM_145453)	promoter-TSS (NM_145453)	80	NM_145453	69085	Mm.52356	NM_145453	ENSMUSG00000021621	Zcchc9	1810019C21Rik	zinc finger, CCHC domain containing 9	protein-coding
mm_17830.1	chr2	33942126	33942151	-	1	NA	Intergenic	GA-rich|Low_complexity|Low_complexity	-54192	NM_175184	72543	Mm.254914	NM_175184	ENSMUSG00000038740	Mvb12b	2610200O14Rik|2610528K11Rik|AI414895|Fam125b	multivesicular body subunit 12B	protein-coding
mm_163664.1	chr13	77708744	77708750	+	1	NA	promoter-TSS (NR_028109)	promoter-TSS (NR_028109)	57	NM_001163419	68675	Mm.343005	NM_138312	ENSMUSG00000064138	Fam172a	1110033M05Rik|2610318O14Rik|53-E6|9430037D06Rik|AF064782|pEN87	family with sequence similarity 172, member A	protein-coding
mm_125017.1	chr15	25626450	25626472	+	1	NA	intron (NM_019472, intron 1 of 40)	intron (NM_019472, intron 1 of 40)	3911	NM_019472	17909	Mm.60590	NM_019472	ENSMUSG00000022272	Myo10	AW048724|D15Ertd600e|mKIAA0799|myosin-X	myosin X	protein-coding
mm_16333.1	chr2	174329984	174329994	+	1	NA	promoter-TSS (NM_001077510)	promoter-TSS (NM_001077510)	-81	NM_201616	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_112146.1	chr12	113259541	113259549	-	1	NA	Intergenic	Intergenic	73642	NM_153776	69195	Mm.313244	NM_153776	ENSMUSG00000049036	Tmem121	2410008J05Rik|Hole	transmembrane protein 121	protein-coding
mm_27675.1	chr3	65922594	65922595	-	1	NA	Intergenic	Intergenic	35631	NM_019937	56706	Mm.175612	NM_019937	ENSMUSG00000027829	Ccnl1	2610030E23Rik|AU018493|Ccnl|ania-6a	cyclin L1	protein-coding
mm_111860.1	chr12	107960215	107960219	-	1	NA	intron (NM_001286343, intron 1 of 1)	intron (NM_001286343, intron 1 of 1)	43197	NM_001079883	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_141327.1	chr17	28455649	28455651	-	1	NA	intron (NM_010220, intron 1 of 10)	B1_Mur4|SINE|Alu	30499	NM_010220	14229	Mm.276405	NM_010220	ENSMUSG00000024222	Fkbp5	D17Ertd592e|Dit1|FKBP-5|FKBP51	FK506 binding protein 5	protein-coding
mm_8792.1	chr1	161788360	161788375	-	1	NA	5' UTR (NM_001205243, exon 1 of 3)	5' UTR (NM_001205243, exon 1 of 3)	128	NM_001205243	14103	Mm.3355	NM_010177	ENSMUSG00000000817	Fasl	APT1LG1|CD178|CD95-L|CD95L|Fas-L|Faslg|Tnfsf6|Tnlg1a|gld	Fas ligand (TNF superfamily, member 6)	protein-coding
mm_60615.1	chr7	44593017	44593025	+	1	NA	intron (NM_008422, intron 1 of 3)	intron (NM_008422, intron 1 of 3)	2135	NM_001290682	16504	Mm.40312	NM_008422	ENSMUSG00000062785	Kcnc3	KShIIID|Kcr2-3|Kv3.3	potassium voltage gated channel, Shaw-related subfamily, member 3	protein-coding
mm_131225.1	chr16	9133296	9133310	+	1	NA	Intergenic	RLTR41C|LTR|ERV1	303203	NM_001081400	69053	Mm.390868	NM_001081400	ENSMUSG00000022507	1810013L24Rik	1110017P05Rik|3010002C02Rik|AA792997|AW124177|Gm19906|R74903	RIKEN cDNA 1810013L24 gene	protein-coding
mm_164384.1	chr16	31740457	31740473	+	1	NA	intron (NR_045516, intron 4 of 24)	RMER17D2|LTR|ERVK	-13885	NM_001252436	13383	Mm.382	NM_007862	ENSMUSG00000022770	Dlg1	B130052P05Rik|Dlgh1|E-dlg/SAP97|SAP-97|SAP97|mKIAA4187	discs, large homolog 1 (Drosophila)	protein-coding
mm_102412.1	chr11	59201683	59201697	-	1	NA	promoter-TSS (NM_026035)	promoter-TSS (NM_026035)	741	NR_037964	72203	Mm.339566	NR_037964		2610507I01Rik	5033414D05Rik	RIKEN cDNA 2610507I01 gene	ncRNA
mm_12714.1	chr2	76968448	76968471	+	1	NA	exon (NM_011652, exon 9 of 313)	exon (NM_011652, exon 9 of 313)	14088	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_131031.1	chr16	3744147	3744157	+	1	NA	promoter-TSS (NM_148924)	promoter-TSS (NM_148924)	53	NM_148924	74120	Mm.29081	NM_148924	ENSMUSG00000022529	Zfp263	1200014J04Rik|AI326880|AU020888|NT2|mFPM315	zinc finger protein 263	protein-coding
mm_25926.1	chr3	131189792	131189795	+	1	NA	intron (NM_001276402, intron 5 of 9)	intron (NM_001276402, intron 5 of 9)	77002	NM_001276403	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_86293.1	chr9	122187563	122187570	-	1	NA	intron (NM_001271873, intron 12 of 12)	intron (NM_001271873, intron 12 of 12)	70300	NM_133741	20623	Mm.257989	NM_133741	ENSMUSG00000038145	Snrk	2010012F07Rik|AI448042|AW547029|E030034B15|R74830|mKIAA0096	SNF related kinase	protein-coding
mm_43653.1	chr5	138341942	138341975	+	1	NA	Intergenic	Intergenic	61449	NM_016964	50878	Mm.285609	NM_016964	ENSMUSG00000036928	Stag3	SA-2	stromal antigen 3	protein-coding
mm_105677.1	chr11	107470788	107470798	-	1	NA	promoter-TSS (NM_145823)	promoter-TSS (NM_145823)	-73	NM_145823	71795	Mm.397413	NM_145823	ENSMUSG00000040430	Pitpnc1	1110020B03Rik|5830436L09Rik|AI662802|AI851387|C330017I21Rik|Dnr411|RDGBB|RDGBB1|rdgB-beta	phosphatidylinositol transfer protein, cytoplasmic 1	protein-coding
mm_95685.1	chr11	54270829	54270830	+	1	NA	Intergenic	Intergenic	-3550	NM_010556	16187	Mm.983	NM_010556	ENSMUSG00000018914	Il3	BPA|Csfmu|HCGF|Il-3|MCGF|PSF	interleukin 3	protein-coding
mm_166733.1	chr6	122801748	122801756	-	1	NA	Intergenic	CpG	-18432	NM_021899	60611	Mm.87142	NM_021899	ENSMUSG00000003154	Foxj2	Fhx	forkhead box J2	protein-coding
mm_164897.1	chr18	65698135	65698156	+	1	NA	promoter-TSS (NM_177028)	promoter-TSS (NM_177028)	-123	NM_177028	319888	Mm.183576	NM_177028	ENSMUSG00000046610	Oacyl	5330437I02Rik|Acyl3	O-acyltransferase like	protein-coding
mm_17263.1	chr2	26005323	26005326	-	1	NA	intron (NM_133835, intron 9 of 9)	intron (NM_133835, intron 9 of 9)	16436	NM_133835	98766	Mm.247824	NM_133835	ENSMUSG00000036352	Ubac1	1110033G07Rik|AA407978|GBDR1|Gdbr1|Kpc2|Ubadc1	ubiquitin associated domain containing 1	protein-coding
mm_5155.1	chr1	9944105	9944127	-	1	NA	promoter-TSS (NR_024067)	promoter-TSS (NR_024067)	2	NR_024067	73824	Mm.28311	NR_024067	ENSMUSG00000098234	Snhg6	1110008H02Rik	small nucleolar RNA host gene 6	ncRNA
mm_70235.1	chr8	3311868	3311873	+	1	NA	Intergenic	ID_B1|SINE|B4	-32253	NM_001330056	16337	Mm.268003	NM_010568	ENSMUSG00000005534	Insr	4932439J01Rik|CD220|D630014A15Rik|IR|IR-A|IR-B	insulin receptor	protein-coding
mm_34282.1	chr4	141424675	141424685	+	1	NA	3' UTR (NM_013868, exon 3 of 3)	3' UTR (NM_013868, exon 3 of 3)	3901	NM_013868	29818	Mm.46181	NM_013868	ENSMUSG00000006221	Hspb7	27kDa|Hsp25-2|cvHsp	heat shock protein family, member 7 (cardiovascular)	protein-coding
mm_99967.1	chr11	113684611	113684621	+	1	NA	promoter-TSS (NM_138598)	promoter-TSS (NM_138598)	204	NM_177777	276852	Mm.239566	NM_177777	ENSMUSG00000041623	D11Wsu47e	-	DNA segment, Chr 11, Wayne State University 47, expressed	protein-coding
mm_164370.1	chr16	24193422	24193435	-	1	NA	Intergenic	Intergenic	-199922	NM_178665	210126	Mm.209385	NM_178665	ENSMUSG00000033306	Lpp	9430020K16Rik|AA959454|AU024130|B130055L10Rik|C79715|D630048H16	LIM domain containing preferred translocation partner in lipoma	protein-coding
mm_172714.1	chr8	70493304	70493307	+	1	NA	exon (NM_018827, exon 1 of 9)	exon (NM_018827, exon 1 of 9)	174	NM_018827	12931	Mm.335584	NM_018827	ENSMUSG00000007888	Crlf1	CLF-1|CRLM-3|CRLM3|NR6|NR6.1	cytokine receptor-like factor 1	protein-coding
mm_125621.1	chr15	61988019	61988116	+	1	NA	exon (NM_001177354, exon 2 of 3)	exon (NM_001177354, exon 2 of 3)	2726	NM_001177352	17869	Mm.2444	NM_010849	ENSMUSG00000022346	Myc	AU016757|Myc2|Niard|Nird|bHLHe39	myelocytomatosis oncogene	protein-coding
mm_63007.1	chr7	120876205	120876227	+	1	NA	intron (NM_007908, intron 3 of 17)	L2b|LINE|L2	25027	NM_001267711	13631	Mm.25997	NM_007908	ENSMUSG00000035064	Eef2k	C86191|eEF-2K	eukaryotic elongation factor-2 kinase	protein-coding
mm_40596.1	chr5	64230618	64230619	+	1	NA	intron (NM_001289514, intron 1 of 18)	CpG	261	NM_001289514	57915	Mm.286353	NM_019636	ENSMUSG00000029174	Tbc1d1	1110062G02Rik|AI385682|AW555803|Nob1|Nobq1|Tbc1|mKIAA1108	TBC1 domain family, member 1	protein-coding
mm_83465.1	chr9	45264241	45264251	-	1	NA	intron (NR_136903, intron 4 of 5)	intron (NR_136903, intron 4 of 5)	2461	NR_106054	102466803		NR_106054	ENSMUSG00000098361	Mir7086	Gm27643|mmu-mir-7086	microRNA 7086	ncRNA
mm_167233.1	chr8	13600596	13600608	+	1	NA	intron (NM_009025, intron 4 of 23)	intron (NM_009025, intron 4 of 23)	-38141	NM_001080781	66501	Mm.46136	NM_025601	ENSMUSG00000031452	1700029H14Rik	-	RIKEN cDNA 1700029H14 gene	protein-coding
mm_16360.1	chr2	174450679	174450708	+	1	NA	promoter-TSS (NM_001080971)	promoter-TSS (NM_001080971)	98	NM_001080971	545486	Mm.45285	NM_001080971	ENSMUSG00000016255	Tubb1	2810484G07Rik|M(beta)1	tubulin, beta 1 class VI	protein-coding
mm_17417.1	chr2	27392196	27392236	-	1	NA	intron (NM_009500, intron 1 of 27)	intron (NM_009500, intron 1 of 27)	35392	NR_133905	22325	Mm.179011	NM_009500	ENSMUSG00000009621	Vav2	2810040F13Rik|AI847175|Vav-2	vav 2 oncogene	protein-coding
mm_88459.1	chr10	77561002	77561008	+	1	NA	intron (NM_008404, intron 13 of 15)	intron (NM_008404, intron 13 of 15)	-20762	NM_145925	108705	Mm.28853	NM_145925	ENSMUSG00000009291	Pttg1ip	1810010L20Rik|AI314311|AU018448|C79540	pituitary tumor-transforming 1 interacting protein	protein-coding
mm_12713.1	chr2	76695817	76695835	+	1	NA	3' UTR (NM_031256, exon 8 of 8)	3' UTR (NM_031256, exon 8 of 8)	20511	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_143753.1	chr17	81582238	81582251	-	1	NA	intron (NR_104580, intron 2 of 8)	intron (NR_104580, intron 2 of 8)	156143	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_35094.1	chr4	8648439	8648459	-	1	NA	Intergenic	Intergenic	-41957	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_9929.1	chr1	189899632	189899653	-	1	NA	intron (NM_026796, intron 3 of 11)	intron (NM_026796, intron 3 of 11)	22646	NM_026796	226830	Mm.156895	NM_026796	ENSMUSG00000026603	Smyd2	1110020E07Rik|4930402C15|KMT3C|Zmynd14	SET and MYND domain containing 2	protein-coding
mm_157325.1	chrX	23285533	23285578	-	1	NA	promoter-TSS (NM_001290476)	promoter-TSS (NM_001290476)	4	NM_001290476	67455	Mm.224306	NM_026167	ENSMUSG00000036782	Klhl13	1200009K10Rik|AI451128|Bklhd2|D130072F20Rik	kelch-like 13	protein-coding
mm_54427.1	chr6	33992176	33992209	-	1	NA	Intergenic	Intergenic	-37256	NM_028886	74354	Mm.127952	NM_028886	ENSMUSG00000056215	Lrguk	4921528H16Rik	leucine-rich repeats and guanylate kinase domain containing	protein-coding
mm_152665.1	chr19	14543401	14543405	-	1	NA	intron (NM_001302950, intron 5 of 18)	intron (NM_001302950, intron 5 of 18)	53810	NM_001302951	21888	Mm.103638	NM_011600	ENSMUSG00000024642	Tle4	5730411M05Rik|AA792082|Bce-1|Bce1|ESTM13|ESTM14|Grg4|X83332|X83333|grg-4	transducin-like enhancer of split 4	protein-coding
mm_15021.1	chr2	152685289	152685297	+	1	NA	TTS (NM_001159553)	TTS (NM_001159553)	-1855	NM_025543	66405	Mm.440291	NM_025543	ENSMUSG00000042814	Mcts2	2400002F11Rik|MCT-2	malignant T cell amplified sequence 2	protein-coding
mm_125618.1	chr15	61987609	61987623	+	1	NA	exon (NM_001177354, exon 2 of 3)	exon (NM_001177354, exon 2 of 3)	2275	NM_001177352	17869	Mm.2444	NM_010849	ENSMUSG00000022346	Myc	AU016757|Myc2|Niard|Nird|bHLHe39	myelocytomatosis oncogene	protein-coding
mm_162105.1	chrX	43274896	43274896	-	1	NA	promoter-TSS (NM_011855)	promoter-TSS (NM_011855)	-112	NM_011855	23963	Mm.327698	NM_011855	ENSMUSG00000016150	Tenm1	Odz1|Odz2|TCAP-1|Ten-m1|ten-1	teneurin transmembrane protein 1	protein-coding
mm_74954.1	chr8	26001971	26001987	-	1	NA	intron (NM_008033, intron 6 of 8)	B1_Mur1|SINE|Alu	-7858	NM_029037	74653	Mm.17631	NM_029037	ENSMUSG00000037251	Pomk	4930444A02Rik|Sgk196	protein-O-mannose kinase	protein-coding
mm_134505.1	chr16	19063466	19063504	-	1	NA	Intergenic	Intergenic	186735	NM_010435	15260	Mm.15694	NM_010435	ENSMUSG00000022702	Hira	AA138857|D16Ertd95e|Gm15797|N28177|OTTMUSG00000026264|Tuple1	histone cell cycle regulator	protein-coding
mm_143899.1	chr17	84716689	84716717	-	1	NA	exon (NM_028233, exon 31 of 38)	exon (NM_028233, exon 31 of 38)	33582	NM_026180	67470	Mm.26581	NM_026180	ENSMUSG00000024254	Abcg8	1300003C16Rik|AI114946|sterolin-2	ATP-binding cassette, sub-family G (WHITE), member 8	protein-coding
mm_58610.1	chr7	5061358	5061383	+	1	NA	promoter-TSS (NM_001205231)	promoter-TSS (NM_001205231)	-773	NM_133671	22185	Mm.360389	NM_133671	ENSMUSG00000030435	U2af2	65kDa	U2 small nuclear ribonucleoprotein auxiliary factor (U2AF) 2	protein-coding
mm_10054.1	chr1	193241508	193241533	-	1	NA	intron (NM_008288, intron 2 of 6)	intron (NM_008288, intron 2 of 6)	840	NM_001044751	15483	Mm.28328	NM_008288	ENSMUSG00000016194	Hsd11b1	-	hydroxysteroid 11-beta dehydrogenase 1	protein-coding
mm_87462.1	chr10	51485113	51485122	+	1	NA	intron (NM_001291892, intron 7 of 8)	intron (NM_001291892, intron 7 of 8)	4505	NM_001291892	14727	Mm.439661	NM_008147	ENSMUSG00000062593	Lilr4b	Gp49a|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4B	protein-coding
mm_1549.1	chr1	72863900	72863915	+	1	NA	exon (NM_010518, exon 2 of 4)	exon (NM_010518, exon 2 of 4)	10958	NM_010518	16011	Mm.405761	NM_010518	ENSMUSG00000026185	Igfbp5	AI256729|AW208790|IGFBP-5|IGFBP-5P	insulin-like growth factor binding protein 5	protein-coding
mm_24062.1	chr3	87915538	87915548	+	1	NA	3' UTR (NM_008231, exon 6 of 6)	3' UTR (NM_008231, exon 6 of 6)	-4001	NM_026591	67707	Mm.393802	NM_026591	ENSMUSG00000019710	Mrpl24	2010005E08Rik|2810470K06Rik|6720473G22Rik|AA407670	mitochondrial ribosomal protein L24	protein-coding
mm_2491.1	chr1	105990974	105990999	+	1	NA	exon (NM_001122675, exon 1 of 13)	exon (NM_001122675, exon 1 of 13)	580	NM_001122675	227449	Mm.210188	NM_001122675	ENSMUSG00000038866	Zcchc2	9930114B20Rik|AW212015	zinc finger, CCHC domain containing 2	protein-coding
mm_124542.1	chr14	122464820	122464877	-	1	NA	exon (NM_022987, exon 1 of 2)	exon (NM_022987, exon 1 of 2)	810	NM_022987	65100	Mm.390761	NM_022987	ENSMUSG00000041703	Zic5	1700049L20Rik|Opr	zinc finger protein of the cerebellum 5	protein-coding
mm_137717.1	chr17	29100271	29100281	+	1	NA	3' UTR (NM_007669, exon 3 of 3)	3' UTR (NM_007669, exon 3 of 3)	6507	NM_007669	12575	Mm.195663	NM_007669	ENSMUSG00000023067	Cdkn1a	CAP20|CDKI|CIP1|Cdkn1|P21|SDI1|Waf1|mda6|p21Cip1|p21WAF	cyclin-dependent kinase inhibitor 1A (P21)	protein-coding
mm_26546.1	chr3	146186284	146186290	+	1	NA	intron (NM_001005846, intron 11 of 13)	intron (NM_001005846, intron 11 of 13)	-34674	NM_022983	65086	Mm.155520	NM_022983	ENSMUSG00000036832	Lpar3	Edg7|lpA3	lysophosphatidic acid receptor 3	protein-coding
mm_134502.1	chr16	18876656	18876668	-	1	NA	promoter-TSS (NM_010922)	promoter-TSS (NM_010922)	-25	NM_010922	18100	Mm.20918	NM_010922	ENSMUSG00000022706	Mrpl40	Nlvcf	mitochondrial ribosomal protein L40	protein-coding
mm_154994.1	chrX	38600450	38600460	+	1	NA	promoter-TSS (NM_026902)	promoter-TSS (NM_026902)	-203	NM_026902	68995	Mm.262453	NM_026902	ENSMUSG00000000355	Mcts1	1500019M23Rik|MCT-1	malignant T cell amplified sequence 1	protein-coding
mm_7828.1	chr1	132116627	132116658	-	1	NA	exon (NM_008795, exon 12 of 16)	exon (NM_008795, exon 12 of 16)	23043	NM_008795	18557	Mm.28130	NM_008795	ENSMUSG00000026437	Cdk18	AA682070|Ctk18|Pctk3	cyclin-dependent kinase 18	protein-coding
mm_6505.1	chr1	74304147	74304187	-	1	NA	5' UTR (NM_027154, exon 1 of 12)	5' UTR (NM_027154, exon 1 of 12)	169	NM_027154	69660	Mm.261182	NM_027154	ENSMUSG00000006301	Tmbim1	2310061B02Rik|AA960455|AU024746|C78899|RECS1|Tmbib1|mKIAA4161	transmembrane BAX inhibitor motif containing 1	protein-coding
mm_69619.1	chr7	137313874	137313882	-	1	NA	exon (NM_001113414, exon 1 of 16)	exon (NM_001113414, exon 1 of 16)	567	NM_001113415	13593	Mm.258708	NM_010096	ENSMUSG00000010476	Ebf3	3110018A08Rik|O/E-2|mKIAA4201	early B cell factor 3	protein-coding
mm_12022.1	chr2	58157200	58157227	+	1	NA	intron (NM_139200, intron 1 of 7)	intron (NM_139200, intron 1 of 7)	2909	NM_139200	227929	Mm.273905	NM_139200	ENSMUSG00000026832	Cytip	A130053M09Rik|AI462064|C80816|Cbp|Cybr|Pscdbp	cytohesin 1 interacting protein	protein-coding
mm_140106.1	chr17	78573872	78573882	+	1	NA	intron (NM_028813, intron 4 of 13)	intron (NM_028813, intron 4 of 13)	65814	NM_028813	74199	Mm.292983	NM_028813	ENSMUSG00000024076	Vit	1700052E02Rik|1700110E08Rik|2810429K11Rik	vitrin	protein-coding
mm_809.1	chr1	45795486	45795515	+	1	NA	promoter-TSS (NM_028599)	promoter-TSS (NM_028599)	-1	NM_028599	73674	Mm.270376	NM_028599	ENSMUSG00000025995	Wdr75	1300003A18Rik|2410118I19Rik|C77608	WD repeat domain 75	protein-coding
mm_2741.1	chr1	128570565	128570607	+	1	NA	Intergenic	Intergenic	21713	NM_009911	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding
mm_105937.1	chr11	115187259	115187284	-	1	NA	promoter-TSS (NM_025400)	promoter-TSS (NM_025400)	45	NM_025400	66176	Mm.86823	NM_025400	ENSMUSG00000015542	Nat9	1110028N05Rik	N-acetyltransferase 9 (GCN5-related, putative)	protein-coding
mm_71656.1	chr8	60518239	60518242	+	1	NA	intron (NM_011834, intron 3 of 12)	intron (NM_011834, intron 3 of 12)	12116	NM_011834	23923	Mm.35020	NM_011834	ENSMUSG00000057228	Aadat	AI875679|Aadt|KATII|Kat2|Kyat2|mKat-2	aminoadipate aminotransferase	protein-coding
mm_17613.1	chr2	30928953	30928998	-	1	NA	Intergenic	ID_B1|SINE|B4	-24026	NM_133673	30934	Mm.249164	NM_133673	ENSMUSG00000026848	Tor1b	2610016F05Rik|DQ1|torsinB	torsin family 1, member B	protein-coding
mm_12706.1	chr2	76650265	76650278	+	1	NA	promoter-TSS (NM_001080711)	promoter-TSS (NM_001080711)	-2	NM_001080711	381375	Mm.330312	NM_001080711	ENSMUSG00000075267	Dfnb59	Gm1001|Pjvk	deafness, autosomal recessive 59 (human)	protein-coding
mm_56990.1	chr6	120822714	120822756	-	1	NA	promoter-TSS (NM_007510)	promoter-TSS (NM_007510)	-50	NM_007510	11973	Mm.29045	NM_007510	ENSMUSG00000019210	Atp6v1e1	2410029D23Rik|Atp6e|Atp6e2|Atp6v1e|D6Ertd385e|E2|P31|Vma4	ATPase, H+ transporting, lysosomal V1 subunit E1	protein-coding
mm_157094.1	chrX	9437255	9437267	-	1	NA	3' UTR (NM_007807, exon 13 of 13)	3' UTR (NM_007807, exon 13 of 13)	32063	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_66259.1	chr7	35647442	35647519	-	1	NA	promoter-TSS (NM_019746)	promoter-TSS (NM_019746)	2	NM_019746	56330	Mm.371609	NM_019746	ENSMUSG00000030417	Pdcd5	2200003D22Rik|AA408513|Tfar19	programmed cell death 5	protein-coding
mm_150634.1	chr19	41482957	41483004	+	1	NA	Intergenic	GC_rich|Low_complexity|Low_complexity	-42272	NM_001326287	627352	Mm.395111	NM_001326287		Morf4l1b	EG627352|Gm6747	mortality factor 4 like 1B	protein-coding
mm_150047.1	chr19	29380426	29380449	+	1	NA	exon (NM_021893, exon 4 of 7)	exon (NM_021893, exon 4 of 7)	12999	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_92761.1	chr10	81092541	81092546	-	1	NA	5' UTR (NM_145365, exon 3 of 12)	5' UTR (NM_145365, exon 3 of 12)	6329	NM_145365	208677	Mm.294693	NM_145365	ENSMUSG00000035041	Creb3l3	BC010786|CREB-H|D10Bur1e	cAMP responsive element binding protein 3-like 3	protein-coding
mm_21482.1	chr2	163031428	163031438	-	1	NA	intron (NM_172150, intron 8 of 12)	intron (NM_172150, intron 8 of 12)	13961	NM_172150	245866	Mm.34034	NM_172150	ENSMUSG00000017858	Ift52	BC037708|NGD5	intraflagellar transport 52	protein-coding
mm_12290.1	chr2	69031435	69031453	+	1	NA	intron (NM_172856, intron 4 of 9)	Lx7|LINE|L1	-104356	NM_181547	329416	Mm.90047	NM_181547	ENSMUSG00000034738	Nostrin	Daip2|mDaIP2	nitric oxide synthase trafficker	protein-coding
mm_1450.1	chr1	67230597	67230602	+	1	NA	3' UTR (NM_001080809, exon 38 of 38)	3' UTR (NM_001080809, exon 38 of 38)	107572	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_95415.1	chr11	50025389	50025395	+	1	NA	promoter-TSS (NM_021540)	promoter-TSS (NM_021540)	61	NM_001290750	59044	Mm.359004	NM_021540	ENSMUSG00000020376	Rnf130	2510042A13Rik|G1RZFP|G1rp|GOLIATH|GP	ring finger protein 130	protein-coding
mm_122863.1	chr14	54908911	54908926	-	1	NA	exon (NM_021551, exon 4 of 9)	exon (NM_021551, exon 4 of 9)	4214	NM_021551	59049	Mm.27435	NM_021551	ENSMUSG00000022199	Slc22a17	1700094C23Rik|24p3R|AU041908|AW555662|BOIT|Boct	solute carrier family 22 (organic cation transporter), member 17	protein-coding
mm_129764.1	chr15	82620932	82620947	-	1	NA	promoter-TSS (NM_145474)	promoter-TSS (NM_145474)	-32	NM_145474	223706	Mm.436843	NM_145474	ENSMUSG00000094559	Cyp2d34	-	cytochrome P450, family 2, subfamily d, polypeptide 34	protein-coding
mm_81393.1	chr9	108988308	108988364	+	1	NA	Intergenic	Intergenic	2173	NM_145077	171530	Mm.388865	NM_145077	ENSMUSG00000049699	Ucn2	Ucn II|Ucn-2|ucn-II	urocortin 2	protein-coding
mm_121254.1	chr14	103057626	103057635	+	1	NA	Intergenic	B4A|SINE|B4	10618	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_16038.1	chr2	167690274	167690296	+	1	NA	promoter-TSS (NR_015500)	promoter-TSS (NR_015500)	-474	NR_110334	329562	Mm.123101	NM_177851	ENSMUSG00000006462	A530013C23Rik	-	RIKEN cDNA A530013C23 gene	ncRNA
mm_108725.1	chr12	87200525	87200544	+	1	NA	promoter-TSS (NM_001290288)	promoter-TSS (NM_001290288)	-9	NM_001290288	238333	Mm.302304	NM_001290288	ENSMUSG00000090812	Samd15	Gm263	sterile alpha motif domain containing 15	protein-coding
mm_122246.1	chr14	33609916	33609917	-	1	NA	intron (NM_008978, intron 4 of 11)	Lx8|LINE|L1	20646	NM_008978	19256	Mm.8019	NM_008978	ENSMUSG00000021940	Ptpn20	typ	protein tyrosine phosphatase, non-receptor type 20	protein-coding
mm_141643.1	chr17	33394569	33394644	-	1	NA	promoter-TSS (NM_009542)	promoter-TSS (NM_009542)	31	NM_009542	22643	Mm.4417	NM_009542	ENSMUSG00000055240	Zfp101	AI316498|AI325003	zinc finger protein 101	protein-coding
mm_2176.1	chr1	88407003	88407101	+	1	NA	promoter-TSS (NM_029269)	promoter-TSS (NM_029269)	42	NM_029269	75396	Mm.173058	NM_029269	ENSMUSG00000026295	Spp2	0610038O04Rik|pp-24|spp24	secreted phosphoprotein 2	protein-coding
mm_119718.1	chr14	53881587	53881605	+	1	NA	Intergenic	Intergenic	372333	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_156948.1	chrX	169983951	169983992	+	1	NA	exon (NM_001290504, exon 6 of 10)	exon (NM_001290504, exon 6 of 10)	-5054	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_132178.1	chr16	32400658	32400668	+	1	NA	5' UTR (NM_001160402, exon 1 of 5)	5' UTR (NM_001160402, exon 1 of 5)	157	NM_001160402	277203	Mm.484240	NM_001160402	ENSMUSG00000079625	Tm4sf19	EG277203	transmembrane 4 L six family member 19	protein-coding
mm_81454.1	chr9	109832999	109833058	+	1	NA	intron (NM_018757, intron 1 of 6)	intron (NM_018757, intron 1 of 6)	234	NM_018757	54369	Mm.12951	NM_018757	ENSMUSG00000032478	Nme6	nm23-M6	NME/NM23 nucleoside diphosphate kinase 6	protein-coding
mm_118252.1	chr13	112289149	112289152	-	1	NA	intron (NM_001168405, intron 1 of 5)	intron (NM_001168405, intron 1 of 5)	632	NM_001168404	77318	Mm.159895	NM_029898	ENSMUSG00000049985	Ankrd55	C030011J08Rik	ankyrin repeat domain 55	protein-coding
mm_46591.1	chr5	107725443	107725458	-	1	NA	intron (NM_001267621, intron 1 of 6)	CpG	355	NM_001267621	14581	Mm.2078	NM_010278	ENSMUSG00000029275	Gfi1	AW495828|Gfi-1|Pal-1|Pal1	growth factor independent 1	protein-coding
mm_128327.1	chr15	38078843	38078860	-	1	NA	promoter-TSS (NM_001081359)	promoter-TSS (NM_001081359)	3	NM_001112721	70790	Mm.476840	NM_027553	ENSMUSG00000037487	Ubr5	Edd|Edd1	ubiquitin protein ligase E3 component n-recognin 5	protein-coding
mm_171851.1	chr5	16941118	16941120	+	1	NA	Intergenic	L1Md_T|LINE|L1	387218	NM_001289461	15234	Mm.267078	NM_010427	ENSMUSG00000028864	Hgf	C230052L06Rik|HGF/SF|NK1|NK2|SF|SF/HGF	hepatocyte growth factor	protein-coding
mm_5232.1	chr1	14310199	14310218	-	1	NA	promoter-TSS (NM_001252192)	promoter-TSS (NM_001252192)	-9	NM_010164	14048	Mm.250185	NM_010164	ENSMUSG00000025932	Eya1	bor	EYA transcriptional coactivator and phosphatase 1	protein-coding
mm_97061.1	chr11	72713726	72713736	+	1	NA	intron (NM_009671, intron 2 of 24)	B1F|SINE|Alu	23729	NM_009671	11736	Mm.10313	NM_009671	ENSMUSG00000020790	Ankfy1	Ankhzn|ZFYVE14|mKIAA1255	ankyrin repeat and FYVE domain containing 1	protein-coding
mm_82268.1	chr9	7221542	7221553	-	1	NA	Intergenic	Intergenic	36981	NM_029775	76863	Mm.27293	NM_029775	ENSMUSG00000032002	Dcun1d5	3110001A18Rik|4833420K19Rik|AW060460|D430047L21Rik	DCN1, defective in cullin neddylation 1, domain containing 5 (S. cerevisiae)	protein-coding
mm_162864.1	chr10	93309083	93309102	-	1	NA	intron (NM_013508, intron 1 of 4)	intron (NM_013508, intron 1 of 4)	2067	NM_001322268	13713	Mm.4454	NM_013508	ENSMUSG00000008398	Elk3	D430049E23Rik|Erp|Etrp|Net|Sap-2	ELK3, member of ETS oncogene family	protein-coding
mm_98453.1	chr11	94945804	94945832	+	1	NA	exon (NM_007742, exon 32 of 51)	exon (NM_007742, exon 32 of 51)	9594	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_163344.1	chr12	16622371	16622373	+	1	NA	Intergenic	ORR1A0|LTR|ERVL-MaLR	-31098	NM_008747	18217	Mm.281715	NM_008747	ENSMUSG00000020591	Ntsr2	NT2R|NTRL	neurotensin receptor 2	protein-coding
mm_81198.1	chr9	107554796	107554809	+	1	NA	exon (NM_019713, exon 1 of 5)	exon (NM_019713, exon 1 of 5)	219	NM_019713	56289	Mm.12091	NM_019713	ENSMUSG00000010067	Rassf1	123F2|AA536941|AU044980|NORE2A|RDA32|REH3P21|Rassf1A|Rassf1B|Rassf1C	Ras association (RalGDS/AF-6) domain family member 1	protein-coding
mm_12781.1	chr2	79330595	79330606	+	1	NA	3' UTR (NM_010576, exon 28 of 28)	3' UTR (NM_010576, exon 28 of 28)	75174	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D|Itga4B	integrin alpha 4	protein-coding
mm_47866.1	chr5	134639029	134639044	-	1	NA	intron (NM_001312867, intron 1 of 5)	CpG	373	NM_001312867	22384	Mm.27955	NM_033561	ENSMUSG00000040731	Eif4h	AU018978|D5Ertd355e|E430026L18Rik|Ef4h|Wbscr1|Wscr1|eIF-4H	eukaryotic translation initiation factor 4H	protein-coding
mm_127350.1	chr15	100619671	100619688	+	1	NA	3' UTR (NM_011873, exon 4 of 4)	3' UTR (NM_011873, exon 4 of 4)	4017	NM_011873	23994	Mm.486175	NM_011873	ENSMUSG00000000346	Dazap2	AI314727|Brbp|Gcap28|Prtb|gt6-12|mKIAA0058	DAZ associated protein 2	protein-coding
mm_132313.1	chr16	33726396	33726419	+	1	NA	exon (NM_175256, exon 4 of 15)	exon (NM_175256, exon 4 of 15)	41941	NM_175256	77446	Mm.245741	NM_172934	ENSMUSG00000075254	Heg1	4632417D23Rik|5530401I02Rik|9530025L16Rik|BC038614|Gm629|OTTMUSG00000027315	heart development protein with EGF-like domains 1	protein-coding
mm_78336.1	chr9	25263178	25263190	+	1	NA	intron (NM_001205367, intron 1 of 12)	L2|LINE|L2	10745	NM_001205367	235072	Mm.270259	NM_009859	ENSMUSG00000001833	Sept7	Cdc10|E430034N22	septin 7	protein-coding
mm_61982.1	chr7	90965787	90965799	+	1	NA	Intergenic	Intergenic	-124993	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_52335.1	chr6	110645573	110645588	+	1	NA	promoter-TSS (NM_177328)	promoter-TSS (NM_177328)	-18	NM_177328	108073	Mm.240881	NM_177328	ENSMUSG00000056755	Grm7	6330570A01Rik|BB176677|C030018L03|E130018M02Rik|Gpr1g|Gprc1g|SMN2|Tg(SMN2)89Ahmb|mGluR7	glutamate receptor, metabotropic 7	protein-coding
mm_82321.1	chr9	8004560	8004577	-	1	NA	promoter-TSS (NM_001171147)	promoter-TSS (NM_001171147)	28	NM_001171147	22601	Mm.221992	NM_009534	ENSMUSG00000053110	Yap1	AI325207|Yap|Yap65|Yki|Yorkie	yes-associated protein 1	protein-coding
mm_74305.1	chr8	126556688	126556691	+	1	NA	Intergenic	Intergenic	36747	NM_001164598	270110	Mm.334918	NM_001164598	ENSMUSG00000051495	Irf2bp2	E130305N23Rik|IRF-2BP2	interferon regulatory factor 2 binding protein 2	protein-coding
mm_75444.1	chr8	47533440	47533477	-	1	NA	promoter-TSS (NM_203507)	promoter-TSS (NM_203507)	12	NM_177240	320714	Mm.39461	NM_177240	ENSMUSG00000038102	Trappc11	AW558465|D030016E14Rik|R75422	trafficking protein particle complex 11	protein-coding
mm_110759.1	chr12	70111949	70111959	-	1	NA	promoter-TSS (NM_001286080)	promoter-TSS (NM_001286080)	81	NM_001286080	18080	Mm.244047	NM_008697	ENSMUSG00000021068	Nin	3110068G20Rik|AI385615|AU024711|mKIAA1565	ninein	protein-coding
mm_37472.1	chr4	123564673	123564701	-	1	NA	intron (NM_001199136, intron 1 of 97)	intron (NM_001199136, intron 1 of 97)	-51733	NR_105824	102465214		NR_105824	ENSMUSG00000099005	Mir6398	Gm27657|mmu-mir-6398	microRNA 6398	ncRNA
mm_147822.1	chr18	61911748	61911758	-	1	NA	promoter-TSS (NM_001164491)	promoter-TSS (NM_001164491)	71	NM_198649	319713	Mm.329478	NM_198649	ENSMUSG00000032735	Ablim3	AW990719|D930036B08Rik	actin binding LIM protein family, member 3	protein-coding
mm_114175.1	chr13	55600056	55600135	+	1	NA	5' UTR (NM_146045, exon 1 of 6)	5' UTR (NM_146045, exon 1 of 6)	199	NM_001311137	218271	Mm.139825	NM_146045	ENSMUSG00000021504	B4galt7	-	xylosylprotein beta1,4-galactosyltransferase, polypeptide 7 (galactosyltransferase I)	protein-coding
mm_111219.1	chr12	84450945	84451018	-	1	NA	promoter-TSS (NM_134042)	promoter-TSS (NM_134042)	43	NM_134042	104776	Mm.247510	NM_134042	ENSMUSG00000021238	Aldh6a1	1110038I05Rik|Mmsdh	aldehyde dehydrogenase family 6, subfamily A1	protein-coding
mm_30594.1	chr4	6365697	6365720	+	1	NA	promoter-TSS (NM_016807)	promoter-TSS (NM_016807)	28	NM_001098227	53378	Mm.247473	NM_016807	ENSMUSG00000028249	Sdcbp	MDA-9|Sycl|syntenin-1	syndecan binding protein	protein-coding
mm_125492.1	chr15	54952940	54952975	+	1	NA	Intergenic	Intergenic	-32811	NM_001285994	18606	Mm.250256	NM_015744	ENSMUSG00000022425	Enpp2	ATX|E-NPP 2|Npps2|PD-Ialpha|Pdnp2|lysoPLD	ectonucleotide pyrophosphatase/phosphodiesterase 2	protein-coding
mm_7656.1	chr1	128359598	128359609	-	1	NA	5' UTR (NM_008567, exon 1 of 17)	5' UTR (NM_008567, exon 1 of 17)	102	NM_008567	17219	Mm.4933	NM_008567	ENSMUSG00000026355	Mcm6	ASP-l1|D1Wsu22e|Mcmd6	minichromosome maintenance complex component 6	protein-coding
mm_144806.1	chr18	36281447	36281459	+	1	NA	5' UTR (NM_008989, exon 1 of 2)	5' UTR (NM_008989, exon 1 of 2)	291	NM_008989	19290	Mm.231802	NM_008989	ENSMUSG00000043991	Pura	CAGER-1|Pur-alpha|ssCRE-BP	purine rich element binding protein A	protein-coding
mm_101043.1	chr11	8624174	8624219	-	1	NA	intron (NM_001083587, intron 1 of 30)	intron (NM_001083587, intron 1 of 30)	40339	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_116665.1	chr13	49204067	49204109	-	1	NA	intron (NM_026738, intron 3 of 5)	intron (NM_026738, intron 3 of 5)	11938	NM_026738	68480	Mm.3336	NM_026738	ENSMUSG00000037960	Card19	1110007C09Rik|AI851695|Bincard	caspase recruitment domain family, member 19	protein-coding
mm_109903.1	chr12	7950148	7950169	-	1	NA	Intergenic	Intergenic	-27519	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_55222.1	chr6	52230948	52230950	-	1	NA	promoter-TSS (NR_029912)	promoter-TSS (NR_029912)	-784	NR_029912	723820		NR_029912	ENSMUSG00000065443	Mir196b	Mirn196b|mir-196b	microRNA 196b	ncRNA
mm_131906.1	chr16	23269335	23269356	+	1	NA	intron (NM_001252505, intron 2 of 7)	RMER13A2|LTR|ERVK	-21125	NM_001252506	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_127461.1	chr15	101272211	101272234	+	1	NA	exon (NM_010444, exon 4 of 7)	exon (NM_010444, exon 4 of 7)	5376	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_103877.1	chr11	83529100	83529117	-	1	NA	intron (NM_013653, intron 2 of 2)	intron (NM_013653, intron 2 of 2)	1410	NM_013653	20304	Mm.284248	NM_013653	ENSMUSG00000035042	Ccl5	MuRantes|RANTES|SISd|Scya5|TCP228	chemokine (C-C motif) ligand 5	protein-coding
mm_70093.1	chr7	142657473	142657486	-	1	NA	promoter-TSS (NM_001122737)	promoter-TSS (NM_001122737)	17	NM_001122737	16002	Mm.3862	NM_010514	ENSMUSG00000048583	Igf2	AL033362|Igf-2|Igf-II|M6pr|Mpr|Peg2	insulin-like growth factor 2	protein-coding
mm_153422.1	chr19	40665942	40665950	-	1	NA	intron (NM_009848, intron 1 of 9)	intron (NM_009848, intron 1 of 9)	6176	NM_009848	12495	Mm.2824	NM_009848	ENSMUSG00000048120	Entpd1	2610206B08Rik|AA408691|Cd39|NTPDase-1	ectonucleoside triphosphate diphosphohydrolase 1	protein-coding
mm_134876.1	chr16	28929827	28929847	-	1	NA	promoter-TSS (NM_177718)	promoter-TSS (NM_177718)	-139	NM_177718	239796	Mm.155887	NM_177718	ENSMUSG00000051065	Mb21d2	1600021P15Rik|A430031N04|C87006	Mab-21 domain containing 2	protein-coding
mm_169629.1	chr15	4419812	4419812	-	1	NA	intron (NM_177355, intron 1 of 2)	L1Md_T|LINE|L1	44321	NM_177355	239318	Mm.308996	NM_177355	ENSMUSG00000049148	Plcxd3	B130016O10Rik	phosphatidylinositol-specific phospholipase C, X domain containing 3	protein-coding
mm_159691.1	chr5	21865579	21865579	-	1	NA	promoter-TSS (NM_030727)	promoter-TSS (NM_030727)	25	NM_030727	80979	Mm.160370	NM_030727	ENSMUSG00000029015	Slc26a5	Pres|prestin	solute carrier family 26, member 5	protein-coding
mm_138073.1	chr17	33949413	33949424	+	1	NA	TTS (NM_019420)	TTS (NM_019420)	2070	NM_019420	54218	Mm.11132	NM_019420	ENSMUSG00000067370	B3galt4	Gal-T2|Galt2	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 4	protein-coding
mm_155451.1	chrX	73495429	73495452	+	1	NA	3' UTR (NM_007542, exon 8 of 8)	3' UTR (NM_007542, exon 8 of 8)	-7646	NM_001310537	320707	Mm.210095	NM_177236	ENSMUSG00000031376	Atp2b3	6430519O13Rik|Pmca3	ATPase, Ca++ transporting, plasma membrane 3	protein-coding
mm_70741.1	chr8	19141483	19141496	+	1	NA	exon (NM_001034905, exon 2 of 2)	exon (NM_001034905, exon 2 of 2)	730	NM_001286493	546038	Mm.99206	NM_001034905	ENSMUSG00000059463	Spag11b	EG546038|Ep2c/h|Spag11c/h	sperm associated antigen 11B	protein-coding
mm_57147.1	chr6	122699065	122699065	-	1	NA	Intergenic	Intergenic	-8424	NM_001289831	71950	Mm.6047	NM_028016	ENSMUSG00000012396	Nanog	2410002E02Rik|ENK|ecat4	Nanog homeobox	protein-coding
mm_11869.1	chr2	48974418	48974422	+	1	NA	intron (NM_029924, intron 1 of 16)	intron (NM_029924, intron 1 of 16)	24912	NM_029924	109241	Mm.440436	NM_029924	ENSMUSG00000036792	Mbd5	9430004D19Rik|AA536666|AI426407|C030040A15Rik|Gm1630|OTTMUSG00000012483	methyl-CpG binding domain protein 5	protein-coding
mm_34666.1	chr4	150910042	150910091	+	1	NA	promoter-TSS (NM_020569)	promoter-TSS (NM_020569)	-145	NM_020569	57320	Mm.277349	NM_020569	ENSMUSG00000028964	Park7	DJ-1|Dj1	Parkinson disease (autosomal recessive, early onset) 7	protein-coding
mm_146993.1	chr18	34347088	34347108	-	1	NA	3' UTR (NM_007874, exon 5 of 5)	3' UTR (NM_007874, exon 5 of 5)	15953	NM_025527	66384	Mm.29452	NM_025527	ENSMUSG00000014504	Srp19	2310020D23Rik	signal recognition particle 19	protein-coding
mm_30829.1	chr4	21879663	21879702	+	1	NA	promoter-TSS (NM_172687)	promoter-TSS (NM_172687)	7	NM_172687	230027	Mm.5662	NM_172687	ENSMUSG00000028247	Coq3	4732433J24|C77934	coenzyme Q3 methyltransferase	protein-coding
mm_24721.1	chr3	95235257	95235301	+	1	NA	3' UTR (NM_172395, exon 5 of 5)	3' UTR (NM_172395, exon 5 of 5)	5830	NM_001024841	229588	Mm.387177	NM_001024841	ENSMUSG00000068860	Gm128	Ment|pmis1	predicted gene 128	protein-coding
mm_93168.1	chr10	93306111	93306112	-	1	NA	intron (NM_013508, intron 1 of 4)	intron (NM_013508, intron 1 of 4)	5048	NM_001322268	13713	Mm.4454	NM_013508	ENSMUSG00000008398	Elk3	D430049E23Rik|Erp|Etrp|Net|Sap-2	ELK3, member of ETS oncogene family	protein-coding
mm_122350.1	chr14	38804047	38804063	-	1	NA	intron (NM_001190187, intron 2 of 9)	Lx7|LINE|L1	-94247	NR_045713	75170	Mm.372967	NR_045713	ENSMUSG00000093528	Nrg3os	4930529F24Rik	neuregulin 3, opposite strand	ncRNA
mm_69019.1	chr7	126776775	126776855	-	1	NA	promoter-TSS (NM_026875)	promoter-TSS (NM_026875)	-160	NM_026875	66090	Mm.27114	NM_025347	ENSMUSG00000042675	Ypel3	0610043B10Rik|1190001G19Rik|Suap	yippee-like 3 (Drosophila)	protein-coding
mm_12009.1	chr2	57330162	57330201	+	1	NA	intron (NM_001145820, intron 6 of 16)	PB1D7|SINE|Alu	91799	NM_010274	14571	Mm.3711	NM_010274	ENSMUSG00000026827	Gpd2	AA408484|AI448216|AU021455|AW494132|GPDH|Gdm1|Gpd-m|Gpdh-m|TISP38	glycerol phosphate dehydrogenase 2, mitochondrial	protein-coding
mm_168116.1	chr10	15634735	15634744	+	1	NA	Intergenic	Lx|LINE|L1	-157038	NR_131087	77538	Mm.128235	NR_131087		C330004P14Rik	-	RIKEN cDNA C330004P14 gene	ncRNA
mm_114312.1	chr13	59823287	59823328	+	1	NA	promoter-TSS (NM_153538)	promoter-TSS (NM_153538)	-160	NM_153538	214290	Mm.233082	NM_153538	ENSMUSG00000035248	Zcchc6	6030448M23Rik|AA420405	zinc finger, CCHC domain containing 6	protein-coding
mm_124716.1	chr15	6579818	6579839	+	1	NA	promoter-TSS (NM_001278269)	promoter-TSS (NM_001278269)	-19	NM_001278269	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_28232.1	chr3	88455303	88455311	-	1	NA	intron (NM_001163489, intron 1 of 14)	intron (NM_001163489, intron 1 of 14)	454	NM_013658	20351	Mm.439752	NM_013658	ENSMUSG00000028064	Sema4a	AI132332|SemB|Semab	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A	protein-coding
mm_111486.1	chr12	98877758	98877761	-	1	NA	intron (NM_001081191, intron 4 of 43)	Lx8|LINE|L1	23725	NM_001081191	319670	Mm.390484	NM_001081191	ENSMUSG00000051166	Eml5	BC027154|C130068M19Rik	echinoderm microtubule associated protein like 5	protein-coding
mm_27286.1	chr3	41522591	41522593	-	1	NA	intron (NR_130791, intron 2 of 5)	intron (NR_130791, intron 2 of 5)	5882	NR_130791	78648	Mm.366093	NR_130791		2400006E01Rik	lncRNA-JADE	RIKEN cDNA 2400006E01 gene	ncRNA
mm_11495.1	chr2	32493632	32493647	+	1	NA	Intergenic	Intergenic	-41720	NM_153560	98952	Mm.4065	NM_153560	ENSMUSG00000039157	Fam102a	AI426465|C230093N12Rik|Eeig1	family with sequence similarity 102, member A	protein-coding
mm_146826.1	chr18	21651814	21651843	-	1	NA	exon (NM_001081403, exon 1 of 8)	exon (NM_001081403, exon 1 of 8)	263	NM_001271580	74644	Mm.329311	NM_001271580		4930426D05Rik	-	RIKEN cDNA 4930426D05 gene	protein-coding
mm_87498.1	chr10	51528014	51528071	+	1	NA	Intergenic	MuRRS4-int|LTR|ERV1	37144	NM_013532	14728	Mm.34408	NM_013532	ENSMUSG00000062593	Lilrb4a	CD85K|Gp49b|HM18|ILT3|LIR-5|Lilrb4|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4A	protein-coding
mm_89790.1	chr10	102178428	102178429	+	1	NA	intron (NM_001162369, intron 1 of 5)	intron (NM_001162369, intron 1 of 5)	19349	NM_001162369	67569	Mm.25252	NM_026243	ENSMUSG00000019888	Mgat4c	9130411I17Rik|GntIVh	MGAT4 family, member C	protein-coding
mm_95116.1	chr11	34078111	34078119	+	1	NA	intron (NM_010696, intron 10 of 20)	intron (NM_010696, intron 10 of 20)	30914	NM_010696	16822	Mm.265350	NM_010696	ENSMUSG00000002699	Lcp2	AI323664|BB161688|SLP-76|SLP76|m1Khoe|twm	lymphocyte cytosolic protein 2	protein-coding
mm_169432.1	chr14	53795384	53795402	+	1	NA	Intergenic	Intergenic	458536	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_133215.1	chr16	75859403	75859418	+	1	NA	3' UTR (NM_023380, exon 8 of 8)	3' UTR (NM_023380, exon 8 of 8)	49856	NM_023380	67742	Mm.131406	NM_023380	ENSMUSG00000022876	Samsn1	4930571B16Rik|930571B16Rik|Hacs1|SLy2	SAM domain, SH3 domain and nuclear localization signals, 1	protein-coding
mm_83830.1	chr9	54068562	54068569	-	1	NA	promoter-TSS (NM_001033535)	promoter-TSS (NM_001033535)	-154	NM_001033535	244882	Mm.325589	NM_001033535	ENSMUSG00000074345	Tnfaip8l3	9930029P06Rik|Gm517	tumor necrosis factor, alpha-induced protein 8-like 3	protein-coding
mm_30765.1	chr4	15988986	15989009	+	1	NA	intron (NM_013752, intron 13 of 15)	intron (NM_013752, intron 13 of 15)	24880	NM_145950	209212	Mm.46455	NM_145950	ENSMUSG00000041153	Osgin2	BC010311|C230027H09Rik	oxidative stress induced growth inhibitor family member 2	protein-coding
mm_125696.1	chr15	66891458	66891468	+	1	NA	promoter-TSS (NM_018865)	promoter-TSS (NM_018865)	70	NM_018865	22402	Mm.10222	NM_018865	ENSMUSG00000005124	Wisp1	AW146261|CCN4|Elm1	WNT1 inducible signaling pathway protein 1	protein-coding
mm_11832.1	chr2	45106276	45106283	+	1	NA	intron (NM_001289521, intron 1 of 8)	intron (NM_001289521, intron 1 of 8)	3998	NM_001289521	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_17132.1	chr2	24935120	24935137	-	1	NA	exon (NM_001162485, exon 1 of 8)	exon (NM_001162485, exon 1 of 8)	153	NR_027876	215705	Mm.45275	NM_178408	ENSMUSG00000026972	Arrdc1	AI957342|BC004091	arrestin domain containing 1	protein-coding
mm_154213.1	chr19	59296902	59296910	-	1	NA	TTS (NM_172523)	TTS (NM_172523)	36028	NM_172523	214084	Mm.268797	NM_172523	ENSMUSG00000025094	Slc18a2	1110037L13Rik|9330105E13|Vmat2	solute carrier family 18 (vesicular monoamine), member 2	protein-coding
mm_145340.1	chr18	56469216	56469238	+	1	NA	intron (NM_026240, intron 1 of 13)	intron (NM_026240, intron 1 of 13)	37095	NM_026240	107022	Mm.24356	NM_026240	ENSMUSG00000001700	Gramd3	9030613F08Rik|9130427A09Rik|AW061306|NS3TP2	GRAM domain containing 3	protein-coding
mm_86633.1	chr10	14046120	14046123	+	1	NA	intron (NM_010437, intron 1 of 8)	intron (NM_010437, intron 1 of 8)	79742	NM_010437	15273	Mm.42157	NM_010437	ENSMUSG00000015501	Hivep2	Gm20114|MIBP1|Schnurri-2|Shn-2	human immunodeficiency virus type I enhancer binding protein 2	protein-coding
mm_153121.1	chr19	33447796	33447807	-	1	NA	Intergenic	Intergenic	-55506	NM_001146342	67795	Mm.204591	NM_001146342	ENSMUSG00000071573	Rnls	6530404N21Rik|AI452315|AW060440|C10orf59	renalase, FAD-dependent amine oxidase	protein-coding
mm_33720.1	chr4	134065623	134065674	+	1	NA	Intergenic	Intergenic	-2804	NM_001162970	230806	Mm.240080	NM_001162970	ENSMUSG00000012123	Aim1l	-	absent in melanoma 1-like	protein-coding
mm_112496.1	chr13	6888753	6888760	+	1	NA	Intergenic	Intergenic	-239985	NM_001291071	56421	Mm.273874	NM_019703	ENSMUSG00000021196	Pfkp	1200015H23Rik|9330125N24Rik|ATP-PFK|PFK-C|PFK-P	phosphofructokinase, platelet	protein-coding
mm_34172.1	chr4	140131867	140131881	+	1	NA	intron (NM_198610, intron 2 of 9)	intron (NM_198610, intron 2 of 9)	114937	NM_198610	230868	Mm.298731	NM_198610	ENSMUSG00000040972	Igsf21	BC055811|Gm141	immunoglobulin superfamily, member 21	protein-coding
mm_91883.1	chr10	59858789	59858791	-	1	NA	intron (NM_001291443, intron 11 of 12)	intron (NM_001291443, intron 11 of 12)	-20801	NM_019965	56709	Mm.103610	NM_019965	ENSMUSG00000020109	Dnajb12	Dj10|mDj10	DnaJ heat shock protein family (Hsp40) member B12	protein-coding
mm_136410.1	chr16	93794883	93794918	-	1	NA	intron (NM_027293, intron 27 of 36)	intron (NM_027293, intron 27 of 36)	-37221	NM_001045529	338467	Mm.287329	NM_001045529	ENSMUSG00000039456	Morc3	1110051N18Rik|AI452146|BF318192|D16Jhu32e|NXP2|Zcwcc3	microrchidia 3	protein-coding
mm_42838.1	chr5	122103169	122103187	+	1	NA	intron (NM_010861, intron 3 of 6)	intron (NM_010861, intron 3 of 6)	2198	NM_010861	17906	Mm.1529	NM_010861	ENSMUSG00000013936	Myl2	MLC-2|MLC-2s/v|MLC-2v|Mlc2v|Mylpc	myosin, light polypeptide 2, regulatory, cardiac, slow	protein-coding
mm_146262.1	chr18	77825380	77825401	+	1	NA	intron (NM_013831, intron 1 of 14)	intron (NM_013831, intron 1 of 14)	30840	NM_013831	19201	Mm.57174	NM_013831	ENSMUSG00000025429	Pstpip2	MAYP|cmo	proline-serine-threonine phosphatase-interacting protein 2	protein-coding
mm_85510.1	chr9	106247861	106247874	-	1	NA	promoter-TSS (NM_020559)	promoter-TSS (NM_020559)	87	NM_020559	11655	Mm.290578	NM_020559	ENSMUSG00000032786	Alas1	ALAS|ALAS-N|Alas-1|Alas-h	aminolevulinic acid synthase 1	protein-coding
mm_96438.1	chr11	67308570	67308596	+	1	NA	TTS (NM_177369)	TTS (NM_177369)	-18520	NM_001081250	544791	Mm.461064	NM_001081250	ENSMUSG00000060180	Myh13	MyHC-eo	myosin, heavy polypeptide 13, skeletal muscle	protein-coding
mm_165487.1	chr2	164373353	164373391	-	1	NA	Intergenic	Intergenic	-16865	NM_011414	20568	Mm.371583	NM_011414	ENSMUSG00000017002	Slpi	-	secretory leukocyte peptidase inhibitor	protein-coding
mm_63567.1	chr7	128116800	128116824	+	1	NA	exon (NM_008401, exon 29 of 30)	exon (NM_008401, exon 29 of 30)	-12756	NM_021334	16411	Mm.22378	NM_021334	ENSMUSG00000030789	Itgax	AI449405|Cd11c|Cr4|N418	integrin alpha X	protein-coding
mm_145401.1	chr18	57354837	57354845	+	1	NA	5' UTR (NM_028447, exon 1 of 9)	5' UTR (NM_028447, exon 1 of 9)	108	NM_028447	73137	Mm.29889	NM_028447	ENSMUSG00000024594	Prrc1	1190002C06Rik|2310058D16Rik|3110038B19Rik|9430085A19Rik	proline-rich coiled-coil 1	protein-coding
mm_6770.1	chr1	84131202	84131217	-	1	NA	intron (NM_001003948, intron 2 of 2)	intron (NM_001003948, intron 2 of 2)	87752	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_75239.1	chr8	39631308	39631318	-	1	NA	exon (NM_031195, exon 3 of 9)	exon (NM_031195, exon 3 of 9)	11365	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_81952.1	chr9	120555586	120555588	+	1	NA	intron (NM_178676, intron 4 of 10)	intron (NM_178676, intron 4 of 10)	15769	NM_178676	215446	Mm.76648	NM_178676	ENSMUSG00000041608	Entpd3	Cd39l3|HB6|NTPDase-3	ectonucleoside triphosphate diphosphohydrolase 3	protein-coding
mm_163732.1	chr13	119649407	119649445	+	1	NA	intron (NM_020279, intron 2 of 2)	intron (NM_020279, intron 2 of 2)	25607	NM_020279	56838	Mm.143745	NM_020279	ENSMUSG00000074715	Ccl28	CCK1|MEC|Scya28	chemokine (C-C motif) ligand 28	protein-coding
mm_18192.1	chr2	45113901	45113927	-	1	NA	promoter-TSS (NM_015753)	promoter-TSS (NM_015753)	-635	NM_015753	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_145291.1	chr18	53245737	53245786	+	1	NA	promoter-TSS (NM_029394)	promoter-TSS (NM_029394)	99	NM_029394	69226	Mm.32414	NM_029394	ENSMUSG00000024535	Snx24	2810011K15Rik|5730433I16Rik|AI451341	sorting nexing 24	protein-coding
mm_167239.1	chr8	19157847	19157853	+	1	NA	promoter-TSS (NM_153115)	promoter-TSS (NM_153115)	-37	NM_153115	78128	Mm.229357	NM_153115	ENSMUSG00000079842	Spag11a	9230111C08Rik|Bin1b|EP2Q|EP2e|Spag11	sperm associated antigen 11A	protein-coding
mm_17427.1	chr2	27464567	27464581	-	1	NA	intron (NM_001113573, intron 1 of 11)	intron (NM_001113573, intron 1 of 11)	10824	NM_023336	67382	Mm.28721	NM_023336	ENSMUSG00000026918	Brd3	2410084F24Rik|AW060456|Fsrg2|ORFX|RINGL3	bromodomain containing 3	protein-coding
mm_50654.1	chr6	51470434	51470478	+	1	NA	promoter-TSS (NM_007624)	promoter-TSS (NM_007624)	-160	NM_007624	12417	Mm.280968	NM_007624	ENSMUSG00000029836	Cbx3	HP1g|M32	chromobox 3	protein-coding
mm_35314.1	chr4	25615412	25615413	-	1	NA	3' UTR (NM_010243, exon 3 of 3)	3' UTR (NM_010243, exon 3 of 3)	184591	NM_010243	14348	Mm.39101	NM_010243	ENSMUSG00000055373	Fut9	AI746471|AU067636|mFUT9|mFuc-TIX	fucosyltransferase 9	protein-coding
mm_147182.1	chr18	36772372	36772385	-	1	NA	exon (NM_008214, exon 5 of 13)	exon (NM_008214, exon 5 of 13)	-6164	NM_173383	213236	Mm.234464	NM_173383	ENSMUSG00000044595	Dnd1	BC034897|RBMS4|Ter	DND microRNA-mediated repression inhibitor 1	protein-coding
mm_142243.1	chr17	37482538	37482559	-	1	NA	exon (NM_008204, exon 3 of 4)	exon (NM_008204, exon 3 of 4)	981	NM_008204	14990	Mm.329041	NM_008204	ENSMUSG00000016283	H2-M2	H-2M2|Thy19.4	histocompatibility 2, M region locus 2	protein-coding
mm_90298.1	chr10	125551543	125551544	+	1	NA	Intergenic	Intergenic	-223008	NM_011391	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|Mct2	solute carrier family 16 (monocarboxylic acid transporters), member 7	protein-coding
mm_157852.1	chrX	74428872	74428887	-	1	NA	promoter-TSS (NM_178590)	promoter-TSS (NM_178590)	282	NM_008062	14381	Mm.27210	NM_008062	ENSMUSG00000031400	G6pdx	G28A|G6pd|Gpdx	glucose-6-phosphate dehydrogenase X-linked	protein-coding
mm_55355.1	chr6	56901822	56901838	-	1	NA	promoter-TSS (NM_001252374)	promoter-TSS (NM_001252374)	56	NM_001252374	107569	Mm.158936	NM_026004	ENSMUSG00000029780	Nt5c3	1600024P05Rik|2610206B05Rik|3110004A18Rik|AI842776|Nt5c3a|Nt5y|PN-1|PN-I|PSN1|UMPH|Umph-1|Umph1|cN-III|lupin|p36	5'-nucleotidase, cytosolic III	protein-coding
mm_68546.1	chr7	114237623	114237631	-	1	NA	exon (NM_033370, exon 9 of 22)	exon (NM_033370, exon 9 of 22)	17053	NM_033370	70349	Mm.277024	NM_033370	ENSMUSG00000030754	Copb1	2610019B04Rik	coatomer protein complex, subunit beta 1	protein-coding
mm_24683.1	chr3	94933102	94933108	+	1	NA	promoter-TSS (NM_009150)	promoter-TSS (NM_009150)	22	NM_009150	20341	Mm.196558	NM_009150	ENSMUSG00000068874	Selenbp1	Lp56|Lpsb|SBP56	selenium binding protein 1	protein-coding
mm_97541.1	chr11	78920820	78920834	+	1	NA	promoter-TSS (NM_010927)	promoter-TSS (NM_010927)	40	NM_010927	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_58564.1	chr7	4782941	4782959	+	1	NA	promoter-TSS (NM_030028)	promoter-TSS (NM_030028)	10	NM_030028	78052	Mm.160043	NM_030028	ENSMUSG00000013091	Tmem190	4930572D21Rik	transmembrane protein 190	protein-coding
mm_126712.1	chr15	85329370	85329382	+	1	NA	Intergenic	Intergenic	-7005	NM_016843	54138	Mm.248906	NM_016843	ENSMUSG00000016541	Atxn10	AI325283|C77170|E46|Sca10|TEG-169|Tex169	ataxin 10	protein-coding
mm_84631.1	chr9	70934581	70934585	-	1	NA	5' UTR (NM_008280, exon 1 of 9)	5' UTR (NM_008280, exon 1 of 9)	225	NM_008280	15450	Mm.390187	NM_008280	ENSMUSG00000032207	Lipc	AI256194|HL|Hpl	lipase, hepatic	protein-coding
mm_110483.1	chr12	51925404	51925408	-	1	NA	exon (NM_177171, exon 15 of 36)	exon (NM_177171, exon 15 of 36)	45915	NM_177171	320487	Mm.131941	NM_177171	ENSMUSG00000035181	Heatr5a	C230081H03Rik|D930036F22Rik|mKIAA1316	HEAT repeat containing 5A	protein-coding
mm_156573.1	chrX	151919794	151919808	+	1	NA	exon (NM_021523, exon 67 of 83)	exon (NM_021523, exon 67 of 83)	6587	NR_029753	723947		NR_029753	ENSMUSG00000065536	Mir98	Mirn98|mir-98|mmu-mir-98	microRNA 98	ncRNA
mm_89110.1	chr10	84622366	84622410	+	1	NA	promoter-TSS (NM_027423)	promoter-TSS (NM_027423)	-49	NM_027423	70428	Mm.335007	NM_027423	ENSMUSG00000034453	Polr3b	2700078H01Rik|A330032P03Rik|C85372|RPC2	polymerase (RNA) III (DNA directed) polypeptide B	protein-coding
mm_106156.1	chr11	116624239	116624256	-	1	NA	promoter-TSS (NM_001167680)	promoter-TSS (NM_001167680)	5	NM_001167680	217344	Mm.89695	NM_172572	ENSMUSG00000020806	Rhbdf2	4732465I17Rik|Rhbdl6|cub	rhomboid 5 homolog 2	protein-coding
mm_66195.1	chr7	34223744	34223755	-	1	NA	intron (NM_008155, intron 4 of 17)	Lx5c|LINE|L1	6587	NM_008155	14751	Mm.589	NM_008155	ENSMUSG00000036427	Gpi1	Amf|Gpi|Gpi-1|Gpi-1r|Gpi-1s|Gpi-1t|Gpi1-r|Gpi1-s|Gpi1-t|Gpi1s|MF|NK|NK/GPI|Nlk|Org|Pgi|Phi	glucose phosphate isomerase 1	protein-coding
mm_7350.1	chr1	106543296	106543306	-	1	NA	exon (NM_009741, exon 2 of 2)	exon (NM_009741, exon 2 of 2)	3330	NR_106164	102466254		NR_106164	ENSMUSG00000098344	Mir3473f	Gm27846|mmu-mir-3473f	microRNA 3473f	ncRNA
mm_75784.1	chr8	70042690	70042713	-	1	NA	promoter-TSS (NM_027481)	promoter-TSS (NM_027481)	33	NM_001167939	74549	Mm.269061	NM_028993	ENSMUSG00000031858	Mau2	9130404D08Rik|A930019L04Rik|C77863|C79014|Mau-2|mKIAA0892	MAU2 sister chromatid cohesion factor	protein-coding
mm_69883.1	chr7	141636933	141636945	-	1	NA	intron (NM_001330001, intron 31 of 33)	intron (NM_001330001, intron 31 of 33)	16238	NR_106030	102466798		NR_106030	ENSMUSG00000098759	Mir7063	Gm27654|mmu-mir-7063	microRNA 7063	ncRNA
mm_7481.1	chr1	120517662	120517669	-	1	NA	Intergenic	Intergenic	-12581	NM_010766	17167	Mm.1856	NM_010766	ENSMUSG00000026390	Marco	AI323439|Ly112|Scara2	macrophage receptor with collagenous structure	protein-coding
mm_32026.1	chr4	95161514	95161522	+	1	NA	Intergenic	Intergenic	-109296	NM_010591	16476	Mm.275071	NM_010591	ENSMUSG00000052684	Jun	AP-1|Junc|c-jun	jun proto-oncogene	protein-coding
mm_101309.1	chr11	22613462	22613470	-	1	NA	Intergenic	RLTR41A2|LTR|ERV1	101183	NM_153596	103765	Mm.221274	NM_153596	ENSMUSG00000049904	Tmem17	AI503894|AW049890	transmembrane protein 17	protein-coding
mm_132945.1	chr16	49904737	49904747	+	1	NA	intron (NM_010581, intron 8 of 9)	intron (NM_010581, intron 8 of 9)	49088	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_134964.1	chr16	31935366	31935390	-	1	NA	intron (NM_172822, intron 1 of 2)	intron (NM_172822, intron 1 of 2)	1527	NM_172822	239827	Mm.440388	NM_172822	ENSMUSG00000045625	Pigz	F630022B06Rik	phosphatidylinositol glycan anchor biosynthesis, class Z	protein-coding
mm_152285.1	chr19	8929182	8929204	-	1	NA	promoter-TSS (NM_144872)	promoter-TSS (NM_144872)	163	NM_009073	19881	Mm.426094	NM_009073	ENSMUSG00000071648	Rom1	M101156|Rgsc1156|Rom-1|Rosp1|Tspan23	rod outer segment membrane protein 1	protein-coding
mm_73756.1	chr8	114987850	114987850	+	1	NA	intron (NM_019573, intron 8 of 8)	intron (NM_019573, intron 8 of 8)	548198	NM_019573	80707	Mm.440420	NM_019573	ENSMUSG00000004637	Wwox	5330426P09Rik|9030416C10Rik|WOX1	WW domain-containing oxidoreductase	protein-coding
mm_20587.1	chr2	131160007	131160051	-	1	NA	promoter-TSS (NM_026091)	promoter-TSS (NM_026091)	-9	NM_026091	67326	Mm.27711	NM_026091	ENSMUSG00000027327	1700037H04Rik	-	RIKEN cDNA 1700037H04 gene	protein-coding
mm_22353.1	chr2	180935998	180936011	-	1	NA	exon (NM_021426, exon 6 of 7)	exon (NM_021426, exon 6 of 7)	6981	NM_001163247	329581	Mm.187879	NM_001163247	ENSMUSG00000038840	Birc7	E130019N06|KIAP|Livin|ML-IAP	baculoviral IAP repeat-containing 7 (livin)	protein-coding
mm_135543.1	chr16	49790952	49790973	-	1	NA	Intergenic	Intergenic	-64692	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_94757.1	chr11	21148821	21148834	+	1	NA	3' UTR (NM_023324, exon 7 of 7)	3' UTR (NM_023324, exon 7 of 7)	57503	NM_023324	67245	Mm.28957	NM_023324	ENSMUSG00000020134	Peli1	2810468L03Rik|A930031K15Rik|AA409794|AI586297|D11Ertd676e	pellino 1	protein-coding
mm_142399.1	chr17	45433563	45433583	-	1	NA	promoter-TSS (NR_130961)	promoter-TSS (NR_130961)	134	NM_152810	71702	Mm.28270	NM_152810	ENSMUSG00000023932	Cdc5l	1200002I02Rik|AA408004|PCDC5RP	cell division cycle 5-like (S. pombe)	protein-coding
mm_102053.1	chr11	52120961	52120975	-	1	NA	exon (NM_019411, exon 6 of 7)	exon (NM_019411, exon 6 of 7)	-5778	NR_037221	100526467		NR_037221	ENSMUSG00000092870	Mir3061	mir-3061|mmu-mir-3061	microRNA 3061	ncRNA
mm_21595.1	chr2	164237726	164237744	-	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	606	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_70768.1	chr8	21969770	21969780	+	1	NA	promoter-TSS (NM_026459)	promoter-TSS (NM_026459)	-821	NM_026459	67929	Mm.60688	NM_026459	ENSMUSG00000017049	Ccdc70	1700112P19Rik	coiled-coil domain containing 70	protein-coding
mm_54437.1	chr6	34345078	34345098	-	1	NA	Intergenic	MER31A|LTR|ERV1	-9076	NM_008012	14187	Mm.5378	NM_008012	ENSMUSG00000029762	Akr1b8	FR-1|Fgfrp|Fgrp	aldo-keto reductase family 1, member B8	protein-coding
mm_100510.1	chr11	120530077	120530101	+	1	NA	promoter-TSS (NM_008101)	promoter-TSS (NM_008101)	-638	NM_008101	14527	Mm.22329	NM_008101	ENSMUSG00000025127	Gcgr	GR	glucagon receptor	protein-coding
mm_55213.1	chr6	52225217	52225231	-	1	NA	intron (NM_001277238, intron 2 of 2)	intron (NM_001277238, intron 2 of 2)	2146	NM_010456	15405	Mm.4694	NM_010456	ENSMUSG00000038227	Hoxa9	D6a9|Hox-1.7	homeobox A9	protein-coding
mm_135011.1	chr16	32477628	32477634	-	1	NA	exon (NM_145932, exon 6 of 9)	exon (NM_145932, exon 6 of 9)	10248	NM_145932	106407	Mm.476915	NM_145932	ENSMUSG00000035699	Slc51a	AV001382|AW261577|D630035O19Rik|OSTalpha|Osta	solute carrier family 51, alpha subunit	protein-coding
mm_63486.1	chr7	127748138	127748155	+	1	NA	intron (NM_172748, intron 1 of 10)	intron (NM_172748, intron 1 of 10)	1371	NM_172748	233902	Mm.259353	NM_172748	ENSMUSG00000030811	Fbxl19	6030430O11|BC059812|Fbl19	F-box and leucine-rich repeat protein 19	protein-coding
mm_66464.1	chr7	44928670	44928681	-	1	NA	intron (NM_007458, intron 1 of 23)	intron (NM_007458, intron 1 of 23)	815	NM_007458	11771	Mm.6877	NM_007458	ENSMUSG00000060279	Ap2a1	Adtaa	adaptor-related protein complex 2, alpha 1 subunit	protein-coding
mm_117292.1	chr13	66932930	66932947	-	1	NA	5' UTR (NM_025547, exon 1 of 8)	5' UTR (NM_025547, exon 1 of 8)	108	NM_008959	19210	Mm.281464	NM_008959	ENSMUSG00000021518	Ptdss1	AU044268|AW539008|PSS-1|mKIAA0024	phosphatidylserine synthase 1	protein-coding
mm_115364.1	chr13	112987953	112987977	+	1	NA	exon (NM_001081062, exon 1 of 3)	exon (NM_001081062, exon 1 of 3)	163	NM_001081062	218630	Mm.25457	NM_001081062	ENSMUSG00000042417	Ccno	C86987|Ccnu|E130318K11|Ung2	cyclin O	protein-coding
mm_63374.1	chr7	127209275	127209292	+	1	NA	promoter-TSS (NM_144522)	promoter-TSS (NM_144522)	384	NM_001347655	17907	Mm.14526	NM_016754	ENSMUSG00000030672	Mylpf	2410014J02Rik|MLC-2|Mlc2	myosin light chain, phosphorylatable, fast skeletal muscle	protein-coding
mm_96196.1	chr11	62005396	62005411	+	1	NA	intron (NM_001310526, intron 1 of 7)	intron (NM_001310526, intron 1 of 7)	48640	NM_001310526	432572	Mm.438022	NM_001029936	ENSMUSG00000042331	Specc1	2810012G08Rik|B230396K10Rik|Cytsb	sperm antigen with calponin homology and coiled-coil domains 1	protein-coding
mm_59808.1	chr7	29168394	29168402	+	1	NA	intron (NM_182927, intron 1 of 5)	intron (NM_182927, intron 1 of 5)	249	NM_182927	101809	Mm.377262	NM_182927	ENSMUSG00000037239	Spred3	AW047143|D130060H24Rik|Spred-3	sprouty-related, EVH1 domain containing 3	protein-coding
mm_37875.1	chr4	132356943	132356958	-	1	NA	3' UTR (NM_175306, exon 14 of 14)	3' UTR (NM_175306, exon 14 of 14)	-3264	NR_003270	399101	Mm.486919	NR_002904	ENSMUSG00000085241	Snhg3	Rnu17d|U17HG	small nucleolar RNA host gene 3	ncRNA
mm_26940.1	chr3	20265380	20265418	-	1	NA	exon (NM_029706, exon 6 of 11)	exon (NM_029706, exon 6 of 11)	10334	NM_029706	76703	Mm.34692	NM_029706	ENSMUSG00000011463	Cpb1	0910001A18Rik|1810063F02Rik|2210008M23Rik|AI504870	carboxypeptidase B1 (tissue)	protein-coding
mm_56619.1	chr6	112696379	112696394	-	1	NA	intron (NM_001167730, intron 1 of 13)	CpG	284	NM_021385	58186	Mm.103812	NM_021385	ENSMUSG00000030254	Rad18	2810024C04Rik|Rad18sc	RAD18 E3 ubiquitin protein ligase	protein-coding
mm_114492.1	chr13	69809864	69809899	+	1	NA	promoter-TSS (NM_138596)	promoter-TSS (NM_138596)	-1	NM_138596	28077	Mm.52583	NM_138596	ENSMUSG00000021598	Med10	AA959813|AI385605|C78613|D13Wsu50e	mediator complex subunit 10	protein-coding
mm_159912.1	chr6	48445030	48445030	-	1	NA	promoter-TSS (NM_001085415)	promoter-TSS (NM_001085415)	60	NM_001085415	68910	Mm.2464	NM_020589	ENSMUSG00000068551	Zfp467	1190001I08Rik|AB041616|AI426952|AV017623|EZI|MNCb-3350|Znf467	zinc finger protein 467	protein-coding
mm_87078.1	chr10	29216017	29216021	+	1	NA	intron (NM_001162537, intron 1 of 5)	intron (NM_001162537, intron 1 of 5)	4376	NM_001162537	212448	Mm.132789	NM_001162537	ENSMUSG00000004360	9330159F19Rik	-	RIKEN cDNA 9330159F19 gene	protein-coding
mm_165477.1	chr2	164333373	164333377	+	1	NA	exon (NM_009301, exon 2 of 3)	exon (NM_009301, exon 2 of 3)	610	NM_009301	20944	Mm.140154	NM_009301	ENSMUSG00000017004	Svs5	BB115186|Semg1|Svp-1|Svp1|Svp5	seminal vesicle secretory protein 5	protein-coding
mm_99652.1	chr11	105590055	105590090	+	1	NA	promoter-TSS (NM_181071)	promoter-TSS (NM_181071)	86	NM_181071	77097	Mm.22501	NM_175492	ENSMUSG00000053580	Tanc2	3526402J09Rik|5730590C14Rik	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2	protein-coding
mm_146090.1	chr18	73572843	73572882	+	1	NA	5' UTR (NM_001039214, exon 1 of 2)	5' UTR (NM_001039214, exon 1 of 2)	157	NM_001039214	240396	Mm.24131	NM_001039214	ENSMUSG00000037253	Mex3c	A130001D14Rik|BC035207|BM-013|Rkhd2	mex3 RNA binding family member C	protein-coding
mm_80784.1	chr9	95857695	95857710	+	1	NA	promoter-TSS (NR_073361)	promoter-TSS (NR_073361)	105	NM_019864	245000	Mm.212462	NM_019864	ENSMUSG00000032409	Atr	-	ataxia telangiectasia and Rad3 related	protein-coding
mm_143953.1	chr17	86831278	86831285	-	1	NA	3' UTR (NM_010137, exon 16 of 16)	3' UTR (NM_010137, exon 16 of 16)	77417	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_150082.1	chr19	29387253	29387272	+	1	NA	3' UTR (NM_021893, exon 7 of 7)	3' UTR (NM_021893, exon 7 of 7)	19824	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_3310.1	chr1	137899401	137899415	+	1	NA	Intergenic	Intergenic	-67047	NR_029795	735252		NR_029795	ENSMUSG00000065565	Mir181a-1	Mirn181a-1|Mirn213|miR-213|mir-181a-1|mmu-mir-213	microRNA 181a-1	ncRNA
mm_45685.1	chr5	77355588	77355602	-	1	NA	exon (NM_008048, exon 2 of 5)	exon (NM_008048, exon 2 of 5)	45111	NM_153798	231329	Mm.273217	NM_153798	ENSMUSG00000029250	Polr2b	Pol2rb|Rpb140|Rpb2	polymerase (RNA) II (DNA directed) polypeptide B	protein-coding
mm_135918.1	chr16	67620806	67620816	-	1	NA	promoter-TSS (NM_178721)	promoter-TSS (NM_178721)	97	NM_001347247	239857	Mm.394300	NM_178721	ENSMUSG00000064115	Cadm2	2900078E11Rik|9330131D06|A830029E02Rik|Igdf4d|Igsf4d|NECL3|SynCAM 2|SynCAM2	cell adhesion molecule 2	protein-coding
mm_143152.1	chr17	57222945	57222949	-	1	NA	exon (NM_009778, exon 13 of 41)	exon (NM_009778, exon 13 of 41)	5189	NM_009778	12266	Mm.19131	NM_009778	ENSMUSG00000024164	C3	AI255234|ASP|HSE-MSF|Plp	complement component 3	protein-coding
mm_49136.1	chr6	8949053	8949068	+	1	NA	promoter-TSS (NM_008751)	promoter-TSS (NM_008751)	-959	NM_008751	18231	Mm.46954	NM_008751	ENSMUSG00000046178	Nxph1	C130005L03Rik	neurexophilin 1	protein-coding
mm_116578.1	chr13	47105685	47105702	-	1	NA	exon (NM_025900, exon 2 of 11)	exon (NM_025900, exon 2 of 11)	528	NM_025900	110052	Mm.131150	NM_025900	ENSMUSG00000021377	Dek	1810019E15Rik|D13H6S231E	DEK oncogene (DNA binding)	protein-coding
mm_166093.1	chr4	141477518	141477524	-	1	NA	exon (NM_019763, exon 12 of 16)	exon (NM_019763, exon 12 of 16)	32848	NM_009541	22642	Mm.389590	NM_009541	ENSMUSG00000006215	Zbtb17	AA589413|Lp-1|Miz1|Zfp100|mZ13	zinc finger and BTB domain containing 17	protein-coding
mm_21085.1	chr2	152951689	152951700	-	1	NA	promoter-TSS (NM_001159376)	promoter-TSS (NM_001159376)	-112	NM_001159376	252864	Mm.330671	NM_145744	ENSMUSG00000042662	Dusp15	AI851682|LMW-DSP10|T-DSP10	dual specificity phosphatase-like 15	protein-coding
mm_118323.1	chr13	113615065	113615089	-	1	NA	intron (NM_130796, intron 1 of 1)	intron (NM_130796, intron 1 of 1)	3487	NM_130796	170625	Mm.33721	NM_130796	ENSMUSG00000042364	Snx18	Snag1	sorting nexin 18	protein-coding
mm_23910.1	chr3	83043220	83043250	+	1	NA	exon (NM_181849, exon 7 of 8)	exon (NM_181849, exon 7 of 8)	6628	NM_181849	110135	Mm.30063	NM_181849	ENSMUSG00000033831	Fgb	2510049G14Rik	fibrinogen beta chain	protein-coding
mm_121941.1	chr14	24081948	24081959	-	1	NA	Intergenic	Intergenic	-6924	NR_106069	102465697		NR_106069	ENSMUSG00000105723	Mir7210	mir-7210|mmu-mir-7210	microRNA 7210	ncRNA
mm_106597.1	chr11	120730878	120730887	-	1	NA	exon (NM_007621, exon 3 of 8)	exon (NM_007621, exon 3 of 8)	1139	NM_007621	12409	Mm.21454	NM_007621	ENSMUSG00000025150	Cbr2	MLCR	carbonyl reductase 2	protein-coding
mm_103052.1	chr11	69816900	69816902	-	1	NA	exon (NM_175368, exon 3 of 3)	exon (NM_175368, exon 3 of 3)	1539	NM_175368	108803	Mm.73263	NM_175368	ENSMUSG00000044084	4933402P03Rik	-	RIKEN cDNA 4933402P03 gene	protein-coding
mm_38533.1	chr4	141566354	141566381	-	1	NA	Intergenic	Intergenic	20205	NR_030695	320456	Mm.32859	NM_177163		B330016D10Rik	-	RIKEN cDNA B330016D10 gene	ncRNA
mm_29761.1	chr3	127162400	127162416	-	1	NA	intron (NR_105029, intron 2 of 3)	intron (NR_105029, intron 2 of 3)	1103	NR_105029	100862268	Mm.444603	NR_105029	ENSMUSG00000097456	LOC100862268	-	uncharacterized LOC100862268	ncRNA
mm_163769.1	chr13	120018082	120018127	+	1	NA	Intergenic	Intergenic	34100	NM_001302966	100861753	Mm.165042	NM_001302966	ENSMUSG00000095609	Gm21188	-	predicted gene, 21188	protein-coding
mm_98319.1	chr11	90249514	90249532	+	1	NA	promoter-TSS (NM_026178)	promoter-TSS (NM_026178)	47	NM_026178	67468	Mm.277518	NM_026178	ENSMUSG00000003948	Mmd	1200017E07Rik|1810073C06Rik|AA690185	monocyte to macrophage differentiation-associated	protein-coding
mm_122314.1	chr14	36919376	36919385	-	1	NA	5' UTR (NM_001347503, exon 1 of 8)	5' UTR (NM_001347503, exon 1 of 8)	155	NM_001347503	72972	Mm.27621	NM_027045	ENSMUSG00000058690	Ccser2	1700012P13Rik|2900054P12Rik|AI035535|AW108503|Fam190b|Gcap14	coiled-coil serine rich 2	protein-coding
mm_37700.1	chr4	129335325	129335377	-	1	NA	promoter-TSS (NM_009030)	promoter-TSS (NM_009030)	19	NM_009030	19646	Mm.12145	NM_009030	ENSMUSG00000057236	Rbbp4	RBAP48|mRbAp48	retinoblastoma binding protein 4	protein-coding
mm_95817.1	chr11	55204320	55204386	+	1	NA	promoter-TSS (NM_153139)	promoter-TSS (NM_153139)	13	NM_153139	215335	Mm.35732	NM_153139	ENSMUSG00000020261	Slc36a1	5830411H19Rik|AI839897|Pat1	solute carrier family 36 (proton/amino acid symporter), member 1	protein-coding
mm_123681.1	chr14	69503350	69503367	-	1	NA	Intergenic	CpG	9191	NM_173420	239167	Mm.259889	NM_173420	ENSMUSG00000047977	Synb	D930020E02Rik|syncytin-B	syncytin b	protein-coding
mm_26963.1	chr3	22076074	22076104	-	1	NA	promoter-TSS (NM_030732)	promoter-TSS (NM_030732)	-563	NM_030732	81004	Mm.202966	NM_030732	ENSMUSG00000027630	Tbl1xr1	8030499H02Rik|A630076E03Rik|AW539987|C21|C230089I12Rik|DC42|Ira1|TBLR1	transducin (beta)-like 1X-linked receptor 1	protein-coding
mm_168649.1	chr11	8605359	8605360	-	1	NA	intron (NM_001083587, intron 2 of 30)	RLTR11A2|LTR|ERVK	59176	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_80344.1	chr9	75166313	75166351	+	1	NA	intron (NM_010864, intron 18 of 40)	intron (NM_010864, intron 18 of 40)	-65682	NM_001081322	208943	Mm.41339	NM_001081322	ENSMUSG00000033590	Myo5c	9130003O20Rik|BB085560|C330029I24	myosin VC	protein-coding
mm_117838.1	chr13	98692152	98692185	-	1	NA	exon (NM_001025606, exon 2 of 4)	exon (NM_001025606, exon 2 of 4)	2663	NM_001025606	380863	Mm.28264	NM_001025606	ENSMUSG00000052485	Tmem171	Gm905	transmembrane protein 171	protein-coding
mm_105258.1	chr11	102356438	102356450	-	1	NA	exon (NM_011403, exon 12 of 20)	exon (NM_011403, exon 12 of 20)	8837	NM_011403	20533	Mm.7248	NM_011403	ENSMUSG00000006574	Slc4a1	Ae1|CD233|Empb3|l11Jus51	solute carrier family 4 (anion exchanger), member 1	protein-coding
mm_13546.1	chr2	112000329	112000343	+	1	NA	Intergenic	Intergenic	8848	NM_146449	258441	Mm.377504	NM_146449	ENSMUSG00000108827	Olfr1310	MOR245-3	olfactory receptor 1310	protein-coding
mm_92396.1	chr10	76614406	76614453	-	1	NA	exon (NM_146007, exon 3 of 28)	exon (NM_146007, exon 3 of 28)	8975	NM_146007	12834	Mm.1949	NM_146007	ENSMUSG00000020241	Col6a2	Col6a-2	collagen, type VI, alpha 2	protein-coding
mm_6071.1	chr1	60910722	60910746	-	1	NA	intron (NM_001281976, intron 1 of 2)	intron (NM_001281976, intron 1 of 2)	1709	NM_001281976	12477	Mm.390	NM_009843	ENSMUSG00000026011	Ctla4	Cd152|Ctla-4|Ly-56	cytotoxic T-lymphocyte-associated protein 4	protein-coding
mm_75330.1	chr8	43180267	43180281	-	1	NA	Intergenic	B1F|SINE|Alu	-2848	NM_001160412	622117	Mm.390031	NM_001160412	ENSMUSG00000091490	Triml2	EG622117|Tu4	tripartite motif family-like 2	protein-coding
mm_83531.1	chr9	46230301	46230315	-	1	NA	exon (NM_009692, exon 4 of 4)	exon (NM_009692, exon 4 of 4)	1678	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2|apo-AI|apoA-I	apolipoprotein A-I	protein-coding
mm_22632.1	chr3	14770164	14770190	+	1	NA	exon (NM_001083957, exon 5 of 7)	exon (NM_001083957, exon 5 of 7)	8283	NM_001083957	12346	Mm.273195	NM_009799	ENSMUSG00000027556	Car1	AW555628|Ca1|Car-1	carbonic anhydrase 1	protein-coding
mm_160940.1	chr11	94704499	94704499	-	1	NA	promoter-TSS (NM_001007584)	promoter-TSS (NM_001007584)	0	NM_001007584	432589	Mm.342314	NM_001007584	ENSMUSG00000056008	Gm11541	OTTMUSG00000002038	predicted gene 11541	protein-coding
mm_137077.1	chr17	21009018	21009034	+	1	NA	promoter-TSS (NM_145483)	promoter-TSS (NM_145483)	85	NM_145483	224585	Mm.296036	NM_145483	ENSMUSG00000067942	Zfp160	6720480D16Rik|F11|HKr18|HZF5|KR18|mKIAA1611|mszf47	zinc finger protein 160	protein-coding
mm_21174.1	chr2	154871485	154871492	-	1	NA	TTS (NM_026030)	TTS (NM_026030)	21418	NM_026030	67204	Mm.377134	NM_026030	ENSMUSG00000074656	Eif2s2	2810026E11Rik|38kDa|AA408636|AA571381|AA986487|AW822225|D2Ertd303e|EIF2|EIF2B	eukaryotic translation initiation factor 2, subunit 2 (beta)	protein-coding
mm_99107.1	chr11	100133635	100133676	+	1	NA	exon (NM_008469, exon 4 of 8)	exon (NM_008469, exon 4 of 8)	2294	NM_008469	16665	Mm.440010	NM_008469	ENSMUSG00000054146	Krt15	AI528832|K15|Krt1-15	keratin 15	protein-coding
mm_117957.1	chr13	99447347	99447393	-	1	NA	intron (NM_008634, intron 2 of 6)	intron (NM_008634, intron 2 of 6)	-34544	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_118704.1	chr14	22164100	22164128	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	144402	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_123262.1	chr14	61305268	61305312	-	1	NA	promoter-TSS (NR_033788)	promoter-TSS (NR_033788)	44	NR_033788	67355	Mm.193728	NR_033788	ENSMUSG00000101505	1700109G14Rik	1700126G13Rik	RIKEN cDNA 1700109G14 gene	ncRNA
mm_120945.1	chr14	76690625	76690629	+	1	NA	Intergenic	MLT1D|LTR|ERVL-MaLR	13059	NR_015485	73272	Mm.116804	NR_015485	ENSMUSG00000101009	1700108F19Rik	1700020I02Rik|BB065030	RIKEN cDNA 1700108F19 gene	ncRNA
mm_142947.1	chr17	56109718	56109737	-	1	NA	promoter-TSS (NM_020568)	promoter-TSS (NM_020568)	75	NM_020568	57435	Mm.12966	NM_020568	ENSMUSG00000002831	Plin4	S3-12|mKIAA1881	perilipin 4	protein-coding
mm_62365.1	chr7	100580279	100580302	+	1	NA	intron (NR_003559, intron 1 of 7)	intron (NR_003559, intron 1 of 7)	2840	NM_198831	52443	Mm.473730	NM_198831	ENSMUSG00000030706	Mrpl48	1810030E20Rik|2610028L11Rik|CGI-118|D4Ertd786e	mitochondrial ribosomal protein L48	protein-coding
mm_8520.1	chr1	154883984	154884000	-	1	NA	Intergenic	Intergenic	-158072	NM_009782	12290	Mm.267517	NM_009782	ENSMUSG00000004110	Cacna1e	A430040I15|BII|Cach6|Cacnl1a6|Cav2.3|Cchra1|alpha1E	calcium channel, voltage-dependent, R type, alpha 1E subunit	protein-coding
mm_77238.1	chr8	115705100	115705113	-	1	NA	3' UTR (NM_001025577, exon 1 of 1)	3' UTR (NM_001025577, exon 1 of 1)	1788	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_22172.1	chr2	173154005	173154034	-	1	NA	exon (NM_011044, exon 3 of 10)	exon (NM_011044, exon 3 of 10)	946	NM_011044	18534	Mm.266867	NM_011044	ENSMUSG00000027513	Pck1	AI265463|PEPCK|Pck-1	phosphoenolpyruvate carboxykinase 1, cytosolic	protein-coding
mm_8882.1	chr1	162866464	162866468	-	1	NA	5' UTR (NM_010231, exon 1 of 9)	5' UTR (NM_010231, exon 1 of 9)	144	NM_010231	14261	Mm.976	NM_010231	ENSMUSG00000040181	Fmo1	-	flavin containing monooxygenase 1	protein-coding
mm_6354.1	chr1	71653163	71653181	-	1	NA	promoter-TSS (NM_001276413)	promoter-TSS (NM_001276413)	62	NM_010233	14268	Mm.193099	NM_010233	ENSMUSG00000026193	Fn1	E330027I09|Fn|Fn-1	fibronectin 1	protein-coding
mm_26778.1	chr3	9004455	9004467	-	1	NA	promoter-TSS (NM_009412)	promoter-TSS (NM_009412)	54	NM_009412	21985	Mm.371590	NM_009412	ENSMUSG00000027506	Tpd52	AI043038|mD52	tumor protein D52	protein-coding
mm_90088.1	chr10	116914188	116914198	+	1	NA	exon (NM_001003950, exon 7 of 10)	exon (NM_001003950, exon 7 of 10)	-17314	NM_001033333	237558	Mm.336386	NM_001033333	ENSMUSG00000034057	Myrfl	Gm239	myelin regulatory factor-like	protein-coding
mm_107964.1	chr12	72745744	72745767	+	1	NA	Intergenic	RMER10A|LTR|ERVL	-15456	NM_008910	19042	Mm.261045	NM_008910	ENSMUSG00000021096	Ppm1a	2310003C21Rik|2900017D14Rik|AI427932|AU017636|MMPa-2|MPPa-1	protein phosphatase 1A, magnesium dependent, alpha isoform	protein-coding
mm_167204.1	chr7	143866886	143866893	+	1	NA	Intergenic	Intergenic	43722	NM_007856	13360	Mm.249342	NM_007856	ENSMUSG00000058454	Dhcr7	AA409147	7-dehydrocholesterol reductase	protein-coding
mm_21105.1	chr2	153241710	153241724	-	1	NA	promoter-TSS (NM_018807)	promoter-TSS (NM_018807)	185	NM_080463	140484	Mm.293761	NM_080463	ENSMUSG00000046020	Pofut1	O-FucT-1|mKIAA0180	protein O-fucosyltransferase 1	protein-coding
mm_18529.1	chr2	63184459	63184469	-	1	NA	promoter-TSS (NM_133207)	promoter-TSS (NM_133207)	-177	NM_133207	170738	Mm.242532	NM_133207	ENSMUSG00000059742	Kcnh7	9330137I11Rik|Kv11.3|erg3	potassium voltage-gated channel, subfamily H (eag-related), member 7	protein-coding
mm_4964.1	chr1	191275832	191275840	+	1	NA	Intergenic	RMER30|DNA|hAT-Charlie	42282	NM_025424	66208	Mm.46444	NM_025424	ENSMUSG00000037499	Nenf	1110060M21Rik|SCIRP10|Spuf	neuron derived neurotrophic factor	protein-coding
mm_122889.1	chr14	54948158	54948171	-	1	NA	TTS (NR_029724)	TTS (NR_029724)	978	NR_029724	387204		NR_029724	ENSMUSG00000065432	Mir208a	Mirn208|Mirn208a|mir-208|mir-208a|mmu-mir-208	microRNA 208a	ncRNA
mm_134370.1	chr16	17125131	17125146	-	1	NA	promoter-TSS (NM_183287)	promoter-TSS (NM_183287)	-32	NM_183287	70458	Mm.234165	NM_183287	ENSMUSG00000049916	2610318N02Rik	AL033325	RIKEN cDNA 2610318N02 gene	protein-coding
mm_85685.1	chr9	107985864	107985893	-	1	NA	promoter-TSS (NM_026597)	promoter-TSS (NM_026597)	38	NM_026597	68176	Mm.76166	NM_026597	ENSMUSG00000042106	Fam212a	6230427J02Rik|Inka1	family with sequence similarity 212, member A	protein-coding
mm_54352.1	chr6	31052519	31052522	-	1	NA	Intergenic	Intergenic	10227	NR_029744	387222		NR_029744	ENSMUSG00000065610	Mir29a	Mirn29a|mir-29a|mmu-mir-29a	microRNA 29a	ncRNA
mm_54227.1	chr6	28135082	28135111	-	1	NA	promoter-TSS (NM_008174)	promoter-TSS (NM_008174)	-727	NM_008174	14823	Mm.320732	NM_008174	ENSMUSG00000024211	Grm8	A230002O04|Gprc1h|mGluR8	glutamate receptor, metabotropic 8	protein-coding
mm_96168.1	chr11	61488338	61488349	+	1	NA	TTS (NM_001291037)	TTS (NM_001291037)	2899	NM_029568	76293	Mm.272278	NM_029568	ENSMUSG00000042436	Mfap4	1110007F23Rik	microfibrillar-associated protein 4	protein-coding
mm_44932.1	chr5	36317548	36317550	-	1	NA	intron (NM_030889, intron 1 of 26)	B4A|SINE|B4	15979	NR_106162	102465792		NR_106162	ENSMUSG00000098884	Mir7689	Gm27434|mmu-mir-7689	microRNA 7689	ncRNA
mm_121500.1	chr14	121916155	121916161	+	1	NA	promoter-TSS (NM_182806)	promoter-TSS (NM_182806)	-384	NM_182806	110168	Mm.37405	NM_182806	ENSMUSG00000050350	Gpr18	-	G protein-coupled receptor 18	protein-coding
mm_95386.1	chr11	49244228	49244283	+	1	NA	promoter-TSS (NM_010794)	promoter-TSS (NM_010794)	64	NM_001110148	17308	Mm.196933	NM_010794	ENSMUSG00000020346	Mgat1	Mgat-1	mannoside acetylglucosaminyltransferase 1	protein-coding
mm_39918.1	chr5	31494737	31494778	+	1	NA	promoter-TSS (NM_133756)	promoter-TSS (NM_133756)	-4	NM_133756	74254	Mm.348649	NM_133756	ENSMUSG00000064037	Gpn1	2410004J02Rik|AI449615|MBDIN|NTPBP|Xab1	GPN-loop GTPase 1	protein-coding
mm_22931.1	chr3	31149965	31149979	+	1	NA	promoter-TSS (NM_008770)	promoter-TSS (NM_008770)	52	NM_008770	18417	Mm.4425	NM_008770	ENSMUSG00000037625	Cldn11	Claudin-11|Claudin11|Osp|Otm	claudin 11	protein-coding
mm_120645.1	chr14	70530561	70530571	+	1	NA	promoter-TSS (NM_145219)	promoter-TSS (NM_145219)	-255	NM_145219	213469	Mm.41708	NM_145219	ENSMUSG00000033595	Lgi3	AI841179|AW049851	leucine-rich repeat LGI family, member 3	protein-coding
mm_38556.1	chr4	141642169	141642201	-	1	NA	intron (NM_001347237, intron 3 of 18)	intron (NM_001347237, intron 3 of 18)	-18351	NM_001013780	384071	Mm.295682	NM_001013780	ENSMUSG00000040740	Slc25a34	Gm1369	solute carrier family 25, member 34	protein-coding
mm_135966.1	chr16	74828846	74828850	-	1	NA	Intergenic	Intergenic	-417936	NM_175549	268902	Mm.171736	NM_175549	ENSMUSG00000052516	Robo2	2600013A04Rik|9430089E08Rik|BB097918|D230004I22Rik|mKIAA1568	roundabout guidance receptor 2	protein-coding
mm_910.1	chr1	54585734	54585765	+	1	NA	Intergenic	Intergenic	-28065	NM_001163314	241062	Mm.103539	NM_175508	ENSMUSG00000073678	Pgap1	5033403E17Rik|9030223K07Rik|A530084K22|D230012E17Rik|oto	post-GPI attachment to proteins 1	protein-coding
mm_80110.1	chr9	70512208	70512220	+	1	NA	Intergenic	Intergenic	-8489	NM_033604	93836	Mm.29783	NM_033604	ENSMUSG00000032217	Rnf111	ARK|Arkadia	ring finger 111	protein-coding
mm_51410.1	chr6	78380742	78380765	+	1	NA	promoter-TSS (NM_011259)	promoter-TSS (NM_011259)	44	NM_011259	19694	Mm.2552	NM_011259	ENSMUSG00000079516	Reg3a	AV063448	regenerating islet-derived 3 alpha	protein-coding
mm_93658.1	chr10	117690428	117690439	-	1	NA	exon (NM_010786, exon 12 of 12)	exon (NM_010786, exon 12 of 12)	20325	NM_010786	17246	Mm.22670	NM_010786	ENSMUSG00000020184	Mdm2	1700007J15Rik|AA415488|Mdm-2	transformed mouse 3T3 cell double minute 2	protein-coding
mm_82994.1	chr9	36637227	36637238	-	1	NA	3' UTR (NM_001033325, exon 3 of 4)	3' UTR (NM_001033325, exon 3 of 4)	1370	NM_001033325	235973	Mm.118804	NM_001033325	ENSMUSG00000070313	A630095E13Rik	Gm191|Pate14|Sslp-1|Sslp1	RIKEN cDNA A630095E13 gene	protein-coding
mm_15875.1	chr2	164835682	164835692	+	1	NA	exon (NM_008906, exon 7 of 15)	exon (NM_008906, exon 7 of 15)	1914	NM_008906	19025	Mm.359633	NM_008906	ENSMUSG00000017760	Ctsa	AU019505|PPCA|Ppgb	cathepsin A	protein-coding
mm_84112.1	chr9	58370440	58370450	-	1	NA	promoter-TSS (NR_040727)	promoter-TSS (NR_040727)	-59	NR_040727	73529	Mm.490924	NR_040727	ENSMUSG00000100487	1700072B07Rik	-	RIKEN cDNA 1700072B07 gene	ncRNA
mm_109208.1	chr12	108677190	108677193	+	1	NA	intron (NM_001163394, intron 7 of 13)	intron (NM_001163394, intron 7 of 13)	18571	NR_029771	723909		NR_029771	ENSMUSG00000065436	Mir342	Mirn342|mmu-mir-342	microRNA 342	ncRNA
mm_127907.1	chr15	9528044	9528052	-	1	NA	intron (NM_008372, intron 1 of 7)	intron (NM_008372, intron 1 of 7)	1828	NM_008372	16197	Mm.389	NM_008372	ENSMUSG00000003882	Il7r	CD127|IL-7Ralpha	interleukin 7 receptor	protein-coding
mm_102553.1	chr11	61378053	61378085	-	1	NA	promoter-TSS (NM_026183)	promoter-TSS (NM_026183)	6	NM_026183	67473	Mm.100741	NM_026183	ENSMUSG00000010122	Slc47a1	1300013J15Rik|AI036982|MATE1|mMATE1	solute carrier family 47, member 1	protein-coding
mm_105002.1	chr11	100374194	100374211	-	1	NA	intron (NM_010593, intron 10 of 13)	intron (NM_010593, intron 10 of 13)	-18061	NM_010404	15114	Mm.281700	NM_010404	ENSMUSG00000006930	Hap1	HAP-1	huntingtin-associated protein 1	protein-coding
mm_116970.1	chr13	56178652	56178721	-	1	NA	5' UTR (NM_001168615, exon 1 of 3)	5' UTR (NM_001168615, exon 1 of 3)	199	NM_145976	212937	Mm.116697	NM_145976	ENSMUSG00000049625	Tifab	-	TRAF-interacting protein with forkhead-associated domain, family member B	protein-coding
mm_54537.1	chr6	36738882	36738884	-	1	NA	intron (NM_008973, intron 4 of 4)	intron (NM_008973, intron 4 of 4)	72478	NM_008973	19242	Mm.279690	NM_008973	ENSMUSG00000029838	Ptn	HARP|HB-GAM|HBBN|HBGF-8|HBNF|OSF|Osf-1|Osf1	pleiotrophin	protein-coding
mm_90755.1	chr10	5550142	5550163	-	1	NA	intron (NM_001347732, intron 1 of 145)	intron (NM_001347732, intron 1 of 145)	540	NM_153399	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_126163.1	chr15	78449381	78449386	+	1	NA	intron (NM_027902, intron 10 of 17)	intron (NM_027902, intron 10 of 17)	19251	NM_027902	71753	Mm.34056	NM_027902	ENSMUSG00000016942	Tmprss6	1300008A22Rik	transmembrane serine protease 6	protein-coding
mm_36110.1	chr4	58867169	58867181	-	1	NA	intron (NM_172381, intron 7 of 48)	intron (NM_172381, intron 7 of 48)	45550	NM_172381	230249	Mm.234801	NM_172381	ENSMUSG00000050812	AI314180	AW558785|BB181316|mKIAA0368	expressed sequence AI314180	protein-coding
mm_48123.1	chr5	137146697	137146706	-	1	NA	Intergenic	Intergenic	-30494	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_130910.1	chr15	102517837	102517856	-	1	NA	promoter-TSS (NM_001163643)	promoter-TSS (NM_001163643)	-346	NM_001253795	21357	Mm.291485	NM_009319	ENSMUSG00000023051	Tarbp2	Prbp|TRBP	TARBP2, RISC loading complex RNA binding subunit	protein-coding
mm_154767.1	chrX	12587792	12587846	+	1	NA	promoter-TSS (NM_027439)	promoter-TSS (NM_027439)	60	NM_027439	70495	Mm.25148	NM_027439	ENSMUSG00000031007	Atp6ap2	(P)RR|5730403E06Rik|APT6M8-9|ATP6M8-9|Atp6ip2|M8-9|PRR	ATPase, H+ transporting, lysosomal accessory protein 2	protein-coding
mm_94573.1	chr11	11690083	11690103	+	1	NA	promoter-TSS (NM_001301865)	promoter-TSS (NM_001301865)	-84	NM_001301865	22778	Mm.103545	NM_009578	ENSMUSG00000018654	Ikzf1	5832432G11Rik|Ikaros|LyF-1|Zfpn1a1|Znfn1a1|hlk-1|mKIAA4227	IKAROS family zinc finger 1	protein-coding
mm_161660.1	chr17	8141641	8141641	-	1	NA	exon (NM_001083938, exon 4 of 9)	exon (NM_001083938, exon 4 of 9)	6147	NM_001083938	100037283	Mm.426736	NM_001083938	ENSMUSG00000095687	Rnaset2a	0610007O07Rik|4833423A10Rik|4930532K22Rik|C79750|RNASE6PL|Rnaset2	ribonuclease T2A	protein-coding
mm_48701.1	chr5	147018350	147018363	-	1	NA	3' UTR (NM_080795, exon 10 of 10)	3' UTR (NM_080795, exon 10 of 10)	-54559	NM_001256100	76366	Mm.486234	NM_029581	ENSMUSG00000016510	Mtif3	2810012L14Rik|AI414549	mitochondrial translational initiation factor 3	protein-coding
mm_60494.1	chr7	44478733	44478746	+	1	NA	Intergenic	Intergenic	-5778	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_125034.1	chr15	25755244	25755248	+	1	NA	intron (NM_019472, intron 19 of 40)	intron (NM_019472, intron 19 of 40)	-88052	NM_001034851	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_64872.1	chr7	14333571	14333574	-	1	NA	Intergenic	Intergenic	-78702	NM_001081325	629219	Mm.439627	NM_001081325	ENSMUSG00000070810	Sult2a6	EG629219|Gm6957	sulfotransferase family 2A, dehydroepiandrosterone (DHEA)-preferring, member 6	protein-coding
mm_151799.1	chr19	5424251	5424287	-	1	NA	promoter-TSS (NM_001256515)	promoter-TSS (NM_001256515)	710	NM_024176	66556	Mm.275446	NM_024176	ENSMUSG00000024914	Drap1	2310074H19Rik|NC2-alpha	Dr1 associated protein 1 (negative cofactor 2 alpha)	protein-coding
mm_144544.1	chr18	28189065	28189086	+	1	NA	Intergenic	Intergenic	-371089	NR_045398	320624	Mm.50107	NR_045398		4930474G06Rik	-	RIKEN cDNA 4930474G06 gene	ncRNA
mm_89231.1	chr10	87548979	87549005	+	1	NA	intron (NM_008777, intron 3 of 12)	intron (NM_008777, intron 3 of 12)	27197	NM_008777	18478	Mm.263539	NM_008777	ENSMUSG00000020051	Pah	AW106920	phenylalanine hydroxylase	protein-coding
mm_22040.1	chr2	168207017	168207025	-	1	NA	promoter-TSS (NM_009628)	promoter-TSS (NM_009628)	91	NM_009628	11538	Mm.201322	NM_009628	ENSMUSG00000051149	Adnp	AA589558|mKIAA0784	activity-dependent neuroprotective protein	protein-coding
mm_83700.1	chr9	50659494	50659564	-	1	NA	5' UTR (NM_145614, exon 1 of 14)	5' UTR (NM_145614, exon 1 of 14)	251	NM_145614	235339	Mm.285076	NM_145614	ENSMUSG00000000168	Dlat	6332404G05Rik|DLTA|PDC-E2	dihydrolipoamide S-acetyltransferase (E2 component of pyruvate dehydrogenase complex)	protein-coding
mm_65132.1	chr7	19508322	19508377	-	1	NA	promoter-TSS (NM_177692)	promoter-TSS (NM_177692)	-18	NM_177692	232946	Mm.64557	NM_177692	ENSMUSG00000057667	Bloc1s3	BC043666|Blos3|E230011O18|rp	biogenesis of lysosomal organelles complex-1, subunit 3	protein-coding
mm_136747.1	chr17	8525175	8525190	+	1	NA	Intergenic	Intergenic	-1619	NM_001290707	23984	Mm.87161	NM_011866	ENSMUSG00000023868	Pde10a	-	phosphodiesterase 10A	protein-coding
mm_91804.1	chr10	53751195	53751266	-	1	NA	promoter-TSS (NM_001081428)	promoter-TSS (NM_001081428)	-321	NM_001081428	75906	Mm.436785	NM_001081428	ENSMUSG00000019856	Fam184a	3110012E06Rik|4930438C08Rik|4930589M24Rik	family with sequence similarity 184, member A	protein-coding
mm_53739.1	chr6	145123484	145123485	+	1	NA	intron (NM_008511, intron 1 of 18)	intron (NM_008511, intron 1 of 18)	1745	NM_008511	16970	Mm.843	NM_008511	ENSMUSG00000030263	Lrmp	D6Int3|D6Int4|D6Int5|D6Int7|D6Int8|Jaw1	lymphoid-restricted membrane protein	protein-coding
mm_73844.1	chr8	117504002	117504007	+	1	NA	intron (NM_172285, intron 1 of 32)	intron (NM_172285, intron 1 of 32)	5729	NM_172285	234779	Mm.192699	NM_172285	ENSMUSG00000034330	Plcg2	PLC-gamma-2|PLCgamma2|Plcg-2	phospholipase C, gamma 2	protein-coding
mm_14855.1	chr2	148681155	148681197	+	1	NA	promoter-TSS (NM_028986)	promoter-TSS (NM_028986)	56	NM_028986	74533	Mm.136913	NM_028986	ENSMUSG00000027439	Gzf1	8430437G08Rik|Zfp336|mGZF1	GDNF-inducible zinc finger protein 1	protein-coding
mm_60566.1	chr7	44481417	44481423	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-3097	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_103140.1	chr11	70238465	70238475	-	1	NA	promoter-TSS (NM_001177601)	promoter-TSS (NM_001177601)	-556	NM_145758	104457	Mm.30016	NM_026757	ENSMUSG00000020831	0610010K14Rik	1110020A23Rik|AL033328|AU045833|Bap18	RIKEN cDNA 0610010K14 gene	protein-coding
mm_82108.1	chr9	123112919	123112932	+	1	NA	promoter-TSS (NM_001081188)	promoter-TSS (NM_001081188)	280	NM_026917	69035	Mm.28300	NM_026917	ENSMUSG00000025786	Zdhhc3	1110020O22Rik|1810006O10Rik|2210017C02Rik|DHHC-3|GODZ|Gramp1|Zfp373	zinc finger, DHHC domain containing 3	protein-coding
mm_160598.1	chr9	75311382	75311382	+	1	NA	5' UTR (NM_010313, exon 2 of 13)	5' UTR (NM_010313, exon 2 of 13)	-2686	NR_073186	14697	Mm.17604	NM_010313	ENSMUSG00000032192	Gnb5	GBS|Gbeta5|flr	guanine nucleotide binding protein (G protein), beta 5	protein-coding
mm_70711.1	chr8	15060153	15060218	+	1	NA	intron (NM_008664, intron 1 of 36)	intron (NM_008664, intron 1 of 36)	2532	NM_008664	17930	Mm.272115	NM_008664	ENSMUSG00000031461	Myom2	AW146149	myomesin 2	protein-coding
mm_150812.1	chr19	44396409	44396426	+	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	11292	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_171821.1	chr5	14180616	14180618	-	1	NA	intron (NM_011348, intron 4 of 16)	intron (NM_011348, intron 4 of 16)	155341	NM_011348	20349	Mm.134093	NM_011348	ENSMUSG00000063531	Sema3e	6430702L12|AA408817|Semah|mKIAA0331	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	protein-coding
mm_151963.1	chr19	5801685	5801706	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	977	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_151222.1	chr19	53700642	53700653	+	1	NA	intron (NM_001170847, intron 1 of 13)	RCHARR1|DNA|hAT-Charlie	23341	NM_001170847	73713	Mm.313695	NM_001170847	ENSMUSG00000043639	Rbm20	1110018J23Rik|2010003H22Rik|AI646761	RNA binding motif protein 20	protein-coding
mm_90976.1	chr10	13540317	13540319	-	1	NA	intron (NM_001347361, intron 3 of 11)	intron (NM_001347361, intron 3 of 11)	-12589	NM_025748	66757	Mm.331841	NM_025748	ENSMUSG00000019808	Adat2	4933426M09Rik|Deadc1	adenosine deaminase, tRNA-specific 2	protein-coding
mm_168404.1	chr11	30143110	30143111	-	1	NA	exon (NM_009260, exon 10 of 31)	exon (NM_009260, exon 10 of 31)	55147	NM_009260	20742	Mm.123110	NM_009260	ENSMUSG00000020315	Sptbn1	9930031C03Rik|AL033301|SPTB2|Spnb-2|Spnb2|elf1|elf3|mKIAA4049	spectrin beta, non-erythrocytic 1	protein-coding
mm_150730.1	chr19	43711418	43711460	+	1	NA	intron (NM_053103, intron 5 of 12)	intron (NM_053103, intron 5 of 12)	21750	NM_053103	93685	Mm.248237	NM_053103	ENSMUSG00000025192	Entpd7	1810012B13Rik|1810020C02Rik|2810003F23Rik|LALP1|Lysal2	ectonucleoside triphosphate diphosphohydrolase 7	protein-coding
mm_120573.1	chr14	69171940	69171964	+	1	NA	promoter-TSS (NR_045931)	promoter-TSS (NR_045931)	-109	NR_045931	73554	Mm.320005	NR_045931	ENSMUSG00000092499	1700092C10Rik	-	RIKEN cDNA 1700092C10 gene	ncRNA
mm_30384.1	chr3	152244072	152244078	-	1	NA	intron (NM_199465, intron 8 of 12)	intron (NM_199465, intron 8 of 12)	22245	NM_199465	68810	Mm.200188	NM_199465	ENSMUSG00000039103	Nexn	1110046H09Rik|AA553326|NELIN	nexilin	protein-coding
mm_161644.1	chr16	97851220	97851220	-	1	NA	promoter-TSS (NM_144789)	promoter-TSS (NM_144789)	7	NM_144789	114604	Mm.328741	NM_144789	ENSMUSG00000014039	Prdm15	C21orf83|E130018M06Rik|ORF62|Zfp298	PR domain containing 15	protein-coding
mm_67410.1	chr7	80096577	80096591	-	1	NA	intron (NM_173011, intron 7 of 10)	RSINE1|SINE|B4	18766	NM_173011	269951	Mm.246432	NM_173011	ENSMUSG00000030541	Idh2	E430004F23|IDPm|Idh-2	isocitrate dehydrogenase 2 (NADP+), mitochondrial	protein-coding
mm_51583.1	chr6	83795003	83795015	+	1	NA	promoter-TSS (NM_001164187)	promoter-TSS (NM_001164187)	9	NM_001347315	56174	Mm.190650	NM_019542	ENSMUSG00000034744	Nagk	Gnk	N-acetylglucosamine kinase	protein-coding
mm_44741.1	chr5	31193056	31193075	-	1	NA	promoter-TSS (NM_001127356)	promoter-TSS (NM_001127356)	74	NM_001127355	13667	Mm.29394	NM_010122	ENSMUSG00000029145	Eif2b4	Eif2b	eukaryotic translation initiation factor 2B, subunit 4 delta	protein-coding
mm_64461.1	chr7	142660732	142660760	+	1	NA	non-coding (NR_002855, exon 1 of 4)	non-coding (NR_002855, exon 1 of 4)	525	NM_001122736	16002	Mm.3862	NM_010514	ENSMUSG00000048583	Igf2	AL033362|Igf-2|Igf-II|M6pr|Mpr|Peg2	insulin-like growth factor 2	protein-coding
mm_9497.1	chr1	173730035	173730045	-	1	NA	exon (NM_001204910, exon 5 of 8)	exon (NM_001204910, exon 5 of 8)	11769	NM_001204910	226691	Mm.440876	NM_001204910	ENSMUSG00000073490	Ifi207	AI607873|Pyhin-A	interferon activated gene 207	protein-coding
mm_115516.1	chr13	5822717	5822721	-	1	NA	Intergenic	Intergenic	35373	NR_045891	71867	Mm.179181	NR_045891	ENSMUSG00000100625	1700016G22Rik	-	RIKEN cDNA 1700016G22 gene	ncRNA
mm_108915.1	chr12	100207570	100207586	+	1	NA	3' UTR (NM_009790, exon 6 of 6)	3' UTR (NM_009790, exon 6 of 6)	7434	NM_001313934	12313	Mm.285993	NM_009790	ENSMUSG00000001175	Calm1	AI256814|AI327027|AI461935|AL024000|CaM|Calm	calmodulin 1	protein-coding
mm_124800.1	chr15	8445411	8445420	+	1	NA	promoter-TSS (NM_027707)	promoter-TSS (NM_027707)	-952	NM_201232	71175	Mm.240329	NM_027707	ENSMUSG00000022141	Nipbl	Idn3	Nipped-B homolog (Drosophila)	protein-coding
mm_172835.1	chr9	25252669	25252674	+	1	NA	exon (NM_001205367, exon 1 of 13)	exon (NM_001205367, exon 1 of 13)	232	NM_001205367	235072	Mm.270259	NM_009859	ENSMUSG00000001833	Sept7	Cdc10|E430034N22	septin 7	protein-coding
mm_156048.1	chrX	109095360	109095391	+	1	NA	promoter-TSS (NM_019989)	promoter-TSS (NM_019989)	-32	NM_019989	56726	Mm.260760	NM_019989	ENSMUSG00000031246	Sh3bgrl	1190008F14Rik	SH3-binding domain glutamic acid-rich protein like	protein-coding
mm_140599.1	chr17	10319261	10319282	-	1	NA	promoter-TSS (NM_001159517)	promoter-TSS (NM_001159517)	90	NM_021881	19317	Mm.130694	NM_021881	ENSMUSG00000062078	Qk	1110003F05Rik|1500005P18|QkI|l(17)-1Wis|l17Wis1	quaking	protein-coding
mm_128509.1	chr15	53277904	53277925	-	1	NA	intron (NM_010162, intron 1 of 10)	intron (NM_010162, intron 1 of 10)	68269	NM_010162	14042	Mm.309395	NM_010162	ENSMUSG00000061731	Ext1	AA409028	exostoses (multiple) 1	protein-coding
mm_9386.1	chr1	172213370	172213398	-	1	NA	exon (NM_009813, exon 8 of 11)	exon (NM_009813, exon 8 of 11)	6511	NM_009813	12372	Mm.12829	NM_009813	ENSMUSG00000007122	Casq1	CSQ|CSQ-1|CSQ1|sCSQ	calsequestrin 1	protein-coding
mm_117969.1	chr13	99900787	99900789	-	1	NA	promoter-TSS (NM_001081493)	promoter-TSS (NM_001081493)	-105	NM_001081493	27220	Mm.75498	NM_013732	ENSMUSG00000021647	Cartpt	Cart	CART prepropeptide	protein-coding
mm_104598.1	chr11	97142283	97142286	-	1	NA	intron (NM_198100, intron 6 of 8)	intron (NM_198100, intron 6 of 8)	4135	NR_106094	102466822		NR_106094	ENSMUSG00000099286	Mir7235	Gm27986|mmu-mir-7235	microRNA 7235	ncRNA
mm_30018.1	chr3	135665303	135665310	-	1	NA	intron (NM_008689, intron 3 of 24)	intron (NM_008689, intron 3 of 24)	26241	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_65656.1	chr7	28137126	28137132	-	1	NA	exon (NM_001164655, exon 4 of 20)	exon (NM_001164655, exon 4 of 20)	7663	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_125013.1	chr15	25622760	25622777	+	1	NA	5' UTR (NM_019472, exon 1 of 41)	5' UTR (NM_019472, exon 1 of 41)	218	NM_019472	17909	Mm.60590	NM_019472	ENSMUSG00000022272	Myo10	AW048724|D15Ertd600e|mKIAA0799|myosin-X	myosin X	protein-coding
mm_13187.1	chr2	93187575	93187641	+	1	NA	promoter-TSS (NM_001025246)	promoter-TSS (NM_001025246)	24	NM_001025246	277414	Mm.41033	NM_001025246	ENSMUSG00000068735	Trp53i11	Tp53i11	transformation related protein 53 inducible protein 11	protein-coding
mm_76696.1	chr8	94180258	94180291	-	1	NA	TTS (NM_013602)	TTS (NM_013602)	1185	NM_013602	17748	Mm.192991	NM_013602	ENSMUSG00000031765	Mt1	MT-I|Mt-1	metallothionein 1	protein-coding
mm_166632.1	chr6	78467883	78467895	+	1	NA	exon (NM_011260, exon 3 of 6)	exon (NM_011260, exon 3 of 6)	985	NM_011260	19695	Mm.252385	NM_011260	ENSMUSG00000030017	Reg3g	AI449515|REG-3-gamma|reg III-gamma	regenerating islet-derived 3 gamma	protein-coding
mm_14205.1	chr2	127247999	127248037	+	1	NA	promoter-TSS (NM_175145)	promoter-TSS (NM_175145)	43	NM_175145	69470	Mm.200889	NM_175145	ENSMUSG00000034850	Tmem127	2310003P10Rik|AI314202|AI317350	transmembrane protein 127	protein-coding
mm_2564.1	chr1	118321835	118321882	+	1	NA	promoter-TSS (NM_026472)	promoter-TSS (NM_026472)	15	NM_026472	67949	Mm.280311	NM_026472	ENSMUSG00000026377	Nifk	AI852665|C130020J04Rik|Mki67ip	nucleolar protein interacting with the FHA domain of MKI67	protein-coding
mm_112706.1	chr13	18717681	18717687	+	1	NA	intron (NM_172120, intron 1 of 28)	intron (NM_172120, intron 1 of 28)	392	NM_172120	218035	Mm.27389	NM_172120	ENSMUSG00000041236	Vps41	AI317346|Vam2|mVam2	VPS41 HOPS complex subunit	protein-coding
mm_28027.1	chr3	83046741	83046758	-	1	NA	exon (NM_181849, exon 2 of 8)	exon (NM_181849, exon 2 of 8)	3114	NM_181849	110135	Mm.30063	NM_181849	ENSMUSG00000033831	Fgb	2510049G14Rik	fibrinogen beta chain	protein-coding
mm_67992.1	chr7	100894574	100894584	-	1	NA	intron (NM_001081116, intron 1 of 20)	CpG	-12170	NR_037289	100526508		NR_037289	ENSMUSG00000093296	Mir3102	mmu-mir-3102	microRNA 3102	ncRNA
mm_139184.1	chr17	47594606	47594626	+	1	NA	intron (NM_001081635, intron 3 of 6)	intron (NM_001081635, intron 3 of 6)	1149	NM_007632	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_168865.1	chr12	30911589	30911591	-	1	NA	promoter-TSS (NM_013709)	promoter-TSS (NM_013709)	22	NM_021330	11431	Mm.359831	NM_021330	ENSMUSG00000044573	Acp1	4632432E04Rik|AI427468|Acp-1|LMW-PTP|Lmptp	acid phosphatase 1, soluble	protein-coding
mm_58448.1	chr7	3303644	3303654	+	1	NA	5' UTR (NM_011102, exon 1 of 18)	5' UTR (NM_011102, exon 1 of 18)	117	NM_011102	18752	Mm.7980	NM_011102	ENSMUSG00000078816	Prkcg	PKCgamma|Pkcc|Prkcc	protein kinase C, gamma	protein-coding
mm_139419.1	chr17	53479338	53479387	+	1	NA	5' UTR (NM_025887, exon 1 of 6)	5' UTR (NM_025887, exon 1 of 6)	128	NM_025887	271457	Mm.329123	NM_025887	ENSMUSG00000017831	Rab5a	2410015H04Rik|AI663973|AU021172|nnyRab5a	RAB5A, member RAS oncogene family	protein-coding
mm_23819.1	chr3	80387545	80387548	+	1	NA	Intergenic	Intergenic	415245	NM_013540	14800	Mm.220224	NM_013540	ENSMUSG00000033981	Gria2	GluA2|GluR-B|Glur-2|Glur2	glutamate receptor, ionotropic, AMPA2 (alpha 2)	protein-coding
mm_60737.1	chr7	45439846	45439852	+	1	NA	intron (NM_030678, intron 4 of 15)	intron (NM_030678, intron 4 of 15)	5010	NM_030678	14936	Mm.275654	NM_030678	ENSMUSG00000003865	Gys1	Gys3|MGS	glycogen synthase 1, muscle	protein-coding
mm_27814.1	chr3	78594572	78594617	-	1	NA	Intergenic	Intergenic	550293	NM_001310536	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_21629.1	chr2	164277268	164277292	-	1	NA	exon (NM_009300, exon 2 of 3)	exon (NM_009300, exon 2 of 3)	1027	NM_009300	20941	Mm.1286	NM_009300	ENSMUSG00000016998	Svs4	SVS-IV|Svp-2|Svp-4|Svp2|Svp4	seminal vesicle secretory protein 4	protein-coding
mm_112183.1	chr12	113422236	113422271	-	1	NA	Intergenic	Intergenic	-67312	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_4969.1	chr1	191281468	191281479	+	1	NA	Intergenic	Intergenic	36645	NM_025424	66208	Mm.46444	NM_025424	ENSMUSG00000037499	Nenf	1110060M21Rik|SCIRP10|Spuf	neuron derived neurotrophic factor	protein-coding
mm_50076.1	chr6	41339819	41339851	+	1	NA	Intergenic	Intergenic	-14270	NM_001038996	436522	Mm.443385	NM_001038996	ENSMUSG00000071521	Try10	-	trypsin 10	protein-coding
mm_159498.1	chr4	43631798	43631798	+	1	NA	promoter-TSS (NM_173788)	promoter-TSS (NM_173788)	-137	NM_173788	230103	Mm.103477	NM_173788	ENSMUSG00000028469	Npr2	GC-B|GC-B2|GC-B3|cn|mNPR-B|pwe	natriuretic peptide receptor 2	protein-coding
mm_115810.1	chr13	19395795	19395795	-	1	NA	promoter-TSS (NM_024270)	promoter-TSS (NM_024270)	18	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_68410.1	chr7	109637423	109637436	-	1	NA	Intergenic	Intergenic	-20282	NM_029811	76954	Mm.252009	NM_029811	ENSMUSG00000031024	St5	2010004M01Rik|2610305K15Rik	suppression of tumorigenicity 5	protein-coding
mm_107123.1	chr12	19288479	19288524	+	1	NA	Intergenic	CpG	773991	NM_001201330	236366	Mm.352227	NM_001033157	ENSMUSG00000073197	5730507C01Rik	-	RIKEN cDNA 5730507C01 gene	protein-coding
mm_27141.1	chr3	32616674	32616689	-	1	NA	promoter-TSS (NM_013531)	promoter-TSS (NM_013531)	-146	NM_013531	14696	Mm.139192	NM_013531	ENSMUSG00000027669	Gnb4	6720453A21Rik|G(beta)4	guanine nucleotide binding protein (G protein), beta 4	protein-coding
mm_12361.1	chr2	69749939	69749951	+	1	NA	exon (NM_001081086, exon 14 of 14)	exon (NM_001081086, exon 14 of 14)	26857	NM_001081086	228005	Mm.11815	NM_001081086	ENSMUSG00000042133	Ppig	AU019516|AU022200|B230312B02Rik|CYP|SRCyp	peptidyl-prolyl isomerase G (cyclophilin G)	protein-coding
mm_6359.1	chr1	72146899	72146908	-	1	NA	Intergenic	Intergenic	65404	NM_001005423	381269	Mm.422636	NM_001005423	ENSMUSG00000039395	Mreg	Gm974|Wdt2|dsu	melanoregulin	protein-coding
mm_42345.1	chr5	114911012	114911022	+	1	NA	exon (NM_011854, exon 6 of 6)	exon (NM_011854, exon 6 of 6)	-12223	NM_145209	231655	Mm.95479	NM_145209	ENSMUSG00000041827	Oasl1	7530414C13Rik|oasl9	2'-5' oligoadenylate synthetase-like 1	protein-coding
mm_100258.1	chr11	117332278	117332284	+	1	NA	promoter-TSS (NM_001113488)	promoter-TSS (NM_001113488)	-32	NM_001113488	53860	Mm.38450	NM_017380	ENSMUSG00000059248	Sept9	MSF1|Msf|PNUTL4|Sint1	septin 9	protein-coding
mm_46081.1	chr5	92328043	92328065	-	1	NA	promoter-TSS (NM_008599)	promoter-TSS (NM_008599)	25	NM_008599	17329	Mm.766	NM_008599	ENSMUSG00000029417	Cxcl9	BB139920|CMK|Mig|MuMIG|Scyb9|crg-10	chemokine (C-X-C motif) ligand 9	protein-coding
mm_51694.1	chr6	86547958	86548007	+	1	NA	intron (NR_037960, intron 3 of 4)	intron (NR_037960, intron 3 of 4)	20581	NR_037961	72012	Mm.349174	NR_037960	ENSMUSG00000097048	1600020E01Rik	-	RIKEN cDNA 1600020E01 gene	ncRNA
mm_84144.1	chr9	59393196	59393218	-	1	NA	3' UTR (NM_019927, exon 14 of 14)	3' UTR (NM_019927, exon 14 of 14)	-39699	NM_175325	102774	Mm.200714	NM_175325	ENSMUSG00000025235	Bbs4	AW537059|AW742241|D9Ertd464e	Bardet-Biedl syndrome 4 (human)	protein-coding
mm_72937.1	chr8	91363262	91363266	+	1	NA	intron (NM_011936, intron 1 of 8)	intron (NM_011936, intron 1 of 8)	49739	NM_011936	26383	Mm.4375	NM_011936	ENSMUSG00000055932	Fto	AW743446|mKIAA1752	fat mass and obesity associated	protein-coding
mm_69108.1	chr7	127021206	127021216	-	1	NA	promoter-TSS (NM_001102563)	promoter-TSS (NM_001102563)	0	NM_001102563	69017	Mm.392047	NM_001102563	ENSMUSG00000045114	Prrt2	1500031I19Rik|AI195361|DSPB3	proline-rich transmembrane protein 2	protein-coding
mm_11513.1	chr2	32587058	32587123	+	1	NA	promoter-TSS (NM_011373)	promoter-TSS (NM_011373)	12	NM_011373	20448	Mm.27446	NM_011373	ENSMUSG00000079442	St6galnac4	SIAT7-D|ST6GalNAcIV|Siat7d	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 4	protein-coding
mm_19511.1	chr2	93957041	93957054	-	1	NA	promoter-TSS (NM_001145034)	promoter-TSS (NM_001145034)	53	NM_001145034	620695	Mm.482106	NM_001145034	ENSMUSG00000087006	Gm13889	Ag2|OTTMUSG00000014994	predicted gene 13889	protein-coding
mm_154081.1	chr19	56617423	56617425	-	1	NA	Intergenic	(CTG)n|Simple_repeat|Simple_repeat	69163	NM_025811	66866	Mm.46346	NM_025811	ENSMUSG00000025078	Nhlrc2	1200003G01Rik|AI835049|AV002846|AW496455	NHL repeat containing 2	protein-coding
mm_56100.1	chr6	87459270	87459293	-	1	NA	non-coding (NR_104483, exon 11 of 11)	non-coding (NR_104483, exon 11 of 11)	30287	NM_009756	12154	Mm.483321	NM_009756	ENSMUSG00000030046	Bmp10	-	bone morphogenetic protein 10	protein-coding
mm_40956.1	chr5	76928345	76928376	+	1	NA	intron (NM_172146, intron 1 of 10)	intron (NM_172146, intron 1 of 10)	-22846	NM_173765	231326	Mm.39271	NM_173765	ENSMUSG00000055923	Aasdh	A230062G08Rik|A830035E16|Acsf4|U26	aminoadipate-semialdehyde dehydrogenase	protein-coding
mm_85479.1	chr9	105960678	105960688	-	1	NA	promoter-TSS (NM_001167923)	promoter-TSS (NM_001167923)	-40	NM_001167923	665033	Mm.39826	NM_001167923	ENSMUSG00000091345	Col6a5	Col29a1|EG665033|Gm7455	collagen, type VI, alpha 5	protein-coding
mm_12779.1	chr2	79329182	79329221	+	1	NA	3' UTR (NM_010576, exon 28 of 28)	3' UTR (NM_010576, exon 28 of 28)	73775	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D|Itga4B	integrin alpha 4	protein-coding
mm_55795.1	chr6	82751867	82751880	-	1	NA	intron (NM_013820, intron 2 of 17)	intron (NM_013820, intron 2 of 17)	22581	NM_013820	15277	Mm.255848	NM_013820	ENSMUSG00000000628	Hk2	AI642394|HKII	hexokinase 2	protein-coding
mm_108146.1	chr12	76255454	76255472	+	1	NA	5' UTR (NM_138745, exon 1 of 28)	5' UTR (NM_138745, exon 1 of 28)	231	NM_138745	108156	Mm.29584	NM_138745	ENSMUSG00000021048	Mthfd1	Dcs|E430024A07Rik|Mthfd	methylenetetrahydrofolate dehydrogenase (NADP+ dependent), methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthase	protein-coding
mm_89641.1	chr10	96630008	96630011	+	1	NA	Intergenic	Intergenic	13008	NM_007569	12226	Mm.23811	NM_007569	ENSMUSG00000036478	Btg1	AI426953|AW546738	B cell translocation gene 1, anti-proliferative	protein-coding
mm_29966.1	chr3	133467744	133467756	-	1	NA	exon (NM_001346736, exon 12 of 12)	exon (NM_001346736, exon 12 of 12)	76640	NM_001346736	214133	Mm.347816	NM_145989	ENSMUSG00000040943	Tet2	Ayu17-449|E130014J05Rik|mKIAA1546	tet methylcytosine dioxygenase 2	protein-coding
mm_142013.1	chr17	35200444	35200455	-	1	NA	exon (NM_013693, exon 4 of 4)	exon (NM_013693, exon 4 of 4)	1558	NM_013693	21926	Mm.1293	NM_013693	ENSMUSG00000024401	Tnf	DIF|TNF-a|TNF-alpha|TNFSF2|TNFalpha|Tnfa|Tnfsf1a|Tnlg1f	tumor necrosis factor	protein-coding
mm_75487.1	chr8	48843663	48843684	-	1	NA	Intergenic	CpG	-168983	NM_011857	23965	Mm.42191	NM_011857	ENSMUSG00000031561	Tenm3	2610100B16Rik|Odz1|Odz3|Ten-m3|mKIAA1455	teneurin transmembrane protein 3	protein-coding
mm_12347.1	chr2	69749004	69749018	+	1	NA	exon (NM_001081086, exon 13 of 14)	exon (NM_001081086, exon 13 of 14)	25923	NM_001081086	228005	Mm.11815	NM_001081086	ENSMUSG00000042133	Ppig	AU019516|AU022200|B230312B02Rik|CYP|SRCyp	peptidyl-prolyl isomerase G (cyclophilin G)	protein-coding
mm_151091.1	chr19	47731775	47731797	+	1	NA	promoter-TSS (NM_026377)	promoter-TSS (NM_026377)	30	NM_026377	67788	Mm.181610	NM_026377	ENSMUSG00000025066	Sfr1	6330577E15Rik|Meir5	SWI5 dependent recombination repair 1	protein-coding
mm_112549.1	chr13	12395363	12395415	+	1	NA	promoter-TSS (NM_144835)	promoter-TSS (NM_144835)	14	NM_144835	217995	Mm.171186	NM_144835	ENSMUSG00000050244	Heatr1	AA517551|B130016L12Rik|BC019693	HEAT repeat containing 1	protein-coding
mm_127600.1	chr15	102401934	102401936	+	1	NA	Intergenic	Intergenic	-4381	NM_013672	20683	Mm.4618	NM_013672	ENSMUSG00000001280	Sp1	1110003E12Rik|AA450830|AI845540|Sp1-1	trans-acting transcription factor 1	protein-coding
mm_74726.1	chr8	17535230	17535240	-	1	NA	5' UTR (NM_053171, exon 1 of 70)	5' UTR (NM_053171, exon 1 of 70)	150	NM_053171	94109	Mm.436988	NM_053171	ENSMUSG00000060924	Csmd1	B930082H09|mKIAA1890	CUB and Sushi multiple domains 1	protein-coding
mm_83056.1	chr9	37545168	37545188	-	1	NA	TTS (NM_020518)	TTS (NM_020518)	5923	NM_020518	57276	Mm.27478	NM_020518	ENSMUSG00000001943	Vsig2	1190004B15Rik|2210413P10Rik|AU040484|CTX|Ctm	V-set and immunoglobulin domain containing 2	protein-coding
mm_147307.1	chr18	39734958	39734963	-	1	NA	Intergenic	Intergenic	-38537	NM_011033	18459	Mm.9493	NM_011033	ENSMUSG00000051732	Pabpc2	Pabp|Pabp+|Pabp2	poly(A) binding protein, cytoplasmic 2	protein-coding
mm_83292.1	chr9	43200228	43200236	-	1	NA	intron (NM_011139, intron 1 of 12)	intron (NM_011139, intron 1 of 12)	5523	NM_011139	18988	Mm.436650	NM_011139	ENSMUSG00000032015	Pou2f3	Epoc-1|Oct-11a|Oct11|Otf-11|Otf11|Skin|Skin-1a|Skn-1a|Skn-li	POU domain, class 2, transcription factor 3	protein-coding
mm_162700.1	chr10	21145158	21145166	+	1	NA	exon (NM_001198914, exon 10 of 16)	exon (NM_001198914, exon 10 of 16)	15822	NM_001198914	17863	Mm.52109	NM_010848	ENSMUSG00000019982	Myb	AI550390|M16449|c-myb	myeloblastosis oncogene	protein-coding
mm_6575.1	chr1	75216439	75216450	-	1	NA	TTS (NM_011494)	TTS (NM_011494)	2850	NM_001313723	22145	Mm.1155	NM_009447	ENSMUSG00000026202	Tuba4a	M[a]4|Tuba4	tubulin, alpha 4A	protein-coding
mm_169497.1	chr14	76495014	76495014	-	1	NA	intron (NM_001177751, intron 1 of 2)	intron (NM_001177751, intron 1 of 2)	6578	NM_001177751	21807	Mm.153272	NM_009366	ENSMUSG00000022010	Tsc22d1	AA589566|AW105905|Egr5|TSC-22|Tgfb1i4|Tsc|Tsc22	TSC22 domain family, member 1	protein-coding
mm_119529.1	chr14	47649103	47649120	+	1	NA	promoter-TSS (NM_001293636)	promoter-TSS (NM_001293636)	-200	NM_001347527	16709	Mm.3110	NM_008477	ENSMUSG00000021843	Ktn1	-	kinectin 1	protein-coding
mm_83836.1	chr9	54237260	54237266	-	1	NA	Intergenic	Intergenic	-43821	NM_007810	13075	Mm.5199	NM_007810	ENSMUSG00000032274	Cyp19a1	Ar|ArKO|Cyp19|Int-5|Int5|p450arom	cytochrome P450, family 19, subfamily a, polypeptide 1	protein-coding
mm_100087.1	chr11	115475973	115475976	+	1	NA	exon (NM_177778, exon 1 of 3)	exon (NM_177778, exon 1 of 3)	297	NM_177778	276905	Mm.38019	NM_177778	ENSMUSG00000057219	Armc7	A630084C13|BC023126	armadillo repeat containing 7	protein-coding
mm_19070.1	chr2	77706063	77706073	-	1	NA	intron (NM_178723, intron 3 of 9)	B4A|SINE|B4	-2796	NM_001113399	241494	Mm.490320	NM_178723	ENSMUSG00000027016	Zfp385b	B830010L13Rik|C130013B13Rik|Zfp533|Znf385b	zinc finger protein 385B	protein-coding
mm_2861.1	chr1	131696658	131696668	+	1	NA	intron (NM_001311096, intron 1 of 4)	intron (NM_001311096, intron 1 of 4)	7968	NM_001311096	226421	Mm.44508	NM_145509	ENSMUSG00000052688	Rab7b	5430435G22Rik	RAB7B, member RAS oncogene family	protein-coding
mm_147944.1	chr18	66291771	66291840	-	1	NA	promoter-TSS (NM_178793)	promoter-TSS (NM_178793)	33	NM_178793	320924	Mm.442049	NM_178793	ENSMUSG00000046318	Ccbe1	4933426F18Rik|9430093N24Rik|mKIAA1983	collagen and calcium binding EGF domains 1	protein-coding
mm_76855.1	chr8	105349251	105349269	-	1	NA	5' UTR (NM_001081332, exon 1 of 16)	5' UTR (NM_001081332, exon 1 of 16)	1002	NM_001081332	277973	Mm.334766	NM_001081332	ENSMUSG00000014786	Slc9a5	Gm696	solute carrier family 9 (sodium/hydrogen exchanger), member 5	protein-coding
mm_77943.1	chr9	7357865	7357884	+	1	NA	exon (NM_008605, exon 9 of 10)	exon (NM_008605, exon 9 of 10)	10500	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_74059.1	chr8	122356237	122356245	+	1	NA	TTS (NM_133202)	TTS (NM_133202)	4505	NM_133202	170732	Mm.154808	NM_133202	ENSMUSG00000039079	Trhr2	TRH-R2	thyrotropin releasing hormone receptor 2	protein-coding
mm_136394.1	chr16	93150441	93150444	-	1	NA	Intergenic	Intergenic	202747	NR_040486	69857	Mm.81192	NR_040486	ENSMUSG00000100277	1810053B23Rik	1810008L18Rik|1810056K14Rik	RIKEN cDNA 1810053B23 gene	ncRNA
mm_75071.1	chr8	33843546	33843556	-	1	NA	intron (NM_001042674, intron 4 of 7)	intron (NM_001042674, intron 4 of 7)	86312	NM_019733	19663	Mm.323997	NM_019733	ENSMUSG00000031586	Rbpms	2010300K22Rik|2700019M19Rik|AU017537|RBP-MS|hermes	RNA binding protein gene with multiple splicing	protein-coding
mm_94544.1	chr11	9193416	9193428	+	1	NA	intron (NM_178259, intron 1 of 61)	intron (NM_178259, intron 1 of 61)	1480	NM_178259	268379	Mm.39270	NM_178259	ENSMUSG00000004668	Abca13	9830132L24|A930002G16Rik|AI956815	ATP-binding cassette, sub-family A (ABC1), member 13	protein-coding
mm_48266.1	chr5	137921613	137921628	-	1	NA	promoter-TSS (NM_007819)	promoter-TSS (NM_007819)	-1	NM_007819	13113	Mm.289886	NM_007819	ENSMUSG00000029727	Cyp3a13	IIIAm2	cytochrome P450, family 3, subfamily a, polypeptide 13	protein-coding
mm_61117.1	chr7	54835778	54835786	+	1	NA	5' UTR (NM_178705, exon 1 of 12)	5' UTR (NM_178705, exon 1 of 12)	537	NM_178705	233271	Mm.387344	NM_178705	ENSMUSG00000063297	Luzp2	9330154K17Rik|D130073E01	leucine zipper protein 2	protein-coding
mm_66878.1	chr7	57509996	57510056	-	1	NA	promoter-TSS (NM_176942)	promoter-TSS (NM_176942)	-17	NM_176942	110886	Mm.273114	NM_176942	ENSMUSG00000055078	Gabra5	A230018I05Rik	gamma-aminobutyric acid (GABA) A receptor, subunit alpha 5	protein-coding
mm_83011.1	chr9	36779839	36779850	-	1	NA	3' UTR (NM_001199494, exon 11 of 11)	3' UTR (NM_001199494, exon 11 of 11)	-12266	NM_008408	16430	Mm.2863	NM_008408	ENSMUSG00000032116	Stt3a	AA408947|BB081708|Itm1	STT3, subunit of the oligosaccharyltransferase complex, homolog A (S. cerevisiae)	protein-coding
mm_58848.1	chr7	16843176	16843211	+	1	NA	5' UTR (NM_178900, exon 1 of 18)	5' UTR (NM_178900, exon 1 of 18)	128	NM_178900	101540	Mm.1881	NM_178900	ENSMUSG00000041187	Prkd2	AI325941|PKD2	protein kinase D2	protein-coding
mm_109040.1	chr12	104214539	104214549	+	1	NA	promoter-TSS (NM_001168295)	promoter-TSS (NM_001168295)	0	NM_001168294	238393	Mm.483584	NM_001033335	ENSMUSG00000066363	Serpina3f	2A1|BC049975	serine (or cysteine) peptidase inhibitor, clade A, member 3F	protein-coding
mm_78075.1	chr9	15538777	15538823	+	1	NA	intron (NM_133214, intron 2 of 2)	intron (NM_133214, intron 2 of 2)	33305	NM_133214	170748	Mm.86572	NM_133214	ENSMUSG00000058173	Smco4	Fn5	single-pass membrane protein with coiled-coil domains 4	protein-coding
mm_51984.1	chr6	92091379	92091389	+	1	NA	promoter-TSS (NM_011630)	promoter-TSS (NM_011630)	-34	NM_011630	22026	Mm.87062	NM_011630	ENSMUSG00000005893	Nr2c2	TAK1|Tr4|mKIAA4145	nuclear receptor subfamily 2, group C, member 2	protein-coding
mm_124078.1	chr14	78644408	78644418	-	1	NA	promoter-TSS (NR_104044)	promoter-TSS (NR_104044)	38	NR_104044	380921	Mm.89591	NM_001081336	ENSMUSG00000034731	Dgkh	5930402B05Rik|D130015C16|DGK	diacylglycerol kinase, eta	protein-coding
mm_62492.1	chr7	101934077	101934190	+	1	NA	promoter-TSS (NM_027053)	promoter-TSS (NM_027053)	-276	NM_001162973	69358	Mm.214841	NM_027053	ENSMUSG00000064307	Lrrc51	1700008D07Rik|Lrtomt	leucine rich repeat containing 51	protein-coding
mm_5682.1	chr1	43163875	43163890	-	1	NA	promoter-TSS (NM_010212)	promoter-TSS (NM_010212)	79	NM_010212	14200	Mm.6799	NM_010212	ENSMUSG00000008136	Fhl2	FHL-2|SLIM-3|SLIM3	four and a half LIM domains 2	protein-coding
mm_23290.1	chr3	52070110	52070159	+	1	NA	intron (NM_001004176, intron 1 of 4)	AmnSINE1|SINE|Deu	34872	NM_001004176	433586	Mm.234972	NM_001004176	ENSMUSG00000061143	Maml3	AV234550|BC049812|Mam-2|mKIAA1816	mastermind like 3 (Drosophila)	protein-coding
mm_95926.1	chr11	58307123	58307143	+	1	NA	promoter-TSS (NM_001040686)	promoter-TSS (NM_001040686)	64	NM_001040686	103836	Mm.41440	NM_182996	ENSMUSG00000037243	Zfp692	AI746306|AI839920|Zfp692-ps|Znf692	zinc finger protein 692	protein-coding
mm_104531.1	chr11	96289526	96289528	-	1	NA	exon (NM_010460, exon 2 of 2)	exon (NM_010460, exon 2 of 2)	2881	NM_010460	15415	Mm.390366	NM_010460	ENSMUSG00000038721	Hoxb7	AI325018|Hox-2.3	homeobox B7	protein-coding
mm_160652.1	chr9	111373548	111373548	+	1	NA	intron (NM_001164659, intron 13 of 21)	intron (NM_001164659, intron 13 of 21)	61809	NM_001164659	320429	Mm.270754	NM_001164659	ENSMUSG00000062296	Trank1	A230061D21Rik|C030048J01Rik|Gm187|Lba1	tetratricopeptide repeat and ankyrin repeat containing 1	protein-coding
mm_86603.1	chr10	13501151	13501190	+	1	NA	exon (NM_001330198, exon 1 of 8)	exon (NM_001330198, exon 1 of 8)	142	NM_025799	66848	Mm.26625	NM_025799	ENSMUSG00000019810	Fuca2	0610025O11Rik|5530401P20Rik	fucosidase, alpha-L- 2, plasma	protein-coding
mm_118502.1	chr14	13670868	13670919	+	1	NA	promoter-TSS (NM_177624)	promoter-TSS (NM_177624)	17	NM_177624	218739	Mm.39919	NM_177624	ENSMUSG00000044772	Sntn	A430083B19Rik	sentan, cilia apical structure protein	protein-coding
mm_25760.1	chr3	123761250	123761299	+	1	NA	Intergenic	Intergenic	-70422	NR_121616	83398	Mm.443908	NM_031186	ENSMUSG00000027977	Ndst3	4921531K01Rik|4930511P15Rik|N-HSST 3|NDST-3	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 3	protein-coding
mm_52768.1	chr6	121137482	121137496	+	1	NA	Intergenic	MTC|LTR|ERVL-MaLR	-6467	NM_001270475	194401	Mm.122399	NM_153396	ENSMUSG00000051586	Mical3	C130040D16Rik|Mical-3|mKIAA1364	microtubule associated monooxygenase, calponin and LIM domain containing 3	protein-coding
mm_130103.1	chr15	89429398	89429441	-	1	NA	non-coding (NR_004843, exon 1 of 27)	non-coding (NR_004843, exon 1 of 27)	508	NR_037154	12651	Mm.485045	NM_007692	ENSMUSG00000022617	Chkb	Chetk|Chkl|Ck|Ck/Ek|Ck/Ek-beta|Ckb|Ckekb|Ek	choline kinase beta	protein-coding
mm_95967.1	chr11	58917947	58917962	+	1	NA	promoter-TSS (NM_138678)	promoter-TSS (NM_138678)	-103	NM_138678	192194	Mm.22540	NM_138678	ENSMUSG00000020490	Btnl10	BUTR-1|Butr1	butyrophilin-like 10	protein-coding
mm_136322.1	chr16	91964667	91964685	-	1	NA	Intergenic	Intergenic	-33046	NM_138597	28080	Mm.41	NM_138597	ENSMUSG00000022956	Atp5o	ATPO|D12Wsu28e|OSCP	ATP synthase, H+ transporting, mitochondrial F1 complex, O subunit	protein-coding
mm_35751.1	chr4	45530753	45530816	-	1	NA	promoter-TSS (NM_001033306)	promoter-TSS (NM_001033306)	44	NM_001033306	230126	Mm.251716	NM_001033306	ENSMUSG00000044813	Shb	BC028832	src homology 2 domain-containing transforming protein B	protein-coding
mm_41149.1	chr5	87929729	87929739	+	1	NA	exon (NM_007786, exon 4 of 5)	exon (NM_007786, exon 4 of 5)	4101	NM_007786	12994	Mm.296303	NM_007786	ENSMUSG00000001622	Csn3	AW208918|CSN10|Csnk	casein kappa	protein-coding
mm_134754.1	chr16	23181595	23181604	-	1	NA	Intergenic	Intergenic	35063	NM_009605	11450	Mm.3969	NM_009605	ENSMUSG00000022878	Adipoq	30kDa|APN|Acdc|Acrp30|Ad|GBP28|adipo|apM1	adiponectin, C1Q and collagen domain containing	protein-coding
mm_37496.1	chr4	123665502	123665513	-	1	NA	promoter-TSS (NR_136925)	promoter-TSS (NR_136925)	-374	NR_136925	102633214	Mm.399387	NR_136925		Gm12925	OTTMUSG00000009214	predicted gene 12925	ncRNA
mm_166069.1	chr4	135152274	135152293	+	1	NA	intron (NM_019732, intron 1 of 5)	CpG	31638	NM_019732	12399	Mm.378894	NM_019732	ENSMUSG00000070691	Runx3	AML2|Cbfa3|Pebp2a3	runt related transcription factor 3	protein-coding
mm_118453.1	chr14	8368236	8368255	+	1	NA	intron (NM_146050, intron 1 of 9)	intron (NM_146050, intron 1 of 9)	10518	NM_146050	18300	Mm.25351	NM_146050	ENSMUSG00000021749	Oit1	2310076N21Rik|AV067083|EF-7|Fam3d	oncoprotein induced transcript 1	protein-coding
mm_48835.1	chr5	149244688	149244698	-	1	NA	Intergenic	Intergenic	-20311	NM_001308462	11690	Mm.19844	NM_009663	ENSMUSG00000060063	Alox5ap	Flap	arachidonate 5-lipoxygenase activating protein	protein-coding
mm_166010.1	chr4	118024593	118024593	-	1	NA	intron (NM_009176, intron 4 of 11)	RMER6A|LTR|ERVK	-94830	NM_001284192	11876	Mm.56897	NM_009711	ENSMUSG00000028539	Artn	neublastin	artemin	protein-coding
mm_109268.1	chr12	109545512	109545526	+	1	NA	TTS (NR_035440).2	TTS (NR_035440).2	121	NR_003633	17263	Mm.289645	NM_144513	ENSMUSG00000021268	Meg3	2900016C05Rik|3110050O07Rik|6330408G06Rik|AI425946|AW108224|D12Bwg1266e|Gtl2|R74756|R75394	maternally expressed 3	ncRNA
mm_121933.1	chr14	23989383	23989386	-	1	NA	intron (NM_001253366, intron 1 of 29)	intron (NM_001253366, intron 1 of 29)	14821	NM_001253375	16531	Mm.343607	NM_010610	ENSMUSG00000063142	Kcnma1	5730414M22Rik|BKCa|MaxiK|Slo|Slo1|mSlo|mSlo1	potassium large conductance calcium-activated channel, subfamily M, alpha member 1	protein-coding
mm_14257.1	chr2	128169751	128169759	+	1	NA	Intergenic	Intergenic	42180	NM_001284410	12125	Mm.141083	NM_009754	ENSMUSG00000027381	Bcl2l11	1500006F24Rik|Bim|Bod|bcl2-L-11	BCL2-like 11 (apoptosis facilitator)	protein-coding
mm_75417.1	chr8	46735552	46735560	-	1	NA	intron (NR_045750, intron 2 of 2)	intron (NR_045750, intron 2 of 2)	3959	NR_045750	100503498	Mm.187358	NR_045750	ENSMUSG00000097534	Gm16675	-	predicted gene, 16675	ncRNA
mm_94734.1	chr11	21048251	21048259	+	1	NA	Intergenic	Intergenic	-43069	NM_023324	67245	Mm.28957	NM_023324	ENSMUSG00000020134	Peli1	2810468L03Rik|A930031K15Rik|AA409794|AI586297|D11Ertd676e	pellino 1	protein-coding
mm_173277.1	chrY	10374956	10374959	+	1	NA	Intergenic	IAPEY_LTR|LTR|ERVK	822891	NM_001199331	100040022	Mm.485767	NM_001199331	ENSMUSG00000095172	Gm20822	-	predicted gene, 20822	protein-coding
mm_65172.1	chr7	19681397	19681467	-	1	NA	promoter-TSS (NM_007385)	promoter-TSS (NM_007385)	28	NM_007385	11425	Mm.477720	NM_007385	ENSMUSG00000074336	Apoc4	Acl|apo-CIV|apoC-IV	apolipoprotein C-IV	protein-coding
mm_45273.1	chr5	64804119	64804149	-	1	NA	intron (NM_008453, intron 1 of 5)	CpG	611	NM_008453	16599	Mm.392759	NM_008453	ENSMUSG00000029178	Klf3	9930027G08Rik|AL024007|Bklf|Tef-2	Kruppel-like factor 3 (basic)	protein-coding
mm_61620.1	chr7	80186699	80186731	+	1	NA	promoter-TSS (NM_013659)	promoter-TSS (NM_013659)	-126	NM_013659	20352	Mm.275909	NM_013659	ENSMUSG00000030539	Sema4b	SemC|Semac|mKIAA1745	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B	protein-coding
mm_25969.1	chr3	132818063	132818067	+	1	NA	intron (NM_001163455, intron 25 of 25)	intron (NM_001163455, intron 25 of 25)	60531	NR_102297	101243624	Mm.306256	NR_102297	ENSMUSG00000106230	Gm29811	-	predicted gene, 29811	ncRNA
mm_1141.1	chr1	60705232	60705249	+	1	NA	Intergenic	Intergenic	-41148	NM_007642	12487	Mm.255003	NM_007642	ENSMUSG00000026012	Cd28	-	CD28 antigen	protein-coding
mm_80977.1	chr9	103183338	103183348	+	1	NA	3' UTR (NM_173781, exon 8 of 8)	3' UTR (NM_173781, exon 8 of 8)	18722	NM_009275	20818	Mm.273053	NM_009275	ENSMUSG00000032553	Srprb	AA409543	signal recognition particle receptor, B subunit	protein-coding
mm_98075.1	chr11	86484648	86484716	+	1	NA	promoter-TSS (NM_029788)	promoter-TSS (NM_029788)	25	NM_029788	76892	Mm.262707	NM_029788	ENSMUSG00000020521	Rnft1	0610013E23Rik|AV007605	ring finger protein, transmembrane 1	protein-coding
mm_134866.1	chr16	28640790	28640824	-	1	NA	intron (NM_010199, intron 2 of 5)	(GA)n|Simple_repeat|Simple_repeat	-40764	NR_030463	751543		NR_030463	ENSMUSG00000076064	Mir690	Mirn690|mir-690|mmu-mir-690	microRNA 690	ncRNA
mm_80105.1	chr9	70370407	70370418	+	1	NA	exon (NM_181072, exon 22 of 28)	exon (NM_181072, exon 22 of 28)	35341	NR_049200	100885839		NR_049200	ENSMUSG00000093763	Mir5626	Gm25590|mir-5626|mmu-mir-5626	microRNA 5626	ncRNA
mm_101300.1	chr11	22286924	22286969	-	1	NA	promoter-TSS (NM_153078)	promoter-TSS (NM_153078)	-151	NM_001252515	216565	Mm.491265	NM_153078	ENSMUSG00000042302	Ehbp1	AF424697|Flj21950|NACSIN	EH domain binding protein 1	protein-coding
mm_145354.1	chr18	56588343	56588359	+	1	NA	promoter-TSS (NM_026099)	promoter-TSS (NM_026099)	3	NM_026099	67343	Mm.87057	NM_026099	ENSMUSG00000032900	Tex43	1700065I17Rik|Tseg7	testis expressed 43	protein-coding
mm_106485.1	chr11	120231579	120231607	-	1	NA	Intergenic	CpG	-1354	NM_001347621	268515	Mm.309498	NM_198423	ENSMUSG00000039741	Bahcc1	B930044J06|BC060615	BAH domain and coiled-coil containing 1	protein-coding
mm_47053.1	chr5	116288979	116288999	-	1	NA	promoter-TSS (NM_177759)	promoter-TSS (NM_177759)	-4	NM_177759	269693	Mm.10946	NM_177759	ENSMUSG00000043913	Ccdc60	AU018954|C130098D09	coiled-coil domain containing 60	protein-coding
mm_111714.1	chr12	103707306	103707314	-	1	NA	Intergenic	Intergenic	-11781	NM_026687	68348	Mm.20149	NM_026687	ENSMUSG00000021081	Serpina1f	0610012A11Rik|AI327419|Serpina2|epserin	serine (or cysteine) peptidase inhibitor, clade A, member 1F	protein-coding
mm_103499.1	chr11	76571625	76571636	-	1	NA	promoter-TSS (NM_198895)	promoter-TSS (NM_198895)	-246	NM_198895	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_117333.1	chr13	68999519	68999565	-	1	NA	promoter-TSS (NM_153534)	promoter-TSS (NM_153534)	-1	NM_153534	210044	Mm.390617	NM_153534	ENSMUSG00000021536	Adcy2	mKIAA1060	adenylate cyclase 2	protein-coding
mm_55974.1	chr6	85865883	85865894	-	1	NA	3' UTR (NM_053096, exon 3 of 3)	3' UTR (NM_053096, exon 3 of 3)	3249	NM_053096	93673	Mm.24251	NM_053096	ENSMUSG00000033634	Nat8f2	Cml2	N-acetyltransferase 8 (GCN5-related) family member 2	protein-coding
mm_142145.1	chr17	36006325	36006341	-	1	NA	3' UTR (NM_008207, exon 6 of 6)	3' UTR (NM_008207, exon 6 of 6)	11829	NR_015618	77810	Mm.483143	NR_015618		A930015D03Rik	-	RIKEN cDNA A930015D03 gene	ncRNA
mm_18392.1	chr2	60209782	60209816	-	1	NA	promoter-TSS (NM_020575)	promoter-TSS (NM_020575)	-137	NM_020575	57438	Mm.260635	NM_020575	ENSMUSG00000026977	March7	Axo|Axot|Gtrgeo17	membrane-associated ring finger (C3HC4) 7	protein-coding
mm_37493.1	chr4	123613822	123613833	-	1	NA	intron (NM_001199136, intron 1 of 97)	intron (NM_001199136, intron 1 of 97)	-2593	NR_105824	102465214		NR_105824	ENSMUSG00000099005	Mir6398	Gm27657|mmu-mir-6398	microRNA 6398	ncRNA
mm_48022.1	chr5	136217366	136217372	-	1	NA	TTS (NM_018825)	TTS (NM_018825)	-18415	NM_025774	66801	Mm.425295	NM_025774	ENSMUSG00000039737	Prkrip1	8430424D23Rik|C114	Prkr interacting protein 1 (IL11 inducible)	protein-coding
mm_84266.1	chr9	62666047	62666062	-	1	NA	Intergenic	Intergenic	-11801	NM_176922	319480	Mm.34883	NM_176922	ENSMUSG00000032243	Itga11	4732459H24Rik	integrin alpha 11	protein-coding
mm_41626.1	chr5	96963166	96963192	+	1	NA	Intergenic	B1F|SINE|Alu	-34510	NM_080708	140780	Mm.281490	NM_080708	ENSMUSG00000034663	Bmp2k	4933417M22Rik|AA673486|AV128808|BIKE	BMP2 inducible kinase	protein-coding
mm_110059.1	chr12	21286177	21286268	-	1	NA	promoter-TSS (NM_008403)	promoter-TSS (NM_008403)	15	NM_008403	16413	Mm.273333	NM_008403	ENSMUSG00000062352	Itgb1bp1	AI449260|AU019480|Icap1	integrin beta 1 binding protein 1	protein-coding
mm_77981.1	chr9	7871977	7871987	+	1	NA	intron (NM_007464, intron 1 of 8)	B1F2|SINE|Alu	1188	NM_007464	11796	Mm.2026	NM_007464	ENSMUSG00000032000	Birc3	AW107670|Api1|Api2|Birc2|C-IAP2|HIAP2|IAP1|IAP2|MIAP1|MIAP2|MIHB|MIHC|RNF49|cIAP-1|cIAP-2|cIAP1|cIAP2	baculoviral IAP repeat-containing 3	protein-coding
mm_61755.1	chr7	82771389	82771440	+	1	NA	intron (NM_175317, intron 18 of 19)	C-rich|Low_complexity|Low_complexity	-15770	NR_046004	77800	Mm.444811	NR_046004	ENSMUSG00000086690	4933406J10Rik	A930009F24Rik	RIKEN cDNA 4933406J10 gene	ncRNA
mm_143924.1	chr17	85618573	85618581	-	1	NA	promoter-TSS (NR_015387)	promoter-TSS (NR_015387)	-181	NR_038082	100043902	Mm.150838	NR_015385	ENSMUSG00000093460	Six3os1	D17Mgi26|E130112H22Rik|Rncr1|Six3os	SIX homeobox 3, opposite strand 1	ncRNA
mm_5564.1	chr1	38836677	38836698	-	1	NA	Intergenic	CpG	-15472	NM_001029878	381338	Mm.487137	NM_028403	ENSMUSG00000048814	Lonrf2	2900060P06Rik|AI851349	LON peptidase N-terminal domain and ring finger 2	protein-coding
mm_159882.1	chr6	18866273	18866273	+	1	NA	promoter-TSS (NM_029202)	promoter-TSS (NM_029202)	-45	NM_029202	75196	Mm.67665	NM_029202	ENSMUSG00000029517	Ankrd7	4930532L20Rik|AV278427	ankyrin repeat domain 7	protein-coding
mm_44466.1	chr5	23386886	23386924	-	1	NA	Intergenic	Intergenic	47448	NR_040469	269630	Mm.425231	NR_040469	ENSMUSG00000073147	5031425E22Rik	-	RIKEN cDNA 5031425E22 gene	ncRNA
mm_57846.1	chr6	129467652	129467669	-	1	NA	exon (NM_020008, exon 4 of 6)	exon (NM_020008, exon 4 of 6)	5119	NM_001309637	56644	Mm.239516	NM_020008	ENSMUSG00000079293	Clec7a	BGR|Clecsf12|beta-GR	C-type lectin domain family 7, member a	protein-coding
mm_159747.1	chr5	75156245	75156245	+	1	NA	promoter-TSS (NM_001083316)	promoter-TSS (NM_001083316)	79	NM_001083316	18595	Mm.221403	NM_011058	ENSMUSG00000029231	Pdgfra	AI115593|CD140a|Pdgfr-2	platelet derived growth factor receptor, alpha polypeptide	protein-coding
mm_30528.1	chr4	3090474	3090497	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	-81598	NM_001167534	100312470	Mm.480297	NM_001167534	ENSMUSG00000094798	Vmn1r2	Gm11776|OTTMUSG00000004179	vomeronasal 1 receptor 2	protein-coding
mm_77951.1	chr9	7558449	7558465	+	1	NA	promoter-TSS (NM_008611)	promoter-TSS (NM_008611)	28	NM_008611	17394	Mm.16415	NM_008611	ENSMUSG00000005800	Mmp8	BB138268	matrix metallopeptidase 8	protein-coding
mm_25704.1	chr3	122419986	122420000	+	1	NA	5' UTR (NM_013867, exon 1 of 12)	5' UTR (NM_013867, exon 1 of 12)	213	NM_013867	29815	Mm.45815	NM_013867	ENSMUSG00000028121	Bcar3	AI131758|AND-34	breast cancer anti-estrogen resistance 3	protein-coding
mm_126827.1	chr15	88862179	88862193	+	1	NA	promoter-TSS (NM_145478)	promoter-TSS (NM_145478)	-8	NM_145478	223775	Mm.400129	NM_145478	ENSMUSG00000035828	Pim3	BC026639|Kid1	proviral integration site 3	protein-coding
mm_168288.1	chr11	101604842	101604846	+	1	NA	Intergenic	Intergenic	-5856	NM_001256318	666331	Mm.303457	NM_001256318		LOC666331	-	uncharacterized LOC666331	protein-coding
mm_57688.1	chr6	128513835	128513845	-	1	NA	exon (NM_007376, exon 11 of 36)	exon (NM_007376, exon 11 of 36)	12880	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_18418.1	chr2	60722532	60722542	-	1	NA	promoter-TSS (NM_001159564)	promoter-TSS (NM_001159564)	66	NM_001159564	16420	Mm.98193	NM_021359	ENSMUSG00000026971	Itgb6	2210409C20Rik|4831415H04Rik	integrin beta 6	protein-coding
mm_151480.1	chr19	58676231	58676231	+	1	NA	exon (NM_026925, exon 7 of 13)	exon (NM_026925, exon 7 of 13)	5866	NM_026925	69060	Mm.20407	NM_026925	ENSMUSG00000046008	Pnlip	1810007A24Rik|PL|PTL	pancreatic lipase	protein-coding
mm_82127.1	chr9	123510050	123510069	+	1	NA	intron (NM_013860, intron 2 of 7)	intron (NM_013860, intron 2 of 7)	-19823	NM_030692	83493	Mm.273671	NM_030692	ENSMUSG00000025240	Sacm1l	SAC1|Sac1p|mKIAA0851	SAC1 suppressor of actin mutations 1-like (yeast)	protein-coding
mm_169962.1	chr16	94855255	94855274	+	1	NA	intron (NM_001025584, intron 2 of 4)	BGLII|LTR|ERVK	1426	NM_001025590	16522	Mm.328720	NM_010606	ENSMUSG00000043301	Kcnj6	BIR1|GIRK2|KATP2|KCNJ7|Kir3.2|weaver|wv	potassium inwardly-rectifying channel, subfamily J, member 6	protein-coding
mm_110411.1	chr12	45573310	45573310	-	1	NA	Intergenic	Intergenic	-498827	NM_144552	217517	Mm.285400	NM_144552	ENSMUSG00000046314	Stxbp6	BC024598|C85317	syntaxin binding protein 6 (amisyn)	protein-coding
mm_123147.1	chr14	57099332	57099347	-	1	NA	3' UTR (NM_008125, exon 2 of 2)	3' UTR (NM_008125, exon 2 of 2)	5363	NM_008125	14619	Mm.390683	NM_008125	ENSMUSG00000046352	Gjb2	AI325222|Cnx26|Cx26|Gjb-2	gap junction protein, beta 2	protein-coding
mm_37855.1	chr4	132220468	132220471	-	1	NA	TTS (NM_020273)	TTS (NM_020273)	120	NR_036572	664903	Mm.425212	NR_036572		Rps15a-ps4	Gm13253|Lethe|OTTMUSG00000011114	ribosomal protein S15A, pseudogene 4	pseudo
mm_167681.1	chr9	80288109	80288133	+	1	NA	exon (NM_001039546, exon 26 of 33)	exon (NM_001039546, exon 26 of 33)	123087	NM_001039546	17920	Mm.4040	NM_008662	ENSMUSG00000033577	Myo6	BC029719|Tlc|sv	myosin VI	protein-coding
mm_88270.1	chr10	74967128	74967162	+	1	NA	promoter-TSS (NM_010311)	promoter-TSS (NM_010311)	-86	NM_010311	14687	Mm.32595	NM_010311	ENSMUSG00000040009	Gnaz	AI847979|Gz	guanine nucleotide binding protein, alpha z subunit	protein-coding
mm_167801.1	chr9	123927946	123927957	-	1	NA	Intergenic	Intergenic	40741	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_7539.1	chr1	124485677	124485679	-	1	NA	Intergenic	Intergenic	-440119	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_77996.1	chr9	8900410	8900425	+	1	NA	5' UTR (NM_008829, exon 1 of 8)	5' UTR (NM_008829, exon 1 of 8)	584	NM_008829	18667	Mm.12798	NM_008829	ENSMUSG00000031870	Pgr	9930019P03Rik|BB114106|ENSMUSG00000074510|NR3C3|PR|PR-A|PR-B	progesterone receptor	protein-coding
mm_24085.1	chr3	87971072	87971089	+	1	NA	promoter-TSS (NM_016701)	promoter-TSS (NM_016701)	-13	NM_016701	18008	Mm.331129	NM_016701	ENSMUSG00000004891	Nes	AA166324|C78523|ESTM46	nestin	protein-coding
mm_14499.1	chr2	132028345	132028354	+	1	NA	intron (NM_175445, intron 1 of 10)	intron (NM_175445, intron 1 of 10)	1639	NM_175445	215653	Mm.204737	NM_175445	ENSMUSG00000027339	Rassf2	3830431H01Rik|9030412M04Rik|AI852669|AW495050	Ras association (RalGDS/AF-6) domain family member 2	protein-coding
mm_153263.1	chr19	36926028	36926056	-	1	NA	promoter-TSS (NM_001080706)	promoter-TSS (NM_001080706)	-37	NM_001080706	107182	Mm.295062	NM_001080706	ENSMUSG00000040565	Btaf1	AI414500|AI447930|E430027O22Rik|TAF170	B-TFIID TATA-box binding protein associated factor 1	protein-coding
mm_107361.1	chr12	32839236	32839247	+	1	NA	exon (NM_021524, exon 6 of 11)	exon (NM_021524, exon 6 of 11)	15125	NR_045032	100504486	Mm.440246	NR_045032		Gdap10	Gdap-ps	ganglioside-induced differentiation-associated-protein 10	ncRNA
mm_102513.1	chr11	60808820	60808830	-	1	NA	intron (NM_009171, intron 1 of 11)	intron (NM_009171, intron 1 of 11)	2440	NM_009171	20425	Mm.364956	NM_009171	ENSMUSG00000020534	Shmt1	AI324848|AI385541|C81125|Shmt|mshmt|mshmt1|mshmt2	serine hydroxymethyltransferase 1 (soluble)	protein-coding
mm_108134.1	chr12	76086720	76086749	+	1	NA	intron (NM_001005510, intron 99 of 115)	intron (NM_001005510, intron 99 of 115)	90525	NM_010157	13983	Mm.2561	NM_010157	ENSMUSG00000021055	Esr2	ER[b]|ERbeta|Estrb	estrogen receptor 2 (beta)	protein-coding
mm_158085.1	chrX	101267354	101267375	-	1	NA	exon (NM_001308535, exon 3 of 8)	exon (NM_001308535, exon 3 of 8)	891	NM_001308535	16186	Mm.2923	NM_013563	ENSMUSG00000031304	Il2rg	CD132|[g]c|gamma(c)|gc|p64	interleukin 2 receptor, gamma chain	protein-coding
mm_40207.1	chr5	37047028	37047044	+	1	NA	Intergenic	Intergenic	-3821	NM_178394	76071	Mm.85280	NM_178394	ENSMUSG00000063646	Jakmip1	5830437M04Rik|C330021K24Rik|Gababrbp|Marlin-1	janus kinase and microtubule interacting protein 1	protein-coding
mm_92172.1	chr10	67585963	67585969	-	1	NA	Intergenic	Intergenic	-37011	NM_001005419	211488	Mm.297250	NM_001005419	ENSMUSG00000057134	Ado	Gm237	2-aminoethanethiol (cysteamine) dioxygenase	protein-coding
mm_90153.1	chr10	118204823	118204827	+	1	NA	promoter-TSS (NM_016971)	promoter-TSS (NM_016971)	-139	NM_016971	50929	Mm.103585	NM_016971	ENSMUSG00000074695	Il22	IL-22|IL-22a|ILTIFa|Iltif	interleukin 22	protein-coding
mm_108619.1	chr12	85598241	85598275	+	1	NA	promoter-TSS (NM_001205052)	promoter-TSS (NM_001205052)	-847	NM_001205052	81703	Mm.103560	NM_030887	ENSMUSG00000034271	Jdp2	Jundm2|Jundp2|TIF	Jun dimerization protein 2	protein-coding
mm_126297.1	chr15	79348392	79348407	+	1	NA	promoter-TSS (NM_001304832)	promoter-TSS (NM_001304832)	-3	NM_001304832	17133	Mm.86646	NM_010755	ENSMUSG00000042622	Maff	-	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein F (avian)	protein-coding
mm_51522.1	chr6	83165921	83165977	+	1	NA	promoter-TSS (NM_001198867)	promoter-TSS (NM_001198867)	25	NM_001198867	13191	Mm.6919	NM_007835	ENSMUSG00000031865	Dctn1	AL022633|DAP-150|DP-150|Glued|p150|p150-glued|p150<glued>	dynactin 1	protein-coding
mm_165613.1	chr3	55516358	55516398	+	1	NA	intron (NM_019978, intron 15 of 16)	intron (NM_019978, intron 15 of 16)	54620	NM_001195540	13175	Mm.393242	NM_019978	ENSMUSG00000027797	Dclk1	1700113D08Rik|2810480F11Rik|AI836758|Click-I|Cpg16|Dcamkl1|Dcl|Dclk|mKIAA0369	doublecortin-like kinase 1	protein-coding
mm_111570.1	chr12	101818516	101818540	-	1	NA	intron (NM_011812, intron 1 of 10)	intron (NM_011812, intron 1 of 10)	591	NM_011812	23876	Mm.288381	NM_011812	ENSMUSG00000021186	Fbln5	A55|DANCE|EVEC	fibulin 5	protein-coding
mm_4446.1	chr1	172555933	172555942	+	1	NA	promoter-TSS (NM_177723)	promoter-TSS (NM_177723)	-1	NM_177723	240916	Mm.71940	NM_177723	ENSMUSG00000049598	Vsig8	A030011M19|EG240916	V-set and immunoglobulin domain containing 8	protein-coding
mm_96740.1	chr11	69800775	69800795	+	1	NA	intron (NM_001291104, intron 1 of 5)	intron (NM_001291104, intron 1 of 5)	931	NM_001291104	14166	Mm.269011	NM_010198	ENSMUSG00000042826	Fgf11	Fgf-11|Fhf-3|Fhf3	fibroblast growth factor 11	protein-coding
mm_117870.1	chr13	98890788	98890805	-	1	NA	intron (NM_178716, intron 1 of 23)	intron (NM_178716, intron 1 of 23)	246	NM_001048267	238799	Mm.173286	NM_178716	ENSMUSG00000009470	Tnpo1	AU021749|D13Ertd688e|IPO2|Kpnb2|MIP|MIP1|TRN	transportin 1	protein-coding
mm_154282.1	chr19	60812190	60812208	-	1	NA	intron (NM_001347464, intron 1 of 7)	intron (NM_001347464, intron 1 of 7)	629	NM_001167829	67894	Mm.26148	NM_026437	ENSMUSG00000024993	Fam45a	1810055E12Rik	family with sequence similarity 45, member A	protein-coding
mm_38644.1	chr4	143243271	143243291	-	1	NA	Intergenic	Intergenic	-30572	NM_001256380	110593	Mm.332020	NM_001081355	ENSMUSG00000057637	Prdm2	4833427P12Rik|E330024L24Rik|Gm1033|Gm19732|KMT8|Riz|Riz1|Znfpr1c1	PR domain containing 2, with ZNF domain	protein-coding
mm_99049.1	chr11	99045125	99045129	+	1	NA	intron (NM_010517, intron 1 of 3)	intron (NM_010517, intron 1 of 3)	3867	NM_010517	16010	Mm.233799	NM_010517	ENSMUSG00000017493	Igfbp4	AI875747|Deb2|IGFBP-4	insulin-like growth factor binding protein 4	protein-coding
mm_120801.1	chr14	74746766	74746790	+	1	NA	intron (NM_001285423, intron 8 of 8)	(TG)n|Simple_repeat|Simple_repeat	14481	NM_016903	13885	Mm.38055	NM_016903	ENSMUSG00000021996	Esd	Es-10|Es10|FGH|sid478	esterase D/formylglutathione hydrolase	protein-coding
mm_9543.1	chr1	173912934	173912938	-	1	NA	5' UTR (NM_001301745, exon 1 of 7)	5' UTR (NM_001301745, exon 1 of 7)	110	NM_001301745	381308	Mm.490248	NM_001033450	ENSMUSG00000026536	Ifi211	A730048F03|Ifi205b|Mnda|ifi-205-B	interferon activated gene 211	protein-coding
mm_104707.1	chr11	98018309	98018363	-	1	NA	promoter-TSS (NM_001159320)	promoter-TSS (NM_001159320)	36	NM_001159320	12295	Mm.41252	NM_031173	ENSMUSG00000020882	Cacnb1	CAB1|Cchb1|Cchlb1	calcium channel, voltage-dependent, beta 1 subunit	protein-coding
mm_168714.1	chr12	102695777	102695780	-	1	NA	intron (NM_172584, intron 1 of 9)	intron (NM_172584, intron 1 of 9)	9091	NM_172584	217837	Mm.482192	NM_172584	ENSMUSG00000057963	Itpk1	BC031182	inositol 1,3,4-triphosphate 5/6 kinase	protein-coding
mm_75375.1	chr8	45333190	45333208	-	1	NA	promoter-TSS (NM_133969)	promoter-TSS (NM_133969)	-3	NM_133969	102294	Mm.245297	NM_133969	ENSMUSG00000079057	Cyp4v3	AU043077|AW111961|Cyp4v2	cytochrome P450, family 4, subfamily v, polypeptide 3	protein-coding
mm_82725.1	chr9	25151242	25151252	-	1	NA	5' UTR (NM_020586, exon 1 of 8)	5' UTR (NM_020586, exon 1 of 8)	534	NM_020586	80517	Mm.142843	NM_020586	ENSMUSG00000008429	Herpud2	5031400M07Rik|AB041580	HERPUD family member 2	protein-coding
mm_164359.1	chr16	22654651	22654668	+	1	NA	intron (NM_001346673, intron 1 of 23)	intron (NM_001346673, intron 1 of 23)	2572	NM_138650	110197	Mm.194986	NM_138650	ENSMUSG00000022861	Dgkg	2900055E17Rik|90kDa|AI854428|Dagk3|E430001K23Rik|mKIAA4131	diacylglycerol kinase, gamma	protein-coding
mm_115705.1	chr13	14522442	14522459	-	1	NA	intron (NM_001081348, intron 1 of 28)	intron (NM_001081348, intron 1 of 28)	776	NM_001081348	94253	Mm.125298	NM_153130	ENSMUSG00000021301	Hecw1	9330116H24Rik|AV273951|E130207I19Rik|Nedl1	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	protein-coding
mm_157911.1	chrX	78544958	78544959	-	1	NA	intron (NM_027322, intron 1 of 3)	intron (NM_027322, intron 1 of 3)	38847	NM_001164275	546336	Mm.211712	NM_027322	ENSMUSG00000047996	Prrg1	2010007L08Rik	proline rich Gla (G-carboxyglutamic acid) 1	protein-coding
mm_67303.1	chr7	79386708	79386762	-	1	NA	5' UTR (NM_020599, exon 1 of 9)	5' UTR (NM_020599, exon 1 of 9)	292	NM_020599	19771	Mm.41653	NM_020599	ENSMUSG00000039194	Rlbp1	3110056M11Rik|CRALBP	retinaldehyde binding protein 1	protein-coding
mm_41096.1	chr5	87694721	87694752	+	1	NA	exon (NM_001286023, exon 5 of 7)	exon (NM_001286023, exon 5 of 7)	4689	NM_001286020	12991	Mm.268737	NM_009972	ENSMUSG00000063157	Csn2	Csnb	casein beta	protein-coding
mm_66251.1	chr7	35585578	35585602	-	1	NA	promoter-TSS (NM_178263)	promoter-TSS (NM_178263)	-8	NM_145840	243923	Mm.222680	NM_145840	ENSMUSG00000056043	Rgs9bp	R9AP|Rgs9-1bp	regulator of G-protein signalling 9 binding protein	protein-coding
mm_87717.1	chr10	60106167	60106178	+	1	NA	promoter-TSS (NM_052994)	promoter-TSS (NM_052994)	-85	NM_052994	94214	Mm.153429	NM_052994	ENSMUSG00000058297	Spock2	AA407235|Gcap26|mKIAA0275	sparc/osteonectin, cwcv and kazal-like domains proteoglycan 2	protein-coding
mm_36688.1	chr4	96591369	96591395	-	1	NA	5' UTR (NM_028979, exon 1 of 9)	5' UTR (NM_028979, exon 1 of 9)	103	NM_028979	74519	Mm.458387	NM_028979	ENSMUSG00000015224	Cyp2j9	8430417E17Rik	cytochrome P450, family 2, subfamily j, polypeptide 9	protein-coding
mm_133278.1	chr16	77419746	77419759	+	1	NA	intron (NR_015543, intron 2 of 4)	intron (NR_015543, intron 2 of 4)	90424	NR_015543	77994	Mm.394688	NR_015543	ENSMUSG00000090386	Mir99ahg	2810055G20Rik|D730043B02Rik	Mir99a and Mirlet7c-1 host gene (non-protein coding)	ncRNA
mm_149738.1	chr19	22441014	22441031	+	1	NA	intron (NM_001035243, intron 1 of 23)	intron (NM_001035243, intron 1 of 23)	-7186	NM_177341	226025	Mm.131943	NM_177341	ENSMUSG00000052387	Trpm3	6330504P12Rik|9330180E14|AU018608|B930001P07Rik|LTRPC3|MLSN2	transient receptor potential cation channel, subfamily M, member 3	protein-coding
mm_105428.1	chr11	103822718	103822733	-	1	NA	3' UTR (NM_008740, exon 21 of 21)	3' UTR (NM_008740, exon 21 of 21)	48550	NM_009521	22415	Mm.159091	NM_009521	ENSMUSG00000000125	Wnt3	Int-4|Wnt-3	wingless-type MMTV integration site family, member 3	protein-coding
mm_34696.1	chr4	152039316	152039356	+	1	NA	promoter-TSS (NM_028727)	promoter-TSS (NM_028727)	15	NM_028727	74035	Mm.275803	NM_028727	ENSMUSG00000028948	Nol9	4632412I24Rik|6030462G04Rik|AI449622|AW490720	nucleolar protein 9	protein-coding
mm_71696.1	chr8	61600282	61600283	+	1	NA	intron (NM_001293772, intron 10 of 21)	intron (NM_001293772, intron 10 of 21)	-9113	NM_001293774	72333	Mm.29933	NM_001081390	ENSMUSG00000058056	Palld	2410003B16Rik|6030492A02	palladin, cytoskeletal associated protein	protein-coding
mm_73238.1	chr8	104142978	104142989	+	1	NA	exon (NM_009868, exon 12 of 12)	exon (NM_009868, exon 12 of 12)	-27530	NM_001141924	65115	Mm.41849	NM_001141922	ENSMUSG00000031872	Bean1	Bean	brain expressed, associated with Nedd4, 1	protein-coding
mm_71112.1	chr8	35765718	35765736	+	1	NA	Intergenic	CpG	60832	NM_027998	71908	Mm.37817	NM_027998	ENSMUSG00000055976	Cldn23	2310014B08Rik	claudin 23	protein-coding
mm_2541.1	chr1	107511434	107511457	+	1	NA	promoter-TSS (NM_001174170)	promoter-TSS (NM_001174170)	22	NM_001174170	18788	Mm.271870	NM_011111	ENSMUSG00000062345	Serpinb2	PAI-2|Planh2|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 2	protein-coding
mm_110697.1	chr12	69198372	69198385	-	1	NA	promoter-TSS (NM_027269)	promoter-TSS (NM_027269)	51	NM_027269	109065	Mm.107180	NM_027269	ENSMUSG00000020973	Dnaaf2	Ktu|TU54|kintoun|mknt	dynein, axonemal assembly factor 2	protein-coding
mm_92624.1	chr10	80261005	80261013	-	1	NA	promoter-TSS (NM_001347119)	promoter-TSS (NM_001347119)	3	NM_001347119	14431	Mm.7329	NM_010255	ENSMUSG00000020150	Gamt	AA571402|Spintz1	guanidinoacetate methyltransferase	protein-coding
mm_100644.1	chr11	121847035	121847038	+	1	NA	Intergenic	MT2B1|LTR|ERVL	16818	NM_029049	74675	Mm.61213	NM_029049	ENSMUSG00000039198	Ptchd3	4930451E13Rik|4933440L20Rik|RNDEu-3	patched domain containing 3	protein-coding
mm_86638.1	chr10	14087864	14087869	+	1	NA	intron (NM_010437, intron 2 of 8)	intron (NM_010437, intron 2 of 8)	121487	NM_010437	15273	Mm.42157	NM_010437	ENSMUSG00000015501	Hivep2	Gm20114|MIBP1|Schnurri-2|Shn-2	human immunodeficiency virus type I enhancer binding protein 2	protein-coding
mm_143511.1	chr17	72604659	72604676	-	1	NA	promoter-TSS (NM_007439)	promoter-TSS (NM_007439)	-360	NM_007439	11682	Mm.311854	NM_007439	ENSMUSG00000055471	Alk	CD246|Tcrz	anaplastic lymphoma kinase	protein-coding
mm_54243.1	chr6	28256497	28256538	-	1	NA	exon (NM_001081678, exon 3 of 6)	exon (NM_001081678, exon 3 of 6)	5084	NM_001081678	627049	Mm.84441	NM_001081678	ENSMUSG00000039841	Zfp800	AA407452|Znf800	zinc finger protein 800	protein-coding
mm_112286.1	chr12	114462738	114462745	-	1	NA	Intergenic	Intergenic	6725	NR_106062	102465663		NR_106062	ENSMUSG00000105438	Mir7094-1	mmu-mir-7094-1	microRNA 7094-1	ncRNA
mm_119438.1	chr14	46387529	46387559	+	1	NA	intron (NM_007554, intron 1 of 3)	CpG	3125	NM_001316360	12159	Mm.6813	NM_007554	ENSMUSG00000021835	Bmp4	Bmp-4|Bmp2b|Bmp2b-1|Bmp2b1	bone morphogenetic protein 4	protein-coding
mm_109630.1	chr12	112767554	112767580	+	1	NA	exon (NM_178911, exon 8 of 11)	exon (NM_178911, exon 8 of 11)	6912	NM_178911	104759	Mm.203915	NM_178911	ENSMUSG00000052160	Pld4	AI132321|thss	phospholipase D family, member 4	protein-coding
mm_134137.1	chr16	10683555	10683563	-	1	NA	intron (NM_001204229, intron 18 of 22)	L1ME3G|LINE|L1	101977	NM_009896	12703	Mm.130	NM_009896	ENSMUSG00000038037	Socs1	Cish1|Cish7|JAB|SOCS-1|SSI-1	suppressor of cytokine signaling 1	protein-coding
mm_52082.1	chr6	97828353	97828362	+	1	NA	intron (NM_001113198, intron 1 of 9)	intron (NM_001113198, intron 1 of 9)	21299	NM_001113198	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_103280.1	chr11	72207214	72207279	-	1	NA	promoter-TSS (NM_026559)	promoter-TSS (NM_026559)	-308	NM_026559	52700	Mm.27670	NM_026559	ENSMUSG00000020803	Txndc17	4831443O22Rik|D11Ertd672e|TRP14|Txnl5	thioredoxin domain containing 17	protein-coding
mm_19443.1	chr2	91976309	91976346	-	1	NA	Intergenic	Intergenic	-12764	NM_138306	104418	Mm.314923	NM_138306	ENSMUSG00000040479	Dgkz	E130307B02Rik|ENSMUSG00000075035|F730209L11Rik|mDGK[z]	diacylglycerol kinase zeta	protein-coding
mm_59727.1	chr7	28788940	28788942	+	1	NA	promoter-TSS (NM_177158)	promoter-TSS (NM_177158)	-28	NM_177158	320435	Mm.74632	NM_177158	ENSMUSG00000051735	Rinl	5830482F20Rik|9930116N10Rik	Ras and Rab interactor-like	protein-coding
mm_77612.1	chr8	123893636	123893644	-	1	NA	exon (NM_009606, exon 2 of 7)	exon (NM_009606, exon 2 of 7)	1135	NM_001272041	11459	Mm.214950	NM_009606	ENSMUSG00000031972	Acta1	AA959943|Acta-2|Acts|Actsk-1	actin, alpha 1, skeletal muscle	protein-coding
mm_65806.1	chr7	28977910	28977950	-	1	NA	exon (NM_028659, exon 3 of 8)	exon (NM_028659, exon 3 of 8)	3958	NM_001285943	73830	Mm.29714	NM_028659	ENSMUSG00000053565	Eif3k	1200009C21Rik|Eif3s12	eukaryotic translation initiation factor 3, subunit K	protein-coding
mm_14067.1	chr2	122738608	122738616	+	1	NA	5' UTR (NM_019788, exon 1 of 5)	5' UTR (NM_019788, exon 1 of 5)	107	NM_019788	18457	Mm.268921	NM_019788	ENSMUSG00000005804	Bloc1s6	BLOC-1|Pldn|Stx13bp1|pa	biogenesis of lysosomal organelles complex-1, subunit 6, pallidin	protein-coding
mm_21810.1	chr2	165090740	165090752	-	1	NA	promoter-TSS (NR_033448)	promoter-TSS (NR_033448)	4	NR_033448	72211	Mm.482899	NR_033448	ENSMUSG00000078935	1700025C18Rik	-	RIKEN cDNA 1700025C18 gene	ncRNA
mm_20146.1	chr2	121506640	121506667	-	1	NA	promoter-TSS (NM_030234)	promoter-TSS (NM_030234)	3	NM_026220	67532	Mm.440764	NM_026220	ENSMUSG00000068479	Mfap1a	4432409M24Rik|Mfap1	microfibrillar-associated protein 1A	protein-coding
mm_51827.1	chr6	89364617	89364648	+	1	NA	Intergenic	Intergenic	-2019	NM_008881	18844	Mm.3789	NM_008881	ENSMUSG00000030084	Plxna1	2600013D04Rik|NOV|PlexA1|Plxn1|mKIAA4053	plexin A1	protein-coding
mm_151118.1	chr19	47864641	47864656	+	1	NA	promoter-TSS (NM_030051)	promoter-TSS (NM_030051)	-897	NM_030051	68214	Mm.63791	NM_026619	ENSMUSG00000025069	Gsto2	1700020F09Rik|4930425C18Rik|GSTO 2-2	glutathione S-transferase omega 2	protein-coding
mm_114856.1	chr13	93304067	93304138	+	1	NA	5' UTR (NM_011982, exon 1 of 5)	5' UTR (NM_011982, exon 1 of 5)	345	NM_011982	26556	Mm.37533	NM_011982	ENSMUSG00000007617	Homer1	PSD-Zip45|SYN47|Ves-1|homer-1|vesl-1	homer scaffolding protein 1	protein-coding
mm_119575.1	chr14	50807491	50807511	+	1	NA	promoter-TSS (NM_009632)	promoter-TSS (NM_009632)	270	NR_002142	85029		NR_002142	ENSMUSG00000092837	Rpph1	Gm24821|H1RNA|Rmrp5|Rpr	ribonuclease P RNA component H1	ncRNA
mm_84038.1	chr9	57765880	57765908	-	1	NA	promoter-TSS (NM_007713)	promoter-TSS (NM_007713)	-34	NM_007713	102414	Mm.25720	NM_007713	ENSMUSG00000032316	Clk3	AI256811	CDC-like kinase 3	protein-coding
mm_78318.1	chr9	24341717	24341719	+	1	NA	Intergenic	Intergenic	161422	NM_172920	244745	Mm.38526	NM_172920	ENSMUSG00000043067	Dpy19l1	1100001I19Rik|6030402K12|AI225861|AW558481	dpy-19-like 1 (C. elegans)	protein-coding
mm_148356.1	chr18	84951429	84951442	-	1	NA	promoter-TSS (NM_025969)	promoter-TSS (NM_025969)	89	NM_025969	67105	Mm.250617	NM_025969	ENSMUSG00000024645	Timm21	1700034H14Rik|2700002I20Rik	tranlocase of inner mitochondrial membrane 21	protein-coding
mm_58483.1	chr7	3617574	3617587	+	1	NA	intron (NM_025348, intron 1 of 3)	intron (NM_025348, intron 1 of 3)	207	NM_025348	66091	Mm.17851	NM_025348	ENSMUSG00000035674	Ndufa3	1010001M12Rik|1700022J01Rik	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 3	protein-coding
mm_118848.1	chr14	25665933	25665950	+	1	NA	3' UTR (NM_183208, exon 24 of 24)	3' UTR (NM_183208, exon 24 of 24)	-28229	NM_134084	105675	Mm.41656	NM_134084	ENSMUSG00000021868	Ppif	AW457192|CyP-D|CyP-F|CypD|PPIase	peptidylprolyl isomerase F (cyclophilin F)	protein-coding
mm_78553.1	chr9	35424876	35424888	+	1	NA	Intergenic	Intergenic	-27194	NM_021339	57810	Mm.80509	NM_021339	ENSMUSG00000038119	Cdon	CDO|Cd0|Orcam	cell adhesion molecule-related/down-regulated by oncogenes	protein-coding
mm_105949.1	chr11	115291535	115291558	-	1	NA	intron (NM_178035, intron 2 of 5)	intron (NM_178035, intron 2 of 5)	6000	NM_178035	328035	Mm.21995	NM_178035	ENSMUSG00000044788	Fads6	BC044804|OTTMUSG00000021749	fatty acid desaturase domain family, member 6	protein-coding
mm_124960.1	chr15	13155228	13155238	+	1	NA	intron (NM_007666, intron 1 of 11)	intron (NM_007666, intron 1 of 11)	18442	NM_007666	12563	Mm.57048	NM_007666	ENSMUSG00000039385	Cdh6	cad6	cadherin 6	protein-coding
mm_139890.1	chr17	70849461	70849469	+	1	NA	intron (NM_001164074, intron 1 of 2)	intron (NM_001164074, intron 1 of 2)	325	NM_001164076	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_53831.1	chr6	148047410	148047424	+	1	NA	promoter-TSS (NM_178797)	promoter-TSS (NM_178797)	1	NM_178797	330450	Mm.447274	NM_178797	ENSMUSG00000030303	Far2	A230046P18|AW048109|BC055759|Mlstd1	fatty acyl CoA reductase 2	protein-coding
mm_57219.1	chr6	122952540	122952552	-	1	NA	promoter-TSS (NM_153197)	promoter-TSS (NM_153197)	31	NM_001204241	73149	Mm.25684	NM_153197	ENSMUSG00000043832	Clec4a3	3110037K17Rik|Dcir3	C-type lectin domain family 4, member a3	protein-coding
mm_140604.1	chr17	10319597	10319614	-	1	NA	promoter-TSS (NM_001159517)	promoter-TSS (NM_001159517)	-244	NM_001159517	19317	Mm.130694	NM_021881	ENSMUSG00000062078	Qk	1110003F05Rik|1500005P18|QkI|l(17)-1Wis|l17Wis1	quaking	protein-coding
mm_20411.1	chr2	129300192	129300230	-	1	NA	3' UTR (NM_010554, exon 7 of 7)	3' UTR (NM_010554, exon 7 of 7)	2841	NR_040371	100503468	Mm.446943	NR_040371	ENSMUSG00000085498	Gm14023	OTTMUSG00000015408	predicted gene 14023	ncRNA
mm_59039.1	chr7	19342260	19342265	+	1	NA	Intergenic	CpG	-2809	NM_001127324	13870	Mm.280913	NM_007948	ENSMUSG00000003549	Ercc1	Ercc-1	excision repair cross-complementing rodent repair deficiency, complementation group 1	protein-coding
mm_56358.1	chr6	93806406	93806409	-	1	NA	intron (NM_001083321, intron 2 of 21)	intron (NM_001083321, intron 2 of 21)	106556	NR_104594	14924	Mm.217216	NM_010367	ENSMUSG00000045095	Magi1	AIP3|BAP1|Baiap1|Gukmi1|MAGI1c|Magi-1|TNRC19|WWP3|mKIAA4129	membrane associated guanylate kinase, WW and PDZ domain containing 1	protein-coding
mm_10565.1	chr2	18055705	18055733	+	1	NA	intron (NM_010804, intron 1 of 22)	intron (NM_010804, intron 1 of 22)	482	NM_010804	17354	Mm.209175	NM_010804	ENSMUSG00000026743	Mllt10	Af10|B130021D15Rik|D630001B22Rik|mKIAA4140	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 10	protein-coding
mm_106265.1	chr11	117968712	117968745	-	1	NA	intron (NM_007707, intron 1 of 1)	CpG	638	NM_007707	12702	Mm.3468	NM_007707	ENSMUSG00000053113	Socs3	Cis3|Cish3|EF-10|Ef10|SSI-3|Ssi3	suppressor of cytokine signaling 3	protein-coding
mm_136524.1	chr16	97459848	97459861	-	1	NA	intron (NR_003520, intron 2 of 8)	MTD|LTR|ERVL-MaLR	3051	NM_010846	17857	Mm.33996	NM_010846	ENSMUSG00000000386	Mx1	AI893580|Mx|Mx-1	MX dynamin-like GTPase 1	protein-coding
mm_101777.1	chr11	44950401	44950408	-	1	NA	intron (NM_007897, intron 10 of 15)	intron (NM_007897, intron 10 of 15)	166524	NR_045100	100504255	Mm.123608	NR_045100	ENSMUSG00000084773	Gm12159	OTTMUSG00000005475	predicted gene 12159	ncRNA
mm_109144.1	chr12	107141505	107141517	+	1	NA	Intergenic	Intergenic	-425187	NR_015512	71033	Mm.159404	NR_015512	ENSMUSG00000085820	4933406K04Rik	4930426M03Rik|4930485I22Rik|4933427G14Rik	RIKEN cDNA 4933406K04 gene	ncRNA
mm_68211.1	chr7	104400870	104400880	-	1	NA	Intergenic	Intergenic	-42229	NM_175648	244183	Mm.347647	NM_175648	ENSMUSG00000052749	Trim30b	A530023O14Rik|Trim30-1	tripartite motif-containing 30B	protein-coding
mm_145072.1	chr18	42053693	42053724	+	1	NA	promoter-TSS (NM_001146299)	promoter-TSS (NM_001146299)	-2	NM_172966	269016	Mm.45472	NM_172966	ENSMUSG00000057719	Sh3rf2	2310046K19|9130023G24Rik|AI452083|Ppp1r39|RNF158	SH3 domain containing ring finger 2	protein-coding
mm_80.1	chr1	6734903	6734926	+	1	NA	intron (NM_173868, intron 1 of 21)	intron (NM_173868, intron 1 of 21)	4863	NR_045188	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding
mm_93251.1	chr10	95494792	95494795	-	1	NA	intron (NM_026065, intron 3 of 5)	intron (NM_026065, intron 3 of 5)	7134	NM_026065	67270	Mm.30008	NM_026065	ENSMUSG00000062981	Mrpl42	2700009F22Rik|2900055D03Rik|D10Ertd322e|HSPC204|L31mt|MRP-L31|PTD007|Rpml31	mitochondrial ribosomal protein L42	protein-coding
mm_48427.1	chr5	140596549	140596580	-	1	NA	Intergenic	Intergenic	-10777	NM_008494	16848	Mm.12834	NM_008494	ENSMUSG00000029570	Lfng	AW061165	LFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	protein-coding
mm_10670.1	chr2	20969069	20969097	+	1	NA	non-coding (NR_033225, exon 1 of 2)	non-coding (NR_033225, exon 1 of 2)	209	NR_033225	433408	Mm.386941	NR_033225		Gm13375	OTTMUSG00000011664	predicted gene 13375	ncRNA
mm_60996.1	chr7	49276721	49276740	+	1	NA	intron (NM_175272, intron 1 of 37)	intron (NM_175272, intron 1 of 37)	30541	NM_175272	78286	Mm.333881	NM_175272	ENSMUSG00000052512	Nav2	5330421F07Rik|AU067780|BQ960892|HELAD1|POMFIL2|RAINB1|RAINB2|Unc53H2|mKIAA3015	neuron navigator 2	protein-coding
mm_77831.1	chr9	4309800	4309825	+	1	NA	promoter-TSS (NM_026962)	promoter-TSS (NM_026962)	-4	NM_026962	69149	Mm.25946	NM_026962	ENSMUSG00000025893	Kbtbd3	2200003A07Rik|Bklhd3	kelch repeat and BTB (POZ) domain containing 3	protein-coding
mm_70489.1	chr8	12439361	12439379	+	1	NA	Intergenic	Intergenic	43851	NM_009233	20664	Mm.39088	NM_009233	ENSMUSG00000096014	Sox1	BB176347|Sox-1	SRY (sex determining region Y)-box 1	protein-coding
mm_144814.1	chr18	36288013	36288038	+	1	NA	exon (NM_008989, exon 2 of 2)	exon (NM_008989, exon 2 of 2)	6863	NM_008989	19290	Mm.231802	NM_008989	ENSMUSG00000043991	Pura	CAGER-1|Pur-alpha|ssCRE-BP	purine rich element binding protein A	protein-coding
mm_135102.1	chr16	35490780	35490792	-	1	NA	promoter-TSS (NM_028295)	promoter-TSS (NM_028295)	87	NM_028295	72599	Mm.71015	NM_028295	ENSMUSG00000022844	Pdia5	2700053F16Rik|AU015525|Pdir	protein disulfide isomerase associated 5	protein-coding
mm_152093.1	chr19	6908856	6908868	-	1	NA	promoter-TSS (NM_026306)	promoter-TSS (NM_026306)	783	NM_012021	54683	Mm.279782	NM_012021	ENSMUSG00000024953	Prdx5	AOEB166|AOPP|Pmp20|Prdx6|PrxV	peroxiredoxin 5	protein-coding
mm_69731.1	chr7	140856703	140856722	-	1	NA	promoter-TSS (NM_053194)	promoter-TSS (NM_053194)	-329	NM_018742	54399	Mm.155696	NM_018742	ENSMUSG00000025484	Bet1l	2610021K23Rik|Gs15	Bet1 golgi vesicular membrane trafficking protein like	protein-coding
mm_9608.1	chr1	176213674	176213684	-	1	NA	5' UTR (NM_001195816, exon 1 of 10)	5' UTR (NM_001195816, exon 1 of 10)	263	NM_001195816	319455	Mm.338001	NM_176916	ENSMUSG00000055214	Pld5	B230365F16Rik	phospholipase D family, member 5	protein-coding
mm_145474.1	chr18	60373608	60373624	+	1	NA	Intergenic	Intergenic	-2413	NM_021792	60440	Mm.261140	NM_021792	ENSMUSG00000054072	Iigp1	2900074L10Rik|AI046432|AW111922|Ifgga1|Iigp|Irga6	interferon inducible GTPase 1	protein-coding
mm_128688.1	chr15	61441658	61441686	-	1	NA	Intergenic	Intergenic	332779	NR_040350	432956	Mm.404918	NR_040350		D030024E09Rik	-	RIKEN cDNA D030024E09 gene	ncRNA
mm_67181.1	chr7	73788343	73788359	-	1	NA	Intergenic	Intergenic	28152	NR_077222	100579147	Mm.109205	NR_077222	ENSMUSG00000074067	Gm10619	4932443D20|ENSMUSG00000074067	predicted gene 10619	ncRNA
mm_51380.1	chr6	73633099	73633105	+	1	NA	Intergenic	Intergenic	-162081	NR_108032	73408	Mm.233629	NR_108032	ENSMUSG00000107408	1700065L07Rik	-	RIKEN cDNA 1700065L07 gene	ncRNA
mm_20541.1	chr2	131063509	131063559	-	1	NA	non-coding (NR_136922, exon 1 of 22)	non-coding (NR_136922, exon 1 of 22)	280	NR_136922	110751	Mm.108550	NM_033615	ENSMUSG00000027318	Adam33	Adaml	a disintegrin and metallopeptidase domain 33	protein-coding
mm_141745.1	chr17	34187329	34187345	-	1	NA	promoter-TSS (NM_001161730)	promoter-TSS (NM_001161730)	-7	NM_013585	16912	Mm.390983	NM_013585	ENSMUSG00000096727	Psmb9	Lmp-2|Lmp2	proteasome (prosome, macropain) subunit, beta type 9 (large multifunctional peptidase 2)	protein-coding
mm_55456.1	chr6	67376135	67376144	-	1	NA	promoter-TSS (NM_008354)	promoter-TSS (NM_008354)	-2	NM_008354	16162	Mm.188337	NM_008354	ENSMUSG00000018341	Il12rb2	A930027I18Rik|IL-12RB2|Ifnm	interleukin 12 receptor, beta 2	protein-coding
mm_129278.1	chr15	77153640	77153648	-	1	NA	5' UTR (NM_001110830, exon 1 of 13)	5' UTR (NM_001110830, exon 1 of 13)	168	NM_001110830	93686	Mm.202774	NM_053104	ENSMUSG00000033565	Rbfox2	Fbm2|Fxh|Hrnbp2|Rbm9	RNA binding protein, fox-1 homolog (C. elegans) 2	protein-coding
mm_14094.1	chr2	125164807	125164808	+	1	NA	intron (NM_001079690, intron 5 of 27)	MER34A1|LTR|ERV1	12207	NM_001079690	20495	Mm.3914	NM_011389	ENSMUSG00000027202	Slc12a1	AI788571|D630042G03Rik|Nkcc2|mBSC1|urehr3	solute carrier family 12, member 1	protein-coding
mm_3238.1	chr1	135851355	135851378	+	1	NA	exon (NM_001130176, exon 11 of 13)	exon (NM_001130176, exon 11 of 13)	10505	NM_001130176	21956	Mm.247470	NM_011619	ENSMUSG00000026414	Tnnt2	Tnt|cTnT	troponin T2, cardiac	protein-coding
mm_14758.1	chr2	144740026	144740034	+	1	NA	intron (NM_025314, intron 4 of 5)	U1|snRNA|snRNA	-83636	NM_025490	66328	Mm.45377	NM_025490	ENSMUSG00000027431	Scp2d1	1700010M22Rik	SCP2 sterol-binding domain containing 1	protein-coding
mm_51275.1	chr6	72132051	72132077	+	1	NA	exon (NM_011375, exon 3 of 7)	exon (NM_011375, exon 3 of 7)	-8867	NR_045165	71265	Mm.442035	NR_045163	ENSMUSG00000108709	4933431G14Rik	4930565C19Rik	RIKEN cDNA 4933431G14 gene	ncRNA
mm_154914.1	chrX	21487310	21487335	+	1	NA	3' UTR (NM_007429, exon 3 of 3)	3' UTR (NM_007429, exon 3 of 3)	2698	NM_007429	11609	Mm.2679	NM_007429	ENSMUSG00000068122	Agtr2	AI316812|AW107640	angiotensin II receptor, type 2	protein-coding
mm_8757.1	chr1	160351992	160352005	-	1	NA	promoter-TSS (NM_001038621)	promoter-TSS (NM_001038621)	-427	NM_001038621	29809	Mm.25833	NM_013862	ENSMUSG00000026721	Rabgap1l	5830411O09Rik|8430421H08Rik|9630005B12Rik|AW049894|HHL|Hh1|mKIAA0471	RAB GTPase activating protein 1-like	protein-coding
mm_155301.1	chrX	61185742	61185769	+	1	NA	promoter-TSS (NM_001166658)	promoter-TSS (NM_001166658)	-197	NM_001166658	631990	Mm.401324	NM_001166658	ENSMUSG00000090546	Cdr1	100039759|Cdr|Cdr34|EG631990|Gm2409|Gm7077	cerebellar degeneration related antigen 1	protein-coding
mm_33795.1	chr4	134924383	134924400	+	1	NA	exon (NM_023665, exon 2 of 5)	exon (NM_023665, exon 2 of 5)	766	NM_023665	27981	Mm.331964	NM_023665	ENSMUSG00000037266	Rsrp1	2700043I21Rik|D4Ucla2|D4Wsu53e	arginine/serine rich protein 1	protein-coding
mm_163144.1	chr11	80978032	80978034	+	1	NA	intron (NM_001034013, intron 1 of 9)	intron (NM_001034013, intron 1 of 9)	119644	NM_029367	75622	Mm.26988	NM_029367	ENSMUSG00000053184	Spaca3	1700025M08Rik|ALLP17|Lyc3|SLLP1|mSLLP1	sperm acrosome associated 3	protein-coding
mm_98810.1	chr11	97187701	97187711	+	1	NA	5' UTR (NM_008379, exon 1 of 22)	5' UTR (NM_008379, exon 1 of 22)	186	NM_008379	16211	Mm.251013	NM_008379	ENSMUSG00000001440	Kpnb1	AA409963|IPOB|Impnb	karyopherin (importin) beta 1	protein-coding
mm_49420.1	chr6	29212406	29212427	+	1	NA	promoter-TSS (NM_011829)	promoter-TSS (NM_011829)	-119	NM_011829	23917	Mm.260707	NM_011829	ENSMUSG00000003500	Impdh1	B930086D20Rik|IMPDH-I	inosine 5'-phosphate dehydrogenase 1	protein-coding
mm_47617.1	chr5	125179141	125179147	-	1	NA	promoter-TSS (NM_001253904)	promoter-TSS (NM_001253904)	70	NM_001253905	20602	Mm.278646	NM_011424	ENSMUSG00000029478	Ncor2	N-CoR|SMRT|SMRTe	nuclear receptor co-repressor 2	protein-coding
mm_5541.1	chr1	38321982	38321997	-	1	NA	intron (NM_001290814, intron 7 of 21)	intron (NM_001290814, intron 7 of 21)	-192327	NM_019570	56210	Mm.389103	NM_019570	ENSMUSG00000026082	Rev1	1110027I23Rik|AU022044|Rev1l	REV1, DNA directed polymerase	protein-coding
mm_152168.1	chr19	7297640	7297648	-	1	NA	intron (NM_007928, intron 1 of 17)	intron (NM_007928, intron 1 of 17)	-2197	NM_001080390	13728	Mm.258986	NM_007928	ENSMUSG00000024969	Mark2	EMK-1|Emk|Par-1|Par-1b	MAP/microtubule affinity regulating kinase 2	protein-coding
mm_160059.1	chr7	4812351	4812351	-	1	NA	promoter-TSS (NM_133777)	promoter-TSS (NM_133777)	-11	NM_133777	77891	Mm.389787	NM_133777	ENSMUSG00000060860	Ube2s	0910001J09Rik|6720465F12Rik|AA409170|E2-EPF	ubiquitin-conjugating enzyme E2S	protein-coding
mm_38511.1	chr4	141284156	141284176	-	1	NA	Intergenic	Intergenic	-17055	NM_010139	13836	Mm.2581	NM_010139	ENSMUSG00000006445	Epha2	AW545284|Eck|Myk2|Sek-2|Sek2	Eph receptor A2	protein-coding
mm_94867.1	chr11	24078207	24078219	+	1	NA	5' UTR (NM_001242934, exon 1 of 4)	5' UTR (NM_001242934, exon 1 of 4)	157	NM_001159289	14025	Mm.53687	NM_016707	ENSMUSG00000000861	Bcl11a	2810047E18Rik|BCL-11A|Ctip1|D930021L15Rik|Evi9|Evi9a|Evi9b|Evi9c|mKIAA1809	B cell CLL/lymphoma 11A (zinc finger protein)	protein-coding
mm_144108.1	chr18	4165885	4165894	+	1	NA	promoter-TSS (NM_026092)	promoter-TSS (NM_026092)	57	NM_026092	67328	Mm.158148	NM_026092	ENSMUSG00000024233	Lyzl1	1700038F02Rik|Lyc2|Lyzd1	lysozyme-like 1	protein-coding
mm_42266.1	chr5	114132211	114132229	+	1	NA	exon (NM_011677, exon 2 of 6)	exon (NM_011677, exon 2 of 6)	1064	NM_011677	22256	Mm.1393	NM_011677	ENSMUSG00000029591	Ung	UNG1|UNG2	uracil DNA glycosylase	protein-coding
mm_97819.1	chr11	82963447	82963458	+	1	NA	3' UTR (NM_183201, exon 6 of 6)	3' UTR (NM_183201, exon 6 of 6)	-2771	NR_045932	76392	Mm.295205	NR_045932	ENSMUSG00000086327	Slfn5os	1700003F17Rik	schlafen 5, opposite strand	ncRNA
mm_158022.1	chrX	96163404	96163448	-	1	NA	exon (NM_010833, exon 9 of 13)	exon (NM_010833, exon 9 of 13)	67381	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_87493.1	chr10	51495758	51495787	+	1	NA	intron (NM_001291894, intron 7 of 8)	intron (NM_001291894, intron 7 of 8)	4874	NM_013532	14728	Mm.34408	NM_013532	ENSMUSG00000062593	Lilrb4a	CD85K|Gp49b|HM18|ILT3|LIR-5|Lilrb4|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4A	protein-coding
mm_43293.1	chr5	134313674	134313696	+	1	NA	intron (NM_001080746, intron 1 of 34)	CpG	1075	NM_001080746	14886	Mm.261570	NM_010365	ENSMUSG00000060261	Gtf2i	6030441I21Rik|BAP-135|Diws1t|GtfII-I|Spin|TFII-I|WBSCR6	general transcription factor II I	protein-coding
mm_34709.1	chr4	152116278	152116284	+	1	NA	promoter-TSS (NM_033042)	promoter-TSS (NM_033042)	-62	NM_033042	85030	Mm.101198	NM_033042	ENSMUSG00000024793	Tnfrsf25	APO-3|DDR3|DR3|LARD|TR3|TRAMP|Tnfrsf12|WSL-1|WSL-LR|Wsl	tumor necrosis factor receptor superfamily, member 25	protein-coding
mm_4978.1	chr1	191339454	191339462	+	1	NA	intron (NM_025864, intron 3 of 7)	B2_Mm1t|SINE|B2	13493	NM_025864	66950	Mm.236300	NM_025864	ENSMUSG00000026627	Tmem206	2310028N02Rik|AI118576	transmembrane protein 206	protein-coding
mm_121143.1	chr14	101898512	101898525	+	1	NA	intron (NM_001347628, intron 9 of 26)	intron (NM_001347628, intron 9 of 26)	57895	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_160785.1	chr10	128237823	128237823	+	1	NA	promoter-TSS (NM_011589)	promoter-TSS (NM_011589)	-243	NM_011589	21853	Mm.6458	NM_011589	ENSMUSG00000039994	Timeless	C77407|Debt69|tim	timeless circadian clock 1	protein-coding
mm_38123.1	chr4	134563325	134563329	-	1	NA	3' UTR (NM_207237, exon 12 of 12)	3' UTR (NM_207237, exon 12 of 12)	4524	NR_105829	102465216		NR_105829	ENSMUSG00000099289	Mir6403	Gm27992|mmu-mir-6403	microRNA 6403	ncRNA
mm_24703.1	chr3	95127426	95127460	+	1	NA	intron (NM_016712, intron 5 of 9)	intron (NM_016712, intron 5 of 9)	2929	NM_016712	50874	Mm.71935	NM_016712	ENSMUSG00000005628	Tmod4	MTMOD|Sk-Tmod	tropomodulin 4	protein-coding
mm_33791.1	chr4	134924073	134924099	+	1	NA	exon (NM_023665, exon 2 of 5)	exon (NM_023665, exon 2 of 5)	461	NM_023665	27981	Mm.331964	NM_023665	ENSMUSG00000037266	Rsrp1	2700043I21Rik|D4Ucla2|D4Wsu53e	arginine/serine rich protein 1	protein-coding
mm_52580.1	chr6	116650614	116650618	+	1	NA	promoter-TSS (NM_001166580)	promoter-TSS (NM_001166580)	-68	NM_145980	213393	Mm.38231	NM_145980	ENSMUSG00000048489	8430408G22Rik	Depp|Fseg	RIKEN cDNA 8430408G22 gene	protein-coding
mm_124735.1	chr15	6580961	6580979	+	1	NA	exon (NM_001278269, exon 1 of 17)	exon (NM_001278269, exon 1 of 17)	1123	NM_011815	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_165993.1	chr4	110687375	110687378	+	1	NA	intron (NM_001048189, intron 3 of 12)	intron (NM_001048189, intron 3 of 12)	289678	NM_030231	78933	Mm.435620	NM_030231	ENSMUSG00000061298	Agbl4	4930578N11Rik|4931433A01Rik	ATP/GTP binding protein-like 4	protein-coding
mm_141739.1	chr17	34122260	34122282	-	1	NA	promoter-TSS (NM_010238)	promoter-TSS (NM_010238)	336	NM_001204973	14312	Mm.3444	NM_010238	ENSMUSG00000024335	Brd2	AW228947|D17H6S113E|Frg-1|Fsrg-1|Fsrg1|Nat|Ring3|Rnf3|mKIAA4005	bromodomain containing 2	protein-coding
mm_113889.1	chr13	49190330	49190331	+	1	NA	intron (NM_013610, intron 1 of 3)	intron (NM_013610, intron 1 of 3)	2783	NM_013610	18081	Mm.18503	NM_013610	ENSMUSG00000037966	Ninj1	AU024536	ninjurin 1	protein-coding
mm_94718.1	chr11	20543308	20543336	+	1	NA	promoter-TSS (NM_021372)	promoter-TSS (NM_021372)	69	NM_021372	58172	Mm.339676	NM_021372	ENSMUSG00000049800	Sertad2	AB041541|AU021878|Kiaa0127|MNCb-1504|SEI-2|Sei2|TRIP-Br2|mKIAA0127	SERTA domain containing 2	protein-coding
mm_6119.1	chr1	64121457	64121463	-	1	NA	promoter-TSS (NM_033563)	promoter-TSS (NM_033563)	-71	NM_033563	93691	Mm.29466	NM_033563	ENSMUSG00000025959	Klf7	9830124P08Rik	Kruppel-like factor 7 (ubiquitous)	protein-coding
mm_12905.1	chr2	84827013	84827067	+	1	NA	promoter-TSS (NM_013899)	promoter-TSS (NM_013899)	19	NM_013899	30059	Mm.21826	NM_013899	ENSMUSG00000027076	Timm10	Tim13|Timm13a	translocase of inner mitochondrial membrane 10	protein-coding
mm_53030.1	chr6	124493176	124493178	+	1	NA	promoter-TSS (NM_181344)	promoter-TSS (NM_181344)	64	NM_181344	232371	Mm.132974	NM_181344	ENSMUSG00000038527	C1rl	C1r-LP|C1rl1|C1rlp	complement component 1, r subcomponent-like	protein-coding
mm_57175.1	chr6	122848171	122848199	-	1	NA	3' UTR (NM_009779, exon 2 of 2)	3' UTR (NM_009779, exon 2 of 2)	7972	NM_009779	12267	Mm.2408	NM_009779	ENSMUSG00000040552	C3ar1	AZ3B|C3AR|HNFAG09	complement component 3a receptor 1	protein-coding
mm_139250.1	chr17	47734330	47734337	+	1	NA	exon (NM_025973, exon 9 of 9)	exon (NM_025973, exon 9 of 9)	-2704	NM_001161722	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_117380.1	chr13	73327961	73327976	-	1	NA	intron (NM_010888, intron 1 of 3)	RMER10B|LTR|ERVL	514	NR_033306	407785	Mm.29897	NM_010888	ENSMUSG00000021606	Ndufs6	BC059730|IP13	NADH dehydrogenase (ubiquinone) Fe-S protein 6	protein-coding
mm_141788.1	chr17	34305716	34305728	-	1	NA	promoter-TSS (NM_010382)	promoter-TSS (NM_010382)	-145	NM_010382	14969	Mm.22564	NM_010382	ENSMUSG00000060586	H2-Eb1	Eb|H-2Eb|H2Eb|Ia-4|Ia4	histocompatibility 2, class II antigen E beta	protein-coding
mm_147498.1	chr18	48444417	48444418	-	1	NA	Intergenic	Intergenic	399082	NM_001025388	433182	Mm.70666	NM_001025388	ENSMUSG00000059040	Eno1b	EG433182|Eno1|Gm5506	enolase 1B, retrotransposed	protein-coding
mm_161715.1	chr17	25735920	25735920	+	1	NA	promoter-TSS (NM_177822)	promoter-TSS (NM_177822)	-120	NM_177822	328783	Mm.183275	NM_177822	ENSMUSG00000041062	Mslnl	4732467B22	mesothelin-like	protein-coding
mm_133252.1	chr16	77302012	77302051	+	1	NA	Intergenic	Intergenic	-27297	NR_015543	77994	Mm.394688	NR_015543	ENSMUSG00000090386	Mir99ahg	2810055G20Rik|D730043B02Rik	Mir99a and Mirlet7c-1 host gene (non-protein coding)	ncRNA
mm_2286.1	chr1	91351030	91351100	+	1	NA	promoter-TSS (NM_027551)	promoter-TSS (NM_027551)	-8	NM_027551	70788	Mm.68617	NM_027551	ENSMUSG00000026308	Klhl30	4631423F02Rik	kelch-like 30	protein-coding
mm_143016.1	chr17	56476463	56476480	-	1	NA	promoter-TSS (NM_001252453)	promoter-TSS (NM_001252453)	9	NM_001252455	19280	Mm.258771	NM_011218	ENSMUSG00000013236	Ptprs	AL022616|PTP|PTP-NU3|PTPNU-3|PTPsigma|Ptpt9|R-PTP-S|RPTPsigma	protein tyrosine phosphatase, receptor type, S	protein-coding
mm_71950.1	chr8	70493141	70493154	+	1	NA	promoter-TSS (NM_018827)	promoter-TSS (NM_018827)	16	NM_018827	12931	Mm.335584	NM_018827	ENSMUSG00000007888	Crlf1	CLF-1|CRLM-3|CRLM3|NR6|NR6.1	cytokine receptor-like factor 1	protein-coding
mm_70385.1	chr8	10481147	10481164	+	1	NA	intron (NM_001319151, intron 23 of 34)	intron (NM_001319151, intron 23 of 34)	327244	NM_001319151	244281	Mm.422761	NM_001081397	ENSMUSG00000039057	Myo16	BM140241|C230040D10Rik|Gm1105|NYAP3|mKIAA0865	myosin XVI	protein-coding
mm_65129.1	chr7	19459236	19459253	-	1	NA	promoter-TSS (NM_172279)	promoter-TSS (NM_172279)	-750	NM_172279	232944	Mm.260504	NM_172279	ENSMUSG00000030397	Mark4	2410090P21Rik|C79806|Markl1	MAP/microtubule affinity regulating kinase 4	protein-coding
mm_117129.1	chr13	60934816	60934825	-	1	NA	3' UTR (NM_001145799, exon 5 of 5)	3' UTR (NM_001145799, exon 5 of 5)	1746	NM_001145799	13024	Mm.482089	NM_007796	ENSMUSG00000044258	Ctla2a	Ctla-2a	cytotoxic T lymphocyte-associated protein 2 alpha	protein-coding
mm_65773.1	chr7	28762129	28762137	-	1	NA	intron (NM_001306222, intron 1 of 5)	intron (NM_001306222, intron 1 of 5)	4511	NM_001306222	18036	Mm.220333	NM_010908	ENSMUSG00000030595	Nfkbib	I(Kappa)B(beta)|I-kappa-B-beta|IKB-beta|IKappaBbeta|IkB|IkBb|NF-kappa-BIB|ikB-B	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, beta	protein-coding
mm_40089.1	chr5	34543432	34543442	+	1	NA	promoter-TSS (NM_001145858)	promoter-TSS (NM_001145858)	72	NM_001145858	24055	Mm.5012	NM_011893	ENSMUSG00000054520	Sh3bp2	3BP2	SH3-domain binding protein 2	protein-coding
mm_157661.1	chrX	57393030	57393040	-	1	NA	promoter-TSS (NM_001166623)	promoter-TSS (NM_001166623)	1	NM_011252	19655	Mm.28275	NM_011252	ENSMUSG00000031134	Rbmx	hnRNP G	RNA binding motif protein, X chromosome	protein-coding
mm_27015.1	chr3	26027256	26027266	-	1	NA	intron (NM_138666, intron 3 of 7)	B3A|SINE|B2	126046	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_36843.1	chr4	106678681	106678704	-	1	NA	promoter-TSS (NM_001172073)	promoter-TSS (NM_001172073)	-6	NM_001172073	72354	Mm.25806	NM_028209	ENSMUSG00000025413	Ttc4	2810002P21Rik|AF007005|L62	tetratricopeptide repeat domain 4	protein-coding
mm_166534.1	chr6	30304611	30304618	+	1	NA	promoter-TSS (NM_009459)	promoter-TSS (NM_009459)	-75	NM_001169576	22214	Mm.332967	NM_009459	ENSMUSG00000039159	Ube2h	1500009C23Rik|AI181839|AI326965|AI462483|AW227540|E2-20K|Gid3|N28148|Ubc8	ubiquitin-conjugating enzyme E2H	protein-coding
mm_56189.1	chr6	88518761	88518880	-	1	NA	promoter-TSS (NM_016906)	promoter-TSS (NM_016906)	-20	NM_016906	53421	Mm.28375	NM_016906	ENSMUSG00000030082	Sec61a1	AA408394|AA410007|Sec61a	Sec61 alpha 1 subunit (S. cerevisiae)	protein-coding
mm_21073.1	chr2	152830411	152830417	-	1	NA	5' UTR (NM_001289716, exon 1 of 3)	5' UTR (NM_001289716, exon 1 of 3)	303	NM_001289716	12048	Mm.238213	NM_009743	ENSMUSG00000007659	Bcl2l1	Bcl(X)L|Bcl-XL|Bcl2l|BclX|bcl-x|bcl2-L-1	BCL2-like 1	protein-coding
mm_166108.1	chr4	146932504	146932520	+	1	NA	Intergenic	CpG	-89338	NM_001177767	100043034	Mm.422606	NM_001177767	ENSMUSG00000067919	Rex2	Gm13138|OTTMUSG00000010655	reduced expression 2	protein-coding
mm_22147.1	chr2	172370879	172370922	-	1	NA	promoter-TSS (NM_001291185)	promoter-TSS (NM_001291185)	-103	NM_024199	67337	Mm.26944	NM_024199	ENSMUSG00000027498	Cstf1	1700057K18Rik|AI788832	cleavage stimulation factor, 3' pre-RNA, subunit 1	protein-coding
mm_69292.1	chr7	128220869	128220879	-	1	NA	Intergenic	Intergenic	-14508	NM_009943	12862	Mm.43824	NM_009943	ENSMUSG00000030785	Cox6a2	CoxVIaH|VIaH	cytochrome c oxidase subunit VIa polypeptide 2	protein-coding
mm_108984.1	chr12	102757749	102757759	+	1	NA	promoter-TSS (NM_001142939)	promoter-TSS (NM_001142939)	56	NM_001142939	100859931	Mm.291222	NM_001142939	ENSMUSG00000041716	Gm20604	AK010878-Moap1	predicted gene 20604	protein-coding
mm_130666.1	chr15	100669536	100669560	-	1	NA	promoter-TSS (NM_001270537)	promoter-TSS (NM_001270537)	-48	NM_001270537	668218	Mm.451225	NM_001270537	ENSMUSG00000098112	Bin2	-	bridging integrator 2	protein-coding
mm_115034.1	chr13	99248013	99248029	+	1	NA	TTS (NM_001004149)	TTS (NM_001004149)	63198	NM_001004149	238803	Mm.343207	NM_001004149	ENSMUSG00000050919	Zfp366	DC-SCRIPT|Znf366	zinc finger protein 366	protein-coding
mm_130169.1	chr15	93275123	93275143	-	1	NA	promoter-TSS (NM_001033275)	promoter-TSS (NM_001033275)	46	NM_001346785	223827	Mm.22819	NM_001033275	ENSMUSG00000036197	Gxylt1	Glt8d3|Gm1228|Gm87	glucoside xylosyltransferase 1	protein-coding
mm_162271.1	chr1	10261685	10261719	+	1	NA	Intergenic	L2a|LINE|L2	-29032	NM_001102430	211673	Mm.229141	NM_001102430	ENSMUSG00000067851	Arfgef1	ARFGEP1|BIG1|D130059B05Rik|D730028O18Rik|P200	ADP-ribosylation factor guanine nucleotide-exchange factor 1(brefeldin A-inhibited)	protein-coding
mm_69470.1	chr7	133709052	133709067	-	1	NA	promoter-TSS (NM_025392)	promoter-TSS (NM_025392)	236	NM_009479	22276	Mm.3160	NM_009479	ENSMUSG00000030979	Uros	AI415298|UROIIIS|Uros3	uroporphyrinogen III synthase	protein-coding
mm_62881.1	chr7	114768753	114768763	+	1	NA	intron (NM_173767, intron 1 of 12)	intron (NM_173767, intron 1 of 12)	22992	NM_173767	233752	Mm.83037	NM_173767	ENSMUSG00000048782	Insc	3830422K02Rik|C730020D23	inscuteable homolog (Drosophila)	protein-coding
mm_5594.1	chr1	39558302	39558325	-	1	NA	intron (NM_001033135, intron 5 of 6)	intron (NM_001033135, intron 5 of 6)	-9473	NR_028555	100217461		NR_028555	ENSMUSG00000077704	Snord89	MBII-289	small nucleolar RNA, C/D box 89	snoRNA
mm_12237.1	chr2	68830758	68830778	+	1	NA	Intergenic	Intergenic	-30673	NM_172856	241447	Mm.222222	NM_172856	ENSMUSG00000027035	Cers6	4732462C07Rik|AW544719|Lass6|T1L	ceramide synthase 6	protein-coding
mm_84155.1	chr9	59486648	59486679	-	1	NA	promoter-TSS (NM_019927)	promoter-TSS (NM_019927)	-289	NM_019927	23806	Mm.305925	NM_019927	ENSMUSG00000025234	Arih1	AU021774|Ari|Ari1|Hari|Hhari|Ubch7bp|Uip77	ariadne RBR E3 ubiquitin protein ligase 1	protein-coding
mm_63761.1	chr7	131112199	131112217	+	1	NA	exon (NM_007769, exon 44 of 47)	exon (NM_007769, exon 44 of 47)	34075	NM_173409	233918	Mm.78341	NM_173409	ENSMUSG00000013668	4933402N03Rik	4930412O05	RIKEN cDNA 4933402N03 gene	protein-coding
mm_144835.1	chr18	36529206	36529208	+	1	NA	intron (NM_172830, intron 2 of 20)	intron (NM_172830, intron 2 of 20)	1055	NM_001271544	240215	Mm.135463	NM_172830	ENSMUSG00000024485	Slc4a9	AE4|D630003B07|D630024F24Rik	solute carrier family 4, sodium bicarbonate cotransporter, member 9	protein-coding
mm_131885.1	chr16	23225428	23225448	+	1	NA	promoter-TSS (NM_001252505)	promoter-TSS (NM_001252505)	-583	NM_001252505	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_163017.1	chr11	46083701	46083716	+	1	NA	intron (NM_001291890, intron 3 of 22)	intron (NM_001291890, intron 3 of 22)	-18562	NR_106177	102465996		NR_106177	ENSMUSG00000098942	Mir8100	Gm27638|mmu-mir-8100	microRNA 8100	ncRNA
mm_46040.1	chr5	91963081	91963105	-	1	NA	promoter-TSS (NM_001271797)	promoter-TSS (NM_001271797)	-25	NM_001271797	68098	Mm.159453	NM_026557	ENSMUSG00000029397	Rchy1	ARNIP|CHIMP|Pirh2|Zfp363|Znf363	ring finger and CHY zinc finger domain containing 1	protein-coding
mm_47774.1	chr5	131616600	131616611	-	1	NA	intron (NM_177047, intron 5 of 18)	CpG	-263664	NR_040704	75369	Mm.389696	NR_040704	ENSMUSG00000105773	4930563F08Rik	-	RIKEN cDNA 4930563F08 gene	ncRNA
mm_103050.1	chr11	69813957	69813966	-	1	NA	Intergenic	(CTGGGG)n|Simple_repeat|Simple_repeat	4479	NM_175368	108803	Mm.73263	NM_175368	ENSMUSG00000044084	4933402P03Rik	-	RIKEN cDNA 4933402P03 gene	protein-coding
mm_31444.1	chr4	48585228	48585245	+	1	NA	promoter-TSS (NM_021436)	promoter-TSS (NM_021436)	43	NM_021436	230157	Mm.422686	NM_021436	ENSMUSG00000028347	Tmeff1	A830033E11|M7365|Tr1	transmembrane protein with EGF-like and two follistatin-like domains 1	protein-coding
mm_18228.1	chr2	51678187	51678190	-	1	NA	intron (NR_040639, intron 2 of 6)	MIR|SINE|MIR	50677	NM_199158	387511	Mm.377918	NM_199158	ENSMUSG00000056115	Tas2r134	T2R134|Tas2r34	taste receptor, type 2, member 134	protein-coding
mm_153846.1	chr19	46332915	46332928	-	1	NA	intron (NM_001164291, intron 1 of 8)	intron (NM_001164291, intron 1 of 8)	4737	NM_133694	68431	Mm.19973	NM_133694	ENSMUSG00000025226	Fbxl15	0710008C12Rik|Fbxo37	F-box and leucine-rich repeat protein 15	protein-coding
mm_29743.1	chr3	126923025	126923037	-	1	NA	3' UTR (NM_178655, exon 25 of 25)	3' UTR (NM_178655, exon 25 of 25)	20355	NM_001034168	109676	Mm.220242	NM_178655	ENSMUSG00000032826	Ank2	100043364|AI835472|AW491075|Ank-2|Gm4392	ankyrin 2, brain	protein-coding
mm_107579.1	chr12	44525639	44525660	+	1	NA	intron (NM_001146031, intron 3 of 27)	intron (NM_001146031, intron 3 of 27)	196764	NM_001146031	319504	Mm.208439	NM_176930	ENSMUSG00000020598	Nrcam	Bravo|C030017F07Rik|C130076O07Rik|mKIAA0343	neuronal cell adhesion molecule	protein-coding
mm_115772.1	chr13	19308035	19308039	-	1	NA	Intergenic	Intergenic	87776	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_167124.1	chr7	122402122	122402126	-	1	NA	intron (NM_001316672, intron 2 of 16)	MTD|LTR|ERVL-MaLR	112999	NM_008855	18751	Mm.207496	NM_008855	ENSMUSG00000052889	Prkcb	PKC-B|PKC-Beta|Pkcb|Prkcb1|Prkcb2	protein kinase C, beta	protein-coding
mm_15200.1	chr2	154206500	154206505	+	1	NA	exon (NM_153418, exon 5 of 16)	exon (NM_153418, exon 5 of 16)	6122	NM_153418	228801	Mm.3783	NM_153418	ENSMUSG00000027485	Bpifb1	Lplunc1	BPI fold containing family B, member 1	protein-coding
mm_60694.1	chr7	45175158	45175163	+	1	NA	3' UTR (NM_182993, exon 12 of 12)	3' UTR (NM_182993, exon 12 of 12)	1857	NR_106022	102465638		NR_106022	ENSMUSG00000106470	Mir7055	mmu-mir-7055	microRNA 7055	ncRNA
mm_33565.1	chr4	131921199	131921207	+	1	NA	promoter-TSS (NM_001201367)	promoter-TSS (NM_001201367)	-568	NM_001201367	623230	Mm.421179	NM_001201367	ENSMUSG00000070720	Tmem200b	EG623230	transmembrane protein 200B	protein-coding
mm_51849.1	chr6	90364202	90364205	+	1	NA	3' UTR (NM_144940, exon 20 of 20)	3' UTR (NM_144940, exon 20 of 20)	-5291	NM_173002	80292	Mm.100116	NM_030260	ENSMUSG00000034430	Zxdc	A930012H20|B930086F11Rik|BC003332	ZXD family zinc finger C	protein-coding
mm_100816.1	chr11	5129221	5129260	-	1	NA	intron (NM_080595, intron 10 of 14)	intron (NM_080595, intron 10 of 14)	22982	NM_080595	140703	Mm.840	NM_080595	ENSMUSG00000034164	Emid1	AW122071|CO-5|Emu1	EMI domain containing 1	protein-coding
mm_62151.1	chr7	97132678	97132683	+	1	NA	intron (NM_001162477, intron 1 of 9)	L1_Mur1|LINE|L1	50929	NM_010248	14389	Mm.42033	NM_010248	ENSMUSG00000004508	Gab2	AI463667|D130058I17Rik|p97	growth factor receptor bound protein 2-associated protein 2	protein-coding
mm_66191.1	chr7	34209883	34209921	-	1	NA	intron (NM_008155, intron 9 of 17)	intron (NM_008155, intron 9 of 17)	-13255	NM_026549	68079	Mm.38173	NM_026549	ENSMUSG00000002635	Pdcd2l	6030457N17Rik	programmed cell death 2-like	protein-coding
mm_173304.1	chrY	74574054	74574055	+	1	NA	Intergenic	Intergenic	-621802	NM_201530	382301	Mm.304354	NM_201530	ENSMUSG00000101155	Sly	-	Sycp3 like Y-linked	protein-coding
mm_47752.1	chr5	131168580	131168580	-	1	NA	intron (NM_145218, intron 1 of 10)	ORR1D2|LTR|ERVL-MaLR	138942	NM_145218	212996	Mm.299204	NM_145218	ENSMUSG00000034040	Wbscr17	AA388321|E330012B09Rik	Williams-Beuren syndrome chromosome region 17 homolog (human)	protein-coding
mm_151341.1	chr19	55895434	55895454	+	1	NA	5' UTR (NM_001142924, exon 1 of 12)	5' UTR (NM_001142924, exon 1 of 12)	123	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_134701.1	chr16	22657249	22657260	-	1	NA	promoter-TSS (NM_138650)	promoter-TSS (NM_138650)	-23	NM_001346673	110197	Mm.194986	NM_138650	ENSMUSG00000022861	Dgkg	2900055E17Rik|90kDa|AI854428|Dagk3|E430001K23Rik|mKIAA4131	diacylglycerol kinase, gamma	protein-coding
mm_30726.1	chr4	13751368	13751392	+	1	NA	promoter-TSS (NM_001111027)	promoter-TSS (NM_001111027)	83	NM_001111027	12395	Mm.4909	NM_009822	ENSMUSG00000006586	Runx1t1	Cbfa2t1h|ETO|MTG8	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	protein-coding
mm_149680.1	chr19	20492607	20492617	+	1	NA	promoter-TSS (NR_015502)	promoter-TSS (NR_015502)	-103	NR_015502	320092	Mm.482524	NR_015502		E030003E18Rik	1700127G21Rik	RIKEN cDNA E030003E18 gene	ncRNA
mm_140771.1	chr17	17826862	17826872	-	1	NA	Intergenic	Intergenic	-3321	NR_029536	387230		NR_029536	ENSMUSG00000065396	Mir99b	Mirn99b|mmu-mir-99b	microRNA 99b	ncRNA
mm_14887.1	chr2	148872852	148872891	+	1	NA	exon (NM_009976, exon 2 of 3)	exon (NM_009976, exon 2 of 3)	2641	NM_009976	13010	Mm.4263	NM_009976	ENSMUSG00000027447	Cst3	CysC	cystatin C	protein-coding
mm_74165.1	chr8	123418096	123418114	+	1	NA	exon (NM_023279, exon 2 of 4)	exon (NM_023279, exon 2 of 4)	6541	NM_023279	22152	Mm.40068	NM_023279	ENSMUSG00000062380	Tubb3	3200002H15Rik|M(beta)3|M(beta)6	tubulin, beta 3 class III	protein-coding
mm_84225.1	chr9	61946755	61946765	-	1	NA	promoter-TSS (NM_024245)	promoter-TSS (NM_024245)	39	NM_024245	71819	Mm.259374	NM_024245	ENSMUSG00000032254	Kif23	3110001D19Rik|C87313|CHO1|Knsl5|MKLP-1|MKLP1	kinesin family member 23	protein-coding
mm_13643.1	chr2	114050286	114050304	+	1	NA	exon (NM_009608, exon 3 of 7)	exon (NM_009608, exon 3 of 7)	2580	NM_009608	11464	Mm.686	NM_009608	ENSMUSG00000068614	Actc1	Actc-1	actin, alpha, cardiac muscle 1	protein-coding
mm_138886.1	chr17	43389580	43389594	+	1	NA	5' UTR (NM_001081178, exon 1 of 21)	5' UTR (NM_001081178, exon 1 of 21)	121	NM_001081178	224792	Mm.23478	NM_001081178	ENSMUSG00000056492	Adgrf5	8430401C09Rik|9330185D23|AI528491|Gpr116|mKIAA0758	adhesion G protein-coupled receptor F5	protein-coding
mm_51985.1	chr6	92091406	92091423	+	1	NA	promoter-TSS (NM_011630)	promoter-TSS (NM_011630)	-4	NM_011630	22026	Mm.87062	NM_011630	ENSMUSG00000005893	Nr2c2	TAK1|Tr4|mKIAA4145	nuclear receptor subfamily 2, group C, member 2	protein-coding
mm_148142.1	chr18	77040200	77040209	-	1	NA	intron (NM_027721, intron 1 of 13)	RMER19B|LTR|ERVK	7092	NM_027721	71206	Mm.35803	NM_027721	ENSMUSG00000025420	Katnal2	3110023G01Rik|4933439B08Rik	katanin p60 subunit A-like 2	protein-coding
mm_73289.1	chr8	104926305	104926315	+	1	NA	promoter-TSS (NM_001163756)	promoter-TSS (NM_001163756)	50	NM_172759	234673	Mm.441134	NM_172759	ENSMUSG00000031886	Ces2e	9030624L02Rik|Ces5	carboxylesterase 2E	protein-coding
mm_58487.1	chr7	3645268	3645321	+	1	NA	promoter-TSS (NM_146176)	promoter-TSS (NM_146176)	25	NM_146176	232791	Mm.358731	NM_146176	ENSMUSG00000035632	Cnot3	A930039N10Rik	CCR4-NOT transcription complex, subunit 3	protein-coding
mm_87241.1	chr10	40883820	40883862	+	1	NA	promoter-TSS (NM_027879)	promoter-TSS (NM_027879)	307	NM_031877	83767	Mm.41353	NM_031877	ENSMUSG00000019831	Wasf1	AI195380|AI838537|Scar|WAVE|WAVE-1	WAS protein family, member 1	protein-coding
mm_67166.1	chr7	73550655	73550668	-	1	NA	intron (NR_037569, intron 3 of 4)	B1_Mm|SINE|Alu	7734	NR_037569	69170	Mm.34539	NR_037569	ENSMUSG00000101970	1810026B05Rik	-	RIKEN cDNA 1810026B05 gene	ncRNA
mm_20526.1	chr2	130906286	130906294	-	1	NA	promoter-TSS (NM_009730)	promoter-TSS (NM_009730)	106	NR_015523	613258	Mm.271990	NR_015523		A730017L22Rik	-	RIKEN cDNA A730017L22 gene	ncRNA
mm_133768.1	chr16	94569906	94569953	+	1	NA	promoter-TSS (NM_001113389)	promoter-TSS (NM_001113389)	-277	NM_007890	13548	Mm.310973	NM_007890	ENSMUSG00000022897	Dyrk1a	2310043O08Rik|D16Ertd272e|D16Ertd493e|Dyrk|ENSMUSG00000074897|Gm10783|Mnbh|Mp86|mmb	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1a	protein-coding
mm_82036.1	chr9	122117339	122117367	+	1	NA	promoter-TSS (NM_133741)	promoter-TSS (NM_133741)	87	NM_133741	20623	Mm.257989	NM_133741	ENSMUSG00000038145	Snrk	2010012F07Rik|AI448042|AW547029|E030034B15|R74830|mKIAA0096	SNF related kinase	protein-coding
mm_73031.1	chr8	94179806	94179861	+	1	NA	exon (NM_013602, exon 2 of 3)	exon (NM_013602, exon 2 of 3)	744	NM_013602	17748	Mm.192991	NM_013602	ENSMUSG00000031765	Mt1	MT-I|Mt-1	metallothionein 1	protein-coding
mm_153948.1	chr19	47580889	47580892	-	1	NA	intron (NM_009289, intron 1 of 18)	intron (NM_009289, intron 1 of 18)	871	NM_001164639	20874	Mm.281011	NM_009289	ENSMUSG00000025060	Slk	9A2|AV021402|AW411554|Etk4|SMAK|Stk2|mKIAA0204|mSLK	STE20-like kinase	protein-coding
mm_73827.1	chr8	117459778	117459785	+	1	NA	TTS (NR_106046)	TTS (NR_106046)	516	NR_106046	102465653		NR_106046	ENSMUSG00000098483	Mir7078	Gm27386|mmu-mir-7078	microRNA 7078	ncRNA
mm_168610.1	chr1	175978924	175978945	-	1	NA	intron (NM_176916, intron 7 of 9)	intron (NM_176916, intron 7 of 9)	58605	NM_001290692	226720	Mm.11282	NM_001290692	ENSMUSG00000104158	Becn2	Beclin-2|Gm104	beclin 2	protein-coding
mm_173305.1	chrY	77701264	77701264	+	1	NA	Intergenic	Intergenic	1135455	NM_001160135	100039574	Mm.458579	NM_001160135	ENSMUSG00000094739	Gm20806	-	predicted gene, 20806	protein-coding
mm_97284.1	chr11	76179659	76179696	+	1	NA	promoter-TSS (NM_026664)	promoter-TSS (NM_026664)	-47	NM_026664	68299	Mm.46397	NM_026664	ENSMUSG00000017288	Vps53	2010002A08Rik|2310040I21Rik|3100002B05Rik|Hccs1	VPS53 GARP complex subunit	protein-coding
mm_9652.1	chr1	177643133	177643148	-	1	NA	promoter-TSS (NR_037994)	promoter-TSS (NR_037994)	-197	NR_037994	75589	Mm.86666	NR_037994	ENSMUSG00000101746	2310043L19Rik	-	RIKEN cDNA 2310043L19 gene	ncRNA
mm_124820.1	chr15	9071613	9071621	+	1	NA	exon (NM_001085410, exon 1 of 14)	exon (NM_001085410, exon 1 of 14)	357	NM_001040395	68646	Mm.244226	NM_001040395	ENSMUSG00000022253	Nadk2	MNADK|Nadkd1	NAD kinase 2, mitochondrial	protein-coding
mm_77603.1	chr8	123893012	123893027	-	1	NA	intron (NM_001272041, intron 4 of 7)	intron (NM_001272041, intron 4 of 7)	1756	NM_001272041	11459	Mm.214950	NM_009606	ENSMUSG00000031972	Acta1	AA959943|Acta-2|Acts|Actsk-1	actin, alpha 1, skeletal muscle	protein-coding
mm_18914.1	chr2	76736859	76736872	-	1	NA	exon (NM_011652, exon 275 of 313)	exon (NM_011652, exon 275 of 313)	61550	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_24722.1	chr3	95281329	95281348	+	1	NA	intron (NM_173347, intron 1 of 7)	CpG	738	NM_173347	229589	Mm.14155	NM_173347	ENSMUSG00000015711	Prune1	9230112O05Rik|C130058A12|DRES-17|HTCD37|PRUNEM1|Prune|Prune-M1	prune exopolyphosphatase	protein-coding
mm_88178.1	chr10	69925767	69925786	+	1	NA	5' UTR (NM_009670, exon 1 of 20)	5' UTR (NM_009670, exon 1 of 20)	244	NM_009670	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_115002.1	chr13	98263263	98263302	+	1	NA	promoter-TSS (NM_178918)	promoter-TSS (NM_178918)	206	NM_001271388	68558	Mm.209642	NM_023472	ENSMUSG00000021661	Ankra2	1110004M18Rik|Ankra	ankyrin repeat, family A (RFXANK-like), 2	protein-coding
mm_48772.1	chr5	148505849	148505861	-	1	NA	3' UTR (NM_011908, exon 5 of 5)	3' UTR (NM_011908, exon 5 of 5)	46933	NM_011908	24109	Mm.21846	NM_011908	ENSMUSG00000001687	Ubl3	AW108023|HCG	ubiquitin-like 3	protein-coding
mm_54333.1	chr6	30641784	30641803	-	1	NA	exon (NM_025350, exon 6 of 10)	exon (NM_025350, exon 6 of 10)	2575	NM_025350	109697	Mm.25377	NM_025350	ENSMUSG00000054446	Cpa1	0910001L12Rik|Cpa	carboxypeptidase A1, pancreatic	protein-coding
mm_30708.1	chr4	12095667	12095670	+	1	NA	3' UTR (NM_198957, exon 4 of 4)	3' UTR (NM_198957, exon 4 of 4)	6298	NM_198957	77604	Mm.474129	NM_198957	ENSMUSG00000052137	Rbm12b2	AV299215|C430048L16Rik|Rbm12bb	RNA binding motif protein 12 B2	protein-coding
mm_14037.1	chr2	122160702	122160737	+	1	NA	promoter-TSS (NM_080510)	promoter-TSS (NM_080510)	19	NM_080510	70928	Mm.379188	NM_080510	ENSMUSG00000033368	Trim69	4921519C19Rik|Rnf36|Trif|Trimless	tripartite motif-containing 69	protein-coding
mm_82814.1	chr9	30921214	30921217	-	1	NA	promoter-TSS (NM_001329420)	promoter-TSS (NM_001329420)	-265	NM_001329420	235130	Mm.65867	NM_001024139	ENSMUSG00000033453	Adamts15	-	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 15	protein-coding
mm_22587.1	chr3	13472451	13472469	+	1	NA	intron (NM_001163328, intron 1 of 8)	intron (NM_001163328, intron 1 of 8)	805	NM_001163328	76897	Mm.422625	NM_178631	ENSMUSG00000039717	Ralyl	0710005M24Rik	RALY RNA binding protein-like	protein-coding
mm_147416.1	chr18	46141642	46141648	-	1	NA	Intergenic	MTC-int|LTR|ERVL-MaLR	57173	NM_001170855	28105	Mm.277382	NM_178872	ENSMUSG00000033949	Trim36	D18Wsu100e|haprin	tripartite motif-containing 36	protein-coding
mm_163489.1	chr12	109453637	109453643	+	1	NA	non-coding (NR_033813, exon 2 of 6)	non-coding (NR_033813, exon 2 of 6)	185	NM_010052	13386	Mm.157069	NM_010052	ENSMUSG00000040856	Dlk1	AW742678|DLK-1|DlkI|FA1|Ly107|Peg9|SCP1|ZOG|pG2|pref-1	delta-like 1 homolog (Drosophila)	protein-coding
mm_96607.1	chr11	69091509	69091521	+	1	NA	3' UTR (NM_009497, exon 5 of 5)	3' UTR (NM_009497, exon 5 of 5)	2987	NM_009497	22318	Mm.28643	NM_009497	ENSMUSG00000020894	Vamp2	Syb-2|Syb2|sybII	vesicle-associated membrane protein 2	protein-coding
mm_114844.1	chr13	92683369	92683400	+	1	NA	exon (NM_172588, exon 4 of 12)	exon (NM_172588, exon 4 of 12)	72246	NM_172588	218442	Mm.297970	NM_172588	ENSMUSG00000021703	Serinc5	A130038L21Rik|AIGP3|C86123|TPO1	serine incorporator 5	protein-coding
mm_105727.1	chr11	109011989	109012000	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	91645	NM_015732	12006	Mm.71710	NM_015732	ENSMUSG00000000142	Axin2	Axi1|Axil|Conductin	axin 2	protein-coding
mm_23424.1	chr3	58692612	58692623	+	1	NA	promoter-TSS (NM_009174)	promoter-TSS (NM_009174)	28	NR_045167	71301	Mm.254475	NR_045167	ENSMUSG00000097725	4930593A02Rik	4933440I01Rik	RIKEN cDNA 4930593A02 gene	ncRNA
mm_93426.1	chr10	108879773	108879783	-	1	NA	intron (NM_001252341, intron 3 of 11)	intron (NM_001252341, intron 3 of 11)	131197	NM_009306	20979	Mm.289702	NM_009306	ENSMUSG00000035864	Syt1	AW124717|G630098F17Rik|SytI	synaptotagmin I	protein-coding
mm_94849.1	chr11	23771146	23771164	+	1	NA	promoter-TSS (NM_009044)	promoter-TSS (NM_009044)	-185	NM_009044	19696	Mm.4869	NM_009044	ENSMUSG00000020275	Rel	c-Rel	reticuloendotheliosis oncogene	protein-coding
mm_120778.1	chr14	74641300	74641317	+	1	NA	5' UTR (NM_172812, exon 1 of 3)	5' UTR (NM_172812, exon 1 of 3)	468	NM_172812	15558	Mm.214351	NM_172812	ENSMUSG00000034997	Htr2a	E030013E04|Htr-2|Htr2	5-hydroxytryptamine (serotonin) receptor 2A	protein-coding
mm_47158.1	chr5	120683415	120683461	-	1	NA	exon (NM_008052, exon 5 of 10)	exon (NM_008052, exon 5 of 10)	28231	NM_008052	14357	Mm.1645	NM_008052	ENSMUSG00000029603	Dtx1	Fxit1|mKIAA4160	deltex 1, E3 ubiquitin ligase	protein-coding
mm_31692.1	chr4	62380016	62380017	+	1	NA	intron (NM_175090, intron 1 of 4)	intron (NM_175090, intron 1 of 4)	19315	NM_175090	20529	Mm.248637	NM_175090	ENSMUSG00000066150	Slc31a1	4930445G01Rik|AI787263|AU016967|Ctr1	solute carrier family 31, member 1	protein-coding
mm_35899.1	chr4	49597403	49597416	-	1	NA	intron (NM_025944, intron 1 of 1)	CpG	461	NM_025944	67063	Mm.490285	NM_025944	ENSMUSG00000039611	Tmem246	2810432L12Rik|9330170P15Rik|AI835809	transmembrane protein 246	protein-coding
mm_5098.1	chr1	4910241	4910244	-	1	NA	3' UTR (NM_001290372, exon 5 of 5)	3' UTR (NM_001290372, exon 5 of 5)	51914	NM_001159751	21399	Mm.207263	NM_011541	ENSMUSG00000033813	Tcea1	S-II	transcription elongation factor A (SII) 1	protein-coding
mm_158735.1	chrX	164028001	164028029	-	1	NA	promoter-TSS (NM_181315)	promoter-TSS (NM_181315)	-5	NM_181315	56078	Mm.180953	NM_181315	ENSMUSG00000031373	Car5b	7330410H16Rik|CAVB|Ca5b|CarVb|D730005F19Rik	carbonic anhydrase 5b, mitochondrial	protein-coding
mm_61484.1	chr7	75697358	75697382	+	1	NA	exon (NM_029332, exon 16 of 37)	exon (NM_029332, exon 16 of 37)	-150968	NM_001122780	207952	Mm.206223	NM_029652	ENSMUSG00000055652	Klhl25	2810402K13Rik|BC027373|Enc-1	kelch-like 25	protein-coding
mm_115395.1	chr13	113794516	113794572	+	1	NA	promoter-TSS (NM_172595)	promoter-TSS (NM_172595)	36	NM_172595	218639	Mm.79837	NM_172595	ENSMUSG00000042348	Arl15	A430036I03|Arfrp2|C230032K13Rik	ADP-ribosylation factor-like 15	protein-coding
mm_59309.1	chr7	25282194	25282216	+	1	NA	promoter-TSS (NM_027882)	promoter-TSS (NM_027882)	26	NM_027882	71722	Mm.28833	NM_027882	ENSMUSG00000005442	Cic	1200010B10Rik|mKIAA0306	capicua transcriptional repressor	protein-coding
mm_45828.1	chr5	87694625	87694639	-	1	NA	exon (NM_001286023, exon 5 of 7)	exon (NM_001286023, exon 5 of 7)	4793	NM_001286020	12991	Mm.268737	NM_009972	ENSMUSG00000063157	Csn2	Csnb	casein beta	protein-coding
mm_34034.1	chr4	138147416	138147420	+	1	NA	intron (NM_172703, intron 13 of 34)	intron (NM_172703, intron 13 of 34)	-8900	NR_126429	73563	Mm.444294	NR_126429	ENSMUSG00000084804	1700095J12Rik	-	RIKEN cDNA 1700095J12 gene	ncRNA
mm_150131.1	chr19	30035501	30035535	+	1	NA	intron (NM_144873, intron 1 of 15)	RSINE1|SINE|B4	5005	NM_144873	109113	Mm.313364	NM_144873	ENSMUSG00000024817	Uhrf2	2310065A22Rik|AI426270|AW214556|D130071B19Rik|Nirf	ubiquitin-like, containing PHD and RING finger domains 2	protein-coding
mm_7934.1	chr1	133912427	133912449	-	1	NA	3' UTR (NM_054077, exon 3 of 3)	3' UTR (NM_054077, exon 3 of 3)	-4439	NM_001160420	269120	Mm.59985	NM_054076	ENSMUSG00000010311	Optc	-	opticin	protein-coding
mm_169889.1	chr16	4684095	4684095	+	1	NA	promoter-TSS (NM_023646)	promoter-TSS (NM_023646)	25	NM_001135112	83945	Mm.248337	NM_023646	ENSMUSG00000004069	Dnaja3	1200003J13Rik|1810053A11Rik|C81173|Tid-1|Tid1l	DnaJ heat shock protein family (Hsp40) member A3	protein-coding
mm_131213.1	chr16	8830038	8830058	+	1	NA	promoter-TSS (NM_001081400)	promoter-TSS (NM_001081400)	-52	NM_001081400	69053	Mm.390868	NM_001081400	ENSMUSG00000022507	1810013L24Rik	1110017P05Rik|3010002C02Rik|AA792997|AW124177|Gm19906|R74903	RIKEN cDNA 1810013L24 gene	protein-coding
mm_75519.1	chr8	54886965	54886999	-	1	NA	intron (NM_001253754, intron 1 of 6)	intron (NM_001253754, intron 1 of 6)	-67746	NM_153581	234267	Mm.241700	NM_153581	ENSMUSG00000031517	Gpm6a	Gpm6|M6A	glycoprotein m6a	protein-coding
mm_72422.1	chr8	82401929	82401974	+	1	NA	intron (NM_001254747, intron 1 of 7)	intron (NM_001254747, intron 1 of 7)	635	NM_001254747	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_39878.1	chr5	31077178	31077186	+	1	NA	exon (NM_001289522, exon 39 of 43)	exon (NM_001289522, exon 39 of 43)	16345	NM_011773	22784	Mm.1396	NM_011773	ENSMUSG00000029151	Slc30a3	Znt3	solute carrier family 30 (zinc transporter), member 3	protein-coding
mm_10274.1	chr2	9882217	9882227	+	1	NA	TTS (NR_040511)	TTS (NR_040511)	976	NR_024257	381347	Mm.441450	NR_024257		4930412O13Rik	ENSMUSG00000075535|Gm10853	RIKEN cDNA 4930412O13 gene	ncRNA
mm_159036.1	chr1	178187649	178187649	+	1	NA	5' UTR (NM_024282, exon 1 of 5)	5' UTR (NM_024282, exon 1 of 5)	232	NM_024282	78825	Mm.440132	NM_024282	ENSMUSG00000026502	Desi2	5830417C01Rik|DeSI-2|Fam152a|Pppde1	desumoylating isopeptidase 2	protein-coding
mm_92411.1	chr10	76723419	76723439	-	1	NA	exon (NM_009933, exon 3 of 35)	exon (NM_009933, exon 3 of 35)	2615	NM_009933	12833	Mm.2509	NM_009933	ENSMUSG00000001119	Col6a1	AI747156|Col6a-1	collagen, type VI, alpha 1	protein-coding
mm_144190.1	chr18	7869308	7869329	+	1	NA	5' UTR (NM_001146298, exon 1 of 13)	5' UTR (NM_001146298, exon 1 of 13)	121	NM_153085	225131	Mm.204524	NM_153085	ENSMUSG00000024283	Wac	1110067P07Rik|A230035H12Rik|AI256735|AI256776|Wwp4	WW domain containing adaptor with coiled-coil	protein-coding
mm_114314.1	chr13	59876046	59876056	+	1	NA	Intergenic	Intergenic	-52904	NM_153538	214290	Mm.233082	NM_153538	ENSMUSG00000035248	Zcchc6	6030448M23Rik|AA420405	zinc finger, CCHC domain containing 6	protein-coding
mm_64036.1	chr7	140770935	140770954	+	1	NA	exon (NM_021282, exon 6 of 9)	exon (NM_021282, exon 6 of 9)	7112	NM_021282	13106	Mm.21758	NM_021282	ENSMUSG00000025479	Cyp2e1	Cyp2e	cytochrome P450, family 2, subfamily e, polypeptide 1	protein-coding
mm_98013.1	chr11	84818833	84818870	+	1	NA	exon (NM_145433, exon 1 of 5)	exon (NM_145433, exon 1 of 5)	664	NM_145433	217038	Mm.280825	NM_145433	ENSMUSG00000018405	Mrm1	A530065E19Rik|ENSMUSG00000054212	mitochondrial rRNA methyltransferase 1	protein-coding
mm_48436.1	chr5	140623410	140623445	-	1	NA	3' UTR (NM_175274, exon 14 of 14)	3' UTR (NM_175274, exon 14 of 14)	16086	NM_008494	16848	Mm.12834	NM_008494	ENSMUSG00000029570	Lfng	AW061165	LFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	protein-coding
mm_20491.1	chr2	130274228	130274284	-	1	NA	promoter-TSS (NM_024193)	promoter-TSS (NM_024193)	-156	NM_024193	67134	Mm.29363	NM_024193	ENSMUSG00000027405	Nop56	2310044F10Rik|Nol5a	NOP56 ribonucleoprotein	protein-coding
mm_104961.1	chr11	100143564	100143587	-	1	NA	intron (NM_008471, intron 1 of 5)	intron (NM_008471, intron 1 of 5)	124	NM_001313963	16669	Mm.439699	NM_008471	ENSMUSG00000020911	Krt19	AI663979|CK-19|EndoC|K19|Krt-1.19|Krt1-19	keratin 19	protein-coding
mm_20885.1	chr2	148851124	148851130	-	1	NA	promoter-TSS (NM_029960)	promoter-TSS (NM_029960)	-193	NM_029960	77705	Mm.159975	NM_029960	ENSMUSG00000027446	9230104L09Rik	mCST E2	RIKEN cDNA 9230104L09 gene	protein-coding
mm_145103.1	chr18	44104317	44104329	+	1	NA	promoter-TSS (NM_030061)	promoter-TSS (NM_030061)	-200	NM_030061	78242	Mm.99782	NM_030061	ENSMUSG00000061144	Spink12	9230117E20Rik	serine peptidase inhibitor, Kazal type 12	protein-coding
mm_71799.1	chr8	68009085	68009088	+	1	NA	Intergenic	Intergenic	-34512	NM_177698	234353	Mm.32525	NM_027626	ENSMUSG00000030465	Psd3	4931420C21Rik|AI661273|BC003498|D430018P08|EFA6D	pleckstrin and Sec7 domain containing 3	protein-coding
mm_86662.1	chr10	17802514	17802518	+	1	NA	intron (NM_138628, intron 2 of 9)	intron (NM_138628, intron 2 of 9)	6297	NM_138628	378431	Mm.283493	NM_138628	ENSMUSG00000039891	Txlnb	2310001N14Rik|Mdp77	taxilin beta	protein-coding
mm_67820.1	chr7	98178890	98178894	-	1	NA	promoter-TSS (NM_007602)	promoter-TSS (NM_007602)	-618	NM_007602	12337	Mm.326847	NM_007602	ENSMUSG00000035547	Capn5	nCL-3	calpain 5	protein-coding
mm_8844.1	chr1	162702236	162702246	-	1	NA	exon (NM_001081290, exon 17 of 35)	exon (NM_001081290, exon 17 of 35)	38315	NM_001081290	226562	Mm.245446	NM_001081290	ENSMUSG00000040225	Prrc2c	1810043M20Rik|9630039I18Rik|A630006J20|Bat2d|Bat2d1|Bat2l2|E130112L15Rik|Prrc3|mKIAA1096	proline-rich coiled-coil 2C	protein-coding
mm_51503.1	chr6	83117713	83117732	+	1	NA	exon (NM_020619, exon 4 of 4)	exon (NM_020619, exon 4 of 4)	2216	NM_020619	57377	Mm.28188	NM_020619	ENSMUSG00000030036	Mogs	1810017N02Rik|AI181835|Gcs1	mannosyl-oligosaccharide glucosidase	protein-coding
mm_29536.1	chr3	116662644	116662654	-	1	NA	promoter-TSS (NM_008246)	promoter-TSS (NM_008246)	28	NM_008246	15247	Mm.280077	NM_008246	ENSMUSG00000089911	Mfsd14a	Hiat1	major facilitator superfamily domain containing 14A	protein-coding
mm_45620.1	chr5	75940791	75940794	-	1	NA	intron (NM_010612, intron 27 of 29)	intron (NM_010612, intron 27 of 29)	37636	NM_010612	16542	Mm.285	NM_010612	ENSMUSG00000062960	Kdr	6130401C07|Flk-1|Flk1|Krd-1|Ly73|VEGFR-2|VEGFR2|sVEGFR-2	kinase insert domain protein receptor	protein-coding
mm_16290.1	chr2	174111143	174111156	+	1	NA	exon (NM_213733, exon 2 of 12)	exon (NM_213733, exon 2 of 12)	798	NM_213733	228961	Mm.295629	NM_213733	ENSMUSG00000039263	Npepl1	BC023239|C85514|mKIAA1974	aminopeptidase-like 1	protein-coding
mm_124013.1	chr14	76152646	76152666	-	1	NA	Intergenic	Intergenic	41765	NM_013745	27275	Mm.21138	NM_013745	ENSMUSG00000022009	Nufip1	Nufip	nuclear fragile X mental retardation protein interacting protein 1	protein-coding
mm_70082.1	chr7	142653967	142653994	-	1	NA	TTS (NR_030251)	TTS (NR_030251)	1016	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_114251.1	chr13	56702427	56702435	+	1	NA	promoter-TSS (NM_008541)	promoter-TSS (NM_008541)	-579	NM_008541	17129	Mm.272920	NM_008541	ENSMUSG00000021540	Smad5	1110051M15Rik|AI451355|Dwf-C|Madh5|MusMLP	SMAD family member 5	protein-coding
mm_33464.1	chr4	130795360	130795364	+	1	NA	intron (NM_011520, intron 1 of 4)	intron (NM_011520, intron 1 of 4)	2825	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_159341.1	chr3	58885020	58885020	-	1	NA	exon (NM_153386, exon 1 of 2)	exon (NM_153386, exon 1 of 2)	192	NM_153386	229320	Mm.131502	NM_153384	ENSMUSG00000043850	Clrn1	A130002D11Rik|USH3|Ush3a|clarin-1	clarin 1	protein-coding
mm_24232.1	chr3	88950639	88950668	+	1	NA	promoter-TSS (NM_022994)	promoter-TSS (NM_022994)	-371	NM_001164533	65111	Mm.29028	NM_022994	ENSMUSG00000068921	Dap3	4921514D13Rik|DAP-3|MRP-S29|S29mt	death associated protein 3	protein-coding
mm_103444.1	chr11	76069685	76069687	-	1	NA	intron (NM_026664, intron 17 of 21)	intron (NM_026664, intron 17 of 21)	-41904	NM_029658	76566	Mm.34131	NM_029658	ENSMUSG00000020846	Rflnb	1500005K14Rik|Fam101b|RefilinB|cfm	refilin B	protein-coding
mm_48975.1	chr6	4754247	4754275	+	1	NA	exon (NM_130877, exon 2 of 2)	exon (NM_130877, exon 2 of 2)	6955	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_162559.1	chr1	172206681	172206683	-	1	NA	5' UTR (NM_001329871, exon 1 of 4)	5' UTR (NM_001329871, exon 1 of 4)	122	NM_001329871	18611	Mm.544	NM_011063	ENSMUSG00000013698	Pea15a	Mat1|PEA-15|Pea15|Pkcs15	phosphoprotein enriched in astrocytes 15A	protein-coding
mm_115531.1	chr13	6109098	6109108	-	1	NA	Intergenic	Intergenic	247614	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_30662.1	chr4	9844350	9844368	+	1	NA	promoter-TSS (NM_013526)	promoter-TSS (NM_013526)	-13	NM_013526	242316	Mm.302555	NM_013526	ENSMUSG00000051279	Gdf6	BMP-13|BMP13|GDF16	growth differentiation factor 6	protein-coding
mm_86345.1	chr9	123529572	123529611	-	1	NA	promoter-TSS (NM_030692)	promoter-TSS (NM_030692)	-291	NM_030692	83493	Mm.273671	NM_030692	ENSMUSG00000025240	Sacm1l	SAC1|Sac1p|mKIAA0851	SAC1 suppressor of actin mutations 1-like (yeast)	protein-coding
mm_43705.1	chr5	139352608	139352623	+	1	NA	promoter-TSS (NM_001160265)	promoter-TSS (NM_001160265)	-2	NM_001160265	545817	Mm.482474	NM_001160265	ENSMUSG00000029541	Cyp2w1	Gm455	cytochrome P450, family 2, subfamily w, polypeptide 1	protein-coding
mm_100132.1	chr11	115974741	115974752	+	1	NA	promoter-TSS (NM_133663)	promoter-TSS (NM_133663)	21	NM_133663	192897	Mm.213873	NM_133663	ENSMUSG00000020758	Itgb4	AA407042|C230078O20|CD104	integrin beta 4	protein-coding
mm_165729.1	chr3	105959200	105959211	-	1	NA	promoter-TSS (NM_027432)	promoter-TSS (NM_027432)	-293	NM_027432	70465	Mm.5110	NM_027432	ENSMUSG00000000561	Wdr77	2610003I18Rik|2610312E17Rik|C79984|p44/MEP50	WD repeat domain 77	protein-coding
mm_33316.1	chr4	129077467	129077469	+	1	NA	intron (NM_029219, intron 5 of 8)	B2_Mm2|SINE|B2	19197	NM_029219	75234	Mm.259672	NM_029219	ENSMUSG00000028793	Rnf19b	4930534K13Rik|4930555L03Rik|Ibrdc3	ring finger protein 19B	protein-coding
mm_10124.1	chr2	3749327	3749364	+	1	NA	intron (NM_025626, intron 1 of 3)	intron (NM_025626, intron 1 of 3)	35887	NM_025626	66540	Mm.277864	NM_025626	ENSMUSG00000026655	Fam107b	3110001A13Rik|AA589595|AA959793|AI132312	family with sequence similarity 107, member B	protein-coding
mm_82063.1	chr9	122747225	122747241	+	1	NA	promoter-TSS (NM_001199736)	promoter-TSS (NM_001199736)	-113	NM_001199736	671232	Mm.296421	NM_001199736	ENSMUSG00000094985	Topaz1	Gm9524	testis and ovary specific PAZ domain containing 1	protein-coding
mm_126332.1	chr15	79894987	79895015	+	1	NA	promoter-TSS (NM_001347041)	promoter-TSS (NM_001347041)	-22	NM_001347041	80287	Mm.284059	NM_030255	ENSMUSG00000009585	Apobec3	Apobec|Arp3|BC003314|Cem15|Rfv3	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 3	protein-coding
mm_91184.1	chr10	21065776	21065808	-	1	NA	intron (NM_001177776, intron 4 of 6)	intron (NM_001177776, intron 4 of 6)	24972	NM_001177776	52906	Mm.253280	NM_026203	ENSMUSG00000019986	Ahi1	1700015F03Rik|Ahi-1|D10Bwg0629e	Abelson helper integration site 1	protein-coding
mm_49898.1	chr6	38923168	38923171	+	1	NA	intron (NM_011539, intron 1 of 12)	intron (NM_011539, intron 1 of 12)	4183	NM_011539	21391	Mm.4054	NM_011539	ENSMUSG00000029925	Tbxas1	CYP5|CYP5A1|THAS|TS|TXAS|TXS	thromboxane A synthase 1, platelet	protein-coding
mm_30974.1	chr4	34550901	34550916	+	1	NA	5' UTR (NM_001007589, exon 1 of 5)	5' UTR (NM_001007589, exon 1 of 5)	293	NM_001007589	433693	Mm.389532	NM_026019	ENSMUSG00000028291	Akirin2	2700059D21Rik|AA114675|AA522011|AU019887|Akirin-2	akirin 2	protein-coding
mm_65673.1	chr7	28301773	28301791	-	1	NA	promoter-TSS (NM_007866)	promoter-TSS (NM_007866)	3	NM_007866	13389	Mm.12896	NM_007866	ENSMUSG00000003436	Dll3	pu|pudgy	delta-like 3 (Drosophila)	protein-coding
mm_159514.1	chr4	60070476	60070476	-	1	NA	promoter-TSS (NM_001134675)	promoter-TSS (NM_001134675)	-1	NM_001134675	100041658	Mm.457982	NM_001134675	ENSMUSG00000073842	Mup7	Gm12546|Mup3|OTTMUSG00000007428	major urinary protein 7	protein-coding
mm_87196.1	chr10	39532097	39532102	+	1	NA	exon (NM_008054, exon 10 of 14)	exon (NM_008054, exon 10 of 14)	-80835	NM_134000	103213	Mm.436686	NM_134000	ENSMUSG00000019842	Traf3ip2	AI429613|Act1|CIKS	TRAF3 interacting protein 2	protein-coding
mm_32410.1	chr4	107002594	107002628	+	1	NA	intron (NM_023672, intron 4 of 17)	intron (NM_023672, intron 4 of 17)	64255	NM_025500	56280	Mm.29517	NM_025500	ENSMUSG00000028622	Mrpl37	2300004O14Rik|AI132596|MRP-L2|Rpml2	mitochondrial ribosomal protein L37	protein-coding
mm_150123.1	chr19	29959514	29959521	+	1	NA	3' UTR (NM_001164724, exon 8 of 8)	3' UTR (NM_001164724, exon 8 of 8)	13727	NM_001164724	77125	Mm.182359	NM_133775	ENSMUSG00000024810	Il33	9230117N10Rik|Il-33|Il1f11|NF-HEV	interleukin 33	protein-coding
mm_153695.1	chr19	44397330	44397372	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	10358	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_30257.1	chr3	146651305	146651327	-	1	NA	promoter-TSS (NM_029144)	promoter-TSS (NM_029144)	1	NM_029144	75015	Mm.250432	NM_029144	ENSMUSG00000048652	4930503B20Rik	1700013A07Rik|1700095G21Rik|4930483N21Rik|Gm1652|Samd13	RIKEN cDNA 4930503B20 gene	protein-coding
mm_93342.1	chr10	99759637	99759652	-	1	NA	promoter-TSS (NM_027945)	promoter-TSS (NM_027945)	14	NM_027945	71832	Mm.483162	NM_027945	ENSMUSG00000046934	Csl	1700007H16Rik	citrate synthase like	protein-coding
mm_73712.1	chr8	111689143	111689193	+	1	NA	TTS (NR_106044)	TTS (NR_106044)	506	NR_106044	102466993		NR_106044	ENSMUSG00000099129	Mir7076	Gm27318|mmu-mir-7076	microRNA 7076	ncRNA
mm_165872.1	chr4	40703139	40703150	-	1	NA	promoter-TSS (NM_025545)	promoter-TSS (NM_025545)	50	NM_001025444	66408	Mm.430710	NM_025545	ENSMUSG00000028411	Aptx	2410016G21Rik|AA388047|FHA-HIT	aprataxin	protein-coding
mm_25222.1	chr3	103853245	103853253	+	1	NA	intron (NM_001142960, intron 3 of 3)	intron (NM_001142960, intron 3 of 3)	-6546	NR_104070	19260	Mm.395	NM_008979	ENSMUSG00000027843	Ptpn22	70zpep|PEP|Ptpn8	protein tyrosine phosphatase, non-receptor type 22 (lymphoid)	protein-coding
mm_148916.1	chr19	6975139	6975158	+	1	NA	promoter-TSS (NM_008889)	promoter-TSS (NM_008889)	100	NM_008889	18938	Mm.140	NM_008889	ENSMUSG00000056612	Ppp1r14b	AOM172|PHI-1|PLCB3N|Png	protein phosphatase 1, regulatory (inhibitor) subunit 14B	protein-coding
mm_74328.1	chr8	126909046	126909073	+	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	36862	NM_024214	67952	Mm.6932	NM_024214	ENSMUSG00000093904	Tomm20	1810060K07Rik|BB284719|Gm19268|MAS20|MOM19|TOM20|mKIAA0016	translocase of outer mitochondrial membrane 20 homolog (yeast)	protein-coding
mm_130681.1	chr15	100678174	100678178	-	1	NA	intron (NM_033612, intron 6 of 7)	intron (NM_033612, intron 6 of 7)	-8676	NM_001270537	668218	Mm.451225	NM_001270537	ENSMUSG00000098112	Bin2	-	bridging integrator 2	protein-coding
mm_41496.1	chr5	92323797	92323804	+	1	NA	exon (NM_008599, exon 4 of 4)	exon (NM_008599, exon 4 of 4)	4279	NM_008599	17329	Mm.766	NM_008599	ENSMUSG00000029417	Cxcl9	BB139920|CMK|Mig|MuMIG|Scyb9|crg-10	chemokine (C-X-C motif) ligand 9	protein-coding
mm_19163.1	chr2	83941202	83941213	-	1	NA	promoter-TSS (NM_027964)	promoter-TSS (NM_027964)	19	NM_027964	71861	Mm.116957	NM_027964	ENSMUSG00000034552	Zswim2	1700025P14Rik|4933437F18Rik|MEX	zinc finger SWIM-type containing 2	protein-coding
mm_9078.1	chr1	168431565	168431591	-	1	NA	5' UTR (NM_001291509, exon 1 of 7)	5' UTR (NM_001291509, exon 1 of 7)	591	NM_001291508	18514	Mm.43358	NM_008783	ENSMUSG00000052534	Pbx1	2310056B04Rik|D230003C07Rik|Pbx-1	pre B cell leukemia homeobox 1	protein-coding
mm_53631.1	chr6	140530961	140530964	+	1	NA	intron (NM_144920, intron 7 of 30)	intron (NM_144920, intron 7 of 30)	-91701	NM_178803	11569	Mm.86453	NM_009637	ENSMUSG00000030232	Aebp2	AU023766|B230313N05Rik	AE binding protein 2	protein-coding
mm_145971.1	chr18	67933501	67933521	+	1	NA	intron (NM_172631, intron 1 of 5)	CpG	254	NM_172631	52662	Mm.440183	NM_172631	ENSMUSG00000024544	Ldlrad4	8230401C20Rik|A430083H02|A430108L08Rik|C18orf1|D18Ertd653e|D330030L18Rik	low density lipoprotein receptor class A domain containing 4	protein-coding
mm_86941.1	chr10	24595624	24595630	+	1	NA	5' UTR (NM_010217, exon 1 of 5)	5' UTR (NM_010217, exon 1 of 5)	185	NM_010217	14219	Mm.390287	NM_010217	ENSMUSG00000019997	Ctgf	Ccn2|Fisp12|Hcs24|fisp-12	connective tissue growth factor	protein-coding
mm_98376.1	chr11	94044325	94044329	+	1	NA	5' UTR (NM_001199205, exon 1 of 27)	5' UTR (NM_001199205, exon 1 of 27)	122	NM_001025429	70834	Mm.260737	NM_027569	ENSMUSG00000020859	Spag9	3110018C07Rik|4733401I23Rik|4831406C20Rik|AW552012|JLP|JSAP2|JSAP2a|Jip4|Mapk8ip4|syd1	sperm associated antigen 9	protein-coding
mm_98906.1	chr11	98026940	98026968	+	1	NA	promoter-TSS (NM_009078)	promoter-TSS (NM_009078)	30	NM_009078	19921	Mm.10247	NM_009078	ENSMUSG00000017404	Rpl19	-	ribosomal protein L19	protein-coding
mm_123550.1	chr14	66834254	66834298	-	1	NA	exon (NM_009955, exon 4 of 14)	exon (NM_009955, exon 4 of 14)	34324	NM_009955	12934	Mm.352648	NM_009955	ENSMUSG00000022048	Dpysl2	AI851130|Crmp2|DRP2|Musunc33|TOAD-64|Ulip2	dihydropyrimidinase-like 2	protein-coding
mm_27873.1	chr3	79166025	79166044	-	1	NA	Intergenic	Intergenic	-20159	NM_001099624	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_52116.1	chr6	97915419	97915429	+	1	NA	intron (NM_001113198, intron 1 of 9)	ID_B1|SINE|B4	-14393	NM_001178049	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_13718.1	chr2	117181753	117181764	+	1	NA	3' UTR (NM_033524, exon 7 of 7)	3' UTR (NM_033524, exon 7 of 7)	-3369	NR_030440	732489		NR_030440	ENSMUSG00000076376	Mir674	Mirn674|mir-674|mmu-mir-674	microRNA 674	ncRNA
mm_32963.1	chr4	119814534	119814563	+	1	NA	promoter-TSS (NM_010657)	promoter-TSS (NM_010657)	-130	NM_010657	16656	Mm.302758	NM_010657	ENSMUSG00000028634	Hivep3	2900056N03Rik|A130075N07|AI848000|E030045D18Rik|KBP-1|KBP1|Krc|Rc|Schnurri-3|Shn3|Zas3	human immunodeficiency virus type I enhancer binding protein 3	protein-coding
mm_11952.1	chr2	52967689	52967699	+	1	NA	intron (NM_172409, intron 1 of 26)	intron (NM_172409, intron 1 of 26)	109826	NM_172409	71409	Mm.394427	NM_172409	ENSMUSG00000036053	Fmnl2	5430425K04Rik|Man	formin-like 2	protein-coding
mm_129182.1	chr15	76306695	76306705	-	1	NA	intron (NM_153122, intron 1 of 26)	intron (NM_153122, intron 1 of 26)	545	NM_153122	75475	Mm.322738	NM_153122	ENSMUSG00000022562	Oplah	1700010G02Rik	5-oxoprolinase (ATP-hydrolysing)	protein-coding
mm_168124.1	chr10	22144366	22144379	-	1	NA	TTS (NM_001254745)	TTS (NM_001254745)	4898	NM_001254744	319887	Mm.177746	NM_001254744	ENSMUSG00000097327	E030030I06Rik	-	RIKEN cDNA E030030I06 gene	protein-coding
mm_150568.1	chr19	40089700	40089723	+	1	NA	promoter-TSS (NM_001167877)	promoter-TSS (NM_001167877)	32	NM_001167875	107141	Mm.474575	NM_134144	ENSMUSG00000054827	Cyp2c50	AI266900	cytochrome P450, family 2, subfamily c, polypeptide 50	protein-coding
mm_97627.1	chr11	78958823	78958833	+	1	NA	intron (NM_001313921, intron 25 of 25)	PB1D10|SINE|Alu	26096	NM_001159301	16859	Mm.341434	NM_010708	ENSMUSG00000001123	Lgals9	AA407335|AI194909|AI265545|LGALS35|Lgals5|gal-9|galectin-9	lectin, galactose binding, soluble 9	protein-coding
mm_81687.1	chr9	111119424	111119447	+	1	NA	intron (NM_027742, intron 1 of 13)	intron (NM_027742, intron 1 of 13)	1324	NM_001164838	71268	Mm.302287	NM_027742	ENSMUSG00000032497	Lrrfip2	5133400F20Rik|AI850587	leucine rich repeat (in FLII) interacting protein 2	protein-coding
mm_39643.1	chr5	24587138	24587165	+	1	NA	5' UTR (NM_133913, exon 1 of 4)	5' UTR (NM_133913, exon 1 of 4)	401	NM_133913	100910	Mm.140672	NM_133913	ENSMUSG00000038181	Chpf2	2010209O12Rik|AW060945|mKIAA1402|mir-671	chondroitin polymerizing factor 2	protein-coding
mm_106009.1	chr11	115813605	115813609	-	1	NA	promoter-TSS (NM_080643)	promoter-TSS (NM_080643)	-15	NM_080643	140721	Mm.383737	NM_080643	ENSMUSG00000034471	Caskin2	1600028L06Rik|mKIAA1139	CASK-interacting protein 2	protein-coding
mm_5102.1	chr1	5070282	5070288	-	1	NA	promoter-TSS (NM_001177795)	promoter-TSS (NM_001177795)	0	NM_001177795	58175	Mm.103771	NM_021374	ENSMUSG00000002459	Rgs20	2900073E09Rik|Rgsz1	regulator of G-protein signaling 20	protein-coding
mm_120850.1	chr14	75216385	75216426	+	1	NA	exon (NM_001247984, exon 13 of 16)	exon (NM_001247984, exon 13 of 16)	-25882	NM_019775	56373	Mm.24242	NM_019775	ENSMUSG00000021999	Cpb2	1110032P04Rik|4930405E17Rik|AI255929|CPR|Cpu|TAFI	carboxypeptidase B2 (plasma)	protein-coding
mm_111499.1	chr12	99392914	99392996	-	1	NA	intron (NM_183186, intron 1 of 5)	CpG	57119	NM_183186	71375	Mm.341972	NM_183186	ENSMUSG00000033713	Foxn3	5430426H20Rik|AA589593|AW556347|Ches1|Ches1l|HTLFL1	forkhead box N3	protein-coding
mm_111491.1	chr12	99011639	99011675	-	1	NA	Intergenic	Intergenic	91045	NM_198311	76260	Mm.282660	NM_029553	ENSMUSG00000021013	Ttc8	0610012F22Rik|AV001447|BBS8	tetratricopeptide repeat domain 8	protein-coding
mm_1982.1	chr1	86789262	86789265	+	1	NA	intron (NM_153530, intron 5 of 20)	L1_Mus3|LINE|L1	85459	NM_001172157	208718	Mm.389152	NM_153530	ENSMUSG00000053333	Dis3l2	4930429A22Rik|8030493P09Rik	DIS3 like 3'-5' exoribonuclease 2	protein-coding
mm_28728.1	chr3	95735313	95735324	-	1	NA	promoter-TSS (NR_105981)	promoter-TSS (NR_105981)	-345	NR_105981	102466787		NR_105981	ENSMUSG00000098737	Mir7014	Gm27837|mmu-mir-7014	microRNA 7014	ncRNA
mm_127989.1	chr15	12549899	12549909	-	1	NA	intron (NM_001081064, intron 1 of 23)	intron (NM_001081064, intron 1 of 23)	42652	NM_001081064	68070	Mm.423205	NM_001081064	ENSMUSG00000022197	Pdzd2	4930537L06Rik|A930022H17Rik|Gm21706|Gm82|Pdzk3|mKIAA0300	PDZ domain containing 2	protein-coding
mm_47145.1	chr5	120560374	120560402	-	1	NA	intron (NM_145853, intron 2 of 27)	ORR1B1|LTR|ERVL-MaLR	28225	NM_145853	252972	Mm.114054	NM_145853	ENSMUSG00000032741	Tpcn1	5730403B01Rik|Tpc1|mKIAA1169	two pore channel 1	protein-coding
mm_70636.1	chr8	13896283	13896287	+	1	NA	Intergenic	Intergenic	-6014	NM_025556	66423	Mm.29063	NM_025556	ENSMUSG00000031458	Coprs	1700029I03Rik|2410022L05Rik|AA409325|AI256813|C85432|Copr5	coordinator of PRMT5, differentiation stimulator	protein-coding
mm_113665.1	chr13	42682097	42682125	+	1	NA	intron (NM_001302635, intron 1 of 13)	intron (NM_001302635, intron 1 of 13)	1312	NM_001302635	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding
mm_122396.1	chr14	40994214	40994225	-	1	NA	3' UTR (NM_001316734, exon 6 of 6)	3' UTR (NM_001316734, exon 6 of 6)	12701	NM_001316739	70564	Mm.27227	NM_027464	ENSMUSG00000021792	Fam213a	5730469M10Rik|AU040822|Adrx|Pamm	family with sequence similarity 213, member A	protein-coding
mm_58114.1	chr6	138424594	138424611	-	1	NA	intron (NR_126072, intron 1 of 3)	intron (NR_126072, intron 1 of 3)	1497	NR_126072	319702	Mm.403785	NR_126072	ENSMUSG00000089957	A830011K09Rik	-	RIKEN cDNA A830011K09 gene	ncRNA
mm_96119.1	chr11	60728414	60728454	+	1	NA	promoter-TSS (NM_001009927)	promoter-TSS (NM_001009927)	36	NM_001009927	237781	Mm.339760	NM_001009927	ENSMUSG00000018599	Mief2	AI482195|Gm11|Smcr7	mitochondrial elongation factor 2	protein-coding
mm_129745.1	chr15	82244689	82244715	-	1	NA	promoter-TSS (NM_001080158)	promoter-TSS (NM_001080158)	45	NM_178269	66570	Mm.23596	NM_025639	ENSMUSG00000068101	Cenpm	2610019I03Rik|AI853711|Pane1	centromere protein M	protein-coding
mm_133001.1	chr16	55966339	55966371	+	1	NA	promoter-TSS (NM_024218)	promoter-TSS (NM_024218)	80	NM_024218	68193	Mm.29221	NM_024218	ENSMUSG00000098274	Rpl24	0610008L05Rik|Bst	ribosomal protein L24	protein-coding
mm_153883.1	chr19	46943939	46943955	-	1	NA	intron (NM_001164365, intron 2 of 17)	ID_B1|SINE|B4	18404	NM_029810	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_78763.1	chr9	43307665	43307678	+	1	NA	Intergenic	Intergenic	-3092	NM_023655	72169	Mm.273277	NM_023655	ENSMUSG00000032013	Trim29	1110047J21Rik|2810431N19Rik|4732461M22Rik|AI119726	tripartite motif-containing 29	protein-coding
mm_90370.1	chr10	127170946	127170948	+	1	NA	exon (NM_027739, exon 9 of 10)	exon (NM_027739, exon 9 of 10)	5116	NM_001244618	14421	Mm.386762	NM_008080	ENSMUSG00000006731	B4galnt1	4933429D13Rik|Gal-NAc-T|GalNAc-T|GalNAcT|Galgt1|Ggm-2|Ggm2	beta-1,4-N-acetyl-galactosaminyl transferase 1	protein-coding
mm_106719.1	chr12	3856331	3856350	+	1	NA	intron (NM_007872, intron 3 of 22)	intron (NM_007872, intron 3 of 22)	5904	NR_045884	100038522	Mm.417270	NR_045884	ENSMUSG00000073242	Dnmt3aos	ENSMUSG00000073242|Gm10485	DNA methyltransferase 3A, opposite strand	ncRNA
mm_123576.1	chr14	67000464	67000485	-	1	NA	intron (NM_009761, intron 1 of 5)	intron (NM_009761, intron 1 of 5)	8403	NM_009761	12177	Mm.29820	NM_009761	ENSMUSG00000022051	Bnip3l	C86132|D14Ertd719e|Nip3L|Nix	BCL2/adenovirus E1B interacting protein 3-like	protein-coding
mm_154120.1	chr19	57197378	57197417	-	1	NA	5' UTR (NM_001103177, exon 1 of 22)	5' UTR (NM_001103177, exon 1 of 22)	234	NM_001103177	226251	Mm.217161	NM_178688	ENSMUSG00000025085	Ablim1	2210411C18Rik|2610209L21Rik|4833406P10Rik|9330196J19Rik|AV079770|AW060987|AW215784|Limab1|mKIAA0059	actin-binding LIM protein 1	protein-coding
mm_97185.1	chr11	75567980	75567993	+	1	NA	intron (NM_173388, intron 10 of 13)	intron (NM_173388, intron 10 of 13)	16557	NR_039553	100628624		NR_039553	ENSMUSG00000093100	Mir3971	mmu-mir-3971|mu-mir-3971	microRNA 3971	ncRNA
mm_90613.1	chr10	128362115	128362133	+	1	NA	TTS (NM_001081040)	TTS (NM_001081040)	7913	NM_001081040	210582	Mm.296876	NM_001081040	ENSMUSG00000039914	Coq10a	Gm1	coenzyme Q10A	protein-coding
mm_119798.1	chr14	54207816	54207827	+	1	NA	Intergenic	MIR3|SINE|MIR	46108	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_124880.1	chr15	10224048	10224062	+	1	NA	5' UTR (NM_001253781, exon 1 of 10)	5' UTR (NM_001253781, exon 1 of 10)	149	NM_001253781	19116	Mm.10516	NM_011169	ENSMUSG00000005268	Prlr	AI987712|Pr-1|Pr-3|Prlr-rs1	prolactin receptor	protein-coding
mm_46527.1	chr5	105415719	105415729	-	1	NA	promoter-TSS (NM_001033550)	promoter-TSS (NM_001033550)	-51	NM_001033550	433926	Mm.439781	NM_001033550	ENSMUSG00000070639	Lrrc8b	R75581|Ta-lrrp|mKIAA0231	leucine rich repeat containing 8 family, member B	protein-coding
mm_193.1	chr1	15804369	15804373	+	1	NA	Intergenic	RMER17A|LTR|ERVK	-1275	NM_009352	21749	Mm.4306	NM_009352	ENSMUSG00000025925	Terf1	Pin2|Trbf1|Trf1	telomeric repeat binding factor 1	protein-coding
mm_104150.1	chr11	87086733	87086743	-	1	NA	promoter-TSS (NM_024262)	promoter-TSS (NM_024262)	39	NM_024262	74133	Mm.23257	NM_024262	ENSMUSG00000020495	Smg8	1200011M11Rik	smg-8 homolog, nonsense mediated mRNA decay factor (C. elegans)	protein-coding
mm_163510.1	chr12	113258741	113258788	-	1	NA	Intergenic	Intergenic	72861	NM_153776	69195	Mm.313244	NM_153776	ENSMUSG00000049036	Tmem121	2410008J05Rik|Hole	transmembrane protein 121	protein-coding
mm_120791.1	chr14	74733457	74733471	+	1	NA	intron (NM_001285423, intron 1 of 8)	intron (NM_001285423, intron 1 of 8)	1167	NM_016903	13885	Mm.38055	NM_016903	ENSMUSG00000021996	Esd	Es-10|Es10|FGH|sid478	esterase D/formylglutathione hydrolase	protein-coding
mm_34253.1	chr4	141301229	141301250	+	1	NA	promoter-TSS (NM_010139)	promoter-TSS (NM_010139)	18	NM_010139	13836	Mm.2581	NM_010139	ENSMUSG00000006445	Epha2	AW545284|Eck|Myk2|Sek-2|Sek2	Eph receptor A2	protein-coding
mm_24768.1	chr3	95502524	95502551	+	1	NA	intron (NM_007802, intron 4 of 7)	intron (NM_007802, intron 4 of 7)	3327	NM_007802	13038	Mm.272085	NM_007802	ENSMUSG00000028111	Ctsk	AI323530|MMS10-Q|Ms10q|catK	cathepsin K	protein-coding
mm_15428.1	chr2	157101054	157101166	+	1	NA	intron (NM_018851, intron 15 of 15)	(TG)n|Simple_repeat|Simple_repeat	14055	NM_001177439	383766	Mm.480305	NM_001177439	ENSMUSG00000074628	Tldc2	Gm1332	TBC/LysM associated domain containing 2	protein-coding
mm_130983.1	chr15	103344807	103344833	-	1	NA	3' UTR (NM_010577, exon 30 of 30)	3' UTR (NM_010577, exon 30 of 30)	-4734	NM_013866	29813	Mm.14099	NM_013866	ENSMUSG00000000552	Zfp385a	Hzf|Zfp385|Znf385a	zinc finger protein 385A	protein-coding
mm_154534.1	chrM	13836	13846	-	1	NA	NA	Intergenic	NA	NA								
mm_119386.1	chr14	41136634	41136646	+	1	NA	TTS (NM_023134)	TTS (NM_023134)	4852	NM_023134	20387	Mm.46062	NM_023134	ENSMUSG00000021789	Sftpa1	SP-A|Sftp-1|Sftp1	surfactant associated protein A1	protein-coding
mm_168746.1	chr12	115461477	115461485	-	1	NA	Intergenic	Intergenic	234313	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
mm_4631.1	chr1	179668203	179668268	+	1	NA	promoter-TSS (NM_178653)	promoter-TSS (NM_178653)	4	NM_178653	109232	Mm.136458	NM_178653	ENSMUSG00000038936	Sccpdh	AW214504|C330023F11Rik	saccharopine dehydrogenase (putative)	protein-coding
mm_101724.1	chr11	42182514	42182520	-	1	NA	5' UTR (NM_010250, exon 1 of 10)	5' UTR (NM_010250, exon 1 of 10)	413	NM_010250	14394	Mm.439668	NM_010250	ENSMUSG00000010803	Gabra1	Gabra-1	gamma-aminobutyric acid (GABA) A receptor, subunit alpha 1	protein-coding
mm_148767.1	chr19	6080030	6080042	+	1	NA	promoter-TSS (NM_001111317)	promoter-TSS (NM_001111317)	-2	NM_001111317	433215	Mm.437186	NM_001111317	ENSMUSG00000047733	Tmem262	-	transmembrane protein 262	protein-coding
mm_149113.1	chr19	8967032	8967050	+	1	NA	promoter-TSS (NM_026007)	promoter-TSS (NM_026007)	0	NM_026007	67160	Mm.247762	NM_026007	ENSMUSG00000071644	Eef1g	2610301D06Rik|AA407312|EF1G	eukaryotic translation elongation factor 1 gamma	protein-coding
mm_145996.1	chr18	68344451	68344465	+	1	NA	Intergenic	MTC-int|LTR|ERVL-MaLR	6855	NM_013596	17203	Mm.8003	NM_013596	ENSMUSG00000007480	Mc5r	-	melanocortin 5 receptor	protein-coding
mm_68358.1	chr7	106511532	106511553	-	1	NA	Intergenic	Intergenic	-70469	NR_003967	209380	Mm.461779	NM_001001318		Gm4759	EG209380	GTPase, very large interferon inducible 1 pseudogene	pseudo
mm_135012.1	chr16	32486169	32486175	-	1	NA	exon (NM_145932, exon 2 of 9)	exon (NM_145932, exon 2 of 9)	1707	NM_145932	106407	Mm.476915	NM_145932	ENSMUSG00000035699	Slc51a	AV001382|AW261577|D630035O19Rik|OSTalpha|Osta	solute carrier family 51, alpha subunit	protein-coding
mm_8086.1	chr1	135634041	135634051	-	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-48691	NM_173437	215690	Mm.34977	NM_173437	ENSMUSG00000009418	Nav1	9530089B19|9930003A20Rik|C230080M11Rik|Pomfil3|Unc53h1|mKIAA1151|steerin-1	neuron navigator 1	protein-coding
mm_10040.1	chr1	192855895	192855907	-	1	NA	promoter-TSS (NM_198247)	promoter-TSS (NM_198247)	-149	NM_198247	214791	Mm.22806	NM_198247	ENSMUSG00000016262	Sertad4	4833404A09|C130018M11Rik	SERTA domain containing 4	protein-coding
mm_101750.1	chr11	43380168	43380210	-	1	NA	Intergenic	Intergenic	-5728	NR_029558	387164		NR_029558	ENSMUSG00000065601	Mir146	Mirn146|miR-146a|mmu-mir-146	microRNA 146	ncRNA
mm_3931.1	chr1	163358383	163358387	+	1	NA	Intergenic	Intergenic	-44735	NM_175686	18933	Mm.288642	NM_011127	ENSMUSG00000026586	Prrx1	A230024N07Rik|AA755424|AI385634|AI843499|K-2|Pmx|Pmx1|Prx1|mHox	paired related homeobox 1	protein-coding
mm_115251.1	chr13	110396992	110397002	+	1	NA	intron (NM_152804, intron 5 of 13)	intron (NM_152804, intron 5 of 13)	1953	NM_152804	20620	Mm.380	NM_152804	ENSMUSG00000021701	Plk2	Snk	polo-like kinase 2	protein-coding
mm_44501.1	chr5	23783701	23783709	-	1	NA	promoter-TSS (NM_001289780)	promoter-TSS (NM_001289780)	6	NM_001289780	78697	Mm.58660	NM_178403	ENSMUSG00000057541	Pus7	C330017I15Rik	pseudouridylate synthase 7	protein-coding
mm_18301.1	chr2	53145351	53145376	-	1	NA	exon (NM_018785, exon 20 of 26)	exon (NM_018785, exon 20 of 26)	45824	NM_018785	56194	Mm.257474	NM_018785	ENSMUSG00000061136	Prpf40a	2810012K09Rik|FBP-11|FBP11|Fnbp11|Fnbp3	pre-mRNA processing factor 40A	protein-coding
mm_9602.1	chr1	175615841	175615856	-	1	NA	intron (NM_010209, intron 3 of 9)	intron (NM_010209, intron 3 of 9)	9787	NM_010209	14194	Mm.41502	NM_010209	ENSMUSG00000026526	Fh1	Fh|Fh-1	fumarate hydratase 1	protein-coding
mm_133190.1	chr16	72663788	72663815	+	1	NA	5' UTR (NM_019413, exon 1 of 29)	5' UTR (NM_019413, exon 1 of 29)	652	NM_019413	19876	Mm.310772	NM_019413	ENSMUSG00000022883	Robo1	AW494633|AW742721|DUTT1|Gm310	roundabout guidance receptor 1	protein-coding
mm_167881.1	chrX	45940903	45940904	-	1	NA	Intergenic	Intergenic	388008	NR_045440	75133	Mm.417818	NR_045440	ENSMUSG00000085157	4930515L19Rik	-	RIKEN cDNA 4930515L19 gene	ncRNA
mm_71014.1	chr8	31187368	31187392	+	1	NA	promoter-TSS (NM_001286425)	promoter-TSS (NM_001286425)	49	NM_001286425	171167	Mm.334477	NM_134161	ENSMUSG00000046152	Fut10	fuc-TX|fut10A	fucosyltransferase 10	protein-coding
mm_36938.1	chr4	108579322	108579329	-	1	NA	promoter-TSS (NM_172697)	promoter-TSS (NM_172697)	11	NM_172697	230596	Mm.157534	NM_172697	ENSMUSG00000063800	Prpf38a	2410002M20Rik	PRP38 pre-mRNA processing factor 38 (yeast) domain containing A	protein-coding
mm_82483.1	chr9	18385956	18385978	-	1	NA	promoter-TSS (NM_028279)	promoter-TSS (NM_028279)	-39	NM_028279	72560	Mm.474510	NM_028279	ENSMUSG00000043943	Naalad2	2700022G20Rik|D9Ertd285e|Folh1b|GCP3|GCPIII|NAADALASE2|NAALADASE2	N-acetylated alpha-linked acidic dipeptidase 2	protein-coding
mm_75046.1	chr8	32820242	32820253	-	1	NA	Intergenic	Intergenic	129779	NM_001177589	100042715	Mm.291093	NM_001177589		Gm3985	-	predicted gene 3985	protein-coding
mm_34288.1	chr4	141546801	141546829	+	1	NA	non-coding (NR_030695, exon 1 of 1)	non-coding (NR_030695, exon 1 of 1)	653	NR_030695	320456	Mm.32859	NM_177163		B330016D10Rik	-	RIKEN cDNA B330016D10 gene	ncRNA
mm_117666.1	chr13	93499804	93499825	-	1	NA	promoter-TSS (NM_021310)	promoter-TSS (NM_021310)	-6	NM_021310	57748	Mm.100273	NM_021310	ENSMUSG00000021690	Jmy	-	junction-mediating and regulatory protein	protein-coding
mm_71230.1	chr8	40905814	40905824	+	1	NA	intron (NM_007514, intron 6 of 11)	intron (NM_007514, intron 6 of 11)	-20414	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_61279.1	chr7	66743718	66743724	+	1	NA	exon (NM_001164201, exon 1 of 11)	exon (NM_001164201, exon 1 of 11)	217	NM_001164201	545975	Mm.380104	NM_001164201	ENSMUSG00000030510	Cers3	4930550L11Rik|Gm488|Lass3|T3L	ceramide synthase 3	protein-coding
mm_28441.1	chr3	90506371	90506381	-	1	NA	5' UTR (NM_001293782, exon 3 of 6)	5' UTR (NM_001293782, exon 3 of 6)	3122	NM_001293776	66511	Mm.154136	NM_023215	ENSMUSG00000001017	Chtop	2500003M10Rik|Fop|Srag	chromatin target of PRMT1	protein-coding
mm_21368.1	chr2	157135201	157135215	-	1	NA	promoter-TSS (NM_001139520)	promoter-TSS (NM_001139520)	14	NM_001139520	56045	Mm.248478	NM_018851	ENSMUSG00000027639	Samhd1	E330031J07Rik|Mg11	SAM domain and HD domain, 1	protein-coding
mm_163350.1	chr12	18229880	18229884	+	1	NA	Intergenic	Intergenic	-284628	NM_001033157	236366	Mm.352227	NM_001033157	ENSMUSG00000073197	5730507C01Rik	-	RIKEN cDNA 5730507C01 gene	protein-coding
mm_15281.1	chr2	155276481	155276494	+	1	NA	non-coding (NR_046364, exon 1 of 3)	non-coding (NR_046364, exon 1 of 3)	123	NR_046364	66734	Mm.196239	NM_025735	ENSMUSG00000027602	Map1lc3a	1010001H21Rik|4922501H04Rik|LC3|LC3a	microtubule-associated protein 1 light chain 3 alpha	protein-coding
mm_2348.1	chr1	92910641	92910665	+	1	NA	promoter-TSS (NM_181405)	promoter-TSS (NM_181405)	36	NR_138577	75995	Mm.46179	NR_138577	ENSMUSG00000097251	5033417F24Rik	6330419D11Rik	RIKEN cDNA 5033417F24 gene	ncRNA
mm_117841.1	chr13	98692726	98692734	-	1	NA	intron (NM_001025606, intron 1 of 3)	intron (NM_001025606, intron 1 of 3)	2101	NM_001025606	380863	Mm.28264	NM_001025606	ENSMUSG00000052485	Tmem171	Gm905	transmembrane protein 171	protein-coding
mm_47658.1	chr5	125393314	125393321	-	1	NA	Intergenic	Intergenic	-3300	NM_019639	22190	Mm.331	NM_019639	ENSMUSG00000008348	Ubc	2700054O04Rik|AI194771|Rps27a|TI-225|Uba52|Ubb	ubiquitin C	protein-coding
mm_28808.1	chr3	96256245	96256255	-	1	NA	Intergenic	Intergenic	7067	NM_033596	97122	Mm.227295	NM_033596	ENSMUSG00000091405	Hist2h4	H4|X04652	histone cluster 2, H4	protein-coding
mm_171366.1	chr4	118943423	118943426	-	1	NA	Intergenic	Intergenic	-8584	NM_146399	258394	Mm.434316	NM_146399	ENSMUSG00000111259	Olfr1328	MOR259-1|MOR259-13|Olfr1519	olfactory receptor 1328	protein-coding
mm_38616.1	chr4	141952112	141952143	-	1	NA	intron (NM_177868, intron 12 of 31)	B4A|SINE|B4	-30865	NR_040672	545691	Mm.332015	NR_040672	ENSMUSG00000085424	Fhad1os1	Gm13037|OTTMUSG00000010113	forkhead-associated (FHA) phosphopeptide binding domain 1, opposite strand 1	ncRNA
mm_146841.1	chr18	23041554	23041566	-	1	NA	promoter-TSS (NM_199024)	promoter-TSS (NM_199024)	93	NM_199024	319211	Mm.209896	NM_199024	ENSMUSG00000041923	Nol4	1700013J13Rik|4930568N03Rik|Gm1262	nucleolar protein 4	protein-coding
mm_167375.1	chr8	91759148	91759152	+	1	NA	Intergenic	Intergenic	42504	NM_001253822	16373	Mm.238044	NM_008393	ENSMUSG00000031734	Irx3	AI894186	Iroquois related homeobox 3	protein-coding
mm_86573.1	chr10	12846013	12846014	+	1	NA	intron (NM_011682, intron 1 of 73)	intron (NM_011682, intron 1 of 73)	15722	NM_011682	22288	Mm.331784	NM_011682	ENSMUSG00000019820	Utrn	AA589569|DRP|Dmdl	utrophin	protein-coding
mm_108931.1	chr12	101083757	101083802	+	1	NA	promoter-TSS (NM_001160214)	promoter-TSS (NM_001160214)	-77	NM_001160214	68734	Mm.87077	NM_211355	ENSMUSG00000041846	Smek1	1110034C04Rik|BC064465|Ppp4r3a|mKIAA2010	SMEK homolog 1, suppressor of mek1 (Dictyostelium)	protein-coding
mm_106440.1	chr11	119758452	119758452	-	1	NA	intron (NM_028898, intron 6 of 33)	intron (NM_028898, intron 6 of 33)	75913	NR_045313	319454	Mm.442144	NR_045312	ENSMUSG00000085081	Rptoros	A430071A18Rik	regulatory associated protein of MTOR, complex 1, opposite strand	ncRNA
mm_7980.1	chr1	134099150	134099160	-	1	NA	Intergenic	Intergenic	-12087	NM_001284524	71884	Mm.328268	NM_027979	ENSMUSG00000026450	Chit1	2300002L19Rik	chitinase 1 (chitotriosidase)	protein-coding
mm_40962.1	chr5	76965940	76965942	+	1	NA	intron (NM_025939, intron 7 of 8)	intron (NM_025939, intron 7 of 8)	-8760	NM_025691	66661	Mm.296976	NM_025691	ENSMUSG00000036323	Srp72	5730576P14Rik|72kDa|AI132477|BC019196|C77589	signal recognition particle 72	protein-coding
mm_149287.1	chr19	10634314	10634324	+	1	NA	promoter-TSS (NM_027913)	promoter-TSS (NM_027913)	86	NM_027913	71768	Mm.169261	NM_027913	ENSMUSG00000043789	Vwce	1300015B04Rik	von Willebrand factor C and EGF domains	protein-coding
mm_172550.1	chr8	102666751	102666759	-	1	NA	intron (NM_009866, intron 6 of 12)	B3|SINE|B2	118356	NM_009866	12552	Mm.1571	NM_009866	ENSMUSG00000031673	Cdh11	Cad11|OSF-4	cadherin 11	protein-coding
mm_98217.1	chr11	87986635	87986638	+	1	NA	promoter-TSS (NM_001168472)	promoter-TSS (NM_001168472)	-51	NM_001168472	68097	Mm.246436	NM_026556	ENSMUSG00000020483	Dynll2	1700064A15Rik|6720463E02Rik|C87222|DLC8|DLC8b|Dlc2	dynein light chain LC8-type 2	protein-coding
mm_148625.1	chr19	5447693	5447711	+	1	NA	promoter-TSS (NM_010235)	promoter-TSS (NM_010235)	4	NM_010235	14283	Mm.6215	NM_010235	ENSMUSG00000024912	Fosl1	AW538199|Fra1|fra-1	fos-like antigen 1	protein-coding
mm_36188.1	chr4	62228545	62228557	-	1	NA	Intergenic	Intergenic	-20005	NM_001290350	22696	Mm.5011	NM_009554	ENSMUSG00000028389	Zfp37	Tzn|Zfp-37	zinc finger protein 37	protein-coding
mm_165812.1	chr3	145758788	145758794	+	1	NA	promoter-TSS (NM_026993)	promoter-TSS (NM_026993)	99	NM_026993	69219	Mm.234247	NM_026993	ENSMUSG00000028194	Ddah1	2410006N07Rik|2510015N06Rik|AI987801|AW050362	dimethylarginine dimethylaminohydrolase 1	protein-coding
mm_160551.1	chr9	46123287	46123287	+	1	NA	exon (NM_027498, exon 2 of 25)	exon (NM_027498, exon 2 of 25)	-105343	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2|apo-AI|apoA-I	apolipoprotein A-I	protein-coding
mm_11588.1	chr2	33216024	33216034	+	1	NA	promoter-TSS (NM_011923)	promoter-TSS (NM_011923)	68	NM_011923	26360	Mm.208919	NM_011923	ENSMUSG00000004105	Angptl2	AI593246|AW260363|Arp2	angiopoietin-like 2	protein-coding
mm_160662.1	chr9	119719075	119719075	-	1	NA	promoter-TSS (NM_001205321)	promoter-TSS (NM_001205321)	-43	NM_001205321	20264	Mm.247042	NM_009134	ENSMUSG00000034533	Scn10a	Nav1.8|PN3|SNS	sodium channel, voltage-gated, type X, alpha	protein-coding
mm_130567.1	chr15	99435650	99435652	-	1	NA	intron (NM_001001884, intron 2 of 12)	intron (NM_001001884, intron 2 of 12)	22097	NM_001001884	380969	Mm.22915	NM_001001884	ENSMUSG00000023009	Nckap5l	C230021P08Rik|Cep169	NCK-associated protein 5-like	protein-coding
mm_53053.1	chr6	124808899	124808933	+	1	NA	promoter-TSS (NM_001306053)	promoter-TSS (NM_001306053)	-2	NM_013539	14794	Mm.261906	NM_013539	ENSMUSG00000038451	Spsb2	AI461677|C9|Grcc9|SSB2	splA/ryanodine receptor domain and SOCS box containing 2	protein-coding
mm_56821.1	chr6	116735358	116735375	-	1	NA	Intergenic	MER44B|DNA|TcMar-Tigger	-18608	NM_178768	319776	Mm.133120	NM_178768	ENSMUSG00000048108	Tmem72	C230095G01Rik	transmembrane protein 72	protein-coding
mm_62673.1	chr7	109439158	109439165	+	1	NA	promoter-TSS (NM_054103)	promoter-TSS (NM_054103)	-108	NM_054103	117229	Mm.389950	NM_054103	ENSMUSG00000031027	Stk33	4921505G21Rik|AW061264	serine/threonine kinase 33	protein-coding
mm_14070.1	chr2	122746063	122746066	+	1	NA	exon (NM_019788, exon 4 of 5)	exon (NM_019788, exon 4 of 5)	7559	NM_019788	18457	Mm.268921	NM_019788	ENSMUSG00000005804	Bloc1s6	BLOC-1|Pldn|Stx13bp1|pa	biogenesis of lysosomal organelles complex-1, subunit 6, pallidin	protein-coding
mm_113951.1	chr13	51100474	51100492	+	1	NA	promoter-TSS (NM_001283028)	promoter-TSS (NM_001283028)	244	NR_029463	77428	Mm.405630	NR_029463		9430083A17Rik	-	RIKEN cDNA 9430083A17 gene	ncRNA
mm_120600.1	chr14	70079242	70079264	+	1	NA	exon (NM_001289927, exon 2 of 2)	exon (NM_001289927, exon 2 of 2)	1458	NM_001289927	13655	Mm.103737	NM_018781	ENSMUSG00000033730	Egr3	Pilot	early growth response 3	protein-coding
mm_133115.1	chr16	65562785	65562847	+	1	NA	promoter-TSS (NM_026879)	promoter-TSS (NM_026879)	-119	NM_026879	68942	Mm.432944	NM_026879	ENSMUSG00000004843	Chmp2b	1190006E07Rik	charged multivesicular body protein 2B	protein-coding
mm_155160.1	chrX	52988083	52988115	+	1	NA	promoter-TSS (NM_013556)	promoter-TSS (NM_013556)	21	NM_013556	15452	Mm.299381	NM_013556	ENSMUSG00000025630	Hprt	C81579|HPGRT|Hprt1	hypoxanthine guanine phosphoribosyl transferase	protein-coding
mm_46795.1	chr5	112790715	112790732	-	1	NA	intron (NM_028901, intron 30 of 43)	intron (NM_028901, intron 30 of 43)	-2569	NR_040675	67360	Mm.59218	NR_040675	ENSMUSG00000098230	1700095B10Rik	-	RIKEN cDNA 1700095B10 gene	ncRNA
mm_35101.1	chr4	8980269	8980270	-	1	NA	Intergenic	Intergenic	-289048	NM_028940	74438	Mm.473368	NM_028940	ENSMUSG00000041216	Clvs1	4933402J24Rik|Clvl1|Rlbp1l1	clavesin 1	protein-coding
mm_101571.1	chr11	34227548	34227565	-	1	NA	3' UTR (NM_033374, exon 52 of 52)	3' UTR (NM_033374, exon 52 of 52)	-19467	NM_023907	14233	Mm.32926	NM_023907	ENSMUSG00000047861	Foxi1	5830401E05Rik|FREAC6|Fkh10|HFH-3|Hfh3	forkhead box I1	protein-coding
mm_60103.1	chr7	35353526	35353542	+	1	NA	intron (NM_027897, intron 1 of 14)	Lx9|LINE|L1	19297	NM_027897	52428	Mm.286600	NM_027897	ENSMUSG00000030494	Rhpn2	1300002E07Rik|AA536890|C85860|D7Ertd784e	rhophilin, Rho GTPase binding protein 2	protein-coding
mm_81855.1	chr9	118703436	118703446	+	1	NA	intron (NM_133721, intron 15 of 27)	intron (NM_133721, intron 15 of 27)	-8251	NM_001113514	104099	Mm.335520	NM_133721	ENSMUSG00000039115	Itga9	(alpha)9|2610002H11Rik|6720458D17Rik|AI461869|D130073C02|D9Ertd428e	integrin alpha 9	protein-coding
mm_59312.1	chr7	25282785	25282795	+	1	NA	5' UTR (NM_027882, exon 1 of 20)	5' UTR (NM_027882, exon 1 of 20)	611	NM_027882	71722	Mm.28833	NM_027882	ENSMUSG00000005442	Cic	1200010B10Rik|mKIAA0306	capicua transcriptional repressor	protein-coding
mm_168698.1	chr11	97778354	97778371	-	1	NA	exon (NM_022891, exon 4 of 5)	exon (NM_022891, exon 4 of 5)	-2444	NM_028156	72215	Mm.269049	NM_028156	ENSMUSG00000018543	1700001P01Rik	-	RIKEN cDNA 1700001P01 gene	protein-coding
mm_7207.1	chr1	93076198	93076208	-	1	NA	exon (NM_008440, exon 6 of 48)	exon (NM_008440, exon 6 of 48)	6277	NM_001294150	16560	Mm.276408	NM_008440	ENSMUSG00000014602	Kif1a	ATSV|C630002N23Rik|Gm1626|Kns1	kinesin family member 1A	protein-coding
mm_171200.1	chr3	51415979	51415979	+	1	NA	promoter-TSS (NM_053089)	promoter-TSS (NM_053089)	-37	NM_053089	74838	Mm.275281	NM_053089	ENSMUSG00000063273	Naa15	5730450D16Rik|6330400I15|ASTBDN|Narg1|Tbdn-1|mNAT1	N(alpha)-acetyltransferase 15, NatA auxiliary subunit	protein-coding
mm_25093.1	chr3	100922483	100922499	+	1	NA	promoter-TSS (NM_001165953)	promoter-TSS (NM_001165953)	-2	NM_001165952	229644	Mm.189351	NM_194343	ENSMUSG00000033233	Trim45	4921530N01Rik	tripartite motif-containing 45	protein-coding
mm_73577.1	chr8	109778851	109778861	+	1	NA	5' UTR (NM_009677, exon 1 of 24)	5' UTR (NM_009677, exon 1 of 24)	273	NM_001301211	11765	Mm.37210	NM_009677	ENSMUSG00000031731	Ap1g1	AA409002|AU041323|AW551707|Adtg|D8Ertd374e	adaptor protein complex AP-1, gamma 1 subunit	protein-coding
mm_170063.1	chr17	30626962	30626963	+	1	NA	promoter-TSS (NR_045287)	promoter-TSS (NR_045287)	26	NM_013811	13417	Mm.426017	NM_013811	ENSMUSG00000033826	Dnah8	ATPase|Dnahc8|Hst6.7b|P1-Loop	dynein, axonemal, heavy chain 8	protein-coding
mm_67134.1	chr7	72279706	72279708	-	1	NA	intron (NM_001024703, intron 1 of 22)	intron (NM_001024703, intron 1 of 22)	26888	NM_001024703	244049	Mm.217412	NM_001024703	ENSMUSG00000032776	Mctp2	Gm489	multiple C2 domains, transmembrane 2	protein-coding
mm_114454.1	chr13	67125103	67125112	+	1	NA	Intergenic	Intergenic	-3121	NM_172392	268670	Mm.56274	NM_172392	ENSMUSG00000057396	Zfp759	BC028265|Rslcan-8|Rslcan8	zinc finger protein 759	protein-coding
mm_19772.1	chr2	105787548	105787550	-	1	NA	intron (NM_023876, intron 9 of 9)	intron (NM_023876, intron 9 of 9)	105086	NM_001310145	18508	Mm.3608	NM_013627	ENSMUSG00000027168	Pax6	1500038E17Rik|AEY11|Dey|Gsfaey11|Pax-6|Sey	paired box 6	protein-coding
mm_56166.1	chr6	87994131	87994153	-	1	NA	Intergenic	Intergenic	12459	NR_026990	434064	Mm.371796	NR_026990	ENSMUSG00000084950	Gm5577	EG434064	predicted gene 5577	ncRNA
mm_87052.1	chr10	28824304	28824315	+	1	NA	intron (NM_001305663, intron 5 of 5)	L1M2|LINE|L1	99198	NR_033601	114676	Mm.390292	NR_033601		4930519F09Rik	-	pyruvate dehydrogenase E1 alpha 1 pseudogene	pseudo
mm_8748.1	chr1	160307325	160307349	-	1	NA	intron (NM_001038621, intron 2 of 8)	intron (NM_001038621, intron 2 of 8)	-11365	NR_035448	100316784		NR_035448	ENSMUSG00000089204	Mir1927	mmu-mir-1927	microRNA 1927	ncRNA
mm_163889.1	chr14	26442761	26442764	-	1	NA	intron (NM_001347494, intron 10 of 19)	intron (NM_001347494, intron 10 of 19)	85215	NR_038005	71106	Mm.158564	NR_038005	ENSMUSG00000021874	4933413J09Rik	GCSE	RIKEN cDNA 4933413J09 gene	ncRNA
mm_87365.1	chr10	43927962	43927970	+	1	NA	intron (NM_130892, intron 5 of 8)	intron (NM_130892, intron 5 of 8)	26159	NM_130892	170728	Mm.390253	NM_130892	ENSMUSG00000019864	Rtn4ip1	D10Ertd690e|NIMP	reticulon 4 interacting protein 1	protein-coding
mm_168276.1	chr1	10294742	10294745	-	1	NA	Intergenic	RLTR27|LTR|ERVK	-62073	NM_001102430	211673	Mm.229141	NM_001102430	ENSMUSG00000067851	Arfgef1	ARFGEP1|BIG1|D130059B05Rik|D730028O18Rik|P200	ADP-ribosylation factor guanine nucleotide-exchange factor 1(brefeldin A-inhibited)	protein-coding
mm_142645.1	chr17	47465830	47465841	-	1	NA	exon (NM_145489, exon 4 of 5)	exon (NM_145489, exon 4 of 5)	-28460	NM_029296	75462	Mm.46129	NM_029296	ENSMUSG00000047150	1700001C19Rik	-	RIKEN cDNA 1700001C19 gene	protein-coding
mm_168405.1	chr11	30149959	30149975	-	1	NA	exon (NM_009260, exon 5 of 31)	exon (NM_009260, exon 5 of 31)	48290	NM_009260	20742	Mm.123110	NM_009260	ENSMUSG00000020315	Sptbn1	9930031C03Rik|AL033301|SPTB2|Spnb-2|Spnb2|elf1|elf3|mKIAA4049	spectrin beta, non-erythrocytic 1	protein-coding
mm_51386.1	chr6	77242716	77242729	+	1	NA	promoter-TSS (NM_028880)	promoter-TSS (NM_028880)	5	NM_028880	74342	Mm.292568	NM_028880	ENSMUSG00000060780	Lrrtm1	4632401D06Rik|AW125451	leucine rich repeat transmembrane neuronal 1	protein-coding
mm_60621.1	chr7	44602633	44602643	+	1	NA	3' UTR (NM_001290682, exon 5 of 5)	3' UTR (NM_001290682, exon 5 of 5)	11752	NM_001290682	16504	Mm.40312	NM_008422	ENSMUSG00000062785	Kcnc3	KShIIID|Kcr2-3|Kv3.3	potassium voltage gated channel, Shaw-related subfamily, member 3	protein-coding
mm_8242.1	chr1	138536202	138536205	-	1	NA	intron (NM_001311148, intron 3 of 7)	intron (NM_001311148, intron 3 of 7)	83554	NM_021605	59125	Mm.143817	NM_021605	ENSMUSG00000026393	Nek7	2810460C19Rik|AU020186	NIMA (never in mitosis gene a)-related expressed kinase 7	protein-coding
mm_49600.1	chr6	30723542	30723552	+	1	NA	Intergenic	Intergenic	-9959	NM_001252293	17294	Mm.335639	NM_008590	ENSMUSG00000051855	Mest	AA408879|AI256745|Peg1	mesoderm specific transcript	protein-coding
mm_161880.1	chr18	37489471	37489471	+	1	NA	promoter-TSS (NM_053143)	promoter-TSS (NM_053143)	6	NM_053143	93889	Mm.196852	NM_053143	ENSMUSG00000048347	Pcdhb18	Pcdhb9|PcdhbR	protocadherin beta 18	protein-coding
mm_77001.1	chr8	107389084	107389097	-	1	NA	exon (NM_008706, exon 6 of 6)	exon (NM_008706, exon 6 of 6)	14115	NM_008706	18104	Mm.252	NM_008706	ENSMUSG00000003849	Nqo1	AV001255|Dia4|Dtd|Nmo-1|Nmo1|Nmor1|Ox-1|Ox1|Qr1	NAD(P)H dehydrogenase, quinone 1	protein-coding
mm_125780.1	chr15	74716015	74716032	+	1	NA	exon (NM_028216, exon 2 of 3)	exon (NM_028216, exon 2 of 3)	1184	NM_028216	72373	Mm.46395	NM_028216	ENSMUSG00000022598	Psca	2210408B04Rik	prostate stem cell antigen	protein-coding
mm_119220.1	chr14	33217039	33217046	+	1	NA	5' UTR (NM_153800, exon 2 of 11)	5' UTR (NM_153800, exon 2 of 11)	219	NM_153800	239027	Mm.318350	NM_153800	ENSMUSG00000063506	Arhgap22	B230341L19Rik|RHOGAP2|p68RacGAP	Rho GTPase activating protein 22	protein-coding
mm_15423.1	chr2	156872499	156872514	+	1	NA	TTS (NM_029983)	TTS (NM_029983)	9384	NM_026124	67388	Mm.29264	NM_026124	ENSMUSG00000027637	1110008F13Rik	AI316789	RIKEN cDNA 1110008F13 gene	protein-coding
mm_151528.1	chr19	58744096	58744113	+	1	NA	TTS (NM_018874)	TTS (NM_018874)	15217	NM_018874	18946	Mm.10753	NM_018874	ENSMUSG00000042179	Pnliprp1	Plrp1	pancreatic lipase related protein 1	protein-coding
mm_47325.1	chr5	122480408	122480415	-	1	NA	intron (NM_001110140, intron 5 of 19)	B2_Mm2|SINE|B2	21814	NM_001110140	11938	Mm.227583	NM_009722	ENSMUSG00000029467	Atp2a2	9530097L16Rik|D5Wsu150e|SERCA2|SERCA2B|Serca2a|mKIAA4195	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	protein-coding
mm_145047.1	chr18	39791922	39791925	+	1	NA	Intergenic	B1_Mus2|SINE|Alu	18426	NM_011033	18459	Mm.9493	NM_011033	ENSMUSG00000051732	Pabpc2	Pabp|Pabp+|Pabp2	poly(A) binding protein, cytoplasmic 2	protein-coding
mm_70854.1	chr8	23776585	23776608	+	1	NA	intron (NM_001277239, intron 2 of 7)	intron (NM_001277239, intron 2 of 7)	106935	NM_177086	320158	Mm.121274	NM_177086	ENSMUSG00000037492	Zmat4	9630048M01Rik	zinc finger, matrin type 4	protein-coding
mm_28435.1	chr3	90466330	90466358	-	1	NA	promoter-TSS (NM_008727)	promoter-TSS (NM_008727)	-478	NM_008727	18160	Mm.4627	NM_008727	ENSMUSG00000027931	Npr1	AI893888|GC-A|NPR-A|NPRA|Pndr	natriuretic peptide receptor 1	protein-coding
mm_144227.1	chr18	10181304	10181314	+	1	NA	exon (NM_009071, exon 1 of 33)	exon (NM_009071, exon 1 of 33)	483	NM_009071	19877	Mm.6710	NM_009071	ENSMUSG00000024290	Rock1	1110055K06Rik|Rock-I	Rho-associated coiled-coil containing protein kinase 1	protein-coding
mm_106236.1	chr11	117774755	117774765	-	1	NA	TTS (NM_181321)	TTS (NM_181321)	5861	NM_181321	217353	Mm.286963	NM_145439	ENSMUSG00000025572	Tmc6	D11Ertd204e|EVER1	transmembrane channel-like gene family 6	protein-coding
mm_145975.1	chr18	67934111	67934136	+	1	NA	intron (NM_172631, intron 1 of 5)	CpG	866	NM_172631	52662	Mm.440183	NM_172631	ENSMUSG00000024544	Ldlrad4	8230401C20Rik|A430083H02|A430108L08Rik|C18orf1|D18Ertd653e|D330030L18Rik	low density lipoprotein receptor class A domain containing 4	protein-coding
mm_26234.1	chr3	141211891	141211900	+	1	NA	5' UTR (NM_008811, exon 1 of 1)	5' UTR (NM_008811, exon 1 of 1)	460	NM_008811	18598	Mm.4223	NM_008811	ENSMUSG00000047674	Pdha2	Pdhal	pyruvate dehydrogenase E1 alpha 2	protein-coding
mm_132887.1	chr16	48842532	48842580	+	1	NA	promoter-TSS (NM_020509)	promoter-TSS (NM_020509)	4	NM_020509	57262	Mm.441868	NM_020509	ENSMUSG00000061100	Retnla	1810019L16Rik|Fizz-1|Fizz1|HIMF|RELM-alpha|RELMa|RELMalpha|Xcp2	resistin like alpha	protein-coding
mm_35924.1	chr4	53032181	53032198	-	1	NA	3' UTR (NM_013454, exon 50 of 50)	3' UTR (NM_013454, exon 50 of 50)	20309	NM_025623	66536	Mm.38244	NM_025623	ENSMUSG00000015247	Nipsnap3b	2700063N13Rik|Nipsnap3a	nipsnap homolog 3B (C. elegans)	protein-coding
mm_153545.1	chr19	42075465	42075493	-	1	NA	3' UTR (NM_198108, exon 5 of 5)	3' UTR (NM_198108, exon 5 of 5)	10891	NM_198108	226123	Mm.259441	NM_198108	ENSMUSG00000049670	Morn4	-	MORN repeat containing 4	protein-coding
mm_153758.1	chr19	45441815	45441853	-	1	NA	intron (NM_001286465, intron 2 of 14)	intron (NM_001286465, intron 2 of 14)	78100	NM_001037758	12234	Mm.119717	NM_009771	ENSMUSG00000025217	Btrc	Beta-Trcp1|E3RS-IkappaB|E3RSIkappaB|FWD1|Fbw1a|HOS|Slimb|b-TrCP|beta-TrCP	beta-transducin repeat containing protein	protein-coding
mm_169643.1	chr1	55088369	55088370	+	1	NA	promoter-TSS (NM_010477)	promoter-TSS (NM_010477)	221	NM_008303	15528	Mm.215667	NM_008303	ENSMUSG00000073676	Hspe1	10kDa|Hsp10|mt-cpn10	heat shock protein 1 (chaperonin 10)	protein-coding
mm_128826.1	chr15	67146454	67146497	-	1	NA	intron (NM_009177, intron 2 of 8)	intron (NM_009177, intron 2 of 8)	30407	NM_009177	20442	Mm.248334	NM_009177	ENSMUSG00000013846	St3gal1	5330418N22Rik|AI467004|ST3GalI|Siat4|Siat4a|St3gal-1	ST3 beta-galactoside alpha-2,3-sialyltransferase 1	protein-coding
mm_96527.1	chr11	68503070	68503076	+	1	NA	promoter-TSS (NM_001081566)	promoter-TSS (NM_001081566)	54	NR_126154	104709	Mm.234573	NM_001004435	ENSMUSG00000046207	Pik3r6	BB220380|p84|p84 PIKAP|p87(PIKAP)|p87PIKAP	phosphoinositide-3-kinase, regulatory subunit 6	protein-coding
mm_153065.1	chr19	32210134	32210144	-	1	NA	intron (NM_001168525, intron 5 of 9)	intron (NM_001168525, intron 5 of 9)	874	NM_001168526	208449	Mm.329810	NM_144792	ENSMUSG00000040451	Sgms1	9530058O11Rik|AI841905|C80702|Mob|Sms1|Sor1|Tmem23	sphingomyelin synthase 1	protein-coding
mm_110052.1	chr12	20815546	20815558	-	1	NA	non-coding (NR_015521, exon 1 of 2)	non-coding (NR_015521, exon 1 of 2)	227	NR_015521	69513	Mm.273972	NR_015521	ENSMUSG00000099759	1700030C10Rik	-	RIKEN cDNA 1700030C10 gene	ncRNA
mm_165900.1	chr4	46752580	46752606	+	1	NA	intron (NM_001081141, intron 7 of 18)	intron (NM_001081141, intron 7 of 18)	-102394	NM_198664	381605	Mm.331595	NM_198664	ENSMUSG00000039813	Tbc1d2	A630005A06Rik|BC022630|Gm1037|PARIS-1|PARIS1	TBC1 domain family, member 2	protein-coding
mm_19473.1	chr2	92460450	92460524	-	1	NA	promoter-TSS (NM_145832)	promoter-TSS (NM_145832)	31	NM_145832	228368	Mm.273990	NM_145832	ENSMUSG00000049922	Slc35c1	E430007K15Rik|fuct1	solute carrier family 35, member C1	protein-coding
mm_130864.1	chr15	102203401	102203443	-	1	NA	promoter-TSS (NM_001289691)	promoter-TSS (NM_001289691)	-223	NM_001289694	68744	Mm.352945	NM_153194	ENSMUSG00000046897	Zfp740	1110034O07Rik|AW548228|Znf740	zinc finger protein 740	protein-coding
mm_64087.1	chr7	140967378	140967388	+	1	NA	promoter-TSS (NM_001112715)	promoter-TSS (NM_001112715)	-46	NM_026820	68713	Mm.175661	NM_026820	ENSMUSG00000025491	Ifitm1	1110036C17Rik|DSPA2a|Mil-2|Mil2	interferon induced transmembrane protein 1	protein-coding
mm_91038.1	chr10	18235596	18235606	-	1	NA	promoter-TSS (NM_144820)	promoter-TSS (NM_144820)	-620	NM_144820	215814	Mm.296565	NM_144820	ENSMUSG00000059554	Ccdc28a	1700009P13Rik|AI480677	coiled-coil domain containing 28A	protein-coding
mm_106284.1	chr11	118202529	118202571	-	1	NA	intron (NM_001112699, intron 1 of 12)	intron (NM_001112699, intron 1 of 12)	10192	NM_001112700	19157	Mm.86413	NM_011180	ENSMUSG00000017132	Cyth1	CLM1|CTH-1|CYTIP|Pscd1	cytohesin 1	protein-coding
mm_30212.1	chr3	144932524	144932536	-	1	NA	promoter-TSS (NM_001033199)	promoter-TSS (NM_001033199)	-1	NM_001033199	99709	Mm.440040	NM_001033199	ENSMUSG00000074195	Clca4b	AI747448|Clca7	chloride channel accessory 4B	protein-coding
mm_109121.1	chr12	105705971	105705987	+	1	NA	promoter-TSS (NM_030187)	promoter-TSS (NM_030187)	-3	NM_030187	78801	Mm.36006	NM_030187	ENSMUSG00000041323	Ak7	4930502N02Rik|AK 7	adenylate kinase 7	protein-coding
mm_83291.1	chr9	43171429	43171431	-	1	NA	intron (NM_011139, intron 3 of 12)	ID_B1|SINE|B4	34325	NM_011139	18988	Mm.436650	NM_011139	ENSMUSG00000032015	Pou2f3	Epoc-1|Oct-11a|Oct11|Otf-11|Otf11|Skin|Skin-1a|Skn-1a|Skn-li	POU domain, class 2, transcription factor 3	protein-coding
mm_145855.1	chr18	65454173	65454185	+	1	NA	intron (NM_172833, intron 8 of 15)	intron (NM_172833, intron 8 of 15)	23182	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_67948.1	chr7	100467254	100467266	-	1	NA	intron (NM_001017985, intron 32 of 32)	intron (NM_001017985, intron 32 of 32)	-5731	NM_009464	22229	Mm.6254	NM_009464	ENSMUSG00000032942	Ucp3	AI645527|Slc25a9|UCP-3	uncoupling protein 3 (mitochondrial, proton carrier)	protein-coding
mm_89499.1	chr10	94035450	94035471	+	1	NA	promoter-TSS (NM_053072)	promoter-TSS (NM_053072)	282	NM_001304720	215008	Mm.124177	NM_172538	ENSMUSG00000036099	Vezt	A630071D13Rik|AI848282	vezatin, adherens junctions transmembrane protein	protein-coding
mm_56808.1	chr6	116659511	116659528	-	1	NA	intron (NM_178045, intron 3 of 10)	intron (NM_178045, intron 3 of 10)	8835	NM_001166580	213393	Mm.38231	NM_145980	ENSMUSG00000048489	8430408G22Rik	Depp|Fseg	RIKEN cDNA 8430408G22 gene	protein-coding
mm_120337.1	chr14	63451473	63451501	+	1	NA	intron (NM_177628, intron 2 of 3)	intron (NM_177628, intron 2 of 3)	15093	NM_177628	219148	Mm.37882	NM_177628	ENSMUSG00000035095	Fam167a	A030013D21	family with sequence similarity 167, member A	protein-coding
mm_120757.1	chr14	73364531	73364593	+	1	NA	exon (NM_008410, exon 5 of 6)	exon (NM_008410, exon 5 of 6)	20709	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_6619.1	chr1	75506640	75506650	-	1	NA	promoter-TSS (NM_178884)	promoter-TSS (NM_178884)	-193	NM_001310679	98733	Mm.236454	NM_178884	ENSMUSG00000026211	Obsl1	AW822216	obscurin-like 1	protein-coding
mm_156408.1	chrX	140461120	140461123	+	1	NA	intron (NM_021463, intron 1 of 6)	intron (NM_021463, intron 1 of 6)	4518	NM_021463	19139	Mm.287178	NM_021463	ENSMUSG00000031432	Prps1	2310010D17Rik|C76571|C76678|PRS-I|Prps-1	phosphoribosyl pyrophosphate synthetase 1	protein-coding
mm_47539.1	chr5	124249785	124249827	-	1	NA	promoter-TSS (NM_011256)	promoter-TSS (NM_011256)	-46	NM_011256	19679	Mm.44261	NM_011256	ENSMUSG00000029406	Pitpnm2	NIR3|RDGBA2|Rdgb2|mKIAA1457	phosphatidylinositol transfer protein, membrane-associated 2	protein-coding
mm_152002.1	chr19	5912772	5912822	-	1	NA	promoter-TSS (NM_001291078)	promoter-TSS (NM_001291078)	74	NM_011262	19708	Mm.2651	NM_011262	ENSMUSG00000024826	Dpf2	2210010M07Rik|BAF45D|Req|ubi-d4	D4, zinc and double PHD fingers family 2	protein-coding
mm_5052.1	chr1	194938971	194938981	+	1	NA	exon (NM_133654, exon 1 of 8)	exon (NM_133654, exon 1 of 8)	155	NM_001111059	12490	Mm.29798	NM_133654	ENSMUSG00000016494	Cd34	AU040960	CD34 antigen	protein-coding
mm_166481.1	chr5	145214534	145214539	+	1	NA	intron (NM_016683, intron 4 of 5)	MTEa|LTR|ERVL-MaLR	9977	NM_001167944	22757	Mm.332842	NM_016683	ENSMUSG00000055991	Zkscan5	AI132486|AI326970|Zfp95|hKraba1	zinc finger with KRAB and SCAN domains 5	protein-coding
mm_13634.1	chr2	114036461	114036465	+	1	NA	Intergenic	Intergenic	16412	NM_009608	11464	Mm.686	NM_009608	ENSMUSG00000068614	Actc1	Actc-1	actin, alpha, cardiac muscle 1	protein-coding
mm_123098.1	chr14	55878358	55878359	-	1	NA	TTS (NM_019820)	TTS (NM_019820)	5898	NM_019820	56410	Mm.97163	NM_019820	ENSMUSG00000040380	Cbln3	-	cerebellin 3 precursor protein	protein-coding
mm_64553.1	chr7	144553941	144553949	+	1	NA	promoter-TSS (NM_001195086)	promoter-TSS (NM_001195086)	-216	NM_001195086	233977	Mm.490347	NM_001033319	ENSMUSG00000037519	Ppfia1	C030014K08Rik|C87158|LIP.1|LIP1	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1	protein-coding
mm_61684.1	chr7	81004968	81004978	+	1	NA	intron (NM_178707, intron 1 of 9)	intron (NM_178707, intron 1 of 9)	11289	NM_178707	233410	Mm.29525	NM_178707	ENSMUSG00000005621	Zfp592	8430405N24|A730014M16Rik|Znf592|mKIAA0211	zinc finger protein 592	protein-coding
mm_12821.1	chr2	80316989	80316994	+	1	NA	intron (NM_024181, intron 1 of 22)	RLTR31D_MM|LTR|ERVK	1525	NM_024181	66861	Mm.21762	NM_024181	ENSMUSG00000027006	Dnajc10	1200006L06Rik|D2Ertd706e|ERdj5|JPDI	DnaJ heat shock protein family (Hsp40) member C10	protein-coding
mm_34749.1	chr4	152297275	152297326	+	1	NA	promoter-TSS (NM_133788)	promoter-TSS (NM_133788)	86	NM_133788	57295	Mm.277464	NM_133788	ENSMUSG00000039662	Icmt	1700008E11Rik|C80758|Gm13095|HSTE14|OTTMUSG00000010406|PPMT|STE14|pcCMT	isoprenylcysteine carboxyl methyltransferase	protein-coding
mm_113588.1	chr13	40917627	40917657	+	1	NA	promoter-TSS (NM_133219)	promoter-TSS (NM_133219)	8	NM_133219	14538	Mm.314757	NM_008105	ENSMUSG00000021360	Gcnt2	5330430K10Rik|IGnT|IGnTA|IGnTB|IGnTC	glucosaminyl (N-acetyl) transferase 2, I-branching enzyme	protein-coding
mm_151059.1	chr19	47179382	47179412	+	1	NA	5' UTR (NM_021360, exon 1 of 6)	5' UTR (NM_021360, exon 1 of 6)	577	NM_021360	18011	Mm.313651	NM_021360	ENSMUSG00000006435	Neurl1a	2410129E16Rik|AI450910|AI481072|Neu1|Neur1|Neurl|Neurl1|Nlz|Rnf67	neuralized E3 ubiquitin protein ligase 1A	protein-coding
mm_117342.1	chr13	69594996	69595006	-	1	NA	exon (NM_175283, exon 3 of 5)	exon (NM_175283, exon 3 of 5)	16462	NM_175283	78925	Mm.451912	NM_175283	ENSMUSG00000021594	Srd5a1	0610031P22Rik|4930435F02Rik|S5AR 1|Srd5a-1	steroid 5 alpha-reductase 1	protein-coding
mm_123642.1	chr14	68655692	68655697	-	1	NA	non-coding (NR_102399, exon 1 of 22)	non-coding (NR_102399, exon 1 of 22)	148	NM_010082	13522	Mm.117450	NM_010082	ENSMUSG00000014725	Adam28	C130072N01Rik|D430033C21Rik|Dtgn1|MDC-L|MDCL|TECADAM|eMDCII	a disintegrin and metallopeptidase domain 28	protein-coding
mm_45411.1	chr5	66333435	66333437	-	1	NA	intron (NM_001310626, intron 10 of 15)	intron (NM_001310626, intron 10 of 15)	4229	NM_001201416	11787	Mm.5159	NM_009686	ENSMUSG00000029207	Apbb2	2310007D03Rik|FE65L1|Rirl1|TR2L|Zfra	amyloid beta (A4) precursor protein-binding, family B, member 2	protein-coding
mm_78933.1	chr9	45103867	45103893	+	1	NA	intron (NM_001005421, intron 9 of 10)	intron (NM_001005421, intron 9 of 10)	-13996	NM_001014761	72821	Mm.229373	NM_001014761	ENSMUSG00000070304	Scn2b	2810451E09Rik|AI840361|Gm183	sodium channel, voltage-gated, type II, beta	protein-coding
mm_124314.1	chr14	103218992	103219025	-	1	NA	intron (NM_207215, intron 33 of 84)	RSINE1|SINE|B4	-119442	NM_001347600	50789	Mm.214746	NM_015822	ENSMUSG00000022124	Fbxl3	AU041772|AW212966|FBK|Fbl3a|Fbxl3a|Ovtm|Play68	F-box and leucine-rich repeat protein 3	protein-coding
mm_40868.1	chr5	73972815	73972817	+	1	NA	Intergenic	Intergenic	95595	NM_177561	69727	Mm.48795	NM_177561	ENSMUSG00000054814	Usp46	1190009E20Rik|2410018I08Rik|AI451644	ubiquitin specific peptidase 46	protein-coding
mm_25225.1	chr3	103859741	103859751	+	1	NA	promoter-TSS (NM_008979)	promoter-TSS (NM_008979)	-49	NR_104070	19260	Mm.395	NM_008979	ENSMUSG00000027843	Ptpn22	70zpep|PEP|Ptpn8	protein tyrosine phosphatase, non-receptor type 22 (lymphoid)	protein-coding
mm_4303.1	chr1	171840558	171840570	+	1	NA	intron (NM_001289470, intron 1 of 8)	intron (NM_001289470, intron 1 of 8)	867	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_101114.1	chr11	11962027	11962037	-	1	NA	intron (NM_010345, intron 4 of 16)	intron (NM_010345, intron 4 of 16)	-63888	NM_001190448	13195	Mm.12906	NM_016672	ENSMUSG00000020182	Ddc	Aadc	dopa decarboxylase	protein-coding
mm_60821.1	chr7	45705361	45705392	+	1	NA	TTS (NM_009800)	TTS (NM_009800)	129	NM_016974	13170	Mm.24222	NM_016974	ENSMUSG00000059824	Dbp	-	D site albumin promoter binding protein	protein-coding
mm_123362.1	chr14	63143128	63143138	-	1	NA	3' UTR (NM_007798, exon 10 of 10)	3' UTR (NM_007798, exon 10 of 10)	20671	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_127444.1	chr15	101270501	101270514	+	1	NA	exon (NM_010444, exon 2 of 7)	exon (NM_010444, exon 2 of 7)	3661	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_55658.1	chr6	72390622	72390639	-	1	NA	promoter-TSS (NM_016794)	promoter-TSS (NM_016794)	37	NM_016794	22320	Mm.1838	NM_016794	ENSMUSG00000050732	Vamp8	AU041171|Edb|endobrevin	vesicle-associated membrane protein 8	protein-coding
mm_30558.1	chr4	3779157	3779174	+	1	NA	intron (NM_010747, intron 10 of 12)	intron (NM_010747, intron 10 of 12)	56490	NM_026147	67427	Mm.21938	NM_026147	ENSMUSG00000028234	Rps20	4632426K06Rik|Dsk4	ribosomal protein S20	protein-coding
mm_95153.1	chr11	35769622	35769652	+	1	NA	5' UTR (NM_145962, exon 1 of 7)	5' UTR (NM_145962, exon 1 of 7)	142	NM_145962	211347	Mm.255044	NM_145962	ENSMUSG00000018846	Pank3	-	pantothenate kinase 3	protein-coding
mm_40050.1	chr5	33983716	33983734	+	1	NA	intron (NM_001310547, intron 1 of 3)	CpG	292	NM_001310546	381633	Mm.4923	NM_001033458	ENSMUSG00000070858	Gm1673	-	predicted gene 1673	protein-coding
mm_46508.1	chr5	105136175	105136206	-	1	NA	intron (NM_008620, intron 2 of 10)	intron (NM_008620, intron 2 of 10)	3362	NM_008620	17472	Mm.440525	NM_008620	ENSMUSG00000079363	Gbp4	AW228052|Mag-2|Mpa-2|Mpa2	guanylate binding protein 4	protein-coding
mm_171581.1	chr4	147492409	147492434	+	1	NA	intron (NM_001039209, intron 1 of 2)	intron (NM_001039209, intron 1 of 2)	-60856	NM_001014397	433804	Mm.332047	NM_001014397	ENSMUSG00000065999	Zfp985	Gm13154|OTTMUSG00000010673	zinc finger protein 985	protein-coding
mm_88569.1	chr10	79669470	79669480	+	1	NA	promoter-TSS (NM_148934)	promoter-TSS (NM_148934)	65	NM_148934	110012	Mm.22623	NM_148934	ENSMUSG00000020308	Tpgs1	AV005629|Gm16517|Gtrgeo22|PGs1	tubulin polyglutamylase complex subunit 1	protein-coding
mm_135026.1	chr16	32550131	32550176	-	1	NA	Intergenic	B1_Mur2|SINE|Alu	53872	NM_199309	245308	Mm.76859	NM_199309	ENSMUSG00000052363	Zdhhc19	Gm1744|Gm616	zinc finger, DHHC domain containing 19	protein-coding
mm_2313.1	chr1	91801454	91801487	+	1	NA	promoter-TSS (NM_007855)	promoter-TSS (NM_007855)	9	NM_007855	13345	Mm.9474	NM_007855	ENSMUSG00000007805	Twist2	Dermo1|bHLHa39	twist basic helix-loop-helix transcription factor 2	protein-coding
mm_169229.1	chr13	67234092	67234111	+	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	34967	NM_001001152	238690	Mm.306358	NM_001001152	ENSMUSG00000055480	Zfp458	BC062958|Rslcan-7|Znf728|mszf59-2	zinc finger protein 458	protein-coding
mm_68679.1	chr7	118995067	118995079	-	1	NA	5' UTR (NM_001195774, exon 1 of 4)	5' UTR (NM_001195774, exon 1 of 4)	138	NM_022420	64297	Mm.103439	NM_022420	ENSMUSG00000008734	Gprc5b	AW125761|Raig2	G protein-coupled receptor, family C, group 5, member B	protein-coding
mm_85117.1	chr9	95407351	95407361	-	1	NA	promoter-TSS (NM_018763)	promoter-TSS (NM_018763)	-86	NM_018763	54371	Mm.212446	NM_018763	ENSMUSG00000033350	Chst2	AI428561|AW121776|C130041E03Rik|Chts2|GST-2|GlcNAc6ST|Gn6st	carbohydrate sulfotransferase 2	protein-coding
mm_82895.1	chr9	32608980	32609001	-	1	NA	Intergenic	Intergenic	-67538	NM_008026	14247	Mm.258908	NM_008026	ENSMUSG00000016087	Fli1	EWSR2|Fli-1|SIC-1|Sic1	Friend leukemia integration 1	protein-coding
mm_110537.1	chr12	55080131	55080139	-	1	NA	promoter-TSS (NM_011899)	promoter-TSS (NM_011899)	-25	NM_028314	72658	Mm.434380	NM_028314	ENSMUSG00000062198	2700097O09Rik	AW552125	RIKEN cDNA 2700097O09 gene	protein-coding
mm_137046.1	chr17	17917485	17917495	+	1	NA	Intergenic	MER20|DNA|hAT-Charlie	29666	NM_008039	14289	Mm.378918	NM_008039	ENSMUSG00000052270	Fpr2	E330010I07Rik|Fpr-rs2	formyl peptide receptor 2	protein-coding
mm_92257.1	chr10	70644876	70644888	-	1	NA	intron (NR_045291, intron 1 of 5)	intron (NR_045291, intron 1 of 5)	7043	NR_045291	319646	Mm.483039	NR_045291	ENSMUSG00000037747	D630013N20Rik	-	RIKEN cDNA D630013N20 gene	ncRNA
mm_24064.1	chr3	87915579	87915603	+	1	NA	3' UTR (NM_008231, exon 6 of 6)	3' UTR (NM_008231, exon 6 of 6)	-3953	NM_026591	67707	Mm.393802	NM_026591	ENSMUSG00000019710	Mrpl24	2010005E08Rik|2810470K06Rik|6720473G22Rik|AA407670	mitochondrial ribosomal protein L24	protein-coding
mm_18047.1	chr2	39065506	39065570	-	1	NA	promoter-TSS (NR_110968)	promoter-TSS (NR_110968)	3	NR_110968	76899	Mm.131098	NM_029793	ENSMUSG00000026754	Golga1	0710001G09Rik|2210418B03Rik|AW107649|Golgi97|awag|golgin-97	golgi autoantigen, golgin subfamily a, 1	protein-coding
mm_18790.1	chr2	73775252	73775262	-	1	NA	promoter-TSS (NM_001113246)	promoter-TSS (NM_001113246)	89	NM_001166603	108699	Mm.257073	NM_029716	ENSMUSG00000056486	Chn1	0610007I19Rik|0710001E19Rik|1700112L09Rik|2900046J01Rik|AI413815|ARHGAP2	chimerin 1	protein-coding
mm_125252.1	chr15	35267531	35267565	+	1	NA	Intergenic	Intergenic	-28564	NM_054049	107587	Mm.46336	NM_054049	ENSMUSG00000022330	Osr2	5430409I15Rik|Osr2A|Osr2B	odd-skipped related 2	protein-coding
mm_125264.1	chr15	35431382	35431395	+	1	NA	intron (NM_177151, intron 7 of 61)	(T)n|Simple_repeat|Simple_repeat	59842	NM_177151	666173	Mm.309250	NM_177151	ENSMUSG00000037646	Vps13b	1810042B05Rik|2310042E16Rik|4732488H20|C330002D13Rik|C87206|Coh1|D230005K13|mKIAA0532|mKIAA5032	vacuolar protein sorting 13B	protein-coding
mm_20118.1	chr2	121171108	121171158	-	1	NA	promoter-TSS (NR_110985)	promoter-TSS (NR_110985)	-8	NM_001290820	99334	Mm.188422	NM_178889	ENSMUSG00000050619	Zscan29	AW125441|Zfp690	zinc finger SCAN domains 29	protein-coding
mm_3136.1	chr1	135131810	135131859	+	1	NA	promoter-TSS (NM_177081)	promoter-TSS (NM_177081)	741	NM_007955	13924	Mm.4450	NM_007955		Ptprv	Esp|OST|OST-PTP|mOST-PTP	protein tyrosine phosphatase, receptor type, V	protein-coding
mm_79731.1	chr9	62342090	62342112	+	1	NA	intron (NM_009672, intron 1 of 6)	CpG	758	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	protein-coding
mm_8231.1	chr1	138175654	138175660	-	1	NA	promoter-TSS (NM_001268286)	promoter-TSS (NM_001268286)	-352	NM_001268286	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_27138.1	chr3	32615292	32615297	-	1	NA	intron (NM_013531, intron 1 of 9)	intron (NM_013531, intron 1 of 9)	1241	NM_013531	14696	Mm.139192	NM_013531	ENSMUSG00000027669	Gnb4	6720453A21Rik|G(beta)4	guanine nucleotide binding protein (G protein), beta 4	protein-coding
mm_34294.1	chr4	141614341	141614389	+	1	NA	promoter-TSS (NR_033566)	promoter-TSS (NR_033566)	-5	NR_033566	100165	Mm.439819	NR_033566	ENSMUSG00000073731	AI507597	-	expressed sequence AI507597	ncRNA
mm_46777.1	chr5	112394837	112394880	-	1	NA	Intergenic	CpG	-2645	NM_028386	72898	Mm.151745	NM_028386	ENSMUSG00000029348	Asphd2	2900006N09Rik|9230106G13Rik	aspartate beta-hydroxylase domain containing 2	protein-coding
mm_81253.1	chr9	107982992	107983037	+	1	NA	intron (NM_023738, intron 21 of 23)	intron (NM_023738, intron 21 of 23)	2902	NM_026597	68176	Mm.76166	NM_026597	ENSMUSG00000042106	Fam212a	6230427J02Rik|Inka1	family with sequence similarity 212, member A	protein-coding
mm_37747.1	chr4	129619053	129619063	-	1	NA	promoter-TSS (NM_198026)	promoter-TSS (NM_198026)	35	NM_198026	230767	Mm.441132	NM_198026	ENSMUSG00000040795	Iqcc	BC026978	IQ motif containing C	protein-coding
mm_18899.1	chr2	76715329	76715337	-	1	NA	exon (NM_011652, exon 305 of 313)	exon (NM_011652, exon 305 of 313)	40018	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_126416.1	chr15	80287302	80287313	+	1	NA	promoter-TSS (NM_001044308)	promoter-TSS (NM_001044308)	69	NM_001044308	239556	Mm.291058	NM_001044308	ENSMUSG00000022416	Cacna1i	Ca(V)3.3	calcium channel, voltage-dependent, alpha 1I subunit	protein-coding
mm_110304.1	chr12	32851605	32851608	-	1	NA	3' UTR (NM_021524, exon 11 of 11)	3' UTR (NM_021524, exon 11 of 11)	27490	NR_045032	100504486	Mm.440246	NR_045032		Gdap10	Gdap-ps	ganglioside-induced differentiation-associated-protein 10	ncRNA
mm_122073.1	chr14	30599365	30599383	-	1	NA	exon (NM_001310682, exon 15 of 17)	exon (NM_001310682, exon 15 of 17)	10936	NM_001310682	18753	Mm.2314	NM_011103	ENSMUSG00000021948	Prkcd	AI385711|D14Ertd420e|PKC[d]|PKCdelta|Pkcd	protein kinase C, delta	protein-coding
mm_27052.1	chr3	27258693	27258708	-	1	NA	Intergenic	MuRRS-int|LTR|ERV1	-58377	NM_009425	22035	Mm.1062	NM_009425	ENSMUSG00000039304	Tnfsf10	A330042I21Rik|AI448571|APO-2L|Ly81|TL2|Tnlg6a|Trail	tumor necrosis factor (ligand) superfamily, member 10	protein-coding
mm_35253.1	chr4	19877876	19877886	-	1	NA	3' UTR (NM_175406, exon 8 of 8)	3' UTR (NM_175406, exon 8 of 8)	44685	NM_175406	242341	Mm.19298	NM_175406	ENSMUSG00000028238	Atp6v0d2	1620401A02Rik|AI324824|V-ATPase	ATPase, H+ transporting, lysosomal V0 subunit D2	protein-coding
mm_147847.1	chr18	63682255	63682265	-	1	NA	exon (NM_016792, exon 2 of 8)	exon (NM_016792, exon 2 of 8)	10099	NM_016792	53382	Mm.19169	NM_016792	ENSMUSG00000024583	Txnl1	32kDa|TRP32|Txnl	thioredoxin-like 1	protein-coding
mm_142765.1	chr17	49509881	49509897	-	1	NA	intron (NM_001008231, intron 1 of 25)	intron (NM_001008231, intron 1 of 25)	54448	NM_001008231	76441	Mm.211275	NM_001008231	ENSMUSG00000040260	Daam2	2310016D11Rik|AI843643|AW557870	dishevelled associated activator of morphogenesis 2	protein-coding
mm_8825.1	chr1	162477947	162478001	-	1	NA	promoter-TSS (NM_172646)	promoter-TSS (NM_172646)	56	NM_001038619	103967	Mm.441620	NM_172646	ENSMUSG00000040265	Dnm3	9630020E24Rik|AW061159|B230343F03Rik|C530045C17|mKIAA0820	dynamin 3	protein-coding
mm_113770.1	chr13	44840709	44840727	+	1	NA	intron (NM_001205044, intron 3 of 18)	intron (NM_001205044, intron 3 of 18)	109447	NM_001205043	16468	Mm.25059	NM_021878	ENSMUSG00000038518	Jarid2	Jmj|jumonji	jumonji, AT rich interactive domain 2	protein-coding
mm_116143.1	chr13	29748361	29748364	-	1	NA	intron (NR_131896, intron 5 of 16)	B4|SINE|B4	107311	NR_131896	68916	Mm.212227	NM_144536	ENSMUSG00000006191	Cdkal1	1190005B03Rik|6620401C13Rik	CDK5 regulatory subunit associated protein 1-like 1	protein-coding
mm_149569.1	chr19	12804859	12804874	+	1	NA	intron (NM_134152, intron 2 of 8)	intron (NM_134152, intron 2 of 8)	6257	NM_134152	107321	Mm.313136	NM_134152	ENSMUSG00000024696	Lpxn	4933402K05Rik|A530083L21Rik|AV278559|LDPL	leupaxin	protein-coding
mm_103464.1	chr11	76437186	76437197	-	1	NA	intron (NM_001346670, intron 15 of 21)	CpG	30048	NM_019818	56322	Mm.18803	NM_019818	ENSMUSG00000020843	Timm22	Tim22	translocase of inner mitochondrial membrane 22	protein-coding
mm_155833.1	chrX	100767720	100767742	+	1	NA	promoter-TSS (NM_001290402)	promoter-TSS (NM_001290402)	9	NM_001290402	53310	Mm.4615	NM_016747	ENSMUSG00000000881	Dlg3	Dlgh3|SAP102|mKIAA1232	discs, large homolog 3 (Drosophila)	protein-coding
mm_33696.1	chr4	133574729	133574771	+	1	NA	promoter-TSS (NM_172876)	promoter-TSS (NM_172876)	5	NM_172876	242691	Mm.40110	NM_172876	ENSMUSG00000028850	Gpatch3	D930035B09Rik|Gpatc3	G patch domain containing 3	protein-coding
mm_139179.1	chr17	47593517	47593545	+	1	NA	promoter-TSS (NM_007632)	promoter-TSS (NM_007632)	64	NM_007632	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_76775.1	chr8	95888378	95888415	-	1	NA	promoter-TSS (NM_010325)	promoter-TSS (NM_010325)	-31	NM_010325	14719	Mm.230169	NM_010325	ENSMUSG00000031672	Got2	AL022787|FABP-pm|Got-2|Kyat4|mAspAT	glutamatic-oxaloacetic transaminase 2, mitochondrial	protein-coding
mm_115924.1	chr13	23562377	23562392	-	1	NA	promoter-TSS (NM_178205)	promoter-TSS (NM_178205)	-19	NM_178205	319151	Mm.261658	NM_178205	ENSMUSG00000069273	Hist1h3e	H3-f|H3.1	histone cluster 1, H3e	protein-coding
mm_82284.1	chr9	7593440	7593443	-	1	NA	Intergenic	Intergenic	22045	NM_001310717	234911	Mm.334940	NM_001030289	ENSMUSG00000070323	Mmp27	Gm180	matrix metallopeptidase 27	protein-coding
mm_66261.1	chr7	35723525	35723528	-	1	NA	intron (NM_178704, intron 6 of 18)	intron (NM_178704, intron 6 of 18)	30928	NM_178704	233115	Mm.257808	NM_178704	ENSMUSG00000043671	Dpy19l3	6030410G08|9330164H19Rik	dpy-19-like 3 (C. elegans)	protein-coding
mm_142054.1	chr17	35638295	35638303	-	1	NA	exon (NM_001033366, exon 2 of 3)	exon (NM_001033366, exon 2 of 3)	5396	NM_001033366	268949	Mm.296301	NM_001033366	ENSMUSG00000073408	Dpcr1	Gm630	diffuse panbronchiolitis critical region 1 (human)	protein-coding
mm_160760.1	chr10	87521665	87521665	+	1	NA	promoter-TSS (NM_008777)	promoter-TSS (NM_008777)	-130	NM_008777	18478	Mm.263539	NM_008777	ENSMUSG00000020051	Pah	AW106920	phenylalanine hydroxylase	protein-coding
mm_41026.1	chr5	81794367	81794377	+	1	NA	exon (NM_198702, exon 28 of 28)	exon (NM_198702, exon 28 of 28)	330341	NR_138557	67327	Mm.87058	NR_138557		1700031L13Rik	-	RIKEN cDNA 1700031L13 gene	ncRNA
mm_148772.1	chr19	6095858	6095875	+	1	NA	Intergenic	Intergenic	-9932	NM_001009546	381204	Mm.359041	NM_001009546	ENSMUSG00000054999	Naaladl1	Gm964|Naaladasel	N-acetylated alpha-linked acidic dipeptidase-like 1	protein-coding
mm_144530.1	chr18	25066124	25066136	+	1	NA	intron (NM_175276, intron 15 of 26)	intron (NM_175276, intron 15 of 26)	99835	NM_001142697	66648	Mm.263189	NM_001004361	ENSMUSG00000024269	Tpgs2	5730437P09Rik|5730494M16Rik|AI666318|Pgs2	tubulin polyglutamylase complex subunit 2	protein-coding
mm_6073.1	chr1	60913336	60913348	-	1	NA	intron (NM_009843, intron 3 of 3)	intron (NM_009843, intron 3 of 3)	4317	NM_001281976	12477	Mm.390	NM_009843	ENSMUSG00000026011	Ctla4	Cd152|Ctla-4|Ly-56	cytotoxic T-lymphocyte-associated protein 4	protein-coding
mm_23034.1	chr3	34653587	34653593	+	1	NA	intron (NR_015580, intron 4 of 4)	intron (NR_015580, intron 4 of 4)	3595	NM_011443	20674	Mm.65396	NM_011443	ENSMUSG00000074637	Sox2	Sox-2|lcc|ysb	SRY (sex determining region Y)-box 2	protein-coding
mm_54864.1	chr6	42597569	42597581	-	1	NA	promoter-TSS (NM_203396)	promoter-TSS (NM_203396)	-203	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_144330.1	chr18	12991527	12991531	+	1	NA	3' UTR (NM_008378, exon 11 of 11)	3' UTR (NM_008378, exon 11 of 11)	-15461	NM_153087	225192	Mm.207073	NM_153087	ENSMUSG00000037346	Hrh4	AXOR35|BG26|GPCR105|GPRv53|H4|H4R|HH4R	histamine receptor H4	protein-coding
mm_6149.1	chr1	64937809	64937821	-	1	NA	exon (NM_001039493, exon 2 of 8)	exon (NM_001039493, exon 2 of 8)	19009	NM_001039493	241075	Mm.239534	NM_175509	ENSMUSG00000051344	Plekhm3	9430067K14Rik|A230102O09Rik|AI449570|DAPR|Plekhm1l	pleckstrin homology domain containing, family M, member 3	protein-coding
mm_117073.1	chr13	59490740	59490754	-	1	NA	intron (NM_023328, intron 17 of 25)	intron (NM_023328, intron 17 of 25)	53704	NM_001284221	67269	Mm.153008	NM_023328	ENSMUSG00000021557	Agtpbp1	1700020N17Rik|2310001G17Rik|2900054O13Rik|4930445M19Rik|5730402G09Rik|CCP1|Nna1|nmf243|pcd	ATP/GTP binding protein 1	protein-coding
mm_46400.1	chr5	104092921	104092963	-	1	NA	exon (NM_010097, exon 4 of 11)	exon (NM_010097, exon 4 of 11)	-15334	NM_001163772	100271704	Mm.366664	NM_001163772	ENSMUSG00000091034	Gm17660	Scpppq1	predicted gene, 17660	protein-coding
mm_120301.1	chr14	63139092	63139096	+	1	NA	exon (NM_007798, exon 8 of 10)	exon (NM_007798, exon 8 of 10)	16632	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_74485.1	chr8	4677320	4677339	-	1	NA	Intergenic	CpG	64159	NM_145591	233987	Mm.102799	NM_145591	ENSMUSG00000058748	Zfp958	-	zinc finger protein 958	protein-coding
mm_2505.1	chr1	106206572	106206573	+	1	NA	intron (NM_133821, intron 1 of 16)	intron (NM_133821, intron 1 of 16)	34703	NM_133821	98432	Mm.24115	NM_133821	ENSMUSG00000044340	Phlpp1	AI836256|Phlpp|Plekhe1|SCOP|mKIAA0606	PH domain and leucine rich repeat protein phosphatase 1	protein-coding
mm_28734.1	chr3	95736547	95736565	-	1	NA	exon (NM_007899, exon 7 of 11)	exon (NM_007899, exon 7 of 11)	-1583	NR_105981	102466787		NR_105981	ENSMUSG00000098737	Mir7014	Gm27837|mmu-mir-7014	microRNA 7014	ncRNA
mm_35212.1	chr4	19631988	19631994	-	1	NA	intron (NR_074089, intron 16 of 23)	B1F|SINE|Alu	56925	NM_025476	66302	Mm.440686	NM_025476	ENSMUSG00000028229	Rmdn1	Fam82b|RMD-1	regulator of microtubule dynamics 1	protein-coding
mm_172046.1	chr6	128473480	128473481	+	1	NA	non-coding (NR_028592, exon 3 of 3)	non-coding (NR_028592, exon 3 of 3)	34723	NR_028592	791299	Mm.297516	NR_028592	ENSMUSG00000059659	Gm10069	ENSMUSG00000059659	predicted gene 10069	ncRNA
mm_76911.1	chr8	105932055	105932097	-	1	NA	TTS (NM_173432)	TTS (NM_173432)	1786	NM_023182	109660	Mm.2745	NM_023182	ENSMUSG00000031896	Ctrl	0910001G08Rik|1810004D15Rik|AV005227|Ctra-1|Ctra1|chymopasin|mFLJ00366	chymotrypsin-like	protein-coding
mm_82244.1	chr9	4507962	4507965	-	1	NA	intron (NM_019691, intron 7 of 16)	L1VL4|LINE|L1	124426	NM_145609	78100	Mm.206549	NM_145609	ENSMUSG00000041124	Msantd4	8430410K20Rik|Mysantd4	Myb/SANT-like DNA-binding domain containing 4 with coiled-coils	protein-coding
mm_51183.1	chr6	70844500	70844579	+	1	NA	promoter-TSS (NM_010121)	promoter-TSS (NM_010121)	24	NM_001313918	13666	Mm.247167	NM_010121	ENSMUSG00000031668	Eif2ak3	Pek|Perk	eukaryotic translation initiation factor 2 alpha kinase 3	protein-coding
mm_53248.1	chr6	127577982	127578000	+	1	NA	promoter-TSS (NM_001033464)	promoter-TSS (NM_001033464)	16	NM_001033464	381812	Mm.296093	NM_001033464	ENSMUSG00000061414	Cracr2a	Efcab4b|Gm1073|Gm462	calcium release activated channel regulator 2A	protein-coding
mm_125962.1	chr15	76268077	76268093	+	1	NA	promoter-TSS (NM_028852)	promoter-TSS (NM_028852)	-4	NM_028852	74281	Mm.159156	NM_028852	ENSMUSG00000049653	Spatc1	1700084J23Rik|speriolin	spermatogenesis and centriole associated 1	protein-coding
mm_57486.1	chr6	125265347	125265354	-	1	NA	promoter-TSS (NR_015527)	promoter-TSS (NR_015527)	-175	NR_015527	73870	Mm.440681	NR_015527	ENSMUSG00000108129	4930417O13Rik	-	RIKEN cDNA 4930417O13 gene	ncRNA
mm_165314.1	chr2	103372684	103372689	-	1	NA	promoter-TSS (NR_040332)	promoter-TSS (NR_040332)	78	NR_040332	319854	Mm.403818	NR_040332	ENSMUSG00000087278	A930006I01Rik	-	RIKEN cDNA A930006I01 gene	ncRNA
mm_114550.1	chr13	73963854	73963888	+	1	NA	promoter-TSS (NM_027704)	promoter-TSS (NM_027704)	9	NM_027704	71164	Mm.66995	NM_027704	ENSMUSG00000069189	Zdhhc11	4933421L13Rik|DHHC-11|Zdhhc20	zinc finger, DHHC domain containing 11	protein-coding
mm_158061.1	chrX	101084247	101084259	-	1	NA	5' UTR (NM_007515, exon 3 of 13)	5' UTR (NM_007515, exon 3 of 13)	1152	NM_001301840	11989	Mm.5140	NM_007515	ENSMUSG00000031297	Slc7a3	Atrc3|CAT-3|CAT3|SLC7A1|SLC7A2	solute carrier family 7 (cationic amino acid transporter, y+ system), member 3	protein-coding
mm_104904.1	chr11	99643553	99643567	-	1	NA	exon (NM_029613, exon 1 of 1)	exon (NM_029613, exon 1 of 1)	529	NM_029613	76444	Mm.348022	NM_029613	ENSMUSG00000045109	Krtap4-7	2310037K05Rik|KAP4.7|KRTAP4.7	keratin associated protein 4-7	protein-coding
mm_127415.1	chr15	101258680	101258700	+	1	NA	Intergenic	Intergenic	-8156	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_106222.1	chr11	117078952	117078955	-	1	NA	TTS (NR_027059)	TTS (NR_027059)	1605	NR_105853	102465258		NR_105853	ENSMUSG00000104740	Mir6516	mmu-mir-6516	microRNA 6516	ncRNA
mm_109534.1	chr12	111542173	111542201	+	1	NA	exon (NM_178041, exon 8 of 12)	exon (NM_178041, exon 8 of 12)	1241	NR_033168	100316932	Mm.484709	NR_033168	ENSMUSG00000064493	Snora28	MBI-13	small nucleolar RNA, H/ACA box 28	snoRNA
mm_5366.1	chr1	26687459	26687462	-	1	NA	promoter-TSS (NM_001033764)	promoter-TSS (NM_001033764)	0	NM_001033764	210940	Mm.297614	NM_001033764	ENSMUSG00000073722	4931408C20Rik	-	RIKEN cDNA 4931408C20 gene	protein-coding
mm_83063.1	chr9	37546957	37546960	-	1	NA	intron (NM_022029, intron 1 of 3)	intron (NM_022029, intron 1 of 3)	5787	NM_022029	64011	Mm.335065	NM_022029	ENSMUSG00000053310	Nrgn	0710001B06Rik|AI838505|NG|NG/RC3|Pss1|R75334|RC3	neurogranin	protein-coding
mm_75173.1	chr8	36732898	36732908	-	1	NA	5' UTR (NM_001194941, exon 1 of 14)	5' UTR (NM_001194941, exon 1 of 14)	151	NM_001194941	50768	Mm.125155	NM_015802	ENSMUSG00000031523	Dlc1	A730069N07Rik|Arhgap7|HP|STARD12|dlc-1	deleted in liver cancer 1	protein-coding
mm_99400.1	chr11	102189811	102189833	+	1	NA	5' UTR (NM_175935, exon 1 of 6)	5' UTR (NM_175935, exon 1 of 6)	123	NM_175935	68401	Mm.22385	NM_175935	ENSMUSG00000034793	G6pc3	0710001K01Rik|AU019276|AU045429|AV128920|AW545836|UGRP	glucose 6 phosphatase, catalytic, 3	protein-coding
mm_140561.1	chr17	8147705	8147734	-	1	NA	promoter-TSS (NM_001083938)	promoter-TSS (NM_001083938)	69	NM_001083938	100037283	Mm.426736	NM_001083938	ENSMUSG00000095687	Rnaset2a	0610007O07Rik|4833423A10Rik|4930532K22Rik|C79750|RNASE6PL|Rnaset2	ribonuclease T2A	protein-coding
mm_102724.1	chr11	67237452	67237457	-	1	NA	promoter-TSS (NM_010855)	promoter-TSS (NM_010855)	-358	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_92207.1	chr10	68150164	68150168	-	1	NA	intron (NM_023598, intron 4 of 9)	intron (NM_023598, intron 4 of 9)	128560	NM_023598	71371	Mm.440357	NM_023598	ENSMUSG00000019947	Arid5b	4930580B11|5430435G07Rik|AI467247|Desrt|Mrf2|Mrf2alpha|Mrf2beta	AT rich interactive domain 5B (MRF1-like)	protein-coding
mm_63879.1	chr7	137129259	137129263	+	1	NA	Intergenic	Intergenic	-105422	NR_045885	100038555	Mm.444788	NR_045885	ENSMUSG00000109722	Gm10578	ENSMUSG00000073800	predicted gene 10578	ncRNA
mm_101974.1	chr11	50325600	50325666	-	1	NA	promoter-TSS (NM_001110500)	promoter-TSS (NM_001110500)	40	NM_001110499	12330	Mm.248827	NM_007597	ENSMUSG00000020368	Canx	1110069N15Rik|AI988026|Cnx|D11Ertd153e	calnexin	protein-coding
mm_35981.1	chr4	54190158	54190187	-	1	NA	Intergenic	Intergenic	364127	NM_028053	52076	Mm.27184	NM_028053	ENSMUSG00000028420	Tmem38b	1600017F22Rik|AA437809|AV051057|D4Ertd89e|TRIC-B|mg33b	transmembrane protein 38B	protein-coding
mm_27419.1	chr3	51517758	51517770	-	1	NA	3' UTR (NM_080793, exon 8 of 8)	3' UTR (NM_080793, exon 8 of 8)	33798	NM_016858	19338	Mm.1664	NM_016858	ENSMUSG00000027739	Rab33b	-	RAB33B, member RAS oncogene family	protein-coding
mm_123929.1	chr14	73366356	73366397	-	1	NA	exon (NM_008410, exon 3 of 6)	exon (NM_008410, exon 3 of 6)	18895	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_140926.1	chr17	24220739	24220803	-	1	NA	promoter-TSS (NM_028056)	promoter-TSS (NM_028056)	-2	NM_028056	72016	Mm.23881	NM_028056	ENSMUSG00000024118	1600002H07Rik	-	RIKEN cDNA 1600002H07 gene	protein-coding
mm_84141.1	chr9	59330151	59330153	-	1	NA	intron (NM_175325, intron 9 of 15)	intron (NM_175325, intron 9 of 15)	23356	NM_175325	102774	Mm.200714	NM_175325	ENSMUSG00000025235	Bbs4	AW537059|AW742241|D9Ertd464e	Bardet-Biedl syndrome 4 (human)	protein-coding
mm_120650.1	chr14	70530850	70530879	+	1	NA	promoter-TSS (NM_145219)	promoter-TSS (NM_145219)	43	NM_145219	213469	Mm.41708	NM_145219	ENSMUSG00000033595	Lgi3	AI841179|AW049851	leucine-rich repeat LGI family, member 3	protein-coding
mm_33941.1	chr4	136945702	136945706	+	1	NA	exon (NM_007939, exon 3 of 17)	exon (NM_007939, exon 3 of 17)	11112	NM_007939	13842	Mm.1390	NM_007939	ENSMUSG00000028661	Epha8	AW047546|Eek|Hek3|mKIAA1459	Eph receptor A8	protein-coding
mm_19718.1	chr2	104410604	104410625	-	1	NA	promoter-TSS (NM_001033347)	promoter-TSS (NM_001033347)	-280	NM_001033347	241589	Mm.358909	NM_001033347	ENSMUSG00000068373	D430041D05Rik	9630056G07Rik|G2	RIKEN cDNA D430041D05 gene	protein-coding
mm_141381.1	chr17	29079024	29079041	-	1	NA	promoter-TSS (NR_036469)	promoter-TSS (NR_036469)	94	NR_036469	100504267	Mm.438550	NR_036469	ENSMUSG00000085912	Trp53cor1	Gm16197|OTTMUSG00000031656|linc-p21|lincRNA-p21	tumor protein p53 pathway corepressor 1	ncRNA
mm_33813.1	chr4	135272174	135272182	+	1	NA	intron (NM_013885, intron 1 of 5)	intron (NM_013885, intron 1 of 5)	582	NM_013885	29876	Mm.257765	NM_013885	ENSMUSG00000037242	Clic4	D0Jmb3|TU-74|mc3s5|mtCLIC	chloride intracellular channel 4 (mitochondrial)	protein-coding
mm_38165.1	chr4	135216823	135216834	-	1	NA	3' UTR (NM_013885, exon 6 of 6)	3' UTR (NM_013885, exon 6 of 6)	55932	NM_013885	29876	Mm.257765	NM_013885	ENSMUSG00000037242	Clic4	D0Jmb3|TU-74|mc3s5|mtCLIC	chloride intracellular channel 4 (mitochondrial)	protein-coding
mm_110677.1	chr12	66284417	66284429	-	1	NA	promoter-TSS (NM_001162933)	promoter-TSS (NM_001162933)	-22	NM_001162933	238217	Mm.188575	NM_001162933	ENSMUSG00000060499	Rpl10l	EG238217	ribosomal protein L10-like	protein-coding
mm_77849.1	chr9	5303632	5303653	+	1	NA	exon (NM_009807, exon 6 of 10)	exon (NM_009807, exon 6 of 10)	5125	NM_009807	12362	Mm.1051	NM_009807	ENSMUSG00000025888	Casp1	ICE|Il1bc	caspase 1	protein-coding
mm_125271.1	chr15	36174021	36174072	+	1	NA	promoter-TSS (NM_001039368)	promoter-TSS (NM_001039368)	36	NM_001039368	17749	Mm.27375	NM_023127	ENSMUSG00000045996	Polr2k	ABC10-alpha|MafY|Mt1a|RPABC4|RPB10alpha|RPB12|RPB7.0	polymerase (RNA) II (DNA directed) polypeptide K	protein-coding
mm_78035.1	chr9	13833051	13833075	+	1	NA	exon (NM_176836, exon 5 of 10)	exon (NM_176836, exon 5 of 10)	5336	NM_176836	72826	Mm.246174	NM_176836	ENSMUSG00000037808	Fam76b	2810485I05Rik|C78303	family with sequence similarity 76, member B	protein-coding
mm_165092.1	chr19	53319265	53319266	+	1	NA	intron (NM_001008542, intron 1 of 5)	intron (NM_001008542, intron 1 of 5)	8759	NM_001008542	17859	Mm.2154	NM_010847	ENSMUSG00000025025	Mxi1	ENSMUSG00000067085|Gm10197|Mad2|bHLHc11	MAX interactor 1, dimerization protein	protein-coding
mm_86778.1	chr10	20170726	20170758	+	1	NA	intron (NM_001198635, intron 1 of 17)	intron (NM_001198635, intron 1 of 17)	21822	NM_001198635	17761	Mm.20928	NM_008635	ENSMUSG00000019996	Map7	E-MAP-115|MAP-7|Mtap7|R75000|mshi|mste|ste	microtubule-associated protein 7	protein-coding
mm_114693.1	chr13	81784174	81784176	+	1	NA	intron (NM_007684, intron 1 of 4)	intron (NM_007684, intron 1 of 4)	883	NM_007684	12626	Mm.12481	NM_007684	ENSMUSG00000021537	Cetn3	MmCEN3	centrin 3	protein-coding
mm_9895.1	chr1	186705327	186705356	-	1	NA	5' UTR (NM_009367, exon 1 of 7)	5' UTR (NM_009367, exon 1 of 7)	648	NM_009367	21808	Mm.18213	NM_009367	ENSMUSG00000039239	Tgfb2	BB105277|Tgf-beta2|Tgfb-2	transforming growth factor, beta 2	protein-coding
mm_57096.1	chr6	122590360	122590395	-	1	NA	intron (NM_001134391, intron 4 of 7)	(TG)n|Simple_repeat|Simple_repeat	12067	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_162125.1	chrX	71991844	71991844	+	1	NA	promoter-TSS (NM_007724)	promoter-TSS (NM_007724)	-5	NM_007724	12789	Mm.5097	NM_007724	ENSMUSG00000005864	Cnga2	CNG2|Cnca|Cncg4|OCNC1	cyclic nucleotide gated channel alpha 2	protein-coding
mm_69083.1	chr7	127016541	127016603	-	1	NA	TTS (NM_001102563)	TTS (NM_001102563)	780	NM_030240	67278	Mm.345385	NM_030240	ENSMUSG00000030680	Pagr1a	2900092E17Rik|C77040|PA1|PAGR1	PAXIP1 associated glutamate rich protein 1A	protein-coding
mm_115249.1	chr13	110396831	110396841	+	1	NA	intron (NM_152804, intron 4 of 13)	intron (NM_152804, intron 4 of 13)	1792	NM_152804	20620	Mm.380	NM_152804	ENSMUSG00000021701	Plk2	Snk	polo-like kinase 2	protein-coding
mm_35737.1	chr4	45320271	45320283	-	1	NA	exon (NM_025513, exon 1 of 4)	exon (NM_025513, exon 1 of 4)	326	NM_025513	66362	Mm.275788	NM_025513	ENSMUSG00000028322	Exosc3	2310005D06Rik|AI593501|Rrp40	exosome component 3	protein-coding
mm_99722.1	chr11	106300339	106300368	+	1	NA	TTS (NM_008117)	TTS (NM_008117)	1543	NM_008117	14599	Mm.343934	NM_008117	ENSMUSG00000020713	Gh	Gh1|Ghb1	growth hormone	protein-coding
mm_75539.1	chr8	57332830	57332891	-	1	NA	intron (NR_131041, intron 1 of 2)	intron (NR_131041, intron 1 of 2)	425	NR_131041	75996	Mm.399754	NR_131041	ENSMUSG00000097910	5033428I22Rik	-	RIKEN cDNA 5033428I22 gene	ncRNA
mm_54376.1	chr6	31202324	31202336	-	1	NA	intron (NR_110469, intron 1 of 3)	Lx8|LINE|L1	16144	NR_110470	232685	Mm.443019	NM_144555	ENSMUSG00000044471	Lncpint	Lincpint|MNCb-1768|Pint|linc-Pint	long non-protein coding RNA, Trp53 induced transcript	ncRNA
mm_25641.1	chr3	121291822	121291832	+	1	NA	promoter-TSS (NM_024178)	promoter-TSS (NM_024178)	10	NM_024178	66789	Mm.269881	NM_024178	ENSMUSG00000039887	Alg14	5430428G01Rik|AI854024	asparagine-linked glycosylation 14	protein-coding
mm_143976.1	chr17	87438520	87438536	-	1	NA	intron (NM_007589, intron 2 of 5)	intron (NM_007589, intron 2 of 5)	8407	NM_007589	12314	Mm.329243	NM_007589	ENSMUSG00000036438	Calm2	1500001E21Rik|AL024017	calmodulin 2	protein-coding
mm_172943.1	chr9	81435947	81435948	+	1	NA	Intergenic	L1Md_F2|LINE|L1	-195983	NR_040394	319405	Mm.246494	NR_040393	ENSMUSG00000097466	D430036J16Rik	-	RIKEN cDNA D430036J16 gene	ncRNA
mm_68272.1	chr7	105596324	105596355	-	1	NA	exon (NM_017371, exon 5 of 10)	exon (NM_017371, exon 5 of 10)	3777	NM_017371	15458	Mm.3485	NM_017371	ENSMUSG00000030895	Hpx	Hpxn|hx	hemopexin	protein-coding
mm_97745.1	chr11	80472612	80472621	+	1	NA	TTS (NM_178616)	TTS (NM_178616)	-4430	NM_009871	12569	Mm.142275	NM_009871	ENSMUSG00000048895	Cdk5r1	Cdk5r|D11Bwg0379e|p25|p35	cyclin-dependent kinase 5, regulatory subunit 1 (p35)	protein-coding
mm_10949.1	chr2	25608525	25608551	+	1	NA	promoter-TSS (NM_001024616)	promoter-TSS (NM_001024616)	-92	NM_001024616	227624	Mm.29600	NM_001024616	ENSMUSG00000015087	Rabl6	B230208H17Rik|Rbel1|Rbel1a|Rbel1b|parf	RAB, member RAS oncogene family-like 6	protein-coding
mm_72369.1	chr8	80948995	80949000	+	1	NA	Intergenic	Intergenic	65909	NM_027554	74841	Mm.246018	NM_027554	ENSMUSG00000038250	Usp38	4631402N15Rik|4833420O05Rik|AA536967|AU044701|AW544820|mKIAA1891	ubiquitin specific peptidase 38	protein-coding
mm_46779.1	chr5	112475776	112475780	-	1	NA	intron (NM_001253917, intron 1 of 15)	intron (NM_001253917, intron 1 of 15)	26352	NM_001177504	625464	Mm.389676	NM_001177504	ENSMUSG00000072722	Gm6588	EG625464	predicted gene 6588	protein-coding
mm_9898.1	chr1	186706049	186706060	-	1	NA	promoter-TSS (NM_009367)	promoter-TSS (NM_009367)	-65	NM_001329107	21808	Mm.18213	NM_009367	ENSMUSG00000039239	Tgfb2	BB105277|Tgf-beta2|Tgfb-2	transforming growth factor, beta 2	protein-coding
mm_68075.1	chr7	101869258	101869277	-	1	NA	5' UTR (NM_008034, exon 2 of 7)	5' UTR (NM_008034, exon 2 of 7)	1521	NM_001252554	14275	Mm.2135	NM_008034	ENSMUSG00000001827	Folr1	FBP1|Folbp-1|Folbp1	folate receptor 1 (adult)	protein-coding
mm_100661.1	chr11	3266343	3266353	-	1	NA	promoter-TSS (NM_007879)	promoter-TSS (NM_007879)	38	NM_007879	13494	Mm.3250	NM_007879	ENSMUSG00000020457	Drg1	AA408859|AI132520|Nedd3	developmentally regulated GTP binding protein 1	protein-coding
mm_51066.1	chr6	66264123	66264170	+	1	NA	Intergenic	ORR1D1-int|LTR|ERVL-MaLR	-8359	NR_136927	102633773	Mm.272086	NR_136927	ENSMUSG00000107653	Gm31520	-	sterol-C5-desaturase pseudogene	pseudo
mm_105454.1	chr11	104503509	104503536	-	1	NA	3' UTR (NM_145436, exon 19 of 19)	3' UTR (NM_145436, exon 19 of 19)	47098	NM_001285990	217232	Mm.89845	NM_145436	ENSMUSG00000020687	Cdc27	AI452358|APC3|BC023187	cell division cycle 27	protein-coding
mm_156697.1	chrX	159482986	159483001	+	1	NA	exon (NM_001081124, exon 10 of 17)	exon (NM_001081124, exon 10 of 17)	23868	NM_001313753	78283	Mm.160079	NM_001081124	ENSMUSG00000041020	Map7d2	1600028E09Rik|2900002G04Rik|5330432J06Rik|C030036K04Rik|Mtap7d2	MAP7 domain containing 2	protein-coding
mm_18022.1	chr2	38613710	38613720	-	1	NA	intron (NM_011187, intron 5 of 7)	intron (NM_011187, intron 5 of 7)	30191	NM_011187	19177	Mm.389251	NM_011187	ENSMUSG00000026750	Psmb7	AU020723|MC14	proteasome (prosome, macropain) subunit, beta type 7	protein-coding
mm_171309.1	chr3	94604796	94604813	-	1	NA	Intergenic	CpG	-22088	NM_029721	76742	Mm.28160	NM_029721	ENSMUSG00000028136	Snx27	5730552M22Rik|ESTM45|ESTM47|R75405	sorting nexin family member 27	protein-coding
mm_71196.1	chr8	40882376	40882384	+	1	NA	intron (NM_007514, intron 1 of 11)	intron (NM_007514, intron 1 of 11)	20013	NM_001044740	11988	Mm.4676	NM_007514	ENSMUSG00000031596	Slc7a2	20.5|AI158848|Atrc2|CAT-2|Cat2|Tea	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	protein-coding
mm_31205.1	chr4	43730427	43730451	+	1	NA	intron (NR_033355, intron 1 of 1)	intron (NR_033355, intron 1 of 1)	405	NR_033355	71406	Mm.33063	NM_027789	ENSMUSG00000028475	5430416O09Rik	AI481365	RIKEN cDNA 5430416O09 gene	ncRNA
mm_50422.1	chr6	48833825	48833840	+	1	NA	TTS (NM_001164209)	TTS (NM_001164209)	7156	NM_023056	65963	Mm.28385	NM_023056	ENSMUSG00000029810	Tmem176b	1810009M01Rik|Clast1|Lr8	transmembrane protein 176B	protein-coding
mm_43355.1	chr5	135187305	135187333	+	1	NA	promoter-TSS (NM_011714)	promoter-TSS (NM_011714)	-4	NM_011714	22385	Mm.40331	NM_011714	ENSMUSG00000002748	Baz1b	C87820|WSTF|Wbscr9	bromodomain adjacent to zinc finger domain, 1B	protein-coding
mm_92403.1	chr10	76709492	76709511	-	1	NA	3' UTR (NM_009933, exon 35 of 35)	3' UTR (NM_009933, exon 35 of 35)	16543	NM_009933	12833	Mm.2509	NM_009933	ENSMUSG00000001119	Col6a1	AI747156|Col6a-1	collagen, type VI, alpha 1	protein-coding
mm_57373.1	chr6	124812483	124812503	-	1	NA	exon (NM_009415, exon 4 of 7)	exon (NM_009415, exon 4 of 7)	1803	NM_009415	21991	Mm.4222	NM_009415	ENSMUSG00000023456	Tpi1	AI255506|Tpi|Tpi-1	triosephosphate isomerase 1	protein-coding
mm_122459.1	chr14	45442477	45442496	-	1	NA	Intergenic	ID4|SINE|ID	-53690	NM_019425	54342	Mm.312945	NM_019425	ENSMUSG00000037722	Gnpnat1	AU017428|AU040593|EMeg32|Gpnat1|Gsnpat	glucosamine-phosphate N-acetyltransferase 1	protein-coding
mm_122911.1	chr14	54957393	54957438	-	1	NA	exon (NM_010856, exon 17 of 39)	exon (NM_010856, exon 17 of 39)	-8273	NR_029724	387204		NR_029724	ENSMUSG00000065432	Mir208a	Mirn208|Mirn208a|mir-208|mir-208a|mmu-mir-208	microRNA 208a	ncRNA
mm_56483.1	chr6	99096262	99096272	-	1	NA	intron (NM_001347345, intron 5 of 19)	intron (NM_001347345, intron 5 of 19)	-67969	NM_001197322	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_78832.1	chr9	44140591	44140609	+	1	NA	exon (NM_023061, exon 13 of 16)	exon (NM_023061, exon 13 of 16)	5942	NM_023061	84004	Mm.275003	NM_023061	ENSMUSG00000032135	Mcam	1-gicerin|AV025631|CD146|CD149|Muc18|s-endo|s-gicerin	melanoma cell adhesion molecule	protein-coding
mm_116854.1	chr13	54762696	54762709	-	1	NA	exon (NM_033610, exon 4 of 6)	exon (NM_033610, exon 4 of 6)	3738	NM_033610	104069	Mm.200843	NM_033610	ENSMUSG00000034891	Sncb	AI838531|betaSYN	synuclein, beta	protein-coding
mm_93989.1	chr10	127522340	127522356	-	1	NA	promoter-TSS (NM_028230)	promoter-TSS (NM_028230)	96	NM_001252316	108037	Mm.29890	NM_028230	ENSMUSG00000025403	Shmt2	2700043D08Rik|AA408223|AA986903	serine hydroxymethyltransferase 2 (mitochondrial)	protein-coding
mm_124237.1	chr14	101477256	101477317	-	1	NA	intron (NM_001081278, intron 9 of 18)	intron (NM_001081278, intron 9 of 18)	131905	NM_001081278	210789	Mm.320639	NM_173380	ENSMUSG00000033083	Tbc1d4	5930406J04Rik|A930035N22|AV295684|As160	TBC1 domain family, member 4	protein-coding
mm_156326.1	chrX	138914393	138914403	+	1	NA	promoter-TSS (NM_013724)	promoter-TSS (NM_013724)	-32	NM_013724	27206	Mm.482319	NM_013724	ENSMUSG00000052854	Nrk	AA407323|AA409510|AI225895|AV168563|AW538185|Nesk	Nik related kinase	protein-coding
mm_32784.1	chr4	116708702	116708712	+	1	NA	promoter-TSS (NM_026714)	promoter-TSS (NM_026714)	-223	NM_026714	68394	Mm.425201	NM_026714	ENSMUSG00000028689	Ccdc163	0610037D15Rik|4933430J04Rik	coiled-coil domain containing 163	protein-coding
mm_63747.1	chr7	130949085	130949088	+	1	NA	intron (NM_019564, intron 1 of 8)	intron (NM_019564, intron 1 of 8)	12883	NM_019564	56213	Mm.30156	NM_019564	ENSMUSG00000006205	Htra1	AI429470|HTRA|L56|Prss11|RSPP11	HtrA serine peptidase 1	protein-coding
mm_167422.1	chr8	111596095	111596107	+	1	NA	intron (NM_001168623, intron 1 of 4)	intron (NM_001168623, intron 1 of 4)	34221	NM_027570	52815	Mm.27589	NM_027570	ENSMUSG00000031958	Ldhd	4733401P21Rik|D8Bwg1320e	lactate dehydrogenase D	protein-coding
mm_28359.1	chr3	89773222	89773279	-	1	NA	promoter-TSS (NM_027315)	promoter-TSS (NM_027315)	150	NR_130957	74034	Mm.386816	NR_130957	ENSMUSG00000042579	4632404H12Rik	-	RIKEN cDNA 4632404H12 gene	ncRNA
mm_118814.1	chr14	25466732	25466746	+	1	NA	intron (NM_001310666, intron 1 of 23)	intron (NM_001310666, intron 1 of 23)	7554	NM_183208	328365	Mm.227484	NM_183208	ENSMUSG00000007817	Zmiz1	BC065120|E330020C23|ENSMUSG00000072684|Gm10397|I920194n01|Rai17|Zimp10	zinc finger, MIZ-type containing 1	protein-coding
mm_30658.1	chr4	8939750	8939768	+	1	NA	Intergenic	Intergenic	249353	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_62045.1	chr7	92324660	92324663	+	1	NA	intron (NM_011807, intron 14 of 22)	intron (NM_011807, intron 14 of 22)	89691	NM_001243047	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_61344.1	chr7	68286134	68286153	+	1	NA	intron (NM_001013811, intron 1 of 8)	intron (NM_001013811, intron 1 of 8)	-9549	NR_040340	100504026	Mm.426764	NR_040340	ENSMUSG00000086628	Gm16157	OTTMUSG00000031023	predicted gene 16157	ncRNA
mm_110783.1	chr12	71114061	71114076	-	1	NA	intron (NM_029227, intron 2 of 4)	intron (NM_029227, intron 2 of 4)	2640	NM_029227	75266	Mm.402075	NM_029227	ENSMUSG00000021078	Tomm20l	4930553D19Rik	translocase of outer mitochondrial membrane 20 homolog (yeast)-like	protein-coding
mm_79699.1	chr9	60837903	60837914	+	1	NA	intron (NM_028283, intron 1 of 18)	intron (NM_028283, intron 1 of 18)	43360	NM_028283	72565	Mm.68819	NM_028283	ENSMUSG00000034485	Uaca	2700059D02Rik|nucling	uveal autoantigen with coiled-coil domains and ankyrin repeats	protein-coding
mm_60701.1	chr7	45213043	45213044	+	1	NA	Intergenic	Intergenic	-1160	NM_015789	50722	Mm.27287	NM_015789	ENSMUSG00000030792	Dkkl1	AI414495|SGY|SGY-1|SGY1|Soggy|mSgy	dickkopf-like 1	protein-coding
mm_41259.1	chr5	88992876	88992878	+	1	NA	intron (NM_001197147, intron 3 of 25)	intron (NM_001197147, intron 3 of 25)	105617	NM_018760	54403	Mm.41044	NM_018760	ENSMUSG00000060961	Slc4a4	AI835705|NBC|NBC1	solute carrier family 4 (anion exchanger), member 4	protein-coding
mm_147489.1	chr18	47333312	47333373	-	1	NA	intron (NM_001311097, intron 1 of 17)	intron (NM_001311097, intron 1 of 17)	35526	NM_018744	20358	Mm.40909	NM_018744	ENSMUSG00000019647	Sema6a	A730020P05Rik|AI851735|Sema6A-1|Semaq|VIa	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A	protein-coding
mm_136454.1	chr16	94997608	94997616	-	1	NA	promoter-TSS (NM_010606)	promoter-TSS (NM_010606)	84	NM_001025584	16522	Mm.328720	NM_010606	ENSMUSG00000043301	Kcnj6	BIR1|GIRK2|KATP2|KCNJ7|Kir3.2|weaver|wv	potassium inwardly-rectifying channel, subfamily J, member 6	protein-coding
mm_61653.1	chr7	80472426	80472437	+	1	NA	intron (NM_001042527, intron 15 of 21)	intron (NM_001042527, intron 15 of 21)	62567	NM_007550	12144	Mm.12932	NM_007550	ENSMUSG00000030528	Blm	-	Bloom syndrome, RecQ helicase-like	protein-coding
mm_50911.1	chr6	57582776	57582790	+	1	NA	intron (NM_025992, intron 1 of 22)	intron (NM_025992, intron 1 of 22)	1791	NM_025992	67138	Mm.297393	NM_025992	ENSMUSG00000029798	Herc6	1700121D12Rik|2510038N07Rik|4930427L17Rik|AI451296|CEB1|Herc5	hect domain and RLD 6	protein-coding
mm_101203.1	chr11	19018957	19018973	-	1	NA	promoter-TSS (NM_010789)	promoter-TSS (NM_010789)	4	NM_001193271	17268	Mm.356578	NM_010789	ENSMUSG00000020160	Meis1	C530044H18Rik|Evi8	Meis homeobox 1	protein-coding
mm_128769.1	chr15	66500858	66500905	-	1	NA	promoter-TSS (NM_019457)	promoter-TSS (NM_019457)	29	NM_019457	54562	Mm.244890	NM_019457	ENSMUSG00000022375	Lrrc6	LRTP	leucine rich repeat containing 6 (testis)	protein-coding
mm_87150.1	chr10	34898778	34898784	+	1	NA	Intergenic	Intergenic	415381	NM_010237	14302	Mm.332432	NM_010237	ENSMUSG00000019779	Frk	BSK|BSK/IYK|C85044|GTK|RAK	fyn-related kinase	protein-coding
mm_23768.1	chr3	75165085	75165108	+	1	NA	Intergenic	Intergenic	-21324	NM_172515	213234	Mm.80075	NM_172515	ENSMUSG00000034151	Zbbx	4931432L23	zinc finger, B-box domain containing	protein-coding
mm_97378.1	chr11	77711555	77711567	+	1	NA	3' UTR (NM_001024205, exon 4 of 4)	3' UTR (NM_001024205, exon 4 of 4)	13732	NM_001313933	12957	Mm.22830	NM_009965	ENSMUSG00000000724	Cryba1	BA3/A1|Cryb	crystallin, beta A1	protein-coding
mm_143389.1	chr17	69274602	69274605	-	1	NA	TTS (NR_045428)	TTS (NR_045428)	2603	NR_045428	69750	Mm.439063	NR_045428	ENSMUSG00000100572	2410021H03Rik	-	RIKEN cDNA 2410021H03 gene	ncRNA
mm_134995.1	chr16	32164373	32164378	-	1	NA	intron (NM_146069, intron 1 of 3)	intron (NM_146069, intron 1 of 3)	1101	NM_146069	224109	Mm.33498	NM_146069	ENSMUSG00000052384	Nrros	E430025L02Rik|Lrcc33|Lrrc33	negative regulator of reactive oxygen species	protein-coding
mm_34984.1	chr4	156026121	156026132	+	1	NA	promoter-TSS (NM_009400)	promoter-TSS (NM_009400)	-216	NM_009400	21936	Mm.3180	NM_009400	ENSMUSG00000041954	Tnfrsf18	AITR|Gitr	tumor necrosis factor receptor superfamily, member 18	protein-coding
mm_108503.1	chr12	83950084	83950090	+	1	NA	promoter-TSS (NM_023633)	promoter-TSS (NM_023633)	-521	NM_023633	71952	Mm.251483	NM_023633	ENSMUSG00000046791	2410016O06Rik	MAPJD|NO66	RIKEN cDNA 2410016O06 gene	protein-coding
mm_134781.1	chr16	23981285	23981292	-	1	NA	intron (NM_009744, intron 1 of 9)	intron (NM_009744, intron 1 of 9)	7324	NM_009744	12053	Mm.347398	NM_009744	ENSMUSG00000022508	Bcl6	Bcl5	B cell leukemia/lymphoma 6	protein-coding
mm_155194.1	chrX	56454920	56454928	+	1	NA	promoter-TSS (NM_172779)	promoter-TSS (NM_172779)	85	NM_172779	236790	Mm.474772	NM_172779	ENSMUSG00000035967	Ints6l	4930535D10Rik|6330505F04Rik|D130066O12|Ddx26b	integrator complex subunit 6 like	protein-coding
mm_40786.1	chr5	67404603	67404614	+	1	NA	intron (NM_001164806, intron 3 of 4)	intron (NM_001164806, intron 3 of 4)	23191	NM_001164806	666938	Mm.101339	NM_001164806	ENSMUSG00000092060	Bend4	D330027G24Rik|EG666938	BEN domain containing 4	protein-coding
mm_112214.1	chr12	113428640	113428651	-	1	NA	Intergenic	Intergenic	-60920	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_58826.1	chr7	16734407	16734408	+	1	NA	Intergenic	ORR1A1|LTR|ERVL-MaLR	-4037	NM_198613	232910	Mm.333597	NM_198613	ENSMUSG00000008036	Ap2s1	AI043088	adaptor-related protein complex 2, sigma 1 subunit	protein-coding
mm_121262.1	chr14	103073267	103073296	+	1	NA	exon (NM_001033242, exon 3 of 4)	exon (NM_001033242, exon 3 of 4)	3065	NM_001033242	211286	Mm.295289	NM_001033242	ENSMUSG00000022125	Cln5	A730075N08Rik	ceroid-lipofuscinosis, neuronal 5	protein-coding
mm_167011.1	chr7	59324146	59324153	-	1	NA	promoter-TSS (NR_015479)	promoter-TSS (NR_015479)	0	NR_015479	330544	Mm.9002	NR_015479	ENSMUSG00000100826	C230091D08Rik	-	RIKEN cDNA C230091D08 gene	ncRNA
mm_73884.1	chr8	119345240	119345260	+	1	NA	intron (NM_024219, intron 2 of 3)	B3A|SINE|B2	712	NM_024219	68196	Mm.358714	NM_024219	ENSMUSG00000031839	Hsbp1	0610007A03Rik|AA408769|Hsp25	heat shock factor binding protein 1	protein-coding
mm_159623.1	chr4	135398216	135398216	-	1	NA	promoter-TSS (NM_001243306)	promoter-TSS (NM_001243306)	11	NM_001243306	230822	Mm.35548	NM_145555	ENSMUSG00000043924	Ncmap	A330049M08Rik|AA545175|Mp11	noncompact myelin associated protein	protein-coding
mm_15765.1	chr2	164316731	164316756	+	1	NA	promoter-TSS (NM_013679)	promoter-TSS (NM_013679)	-8	NM_013679	20945	Mm.439686	NM_013679	ENSMUSG00000017000	Svs6	MSVSP99|Svp6	seminal vesicle secretory protein 6	protein-coding
mm_12797.1	chr2	79639195	79639207	+	1	NA	intron (NM_080558, intron 2 of 17)	intron (NM_080558, intron 2 of 17)	3776	NM_080558	70599	Mm.272881	NM_080558	ENSMUSG00000027007	Ssfa2	5730488C15Rik|CS-1|CS1|KRAP|SPAG13|mKIAA1927	sperm specific antigen 2	protein-coding
mm_53471.1	chr6	134924647	134924666	+	1	NA	3' UTR (NM_009875, exon 3 of 3)	3' UTR (NM_009875, exon 3 of 3)	4255	NM_009875	12576	Mm.2958	NM_009875	ENSMUSG00000003031	Cdkn1b	AA408329|AI843786|Kip1|p27|p27Kip1	cyclin-dependent kinase inhibitor 1B	protein-coding
mm_171982.1	chr5	92083658	92083658	-	1	NA	promoter-TSS (NM_011816)	promoter-TSS (NM_011816)	-60	NM_001080796	23881	Mm.290530	NM_011816	ENSMUSG00000029405	G3bp2	AA409541|E430034L04Rik|G3BP|mKIAA0660	GTPase activating protein (SH3 domain) binding protein 2	protein-coding
mm_23934.1	chr3	84039379	84039382	+	1	NA	exon (NM_172681, exon 2 of 35)	exon (NM_172681, exon 2 of 35)	781	NM_172681	229473	Mm.28838	NM_172681	ENSMUSG00000033767	D930015E06Rik	Kiaa0922|mKIAA0922	RIKEN cDNA D930015E06 gene	protein-coding
mm_41075.1	chr5	87670999	87671016	+	1	NA	exon (NM_007784, exon 7 of 34)	exon (NM_007784, exon 7 of 34)	4799	NM_001286016	12990	Mm.427467	NM_007784	ENSMUSG00000070702	Csn1s1	AA959832|AW212882|Csna	casein alpha s1	protein-coding
mm_110727.1	chr12	69724831	69724885	-	1	NA	promoter-TSS (NM_026536)	promoter-TSS (NM_026536)	16	NM_145443	217666	Mm.103362	NM_145443	ENSMUSG00000020988	L2hgdh	BC016226	L-2-hydroxyglutarate dehydrogenase	protein-coding
mm_72711.1	chr8	84990586	84990649	+	1	NA	promoter-TSS (NM_001167991)	promoter-TSS (NM_001167991)	22	NM_001167991	170833	Mm.247775	NM_133255	ENSMUSG00000052566	Hook2	A630054I03Rik	hook microtubule tethering protein 2	protein-coding
mm_101510.1	chr11	32267584	32267677	-	1	NA	promoter-TSS (NM_001284360)	promoter-TSS (NM_001284360)	77	NM_181569	17168	Mm.263161	NM_181569	ENSMUSG00000020289	Nprl3	Aag|CGTHBA|HS-26|HS-40|Mare|Phg|Prox1|m(alpha)RE	nitrogen permease regulator-like 3	protein-coding
mm_155891.1	chrX	101652387	101652411	+	1	NA	intron (NM_139144, intron 4 of 21)	intron (NM_139144, intron 4 of 21)	12181	NM_001290535	108155	Mm.487332	NM_139144	ENSMUSG00000034160	Ogt	1110038P24Rik|4831420N21Rik|AI115525|Ogtl	O-linked N-acetylglucosamine (GlcNAc) transferase (UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase)	protein-coding
mm_86471.1	chr10	4611839	4611863	+	1	NA	promoter-TSS (NR_126357)	promoter-TSS (NR_126357)	-138	NM_001302532	13982	Mm.9213	NM_007956	ENSMUSG00000019768	Esr1	ER|ER-alpha|ERa|ERalpha|ESR|Estr|Estra|Nr3a1	estrogen receptor 1 (alpha)	protein-coding
mm_134847.1	chr16	26831620	26831625	-	1	NA	Intergenic	U2|snRNA|snRNA	-76120	NR_105063	100504628	Mm.393275	NR_105063	ENSMUSG00000092545	Gm20319	-	predicted gene, 20319	ncRNA
mm_103158.1	chr11	70433298	70433333	-	1	NA	intron (NM_001271359, intron 1 of 15)	intron (NM_001271359, intron 1 of 15)	735	NM_001271358	216869	Mm.203747	NM_145429	ENSMUSG00000060216	Arrb2	AI326910|AW122872	arrestin, beta 2	protein-coding
mm_160014.1	chr6	128300835	128300835	-	1	NA	promoter-TSS (NM_001080979)	promoter-TSS (NM_001080979)	-22	NM_011567	21679	Mm.14774	NM_011567	ENSMUSG00000030353	Tead4	ETFR-2|Etfr2|FR-19|Rtef1|TEAD-4|TEF-3|Tcf13r1|Tef3|Tefr|Tefr1|Tefr1a	TEA domain family member 4	protein-coding
mm_55245.1	chr6	52640271	52640281	-	1	NA	promoter-TSS (NM_145567)	promoter-TSS (NM_145567)	24	NM_145567	58875	Mm.286458	NM_145567	ENSMUSG00000029776	Hibadh	6430402H10Rik|AI265272	3-hydroxyisobutyrate dehydrogenase	protein-coding
mm_25807.1	chr3	127789901	127789929	+	1	NA	promoter-TSS (NM_145133)	promoter-TSS (NM_145133)	2	NM_145133	211550	Mm.31852	NM_145133	ENSMUSG00000046688	Tifa	T2bp	TRAF-interacting protein with forkhead-associated domain	protein-coding
mm_50193.1	chr6	41852749	41852790	+	1	NA	TTS (NM_008843)	TTS (NM_008843)	5220	NM_008843	18716	Mm.214755	NM_008843	ENSMUSG00000058499	Pip	GCDFP-15|GP17|mSMGP	prolactin induced protein	protein-coding
mm_26007.1	chr3	135298848	135298861	+	1	NA	intron (NM_001172055, intron 7 of 9)	intron (NM_001172055, intron 7 of 9)	-8846	NM_178877	97086	Mm.441764	NM_178877	ENSMUSG00000037994	Slc9b2	C80638|NHA2|NHE10|Nhedc2|nha-oc|nhaoc	solute carrier family 9, subfamily B (NHA2, cation proton antiporter 2), member 2	protein-coding
mm_134915.1	chr16	30310795	30310813	-	1	NA	promoter-TSS (NM_008148)	promoter-TSS (NM_008148)	-23	NM_008148	14729	Mm.3519	NM_008148	ENSMUSG00000047953	Gp5	GPV	glycoprotein 5 (platelet)	protein-coding
mm_15236.1	chr2	154650859	154650865	+	1	NA	Intergenic	RMER17C|LTR|ERVK	-6164	NM_029362	75608	Mm.262480	NM_029362	ENSMUSG00000038467	Chmp4b	2010012F05Rik|C76846|Snf7-2	charged multivesicular body protein 4B	protein-coding
mm_31265.1	chr4	45297151	45297175	+	1	NA	promoter-TSS (NM_027266)	promoter-TSS (NM_027266)	-5	NM_027266	69934	Mm.46761	NM_027266	ENSMUSG00000035601	Trmt10b	2610042J10Rik|Rg9mtd3|Rnmtd3	tRNA methyltransferase 10B	protein-coding
mm_118643.1	chr14	21500880	21500897	+	1	NA	intron (NM_017479, intron 1 of 16)	CpG	1103	NM_017479	54169	Mm.248967	NM_017479	ENSMUSG00000021767	Kat6b	AI507552|B130044K16Rik|MYST-4|Morf|Myst4|mKIAA0383|qkf|querkopf	K(lysine) acetyltransferase 6B	protein-coding
mm_82911.1	chr9	34589300	34589313	-	1	NA	intron (NM_001190912, intron 1 of 15)	intron (NM_001190912, intron 1 of 15)	100575	NM_001190911	67703	Mm.220710	NM_026324	ENSMUSG00000032036	Kirrel3	1500010O20Rik|2900036G11Rik|NEPH2|SST4|mKIAA1867	kin of IRRE like 3 (Drosophila)	protein-coding
mm_7075.1	chr1	88213940	88213953	-	1	NA	intron (NM_201645, intron 1 of 4)	intron (NM_201645, intron 1 of 4)	1987	NM_201645	394436	Mm.300095	NM_201645	ENSMUSG00000089960	Ugt1a1	Gnt1|UDPGT 1-1|UGT1A01|Udpgt-1a|UgtBr1	UDP glucuronosyltransferase 1 family, polypeptide A1	protein-coding
mm_105910.1	chr11	114983581	114983594	-	1	NA	3' UTR (NM_145437, exon 4 of 4)	3' UTR (NM_145437, exon 4 of 4)	6299	NM_145437	217305	Mm.275986	NM_145437	ENSMUSG00000034641	Cd300ld	4732429D16Rik|CLM5|Cd300ld1|LMIR4|MAIR-IV|clm-5	CD300 molecule like family member d	protein-coding
mm_116706.1	chr13	50991356	50991376	-	1	NA	Intergenic	Intergenic	109361	NR_029463	77428	Mm.405630	NR_029463		9430083A17Rik	-	RIKEN cDNA 9430083A17 gene	ncRNA
mm_160445.1	chr8	104534634	104534634	+	1	NA	promoter-TSS (NM_144931)	promoter-TSS (NM_144931)	3	NM_144931	234664	Mm.237670	NM_144931	ENSMUSG00000031878	Nae1	59kDa|Appbp1	NEDD8 activating enzyme E1 subunit 1	protein-coding
mm_82960.1	chr9	35611862	35611878	-	1	NA	promoter-TSS (NM_020264)	promoter-TSS (NM_020264)	15	NM_020264	56872	Mm.390143	NM_020264	ENSMUSG00000032099	Pate4	9530004K16Rik|Pate-B|Svs7	prostate and testis expressed 4	protein-coding
mm_52246.1	chr6	106118925	106118952	+	1	NA	5' UTR (NM_001109751, exon 1 of 19)	5' UTR (NM_001109751, exon 1 of 19)	173	NM_001109751	269784	Mm.321683	NM_173004	ENSMUSG00000064293	Cntn4	9630050B05|Axcam|BIG-2	contactin 4	protein-coding
mm_151569.1	chr19	60766322	60766348	+	1	NA	exon (NM_010123, exon 19 of 22)	exon (NM_010123, exon 19 of 22)	8050	NR_034047	100217439		NR_034047		Snora19	MBI-51	small nucleolar RNA, H/ACA box 19	snoRNA
mm_41987.1	chr5	107724197	107724213	+	1	NA	5' UTR (NM_010278, exon 1 of 6)	5' UTR (NM_010278, exon 1 of 6)	138	NM_010278	14581	Mm.2078	NM_010278	ENSMUSG00000029275	Gfi1	AW495828|Gfi-1|Pal-1|Pal1	growth factor independent 1	protein-coding
mm_165097.1	chr19	55183655	55183685	+	1	NA	intron (NM_009348, intron 2 of 9)	intron (NM_009348, intron 2 of 9)	2785	NM_009348	21684	Mm.42139	NM_009348	ENSMUSG00000024979	Tectb	Tctnb	tectorin beta	protein-coding
mm_109058.1	chr12	104340644	104340670	+	1	NA	exon (NM_011458, exon 2 of 5)	exon (NM_011458, exon 2 of 5)	2171	NM_011458	20714	Mm.291569	NM_011458	ENSMUSG00000058207	Serpina3k	1300001I07Rik|D12Rp54|MMCM2|MMSpi2|RP54|Spi-2|Spi2|contrapsin	serine (or cysteine) peptidase inhibitor, clade A, member 3K	protein-coding
mm_32328.1	chr4	104232960	104232966	+	1	NA	Intergenic	Intergenic	-134575	NR_104385	13131	Mm.289682	NM_010014	ENSMUSG00000028519	Dab1	AI956902|C630028C02Rik|scm|scr|scrambler|yot	disabled 1	protein-coding
mm_68889.1	chr7	126448234	126448244	-	1	NA	exon (NM_007504, exon 16 of 23)	exon (NM_007504, exon 16 of 23)	14834	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_12790.1	chr2	79635271	79635290	+	1	NA	promoter-TSS (NM_080558)	promoter-TSS (NM_080558)	-145	NM_080558	70599	Mm.272881	NM_080558	ENSMUSG00000027007	Ssfa2	5730488C15Rik|CS-1|CS1|KRAP|SPAG13|mKIAA1927	sperm specific antigen 2	protein-coding
mm_40750.1	chr5	66770936	66770942	+	1	NA	intron (NM_001001980, intron 1 of 25)	intron (NM_001001980, intron 1 of 25)	25099	NM_001001980	77569	Mm.374778	NM_001001980	ENSMUSG00000037736	Limch1	3732412D22Rik|mKIAA1102	LIM and calponin homology domains 1	protein-coding
mm_113103.1	chr13	24397381	24397391	+	1	NA	intron (NM_001284519, intron 3 of 17)	intron (NM_001284519, intron 3 of 17)	-17736	NM_007717	12763	Mm.8396	NM_007717	ENSMUSG00000016756	Cmah	-	cytidine monophospho-N-acetylneuraminic acid hydroxylase	protein-coding
mm_24951.1	chr3	96635463	96635475	+	1	NA	promoter-TSS (NR_027844)	promoter-TSS (NR_027844)	39	NM_001162387	18632	Mm.20901	NM_011069	ENSMUSG00000028102	Pex11b	PEX11beta|Pex11pbeta	peroxisomal biogenesis factor 11 beta	protein-coding
mm_152423.1	chr19	10675102	10675108	-	1	NA	exon (NM_021453, exon 3 of 9)	exon (NM_021453, exon 3 of 9)	2966	NM_021453	58803	Mm.34037	NM_021453	ENSMUSG00000024738	Pga5	1110035E17Rik|Pepf	pepsinogen 5, group I	protein-coding
mm_101652.1	chr11	36628809	36628820	-	1	NA	intron (NM_011856, intron 2 of 28)	B3A|SINE|B2	315427	NM_001290702	23964	Mm.439889	NM_011856	ENSMUSG00000049336	Tenm2	Odz2|Odz3|Ten-2|Ten-m2	teneurin transmembrane protein 2	protein-coding
mm_86023.1	chr9	112235901	112235911	-	1	NA	non-coding (NR_015468, exon 2 of 2)	non-coding (NR_015468, exon 2 of 2)	-1065	NM_001177619	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_136182.1	chr16	88896475	88896489	-	1	NA	promoter-TSS (NM_010676)	promoter-TSS (NM_010676)	-33	NM_010676	16704	Mm.3503	NM_010676	ENSMUSG00000051802	Krtap19-5	Krtap8-2	keratin associated protein 19-5	protein-coding
mm_164644.1	chr17	35236685	35236693	+	1	NA	promoter-TSS (NM_010909)	promoter-TSS (NM_010909)	93	NM_023179	66237	Mm.396107	NM_023179	ENSMUSG00000024403	Atp6v1g2	1500002D01Rik|Atp6g2|NG38|VAG2	ATPase, H+ transporting, lysosomal V1 subunit G2	protein-coding
mm_52141.1	chr6	97972599	97972607	+	1	NA	intron (NM_001113198, intron 2 of 9)	intron (NM_001113198, intron 2 of 9)	-19180	NM_008601	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_92253.1	chr10	70599285	70599301	-	1	NA	promoter-TSS (NM_178621)	promoter-TSS (NM_178621)	-2	NM_178621	70911	Mm.19825	NM_178621	ENSMUSG00000037747	Phyhipl	4921522K17Rik|AI267048	phytanoyl-CoA hydroxylase interacting protein-like	protein-coding
mm_3314.1	chr1	137906762	137906770	+	1	NA	Intergenic	Intergenic	-59689	NR_029795	735252		NR_029795	ENSMUSG00000065565	Mir181a-1	Mirn181a-1|Mirn213|miR-213|mir-181a-1|mmu-mir-213	microRNA 181a-1	ncRNA
mm_81551.1	chr9	110333277	110333322	+	1	NA	promoter-TSS (NM_001001144)	promoter-TSS (NM_001001144)	11	NM_001103162	235623	Mm.288741	NM_001001144	ENSMUSG00000032485	Scap	9530044G19|mKIAA0199	SREBF chaperone	protein-coding
mm_48098.1	chr5	137063060	137063082	-	1	NA	3' UTR (NM_008871, exon 9 of 9)	3' UTR (NM_008871, exon 9 of 9)	9201	NM_008871	18787	Mm.250422	NM_008871	ENSMUSG00000037411	Serpine1	PAI-1|PAI1|Planh1	serine (or cysteine) peptidase inhibitor, clade E, member 1	protein-coding
mm_88662.1	chr10	80016663	80016677	+	1	NA	promoter-TSS (NM_001142701)	promoter-TSS (NM_001142701)	-2	NM_001142701	70719	Mm.243954	NM_027521	ENSMUSG00000035697	Hmha1	6330406L22Rik|AW539505|Ha-1	histocompatibility (minor) HA-1	protein-coding
mm_44419.1	chr5	18495201	18495225	-	1	NA	Intergenic	RMER17B|LTR|ERVK	-134800	NM_010305	14677	Mm.254629	NM_010305	ENSMUSG00000057614	Gnai1	AU046200|Gialpha1|Gnai-1	guanine nucleotide binding protein (G protein), alpha inhibiting 1	protein-coding
mm_59921.1	chr7	30422273	30422295	+	1	NA	Intergenic	CpG	-1020	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_125113.1	chr15	28154926	28154968	+	1	NA	Intergenic	Intergenic	-48819	NM_133365	110082	Mm.248464	NM_133365	ENSMUSG00000022262	Dnah5	AU022615|Dnahc5|Mdnah5|b2b1134Clo|b2b1154Clo|b2b1537Clo|b2b1565Clo|b2b601Clo|mKIAA1603	dynein, axonemal, heavy chain 5	protein-coding
mm_10696.1	chr2	22622532	22622592	+	1	NA	5' UTR (NM_008078, exon 1 of 16)	5' UTR (NM_008078, exon 1 of 16)	235	NM_008078	14417	Mm.4784	NM_008078	ENSMUSG00000026787	Gad2	6330404F12Rik|GAD(65)|GAD65|Gad-2	glutamic acid decarboxylase 2	protein-coding
mm_124985.1	chr15	21111343	21111356	+	1	NA	promoter-TSS (NM_001008420)	promoter-TSS (NM_001008420)	-103	NM_001008420	215654	Mm.300909	NM_001008420	ENSMUSG00000040452	Cdh12	Cdhb	cadherin 12	protein-coding
mm_136271.1	chr16	91056411	91056421	-	1	NA	intron (NM_001163695, intron 1 of 1)	intron (NM_001163695, intron 1 of 1)	-12037	NM_026110	67367	Mm.347	NM_026110	ENSMUSG00000022974	Paxbp1	1810007M14Rik|C21orf66|Gcfc|Gcfc1|Pax3/7bp	PAX3 and PAX7 binding protein 1	protein-coding
mm_14919.1	chr2	151039502	151039517	+	1	NA	promoter-TSS (NM_026086)	promoter-TSS (NM_026086)	-130	NM_026086	67311	Mm.480682	NM_026086	ENSMUSG00000053916	Nanp	1600031M04Rik|Hdhd4	N-acetylneuraminic acid phosphatase	protein-coding
mm_162679.1	chr10	10334649	10334653	-	1	NA	Intergenic	Intergenic	137663	NM_001127353	215772	Mm.246573	NM_172547	ENSMUSG00000050994	Adgb	9130014G24Rik	androglobin	protein-coding
mm_104748.1	chr11	98463436	98463458	-	1	NA	Intergenic	IMPB_01|Satellite|Satellite	16613	NM_010346	14786	Mm.276702	NM_010346	ENSMUSG00000019312	Grb7	mKIAA4028	growth factor receptor bound protein 7	protein-coding
mm_128419.1	chr15	45114864	45114872	-	1	NA	promoter-TSS (NM_026200)	promoter-TSS (NM_026200)	66	NM_026200	67498	Mm.300079	NM_026200	ENSMUSG00000022342	Kcnv1	2700023A03Rik|vibe	potassium channel, subfamily V, member 1	protein-coding
mm_163528.1	chr13	6123862	6123866	+	1	NA	Intergenic	B4A|SINE|B4	262375	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_68170.1	chr7	103813914	103813927	-	1	NA	promoter-TSS (NM_016956)	promoter-TSS (NM_016956)	3	NM_016956	15130	Mm.288567	NM_016956		Hbb-b2	AI036344|Hbb2|Hbbt2|beta2	hemoglobin, beta adult minor chain	protein-coding
mm_15414.1	chr2	156839816	156839826	+	1	NA	promoter-TSS (NM_001291124)	promoter-TSS (NM_001291124)	-186	NM_001291124	228839	Mm.315625	NM_173396	ENSMUSG00000062175	Tgif2	4921501K24|5730599O09Rik|C80753|C81206	TGFB-induced factor homeobox 2	protein-coding
mm_114195.1	chr13	55905069	55905076	+	1	NA	Intergenic	Intergenic	-73647	NM_011097	18740	Mm.135195	NM_011097	ENSMUSG00000021506	Pitx1	Bft|P-OTX|Potx|Ptx1	paired-like homeodomain transcription factor 1	protein-coding
mm_7203.1	chr1	93023142	93023153	-	1	NA	intron (NM_001294150, intron 39 of 46)	intron (NM_001294150, intron 39 of 46)	16813	NM_001159658	208760	Mm.235537	NM_177587	ENSMUSG00000045091	Aqp12	AB084104|mAQP12	aquaporin 12	protein-coding
mm_51505.1	chr6	83121735	83121751	+	1	NA	promoter-TSS (NM_001083922)	promoter-TSS (NM_001083922)	-282	NM_001083922	22377	Mm.1109	NM_016757	ENSMUSG00000030035	Wbp1	AI255152	WW domain binding protein 1	protein-coding
mm_37291.1	chr4	119176813	119176833	-	1	NA	3' UTR (NM_013848, exon 13 of 13)	3' UTR (NM_013848, exon 13 of 13)	-2628	NM_001145936	195522	Mm.169620	NM_183140	ENSMUSG00000045268	Zfp691	6430544H17Rik|Znf691	zinc finger protein 691	protein-coding
mm_106779.1	chr12	4635590	4635610	+	1	NA	exon (NM_001198969, exon 13 of 17)	exon (NM_001198969, exon 13 of 17)	42592	NM_001198968	20403	Mm.341204	NM_011365	ENSMUSG00000020640	Itsn2	AI327390|Ese2|Sh3d1B|Sh3p18|mKIAA1256	intersectin 2	protein-coding
mm_137735.1	chr17	29347991	29348001	+	1	NA	promoter-TSS (NM_019880)	promoter-TSS (NM_019880)	-64	NM_001347335	56462	Mm.285322	NM_019880	ENSMUSG00000024012	Mtch1	2310034O17Rik|AI255158|AU018396|C77849|PSAP	mitochondrial carrier 1	protein-coding
mm_42101.1	chr5	110448342	110448357	+	1	NA	5' UTR (NM_001142642, exon 1 of 19)	5' UTR (NM_001142642, exon 1 of 19)	154	NM_001317042	381668	Mm.348782	NM_028596	ENSMUSG00000043323	Fbrsl1	2410025L10Rik|AI467568|Gm1049|Gm29766|mKIAA1545	fibrosin-like 1	protein-coding
mm_9167.1	chr1	170976005	170976015	-	1	NA	promoter-TSS (NM_001077189)	promoter-TSS (NM_001077189)	61	NM_001077189	14130	Mm.425062	NM_010187	ENSMUSG00000026656	Fcgr2b	AI528646|CD32|F630109E10Rik|Fc[g]RII|FcgRII|Fcgr2|Fcgr2a|Fcr-2|Fcr-3|Ly-17|Ly-m20|LyM-1|Lym-1|fcRII	Fc receptor, IgG, low affinity IIb	protein-coding
mm_103441.1	chr11	76015429	76015445	-	1	NA	Intergenic	Intergenic	12345	NM_029658	76566	Mm.34131	NM_029658	ENSMUSG00000020846	Rflnb	1500005K14Rik|Fam101b|RefilinB|cfm	refilin B	protein-coding
mm_26824.1	chr3	10335716	10335724	-	1	NA	promoter-TSS (NM_001010834)	promoter-TSS (NM_001010834)	-64	NM_001010834	241877	Mm.442146	NM_001010834	ENSMUSG00000058921	Slc10a5	Gm405|mP5	solute carrier family 10 (sodium/bile acid cotransporter family), member 5	protein-coding
mm_14656.1	chr2	137028102	137028112	+	1	NA	intron (NM_001038641, intron 4 of 7)	intron (NM_001038641, intron 4 of 7)	88413	NM_013822	16449	Mm.22398	NM_013822	ENSMUSG00000027276	Jag1	ABE2|Gsfabe2|Htu|Ozz|Ser-1	jagged 1	protein-coding
mm_84040.1	chr9	57766215	57766229	-	1	NA	promoter-TSS (NM_007713)	promoter-TSS (NM_007713)	-362	NM_007713	102414	Mm.25720	NM_007713	ENSMUSG00000032316	Clk3	AI256811	CDC-like kinase 3	protein-coding
mm_128508.1	chr15	53266945	53266960	-	1	NA	intron (NM_010162, intron 1 of 10)	intron (NM_010162, intron 1 of 10)	79231	NM_010162	14042	Mm.309395	NM_010162	ENSMUSG00000061731	Ext1	AA409028	exostoses (multiple) 1	protein-coding
mm_72391.1	chr8	81767627	81767650	+	1	NA	intron (NM_001297593, intron 4 of 23)	intron (NM_001297593, intron 4 of 23)	425076	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_68076.1	chr7	101869293	101869302	-	1	NA	5' UTR (NM_008034, exon 2 of 7)	5' UTR (NM_008034, exon 2 of 7)	1491	NM_001252554	14275	Mm.2135	NM_008034	ENSMUSG00000001827	Folr1	FBP1|Folbp-1|Folbp1	folate receptor 1 (adult)	protein-coding
mm_41533.1	chr5	92809373	92809436	+	1	NA	promoter-TSS (NM_001077595)	promoter-TSS (NM_001077595)	22	NM_001077595	27428	Mm.46014	NM_015756	ENSMUSG00000029381	Shroom3	AL022960|D5Ertd287e|Shrm|Shrm3	shroom family member 3	protein-coding
mm_165626.1	chr3	65473351	65473351	+	1	NA	Intergenic	ORR1D2|LTR|ERVL-MaLR	-55096	NM_178892	99929	Mm.246398	NM_178892	ENSMUSG00000034640	Tiparp	ARTD14|AW558171|PARP7	TCDD-inducible poly(ADP-ribose) polymerase	protein-coding
mm_161302.1	chr14	30879503	30879503	+	1	NA	5' UTR (NM_181390, exon 1 of 3)	5' UTR (NM_181390, exon 1 of 3)	246	NM_181390	66175	Mm.220895	NM_181390	ENSMUSG00000042485	Mustn1	1110028G01Rik|Mustang	musculoskeletal, embryonic nuclear protein 1	protein-coding
mm_168171.1	chr10	55504823	55504826	-	1	NA	Intergenic	Intergenic	-602093	NM_001163833	73390	Mm.181475	NM_133751	ENSMUSG00000047669	Msl3l2	1700060H10Rik	male-specific lethal 3-like 2 (Drosophila)	protein-coding
mm_78002.1	chr9	9434629	9434653	+	1	NA	Intergenic	L1_Mus2|LINE|L1	-195628	NM_027823	71544	Mm.334955	NM_027823	ENSMUSG00000050730	Arhgap42	9030420J04Rik|BE136619	Rho GTPase activating protein 42	protein-coding
mm_97519.1	chr11	78499869	78499881	+	1	NA	exon (NM_011707, exon 3 of 8)	exon (NM_011707, exon 3 of 8)	755	NM_011707	22370	Mm.3667	NM_011707	ENSMUSG00000017344	Vtn	AI256434|Vn	vitronectin	protein-coding
mm_12346.1	chr2	69748989	69748999	+	1	NA	exon (NM_001081086, exon 13 of 14)	exon (NM_001081086, exon 13 of 14)	25906	NM_001081086	228005	Mm.11815	NM_001081086	ENSMUSG00000042133	Ppig	AU019516|AU022200|B230312B02Rik|CYP|SRCyp	peptidyl-prolyl isomerase G (cyclophilin G)	protein-coding
mm_70390.1	chr8	10899948	10899956	+	1	NA	promoter-TSS (NR_102285)	promoter-TSS (NR_102285)	30	NR_102285	71624	Mm.139075	NR_102285	ENSMUSG00000109089	4833411C07Rik	-	RIKEN cDNA 4833411C07 gene	ncRNA
mm_149645.1	chr19	17479679	17479691	+	1	NA	intron (NM_001190483, intron 24 of 37)	B1_Mur1|SINE|Alu	85642	NM_019437	54391	Mm.7013	NM_019437	ENSMUSG00000024712	Rfk	0610038L10Rik|AF031381|KOI-4	riboflavin kinase	protein-coding
mm_93779.1	chr10	120476473	120476483	-	1	NA	promoter-TSS (NM_010441)	promoter-TSS (NM_010441)	-9	NM_010441	15364	Mm.157190	NM_010441	ENSMUSG00000056758	Hmga2	9430083A20Rik|HMGI-C|Hmgic|pg|pygmy	high mobility group AT-hook 2	protein-coding
mm_167255.1	chr8	25068147	25068159	+	1	NA	intron (NM_031257, intron 3 of 11)	intron (NM_031257, intron 3 of 11)	-29191	NM_001081187	330723	Mm.334452	NM_001081187	ENSMUSG00000037406	Htra4	B430206E18Rik	HtrA serine peptidase 4	protein-coding
mm_15133.1	chr2	153938219	153938223	+	1	NA	Intergenic	Intergenic	-2641	NM_001034875	381399	Mm.315572	NM_001034875	ENSMUSG00000074665	Bpifb4	Gm1006|Lplunc4	BPI fold containing family B, member 4	protein-coding
mm_79425.1	chr9	55430389	55430402	+	1	NA	exon (NM_172923, exon 9 of 11)	exon (NM_172923, exon 9 of 11)	81848	NM_145615	110842	Mm.290853	NM_145615	ENSMUSG00000032314	Etfa	2010200I21Rik|D9Ertd394e	electron transferring flavoprotein, alpha polypeptide	protein-coding
mm_89451.1	chr10	93160646	93160685	+	1	NA	promoter-TSS (NM_146239)	promoter-TSS (NM_146239)	-211	NM_146239	237459	Mm.217404	NM_146239	ENSMUSG00000020015	Cdk17	6430598J10Rik|Pctk2	cyclin-dependent kinase 17	protein-coding
mm_71036.1	chr8	33653655	33653659	+	1	NA	exon (NM_010344, exon 1 of 13)	exon (NM_010344, exon 1 of 13)	419	NM_010344	14782	Mm.283573	NM_010344	ENSMUSG00000031584	Gsr	AI325518|D8Ertd238e|Gr-1|Gr1	glutathione reductase	protein-coding
mm_122045.1	chr14	30024590	30024616	-	1	NA	intron (NM_175343, intron 1 of 7)	L1MB4|LINE|L1	1970	NM_175343	218865	Mm.259916	NM_172264	ENSMUSG00000015970	Chdh	AU041472|D630034H06Rik	choline dehydrogenase	protein-coding
mm_149763.1	chr19	22887911	22887914	+	1	NA	intron (NM_001035243, intron 11 of 23)	intron (NM_001035243, intron 11 of 23)	137307	NR_029591	387200		NR_029591	ENSMUSG00000065507	Mir204	Mirn204|mir-204|mmu-mir-204	microRNA 204	ncRNA
mm_46343.1	chr5	102053019	102053033	-	1	NA	intron (NM_172882, intron 1 of 66)	intron (NM_172882, intron 1 of 66)	16895	NM_172882	72145	Mm.332522	NM_172882	ENSMUSG00000043940	Wdfy3	2610509D04Rik|ALFY|AW319683|B930017C24|BWF1|Bchs|D5Ertd66e|Ggtb3|ZFYVE25|mKIAA0993	WD repeat and FYVE domain containing 3	protein-coding
mm_129876.1	chr15	83432820	83432859	-	1	NA	promoter-TSS (NM_001159510)	promoter-TSS (NM_001159510)	11	NM_011862	23970	Mm.23978	NM_011862	ENSMUSG00000016664	Pacsin2	AI197433	protein kinase C and casein kinase substrate in neurons 2	protein-coding
mm_119084.1	chr14	30889613	30889623	+	1	NA	exon (NM_001289633, exon 3 of 22)	exon (NM_001289633, exon 3 of 22)	3142	NM_001289632	16427	Mm.34819	NM_018746	ENSMUSG00000021922	Itih4	ITI-HC4|Itih-4|PK-120	inter alpha-trypsin inhibitor, heavy chain 4	protein-coding
mm_106843.1	chr12	8007503	8007512	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	29830	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_85487.1	chr9	106106182	106106207	-	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	-9503	NM_026763	68553	Mm.28854	NM_026763	ENSMUSG00000032572	Col6a4	1110001D15Rik|AI413310|AU023415|Dvwa|EG235580|Vwa6	collagen, type VI, alpha 4	protein-coding
mm_64343.1	chr7	142380784	142380798	+	1	NA	exon (NM_009983, exon 5 of 9)	exon (NM_009983, exon 5 of 9)	-7045	NM_001347541	320802	Mm.154486	NM_177265	ENSMUSG00000045777	Ifitm10	6330512M04Rik|AI848576|DSPA3	interferon induced transmembrane protein 10	protein-coding
mm_166714.1	chr6	118197342	118197346	-	1	NA	5' UTR (NM_009050, exon 1 of 20)	5' UTR (NM_009050, exon 1 of 20)	400	NM_009050	19713	Mm.57199	NM_009050	ENSMUSG00000030110	Ret	PTC|RET51|RET9|c-Ret	ret proto-oncogene	protein-coding
mm_146256.1	chr18	77794362	77794382	+	1	NA	promoter-TSS (NM_013831)	promoter-TSS (NM_013831)	-178	NM_013831	19201	Mm.57174	NM_013831	ENSMUSG00000025429	Pstpip2	MAYP|cmo	proline-serine-threonine phosphatase-interacting protein 2	protein-coding
mm_27876.1	chr3	79169877	79169889	-	1	NA	Intergenic	Intergenic	-24008	NM_001099624	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_172940.1	chr9	78821890	78821893	-	1	NA	Intergenic	CpG	206345	NM_153098	235505	Mm.32955	NM_153098	ENSMUSG00000046186	Cd109	9930012E15Rik|AI480638|GARP	CD109 antigen	protein-coding
mm_169899.1	chr16	52083660	52083664	+	1	NA	intron (NM_001033238, intron 3 of 17)	intron (NM_001033238, intron 3 of 17)	52113	NM_001033238	208650	Mm.328206	NM_001033238	ENSMUSG00000022637	Cblb	AI429560|AI851073|Cbl-b	Casitas B-lineage lymphoma b	protein-coding
mm_37612.1	chr4	126968051	126968114	-	1	NA	promoter-TSS (NM_001114399)	promoter-TSS (NM_001114399)	-159	NM_001114399	67785	Mm.165401	NM_001114399	ENSMUSG00000042446	Zmym4	6330503C17Rik|AI480785|AW493829|CDIR|D630001M21|MYM|Zfp262|Znf262|mKIAA0425	zinc finger, MYM-type 4	protein-coding
mm_11644.1	chr2	34958351	34958355	+	1	NA	intron (NM_009421, intron 4 of 10)	intron (NM_009421, intron 4 of 10)	3419	NM_009421	22029	Mm.239514	NM_009421	ENSMUSG00000026875	Traf1	4732496E14Rik	TNF receptor-associated factor 1	protein-coding
mm_24364.1	chr3	90080486	90080498	+	1	NA	intron (NM_001293749, intron 1 of 7)	intron (NM_001293749, intron 1 of 7)	971	NM_001293749	59069	Mm.240839	NM_022314	ENSMUSG00000027940	Tpm3	TM30nm|TMnm|Tm5NM|Tpm-5|Tpm5|Trop-5|gamma-TM|hTM30nm|hTMnm	tropomyosin 3, gamma	protein-coding
mm_159163.1	chr2	91653210	91653210	+	1	NA	promoter-TSS (NM_146124)	promoter-TSS (NM_146124)	2	NM_146124	228359	Mm.22413	NM_146124	ENSMUSG00000027247	Arhgap1	B230365D05Rik|C76222|Cdc42GAP|p50rhoGAP	Rho GTPase activating protein 1	protein-coding
mm_104155.1	chr11	87122064	87122064	-	1	NA	3' UTR (NM_025377, exon 4 of 4)	3' UTR (NM_025377, exon 4 of 4)	-5011	NM_197987	68729	Mm.17436	NM_197987	ENSMUSG00000018548	Trim37	1110032A10Rik|2810004E07Rik|AI848587|AU043018|MUL|TEF3|mKIAA0898	tripartite motif-containing 37	protein-coding
mm_46447.1	chr5	105110065	105110082	-	1	NA	intron (NM_172777, intron 1 of 10)	intron (NM_172777, intron 1 of 10)	219	NM_172777	236573	Mm.425261	NM_172777	ENSMUSG00000029298	Gbp9	-	guanylate-binding protein 9	protein-coding
mm_49564.1	chr6	30610985	30611026	+	1	NA	promoter-TSS (NM_144537)	promoter-TSS (NM_144537)	-5	NM_144537	74649	Mm.159276	NM_144537	ENSMUSG00000029788	Cpa5	4930430M09Rik	carboxypeptidase A5	protein-coding
mm_80284.1	chr9	73044868	73044881	+	1	NA	promoter-TSS (NM_023635)	promoter-TSS (NM_023635)	64	NM_001301230	11891	Mm.34867	NM_023635	ENSMUSG00000032202	Rab27a	2210402C08Rik|2410003M20Rik|4933437C11Rik|ash	RAB27A, member RAS oncogene family	protein-coding
mm_49817.1	chr6	37213087	37213094	+	1	NA	intron (NM_001347104, intron 1 of 32)	intron (NM_001347104, intron 1 of 32)	86886	NM_001081206	320127	Mm.119469	NM_001081206	ENSMUSG00000038665	Dgki	C130010K08Rik	diacylglycerol kinase, iota	protein-coding
mm_164631.1	chr17	33629364	33629403	+	1	NA	intron (NM_026712, intron 1 of 5)	intron (NM_026712, intron 1 of 5)	291	NM_026712	328801	Mm.181488	NM_026712	ENSMUSG00000073423	Zfp414	0610030H11Rik|Znf414	zinc finger protein 414	protein-coding
mm_136798.1	chr17	12119366	12119377	+	1	NA	promoter-TSS (NM_026644)	promoter-TSS (NM_026644)	87	NM_026644	68262	Mm.258300	NM_026644	ENSMUSG00000023827	Agpat4	1500003P24Rik	1-acylglycerol-3-phosphate O-acyltransferase 4 (lysophosphatidic acid acyltransferase, delta)	protein-coding
mm_70286.1	chr8	3648621	3648648	+	1	NA	Intergenic	AT_rich|Low_complexity|Low_complexity	-7136	NM_001204959	57264	Mm.1181	NM_022984	ENSMUSG00000012705	Retn	ADSF|Fizz3|Rstn|Xcp4	resistin	protein-coding
mm_22416.1	chr2	181496979	181497008	-	1	NA	promoter-TSS (NM_001291200)	promoter-TSS (NM_001291200)	-149	NM_001291203	66314	Mm.136648	NM_025482	ENSMUSG00000000827	Tpd52l2	2810411G23Rik|AU016537|C86069|D54	tumor protein D52-like 2	protein-coding
mm_51648.1	chr6	86028804	86028814	+	1	NA	5' UTR (NM_001271860, exon 1 of 13)	5' UTR (NM_001271860, exon 1 of 13)	128	NM_001271860	11519	Mm.104155	NM_013458	ENSMUSG00000030000	Add2	2900072M03Rik|add97	adducin 2 (beta)	protein-coding
mm_73530.1	chr8	108612259	108612278	+	1	NA	Intergenic	Intergenic	-27591	NR_077224	109215	Mm.65282	NR_077224	ENSMUSG00000110613	Lncbate1	3010033K07Rik|Lnc-BATE1	brown adipose tissue enriched long non-coding RNA 1	ncRNA
mm_87939.1	chr10	62892477	62892485	+	1	NA	Intergenic	PB1D9|SINE|Alu	-12467	NM_001253857	52463	Mm.17774	NM_027384	ENSMUSG00000047146	Tet1	2510010B09Rik|AA517754|BB001228|Cxxc6|D10Ertd17e|LCX|mKIAA1676	tet methylcytosine dioxygenase 1	protein-coding
mm_107922.1	chr12	71063257	71063279	+	1	NA	exon (NM_001081195, exon 15 of 24)	exon (NM_001081195, exon 15 of 24)	47301	NM_001081195	238247	Mm.241601	NM_001081195	ENSMUSG00000048118	Arid4a	A630009N03|A630067N03Rik|MmRBBP1|Rbbp1	AT rich interactive domain 4A (RBP1-like)	protein-coding
mm_31110.1	chr4	42921864	42921872	+	1	NA	intron (NM_001346526, intron 1 of 8)	intron (NM_001346526, intron 1 of 8)	4617	NM_172690	230085	Mm.240965	NM_172690	ENSMUSG00000036062	Phf24	GINIP|N28178	PHD finger protein 24	protein-coding
mm_142506.1	chr17	46096659	46096667	-	1	NA	Intergenic	Intergenic	-14341	NM_026768	68565	Mm.287443	NM_026768	ENSMUSG00000023967	Mrps18a	1110004O20Rik|C79712	mitochondrial ribosomal protein S18A	protein-coding
mm_93134.1	chr10	92162694	92162708	-	1	NA	intron (NR_028262, intron 2 of 12)	intron (NR_028262, intron 2 of 12)	2477	NR_028262	110333	Mm.429764	NR_028262		Rmst	100041799|AI853140|C230053E11Rik|D930049J19Rik|Dmt2|Gm3515|M2|Ncrms	rhabdomyosarcoma 2 associated transcript (non-coding RNA)	ncRNA
mm_13782.1	chr2	118779815	118779819	+	1	NA	promoter-TSS (NM_170593)	promoter-TSS (NM_170593)	98	NM_170593	214240	Mm.221499	NM_170593	ENSMUSG00000040035	Disp2	AI840597|B230210L08Rik|DispB|mKIAA1742	dispatched RND tramsporter family member 2	protein-coding
mm_143413.1	chr17	70834562	70834573	-	1	NA	Intergenic	CpG	12210	NM_001164077	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_148857.1	chr19	6398141	6398155	+	1	NA	exon (NM_011224, exon 20 of 20)	exon (NM_011224, exon 20 of 20)	-2435	NM_011242	19395	Mm.77017	NM_011242	ENSMUSG00000032946	Rasgrp2	CDC25L|Caldaggef1	RAS, guanyl releasing protein 2	protein-coding
mm_172438.1	chr7	29921890	29921898	-	1	NA	Intergenic	RLTR17|LTR|ERVK	13377	NM_001243908	73729	Mm.333743	NM_001243908	ENSMUSG00000099689	Zfp383	1110003H10Rik	zinc finger protein 383	protein-coding
mm_56215.1	chr6	89362582	89362637	-	1	NA	promoter-TSS (NM_008881)	promoter-TSS (NM_008881)	4	NM_008881	18844	Mm.3789	NM_008881	ENSMUSG00000030084	Plxna1	2600013D04Rik|NOV|PlexA1|Plxn1|mKIAA4053	plexin A1	protein-coding
mm_136547.1	chr16	97965204	97965207	-	1	NA	Intergenic	RMER12B|LTR|ERVK	-2583	NM_001320385	114565	Mm.474489	NM_175428	ENSMUSG00000046962	Zbtb21	5430437K12Rik|B430213I24Rik|Zfp295|Znf295|mKIAA1227	zinc finger and BTB domain containing 21	protein-coding
mm_16615.1	chr2	5410937	5410941	-	1	NA	intron (NR_030601, intron 1 of 1)	intron (NR_030601, intron 1 of 1)	31549	NR_030601	100124465		NR_030601	ENSMUSG00000078031	Mir466d	Mirn466d	microRNA 466d	ncRNA
mm_145306.1	chr18	53463745	53463785	+	1	NA	promoter-TSS (NM_001033281)	promoter-TSS (NM_001033281)	-781	NM_001033281	225518	Mm.297645	NM_001033281	ENSMUSG00000069378	Prdm6	Gm92|PRISM	PR domain containing 6	protein-coding
mm_151720.1	chr19	4802606	4802625	-	1	NA	exon (NM_019869, exon 2 of 3)	exon (NM_019869, exon 2 of 3)	-8606	NM_001290123	19653	Mm.426069	NM_009032	ENSMUSG00000094936	Rbm4	4921506I22Rik|Lark1|Mlark|Rbm4a|lark	RNA binding motif protein 4	protein-coding
mm_134535.1	chr16	19673249	19673257	-	1	NA	intron (NM_177356, intron 5 of 5)	intron (NM_177356, intron 5 of 5)	33112	NM_177356	239739	Mm.258059	NM_177356	ENSMUSG00000041247	Lamp3	1200002D17Rik|Cd208|DC-LAMP|DCLAMP|LAMP|TSC403	lysosomal-associated membrane protein 3	protein-coding
mm_152828.1	chr19	23140968	23140973	-	1	NA	promoter-TSS (NM_010638)	promoter-TSS (NM_010638)	-256	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_135838.1	chr16	58524165	58524179	-	1	NA	promoter-TSS (NM_018784)	promoter-TSS (NM_018784)	-860	NM_018784	54613	Mm.212742	NM_018784	ENSMUSG00000022747	St3gal6	1700023B24Rik|AI930218|AW552396|Siat10|St3galVI	ST3 beta-galactoside alpha-2,3-sialyltransferase 6	protein-coding
mm_167905.1	chrX	78059339	78059340	+	1	NA	Intergenic	Intergenic	32035	NM_008754	18249	Mm.430771	NM_008754	ENSMUSG00000067684	Obp1a	OBP-1a|OBP5	odorant binding protein IA	protein-coding
mm_32741.1	chr4	116636509	116636517	+	1	NA	TTS (NM_021473)	TTS (NM_021473)	-8562	NM_016777	50927	Mm.257181	NM_016777	ENSMUSG00000028693	Nasp	5033430J04Rik|AI131596|AI317140|D4Ertd767e|Epcs32|Nasp-T	nuclear autoantigenic sperm protein (histone-binding)	protein-coding
mm_35660.1	chr4	43562162	43562172	-	1	NA	promoter-TSS (NM_013497)	promoter-TSS (NM_013497)	416	NM_011602	21894	Mm.208601	NM_011602	ENSMUSG00000028465	Tln1	Tln	talin 1	protein-coding
mm_141474.1	chr17	31039701	31039746	-	1	NA	Intergenic	Intergenic	-17971	NM_009593	11307	Mm.15691	NM_009593	ENSMUSG00000024030	Abcg1	AW413978|Abc8|White	ATP-binding cassette, sub-family G (WHITE), member 1	protein-coding
mm_40693.1	chr5	65767411	65767414	+	1	NA	intron (NM_001024917, intron 1 of 19)	B1_Mur2|SINE|Alu	3891	NM_001024917	333789	Mm.332398	NM_001024917	ENSMUSG00000037795	N4bp2	B3bp|E430014I16|Gm1791|Gm868	NEDD4 binding protein 2	protein-coding
mm_106836.1	chr12	8006385	8006392	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	28711	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_70400.1	chr8	11312533	11312557	+	1	NA	promoter-TSS (NM_009932)	promoter-TSS (NM_009932)	-260	NM_009932	12827	Mm.181021	NM_009932	ENSMUSG00000031503	Col4a2	Col4a-2	collagen, type IV, alpha 2	protein-coding
mm_127271.1	chr15	99723834	99723857	+	1	NA	3' UTR (NM_010271, exon 8 of 8)	3' UTR (NM_010271, exon 8 of 8)	-1773	NM_183256	66379	Mm.5265	NM_183256	ENSMUSG00000023020	Cox14	2310016M24Rik|AA959804	cytochrome c oxidase assembly protein 14	protein-coding
mm_146874.1	chr18	25478997	25478999	-	1	NA	3' UTR (NM_001146294, exon 13 of 13)	3' UTR (NM_001146294, exon 13 of 13)	274985	NM_133195	108013	Mm.266435	NM_133195	ENSMUSG00000024268	Celf4	A230070D14Rik|BRUNOL-4|Brul4|Brunol4|C130060B05Rik	CUGBP, Elav-like family member 4	protein-coding
mm_30245.1	chr3	146521397	146521430	-	1	NA	promoter-TSS (NM_027332)	promoter-TSS (NM_027332)	10	NM_027332	70285	Mm.28128	NM_027332	ENSMUSG00000028187	Rpf1	2210420E24Rik|2310066N05Rik|Bxdc5	ribosome production factor 1 homolog	protein-coding
mm_155686.1	chrX	93807006	93807012	+	1	NA	intron (NM_145630, intron 3 of 11)	RMER19B|LTR|ERVK	25086	NM_145630	236900	Mm.12775	NM_145630	ENSMUSG00000035232	Pdk3	2610001M10Rik|AI035637	pyruvate dehydrogenase kinase, isoenzyme 3	protein-coding
mm_84487.1	chr9	66845753	66845841	-	1	NA	3' UTR (NM_173413, exon 8 of 8)	3' UTR (NM_173413, exon 8 of 8)	-11091	NM_026674	68318	Mm.284229	NM_026674	ENSMUSG00000053040	Aph1c	0610008A10Rik|APH-1b|Aph1b	aph1 homolog C, gamma secretase subunit	protein-coding
mm_41847.1	chr5	104436536	104436549	+	1	NA	exon (NM_001204203, exon 3 of 7)	exon (NM_001204203, exon 3 of 7)	350	NM_001204233	20750	Mm.288474	NM_009263	ENSMUSG00000029304	Spp1	2AR|Apl-1|BNSP|BSPI|Bsp|ETA-1|Eta|OP|Opn|Opnl|Ric|Spp-1	secreted phosphoprotein 1	protein-coding
mm_131901.1	chr16	23263018	23263045	+	1	NA	intron (NM_001252505, intron 2 of 7)	L1ME2|LINE|L1	-27439	NM_001252506	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_71206.1	chr8	40890327	40890333	+	1	NA	intron (NM_007514, intron 1 of 11)	MLT1B|LTR|ERVL-MaLR	27963	NM_001044740	11988	Mm.4676	NM_007514	ENSMUSG00000031596	Slc7a2	20.5|AI158848|Atrc2|CAT-2|Cat2|Tea	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	protein-coding
mm_104586.1	chr11	96988487	96988488	-	1	NA	Intergenic	Intergenic	-10799	NM_001080964	78912	Mm.491183	NM_030220	ENSMUSG00000018678	Sp2	4930480I16Rik|mKIAA0048	Sp2 transcription factor	protein-coding
mm_116975.1	chr13	56178988	56179001	-	1	NA	promoter-TSS (NM_001168615)	promoter-TSS (NM_001168615)	-109	NM_001168615	212937	Mm.116697	NM_145976	ENSMUSG00000049625	Tifab	-	TRAF-interacting protein with forkhead-associated domain, family member B	protein-coding
mm_154740.1	chrX	10276646	10276661	+	1	NA	exon (NM_008769, exon 4 of 10)	exon (NM_008769, exon 4 of 10)	24348	NM_008769	18416	Mm.2611	NM_008769	ENSMUSG00000031173	Otc	AI265390|Sf|spf	ornithine transcarbamylase	protein-coding
mm_82969.1	chr9	35777941	35777952	-	1	NA	5' UTR (NM_001167673, exon 1 of 3)	5' UTR (NM_001167673, exon 1 of 3)	163	NM_001167673	100312986	Mm.437659	NM_001167673	ENSMUSG00000090738	Gm17727	Pate-e|Pate7	predicted gene, 17727	protein-coding
mm_2867.1	chr1	131744179	131744195	+	1	NA	intron (NM_177243, intron 1 of 20)	intron (NM_177243, intron 1 of 20)	165	NM_177243	320718	Mm.482704	NM_177243	ENSMUSG00000042268	Slc26a9	E030002L01Rik	solute carrier family 26, member 9	protein-coding
mm_135228.1	chr16	36828225	36828269	-	1	NA	promoter-TSS (NM_177128)	promoter-TSS (NM_177128)	12	NM_001113401	106389	Mm.432078	NM_134111	ENSMUSG00000022838	Eaf2	AW048865|FESTA-L|FESTA-S|Festa|Traits|U19	ELL associated factor 2	protein-coding
mm_63998.1	chr7	140125652	140125727	+	1	NA	promoter-TSS (NM_001346725)	promoter-TSS (NM_001346725)	4	NM_153783	212503	Mm.486735	NM_153783	ENSMUSG00000025464	Paox	2410012F02Rik|AI118225|Pao	polyamine oxidase (exo-N4-amino)	protein-coding
mm_164505.1	chr16	93002751	93002755	+	1	NA	Intergenic	Intergenic	-176679	NM_001111022	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_39011.1	chr4	152117630	152117638	-	1	NA	intron (NM_033042, intron 3 of 6)	intron (NM_033042, intron 3 of 6)	1291	NM_033042	85030	Mm.101198	NM_033042	ENSMUSG00000024793	Tnfrsf25	APO-3|DDR3|DR3|LARD|TR3|TRAMP|Tnfrsf12|WSL-1|WSL-LR|Wsl	tumor necrosis factor receptor superfamily, member 25	protein-coding
mm_30670.1	chr4	11156412	11156453	+	1	NA	promoter-TSS (NM_001199105)	promoter-TSS (NM_001199105)	-9	NM_001199105	60599	Mm.393018	NM_021897	ENSMUSG00000028211	Trp53inp1	2700057G22Rik|SIP|SIP18|SIP27|Stinp|Teap	transformation related protein 53 inducible nuclear protein 1	protein-coding
mm_128828.1	chr15	67176748	67176791	-	1	NA	5' UTR (NM_009177, exon 1 of 9)	5' UTR (NM_009177, exon 1 of 9)	113	NM_009177	20442	Mm.248334	NM_009177	ENSMUSG00000013846	St3gal1	5330418N22Rik|AI467004|ST3GalI|Siat4|Siat4a|St3gal-1	ST3 beta-galactoside alpha-2,3-sialyltransferase 1	protein-coding
mm_82240.1	chr9	3260873	3260875	-	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	-61061	NR_027988	114673	Mm.422774	NM_053265	ENSMUSG00000042360	4930433N12Rik	-	RIKEN cDNA 4930433N12 gene	ncRNA
mm_15255.1	chr2	154891808	154891815	+	1	NA	intron (NM_026030, intron 1 of 8)	intron (NM_026030, intron 1 of 8)	1095	NM_026030	67204	Mm.377134	NM_026030	ENSMUSG00000074656	Eif2s2	2810026E11Rik|38kDa|AA408636|AA571381|AA986487|AW822225|D2Ertd303e|EIF2|EIF2B	eukaryotic translation initiation factor 2, subunit 2 (beta)	protein-coding
mm_42055.1	chr5	108669351	108669357	+	1	NA	TTS (NM_001310692)	TTS (NM_001310692)	5442	NM_001310692	231583	Mm.440571	NM_174870	ENSMUSG00000046959	Slc26a1	Sat1	solute carrier family 26 (sulfate transporter), member 1	protein-coding
mm_75021.1	chr8	31167817	31167824	-	1	NA	intron (NM_026453, intron 1 of 9)	AT_rich|Low_complexity|Low_complexity	904	NM_026453	67920	Mm.289818	NM_026453	ENSMUSG00000031578	Mak16	2600016B03Rik|AI314911|Rbm13	MAK16 homolog	protein-coding
mm_24965.1	chr3	96727532	96727572	+	1	NA	promoter-TSS (NM_026406)	promoter-TSS (NM_026406)	-59	NM_026406	67845	Mm.386792	NM_026406	ENSMUSG00000028098	Rnf115	2610028E05Rik|AU042696|Zfp364	ring finger protein 115	protein-coding
mm_141154.1	chr17	26506544	26506563	-	1	NA	exon (NM_013642, exon 4 of 4)	exon (NM_013642, exon 4 of 4)	1919	NM_013642	19252	Mm.239041	NM_013642	ENSMUSG00000024190	Dusp1	3CH134|MKP1|Ptpn16|U19515|erp|mkp-1	dual specificity phosphatase 1	protein-coding
mm_92212.1	chr10	68225731	68225750	-	1	NA	intron (NM_023598, intron 3 of 9)	intron (NM_023598, intron 3 of 9)	52986	NM_023598	71371	Mm.440357	NM_023598	ENSMUSG00000019947	Arid5b	4930580B11|5430435G07Rik|AI467247|Desrt|Mrf2|Mrf2alpha|Mrf2beta	AT rich interactive domain 5B (MRF1-like)	protein-coding
mm_10531.1	chr2	16408529	16408540	+	1	NA	intron (NM_026162, intron 1 of 13)	intron (NM_026162, intron 1 of 13)	52230	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding
mm_23365.1	chr3	55247104	55247150	+	1	NA	intron (NM_019978, intron 1 of 16)	intron (NM_019978, intron 1 of 16)	4601	NM_001195538	13175	Mm.393242	NM_019978	ENSMUSG00000027797	Dclk1	1700113D08Rik|2810480F11Rik|AI836758|Click-I|Cpg16|Dcamkl1|Dcl|Dclk|mKIAA0369	doublecortin-like kinase 1	protein-coding
mm_49675.1	chr6	31619961	31619984	+	1	NA	Intergenic	L2a|LINE|L2	-56035	NM_013723	27205	Mm.89918	NM_013723	ENSMUSG00000025608	Podxl	AW121214|Ly102|PC|PCLP-1|Pclp1	podocalyxin-like	protein-coding
mm_30171.1	chr3	144202301	144202345	-	1	NA	promoter-TSS (NM_001161769)	promoter-TSS (NM_001161769)	9	NM_001161770	16911	Mm.29187	NM_010723	ENSMUSG00000028266	Lmo4	A730077C12Rik|Crp3|Etohi4	LIM domain only 4	protein-coding
mm_15348.1	chr2	156144204	156144245	+	1	NA	promoter-TSS (NM_025946)	promoter-TSS (NM_025946)	-9	NM_025946	67067	Mm.371623	NM_025946	ENSMUSG00000067847	Romo1	2010100O12Rik|AI853864	reactive oxygen species modulator 1	protein-coding
mm_129533.1	chr15	79323336	79323349	-	1	NA	intron (NM_016915, intron 1 of 15)	intron (NM_016915, intron 1 of 15)	5029	NM_016915	53357	Mm.155620	NM_016915	ENSMUSG00000042632	Pla2g6	BB112799|PNPLA9|iPLA(2)beta|iPLA2|iPLA2beta	phospholipase A2, group VI	protein-coding
mm_78419.1	chr9	31030730	31030751	+	1	NA	promoter-TSS (NM_001115130)	promoter-TSS (NM_001115130)	96	NM_172765	235132	Mm.239355	NM_172765	ENSMUSG00000047412	Zbtb44	6030404E16Rik|Btbd15|E230011F09	zinc finger and BTB domain containing 44	protein-coding
mm_48661.1	chr5	145880057	145880057	-	1	NA	promoter-TSS (NM_007818)	promoter-TSS (NM_007818)	-203	NM_007818	13112	Mm.332844	NM_007818	ENSMUSG00000056035	Cyp3a11	AI256190|Cyp3a|IIIAm1|Pcn	cytochrome P450, family 3, subfamily a, polypeptide 11	protein-coding
mm_41452.1	chr5	90905516	90905527	+	1	NA	3' UTR (NM_009140, exon 4 of 4)	3' UTR (NM_009140, exon 4 of 4)	1622	NM_009140	20310	Mm.4979	NM_009140	ENSMUSG00000058427	Cxcl2	CINC-2a|GROb|Gro2|MIP-2|MIP-2a|Mgsa-b|Mip2|Scyb|Scyb2	chemokine (C-X-C motif) ligand 2	protein-coding
mm_3166.1	chr1	135363858	135363868	+	1	NA	exon (NM_053106, exon 2 of 3)	exon (NM_053106, exon 2 of 3)	11200	NM_175259	77552	Mm.41407	NM_175259	ENSMUSG00000041889	Shisa4	9330132O05Rik|Tmem58|mShisa4	shisa family member 4	protein-coding
mm_164946.1	chr19	4231613	4231657	-	1	NA	promoter-TSS (NM_027196)	promoter-TSS (NM_027196)	-258	NM_027196	69745	Mm.32518	NM_027196	ENSMUSG00000024854	Pold4	2410012M21Rik|AI463381|AW060307|Polds|p12	polymerase (DNA-directed), delta 4	protein-coding
mm_142202.1	chr17	36970610	36970620	-	1	NA	Intergenic	Intergenic	10622	NM_029747	76797	Mm.159787	NM_029747	ENSMUSG00000064308	2410137M14Rik	-	RIKEN cDNA 2410137M14 gene	protein-coding
mm_57913.1	chr6	133767410	133767414	-	1	NA	promoter-TSS (NM_001177652)	promoter-TSS (NM_001177652)	-4	NR_111985	545886	Mm.449716	NM_001177652	ENSMUSG00000108106	Gm5886	EG545886|smarp	predicted gene 5886	protein-coding
mm_22906.1	chr3	30864314	30864324	+	1	NA	intron (NM_001286994, intron 1 of 3)	MTD|LTR|ERVL-MaLR	8369	NM_001286994	71862	Mm.272019	NM_027965	ENSMUSG00000037661	Gpr160	1700025D19Rik|GPCR150	G protein-coupled receptor 160	protein-coding
mm_105296.1	chr11	102480775	102480788	-	1	NA	exon (NM_001159492, exon 8 of 8)	exon (NM_001159492, exon 8 of 8)	-10898	NM_010575	16399	Mm.26646	NM_010575	ENSMUSG00000034664	Itga2b	AI172977|CD41|CD41B|GpIIb|alphaIIb	integrin alpha 2b	protein-coding
mm_70021.1	chr7	142575780	142575793	-	1	NA	non-coding (NR_130974, exon 5 of 5)	non-coding (NR_130974, exon 5 of 5)	1361	NR_030416	735280		NR_030416	ENSMUSG00000076275	Mir675	Mirn675|mir-675|mmu-mir-675	microRNA 675	ncRNA
mm_15678.1	chr2	163547339	163547350	+	1	NA	exon (NM_008261, exon 1 of 10)	exon (NM_008261, exon 1 of 10)	189	NM_008261	15378	Mm.202383	NM_008261	ENSMUSG00000017950	Hnf4a	HNF-4|Hnf4|Hnf4alpha|MODY1|Nr2a1|TCF-14|Tcf14	hepatic nuclear factor 4, alpha	protein-coding
mm_405.1	chr1	34187797	34187808	+	1	NA	intron (NM_133833, intron 35 of 92)	intron (NM_133833, intron 35 of 92)	27472	NM_010081	13518	Mm.336625	NM_010081	ENSMUSG00000026131	Dst	2310001O04Rik|A830042E19Rik|AW554249|BP230|BPAG1-n|Bpag|Bpag1|Macf2|ah|athetoid|dt|mKIAA0728|nmf203|nmf339	dystonin	protein-coding
mm_8330.1	chr1	149961672	149961697	-	1	NA	promoter-TSS (NM_008869)	promoter-TSS (NM_008869)	-394	NM_008869	18783	Mm.4186	NM_008869	ENSMUSG00000056220	Pla2g4a	Pla2g4|cPLA2|cPLA2-alpha|cPLA2alpha	phospholipase A2, group IVA (cytosolic, calcium-dependent)	protein-coding
mm_167342.1	chr8	77689133	77689135	-	1	NA	exon (NM_010332, exon 3 of 8)	exon (NM_010332, exon 3 of 8)	35318	NM_010332	13617	Mm.283168	NM_010332	ENSMUSG00000031616	Ednra	ET-AR|ETa|Gpcr10	endothelin receptor type A	protein-coding
mm_67525.1	chr7	80993553	80993583	-	1	NA	promoter-TSS (NM_178707)	promoter-TSS (NM_178707)	-116	NM_178707	233410	Mm.29525	NM_178707	ENSMUSG00000005621	Zfp592	8430405N24|A730014M16Rik|Znf592|mKIAA0211	zinc finger protein 592	protein-coding
mm_107871.1	chr12	69907938	69907940	+	1	NA	5' UTR (NM_178628, exon 2 of 15)	5' UTR (NM_178628, exon 2 of 15)	-14776	NM_201519	399510	Mm.291936	NM_201519	ENSMUSG00000034761	Map4k5	4432415E19Rik|GCKR|KHS|MAPKKKK5	mitogen-activated protein kinase kinase kinase kinase 5	protein-coding
mm_81105.1	chr9	106448661	106448683	+	1	NA	promoter-TSS (NM_145919)	promoter-TSS (NM_145919)	32	NM_029631	76491	Mm.335427	NM_029631	ENSMUSG00000042073	Abhd14b	1810013B01Rik	abhydrolase domain containing 14b	protein-coding
mm_71315.1	chr8	43321205	43321223	+	1	NA	Intergenic	MLT1A0|LTR|ERVL-MaLR	-14205	NM_009556	22702	Mm.285848	NM_009556	ENSMUSG00000051176	Zfp42	Rex-1|Rex1|Zfp-42	zinc finger protein 42	protein-coding
mm_104117.1	chr11	86738918	86738966	-	1	NA	intron (NM_001003908, intron 1 of 31)	intron (NM_001003908, intron 1 of 31)	18550	NM_001003908	67300	Mm.254588	NM_001003908	ENSMUSG00000047126	Cltc	3110065L21Rik|CHC|R74732	clathrin, heavy polypeptide (Hc)	protein-coding
mm_146925.1	chr18	31949695	31949710	-	1	NA	promoter-TSS (NM_001025381)	promoter-TSS (NM_001025381)	-66	NM_001025381	574402	Mm.391108	NM_001025381	ENSMUSG00000052229	Gpr17	AI853548	G protein-coupled receptor 17	protein-coding
mm_106821.1	chr12	7985279	7985302	+	1	NA	exon (NM_009693, exon 7 of 29)	exon (NM_009693, exon 7 of 29)	7613	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_69990.1	chr7	142383450	142383466	-	1	NA	exon (NM_009983, exon 3 of 9)	exon (NM_009983, exon 3 of 9)	4412	NM_009983	13033	Mm.231395	NM_009983	ENSMUSG00000007891	Ctsd	CD|CatD	cathepsin D	protein-coding
mm_20779.1	chr2	143988453	143988475	-	1	NA	exon (NM_133626, exon 2 of 3)	exon (NM_133626, exon 2 of 3)	22799	NM_133626	81910	Mm.13705	NM_024281	ENSMUSG00000027422	Rrbp1	1700087N07Rik|5730465C04Rik|ES/130|mKIAA1398|mRRp0|mRRp1.8|mRRp10|mRRp15a|mRRp15b|mRRp16.8|mRRp2|mRRp41|mRRp47|mRRp5.4|p180	ribosome binding protein 1	protein-coding
mm_101267.1	chr11	21239531	21239548	-	1	NA	intron (NM_139061, intron 1 of 22)	CpG	507	NM_001290628	245944	Mm.170103	NM_139061	ENSMUSG00000020128	Vps54	Hcc8|Vps54l|mSLP8|wr	VPS54 GARP complex subunit	protein-coding
mm_77848.1	chr9	5303551	5303563	+	1	NA	exon (NM_009807, exon 6 of 10)	exon (NM_009807, exon 6 of 10)	5040	NM_009807	12362	Mm.1051	NM_009807	ENSMUSG00000025888	Casp1	ICE|Il1bc	caspase 1	protein-coding
mm_67504.1	chr7	80779369	80779378	-	1	NA	intron (NM_016721, intron 2 of 37)	intron (NM_016721, intron 2 of 37)	23958	NM_016721	29875	Mm.207619	NM_016721	ENSMUSG00000030536	Iqgap1	AA682088|D7Ertd237e|D7Ertd257e|mKIAA0051	IQ motif containing GTPase activating protein 1	protein-coding
mm_159778.1	chr5	104860000	104860000	-	1	NA	promoter-TSS (NM_001039231)	promoter-TSS (NM_001039231)	68	NM_001039231	626391	Mm.385405	NM_001039231	ENSMUSG00000072774	Zfp951	C230055K05Rik	zinc finger protein 951	protein-coding
mm_97958.1	chr11	83731344	83731348	+	1	NA	Intergenic	RLTR20B2|LTR|ERVK	-15594	NM_183249	66107	Mm.902	NM_183249	ENSMUSG00000051748	Wfdc21	1100001G20Rik|Wdnm1-like	WAP four-disulfide core domain 21	protein-coding
mm_32618.1	chr4	114406036	114406053	+	1	NA	promoter-TSS (NM_001085549)	promoter-TSS (NM_001085549)	-680	NM_001085549	666048	Mm.331779	NM_001085549	ENSMUSG00000070867	Trabd2b	Gm12824|Hkat|OTTMUSG00000008561	TraB domain containing 2B	protein-coding
mm_32444.1	chr4	107291842	107291853	+	1	NA	3' UTR (NM_007860, exon 4 of 4)	3' UTR (NM_007860, exon 4 of 4)	15321	NM_007860	13370	Mm.148342	NM_007860	ENSMUSG00000034785	Dio1	5DI|D1|ITDI1|TXDI1	deiodinase, iodothyronine, type I	protein-coding
mm_94869.1	chr11	24078271	24078290	+	1	NA	5' UTR (NM_001242934, exon 1 of 4)	5' UTR (NM_001242934, exon 1 of 4)	224	NM_001159289	14025	Mm.53687	NM_016707	ENSMUSG00000000861	Bcl11a	2810047E18Rik|BCL-11A|Ctip1|D930021L15Rik|Evi9|Evi9a|Evi9b|Evi9c|mKIAA1809	B cell CLL/lymphoma 11A (zinc finger protein)	protein-coding
mm_161428.1	chr15	44747815	44747815	-	1	NA	intron (NM_178765, intron 2 of 7)	intron (NM_178765, intron 2 of 7)	857	NM_001285840	319613	Mm.207715	NM_176998	ENSMUSG00000022340	Sybu	Golsyn	syntabulin (syntaxin-interacting)	protein-coding
mm_40746.1	chr5	66745423	66745440	+	1	NA	promoter-TSS (NM_001001980)	promoter-TSS (NM_001001980)	-409	NM_001001980	77569	Mm.374778	NM_001001980	ENSMUSG00000037736	Limch1	3732412D22Rik|mKIAA1102	LIM and calponin homology domains 1	protein-coding
mm_100224.1	chr11	117115134	117115186	+	1	NA	promoter-TSS (NM_001166506)	promoter-TSS (NM_001166506)	-12	NR_029459	74136	Mm.272312	NM_028777	ENSMUSG00000020823	Sec14l1	1200017E04Rik|2810012L19Rik|Naa-35	SEC14-like lipid binding 1	protein-coding
mm_152322.1	chr19	9936704	9936731	-	1	NA	Intergenic	Intergenic	-37184	NM_016692	16319	Mm.29755	NM_016692	ENSMUSG00000024660	Incenp	2700067E22Rik|AU019509|C130081E20|C77457	inner centromere protein	protein-coding
mm_152277.1	chr19	8838102	8838142	-	1	NA	3' UTR (NM_010316, exon 3 of 3)	3' UTR (NM_010316, exon 3 of 3)	655	NM_001136064	14705	Mm.345134	NM_008144	ENSMUSG00000071657	Bscl2	2900097C17Rik|AI046355|Gng3lg	Berardinelli-Seip congenital lipodystrophy 2 (seipin)	protein-coding
mm_139705.1	chr17	57453508	57453529	+	1	NA	intron (NM_010130, intron 17 of 21)	Lx3A|LINE|L1	91796	NM_001104591	224916	Mm.469889	NM_001104591	ENSMUSG00000090655	Vmn2r120	EG224916	vomeronasal 2, receptor 120	protein-coding
mm_142090.1	chr17	35834046	35834073	-	1	NA	3' UTR (NM_011655, exon 4 of 4)	3' UTR (NM_011655, exon 4 of 4)	4242	NM_011655	22154	Mm.273538	NM_011655	ENSMUSG00000001525	Tubb5	AA408537|AI596182|B130022C14Rik|M(beta)5	tubulin, beta 5 class I	protein-coding
mm_104405.1	chr11	94521473	94521516	-	1	NA	promoter-TSS (NM_170671)	promoter-TSS (NM_170671)	8	NM_170671	104601	Mm.84725	NM_170671	ENSMUSG00000039110	Mycbpap	4932408B01Rik|AMAP-1|AW125474	MYCBP associated protein	protein-coding
mm_109174.1	chr12	108410574	108410585	+	1	NA	promoter-TSS (NM_001043336)	promoter-TSS (NM_001043336)	-54	NM_001043336	68519	Mm.236645	NM_001043335	ENSMUSG00000058070	Eml1	1110008N23Rik|A930030P13Rik|AA171013|AI847476|AI853955|ELP79|EMAP|EMAPL|heco	echinoderm microtubule associated protein like 1	protein-coding
mm_142984.1	chr17	56276751	56276773	-	1	NA	promoter-TSS (NM_174989)	promoter-TSS (NM_174989)	5	NM_174989	106759	Mm.203952	NM_174989	ENSMUSG00000047123	Ticam1	AW046014|AW547018|TICAM-1|TRIF	toll-like receptor adaptor molecule 1	protein-coding
mm_114127.1	chr13	55210925	55210958	+	1	NA	intron (NM_008739, intron 1 of 22)	CpG	1159	NM_008739	18193	Mm.12964	NM_008739	ENSMUSG00000021488	Nsd1	AI528500|KMT3B	nuclear receptor-binding SET-domain protein 1	protein-coding
mm_166702.1	chr6	115687863	115687864	+	1	NA	Intergenic	RSINE1|SINE|B4	-11228	NM_029780	110157	Mm.184163	NM_029780	ENSMUSG00000000441	Raf1	6430402F14Rik|AA990557|BB129353|Craf1|D830050J10Rik|Raf-1|c-Raf|v-Raf	v-raf-leukemia viral oncogene 1	protein-coding
mm_33430.1	chr4	130055280	130055284	+	1	NA	intron (NM_028266, intron 9 of 69)	intron (NM_028266, intron 9 of 69)	7442	NM_028266	107581	Mm.41860	NM_028266	ENSMUSG00000040690	Col16a1	2700007F12Rik|A530052M23Rik|AI838662|CA1F	collagen, type XVI, alpha 1	protein-coding
mm_168294.1	chr11	104442792	104442802	-	1	NA	promoter-TSS (NM_001081045)	promoter-TSS (NM_001081045)	-506	NM_001081045	76719	Mm.136418	NM_001081045	ENSMUSG00000018412	Kansl1	1700081L11Rik|9430041J06Rik|mKIAA1267	KAT8 regulatory NSL complex subunit 1	protein-coding
mm_62021.1	chr7	91543065	91543095	+	1	NA	intron (NM_011807, intron 2 of 22)	intron (NM_011807, intron 2 of 22)	452294	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_104267.1	chr11	88996501	88996533	-	1	NA	Intergenic	Intergenic	-2886	NM_009546	217069	Mm.248445	NM_009546	ENSMUSG00000000275	Trim25	AA960166|AL022677|EFP|Zfp147	tripartite motif-containing 25	protein-coding
mm_108740.1	chr12	88722867	88722893	+	1	NA	Intergenic	Intergenic	-71624	NM_001198587	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding
mm_35994.1	chr4	55532466	55532485	-	1	NA	promoter-TSS (NM_010637)	promoter-TSS (NM_010637)	0	NM_010637	16600	Mm.4325	NM_010637	ENSMUSG00000003032	Klf4	EZF|Gklf|Zie	Kruppel-like factor 4 (gut)	protein-coding
mm_109792.1	chr12	3255840	3255844	-	1	NA	intron (NM_016676, intron 3 of 5)	intron (NM_016676, intron 3 of 5)	20051	NR_015551	74173	Mm.309774	NM_028796	ENSMUSG00000079179	Rab10os	1700012B15Rik|1810036A22Rik	RAB10, member RAS oncogene family, opposite strand	ncRNA
mm_61662.1	chr7	80774514	80774520	+	1	NA	intron (NM_016721, intron 2 of 37)	MIR|SINE|MIR	28814	NM_016721	29875	Mm.207619	NM_016721	ENSMUSG00000030536	Iqgap1	AA682088|D7Ertd237e|D7Ertd257e|mKIAA0051	IQ motif containing GTPase activating protein 1	protein-coding
mm_97989.1	chr11	83955981	83956007	+	1	NA	exon (NM_030096, exon 12 of 15)	exon (NM_030096, exon 12 of 15)	-8437	NM_194341	217030	Mm.82680	NM_194341	ENSMUSG00000034940	Synrg	Ap1gbp1|SYNG	synergin, gamma	protein-coding
mm_125629.1	chr15	61989483	61989494	+	1	NA	exon (NM_001177354, exon 3 of 3)	exon (NM_001177354, exon 3 of 3)	4147	NM_001177352	17869	Mm.2444	NM_010849	ENSMUSG00000022346	Myc	AU016757|Myc2|Niard|Nird|bHLHe39	myelocytomatosis oncogene	protein-coding
mm_43468.1	chr5	136693615	136693642	+	1	NA	promoter-TSS (NM_001303021)	promoter-TSS (NM_001303021)	-48	NM_001303021	59310	Mm.5178	NM_021611	ENSMUSG00000005474	Myl10	1700027I08Rik|Mylc2pl|PLRLC	myosin, light chain 10, regulatory	protein-coding
mm_72103.1	chr8	71597699	71597718	+	1	NA	promoter-TSS (NM_001166213)	promoter-TSS (NM_001166213)	62	NM_001166213	100037278	Mm.482159	NM_001166213	ENSMUSG00000043243	Fam129c	Bcnp1	family with sequence similarity 129, member C	protein-coding
mm_135250.1	chr16	37539782	37539796	-	1	NA	promoter-TSS (NM_001042499)	promoter-TSS (NM_001042499)	-20	NM_028812	74197	Mm.287795	NM_028812	ENSMUSG00000022828	Gtf2e1	2610024P03Rik|56kDa|AI303800|FE|TFIIE-A	general transcription factor II E, polypeptide 1 (alpha subunit)	protein-coding
mm_165164.1	chr2	25470015	25470019	-	1	NA	promoter-TSS (NM_008963)	promoter-TSS (NM_008963)	-268	NM_008963	19215	Mm.1008	NM_008963	ENSMUSG00000015090	Ptgds	21kDa|L-PGDS|PGD2|PGDS|PGDS2|Ptgs3	prostaglandin D2 synthase (brain)	protein-coding
mm_136940.1	chr17	14249885	14249897	+	1	NA	Intergenic	Intergenic	-29615	NM_022315	64074	Mm.30162	NM_022315	ENSMUSG00000023886	Smoc2	1700056C05Rik|5430426J21Rik|Smoc2l	SPARC related modular calcium binding 2	protein-coding
mm_108155.1	chr12	76324911	76324932	+	1	NA	promoter-TSS (NM_001101471)	promoter-TSS (NM_001101471)	30	NM_001101471	238276	Mm.311452	NM_001101471	ENSMUSG00000021057	Akap5	3526401B18Rik|AKAP 150|AKAP-5|AKAP150|BB098886|Gm258|P150	A kinase (PRKA) anchor protein 5	protein-coding
mm_25150.1	chr3	102775105	102775111	+	1	NA	Intergenic	Intergenic	7606	NM_009432	22094	Mm.110730	NM_009432	ENSMUSG00000027857	Tshb	-	thyroid stimulating hormone, beta subunit	protein-coding
mm_9795.1	chr1	181842308	181842313	-	1	NA	promoter-TSS (NM_133815)	promoter-TSS (NM_133815)	91	NM_133815	98386	Mm.4538	NM_133815	ENSMUSG00000004880	Lbr	AI505894|ic	lamin B receptor	protein-coding
mm_43835.1	chr5	142972441	142972496	+	1	NA	3' UTR (NM_007984, exon 5 of 5)	3' UTR (NM_007984, exon 5 of 5)	12113	NM_007984	14086	Mm.289707	NM_007984	ENSMUSG00000029581	Fscn1	AI663989|Fan1|fascin-1	fascin actin-bundling protein 1	protein-coding
mm_85799.1	chr9	110117331	110117353	-	1	NA	intron (NM_001252682, intron 1 of 22)	CpG	274	NM_001252682	72831	Mm.276305	NM_133347	ENSMUSG00000032480	Dhx30	2810477H02Rik|C130058C04Rik|Ddx30|HELG|Ret-CoR	DEAH (Asp-Glu-Ala-His) box polypeptide 30	protein-coding
mm_144374.1	chr18	20558039	20558086	+	1	NA	promoter-TSS (NM_007883)	promoter-TSS (NM_007883)	-12	NM_007883	13511	Mm.345891	NM_007883	ENSMUSG00000044393	Dsg2	AA408168|D18Ertd293e	desmoglein 2	protein-coding
mm_82047.1	chr9	122351776	122351784	+	1	NA	5' UTR (NM_026179, exon 1 of 7)	5' UTR (NM_026179, exon 1 of 7)	164	NM_026179	67469	Mm.280254	NM_026179	ENSMUSG00000032540	Abhd5	1300003D03Rik|2010002J10Rik|CDS|CGI-58|IECN5|NCIE2	abhydrolase domain containing 5	protein-coding
mm_69985.1	chr7	142380927	142380934	-	1	NA	exon (NM_009983, exon 5 of 9)	exon (NM_009983, exon 5 of 9)	6940	NM_009983	13033	Mm.231395	NM_009983	ENSMUSG00000007891	Ctsd	CD|CatD	cathepsin D	protein-coding
mm_81115.1	chr9	106453948	106453961	+	1	NA	5' UTR (NM_021567, exon 1 of 13)	5' UTR (NM_021567, exon 1 of 13)	116	NM_021567	59092	Mm.286394	NM_021567	ENSMUSG00000023495	Pcbp4	1200003L19Rik|AlphaCP-4	poly(rC) binding protein 4	protein-coding
mm_73499.1	chr8	107205317	107205353	+	1	NA	Intergenic	Intergenic	-50829	NR_039557	100628577		NR_039557	ENSMUSG00000093061	Mir5098	mmu-mir-5098|mu-mir-5098	microRNA 5098	ncRNA
mm_70284.1	chr8	3631110	3631169	+	1	NA	promoter-TSS (NM_011503)	promoter-TSS (NM_011503)	-21	NM_011503	20911	Mm.7247	NM_011503	ENSMUSG00000004626	Stxbp2	C79054|Munc-18-2|Munc-18b|Munc18b|Sxtbp2|Sxtp2|Unc18-2|Unc18b|muSec1	syntaxin binding protein 2	protein-coding
mm_129905.1	chr15	84055072	84055099	-	1	NA	intron (NM_029946, intron 1 of 31)	MER5A|DNA|hAT-Charlie	10264	NM_029946	77627	Mm.196288	NM_029946	ENSMUSG00000022441	Efcab6	4931407K02Rik|4932408N08Rik|bM150J22.2|mKIAA1672	EF-hand calcium binding domain 6	protein-coding
mm_56852.1	chr6	118139046	118139070	-	1	NA	promoter-TSS (NM_030165)	promoter-TSS (NM_030165)	82	NM_030165	78752	Mm.300317	NM_030165	ENSMUSG00000042042	Csgalnact2	4632415D10Rik|Galnact2	chondroitin sulfate N-acetylgalactosaminyltransferase 2	protein-coding
mm_10006.1	chr1	191575538	191575549	-	1	NA	promoter-TSS (NM_178632)	promoter-TSS (NM_178632)	1	NM_001305233	76843	Mm.189102	NM_029766	ENSMUSG00000037474	Dtl	2810047L02Rik|5730564G15Rik|L2dtl|Ramp	denticleless E3 ubiquitin protein ligase	protein-coding
mm_135139.1	chr16	35853595	35853609	-	1	NA	exon (NM_001039530, exon 7 of 17)	exon (NM_001039530, exon 7 of 17)	17780	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_87833.1	chr10	60371813	60371825	+	1	NA	3' UTR (NM_001159572, exon 7 of 7)	3' UTR (NM_001159572, exon 7 of 7)	24968	NM_028732	74048	Mm.273584	NM_028732	ENSMUSG00000020101	Vsir	4632428N05Rik|Dies1|PD-1H|VISTA	V-set immunoregulatory receptor	protein-coding
mm_99306.1	chr11	101376624	101376630	+	1	NA	exon (NM_008061, exon 5 of 5)	exon (NM_008061, exon 5 of 5)	8911	NM_008061	14377	Mm.18064	NM_008061	ENSMUSG00000078650	G6pc	AW107337|G6Pase|G6pt|Glc-6-Pase	glucose-6-phosphatase, catalytic	protein-coding
mm_100381.1	chr11	119300188	119300203	+	1	NA	promoter-TSS (NM_138669)	promoter-TSS (NM_138669)	-152	NM_138669	192170	Mm.197555	NM_138669	ENSMUSG00000025580	Eif4a3	2400003O03Rik|Ddx48|eIF4A-III|mKIAA0111	eukaryotic translation initiation factor 4A3	protein-coding
mm_33625.1	chr4	132768326	132768390	+	1	NA	promoter-TSS (NM_011284)	promoter-TSS (NM_011284)	-2	NM_011284	19891	Mm.2870	NM_011284	ENSMUSG00000028884	Rpa2	AA409079|AI325195|AU020965|RPA34|Rf-A2	replication protein A2	protein-coding
mm_53530.1	chr6	136555059	136555075	+	1	NA	intron (NM_019426, intron 1 of 14)	intron (NM_019426, intron 1 of 14)	36216	NM_019426	54343	Mm.173271	NM_019426	ENSMUSG00000030213	Atf7ip	2610204M12Rik|AM|Mcaf1	activating transcription factor 7 interacting protein	protein-coding
mm_144543.1	chr18	27745615	27745619	+	1	NA	Intergenic	Intergenic	-814547	NR_045398	320624	Mm.50107	NR_045398		4930474G06Rik	-	RIKEN cDNA 4930474G06 gene	ncRNA
mm_64460.1	chr7	142660655	142660667	+	1	NA	non-coding (NR_002855, exon 1 of 4)	non-coding (NR_002855, exon 1 of 4)	610	NM_001122736	16002	Mm.3862	NM_010514	ENSMUSG00000048583	Igf2	AL033362|Igf-2|Igf-II|M6pr|Mpr|Peg2	insulin-like growth factor 2	protein-coding
mm_56144.1	chr6	87809793	87809814	-	1	NA	promoter-TSS (NM_133717)	promoter-TSS (NM_133717)	-46	NM_133717	69834	Mm.37380	NM_133717	ENSMUSG00000030055	Rab43	1810048P08Rik|2500004H21Rik|AW490415	RAB43, member RAS oncogene family	protein-coding
mm_35958.1	chr4	53130992	53131004	-	1	NA	intron (NM_013454, intron 3 of 49)	intron (NM_013454, intron 3 of 49)	28897	NM_013454	11303	Mm.277376	NM_013454	ENSMUSG00000015243	Abca1	ABC-1|Abc1	ATP-binding cassette, sub-family A (ABC1), member 1	protein-coding
mm_22150.1	chr2	172401112	172401123	-	1	NA	intron (NM_001080820, intron 1 of 6)	intron (NM_001080820, intron 1 of 6)	7323	NM_001276423	320664	Mm.210195	NM_001033538	ENSMUSG00000074570	Cass4	F730031O20Rik	Cas scaffolding protein family member 4	protein-coding
mm_88143.1	chr10	69533594	69533632	+	1	NA	promoter-TSS (NM_170688)	promoter-TSS (NM_170688)	-95	NM_170729	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_154461.1	chrM	3154	3165	-	1	NA	NA	Intergenic	NA	NA								
mm_61686.1	chr7	81005027	81005037	+	1	NA	intron (NM_178707, intron 1 of 9)	intron (NM_178707, intron 1 of 9)	11348	NM_178707	233410	Mm.29525	NM_178707	ENSMUSG00000005621	Zfp592	8430405N24|A730014M16Rik|Znf592|mKIAA0211	zinc finger protein 592	protein-coding
mm_61683.1	chr7	81004841	81004841	+	1	NA	intron (NM_178707, intron 1 of 9)	intron (NM_178707, intron 1 of 9)	11157	NM_178707	233410	Mm.29525	NM_178707	ENSMUSG00000005621	Zfp592	8430405N24|A730014M16Rik|Znf592|mKIAA0211	zinc finger protein 592	protein-coding
mm_108650.1	chr12	86082556	86082603	+	1	NA	promoter-TSS (NM_029601)	promoter-TSS (NM_029601)	18	NM_001199843	76411	Mm.292345	NM_029601	ENSMUSG00000007867	Ift43	1700019E19Rik|R75064	intraflagellar transport 43	protein-coding
mm_29656.1	chr3	122513000	122513049	-	1	NA	intron (NM_013867, intron 7 of 11)	intron (NM_013867, intron 7 of 11)	28657	NR_106117	102465764		NR_106117	ENSMUSG00000104773	Mir7657	mmu-mir-7657	microRNA 7657	ncRNA
mm_105975.1	chr11	115535805	115535863	-	1	NA	intron (NM_133354, intron 1 of 3)	CpG	396	NM_133354	170930	Mm.29923	NM_133354	ENSMUSG00000020738	Sumo2	SUMO-2|Smt3A|Smt3b|Smt3h2	small ubiquitin-like modifier 2	protein-coding
mm_39090.1	chr4	154636964	154636986	-	1	NA	promoter-TSS (NM_027504)	promoter-TSS (NM_027504)	-102	NM_027504	70673	Mm.257785	NM_027504	ENSMUSG00000039410	Prdm16	5730557K01Rik|csp1|mel1	PR domain containing 16	protein-coding
mm_60691.1	chr7	45169819	45169834	+	1	NA	exon (NM_182993, exon 3 of 12)	exon (NM_182993, exon 3 of 12)	-3477	NR_106022	102465638		NR_106022	ENSMUSG00000106470	Mir7055	mmu-mir-7055	microRNA 7055	ncRNA
mm_46010.1	chr5	90786657	90786673	-	1	NA	exon (NM_203320, exon 3 of 4)	exon (NM_203320, exon 3 of 4)	564	NM_203320	330122	Mm.244289	NM_203320	ENSMUSG00000029379	Cxcl3	Dcip1|Gm1960	chemokine (C-X-C motif) ligand 3	protein-coding
mm_26379.1	chr3	142568287	142568302	+	1	NA	intron (NM_001289493, intron 7 of 10)	intron (NM_001289493, intron 7 of 10)	7798	NM_001289493	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_40864.1	chr5	73651377	73651394	+	1	NA	promoter-TSS (NM_178387)	promoter-TSS (NM_178387)	5	NM_178387	73472	Mm.87067	NM_178387	ENSMUSG00000029155	Spata18	1700067I02Rik	spermatogenesis associated 18	protein-coding
mm_8858.1	chr1	162715695	162715712	-	1	NA	exon (NM_001081290, exon 8 of 35)	exon (NM_001081290, exon 8 of 35)	24853	NM_001081290	226562	Mm.245446	NM_001081290	ENSMUSG00000040225	Prrc2c	1810043M20Rik|9630039I18Rik|A630006J20|Bat2d|Bat2d1|Bat2l2|E130112L15Rik|Prrc3|mKIAA1096	proline-rich coiled-coil 2C	protein-coding
mm_172688.1	chr8	57512621	57512629	+	1	NA	exon (NM_008252, exon 2 of 5)	exon (NM_008252, exon 2 of 5)	782	NM_008252	97165	Mm.276881	NM_008252	ENSMUSG00000054717	Hmgb2	C80539|HMG-2|Hmg2	high mobility group box 2	protein-coding
mm_85806.1	chr9	110305058	110305120	-	1	NA	promoter-TSS (NM_001081381)	promoter-TSS (NM_001081381)	-103	NM_001081381	72341	Mm.374250	NM_001081381	ENSMUSG00000054836	Elp6	2610001P13Rik|2610002I17Rik|AV159994|Tmem103	elongator acetyltransferase complex subunit 6	protein-coding
mm_99830.1	chr11	108921671	108921684	+	1	NA	intron (NM_015732, intron 1 of 10)	CpG	1328	NM_015732	12006	Mm.71710	NM_015732	ENSMUSG00000000142	Axin2	Axi1|Axil|Conductin	axin 2	protein-coding
mm_46235.1	chr5	99217998	99218001	-	1	NA	3' UTR (NM_181318, exon 14 of 14)	3' UTR (NM_181318, exon 14 of 14)	34928	NM_181318	320292	Mm.259074	NM_145839	ENSMUSG00000089809	Rasgef1b	4732452O09Rik|GPIgamma4|Gpig4	RasGEF domain family, member 1B	protein-coding
mm_19023.1	chr2	76954653	76954667	-	1	NA	exon (NM_011652, exon 15 of 313)	exon (NM_011652, exon 15 of 313)	27887	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_1358.1	chr1	66322080	66322090	+	1	NA	5' UTR (NM_001310634, exon 1 of 15)	5' UTR (NM_001310634, exon 1 of 15)	361	NM_001310634	17756	Mm.256966	NM_008632	ENSMUSG00000015222	Map2	G1-397-34|MAP-2|Mtap-2|Mtap2|repro4	microtubule-associated protein 2	protein-coding
mm_23620.1	chr3	65703559	65703562	+	1	NA	intron (NM_001166659, intron 3 of 12)	L1_Mur3|LINE|L1	37332	NM_001166659	624866	Mm.296317	NM_001037923	ENSMUSG00000074579	Lekr1	EG546798|EG624866|Gm6534	leucine, glutamate and lysine rich 1	protein-coding
mm_89344.1	chr10	87937726	87937733	+	1	NA	TTS (NM_010512)	TTS (NM_010512)	-28942	NR_000040	22172	Mm.391420	NR_000040		Tyms-ps	-	thymidylate synthase, pseudogene	pseudo
mm_56672.1	chr6	113660534	113660542	-	1	NA	intron (NM_001113553, intron 2 of 11)	ORR1D2|LTR|ERVL-MaLR	22071	NM_001113553	108960	Mm.152142	NM_172161	ENSMUSG00000060477	Irak2	6330415L08Rik|AI649099|IRAK-2	interleukin-1 receptor-associated kinase 2	protein-coding
mm_3574.1	chr1	150625291	150625301	+	1	NA	intron (NM_001024720, intron 77 of 106)	L1MB7|LINE|L1	-159131	NM_001110146	96875	Mm.174256	NM_021400	ENSMUSG00000006014	Prg4	CACP|DOL54|JCAP|MSF|SZP|lubricin	proteoglycan 4 (megakaryocyte stimulating factor, articular superficial zone protein)	protein-coding
mm_95483.1	chr11	51289739	51289754	+	1	NA	promoter-TSS (NM_153393)	promoter-TSS (NM_153393)	-174	NM_153393	237759	Mm.154093	NM_153393	ENSMUSG00000063564	Col23a1	2810458L13Rik|AI429655	collagen, type XXIII, alpha 1	protein-coding
mm_156335.1	chrX	139009058	139009077	+	1	NA	TTS (NM_013724)	TTS (NM_013724)	76169	NM_177920	331535	Mm.211704	NM_177920	ENSMUSG00000031271	Serpina7	C730040N12Rik|Tbg	serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 7	protein-coding
mm_124965.1	chr15	16824998	16825008	+	1	NA	intron (NM_009869, intron 2 of 10)	Lx9|LINE|L1	46902	NM_009869	12565	Mm.439758	NM_009869	ENSMUSG00000025370	Cdh9	-	cadherin 9	protein-coding
mm_23071.1	chr3	36151114	36151124	+	1	NA	promoter-TSS (NM_001101478)	promoter-TSS (NM_001101478)	39	NM_001101478	241944	Mm.260056	NM_001101478	ENSMUSG00000033883	D3Ertd254e	-	DNA segment, Chr 3, ERATO Doi 254, expressed	protein-coding
mm_153764.1	chr19	45591900	45591910	-	1	NA	intron (NM_013907, intron 5 of 8)	intron (NM_013907, intron 5 of 8)	31290	NM_172639	226162	Mm.21978	NM_172639	ENSMUSG00000041035	Dpcd	5330431N19Rik|Ndac	deleted in primary ciliary dyskinesia	protein-coding
mm_99289.1	chr11	101322847	101322897	+	1	NA	3' UTR (NM_011192, exon 11 of 11)	3' UTR (NM_011192, exon 11 of 11)	-2191	NM_178932	237940	Mm.302277	NM_178932	ENSMUSG00000078651	Aoc2	RAO	amine oxidase, copper containing 2 (retina-specific)	protein-coding
mm_170089.1	chr17	35935959	35935978	-	1	NA	Intergenic	Intergenic	-11186	NR_028278	667766	Mm.29385	NR_028278		Gm8801	-	protein phosphatase 1, regulatory subunit 10 pseudogene	pseudo
mm_8237.1	chr1	138175914	138175936	-	1	NA	promoter-TSS (NM_001268286)	promoter-TSS (NM_001268286)	-620	NM_001268286	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_127764.1	chr15	103562828	103562865	+	1	NA	TTS (NM_008134)	TTS (NM_008134)	2235	NM_001289587	14663	Mm.219621	NM_008134	ENSMUSG00000022491	Glycam1	MC26|Sgp50|glyCAM-1	glycosylation dependent cell adhesion molecule 1	protein-coding
mm_58555.1	chr7	4740814	4740883	+	1	NA	intron (NM_146177, intron 1 of 8)	intron (NM_146177, intron 1 of 8)	721	NM_001115018	232811	Mm.247844	NM_146177	ENSMUSG00000059851	Kmt5c	BC024816|Suv4-20h2|Suv420h2	lysine methyltransferase 5C	protein-coding
mm_106385.1	chr11	118513251	118513269	-	1	NA	exon (NM_001039167, exon 5 of 15)	exon (NM_001039167, exon 5 of 15)	36300	NM_172573	217364	Mm.473963	NM_172573	ENSMUSG00000033857	Engase	C130099A03|D230014K01Rik	endo-beta-N-acetylglucosaminidase	protein-coding
mm_170809.1	chr2	175965317	175965336	+	1	NA	intron (NM_001177480, intron 4 of 4).2	intron (NM_001177480, intron 4 of 4).2	-34226	NM_001177406	100303732	Mm.484983	NM_001177404	ENSMUSG00000095199	Zfp967	Gm14431|OTTMUSG00000016608	zinc finger protein 967	protein-coding
mm_26261.1	chr3	142500621	142500632	+	1	NA	exon (NM_153564, exon 2 of 11)	exon (NM_153564, exon 2 of 11)	3692	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_69306.1	chr7	128393647	128393656	-	1	NA	intron (NM_026418, intron 3 of 4)	intron (NM_026418, intron 3 of 4)	24521	NM_026418	67865	Mm.18635	NM_026418	ENSMUSG00000030844	Rgs10	2310010N19Rik	regulator of G-protein signalling 10	protein-coding
mm_50377.1	chr6	48684571	48684586	+	1	NA	promoter-TSS (NM_001243199)	promoter-TSS (NM_001243199)	0	NM_001243200	107526	Mm.333048	NM_174990	ENSMUSG00000054435	Gimap4	AU019574|E430007K16Rik|Ian-1|Ian1|Imap4	GTPase, IMAP family member 4	protein-coding
mm_106748.1	chr12	3959997	3960061	+	1	NA	exon (NM_008895, exon 3 of 3)	exon (NM_008895, exon 3 of 3)	5084	NM_001278583	18976	Mm.277996	NM_008895	ENSMUSG00000020660	Pomc	ACTH|BE|Beta-LPH|Clip|Gamma-LPH|Npp|Pomc-1|Pomc1|alpha-MSH|alphaMSH|beta-MSH|gamma-MSH	pro-opiomelanocortin-alpha	protein-coding
mm_62692.1	chr7	110062105	110062123	+	1	NA	intron (NM_009281, intron 1 of 15)	CpG	412	NM_009281	20841	Mm.10815	NM_009281	ENSMUSG00000061079	Zfp143	AA959806|AU015869|D7Ertd805e|KRAB14|SBF|Staf|Zfp79|Zfp80-rs1|Znf143|pHZ-1	zinc finger protein 143	protein-coding
mm_54339.1	chr6	30669312	30669322	-	1	NA	intron (NR_130781, intron 3 of 11)	intron (NR_130781, intron 3 of 11)	24432	NM_031998	83922	Mm.65389	NM_031998	ENSMUSG00000029790	Cep41	1700017E11Rik|2810431D15Rik|Tsga14	centrosomal protein 41	protein-coding
mm_149938.1	chr19	27217102	27217131	+	1	NA	promoter-TSS (NM_013703)	promoter-TSS (NM_013703)	96	NM_001161420	22359	Mm.4141	NM_013703	ENSMUSG00000024924	Vldlr	AA408956|AI451093|AW047288	very low density lipoprotein receptor	protein-coding
mm_59490.1	chr7	27499316	27499331	+	1	NA	promoter-TSS (NM_019412)	promoter-TSS (NM_019412)	-1	NM_198048	19153	Mm.10119	NM_019412	ENSMUSG00000053198	Prx	L-Periaxin	periaxin	protein-coding
mm_131041.1	chr16	3884719	3884738	+	1	NA	5' UTR (NM_001290689, exon 1 of 6)	5' UTR (NM_001290689, exon 1 of 6)	109	NM_001290689	74763	Mm.28403	NM_029090	ENSMUSG00000005982	Naa60	1200013P24Rik|AI315146|Nat15	N(alpha)-acetyltransferase 60, NatF catalytic subunit	protein-coding
mm_22223.1	chr2	174427956	174427984	-	1	NA	TTS (NM_020580)	TTS (NM_020580)	11069	NM_022325	64138	Mm.156919	NM_022325	ENSMUSG00000016256	Ctsz	AI787083|AU019819|CTSX|D2Wsu143e	cathepsin Z	protein-coding
mm_44123.1	chr5	149636411	149636455	+	1	NA	promoter-TSS (NM_013559)	promoter-TSS (NM_013559)	-97	NM_001347534	15505	Mm.270681	NM_013559	ENSMUSG00000029657	Hsph1	105kDa|AI790491|Hsp105|Hsp110|hsp-E7I|hsp110/105	heat shock 105kDa/110kDa protein 1	protein-coding
mm_142370.1	chr17	44643578	44643579	-	1	NA	intron (NM_001271631, intron 2 of 4)	MIRc|SINE|MIR	92598	NR_073425	12393	Mm.391013	NM_009820	ENSMUSG00000039153	Runx2	AML3|Cbf|Cbfa-1|Cbfa1|LS3|Osf2|PEBP2aA|Pebp2a1|Pebpa2a	runt related transcription factor 2	protein-coding
mm_9222.1	chr1	171234608	171234620	-	1	NA	promoter-TSS (NM_010185)	promoter-TSS (NM_010185)	-265	NM_010185	14127	Mm.22673	NM_010185	ENSMUSG00000058715	Fcer1g	AI573376|CD23|FcR-gamma|FcR[g]|FcRgamma|Fce1g|FcepsilonRI|Ly-50	Fc receptor, IgE, high affinity I, gamma polypeptide	protein-coding
mm_166305.1	chr5	105702703	105702738	-	1	NA	intron (NM_178701, intron 1 of 2)	intron (NM_178701, intron 1 of 2)	1910	NM_178701	231549	Mm.23837	NM_178701	ENSMUSG00000046079	Lrrc8d	2810473G09Rik|4930525N13Rik|A930019F03|Lrrc5	leucine rich repeat containing 8D	protein-coding
mm_170324.1	chr18	4199335	4199335	-	1	NA	Intergenic	Intergenic	33503	NM_026092	67328	Mm.158148	NM_026092	ENSMUSG00000024233	Lyzl1	1700038F02Rik|Lyc2|Lyzd1	lysozyme-like 1	protein-coding
mm_52695.1	chr6	118880165	118880175	+	1	NA	promoter-TSS (NR_046053)	promoter-TSS (NR_046053)	12	NR_046053	74363	Mm.399403	NR_046053		4931430N09Rik	-	RIKEN cDNA 4931430N09 gene	ncRNA
mm_152899.1	chr19	25002911	25002935	-	1	NA	intron (NM_028785, intron 1 of 47)	intron (NM_028785, intron 1 of 47)	3394	NM_028785	76088	Mm.102485	NM_028785	ENSMUSG00000052085	Dock8	1200017A24Rik|5830472H07Rik|A130095G14Rik|AI461977	dedicator of cytokinesis 8	protein-coding
mm_102129.1	chr11	53430418	53430433	-	1	NA	intron (NM_001326614, intron 2 of 2)	intron (NM_001326614, intron 2 of 2)	406	NM_025352	22272	Mm.251621	NM_025352	ENSMUSG00000044894	Uqcrq	1100001F06Rik|1500040F11Rik|5830407L17Rik|9.5kDa|AA959903|QP-C|Qpc|Uqcrb|c1502	ubiquinol-cytochrome c reductase, complex III subunit VII	protein-coding
mm_152690.1	chr19	16780873	16780897	-	1	NA	promoter-TSS (NM_173028)	promoter-TSS (NM_173028)	48	NM_173028	271564	Mm.211963	NM_173028	ENSMUSG00000046230	Vps13a	4930425F11|4930516E05Rik|4930543C13Rik|9930023P20|Chac|Chorein|D330038K10Rik|mKIAA0986	vacuolar protein sorting 13A	protein-coding
mm_24220.1	chr3	88685425	88685442	+	1	NA	promoter-TSS (NM_028814)	promoter-TSS (NM_028814)	-361	NM_028814	74200	Mm.251800	NM_028814	ENSMUSG00000028060	2810403A07Rik	A430106P18Rik|AI256352|AI451678|Blom7|Kiaa0907	RIKEN cDNA 2810403A07 gene	protein-coding
mm_133729.1	chr16	93788691	93788711	+	1	NA	intron (NM_027293, intron 26 of 36)	intron (NM_027293, intron 26 of 36)	-43420	NM_001045529	338467	Mm.287329	NM_001045529	ENSMUSG00000039456	Morc3	1110051N18Rik|AI452146|BF318192|D16Jhu32e|NXP2|Zcwcc3	microrchidia 3	protein-coding
mm_4000.1	chr1	164631744	164631754	+	1	NA	Intergenic	Intergenic	-164983	NM_019759	56429	Mm.28935	NM_019759	ENSMUSG00000026574	Dpt	1810032B19Rik|5033416F05Rik|EQ-1|Eq1	dermatopontin	protein-coding
mm_127620.1	chr15	102460593	102460616	+	1	NA	exon (NM_025385, exon 4 of 5)	exon (NM_025385, exon 4 of 5)	1434	NM_025385	66151	Mm.393955	NM_025385	ENSMUSG00000023048	Prr13	1110020C13Rik|2010324E22Rik	proline rich 13	protein-coding
mm_27071.1	chr3	28264236	28264249	-	1	NA	intron (NM_026910, intron 1 of 32)	intron (NM_026910, intron 1 of 32)	1028	NM_001163009	665113	Mm.126193	NM_026910	ENSMUSG00000027692	Tnik	1500031A17Rik|4831440I19Rik|AI451411|C530008O15Rik|C630040K21Rik	TRAF2 and NCK interacting kinase	protein-coding
mm_16201.1	chr2	173022361	173022388	+	1	NA	intron (NM_019547, intron 1 of 3)	CpG	472	NM_019547	56190	Mm.485782	NM_019547	ENSMUSG00000027510	Rbm38	Rnpc1|Seb4|Seb4l	RNA binding motif protein 38	protein-coding
mm_139041.1	chr17	46227804	46227808	+	1	NA	exon (NM_028198, exon 18 of 32)	exon (NM_028198, exon 18 of 32)	-3725	NR_030466	751553		NR_030466	ENSMUSG00000076141	Mir693	Mirn693|mir-693|mmu-mir-693	microRNA 693	ncRNA
mm_44229.1	chr5	5120019	5120022	-	1	NA	intron (NM_011074, intron 6 of 14)	intron (NM_011074, intron 6 of 14)	146048	NM_001310448	18647	Mm.389061	NM_011074	ENSMUSG00000028926	Cdk14	Pftk1|mKIAA0834	cyclin-dependent kinase 14	protein-coding
mm_160811.1	chr11	20741534	20741534	-	1	NA	promoter-TSS (NM_001252503)	promoter-TSS (NM_001252503)	22	NM_001290545	216549	Mm.356580	NM_181411	ENSMUSG00000049659	Aftph	-	aftiphilin	protein-coding
mm_142270.1	chr17	39846897	39846909	-	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	3906	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_142152.1	chr17	36030621	36030653	-	1	NA	exon (NM_010398, exon 5 of 7)	exon (NM_010398, exon 5 of 7)	2064	NM_010398	15040	Mm.439648	NM_010398	ENSMUSG00000067212	H2-T23	37b|37c|H-2T23|H2-Qa1|Qa-1|Qa-1(b)|Qa1|Qed-1|T18c|T18c(37)|T23b|T23d	histocompatibility 2, T region locus 23	protein-coding
mm_65100.1	chr7	19302942	19302952	-	1	NA	3' UTR (NM_008036, exon 4 of 4)	3' UTR (NM_008036, exon 4 of 4)	7098	NM_008036	14282	Mm.248335	NM_008036	ENSMUSG00000003545	Fosb	-	FBJ osteosarcoma oncogene B	protein-coding
mm_56145.1	chr6	87811653	87811667	-	1	NA	5' UTR (NM_001039394, exon 1 of 3)	5' UTR (NM_001039394, exon 1 of 3)	119	NM_001039394	69834	Mm.37380	NM_133717	ENSMUSG00000030055	Rab43	1810048P08Rik|2500004H21Rik|AW490415	RAB43, member RAS oncogene family	protein-coding
mm_151088.1	chr19	47705784	47705806	+	1	NA	Intergenic	Intergenic	-13753	NM_001290825	12821	Mm.1225	NM_007732	ENSMUSG00000025064	Col17a1	BP180|Bpag|Bpag2	collagen, type XVII, alpha 1	protein-coding
mm_103916.1	chr11	83588916	83588928	-	1	NA	exon (NM_009139, exon 4 of 4)	exon (NM_009139, exon 4 of 4)	4165	NM_009139	20305	Mm.137	NM_009139	ENSMUSG00000018927	Ccl6	MRP-1|Scya6|c10	chemokine (C-C motif) ligand 6	protein-coding
mm_12873.1	chr2	84525472	84525475	+	1	NA	Intergenic	Intergenic	-18600	NR_046046	672763	Mm.491046	NR_046046	ENSMUSG00000087362	Gm13710	OTTMUSG00000013441	predicted gene 13710	ncRNA
mm_10806.1	chr2	24349865	24349877	+	1	NA	3' UTR (NM_031167, exon 5 of 5)	3' UTR (NM_031167, exon 5 of 5)	4500	NM_001039701	16181	Mm.882	NM_031167	ENSMUSG00000026981	Il1rn	F630041P17Rik|IL-1ra	interleukin 1 receptor antagonist	protein-coding
mm_141402.1	chr17	29332363	29332405	-	1	NA	3' UTR (NM_019880, exon 12 of 12)	3' UTR (NM_019880, exon 12 of 12)	13502	NM_023734	74116	Mm.30950	NM_023734	ENSMUSG00000024011	Pi16	1200009H11Rik|Cripi|PI-16	peptidase inhibitor 16	protein-coding
mm_154386.1	chrM	11679	11685	+	1	NA	NA	Intergenic	NA	NA								
mm_104734.1	chr11	98329605	98329637	-	1	NA	promoter-TSS (NM_010895)	promoter-TSS (NM_010895)	24	NM_010895	18013	Mm.4814	NM_010895	ENSMUSG00000038255	Neurod2	Ndrf|bHLHa1	neurogenic differentiation 2	protein-coding
mm_100593.1	chr11	120958393	120958426	+	1	NA	3' UTR (NM_001038654, exon 5 of 5)	3' UTR (NM_001038654, exon 5 of 5)	9342	NM_001038654	80879	Mm.28632	NM_030696	ENSMUSG00000025161	Slc16a3	Mct3|Mct4	solute carrier family 16 (monocarboxylic acid transporters), member 3	protein-coding
mm_136049.1	chr16	78576596	78576618	-	1	NA	promoter-TSS (NM_001252440)	promoter-TSS (NM_001252440)	81	NM_001252438	67102	Mm.37332	NM_025967	ENSMUSG00000022864	D16Ertd472e	1700010I10Rik|2310009O17Rik|E330003K22Rik|Eurl	DNA segment, Chr 16, ERATO Doi 472, expressed	protein-coding
mm_43250.1	chr5	130187190	130187203	+	1	NA	promoter-TSS (NM_019983)	promoter-TSS (NM_019983)	16	NM_019983	56715	Mm.288639	NM_019983	ENSMUSG00000025340	Rabgef1	Rab5ef|Rabex5|Rin2	RAB guanine nucleotide exchange factor (GEF) 1	protein-coding
mm_135361.1	chr16	43980256	43980275	-	1	NA	TTS (NM_001172107)	TTS (NM_001172107)	-1215	NM_001007460	332175	Mm.327852	NM_001007460	ENSMUSG00000036304	Zdhhc23	Gm1751|Gm779|nidd	zinc finger, DHHC domain containing 23	protein-coding
mm_63505.1	chr7	127841818	127841847	+	1	NA	promoter-TSS (NM_009294)	promoter-TSS (NM_009294)	24	NM_009294	20909	Mm.24867	NM_009294	ENSMUSG00000030805	Stx4a	Stx4|Syn-4|Syn4	syntaxin 4A (placental)	protein-coding
mm_152916.1	chr19	27762338	27762357	-	1	NA	3' UTR (NM_001166414, exon 18 of 18)	3' UTR (NM_001166414, exon 18 of 18)	220601	NM_001166414	19726	Mm.313321	NM_011265	ENSMUSG00000040929	Rfx3	C230093O12Rik|MRFX3	regulatory factor X, 3 (influences HLA class II expression)	protein-coding
mm_80486.1	chr9	78340489	78340491	+	1	NA	intron (NM_008182, intron 2 of 6)	intron (NM_008182, intron 2 of 6)	6655	NM_008182	14858	Mm.422778	NM_008182	ENSMUSG00000057933	Gsta2	Gst2-2|Gstc-2|Gstc2	glutathione S-transferase, alpha 2 (Yc2)	protein-coding
mm_132312.1	chr16	33725482	33725485	+	1	NA	exon (NM_175256, exon 3 of 15)	exon (NM_175256, exon 3 of 15)	41017	NM_175256	77446	Mm.245741	NM_172934	ENSMUSG00000075254	Heg1	4632417D23Rik|5530401I02Rik|9530025L16Rik|BC038614|Gm629|OTTMUSG00000027315	heart development protein with EGF-like domains 1	protein-coding
mm_130292.1	chr15	97010141	97010160	-	1	NA	exon (NM_027052, exon 8 of 16)	exon (NM_027052, exon 8 of 16)	45806	NM_027052	69354	Mm.250980	NM_027052	ENSMUSG00000022464	Slc38a4	1110012E16Rik|1700012A18Rik|Ata3|mATA3|mNAT3	solute carrier family 38, member 4	protein-coding
mm_8687.1	chr1	157108633	157108664	-	1	NA	promoter-TSS (NM_001305061)	promoter-TSS (NM_001305061)	2	NM_001305059	73435	Mm.116705	NM_028540	ENSMUSG00000026592	Tex35	1700057K13Rik	testis expressed 35	protein-coding
mm_81530.1	chr9	110063013	110063100	+	1	NA	exon (NM_008633, exon 9 of 19)	exon (NM_008633, exon 9 of 19)	11035	NM_001311164	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_148131.1	chr18	75697531	75697583	-	1	NA	5' UTR (NM_201354, exon 1 of 12)	5' UTR (NM_201354, exon 1 of 12)	139	NM_201354	269037	Mm.36745	NM_201354	ENSMUSG00000052928	Ctif	Gm672	CBP80/20-dependent translation initiation factor	protein-coding
mm_102111.1	chr11	53266989	53267016	-	1	NA	exon (NM_008300, exon 14 of 19)	exon (NM_008300, exon 14 of 19)	33477	NM_008300	15525	Mm.239865	NM_008300	ENSMUSG00000020361	Hspa4	70kDa|AI317151|APG-2|Hsp110|Hsp70RY|mKIAA4025	heat shock protein 4	protein-coding
mm_157500.1	chrX	48513445	48513459	-	1	NA	5' UTR (NM_001290364, exon 1 of 16)	5' UTR (NM_001290364, exon 1 of 16)	111	NM_001290364	26926	Mm.240434	NM_012019	ENSMUSG00000036932	Aifm1	AIF|AIFsh2|Hq|Pdcd8	apoptosis-inducing factor, mitochondrion-associated 1	protein-coding
mm_49555.1	chr6	30544886	30544910	+	1	NA	exon (NM_001024698, exon 3 of 11)	exon (NM_001024698, exon 3 of 11)	3256	NM_001024698	232680	Mm.268855	NM_001024698	ENSMUSG00000071553	Cpa2	-	carboxypeptidase A2, pancreatic	protein-coding
mm_28181.1	chr3	88001016	88001043	-	1	NA	promoter-TSS (NM_001109758)	promoter-TSS (NM_001109758)	-673	NM_001109758	12032	Mm.4598	NM_007529	ENSMUSG00000004892	Bcan	Cspg7	brevican	protein-coding
mm_58507.1	chr7	3981154	3981160	+	1	NA	Intergenic	Intergenic	-65656	NR_028115	18726	Mm.440989	NM_011090	ENSMUSG00000030427	Lilra6	7M1|Pira3	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	protein-coding
mm_131280.1	chr16	11077867	11077891	+	1	NA	intron (NM_134105, intron 4 of 4)	intron (NM_134105, intron 4 of 4)	10051	NM_134105	106200	Mm.291015	NM_029582	ENSMUSG00000022498	Txndc11	2810408E11Rik|AI427833|EFP1|Txdc11	thioredoxin domain containing 11	protein-coding
mm_128012.1	chr15	13173661	13173706	-	1	NA	promoter-TSS (NM_007666)	promoter-TSS (NM_007666)	-8	NM_007666	12563	Mm.57048	NM_007666	ENSMUSG00000039385	Cdh6	cad6	cadherin 6	protein-coding
mm_170803.1	chr2	175703677	175703683	-	1	NA	promoter-TSS (NM_001177404)	promoter-TSS (NM_001177404)	18	NM_001177406	100303732	Mm.484983	NM_001177404	ENSMUSG00000095199	Zfp967	Gm14431|OTTMUSG00000016608	zinc finger protein 967	protein-coding
mm_941.1	chr1	56451364	56451373	+	1	NA	Intergenic	Intergenic	186083	NM_027661	71066	Mm.152656	NM_027661	ENSMUSG00000045336	Hsfy2	4933413G11Rik|Hspy2l	heat shock transcription factor, Y-linked 2	protein-coding
mm_79213.1	chr9	49055636	49055682	+	1	NA	promoter-TSS (NM_012039)	promoter-TSS (NM_012039)	78	NM_012039	26951	Mm.24791	NM_012039	ENSMUSG00000032264	Zw10	6330566F14Rik|MmZw10	zw10 kinetochore protein	protein-coding
mm_78098.1	chr9	18645191	18645215	+	1	NA	Intergenic	Intergenic	110430	NM_146606	18322	Mm.246530	NM_146606	ENSMUSG00000054141	Olfr24	MOR132-1|MTPCR51	olfactory receptor 24	protein-coding
mm_69103.1	chr7	127020322	127020336	-	1	NA	5' UTR (NM_001102563, exon 2 of 4)	5' UTR (NM_001102563, exon 2 of 4)	882	NM_001102563	69017	Mm.392047	NM_001102563	ENSMUSG00000045114	Prrt2	1500031I19Rik|AI195361|DSPB3	proline-rich transmembrane protein 2	protein-coding
mm_85353.1	chr9	103211877	103211924	-	1	NA	exon (NM_133977, exon 15 of 17)	exon (NM_133977, exon 15 of 17)	-9835	NM_009275	20818	Mm.273053	NM_009275	ENSMUSG00000032553	Srprb	AA409543	signal recognition particle receptor, B subunit	protein-coding
mm_168546.1	chr1	162740489	162740489	-	1	NA	promoter-TSS (NM_001081290)	promoter-TSS (NM_001081290)	67	NM_001081290	226562	Mm.245446	NM_001081290	ENSMUSG00000040225	Prrc2c	1810043M20Rik|9630039I18Rik|A630006J20|Bat2d|Bat2d1|Bat2l2|E130112L15Rik|Prrc3|mKIAA1096	proline-rich coiled-coil 2C	protein-coding
mm_92012.1	chr10	62342634	62342642	-	1	NA	intron (NR_038038, intron 1 of 1)	intron (NR_038038, intron 1 of 1)	2031	NR_038038	70162	Mm.441212	NR_038038		Hk1os	2210417K05Rik	hexokinase 1, opposite strand	ncRNA
mm_113559.1	chr13	38151434	38151444	+	1	NA	5' UTR (NM_023842, exon 1 of 24)	5' UTR (NM_023842, exon 1 of 24)	145	NM_023842	109620	Mm.355327	NM_023842	ENSMUSG00000054889	Dsp	2300002E22Rik|5730453H04Rik|AA407887|AA407888|AW109828|DP|rul	desmoplakin	protein-coding
mm_53527.1	chr6	136532941	136532976	+	1	NA	intron (NM_019426, intron 1 of 14)	intron (NM_019426, intron 1 of 14)	14107	NM_019426	54343	Mm.173271	NM_019426	ENSMUSG00000030213	Atf7ip	2610204M12Rik|AM|Mcaf1	activating transcription factor 7 interacting protein	protein-coding
mm_81950.1	chr9	120539802	120539864	+	1	NA	promoter-TSS (NM_178676)	promoter-TSS (NM_178676)	15	NM_178676	215446	Mm.76648	NM_178676	ENSMUSG00000041608	Entpd3	Cd39l3|HB6|NTPDase-3	ectonucleoside triphosphate diphosphohydrolase 3	protein-coding
mm_75250.1	chr8	40308395	40308431	-	1	NA	promoter-TSS (NR_106126)	promoter-TSS (NR_106126)	362	NM_030110	78506	Mm.169893	NM_030110	ENSMUSG00000039478	Micu3	2900075B16Rik|Efha2	mitochondrial calcium uptake family, member 3	protein-coding
mm_26662.1	chr3	154707620	154707627	+	1	NA	Intergenic	MLT1J|LTR|ERVL-MaLR	-3510	NM_175176	209601	Mm.331454	NM_175176	ENSMUSG00000078161	Erich3	1700013E18Rik|4922501L14Rik|5031409G23Rik|AI596448|Gm133	glutamate rich 3	protein-coding
mm_73218.1	chr8	97163765	97163783	+	1	NA	Intergenic	Intergenic	-617801	NR_039538	100628567		NR_039538	ENSMUSG00000104794	Mir28c	mmu-mir-28c	microRNA 28c	ncRNA
mm_88717.1	chr10	80158039	80158060	+	1	NA	3' UTR (NM_001305798, exon 8 of 8)	3' UTR (NM_001305798, exon 8 of 8)	8367	NM_001305799	59090	Mm.143813	NM_021565	ENSMUSG00000035621	Midn	3000003C15Rik	midnolin	protein-coding
mm_139616.1	chr17	57361693	57361701	+	1	NA	exon (NM_010130, exon 2 of 22)	exon (NM_010130, exon 2 of 22)	3011	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_91818.1	chr10	55215180	55215181	-	1	NA	Intergenic	Intergenic	-891737	NM_001163833	73390	Mm.181475	NM_133751	ENSMUSG00000047669	Msl3l2	1700060H10Rik	male-specific lethal 3-like 2 (Drosophila)	protein-coding
mm_110988.1	chr12	77134336	77134356	-	1	NA	Intergenic	RLTR30D2_MM|LTR|ERV1	-103758	NM_001252614	53618	Mm.35628	NM_016893	ENSMUSG00000021065	Fut8	-	fucosyltransferase 8	protein-coding
mm_72365.1	chr8	80859374	80859384	+	1	NA	intron (NM_021356, intron 1 of 9)	intron (NM_021356, intron 1 of 9)	21100	NM_021356	14388	Mm.277409	NM_021356	ENSMUSG00000031714	Gab1	AA408973|AW107238	growth factor receptor bound protein 2-associated protein 1	protein-coding
mm_164781.1	chr18	5671157	5671159	+	1	NA	intron (NM_011546, intron 1 of 7)	L1_Mus3|LINE|L1	-78721	NR_033552	791318	Mm.84339	NR_033552	ENSMUSG00000063087	Gm10125	ENSMUSG00000063087|Zeb1os	predicted gene 10125	ncRNA
mm_86517.1	chr10	7709033	7709070	+	1	NA	intron (NM_010690, intron 5 of 7)	B4A|SINE|B4	-16949	NM_011835	23924	Mm.28127	NM_011835	ENSMUSG00000019794	Katna1	-	katanin p60 (ATPase-containing) subunit A1	protein-coding
mm_96099.1	chr11	60454588	60454657	+	1	NA	promoter-TSS (NM_021354)	promoter-TSS (NM_021354)	5	NM_021354	13495	Mm.41803	NM_021354	ENSMUSG00000020537	Drg2	AI255295|AI461605	developmentally regulated GTP binding protein 2	protein-coding
mm_69296.1	chr7	128271679	128271719	-	1	NA	3' UTR (NM_145590, exon 13 of 13)	3' UTR (NM_145590, exon 13 of 13)	6002	NM_133254	246787	Mm.38870	NM_133254	ENSMUSG00000030781	Slc5a2	Sglt2	solute carrier family 5 (sodium/glucose cotransporter), member 2	protein-coding
mm_12249.1	chr2	68891383	68891386	+	1	NA	intron (NM_172856, intron 1 of 9)	AT_rich|Low_complexity|Low_complexity	29943	NM_001347161	241447	Mm.222222	NM_172856	ENSMUSG00000027035	Cers6	4732462C07Rik|AW544719|Lass6|T1L	ceramide synthase 6	protein-coding
mm_136263.1	chr16	91028842	91028845	-	1	NA	intron (NM_026110, intron 8 of 17)	intron (NM_026110, intron 8 of 17)	15536	NM_026110	67367	Mm.347	NM_026110	ENSMUSG00000022974	Paxbp1	1810007M14Rik|C21orf66|Gcfc|Gcfc1|Pax3/7bp	PAX3 and PAX7 binding protein 1	protein-coding
mm_154430.1	chrM	631	641	-	1	NA	NA	Intergenic	NA	NA								
mm_33070.1	chr4	123630252	123630256	+	1	NA	intron (NM_001199136, intron 1 of 97)	intron (NM_001199136, intron 1 of 97)	13834	NR_105824	102465214		NR_105824	ENSMUSG00000099005	Mir6398	Gm27657|mmu-mir-6398	microRNA 6398	ncRNA
mm_86351.1	chr9	123632529	123632543	-	1	NA	promoter-TSS (NM_011731)	promoter-TSS (NM_011731)	29	NM_011731	22599	Mm.41963	NM_011731	ENSMUSG00000025243	Slc6a20b	AA986306|Sit1|Slc6a20|XT3|Xtrp3	solute carrier family 6 (neurotransmitter transporter), member 20B	protein-coding
mm_43711.1	chr5	139380633	139380707	+	1	NA	promoter-TSS (NM_030258)	promoter-TSS (NM_030258)	3	NM_030258	80290	Mm.270003	NM_030258	ENSMUSG00000044197	Gpr146	BC003323|PGR8	G protein-coupled receptor 146	protein-coding
mm_38451.1	chr4	140246752	140246793	-	1	NA	promoter-TSS (NM_198610)	promoter-TSS (NM_198610)	39	NM_198610	230868	Mm.298731	NM_198610	ENSMUSG00000040972	Igsf21	BC055811|Gm141	immunoglobulin superfamily, member 21	protein-coding
mm_10007.1	chr1	191575551	191575557	-	1	NA	promoter-TSS (NM_178632)	promoter-TSS (NM_178632)	-10	NM_029766	76843	Mm.189102	NM_029766	ENSMUSG00000037474	Dtl	2810047L02Rik|5730564G15Rik|L2dtl|Ramp	denticleless E3 ubiquitin protein ligase	protein-coding
mm_150386.1	chr19	36348471	36348500	+	1	NA	Intergenic	Intergenic	-30582	NM_029508	76073	Mm.259180	NM_029508	ENSMUSG00000024805	Pcgf5	0610009F02Rik|1110054A01Rik|5830406C17Rik|5830443C21Rik|9530023M17Rik|AI324127	polycomb group ring finger 5	protein-coding
mm_96180.1	chr11	61653260	61653353	+	1	NA	promoter-TSS (NM_027817)	promoter-TSS (NM_027817)	-15	NM_027817	71520	Mm.202760	NM_027817	ENSMUSG00000004837	Grap	8430435N19Rik|BB233594	GRB2-related adaptor protein	protein-coding
mm_141290.1	chr17	28067088	28067097	-	1	NA	exon (NM_013687, exon 10 of 10)	exon (NM_013687, exon 10 of 10)	13492	NM_013687	21463	Mm.29758	NM_013687	ENSMUSG00000062859	Tcp11	D17Ken1|Tcp-11	t-complex protein 11	protein-coding
mm_101088.1	chr11	11836260	11836276	-	1	NA	intron (NM_001190448, intron 8 of 14)	intron (NM_001190448, intron 8 of 14)	-27306	NM_001163360	60530	Mm.236114	NM_021891	ENSMUSG00000035455	Fignl1	-	fidgetin-like 1	protein-coding
mm_141410.1	chr17	29398116	29398146	-	1	NA	Intergenic	Intergenic	37217	NM_001159538	26382	Mm.279187	NM_013710	ENSMUSG00000024013	Fgd2	Tcd-2|Tcd2|ZFYVE4|tcs-2|tcs2	FYVE, RhoGEF and PH domain containing 2	protein-coding
mm_85036.1	chr9	88522877	88522895	-	1	NA	promoter-TSS (NR_040721)	promoter-TSS (NR_040721)	11	NR_040721	72655	Mm.21798	NR_040721	ENSMUSG00000097195	Snhg5	2810026P18Rik|4933428I09Rik|mU50HG-b	small nucleolar RNA host gene 5	ncRNA
mm_99617.1	chr11	104608027	104608037	+	1	NA	promoter-TSS (NM_016780)	promoter-TSS (NM_016780)	32	NM_016780	16416	Mm.87150	NM_016780	ENSMUSG00000020689	Itgb3	CD61|GP3A|INGRB3	integrin beta 3	protein-coding
mm_121209.1	chr14	103053857	103053865	+	1	NA	intron (NM_008392, intron 4 of 4)	intron (NM_008392, intron 4 of 4)	6849	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_13472.1	chr2	105682729	105682745	+	1	NA	intron (NM_001310146, intron 1 of 9)	intron (NM_001310146, intron 1 of 9)	274	NM_001310145	18508	Mm.3608	NM_013627	ENSMUSG00000027168	Pax6	1500038E17Rik|AEY11|Dey|Gsfaey11|Pax-6|Sey	paired box 6	protein-coding
mm_123044.1	chr14	55590919	55590969	-	1	NA	promoter-TSS (NM_011190)	promoter-TSS (NM_011190)	77	NM_011190	19188	Mm.371573	NM_011190	ENSMUSG00000079197	Psme2	AA589371|AI788882|PA28b	proteasome (prosome, macropain) activator subunit 2 (PA28 beta)	protein-coding
mm_83883.1	chr9	55410560	55410563	-	1	NA	intron (NM_172923, intron 5 of 10)	MT2A|LTR|ERVL	83612	NM_172923	244886	Mm.24361	NM_172923	ENSMUSG00000032313	Tmem266	9630029F15|AI118078|HVRP1	transmembrane protein 266	protein-coding
mm_107081.1	chr12	17266572	17266601	+	1	NA	promoter-TSS (NM_027959)	promoter-TSS (NM_027959)	-9	NM_027959	71853	Mm.222825	NM_027959	ENSMUSG00000020571	Pdia6	1700015E05Rik|AL023058|C77895|CaBP5|P5|Txndc7	protein disulfide isomerase associated 6	protein-coding
mm_81095.1	chr9	106374208	106374219	+	1	NA	3' UTR (NM_153459, exon 3 of 3)	3' UTR (NM_153459, exon 3 of 3)	5581	NM_153459	235584	Mm.275584	NM_153459	ENSMUSG00000053716	Dusp7	AU015694|Mkpx|Pyst2	dual specificity phosphatase 7	protein-coding
mm_146037.1	chr18	69550390	69550397	+	1	NA	intron (NM_013685, intron 6 of 19)	RMER4A|LTR|ERVK	204672	NM_001083967	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding
mm_133916.1	chr16	97557912	97557922	+	1	NA	intron (NM_013606, intron 12 of 13)	MTEb|LTR|ERVL-MaLR	21834	NM_013606	17858	Mm.14157	NM_013606	ENSMUSG00000023341	Mx2	AI528743|Mx-2	MX dynamin-like GTPase 2	protein-coding
mm_156925.1	chrX	169267590	169267594	+	1	NA	intron (NR_109847, intron 9 of 14)	AT_rich|Low_complexity|Low_complexity	52780	NM_001331050	15159	Mm.284033	NM_008222	ENSMUSG00000031352	Hccs	-	holocytochrome c synthetase	protein-coding
mm_24517.1	chr3	92690954	92690964	+	1	NA	Intergenic	T-rich|Low_complexity|Low_complexity	-3749	NM_027137	69611	Mm.176243	NM_027137	ENSMUSG00000103243	Lce1d	2310037L11Rik|AI415320|Sprrl7	late cornified envelope 1D	protein-coding
mm_31820.1	chr4	66841893	66841909	+	1	NA	3' UTR (NM_021297, exon 3 of 3)	3' UTR (NM_021297, exon 3 of 3)	14350	NM_021297	21898	Mm.38049	NM_021297	ENSMUSG00000039005	Tlr4	Lps|Ly87|Ran/M1|Rasl2-8	toll-like receptor 4	protein-coding
mm_137816.1	chr17	30077507	30077516	+	1	NA	intron (NM_148926, intron 2 of 4)	B2_Mm2|SINE|B2	72424	NM_148926	21769	Mm.220972	NM_148926	ENSMUSG00000044477	Zfand3	AW539211|TEG-27|Tex27	zinc finger, AN1-type domain 3	protein-coding
mm_97182.1	chr11	75550133	75550155	+	1	NA	intron (NM_173388, intron 5 of 13)	intron (NM_173388, intron 5 of 13)	-1285	NR_039553	100628624		NR_039553	ENSMUSG00000093100	Mir3971	mmu-mir-3971|mu-mir-3971	microRNA 3971	ncRNA
mm_50659.1	chr6	51470634	51470673	+	1	NA	promoter-TSS (NM_007624)	promoter-TSS (NM_007624)	37	NM_007624	12417	Mm.280968	NM_007624	ENSMUSG00000029836	Cbx3	HP1g|M32	chromobox 3	protein-coding
mm_138109.1	chr17	34121412	34121433	+	1	NA	intron (NM_001204973, intron 1 of 12)	CpG-6274	325	NM_010238	14312	Mm.3444	NM_010238	ENSMUSG00000024335	Brd2	AW228947|D17H6S113E|Frg-1|Fsrg-1|Fsrg1|Nat|Ring3|Rnf3|mKIAA4005	bromodomain containing 2	protein-coding
mm_109747.1	chr12	117626358	117626385	+	1	NA	intron (NM_175930, intron 9 of 27)	intron (NM_175930, intron 9 of 27)	109892	NM_175930	217944	Mm.227642	NM_175930	ENSMUSG00000041992	Rapgef5	4932413M22|C86120|D030051B22Rik|GFR|Mrgef|mKIAA0277|mmr-gef	Rap guanine nucleotide exchange factor (GEF) 5	protein-coding
mm_30838.1	chr4	22486941	22486952	+	1	NA	exon (NM_008899, exon 1 of 1)	exon (NM_008899, exon 1 of 1)	1420	NM_008899	18992	Mm.129387	NM_008899	ENSMUSG00000095139	Pou3f2	9430075J19Rik|A230098E07Rik|Brn-2|Brn2|OTF-7|Otf7|oct-7	POU domain, class 3, transcription factor 2	protein-coding
mm_106820.1	chr12	7983915	7983934	+	1	NA	exon (NM_009693, exon 6 of 29)	exon (NM_009693, exon 6 of 29)	6247	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_136970.1	chr17	15735759	15735807	+	1	NA	exon (NM_007690, exon 12 of 36)	exon (NM_007690, exon 12 of 36)	30816	NM_007690	12648	Mm.8137	NM_007690	ENSMUSG00000023852	Chd1	4930525N21Rik|AI851787|AW555109	chromodomain helicase DNA binding protein 1	protein-coding
mm_92371.1	chr10	76110957	76110962	-	1	NA	promoter-TSS (NM_023219)	promoter-TSS (NM_023219)	59	NM_023219	64454	Mm.155678	NM_023219	ENSMUSG00000020226	Slc5a4b	2010104G07Rik|SAAT1|SGLT3-b|SGLT3b|pSGLT2	solute carrier family 5 (neutral amino acid transporters, system A), member 4b	protein-coding
mm_74600.1	chr8	11635746	11635765	-	1	NA	promoter-TSS (NM_001167967)	promoter-TSS (NM_001167967)	2	NM_133971	102334	Mm.12459	NM_133971	ENSMUSG00000031508	Ankrd10	4833425P12Rik|AW549277	ankyrin repeat domain 10	protein-coding
mm_112172.1	chr12	113421116	113421132	-	1	NA	Intergenic	Intergenic	-68441	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_62895.1	chr7	116093340	116093372	+	1	NA	promoter-TSS (NM_019772)	promoter-TSS (NM_019772)	-24	NM_019772	56372	Mm.24231	NM_019772	ENSMUSG00000030663	1110004F10Rik	Smacp|Smap|sid2057|sid2057p	RIKEN cDNA 1110004F10 gene	protein-coding
mm_107288.1	chr12	29937977	29937987	+	1	NA	promoter-TSS (NM_181395)	promoter-TSS (NM_181395)	-54	NM_181395	69675	Mm.251774	NM_181395	ENSMUSG00000020674	Pxdn	2310075M15Rik|C85409|E330004E07|VPO1|mKIAA0230	peroxidasin	protein-coding
mm_157875.1	chrX	75673330	75673350	-	1	NA	Intergenic	Intergenic	91359	NR_029443	74396	Mm.162493	NR_029443	ENSMUSG00000087396	4933407K13Rik	A130080L05Rik	RIKEN cDNA 4933407K13 gene	ncRNA
mm_159506.1	chr4	47057253	47057253	-	1	NA	promoter-TSS (NM_001024136)	promoter-TSS (NM_001024136)	53	NM_001024136	75691	Mm.86866	NM_001024136	ENSMUSG00000066191	Anks6	2210417J20Rik|Ankrd14|Gm635|SamCystin|Samd6|b2b1801.1Clo	ankyrin repeat and sterile alpha motif domain containing 6	protein-coding
mm_37560.1	chr4	126195158	126195162	-	1	NA	intron (NM_146153, intron 1 of 10)	intron (NM_146153, intron 1 of 10)	7550	NM_146153	230753	Mm.29813	NM_146153	ENSMUSG00000043962	Thrap3	9330151F09Rik|B230333E16Rik|Trap150	thyroid hormone receptor associated protein 3	protein-coding
mm_51137.1	chr6	68939557	68939585	+	1	NA	Intergenic	Intergenic	387603	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_98159.1	chr11	87662619	87662680	+	1	NA	promoter-TSS (NM_172448)	promoter-TSS (NM_172448)	-438	NM_172448	207742	Mm.440230	NM_172448	ENSMUSG00000034177	Rnf43	4732452J19Rik	ring finger protein 43	protein-coding
mm_132328.1	chr16	33799494	33799508	+	1	NA	exon (NM_010739, exon 3 of 13)	exon (NM_010739, exon 3 of 13)	5464	NM_010739	17063	Mm.3177	NM_010739	ENSMUSG00000022824	Muc13	114/A10|14/A10|AI159736|Lrrp|Ly64|NJ-1	mucin 13, epithelial transmembrane	protein-coding
mm_165849.1	chr4	8843036	8843038	+	1	NA	intron (NM_001277149, intron 19 of 37)	L1MA5A|LINE|L1	152631	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_100207.1	chr11	116852486	116852574	+	1	NA	intron (NM_011358, intron 1 of 2)	CpG	564	NM_011358	20382	Mm.21841	NM_011358	ENSMUSG00000034120	Srsf2	D11Wsu175e|MRF-1|Pr264|SC35|Sfrs10|Sfrs2	serine/arginine-rich splicing factor 2	protein-coding
mm_136062.1	chr16	84621565	84621570	-	1	NA	Intergenic	Intergenic	-58222	NR_040537	78023	Mm.243853	NR_040537		4930529L06Rik	-	RIKEN cDNA 4930529L06 gene	ncRNA
mm_127459.1	chr15	101272158	101272166	+	1	NA	exon (NM_010444, exon 4 of 7)	exon (NM_010444, exon 4 of 7)	5316	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_136356.1	chr16	92762163	92762173	-	1	NA	intron (NM_001111022, intron 2 of 6)	intron (NM_001111022, intron 2 of 6)	63906	NM_001111021	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_9357.1	chr1	172197889	172197911	-	1	NA	3' UTR (NM_001329871, exon 4 of 4)	3' UTR (NM_001329871, exon 4 of 4)	8904	NM_001329871	18611	Mm.544	NM_011063	ENSMUSG00000013698	Pea15a	Mat1|PEA-15|Pea15|Pkcs15	phosphoprotein enriched in astrocytes 15A	protein-coding
mm_139062.1	chr17	46496754	46496809	+	1	NA	promoter-TSS (NM_207161)	promoter-TSS (NM_207161)	-8	NM_207161	381101	Mm.35801	NM_207161	ENSMUSG00000040658	Dnph1	C76683|Rcl	2'-deoxynucleoside 5'-phosphate N-hydrolase 1	protein-coding
mm_93647.1	chr10	117361047	117361063	-	1	NA	exon (NM_001013391, exon 6 of 10)	exon (NM_001013391, exon 6 of 10)	15918	NM_001013391	432508	Mm.478881	NM_001013391	ENSMUSG00000055531	Cpsf6	4733401N12Rik|AI256641|CFIM|CFIM68|HPBRII-4|HPBRII-7	cleavage and polyadenylation specific factor 6	protein-coding
mm_119091.1	chr14	30892339	30892357	+	1	NA	exon (NM_001289633, exon 10 of 22)	exon (NM_001289633, exon 10 of 22)	5872	NM_001289632	16427	Mm.34819	NM_018746	ENSMUSG00000021922	Itih4	ITI-HC4|Itih-4|PK-120	inter alpha-trypsin inhibitor, heavy chain 4	protein-coding
mm_91930.1	chr10	60380223	60380232	-	1	NA	intron (NR_045556, intron 33 of 68)	intron (NR_045556, intron 33 of 68)	-19499	NM_001164374	100302688	Mm.444135	NM_001164374	ENSMUSG00000090439	Gm17455	-	predicted gene, 17455	protein-coding
mm_51673.1	chr6	86405878	86405882	+	1	NA	intron (NM_001164079, intron 1 of 9)	ID_B1|SINE|B4	1661	NM_001164078	21841	Mm.333219	NM_011585	ENSMUSG00000071337	Tia1	2310050N03Rik|AI256674|TIA-1|mTIA-1	cytotoxic granule-associated RNA binding protein 1	protein-coding
mm_51198.1	chr6	71284299	71284319	+	1	NA	exon (NM_145568, exon 4 of 4)	exon (NM_145568, exon 4 of 4)	12290	NM_145568	57896	Mm.250569	NM_145568	ENSMUSG00000053012	Krcc1	AA792894	lysine-rich coiled-coil 1	protein-coding
mm_39196.1	chr4	156013735	156013747	-	1	NA	promoter-TSS (NM_011659)	promoter-TSS (NM_011659)	46	NM_011659	22163	Mm.13885	NM_011659	ENSMUSG00000029075	Tnfrsf4	ACT35|CD134|Ly-70|Ox40|TXGP1L|Txgp1	tumor necrosis factor receptor superfamily, member 4	protein-coding
mm_148918.1	chr19	6976374	6976384	+	1	NA	intron (NM_008889, intron 1 of 3)	intron (NM_008889, intron 1 of 3)	1331	NM_008889	18938	Mm.140	NM_008889	ENSMUSG00000056612	Ppp1r14b	AOM172|PHI-1|PLCB3N|Png	protein phosphatase 1, regulatory (inhibitor) subunit 14B	protein-coding
mm_141103.1	chr17	26021743	26021757	-	1	NA	5' UTR (NM_153140, exon 1 of 12)	5' UTR (NM_153140, exon 1 of 12)	110	NM_153140	215445	Mm.41191	NM_153140	ENSMUSG00000037098	Rab11fip3	Cart1|D030060O14Rik|Rab11-FIP3|mKIAA0665	RAB11 family interacting protein 3 (class II)	protein-coding
mm_168508.1	chr1	156366036	156366036	+	1	NA	intron (NM_001198597, intron 10 of 10)	RLTR28|LTR|ERVL	33954	NM_001198597	77352	Mm.428709	NM_001033180	ENSMUSG00000026601	Axdnd1	9430070O13Rik|Gm979	axonemal dynein light chain domain containing 1	protein-coding
mm_44059.1	chr5	148265266	148265305	+	1	NA	intron (NM_029920, intron 7 of 14)	intron (NM_029920, intron 7 of 14)	127530	NM_001301424	11987	Mm.275489	NM_007513	ENSMUSG00000041313	Slc7a1	4831426K01Rik|AI447493|Atrc-1|Atrc1|Cat1|Rec-1|Rev-1|mCAT-1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 1	protein-coding
mm_111601.1	chr12	102302406	102302415	-	1	NA	intron (NM_001161365, intron 1 of 9)	intron (NM_001161365, intron 1 of 9)	18769	NM_001161365	217835	Mm.24145	NM_177620	ENSMUSG00000044456	Rin3	6430500K07|C86933	Ras and Rab interactor 3	protein-coding
mm_112852.1	chr13	20836200	20836210	+	1	NA	intron (NM_012054, intron 2 of 20)	intron (NM_012054, intron 2 of 20)	42092	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_48074.1	chr5	136623124	136623141	-	1	NA	Intergenic	Intergenic	-55642	NM_001291238	13047	Mm.320317	NM_009986	ENSMUSG00000029705	Cux1	CDP|Cutl1|Cux|Cux-1	cut-like homeobox 1	protein-coding
mm_147813.1	chr18	61725426	61725468	-	1	NA	promoter-TSS (NR_029432)	promoter-TSS (NR_029432)	884	NM_021296	17714	Mm.269657	NM_021296	ENSMUSG00000024580	Grpel2	mt-GrpE#2|mt-Grpel2	GrpE-like 2, mitochondrial	protein-coding
mm_107398.1	chr12	33333154	33333155	+	1	NA	intron (NM_001033436, intron 2 of 7)	intron (NM_001033436, intron 2 of 7)	30639	NM_001033436	380753	Mm.41540	NM_028139	ENSMUSG00000020564	Atxn7l1	2810423G08Rik|Atxn7l4	ataxin 7-like 1	protein-coding
mm_147222.1	chr18	38192122	38192128	-	1	NA	Intergenic	Intergenic	17637	NM_029357	75599	Mm.36560	NM_029357	ENSMUSG00000051375	Pcdh1	2010005A06Rik|AI585920	protocadherin 1	protein-coding
mm_42986.1	chr5	123302403	123302411	+	1	NA	Intergenic	Intergenic	-42041	NM_029850	77045	Mm.151960	NM_029850	ENSMUSG00000029438	Bcl7a	4432415N06Rik|AI448316	B cell CLL/lymphoma 7A	protein-coding
mm_34211.1	chr4	140961373	140961402	+	1	NA	5' UTR (NM_023374, exon 1 of 8)	5' UTR (NM_023374, exon 1 of 8)	116	NM_023374	67680	Mm.246965	NM_023374	ENSMUSG00000009863	Sdhb	0710008N11Rik	succinate dehydrogenase complex, subunit B, iron sulfur (Ip)	protein-coding
mm_123636.1	chr14	68533823	68533825	-	1	NA	promoter-TSS (NM_007402)	promoter-TSS (NM_007402)	-135	NM_007402	11500	Mm.261495	NM_007402	ENSMUSG00000022056	Adam7	ADAM 7|EAP1|EAPI	a disintegrin and metallopeptidase domain 7	protein-coding
mm_67304.1	chr7	79386786	79386796	-	1	NA	5' UTR (NM_020599, exon 1 of 9)	5' UTR (NM_020599, exon 1 of 9)	236	NM_020599	19771	Mm.41653	NM_020599	ENSMUSG00000039194	Rlbp1	3110056M11Rik|CRALBP	retinaldehyde binding protein 1	protein-coding
mm_120022.1	chr14	55765835	55765867	+	1	NA	promoter-TSS (NM_008519)	promoter-TSS (NM_008519)	-111	NM_008519	16995	Mm.20853	NM_008519	ENSMUSG00000046908	Ltb4r1	BLT1|BLTR|Ltb4r|mBLTR	leukotriene B4 receptor 1	protein-coding
mm_124848.1	chr15	9524330	9524340	+	1	NA	intron (NM_008372, intron 2 of 7)	intron (NM_008372, intron 2 of 7)	5541	NM_008372	16197	Mm.389	NM_008372	ENSMUSG00000003882	Il7r	CD127|IL-7Ralpha	interleukin 7 receptor	protein-coding
mm_71595.1	chr8	54955141	54955183	+	1	NA	5' UTR (NM_153581, exon 1 of 7)	5' UTR (NM_153581, exon 1 of 7)	434	NM_001253756	234267	Mm.241700	NM_153581	ENSMUSG00000031517	Gpm6a	Gpm6|M6A	glycoprotein m6a	protein-coding
mm_158431.1	chrX	139871616	139871630	-	1	NA	promoter-TSS (NM_001193309)	promoter-TSS (NM_001193309)	31	NM_029413	75746	Mm.23269	NM_029413	ENSMUSG00000031434	Morc4	1600017G11Rik|5630401M14Rik|AA117449|Zcwcc2	microrchidia 4	protein-coding
mm_153060.1	chr19	32182184	32182194	-	1	NA	intron (NM_001168525, intron 5 of 9)	intron (NM_001168525, intron 5 of 9)	28824	NM_001168526	208449	Mm.329810	NM_144792	ENSMUSG00000040451	Sgms1	9530058O11Rik|AI841905|C80702|Mob|Sms1|Sor1|Tmem23	sphingomyelin synthase 1	protein-coding
mm_71538.1	chr8	47094808	47094816	+	1	NA	3' UTR (NM_177304, exon 8 of 8)	3' UTR (NM_177304, exon 8 of 8)	107925	NM_177304	320981	Mm.211429	NM_177304	ENSMUSG00000038173	Enpp6	4833421B01Rik|B830047L21Rik|D8Ertd514e|E-NPP 6|GPC-Cpde|Npp6	ectonucleotide pyrophosphatase/phosphodiesterase 6	protein-coding
mm_48334.1	chr5	139129663	139129752	-	1	NA	promoter-TSS (NM_008923)	promoter-TSS (NM_008923)	45	NM_008923	19085	Mm.306163	NM_008923	ENSMUSG00000025855	Prkar1b	AI385716|RIbeta	protein kinase, cAMP dependent regulatory, type I beta	protein-coding
mm_106245.1	chr11	117782207	117782221	-	1	NA	promoter-TSS (NM_181856)	promoter-TSS (NM_181856)	-83	NM_001195090	217356	Mm.116675	NM_181856	ENSMUSG00000050106	Tmc8	EVIN2|Ever2|mFLJ00400	transmembrane channel-like gene family 8	protein-coding
mm_139688.1	chr17	57420842	57420862	+	1	NA	intron (NM_010130, intron 12 of 21)	intron (NM_010130, intron 12 of 21)	62166	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_111800.1	chr12	104998683	104998710	-	1	NA	promoter-TSS (NM_001042699)	promoter-TSS (NM_001042699)	-19	NM_001042699	212073	Mm.212688	NM_172500	ENSMUSG00000054150	Syne3	nesprin-3	spectrin repeat containing, nuclear envelope family member 3	protein-coding
mm_168014.1	chrY	57896555	57896590	-	1	NA	Intergenic	Intergenic	-362846	NM_001017393	434935	Mm.426195	NM_001017393	ENSMUSG00000096122	Gm21943	-	predicted gene, 21943	protein-coding
mm_47878.1	chr5	134703016	134703025	-	1	NA	3' UTR (NM_007925, exon 37 of 37)	3' UTR (NM_007925, exon 37 of 37)	-14430	NM_010717	16885	Mm.15409	NM_010717	ENSMUSG00000029674	Limk1	KIZ-1|LIMK-1|Limk	LIM-domain containing, protein kinase	protein-coding
mm_148051.1	chr18	71741563	71741572	-	1	NA	intron (NM_007831, intron 5 of 28)	RMER15|LTR|ERVL	609502	NM_007831	13176	Mm.167882	NM_007831	ENSMUSG00000060534	Dcc	C030036D22Rik|Igdcc1	deleted in colorectal carcinoma	protein-coding
mm_8666.1	chr1	156656508	156656533	-	1	NA	exon (NM_023141, exon 5 of 6)	exon (NM_023141, exon 5 of 6)	17819	NM_023141	30935	Mm.206737	NM_023141	ENSMUSG00000060519	Tor3a	Adir	torsin family 3, member A	protein-coding
mm_32845.1	chr4	117849362	117849375	+	1	NA	intron (NM_008135, intron 2 of 13)	intron (NM_008135, intron 2 of 13)	14110	NM_008135	14664	Mm.244549	NM_008135	ENSMUSG00000028542	Slc6a9	Glyt-1|Glyt1	solute carrier family 6 (neurotransmitter transporter, glycine), member 9	protein-coding
mm_173079.1	chrX	141747866	141747867	-	1	NA	Intergenic	Intergenic	-22649	NM_010572	16370	Mm.261591	NM_010572	ENSMUSG00000054667	Irs4	IRS-4	insulin receptor substrate 4	protein-coding
mm_52510.1	chr6	115361215	115361223	+	1	NA	promoter-TSS (NM_001308352)	promoter-TSS (NM_001308352)	75	NM_001308352	19016	Mm.3020	NM_011146	ENSMUSG00000000440	Pparg	Nr1c3|PPAR-gamma|PPAR-gamma2|PPARgamma|PPARgamma2	peroxisome proliferator activated receptor gamma	protein-coding
mm_82068.1	chr9	122873925	122873930	+	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	-7921	NM_173364	235682	Mm.326477	NM_173364	ENSMUSG00000047036	Zfp445	AW610627|ZNF168|Znf445|mszf29|mszf50	zinc finger protein 445	protein-coding
mm_80038.1	chr9	68969129	68969141	+	1	NA	intron (NM_013646, intron 1 of 10)	MTE2b|LTR|ERVL-MaLR	203789	NR_033299	320440	Mm.483129	NM_177159		9530091C08Rik	-	RIKEN cDNA 9530091C08 gene	ncRNA
mm_104672.1	chr11	97663570	97663578	-	1	NA	exon (NM_139311, exon 1 of 20)	exon (NM_139311, exon 1 of 20)	162	NM_139311	246198	Mm.23685	NM_139311	ENSMUSG00000038437	Mllt6	AI315037|Af17	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 6	protein-coding
mm_109790.1	chr12	3249747	3249828	-	1	NA	exon (NM_016676, exon 6 of 6)	exon (NM_016676, exon 6 of 6)	13996	NR_015551	74173	Mm.309774	NM_028796	ENSMUSG00000079179	Rab10os	1700012B15Rik|1810036A22Rik	RAB10, member RAS oncogene family, opposite strand	ncRNA
mm_75696.1	chr8	68212099	68212115	-	1	NA	Intergenic	Intergenic	-64421	NM_028182	72281	Mm.40974	NM_028182	ENSMUSG00000053886	Sh2d4a	2210402M20Rik|SH2A	SH2 domain containing 4A	protein-coding
mm_141440.1	chr17	29658338	29658352	-	1	NA	intron (NR_132314, intron 7 of 27)	intron (NR_132314, intron 7 of 27)	-2250	NM_028791	74157	Mm.390979	NM_028791	ENSMUSG00000024019	Cmtr1	1300018I05Rik|AI451264|Ftsjd2|MTr1	cap methyltransferase 1	protein-coding
mm_68500.1	chr7	111079317	111079337	-	1	NA	exon (NM_013507, exon 5 of 22)	exon (NM_013507, exon 5 of 22)	3703	NM_001040131	13690	Mm.185453	NM_013507	ENSMUSG00000005610	Eif4g2	DAP-5|E130105L11Rik|Nat1|Natm1|p97	eukaryotic translation initiation factor 4, gamma 2	protein-coding
mm_148004.1	chr18	67774682	67774704	-	1	NA	promoter-TSS (NM_001039088)	promoter-TSS (NM_001039088)	-183	NM_028112	72124	Mm.307315	NM_028112	ENSMUSG00000079614	Seh1l	2610007A16Rik|AW540070|SEC13L|SEH1A|SEH1B|Seh1	SEH1-like (S. cerevisiae	protein-coding
mm_6701.1	chr1	80758692	80758709	-	1	NA	promoter-TSS (NM_175291)	promoter-TSS (NM_175291)	-147	NM_175291	210293	Mm.133473	NM_175291	ENSMUSG00000038608	Dock10	9330153B10Rik|A630054M16Rik|Jr4|Jr5|R75174|ZIZ3|Zizimin3|mKIAA0694	dedicator of cytokinesis 10	protein-coding
mm_95112.1	chr11	34075237	34075266	+	1	NA	exon (NM_010696, exon 10 of 21)	exon (NM_010696, exon 10 of 21)	28050	NM_010696	16822	Mm.265350	NM_010696	ENSMUSG00000002699	Lcp2	AI323664|BB161688|SLP-76|SLP76|m1Khoe|twm	lymphocyte cytosolic protein 2	protein-coding
mm_154832.1	chrX	18162693	18162701	+	1	NA	5' UTR (NM_009483, exon 1 of 29)	5' UTR (NM_009483, exon 1 of 29)	122	NM_001310444	22289	Mm.257498	NM_009483	ENSMUSG00000037369	Kdm6a	Utx	lysine (K)-specific demethylase 6A	protein-coding
mm_85849.1	chr9	110654067	110654081	-	1	NA	promoter-TSS (NM_183276)	promoter-TSS (NM_183276)	87	NM_183276	235627	Mm.335481	NM_183276	ENSMUSG00000056724	Nbeal2	1110014F23Rik|BC042396|mKIAA0540	neurobeachin-like 2	protein-coding
mm_42585.1	chr5	117319293	117319326	+	1	NA	promoter-TSS (NM_001033311)	promoter-TSS (NM_001033311)	43	NM_001033311	231668	Mm.298603	NM_001033311	ENSMUSG00000066894	Vsig10	-	V-set and immunoglobulin domain containing 10	protein-coding
mm_21340.1	chr2	157107537	157107554	-	1	NA	exon (NM_001139520, exon 12 of 17)	exon (NM_001139520, exon 12 of 17)	20490	NM_001177439	383766	Mm.480305	NM_001177439	ENSMUSG00000074628	Tldc2	Gm1332	TBC/LysM associated domain containing 2	protein-coding
mm_38224.1	chr4	135987157	135987179	-	1	NA	promoter-TSS (NM_025411)	promoter-TSS (NM_025411)	76	NM_025411	66193	Mm.29131	NM_025411	ENSMUSG00000028669	Pithd1	1110049F12Rik|AA408179|Trp26	PITH (C-terminal proteasome-interacting domain of thioredoxin-like) domain containing 1	protein-coding
mm_37112.1	chr4	116641112	116641128	-	1	NA	exon (NM_021473, exon 4 of 9)	exon (NM_021473, exon 4 of 9)	10554	NM_021473	58810	Mm.30085	NM_021473	ENSMUSG00000028692	Akr1a1	2610201A18Rik|Akr1a4	aldo-keto reductase family 1, member A1 (aldehyde reductase)	protein-coding
mm_57881.1	chr6	131293188	131293248	-	1	NA	promoter-TSS (NM_025564)	promoter-TSS (NM_025564)	26	NM_001327860	66441	Mm.46623	NM_025564	ENSMUSG00000030188	Magohb	2010012C16Rik|Mago|Magoh|Magoh-rs1	mago homolog B, exon junction complex core component	protein-coding
mm_88441.1	chr10	77546109	77546119	+	1	NA	exon (NM_008404, exon 4 of 16)	exon (NM_008404, exon 4 of 16)	15766	NM_008404	16414	Mm.1137	NM_008404	ENSMUSG00000000290	Itgb2	2E6|AI528527|Cd18|LAD|LCAMB|Lfa1|MF17	integrin beta 2	protein-coding
mm_74310.1	chr8	126594694	126594712	+	1	NA	Intergenic	CpG-14677	-1267	NM_001164598	270110	Mm.334918	NM_001164598	ENSMUSG00000051495	Irf2bp2	E130305N23Rik|IRF-2BP2	interferon regulatory factor 2 binding protein 2	protein-coding
mm_25063.1	chr3	99240329	99240337	+	1	NA	Intergenic	GC_rich|Low_complexity|Low_complexity	-13427	NM_009323	21384	Mm.88761	NM_009323	ENSMUSG00000027868	Tbx15	Tbx14|Tbx8|de	T-box 15	protein-coding
mm_47532.1	chr5	124189737	124189740	-	1	NA	intron (NM_011256, intron 2 of 24)	intron (NM_011256, intron 2 of 24)	-2556	NM_001289472	19679	Mm.44261	NM_011256	ENSMUSG00000029406	Pitpnm2	NIR3|RDGBA2|Rdgb2|mKIAA1457	phosphatidylinositol transfer protein, membrane-associated 2	protein-coding
mm_27377.1	chr3	50443513	50443520	-	1	NA	promoter-TSS (NM_011990)	promoter-TSS (NM_011990)	97	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_148745.1	chr19	6046630	6046645	+	1	NA	promoter-TSS (NM_028769)	promoter-TSS (NM_028769)	61	NM_028769	74126	Mm.149870	NM_028769	ENSMUSG00000024807	Syvn1	1200010C09Rik|AW211966|C85322|D530017H19Rik|Hrd1	synovial apoptosis inhibitor 1, synoviolin	protein-coding
mm_86096.1	chr9	115282067	115282075	-	1	NA	promoter-TSS (NR_029430)	promoter-TSS (NR_029430)	-1	NR_029430	111186	Mm.484753	NR_029430		Stmn1-rs1	Lag-rs1|Lap18-rs1	stathmin 1, related sequence 1	pseudo
mm_43456.1	chr5	136228422	136228428	+	1	NA	intron (NM_001302939, intron 2 of 5)	intron (NM_001302939, intron 2 of 5)	16515	NM_001302939	23921	Mm.425294	NM_018825	ENSMUSG00000005057	Sh2b2	Aps	SH2B adaptor protein 2	protein-coding
mm_26871.1	chr3	17326563	17326568	-	1	NA	Intergenic	Intergenic	-463356	NR_033490	70441	Mm.458192	NR_033490	ENSMUSG00000100252	Mir124-2hg	100040120|2610100L16Rik|6430547I21Rik|A930005K07Rik|AW125202|Gm2612	Mir124-2 host gene (non-protein coding)	ncRNA
mm_122483.1	chr14	46386427	46386436	-	1	NA	intron (NM_001316360, intron 1 of 2)	intron (NM_001316360, intron 1 of 2)	4238	NM_001316360	12159	Mm.6813	NM_007554	ENSMUSG00000021835	Bmp4	Bmp-4|Bmp2b|Bmp2b-1|Bmp2b1	bone morphogenetic protein 4	protein-coding
mm_136512.1	chr16	97170906	97170945	-	1	NA	promoter-TSS (NM_031174)	promoter-TSS (NM_031174)	-190	NM_031174	13508	Mm.102437	NM_031174	ENSMUSG00000050272	Dscam	4932410A21Rik	Down syndrome cell adhesion molecule	protein-coding
mm_80525.1	chr9	80112907	80112911	+	1	NA	intron (NM_001311110, intron 8 of 23)	intron (NM_001311110, intron 8 of 23)	46006	NM_146003	215351	Mm.28232	NM_146003	ENSMUSG00000034252	Senp6	2810017C20Rik|E130319N12Rik|Susp1|mKIAA0797	SUMO/sentrin specific peptidase 6	protein-coding
mm_19033.1	chr2	76969726	76969742	-	1	NA	exon (NM_011652, exon 7 of 313)	exon (NM_011652, exon 7 of 313)	12813	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_92588.1	chr10	80075051	80075090	-	1	NA	intron (NM_183426, intron 4 of 31)	intron (NM_183426, intron 4 of 31)	21051	NM_001037741	625249	Mm.332810	NM_008162	ENSMUSG00000075706	Gpx4	GPx-4|GSHPx-4|PHGPx|mtPHGPx|snGPx	glutathione peroxidase 4	protein-coding
mm_34642.1	chr4	150678138	150678141	+	1	NA	Intergenic	RMER10A|LTR|ERVL	-25965	NM_173774	242773	Mm.29280	NM_173774	ENSMUSG00000039838	Slc45a1	C230078B22|Dnb5	solute carrier family 45, member 1	protein-coding
mm_12252.1	chr2	68905681	68905718	+	1	NA	intron (NM_172856, intron 1 of 9)	MIR|SINE|MIR	44258	NM_001347161	241447	Mm.222222	NM_172856	ENSMUSG00000027035	Cers6	4732462C07Rik|AW544719|Lass6|T1L	ceramide synthase 6	protein-coding
mm_150015.1	chr19	29367448	29367468	+	1	NA	promoter-TSS (NM_021893)	promoter-TSS (NM_021893)	20	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_123639.1	chr14	68582098	68582121	-	1	NA	promoter-TSS (NM_021475)	promoter-TSS (NM_021475)	-37	NM_021475	58860	Mm.36742	NM_021475	ENSMUSG00000022057	Adamdec1	2210414L24Rik|AI574231|Dcsn	ADAM-like, decysin 1	protein-coding
mm_146768.1	chr18	20002018	20002063	-	1	NA	promoter-TSS (NM_001291809)	promoter-TSS (NM_001291809)	57	NM_007882	13507	Mm.89935	NM_007882	ENSMUSG00000059898	Dsc3	5430426I24Rik	desmocollin 3	protein-coding
mm_82224.1	chr9	3025532	3025558	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	13198	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_25745.1	chr3	123085674	123085678	+	1	NA	intron (NM_080451, intron 4 of 4)	MTD|LTR|ERVL-MaLR	-50689	NM_021503	59006	Mm.141157	NM_021503	ENSMUSG00000028116	Myoz2	1110012I24Rik|Fatz-2|Myozl2	myozenin 2	protein-coding
mm_158132.1	chrX	103186443	103186453	-	1	NA	5' UTR (NM_008671, exon 1 of 1)	5' UTR (NM_008671, exon 1 of 1)	216	NM_008671	17954	Mm.388694	NM_008671	ENSMUSG00000082229	Nap1l2	Bpx	nucleosome assembly protein 1-like 2	protein-coding
mm_158303.1	chrX	121672849	121672849	-	1	NA	Intergenic	RMER17A|LTR|ERVK	724536	NM_138742	54561	Mm.490573	NM_138742	ENSMUSG00000055733	Nap1l3	MB20	nucleosome assembly protein 1-like 3	protein-coding
mm_140308.1	chr17	85691241	85691258	+	1	NA	Intergenic	Intergenic	-2995	NM_011380	20472	Mm.5039	NM_011380	ENSMUSG00000024134	Six2	-	sine oculis-related homeobox 2	protein-coding
mm_124415.1	chr14	118030686	118030687	-	1	NA	intron (NM_010024, intron 6 of 7)	intron (NM_010024, intron 6 of 7)	21560	NM_010024	13190	Mm.19987	NM_010024	ENSMUSG00000022129	Dct	DT|TRP-2|TRP2|Tyrp-2|Tyrp2|slaty|slt	dopachrome tautomerase	protein-coding
mm_52843.1	chr6	121838490	121838510	+	1	NA	promoter-TSS (NM_008645)	promoter-TSS (NM_008645)	-41	NM_008645	17836	Mm.1311	NM_008645	ENSMUSG00000059908	Mug1	-	murinoglobulin 1	protein-coding
mm_135476.1	chr16	45953498	45953562	-	1	NA	Intergenic	Intergenic	56883	NM_001134480	433022	Mm.380993	NM_001134480	ENSMUSG00000087141	Plcxd2	AW494639|EG433022	phosphatidylinositol-specific phospholipase C, X domain containing 2	protein-coding
mm_61377.1	chr7	70381748	70381752	+	1	NA	intron (NR_045850, intron 1 of 10)	intron (NR_045850, intron 1 of 10)	-15004	NM_183261	11819	Mm.158143	NM_009697	ENSMUSG00000030551	Nr2f2	2700033K02Rik|9430015G03Rik|ARP-1|Aporp1|COUP-TF2|COUP-TFII|COUPTFB|EAR3|SVP40|Tcfcoup2	nuclear receptor subfamily 2, group F, member 2	protein-coding
mm_50120.1	chr6	41535469	41535479	+	1	NA	Intergenic	Intergenic	13698	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_124496.1	chr14	121797814	121797860	-	1	NA	promoter-TSS (NM_134074)	promoter-TSS (NM_134074)	-103	NM_134074	105445	Mm.378591	NM_134074	ENSMUSG00000025558	Dock9	AA959601|AW538057|B230309H04Rik|D14Wsu89e|Zizimin1|mKIAA1058	dedicator of cytokinesis 9	protein-coding
mm_144153.1	chr18	5591911	5591919	+	1	NA	promoter-TSS (NM_011546)	promoter-TSS (NM_011546)	55	NM_011546	21417	Mm.3929	NM_011546	ENSMUSG00000024238	Zeb1	3110032K11Rik|AREB6|BZP|MEB1|Nil2|TCF-8|Tcf18|Tcf8|Tw|ZEB|Zfhep|Zfhx1a|Zfx1a|Zfx1ha|[delta]EF1	zinc finger E-box binding homeobox 1	protein-coding
mm_86541.1	chr10	8874220	8874240	+	1	NA	intron (NM_175155, intron 1 of 19)	intron (NM_175155, intron 1 of 19)	11840	NM_175155	70097	Mm.338275	NM_175155	ENSMUSG00000015305	Sash1	1100001C18Rik|2500002E12Rik|A330076K04Rik|mKIAA0790	SAM and SH3 domain containing 1	protein-coding
mm_95054.1	chr11	32385079	32385093	+	1	NA	intron (NM_177364, intron 3 of 12)	intron (NM_177364, intron 3 of 12)	37275	NM_177364	268396	Mm.227616	NM_177364	ENSMUSG00000040711	Sh3pxd2b	G431001E03Rik|TSK4|fad49	SH3 and PX domains 2B	protein-coding
mm_89963.1	chr10	111298683	111298689	+	1	NA	promoter-TSS (NM_027914)	promoter-TSS (NM_027914)	7	NM_027914	71769	Mm.45256	NM_027914	ENSMUSG00000035759	Bbs10	1300007O09Rik|AI452285	Bardet-Biedl syndrome 10 (human)	protein-coding
mm_167643.1	chr9	64814546	64814549	+	1	NA	intron (NM_001162917, intron 2 of 34)	intron (NM_001162917, intron 2 of 34)	3536	NM_001162917	102442	Mm.222473	NM_176935	ENSMUSG00000053641	Dennd4a	AI115600|AI851943|F730015K02Rik	DENN/MADD domain containing 4A	protein-coding
mm_130885.1	chr15	102257380	102257417	-	1	NA	5' UTR (NM_011244, exon 1 of 10)	5' UTR (NM_011244, exon 1 of 10)	124	NM_011244	19411	Mm.1273	NM_011244	ENSMUSG00000001288	Rarg	Nr1b3|RAR-gamma|RARD|RARgamma2	retinoic acid receptor, gamma	protein-coding
mm_76597.1	chr8	89147249	89147251	-	1	NA	Intergenic	Intergenic	-103088	NM_021390	58198	Mm.214361	NM_021390	ENSMUSG00000031665	Sall1	Msal-3	sal-like 1 (Drosophila)	protein-coding
mm_12370.1	chr2	69821941	69821991	+	1	NA	promoter-TSS (NM_177784)	promoter-TSS (NM_177784)	-404	NM_177784	277396	Mm.138073	NM_177784	ENSMUSG00000042155	Klhl23	C130068N17Rik	kelch-like 23	protein-coding
mm_24529.1	chr3	93277584	93277591	+	1	NA	Intergenic	Intergenic	-42162	NM_133698	68723	Mm.208047	NM_133698	ENSMUSG00000041991	Hrnr	1110033K19Rik|A530063N20Rik|S100a18	hornerin	protein-coding
mm_39391.1	chr5	13399496	13399519	+	1	NA	5' UTR (NM_009152, exon 1 of 17)	5' UTR (NM_009152, exon 1 of 17)	198	NM_009152	20346	Mm.372039	NM_009152	ENSMUSG00000028883	Sema3a	Hsema-I|SEMA1|SemD|Semad|coll-1	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	protein-coding
mm_59264.1	chr7	24884810	24884826	+	1	NA	5' UTR (NM_023133, exon 1 of 6)	5' UTR (NM_023133, exon 1 of 6)	104	NM_023133	20085	Mm.300281	NM_023133	ENSMUSG00000040952	Rps19	Dsk3	ribosomal protein S19	protein-coding
mm_35129.1	chr4	11248207	11248231	-	1	NA	exon (NM_001159595, exon 3 of 27)	exon (NM_001159595, exon 3 of 27)	6040	NM_178112	72656	Mm.246713	NM_178112	ENSMUSG00000040738	Ints8	2810013E07Rik|AV063769|D130008D20Rik	integrator complex subunit 8	protein-coding
mm_44192.1	chr5	3501655	3501664	-	1	NA	intron (NM_009873, intron 5 of 7)	intron (NM_009873, intron 5 of 7)	-42174	NM_001042501	68152	Mm.240265	NM_026583	ENSMUSG00000058503	Fam133b	2900022K02Rik|5830415L20Rik	family with sequence similarity 133, member B	protein-coding
mm_44791.1	chr5	32354816	32354832	-	1	NA	exon (NM_001081407, exon 56 of 59)	exon (NM_001081407, exon 56 of 59)	1244	NM_172147	665270	Mm.160067	NM_030072	ENSMUSG00000029134	Plb1	4632413E21Rik|4930433E17Rik|4930539A06Rik|BC033606	phospholipase B1	protein-coding
mm_8064.1	chr1	135430491	135430505	-	1	NA	promoter-TSS (NM_153774)	promoter-TSS (NM_153774)	-7	NM_153774	226432	Mm.271642	NM_153774	ENSMUSG00000041879	Ipo9	0710008K06Rik|AI845704|C78347|Imp9|Ranbp9|mKIAA1192	importin 9	protein-coding
mm_45884.1	chr5	88521207	88521209	-	1	NA	3' UTR (NM_152839, exon 4 of 4)	3' UTR (NM_152839, exon 4 of 4)	6689	NM_152839	16069	Mm.1192	NM_152839	ENSMUSG00000067149	Jchain	9530090F24Rik|AI323815|Igj|Jch	immunoglobulin joining chain	protein-coding
mm_119528.1	chr14	47648448	47648470	+	1	NA	promoter-TSS (NM_001293636)	promoter-TSS (NM_001293636)	-852	NM_001347527	16709	Mm.3110	NM_008477	ENSMUSG00000021843	Ktn1	-	kinectin 1	protein-coding
mm_17312.1	chr2	26409162	26409209	-	1	NA	promoter-TSS (NM_033134)	promoter-TSS (NM_033134)	34	NM_033134	64436	Mm.330070	NM_033134	ENSMUSG00000026925	Inpp5e	1200002L24Rik|72kDa|mKIAA0123	inositol polyphosphate-5-phosphatase E	protein-coding
mm_169257.1	chr1	37997196	37997198	-	1	NA	promoter-TSS (NM_172054)	promoter-TSS (NM_172054)	11	NM_172054	98258	Mm.28438	NM_172054	ENSMUSG00000058407	Txndc9	AI098020|APACD	thioredoxin domain containing 9	protein-coding
mm_158150.1	chrX	103469729	103469741	-	1	NA	non-coding (NR_001570, exon 4 of 8)	non-coding (NR_001570, exon 4 of 8)	13498	NR_001570	213742	Mm.274770	NR_001463	ENSMUSG00000086503	Xist	A430022B11|AI314753	inactive X specific transcripts	ncRNA
mm_157621.1	chrX	56549676	56549679	-	1	NA	promoter-TSS (NM_001033372)	promoter-TSS (NM_001033372)	-71	NM_001033372	270599	Mm.424438	NM_001033372	ENSMUSG00000064016	Gm648	-	predicted gene 648	protein-coding
mm_82448.1	chr9	15326536	15326559	-	1	NA	promoter-TSS (NR_028568)	promoter-TSS (NR_028568)	-217	NR_028568	100216535		NR_028568		Scarna9	Z32	small Cajal body-specific RNA 9	ncRNA
mm_35143.1	chr4	11558755	11558763	-	1	NA	promoter-TSS (NM_001256145)	promoter-TSS (NM_001256145)	-161	NM_001039556	623474	Mm.491200	NM_177285	ENSMUSG00000078773	Rad54b	E130016E03Rik	RAD54 homolog B (S. cerevisiae)	protein-coding
mm_156893.1	chrX	166674539	166674540	+	1	NA	intron (NR_046015, intron 6 of 8)	intron (NR_046015, intron 6 of 8)	12514	NR_046015	382255	Mm.336320	NR_046015	ENSMUSG00000086860	Gm1720	-	predicted gene 1720	ncRNA
mm_63947.1	chr7	139834356	139834370	+	1	NA	5' UTR (NM_177469, exon 1 of 8)	5' UTR (NM_177469, exon 1 of 8)	189	NM_177469	52389	Mm.39863	NM_177469	ENSMUSG00000025475	Adgra1	2900059M17Rik|D7Ertd680e|Gpr123	adhesion G protein-coupled receptor A1	protein-coding
mm_112155.1	chr12	113288747	113288762	-	1	NA	Intergenic	Intergenic	102851	NM_153776	69195	Mm.313244	NM_153776	ENSMUSG00000049036	Tmem121	2410008J05Rik|Hole	transmembrane protein 121	protein-coding
mm_92896.1	chr10	83153974	83153984	-	1	NA	intron (NM_021439, intron 2 of 2)	intron (NM_021439, intron 2 of 2)	168482	NM_021439	58250	Mm.360747	NM_021439	ENSMUSG00000034612	Chst11	1110020P09Rik|C4ST|C4ST-1|C4ST1|C4s	carbohydrate sulfotransferase 11	protein-coding
mm_39883.1	chr5	31108308	31108341	+	1	NA	promoter-TSS (NM_177677)	promoter-TSS (NM_177677)	5	NM_177677	231098	Mm.189696	NM_177677	ENSMUSG00000053856	Dnajc5g	4922503E23Rik	DnaJ heat shock protein family (Hsp40) member C5 gamma	protein-coding
mm_57026.1	chr6	122282891	122282908	-	1	NA	promoter-TSS (NM_016970)	promoter-TSS (NM_016970)	-66	NM_016970	50928	Mm.20434	NM_016970	ENSMUSG00000030114	Klrg1	2F1-Ag|MAFA|MAFA-L	killer cell lectin-like receptor subfamily G, member 1	protein-coding
mm_65146.1	chr7	19586418	19586430	-	1	NA	non-coding (NR_125836, exon 11 of 18)	non-coding (NR_125836, exon 11 of 18)	9137	NM_022409	63872	Mm.23310	NM_022409	ENSMUSG00000011267	Zfp296	2210018A16Rik|Znf296	zinc finger protein 296	protein-coding
mm_156485.1	chrX	144335904	144335927	+	1	NA	intron (NR_037145, intron 3 of 26)	intron (NR_037145, intron 3 of 26)	17949	NM_026247	67574	Mm.249084	NM_026247	ENSMUSG00000041718	Alg13	2810046O15Rik|4833435D08Rik|Glt28d1|MDS031|OTTMUSG00000018917	asparagine-linked glycosylation 13	protein-coding
mm_121560.1	chr14	122484393	122484402	+	1	NA	Intergenic	Intergenic	9013	NM_009574	22772	Mm.308936	NM_009574	ENSMUSG00000061524	Zic2	HPE5|Ku	zinc finger protein of the cerebellum 2	protein-coding
mm_63531.1	chr7	127968804	127968807	+	1	NA	intron (NM_001347649, intron 1 of 14)	intron (NM_001347649, intron 1 of 14)	1326	NM_139149	233908	Mm.277680	NM_139149	ENSMUSG00000030795	Fus	D430004D17Rik|D930039C12Rik|Fus1|Tls	fused in sarcoma	protein-coding
mm_70904.1	chr8	25640734	25640841	+	1	NA	exon (NM_001081269, exon 1 of 23)	exon (NM_001081269, exon 1 of 23)	210	NM_001081269	234135	Mm.217337	NM_001001735	ENSMUSG00000054823	Whsc1l1	6720429E03|A530023P05|AI528490|NSD3|WHISTLE	Wolf-Hirschhorn syndrome candidate 1-like 1 (human)	protein-coding
mm_53884.1	chr6	3345996	3346008	-	1	NA	Intergenic	Intergenic	53569	NM_010156	209086	Mm.196013	NM_010156	ENSMUSG00000047735	Samd9l	AA175286|ESTM25|mKIAA2005	sterile alpha motif domain containing 9-like	protein-coding
mm_75651.1	chr8	65129410	65129424	-	1	NA	non-coding (NR_033217, exon 1 of 3)	non-coding (NR_033217, exon 1 of 3)	120	NR_033217	407795	Mm.387876	NR_033217	ENSMUSG00000074300	BC030870	-	cDNA sequence BC030870	ncRNA
mm_99848.1	chr11	109362707	109362739	+	1	NA	promoter-TSS (NM_010303)	promoter-TSS (NM_010303)	-71	NM_010303	14674	Mm.193925	NM_010303	ENSMUSG00000020611	Gna13	AU024132|AU043124|Galpha13	guanine nucleotide binding protein, alpha 13	protein-coding
mm_57808.1	chr6	129451740	129451752	-	1	NA	5' UTR (NM_175526, exon 1 of 6)	5' UTR (NM_175526, exon 1 of 6)	254	NM_175526	243653	Mm.131289	NM_175526	ENSMUSG00000033082	Clec1a	5930406N14Rik	C-type lectin domain family 1, member a	protein-coding
mm_121186.1	chr14	103049392	103049397	+	1	NA	exon (NM_008392, exon 2 of 5)	exon (NM_008392, exon 2 of 5)	2382	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_34783.1	chr4	154142397	154142418	+	1	NA	promoter-TSS (NM_021499)	promoter-TSS (NM_021499)	35	NM_021499	59002	Mm.46508	NM_021499	ENSMUSG00000029029	Wrap73	2610044M17Rik|5330425N03Rik|Dd57|Wdr8	WD repeat containing, antisense to Trp73	protein-coding
mm_27165.1	chr3	33143228	33143266	-	1	NA	promoter-TSS (NM_001163516)	promoter-TSS (NM_001163516)	-56	NM_001163516	58869	Mm.151332	NM_021483	ENSMUSG00000027674	Pex5l	1700016J08Rik|PXR2|Pex2|TRIP8b|pex5Rp	peroxisomal biogenesis factor 5-like	protein-coding
mm_10246.1	chr2	9141663	9141700	+	1	NA	Intergenic	MER44B|DNA|TcMar-Tigger	-47834	NR_038180	73438	Mm.23558	NR_038180	ENSMUSG00000085580	1700061F12Rik	-	RIKEN cDNA 1700061F12 gene	ncRNA
mm_141812.1	chr17	34603710	34603724	-	1	NA	promoter-TSS (NM_019403)	promoter-TSS (NM_019403)	-156	NM_019403	54197	Mm.274542	NM_019403	ENSMUSG00000015478	Rnf5	2410131O05Rik|AA407576|NG2	ring finger protein 5	protein-coding
mm_94754.1	chr11	21118179	21118220	+	1	NA	intron (NM_023324, intron 1 of 6)	B1_Mm|SINE|Alu	26875	NM_023324	67245	Mm.28957	NM_023324	ENSMUSG00000020134	Peli1	2810468L03Rik|A930031K15Rik|AA409794|AI586297|D11Ertd676e	pellino 1	protein-coding
mm_37826.1	chr4	131960335	131960338	-	1	NA	intron (NM_001128606, intron 12 of 17)	intron (NM_001128606, intron 12 of 17)	38565	NM_001201367	623230	Mm.421179	NM_001201367	ENSMUSG00000070720	Tmem200b	EG623230	transmembrane protein 200B	protein-coding
mm_158575.1	chrX	150594776	150594781	-	1	NA	intron (NM_008824, intron 1 of 13)	intron (NM_008824, intron 1 of 13)	4857	NM_008824	18639	Mm.249131	NM_008824	ENSMUSG00000025271	Pfkfb1	PFK/FBPase 1	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1	protein-coding
mm_73485.1	chr8	107031236	107031246	+	1	NA	promoter-TSS (NM_126165)	promoter-TSS (NM_126165)	-85	NM_126165	116733	Mm.236004	NM_126165	ENSMUSG00000031913	Vps4a	4930589C15Rik|AI325971|AW553189	vacuolar protein sorting 4A	protein-coding
mm_140363.1	chr17	86917442	86917458	+	1	NA	5' UTR (NM_030104, exon 1 of 3)	5' UTR (NM_030104, exon 1 of 3)	102	NM_030104	78469	Mm.67234	NM_030104	ENSMUSG00000037689	Tmem247	1700090G07Rik	transmembrane protein 247	protein-coding
mm_46248.1	chr5	99248595	99248607	-	1	NA	intron (NM_145839, intron 1 of 13)	intron (NM_145839, intron 1 of 13)	4326	NM_181318	320292	Mm.259074	NM_145839	ENSMUSG00000089809	Rasgef1b	4732452O09Rik|GPIgamma4|Gpig4	RasGEF domain family, member 1B	protein-coding
mm_550.1	chr1	38019150	38019163	+	1	NA	exon (NM_198303, exon 4 of 24)	exon (NM_198303, exon 4 of 24)	21146	NM_198303	226982	Mm.260943	NM_198303	ENSMUSG00000026083	Eif5b	A030003E17Rik|BC018347|IF2	eukaryotic translation initiation factor 5B	protein-coding
mm_106148.1	chr11	116581447	116581472	-	1	NA	promoter-TSS (NM_173755)	promoter-TSS (NM_173755)	-12	NM_173755	217342	Mm.243950	NM_173755	ENSMUSG00000020802	Ube2o	9630022H21|B230113M03Rik|E2-230K|mKIAA1734	ubiquitin-conjugating enzyme E2O	protein-coding
mm_53196.1	chr6	125538735	125538741	+	1	NA	Intergenic	Intergenic	-14210	NM_011708	22371	Mm.22339	NM_011708	ENSMUSG00000001930	Vwf	6820430P06Rik|AI551257|B130011O06Rik|C630030D09|F8VWF|VWD	Von Willebrand factor	protein-coding
mm_119650.1	chr14	52014956	52014978	+	1	NA	promoter-TSS (NM_001253695)	promoter-TSS (NM_001253695)	-409	NM_001253695	69890	Mm.475652	NM_027248	ENSMUSG00000049295	Zfp219	2010302A17Rik	zinc finger protein 219	protein-coding
mm_122818.1	chr14	54632304	54632314	-	1	NA	exon (NM_199470, exon 12 of 12)	exon (NM_199470, exon 12 of 12)	6999	NM_175204	73902	Mm.32009	NM_175204	ENSMUSG00000072423	Psmb11	5830406J20Rik|beta5t	proteasome (prosome, macropain) subunit, beta type, 11	protein-coding
mm_67897.1	chr7	99536041	99536053	-	1	NA	intron (NM_177231, intron 1 of 15)	intron (NM_177231, intron 1 of 15)	561	NM_177231	109689	Mm.260193	NM_177231	ENSMUSG00000018909	Arrb1	1200006I17Rik|AW208571|G430100A01Rik	arrestin, beta 1	protein-coding
mm_106913.1	chr12	8216603	8216609	+	1	NA	intron (NM_001167767, intron 1 of 5)	intron (NM_001167767, intron 1 of 5)	8479	NM_001167767	68832	Mm.25608	NM_172401	ENSMUSG00000037669	Ldah	1110057K04Rik|mLDAH	lipid droplet associated hydrolase	protein-coding
mm_133218.1	chr16	75907107	75907139	+	1	NA	intron (NM_023380, intron 1 of 7)	intron (NM_023380, intron 1 of 7)	2143	NM_023380	67742	Mm.131406	NM_023380	ENSMUSG00000022876	Samsn1	4930571B16Rik|930571B16Rik|Hacs1|SLy2	SAM domain, SH3 domain and nuclear localization signals, 1	protein-coding
mm_91080.1	chr10	19011949	19011973	-	1	NA	promoter-TSS (NM_001166402)	promoter-TSS (NM_001166402)	2	NM_001166402	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_6868.1	chr1	84281938	84281949	-	1	NA	intron (NM_001003948, intron 1 of 2)	intron (NM_001003948, intron 1 of 2)	2702	NM_001003948	98496	Mm.187470	NM_001003948	ENSMUSG00000045658	Pid1	5033414K04Rik|NYGGF4	phosphotyrosine interaction domain containing 1	protein-coding
mm_162735.1	chr10	54119448	54119464	+	1	NA	Intergenic	Intergenic	43534	NR_038016	100502920	Mm.403982	NR_038016	ENSMUSG00000097069	Gm16998	-	predicted gene, 16998	ncRNA
mm_62351.1	chr7	100498829	100498830	+	1	NA	exon (NM_011671, exon 7 of 8)	exon (NM_011671, exon 7 of 8)	5471	NM_011671	22228	Mm.171378	NM_011671	ENSMUSG00000033685	Ucp2	Slc25a8	uncoupling protein 2 (mitochondrial, proton carrier)	protein-coding
mm_35721.1	chr4	44640583	44640588	-	1	NA	intron (NM_008782, intron 6 of 9)	intron (NM_008782, intron 6 of 9)	-62215	NR_073462	70602	Mm.491142	NR_073462	ENSMUSG00000103995	5730488B01Rik	-	RIKEN cDNA 5730488B01 gene	ncRNA
mm_163998.1	chr14	65262367	65262373	-	1	NA	promoter-TSS (NM_021458)	promoter-TSS (NM_021458)	93	NM_021458	14365	Mm.214687	NM_021458	ENSMUSG00000007989	Fzd3	AU020229|D930050A07Rik|Fz3	frizzled class receptor 3	protein-coding
mm_86195.1	chr9	119895138	119895141	-	1	NA	intron (NM_026236, intron 1 of 18)	CpG	244	NM_026236	67561	Mm.104789	NM_026236	ENSMUSG00000032512	Wdr48	8430408H12Rik|Uaf1|mKIAA1449	WD repeat domain 48	protein-coding
mm_43555.1	chr5	137601560	137601560	+	1	NA	promoter-TSS (NM_030037)	promoter-TSS (NM_030037)	-501	NM_030037	68929	Mm.41355	NM_030037	ENSMUSG00000037221	Mospd3	1190005J19Rik|5133401H10Rik|Gtig2|R124	motile sperm domain containing 3	protein-coding
mm_43947.1	chr5	145131445	145131480	+	1	NA	exon (NM_001033313, exon 5 of 6)	exon (NM_001033313, exon 5 of 6)	8627	NM_001033313	231887	Mm.188851	NM_001033313	ENSMUSG00000029623	Pdap1	HASPP28|PAP|PAP1	PDGFA associated protein 1	protein-coding
mm_103357.1	chr11	74851857	74851863	-	1	NA	intron (NM_197943, intron 20 of 22)	intron (NM_197943, intron 20 of 22)	16334	NR_105891	102465558		NR_105891	ENSMUSG00000098317	Mir6926	Gm27949|mmu-mir-6926	microRNA 6926	ncRNA
mm_71718.1	chr8	61947688	61947703	+	1	NA	intron (NM_001293783, intron 6 of 37)	intron (NM_001293783, intron 6 of 37)	19608	NM_001293783	234311	Mm.275233	NM_144928	ENSMUSG00000037921	Ddx60	9830118M07	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	protein-coding
mm_7434.1	chr1	119913163	119913202	-	1	NA	promoter-TSS (NM_175106)	promoter-TSS (NM_175106)	-14	NM_175106	66343	Mm.49942	NM_175106	ENSMUSG00000036975	Tmem177	2300008B03Rik	transmembrane protein 177	protein-coding
mm_90187.1	chr10	120165391	120165395	+	1	NA	intron (NM_028679, intron 7 of 11)	RMER17C|LTR|ERVK	36144	NM_028679	73914	Mm.146194	NM_028679	ENSMUSG00000020227	Irak3	4833428C18Rik|AI563835|IRAK-M	interleukin-1 receptor-associated kinase 3	protein-coding
mm_106018.1	chr11	116022649	116022677	-	1	NA	3' UTR (NM_008211, exon 4 of 4)	3' UTR (NM_008211, exon 4 of 4)	1841	NM_008211	15081	Mm.18516	NM_008211	ENSMUSG00000016559	H3f3b	9430068D06Rik|H3.3B	H3 histone, family 3B	protein-coding
mm_154047.1	chr19	55095725	55095764	-	1	NA	intron (NM_008149, intron 3 of 20)	intron (NM_008149, intron 3 of 20)	3703	NM_008149	14732	Mm.210196	NM_008149	ENSMUSG00000024978	Gpam	GPAT|GPAT1	glycerol-3-phosphate acyltransferase, mitochondrial	protein-coding
mm_167015.1	chr7	63875735	63875736	+	1	NA	Intergenic	Intergenic	-41122	NM_001256311	381994	Mm.425466	NM_001256311	ENSMUSG00000095061	E030018B13Rik	Gm1697	RIKEN cDNA E030018B13 gene	protein-coding
mm_2987.1	chr1	133131810	133131824	+	1	NA	exon (NM_133819, exon 1 of 2)	exon (NM_133819, exon 1 of 2)	651	NM_133819	108954	Mm.293628	NM_133819	ENSMUSG00000046062	Ppp1r15b	1810033K10Rik|AI606441|C530022L24Rik|CReP	protein phosphatase 1, regulatory (inhibitor) subunit 15b	protein-coding
mm_144837.1	chr18	36529244	36529251	+	1	NA	exon (NM_001271545, exon 3 of 21)	exon (NM_001271545, exon 3 of 21)	1095	NM_001271544	240215	Mm.135463	NM_172830	ENSMUSG00000024485	Slc4a9	AE4|D630003B07|D630024F24Rik	solute carrier family 4, sodium bicarbonate cotransporter, member 9	protein-coding
mm_92584.1	chr10	80036756	80036766	-	1	NA	intron (NM_025554, intron 5 of 6)	intron (NM_025554, intron 5 of 6)	2898	NM_025554	66420	Mm.18579	NM_025554	ENSMUSG00000004667	Polr2e	2410021N14Rik|25kDa|AW208866|RPB5|XAP4	polymerase (RNA) II (DNA directed) polypeptide E	protein-coding
mm_80521.1	chr9	80067088	80067119	+	1	NA	5' UTR (NM_146003, exon 1 of 23)	5' UTR (NM_146003, exon 1 of 23)	200	NM_146003	215351	Mm.28232	NM_146003	ENSMUSG00000034252	Senp6	2810017C20Rik|E130319N12Rik|Susp1|mKIAA0797	SUMO/sentrin specific peptidase 6	protein-coding
mm_120983.1	chr14	78849172	78849220	+	1	NA	promoter-TSS (NM_027906)	promoter-TSS (NM_027906)	18	NM_173758	219189	Mm.159651	NM_027906	ENSMUSG00000058997	Vwa8	1300010F03Rik|4932416F07Rik|AI957255|Kiaa0564|mKIAA0564	von Willebrand factor A domain containing 8	protein-coding
mm_61605.1	chr7	80028370	80028374	+	1	NA	intron (NM_175433, intron 1 of 4)	intron (NM_175433, intron 1 of 4)	2144	NM_175433	209225	Mm.290925	NM_175433	ENSMUSG00000048897	Zfp710	5430400N05Rik|9830165K13|AI324798|Znf710	zinc finger protein 710	protein-coding
mm_83801.1	chr9	53178628	53178630	-	1	NA	intron (NM_029936, intron 13 of 17)	intron (NM_029936, intron 13 of 17)	69483	NM_029936	77591	Mm.133560	NM_029936	ENSMUSG00000053289	Ddx10	4632415A01Rik|AI646054	DEAD (Asp-Glu-Ala-Asp) box polypeptide 10	protein-coding
mm_125748.1	chr15	73729149	73729167	+	1	NA	intron (NM_001166388, intron 1 of 5)	intron (NM_001166388, intron 1 of 5)	4228	NM_001166388	19245	Mm.390807	NM_008975	ENSMUSG00000059895	Ptp4a3	AV088979|Prl-3|pPtp4a3	protein tyrosine phosphatase 4a3	protein-coding
mm_53489.1	chr6	135084173	135084195	+	1	NA	3' UTR (NM_181444, exon 4 of 4)	3' UTR (NM_181444, exon 4 of 4)	18522	NM_181444	232431	Mm.23575	NM_181444	ENSMUSG00000046733	Gprc5a	Rai3|Raig1	G protein-coupled receptor, family C, group 5, member A	protein-coding
mm_35372.1	chr4	33031255	33031272	-	1	NA	promoter-TSS (NM_019586)	promoter-TSS (NM_019586)	60	NR_036602	100504166	Mm.426309	NR_036602	ENSMUSG00000085037	4933421O10Rik	-	RIKEN cDNA 4933421O10 gene	ncRNA
mm_71403.1	chr8	46432852	46432860	+	1	NA	Intergenic	Intergenic	-38181	NM_007981	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_62498.1	chr7	101970643	101970689	+	1	NA	intron (NM_133947, intron 1 of 24)	intron (NM_133947, intron 1 of 24)	823	NM_133947	101706	Mm.27259	NM_133947	ENSMUSG00000066306	Numa1	6720401E04Rik|AA764025|AL022610|AU014979|NuMA	nuclear mitotic apparatus protein 1	protein-coding
mm_35598.1	chr4	43031378	43031427	-	1	NA	promoter-TSS (NM_023231)	promoter-TSS (NM_023231)	-18	NM_023231	66592	Mm.331565	NM_023231	ENSMUSG00000028455	Stoml2	0610038F01Rik|MSLP2|SLP-2	stomatin (Epb7.2)-like 2	protein-coding
mm_115855.1	chr13	21289909	21289920	-	1	NA	intron (NM_010343, intron 2 of 4)	(A)n|Simple_repeat|Simple_repeat	2772	NM_010343	14780	Mm.1332	NM_010343	ENSMUSG00000004344	Gpx5	AV379049|Arep	glutathione peroxidase 5	protein-coding
mm_93950.1	chr10	127247620	127247630	-	1	NA	exon (NM_001039000, exon 4 of 29)	exon (NM_001039000, exon 4 of 29)	15738	NM_008447	16572	Mm.30355	NM_008447	ENSMUSG00000074657	Kif5a	D10Bwg0738e|Khc|Kif5|Kns|mKIAA4086	kinesin family member 5A	protein-coding
mm_38064.1	chr4	134018850	134018862	-	1	NA	promoter-TSS (NM_145833)	promoter-TSS (NM_145833)	-40	NM_145833	83557	Mm.302567	NM_145833	ENSMUSG00000050966	Lin28a	AL024421|ENSMUSG00000070700|Gm10299|Lin-28|Lin28|Tex17|lin-28A	lin-28 homolog A (C. elegans)	protein-coding
mm_57787.1	chr6	129269665	129269702	-	1	NA	intron (NM_001033122, intron 3 of 4)	intron (NM_001033122, intron 3 of 4)	5686	NM_001033122	12515	Mm.74745	NM_001033122	ENSMUSG00000030156	Cd69	5830438K24Rik|AI452015|AIM|VEA	CD69 antigen	protein-coding
mm_26256.1	chr3	142496874	142496892	+	1	NA	promoter-TSS (NM_153564)	promoter-TSS (NM_153564)	-51	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_105286.1	chr11	102444797	102444803	-	1	NA	intron (NM_199200, intron 1 of 7)	intron (NM_199200, intron 1 of 7)	2863	NM_199200	217219	Mm.259924	NM_199200	ENSMUSG00000034685	Fam171a2	-	family with sequence similarity 171, member A2	protein-coding
mm_161240.1	chr13	96489791	96489791	-	1	NA	intron (NR_144624, intron 6 of 10)	intron (NR_144624, intron 6 of 10)	-18631	NM_001042714	271144	Mm.470057	NM_001042714	ENSMUSG00000047117	Ankdd1b	9330128J19Rik	ankyrin repeat and death domain containing 1B	protein-coding
mm_30193.1	chr3	144706640	144706700	-	1	NA	exon (NM_019464, exon 4 of 9)	exon (NM_019464, exon 4 of 9)	13665	NM_001282042	54673	Mm.271775	NM_019464	ENSMUSG00000037062	Sh3glb1	AA409932|AI314629|AU015566|Bif-1|mKIAA0491	SH3-domain GRB2-like B1 (endophilin)	protein-coding
mm_143430.1	chr17	70851110	70851118	-	1	NA	promoter-TSS (NM_009372)	promoter-TSS (NM_009372)	96	NM_009372	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_130069.1	chr15	89315254	89315312	-	1	NA	promoter-TSS (NM_001170561)	promoter-TSS (NM_001170561)	28	NM_001081030	77980	Mm.35483	NM_030019	ENSMUSG00000036529	Sbf1	2610510A08Rik|B230113C15Rik|Mtmr5|mKIAA3020	SET binding factor 1	protein-coding
mm_131591.1	chr16	18811773	18811787	+	1	NA	promoter-TSS (NM_001161623)	promoter-TSS (NM_001161623)	-141	NM_001161623	12544	Mm.1248	NM_009862	ENSMUSG00000000028	Cdc45	Cdc45l	cell division cycle 45	protein-coding
mm_11121.1	chr2	28214140	28214155	+	1	NA	3' UTR (NM_001038614, exon 4 of 4)	3' UTR (NM_001038614, exon 4 of 4)	8458	NM_019498	56177	Mm.43278	NM_019498	ENSMUSG00000026833	Olfm1	AMY|AW742568|Noe1|OlfA|Pancortin|Pancortin3	olfactomedin 1	protein-coding
mm_80135.1	chr9	70679022	70679116	+	1	NA	promoter-TSS (NM_007399)	promoter-TSS (NM_007399)	87	NM_007399	11487	Mm.3037	NM_007399	ENSMUSG00000054693	Adam10	1700031C13Rik|MADM|kuz|kuzbanian	a disintegrin and metallopeptidase domain 10	protein-coding
mm_150287.1	chr19	34492317	34492320	+	1	NA	TTS (NM_021460)	TTS (NM_021460)	-17183	NM_009890	12642	Mm.30824	NM_009890	ENSMUSG00000050370	Ch25h	AI462618|m25OH	cholesterol 25-hydroxylase	protein-coding
mm_81407.1	chr9	109051953	109051975	+	1	NA	intron (NM_025858, intron 3 of 5)	intron (NM_025858, intron 3 of 5)	-2902	NM_026381	66940	Mm.196533	NM_025858	ENSMUSG00000025647	Shisa5	2310008D10Rik|6430628I05Rik|Scotin|mShisa5	shisa family member 5	protein-coding
mm_1118.1	chr1	59913054	59913064	+	1	NA	promoter-TSS (NM_001037725)	promoter-TSS (NM_001037725)	53	NM_001037725	72750	Mm.258250	NM_001037725	ENSMUSG00000041040	Fam117b	2810425F24Rik|6330416D14Rik|Als2cr13	family with sequence similarity 117, member B	protein-coding
mm_171385.1	chr4	121016884	121016892	-	1	NA	5' UTR (NM_133716, exon 1 of 10)	5' UTR (NM_133716, exon 1 of 10)	359	NM_133716	69780	Mm.271819	NM_133716	ENSMUSG00000032870	Smap2	1810031K02Rik|AA408614|Smap1l	small ArfGAP 2	protein-coding
mm_94445.1	chr11	6366141	6366153	+	1	NA	Intergenic	Intergenic	-28978	NM_001005867	52915	Mm.1144	NM_028601	ENSMUSG00000041164	Zmiz2	Zimp7	zinc finger, MIZ-type containing 2	protein-coding
mm_80850.1	chr9	98331252	98331252	+	1	NA	intron (NM_144533, intron 1 of 4)	(TATATG)n|Simple_repeat|Simple_repeat	34669	NM_144533	74080	Mm.294082	NM_144533	ENSMUSG00000032456	Nmnat3	4933408N02Rik|PNAT3	nicotinamide nucleotide adenylyltransferase 3	protein-coding
mm_39841.1	chr5	30888928	30888997	+	1	NA	promoter-TSS (NR_122117)	promoter-TSS (NR_122117)	27	NR_122116	231093	Mm.440364	NM_174849	ENSMUSG00000029165	Agbl5	9430057O19Rik|CCP5	ATP/GTP binding protein-like 5	protein-coding
mm_38621.1	chr4	142048459	142048468	-	1	NA	intron (NM_145402, intron 1 of 2)	MLT1J|LTR|ERVL-MaLR	30565	NR_131014	78917	Mm.139995	NR_131014	ENSMUSG00000085761	4930455G09Rik	-	RIKEN cDNA 4930455G09 gene	ncRNA
mm_147088.1	chr18	35648398	35648412	-	1	NA	intron (NM_027222, intron 1 of 3)	intron (NM_027222, intron 1 of 3)	962	NM_027222	69816	Mm.27252	NM_027222	ENSMUSG00000024353	Mzb1	2010001M09Rik|AV064572|PACAP|pERp1	marginal zone B and B1 cell-specific protein 1	protein-coding
mm_51264.1	chr6	72097764	72097785	+	1	NA	exon (NM_001035228, exon 1 of 7)	exon (NM_001035228, exon 1 of 7)	166	NM_011375	20454	Mm.38248	NM_011375	ENSMUSG00000056091	St3gal5	3S-T|Siat9|[a]2	ST3 beta-galactoside alpha-2,3-sialyltransferase 5	protein-coding
mm_104218.1	chr11	88366949	88366955	-	1	NA	intron (NM_054043, intron 10 of 13)	intron (NM_054043, intron 10 of 13)	14179	NR_039545	100628571		NR_039545	ENSMUSG00000092985	Mir378b	mir-378b|mmu-mir-378b	microRNA 378b	ncRNA
mm_167030.1	chr7	68284146	68284169	+	1	NA	intron (NM_001013811, intron 1 of 8)	L1MB3|LINE|L1	-7563	NR_040340	100504026	Mm.426764	NR_040340	ENSMUSG00000086628	Gm16157	OTTMUSG00000031023	predicted gene 16157	ncRNA
mm_34300.1	chr4	141746731	141746759	+	1	NA	promoter-TSS (NM_001081408)	promoter-TSS (NM_001081408)	70	NM_001081408	75986	Mm.30032	NM_001081408	ENSMUSG00000040706	Agmat	5033405N08Rik	agmatine ureohydrolase (agmatinase)	protein-coding
mm_30834.1	chr4	21964708	21964709	+	1	NA	intron (NM_175234, intron 4 of 5)	intron (NM_175234, intron 4 of 5)	33382	NM_175234	76132	Mm.159689	NM_175234	ENSMUSG00000028246	Faxc	6230409E13Rik|AW742931	failed axon connections homolog	protein-coding
mm_140441.1	chr17	88530212	88530234	+	1	NA	promoter-TSS (NM_028658)	promoter-TSS (NM_028658)	99	NM_028658	73825	Mm.271817	NM_028658	ENSMUSG00000034709	Ppp1r21	1110018J12Rik|AI426045|AW550781|Ccdc128|Klraq1	protein phosphatase 1, regulatory subunit 21	protein-coding
mm_60663.1	chr7	44997661	44997700	+	1	NA	promoter-TSS (NM_016849)	promoter-TSS (NM_016849)	32	NM_016849	54131	Mm.3960	NM_016849	ENSMUSG00000003184	Irf3	C920001K05Rik|IRF-3	interferon regulatory factor 3	protein-coding
mm_109525.1	chr12	111537193	111537205	+	1	NA	promoter-TSS (NM_178041)	promoter-TSS (NM_178041)	-902	NM_178041	217869	Mm.271222	NM_173363	ENSMUSG00000021282	Eif5	2810011H21Rik|D12Ertd549e	eukaryotic translation initiation factor 5	protein-coding
mm_151178.1	chr19	53313425	53313435	+	1	NA	intron (NM_001008542, intron 1 of 5)	CpG	2924	NM_001008542	17859	Mm.2154	NM_010847	ENSMUSG00000025025	Mxi1	ENSMUSG00000067085|Gm10197|Mad2|bHLHc11	MAX interactor 1, dimerization protein	protein-coding
mm_71572.1	chr8	54106955	54106958	+	1	NA	intron (NM_009506, intron 1 of 6)	intron (NM_009506, intron 1 of 6)	29424	NM_009506	22341	Mm.1402	NM_009506	ENSMUSG00000031520	Vegfc	AW228853|VEGF-C	vascular endothelial growth factor C	protein-coding
mm_114501.1	chr13	70573231	70573243	+	1	NA	promoter-TSS (NR_045934)	promoter-TSS (NR_045934)	-4	NR_045934	73584	Mm.442491	NR_045934	ENSMUSG00000101051	1700100L14Rik	-	RIKEN cDNA 1700100L14 gene	ncRNA
mm_69268.1	chr7	127922691	127922701	-	1	NA	intron (NM_026370, intron 6 of 10)	intron (NM_026370, intron 6 of 10)	7417	NM_133351	76560	Mm.5875	NM_133351	ENSMUSG00000030800	Prss8	2410039E18Rik|AI313909|C79772|CAP1|fr|mCAP1	protease, serine 8 (prostasin)	protein-coding
mm_154390.1	chrM	12953	12974	+	1	NA	NA	Intergenic	NA	NA								
mm_79411.1	chr9	55150051	55150083	+	1	NA	promoter-TSS (NM_001346658)	promoter-TSS (NM_001346658)	-16	NM_001346658	109161	Mm.207894	NM_180600	ENSMUSG00000032307	Ube2q2	3010021M21Rik	ubiquitin-conjugating enzyme E2Q family member 2	protein-coding
mm_147718.1	chr18	60817167	60817170	-	1	NA	intron (NM_001198984, intron 22 of 25)	intron (NM_001198984, intron 22 of 25)	5092	NR_039567	100628611		NR_039567	ENSMUSG00000093327	Mir5107	mir-5107|mmu-mir-5107|mu-mir-5107	microRNA 5107	ncRNA
mm_98721.1	chr11	96332434	96332457	+	1	NA	intron (NM_001079869, intron 1 of 3)	intron (NM_001079869, intron 1 of 3)	9319	NM_001079869	15410	Mm.342481	NM_010458	ENSMUSG00000048763	Hoxb3	Hox-2.7	homeobox B3	protein-coding
mm_131135.1	chr16	6298891	6298922	+	1	NA	intron (NM_021477, intron 2 of 16)	B4|SINE|B4	323319	NR_045799	68238	Mm.434605	NR_045799	ENSMUSG00000101481	1700123O21Rik	-	RIKEN cDNA 1700123O21 gene	ncRNA
mm_48541.1	chr5	142905313	142905340	-	1	NA	exon (NM_007393, exon 3 of 6)	exon (NM_007393, exon 3 of 6)	1428	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_15308.1	chr2	155517685	155517714	+	1	NA	promoter-TSS (NM_019811)	promoter-TSS (NM_019811)	-344	NM_019811	60525	Mm.255026	NM_019811	ENSMUSG00000027605	Acss2	1110017C11Rik|ACAS|Acas1|Acas2|AceCS1|Acs1	acyl-CoA synthetase short-chain family member 2	protein-coding
mm_28397.1	chr3	90052609	90052627	-	1	NA	promoter-TSS (NM_001165987)	promoter-TSS (NM_001165987)	-103	NM_001165984	74383	Mm.25610	NM_028475	ENSMUSG00000042520	Ubap2l	3110083O19Rik|4932431F02Rik|A430103N23Rik|C77168|Nice-4|mKIAA0144	ubiquitin-associated protein 2-like	protein-coding
mm_119610.1	chr14	51105164	51105181	+	1	NA	exon (NM_201239, exon 2 of 2)	exon (NM_201239, exon 2 of 2)	9172	NM_201239	58809	Mm.202665	NM_021472	ENSMUSG00000021876	Rnase4	C730049F20Rik|Rab1	ribonuclease, RNase A family 4	protein-coding
mm_25874.1	chr3	130180883	130180899	+	1	NA	promoter-TSS (NM_001244952)	promoter-TSS (NM_001244952)	46	NM_001244952	77018	Mm.91728	NM_029838	ENSMUSG00000058897	Col25a1	2700062B08Rik|CLAC-P	collagen, type XXV, alpha 1	protein-coding
mm_1817.1	chr1	82339079	82339086	+	1	NA	promoter-TSS (NM_001122685)	promoter-TSS (NM_001122685)	33	NM_001122685	76867	Mm.226994	NM_029777	ENSMUSG00000026142	Rhbdd1	4930418P06Rik|RRP4|mRHBDD1	rhomboid domain containing 1	protein-coding
mm_40614.1	chr5	64803364	64803374	+	1	NA	promoter-TSS (NM_008453)	promoter-TSS (NM_008453)	-154	NM_008453	16599	Mm.392759	NM_008453	ENSMUSG00000029178	Klf3	9930027G08Rik|AL024007|Bklf|Tef-2	Kruppel-like factor 3 (basic)	protein-coding
mm_141522.1	chr17	31729551	31729553	-	1	NA	Intergenic	Intergenic	51621	NM_001278570	12954	Mm.1228	NM_013501	ENSMUSG00000024041	Cryaa	Acry-1|Crya-1|Crya1|DAcry-1|lop18	crystallin, alpha A	protein-coding
mm_84036.1	chr9	57765800	57765816	-	1	NA	promoter-TSS (NM_007713)	promoter-TSS (NM_007713)	52	NM_007713	102414	Mm.25720	NM_007713	ENSMUSG00000032316	Clk3	AI256811	CDC-like kinase 3	protein-coding
mm_86976.1	chr10	25425881	25425920	+	1	NA	intron (NM_013511, intron 1 of 19)	(T)n|Simple_repeat|Simple_repeat	17532	NM_013511	13822	Mm.306026	NM_013511	ENSMUSG00000019978	Epb41l2	4.1G|AW555191|D10Ertd398e|Epb4.1l2|NBL2	erythrocyte membrane protein band 4.1 like 2	protein-coding
mm_84517.1	chr9	67036106	67036137	-	1	NA	exon (NM_001164251, exon 3 of 10)	exon (NM_001164251, exon 3 of 10)	7750	NM_001164252	22003	Mm.121878	NM_024427	ENSMUSG00000032366	Tpm1	AA986836|AI854628|TM2|Tm3|Tmpa|Tpm-1|alpha-TM	tropomyosin 1, alpha	protein-coding
mm_164779.1	chr18	4909200	4909207	+	1	NA	Intergenic	L1MC4a|LINE|L1	96717	NR_045881	100038439	Mm.387569	NR_045881	ENSMUSG00000097043	Gm10556	ENSMUSG00000073646	predicted gene 10556	ncRNA
mm_92436.1	chr10	77199330	77199338	-	1	NA	Intergenic	Intergenic	-32804	NM_009929	12822	Mm.4352	NM_009929	ENSMUSG00000001435	Col18a1	-	collagen, type XVIII, alpha 1	protein-coding
mm_165244.1	chr2	67208472	67208472	+	1	NA	Intergenic	Intergenic	34638	NM_001033477	383709	Mm.244520	NM_001033477		Gm1322	-	predicted gene 1322	protein-coding
mm_40123.1	chr5	34989631	34989675	+	1	NA	intron (NM_173402, intron 3 of 16)	intron (NM_173402, intron 3 of 16)	-9425	NM_001163512	71729	Mm.196208	NM_173402	ENSMUSG00000029101	Rgs12	1200016K18Rik|4632412M04Rik|AI481290|E130309H11	regulator of G-protein signaling 12	protein-coding
mm_164333.1	chr16	10796359	10796370	+	1	NA	TTS (NM_013637)	TTS (NM_013637)	459	NM_013637	19118	Mm.42733	NM_013637	ENSMUSG00000022501	Prm1	Prm-1	protamine 1	protein-coding
mm_91310.1	chr10	24921841	24921857	-	1	NA	intron (NM_007482, intron 2 of 7)	L1ME1|LINE|L1	5621	NM_007482	11846	Mm.154144	NM_007482	ENSMUSG00000019987	Arg1	AI|AI256583|Arg-1|PGIF	arginase, liver	protein-coding
mm_6707.1	chr1	82286817	82286829	-	1	NA	exon (NM_010570, exon 1 of 2)	exon (NM_010570, exon 1 of 2)	4616	NM_010570	16367	Mm.4952	NM_010570	ENSMUSG00000055980	Irs1	G972R|IRS-1	insulin receptor substrate 1	protein-coding
mm_93501.1	chr10	112928885	112928901	-	1	NA	5' UTR (NM_001033474, exon 1 of 1)	5' UTR (NM_001033474, exon 1 of 1)	133	NM_001033474	382423	Mm.431239	NM_001033474	ENSMUSG00000074748	Atxn7l3b	4921506J03Rik|6230409E21Rik|AI315132|ENSMUSG00000074747	ataxin 7-like 3B	protein-coding
mm_56313.1	chr6	92214898	92214906	-	1	NA	promoter-TSS (NM_030081)	promoter-TSS (NM_030081)	-91	NM_030081	78287	Mm.290734	NM_030081	ENSMUSG00000014550	Rbsn	5330426D11Rik|Zfyve20	rabenosyn, RAB effector	protein-coding
mm_87266.1	chr10	41528749	41528759	+	1	NA	exon (NM_016898, exon 6 of 6)	exon (NM_016898, exon 6 of 6)	9254	NM_016898	53599	Mm.269815	NM_016898	ENSMUSG00000019818	Cd164	A115|A24|AA589639|AW540279|MGC-24|MSSP	CD164 antigen	protein-coding
mm_82529.1	chr9	20668000	20668014	-	1	NA	TTS (NM_173777)	TTS (NM_173777)	15877	NM_023371	23988	Mm.7906	NM_023371	ENSMUSG00000032171	Pin1	0610025L01Rik|D9Bwg1161e	protein (peptidyl-prolyl cis/trans isomerase) NIMA-interacting 1	protein-coding
mm_53284.1	chr6	128914259	128914273	+	1	NA	Intergenic	Intergenic	17579	NR_106107	102465757		NR_106107	ENSMUSG00000098359	Mir7649	mmu-mir-7649	microRNA 7649	ncRNA
mm_168210.1	chr10	75860183	75860184	-	1	NA	promoter-TSS (NM_010798)	promoter-TSS (NM_010798)	67	NM_010798	17319	Mm.2326	NM_010798	ENSMUSG00000033307	Mif	GIF|Glif	macrophage migration inhibitory factor	protein-coding
mm_135402.1	chr16	44703750	44703798	-	1	NA	Intergenic	Intergenic	-20527	NM_145972	212547	Mm.310573	NM_145972	ENSMUSG00000036208	Nepro	-	nucleolus and neural progenitor protein	protein-coding
mm_114672.1	chr13	80207654	80207656	+	1	NA	Intergenic	Intergenic	-675767	NM_001042591	105171	Mm.423137	NM_001042591	ENSMUSG00000074794	Arrdc3	AI450344|mKIAA1376	arrestin domain containing 3	protein-coding
mm_122156.1	chr14	31374257	31374274	-	1	NA	3' UTR (NM_001347585, exon 8 of 8)	3' UTR (NM_001347585, exon 8 of 8)	37541	NM_009796	12339	Mm.201535	NM_009796	ENSMUSG00000021893	Capn7	AU022319|PalBH	calpain 7	protein-coding
mm_72703.1	chr8	84978614	84978629	+	1	NA	5' UTR (NM_008416, exon 1 of 1)	5' UTR (NM_008416, exon 1 of 1)	127	NM_008416	16477	Mm.1167	NM_008416	ENSMUSG00000052837	Junb	-	jun B proto-oncogene	protein-coding
mm_54418.1	chr6	32897040	32897060	-	1	NA	intron (NM_025336, intron 4 of 7)	intron (NM_025336, intron 4 of 7)	163102	NM_025336	66075	Mm.21501	NM_025336	ENSMUSG00000053768	Chchd3	0610041L09Rik|1700039J09Rik|AW558177	coiled-coil-helix-coiled-coil-helix domain containing 3	protein-coding
mm_123638.1	chr14	68582079	68582092	-	1	NA	promoter-TSS (NM_021475)	promoter-TSS (NM_021475)	-13	NM_021475	58860	Mm.36742	NM_021475	ENSMUSG00000022057	Adamdec1	2210414L24Rik|AI574231|Dcsn	ADAM-like, decysin 1	protein-coding
mm_80803.1	chr9	96268479	96268522	+	1	NA	intron (NM_001184710, intron 1 of 9)	B1F|SINE|Alu	9252	NM_001184710	211586	Mm.17977	NM_178667	ENSMUSG00000032411	Tfdp2	1110029I05Rik|A330080J22Rik|DP-3|DP3	transcription factor Dp 2	protein-coding
mm_38521.1	chr4	141424035	141424074	-	1	NA	exon (NM_013868, exon 3 of 3)	exon (NM_013868, exon 3 of 3)	3275	NM_013868	29818	Mm.46181	NM_013868	ENSMUSG00000006221	Hspb7	27kDa|Hsp25-2|cvHsp	heat shock protein family, member 7 (cardiovascular)	protein-coding
mm_37663.1	chr4	129111795	129111830	-	1	NA	TTS (NM_001290706)	TTS (NM_001290706)	6264	NM_001290706	66260	Mm.25295	NM_025452	ENSMUSG00000028786	Tmem54	1810017F10Rik|AI507302	transmembrane protein 54	protein-coding
mm_91856.1	chr10	59322227	59322231	-	1	NA	Intergenic	Intergenic	-1067	NM_001316371	18451	Mm.2212	NM_011030	ENSMUSG00000019916	P4ha1	AL022634|P4ha	procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha 1 polypeptide	protein-coding
mm_45570.1	chr5	73338555	73338576	-	1	NA	5' UTR (NM_001310636, exon 1 of 6)	5' UTR (NM_001310636, exon 1 of 6)	382	NM_026950	433904	Mm.274892	NM_026950	ENSMUSG00000029153	Ociad2	1810027I20Rik	OCIA domain containing 2	protein-coding
mm_17368.1	chr2	26910534	26910563	-	1	NA	promoter-TSS (NM_001033908)	promoter-TSS (NM_001033908)	94	NM_011513	20933	Mm.397932	NM_011513	ENSMUSG00000015776	Med22	AW212655|AW558812|Surf-5|Surf5	mediator complex subunit 22	protein-coding
mm_119641.1	chr14	51918419	51918430	+	1	NA	promoter-TSS (NM_001128634)	promoter-TSS (NM_001128634)	-337	NM_001128634	219038	Mm.296425	NM_001128634	ENSMUSG00000008813	Tppp2	Gm1790|Gm77	tubulin polymerization-promoting protein family member 2	protein-coding
mm_38889.1	chr4	149749432	149749440	-	1	NA	intron (NM_027460, intron 5 of 6)	intron (NM_027460, intron 5 of 6)	-11368	NM_177672	230917	Mm.266704	NM_177672	ENSMUSG00000044700	Tmem201	AV028368|D4Ertd429e|Net5|Samp1	transmembrane protein 201	protein-coding
mm_77020.1	chr8	108584468	108584477	-	1	NA	non-coding (NR_077224, exon 1 of 2)	non-coding (NR_077224, exon 1 of 2)	205	NR_077224	109215	Mm.65282	NR_077224	ENSMUSG00000110613	Lncbate1	3010033K07Rik|Lnc-BATE1	brown adipose tissue enriched long non-coding RNA 1	ncRNA
mm_159693.1	chr5	24394067	24394067	+	1	NA	promoter-TSS (NM_029020)	promoter-TSS (NM_029020)	-89	NM_029020	74610	Mm.283914	NM_029020	ENSMUSG00000028973	Abcb8	4833412N02Rik|AA409895	ATP-binding cassette, sub-family B (MDR/TAP), member 8	protein-coding
mm_22439.1	chr2	181693563	181693590	-	1	NA	5' UTR (NM_001291208, exon 1 of 5)	5' UTR (NM_001291208, exon 1 of 5)	234	NM_001291206	56470	Mm.274366	NM_026446	ENSMUSG00000002458	Rgs19	2610042F04Rik|AI324841|AW547781|GAIP	regulator of G-protein signaling 19	protein-coding
mm_31800.1	chr4	63998335	63998337	+	1	NA	intron (NM_011607, intron 12 of 25)	MT2B1|LTR|ERVL	48679	NM_011607	21923	Mm.980	NM_011607	ENSMUSG00000028364	Tnc	AI528729|C130033P17Rik|Hxb|TN|TN-C|Ten|cytotactin|tenascin-C	tenascin C	protein-coding
mm_136584.1	chr17	4880580	4880581	+	1	NA	Intergenic	Intergenic	-114494	NM_001085355	239985	Mm.133401	NM_001085355	ENSMUSG00000069729	Arid1b	8030481M12|9330189K18Rik|AI836955|Ardi1b|B230217J03Rik|mKIAA1235	AT rich interactive domain 1B (SWI-like)	protein-coding
mm_45864.1	chr5	87929977	87929980	-	1	NA	exon (NM_007786, exon 4 of 5)	exon (NM_007786, exon 4 of 5)	4345	NM_007786	12994	Mm.296303	NM_007786	ENSMUSG00000001622	Csn3	AW208918|CSN10|Csnk	casein kappa	protein-coding
mm_86963.1	chr10	25221001	25221028	+	1	NA	intron (NM_018747, intron 6 of 7)	intron (NM_018747, intron 6 of 7)	-20844	NM_001347460	432442	Mm.485937	NM_018747	ENSMUSG00000039166	Akap7	6430401D08|AI662165|AKAP15|Akap18|BB170514	A kinase (PRKA) anchor protein 7	protein-coding
mm_162035.1	chr19	55253362	55253362	+	1	NA	promoter-TSS (NM_027976)	promoter-TSS (NM_027976)	-7	NM_027976	433256	Mm.292056	NM_027976	ENSMUSG00000024981	Acsl5	1700030F05Rik|ACS2|ACS5|Facl5	acyl-CoA synthetase long-chain family member 5	protein-coding
mm_147663.1	chr18	60610091	60610112	-	1	NA	promoter-TSS (NM_001109975)	promoter-TSS (NM_001109975)	3	NM_001109975	104027	Mm.252321	NM_177340	ENSMUSG00000043079	Synpo	9030217H17Rik|9130229N11|9330140I15Rik|AW046661	synaptopodin	protein-coding
mm_49734.1	chr6	34745661	34745690	+	1	NA	exon (NM_145575, exon 3 of 12)	exon (NM_145575, exon 3 of 12)	-34757	NM_001289657	76223	Mm.150047	NM_178630	ENSMUSG00000038836	Agbl3	2900053G10Rik|4930431N21Rik|6530406M24Rik|CCP3	ATP/GTP binding protein-like 3	protein-coding
mm_93427.1	chr10	108894895	108894905	-	1	NA	intron (NM_001252341, intron 3 of 11)	intron (NM_001252341, intron 3 of 11)	116075	NM_009306	20979	Mm.289702	NM_009306	ENSMUSG00000035864	Syt1	AW124717|G630098F17Rik|SytI	synaptotagmin I	protein-coding
mm_119062.1	chr14	30732878	30732882	+	1	NA	intron (NM_001166532, intron 1 of 20)	L1M2|LINE|L1	17265	NM_001166532	54650	Mm.294662	NM_019460	ENSMUSG00000006527	Sfmbt1	4930442N21Rik|9330180L21Rik|AA536974|Sfmbt|Smr	Scm-like with four mbt domains 1	protein-coding
mm_124818.1	chr15	9071328	9071340	+	1	NA	promoter-TSS (NM_001085410)	promoter-TSS (NM_001085410)	74	NM_001040395	68646	Mm.244226	NM_001040395	ENSMUSG00000022253	Nadk2	MNADK|Nadkd1	NAD kinase 2, mitochondrial	protein-coding
mm_159500.1	chr4	43700808	43700808	-	1	NA	promoter-TSS (NM_019485)	promoter-TSS (NM_019485)	-1	NM_019485	56014	Mm.331571	NM_019485	ENSMUSG00000050215	Olfr70	MOR262-10|mOR6	olfactory receptor 70	protein-coding
mm_159992.1	chr6	116134564	116134564	-	1	NA	intron (NM_177412, intron 2 of 5)	intron (NM_177412, intron 2 of 5)	58810	NM_177412	330401	Mm.425352	NM_177412	ENSMUSG00000030126	Tmcc1	3632431M01Rik|mKIAA0779	transmembrane and coiled coil domains 1	protein-coding
mm_131995.1	chr16	25059362	25059380	+	1	NA	promoter-TSS (NR_040374)	promoter-TSS (NR_040374)	-268	NR_040374	319487	Mm.137341	NR_040374	ENSMUSG00000096960	A230028O05Rik	-	RIKEN cDNA A230028O05 gene	ncRNA
mm_3971.1	chr1	164193043	164193053	+	1	NA	exon (NM_007976, exon 13 of 25)	exon (NM_007976, exon 13 of 25)	-40831	NR_037987	100503816	Mm.398579	NR_037987	ENSMUSG00000086593	Gm16548	-	predicted gene 16548	ncRNA
mm_161038.1	chr12	30132643	30132643	-	1	NA	promoter-TSS (NM_009417)	promoter-TSS (NM_009417)	-19	NM_009417	22018	Mm.4991	NM_009417	ENSMUSG00000020673	Tpo	-	thyroid peroxidase	protein-coding
mm_111590.1	chr12	101975766	101975776	-	1	NA	promoter-TSS (NM_016856)	promoter-TSS (NM_016856)	-203	NM_016856	51786	Mm.716	NM_016856	ENSMUSG00000041781	Cpsf2	100kDa|2610024B04Rik|AI662483|Cpsf|MCPSF|mKIAA1367	cleavage and polyadenylation specific factor 2	protein-coding
mm_120629.1	chr14	70466456	70466467	+	1	NA	intron (NM_145981, intron 4 of 4)	intron (NM_145981, intron 4 of 4)	8944	NM_145981	105653	Mm.192598	NM_145981	ENSMUSG00000003469	Phyhip	AW049870|C630010D02Rik|Lnap1ip|PAHX-AP#1|PAHX-AP1	phytanoyl-CoA hydroxylase interacting protein	protein-coding
mm_107635.1	chr12	52097738	52097775	+	1	NA	promoter-TSS (NM_029760)	promoter-TSS (NM_029760)	10	NM_029760	76826	Mm.244781	NM_029760	ENSMUSG00000035142	Nubpl	2410170E07Rik	nucleotide binding protein-like	protein-coding
mm_43916.1	chr5	144556577	144556580	+	1	NA	3' UTR (NM_016789, exon 5 of 5)	3' UTR (NM_016789, exon 5 of 5)	10691	NM_016789	53324	Mm.10099	NM_016789	ENSMUSG00000059991	Nptx2	Narp|np2	neuronal pentraxin 2	protein-coding
mm_7480.1	chr1	120517619	120517626	-	1	NA	Intergenic	Intergenic	-12538	NM_010766	17167	Mm.1856	NM_010766	ENSMUSG00000026390	Marco	AI323439|Ly112|Scara2	macrophage receptor with collagenous structure	protein-coding
mm_27274.1	chr3	40746441	40746450	-	1	NA	intron (NM_011020, intron 1 of 18)	intron (NM_011020, intron 1 of 18)	832	NM_011020	18415	Mm.39330	NM_011020	ENSMUSG00000025757	Hspa4l	94kDa|AI461691|APG-1|Osp94	heat shock protein 4 like	protein-coding
mm_118602.1	chr14	20707557	20707616	+	1	NA	promoter-TSS (NM_001252082)	promoter-TSS (NM_001252082)	34	NM_001252082	268721	Mm.275082	NM_027996	ENSMUSG00000021819	Zswim8	2310021P13Rik|4832404P21Rik|Kiaa0913|mKIAA0913	zinc finger SWIM-type containing 8	protein-coding
mm_67342.1	chr7	79822172	79822195	-	1	NA	3' UTR (NM_008486, exon 20 of 20)	3' UTR (NM_008486, exon 20 of 20)	11456	NM_008589	17293	Mm.31472	NM_008589	ENSMUSG00000030543	Mesp2	bHLHc6	mesoderm posterior 2	protein-coding
mm_20702.1	chr2	132945736	132945751	-	1	NA	5' UTR (NM_198029, exon 1 of 15)	5' UTR (NM_198029, exon 1 of 15)	293	NM_198029	241639	Mm.209784	NM_198029	ENSMUSG00000027356	Fermt1	5830467P10Rik|Kindlin-1	fermitin family member 1	protein-coding
mm_108497.1	chr12	83731571	83731591	+	1	NA	intron (NM_008943, intron 10 of 11)	PB1D10|SINE|Alu	-32053	NM_001205343	170721	Mm.133443	NM_130887	ENSMUSG00000021223	Papln	E030033C16Rik	papilin, proteoglycan-like sulfated glycoprotein	protein-coding
mm_86182.1	chr9	119209097	119209109	-	1	NA	promoter-TSS (NM_133980)	promoter-TSS (NM_133980)	2	NM_133980	102570	Mm.38775	NM_133980	ENSMUSG00000074028	Slc22a13	AI648912|OCTL1|OCTL3|ORCTL3	solute carrier family 22 (organic cation transporter), member 13	protein-coding
mm_83738.1	chr9	51101781	51101790	-	1	NA	exon (NM_177702, exon 1 of 6)	exon (NM_177702, exon 1 of 6)	293	NM_177702	235345	Mm.72828	NM_177702	ENSMUSG00000032057	4833427G06Rik	-	RIKEN cDNA 4833427G06 gene	protein-coding
mm_43542.1	chr5	137527283	137527285	+	1	NA	TTS (NM_010312)	TTS (NM_010312)	2310	NR_105846	102465227		NR_105846	ENSMUSG00000098597	Mir6418	Gm27629|mir-6418|mmu-mir-6418	microRNA 6418	ncRNA
mm_150647.1	chr19	41911876	41911895	+	1	NA	promoter-TSS (NM_023418)	promoter-TSS (NM_023418)	14	NM_023418	18648	Mm.16783	NM_023418	ENSMUSG00000011752	Pgam1	2310050F24Rik|Pgam-1	phosphoglycerate mutase 1	protein-coding
mm_58523.1	chr7	4147325	4147340	+	1	NA	TTS (NM_175529)	TTS (NM_175529)	2540	NM_175529	243813	Mm.347643	NM_175529	ENSMUSG00000043432	Leng9	9530024C23Rik|F630035L11Rik	leukocyte receptor cluster (LRC) member 9	protein-coding
mm_28055.1	chr3	84191224	84191236	-	1	NA	exon (NM_030706, exon 6 of 12)	exon (NM_030706, exon 6 of 12)	16592	NR_036654	624713	Mm.442604	NR_036654		Gm6525	EG624713	ribosomal protein L36a pseudogene	pseudo
mm_164405.1	chr16	35568162	35568164	+	1	NA	intron (NM_013661, intron 1 of 21)	Tigger15a|DNA|TcMar-Tigger	26801	NM_013661	20357	Mm.42015	NM_013661	ENSMUSG00000052133	Sema5b	AI893641|SemG|Semag|mKIAA1445	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B	protein-coding
mm_62852.1	chr7	114415378	114415384	+	1	NA	promoter-TSS (NR_029438)	promoter-TSS (NR_029438)	127	NM_011055	18576	Mm.430730	NM_011055	ENSMUSG00000030671	Pde3b	9830102A01Rik|AI847709	phosphodiesterase 3B, cGMP-inhibited	protein-coding
mm_34350.1	chr4	144529409	144529423	+	1	NA	TTS (NM_198662)	TTS (NM_198662)	9594	NM_198662	381572	Mm.184290	NM_198662	ENSMUSG00000028593	9430007A20Rik	Aadacl4|Gm1034	RIKEN cDNA 9430007A20 gene	protein-coding
mm_82125.1	chr9	123509223	123509236	+	1	NA	intron (NM_013860, intron 2 of 7)	intron (NM_013860, intron 2 of 7)	-20653	NM_030692	83493	Mm.273671	NM_030692	ENSMUSG00000025240	Sacm1l	SAC1|Sac1p|mKIAA0851	SAC1 suppressor of actin mutations 1-like (yeast)	protein-coding
mm_129235.1	chr15	76617116	76617126	-	1	NA	promoter-TSS (NM_028064)	promoter-TSS (NM_028064)	-269	NM_028064	72027	Mm.276829	NM_028064	ENSMUSG00000063354	Slc39a4	1600025H15Rik|AU041686|AWMS2|ZIP4	solute carrier family 39 (zinc transporter), member 4	protein-coding
mm_101351.1	chr11	23739753	23739764	-	1	NA	Intergenic	Intergenic	31212	NM_009044	19696	Mm.4869	NM_009044	ENSMUSG00000020275	Rel	c-Rel	reticuloendotheliosis oncogene	protein-coding
mm_4351.1	chr1	171896921	171896943	+	1	NA	Intergenic	RLTR20A3_MM|LTR|ERVK	-20530	NM_001347187	30925	Mm.486404	NM_030710	ENSMUSG00000015314	Slamf6	KAL1|KAL1b|Ly108|NTB-A|NTBA|SF2000	SLAM family member 6	protein-coding
mm_8615.1	chr1	156036384	156036400	-	1	NA	promoter-TSS (NM_144791)	promoter-TSS (NM_144791)	88	NM_144791	208263	Mm.211654	NM_144791	ENSMUSG00000026466	Tor1aip1	LAP1|Lap1B	torsin A interacting protein 1	protein-coding
mm_15141.1	chr2	153974815	153974830	+	1	NA	promoter-TSS (NM_001080811)	promoter-TSS (NM_001080811)	-123	NM_001080811	545477	Mm.379973	NM_001080811	ENSMUSG00000078998	Bpifa6	EG545477|Gm5840|Splunc6	BPI fold containing family A, member 6	protein-coding
mm_115415.1	chr13	115089467	115089486	+	1	NA	exon (NM_134058, exon 1 of 2)	exon (NM_134058, exon 1 of 2)	682	NM_134058	105083	Mm.486295	NM_134058	ENSMUSG00000042275	Pelo	AA409897|AI852218	pelota homolog (Drosophila)	protein-coding
mm_16336.1	chr2	174330068	174330098	+	1	NA	promoter-TSS (NM_001077510)	promoter-TSS (NM_001077510)	-6	NM_001077510	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_21092.1	chr2	153191522	153191536	-	1	NA	intron (NM_133847, intron 8 of 17)	intron (NM_133847, intron 8 of 17)	30228	NM_133847	99237	Mm.330674	NM_133847	ENSMUSG00000068040	Tm9sf4	AA986553|AU045326|B930079E06|mKIAA0255	transmembrane 9 superfamily protein member 4	protein-coding
mm_16649.1	chr2	6256285	6256288	-	1	NA	intron (NR_040333, intron 3 of 6)	intron (NR_040333, intron 3 of 6)	-43292	NM_024208	67856	Mm.38342	NM_024208	ENSMUSG00000039063	Echdc3	2310005D12Rik|AI662097	enoyl Coenzyme A hydratase domain containing 3	protein-coding
mm_124309.1	chr14	103099561	103099571	-	1	NA	promoter-TSS (NM_015822)	promoter-TSS (NM_015822)	0	NM_001347600	50789	Mm.214746	NM_015822	ENSMUSG00000022124	Fbxl3	AU041772|AW212966|FBK|Fbl3a|Fbxl3a|Ovtm|Play68	F-box and leucine-rich repeat protein 3	protein-coding
mm_28830.1	chr3	96414826	96414839	-	1	NA	promoter-TSS (NR_001579)	promoter-TSS (NR_001579)	1	NR_001579	21748		NR_001579	ENSMUSG00000064796	Terc	mTER|mTR	telomerase RNA component	ncRNA
mm_43348.1	chr5	135168352	135168373	+	1	NA	promoter-TSS (NM_009745)	promoter-TSS (NM_009745)	-10	NM_009745	12054	Mm.405834	NM_009745	ENSMUSG00000029681	Bcl7b	-	B cell CLL/lymphoma 7B	protein-coding
mm_68305.1	chr7	105746600	105746619	-	1	NA	3' UTR (NM_009906, exon 13 of 13)	3' UTR (NM_009906, exon 13 of 13)	-2271	NM_020024	24075	Mm.274846	NM_020024	ENSMUSG00000043866	Taf10	30kDa|AU041226|TAFII30|Taf2h	TATA-box binding protein associated factor 10	protein-coding
mm_163505.1	chr12	113140593	113140599	+	1	NA	promoter-TSS (NM_001347443)	promoter-TSS (NM_001347443)	-9	NM_001347443	68337	Mm.133825	NM_024223	ENSMUSG00000006356	Crip2	0610010I23Rik|AW743261|C77570|CRP2|CRP4|Crp|ESP1|Hlp	cysteine rich protein 2	protein-coding
mm_157148.1	chrX	9461864	9461874	-	1	NA	intron (NM_007807, intron 3 of 12)	intron (NM_007807, intron 3 of 12)	7455	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_30312.1	chr3	151731064	151731067	-	1	NA	3' UTR (NM_133871, exon 8 of 8)	3' UTR (NM_133871, exon 8 of 8)	18894	NM_133871	99899	Mm.30756	NM_133871	ENSMUSG00000028037	Ifi44	A430056A10Rik|AW261460|MTAP44|p44	interferon-induced protein 44	protein-coding
mm_36324.1	chr4	70378220	70378262	-	1	NA	intron (NM_145990, intron 4 of 36)	GSAT_MM|Satellite|Satellite	32194	NM_001313762	214444	Mm.370777	NM_145990	ENSMUSG00000039298	Cdk5rap2	2900018K03Rik|an|mKIAA1633	CDK5 regulatory subunit associated protein 2	protein-coding
mm_10539.1	chr2	16458860	16458908	+	1	NA	intron (NM_026162, intron 1 of 13)	intron (NM_026162, intron 1 of 13)	102580	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding
mm_141885.1	chr17	34860861	34860872	-	1	NA	exon (NM_008198, exon 4 of 18)	exon (NM_008198, exon 4 of 18)	1648	NM_001142706	14962	Mm.653	NM_008198	ENSMUSG00000090231	Cfb	AI195813|AI255840|B|Bf|C2|Fb|H2-Bf	complement factor B	protein-coding
mm_119321.1	chr14	37068014	37068024	+	1	NA	promoter-TSS (NM_173418)	promoter-TSS (NM_173418)	-30	NM_173418	239038	Mm.134302	NM_173418	ENSMUSG00000043418	Lrit2	A930010E21Rik|Lrrc22	leucine-rich repeat, immunoglobulin-like and transmembrane domains 2	protein-coding
mm_125169.1	chr15	31337016	31337025	+	1	NA	intron (NM_027496, intron 1 of 3)	intron (NM_027496, intron 1 of 3)	30739	NM_001164441	67434	Mm.102470	NM_026153	ENSMUSG00000022237	Ankrd33b	0610012A05Rik|3021401C12Rik|5730557B15Rik	ankyrin repeat domain 33B	protein-coding
mm_101661.1	chr11	36677914	36677939	-	1	NA	intron (NM_011856, intron 2 of 28)	intron (NM_011856, intron 2 of 28)	266315	NM_001290702	23964	Mm.439889	NM_011856	ENSMUSG00000049336	Tenm2	Odz2|Odz3|Ten-2|Ten-m2	teneurin transmembrane protein 2	protein-coding
mm_124805.1	chr15	8832280	8832293	+	1	NA	Intergenic	Intergenic	-121479	NM_148938	20512	Mm.204834	NM_148938	ENSMUSG00000005360	Slc1a3	AI504299|B430115D02Rik|Eaat1|GLAST|GLAST-1|GLU-T|GluT-1|Gmt1|MGluT1	solute carrier family 1 (glial high affinity glutamate transporter), member 3	protein-coding
mm_171750.1	chr5	101888114	101888117	-	1	NA	exon (NM_172882, exon 39 of 67)	exon (NM_172882, exon 39 of 67)	122985	NM_173370	74596	Mm.46764	NM_173370	ENSMUSG00000029330	Cds1	4833409J18Rik|AI314024|AW125888	CDP-diacylglycerol synthase 1	protein-coding
mm_108266.1	chr12	78748866	78748920	+	1	NA	promoter-TSS (NM_019579)	promoter-TSS (NM_019579)	-54	NM_019579	56217	Mm.425777	NM_019579	ENSMUSG00000021112	Mpp5	3830420B02Rik|AI255216|AI644496|Pals1	membrane protein, palmitoylated 5 (MAGUK p55 subfamily member 5)	protein-coding
mm_126457.1	chr15	80931289	80931322	+	1	NA	3' UTR (NM_177124, exon 22 of 22)	3' UTR (NM_177124, exon 22 of 22)	-8734	NR_039573	100628612		NR_039573	ENSMUSG00000092868	Mir5113	mir-5113|mmu-mir-5113|mu-mir-5113	microRNA 5113	ncRNA
mm_154350.1	chrM	5818	5829	+	1	NA	NA	Intergenic	NA	NA								
mm_91915.1	chr10	60299146	60299172	-	1	NA	exon (NM_011179, exon 9 of 15)	exon (NM_011179, exon 9 of 15)	14698	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_50033.1	chr6	41135092	41135100	+	1	NA	Intergenic	Intergenic	-99587	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_76845.1	chr8	105295935	105295948	-	1	NA	5' UTR (NM_177788, exon 1 of 14)	5' UTR (NM_177788, exon 1 of 14)	157	NM_177788	277978	Mm.40228	NM_177788	ENSMUSG00000043251	Exoc3l	C730015A04Rik|Exoc3l1	exocyst complex component 3-like	protein-coding
mm_33756.1	chr4	134343494	134343506	+	1	NA	promoter-TSS (NM_001346578)	promoter-TSS (NM_001346578)	34	NM_001346578	230810	Mm.358876	NM_001039677	ENSMUSG00000028836	Slc30a2	ZnT-2|Znt2	solute carrier family 30 (zinc transporter), member 2	protein-coding
mm_71193.1	chr8	40875632	40875640	+	1	NA	intron (NM_007514, intron 1 of 11)	intron (NM_007514, intron 1 of 11)	13269	NM_001044740	11988	Mm.4676	NM_007514	ENSMUSG00000031596	Slc7a2	20.5|AI158848|Atrc2|CAT-2|Cat2|Tea	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	protein-coding
mm_108772.1	chr12	89812442	89812465	+	1	NA	promoter-TSS (NM_001252074)	promoter-TSS (NM_001252074)	-30	NM_001252074	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding
mm_73249.1	chr8	104295731	104295733	+	1	NA	intron (NM_181990, intron 3 of 3)	RLTR43C|LTR|ERVK	-2551	NM_027022	73381	Mm.272746	NM_027022	ENSMUSG00000074127	Cmtm2a	1700001K04Rik|1700041N15Rik|1700063K20Rik|AI449770|ARR19|C32|CKLF3|CKLF4|CKLF5|Cklf|Cklf1|Cklfsf2-1b|Cklfsf2a|UCK-1	CKLF-like MARVEL transmembrane domain containing 2A	protein-coding
mm_26459.1	chr3	143017123	143017148	+	1	NA	Intergenic	Intergenic	-135131	NM_178654	109333	Mm.244236	NM_178654	ENSMUSG00000004591	Pkn2	6030436C20Rik|AI507382|PRK2|Prkcl2|Stk7	protein kinase N2	protein-coding
mm_10213.1	chr2	5845244	5845311	+	1	NA	promoter-TSS (NM_133837)	promoter-TSS (NM_133837)	243	NM_016918	53893	Mm.251904	NM_016918	ENSMUSG00000025817	Nudt5	-	nudix (nucleoside diphosphate linked moiety X)-type motif 5	protein-coding
mm_111490.1	chr12	98901479	98901492	-	1	NA	promoter-TSS (NM_001081191)	promoter-TSS (NM_001081191)	-1	NM_001081191	319670	Mm.390484	NM_001081191	ENSMUSG00000051166	Eml5	BC027154|C130068M19Rik	echinoderm microtubule associated protein like 5	protein-coding
mm_147534.1	chr18	53417966	53418003	-	1	NA	promoter-TSS (NM_008908)	promoter-TSS (NM_008908)	23	NM_008908	19038	Mm.4587	NM_008908	ENSMUSG00000024538	Ppic	CyP-20c	peptidylprolyl isomerase C	protein-coding
mm_49438.1	chr6	29313508	29313541	+	1	NA	Intergenic	L1M6|LINE|L1	-5616	NM_001289663	330277	Mm.87624	NM_207258	ENSMUSG00000039742	Fam71f1	GARI-L1|Gm764|NYD-SP18	family with sequence similarity 71, member F1	protein-coding
mm_110577.1	chr12	56497730	56497733	-	1	NA	intron (NR_045082, intron 5 of 6)	L1MB5|LINE|L1	31689	NR_045082	104798	Mm.310950	NR_045082		E030019B13Rik	AI413669	RIKEN cDNA E030019B13 gene	ncRNA
mm_73094.1	chr8	94555971	94555989	+	1	NA	exon (NM_153507, exon 9 of 16)	exon (NM_153507, exon 9 of 16)	22952	NM_153507	234577	Mm.291815	NM_153507	ENSMUSG00000034361	Cpne2	3322401K10Rik	copine II	protein-coding
mm_169123.1	chr13	52359387	52359400	-	1	NA	Intergenic	RLTR9D|LTR|ERVK	171443	NM_001024474	68203	Mm.29362	NM_001024474	ENSMUSG00000047842	Diras2	2900052J15Rik|AI414999	DIRAS family, GTP-binding RAS-like 2	protein-coding
mm_84392.1	chr9	65512707	65512719	-	1	NA	Intergenic	Intergenic	51776	NM_138584	27965	Mm.272475	NM_138584	ENSMUSG00000032388	Spg21	ACP33|BM-019|C78576|D9Wsu18e|GL010|MAST	spastic paraplegia 21 homolog (human)	protein-coding
mm_41752.1	chr5	102845272	102845292	+	1	NA	5' UTR (NM_001346585, exon 1 of 7)	5' UTR (NM_001346585, exon 1 of 7)	275	NM_001346585	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding
mm_159598.1	chr4	126923117	126923117	-	1	NA	exon (NM_001114399, exon 5 of 30)	exon (NM_001114399, exon 5 of 30)	44806	NM_001114399	67785	Mm.165401	NM_001114399	ENSMUSG00000042446	Zmym4	6330503C17Rik|AI480785|AW493829|CDIR|D630001M21|MYM|Zfp262|Znf262|mKIAA0425	zinc finger, MYM-type 4	protein-coding
mm_1109.1	chr1	59764305	59764326	+	1	NA	promoter-TSS (NM_007561)	promoter-TSS (NM_007561)	36	NM_007561	12168	Mm.7106	NM_007561	ENSMUSG00000067336	Bmpr2	2610024H22Rik|AL117858|AW546137|BB189135|BMP-2|BMPR-2|BMPR-II|BMPRII|BRK-3|Gm20272	bone morphogenetic protein receptor, type II (serine/threonine kinase)	protein-coding
mm_169780.1	chr16	11144126	11144128	+	1	NA	intron (NR_027502, intron 19 of 22)	LSU-rRNA_Hsa|rRNA|rRNA	-9595	NM_029582	106200	Mm.291015	NM_029582	ENSMUSG00000022498	Txndc11	2810408E11Rik|AI427833|EFP1|Txdc11	thioredoxin domain containing 11	protein-coding
mm_87321.1	chr10	42860683	42860692	+	1	NA	5' UTR (NM_172938, exon 1 of 9)	5' UTR (NM_172938, exon 1 of 9)	175	NM_172938	268297	Mm.98731	NM_172938	ENSMUSG00000044770	Scml4	9330161D17|mFLJ00197	sex comb on midleg-like 4 (Drosophila)	protein-coding
mm_110567.1	chr12	55821197	55821207	-	1	NA	5' UTR (NM_019994, exon 1 of 41)	5' UTR (NM_019994, exon 1 of 41)	314	NM_019994	56784	Mm.292180	NM_019994	ENSMUSG00000021027	Ralgapa1	2310003F20Rik|4930400K19Rik|AI563624|GRIPE|Garnl1|Tulip1|mKIAA0884	Ral GTPase activating protein, alpha subunit 1	protein-coding
mm_116410.1	chr13	41473551	41473584	-	1	NA	intron (NM_001111324, intron 1 of 7)	intron (NM_001111324, intron 1 of 7)	13793	NM_001111324	18003	Mm.288980	NM_017464	ENSMUSG00000021365	Nedd9	Cas-L|CasL|HEF1|MEF1|Nedd-9|p105	neural precursor cell expressed, developmentally down-regulated gene 9	protein-coding
mm_29538.1	chr3	116711821	116711847	-	1	NA	intron (NM_144902, intron 1 of 7)	CpG	446	NM_144902	229782	Mm.190758	NM_144902	ENSMUSG00000027957	Slc35a3	2310050P13Rik	solute carrier family 35 (UDP-N-acetylglucosamine (UDP-GlcNAc) transporter), member 3	protein-coding
mm_4336.1	chr1	171855909	171855928	+	1	NA	TTS (NM_001252472)	TTS (NM_001252472)	16221	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_118336.1	chr13	114156985	114157010	-	1	NA	3' UTR (NM_172595, exon 5 of 5)	3' UTR (NM_172595, exon 5 of 5)	-5405	NR_045836	319803	Mm.386896	NM_177004		A430090L17Rik	-	RIKEN cDNA A430090L17 gene	ncRNA
mm_130159.1	chr15	91192011	91192027	-	1	NA	promoter-TSS (NM_011994)	promoter-TSS (NM_011994)	-212	NM_011994	26874	Mm.295456	NM_011994	ENSMUSG00000055782	Abcd2	ABC39|ALDL1|ALDR|ALDRP	ATP-binding cassette, sub-family D (ALD), member 2	protein-coding
mm_79936.1	chr9	65890525	65890538	+	1	NA	intron (NM_026515, intron 1 of 3)	intron (NM_026515, intron 1 of 3)	208	NM_026515	68026	Mm.351273	NM_026515	ENSMUSG00000040204	Pclaf	2810417H13Rik|AA409629|Ns5apt9|Ns5atp9|PAF15|Paf|mKIAA0101|p15(PAF)	PCNA clamp associated factor	protein-coding
mm_139471.1	chr17	55970590	55970603	+	1	NA	5' UTR (NM_009168, exon 1 of 7)	5' UTR (NM_009168, exon 1 of 7)	114	NM_009168	20420	Mm.20908	NM_009168	ENSMUSG00000039154	Shd	AI413439	src homology 2 domain-containing transforming protein D	protein-coding
mm_71428.1	chr8	46492790	46492801	+	1	NA	intron (NM_001302163, intron 1 of 20)	intron (NM_001302163, intron 1 of 20)	1829	NM_001302163	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_104114.1	chr11	86726443	86726461	-	1	NA	exon (NM_001003908, exon 7 of 32)	exon (NM_001003908, exon 7 of 32)	31040	NM_001003908	67300	Mm.254588	NM_001003908	ENSMUSG00000047126	Cltc	3110065L21Rik|CHC|R74732	clathrin, heavy polypeptide (Hc)	protein-coding
mm_44256.1	chr5	5479064	5479075	-	1	NA	promoter-TSS (NM_001200025)	promoter-TSS (NM_001200025)	74	NM_001200025	381716	Mm.276086	NM_001200025	ENSMUSG00000079666	1700015F17Rik	Gm1686	RIKEN cDNA 1700015F17 gene	protein-coding
mm_170905.1	chr2	30131060	30131065	-	1	NA	Intergenic	LTRIS2|LTR|ERV1	-2684	NM_146252	70296	Mm.19172	NM_146252	ENSMUSG00000039678	Tbc1d13	2600014A06Rik|BC025586	TBC1 domain family, member 13	protein-coding
mm_80749.1	chr9	95162923	95162941	+	1	NA	intron (NM_177909, intron 14 of 15)	intron (NM_177909, intron 14 of 15)	244338	NM_018763	54371	Mm.212446	NM_018763	ENSMUSG00000033350	Chst2	AI428561|AW121776|C130041E03Rik|Chts2|GST-2|GlcNAc6ST|Gn6st	carbohydrate sulfotransferase 2	protein-coding
mm_159840.1	chr5	134609115	134609115	-	1	NA	intron (NM_020044, intron 1 of 12)	intron (NM_020044, intron 1 of 12)	5910	NM_022964	56743	Mm.391375	NM_020044	ENSMUSG00000040751	Lat2	AW125574|LAB|NTAL|WSCR5|Wbscr15|Wbscr5	linker for activation of T cells family, member 2	protein-coding
mm_32244.1	chr4	102511182	102511227	+	1	NA	intron (NM_019840, intron 5 of 14)	intron (NM_019840, intron 5 of 14)	-58856	NM_001177980	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_96931.1	chr11	70519169	70519175	+	1	NA	promoter-TSS (NM_146020)	promoter-TSS (NM_146020)	-37	NM_146020	216871	Mm.22551	NM_146020	ENSMUSG00000046811	Gltpd2	C730027E14Rik	glycolipid transfer protein domain containing 2	protein-coding
mm_41386.1	chr5	90768512	90768526	+	1	NA	promoter-TSS (NM_023785)	promoter-TSS (NM_023785)	1	NM_023785	57349	Mm.293614	NM_023785	ENSMUSG00000029372	Ppbp	2400003M24Rik|AI854500|CTAP3|CTAPIII|Cxcl7|LA-PF4|LDGF|MDGF|NAP-2|NAP-2-L1|Scyb7|TGB|TGB1|THBGB1|b-TG1|beta-TG	pro-platelet basic protein	protein-coding
mm_158761.1	chrX	166498858	166498873	-	1	NA	TTS (NM_001007577)	TTS (NM_001007577)	11613	NM_001007577	245695	Mm.336318	NM_001007577	ENSMUSG00000051224	Tceanc	A630018P17Rik|Gm390	transcription elongation factor A (SII) N-terminal and central domain containing	protein-coding
mm_21189.1	chr2	155357393	155357431	-	1	NA	promoter-TSS (NM_001004721)	promoter-TSS (NM_001004721)	12	NM_001004721	228812	Mm.5434	NM_001004721	ENSMUSG00000038383	Pigu	5430426F17Rik|BC028278|Cdc91l1	phosphatidylinositol glycan anchor biosynthesis, class U	protein-coding
mm_34009.1	chr4	137993017	137993036	+	1	NA	promoter-TSS (NM_001256198)	promoter-TSS (NM_001256198)	-430	NM_001256198	230861	Mm.268903	NM_172703	ENSMUSG00000028760	Eif4g3	1500002J22Rik|4930523M17Rik|G1-419-52|eIF4GII|repro8	eukaryotic translation initiation factor 4 gamma, 3	protein-coding
mm_34762.1	chr4	152353592	152353604	+	1	NA	exon (NM_001081376, exon 3 of 42)	exon (NM_001081376, exon 3 of 42)	14947	NM_001081376	269610	Mm.40192	NM_029216	ENSMUSG00000005045	Chd5	4930532L22Rik|AW060752|B230399N07Rik|CHD-5	chromodomain helicase DNA binding protein 5	protein-coding
mm_116864.1	chr13	54930230	54930246	-	1	NA	Intergenic	Intergenic	-19173	NM_001311128	107448	Mm.23573	NM_153131	ENSMUSG00000025876	Unc5a	Unc5h1|mKIAA1976	unc-5 netrin receptor A	protein-coding
mm_165387.1	chr2	131103546	131103555	+	1	NA	Intergenic	ID|SINE|ID	-16785	NM_011426	20612	Mm.1374	NM_011426	ENSMUSG00000027322	Siglec1	Cd169|Siglec-1|Sn	sialic acid binding Ig-like lectin 1, sialoadhesin	protein-coding
mm_135551.1	chr16	49847649	49847676	-	1	NA	Intergenic	MER5A|DNA|hAT-Charlie	-7992	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_55471.1	chr6	68769116	68769141	-	1	NA	Intergenic	Intergenic	558046	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_14689.1	chr2	140589532	140589537	+	1	NA	intron (NM_001013802, intron 3 of 18)	L1_Rod|LINE|L1	81942	NM_001172160	71436	Mm.426781	NM_178382	ENSMUSG00000051379	Flrt3	5530600M07Rik|C430047I10Rik|mKIAA1469	fibronectin leucine rich transmembrane protein 3	protein-coding
mm_144917.1	chr18	37518342	37518359	+	1	NA	promoter-TSS (NM_053147)	promoter-TSS (NM_053147)	-3	NM_053147	93893	Mm.348054	NM_053147	ENSMUSG00000073591	Pcdhb22	Pcdhb15|PcdhbV	protocadherin beta 22	protein-coding
mm_20368.1	chr2	128422219	128422241	-	1	NA	intron (NR_028591, intron 1 of 1)	intron (NR_028591, intron 1 of 1)	7121	NR_028591	100043424	Mm.297222	NR_028589		Gm14005	OTTMUSG00000015351	predicted gene 14005	ncRNA
mm_152451.1	chr19	10830046	10830063	-	1	NA	promoter-TSS (NM_009852)	promoter-TSS (NM_009852)	4	NM_001037801	12511	Mm.290897	NM_009852	ENSMUSG00000024670	Cd6	-	CD6 antigen	protein-coding
mm_93116.1	chr10	91138417	91138442	-	1	NA	Intergenic	ORR1B2|LTR|ERVL-MaLR	-14466	NM_133668	18674	Mm.298	NM_133668	ENSMUSG00000061904	Slc25a3	5730556H19Rik|PTP|Phc	solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 3	protein-coding
mm_144962.1	chr18	37821520	37821526	+	1	NA	exon (NM_033583, exon 1 of 4)	exon (NM_033583, exon 1 of 4)	1977	NM_033583	93708	Mm.247203	NM_033583	ENSMUSG00000102543	Pcdhgc5	-	protocadherin gamma subfamily C, 5	protein-coding
mm_168059.1	chr10	100212515	100212526	+	1	NA	Intergenic	Intergenic	-123156	NM_001166636	100043247	Mm.478257	NM_001166636	ENSMUSG00000096640	Gm4312	-	predicted gene 4312	protein-coding
mm_157935.1	chrX	83487781	83487791	-	1	NA	5' UTR (NM_021898, exon 1 of 2)	5' UTR (NM_021898, exon 1 of 2)	138	NM_021898	100502723	Mm.383210	NM_021898	ENSMUSG00000035522	Tsga8	Halap-X|Halapx	testis specific gene A8	protein-coding
mm_100022.1	chr11	114903481	114903496	+	1	NA	3' UTR (NM_170758, exon 7 of 7)	3' UTR (NM_170758, exon 7 of 7)	13447	NM_170758	217303	Mm.294439	NM_170758	ENSMUSG00000034652	Cd300a	B230315M08Rik|Clm8|LMIR1|MAIR-I|MAIR-Ia|MMAC8|Pigr4|mcpir1	CD300A molecule	protein-coding
mm_147668.1	chr18	60624202	60624247	-	1	NA	promoter-TSS (NM_177340)	promoter-TSS (NM_177340)	81	NM_177340	104027	Mm.252321	NM_177340	ENSMUSG00000043079	Synpo	9030217H17Rik|9130229N11|9330140I15Rik|AW046661	synaptopodin	protein-coding
mm_52595.1	chr6	116970984	116970984	+	1	NA	Intergenic	Intergenic	-197551	NM_001012477	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_43198.1	chr5	129020460	129020501	+	1	NA	intron (NM_009391, intron 1 of 6)	CpG	324	NM_009391	19384	Mm.297440	NM_009391	ENSMUSG00000029430	Ran	-	RAN, member RAS oncogene family	protein-coding
mm_81573.1	chr9	110421711	110421745	+	1	NA	exon (NM_008694, exon 3 of 4)	exon (NM_008694, exon 3 of 4)	1920	NM_008694	18054	Mm.236225	NM_008694	ENSMUSG00000032484	Ngp	bectenecin	neutrophilic granule protein	protein-coding
mm_73211.1	chr8	95715902	95715932	+	1	NA	promoter-TSS (NM_001035123)	promoter-TSS (NM_001035123)	4	NM_001035123	66083	Mm.261321	NM_001035123	ENSMUSG00000031671	Setd6	0610039J04Rik|3110004G14Rik|AI413388|C76402	SET domain containing 6	protein-coding
mm_64055.1	chr7	140847771	140847779	+	1	NA	promoter-TSS (NM_027019)	promoter-TSS (NM_027019)	-141	NM_027019	69287	Mm.56404	NM_027019	ENSMUSG00000025482	Odf3	1700011O04Rik|SHIPPO1	outer dense fiber of sperm tails 3	protein-coding
mm_42020.1	chr5	108269420	108269441	+	1	NA	5' UTR (NM_026106, exon 1 of 3)	5' UTR (NM_026106, exon 1 of 3)	533	NM_026106	13486	Mm.303534	NM_026106	ENSMUSG00000029265	Dr1	1700121L09Rik|Dr1l|NC2|NC2beta	down-regulator of transcription 1	protein-coding
mm_118239.1	chr13	111771152	111771156	-	1	NA	intron (NM_011945, intron 3 of 19)	Charlie1a|DNA|hAT-Charlie	37829	NM_011945	26401	Mm.15918	NM_011945	ENSMUSG00000021754	Map3k1	MAPKKK1|MEKK1|Mekk	mitogen-activated protein kinase kinase kinase 1	protein-coding
mm_15608.1	chr2	160732636	160732638	+	1	NA	intron (NM_021280, intron 2 of 33)	intron (NM_021280, intron 2 of 33)	1327	NM_021280	18803	Mm.44463	NM_021280	ENSMUSG00000016933	Plcg1	AI894140|Cded|Plc-1|Plc-gamma1|Plcg-1	phospholipase C, gamma 1	protein-coding
mm_89909.1	chr10	111167592	111167620	+	1	NA	intron (NM_175489, intron 1 of 23)	intron (NM_175489, intron 1 of 23)	2804	NM_175489	237542	Mm.220204	NM_175489	ENSMUSG00000020189	Osbpl8	AA536976|AA536995|C730029P18Rik|D330025H14Rik|ORP-8	oxysterol binding protein-like 8	protein-coding
mm_4156.1	chr1	171025580	171025593	+	1	NA	exon (NM_144559, exon 4 of 5)	exon (NM_144559, exon 4 of 5)	6660	NM_144559	246256	Mm.251254	NM_144559	ENSMUSG00000059089	Fcgr4	4833442P21Rik|CD16-2|FcgRIV|FcgammaRIV|Fcgr3a|Fcrl3	Fc receptor, IgG, low affinity IV	protein-coding
mm_51764.1	chr6	87913937	87913976	+	1	NA	promoter-TSS (NM_173737)	promoter-TSS (NM_173737)	-20	NM_173737	232210	Mm.246241	NM_173737	ENSMUSG00000030060	Hmces	8430410A17Rik|C85376	5-hydroxymethylcytosine (hmC) binding, ES cell specific	protein-coding
mm_35855.1	chr4	49446294	49446312	-	1	NA	3' UTR (NM_001164565, exon 3 of 3)	3' UTR (NM_001164565, exon 3 of 3)	4806	NM_001164565	230161	Mm.30101	NM_001164565	ENSMUSG00000070985	Acnat1	AI132189	acyl-coenzyme A amino acid N-acyltransferase 1	protein-coding
mm_71905.1	chr8	70072984	70073006	+	1	NA	promoter-TSS (NM_001293795)	promoter-TSS (NM_001293795)	71	NM_181540	107770	Mm.37974	NM_181540	ENSMUSG00000036151	Tm6sf2	-	transmembrane 6 superfamily member 2	protein-coding
mm_37817.1	chr4	131821632	131821663	-	1	NA	intron (NM_001083119, intron 2 of 30)	intron (NM_001083119, intron 2 of 30)	16631	NM_011214	19273	Mm.4860	NM_011214	ENSMUSG00000028909	Ptpru	Ftp-1|PCP-2|PTP|PTP-lambda|PTPlambda|Pcp2|Ptpf|Ptprl|R-PTP-U|R-PTP-psi|RPTPlambda	protein tyrosine phosphatase, receptor type, U	protein-coding
mm_133288.1	chr16	77466126	77466150	+	1	NA	intron (NR_015543, intron 3 of 4)	Plat_L3|LINE|CR1	-132798	NR_029535	387229		NR_029535	ENSMUSG00000065530	Mir99a	Mirn99a|mir-99a|mmu-mir-99a	microRNA 99a	ncRNA
mm_33089.1	chr4	124695829	124695835	+	1	NA	Intergenic	Intergenic	-2278	NM_026031	67205	Mm.259121	NM_026031	ENSMUSG00000028907	Utp11l	2700082D03Rik|CGI-94|Cgi94|Utp11	UTP11-like, U3 small nucleolar ribonucleoprotein, (yeast)	protein-coding
mm_14677.1	chr2	139579469	139579478	+	1	NA	intron (NM_175467, intron 7 of 12)	intron (NM_175467, intron 7 of 12)	85553	NM_175467	228677	Mm.100450	NM_175467	ENSMUSG00000039092	Sptlc3	C130053K05Rik	serine palmitoyltransferase, long chain base subunit 3	protein-coding
mm_142128.1	chr17	35900722	35900740	-	1	NA	3' UTR (NM_028476, exon 10 of 10)	3' UTR (NM_028476, exon 10 of 10)	-3353	NM_001033630	69662	Mm.260159	NM_001033630	ENSMUSG00000050705	2310061I04Rik	-	RIKEN cDNA 2310061I04 gene	protein-coding
mm_24080.1	chr3	87948688	87948704	+	1	NA	promoter-TSS (NM_007759)	promoter-TSS (NM_007759)	3	NM_007759	12904	Mm.4757	NM_007759	ENSMUSG00000004885	Crabp2	AI893628|Crabp-2|CrabpII	cellular retinoic acid binding protein II	protein-coding
mm_126499.1	chr15	81745140	81745169	+	1	NA	5' UTR (NM_001081016, exon 1 of 23)	5' UTR (NM_001081016, exon 1 of 23)	306	NM_001081016	20286	Mm.432075	NM_001081016	ENSMUSG00000022390	Zc3h7b	Gm627|Scrg3|Zc2h7b|mKIAA1031	zinc finger CCCH type containing 7B	protein-coding
mm_131973.1	chr16	24951275	24951278	+	1	NA	intron (NM_001145954, intron 5 of 7)	intron (NM_001145954, intron 5 of 7)	-108363	NR_040374	319487	Mm.137341	NR_040374	ENSMUSG00000096960	A230028O05Rik	-	RIKEN cDNA A230028O05 gene	ncRNA
mm_54457.1	chr6	34824450	34824465	-	1	NA	intron (NM_178630, intron 12 of 18)	ID|SINE|ID	-38689	NM_197986	68487	Mm.248440	NM_197986	ENSMUSG00000057137	Tmem140	1110007F12Rik	transmembrane protein 140	protein-coding
mm_16285.1	chr2	174097704	174097718	+	1	NA	3' UTR (NM_001102425, exon 8 of 8)	3' UTR (NM_001102425, exon 8 of 8)	-12640	NM_213733	228961	Mm.295629	NM_213733	ENSMUSG00000039263	Npepl1	BC023239|C85514|mKIAA1974	aminopeptidase-like 1	protein-coding
mm_68625.1	chr7	118126586	118126591	-	1	NA	intron (NM_019419, intron 2 of 5)	intron (NM_019419, intron 2 of 5)	3037	NM_019419	54208	Mm.29924	NM_019419	ENSMUSG00000030654	Arl6ip1	AIP-6|AL022945|ARMER|AU042858|Aip-1|Arl6ip|C85138|mKIAA0069	ADP-ribosylation factor-like 6 interacting protein 1	protein-coding
mm_75350.1	chr8	43699490	43699506	-	1	NA	promoter-TSS (NM_001079931)	promoter-TSS (NM_001079931)	-7	NM_001079931	384814	Mm.491652	NM_001079931		Gm5347	EG384814	predicted gene 5347	protein-coding
mm_18425.1	chr2	60752936	60752953	-	1	NA	3' UTR (NM_001141932, exon 15 of 15)	3' UTR (NM_001141932, exon 15 of 15)	-30341	NM_001159564	16420	Mm.98193	NM_021359	ENSMUSG00000026971	Itgb6	2210409C20Rik|4831415H04Rik	integrin beta 6	protein-coding
mm_132633.1	chr16	39026189	39026195	+	1	NA	3' UTR (NM_170599, exon 7 of 7)	3' UTR (NM_170599, exon 7 of 7)	123847	NM_170599	207683	Mm.245564	NM_170599	ENSMUSG00000022790	Igsf11	1700025L02Rik|BT-IgSF|Igsf13	immunoglobulin superfamily, member 11	protein-coding
mm_87308.1	chr10	42700727	42700729	+	1	NA	3' UTR (NM_172416, exon 6 of 6)	3' UTR (NM_172416, exon 6 of 6)	21812	NM_172416	14628	Mm.46636	NM_172416	ENSMUSG00000038280	Ostm1	1200002H13Rik|HSPC019|gl	osteopetrosis associated transmembrane protein 1	protein-coding
mm_81697.1	chr9	111205743	111205749	+	1	NA	intron (NM_027742, intron 7 of 13)	intron (NM_027742, intron 7 of 13)	65862	NM_026810	17350	Mm.486383	NM_026810	ENSMUSG00000032498	Mlh1	1110035C23Rik|AI317206|AI325952|AI561766	mutL homolog 1	protein-coding
mm_129624.1	chr15	80091823	80091840	-	1	NA	intron (NM_207708, intron 1 of 3)	CpG	497	NM_207708	20972	Mm.230301	NM_009303	ENSMUSG00000022415	Syngr1	R75468|Syngr1b|p29	synaptogyrin 1	protein-coding
mm_100542.1	chr11	120673370	120673393	+	1	NA	intron (NM_026877, intron 1 of 15)	CpG	408	NM_026877	68938	Mm.294020	NM_026877	ENSMUSG00000025142	Aspscr1	1190006K01Rik|ASPC|ASPCR1|ASPL|ASPS|RCC17|TUG	alveolar soft part sarcoma chromosome region, candidate 1 (human)	protein-coding
mm_68251.1	chr7	105569283	105569315	-	1	NA	promoter-TSS (NM_001253887)	promoter-TSS (NM_001253887)	19	NM_001253887	11785	Mm.38469	NM_009685	ENSMUSG00000037032	Apbb1	Fe65|Rir	amyloid beta (A4) precursor protein-binding, family B, member 1	protein-coding
mm_52923.1	chr6	122882898	122882908	+	1	NA	exon (NM_026267, exon 6 of 8)	exon (NM_026267, exon 6 of 8)	8346	NM_026267	67602	Mm.288114	NM_026267	ENSMUSG00000030327	Necap1	1200016B17Rik|AI747569|mFLJ00061	NECAP endocytosis associated 1	protein-coding
mm_31058.1	chr4	41275487	41275497	+	1	NA	promoter-TSS (NM_026872)	promoter-TSS (NM_026872)	-357	NM_026872	68926	Mm.41864	NM_026872	ENSMUSG00000028433	Ubap2	1190005K07Rik|AA408600|AU045235|UBAP-2|mKIAA1491	ubiquitin-associated protein 2	protein-coding
mm_9858.1	chr1	184811171	184811203	-	1	NA	5' UTR (NM_001290273, exon 1 of 7)	5' UTR (NM_001290273, exon 1 of 7)	113	NM_001290273	66112	Mm.272457	NM_001081361	ENSMUSG00000026621	Marc1	1300013F15Rik|Mosc1	mitochondrial amidoxime reducing component 1	protein-coding
mm_141882.1	chr17	34860312	34860326	-	1	NA	exon (NM_008198, exon 6 of 18)	exon (NM_008198, exon 6 of 18)	2195	NM_001142706	14962	Mm.653	NM_008198	ENSMUSG00000090231	Cfb	AI195813|AI255840|B|Bf|C2|Fb|H2-Bf	complement factor B	protein-coding
mm_3961.1	chr1	164135669	164135678	+	1	NA	intron (NM_011347, intron 8 of 15)	intron (NM_011347, intron 8 of 15)	-16162	NM_007976	14067	Mm.12900	NM_007976	ENSMUSG00000026579	F5	AI173222|Cf-5|Cf5	coagulation factor V	protein-coding
mm_16771.1	chr2	9879590	9879611	-	1	NA	promoter-TSS (NM_008091)	promoter-TSS (NM_008091)	-1000	NM_008091	14462	Mm.313866	NM_008091	ENSMUSG00000015619	Gata3	Gata-3|jal	GATA binding protein 3	protein-coding
mm_81030.1	chr9	104569673	104569683	+	1	NA	promoter-TSS (NM_028719)	promoter-TSS (NM_028719)	-110	NM_028719	74020	Mm.326240	NM_028719	ENSMUSG00000032564	Cpne4	3632411M23Rik|4933406O10Rik	copine IV	protein-coding
mm_74086.1	chr8	122550652	122550698	+	1	NA	intron (NM_001037298, intron 1 of 50)	intron (NM_001037298, intron 1 of 50)	654	NM_001037298	234839	Mm.37324	NM_001037298	ENSMUSG00000014444	Piezo1	9630020g22|Fam38a|mKIAA0233	piezo-type mechanosensitive ion channel component 1	protein-coding
mm_52803.1	chr6	121342457	121342467	+	1	NA	promoter-TSS (NM_001347433)	promoter-TSS (NM_001347433)	-614	NM_001347433	14411	Mm.274506	NM_133661	ENSMUSG00000030109	Slc6a12	BGT1|GAT-2|GAT2|Gabt2	solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12	protein-coding
mm_155246.1	chrX	57223643	57223649	+	1	NA	3' UTR (NM_011616, exon 5 of 5)	3' UTR (NM_011616, exon 5 of 5)	11503	NM_011616	21947	Mm.4861	NM_011616	ENSMUSG00000031132	Cd40lg	CD154|CD40-L|Cd40l|HIGM1|IGM|IMD3|Ly-62|Ly62|T-BAM|TRAP|Tnfsf5|Tnlg8b|gp39	CD40 ligand	protein-coding
mm_69002.1	chr7	126700379	126700398	-	1	NA	exon (NM_009898, exon 10 of 11)	exon (NM_009898, exon 10 of 11)	3832	NM_001301374	12721	Mm.290482	NM_009898	ENSMUSG00000030707	Coro1a	Clabp|Lmb3|TACO|p57	coronin, actin binding protein 1A	protein-coding
mm_33604.1	chr4	132579537	132579563	+	1	NA	exon (NM_001081211, exon 2 of 2)	exon (NM_001081211, exon 2 of 2)	15483	NM_001081211	19204	Mm.89389	NM_001081211	ENSMUSG00000056529	Ptafr	PAFR	platelet-activating factor receptor	protein-coding
mm_24752.1	chr3	95320471	95320493	+	1	NA	intron (NM_029789, intron 2 of 10)	intron (NM_029789, intron 2 of 10)	1652	NM_001320492	76893	Mm.181009	NM_029789	ENSMUSG00000015714	Cers2	0610013I17Rik|AI225939|Lass2|TRH3	ceramide synthase 2	protein-coding
mm_155641.1	chrX	85249710	85249718	+	1	NA	promoter-TSS (NM_028046)	promoter-TSS (NM_028046)	37	NM_028046	71996	Mm.20201	NM_028046	ENSMUSG00000035491	Fthl17a	1600014K23Rik|AI324104	ferritin, heavy polypeptide-like 17, member A	protein-coding
mm_156477.1	chrX	143784233	143784235	+	1	NA	intron (NM_008778, intron 13 of 14)	intron (NM_008778, intron 13 of 14)	43178	NM_007603	12338	Mm.30290	NM_007603	ENSMUSG00000067276	Capn6	-	calpain 6	protein-coding
mm_172446.1	chr7	30195228	30195228	-	1	NA	promoter-TSS (NM_009795)	promoter-TSS (NM_009795)	-180	NM_009795	12336	Mm.439782	NM_009795	ENSMUSG00000001794	Capns1	Capa-4|Capa4|Capn4|D7Ertd146e	calpain, small subunit 1	protein-coding
mm_36347.1	chr4	73790994	73791053	-	1	NA	promoter-TSS (NR_046042)	promoter-TSS (NR_046042)	-221	NR_046042	667768	Mm.244966	NR_046041	ENSMUSG00000085034	Gm11240	OTTMUSG00000000286	predicted gene 11240	ncRNA
mm_3768.1	chr1	156310717	156310734	+	1	NA	promoter-TSS (NM_130456)	promoter-TSS (NM_130456)	6	NM_130456	170484	Mm.289099	NM_130456	ENSMUSG00000026602	Nphs2	PDCN|SRN1	nephrosis 2, podocin	protein-coding
mm_22437.1	chr2	181691805	181691831	-	1	NA	promoter-TSS (NM_001291205)	promoter-TSS (NM_001291205)	-1	NM_001291205	56470	Mm.274366	NM_026446	ENSMUSG00000002458	Rgs19	2610042F04Rik|AI324841|AW547781|GAIP	regulator of G-protein signaling 19	protein-coding
mm_122949.1	chr14	54966602	54966608	-	1	NA	promoter-TSS (NM_010856)	promoter-TSS (NM_010856)	2	NM_001164171	17888	Mm.290003	NM_010856	ENSMUSG00000040752	Myh6	A830009F23Rik|AA517445|Myhc-a|Myhca|alpha-MHC	myosin, heavy polypeptide 6, cardiac muscle, alpha	protein-coding
mm_38879.1	chr4	149698599	149698617	-	1	NA	promoter-TSS (NM_001164049)	promoter-TSS (NM_001164049)	100	NM_001164050	18707	Mm.229108	NM_008840	ENSMUSG00000039936	Pik3cd	2410099E07Rik|2610208K16Rik|AW545373|p110delta	phosphatidylinositol 3-kinase catalytic delta polypeptide	protein-coding
mm_36822.1	chr4	105109733	105109743	-	1	NA	exon (NM_178143, exon 1 of 9)	exon (NM_178143, exon 1 of 9)	160	NM_178143	108079	Mm.48638	NM_178143	ENSMUSG00000028518	Prkaa2	2310008I11Rik|A830082D05|AMPKalpha2	protein kinase, AMP-activated, alpha 2 catalytic subunit	protein-coding
mm_80699.1	chr9	92222287	92222287	+	1	NA	Intergenic	Lx9|LINE|L1	-27907	NM_011636	22038	Mm.421956	NM_011636	ENSMUSG00000032369	Plscr1	MmTRA1a|MmTRA1b|Nor1|Tra1|Tra1a|Tra1b|Tras1|Tras2	phospholipid scramblase 1	protein-coding
mm_167026.1	chr7	67373161	67373178	+	1	NA	promoter-TSS (NM_001291196)	promoter-TSS (NM_001291196)	-311	NM_001291195	17258	Mm.132788	NM_001033713	ENSMUSG00000030557	Mef2a	A430079H05Rik	myocyte enhancer factor 2A	protein-coding
mm_170422.1	chr18	70648068	70648083	-	1	NA	Intergenic	Intergenic	79783	NM_010773	17191	Mm.322	NM_010773	ENSMUSG00000024513	Mbd2	MBD2a	methyl-CpG binding domain protein 2	protein-coding
mm_63252.1	chr7	126623246	126623255	+	1	NA	TTS (NM_019738)	TTS (NM_019738)	2220	NM_019738	56312	Mm.18742	NM_019738	ENSMUSG00000030717	Nupr1	2310032H04Rik|Com1|p8	nuclear protein transcription regulator 1	protein-coding
mm_95642.1	chr11	53720082	53720088	+	1	NA	promoter-TSS (NM_010558)	promoter-TSS (NM_010558)	-709	NM_010558	16191	Mm.4461	NM_010558	ENSMUSG00000036117	Il5	Il-5	interleukin 5	protein-coding
mm_149449.1	chr19	11486002	11486017	+	1	NA	Intergenic	RMER19B2|LTR|ERVK	-6029	NM_001164202	666926	Mm.486382	NM_001164202	ENSMUSG00000058470	Gm8369	EG666926	predicted gene 8369	protein-coding
mm_140485.1	chr17	3115749	3115768	-	1	NA	intron (NM_134123, intron 1 of 19)	intron (NM_134123, intron 1 of 19)	786	NM_134123	106583	Mm.124373	NM_134123	ENSMUSG00000046201	Scaf8	A630086M08Rik|A930036P18Rik|AA408306|AI447644|AI448652|AU015035|Rbm16|mKIAA1116	SR-related CTD-associated factor 8	protein-coding
mm_171090.1	chr3	127692454	127692470	-	1	NA	intron (NM_027808, intron 4 of 13)	intron (NM_027808, intron 4 of 13)	59317	NM_009718	11924	Mm.42017	NM_009718	ENSMUSG00000027967	Neurog2	Atoh4|Math4A|bHLHa8|ngn-2|ngn2	neurogenin 2	protein-coding
mm_61435.1	chr7	74220180	74220184	+	1	NA	Intergenic	Lx10|LINE|L1	-206500	NM_009181	20450	Mm.4954	NM_009181	ENSMUSG00000025789	St8sia2	AI323367|ST8SiaII|STX|Siat8b	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 2	protein-coding
mm_112148.1	chr12	113259975	113259982	-	1	NA	Intergenic	Intergenic	74075	NM_153776	69195	Mm.313244	NM_153776	ENSMUSG00000049036	Tmem121	2410008J05Rik|Hole	transmembrane protein 121	protein-coding
mm_138508.1	chr17	35236557	35236607	+	1	NA	promoter-TSS (NM_010909)	promoter-TSS (NM_010909)	-14	NM_023179	66237	Mm.396107	NM_023179	ENSMUSG00000024403	Atp6v1g2	1500002D01Rik|Atp6g2|NG38|VAG2	ATPase, H+ transporting, lysosomal V1 subunit G2	protein-coding
mm_47234.1	chr5	121445384	121445415	-	1	NA	exon (NM_026129, exon 3 of 3)	exon (NM_026129, exon 3 of 3)	7075	NM_026129	67397	Mm.154570	NM_026129	ENSMUSG00000029616	Erp29	1200015M03Rik|2810446M09Rik|AW209030|Erp28|Erp31|PDI-Db	endoplasmic reticulum protein 29	protein-coding
mm_24500.1	chr3	92418080	92418088	+	1	NA	promoter-TSS (NR_003185)	promoter-TSS (NR_003185)	-3	NR_003185	20764	Mm.57084	NR_003185	ENSMUSG00000027925	Sprr2j-ps	Sprr2j	small proline-rich protein 2J, pseudogene	pseudo
mm_49395.1	chr6	28423535	28423537	+	1	NA	promoter-TSS (NM_007480)	promoter-TSS (NM_007480)	-104	NM_007480	11844	Mm.389075	NM_007480	ENSMUSG00000020440	Arf5	-	ADP-ribosylation factor 5	protein-coding
mm_14987.1	chr2	152226809	152226839	+	1	NA	promoter-TSS (NM_007788)	promoter-TSS (NM_007788)	-16	NM_007788	12995	Mm.23692	NM_007788	ENSMUSG00000074698	Csnk2a1	Csnk2a1-rs4	casein kinase 2, alpha 1 polypeptide	protein-coding
mm_116841.1	chr13	54688265	54688284	-	1	NA	promoter-TSS (NM_001146025)	promoter-TSS (NM_001146025)	-74	NM_001146027	105239	Mm.25366	NM_134064	ENSMUSG00000034928	Rnf44	AI854545|mKIAA1100	ring finger protein 44	protein-coding
mm_140068.1	chr17	75005483	75005488	+	1	NA	promoter-TSS (NM_019919)	promoter-TSS (NM_019919)	-44	NM_019919	268977	Mm.269747	NM_019919	ENSMUSG00000001870	Ltbp1	9430031G15Rik|9830146M04|Ltbp-1|Ltbp1L|TGF-beta1-BP-1|Tgfb|b2b1000Clo	latent transforming growth factor beta binding protein 1	protein-coding
mm_29180.1	chr3	106528252	106528271	-	1	NA	intron (NM_001293694, intron 4 of 8)	intron (NM_001293694, intron 4 of 8)	-19537	NM_001286986	67171	Mm.290488	NM_026013	ENSMUSG00000027900	Dram2	2010305N14Rik|2610318G18Rik|AI647667|Tmem77	DNA-damage regulated autophagy modulator 2	protein-coding
mm_54224.1	chr6	27810131	27810171	-	1	NA	intron (NM_001311072, intron 2 of 9)	intron (NM_001311072, intron 2 of 9)	126599	NR_030420	735266		NR_030420	ENSMUSG00000076067	Mir592	Mirn592|mir-592|mmu-mir-592	microRNA 592	ncRNA
mm_28085.1	chr3	84913558	84913565	-	1	NA	intron (NM_001177773, intron 4 of 13)	intron (NM_001177773, intron 4 of 13)	-38650	NM_080428	50754	Mm.196475	NM_080428	ENSMUSG00000028086	Fbxw7	1110001A17Rik|AGO|Cdc4|Fbw7|Fbwd6|Fbx30|Fbxo30|Fbxw6|SEL-10	F-box and WD-40 domain protein 7	protein-coding
mm_57266.1	chr6	123286483	123286492	-	1	NA	exon (NM_019948, exon 3 of 6)	exon (NM_019948, exon 3 of 6)	3384	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_21559.1	chr2	164182619	164182634	-	1	NA	exon (NM_145369, exon 1 of 4)	exon (NM_145369, exon 1 of 4)	116	NM_145369	209232	Mm.218273	NM_145369	ENSMUSG00000040154	Wfdc5	BC019734|Prg5|Wap1	WAP four-disulfide core domain 5	protein-coding
mm_135347.1	chr16	43664105	43664126	-	1	NA	promoter-TSS (NM_001146325)	promoter-TSS (NM_001146325)	69	NM_001146325	100043314	Mm.390896	NM_001146325	ENSMUSG00000071552	Tigit	ENSMUSG00000071552|Vstm3	T cell immunoreceptor with Ig and ITIM domains	protein-coding
mm_171456.1	chr4	145514867	145514868	+	1	NA	intron (NM_001324553, intron 1 of 3)	intron (NM_001324553, intron 1 of 3)	4108	NM_001324553	101056073	Mm.276881	NM_001324553	ENSMUSG00000078503	LOC101056073	-	zinc finger protein 501-like	protein-coding
mm_73932.1	chr8	119947706	119947729	+	1	NA	exon (NM_009462, exon 6 of 14)	exon (NM_009462, exon 6 of 14)	37357	NM_001310630	22224	Mm.256910	NM_009462	ENSMUSG00000031826	Usp10	2610014N07Rik|UBPO|Uchrp|mKIAA0190	ubiquitin specific peptidase 10	protein-coding
mm_72151.1	chr8	72144664	72144683	+	1	NA	intron (NM_001001491, intron 3 of 7)	intron (NM_001001491, intron 3 of 7)	9381	NM_001001491	326618	Mm.295124	NM_001001491	ENSMUSG00000031799	Tpm4	2610528G24Rik|Tpm4.2|Tpm4.2cy	tropomyosin 4	protein-coding
mm_10924.1	chr2	25428645	25428686	+	1	NA	promoter-TSS (NM_007379)	promoter-TSS (NM_007379)	-9	NM_007379	11305	Mm.2210	NM_007379	ENSMUSG00000026944	Abca2	AI413825|Abc2|D2H0S1474E|mKIAA1062	ATP-binding cassette, sub-family A (ABC1), member 2	protein-coding
mm_45292.1	chr5	65019261	65019276	-	1	NA	intron (NM_026667, intron 7 of 13)	intron (NM_026667, intron 7 of 13)	48950	NR_030577	100124451		NR_030577	ENSMUSG00000077042	Mir574	Mirn574|mir-574|mmu-mir-574	microRNA 574	ncRNA
mm_27530.1	chr3	57501762	57501770	-	1	NA	exon (NM_133784, exon 3 of 7)	exon (NM_133784, exon 3 of 7)	74110	NM_133784	97064	Mm.405029	NM_133784	ENSMUSG00000027803	Wwtr1	2310058J06Rik|2610021I22Rik|C78399|Taz	WW domain containing transcription regulator 1	protein-coding
mm_114006.1	chr13	52596862	52596911	+	1	NA	promoter-TSS (NM_011518)	promoter-TSS (NM_011518)	4	NM_011518	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_85720.1	chr9	108275088	108275134	-	1	NA	Intergenic	Intergenic	-11153	NM_001276486	13138	Mm.7524	NM_010017	ENSMUSG00000039952	Dag1	D9Wsu13e|DG|Dp427|Dp71	dystroglycan 1	protein-coding
mm_73461.1	chr8	106653585	106653595	+	1	NA	exon (NM_009864, exon 4 of 16)	exon (NM_009864, exon 4 of 16)	-29478	NM_173037	272538	Mm.87151	NM_173037	ENSMUSG00000041949	Tango6	AW413431|E330010G16|Tmco7	transport and golgi organization 6	protein-coding
mm_164580.1	chr17	25317561	25317586	+	1	NA	Intergenic	RMER5|LTR|ERV1	-1081	NM_053260	114662	Mm.207082	NM_053260	ENSMUSG00000034039	Prss29	D19363|Isp2|mISP-2	protease, serine 29	protein-coding
mm_65230.1	chr7	19717493	19717511	-	1	NA	3' UTR (NM_008990, exon 9 of 9)	3' UTR (NM_008990, exon 9 of 9)	-2073	NM_016871	53333	Mm.61682	NM_016871	ENSMUSG00000002984	Tomm40	AW539759|Mom35|Tom40	translocase of outer mitochondrial membrane 40 homolog (yeast)	protein-coding
mm_111821.1	chr12	106634511	106634517	-	1	NA	Intergenic	Intergenic	81810	NR_015512	71033	Mm.159404	NR_015512	ENSMUSG00000085820	4933406K04Rik	4930426M03Rik|4930485I22Rik|4933427G14Rik	RIKEN cDNA 4933406K04 gene	ncRNA
mm_166491.1	chr5	149587986	149587986	+	1	NA	intron (NM_029440, intron 14 of 22)	intron (NM_029440, intron 14 of 22)	48329	NM_013559	15505	Mm.270681	NM_013559	ENSMUSG00000029657	Hsph1	105kDa|AI790491|Hsp105|Hsp110|hsp-E7I|hsp110/105	heat shock 105kDa/110kDa protein 1	protein-coding
mm_32712.1	chr4	116151450	116151477	+	1	NA	promoter-TSS (NM_001290658)	promoter-TSS (NM_001290658)	32	NM_001290658	68273	Mm.196045	NM_026651	ENSMUSG00000028700	Pomgnt1	0610016I07Rik|4930467B06Rik	protein O-linked mannose beta 1,2-N-acetylglucosaminyltransferase	protein-coding
mm_90437.1	chr10	127643036	127643044	+	1	NA	promoter-TSS (NM_009284)	promoter-TSS (NM_009284)	54	NM_009284	20852	Mm.121721	NM_009284	ENSMUSG00000002147	Stat6	-	signal transducer and activator of transcription 6	protein-coding
mm_42102.1	chr5	110467235	110467261	+	1	NA	Intergenic	Intergenic	-18745	NM_001142642	381668	Mm.348782	NM_028596	ENSMUSG00000043323	Fbrsl1	2410025L10Rik|AI467568|Gm1049|Gm29766|mKIAA1545	fibrosin-like 1	protein-coding
mm_61124.1	chr7	55794147	55794217	+	1	NA	promoter-TSS (NM_146190)	promoter-TSS (NM_146190)	34	NM_146190	233276	Mm.284306	NM_146190	ENSMUSG00000033790	Tubgcp5	B130010C12Rik|GCP5|mKIAA1899	tubulin, gamma complex associated protein 5	protein-coding
mm_20461.1	chr2	129367232	129367243	-	1	NA	intron (NM_008361, intron 5 of 6)	intron (NM_008361, intron 5 of 6)	-2665	NR_015474	329514	Mm.207315	NM_177848	ENSMUSG00000074805	Il1bos	9430083I22|Gm14047|OTTMUSG00000015529	interleukin 1 beta, opposite strand	ncRNA
mm_16937.1	chr2	14059900	14059915	-	1	NA	Intergenic	Intergenic	-3872	NM_013935	30963	Mm.241205	NM_013935	ENSMUSG00000063275	Hacd1	Ptpla	3-hydroxyacyl-CoA dehydratase 1	protein-coding
mm_114306.1	chr13	59656568	59656582	+	1	NA	intron (NM_027307, intron 4 of 10)	ORR1C1|LTR|ERVL-MaLR	19209	NM_001035122	105348	Mm.171335	NM_027307	ENSMUSG00000021556	Golm1	2310001L02Rik|AW125446|D030064E01Rik|GP73|Golph2|PSEC0257	golgi membrane protein 1	protein-coding
mm_51625.1	chr6	85451984	85452003	+	1	NA	promoter-TSS (NM_001163427)	promoter-TSS (NM_001163427)	-23	NR_028081	73327	Mm.379221	NM_028505	ENSMUSG00000030008	Pradc1	1700040I03Rik|Pap21	protease-associated domain containing 1	protein-coding
mm_65358.1	chr7	25000690	25000699	-	1	NA	exon (NM_001290469, exon 4 of 23)	exon (NM_001290469, exon 4 of 23)	5243	NM_001290469	232975	Mm.44101	NM_144921	ENSMUSG00000040907	Atp1a3	Atpa-2	ATPase, Na+/K+ transporting, alpha 3 polypeptide	protein-coding
mm_50062.1	chr6	41188199	41188207	+	1	NA	Intergenic	Intergenic	-114069	NM_011646	22074	Mm.383263	NM_011646	ENSMUSG00000054106	Try4	0910001B19Rik|Td	trypsin 4	protein-coding
mm_104340.1	chr11	94180320	94180342	-	1	NA	Intergenic	Intergenic	-31123	NM_009427	22057	Mm.259673	NM_009427	ENSMUSG00000037573	Tob1	Tob|Trob	transducer of ErbB-2.1	protein-coding
mm_92282.1	chr10	71285254	71285264	-	1	NA	promoter-TSS (NM_145420)	promoter-TSS (NM_145420)	3	NM_145420	216080	Mm.270530	NM_145420	ENSMUSG00000019927	Ube2d1	UBCH5	ubiquitin-conjugating enzyme E2D 1	protein-coding
mm_25501.1	chr3	109507812	109507824	+	1	NA	intron (NM_020505, intron 7 of 26)	intron (NM_020505, intron 7 of 26)	-66189	NM_146139	57257	Mm.282257	NM_020505	ENSMUSG00000033721	Vav3	A530094I06Rik|AA986410|Idd18.1	vav 3 oncogene	protein-coding
mm_55975.1	chr6	85867425	85867435	-	1	NA	3' UTR (NM_053096, exon 3 of 3)	3' UTR (NM_053096, exon 3 of 3)	1707	NM_053096	93673	Mm.24251	NM_053096	ENSMUSG00000033634	Nat8f2	Cml2	N-acetyltransferase 8 (GCN5-related) family member 2	protein-coding
mm_111970.1	chr12	109948318	109948356	-	1	NA	Intergenic	Intergenic	200459	NR_037233	100499517		NR_037233	ENSMUSG00000093351	Mir3072	mir-3072|mmu-mir-3072	microRNA 3072	ncRNA
mm_104777.1	chr11	98546027	98546045	-	1	NA	promoter-TSS (NM_011771)	promoter-TSS (NM_011771)	-5	NM_011771	22780	Mm.133367	NM_011771	ENSMUSG00000018168	Ikzf3	5830411O07Rik|Aiolos|Zfpn1a3|Znfn1a3	IKAROS family zinc finger 3	protein-coding
mm_115695.1	chr13	14063269	14063278	-	1	NA	promoter-TSS (NM_194262)	promoter-TSS (NM_194262)	215	NM_001331119	14593	Mm.148039	NM_010282	ENSMUSG00000021302	Ggps1	1810026C22Rik|9530089B04Rik|AI843169|C79210	geranylgeranyl diphosphate synthase 1	protein-coding
mm_104862.1	chr11	99386088	99386099	-	1	NA	exon (NM_010660, exon 7 of 8)	exon (NM_010660, exon 7 of 8)	3271	NM_010660	16661	Mm.22662	NM_010660	ENSMUSG00000019761	Krt10	D130054E02Rik|K10|K1C1|Krt-1.10|Krt1-10	keratin 10	protein-coding
mm_52407.1	chr6	113388958	113388986	+	1	NA	promoter-TSS (NM_001142732)	promoter-TSS (NM_001142732)	-288	NM_001142732	101100	Mm.388573	NM_133923	ENSMUSG00000030276	Ttll3	4833441J24Rik|AI450050	tubulin tyrosine ligase-like family, member 3	protein-coding
mm_158813.1	chrX	167308014	167308030	-	1	NA	exon (NM_001290758, exon 4 of 4)	exon (NM_001290758, exon 4 of 4)	22549	NM_001290757	170743	Mm.23979	NM_133211	ENSMUSG00000044583	Tlr7	-	toll-like receptor 7	protein-coding
mm_158306.1	chrX	122397340	122397349	-	1	NA	promoter-TSS (NM_138742)	promoter-TSS (NM_138742)	41	NM_138742	54561	Mm.490573	NM_138742	ENSMUSG00000055733	Nap1l3	MB20	nucleosome assembly protein 1-like 3	protein-coding
mm_38372.1	chr4	138456816	138456883	-	1	NA	3' UTR (NM_025451, exon 2 of 2)	3' UTR (NM_025451, exon 2 of 2)	1701	NM_025451	66259	Mm.41603	NM_025451	ENSMUSG00000046447	Camk2n1	1810006K23Rik|AI848599|AI891706	calcium/calmodulin-dependent protein kinase II inhibitor 1	protein-coding
mm_79033.1	chr9	46083872	46083898	+	1	NA	intron (NM_027498, intron 1 of 24)	intron (NM_027498, intron 1 of 24)	71065	NM_027498	70661	Mm.219459	NM_027498	ENSMUSG00000034135	Sik3	5730525O22Rik|9030204A07Rik|AI447252|AI846254|AI849445|Qsk|SIK-3|mKIAA0999	SIK family kinase 3	protein-coding
mm_87499.1	chr10	51533838	51533849	+	1	NA	Intergenic	LTRIS6|LTR|ERV1	42945	NM_013532	14728	Mm.34408	NM_013532	ENSMUSG00000062593	Lilrb4a	CD85K|Gp49b|HM18|ILT3|LIR-5|Lilrb4|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4A	protein-coding
mm_134499.1	chr16	18876523	18876570	-	1	NA	promoter-TSS (NM_010922)	promoter-TSS (NM_010922)	91	NM_010922	18100	Mm.20918	NM_010922	ENSMUSG00000022706	Mrpl40	Nlvcf	mitochondrial ribosomal protein L40	protein-coding
mm_30582.1	chr4	5611847	5611856	+	1	NA	Intergenic	RSINE1|SINE|B4	-20477	NR_038183	73872	Mm.427301	NR_038183	ENSMUSG00000086066	4930423M02Rik	-	RIKEN cDNA 4930423M02 gene	ncRNA
mm_93926.1	chr10	127162923	127162948	-	1	NA	Intergenic	Intergenic	-2221	NR_045166	14421	Mm.386762	NM_008080	ENSMUSG00000006731	B4galnt1	4933429D13Rik|Gal-NAc-T|GalNAc-T|GalNAcT|Galgt1|Ggm-2|Ggm2	beta-1,4-N-acetyl-galactosaminyl transferase 1	protein-coding
mm_40091.1	chr5	34549545	34549552	+	1	NA	promoter-TSS (NM_001145859)	promoter-TSS (NM_001145859)	-28	NM_001145859	24055	Mm.5012	NM_011893	ENSMUSG00000054520	Sh3bp2	3BP2	SH3-domain binding protein 2	protein-coding
mm_131148.1	chr16	6563114	6563127	+	1	NA	intron (NM_021477, intron 3 of 16)	ORR1B2|LTR|ERVL-MaLR	-506715	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_104585.1	chr11	96977661	96977693	-	1	NA	promoter-TSS (NM_030220)	promoter-TSS (NM_030220)	11	NM_030220	78912	Mm.491183	NM_030220	ENSMUSG00000018678	Sp2	4930480I16Rik|mKIAA0048	Sp2 transcription factor	protein-coding
mm_117370.1	chr13	71960370	71960384	-	1	NA	intron (NM_010573, intron 1 of 3)	intron (NM_010573, intron 1 of 3)	3346	NM_010573	16371	Mm.316056	NM_010573	ENSMUSG00000060969	Irx1	-	Iroquois related homeobox 1 (Drosophila)	protein-coding
mm_69275.1	chr7	127946509	127946516	-	1	NA	5' UTR (NM_001319147, exon 1 of 15)	5' UTR (NM_001319147, exon 1 of 15)	213	NM_001319147	77613	Mm.334253	NM_001081374	ENSMUSG00000070371	Prss36	C330007D15Rik	protease, serine 36	protein-coding
mm_135832.1	chr16	58523505	58523520	-	1	NA	promoter-TSS (NM_018784)	promoter-TSS (NM_018784)	-200	NM_018784	54613	Mm.212742	NM_018784	ENSMUSG00000022747	St3gal6	1700023B24Rik|AI930218|AW552396|Siat10|St3galVI	ST3 beta-galactoside alpha-2,3-sialyltransferase 6	protein-coding
mm_132668.1	chr16	42750764	42750764	+	1	NA	intron (NR_040521, intron 1 of 3)	B4A|SINE|B4	124823	NR_040521	75722	Mm.243747	NR_040521	ENSMUSG00000075070	4932412D23Rik	ENSMUSG00000075070|Gm10809	RIKEN cDNA 4932412D23 gene	ncRNA
mm_53343.1	chr6	129275462	129275491	+	1	NA	promoter-TSS (NM_001033122)	promoter-TSS (NM_001033122)	-107	NM_001033122	12515	Mm.74745	NM_001033122	ENSMUSG00000030156	Cd69	5830438K24Rik|AI452015|AIM|VEA	CD69 antigen	protein-coding
mm_58753.1	chr7	13324589	13324600	+	1	NA	Intergenic	MER54B|LTR|ERVL	-1073	NM_001168504	232889	Mm.223639	NM_001004762	ENSMUSG00000033847	Pla2g4c	D7Ertd445e	phospholipase A2, group IVC (cytosolic, calcium-independent)	protein-coding
mm_99358.1	chr11	101610687	101610693	+	1	NA	promoter-TSS (NM_001256318)	promoter-TSS (NM_001256318)	-10	NM_001256318	666331	Mm.303457	NM_001256318		LOC666331	-	uncharacterized LOC666331	protein-coding
mm_37432.1	chr4	122933963	122933997	-	1	NA	Intergenic	B1F2|SINE|Alu	27208	NM_029662	76574	Mm.331842	NM_029662	ENSMUSG00000028655	Mfsd2a	1700018O18Rik|Mfsd2|NLS1	major facilitator superfamily domain containing 2A	protein-coding
mm_98793.1	chr11	96944235	96944285	+	1	NA	promoter-TSS (NM_134021)	promoter-TSS (NM_134021)	114	NR_003293	319371	Mm.436865	NR_003293	ENSMUSG00000078700	D030028A08Rik	-	RIKEN cDNA D030028A08 gene	ncRNA
mm_67575.1	chr7	81992669	81992679	-	1	NA	promoter-TSS (NM_007562)	promoter-TSS (NM_007562)	-375	NM_007562	12173	Mm.243802	NM_007562	ENSMUSG00000025105	Bnc1	AI047752|AW546376|Bnc	basonuclin 1	protein-coding
mm_20935.1	chr2	150858874	150858889	-	1	NA	intron (NM_024465, intron 1 of 12)	intron (NM_024465, intron 1 of 12)	45850	NM_024465	76192	Mm.112632	NM_024465	ENSMUSG00000032046	Abhd12	1500011G07Rik|6330583M11Rik|AI431047|AW547313	abhydrolase domain containing 12	protein-coding
mm_11494.1	chr2	32493617	32493622	+	1	NA	Intergenic	Intergenic	-41740	NM_153560	98952	Mm.4065	NM_153560	ENSMUSG00000039157	Fam102a	AI426465|C230093N12Rik|Eeig1	family with sequence similarity 102, member A	protein-coding
mm_164490.1	chr16	86303105	86303105	+	1	NA	Intergenic	Intergenic	-401980	NM_011782	23794	Mm.112933	NM_011782	ENSMUSG00000022894	Adamts5	9530092O11Rik|ADAM-TS5|ADAMTS1|ADAMTS11|ADMP-2|AI481094|ASMP-2	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)	protein-coding
mm_45826.1	chr5	87694578	87694584	-	1	NA	exon (NM_001286023, exon 5 of 7)	exon (NM_001286023, exon 5 of 7)	4844	NM_001286020	12991	Mm.268737	NM_009972	ENSMUSG00000063157	Csn2	Csnb	casein beta	protein-coding
mm_162474.1	chr1	133133545	133133557	-	1	NA	exon (NM_133819, exon 1 of 2)	exon (NM_133819, exon 1 of 2)	2385	NM_133819	108954	Mm.293628	NM_133819	ENSMUSG00000046062	Ppp1r15b	1810033K10Rik|AI606441|C530022L24Rik|CReP	protein phosphatase 1, regulatory (inhibitor) subunit 15b	protein-coding
mm_118980.1	chr14	28284568	28284570	+	1	NA	intron (NM_177814, intron 14 of 15)	intron (NM_177814, intron 14 of 15)	-220904	NM_009524	22418	Mm.287544	NM_009524	ENSMUSG00000021994	Wnt5a	8030457G12Rik|Wnt-5a	wingless-type MMTV integration site family, member 5A	protein-coding
mm_46810.1	chr5	113078451	113078463	-	1	NA	exon (NM_021352, exon 4 of 6)	exon (NM_021352, exon 4 of 6)	3127	NM_001159650	12962	Mm.378899	NM_021352	ENSMUSG00000029352	Crybb3	AI852419	crystallin, beta B3	protein-coding
mm_15060.1	chr2	152962487	152962510	+	1	NA	promoter-TSS (NM_029064)	promoter-TSS (NM_029064)	13	NM_001083618	74711	Mm.44746	NM_029064	ENSMUSG00000074673	Ttll9	1700016F23Rik|4930509O20Rik|AW046572	tubulin tyrosine ligase-like family, member 9	protein-coding
mm_122315.1	chr14	36919428	36919443	-	1	NA	promoter-TSS (NM_001347503)	promoter-TSS (NM_001347503)	100	NM_001347503	72972	Mm.27621	NM_027045	ENSMUSG00000058690	Ccser2	1700012P13Rik|2900054P12Rik|AI035535|AW108503|Fam190b|Gcap14	coiled-coil serine rich 2	protein-coding
mm_57461.1	chr6	125187107	125187146	-	1	NA	promoter-TSS (NR_028517)	promoter-TSS (NR_028517)	-695	NR_028517	100217413		NR_028517		Scarna10	MBI-52	small Cajal body-specific RNA 10	ncRNA
mm_101658.1	chr11	36677773	36677786	-	1	NA	intron (NM_011856, intron 2 of 28)	intron (NM_011856, intron 2 of 28)	266462	NM_001290702	23964	Mm.439889	NM_011856	ENSMUSG00000049336	Tenm2	Odz2|Odz3|Ten-2|Ten-m2	teneurin transmembrane protein 2	protein-coding
mm_39480.1	chr5	20702130	20702214	+	1	NA	3' UTR (NM_001170745, exon 21 of 21)	3' UTR (NM_001170745, exon 21 of 21)	179952	NM_172992	68770	Mm.86410	NM_172992	ENSMUSG00000039987	Phtf2	1110054G21Rik|9530062N20Rik|AI447096|C77923	putative homeodomain transcription factor 2	protein-coding
mm_62554.1	chr7	102442733	102442752	+	1	NA	intron (NM_009103, intron 1 of 18)	B1_Mur4|SINE|Alu	1047	NM_009103	20133	Mm.197486	NM_009103	ENSMUSG00000030978	Rrm1	RnrM1	ribonucleotide reductase M1	protein-coding
mm_168377.1	chr1	122086608	122086624	+	1	NA	Intergenic	L1Md_T|LINE|L1	-518636	NM_025860	66942	Mm.44219	NM_025860	ENSMUSG00000001674	Ddx18	2310005B10Rik	DEAD (Asp-Glu-Ala-Asp) box polypeptide 18	protein-coding
mm_41233.1	chr5	88758079	88758092	+	1	NA	3' UTR (NM_026735, exon 6 of 6)	3' UTR (NM_026735, exon 6 of 6)	-6928	NM_007832	13178	Mm.298892	NM_007832	ENSMUSG00000029366	Dck	-	deoxycytidine kinase	protein-coding
mm_121898.1	chr14	21848281	21848296	-	1	NA	exon (NM_026965, exon 3 of 7)	exon (NM_026965, exon 3 of 7)	622	NM_026965	69156	Mm.11827	NM_026965	ENSMUSG00000021773	Comtd1	1810030M08Rik|MT773	catechol-O-methyltransferase domain containing 1	protein-coding
mm_84375.1	chr9	65021646	65021717	-	1	NA	promoter-TSS (NM_021345)	promoter-TSS (NM_021345)	36	NM_021345	57874	Mm.308180	NM_021345	ENSMUSG00000033629	Hacd3	4930523M17Rik|AW742319|B-ind1|Hcad3|Hspc121|Ptplad1	3-hydroxyacyl-CoA dehydratase 3	protein-coding
mm_41735.1	chr5	102704162	102704170	+	1	NA	intron (NM_146161, intron 2 of 8)	intron (NM_146161, intron 2 of 8)	-64644	NM_001286468	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding
mm_146115.1	chr18	74283099	74283131	+	1	NA	promoter-TSS (NM_028948)	promoter-TSS (NM_028948)	15	NM_028948	74453	Mm.182293	NM_028948	ENSMUSG00000035394	Cfap53	4933415I03Rik|Ccdc11	cilia and flagella associated protein 53	protein-coding
mm_132727.1	chr16	43622973	43623006	+	1	NA	Intergenic	Intergenic	-17666	NR_030576	100124467		NR_030576	ENSMUSG00000076372	Mir568	Mirn568|mmu-mir-568	microRNA 568	ncRNA
mm_165128.1	chr2	7200969	7200970	-	1	NA	intron (NM_001110231, intron 2 of 15)	Lx6|LINE|L1	-119667	NM_001160292	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_78506.1	chr9	32752852	32752860	+	1	NA	exon (NM_001038642, exon 6 of 7)	exon (NM_001038642, exon 6 of 7)	56814	NM_001038642	23871	Mm.292415	NM_011808	ENSMUSG00000032035	Ets1	AI196000|AI448617|D230050P06|Ets-1|Tpl1|vs	E26 avian leukemia oncogene 1, 5' domain	protein-coding
mm_36285.1	chr4	63861279	63861293	-	1	NA	promoter-TSS (NM_009403)	promoter-TSS (NM_009403)	-2	NM_009403	21949	Mm.4664	NM_009403	ENSMUSG00000028362	Tnfsf8	CD153|CD30LG|Cd30l|Tnlg3a	tumor necrosis factor (ligand) superfamily, member 8	protein-coding
mm_109880.1	chr12	4918231	4918249	-	1	NA	intron (NM_001099628, intron 1 of 30)	intron (NM_001099628, intron 1 of 30)	887	NM_001099628	320817	Mm.210966	NM_001099628	ENSMUSG00000052812	Atad2b	1110014E10Rik|BC032887|C79189|D530031C13Rik	ATPase family, AAA domain containing 2B	protein-coding
mm_112292.1	chr12	114523944	114523959	-	1	NA	Intergenic	Intergenic	-10257	NR_106063	102465664		NR_106063	ENSMUSG00000098357	Mir7094-2	Gm27508|mmu-mir-7094-2	microRNA 7094-2	ncRNA
mm_660.1	chr1	40439643	40439649	+	1	NA	promoter-TSS (NM_010743)	promoter-TSS (NM_010743)	17	NM_010743	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_109350.1	chr12	109607799	109607802	+	1	NA	intron (NR_028261, intron 2 of 20)	intron (NR_028261, intron 2 of 20)	-3700	NR_029770	723846		NR_029770	ENSMUSG00000070101	Mir341	Mirn341|mmu-mir-341	microRNA 341	ncRNA
mm_67261.1	chr7	75774134	75774157	-	1	NA	Intergenic	MTC-int|LTR|ERVL-MaLR	-74193	NM_001122780	207952	Mm.206223	NM_029652	ENSMUSG00000055652	Klhl25	2810402K13Rik|BC027373|Enc-1	kelch-like 25	protein-coding
mm_20621.1	chr2	131855830	131855840	-	1	NA	exon (NM_001166206, exon 2 of 2)	exon (NM_001166206, exon 2 of 2)	3912	NM_001166206	71995	Mm.22	NM_028045	ENSMUSG00000037482	Erv3	1600014E20Rik|AA389086|AI426069|AI448024|D19349	endogenous retroviral sequence 3	protein-coding
mm_142668.1	chr17	47728876	47728908	-	1	NA	exon (NM_025973, exon 2 of 9)	exon (NM_025973, exon 2 of 9)	2050	NM_025973	109820	Mm.22957	NM_025973	ENSMUSG00000023987	Pgc	2210410L06Rik|Upg-1|Upg1	progastricsin (pepsinogen C)	protein-coding
mm_85820.1	chr9	110419955	110419963	-	1	NA	exon (NM_008694, exon 1 of 4)	exon (NM_008694, exon 1 of 4)	151	NM_008694	18054	Mm.236225	NM_008694	ENSMUSG00000032484	Ngp	bectenecin	neutrophilic granule protein	protein-coding
mm_58411.1	chr7	3289217	3289232	+	1	NA	5' UTR (NM_001093764, exon 1 of 3)	5' UTR (NM_001093764, exon 1 of 3)	186	NM_001093764	50918	Mm.29874	NM_016969	ENSMUSG00000068566	Myadm	D7Wsu62e	myeloid-associated differentiation marker	protein-coding
mm_132971.1	chr16	52031586	52031646	+	1	NA	promoter-TSS (NM_001033238)	promoter-TSS (NM_001033238)	67	NM_001033238	208650	Mm.328206	NM_001033238	ENSMUSG00000022637	Cblb	AI429560|AI851073|Cbl-b	Casitas B-lineage lymphoma b	protein-coding
mm_127425.1	chr15	101267876	101267896	+	1	NA	intron (NM_010444, intron 1 of 6)	intron (NM_010444, intron 1 of 6)	1040	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_91656.1	chr10	42583647	42583664	-	1	NA	promoter-TSS (NM_152229)	promoter-TSS (NM_152229)	-67	NM_152229	21907	Mm.287100	NM_152229	ENSMUSG00000019803	Nr2e1	Mtl1|Mtll|TLL|Tlx|XTLL|fierce|frc|tailless	nuclear receptor subfamily 2, group E, member 1	protein-coding
mm_87282.1	chr10	42140938	42140952	+	1	NA	Intergenic	Intergenic	-122563	NM_001034858	213402	Mm.211320	NM_001034858	ENSMUSG00000071324	Armc2	2610018I05Rik	armadillo repeat containing 2	protein-coding
mm_78932.1	chr9	45103837	45103862	+	1	NA	intron (NM_001005421, intron 9 of 10)	intron (NM_001005421, intron 9 of 10)	-14027	NM_001014761	72821	Mm.229373	NM_001014761	ENSMUSG00000070304	Scn2b	2810451E09Rik|AI840361|Gm183	sodium channel, voltage-gated, type II, beta	protein-coding
mm_17750.1	chr2	32716683	32716687	-	1	NA	Intergenic	RMER19B|LTR|ERVK	-3713	NR_039536	100628606		NR_039536	ENSMUSG00000105841	Mir3960	mmu-mir-3960	microRNA 3960	ncRNA
mm_120174.1	chr14	61129379	61129388	+	1	NA	Intergenic	Intergenic	-9074	NM_172809	50720	Mm.440703	NM_015788	ENSMUSG00000048279	Sacs	A230052M14|DNAJC29|E130115J16Rik|mKIAA0730	sacsin	protein-coding
mm_151904.1	chr19	5799369	5799382	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	3297	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_161802.1	chr17	55945254	55945254	-	1	NA	promoter-TSS (NM_146249)	promoter-TSS (NM_146249)	5	NM_146249	240120	Mm.441018	NM_146249	ENSMUSG00000062101	Zfp119b	-	zinc finger protein 119b	protein-coding
mm_169296.1	chr14	100314389	100314389	+	1	NA	Intergenic	Intergenic	-164593	NM_010636	16597	Mm.396499	NM_010636	ENSMUSG00000072294	Klf12	2700063E05Rik|AI225908|AI315654|AP-2rep|B130052C06Rik|D530033K05Rik	Kruppel-like factor 12	protein-coding
mm_10571.1	chr2	18064417	18064429	+	1	NA	promoter-TSS (NM_001252561)	promoter-TSS (NM_001252561)	-162	NM_001252560	17354	Mm.209175	NM_010804	ENSMUSG00000026743	Mllt10	Af10|B130021D15Rik|D630001B22Rik|mKIAA4140	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 10	protein-coding
mm_61266.1	chr7	66109531	66109539	+	1	NA	promoter-TSS (NM_001081163)	promoter-TSS (NM_001081163)	20	NM_001081163	269941	Mm.333916	NM_001081163	ENSMUSG00000032640	Chsy1	mKIAA0990	chondroitin sulfate synthase 1	protein-coding
mm_16489.1	chr2	180974322	180974325	+	1	NA	intron (NM_001177709, intron 7 of 11)	intron (NM_001177709, intron 7 of 11)	7023	NM_001177706	228998	Mm.33765	NM_145760	ENSMUSG00000027575	Arfgap1	AI115377|Arf1gap	ADP-ribosylation factor GTPase activating protein 1	protein-coding
mm_153918.1	chr19	47272034	47272058	-	1	NA	exon (NM_008018, exon 13 of 15)	exon (NM_008018, exon 13 of 15)	1543	NR_105961	102466782		NR_105961	ENSMUSG00000098786	Mir6995	Gm27576|mmu-mir-6995	microRNA 6995	ncRNA
mm_41419.1	chr5	90881998	90882013	+	1	NA	Intergenic	(CTCTG)n|Simple_repeat|Simple_repeat	-9240	NM_008176	14825	Mm.21013	NM_008176	ENSMUSG00000029380	Cxcl1	Fsp|Gro1|KC|Mgsa|N51|Scyb1|gro	chemokine (C-X-C motif) ligand 1	protein-coding
mm_127225.1	chr15	99397879	99397883	+	1	NA	intron (NM_001171036, intron 2 of 10)	ID4_|SINE|ID	4662	NM_001171035	110213	Mm.16769	NM_026669	ENSMUSG00000023010	Tmbim6	5031406P05Rik|Bi1|Tegt	transmembrane BAX inhibitor motif containing 6	protein-coding
mm_148325.1	chr18	84058096	84058112	-	1	NA	intron (NM_001081300, intron 1 of 1)	intron (NM_001081300, intron 1 of 1)	28458	NM_001081300	110796	Mm.102136	NM_001081300	ENSMUSG00000046982	Tshz1	5730407I04Rik|D18Bwg1409e|Mtsh1|NY-CO-33|Sdccag33|Tsh1|mKIAA4206|teashirt1	teashirt zinc finger family member 1	protein-coding
mm_83930.1	chr9	56635861	56635880	-	1	NA	promoter-TSS (NM_001311076)	promoter-TSS (NM_001311076)	-222	NM_001311076	235402	Mm.246605	NM_181074	ENSMUSG00000049556	Lingo1	4930471K13Rik|AV148400|LERN1|LINGO-1|Lrrn6a|UNQ201	leucine rich repeat and Ig domain containing 1	protein-coding
mm_158570.1	chrX	150588045	150588057	-	1	NA	exon (NM_029943, exon 1 of 6)	exon (NM_029943, exon 1 of 6)	104	NM_029943	77622	Mm.440275	NM_029943	ENSMUSG00000025269	Apex2	C430040P13Rik|ape2	apurinic/apyrimidinic endonuclease 2	protein-coding
mm_73138.1	chr8	94977297	94977309	+	1	NA	5' UTR (NM_001198894, exon 1 of 14)	5' UTR (NM_001198894, exon 1 of 14)	194	NM_001198894	14766	Mm.290834	NM_018882	ENSMUSG00000031785	Adgrg1	Cyt28|Gpr56|TM7LN4|TM7XN1	adhesion G protein-coupled receptor G1	protein-coding
mm_131769.1	chr16	22894230	22894241	+	1	NA	intron (NR_075099, intron 1 of 5)	intron (NR_075099, intron 1 of 5)	151	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_85693.1	chr9	108079700	108079710	-	1	NA	promoter-TSS (NM_008243)	promoter-TSS (NM_008243)	-330	NM_032543	84585	Mm.379272	NM_032543	ENSMUSG00000041528	Rnf123	BC003945|Kpc1	ring finger protein 123	protein-coding
mm_140040.1	chr17	74487228	74487241	+	1	NA	Intergenic	Intergenic	-2259	NM_026417	67864	Mm.41891	NM_026417	ENSMUSG00000024072	Yipf4	2310034L04Rik	Yip1 domain family, member 4	protein-coding
mm_167713.1	chr9	97015996	97015999	+	1	NA	intron (NM_145134, intron 1 of 2)	intron (NM_145134, intron 1 of 2)	2358	NM_145134	211949	Mm.491271	NM_145134	ENSMUSG00000046997	Spsb4	D030068E18Rik|SSB-4|Ssb4	splA/ryanodine receptor domain and SOCS box containing 4	protein-coding
mm_52080.1	chr6	97828301	97828312	+	1	NA	intron (NM_001113198, intron 1 of 9)	intron (NM_001113198, intron 1 of 9)	21248	NM_001113198	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_100558.1	chr11	120729559	120729638	+	1	NA	3' UTR (NM_007621, exon 8 of 8)	3' UTR (NM_007621, exon 8 of 8)	-2314	NM_001347608	67880	Mm.231091	NM_026428	ENSMUSG00000039450	Dcxr	0610038K04Rik|1810027P18Rik|XR	dicarbonyl L-xylulose reductase	protein-coding
mm_83672.1	chr9	49794458	49794461	-	1	NA	intron (NM_001081445, intron 1 of 17)	intron (NM_001081445, intron 1 of 17)	4610	NM_001081445	17967	Mm.4974	NM_010875	ENSMUSG00000039542	Ncam1	CD56|E-NCAM|NCAM-1|Ncam	neural cell adhesion molecule 1	protein-coding
mm_89001.1	chr10	81620536	81620541	+	1	NA	Intergenic	Intergenic	6784	NM_001163430	50721	Mm.25643	NM_181586	ENSMUSG00000034748	Sirt6	2810449N18Rik|AI043036|Sir2l6	sirtuin 6	protein-coding
mm_88356.1	chr10	75935879	75935908	+	1	NA	5' UTR (NM_175329, exon 1 of 4)	5' UTR (NM_175329, exon 1 of 4)	320	NM_175329	103172	Mm.333849	NM_175329	ENSMUSG00000049422	Chchd10	1620401E04Rik|AI267078|Ndg2	coiled-coil-helix-coiled-coil-helix domain containing 10	protein-coding
mm_148617.1	chr19	5394633	5394637	+	1	NA	Intergenic	Intergenic	-5932	NM_016882	20227	Mm.34562	NM_016882	ENSMUSG00000039148	Sart1	U5-110K	squamous cell carcinoma antigen recognized by T cells 1	protein-coding
mm_24717.1	chr3	95231477	95231511	+	1	NA	intron (NM_001038708, intron 1 of 4)	intron (NM_001038708, intron 1 of 4)	2551	NM_001038708	57912	Mm.28189	NM_172395	ENSMUSG00000046722	Cdc42se1	1300002M12Rik|AW558204|Cdcse1|SCIP1|Spec1	CDC42 small effector 1	protein-coding
mm_152477.1	chr19	11018052	11018060	-	1	NA	promoter-TSS (NM_001251849)	promoter-TSS (NM_001251849)	-93	NM_001251849	76002	Mm.139320	NM_001251849	ENSMUSG00000094584	Ms4a18	5033428B15Rik	membrane-spanning 4-domains, subfamily A, member 18	protein-coding
mm_4719.1	chr1	181062059	181062075	+	1	NA	Intergenic	Intergenic	10830	NM_001033819	619326	Mm.355174	NM_001033819	ENSMUSG00000038768	9130409I23Rik	-	RIKEN cDNA 9130409I23 gene	protein-coding
mm_153022.1	chr19	31351461	31351470	-	1	NA	intron (NM_011160, intron 2 of 17)	intron (NM_011160, intron 2 of 17)	-135069	NR_002849	78103	Mm.445198	NR_002849		8430431K14Rik	-	RIKEN cDNA 8430431K14 gene	ncRNA
mm_23189.1	chr3	40950780	40950838	+	1	NA	intron (NM_001040399, intron 1 of 9)	CpG-9127	178	NM_001040399	214048	Mm.46782	NM_027663	ENSMUSG00000025762	Larp1b	1700108L22Rik|4933421B21Rik|AA690246|Larp2	La ribonucleoprotein domain family, member 1B	protein-coding
mm_130614.1	chr15	99967056	99967066	-	1	NA	Intergenic	Intergenic	-3004	NM_001080948	207214	Mm.28811	NM_001024526	ENSMUSG00000023025	Larp4	DXErtd793|DXErtd793e	La ribonucleoprotein domain family, member 4	protein-coding
mm_108012.1	chr12	73586157	73586191	+	1	NA	intron (NM_008856, intron 1 of 13)	intron (NM_008856, intron 1 of 13)	1378	NM_008856	18755	Mm.341677	NM_008856	ENSMUSG00000021108	Prkch	Pkch	protein kinase C, eta	protein-coding
mm_112620.1	chr13	15550918	15550922	+	1	NA	intron (NM_008130, intron 3 of 14)	intron (NM_008130, intron 3 of 14)	87197	NM_008130	14634	Mm.5098	NM_008130	ENSMUSG00000021318	Gli3	AI854843|AU023367|Bph|GLI3-190|GLI3FL|Pdn|Xt|add	GLI-Kruppel family member GLI3	protein-coding
mm_118963.1	chr14	27438833	27438836	+	1	NA	intron (NM_028945, intron 2 of 23)	intron (NM_028945, intron 2 of 23)	9987	NM_001114879	218850	Mm.247767	NM_028945	ENSMUSG00000040651	Fam208a	4732418E12|4933409E02Rik|D14Abb1e|MommeD6	family with sequence similarity 208, member A	protein-coding
mm_21093.1	chr2	153225034	153225052	-	1	NA	exon (NM_198617, exon 1 of 1)	exon (NM_198617, exon 1 of 1)	398	NM_198617	241732	Mm.277243	NM_198617	ENSMUSG00000074671	Tspyl3	AW212607|Gm36	TSPY-like 3	protein-coding
mm_127431.1	chr15	101270131	101270140	+	1	NA	exon (NM_010444, exon 2 of 7)	exon (NM_010444, exon 2 of 7)	3289	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_97365.1	chr11	77513512	77513537	+	1	NA	promoter-TSS (NM_001024920)	promoter-TSS (NM_001024920)	-251	NM_001024920	216964	Mm.341211	NM_001024920	ENSMUSG00000044328	Trp53i13	2410019G02Rik|Tp53i13	transformation related protein 53 inducible protein 13	protein-coding
mm_77607.1	chr8	123893258	123893279	-	1	NA	exon (NM_009606, exon 3 of 7)	exon (NM_009606, exon 3 of 7)	1507	NM_001272041	11459	Mm.214950	NM_009606	ENSMUSG00000031972	Acta1	AA959943|Acta-2|Acts|Actsk-1	actin, alpha 1, skeletal muscle	protein-coding
mm_16194.1	chr2	172979828	172979879	+	1	NA	promoter-TSS (NM_001083959)	promoter-TSS (NM_001083959)	11	NM_001305434	26972	Mm.23495	NM_012046	ENSMUSG00000005883	Spo11	AI449549|Spo11a|Spo11b	SPO11 meiotic protein covalently bound to DSB	protein-coding
mm_172711.1	chr8	69575804	69575805	-	1	NA	Intergenic	Intergenic	49371	NM_001045553	234362	Mm.458487	NM_172754	ENSMUSG00000060427	Zfp868	AI449175|AW108241|C530032E20|mszf62	zinc finger protein 868	protein-coding
mm_159065.1	chr2	22227519	22227519	+	1	NA	promoter-TSS (NM_148413)	promoter-TSS (NM_148413)	16	NM_148413	667663	Mm.330033	NM_148413	ENSMUSG00000025716	Myo3a	9030416P08Rik	myosin IIIA	protein-coding
mm_110168.1	chr12	27335575	27335585	-	1	NA	3' UTR (NM_009234, exon 1 of 1)	3' UTR (NM_009234, exon 1 of 1)	7138	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding
mm_114294.1	chr13	58808264	58808286	+	1	NA	intron (NM_001025074, intron 1 of 17)	CpG	578	NM_001025074	18212	Mm.130054	NM_008745	ENSMUSG00000055254	Ntrk2	GP145-TrkB/GP95-TrkB|Tkrb|trk-B|trkB	neurotrophic tyrosine kinase, receptor, type 2	protein-coding
mm_162261.1	chrY	2663891	2663891	-	1	NA	promoter-TSS (NM_011564)	promoter-TSS (NM_011564)	-233	NM_011564	21674	Mm.377114	NM_011564	ENSMUSG00000069036	Sry	Tdf|Tdy	sex determining region of Chr Y	protein-coding
mm_51493.1	chr6	83057267	83057300	+	1	NA	promoter-TSS (NM_033606)	promoter-TSS (NM_033606)	-561	NM_033606	93838	Mm.140332	NM_033606	ENSMUSG00000009145	Dqx1	2310066E11Rik	DEAQ RNA-dependent ATPase	protein-coding
mm_55043.1	chr6	48988169	48988174	-	1	NA	exon (NM_172888, exon 1 of 5)	exon (NM_172888, exon 1 of 5)	1310	NM_172888	243377	Mm.446302	NM_172888	ENSMUSG00000039215	Svs1	9530003A11	seminal vesicle secretory protein 1	protein-coding
mm_52052.1	chr6	97217973	97217996	+	1	NA	intron (NM_022992, intron 1 of 2)	(T)n|Simple_repeat|Simple_repeat	7192	NM_022992	65106	Mm.291014	NM_022992	ENSMUSG00000035199	Arl6ip5	5930404D22Rik|AV001879|Aip-5|Gtrap3-18|addiscin	ADP-ribosylation factor-like 6 interacting protein 5	protein-coding
mm_116396.1	chr13	41220202	41220225	-	1	NA	promoter-TSS (NM_001311121)	promoter-TSS (NM_001311121)	-51	NM_001311121	54326	Mm.2567	NM_019423	ENSMUSG00000021364	Elovl2	AI317360|Ssc2	elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 2	protein-coding
mm_117982.1	chr13	100113997	100114038	-	1	NA	exon (NM_011353, exon 3 of 3)	exon (NM_011353, exon 3 of 3)	5998	NM_011353	20365	Mm.286177	NM_011353	ENSMUSG00000021643	Serf1	4F5|Msmac1|m4F5	small EDRK-rich factor 1	protein-coding
mm_152015.1	chr19	5989348	5989360	-	1	NA	3' UTR (NM_007600, exon 22 of 22)	3' UTR (NM_007600, exon 22 of 22)	-3211	NM_198650	381203	Mm.329638	NM_198650	ENSMUSG00000037451	Slc22a20	Gm963|OAT1-L|mOAT6	solute carrier family 22 (organic anion transporter), member 20	protein-coding
mm_157248.1	chrX	19146890	19146904	-	1	NA	promoter-TSS (NR_029806)	promoter-TSS (NR_029806)	74	NR_029807	723828		NR_029807	ENSMUSG00000065471	Mir222	Mirn222|mir-222|mmu-mir-222	microRNA 222	ncRNA
mm_50935.1	chr6	57702915	57702925	+	1	NA	5' UTR (NM_133737, exon 1 of 9)	5' UTR (NM_133737, exon 1 of 9)	465	NM_133737	71835	Mm.274904	NM_133737	ENSMUSG00000062190	Lancl2	1700003F10Rik	LanC (bacterial lantibiotic synthetase component C)-like 2	protein-coding
mm_156027.1	chrX	107172295	107172298	+	1	NA	3' UTR (NM_175442, exon 2 of 2)	3' UTR (NM_175442, exon 2 of 2)	22681	NM_175442	213438	Mm.265244	NM_175442	ENSMUSG00000054293	A630033H20Rik	AI662791|P2ry10	RIKEN cDNA A630033H20 gene	protein-coding
mm_88864.1	chr10	80940077	80940096	+	1	NA	Intergenic	Intergenic	9995	NM_008655	17873	Mm.1360	NM_008655	ENSMUSG00000015312	Gadd45b	AI323528|Myd118	growth arrest and DNA-damage-inducible 45 beta	protein-coding
mm_103070.1	chr11	69880857	69880863	-	1	NA	TTS (NM_153788)	TTS (NM_153788)	125	NM_153143	216858	Mm.239498	NM_153143	ENSMUSG00000046731	Kctd11	AF465352|Ren	potassium channel tetramerisation domain containing 11	protein-coding
mm_19158.1	chr2	83353970	83353976	-	1	NA	Intergenic	Intergenic	-290605	NM_026934	69082	Mm.27804	NM_026934	ENSMUSG00000027091	Zc3h15	1700006A17Rik|1810012H02Rik|2610312B22Rik|FM22|Ierepo4	zinc finger CCCH-type containing 15	protein-coding
mm_143526.1	chr17	73899804	73899807	-	1	NA	intron (NM_011723, intron 26 of 35)	intron (NM_011723, intron 26 of 35)	50391	NM_011723	22436	Mm.11223	NM_011723	ENSMUSG00000024066	Xdh	XO|Xor|Xox-1|Xox1	xanthine dehydrogenase	protein-coding
mm_55870.1	chr6	83506817	83506823	-	1	NA	exon (NM_001162521, exon 1 of 6)	exon (NM_001162521, exon 1 of 6)	149	NM_013764	27369	Mm.42234	NM_013764	ENSMUSG00000014554	Dguok	dGK|dGK1|dGK2|dGK3	deoxyguanosine kinase	protein-coding
mm_168221.1	chr10	78043529	78043529	-	1	NA	promoter-TSS (NM_001271556)	promoter-TSS (NM_001271556)	81	NM_001271552	11634	Mm.35300	NM_009646	ENSMUSG00000000731	Aire	-	autoimmune regulator (autoimmune polyendocrinopathy candidiasis ectodermal dystrophy)	protein-coding
mm_93206.1	chr10	94855557	94855573	-	1	NA	intron (NM_018797, intron 9 of 30)	MTC|LTR|ERVL-MaLR	89013	NM_018797	54712	Mm.256712	NM_018797	ENSMUSG00000074785	Plxnc1	2510048K12Rik|AW742158|CD232|Vespr	plexin C1	protein-coding
mm_73793.1	chr8	117257083	117257107	+	1	NA	promoter-TSS (NM_001163262)	promoter-TSS (NM_001163262)	76	NM_001163262	74440	Mm.233181	NM_028941	ENSMUSG00000034390	Cmip	4933407C03Rik|5830471E12Rik|AI314065|AI464126	c-Maf inducing protein	protein-coding
mm_71815.1	chr8	68884470	68884493	+	1	NA	intron (NM_008509, intron 1 of 9)	intron (NM_008509, intron 1 of 9)	3926	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_93044.1	chr10	88471151	88471185	-	1	NA	intron (NM_011517, intron 7 of 8)	intron (NM_011517, intron 7 of 8)	11581	NM_011517	20962	Mm.297977	NM_011517	ENSMUSG00000020059	Sycp3	Cor1|Scp3	synaptonemal complex protein 3	protein-coding
mm_25078.1	chr3	100008323	100008323	+	1	NA	intron (NM_028892, intron 7 of 48)	intron (NM_028892, intron 7 of 48)	122906	NM_028892	74362	Mm.55847	NM_028892	ENSMUSG00000027867	Spag17	4931427F14Rik|PF6|Spag17-ps	sperm associated antigen 17	protein-coding
mm_27632.1	chr3	61363131	61363141	-	1	NA	Intergenic	Intergenic	-1371	NM_028712	74012	Mm.422674	NM_028712	ENSMUSG00000036894	Rap2b	4021402C18Rik|AA408554	RAP2B, member of RAS oncogene family	protein-coding
mm_136380.1	chr16	92825936	92825946	-	1	NA	5' UTR (NM_001111021, exon 1 of 8)	5' UTR (NM_001111021, exon 1 of 8)	133	NM_001111021	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_46046.1	chr5	92050594	92050595	-	1	NA	Intergenic	Intergenic	-7552	NM_016912	53886	Mm.44963	NM_016912	ENSMUSG00000029403	Cdkl2	5330436L21Rik|AI505225|KKIAMRE|Kkm	cyclin-dependent kinase-like 2 (CDC2-related kinase)	protein-coding
mm_4251.1	chr1	171408161	171408178	+	1	NA	exon (NM_001005508, exon 12 of 12)	exon (NM_001005508, exon 12 of 12)	-3144	NM_001305678	22278	Mm.8	NM_009480	ENSMUSG00000026641	Usf1	bHLHb11	upstream transcription factor 1	protein-coding
mm_94449.1	chr11	6389118	6389137	+	1	NA	Intergenic	Intergenic	-5998	NM_001005867	52915	Mm.1144	NM_028601	ENSMUSG00000041164	Zmiz2	Zimp7	zinc finger, MIZ-type containing 2	protein-coding
mm_63136.1	chr7	123057136	123057139	+	1	NA	Intergenic	(T)n|Simple_repeat|Simple_repeat	-66748	NM_144925	233833	Mm.102305	NM_144925	ENSMUSG00000052707	Tnrc6a	2010321I05Rik|3110054G10Rik|AW557223|CAGH26|D130023A07Rik|GW182|Tnrc6	trinucleotide repeat containing 6a	protein-coding
mm_64184.1	chr7	141459642	141459664	+	1	NA	non-coding (NR_028142, exon 10 of 10)	non-coding (NR_028142, exon 10 of 10)	-1441	NM_001025103	213573	Mm.386851	NM_001025103	ENSMUSG00000048200	Cracr2b	6330520A15Rik|BC026645|Cracr2a|Efcab4|Efcab4a	calcium release activated channel regulator 2B	protein-coding
mm_57527.1	chr6	126365938	126365952	-	1	NA	Intergenic	Intergenic	-37259	NR_045480	100038574	Mm.399353	NR_045480	ENSMUSG00000107623	Gm10415	ENSMUSG00000072759	predicted gene 10415	ncRNA
mm_46598.1	chr5	107837501	107837501	-	1	NA	intron (NM_007964, intron 2 of 17)	intron (NM_007964, intron 2 of 17)	7339	NM_001276397	73318	Mm.441500	NM_028502	ENSMUSG00000063447	Ube2d2b	1700013N18Rik	ubiquitin-conjugating enzyme E2D 2B	protein-coding
mm_39783.1	chr5	30159921	30159940	+	1	NA	intron (NM_001289798, intron 1 of 15)	MLT1F|LTR|ERVL-MaLR	4677	NM_001289798	231086	Mm.291463	NM_145558	ENSMUSG00000059447	Hadhb	4930479F15Rik|Mtpb|TP-beta	hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), beta subunit	protein-coding
mm_22552.1	chr3	9608804	9608824	+	1	NA	intron (NM_133218, intron 1 of 8)	intron (NM_133218, intron 1 of 8)	1271	NM_133218	170753	Mm.212908	NM_133218	ENSMUSG00000040209	Zfp704	C030026M03|C030034L19Rik|Gig1|Znf704	zinc finger protein 704	protein-coding
mm_152626.1	chr19	12473425	12473433	-	1	NA	intron (NM_172442, intron 7 of 8)	intron (NM_172442, intron 7 of 8)	12650	NM_010821	17476	Mm.3999	NM_010821	ENSMUSG00000046805	Mpeg1	MPS1|Mpg-1	macrophage expressed gene 1	protein-coding
mm_129478.1	chr15	78718846	78718879	-	1	NA	promoter-TSS (NM_183141)	promoter-TSS (NM_183141)	-749	NM_183141	207393	Mm.323188	NM_183141	ENSMUSG00000043460	Elfn2	6330514E13|AW048948|BC094219|Lrrc62|Ppp1r29	leucine rich repeat and fibronectin type III, extracellular 2	protein-coding
mm_132746.1	chr16	44146319	44146322	+	1	NA	intron (NM_028108, intron 1 of 4)	B2_Mm1a|SINE|B2	6511	NM_028108	72117	Mm.278726	NM_028108	ENSMUSG00000022698	Naa50	2600005K24Rik|2810441M03Rik|AW112078|Mak3|Mak3p|Nat13|Nat5|San	N(alpha)-acetyltransferase 50, NatE catalytic subunit	protein-coding
mm_14584.1	chr2	135764959	135764973	+	1	NA	intron (NM_013829, intron 1 of 36)	intron (NM_013829, intron 1 of 36)	23136	NM_013829	18798	Mm.38009	NM_013829	ENSMUSG00000039943	Plcb4	A930039J07Rik|AI854601|C230058B11Rik	phospholipase C, beta 4	protein-coding
mm_42126.1	chr5	110906478	110906491	+	1	NA	intron (NM_001267622, intron 2 of 22)	intron (NM_001267622, intron 2 of 22)	26681	NM_001267622	209683	Mm.295660	NM_024477	ENSMUSG00000033209	Ttc28	2310015L07Rik|6030435N04|AI428795|AI851761|BC002262|TPRBK	tetratricopeptide repeat domain 28	protein-coding
mm_108496.1	chr12	83688252	83688268	+	1	NA	promoter-TSS (NM_008943)	promoter-TSS (NM_008943)	-303	NM_008943	19164	Mm.998	NM_008943	ENSMUSG00000019969	Psen1	Ad3h|PS-1|PS1|S182	presenilin 1	protein-coding
mm_136173.1	chr16	88671722	88671726	-	1	NA	promoter-TSS (NM_001163105)	promoter-TSS (NM_001163105)	-70	NM_001163105	239933	Mm.478807	NM_001163105	ENSMUSG00000090515	Krtap27-1	EG239933	keratin associated protein 27-1	protein-coding
mm_37266.1	chr4	118489790	118489831	-	1	NA	promoter-TSS (NM_011587)	promoter-TSS (NM_011587)	39	NM_011587	21846	Mm.4345	NM_011587	ENSMUSG00000033191	Tie1	D430008P04Rik|TIE|tie-1	tyrosine kinase with immunoglobulin-like and EGF-like domains 1	protein-coding
mm_70864.1	chr8	24595778	24595782	+	1	NA	promoter-TSS (NM_001293690)	promoter-TSS (NM_001293690)	-114	NM_001293690	15930	Mm.392	NM_008324	ENSMUSG00000031551	Ido1	Ido|Indo	indoleamine 2,3-dioxygenase 1	protein-coding
mm_1648.1	chr1	74661551	74661568	+	1	NA	promoter-TSS (NM_001014974)	promoter-TSS (NM_001014974)	-195	NM_001014974	67534	Mm.260714	NM_001014974	ENSMUSG00000033257	Ttll4	4632407P03Rik|AI451681|mKIAA0173	tubulin tyrosine ligase-like family, member 4	protein-coding
mm_166605.1	chr6	67875985	67875986	+	1	NA	Intergenic	Intergenic	-310286	NR_003100	75070	Mm.463364	NR_003100		4930515G16Rik	-	myc induced nuclear antigen pseudogene	pseudo
mm_147981.1	chr18	67549245	67549269	-	1	NA	promoter-TSS (NM_176832)	promoter-TSS (NM_176832)	-84	NM_176832	68166	Mm.208723	NM_176832	ENSMUSG00000024533	Spire1	6030430B19Rik|AI415299|AU022898|AW550622|Spir-1	spire homolog 1 (Drosophila)	protein-coding
mm_128066.1	chr15	26895540	26895558	-	1	NA	promoter-TSS (NM_176959)	promoter-TSS (NM_176959)	15	NM_176959	448987	Mm.253378	NM_176959	ENSMUSG00000043556	Fbxl7	AL023057|D230018M15Rik|FBL7|Fbl6	F-box and leucine-rich repeat protein 7	protein-coding
mm_88546.1	chr10	78577056	78577075	+	1	NA	intron (NM_173751, intron 4 of 15)	intron (NM_173751, intron 4 of 15)	2565	NM_173751	216136	Mm.2644	NM_173751	ENSMUSG00000032763	Ilvbl	5830463I21|AI415009	ilvB (bacterial acetolactate synthase)-like	protein-coding
mm_78903.1	chr9	44772910	44772949	+	1	NA	promoter-TSS (NM_023831)	promoter-TSS (NM_023831)	-80	NM_023831	76568	Mm.278597	NM_023831	ENSMUSG00000002031	Ift46	1500035H01Rik|AA408110|AI663846|R75047|c11orf2	intraflagellar transport 46	protein-coding
mm_93613.1	chr10	117238648	117238654	-	1	NA	promoter-TSS (NM_029906)	promoter-TSS (NM_029906)	30	NM_029906	77397	Mm.118350	NM_029906	ENSMUSG00000020177	9530003J23Rik	Lyzf1	RIKEN cDNA 9530003J23 gene	protein-coding
mm_147715.1	chr18	60812536	60812562	-	1	NA	TTS (NR_039567)	TTS (NR_039567)	473	NR_039567	100628611		NR_039567	ENSMUSG00000093327	Mir5107	mir-5107|mmu-mir-5107|mu-mir-5107	microRNA 5107	ncRNA
mm_158977.1	chr1	119995271	119995271	-	1	NA	promoter-TSS (NM_001115074)	promoter-TSS (NM_001115074)	-61	NM_001115074	226356	Mm.297290	NM_001115074	ENSMUSG00000036962	Cfap221	Gm101|Pcdp1	cilia and flagella associated protein 221	protein-coding
mm_140504.1	chr17	5217280	5217309	-	1	NA	intron (NM_001085355, intron 4 of 19)	intron (NM_001085355, intron 4 of 19)	201473	NM_175349	106557	Mm.432764	NM_175349	ENSMUSG00000101959	Ldhal6b	4933402O15Rik|AI326310|LDHL|Ldhal	lactate dehydrogenase A-like 6B	protein-coding
mm_117883.1	chr13	99344653	99344706	-	1	NA	promoter-TSS (NM_026873)	promoter-TSS (NM_026873)	-1	NM_026873	68927	Mm.276502	NM_026873	ENSMUSG00000021650	Ptcd2	1190005P08Rik	pentatricopeptide repeat domain 2	protein-coding
mm_160853.1	chr11	55607890	55607890	-	1	NA	5' UTR (NM_020492, exon 1 of 9)	5' UTR (NM_020492, exon 1 of 9)	308	NM_001290821	14654	Mm.89320	NM_020492	ENSMUSG00000000263	Glra1	nmf11|oscillator|ot|spasmodic|spd	glycine receptor, alpha 1 subunit	protein-coding
mm_97248.1	chr11	75751948	75752007	+	1	NA	exon (NM_009536, exon 2 of 6)	exon (NM_009536, exon 2 of 6)	19090	NM_009536	22627	Mm.234700	NM_009536	ENSMUSG00000020849	Ywhae	AU019196	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide	protein-coding
mm_110057.1	chr12	20921256	20921273	-	1	NA	Intergenic	CpG	-105485	NR_015521	69513	Mm.273972	NR_015521	ENSMUSG00000099759	1700030C10Rik	-	RIKEN cDNA 1700030C10 gene	ncRNA
mm_735.1	chr1	43445737	43445830	+	1	NA	promoter-TSS (NM_010879)	promoter-TSS (NM_010879)	32	NM_010879	17974	Mm.389903	NM_010879	ENSMUSG00000066877	Nck2	4833426I10Rik|Grb4|NCKbeta|Nck-2	non-catalytic region of tyrosine kinase adaptor protein 2	protein-coding
mm_117737.1	chr13	95671430	95671445	-	1	NA	exon (NM_027711, exon 21 of 36)	exon (NM_027711, exon 21 of 36)	-25483	NM_010170	14064	Mm.440952	NM_010170	ENSMUSG00000021675	F2rl2	F730031A08|PAR3	coagulation factor II (thrombin) receptor-like 2	protein-coding
mm_156603.1	chrX	153139942	153140011	+	1	NA	promoter-TSS (NM_001004154)	promoter-TSS (NM_001004154)	18	NM_001004154	245670	Mm.190922	NM_001004154	ENSMUSG00000041658	Rragb	-	Ras-related GTP binding B	protein-coding
mm_143445.1	chr17	70873422	70873438	-	1	NA	Intergenic	Intergenic	-19898	NM_001164074	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_56832.1	chr6	117174656	117174662	-	1	NA	3' UTR (NM_021704, exon 3 of 3)	3' UTR (NM_021704, exon 3 of 3)	6124	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_53901.1	chr6	3494528	3494542	-	1	NA	promoter-TSS (NM_178899)	promoter-TSS (NM_178899)	-37	NM_178899	101202	Mm.206911	NM_178899	ENSMUSG00000044156	Hepacam2	AI987662	HEPACAM family member 2	protein-coding
mm_27999.1	chr3	82903918	82903928	-	1	NA	promoter-TSS (NR_040381)	promoter-TSS (NR_040381)	51	NM_023624	79235	Mm.33921	NM_023624	ENSMUSG00000028003	Lrat	1300010A18Rik|AI449251	lecithin-retinol acyltransferase (phosphatidylcholine-retinol-O-acyltransferase)	protein-coding
mm_107538.1	chr12	40572805	40572811	+	1	NA	intron (NM_172803, intron 1 of 52)	intron (NM_172803, intron 1 of 52)	126755	NM_172803	238130	Mm.341423	NM_172803	ENSMUSG00000035954	Dock4	5330406C03|6330411N01Rik|AF263288|C030023J22|mKIAA0716	dedicator of cytokinesis 4	protein-coding
mm_140350.1	chr17	86831249	86831270	+	1	NA	3' UTR (NM_010137, exon 16 of 16)	3' UTR (NM_010137, exon 16 of 16)	77395	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_73224.1	chr8	101591007	101591010	+	1	NA	Intergenic	Intergenic	1194103	NM_009866	12552	Mm.1571	NM_009866	ENSMUSG00000031673	Cdh11	Cad11|OSF-4	cadherin 11	protein-coding
mm_124042.1	chr14	77036851	77036886	-	1	NA	promoter-TSS (NM_172488)	promoter-TSS (NM_172488)	96	NM_001310649	108811	Mm.102168	NM_175369	ENSMUSG00000034795	Ccdc122	4933415L06Rik	coiled-coil domain containing 122	protein-coding
mm_37409.1	chr4	122859172	122859176	-	1	NA	TTS (NM_008917)	TTS (NM_008917)	22947	NM_008917	19063	Mm.277719	NM_008917	ENSMUSG00000028657	Ppt1	9530043G02Rik|AA960502|C77813|CLN1|D4Ertd184e|INCL|PPT	palmitoyl-protein thioesterase 1	protein-coding
mm_95713.1	chr11	54516299	54516320	+	1	NA	3' UTR (NM_173753, exon 18 of 18)	3' UTR (NM_173753, exon 18 of 18)	-6536	NM_001252494	192786	Mm.254404	NM_175258	ENSMUSG00000037533	Rapgef6	A530068K01|AI844632|BB085664|C030018K18Rik|PDZ-GEF2|Pdzgef2|RA-GEF-2|Ragef2|mKIAA4052	Rap guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_104956.1	chr11	100141629	100141646	-	1	NA	exon (NM_008471, exon 4 of 6)	exon (NM_008471, exon 4 of 6)	2062	NM_001313963	16669	Mm.439699	NM_008471	ENSMUSG00000020911	Krt19	AI663979|CK-19|EndoC|K19|Krt-1.19|Krt1-19	keratin 19	protein-coding
mm_107712.1	chr12	55836333	55836361	+	1	NA	promoter-TSS (NM_001037756)	promoter-TSS (NM_001037756)	-19	NM_001037756	52592	Mm.24761	NM_027867	ENSMUSG00000012076	Brms1l	0710008O11Rik|AI159718|BRMS1|D12Ertd407e	breast cancer metastasis-suppressor 1-like	protein-coding
mm_146895.1	chr18	29496546	29496555	-	1	NA	promoter-TSS (NR_045391)	promoter-TSS (NR_045391)	-134	NR_045391	78058	Mm.416952	NR_045391		4930578E11Rik	-	RIKEN cDNA 4930578E11 gene	ncRNA
mm_93820.1	chr10	121475806	121475820	-	1	NA	intron (NM_138956, intron 1 of 4)	CpG	437	NM_138956	192678	Mm.41265	NM_138956	ENSMUSG00000025795	Rassf3	AW212023|AW322379	Ras association (RalGDS/AF-6) domain family member 3	protein-coding
mm_103941.1	chr11	83849666	83849677	-	1	NA	Intergenic	Intergenic	-1198	NM_001291268	21410	Mm.7226	NM_009330	ENSMUSG00000020679	Hnf1b	HNF-1-beta|HNF-1B|HNF-1Beta|Hnf1beta|LFB3|Tcf-2|Tcf2|vHNF1	HNF1 homeobox B	protein-coding
mm_112301.1	chr12	114736728	114736734	-	1	NA	Intergenic	Intergenic	-223037	NR_106063	102465664		NR_106063	ENSMUSG00000098357	Mir7094-2	Gm27508|mmu-mir-7094-2	microRNA 7094-2	ncRNA
mm_144615.1	chr18	32837230	32837240	+	1	NA	promoter-TSS (NM_001110015)	promoter-TSS (NM_001110015)	10	NM_001110016	225348	Mm.38816	NM_144863	ENSMUSG00000038299	Wdr36	5730444A13Rik|Ta-wdrp	WD repeat domain 36	protein-coding
mm_130693.1	chr15	100682921	100682943	-	1	NA	exon (NM_033612, exon 5 of 8)	exon (NM_033612, exon 5 of 8)	4988	NM_033612	109901	Mm.2131	NM_033612	ENSMUSG00000023031	Cela1	1810009A17Rik|1810062B19Rik|Ela-1|Ela1|PC-TsF	chymotrypsin-like elastase family, member 1	protein-coding
mm_90168.1	chr10	119468724	119468725	+	1	NA	intron (NM_133442, intron 1 of 21)	intron (NM_133442, intron 1 of 21)	14690	NM_001277293	74053	Mm.196692	NM_028736	ENSMUSG00000034813	Grip1	4931400F03Rik|GRIP|eb	glutamate receptor interacting protein 1	protein-coding
mm_42797.1	chr5	121711786	121711859	+	1	NA	exon (NM_009125, exon 1 of 25)	exon (NM_009125, exon 1 of 25)	213	NM_009125	20239	Mm.260900	NM_009125	ENSMUSG00000042605	Atxn2	9630045M23Rik|ATX2|AW544490|Sca2	ataxin 2	protein-coding
mm_87389.1	chr10	45107514	45107522	+	1	NA	intron (NM_011156, intron 6 of 14)	ORR1E|LTR|ERVL-MaLR	40304	NM_011156	19072	Mm.10281	NM_011156	ENSMUSG00000019849	Prep	AI047692|AI450383|D10Wsu136e|PEP|Pop	prolyl endopeptidase	protein-coding
mm_100006.1	chr11	114851908	114851962	+	1	NA	promoter-TSS (NM_147217)	promoter-TSS (NM_147217)	-95	NM_147217	70355	Mm.242413	NM_147217	ENSMUSG00000051043	Gprc5c	1110028I06Rik|3200002M13Rik|Raig3	G protein-coupled receptor, family C, group 5, member C	protein-coding
mm_86179.1	chr9	119190366	119190374	-	1	NA	promoter-TSS (NM_001037749)	promoter-TSS (NM_001037749)	23	NM_001037749	382113	Mm.335525	NM_001037749	ENSMUSG00000070280	Slc22a14	Gm1128	solute carrier family 22 (organic cation transporter), member 14	protein-coding
mm_43539.1	chr5	137350197	137350205	+	1	NA	promoter-TSS (NM_010144)	promoter-TSS (NM_010144)	92	NM_010144	13846	Mm.34533	NM_010144	ENSMUSG00000029710	Ephb4	AI042935|Htk|MDK2|Myk1|Tyro11	Eph receptor B4	protein-coding
mm_87091.1	chr10	32889810	32889821	+	1	NA	promoter-TSS (NM_001025286)	promoter-TSS (NM_001025286)	100	NM_001013411	432450	Mm.49665	NM_001013411	ENSMUSG00000069670	Nkain2	6330571D19Rik|AW455467|Tcba1	Na+/K+ transporting ATPase interacting 2	protein-coding
mm_111415.1	chr12	91557007	91557027	-	1	NA	3' UTR (NM_031391, exon 9 of 9)	3' UTR (NM_031391, exon 9 of 9)	32632	NM_031391	83602	Mm.275728	NM_031391	ENSMUSG00000020962	Gtf2a1	6330549H03Rik|AA536742|AA959775|AW060250|TfIIAa/b|Tfiia1	general transcription factor II A, 1	protein-coding
mm_128981.1	chr15	74833674	74833682	-	1	NA	Intergenic	Intergenic	7965	NM_001033229	110115	Mm.322606	NM_001033229	ENSMUSG00000075604	Cyp11b1	AA389061|CPN1|Cyp11b|Cyp11b-1|FHI	cytochrome P450, family 11, subfamily b, polypeptide 1	protein-coding
mm_31490.1	chr4	52989272	52989308	+	1	NA	promoter-TSS (NM_028529)	promoter-TSS (NM_028529)	6	NM_028529	73398	Mm.252738	NM_028529	ENSMUSG00000015242	Nipsnap3a	1700054F22Rik|AI429120	nipsnap homolog 3A (C. elegans)	protein-coding
mm_116798.1	chr13	53639208	53639212	-	1	NA	promoter-TSS (NR_131079)	promoter-TSS (NR_131079)	-9	NR_131079	77398	Mm.174307	NR_131079		9530014B07Rik	-	RIKEN cDNA 9530014B07 gene	ncRNA
mm_9410.1	chr1	172278919	172278927	-	1	NA	exon (NM_178405, exon 18 of 23)	exon (NM_178405, exon 18 of 23)	19141	NM_178405	98660	Mm.207432	NM_178405	ENSMUSG00000007097	Atp1a2	AW060654|Atpa-3|mKIAA0778	ATPase, Na+/K+ transporting, alpha 2 polypeptide	protein-coding
mm_80775.1	chr9	95563755	95563757	+	1	NA	Intergenic	Intergenic	3939	NM_198414	75552	Mm.151485	NM_198414	ENSMUSG00000064225	Paqr9	1700020G04Rik	progestin and adipoQ receptor family member IX	protein-coding
mm_153577.1	chr19	43388293	43388305	-	1	NA	promoter-TSS (NM_001081257)	promoter-TSS (NM_001081257)	56	NM_001081257	545291	Mm.442200	NM_001081257	ENSMUSG00000074852	Hpse2	Gm968|Hpa2	heparanase 2	protein-coding
mm_41393.1	chr5	90771626	90771630	+	1	NA	promoter-TSS (NM_019932)	promoter-TSS (NM_019932)	-807	NM_019932	56744	Mm.332490	NM_019932	ENSMUSG00000029373	Pf4	Cxcl4|Scyb4	platelet factor 4	protein-coding
mm_62032.1	chr7	91754608	91754623	+	1	NA	intron (NM_011807, intron 3 of 22)	intron (NM_011807, intron 3 of 22)	-307779	NM_001243046	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_97326.1	chr11	76945808	76945816	+	1	NA	5' UTR (NM_178645, exon 1 of 12)	5' UTR (NM_178645, exon 1 of 12)	156	NM_178645	104184	Mm.399785	NM_178645	ENSMUSG00000020840	Blmh	AI035728|Bh|Bmh	bleomycin hydrolase	protein-coding
mm_57312.1	chr6	124724591	124724604	-	1	NA	intron (NM_001077705, intron 11 of 15)	intron (NM_001077705, intron 11 of 15)	-6207	NR_029792	723944		NR_029792	ENSMUSG00000065462	Mir200c	Mirn200c|mir-200c	microRNA 200c	ncRNA
mm_136730.1	chr17	8283417	8283441	+	1	NA	promoter-TSS (NM_018819)	promoter-TSS (NM_018819)	-384	NM_018819	55951	Mm.288510	NM_018819	ENSMUSG00000023861	Mpc1	0610006G08Rik|3830411I18Rik|Brp44l	mitochondrial pyruvate carrier 1	protein-coding
mm_152341.1	chr19	9982547	9982567	-	1	NA	promoter-TSS (NM_010239)	promoter-TSS (NM_010239)	-89	NM_010239	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
mm_113439.1	chr13	34888152	34888164	+	1	NA	exon (NM_013830, exon 4 of 15)	exon (NM_013830, exon 4 of 15)	12664	NM_013830	19134	Mm.10027	NM_013830	ENSMUSG00000021413	Prpf4b	2610037H07|Prp4|Prp4k|Prpk|cbp143	pre-mRNA processing factor 4B	protein-coding
mm_79136.1	chr9	47623289	47623291	+	1	NA	intron (NM_001025600, intron 1 of 8)	intron (NM_001025600, intron 1 of 8)	92938	NM_018770	54725	Mm.234832	NM_018770	ENSMUSG00000032076	Cadm1	2900073G06Rik|3100001I08Rik|AI987920|Bl2|Igsf4|Igsf4a|Necl2|RA175|RA175A|RA175B|RA175C|RA175N|ST17|SgIGSF|SynCam|Tslc1	cell adhesion molecule 1	protein-coding
mm_139699.1	chr17	57449858	57449915	+	1	NA	exon (NM_010130, exon 17 of 22)	exon (NM_010130, exon 17 of 22)	91200	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_101668.1	chr11	37059285	37059287	-	1	NA	Intergenic	Intergenic	-115045	NM_011856	23964	Mm.439889	NM_011856	ENSMUSG00000049336	Tenm2	Odz2|Odz3|Ten-2|Ten-m2	teneurin transmembrane protein 2	protein-coding
mm_53100.1	chr6	125049973	125049986	+	1	NA	promoter-TSS (NM_016845)	promoter-TSS (NM_016845)	52	NM_016845	54137	Mm.347910	NM_016845	ENSMUSG00000072770	Acrbp	OY-TES-1|sp32	proacrosin binding protein	protein-coding
mm_25711.1	chr3	122512171	122512206	+	1	NA	intron (NM_013867, intron 6 of 11)	intron (NM_013867, intron 6 of 11)	29493	NR_106117	102465764		NR_106117	ENSMUSG00000104773	Mir7657	mmu-mir-7657	microRNA 7657	ncRNA
mm_70789.1	chr8	22506519	22506540	+	1	NA	intron (NM_011394, intron 1 of 10)	intron (NM_011394, intron 1 of 10)	-29650	NM_001146117	102032	Mm.378231	NM_001012667	ENSMUSG00000031534	Smim19	AI316807|BG694986|EST-c39	small integral membrane protein 19	protein-coding
mm_48940.1	chr6	4539479	4539491	+	1	NA	exon (NM_007743, exon 51 of 52)	exon (NM_007743, exon 51 of 52)	33867	NM_007743	12843	Mm.277792	NM_007743	ENSMUSG00000029661	Col1a2	AA960264|AI325291|Col1a-2|Cola-2|Cola2|oim	collagen, type I, alpha 2	protein-coding
mm_7186.1	chr1	92837884	92837901	-	1	NA	intron (NM_016696, intron 1 of 8)	intron (NM_016696, intron 1 of 8)	6206	NM_016696	14733	Mm.297976	NM_016696	ENSMUSG00000034220	Gpc1	AI462976	glypican 1	protein-coding
mm_1652.1	chr1	74661795	74661832	+	1	NA	promoter-TSS (NM_001014974)	promoter-TSS (NM_001014974)	59	NM_001014974	67534	Mm.260714	NM_001014974	ENSMUSG00000033257	Ttll4	4632407P03Rik|AI451681|mKIAA0173	tubulin tyrosine ligase-like family, member 4	protein-coding
mm_129134.1	chr15	76198148	76198204	-	1	NA	promoter-TSS (NM_201393)	promoter-TSS (NM_201393)	33	NM_201393	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
mm_123230.1	chr14	60086833	60086890	-	1	NA	promoter-TSS (NM_015803)	promoter-TSS (NM_015803)	-27	NM_015803	50769	Mm.319599	NM_015803	ENSMUSG00000021983	Atp8a2	AI415030|Atpc1b|agil|wl	ATPase, aminophospholipid transporter-like, class I, type 8A, member 2	protein-coding
mm_159766.1	chr5	96811125	96811125	+	1	NA	exon (NM_013470, exon 3 of 13)	exon (NM_013470, exon 3 of 13)	17740	NM_013470	11745	Mm.7214	NM_013470	ENSMUSG00000029484	Anxa3	Anx3	annexin A3	protein-coding
mm_1661.1	chr1	74713552	74713568	+	1	NA	promoter-TSS (NM_024264)	promoter-TSS (NM_024264)	25	NM_024264	104086	Mm.85083	NM_024264	ENSMUSG00000026170	Cyp27a1	1300013A03Rik|Cyp27	cytochrome P450, family 27, subfamily a, polypeptide 1	protein-coding
mm_111097.1	chr12	80643859	80643869	-	1	NA	promoter-TSS (NM_026244)	promoter-TSS (NM_026244)	247	NM_007951	13877	Mm.246551	NM_007951	ENSMUSG00000021131	Erh	Mer|Prei1	enhancer of rudimentary homolog (Drosophila)	protein-coding
mm_147796.1	chr18	61657882	61657927	-	1	NA	intron (NR_045402, intron 1 of 4)	(TG)n|Simple_repeat|Simple_repeat	7634	NR_045402	328968	Mm.392305	NR_045402		Carmn	Carmen|E330013P06|Gm16908|Mir143hg	cardiac mesoderm enhancer-associated non-coding RNA	ncRNA
mm_52208.1	chr6	100839154	100839157	+	1	NA	intron (NM_182939, intron 2 of 8)	RMER15|LTR|ERVL	5517	NM_182939	232314	Mm.27223	NM_182939	ENSMUSG00000052144	Ppp4r2	BE691708|C230060M08Rik	protein phosphatase 4, regulatory subunit 2	protein-coding
mm_41772.1	chr5	103516127	103516137	+	1	NA	intron (NM_011204, intron 7 of 47)	intron (NM_011204, intron 7 of 47)	90940	NM_011204	19249	Mm.3414	NM_011204	ENSMUSG00000034573	Ptpn13	AI324989|PTP-BL|PTPL1|Ptpri|RIP	protein tyrosine phosphatase, non-receptor type 13	protein-coding
mm_51010.1	chr6	65002419	65002434	+	1	NA	Intergenic	ORR1C1|LTR|ERVL-MaLR	-40241	NM_007958	13990	Mm.99113	NM_007958	ENSMUSG00000029920	Smarcad1	AV081750|AW226546|D6Pas1|Etl1|mKIAA1122	SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1	protein-coding
mm_102299.1	chr11	55461180	55461190	-	1	NA	promoter-TSS (NM_009720)	promoter-TSS (NM_009720)	-47	NM_009720	11927	Mm.217759	NM_009720	ENSMUSG00000018585	Atox1	AI256639|Atx1	antioxidant 1 copper chaperone	protein-coding
mm_60084.1	chr7	34313019	34313026	+	1	NA	Intergenic	CpG	-27413	NM_172741	233103	Mm.491097	NM_172741	ENSMUSG00000066571	4931406P16Rik	AA553327|mKIAA0355	RIKEN cDNA 4931406P16 gene	protein-coding
mm_75695.1	chr8	68212072	68212088	-	1	NA	Intergenic	Intergenic	-64448	NM_028182	72281	Mm.40974	NM_028182	ENSMUSG00000053886	Sh2d4a	2210402M20Rik|SH2A	SH2 domain containing 4A	protein-coding
mm_48117.1	chr5	137138309	137138320	-	1	NA	Intergenic	Intergenic	-22107	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_41305.1	chr5	90467808	90467811	+	1	NA	intron (NM_009654, intron 7 of 14)	intron (NM_009654, intron 7 of 14)	6939	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_97767.1	chr11	82036481	82036498	+	1	NA	exon (NM_011333, exon 2 of 3)	exon (NM_011333, exon 2 of 3)	912	NM_011333	20296	Mm.290320	NM_011333	ENSMUSG00000035385	Ccl2	AI323594|HC11|JE|MCAF|MCP-1|MCP1|SMC-CF|Scya2|Sigje	chemokine (C-C motif) ligand 2	protein-coding
mm_163348.1	chr12	17416360	17416362	+	1	NA	intron (NM_001008421, intron 18 of 20)	intron (NM_001008421, intron 18 of 20)	60969	NR_037226	100526470		NR_037226	ENSMUSG00000093037	Mir3066	mir-3066|mmu-mir-3066	microRNA 3066	ncRNA
mm_51268.1	chr6	72099930	72099939	+	1	NA	intron (NM_011375, intron 1 of 6)	MTD|LTR|ERVL-MaLR	2326	NM_011375	20454	Mm.38248	NM_011375	ENSMUSG00000056091	St3gal5	3S-T|Siat9|[a]2	ST3 beta-galactoside alpha-2,3-sialyltransferase 5	protein-coding
mm_163124.1	chr11	77078509	77078528	+	1	NA	promoter-TSS (NR_030756)	promoter-TSS (NR_030756)	-81	NM_001012309	237859	Mm.156195	NM_001012309	ENSMUSG00000037958	Nsrp1	8030451K07|AI851076|AL022898|Ccdc55|NSpr70|NSrp70	nuclear speckle regulatory protein 1	protein-coding
mm_72861.1	chr8	88521349	88521371	+	1	NA	promoter-TSS (NM_027280)	promoter-TSS (NM_027280)	16	NM_027280	93960	Mm.30219	NM_027280	ENSMUSG00000031661	Nkd1	2810434J10Rik|9030215G15Rik|Nkd	naked cuticle 1 homolog (Drosophila)	protein-coding
mm_147601.1	chr18	56791493	56791496	-	1	NA	intron (NM_177115, intron 3 of 4)	intron (NM_177115, intron 3 of 4)	83681	NM_010721	16906	Mm.4105	NM_010721	ENSMUSG00000024590	Lmnb1	-	lamin B1	protein-coding
mm_80573.1	chr9	84003000	84003002	+	1	NA	intron (NM_001305935, intron 6 of 10)	intron (NM_001305935, intron 6 of 10)	54220	NM_199195	12040	Mm.12819	NM_199195	ENSMUSG00000032263	Bckdhb	BCKDE1B|BCKDH E1-beta	branched chain ketoacid dehydrogenase E1, beta polypeptide	protein-coding
mm_70486.1	chr8	12396268	12396279	+	1	NA	5' UTR (NM_009233, exon 1 of 1)	5' UTR (NM_009233, exon 1 of 1)	754	NM_009233	20664	Mm.39088	NM_009233	ENSMUSG00000096014	Sox1	BB176347|Sox-1	SRY (sex determining region Y)-box 1	protein-coding
mm_150085.1	chr19	29387835	29387845	+	1	NA	3' UTR (NM_021893, exon 7 of 7)	3' UTR (NM_021893, exon 7 of 7)	20402	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_113182.1	chr13	24905617	24905633	+	1	NA	promoter-TSS (NR_045182)	promoter-TSS (NR_045182)	25	NR_045182	73326	Mm.458692	NR_045182		4932702P03Rik	1700047I16Rik	RIKEN cDNA 4932702P03 gene	ncRNA
mm_165605.1	chr3	50443513	50443540	+	1	NA	promoter-TSS (NM_011990)	promoter-TSS (NM_011990)	87	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_83845.1	chr9	54474416	54474422	-	1	NA	intron (NM_172771, intron 3 of 43)	intron (NM_172771, intron 3 of 43)	27207	NM_172771	235380	Mm.93636	NM_172771	ENSMUSG00000041268	Dmxl2	6330586A12|6430411K14Rik|E130119P06Rik|mKIAA0856	Dmx-like 2	protein-coding
mm_53274.1	chr6	128523963	128524001	+	1	NA	exon (NM_007376, exon 3 of 36)	exon (NM_007376, exon 3 of 36)	2738	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_19555.1	chr2	98666790	98666791	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	1199133	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_125749.1	chr15	73742857	73742859	+	1	NA	intron (NM_001166388, intron 1 of 5)	intron (NM_001166388, intron 1 of 5)	-5168	NM_008975	19245	Mm.390807	NM_008975	ENSMUSG00000059895	Ptp4a3	AV088979|Prl-3|pPtp4a3	protein tyrosine phosphatase 4a3	protein-coding
mm_41665.1	chr5	99336744	99336754	+	1	NA	intron (NR_030692, intron 3 of 3)	intron (NR_030692, intron 3 of 3)	-83822	NM_145839	320292	Mm.259074	NM_145839	ENSMUSG00000089809	Rasgef1b	4732452O09Rik|GPIgamma4|Gpig4	RasGEF domain family, member 1B	protein-coding
mm_147858.1	chr18	63708552	63708574	-	1	NA	promoter-TSS (NM_001014981)	promoter-TSS (NM_001014981)	-132	NM_001014981	104082	Mm.30850	NM_001014981	ENSMUSG00000040560	Wdr7	AI462727|TRAG|mKIAA0541	WD repeat domain 7	protein-coding
mm_94404.1	chr11	5788481	5788560	+	1	NA	promoter-TSS (NM_001146309)	promoter-TSS (NM_001146309)	37	NM_013810	13169	Mm.256925	NM_013810	ENSMUSG00000020476	Dbnl	Abp1|SH3P7|mAbp1	drebrin-like	protein-coding
mm_18573.1	chr2	65567311	65567336	-	1	NA	5' UTR (NM_018732, exon 1 of 27)	5' UTR (NM_018732, exon 1 of 27)	169	NM_018732	20269	Mm.330256	NM_018732	ENSMUSG00000057182	Scn3a	Gm1000|Nav1.3	sodium channel, voltage-gated, type III, alpha	protein-coding
mm_150244.1	chr19	34085478	34085486	+	1	NA	TTS (NM_027340)	TTS (NM_027340)	-15461	NM_023903	78753	Mm.195937	NM_023903	ENSMUSG00000056078	Lipm	4632427C23Rik|AW227514|Lipl3	lipase, family member M	protein-coding
mm_5985.1	chr1	58424008	58424028	-	1	NA	promoter-TSS (NM_001042634)	promoter-TSS (NM_001042634)	70	NR_027853	12747	Mm.1761	NM_009905	ENSMUSG00000026034	Clk1	STY	CDC-like kinase 1	protein-coding
mm_20083.1	chr2	120692899	120692905	-	1	NA	Intergenic	Intergenic	38615	NM_026891	68968	Mm.2289	NM_026891	ENSMUSG00000027284	Cdan1	1500015A01Rik|AI448026|AW492297|CDA-I|CDA1|CDAI	congenital dyserythropoietic anemia, type I (human)	protein-coding
mm_107729.1	chr12	57475443	57475446	+	1	NA	Intergenic	Intergenic	70677	NM_008259	15375	Mm.4578	NM_008259	ENSMUSG00000035451	Foxa1	Hnf-3a|Hnf3a|Tcf-3a|Tcf3a	forkhead box A1	protein-coding
mm_9259.1	chr1	171607322	171607363	-	1	NA	promoter-TSS (NM_001277968)	promoter-TSS (NM_001277968)	-8	NR_102726	17085	Mm.560	NM_008534	ENSMUSG00000004707	Ly9	AI893573|CD229|Lgp100|Ly-9|SLAMF3|T100	lymphocyte antigen 9	protein-coding
mm_127857.1	chr15	8350422	8350440	-	1	NA	exon (NM_027707, exon 10 of 47)	exon (NM_027707, exon 10 of 47)	94032	NM_027707	71175	Mm.240329	NM_027707	ENSMUSG00000022141	Nipbl	Idn3	Nipped-B homolog (Drosophila)	protein-coding
mm_85387.1	chr9	103228421	103228437	-	1	NA	intron (NM_133977, intron 1 of 16)	intron (NM_133977, intron 1 of 16)	1857	NM_133977	22041	Mm.37214	NM_133977	ENSMUSG00000032554	Trf	AI266983|Cd176|HP|Tf|Tfn|hpx	transferrin	protein-coding
mm_61807.1	chr7	87246688	87246692	+	1	NA	promoter-TSS (NM_001285835)	promoter-TSS (NM_001285835)	41	NM_001285833	50490	Mm.31748	NM_015760	ENSMUSG00000030562	Nox4	AI648021	NADPH oxidase 4	protein-coding
mm_137664.1	chr17	28692593	28692616	+	1	NA	promoter-TSS (NM_001168513)	promoter-TSS (NM_001168513)	36	NM_001168513	26416	Mm.311337	NM_011951	ENSMUSG00000053436	Mapk14	CSBP2|Crk1|Csbp1|Mxi2|PRKM14|PRKM15|p38|p38-alpha|p38MAPK|p38a|p38alpha	mitogen-activated protein kinase 14	protein-coding
mm_14625.1	chr2	136777331	136777341	+	1	NA	exon (NM_001291056, exon 7 of 8)	exon (NM_001291056, exon 7 of 8)	63886	NM_001291056	20614	Mm.45953	NM_011428	ENSMUSG00000027273	Snap25	Bdr|GENA70|SNAP-25|SUP|sp	synaptosomal-associated protein 25	protein-coding
mm_147045.1	chr18	34924902	34924918	-	1	NA	intron (NM_144866, intron 2 of 10)	intron (NM_144866, intron 2 of 10)	7093	NM_144866	225363	Mm.329353	NM_144866	ENSMUSG00000024360	Etf1	AI463371|D6Ertd109e|ERF|ERF1|SUP45L1|TB3-1	eukaryotic translation termination factor 1	protein-coding
mm_115788.1	chr13	19337180	19337190	-	1	NA	Intergenic	Intergenic	58628	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_28920.1	chr3	98858007	98858017	-	1	NA	5' UTR (NM_001304800, exon 2 of 4)	5' UTR (NM_001304800, exon 2 of 4)	1782	NM_001304800	15492	Mm.140811	NM_008293	ENSMUSG00000027871	Hsd3b1	3-beta-HSD I|D3Ertd383e	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1	protein-coding
mm_143980.1	chr17	87459454	87459483	-	1	NA	Intergenic	Intergenic	-12533	NM_007589	12314	Mm.329243	NM_007589	ENSMUSG00000036438	Calm2	1500001E21Rik|AL024017	calmodulin 2	protein-coding
mm_55508.1	chr6	69901001	69901017	-	1	NA	Intergenic	Intergenic	-573835	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_139775.1	chr17	64895807	64895822	+	1	NA	Intergenic	Intergenic	-59743	NM_030031	78057	Mm.109380	NM_030031	ENSMUSG00000024088	4930583I09Rik	-	RIKEN cDNA 4930583I09 gene	protein-coding
mm_169052.1	chr13	20748568	20748577	+	1	NA	Intergenic	Intergenic	-45541	NM_001281854	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_141626.1	chr17	32917032	32917042	-	1	NA	promoter-TSS (NM_022434)	promoter-TSS (NM_022434)	50	NM_022434	64385	Mm.486449	NM_022434	ENSMUSG00000024292	Cyp4f14	1300014O15Rik|cyp4f-14	cytochrome P450, family 4, subfamily f, polypeptide 14	protein-coding
mm_61449.1	chr7	75586204	75586220	+	1	NA	exon (NM_029332, exon 5 of 37)	exon (NM_029332, exon 5 of 37)	130678	NM_029332	75547	Mm.216107	NM_029332	ENSMUSG00000066406	Akap13	1700026G02Rik|5730522G15Rik|5830460E08Rik|AKAP-13|AKAP-Lbc|BRX|Ht31|LBC|PROTO-LB|PROTO-LBC	A kinase (PRKA) anchor protein 13	protein-coding
mm_38975.1	chr4	150909429	150909459	-	1	NA	intron (NM_020569, intron 1 of 6)	intron (NM_020569, intron 1 of 6)	477	NM_020569	57320	Mm.277349	NM_020569	ENSMUSG00000028964	Park7	DJ-1|Dj1	Parkinson disease (autosomal recessive, early onset) 7	protein-coding
mm_142868.1	chr17	51815314	51815330	-	1	NA	intron (NM_001163632, intron 1 of 10)	intron (NM_001163632, intron 1 of 10)	-3268	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_124145.1	chr14	88123825	88123835	-	1	NA	Intergenic	Intergenic	347566	NM_178685	219257	Mm.128861	NM_178685	ENSMUSG00000050505	Pcdh20	C630015B17Rik|Pcdh13	protocadherin 20	protein-coding
mm_15705.1	chr2	163995272	163995282	+	1	NA	promoter-TSS (NM_018753)	promoter-TSS (NM_018753)	80	NM_018753	54401	Mm.34319	NM_018753	ENSMUSG00000018326	Ywhab	1300003C17Rik|14-3-3b	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta polypeptide	protein-coding
mm_75143.1	chr8	35480560	35480564	-	1	NA	intron (NM_026067, intron 3 of 6)	AT_rich|Low_complexity|Low_complexity	14971	NM_026067	67276	Mm.207534	NM_026067	ENSMUSG00000031527	Eri1	3'hexo|3110010F15Rik|Thex1|eri-1	exoribonuclease 1	protein-coding
mm_81038.1	chr9	105053249	105053259	+	1	NA	promoter-TSS (NM_053159)	promoter-TSS (NM_053159)	-14	NM_053159	94062	Mm.29746	NM_053159	ENSMUSG00000032563	Mrpl3	2010320L16Rik|5930422H18Rik|AA407889	mitochondrial ribosomal protein L3	protein-coding
mm_110973.1	chr12	76962105	76962111	-	1	NA	5' UTR (NM_001146176, exon 1 of 4)	5' UTR (NM_001146176, exon 1 of 4)	140	NM_008558	17187	Mm.268548	NM_008558	ENSMUSG00000059436	Max	AA960152|AI875693|bHLHd4|bHLHd5|bHLHd6|bHLHd7|bHLHd8	Max protein	protein-coding
mm_166322.1	chr5	111509385	111509397	+	1	NA	Intergenic	Intergenic	-72170	NR_015546	330164	Mm.193276	NM_177875	ENSMUSG00000052848	C130026L21Rik	-	RIKEN cDNA C130026L21 gene	ncRNA
mm_7255.1	chr1	93754770	93754806	-	1	NA	promoter-TSS (NM_025920)	promoter-TSS (NM_025920)	50	NM_025920	67026	Mm.272356	NM_025920	ENSMUSG00000026279	Thap4	2010320B01Rik	THAP domain containing 4	protein-coding
mm_144478.1	chr18	23944923	23944954	+	1	NA	Intergenic	Intergenic	-9750	NM_027007	69256	Mm.218343	NM_027007	ENSMUSG00000024276	Zfp397	2810411K16Rik|6720480F11Rik|AI461664	zinc finger protein 397	protein-coding
mm_100957.1	chr11	6635537	6635541	-	1	NA	TTS (NM_011709)	TTS (NM_011709)	3110	NM_011709	22373	Mm.268094	NM_011709	ENSMUSG00000000381	Wap	-	whey acidic protein	protein-coding
mm_26405.1	chr3	142606782	142606799	+	1	NA	exon (NM_010259, exon 7 of 11)	exon (NM_010259, exon 7 of 11)	11943	NM_010259	14468	Mm.457978	NM_010259	ENSMUSG00000040264	Gbp2b	Gbp-1|Gbp1|Mag-1|Mpa-1|Mpa1	guanylate binding protein 2b	protein-coding
mm_35419.1	chr4	35125337	35125348	-	1	NA	intron (NM_178061, intron 1 of 3)	intron (NM_178061, intron 1 of 3)	-26713	NM_199157	387510	Mm.386929	NM_199157	ENSMUSG00000042993	Ifnk	-	interferon kappa	protein-coding
mm_108564.1	chr12	84762797	84762808	+	1	NA	intron (NM_023409, intron 2 of 3)	intron (NM_023409, intron 2 of 3)	10310	NM_023409	67963	Mm.282556	NM_023409	ENSMUSG00000021242	Npc2	2700012J19Rik|AA408070|AU045843|HE1	Niemann-Pick type C2	protein-coding
mm_135418.1	chr16	45158625	45158645	-	1	NA	promoter-TSS (NM_028756)	promoter-TSS (NM_028756)	38	NM_028756	74102	Mm.264984	NM_028756	ENSMUSG00000022664	Slc35a5	1010001J06Rik|AU021179|BB097433|D16Ertd450e|D730043G07Rik	solute carrier family 35, member A5	protein-coding
mm_119013.1	chr14	29978374	29978418	+	1	NA	promoter-TSS (NM_027493)	promoter-TSS (NM_027493)	59	NM_027493	56249	Mm.215110	NM_027493	ENSMUSG00000015971	Actr8	5730542K05Rik|ARP8	ARP8 actin-related protein 8	protein-coding
mm_172221.1	chr6	65318366	65318367	+	1	NA	Intergenic	Intergenic	-62928	NM_175524	243407	Mm.389758	NM_175524	ENSMUSG00000029917	C130060K24Rik	-	RIKEN cDNA C130060K24 gene	protein-coding
mm_110611.1	chr12	56537527	56537557	-	1	NA	promoter-TSS (NM_009385)	promoter-TSS (NM_009385)	-634	NM_009385	21869	Mm.89972	NM_009385	ENSMUSG00000001496	Nkx2-1	AV026640|Nkx2.1|T/EBP|Titf1|Ttf-1	NK2 homeobox 1	protein-coding
mm_84449.1	chr9	66514501	66514526	-	1	NA	promoter-TSS (NM_175206)	promoter-TSS (NM_175206)	80	NM_175206	74165	Mm.297998	NM_175206	ENSMUSG00000050503	Fbxl22	1110004B15Rik	F-box and leucine-rich repeat protein 22	protein-coding
mm_41809.1	chr5	103754795	103754798	+	1	NA	intron (NM_001080798, intron 1 of 19)	intron (NM_001080798, intron 1 of 19)	223	NM_001080798	17355	Mm.6949	NM_133919	ENSMUSG00000029313	Aff1	9630032B01Rik|AW319193|Af4|Mllt2h|Rob	AF4/FMR2 family, member 1	protein-coding
mm_9731.1	chr1	180229027	180229028	-	1	NA	intron (NM_001128605, intron 9 of 10)	intron (NM_001128605, intron 9 of 10)	16923	NM_011183	19165	Mm.330850	NM_011183	ENSMUSG00000010609	Psen2	ALG-3|Ad4h|Alg3|PS-2|PS2|Psnl2|STM2	presenilin 2	protein-coding
mm_68863.1	chr7	126414850	126414854	-	1	NA	promoter-TSS (NM_009844)	promoter-TSS (NM_009844)	18	NM_009844	12478	Mm.4360	NM_009844	ENSMUSG00000030724	Cd19	AW495831	CD19 antigen	protein-coding
mm_52223.1	chr6	103511084	103511088	+	1	NA	5' UTR (NM_007697, exon 1 of 27)	5' UTR (NM_007697, exon 1 of 27)	210	NM_007697	12661	Mm.251288	NM_007697	ENSMUSG00000030077	Chl1	A530023M13Rik|AI465420|CALL|LICAM2	cell adhesion molecule L1-like	protein-coding
mm_91291.1	chr10	24915493	24915493	-	1	NA	3' UTR (NM_007482, exon 8 of 8)	3' UTR (NM_007482, exon 8 of 8)	4829	NR_105870	102465545		NR_105870	ENSMUSG00000099181	Mir6905	Gm27879|mmu-mir-6905	microRNA 6905	ncRNA
mm_130917.1	chr15	102670962	102670970	-	1	NA	promoter-TSS (NM_026468)	promoter-TSS (NM_026468)	81	NM_026468	67942	Mm.10314	NM_026468	ENSMUSG00000062683	Atp5g2	1810041M08Rik	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit C2 (subunit 9)	protein-coding
mm_135892.1	chr16	64919108	64919115	-	1	NA	Intergenic	Intergenic	67026	NM_178647	106143	Mm.10160	NM_178647	ENSMUSG00000054604	Cggbp1	AA960172|AL023996|AW045841	CGG triplet repeat binding protein 1	protein-coding
mm_51159.1	chr6	70723539	70723547	+	1	NA	Intergenic	Intergenic	68632	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_5819.1	chr1	52727128	52727161	-	1	NA	5' UTR (NM_133829, exon 1 of 7)	5' UTR (NM_133829, exon 1 of 7)	174	NM_178081	98682	Mm.491173	NM_133829	ENSMUSG00000041439	Mfsd6	2210010L05Rik|9630025I22Rik|AI836200|AW212394|MMR2	major facilitator superfamily domain containing 6	protein-coding
mm_49542.1	chr6	30353025	30353030	+	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	37983	NM_172735	232679	Mm.29780	NM_172735	ENSMUSG00000039130	Zc3hc1	1110054L24Rik|AU018540|AU019789|HSPC216|Nipa	zinc finger, C3HC type 1	protein-coding
mm_107586.1	chr12	45094002	45094019	+	1	NA	Intergenic	Intergenic	-19527	NM_144552	217517	Mm.285400	NM_144552	ENSMUSG00000046314	Stxbp6	BC024598|C85317	syntaxin binding protein 6 (amisyn)	protein-coding
mm_121235.1	chr14	103056090	103056102	+	1	NA	3' UTR (NM_008392, exon 5 of 5)	3' UTR (NM_008392, exon 5 of 5)	9084	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_91757.1	chr10	50894495	50894516	-	1	NA	Intergenic	CpG	-1146	NM_011376	20464	Mm.4774	NM_011376	ENSMUSG00000019913	Sim1	bHLHe14|mSIM1	single-minded homolog 1 (Drosophila)	protein-coding
mm_33.1	chr1	6249312	6249329	+	1	NA	exon (NM_009826, exon 15 of 24)	exon (NM_009826, exon 15 of 24)	34658	NM_009826	12421	Mm.293811	NM_009826	ENSMUSG00000025907	Rb1cc1	2900055E04Rik|5930404L04Rik|Cc1|FIP200|LaXp180	RB1-inducible coiled-coil 1	protein-coding
mm_51529.1	chr6	83186329	83186349	+	1	NA	5' UTR (NM_001347310, exon 1 of 27)	5' UTR (NM_001347310, exon 1 of 27)	393	NM_001347310	13191	Mm.6919	NM_007835	ENSMUSG00000031865	Dctn1	AL022633|DAP-150|DP-150|Glued|p150|p150-glued|p150<glued>	dynactin 1	protein-coding
mm_46888.1	chr5	113974767	113974780	-	1	NA	intron (NM_198109, intron 2 of 14)	intron (NM_198109, intron 2 of 14)	18984	NM_198109	231637	Mm.389682	NM_198109	ENSMUSG00000042121	Ssh1	AW551225|Gm1394|Gm1395|SSH-1|SSH-1L	slingshot homolog 1 (Drosophila)	protein-coding
mm_128221.1	chr15	36367116	36367121	-	1	NA	Intergenic	Intergenic	-83971	NM_013923	30945	Mm.5181	NM_013923	ENSMUSG00000022280	Rnf19a	AA032313|Dorfin|Rnf19|UIP117|Ubce7ip2|XYbp	ring finger protein 19A	protein-coding
mm_117340.1	chr13	69534578	69534616	-	1	NA	promoter-TSS (NM_198600)	promoter-TSS (NM_198600)	-733	NM_001169131	210106	Mm.315959	NM_198600	ENSMUSG00000034575	Papd7	LAK-1|POLK|Pols|TRF4|TRF4-1	PAP associated domain containing 7	protein-coding
mm_149040.1	chr19	8820129	8820139	+	1	NA	promoter-TSS (NM_027412)	promoter-TSS (NM_027412)	733	NM_001081196	68693	Mm.476519	NM_001081196	ENSMUSG00000071659	Hnrnpul2	1110031M08Rik|AI465155|Hnrpul2	heterogeneous nuclear ribonucleoprotein U-like 2	protein-coding
mm_43015.1	chr5	123907240	123907292	+	1	NA	promoter-TSS (NM_026603)	promoter-TSS (NM_026603)	-9	NM_026603	68184	Mm.28549	NM_026603	ENSMUSG00000023106	Denr	1500003K04Rik	density-regulated protein	protein-coding
mm_13207.1	chr2	93642280	93642294	+	1	NA	promoter-TSS (NM_007442)	promoter-TSS (NM_007442)	-147	NM_007442	11695	Mm.389389	NM_007442	ENSMUSG00000040310	Alx4	lst	aristaless-like homeobox 4	protein-coding
mm_112528.1	chr13	9278175	9278178	+	1	NA	intron (NM_001081426, intron 1 of 36)	intron (NM_001081426, intron 1 of 36)	1651	NM_001081426	208440	Mm.217326	NM_172459	ENSMUSG00000048264	Dip2c	2900024P20Rik|9630044M06|mKIAA0934	disco interacting protein 2 homolog C	protein-coding
mm_74955.1	chr8	26015578	26015626	-	1	NA	promoter-TSS (NM_008033)	promoter-TSS (NM_008033)	-1	NM_008033	14272	Mm.3496	NM_008033	ENSMUSG00000015994	Fnta	FTA	farnesyltransferase, CAAX box, alpha	protein-coding
mm_130283.1	chr15	96953537	96953550	-	1	NA	Intergenic	Intergenic	102413	NM_027052	69354	Mm.250980	NM_027052	ENSMUSG00000022464	Slc38a4	1110012E16Rik|1700012A18Rik|Ata3|mATA3|mNAT3	solute carrier family 38, member 4	protein-coding
mm_137589.1	chr17	28040781	28040811	+	1	NA	intron (NM_001286040, intron 13 of 24)	intron (NM_001286040, intron 13 of 24)	39788	NM_013687	21463	Mm.29758	NM_013687	ENSMUSG00000062859	Tcp11	D17Ken1|Tcp-11	t-complex protein 11	protein-coding
mm_165696.1	chr3	93445257	93445261	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	2929	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_120511.1	chr14	66344370	66344380	+	1	NA	promoter-TSS (NM_019675)	promoter-TSS (NM_019675)	79	NM_019675	56471	Mm.35474	NM_019675	ENSMUSG00000022044	Stmn4	Lagl|R75359|RB3	stathmin-like 4	protein-coding
mm_161372.1	chr14	66868797	66868797	+	1	NA	promoter-TSS (NM_001034881)	promoter-TSS (NM_001034881)	-53	NM_001034881	432870	Mm.425890	NM_001034881	ENSMUSG00000075553	Gm5464	EG432870	predicted gene 5464	protein-coding
mm_79586.1	chr9	58253320	58253333	+	1	NA	exon (NM_026942, exon 1 of 7)	exon (NM_026942, exon 1 of 7)	162	NM_026942	69106	Mm.216502	NM_026942	ENSMUSG00000032333	Stoml1	1810015E19Rik|AI847431|SLP1|STORP|UNC24|WPB72	stomatin-like 1	protein-coding
mm_118361.1	chr13	115101755	115101778	-	1	NA	5' UTR (NM_001033228, exon 1 of 29)	5' UTR (NM_001033228, exon 1 of 29)	198	NM_001033228	109700	Mm.317280	NM_001033228	ENSMUSG00000042284	Itga1	CD49A|E130012M19Rik|Vla1	integrin alpha 1	protein-coding
mm_65007.1	chr7	17056829	17056874	-	1	NA	promoter-TSS (NM_016868)	promoter-TSS (NM_016868)	-172	NM_016868	53417	Mm.135110	NM_016868	ENSMUSG00000004328	Hif3a	Ipas|MOP7|NEPAS|bHLHe17	hypoxia inducible factor 3, alpha subunit	protein-coding
mm_138623.1	chr17	35841492	35841505	+	1	NA	promoter-TSS (NM_001010833)	promoter-TSS (NM_001010833)	0	NM_001010833	240087	Mm.218511	NM_001010833	ENSMUSG00000061607	Mdc1	6820401C03|AA413496|Nfbd1|mKIAA0170	mediator of DNA damage checkpoint 1	protein-coding
mm_94878.1	chr11	24158301	24158311	+	1	NA	exon (NM_001242934, exon 3 of 4)	exon (NM_001242934, exon 3 of 4)	77611	NM_001159290	14025	Mm.53687	NM_016707	ENSMUSG00000000861	Bcl11a	2810047E18Rik|BCL-11A|Ctip1|D930021L15Rik|Evi9|Evi9a|Evi9b|Evi9c|mKIAA1809	B cell CLL/lymphoma 11A (zinc finger protein)	protein-coding
mm_159544.1	chr4	88841795	88841795	+	1	NA	promoter-TSS (NM_010504)	promoter-TSS (NM_010504)	-21	NM_010504	15967	Mm.377088	NM_010504	ENSMUSG00000070904	Ifna4	Ifa4	interferon alpha 4	protein-coding
mm_38160.1	chr4	135214529	135214546	-	1	NA	3' UTR (NM_013885, exon 6 of 6)	3' UTR (NM_013885, exon 6 of 6)	58223	NM_013885	29876	Mm.257765	NM_013885	ENSMUSG00000037242	Clic4	D0Jmb3|TU-74|mc3s5|mtCLIC	chloride intracellular channel 4 (mitochondrial)	protein-coding
mm_138426.1	chr17	35076874	35076915	+	1	NA	promoter-TSS (NM_027366)	promoter-TSS (NM_027366)	-48	NM_027366	70274	Mm.250491	NM_027366	ENSMUSG00000013766	Ly6g6e	2310011I02Rik|G6e	lymphocyte antigen 6 complex, locus G6E	protein-coding
mm_69046.1	chr7	126831467	126831481	-	1	NA	promoter-TSS (NM_183131)	promoter-TSS (NM_183131)	22	NM_183131	78118	Mm.107753	NM_183131	ENSMUSG00000045989	4930451I11Rik	-	RIKEN cDNA 4930451I11 gene	protein-coding
mm_67788.1	chr7	97579429	97579501	-	1	NA	promoter-TSS (NM_183251)	promoter-TSS (NM_183251)	32	NM_001177945	66273	Mm.41583	NM_183251	ENSMUSG00000035642	Aamdc	1810020D17Rik|1810037D19Rik|LI2	adipogenesis associated Mth938 domain containing	protein-coding
mm_14003.1	chr2	122014806	122014809	+	1	NA	3' UTR (NM_001290992, exon 13 of 13)	3' UTR (NM_001290992, exon 13 of 13)	-13773	NM_144545	78655	Mm.458184	NM_144545	ENSMUSG00000027236	Eif3j1	1810016I04Rik|2700079K05Rik|AA409117|AA409446|C78575|Eif3j|Eif3j-1|Eif3j-2|Eif3j2|Eif3s1|eIF-3-alpha-A|eIF-3-alpha-B|eIF3-alpha|eIF3-p35|eIF3j-A|eIF3j-B	eukaryotic translation initiation factor 3, subunit J1	protein-coding
mm_126650.1	chr15	84127358	84127366	+	1	NA	Intergenic	Intergenic	-4187	NM_029427	75772	Mm.159565	NM_029427	ENSMUSG00000018868	Pnpla5	4833426H19Rik|GS2L	patatin-like phospholipase domain containing 5	protein-coding
mm_70656.1	chr8	14534463	14534475	+	1	NA	intron (NM_172910, intron 4 of 15)	intron (NM_172910, intron 4 of 15)	-354067	NM_012000	26889	Mm.254027	NM_012000	ENSMUSG00000026317	Cln8	mnd	ceroid-lipofuscinosis, neuronal 8	protein-coding
mm_43286.1	chr5	134099705	134099760	+	1	NA	promoter-TSS (NM_030719)	promoter-TSS (NM_030719)	-16	NM_030719	80909	Mm.45218	NM_030719	ENSMUSG00000015944	Gatsl2	7530428J21Rik|AW742413|Gats|Gatsl1	GATS protein-like 2	protein-coding
mm_116255.1	chr13	34050564	34050574	-	1	NA	intron (NM_026512, intron 4 of 6)	intron (NM_026512, intron 4 of 6)	12928	NM_026512	68021	Mm.140243	NM_026512	ENSMUSG00000038286	Bphl	2010012D11Rik|5730533B08Rik|AI115341	biphenyl hydrolase-like (serine hydrolase, breast epithelial mucin-associated antigen)	protein-coding
mm_29980.1	chr3	134249452	134249452	-	1	NA	intron (NM_001004367, intron 3 of 3)	intron (NM_001004367, intron 3 of 3)	-8869	NR_035435	100316832		NR_035435	ENSMUSG00000084564	Mir1895	Mirn1895|mmu-mir-1895	microRNA 1895	ncRNA
mm_121325.1	chr14	113900973	113900989	+	1	NA	Intergenic	Intergenic	-930984	NR_045661	75822	Mm.410813	NR_045661		4930524C18Rik	-	RIKEN cDNA 4930524C18 gene	ncRNA
mm_18218.1	chr2	50296681	50296736	-	1	NA	promoter-TSS (NM_133839)	promoter-TSS (NM_133839)	-31	NM_133839	109129	Mm.29214	NM_133839	ENSMUSG00000026766	Mmadhc	2010311D03Rik|AI314967|CblD	methylmalonic aciduria (cobalamin deficiency) cblD type, with homocystinuria	protein-coding
mm_138855.1	chr17	41752549	41752556	+	1	NA	Intergenic	ORR1C1|LTR|ERVL-MaLR	-563395	NM_028474	627626	Mm.390999	NM_028474	ENSMUSG00000042256	Ptchd4	3110082D06Rik|Gm321	patched domain containing 4	protein-coding
mm_41992.1	chr5	107726875	107726880	+	1	NA	Intergenic	Intergenic	-1072	NM_001267621	14581	Mm.2078	NM_010278	ENSMUSG00000029275	Gfi1	AW495828|Gfi-1|Pal-1|Pal1	growth factor independent 1	protein-coding
mm_106292.1	chr11	118212716	118212748	-	1	NA	promoter-TSS (NM_001112700)	promoter-TSS (NM_001112700)	10	NM_001112700	19157	Mm.86413	NM_011180	ENSMUSG00000017132	Cyth1	CLM1|CTH-1|CYTIP|Pscd1	cytohesin 1	protein-coding
mm_27546.1	chr3	57847479	57847610	-	1	NA	5' UTR (NM_019410, exon 1 of 3)	5' UTR (NM_019410, exon 1 of 3)	213	NM_019410	18645	Mm.271744	NM_019410	ENSMUSG00000027805	Pfn2	Pfn	profilin 2	protein-coding
mm_137047.1	chr17	17917576	17917586	+	1	NA	Intergenic	MER20|DNA|hAT-Charlie	29757	NM_008039	14289	Mm.378918	NM_008039	ENSMUSG00000052270	Fpr2	E330010I07Rik|Fpr-rs2	formyl peptide receptor 2	protein-coding
mm_140201.1	chr17	83706212	83706260	+	1	NA	promoter-TSS (NM_001171052)	promoter-TSS (NM_001171052)	73	NM_001171052	116871	Mm.277668	NM_054082	ENSMUSG00000055817	Mta3	1110002J22Rik|mKIAA1266	metastasis associated 3	protein-coding
mm_137520.1	chr17	27203342	27203346	+	1	NA	intron (NM_146075, intron 1 of 8)	intron (NM_146075, intron 1 of 8)	1094	NM_146075	224640	Mm.29689	NM_146075	ENSMUSG00000044857	Lemd2	BC026588|Lem2|NET25	LEM domain containing 2	protein-coding
mm_51931.1	chr6	91515970	91515993	+	1	NA	promoter-TSS (NM_009531)	promoter-TSS (NM_009531)	-54	NM_026309	67678	Mm.246693	NM_026309	ENSMUSG00000034192	Lsm3	1010001J12Rik|2610005D18Rik|6030401D18Rik|SMX4|USS2	LSM3 homolog, U6 small nuclear RNA and mRNA degradation associated	protein-coding
mm_50417.1	chr6	48746708	48746718	+	1	NA	intron (NM_175035, intron 1 of 2)	intron (NM_175035, intron 1 of 2)	516	NM_175035	317757	Mm.455917	NM_175035	ENSMUSG00000043505	Gimap5	D630024P16|E230026N22Rik	GTPase, IMAP family member 5	protein-coding
mm_145749.1	chr18	64511784	64511817	+	1	NA	exon (NM_027350, exon 4 of 15)	exon (NM_027350, exon 4 of 15)	4757	NM_027350	70223	Mm.29192	NM_027350	ENSMUSG00000024587	Nars	3010001M15Rik|AA960128|ASNRS|C78150	asparaginyl-tRNA synthetase	protein-coding
mm_32024.1	chr4	95104344	95104345	+	1	NA	Intergenic	B1F|SINE|Alu	-52122	NM_010591	16476	Mm.275071	NM_010591	ENSMUSG00000052684	Jun	AP-1|Junc|c-jun	jun proto-oncogene	protein-coding
mm_75254.1	chr8	40511278	40511297	-	1	NA	promoter-TSS (NM_033560)	promoter-TSS (NM_033560)	467	NM_001271543	18983	Mm.272551	NM_011135	ENSMUSG00000031601	Cnot7	AU022737|CAF-1|Caf1|Pop2	CCR4-NOT transcription complex, subunit 7	protein-coding
mm_11239.1	chr2	29881984	29881994	+	1	NA	3' UTR (NM_207298, exon 12 of 12)	3' UTR (NM_207298, exon 12 of 12)	-7731	NM_001177661	18286	Mm.330116	NM_013615	ENSMUSG00000026790	Odf2	AI848335|MMTEST29	outer dense fiber of sperm tails 2	protein-coding
mm_97022.1	chr11	71750999	71751039	+	1	NA	intron (NM_177618, intron 1 of 8)	CpG	316	NM_177618	216881	Mm.48648	NM_177618	ENSMUSG00000020811	Wscd1	mKIAA0523	WSC domain containing 1	protein-coding
mm_57871.1	chr6	129678909	129678933	-	1	NA	promoter-TSS (NM_001288664)	promoter-TSS (NM_001288664)	52	NM_001288664	16641	Mm.56899	NM_010652	ENSMUSG00000030167	Klrc1	CD159a|NKG2A|NKG2B	killer cell lectin-like receptor subfamily C, member 1	protein-coding
mm_123525.1	chr14	66750109	66750113	-	1	NA	intron (NM_001271761, intron 2 of 2)	intron (NM_001271761, intron 2 of 2)	114860	NM_001271760	11549	Mm.57064	NM_013461	ENSMUSG00000045875	Adra1a	Adra1c	adrenergic receptor, alpha 1a	protein-coding
mm_80147.1	chr9	70914125	70914164	+	1	NA	intron (NM_001324473, intron 1 of 8)	B1_Mus2|SINE|Alu	20664	NM_008280	15450	Mm.390187	NM_008280	ENSMUSG00000032207	Lipc	AI256194|HL|Hpl	lipase, hepatic	protein-coding
mm_106634.1	chr11	120932833	120932876	-	1	NA	promoter-TSS (NM_027745)	promoter-TSS (NM_027745)	18	NM_027745	71276	Mm.275751	NM_027745	ENSMUSG00000048445	Ccdc57	4933434G05Rik	coiled-coil domain containing 57	protein-coding
mm_12195.1	chr2	65668731	65668746	+	1	NA	promoter-TSS (NM_001346680)	promoter-TSS (NM_001346680)	52	NM_001346680	110876	Mm.220329	NM_001099298	ENSMUSG00000075318	Scn2a	6430408L10|A230052E19Rik|Nav1.2|Scn2a1	sodium channel, voltage-gated, type II, alpha	protein-coding
mm_127508.1	chr15	101473473	101473478	+	1	NA	promoter-TSS (NM_010667)	promoter-TSS (NM_010667)	-3	NM_010667	16679	Mm.383183	NM_010667	ENSMUSG00000067614	Krt86	5430421N21Rik|AI325212|Khb4|Krt2-10|Krt2-11|MHb4	keratin 86	protein-coding
mm_157383.1	chrX	38043106	38043137	-	1	NA	promoter-TSS (NM_001034856)	promoter-TSS (NM_001034856)	-7	NM_001034856	194735	Mm.422929	NM_001034856	ENSMUSG00000098348	Btg1-ps2	4930430D24Rik	B cell translocation gene 1, anti-proliferative, pseudogene 2	protein-coding
mm_75646.1	chr8	65097738	65097740	-	1	NA	intron (NR_033217, intron 2 of 2)	intron (NR_033217, intron 2 of 2)	31798	NR_033217	407795	Mm.387876	NR_033217	ENSMUSG00000074300	BC030870	-	cDNA sequence BC030870	ncRNA
mm_97813.1	chr11	82962774	82962785	+	1	NA	3' UTR (NM_183201, exon 6 of 6)	3' UTR (NM_183201, exon 6 of 6)	-2098	NR_045932	76392	Mm.295205	NR_045932	ENSMUSG00000086327	Slfn5os	1700003F17Rik	schlafen 5, opposite strand	ncRNA
mm_38700.1	chr4	145214986	145215008	-	1	NA	3' UTR (NM_011610, exon 10 of 10)	3' UTR (NM_011610, exon 10 of 10)	-19992	NM_001276465	230895	Mm.240310	NM_001033190	ENSMUSG00000020220	Vps13d	-	vacuolar protein sorting 13D	protein-coding
mm_35368.1	chr4	32923391	32923436	-	1	NA	promoter-TSS (NM_080471)	promoter-TSS (NM_080471)	92	NM_080471	140577	Mm.214766	NM_080471	ENSMUSG00000040183	Ankrd6	-	ankyrin repeat domain 6	protein-coding
mm_21545.1	chr2	164054345	164054355	-	1	NA	3' UTR (NM_001291155, exon 7 of 7)	3' UTR (NM_001291155, exon 7 of 7)	16752	NM_025996	67145	Mm.23173	NM_025996	ENSMUSG00000018322	Tomm34	2610100K07Rik|TOM34	translocase of outer mitochondrial membrane 34	protein-coding
mm_97761.1	chr11	80858400	80858428	+	1	NA	promoter-TSS (NM_029367)	promoter-TSS (NM_029367)	25	NM_029367	75622	Mm.26988	NM_029367	ENSMUSG00000053184	Spaca3	1700025M08Rik|ALLP17|Lyc3|SLLP1|mSLLP1	sperm acrosome associated 3	protein-coding
mm_122912.1	chr14	54957780	54957813	-	1	NA	exon (NM_010856, exon 16 of 39)	exon (NM_010856, exon 16 of 39)	-8654	NR_029724	387204		NR_029724	ENSMUSG00000065432	Mir208a	Mirn208|Mirn208a|mir-208|mir-208a|mmu-mir-208	microRNA 208a	ncRNA
mm_171672.1	chr4	4883636	4883642	-	1	NA	Intergenic	IAPLTR1_Mm|LTR|ERVK	-90333	NM_177730	242291	Mm.218889	NM_177730	ENSMUSG00000066324	Impad1	1110001C20Rik|AA408880|AI451589|AL022796|B230207P20|Jaws|gPAPP	inositol monophosphatase domain containing 1	protein-coding
mm_170210.1	chr1	7709319	7709330	-	1	NA	Intergenic	MMVL30-int|LTR|ERV1	620404	NM_183028	319263	Mm.21539	NM_183028	ENSMUSG00000051285	Pcmtd1	8430411F12Rik|A030012M09Rik	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding
mm_162199.1	chrX	126815976	126815976	-	1	NA	intron (NM_177705, intron 2 of 2)	intron (NM_177705, intron 2 of 2)	18028	NM_177705	237029	Mm.60998	NM_177705	ENSMUSG00000058670	4932411N23Rik	-	RIKEN cDNA 4932411N23 gene	protein-coding
mm_166871.1	chr7	25178625	25178630	-	1	NA	Intergenic	Intergenic	23558	NR_045848	434147	Mm.59171	NM_001033781	ENSMUSG00000074274	D930028M14Rik	EG434147	RIKEN cDNA D930028M14 gene	ncRNA
mm_45804.1	chr5	87569024	87569038	-	1	NA	promoter-TSS (NM_016771)	promoter-TSS (NM_016771)	-25	NM_016771	53315	Mm.6824	NM_016771	ENSMUSG00000029273	Sult1d1	5033411P13Rik|AI987815|ST1d1|SULT-N|Sultn	sulfotransferase family 1D, member 1	protein-coding
mm_84458.1	chr9	66580316	66580321	-	1	NA	intron (NM_001302116, intron 1 of 13)	ORR1B1-int|LTR|ERVL-MaLR	12797	NM_144937	235441	Mm.32465	NM_144937	ENSMUSG00000032376	Usp3	AA409661|BC017156	ubiquitin specific peptidase 3	protein-coding
mm_41818.1	chr5	103824452	103824456	+	1	NA	intron (NM_001080798, intron 7 of 19)	intron (NM_001080798, intron 7 of 19)	69881	NM_001080798	17355	Mm.6949	NM_133919	ENSMUSG00000029313	Aff1	9630032B01Rik|AW319193|Af4|Mllt2h|Rob	AF4/FMR2 family, member 1	protein-coding
mm_167826.1	chr9	124423309	124423362	-	1	NA	promoter-TSS (NR_015516)	promoter-TSS (NR_015516)	84	NR_027950	75135	Mm.476814	NR_015516		4930526I15Rik	1600027J15Rik	RIKEN cDNA 4930526I15 gene	ncRNA
mm_72683.1	chr8	84949915	84949921	+	1	NA	5' UTR (NM_144929, exon 2 of 6)	5' UTR (NM_144929, exon 2 of 6)	2927	NM_144929	234542	Mm.461701	NM_144929	ENSMUSG00000048617	Rtbdn	A330096I21Rik|BC022744|Rtbnd	retbindin	protein-coding
mm_56427.1	chr6	97312024	97312038	-	1	NA	intron (NM_001346639, intron 11 of 22)	intron (NM_001346639, intron 11 of 22)	-59251	NM_001081157	320502	Mm.68163	NM_001081157	ENSMUSG00000044086	Lmod3	5430424A14Rik	leiomodin 3 (fetal)	protein-coding
mm_105966.1	chr11	115490669	115490684	-	1	NA	promoter-TSS (NR_136931)	promoter-TSS (NR_136931)	-853	NR_136931	102634812	Mm.390379	NR_136931		LOC102634812	-	ribosomal protein L39 pseudogene	pseudo
mm_31157.1	chr4	43442361	43442369	+	1	NA	promoter-TSS (NM_011571)	promoter-TSS (NM_011571)	88	NM_011571	21754	Mm.485441	NM_011571	ENSMUSG00000028458	Tesk1	AI326901	testis specific protein kinase 1	protein-coding
mm_122957.1	chr14	54968100	54968102	-	1	NA	promoter-TSS (NR_033497)	promoter-TSS (NR_033497)	-686	NR_033497	791403	Mm.319176	NR_033497	ENSMUSG00000097652	Mhrt	D830015G02Rik|ENSMUSG00000053118|Myheart	myosin heavy chain associated RNA transcript	ncRNA
mm_51611.1	chr6	84812164	84812165	+	1	NA	intron (NM_177077, intron 18 of 21)	intron (NM_177077, intron 18 of 21)	-218256	NM_001177713	232174	Mm.255246	NM_175475	ENSMUSG00000063415	Cyp26b1	CP26|P450RAI-2	cytochrome P450, family 26, subfamily b, polypeptide 1	protein-coding
mm_123194.1	chr14	57999237	57999273	-	1	NA	promoter-TSS (NM_028643)	promoter-TSS (NM_028643)	7	NM_028643	68514	Mm.26834	NM_028643	ENSMUSG00000021973	Micu2	1110008L20Rik|4833427E09Rik|AU041871|Efha1|Smhs2	mitochondrial calcium uptake 2	protein-coding
mm_5581.1	chr1	39552135	39552157	-	1	NA	3' UTR (NM_001033135, exon 7 of 7)	3' UTR (NM_001033135, exon 7 of 7)	-3306	NR_028555	100217461		NR_028555	ENSMUSG00000077704	Snord89	MBII-289	small nucleolar RNA, C/D box 89	snoRNA
mm_70027.1	chr7	142576317	142576327	-	1	NA	TTS (NR_030416)	TTS (NR_030416)	825	NR_030416	735280		NR_030416	ENSMUSG00000076275	Mir675	Mirn675|mir-675|mmu-mir-675	microRNA 675	ncRNA
mm_105506.1	chr11	106193512	106193584	-	1	NA	promoter-TSS (NM_001252449)	promoter-TSS (NM_001252449)	55	NM_001252448	72149	Mm.403722	NM_028126	ENSMUSG00000069631	Strada	2610019A05Rik|6030402H20Rik|AI480680|E130112C09Rik	STE20-related kinase adaptor alpha	protein-coding
mm_126439.1	chr15	80671623	80671633	+	1	NA	promoter-TSS (NM_145986)	promoter-TSS (NM_145986)	-219	NM_145986	213956	Mm.132439	NM_145986	ENSMUSG00000022408	Fam83f	AW544981	family with sequence similarity 83, member F	protein-coding
mm_167468.1	chr8	126029362	126029364	+	1	NA	intron (NM_008430, intron 2 of 2)	intron (NM_008430, intron 2 of 2)	34261	NM_008430	16525	Mm.10800	NM_008430	ENSMUSG00000033998	Kcnk1	AI788889|TWIK-1	potassium channel, subfamily K, member 1	protein-coding
mm_99007.1	chr11	98832535	98832551	+	1	NA	3' UTR (NM_138660, exon 14 of 14)	3' UTR (NM_138660, exon 14 of 14)	-4242	NM_001080925	268480	Mm.340766	NM_001080925	ENSMUSG00000038020	Rapgefl1	B230105J10	Rap guanine nucleotide exchange factor (GEF)-like 1	protein-coding
mm_127586.1	chr15	102331701	102331777	+	1	NA	promoter-TSS (NM_021713)	promoter-TSS (NM_021713)	30	NM_021713	60315	Mm.251638	NM_021713	ENSMUSG00000001285	Myg1	0610023A07Rik|2810433J21Rik|5830429P19Rik|AI325965|Gamm1	melanocyte proliferating gene 1	protein-coding
mm_121402.1	chr14	119172884	119172914	+	1	NA	intron (NM_015820, intron 1 of 1)	intron (NM_015820, intron 1 of 1)	34634	NM_015820	50787	Mm.445777	NM_015820	ENSMUSG00000053465	Hs6st3	6OST3|HS6ST-3	heparan sulfate 6-O-sulfotransferase 3	protein-coding
mm_122032.1	chr14	29721891	29721912	-	1	NA	promoter-TSS (NM_009785)	promoter-TSS (NM_009785)	-37	NM_009785	12294	Mm.386754	NM_009785	ENSMUSG00000021991	Cacna2d3	Cacnad3|alapha2delta3	calcium channel, voltage-dependent, alpha2/delta subunit 3	protein-coding
mm_62975.1	chr7	120102368	120102431	+	1	NA	promoter-TSS (NM_145586)	promoter-TSS (NM_145586)	-27	NM_145586	233806	Mm.257952	NM_145586	ENSMUSG00000030917	Tmem159	8430420C20Rik	transmembrane protein 159	protein-coding
mm_62782.1	chr7	112427867	112427882	+	1	NA	5' UTR (NM_020606, exon 1 of 13)	5' UTR (NM_020606, exon 1 of 13)	168	NM_020606	57342	Mm.143763	NM_020606	ENSMUSG00000030770	Parva	2010012A22Rik|5430400F08Rik|AI225929|AU042898|Actp|CH-ILKBP|Parvin	parvin, alpha	protein-coding
mm_104059.1	chr11	86581366	86581369	-	1	NA	Intergenic	RSINE1|SINE|B4	2791	NR_029738	387140		NR_029738	ENSMUSG00000065455	Mir21a	Mir21|Mirn21|mmu-mir-21|mmu-mir-21a	microRNA 21a	ncRNA
mm_157674.1	chrX	59134729	59134785	-	1	NA	promoter-TSS (NM_010200)	promoter-TSS (NM_010200)	-321	NM_010200	14168	Mm.7995	NM_010200	ENSMUSG00000031137	Fgf13	Fhf2	fibroblast growth factor 13	protein-coding
mm_81779.1	chr9	114688837	114688846	+	1	NA	promoter-TSS (NM_146229)	promoter-TSS (NM_146229)	10	NM_146229	235661	Mm.128627	NM_146229	ENSMUSG00000032435	Dync1li1	1110053F02Rik|Dnclic1|LIC-1	dynein cytoplasmic 1 light intermediate chain 1	protein-coding
mm_81165.1	chr9	107299352	107299365	+	1	NA	intron (NM_001317354, intron 1 of 1)	intron (NM_001317354, intron 1 of 1)	2699	NM_009895	12700	Mm.4592	NM_009895	ENSMUSG00000032578	Cish	CIS-1|CIS1|Cis|F17|F23|SOCS	cytokine inducible SH2-containing protein	protein-coding
mm_126597.1	chr15	82358586	82358597	+	1	NA	Intergenic	Intergenic	-4300	NM_025987	67130	Mm.27570	NM_025987	ENSMUSG00000022450	Ndufa6	14kDa|2700038D15Rik|B230217P19Rik	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 6 (B14)	protein-coding
mm_157378.1	chrX	37879034	37879037	-	1	NA	promoter-TSS (NM_001004193)	promoter-TSS (NM_001004193)	-91	NM_001004193	434768	Mm.336025	NM_001004193	ENSMUSG00000064137	Rhox8	Tox	reproductive homeobox 8	protein-coding
mm_122087.1	chr14	30625096	30625105	-	1	NA	intron (NM_011103, intron 1 of 17)	intron (NM_011103, intron 1 of 17)	1108	NM_011103	18753	Mm.2314	NM_011103	ENSMUSG00000021948	Prkcd	AI385711|D14Ertd420e|PKC[d]|PKCdelta|Pkcd	protein kinase C, delta	protein-coding
mm_57188.1	chr6	122849030	122849039	-	1	NA	3' UTR (NM_009779, exon 2 of 2)	3' UTR (NM_009779, exon 2 of 2)	7123	NM_009779	12267	Mm.2408	NM_009779	ENSMUSG00000040552	C3ar1	AZ3B|C3AR|HNFAG09	complement component 3a receptor 1	protein-coding
mm_139470.1	chr17	55970497	55970577	+	1	NA	promoter-TSS (NM_009168)	promoter-TSS (NM_009168)	55	NM_009168	20420	Mm.20908	NM_009168	ENSMUSG00000039154	Shd	AI413439	src homology 2 domain-containing transforming protein D	protein-coding
mm_21530.1	chr2	163645108	163645112	-	1	NA	promoter-TSS (NM_012032)	promoter-TSS (NM_012032)	33	NM_012032	26943	Mm.218473	NM_012032	ENSMUSG00000017707	Serinc3	AA959945|AA960047|AIGP1|DIFF33|TMS-1|Tde1	serine incorporator 3	protein-coding
mm_103959.1	chr11	84129624	84129634	-	1	NA	promoter-TSS (NM_172562)	promoter-TSS (NM_172562)	-61	NM_172562	217031	Mm.45159	NM_172562	ENSMUSG00000018651	Tada2a	AV319371|D030022J10Rik|Tada2l	transcriptional adaptor 2A	protein-coding
mm_4950.1	chr1	191224444	191224461	+	1	NA	Intergenic	CpG	-41119	NM_007498	11910	Mm.2706	NM_007498	ENSMUSG00000026628	Atf3	LRG-21	activating transcription factor 3	protein-coding
mm_73962.1	chr8	120488180	120488200	+	1	NA	promoter-TSS (NM_198671)	promoter-TSS (NM_198671)	-676	NM_198671	382034	Mm.334856	NM_198671	ENSMUSG00000031822	Gse1	2210013I18Rik|mKIAA0182	genetic suppressor element 1, coiled-coil protein	protein-coding
mm_96701.1	chr11	69642787	69642788	+	1	NA	intron (NM_011814, intron 6 of 16)	B1_Mus2|SINE|Alu	9816	NM_011814	23879	Mm.41930	NM_011814	ENSMUSG00000018765	Fxr2	Fxr2h	fragile X mental retardation, autosomal homolog 2	protein-coding
mm_8766.1	chr1	160792909	160792969	-	1	NA	promoter-TSS (NM_013862)	promoter-TSS (NM_013862)	-1	NM_013862	29809	Mm.25833	NM_013862	ENSMUSG00000026721	Rabgap1l	5830411O09Rik|8430421H08Rik|9630005B12Rik|AW049894|HHL|Hh1|mKIAA0471	RAB GTPase activating protein 1-like	protein-coding
mm_166560.1	chr6	45808888	45808889	-	1	NA	intron (NM_001004357, intron 3 of 23)	intron (NM_001004357, intron 3 of 23)	748827	NM_001004357	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding
mm_28153.1	chr3	87748557	87748568	-	1	NA	promoter-TSS (NM_028971)	promoter-TSS (NM_028971)	61	NM_028971	74485	Mm.474494	NM_028971	ENSMUSG00000023084	Lrrc71	4933430H15Rik	leucine rich repeat containing 71	protein-coding
mm_45746.1	chr5	86632418	86632431	-	1	NA	promoter-TSS (NM_178730)	promoter-TSS (NM_178730)	0	NM_178730	243083	Mm.106867	NM_178730	ENSMUSG00000048764	Tmprss11f	4631408C20|4732406D01Rik	transmembrane protease, serine 11f	protein-coding
mm_48324.1	chr5	138995327	138995364	-	1	NA	promoter-TSS (NM_008808)	promoter-TSS (NM_008808)	-392	NM_008808	18590	Mm.2675	NM_008808	ENSMUSG00000025856	Pdgfa	-	platelet derived growth factor, alpha	protein-coding
mm_73502.1	chr8	107293501	107293517	+	1	NA	promoter-TSS (NM_018823)	promoter-TSS (NM_018823)	39	NM_133957	54446	Mm.390057	NM_018823	ENSMUSG00000003847	Nfat5	AI225870|B130038B15Rik|CAG-8|CAG80|NFATL1|OREBP|TonEBP|mKIAA0827|nfatz	nuclear factor of activated T cells 5	protein-coding
mm_41215.1	chr5	88581475	88581487	+	1	NA	intron (NM_001289774, intron 1 of 17)	intron (NM_001289774, intron 1 of 17)	-2032	NM_001289777	52822	Mm.270469	NM_027530	ENSMUSG00000029291	Rufy3	2810428M05Rik|6330416M07Rik|AW455998|AW538594|D5Bwg0860e|Ripx|Rpipx	RUN and FYVE domain containing 3	protein-coding
mm_67378.1	chr7	79842105	79842113	-	1	NA	exon (NM_008486, exon 1 of 20)	exon (NM_008486, exon 1 of 20)	243	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_20738.1	chr2	137116625	137116628	-	1	NA	promoter-TSS (NM_013822)	promoter-TSS (NM_013822)	-106	NM_013822	16449	Mm.22398	NM_013822	ENSMUSG00000027276	Jag1	ABE2|Gsfabe2|Htu|Ozz|Ser-1	jagged 1	protein-coding
mm_11319.1	chr2	30392448	30392458	+	1	NA	exon (NM_020329, exon 1 of 8)	exon (NM_020329, exon 1 of 8)	199	NM_001290508	57170	Mm.285167	NM_020329	ENSMUSG00000026856	Dolpp1	0610011H20Rik|AB030189|LSFR2	dolichyl pyrophosphate phosphatase 1	protein-coding
mm_29757.1	chr3	127162144	127162174	-	1	NA	intron (NR_105029, intron 2 of 3)	intron (NR_105029, intron 2 of 3)	854	NR_105029	100862268	Mm.444603	NR_105029	ENSMUSG00000097456	LOC100862268	-	uncharacterized LOC100862268	ncRNA
mm_163936.1	chr14	50397083	50397092	-	1	NA	Intergenic	L1_Mur3|LINE|L1	4329	NM_146666	258660	Mm.377623	NM_146666	ENSMUSG00000047716	Olfr736	MOR106-5	olfactory receptor 736	protein-coding
mm_64264.1	chr7	141749528	141749539	+	1	NA	exon (NM_023566, exon 36 of 46)	exon (NM_023566, exon 36 of 46)	-39478	NM_010844	17833	Mm.334332	NM_010844	ENSMUSG00000037974	Muc5ac	2210005L13Rik|MGM	mucin 5, subtypes A and C, tracheobronchial/gastric	protein-coding
mm_97059.1	chr11	72689998	72690015	+	1	NA	promoter-TSS (NM_009671)	promoter-TSS (NM_009671)	4	NM_009671	11736	Mm.10313	NM_009671	ENSMUSG00000020790	Ankfy1	Ankhzn|ZFYVE14|mKIAA1255	ankyrin repeat and FYVE domain containing 1	protein-coding
mm_81515.1	chr9	110035371	110035380	+	1	NA	exon (NM_008633, exon 7 of 19)	exon (NM_008633, exon 7 of 19)	-16646	NM_001311163	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_164861.1	chr18	53744481	53744492	-	1	NA	promoter-TSS (NM_178686)	promoter-TSS (NM_178686)	61	NM_178686	225523	Mm.193678	NM_178686	ENSMUSG00000048799	Cep120	A230075C01|AU016693|Ccdc100	centrosomal protein 120	protein-coding
mm_173214.1	chrX	73243049	73243053	-	1	NA	promoter-TSS (NM_183094)	promoter-TSS (NM_183094)	79	NM_183094	72891	Mm.104764	NM_183094	ENSMUSG00000031362	Xlr4c	2900036K24Rik	X-linked lymphocyte-regulated 4C	protein-coding
mm_26800.1	chr3	9884725	9884741	-	1	NA	Intergenic	Intergenic	-51054	NM_001195031	94212	Mm.23897	NM_053182	ENSMUSG00000027508	Pag1	Cbp|F730007C19Rik|Pag	phosphoprotein associated with glycosphingolipid microdomains 1	protein-coding
mm_3577.1	chr1	151089194	151089196	+	1	NA	Intergenic	RLTR14|LTR|ERV1	-48839	NR_038011	402734	Mm.337666	NR_038011		C730036E19Rik	lncLSTR	RIKEN cDNA C730036E19 gene	ncRNA
mm_46344.1	chr5	102053040	102053087	-	1	NA	intron (NM_172882, intron 1 of 66)	intron (NM_172882, intron 1 of 66)	16858	NM_172882	72145	Mm.332522	NM_172882	ENSMUSG00000043940	Wdfy3	2610509D04Rik|ALFY|AW319683|B930017C24|BWF1|Bchs|D5Ertd66e|Ggtb3|ZFYVE25|mKIAA0993	WD repeat and FYVE domain containing 3	protein-coding
mm_157045.1	chrX	8005933	8005949	-	1	NA	intron (NM_027227, intron 2 of 3)	intron (NM_027227, intron 2 of 3)	12551	NM_027227	69824	Mm.279756	NM_027227	ENSMUSG00000031163	Glod5	2010001H14Rik|AV061890	glyoxalase domain containing 5	protein-coding
mm_32530.1	chr4	108879155	108879161	+	1	NA	promoter-TSS (NM_023537)	promoter-TSS (NM_023537)	88	NM_023537	69908	Mm.41580	NM_023537	ENSMUSG00000003411	Rab3b	2610528C18Rik	RAB3B, member RAS oncogene family	protein-coding
mm_149379.1	chr19	11377107	11377119	+	1	NA	intron (NM_001310331, intron 1 of 6)	AT_rich|Low_complexity|Low_complexity	1625	NM_001310331	666907		NM_001310331	ENSMUSG00000101389	Ms4a4a	EG666907	membrane-spanning 4-domains, subfamily A, member 4A	protein-coding
mm_39370.1	chr5	10460398	10460398	+	1	NA	Intergenic	MTE-int|LTR|ERVL-MaLR	-404631	NR_003596	623849	Mm.335888	NR_003596	ENSMUSG00000091422	Gm6455	EG623849	predicted gene 6455	pseudo
mm_96014.1	chr11	59542882	59542892	+	1	NA	intron (NM_145827, intron 1 of 9)	intron (NM_145827, intron 1 of 9)	201	NM_145827	216799	Mm.54174	NM_145827	ENSMUSG00000032691	Nlrp3	AGTAVPRL|AII/AVP|Cias1|FCAS|FCU|MWS|Mmig1|NALP3|Pypaf1	NLR family, pyrin domain containing 3	protein-coding
mm_102039.1	chr11	51857989	51858043	-	1	NA	promoter-TSS (NM_199299)	promoter-TSS (NM_199299)	-535	NM_199299	76901	Mm.259996	NM_199299	ENSMUSG00000020387	Jade2	1200017K05Rik|AI480685|Phf15|mKIAA0239	jade family PHD finger 2	protein-coding
mm_66854.1	chr7	52005679	52005719	-	1	NA	promoter-TSS (NR_027704)	promoter-TSS (NR_027704)	15	NR_027704	75744	Mm.386823	NM_001160345	ENSMUSG00000074093	Svip	1700006C13Rik|6620401M08Rik	small VCP/p97-interacting protein	protein-coding
mm_153598.1	chr19	43752892	43752902	-	1	NA	promoter-TSS (NM_001113562)	promoter-TSS (NM_001113562)	103	NM_144874	226139	Mm.248237	NM_144874	ENSMUSG00000040018	Cox15	2900026G05Rik	cytochrome c oxidase assembly protein 15	protein-coding
mm_24144.1	chr3	88325031	88325075	+	1	NA	promoter-TSS (NM_020003)	promoter-TSS (NM_020003)	30	NM_020003	56700	Mm.439922	NM_020003	ENSMUSG00000001418	Glmp	0610031J06Rik|AB027141|NCU-G1	glycosylated lysosomal membrane protein	protein-coding
mm_10516.1	chr2	16356677	16356704	+	1	NA	5' UTR (NM_026162, exon 1 of 14)	5' UTR (NM_026162, exon 1 of 14)	386	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding
mm_146551.1	chr18	6220925	6220933	-	1	NA	exon (NM_008448, exon 12 of 26)	exon (NM_008448, exon 12 of 26)	20595	NM_008448	16573	Mm.223744	NM_008448	ENSMUSG00000006740	Kif5b	AL022807|Khc|Khcs|Kns1|Ukhc	kinesin family member 5B	protein-coding
mm_69249.1	chr7	127824837	127824849	-	1	NA	promoter-TSS (NM_024414)	promoter-TSS (NM_024414)	-312	NM_024414	56216	Mm.439759	NM_024414	ENSMUSG00000030806	Stx1b	Stx1b2|Stx1bl|Syn1b	syntaxin 1B	protein-coding
mm_92236.1	chr10	69213093	69213130	-	1	NA	promoter-TSS (NM_001252638)	promoter-TSS (NM_001252638)	-13	NM_001331193	320700	Mm.396529	NM_001331193	ENSMUSG00000090622	A930033H14Rik	-	RIKEN cDNA A930033H14 gene	protein-coding
mm_24507.1	chr3	92502554	92502554	+	1	NA	Intergenic	Intergenic	-2061	NM_173070	229562	Mm.246590	NM_173070	ENSMUSG00000045566	Sprr4	-	small proline-rich protein 4	protein-coding
mm_126704.1	chr15	85206023	85206045	+	1	NA	promoter-TSS (NM_010180)	promoter-TSS (NM_010180)	26	NM_010180	14114	Mm.297992	NM_010180	ENSMUSG00000006369	Fbln1	-	fibulin 1	protein-coding
mm_72934.1	chr8	91313561	91313575	+	1	NA	promoter-TSS (NM_173431)	promoter-TSS (NM_173431)	43	NM_011936	26383	Mm.4375	NM_011936	ENSMUSG00000055932	Fto	AW743446|mKIAA1752	fat mass and obesity associated	protein-coding
mm_23732.1	chr3	69029396	69029414	+	1	NA	exon (NM_133786, exon 17 of 24)	exon (NM_133786, exon 17 of 24)	15337	NM_025863	66949	Mm.176695	NM_025863	ENSMUSG00000034317	Trim59	2310035M22Rik|2700022F13Rik|Mrf1|TSBF1	tripartite motif-containing 59	protein-coding
mm_171959.1	chr5	8266596	8266599	+	1	NA	intron (NM_001310440, intron 3 of 30)	intron (NM_001310440, intron 3 of 30)	101563	NM_001007221	11496	Mm.275895	NM_001007220	ENSMUSG00000040537	Adam22	2900022I03Rik|AI854032|MDC2	a disintegrin and metallopeptidase domain 22	protein-coding
mm_170491.1	chr19	22852040	22852058	+	1	NA	intron (NM_001035243, intron 8 of 23)	LSU-rRNA_Hsa|rRNA|rRNA	101444	NR_029591	387200		NR_029591	ENSMUSG00000065507	Mir204	Mirn204|mir-204|mmu-mir-204	microRNA 204	ncRNA
mm_123283.1	chr14	61437049	61437054	-	1	NA	intron (NM_008466, intron 1 of 16)	intron (NM_008466, intron 1 of 16)	2896	NM_008466	16648	Mm.25548	NM_008466	ENSMUSG00000021929	Kpna3	IPOA4	karyopherin (importin) alpha 3	protein-coding
mm_53200.1	chr6	125565586	125565597	+	1	NA	intron (NM_011708, intron 3 of 51)	intron (NM_011708, intron 3 of 51)	12643	NM_011708	22371	Mm.22339	NM_011708	ENSMUSG00000001930	Vwf	6820430P06Rik|AI551257|B130011O06Rik|C630030D09|F8VWF|VWD	Von Willebrand factor	protein-coding
mm_4545.1	chr1	177139859	177139864	+	1	NA	intron (NM_011785, intron 1 of 12)	RMER19B|LTR|ERVK	108906	NM_011785	23797	Mm.235194	NM_011785	ENSMUSG00000019699	Akt3	AI851531|D930002M15Rik|Nmf350	thymoma viral proto-oncogene 3	protein-coding
mm_152243.1	chr19	8713887	8713893	-	1	NA	promoter-TSS (NM_008577)	promoter-TSS (NM_008577)	7	NM_008577	17254	Mm.4114	NM_008577	ENSMUSG00000010095	Slc3a2	4F2|4F2HC|AI314110|Cd98|Ly-10|Ly-m10|Ly10|Mdu1|Mgp-2hc|NACAE	solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2	protein-coding
mm_123537.1	chr14	66814999	66815009	-	1	NA	exon (NM_009955, exon 10 of 14)	exon (NM_009955, exon 10 of 14)	53596	NM_009955	12934	Mm.352648	NM_009955	ENSMUSG00000022048	Dpysl2	AI851130|Crmp2|DRP2|Musunc33|TOAD-64|Ulip2	dihydropyrimidinase-like 2	protein-coding
mm_161168.1	chr13	36117634	36117634	+	1	NA	promoter-TSS (NM_024274)	promoter-TSS (NM_024274)	-9	NM_024274	69955	Mm.70690	NM_024274	ENSMUSG00000021420	Fars2	Fars1|pheRS	phenylalanine-tRNA synthetase 2 (mitochondrial)	protein-coding
mm_66494.1	chr7	45057056	45057064	-	1	NA	intron (NM_022999, intron 4 of 6)	intron (NM_022999, intron 4 of 6)	-4179	NM_175022	233210	Mm.219137	NM_175022	ENSMUSG00000046574	Prr12	6720469B10|BC058674	proline rich 12	protein-coding
mm_97259.1	chr11	75759291	75759336	+	1	NA	exon (NM_009536, exon 5 of 6)	exon (NM_009536, exon 5 of 6)	26426	NM_009536	22627	Mm.234700	NM_009536	ENSMUSG00000020849	Ywhae	AU019196	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide	protein-coding
mm_117968.1	chr13	99900646	99900669	-	1	NA	promoter-TSS (NM_001081493)	promoter-TSS (NM_001081493)	26	NM_013732	27220	Mm.75498	NM_013732	ENSMUSG00000021647	Cartpt	Cart	CART prepropeptide	protein-coding
mm_17440.1	chr2	28084878	28084891	-	1	NA	promoter-TSS (NM_010190)	promoter-TSS (NM_010190)	-6	NM_010190	14134	Mm.182935	NM_010190	ENSMUSG00000026835	Fcnb	Fcn2	ficolin B	protein-coding
mm_70051.1	chr7	142578140	142578154	-	1	NA	promoter-TSS (NR_130974)	promoter-TSS (NR_130974)	-1	NR_130973	14955	Mm.14802	NR_001592	ENSMUSG00000000031	H19	AI747191	H19, imprinted maternally expressed transcript	ncRNA
mm_60223.1	chr7	43567614	43567616	+	1	NA	intron (NM_001008549, intron 3 of 4)	intron (NM_001008549, intron 3 of 4)	5245	NM_001008549	210104	Mm.333821	NM_001008549	ENSMUSG00000056592	Zfp658	-	zinc finger protein 658	protein-coding
mm_119372.1	chr14	41122789	41122797	+	1	NA	3' UTR (NM_133653, exon 10 of 10)	3' UTR (NM_133653, exon 10 of 10)	-8995	NM_023134	20387	Mm.46062	NM_023134	ENSMUSG00000021789	Sftpa1	SP-A|Sftp-1|Sftp1	surfactant associated protein A1	protein-coding
mm_25662.1	chr3	121723602	121723618	+	1	NA	promoter-TSS (NM_010171)	promoter-TSS (NM_010171)	73	NM_010171	14066	Mm.273188	NM_010171	ENSMUSG00000028128	F3	AA409063|CD142|Cf-3|Cf3|TF	coagulation factor III	protein-coding
mm_7200.1	chr1	93016050	93016065	-	1	NA	3' UTR (NM_008440, exon 48 of 48)	3' UTR (NM_008440, exon 48 of 48)	9723	NM_001159658	208760	Mm.235537	NM_177587	ENSMUSG00000045091	Aqp12	AB084104|mAQP12	aquaporin 12	protein-coding
mm_130285.1	chr15	96996974	96996984	-	1	NA	3' UTR (NM_027052, exon 16 of 16)	3' UTR (NM_027052, exon 16 of 16)	58977	NM_027052	69354	Mm.250980	NM_027052	ENSMUSG00000022464	Slc38a4	1110012E16Rik|1700012A18Rik|Ata3|mATA3|mNAT3	solute carrier family 38, member 4	protein-coding
mm_59835.1	chr7	29307975	29308057	+	1	NA	intron (NM_013874, intron 1 of 11)	CpG	4011	NM_013874	29861	Mm.101885	NM_013874	ENSMUSG00000030584	Dpf1	Neud4	D4, zinc and double PHD fingers family 1	protein-coding
mm_74885.1	chr8	25101735	25101792	-	1	NA	promoter-TSS (NM_031257)	promoter-TSS (NM_031257)	48	NM_031257	83436	Mm.261122	NM_031257	ENSMUSG00000031557	Plekha2	6430512N22Rik|AI851530|AU041791|TAPP2|W91773	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 2	protein-coding
mm_95353.1	chr11	48817566	48817585	+	1	NA	promoter-TSS (NM_145377)	promoter-TSS (NM_145377)	-184	NM_145377	211007	Mm.794	NM_145377	ENSMUSG00000040365	Trim41	AW552703|BC020156|R75223|RINCK	tripartite motif-containing 41	protein-coding
mm_30184.1	chr3	144570137	144570227	-	1	NA	promoter-TSS (NM_053102)	promoter-TSS (NM_053102)	34	NM_011828	23908	Mm.12863	NM_011828	ENSMUSG00000040151	Hs2st1	AW214369|Hs2st|mKIAA0448	heparan sulfate 2-O-sulfotransferase 1	protein-coding
mm_12597.1	chr2	74673953	74673955	+	1	NA	Intergenic	Intergenic	-1059	NM_008274	15432	Mm.57124	NM_008274	ENSMUSG00000001823	Hoxd12	Hox-4.7|Hox-5.6	homeobox D12	protein-coding
mm_2368.1	chr1	93211723	93211724	+	1	NA	intron (NM_001310428, intron 21 of 31)	intron (NM_001310428, intron 21 of 31)	-24174	NM_172463	208777	Mm.271897	NM_172463	ENSMUSG00000047793	Sned1	6720455I24Rik|AI197264|AI642697|D430044C15Rik|SST3|Snep	sushi, nidogen and EGF-like domains 1	protein-coding
mm_3193.1	chr1	135810878	135810886	+	1	NA	3' UTR (NM_021467, exon 9 of 9)	3' UTR (NM_021467, exon 9 of 9)	-7716	NM_133664	16763	Mm.36726	NM_133664	ENSMUSG00000041782	Lad1	-	ladinin	protein-coding
mm_72148.1	chr8	72144560	72144585	+	1	NA	intron (NM_001001491, intron 3 of 7)	intron (NM_001001491, intron 3 of 7)	9280	NM_001001491	326618	Mm.295124	NM_001001491	ENSMUSG00000031799	Tpm4	2610528G24Rik|Tpm4.2|Tpm4.2cy	tropomyosin 4	protein-coding
mm_50361.1	chr6	48647389	48647404	+	1	NA	promoter-TSS (NM_001286629)	promoter-TSS (NM_001286629)	35	NM_212486	243374	Mm.86514	NM_212486	ENSMUSG00000064262	Gimap8	Gm457|IAN9|IMAP8	GTPase, IMAP family member 8	protein-coding
mm_31828.1	chr4	70378118	70378127	+	1	NA	intron (NM_145990, intron 4 of 36)	GSAT_MM|Satellite|Satellite	32313	NM_001313762	214444	Mm.370777	NM_145990	ENSMUSG00000039298	Cdk5rap2	2900018K03Rik|an|mKIAA1633	CDK5 regulatory subunit associated protein 2	protein-coding
mm_118246.1	chr13	111884313	111884333	-	1	NA	Intergenic	Intergenic	16387	NR_130345	102636620	Mm.402328	NR_130345	ENSMUSG00000086111	Gm15326	OTTMUSG00000020187	predicted gene 15326	ncRNA
mm_85894.1	chr9	111055548	111055559	-	1	NA	exon (NM_017466, exon 2 of 2)	exon (NM_017466, exon 2 of 2)	1691	NM_001302377	54199	Mm.7336	NM_017466	ENSMUSG00000043953	Ccrl2	1810047I05Rik|Ackr5|CCR11|Cmkbr1l2|E01|L-CCR	chemokine (C-C motif) receptor-like 2	protein-coding
mm_93539.1	chr10	115384477	115384509	-	1	NA	promoter-TSS (NM_025780)	promoter-TSS (NM_025780)	-58	NM_025780	66816	Mm.32314	NM_025780	ENSMUSG00000020137	Thap2	2900040O07Rik|9030625G08Rik|AI450385|AI649097	THAP domain containing, apoptosis associated protein 2	protein-coding
mm_93117.1	chr10	91153850	91153856	-	1	NA	intron (NM_001080129, intron 4 of 8)	BC1_Mm|scRNA|scRNA	16697	NM_001283048	21917	Mm.159684	NM_011605	ENSMUSG00000019961	Tmpo	5630400D24Rik|AI195756|AI606875|AW214352|AW547477|LAP2|TP	thymopoietin	protein-coding
mm_68114.1	chr7	102099896	102099906	-	1	NA	non-coding (NR_111935, exon 1 of 6)	non-coding (NR_111935, exon 1 of 6)	328	NR_111935	11875	Mm.2816	NM_007491	ENSMUSG00000070424	Art5	ARTC5|Yac-2	ADP-ribosyltransferase 5	protein-coding
mm_98205.1	chr11	87797317	87797331	+	1	NA	exon (NM_010824, exon 8 of 14)	exon (NM_010824, exon 8 of 14)	3540	NM_010824	17523	Mm.4668	NM_010824	ENSMUSG00000009350	Mpo	mKIAA4033	myeloperoxidase	protein-coding
mm_47940.1	chr5	135351289	135351302	-	1	NA	Intergenic	Intergenic	-1251	NM_001277891	94244	Mm.26037	NM_033571	ENSMUSG00000040013	Fkbp6	1700008G22Rik|36kDa|AU017274|D5Ertd724e|FKBP-36|FKBP-6	FK506 binding protein 6	protein-coding
mm_106522.1	chr11	120561189	120561269	-	1	NA	exon (NM_011032, exon 11 of 11)	exon (NM_011032, exon 11 of 11)	-10097	NM_026814	68701	Mm.46477	NM_026814	ENSMUSG00000025129	Ppp1r27	1110033I14Rik|Dysfip1|toonin	protein phosphatase 1, regulatory subunit 27	protein-coding
mm_166306.1	chr5	105731852	105731873	+	1	NA	intron (NM_178701, intron 1 of 2)	intron (NM_178701, intron 1 of 2)	31052	NM_178701	231549	Mm.23837	NM_178701	ENSMUSG00000046079	Lrrc8d	2810473G09Rik|4930525N13Rik|A930019F03|Lrrc5	leucine rich repeat containing 8D	protein-coding
mm_118425.1	chr14	7937287	7937297	+	1	NA	intron (NM_134080, intron 41 of 45)	intron (NM_134080, intron 41 of 45)	56890	NM_007870	13421	Mm.272258	NM_007870	ENSMUSG00000025279	Dnase1l3	DNasegamma|Dhp2|Lsd	deoxyribonuclease 1-like 3	protein-coding
mm_158602.1	chrX	152016270	152016302	-	1	NA	promoter-TSS (NM_025660)	promoter-TSS (NM_025660)	9	NM_025660	66611	Mm.158120	NM_025660	ENSMUSG00000025257	Ribc1	2610028I09Rik|W08639	RIB43A domain with coiled-coils 1	protein-coding
mm_166393.1	chr5	135010022	135010032	+	1	NA	exon (NM_145215, exon 2 of 6)	exon (NM_145215, exon 2 of 6)	571	NR_033794	68758	Mm.389700	NM_145215	ENSMUSG00000040532	Abhd11	1110054D16Rik|A630008N09Rik|Wbscr21	abhydrolase domain containing 11	protein-coding
mm_31335.1	chr4	46468666	46468677	+	1	NA	exon (NM_130889, exon 4 of 7)	exon (NM_130889, exon 4 of 7)	17745	NM_130889	67628	Mm.263913	NM_130889	ENSMUSG00000028333	Anp32b	2410015B15Rik|PAL31|PHAPI2a|Ssp29	acidic (leucine-rich) nuclear phosphoprotein 32 family, member B	protein-coding
mm_158846.1	chrX	169978857	169978882	-	1	NA	promoter-TSS (NR_029457)	promoter-TSS (NR_029457)	48	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_77311.1	chr8	117673664	117673674	-	1	NA	Intergenic	Intergenic	-2154	NM_028725	74032	Mm.296302	NM_028725	ENSMUSG00000034308	Sdr42e1	4632417N05Rik|AI117603	short chain dehydrogenase/reductase family 42E, member 1	protein-coding
mm_48121.1	chr5	137139122	137139140	-	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	-22924	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_123063.1	chr14	55672065	55672125	-	1	NA	promoter-TSS (NM_177992)	promoter-TSS (NM_177992)	-140	NM_177992	105446	Mm.390685	NM_177992	ENSMUSG00000002326	Gmpr2	1810008P16Rik|5730544D12Rik|AA959850|GMPR 2	guanosine monophosphate reductase 2	protein-coding
mm_121099.1	chr14	99339137	99339179	+	1	NA	Intergenic	Intergenic	40467	NM_009769	12224	Mm.30262	NM_009769	ENSMUSG00000005148	Klf5	4930520J07Rik|Bteb2|CKLF|IKLF	Kruppel-like factor 5	protein-coding
mm_122963.1	chr14	54973152	54973187	-	1	NA	exon (NM_080728, exon 37 of 41)	exon (NM_080728, exon 37 of 41)	2607	NR_030607	100124433		NR_030607	ENSMUSG00000077928	Mir208b	Mirn208b|mir-208b	microRNA 208b	ncRNA
mm_26286.1	chr3	142506649	142506652	+	1	NA	intron (NM_153564, intron 7 of 10)	intron (NM_153564, intron 7 of 10)	9716	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_72825.1	chr8	88199514	88199555	+	1	NA	intron (NM_001164498, intron 1 of 12)	CpG	321	NM_001164498	214627	Mm.491211	NM_001164497	ENSMUSG00000036779	Papd5	5730445M16Rik|5830428A09	PAP associated domain containing 5	protein-coding
mm_116957.1	chr13	56137177	56137188	-	1	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	-1632	NM_001159513	26914	Mm.283802	NM_012015	ENSMUSG00000015937	H2afy	H2AF12M|mH2a1|macroH2A1	H2A histone family, member Y	protein-coding
mm_41117.1	chr5	87780957	87780959	+	1	NA	intron (NM_007785, intron 8 of 13)	intron (NM_007785, intron 8 of 13)	6508	NM_007785	12993	Mm.4908	NM_007785	ENSMUSG00000061937	Csn1s2a	Csng|PP22	casein alpha s2-like A	protein-coding
mm_21583.1	chr2	164237286	164237295	-	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	1051	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_90514.1	chr10	128043119	128043128	+	1	NA	exon (NM_001113199, exon 3 of 9)	exon (NM_001113199, exon 3 of 9)	7777	NM_001113199	17938	Mm.3746	NM_013608	ENSMUSG00000061315	Naca	AL022831|AL024382|Gm1878|mKIAA0363|skNAC	nascent polypeptide-associated complex alpha polypeptide	protein-coding
mm_47490.1	chr5	124005618	124005648	-	1	NA	3' UTR (NM_177876, exon 4 of 4)	3' UTR (NM_177876, exon 4 of 4)	8781	NR_105999	102465625		NR_105999	ENSMUSG00000098454	Mir7032	Gm27309|mmu-mir-7032	microRNA 7032	ncRNA
mm_151305.1	chr19	55742281	55742303	+	1	NA	non-coding (NR_138565, exon 1 of 16)	non-coding (NR_138565, exon 1 of 16)	482	NM_001142923	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_71500.1	chr8	46806470	46806482	+	1	NA	exon (NM_008391, exon 3 of 9)	exon (NM_008391, exon 3 of 9)	66731	NM_008391	16363	Mm.1149	NM_008391	ENSMUSG00000031627	Irf2	9830146E22Rik|AI646973|Irf-2	interferon regulatory factor 2	protein-coding
mm_155779.1	chrX	96455512	96455522	+	1	NA	promoter-TSS (NM_010417)	promoter-TSS (NM_010417)	81	NM_010417	15203	Mm.277092	NM_010417	ENSMUSG00000031209	Heph	C130006F04Rik|Cpl|mKIAA0698|sla	hephaestin	protein-coding
mm_97214.1	chr11	75630775	75630803	+	1	NA	promoter-TSS (NM_008916)	promoter-TSS (NM_008916)	-231	NM_008916	19062	Mm.1458	NM_008916	ENSMUSG00000006127	Inpp5k	C62|Pps|SKIP	inositol polyphosphate 5-phosphatase K	protein-coding
mm_13061.1	chr2	91115361	91115390	+	1	NA	exon (NM_011355, exon 5 of 5)	exon (NM_011355, exon 5 of 5)	-2769	NM_008653	17868	Mm.10728	NM_008653	ENSMUSG00000002100	Mybpc3	-	myosin binding protein C, cardiac	protein-coding
mm_150525.1	chr19	39060999	39061015	+	1	NA	promoter-TSS (NM_028191)	promoter-TSS (NM_028191)	1	NM_028191	72303	Mm.482578	NM_028191	ENSMUSG00000067231	Cyp2c65	2210009K14Rik	cytochrome P450, family 2, subfamily c, polypeptide 65	protein-coding
mm_164375.1	chr16	26692723	26692728	-	1	NA	intron (NM_001159318, intron 4 of 10)	intron (NM_001159318, intron 4 of 10)	62777	NR_105063	100504628	Mm.393275	NR_105063	ENSMUSG00000092545	Gm20319	-	predicted gene, 20319	ncRNA
mm_168376.1	chr11	21906984	21906986	+	1	NA	Intergenic	Intergenic	94666	NM_011023	18423	Mm.129663	NM_011023	ENSMUSG00000005917	Otx1	A730044F23Rik|jv	orthodenticle homeobox 1	protein-coding
mm_122624.1	chr14	51145636	51145642	-	1	NA	exon (NM_011271, exon 2 of 2)	exon (NM_011271, exon 2 of 2)	1128	NM_011271	19752	Mm.235538	NM_011271	ENSMUSG00000035896	Rnase1	AI574248|Rib-1|Rib1	ribonuclease, RNase A family, 1 (pancreatic)	protein-coding
mm_62646.1	chr7	107670346	107670351	+	1	NA	intron (NM_001163557, intron 3 of 25)	intron (NM_001163557, intron 3 of 25)	63504	NM_001163557	19024	Mm.2817	NM_008905	ENSMUSG00000036528	Ppfibp2	Cclp1	PTPRF interacting protein, binding protein 2 (liprin beta 2)	protein-coding
mm_7999.1	chr1	134405631	134405635	-	1	NA	promoter-TSS (NM_028057)	promoter-TSS (NM_028057)	-357	NM_028057	72017	Mm.280230	NM_028057	ENSMUSG00000026456	Cyb5r1	1500005G05Rik|B5R.1|C80155|Nqo3a2	cytochrome b5 reductase 1	protein-coding
mm_108486.1	chr12	83668086	83668104	+	1	NA	exon (NM_027349, exon 11 of 19)	exon (NM_027349, exon 11 of 19)	-20468	NM_008943	19164	Mm.998	NM_008943	ENSMUSG00000019969	Psen1	Ad3h|PS-1|PS1|S182	presenilin 1	protein-coding
mm_42858.1	chr5	122210632	122210635	+	1	NA	intron (NM_028752, intron 1 of 6)	intron (NM_028752, intron 1 of 6)	346	NM_028752	74096	Mm.28804	NM_028752	ENSMUSG00000064267	Hvcn1	0610039P13Rik|AI450555|BTS|HV1|Vsop.|mVSOP	hydrogen voltage-gated channel 1	protein-coding
mm_135491.1	chr16	46120139	46120181	-	1	NA	promoter-TSS (NM_032465)	promoter-TSS (NM_032465)	88	NM_032465	84544	Mm.29204	NM_032465	ENSMUSG00000022657	Cd96	1700109I12Rik|Tactile	CD96 antigen	protein-coding
mm_17939.1	chr2	36049366	36049376	-	1	NA	promoter-TSS (NM_029309)	promoter-TSS (NM_029309)	-79	NM_026703	68375	Mm.19834	NM_026703	ENSMUSG00000026895	Ndufa8	0610033L03Rik|AW261656	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 8	protein-coding
mm_12759.1	chr2	79255555	79255652	+	1	NA	5' UTR (NM_010576, exon 1 of 28)	5' UTR (NM_010576, exon 1 of 28)	177	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D|Itga4B	integrin alpha 4	protein-coding
mm_6188.1	chr1	65113536	65113537	-	1	NA	intron (NM_175293, intron 5 of 7)	intron (NM_175293, intron 5 of 7)	9678	NM_175293	98303	Mm.348057	NM_175293	ENSMUSG00000044816	D630023F18Rik	AI314969	RIKEN cDNA D630023F18 gene	protein-coding
mm_138643.1	chr17	35866678	35866699	+	1	NA	promoter-TSS (NM_175242)	promoter-TSS (NM_175242)	73	NM_175242	76448	Mm.359982	NM_175242	ENSMUSG00000034595	Ppp1r18	2310014H01Rik|AA407849|AI450394	protein phosphatase 1, regulatory subunit 18	protein-coding
mm_83888.1	chr9	55540894	55540925	-	1	NA	promoter-TSS (NM_027397)	promoter-TSS (NM_027397)	-240	NM_027397	104360	Mm.273996	NM_027397	ENSMUSG00000032318	Isl2	3110001N10Rik	insulin related protein 2 (islet 2)	protein-coding
mm_120331.1	chr14	63339967	63339972	+	1	NA	Intergenic	RMER30|DNA|hAT-Charlie	77218	NM_007549	12143	Mm.3962	NM_007549	ENSMUSG00000014453	Blk	-	B lymphoid kinase	protein-coding
mm_100123.1	chr11	115900126	115900190	+	1	NA	promoter-TSS (NM_183259)	promoter-TSS (NM_183259)	19	NM_183259	66528	Mm.275740	NM_183259	ENSMUSG00000048442	Smim5	2210020M01Rik	small integral membrane protein 5	protein-coding
mm_82122.1	chr9	123478739	123478782	+	1	NA	promoter-TSS (NM_013860)	promoter-TSS (NM_013860)	59	NM_013860	29806	Mm.10987	NM_013860	ENSMUSG00000025239	Limd1	AW822033|D9Ertd192e	LIM domains containing 1	protein-coding
mm_71685.1	chr8	61224221	61224251	+	1	NA	promoter-TSS (NM_021506)	promoter-TSS (NM_021506)	65	NM_021506	59009	Mm.27949	NM_021506	ENSMUSG00000031642	Sh3rf1	2200003J05Rik|Posh|R75531|Sh3md2	SH3 domain containing ring finger 1	protein-coding
mm_132278.1	chr16	32975792	32975810	+	1	NA	exon (NM_001310673, exon 8 of 19)	exon (NM_001310673, exon 8 of 19)	61701	NM_001310672	70144	Mm.491178	NM_001081255	ENSMUSG00000022801	Lrch3	2210409B11Rik|AW215594|Gm1742	leucine-rich repeats and calponin homology (CH) domain containing 3	protein-coding
mm_165667.1	chr3	88563764	88563801	+	1	NA	intron (NM_033526, intron 6 of 10)	intron (NM_033526, intron 6 of 10)	10066	NM_033526	94232	Mm.303059	NM_033526	ENSMUSG00000008604	Ubqln4	A1Up|A1u|AI663987|CIP75|UBIN	ubiquilin 4	protein-coding
mm_161343.1	chr14	52237800	52237800	-	1	NA	promoter-TSS (NM_201637)	promoter-TSS (NM_201637)	-228	NM_201637	67772	Mm.289934	NM_201637	ENSMUSG00000053754	Chd8	5830451P18Rik|AU015341|Duplin|HELSNF1|mKIAA1564	chromodomain helicase DNA binding protein 8	protein-coding
mm_36730.1	chr4	99120947	99120962	-	1	NA	promoter-TSS (NM_026082)	promoter-TSS (NM_026082)	-39	NM_026082	67299	Mm.260623	NM_026082	ENSMUSG00000028556	Dock7	3110056M06Rik|Gm430	dedicator of cytokinesis 7	protein-coding
mm_129262.1	chr15	76817023	76817033	-	1	NA	intron (NM_198420, intron 1 of 10)	intron (NM_198420, intron 1 of 10)	1142	NM_001168288	223666	Mm.322931	NM_198420	ENSMUSG00000033697	Arhgap39	9530053N22|AI843066|D15Wsu169e|Kiaa1688|Porf-2	Rho GTPase activating protein 39	protein-coding
mm_72691.1	chr8	84969687	84969706	+	1	NA	promoter-TSS (NM_011563)	promoter-TSS (NM_011563)	74	NM_011563	21672	Mm.347009	NM_011563	ENSMUSG00000005161	Prdx2	AL022839|Band-8|NkefB|PRP|PrxII|TDX1|TPx|TPx-B|TR|TSA|Tdpx1|Torin	peroxiredoxin 2	protein-coding
mm_92454.1	chr10	77799186	77799191	-	1	NA	promoter-TSS (NM_001205034)	promoter-TSS (NM_001205034)	-55	NM_001205034	100503388	Mm.482880	NM_001205034	ENSMUSG00000096380	Gm19668	-	predicted gene, 19668	protein-coding
mm_135197.1	chr16	36455379	36455400	-	1	NA	promoter-TSS (NM_025288)	promoter-TSS (NM_025288)	3	NM_025288	20863	Mm.136573	NM_025288	ENSMUSG00000054905	Stfa3	Stf3	stefin A3	protein-coding
mm_164410.1	chr16	36580174	36580184	+	1	NA	Intergenic	Intergenic	-18045	NM_013803	12374	Mm.103619	NM_013803	ENSMUSG00000051980	Casr	CaR|Gprc2a	calcium-sensing receptor	protein-coding
mm_171455.1	chr4	145510786	145510804	+	1	NA	promoter-TSS (NM_001324553)	promoter-TSS (NM_001324553)	36	NM_001324553	101056073	Mm.276881	NM_001324553	ENSMUSG00000078503	LOC101056073	-	zinc finger protein 501-like	protein-coding
mm_80358.1	chr9	75211631	75211634	+	1	NA	intron (NM_010864, intron 37 of 40)	intron (NM_010864, intron 37 of 40)	-20382	NM_001081322	208943	Mm.41339	NM_001081322	ENSMUSG00000033590	Myo5c	9130003O20Rik|BB085560|C330029I24	myosin VC	protein-coding
mm_106026.1	chr11	116027962	116027978	-	1	NA	Intergenic	MIR3|SINE|MIR	-2346	NM_001286006	217331	Mm.297706	NM_172569	ENSMUSG00000020770	Unk	B230379M23Rik|Zc3h5|Zc3hdc5|mKIAA1753	unkempt family zinc finger	protein-coding
mm_12691.1	chr2	76369968	76370024	+	1	NA	promoter-TSS (NM_153405)	promoter-TSS (NM_153405)	12	NM_153405	241490	Mm.33310	NM_153405	ENSMUSG00000042369	Rbm45	Drb1|Drbp1|G430095G15Rik	RNA binding motif protein 45	protein-coding
mm_147729.1	chr18	61014166	61014180	-	1	NA	promoter-TSS (NM_201353)	promoter-TSS (NM_201353)	26	NM_201353	240332	Mm.39846	NM_201353	ENSMUSG00000052026	Slc6a7	AW455934|PROT	solute carrier family 6 (neurotransmitter transporter, L-proline), member 7	protein-coding
mm_104620.1	chr11	97284715	97284750	-	1	NA	Intergenic	Intergenic	-4156	NM_008942	19155	Mm.29824	NM_008942	ENSMUSG00000001441	Npepps	AAP-S|MP100|Psa|R74825|goku	aminopeptidase puromycin sensitive	protein-coding
mm_97369.1	chr11	77607955	77607965	+	1	NA	promoter-TSS (NM_144825)	promoter-TSS (NM_144825)	-145	NM_144825	216965	Mm.340436	NM_144825	ENSMUSG00000017291	Taok1	2810468K05Rik|AU020252|D130018F14Rik|Map3k16|Markk|Psk2|mKIAA1361	TAO kinase 1	protein-coding
mm_68901.1	chr7	126450503	126450510	-	1	NA	exon (NM_007504, exon 13 of 23)	exon (NM_007504, exon 13 of 23)	12567	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_26062.1	chr3	135826276	135826329	+	1	NA	5' UTR (NM_001135150, exon 2 of 9)	5' UTR (NM_001135150, exon 2 of 9)	512	NM_001135150	67547	Mm.30239	NM_026228	ENSMUSG00000053897	Slc39a8	4933419D20Rik|AA986696|BIGM103|ZIP-8|Zip8	solute carrier family 39 (metal ion transporter), member 8	protein-coding
mm_23498.1	chr3	60524350	60524362	+	1	NA	intron (NM_001253710, intron 1 of 7)	intron (NM_001253710, intron 1 of 7)	23177	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_138958.1	chr17	44188666	44188676	+	1	NA	promoter-TSS (NM_172621)	promoter-TSS (NM_172621)	99	NM_172621	224796	Mm.37666	NM_172621	ENSMUSG00000023959	Clic5	5730531E12Rik|B330005L24|Gm322|jbg	chloride intracellular channel 5	protein-coding
mm_63079.1	chr7	122219676	122219688	+	1	NA	5' UTR (NM_027363, exon 1 of 7)	5' UTR (NM_027363, exon 1 of 7)	186	NM_027363	70261	Mm.96997	NM_027363	ENSMUSG00000030865	Chp2	2010110P09Rik|Cbhp2	calcineurin-like EF hand protein 2	protein-coding
mm_47964.1	chr5	135744160	135744180	-	1	NA	promoter-TSS (NM_172541)	promoter-TSS (NM_172541)	2	NM_172541	215210	Mm.11688	NM_172541	ENSMUSG00000039886	Tmem120a	2010310D06Rik|Tmpit	transmembrane protein 120A	protein-coding
mm_141662.1	chr17	33780617	33780656	-	1	NA	exon (NM_020581, exon 3 of 7)	exon (NM_020581, exon 3 of 7)	939	NM_020581	57875	Mm.196189	NM_020581	ENSMUSG00000002289	Angptl4	Arp4|Bk89|Fiaf|Hfarp|Ng27|Pgar|Pgarg|Pp1158	angiopoietin-like 4	protein-coding
mm_32796.1	chr4	117019401	117019437	+	1	NA	promoter-TSS (NM_001111277)	promoter-TSS (NM_001111277)	11	NM_001111277	108067	Mm.34612	NM_175135	ENSMUSG00000028683	Eif2b3	1190002P15Rik	eukaryotic translation initiation factor 2B, subunit 3	protein-coding
mm_26375.1	chr3	142565320	142565399	+	1	NA	exon (NM_018734, exon 5 of 11)	exon (NM_018734, exon 5 of 11)	4863	NM_001289493	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_29629.1	chr3	121548154	121548164	-	1	NA	Intergenic	Intergenic	-15815	NM_145394	213603	Mm.33062	NM_145394	ENSMUSG00000039865	Slc44a3	BC010552	solute carrier family 44, member 3	protein-coding
mm_150744.1	chr19	43783042	43783051	+	1	NA	intron (NM_013806, intron 1 of 31)	B1_Mur3|SINE|Alu	738	NM_013806	12780	Mm.39054	NM_013806	ENSMUSG00000025194	Abcc2	AI173996|Abc30|Cmoat|Mrp2|cMRP	ATP-binding cassette, sub-family C (CFTR/MRP), member 2	protein-coding
mm_154197.1	chr19	58943595	58943648	-	1	NA	promoter-TSS (NM_001327998)	promoter-TSS (NM_001327998)	51	NM_001327998	73442	Mm.39739	NM_175199	ENSMUSG00000025092	Hspa12a	1700063D12Rik|AI118035|AI840429|AW048913|AW556406|D5Mgi40|Gm19925|mKIAA0417	heat shock protein 12A	protein-coding
mm_123572.1	chr14	66911096	66911106	-	1	NA	promoter-TSS (NM_175498)	promoter-TSS (NM_175498)	-107	NM_175498	239157	Mm.44358	NM_175498	ENSMUSG00000046204	Pnma2	A830049P17Rik|mKIAA0883	paraneoplastic antigen MA2	protein-coding
mm_167748.1	chr9	109848424	109848439	+	1	NA	exon (NM_009921, exon 3 of 4)	exon (NM_009921, exon 3 of 4)	1025	NM_009921	12796	Mm.3834	NM_009921	ENSMUSG00000038357	Camp	CAP18|Cnlp|Cramp|FALL39|MCLP	cathelicidin antimicrobial peptide	protein-coding
mm_60506.1	chr7	44479510	44479528	+	1	NA	Intergenic	L1MC4|LINE|L1	-4998	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_143737.1	chr17	81481491	81481495	-	1	NA	intron (NR_104580, intron 2 of 8)	intron (NR_104580, intron 2 of 8)	256894	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_7355.1	chr1	106642265	106642275	-	1	NA	intron (NM_009741, intron 1 of 1)	intron (NM_009741, intron 1 of 1)	72020	NM_009741	12043	Mm.257460	NM_009741	ENSMUSG00000057329	Bcl2	AW986256|Bcl-2|C430015F12Rik|D630044D05Rik|D830018M01Rik	B cell leukemia/lymphoma 2	protein-coding
mm_117684.1	chr13	94246582	94246596	-	1	NA	intron (NM_001346609, intron 2 of 8)	intron (NM_001346609, intron 2 of 8)	38692	NM_029153	107767	Mm.201455	NM_029153	ENSMUSG00000021687	Scamp1	4930505M11Rik|AI415563|AW122395	secretory carrier membrane protein 1	protein-coding
mm_22446.1	chr2	181697830	181697834	-	1	NA	intron (NM_199023, intron 1 of 3)	intron (NM_199023, intron 1 of 3)	610	NM_199023	277496	Mm.212749	NM_199023	ENSMUSG00000045794	Lkaaear1	4930526D03Rik|Gm692	LKAAEAR motif containing 1 (IKAAEAR murine motif)	protein-coding
mm_79657.1	chr9	59656549	59656584	+	1	NA	5' UTR (NM_011099, exon 1 of 11)	5' UTR (NM_011099, exon 1 of 11)	198	NM_001253883	18746	Mm.326167	NM_011099	ENSMUSG00000032294	Pkm	AA414905|AL024370|AL024424|Pk-2|Pk-3|Pk3|Pkm2	pyruvate kinase, muscle	protein-coding
mm_105805.1	chr11	110251694	110251704	-	1	NA	promoter-TSS (NM_147218)	promoter-TSS (NM_147218)	77	NM_147218	76184	Mm.159704	NM_147218	ENSMUSG00000044749	Abca6	6330565N06Rik	ATP-binding cassette, sub-family A (ABC1), member 6	protein-coding
mm_67569.1	chr7	81934293	81934311	-	1	NA	5' UTR (NM_013886, exon 1 of 6)	5' UTR (NM_013886, exon 1 of 6)	157	NM_013886	29877	Mm.392934	NM_013886	ENSMUSG00000025104	Hdgfrp3	2700022B06Rik|HRP-3	hepatoma-derived growth factor, related protein 3	protein-coding
mm_20929.1	chr2	150855919	150855946	-	1	NA	intron (NM_024465, intron 2 of 12)	intron (NM_024465, intron 2 of 12)	48799	NM_024465	76192	Mm.112632	NM_024465	ENSMUSG00000032046	Abhd12	1500011G07Rik|6330583M11Rik|AI431047|AW547313	abhydrolase domain containing 12	protein-coding
mm_82556.1	chr9	20979307	20979315	-	1	NA	Intergenic	RSINE1|SINE|B4	-2518	NM_010333	14739	Mm.46493	NM_010333	ENSMUSG00000043895	S1pr2	1100001A16Rik|Edg5|Gpcr13|H218|LPb2|S1P2	sphingosine-1-phosphate receptor 2	protein-coding
mm_20410.1	chr2	129300163	129300177	-	1	NA	3' UTR (NM_010554, exon 7 of 7)	3' UTR (NM_010554, exon 7 of 7)	2800	NR_040371	100503468	Mm.446943	NR_040371	ENSMUSG00000085498	Gm14023	OTTMUSG00000015408	predicted gene 14023	ncRNA
mm_112020.1	chr12	111377787	111377799	-	1	NA	promoter-TSS (NM_183016)	promoter-TSS (NM_183016)	-75	NM_183016	217866	Mm.27397	NM_183016	ENSMUSG00000021279	Cdc42bpb	MRCKb	CDC42 binding protein kinase beta	protein-coding
mm_64405.1	chr7	142511272	142511315	+	1	NA	exon (NM_001163669, exon 11 of 17)	exon (NM_001163669, exon 11 of 17)	-4522	NR_033261	677289	Mm.350054	NR_033261	ENSMUSG00000043795	Prr33	ENSMUSG00000043795|Gm14492|OTTMUSG00000016823	proline rich 33	ncRNA
mm_125729.1	chr15	73155597	73155606	+	1	NA	intron (NM_153178, intron 1 of 18)	intron (NM_153178, intron 1 of 18)	29346	NM_153178	239528	Mm.23095	NM_153178	ENSMUSG00000036698	Ago2	1110029L17Rik|2310051F07Rik|AI225898|AL022874|AW546247|ENSMUSG00000072493|Eif2c2|Gerp95|Gm10365|mKIAA4215	argonaute RISC catalytic subunit 2	protein-coding
mm_153585.1	chr19	43507000	43507029	-	1	NA	exon (NM_010324, exon 5 of 9)	exon (NM_010324, exon 5 of 9)	17591	NM_010324	14718	Mm.19039	NM_010324	ENSMUSG00000025190	Got1	AI789014|Got-1|cAspAT|cCAT	glutamic-oxaloacetic transaminase 1, soluble	protein-coding
mm_24262.1	chr3	89187476	89187488	+	1	NA	exon (NM_001014995, exon 9 of 12)	exon (NM_001014995, exon 9 of 12)	4257	NM_001014995	68521	Mm.274708	NM_001014995	ENSMUSG00000032657	Fam189b	1110013L07Rik	family with sequence similarity 189, member B	protein-coding
mm_37243.1	chr4	118144280	118144293	-	1	NA	intron (NM_172382, intron 17 of 18)	intron (NM_172382, intron 17 of 18)	-9340	NM_001161774	20441	Mm.251002	NM_009176	ENSMUSG00000028538	St3gal3	ST3GalIII|ST3N|Siat3|Siat6	ST3 beta-galactoside alpha-2,3-sialyltransferase 3	protein-coding
mm_170135.1	chr17	39847707	39847709	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	4711	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_49539.1	chr6	30175816	30175835	+	1	NA	promoter-TSS (NR_038124)	promoter-TSS (NR_038124)	-798	NR_038124	100463519	Mm.361139	NR_038124		BB283400	BF465573|Rncr4	expressed sequence BB283400	ncRNA
mm_1220.1	chr1	62735405	62735426	+	1	NA	intron (NM_001077405, intron 2 of 15)	intron (NM_001077405, intron 2 of 15)	32098	NM_001077405	18187	Mm.266341	NM_010939	ENSMUSG00000025969	Nrp2	1110048P06Rik|Np-2|Np2|Npn-2|Npn2	neuropilin 2	protein-coding
mm_100696.1	chr11	3530047	3530065	-	1	NA	exon (NM_001284429, exon 11 of 22)	exon (NM_001284429, exon 11 of 22)	9236	NM_013870	29856	Mm.188516	NM_013870	ENSMUSG00000020439	Smtn	smsmo	smoothelin	protein-coding
mm_159939.1	chr6	82402282	82402282	+	1	NA	promoter-TSS (NM_009313)	promoter-TSS (NM_009313)	-193	NM_009313	21336	Mm.8055	NM_009313	ENSMUSG00000030043	Tacr1	Nk1r|Spr|Tac1r	tachykinin receptor 1	protein-coding
mm_14904.1	chr2	150305751	150305757	+	1	NA	Intergenic	Intergenic	48237	NM_001142410	100216455	Mm.484816	NM_001142410	ENSMUSG00000079008	Gm14124	EG640962|ENSMUSG00000074735|Gm10749|OTTMUSG00000015734	predicted gene 14124	protein-coding
mm_15449.1	chr2	157403053	157403053	+	1	NA	Intergenic	MLT1D|LTR|ERVL-MaLR	-21240	NM_009271	20779	Mm.22845	NM_009271	ENSMUSG00000027646	Src	AW259666|pp60c-src	Rous sarcoma oncogene	protein-coding
mm_46031.1	chr5	91761681	91761686	-	1	NA	Intergenic	Intergenic	5617	NR_045383	73452	Mm.396233	NR_045383	ENSMUSG00000101978	1700063O14Rik	-	RIKEN cDNA 1700063O14 gene	ncRNA
mm_2808.1	chr1	130865788	130865804	+	1	NA	promoter-TSS (NM_026976)	promoter-TSS (NM_026976)	19	NM_026976	69169	Mm.46042	NM_026976	ENSMUSG00000042474	Fcmr	1810037B05Rik|Faim3|FcmuR|Toso	Fc fragment of IgM receptor	protein-coding
mm_29592.1	chr3	119737720	119737723	-	1	NA	intron (NM_001310711, intron 8 of 13)	intron (NM_001310711, intron 8 of 13)	45667	NM_001310711	56195	Mm.29966	NM_019550	ENSMUSG00000028134	Ptbp2	Ptb2|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding
mm_142232.1	chr17	37481002	37481015	-	1	NA	3' UTR (NM_008204, exon 4 of 4)	3' UTR (NM_008204, exon 4 of 4)	2521	NM_008204	14990	Mm.329041	NM_008204	ENSMUSG00000016283	H2-M2	H-2M2|Thy19.4	histocompatibility 2, M region locus 2	protein-coding
mm_67830.1	chr7	98360436	98360470	-	1	NA	intron (NM_001168541, intron 1 of 3)	intron (NM_001168541, intron 1 of 3)	835	NM_001168540	244152	Mm.25317	NM_001024619	ENSMUSG00000049580	Tsku	9530051K01Rik|E2ig4|Lrrc54|Tsk	tsukushi, small leucine rich proteoglycan	protein-coding
mm_15299.1	chr2	155385891	155385916	+	1	NA	exon (NM_178111, exon 3 of 4)	exon (NM_178111, exon 3 of 4)	4047	NM_178111	68728	Mm.293605	NM_178111	ENSMUSG00000038375	Trp53inp2	1110029F20Rik|Tp53inp2	transformation related protein 53 inducible nuclear protein 2	protein-coding
mm_62232.1	chr7	98563190	98563196	+	1	NA	Intergenic	Intergenic	68971	NM_001113379	434215	Mm.323057	NM_001113379	ENSMUSG00000090958	Lrrc32	AI426318|D11S833Eh|D7H11S833E|EG434215|Garp	leucine rich repeat containing 32	protein-coding
mm_132348.1	chr16	33891937	33891964	+	1	NA	intron (NM_010580, intron 5 of 14)	intron (NM_010580, intron 5 of 14)	62285	NM_001145884	16419	Mm.6424	NM_010580	ENSMUSG00000022817	Itgb5	AA475909|AI874634|ESTM23|[b]-5|[b]5|[b]5A|[b]5B|beta-5|beta5	integrin beta 5	protein-coding
mm_97142.1	chr11	75272080	75272080	+	1	NA	Intergenic	Intergenic	76303	NM_001164223	68275	Mm.102574	NM_026653	ENSMUSG00000000751	Rpa1	5031405K23Rik|70kDa|AA589576|AW557552|RF-A|RP-A|Rpa	replication protein A1	protein-coding
mm_13454.1	chr2	105660774	105660785	+	1	NA	non-coding (NR_117095, exon 1 of 1)	non-coding (NR_117095, exon 1 of 1)	564	NR_117095	103164605	Mm.444995	NR_117095	ENSMUSG00000102424	Paupar	-	Pax6 upstream antisense RNA	ncRNA
mm_127737.1	chr15	103298786	103298808	+	1	NA	3' UTR (NM_019817, exon 9 of 9)	3' UTR (NM_019817, exon 9 of 9)	11641	NM_030720	80910	Mm.160369	NM_030720	ENSMUSG00000063234	Gpr84	EX33	G protein-coupled receptor 84	protein-coding
mm_84972.1	chr9	85323390	85323393	-	1	NA	3' UTR (NM_001160378, exon 3 of 3)	3' UTR (NM_001160378, exon 3 of 3)	3733	NM_001160378	212943	Mm.74610	NM_001160378	ENSMUSG00000032265	Fam46a	BAP014|D930050G01Rik	family with sequence similarity 46, member A	protein-coding
mm_45182.1	chr5	51797222	51797226	-	1	NA	Intergenic	Intergenic	-229499	NR_132764	19017	Mm.259072	NM_008904	ENSMUSG00000029167	Ppargc1a	A830037N07Rik|ENSMUSG00000079510|Gm11133|PGC-1|PPARGC-1-alpha|Pgc-1alpha|Pgc1|Pgco1|Ppargc1	peroxisome proliferative activated receptor, gamma, coactivator 1 alpha	protein-coding
mm_99844.1	chr11	109361936	109361942	+	1	NA	promoter-TSS (NM_010303)	promoter-TSS (NM_010303)	-855	NM_010303	14674	Mm.193925	NM_010303	ENSMUSG00000020611	Gna13	AU024132|AU043124|Galpha13	guanine nucleotide binding protein, alpha 13	protein-coding
mm_79043.1	chr9	46216124	46216132	+	1	NA	intron (NM_027498, intron 21 of 24)	intron (NM_027498, intron 21 of 24)	-12502	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2|apo-AI|apoA-I	apolipoprotein A-I	protein-coding
mm_117890.1	chr13	99422856	99422867	-	1	NA	3' UTR (NM_008634, exon 7 of 7)	3' UTR (NM_008634, exon 7 of 7)	-10035	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_134984.1	chr16	32099698	32099752	-	1	NA	promoter-TSS (NM_025892)	promoter-TSS (NM_025892)	2	NM_001111025	72084	Mm.37613	NM_024464	ENSMUSG00000023791	Pigx	2010319C14Rik|PIG-X	phosphatidylinositol glycan anchor biosynthesis, class X	protein-coding
mm_112435.1	chr13	4725580	4725594	+	1	NA	Intergenic	RMER17A|LTR|ERVK	-116423	NM_018859	56043	Mm.251908	NM_018859	ENSMUSG00000045410	Akr1e1	1810061I10Rik|Akr1e2	aldo-keto reductase family 1, member E1	protein-coding
mm_62475.1	chr7	101863744	101863771	+	1	NA	intron (NM_001252552, intron 4 of 6)	intron (NM_001252552, intron 4 of 6)	-6567	NM_001303239	14276	Mm.439666	NM_008035	ENSMUSG00000032725	Folr2	FBP2|FR-P3|FR-beta|Folbp-2|Folbp2	folate receptor 2 (fetal)	protein-coding
mm_140030.1	chr17	74316464	74316476	+	1	NA	promoter-TSS (NM_001146223)	promoter-TSS (NM_001146223)	-37	NM_001146223	66310	Mm.28536	NM_024428	ENSMUSG00000024067	Dpy30	2810410M20Rik|C87842	dpy-30, histone methyltransferase complex regulatory subunit	protein-coding
mm_49460.1	chr6	29402872	29402921	+	1	NA	intron (NM_001347071, intron 4 of 17)	CpG	3970	NM_001201378	232664	Mm.251303	NM_145574	ENSMUSG00000029769	Ccdc136	4921511K06Rik|BC006583	coiled-coil domain containing 136	protein-coding
mm_15187.1	chr2	154200372	154200385	+	1	NA	promoter-TSS (NM_153418)	promoter-TSS (NM_153418)	-2	NM_153418	228801	Mm.3783	NM_153418	ENSMUSG00000027485	Bpifb1	Lplunc1	BPI fold containing family B, member 1	protein-coding
mm_10545.1	chr2	16565403	16565409	+	1	NA	intron (NM_026162, intron 4 of 13)	intron (NM_026162, intron 4 of 13)	209102	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding
mm_95736.1	chr11	54691423	54691442	+	1	NA	exon (NM_001252494, exon 27 of 29)	exon (NM_001252494, exon 27 of 29)	95286	NM_001252497	192786	Mm.254404	NM_175258	ENSMUSG00000037533	Rapgef6	A530068K01|AI844632|BB085664|C030018K18Rik|PDZ-GEF2|Pdzgef2|RA-GEF-2|Ragef2|mKIAA4052	Rap guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_36902.1	chr4	107803675	107803697	-	1	NA	intron (NR_033496, intron 2 of 20)	CpG-10112	1427	NM_001080926	16975	Mm.442134	NM_053073	ENSMUSG00000028613	Lrp8	4932703M08Rik|AA921429|AI848122|ApoER2|Lr8b	low density lipoprotein receptor-related protein 8, apolipoprotein e receptor	protein-coding
mm_165923.1	chr4	62280379	62280379	+	1	NA	Intergenic	L1MB2|LINE|L1	-6050	NM_025286	20530	Mm.292539	NM_025286	ENSMUSG00000066152	Slc31a2	AI604396|CTR2	solute carrier family 31, member 2	protein-coding
mm_110572.1	chr12	56345863	56345888	-	1	NA	promoter-TSS (NM_145442)	promoter-TSS (NM_145442)	19	NM_145442	217588	Mm.25656	NM_145442	ENSMUSG00000021028	Mbip	4933408E06Rik	MAP3K12 binding inhibitory protein 1	protein-coding
mm_127549.1	chr15	102144716	102144727	+	1	NA	exon (NM_008344, exon 1 of 4)	exon (NM_008344, exon 1 of 4)	535	NM_008344	16012	Mm.358609	NM_008344	ENSMUSG00000023046	Igfbp6	IGFBP-6	insulin-like growth factor binding protein 6	protein-coding
mm_91219.1	chr10	22010110	22010112	-	1	NA	Intergenic	ID_B1|SINE|B4	15445	NM_011361	20393	Mm.28405	NM_011361	ENSMUSG00000019970	Sgk1	Sgk	serum/glucocorticoid regulated kinase 1	protein-coding
mm_145458.1	chr18	60238848	60238893	+	1	NA	intron (NM_001033767, intron 2 of 2)	intron (NM_001033767, intron 2 of 2)	26793	NM_001033767	240327	Mm.357104	NM_001033767	ENSMUSG00000073555	Gm4951	EG240327|Ifgga2	predicted gene 4951	protein-coding
mm_120507.1	chr14	66297030	66297083	+	1	NA	promoter-TSS (NM_029979)	promoter-TSS (NM_029979)	31	NM_029979	66854	Mm.43871	NM_029979	ENSMUSG00000022043	Trim35	0710005M05Rik|A430106H13Rik|AW046487|HLS5|Mair|NC8|mKIAA1098	tripartite motif-containing 35	protein-coding
mm_91254.1	chr10	22820127	22820150	-	1	NA	promoter-TSS (NM_011545)	promoter-TSS (NM_011545)	-10	NM_011545	21412	Mm.16497	NM_011545	ENSMUSG00000045680	Tcf21	Pod-1|Pod1|bHLHa23|capsulin|epc|epicardin	transcription factor 21	protein-coding
mm_29528.1	chr3	116655571	116655575	-	1	NA	intron (NM_008246, intron 1 of 11)	intron (NM_008246, intron 1 of 11)	7104	NM_008246	15247	Mm.280077	NM_008246	ENSMUSG00000089911	Mfsd14a	Hiat1	major facilitator superfamily domain containing 14A	protein-coding
mm_61779.1	chr7	83653859	83653880	+	1	NA	intron (NM_010551, intron 13 of 18)	intron (NM_010551, intron 13 of 18)	21852	NM_023377	170460	Mm.357953	NM_023377	ENSMUSG00000046027	Stard5	2310058G22Rik|AI607880|D7Ertd152e	StAR-related lipid transfer (START) domain containing 5	protein-coding
mm_38417.1	chr4	139131059	139131061	-	1	NA	promoter-TSS (NR_033745)	promoter-TSS (NR_033745)	-23	NR_033745	433771	Mm.305990	NM_001163006	ENSMUSG00000050608	Minos1	2310028O11Rik	mitochondrial inner membrane organizing system 1	protein-coding
mm_78959.1	chr9	45189492	45189514	+	1	NA	intron (NM_145403, intron 2 of 12)	intron (NM_145403, intron 2 of 12)	-6263	NM_001198971	408059	Mm.249297	NM_001198971	ENSMUSG00000091996	BC049352	-	cDNA sequence BC049352	protein-coding
mm_126425.1	chr15	80572538	80572560	+	1	NA	promoter-TSS (NM_001289442)	promoter-TSS (NM_001289442)	-48	NM_001289442	17444	Mm.12947	NM_010815	ENSMUSG00000042351	Grap2	GRAP-2|GRB2L|GRBLG|GRID|Gads|GrbX|Grf40|GrpL|Mona|P38	GRB2-related adaptor protein 2	protein-coding
mm_165105.1	chr19	56397076	56397095	+	1	NA	promoter-TSS (NM_007611)	promoter-TSS (NM_007611)	-44	NM_007611	12369	Mm.35687	NM_007611	ENSMUSG00000025076	Casp7	AI314680|CMH-1|ICE-IAP3|Mch3|caspase-7|mCASP-7	caspase 7	protein-coding
mm_36413.1	chr4	78180890	78180892	-	1	NA	intron (NM_011211, intron 1 of 39)	intron (NM_011211, intron 1 of 39)	31004	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding
mm_138114.1	chr17	34137295	34137311	+	1	NA	exon (NM_010386, exon 3 of 6)	exon (NM_010386, exon 3 of 6)	-8113	NM_010388	15000	Mm.195060	NM_010388	ENSMUSG00000037548	H2-DMb2	H-2Mb2|H2-Mb2	histocompatibility 2, class II, locus Mb2	protein-coding
mm_128349.1	chr15	39857460	39857476	-	1	NA	promoter-TSS (NM_001164466)	promoter-TSS (NM_001164466)	2	NM_001164466	64705	Mm.275974	NM_022722	ENSMUSG00000022304	Dpys	1200017I10Rik|1300004I01Rik|DHP|DHPase	dihydropyrimidinase	protein-coding
mm_138890.1	chr17	43535180	43535228	+	1	NA	intron (NM_001254953, intron 2 of 2)	intron (NM_001254953, intron 2 of 2)	8435	NM_001254953	100043332	Mm.17626	NM_001254953	ENSMUSG00000096140	Ankrd66	AU041848|D730048J04Rik|Gm4368	ankyrin repeat domain 66	protein-coding
mm_133894.1	chr16	97535291	97535319	+	1	NA	promoter-TSS (NR_003508)	promoter-TSS (NR_003508)	-776	NR_003508	17858	Mm.14157	NM_013606	ENSMUSG00000023341	Mx2	AI528743|Mx-2	MX dynamin-like GTPase 2	protein-coding
mm_172796.1	chr9	110960715	110960719	+	1	NA	intron (NM_028838, intron 2 of 8)	intron (NM_028838, intron 2 of 8)	9172	NM_028838	74249	Mm.307615	NM_028838	ENSMUSG00000032495	Lrrc2	2400002D05Rik|4933431K03Rik	leucine rich repeat containing 2	protein-coding
mm_86661.1	chr10	17796275	17796339	+	1	NA	promoter-TSS (NM_138628)	promoter-TSS (NM_138628)	88	NM_138628	378431	Mm.283493	NM_138628	ENSMUSG00000039891	Txlnb	2310001N14Rik|Mdp77	taxilin beta	protein-coding
mm_31197.1	chr4	43664050	43664058	+	1	NA	intron (NM_175517, intron 3 of 6)	intron (NM_175517, intron 3 of 6)	4805	NM_175517	242408	Mm.440423	NM_175517	ENSMUSG00000043633	Fam221b	4930412F15Rik	family with sequence similarity 221, member B	protein-coding
mm_142439.1	chr17	45571504	45571559	-	1	NA	exon (NM_008302, exon 3 of 11)	exon (NM_008302, exon 3 of 11)	1730	NM_008302	15516	Mm.2180	NM_008302	ENSMUSG00000023944	Hsp90ab1	90kDa|AL022974|C81438|Hsp84|Hsp84-1|Hsp90|Hspcb	heat shock protein 90 alpha (cytosolic), class B member 1	protein-coding
mm_147051.1	chr18	34932006	34932009	-	1	NA	promoter-TSS (NM_144866)	promoter-TSS (NM_144866)	-4	NM_144866	225363	Mm.329353	NM_144866	ENSMUSG00000024360	Etf1	AI463371|D6Ertd109e|ERF|ERF1|SUP45L1|TB3-1	eukaryotic translation termination factor 1	protein-coding
mm_93830.1	chr10	121585902	121585910	-	1	NA	intron (NM_019786, intron 1 of 20)	intron (NM_019786, intron 1 of 20)	888	NM_019786	56480	Mm.34580	NM_019786	ENSMUSG00000020115	Tbk1	1200008B05Rik|AI462036|AW048562	TANK-binding kinase 1	protein-coding
mm_117690.1	chr13	94285894	94285901	-	1	NA	promoter-TSS (NM_029153)	promoter-TSS (NM_029153)	-66	NM_001346609	107767	Mm.201455	NM_029153	ENSMUSG00000021687	Scamp1	4930505M11Rik|AI415563|AW122395	secretory carrier membrane protein 1	protein-coding
mm_65823.1	chr7	29176121	29176135	-	1	NA	exon (NM_026545, exon 5 of 7)	exon (NM_026545, exon 5 of 7)	4545	NM_026545	57296	Mm.273152	NM_026545	ENSMUSG00000030591	Psmd8	6720456J22Rik|AA407360|AL033291|AL033322|AL033323|C76433	proteasome (prosome, macropain) 26S subunit, non-ATPase, 8	protein-coding
mm_156471.1	chrX	143518727	143518737	+	1	NA	5' UTR (NM_001195048, exon 1 of 16)	5' UTR (NM_001195048, exon 1 of 16)	141	NM_001195048	18481	Mm.40035	NM_008778	ENSMUSG00000031284	Pak3	PAK-3|Pak65alpha|Pak65beta|Stk4	p21 protein (Cdc42/Rac)-activated kinase 3	protein-coding
mm_106494.1	chr11	120348180	120348189	-	1	NA	promoter-TSS (NR_105900)	promoter-TSS (NR_105900)	311	NM_001313923	11465	Mm.196173	NM_009609	ENSMUSG00000062825	Actg1	AL023024|Actg|Actl|E51	actin, gamma, cytoplasmic 1	protein-coding
mm_63492.1	chr7	127769859	127769863	+	1	NA	promoter-TSS (NM_198424)	promoter-TSS (NM_198424)	46	NM_198424	269999	Mm.36852	NM_198424	ENSMUSG00000043964	Orai3	9930124N15|BC061259|Tmem142c	ORAI calcium release-activated calcium modulator 3	protein-coding
mm_89087.1	chr10	83722882	83722947	+	1	NA	promoter-TSS (NM_001145198)	promoter-TSS (NM_001145198)	49	NM_001145198	69784	Mm.271188	NM_001145198	ENSMUSG00000087651	1500009L16Rik	2700050C19Rik|OCC-1	RIKEN cDNA 1500009L16 gene	protein-coding
mm_56887.1	chr6	119032715	119032726	-	1	NA	intron (NM_001256002, intron 3 of 47)	ID4_|SINE|ID	75775	NM_001159534	12288	Mm.41628	NM_009781	ENSMUSG00000051331	Cacna1c	Cav1.2|Cchl1a1|D930026N18Rik|MBC|MELC-CC	calcium channel, voltage-dependent, L type, alpha 1C subunit	protein-coding
mm_136310.1	chr16	91685638	91685665	-	1	NA	intron (NM_021720, intron 3 of 9)	intron (NM_021720, intron 3 of 9)	3077	NM_021720	60364	Mm.328698	NM_021720	ENSMUSG00000022960	Donson	1110025J21Rik|AI845729|ORF60	downstream neighbor of SON	protein-coding
mm_80212.1	chr9	72461795	72461798	+	1	NA	intron (NM_009359, intron 11 of 11)	intron (NM_009359, intron 11 of 11)	23267	NM_008613	17427	Mm.387671	NM_008613	ENSMUSG00000032221	Mns1	AW546487	meiosis-specific nuclear structural protein 1	protein-coding
mm_148944.1	chr19	7217862	7217868	+	1	NA	promoter-TSS (NM_007750)	promoter-TSS (NM_007750)	-249	NM_007750	12868	Mm.14022	NM_007750	ENSMUSG00000035885	Cox8a	COX8L	cytochrome c oxidase subunit VIIIa	protein-coding
mm_137880.1	chr17	31564949	31564963	+	1	NA	intron (NM_016670, intron 1 of 10)	CpG	183	NM_016670	18771	Mm.259295	NM_016670	ENSMUSG00000006705	Pknox1	D17Wsu76e|PREP1	Pbx/knotted 1 homeobox	protein-coding
mm_61119.1	chr7	54877175	54877224	+	1	NA	intron (NM_178705, intron 1 of 11)	L1_Mur3|LINE|L1	41954	NM_178705	233271	Mm.387344	NM_178705	ENSMUSG00000063297	Luzp2	9330154K17Rik|D130073E01	leucine zipper protein 2	protein-coding
mm_17153.1	chr2	25214629	25214633	-	1	NA	promoter-TSS (NM_028961)	promoter-TSS (NM_028961)	-1	NM_028961	74472	Mm.176944	NM_028961	ENSMUSG00000036770	Stpg3	4933433C11Rik	sperm tail PG rich repeat containing 3	protein-coding
mm_104552.1	chr11	96788989	96789008	-	1	NA	promoter-TSS (NM_007622)	promoter-TSS (NM_007622)	-138	NM_007622	12412	Mm.29055	NM_007622	ENSMUSG00000018666	Cbx1	Cbx|Cbx-rs2|E430007M08Rik|HP1B|Hp1beta|M31|MOD1	chromobox 1	protein-coding
mm_63490.1	chr7	127767505	127767517	+	1	NA	exon (NM_172748, exon 10 of 11)	exon (NM_172748, exon 10 of 11)	-2304	NM_198424	269999	Mm.36852	NM_198424	ENSMUSG00000043964	Orai3	9930124N15|BC061259|Tmem142c	ORAI calcium release-activated calcium modulator 3	protein-coding
mm_128174.1	chr15	34443210	34443227	-	1	NA	promoter-TSS (NR_028101)	promoter-TSS (NR_028101)	7	NM_009083	19946	Mm.358632	NM_009083	ENSMUSG00000058600	Rpl30	-	ribosomal protein L30	protein-coding
mm_53655.1	chr6	141274976	141274991	+	1	NA	intron (NM_018779, intron 1 of 15)	intron (NM_018779, intron 1 of 15)	25714	NM_018779	54611	Mm.103728	NM_018779	ENSMUSG00000041741	Pde3a	A930022O17Rik|C87899	phosphodiesterase 3A, cGMP inhibited	protein-coding
mm_55821.1	chr6	83054380	83054409	-	1	NA	promoter-TSS (NR_125891)	promoter-TSS (NR_125891)	-127	NR_125891	11993	Mm.386752	NM_007517	ENSMUSG00000068328	Aup1	AA589454	ancient ubiquitous protein 1	protein-coding
mm_161789.1	chr17	46028394	46028394	-	1	NA	exon (NM_001025250, exon 2 of 8)	exon (NM_001025250, exon 2 of 8)	-3231	NM_001110268	22339	Mm.282184	NM_009505	ENSMUSG00000023951	Vegfa	Vegf|Vpf	vascular endothelial growth factor A	protein-coding
mm_41333.1	chr5	90495960	90495965	+	1	NA	intron (NM_007423, intron 3 of 14)	intron (NM_007423, intron 3 of 14)	5248	NM_007423	11576	Mm.358570	NM_007423	ENSMUSG00000054932	Afp	-	alpha fetoprotein	protein-coding
mm_147995.1	chr18	67675758	67675769	-	1	NA	exon (NM_001127177, exon 8 of 9)	exon (NM_001127177, exon 8 of 9)	34164	NM_134138	107047	Mm.150701	NM_134138	ENSMUSG00000024537	Psmg2	1700017I17Rik|AW545363|Clast3|Tnfsf5ip1	proteasome (prosome, macropain) assembly chaperone 2	protein-coding
mm_103614.1	chr11	78550675	78550749	-	1	NA	promoter-TSS (NM_133706)	promoter-TSS (NM_133706)	23	NM_133706	69071	Mm.29431	NM_133706	ENSMUSG00000037278	Tmem97	1810014L12Rik|AI115531|AL022956|D11Bhm182e	transmembrane protein 97	protein-coding
mm_50326.1	chr6	48395692	48395713	+	1	NA	5' UTR (NM_133922, exon 1 of 18)	5' UTR (NM_133922, exon 1 of 18)	116	NM_001347153	77827	Mm.107646	NM_133922	ENSMUSG00000042810	Krba1	A930040G15Rik|AI448780	KRAB-A domain containing 1	protein-coding
mm_144244.1	chr18	10726246	10726271	+	1	NA	5' UTR (NM_144860, exon 1 of 21)	5' UTR (NM_144860, exon 1 of 21)	633	NM_144860	225164	Mm.21500	NM_144860	ENSMUSG00000024294	Mib1	DIP-1|E430019M12Rik|Mib|mKIAA1323	mindbomb E3 ubiquitin protein ligase 1	protein-coding
mm_145164.1	chr18	46741002	46741016	+	1	NA	promoter-TSS (NM_009681)	promoter-TSS (NM_009681)	570	NM_026217	67526	Mm.9852	NM_026217	ENSMUSG00000032905	Atg12	4931423H11Rik|A330058M13Rik|Apg12l|Atg12l	autophagy related 12	protein-coding
mm_125152.1	chr15	30646937	30646956	+	1	NA	exon (NM_008729, exon 7 of 23)	exon (NM_008729, exon 7 of 23)	-392180	NR_045186	73784	Mm.66947	NR_045186		4930430F21Rik	-	RIKEN cDNA 4930430F21 gene	ncRNA
mm_82732.1	chr9	25185985	25186025	-	1	NA	Intergenic	L1MC|LINE|L1	-34224	NM_020586	80517	Mm.142843	NM_020586	ENSMUSG00000008429	Herpud2	5031400M07Rik|AB041580	HERPUD family member 2	protein-coding
mm_46939.1	chr5	114813944	114813964	-	1	NA	promoter-TSS (NR_027818)	promoter-TSS (NR_027818)	22	NR_027818	66236	Mm.268546	NR_027817	ENSMUSG00000072694	1500011B03Rik	AI415201|AV141149|AW556386	RIKEN cDNA 1500011B03 gene	ncRNA
mm_99161.1	chr11	100622922	100622970	+	1	NA	promoter-TSS (NM_028024)	promoter-TSS (NM_028024)	-9	NM_028024	71966	Mm.274734	NM_028024	ENSMUSG00000017837	Nkiras2	2410003M04Rik|4930527H08Rik|D630018G21Rik|KBRAS2	NFKB inhibitor interacting Ras-like protein 2	protein-coding
mm_144155.1	chr18	5593567	5593586	+	1	NA	intron (NM_011546, intron 1 of 7)	intron (NM_011546, intron 1 of 7)	-1139	NR_033552	791318	Mm.84339	NR_033552	ENSMUSG00000063087	Gm10125	ENSMUSG00000063087|Zeb1os	predicted gene 10125	ncRNA
mm_156192.1	chrX	134059138	134059213	+	1	NA	promoter-TSS (NM_133196)	promoter-TSS (NM_133196)	-1	NM_001290398	108062	Mm.67938	NM_133196	ENSMUSG00000031256	Cstf2	C630034J23Rik|Cstf64|mir-3112	cleavage stimulation factor, 3' pre-RNA subunit 2	protein-coding
mm_17107.1	chr2	24049390	24049400	-	1	NA	promoter-TSS (NM_080462)	promoter-TSS (NM_080462)	-16	NM_080462	140483	Mm.33120	NM_080462	ENSMUSG00000026986	Hnmt	1500031F01Rik|AI788969	histamine N-methyltransferase	protein-coding
mm_74082.1	chr8	122523650	122523658	+	1	NA	intron (NM_001037298, intron 1 of 50)	intron (NM_001037298, intron 1 of 50)	27675	NM_001037298	234839	Mm.37324	NM_001037298	ENSMUSG00000014444	Piezo1	9630020g22|Fam38a|mKIAA0233	piezo-type mechanosensitive ion channel component 1	protein-coding
mm_24368.1	chr3	90104129	90104143	+	1	NA	promoter-TSS (NM_029937)	promoter-TSS (NM_029937)	4	NM_029937	77595	Mm.159949	NM_029937	ENSMUSG00000027939	Nup210l	4930548O11Rik|R26-EGFP|Tg(Gt(ROSA)26Sor-EGFP)130910Eps	nucleoporin 210-like	protein-coding
mm_151100.1	chr19	47855208	47855225	+	1	NA	exon (NM_010362, exon 2 of 6)	exon (NM_010362, exon 2 of 6)	243	NM_010362	14873	Mm.378931	NM_010362	ENSMUSG00000025068	Gsto1	AA407097|AI194287|AU018802|Gsto-1|Gstx|Spg-r|p28	glutathione S-transferase omega 1	protein-coding
mm_90612.1	chr10	128361389	128361406	+	1	NA	3' UTR (NM_026444, exon 11 of 11)	3' UTR (NM_026444, exon 11 of 11)	8640	NM_001081040	210582	Mm.296876	NM_001081040	ENSMUSG00000039914	Coq10a	Gm1	coenzyme Q10A	protein-coding
mm_117361.1	chr13	70637770	70637825	-	1	NA	promoter-TSS (NM_144837)	promoter-TSS (NM_144837)	-163	NM_144837	218333	Mm.139738	NM_144837	ENSMUSG00000034525	Ice1	C77245|mKIAA0947	interactor of little elongation complex ELL subunit 1	protein-coding
mm_15503.1	chr2	158028548	158028568	+	1	NA	promoter-TSS (NM_027434)	promoter-TSS (NM_027434)	61	NM_001291135	70470	Mm.290810	NM_027434	ENSMUSG00000027651	Rprd1b	2610304G08Rik|2810446G03Rik|Crept	regulation of nuclear pre-mRNA domain containing 1B	protein-coding
mm_88436.1	chr10	77530629	77530642	+	1	NA	intron (NM_008404, intron 1 of 15)	intron (NM_008404, intron 1 of 15)	287	NM_008404	16414	Mm.1137	NM_008404	ENSMUSG00000000290	Itgb2	2E6|AI528527|Cd18|LAD|LCAMB|Lfa1|MF17	integrin beta 2	protein-coding
mm_135876.1	chr16	62881433	62881439	-	1	NA	intron (NM_011173, intron 1 of 14)	intron (NM_011173, intron 1 of 14)	27129	NM_011173	19128	Mm.127156	NM_011173	ENSMUSG00000022912	Pros1	AW214361	protein S (alpha)	protein-coding
mm_20011.1	chr2	119229850	119229877	-	1	NA	promoter-TSS (NM_028104)	promoter-TSS (NM_028104)	2	NM_028104	72112	Mm.46317	NM_028104	ENSMUSG00000027317	Ppp1r14d	2010107K19Rik|GBPI-1|Ppp1r14	protein phosphatase 1, regulatory (inhibitor) subunit 14D	protein-coding
mm_30707.1	chr4	12089374	12089395	+	1	NA	promoter-TSS (NM_198957)	promoter-TSS (NM_198957)	14	NM_198957	77604	Mm.474129	NM_198957	ENSMUSG00000052137	Rbm12b2	AV299215|C430048L16Rik|Rbm12bb	RNA binding motif protein 12 B2	protein-coding
mm_169572.1	chr1	52119438	52119456	+	1	NA	promoter-TSS (NM_001205314)	promoter-TSS (NM_001205314)	9	NM_001205314	20846	Mm.277406	NM_009283	ENSMUSG00000026104	Stat1	2010005J02Rik|AA408197	signal transducer and activator of transcription 1	protein-coding
mm_7737.1	chr1	130876158	130876161	-	1	NA	exon (NM_026976, exon 4 of 8)	exon (NM_026976, exon 4 of 8)	10382	NM_026976	69169	Mm.46042	NM_026976	ENSMUSG00000042474	Fcmr	1810037B05Rik|Faim3|FcmuR|Toso	Fc fragment of IgM receptor	protein-coding
mm_134415.1	chr16	17722469	17722508	-	1	NA	intron (NM_001285886, intron 1 of 16)	intron (NM_001285886, intron 1 of 16)	412	NM_001285886	94112	Mm.208970	NM_033609	ENSMUSG00000012114	Med15	A230074L19Rik|AW536074|Pcqap|mPcqap	mediator complex subunit 15	protein-coding
mm_142222.1	chr17	37185543	37185549	-	1	NA	Intergenic	Intergenic	-8346	NM_023137	24108	Mm.140210	NM_023137	ENSMUSG00000035186	Ubd	FAT10	ubiquitin D	protein-coding
mm_77717.1	chr8	126594004	126594014	-	1	NA	promoter-TSS (NM_001164598)	promoter-TSS (NM_001164598)	-573	NM_001164598	270110	Mm.334918	NM_001164598	ENSMUSG00000051495	Irf2bp2	E130305N23Rik|IRF-2BP2	interferon regulatory factor 2 binding protein 2	protein-coding
mm_46869.1	chr5	113830423	113830506	-	1	NA	promoter-TSS (NM_009151)	promoter-TSS (NM_009151)	37	NM_009151	20345	Mm.332590	NM_009151	ENSMUSG00000048163	Selplg	CD162|Psgl-1|Psgl1|Selp1|Selpl	selectin, platelet (p-selectin) ligand	protein-coding
mm_21336.1	chr2	157105663	157105679	-	1	NA	intron (NM_018851, intron 13 of 15)	intron (NM_018851, intron 13 of 15)	18616	NM_001177439	383766	Mm.480305	NM_001177439	ENSMUSG00000074628	Tldc2	Gm1332	TBC/LysM associated domain containing 2	protein-coding
mm_47362.1	chr5	122899110	122899113	-	1	NA	intron (NM_001003953, intron 12 of 22)	intron (NM_001003953, intron 12 of 22)	1239	NM_013910	30841	Mm.86406	NM_013910	ENSMUSG00000029475	Kdm2b	Cxxc2|Fbl10|Fbxl10|Jhdm1b|PCCX2	lysine (K)-specific demethylase 2B	protein-coding
mm_144632.1	chr18	32939417	32939436	+	1	NA	exon (NM_009793, exon 1 of 11)	exon (NM_009793, exon 1 of 11)	385	NM_009793	12326	Mm.222329	NM_009793	ENSMUSG00000038128	Camk4	A430110E23Rik|AI666733|CaMKIV|CaMKIV/Gr|D18Bwg0362e	calcium/calmodulin-dependent protein kinase IV	protein-coding
mm_59145.1	chr7	24349189	24349201	+	1	NA	promoter-TSS (NM_029806)	promoter-TSS (NM_029806)	-29	NM_029806	76942	Mm.261468	NM_029806	ENSMUSG00000030484	Lypd5	2210003I03Rik	Ly6/Plaur domain containing 5	protein-coding
mm_16541.1	chr2	181656880	181656900	+	1	NA	Intergenic	Intergenic	14750	NM_009236	20672	Mm.264904	NM_009236	ENSMUSG00000046470	Sox18	AI385749|Ra|Ragl	SRY (sex determining region Y)-box 18	protein-coding
mm_91500.1	chr10	37136093	37136101	-	1	NA	3' UTR (NM_008538, exon 2 of 2)	3' UTR (NM_008538, exon 2 of 2)	2829	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_100116.1	chr11	115877498	115877548	+	1	NA	Intergenic	Intergenic	-22616	NM_183259	66528	Mm.275740	NM_183259	ENSMUSG00000048442	Smim5	2210020M01Rik	small integral membrane protein 5	protein-coding
mm_54089.1	chr6	15846079	15846087	-	1	NA	Intergenic	LTR33A_|LTR|ERVL	125422	NM_175088	16543	Mm.1314	NM_175088	ENSMUSG00000041390	Mdfic	Kdt1|Mdfid	MyoD family inhibitor domain containing	protein-coding
mm_32742.1	chr4	116637747	116637757	+	1	NA	intron (NM_021473, intron 8 of 8)	intron (NM_021473, intron 8 of 8)	-9801	NM_016777	50927	Mm.257181	NM_016777	ENSMUSG00000028693	Nasp	5033430J04Rik|AI131596|AI317140|D4Ertd767e|Epcs32|Nasp-T	nuclear autoantigenic sperm protein (histone-binding)	protein-coding
mm_152518.1	chr19	11283882	11283884	-	1	NA	promoter-TSS (NM_183190)	promoter-TSS (NM_183190)	-70	NM_183190	269063	Mm.268940	NM_183190	ENSMUSG00000054523	Ms4a5	-	membrane-spanning 4-domains, subfamily A, member 5	protein-coding
mm_1990.1	chr1	87125932	87125938	+	1	NA	exon (NM_007432, exon 5 of 11)	exon (NM_007432, exon 5 of 11)	927	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_87957.1	chr10	63243786	63243846	+	1	NA	promoter-TSS (NM_026101)	promoter-TSS (NM_026101)	19	NM_026101	67345	Mm.234437	NM_026101	ENSMUSG00000020064	Herc4	1700056O17Rik|4921531D01Rik|9530080M15Rik|mKIAA1593	hect domain and RLD 4	protein-coding
mm_112759.1	chr13	19347087	19347090	+	1	NA	Intergenic	B1_Mur1|SINE|Alu	48725	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_79553.1	chr9	57998037	57998058	+	1	NA	promoter-TSS (NM_001346787)	promoter-TSS (NM_001346787)	23	NM_001346787	13070	Mm.302865	NM_019779	ENSMUSG00000032323	Cyp11a1	Cyp11a|Cypxia1|D9Ertd411e|P450scc|Scc|cscc	cytochrome P450, family 11, subfamily a, polypeptide 1	protein-coding
mm_88833.1	chr10	80806831	80806840	+	1	NA	exon (NM_007445, exon 5 of 5)	exon (NM_007445, exon 5 of 5)	1587	NM_007445	11705	Mm.376094	NM_007445	ENSMUSG00000035262	Amh	MIS	anti-Mullerian hormone	protein-coding
mm_31006.1	chr4	40184951	40184989	+	1	NA	exon (NM_007386, exon 14 of 21)	exon (NM_007386, exon 14 of 21)	41705	NM_007386	11428	Mm.331547	NM_007386	ENSMUSG00000028405	Aco1	Aco-1|Irebp|Irp1	aconitase 1	protein-coding
mm_147024.1	chr18	34651696	34651702	-	1	NA	promoter-TSS (NM_178347)	promoter-TSS (NM_178347)	37	NM_178347	52563	Mm.196638	NM_178347	ENSMUSG00000024370	Cdc23	6030435O18|D18Ertd243e	CDC23 cell division cycle 23	protein-coding
mm_104567.1	chr11	96916449	96916531	-	1	NA	promoter-TSS (NM_030248)	promoter-TSS (NM_030248)	24	NM_001308183	80280	Mm.28297	NM_030248	ENSMUSG00000018669	Cdk5rap3	1810007E24Rik|BC002318|C53|C81486|HSF-27|IC53|LZAP|MST016	CDK5 regulatory subunit associated protein 3	protein-coding
mm_110402.1	chr12	44268996	44269007	-	1	NA	promoter-TSS (NM_026164)	promoter-TSS (NM_026164)	-153	NM_026164	67452	Mm.54126	NM_026164	ENSMUSG00000036257	Pnpla8	1200006O19Rik|AI467579|Ipla2(gamma)	patatin-like phospholipase domain containing 8	protein-coding
mm_34019.1	chr4	138017315	138017345	+	1	NA	intron (NM_172703, intron 2 of 34)	intron (NM_172703, intron 2 of 34)	23874	NM_172703	230861	Mm.268903	NM_172703	ENSMUSG00000028760	Eif4g3	1500002J22Rik|4930523M17Rik|G1-419-52|eIF4GII|repro8	eukaryotic translation initiation factor 4 gamma, 3	protein-coding
mm_85061.1	chr9	90243122	90243133	-	1	NA	intron (NM_194334, intron 2 of 12)	intron (NM_194334, intron 2 of 12)	27642	NM_194334	67016	Mm.335347	NM_194334	ENSMUSG00000037410	Tbc1d2b	1810061M12Rik|AI480956|AV021536|AV023399|AW491493|mKIAA1055	TBC1 domain family, member 2B	protein-coding
mm_153699.1	chr19	44397544	44397554	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	10160	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_94983.1	chr11	31831793	31831798	+	1	NA	Intergenic	Intergenic	-7248	NR_102312	414116	Mm.150222	NR_102310	ENSMUSG00000085772	D630024D03Rik	-	RIKEN cDNA D630024D03 gene	ncRNA
mm_130976.1	chr15	103340103	103340125	-	1	NA	promoter-TSS (NM_013866)	promoter-TSS (NM_013866)	-28	NM_013866	29813	Mm.14099	NM_013866	ENSMUSG00000000552	Zfp385a	Hzf|Zfp385|Znf385a	zinc finger protein 385A	protein-coding
mm_147889.1	chr18	64999373	64999380	-	1	NA	intron (NM_001114386, intron 2 of 30)	intron (NM_001114386, intron 2 of 30)	-24151	NM_031881	83814	Mm.98668	NM_031881	ENSMUSG00000024589	Nedd4l	1300012C07Rik|Nedd4-2|Nedd4b	neural precursor cell expressed, developmentally down-regulated gene 4-like	protein-coding
mm_78362.1	chr9	26733846	26733856	+	1	NA	promoter-TSS (NM_001310766)	promoter-TSS (NM_001310766)	43	NM_001310766	76898	Mm.218788	NM_029792	ENSMUSG00000045994	B3gat1	0710007K08Rik|AI846286|GlcAT-P|Glcatp|Hnk1	beta-1,3-glucuronyltransferase 1 (glucuronosyltransferase P)	protein-coding
mm_59503.1	chr7	27556682	27556684	+	1	NA	intron (NM_175107, intron 2 of 9)	intron (NM_175107, intron 2 of 9)	3393	NM_175107	66367	Mm.29831	NM_175107	ENSMUSG00000049643	2310022A10Rik	-	RIKEN cDNA 2310022A10 gene	protein-coding
mm_73804.1	chr8	117307733	117307736	+	1	NA	intron (NM_001163262, intron 1 of 20)	intron (NM_001163262, intron 1 of 20)	-41436	NM_028941	74440	Mm.233181	NM_028941	ENSMUSG00000034390	Cmip	4933407C03Rik|5830471E12Rik|AI314065|AI464126	c-Maf inducing protein	protein-coding
mm_44911.1	chr5	35663778	35663789	-	1	NA	intron (NM_001042615, intron 6 of 6)	intron (NM_001042615, intron 6 of 6)	15997	NM_001042615	78558	Mm.274255	NM_030127	ENSMUSG00000029096	Htra3	2210021K23Rik|9530081K03Rik|Prsp|Tasp	HtrA serine peptidase 3	protein-coding
mm_73325.1	chr8	105276433	105276436	+	1	NA	promoter-TSS (NM_030152)	promoter-TSS (NM_030152)	-13	NM_030152	78688	Mm.475715	NM_030152	ENSMUSG00000014776	Nol3	ARC|B430311C09Rik|MYC|NOP|Nop30	nucleolar protein 3 (apoptosis repressor with CARD domain)	protein-coding
mm_160137.1	chr7	30821671	30821671	-	1	NA	promoter-TSS (NM_001168512)	promoter-TSS (NM_001168512)	-23	NM_001168509	233079	Mm.97338	NM_146187	ENSMUSG00000051314	Ffar2	GPCR43|Gpr43	free fatty acid receptor 2	protein-coding
mm_33971.1	chr4	137614540	137614543	+	1	NA	intron (NM_130879, intron 9 of 27)	AT_rich|Low_complexity|Low_complexity	20352	NM_130879	170707	Mm.218478	NM_130879	ENSMUSG00000043411	Usp48	2810449C13Rik|AI115503|BC021769|D330022K21Rik|Usp31	ubiquitin specific peptidase 48	protein-coding
mm_63389.1	chr7	127233045	127233073	+	1	NA	promoter-TSS (NM_146201)	promoter-TSS (NM_146201)	71	NR_030674	100043580	Mm.482209	NR_030674	ENSMUSG00000000486	Gm4532	-	predicted gene 4532	ncRNA
mm_34353.1	chr4	144613641	144613653	+	1	NA	promoter-TSS (NM_001081248)	promoter-TSS (NM_001081248)	-60	NM_001081248	435815	Mm.439623	NM_001081248	ENSMUSG00000070609	Gm13177	OTTMUSG00000010747	predicted gene 13177	protein-coding
mm_54397.1	chr6	31480118	31480139	-	1	NA	intron (NM_013791, intron 12 of 17)	intron (NM_013791, intron 12 of 17)	81300	NM_013791	27418	Mm.238038	NM_013791	ENSMUSG00000025609	Mkln1	A130067F06Rik|AU015903|BB154892	muskelin 1, intracellular mediator containing kelch motifs	protein-coding
mm_46958.1	chr5	115103541	115103560	-	1	NA	intron (NM_001271590, intron 1 of 1)	intron (NM_001271590, intron 1 of 1)	4412	NM_001271591	100502825	Mm.361657	NM_001271590		Rpl37rt	Gm13826|OTTMUSG00000014624	ribosomal protein L37, retrotransposed	protein-coding
mm_36088.1	chr4	58444117	58444120	-	1	NA	intron (NM_001290486, intron 2 of 2)	intron (NM_001290486, intron 2 of 2)	-3020	NR_037278	100526502		NR_037278	ENSMUSG00000093293	Mir3095	mir-3095|mmu-mir-3095	microRNA 3095	ncRNA
mm_90319.1	chr10	127064207	127064244	+	1	NA	5' UTR (NM_009870, exon 2 of 8)	5' UTR (NM_009870, exon 2 of 8)	622	NM_009870	12567	Mm.6839	NM_009870	ENSMUSG00000006728	Cdk4	Crk3	cyclin-dependent kinase 4	protein-coding
mm_121779.1	chr14	19890590	19890608	-	1	NA	intron (NM_001038637, intron 4 of 4)	B4A|SINE|B4	51674	NR_105025	52512	Mm.483998	NR_105025		D14Ertd670e	-	DNA segment, Chr 14, ERATO Doi 670, expressed	ncRNA
mm_104349.1	chr11	94296964	94296983	-	1	NA	exon (NM_026313, exon 8 of 11)	exon (NM_026313, exon 8 of 11)	24938	NM_026313	67684	Mm.30927	NM_026313	ENSMUSG00000020863	Luc7l3	3300001P08Rik|Luc7a	LUC7-like 3 (S. cerevisiae)	protein-coding
mm_21414.1	chr2	158124146	158124182	-	1	NA	exon (NM_009373, exon 10 of 13)	exon (NM_009373, exon 10 of 13)	22228	NM_009373	21817	Mm.330731	NM_009373	ENSMUSG00000037820	Tgm2	G[a]h|TG2|TGase2|tTG|tTGas	transglutaminase 2, C polypeptide	protein-coding
mm_159590.1	chr4	123323587	123323587	-	1	NA	promoter-TSS (NM_022033)	promoter-TSS (NM_022033)	92	NM_022033	64059	Mm.270287	NM_022033	ENSMUSG00000076436	Oxct2a	Oxct|Oxct2|Scot|Scot-t1	3-oxoacid CoA transferase 2A	protein-coding
mm_99399.1	chr11	102189771	102189791	+	1	NA	promoter-TSS (NM_175935)	promoter-TSS (NM_175935)	82	NM_175935	68401	Mm.22385	NM_175935	ENSMUSG00000034793	G6pc3	0710001K01Rik|AU019276|AU045429|AV128920|AW545836|UGRP	glucose 6 phosphatase, catalytic, 3	protein-coding
mm_158770.1	chrX	166618661	166618666	-	1	NA	Intergenic	MLTR25A|LTR|ERVK	-32947	NM_019397	54156	Mm.37707	NM_019397	ENSMUSG00000000402	Egfl6	Maeg	EGF-like-domain, multiple 6	protein-coding
mm_122359.1	chr14	39223336	39223341	-	1	NA	intron (NM_001190187, intron 1 of 9)	intron (NM_001190187, intron 1 of 9)	-249091	NR_131973	432842	Mm.352566	NR_131973		LOC432842	-	uncharacterized LOC432842	ncRNA
mm_34616.1	chr4	150406618	150406643	+	1	NA	exon (NM_001085492, exon 2 of 23)	exon (NM_001085492, exon 2 of 23)	124714	NM_001085492	68703	Mm.291274	NM_001085492	ENSMUSG00000039852	Rere	1110033A15Rik|AI414665|ARG|ARP|ATN1L|AW742570|Atr2|DNB1|eye<m03Jus>|eyes3|mKIAA0458	arginine glutamic acid dipeptide (RE) repeats	protein-coding
mm_14424.1	chr2	130503982	130503986	+	1	NA	intron (NM_001163688, intron 2 of 20)	intron (NM_001163688, intron 2 of 20)	53706	NM_001163688	19262	Mm.224246	NM_008980	ENSMUSG00000027303	Ptpra	Ptpa|Ptpalpha|Rptpalpha|Rptra|Rptralpha	protein tyrosine phosphatase, receptor type, A	protein-coding
mm_40449.1	chr5	53596117	53596133	+	1	NA	intron (NM_001080927, intron 1 of 10)	(GGGAGA)n|Simple_repeat|Simple_repeat	5639	NM_001080927	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_12296.1	chr2	69075523	69075536	+	1	NA	intron (NM_172856, intron 8 of 9)	RMER5|LTR|ERV1	-60271	NM_181547	329416	Mm.90047	NM_181547	ENSMUSG00000034738	Nostrin	Daip2|mDaIP2	nitric oxide synthase trafficker	protein-coding
mm_66357.1	chr7	43527909	43527929	-	1	NA	3' UTR (NM_001111058, exon 7 of 7)	3' UTR (NM_001111058, exon 7 of 7)	5252	NM_001111058	12489	Mm.140157	NM_021293	ENSMUSG00000004609	Cd33	Siglec-3|gp67	CD33 antigen	protein-coding
mm_134213.1	chr16	11200380	11200384	-	1	NA	intron (NM_025546, intron 3 of 8)	B1_Mus1|SINE|Alu	2910	NM_025546	66409	Mm.28291	NM_025546	ENSMUSG00000005846	Rsl1d1	2410005K20Rik|C76439|pBK1	ribosomal L1 domain containing 1	protein-coding
mm_144259.1	chr18	11052459	11052479	+	1	NA	promoter-TSS (NR_105023)	promoter-TSS (NR_105023)	-41	NM_010258	14465	Mm.329287	NM_010258	ENSMUSG00000005836	Gata6	AA410133|GATA-6	GATA binding protein 6	protein-coding
mm_166133.1	chr4	155625231	155625240	+	1	NA	promoter-TSS (NR_040441)	promoter-TSS (NR_040441)	366	NM_007661	12537	Mm.267410	NM_007661	ENSMUSG00000029062	Cdk11b	AA989746|CDK11-p110|CDK11-p46|CDK11-p58|Cdc11b|Cdc2l1|Cdc2l2|Cdk11|p58	cyclin-dependent kinase 11B	protein-coding
mm_66444.1	chr7	44854529	44854548	-	1	NA	intron (NM_026270, intron 4 of 4)	CpG	-2608	NM_021549	59047	Mm.238254	NM_021549	ENSMUSG00000002963	Pnkp	1810009G08Rik|PNK	polynucleotide kinase 3'- phosphatase	protein-coding
mm_31515.1	chr4	53832571	53832582	+	1	NA	intron (NM_028053, intron 1 of 5)	intron (NM_028053, intron 1 of 5)	6531	NM_028053	52076	Mm.27184	NM_028053	ENSMUSG00000028420	Tmem38b	1600017F22Rik|AA437809|AV051057|D4Ertd89e|TRIC-B|mg33b	transmembrane protein 38B	protein-coding
mm_121564.1	chr14	122534306	122534367	+	1	NA	promoter-TSS (NM_144844)	promoter-TSS (NM_144844)	8	NM_144844	110821	Mm.23876	NM_144844	ENSMUSG00000041650	Pcca	C79630	propionyl-Coenzyme A carboxylase, alpha polypeptide	protein-coding
mm_162637.1	chr1	191280828	191280829	-	1	NA	Intergenic	Intergenic	37290	NM_025424	66208	Mm.46444	NM_025424	ENSMUSG00000037499	Nenf	1110060M21Rik|SCIRP10|Spuf	neuron derived neurotrophic factor	protein-coding
mm_99551.1	chr11	103445547	103445550	+	1	NA	Intergenic	RMER3D-int|LTR|ERVK	-32884	NM_183034	353047	Mm.18556	NM_183034	ENSMUSG00000034247	Plekhm1	AP162|B2|BC038943|D330036J23Rik	pleckstrin homology domain containing, family M (with RUN domain) member 1	protein-coding
mm_128582.1	chr15	58034290	58034298	-	1	NA	promoter-TSS (NM_029418)	promoter-TSS (NM_029418)	0	NM_029418	75758	Mm.455792	NM_029418	ENSMUSG00000101892	9130401M01Rik	AI849328	RIKEN cDNA 9130401M01 gene	protein-coding
mm_84821.1	chr9	77707848	77707871	-	1	NA	Intergenic	Intergenic	-46676	NM_010295	14629	Mm.89888	NM_010295	ENSMUSG00000032350	Gclc	D9Wsu168e|GLCL-H|Ggcs-hs|Glclc	glutamate-cysteine ligase, catalytic subunit	protein-coding
mm_32485.1	chr4	107890274	107890295	+	1	NA	intron (NM_001347160, intron 2 of 7)	intron (NM_001347160, intron 2 of 7)	385	NM_028754	74098	Mm.274853	NM_028754	ENSMUSG00000028608	0610037L13Rik	1110008H16Rik	RIKEN cDNA 0610037L13 gene	protein-coding
mm_63468.1	chr7	127585314	127585326	+	1	NA	intron (NM_001033040, intron 5 of 8)	intron (NM_001033040, intron 5 of 8)	3275	NM_001033040	233899	Mm.25220	NM_001033040	ENSMUSG00000057176	Ccdc189	Gm166	coiled-coil domain containing 189	protein-coding
mm_990.1	chr1	58652589	58652626	+	1	NA	promoter-TSS (NR_045007)	promoter-TSS (NR_045007)	-34	NR_045007	100504501	Mm.440933	NR_045007	ENSMUSG00000102059	Gm20257	-	caspase 8 pseudogene	pseudo
mm_161522.1	chr15	100353188	100353188	+	1	NA	promoter-TSS (NM_001024672)	promoter-TSS (NM_001024672)	-12	NM_001024672	554292	Mm.268451	NM_001024672	ENSMUSG00000093789	Methig1	Mettl7a2-Higd1c|Mettl7a2Higd1c|Mettl7a2higd1c|UbiE-YGHL1	methyltransferase hypoxia inducible domain containing 1	protein-coding
mm_104232.1	chr11	88643549	88643552	-	1	NA	intron (NM_054043, intron 5 of 13)	intron (NM_054043, intron 5 of 13)	24299	NR_131025	68397	Mm.426889	NR_131025		0610039H22Rik	-	RIKEN cDNA 0610039H22 gene	ncRNA
mm_36795.1	chr4	103114563	103114578	-	1	NA	promoter-TSS (NM_146254)	promoter-TSS (NM_146254)	180	NM_001286222	71148	Mm.288721	NM_027696	ENSMUSG00000028522	Mier1	4933425I22Rik|5830411K19Rik|er1	MEIR1 treanscription regulator	protein-coding
mm_66349.1	chr7	43518563	43518572	-	1	NA	Intergenic	Intergenic	-12629	NM_028737	74054	Mm.195732	NM_028737	ENSMUSG00000013353	4931406B18Rik	4930538L19Rik	RIKEN cDNA 4931406B18 gene	protein-coding
mm_15476.1	chr2	157560665	157560675	+	1	NA	intron (NM_001291128, intron 2 of 2)	intron (NM_001291128, intron 2 of 2)	592	NM_180960	18111	Mm.34330	NM_010923	ENSMUSG00000067786	Nnat	5730414I02Rik|AW107673|Peg5	neuronatin	protein-coding
mm_122280.1	chr14	34502523	34502574	-	1	NA	promoter-TSS (NM_009758)	promoter-TSS (NM_009758)	-2	NM_009758	12166	Mm.237825	NM_009758	ENSMUSG00000021796	Bmpr1a	1110037I22Rik|ALK3|AU045487|BMPR-IA|Bmpr	bone morphogenetic protein receptor, type 1A	protein-coding
mm_137282.1	chr17	24728250	24728259	+	1	NA	intron (NM_001163945, intron 1 of 9)	intron (NM_001163945, intron 1 of 9)	425	NM_001163945	66211	Mm.46198	NM_025425	ENSMUSG00000002500	Rpl3l	1110057H16Rik	ribosomal protein L3-like	protein-coding
mm_102795.1	chr11	68838746	68838752	-	1	NA	intron (NM_023668, intron 5 of 8)	A-rich|Low_complexity|Low_complexity	14382	NM_023668	83431	Mm.31979	NM_023668	ENSMUSG00000018736	Ndel1	2600006O07Rik|MITAP1|NUDEL|mNudel	nudE neurodevelopment protein 1 like 1	protein-coding
mm_130971.1	chr15	103323496	103323566	-	1	NA	intron (NM_013866, intron 2 of 7)	CpG	-13093	NM_030720	80910	Mm.160369	NM_030720	ENSMUSG00000063234	Gpr84	EX33	G protein-coupled receptor 84	protein-coding
mm_18707.1	chr2	71873051	71873092	-	1	NA	promoter-TSS (NM_172665)	promoter-TSS (NM_172665)	-153	NM_172665	228026	Mm.34411	NM_172665	ENSMUSG00000006494	Pdk1	B830012B01|D530020C15Rik	pyruvate dehydrogenase kinase, isoenzyme 1	protein-coding
mm_5369.1	chr1	28895581	28895607	-	1	NA	Intergenic	B3A|SINE|B2	-115342	NM_001013750	210962	Mm.214178	NM_001013750	ENSMUSG00000048411	Gm597	-	predicted gene 597	protein-coding
mm_57077.1	chr6	122581429	122581454	-	1	NA	exon (NM_031159, exon 6 of 8)	exon (NM_031159, exon 6 of 8)	21003	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_18689.1	chr2	71529656	71529668	-	1	NA	TTS (NR_002854)	TTS (NR_002854)	217	NM_010053	13390	Mm.475101	NM_010053	ENSMUSG00000041911	Dlx1	Dlx|Dlx-1	distal-less homeobox 1	protein-coding
mm_13528.1	chr2	110135057	110135060	+	1	NA	Intergenic	Intergenic	-84579	NR_040508	75517	Mm.363927	NR_040508	ENSMUSG00000086186	Ccdc34os	1700024P03Rik	coiled-coil domain containing 34, opposite strand	ncRNA
mm_87496.1	chr10	51526330	51526360	+	1	NA	Intergenic	LTRIS2|LTR|ERV1	35447	NM_013532	14728	Mm.34408	NM_013532	ENSMUSG00000062593	Lilrb4a	CD85K|Gp49b|HM18|ILT3|LIR-5|Lilrb4|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4A	protein-coding
mm_7906.1	chr1	133661388	133661399	-	1	NA	promoter-TSS (NM_001166552)	promoter-TSS (NM_001166552)	6	NM_001276767	70579	Mm.245357	NM_144530	ENSMUSG00000102976	Zc3h11a	1110003F06Rik|5730454B08Rik|G630041M05Rik|Zc3hdc11a|Zc3hh11a|mKIAA0663	zinc finger CCCH type containing 11A	protein-coding
mm_54715.1	chr6	39810882	39810905	-	1	NA	promoter-TSS (NM_010270)	promoter-TSS (NM_010270)	43	NM_010270	14548	Mm.377071	NM_010270	ENSMUSG00000029918	Mrps33	AI841153|CGI-139|Gdap3|MRP-S33|PTD003	mitochondrial ribosomal protein S33	protein-coding
mm_152523.1	chr19	11314424	11314434	-	1	NA	Intergenic	Intergenic	20266	NM_001276398	109225	Mm.491251	NM_027836	ENSMUSG00000024672	Ms4a7	9130422I10Rik|A430103C15Rik|CD20l4|CFFMA	membrane-spanning 4-domains, subfamily A, member 7	protein-coding
mm_145063.1	chr18	40523097	40523107	+	1	NA	intron (NM_026135, intron 1 of 1)	intron (NM_026135, intron 1 of 1)	264741	NM_026135	383348	Mm.76366	NM_026135	ENSMUSG00000051401	Kctd16	4930434H12Rik|Gm1267	potassium channel tetramerisation domain containing 16	protein-coding
mm_25605.1	chr3	117575269	117575282	+	1	NA	promoter-TSS (NM_029425)	promoter-TSS (NM_029425)	48	NM_001305451	75769	Mm.72187	NM_029425	ENSMUSG00000033342	Plppr5	4833424O15Rik|Lppr5|PRG-5|Pap2d	phospholipid phosphatase related 5	protein-coding
mm_6517.1	chr1	74395580	74395590	-	1	NA	3' UTR (NM_153088, exon 7 of 7)	3' UTR (NM_153088, exon 7 of 7)	1275	NR_029743	387219		NR_029743	ENSMUSG00000065468	Mir26b	Mirn26b|mir-26b|mmu-mir-26b	microRNA 26b	ncRNA
mm_78120.1	chr9	20643608	20643634	+	1	NA	promoter-TSS (NM_013911)	promoter-TSS (NM_013911)	303	NM_025401	66177	Mm.390165	NM_025401	ENSMUSG00000084786	Ubl5	1110030M22Rik|beacon	ubiquitin-like 5	protein-coding
mm_77465.1	chr8	122425018	122425028	-	1	NA	exon (NM_007806, exon 6 of 6)	exon (NM_007806, exon 6 of 6)	2938	NM_145834	234836	Mm.222808	NM_145834	ENSMUSG00000046108	Il17c	IL-17C	interleukin 17C	protein-coding
mm_128093.1	chr15	27788541	27788558	-	1	NA	intron (NM_001081302, intron 34 of 56)	intron (NM_001081302, intron 34 of 56)	-107007	NM_001242423	223433	Mm.266485	NM_198301	ENSMUSG00000056069	Fam105a	9830126M18	family with sequence similarity 105, member A	protein-coding
mm_118732.1	chr14	22252948	22252969	+	1	NA	intron (NM_028275, intron 2 of 6)	(TTTTG)n|Simple_repeat|Simple_repeat	233246	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_119810.1	chr14	54222775	54222789	+	1	NA	Intergenic	Intergenic	31147	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_135950.1	chr16	74411808	74411832	-	1	NA	promoter-TSS (NM_175549)	promoter-TSS (NM_175549)	-908	NM_175549	268902	Mm.171736	NM_175549	ENSMUSG00000052516	Robo2	2600013A04Rik|9430089E08Rik|BB097918|D230004I22Rik|mKIAA1568	roundabout guidance receptor 2	protein-coding
mm_138416.1	chr17	35069373	35069386	+	1	NA	exon (NM_023463, exon 3 of 3)	exon (NM_023463, exon 3 of 3)	2054	NM_023463	68468	Mm.215096	NM_023463	ENSMUSG00000092586	Ly6g6c	1110003M04Rik|AU016360|G6c|NG24	lymphocyte antigen 6 complex, locus G6C	protein-coding
mm_13516.1	chr2	109917680	109917686	+	1	NA	promoter-TSS (NM_172671)	promoter-TSS (NM_172671)	36	NM_172671	107515	Mm.277351	NM_172671	ENSMUSG00000050199	Lgr4	9130225G07|A330106J01Rik|A930009A08Rik|Gpr48	leucine-rich repeat-containing G protein-coupled receptor 4	protein-coding
mm_89814.1	chr10	103369377	103369381	+	1	NA	5' UTR (NM_175328, exon 2 of 13)	5' UTR (NM_175328, exon 2 of 13)	1571	NM_175328	103098	Mm.458408	NM_175328	ENSMUSG00000019894	Slc6a15	AA536730|AI326450|AI326451|v7-3	solute carrier family 6 (neurotransmitter transporter), member 15	protein-coding
mm_136899.1	chr17	13015129	13015140	+	1	NA	exon (NM_013671, exon 5 of 5)	exon (NM_013671, exon 5 of 5)	7295	NM_013671	20656	Mm.290876	NM_013671	ENSMUSG00000006818	Sod2	MnSOD|Sod-2	superoxide dismutase 2, mitochondrial	protein-coding
mm_80334.1	chr9	75052084	75052090	+	1	NA	intron (NM_021548, intron 1 of 2)	intron (NM_021548, intron 1 of 2)	14355	NM_021548	59046	Mm.247837	NM_021548	ENSMUSG00000007656	Arpp19	19kDa|2700024H10Rik|ARPP-19|AW559096|Arpp12	cAMP-regulated phosphoprotein 19	protein-coding
mm_79153.1	chr9	47745403	47745408	+	1	NA	intron (NM_001025600, intron 1 of 8)	intron (NM_001025600, intron 1 of 8)	72803	NR_046048	100038460	Mm.447649	NR_046048		Gm10677	ENSMUSG00000074363	predicted gene 10677	ncRNA
mm_83104.1	chr9	40345217	40345221	-	1	NA	intron (NM_172768, intron 2 of 19)	intron (NM_172768, intron 2 of 19)	11747	NR_040728	73558	Mm.398307	NR_040728		1700110K17Rik	-	RIKEN cDNA 1700110K17 gene	ncRNA
mm_72917.1	chr8	91073974	91073994	+	1	NA	intron (NM_011250, intron 1 of 21)	MLT1G3|LTR|ERVL-MaLR	3927	NM_001282000	19651	Mm.235580	NM_011250	ENSMUSG00000031666	Rbl2	PRB2|RBR-2|Rb2|p130	retinoblastoma-like 2	protein-coding
mm_150862.1	chr19	45017430	45017485	+	1	NA	promoter-TSS (NM_001130526)	promoter-TSS (NM_001130526)	-678	NM_001130526	226154	Mm.28204	NM_145503	ENSMUSG00000035342	Lzts2	BC014695|LAPSER1|mKIAA1813	leucine zipper, putative tumor suppressor 2	protein-coding
mm_134054.1	chr16	5949935	5949945	-	1	NA	intron (NM_021477, intron 1 of 16)	intron (NM_021477, intron 1 of 16)	-25647	NR_045799	68238	Mm.434605	NR_045799	ENSMUSG00000101481	1700123O21Rik	-	RIKEN cDNA 1700123O21 gene	ncRNA
mm_150806.1	chr19	44333855	44333866	+	1	NA	intron (NM_183216, intron 1 of 5)	intron (NM_183216, intron 1 of 5)	534	NM_183216	329065	Mm.313583	NM_183216	ENSMUSG00000050195	Scd4	ACOD4	stearoyl-coenzyme A desaturase 4	protein-coding
mm_169524.1	chr14	90085257	90085271	-	1	NA	Intergenic	ERVB4_2-LTR_MM|LTR|ERVK	-41627	NR_045712	74967	Mm.390704	NR_045712		4930474H20Rik	-	RIKEN cDNA 4930474H20 gene	ncRNA
mm_135899.1	chr16	66744589	66744601	-	1	NA	intron (NM_001347247, intron 7 of 9)	RSINE1|SINE|B4	87477	NR_040512	75501	Mm.394300	NR_040512	ENSMUSG00000092599	1700010K23Rik	-	RIKEN cDNA 1700010K23 gene	ncRNA
mm_2593.1	chr1	119453953	119453961	+	1	NA	Intergenic	Intergenic	-31709	NM_008381	16324	Mm.3092	NM_008381	ENSMUSG00000037035	Inhbb	-	inhibin beta-B	protein-coding
mm_39105.1	chr4	154921767	154921778	-	1	NA	TTS (NM_178931)	TTS (NM_178931)	6305	NM_178931	230979	Mm.215147	NM_178931	ENSMUSG00000042333	Tnfrsf14	Atar|HveA|Hvem|Tnfrs14	tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)	protein-coding
mm_10097.1	chr2	3439310	3439330	+	1	NA	intron (NM_001302684, intron 8 of 14)	B4|SINE|B4	15189	NM_001302684	227525	Mm.23483	NM_146114	ENSMUSG00000026648	Dclre1c	9930121L06Rik|AI661365|Art|Snm1l	DNA cross-link repair 1C	protein-coding
mm_164711.1	chr17	53565900	53565902	+	1	NA	Intergenic	B1_Mur1|SINE|Alu	-1070	NM_020005	18519	Mm.255025	NM_020005	ENSMUSG00000000708	Kat2b	A930006P13Rik|AI461839|AW536563|Pcaf|p/CAF	K(lysine) acetyltransferase 2B	protein-coding
mm_9461.1	chr1	172895009	172895015	-	1	NA	promoter-TSS (NM_011318)	promoter-TSS (NM_011318)	42	NM_011318	20219	Mm.330510	NM_011318	ENSMUSG00000026542	Apcs	Sap	serum amyloid P-component	protein-coding
mm_113106.1	chr13	24414502	24414518	+	1	NA	promoter-TSS (NM_001284520)	promoter-TSS (NM_001284520)	-612	NM_007717	12763	Mm.8396	NM_007717	ENSMUSG00000016756	Cmah	-	cytidine monophospho-N-acetylneuraminic acid hydroxylase	protein-coding
mm_103279.1	chr11	72206997	72207011	-	1	NA	promoter-TSS (NM_026559)	promoter-TSS (NM_026559)	-550	NM_026559	52700	Mm.27670	NM_026559	ENSMUSG00000020803	Txndc17	4831443O22Rik|D11Ertd672e|TRP14|Txnl5	thioredoxin domain containing 17	protein-coding
mm_117258.1	chr13	64368150	64368227	-	1	NA	exon (NM_009984, exon 3 of 8)	exon (NM_009984, exon 3 of 8)	2332	NM_009984	13039	Mm.930	NM_009984	ENSMUSG00000021477	Ctsl	1190035F06Rik|CatL|Ctsl1|MEP|fs|nkt	cathepsin L	protein-coding
mm_17272.1	chr2	26091915	26091923	-	1	NA	5' UTR (NM_001037098, exon 1 of 6)	5' UTR (NM_001037098, exon 1 of 6)	477	NM_001037098	67991	Mm.131074	NM_026495	ENSMUSG00000026932	Nacc2	0610020I02Rik|AI448087|Btbd14a|C030048H19Rik	nucleus accumbens associated 2, BEN and BTB (POZ) domain containing	protein-coding
mm_139609.1	chr17	57316395	57316422	+	1	NA	intron (NM_001163816, intron 23 of 25)	intron (NM_001163816, intron 23 of 25)	37308	NM_001163815	22324	Mm.248172	NM_011691	ENSMUSG00000034116	Vav1	Vav|vav-T	vav 1 oncogene	protein-coding
mm_113346.1	chr13	31806661	31806673	+	1	NA	promoter-TSS (NM_008592)	promoter-TSS (NM_008592)	21	NM_008592	17300	Mm.12949	NM_008592	ENSMUSG00000050295	Foxc1	FREAC3|Fkh1|Mf1|Mf4|ch|fkh-1|frkhda	forkhead box C1	protein-coding
mm_104407.1	chr11	94570542	94570551	-	1	NA	intron (NM_153807, intron 7 of 15)	intron (NM_153807, intron 7 of 15)	5472	NM_007689	12643	Mm.440523	NM_007689	ENSMUSG00000039084	Chad	SLRR4A	chondroadherin	protein-coding
mm_157954.1	chrX	87762704	87762707	-	1	NA	intron (NM_001160403, intron 2 of 10)	intron (NM_001160403, intron 2 of 10)	352918	NM_001160403	331461	Mm.121680	NM_001160403	ENSMUSG00000052372	Il1rapl1	6330532G10Rik|C030039N24|IL1R8|IL1RAPL|MRX34|OPHN4|TIGIRR-2	interleukin 1 receptor accessory protein-like 1	protein-coding
mm_30067.1	chr3	137954729	137954736	-	1	NA	intron (NM_011932, intron 3 of 8)	intron (NM_011932, intron 3 of 8)	26817	NM_011932	26377	Mm.254835	NM_011932	ENSMUSG00000028159	Dapp1	Bam32	dual adaptor for phosphotyrosine and 3-phosphoinositides 1	protein-coding
mm_6521.1	chr1	74505681	74505713	-	1	NA	promoter-TSS (NM_021383)	promoter-TSS (NM_021383)	124	NM_001310662	319651	Mm.66568	NM_176972	ENSMUSG00000033364	Usp37	4932415L06Rik|C330008N13Rik	ubiquitin specific peptidase 37	protein-coding
mm_156201.1	chrX	134425222	134425236	+	1	NA	intron (NM_010078, intron 2 of 22)	(T)n|Simple_repeat|Simple_repeat	20449	NM_010078	13497	Mm.121662	NM_010078	ENSMUSG00000000223	Drp2	AW495265|DRP-2	dystrophin related protein 2	protein-coding
mm_121595.1	chr14	7994136	7994150	-	1	NA	promoter-TSS (NM_007870)	promoter-TSS (NM_007870)	39	NM_007870	13421	Mm.272258	NM_007870	ENSMUSG00000025279	Dnase1l3	DNasegamma|Dhp2|Lsd	deoxyribonuclease 1-like 3	protein-coding
mm_158780.1	chrX	167207208	167207232	-	1	NA	3' UTR (NM_021278, exon 3 of 3)	3' UTR (NM_021278, exon 3 of 3)	1998	NM_021278	19241	Mm.142729	NM_021278	ENSMUSG00000049775	Tmsb4x	Ptmb4|Tb4	thymosin, beta 4, X chromosome	protein-coding
mm_167741.1	chr9	107614724	107614768	-	1	NA	3' UTR (NM_008138, exon 9 of 9)	3' UTR (NM_008138, exon 9 of 9)	-5505	NM_001291539	20347	Mm.4083	NM_009153	ENSMUSG00000057969	Sema3b	SemA|Semaa|sema5|semaV	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B	protein-coding
mm_79651.1	chr9	59617239	59617282	+	1	NA	promoter-TSS (NM_029922)	promoter-TSS (NM_029922)	-24	NR_038075	67287	Mm.439943	NM_029922	ENSMUSG00000025237	Parp6	1700119G14Rik|2310028P13Rik|3110038K10Rik|ARTD17|C030013N01Rik|PARP-6	poly (ADP-ribose) polymerase family, member 6	protein-coding
mm_14529.1	chr2	132780707	132780730	+	1	NA	promoter-TSS (NM_007694)	promoter-TSS (NM_007694)	-560	NM_007694	12653	Mm.255241	NM_007694	ENSMUSG00000027350	Chgb	Scg-1	chromogranin B	protein-coding
mm_155753.1	chrX	96167393	96167413	+	1	NA	3' UTR (NM_010833, exon 13 of 13)	3' UTR (NM_010833, exon 13 of 13)	71358	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_59626.1	chr7	28154721	28154730	+	1	NA	exon (NM_001164655, exon 13 of 20)	exon (NM_001164655, exon 13 of 20)	-15023	NM_007991	14113	Mm.4595	NM_007991	ENSMUSG00000046865	Fbl	AL022665|FIB|FLRN|RNU3IP1	fibrillarin	protein-coding
mm_18139.1	chr2	45037101	45037112	-	1	NA	intron (NM_001289521, intron 1 of 8)	intron (NM_001289521, intron 1 of 8)	-13929	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_105370.1	chr11	103208543	103208555	-	1	NA	promoter-TSS (NM_001254724)	promoter-TSS (NM_001254724)	-1	NM_001254724	69441	Mm.380648	NM_027082	ENSMUSG00000020940	1700023F06Rik	-	RIKEN cDNA 1700023F06 gene	protein-coding
mm_102920.1	chr11	69600235	69600237	-	1	NA	3' UTR (NM_013415, exon 7 of 7)	3' UTR (NM_013415, exon 7 of 7)	5724	NM_013415	11932	Mm.235204	NM_013415	ENSMUSG00000041329	Atp1b2	Amog|Atpb-2	ATPase, Na+/K+ transporting, beta 2 polypeptide	protein-coding
mm_34839.1	chr4	155397056	155397069	+	1	NA	intron (NM_008072, intron 1 of 8)	intron (NM_008072, intron 1 of 8)	1007	NM_008072	14403	Mm.388925	NM_008072	ENSMUSG00000029054	Gabrd	AI853201	gamma-aminobutyric acid (GABA) A receptor, subunit delta	protein-coding
mm_44339.1	chr5	17397903	17397909	-	1	NA	Intergenic	Intergenic	-78216	NM_027609	70935	Mm.332225	NM_027609	ENSMUSG00000058643	Speer4f1	4922502J04Rik|SPEER-4F|Speer4f	spermatogenesis associated glutamate (E)-rich protein 4F1	protein-coding
mm_137714.1	chr17	29099805	29099816	+	1	NA	3' UTR (NM_007669, exon 3 of 3)	3' UTR (NM_007669, exon 3 of 3)	6041	NM_007669	12575	Mm.195663	NM_007669	ENSMUSG00000023067	Cdkn1a	CAP20|CDKI|CIP1|Cdkn1|P21|SDI1|Waf1|mda6|p21Cip1|p21WAF	cyclin-dependent kinase inhibitor 1A (P21)	protein-coding
mm_161120.1	chr12	108423030	108423030	+	1	NA	5' UTR (NM_001043335, exon 1 of 22)	5' UTR (NM_001043335, exon 1 of 22)	214	NM_001043335	68519	Mm.236645	NM_001043335	ENSMUSG00000058070	Eml1	1110008N23Rik|A930030P13Rik|AA171013|AI847476|AI853955|ELP79|EMAP|EMAPL|heco	echinoderm microtubule associated protein like 1	protein-coding
mm_22452.1	chr3	3187925	3187937	+	1	NA	Intergenic	Intergenic	-320099	NM_013920	30942	Mm.330897	NM_013920	ENSMUSG00000017688	Hnf4g	NR2A2	hepatocyte nuclear factor 4, gamma	protein-coding
mm_150380.1	chr19	36235473	36235481	+	1	NA	Intergenic	RLTR41|LTR|ERV1	-115633	NM_013468	107765	Mm.10279	NM_013468	ENSMUSG00000024803	Ankrd1	Alrp|CARP|Crap|MARP1	ankyrin repeat domain 1 (cardiac muscle)	protein-coding
mm_25316.1	chr3	106482558	106482571	+	1	NA	non-coding (NR_033207, exon 2 of 2)	non-coding (NR_033207, exon 2 of 2)	114	NM_001278941	72121	Mm.14816	NM_028110	ENSMUSG00000027901	Dennd2d	2010308M01Rik|AI451421	DENN/MADD domain containing 2D	protein-coding
mm_27225.1	chr3	36222279	36222294	-	1	NA	promoter-TSS (NM_198192)	promoter-TSS (NM_198192)	-11	NM_198192	229214	Mm.330975	NM_198192	ENSMUSG00000058400	Qrfpr	AQ27|Gpr103|SP9155	pyroglutamylated RFamide peptide receptor	protein-coding
mm_69803.1	chr7	141183422	141183428	-	1	NA	Intergenic	PB1D10|SINE|Alu	-10574	NM_001172100	107702	Mm.197493	NM_145135	ENSMUSG00000038650	Rnh1	AW546468|C80305|RNH	ribonuclease/angiogenin inhibitor 1	protein-coding
mm_95960.1	chr11	58867205	58867229	+	1	NA	promoter-TSS (NM_172403)	promoter-TSS (NM_172403)	-23	NM_172403	69944	Mm.32118	NM_172403	ENSMUSG00000020491	2810021J22Rik	AI449137	RIKEN cDNA 2810021J22 gene	protein-coding
mm_18514.1	chr2	62627823	62627825	-	1	NA	intron (NM_001164477, intron 2 of 14)	intron (NM_001164477, intron 2 of 14)	18431	NM_027835	71586	Mm.136224	NM_027835	ENSMUSG00000026896	Ifih1	9130009C22Rik|Helicard|Hlcd|MDA5|RLR-2	interferon induced with helicase C domain 1	protein-coding
mm_18376.1	chr2	59953761	59953767	-	1	NA	intron (NM_001001182, intron 12 of 35)	intron (NM_001001182, intron 12 of 35)	-71158	NM_028118	72137	Mm.288734	NM_028118	ENSMUSG00000026988	Wdsub1	1700048E19Rik|2610014F08Rik	WD repeat, SAM and U-box domain containing 1	protein-coding
mm_129112.1	chr15	76070923	76070940	-	1	NA	exon (NM_028364, exon 11 of 12)	exon (NM_028364, exon 11 of 12)	-1147	NM_001310542	105782	Mm.25568	NM_134089	ENSMUSG00000022568	Scrib	AI118201|CRIB|Crc|SCRIB1|Scrb1|mKIAA0147|vartul	scribbled planar cell polarity	protein-coding
mm_4414.1	chr1	172499888	172499912	+	1	NA	promoter-TSS (NM_178598)	promoter-TSS (NM_178598)	-346	NM_178598	21346	Mm.271711	NM_178598	ENSMUSG00000026547	Tagln2	2700094C18Rik|SM22beta|Sm22B|Sm22a	transgelin 2	protein-coding
mm_156288.1	chrX	136837444	136837457	+	1	NA	3' UTR (NM_011123, exon 7 of 7)	3' UTR (NM_011123, exon 7 of 7)	14704	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_124834.1	chr15	9197032	9197060	+	1	NA	3' UTR (NM_177178, exon 18 of 18)	3' UTR (NM_177178, exon 18 of 18)	-41621	NM_001285980	27401	Mm.35584	NM_013787	ENSMUSG00000054115	Skp2	4930500A04Rik|FBXL1|FWD1|p45	S-phase kinase-associated protein 2 (p45)	protein-coding
mm_130906.1	chr15	102510769	102510797	-	1	NA	intron (NM_001163643, intron 1 of 15)	CpG	6221	NM_001163643	26404	Mm.172897	NM_009582	ENSMUSG00000023050	Map3k12	DLK|MUK|Zpk	mitogen-activated protein kinase kinase kinase 12	protein-coding
mm_78007.1	chr9	12839131	12839135	+	1	NA	Intergenic	L2a|LINE|L2	266722	NR_040755	78219	Mm.414868	NR_040755	ENSMUSG00000111830	4930568E12Rik	-	RIKEN cDNA 4930568E12 gene	ncRNA
mm_22556.1	chr3	9801888	9801931	+	1	NA	intron (NM_001195031, intron 1 of 8)	L1MDa|LINE|L1	31770	NM_053182	94212	Mm.23897	NM_053182	ENSMUSG00000027508	Pag1	Cbp|F730007C19Rik|Pag	phosphoprotein associated with glycosphingolipid microdomains 1	protein-coding
mm_134506.1	chr16	19063522	19063560	-	1	NA	Intergenic	Intergenic	186791	NM_010435	15260	Mm.15694	NM_010435	ENSMUSG00000022702	Hira	AA138857|D16Ertd95e|Gm15797|N28177|OTTMUSG00000026264|Tuple1	histone cell cycle regulator	protein-coding
mm_156969.1	chrX	169997294	169997316	+	1	NA	Intergenic	CpG	-18388	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_54128.1	chr6	18514803	18514860	-	1	NA	promoter-TSS (NM_080285)	promoter-TSS (NM_080285)	-6	NM_080285	30785	Mm.224189	NM_080285	ENSMUSG00000000416	Cttnbp2	3010022N24Rik|4732477G22Rik|6430526E05|9130022E09Rik|AU040881|Cortbp2|ORF4|mKIAA1758	cortactin binding protein 2	protein-coding
mm_153487.1	chr19	41308473	41308493	-	1	NA	exon (NM_031376, exon 9 of 17)	exon (NM_031376, exon 9 of 17)	-44479	NM_133352	107358	Mm.246440	NM_133352	ENSMUSG00000025016	Tm9sf3	1810073M23Rik|2810031D16Rik|AI115521|AI413748|AW146116|AW549777|Smbp|mKIAA4036	transmembrane 9 superfamily member 3	protein-coding
mm_169705.1	chr15	75135144	75135149	-	1	NA	Intergenic	Intergenic	-20115	NM_001310438	546644		NM_008531	ENSMUSG00000022582	Ly6g	Gr-1|Gr1|Ly-6G	lymphocyte antigen 6 complex, locus G	protein-coding
mm_68205.1	chr7	104395213	104395222	-	1	NA	Intergenic	MYSERV6-int|LTR|ERVK	-36571	NM_175648	244183	Mm.347647	NM_175648	ENSMUSG00000052749	Trim30b	A530023O14Rik|Trim30-1	tripartite motif-containing 30B	protein-coding
mm_1883.1	chr1	85665273	85665322	+	1	NA	exon (NM_013673, exon 5 of 20)	exon (NM_013673, exon 5 of 20)	15309	NM_001313714	20684	Mm.290906	NM_013673	ENSMUSG00000026222	Sp100	A430075G10Rik	nuclear antigen Sp100	protein-coding
mm_54784.1	chr6	41544378	41544390	-	1	NA	Intergenic	Intergenic	22608	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_170060.1	chr17	30624380	30624381	+	1	NA	non-coding (NR_045287, exon 3 of 4)	non-coding (NR_045287, exon 3 of 4)	2525	NR_045287	67522	Mm.254797	NR_045287	ENSMUSG00000099474	1700097N02Rik	-	RIKEN cDNA 1700097N02 gene	ncRNA
mm_43000.1	chr5	123429050	123429055	+	1	NA	intron (NM_133917, intron 1 of 16)	intron (NM_133917, intron 1 of 16)	34254	NM_177582	208104	Mm.83277	NM_133917	ENSMUSG00000038342	Mlxip	AW228700|Mir|bHLHe36	MLX interacting protein	protein-coding
mm_25141.1	chr3	102520355	102520403	+	1	NA	exon (NM_013609, exon 4 of 4)	exon (NM_013609, exon 4 of 4)	50460	NM_013609	18049	Mm.1259	NM_013609	ENSMUSG00000027859	Ngf	Ngfb	nerve growth factor	protein-coding
mm_16794.1	chr2	10094824	10094828	-	1	NA	exon (NM_010582, exon 21 of 21)	exon (NM_010582, exon 21 of 21)	14214	NM_025280	16588	Mm.35498	NM_025280	ENSMUSG00000037262	Kin	Kin17	Kin17 DNA and RNA binding protein	protein-coding
mm_91746.1	chr10	49534099	49534104	-	1	NA	intron (NM_001111268, intron 5 of 16)	(A)n|Simple_repeat|Simple_repeat	254653	NM_010349	14806	Mm.332838	NM_010349	ENSMUSG00000056073	Grik2	AW124492|GluK2|Glur-6|Glur6|Glurbeta2	glutamate receptor, ionotropic, kainate 2 (beta 2)	protein-coding
mm_100030.1	chr11	114929870	114929888	+	1	NA	intron (NM_199221, intron 1 of 3)	intron (NM_199221, intron 1 of 3)	4507	NM_001347651	217304	Mm.185355	NM_199221	ENSMUSG00000063193	Cd300lb	CLM-7|Clm7|Gm253|LMIR5	CD300 molecule like family member B	protein-coding
mm_70403.1	chr8	11325486	11325492	+	1	NA	intron (NM_009932, intron 3 of 47)	B4A|SINE|B4	-12663	NM_009931	12826	Mm.738	NM_009931	ENSMUSG00000031502	Col4a1	Bru|Col4a-1|Raw|Svc	collagen, type IV, alpha 1	protein-coding
mm_47531.1	chr5	124189715	124189732	-	1	NA	intron (NM_011256, intron 2 of 24)	intron (NM_011256, intron 2 of 24)	-2541	NM_001289472	19679	Mm.44261	NM_011256	ENSMUSG00000029406	Pitpnm2	NIR3|RDGBA2|Rdgb2|mKIAA1457	phosphatidylinositol transfer protein, membrane-associated 2	protein-coding
mm_51711.1	chr6	86748931	86748962	+	1	NA	exon (NM_001331120, exon 9 of 13)	exon (NM_001331120, exon 9 of 13)	-15568	NM_011818	23885	Mm.321452	NM_011818	ENSMUSG00000001157	Gmcl1	2810049L19Rik|Btbd13|DIP|Gcl|Gcl-1|glc-1|mglc-1	germ cell-less, spermatogenesis associated 1	protein-coding
mm_115443.1	chr13	117724900	117724900	+	1	NA	intron (NM_010408, intron 2 of 7)	intron (NM_010408, intron 2 of 7)	-4889	NR_045508	71100	Mm.414841	NR_045508	ENSMUSG00000079048	4933413L06Rik	-	RIKEN cDNA 4933413L06 gene	ncRNA
mm_52724.1	chr6	120039902	120039926	+	1	NA	Intergenic	Intergenic	-1259	NM_001185021	232341	Mm.333349	NM_198703	ENSMUSG00000045962	Wnk1	6430573H23Rik|EG406236|Hsn2|Prkwnk1|mKIAA0344	WNK lysine deficient protein kinase 1	protein-coding
mm_31128.1	chr4	43058977	43059011	+	1	NA	promoter-TSS (NM_021468)	promoter-TSS (NM_021468)	41	NM_001310758	22249	Mm.128892	NM_021468	ENSMUSG00000028456	Unc13b	Munc13-1|Munc13-2|Unc13a|Unc13h1|Unc13h2	unc-13 homolog B (C. elegans)	protein-coding
mm_144182.1	chr18	6788907	6788911	+	1	NA	3' UTR (NM_181070, exon 7 of 7)	3' UTR (NM_181070, exon 7 of 7)	23742	NM_001278447	19330	Mm.132802	NM_181070	ENSMUSG00000073639	Rab18	AA959686	RAB18, member RAS oncogene family	protein-coding
mm_123872.1	chr14	72589897	72589928	-	1	NA	exon (NM_207636, exon 5 of 26)	exon (NM_207636, exon 5 of 26)	120091	NM_207636	319448	Mm.205421	NM_207636	ENSMUSG00000033487	Fndc3a	1700094E19Rik|D14Ertd453e|F730017H24Rik|Fndc3|sys	fibronectin type III domain containing 3A	protein-coding
mm_68968.1	chr7	126584617	126584627	-	1	NA	promoter-TSS (NM_138310)	promoter-TSS (NM_138310)	-386	NM_138310	171504	Mm.170665	NM_138310	ENSMUSG00000042759	Apobr	Apob-48r|Apob48r	apolipoprotein B receptor	protein-coding
mm_87149.1	chr10	34898698	34898710	+	1	NA	Intergenic	Intergenic	415304	NM_010237	14302	Mm.332432	NM_010237	ENSMUSG00000019779	Frk	BSK|BSK/IYK|C85044|GTK|RAK	fyn-related kinase	protein-coding
mm_26924.1	chr3	20249646	20249713	-	1	NA	exon (NM_029706, exon 11 of 11)	exon (NM_029706, exon 11 of 11)	-7498	NM_007753	12873	Mm.1135	NM_007753	ENSMUSG00000001865	Cpa3	MC-CPA	carboxypeptidase A3, mast cell	protein-coding
mm_61938.1	chr7	90176735	90176748	+	1	NA	exon (NM_001252521, exon 11 of 20)	exon (NM_001252521, exon 11 of 20)	46509	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_20968.1	chr2	151972961	151972974	-	1	NA	intron (NM_146127, intron 1 of 1)	intron (NM_146127, intron 1 of 1)	427	NM_001289151	73847	Mm.272444	NM_028666	ENSMUSG00000027459	Fam110a	1700008J10Rik|5430432M24Rik|AI747080	family with sequence similarity 110, member A	protein-coding
mm_5669.1	chr1	42695413	42695457	-	1	NA	promoter-TSS (NR_027826)	promoter-TSS (NR_027826)	-610	NR_027826	66297	Mm.45203	NM_183252	ENSMUSG00000060424	Pantr1	2610017I09Rik|Pou3f3os|linc-Brn1a	POU domain, class 3, transcription factor 3 adjacent noncoding transcript 1	ncRNA
mm_37709.1	chr4	129490761	129490776	-	1	NA	promoter-TSS (NM_080442)	promoter-TSS (NM_080442)	2	NM_080442	58864	Mm.143802	NM_080442	ENSMUSG00000000411	Tssk3	1700014N07Rik|4930594I21Rik|Stk22c|Stk22d|Tsk-3|Tssk-3|Tssk3b	testis-specific serine kinase 3	protein-coding
mm_44175.1	chr5	150973555	150973564	+	1	NA	intron (NM_013823, intron 1 of 4)	B4|SINE|B4	20952	NM_013823	16591	Mm.6500	NM_013823	ENSMUSG00000058488	Kl	alpha-kl	klotho	protein-coding
mm_137648.1	chr17	28558213	28558219	+	1	NA	TTS (NR_105935)	TTS (NR_105935)	285	NR_105935	102465585		NR_105935	ENSMUSG00000099152	Mir6969	Gm27305|mmu-mir-6969	microRNA 6969	ncRNA
mm_103293.1	chr11	72441220	72441276	-	1	NA	promoter-TSS (NM_016776)	promoter-TSS (NM_016776)	-130	NM_016776	18432	Mm.147946	NM_016776	ENSMUSG00000040463	Mybbp1a	AL024407|AU019902|P160|p160MBP|p67MBP	MYB binding protein (P160) 1a	protein-coding
mm_128541.1	chr15	54952654	54952694	-	1	NA	Intergenic	CpG	-32528	NM_001285994	18606	Mm.250256	NM_015744	ENSMUSG00000022425	Enpp2	ATX|E-NPP 2|Npps2|PD-Ialpha|Pdnp2|lysoPLD	ectonucleotide pyrophosphatase/phosphodiesterase 2	protein-coding
mm_33541.1	chr4	130934546	130934550	+	1	NA	exon (NM_010686, exon 8 of 8)	exon (NM_010686, exon 8 of 8)	-9837	NM_010769	17180	Mm.271796	NM_010769	ENSMUSG00000040533	Matn1	CMP|Crtm|Mat1|matrilin-1	matrilin 1, cartilage matrix protein	protein-coding
mm_44996.1	chr5	38159540	38159546	-	1	NA	promoter-TSS (NM_010942)	promoter-TSS (NM_010942)	-76	NM_010942	18196	Mm.7414	NM_010942	ENSMUSG00000029126	Nsg1	Neep21|m234|p21	neuron specific gene family member 1	protein-coding
mm_168304.1	chr11	106787004	106787005	-	1	NA	exon (NM_007840, exon 2 of 13)	exon (NM_007840, exon 2 of 13)	1490	NM_007840	13207	Mm.491096	NM_007840	ENSMUSG00000020719	Ddx5	2600009A06Rik|G17P1|HUMP68|Hlr1|p68	DEAD (Asp-Glu-Ala-Asp) box polypeptide 5	protein-coding
mm_12942.1	chr2	85136523	85136531	+	1	NA	5' UTR (NM_011784, exon 1 of 1)	5' UTR (NM_011784, exon 1 of 1)	167	NM_011784	23796	Mm.29368	NM_011784	ENSMUSG00000044338	Aplnr	APJ|Agtrl1|msr/apj	apelin receptor	protein-coding
mm_64152.1	chr7	141328143	141328179	+	1	NA	promoter-TSS (NM_001282076)	promoter-TSS (NM_001282076)	31	NM_027797	71448	Mm.248960	NM_027797	ENSMUSG00000025505	Tmem80	5530601I19Rik	transmembrane protein 80	protein-coding
mm_91372.1	chr10	29535858	29535880	-	1	NA	promoter-TSS (NM_028351)	promoter-TSS (NM_028351)	-2	NM_028351	72780	Mm.45191	NM_028351	ENSMUSG00000019880	Rspo3	2810459H04Rik|AW742308|Cristin1|Thsd2	R-spondin 3	protein-coding
mm_13259.1	chr2	98666242	98666261	+	1	NA	Intergenic	SYNREP_MM|Satellite|Satellite	1198594	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_117449.1	chr13	74807914	74807989	-	1	NA	promoter-TSS (NM_009817)	promoter-TSS (NM_009817)	9	NM_009817	12380	Mm.29163	NM_009817	ENSMUSG00000021585	Cast	-	calpastatin	protein-coding
mm_143902.1	chr17	84855354	84855359	-	1	NA	Intergenic	Intergenic	-64570	NM_028233	72416	Mm.217027	NM_028233	ENSMUSG00000024120	Lrpprc	3110001K13Rik|C76645|Gp130|Lrp130|Lsfc	leucine-rich PPR-motif containing	protein-coding
mm_131918.1	chr16	23317549	23317567	+	1	NA	intron (NM_001252506, intron 1 of 6)	intron (NM_001252506, intron 1 of 6)	27088	NM_001252506	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_68338.1	chr7	106505342	106505391	-	1	NA	Intergenic	Intergenic	-64293	NR_003967	209380	Mm.461779	NM_001001318		Gm4759	EG209380	GTPase, very large interferon inducible 1 pseudogene	pseudo
mm_42582.1	chr5	117318739	117318759	+	1	NA	promoter-TSS (NM_001033311)	promoter-TSS (NM_001033311)	-517	NM_001033311	231668	Mm.298603	NM_001033311	ENSMUSG00000066894	Vsig10	-	V-set and immunoglobulin domain containing 10	protein-coding
mm_131415.1	chr16	14705596	14705618	+	1	NA	promoter-TSS (NM_011415)	promoter-TSS (NM_011415)	-252	NM_011415	20583	Mm.4272	NM_011415	ENSMUSG00000022676	Snai2	Slug|Slugh|Snail2	snail family zinc finger 2	protein-coding
mm_142780.1	chr17	50124299	50124314	-	1	NA	intron (NM_181397, intron 2 of 9)	B1F|SINE|Alu	66191	NM_181397	76438	Mm.41854	NM_181397	ENSMUSG00000039316	Rftn1	2310015N21Rik|AI853526	raftlin lipid raft linker 1	protein-coding
mm_74497.1	chr8	5105402	5105409	-	1	NA	promoter-TSS (NM_011388)	promoter-TSS (NM_011388)	-118	NM_011388	20494	Mm.3500	NM_011388	ENSMUSG00000023073	Slc10a2	9130221J18Rik|AI605518|ASBT|IBAT|ISBT	solute carrier family 10, member 2	protein-coding
mm_66381.1	chr7	43954080	43954098	-	1	NA	exon (NM_008457, exon 3 of 5)	exon (NM_008457, exon 3 of 5)	3423	NM_008457	16624	Mm.435488	NM_008457	ENSMUSG00000063089	Klk1b8	Klk8|Nrpn|TADG14|kallikrein|mGK-8	kallikrein 1-related peptidase b8	protein-coding
mm_102594.1	chr11	61930247	61930257	-	1	NA	promoter-TSS (NM_019921)	promoter-TSS (NM_019921)	5	NM_019921	56697	Mm.274404	NM_019921	ENSMUSG00000047804	Akap10	1500031L16Rik|B130049N18Rik|D-AKAP-2|D-AKAP2|PRKA10	A kinase (PRKA) anchor protein 10	protein-coding
mm_4152.1	chr1	171019847	171019859	+	1	NA	intron (NM_144559, intron 2 of 4)	intron (NM_144559, intron 2 of 4)	927	NM_144559	246256	Mm.251254	NM_144559	ENSMUSG00000059089	Fcgr4	4833442P21Rik|CD16-2|FcgRIV|FcgammaRIV|Fcgr3a|Fcrl3	Fc receptor, IgG, low affinity IV	protein-coding
mm_50520.1	chr6	49042886	49042894	+	1	NA	exon (NM_053110, exon 2 of 11)	exon (NM_053110, exon 2 of 11)	6372	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_165962.1	chr4	93334778	93334816	+	1	NA	3' UTR (NM_026954, exon 1 of 1)	3' UTR (NM_026954, exon 1 of 1)	714	NM_026954	69136	Mm.171558	NM_026954	ENSMUSG00000054000	Tusc1	2200001D17Rik|TSG-9	tumor suppressor candidate 1	protein-coding
mm_158441.1	chrX	140385859	140385870	-	1	NA	intron (NM_001320946, intron 5 of 14)	intron (NM_001320946, intron 5 of 14)	18370	NM_177750	245643	Mm.208683	NM_177750	ENSMUSG00000042425	Frmpd3	B930041G04|EG245643|Gm29750	FERM and PDZ domain containing 3	protein-coding
mm_5553.1	chr1	38664935	38664945	-	1	NA	Intergenic	Intergenic	-37696	NM_001290814	16764	Mm.336679	NM_010678	ENSMUSG00000037138	Aff3	3222402O04Rik|A730046J16|LAF-4|Laf4	AF4/FMR2 family, member 3	protein-coding
mm_115757.1	chr13	19192792	19192803	-	1	NA	Intergenic	Intergenic	203016	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_40096.1	chr5	34559438	34559472	+	1	NA	exon (NM_001145859, exon 8 of 13)	exon (NM_001145859, exon 8 of 13)	9879	NM_001145859	24055	Mm.5012	NM_011893	ENSMUSG00000054520	Sh3bp2	3BP2	SH3-domain binding protein 2	protein-coding
mm_140465.1	chr17	92409813	92409818	+	1	NA	Intergenic	Intergenic	-789202	NM_001315503	11516	Mm.3407	NM_009625	ENSMUSG00000024256	Adcyap1	PACAP	adenylate cyclase activating polypeptide 1	protein-coding
mm_109511.1	chr12	111453900	111453911	+	1	NA	3' UTR (NM_009396, exon 12 of 12)	3' UTR (NM_009396, exon 12 of 12)	11244	NM_009396	21928	Mm.255332	NM_009396	ENSMUSG00000021281	Tnfaip2	B94|Exoc3l3|M-sec|Tnfip2|tnfb94	tumor necrosis factor, alpha-induced protein 2	protein-coding
mm_72847.1	chr8	88309708	88309728	+	1	NA	exon (NM_001037724, exon 6 of 28)	exon (NM_001037724, exon 6 of 28)	15514	NM_001037724	11513	Mm.288206	NM_007406	ENSMUSG00000031659	Adcy7	AA407758	adenylate cyclase 7	protein-coding
mm_41347.1	chr5	90501445	90501531	+	1	NA	exon (NM_007423, exon 8 of 15)	exon (NM_007423, exon 8 of 15)	10774	NM_007423	11576	Mm.358570	NM_007423	ENSMUSG00000054932	Afp	-	alpha fetoprotein	protein-coding
mm_159733.1	chr5	61808807	61808807	+	1	NA	promoter-TSS (NM_019468)	promoter-TSS (NM_019468)	-36	NM_019468	14380	Mm.347430	NM_019468	ENSMUSG00000089992	G6pd2	G6pdx-ps1|Gpd-2|Gpd2	glucose-6-phosphate dehydrogenase 2	protein-coding
mm_77324.1	chr8	119424331	119424343	-	1	NA	Intergenic	Intergenic	-12825	NM_027950	71839	Mm.272357	NM_027950	ENSMUSG00000074063	Osgin1	1700012B18Rik|Okl38	oxidative stress induced growth inhibitor 1	protein-coding
mm_56548.1	chr6	100181718	100181733	-	1	NA	Intergenic	Intergenic	105633	NM_019743	56353	Mm.321633	NM_019743	ENSMUSG00000072872	Rybp	2410018J24Rik|DEDAF|YEAF1	RING1 and YY1 binding protein	protein-coding
mm_144273.1	chr18	11633364	11633381	+	1	NA	promoter-TSS (NM_001252495)	promoter-TSS (NM_001252495)	96	NR_045527	225182	Mm.154275	NM_175458	ENSMUSG00000041238	Rbbp8	9930104E21Rik|CtIP|RBBP-8|RIM|SAE2	retinoblastoma binding protein 8	protein-coding
mm_6404.1	chr1	72862330	72862379	-	1	NA	3' UTR (NM_010518, exon 4 of 4)	3' UTR (NM_010518, exon 4 of 4)	12511	NM_010518	16011	Mm.405761	NM_010518	ENSMUSG00000026185	Igfbp5	AI256729|AW208790|IGFBP-5|IGFBP-5P	insulin-like growth factor binding protein 5	protein-coding
mm_112861.1	chr13	20846033	20846036	+	1	NA	intron (NM_012054, intron 3 of 20)	RMER1B|Other|Other	51921	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_56571.1	chr6	105677570	105677603	-	1	NA	promoter-TSS (NM_173004)	promoter-TSS (NM_173004)	-5	NR_132434	102638038	Mm.360282	NR_132434		Gm15631	OTTMUSG00000024600	predicted gene 15631	ncRNA
mm_102033.1	chr11	51763597	51763637	-	1	NA	promoter-TSS (NM_025535)	promoter-TSS (NM_025535)	-46	NM_025535	66397	Mm.196592	NM_025535	ENSMUSG00000020386	Sar1b	2310075M17Rik|2900019I22Rik|CMRD|Sara1b|Sara2|Sarb	secretion associated Ras related GTPase 1B	protein-coding
mm_108970.1	chr12	102554230	102554259	+	1	NA	promoter-TSS (NM_007693)	promoter-TSS (NM_007693)	-697	NM_007693	12652	Mm.4137	NM_007693	ENSMUSG00000021194	Chga	ChrA|cgA	chromogranin A	protein-coding
mm_129872.1	chr15	83423743	83423751	-	1	NA	intron (NM_001159509, intron 1 of 10)	intron (NM_001159509, intron 1 of 10)	9103	NM_011862	23970	Mm.23978	NM_011862	ENSMUSG00000016664	Pacsin2	AI197433	protein kinase C and casein kinase substrate in neurons 2	protein-coding
mm_59797.1	chr7	29001567	29001591	+	1	NA	intron (NM_008279, intron 27 of 31)	intron (NM_008279, intron 27 of 31)	18725	NM_008279	26411	Mm.148278	NM_008279	ENSMUSG00000037337	Map4k1	Hpk1|mHPK1	mitogen-activated protein kinase kinase kinase kinase 1	protein-coding
mm_116165.1	chr13	30781999	30782008	-	1	NA	Intergenic	Intergenic	32770	NM_013674	16364	Mm.4677	NM_013674	ENSMUSG00000021356	Irf4	AI385587|IRF-4|LSIRF|NF-EM5|Spip	interferon regulatory factor 4	protein-coding
mm_167207.1	chr7	144406905	144406911	-	1	NA	intron (NM_001113373, intron 12 of 15)	intron (NM_001113373, intron 12 of 15)	36525	NR_037302	100499519		NR_037302	ENSMUSG00000093912	Mir3470b	mmu-mir-3470b	microRNA 3470b	ncRNA
mm_26458.1	chr3	142927468	142927491	+	1	NA	Intergenic	RMER1B|Other|Other	-45475	NM_178654	109333	Mm.244236	NM_178654	ENSMUSG00000004591	Pkn2	6030436C20Rik|AI507382|PRK2|Prkcl2|Stk7	protein kinase N2	protein-coding
mm_161025.1	chr12	3572959	3572959	+	1	NA	promoter-TSS (NM_007886)	promoter-TSS (NM_007886)	-82	NM_007886	13528	Mm.286202	NM_007886	ENSMUSG00000071454	Dtnb	-	dystrobrevin, beta	protein-coding
mm_113016.1	chr13	21981219	21981223	+	1	NA	promoter-TSS (NM_001162929)	promoter-TSS (NM_001162929)	27	NM_001162929	195236	Mm.204664	NM_001162928	ENSMUSG00000016982	Pom121l2	Gm24	POM121 membrane glycoprotein-like 2 (rat)	protein-coding
mm_39713.1	chr5	27952008	27952050	+	1	NA	Intergenic	(AGTTG)n|Simple_repeat|Simple_repeat	110082	NM_008314	15563	Mm.4835	NM_008314	ENSMUSG00000039106	Htr5a	Htr5	5-hydroxytryptamine (serotonin) receptor 5A	protein-coding
mm_57148.1	chr6	122728327	122728338	-	1	NA	3' UTR (NM_011401, exon 10 of 10)	3' UTR (NM_011401, exon 10 of 10)	14413	NM_011401	20527	Mm.395108	NM_011401	ENSMUSG00000003153	Slc2a3	AA408729|AL023014|AL024341|AU040424|C78366|Glut-3|Glut3	solute carrier family 2 (facilitated glucose transporter), member 3	protein-coding
mm_122452.1	chr14	45314790	45314795	-	1	NA	intron (NM_015774, intron 1 of 15)	intron (NM_015774, intron 1 of 15)	3780	NM_015774	50527	Mm.387108	NM_015774	ENSMUSG00000021831	Ero1l	ERO1-L|Ero1a	ERO1-like (S. cerevisiae)	protein-coding
mm_101227.1	chr11	20289688	20289693	-	1	NA	Intergenic	RLTR48B|LTR|ERV1	-40266	NM_172260	216543	Mm.260314	NM_172260	ENSMUSG00000044066	Cep68	6030463E10Rik|AI481761|BC027174|Kiaa0582	centrosomal protein 68	protein-coding
mm_115652.1	chr13	12332416	12332436	-	1	NA	intron (NM_033268, intron 1 of 20)	B3A|SINE|B2	8306	NM_033268	11472	Mm.37638	NM_033268	ENSMUSG00000052374	Actn2	1110008F24Rik	actinin alpha 2	protein-coding
mm_135530.1	chr16	49768696	49768709	-	1	NA	Intergenic	ORR1D1|LTR|ERVL-MaLR	69408	NM_028680	73916	Mm.241276	NM_028680	ENSMUSG00000032965	Ift57	4833420A15Rik|Esrrbl1|Hippi|MHS4R2	intraflagellar transport 57	protein-coding
mm_64115.1	chr7	141078267	141078314	+	1	NA	promoter-TSS (NM_001162924)	promoter-TSS (NM_001162924)	61	NM_001162924	56460	Mm.350037	NM_019762	ENSMUSG00000054065	Pkp3	2310056L12Rik	plakophilin 3	protein-coding
mm_131608.1	chr16	19236343	19236352	+	1	NA	Intergenic	L1_Mur2|LINE|L1	50394	NM_146451	258443	Mm.377506	NM_146451	ENSMUSG00000050742	Olfr164	MOR279-2	olfactory receptor 164	protein-coding
mm_132234.1	chr16	32750401	32750411	+	1	NA	exon (NM_080457, exon 2 of 27)	exon (NM_080457, exon 2 of 27)	14520	NM_080457	140474	Mm.214599	NM_080457	ENSMUSG00000079620	Muc4	4933405I11Rik|Asgp	mucin 4	protein-coding
mm_82264.1	chr9	7015853	7015856	-	1	NA	intron (NM_029851, intron 71 of 88)	intron (NM_029851, intron 71 of 88)	161192	NM_029851	110350	Mm.237596	NM_029851	ENSMUSG00000047193	Dync2h1	4432416O06Rik|AI448217|D030010H02Rik|D330044F14Rik|DHC1b|DHC2|Dnchc2|b2b414Clo|mKIAA1997	dynein cytoplasmic 2 heavy chain 1	protein-coding
mm_104610.1	chr11	97207002	97207017	-	1	NA	3' UTR (NM_008942, exon 23 of 23)	3' UTR (NM_008942, exon 23 of 23)	-19117	NM_008379	16211	Mm.251013	NM_008379	ENSMUSG00000001440	Kpnb1	AA409963|IPOB|Impnb	karyopherin (importin) beta 1	protein-coding
mm_97590.1	chr11	78945892	78945898	+	1	NA	exon (NM_010927, exon 15 of 27)	exon (NM_010927, exon 15 of 27)	20604	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_81302.1	chr9	108339309	108339310	+	1	NA	5' UTR (NM_008160, exon 1 of 2)	5' UTR (NM_008160, exon 1 of 2)	229	NM_001329528	14775	Mm.1090	NM_008160	ENSMUSG00000063856	Gpx1	AI195024|AL033363|CGPx|GPx-1|GSHPx-1|Gpx	glutathione peroxidase 1	protein-coding
mm_143702.1	chr17	80577411	80577439	-	1	NA	Intergenic	CpG	-13591	NM_001033443	381113	Mm.329216	NM_001033443	ENSMUSG00000033966	Cdkl4	AU067824|Gm942	cyclin-dependent kinase-like 4	protein-coding
mm_74547.1	chr8	10534903	10534916	-	1	NA	intron (NM_001319151, intron 28 of 34)	intron (NM_001319151, intron 28 of 34)	347545	NR_040705	320014	Mm.403203	NR_040705	ENSMUSG00000109473	B930025P03Rik	-	RIKEN cDNA B930025P03 gene	ncRNA
mm_68949.1	chr7	126563269	126563309	-	1	NA	exon (NM_146200, exon 6 of 21)	exon (NM_146200, exon 6 of 21)	3077	NM_146200	56347	Mm.22776	NM_146200	ENSMUSG00000030738	Eif3c	110kDa|3230401O13Rik|Eif3s8|NIPIL(A3)|NipilA3|Xs|Xsl	eukaryotic translation initiation factor 3, subunit C	protein-coding
mm_29461.1	chr3	113574642	113574652	-	1	NA	5' UTR (NM_007446, exon 1 of 11)	5' UTR (NM_007446, exon 1 of 11)	115	NM_007446	11722	Mm.439727	NM_007446	ENSMUSG00000074264	Amy1	Amy-1|Amy1a|C030014B17Rik	amylase 1, salivary	protein-coding
mm_53388.1	chr6	129533369	129533401	+	1	NA	promoter-TSS (NR_045270)	promoter-TSS (NR_045270)	-101	NR_045270	100504641	Mm.398286	NR_045270	ENSMUSG00000097675	1700101I11Rik	-	RIKEN cDNA 1700101I11 gene	ncRNA
mm_48274.1	chr5	137963063	137963073	-	1	NA	promoter-TSS (NM_080450)	promoter-TSS (NM_080450)	-109	NM_080450	118446	Mm.332771	NM_080450	ENSMUSG00000056966	Gjc3	Cx29|Gje1	gap junction protein, gamma 3	protein-coding
mm_139520.1	chr17	56613356	56613358	+	1	NA	promoter-TSS (NM_018730)	promoter-TSS (NM_018730)	-38	NM_018730	54217	Mm.11376	NM_018730	ENSMUSG00000057863	Rpl36	-	ribosomal protein L36	protein-coding
mm_17580.1	chr2	30415439	30415449	-	1	NA	promoter-TSS (NM_138748)	promoter-TSS (NM_138748)	304	NM_007760	12908	Mm.20396	NM_007760	ENSMUSG00000026853	Crat	AW107812|CARAT	carnitine acetyltransferase	protein-coding
mm_123766.1	chr14	70208294	70208314	-	1	NA	promoter-TSS (NM_011366)	promoter-TSS (NM_011366)	-633	NM_011366	20410	Mm.5068	NM_011366	ENSMUSG00000022091	Sorbs3	SCAM-1|SH3P3|Sh3d4|vinexin-g	sorbin and SH3 domain containing 3	protein-coding
mm_117161.1	chr13	62624136	62624182	-	1	NA	promoter-TSS (NM_001324406)	promoter-TSS (NM_001324406)	23	NM_001324406	211378	Mm.247448	NM_173381	ENSMUSG00000072066	6720489N17Rik	9330128I06	RIKEN cDNA 6720489N17 gene	protein-coding
mm_6401.1	chr1	72862202	72862223	-	1	NA	3' UTR (NM_010518, exon 4 of 4)	3' UTR (NM_010518, exon 4 of 4)	12653	NM_010518	16011	Mm.405761	NM_010518	ENSMUSG00000026185	Igfbp5	AI256729|AW208790|IGFBP-5|IGFBP-5P	insulin-like growth factor binding protein 5	protein-coding
mm_151179.1	chr19	53329425	53329478	+	1	NA	promoter-TSS (NM_010847)	promoter-TSS (NM_010847)	38	NM_010847	17859	Mm.2154	NM_010847	ENSMUSG00000025025	Mxi1	ENSMUSG00000067085|Gm10197|Mad2|bHLHc11	MAX interactor 1, dimerization protein	protein-coding
mm_80210.1	chr9	72448619	72448632	+	1	NA	exon (NM_008613, exon 5 of 10)	exon (NM_008613, exon 5 of 10)	10096	NM_008613	17427	Mm.387671	NM_008613	ENSMUSG00000032221	Mns1	AW546487	meiosis-specific nuclear structural protein 1	protein-coding
mm_6197.1	chr1	65179059	65179121	-	1	NA	promoter-TSS (NM_010497)	promoter-TSS (NM_010497)	52	NM_010497	15926	Mm.9925	NM_010497	ENSMUSG00000025950	Idh1	AI314845|AI788952|E030024J03Rik|Id-1|Idh-1|Idpc	isocitrate dehydrogenase 1 (NADP+), soluble	protein-coding
mm_92344.1	chr10	75837341	75837383	-	1	NA	Intergenic	CpG	-2481	NM_010361	14872	Mm.24118	NM_010361	ENSMUSG00000033318	Gstt2	AI266894|Yrs|mGSTT2	glutathione S-transferase, theta 2	protein-coding
mm_115040.1	chr13	99435066	99435084	+	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-22249	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_84420.1	chr9	65629453	65629496	-	1	NA	Intergenic	CpG	-1108	NM_028030	71973	Mm.29148	NM_028030	ENSMUSG00000032387	Rbpms2	2400008B06Rik|AI316523	RNA binding protein with multiple splicing 2	protein-coding
mm_65872.1	chr7	29505793	29505822	-	1	NA	promoter-TSS (NM_001081028)	promoter-TSS (NM_001081028)	-347	NM_001081028	74206	Mm.447042	NM_001081028	ENSMUSG00000030583	Sipa1l3	2610511M17Rik	signal-induced proliferation-associated 1 like 3	protein-coding
mm_21182.1	chr2	155065055	155065067	-	1	NA	intron (NM_016661, intron 4 of 9)	intron (NM_016661, intron 4 of 9)	9436	NM_016661	269378	Mm.330692	NM_016661	ENSMUSG00000027597	Ahcy	AA987153|AL024110|CuBP|SAHH	S-adenosylhomocysteine hydrolase	protein-coding
mm_26730.1	chr3	5357885	5357928	-	1	NA	intron (NM_030708, intron 4 of 10)	intron (NM_030708, intron 4 of 10)	-137083	NR_045905	72608	Mm.384359	NR_045905		2700069I18Rik	-	RIKEN cDNA 2700069I18 gene	ncRNA
mm_18922.1	chr2	76742737	76742752	-	1	NA	exon (NM_011652, exon 275 of 313)	exon (NM_011652, exon 275 of 313)	67429	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_158842.1	chrX	169320119	169320133	-	1	NA	5' UTR (NM_001331049, exon 1 of 7)	5' UTR (NM_001331049, exon 1 of 7)	246	NM_001331050	15159	Mm.284033	NM_008222	ENSMUSG00000031352	Hccs	-	holocytochrome c synthetase	protein-coding
mm_159088.1	chr2	31474715	31474715	+	1	NA	non-coding (NR_002687, exon 2 of 16)	non-coding (NR_002687, exon 2 of 16)	4407	NR_002687	432466	Mm.333323	NR_002687	ENSMUSG00000046687	Gm5424	EG432466	argininosuccinate synthase pseudogene	pseudo
mm_159158.1	chr2	89816425	89816425	+	1	NA	promoter-TSS (NM_146977)	promoter-TSS (NM_146977)	97	NM_146977	258979	Mm.377775	NM_146977	ENSMUSG00000045148	Olfr1255	MOR232-4	olfactory receptor 1255	protein-coding
mm_126478.1	chr15	81523833	81523871	+	1	NA	Intergenic	Intergenic	57536	NM_019712	56438	Mm.29405	NM_019712	ENSMUSG00000022400	Rbx1	1500002P15Rik|AA517855|ROC1	ring-box 1	protein-coding
mm_40475.1	chr5	53998696	53998707	+	1	NA	5' UTR (NM_001081103, exon 1 of 12)	5' UTR (NM_001081103, exon 1 of 12)	178	NM_001081103	116873	Mm.265985	NM_054083	ENSMUSG00000039156	Stim2	-	stromal interaction molecule 2	protein-coding
mm_85148.1	chr9	95857882	95857895	-	1	NA	promoter-TSS (NM_001271569)	promoter-TSS (NM_001271569)	-6	NM_001271569	73410	Mm.443314	NM_028533	ENSMUSG00000096655	1700065D16Rik	-	RIKEN cDNA 1700065D16 gene	protein-coding
mm_87361.1	chr10	43828787	43828790	+	1	NA	intron (NR_131055, intron 1 of 2)	RMER20C_Mm|LTR|ERVK	2881	NR_131055	71018	Mm.410796	NR_131055	ENSMUSG00000111342	4933404K13Rik	-	RIKEN cDNA 4933404K13 gene	ncRNA
mm_19776.1	chr2	106650322	106650338	-	1	NA	promoter-TSS (NR_137201)	promoter-TSS (NR_137201)	34	NR_137201	102640562	Mm.404175	NR_137201	ENSMUSG00000085218	BB218582	-	expressed sequence BB218582	ncRNA
mm_2086.1	chr1	87676484	87676495	+	1	NA	intron (NM_010566, intron 6 of 26)	intron (NM_010566, intron 6 of 26)	56177	NM_001110193	16331	Mm.15105	NM_010566	ENSMUSG00000026288	Inpp5d	SHIP|SHIP-1|SHIP1|SIP-145|p150Ship|s-SHIP	inositol polyphosphate-5-phosphatase D	protein-coding
mm_49209.1	chr6	15720995	15720999	+	1	NA	intron (NM_175088, intron 1 of 4)	CpG	336	NM_175088	16543	Mm.1314	NM_175088	ENSMUSG00000041390	Mdfic	Kdt1|Mdfid	MyoD family inhibitor domain containing	protein-coding
mm_132067.1	chr16	30064165	30064196	+	1	NA	Intergenic	CpG	-1177	NM_008235	15205	Mm.390859	NM_008235	ENSMUSG00000022528	Hes1	Hry|bHLHb39	hairy and enhancer of split 1 (Drosophila)	protein-coding
mm_3082.1	chr1	134405726	134405736	+	1	NA	promoter-TSS (NM_028057)	promoter-TSS (NM_028057)	-259	NM_028057	72017	Mm.280230	NM_028057	ENSMUSG00000026456	Cyb5r1	1500005G05Rik|B5R.1|C80155|Nqo3a2	cytochrome b5 reductase 1	protein-coding
mm_156847.1	chrX	164394504	164394530	+	1	NA	exon (NM_010216, exon 4 of 7)	exon (NM_010216, exon 4 of 7)	20995	NM_010216	14205	Mm.297978	NM_010216	ENSMUSG00000031380	Vegfd	AI325264|Figf|VEGF-D	vascular endothelial growth factor D	protein-coding
mm_65173.1	chr7	19691947	19691956	-	1	NA	exon (NM_001110009, exon 3 of 4)	exon (NM_001110009, exon 3 of 4)	708	NM_001110009	11812	Mm.182440	NM_007469	ENSMUSG00000040564	Apoc1	Apo-CIB|ApoC-IB|apo-CI|apoC-I	apolipoprotein C-I	protein-coding
mm_17450.1	chr2	28555891	28555895	-	1	NA	TTS (NM_009885)	TTS (NM_009885)	7510	NM_009885	12613	Mm.236017	NM_009885	ENSMUSG00000026818	Cel	1810036E18Rik|BAL	carboxyl ester lipase	protein-coding
mm_77745.1	chr8	126979512	126979519	-	1	NA	Intergenic	Intergenic	-8436	NM_172762	52202	Mm.28199	NM_172762	ENSMUSG00000033931	Rbm34	4930547K05Rik|6330444B11|D8Ertd233e	RNA binding motif protein 34	protein-coding
mm_681.1	chr1	40500372	40500383	+	1	NA	3' UTR (NM_008365, exon 11 of 11)	3' UTR (NM_008365, exon 11 of 11)	-14985	NM_010553	16174	Mm.20466	NM_010553	ENSMUSG00000026068	Il18rap	AcPL|IL-18R-beta|IL-18RAcP|IL-18Rbeta|IL-1RAcPL	interleukin 18 receptor accessory protein	protein-coding
mm_59252.1	chr7	24853899	24853924	+	1	NA	Intergenic	Intergenic	15780	NM_182785	232973	Mm.189648	NM_182785	ENSMUSG00000062732	Lypd4	4933400F01Rik	Ly6/Plaur domain containing 4	protein-coding
mm_123275.1	chr14	61370733	61370754	-	1	NA	exon (NM_008466, exon 14 of 17)	exon (NM_008466, exon 14 of 17)	-10298	NM_026598	68177	Mm.22758	NM_026598	ENSMUSG00000021928	Ebpl	5730442K12Rik|EBRP	emopamil binding protein-like	protein-coding
mm_119407.1	chr14	44988457	44988472	+	1	NA	5' UTR (NM_008964, exon 1 of 2)	5' UTR (NM_008964, exon 1 of 2)	353	NM_008964	19217	Mm.4630	NM_008964	ENSMUSG00000037759	Ptger2	EP2|Ptgerep2	prostaglandin E receptor 2 (subtype EP2)	protein-coding
mm_123094.1	chr14	55788716	55788729	-	1	NA	5' UTR (NM_019955, exon 1 of 10)	5' UTR (NM_019955, exon 1 of 10)	135	NM_001164107	56532	Mm.46612	NM_019955	ENSMUSG00000022221	Ripk3	2610528K09Rik|AW107945|Rip3	receptor-interacting serine-threonine kinase 3	protein-coding
mm_153681.1	chr19	44396671	44396685	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	11031	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_100020.1	chr11	114891013	114891045	+	1	NA	intron (NM_001347654, intron 1 of 6)	intron (NM_001347654, intron 1 of 6)	988	NM_170758	217303	Mm.294439	NM_170758	ENSMUSG00000034652	Cd300a	B230315M08Rik|Clm8|LMIR1|MAIR-I|MAIR-Ia|MMAC8|Pigr4|mcpir1	CD300A molecule	protein-coding
mm_33287.1	chr4	128846164	128846166	+	1	NA	Intergenic	Intergenic	-37975	NM_178110	67525	Mm.30653	NM_178110	ENSMUSG00000041000	Trim62	6330414G21Rik|AI450348|Dear1	tripartite motif-containing 62	protein-coding
mm_86776.1	chr10	20148694	20148705	+	1	NA	promoter-TSS (NM_008635)	promoter-TSS (NM_008635)	-221	NM_008635	17761	Mm.20928	NM_008635	ENSMUSG00000019996	Map7	E-MAP-115|MAP-7|Mtap7|R75000|mshi|mste|ste	microtubule-associated protein 7	protein-coding
mm_4732.1	chr1	181576574	181576578	+	1	NA	Intergenic	Intergenic	-65125	NM_207280	403180	Mm.220754	NM_207280	ENSMUSG00000050625	Ccdc121	6530421E24Rik|Gm755	coiled-coil domain containing 121	protein-coding
mm_129620.1	chr15	80081054	80081081	-	1	NA	intron (NM_013762, intron 3 of 9)	intron (NM_013762, intron 3 of 9)	1839	NR_028281	100302600		NR_028281		Snord43	MBII-47	small nucleolar RNA, C/D box 43	snoRNA
mm_64212.1	chr7	141476405	141476407	+	1	NA	promoter-TSS (NM_001252588)	promoter-TSS (NM_001252588)	26	NM_001252588	64540	Mm.489619	NM_053082	ENSMUSG00000025511	Tspan4	AI325509|AI746565|D130042I01Rik|NAG-2|Tm4sf7|Tspan-4	tetraspanin 4	protein-coding
mm_166417.1	chr5	137151607	137151614	+	1	NA	Intergenic	Intergenic	-35403	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_167957.1	chrX	141627898	141627903	+	1	NA	intron (NM_007736, intron 31 of 51)	intron (NM_007736, intron 31 of 51)	97317	NM_010572	16370	Mm.261591	NM_010572	ENSMUSG00000054667	Irs4	IRS-4	insulin receptor substrate 4	protein-coding
mm_153571.1	chr19	42752711	42752721	-	1	NA	promoter-TSS (NM_029011)	promoter-TSS (NM_029011)	59	NM_029011	74580	Mm.329858	NM_029011	ENSMUSG00000060224	Pyroxd2	3830409H07Rik|4833409A17Rik	pyridine nucleotide-disulphide oxidoreductase domain 2	protein-coding
mm_48497.1	chr5	142800423	142800442	-	1	NA	intron (NM_178242, intron 2 of 15)	intron (NM_178242, intron 2 of 15)	16955	NM_178242	231861	Mm.354649	NM_178242	ENSMUSG00000039477	Tnrc18	BC025631|EG381742|Zfp469	trinucleotide repeat containing 18	protein-coding
mm_136551.1	chr16	98082433	98082439	-	1	NA	promoter-TSS (NR_015491)	promoter-TSS (NR_015491)	3	NR_015491	320586	Mm.442230	NR_015491		A630089N07Rik	-	RIKEN cDNA A630089N07 gene	ncRNA
mm_129206.1	chr15	76518358	76518381	-	1	NA	3' UTR (NM_130893, exon 2 of 2)	3' UTR (NM_130893, exon 2 of 2)	3760	NM_130893	170729	Mm.218747	NM_130893	ENSMUSG00000048385	Scrt1	-	scratch family zinc finger 1	protein-coding
mm_148052.1	chr18	71803429	71803459	-	1	NA	intron (NM_007831, intron 5 of 28)	intron (NM_007831, intron 5 of 28)	547625	NM_007831	13176	Mm.167882	NM_007831	ENSMUSG00000060534	Dcc	C030036D22Rik|Igdcc1	deleted in colorectal carcinoma	protein-coding
mm_35125.1	chr4	11156243	11156258	-	1	NA	promoter-TSS (NM_001199105)	promoter-TSS (NM_001199105)	-191	NM_001199105	60599	Mm.393018	NM_021897	ENSMUSG00000028211	Trp53inp1	2700057G22Rik|SIP|SIP18|SIP27|Stinp|Teap	transformation related protein 53 inducible nuclear protein 1	protein-coding
mm_105.1	chr1	9548115	9548125	+	1	NA	promoter-TSS (NM_175236)	promoter-TSS (NM_175236)	74	NR_027664	76187	Mm.28514	NM_175236	ENSMUSG00000025911	Adhfe1	6330565B14Rik|AI043035|Adh8	alcohol dehydrogenase, iron containing, 1	protein-coding
mm_114767.1	chr13	88521219	88521230	+	1	NA	Intergenic	L1_Mus1|LINE|L1	-300248	NM_010103	13612	Mm.125580	NM_010103	ENSMUSG00000034488	Edil3	Del-1|Del1	EGF-like repeats and discoidin I-like domains 3	protein-coding
mm_84652.1	chr9	71592347	71592372	-	1	NA	promoter-TSS (NM_001033208)	promoter-TSS (NM_001033208)	1	NM_001033208	102371	Mm.27585	NM_001033208	ENSMUSG00000041361	Myzap	AA407270|AV006038|Gcom1|Gm640|Grinl1a7|Myozap	myocardial zonula adherens protein	protein-coding
mm_120139.1	chr14	60377604	60377610	+	1	NA	promoter-TSS (NM_001164705)	promoter-TSS (NM_001164705)	-679	NM_028113	72125	Mm.275499	NM_028113	ENSMUSG00000021986	Amer2	2600011E07Rik|Fam123a	APC membrane recruitment 2	protein-coding
mm_162875.1	chr10	97506602	97506608	+	1	NA	exon (NM_007833, exon 4 of 8)	exon (NM_007833, exon 4 of 8)	24274	NM_007833	13179	Mm.56769	NM_007833	ENSMUSG00000019929	Dcn	DC|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding
mm_99357.1	chr11	101610649	101610662	+	1	NA	promoter-TSS (NM_001256318)	promoter-TSS (NM_001256318)	-45	NM_001256318	666331	Mm.303457	NM_001256318		LOC666331	-	uncharacterized LOC666331	protein-coding
mm_123417.1	chr14	64327578	64327597	-	1	NA	intron (NM_001253712, intron 1 of 5)	MLT1F1|LTR|ERVL-MaLR	89369	NM_001253716	110265	Mm.26713	NM_026322	ENSMUSG00000054733	Msra	2310045J23Rik|6530413P12Rik|MSR-A	methionine sulfoxide reductase A	protein-coding
mm_172672.1	chr8	44938228	44938228	+	1	NA	Intergenic	CpG	-11980	NM_001081286	14107	Mm.27365	NM_001081286	ENSMUSG00000070047	Fat1	2310038E12Rik|AU023433|Fath|mFat1	FAT atypical cadherin 1	protein-coding
mm_21210.1	chr2	155653536	155653554	-	1	NA	exon (NM_001163452, exon 8 of 19)	exon (NM_001163452, exon 8 of 19)	30665	NR_030757	735275		NR_030757	ENSMUSG00000076312	Mir499	Mirn499|mir-499|mmu-mir-499	microRNA 499	ncRNA
mm_12924.1	chr2	85037170	85037205	+	1	NA	promoter-TSS (NM_001136081)	promoter-TSS (NM_001136081)	67	NM_182990	20833	Mm.219793	NM_182990	ENSMUSG00000027067	Ssrp1	C81323|Hmg1-rs1|Hmgi-rs3|Hmgox|T160	structure specific recognition protein 1	protein-coding
mm_84555.1	chr9	67707030	67707031	-	1	NA	Intergenic	Intergenic	20750	NR_106100	102466824		NR_106100	ENSMUSG00000098937	Mir7241	Gm27918|mmu-mir-7241	microRNA 7241	ncRNA
mm_41915.1	chr5	105596093	105596121	+	1	NA	intron (NM_133897, intron 3 of 3)	intron (NM_133897, intron 3 of 3)	76636	NM_133897	100604	Mm.319847	NM_133897	ENSMUSG00000054720	Lrrc8c	AD158|AI326115|E430036I04Rik|fad158	leucine rich repeat containing 8 family, member C	protein-coding
mm_149823.1	chr19	24416023	24416031	+	1	NA	intron (NM_008846, intron 3 of 14)	intron (NM_008846, intron 3 of 14)	61447	NM_026520	68034	Mm.440181	NM_026520	ENSMUSG00000074922	Fam122a	2410124L17Rik|2900009I07Rik|ENSMUSG00000051082|Gm9849	family with sequence similarity 122, member A	protein-coding
mm_66830.1	chr7	48845212	48845223	-	1	NA	intron (NM_001198841, intron 1 of 5)	intron (NM_001198841, intron 1 of 5)	-1546	NM_013808	13009	Mm.17235	NM_013808	ENSMUSG00000030470	Csrp3	CRP3|MLP|MMLP	cysteine and glycine-rich protein 3	protein-coding
mm_19479.1	chr2	93014574	93014598	-	1	NA	intron (NM_001177536, intron 1 of 6)	intron (NM_001177536, intron 1 of 6)	-14762	NR_110333	433456	Mm.235231	NM_001002794	ENSMUSG00000075027	4631405J19Rik	-	RIKEN cDNA 4631405J19 gene	ncRNA
mm_40383.1	chr5	52368820	52368845	+	1	NA	3' UTR (NM_011435, exon 2 of 2)	3' UTR (NM_011435, exon 2 of 2)	5028	NM_011435	20657	Mm.2407	NM_011435	ENSMUSG00000072941	Sod3	AI314465|EC-SOD	superoxide dismutase 3, extracellular	protein-coding
mm_136896.1	chr17	13014553	13014556	+	1	NA	intron (NM_013671, intron 4 of 4)	intron (NM_013671, intron 4 of 4)	6715	NM_013671	20656	Mm.290876	NM_013671	ENSMUSG00000006818	Sod2	MnSOD|Sod-2	superoxide dismutase 2, mitochondrial	protein-coding
mm_63605.1	chr7	128149167	128149179	+	1	NA	exon (NM_021334, exon 29 of 30)	exon (NM_021334, exon 29 of 30)	19605	NM_021334	16411	Mm.22378	NM_021334	ENSMUSG00000030789	Itgax	AI449405|Cd11c|Cr4|N418	integrin alpha X	protein-coding
mm_154540.1	chrM	14143	14181	-	1	NA	NA	Intergenic	NA	NA								
mm_57465.1	chr6	125192097	125192117	-	1	NA	promoter-TSS (NM_025595)	promoter-TSS (NM_025595)	-93	NM_025595	66493	Mm.138749	NM_025595	ENSMUSG00000030335	Mrpl51	2610511M02Rik|CDA09|HSPC241|Mrp64	mitochondrial ribosomal protein L51	protein-coding
mm_84701.1	chr9	72663251	72663270	-	1	NA	intron (NM_010890, intron 1 of 28)	intron (NM_010890, intron 1 of 28)	913	NM_010890	17999	Mm.279923	NM_010890	ENSMUSG00000032216	Nedd4	AA959633|AL023035|AU019897|E430025J12Rik|Nedd4-1|Nedd4a|mKIAA0093	neural precursor cell expressed, developmentally down-regulated 4	protein-coding
mm_129560.1	chr15	79545740	79545743	-	1	NA	intron (NM_199080, intron 1 of 12)	intron (NM_199080, intron 1 of 12)	818	NM_199079	67040	Mm.29644	NM_152806	ENSMUSG00000055065	Ddx17	2610007K22Rik|A430025E01Rik|AI047725|C80929|Gm926|p72	DEAD (Asp-Glu-Ala-Asp) box polypeptide 17	protein-coding
mm_168960.1	chr12	80221157	80221157	-	1	NA	intron (NM_001346669, intron 1 of 20)	intron (NM_001346669, intron 1 of 20)	39214	NM_134156	109711	Mm.253564	NM_134156	ENSMUSG00000015143	Actn1	3110023F10Rik|Actn1a	actinin, alpha 1	protein-coding
mm_99579.1	chr11	104231443	104231453	+	1	NA	promoter-TSS (NM_010838)	promoter-TSS (NM_010838)	12	NM_001285454	17762	Mm.1287	NM_010838	ENSMUSG00000018411	Mapt	AI413597|AW045860|Mtapt|Tau	microtubule-associated protein tau	protein-coding
mm_72090.1	chr8	71580464	71580481	+	1	NA	intron (NM_011977, intron 6 of 13)	intron (NM_011977, intron 6 of 13)	11545	NM_011977	26457	Mm.38165	NM_011977	ENSMUSG00000031808	Slc27a1	FATP1|Fatp	solute carrier family 27 (fatty acid transporter), member 1	protein-coding
mm_58022.1	chr6	136661775	136661784	-	1	NA	5' UTR (NM_025806, exon 1 of 11)	5' UTR (NM_025806, exon 1 of 11)	114	NM_025806	66857	Mm.3311	NM_025806	ENSMUSG00000030214	Plbd1	1100001H23Rik	phospholipase B domain containing 1	protein-coding
mm_146954.1	chr18	32560126	32560145	-	1	NA	promoter-TSS (NM_001048207)	promoter-TSS (NM_001048207)	-101	NM_001048207	71683	Mm.292145	NM_027863	ENSMUSG00000090523	Gypc	0610037F22Rik|Cd236r	glycophorin C	protein-coding
mm_127242.1	chr15	99592461	99592477	+	1	NA	intron (NM_009701, intron 1 of 3)	intron (NM_009701, intron 1 of 3)	1441	NM_009701	11830	Mm.45580	NM_009701	ENSMUSG00000044217	Aqp5	-	aquaporin 5	protein-coding
mm_136700.1	chr17	7324661	7324677	+	1	NA	promoter-TSS (NM_011553)	promoter-TSS (NM_011553)	9	NR_046291	21461	Mm.264651	NM_011553	ENSMUSG00000071322	Tcp10a	D17Leh66A|D17Leh66aa|Gm10326|T66A-a|Tcp-10a	t-complex protein 10a	protein-coding
mm_140727.1	chr17	15498283	15498304	-	1	NA	promoter-TSS (NM_011185)	promoter-TSS (NM_011185)	-17	NM_011185	19170	Mm.32912	NM_011185	ENSMUSG00000014769	Psmb1	AA409053|C81484|Lmpc5	proteasome (prosome, macropain) subunit, beta type 1	protein-coding
mm_150823.1	chr19	44511233	44511242	+	1	NA	exon (NM_011720, exon 5 of 6)	exon (NM_011720, exon 5 of 6)	17765	NM_011720	22423	Mm.88365	NM_011720	ENSMUSG00000036961	Wnt8b	-	wingless-type MMTV integration site family, member 8B	protein-coding
mm_70108.1	chr7	142664695	142664713	-	1	NA	intron (NR_002855, intron 1 of 3)	intron (NR_002855, intron 1 of 3)	2112	NM_001315488	16002	Mm.3862	NM_010514	ENSMUSG00000048583	Igf2	AL033362|Igf-2|Igf-II|M6pr|Mpr|Peg2	insulin-like growth factor 2	protein-coding
mm_44513.1	chr5	24344530	24344544	-	1	NA	intron (NM_013569, intron 2 of 14)	intron (NM_013569, intron 2 of 14)	7067	NM_013569	16511	Mm.6539	NM_013569	ENSMUSG00000038319	Kcnh2	AI326795|ERG1|LQT|Lqt2|M-erg|Merg1|merg1a|merg1b	potassium voltage-gated channel, subfamily H (eag-related), member 2	protein-coding
mm_54170.1	chr6	23272525	23272530	-	1	NA	intron (NM_001252110, intron 26 of 27)	intron (NM_001252110, intron 26 of 27)	-24263	NM_028462	73191	Mm.55115	NM_028462	ENSMUSG00000029697	Fezf1	3110069A13Rik|Fez|Zfp312-like|fez-like	Fez family zinc finger 1	protein-coding
mm_6026.1	chr1	59237176	59237256	-	1	NA	promoter-TSS (NM_001159948)	promoter-TSS (NM_001159948)	15	NM_028717	74018	Mm.272078	NM_028717	ENSMUSG00000026024	Als2	3222402C23Rik|9430073A21Rik|Als2cr6|Alsin|mKIAA1563	amyotrophic lateral sclerosis 2 (juvenile)	protein-coding
mm_2981.1	chr1	133131240	133131254	+	1	NA	promoter-TSS (NM_133819)	promoter-TSS (NM_133819)	81	NM_133819	108954	Mm.293628	NM_133819	ENSMUSG00000046062	Ppp1r15b	1810033K10Rik|AI606441|C530022L24Rik|CReP	protein phosphatase 1, regulatory (inhibitor) subunit 15b	protein-coding
mm_56458.1	chr6	98342662	98342691	-	1	NA	promoter-TSS (NM_001128092)	promoter-TSS (NM_001128092)	78	NM_001128092	330390	Mm.484161	NM_001128092	ENSMUSG00000090667	Gm765	-	predicted gene 765	protein-coding
mm_111088.1	chr12	80260521	80260543	-	1	NA	promoter-TSS (NM_134156)	promoter-TSS (NM_134156)	-151	NM_001346669	109711	Mm.253564	NM_134156	ENSMUSG00000015143	Actn1	3110023F10Rik|Actn1a	actinin, alpha 1	protein-coding
mm_19883.1	chr2	114049665	114049679	-	1	NA	exon (NM_009608, exon 4 of 7)	exon (NM_009608, exon 4 of 7)	3203	NM_009608	11464	Mm.686	NM_009608	ENSMUSG00000068614	Actc1	Actc-1	actin, alpha, cardiac muscle 1	protein-coding
mm_86041.1	chr9	114461726	114461739	-	1	NA	intron (NR_108101, intron 13 of 14)	B4A|SINE|B4	34812	NM_009916	12773	Mm.1337	NM_009916	ENSMUSG00000047898	Ccr4	C-C CKR-4|CHEMR1|Cmkbr4|LESTR|Sdf1r	chemokine (C-C motif) receptor 4	protein-coding
mm_43401.1	chr5	135806860	135806902	+	1	NA	Intergenic	Intergenic	-11225	NM_021403	58212	Mm.271230	NM_021403	ENSMUSG00000039860	Srrm3	2900083I11Rik|AB041661|SRm300-like|Srrm2l	serine/arginine repetitive matrix 3	protein-coding
mm_132220.1	chr16	32631203	32631215	+	1	NA	3' UTR (NM_011638, exon 19 of 19)	3' UTR (NM_011638, exon 19 of 19)	-13434	NM_001110147	51789	Mm.251115	NM_016788	ENSMUSG00000022791	Tnk2	Ack|Ack-1|Ack1|Cdgip|Pyk1	tyrosine kinase, non-receptor, 2	protein-coding
mm_53463.1	chr6	134898070	134898110	+	1	NA	promoter-TSS (NM_001167694)	promoter-TSS (NM_001167694)	129	NR_029441	72813	Mm.409034	NR_029441	ENSMUSG00000100876	2810454H06Rik	-	RIKEN cDNA 2810454H06 gene	ncRNA
mm_20445.1	chr2	129310145	129310178	-	1	NA	promoter-TSS (NM_010554)	promoter-TSS (NM_010554)	-189	NM_010554	16175	Mm.15534	NM_010554	ENSMUSG00000027399	Il1a	Il-1a	interleukin 1 alpha	protein-coding
mm_60221.1	chr7	43562292	43562317	+	1	NA	promoter-TSS (NM_001008549)	promoter-TSS (NM_001008549)	-66	NM_001008549	210104	Mm.333821	NM_001008549	ENSMUSG00000056592	Zfp658	-	zinc finger protein 658	protein-coding
mm_65590.1	chr7	27327478	27327494	-	1	NA	exon (NM_175641, exon 12 of 33)	exon (NM_175641, exon 12 of 33)	6162	NM_001113549	108075	Mm.272251	NM_175641	ENSMUSG00000040488	Ltbp4	2310046A13Rik	latent transforming growth factor beta binding protein 4	protein-coding
mm_66955.1	chr7	62419434	62419455	-	1	NA	exon (NM_011746, exon 1 of 1)	exon (NM_011746, exon 1 of 1)	695	NM_011746	22652	Mm.146	NM_011746	ENSMUSG00000070527	Mkrn3	D7H15S9-1|Zfp127	makorin, ring finger protein, 3	protein-coding
mm_81036.1	chr9	105018369	105018378	+	1	NA	intron (NM_028719, intron 11 of 15)	intron (NM_028719, intron 11 of 15)	-34895	NM_053159	94062	Mm.29746	NM_053159	ENSMUSG00000032563	Mrpl3	2010320L16Rik|5930422H18Rik|AA407889	mitochondrial ribosomal protein L3	protein-coding
mm_121139.1	chr14	101891311	101891314	+	1	NA	intron (NM_001347628, intron 8 of 26)	MER20|DNA|hAT-Charlie	50689	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_56154.1	chr6	87845310	87845329	-	1	NA	exon (NM_013493, exon 4 of 5)	exon (NM_013493, exon 4 of 5)	5787	NM_001109746	12785	Mm.290251	NM_013493	ENSMUSG00000030057	Cnbp	AA408710|Cnbp1|Znf9	cellular nucleic acid binding protein	protein-coding
mm_93465.1	chr10	111009980	111009984	-	1	NA	promoter-TSS (NM_172554)	promoter-TSS (NM_172554)	84	NM_172554	320150	Mm.339281	NM_172554	ENSMUSG00000035798	Zdhhc17	A230053P19Rik|BB187739|D130071N24Rik|Hip14	zinc finger, DHHC domain containing 17	protein-coding
mm_143431.1	chr17	70851190	70851216	-	1	NA	promoter-TSS (NM_009372)	promoter-TSS (NM_009372)	7	NM_009372	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_53609.1	chr6	139587199	139587230	+	1	NA	Intergenic	Intergenic	-85305	NM_001128090	632971	Mm.475610	NM_001128090	ENSMUSG00000092164	Rergl	EG632971	RERG/RAS-like	protein-coding
mm_100602.1	chr11	121237306	121237317	+	1	NA	promoter-TSS (NM_026272)	promoter-TSS (NM_026272)	75	NM_026272	67608	Mm.291832	NM_026272	ENSMUSG00000000056	Narf	4430402O11Rik	nuclear prelamin A recognition factor	protein-coding
mm_134416.1	chr16	17722880	17722936	-	1	NA	promoter-TSS (NM_001040683)	promoter-TSS (NM_001040683)	-8	NM_001285886	94112	Mm.208970	NM_033609	ENSMUSG00000012114	Med15	A230074L19Rik|AW536074|Pcqap|mPcqap	mediator complex subunit 15	protein-coding
mm_34026.1	chr4	138057960	138057991	+	1	NA	5' UTR (NM_001256198, exon 4 of 33)	5' UTR (NM_001256198, exon 4 of 33)	64519	NM_172703	230861	Mm.268903	NM_172703	ENSMUSG00000028760	Eif4g3	1500002J22Rik|4930523M17Rik|G1-419-52|eIF4GII|repro8	eukaryotic translation initiation factor 4 gamma, 3	protein-coding
mm_173320.1	chrY	90736931	90736945	+	1	NA	Intergenic	IMPB_01|Satellite|Satellite	18112	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_82656.1	chr9	22071369	22071416	-	1	NA	promoter-TSS (NM_177318)	promoter-TSS (NM_177318)	-16	NM_001310759	319601	Mm.347707	NM_177318	ENSMUSG00000038895	Zfp653	E430039K05Rik|Znf653	zinc finger protein 653	protein-coding
mm_50555.1	chr6	49047749	49047757	+	1	NA	exon (NM_053110, exon 6 of 11)	exon (NM_053110, exon 6 of 11)	11235	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_93537.1	chr10	115384338	115384375	-	1	NA	promoter-TSS (NM_025780)	promoter-TSS (NM_025780)	79	NM_025780	66816	Mm.32314	NM_025780	ENSMUSG00000020137	Thap2	2900040O07Rik|9030625G08Rik|AI450385|AI649097	THAP domain containing, apoptosis associated protein 2	protein-coding
mm_81701.1	chr9	111271813	111271823	+	1	NA	promoter-TSS (NM_026810)	promoter-TSS (NM_026810)	-27	NM_175266	77781	Mm.209005	NM_175266	ENSMUSG00000046785	Epm2aip1	A930003G21Rik|mKIAA0766	EPM2A (laforin) interacting protein 1	protein-coding
mm_25406.1	chr3	107279015	107279025	+	1	NA	exon (NM_026774, exon 1 of 4)	exon (NM_026774, exon 1 of 4)	162	NM_026774	68576	Mm.290035	NM_026774	ENSMUSG00000087260	Lamtor5	1110003H18Rik|Hbxip|XIP	late endosomal/lysosomal adaptor, MAPK and MTOR activator 5	protein-coding
mm_32911.1	chr4	119132625	119132638	+	1	NA	exon (NM_011400, exon 4 of 10)	exon (NM_011400, exon 4 of 10)	23886	NM_011400	20525	Mm.21002	NM_011400	ENSMUSG00000028645	Slc2a1	Glut-1|Glut1	solute carrier family 2 (facilitated glucose transporter), member 1	protein-coding
mm_116565.1	chr13	47010765	47010777	-	1	NA	Intergenic	Intergenic	4079	NM_175340	105193	Mm.25593	NM_175340	ENSMUSG00000044231	Nhlrc1	AI505271|B230309E09Rik|EPM2B	NHL repeat containing 1	protein-coding
mm_104786.1	chr11	98706555	98706570	-	1	NA	intron (NM_011869, intron 22 of 25)	intron (NM_011869, intron 22 of 25)	5249	NM_009971	12985	Mm.1238	NM_009971	ENSMUSG00000038067	Csf3	Csfg|G-CSF|MGI-IG	colony stimulating factor 3 (granulocyte)	protein-coding
mm_61113.1	chr7	54835590	54835610	+	1	NA	5' UTR (NM_178705, exon 1 of 12)	5' UTR (NM_178705, exon 1 of 12)	355	NM_178705	233271	Mm.387344	NM_178705	ENSMUSG00000063297	Luzp2	9330154K17Rik|D130073E01	leucine zipper protein 2	protein-coding
mm_83047.1	chr9	37544554	37544563	-	1	NA	TTS (NM_022029)	TTS (NM_022029)	5303	NM_020518	57276	Mm.27478	NM_020518	ENSMUSG00000001943	Vsig2	1190004B15Rik|2210413P10Rik|AU040484|CTX|Ctm	V-set and immunoglobulin domain containing 2	protein-coding
mm_165435.1	chr2	153686908	153686929	+	1	NA	3' UTR (NM_010068, exon 21 of 21)	3' UTR (NM_010068, exon 21 of 21)	37469	NM_001271747	13436	Mm.89772	NM_010068	ENSMUSG00000027478	Dnmt3b	MmuIIIB	DNA methyltransferase 3B	protein-coding
mm_125419.1	chr15	41831008	41831018	+	1	NA	promoter-TSS (NM_001130164)	promoter-TSS (NM_001130164)	55	NM_001130164	170719	Mm.254267	NM_130885	ENSMUSG00000022307	Oxr1	2210416C20Rik|C7|C7B	oxidation resistance 1	protein-coding
mm_63260.1	chr7	126663946	126663971	+	1	NA	exon (NM_029339, exon 3 of 10)	exon (NM_029339, exon 3 of 10)	12399	NM_133670	20887	Mm.368982	NM_133670	ENSMUSG00000030711	Sult1a1	AI266890|PST|ST1A1|Stp|Stp1	sulfotransferase family 1A, phenol-preferring, member 1	protein-coding
mm_15601.1	chr2	160670175	160670182	+	1	NA	exon (NM_009408, exon 3 of 21)	exon (NM_009408, exon 3 of 21)	24281	NM_009408	21969	Mm.217233	NM_009408	ENSMUSG00000070544	Top1	AI467334|D130064I21Rik|Top-1	topoisomerase (DNA) I	protein-coding
mm_14538.1	chr2	132792435	132792469	+	1	NA	exon (NM_007694, exon 4 of 5)	exon (NM_007694, exon 4 of 5)	11174	NM_007694	12653	Mm.255241	NM_007694	ENSMUSG00000027350	Chgb	Scg-1	chromogranin B	protein-coding
mm_109218.1	chr12	108765966	108765971	+	1	NA	Intergenic	Intergenic	-27343	NM_009537	22632	Mm.3868	NM_009537	ENSMUSG00000021264	Yy1	AW488674|NF-E1	YY1 transcription factor	protein-coding
mm_133681.1	chr16	92470929	92470968	+	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	-4779	NM_001081549	54720	Mm.265744	NM_019466	ENSMUSG00000022951	Rcan1	Adapt78|CALP1L|CSP1|DSC1|Dscr1|MCIP1|RCN1	regulator of calcineurin 1	protein-coding
mm_138600.1	chr17	35555210	35555224	+	1	NA	exon (NM_001008424, exon 2 of 2)	exon (NM_001008424, exon 2 of 2)	3089	NM_001008424	386463	Mm.426664	NM_001008424	ENSMUSG00000039518	Cdsn	AI747712	corneodesmosin	protein-coding
mm_89072.1	chr10	82985444	82985454	+	1	NA	promoter-TSS (NM_021439)	promoter-TSS (NM_021439)	-48	NM_021439	58250	Mm.360747	NM_021439	ENSMUSG00000034612	Chst11	1110020P09Rik|C4ST|C4ST-1|C4ST1|C4s	carbohydrate sulfotransferase 11	protein-coding
mm_72521.1	chr8	83973049	83973059	+	1	NA	promoter-TSS (NM_008854)	promoter-TSS (NM_008854)	76	NM_008854	18747	Mm.19111	NM_008854	ENSMUSG00000005469	Prkaca	PKCD|Pkaca	protein kinase, cAMP dependent, catalytic, alpha	protein-coding
mm_30556.1	chr4	3700818	3700828	+	1	NA	intron (NM_010747, intron 1 of 12)	intron (NM_010747, intron 1 of 12)	-14141	NR_028126	70720	Mm.445696	NR_028126		6330407A03Rik	-	RIKEN cDNA 6330407A03 gene	ncRNA
mm_74791.1	chr8	22186970	22186980	-	1	NA	Intergenic	RMER17C|LTR|ERVK	-1156	NM_001004140	80986	Mm.22448	NM_001004140	ENSMUSG00000037725	Ckap2	AI461656|AW228814|LB1	cytoskeleton associated protein 2	protein-coding
mm_69011.1	chr7	126704523	126704542	-	1	NA	promoter-TSS (NM_001301374)	promoter-TSS (NM_001301374)	284	NM_009898	12721	Mm.290482	NM_009898	ENSMUSG00000030707	Coro1a	Clabp|Lmb3|TACO|p57	coronin, actin binding protein 1A	protein-coding
mm_92567.1	chr10	79874600	79874610	-	1	NA	promoter-TSS (NM_001170935)	promoter-TSS (NM_001170935)	29	NM_181681	216152	Mm.29678	NM_181681	ENSMUSG00000035835	Plppr3	Lppr3|Prg2	phospholipid phosphatase related 3	protein-coding
mm_162172.1	chrX	101418969	101418969	-	1	NA	intron (NM_001177987, intron 1 of 6)	intron (NM_001177987, intron 1 of 6)	945	NM_001177986	56364	Mm.23458	NM_019831	ENSMUSG00000031310	Zmym3	9030216B10Rik|AW122925|DXS6673El|Zfp261	zinc finger, MYM-type 3	protein-coding
mm_75709.1	chr8	68901300	68901314	-	1	NA	exon (NM_008509, exon 8 of 10)	exon (NM_008509, exon 8 of 10)	20752	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_153576.1	chr19	43388198	43388224	-	1	NA	exon (NM_001081257, exon 1 of 12)	exon (NM_001081257, exon 1 of 12)	144	NM_001081257	545291	Mm.442200	NM_001081257	ENSMUSG00000074852	Hpse2	Gm968|Hpa2	heparanase 2	protein-coding
mm_91330.1	chr10	25271653	25271656	-	1	NA	intron (NM_018747, intron 3 of 7)	intron (NM_018747, intron 3 of 7)	27509	NM_018747	432442	Mm.485937	NM_018747	ENSMUSG00000039166	Akap7	6430401D08|AI662165|AKAP15|Akap18|BB170514	A kinase (PRKA) anchor protein 7	protein-coding
mm_149946.1	chr19	27322610	27322617	+	1	NA	promoter-TSS (NM_183179)	promoter-TSS (NM_183179)	-6	NM_183179	240595	Mm.269759	NM_183179	ENSMUSG00000047298	Kcnv2	KV11.1	potassium channel, subfamily V, member 2	protein-coding
mm_101126.1	chr11	12054300	12054307	-	1	NA	Intergenic	U1|snRNA|snRNA	-16883	NM_010345	14783	Mm.273117	NM_010345	ENSMUSG00000020176	Grb10	5730571D09Rik|AI325020|Meg1|mKIAA0207	growth factor receptor bound protein 10	protein-coding
mm_170477.1	chr19	11912172	11912182	-	1	NA	promoter-TSS (NM_172635)	promoter-TSS (NM_172635)	-222	NM_172635	225929	Mm.42711	NM_172635	ENSMUSG00000046139	Patl1	AV312086|Pat1b	protein associated with topoisomerase II homolog 1 (yeast)	protein-coding
mm_150347.1	chr19	34643066	34643082	+	1	NA	intron (NM_008331, intron 1 of 1)	intron (NM_008331, intron 1 of 1)	2185	NM_008331	15957	Mm.439751	NM_008331	ENSMUSG00000034459	Ifit1	ISG56|Ifi56|P56	interferon-induced protein with tetratricopeptide repeats 1	protein-coding
mm_43057.1	chr5	124194861	124194869	+	1	NA	intron (NM_011256, intron 2 of 24)	intron (NM_011256, intron 2 of 24)	-7683	NM_001289472	19679	Mm.44261	NM_011256	ENSMUSG00000029406	Pitpnm2	NIR3|RDGBA2|Rdgb2|mKIAA1457	phosphatidylinositol transfer protein, membrane-associated 2	protein-coding
mm_46310.1	chr5	100565081	100565085	-	1	NA	intron (NM_139198, intron 1 of 4)	intron (NM_139198, intron 1 of 4)	7122	NM_139198	231507	Mm.34609	NM_139198	ENSMUSG00000029322	Plac8	C15|D5Wsu111e	placenta-specific 8	protein-coding
mm_165685.1	chr3	90695169	90695173	-	1	NA	exon (NM_001281852, exon 2 of 3)	exon (NM_001281852, exon 2 of 3)	550	NM_001281852	20202	Mm.2128	NM_009114	ENSMUSG00000056071	S100a9	60B8Ag|AW546964|BEE22|Cagb|GAGB|L1Ag|MRP14|p14	S100 calcium binding protein A9 (calgranulin B)	protein-coding
mm_23436.1	chr3	59304951	59304953	+	1	NA	intron (NM_177855, intron 42 of 43)	intron (NM_177855, intron 42 of 43)	39304	NM_001162884	242050	Mm.228086	NM_001162884	ENSMUSG00000036334	Igsf10	6530405F15Rik|9030224D03|AA409708|AA536958|AI414626|Adlican2|CMF608	immunoglobulin superfamily, member 10	protein-coding
mm_161361.1	chr14	57057995	57057995	-	1	NA	promoter-TSS (NM_016975)	promoter-TSS (NM_016975)	35	NM_016975	14611	Mm.57207	NM_016975	ENSMUSG00000048582	Gja3	Cnx46|Cx43|Cx46|Gja-3	gap junction protein, alpha 3	protein-coding
mm_127347.1	chr15	100616320	100616339	+	1	NA	intron (NM_011873, intron 1 of 3)	intron (NM_011873, intron 1 of 3)	667	NM_011873	23994	Mm.486175	NM_011873	ENSMUSG00000000346	Dazap2	AI314727|Brbp|Gcap28|Prtb|gt6-12|mKIAA0058	DAZ associated protein 2	protein-coding
mm_45128.1	chr5	48749336	48749351	-	1	NA	intron (NM_001199244, intron 1 of 7)	RMER1A|Other|Other	140214	NM_030265	80334	Mm.160172	NM_030265	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding
mm_137052.1	chr17	17927994	17928022	+	1	NA	Intergenic	RMER12|LTR|ERVK	40184	NM_008039	14289	Mm.378918	NM_008039	ENSMUSG00000052270	Fpr2	E330010I07Rik|Fpr-rs2	formyl peptide receptor 2	protein-coding
mm_52509.1	chr6	115361115	115361129	+	1	NA	promoter-TSS (NM_001308352)	promoter-TSS (NM_001308352)	-22	NM_001308352	19016	Mm.3020	NM_011146	ENSMUSG00000000440	Pparg	Nr1c3|PPAR-gamma|PPAR-gamma2|PPARgamma|PPARgamma2	peroxisome proliferator activated receptor gamma	protein-coding
mm_125352.1	chr15	39391790	39391800	+	1	NA	intron (NM_001256382, intron 3 of 26)	intron (NM_001256382, intron 3 of 26)	193509	NM_053271	116838	Mm.309296	NM_053271	ENSMUSG00000037386	Rims2	2810036I15Rik|AW048769|RIM2|Rab3ip2|Rim2(+40A)|Rim2(+44A)|Rim2(+4A)|Serg2|Syt3-rs|mKIAA0751	regulating synaptic membrane exocytosis 2	protein-coding
mm_36470.1	chr4	82705663	82705703	-	1	NA	Intergenic	Intergenic	153978	NM_026647	68268	Mm.32047	NM_026647	ENSMUSG00000028403	Zdhhc21	9130404H11Rik|AL024349|D130004H04Rik|dep	zinc finger, DHHC domain containing 21	protein-coding
mm_2679.1	chr1	127300418	127300449	+	1	NA	intron (NM_145128, intron 2 of 17)	intron (NM_145128, intron 2 of 17)	95447	NM_145128	107895	Mm.214682	NM_145128	ENSMUSG00000036155	Mgat5	4930471A21Rik|5330407H02Rik|AI480971|GlcNAc-TV	mannoside acetylglucosaminyltransferase 5	protein-coding
mm_148928.1	chr19	7014352	7014399	+	1	NA	exon (NM_153795, exon 4 of 15)	exon (NM_153795, exon 4 of 15)	5094	NM_153795	108101	Mm.157591	NM_153795	ENSMUSG00000024965	Fermt3	C79673|Kindlin3	fermitin family member 3	protein-coding
mm_69042.1	chr7	126800355	126800430	-	1	NA	promoter-TSS (NM_001177308)	promoter-TSS (NM_001177308)	55	NM_001177308	11674	Mm.275831	NM_007438	ENSMUSG00000030695	Aldoa	Aldo-1|Aldo1	aldolase A, fructose-bisphosphate	protein-coding
mm_8384.1	chr1	151344053	151344069	-	1	NA	promoter-TSS (NM_001039512)	promoter-TSS (NM_001039512)	-437	NM_001039512	117198	Mm.33764	NM_028582	ENSMUSG00000023150	Ivns1abp	1190004M08Rik|1700126I16Rik|AA960440|HSPC068|ND1|NS-1|NS1-BP|Nd1-L|Nd1-S|mKIAA0850	influenza virus NS1A binding protein	protein-coding
mm_148441.1	chr19	3948860	3948871	+	1	NA	exon (NM_019449, exon 11 of 11)	exon (NM_019449, exon 11 of 11)	-9943	NM_028545	73458	Mm.482922	NM_028545	ENSMUSG00000037263	Aldh3b3	1700055N04Rik	aldehyde dehydrogenase 3 family, member B3	protein-coding
mm_141287.1	chr17	28008553	28008580	-	1	NA	intron (NM_001286040, intron 12 of 24)	intron (NM_001286040, intron 12 of 24)	72018	NM_013687	21463	Mm.29758	NM_013687	ENSMUSG00000062859	Tcp11	D17Ken1|Tcp-11	t-complex protein 11	protein-coding
mm_58878.1	chr7	16993799	16993812	+	1	NA	promoter-TSS (NM_001101535)	promoter-TSS (NM_001101535)	-783	NM_001101535	434130	Mm.459162	NM_001101535	ENSMUSG00000041117	Ccdc8	ENSMUSG00000041117	coiled-coil domain containing 8	protein-coding
mm_140783.1	chr17	17893950	17893961	-	1	NA	TTS (NM_008039)	TTS (NM_008039)	6131	NM_008039	14289	Mm.378918	NM_008039	ENSMUSG00000052270	Fpr2	E330010I07Rik|Fpr-rs2	formyl peptide receptor 2	protein-coding
mm_152239.1	chr19	8712889	8712952	-	1	NA	intron (NM_001161413, intron 2 of 9)	intron (NM_001161413, intron 2 of 9)	977	NM_008577	17254	Mm.4114	NM_008577	ENSMUSG00000010095	Slc3a2	4F2|4F2HC|AI314110|Cd98|Ly-10|Ly-m10|Ly10|Mdu1|Mgp-2hc|NACAE	solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2	protein-coding
mm_165966.1	chr4	95505130	95505131	+	1	NA	Intergenic	Intergenic	-52377	NM_001113412	75578	Mm.276098	NM_029347	ENSMUSG00000028573	Fggy	2310009E04Rik	FGGY carbohydrate kinase domain containing	protein-coding
mm_10566.1	chr2	18057129	18057145	+	1	NA	promoter-TSS (NR_106115)	promoter-TSS (NR_106115)	-709	NR_106115	102466840		NR_106115	ENSMUSG00000099050	Mir7655	Gm27794|mmu-mir-7655	microRNA 7655	ncRNA
mm_16640.1	chr2	5942741	5942804	-	1	NA	promoter-TSS (NM_001081131)	promoter-TSS (NM_001081131)	20	NM_001081131	209692	Mm.222517	NM_001081131	ENSMUSG00000025815	Dhtkd1	C330018I04Rik	dehydrogenase E1 and transketolase domain containing 1	protein-coding
mm_99348.1	chr11	101583417	101583476	+	1	NA	intron (NM_144830, intron 2 of 8)	intron (NM_144830, intron 2 of 8)	1204	NM_144830	217203	Mm.280559	NM_144830	ENSMUSG00000034947	Tmem106a	0610008L10Rik|AI043106|BC022145	transmembrane protein 106A	protein-coding
mm_85827.1	chr9	110422505	110422513	-	1	NA	3' UTR (NM_008694, exon 4 of 4)	3' UTR (NM_008694, exon 4 of 4)	2701	NM_008694	18054	Mm.236225	NM_008694	ENSMUSG00000032484	Ngp	bectenecin	neutrophilic granule protein	protein-coding
mm_81189.1	chr9	107547289	107547379	+	1	NA	promoter-TSS (NM_053253)	promoter-TSS (NM_053253)	24	NM_053253	114602	Mm.28331	NM_053253	ENSMUSG00000010044	Zmynd10	Blu	zinc finger, MYND domain containing 10	protein-coding
mm_29797.1	chr3	127780031	127780040	-	1	NA	intron (NM_027808, intron 1 of 13)	intron (NM_027808, intron 1 of 13)	492	NM_027808	71481	Mm.158704	NM_027808	ENSMUSG00000028028	Alpk1	8430410J10Rik|LAK	alpha-kinase 1	protein-coding
mm_109889.1	chr12	5491447	5491449	-	1	NA	Intergenic	Intergenic	114946	NR_015579	72669	Mm.10434	NM_028318		2810032G03Rik	AI461720	RIKEN cDNA 2810032G03 gene	ncRNA
mm_162459.1	chr1	128586918	128586941	-	1	NA	Intergenic	Intergenic	5370	NM_009911	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding
mm_91312.1	chr10	24922138	24922148	-	1	NA	intron (NM_007482, intron 2 of 7)	intron (NM_007482, intron 2 of 7)	5327	NM_007482	11846	Mm.154144	NM_007482	ENSMUSG00000019987	Arg1	AI|AI256583|Arg-1|PGIF	arginase, liver	protein-coding
mm_42948.1	chr5	122995100	122995102	+	1	NA	intron (NR_045820, intron 2 of 2)	intron (NR_045820, intron 2 of 2)	5747	NR_045820	109202	Mm.30769	NM_175405	ENSMUSG00000056735	A930024E05Rik	-	RIKEN cDNA A930024E05 gene	ncRNA
mm_11778.1	chr2	38998303	38998340	+	1	NA	promoter-TSS (NM_029687)	promoter-TSS (NM_029687)	12	NM_029687	76646	Mm.358777	NM_029687	ENSMUSG00000035295	Wdr38	1700123D08Rik	WD repeat domain 38	protein-coding
mm_62317.1	chr7	100319031	100319048	+	1	NA	3' UTR (NM_177161, exon 13 of 13)	3' UTR (NM_177161, exon 13 of 13)	33519	NM_177161	320452	Mm.150294	NM_177161	ENSMUSG00000051048	P4ha3	D930031A02Rik	procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide III	protein-coding
mm_112684.1	chr13	16029956	16029974	+	1	NA	3' UTR (NM_008380, exon 5 of 5)	3' UTR (NM_008380, exon 5 of 5)	18114	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_24976.1	chr3	96824105	96824123	+	1	NA	intron (NM_001163496, intron 1 of 4)	intron (NM_001163496, intron 1 of 4)	5237	NM_001163497	54215	Mm.34693	NM_018767	ENSMUSG00000038304	Cd160	AU045688|By55	CD160 antigen	protein-coding
mm_162577.1	chr1	177447851	177447862	+	1	NA	exon (NM_013915, exon 1 of 1)	exon (NM_013915, exon 1 of 1)	2035	NM_013915	30928	Mm.330700	NM_013915	ENSMUSG00000063659	Zbtb18	RP58|Zfp238|Znf238	zinc finger and BTB domain containing 18	protein-coding
mm_158613.1	chrX	152644135	152644162	-	1	NA	promoter-TSS (NM_001290687)	promoter-TSS (NM_001290687)	1	NM_001290687	110380	Mm.40796	NM_172441	ENSMUSG00000045180	Shroom2	4832440C16|Apxl|C630003H05Rik|Shrm2	shroom family member 2	protein-coding
mm_18177.1	chr2	45110242	45110265	-	1	NA	promoter-TSS (NM_001289521)	promoter-TSS (NM_001289521)	24	NM_001289521	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_51424.1	chr6	78427375	78427388	+	1	NA	exon (NM_009042, exon 4 of 6)	exon (NM_009042, exon 4 of 6)	1398	NM_009042	19692	Mm.142731	NM_009042	ENSMUSG00000059654	Reg1	-	regenerating islet-derived 1	protein-coding
mm_137716.1	chr17	29100133	29100146	+	1	NA	3' UTR (NM_007669, exon 3 of 3)	3' UTR (NM_007669, exon 3 of 3)	6370	NM_007669	12575	Mm.195663	NM_007669	ENSMUSG00000023067	Cdkn1a	CAP20|CDKI|CIP1|Cdkn1|P21|SDI1|Waf1|mda6|p21Cip1|p21WAF	cyclin-dependent kinase inhibitor 1A (P21)	protein-coding
mm_46018.1	chr5	90904202	90904227	-	1	NA	exon (NM_009140, exon 2 of 4)	exon (NM_009140, exon 2 of 4)	315	NM_009140	20310	Mm.4979	NM_009140	ENSMUSG00000058427	Cxcl2	CINC-2a|GROb|Gro2|MIP-2|MIP-2a|Mgsa-b|Mip2|Scyb|Scyb2	chemokine (C-X-C motif) ligand 2	protein-coding
mm_139117.1	chr17	47436586	47436595	+	1	NA	promoter-TSS (NM_145489)	promoter-TSS (NM_145489)	-49	NM_145489	224833	Mm.218444	NM_145489	ENSMUSG00000034382	AI661453	-	expressed sequence AI661453	protein-coding
mm_7679.1	chr1	128589276	128589285	-	1	NA	exon (NM_009911, exon 2 of 2)	exon (NM_009911, exon 2 of 2)	3019	NM_009911	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding
mm_55536.1	chr6	70766409	70766412	-	1	NA	3' UTR (NM_009075, exon 9 of 9)	3' UTR (NM_009075, exon 9 of 9)	25765	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_88663.1	chr10	80016697	80016733	+	1	NA	promoter-TSS (NM_001142701)	promoter-TSS (NM_001142701)	43	NM_001142701	70719	Mm.243954	NM_027521	ENSMUSG00000035697	Hmha1	6330406L22Rik|AW539505|Ha-1	histocompatibility (minor) HA-1	protein-coding
mm_40477.1	chr5	54045909	54045921	+	1	NA	intron (NM_001081103, intron 1 of 11)	intron (NM_001081103, intron 1 of 11)	47392	NM_001081103	116873	Mm.265985	NM_054083	ENSMUSG00000039156	Stim2	-	stromal interaction molecule 2	protein-coding
mm_36804.1	chr4	103173461	103173465	-	1	NA	3' UTR (NM_177732, exon 10 of 10)	3' UTR (NM_177732, exon 10 of 10)	41421	NM_177732	242585	Mm.281800	NM_177732	ENSMUSG00000028521	Slc35d1	AI834976|C330011J09|UGTREL7|mKIAA0260	solute carrier family 35 (UDP-glucuronic acid/UDP-N-acetylgalactosamine dual transporter), member D1	protein-coding
mm_76461.1	chr8	85365042	85365062	-	1	NA	exon (NM_175441, exon 1 of 13)	exon (NM_175441, exon 1 of 13)	272	NM_175441	213435	Mm.32804	NM_175441	ENSMUSG00000031698	Mylk3	D830007F02Rik|MLCK	myosin light chain kinase 3	protein-coding
mm_159584.1	chr4	121188439	121188439	-	1	NA	intron (NM_001346660, intron 2 of 7)	intron (NM_001346660, intron 2 of 7)	26645	NM_001346660	109263	Mm.215745	NM_001081013	ENSMUSG00000049878	Rlf	9230110M18Rik|AI195322|MommeD8	rearranged L-myc fusion sequence	protein-coding
mm_35418.1	chr4	35113624	35113672	-	1	NA	intron (NM_178061, intron 1 of 3)	intron (NM_178061, intron 1 of 3)	-38407	NM_199157	387510	Mm.386929	NM_199157	ENSMUSG00000042993	Ifnk	-	interferon kappa	protein-coding
mm_157866.1	chrX	75272957	75272972	-	1	NA	intron (NM_007977, intron 14 of 25)	intron (NM_007977, intron 14 of 25)	107077	NM_007977	14069	Mm.1805	NM_007977	ENSMUSG00000031196	F8	Cf-8|Cf8|FVIII	coagulation factor VIII	protein-coding
mm_13064.1	chr2	91115587	91115597	+	1	NA	3' UTR (NM_011355, exon 5 of 5)	3' UTR (NM_011355, exon 5 of 5)	-2552	NM_008653	17868	Mm.10728	NM_008653	ENSMUSG00000002100	Mybpc3	-	myosin binding protein C, cardiac	protein-coding
mm_168240.1	chr10	81846503	81846517	+	1	NA	Intergenic	CpG	-17424	NM_001243067	73610	Mm.490466	NM_001243067	ENSMUSG00000096795	Zfp433	1700123A16Rik	zinc finger protein 433	protein-coding
mm_143537.1	chr17	73950396	73950418	-	1	NA	promoter-TSS (NM_011723)	promoter-TSS (NM_011723)	-211	NM_011723	22436	Mm.11223	NM_011723	ENSMUSG00000024066	Xdh	XO|Xor|Xox-1|Xox1	xanthine dehydrogenase	protein-coding
mm_138538.1	chr17	35251215	35251237	+	1	NA	promoter-TSS (NR_106169)	promoter-TSS (NR_106169)	-63	NR_106169	102465886		NR_106169	ENSMUSG00000098269	Mir8094	Gm27513|mmu-mir-8094	microRNA 8094	ncRNA
mm_153010.1	chr19	30539701	30539726	-	1	NA	promoter-TSS (NR_003650)	promoter-TSS (NR_003650)	-34	NR_003650	546723	Mm.301509	NM_001037169		Ppp1r2-ps3	EG546723|Gm5972	protein phosphatase 1, regulatory (inhibitor) subunit 2, pseudogene 3	pseudo
mm_11671.1	chr2	35284772	35284787	+	1	NA	exon (NM_001206369, exon 3 of 17)	exon (NM_001206369, exon 3 of 17)	2399	NM_146120	227753	Mm.443	NM_146120	ENSMUSG00000026879	Gsn	ADF	gelsolin	protein-coding
mm_82376.1	chr9	14615446	14615455	-	1	NA	promoter-TSS (NM_001081395)	promoter-TSS (NM_001081395)	-450	NM_001081395	75723	Mm.159552	NM_001081395	ENSMUSG00000013076	Amotl1	2310010G08Rik|2310067L22Rik|4932416D09Rik|JEAP|mFLJ00155	angiomotin-like 1	protein-coding
mm_49230.1	chr6	17065130	17065233	+	1	NA	promoter-TSS (NM_207176)	promoter-TSS (NM_207176)	32	NM_207176	21753	Mm.436548	NM_011570	ENSMUSG00000029552	Tes	D6Ertd352e|TESS|Tes1|Tes2|testin2	testis derived transcript	protein-coding
mm_171752.1	chr5	104571710	104571721	+	1	NA	promoter-TSS (NM_001346671)	promoter-TSS (NM_001346671)	43	NM_001346671	69623	Mm.69919	NM_027142		Zfp33b	2310012P17Rik	zinc finger protein 33B	protein-coding
mm_31344.1	chr4	46508396	46508397	+	1	NA	intron (NM_029077, intron 5 of 5)	intron (NM_029077, intron 5 of 5)	19067	NM_053179	94181	Mm.249349	NM_053179	ENSMUSG00000028334	Nans	4632418E04Rik|BB056474|Sas	N-acetylneuraminic acid synthase (sialic acid synthase)	protein-coding
mm_90812.1	chr10	7824580	7824599	-	1	NA	Intergenic	Intergenic	-7881	NM_172785	237256	Mm.140055	NM_172785	ENSMUSG00000039981	Zc3h12d	D730019B10Rik|TFL	zinc finger CCCH type containing 12D	protein-coding
mm_2231.1	chr1	91022723	91022727	+	1	NA	intron (NM_001111312, intron 1 of 12)	intron (NM_001111312, intron 1 of 12)	23998	NM_001111312	16978	Mm.45039	NM_008515	ENSMUSG00000026305	Lrrfip1	AU024550|Fliiap1	leucine rich repeat (in FLII) interacting protein 1	protein-coding
mm_11045.1	chr2	27165500	27165515	+	1	NA	promoter-TSS (NM_138942)	promoter-TSS (NM_138942)	0	NM_138942	13166	Mm.167781	NM_138942	ENSMUSG00000000889	Dbh	-	dopamine beta hydroxylase	protein-coding
mm_14834.1	chr2	147365014	147365033	+	1	NA	promoter-TSS (NM_008780)	promoter-TSS (NM_008780)	29	NM_008780	18503	Mm.315502	NM_008780	ENSMUSG00000037034	Pax1	Pax-1|hbs|hunchback|un|undulated|wt	paired box 1	protein-coding
mm_152836.1	chr19	23273894	23273918	-	1	NA	promoter-TSS (NM_001252684)	promoter-TSS (NM_001252684)	-9	NM_001252684	226026	Mm.23267	NM_153808	ENSMUSG00000024943	Smc5	MLZ-453|SMC-5|Smc5l1|mKIAA0594|mSMC5	structural maintenance of chromosomes 5	protein-coding
mm_121252.1	chr14	103057533	103057539	+	1	NA	TTS (NM_008392)	TTS (NM_008392)	10524	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_21169.1	chr2	154658000	154658034	-	1	NA	intron (NM_029362, intron 1 of 4)	intron (NM_029362, intron 1 of 4)	991	NM_029362	75608	Mm.262480	NM_029362	ENSMUSG00000038467	Chmp4b	2010012F05Rik|C76846|Snf7-2	charged multivesicular body protein 4B	protein-coding
mm_27432.1	chr3	51560596	51560686	-	1	NA	5' UTR (NM_080793, exon 1 of 8)	5' UTR (NM_080793, exon 1 of 8)	182	NM_080793	73251	Mm.192111	NM_080793	ENSMUSG00000037111	Setd7	1600028F23Rik|H3K4MT|KMT7|Set7|Set7/9|mKIAA1717	SET domain containing (lysine methyltransferase) 7	protein-coding
mm_93374.1	chr10	105474139	105474143	-	1	NA	intron (NM_177368, intron 1 of 11)	intron (NM_177368, intron 1 of 11)	100338	NM_177368	278279	Mm.25225	NM_177368	ENSMUSG00000036019	Tmtc2	8430438D04Rik|D330034A10Rik	transmembrane and tetratricopeptide repeat containing 2	protein-coding
mm_12606.1	chr2	74682019	74682030	+	1	NA	promoter-TSS (NM_008273)	promoter-TSS (NM_008273)	-299	NM_008273	15431	Mm.207763	NM_008273	ENSMUSG00000042499	Hoxd11	E230017H14Rik|Hox-4.6|Hox-5.4|Hox-5.5	homeobox D11	protein-coding
mm_56395.1	chr6	96033276	96033297	-	1	NA	Intergenic	Intergenic	-79868	NM_182808	320265	Mm.489890	NM_182808	ENSMUSG00000059187	Fam19a1	C630007B19Rik|FAM19A1 TAFA-1|TAFA1|Tafa-1	family with sequence similarity 19, member A1	protein-coding
mm_107418.1	chr12	34984819	34984838	+	1	NA	promoter-TSS (NM_029294)	promoter-TSS (NM_029294)	67	NM_029294	75456	Mm.79179	NM_029294	ENSMUSG00000092305	Prps1l1	1700011K15Rik	phosphoribosyl pyrophosphate synthetase 1-like 1	protein-coding
mm_128684.1	chr15	60824920	60824924	-	1	NA	5' UTR (NM_001162926, exon 1 of 2)	5' UTR (NM_001162926, exon 1 of 2)	158	NM_001162926	399603	Mm.411968	NM_207269	ENSMUSG00000072568	Fam84b	BF642811|D330050I23Rik	family with sequence similarity 84, member B	protein-coding
mm_124613.1	chr15	3279525	3279537	+	1	NA	exon (NM_009155, exon 5 of 5)	exon (NM_009155, exon 5 of 5)	8554	NM_009155	20363	Mm.392203	NM_009155	ENSMUSG00000064373	Selenop	AU018766|D15Ucla1|Se-P|Sepp1|selp	selenoprotein P	protein-coding
mm_137383.1	chr17	25773788	25773824	+	1	NA	promoter-TSS (NM_026238)	promoter-TSS (NM_026238)	30	NM_026238	67563	Mm.24201	NM_026238	ENSMUSG00000002280	Narfl	9030612I22Rik|AI504405|PRN	nuclear prelamin A recognition factor-like	protein-coding
mm_110674.1	chr12	65172561	65172618	-	1	NA	promoter-TSS (NM_172578)	promoter-TSS (NM_172578)	-9	NM_172578	217653	Mm.21144	NM_172578	ENSMUSG00000047534	Mis18bp1	6720403H11|C79407|Knl2|mKIAA1903	MIS18 binding protein 1	protein-coding
mm_127331.1	chr15	100421672	100421683	+	1	NA	intron (NM_008732, intron 1 of 16)	B1F2|SINE|Alu	1378	NM_001146161	18174	Mm.234608	NM_008732	ENSMUSG00000023030	Slc11a2	DCT1|DMT1|Nramp2|mk|van	solute carrier family 11 (proton-coupled divalent metal ion transporters), member 2	protein-coding
mm_136811.1	chr17	12391780	12391791	+	1	NA	exon (NM_008877, exon 6 of 19)	exon (NM_008877, exon 6 of 19)	13176	NM_008877	18815	Mm.971	NM_008877	ENSMUSG00000059481	Plg	AI649309|Pg	plasminogen	protein-coding
mm_19794.1	chr2	109280719	109280767	-	1	NA	promoter-TSS (NM_139303)	promoter-TSS (NM_139303)	5	NM_139303	228421	Mm.274086	NM_139303	ENSMUSG00000027115	Kif18a	AU024633|B130001M12Rik|gcd2	kinesin family member 18A	protein-coding
mm_138204.1	chr17	34299648	34299675	+	1	NA	Intergenic	Intergenic	-6206	NM_010382	14969	Mm.22564	NM_010382	ENSMUSG00000060586	H2-Eb1	Eb|H-2Eb|H2Eb|Ia-4|Ia4	histocompatibility 2, class II antigen E beta	protein-coding
mm_137809.1	chr17	30004854	30004876	+	1	NA	promoter-TSS (NM_148926)	promoter-TSS (NM_148926)	-222	NM_148926	21769	Mm.220972	NM_148926	ENSMUSG00000044477	Zfand3	AW539211|TEG-27|Tex27	zinc finger, AN1-type domain 3	protein-coding
mm_119646.1	chr14	51984827	51984856	+	1	NA	promoter-TSS (NM_001145922)	promoter-TSS (NM_001145922)	8	NM_198249	268739	Mm.9239	NM_198249	ENSMUSG00000004562	Arhgef40	E130112L23Rik|Gm669|Solo	Rho guanine nucleotide exchange factor (GEF) 40	protein-coding
mm_61989.1	chr7	91090889	91090902	+	1	NA	5' UTR (NM_011807, exon 1 of 23)	5' UTR (NM_011807, exon 1 of 23)	109	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_90314.1	chr10	127059359	127059371	+	1	NA	intron (NM_001033262, intron 1 of 3)	CpG	819	NM_001033262	216438	Mm.37892	NM_001033262	ENSMUSG00000040502	March9	AI608492|BC019560	membrane-associated ring finger (C3HC4) 9	protein-coding
mm_112410.1	chr13	3611325	3611350	+	1	NA	promoter-TSS (NM_134063)	promoter-TSS (NM_134063)	-229	NM_134063	105203	Mm.221609	NM_134063	ENSMUSG00000033799	Fam208b	AI645998|Pap20|mKIAA2006	family with sequence similarity 208, member B	protein-coding
mm_153049.1	chr19	32069675	32069681	-	1	NA	intron (NM_018830, intron 2 of 23)	intron (NM_018830, intron 2 of 23)	33462	NM_018830	54447	Mm.491229	NM_018830	ENSMUSG00000024887	Asah2	AI585898	N-acylsphingosine amidohydrolase 2	protein-coding
mm_95959.1	chr11	58847154	58847226	+	1	NA	Intergenic	CpG	6074	NM_146537	258530	Mm.377556	NM_146537	ENSMUSG00000094805	Olfr311	MOR222-1	olfactory receptor 311	protein-coding
mm_118702.1	chr14	22159108	22159121	+	1	NA	intron (NM_028275, intron 2 of 6)	B4|SINE|B4	139402	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_53840.1	chr6	148354858	148354867	+	1	NA	non-coding (NR_003634, exon 1 of 1)	non-coding (NR_003634, exon 1 of 1)	206	NR_003634	66184	Mm.391542	NM_025405	ENSMUSG00000063171	Rps4l	1110033J19Rik|AA407494|Rps4y2	ribosomal protein S4-like	pseudo
mm_107708.1	chr12	55565189	55565257	+	1	NA	promoter-TSS (NM_001277340)	promoter-TSS (NM_001277340)	18	NM_001277340	79459	Mm.392781	NM_001277340	ENSMUSG00000063129	Aldoart2	4933425L11Rik|Aldo1-ps1|Aldoa-ps1	aldolase 1 A, retrogene 2	protein-coding
mm_134222.1	chr16	11254269	11254303	-	1	NA	promoter-TSS (NM_001130008)	promoter-TSS (NM_001130008)	39	NM_001130008	14852	Mm.325827	NM_146066	ENSMUSG00000062203	Gspt1	AI314175|AI326449|AV307676|C79774|G1st|Gst-1	G1 to S phase transition 1	protein-coding
mm_106211.1	chr11	116852114	116852153	-	1	NA	exon (NM_011358, exon 2 of 3)	exon (NM_011358, exon 2 of 3)	961	NM_011358	20382	Mm.21841	NM_011358	ENSMUSG00000034120	Srsf2	D11Wsu175e|MRF-1|Pr264|SC35|Sfrs10|Sfrs2	serine/arginine-rich splicing factor 2	protein-coding
mm_170949.1	chr2	53191185	53191187	-	1	NA	promoter-TSS (NM_018785)	promoter-TSS (NM_018785)	1	NM_018785	56194	Mm.257474	NM_018785	ENSMUSG00000061136	Prpf40a	2810012K09Rik|FBP-11|FBP11|Fnbp11|Fnbp3	pre-mRNA processing factor 40A	protein-coding
mm_152795.1	chr19	21472553	21472606	-	1	NA	promoter-TSS (NM_010266)	promoter-TSS (NM_010266)	82	NM_010266	14544	Mm.45054	NM_010266	ENSMUSG00000058624	Gda	AU015411|AW047581|GAH	guanine deaminase	protein-coding
mm_107279.1	chr12	29535210	29535237	+	1	NA	5' UTR (NM_001093776, exon 1 of 25)	5' UTR (NM_001093776, exon 1 of 25)	318	NM_001093776	17933	Mm.253067	NM_008666	ENSMUSG00000061911	Myt1l	2900046C06Rik|2900093J19Rik|C630034G21Rik|Nztf1|Pmng1|Png-1|mKIAA1106	myelin transcription factor 1-like	protein-coding
mm_123848.1	chr14	70708035	70708037	-	1	NA	intron (NM_023045, intron 1 of 27)	intron (NM_023045, intron 1 of 27)	-54952	NM_181345	328440	Mm.347749	NM_181345	ENSMUSG00000047911	Npm2	-	nucleophosmin/nucleoplasmin 2	protein-coding
mm_28996.1	chr3	101536436	101536446	-	1	NA	Intergenic	Intergenic	68266	NM_144900	11928	Mm.193670	NM_144900	ENSMUSG00000033161	Atp1a1	Atpa-1|BC010319	ATPase, Na+/K+ transporting, alpha 1 polypeptide	protein-coding
mm_125585.1	chr15	59612106	59612110	+	1	NA	Intergenic	Intergenic	-36546	NM_144549	211770	Mm.40298	NM_144549	ENSMUSG00000032501	Trib1	A530090O15Rik|TRB-1|Trb1	tribbles pseudokinase 1	protein-coding
mm_122613.1	chr14	51060877	51060880	-	1	NA	Intergenic	Intergenic	-3636	NM_001011875	497106	Mm.379740	NM_001011875	ENSMUSG00000068407	Rnase12	Rai1	ribonuclease, RNase A family, 12 (non-active)	protein-coding
mm_9511.1	chr1	173741691	173741701	-	1	NA	5' UTR (NM_001204910, exon 1 of 8)	5' UTR (NM_001204910, exon 1 of 8)	113	NM_001204910	226691	Mm.440876	NM_001204910	ENSMUSG00000073490	Ifi207	AI607873|Pyhin-A	interferon activated gene 207	protein-coding
mm_137837.1	chr17	30919584	30919615	+	1	NA	intron (NM_021332, intron 5 of 12)	(CA)n|Simple_repeat|Simple_repeat	17732	NM_021332	14652	Mm.390969	NM_021332	ENSMUSG00000024027	Glp1r	GLP-1R|GLP1Rc	glucagon-like peptide 1 receptor	protein-coding
mm_111442.1	chr12	96736552	96736557	-	1	NA	Intergenic	Intergenic	-689332	NR_103800	69423	Mm.46121	NM_027076		1700019M22Rik	-	NFX-like protein	pseudo
mm_169682.1	chr15	70857294	70857302	-	1	NA	Intergenic	L1Md_T|LINE|L1	870540	NM_177819	70363	Mm.126450	NM_177819	ENSMUSG00000036800	Fam135b	1700010C24Rik|A830008O07Rik	family with sequence similarity 135, member B	protein-coding
mm_115792.1	chr13	19338764	19338775	-	1	NA	Intergenic	L1M2|LINE|L1	57044	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_1822.1	chr1	82586943	82586988	+	1	NA	promoter-TSS (NM_007735)	promoter-TSS (NM_007735)	44	NM_007734	12828	Mm.389135	NM_007734	ENSMUSG00000079465	Col4a3	[a]3(IV)|alpha3(IV)	collagen, type IV, alpha 3	protein-coding
mm_119956.1	chr14	55095031	55095044	+	1	NA	5' UTR (NM_153083, exon 1 of 2)	5' UTR (NM_153083, exon 1 of 2)	253	NM_153083	105663	Mm.319204	NM_153083	ENSMUSG00000045691	Thtpa	AW122966	thiamine triphosphatase	protein-coding
mm_29860.1	chr3	130060736	130060758	-	1	NA	5' UTR (NM_207209, exon 1 of 24)	5' UTR (NM_207209, exon 1 of 24)	160	NM_207209	99683	Mm.192303	NM_207209	ENSMUSG00000001052	Sec24b	AI605202|SEC24	Sec24 related gene family, member B (S. cerevisiae)	protein-coding
mm_28719.1	chr3	95673783	95673793	-	1	NA	Intergenic	Intergenic	14129	NM_144899	229595	Mm.490574	NM_144899	ENSMUSG00000015850	Adamtsl4	ADAMTSL-4|Tsrc1	ADAMTS-like 4	protein-coding
mm_164484.1	chr16	75909189	75909203	-	1	NA	promoter-TSS (NM_023380)	promoter-TSS (NM_023380)	70	NM_023380	67742	Mm.131406	NM_023380	ENSMUSG00000022876	Samsn1	4930571B16Rik|930571B16Rik|Hacs1|SLy2	SAM domain, SH3 domain and nuclear localization signals, 1	protein-coding
mm_46647.1	chr5	108587815	108587819	-	1	NA	intron (NM_001282052, intron 17 of 26)	intron (NM_001282052, intron 17 of 26)	-37790	NM_007756	12889	Mm.5195	NM_007756	ENSMUSG00000033615	Cplx1	921-S	complexin 1	protein-coding
mm_67602.1	chr7	83735535	83735543	-	1	NA	promoter-TSS (NM_010551)	promoter-TSS (NM_010551)	-49	NM_010551	16170	Mm.10137	NM_010551	ENSMUSG00000001741	Il16	mKIAA4048	interleukin 16	protein-coding
mm_88957.1	chr10	81390340	81390369	+	1	NA	Intergenic	Intergenic	-2710	NM_001099917	72273	Mm.253147	NM_001099917	ENSMUSG00000078439	Smim24	2210404O07Rik	small integral membrane protein 24	protein-coding
mm_144598.1	chr18	32377177	32377289	+	1	NA	promoter-TSS (NM_009668)	promoter-TSS (NM_009668)	16	NM_009668	30948	Mm.4383	NM_009668	ENSMUSG00000024381	Bin1	ALP-1|Amphl|BRAMP-2|SH3P9	bridging integrator 1	protein-coding
mm_45368.1	chr5	66019267	66019293	-	1	NA	exon (NM_139065, exon 7 of 7)	exon (NM_139065, exon 7 of 7)	-14995	NR_027961	231253	Mm.436542	NM_177679	ENSMUSG00000054598	9130230L23Rik	-	RIKEN cDNA 9130230L23 gene	ncRNA
mm_96047.1	chr11	59559112	59559159	+	1	NA	intron (NM_145827, intron 7 of 9)	B1_Mur2|SINE|Alu	12603	NM_001011789	257962	Mm.377316	NM_001011789	ENSMUSG00000059610	Olfr222	MOR256-45P	olfactory receptor 222	protein-coding
mm_122501.1	chr14	46822031	46822061	-	1	NA	intron (NM_022023, intron 1 of 6)	CpG	196	NM_022023	63985	Mm.87312	NM_022023	ENSMUSG00000062014	Gmfb	3110001H22Rik|3110001O16Rik|AI851627|C79176|D14Ertd630e	glia maturation factor, beta	protein-coding
mm_40802.1	chr5	68031776	68031798	+	1	NA	promoter-TSS (NM_001018019)	promoter-TSS (NM_001018019)	-48	NM_001018019	433899	Mm.332422	NM_001018019	ENSMUSG00000068082	Grxcr1	Tg(Eno2-Gabrb3)0370Brll|pi|tde	glutaredoxin, cysteine rich 1	protein-coding
mm_40803.1	chr5	69461044	69461065	+	1	NA	Intergenic	Intergenic	81593	NM_023784	75581	Mm.154776	NM_023784	ENSMUSG00000029158	Yipf7	2310016N21Rik|Yip1b	Yip1 domain family, member 7	protein-coding
mm_6021.1	chr1	59119749	59119795	-	1	NA	promoter-TSS (NM_001037812)	promoter-TSS (NM_001037812)	34	NM_001037812	381259	Mm.261275	NM_001033449	ENSMUSG00000038079	Tmem237	AI853305|Als2cr4|Gm972	transmembrane protein 237	protein-coding
mm_146902.1	chr18	31243143	31243186	-	1	NA	exon (NM_009065, exon 2 of 5)	exon (NM_009065, exon 2 of 5)	73964	NM_009065	19762	Mm.5163	NM_009065	ENSMUSG00000057455	Rit2	RIBA|Rin|Roc2	Ras-like without CAAX 2	protein-coding
mm_138617.1	chr17	35823426	35823436	+	1	NA	promoter-TSS (NM_008027)	promoter-TSS (NM_008027)	74	NM_008027	14251	Mm.2931	NM_008027	ENSMUSG00000059714	Flot1	reggie-2	flotillin 1	protein-coding
mm_111085.1	chr12	80260357	80260371	-	1	NA	promoter-TSS (NM_134156)	promoter-TSS (NM_134156)	7	NM_134156	109711	Mm.253564	NM_134156	ENSMUSG00000015143	Actn1	3110023F10Rik|Actn1a	actinin, alpha 1	protein-coding
mm_114380.1	chr13	63240057	63240093	+	1	NA	promoter-TSS (NR_110521)	promoter-TSS (NR_110521)	46	NR_110521	72061	Mm.188105	NM_028079	ENSMUSG00000021458	2010111I01Rik	2300006M17Rik|AP-O|AW742919|Aopep|ApO|mir-23b|mir-24-1|mir-27b	RIKEN cDNA 2010111I01 gene	protein-coding
mm_147418.1	chr18	46175998	46176015	-	1	NA	exon (NM_001170855, exon 6 of 10)	exon (NM_001170855, exon 6 of 10)	22812	NM_001170855	28105	Mm.277382	NM_178872	ENSMUSG00000033949	Trim36	D18Wsu100e|haprin	tripartite motif-containing 36	protein-coding
mm_120710.1	chr14	71880682	71880715	+	1	NA	intron (NR_046274, intron 3 of 6)	intron (NR_046274, intron 3 of 6)	23989	NR_046274	74667	Mm.159286	NR_046274		4930434J06Rik	-	RIKEN cDNA 4930434J06 gene	ncRNA
mm_151848.1	chr19	5771377	5771408	-	1	NA	promoter-TSS (NM_023912)	promoter-TSS (NM_023912)	9	NM_023912	78891	Mm.276063	NM_023912	ENSMUSG00000024941	Scyl1	2810011O19Rik|C85140|Ntkl|mdf|mfd|p105	SCY1-like 1 (S. cerevisiae)	protein-coding
mm_165348.1	chr2	119186236	119186240	+	1	NA	intron (NM_139139, intron 2 of 10)	intron (NM_139139, intron 2 of 10)	11729	NM_001039223	623781	Mm.389344	NM_001039223	ENSMUSG00000055926	Gm14137	OTTMUSG00000015762	predicted gene 14137	protein-coding
mm_35942.1	chr4	53096400	53096420	-	1	NA	intron (NM_013454, intron 7 of 49)	intron (NM_013454, intron 7 of 49)	63485	NM_013454	11303	Mm.277376	NM_013454	ENSMUSG00000015243	Abca1	ABC-1|Abc1	ATP-binding cassette, sub-family A (ABC1), member 1	protein-coding
mm_76784.1	chr8	99416506	99416516	-	1	NA	promoter-TSS (NM_001285913)	promoter-TSS (NM_001285913)	-40	NR_133570	12564	Mm.441131	NM_007667	ENSMUSG00000036510	Cdh8	AI851472|cad8	cadherin 8	protein-coding
mm_36348.1	chr4	73791139	73791153	-	1	NA	promoter-TSS (NR_046042)	promoter-TSS (NR_046042)	-98	NR_046042	667768	Mm.244966	NR_046041	ENSMUSG00000085034	Gm11240	OTTMUSG00000000286	predicted gene 11240	ncRNA
mm_171393.1	chr4	12232804	12232805	+	1	NA	Intergenic	Intergenic	-60789	NM_026558	68099	Mm.25340	NM_026558	ENSMUSG00000028218	Fam92a	6720467C03Rik|Fam92a1	family with sequence similarity 92, member A	protein-coding
mm_4111.1	chr1	167618247	167618299	+	1	NA	promoter-TSS (NM_001159731)	promoter-TSS (NM_001159731)	8	NM_001159731	20183	Mm.3475	NM_009107	ENSMUSG00000015843	Rxrg	Nr2b3	retinoid X receptor gamma	protein-coding
mm_56062.1	chr6	86780698	86780706	-	1	NA	intron (NM_013471, intron 1 of 12)	B1_Mus1|SINE|Alu	-5588	NM_001331120	11746	Mm.259702	NM_013471	ENSMUSG00000029994	Anxa4	AI265406|AIV|AW106930|Anx4|Xanx-4	annexin A4	protein-coding
mm_130882.1	chr15	102249090	102249092	-	1	NA	intron (NM_011244, intron 3 of 9)	intron (NM_011244, intron 3 of 9)	-2591	NM_001042727	19411	Mm.1273	NM_011244	ENSMUSG00000001288	Rarg	Nr1b3|RAR-gamma|RARD|RARgamma2	retinoic acid receptor, gamma	protein-coding
mm_23933.1	chr3	83863254	83863302	+	1	NA	Intergenic	Intergenic	-21670	NM_011905	24088	Mm.87596	NM_011905	ENSMUSG00000027995	Tlr2	Ly105	toll-like receptor 2	protein-coding
mm_48502.1	chr5	142816592	142816625	-	1	NA	intron (NM_178242, intron 1 of 15)	CpG-11746	779	NM_178242	231861	Mm.354649	NM_178242	ENSMUSG00000039477	Tnrc18	BC025631|EG381742|Zfp469	trinucleotide repeat containing 18	protein-coding
mm_166030.1	chr4	126103217	126103239	-	1	NA	promoter-TSS (NM_028800)	promoter-TSS (NM_028800)	-729	NM_028800	74178	Mm.440269	NM_028800	ENSMUSG00000042608	Stk40	2310004N11Rik|AI428792	serine/threonine kinase 40	protein-coding
mm_153874.1	chr19	46863557	46863569	-	1	NA	intron (NM_033569, intron 4 of 7)	intron (NM_033569, intron 4 of 7)	98788	NM_029810	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_101612.1	chr11	35828692	35828716	-	1	NA	exon (NM_025936, exon 3 of 15)	exon (NM_025936, exon 3 of 15)	5824	NM_025936	104458	Mm.284906	NM_025936	ENSMUSG00000018848	Rars	2610011N19Rik|2610037E21Rik|AL033339|AW985894	arginyl-tRNA synthetase	protein-coding
mm_7655.1	chr1	128343468	128343480	-	1	NA	exon (NM_008567, exon 10 of 17)	exon (NM_008567, exon 10 of 17)	-15156	NM_001081078	226413	Mm.26930	NM_001081078	ENSMUSG00000026354	Lct	Gm100|LAC|LPH|Lphl	lactase	protein-coding
mm_96782.1	chr11	69941064	69941078	+	1	NA	exon (NM_016875, exon 8 of 9)	exon (NM_016875, exon 8 of 9)	4743	NM_001347634	53422	Mm.29286	NM_016875	ENSMUSG00000018554	Ybx2	Msy2	Y box protein 2	protein-coding
mm_60493.1	chr7	44478697	44478721	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-5808	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_6035.1	chr1	59592203	59592228	-	1	NA	intron (NM_001013771, intron 12 of 19)	intron (NM_001013771, intron 12 of 19)	75951	NM_001013771	381260	Mm.486706	NM_001013771	ENSMUSG00000047361	Gm973	AW554518	predicted gene 973	protein-coding
mm_74905.1	chr8	25203859	25203876	-	1	NA	Intergenic	Intergenic	-2325	NM_177089	320165	Mm.308452	NM_177089	ENSMUSG00000065954	Tacc1	4833447E04Rik|AA960202|B230378H13Rik	transforming, acidic coiled-coil containing protein 1	protein-coding
mm_167854.1	chrX	9862100	9862115	+	1	NA	Intergenic	Intergenic	12404	NM_029229	385317	Mm.108656	NM_029229	ENSMUSG00000048994	H2al3	4930557A04Rik	H2A histone family member L3	protein-coding
mm_107025.1	chr12	12942562	12942574	+	1	NA	promoter-TSS (NM_008709)	promoter-TSS (NM_008709)	-732	NM_008709	18109	Mm.16469	NM_008709	ENSMUSG00000037169	Mycn	N-myc|Nmyc|Nmyc-1|Nmyc1|bHLHe37|c-nmyc	v-myc avian myelocytomatosis viral related oncogene, neuroblastoma derived	protein-coding
mm_74393.1	chr8	3176923	3176952	-	1	NA	intron (NM_010568, intron 10 of 20)	intron (NM_010568, intron 10 of 20)	102680	NM_010568	16337	Mm.268003	NM_010568	ENSMUSG00000005534	Insr	4932439J01Rik|CD220|D630014A15Rik|IR|IR-A|IR-B	insulin receptor	protein-coding
mm_42642.1	chr5	118561155	118561172	+	1	NA	intron (NM_001347445, intron 1 of 30)	CpG-11438	444	NM_172424	76199	Mm.206238	NM_172424	ENSMUSG00000018076	Med13l	2210413I17Rik|6330591G05Rik|9030618F05Rik|Thrap2|Trap240L|mKIAA1025	mediator complex subunit 13-like	protein-coding
mm_150395.1	chr19	36409912	36409920	+	1	NA	intron (NM_029508, intron 1 of 8)	CpG	30849	NM_029508	76073	Mm.259180	NM_029508	ENSMUSG00000024805	Pcgf5	0610009F02Rik|1110054A01Rik|5830406C17Rik|5830443C21Rik|9530023M17Rik|AI324127	polycomb group ring finger 5	protein-coding
mm_167724.1	chr9	101074388	101074453	-	1	NA	promoter-TSS (NM_001100451)	promoter-TSS (NM_001100451)	-342	NM_001100451	77853	Mm.326206	NM_001100451	ENSMUSG00000066415	Msl2	E130103E02Rik|Msl2l1|Rnf184	male-specific lethal 2 homolog (Drosophila)	protein-coding
mm_138254.1	chr17	34590451	34590464	+	1	NA	intron (NM_134116, intron 1 of 3)	intron (NM_134116, intron 1 of 3)	651	NM_134116	106512	Mm.26584	NM_134116	ENSMUSG00000034786	Gpsm3	AA960287|AGS4	G-protein signalling modulator 3 (AGS3-like, C. elegans)	protein-coding
mm_19067.1	chr2	77703253	77703265	-	1	NA	promoter-TSS (NM_001113399)	promoter-TSS (NM_001113399)	13	NM_001113399	241494	Mm.490320	NM_178723	ENSMUSG00000027016	Zfp385b	B830010L13Rik|C130013B13Rik|Zfp533|Znf385b	zinc finger protein 385B	protein-coding
mm_72803.1	chr8	87472806	87472822	+	1	NA	promoter-TSS (NM_019626)	promoter-TSS (NM_019626)	2	NR_033430	100040294	Mm.213632	NR_033430	ENSMUSG00000097248	Gm2694	C230036H16Rik|linc1582	predicted gene 2694	ncRNA
mm_85114.1	chr9	95407241	95407276	-	1	NA	promoter-TSS (NM_018763)	promoter-TSS (NM_018763)	12	NM_018763	54371	Mm.212446	NM_018763	ENSMUSG00000033350	Chst2	AI428561|AW121776|C130041E03Rik|Chts2|GST-2|GlcNAc6ST|Gn6st	carbohydrate sulfotransferase 2	protein-coding
mm_22561.1	chr3	9942932	9942941	+	1	NA	Intergenic	L2|LINE|L2	-69649	NM_001272097	16592	Mm.741	NM_010634	ENSMUSG00000027533	Fabp5	E-FABP|Fabpe|Klbp|PA-FABP|mal1	fatty acid binding protein 5, epidermal	protein-coding
mm_27634.1	chr3	61365808	61365818	-	1	NA	3' UTR (NM_028712, exon 1 of 1)	3' UTR (NM_028712, exon 1 of 1)	1306	NM_028712	74012	Mm.422674	NM_028712	ENSMUSG00000036894	Rap2b	4021402C18Rik|AA408554	RAP2B, member of RAS oncogene family	protein-coding
mm_106615.1	chr11	120817179	120817193	-	1	NA	exon (NM_007988, exon 13 of 43)	exon (NM_007988, exon 13 of 43)	7361	NM_007988	14104	Mm.236443	NM_007988	ENSMUSG00000025153	Fasn	A630082H08Rik|FAS	fatty acid synthase	protein-coding
mm_67310.1	chr7	79466013	79466028	-	1	NA	intron (NM_017462, intron 1 of 22)	CpG	253	NM_017462	18975	Mm.3616	NM_017462	ENSMUSG00000039176	Polg	AA409516|PolgA	polymerase (DNA directed), gamma	protein-coding
mm_157261.1	chrX	19161942	19161956	-	1	NA	Intergenic	Intergenic	-14978	NR_029807	723828		NR_029807	ENSMUSG00000065471	Mir222	Mirn222|mir-222|mmu-mir-222	microRNA 222	ncRNA
mm_41679.1	chr5	99978572	99978633	+	1	NA	exon (NM_007516, exon 1 of 8)	exon (NM_007516, exon 1 of 8)	336	NM_001077266	11991	Mm.150231	NM_007516	ENSMUSG00000000568	Hnrnpd	Auf1|Hnrpd	heterogeneous nuclear ribonucleoprotein D	protein-coding
mm_133666.1	chr16	92058314	92058328	+	1	NA	promoter-TSS (NM_080456)	promoter-TSS (NM_080456)	-1	NM_017391	53881	Mm.217354	NM_017391	ENSMUSG00000089774	Slc5a3	AA623876|BF642829|Smit1	solute carrier family 5 (inositol transporters), member 3	protein-coding
mm_26247.1	chr3	141531861	141531877	+	1	NA	intron (NM_001293561, intron 1 of 16)	intron (NM_001293561, intron 1 of 16)	66305	NM_001293561	22253	Mm.24430	NM_009472	ENSMUSG00000059921	Unc5c	B130051O18Rik|Unc5h3|rcm	unc-5 netrin receptor C	protein-coding
mm_26864.1	chr3	16006329	16006335	-	1	NA	promoter-TSS (NM_001081687)	promoter-TSS (NM_001081687)	0	NM_001081687	381484	Mm.217376	NM_001081687	ENSMUSG00000078780	Gm5150	-	predicted gene 5150	protein-coding
mm_32298.1	chr4	103119435	103119447	+	1	NA	promoter-TSS (NM_001039081)	promoter-TSS (NM_001039081)	51	NM_001039081	71148	Mm.288721	NM_027696	ENSMUSG00000028522	Mier1	4933425I22Rik|5830411K19Rik|er1	MEIR1 treanscription regulator	protein-coding
mm_21133.1	chr2	154207157	154207171	-	1	NA	exon (NM_153418, exon 6 of 16)	exon (NM_153418, exon 6 of 16)	6784	NM_153418	228801	Mm.3783	NM_153418	ENSMUSG00000027485	Bpifb1	Lplunc1	BPI fold containing family B, member 1	protein-coding
mm_165163.1	chr2	25429387	25429396	+	1	NA	intron (NM_007379, intron 1 of 47)	intron (NM_007379, intron 1 of 47)	717	NM_007379	11305	Mm.2210	NM_007379	ENSMUSG00000026944	Abca2	AI413825|Abc2|D2H0S1474E|mKIAA1062	ATP-binding cassette, sub-family A (ABC1), member 2	protein-coding
mm_171251.1	chr3	7910595	7910595	+	1	NA	Intergenic	L1Md_T|LINE|L1	44292	NR_040587	75476	Mm.491752	NR_040587	ENSMUSG00000100010	1700010I02Rik	-	RIKEN cDNA 1700010I02 gene	ncRNA
mm_125481.1	chr15	54600731	54600737	+	1	NA	exon (NM_178920, exon 4 of 4)	exon (NM_178920, exon 4 of 4)	29368	NM_178920	105853	Mm.410994	NM_178920	ENSMUSG00000024479	Mal2	AI461653	mal, T cell differentiation protein 2	protein-coding
mm_107441.1	chr12	36314217	36314232	+	1	NA	promoter-TSS (NM_025312)	promoter-TSS (NM_025312)	55	NM_025312	66042	Mm.43375	NM_025312	ENSMUSG00000036169	Sostdc1	0610006G05Rik|Sostl|USAG-1|Wise|ectodin	sclerostin domain containing 1	protein-coding
mm_138633.1	chr17	35861265	35861271	+	1	NA	promoter-TSS (NM_134122)	promoter-TSS (NM_134122)	-50	NM_134122	106582	Mm.390992	NM_134122	ENSMUSG00000059791	Nrm	2610307M02Rik|AI429796	nurim (nuclear envelope membrane protein)	protein-coding
mm_4628.1	chr1	179549656	179549677	+	1	NA	intron (NM_146105, intron 1 of 10)	intron (NM_146105, intron 1 of 10)	3137	NM_146105	226744	Mm.87662	NM_146105	ENSMUSG00000038949	Cnst	9630058J23Rik	consortin, connexin sorting protein	protein-coding
mm_118931.1	chr14	27091773	27091776	+	1	NA	intron (NM_134437, intron 5 of 12)	intron (NM_134437, intron 5 of 12)	-52219	NM_001289686	71704	Mm.248606	NM_027871	ENSMUSG00000021895	Arhgef3	1200004I24Rik|9830169H03Rik|C76747|Xpln	Rho guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_31771.1	chr4	63554191	63554197	+	1	NA	Intergenic	Intergenic	-6166	NM_144905	230279	Mm.41523	NM_144905	ENSMUSG00000045917	Tmem268	6330416G13Rik|AW492431|bM230C2.2	transmembrane protein 268	protein-coding
mm_54263.1	chr6	28398079	28398109	-	1	NA	Intergenic	Intergenic	23630	NM_028900	74375	Mm.332950	NM_028900	ENSMUSG00000029708	Gcc1	4932417P04Rik	golgi coiled coil 1	protein-coding
mm_89635.1	chr10	96616999	96617015	+	1	NA	promoter-TSS (NM_007569)	promoter-TSS (NM_007569)	6	NM_007569	12226	Mm.23811	NM_007569	ENSMUSG00000036478	Btg1	AI426953|AW546738	B cell translocation gene 1, anti-proliferative	protein-coding
mm_153052.1	chr19	32103107	32103154	-	1	NA	promoter-TSS (NM_018830)	promoter-TSS (NM_018830)	10	NM_018830	54447	Mm.491229	NM_018830	ENSMUSG00000024887	Asah2	AI585898	N-acylsphingosine amidohydrolase 2	protein-coding
mm_89485.1	chr10	93641171	93641216	+	1	NA	5' UTR (NM_021320, exon 1 of 10)	5' UTR (NM_021320, exon 1 of 10)	144	NM_021320	57764	Mm.483868	NM_021320	ENSMUSG00000020019	Ntn4	-	netrin 4	protein-coding
mm_63094.1	chr7	122366536	122366558	+	1	NA	intron (NM_001316672, intron 2 of 16)	(CACAC)n|Simple_repeat|Simple_repeat	77422	NM_008855	18751	Mm.207496	NM_008855	ENSMUSG00000052889	Prkcb	PKC-B|PKC-Beta|Pkcb|Prkcb1|Prkcb2	protein kinase C, beta	protein-coding
mm_15301.1	chr2	155386111	155386134	+	1	NA	exon (NM_178111, exon 3 of 4)	exon (NM_178111, exon 3 of 4)	4266	NM_178111	68728	Mm.293605	NM_178111	ENSMUSG00000038375	Trp53inp2	1110029F20Rik|Tp53inp2	transformation related protein 53 inducible nuclear protein 2	protein-coding
mm_132293.1	chr16	33380796	33380823	+	1	NA	promoter-TSS (NM_011749)	promoter-TSS (NM_011749)	34	NM_011749	22661	Mm.392667	NM_011749	ENSMUSG00000022811	Zfp148	2210405J08Rik|AI480666|AW045217|BERF-1|BFCOL1|ZBP-89|Znf148	zinc finger protein 148	protein-coding
mm_5168.1	chr1	10180946	10180957	-	1	NA	exon (NM_001102430, exon 17 of 38)	exon (NM_001102430, exon 17 of 38)	51719	NM_001102430	211673	Mm.229141	NM_001102430	ENSMUSG00000067851	Arfgef1	ARFGEP1|BIG1|D130059B05Rik|D730028O18Rik|P200	ADP-ribosylation factor guanine nucleotide-exchange factor 1(brefeldin A-inhibited)	protein-coding
mm_113192.1	chr13	24943166	24943176	+	1	NA	promoter-TSS (NM_008156)	promoter-TSS (NM_008156)	19	NM_008156	14756	Mm.291831	NM_008156	ENSMUSG00000021340	Gpld1	6330541J12Rik|AW546131	glycosylphosphatidylinositol specific phospholipase D1	protein-coding
mm_32432.1	chr4	107200353	107200363	+	1	NA	intron (NM_029565, intron 7 of 7)	intron (NM_029565, intron 7 of 7)	-8822	NM_001081272	546840	Mm.331755	NM_001081272	ENSMUSG00000070877	Ldlrad1	OTTMUSG00000008594	low density lipoprotein receptor class A domain containing 1	protein-coding
mm_46847.1	chr5	113596436	113596468	-	1	NA	Intergenic	MTC|LTR|ERVL-MaLR	46032	NM_177292	320916	Mm.102783	NM_177292	ENSMUSG00000063430	Wscd2	4933413A10Rik|C530024P05Rik|Gm450	WSC domain containing 2	protein-coding
mm_108327.1	chr12	79863254	79863254	+	1	NA	Intergenic	Intergenic	61479	NR_131075	77290	Mm.395042	NR_131073		9430078K24Rik	-	RIKEN cDNA 9430078K24 gene	ncRNA
mm_71938.1	chr8	70329883	70329904	+	1	NA	5' UTR (NM_001163282, exon 7 of 8)	5' UTR (NM_001163282, exon 7 of 8)	128	NM_008107	14559	Mm.258280	NM_008107	ENSMUSG00000087408	Gdf1	AI385651|Gdf-1	growth differentiation factor 1	protein-coding
mm_131363.1	chr16	13780700	13780755	+	1	NA	promoter-TSS (NM_001039521)	promoter-TSS (NM_001039521)	28	NM_001039521	106298	Mm.288606	NM_001039521	ENSMUSG00000022682	Rrn3	AL023001|E130302O19Rik|R75565|TIF-1A|Tif1a	RRN3 RNA polymerase I transcription factor homolog (yeast)	protein-coding
mm_63263.1	chr7	126700662	126700666	+	1	NA	intron (NM_001301374, intron 8 of 10)	intron (NM_001301374, intron 8 of 10)	3556	NM_001301374	12721	Mm.290482	NM_009898	ENSMUSG00000030707	Coro1a	Clabp|Lmb3|TACO|p57	coronin, actin binding protein 1A	protein-coding
mm_132606.1	chr16	38562877	38562886	+	1	NA	promoter-TSS (NM_026407)	promoter-TSS (NM_026407)	67	NM_026407	67846	Mm.310476	NM_026407	ENSMUSG00000002845	Tmem39a	2610033C09Rik	transmembrane protein 39a	protein-coding
mm_37053.1	chr4	116018121	116018131	-	1	NA	promoter-TSS (NM_010173)	promoter-TSS (NM_010173)	-224	NM_010173	14073	Mm.256025	NM_010173	ENSMUSG00000034171	Faah	AW412498	fatty acid amide hydrolase	protein-coding
mm_92368.1	chr10	76027026	76027030	-	1	NA	Intergenic	Intergenic	-5584	NM_177475	64453	Mm.80609	NM_177475	ENSMUSG00000049764	Zfp280b	D10Jhu82e|Suhw2	zinc finger protein 280B	protein-coding
mm_137604.1	chr17	28221747	28221748	+	1	NA	intron (NM_027185, intron 5 of 10)	intron (NM_027185, intron 5 of 10)	-11007	NM_011145	19015	Mm.328914	NM_011145	ENSMUSG00000002250	Ppard	NUC-1|NUC1|Nr1c2|PPAR-beta|PPAR-delta|PPAR[b]|PPARdelta|Pparb|Pparb/d	peroxisome proliferator activator receptor delta	protein-coding
mm_11695.1	chr2	35736319	35736334	+	1	NA	Intergenic	B1_Mur3|SINE|Alu	39594	NM_001290639	69601	Mm.29629	NM_001001602	ENSMUSG00000026883	Dab2ip	2310011D08Rik|AI480459|Aip1|mKIAA1743	disabled 2 interacting protein	protein-coding
mm_48460.1	chr5	140812084	140812086	-	1	NA	intron (NM_010302, intron 1 of 3)	MTE2b|LTR|ERVL-MaLR	18346	NM_010302	14673	Mm.370185	NM_010302	ENSMUSG00000000149	Gna12	AI414047|AI504261|Galpha12	guanine nucleotide binding protein, alpha 12	protein-coding
mm_4381.1	chr1	172165524	172165532	+	1	NA	intron (NM_153555, intron 2 of 13)	intron (NM_153555, intron 2 of 13)	17513	NM_153555	98193	Mm.159915	NM_153555	ENSMUSG00000026554	Dcaf8	AA408877|AA433120|AA792214|AU018973|C76055|D1Dau35e|D1Ucla4|H326|Wdr42a	DDB1 and CUL4 associated factor 8	protein-coding
mm_141096.1	chr17	26004804	26004820	-	1	NA	intron (NM_153140, intron 4 of 11)	intron (NM_153140, intron 4 of 11)	17048	NM_153140	215445	Mm.41191	NM_153140	ENSMUSG00000037098	Rab11fip3	Cart1|D030060O14Rik|Rab11-FIP3|mKIAA0665	RAB11 family interacting protein 3 (class II)	protein-coding
mm_13467.1	chr2	105675707	105675716	+	1	NA	promoter-TSS (NM_013627)	promoter-TSS (NM_013627)	-33	NM_001244200	18508	Mm.3608	NM_013627	ENSMUSG00000027168	Pax6	1500038E17Rik|AEY11|Dey|Gsfaey11|Pax-6|Sey	paired box 6	protein-coding
mm_123741.1	chr14	70190771	70190774	-	1	NA	exon (NM_001271407, exon 16 of 21)	exon (NM_001271407, exon 16 of 21)	1474	NM_001271409	20410	Mm.5068	NM_011366	ENSMUSG00000022091	Sorbs3	SCAM-1|SH3P3|Sh3d4|vinexin-g	sorbin and SH3 domain containing 3	protein-coding
mm_59319.1	chr7	25301367	25301380	+	1	NA	promoter-TSS (NM_001081294)	promoter-TSS (NM_001081294)	14	NM_001081294	623131	Mm.172160	NM_001081294	ENSMUSG00000058741	Prr19	EG623131	proline rich 19	protein-coding
mm_35118.1	chr4	10998649	10998652	-	1	NA	intron (NM_175175, intron 1 of 1)	intron (NM_175175, intron 1 of 1)	8969	NM_175175	71801	Mm.34351	NM_175175	ENSMUSG00000049969	Plekhf2	1110070J07Rik|AA673237|ZFYVE18	pleckstrin homology domain containing, family F (with FYVE domain) member 2	protein-coding
mm_29291.1	chr3	107760188	107760227	-	1	NA	5' UTR (NM_007778, exon 1 of 9)	5' UTR (NM_007778, exon 1 of 9)	262	NM_001113530	12977	Mm.795	NM_007778	ENSMUSG00000014599	Csf1	C87615|Csfm|MCSF|op	colony stimulating factor 1 (macrophage)	protein-coding
mm_33303.1	chr4	129010761	129010764	+	1	NA	non-coding (NR_138540, exon 7 of 7)	non-coding (NR_138540, exon 7 of 7)	17538	NM_001033966	11637	Mm.29460	NM_016895	ENSMUSG00000028792	Ak2	Ak-2|D4Ertd220e	adenylate kinase 2	protein-coding
mm_169102.1	chr13	44478997	44478997	-	1	NA	Intergenic	LTRIS3|LTR|ERV1	39270	NR_045489	69491	Mm.392410	NR_045489	ENSMUSG00000098144	1700029N11Rik	-	RIKEN cDNA 1700029N11 gene	ncRNA
mm_129831.1	chr15	83149024	83149056	-	1	NA	promoter-TSS (NR_004432)	promoter-TSS (NR_004432)	296	NM_178627	73826	Mm.23758	NM_178627	ENSMUSG00000041815	Poldip3	1110008P04Rik|AA408269|AL022852|C77954|PDIP46|SKAR|mKIAA1649	polymerase (DNA-directed), delta interacting protein 3	protein-coding
mm_162116.1	chrX	53797706	53797706	-	1	NA	promoter-TSS (NM_001291748)	promoter-TSS (NM_001291748)	0	NM_001291747	22441	Mm.379041	NM_011725	ENSMUSG00000054626	Xlr	-	X-linked lymphocyte-regulated	protein-coding
mm_35227.1	chr4	19695280	19695285	-	1	NA	intron (NR_074089, intron 1 of 23)	intron (NR_074089, intron 1 of 23)	13722	NM_177327	107568	Mm.78312	NM_177327	ENSMUSG00000041058	Wwp1	8030445B08Rik|AIP5|SDRP1|Tiul1	WW domain containing E3 ubiquitin protein ligase 1	protein-coding
mm_76449.1	chr8	85080680	85080721	-	1	NA	promoter-TSS (NM_026399)	promoter-TSS (NM_026399)	46	NM_026399	67836	Mm.334680	NM_026399	ENSMUSG00000005150	Wdr83	1500041N16Rik|Morg1	WD repeat domain containing 83	protein-coding
mm_79903.1	chr9	65400869	65400879	+	1	NA	intron (NM_001033158, intron 1 of 4)	intron (NM_001033158, intron 1 of 4)	2386	NM_001033158	70784	Mm.35827	NM_001033158	ENSMUSG00000041696	Rasl12	4631404I11Rik	RAS-like, family 12	protein-coding
mm_76260.1	chr8	83748740	83748750	-	1	NA	Intergenic	Intergenic	-7434	NM_001163031	26364	Mm.334648	NM_011925	ENSMUSG00000002885	Adgre5	AA409984|Cd97|TM7LN1	adhesion G protein-coupled receptor E5	protein-coding
mm_151384.1	chr19	56319716	56319724	+	1	NA	TTS (NM_198059)	TTS (NM_198059)	31808	NM_146101	226243	Mm.25791	NM_146101	ENSMUSG00000025075	Habp2	AI035669|FSAP|HABP|HGFAL|PHBP	hyaluronic acid binding protein 2	protein-coding
mm_150017.1	chr19	29369051	29369061	+	1	NA	intron (NM_021893, intron 1 of 6)	intron (NM_021893, intron 1 of 6)	1618	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_84534.1	chr9	67208349	67208368	-	1	NA	Intergenic	Intergenic	28368	NR_029576	387185		NR_029576	ENSMUSG00000076379	Mir190a	Mir190|Mirn190|mir-190|mir-190a|mmu-mir-190|mmu-mir-190a	microRNA 190a	ncRNA
mm_32531.1	chr4	108942351	108942354	+	1	NA	TTS (NR_040664)	TTS (NR_040664)	29725	NR_040664	77173	Mm.402545	NR_040664	ENSMUSG00000086483	8030443G20Rik	-	RIKEN cDNA 8030443G20 gene	ncRNA
mm_27766.1	chr3	70807248	70807267	-	1	NA	promoter-TSS (NR_040556)	promoter-TSS (NR_040556)	34	NR_040556	625901	Mm.366028	NR_040556	ENSMUSG00000097252	Gm6634	EG625901	predicted gene 6634	ncRNA
mm_104749.1	chr11	98463480	98463486	-	1	NA	Intergenic	IMPB_01|Satellite|Satellite	16649	NM_010346	14786	Mm.276702	NM_010346	ENSMUSG00000019312	Grb7	mKIAA4028	growth factor receptor bound protein 7	protein-coding
mm_68046.1	chr7	101521450	101521452	-	1	NA	Intergenic	ID_B1|SINE|B4	34351	NM_007490	11871	Mm.439746	NM_007490	ENSMUSG00000092517	Art2a-ps	ARTC2|Art2a|Ly92a|Rt-6|Rt6|Rt6-1	ADP-ribosyltransferase 2a, pseudogene	protein-coding
mm_160130.1	chr7	29214024	29214024	-	1	NA	promoter-TSS (NM_001164658)	promoter-TSS (NM_001164658)	9	NM_001164658	320225	Mm.349382	NM_001039721	ENSMUSG00000049676	Catsperg1	A230107C01Rik|Catsperg	catsper channel auxiliary subunit gamma 1	protein-coding
mm_104236.1	chr11	88717792	88717838	-	1	NA	promoter-TSS (NR_038058)	promoter-TSS (NR_038058)	414	NM_054043	76626	Mm.400451	NM_054043	ENSMUSG00000069769	Msi2	1700105C15Rik|AI451722|AI563628|AW489193|Msi2h	musashi RNA-binding protein 2	protein-coding
mm_103640.1	chr11	78963333	78963356	-	1	NA	3' UTR (NM_010708, exon 11 of 11)	3' UTR (NM_010708, exon 11 of 11)	21580	NM_001159301	16859	Mm.341434	NM_010708	ENSMUSG00000001123	Lgals9	AA407335|AI194909|AI265545|LGALS35|Lgals5|gal-9|galectin-9	lectin, galactose binding, soluble 9	protein-coding
mm_119672.1	chr14	52622497	52622518	+	1	NA	Intergenic	Intergenic	-126812	NM_001170918	57269	Mm.88822	NM_020512	ENSMUSG00000059887	Olfr1507	MOR244-1|Mor28|Or28	olfactory receptor 1507	protein-coding
mm_125211.1	chr15	34082222	34082232	+	1	NA	promoter-TSS (NM_026002)	promoter-TSS (NM_026002)	-492	NM_026002	67154	Mm.130883	NM_026002	ENSMUSG00000022255	Mtdh	2610103J23Rik|3D3|3D3/Lyric|AEG-1|AV353288|D8Bwg1112e|Lyric	metadherin	protein-coding
mm_60115.1	chr7	35586296	35586310	+	1	NA	promoter-TSS (NM_178263)	promoter-TSS (NM_178263)	56	NM_178263	245886	Mm.272620	NM_145633	ENSMUSG00000034867	Ankrd27	AA408090|BC016493|D330003H11Rik|Varp	ankyrin repeat domain 27 (VPS9 domain)	protein-coding
mm_166813.1	chr7	16258043	16258066	+	1	NA	intron (NM_007577, intron 2 of 2)	intron (NM_007577, intron 2 of 2)	1284	NM_001173550	12273	Mm.247623	NM_007577	ENSMUSG00000049130	C5ar1	C5aR|C5r1|Cd88|D7Msu1	complement component 5a receptor 1	protein-coding
mm_86921.1	chr10	23851538	23851548	+	1	NA	promoter-TSS (NM_011979)	promoter-TSS (NM_011979)	81	NM_011979	26464	Mm.27334	NM_011979	ENSMUSG00000020010	Vnn3	-	vanin 3	protein-coding
mm_77494.1	chr8	122576831	122576892	-	1	NA	promoter-TSS (NM_009698)	promoter-TSS (NM_009698)	46	NM_009698	11821	Mm.1786	NM_009698	ENSMUSG00000006589	Aprt	C85684	adenine phosphoribosyl transferase	protein-coding
mm_148371.1	chr18	88927448	88927481	-	1	NA	Intergenic	Intergenic	-33257	NM_018821	54607	Mm.91920	NM_018821	ENSMUSG00000056153	Socs6	1500012M23Rik|5830401B18Rik|AI447482|Cis4|Cish4|HSPC060|SOCS-4|SOCS-6|SSI4|STAI4|STATI4|Socs4	suppressor of cytokine signaling 6	protein-coding
mm_27525.1	chr3	57302000	57302009	-	1	NA	promoter-TSS (NM_008536)	promoter-TSS (NM_008536)	-85	NM_008536	17112	Mm.856	NM_008536	ENSMUSG00000027800	Tm4sf1	L6|M3s1	transmembrane 4 superfamily member 1	protein-coding
mm_113220.1	chr13	27057602	27057611	+	1	NA	promoter-TSS (NM_011164)	promoter-TSS (NM_011164)	36	NM_011164	19109	Mm.1270	NM_011164	ENSMUSG00000021342	Prl	AV290867|Gha1|Prl1a1	prolactin	protein-coding
mm_31813.1	chr4	66827700	66827723	+	1	NA	5' UTR (NM_021297, exon 1 of 3)	5' UTR (NM_021297, exon 1 of 3)	160	NM_021297	21898	Mm.38049	NM_021297	ENSMUSG00000039005	Tlr4	Lps|Ly87|Ran/M1|Rasl2-8	toll-like receptor 4	protein-coding
mm_125725.1	chr15	73149836	73149884	+	1	NA	intron (NM_153178, intron 1 of 18)	intron (NM_153178, intron 1 of 18)	35087	NM_153178	239528	Mm.23095	NM_153178	ENSMUSG00000036698	Ago2	1110029L17Rik|2310051F07Rik|AI225898|AL022874|AW546247|ENSMUSG00000072493|Eif2c2|Gerp95|Gm10365|mKIAA4215	argonaute RISC catalytic subunit 2	protein-coding
mm_49286.1	chr6	17666047	17666074	+	1	NA	3' UTR (NM_007604, exon 10 of 10)	3' UTR (NM_007604, exon 10 of 10)	-27934	NM_001289624	64213	Mm.12051	NM_022332	ENSMUSG00000029534	St7	9430001H04Rik|Fam4a2|HELG|RAY1|SEN4|TSG7	suppression of tumorigenicity 7	protein-coding
mm_145598.1	chr18	61045140	61045206	+	1	NA	promoter-TSS (NM_001146268)	promoter-TSS (NM_001146268)	23	NM_008809	18596	Mm.4146	NM_008809	ENSMUSG00000024620	Pdgfrb	AI528809|CD140b|PDGFR-1|Pdgfr	platelet derived growth factor receptor, beta polypeptide	protein-coding
mm_117115.1	chr13	60602585	60602596	-	1	NA	exon (NM_134062, exon 2 of 27)	exon (NM_134062, exon 2 of 27)	379	NM_134062	69635	Mm.24103	NM_029653	ENSMUSG00000021559	Dapk1	D13Ucla1|DAP-Kinase	death associated protein kinase 1	protein-coding
mm_161932.1	chr18	82406760	82406760	-	1	NA	promoter-TSS (NM_008082)	promoter-TSS (NM_008082)	17	NM_008082	14427	Mm.6219	NM_008082	ENSMUSG00000024553	Galr1	Galnr1	galanin receptor 1	protein-coding
mm_98394.1	chr11	94281832	94281865	+	1	NA	Intergenic	Intergenic	-39269	NM_181819	278507	Mm.342216	NM_181819	ENSMUSG00000044177	Wfikkn2	2610304F08Rik|AY100450|Gasp1|WFIKKNRP	WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 2	protein-coding
mm_14995.1	chr2	152345627	152345637	+	1	NA	promoter-TSS (NR_033505)	promoter-TSS (NR_033505)	-37	NR_033505	791417	Mm.451219	NR_033505	ENSMUSG00000068062	Gm14164	OTTMUSG00000015846	predicted gene 14164	ncRNA
mm_33618.1	chr4	132639029	132639118	+	1	NA	promoter-TSS (NM_010166)	promoter-TSS (NM_010166)	27	NM_010166	14050	Mm.227733	NM_010166	ENSMUSG00000028886	Eya3	AI844637	EYA transcriptional coactivator and phosphatase 3	protein-coding
mm_156723.1	chrX	159840464	159840472	+	1	NA	promoter-TSS (NM_001135728)	promoter-TSS (NM_001135728)	0	NM_001135728	58194	Mm.286495	NM_021389	ENSMUSG00000040990	Sh3kbp1	1200007H22Rik|1700125L08Rik|5830464D22Rik|AI447724|Cin85|IN85|Ruk|Seta	SH3-domain kinase binding protein 1	protein-coding
mm_160800.1	chr11	5100139	5100139	+	1	NA	promoter-TSS (NM_001290493)	promoter-TSS (NM_001290493)	-26	NM_001290493	279766	Mm.260866	NM_177370	ENSMUSG00000034175	Rhbdd3	Ptag	rhomboid domain containing 3	protein-coding
mm_61583.1	chr7	79869383	79869387	+	1	NA	Intergenic	Intergenic	-27033	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_15349.1	chr2	156172924	156172991	+	1	NA	exon (NM_001291114, exon 4 of 17)	exon (NM_001291114, exon 4 of 17)	6623	NM_001291115	170791	Mm.392436	NM_133242	ENSMUSG00000027620	Rbm39	1500012C14Rik|2310040E03Rik|B330012G18Rik|C79248|R75070|Rnpc2|caper	RNA binding motif protein 39	protein-coding
mm_67451.1	chr7	80398874	80398898	-	1	NA	5' UTR (NM_001081454, exon 2 of 16)	5' UTR (NM_001081454, exon 2 of 16)	3926	NM_011046	18550	Mm.5241	NM_011046	ENSMUSG00000030530	Furin	9130404I01Rik|Fur|PACE|Pcsk3|SPC1	furin (paired basic amino acid cleaving enzyme)	protein-coding
mm_20811.1	chr2	144474430	144474439	-	1	NA	3' UTR (NM_172859, exon 21 of 21)	3' UTR (NM_172859, exon 21 of 21)	9258	NR_038065	171588	Mm.450554	NR_038065	ENSMUSG00000083674	Gm38402	-	zinc finger protein pseudogene	pseudo
mm_115081.1	chr13	102688395	102688429	+	1	NA	Intergenic	LTR104_Mam|LTR|Gypsy	-5146	NM_008533	17079	Mm.373974	NM_008533	ENSMUSG00000021624	Cd180	F630107B15|Ly78|RP105	CD180 antigen	protein-coding
mm_32459.1	chr4	107381123	107381125	+	1	NA	intron (NM_028355, intron 6 of 17)	intron (NM_028355, intron 6 of 17)	13340	NM_028355	72787	Mm.28478	NM_028355	ENSMUSG00000028614	Ndc1	2810475A17Rik|AI450313|Tmem48|sks	NDC1 transmembrane nucleoporin	protein-coding
mm_47897.1	chr5	134747248	134747264	-	1	NA	promoter-TSS (NM_007925)	promoter-TSS (NM_007925)	67	NM_007925	13717	Mm.275320	NM_007925	ENSMUSG00000029675	Eln	AI385707|AI480567|E030024M20Rik	elastin	protein-coding
mm_121187.1	chr14	103049603	103049608	+	1	NA	intron (NM_008392, intron 2 of 4)	intron (NM_008392, intron 2 of 4)	2593	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_136921.1	chr17	13846096	13846119	+	1	NA	intron (NM_010806, intron 13 of 32)	intron (NM_010806, intron 13 of 32)	-84713	NM_022311	21646	Mm.486358	NM_022311	ENSMUSG00000038347	Tcte2	AI429268|Tcte-2	t-complex-associated testis expressed 2	protein-coding
mm_75723.1	chr8	69084849	69084855	-	1	NA	intron (NM_153054, intron 1 of 16)	intron (NM_153054, intron 1 of 16)	-3884	NM_007509	11966	Mm.249096	NM_007509	ENSMUSG00000006273	Atp6v1b2	AI194269|AI790362|Atp6b2|HO57|R74844	ATPase, H+ transporting, lysosomal V1 subunit B2	protein-coding
mm_161811.1	chr17	63911214	63911214	+	1	NA	intron (NM_001037997, intron 3 of 18)	Lx9|LINE|L1	-26758	NM_008000	14158	Mm.23039	NM_008000	ENSMUSG00000000127	Fer	AV082135|C330004K01Rik|Fert|Fert2	fer (fms/fps related) protein kinase	protein-coding
mm_126811.1	chr15	87655004	87655019	+	1	NA	intron (NM_134096, intron 1 of 3)	intron (NM_134096, intron 1 of 3)	29781	NM_134096	106014	Mm.244319	NM_134096	ENSMUSG00000054863	Fam19a5	TAFA5|Tafa-5|Tara-5	family with sequence similarity 19, member A5	protein-coding
mm_103836.1	chr11	83020771	83020783	-	1	NA	promoter-TSS (NM_001167743)	promoter-TSS (NM_001167743)	33	NM_181545	276950	Mm.491599	NM_181545	ENSMUSG00000035208	Slfn8	-	schlafen 8	protein-coding
mm_147373.1	chr18	43477765	43477801	-	1	NA	Intergenic	CpG	-39497	NM_001291455	22240	Mm.8180	NM_009468	ENSMUSG00000024501	Dpysl3	CRMP-4|DRP-3|TUC4|ULIP-1|Ulip|Ulip1	dihydropyrimidinase-like 3	protein-coding
mm_27477.1	chr3	53557557	53557571	-	1	NA	intron (NM_172862, intron 6 of 23)	intron (NM_172862, intron 6 of 23)	68771	NM_153156	229277	Mm.222810	NM_153156	ENSMUSG00000027744	Stoml3	Epb7.2l|SLP3|sro	stomatin (Epb7.2)-like 3	protein-coding
mm_18730.1	chr2	72979264	72979342	-	1	NA	promoter-TSS (NR_045269)	promoter-TSS (NR_045269)	-22	NM_001098425	20687	Mm.124328	NM_011450	ENSMUSG00000027109	Sp3	D130027J01Rik	trans-acting transcription factor 3	protein-coding
mm_145534.1	chr18	60805007	60805017	+	1	NA	intron (NM_001042605, intron 1 of 8)	intron (NM_001042605, intron 1 of 8)	1163	NM_010545	16149	Mm.439737	NM_010545	ENSMUSG00000024610	Cd74	CLIP|DHLAG|HLADG|Ia-GAMMA|Ii	CD74 antigen (invariant polypeptide of major histocompatibility complex, class II antigen-associated)	protein-coding
mm_144995.1	chr18	38296962	38296987	+	1	NA	5' UTR (NM_001164621, exon 1 of 10)	5' UTR (NM_001164621, exon 1 of 10)	169	NM_001164621	56736	Mm.228903	NM_020012	ENSMUSG00000060450	Rnf14	2310075C09Rik|2610005D23Rik|AA986456|AU041447|D18Ertd188e|D7Bwg0165e|Triad2	ring finger protein 14	protein-coding
mm_77606.1	chr8	123893239	123893249	-	1	NA	exon (NM_009606, exon 3 of 7)	exon (NM_009606, exon 3 of 7)	1531	NM_001272041	11459	Mm.214950	NM_009606	ENSMUSG00000031972	Acta1	AA959943|Acta-2|Acts|Actsk-1	actin, alpha 1, skeletal muscle	protein-coding
mm_7324.1	chr1	100252502	100252519	-	1	NA	intron (NM_172851, intron 11 of 23)	intron (NM_172851, intron 11 of 23)	479745	NM_172851	241175	Mm.251301	NM_172851	ENSMUSG00000067028	Cntnap5b	C230078M14Rik|Caspr5-2	contactin associated protein-like 5B	protein-coding
mm_82796.1	chr9	29412286	29412298	-	1	NA	intron (NM_172290, intron 1 of 7)	CpG	550837	NM_172290	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding
mm_8641.1	chr1	156429468	156429488	-	1	NA	3' UTR (NM_009230, exon 16 of 16)	3' UTR (NM_009230, exon 16 of 16)	-8563	NM_001346967	77352	Mm.428709	NM_001033180	ENSMUSG00000026601	Axdnd1	9430070O13Rik|Gm979	axonemal dynein light chain domain containing 1	protein-coding
mm_22736.1	chr3	19707418	19707418	+	1	NA	Intergenic	Intergenic	-12022	NM_205769	12918	Mm.290689	NM_205769	ENSMUSG00000049796	Crh	CRF|Gm1347	corticotropin releasing hormone	protein-coding
mm_53083.1	chr6	124996682	124996756	+	1	NA	promoter-TSS (NM_175696)	promoter-TSS (NM_175696)	-1	NM_175696	319352	Mm.295327	NM_175696	ENSMUSG00000030329	Pianp	AI255183|AU067746|C530028O21Rik|Panp	PILR alpha associated neural protein	protein-coding
mm_150175.1	chr19	32595728	32595745	+	1	NA	promoter-TSS (NM_001201470)	promoter-TSS (NM_001201470)	21	NM_001201470	23972	Mm.203916	NM_011864	ENSMUSG00000024899	Papss2	1810018P12Rik|AI159688|AtpsU2|Atpsk2|Sk2|bm	3'-phosphoadenosine 5'-phosphosulfate synthase 2	protein-coding
mm_116629.1	chr13	48968035	48968068	-	1	NA	promoter-TSS (NR_015601)	promoter-TSS (NR_015601)	-61	NR_015601	68128	Mm.426304	NR_015601		Fam120aos	C030044B11Rik	family with sequence similarity 120A, opposite strand	ncRNA
mm_154583.1	chrX	7572674	7572689	+	1	NA	promoter-TSS (NR_029473)	promoter-TSS (NR_029473)	-919	NR_029473	78185	Mm.160055	NR_029473	ENSMUSG00000039545	Ppp1r3fos	4930524L23Rik	protein phosphatase 1, regulatory subunit 3F, opposite strand	ncRNA
mm_36513.1	chr4	83527766	83527767	-	1	NA	intron (NM_001081012, intron 1 of 25)	U4|snRNA|snRNA	2221	NM_001081012	320226	Mm.180032	NM_029117	ENSMUSG00000052407	Ccdc171	4930418J05Rik|4930473A06Rik|A330015D16Rik	coiled-coil domain containing 171	protein-coding
mm_138240.1	chr17	34564296	34564299	+	1	NA	promoter-TSS (NM_010929)	promoter-TSS (NM_010929)	2	NM_010929	18132	Mm.173813	NM_010929	ENSMUSG00000015468	Notch4	Int-3|Int3|N4	notch 4	protein-coding
mm_117840.1	chr13	98692716	98692725	-	1	NA	intron (NM_001025606, intron 1 of 3)	intron (NM_001025606, intron 1 of 3)	2111	NM_001025606	380863	Mm.28264	NM_001025606	ENSMUSG00000052485	Tmem171	Gm905	transmembrane protein 171	protein-coding
mm_121618.1	chr14	8297111	8297136	-	1	NA	3' UTR (NM_183187, exon 4 of 4)	3' UTR (NM_183187, exon 4 of 4)	12653	NM_183187	268709	Mm.256058	NM_183187	ENSMUSG00000021750	Fam107a	DRR1	family with sequence similarity 107, member A	protein-coding
mm_69704.1	chr7	140082247	140082284	-	1	NA	promoter-TSS (NM_001190386)	promoter-TSS (NM_001190386)	36	NM_001190386	68566	Mm.44241	NM_026769	ENSMUSG00000025468	Caly	0710001P07Rik|1110004A22Rik|Calcyon|Drd1ip	calcyon neuron-specific vesicular protein	protein-coding
mm_16617.1	chr2	5538732	5538744	-	1	NA	intron (NM_177343, intron 2 of 10)	intron (NM_177343, intron 2 of 10)	137308	NM_001290376	227541	Mm.191949	NM_177343	ENSMUSG00000039145	Camk1d	A630059D12Rik|CKLiK|CaMKIdelta|E030025C11Rik|mCKLiK	calcium/calmodulin-dependent protein kinase ID	protein-coding
mm_76611.1	chr8	91133950	91134022	-	1	NA	promoter-TSS (NM_001302337)	promoter-TSS (NM_001302337)	41	NM_001302337	14339	Mm.324588	NM_010241	ENSMUSG00000031667	Aktip	AL023020|Fif|Ft|Ft1|Fts	thymoma viral proto-oncogene 1 interacting protein	protein-coding
mm_136194.1	chr16	89507739	89507743	-	1	NA	TTS (NM_027771)	TTS (NM_027771)	582	NM_027771	71363	Mm.158680	NM_027771	ENSMUSG00000056706	Krtap7-1	5430433J05Rik	keratin associated protein 7-1	protein-coding
mm_68422.1	chr7	109752194	109752208	-	1	NA	promoter-TSS (NM_020050)	promoter-TSS (NM_020050)	62	NM_020050	56786	Mm.240668	NM_020050	ENSMUSG00000031021	Tmem9b	2310004K06Rik|AW539847|D7H11orf15|ICRFP703B1614Q5.3	TMEM9 domain family, member B	protein-coding
mm_145648.1	chr18	61127837	61127925	+	1	NA	exon (NM_001037859, exon 16 of 22)	exon (NM_001037859, exon 16 of 22)	10413	NR_105949	102466212		NR_105949	ENSMUSG00000098389	Mir6983	Gm27496|mmu-mir-6983	microRNA 6983	ncRNA
mm_73398.1	chr8	105850858	105850877	+	1	NA	intron (NM_177150, intron 1 of 12)	ID2|SINE|ID	1141	NM_177150	320394	Mm.334775	NM_177150	ENSMUSG00000036672	Cenpt	G630055P03Rik	centromere protein T	protein-coding
mm_88861.1	chr10	80930910	80930924	+	1	NA	intron (NM_008655, intron 2 of 3)	intron (NM_008655, intron 2 of 3)	826	NM_008655	17873	Mm.1360	NM_008655	ENSMUSG00000015312	Gadd45b	AI323528|Myd118	growth arrest and DNA-damage-inducible 45 beta	protein-coding
mm_88648.1	chr10	79960146	79960162	+	1	NA	promoter-TSS (NM_175450)	promoter-TSS (NM_175450)	2	NM_175450	216156	Mm.35828	NM_175450	ENSMUSG00000035754	Wdr18	2310012I10Rik|AU044733|AW122032	WD repeat domain 18	protein-coding
mm_18299.1	chr2	52998154	52998158	-	1	NA	intron (NM_172409, intron 1 of 26)	intron (NM_172409, intron 1 of 26)	140288	NM_172409	71409	Mm.394427	NM_172409	ENSMUSG00000036053	Fmnl2	5430425K04Rik|Man	formin-like 2	protein-coding
mm_32879.1	chr4	118625524	118625525	+	1	NA	promoter-TSS (NR_029469)	promoter-TSS (NR_029469)	-880	NR_029469	100041290	Mm.472885	NR_029469		D4Ertd617e	-	DNA segment, Chr 4, ERATO Doi 617, expressed	ncRNA
mm_111979.1	chr12	110278959	110278991	-	1	NA	promoter-TSS (NR_002866)	promoter-TSS (NR_002866)	-255	NM_172119	107585	Mm.154427	NM_172119	ENSMUSG00000075707	Dio3	-	deiodinase, iodothyronine type III	protein-coding
mm_364.1	chr1	33908078	33908090	+	1	NA	promoter-TSS (NM_001310484)	promoter-TSS (NM_001310484)	-141	NM_001276764	13518	Mm.336625	NM_010081	ENSMUSG00000026131	Dst	2310001O04Rik|A830042E19Rik|AW554249|BP230|BPAG1-n|Bpag|Bpag1|Macf2|ah|athetoid|dt|mKIAA0728|nmf203|nmf339	dystonin	protein-coding
mm_19841.1	chr2	112678263	112678275	-	1	NA	intron (NM_177652, intron 71 of 103)	intron (NM_177652, intron 71 of 103)	118587	NM_001165935	74268	Mm.315125	NM_028844	ENSMUSG00000003604	Aven	1700013A01Rik|1700056A21Rik|mAven-L|mAven-S	apoptosis, caspase activation inhibitor	protein-coding
mm_127559.1	chr15	102177319	102177321	+	1	NA	3' UTR (NM_144942, exon 15 of 15)	3' UTR (NM_144942, exon 15 of 15)	11723	NM_144942	246277	Mm.296382	NM_144942	ENSMUSG00000023044	Csad	Csd	cysteine sulfinic acid decarboxylase	protein-coding
mm_73672.1	chr8	111435826	111435847	+	1	NA	Intergenic	B4A|SINE|B4	-14364	NR_105819	102466970		NR_105819	ENSMUSG00000098410	Mir1957b	Gm27725|mmu-mir-1957b	microRNA 1957b	ncRNA
mm_55188.1	chr6	52190592	52190606	-	1	NA	exon (NM_008265, exon 2 of 2)	exon (NM_008265, exon 2 of 2)	1104	NM_008265	15401	Mm.439647	NM_008265	ENSMUSG00000000942	Hoxa4	AV206827|Hox-1.4	homeobox A4	protein-coding
mm_140996.1	chr17	24885901	24885909	-	1	NA	promoter-TSS (NM_001163750)	promoter-TSS (NM_001163750)	445	NM_011956	26426	Mm.36718	NM_011956	ENSMUSG00000039183	Nubp2	D17Wsu11e	nucleotide binding protein 2	protein-coding
mm_88703.1	chr10	80148249	80148253	+	1	NA	promoter-TSS (NM_001305798)	promoter-TSS (NM_001305798)	-21	NM_001305798	59090	Mm.143813	NM_021565	ENSMUSG00000035621	Midn	3000003C15Rik	midnolin	protein-coding
mm_114081.1	chr13	54575021	54575093	+	1	NA	promoter-TSS (NM_019968)	promoter-TSS (NM_019968)	44	NM_019968	56795	Mm.89484	NM_019968	ENSMUSG00000025870	Arl10	Arl10a|Arm1	ADP-ribosylation factor-like 10	protein-coding
mm_103017.1	chr11	69734909	69734919	-	1	NA	exon (NM_001291068, exon 29 of 29)	exon (NM_001291068, exon 29 of 29)	23719	NM_001291068	20020	Mm.16533	NM_009089	ENSMUSG00000005198	Polr2a	220kDa|Rpb1|Rpo2-1	polymerase (RNA) II (DNA directed) polypeptide A	protein-coding
mm_84064.1	chr9	58201302	58201316	-	1	NA	exon (NM_001161535, exon 1 of 2)	exon (NM_001161535, exon 1 of 2)	406	NM_001161535	320563	Mm.186499	NM_177193	ENSMUSG00000051243	Islr2	B930052A04Rik|Linx|Mbu-3|mKIAA1465	immunoglobulin superfamily containing leucine-rich repeat 2	protein-coding
mm_160838.1	chr11	49050773	49050773	+	1	NA	promoter-TSS (NM_010999)	promoter-TSS (NM_010999)	40	NM_010999	18356	Mm.24769	NM_010999	ENSMUSG00000040328	Olfr56	IF7|MOR276-1	olfactory receptor 56	protein-coding
mm_170674.1	chr2	121449412	121449419	+	1	NA	non-coding (NR_110986, exon 1 of 3)	non-coding (NR_110986, exon 1 of 3)	217	NR_110986	378702	Mm.262252	NM_011354	ENSMUSG00000074884	Serf2	C80083|Msmac1l|m4F5rel	small EDRK-rich factor 2	protein-coding
mm_65385.1	chr7	25091253	25091283	-	1	NA	3' UTR (NM_001163556, exon 14 of 14)	3' UTR (NM_001163556, exon 14 of 14)	5907	NR_105855	102465968		NR_105855	ENSMUSG00000098441	Mir6537	Gm27808|mmu-mir-6537	microRNA 6537	ncRNA
mm_103535.1	chr11	77489671	77489687	-	1	NA	promoter-TSS (NM_172945)	promoter-TSS (NM_172945)	-1	NM_172945	268445	Mm.39296	NM_172945	ENSMUSG00000037907	Ankrd13b	AW124583|B930093C12Rik	ankyrin repeat domain 13b	protein-coding
mm_163620.1	chr13	55322164	55322175	+	1	NA	promoter-TSS (NM_009000)	promoter-TSS (NM_009000)	114	NM_025596	66494	Mm.439805	NM_025596	ENSMUSG00000021486	Prelid1	2610524G07Rik|Preli	PRELI domain containing 1	protein-coding
mm_56881.1	chr6	119017037	119017041	-	1	NA	intron (NM_001256002, intron 3 of 47)	intron (NM_001256002, intron 3 of 47)	91456	NM_001159534	12288	Mm.41628	NM_009781	ENSMUSG00000051331	Cacna1c	Cav1.2|Cchl1a1|D930026N18Rik|MBC|MELC-CC	calcium channel, voltage-dependent, L type, alpha 1C subunit	protein-coding
mm_63488.1	chr7	127767448	127767468	+	1	NA	exon (NM_172748, exon 10 of 11)	exon (NM_172748, exon 10 of 11)	-2357	NM_198424	269999	Mm.36852	NM_198424	ENSMUSG00000043964	Orai3	9930124N15|BC061259|Tmem142c	ORAI calcium release-activated calcium modulator 3	protein-coding
mm_52396.1	chr6	113307161	113307230	+	1	NA	promoter-TSS (NM_001282127)	promoter-TSS (NM_001282127)	58	NM_001282126	78783	Mm.356059	NM_030178	ENSMUSG00000001632	Brpf1	4833438B11Rik|4930540D11Rik|Brpf2	bromodomain and PHD finger containing, 1	protein-coding
mm_109243.1	chr12	109452780	109452791	+	1	NA	promoter-TSS (NM_010052)	promoter-TSS (NM_010052)	-38	NR_033813	13386	Mm.157069	NM_010052	ENSMUSG00000040856	Dlk1	AW742678|DLK-1|DlkI|FA1|Ly107|Peg9|SCP1|ZOG|pG2|pref-1	delta-like 1 homolog (Drosophila)	protein-coding
mm_97636.1	chr11	78973755	78973766	+	1	NA	intron (NM_001159301, intron 2 of 9)	MTD|LTR|ERVL-MaLR	11164	NM_001159301	16859	Mm.341434	NM_010708	ENSMUSG00000001123	Lgals9	AA407335|AI194909|AI265545|LGALS35|Lgals5|gal-9|galectin-9	lectin, galactose binding, soluble 9	protein-coding
mm_143319.1	chr17	66266902	66266929	-	1	NA	Intergenic	Intergenic	143395	NM_001003919	320209	Mm.259605	NM_001003919	ENSMUSG00000035842	Ddx11	4732462I11Rik|CHL1|CHLR1|KRG2|essa15a	DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11	protein-coding
mm_166209.1	chr5	48188040	48188047	-	1	NA	intron (NR_111900, intron 7 of 35)	intron (NR_111900, intron 7 of 35)	-35899	NR_029798	723822		NR_029798	ENSMUSG00000065603	Mir218-1	Mirn218-1|mir-218-1	microRNA 218-1	ncRNA
mm_12727.1	chr2	78868726	78868756	+	1	NA	promoter-TSS (NM_009454)	promoter-TSS (NM_009454)	-306	NM_009454	22193	Mm.1485	NM_009454	ENSMUSG00000027011	Ube2e3	Ubce4|ubcM2	ubiquitin-conjugating enzyme E2E 3	protein-coding
mm_81933.1	chr9	120180015	120180026	+	1	NA	Intergenic	L1ME3Cz|LINE|L1	30278	NM_001039364	17433	Mm.486167	NM_008614	ENSMUSG00000032517	Mobp	AI835053|AI839848|MOBP155|MOBP170|MOBP69|MOBP73|MOBP81|R74645	myelin-associated oligodendrocytic basic protein	protein-coding
mm_154473.1	chrM	3884	3895	-	1	NA	NA	Intergenic	NA	NA								
mm_121226.1	chr14	103055538	103055560	+	1	NA	3' UTR (NM_008392, exon 5 of 5)	3' UTR (NM_008392, exon 5 of 5)	8537	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_121800.1	chr14	20143689	20143713	-	1	NA	intron (NM_021542, intron 4 of 4)	intron (NM_021542, intron 4 of 4)	38081	NM_021542	16529	Mm.68998	NM_021542	ENSMUSG00000023243	Kcnk5	KCNK5b|TASK-2	potassium channel, subfamily K, member 5	protein-coding
mm_5453.1	chr1	36269539	36269550	-	1	NA	exon (NM_153408, exon 2 of 4)	exon (NM_153408, exon 2 of 4)	3881	NM_153408	214854	Mm.389110	NM_153408	ENSMUSG00000047180	Neurl3	2010300P06Rik|Lincr	neuralized E3 ubiquitin protein ligase 3	protein-coding
mm_129921.1	chr15	84239926	84239943	-	1	NA	intron (NM_133167, intron 1 of 12)	intron (NM_133167, intron 1 of 12)	7891	NM_133167	170736	Mm.323892	NM_133167	ENSMUSG00000022438	Parvb	AI595373|AW742462|D15Gsk1|affixin	parvin, beta	protein-coding
mm_168046.1	chrY	90811624	90811639	+	1	NA	intron (NM_133362, intron 2 of 3)	IMPB_01|Satellite|Satellite	26189	NM_133362	170942	Mm.76062	NM_133362	ENSMUSG00000096768	Erdr1	edr	erythroid differentiation regulator 1	protein-coding
mm_99490.1	chr11	102761564	102761620	+	1	NA	5' UTR (NM_009613, exon 1 of 27)	5' UTR (NM_009613, exon 1 of 27)	157	NM_001110778	11488	Mm.89854	NM_009613	ENSMUSG00000020926	Adam11	AW060611|Mdc	a disintegrin and metallopeptidase domain 11	protein-coding
mm_73220.1	chr8	99416586	99416599	+	1	NA	promoter-TSS (NM_001285913)	promoter-TSS (NM_001285913)	-82	NR_132435	234624	Mm.124595	NM_175479	ENSMUSG00000052479	A330008L17Rik	-	RIKEN cDNA A330008L17 gene	ncRNA
mm_57242.1	chr6	123283133	123283157	-	1	NA	3' UTR (NM_019948, exon 6 of 6)	3' UTR (NM_019948, exon 6 of 6)	6726	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_54566.1	chr6	37870424	37870467	-	1	NA	promoter-TSS (NM_145076)	promoter-TSS (NM_145076)	-366	NM_001272064	21848	Mm.41063	NM_145076	ENSMUSG00000029833	Trim24	A130082H20Rik|AI447469|D430004I05Rik|TIF1|TIF1-alpha|TIF1alpha|Tif1a	tripartite motif-containing 24	protein-coding
mm_48479.1	chr5	141000635	141000649	-	1	NA	promoter-TSS (NM_175362)	promoter-TSS (NM_175362)	-46	NM_175362	108723	Mm.46187	NM_175362	ENSMUSG00000036526	Card11	0610008L17Rik|2410011D02Rik|BIMP3|CARMA1	caspase recruitment domain family, member 11	protein-coding
mm_140418.1	chr17	87672524	87672580	+	1	NA	promoter-TSS (NM_008628)	promoter-TSS (NM_008628)	-5	NM_008628	17685	Mm.4619	NM_008628	ENSMUSG00000024151	Msh2	AI788990	mutS homolog 2	protein-coding
mm_126400.1	chr15	80234072	80234146	+	1	NA	promoter-TSS (NM_178719)	promoter-TSS (NM_178719)	29	NM_178719	239555	Mm.307163	NM_178719	ENSMUSG00000022412	Mief1	A230016E22|AI452372|Smcr7l	mitochondrial elongation factor 1	protein-coding
mm_121211.1	chr14	103054056	103054068	+	1	NA	intron (NM_008392, intron 4 of 4)	intron (NM_008392, intron 4 of 4)	7050	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_56205.1	chr6	88903892	88903930	-	1	NA	intron (NM_011906, intron 1 of 11)	intron (NM_011906, intron 1 of 11)	1660	NM_011906	24100	Mm.284480	NM_011906	ENSMUSG00000002871	Tpra1	40kDa|Gpr175|Tpra40	transmembrane protein, adipocyte asscociated 1	protein-coding
mm_161008.1	chr11	118129123	118129123	-	1	NA	promoter-TSS (NM_001167746)	promoter-TSS (NM_001167746)	96	NM_001167746	69926	Mm.473893	NM_001167746	ENSMUSG00000033987	Dnah17	2810003K23Rik|Dnahc17|Dnahcl1|Gm1178|mKIAA3028	dynein, axonemal, heavy chain 17	protein-coding
mm_36613.1	chr4	89282182	89282188	-	1	NA	promoter-TSS (NM_001040654)	promoter-TSS (NM_001040654)	7	NM_001040654	12578	Mm.4733	NM_009877	ENSMUSG00000044303	Cdkn2a	ARF-INK4a|Arf|INK4a-ARF|Ink4a/Arf|MTS1|Pctr1|p16|p16(INK4a)|p16INK4a|p19<ARF>|p19ARF	cyclin-dependent kinase inhibitor 2A	protein-coding
mm_28296.1	chr3	89101859	89101898	-	1	NA	promoter-TSS (NM_001253751)	promoter-TSS (NM_001253751)	89	NM_134469	110196	Mm.39472	NM_134469	ENSMUSG00000059743	Fdps	6030492I17Rik|AI256750|Fdpsl1|mKIAA1293	farnesyl diphosphate synthetase	protein-coding
mm_98259.1	chr11	88851642	88851652	+	1	NA	promoter-TSS (NR_126433)	promoter-TSS (NR_126433)	43	NR_126433	75285	Mm.402023	NR_126433	ENSMUSG00000092399	4930556N13Rik	-	RIKEN cDNA 4930556N13 gene	ncRNA
mm_55908.1	chr6	83710851	83710865	-	1	NA	promoter-TSS (NR_002873)	promoter-TSS (NR_002873)	-52	NR_075094	574519	Mm.487605	NR_002871	ENSMUSG00000085794	Vax2os	Vas2os|Vax2os1|Vax2os2	ventral anterior homeobox 2, opposite strand	ncRNA
mm_134854.1	chr16	28307172	28307175	-	1	NA	intron (NM_001276419, intron 3 of 4)	intron (NM_001276419, intron 3 of 4)	138902	NM_183064	14167	Mm.7996	NM_010199	ENSMUSG00000022523	Fgf12	AV114868|B230343J05Rik|FGF-12|FHF-1|Fhf1	fibroblast growth factor 12	protein-coding
mm_72174.1	chr8	72318882	72318892	+	1	NA	promoter-TSS (NM_008452)	promoter-TSS (NM_008452)	-175	NM_008452	16598	Mm.26938	NM_008452	ENSMUSG00000055148	Klf2	Lklf	Kruppel-like factor 2 (lung)	protein-coding
mm_171912.1	chr5	53555843	53555844	+	1	NA	promoter-TSS (NM_001080928)	promoter-TSS (NM_001080928)	64	NM_001080928	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_4546.1	chr1	177257444	177257454	+	1	NA	Intergenic	CpG	-8682	NM_011785	23797	Mm.235194	NM_011785	ENSMUSG00000019699	Akt3	AI851531|D930002M15Rik|Nmf350	thymoma viral proto-oncogene 3	protein-coding
mm_155241.1	chrX	57213402	57213431	+	1	NA	intron (NM_011616, intron 1 of 4)	intron (NM_011616, intron 1 of 4)	1273	NM_011616	21947	Mm.4861	NM_011616	ENSMUSG00000031132	Cd40lg	CD154|CD40-L|Cd40l|HIGM1|IGM|IMD3|Ly-62|Ly62|T-BAM|TRAP|Tnfsf5|Tnlg8b|gp39	CD40 ligand	protein-coding
mm_31209.1	chr4	43937342	43937380	+	1	NA	exon (NM_016678, exon 17 of 21)	exon (NM_016678, exon 17 of 21)	-20341	NM_027450	384009	Mm.22213	NM_027450	ENSMUSG00000028480	Glipr2	5730414A08Rik|C77180|GAPR-1	GLI pathogenesis-related 2	protein-coding
mm_135663.1	chr16	52407624	52407669	-	1	NA	intron (NM_009655, intron 1 of 15)	B4A|SINE|B4	45435	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_71438.1	chr8	46511537	46511547	+	1	NA	intron (NM_001302163, intron 5 of 20)	intron (NM_001302163, intron 5 of 20)	20576	NM_001302163	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_161017.1	chr11	120361445	120361445	+	1	NA	promoter-TSS (NM_172802)	promoter-TSS (NM_172802)	-89	NM_172802	238021	Mm.481403	NM_172802	ENSMUSG00000025380	Fscn2	A930022G03|Ahl8|C630046B20Rik	fascin actin-bundling protein 2	protein-coding
mm_51451.1	chr6	80517245	80517264	+	1	NA	intron (NM_001347261, intron 2 of 2)	Lx8|LINE|L1	497611	NM_178731	243499	Mm.483425	NM_178731	ENSMUSG00000052581	Lrrtm4	7530419J18Rik|A230052N11	leucine rich repeat transmembrane neuronal 4	protein-coding
mm_98412.1	chr11	94507437	94507451	+	1	NA	intron (NM_170671, intron 12 of 18)	intron (NM_170671, intron 12 of 18)	-7470	NM_027984	71889	Mm.248620	NM_027984	ENSMUSG00000010080	Epn3	2310022G12Rik	epsin 3	protein-coding
mm_65926.1	chr7	30263956	30263958	-	1	NA	intron (NM_146186, intron 9 of 32)	HAL1M8|LINE|L1	-16137	NR_144498	108167416	Mm.471845	NR_144498		LOC108167416	-	uncharacterized LOC108167416	ncRNA
mm_46393.1	chr5	104022132	104022186	-	1	NA	promoter-TSS (NM_053262)	promoter-TSS (NM_053262)	-363	NM_053262	114664	Mm.46019	NM_053262	ENSMUSG00000029311	Hsd17b11	Dhrs8|Pan1b|SDR2|retSDR2	hydroxysteroid (17-beta) dehydrogenase 11	protein-coding
mm_18486.1	chr2	62601488	62601500	-	1	NA	exon (NM_027835, exon 13 of 16)	exon (NM_027835, exon 13 of 16)	-27473	NM_007986	14089	Mm.41816	NM_007986	ENSMUSG00000000392	Fap	SIMP	fibroblast activation protein	protein-coding
mm_30372.1	chr3	152193804	152193831	-	1	NA	promoter-TSS (NM_025926)	promoter-TSS (NM_025926)	28	NM_025926	67035	Mm.46746	NM_025926	ENSMUSG00000028035	Dnajb4	1700029A20Rik|2010306G19Rik|5730460G06Rik	DnaJ heat shock protein family (Hsp40) member B4	protein-coding
mm_49850.1	chr6	38376735	38376738	+	1	NA	Intergenic	Intergenic	-4788	NM_153600	264134	Mm.253446	NM_153600	ENSMUSG00000056832	Ttc26	9330141E21Rik|9430097H08Rik|hop|hpy	tetratricopeptide repeat domain 26	protein-coding
mm_154338.1	chrM	4287	4297	+	1	NA	NA	Intergenic	NA	NA								
mm_172794.1	chr9	110946051	110946053	-	1	NA	5' UTR (NM_011562, exon 1 of 6)	5' UTR (NM_011562, exon 1 of 6)	106	NM_011562	21667	Mm.5090	NM_011562	ENSMUSG00000032494	Tdgf1	CR1|cripto	teratocarcinoma-derived growth factor 1	protein-coding
mm_129828.1	chr15	83127996	83128008	-	1	NA	exon (NM_178627, exon 9 of 9)	exon (NM_178627, exon 9 of 9)	-5201	NM_029101	74778	Mm.30056	NM_029101	ENSMUSG00000018040	Rrp7a	1110014J01Rik|AA408146|Kheg1	ribosomal RNA processing 7 homolog A (S. cerevisiae)	protein-coding
mm_63292.1	chr7	126799608	126799627	+	1	NA	promoter-TSS (NM_001177307)	promoter-TSS (NM_001177307)	-363	NM_007438	11674	Mm.275831	NM_007438	ENSMUSG00000030695	Aldoa	Aldo-1|Aldo1	aldolase A, fructose-bisphosphate	protein-coding
mm_113339.1	chr13	31785113	31785120	+	1	NA	Intergenic	Intergenic	-21530	NM_008592	17300	Mm.12949	NM_008592	ENSMUSG00000050295	Foxc1	FREAC3|Fkh1|Mf1|Mf4|ch|fkh-1|frkhda	forkhead box C1	protein-coding
mm_112956.1	chr13	21179900	21179942	+	1	NA	promoter-TSS (NM_009054)	promoter-TSS (NM_009054)	-10	NM_009054	19720	Mm.314056	NM_009054	ENSMUSG00000021326	Trim27	AW538890|Gm19403|Rfp	tripartite motif-containing 27	protein-coding
mm_83591.1	chr9	48480489	48480502	-	1	NA	exon (NM_024233, exon 1 of 7)	exon (NM_024233, exon 1 of 7)	116	NM_024233	104444	Mm.21911	NM_024233	ENSMUSG00000032026	Rexo2	1810038D15Rik|AW107347|Rex2|Sfn|Smfn	RNA exonuclease 2	protein-coding
mm_144972.1	chr18	37874548	37874550	+	1	NA	intron (NM_007858, intron 16 of 26)	intron (NM_007858, intron 16 of 26)	-19889	NR_105945	102465592		NR_105945	ENSMUSG00000098706	Mir6979	Gm27524|mmu-mir-6979	microRNA 6979	ncRNA
mm_163409.1	chr12	76909515	76909519	+	1	NA	intron (NM_145927, intron 8 of 11)	intron (NM_145927, intron 8 of 11)	52731	NM_008558	17187	Mm.268548	NM_008558	ENSMUSG00000059436	Max	AA960152|AI875693|bHLHd4|bHLHd5|bHLHd6|bHLHd7|bHLHd8	Max protein	protein-coding
mm_4165.1	chr1	171032855	171032858	+	1	NA	Intergenic	RMER17C|LTR|ERVK	13930	NM_144559	246256	Mm.251254	NM_144559	ENSMUSG00000059089	Fcgr4	4833442P21Rik|CD16-2|FcgRIV|FcgammaRIV|Fcgr3a|Fcrl3	Fc receptor, IgG, low affinity IV	protein-coding
mm_8429.1	chr1	152552595	152552598	-	1	NA	exon (NM_016846, exon 7 of 18)	exon (NM_016846, exon 7 of 18)	72621	NM_016846	19731	Mm.245270	NM_016846	ENSMUSG00000026482	Rgl1	Rgl|mKIAA0959	ral guanine nucleotide dissociation stimulator,-like 1	protein-coding
mm_43592.1	chr5	137758254	137758263	+	1	NA	intron (NM_029805, intron 3 of 5)	intron (NM_029805, intron 3 of 5)	12289	NM_029805	78829	Mm.286399	NM_023910	ENSMUSG00000029723	Tsc22d4	0610009M14Rik|1700023B23Rik|AI415410|Thg-1pit|Tilz2	TSC22 domain family, member 4	protein-coding
mm_21246.1	chr2	156176572	156176586	-	1	NA	intron (NM_133242, intron 3 of 16)	intron (NM_133242, intron 3 of 16)	3001	NM_001291115	170791	Mm.392436	NM_133242	ENSMUSG00000027620	Rbm39	1500012C14Rik|2310040E03Rik|B330012G18Rik|C79248|R75070|Rnpc2|caper	RNA binding motif protein 39	protein-coding
mm_20142.1	chr2	121450196	121450213	-	1	NA	TTS (NM_001025371)	TTS (NM_001025371)	1006	NR_110986	378702	Mm.262252	NM_011354	ENSMUSG00000074884	Serf2	C80083|Msmac1l|m4F5rel	small EDRK-rich factor 2	protein-coding
mm_7682.1	chr1	128589373	128589379	-	1	NA	exon (NM_009911, exon 2 of 2)	exon (NM_009911, exon 2 of 2)	2923	NM_009911	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding
mm_111958.1	chr12	109560862	109560872	-	1	NA	non-coding (NR_003633, exon 5 of 5)	non-coding (NR_003633, exon 5 of 5)	-2825	NR_030427	791079		NR_030427	ENSMUSG00000076451	Mir770	Mirn770|mir-770|mmu-mir-770	microRNA 770	ncRNA
mm_23540.1	chr3	61363895	61363907	+	1	NA	promoter-TSS (NM_028712)	promoter-TSS (NM_028712)	-606	NM_028712	74012	Mm.422674	NM_028712	ENSMUSG00000036894	Rap2b	4021402C18Rik|AA408554	RAP2B, member of RAS oncogene family	protein-coding
mm_21123.1	chr2	153871062	153871072	-	1	NA	promoter-TSS (NM_001305048)	promoter-TSS (NM_001305048)	17	NM_001305048	76407	Mm.33629	NM_029599	ENSMUSG00000027480	Sun5	1700021O15Rik|SPAG4L-2|SRG4|Spag4l	Sad1 and UNC84 domain containing 5	protein-coding
mm_20861.1	chr2	148438257	148438275	-	1	NA	3' UTR (NM_010740, exon 2 of 2)	3' UTR (NM_010740, exon 2 of 2)	5269	NM_010740	17064	Mm.681	NM_010740	ENSMUSG00000027435	Cd93	6030404G09Rik|AA145088|AA4.1|AW555904|C1qr1|C1qrp|Ly68	CD93 antigen	protein-coding
mm_7997.1	chr1	134344658	134344729	-	1	NA	Intergenic	CpG	-11765	NM_001144855	68507	Mm.295105	NM_001144855	ENSMUSG00000026458	Ppfia4	100042382|1110008G13Rik|AI448359|AI852265|C81506|Gm3812	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 4	protein-coding
mm_77706.1	chr8	126591649	126591672	-	1	NA	exon (NM_001164598, exon 2 of 2)	exon (NM_001164598, exon 2 of 2)	1776	NM_001164598	270110	Mm.334918	NM_001164598	ENSMUSG00000051495	Irf2bp2	E130305N23Rik|IRF-2BP2	interferon regulatory factor 2 binding protein 2	protein-coding
mm_14692.1	chr2	140965928	140965946	+	1	NA	intron (NM_001013802, intron 4 of 18)	intron (NM_001013802, intron 4 of 18)	-294461	NM_178382	71436	Mm.426781	NM_178382	ENSMUSG00000051379	Flrt3	5530600M07Rik|C430047I10Rik|mKIAA1469	fibronectin leucine rich transmembrane protein 3	protein-coding
mm_12418.1	chr2	70562008	70562037	+	1	NA	promoter-TSS (NM_008077)	promoter-TSS (NM_008077)	-107	NM_001312900	14415	Mm.272120	NM_008077	ENSMUSG00000070880	Gad1	EP10|Gad-1	glutamate decarboxylase 1	protein-coding
mm_86295.1	chr9	122294344	122294355	-	1	NA	promoter-TSS (NM_133979)	promoter-TSS (NM_133979)	74	NM_001271873	102566	Mm.87676	NM_133979	ENSMUSG00000037949	Ano10	AI604832|Tmem16k	anoctamin 10	protein-coding
mm_43655.1	chr5	138610700	138610709	+	1	NA	intron (NM_013844, intron 5 of 5)	intron (NM_013844, intron 5 of 5)	9039	NM_001163797	24135	Mm.27575	NM_013844	ENSMUSG00000058291	Zfp68	KRAB3|KRAZ2|Zfp70|mszf22|mszf49	zinc finger protein 68	protein-coding
mm_74444.1	chr8	4040491	4040508	-	1	NA	Intergenic	Intergenic	65265	NM_026956	69142	Mm.171061	NM_026956	ENSMUSG00000051906	Cd209f	1810029C22Rik|AI647041|SIGNR8	CD209f antigen	protein-coding
mm_90371.1	chr10	127172033	127172046	+	1	NA	TTS (NM_177615)	TTS (NM_177615)	6208	NM_001244618	14421	Mm.386762	NM_008080	ENSMUSG00000006731	B4galnt1	4933429D13Rik|Gal-NAc-T|GalNAc-T|GalNAcT|Galgt1|Ggm-2|Ggm2	beta-1,4-N-acetyl-galactosaminyl transferase 1	protein-coding
mm_103935.1	chr11	83649085	83649090	-	1	NA	intron (NM_011337, intron 1 of 2)	intron (NM_011337, intron 1 of 2)	291	NM_011337	20302	Mm.1282	NM_011337	ENSMUSG00000000982	Ccl3	AI323804|G0S19-1|LD78alpha|MIP-1alpha|MIP1-(a)|MIP1-alpha|Mip1a|Scya3	chemokine (C-C motif) ligand 3	protein-coding
mm_94272.1	chr11	3655694	3655712	+	1	NA	intron (NM_001159288, intron 2 of 26)	B2_Mm1t|SINE|B2	-2997	NM_198162	74522	Mm.139127	NM_198162	ENSMUSG00000034543	Morc2a	8430403M08Rik|Zcwcc1	microrchidia 2A	protein-coding
mm_3998.1	chr1	164503307	164503330	+	1	NA	Intergenic	Intergenic	-44963	NM_009721	11931	Mm.4550	NM_009721	ENSMUSG00000026576	Atp1b1	Atp4b|Atpb|Atpb-1|NKbeta1	ATPase, Na+/K+ transporting, beta 1 polypeptide	protein-coding
mm_171730.1	chr4	92903463	92903474	-	1	NA	Intergenic	RLTR9D|LTR|ERVK	432043	NM_026954	69136	Mm.171558	NM_026954	ENSMUSG00000054000	Tusc1	2200001D17Rik|TSG-9	tumor suppressor candidate 1	protein-coding
mm_110076.1	chr12	23010217	23010232	-	1	NA	promoter-TSS (NR_015504)	promoter-TSS (NR_015504)	19	NR_015504	69732	Mm.391403	NM_028362	ENSMUSG00000073164	2410018L13Rik	2810480C08Rik	RIKEN cDNA 2410018L13 gene	ncRNA
mm_136196.1	chr16	89571145	89571153	-	1	NA	promoter-TSS (NM_001113406)	promoter-TSS (NM_001113406)	34	NM_001113406	16693	Mm.310906	NM_001113406	ENSMUSG00000091212	Krtap11-1	AA162070|AA589467|AV018433|Hacl1|KAP11.1|PRED29	keratin associated protein 11-1	protein-coding
mm_20338.1	chr2	127633601	127633617	-	1	NA	3' UTR (NM_001171187, exon 3 of 3)	3' UTR (NM_001171187, exon 3 of 3)	23086	NM_010762	17153	Mm.39040	NM_010762	ENSMUSG00000027375	Mal	Mpv17|Vip17	myelin and lymphocyte protein, T cell differentiation protein	protein-coding
mm_102421.1	chr11	59228209	59228247	-	1	NA	promoter-TSS (NM_007476)	promoter-TSS (NM_007476)	39	NM_007476	11840	Mm.371546	NM_007476	ENSMUSG00000048076	Arf1	-	ADP-ribosylation factor 1	protein-coding
mm_6415.1	chr1	73140653	73140692	-	1	NA	Intergenic	Intergenic	116086	NR_038002	69449	Mm.250447	NR_038001	ENSMUSG00000101968	1700027A15Rik	-	RIKEN cDNA 1700027A15 gene	ncRNA
mm_44101.1	chr5	149289631	149289643	+	1	NA	Intergenic	IMPB_01|Satellite|Satellite	24633	NM_009663	11690	Mm.19844	NM_009663	ENSMUSG00000060063	Alox5ap	Flap	arachidonate 5-lipoxygenase activating protein	protein-coding
mm_8249.1	chr1	138619646	138619654	-	1	NA	5' UTR (NM_021605, exon 1 of 10)	5' UTR (NM_021605, exon 1 of 10)	107	NM_021605	59125	Mm.143817	NM_021605	ENSMUSG00000026393	Nek7	2810460C19Rik|AU020186	NIMA (never in mitosis gene a)-related expressed kinase 7	protein-coding
mm_103967.1	chr11	84491568	84491578	-	1	NA	intron (NM_019816, intron 5 of 12)	intron (NM_019816, intron 5 of 12)	21928	NM_019816	56321	Mm.257482	NM_019816	ENSMUSG00000018697	Aatf	4933415H02Rik|5830465M17Rik|Che-1|Trb	apoptosis antagonizing transcription factor	protein-coding
mm_76809.1	chr8	104437640	104437657	-	1	NA	intron (NM_001013380, intron 3 of 12)	intron (NM_001013380, intron 3 of 12)	5399	NM_001013380	234663	Mm.289583	NM_001013380	ENSMUSG00000035770	Dync1li2	AA409702|C920003I06|Dncli2|Dnclic2|LIC2	dynein, cytoplasmic 1 light intermediate chain 2	protein-coding
mm_136907.1	chr17	13016590	13016594	+	1	NA	3' UTR (NM_013671, exon 5 of 5)	3' UTR (NM_013671, exon 5 of 5)	8753	NM_013671	20656	Mm.290876	NM_013671	ENSMUSG00000006818	Sod2	MnSOD|Sod-2	superoxide dismutase 2, mitochondrial	protein-coding
mm_144686.1	chr18	34777591	34777646	+	1	NA	intron (NM_001081256, intron 1 of 23)	CpG	610	NM_001081256	277250	Mm.277906	NM_029518	ENSMUSG00000038773	Kdm3b	5830462I21Rik|JHDM2B|Jmjd1b|mKIAA1082	KDM3B lysine (K)-specific demethylase 3B	protein-coding
mm_463.1	chr1	36308138	36308149	+	1	NA	intron (NM_001172206, intron 1 of 6)	CpG	410	NM_001172205	214855	Mm.34316	NM_145996	ENSMUSG00000037447	Arid5a	D430024K22Rik|Mrf1	AT rich interactive domain 5A (MRF1-like)	protein-coding
mm_51484.1	chr6	83051270	83051285	+	1	NA	TTS (NM_019752)	TTS (NM_019752)	1566	NR_106007	102465630		NR_106007	ENSMUSG00000099035	Mir7040	Gm27489|mmu-mir-7040	microRNA 7040	ncRNA
mm_42271.1	chr5	114146441	114146449	+	1	NA	Intergenic	Intergenic	15289	NM_011677	22256	Mm.1393	NM_011677	ENSMUSG00000029591	Ung	UNG1|UNG2	uracil DNA glycosylase	protein-coding
mm_118904.1	chr14	26655985	26655997	+	1	NA	3' UTR (NM_007479, exon 6 of 6)	3' UTR (NM_007479, exon 6 of 6)	13617	NR_106132	102465773		NR_106132	ENSMUSG00000098751	Mir7672	Gm27314|mmu-mir-7672	microRNA 7672	ncRNA
mm_40211.1	chr5	37047421	37047457	+	1	NA	Intergenic	Intergenic	-3418	NM_178394	76071	Mm.85280	NM_178394	ENSMUSG00000063646	Jakmip1	5830437M04Rik|C330021K24Rik|Gababrbp|Marlin-1	janus kinase and microtubule interacting protein 1	protein-coding
mm_37206.1	chr4	117872597	117872614	-	1	NA	promoter-TSS (NM_001034876)	promoter-TSS (NM_001034876)	-135	NM_001034876	381546	Mm.440118	NM_001034876	ENSMUSG00000078588	Ccdc24	Gm1028	coiled-coil domain containing 24	protein-coding
mm_99407.1	chr11	102262222	102262230	+	1	NA	exon (NM_153544, exon 9 of 10)	exon (NM_153544, exon 9 of 10)	-6597	NM_148953	217217	Mm.216432	NM_148953	ENSMUSG00000034768	Asb16	-	ankyrin repeat and SOCS box-containing 16	protein-coding
mm_172492.1	chr7	56805481	56805497	-	1	NA	intron (NM_008074, intron 5 of 9)	intron (NM_008074, intron 5 of 9)	565718	NM_021879	18431	Mm.137052	NM_021879	ENSMUSG00000030450	Oca2	D7H15S12|D7Icr28RN|D7Nic1|p|p<cas>	oculocutaneous albinism II	protein-coding
mm_115681.1	chr13	13393526	13393561	-	1	NA	promoter-TSS (NM_031999)	promoter-TSS (NM_031999)	81	NM_031999	83924	Mm.379269	NM_031999	ENSMUSG00000021306	Gpr137b	AI788917|AU016435|AW546472|C730041E01|C80550|C80741|D13Abb1e|Tm7sf1	G protein-coupled receptor 137B	protein-coding
mm_64393.1	chr7	142489301	142489328	+	1	NA	intron (NM_001271508, intron 6 of 10)	intron (NM_001271508, intron 6 of 10)	-9522	NM_001347549	21957	Mm.389992	NM_011620	ENSMUSG00000061723	Tnnt3	fTnT	troponin T3, skeletal, fast	protein-coding
mm_114478.1	chr13	69141199	69141207	+	1	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	-141662	NM_153534	210044	Mm.390617	NM_153534	ENSMUSG00000021536	Adcy2	mKIAA1060	adenylate cyclase 2	protein-coding
mm_141207.1	chr17	27057190	27057203	-	1	NA	promoter-TSS (NM_080553)	promoter-TSS (NM_080553)	-108	NM_080553	16440	Mm.458106	NM_080553	ENSMUSG00000042644	Itpr3	IP3R 3|Ip3r3|Itpr-3|tf	inositol 1,4,5-triphosphate receptor 3	protein-coding
mm_120417.1	chr14	65358591	65358615	+	1	NA	promoter-TSS (NM_199029)	promoter-TSS (NM_199029)	-73	NM_199029	380912	Mm.270087	NM_199029	ENSMUSG00000034522	Zfp395	BC053701|Gm910	zinc finger protein 395	protein-coding
mm_52712.1	chr6	119481383	119481394	+	1	NA	3' UTR (NM_133940, exon 1 of 1)	3' UTR (NM_133940, exon 1 of 1)	1720	NM_133940	101358	Mm.125477	NM_133940	ENSMUSG00000030019	Fbxl14	AW322056|Fbx14l	F-box and leucine-rich repeat protein 14	protein-coding
mm_124695.1	chr15	6438993	6439003	+	1	NA	3' UTR (NM_001102400, exon 13 of 13)	3' UTR (NM_001102400, exon 13 of 13)	-6335	NM_013485	12279	Mm.29095	NM_013485	ENSMUSG00000022149	C9	-	complement component 9	protein-coding
mm_8663.1	chr1	156654499	156654509	-	1	NA	3' UTR (NM_023141, exon 6 of 6)	3' UTR (NM_023141, exon 6 of 6)	19835	NM_023141	30935	Mm.206737	NM_023141	ENSMUSG00000060519	Tor3a	Adir	torsin family 3, member A	protein-coding
mm_167544.1	chr9	26792001	26792002	-	1	NA	intron (NM_001310768, intron 4 of 18)	intron (NM_001310768, intron 4 of 18)	14416	NM_153803	244757	Mm.293696	NM_153803	ENSMUSG00000036395	Glb1l2	-	galactosidase, beta 1-like 2	protein-coding
mm_160773.1	chr10	119454161	119454161	+	1	NA	5' UTR (NM_001277293, exon 1 of 25)	5' UTR (NM_001277293, exon 1 of 25)	127	NM_001277293	74053	Mm.196692	NM_028736	ENSMUSG00000034813	Grip1	4931400F03Rik|GRIP|eb	glutamate receptor interacting protein 1	protein-coding
mm_2693.1	chr1	127731349	127731382	+	1	NA	intron (NM_001033041, intron 1 of 9)	intron (NM_001033041, intron 1 of 9)	1952	NM_001033041	266645	Mm.25735	NM_001033041	ENSMUSG00000026348	Acmsd	-	amino carboxymuconate semialdehyde decarboxylase	protein-coding
mm_48467.1	chr5	140830404	140830425	-	1	NA	promoter-TSS (NM_010302)	promoter-TSS (NM_010302)	17	NM_010302	14673	Mm.370185	NM_010302	ENSMUSG00000000149	Gna12	AI414047|AI504261|Galpha12	guanine nucleotide binding protein, alpha 12	protein-coding
mm_153534.1	chr19	41911752	41911779	-	1	NA	promoter-TSS (NM_023418)	promoter-TSS (NM_023418)	-106	NM_023418	18648	Mm.16783	NM_023418	ENSMUSG00000011752	Pgam1	2310050F24Rik|Pgam-1	phosphoglycerate mutase 1	protein-coding
mm_22224.1	chr2	174428627	174428643	-	1	NA	exon (NM_022325, exon 5 of 6)	exon (NM_022325, exon 5 of 6)	10404	NM_022325	64138	Mm.156919	NM_022325	ENSMUSG00000016256	Ctsz	AI787083|AU019819|CTSX|D2Wsu143e	cathepsin Z	protein-coding
mm_7921.1	chr1	133800997	133801023	-	1	NA	Intergenic	Intergenic	-47263	NM_213616	381290	Mm.188617	NM_213616	ENSMUSG00000026463	Atp2b4	Pmca4	ATPase, Ca++ transporting, plasma membrane 4	protein-coding
mm_160141.1	chr7	34285464	34285464	-	1	NA	5' UTR (NM_172741, exon 1 of 13)	5' UTR (NM_172741, exon 1 of 13)	145	NM_172741	233103	Mm.491097	NM_172741	ENSMUSG00000066571	4931406P16Rik	AA553327|mKIAA0355	RIKEN cDNA 4931406P16 gene	protein-coding
mm_169790.1	chr16	14067756	14067758	+	1	NA	intron (NM_144518, intron 2 of 5)	intron (NM_144518, intron 2 of 5)	-80890	NM_001270718	74482	Mm.484026	NM_028968	ENSMUSG00000065968	Ifitm7	4933438K12Rik|Mil4	interferon induced transmembrane protein 7	protein-coding
mm_99666.1	chr11	105956006	105956020	+	1	NA	Intergenic	Intergenic	-11866	NM_007805	13056	Mm.149403	NM_007805	ENSMUSG00000019590	Cyb561	-	cytochrome b-561	protein-coding
mm_6712.1	chr1	82290899	82290917	-	1	NA	5' UTR (NM_010570, exon 1 of 2)	5' UTR (NM_010570, exon 1 of 2)	531	NM_010570	16367	Mm.4952	NM_010570	ENSMUSG00000055980	Irs1	G972R|IRS-1	insulin receptor substrate 1	protein-coding
mm_35758.1	chr4	45826820	45826834	-	1	NA	promoter-TSS (NM_018741)	promoter-TSS (NM_018741)	0	NM_018741	75426	Mm.3919	NM_018741	ENSMUSG00000035551	Igfbpl1	2810011G06Rik|2810453O06Rik|IGFBPL	insulin-like growth factor binding protein-like 1	protein-coding
mm_146321.1	chr18	80612485	80612497	+	1	NA	intron (NM_198429, intron 9 of 9)	intron (NM_198429, intron 9 of 9)	-67945	NR_028424	100039348	Mm.254722	NR_028424		Gm2176	A430076E10Rik	glucosamine-6-phosphate deaminase 1 pseudogene	pseudo
mm_138823.1	chr17	39847790	39847812	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	4804	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_164657.1	chr17	36271800	36271813	-	1	NA	promoter-TSS (NM_178281)	promoter-TSS (NM_178281)	198	NM_024468	79263	Mm.40624	NM_024468	ENSMUSG00000045409	Trim39	1100001D15Rik|E130103K13Rik|RBCC-B30.2|Rnf23|mKIAA4179|tfp	tripartite motif-containing 39	protein-coding
mm_168911.1	chr12	55230438	55230440	+	1	NA	promoter-TSS (NM_001100110)	promoter-TSS (NM_001100110)	-39	NM_001100110	100101806	Mm.471968	NM_001100110	ENSMUSG00000079108	Srp54c	E330029E12Rik	signal recognition particle 54C	protein-coding
mm_3885.1	chr1	161070925	161071006	+	1	NA	promoter-TSS (NM_172644)	promoter-TSS (NM_172644)	198	NR_131028	70454	Mm.248212	NM_027429	ENSMUSG00000026708	Cenpl	2610300B10Rik|AW121806|AW550697|CENP-L	centromere protein L	protein-coding
mm_92657.1	chr10	80412709	80412720	-	1	NA	intron (NM_001164150, intron 17 of 18)	intron (NM_001164150, intron 17 of 18)	-5893	NM_025650	66594	Mm.379119	NM_025650	ENSMUSG00000020163	Uqcr11	0710008D09Rik|AL022707|Uqcr	ubiquinol-cytochrome c reductase, complex III subunit XI	protein-coding
mm_93215.1	chr10	94944963	94944992	-	1	NA	promoter-TSS (NM_018797)	promoter-TSS (NM_018797)	-399	NM_018797	54712	Mm.256712	NM_018797	ENSMUSG00000074785	Plxnc1	2510048K12Rik|AW742158|CD232|Vespr	plexin C1	protein-coding
mm_110924.1	chr12	76369386	76369469	-	1	NA	promoter-TSS (NM_001172104)	promoter-TSS (NM_001172104)	37	NM_001172104	109929	Mm.41880	NM_028356	ENSMUSG00000056459	Zbtb25	2810462M08Rik|2900064P18Rik|AI842128|Kup|Zfp-50|Zfp50	zinc finger and BTB domain containing 25	protein-coding
mm_1428.1	chr1	67176975	67176997	+	1	NA	exon (NM_001080809, exon 20 of 38)	exon (NM_001080809, exon 20 of 38)	53959	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_32549.1	chr4	109394163	109394177	+	1	NA	Intergenic	Intergenic	12087	NR_131195	102635290	Mm.427859	NR_131195		Ttc39aos1	Gm12750|OTTMUSG00000008290|lincRNA-EPS	Ttc39a opposite strand RNA 1	ncRNA
mm_151766.1	chr19	5272983	5273000	-	1	NA	TTS (NM_030109)	TTS (NM_030109)	128	NM_153129	107975	Mm.234923	NM_153129	ENSMUSG00000024855	Pacs1	AI325977	phosphofurin acidic cluster sorting protein 1	protein-coding
mm_52604.1	chr6	117173573	117173577	+	1	NA	exon (NM_021704, exon 3 of 3)	exon (NM_021704, exon 3 of 3)	5040	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_33193.1	chr4	126262370	126262380	+	1	NA	promoter-TSS (NM_013718)	promoter-TSS (NM_013718)	-30	NM_013718	27096	Mm.8392	NM_013718	ENSMUSG00000028847	Trappc3	1110058K12Rik|AI835942|AU019197|Bet3	trafficking protein particle complex 3	protein-coding
mm_169970.1	chr17	13862830	13862841	-	1	NA	intron (NM_010806, intron 22 of 32)	intron (NM_010806, intron 22 of 32)	-85538	NM_001122977	635895	Mm.388844	NM_001122977	ENSMUSG00000067941	Gm7168	EG635895	predicted gene 7168	protein-coding
mm_119181.1	chr14	32166105	32166123	+	1	NA	intron (NM_019744, intron 1 of 9)	intron (NM_019744, intron 1 of 9)	325	NM_019744	27057	Mm.371598	NM_019744	ENSMUSG00000056234	Ncoa4	ARA70|Rfg	nuclear receptor coactivator 4	protein-coding
mm_100503.1	chr11	120485339	120485354	+	1	NA	exon (NM_027204, exon 2 of 5)	exon (NM_027204, exon 2 of 5)	677	NM_027204	56282	Mm.133851	NM_027204	ENSMUSG00000039640	Mrpl12	0610034O11Rik|1500031N16Rik|MRP-L12|Rpml12	mitochondrial ribosomal protein L12	protein-coding
mm_107267.1	chr12	29528528	29528549	+	1	NA	5' UTR (NM_008666, exon 1 of 25)	5' UTR (NM_008666, exon 1 of 25)	154	NM_008666	17933	Mm.253067	NM_008666	ENSMUSG00000061911	Myt1l	2900046C06Rik|2900093J19Rik|C630034G21Rik|Nztf1|Pmng1|Png-1|mKIAA1106	myelin transcription factor 1-like	protein-coding
mm_10907.1	chr2	25346275	25346281	+	1	NA	intron (NM_001029983, intron 8 of 12)	intron (NM_001029983, intron 8 of 12)	10054	NM_031843	83768	Mm.21440	NM_031843	ENSMUSG00000026958	Dpp7	DPPII|Dpp2|QPP	dipeptidylpeptidase 7	protein-coding
mm_77079.1	chr8	110502349	110502361	-	1	NA	promoter-TSS (NR_105058)	promoter-TSS (NR_105058)	1	NR_105058	100861869	Mm.84499	NR_105058		Gm21283	-	predicted gene, 21283	ncRNA
mm_138546.1	chr17	35263760	35263768	+	1	NA	intron (NM_010380, intron 2 of 7)	CpG-6316	641	NM_001267808	14980	Mm.439675	NM_001267808		H2-L	H-2L	histocompatibility 2, D region locus L	protein-coding
mm_43770.1	chr5	141116325	141116329	+	1	NA	Intergenic	Intergenic	-115731	NM_175362	108723	Mm.46187	NM_175362	ENSMUSG00000036526	Card11	0610008L17Rik|2410011D02Rik|BIMP3|CARMA1	caspase recruitment domain family, member 11	protein-coding
mm_88602.1	chr10	79805987	79806005	+	1	NA	intron (NM_023128, intron 1 of 8)	intron (NM_023128, intron 1 of 8)	12424	NM_001161747	18483	Mm.34650	NM_023128	ENSMUSG00000035863	Palm	-	paralemmin	protein-coding
mm_65866.1	chr7	29505334	29505445	-	1	NA	promoter-TSS (NM_001081028)	promoter-TSS (NM_001081028)	71	NM_001081028	74206	Mm.447042	NM_001081028	ENSMUSG00000030583	Sipa1l3	2610511M17Rik	signal-induced proliferation-associated 1 like 3	protein-coding
mm_115847.1	chr13	21287438	21287446	-	1	NA	exon (NM_010343, exon 5 of 5)	exon (NM_010343, exon 5 of 5)	5244	NM_010343	14780	Mm.1332	NM_010343	ENSMUSG00000004344	Gpx5	AV379049|Arep	glutathione peroxidase 5	protein-coding
mm_114396.1	chr13	63279013	63279025	+	1	NA	intron (NR_110520, intron 2 of 5)	intron (NR_110520, intron 2 of 5)	18128	NR_045794	100504114	Mm.437070	NR_045794	ENSMUSG00000097242	Gm16907	-	predicted gene, 16907	ncRNA
mm_32897.1	chr4	118986943	118986944	+	1	NA	Intergenic	Intergenic	24976	NM_133892	100470	Mm.26698	NM_133892	ENSMUSG00000024903	Lao1	AW990848	L-amino acid oxidase 1	protein-coding
mm_62757.1	chr7	112074652	112074677	+	1	NA	exon (NM_177249, exon 11 of 29)	exon (NM_177249, exon 11 of 29)	51158	NM_177249	74996	Mm.16974	NM_133758	ENSMUSG00000059263	Usp47	4930502N04Rik|A630020C16Rik	ubiquitin specific peptidase 47	protein-coding
mm_39384.1	chr5	13125586	13125610	+	1	NA	Intergenic	Intergenic	-271186	NM_001243072	20346	Mm.372039	NM_009152	ENSMUSG00000028883	Sema3a	Hsema-I|SEMA1|SemD|Semad|coll-1	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	protein-coding
mm_13449.1	chr2	105224315	105224357	+	1	NA	promoter-TSS (NM_028747)	promoter-TSS (NM_028747)	-6	NM_028747	74088	Mm.46188	NM_028747	ENSMUSG00000055312	Them7	0610012H03Rik	thioesterase superfamily member 7	protein-coding
mm_101544.1	chr11	33537402	33537407	-	1	NA	Intergenic	Intergenic	-23658	NM_023146	66011	Mm.383775	NM_023146	ENSMUSG00000040594	Ranbp17	-	RAN binding protein 17	protein-coding
mm_99101.1	chr11	100052261	100052265	+	1	NA	Intergenic	Intergenic	-1712	NM_010659	16660	Mm.439673	NM_010659	ENSMUSG00000048981	Krt31	Ha1|Kha1|Krt1-1|MKHA-1	keratin 31	protein-coding
mm_38054.1	chr4	134004186	134004201	-	1	NA	3' UTR (NM_145833, exon 4 of 4)	3' UTR (NM_145833, exon 4 of 4)	-3329	NM_026144	67422	Mm.100290	NM_026144	ENSMUSG00000012117	Dhdds	3222401G21Rik|CIT|DS|HDS|W91638	dehydrodolichyl diphosphate synthase	protein-coding
mm_140698.1	chr17	14204235	14204251	-	1	NA	promoter-TSS (NM_172826)	promoter-TSS (NM_172826)	-412	NM_172826	240025	Mm.79993	NM_172826	ENSMUSG00000048826	Dact2	2900084M21Rik|A630024E20|Dpr2|Frd2|dapper2	dishevelled-binding antagonist of beta-catenin 2	protein-coding
mm_61585.1	chr7	80010921	80010958	+	1	NA	Intergenic	MTEa|LTR|ERVL-MaLR	-13875	NM_001145999	209225	Mm.290925	NM_175433	ENSMUSG00000048897	Zfp710	5430400N05Rik|9830165K13|AI324798|Znf710	zinc finger protein 710	protein-coding
mm_28642.1	chr3	95220220	95220232	-	1	NA	exon (NM_019914, exon 2 of 2)	exon (NM_019914, exon 2 of 2)	-2284	NM_029885	213054	Mm.224820	NM_029885	ENSMUSG00000038766	Gabpb2	1810015F01Rik|5830427M07|9430006E19Rik|A430024B14Rik|AV050852|Gabpb2-1	GA repeat binding protein, beta 2	protein-coding
mm_53705.1	chr6	143167211	143167267	+	1	NA	promoter-TSS (NM_029250)	promoter-TSS (NM_029250)	9	NM_029250	75320	Mm.272548	NM_029250	ENSMUSG00000030275	Etnk1	1110061E11Rik|4930555L11Rik|AI195356|AI841245|C80956|D6Ertd3e|EKI1	ethanolamine kinase 1	protein-coding
mm_30292.1	chr3	148989713	148989751	-	1	NA	Intergenic	CpG	-35097	NM_001081298	99633	Mm.9776	NM_001081298	ENSMUSG00000028184	Adgrl2	AI450192|CIRL-2|Gm619|Lec1|Lphh1|Lphn2|mKIAA0786	adhesion G protein-coupled receptor L2	protein-coding
mm_51390.1	chr6	78370619	78370629	+	1	NA	promoter-TSS (NM_011036)	promoter-TSS (NM_011036)	-261	NM_011036	18489	Mm.2553	NM_011036	ENSMUSG00000071356	Reg3b	HIP|PAP1|Pap|REG-III	regenerating islet-derived 3 beta	protein-coding
mm_44492.1	chr5	23675942	23675997	-	1	NA	Intergenic	CpG	36698	NR_038090	433855	Mm.205125	NR_015554	ENSMUSG00000105987	AI506816	-	expressed sequence AI506816	ncRNA
mm_29460.1	chr3	113574243	113574269	-	1	NA	intron (NM_001110505, intron 1 of 10)	intron (NM_001110505, intron 1 of 10)	506	NM_007446	11722	Mm.439727	NM_007446	ENSMUSG00000074264	Amy1	Amy-1|Amy1a|C030014B17Rik	amylase 1, salivary	protein-coding
mm_138438.1	chr17	35121516	35121577	+	1	NA	promoter-TSS (NM_009975)	promoter-TSS (NM_009975)	50	NM_001128597	81845	Mm.7405	NM_032460	ENSMUSG00000092417	Gpank1	Bat-4|Bat4|D17H6S54E|G5	G patch domain and ankyrin repeats 1	protein-coding
mm_113201.1	chr13	24964280	24964285	+	1	NA	intron (NM_008156, intron 11 of 25)	B4|SINE|B4	21130	NM_008156	14756	Mm.291831	NM_008156	ENSMUSG00000021340	Gpld1	6330541J12Rik|AW546131	glycosylphosphatidylinositol specific phospholipase D1	protein-coding
mm_154026.1	chr19	53423344	53423362	-	1	NA	Intergenic	Intergenic	-32780	NM_172429	76479	Mm.313687	NM_172429	ENSMUSG00000025024	Smndc1	2410004J23Rik|4933440I19Rik	survival motor neuron domain containing 1	protein-coding
mm_98912.1	chr11	98202816	98202820	+	1	NA	promoter-TSS (NM_026952)	promoter-TSS (NM_026952)	-487	NM_001109628	69131	Mm.260516	NM_026952	ENSMUSG00000003119	Cdk12	1810022J16Rik|AI646528|Crk7|Crkrs|D11Ertd752e|Pksc	cyclin-dependent kinase 12	protein-coding
mm_31661.1	chr4	59944477	59944497	+	1	NA	Intergenic	Intergenic	16178	NM_008648	17843	Mm.457982	NM_008648	ENSMUSG00000041333	Mup4	Mup-4|Mup1	major urinary protein 4	protein-coding
mm_145863.1	chr18	65458368	65458380	+	1	NA	intron (NM_172833, intron 9 of 15)	intron (NM_172833, intron 9 of 15)	27377	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_120938.1	chr14	76515977	76515997	+	1	NA	non-coding (NR_045660, exon 3 of 4)	non-coding (NR_045660, exon 3 of 4)	4868	NR_045660	75789	Mm.159571	NR_045660	ENSMUSG00000097172	4930444M15Rik	-	RIKEN cDNA 4930444M15 gene	ncRNA
mm_83756.1	chr9	51875880	51875887	-	1	NA	promoter-TSS (NR_033560)	promoter-TSS (NR_033560)	2	NR_033560	408028	Mm.393649	NR_033560	ENSMUSG00000074354	Arhgap20os	9230115E21Rik	Rho GTPase activating protein 20, opposite strand	ncRNA
mm_101790.1	chr11	46083798	46083807	-	1	NA	intron (NM_001291890, intron 3 of 22)	intron (NM_001291890, intron 3 of 22)	-18468	NR_106177	102465996		NR_106177	ENSMUSG00000098942	Mir8100	Gm27638|mmu-mir-8100	microRNA 8100	ncRNA
mm_106887.1	chr12	8012142	8012151	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	34469	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_45287.1	chr5	64961032	64961045	-	1	NA	Intergenic	Intergenic	-1004	NM_011604	21899	Mm.42146	NM_011604	ENSMUSG00000051498	Tlr6	-	toll-like receptor 6	protein-coding
mm_110750.1	chr12	69986959	69986967	-	1	NA	promoter-TSS (NM_022028)	promoter-TSS (NM_022028)	39	NM_022028	64010	Mm.390480	NM_022028	ENSMUSG00000021067	Sav1	1700040G09Rik|Salv|Sav|WW45|Wwp3|Wwp4	salvador family WW domain containing 1	protein-coding
mm_118469.1	chr14	11553599	11553615	+	1	NA	promoter-TSS (NM_008981)	promoter-TSS (NM_008981)	54	NM_008981	19270	Mm.431266	NM_008981	ENSMUSG00000021745	Ptprg	5430405N12Rik|AW046354|AW549872|RPTPgamma	protein tyrosine phosphatase, receptor type, G	protein-coding
mm_142893.1	chr17	51833251	51833270	-	1	NA	promoter-TSS (NM_001163632)	promoter-TSS (NM_001163632)	30	NM_001163632	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_106734.1	chr12	3894882	3894896	+	1	NA	intron (NM_153743, intron 1 of 17)	intron (NM_153743, intron 1 of 17)	3145	NM_153743	13435	Mm.5001	NM_007872	ENSMUSG00000020661	Dnmt3a	MmuIIIA	DNA methyltransferase 3A	protein-coding
mm_119206.1	chr14	32856857	32856895	+	1	NA	5' UTR (NM_178791, exon 1 of 8)	5' UTR (NM_178791, exon 1 of 8)	120	NM_178791	320736	Mm.187910	NM_178791	ENSMUSG00000050666	Vstm4	E130203B14Rik	V-set and transmembrane domain containing 4	protein-coding
mm_56612.1	chr6	112490805	112490829	-	1	NA	Intergenic	Intergenic	-1009	NM_001081147	18430	Mm.333310	NM_001081147	ENSMUSG00000049112	Oxtr	OTR	oxytocin receptor	protein-coding
mm_139836.1	chr17	69156792	69156850	+	1	NA	promoter-TSS (NM_013813)	promoter-TSS (NM_013813)	11	NM_013813	13823	Mm.131135	NM_013813	ENSMUSG00000024044	Epb41l3	4.1B|DAL1P|Dal1|Epb4.1l3|NBL3	erythrocyte membrane protein band 4.1 like 3	protein-coding
mm_86990.1	chr10	25498591	25498602	+	1	NA	intron (NM_001199265, intron 14 of 19)	intron (NM_001199265, intron 14 of 19)	37676	NM_001195596	100504474	Mm.46323	NM_001195596	ENSMUSG00000096546	Smlr1	2010003K15Rik	small leucine-rich protein 1	protein-coding
mm_101714.1	chr11	42179655	42179683	-	1	NA	intron (NM_010250, intron 1 of 9)	intron (NM_010250, intron 1 of 9)	3261	NM_010250	14394	Mm.439668	NM_010250	ENSMUSG00000010803	Gabra1	Gabra-1	gamma-aminobutyric acid (GABA) A receptor, subunit alpha 1	protein-coding
mm_18240.1	chr2	52169922	52169950	-	1	NA	exon (NM_010889, exon 135 of 157)	exon (NM_010889, exon 135 of 157)	97099	NM_175238	51869	Mm.254530	NM_175238	ENSMUSG00000036202	Rif1	5730435J01Rik|6530403D07Rik|AU016181|AW549474|D2Ertd145e	replication timing regulatory factor 1	protein-coding
mm_2469.1	chr1	105669331	105669338	+	1	NA	intron (NM_173187, intron 1 of 28)	intron (NM_173187, intron 1 of 28)	5473	NM_173187	227446	Mm.337339	NM_029349	ENSMUSG00000026319	2310035C23Rik	6430401N10|Kiaa1468|mKIAA1468	RIKEN cDNA 2310035C23 gene	protein-coding
mm_152446.1	chr19	10794657	10794678	-	1	NA	exon (NM_009852, exon 7 of 13)	exon (NM_009852, exon 7 of 13)	35391	NM_001037801	12511	Mm.290897	NM_009852	ENSMUSG00000024670	Cd6	-	CD6 antigen	protein-coding
mm_86102.1	chr9	115310166	115310181	-	1	NA	5' UTR (NM_024222, exon 1 of 16)	5' UTR (NM_024222, exon 1 of 16)	248	NM_024222	68292	Mm.296158	NM_024222	ENSMUSG00000032437	Stt3b	1300006C19Rik|Simp	STT3, subunit of the oligosaccharyltransferase complex, homolog B (S. cerevisiae)	protein-coding
mm_49203.1	chr6	15394723	15394734	+	1	NA	exon (NM_001286607, exon 7 of 17)	exon (NM_001286607, exon 7 of 17)	209222	NM_001286607	114142	Mm.332919	NM_053242	ENSMUSG00000029563	Foxp2	2810043D05Rik|AI449000|CAG-16|D0Kist7	forkhead box P2	protein-coding
mm_121466.1	chr14	120897244	120897263	+	1	NA	Intergenic	Intergenic	-13941	NM_023579	70572	Mm.221452	NM_023579	ENSMUSG00000030662	Ipo5	1110011C18Rik|5730478E03Rik|AA409333|C76941|IMB3|Kpnb3|Ranbp5	importin 5	protein-coding
mm_9916.1	chr1	189128136	189128142	-	1	NA	Intergenic	RMER17A|LTR|ERVK	-120299	NM_172650	226823	Mm.209880	NM_172650	ENSMUSG00000026608	Kctd3	4930438A20Rik|9330185B06|E330032J19Rik|NY-REN-45	potassium channel tetramerisation domain containing 3	protein-coding
mm_19834.1	chr2	112363328	112363333	-	1	NA	TTS (NM_133649)	TTS (NM_133649)	4697	NM_026519	68032	Mm.220942	NM_026519	ENSMUSG00000027131	Emc4	2610318K02Rik|Tmem85	ER membrane protein complex subunit 4	protein-coding
mm_148216.1	chr18	80236683	80236708	-	1	NA	intron (NM_001136181, intron 2 of 4)	CpG	10407	NM_001136181	66255	Mm.272341	NM_001136181	ENSMUSG00000078963	Hsbp1l1	1810005K13Rik	heat shock factor binding protein 1-like 1	protein-coding
mm_64994.1	chr7	16917714	16917728	-	1	NA	exon (NM_007590, exon 3 of 6)	exon (NM_007590, exon 3 of 6)	6311	NM_007590	12315	Mm.288630	NM_007590	ENSMUSG00000019370	Calm3	CaMA|R75142	calmodulin 3	protein-coding
mm_167448.1	chr8	122431879	122431891	+	1	NA	intron (NM_001301284, intron 1 of 4)	intron (NM_001301284, intron 1 of 4)	1055	NM_001301284	13057	Mm.271671	NM_007806	ENSMUSG00000006519	Cyba	b558|nmf333|p22-phox|p22phox	cytochrome b-245, alpha polypeptide	protein-coding
mm_56318.1	chr6	92244646	92244649	-	1	NA	promoter-TSS (NM_009426)	promoter-TSS (NM_009426)	3	NM_009426	22044	Mm.1363	NM_009426	ENSMUSG00000005892	Trh	Pro-TRH|Trf	thyrotropin releasing hormone	protein-coding
mm_23094.1	chr3	37063645	37063672	+	1	NA	promoter-TSS (NM_009350)	promoter-TSS (NM_009350)	2	NM_009350	21744	Mm.8122	NM_009350	ENSMUSG00000027719	Adad1	Tenr	adenosine deaminase domain containing 1 (testis specific)	protein-coding
mm_83457.1	chr9	45249979	45250003	-	1	NA	TTS (NM_001198971)	TTS (NM_001198971)	16716	NR_106054	102466803		NR_106054	ENSMUSG00000098361	Mir7086	Gm27643|mmu-mir-7086	microRNA 7086	ncRNA
mm_77781.1	chr9	3022737	3022762	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	15994	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_66620.1	chr7	45474794	45474814	-	1	NA	3' UTR (NM_027903, exon 7 of 7)	3' UTR (NM_027903, exon 7 of 7)	-7906	NM_007527	12028	Mm.19904	NM_007527	ENSMUSG00000003873	Bax	-	BCL2-associated X protein	protein-coding
mm_27613.1	chr3	59220001	59220011	-	1	NA	5' UTR (NM_027571, exon 3 of 4)	5' UTR (NM_027571, exon 3 of 4)	-9124	NM_028808	74191	Mm.90067	NM_028808	ENSMUSG00000036362	P2ry13	2010001L06Rik|GPCR1|GPR94|Gpr86|P2Y13|P2yr13|SP174	purinergic receptor P2Y, G-protein coupled 13	protein-coding
mm_109756.1	chr12	117830882	117830883	+	1	NA	Intergenic	Intergenic	-12979	NM_146040	217946	Mm.281149	NM_146040	ENSMUSG00000021175	Cdca7l	BC006933|JPO2	cell division cycle associated 7 like	protein-coding
mm_81019.1	chr9	104337847	104337872	+	1	NA	promoter-TSS (NM_019807)	promoter-TSS (NM_019807)	-137	NM_207668	56318	Mm.19941	NM_019807	ENSMUSG00000032561	Acpp	5'-NT|A030005E02Rik|FRAP|Lap|PAP|Ppal	acid phosphatase, prostate	protein-coding
mm_29123.1	chr3	105053126	105053151	-	1	NA	promoter-TSS (NM_001163333)	promoter-TSS (NM_001163333)	8	NM_030249	80281	Mm.200327	NM_030249	ENSMUSG00000062127	Cttnbp2nl	AA552995|AA589392|AU018624|BC003236|mKIAA1433	CTTNBP2 N-terminal like	protein-coding
mm_30053.1	chr3	136449443	136449451	-	1	NA	promoter-TSS (NR_040592)	promoter-TSS (NR_040592)	-98	NR_040592	70055	Mm.261063	NR_040592	ENSMUSG00000099508	1700030L20Rik	-	RIKEN cDNA 1700030L20 gene	ncRNA
mm_102889.1	chr11	69413258	69413298	-	1	NA	intron (NM_001017426, intron 1 of 22)	intron (NM_001017426, intron 1 of 22)	397	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_89764.1	chr10	100076295	100076298	+	1	NA	intron (NM_001347156, intron 3 of 8)	intron (NM_001347156, intron 3 of 8)	60475	NM_013598	17311	Mm.45124	NM_013598	ENSMUSG00000019966	Kitl	Clo|Con|Gb|Kitlg|Mgf|SCF|SF|SLF|Sl|blz|contrasted	kit ligand	protein-coding
mm_115079.1	chr13	102349692	102349724	+	1	NA	Intergenic	Intergenic	-343850	NM_008533	17079	Mm.373974	NM_008533	ENSMUSG00000021624	Cd180	F630107B15|Ly78|RP105	CD180 antigen	protein-coding
mm_153513.1	chr19	41385076	41385086	-	1	NA	promoter-TSS (NM_031376)	promoter-TSS (NM_031376)	-11	NM_031376	83490	Mm.222266	NM_031376	ENSMUSG00000025017	Pik3ap1	1810044J04Rik|BCAP	phosphoinositide-3-kinase adaptor protein 1	protein-coding
mm_152099.1	chr19	6910089	6910125	-	1	NA	promoter-TSS (NM_012021)	promoter-TSS (NM_012021)	409	NM_026306	67674	Mm.318804	NM_026306	ENSMUSG00000038812	Trmt112	0610038D11Rik|Trm112p	tRNA methyltransferase 11-2	protein-coding
mm_5345.1	chr1	24679118	24679138	-	1	NA	intron (NM_001310483, intron 1 of 15)	intron (NM_001310483, intron 1 of 15)	210	NM_001310483	68421	Mm.336563	NM_026719	ENSMUSG00000073725	Lmbrd1	0910001K20Rik|AV347960	LMBR1 domain containing 1	protein-coding
mm_27341.1	chr3	50414738	50414748	-	1	NA	intron (NM_011990, intron 6 of 11)	intron (NM_011990, intron 6 of 11)	28870	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_125157.1	chr15	31103306	31103309	+	1	NA	Intergenic	Intergenic	64181	NR_045186	73784	Mm.66947	NR_045186		4930430F21Rik	-	RIKEN cDNA 4930430F21 gene	ncRNA
mm_153962.1	chr19	47835940	47835982	-	1	NA	intron (NM_027559, intron 1 of 37)	intron (NM_027559, intron 1 of 37)	1400	NM_027559	100048534	Mm.29457	NM_027559	ENSMUSG00000044948	Cfap43	4632415N18Rik|4930428C11Rik|4930463G05Rik|AI429486|D19Ertd652e|Wdr96	cilia and flagella associated protein 43	protein-coding
mm_107272.1	chr12	29533429	29533446	+	1	NA	intron (NM_001093778, intron 1 of 24)	intron (NM_001093778, intron 1 of 24)	-1468	NM_001093776	17933	Mm.253067	NM_008666	ENSMUSG00000061911	Myt1l	2900046C06Rik|2900093J19Rik|C630034G21Rik|Nztf1|Pmng1|Png-1|mKIAA1106	myelin transcription factor 1-like	protein-coding
mm_164022.1	chr14	75182485	75182490	-	1	NA	intron (NM_008879, intron 2 of 16)	intron (NM_008879, intron 2 of 16)	46062	NM_008879	18826	Mm.153911	NM_008879	ENSMUSG00000021998	Lcp1	AW536232|D14Ertd310e|LCP-1|Pls2|pp65	lymphocyte cytosolic protein 1	protein-coding
mm_172048.1	chr6	128644861	128644863	+	1	NA	Intergenic	Intergenic	-17523	NM_053165	94071	Mm.197689	NM_053165	ENSMUSG00000030364	Clec2h	Clrf|clr-f	C-type lectin domain family 2, member h	protein-coding
mm_142871.1	chr17	51815990	51816016	-	1	NA	intron (NM_001163632, intron 1 of 10)	intron (NM_001163632, intron 1 of 10)	-3949	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_45191.1	chr5	52154309	52154312	-	1	NA	intron (NR_104311, intron 11 of 13)	intron (NR_104311, intron 11 of 13)	-18293	NR_105845	102466648		NR_105845	ENSMUSG00000098726	Mir6417	Gm27334|mmu-mir-6417	microRNA 6417	ncRNA
mm_25391.1	chr3	107218602	107218634	+	1	NA	exon (NM_001111143, exon 3 of 9)	exon (NM_001111143, exon 3 of 9)	3114	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_16024.1	chr2	167504199	167504214	+	1	NA	intron (NM_030743, intron 3 of 7)	CpG-8879	-11332	NM_170756	263876	Mm.34342	NM_170756	ENSMUSG00000047030	Spata2	AI504642|mKIAA0757	spermatogenesis associated 2	protein-coding
mm_52104.1	chr6	97876152	97876170	+	1	NA	intron (NM_001113198, intron 1 of 9)	B3A|SINE|B2	-53656	NM_001178049	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_107868.1	chr12	69907854	69907863	+	1	NA	5' UTR (NM_178628, exon 2 of 15)	5' UTR (NM_178628, exon 2 of 15)	-14695	NM_201519	399510	Mm.291936	NM_201519	ENSMUSG00000034761	Map4k5	4432415E19Rik|GCKR|KHS|MAPKKKK5	mitogen-activated protein kinase kinase kinase kinase 5	protein-coding
mm_140213.1	chr17	83810648	83810665	+	1	NA	intron (NM_054082, intron 16 of 16)	B4|SINE|B4	36134	NM_025325	107766	Mm.30100	NM_025325	ENSMUSG00000000673	Haao	0610007K21Rik|0610012J07Rik|3-HAO|3-HAOxase|3HAO	3-hydroxyanthranilate 3,4-dioxygenase	protein-coding
mm_159592.1	chr4	125122412	125122412	-	1	NA	intron (NM_153159, intron 2 of 5)	intron (NM_153159, intron 2 of 5)	5469	NM_153159	230738	Mm.402	NM_153159	ENSMUSG00000042677	Zc3h12a	BC036563|MCPIP|MCPIP-1|Mcpip1|Reg1	zinc finger CCCH type containing 12A	protein-coding
mm_167916.1	chrX	99542659	99542663	+	1	NA	Intergenic	Intergenic	-71926	NM_008853	18744	Mm.8211	NM_008853	ENSMUSG00000034403	Pja1	praja-1	praja ring finger 1, E3 ubiquitin protein ligase	protein-coding
mm_137392.1	chr17	25820154	25820178	+	1	NA	3' UTR (NM_001164225, exon 6 of 6)	3' UTR (NM_001164225, exon 6 of 6)	-3461	NM_173741	268933	Mm.95512	NM_173741	ENSMUSG00000025737	Wdr24	BC037651	WD repeat domain 24	protein-coding
mm_30220.1	chr3	145032766	145032781	-	1	NA	promoter-TSS (NM_017474)	promoter-TSS (NM_017474)	3	NM_017474	23844	Mm.33483	NM_017474	ENSMUSG00000028255	Clca1	Clca2|Clca3|gob-5|gob5	chloride channel accessory 1	protein-coding
mm_74556.1	chr8	10900541	10900563	-	1	NA	intron (NR_102285, intron 2 of 2)	A-rich|Low_complexity|Low_complexity	630	NR_102285	71624	Mm.139075	NR_102285	ENSMUSG00000109089	4833411C07Rik	-	RIKEN cDNA 4833411C07 gene	ncRNA
mm_148369.1	chr18	88894293	88894319	-	1	NA	promoter-TSS (NM_018821)	promoter-TSS (NM_018821)	-99	NM_018821	54607	Mm.91920	NM_018821	ENSMUSG00000056153	Socs6	1500012M23Rik|5830401B18Rik|AI447482|Cis4|Cish4|HSPC060|SOCS-4|SOCS-6|SSI4|STAI4|STATI4|Socs4	suppressor of cytokine signaling 6	protein-coding
mm_85953.1	chr9	112120584	112120589	-	1	NA	intron (NM_001177617, intron 13 of 14)	B1F|SINE|Alu	-1875	NR_029823	723815		NR_029823	ENSMUSG00000065441	Mir128-2	Mirn128-2|Mirn128b|mir-128-2|mir-128b	microRNA 128-2	ncRNA
mm_20132.1	chr2	121355321	121355367	-	1	NA	Intergenic	CpG	-3297	NM_009897	12716	Mm.252145	NM_009897	ENSMUSG00000000308	Ckmt1	Mt-CK|ScCKmit|UbCKmit|mi-CK	creatine kinase, mitochondrial 1, ubiquitous	protein-coding
mm_42776.1	chr5	121385449	121385453	+	1	NA	intron (NM_172275, intron 1 of 11)	CpG	164	NM_001163470	231712	Mm.20488	NM_172275	ENSMUSG00000042726	Trafd1	1110008K06Rik|Fln29	TRAF type zinc finger domain containing 1	protein-coding
mm_124620.1	chr15	3280023	3280031	+	1	NA	TTS (NM_001166063)	TTS (NM_001166063)	9050	NM_009155	20363	Mm.392203	NM_009155	ENSMUSG00000064373	Selenop	AU018766|D15Ucla1|Se-P|Sepp1|selp	selenoprotein P	protein-coding
mm_81272.1	chr9	108095193	108095213	+	1	NA	promoter-TSS (NM_146226)	promoter-TSS (NM_146226)	-723	NM_146226	235606	Mm.219639	NM_146226	ENSMUSG00000032590	Apeh	-	acylpeptide hydrolase	protein-coding
mm_77367.1	chr8	119810217	119810227	-	1	NA	3' UTR (NM_028071, exon 4 of 4)	3' UTR (NM_028071, exon 4 of 4)	30357	NM_028071	72042	Mm.393405	NM_028071	ENSMUSG00000031827	Cotl1	1810074P22Rik|2010004C08Rik|Clp	coactosin-like 1 (Dictyostelium)	protein-coding
mm_94935.1	chr11	29706789	29706818	+	1	NA	exon (NM_194051, exon 3 of 9)	exon (NM_194051, exon 3 of 9)	-11760	NM_024226	68585	Mm.192580	NM_024226	ENSMUSG00000020458	Rtn4	1110020G17Rik|AA407876|AA409940|AA960376|ASY|C130026I10Rik|NOGO|NSP-CL|NgA|Nogo-A|Nogo-B|Nogo-C|mKIAA0886|mKIAA4153	reticulon 4	protein-coding
mm_18928.1	chr2	76746083	76746102	-	1	NA	exon (NM_011652, exon 275 of 313)	exon (NM_011652, exon 275 of 313)	70777	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_9593.1	chr1	174921765	174921771	-	1	NA	promoter-TSS (NM_011825)	promoter-TSS (NM_011825)	51	NM_011825	23893	Mm.25760	NM_011825	ENSMUSG00000050069	Grem2	Gremlin2|Prdc	gremlin 2, DAN family BMP antagonist	protein-coding
mm_34865.1	chr4	155557742	155557753	+	1	NA	3' UTR (NM_008142, exon 12 of 12)	3' UTR (NM_008142, exon 12 of 12)	-4645	NM_138671	192185	Mm.28347	NM_138671	ENSMUSG00000029063	Nadk	4432404C02Rik|BC004012	NAD kinase	protein-coding
mm_106194.1	chr11	116842727	116842743	-	1	NA	promoter-TSS (NM_028865)	promoter-TSS (NM_028865)	714	NM_033398	107817	Mm.481684	NM_033398	ENSMUSG00000056962	Jmjd6	5730436I23Rik|D11Ertd195e|PSR|PtdSerR|Ptdsr|mKIAA0585	jumonji domain containing 6	protein-coding
mm_24984.1	chr3	96833219	96833257	+	1	NA	intron (NM_001146001, intron 1 of 8)	intron (NM_001146001, intron 1 of 8)	564	NM_001146001	59020	Mm.489677	NM_021517	ENSMUSG00000038298	Pdzk1	1700023D20Rik|2610507N21Rik|4921513F16Rik|AI267131|AI314638|AL022680|D3Ertd537e|Pdzd1|mPDZK1	PDZ domain containing 1	protein-coding
mm_16695.1	chr2	6885106	6885121	-	1	NA	promoter-TSS (NM_001110228)	promoter-TSS (NM_001110228)	-117	NM_001160293	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_98482.1	chr11	94950872	94950876	+	1	NA	exon (NM_007742, exon 49 of 51)	exon (NM_007742, exon 49 of 51)	14650	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_108377.1	chr12	80854098	80854110	+	1	NA	intron (NM_001242419, intron 3 of 6)	intron (NM_001242419, intron 3 of 6)	63572	NM_001242419	217684	Mm.341776	NM_178682	ENSMUSG00000021133	Susd6	4933426M11Rik|mKIAA0247	sushi domain containing 6	protein-coding
mm_56420.1	chr6	97252769	97252777	-	1	NA	promoter-TSS (NM_001081157)	promoter-TSS (NM_001081157)	7	NM_001081157	320502	Mm.68163	NM_001081157	ENSMUSG00000044086	Lmod3	5430424A14Rik	leiomodin 3 (fetal)	protein-coding
mm_41865.1	chr5	104440756	104440772	+	1	NA	3' UTR (NM_001204203, exon 7 of 7)	3' UTR (NM_001204203, exon 7 of 7)	4572	NM_001204233	20750	Mm.288474	NM_009263	ENSMUSG00000029304	Spp1	2AR|Apl-1|BNSP|BSPI|Bsp|ETA-1|Eta|OP|Opn|Opnl|Ric|Spp-1	secreted phosphoprotein 1	protein-coding
mm_9146.1	chr1	170906995	170906998	-	1	NA	TTS (NM_001029984)	TTS (NM_001029984)	5945	NM_001029984	435653	Mm.337931	NM_001029984	ENSMUSG00000070524	Fcrlb	FREB-2|FREB2|FcRL2|Fcrlm2|Fcry|mFCRL2	Fc receptor-like B	protein-coding
mm_39332.1	chr5	8660634	8660652	+	1	NA	intron (NM_011076, intron 1 of 27)	intron (NM_011076, intron 1 of 27)	551	NM_011076	18671	Mm.207354	NM_011076	ENSMUSG00000040584	Abcb1a	Abcb4|Evi32|Mdr1a|Mdr3|P-gp|Pgp|Pgy-3|Pgy3|mdr-3	ATP-binding cassette, sub-family B (MDR/TAP), member 1A	protein-coding
mm_39510.1	chr5	21251392	21251406	+	1	NA	intron (NM_175437, intron 16 of 30)	Tigger7|DNA|TcMar-Tigger	65132	NM_175437	212167	Mm.121705	NM_175437	ENSMUSG00000039934	Gsap	A530088I07Rik|Pion	gamma-secretase activating protein	protein-coding
mm_16666.1	chr2	6721812	6721867	-	1	NA	promoter-TSS (NM_001310447)	promoter-TSS (NM_001310447)	-177	NM_001310447	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_74029.1	chr8	121792332	121792339	+	1	NA	Intergenic	Intergenic	37234	NM_145605	234825	Mm.209329	NM_145605	ENSMUSG00000040263	Klhdc4	AA408426|AV352552|BC012312|G430025P05Rik	kelch domain containing 4	protein-coding
mm_55982.1	chr6	85915619	85915640	-	1	NA	promoter-TSS (NM_001170488)	promoter-TSS (NM_001170488)	48	NM_023160	66116	Mm.13036	NM_023160	ENSMUSG00000057103	Nat8f1	1110002I11Rik|AI266962|Cml1	N-acetyltransferase 8 (GCN5-related) family member 1	protein-coding
mm_54372.1	chr6	31156776	31156778	-	1	NA	intron (NR_110471, intron 2 of 3)	intron (NR_110471, intron 2 of 3)	61697	NR_110470	232685	Mm.443019	NM_144555	ENSMUSG00000044471	Lncpint	Lincpint|MNCb-1768|Pint|linc-Pint	long non-protein coding RNA, Trp53 induced transcript	ncRNA
mm_1340.1	chr1	66175210	66175220	+	1	NA	promoter-TSS (NM_008632)	promoter-TSS (NM_008632)	-114	NM_008632	17756	Mm.256966	NM_008632	ENSMUSG00000015222	Map2	G1-397-34|MAP-2|Mtap-2|Mtap2|repro4	microtubule-associated protein 2	protein-coding
mm_103956.1	chr11	84101979	84101982	-	1	NA	intron (NM_172562, intron 8 of 15)	intron (NM_172562, intron 8 of 15)	27588	NM_172562	217031	Mm.45159	NM_172562	ENSMUSG00000018651	Tada2a	AV319371|D030022J10Rik|Tada2l	transcriptional adaptor 2A	protein-coding
mm_102340.1	chr11	57832680	57832690	-	1	NA	promoter-TSS (NM_008213)	promoter-TSS (NM_008213)	-538	NM_008213	15110	Mm.4746	NM_008213	ENSMUSG00000037335	Hand1	Ehand1|Hxt|Th1|Thing1|bHLHa27|eHAND	heart and neural crest derivatives expressed transcript 1	protein-coding
mm_83765.1	chr9	52048672	52048678	-	1	NA	promoter-TSS (NR_023357)	promoter-TSS (NR_023357)	30	NR_023357	629557	Mm.422775	NR_023357		Gm6981	EG629557	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_85010.1	chr9	87704226	87704234	-	1	NA	3' UTR (NM_023814, exon 8 of 8)	3' UTR (NM_023814, exon 8 of 8)	27030	NM_023814	76365	Mm.158789	NM_023814	ENSMUSG00000032419	Tbx18	2810012F10Rik|2810404D13Rik	T-box18	protein-coding
mm_70346.1	chr8	4678529	4678538	+	1	NA	Intergenic	CpG	65363	NM_145591	233987	Mm.102799	NM_145591	ENSMUSG00000058748	Zfp958	-	zinc finger protein 958	protein-coding
mm_127114.1	chr15	97964312	97964326	+	1	NA	promoter-TSS (NM_201359)	promoter-TSS (NM_201359)	90	NM_001252153	380967	Mm.196630	NM_201359	ENSMUSG00000052369	Tmem106c	AI046681|BC046621|D15Ertd405e	transmembrane protein 106C	protein-coding
mm_65074.1	chr7	19095557	19095572	-	1	NA	intron (NM_011383, intron 1 of 2)	intron (NM_011383, intron 1 of 2)	1020	NM_011383	20475	Mm.3410	NM_011383	ENSMUSG00000040841	Six5	Dmahp|MDMAHP|TrexBF	sine oculis-related homeobox 5	protein-coding
mm_105009.1	chr11	100397071	100397109	-	1	NA	intron (NM_010593, intron 1 of 13)	intron (NM_010593, intron 1 of 13)	700	NM_010593	16480	Mm.299774	NM_010593	ENSMUSG00000001552	Jup	Ctnng|D930025P04Rik|PG	junction plakoglobin	protein-coding
mm_139763.1	chr17	64601244	64601260	+	1	NA	promoter-TSS (NM_008549)	promoter-TSS (NM_008549)	-397	NM_008549	17158	Mm.2433	NM_008549	ENSMUSG00000024085	Man2a1	Mana-2|Mana2|Map-2	mannosidase 2, alpha 1	protein-coding
mm_90185.1	chr10	120160710	120160731	+	1	NA	intron (NM_028679, intron 8 of 11)	RLTR31B2|LTR|ERVK	40817	NM_028679	73914	Mm.146194	NM_028679	ENSMUSG00000020227	Irak3	4833428C18Rik|AI563835|IRAK-M	interleukin-1 receptor-associated kinase 3	protein-coding
mm_124021.1	chr14	76556643	76556653	-	1	NA	promoter-TSS (NM_001160326)	promoter-TSS (NM_001160326)	39	NM_001160326	72661	Mm.320384	NM_001160326	ENSMUSG00000052584	Serp2	2810032E02Rik	stress-associated endoplasmic reticulum protein family member 2	protein-coding
mm_123540.1	chr14	66824401	66824415	-	1	NA	exon (NM_009955, exon 8 of 14)	exon (NM_009955, exon 8 of 14)	44192	NM_009955	12934	Mm.352648	NM_009955	ENSMUSG00000022048	Dpysl2	AI851130|Crmp2|DRP2|Musunc33|TOAD-64|Ulip2	dihydropyrimidinase-like 2	protein-coding
mm_92084.1	chr10	62791973	62791987	-	1	NA	intron (NM_026201, intron 1 of 24)	CpG	388	NM_026201	67500	Mm.196371	NM_026201	ENSMUSG00000020074	Ccar1	2610511G16Rik|9430036H15Rik|Carp1	cell division cycle and apoptosis regulator 1	protein-coding
mm_133525.1	chr16	90846630	90846631	+	1	NA	intron (NM_001316761, intron 1 of 5)	intron (NM_001316761, intron 1 of 5)	15771	NM_001316761	70967	Mm.253077	NM_027627	ENSMUSG00000039903	Eva1c	1700092M14Rik|4931408A02Rik|Fam176c	eva-1 homolog C (C. elegans)	protein-coding
mm_138288.1	chr17	34613223	34613226	+	1	NA	TTS (NM_152922)	TTS (NM_152922)	2747	NM_152922	81701	Mm.231343	NM_152922	ENSMUSG00000015467	Egfl8	Ng3	EGF-like domain 8	protein-coding
mm_173087.1	chrX	150020076	150020076	+	1	NA	Intergenic	L1Md_A|LINE|L1	78421	NM_001122735	382244	Mm.359506	NM_001122735	ENSMUSG00000095082	Gm15091	OTTMUSG00000018981	predicted gene 15091	protein-coding
mm_170568.1	chr19	5008625	5008639	+	1	NA	Intergenic	Intergenic	-15374	NM_007854	13340	Mm.4930	NM_007854	ENSMUSG00000024891	Slc29a2	Der12|Ent2|Hnp36	solute carrier family 29 (nucleoside transporters), member 2	protein-coding
mm_125520.1	chr15	57694861	57694870	+	1	NA	5' UTR (NM_199449, exon 1 of 4)	5' UTR (NM_199449, exon 1 of 4)	198	NM_199449	387609	Mm.36557	NM_199449	ENSMUSG00000071757	Zhx2	Afr-1|Afr1|Raf|mKIAA0854	zinc fingers and homeoboxes 2	protein-coding
mm_171428.1	chr4	13483208	13483216	-	1	NA	Intergenic	Intergenic	-260090	NM_001111026	12395	Mm.4909	NM_009822	ENSMUSG00000006586	Runx1t1	Cbfa2t1h|ETO|MTG8	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	protein-coding
mm_109171.1	chr12	108371181	108371196	+	1	NA	promoter-TSS (NM_001286346)	promoter-TSS (NM_001286346)	35	NM_001286346	68519	Mm.236645	NM_001043335	ENSMUSG00000058070	Eml1	1110008N23Rik|A930030P13Rik|AA171013|AI847476|AI853955|ELP79|EMAP|EMAPL|heco	echinoderm microtubule associated protein like 1	protein-coding
mm_166573.1	chr6	49073729	49073750	-	1	NA	promoter-TSS (NM_029353)	promoter-TSS (NM_029353)	-56	NM_029353	75593	Mm.439947	NM_029353	ENSMUSG00000029815	Malsu1	2410003K15Rik|Matsu1	mitochondrial assembly of ribosomal large subunit 1	protein-coding
mm_129409.1	chr15	78298180	78298204	-	1	NA	exon (NM_007781, exon 2 of 14)	exon (NM_007781, exon 2 of 14)	7529	NM_007781	12984	Mm.1940	NM_007781	ENSMUSG00000071714	Csf2rb2	AIC2A|BetaIl3|Bil3|Csfgmrb|Il3r|Il3rb|Il3rb2	colony stimulating factor 2 receptor, beta 2, low-affinity (granulocyte-macrophage)	protein-coding
mm_82564.1	chr9	21074878	21074921	-	1	NA	TTS (NR_106050)	TTS (NR_106050)	689	NR_106050	102465656		NR_106050	ENSMUSG00000098907	Mir7082	Gm27933|mmu-mir-7082	microRNA 7082	ncRNA
mm_114799.1	chr13	90089706	90089740	+	1	NA	promoter-TSS (NM_025335)	promoter-TSS (NM_025335)	56	NM_025335	66074	Mm.241387	NM_025335	ENSMUSG00000012422	Tmem167	0610041E09Rik|5730424F14Rik|AU041184|AW537806|ENSMUSG00000060669|Gm10085|Tmem167a	transmembrane protein 167	protein-coding
mm_62238.1	chr7	98703092	98703137	+	1	NA	promoter-TSS (NM_028410)	promoter-TSS (NM_028410)	-186	NR_144495	100040769	Mm.126401	NR_144495		Gm15506	OTTMUSG00000023003	predicted gene 15506	ncRNA
mm_50705.1	chr6	52158407	52158423	+	1	NA	promoter-TSS (NM_010449)	promoter-TSS (NM_010449)	-98	NM_001311118	15394	Mm.197	NM_010449	ENSMUSG00000029844	Hoxa1	ERA1|Hox-1.6	homeobox A1	protein-coding
mm_129344.1	chr15	77849562	77849601	-	1	NA	Intergenic	Intergenic	-7406	NM_022410	17886	Mm.29677	NM_022410	ENSMUSG00000022443	Myh9	Fltn|Myhn-1|Myhn1|NMHCIIA|NMMHC-A|NMMHC-IIA|TU72.6	myosin, heavy polypeptide 9, non-muscle	protein-coding
mm_72049.1	chr8	71346152	71346154	+	1	NA	intron (NM_015742, intron 20 of 39)	intron (NM_015742, intron 20 of 39)	-20695	NM_001145780	67023	Mm.41890	NM_025917	ENSMUSG00000002395	Use1	2010315L10Rik|5730403H22Rik|AV002165|D12|Ed2|Q-snare|p31	unconventional SNARE in the ER 1 homolog (S. cerevisiae)	protein-coding
mm_71746.1	chr8	65209117	65209134	+	1	NA	Intergenic	RLTR9A3A|LTR|ERVK	-79588	NR_033217	407795	Mm.387876	NR_033217	ENSMUSG00000074300	BC030870	-	cDNA sequence BC030870	ncRNA
mm_48580.1	chr5	143506591	143506603	-	1	NA	3' UTR (NM_009007, exon 6 of 6)	3' UTR (NM_009007, exon 6 of 6)	21396	NM_009007	19353	Mm.292510	NM_009007	ENSMUSG00000001847	Rac1	AL023026|D5Ertd559e	RAS-related C3 botulinum substrate 1	protein-coding
mm_137779.1	chr17	29493115	29493128	+	1	NA	intron (NM_008842, intron 4 of 5)	intron (NM_008842, intron 4 of 5)	2076	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_115306.1	chr13	112288517	112288548	+	1	NA	promoter-TSS (NM_029898)	promoter-TSS (NM_029898)	14	NM_001168404	77318	Mm.159895	NM_029898	ENSMUSG00000049985	Ankrd55	C030011J08Rik	ankyrin repeat domain 55	protein-coding
mm_169711.1	chr15	76180905	76180906	-	1	NA	exon (NM_201393, exon 31 of 32)	exon (NM_201393, exon 31 of 32)	14805	NM_201394	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
mm_53365.1	chr6	129397309	129397332	+	1	NA	promoter-TSS (NM_019985)	promoter-TSS (NM_019985)	23	NM_001204239	56760	Mm.30700	NM_019985	ENSMUSG00000030159	Clec1b	1810061I13Rik|Clec-2|Clec2	C-type lectin domain family 1, member b	protein-coding
mm_137177.1	chr17	23816153	23816170	+	1	NA	exon (NM_175229, exon 10 of 14)	exon (NM_175229, exon 10 of 14)	12948	NM_026305	67673	Mm.153758	NM_026305	ENSMUSG00000055839	Elob	0610040H15Rik|Tceb2	elongin B	protein-coding
mm_138874.1	chr17	43088009	43088025	+	1	NA	3' UTR (NM_178589, exon 6 of 6)	3' UTR (NM_178589, exon 6 of 6)	70274	NR_045155	545207	Mm.329050	NR_045153		E130008D07Rik	-	RIKEN cDNA E130008D07 gene	ncRNA
mm_87325.1	chr10	42860777	42860810	+	1	NA	5' UTR (NM_172938, exon 1 of 9)	5' UTR (NM_172938, exon 1 of 9)	281	NM_172938	268297	Mm.98731	NM_172938	ENSMUSG00000044770	Scml4	9330161D17|mFLJ00197	sex comb on midleg-like 4 (Drosophila)	protein-coding
mm_69266.1	chr7	127898446	127898452	-	1	NA	Intergenic	Intergenic	-2832	NM_178600	27973	Mm.29703	NM_178600	ENSMUSG00000096145	Vkorc1	D7Wsu86e	vitamin K epoxide reductase complex, subunit 1	protein-coding
mm_120593.1	chr14	70076908	70076923	+	1	NA	promoter-TSS (NM_001289927)	promoter-TSS (NM_001289927)	-530	NM_018781	13655	Mm.103737	NM_018781	ENSMUSG00000033730	Egr3	Pilot	early growth response 3	protein-coding
mm_164067.1	chr14	118457497	118457499	+	1	NA	Intergenic	Intergenic	91620	NR_045624	73306	Mm.362328	NR_045624	ENSMUSG00000099911	1700044C05Rik	-	RIKEN cDNA 1700044C05 gene	ncRNA
mm_28505.1	chr3	92532979	92532989	-	1	NA	Intergenic	Intergenic	-32491	NM_173070	229562	Mm.246590	NM_173070	ENSMUSG00000045566	Sprr4	-	small proline-rich protein 4	protein-coding
mm_23220.1	chr3	48123500	48123500	+	1	NA	Intergenic	MMERGLN_LTR|LTR|ERV1	-96741	NR_040408	666202	Mm.465057	NR_040408	ENSMUSG00000103257	Gm7977	EG666202	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide pseudogene	pseudo
mm_41761.1	chr5	103366375	103366378	+	1	NA	Intergenic	Intergenic	-58816	NM_011204	19249	Mm.3414	NM_011204	ENSMUSG00000034573	Ptpn13	AI324989|PTP-BL|PTPL1|Ptpri|RIP	protein tyrosine phosphatase, non-receptor type 13	protein-coding
mm_155017.1	chrX	42059531	42059540	+	1	NA	Intergenic	Intergenic	-8301	NM_009688	11798	Mm.259879	NM_009688	ENSMUSG00000025860	Xiap	1110015C02Rik|Aipa|Api3|Birc4|IAP3|ILP-1|MIHA	X-linked inhibitor of apoptosis	protein-coding
mm_169298.1	chr14	101463132	101463132	-	1	NA	intron (NM_001081278, intron 11 of 18)	intron (NM_001081278, intron 11 of 18)	146059	NM_001081278	210789	Mm.320639	NM_173380	ENSMUSG00000033083	Tbc1d4	5930406J04Rik|A930035N22|AV295684|As160	TBC1 domain family, member 4	protein-coding
mm_126045.1	chr15	76904885	76904914	+	1	NA	exon (NM_012053, exon 4 of 6)	exon (NM_012053, exon 4 of 6)	828	NM_012053	26961	Mm.30066	NM_012053	ENSMUSG00000003970	Rpl8	-	ribosomal protein L8	protein-coding
mm_172897.1	chr9	56223947	56223964	-	1	NA	intron (NM_172924, intron 6 of 6)	LSU-rRNA_Hsa|rRNA|rRNA	-62885	NM_019793	56434	Mm.28484	NM_019793	ENSMUSG00000032324	Tspan3	1700055K04Rik|TM4-A|Tm4sf8	tetraspanin 3	protein-coding
mm_85697.1	chr9	108094460	108094487	-	1	NA	promoter-TSS (NM_146226)	promoter-TSS (NM_146226)	7	NM_146226	235606	Mm.219639	NM_146226	ENSMUSG00000032590	Apeh	-	acylpeptide hydrolase	protein-coding
mm_146124.1	chr18	74442552	74442631	+	1	NA	promoter-TSS (NM_201600)	promoter-TSS (NM_201600)	-28	NM_201600	17919	Mm.260098	NM_008661	ENSMUSG00000025885	Myo5b	AI661750|mKIAA1119	myosin VB	protein-coding
mm_32940.1	chr4	119320576	119320630	+	1	NA	promoter-TSS (NM_001110130)	promoter-TSS (NM_001110130)	-80	NM_001110130	66101	Mm.304080	NM_028677	ENSMUSG00000060288	Ppih	1100001J08Rik|2010111B15Rik|4833408F11Rik|AI464484|CYP-20|CYPH|D4Wsu43e	peptidyl prolyl isomerase H	protein-coding
mm_12202.1	chr2	65930118	65930190	+	1	NA	intron (NM_178634, intron 2 of 5)	intron (NM_178634, intron 2 of 5)	-1711	NM_001290665	77771	Mm.102025	NM_153409	ENSMUSG00000044647	Csrnp3	A330102K23Rik|CSRNP-3|Csnrp3|Mbu1|taip-2	cysteine-serine-rich nuclear protein 3	protein-coding
mm_126496.1	chr15	81726375	81726394	+	1	NA	intron (NM_001146174, intron 1 of 15)	intron (NM_001146174, intron 1 of 15)	3535	NM_011241	19387	Mm.270975	NM_011241	ENSMUSG00000022391	Rangap1	C79654|Fug1|mKIAA1835	RAN GTPase activating protein 1	protein-coding
mm_49877.1	chr6	38592938	38592940	+	1	NA	intron (NM_001331223, intron 10 of 12)	intron (NM_001331223, intron 10 of 12)	37216	NM_001331223	192196	Mm.276133	NM_138680	ENSMUSG00000029823	Luc7l2	4930471C18Rik|AA522013|AU015269|CGI59|Cgi74	LUC7-like 2 (S. cerevisiae)	protein-coding
mm_51682.1	chr6	86472818	86472831	+	1	NA	non-coding (NR_131125, exon 4 of 5)	non-coding (NR_131125, exon 4 of 5)	8006	NR_131125	320486	Mm.391625	NR_131125	ENSMUSG00000085589	A430078I02Rik	T25621	RIKEN cDNA A430078I02 gene	ncRNA
mm_84172.1	chr9	59948524	59948543	-	1	NA	intron (NM_013708, intron 4 of 7)	intron (NM_013708, intron 4 of 7)	1546	NM_013708	23958	Mm.103641	NM_013708	ENSMUSG00000032292	Nr2e3	A930035N01Rik|PNR|RNR|rd7	nuclear receptor subfamily 2, group E, member 3	protein-coding
mm_40141.1	chr5	35166380	35166393	+	1	NA	Intergenic	Intergenic	-60689	NM_013587	16976	Mm.277661	NM_013587	ENSMUSG00000029103	Lrpap1	AA617339|AI790446|AU042172|C77774|HBP44|RAP	low density lipoprotein receptor-related protein associated protein 1	protein-coding
mm_136976.1	chr17	15758627	15758638	+	1	NA	exon (NM_007690, exon 28 of 36)	exon (NM_007690, exon 28 of 36)	53665	NM_007690	12648	Mm.8137	NM_007690	ENSMUSG00000023852	Chd1	4930525N21Rik|AI851787|AW555109	chromodomain helicase DNA binding protein 1	protein-coding
mm_158221.1	chrX	106010944	106010947	-	1	NA	intron (NM_025952, intron 1 of 10)	intron (NM_025952, intron 1 of 10)	954	NM_001190409	67075	Mm.275943	NM_025952	ENSMUSG00000031232	Magt1	2410001C15Rik|2610529C04Rik|2810482I07Rik|IAG2|IAP	magnesium transporter 1	protein-coding
mm_160717.1	chr10	63024472	63024472	+	1	NA	promoter-TSS (NM_001079824)	promoter-TSS (NM_001079824)	-40	NM_026085	67307	Mm.368563	NM_026085	ENSMUSG00000020072	Pbld2	3110049J23Rik|Mawbp	phenazine biosynthesis-like protein domain containing 2	protein-coding
mm_87971.1	chr10	63457550	63457555	+	1	NA	promoter-TSS (NM_001164376)	promoter-TSS (NM_001164376)	41	NM_001164376	216033	Mm.444692	NM_177612	ENSMUSG00000060843	Ctnna3	4930429L08Rik|4933408A16|Catna3|Vr22	catenin (cadherin associated protein), alpha 3	protein-coding
mm_140844.1	chr17	23675852	23675888	-	1	NA	TTS (NM_181821)	TTS (NM_181821)	1579	NM_001161746	27279	Mm.28518	NM_013749	ENSMUSG00000023905	Tnfrsf12a	AI255180|C87282|Fn14|HPIP|TWEAK-R|TweakR	tumor necrosis factor receptor superfamily, member 12a	protein-coding
mm_85377.1	chr9	103225165	103225173	-	1	NA	exon (NM_133977, exon 5 of 17)	exon (NM_133977, exon 5 of 17)	5117	NM_133977	22041	Mm.37214	NM_133977	ENSMUSG00000032554	Trf	AI266983|Cd176|HP|Tf|Tfn|hpx	transferrin	protein-coding
mm_56925.1	chr6	119417679	119417707	-	1	NA	promoter-TSS (NM_197985)	promoter-TSS (NM_197985)	-210	NM_197985	68465	Mm.291826	NM_197985	ENSMUSG00000030168	Adipor2	1110001I14Rik|ADCR2|AI115388|AW554121|D6Ucla1e|Paqr2	adiponectin receptor 2	protein-coding
mm_149424.1	chr19	11447522	11447539	+	1	NA	intron (NM_021718, intron 1 of 6)	intron (NM_021718, intron 1 of 6)	3972	NM_021718	60361	Mm.33957	NM_021718	ENSMUSG00000056290	Ms4a4b	AI463180|Chandra|Ly116	membrane-spanning 4-domains, subfamily A, member 4B	protein-coding
mm_137271.1	chr17	24699904	24699905	+	1	NA	TTS (NM_145396)	TTS (NM_145396)	3670	NM_027988	71893	Mm.390971	NM_027988	ENSMUSG00000019320	Noxo1	2310034C04Rik|P41NOX|P41NOXA|P41NOXB|P41NOXC|Snx28|hslt	NADPH oxidase organizer 1	protein-coding
mm_3086.1	chr1	134406018	134406029	+	1	NA	promoter-TSS (NM_028057)	promoter-TSS (NM_028057)	33	NM_028057	72017	Mm.280230	NM_028057	ENSMUSG00000026456	Cyb5r1	1500005G05Rik|B5R.1|C80155|Nqo3a2	cytochrome b5 reductase 1	protein-coding
mm_113455.1	chr13	35870745	35870750	+	1	NA	intron (NM_001123386, intron 5 of 6)	intron (NM_001123386, intron 5 of 6)	35600	NM_145938	208366	Mm.35545	NM_145938	ENSMUSG00000021418	Rpp40	D8Bwg1265e|Rnasep1	ribonuclease P 40 subunit	protein-coding
mm_119814.1	chr14	54223963	54223972	+	1	NA	Intergenic	Intergenic	29962	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_128488.1	chr15	50890397	50890441	-	1	NA	promoter-TSS (NM_032000)	promoter-TSS (NM_032000)	-378	NM_032000	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_134521.1	chr16	19236211	19236213	-	1	NA	Intergenic	L1_Mur2|LINE|L1	50529	NM_146451	258443	Mm.377506	NM_146451	ENSMUSG00000050742	Olfr164	MOR279-2	olfactory receptor 164	protein-coding
mm_91039.1	chr10	18545772	18545778	-	1	NA	exon (NM_019487, exon 1 of 4)	exon (NM_019487, exon 1 of 4)	301	NM_019487	56016	Mm.35551	NM_019487	ENSMUSG00000019853	Hebp2	SOUL	heme binding protein 2	protein-coding
mm_78674.1	chr9	40781077	40781090	+	1	NA	intron (NM_133733, intron 5 of 6)	intron (NM_133733, intron 5 of 6)	-20190	NM_031165	15481	Mm.290774	NM_031165	ENSMUSG00000015656	Hspa8	2410008N15Rik|Hsc70|Hsc71|Hsc73|Hsp73|Hspa10	heat shock protein 8	protein-coding
mm_145808.1	chr18	65412829	65412830	+	1	NA	intron (NR_105742, intron 3 of 6)	intron (NR_105742, intron 3 of 6)	-18168	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_78463.1	chr9	32504330	32504334	+	1	NA	intron (NM_008026, intron 1 of 8)	intron (NM_008026, intron 1 of 8)	37120	NM_008026	14247	Mm.258908	NM_008026	ENSMUSG00000016087	Fli1	EWSR2|Fli-1|SIC-1|Sic1	Friend leukemia integration 1	protein-coding
mm_97455.1	chr11	78194767	78194794	+	1	NA	intron (NM_001045516, intron 1 of 3)	intron (NM_001045516, intron 1 of 3)	1388	NM_001045516	216974	Mm.50974	NM_001045516	ENSMUSG00000044122	Proca1	4933404M19Rik	protein interacting with cyclin A1	protein-coding
mm_18015.1	chr2	38368959	38369004	-	1	NA	exon (NM_010710, exon 5 of 5)	exon (NM_010710, exon 5 of 5)	17673	NM_010710	16870	Mm.142856	NM_010710	ENSMUSG00000000247	Lhx2	LH2A|Lh-2|Lim2|ap|apterous	LIM homeobox protein 2	protein-coding
mm_85590.1	chr9	107333814	107333828	-	1	NA	intron (NM_133984, intron 4 of 10)	intron (NM_133984, intron 4 of 10)	4529	NM_133984	69536	Mm.259467	NM_133984	ENSMUSG00000032579	Hemk1	2310008M14Rik|AW049265	HemK methyltransferase family member 1	protein-coding
mm_21358.1	chr2	157125113	157125130	-	1	NA	intron (NM_018851, intron 3 of 15)	B2_Mm2|SINE|B2	10101	NM_001139520	56045	Mm.248478	NM_018851	ENSMUSG00000027639	Samhd1	E330031J07Rik|Mg11	SAM domain and HD domain, 1	protein-coding
mm_149404.1	chr19	11392700	11392719	+	1	NA	exon (NM_001310331, exon 7 of 7)	exon (NM_001310331, exon 7 of 7)	-14952	NM_029499	64380	Mm.440715	NM_029499	ENSMUSG00000024675	Ms4a4c	5830413L19Rik|AI449185|Ms4a9	membrane-spanning 4-domains, subfamily A, member 4C	protein-coding
mm_100779.1	chr11	4808343	4808351	-	1	NA	intron (NM_001252251, intron 4 of 16)	intron (NM_001252251, intron 4 of 16)	24788	NM_001252253	18016	Mm.297109	NM_010898	ENSMUSG00000009073	Nf2	merlin	neurofibromin 2	protein-coding
mm_78365.1	chr9	26999669	26999686	+	1	NA	promoter-TSS (NM_144543)	promoter-TSS (NM_144543)	0	NM_144543	77862	Mm.16925	NM_144543	ENSMUSG00000035443	Thyn1	D730042P09Rik|HSPC144|MDS012|MY105|Thy28	thymocyte nuclear protein 1	protein-coding
mm_72228.1	chr8	73383392	73383400	+	1	NA	Intergenic	Intergenic	-29856	NM_010687	16795	Mm.324371	NM_010687	ENSMUSG00000004383	Large1	BPFD#36|Gyltl1a|Large|Mbp-1|Mbp1|enr|fg|froggy|myd	LARGE xylosyl- and glucuronyltransferase 1	protein-coding
mm_133559.1	chr16	91391773	91391796	+	1	NA	exon (NM_010509, exon 6 of 9)	exon (NM_010509, exon 6 of 9)	-14451	NM_008349	16155	Mm.4154	NM_008349	ENSMUSG00000022969	Il10rb	6620401D04Rik|AI528744|CRF2-4|Crfb4|D16H21S58|D21S58h|IL-10R2|Il10r2	interleukin 10 receptor, beta	protein-coding
mm_74801.1	chr8	22476810	22476873	-	1	NA	promoter-TSS (NM_001146117)	promoter-TSS (NM_001146117)	38	NM_001012667	102032	Mm.378231	NM_001012667	ENSMUSG00000031534	Smim19	AI316807|BG694986|EST-c39	small integral membrane protein 19	protein-coding
mm_16408.1	chr2	180042497	180042562	+	1	NA	promoter-TSS (NM_178750)	promoter-TSS (NM_178750)	46	NM_178750	269397	Mm.63068	NM_178750	ENSMUSG00000039086	Ss18l1	A230053O16Rik|CREST	SS18, nBAF chromatin remodeling complex subunit like 1	protein-coding
mm_45118.1	chr5	45806680	45806683	-	1	NA	intron (NM_001163073, intron 1 of 6)	intron (NM_001163073, intron 1 of 6)	49871	NM_172153	209707	Mm.71498	NM_172153	ENSMUSG00000015882	Lcorl	Mlr1	ligand dependent nuclear receptor corepressor-like	protein-coding
mm_131644.1	chr16	20517077	20517130	+	1	NA	promoter-TSS (NM_007889)	promoter-TSS (NM_007889)	39	NM_007889	13544	Mm.247259	NM_007889	ENSMUSG00000003233	Dvl3	-	dishevelled segment polarity protein 3	protein-coding
mm_54655.1	chr6	39087522	39087540	-	1	NA	exon (NM_172893, exon 12 of 12)	exon (NM_172893, exon 12 of 12)	-19945	NR_040523	69986	Mm.490941	NR_040523	ENSMUSG00000100121	1700025N23Rik	-	RIKEN cDNA 1700025N23 gene	ncRNA
mm_169339.1	chr14	123793313	123793313	+	1	NA	intron (NM_145467, intron 2 of 10)	L1Md_A|LINE|L1	133173	NM_145467	223272	Mm.383176	NM_145467	ENSMUSG00000032925	Itgbl1	B930011D01Rik	integrin, beta-like 1	protein-coding
mm_139683.1	chr17	57417502	57417516	+	1	NA	intron (NM_010130, intron 10 of 21)	L1_Mus3|LINE|L1	58823	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_96173.1	chr11	61505139	61505210	+	1	NA	promoter-TSS (NM_001330780)	promoter-TSS (NM_001330780)	30	NM_001330781	27078	Mm.261226	NM_013717	ENSMUSG00000001039	B9d1	AW045994|B9|Eppb9	B9 protein domain 1	protein-coding
mm_56955.1	chr6	120022791	120022793	-	1	NA	intron (NM_001185021, intron 1 of 25)	intron (NM_001185021, intron 1 of 25)	11519	NR_030487	735290		NR_030487	ENSMUSG00000076217	Mir706	Mirn706|mir-706|mmu-mir-706	microRNA 706	ncRNA
mm_153336.1	chr19	38224097	38224183	-	1	NA	promoter-TSS (NM_001081075)	promoter-TSS (NM_001081075)	-8	NM_001081075	70567	Mm.30607	NM_001081075	ENSMUSG00000054237	Fra10ac1	5730455O13Rik|AI448293	FRA10AC1 homolog (human)	protein-coding
mm_161652.1	chr17	6601781	6601781	+	1	NA	promoter-TSS (NM_001166630)	promoter-TSS (NM_001166630)	2	NM_001166630	100040563	Mm.457381	NM_001166630	ENSMUSG00000000579	Dynlt1c	100040603|Dynlt1d	dynein light chain Tctex-type 1C	protein-coding
mm_66861.1	chr7	55962467	55962481	-	1	NA	promoter-TSS (NM_023647)	promoter-TSS (NM_023647)	19	NM_001256133	93790	Mm.37249	NM_023647	ENSMUSG00000030452	Nipa2	2600017P10Rik|3830408P04Rik|AB041581	non imprinted in Prader-Willi/Angelman syndrome 2 homolog (human)	protein-coding
mm_143549.1	chr17	74017462	74017471	-	1	NA	TTS (NM_053188)	TTS (NM_053188)	30450	NM_053188	94224	Mm.38933	NM_053188	ENSMUSG00000038541	Srd5a2	5ART2|S5AR 2	steroid 5 alpha-reductase 2	protein-coding
mm_40296.1	chr5	43515807	43515818	+	1	NA	5' UTR (NM_001135172, exon 1 of 3)	5' UTR (NM_001135172, exon 1 of 3)	243	NM_001135172	109323	Mm.275553	NM_175425	ENSMUSG00000061535	C1qtnf7	5530401N20Rik|8430425G24Rik|Ctrp7	C1q and tumor necrosis factor related protein 7	protein-coding
mm_54270.1	chr6	28833416	28833461	-	1	NA	intron (NM_019776, intron 16 of 23)	CpG	-1691	NM_138682	192198	Mm.443660	NM_138682	ENSMUSG00000049939	Lrrc4	MBAG1|NGL-2|NGL2|NLG-2|Nag14	leucine rich repeat containing 4	protein-coding
mm_161024.1	chr12	3451695	3451695	+	1	NA	exon (NM_172421, exon 3 of 11)	exon (NM_172421, exon 3 of 11)	24838	NM_172421	75302	Mm.120475	NM_172421	ENSMUSG00000037486	Asxl2	4930556B16Rik|mKIAA1685	additional sex combs like 2 (Drosophila)	protein-coding
mm_101343.1	chr11	23633533	23633576	-	1	NA	promoter-TSS (NM_001347242)	promoter-TSS (NM_001347242)	77	NM_001347242	71675	Mm.48031	NM_027860	ENSMUSG00000042208	0610010F05Rik	Kiaa1841|mKIAA1841	RIKEN cDNA 0610010F05 gene	protein-coding
mm_5491.1	chr1	36939522	36939532	-	1	NA	promoter-TSS (NM_018872)	promoter-TSS (NM_018872)	0	NM_018872	56030	Mm.186943	NM_018872	ENSMUSG00000026116	Tmem131	2610524E03Rik|CC28|D1Bwg0491e|Neg|RW1|YR-23|mKIAA0257	transmembrane protein 131	protein-coding
mm_91345.1	chr10	26544884	26544888	-	1	NA	Intergenic	Intergenic	129765	NR_033633	667572	Mm.482728	NR_033633	ENSMUSG00000098179	Gm8709	EG667572	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_94476.1	chr11	6560192	6560209	+	1	NA	promoter-TSS (NM_001190344)	promoter-TSS (NM_001190344)	17	NM_001190344	216527	Mm.221271	NM_146014	ENSMUSG00000000378	Ccm2	BC029157	cerebral cavernous malformation 2	protein-coding
mm_119222.1	chr14	33227651	33227662	+	1	NA	intron (NM_153800, intron 2 of 10)	intron (NM_153800, intron 2 of 10)	10833	NM_153800	239027	Mm.318350	NM_153800	ENSMUSG00000063506	Arhgap22	B230341L19Rik|RHOGAP2|p68RacGAP	Rho GTPase activating protein 22	protein-coding
mm_150152.1	chr19	31950616	31950628	+	1	NA	Intergenic	PB1D10|SINE|Alu	81861	NM_001081074	69865	Mm.87538	NM_001081074	ENSMUSG00000052595	A1cf	1810073H04Rik|ACF64|ACF65|ASP|Acf|MCM|MerCreMer|Tg(Myh6-cre/Esr1*)1Jmk|mer	APOBEC1 complementation factor	protein-coding
mm_90846.1	chr10	8762220	8762259	-	1	NA	intron (NM_175155, intron 8 of 19)	intron (NM_175155, intron 8 of 19)	123831	NM_175155	70097	Mm.338275	NM_175155	ENSMUSG00000015305	Sash1	1100001C18Rik|2500002E12Rik|A330076K04Rik|mKIAA0790	SAM and SH3 domain containing 1	protein-coding
mm_133424.1	chr16	87440603	87440637	+	1	NA	promoter-TSS (NM_016924)	promoter-TSS (NM_016924)	-28	NM_016924	53858	Mm.162406	NM_016924	ENSMUSG00000041079	Rwdd2b	ORF5	RWD domain containing 2B	protein-coding
mm_63067.1	chr7	122133037	122133050	+	1	NA	promoter-TSS (NM_001081238)	promoter-TSS (NM_001081238)	2	NM_021608	59288	Mm.478285	NM_021608	ENSMUSG00000030868	Dctn5	4930427E12Rik|C78178|b2b315Clo	dynactin 5	protein-coding
mm_32699.1	chr4	116075345	116075357	+	1	NA	promoter-TSS (NM_153521)	promoter-TSS (NM_153521)	82	NM_153521	230654	Mm.3655	NM_153521	ENSMUSG00000028703	Lrrc41	AA409966|AW555107|D630045E04Rik|D730026A16Rik|MUF1	leucine rich repeat containing 41	protein-coding
mm_136253.1	chr16	90956866	90956910	-	1	NA	intron (NM_001164483, intron 22 of 31)	intron (NM_001164483, intron 22 of 31)	-22039	NM_026502	68001	Mm.45374	NM_026502	ENSMUSG00000022972	1110004E09Rik	-	RIKEN cDNA 1110004E09 gene	protein-coding
mm_126038.1	chr15	76904071	76904092	+	1	NA	promoter-TSS (NM_012053)	promoter-TSS (NM_012053)	10	NM_012053	26961	Mm.30066	NM_012053	ENSMUSG00000003970	Rpl8	-	ribosomal protein L8	protein-coding
mm_171677.1	chr4	53058366	53058369	-	1	NA	intron (NM_013454, intron 34 of 49)	L1Md_T|LINE|L1	46487	NM_025623	66536	Mm.38244	NM_025623	ENSMUSG00000015247	Nipsnap3b	2700063N13Rik|Nipsnap3a	nipsnap homolog 3B (C. elegans)	protein-coding
mm_65064.1	chr7	18910241	18910285	-	1	NA	5' UTR (NM_001033314, exon 1 of 14)	5' UTR (NM_001033314, exon 1 of 14)	141	NM_001033314	232933	Mm.333624	NM_001033314	ENSMUSG00000074358	Ccdc61	C530028I08Rik|Gm159	coiled-coil domain containing 61	protein-coding
mm_82114.1	chr9	123461897	123461910	+	1	NA	3' UTR (NM_153168, exon 21 of 21)	3' UTR (NM_153168, exon 21 of 21)	-16798	NM_013860	29806	Mm.10987	NM_013860	ENSMUSG00000025239	Limd1	AW822033|D9Ertd192e	LIM domains containing 1	protein-coding
mm_66736.1	chr7	46672299	46672311	-	1	NA	5' UTR (NM_009414, exon 1 of 11)	5' UTR (NM_009414, exon 1 of 11)	232	NM_009414	21990	Mm.248684	NM_009414	ENSMUSG00000040046	Tph1	Tph	tryptophan hydroxylase 1	protein-coding
mm_93637.1	chr10	117282386	117282393	-	1	NA	promoter-TSS (NM_017372)	promoter-TSS (NM_017372)	-117	NM_017372	17105	Mm.45436	NM_017372	ENSMUSG00000069516	Lyz2	AI326280|Lys|Lysm|Lyzf2|Lyzs|Lzm|Lzm-s1|Lzp	lysozyme 2	protein-coding
mm_119820.1	chr14	54227679	54227689	+	1	NA	Intergenic	Intergenic	26245	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_64295.1	chr7	141861123	141861125	+	1	NA	exon (NM_028801, exon 31 of 49)	exon (NM_028801, exon 31 of 49)	22052	NM_028801	74180	Mm.200752	NM_028801	ENSMUSG00000066108	Muc5b	2300002I04Rik|A130042M24|AV085033|MUC5|MUC9|mucin 5b	mucin 5, subtype B, tracheobronchial	protein-coding
mm_13785.1	chr2	118813996	118814027	+	1	NA	promoter-TSS (NM_026412)	promoter-TSS (NM_026412)	8	NM_026412	51944	Mm.252695	NM_026412	ENSMUSG00000027331	Knstrn	1700025D04Rik|C15orf23|D2Ertd750e|SKAP|Traf4af1	kinetochore-localized astrin/SPAG5 binding	protein-coding
mm_167007.1	chr7	51880269	51880277	+	1	NA	intron (NM_008087, intron 1 of 7)	intron (NM_008087, intron 1 of 7)	1306	NM_001330607	14453	Mm.207360	NM_008087	ENSMUSG00000030498	Gas2	Gas-2	growth arrest specific 2	protein-coding
mm_58468.1	chr7	3390317	3390337	+	1	NA	Intergenic	G-rich|Low_complexity|Low_complexity	-3715	NM_133190	81905	Mm.357990	NM_133190	ENSMUSG00000053395	Cacng8	-	calcium channel, voltage-dependent, gamma subunit 8	protein-coding
mm_51408.1	chr6	78380701	78380715	+	1	NA	promoter-TSS (NM_011259)	promoter-TSS (NM_011259)	-1	NM_011259	19694	Mm.2552	NM_011259	ENSMUSG00000079516	Reg3a	AV063448	regenerating islet-derived 3 alpha	protein-coding
mm_164662.1	chr17	40239206	40239219	-	1	NA	exon (NM_009639, exon 2 of 8)	exon (NM_009639, exon 2 of 8)	3046	NM_009639	11572	Mm.14138	NM_009639	ENSMUSG00000025433	Crisp3	Aeg2|CRISP-3|CRS3|SGP28	cysteine-rich secretory protein 3	protein-coding
mm_39890.1	chr5	31154255	31154280	+	1	NA	promoter-TSS (NM_001294322)	promoter-TSS (NM_001294322)	-16	NM_008622	17527	Mm.271923	NM_008622	ENSMUSG00000107283	Mpv17	Tg.Mpv17	MpV17 mitochondrial inner membrane protein	protein-coding
mm_74456.1	chr8	4214467	4214485	-	1	NA	exon (NM_207203, exon 6 of 7)	exon (NM_207203, exon 6 of 7)	2836	NM_207203	73072	Mm.477379	NM_207203	ENSMUSG00000064125	Prr36	-	proline rich 36	protein-coding
mm_85644.1	chr9	107656130	107656143	-	1	NA	exon (NM_001199218, exon 10 of 16)	exon (NM_001199218, exon 10 of 16)	11263	NM_023805	76257	Mm.296560	NM_023805	ENSMUSG00000010064	Slc38a3	0610012J02Rik|D9Ucla2|Nat1|Slc38-3|Sn1|Snat3|mNAT	solute carrier family 38, member 3	protein-coding
mm_145914.1	chr18	66504171	66504187	+	1	NA	promoter-TSS (NR_040528)	promoter-TSS (NR_040528)	1	NR_040528	100503565	Mm.98256	NR_040528		Gm9926	ENSMUSG00000053891	predicted gene 9926	ncRNA
mm_121558.1	chr14	122484294	122484301	+	1	NA	Intergenic	Intergenic	8913	NM_009574	22772	Mm.308936	NM_009574	ENSMUSG00000061524	Zic2	HPE5|Ku	zinc finger protein of the cerebellum 2	protein-coding
mm_158590.1	chrX	150954846	150954852	-	1	NA	Intergenic	MLT1M|LTR|ERVL-MaLR	62444	NM_001168600	237107	Mm.45987	NM_198110	ENSMUSG00000025266	Gnl3l	BC020354	guanine nucleotide binding protein-like 3 (nucleolar)-like	protein-coding
mm_49142.1	chr6	10883312	10883338	+	1	NA	Intergenic	Intergenic	91053	NR_033776	57866	Mm.4397	NR_033776		AA545190	-	EST AA545190	ncRNA
mm_90631.1	chr10	128474567	128474577	+	1	NA	intron (NM_198160, intron 13 of 27)	intron (NM_198160, intron 13 of 27)	15336	NM_001114097	68094	Mm.417338	NM_198160	ENSMUSG00000025369	Smarcc2	5930405J04Rik	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2	protein-coding
mm_79938.1	chr9	65903098	65903102	+	1	NA	3' UTR (NM_026515, exon 4 of 4)	3' UTR (NM_026515, exon 4 of 4)	5694	NM_019797	56404	Mm.208379	NM_019797	ENSMUSG00000032386	Trip4	4930558E03Rik|ASC-1|Asc1|BB191711	thyroid hormone receptor interactor 4	protein-coding
mm_101760.1	chr11	43598638	43598647	-	1	NA	exon (NM_008375, exon 2 of 4)	exon (NM_008375, exon 2 of 4)	2920	NM_008375	16204	Mm.142716	NM_008375	ENSMUSG00000020405	Fabp6	GT|I-15P|I-BABP|ILBP|ILBP3|Illbp	fatty acid binding protein 6, ileal (gastrotropin)	protein-coding
mm_154284.1	chr19	60861391	60861462	-	1	NA	promoter-TSS (NM_053198)	promoter-TSS (NM_053198)	4	NM_053198	94281	Mm.48179	NM_053198	ENSMUSG00000063698	Sfxn4	-	sideroflexin 4	protein-coding
mm_19002.1	chr2	76872835	76872853	-	1	NA	exon (NM_011652, exon 99 of 313)	exon (NM_011652, exon 99 of 313)	109703	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_146702.1	chr18	13815656	13815659	-	1	NA	intron (NM_145492, intron 5 of 7)	intron (NM_145492, intron 5 of 7)	157076	NM_145492	225207	Mm.40325	NM_145492	ENSMUSG00000024420	Zfp521	B930086A16Rik|Evi3|Znf521	zinc finger protein 521	protein-coding
mm_32809.1	chr4	117126768	117126774	+	1	NA	promoter-TSS (NM_175030)	promoter-TSS (NM_175030)	-42	NM_175030	242646	Mm.358914	NM_175030	ENSMUSG00000047671	Tctex1d4	4833401D15Rik	Tctex1 domain containing 4	protein-coding
mm_26383.1	chr3	142569127	142569139	+	1	NA	exon (NM_018734, exon 8 of 11)	exon (NM_018734, exon 8 of 11)	8637	NM_001289493	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_27172.1	chr3	33990597	33990606	-	1	NA	Intergenic	RLTR9A3|LTR|ERVK	-29478	NM_001113189	14359	Mm.259021	NM_008053	ENSMUSG00000027680	Fxr1	1110050J02Rik|9530073J07Rik|AI851072|Fxr1h|Fxr1p	fragile X mental retardation gene 1, autosomal homolog	protein-coding
mm_132837.1	chr16	45610418	45610438	+	1	NA	promoter-TSS (NM_008099)	promoter-TSS (NM_008099)	-12	NM_008099	14525	Mm.4799	NM_008099	ENSMUSG00000022659	Gcsam	Gcet|Gcet2|M17|M17-L	germinal center associated, signaling and motility	protein-coding
mm_63337.1	chr7	126952088	126952098	+	1	NA	exon (NM_001252566, exon 2 of 17)	exon (NM_001252566, exon 2 of 17)	1558	NM_001252566	233878	Mm.283926	NM_144926	ENSMUSG00000030683	Sez6l2	AI835913|AW121566|BSRP-A|Psk1	seizure related 6 homolog like 2	protein-coding
mm_80688.1	chr9	91378349	91378373	+	1	NA	intron (NM_009576, intron 2 of 4)	intron (NM_009576, intron 2 of 4)	9389	NM_009576	22774	Mm.8062	NM_009576	ENSMUSG00000036972	Zic4	-	zinc finger protein of the cerebellum 4	protein-coding
mm_163688.1	chr13	96832375	96832379	+	1	NA	Intergenic	Intergenic	-92312	NM_001166065	218476	Mm.483490	NM_001166065	ENSMUSG00000091387	Gcnt4	C2gnt3|Gm279|Gm73	glucosaminyl (N-acetyl) transferase 4, core 2 (beta-1,6-N-acetylglucosaminyltransferase)	protein-coding
mm_39031.1	chr4	152288071	152288074	-	1	NA	intron (NM_008237, intron 2 of 4)	intron (NM_008237, intron 2 of 4)	3590	NM_008237	15207	Mm.3516	NM_008237	ENSMUSG00000028946	Hes3	Hes-3|bHLHb43	hairy and enhancer of split 3 (Drosophila)	protein-coding
mm_60262.1	chr7	43824450	43824460	+	1	NA	promoter-TSS (NM_011177)	promoter-TSS (NM_011177)	-89	NM_001164697	19144	Mm.3944	NM_011177	ENSMUSG00000050063	Klk6	AI849898|BSP|Bssp|Klk29|MSP|Prss18|Prss9|neurosin	kallikrein related-peptidase 6	protein-coding
mm_107356.1	chr12	32830140	32830150	+	1	NA	intron (NM_021524, intron 1 of 10)	intron (NM_021524, intron 1 of 10)	6029	NR_045032	100504486	Mm.440246	NR_045032		Gdap10	Gdap-ps	ganglioside-induced differentiation-associated-protein 10	ncRNA
mm_29871.1	chr3	130730376	130730386	-	1	NA	promoter-TSS (NM_001287581)	promoter-TSS (NM_001287581)	17	NM_001005859	68436	Mm.140568	NM_026724	ENSMUSG00000062006	Rpl34	1100001I22Rik	ribosomal protein L34	protein-coding
mm_39740.1	chr5	29538090	29538095	+	1	NA	non-coding (NR_102704, exon 1 of 1)	non-coding (NR_102704, exon 1 of 1)	143	NR_102704	619355	Mm.426744	NR_102704		Gm6083	ENSMUSG00000078182	developmental pluripotency associated 5 pseudogene	pseudo
mm_70238.1	chr8	3353418	3353468	+	1	NA	promoter-TSS (NM_001033378)	promoter-TSS (NM_001033378)	28	NM_001033378	319493	Mm.234565	NM_001033378	ENSMUSG00000074497	A430078G23Rik	-	RIKEN cDNA A430078G23 gene	protein-coding
mm_153093.1	chr19	32673502	32673518	-	1	NA	3' UTR (NM_026487, exon 10 of 10)	3' UTR (NM_026487, exon 10 of 10)	38788	NM_026487	67979	Mm.27123	NM_026487	ENSMUSG00000013662	Atad1	4921525H23Rik|AW107648|Thorase	ATPase family, AAA domain containing 1	protein-coding
mm_14679.1	chr2	139677178	139677194	+	1	NA	promoter-TSS (NM_001276489)	promoter-TSS (NM_001276489)	-992	NM_001276489	319909	Mm.41113	NM_001126490	ENSMUSG00000074766	Ism1	5430433G21Rik|Ism	isthmin 1, angiogenesis inhibitor	protein-coding
mm_130503.1	chr15	98831499	98831509	-	1	NA	promoter-TSS (NM_016781)	promoter-TSS (NM_016781)	4	NM_016781	19082	Mm.6670	NM_016781	ENSMUSG00000067713	Prkag1	AA571379|BB036179|Prkaac	protein kinase, AMP-activated, gamma 1 non-catalytic subunit	protein-coding
mm_168634.1	chr1	183204956	183204956	-	1	NA	intron (NM_026866, intron 1 of 9)	intron (NM_026866, intron 1 of 9)	16573	NM_001278218	68897	Mm.327216	NM_026866	ENSMUSG00000030768	Disp1	1190008H24Rik|DispA	dispatched RND transporter family member 1	protein-coding
mm_32852.1	chr4	117998628	117998636	+	1	NA	intron (NM_009176, intron 5 of 11)	intron (NM_009176, intron 5 of 11)	-68869	NM_001284192	11876	Mm.56897	NM_009711	ENSMUSG00000028539	Artn	neublastin	artemin	protein-coding
mm_96388.1	chr11	67248683	67248693	+	1	NA	exon (NM_010855, exon 16 of 40)	exon (NM_010855, exon 16 of 40)	10876	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_93968.1	chr10	127289000	127289035	-	1	NA	promoter-TSS (NM_001347171)	promoter-TSS (NM_001347171)	1	NM_001347171	110962	Mm.372826	NM_033072	ENSMUSG00000025409	Mbd6	D10Wsu93e	methyl-CpG binding domain protein 6	protein-coding
mm_120936.1	chr14	76507422	76507443	+	1	NA	3' UTR (NM_207652, exon 3 of 3)	3' UTR (NM_207652, exon 3 of 3)	2922	NM_009366	21807	Mm.153272	NM_009366	ENSMUSG00000022010	Tsc22d1	AA589566|AW105905|Egr5|TSC-22|Tgfb1i4|Tsc|Tsc22	TSC22 domain family, member 1	protein-coding
mm_139404.1	chr17	52457175	52457177	+	1	NA	Intergenic	B3A|SINE|B2	-145533	NM_001031811	211468	Mm.399068	NM_001031811	ENSMUSG00000035580	Kcnh8	C130090D05Rik|ELK|ELK1|ELK3|Kv12.1	potassium voltage-gated channel, subfamily H (eag-related), member 8	protein-coding
mm_141618.1	chr17	32872247	32872251	-	1	NA	Intergenic	RLTR19-int|LTR|ERVK	19354	NM_207245	240066	Mm.26636	NM_207245	ENSMUSG00000095325	Zfp870	AI173952	zinc finger protein 870	protein-coding
mm_123300.1	chr14	61636073	61636120	-	1	NA	intron (NR_028264, intron 2 of 6)	intron (NR_028264, intron 2 of 6)	-3986	NR_029733	387174		NR_029733	ENSMUSG00000093007	Mir15a	Mirn15a|mir-15a|mmu-mir-15a	microRNA 15a	ncRNA
mm_146078.1	chr18	70581061	70581065	+	1	NA	intron (NM_010773, intron 2 of 6)	B1_Mus1|SINE|Alu	12771	NM_010773	17191	Mm.322	NM_010773	ENSMUSG00000024513	Mbd2	MBD2a	methyl-CpG binding domain protein 2	protein-coding
mm_86547.1	chr10	9901291	9901303	+	1	NA	promoter-TSS (NM_001081344)	promoter-TSS (NM_001081344)	-257	NM_001081344	78808	Mm.331751	NM_030191	ENSMUSG00000019790	Stxbp5	0710001E20Rik|4930565N16Rik|AW742610|LGL3|mKIAA1006	syntaxin binding protein 5 (tomosyn)	protein-coding
mm_153181.1	chr19	34495107	34495140	-	1	NA	exon (NM_021460, exon 9 of 10)	exon (NM_021460, exon 9 of 10)	-19988	NM_009890	12642	Mm.30824	NM_009890	ENSMUSG00000050370	Ch25h	AI462618|m25OH	cholesterol 25-hydroxylase	protein-coding
mm_39707.1	chr5	27262257	27262261	+	1	NA	5' UTR (NM_001136060, exon 1 of 26)	5' UTR (NM_001136060, exon 1 of 26)	324	NM_001136060	13483	Mm.42078	NM_010075	ENSMUSG00000061576	Dpp6	B930011P16Rik|D5Buc3|D5Buc4|D5Buc5|DPP VI|Dpp-6|Gm1377|In(5)6H-p|Peplb|Rw	dipeptidylpeptidase 6	protein-coding
mm_17560.1	chr2	30178589	30178600	-	1	NA	promoter-TSS (NM_172660)	promoter-TSS (NM_172660)	-135	NM_172660	227695	Mm.4449	NM_172660	ENSMUSG00000039660	Spout1	9930028P05|AL033358|D2Wsu81e	SPOUT domain containing methyltransferase 1	protein-coding
mm_93671.1	chr10	117710194	117710205	-	1	NA	intron (NM_001288586, intron 1 of 10)	CpG-1528	559	NM_010786	17246	Mm.22670	NM_010786	ENSMUSG00000020184	Mdm2	1700007J15Rik|AA415488|Mdm-2	transformed mouse 3T3 cell double minute 2	protein-coding
mm_166834.1	chr7	19271552	19271558	-	1	NA	non-coding (NR_104069, exon 1 of 11)	non-coding (NR_104069, exon 1 of 11)	299	NM_001282021	22323	Mm.9684	NM_009499	ENSMUSG00000030403	Vasp	-	vasodilator-stimulated phosphoprotein	protein-coding
mm_152049.1	chr19	6234954	6234981	-	1	NA	5' UTR (NM_198168, exon 2 of 14)	5' UTR (NM_198168, exon 2 of 14)	873	NM_198168	225849	Mm.118076	NM_198168	ENSMUSG00000024777	Ppp2r5b	B'beta|BC026670	protein phosphatase 2, regulatory subunit B', beta	protein-coding
mm_20207.1	chr2	125505938	125505944	-	1	NA	intron (NM_007993, intron 1 of 65)	CpG	497	NM_007993	14118	Mm.271644	NM_007993	ENSMUSG00000027204	Fbn1	AI536462|B430209H23|Fib-1|Tsk	fibrillin 1	protein-coding
mm_11193.1	chr2	29122785	29122789	+	1	NA	Intergenic	Lx8|LINE|L1	-2205	NM_198033	269254	Mm.41867	NM_198033	ENSMUSG00000043535	Setx	A130090N03|A930037J23Rik|AOA2|AW060766|Als4|SCAR1|Sen1|mKIAA0625	senataxin	protein-coding
mm_83424.1	chr9	44974346	44974359	-	1	NA	exon (NM_009850, exon 3 of 7)	exon (NM_009850, exon 3 of 7)	6079	NM_009850	12502	Mm.335106	NM_009850	ENSMUSG00000002033	Cd3g	Ctg-3|Ctg3|T3g	CD3 antigen, gamma polypeptide	protein-coding
mm_169423.1	chr14	53259587	53259589	+	1	NA	Intergenic	Intergenic	-763893	NM_001170918	57269	Mm.88822	NM_020512	ENSMUSG00000059887	Olfr1507	MOR244-1|Mor28|Or28	olfactory receptor 1507	protein-coding
mm_160176.1	chr7	45526335	45526335	+	1	NA	promoter-TSS (NM_148927)	promoter-TSS (NM_148927)	5	NM_148927	69217	Mm.274158	NM_148927	ENSMUSG00000040428	Plekha4	2410005C22Rik|C88169|Pepp1	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 4	protein-coding
mm_90093.1	chr10	116962429	116962432	+	1	NA	non-coding (NR_038026, exon 3 of 3)	non-coding (NR_038026, exon 3 of 3)	-2310	NR_027847	103175	Mm.27138	NR_027846	ENSMUSG00000031294	D630029K05Rik	AI314111|AI875589	RIKEN cDNA D630029K05 gene	ncRNA
mm_155958.1	chrX	105499769	105499773	+	1	NA	promoter-TSS (NM_173436)	promoter-TSS (NM_173436)	-1	NM_173436	245566	Mm.250428	NM_173436	ENSMUSG00000090132	Cypt2	Ckt1|Cypt2-ps	cysteine-rich perinuclear theca 2	protein-coding
mm_60359.1	chr7	44428818	44428837	+	1	NA	Intergenic	Intergenic	-13660	NM_198250	272381	Mm.44173	NM_198250	ENSMUSG00000047085	Lrrc4b	A830007M12|Lrig4	leucine rich repeat containing 4B	protein-coding
mm_104724.1	chr11	98203159	98203173	-	1	NA	promoter-TSS (NM_026952)	promoter-TSS (NM_026952)	-139	NM_001109628	69131	Mm.260516	NM_026952	ENSMUSG00000003119	Cdk12	1810022J16Rik|AI646528|Crk7|Crkrs|D11Ertd752e|Pksc	cyclin-dependent kinase 12	protein-coding
mm_168141.1	chr10	3241980	3242009	-	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	25777	NM_001204916	670558	Mm.398582	NM_001204916	ENSMUSG00000091618	H60c	4632413I24Rik|Gm9491	histocompatibility 60c	protein-coding
mm_58079.1	chr6	136941525	136941538	-	1	NA	promoter-TSS (NM_001301305)	promoter-TSS (NM_001301305)	-28	NM_001301305	11857	Mm.2241	NM_007486	ENSMUSG00000030220	Arhgdib	D4|Gdid4|Ly-GDI	Rho, GDP dissociation inhibitor (GDI) beta	protein-coding
mm_100767.1	chr11	4594858	4594875	-	1	NA	promoter-TSS (NM_028860)	promoter-TSS (NM_028860)	-51	NM_028860	74302	Mm.425669	NM_028860	ENSMUSG00000034354	Mtmr3	1700092A20Rik|AI255150|AW557713|FYVE-DSP1|ZFYVE10|mKIAA0371	myotubularin related protein 3	protein-coding
mm_50959.1	chr6	58906545	58906579	+	1	NA	exon (NM_021432, exon 1 of 1)	exon (NM_021432, exon 1 of 1)	564	NM_021432	58243	Mm.389747	NM_021432	ENSMUSG00000055430	Nap1l5	1110020M21Rik	nucleosome assembly protein 1-like 5	protein-coding
mm_46574.1	chr5	107289497	107289525	-	1	NA	promoter-TSS (NM_011578)	promoter-TSS (NM_011578)	84	NM_011578	21814	Mm.200775	NM_011578	ENSMUSG00000029287	Tgfbr3	1110036H20Rik|AU015626|AW215636|TBRIII	transforming growth factor, beta receptor III	protein-coding
mm_8587.1	chr1	156005691	156005709	-	1	NA	3' UTR (NM_144791, exon 7 of 7)	3' UTR (NM_144791, exon 7 of 7)	29117	NM_001160019	208263	Mm.211654	NM_144791	ENSMUSG00000026466	Tor1aip1	LAP1|Lap1B	torsin A interacting protein 1	protein-coding
mm_4738.1	chr1	181842552	181842565	+	1	NA	promoter-TSS (NM_133815)	promoter-TSS (NM_133815)	-157	NM_133815	98386	Mm.4538	NM_133815	ENSMUSG00000004880	Lbr	AI505894|ic	lamin B receptor	protein-coding
mm_68502.1	chr7	111080932	111080946	-	1	NA	exon (NM_013507, exon 3 of 22)	exon (NM_013507, exon 3 of 22)	2091	NM_001040131	13690	Mm.185453	NM_013507	ENSMUSG00000005610	Eif4g2	DAP-5|E130105L11Rik|Nat1|Natm1|p97	eukaryotic translation initiation factor 4, gamma 2	protein-coding
mm_91161.1	chr10	20589519	20589534	-	1	NA	intron (NM_013875, intron 2 of 12)	intron (NM_013875, intron 2 of 12)	-41198	NM_001347366	29863	Mm.425617	NM_013875	ENSMUSG00000019990	Pde7b	-	phosphodiesterase 7B	protein-coding
mm_2381.1	chr1	93478509	93478533	+	1	NA	promoter-TSS (NM_010891)	promoter-TSS (NM_010891)	396	NM_133808	110611	Mm.30012	NM_133808	ENSMUSG00000034088	Hdlbp	1110005P14Rik|AA960365|AI118566|D1Ertd101e	high density lipoprotein (HDL) binding protein	protein-coding
mm_166084.1	chr4	138834896	138834904	+	1	NA	non-coding (NR_002926, exon 5 of 5)	non-coding (NR_002926, exon 5 of 5)	3024	NM_001082531	18780	Mm.4675	NM_011108	ENSMUSG00000058908	Pla2g2a	EF|Mom1|Pla2|sPLA2|sPla2-IIA	phospholipase A2, group IIA (platelets, synovial fluid)	protein-coding
mm_145567.1	chr18	60812558	60812566	+	1	NA	TTS (NM_010545)	TTS (NM_010545)	486	NR_039567	100628611		NR_039567	ENSMUSG00000093327	Mir5107	mir-5107|mmu-mir-5107|mu-mir-5107	microRNA 5107	ncRNA
mm_167780.1	chr9	115186200	115186230	+	1	NA	intron (NM_148958, intron 4 of 9)	intron (NM_148958, intron 4 of 9)	95855	NR_029430	111186	Mm.484753	NR_029430		Stmn1-rs1	Lag-rs1|Lap18-rs1	stathmin 1, related sequence 1	pseudo
mm_54897.1	chr6	47454610	47454627	-	1	NA	intron (NM_012042, intron 1 of 21)	CpG	294	NM_012042	26965	Mm.87611	NM_012042	ENSMUSG00000029686	Cul1	-	cullin 1	protein-coding
mm_68726.1	chr7	120202008	120202029	-	1	NA	promoter-TSS (NM_016669)	promoter-TSS (NM_016669)	-30	NM_016669	12971	Mm.9114	NM_016669	ENSMUSG00000030905	Crym	-	crystallin, mu	protein-coding
mm_71467.1	chr8	46534686	46534696	+	1	NA	3' UTR (NM_007981, exon 21 of 21)	3' UTR (NM_007981, exon 21 of 21)	-17378	NM_027973	71876	Mm.22108	NM_027973	ENSMUSG00000031629	Cenpu	1700029A22Rik|Mlf1ip	centromere protein U	protein-coding
mm_86617.1	chr10	13965780	13965839	+	1	NA	promoter-TSS (NM_010437)	promoter-TSS (NM_010437)	-570	NM_010437	15273	Mm.42157	NM_010437	ENSMUSG00000015501	Hivep2	Gm20114|MIBP1|Schnurri-2|Shn-2	human immunodeficiency virus type I enhancer binding protein 2	protein-coding
mm_127265.1	chr15	99717579	99717594	+	1	NA	promoter-TSS (NM_010271)	promoter-TSS (NM_010271)	-7	NM_010271	14555	Mm.252391	NM_010271	ENSMUSG00000023019	Gpd1	AI747587|Gdc-1|Gdc1|mKIAA4010	glycerol-3-phosphate dehydrogenase 1 (soluble)	protein-coding
mm_118804.1	chr14	25378088	25378097	+	1	NA	Intergenic	Intergenic	-81093	NM_001310666	328365	Mm.227484	NM_183208	ENSMUSG00000007817	Zmiz1	BC065120|E330020C23|ENSMUSG00000072684|Gm10397|I920194n01|Rai17|Zimp10	zinc finger, MIZ-type containing 1	protein-coding
mm_145763.1	chr18	64921106	64921146	+	1	NA	intron (NM_001114386, intron 1 of 30)	intron (NM_001114386, intron 1 of 30)	33370	NM_001114386	83814	Mm.98668	NM_031881	ENSMUSG00000024589	Nedd4l	1300012C07Rik|Nedd4-2|Nedd4b	neural precursor cell expressed, developmentally down-regulated gene 4-like	protein-coding
mm_29813.1	chr3	127895509	127895513	-	1	NA	intron (NM_027482, intron 1 of 1)	AT_rich|Low_complexity|Low_complexity	812	NM_027482	70617	Mm.317049	NM_027482	ENSMUSG00000050549	5730508B09Rik	2700063A17Rik|C80506	RIKEN cDNA 5730508B09 gene	protein-coding
mm_143697.1	chr17	80480436	80480462	-	1	NA	promoter-TSS (NM_009231)	promoter-TSS (NM_009231)	4	NM_009231	20662	Mm.60975	NM_009231	ENSMUSG00000024241	Sos1	4430401P03Rik|9630010N06|AI449023	son of sevenless homolog 1 (Drosophila)	protein-coding
mm_25757.1	chr3	123508551	123508568	+	1	NA	promoter-TSS (NR_028574)	promoter-TSS (NR_028574)	-223	NR_028574	69895	Mm.260791	NR_028574	ENSMUSG00000104960	Snhg8	1110065M07Rik|2010109N14Rik	small nucleolar RNA host gene 8	ncRNA
mm_2414.1	chr1	93996257	93996280	+	1	NA	intron (NM_001039219, intron 4 of 7)	intron (NM_001039219, intron 4 of 7)	5759	NM_001039219	619597	Mm.417228	NM_001039219	ENSMUSG00000073608	Gm6086	EG619597|Gm219	predicted gene 6086	protein-coding
mm_75534.1	chr8	57320403	57320421	-	1	NA	promoter-TSS (NM_010402)	promoter-TSS (NM_010402)	447	NR_110474	102636514		NR_110474	ENSMUSG00000100510	Uph	-	upperhand	ncRNA
mm_68857.1	chr7	126377388	126377399	-	1	NA	non-coding (NR_045537, exon 1 of 13)	non-coding (NR_045537, exon 1 of 13)	541	NM_023712	73658	Mm.11112	NM_023712	ENSMUSG00000030741	Spns1	2210013K02Rik|Spin1|Spinl	spinster homolog 1	protein-coding
mm_137169.1	chr17	23812501	23812522	+	1	NA	exon (NM_175229, exon 9 of 14)	exon (NM_175229, exon 9 of 14)	9324	NM_175229	75956	Mm.5222	NM_175229	ENSMUSG00000039218	Srrm2	5033413A03Rik|AA410130|SRm300|mKIAA0324	serine/arginine repetitive matrix 2	protein-coding
mm_144274.1	chr18	11657353	11657486	+	1	NA	promoter-TSS (NM_001081223)	promoter-TSS (NM_001081223)	70	NM_001081223	225182	Mm.154275	NM_175458	ENSMUSG00000041238	Rbbp8	9930104E21Rik|CtIP|RBBP-8|RIM|SAE2	retinoblastoma binding protein 8	protein-coding
mm_168684.1	chr11	95923417	95923418	-	1	NA	Intergenic	ERVB7_1-LTR_MM|LTR|ERVK	-8546	NM_008081	14422	Mm.340702	NM_008081	ENSMUSG00000013418	B4galnt2	AI593864|Dlb-1|Dlb1|Galg2|Galgt2|Ggm3|Igf2bp1	beta-1,4-N-acetyl-galactosaminyl transferase 2	protein-coding
mm_129837.1	chr15	83154392	83154402	-	1	NA	3' UTR (NM_029787, exon 9 of 9)	3' UTR (NM_029787, exon 9 of 9)	4752	NR_004432	104307	Mm.471434	NR_004432	ENSMUSG00000065176	Rnu12	-	RNA U12, small nuclear	snRNA
mm_644.1	chr1	40405687	40405687	+	1	NA	Intergenic	Intergenic	-23883	NM_001294171	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_110413.1	chr12	46697000	46697024	-	1	NA	3' UTR (NM_021361, exon 5 of 5)	3' UTR (NM_021361, exon 5 of 5)	121763	NM_021361	664883	Mm.247195	NM_021361	ENSMUSG00000021047	Nova1	9430099M15Rik|G630039L02|Nova-1	neuro-oncological ventral antigen 1	protein-coding
mm_3832.1	chr1	159926234	159926252	+	1	NA	Intergenic	Intergenic	-118137	NR_028111	67647	Mm.171518	NM_001024470	ENSMUSG00000090394	4930523C07Rik	-	RIKEN cDNA 4930523C07 gene	protein-coding
mm_166292.1	chr5	102796319	102796322	+	1	NA	intron (NM_001286468, intron 1 of 7)	intron (NM_001286468, intron 1 of 7)	27510	NM_001286468	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding
mm_25053.1	chr3	98382539	98382553	+	1	NA	promoter-TSS (NM_172863)	promoter-TSS (NM_172863)	65	NM_172863	242109	Mm.358911	NM_172863	ENSMUSG00000050064	Zfp697	9430053K19|AI467503|Znf697	zinc finger protein 697	protein-coding
mm_87483.1	chr10	51493935	51493953	+	1	NA	intron (NM_001291894, intron 5 of 8)	MIR3|SINE|MIR	3046	NM_013532	14728	Mm.34408	NM_013532	ENSMUSG00000062593	Lilrb4a	CD85K|Gp49b|HM18|ILT3|LIR-5|Lilrb4|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4A	protein-coding
mm_111338.1	chr12	86884402	86884413	-	1	NA	5' UTR (NM_145836, exon 1 of 1)	5' UTR (NM_145836, exon 1 of 1)	407	NM_145836	238330	Mm.248358	NM_145836	ENSMUSG00000034168	Irf2bpl	6430527G18Rik|Eap1	interferon regulatory factor 2 binding protein-like	protein-coding
mm_42469.1	chr5	115454178	115454188	+	1	NA	TTS (NM_008629)	TTS (NM_008629)	-12083	NM_011107	18778	Mm.20190	NM_011107	ENSMUSG00000029522	Pla2g1b	Pla2a|sPLA2IB	phospholipase A2, group IB, pancreas	protein-coding
mm_18586.1	chr2	66410084	66410134	-	1	NA	intron (NM_018733, intron 1 of 26)	intron (NM_018733, intron 1 of 26)	30728	NM_018733	20265	Mm.439704	NM_018733	ENSMUSG00000064329	Scn1a	B230332M13|Nav1.1	sodium channel, voltage-gated, type I, alpha	protein-coding
mm_123218.1	chr14	59441310	59441310	-	1	NA	promoter-TSS (NM_001320721)	promoter-TSS (NM_001320721)	329	NM_026908	69008	Mm.179091	NM_026908	ENSMUSG00000021981	Cab39l	1500031K13Rik|2810425O13Rik|4930520C08Rik|AA589432|MO2L	calcium binding protein 39-like	protein-coding
mm_9482.1	chr1	173437242	173437249	-	1	NA	intron (NM_001013779, intron 2 of 8)	intron (NM_001013779, intron 2 of 8)	16641	NM_001013779	383619	Mm.131453	NM_001013779	ENSMUSG00000037860	Aim2	Gm1313|Ifi210	absent in melanoma 2	protein-coding
mm_126009.1	chr15	76576353	76576380	+	1	NA	promoter-TSS (NM_172960)	promoter-TSS (NM_172960)	7	NR_073123	268822	Mm.181624	NM_172960	ENSMUSG00000022550	Adck5	A230108P17	aarF domain containing kinase 5	protein-coding
mm_122866.1	chr14	54913038	54913042	-	1	NA	promoter-TSS (NM_021551)	promoter-TSS (NM_021551)	92	NM_021551	59049	Mm.27435	NM_021551	ENSMUSG00000022199	Slc22a17	1700094C23Rik|24p3R|AU041908|AW555662|BOIT|Boct	solute carrier family 22 (organic cation transporter), member 17	protein-coding
mm_139856.1	chr17	69969218	69969234	+	1	NA	5' UTR (NM_001347412, exon 1 of 14)	5' UTR (NM_001347412, exon 1 of 14)	153	NM_001347411	224997	Mm.311840	NM_027712	ENSMUSG00000003279	Dlgap1	4933422O14Rik|9630002F18|AI845682|AI848168|BB075781|D17Bwg0511e|GKAP/SAPAP|GKPA/SAPAP|Gkap|Sapap1|mKIAA4162	discs, large (Drosophila) homolog-associated protein 1	protein-coding
mm_140651.1	chr17	12692037	12692044	-	1	NA	exon (NM_010515, exon 40 of 48)	exon (NM_010515, exon 40 of 48)	-16202	NM_009202	20517	Mm.594	NM_009202	ENSMUSG00000023829	Slc22a1	Lx1|Oct1|Orct|Orct1	solute carrier family 22 (organic cation transporter), member 1	protein-coding
mm_169061.1	chr13	25053008	25053023	+	1	NA	Intergenic	MTEb|LTR|ERVL-MaLR	-2989	NM_001195617	195208	Mm.284719	NM_177577	ENSMUSG00000035910	Dcdc2a	AW492955|Dcdc2|RU2	doublecortin domain containing 2a	protein-coding
mm_54569.1	chr6	38002999	38003000	-	1	NA	intron (NM_177200, intron 14 of 15)	Lx9|LINE|L1	43997	NM_177200	320590	Mm.197449	NM_177200	ENSMUSG00000029830	Svopl	9430071P14Rik	SV2 related protein homolog (rat)-like	protein-coding
mm_41594.1	chr5	95956917	95956933	+	1	NA	promoter-TSS (NM_018866)	promoter-TSS (NM_018866)	-14	NM_018866	55985	Mm.10116	NM_018866	ENSMUSG00000023078	Cxcl13	4631412M08Rik|ANGIE2|Angie|BCA-1|BLC|BLR1L|Scyb13	chemokine (C-X-C motif) ligand 13	protein-coding
mm_51177.1	chr6	70726730	70726732	+	1	NA	Intergenic	Intergenic	65444	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_40491.1	chr5	57717228	57717237	+	1	NA	promoter-TSS (NM_001310606)	promoter-TSS (NM_001310606)	687	NR_015588	319216	Mm.332387	NR_015588	ENSMUSG00000097216	4932441J04Rik	-	RIKEN cDNA 4932441J04 gene	ncRNA
mm_82414.1	chr9	14900796	14900843	-	1	NA	exon (NM_176807, exon 4 of 5)	exon (NM_176807, exon 4 of 5)	3132	NM_176807	64931	Mm.86738	NM_022888	ENSMUSG00000031933	Izumo1r	0910001L11Rik|C86255|Folbp3|Folr4|Juno	IZUMO1 receptor, JUNO	protein-coding
mm_46597.1	chr5	107837476	107837491	-	1	NA	intron (NM_007964, intron 2 of 17)	intron (NM_007964, intron 2 of 17)	7321	NM_001276397	73318	Mm.441500	NM_028502	ENSMUSG00000063447	Ube2d2b	1700013N18Rik	ubiquitin-conjugating enzyme E2D 2B	protein-coding
mm_86161.1	chr9	118406113	118406160	-	1	NA	Intergenic	RLTR11A2|LTR|ERVK	-23703	NR_040716	71196	Mm.73218	NR_040716	ENSMUSG00000111843	4933432G23Rik	-	RIKEN cDNA 4933432G23 gene	ncRNA
mm_43521.1	chr5	137151068	137151092	+	1	NA	Intergenic	Intergenic	-34873	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_104536.1	chr11	96347347	96347359	-	1	NA	3' UTR (NM_010458, exon 2 of 2)	3' UTR (NM_010458, exon 2 of 2)	3584	NM_010458	15410	Mm.342481	NM_010458	ENSMUSG00000048763	Hoxb3	Hox-2.7	homeobox B3	protein-coding
mm_158481.1	chrX	142196955	142196960	-	1	NA	promoter-TSS (NM_001007576)	promoter-TSS (NM_001007576)	-21	NM_001007576	245650	Mm.208511	NM_001007576	ENSMUSG00000042282	Gucy2f	A930002I06|GC-F|GC2	guanylate cyclase 2f	protein-coding
mm_106924.1	chr12	8342933	8342955	+	1	NA	3' UTR (NM_021429, exon 7 of 7)	3' UTR (NM_021429, exon 7 of 7)	29511	NM_021429	58240	Mm.309954	NM_021429	ENSMUSG00000020605	Hs1bp3	-	HCLS1 binding protein 3	protein-coding
mm_81372.1	chr9	108854070	108854084	+	1	NA	promoter-TSS (NM_134420)	promoter-TSS (NM_134420)	34	NM_134420	171429	Mm.45201	NM_134420	ENSMUSG00000023259	Slc26a6	B930010B04Rik|CFEX|Pat-1|Pat1	solute carrier family 26, member 6	protein-coding
mm_16498.1	chr2	181187780	181187808	+	1	NA	intron (NM_025598, intron 2 of 4)	CpG-8989	451	NM_025598	66496	Mm.213943	NM_025598	ENSMUSG00000016344	Ppdpf	0610012G23Rik|2610317A05Rik|2700038C09Rik|3110053G12Rik	pancreatic progenitor cell differentiation and proliferation factor	protein-coding
mm_18974.1	chr2	76841217	76841227	-	1	NA	exon (NM_011652, exon 150 of 313)	exon (NM_011652, exon 150 of 313)	141325	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_31826.1	chr4	69853930	69853941	+	1	NA	Intergenic	Intergenic	556500	NM_001313762	214444	Mm.370777	NM_145990	ENSMUSG00000039298	Cdk5rap2	2900018K03Rik|an|mKIAA1633	CDK5 regulatory subunit associated protein 2	protein-coding
mm_148333.1	chr18	84099347	84099385	-	1	NA	Intergenic	Intergenic	11208	NM_146090	225791	Mm.147052	NM_146090	ENSMUSG00000049090	Zadh2	C530046K17Rik|PTGR-3|Pthr3	zinc binding alcohol dehydrogenase, domain containing 2	protein-coding
mm_85111.1	chr9	95407185	95407191	-	1	NA	promoter-TSS (NM_018763)	promoter-TSS (NM_018763)	82	NM_018763	54371	Mm.212446	NM_018763	ENSMUSG00000033350	Chst2	AI428561|AW121776|C130041E03Rik|Chts2|GST-2|GlcNAc6ST|Gn6st	carbohydrate sulfotransferase 2	protein-coding
mm_121066.1	chr14	95578683	95578690	+	1	NA	Intergenic	Intergenic	-302580	NM_025733	66732	Mm.75060	NM_025733	ENSMUSG00000034689	4921530L21Rik	-	RIKEN cDNA 4921530L21 gene	protein-coding
mm_38872.1	chr4	149676044	149676065	-	1	NA	promoter-TSS (NM_001164051)	promoter-TSS (NM_001164051)	35	NM_001164051	18707	Mm.229108	NM_008840	ENSMUSG00000039936	Pik3cd	2410099E07Rik|2610208K16Rik|AW545373|p110delta	phosphatidylinositol 3-kinase catalytic delta polypeptide	protein-coding
mm_102054.1	chr11	52168118	52168137	-	1	NA	Intergenic	CpG	-10220	NR_034155	257871	Mm.253576	NR_034155		Olfr1372-ps1	GA_x5J8B7TR6JS-3-632|MOR256-54P|NP_TR6JSE50FPA	olfactory receptor 1372, pseudogene 1	pseudo
mm_143950.1	chr17	86810992	86810994	-	1	NA	intron (NM_010137, intron 6 of 15)	intron (NM_010137, intron 6 of 15)	57129	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_56487.1	chr6	99173328	99173365	-	1	NA	intron (NM_001347345, intron 4 of 19)	intron (NM_001347345, intron 4 of 19)	93169	NM_001197321	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_27416.1	chr3	51400756	51400757	-	1	NA	Intergenic	Intergenic	-4209	NR_028121	67749	Mm.273339	NM_026358	ENSMUSG00000037161	Mgarp	4930583H14Rik|AI195347|CESP-1|HUMMR|Osap|Qsap	mitochondria localized glutamic acid rich protein	protein-coding
mm_73862.1	chr8	118309404	118309424	+	1	NA	intron (NM_019707, intron 1 of 13)	RLTR20C1_MM|LTR|ERVK	25803	NM_019707	12554	Mm.334841	NM_019707	ENSMUSG00000031841	Cdh13	4932416G01Rik|Cdht|Tcad	cadherin 13	protein-coding
mm_93788.1	chr10	120628154	120628169	-	1	NA	Intergenic	Intergenic	-137571	NR_038000	70874	Mm.427286	NR_038000	ENSMUSG00000044544	4921513I03Rik	-	RIKEN cDNA 4921513I03 gene	ncRNA
mm_34954.1	chr4	155992401	155992413	+	1	NA	promoter-TSS (NM_011341)	promoter-TSS (NM_011341)	271	NM_080445	117592	Mm.440185	NM_080445	ENSMUSG00000050796	B3galt6	BB129894|GalTII	UDP-Gal:betaGal beta 1,3-galactosyltransferase, polypeptide 6	protein-coding
mm_91899.1	chr10	60162373	60162382	-	1	NA	Intergenic	LTRIS2|LTR|ERV1	35601	NR_105871	102465546		NR_105871	ENSMUSG00000105468	Mir6906	mmu-mir-6906	microRNA 6906	ncRNA
mm_3035.1	chr1	134037464	134037484	+	1	NA	promoter-TSS (NM_021355)	promoter-TSS (NM_021355)	-41	NM_021355	14264	Mm.287146	NM_021355	ENSMUSG00000041559	Fmod	AI131919|AU041740|SLRR2E	fibromodulin	protein-coding
mm_169314.1	chr14	10608901	10608901	+	1	NA	intron (NM_010210, intron 3 of 8)	L1Md_T|LINE|L1	-129652	NR_131139	547334	Mm.434606	NR_131139	ENSMUSG00000089833	Fhitos	Gm16542	fragile histidine triad gene, opposite strand	ncRNA
mm_13647.1	chr2	114054330	114054340	+	1	NA	promoter-TSS (NR_028422)	promoter-TSS (NR_028422)	-61	NR_028422	100303644	Mm.330469	NR_028422	ENSMUSG00000092397	C130080G10Rik	-	RIKEN cDNA C130080G10 gene	ncRNA
mm_17347.1	chr2	26604582	26604625	-	1	NA	promoter-TSS (NM_026212)	promoter-TSS (NM_026212)	-186	NM_026212	67512	Mm.24244	NM_026212	ENSMUSG00000026922	Agpat2	2510002J07Rik|AV000834|BSCL|BSCL1|LPAAB|LPAAT-beta	1-acylglycerol-3-phosphate O-acyltransferase 2 (lysophosphatidic acid acyltransferase, beta)	protein-coding
mm_148824.1	chr19	6306627	6306638	+	1	NA	5' UTR (NM_001033342, exon 1 of 37)	5' UTR (NM_001033342, exon 1 of 37)	175	NM_001033342	240505	Mm.329622	NM_001033342	ENSMUSG00000024769	Cdc42bpg	BC046418|MRCKgamma	CDC42 binding protein kinase gamma (DMPK-like)	protein-coding
mm_133277.1	chr16	77417607	77417645	+	1	NA	intron (NR_015543, intron 2 of 4)	intron (NR_015543, intron 2 of 4)	88298	NR_015543	77994	Mm.394688	NR_015543	ENSMUSG00000090386	Mir99ahg	2810055G20Rik|D730043B02Rik	Mir99a and Mirlet7c-1 host gene (non-protein coding)	ncRNA
mm_42841.1	chr5	122112181	122112225	+	1	NA	intron (NM_001289809, intron 9 of 11)	intron (NM_001289809, intron 9 of 11)	11223	NM_010861	17906	Mm.1529	NM_010861	ENSMUSG00000013936	Myl2	MLC-2|MLC-2s/v|MLC-2v|Mlc2v|Mylpc	myosin, light polypeptide 2, regulatory, cardiac, slow	protein-coding
mm_84168.1	chr9	59941005	59941013	-	1	NA	Intergenic	Intergenic	9070	NM_013708	23958	Mm.103641	NM_013708	ENSMUSG00000032292	Nr2e3	A930035N01Rik|PNR|RNR|rd7	nuclear receptor subfamily 2, group E, member 3	protein-coding
mm_14988.1	chr2	152236735	152236738	+	1	NA	intron (NM_007788, intron 1 of 12)	intron (NM_007788, intron 1 of 12)	9896	NM_007788	12995	Mm.23692	NM_007788	ENSMUSG00000074698	Csnk2a1	Csnk2a1-rs4	casein kinase 2, alpha 1 polypeptide	protein-coding
mm_126917.1	chr15	91641894	91641906	+	1	NA	Intergenic	Intergenic	-31324	NM_025730	66725	Mm.37558	NM_025730	ENSMUSG00000036273	Lrrk2	4921513O20Rik|9330188B09Rik|AW561911|D630001M17Rik|Gm927|cI-46	leucine-rich repeat kinase 2	protein-coding
mm_48560.1	chr5	143165677	143165715	-	1	NA	promoter-TSS (NR_040426)	promoter-TSS (NR_040426)	55	NR_040426	100042605	Mm.332809	NR_040424	ENSMUSG00000104529	Rbakdn	Gm3925	RB-associated KRAB zinc finger downstream neighbor (non-protein coding)	ncRNA
mm_21362.1	chr2	157130739	157130746	-	1	NA	intron (NM_018851, intron 1 of 15)	(TCCC)n|Simple_repeat|Simple_repeat	4480	NM_001139520	56045	Mm.248478	NM_018851	ENSMUSG00000027639	Samhd1	E330031J07Rik|Mg11	SAM domain and HD domain, 1	protein-coding
mm_125354.1	chr15	39391827	39391842	+	1	NA	intron (NM_001256382, intron 3 of 26)	intron (NM_001256382, intron 3 of 26)	193548	NM_053271	116838	Mm.309296	NM_053271	ENSMUSG00000037386	Rims2	2810036I15Rik|AW048769|RIM2|Rab3ip2|Rim2(+40A)|Rim2(+44A)|Rim2(+4A)|Serg2|Syt3-rs|mKIAA0751	regulating synaptic membrane exocytosis 2	protein-coding
mm_51237.1	chr6	71543844	71543868	+	1	NA	promoter-TSS (NM_025783)	promoter-TSS (NM_025783)	2	NM_025783	66700	Mm.181278	NM_025783	ENSMUSG00000053119	Chmp3	25.1|4921505F14Rik|9130011K15Rik|CGI-49|D6Ertd286e|NEDF|Vps24	charged multivesicular body protein 3	protein-coding
mm_159213.1	chr2	122484829	122484829	+	1	NA	promoter-TSS (NM_001085518)	promoter-TSS (NM_001085518)	-112	NM_001085518	381417	Mm.482295	NM_001085518	ENSMUSG00000079071	Gm14085	OTTMUSG00000015615	predicted gene 14085	protein-coding
mm_131985.1	chr16	25041687	25041711	+	1	NA	Intergenic	(T)n|Simple_repeat|Simple_repeat	-17940	NR_040374	319487	Mm.137341	NR_040374	ENSMUSG00000096960	A230028O05Rik	-	RIKEN cDNA A230028O05 gene	ncRNA
mm_125985.1	chr15	76343573	76343583	+	1	NA	promoter-TSS (NM_025567)	promoter-TSS (NM_025567)	55	NM_025567	66445	Mm.29196	NM_025567	ENSMUSG00000022551	Cyc1	2610002H19Rik|AA408921|Cyct1	cytochrome c-1	protein-coding
mm_72313.1	chr8	78013950	78013960	+	1	NA	Intergenic	RLTR9A|LTR|ERVK	-199387	NM_183096	73301	Mm.61243	NM_183096	ENSMUSG00000037101	Ttc29	1700031F13Rik	tetratricopeptide repeat domain 29	protein-coding
mm_45071.1	chr5	43821779	43821799	-	1	NA	intron (NM_009763, intron 3 of 8)	intron (NM_009763, intron 3 of 8)	2896	NM_009763	12182	Mm.246332	NM_009763	ENSMUSG00000029082	Bst1	114/A10|A530073F09|BP-3|Bp3|Bsta1|CD157|Ly65	bone marrow stromal cell antigen 1	protein-coding
mm_170164.1	chr17	53456192	53456196	-	1	NA	intron (NM_172497, intron 1 of 12)	BGLII|LTR|ERVK	7127	NM_172497	211482	Mm.60887	NM_172497	ENSMUSG00000023931	Efhb	4921525D22Rik	EF hand domain family, member B	protein-coding
mm_75629.1	chr8	64692996	64693021	-	1	NA	5' UTR (NM_013494, exon 1 of 9)	5' UTR (NM_013494, exon 1 of 9)	101	NM_013494	12876	Mm.31395	NM_013494	ENSMUSG00000037852	Cpe	CPH|Cph-1|Cph1|R74677|fat	carboxypeptidase E	protein-coding
mm_89789.1	chr10	102167639	102167642	+	1	NA	intron (NM_001162369, intron 1 of 5)	Lx3A|LINE|L1	8561	NM_001162369	67569	Mm.25252	NM_026243	ENSMUSG00000019888	Mgat4c	9130411I17Rik|GntIVh	MGAT4 family, member C	protein-coding
mm_136025.1	chr16	76365119	76365122	-	1	NA	intron (NM_173440, intron 1 of 3)	intron (NM_173440, intron 1 of 3)	7929	NM_173440	268903	Mm.74711	NM_173440	ENSMUSG00000048490	Nrip1	6030458L20Rik|8430438I05Rik|9630050P12|AA959574|AW456757|RIP140	nuclear receptor interacting protein 1	protein-coding
mm_42643.1	chr5	118599169	118599172	+	1	NA	intron (NM_001347445, intron 2 of 30)	intron (NM_001347445, intron 2 of 30)	38451	NM_172424	76199	Mm.206238	NM_172424	ENSMUSG00000018076	Med13l	2210413I17Rik|6330591G05Rik|9030618F05Rik|Thrap2|Trap240L|mKIAA1025	mediator complex subunit 13-like	protein-coding
mm_84567.1	chr9	68956679	68956681	-	1	NA	intron (NM_013646, intron 1 of 10)	intron (NM_013646, intron 1 of 10)	191334	NR_033299	320440	Mm.483129	NM_177159		9530091C08Rik	-	RIKEN cDNA 9530091C08 gene	ncRNA
mm_55944.1	chr6	85126064	85126079	-	1	NA	promoter-TSS (NM_001034902)	promoter-TSS (NM_001034902)	23	NM_001034902	545861	Mm.321419	NM_001034902	ENSMUSG00000072952	Gm5878	EG545861	predicted gene 5878	protein-coding
mm_49279.1	chr6	17637771	17637783	+	1	NA	intron (NM_007604, intron 1 of 9)	intron (NM_007604, intron 1 of 9)	679	NM_007604	12343	Mm.392504	NM_007604	ENSMUSG00000015733	Capza2	1110053K06Rik|AW208808|Cappa2	capping protein (actin filament) muscle Z-line, alpha 2	protein-coding
mm_41927.1	chr5	105696291	105696301	+	1	NA	Intergenic	Intergenic	-3673	NM_001122768	231549	Mm.23837	NM_178701	ENSMUSG00000046079	Lrrc8d	2810473G09Rik|4930525N13Rik|A930019F03|Lrrc5	leucine rich repeat containing 8D	protein-coding
mm_65944.1	chr7	30417384	30417436	-	1	NA	TTS (NM_011827)	TTS (NM_011827)	2444	NM_011827	23900	Mm.379050	NM_011827	ENSMUSG00000064109	Hcst	DAP10|KAP10	hematopoietic cell signal transducer	protein-coding
mm_95199.1	chr11	43441407	43441420	+	1	NA	intron (NM_148673, intron 8 of 16)	intron (NM_148673, intron 8 of 16)	7682	NM_198936	193116	Mm.28200	NM_148673	ENSMUSG00000020409	Slu7	AU018913|D11Ertd730e|D3Bwg0878e	SLU7 splicing factor homolog (S. cerevisiae)	protein-coding
mm_101058.1	chr11	9039580	9039584	-	1	NA	promoter-TSS (NM_001290519)	promoter-TSS (NM_001290519)	9	NM_001290519	194974	Mm.79210	NM_177576	ENSMUSG00000040985	Sun3	Sunc1	Sad1 and UNC84 domain containing 3	protein-coding
mm_141373.1	chr17	29007992	29008002	-	1	NA	promoter-TSS (NM_134115)	promoter-TSS (NM_134115)	-60	NM_134115	106504	Mm.439986	NM_134115	ENSMUSG00000024006	Stk38	5830476G13Rik|9530097A09Rik|AA617404|Ndr1	serine/threonine kinase 38	protein-coding
mm_96865.1	chr11	70166649	70166663	+	1	NA	promoter-TSS (NM_010796)	promoter-TSS (NM_010796)	33	NM_010796	17312	Mm.252405	NM_010796	ENSMUSG00000000318	Clec10a	CD301a|M-ASGP-BP-1|Mgl|Mgl1	C-type lectin domain family 10, member A	protein-coding
mm_119278.1	chr14	34310799	34310809	+	1	NA	promoter-TSS (NM_008133)	promoter-TSS (NM_008133)	77	NM_008133	14661	Mm.10600	NM_008133	ENSMUSG00000021794	Glud1	AI118167|Gdh-X|Glud|Gludl	glutamate dehydrogenase 1	protein-coding
mm_43022.1	chr5	123907623	123907633	+	1	NA	intron (NM_026603, intron 1 of 7)	intron (NM_026603, intron 1 of 7)	353	NM_026603	68184	Mm.28549	NM_026603	ENSMUSG00000023106	Denr	1500003K04Rik	density-regulated protein	protein-coding
mm_112995.1	chr13	21753428	21753454	+	1	NA	promoter-TSS (NM_178201)	promoter-TSS (NM_178201)	471	NM_178183	319169	Mm.370338	NM_178183	ENSMUSG00000063021	Hist1h2ak	-	histone cluster 1, H2ak	protein-coding
mm_135938.1	chr16	74279457	74279470	-	1	NA	intron (NM_175549, intron 2 of 27)	intron (NM_175549, intron 2 of 27)	62604	NR_030464	751561		NR_030464	ENSMUSG00000104758	Mir691	Mirn691|mir-691|mmu-mir-691	microRNA 691	ncRNA
mm_25131.1	chr3	102262450	102262460	+	1	NA	promoter-TSS (NR_040391)	promoter-TSS (NR_040391)	50	NR_040391	319951	Mm.225196	NR_040391	ENSMUSG00000105891	A230001M10Rik	-	RIKEN cDNA A230001M10 gene	ncRNA
mm_30660.1	chr4	9269339	9269362	+	1	NA	promoter-TSS (NM_028940)	promoter-TSS (NM_028940)	33	NM_028940	74438	Mm.473368	NM_028940	ENSMUSG00000041216	Clvs1	4933402J24Rik|Clvl1|Rlbp1l1	clavesin 1	protein-coding
mm_161777.1	chr17	37795215	37795215	+	1	NA	promoter-TSS (NM_146630)	promoter-TSS (NM_146630)	-231	NM_146630	258623	Mm.271474	NM_146630	ENSMUSG00000045202	Olfr123	MOR256-9	olfactory receptor 123	protein-coding
mm_95453.1	chr11	50376912	50376924	+	1	NA	promoter-TSS (NM_021510)	promoter-TSS (NM_021510)	-801	NM_021510	59013	Mm.21740	NM_021510	ENSMUSG00000007850	Hnrnph1	AI642080|E430005G16Rik|Hnrnph|Hnrph1	heterogeneous nuclear ribonucleoprotein H1	protein-coding
mm_60922.1	chr7	46846216	46846237	+	1	NA	promoter-TSS (NM_001136069)	promoter-TSS (NM_001136069)	422	NR_102727	16828	Mm.29324	NM_010699	ENSMUSG00000063229	Ldha	Ldh1|Ldhm|l7R2	lactate dehydrogenase A	protein-coding
mm_58010.1	chr6	136518762	136518772	-	1	NA	promoter-TSS (NM_019426)	promoter-TSS (NM_019426)	-84	NM_019426	54343	Mm.173271	NM_019426	ENSMUSG00000030213	Atf7ip	2610204M12Rik|AM|Mcaf1	activating transcription factor 7 interacting protein	protein-coding
mm_88141.1	chr10	69417565	69417583	+	1	NA	Intergenic	B3|SINE|B2	-64662	NM_007659	12534	Mm.281367	NM_007659	ENSMUSG00000019942	Cdk1	Cdc2|Cdc2a|p34<CDC2>	cyclin-dependent kinase 1	protein-coding
mm_740.1	chr1	43457303	43457315	+	1	NA	intron (NM_010879, intron 1 of 4)	intron (NM_010879, intron 1 of 4)	11558	NM_010879	17974	Mm.389903	NM_010879	ENSMUSG00000066877	Nck2	4833426I10Rik|Grb4|NCKbeta|Nck-2	non-catalytic region of tyrosine kinase adaptor protein 2	protein-coding
mm_92444.1	chr10	77582573	77582612	-	1	NA	intron (NM_145925, intron 1 of 5)	intron (NM_145925, intron 1 of 5)	825	NM_145925	108705	Mm.28853	NM_145925	ENSMUSG00000009291	Pttg1ip	1810010L20Rik|AI314311|AU018448|C79540	pituitary tumor-transforming 1 interacting protein	protein-coding
mm_20495.1	chr2	130279630	130279652	-	1	NA	TTS (NM_024193)	TTS (NM_024193)	1615	NR_028528	100217428		NR_028528	ENSMUSG00000065272	Snord57	MBII-434	small nucleolar RNA, C/D box 57	snoRNA
mm_90720.1	chr10	4432313	4432341	-	1	NA	promoter-TSS (NM_024261)	promoter-TSS (NM_024261)	25	NM_025343	66084	Mm.153111	NM_025343	ENSMUSG00000019763	Rmnd1	0610042C05Rik|AA408137|AI462664|AW536662	required for meiotic nuclear division 1 homolog	protein-coding
mm_127884.1	chr15	8683614	8683616	-	1	NA	intron (NM_148938, intron 3 of 9)	intron (NM_148938, intron 3 of 9)	27192	NM_148938	20512	Mm.204834	NM_148938	ENSMUSG00000005360	Slc1a3	AI504299|B430115D02Rik|Eaat1|GLAST|GLAST-1|GLU-T|GluT-1|Gmt1|MGluT1	solute carrier family 1 (glial high affinity glutamate transporter), member 3	protein-coding
mm_8395.1	chr1	151428441	151428474	-	1	NA	promoter-TSS (NM_025819)	promoter-TSS (NM_025819)	-22	NM_025819	66875	Mm.290905	NM_025819	ENSMUSG00000052748	Swt1	1200016B10Rik|C1orf26	SWT1 RNA endoribonuclease homolog (S. cerevisiae)	protein-coding
mm_47440.1	chr5	123181694	123181699	-	1	NA	intron (NM_008277, intron 3 of 13)	intron (NM_008277, intron 3 of 13)	990	NM_008277	15445	Mm.439709	NM_008277	ENSMUSG00000029445	Hpd	Fla|Flp|Hppd|Laf	4-hydroxyphenylpyruvic acid dioxygenase	protein-coding
mm_96993.1	chr11	70700211	70700300	+	1	NA	promoter-TSS (NM_213729)	promoter-TSS (NM_213729)	-100	NM_001252485	103844	Mm.101581	NM_213729	ENSMUSG00000057054	Inca1	AI842396	inhibitor of CDK, cyclin A1 interacting protein 1	protein-coding
mm_29661.1	chr3	122568786	122568808	-	1	NA	exon (NM_001114665, exon 5 of 16)	exon (NM_001114665, exon 5 of 16)	-27116	NR_106117	102465764		NR_106117	ENSMUSG00000104773	Mir7657	mmu-mir-7657	microRNA 7657	ncRNA
mm_52852.1	chr6	121865727	121865745	+	1	NA	exon (NM_008645, exon 15 of 36)	exon (NM_008645, exon 15 of 36)	27195	NM_008645	17836	Mm.1311	NM_008645	ENSMUSG00000059908	Mug1	-	murinoglobulin 1	protein-coding
mm_165630.1	chr3	68494204	68494232	+	1	NA	promoter-TSS (NM_001282044)	promoter-TSS (NM_001282044)	37	NM_001282044	30953	Mm.331064	NM_013928	ENSMUSG00000027777	Schip1	Nf2ip|Schip-1	schwannomin interacting protein 1	protein-coding
mm_16223.1	chr2	173137106	173137126	+	1	NA	Intergenic	L1MB5|LINE|L1	12367	NR_040321	74161	Mm.208098	NR_040321	ENSMUSG00000087382	Ctcflos	1300015D01Rik|A530094K13	CCCTC-binding factor (zinc finger protein)-like, opposite strand	ncRNA
mm_170768.1	chr2	162390771	162390781	+	1	NA	promoter-TSS (NR_040617)	promoter-TSS (NR_040617)	-37	NR_040617	77645	Mm.447752	NR_040617	ENSMUSG00000084919	Ptprtos	C330008G21Rik	protein tyrosine phosphatase, receptor type T, opposite strand	ncRNA
mm_64844.1	chr7	13013875	13013899	-	1	NA	Intergenic	Intergenic	-4087	NM_001024699	232879	Mm.279272	NM_001024699	ENSMUSG00000049600	Zbtb45	BB161562|Gm157|Zfp499	zinc finger and BTB domain containing 45	protein-coding
mm_83172.1	chr9	40531462	40531473	-	1	NA	Intergenic	Intergenic	-75703	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_143754.1	chr17	81582636	81582646	-	1	NA	intron (NR_104580, intron 2 of 8)	(TC)n|Simple_repeat|Simple_repeat	155746	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_157064.1	chrX	8145714	8145731	-	1	NA	non-coding (NR_033561, exon 1 of 3)	non-coding (NR_033561, exon 1 of 3)	158	NM_001166410	19652	Mm.128512	NM_016809	ENSMUSG00000031167	Rbm3	2600016C11Rik	RNA binding motif protein 3	protein-coding
mm_36544.1	chr4	86669473	86669485	-	1	NA	intron (NM_007408, intron 1 of 7)	intron (NM_007408, intron 1 of 7)	580	NM_007408	11520	Mm.381	NM_007408	ENSMUSG00000028494	Plin2	AA407157|ADPH|Adfp|Adrp	perilipin 2	protein-coding
mm_110798.1	chr12	72211902	72211913	-	1	NA	non-coding (NR_104446, exon 7 of 7)	non-coding (NR_104446, exon 7 of 7)	23839	NR_104446	104001	Mm.221275	NM_153457	ENSMUSG00000021087	Rtn1	Nsp	reticulon 1	protein-coding
mm_19346.1	chr2	90904920	90904940	-	1	NA	promoter-TSS (NM_026688)	promoter-TSS (NM_026688)	144	NM_025991	67136	Mm.330394	NM_025991	ENSMUSG00000005505	Kbtbd4	2510026C23Rik	kelch repeat and BTB (POZ) domain containing 4	protein-coding
mm_72183.1	chr8	72322772	72322797	+	1	NA	Intergenic	Intergenic	3722	NM_008452	16598	Mm.26938	NM_008452	ENSMUSG00000055148	Klf2	Lklf	Kruppel-like factor 2 (lung)	protein-coding
mm_129804.1	chr15	82963781	82963865	-	1	NA	Intergenic	G-rich|Low_complexity|Low_complexity	-4527	NR_037241	100526477		NR_037241	ENSMUSG00000092751	Mir3080	mmu-mir-3080	microRNA 3080	ncRNA
mm_53598.1	chr6	138141649	138141669	+	1	NA	promoter-TSS (NM_001347489)	promoter-TSS (NM_001347489)	65	NM_001347489	56615	Mm.14796	NM_019946	ENSMUSG00000008540	Mgst1	1500002K10Rik|Gst	microsomal glutathione S-transferase 1	protein-coding
mm_118254.1	chr13	112354223	112354227	-	1	NA	intron (NM_001168403, intron 7 of 11)	intron (NM_001168403, intron 7 of 11)	65707	NM_001168404	77318	Mm.159895	NM_029898	ENSMUSG00000049985	Ankrd55	C030011J08Rik	ankyrin repeat domain 55	protein-coding
mm_24113.1	chr3	88144333	88144340	+	1	NA	intron (NM_133665, intron 1 of 10)	intron (NM_133665, intron 1 of 10)	1964	NM_001310593	17261	Mm.28184	NM_133665	ENSMUSG00000001419	Mef2d	C80750	myocyte enhancer factor 2D	protein-coding
mm_6314.1	chr1	71597438	71597451	-	1	NA	exon (NM_010233, exon 40 of 46)	exon (NM_010233, exon 40 of 46)	40288	NM_026195	108147	Mm.38010	NM_026195	ENSMUSG00000026192	Atic	2610509C24Rik|AA536954|AW212393	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	protein-coding
mm_163973.1	chr14	55575706	55575710	+	1	NA	promoter-TSS (NM_026808)	promoter-TSS (NM_026808)	34	NM_026808	68680	Mm.36758	NM_026808	ENSMUSG00000022215	Fitm1	1110028A07Rik|AV010547|Cg10671|Fit1	fat storage-inducing transmembrane protein 1	protein-coding
mm_124383.1	chr14	108913845	108913859	-	1	NA	5' UTR (NM_199065, exon 1 of 1)	5' UTR (NM_199065, exon 1 of 1)	387	NM_199065	76965	Mm.257268	NM_199065	ENSMUSG00000075478	Slitrk1	3200001I04Rik	SLIT and NTRK-like family, member 1	protein-coding
mm_8902.1	chr1	163289323	163289338	-	1	NA	intron (NM_001025570, intron 1 of 2)	intron (NM_001025570, intron 1 of 2)	24320	NM_011127	18933	Mm.288642	NM_011127	ENSMUSG00000026586	Prrx1	A230024N07Rik|AA755424|AI385634|AI843499|K-2|Pmx|Pmx1|Prx1|mHox	paired related homeobox 1	protein-coding
mm_41760.1	chr5	102860099	102860120	+	1	NA	intron (NM_001346585, intron 1 of 6)	intron (NM_001346585, intron 1 of 6)	15102	NM_001346585	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding
mm_32656.1	chr4	115088915	115088925	+	1	NA	5' UTR (NM_001164557, exon 1 of 4)	5' UTR (NM_001164557, exon 1 of 4)	212	NM_001164557	67182	Mm.30181	NM_026018	ENSMUSG00000028716	Pdzk1ip1	0610007F13Rik|2700030M23Rik|AU046042|Map17	PDZK1 interacting protein 1	protein-coding
mm_107738.1	chr12	57951219	57951225	+	1	NA	Intergenic	Intergenic	-260582	NM_009216	20605	Mm.278336	NM_009216	ENSMUSG00000035431	Sstr1	SRIF-2|SS-1-R|SS1-R|SS1R|Smstr-1|Smstr1|sst1	somatostatin receptor 1	protein-coding
mm_85214.1	chr9	96889382	96889438	-	1	NA	promoter-TSS (NM_153420)	promoter-TSS (NM_153420)	64	NM_001289646	235534	Mm.233031	NM_153420	ENSMUSG00000043587	Pxylp1	9430094M07Rik|Acpl2|BB177120|C130099A20Rik	2-phosphoxylose phosphatase 1	protein-coding
mm_82777.1	chr9	27155369	27155387	-	1	NA	promoter-TSS (NM_023277)	promoter-TSS (NM_023277)	43	NM_023277	83964	Mm.28770	NM_023277	ENSMUSG00000031990	Jam3	1110002N23Rik|JAM-3|JAM-C|Jcam3	junction adhesion molecule 3	protein-coding
mm_86732.1	chr10	19065614	19065619	+	1	NA	Intergenic	Intergenic	-50206	NM_009397	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_8881.1	chr1	162866441	162866451	-	1	NA	5' UTR (NM_010231, exon 1 of 9)	5' UTR (NM_010231, exon 1 of 9)	164	NM_010231	14261	Mm.976	NM_010231	ENSMUSG00000040181	Fmo1	-	flavin containing monooxygenase 1	protein-coding
mm_125582.1	chr15	59522989	59522993	+	1	NA	intron (NM_026746, intron 4 of 6)	intron (NM_026746, intron 4 of 6)	-125663	NM_144549	211770	Mm.40298	NM_144549	ENSMUSG00000032501	Trib1	A530090O15Rik|TRB-1|Trb1	tribbles pseudokinase 1	protein-coding
mm_62862.1	chr7	114717330	114717346	+	1	NA	Intergenic	Intergenic	-1305	NM_054084	116903	Mm.273838	NM_054084	ENSMUSG00000030666	Calcb	CGRP2|Calc2	calcitonin-related polypeptide, beta	protein-coding
mm_10425.1	chr2	13582611	13582626	+	1	NA	3' UTR (NM_011701, exon 9 of 9)	3' UTR (NM_011701, exon 9 of 9)	8307	NM_011701	22352	Mm.268000	NM_011701	ENSMUSG00000026728	Vim	-	vimentin	protein-coding
mm_147895.1	chr18	65306051	65306065	-	1	NA	exon (NM_001037294, exon 5 of 13)	exon (NM_001037294, exon 5 of 13)	57197	NR_029600	387231		NR_029600	ENSMUSG00000065402	Mir122	Mir122a|Mirn122a|mir-122|mmu-mir-122	microRNA 122	ncRNA
mm_151893.1	chr19	5798845	5798852	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	-2867	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_50792.1	chr6	54039936	54040016	+	1	NA	promoter-TSS (NM_001163640)	promoter-TSS (NM_001163640)	44	NM_001163640	69993	Mm.321147	NM_023543	ENSMUSG00000004633	Chn2	1700026N20Rik|4930557O16Rik|ARHGAP3|Bch	chimerin 2	protein-coding
mm_16697.1	chr2	6885223	6885237	-	1	NA	promoter-TSS (NM_001110228)	promoter-TSS (NM_001110228)	-234	NM_001160293	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_20210.1	chr2	125506053	125506084	-	1	NA	intron (NM_007993, intron 1 of 65)	CpG	370	NM_007993	14118	Mm.271644	NM_007993	ENSMUSG00000027204	Fbn1	AI536462|B430209H23|Fib-1|Tsk	fibrillin 1	protein-coding
mm_86476.1	chr10	4709816	4709862	+	1	NA	promoter-TSS (NM_001302533)	promoter-TSS (NM_001302533)	-319	NM_001302531	13982	Mm.9213	NM_007956	ENSMUSG00000019768	Esr1	ER|ER-alpha|ERa|ERalpha|ESR|Estr|Estra|Nr3a1	estrogen receptor 1 (alpha)	protein-coding
mm_79999.1	chr9	67047795	67047808	+	1	NA	exon (NM_001164251, exon 2 of 10)	exon (NM_001164251, exon 2 of 10)	1412	NM_001164255	22003	Mm.121878	NM_024427	ENSMUSG00000032366	Tpm1	AA986836|AI854628|TM2|Tm3|Tmpa|Tpm-1|alpha-TM	tropomyosin 1, alpha	protein-coding
mm_167130.1	chr7	126777182	126777192	+	1	NA	5' UTR (NM_026875, exon 1 of 5)	5' UTR (NM_026875, exon 1 of 5)	212	NM_025347	66090	Mm.27114	NM_025347	ENSMUSG00000042675	Ypel3	0610043B10Rik|1190001G19Rik|Suap	yippee-like 3 (Drosophila)	protein-coding
mm_56102.1	chr6	87459476	87459515	-	1	NA	non-coding (NR_104483, exon 11 of 11)	non-coding (NR_104483, exon 11 of 11)	30501	NM_009756	12154	Mm.483321	NM_009756	ENSMUSG00000030046	Bmp10	-	bone morphogenetic protein 10	protein-coding
mm_16724.1	chr2	7395914	7395924	-	1	NA	promoter-TSS (NM_001110232)	promoter-TSS (NM_001110232)	81	NM_001110232	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_11694.1	chr2	35713175	35713183	+	1	NA	exon (NM_001114125, exon 8 of 17)	exon (NM_001114125, exon 8 of 17)	16447	NM_001290639	69601	Mm.29629	NM_001001602	ENSMUSG00000026883	Dab2ip	2310011D08Rik|AI480459|Aip1|mKIAA1743	disabled 2 interacting protein	protein-coding
mm_114628.1	chr13	76130194	76130202	+	1	NA	intron (NM_001081352, intron 18 of 43)	intron (NM_001081352, intron 18 of 43)	31464	NM_001081352	218343	Mm.277964	NM_001081352	ENSMUSG00000033991	Ttc37	mKIAA0372	tetratricopeptide repeat domain 37	protein-coding
mm_55046.1	chr6	49036471	49036481	-	1	NA	promoter-TSS (NM_053110)	promoter-TSS (NM_053110)	-42	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_111820.1	chr12	106444773	106444781	-	1	NA	intron (NR_036593, intron 2 of 3)	intron (NR_036593, intron 2 of 3)	2889	NR_036593	76639	Mm.375609	NR_036593	ENSMUSG00000092066	1700121N20Rik	-	RIKEN cDNA 1700121N20 gene	ncRNA
mm_134331.1	chr16	16455075	16455078	-	1	NA	intron (NM_001301817, intron 10 of 16)	intron (NM_001301817, intron 10 of 16)	72335	NM_001301818	224014	Mm.256131	NM_139232	ENSMUSG00000022788	Fgd4	9030023J02Rik|9330209B17Rik|Frabp|ZFYVE6	FYVE, RhoGEF and PH domain containing 4	protein-coding
mm_47936.1	chr5	135251245	135251277	-	1	NA	promoter-TSS (NM_010246)	promoter-TSS (NM_010246)	-214	NM_010246	14371	Mm.6256	NM_010246	ENSMUSG00000049551	Fzd9	mfz9	frizzled class receptor 9	protein-coding
mm_139888.1	chr17	70834943	70834957	+	1	NA	Intergenic	Intergenic	11827	NM_001164077	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_132239.1	chr16	32750812	32750824	+	1	NA	exon (NM_080457, exon 2 of 27)	exon (NM_080457, exon 2 of 27)	14932	NM_080457	140474	Mm.214599	NM_080457	ENSMUSG00000079620	Muc4	4933405I11Rik|Asgp	mucin 4	protein-coding
mm_38322.1	chr4	137339279	137339282	-	1	NA	intron (NM_009861, intron 1 of 5)	intron (NM_009861, intron 1 of 5)	18479	NM_009861	12540	Mm.1022	NM_009861	ENSMUSG00000006699	Cdc42	AI747189|AU018915	cell division cycle 42	protein-coding
mm_33613.1	chr4	132611162	132611166	+	1	NA	Intergenic	B4A|SINE|B4	-27882	NM_210071	14050	Mm.227733	NM_010166	ENSMUSG00000028886	Eya3	AI844637	EYA transcriptional coactivator and phosphatase 3	protein-coding
mm_72332.1	chr8	79028318	79028350	+	1	NA	promoter-TSS (NM_178267)	promoter-TSS (NM_178267)	-103	NM_001294279	622675	Mm.48724	NM_178267	ENSMUSG00000071064	Zfp827	2810449M09Rik|D630040G17Rik|Znf827	zinc finger protein 827	protein-coding
mm_55391.1	chr6	60403668	60403681	-	1	NA	promoter-TSS (NR_015565)	promoter-TSS (NR_015565)	33	NR_015565	208079	Mm.131226	NM_177329	ENSMUSG00000046764	A530053G22Rik	-	RIKEN cDNA A530053G22 gene	ncRNA
mm_157551.1	chrX	51681451	51681461	-	1	NA	promoter-TSS (NM_015819)	promoter-TSS (NM_015819)	146	NM_001077202	50786	Mm.252561	NM_015819	ENSMUSG00000062184	Hs6st2	6OST2	heparan sulfate 6-O-sulfotransferase 2	protein-coding
mm_108957.1	chr12	102368733	102368761	+	1	NA	exon (NM_001161365, exon 6 of 10)	exon (NM_001161365, exon 6 of 10)	71066	NM_011175	19141	Mm.17185	NM_011175	ENSMUSG00000021190	Lgmn	AEP|AI746452|AU022324|Prsc1	legumain	protein-coding
mm_75727.1	chr8	69134694	69134697	-	1	NA	TTS (NM_199364)	TTS (NM_199364)	6258	NM_199364	211134	Mm.409446	NM_199364	ENSMUSG00000036306	Lzts1	F37|FEZ1|PSD-Zip70	leucine zipper, putative tumor suppressor 1	protein-coding
mm_136372.1	chr16	92825536	92825548	-	1	NA	intron (NM_001111022, intron 2 of 6)	intron (NM_001111022, intron 2 of 6)	532	NM_001111021	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_44738.1	chr5	31180111	31180158	-	1	NA	promoter-TSS (NM_027901)	promoter-TSS (NM_027901)	10	NM_027901	71752	Mm.271923	NM_027901	ENSMUSG00000101678	Gtf3c2	1300004C11Rik|2610510G03Rik|AI225816|AU041069|TFIIIC110|mKIAA0011	general transcription factor IIIC, polypeptide 2, beta	protein-coding
mm_30390.1	chr3	152247957	152247970	-	1	NA	exon (NM_199465, exon 7 of 13)	exon (NM_199465, exon 7 of 13)	18357	NM_199465	68810	Mm.200188	NM_199465	ENSMUSG00000039103	Nexn	1110046H09Rik|AA553326|NELIN	nexilin	protein-coding
mm_820.1	chr1	46748118	46748120	+	1	NA	intron (NM_001310335, intron 51 of 64)	intron (NM_001310335, intron 51 of 64)	105390	NM_172653	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|mKIAA1265	solute carrier family 39 (zinc transporter), member 10	protein-coding
mm_168265.1	chr10	91259848	91259866	-	1	NA	Intergenic	Intergenic	-88238	NM_001080130	21917	Mm.159684	NM_011605	ENSMUSG00000019961	Tmpo	5630400D24Rik|AI195756|AI606875|AW214352|AW547477|LAP2|TP	thymopoietin	protein-coding
mm_133352.1	chr16	84585478	84585480	+	1	NA	Intergenic	Intergenic	-94310	NR_040537	78023	Mm.243853	NR_040537		4930529L06Rik	-	RIKEN cDNA 4930529L06 gene	ncRNA
mm_123339.1	chr14	63135628	63135677	-	1	NA	exon (NM_007798, exon 4 of 10)	exon (NM_007798, exon 4 of 10)	13190	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_63564.1	chr7	128113248	128113268	+	1	NA	exon (NM_008401, exon 21 of 30)	exon (NM_008401, exon 21 of 30)	-16310	NM_021334	16411	Mm.22378	NM_021334	ENSMUSG00000030789	Itgax	AI449405|Cd11c|Cr4|N418	integrin alpha X	protein-coding
mm_95682.1	chr11	54199359	54199366	+	1	NA	intron (NR_045506, intron 2 of 2)	intron (NR_045506, intron 2 of 2)	13926	NR_045506	71056	Mm.56332	NR_045506	ENSMUSG00000086209	4933405E24Rik	-	RIKEN cDNA 4933405E24 gene	ncRNA
mm_117529.1	chr13	81783609	81783653	-	1	NA	intron (NM_007684, intron 1 of 4)	CpG	339	NM_007684	12626	Mm.12481	NM_007684	ENSMUSG00000021537	Cetn3	MmCEN3	centrin 3	protein-coding
mm_26150.1	chr3	138143430	138143477	+	1	NA	promoter-TSS (NM_175389)	promoter-TSS (NM_175389)	-65	NM_001163457	17777	Mm.2941	NM_008642	ENSMUSG00000028158	Mttp	1810043K16Rik|MTP	microsomal triglyceride transfer protein	protein-coding
mm_52779.1	chr6	121246657	121246670	+	1	NA	intron (NM_011909, intron 1 of 10)	MLTR73|LTR|ERV1	757	NM_011909	24110	Mm.326911	NM_011909	ENSMUSG00000030107	Usp18	1110058H21Rik|AW047653|UBP43|Ubp15	ubiquitin specific peptidase 18	protein-coding
mm_38337.1	chr4	137706604	137706627	-	1	NA	promoter-TSS (NM_001331215)	promoter-TSS (NM_001331215)	-9	NR_138594	69808	Mm.437203	NR_138594		Rap1gapos	1810058N05Rik	RAP1 GTPase activating protein, opposite strand	ncRNA
mm_93862.1	chr10	122985637	122985642	-	1	NA	promoter-TSS (NR_029527)	promoter-TSS (NR_029527)	85	NR_029527	387251		NR_029527	ENSMUSG00000065406	Mirlet7i	Mirnlet7i|let-7i|mmu-let-7i	microRNA let7i	ncRNA
mm_39614.1	chr5	24364805	24364824	+	1	NA	promoter-TSS (NM_008713)	promoter-TSS (NM_008713)	-5	NM_008713	18127	Mm.258415	NM_008713	ENSMUSG00000028978	Nos3	2310065A03Rik|Nos-3|eNOS|ecNOS	nitric oxide synthase 3, endothelial cell	protein-coding
mm_68044.1	chr7	101362872	101362884	-	1	NA	intron (NM_001040111, intron 1 of 33)	intron (NM_001040111, intron 1 of 33)	14809	NM_001040111	69710	Mm.277687	NM_027180	ENSMUSG00000032812	Arap1	2410002L19Rik|Centd2|mKIAA0782	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	protein-coding
mm_14199.1	chr2	127208359	127208444	+	1	NA	promoter-TSS (NM_177214)	promoter-TSS (NM_177214)	-3	NM_177214	320632	Mm.215860	NM_177214	ENSMUSG00000003660	Snrnp200	A330064G03Rik|Ascc3l1|BC011390|HELIC2|U5-200-KD|U5-200KD	small nuclear ribonucleoprotein 200 (U5)	protein-coding
mm_157290.1	chrX	20861525	20861537	-	1	NA	exon (NM_013680, exon 13 of 13)	exon (NM_013680, exon 13 of 13)	1651	NR_049190	100885829		NR_049190	ENSMUSG00000093408	Mir5617	Gm25192|mir-5617|mmu-mir-5617	microRNA 5617	ncRNA
mm_99215.1	chr11	101026424	101026438	+	1	NA	intron (NM_001243050, intron 5 of 20)	intron (NM_001243050, intron 5 of 20)	-3909	NR_105893	102466767		NR_105893	ENSMUSG00000098415	Mir6928	Gm27728|mmu-mir-6928	microRNA 6928	ncRNA
mm_12110.1	chr2	61593092	61593102	+	1	NA	promoter-TSS (NM_001164072)	promoter-TSS (NM_001164072)	0	NM_001164072	21353	Mm.244393	NM_011529	ENSMUSG00000064289	Tank	C86182|E430026L09Rik|I-TRAF	TRAF family member-associated Nf-kappa B activator	protein-coding
mm_117496.1	chr13	78198816	78198843	-	1	NA	promoter-TSS (NM_010151)	promoter-TSS (NM_010151)	44	NM_010151	13865	Mm.439653	NM_010151	ENSMUSG00000069171	Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR-3|EAR3|Erbal3|SVP44|Tcfcoup1	nuclear receptor subfamily 2, group F, member 1	protein-coding
mm_127402.1	chr15	101224218	101224231	+	1	NA	promoter-TSS (NM_019518)	promoter-TSS (NM_019518)	17	NM_019518	56149	Mm.276573	NM_019518	ENSMUSG00000000531	Grasp	tamalin	GRP1 (general receptor for phosphoinositides 1)-associated scaffold protein	protein-coding
mm_150125.1	chr19	30003821	30003834	+	1	NA	promoter-TSS (NM_025741)	promoter-TSS (NM_025741)	37	NM_025741	66745	Mm.158128	NM_025741	ENSMUSG00000024815	Trpd52l3	4931412G03Rik	tumor protein D52-like 3	protein-coding
mm_147209.1	chr18	37935430	37935450	-	1	NA	promoter-TSS (NM_001305981)	promoter-TSS (NM_001305981)	36	NM_001305980	13367	Mm.195916	NM_007858	ENSMUSG00000024456	Diaph1	D18Wsu154e|Dia1|Diap1|Drf1|p140mDia	diaphanous related formin 1	protein-coding
mm_117693.1	chr13	94294994	94295010	-	1	NA	Intergenic	MTC|LTR|ERVL-MaLR	-9171	NM_001346609	107767	Mm.201455	NM_029153	ENSMUSG00000021687	Scamp1	4930505M11Rik|AI415563|AW122395	secretory carrier membrane protein 1	protein-coding
mm_79156.1	chr9	47796003	47796006	+	1	NA	intron (NM_001025600, intron 3 of 8)	intron (NM_001025600, intron 3 of 8)	22204	NR_046048	100038460	Mm.447649	NR_046048		Gm10677	ENSMUSG00000074363	predicted gene 10677	ncRNA
mm_27572.1	chr3	58692009	58692015	-	1	NA	promoter-TSS (NR_045167)	promoter-TSS (NR_045167)	376	NM_009174	20439	Mm.2847	NM_009174	ENSMUSG00000036432	Siah2	AA415433|Sinh2	seven in absentia 2	protein-coding
mm_873.1	chr1	52155115	52155131	+	1	NA	intron (NM_001205313, intron 23 of 24)	intron (NM_001205313, intron 23 of 24)	35501	NM_001205313	20846	Mm.277406	NM_009283	ENSMUSG00000026104	Stat1	2010005J02Rik|AA408197	signal transducer and activator of transcription 1	protein-coding
mm_372.1	chr1	33991011	33991018	+	1	NA	intron (NM_001276764, intron 3 of 102)	intron (NM_001276764, intron 3 of 102)	-20811	NM_133833	13518	Mm.336625	NM_010081	ENSMUSG00000026131	Dst	2310001O04Rik|A830042E19Rik|AW554249|BP230|BPAG1-n|Bpag|Bpag1|Macf2|ah|athetoid|dt|mKIAA0728|nmf203|nmf339	dystonin	protein-coding
mm_160058.1	chr7	4546598	4546598	-	1	NA	promoter-TSS (NM_016908)	promoter-TSS (NM_016908)	-31	NM_016908	53420	Mm.358663	NM_016908	ENSMUSG00000004961	Syt5	SytV	synaptotagmin V	protein-coding
mm_140045.1	chr17	74489621	74489631	+	1	NA	5' UTR (NM_026417, exon 1 of 6)	5' UTR (NM_026417, exon 1 of 6)	133	NM_026417	67864	Mm.41891	NM_026417	ENSMUSG00000024072	Yipf4	2310034L04Rik	Yip1 domain family, member 4	protein-coding
mm_141176.1	chr17	26841465	26841497	-	1	NA	promoter-TSS (NM_008700)	promoter-TSS (NM_008700)	84	NM_008700	18091	Mm.41974	NM_008700	ENSMUSG00000015579	Nkx2-5	Csx|Nkx-2.5|Nkx2.5|tinman	NK2 homeobox 5	protein-coding
mm_97547.1	chr11	78926550	78926574	+	1	NA	intron (NM_001313922, intron 1 of 25)	intron (NM_001313922, intron 1 of 25)	1271	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_96441.1	chr11	67344780	67344807	+	1	NA	intron (NM_001081250, intron 14 of 38)	intron (NM_001081250, intron 14 of 38)	17690	NM_001081250	544791	Mm.461064	NM_001081250	ENSMUSG00000060180	Myh13	MyHC-eo	myosin, heavy polypeptide 13, skeletal muscle	protein-coding
mm_9091.1	chr1	168675877	168675888	-	1	NA	Intergenic	Intergenic	185239	NR_105766	102465178		NR_105766	ENSMUSG00000098407	Mir6348	Gm27412|mmu-mir-6348	microRNA 6348	ncRNA
mm_106221.1	chr11	117078096	117078130	-	1	NA	TTS (NR_105853)	TTS (NR_105853)	765	NR_105853	102465258		NR_105853	ENSMUSG00000104740	Mir6516	mmu-mir-6516	microRNA 6516	ncRNA
mm_138992.1	chr17	45539653	45539653	+	1	NA	exon (NM_013688, exon 4 of 5)	exon (NM_013688, exon 4 of 5)	10024	NM_001013749	210573	Mm.329064	NM_001013749	ENSMUSG00000096847	Tmem151b	Gm323	transmembrane protein 151B	protein-coding
mm_153260.1	chr19	36919607	36919622	-	1	NA	promoter-TSS (NM_028263)	promoter-TSS (NM_028263)	-15	NM_028263	72514	Mm.41674	NM_028263	ENSMUSG00000047632	Fgfbp3	2610306H15Rik|Fgf-bp3	fibroblast growth factor binding protein 3	protein-coding
mm_46629.1	chr5	108449095	108449105	-	1	NA	promoter-TSS (NM_172883)	promoter-TSS (NM_172883)	-209	NM_172883	243197	Mm.106818	NM_172883	ENSMUSG00000029490	Mfsd7a	4732482E20Rik|Mfsd7	major facilitator superfamily domain containing 7A	protein-coding
mm_69794.1	chr7	141117805	141117825	-	1	NA	promoter-TSS (NM_178381)	promoter-TSS (NM_178381)	-9	NM_178381	71345	Mm.235813	NM_178381	ENSMUSG00000054662	Ano9	5430425C04Rik|Tmem16j|Tp53i5|Trp53i5	anoctamin 9	protein-coding
mm_149941.1	chr19	27312895	27312904	+	1	NA	Intergenic	Intergenic	-9720	NM_183179	240595	Mm.269759	NM_183179	ENSMUSG00000047298	Kcnv2	KV11.1	potassium channel, subfamily V, member 2	protein-coding
mm_9826.1	chr1	182517448	182517525	-	1	NA	promoter-TSS (NM_009794)	promoter-TSS (NM_009794)	-3	NM_009794	12334	Mm.19306	NM_009794	ENSMUSG00000026509	Capn2	AI326419|Capa-2|Capa2|m-calpain|m-calpin	calpain 2	protein-coding
mm_140621.1	chr17	11973535	11973580	-	1	NA	intron (NM_016694, intron 9 of 11)	intron (NM_016694, intron 9 of 11)	-90368	NR_045808	52027	Mm.442257	NR_045808		D17Ertd648e	-	DNA segment, Chr 17, ERATO Doi 648, expressed	ncRNA
mm_125550.1	chr15	58648507	58648511	+	1	NA	Intergenic	Intergenic	174918	NM_175212	74868	Mm.293754	NM_175212	ENSMUSG00000062373	Tmem65	2610029O13Rik|4930438D12Rik	transmembrane protein 65	protein-coding
mm_49724.1	chr6	34662168	34662191	+	1	NA	5' UTR (NM_001347100, exon 2 of 14)	5' UTR (NM_001347100, exon 2 of 14)	-47265	NM_145575	109624	Mm.308134	NM_145575	ENSMUSG00000029761	Cald1	4833423D12Rik|AI195384|AV071549|AW536160|C920027I18Rik	caldesmon 1	protein-coding
mm_118688.1	chr14	22122839	22122852	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	103133	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_43779.1	chr5	142358040	142358043	+	1	NA	Intergenic	Intergenic	-43456	NM_199068	17425	Mm.24214	NM_010812	ENSMUSG00000056493	Foxk1	A630048H08Rik|AI463295|ENSMUSG00000075577|Gm10868|Mnf	forkhead box K1	protein-coding
mm_92596.1	chr10	80101126	80101139	-	1	NA	intron (NM_183426, intron 1 of 31)	intron (NM_183426, intron 1 of 31)	1570	NM_183426	216161	Mm.262102	NM_183426	ENSMUSG00000035673	Sbno2	BC019206|F730040C21|Sno|Stno	strawberry notch homolog 2 (Drosophila)	protein-coding
mm_78646.1	chr9	40321739	40321751	+	1	NA	intron (NM_172768, intron 4 of 19)	intron (NM_172768, intron 4 of 19)	-11727	NR_040728	73558	Mm.398307	NR_040728		1700110K17Rik	-	RIKEN cDNA 1700110K17 gene	ncRNA
mm_41143.1	chr5	87908759	87908777	+	1	NA	promoter-TSS (NM_001305431)	promoter-TSS (NM_001305431)	-11	NM_001305431	494497	Mm.332472	NM_001305431		BC037156	FDC-SP	cDNA sequence BC037156	protein-coding
mm_43274.1	chr5	130449375	130449438	+	1	NA	5' UTR (NM_021371, exon 1 of 6)	5' UTR (NM_021371, exon 1 of 6)	614	NM_021371	140904	Mm.40875	NM_021371	ENSMUSG00000060371	Caln1	9630012C17Rik|Cabp8|MNCb-0849	calneuron 1	protein-coding
mm_113391.1	chr13	33040261	33040297	+	1	NA	3' UTR (NM_011452, exon 7 of 7)	3' UTR (NM_011452, exon 7 of 7)	12865	NM_011452	20706	Mm.45371	NM_011452	ENSMUSG00000021403	Serpinb9b	1600019A21Rik|R86|SPI-CI|Spi10|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 9b	protein-coding
mm_144951.1	chr18	37808691	37808704	+	1	NA	exon (NM_033581, exon 1 of 4)	exon (NM_033581, exon 1 of 4)	2287	NM_033581	93706	Mm.247203	NM_033581	ENSMUSG00000102918	Pcdhgc3	PC43|Pcdh2	protocadherin gamma subfamily C, 3	protein-coding
mm_37457.1	chr4	123442886	123442891	-	1	NA	intron (NM_001199136, intron 51 of 97)	B3|SINE|B2	-30977	NM_001167918	442834	Mm.483803	NM_001167918		D830031N03Rik	Kiaa0754|mKIAA0754	RIKEN cDNA D830031N03 gene	protein-coding
mm_89124.1	chr10	84917270	84917295	+	1	NA	promoter-TSS (NM_183172)	promoter-TSS (NM_183172)	-331	NM_001013441	237422	Mm.18936	NM_183172	ENSMUSG00000035620	Ric8b	BC051080|Ric-8|Ric-8b	RIC8 guanine nucleotide exchange factor B	protein-coding
mm_64750.1	chr7	4792325	4792330	-	1	NA	promoter-TSS (NM_009081)	promoter-TSS (NM_009081)	-638	NM_009081	19943	Mm.379002	NM_009081	ENSMUSG00000030432	Rpl28	D7Wsu21e	ribosomal protein L28	protein-coding
mm_29237.1	chr3	107215954	107215958	-	1	NA	exon (NM_001111143, exon 5 of 9)	exon (NM_001111143, exon 5 of 9)	5776	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_137167.1	chr17	23808137	23808147	+	1	NA	exon (NM_175229, exon 2 of 14)	exon (NM_175229, exon 2 of 14)	4955	NM_175229	75956	Mm.5222	NM_175229	ENSMUSG00000039218	Srrm2	5033413A03Rik|AA410130|SRm300|mKIAA0324	serine/arginine repetitive matrix 2	protein-coding
mm_168916.1	chr12	57941459	57941460	-	1	NA	Intergenic	L1Md_T|LINE|L1	-270345	NM_009216	20605	Mm.278336	NM_009216	ENSMUSG00000035431	Sstr1	SRIF-2|SS-1-R|SS1-R|SS1R|Smstr-1|Smstr1|sst1	somatostatin receptor 1	protein-coding
mm_82060.1	chr9	122686796	122686802	+	1	NA	Intergenic	Intergenic	3923	NR_029819	387156		NR_029819	ENSMUSG00000065414	Mir138-1	Mirn138|Mirn138-1|mir-138-1	microRNA 138-1	ncRNA
mm_104452.1	chr11	95041267	95041271	-	1	NA	5' UTR (NM_133667, exon 1 of 11)	5' UTR (NM_133667, exon 1 of 11)	102	NM_133667	18604	Mm.29768	NM_133667	ENSMUSG00000038967	Pdk2	-	pyruvate dehydrogenase kinase, isoenzyme 2	protein-coding
mm_64882.1	chr7	15873188	15873194	-	1	NA	promoter-TSS (NM_001113330)	promoter-TSS (NM_001113330)	-806	NM_001113330	12951	Mm.441911	NM_007770	ENSMUSG00000041578	Crx	Crx1	cone-rod homeobox	protein-coding
mm_165392.1	chr2	131855645	131855645	-	1	NA	3' UTR (NM_001166206, exon 2 of 2)	3' UTR (NM_001166206, exon 2 of 2)	4102	NM_001166206	71995	Mm.22	NM_028045	ENSMUSG00000037482	Erv3	1600014E20Rik|AA389086|AI426069|AI448024|D19349	endogenous retroviral sequence 3	protein-coding
mm_1014.1	chr1	58728714	58728724	+	1	NA	intron (NM_001293804, intron 3 of 9)	B1_Mur1|SINE|Alu	-1833	NM_001293805	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_36509.1	chr4	83486392	83486402	-	1	NA	promoter-TSS (NM_001290527)	promoter-TSS (NM_001290527)	51	NM_001290527	101739	Mm.105331	NM_133948	ENSMUSG00000028484	Psip1	AA408851|AU015605|Dfs70|Ledgfa|Ledgfb|Psip2	PC4 and SFRS1 interacting protein 1	protein-coding
mm_56922.1	chr6	119417480	119417530	-	1	NA	promoter-TSS (NM_197985)	promoter-TSS (NM_197985)	-22	NM_197985	68465	Mm.291826	NM_197985	ENSMUSG00000030168	Adipor2	1110001I14Rik|ADCR2|AI115388|AW554121|D6Ucla1e|Paqr2	adiponectin receptor 2	protein-coding
mm_153491.1	chr19	41324335	41324346	-	1	NA	intron (NM_031376, intron 7 of 16)	MIRc|SINE|MIR	-60336	NM_133352	107358	Mm.246440	NM_133352	ENSMUSG00000025016	Tm9sf3	1810073M23Rik|2810031D16Rik|AI115521|AI413748|AW146116|AW549777|Smbp|mKIAA4036	transmembrane 9 superfamily member 3	protein-coding
mm_88228.1	chr10	70520479	70520489	+	1	NA	intron (NM_024244, intron 5 of 13)	intron (NM_024244, intron 5 of 13)	72328	NM_001162846	70911	Mm.19825	NM_178621	ENSMUSG00000037747	Phyhipl	4921522K17Rik|AI267048	phytanoyl-CoA hydroxylase interacting protein-like	protein-coding
mm_89501.1	chr10	94036058	94036121	+	1	NA	promoter-TSS (NM_053072)	promoter-TSS (NM_053072)	88	NM_053072	13998	Mm.269596	NM_053072	ENSMUSG00000020021	Fgd6	AA123052|Etohd4|ZFYVE24	FYVE, RhoGEF and PH domain containing 6	protein-coding
mm_107953.1	chr12	72441872	72441896	+	1	NA	promoter-TSS (NM_001142728)	promoter-TSS (NM_001142728)	18	NM_030070	78257	Mm.266280	NM_030070	ENSMUSG00000021090	Lrrc9	4921529O18Rik|4930432K16Rik	leucine rich repeat containing 9	protein-coding
mm_127353.1	chr15	100619854	100619897	+	1	NA	3' UTR (NM_011873, exon 4 of 4)	3' UTR (NM_011873, exon 4 of 4)	4213	NM_011873	23994	Mm.486175	NM_011873	ENSMUSG00000000346	Dazap2	AI314727|Brbp|Gcap28|Prtb|gt6-12|mKIAA0058	DAZ associated protein 2	protein-coding
mm_26735.1	chr3	5576220	5576231	-	1	NA	promoter-TSS (NM_008994)	promoter-TSS (NM_008994)	23	NM_001163301	19302	Mm.132336	NM_008994	ENSMUSG00000040374	Pex2	D3Ertd138e|PAF-1|PMP35|Pxmp3	peroxisomal biogenesis factor 2	protein-coding
mm_24666.1	chr3	94487734	94487751	+	1	NA	exon (NM_001289613, exon 9 of 13)	exon (NM_001289613, exon 9 of 13)	5020	NR_110353	78784	Mm.44292	NM_172434	ENSMUSG00000028137	Celf3	4930415M08Rik|BRUNOL1|CAGH4|ERDA4|Tnrc4	CUGBP, Elav-like family member 3	protein-coding
mm_64270.1	chr7	141805633	141805639	+	1	NA	exon (NM_010844, exon 30 of 50)	exon (NM_010844, exon 30 of 50)	16625	NM_010844	17833	Mm.334332	NM_010844	ENSMUSG00000037974	Muc5ac	2210005L13Rik|MGM	mucin 5, subtypes A and C, tracheobronchial/gastric	protein-coding
mm_44413.1	chr5	17854223	17854287	-	1	NA	intron (NM_001159558, intron 1 of 15)	intron (NM_001159558, intron 1 of 15)	-4463	NM_001159556	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_21305.1	chr2	157079125	157079149	-	1	NA	5' UTR (NM_001164663, exon 1 of 15)	5' UTR (NM_001164663, exon 1 of 15)	128	NM_001164663	320706	Mm.79466	NM_001164663	ENSMUSG00000055485	Soga1	9830001H06Rik|AI426038|D430036N24Rik|Soga	suppressor of glucose, autophagy associated 1	protein-coding
mm_84111.1	chr9	58370410	58370438	-	1	NA	promoter-TSS (NR_040727)	promoter-TSS (NR_040727)	-55	NM_028854	74286	Mm.252761	NM_028854	ENSMUSG00000036244	Tbc1d21	1700095K08Rik|MgcRabGAP	TBC1 domain family, member 21	protein-coding
mm_94769.1	chr11	21239159	21239178	+	1	NA	5' UTR (NM_001290628, exon 1 of 23)	5' UTR (NM_001290628, exon 1 of 23)	136	NM_001290628	245944	Mm.170103	NM_139061	ENSMUSG00000020128	Vps54	Hcc8|Vps54l|mSLP8|wr	VPS54 GARP complex subunit	protein-coding
mm_81458.1	chr9	109833218	109833226	+	1	NA	5' UTR (NM_018757, exon 2 of 7)	5' UTR (NM_018757, exon 2 of 7)	428	NM_018757	54369	Mm.12951	NM_018757	ENSMUSG00000032478	Nme6	nm23-M6	NME/NM23 nucleoside diphosphate kinase 6	protein-coding
mm_141801.1	chr17	34477291	34477320	-	1	NA	Intergenic	Intergenic	-1368	NM_030746	632126	Mm.484958	NM_030746	ENSMUSG00000058435	Btnl4	Btn3a3|EG632126|NG11	butyrophilin-like 4	protein-coding
mm_84986.1	chr9	86464901	86464943	-	1	NA	promoter-TSS (NM_027394)	promoter-TSS (NM_027394)	-6	NM_027394	70348	Mm.53469	NM_027394	ENSMUSG00000032415	Ube2cbp	2610018I03Rik|Ube3d	ubiquitin-conjugating enzyme E2C binding protein	protein-coding
mm_111325.1	chr12	86470015	86470026	-	1	NA	intron (NM_011934, intron 1 of 6)	intron (NM_011934, intron 1 of 6)	48376	NM_011934	26380	Mm.235550	NM_011934	ENSMUSG00000021255	Esrrb	Err2|Errb|Estrrb|Nr3b2	estrogen related receptor, beta	protein-coding
mm_22927.1	chr3	31121698	31121701	+	1	NA	3' UTR (NM_001039090, exon 7 of 7)	3' UTR (NM_001039090, exon 7 of 7)	26641	NM_001039090	20482	Mm.15406	NM_011386	ENSMUSG00000027660	Skil	Skir|SnoN|sno	SKI-like	protein-coding
mm_51353.1	chr6	72557335	72557343	+	1	NA	intron (NM_001271395, intron 5 of 9)	B3|SINE|B2	7692	NM_001271395	12332	Mm.18626	NM_007599	ENSMUSG00000056737	Capg	gCap39|mbh1	capping protein (actin filament), gelsolin-like	protein-coding
mm_75850.1	chr8	70650420	70650431	-	1	NA	3' UTR (NM_023217, exon 5 of 5)	3' UTR (NM_023217, exon 5 of 5)	9313	NM_023217	66522	Mm.154906	NM_023217	ENSMUSG00000056204	Pgpep1	2810003H13Rik|Gm19458|PAP-I|PGP|PGP-I|PGPI|Pcp	pyroglutamyl-peptidase I	protein-coding
mm_18347.1	chr2	58159194	58159211	-	1	NA	intron (NM_139200, intron 1 of 7)	intron (NM_139200, intron 1 of 7)	920	NM_139200	227929	Mm.273905	NM_139200	ENSMUSG00000026832	Cytip	A130053M09Rik|AI462064|C80816|Cbp|Cybr|Pscdbp	cytohesin 1 interacting protein	protein-coding
mm_155471.1	chrX	73640118	73640129	+	1	NA	intron (NM_029352, intron 1 of 3)	CpG	682	NM_029352	75590	Mm.16479	NM_029352	ENSMUSG00000031383	Dusp9	Dusp4|Mpk4|Pyst3	dual specificity phosphatase 9	protein-coding
mm_110832.1	chr12	72664760	72664813	-	1	NA	promoter-TSS (NM_025522)	promoter-TSS (NM_025522)	42	NM_025522	66375	Mm.289653	NM_025522	ENSMUSG00000021094	Dhrs7	2310016E22Rik|5730564L20Rik|AW061210|Retdsr4|Retsdr4	dehydrogenase/reductase (SDR family) member 7	protein-coding
mm_144754.1	chr18	35726976	35726994	+	1	NA	promoter-TSS (NM_001033168)	promoter-TSS (NM_001033168)	-4	NM_001033168	73449	Mm.379225	NM_001033168	ENSMUSG00000073598	1700066B19Rik	-	RIKEN cDNA 1700066B19 gene	protein-coding
mm_24544.1	chr3	93293167	93293186	+	1	NA	Intergenic	Intergenic	-26573	NM_133698	68723	Mm.208047	NM_133698	ENSMUSG00000041991	Hrnr	1110033K19Rik|A530063N20Rik|S100a18	hornerin	protein-coding
mm_120078.1	chr14	57537488	57537494	+	1	NA	intron (NM_145837, intron 2 of 2)	intron (NM_145837, intron 2 of 2)	12662	NM_145837	239114	Mm.390726	NM_145837	ENSMUSG00000050222	Il17d	AI462269|IL-17D	interleukin 17D	protein-coding
mm_163879.1	chr14	19419675	19419692	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	182904	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_24057.1	chr3	87915057	87915080	+	1	NA	3' UTR (NM_008231, exon 6 of 6)	3' UTR (NM_008231, exon 6 of 6)	-4476	NM_026591	67707	Mm.393802	NM_026591	ENSMUSG00000019710	Mrpl24	2010005E08Rik|2810470K06Rik|6720473G22Rik|AA407670	mitochondrial ribosomal protein L24	protein-coding
mm_88844.1	chr10	80929095	80929101	+	1	NA	promoter-TSS (NM_008655)	promoter-TSS (NM_008655)	-993	NM_008655	17873	Mm.1360	NM_008655	ENSMUSG00000015312	Gadd45b	AI323528|Myd118	growth arrest and DNA-damage-inducible 45 beta	protein-coding
mm_29883.1	chr3	131112140	131112150	-	1	NA	promoter-TSS (NM_001276403)	promoter-TSS (NM_001276403)	-646	NM_001276403	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_8514.1	chr1	154726705	154726714	-	1	NA	promoter-TSS (NM_009782)	promoter-TSS (NM_009782)	-789	NM_009782	12290	Mm.267517	NM_009782	ENSMUSG00000004110	Cacna1e	A430040I15|BII|Cach6|Cacnl1a6|Cav2.3|Cchra1|alpha1E	calcium channel, voltage-dependent, R type, alpha 1E subunit	protein-coding
mm_80881.1	chr9	99139514	99139530	+	1	NA	intron (NM_029094, intron 1 of 23)	intron (NM_029094, intron 1 of 23)	689	NM_029094	74769	Mm.213128	NM_029094	ENSMUSG00000032462	Pik3cb	1110001J02Rik|AI447572|p110beta	phosphatidylinositol 3-kinase, catalytic, beta polypeptide	protein-coding
mm_119631.1	chr14	51253865	51253885	+	1	NA	Intergenic	RLTR25B|LTR|ERVK	2237	NM_053113	93726	Mm.153688	NM_053113	ENSMUSG00000047222	Rnase2a	Ear11	ribonuclease, RNase A family, 2A (liver, eosinophil-derived neurotoxin)	protein-coding
mm_47613.1	chr5	125140895	125140921	-	1	NA	intron (NM_011424, intron 1 of 46)	intron (NM_011424, intron 1 of 46)	38306	NM_001253905	20602	Mm.278646	NM_011424	ENSMUSG00000029478	Ncor2	N-CoR|SMRT|SMRTe	nuclear receptor co-repressor 2	protein-coding
mm_47243.1	chr5	121527261	121527269	-	1	NA	intron (NM_010765, intron 10 of 13)	PB1D10|SINE|Alu	-5570	NM_172126	280668	Mm.1453	NM_172126	ENSMUSG00000072647	Adam1a	Adam1|Ftna	a disintegrin and metallopeptidase domain 1a	protein-coding
mm_1246.1	chr1	62798400	62798411	+	1	NA	intron (NM_010939, intron 15 of 15)	intron (NM_010939, intron 15 of 15)	-3673	NR_040601	74992	Mm.401979	NR_040601		4930487H11Rik	-	RIKEN cDNA 4930487H11 gene	ncRNA
mm_163884.1	chr14	23384437	23384443	+	1	NA	intron (NM_001253366, intron 20 of 29)	intron (NM_001253366, intron 20 of 29)	-289869	NR_033550	791307	Mm.364384	NR_033550	ENSMUSG00000068680	Gm10248	ENSMUSG00000068680	predicted gene 10248	ncRNA
mm_45669.1	chr5	77211393	77211403	-	1	NA	promoter-TSS (NM_001289764)	promoter-TSS (NM_001289764)	73	NM_183284	69982	Mm.46106	NM_183284	ENSMUSG00000053030	Spink2	1700007F22Rik|AV038945|HUSI-II	serine peptidase inhibitor, Kazal type 2	protein-coding
mm_144462.1	chr18	23497499	23497544	+	1	NA	promoter-TSS (NM_001285810)	promoter-TSS (NM_001285810)	39	NM_001285810	13527	Mm.94371	NM_010087	ENSMUSG00000024302	Dtna	2210407P21Rik|DTN-A|Dtn|Gm19389|a-DB-1|adbn	dystrobrevin alpha	protein-coding
mm_9340.1	chr1	172027270	172027313	-	1	NA	promoter-TSS (NM_033509)	promoter-TSS (NM_033509)	4	NM_033509	93840	Mm.36148	NM_033509	ENSMUSG00000026556	Vangl2	C530001F03Rik|Lootl|Lp|Lpp1|Ltap|Vang1l2|loop-tail|ska17|ska<m17Jus>|stbm|strabismus	vang-like 2 (van gogh, Drosophila)	protein-coding
mm_56032.1	chr6	86620089	86620104	-	1	NA	Intergenic	Intergenic	-8078	NM_026414	67855	Mm.183043	NM_026414	ENSMUSG00000033508	Asprv1	2300003P22Rik|AA986851|SASP|SASPase|Taps	aspartic peptidase, retroviral-like 1	protein-coding
mm_3780.1	chr1	156615904	156615933	+	1	NA	intron (NM_001136104, intron 1 of 12)	intron (NM_001136104, intron 1 of 12)	57131	NM_001136104	11352	Mm.329515	NM_009595	ENSMUSG00000026596	Abl2	AA536808|Abll|Arg	v-abl Abelson murine leukemia viral oncogene 2 (arg, Abelson-related gene)	protein-coding
mm_89363.1	chr10	88437481	88437492	+	1	NA	exon (NM_001004164, exon 16 of 21)	exon (NM_001004164, exon 16 of 21)	-22101	NM_011517	20962	Mm.297977	NM_011517	ENSMUSG00000020059	Sycp3	Cor1|Scp3	synaptonemal complex protein 3	protein-coding
mm_15043.1	chr2	152829459	152829475	+	1	NA	exon (NM_009743, exon 2 of 3)	exon (NM_009743, exon 2 of 3)	1250	NM_001289716	12048	Mm.238213	NM_009743	ENSMUSG00000007659	Bcl2l1	Bcl(X)L|Bcl-XL|Bcl2l|BclX|bcl-x|bcl2-L-1	BCL2-like 1	protein-coding
mm_56532.1	chr6	99545814	99545814	-	1	NA	Intergenic	L1MD2|LINE|L1	-24821	NM_001347345	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_27076.1	chr3	28816244	28816254	-	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	10738	NM_026517	68028	Mm.371630	NM_026517	ENSMUSG00000039221	Rpl22l1	3110001N18Rik|AU041196	ribosomal protein L22 like 1	protein-coding
mm_57065.1	chr6	122570850	122570867	-	1	NA	Intergenic	Intergenic	17049	NM_009645	11628	Mm.391503	NM_009645	ENSMUSG00000040627	Aicda	Aid|Arp2	activation-induced cytidine deaminase	protein-coding
mm_107812.1	chr12	65113090	65113104	+	1	NA	intron (NM_178912, intron 14 of 22)	intron (NM_178912, intron 14 of 22)	37491	NM_178912	104806	Mm.374847	NM_178912	ENSMUSG00000055884	Fancm	AI427100|C730036B14Rik|D12Ertd364e	Fanconi anemia, complementation group M	protein-coding
mm_45310.1	chr5	65428399	65428405	-	1	NA	intron (NM_009466, intron 1 of 11)	MLT1A1|LTR|ERVL-MaLR	7440	NM_009466	22235	Mm.344831	NM_009466	ENSMUSG00000029201	Ugdh	Udpgdh	UDP-glucose dehydrogenase	protein-coding
mm_165907.1	chr4	53142630	53142639	-	1	NA	intron (NM_013454, intron 2 of 49)	intron (NM_013454, intron 2 of 49)	17261	NM_013454	11303	Mm.277376	NM_013454	ENSMUSG00000015243	Abca1	ABC-1|Abc1	ATP-binding cassette, sub-family A (ABC1), member 1	protein-coding
mm_59130.1	chr7	19965461	19965467	+	1	NA	promoter-TSS (NM_027839)	promoter-TSS (NM_027839)	52	NM_027839	71601	Mm.98097	NM_027839	ENSMUSG00000070777	Ceacam20	9130012D09Rik	carcinoembryonic antigen-related cell adhesion molecule 20	protein-coding
mm_36580.1	chr4	88032806	88032822	-	1	NA	intron (NM_027326, intron 1 of 10)	CpG	593	NM_027326	70122	Mm.288898	NM_027326	ENSMUSG00000028496	Mllt3	2210011H10Rik|2610012I03Rik|3830408D16Rik|Af9|D4Ertd321e	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 3	protein-coding
mm_29636.1	chr3	121814795	121814816	-	1	NA	intron (NM_008991, intron 1 of 22)	CpG	410	NM_008991	19299	Mm.399042	NM_008991	ENSMUSG00000028127	Abcd3	AI313901|AU018866|AW146054|PMP68|PMP70|Pxmp1	ATP-binding cassette, sub-family D (ALD), member 3	protein-coding
mm_124538.1	chr14	122461613	122461622	-	1	NA	intron (NM_022987, intron 1 of 1)	intron (NM_022987, intron 1 of 1)	4041	NM_022987	65100	Mm.390761	NM_022987	ENSMUSG00000041703	Zic5	1700049L20Rik|Opr	zinc finger protein of the cerebellum 5	protein-coding
mm_60926.1	chr7	46847156	46847168	+	1	NA	promoter-TSS (NM_001136069)	promoter-TSS (NM_001136069)	80	NM_001136069	16828	Mm.29324	NM_010699	ENSMUSG00000063229	Ldha	Ldh1|Ldhm|l7R2	lactate dehydrogenase A	protein-coding
mm_134453.1	chr16	18410779	18410800	-	1	NA	exon (NM_001111062, exon 5 of 6)	exon (NM_001111062, exon 5 of 6)	2705	NM_001111063	12846	Mm.100940	NM_007744	ENSMUSG00000000326	Comt	Comt1|D16Wsu103e|D330014B15Rik	catechol-O-methyltransferase	protein-coding
mm_79991.1	chr9	67032797	67032837	+	1	NA	exon (NM_001164251, exon 5 of 10)	exon (NM_001164251, exon 5 of 10)	11054	NM_001164252	22003	Mm.121878	NM_024427	ENSMUSG00000032366	Tpm1	AA986836|AI854628|TM2|Tm3|Tmpa|Tpm-1|alpha-TM	tropomyosin 1, alpha	protein-coding
mm_124915.1	chr15	11967059	11967114	+	1	NA	promoter-TSS (NR_040447)	promoter-TSS (NR_040447)	24	NR_040447	73339	Mm.231975	NR_040447	ENSMUSG00000099349	1700047G03Rik	-	RIKEN cDNA 1700047G03 gene	ncRNA
mm_147609.1	chr18	56974058	56974067	-	1	NA	intron (NM_029909, intron 1 of 4)	intron (NM_029909, intron 1 of 4)	1317	NM_029909	77422	Mm.256874	NM_029909	ENSMUSG00000024592	C330018D20Rik	AU018666	RIKEN cDNA C330018D20 gene	protein-coding
mm_102623.1	chr11	62494796	62494812	-	1	NA	intron (NM_001039536, intron 2 of 6)	intron (NM_001039536, intron 2 of 6)	36344	NM_001039536	327942	Mm.390358	NM_199026	ENSMUSG00000014245	Pigl	Gm737	phosphatidylinositol glycan anchor biosynthesis, class L	protein-coding
mm_63408.1	chr7	127333603	127333625	+	1	NA	3' UTR (NM_001253873, exon 31 of 31)	3' UTR (NM_001253873, exon 31 of 31)	11700	NM_146202	233890	Mm.23031	NM_146202	ENSMUSG00000047371	Zfp768	BC026432|Znf768	zinc finger protein 768	protein-coding
mm_140285.1	chr17	85090648	85090721	+	1	NA	promoter-TSS (NM_001163624)	promoter-TSS (NM_001163624)	-16	NM_028576	73582	Mm.260753	NM_028576	ENSMUSG00000071037	Camkmt	1700106N22Rik|AI480743|AV099781|CLNMT|CaM KMT	calmodulin-lysine N-methyltransferase	protein-coding
mm_124930.1	chr15	12205010	12205040	+	1	NA	promoter-TSS (NM_172958)	promoter-TSS (NM_172958)	-69	NM_172958	268783	Mm.54460	NM_172958	ENSMUSG00000039458	Mtmr12	3Pap|4932703C11|C730015A02Rik|Pip3ap|mKIAA1682	myotubularin related protein 12	protein-coding
mm_42910.1	chr5	122643879	122643984	+	1	NA	promoter-TSS (NM_011027)	promoter-TSS (NM_011027)	20	NM_001038887	18439	Mm.42026	NM_011027	ENSMUSG00000029468	P2rx7	AI467586|P2X(7)|P2X7R	purinergic receptor P2X, ligand-gated ion channel, 7	protein-coding
mm_127099.1	chr15	97791195	97791210	+	1	NA	3' UTR (NM_026353, exon 3 of 3)	3' UTR (NM_026353, exon 3 of 3)	6837	NM_026353	67739	Mm.28955	NM_026353	ENSMUSG00000081534	Slc48a1	4930570C03Rik	solute carrier family 48 (heme transporter), member 1	protein-coding
mm_137709.1	chr17	29099423	29099463	+	1	NA	3' UTR (NM_007669, exon 3 of 3)	3' UTR (NM_007669, exon 3 of 3)	5674	NM_007669	12575	Mm.195663	NM_007669	ENSMUSG00000023067	Cdkn1a	CAP20|CDKI|CIP1|Cdkn1|P21|SDI1|Waf1|mda6|p21Cip1|p21WAF	cyclin-dependent kinase inhibitor 1A (P21)	protein-coding
mm_5518.1	chr1	37691524	37691526	-	1	NA	intron (NM_028096, intron 1 of 9)	intron (NM_028096, intron 1 of 9)	28286	NM_028096	72097	Mm.142607	NM_028096	ENSMUSG00000026090	2010300C02Rik	-	RIKEN cDNA 2010300C02 gene	protein-coding
mm_52333.1	chr6	109874953	109874957	+	1	NA	Intergenic	RMER19C|LTR|ERVK	-770557	NM_001346640	108073	Mm.240881	NM_177328	ENSMUSG00000056755	Grm7	6330570A01Rik|BB176677|C030018L03|E130018M02Rik|Gpr1g|Gprc1g|SMN2|Tg(SMN2)89Ahmb|mGluR7	glutamate receptor, metabotropic 7	protein-coding
mm_13074.1	chr2	91182184	91182212	+	1	NA	intron (NM_001177719, intron 1 of 34)	intron (NM_001177719, intron 1 of 34)	849	NM_001177719	228355	Mm.36410	NM_145527	ENSMUSG00000040687	Madd	9630059K23Rik|IG20	MAP-kinase activating death domain	protein-coding
mm_58377.1	chr6	149101507	149101589	-	1	NA	5' UTR (NM_177192, exon 1 of 21)	5' UTR (NM_177192, exon 1 of 21)	132	NM_177192	320560	Mm.426874	NM_177192	ENSMUSG00000030313	Dennd5b	9330160C06Rik|AI852444|D030011O10Rik|ENSMUSG00000072657|Gm17524	DENN/MADD domain containing 5B	protein-coding
mm_31959.1	chr4	86874990	86874995	+	1	NA	intron (NM_139306, intron 1 of 5)	intron (NM_139306, intron 1 of 5)	578	NM_139306	230379	Mm.45019	NM_139306	ENSMUSG00000038007	Acer2	2410116I05Rik|Asah3l|CRG-L1|maCER2	alkaline ceramidase 2	protein-coding
mm_114261.1	chr13	56810421	56810459	+	1	NA	exon (NM_012035, exon 6 of 12)	exon (NM_012035, exon 6 of 12)	85349	NM_001302372	26946	Mm.62409	NM_012035	ENSMUSG00000021541	Trpc7	TRP7|Trrp8	transient receptor potential cation channel, subfamily C, member 7	protein-coding
mm_16306.1	chr2	174289877	174289899	+	1	NA	intron (NR_002846, intron 1 of 4)	(CA)n|Simple_repeat|Simple_repeat	5548	NR_002846	56802	Mm.125770	NR_002846	ENSMUSG00000086537	Nespas	Gnas-as|Nespos	neuroendocrine secretory protein antisense	ncRNA
mm_96085.1	chr11	60140067	60140080	+	1	NA	promoter-TSS (NM_001037764)	promoter-TSS (NM_001037764)	-9	NM_001037764	19377	Mm.296366	NM_009021	ENSMUSG00000062115	Rai1	Gt1	retinoic acid induced 1	protein-coding
mm_91179.1	chr10	20839251	20839269	-	1	NA	Intergenic	Intergenic	-113287	NM_026203	52906	Mm.253280	NM_026203	ENSMUSG00000019986	Ahi1	1700015F03Rik|Ahi-1|D10Bwg0629e	Abelson helper integration site 1	protein-coding
mm_148983.1	chr19	8591174	8591180	+	1	NA	promoter-TSS (NM_001164634)	promoter-TSS (NM_001164634)	-77	NM_001164634	19879	Mm.285294	NM_031194	ENSMUSG00000063796	Slc22a8	Oat3|Roct	solute carrier family 22 (organic anion transporter), member 8	protein-coding
mm_55493.1	chr6	69607433	69607443	-	1	NA	Intergenic	Intergenic	-280264	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_153979.1	chr19	47864780	47864789	-	1	NA	promoter-TSS (NM_030051)	promoter-TSS (NM_030051)	-761	NM_030051	68214	Mm.63791	NM_026619	ENSMUSG00000025069	Gsto2	1700020F09Rik|4930425C18Rik|GSTO 2-2	glutathione S-transferase omega 2	protein-coding
mm_99225.1	chr11	101045073	101045090	+	1	NA	intron (NM_001243050, intron 17 of 20)	intron (NM_001243050, intron 17 of 20)	14741	NR_105893	102466767		NR_105893	ENSMUSG00000098415	Mir6928	Gm27728|mmu-mir-6928	microRNA 6928	ncRNA
mm_119574.1	chr14	50769206	50769207	+	1	NA	intron (NM_001080949, intron 8 of 9)	intron (NM_001080949, intron 8 of 9)	16314	NM_177625	219022	Mm.276362	NM_177625	ENSMUSG00000006288	Ttc5	-	tetratricopeptide repeat domain 5	protein-coding
mm_49179.1	chr6	15125485	15125489	+	1	NA	intron (NM_053242, intron 3 of 18)	intron (NM_053242, intron 3 of 18)	-60019	NM_212435	114142	Mm.332919	NM_053242	ENSMUSG00000029563	Foxp2	2810043D05Rik|AI449000|CAG-16|D0Kist7	forkhead box P2	protein-coding
mm_10283.1	chr2	10080601	10080618	+	1	NA	promoter-TSS (NM_001112738)	promoter-TSS (NM_001112738)	-3	NM_025280	16588	Mm.35498	NM_025280	ENSMUSG00000037262	Kin	Kin17	Kin17 DNA and RNA binding protein	protein-coding
mm_120024.1	chr14	55768827	55768837	+	1	NA	TTS (NM_080435)	TTS (NM_080435)	2870	NM_008519	16995	Mm.20853	NM_008519	ENSMUSG00000046908	Ltb4r1	BLT1|BLTR|Ltb4r|mBLTR	leukotriene B4 receptor 1	protein-coding
mm_135376.1	chr16	44139004	44139026	-	1	NA	promoter-TSS (NM_007508)	promoter-TSS (NM_007508)	4	NM_007508	11964	Mm.217787	NM_007508	ENSMUSG00000052459	Atp6v1a	AI647066|Atp6a1|Atp6a2|Atp6v1a1|VA68|VPP2	ATPase, H+ transporting, lysosomal V1 subunit A	protein-coding
mm_90154.1	chr10	118253141	118253151	+	1	NA	Intergenic	Intergenic	41892	NM_054079	116849	Mm.213193	NM_054079	ENSMUSG00000090461	Iltifb	IL-22b|IL-TIFb|Il22b	interleukin 10-related T cell-derived inducible factor beta	protein-coding
mm_151587.1	chr19	61227758	61227761	+	1	NA	intron (NM_009970, intron 1 of 11)	CpG-7695	659	NM_009970	12982	Mm.287228	NM_009970	ENSMUSG00000059326	Csf2ra	CD116|Csfgmra|GM-CSF-Ra|GM-CSFR	colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)	protein-coding
mm_169293.1	chr1	40195098	40195100	+	1	NA	Intergenic	Intergenic	-29981	NM_008362	16177	Mm.896	NM_008362	ENSMUSG00000026072	Il1r1	CD121a|CD121b|IL-1R1|IL-iR|Il1r-1	interleukin 1 receptor, type I	protein-coding
mm_100892.1	chr11	6065738	6065755	-	1	NA	promoter-TSS (NM_001174054)	promoter-TSS (NM_001174054)	2	NM_001174054	12323	Mm.439733	NM_007595	ENSMUSG00000057897	Camk2b	CaMKII	calcium/calmodulin-dependent protein kinase II, beta	protein-coding
mm_7398.1	chr1	118388863	118388888	-	1	NA	promoter-TSS (NM_029709)	promoter-TSS (NM_029709)	-183	NM_001293300	76707	Mm.138740	NM_029709	ENSMUSG00000064302	Clasp1	1700030C23Rik|5730583A19Rik|B130045P17Rik|CLASP1alpha	CLIP associating protein 1	protein-coding
mm_115563.1	chr13	9764585	9764595	-	1	NA	promoter-TSS (NM_001347480)	promoter-TSS (NM_001347480)	-120	NM_001347472	66505	Mm.397307	NM_144516	ENSMUSG00000021156	Zmynd11	2210402G22Rik|BS69	zinc finger, MYND domain containing 11	protein-coding
mm_118396.1	chr13	119353203	119353221	-	1	NA	intron (NM_001308506, intron 14 of 16)	B4|SINE|B4	55799	NM_008710	18115	Mm.132584	NM_008710	ENSMUSG00000025453	Nnt	4930423F13Rik|AI323702|BB168308	nicotinamide nucleotide transhydrogenase	protein-coding
mm_124238.1	chr14	101477412	101477420	-	1	NA	intron (NM_001081278, intron 9 of 18)	intron (NM_001081278, intron 9 of 18)	131775	NM_001081278	210789	Mm.320639	NM_173380	ENSMUSG00000033083	Tbc1d4	5930406J04Rik|A930035N22|AV295684|As160	TBC1 domain family, member 4	protein-coding
mm_71636.1	chr8	57489618	57489631	+	1	NA	intron (NR_126553, intron 1 of 3)	ORR1A2-int|LTR|ERVL-MaLR	1661	NR_126555	78353	Mm.426240	NR_126553	ENSMUSG00000096917	2500002B13Rik	-	RIKEN cDNA 2500002B13 gene	ncRNA
mm_42726.1	chr5	120613144	120613152	+	1	NA	promoter-TSS (NM_029096)	promoter-TSS (NM_029096)	18	NM_028041	71990	Mm.24495	NM_028041	ENSMUSG00000029599	Ddx54	2410015A15Rik|AI414901|DP97	DEAD (Asp-Glu-Ala-Asp) box polypeptide 54	protein-coding
mm_80230.1	chr9	72670033	72670056	+	1	NA	exon (NM_010890, exon 2 of 29)	exon (NM_010890, exon 2 of 29)	7697	NM_010890	17999	Mm.279923	NM_010890	ENSMUSG00000032216	Nedd4	AA959633|AL023035|AU019897|E430025J12Rik|Nedd4-1|Nedd4a|mKIAA0093	neural precursor cell expressed, developmentally down-regulated 4	protein-coding
mm_118753.1	chr14	22365332	22365355	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	177455	NR_046307	74896	Mm.444661	NR_046307		4930405A10Rik	4930456G20Rik	RIKEN cDNA 4930405A10 gene	ncRNA
mm_121175.1	chr14	103037385	103037395	+	1	NA	Intergenic	MTE2a|LTR|ERVL-MaLR	-3587	NR_045657	71264	Mm.399572	NR_045657		4933432I03Rik	-	RIKEN cDNA 4933432I03 gene	ncRNA
mm_15734.1	chr2	164237204	164237207	+	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	1136	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_100886.1	chr11	6029044	6029052	-	1	NA	intron (NM_007595, intron 1 of 20)	intron (NM_007595, intron 1 of 20)	36700	NM_001174054	12323	Mm.439733	NM_007595	ENSMUSG00000057897	Camk2b	CaMKII	calcium/calmodulin-dependent protein kinase II, beta	protein-coding
mm_111305.1	chr12	85747670	85747678	-	1	NA	intron (NM_145447, intron 1 of 9)	intron (NM_145447, intron 1 of 9)	1135	NM_145447	217721	Mm.301076	NM_145447	ENSMUSG00000034258	Mfsd7c	CCT|Flvcr2	major facilitator superfamily domain containing 7C	protein-coding
mm_75947.1	chr8	71592037	71592072	-	1	NA	promoter-TSS (NM_025396)	promoter-TSS (NM_025396)	-130	NM_025396	66171	Mm.282284	NM_025396	ENSMUSG00000031807	Pgls	1110030K05Rik|AI447866|Plgs	6-phosphogluconolactonase	protein-coding
mm_54341.1	chr6	30669444	30669450	-	1	NA	intron (NR_130781, intron 3 of 11)	intron (NR_130781, intron 3 of 11)	24302	NM_031998	83922	Mm.65389	NM_031998	ENSMUSG00000029790	Cep41	1700017E11Rik|2810431D15Rik|Tsga14	centrosomal protein 41	protein-coding
mm_6012.1	chr1	59014071	59014075	-	1	NA	Intergenic	Intergenic	40502	NM_172656	227154	Mm.286006	NM_172656	ENSMUSG00000026027	Stradb	AA792893|Als2cr2|B830008M19|D1Ucla2|ILPIP|ILPIPA|PRO1038|Papk|Syradb	STE20-related kinase adaptor beta	protein-coding
mm_6379.1	chr1	72700545	72700556	-	1	NA	promoter-TSS (NM_176980)	promoter-TSS (NM_176980)	14	NM_176980	319695	Mm.249056	NM_176980	ENSMUSG00000039342	Ankar	4932422E22Rik	ankyrin and armadillo repeat containing	protein-coding
mm_116809.1	chr13	54303492	54303517	-	1	NA	Intergenic	Intergenic	-67845	NM_009946	12890	Mm.268902	NM_009946	ENSMUSG00000025867	Cplx2	921-L|AI413745|AW492120	complexin 2	protein-coding
mm_70251.1	chr8	3485729	3485737	+	1	NA	exon (NM_029598, exon 8 of 9)	exon (NM_029598, exon 8 of 9)	-7405	NM_080461	140482	Mm.299073	NM_080461	ENSMUSG00000047264	Zfp358	Zfend	zinc finger protein 358	protein-coding
mm_139236.1	chr17	47732955	47732965	+	1	NA	intron (NM_025973, intron 6 of 8)	intron (NM_025973, intron 6 of 8)	-4077	NM_001161722	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_119449.1	chr14	46884577	46884585	+	1	NA	5' UTR (NM_028966, exon 2 of 12)	5' UTR (NM_028966, exon 2 of 12)	1616	NM_001037221	74480	Mm.214454	NM_028966	ENSMUSG00000021838	Samd4	1700024G08Rik|1700111L17Rik|4933436G17Rik|Samd4a|Smaug|Smaug1|sunk	sterile alpha motif domain containing 4	protein-coding
mm_18171.1	chr2	45110041	45110049	-	1	NA	exon (NM_015753, exon 2 of 10)	exon (NM_015753, exon 2 of 10)	232	NM_001289521	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_111241.1	chr12	84773088	84773091	-	1	NA	promoter-TSS (NM_028863)	promoter-TSS (NM_028863)	23	NM_023409	67963	Mm.282556	NM_023409	ENSMUSG00000021242	Npc2	2700012J19Rik|AA408070|AU045843|HE1	Niemann-Pick type C2	protein-coding
mm_6050.1	chr1	60097613	60097702	-	1	NA	promoter-TSS (NM_139150)	promoter-TSS (NM_139150)	250	NM_021312	57750	Mm.281079	NM_021312	ENSMUSG00000026019	Wdr12	4933402C23Rik|Ytm1|Ytm1p	WD repeat domain 12	protein-coding
mm_38221.1	chr4	135973523	135973531	-	1	NA	promoter-TSS (NM_011942)	promoter-TSS (NM_011942)	-933	NM_011942	26394	Mm.34302	NM_011942	ENSMUSG00000028670	Lypla2	LysoII	lysophospholipase 2	protein-coding
mm_82602.1	chr9	21359425	21359426	-	1	NA	Intergenic	RLTR30|LTR|ERV1	-8446	NM_001042708	16201	Mm.440026	NM_010561	ENSMUSG00000032178	Ilf3	MBII-26|MPHOSPH4|NF90|NFAR	interleukin enhancer binding factor 3	protein-coding
mm_46384.1	chr5	103990239	103990243	-	1	NA	3' UTR (NM_053262, exon 7 of 7)	3' UTR (NM_053262, exon 7 of 7)	-12853	NM_001163486	243168	Mm.284944	NM_198030	ENSMUSG00000034528	Hsd17b13	AI047820|PAN1B-like|Pan1b	hydroxysteroid (17-beta) dehydrogenase 13	protein-coding
mm_111824.1	chr12	106716342	106716344	-	1	NA	promoter-TSS (NR_015512)	promoter-TSS (NR_015512)	-19	NR_015512	71033	Mm.159404	NR_015512	ENSMUSG00000085820	4933406K04Rik	4930426M03Rik|4930485I22Rik|4933427G14Rik	RIKEN cDNA 4933406K04 gene	ncRNA
mm_151325.1	chr19	55893287	55893291	+	1	NA	intron (NR_138565, intron 4 of 15)	intron (NR_138565, intron 4 of 15)	-2032	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_151948.1	chr19	5801116	5801126	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	1551	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_106488.1	chr11	120235869	120235899	-	1	NA	intron (NM_001347621, intron 1 of 27)	CpG	2937	NM_198423	268515	Mm.309498	NM_198423	ENSMUSG00000039741	Bahcc1	B930044J06|BC060615	BAH domain and coiled-coil containing 1	protein-coding
mm_62624.1	chr7	107567648	107567708	+	1	NA	5' UTR (NM_172907, exon 1 of 3)	5' UTR (NM_172907, exon 1 of 3)	245	NM_172907	244198	Mm.77425	NM_172907	ENSMUSG00000051041	Olfml1	6720478C22|AV321997|BC047207|MVAL564|ONT2|mONT2	olfactomedin-like 1	protein-coding
mm_25428.1	chr3	107885935	107885939	+	1	NA	intron (NM_133867, intron 12 of 18)	intron (NM_133867, intron 12 of 18)	8707	NM_133867	99662	Mm.108491	NM_133867	ENSMUSG00000040600	Eps8l3	AI504489|Eps8r3	EPS8-like 3	protein-coding
mm_125208.1	chr15	33861185	33861188	+	1	NA	Intergenic	Intergenic	-173303	NM_001085421	239364	Mm.60794	NM_001085421	ENSMUSG00000038984	Tspyl5	6330530B20|E130308C19Rik	testis-specific protein, Y-encoded-like 5	protein-coding
mm_77826.1	chr9	3532361	3532448	+	1	NA	promoter-TSS (NM_001033322)	promoter-TSS (NM_001033322)	55	NM_001033322	234889	Mm.91240	NM_001033322	ENSMUSG00000041624	Gucy1a2	6330407I18Rik|A230060L24Rik	guanylate cyclase 1, soluble, alpha 2	protein-coding
mm_126175.1	chr15	78571799	78571811	+	1	NA	intron (NM_009008, intron 1 of 6)	intron (NM_009008, intron 1 of 6)	978	NM_009008	19354	Mm.1972	NM_009008	ENSMUSG00000033220	Rac2	AI323801|AI452260	RAS-related C3 botulinum substrate 2	protein-coding
mm_160715.1	chr10	61418204	61418204	+	1	NA	5' UTR (NM_013611, exon 1 of 3)	5' UTR (NM_013611, exon 1 of 3)	232	NM_013611	18119	Mm.57195	NM_013611	ENSMUSG00000037171	Nodal	Tg.413d	nodal	protein-coding
mm_153.1	chr1	11414266	11414331	+	1	NA	5' UTR (NM_001160369, exon 1 of 14)	5' UTR (NM_001160369, exon 1 of 14)	193	NM_001160371	320492	Mm.52021	NM_177173	ENSMUSG00000057715	A830018L16Rik	-	RIKEN cDNA A830018L16 gene	protein-coding
mm_111117.1	chr12	80967982	80967993	-	1	NA	promoter-TSS (NM_001177561)	promoter-TSS (NM_001177561)	92	NM_011387	20493	Mm.486361	NM_011387	ENSMUSG00000021135	Slc10a1	Ntcp	solute carrier family 10 (sodium/bile acid cotransporter family), member 1	protein-coding
mm_87919.1	chr10	62504129	62504140	+	1	NA	intron (NM_011157, intron 1 of 2)	intron (NM_011157, intron 1 of 2)	3621	NM_011157	19073	Mm.338790	NM_011157	ENSMUSG00000020077	Srgn	Prg|Prg1|Sgc	serglycin	protein-coding
mm_91233.1	chr10	22302560	22302573	-	1	NA	intron (NM_009018, intron 5 of 5)	intron (NM_009018, intron 5 of 5)	-4154	NR_015465	606736	Mm.387042	NR_015465	ENSMUSG00000097352	C920009B18Rik	-	RIKEN cDNA C920009B18 gene	ncRNA
mm_120108.1	chr14	59201966	59201968	+	1	NA	intron (NM_027764, intron 1 of 11)	intron (NM_027764, intron 1 of 11)	739	NM_027764	71330	Mm.234195	NM_027764	ENSMUSG00000035469	Rcbtb1	5430409I18Rik|AW111883|CLLD7|CLLL7	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 1	protein-coding
mm_135525.1	chr16	48994082	48994123	-	1	NA	promoter-TSS (NM_001110017)	promoter-TSS (NM_001110017)	10	NM_001110017	224170	Mm.275138	NM_027341	ENSMUSG00000064061	Dzip3	2310047C04Rik|2A-HUB|6430549P11Rik|A230104G20	DAZ interacting protein 3, zinc finger	protein-coding
mm_4699.1	chr1	180849133	180849144	+	1	NA	Intergenic	Intergenic	-2013	NM_145943	208768	Mm.272625	NM_145943	ENSMUSG00000038806	Sde2	-	SDE2 telomere maintenance homolog (S. pombe)	protein-coding
mm_5088.1	chr1	4496514	4496531	-	1	NA	5' UTR (NM_001289467, exon 1 of 3)	5' UTR (NM_001289467, exon 1 of 3)	832	NM_001289464	20671	Mm.279103	NM_011441	ENSMUSG00000025902	Sox17	-	SRY (sex determining region Y)-box 17	protein-coding
mm_109741.1	chr12	117466181	117466227	+	1	NA	Intergenic	Intergenic	-50275	NM_175930	217944	Mm.227642	NM_175930	ENSMUSG00000041992	Rapgef5	4932413M22|C86120|D030051B22Rik|GFR|Mrgef|mKIAA0277|mmr-gef	Rap guanine nucleotide exchange factor (GEF) 5	protein-coding
mm_115368.1	chr13	112993885	112993895	+	1	NA	promoter-TSS (NM_001037914)	promoter-TSS (NM_001037914)	22	NM_001037914	622408	Mm.360976	NM_001037914	ENSMUSG00000074651	Mcidas	EG622408|Gm6320|Idas|Mci|Mcin	multiciliate differentiation and DNA synthesis associated cell cycle protein	protein-coding
mm_141979.1	chr17	35163005	35163040	-	1	NA	5' UTR (NM_020027, exon 2 of 31)	5' UTR (NM_020027, exon 2 of 31)	1855	NM_001199044	53761	Mm.272462	NM_020027	ENSMUSG00000024393	Prrc2a	3110039B05Rik|Bat-2|Bat2|D17H6S51E|G2|Wbp12|mKIAA4178	proline-rich coiled-coil 2A	protein-coding
mm_127705.1	chr15	102991159	102991176	+	1	NA	exon (NM_010466, exon 1 of 2)	exon (NM_010466, exon 1 of 2)	628	NM_010466	15426	Mm.6167	NM_010466	ENSMUSG00000001657	Hoxc8	D130011F21Rik|Hox-3.1	homeobox C8	protein-coding
mm_119187.1	chr14	32322054	32322069	+	1	NA	promoter-TSS (NM_001081130)	promoter-TSS (NM_001081130)	42	NM_001081130	239017	Mm.318302	NM_001081130	ENSMUSG00000021913	Ogdhl	-	oxoglutarate dehydrogenase-like	protein-coding
mm_144849.1	chr18	36635555	36635557	+	1	NA	intron (NM_175375, intron 20 of 33)	B1_Mur3|SINE|Alu	-28504	NM_201256	108112	Mm.24790	NM_201256	ENSMUSG00000090264	Eif4ebp3	4e-bp3	eukaryotic translation initiation factor 4E binding protein 3	protein-coding
mm_2843.1	chr1	131638355	131638363	+	1	NA	promoter-TSS (NM_007799)	promoter-TSS (NM_007799)	45	NM_007799	13034	Mm.230249	NM_007799	ENSMUSG00000004552	Ctse	A430072O03Rik|C920004C08Rik|CE|CatE	cathepsin E	protein-coding
mm_30033.1	chr3	135691275	135691313	-	1	NA	5' UTR (NM_008689, exon 1 of 25)	5' UTR (NM_008689, exon 1 of 25)	253	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_75802.1	chr8	70139151	70139162	-	1	NA	promoter-TSS (NM_001145552)	promoter-TSS (NM_001145552)	41	NM_011266	19727	Mm.161167	NM_011266	ENSMUSG00000036120	Rfxank	Tvl1	regulatory factor X-associated ankyrin-containing protein	protein-coding
mm_29192.1	chr3	106760470	106760485	-	1	NA	3' UTR (NM_007651, exon 8 of 8)	3' UTR (NM_007651, exon 8 of 8)	29672	NM_007651	12508	Mm.316861	NM_007651	ENSMUSG00000040747	Cd53	AI323659|Ox-44|Tspan25	CD53 antigen	protein-coding
mm_60732.1	chr7	45434834	45434871	+	1	NA	promoter-TSS (NM_030678)	promoter-TSS (NM_030678)	13	NM_030678	14936	Mm.275654	NM_030678	ENSMUSG00000003865	Gys1	Gys3|MGS	glycogen synthase 1, muscle	protein-coding
mm_160676.1	chr10	11281791	11281791	+	1	NA	intron (NM_001168297, intron 1 of 2)	CpG	204	NM_001168297	71865	Mm.276229	NM_027968	ENSMUSG00000047648	Fbxo30	1700026A16Rik|MUSA1	F-box protein 30	protein-coding
mm_10947.1	chr2	25557862	25557923	+	1	NA	promoter-TSS (NM_021519)	promoter-TSS (NM_021519)	-8	NM_021519	59022	Mm.29945	NM_021519	ENSMUSG00000015092	Edf1	0610008L11Rik|AA409425	endothelial differentiation-related factor 1	protein-coding
mm_132231.1	chr16	32736264	32736281	+	1	NA	5' UTR (NM_080457, exon 1 of 27)	5' UTR (NM_080457, exon 1 of 27)	386	NM_080457	140474	Mm.214599	NM_080457	ENSMUSG00000079620	Muc4	4933405I11Rik|Asgp	mucin 4	protein-coding
mm_33114.1	chr4	124739022	124739055	+	1	NA	Intergenic	Intergenic	-2812	NM_008385	16330	Mm.296202	NM_008385	ENSMUSG00000028894	Inpp5b	5PTase|AW260155|INPP5P	inositol polyphosphate-5-phosphatase B	protein-coding
mm_35499.1	chr4	41048003	41048013	-	1	NA	5' UTR (NM_007473, exon 1 of 8)	5' UTR (NM_007473, exon 1 of 8)	128	NM_007473	11832	Mm.8728	NM_007473	ENSMUSG00000028427	Aqp7	AQP7L|AQPap	aquaporin 7	protein-coding
mm_114980.1	chr13	97251365	97251370	+	1	NA	3' UTR (NM_007930, exon 3 of 3)	3' UTR (NM_007930, exon 3 of 3)	10262	NM_007930	13803	Mm.241073	NM_007930	ENSMUSG00000041773	Enc1	Nrpb|PIG10	ectodermal-neural cortex 1	protein-coding
mm_152290.1	chr19	9000123	9000148	-	1	NA	exon (NM_001286518, exon 3 of 7)	exon (NM_001286518, exon 3 of 7)	10851	NM_001286518	66395	Mm.203866	NM_009643	ENSMUSG00000069833	Ahnak	DY6	AHNAK nucleoprotein (desmoyokin)	protein-coding
mm_74318.1	chr8	126828380	126828381	+	1	NA	Intergenic	Intergenic	117541	NM_024214	67952	Mm.6932	NM_024214	ENSMUSG00000093904	Tomm20	1810060K07Rik|BB284719|Gm19268|MAS20|MOM19|TOM20|mKIAA0016	translocase of outer mitochondrial membrane 20 homolog (yeast)	protein-coding
mm_65922.1	chr7	30232187	30232205	-	1	NA	promoter-TSS (NM_025548)	promoter-TSS (NM_025548)	122	NM_027259	69920	Mm.440028	NM_027259	ENSMUSG00000019738	Polr2i	2810002B19Rik	polymerase (RNA) II (DNA directed) polypeptide I	protein-coding
mm_29827.1	chr3	129725075	129725107	-	1	NA	promoter-TSS (NM_001310737)	promoter-TSS (NM_001310737)	-5	NM_001329594	13645	Mm.252481	NM_010113	ENSMUSG00000028017	Egf	AI790464	epidermal growth factor	protein-coding
mm_119764.1	chr14	54173528	54173534	+	1	NA	Intergenic	Intergenic	80398	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_41189.1	chr5	88327889	88327902	+	1	NA	exon (NM_008644, exon 3 of 3)	exon (NM_008644, exon 3 of 3)	10583	NM_008644	17830	Mm.200411	NM_008644	ENSMUSG00000064156	Prol1	Muc10	proline rich, lacrimal 1	protein-coding
mm_345.1	chr1	30950256	30950264	+	1	NA	promoter-TSS (NR_002688)	promoter-TSS (NR_002688)	-505	NM_011200	19243	Mm.491181	NM_011200	ENSMUSG00000026064	Ptp4a1	AA415290|AU019864|C130021B01|Prl-1	protein tyrosine phosphatase 4a1	protein-coding
mm_30180.1	chr3	144232042	144232057	-	1	NA	Intergenic	Intergenic	-26794	NM_010723	16911	Mm.29187	NM_010723	ENSMUSG00000028266	Lmo4	A730077C12Rik|Crp3|Etohi4	LIM domain only 4	protein-coding
mm_116148.1	chr13	29984205	29984215	-	1	NA	5' UTR (NM_001289920, exon 1 of 7)	5' UTR (NM_001289920, exon 1 of 7)	181	NM_001289920	13557	Mm.268356	NM_010093	ENSMUSG00000016477	E2f3	E2F3b|E2f3a	E2F transcription factor 3	protein-coding
mm_76289.1	chr8	84200731	84200750	-	1	NA	Intergenic	Intergenic	-7778	NR_029740	387216		NR_029740	ENSMUSG00000065611	Mir23a	Mirn23a|mir-23a|mmu-mir-23a	microRNA 23a	ncRNA
mm_14176.1	chr2	126735973	126735978	+	1	NA	intron (NM_019729, intron 7 of 18)	intron (NM_019729, intron 7 of 18)	28647	NM_019729	84092	Mm.272629	NM_019729	ENSMUSG00000027363	Usp8	AI574262|AW557536|Ubpy|mKIAA0055	ubiquitin specific peptidase 8	protein-coding
mm_149065.1	chr19	8841181	8841197	+	1	NA	exon (NM_008144, exon 2 of 11)	exon (NM_008144, exon 2 of 11)	686	NM_001290823	14705	Mm.345134	NM_008144	ENSMUSG00000071657	Bscl2	2900097C17Rik|AI046355|Gng3lg	Berardinelli-Seip congenital lipodystrophy 2 (seipin)	protein-coding
mm_110597.1	chr12	56535234	56535249	-	1	NA	intron (NM_009385, intron 1 of 2)	CpG-3195	1667	NM_009385	21869	Mm.89972	NM_009385	ENSMUSG00000001496	Nkx2-1	AV026640|Nkx2.1|T/EBP|Titf1|Ttf-1	NK2 homeobox 1	protein-coding
mm_62375.1	chr7	100706670	100706695	+	1	NA	promoter-TSS (NM_178764)	promoter-TSS (NM_178764)	-20	NM_178764	319604	Mm.260362	NM_178764	ENSMUSG00000029461	Fam168a	2610030B18Rik|B930006L02Rik|mKIAA0280	family with sequence similarity 168, member A	protein-coding
mm_15018.1	chr2	152626986	152627018	+	1	NA	promoter-TSS (NM_009047)	promoter-TSS (NM_009047)	-6	NM_009047	19700	Mm.8752	NM_009047	ENSMUSG00000000359	Rem1	E030011C07Rik|Ras|Rem	rad and gem related GTP binding protein 1	protein-coding
mm_88597.1	chr10	79781153	79781161	+	1	NA	TTS (NM_001042710)	TTS (NM_001042710)	3883	NM_031380	83554	Mm.251710	NM_031380	ENSMUSG00000020325	Fstl3	E030038F23Rik|Flrg	follistatin-like 3	protein-coding
mm_151371.1	chr19	55932300	55932325	+	1	NA	non-coding (NR_138565, exon 16 of 16)	non-coding (NR_138565, exon 16 of 16)	36991	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_48510.1	chr5	142821682	142821705	-	1	NA	Intergenic	Intergenic	-4306	NM_001122730	231861	Mm.354649	NM_178242	ENSMUSG00000039477	Tnrc18	BC025631|EG381742|Zfp469	trinucleotide repeat containing 18	protein-coding
mm_26241.1	chr3	141465543	141465549	+	1	NA	promoter-TSS (NM_009472)	promoter-TSS (NM_009472)	-18	NM_009472	22253	Mm.24430	NM_009472	ENSMUSG00000059921	Unc5c	B130051O18Rik|Unc5h3|rcm	unc-5 netrin receptor C	protein-coding
mm_48397.1	chr5	140118041	140118056	-	1	NA	intron (NM_010752, intron 13 of 17)	intron (NM_010752, intron 13 of 17)	203504	NM_010752	17120	Mm.27250	NM_010752	ENSMUSG00000029554	Mad1l1	AI173502|AW550425|Mad1	MAD1 mitotic arrest deficient 1-like 1	protein-coding
mm_166207.1	chr5	44799591	44799597	-	1	NA	5' UTR (NM_010698, exon 1 of 8)	5' UTR (NM_010698, exon 1 of 8)	152	NM_001347349	16826	Mm.25785	NM_010698	ENSMUSG00000039706	Ldb2	AI035351|AW146358|CLIM1|CLP-36|Ldb3	LIM domain binding 2	protein-coding
mm_143614.1	chr17	78736652	78736670	-	1	NA	promoter-TSS (NM_011500)	promoter-TSS (NM_011500)	-101	NM_011500	268980	Mm.311915	NM_011500	ENSMUSG00000024077	Strn	AU022939|D130055P19	striatin, calmodulin binding protein	protein-coding
mm_77746.1	chr8	127440140	127440140	-	1	NA	intron (NM_001309391, intron 20 of 24)	intron (NM_001309391, intron 20 of 24)	140488	NM_001013580	93742	Mm.299254	NM_033620	ENSMUSG00000025812	Pard3	AA960621|AI256638|Asip|D8Ertd580e|Par-3|Par3|Pard-3|Pard3a|Phip	par-3 family cell polarity regulator	protein-coding
mm_140476.1	chr17	94864887	94864922	+	1	NA	promoter-TSS (NM_001024731)	promoter-TSS (NM_001024731)	-14	NM_001024731	100044193		NM_001024731	ENSMUSG00000095193	Gm20939	-	predicted gene, 20939	protein-coding
mm_4691.1	chr1	180726325	180726351	+	1	NA	exon (NM_133225, exon 1 of 8)	exon (NM_133225, exon 1 of 8)	295	NM_133225	170760	Mm.272981	NM_133225	ENSMUSG00000026499	Acbd3	60kDa|8430407O11Rik|D1Ertd10e|GCP60|GOLPH1|Gocap1|Pap7	acyl-Coenzyme A binding domain containing 3	protein-coding
mm_5762.1	chr1	46893133	46893136	-	1	NA	Intergenic	Intergenic	-39625	NM_172653	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|mKIAA1265	solute carrier family 39 (zinc transporter), member 10	protein-coding
mm_44769.1	chr5	31699386	31699420	-	1	NA	intron (NM_181280, intron 1 of 12)	MIRc|SINE|MIR	1353	NM_144541	107976	Mm.482126	NM_144541	ENSMUSG00000052139	Bre	6030405P19Rik|AI429776|B830038C02Rik	brain and reproductive organ-expressed protein	protein-coding
mm_5981.1	chr1	58393047	58393067	-	1	NA	promoter-TSS (NM_025824)	promoter-TSS (NM_025824)	-79	NM_025824	66882	Mm.21848	NM_025824	ENSMUSG00000051223	Bzw1	1200015E15Rik|mKIAA0005	basic leucine zipper and W2 domains 1	protein-coding
mm_146599.1	chr18	9450098	9450161	-	1	NA	promoter-TSS (NM_026484)	promoter-TSS (NM_026484)	21	NM_026484	67974	Mm.86523	NM_026484	ENSMUSG00000024286	Ccny	1700025H17Rik|3110050L10Rik|4631402G10Rik|5730405I09Rik	cyclin Y	protein-coding
mm_10557.1	chr2	16758939	16758973	+	1	NA	Intergenic	Intergenic	254770	NR_040632	75069	Mm.50378	NR_040632		4930515L03Rik	-	RIKEN cDNA 4930515L03 gene	ncRNA
mm_87439.1	chr10	51480814	51480834	+	1	NA	intron (NM_001291892, intron 1 of 8)	intron (NM_001291892, intron 1 of 8)	212	NM_001291892	14727	Mm.439661	NM_008147	ENSMUSG00000062593	Lilr4b	Gp49a|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4B	protein-coding
mm_13122.1	chr2	91664411	91664446	+	1	NA	intron (NR_027371, intron 5 of 13)	IMPB_01|Satellite|Satellite	11220	NM_146124	228359	Mm.22413	NM_146124	ENSMUSG00000027247	Arhgap1	B230365D05Rik|C76222|Cdc42GAP|p50rhoGAP	Rho GTPase activating protein 1	protein-coding
mm_70172.1	chr7	143628367	143628377	-	1	NA	promoter-TSS (NM_175649)	promoter-TSS (NM_175649)	-527	NM_175649	244237	Mm.247498	NM_175649	ENSMUSG00000045362	Tnfrsf26	Tnfrh3|Tnfrsf24	tumor necrosis factor receptor superfamily, member 26	protein-coding
mm_20585.1	chr2	131158546	131158555	-	1	NA	intron (NM_001311138, intron 1 of 5)	intron (NM_001311138, intron 1 of 5)	1470	NM_026091	67326	Mm.27711	NM_026091	ENSMUSG00000027327	1700037H04Rik	-	RIKEN cDNA 1700037H04 gene	protein-coding
mm_31824.1	chr4	68587906	68587912	+	1	NA	Intergenic	(T)n|Simple_repeat|Simple_repeat	366488	NM_019967	56710	Mm.248788	NM_019967	ENSMUSG00000028351	Brinp1	BRINP|Dbc1|Dbccr1|Fam5a	bone morphogenic protein/retinoic acid inducible neural specific 1	protein-coding
mm_23246.1	chr3	51224462	51224475	+	1	NA	promoter-TSS (NM_009834)	promoter-TSS (NM_009834)	21	NM_009834	12457	Mm.86541	NM_009834	ENSMUSG00000023087	Noct	AU043840|Ccr4|Ccrn4l	nocturnin	protein-coding
mm_72021.1	chr8	70724177	70724185	+	1	NA	5' UTR (NM_201607, exon 1 of 17)	5' UTR (NM_201607, exon 1 of 17)	117	NM_201607	110385	Mm.255180	NM_201607	ENSMUSG00000031842	Pde4c	Dpde1|E130301F19Rik|dunce	phosphodiesterase 4C, cAMP specific	protein-coding
mm_160090.1	chr7	16721868	16721868	+	1	NA	promoter-TSS (NM_011927)	promoter-TSS (NM_011927)	-61	NM_011927	26368	Mm.27096	NM_011927	ENSMUSG00000007209	Ceacam9	AA410097|AW545709|Cea-5|Cea5|mmCGM8	carcinoembryonic antigen-related cell adhesion molecule 9	protein-coding
mm_44721.1	chr5	30960218	30960228	-	1	NA	5' UTR (NM_001294302, exon 1 of 8)	5' UTR (NM_001294302, exon 1 of 8)	104	NM_001294302	50907	Mm.272414	NM_016703	ENSMUSG00000045302	Preb	C85705	prolactin regulatory element binding	protein-coding
mm_63317.1	chr7	126928845	126928899	+	1	NA	promoter-TSS (NM_172747)	promoter-TSS (NM_172747)	-7	NM_172747	233877	Mm.245897	NM_172747	ENSMUSG00000030685	Kctd13	1500003N18Rik|AV259508|PDIP1alpha|Pdip1|Poldip1	potassium channel tetramerisation domain containing 13	protein-coding
mm_71237.1	chr8	40908047	40908165	+	1	NA	exon (NM_001044740, exon 7 of 12)	exon (NM_001044740, exon 7 of 12)	-18127	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_168040.1	chrY	90742962	90742974	-	1	NA	Intergenic	CpG	12082	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_59991.1	chr7	30554924	30554939	+	1	NA	TTS (NM_001290569)	TTS (NM_001290569)	1629	NM_001012401	243912	Mm.34885	NM_001012401	ENSMUSG00000036854	Hspb6	AA387366|Gm479|Hsp20	heat shock protein, alpha-crystallin-related, B6	protein-coding
mm_35331.1	chr4	26346883	26346901	-	1	NA	promoter-TSS (NM_172865)	promoter-TSS (NM_172865)	-240	NM_172865	242362	Mm.245602	NM_172865	ENSMUSG00000040520	Manea	4932703L02Rik	mannosidase, endo-alpha	protein-coding
mm_70561.1	chr8	13086449	13086456	+	1	NA	intron (NM_178708, intron 7 of 13)	intron (NM_178708, intron 7 of 13)	18891	NM_178708	234069	Mm.103427	NM_178708	ENSMUSG00000038542	Pcid2	A730042J05Rik	PCI domain containing 2	protein-coding
mm_51878.1	chr6	90565938	90565969	+	1	NA	intron (NM_027406, intron 7 of 22)	intron (NM_027406, intron 7 of 22)	15105	NM_027406	107747	Mm.30035	NM_027406	ENSMUSG00000030088	Aldh1l1	1810048F20Rik|FDH|Fthfd|Neut2	aldehyde dehydrogenase 1 family, member L1	protein-coding
mm_130935.1	chr15	103213237	103213252	-	1	NA	5' UTR (NM_001110216, exon 3 of 6)	5' UTR (NM_001110216, exon 3 of 6)	2108	NM_007626	12419	Mm.262059	NM_007626	ENSMUSG00000009575	Cbx5	2610029O15Rik|C75991|HP1|Hp1a|Hp1alpha	chromobox 5	protein-coding
mm_109416.1	chr12	110485711	110485755	+	1	NA	promoter-TSS (NM_001081458)	promoter-TSS (NM_001081458)	-6	NM_001081457	26931	Mm.240396	NM_012023	ENSMUSG00000017843	Ppp2r5c	2610043M05Rik|2700063L20Rik|AI060890|AW545884|C85228|D12Bwg0916e|mKIAA0044	protein phosphatase 2, regulatory subunit B', gamma	protein-coding
mm_70570.1	chr8	13159229	13159314	+	1	NA	5' UTR (NM_010684, exon 1 of 9)	5' UTR (NM_010684, exon 1 of 9)	110	NM_010684	16783	Mm.16716	NM_010684	ENSMUSG00000031447	Lamp1	CD107a|LGP-120|LGP-A|Lamp-1|P2B	lysosomal-associated membrane protein 1	protein-coding
mm_14255.1	chr2	128158692	128158697	+	1	NA	3' UTR (NM_009754, exon 4 of 4)	3' UTR (NM_009754, exon 4 of 4)	31119	NM_001284410	12125	Mm.141083	NM_009754	ENSMUSG00000027381	Bcl2l11	1500006F24Rik|Bim|Bod|bcl2-L-11	BCL2-like 11 (apoptosis facilitator)	protein-coding
mm_127429.1	chr15	101270077	101270106	+	1	NA	exon (NM_010444, exon 2 of 7)	exon (NM_010444, exon 2 of 7)	3245	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_134003.1	chr16	4790001	4790009	-	1	NA	promoter-TSS (NM_025670)	promoter-TSS (NM_025670)	-70	NM_025670	66626	Mm.157648	NM_025670	ENSMUSG00000004071	Cdip1	2700048O17Rik|5730403B10Rik|AU018521|AW742692|CDIP	cell death inducing Trp53 target 1	protein-coding
mm_36212.1	chr4	62470869	62470922	-	1	NA	promoter-TSS (NM_023597)	promoter-TSS (NM_023597)	0	NM_001290522	71354	Mm.155573	NM_023597	ENSMUSG00000028391	Wdr31	5430402I10Rik|spWD	WD repeat domain 31	protein-coding
mm_103558.1	chr11	77722638	77722646	-	1	NA	exon (NM_009965, exon 3 of 6)	exon (NM_009965, exon 3 of 6)	2651	NM_001313933	12957	Mm.22830	NM_009965	ENSMUSG00000000724	Cryba1	BA3/A1|Cryb	crystallin, beta A1	protein-coding
mm_137924.1	chr17	32506447	32506473	+	1	NA	promoter-TSS (NM_001101445)	promoter-TSS (NM_001101445)	-2	NM_001101445	208285	Mm.311422	NM_001101445	ENSMUSG00000091586	Cyp4f17	EG208285	cytochrome P450, family 4, subfamily f, polypeptide 17	protein-coding
mm_67006.1	chr7	65313978	65313981	-	1	NA	intron (NM_001163574, intron 19 of 26)	intron (NM_001163574, intron 19 of 26)	57265	NM_001163574	21872	Mm.4342	NM_009386	ENSMUSG00000030516	Tjp1	ZO1	tight junction protein 1	protein-coding
mm_17568.1	chr2	30237627	30237655	-	1	NA	promoter-TSS (NM_177725)	promoter-TSS (NM_177725)	-10	NR_028299	67350	Mm.402683	NR_028299		1700084E18Rik	-	RIKEN cDNA 1700084E18 gene	ncRNA
mm_107217.1	chr12	26448659	26448677	+	1	NA	exon (NM_021384, exon 4 of 6)	exon (NM_021384, exon 4 of 6)	7784	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_110463.1	chr12	51773579	51773593	-	1	NA	intron (NM_144788, intron 22 of 42)	RSINE1|SINE|B4	55950	NM_144788	207304	Mm.249391	NM_144788	ENSMUSG00000035247	Hectd1	A630086P08Rik|AI844876|b2b327Clo|opm	HECT domain containing 1	protein-coding
mm_99489.1	chr11	102761403	102761448	+	1	NA	promoter-TSS (NM_009613)	promoter-TSS (NM_009613)	-10	NM_009613	11488	Mm.89854	NM_009613	ENSMUSG00000020926	Adam11	AW060611|Mdc	a disintegrin and metallopeptidase domain 11	protein-coding
mm_126974.1	chr15	93432899	93432906	+	1	NA	intron (NM_175363, intron 3 of 8)	B1_Mus1|SINE|Alu	34438	NM_001285863	223828	Mm.74208	NM_146062	ENSMUSG00000036167	Pphln1	CR|HSPC206|HSPC232	periphilin 1	protein-coding
mm_83638.1	chr9	49503779	49503790	-	1	NA	3' UTR (NM_001311065, exon 18 of 18)	3' UTR (NM_001311065, exon 18 of 18)	-14504	NR_029465	100036537	Mm.437541	NR_029465	ENSMUSG00000079564	Gm11149	ENSMUSG00000060603|ENSMUSG00000079564	predicted gene 11149	ncRNA
mm_165698.1	chr3	94984837	94984850	+	1	NA	exon (NM_001293715, exon 2 of 12)	exon (NM_001293715, exon 2 of 12)	10112	NM_001293716	107650	Mm.217222	NM_175356	ENSMUSG00000038861	Pi4kb	ESTM41|PI4K-beta|PI4Kbeta|Pik4cb	phosphatidylinositol 4-kinase, catalytic, beta polypeptide	protein-coding
mm_106130.1	chr11	116459931	116459947	-	1	NA	Intergenic	MLT1D|LTR|ERVL-MaLR	-5592	NM_001033267	217341	Mm.387352	NM_001033267	ENSMUSG00000070331	Qrich2	Gm66	glutamine rich 2	protein-coding
mm_157587.1	chrX	53070652	53070669	-	1	NA	exon (NM_019538, exon 3 of 3)	exon (NM_019538, exon 3 of 3)	-13470	NR_038184	72575	Mm.59516	NR_038184		C430049B03Rik	2700063P19Rik|9430052C07Rik|mir-322|mir-351|mir-503	RIKEN cDNA C430049B03 gene	ncRNA
mm_163875.1	chr14	19419429	19419454	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	183146	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_64135.1	chr7	141194123	141194140	+	1	NA	promoter-TSS (NM_001172065)	promoter-TSS (NM_001172065)	1	NM_001172064	70552	Mm.45104	NM_153777	ENSMUSG00000038637	Lrrc56	5730427C23Rik|BB110509|mFLJ00101	leucine rich repeat containing 56	protein-coding
mm_126417.1	chr15	80287510	80287535	+	1	NA	5' UTR (NM_001044308, exon 1 of 37)	5' UTR (NM_001044308, exon 1 of 37)	284	NM_001044308	239556	Mm.291058	NM_001044308	ENSMUSG00000022416	Cacna1i	Ca(V)3.3	calcium channel, voltage-dependent, alpha 1I subunit	protein-coding
mm_102211.1	chr11	54860565	54860603	-	1	NA	promoter-TSS (NM_029327)	promoter-TSS (NM_029327)	7	NM_029327	75530	Mm.83578	NM_029327	ENSMUSG00000020268	Lyrm7	1700024C24Rik|9330147L21Rik	LYR motif containing 7	protein-coding
mm_82844.1	chr9	31168876	31168919	-	1	NA	exon (NM_009691, exon 6 of 16)	exon (NM_009691, exon 6 of 16)	-37098	NM_011176	19143	Mm.243926	NM_011176	ENSMUSG00000031995	St14	Epithin|MT-SP1|Prss14|Tmprss14|mCAP3|matriptase	suppression of tumorigenicity 14 (colon carcinoma)	protein-coding
mm_95792.1	chr11	54961738	54961756	+	1	NA	intron (NM_001199275, intron 1 of 18)	intron (NM_001199275, intron 1 of 18)	1193	NM_021327	57783	Mm.259671	NM_021327	ENSMUSG00000020400	Tnip1	ABIN|ABIN-1|ABIN1|AU018810|Naf1|Nef|VAN	TNFAIP3 interacting protein 1	protein-coding
mm_21214.1	chr2	155692377	155692387	-	1	NA	promoter-TSS (NM_001163452)	promoter-TSS (NM_001163452)	2	NM_019828	56407	Mm.234944	NM_019828	ENSMUSG00000038324	Trpc4ap	4833429F06Rik|D2Ertd113e|Trrp4ap|mFLJ00177|truss	transient receptor potential cation channel, subfamily C, member 4 associated protein	protein-coding
mm_67226.1	chr7	74554633	74554681	-	1	NA	5' UTR (NM_023908, exon 1 of 10)	5' UTR (NM_023908, exon 1 of 10)	123	NM_023908	108116	Mm.425467	NM_023908	ENSMUSG00000025790	Slco3a1	5830414C08Rik|Anr1|MJAM|OATP-D|R75096|Slc21a11	solute carrier organic anion transporter family, member 3a1	protein-coding
mm_108354.1	chr12	80644213	80644265	+	1	NA	promoter-TSS (NM_026244)	promoter-TSS (NM_026244)	24	NM_026244	328133	Mm.238279	NM_026244	ENSMUSG00000048833	Slc39a9	2010002A02Rik|2610511I23Rik|4833420E20Rik|AW209151	solute carrier family 39 (zinc transporter), member 9	protein-coding
mm_8240.1	chr1	138485322	138485326	-	1	NA	3' UTR (NM_021605, exon 10 of 10)	3' UTR (NM_021605, exon 10 of 10)	134433	NM_021605	59125	Mm.143817	NM_021605	ENSMUSG00000026393	Nek7	2810460C19Rik|AU020186	NIMA (never in mitosis gene a)-related expressed kinase 7	protein-coding
mm_91844.1	chr10	57794802	57794815	-	1	NA	intron (NM_020561, intron 1 of 7)	CpG	264	NM_020561	57319	Mm.2379	NM_020561	ENSMUSG00000019872	Smpdl3a	0610010C24Rik|AI529588|ASM3A|ASML3|ASML3A	sphingomyelin phosphodiesterase, acid-like 3A	protein-coding
mm_97502.1	chr11	78404701	78404732	+	1	NA	non-coding (NR_003282, exon 5 of 5)	non-coding (NR_003282, exon 5 of 5)	10231	NR_003282	790911	Mm.457257	NR_003282	ENSMUSG00000085747	Slc13a2os	Gm11194|OTTMUSG00000000132	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 2, opposite strand	ncRNA
mm_16142.1	chr2	171193223	171193229	+	1	NA	Intergenic	Intergenic	461419	NM_001163686	76829	Mm.41633	NM_029761	ENSMUSG00000027560	Dok5	2700055C10Rik	docking protein 5	protein-coding
mm_21620.1	chr2	164276102	164276105	-	1	NA	3' UTR (NM_009300, exon 3 of 3)	3' UTR (NM_009300, exon 3 of 3)	2204	NM_009300	20941	Mm.1286	NM_009300	ENSMUSG00000016998	Svs4	SVS-IV|Svp-2|Svp-4|Svp2|Svp4	seminal vesicle secretory protein 4	protein-coding
mm_135021.1	chr16	32487898	32487918	-	1	NA	promoter-TSS (NM_145932)	promoter-TSS (NM_145932)	-29	NM_145932	106407	Mm.476915	NM_145932	ENSMUSG00000035699	Slc51a	AV001382|AW261577|D630035O19Rik|OSTalpha|Osta	solute carrier family 51, alpha subunit	protein-coding
mm_98287.1	chr11	89066005	89066021	+	1	NA	intron (NR_110336, intron 1 of 3)	intron (NR_110336, intron 1 of 3)	5262	NR_110336	414094	Mm.124287	NM_001001497		Dgkeos	A930013B10Rik	diacylglycerol kinase, epsilon, opposite strand	ncRNA
mm_59301.1	chr7	25206121	25206130	+	1	NA	intron (NM_207677, intron 4 of 4)	intron (NM_207677, intron 4 of 4)	11600	NR_106015	102466794		NR_106015	ENSMUSG00000098325	Mir7048	Gm27274|mmu-mir-7048	microRNA 7048	ncRNA
mm_142878.1	chr17	51826291	51826293	-	1	NA	intron (NM_001163632, intron 1 of 10)	intron (NM_001163632, intron 1 of 10)	296	NM_001163631	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_24889.1	chr3	96108570	96108586	+	1	NA	intron (NM_001025614, intron 1 of 11)	intron (NM_001025614, intron 1 of 11)	4051	NM_001025614	229603	Mm.272336	NM_001025613	ENSMUSG00000038495	Otud7b	2900060B22Rik|4930463P07Rik|AI462125|CEZANNE|Trabid2|Za20d1	OTU domain containing 7B	protein-coding
mm_42147.1	chr5	111418709	111418715	+	1	NA	exon (NM_001081235, exon 1 of 2)	exon (NM_001081235, exon 1 of 2)	546	NM_001081235	433938	Mm.332576	NM_001081235	ENSMUSG00000070576	Mn1	AA003644|AA009236	meningioma 1	protein-coding
mm_125357.1	chr15	39391918	39391935	+	1	NA	intron (NM_001256382, intron 3 of 26)	intron (NM_001256382, intron 3 of 26)	193640	NM_053271	116838	Mm.309296	NM_053271	ENSMUSG00000037386	Rims2	2810036I15Rik|AW048769|RIM2|Rab3ip2|Rim2(+40A)|Rim2(+44A)|Rim2(+4A)|Serg2|Syt3-rs|mKIAA0751	regulating synaptic membrane exocytosis 2	protein-coding
mm_125376.1	chr15	40654882	40654891	+	1	NA	promoter-TSS (NM_011766)	promoter-TSS (NM_011766)	-156	NM_011766	22762	Mm.39496	NM_011766	ENSMUSG00000022306	Zfpm2	B330005D23Rik|FOG-2|FOG2	zinc finger protein, multitype 2	protein-coding
mm_133631.1	chr16	91651679	91651700	+	1	NA	exon (NM_019973, exon 2 of 5)	exon (NM_019973, exon 2 of 5)	3865	NM_178880	20658	Mm.46401	NM_019973	ENSMUSG00000022961	Son	2900011L12Rik|AA409051|AU067731|C81487|mKIAA1019|nrebp	Son DNA binding protein	protein-coding
mm_50906.1	chr6	57581781	57581794	+	1	NA	intron (NM_025992, intron 1 of 22)	B3|SINE|B2	795	NM_025992	67138	Mm.297393	NM_025992	ENSMUSG00000029798	Herc6	1700121D12Rik|2510038N07Rik|4930427L17Rik|AI451296|CEB1|Herc5	hect domain and RLD 6	protein-coding
mm_170758.1	chr2	158400026	158400027	-	1	NA	Intergenic	B1_Mm|SINE|Alu	-9827	NM_001291137	228850	Mm.398185	NM_177227	ENSMUSG00000027652	Ralgapb	AI507211|B230339M05Rik|p170	Ral GTPase activating protein, beta subunit (non-catalytic)	protein-coding
mm_13043.1	chr2	91096711	91096717	+	1	NA	promoter-TSS (NM_011355)	promoter-TSS (NM_011355)	36	NM_011355	20375	Mm.1302	NM_011355	ENSMUSG00000002111	Spi1	Dis-1|Dis1|PU.1|Sfpi-1|Sfpi1|Spi-1|Tcfpu1|Tfpu.1	spleen focus forming virus (SFFV) proviral integration oncogene	protein-coding
mm_165629.1	chr3	67012213	67012214	+	1	NA	intron (NM_025822, intron 3 of 9)	B4A|SINE|B4	26541	NM_025822	66880	Mm.316418	NM_025822	ENSMUSG00000034544	Rsrc1	1200013F24Rik|SRrp53	arginine/serine-rich coiled-coil 1	protein-coding
mm_161305.1	chr14	32599429	32599429	+	1	NA	promoter-TSS (NM_001001796)	promoter-TSS (NM_001001796)	21	NM_001347590	107751	Mm.119274	NM_001001796	ENSMUSG00000041730	Prrxl1	Drg11|Drgx	paired related homeobox protein-like 1	protein-coding
mm_168035.1	chrY	90742385	90742395	-	1	NA	Intergenic	CpG	12660	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_12770.1	chr2	79321463	79321475	+	1	NA	exon (NM_010576, exon 24 of 28)	exon (NM_010576, exon 24 of 28)	66043	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D|Itga4B	integrin alpha 4	protein-coding
mm_146310.1	chr18	80278985	80279005	+	1	NA	intron (NM_025861, intron 4 of 5)	intron (NM_025861, intron 4 of 5)	22689	NM_001164423	66943	Mm.29247	NM_025861	ENSMUSG00000034006	Pqlc1	2310009N05Rik|4933425L21Rik|5730564E11Rik|C78974	PQ loop repeat containing 1	protein-coding
mm_73085.1	chr8	94513306	94513322	+	1	NA	intron (NM_001033207, intron 34 of 48)	ID_B1|SINE|B4	8268	NR_106040	102466800		NR_106040	ENSMUSG00000098511	Mir7072	Gm27665|mmu-mir-7072	microRNA 7072	ncRNA
mm_98714.1	chr11	96314797	96314835	+	1	NA	Intergenic	CpG	-2349	NR_029784	723893		NR_029784	ENSMUSG00000065519	Mir10a	Mirn10a|miR-10a|mmu-mir-10a	microRNA 10a	ncRNA
mm_151062.1	chr19	47229067	47229073	+	1	NA	exon (NM_001163480, exon 1 of 6)	exon (NM_001163480, exon 1 of 6)	227	NM_001163480	18011	Mm.313651	NM_021360	ENSMUSG00000006435	Neurl1a	2410129E16Rik|AI450910|AI481072|Neu1|Neur1|Neurl|Neurl1|Nlz|Rnf67	neuralized E3 ubiquitin protein ligase 1A	protein-coding
mm_115925.1	chr13	23571035	23571056	-	1	NA	promoter-TSS (NM_178196)	promoter-TSS (NM_178196)	175	NM_178187	319166	Mm.261665	NM_178187	ENSMUSG00000069272	Hist1h2ae	1190022L06	histone cluster 1, H2ae	protein-coding
mm_71146.1	chr8	39297970	39298019	+	1	NA	promoter-TSS (NR_044988)	promoter-TSS (NR_044988)	14	NR_044988	621335	Mm.208080	NR_044988	ENSMUSG00000109827	Gm6213	EG621335	predicted gene 6213	ncRNA
mm_98679.1	chr11	96285569	96285591	+	1	NA	TTS (NM_010461)	TTS (NM_010461)	-1066	NM_010460	15415	Mm.390366	NM_010460	ENSMUSG00000038721	Hoxb7	AI325018|Hox-2.3	homeobox B7	protein-coding
mm_105700.1	chr11	108249048	108249050	-	1	NA	intron (NM_011101, intron 2 of 16)	ID_B1|SINE|B4	94839	NM_011101	18750	Mm.222178	NM_011101	ENSMUSG00000050965	Prkca	AI875142|Pkca	protein kinase C, alpha	protein-coding
mm_27437.1	chr3	51662779	51662798	-	1	NA	intron (NM_001310482, intron 1 of 3)	intron (NM_001310482, intron 1 of 3)	1609	NM_001310482	211666	Mm.24679	NM_174995	ENSMUSG00000074604	Mgst2	GST2|MGST-II	microsomal glutathione S-transferase 2	protein-coding
mm_130650.1	chr15	100636743	100636777	-	1	NA	non-coding (NR_104338, exon 1 of 4)	non-coding (NR_104338, exon 1 of 4)	180	NR_104338	207818	Mm.26282	NM_174992	ENSMUSG00000053559	Smagp	-	small cell adhesion glycoprotein	protein-coding
mm_164617.1	chr17	31161537	31161567	+	1	NA	3' UTR (NM_009362, exon 3 of 3)	3' UTR (NM_009362, exon 3 of 3)	3501	NM_009362	21784	Mm.2854	NM_009362	ENSMUSG00000024032	Tff1	Bcei|PS2	trefoil factor 1	protein-coding
mm_136751.1	chr17	8525435	8525444	+	1	NA	Intergenic	Intergenic	-1362	NM_001290707	23984	Mm.87161	NM_011866	ENSMUSG00000023868	Pde10a	-	phosphodiesterase 10A	protein-coding
mm_3523.1	chr1	150108076	150108095	+	1	NA	3' UTR (NM_011198, exon 10 of 10)	3' UTR (NM_011198, exon 10 of 10)	8054	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_103024.1	chr11	69735081	69735092	-	1	NA	exon (NM_001291068, exon 29 of 29)	exon (NM_001291068, exon 29 of 29)	23547	NM_001291068	20020	Mm.16533	NM_009089	ENSMUSG00000005198	Polr2a	220kDa|Rpb1|Rpo2-1	polymerase (RNA) II (DNA directed) polypeptide A	protein-coding
mm_150119.1	chr19	29945783	29945799	+	1	NA	promoter-TSS (NM_001164724)	promoter-TSS (NM_001164724)	1	NM_001164724	77125	Mm.182359	NM_133775	ENSMUSG00000024810	Il33	9230117N10Rik|Il-33|Il1f11|NF-HEV	interleukin 33	protein-coding
mm_114131.1	chr13	55211889	55211921	+	1	NA	intron (NM_008739, intron 1 of 22)	CpG	2123	NM_008739	18193	Mm.12964	NM_008739	ENSMUSG00000021488	Nsd1	AI528500|KMT3B	nuclear receptor-binding SET-domain protein 1	protein-coding
mm_167066.1	chr7	97417462	97417469	-	1	NA	promoter-TSS (NM_009381)	promoter-TSS (NM_009381)	85	NM_009381	21835	Mm.28585	NM_009381	ENSMUSG00000035686	Thrsp	S14|SPOT14	thyroid hormone responsive	protein-coding
mm_68717.1	chr7	120095265	120095312	-	1	NA	Intergenic	Intergenic	-7138	NM_145586	233806	Mm.257952	NM_145586	ENSMUSG00000030917	Tmem159	8430420C20Rik	transmembrane protein 159	protein-coding
mm_62805.1	chr7	112899941	112899953	+	1	NA	3' UTR (NM_001166585, exon 11 of 11)	3' UTR (NM_001166585, exon 11 of 11)	-54015	NM_175279	78748	Mm.349943	NM_175279	ENSMUSG00000098132	Rassf10	4632411J06Rik	Ras association (RalGDS/AF-6) domain family (N-terminal) member 10	protein-coding
mm_43068.1	chr5	124445378	124445388	+	1	NA	promoter-TSS (NM_001310723)	promoter-TSS (NM_001310723)	-116	NM_001310723	67956	Mm.137966	NM_030241	ENSMUSG00000049327	Kmt5a	2410195B05Rik|AA617402|AW536475|PR-SET7|PR/SET07|Setd8	lysine methyltransferase 5A	protein-coding
mm_1601.1	chr1	74377149	74377159	+	1	NA	intron (NM_013612, intron 3 of 14)	intron (NM_013612, intron 3 of 14)	1951	NM_013612	18173	Mm.2913	NM_013612	ENSMUSG00000026177	Slc11a1	Bcg|Ity|Ity1|Lsh|Nramp|Nramp1|ity	solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1	protein-coding
mm_119061.1	chr14	30719829	30719832	+	1	NA	intron (NM_001166532, intron 1 of 20)	intron (NM_001166532, intron 1 of 20)	4215	NM_001166532	54650	Mm.294662	NM_019460	ENSMUSG00000006527	Sfmbt1	4930442N21Rik|9330180L21Rik|AA536974|Sfmbt|Smr	Scm-like with four mbt domains 1	protein-coding
mm_164695.1	chr17	48501999	48502000	+	1	NA	Intergenic	Intergenic	47098	NM_152823	76589	Mm.311629	NM_152823	ENSMUSG00000043592	Unc5cl	2510009H09Rik|BB155270|Zud	unc-5 family C-terminal like	protein-coding
mm_115094.1	chr13	102706944	102706950	+	1	NA	TTS (NM_008533)	TTS (NM_008533)	13389	NM_008533	17079	Mm.373974	NM_008533	ENSMUSG00000021624	Cd180	F630107B15|Ly78|RP105	CD180 antigen	protein-coding
mm_151954.1	chr19	5801341	5801347	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	1328	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_47622.1	chr5	125245839	125245849	-	1	NA	Intergenic	CpG	-66630	NM_001253904	20602	Mm.278646	NM_011424	ENSMUSG00000029478	Ncor2	N-CoR|SMRT|SMRTe	nuclear receptor co-repressor 2	protein-coding
mm_155606.1	chrX	82960563	82960591	+	1	NA	intron (NM_007868, intron 1 of 78)	(T)n|Simple_repeat|Simple_repeat	11707	NM_007868	13405	Mm.275608	NM_007868	ENSMUSG00000045103	Dmd	DXSmh7|DXSmh9|Dp427|Dp71|dys|mdx|pke	dystrophin, muscular dystrophy	protein-coding
mm_109767.1	chr12	118376763	118376765	+	1	NA	Intergenic	Intergenic	-75324	NM_001166385	20688	Mm.34699	NM_009239	ENSMUSG00000025323	Sp4	5730497N03Rik|HF-1b|HF1-b	trans-acting transcription factor 4	protein-coding
mm_80527.1	chr9	80164996	80164998	+	1	NA	promoter-TSS (NM_001039546)	promoter-TSS (NM_001039546)	-37	NM_001039546	17920	Mm.4040	NM_008662	ENSMUSG00000033577	Myo6	BC029719|Tlc|sv	myosin VI	protein-coding
mm_50888.1	chr6	56714892	56714951	+	1	NA	promoter-TSS (NM_030235)	promoter-TSS (NM_030235)	16	NM_030235	78937	Mm.105343	NM_030235	ENSMUSG00000029787	Avl9	5830411G16Rik|D730049P16Rik|mKIAA0241	AVL9 cell migration associated	protein-coding
mm_11974.1	chr2	54905525	54905528	+	1	NA	intron (NM_173030, intron 8 of 12)	intron (NM_173030, intron 8 of 12)	469139	NM_173030	271786	Mm.330227	NM_173030	ENSMUSG00000060988	Galnt13	A230002A12|A230020F20|BB182356	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13	protein-coding
mm_28250.1	chr3	88511111	88511123	-	1	NA	Intergenic	B3|SINE|B2	-7765	NM_001002011	16905	Mm.243014	NM_019390	ENSMUSG00000028063	Lmna	Dhe	lamin A	protein-coding
mm_88691.1	chr10	80117296	80117311	+	1	NA	intron (NR_126043, intron 1 of 10)	CpG	1500	NM_001301854	20869	Mm.44231	NM_011492	ENSMUSG00000003068	Stk11	AA408040|Lkb1|Par-4|R75140	serine/threonine kinase 11	protein-coding
mm_116118.1	chr13	28950450	28950476	-	1	NA	TTS (NM_009238)	TTS (NM_009238)	3219	NM_009238	20677	Mm.240627	NM_009238	ENSMUSG00000076431	Sox4	AA682046|Sox-4	SRY (sex determining region Y)-box 4	protein-coding
mm_72888.1	chr8	89995915	89995918	+	1	NA	Intergenic	Intergenic	352336	NM_172913	244579	Mm.302755	NM_172913	ENSMUSG00000043668	Tox3	500-9|BC052044|C230068E13|CAGF9|Tnrc9	TOX high mobility group box family member 3	protein-coding
mm_90697.1	chr10	130322916	130322924	+	1	NA	promoter-TSS (NM_183264)	promoter-TSS (NM_183264)	68	NM_183264	67596	Mm.131264	NM_183264	ENSMUSG00000034833	Tespa1	5830405N20Rik|A430001F24Rik|AI450549	thymocyte expressed, positive selection associated 1	protein-coding
mm_116803.1	chr13	54072592	54072599	-	1	NA	intron (NM_027324, intron 1 of 10)	MIR|SINE|MIR	750	NM_027324	14057	Mm.134191	NM_027324	ENSMUSG00000021474	Sfxn1	2810002O05Rik|A930015P12Rik|f	sideroflexin 1	protein-coding
mm_70823.1	chr8	23139065	23139076	+	1	NA	promoter-TSS (NM_001310437)	promoter-TSS (NM_001310437)	40	NM_001310437	11733	Mm.334444	NM_031158	ENSMUSG00000031543	Ank1	Ank-1|nb|pale	ankyrin 1, erythroid	protein-coding
mm_80000.1	chr9	67047825	67047840	+	1	NA	exon (NM_001164251, exon 2 of 10)	exon (NM_001164251, exon 2 of 10)	1381	NM_001164255	22003	Mm.121878	NM_024427	ENSMUSG00000032366	Tpm1	AA986836|AI854628|TM2|Tm3|Tmpa|Tpm-1|alpha-TM	tropomyosin 1, alpha	protein-coding
mm_13880.1	chr2	119972396	119972430	+	1	NA	promoter-TSS (NM_011941)	promoter-TSS (NM_011941)	-286	NM_011941	26390	Mm.330501	NM_011941	ENSMUSG00000033902	Mapkbp1	2810483F24Rik|AW123212|JNKBP-1|Jnkbp1|mKIAA0596	mitogen-activated protein kinase binding protein 1	protein-coding
mm_142859.1	chr17	51813532	51813551	-	1	NA	intron (NM_001163632, intron 1 of 10)	CpG	-1487	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_56444.1	chr6	97487774	97487797	-	1	NA	promoter-TSS (NM_001346637)	promoter-TSS (NM_001346637)	35	NM_001346637	232288	Mm.27789	NM_145148	ENSMUSG00000030064	Frmd4b	6030440G05Rik|C87375|GOBLIN|GRSP1|R74720	FERM domain containing 4B	protein-coding
mm_76668.1	chr8	93427146	93427162	-	1	NA	Intergenic	Intergenic	-89945	NM_021456	12623	Mm.22720	NM_021456	ENSMUSG00000057074	Ces1g	Ces-1|Ces1|Ses-1	carboxylesterase 1G	protein-coding
mm_66492.1	chr7	45053951	45053984	-	1	NA	3' UTR (NM_022999, exon 7 of 7)	3' UTR (NM_022999, exon 7 of 7)	-1086	NM_175022	233210	Mm.219137	NM_175022	ENSMUSG00000046574	Prr12	6720469B10|BC058674	proline rich 12	protein-coding
mm_73140.1	chr8	94977353	94977368	+	1	NA	5' UTR (NM_001198894, exon 1 of 14)	5' UTR (NM_001198894, exon 1 of 14)	251	NM_001198894	14766	Mm.290834	NM_018882	ENSMUSG00000031785	Adgrg1	Cyt28|Gpr56|TM7LN4|TM7XN1	adhesion G protein-coupled receptor G1	protein-coding
mm_151622.1	chr19	3907048	3907064	-	1	NA	promoter-TSS (NM_001136091)	promoter-TSS (NM_001136091)	-73	NM_001167784	27060	Mm.271689	NM_016921	ENSMUSG00000001750	Tcirg1	ATP6N1C|ATP6a3|Atp6i|OC-116|OPTB1|Stv1|TIRC7|Vph1|oc	T cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 protein A3	protein-coding
mm_133689.1	chr16	92498766	92498824	+	1	NA	exon (NM_172469, exon 1 of 6)	exon (NM_172469, exon 1 of 6)	648	NM_172469	209195	Mm.44747	NM_172469	ENSMUSG00000022949	Clic6	5730466J16Rik|AL022908|AW045520|CLIC1L	chloride intracellular channel 6	protein-coding
mm_57177.1	chr6	122848269	122848279	-	1	NA	3' UTR (NM_009779, exon 2 of 2)	3' UTR (NM_009779, exon 2 of 2)	7883	NM_009779	12267	Mm.2408	NM_009779	ENSMUSG00000040552	C3ar1	AZ3B|C3AR|HNFAG09	complement component 3a receptor 1	protein-coding
mm_15337.1	chr2	155979043	155979066	+	1	NA	intron (NM_001130000, intron 18 of 32)	intron (NM_001130000, intron 18 of 32)	22496	NM_177217	16328	Mm.288729	NM_008383	ENSMUSG00000038241	Cep250	AW490617|B230210E21Rik|Cep2|Inmp	centrosomal protein 250	protein-coding
mm_44817.1	chr5	33652313	33652327	-	1	NA	TTS (NM_026698)	TTS (NM_026698)	254	NM_001289725	20492	Mm.4172	NM_009193	ENSMUSG00000004642	Slbp	-	stem-loop binding protein	protein-coding
mm_111340.1	chr12	86884704	86884714	-	1	NA	5' UTR (NM_145836, exon 1 of 1)	5' UTR (NM_145836, exon 1 of 1)	105	NM_145836	238330	Mm.248358	NM_145836	ENSMUSG00000034168	Irf2bpl	6430527G18Rik|Eap1	interferon regulatory factor 2 binding protein-like	protein-coding
mm_128199.1	chr15	35295089	35295104	-	1	NA	Intergenic	Intergenic	-1016	NM_054049	107587	Mm.46336	NM_054049	ENSMUSG00000022330	Osr2	5430409I15Rik|Osr2A|Osr2B	odd-skipped related 2	protein-coding
mm_37413.1	chr4	122859831	122859849	-	1	NA	TTS (NM_008917)	TTS (NM_008917)	23613	NM_008917	19063	Mm.277719	NM_008917	ENSMUSG00000028657	Ppt1	9530043G02Rik|AA960502|C77813|CLN1|D4Ertd184e|INCL|PPT	palmitoyl-protein thioesterase 1	protein-coding
mm_147286.1	chr18	39489243	39489297	-	1	NA	Intergenic	CpG	-2025	NM_008173	14815	Mm.129481	NM_008173	ENSMUSG00000024431	Nr3c1	GR|Grl-1|Grl1	nuclear receptor subfamily 3, group C, member 1	protein-coding
mm_114897.1	chr13	94404034	94404050	+	1	NA	exon (NM_009680, exon 5 of 27)	exon (NM_009680, exon 5 of 27)	45082	NM_009680	11774	Mm.21185	NM_009680	ENSMUSG00000021686	Ap3b1	AP-3|AU015684|C78395|Hps2|beta3A|pe|pearl|rim2	adaptor-related protein complex 3, beta 1 subunit	protein-coding
mm_27579.1	chr3	58885321	58885354	-	1	NA	promoter-TSS (NM_153386)	promoter-TSS (NM_153386)	-125	NM_153385	229320	Mm.131502	NM_153384	ENSMUSG00000043850	Clrn1	A130002D11Rik|USH3|Ush3a|clarin-1	clarin 1	protein-coding
mm_122322.1	chr14	36935616	36935618	-	1	NA	promoter-TSS (NM_028407)	promoter-TSS (NM_028407)	-49	NM_028407	72972	Mm.27621	NM_027045	ENSMUSG00000058690	Ccser2	1700012P13Rik|2900054P12Rik|AI035535|AW108503|Fam190b|Gcap14	coiled-coil serine rich 2	protein-coding
mm_114402.1	chr13	64153710	64153720	+	1	NA	promoter-TSS (NM_175494)	promoter-TSS (NM_175494)	-516	NM_175494	238673	Mm.300065	NM_175494	ENSMUSG00000044934	Zfp367	8030486J21Rik|ZFF29a|ZFF29b|Znf367	zinc finger protein 367	protein-coding
mm_75335.1	chr8	43305871	43305880	-	1	NA	intron (NM_009556, intron 1 of 3)	intron (NM_009556, intron 1 of 3)	1134	NM_009556	22702	Mm.285848	NM_009556	ENSMUSG00000051176	Zfp42	Rex-1|Rex1|Zfp-42	zinc finger protein 42	protein-coding
mm_27692.1	chr3	66193529	66193532	-	1	NA	intron (NM_145820, intron 6 of 13)	intron (NM_145820, intron 6 of 13)	-26357	NM_008987	19288	Mm.276776	NM_008987	ENSMUSG00000027832	Ptx3	AI607804|TSG-14	pentraxin related gene	protein-coding
mm_68964.1	chr7	126583548	126583578	-	1	NA	promoter-TSS (NM_009907)	promoter-TSS (NM_009907)	-327	NM_009907	12752	Mm.268930	NM_009907	ENSMUSG00000030720	Cln3	AI323623	ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease)	protein-coding
mm_29721.1	chr3	125935931	125935934	-	1	NA	intron (NM_011674, intron 1 of 5)	intron (NM_011674, intron 1 of 5)	2618	NM_011674	22239	Mm.306021	NM_011674	ENSMUSG00000032854	Ugt8a	AI850488|AW455908|Cgt|Ugt8|mCerGT	UDP galactosyltransferase 8A	protein-coding
mm_61873.1	chr7	89426331	89426353	+	1	NA	promoter-TSS (NR_102276)	promoter-TSS (NR_102276)	36	NR_102276	101521	Mm.26902	NR_102276	ENSMUSG00000109311	AI314278	-	expressed sequence AI314278	ncRNA
mm_87360.1	chr10	43825888	43825918	+	1	NA	promoter-TSS (NR_131055)	promoter-TSS (NR_131055)	-4	NR_131055	71018	Mm.410796	NR_131055	ENSMUSG00000111342	4933404K13Rik	-	RIKEN cDNA 4933404K13 gene	ncRNA
mm_24835.1	chr3	95659099	95659129	+	1	NA	exon (NM_008562, exon 1 of 3)	exon (NM_008562, exon 1 of 3)	393	NM_008562	17210	Mm.1639	NM_008562	ENSMUSG00000038612	Mcl1	AW556805|Mcl-1	myeloid cell leukemia sequence 1	protein-coding
mm_4551.1	chr1	177442413	177442426	+	1	NA	Intergenic	CpG	-2242	NM_001012330	30928	Mm.330700	NM_013915	ENSMUSG00000063659	Zbtb18	RP58|Zfp238|Znf238	zinc finger and BTB domain containing 18	protein-coding
mm_123487.1	chr14	66077695	66077740	-	1	NA	promoter-TSS (NM_009618)	promoter-TSS (NM_009618)	52	NM_009618	11495	Mm.422850	NM_009618	ENSMUSG00000022039	Adam2	AI323749|Ftnb|Ph30-beta	a disintegrin and metallopeptidase domain 2	protein-coding
mm_154604.1	chrX	7641094	7641109	+	1	NA	exon (NM_009305, exon 3 of 7)	exon (NM_009305, exon 3 of 7)	2521	NM_009305	20977	Mm.223674	NM_009305	ENSMUSG00000031144	Syp	A230093K24Rik|AI848995|Syn|p38	synaptophysin	protein-coding
mm_21705.1	chr2	164573417	164573445	-	1	NA	promoter-TSS (NM_001177401)	promoter-TSS (NM_001177401)	25	NM_001177401	629747	Mm.234248	NM_001177401	ENSMUSG00000074596	Spint3	Gm14315|OTTMUSG00000016288	serine peptidase inhibitor, Kunitz type, 3	protein-coding
mm_13979.1	chr2	121457079	121457127	+	1	NA	promoter-TSS (NM_001025371)	promoter-TSS (NM_001025371)	15	NM_026318	67693	Mm.330525	NM_026318	ENSMUSG00000027245	Hypk	2310003F16Rik|HSPC136	huntingtin interacting protein K	protein-coding
mm_72410.1	chr8	81775856	81775871	+	1	NA	intron (NM_001024617, intron 7 of 24)	intron (NM_001024617, intron 7 of 24)	433301	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_168161.1	chr10	4353464	4353465	+	1	NA	exon (NM_031185, exon 3 of 4)	exon (NM_031185, exon 3 of 4)	34644	NM_001033466	381990	Mm.262466	NM_001033466	ENSMUSG00000075327	Zbtb2	Gm1103	zinc finger and BTB domain containing 2	protein-coding
mm_122006.1	chr14	26970448	26970556	-	1	NA	promoter-TSS (NM_145221)	promoter-TSS (NM_145221)	49	NM_145221	72993	Mm.202322	NM_145221	ENSMUSG00000040760	Appl1	2900057D21Rik|7330406P05Rik|AI585782|AW209077|BB022931|C88264|DIP13	adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 1	protein-coding
mm_56394.1	chr6	95718801	95718832	-	1	NA	promoter-TSS (NM_011507)	promoter-TSS (NM_011507)	30	NM_011507	20917	Mm.371585	NM_011507	ENSMUSG00000061838	Suclg2	AF171077|AW556404|D6Wsu120e|G-SCS|GTPSCS|SCS-betaG	succinate-Coenzyme A ligase, GDP-forming, beta subunit	protein-coding
mm_70007.1	chr7	142398075	142398083	-	1	NA	Intergenic	Intergenic	-10209	NM_009983	13033	Mm.231395	NM_009983	ENSMUSG00000007891	Ctsd	CD|CatD	cathepsin D	protein-coding
mm_123628.1	chr14	68124837	68124856	-	1	NA	5' UTR (NM_008691, exon 1 of 3)	intron (NR_045897, intron 1 of 2)	158	NM_008691	18040	Mm.242832	NM_008691	ENSMUSG00000022054	Nefm	NF-M|NF160|NF165|Nef3|Nfm	neurofilament, medium polypeptide	protein-coding
mm_59908.1	chr7	30412918	30412949	+	1	NA	promoter-TSS (NM_011662)	promoter-TSS (NM_011662)	-855	NM_011662	22177	Mm.46301	NM_011662	ENSMUSG00000030579	Tyrobp	DAP12|KARAP|Ly83	TYRO protein tyrosine kinase binding protein	protein-coding
mm_119915.1	chr14	54953339	54953353	+	1	NA	exon (NM_010856, exon 22 of 39)	exon (NM_010856, exon 22 of 39)	-4204	NR_029724	387204		NR_029724	ENSMUSG00000065432	Mir208a	Mirn208|Mirn208a|mir-208|mir-208a|mmu-mir-208	microRNA 208a	ncRNA
mm_62546.1	chr7	102426575	102426582	+	1	NA	intron (NM_009287, intron 8 of 11)	intron (NM_009287, intron 8 of 11)	-15117	NM_009103	20133	Mm.197486	NM_009103	ENSMUSG00000030978	Rrm1	RnrM1	ribonucleotide reductase M1	protein-coding
mm_152491.1	chr19	11055772	11055786	-	1	NA	Intergenic	Lx|LINE|L1	-5213	NR_102366	107350	Mm.6381	NM_001177351	ENSMUSG00000075010	AW112010	-	expressed sequence AW112010	ncRNA
mm_113262.1	chr13	28874293	28874296	+	1	NA	intron (NR_045053, intron 2 of 8)	intron (NR_045053, intron 2 of 8)	11128	NR_045054	72518	Mm.37454	NR_045053		2610307P16Rik	AI666457	RIKEN cDNA 2610307P16 gene	ncRNA
mm_38983.1	chr4	150944949	150944964	-	1	NA	3' UTR (NM_001077508, exon 7 of 7)	3' UTR (NM_001077508, exon 7 of 7)	16957	NM_001077509	21942	Mm.244187	NM_011612	ENSMUSG00000028965	Tnfrsf9	4-1BB|A930040I11Rik|AA408498|AI325004|CDw137|Cd137|ILA|Ly63	tumor necrosis factor receptor superfamily, member 9	protein-coding
mm_113160.1	chr13	24803019	24803035	+	1	NA	5' UTR (NM_024473, exon 1 of 5)	5' UTR (NM_024473, exon 1 of 5)	1370	NM_024473	79555	Mm.266668	NM_024473	ENSMUSG00000019132	BC005537	8030460C05Rik|C78201	cDNA sequence BC005537	protein-coding
mm_39272.1	chr5	3803161	3803193	+	1	NA	promoter-TSS (NM_001003909)	promoter-TSS (NM_001003909)	-4	NR_033173	79264	Mm.32368	NM_030675	ENSMUSG00000000600	Krit1	2010007K12Rik|A630036P20Rik|AA432855|AI450393|AI643869|BB155247|BB235701|Ccm1	KRIT1, ankyrin repeat containing	protein-coding
mm_88620.1	chr10	79859391	79859417	+	1	NA	exon (NM_008956, exon 5 of 13)	exon (NM_008956, exon 5 of 13)	-3183	NR_105875	102465549		NR_105875	ENSMUSG00000098562	Mir6910	Gm27763|mmu-mir-6910	microRNA 6910	ncRNA
mm_45.1	chr1	6500371	6500397	+	1	NA	intron (NM_001244693, intron 2 of 22)	RMER4B|LTR|ERVK	13153	NM_001244692	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding
mm_3350.1	chr1	138152404	138152440	+	1	NA	intron (NM_001111316, intron 1 of 31)	intron (NM_001111316, intron 1 of 31)	22704	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_140107.1	chr17	78573885	78573891	+	1	NA	intron (NM_028813, intron 4 of 13)	intron (NM_028813, intron 4 of 13)	65825	NM_028813	74199	Mm.292983	NM_028813	ENSMUSG00000024076	Vit	1700052E02Rik|1700110E08Rik|2810429K11Rik	vitrin	protein-coding
mm_82532.1	chr9	20726997	20727012	-	1	NA	intron (NM_173777, intron 1 of 5)	CpG	1210	NM_173777	244723	Mm.293552	NM_173777	ENSMUSG00000032172	Olfm2	A030009A06Rik	olfactomedin 2	protein-coding
mm_169958.1	chr16	91248654	91248669	+	1	NA	Intergenic	ETnERV-int|LTR|ERVK	-21108	NM_016968	50914	Mm.39300	NM_016968	ENSMUSG00000046160	Olig1	AI836478|AW494459|Bhlhb6|Olg-1|Oligo1|bHLHe21	oligodendrocyte transcription factor 1	protein-coding
mm_161577.1	chr16	25865701	25865701	+	1	NA	intron (NM_001127259, intron 7 of 13)	intron (NM_001127259, intron 7 of 13)	63785	NM_001127264	22061	Mm.20894	NM_011641	ENSMUSG00000022510	Trp63	AI462811|Ket|P51/P63|P63|P73l|Tp63|Trp53rp1	transformation related protein 63	protein-coding
mm_170111.1	chr17	39845071	39845073	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	2075	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_123785.1	chr14	70348426	70348440	-	1	NA	promoter-TSS (NM_001135152)	promoter-TSS (NM_001135152)	0	NM_001135152	213053	Mm.270647	NM_144808	ENSMUSG00000022094	Slc39a14	FAD-123|ZIP-14|Zip14|fad123	solute carrier family 39 (zinc transporter), member 14	protein-coding
mm_56151.1	chr6	87843627	87843692	-	1	NA	3' UTR (NM_013493, exon 5 of 5)	3' UTR (NM_013493, exon 5 of 5)	-4900	NM_133934	57905	Mm.241546	NM_133934	ENSMUSG00000030056	Isy1	5830446M03Rik|AI181014|AU020769	ISY1 splicing factor homolog	protein-coding
mm_60284.1	chr7	43979063	43979088	+	1	NA	intron (NM_010116, intron 2 of 4)	intron (NM_010116, intron 2 of 4)	3014	NM_010116	13648	Mm.440884	NM_010116	ENSMUSG00000059042	Klk1b9	EGF-BP C|Egfbp-3|Egfbp3|KAL|Klk9|kallikrein|mGk-9	kallikrein 1-related peptidase b9	protein-coding
mm_115445.1	chr13	117971584	117971597	+	1	NA	exon (NM_010408, exon 7 of 8)	exon (NM_010408, exon 7 of 8)	-251579	NR_045508	71100	Mm.414841	NR_045508	ENSMUSG00000079048	4933413L06Rik	-	RIKEN cDNA 4933413L06 gene	ncRNA
mm_69219.1	chr7	127588146	127588190	-	1	NA	promoter-TSS (NM_172281)	promoter-TSS (NM_172281)	427	NM_001033040	233899	Mm.25220	NM_001033040	ENSMUSG00000057176	Ccdc189	Gm166	coiled-coil domain containing 189	protein-coding
mm_24009.1	chr3	87376442	87376459	+	1	NA	promoter-TSS (NM_178165)	promoter-TSS (NM_178165)	63	NM_001136236	229499	Mm.255203	NM_153090	ENSMUSG00000059994	Fcrl1	A230020G22Rik|Bxmas1|Bxmh1|Bxmh1b|Fcrh1|Fcrh1l|Fcrh1s|Ifgp1	Fc receptor-like 1	protein-coding
mm_163357.1	chr12	28800698	28800709	+	1	NA	intron (NM_201357, intron 3 of 8)	intron (NM_201357, intron 3 of 8)	48875	NM_201357	380752	Mm.273724	NM_201357	ENSMUSG00000036613	Tssc1	D12Ertd604e|Eipr1	tumor suppressing subtransferable candidate 1	protein-coding
mm_125417.1	chr15	41820121	41820142	+	1	NA	exon (NM_001130163, exon 7 of 14)	exon (NM_001130163, exon 7 of 14)	-10827	NM_001130164	170719	Mm.254267	NM_130885	ENSMUSG00000022307	Oxr1	2210416C20Rik|C7|C7B	oxidation resistance 1	protein-coding
mm_9609.1	chr1	176213705	176213718	-	1	NA	5' UTR (NM_001195816, exon 1 of 10)	5' UTR (NM_001195816, exon 1 of 10)	231	NM_001195816	319455	Mm.338001	NM_176916	ENSMUSG00000055214	Pld5	B230365F16Rik	phospholipase D family, member 5	protein-coding
mm_137328.1	chr17	25016582	25016588	+	1	NA	5' UTR (NM_134126, exon 1 of 30)	5' UTR (NM_134126, exon 1 of 30)	499	NM_134126	106633	Mm.32802	NM_134126	ENSMUSG00000024169	Ift140	AI661311|Tce5|Wdtc2|mKIAA0590	intraflagellar transport 140	protein-coding
mm_96741.1	chr11	69838526	69838567	+	1	NA	promoter-TSS (NM_026982)	promoter-TSS (NM_026982)	21	NM_026982	69186	Mm.248772	NM_026982	ENSMUSG00000070394	Tmem256	1810027O10Rik|3110009M16Rik	transmembrane protein 256	protein-coding
mm_61841.1	chr7	88290598	88290607	+	1	NA	3' UTR (NM_001311790, exon 4 of 4)	3' UTR (NM_001311790, exon 4 of 4)	12517	NM_001311790	13032	Mm.89295	NM_009982	ENSMUSG00000030560	Ctsc	AI047818|CatC|DPP1|DPPI	cathepsin C	protein-coding
mm_122835.1	chr14	54723572	54723578	-	1	NA	3' UTR (NM_016972, exon 11 of 11)	3' UTR (NM_016972, exon 11 of 11)	-11401	NM_207131	110794	Mm.236223	NM_207131	ENSMUSG00000052435	Cebpe	C/EBPe|CRP1|Gm294	CCAAT/enhancer binding protein (C/EBP), epsilon	protein-coding
mm_51014.1	chr6	65022204	65022214	+	1	NA	Intergenic	Intergenic	-20458	NM_007958	13990	Mm.99113	NM_007958	ENSMUSG00000029920	Smarcad1	AV081750|AW226546|D6Pas1|Etl1|mKIAA1122	SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1	protein-coding
mm_171751.1	chr5	102409799	102409804	+	1	NA	Intergenic	L1Md_T|LINE|L1	-71590	NM_146161	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding
mm_120296.1	chr14	63138414	63138422	+	1	NA	exon (NM_007798, exon 7 of 10)	exon (NM_007798, exon 7 of 10)	15956	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_171379.1	chr4	119293760	119293760	-	1	NA	exon (NM_011732, exon 2 of 8)	exon (NM_011732, exon 2 of 8)	753	NM_011732	22608	Mm.258204	NM_011732	ENSMUSG00000028639	Ybx1	1700102N10Rik|C79409|EF1A|MSY1|Nsep1|YB-1|dbpB|mYB-1a	Y box protein 1	protein-coding
mm_81096.1	chr9	106374305	106374344	+	1	NA	3' UTR (NM_153459, exon 3 of 3)	3' UTR (NM_153459, exon 3 of 3)	5692	NM_153459	235584	Mm.275584	NM_153459	ENSMUSG00000053716	Dusp7	AU015694|Mkpx|Pyst2	dual specificity phosphatase 7	protein-coding
mm_56936.1	chr6	119848094	119848113	-	1	NA	promoter-TSS (NM_178085)	promoter-TSS (NM_178085)	47	NM_053204	111173	Mm.288860	NM_053204	ENSMUSG00000030172	Erc1	4930404L01Rik|5033405M01Rik|9630025C19Rik|B430107L16Rik|CAST2|ELKS|Elks1|RAB6IP2A|RAB6IP2B|Rab6ip2|mKIAA1081	ELKS/RAB6-interacting/CAST family member 1	protein-coding
mm_99144.1	chr11	100441883	100441938	+	1	NA	promoter-TSS (NM_001102650)	promoter-TSS (NM_001102650)	-14	NM_025727	66720	Mm.34168	NM_025727	ENSMUSG00000001558	Klhl10	4921517C11Rik	kelch-like 10	protein-coding
mm_25153.1	chr3	102996124	102996160	+	1	NA	intron (NM_025679, intron 1 of 4)	intron (NM_025679, intron 1 of 4)	402	NM_025679	66641	Mm.33937	NM_025679	ENSMUSG00000027854	Sike1	2810005O12Rik|5730470L24Rik|AI450236|AI839862|Sike|Sikeb	suppressor of IKBKE 1	protein-coding
mm_113571.1	chr13	38350210	38350212	+	1	NA	intron (NM_007556, intron 1 of 6)	intron (NM_007556, intron 1 of 6)	4495	NM_007556	12161	Mm.385759	NM_007556	ENSMUSG00000039004	Bmp6	D13Wsu115e|Vgr1	bone morphogenetic protein 6	protein-coding
mm_133685.1	chr16	92498123	92498175	+	1	NA	promoter-TSS (NM_172469)	promoter-TSS (NM_172469)	2	NM_172469	209195	Mm.44747	NM_172469	ENSMUSG00000022949	Clic6	5730466J16Rik|AL022908|AW045520|CLIC1L	chloride intracellular channel 6	protein-coding
mm_81135.1	chr9	106561713	106561718	+	1	NA	promoter-TSS (NM_026645)	promoter-TSS (NM_026645)	-90	NM_026645	68265	Mm.141451	NM_026645	ENSMUSG00000023577	Iqcf3	1700012F17Rik|AV040440	IQ motif containing F3	protein-coding
mm_96160.1	chr11	61487745	61487756	+	1	NA	intron (NM_001347545, intron 4 of 4)	intron (NM_001347545, intron 4 of 4)	2306	NM_029568	76293	Mm.272278	NM_029568	ENSMUSG00000042436	Mfap4	1110007F23Rik	microfibrillar-associated protein 4	protein-coding
mm_77291.1	chr8	116944183	116944195	-	1	NA	intron (NM_177700, intron 1 of 3)	intron (NM_177700, intron 1 of 3)	796	NM_177700	234776	Mm.259736	NM_177700	ENSMUSG00000047388	Atmin	Asciz|gpg6|mKIAA0431	ATM interactor	protein-coding
mm_8053.1	chr1	135374420	135374434	-	1	NA	exon (NM_175259, exon 2 of 5)	exon (NM_175259, exon 2 of 5)	636	NM_175259	77552	Mm.41407	NM_175259	ENSMUSG00000041889	Shisa4	9330132O05Rik|Tmem58|mShisa4	shisa family member 4	protein-coding
mm_94698.1	chr11	20138080	20138111	+	1	NA	Intergenic	MTEa|LTR|ERVL-MaLR	-25144	NM_146243	66713	Mm.259045	NM_146243	ENSMUSG00000020152	Actr2	4921510D23Rik|AA409782|Arp2|D6Ertd746e	ARP2 actin-related protein 2	protein-coding
mm_98911.1	chr11	98202759	98202801	+	1	NA	promoter-TSS (NM_026952)	promoter-TSS (NM_026952)	-525	NM_001109628	69131	Mm.260516	NM_026952	ENSMUSG00000003119	Cdk12	1810022J16Rik|AI646528|Crk7|Crkrs|D11Ertd752e|Pksc	cyclin-dependent kinase 12	protein-coding
mm_37315.1	chr4	119335544	119335544	-	1	NA	intron (NM_029286, intron 10 of 14)	intron (NM_029286, intron 10 of 14)	-15021	NM_001110130	66101	Mm.304080	NM_028677	ENSMUSG00000060288	Ppih	1100001J08Rik|2010111B15Rik|4833408F11Rik|AI464484|CYP-20|CYPH|D4Wsu43e	peptidyl prolyl isomerase H	protein-coding
mm_121401.1	chr14	119169960	119169963	+	1	NA	intron (NM_015820, intron 1 of 1)	Lx3B|LINE|L1	31696	NM_015820	50787	Mm.445777	NM_015820	ENSMUSG00000053465	Hs6st3	6OST3|HS6ST-3	heparan sulfate 6-O-sulfotransferase 3	protein-coding
mm_130623.1	chr15	100403409	100403428	-	1	NA	intron (NM_008732, intron 9 of 16)	intron (NM_008732, intron 9 of 16)	19637	NM_001146161	18174	Mm.234608	NM_008732	ENSMUSG00000023030	Slc11a2	DCT1|DMT1|Nramp2|mk|van	solute carrier family 11 (proton-coupled divalent metal ion transporters), member 2	protein-coding
mm_41404.1	chr5	90786505	90786515	+	1	NA	intron (NM_203320, intron 2 of 3)	intron (NM_203320, intron 2 of 3)	409	NM_203320	330122	Mm.244289	NM_203320	ENSMUSG00000029379	Cxcl3	Dcip1|Gm1960	chemokine (C-X-C motif) ligand 3	protein-coding
mm_35223.1	chr4	19678847	19678850	-	1	NA	intron (NR_074089, intron 2 of 23)	intron (NR_074089, intron 2 of 23)	30156	NM_177327	107568	Mm.78312	NM_177327	ENSMUSG00000041058	Wwp1	8030445B08Rik|AIP5|SDRP1|Tiul1	WW domain containing E3 ubiquitin protein ligase 1	protein-coding
mm_114639.1	chr13	76472173	76472181	+	1	NA	intron (NM_030174, intron 1 of 20)	intron (NM_030174, intron 1 of 20)	87216	NM_030174	78771	Mm.316249	NM_030174	ENSMUSG00000021596	Mctp1	2810465F10Rik	multiple C2 domains, transmembrane 1	protein-coding
mm_59454.1	chr7	27195139	27195143	+	1	NA	promoter-TSS (NM_001290511)	promoter-TSS (NM_001290511)	619	NM_001046637	53607	Mm.386890	NM_015782	ENSMUSG00000061479	Snrpa	C430021M15Rik|Rnu1a-1|Rnu1a1|U1-A|U1A	small nuclear ribonucleoprotein polypeptide A	protein-coding
mm_103486.1	chr11	76509258	76509307	-	1	NA	5' UTR (NM_198018, exon 1 of 22)	5' UTR (NM_198018, exon 1 of 22)	137	NM_198018	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_118533.1	chr14	15910430	15910433	+	1	NA	Intergenic	Intergenic	-338883	NM_021504	59007	Mm.258381	NM_021504	ENSMUSG00000021785	Ngly1	1110002C09Rik|PNGase|Png1	N-glycanase 1	protein-coding
mm_149584.1	chr19	16025410	16025439	+	1	NA	Intergenic	Intergenic	40349	NR_045355	100502653	Mm.149980	NR_045355	ENSMUSG00000097557	C130060C02Rik	-	RIKEN cDNA C130060C02 gene	ncRNA
mm_156294.1	chrX	136837538	136837566	+	1	NA	3' UTR (NM_011123, exon 7 of 7)	3' UTR (NM_011123, exon 7 of 7)	14806	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_162733.1	chr10	51597374	51597390	-	1	NA	Intergenic	Intergenic	-6922	NM_029894	77296	Mm.30588	NM_029894	ENSMUSG00000019909	Fam162b	9430073N08Rik	family with sequence similarity 162, member B	protein-coding
mm_103616.1	chr11	78550802	78550812	-	1	NA	promoter-TSS (NM_133706)	promoter-TSS (NM_133706)	-72	NM_133706	69071	Mm.29431	NM_133706	ENSMUSG00000037278	Tmem97	1810014L12Rik|AI115531|AL022956|D11Bhm182e	transmembrane protein 97	protein-coding
mm_19882.1	chr2	114049638	114049654	-	1	NA	exon (NM_009608, exon 4 of 7)	exon (NM_009608, exon 4 of 7)	3229	NM_009608	11464	Mm.686	NM_009608	ENSMUSG00000068614	Actc1	Actc-1	actin, alpha, cardiac muscle 1	protein-coding
mm_53457.1	chr6	134830217	134830270	+	1	NA	promoter-TSS (NM_177687)	promoter-TSS (NM_177687)	44	NM_177687	232430	Mm.267010	NM_177687	ENSMUSG00000032652	Crebl2	AI046348|B230205M03	cAMP responsive element binding protein-like 2	protein-coding
mm_157809.1	chrX	73945550	73945554	-	1	NA	intron (NM_008224, intron 23 of 25)	intron (NM_008224, intron 23 of 25)	-14702	NM_001164704	19703	Mm.236969	NM_023132	ENSMUSG00000031387	Renbp	Age|Rnbp	renin binding protein	protein-coding
mm_145703.1	chr18	62657311	62657313	+	1	NA	intron (NM_177829, intron 5 of 8)	intron (NM_177829, intron 5 of 8)	-61048	NM_001001803	408198	Mm.478742	NM_001001803	ENSMUSG00000060201	Spink7	EG408198|Ecg2	serine peptidase inhibitor, Kazal type 7 (putative)	protein-coding
mm_122185.1	chr14	31633688	31633699	-	1	NA	intron (NM_019975, intron 4 of 16)	intron (NM_019975, intron 4 of 16)	7272	NM_019975	56794	Mm.38887	NM_019975	ENSMUSG00000021884	Hacl1	1600020H07Rik|Hpcl|Phyh2	2-hydroxyacyl-CoA lyase 1	protein-coding
mm_53909.1	chr6	3968396	3968417	-	1	NA	promoter-TSS (NM_009364)	promoter-TSS (NM_009364)	-31	NM_009364	21789	Mm.25612	NM_009364	ENSMUSG00000029664	Tfpi2	AV000670|PP5/TFPI-2	tissue factor pathway inhibitor 2	protein-coding
mm_27719.1	chr3	68893078	68893083	-	1	NA	3' UTR (NM_026641, exon 20 of 20)	3' UTR (NM_026641, exon 20 of 20)	23494	NM_001167996	68725	Mm.45741	NM_001167996	ENSMUSG00000046999	1110032F04Rik	AI115547	RIKEN cDNA 1110032F04 gene	protein-coding
mm_16170.1	chr2	172546214	172546224	+	1	NA	Intergenic	Intergenic	-3374	NM_009335	21420	Mm.3629	NM_009335	ENSMUSG00000028640	Tfap2c	AA409384|AP2gamma|Ap-2.2|Stra2|Tcfap2c	transcription factor AP-2, gamma	protein-coding
mm_122450.1	chr14	45306212	45306216	-	1	NA	intron (NM_015774, intron 2 of 15)	RSINE1|SINE|B4	12358	NM_015774	50527	Mm.387108	NM_015774	ENSMUSG00000021831	Ero1l	ERO1-L|Ero1a	ERO1-like (S. cerevisiae)	protein-coding
mm_118527.1	chr14	14963540	14963543	+	1	NA	intron (NM_001195229, intron 28 of 34)	Lx|LINE|L1	142726	NM_001195229	674895	Mm.317563	NM_001034865	ENSMUSG00000042567	Nek10	Gm282	NIMA (never in mitosis gene a)- related kinase 10	protein-coding
mm_169634.1	chr15	47539995	47539996	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	916690	NR_045811	75281	Mm.159487	NR_045811	ENSMUSG00000051198	4930548G14Rik	-	RIKEN cDNA 4930548G14 gene	ncRNA
mm_76137.1	chr8	81014867	81014942	-	1	NA	promoter-TSS (NM_027554)	promoter-TSS (NM_027554)	2	NM_027554	74841	Mm.246018	NM_027554	ENSMUSG00000038250	Usp38	4631402N15Rik|4833420O05Rik|AA536967|AU044701|AW544820|mKIAA1891	ubiquitin specific peptidase 38	protein-coding
mm_2197.1	chr1	89454934	89454948	+	1	NA	5' UTR (NM_178119, exon 1 of 18)	5' UTR (NM_178119, exon 1 of 18)	130	NM_001037136	347722	Mm.291135	NM_178119	ENSMUSG00000055013	Agap1	Centg2|Ggap1|R75364|mKIAA1099	ArfGAP with GTPase domain, ankyrin repeat and PH domain 1	protein-coding
mm_127895.1	chr15	9155414	9155416	-	1	NA	promoter-TSS (NM_001285980)	promoter-TSS (NM_001285980)	10	NM_001285980	27401	Mm.35584	NM_013787	ENSMUSG00000054115	Skp2	4930500A04Rik|FBXL1|FWD1|p45	S-phase kinase-associated protein 2 (p45)	protein-coding
mm_36853.1	chr4	106805086	106805099	-	1	NA	promoter-TSS (NM_001347159)	promoter-TSS (NM_001347159)	-85	NM_001347159	329910	Mm.222956	NM_025590	ENSMUSG00000034853	Acot11	1110020M10Rik|2010309H15Rik|AW060409|BFIT|BFIT1|Thea|Them1|mKIAA0707	acyl-CoA thioesterase 11	protein-coding
mm_162470.1	chr1	132007907	132007917	-	1	NA	5' UTR (NM_007923, exon 1 of 5)	5' UTR (NM_007923, exon 1 of 5)	307	NM_007923	13714	Mm.254233	NM_007923	ENSMUSG00000026436	Elk4	2310011G17Rik|A130026I01Rik|BB162516|SAP-1|Sap1	ELK4, member of ETS oncogene family	protein-coding
mm_20095.1	chr2	120970647	120970703	-	1	NA	promoter-TSS (NM_009461)	promoter-TSS (NM_009461)	40	NM_009461	22222	Mm.389330	NM_009461	ENSMUSG00000027272	Ubr1	AI504731	ubiquitin protein ligase E3 component n-recognin 1	protein-coding
mm_80954.1	chr9	103007956	103007976	+	1	NA	promoter-TSS (NM_033314)	promoter-TSS (NM_033314)	-523	NM_033314	24059	Mm.207106	NM_033314	ENSMUSG00000032548	Slco2a1	2310021C19Rik|Pgt|Slc21a2|mPgt	solute carrier organic anion transporter family, member 2a1	protein-coding
mm_29682.1	chr3	123024853	123024856	-	1	NA	intron (NM_021503, intron 3 of 5)	intron (NM_021503, intron 3 of 5)	10133	NM_021503	59006	Mm.141157	NM_021503	ENSMUSG00000028116	Myoz2	1110012I24Rik|Fatz-2|Myozl2	myozenin 2	protein-coding
mm_6638.1	chr1	79371730	79371732	-	1	NA	Intergenic	URR1B|DNA|hAT-Charlie	68359	NM_009129	20254	Mm.5038	NM_009129	ENSMUSG00000050711	Scg2	Chgc|SgII	secretogranin II	protein-coding
mm_63798.1	chr7	132931200	132931219	+	1	NA	Intergenic	CpG	-18413	NM_207302	360216	Mm.389984	NM_207302	ENSMUSG00000030967	Zranb1	9330160G10Rik|D7Wsu87e|Gm1956|Trabid	zinc finger, RAN-binding domain containing 1	protein-coding
mm_51417.1	chr6	78382046	78382057	+	1	NA	intron (NM_011259, intron 3 of 5)	intron (NM_011259, intron 3 of 5)	1342	NM_011259	19694	Mm.2552	NM_011259	ENSMUSG00000079516	Reg3a	AV063448	regenerating islet-derived 3 alpha	protein-coding
mm_57771.1	chr6	129237087	129237099	-	1	NA	intron (NR_040265, intron 1 of 2)	ORR1E|LTR|ERVL-MaLR	952	NR_040265	76432	Mm.261738	NR_040265	ENSMUSG00000097354	2310001H17Rik	AI646108	RIKEN cDNA 2310001H17 gene	ncRNA
mm_21658.1	chr2	164404813	164404824	-	1	NA	promoter-TSS (NM_013592)	promoter-TSS (NM_013592)	0	NM_013592	17183	Mm.29428	NM_013592	ENSMUSG00000016995	Matn4	matrilin-4	matrilin 4	protein-coding
mm_80587.1	chr9	85327894	85327941	+	1	NA	promoter-TSS (NM_001160378)	promoter-TSS (NM_001160378)	-767	NM_001160379	212943	Mm.74610	NM_001160378	ENSMUSG00000032265	Fam46a	BAP014|D930050G01Rik	family with sequence similarity 46, member A	protein-coding
mm_83331.1	chr9	44234015	44234017	-	1	NA	promoter-TSS (NM_007619)	promoter-TSS (NM_007619)	30	NM_007619	12402	Mm.266871	NM_007619	ENSMUSG00000034342	Cbl	4732447J05Rik|Cbl-2|c-Cbl|cbl	Casitas B-lineage lymphoma	protein-coding
mm_72166.1	chr8	72240316	72240346	+	1	NA	intron (NM_007456, intron 1 of 11)	CpG	313	NM_007456	11767	Mm.290086	NM_007456	ENSMUSG00000003033	Ap1m1	AA408894|AP47|Adtm1A|Cltnm|mu1A	adaptor-related protein complex AP-1, mu subunit 1	protein-coding
mm_7900.1	chr1	133648879	133648883	-	1	NA	intron (NM_001276767, intron 3 of 17)	B2_Mm2|SINE|B2	12004	NM_001166552	667118	Mm.245357	NM_001166552	ENSMUSG00000094410	Zbed6	Gm8466|MGR	zinc finger, BED type containing 6	protein-coding
mm_3822.1	chr1	159276000	159276008	+	1	NA	intron (NM_011931, intron 8 of 19)	intron (NM_011931, intron 8 of 19)	-17769	NR_144489	100846986		NR_144489		Pou5f1-rs1	Gm21053|Oct4P2|Otf-3rs|Otf3-rs1|Otf3a	POU domain, class 5, transcription factor 1, related sequence 1	pseudo
mm_57919.1	chr6	133853651	133853673	-	1	NA	promoter-TSS (NM_010594)	promoter-TSS (NM_010594)	5	NM_010594	16483	Mm.13052	NM_010594	ENSMUSG00000032758	Kap	AW146435|FKSG22	kidney androgen regulated protein	protein-coding
mm_116060.1	chr13	27513182	27513196	-	1	NA	promoter-TSS (NM_023741)	promoter-TSS (NM_023741)	24	NM_023741	74188	Mm.46090	NM_023741	ENSMUSG00000021346	Prl8a8	1600032B14Rik|Ghd14|PLP-Cgamma|Prlpc3	prolactin family 8, subfamily a, member 81	protein-coding
mm_170390.1	chr18	6268588	6268588	-	1	NA	Intergenic	Intergenic	-27064	NM_008448	16573	Mm.223744	NM_008448	ENSMUSG00000006740	Kif5b	AL022807|Khc|Khcs|Kns1|Ukhc	kinesin family member 5B	protein-coding
mm_153101.1	chr19	32712831	32712843	-	1	NA	promoter-TSS (NM_026487)	promoter-TSS (NM_026487)	-539	NM_026487	67979	Mm.27123	NM_026487	ENSMUSG00000013662	Atad1	4921525H23Rik|AW107648|Thorase	ATPase family, AAA domain containing 1	protein-coding
mm_149087.1	chr19	8920497	8920575	+	1	NA	5' UTR (NM_024256, exon 1 of 5)	5' UTR (NM_024256, exon 1 of 5)	143	NM_024256	72727	Mm.259	NM_024256	ENSMUSG00000071649	B3gat3	2810405M13Rik	beta-1,3-glucuronyltransferase 3 (glucuronosyltransferase I)	protein-coding
mm_88634.1	chr10	79888667	79888667	+	1	NA	TTS (NM_015779)	TTS (NM_015779)	-2186	NM_001329541	11537	Mm.4407	NM_013459	ENSMUSG00000061780	Cfd	Adn|DF	complement factor D (adipsin)	protein-coding
mm_59229.1	chr7	24655781	24655786	+	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-5511	NR_030681	100043706	Mm.483825	NR_030681	ENSMUSG00000108470	Gm4598	-	predicted gene 4598	ncRNA
mm_58901.1	chr7	17163260	17163283	+	1	NA	TTS (NM_054059)	TTS (NM_054059)	12871	NM_054059	384557	Mm.486145	NM_054059	ENSMUSG00000053228	Ceacam3	EG384557|Psg24|cea12	carcinoembryonic antigen-related cell adhesion molecule 3	protein-coding
mm_34996.1	chr4	156109972	156110004	+	1	NA	promoter-TSS (NM_145557)	promoter-TSS (NM_145557)	-10	NM_145557	230996	Mm.318925	NM_145557	ENSMUSG00000059939	9430015G10Rik	-	RIKEN cDNA 9430015G10 gene	protein-coding
mm_62005.1	chr7	91262122	91262144	+	1	NA	intron (NM_011807, intron 1 of 22)	intron (NM_011807, intron 1 of 22)	171347	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_55051.1	chr6	49044096	49044149	-	1	NA	exon (NM_053110, exon 3 of 11)	exon (NM_053110, exon 3 of 11)	7604	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_120484.1	chr14	65975840	65975863	+	1	NA	exon (NM_013492, exon 5 of 9)	exon (NM_013492, exon 5 of 9)	7368	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_172913.1	chr9	64173403	64173405	+	1	NA	promoter-TSS (NM_026507)	promoter-TSS (NM_026507)	17	NM_024212	67891	Mm.280083	NM_024212	ENSMUSG00000032399	Rpl4	2010004J23Rik	ribosomal protein L4	protein-coding
mm_160509.1	chr9	20644496	20644496	-	1	NA	promoter-TSS (NM_001310746)	promoter-TSS (NM_001310746)	271	NM_001286529	30843	Mm.24608	NM_013911	ENSMUSG00000066892	Fbxl12	3110048D16Rik|Fbl12	F-box and leucine-rich repeat protein 12	protein-coding
mm_96569.1	chr11	69027976	69027982	+	1	NA	exon (NM_001281465, exon 10 of 23)	exon (NM_001281465, exon 10 of 23)	12068	NM_001013256	68964	Mm.285785	NM_001013256	ENSMUSG00000020898	Ctc1	1500010J02Rik|AAF-132|AAF132	CTS telomere maintenance complex component 1	protein-coding
mm_124661.1	chr15	6299782	6299795	+	1	NA	promoter-TSS (NM_001008702)	promoter-TSS (NM_001008702)	-1	NM_001008702	13132	Mm.240830	NM_023118	ENSMUSG00000022150	Dab2	5730435J12Rik|AA960054|AI957090|D15Wsu122e|D630005B22Rik|Doc-2|Doc2|p96	disabled 2, mitogen-responsive phosphoprotein	protein-coding
mm_137921.1	chr17	32492154	32492161	+	1	NA	intron (NM_177307, intron 13 of 13)	MIRb|SINE|MIR	-14305	NM_001101445	208285	Mm.311422	NM_001101445	ENSMUSG00000091586	Cyp4f17	EG208285	cytochrome P450, family 4, subfamily f, polypeptide 17	protein-coding
mm_26809.1	chr3	10197242	10197266	-	1	NA	promoter-TSS (NM_011598)	promoter-TSS (NM_011598)	29	NM_011598	21884	Mm.26654	NM_011598	ENSMUSG00000027528	Fabp9	1700007P10Rik|Perf|Perf15|Tlbp	fatty acid binding protein 9, testis	protein-coding
mm_16487.1	chr2	180967292	180967303	+	1	NA	promoter-TSS (NM_001177706)	promoter-TSS (NM_001177706)	-3	NM_001177706	228998	Mm.33765	NM_145760	ENSMUSG00000027575	Arfgap1	AI115377|Arf1gap	ADP-ribosylation factor GTPase activating protein 1	protein-coding
mm_83196.1	chr9	41157460	41157470	-	1	NA	promoter-TSS (NM_176860)	promoter-TSS (NM_176860)	29	NM_176860	72828	Mm.133615	NM_176860	ENSMUSG00000032020	Ubash3b	2810457I06Rik|BB125008|TULA-2|p70	ubiquitin associated and SH3 domain containing, B	protein-coding
mm_111269.1	chr12	85280362	85280435	-	1	NA	promoter-TSS (NM_025421)	promoter-TSS (NM_025421)	37	NM_025421	66204	Mm.311985	NM_025421	ENSMUSG00000008822	Acyp1	1110039O14Rik|AI325944	acylphosphatase 1, erythrocyte (common) type	protein-coding
mm_37451.1	chr4	123411865	123411871	-	1	NA	promoter-TSS (NM_001167918)	promoter-TSS (NM_001167918)	43	NM_001167918	442834	Mm.483803	NM_001167918		D830031N03Rik	Kiaa0754|mKIAA0754	RIKEN cDNA D830031N03 gene	protein-coding
mm_104951.1	chr11	100136050	100136087	-	1	NA	promoter-TSS (NM_008469)	promoter-TSS (NM_008469)	-119	NM_008469	16665	Mm.440010	NM_008469	ENSMUSG00000054146	Krt15	AI528832|K15|Krt1-15	keratin 15	protein-coding
mm_46910.1	chr5	114374991	114374996	-	1	NA	exon (NM_001159941, exon 2 of 7)	exon (NM_001159941, exon 2 of 7)	5512	NM_001159941	330171	Mm.238285	NM_026145	ENSMUSG00000001098	Kctd10	AW536343|C87062|mBACURD3	potassium channel tetramerisation domain containing 10	protein-coding
mm_147603.1	chr18	56853410	56853413	-	1	NA	intron (NM_177115, intron 1 of 4)	intron (NM_177115, intron 1 of 4)	72137	NM_177115	320253	Mm.312623	NM_177115	ENSMUSG00000032656	March3	6330411I15Rik|A530081L18Rik|AI843639|MARCH-III	membrane-associated ring finger (C3HC4) 3	protein-coding
mm_112393.1	chr12	119238605	119238609	-	1	NA	promoter-TSS (NM_177290)	promoter-TSS (NM_177290)	-331	NM_177290	320910	Mm.217000	NM_177290	ENSMUSG00000025321	Itgb8	4832412O06Rik	integrin beta 8	protein-coding
mm_163446.1	chr12	86990660	86990662	-	1	NA	Intergenic	Intergenic	-1985	NM_001080943	238331	Mm.185890	NM_001080943	ENSMUSG00000048483	Zdhhc22	Gm262	zinc finger, DHHC-type containing 22	protein-coding
mm_134614.1	chr16	20822677	20822680	-	1	NA	Intergenic	Intergenic	-88167	NM_009379	21832	Mm.3943	NM_009379	ENSMUSG00000022847	Thpo	Mgdf|Ml|Mpllg|Tpo	thrombopoietin	protein-coding
mm_15861.1	chr2	164823060	164823072	+	1	NA	TTS (NM_178375)	TTS (NM_178375)	380	NM_028028	71971	Mm.161149	NM_028028	ENSMUSG00000017764	Zswim1	2410003H12Rik|AI850991|BB046916	zinc finger SWIM-type containing 1	protein-coding
mm_80948.1	chr9	102834980	102834990	+	1	NA	promoter-TSS (NM_013649)	promoter-TSS (NM_013649)	65	NM_001042607	20187	Mm.335391	NM_013649	ENSMUSG00000032547	Ryk	AW536699|ERK-3|Vik	receptor-like tyrosine kinase	protein-coding
mm_95809.1	chr11	55110303	55110329	+	1	NA	3' UTR (NM_010299, exon 4 of 4)	3' UTR (NM_010299, exon 4 of 4)	12331	NM_010299	14667	Mm.287807	NM_010299	ENSMUSG00000000594	Gm2a	AA408702|AW215435|GM2-AP|SAP-3	GM2 ganglioside activator protein	protein-coding
mm_94501.1	chr11	7197781	7197795	+	1	NA	promoter-TSS (NM_008341)	promoter-TSS (NM_008341)	1	NM_008341	16006	Mm.21300	NM_008341	ENSMUSG00000020429	Igfbp1	-	insulin-like growth factor binding protein 1	protein-coding
mm_68840.1	chr7	126351597	126351611	-	1	NA	Intergenic	Intergenic	16441	NR_106025	102466797		NR_106025	ENSMUSG00000099017	Mir7058	Gm27766|mmu-mir-7058	microRNA 7058	ncRNA
mm_60976.1	chr7	48884810	48884816	+	1	NA	Intergenic	Intergenic	-3772	NM_001013368	108961	Mm.240566	NM_001013368	ENSMUSG00000046179	E2f8	4432406C08Rik|AA410048	E2F transcription factor 8	protein-coding
mm_20981.1	chr2	151974189	151974199	-	1	NA	promoter-TSS (NM_001289151)	promoter-TSS (NM_001289151)	-213	NM_028666	73847	Mm.272444	NM_028666	ENSMUSG00000027459	Fam110a	1700008J10Rik|5430432M24Rik|AI747080	family with sequence similarity 110, member A	protein-coding
mm_165595.1	chr3	40902501	40902502	-	1	NA	promoter-TSS (NR_045380)	promoter-TSS (NR_045380)	42	NR_045380	73297	Mm.422673	NM_028494	ENSMUSG00000074619	1700034I23Rik	-	FUN14 domain containing 2 pseudogene	pseudo
mm_28485.1	chr3	92457332	92457341	-	1	NA	exon (NM_011478, exon 2 of 2)	exon (NM_011478, exon 2 of 2)	1384	NM_001204427	20766	Mm.57092	NM_011478	ENSMUSG00000045539	Sprr3	SPR3	small proline-rich protein 3	protein-coding
mm_119931.1	chr14	54970168	54970183	+	1	NA	TTS (NM_080728)	TTS (NM_080728)	1388	NR_033497	791403	Mm.319176	NR_033497	ENSMUSG00000097652	Mhrt	D830015G02Rik|ENSMUSG00000053118|Myheart	myosin heavy chain associated RNA transcript	ncRNA
mm_134470.1	chr16	18533332	18533341	-	1	NA	intron (NR_104347, intron 2 of 8)	intron (NR_104347, intron 2 of 8)	34465	NR_104347	13972	Mm.236139	NM_023120	ENSMUSG00000000884	Gnb1l	ESTM55|Gm16314|Me49f07|OTTMUSG00000033458|Wdr14|Wdvcf	guanine nucleotide binding protein (G protein), beta polypeptide 1-like	protein-coding
mm_35902.1	chr4	49597786	49597830	-	1	NA	promoter-TSS (NM_025944)	promoter-TSS (NM_025944)	62	NM_025944	67063	Mm.490285	NM_025944	ENSMUSG00000039611	Tmem246	2810432L12Rik|9330170P15Rik|AI835809	transmembrane protein 246	protein-coding
mm_14455.1	chr2	131187005	131187027	+	1	NA	promoter-TSS (NM_001111075)	promoter-TSS (NM_001111075)	68	NM_001111075	12531	Mm.38444	NM_023117	ENSMUSG00000027330	Cdc25b	AI604853	cell division cycle 25B	protein-coding
mm_13832.1	chr2	119329750	119329766	+	1	NA	intron (NM_019454, intron 6 of 10)	C-rich|Low_complexity|Low_complexity	-3561	NR_030683	100043609	Mm.185068	NR_030683	ENSMUSG00000074912	Gm14207	Dll4|OTTMUSG00000015946	predicted gene 14207	ncRNA
mm_32369.1	chr4	105267453	105267462	+	1	NA	Intergenic	MTC|LTR|ERVL-MaLR	110110	NM_080555	67916	Mm.348326	NM_080555	ENSMUSG00000028517	Plpp3	1110003O22Rik|2610002D05Rik|AV025606|D4Bwg0538e|D4Bwg1535e|Lpp3|Ppab2b|Ppap2b	phospholipid phosphatase 3	protein-coding
mm_29575.1	chr3	116968970	116969004	-	1	NA	promoter-TSS (NM_023245)	promoter-TSS (NM_023245)	-35	NM_023245	114301	Mm.253736	NM_023245	ENSMUSG00000033377	Palmd	4631423C22Rik|PALML	palmdelphin	protein-coding
mm_123421.1	chr14	64417136	64417162	-	1	NA	promoter-TSS (NM_001253716)	promoter-TSS (NM_001253716)	130	NM_001347639	110265	Mm.26713	NM_026322	ENSMUSG00000054733	Msra	2310045J23Rik|6530413P12Rik|MSR-A	methionine sulfoxide reductase A	protein-coding
mm_68742.1	chr7	121064286	121064296	-	1	NA	3' UTR (NM_030691, exon 6 of 6)	3' UTR (NM_030691, exon 6 of 6)	10239	NM_030691	80719	Mm.160384	NM_030691	ENSMUSG00000035004	Igsf6	-	immunoglobulin superfamily, member 6	protein-coding
mm_129544.1	chr15	79396863	79396879	-	1	NA	intron (NM_172608, intron 1 of 8)	intron (NM_172608, intron 1 of 8)	6048	NM_001253817	223693	Mm.323358	NM_172608	ENSMUSG00000009035	Tmem184b	2610507A11|4732495E13Rik	transmembrane protein 184b	protein-coding
mm_18137.1	chr2	45033558	45033567	-	1	NA	intron (NM_001289521, intron 1 of 8)	intron (NM_001289521, intron 1 of 8)	-10385	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_49251.1	chr6	17335360	17335363	+	1	NA	intron (NM_007616, intron 2 of 2)	intron (NM_007616, intron 2 of 2)	27721	NM_001243064	12389	Mm.28278	NM_007616	ENSMUSG00000007655	Cav1	Cav|Cav-1	caveolin 1, caveolae protein	protein-coding
mm_119001.1	chr14	29018078	29018082	+	1	NA	promoter-TSS (NM_176920)	promoter-TSS (NM_176920)	-128	NM_176920	319476	Mm.95780	NM_176920	ENSMUSG00000045776	Lrtm1	A930016D02Rik	leucine-rich repeats and transmembrane domains 1	protein-coding
mm_147104.1	chr18	35662082	35662092	-	1	NA	promoter-TSS (NM_027733)	promoter-TSS (NM_027733)	99	NM_029485	71242	Mm.151498	NM_027733	ENSMUSG00000024352	Spata24	2700012K08Rik|4930583E11Rik|5133400G04Rik|AU016220|TIPT|TIPT2	spermatogenesis associated 24	protein-coding
mm_80182.1	chr9	72294313	72294315	+	1	NA	intron (NM_001311105, intron 1 of 20)	ID_B1|SINE|B4	19426	NM_001311105	235469	Mm.242791	NM_146224	ENSMUSG00000038535	Zfp280d	A930005F02Rik|BC027163|Suhw4|ZNF634|Znf280d	zinc finger protein 280D	protein-coding
mm_64640.1	chr7	4008009	4008026	-	1	NA	3' UTR (NM_178611, exon 7 of 7)	3' UTR (NM_178611, exon 7 of 7)	55187	NM_001302677	52855	Mm.290880	NM_178611	ENSMUSG00000055541	Lair1	5133400O11Rik|BB115266|D7Bwg0421e|Lair-1	leukocyte-associated Ig-like receptor 1	protein-coding
mm_91501.1	chr10	37136107	37136120	-	1	NA	exon (NM_008538, exon 2 of 2)	exon (NM_008538, exon 2 of 2)	2813	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_26906.1	chr3	19311390	19311403	-	1	NA	promoter-TSS (NM_001122759)	promoter-TSS (NM_001122759)	-74	NM_001122759	18583	Mm.355614	NM_008802	ENSMUSG00000069094	Pde7a	AU015378|AW047537	phosphodiesterase 7A	protein-coding
mm_40528.1	chr5	57919902	57919912	+	1	NA	intron (NM_001122758, intron 2 of 2)	B4A|SINE|B4	201826	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_78745.1	chr9	42122704	42122713	+	1	NA	intron (NM_011436, intron 1 of 47)	intron (NM_011436, intron 1 of 47)	1581	NM_011436	20660	Mm.121920	NM_011436	ENSMUSG00000049313	Sorl1	2900010L19Rik|AI596264|AW261561|LR11|SorLA|gp250|mSorLA	sortilin-related receptor, LDLR class A repeats-containing	protein-coding
mm_42968.1	chr5	123138612	123138635	+	1	NA	Intergenic	Intergenic	-3570	NM_001040398	208043	Mm.250391	NM_177581	ENSMUSG00000038384	Setd1b	AA516740|BC035291|KMT2G|mKIAA1076	SET domain containing 1B	protein-coding
mm_115441.1	chr13	117666485	117666514	+	1	NA	intron (NM_010408, intron 2 of 7)	L1MEc|LINE|L1	53512	NR_045508	71100	Mm.414841	NR_045508	ENSMUSG00000079048	4933413L06Rik	-	RIKEN cDNA 4933413L06 gene	ncRNA
mm_67954.1	chr7	100499450	100499476	-	1	NA	3' UTR (NM_011671, exon 8 of 8)	3' UTR (NM_011671, exon 8 of 8)	6105	NM_011671	22228	Mm.171378	NM_011671	ENSMUSG00000033685	Ucp2	Slc25a8	uncoupling protein 2 (mitochondrial, proton carrier)	protein-coding
mm_1301.1	chr1	64533127	64533145	+	1	NA	intron (NM_001037726, intron 1 of 6)	CpG	332	NM_001037726	12912	Mm.422634	NM_009952	ENSMUSG00000025958	Creb1	2310001E10Rik|3526402H21Rik|AV083133|Creb|Creb-1	cAMP responsive element binding protein 1	protein-coding
mm_163148.1	chr11	83063493	83063526	+	1	NA	Intergenic	RLTR49|LTR|ERVK	-1603	NM_011408	20556	Mm.278689	NM_011408	ENSMUSG00000072620	Slfn2	Shlf2	schlafen 2	protein-coding
mm_22059.1	chr2	168601569	168601615	-	1	NA	promoter-TSS (NM_001291173)	promoter-TSS (NM_001291173)	65	NM_001291171	18019	Mm.116802	NM_010899	ENSMUSG00000027544	Nfatc2	AI607462|NF-ATc2|NF-ATp|NFAT1|NFAT1-D|Nfatp	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 2	protein-coding
mm_172791.1	chr9	109970408	109970425	+	1	NA	intron (NM_001205330, intron 1 of 18)	intron (NM_001205330, intron 1 of 18)	38642	NM_008633	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_16854.1	chr2	11636209	11636224	-	1	NA	Intergenic	Intergenic	-6576	NM_008367	16184	Mm.915	NM_008367	ENSMUSG00000026770	Il2ra	CD25|Il2r|Ly-43	interleukin 2 receptor, alpha chain	protein-coding
mm_44367.1	chr5	17811206	17811237	-	1	NA	exon (NM_001159558, exon 9 of 16)	exon (NM_001159558, exon 9 of 16)	24675	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_149285.1	chr19	10634224	10634245	+	1	NA	promoter-TSS (NM_027913)	promoter-TSS (NM_027913)	1	NM_027913	71768	Mm.169261	NM_027913	ENSMUSG00000043789	Vwce	1300015B04Rik	von Willebrand factor C and EGF domains	protein-coding
mm_96378.1	chr11	67242810	67242818	+	1	NA	exon (NM_010855, exon 8 of 40)	exon (NM_010855, exon 8 of 40)	5002	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_69633.1	chr7	137410972	137410983	-	1	NA	promoter-TSS (NM_029886)	promoter-TSS (NM_029886)	-221	NM_029886	77252	Mm.29184	NM_029886	ENSMUSG00000040139	9430038I01Rik	-	RIKEN cDNA 9430038I01 gene	protein-coding
mm_81108.1	chr9	106452179	106452194	+	1	NA	3' UTR (NM_029631, exon 4 of 4)	3' UTR (NM_029631, exon 4 of 4)	-1652	NM_021567	59092	Mm.286394	NM_021567	ENSMUSG00000023495	Pcbp4	1200003L19Rik|AlphaCP-4	poly(rC) binding protein 4	protein-coding
mm_59394.1	chr7	26764531	26764539	+	1	NA	intron (NM_007814, intron 6 of 8)	intron (NM_007814, intron 6 of 8)	7393	NM_007814	13090	Mm.14098	NM_007814	ENSMUSG00000066704	Cyp2b19	CYPIIB19	cytochrome P450, family 2, subfamily b, polypeptide 19	protein-coding
mm_48003.1	chr5	136161324	136161360	-	1	NA	intron (NM_178751, intron 2 of 2)	RSINE1|SINE|B4	9314	NM_178751	269717	Mm.308396	NM_178751	ENSMUSG00000039747	Orai2	A730041O15Rik|Tmem142b	ORAI calcium release-activated calcium modulator 2	protein-coding
mm_52698.1	chr6	119215350	119215360	+	1	NA	exon (NM_001033379, exon 7 of 9)	exon (NM_001033379, exon 7 of 9)	-18946	NM_001255999	12288	Mm.41628	NM_009781	ENSMUSG00000051331	Cacna1c	Cav1.2|Cchl1a1|D930026N18Rik|MBC|MELC-CC	calcium channel, voltage-dependent, L type, alpha 1C subunit	protein-coding
mm_24962.1	chr3	96697101	96697165	+	1	NA	promoter-TSS (NM_001165949)	promoter-TSS (NM_001165949)	57	NM_018812	229615	Mm.1635	NM_018812	ENSMUSG00000028101	Pias3	Pias3l	protein inhibitor of activated STAT 3	protein-coding
mm_120334.1	chr14	63436491	63436525	+	1	NA	5' UTR (NM_177628, exon 1 of 4)	5' UTR (NM_177628, exon 1 of 4)	114	NM_177628	219148	Mm.37882	NM_177628	ENSMUSG00000035095	Fam167a	A030013D21	family with sequence similarity 167, member A	protein-coding
mm_160956.1	chr11	98192932	98192932	-	1	NA	promoter-TSS (NM_013634)	promoter-TSS (NM_013634)	-26	NM_013634	19014	Mm.12926	NM_013634	ENSMUSG00000018160	Med1	AI480703|CRSP210|DRIP205|PBP|Pparbp|TRAP220|l11Jus15	mediator complex subunit 1	protein-coding
mm_114493.1	chr13	69810160	69810172	+	1	NA	intron (NM_138596, intron 1 of 3)	CpG	284	NM_138596	28077	Mm.52583	NM_138596	ENSMUSG00000021598	Med10	AA959813|AI385605|C78613|D13Wsu50e	mediator complex subunit 10	protein-coding
mm_47632.1	chr5	125300416	125300427	-	1	NA	exon (NM_001205082, exon 4 of 12)	exon (NM_001205082, exon 4 of 12)	40673	NM_016741	20778	Mm.282242	NM_016741	ENSMUSG00000037936	Scarb1	AI120173|CD36|Cd36l1|Chohd1|Cla-1|Cla1|D5Ertd460e|Hdlq1|Hlb398|SR-B1|SR-BI|SRBI|Srb1|mSR-BI	scavenger receptor class B, member 1	protein-coding
mm_156646.1	chrX	157699185	157699205	+	1	NA	non-coding (NR_103722, exon 1 of 6)	non-coding (NR_103722, exon 1 of 6)	222	NR_103722	66106	Mm.140340	NM_025357	ENSMUSG00000041476	Smpx	1010001C09Rik|Csl	small muscle protein, X-linked	protein-coding
mm_7314.1	chr1	98095539	98095553	-	1	NA	promoter-TSS (NM_013626)	promoter-TSS (NM_013626)	86	NM_013626	18484	Mm.5121	NM_013626	ENSMUSG00000026335	Pam	PHM	peptidylglycine alpha-amidating monooxygenase	protein-coding
mm_131368.1	chr16	13819307	13819369	+	1	NA	promoter-TSS (NM_001346106)	promoter-TSS (NM_001346106)	87	NM_001346111	18203	Mm.380410	NM_010946	ENSMUSG00000022681	Ntan1	PNAA|PNAD	N-terminal Asn amidase	protein-coding
mm_20489.1	chr2	130048589	130048599	-	1	NA	3' UTR (NM_009374, exon 13 of 13)	3' UTR (NM_009374, exon 13 of 13)	-32186	NR_105757	102466628		NR_105757	ENSMUSG00000098347	Mir6339	Gm27848|mmu-mir-6339	microRNA 6339	ncRNA
mm_173090.1	chrX	150530174	150530176	+	1	NA	Intergenic	L1Md_T|LINE|L1	-17242	NM_009653	11656	Mm.302724	NM_009653	ENSMUSG00000025270	Alas2	ALAS|ALAS-E|ALASE|Alas-2	aminolevulinic acid synthase 2, erythroid	protein-coding
mm_21477.1	chr2	162644610	162644629	-	1	NA	intron (NM_001291151, intron 1 of 30)	Tigger15a|DNA|TcMar-Tigger	16528	NM_001291151	19281	Mm.235807	NM_021464	ENSMUSG00000053141	Ptprt	R-PTP-T|RPTP-rfo|RPTP-rho|RPTPmam4|RPTPrho|mKIAA0283|mRPTPrho	protein tyrosine phosphatase, receptor type, T	protein-coding
mm_15057.1	chr2	152911764	152911769	+	1	NA	intron (NM_001081044, intron 1 of 11)	intron (NM_001081044, intron 1 of 11)	414	NM_001081044	228785	Mm.250604	NM_001081044	ENSMUSG00000027470	Mylk2	9830004H17Rik|BB138278	myosin, light polypeptide kinase 2, skeletal muscle	protein-coding
mm_20791.1	chr2	144011173	144011197	-	1	NA	promoter-TSS (NM_133626)	promoter-TSS (NM_133626)	78	NM_133626	81910	Mm.13705	NM_024281	ENSMUSG00000027422	Rrbp1	1700087N07Rik|5730465C04Rik|ES/130|mKIAA1398|mRRp0|mRRp1.8|mRRp10|mRRp15a|mRRp15b|mRRp16.8|mRRp2|mRRp41|mRRp47|mRRp5.4|p180	ribosome binding protein 1	protein-coding
mm_160686.1	chr10	21160892	21160892	-	1	NA	promoter-TSS (NM_001198914)	promoter-TSS (NM_001198914)	92	NM_001198914	17863	Mm.52109	NM_010848	ENSMUSG00000019982	Myb	AI550390|M16449|c-myb	myeloblastosis oncogene	protein-coding
mm_1746.1	chr1	75495430	75495436	+	1	NA	TTS (NM_001310679)	TTS (NM_001310679)	11019	NM_178884	98733	Mm.236454	NM_178884	ENSMUSG00000026211	Obsl1	AW822216	obscurin-like 1	protein-coding
mm_15059.1	chr2	152962458	152962469	+	1	NA	promoter-TSS (NM_029064)	promoter-TSS (NM_029064)	-22	NM_029064	74711	Mm.44746	NM_029064	ENSMUSG00000074673	Ttll9	1700016F23Rik|4930509O20Rik|AW046572	tubulin tyrosine ligase-like family, member 9	protein-coding
mm_31748.1	chr4	63344603	63344609	+	1	NA	promoter-TSS (NM_008768)	promoter-TSS (NM_008768)	50	NM_008768	18405	Mm.4777	NM_008768	ENSMUSG00000039196	Orm1	Agp-1|Agp-2|Orm-1	orosomucoid 1	protein-coding
mm_107755.1	chr12	59070424	59070486	+	1	NA	exon (NM_008891, exon 8 of 9)	exon (NM_008891, exon 8 of 9)	3536	NM_008891	18949	Mm.22347	NM_008891	ENSMUSG00000020994	Pnn	AU045199|D12Ertd512e	pinin	protein-coding
mm_102982.1	chr11	69681871	69681896	-	1	NA	promoter-TSS (NM_030702)	promoter-TSS (NM_030702)	87	NM_030702	80886	Mm.284592	NM_030702	ENSMUSG00000005204	Senp3	AA408656|Smt3ip|Smt3ip1	SUMO/sentrin specific peptidase 3	protein-coding
mm_76372.1	chr8	84800394	84800404	-	1	NA	promoter-TSS (NM_010906)	promoter-TSS (NM_010906)	-61	NM_001081982	18032	Mm.9394	NM_010906	ENSMUSG00000001911	Nfix	CTF|NF-I/X|NF1-X|NFI-X	nuclear factor I/X	protein-coding
mm_165116.1	chr19	60580871	60580881	-	1	NA	5' UTR (NM_001172096, exon 1 of 8)	5' UTR (NM_001172096, exon 1 of 8)	147	NM_001172097	78832	Mm.259026	NM_030197	ENSMUSG00000033417	Cacul1	2700078E11Rik|2810417M16Rik|9830127L17Rik|AI450346|D130033C15Rik	CDK2 associated, cullin domain 1	protein-coding
mm_105649.1	chr11	107132645	107132661	-	1	NA	promoter-TSS (NM_176850)	promoter-TSS (NM_176850)	-731	NM_176850	207165	Mm.343986	NM_176850	ENSMUSG00000040481	Bptf	9430093H17Rik|Falz	bromodomain PHD finger transcription factor	protein-coding
mm_170554.1	chr19	41525290	41525291	+	1	NA	promoter-TSS (NM_001326287)	promoter-TSS (NM_001326287)	38	NM_001326287	627352	Mm.395111	NM_001326287		Morf4l1b	EG627352|Gm6747	mortality factor 4 like 1B	protein-coding
mm_70456.1	chr8	11810326	11810350	+	1	NA	exon (NM_001113518, exon 11 of 21)	exon (NM_001113518, exon 11 of 21)	-30183	NM_029326	75528	Mm.440342	NM_029326	ENSMUSG00000031512	Tex29	1700018L24Rik	testis expressed 29	protein-coding
mm_124458.1	chr14	120278976	120278986	-	1	NA	intron (NM_175341, intron 1 of 8)	intron (NM_175341, intron 1 of 8)	3312	NM_175341	105559	Mm.238266	NM_175341	ENSMUSG00000022139	Mbnl2	1110002M11Rik|AI047808|AI837313|AI849185|AL118326|MBLL|R75232|mKIAA4072	muscleblind-like 2	protein-coding
mm_3092.1	chr1	134415397	134415408	+	1	NA	promoter-TSS (NM_001306069)	promoter-TSS (NM_001306069)	24	NM_028320	72674	Mm.259976	NM_028320	ENSMUSG00000026457	Adipor1	2810031L11Rik|ACDCR1|CGI-45|Paqr1	adiponectin receptor 1	protein-coding
mm_91019.1	chr10	17724308	17724352	-	1	NA	exon (NM_010828, exon 2 of 2)	exon (NM_010828, exon 2 of 2)	1102	NM_010828	17684	Mm.272321	NM_010828	ENSMUSG00000039910	Cited2	AI835299|ER154-like|Mrg1|Msg2|p35srj	Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 2	protein-coding
mm_118747.1	chr14	22330678	22330700	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	212109	NR_046307	74896	Mm.444661	NR_046307		4930405A10Rik	4930456G20Rik	RIKEN cDNA 4930405A10 gene	ncRNA
mm_147271.1	chr18	38929379	38929396	-	1	NA	intron (NM_001033789, intron 3 of 4)	intron (NM_001033789, intron 3 of 4)	-10688	NM_010197	14164	Mm.241282	NM_010197	ENSMUSG00000036585	Fgf1	Dffrx|Fam|Fgf-1|Fgfa	fibroblast growth factor 1	protein-coding
mm_141714.1	chr17	34028004	34028006	-	1	NA	promoter-TSS (NM_013543)	promoter-TSS (NM_013543)	50	NM_013543	14979	Mm.275452	NM_013543	ENSMUSG00000073422	H2-Ke6	D17H6S112E|H-2Ke6|Hsd17b8|Ke-6|Ke6|Ring2	H2-K region expressed gene 6	protein-coding
mm_35435.1	chr4	36951690	36951759	-	1	NA	promoter-TSS (NM_001165999)	promoter-TSS (NM_001165999)	20	NM_001165999	242384	Mm.132507	NM_175516	ENSMUSG00000045083	Lingo2	B230217C06Rik|Lern3|Lrrn6c	leucine rich repeat and Ig domain containing 2	protein-coding
mm_15529.1	chr2	158382893	158382901	+	1	NA	3' UTR (NM_175692, exon 5 of 5)	3' UTR (NM_175692, exon 5 of 5)	7259	NM_175692	319317	Mm.294494	NM_175692	ENSMUSG00000044349	Snhg11	A930034L06Rik|AI854265|AL022637|AW319638|E130013N09Rik	small nucleolar RNA host gene 11	protein-coding
mm_78417.1	chr9	31030551	31030561	+	1	NA	promoter-TSS (NM_001115130)	promoter-TSS (NM_001115130)	-88	NM_001115130	235132	Mm.239355	NM_172765	ENSMUSG00000047412	Zbtb44	6030404E16Rik|Btbd15|E230011F09	zinc finger and BTB domain containing 44	protein-coding
mm_56656.1	chr6	113434778	113434788	-	1	NA	intron (NM_178373, intron 1 of 5)	intron (NM_178373, intron 1 of 5)	972	NM_178373	14311	Mm.10026	NM_178373	ENSMUSG00000030278	Cidec	CIDE-3|Fsp27	cell death-inducing DFFA-like effector c	protein-coding
mm_106859.1	chr12	8009268	8009278	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	31596	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_75801.1	chr8	70139101	70139132	-	1	NA	promoter-TSS (NM_001145552)	promoter-TSS (NM_001145552)	81	NM_011266	19727	Mm.161167	NM_011266	ENSMUSG00000036120	Rfxank	Tvl1	regulatory factor X-associated ankyrin-containing protein	protein-coding
mm_95160.1	chr11	36338615	36338636	+	1	NA	intron (NM_011856, intron 3 of 28)	intron (NM_011856, intron 3 of 28)	-358536	NM_170779	211652	Mm.31267	NM_170779	ENSMUSG00000018849	Wwc1	AA408228|AU017197|BC037006|Kibra|mKIAA0869	WW, C2 and coiled-coil domain containing 1	protein-coding
mm_143461.1	chr17	70990929	70990964	-	1	NA	promoter-TSS (NM_023402)	promoter-TSS (NM_023402)	-430	NM_023402	67938	Mm.261329	NM_023402	ENSMUSG00000034868	Myl12b	1500001M02Rik|C77744|Mylc2b|RLC-B	myosin, light chain 12B, regulatory	protein-coding
mm_69345.1	chr7	130200368	130200372	-	1	NA	intron (NM_201601, intron 5 of 15)	intron (NM_201601, intron 5 of 15)	66438	NM_010207	14183	Mm.16340	NM_010207	ENSMUSG00000030849	Fgfr2	AU043015|AW556123|Bek|Fgfr-2|Fgfr-7|Fgfr7|KGFR|KGFRTr|svs	fibroblast growth factor receptor 2	protein-coding
mm_149479.1	chr19	11755784	11755811	+	1	NA	intron (NM_008118, intron 5 of 8)	intron (NM_008118, intron 5 of 8)	8238	NM_008118	14603	Mm.456	NM_008118	ENSMUSG00000024682	Gif	AV073125	gastric intrinsic factor	protein-coding
mm_165818.1	chr3	146651328	146651332	-	1	NA	promoter-TSS (NM_029144)	promoter-TSS (NM_029144)	-13	NM_029144	75015	Mm.250432	NM_029144	ENSMUSG00000048652	4930503B20Rik	1700013A07Rik|1700095G21Rik|4930483N21Rik|Gm1652|Samd13	RIKEN cDNA 4930503B20 gene	protein-coding
mm_64503.1	chr7	143476133	143476160	+	1	NA	5' UTR (NM_008767, exon 2 of 11)	5' UTR (NM_008767, exon 2 of 11)	1030	NM_001042760	18400	Mm.271740	NM_008767	ENSMUSG00000000154	Slc22a18	AW260131|BWR1A|BWSCR1A|HET|ITM|Impt1|Orctl2|Slc22a1l|TSSC5|p45-BWR1A	solute carrier family 22 (organic cation transporter), member 18	protein-coding
mm_18180.1	chr2	45110378	45110388	-	1	NA	promoter-TSS (NM_001289521)	promoter-TSS (NM_001289521)	-106	NM_001289521	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_19478.1	chr2	92978130	92978132	-	1	NA	intron (NM_001177536, intron 6 of 6)	B4|SINE|B4	-51217	NR_110333	433456	Mm.235231	NM_001002794	ENSMUSG00000075027	4631405J19Rik	-	RIKEN cDNA 4631405J19 gene	ncRNA
mm_16163.1	chr2	172461365	172461394	+	1	NA	intron (NM_025542, intron 5 of 8)	MTD|LTR|ERVL-MaLR	-2783	NM_001039560	654821	Mm.389337	NM_001039560	ENSMUSG00000074569	Gcnt7	A330041C17Rik|gnt	glucosaminyl (N-acetyl) transferase family member 7	protein-coding
mm_75134.1	chr8	35053434	35053444	-	1	NA	Intergenic	Intergenic	-87749	NM_175091	21951	Mm.88364	NM_175091	ENSMUSG00000031529	Tnks	4930554K12Rik|AI662855|ARTD5|C86528|D130072O21Rik|TANK1|mTNKS1	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase	protein-coding
mm_47893.1	chr5	134722060	134722063	-	1	NA	exon (NM_007925, exon 15 of 37)	exon (NM_007925, exon 15 of 37)	25262	NM_007925	13717	Mm.275320	NM_007925	ENSMUSG00000029675	Eln	AI385707|AI480567|E030024M20Rik	elastin	protein-coding
mm_89272.1	chr10	87860478	87860492	+	1	NA	promoter-TSS (NM_001111276)	promoter-TSS (NM_001111276)	-626	NM_001111274	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_74914.1	chr8	25306222	25306239	-	1	NA	promoter-TSS (NR_040352)	promoter-TSS (NR_040352)	40	NR_040352	74489	Mm.256468	NR_040352	ENSMUSG00000110140	5430421F17Rik	-	RIKEN cDNA 5430421F17 gene	ncRNA
mm_101921.1	chr11	50200831	50200842	-	1	NA	TTS (NM_026543)	TTS (NM_026543)	9984	NM_001290769	18412	Mm.40828	NM_011018	ENSMUSG00000015837	Sqstm1	A170|OSF-6|Osi|STAP|STONE14|p62	sequestosome 1	protein-coding
mm_44529.1	chr5	24445167	24445220	-	1	NA	promoter-TSS (NM_023229)	promoter-TSS (NM_023229)	42	NM_023229	66587	Mm.28123	NM_023229	ENSMUSG00000028959	Fastk	0610011K02Rik|610011K02Rik	Fas-activated serine/threonine kinase	protein-coding
mm_5231.1	chr1	14310110	14310124	-	1	NA	promoter-TSS (NM_001252192)	promoter-TSS (NM_001252192)	82	NM_001310459	14048	Mm.250185	NM_010164	ENSMUSG00000025932	Eya1	bor	EYA transcriptional coactivator and phosphatase 1	protein-coding
mm_167625.1	chr9	60597855	60597857	+	1	NA	intron (NM_001311095, intron 14 of 15)	intron (NM_001311095, intron 14 of 15)	-51974	NR_040463	100504561	Mm.410770	NR_040463	ENSMUSG00000111761	9230112J17Rik	-	RIKEN cDNA 9230112J17 gene	ncRNA
mm_80990.1	chr9	103331177	103331180	+	1	NA	intron (NM_176979, intron 14 of 27)	intron (NM_176979, intron 14 of 27)	25851	NM_176979	235559	Mm.259893	NM_176979	ENSMUSG00000032555	Topbp1	1110031N14Rik|2810429C13Rik|AI256758|D430026L04Rik|mKIAA0259	topoisomerase (DNA) II binding protein 1	protein-coding
mm_60256.1	chr7	43794144	43794155	+	1	NA	intron (NM_028660, intron 2 of 4)	intron (NM_028660, intron 2 of 4)	2258	NM_028660	101533	Mm.19942	NM_028660	ENSMUSG00000047884	Klk9	1200016C12Rik|AI324041	kallikrein related-peptidase 9	protein-coding
mm_46122.1	chr5	92443618	92443632	-	1	NA	3' UTR (NM_007644, exon 12 of 12)	3' UTR (NM_007644, exon 12 of 12)	-8426	NM_183392	269113	Mm.275289	NM_183392	ENSMUSG00000034826	Nup54	3110079L04Rik|54kDa	nucleoporin 54	protein-coding
mm_11654.1	chr2	34963695	34963709	+	1	NA	Intergenic	Intergenic	-1930	NM_001326601	22029	Mm.239514	NM_009421	ENSMUSG00000026875	Traf1	4732496E14Rik	TNF receptor-associated factor 1	protein-coding
mm_3685.1	chr1	153749415	153749442	+	1	NA	promoter-TSS (NM_011882)	promoter-TSS (NM_011882)	2	NM_011882	24014	Mm.259254	NM_011882	ENSMUSG00000066800	Rnasel	E230029I04Rik	ribonuclease L (2', 5'-oligoisoadenylate synthetase-dependent)	protein-coding
mm_4003.1	chr1	164796697	164796721	+	1	NA	promoter-TSS (NM_019759)	promoter-TSS (NM_019759)	-23	NM_019759	56429	Mm.28935	NM_019759	ENSMUSG00000026574	Dpt	1810032B19Rik|5033416F05Rik|EQ-1|Eq1	dermatopontin	protein-coding
mm_106075.1	chr11	116173277	116173351	-	1	NA	3' UTR (NM_015729, exon 14 of 14)	3' UTR (NM_015729, exon 14 of 14)	-5136	NM_172571	217335	Mm.35241	NM_172571	ENSMUSG00000020776	Fbf1	1110033G01Rik|5930413D20|mKIAA1863	Fas (TNFRSF6) binding factor 1	protein-coding
mm_79019.1	chr9	45852741	45852756	+	1	NA	intron (NM_011792, intron 1 of 8)	intron (NM_011792, intron 1 of 8)	14203	NM_011792	23821	Mm.24044	NM_011792	ENSMUSG00000032086	Bace1	ASP2|Bace|C76936	beta-site APP cleaving enzyme 1	protein-coding
mm_127516.1	chr15	101854754	101854759	+	1	NA	Intergenic	Intergenic	-3970	NM_008473	16678	Mm.183137	NM_008473	ENSMUSG00000046834	Krt1	Krt-2.1|Krt2-1|Krt86	keratin 1	protein-coding
mm_143027.1	chr17	56584595	56584605	-	1	NA	promoter-TSS (NM_001163300)	promoter-TSS (NM_001163300)	-17	NM_001029979	224902	Mm.214973	NM_001029979	ENSMUSG00000042625	Safb2	AA389433|AI255170|mKIAA0138	scaffold attachment factor B2	protein-coding
mm_51333.1	chr6	72367087	72367094	+	1	NA	promoter-TSS (NM_001331167)	promoter-TSS (NM_001331167)	-118	NM_001331167	66510	Mm.170023	NM_025607	ENSMUSG00000055850	Rnf181	1700047F16Rik|2500002L14Rik|6230415N01Rik|C77350	ring finger protein 181	protein-coding
mm_89703.1	chr10	97647120	97647130	+	1	NA	intron (NM_007884, intron 1 of 7)	intron (NM_007884, intron 1 of 7)	3057	NM_007884	13516	Mm.148886	NM_007884	ENSMUSG00000019936	Epyc	Dspg3|PG-Lb|SLRR3B	epiphycan	protein-coding
mm_111506.1	chr12	99563563	99563651	-	1	NA	promoter-TSS (NR_136760)	promoter-TSS (NR_136760)	-234	NR_136760	102639404	Mm.396324	NR_136760	ENSMUSG00000097917	Gm26839	-	predicted gene, 26839	ncRNA
mm_9334.1	chr1	172004139	172004149	-	1	NA	3' UTR (NM_033509, exon 8 of 8)	3' UTR (NM_033509, exon 8 of 8)	23151	NM_033509	93840	Mm.36148	NM_033509	ENSMUSG00000026556	Vangl2	C530001F03Rik|Lootl|Lp|Lpp1|Ltap|Vang1l2|loop-tail|ska17|ska<m17Jus>|stbm|strabismus	vang-like 2 (van gogh, Drosophila)	protein-coding
mm_13261.1	chr2	98666281	98666298	+	1	NA	Intergenic	SYNREP_MM|Satellite|Satellite	1198632	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_34116.1	chr4	139205201	139205208	+	1	NA	intron (NM_001271405, intron 1 of 8)	ORR1D2|LTR|ERVL-MaLR	11093	NM_001271405	12345	Mm.2945	NM_009798	ENSMUSG00000028745	Capzb	1700120C01Rik|AI325129|CPB1|CPB2|CPbeat2|CPbeta1|CPbeta2|Cappb1	capping protein (actin filament) muscle Z-line, beta	protein-coding
mm_79867.1	chr9	65077978	65077988	+	1	NA	exon (NM_028906, exon 19 of 21)	exon (NM_028906, exon 19 of 21)	-23503	NM_001290315	56741	Mm.209041	NM_020043	ENSMUSG00000032816	Igdcc4	DDM36|Nope	immunoglobulin superfamily, DCC subclass, member 4	protein-coding
mm_154113.1	chr19	57134992	57135006	-	1	NA	intron (NM_001290813, intron 4 of 20)	intron (NM_001290813, intron 4 of 20)	-15975	NM_001103178	226251	Mm.217161	NM_178688	ENSMUSG00000025085	Ablim1	2210411C18Rik|2610209L21Rik|4833406P10Rik|9330196J19Rik|AV079770|AW060987|AW215784|Limab1|mKIAA0059	actin-binding LIM protein 1	protein-coding
mm_143403.1	chr17	70755442	70755474	-	1	NA	intron (NM_001347411, intron 9 of 14)	intron (NM_001347411, intron 9 of 14)	91319	NM_001164077	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_16315.1	chr2	174304322	174304327	+	1	NA	intron (NM_001310085, intron 2 of 12)	intron (NM_001310085, intron 2 of 12)	6465	NM_001310085	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_110562.1	chr12	55821022	55821028	-	1	NA	5' UTR (NM_019994, exon 1 of 41)	5' UTR (NM_019994, exon 1 of 41)	491	NM_019994	56784	Mm.292180	NM_019994	ENSMUSG00000021027	Ralgapa1	2310003F20Rik|4930400K19Rik|AI563624|GRIPE|Garnl1|Tulip1|mKIAA0884	Ral GTPase activating protein, alpha subunit 1	protein-coding
mm_83320.1	chr9	44148244	44148278	-	1	NA	Intergenic	Intergenic	13603	NM_023061	84004	Mm.275003	NM_023061	ENSMUSG00000032135	Mcam	1-gicerin|AV025631|CD146|CD149|Muc18|s-endo|s-gicerin	melanoma cell adhesion molecule	protein-coding
mm_87128.1	chr10	33905016	33905047	+	1	NA	promoter-TSS (NM_001162957)	promoter-TSS (NM_001162957)	-80	NM_001162957	212892	Mm.131949	NM_001162957	ENSMUSG00000039552	Rsph4a	A230081C05|Rshl3	radial spoke head 4 homolog A (Chlamydomonas)	protein-coding
mm_61302.1	chr7	67951770	67951772	+	1	NA	promoter-TSS (NM_010513)	promoter-TSS (NM_010513)	-486	NM_010513	16001	Mm.275742	NM_010513	ENSMUSG00000005533	Igf1r	A330103N21Rik|CD221|D930020L01|IGF-1R|hyft	insulin-like growth factor I receptor	protein-coding
mm_134141.1	chr16	10772185	10772205	-	1	NA	Intergenic	Intergenic	13341	NM_009896	12703	Mm.130	NM_009896	ENSMUSG00000038037	Socs1	Cish1|Cish7|JAB|SOCS-1|SSI-1	suppressor of cytokine signaling 1	protein-coding
mm_128833.1	chr15	68258835	68258880	-	1	NA	promoter-TSS (NM_198644)	promoter-TSS (NM_198644)	-1	NM_198644	380993	Mm.309526	NM_198644	ENSMUSG00000022335	Zfat	Gm922|Zfat1|Zfp406	zinc finger and AT hook domain containing	protein-coding
mm_77474.1	chr8	122432925	122432946	-	1	NA	promoter-TSS (NM_007806)	promoter-TSS (NM_007806)	5	NM_001301284	13057	Mm.271671	NM_007806	ENSMUSG00000006519	Cyba	b558|nmf333|p22-phox|p22phox	cytochrome b-245, alpha polypeptide	protein-coding
mm_44498.1	chr5	23712662	23712691	-	1	NA	promoter-TSS (NR_038090)	promoter-TSS (NR_038090)	-9	NR_015554	433855	Mm.205125	NR_015554	ENSMUSG00000105987	AI506816	-	expressed sequence AI506816	ncRNA
mm_122536.1	chr14	47395782	47395788	-	1	NA	exon (NM_144553, exon 14 of 19)	exon (NM_144553, exon 14 of 19)	21925	NM_001145953	16854	Mm.248615	NM_010705	ENSMUSG00000050335	Lgals3	GBP|L-34|Mac-2|gal3	lectin, galactose binding, soluble 3	protein-coding
mm_11813.1	chr2	43976624	43976627	+	1	NA	intron (NM_001301832, intron 7 of 14)	intron (NM_001301832, intron 7 of 14)	88699	NR_040622	320872	Mm.445023	NR_040622	ENSMUSG00000085089	Arhgap15os	A430092G05Rik	Rho GTPase activating protein 15, opposite strand	ncRNA
mm_163540.1	chr13	14487857	14487858	+	1	NA	intron (NM_001081348, intron 1 of 28)	intron (NM_001081348, intron 1 of 28)	35369	NM_001081348	94253	Mm.125298	NM_153130	ENSMUSG00000021301	Hecw1	9330116H24Rik|AV273951|E130207I19Rik|Nedl1	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	protein-coding
mm_153363.1	chr19	40231196	40231211	-	1	NA	intron (NM_016861, intron 4 of 6)	intron (NM_016861, intron 4 of 6)	40413	NM_016861	54132	Mm.5567	NM_016861	ENSMUSG00000055044	Pdlim1	CLP36|Clim1|mClim1	PDZ and LIM domain 1 (elfin)	protein-coding
mm_147997.1	chr18	67677740	67677756	-	1	NA	exon (NM_001127177, exon 7 of 9)	exon (NM_001127177, exon 7 of 9)	36149	NM_134138	107047	Mm.150701	NM_134138	ENSMUSG00000024537	Psmg2	1700017I17Rik|AW545363|Clast3|Tnfsf5ip1	proteasome (prosome, macropain) assembly chaperone 2	protein-coding
mm_116248.1	chr13	33935970	33935986	-	1	NA	promoter-TSS (NR_040707)	promoter-TSS (NR_040707)	-54	NR_040707	68808	Mm.443347	NR_040707	ENSMUSG00000085457	1110046J04Rik	-	RIKEN cDNA 1110046J04 gene	ncRNA
mm_122988.1	chr14	54985148	54985158	-	1	NA	exon (NM_080728, exon 22 of 41)	exon (NM_080728, exon 22 of 41)	-9377	NR_030607	100124433		NR_030607	ENSMUSG00000077928	Mir208b	Mirn208b|mir-208b	microRNA 208b	ncRNA
mm_26228.1	chr3	139075498	139075507	+	1	NA	promoter-TSS (NM_001286759)	promoter-TSS (NM_001286759)	-301	NM_001040690	229877	Mm.28893	NM_145544	ENSMUSG00000028149	Rap1gds1	BC011279|GDS1	RAP1, GTP-GDP dissociation stimulator 1	protein-coding
mm_145605.1	chr18	61096642	61096664	+	1	NA	Intergenic	Intergenic	-8919	NM_001037859	12978	Mm.22574	NM_007779	ENSMUSG00000024621	Csf1r	AI323359|CD115|CSF-1R|Csfmr|Fim-2|Fim2|Fms|M-CSF-R|M-CSFR	colony stimulating factor 1 receptor	protein-coding
mm_121420.1	chr14	119875714	119875730	+	1	NA	Intergenic	Intergenic	126495	NR_045621	75432	Mm.443277	NR_045621	ENSMUSG00000100274	1700006F04Rik	-	RIKEN cDNA 1700006F04 gene	ncRNA
mm_30995.1	chr4	39450317	39450331	+	1	NA	promoter-TSS (NM_001081095)	promoter-TSS (NM_001081095)	31	NM_001081095	75471	Mm.23522	NM_001081095	ENSMUSG00000028287	1700009N14Rik	AI429145	RIKEN cDNA 1700009N14 gene	protein-coding
mm_90395.1	chr10	127323742	127323781	+	1	NA	promoter-TSS (NM_146011)	promoter-TSS (NM_146011)	34	NM_146011	216445	Mm.227198	NM_146011	ENSMUSG00000040345	Arhgap9	AU043488	Rho GTPase activating protein 9	protein-coding
mm_157550.1	chrX	51681367	51681394	-	1	NA	promoter-TSS (NM_015819)	promoter-TSS (NM_015819)	222	NM_001077202	50786	Mm.252561	NM_015819	ENSMUSG00000062184	Hs6st2	6OST2	heparan sulfate 6-O-sulfotransferase 2	protein-coding
mm_61381.1	chr7	71229313	71229314	+	1	NA	Intergenic	Intergenic	-680382	NR_130995	78156	Mm.243818	NR_130995	ENSMUSG00000108669	4930441H08Rik	-	RIKEN cDNA 4930441H08 gene	ncRNA
mm_29465.1	chr3	113577734	113577740	-	1	NA	promoter-TSS (NM_001110505)	promoter-TSS (NM_001110505)	13	NM_001110505	11722	Mm.439727	NM_007446	ENSMUSG00000074264	Amy1	Amy-1|Amy1a|C030014B17Rik	amylase 1, salivary	protein-coding
mm_16164.1	chr2	172472513	172472535	+	1	NA	promoter-TSS (NM_029608)	promoter-TSS (NM_029608)	-30	NM_029608	76426	Mm.46148	NM_029608	ENSMUSG00000027505	Fam209	1700029J11Rik	family with sequence similarity 209	protein-coding
mm_166244.1	chr5	74922082	74922087	+	1	NA	Intergenic	Lx8|LINE|L1	-27110	NR_045866	619945	Mm.359372	NM_001037908	ENSMUSG00000072874	Gm6116	EG619945	predicted gene 6116	ncRNA
mm_92593.1	chr10	80075470	80075478	-	1	NA	intron (NM_183426, intron 4 of 31)	intron (NM_183426, intron 4 of 31)	21455	NM_001037741	625249	Mm.332810	NM_008162	ENSMUSG00000075706	Gpx4	GPx-4|GSHPx-4|PHGPx|mtPHGPx|snGPx	glutathione peroxidase 4	protein-coding
mm_125525.1	chr15	57777313	57777315	+	1	NA	intron (NM_199449, intron 2 of 3)	intron (NM_199449, intron 2 of 3)	82647	NM_199449	387609	Mm.36557	NM_199449	ENSMUSG00000071757	Zhx2	Afr-1|Afr1|Raf|mKIAA0854	zinc fingers and homeoboxes 2	protein-coding
mm_160960.1	chr11	98982994	98982994	-	1	NA	promoter-TSS (NM_178596)	promoter-TSS (NM_178596)	22	NM_178596	353155	Mm.453253	NM_178596	ENSMUSG00000047197	Gjd3	Gja11|Gjc1|cx30.2	gap junction protein, delta 3	protein-coding
mm_165905.1	chr4	51812644	51812647	-	1	NA	Intergenic	U1|snRNA|snRNA	238465	NR_040668	329844	Mm.128934	NR_040668	ENSMUSG00000085515	C630028M04Rik	-	RIKEN cDNA C630028M04 gene	ncRNA
mm_35271.1	chr4	19908543	19908560	-	1	NA	intron (NM_175406, intron 2 of 7)	intron (NM_175406, intron 2 of 7)	14015	NM_175406	242341	Mm.19298	NM_175406	ENSMUSG00000028238	Atp6v0d2	1620401A02Rik|AI324824|V-ATPase	ATPase, H+ transporting, lysosomal V0 subunit D2	protein-coding
mm_69413.1	chr7	132576338	132576355	-	1	NA	promoter-TSS (NM_016978)	promoter-TSS (NM_016978)	52	NM_016978	18242	Mm.13694	NM_016978	ENSMUSG00000030934	Oat	AI194874|rhg	ornithine aminotransferase	protein-coding
mm_46727.1	chr5	110770561	110770629	-	1	NA	5' UTR (NM_029337, exon 1 of 52)	5' UTR (NM_029337, exon 1 of 52)	122	NM_029337	75560	Mm.270487	NM_029337	ENSMUSG00000029505	Ep400	1700020J09Rik|AU023439|mDomino|mKIAA1498|p400	E1A binding protein p400	protein-coding
mm_58115.1	chr6	138426693	138426701	-	1	NA	intron (NR_126072, intron 2 of 3)	intron (NR_126072, intron 2 of 3)	3592	NR_126072	319702	Mm.403785	NR_126072	ENSMUSG00000089957	A830011K09Rik	-	RIKEN cDNA A830011K09 gene	ncRNA
mm_83314.1	chr9	44130174	44130178	-	1	NA	Intergenic	CpG	-4482	NM_023061	84004	Mm.275003	NM_023061	ENSMUSG00000032135	Mcam	1-gicerin|AV025631|CD146|CD149|Muc18|s-endo|s-gicerin	melanoma cell adhesion molecule	protein-coding
mm_140734.1	chr17	15704423	15704431	-	1	NA	promoter-TSS (NM_007690)	promoter-TSS (NM_007690)	-540	NM_007690	12648	Mm.8137	NM_007690	ENSMUSG00000023852	Chd1	4930525N21Rik|AI851787|AW555109	chromodomain helicase DNA binding protein 1	protein-coding
mm_103526.1	chr11	77046468	77046485	-	1	NA	exon (NM_001012309, exon 7 of 7)	exon (NM_001012309, exon 7 of 7)	31696	NR_030756	751519		NR_030756	ENSMUSG00000065518	Mir423	Mirn423|mir-423|mmu-mir-423	microRNA 423	ncRNA
mm_148956.1	chr19	7383124	7383135	+	1	NA	promoter-TSS (NM_001033139)	promoter-TSS (NM_001033139)	-103	NM_001167831	68229	Mm.34766	NM_001033139	ENSMUSG00000024970	AI846148	1700105P06Rik	expressed sequence AI846148	protein-coding
mm_97075.1	chr11	72999129	72999137	+	1	NA	promoter-TSS (NM_008771)	promoter-TSS (NM_008771)	-12	NM_008771	18436	Mm.25722	NM_008771	ENSMUSG00000020787	P2rx1	AI323649|BB122383|P2x|Pdcd3|RP-2	purinergic receptor P2X, ligand-gated ion channel, 1	protein-coding
mm_125530.1	chr15	57975387	57975395	+	1	NA	Intergenic	Intergenic	-10512	NM_173862	239463	Mm.221241	NM_173862	ENSMUSG00000051225	Fam83a	-	family with sequence similarity 83, member A	protein-coding
mm_50473.1	chr6	48987950	48987967	+	1	NA	exon (NM_172888, exon 1 of 5)	exon (NM_172888, exon 1 of 5)	1097	NM_172888	243377	Mm.446302	NM_172888	ENSMUSG00000039215	Svs1	9530003A11	seminal vesicle secretory protein 1	protein-coding
mm_41003.1	chr5	77465484	77465496	+	1	NA	promoter-TSS (NR_131050)	promoter-TSS (NR_131050)	2	NR_131050	69370	Mm.426881	NR_131050	ENSMUSG00000107232	1700017L05Rik	-	RIKEN cDNA 1700017L05 gene	ncRNA
mm_166386.1	chr5	132993070	132993070	+	1	NA	Intergenic	Intergenic	-450727	NM_177047	319974	Mm.409595	NM_177047	ENSMUSG00000029673	Auts2	2700063G02Rik|A730011F23Rik|D830032G16Rik	autism susceptibility candidate 2	protein-coding
mm_13353.1	chr2	103073765	103073788	+	1	NA	promoter-TSS (NM_175094)	promoter-TSS (NM_175094)	101	NM_019735	56369	Mm.24772	NM_019735	ENSMUSG00000010911	Apip	APIP2|CGI-29|Mmrp19	APAF1 interacting protein	protein-coding
mm_114538.1	chr13	73703720	73703724	+	1	NA	intron (NM_027780, intron 1 of 1)	intron (NM_027780, intron 1 of 1)	-3027	NM_028878	74338	Mm.271635	NM_028878	ENSMUSG00000021565	Slc6a19	4632401C08Rik|B<0>AT1	solute carrier family 6 (neurotransmitter transporter), member 19	protein-coding
mm_86442.1	chr10	4089945	4089950	+	1	NA	intron (NM_172308, intron 23 of 27)	intron (NM_172308, intron 23 of 27)	116872	NM_172308	270685	Mm.184752	NM_172308	ENSMUSG00000040675	Mthfd1l	2410004L15Rik|AI647056|Fthfsdc1	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1-like	protein-coding
mm_89798.1	chr10	102512326	102512338	+	1	NA	5' UTR (NM_146240, exon 1 of 2)	5' UTR (NM_146240, exon 1 of 2)	110	NM_146240	237504	Mm.282672	NM_146240	ENSMUSG00000044921	Rassf9	AW322107|Pamci	Ras association (RalGDS/AF-6) domain family (N-terminal) member 9	protein-coding
mm_119534.1	chr14	47668388	47668426	+	1	NA	intron (NM_001347528, intron 3 of 37)	intron (NM_001347528, intron 3 of 37)	4651	NM_001347522	16709	Mm.3110	NM_008477	ENSMUSG00000021843	Ktn1	-	kinectin 1	protein-coding
mm_105298.1	chr11	102481083	102481097	-	1	NA	exon (NM_001159492, exon 8 of 8)	exon (NM_001159492, exon 8 of 8)	-11207	NM_010575	16399	Mm.26646	NM_010575	ENSMUSG00000034664	Itga2b	AI172977|CD41|CD41B|GpIIb|alphaIIb	integrin alpha 2b	protein-coding
mm_29866.1	chr3	130061568	130061585	-	1	NA	promoter-TSS (NM_207209)	promoter-TSS (NM_207209)	-669	NM_207209	99683	Mm.192303	NM_207209	ENSMUSG00000001052	Sec24b	AI605202|SEC24	Sec24 related gene family, member B (S. cerevisiae)	protein-coding
mm_4400.1	chr1	172376601	172376624	+	1	NA	promoter-TSS (NM_026234)	promoter-TSS (NM_026234)	81	NM_026234	67556	Mm.26612	NM_026234	ENSMUSG00000050229	Pigm	4933437L05Rik|AI644422|AV302080|C920011G20Rik	phosphatidylinositol glycan anchor biosynthesis, class M	protein-coding
mm_119910.1	chr14	54952282	54952299	+	1	NA	exon (NM_010856, exon 25 of 39)	exon (NM_010856, exon 25 of 39)	-3148	NR_029724	387204		NR_029724	ENSMUSG00000065432	Mir208a	Mirn208|Mirn208a|mir-208|mir-208a|mmu-mir-208	microRNA 208a	ncRNA
mm_14039.1	chr2	122186269	122186285	+	1	NA	promoter-TSS (NM_028914)	promoter-TSS (NM_028914)	5	NM_028914	74401	Mm.374834	NM_028914	ENSMUSG00000027229	Terb2	4933406J08Rik	telomere repeat binding bouquet formation protein 2	protein-coding
mm_42388.1	chr5	114936950	114936963	+	1	NA	exon (NM_145209, exon 7 of 7)	exon (NM_145209, exon 7 of 7)	-5246	NM_028211	72357	Mm.292672	NM_028211	ENSMUSG00000029559	2210016L21Rik	-	RIKEN cDNA 2210016L21 gene	protein-coding
mm_19133.1	chr2	80292402	80292411	-	1	NA	promoter-TSS (NM_177256)	promoter-TSS (NM_177256)	-64	NM_177256	320769	Mm.60992	NM_177256	ENSMUSG00000050114	Prdx6b	1-cysPrx-P1|4930414C22Rik|Aop2-rs1|Prdx5-rs1|Prdx6-ps1|Prdx6-rs1|Prdx6-rs1-ps	peroxiredoxin 6B	protein-coding
mm_164912.1	chr18	73382833	73382837	+	1	NA	Intergenic	U2|snRNA|snRNA	-189870	NM_001039214	240396	Mm.24131	NM_001039214	ENSMUSG00000037253	Mex3c	A130001D14Rik|BC035207|BM-013|Rkhd2	mex3 RNA binding family member C	protein-coding
mm_108600.1	chr12	85468856	85468867	+	1	NA	Intergenic	Intergenic	-5040	NM_010234	14281	Mm.246513	NM_010234	ENSMUSG00000021250	Fos	D12Rfj1|c-fos|cFos	FBJ osteosarcoma oncogene	protein-coding
mm_121170.1	chr14	103015117	103015124	+	1	NA	intron (NR_045657, intron 2 of 2)	RMER1B|Other|Other	18683	NR_045657	71264	Mm.399572	NR_045657		4933432I03Rik	-	RIKEN cDNA 4933432I03 gene	ncRNA
mm_164279.1	chr15	102150579	102150581	+	1	NA	promoter-TSS (NM_146064)	promoter-TSS (NM_146064)	5	NM_146064	223920	Mm.358862	NM_146064	ENSMUSG00000023045	Soat2	ACAT2|D15Wsu97e	sterol O-acyltransferase 2	protein-coding
mm_41662.1	chr5	99217834	99217849	+	1	NA	3' UTR (NM_181318, exon 14 of 14)	3' UTR (NM_181318, exon 14 of 14)	35086	NM_181318	320292	Mm.259074	NM_145839	ENSMUSG00000089809	Rasgef1b	4732452O09Rik|GPIgamma4|Gpig4	RasGEF domain family, member 1B	protein-coding
mm_15964.1	chr2	166035508	166035523	+	1	NA	intron (NM_008679, intron 2 of 22)	intron (NM_008679, intron 2 of 22)	42878	NM_008679	17979	Mm.469663	NM_008679	ENSMUSG00000027678	Ncoa3	2010305B15Rik|AW321064|Actr|Aib1|KAT13B|Rac3|Src3|Tram-1|Tram1|bHLHe42|p/Cip|pCip	nuclear receptor coactivator 3	protein-coding
mm_125632.1	chr15	61990105	61990109	+	1	NA	3' UTR (NM_001177354, exon 3 of 3)	3' UTR (NM_001177354, exon 3 of 3)	4766	NM_001177352	17869	Mm.2444	NM_010849	ENSMUSG00000022346	Myc	AU016757|Myc2|Niard|Nird|bHLHe39	myelocytomatosis oncogene	protein-coding
mm_168987.1	chr12	97038396	97038410	+	1	NA	Intergenic	L1Md_T|LINE|L1	-991181	NR_103800	69423	Mm.46121	NM_027076		1700019M22Rik	-	NFX-like protein	pseudo
mm_91143.1	chr10	19907623	19907627	-	1	NA	promoter-TSS (NM_008822)	promoter-TSS (NM_008822)	49	NM_008822	18634	Mm.338363	NM_008822	ENSMUSG00000020003	Pex7	MmPEX7	peroxisomal biogenesis factor 7	protein-coding
mm_139136.1	chr17	47509421	47509440	+	1	NA	intron (NM_001081635, intron 1 of 6)	intron (NM_001081635, intron 1 of 6)	4379	NM_001081635	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_4153.1	chr1	171019863	171019873	+	1	NA	intron (NM_144559, intron 2 of 4)	intron (NM_144559, intron 2 of 4)	942	NM_144559	246256	Mm.251254	NM_144559	ENSMUSG00000059089	Fcgr4	4833442P21Rik|CD16-2|FcgRIV|FcgammaRIV|Fcgr3a|Fcrl3	Fc receptor, IgG, low affinity IV	protein-coding
mm_133330.1	chr16	78376118	78376122	+	1	NA	intron (NM_001297747, intron 1 of 4)	CpG	637	NR_002700	654432	Mm.458574	NR_002700	ENSMUSG00000044645	Gm7334	EG654432	B-cell translocation gene 3 pseudogene	pseudo
mm_76044.1	chr8	77517950	77517979	-	1	NA	promoter-TSS (NM_030113)	promoter-TSS (NM_030113)	-57	NM_030113	78514	Mm.165974	NM_030113	ENSMUSG00000037148	Arhgap10	A930033B01Rik|PSGAP-m|PSGAP-s	Rho GTPase activating protein 10	protein-coding
mm_17183.1	chr2	25460907	25460931	-	1	NA	5' UTR (NM_153557, exon 1 of 7)	5' UTR (NM_153557, exon 1 of 7)	175	NM_153557	227622	Mm.261780	NM_153557	ENSMUSG00000047617	BC029214	D930050G13Rik|Paxx	cDNA sequence BC029214	protein-coding
mm_117733.1	chr13	95618480	95618498	-	1	NA	promoter-TSS (NM_010169)	promoter-TSS (NM_010169)	-56	NM_010169	14062	Mm.24816	NM_010169	ENSMUSG00000048376	F2r	AI482343|Cf2r|Par1|ThrR	coagulation factor II (thrombin) receptor	protein-coding
mm_150630.1	chr19	41345224	41345231	+	1	NA	intron (NM_031376, intron 2 of 16)	intron (NM_031376, intron 2 of 16)	39843	NM_031376	83490	Mm.222266	NM_031376	ENSMUSG00000025017	Pik3ap1	1810044J04Rik|BCAP	phosphoinositide-3-kinase adaptor protein 1	protein-coding
mm_68143.1	chr7	102245423	102245427	-	1	NA	intron (NM_019566, intron 1 of 1)	B4|SINE|B4	4693	NM_019566	56212	Mm.259795	NM_019566	ENSMUSG00000073982	Rhog	2810426G09Rik|Arhg|Sid10750	ras homolog family member G	protein-coding
mm_76739.1	chr8	95198704	95198707	-	1	NA	Intergenic	L1MD|LINE|L1	-56165	NM_001145831	16582	Mm.378951	NM_010631	ENSMUSG00000031788	Kifc3	AI325457|BB123200	kinesin family member C3	protein-coding
mm_115686.1	chr13	13564690	13564714	-	1	NA	Intergenic	Intergenic	-25707	NM_010748	17101	Mm.342337	NM_010748	ENSMUSG00000019726	Lyst	D13Sfk13|beige|bg	lysosomal trafficking regulator	protein-coding
mm_71894.1	chr8	69849322	69849341	+	1	NA	intron (NM_001024954, intron 1 of 7)	intron (NM_001024954, intron 1 of 7)	16627	NM_001024954	80720	Mm.210823	NM_030555	ENSMUSG00000031860	Pbx4	2410015M21Rik|AI429113|AW045266	pre B cell leukemia homeobox 4	protein-coding
mm_168227.1	chr10	79960189	79960190	+	1	NA	promoter-TSS (NM_175450)	promoter-TSS (NM_175450)	37	NM_175450	216156	Mm.35828	NM_175450	ENSMUSG00000035754	Wdr18	2310012I10Rik|AU044733|AW122032	WD repeat domain 18	protein-coding
mm_131740.1	chr16	22047593	22047599	+	1	NA	non-coding (NR_027488, exon 17 of 17)	non-coding (NR_027488, exon 17 of 17)	38112	NR_027488	75826	Mm.297431	NM_029457	ENSMUSG00000022855	Senp2	2310007L05Rik|4930538C18Rik|AI646780|AW554757|Smt3ip2|SuPr-1|mKIAA1331	SUMO/sentrin specific peptidase 2	protein-coding
mm_82405.1	chr9	14771157	14771165	-	1	NA	promoter-TSS (NM_029306)	promoter-TSS (NM_029306)	-131	NM_029306	69325	Mm.440453	NM_029306	ENSMUSG00000031927	1700012B09Rik	1700007P19Rik	RIKEN cDNA 1700012B09 gene	protein-coding
mm_126240.1	chr15	79002253	79002263	+	1	NA	promoter-TSS (NR_105921)	promoter-TSS (NR_105921)	35	NR_105921	102465577		NR_105921	ENSMUSG00000099180	Mir6956	Gm27880|mmu-mir-6956	microRNA 6956	ncRNA
mm_43563.1	chr5	137630117	137630123	+	1	NA	intron (NR_033148, intron 1 of 21)	intron (NR_033148, intron 1 of 21)	997	NR_033148	100316903	Mm.200763	NR_033148		Gm20605	Lrch4-sap25	predicted gene 20605	ncRNA
mm_159172.1	chr2	106970477	106970477	-	1	NA	promoter-TSS (NM_173750)	promoter-TSS (NM_173750)	-86	NM_173750	212772	Mm.381231	NM_173750	ENSMUSG00000027122	Arl14ep	2700007P21Rik|4930448O08Rik|ARF7EP	ADP-ribosylation factor-like 14 effector protein	protein-coding
mm_123970.1	chr14	75130909	75130943	-	1	NA	promoter-TSS (NM_001247984)	promoter-TSS (NM_001247984)	-43	NM_027581	70859	Mm.320289	NM_027581	ENSMUSG00000021997	Lrrc63	4921509B22Rik	leucine rich repeat containing 63	protein-coding
mm_9458.1	chr1	172894926	172894958	-	1	NA	5' UTR (NM_011318, exon 1 of 2)	5' UTR (NM_011318, exon 1 of 2)	112	NM_011318	20219	Mm.330510	NM_011318	ENSMUSG00000026542	Apcs	Sap	serum amyloid P-component	protein-coding
mm_40218.1	chr5	37229089	37229091	+	1	NA	Intergenic	Intergenic	-12968	NM_001136058	12933	Mm.290995	NM_007765	ENSMUSG00000029121	Crmp1	CRMP-1|DRP-1|Dpysl1|ULIP-3|Ulip3	collapsin response mediator protein 1	protein-coding
mm_79891.1	chr9	65294441	65294444	+	1	NA	5' UTR (NM_011802, exon 1 of 14)	5' UTR (NM_011802, exon 1 of 14)	182	NM_011802	270166	Mm.30088	NM_011802	ENSMUSG00000015357	Clpx	AU014732|E330029I21	caseinolytic mitochondrial matrix peptidase chaperone subunit	protein-coding
mm_71646.1	chr8	58523277	58523314	+	1	NA	intron (NM_175032, intron 2 of 11)	L1_Mur3|LINE|L1	177501	NM_001177534	100271928	Mm.484123	NM_001177534		Gm15881	OTTMUSG00000027193	predicted gene 15881	protein-coding
mm_90100.1	chr10	116966222	116966246	+	1	NA	promoter-TSS (NR_027846)	promoter-TSS (NR_027846)	-40	NR_027846	103175	Mm.27138	NR_027846	ENSMUSG00000031294	D630029K05Rik	AI314111|AI875589	RIKEN cDNA D630029K05 gene	ncRNA
mm_13858.1	chr2	119711473	119711482	+	1	NA	intron (NM_030112, intron 5 of 17)	intron (NM_030112, intron 5 of 17)	-30860	NM_146125	228550	Mm.65337	NM_146125	ENSMUSG00000027296	Itpka	-	inositol 1,4,5-trisphosphate 3-kinase A	protein-coding
mm_146027.1	chr18	69519916	69519924	+	1	NA	intron (NM_013685, intron 5 of 19)	intron (NM_013685, intron 5 of 19)	174199	NM_001083967	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding
mm_93834.1	chr10	121586814	121586824	-	1	NA	promoter-TSS (NM_019786)	promoter-TSS (NM_019786)	-25	NM_019786	56480	Mm.34580	NM_019786	ENSMUSG00000020115	Tbk1	1200008B05Rik|AI462036|AW048562	TANK-binding kinase 1	protein-coding
mm_64096.1	chr7	141006707	141006711	+	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	4035	NM_025378	66141	Mm.141021	NM_025378	ENSMUSG00000025492	Ifitm3	1110004C05Rik|Cd225|Cdw217|DSPA2b|Fgls|IP15|mil-1	interferon induced transmembrane protein 3	protein-coding
mm_84993.1	chr9	86695671	86695678	-	1	NA	exon (NM_008615, exon 1 of 14)	exon (NM_008615, exon 1 of 14)	232	NR_045835	319556	Mm.386894	NR_045835	ENSMUSG00000087466	A330041J22Rik	-	RIKEN cDNA A330041J22 gene	ncRNA
mm_93370.1	chr10	105315687	105315693	-	1	NA	intron (NM_177368, intron 7 of 11)	intron (NM_177368, intron 7 of 11)	258789	NM_177368	278279	Mm.25225	NM_177368	ENSMUSG00000036019	Tmtc2	8430438D04Rik|D330034A10Rik	transmembrane and tetratricopeptide repeat containing 2	protein-coding
mm_7071.1	chr1	87854247	87854259	-	1	NA	promoter-TSS (NR_136921)	promoter-TSS (NR_136921)	46	NR_136921	100503175	Mm.426422	NR_136921	ENSMUSG00000101942	Gm19582	-	predicted gene, 19582	ncRNA
mm_134162.1	chr16	10792096	10792107	-	1	NA	promoter-TSS (NM_008933)	promoter-TSS (NM_008933)	4	NM_008933	19119	Mm.325769	NM_008933	ENSMUSG00000038015	Prm2	AI528784|Prm-2	protamine 2	protein-coding
mm_54228.1	chr6	28212897	28212897	-	1	NA	Intergenic	L1M5|LINE|L1	48704	NM_001081678	627049	Mm.84441	NM_001081678	ENSMUSG00000039841	Zfp800	AA407452|Znf800	zinc finger protein 800	protein-coding
mm_91223.1	chr10	22058608	22058639	-	1	NA	Intergenic	CpG	9456	NM_053264	114671	Mm.288194	NM_053264	ENSMUSG00000069712	4930444G20Rik	-	RIKEN cDNA 4930444G20 gene	protein-coding
mm_89235.1	chr10	87581848	87581878	+	1	NA	exon (NM_008777, exon 12 of 13)	exon (NM_008777, exon 12 of 13)	60068	NM_008777	18478	Mm.263539	NM_008777	ENSMUSG00000020051	Pah	AW106920	phenylalanine hydroxylase	protein-coding
mm_130107.1	chr15	89429852	89429935	-	1	NA	promoter-TSS (NR_004843)	promoter-TSS (NR_004843)	34	NR_037154	12651	Mm.485045	NM_007692	ENSMUSG00000022617	Chkb	Chetk|Chkl|Ck|Ck/Ek|Ck/Ek-beta|Ckb|Ckekb|Ek	choline kinase beta	protein-coding
mm_150021.1	chr19	29372316	29372324	+	1	NA	intron (NM_021893, intron 1 of 6)	intron (NM_021893, intron 1 of 6)	4882	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_94502.1	chr11	7197805	7197811	+	1	NA	promoter-TSS (NM_008341)	promoter-TSS (NM_008341)	21	NM_008341	16006	Mm.21300	NM_008341	ENSMUSG00000020429	Igfbp1	-	insulin-like growth factor binding protein 1	protein-coding
mm_157107.1	chrX	9437890	9437900	-	1	NA	3' UTR (NM_007807, exon 13 of 13)	3' UTR (NM_007807, exon 13 of 13)	31429	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_34610.1	chr4	150282804	150282806	+	1	NA	intron (NM_001085492, intron 1 of 22)	intron (NM_001085492, intron 1 of 22)	889	NM_001085492	68703	Mm.291274	NM_001085492	ENSMUSG00000039852	Rere	1110033A15Rik|AI414665|ARG|ARP|ATN1L|AW742570|Atr2|DNB1|eye<m03Jus>|eyes3|mKIAA0458	arginine glutamic acid dipeptide (RE) repeats	protein-coding
mm_156250.1	chrX	136340054	136340073	+	1	NA	Intergenic	Intergenic	69810	NM_001110234	12070	Mm.90787	NM_009750	ENSMUSG00000046432	Bex3	AL033356|DXWsu67e|Gcap27|Nade|Ngfrap1	brain expressed X-linked 3	protein-coding
mm_123520.1	chr14	66296965	66296977	-	1	NA	promoter-TSS (NM_029979)	promoter-TSS (NM_029979)	-54	NM_029979	66854	Mm.43871	NM_029979	ENSMUSG00000022043	Trim35	0710005M05Rik|A430106H13Rik|AW046487|HLS5|Mair|NC8|mKIAA1098	tripartite motif-containing 35	protein-coding
mm_161541.1	chr15	103014060	103014060	+	1	NA	promoter-TSS (NM_175730)	promoter-TSS (NM_175730)	52	NM_175730	15424	Mm.103825	NM_175730	ENSMUSG00000022485	Hoxc5	AI181837|Hox-3.4|Hox-6.2	homeobox C5	protein-coding
mm_38483.1	chr4	140750547	140750563	-	1	NA	intron (NM_011061, intron 12 of 15)	intron (NM_011061, intron 12 of 15)	-7912	NM_153106	242726	Mm.271661	NM_153106	ENSMUSG00000040935	Padi6	Pad6|Padi5|ePAD	peptidyl arginine deiminase, type VI	protein-coding
mm_36206.1	chr4	62408648	62408658	-	1	NA	promoter-TSS (NM_027297)	promoter-TSS (NM_027297)	-30	NM_139291	66440	Mm.109930	NM_139291	ENSMUSG00000066149	Cdc26	2010012C09Rik	cell division cycle 26	protein-coding
mm_11060.1	chr2	27506856	27506858	+	1	NA	Intergenic	Intergenic	-8290	NM_080848	140858	Mm.28265	NM_080848	ENSMUSG00000026917	Wdr5	2410008O07Rik|AA408785|AA960360|Big|Big-3	WD repeat domain 5	protein-coding
mm_82151.1	chr9	123775015	123775025	+	1	NA	intron (NM_009913, intron 2 of 2)	intron (NM_009913, intron 2 of 2)	7809	NM_001166625	12769	Mm.440604	NM_009913	ENSMUSG00000029530	Ccr9	A130091K22Rik|Cmkbr10|GPR-9-6	chemokine (C-C motif) receptor 9	protein-coding
mm_67716.1	chr7	90019639	90019657	-	1	NA	Intergenic	Intergenic	-9511	NR_110365	319711	Mm.31753	NR_015614	ENSMUSG00000097585	E230029C05Rik	AI452102|B230337J15	RIKEN cDNA E230029C05 gene	ncRNA
mm_127602.1	chr15	102402395	102402429	+	1	NA	Intergenic	Intergenic	-3904	NM_013672	20683	Mm.4618	NM_013672	ENSMUSG00000001280	Sp1	1110003E12Rik|AA450830|AI845540|Sp1-1	trans-acting transcription factor 1	protein-coding
mm_72608.1	chr8	84589668	84589678	+	1	NA	intron (NM_001252059, intron 29 of 45)	B4|SINE|B4	73179	NM_010499	15936	Mm.399	NM_010499	ENSMUSG00000053560	Ier2	AI317238|Ch1|Pip92	immediate early response 2	protein-coding
mm_48628.1	chr5	145136395	145136411	-	1	NA	intron (NM_001033313, intron 2 of 5)	intron (NM_001033313, intron 2 of 5)	3686	NM_001033313	231887	Mm.188851	NM_001033313	ENSMUSG00000029623	Pdap1	HASPP28|PAP|PAP1	PDGFA associated protein 1	protein-coding
mm_169540.1	chr15	100353179	100353187	+	1	NA	promoter-TSS (NM_001024672)	promoter-TSS (NM_001024672)	-17	NM_001024672	554292	Mm.268451	NM_001024672	ENSMUSG00000093789	Methig1	Mettl7a2-Higd1c|Mettl7a2Higd1c|Mettl7a2higd1c|UbiE-YGHL1	methyltransferase hypoxia inducible domain containing 1	protein-coding
mm_83422.1	chr9	44969772	44969774	-	1	NA	3' UTR (NM_009850, exon 7 of 7)	3' UTR (NM_009850, exon 7 of 7)	-4173	NM_145400	140630	Mm.215069	NM_145400	ENSMUSG00000059890	Ube4a	4732444G18Rik|9930123J21Rik|UFD2b	ubiquitination factor E4A	protein-coding
mm_40599.1	chr5	64264226	64264254	+	1	NA	intron (NM_001310611, intron 5 of 21)	intron (NM_001310611, intron 5 of 21)	33883	NM_001289514	57915	Mm.286353	NM_019636	ENSMUSG00000029174	Tbc1d1	1110062G02Rik|AI385682|AW555803|Nob1|Nobq1|Tbc1|mKIAA1108	TBC1 domain family, member 1	protein-coding
mm_22324.1	chr2	180642603	180642625	-	1	NA	promoter-TSS (NM_178254)	promoter-TSS (NM_178254)	77	NM_178254	277353	Mm.473700	NM_178254	ENSMUSG00000038932	Tcfl5	AV260129|Figlb|Sosf1	transcription factor-like 5 (basic helix-loop-helix)	protein-coding
mm_17402.1	chr2	27215183	27215184	-	1	NA	exon (NM_138665, exon 16 of 21)	exon (NM_138665, exon 16 of 21)	32120	NM_138665	192166	Mm.278467	NM_138665	ENSMUSG00000009614	Sardh	-	sarcosine dehydrogenase	protein-coding
mm_88290.1	chr10	75222126	75222158	+	1	NA	5' UTR (NM_001145826, exon 2 of 19)	5' UTR (NM_001145826, exon 2 of 19)	9752	NM_001145826	74392	Mm.27716	NM_153406	ENSMUSG00000033444	Specc1l	4930470P14Rik|4932439K10Rik|9530057A13Rik|AI317249|Cytsa|mKIAA0376	sperm antigen with calponin homology and coiled-coil domains 1-like	protein-coding
mm_49960.1	chr6	40635073	40635111	+	1	NA	intron (NM_001171003, intron 1 of 47)	intron (NM_001171003, intron 1 of 47)	6261	NM_001171003	232714	Mm.33401	NM_001171003	ENSMUSG00000068587	Mgam	6030407P20Rik|MGA	maltase-glucoamylase	protein-coding
mm_39359.1	chr5	9104823	9104827	+	1	NA	intron (NM_001081029, intron 2 of 4)	intron (NM_001081029, intron 2 of 4)	4088	NM_001081029	652925	Mm.439954	NM_001081029	ENSMUSG00000079659	Tmem243	4930420K17Rik|E030031F02Rik	transmembrane protein 243, mitochondrial	protein-coding
mm_79966.1	chr9	66394324	66394329	+	1	NA	intron (NM_145617, intron 8 of 77)	intron (NM_145617, intron 8 of 77)	43876	NM_145617	235439	Mm.244179	NM_145617	ENSMUSG00000038664	Herc1	2810449H11Rik|B230218H07|D130015N03Rik|tbl	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	protein-coding
mm_35029.1	chr4	4019567	4019576	-	1	NA	promoter-TSS (NM_181989)	promoter-TSS (NM_181989)	92	NM_181989	242285	Mm.98096	NM_181989	ENSMUSG00000028236	Sdr16c5	Rdhe2|Scdr9	short chain dehydrogenase/reductase family 16C, member 5	protein-coding
mm_21687.1	chr2	164432209	164432221	-	1	NA	intron (NM_011521, intron 1 of 4)	intron (NM_011521, intron 1 of 4)	10973	NM_011521	20971	Mm.3815	NM_011521	ENSMUSG00000017009	Sdc4	AA959608|AW108331|S4|Synd4|ryudocan|syndecan-4	syndecan 4	protein-coding
mm_21873.1	chr2	165993730	165993743	-	1	NA	intron (NM_008679, intron 1 of 22)	intron (NM_008679, intron 1 of 22)	1099	NM_008679	17979	Mm.469663	NM_008679	ENSMUSG00000027678	Ncoa3	2010305B15Rik|AW321064|Actr|Aib1|KAT13B|Rac3|Src3|Tram-1|Tram1|bHLHe42|p/Cip|pCip	nuclear receptor coactivator 3	protein-coding
mm_106678.1	chr11	121925315	121925343	-	1	NA	Intergenic	Intergenic	95111	NM_029049	74675	Mm.61213	NM_029049	ENSMUSG00000039198	Ptchd3	4930451E13Rik|4933440L20Rik|RNDEu-3	patched domain containing 3	protein-coding
mm_152245.1	chr19	8714305	8714316	-	1	NA	promoter-TSS (NM_008577)	promoter-TSS (NM_008577)	-413	NM_008577	17254	Mm.4114	NM_008577	ENSMUSG00000010095	Slc3a2	4F2|4F2HC|AI314110|Cd98|Ly-10|Ly-m10|Ly10|Mdu1|Mgp-2hc|NACAE	solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2	protein-coding
mm_48134.1	chr5	137150142	137150146	-	1	NA	Intergenic	Intergenic	-33937	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_114849.1	chr13	92846655	92846669	+	1	NA	intron (NM_001162945, intron 3 of 8)	intron (NM_001162945, intron 3 of 8)	1875	NM_001162945	382793	Mm.296770	NM_001162945	ENSMUSG00000021704	Mtx3	4930470O13Rik|AA409304|AI853833|AU067765|EG624619|Gm1194|Gm6514	metaxin 3	protein-coding
mm_40591.1	chr5	64230326	64230346	+	1	NA	promoter-TSS (NM_001289514)	promoter-TSS (NM_001289514)	-21	NM_001289514	57915	Mm.286353	NM_019636	ENSMUSG00000029174	Tbc1d1	1110062G02Rik|AI385682|AW555803|Nob1|Nobq1|Tbc1|mKIAA1108	TBC1 domain family, member 1	protein-coding
mm_49569.1	chr6	30640515	30640547	+	1	NA	exon (NM_025350, exon 3 of 10)	exon (NM_025350, exon 3 of 10)	1313	NM_025350	109697	Mm.25377	NM_025350	ENSMUSG00000054446	Cpa1	0910001L12Rik|Cpa	carboxypeptidase A1, pancreatic	protein-coding
mm_153492.1	chr19	41324665	41324677	-	1	NA	exon (NM_031376, exon 7 of 17)	exon (NM_031376, exon 7 of 17)	60399	NM_031376	83490	Mm.222266	NM_031376	ENSMUSG00000025017	Pik3ap1	1810044J04Rik|BCAP	phosphoinositide-3-kinase adaptor protein 1	protein-coding
mm_1923.1	chr1	86045921	86045968	+	1	NA	promoter-TSS (NM_001144992)	promoter-TSS (NM_001144992)	81	NM_001144992	72792	Mm.54981	NM_001144992	ENSMUSG00000026227	2810459M11Rik	-	RIKEN cDNA 2810459M11 gene	protein-coding
mm_125155.1	chr15	31004773	31004798	+	1	NA	intron (NM_008729, intron 19 of 22)	intron (NM_008729, intron 19 of 22)	-34341	NR_045186	73784	Mm.66947	NR_045186		4930430F21Rik	-	RIKEN cDNA 4930430F21 gene	ncRNA
mm_67431.1	chr7	80371198	80371368	-	1	NA	promoter-TSS (NM_172903)	promoter-TSS (NM_172903)	92	NM_172903	140481	Mm.269245	NM_172903	ENSMUSG00000038886	Man2a2	1700052O22Rik|4931438M07Rik|AI480988|MX|Man IIx	mannosidase 2, alpha 2	protein-coding
mm_4677.1	chr1	180423441	180423466	+	1	NA	3' UTR (NM_001081175, exon 8 of 8)	3' UTR (NM_001081175, exon 8 of 8)	60051	NM_001081227	381310	Mm.44791	NM_001081227	ENSMUSG00000053963	Stum	6330403A02Rik|ENSMUSG00000056615|Gm10001|R75555	mechanosensory transduction mediator	protein-coding
mm_67846.1	chr7	98563017	98563026	-	1	NA	Intergenic	Intergenic	68799	NM_001113379	434215	Mm.323057	NM_001113379	ENSMUSG00000090958	Lrrc32	AI426318|D11S833Eh|D7H11S833E|EG434215|Garp	leucine rich repeat containing 32	protein-coding
mm_58980.1	chr7	19076072	19076117	+	1	NA	promoter-TSS (NM_010058)	promoter-TSS (NM_010058)	-106	NM_010058	13401	Mm.2852	NM_010058	ENSMUSG00000030410	Dmwd	DMR-N9|Dm9	dystrophia myotonica-containing WD repeat motif	protein-coding
mm_39592.1	chr5	23496499	23496519	+	1	NA	exon (NM_026984, exon 18 of 26)	exon (NM_026984, exon 18 of 26)	62080	NM_026984	69188	Mm.205190	NM_026984	ENSMUSG00000029004	Kmt2e	1810033J14Rik|9530077A04Rik|D230038D11Rik|Mll5|NKp44L	lysine (K)-specific methyltransferase 2E	protein-coding
mm_149659.1	chr19	18713226	18713243	+	1	NA	promoter-TSS (NM_177640)	promoter-TSS (NM_177640)	-2	NM_177640	225995	Mm.28101	NM_177640	ENSMUSG00000047044	D030056L22Rik	-	RIKEN cDNA D030056L22 gene	protein-coding
mm_146160.1	chr18	75043100	75043116	+	1	NA	5' UTR (NM_027727, exon 2 of 17)	5' UTR (NM_027727, exon 2 of 17)	24336	NM_027727	69190	Mm.173826	NM_027727	ENSMUSG00000035765	Dym	1810041M12Rik|4933427L07Rik|C030019K18Rik	dymeclin	protein-coding
mm_131383.1	chr16	14163317	14163352	+	1	NA	promoter-TSS (NM_001285504)	promoter-TSS (NM_001285504)	59	NM_001114085	67203	Mm.24105	NM_023317	ENSMUSG00000022678	Nde1	2810027M15Rik|AU042936|AW822251|Nude|mNudE	nudE neurodevelopment protein 1	protein-coding
mm_144089.1	chr18	3005639	3005665	+	1	NA	Intergenic	Intergenic	117760	NM_001167539	100312476	Mm.480293	NM_001167539	ENSMUSG00000091539	Vmn1r238	-	vomeronasal 1 receptor, 238	protein-coding
mm_115677.1	chr13	13005392	13005394	-	1	NA	promoter-TSS (NM_031191)	promoter-TSS (NM_031191)	-63	NM_031191	18811	Mm.88796	NM_031191	ENSMUSG00000079092	Prl2c2	Ghd2|MRP-1|PLF-1|Plf|Plf1	prolactin family 2, subfamily c, member 2	protein-coding
mm_68341.1	chr7	106506351	106506383	-	1	NA	Intergenic	Intergenic	-65294	NR_003967	209380	Mm.461779	NM_001001318		Gm4759	EG209380	GTPase, very large interferon inducible 1 pseudogene	pseudo
mm_92926.1	chr10	84440660	84440675	-	1	NA	promoter-TSS (NM_001004363)	promoter-TSS (NM_001004363)	-196	NM_001004363	77976	Mm.25874	NM_001004363	ENSMUSG00000020032	Nuak1	AU014801|AW494241|B230104P22Rik|Omphk1	NUAK family, SNF1-like kinase, 1	protein-coding
mm_164311.1	chr15	103897515	103897535	-	1	NA	exon (NM_009267, exon 3 of 4)	exon (NM_009267, exon 3 of 4)	1775	NM_009268	20771	Mm.30276	NM_009268		Mucl1	Spt-2|Spt2	mucin-like 1	protein-coding
mm_96948.1	chr11	70562841	70562897	+	1	NA	promoter-TSS (NM_001045964)	promoter-TSS (NM_001045964)	-12	NM_001045964	50932	Mm.42967	NM_016713	ENSMUSG00000020827	Mink1	B55|MINK|Map4k6|Ysk2	misshapen-like kinase 1 (zebrafish)	protein-coding
mm_9573.1	chr1	173979922	173979934	-	1	NA	intron (NM_008327, intron 1 of 6)	Lx9|LINE|L1	2916	NM_008327	26388	Mm.218770	NM_008327	ENSMUSG00000026535	Ifi202b	Ifbip-1|Ifi202|Ifi202a|p202	interferon activated gene 202B	protein-coding
mm_145367.1	chr18	56733145	56733166	+	1	NA	intron (NM_010721, intron 4 of 10)	intron (NM_010721, intron 4 of 10)	25342	NM_010721	16906	Mm.4105	NM_010721	ENSMUSG00000024590	Lmnb1	-	lamin B1	protein-coding
mm_6704.1	chr1	82237089	82237091	-	1	NA	3' UTR (NM_010570, exon 2 of 2)	3' UTR (NM_010570, exon 2 of 2)	54349	NM_010570	16367	Mm.4952	NM_010570	ENSMUSG00000055980	Irs1	G972R|IRS-1	insulin receptor substrate 1	protein-coding
mm_107592.1	chr12	49377658	49377672	+	1	NA	Intergenic	Intergenic	-5218	NM_001160112	15228	Mm.4704	NM_008241	ENSMUSG00000020950	Foxg1	2900064B05Rik|BF-1|Bf1|Hfh9|Hfhbf1	forkhead box G1	protein-coding
mm_149771.1	chr19	23061566	23061593	+	1	NA	Intergenic	Intergenic	-79647	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_107306.1	chr12	31073948	31073959	+	1	NA	promoter-TSS (NM_027828)	promoter-TSS (NM_027828)	-15	NM_027828	104943	Mm.248938	NM_027828	ENSMUSG00000036136	Fam110c	9030611O19Rik|AU019489	family with sequence similarity 110, member C	protein-coding
mm_127776.1	chr15	3341103	3341106	-	1	NA	intron (NM_001048178, intron 5 of 8)	intron (NM_001048178, intron 5 of 8)	-37578	NM_001166063	100039139	Mm.455610	NM_001166063	ENSMUSG00000091119	Ccdc152	ENSMUSG00000071814	coiled-coil domain containing 152	protein-coding
mm_11037.1	chr2	26973483	26973505	+	1	NA	promoter-TSS (NM_001290463)	promoter-TSS (NM_001290463)	78	NM_001290465	279028	Mm.330084	NM_001001322	ENSMUSG00000014852	Adamts13	ADAM-TS13|ADAMTS-13|Gm710|vWF-CP	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 13	protein-coding
mm_162050.1	chrX	6779288	6779288	+	1	NA	Intergenic	(CCCGAA)n|Simple_repeat|Simple_repeat	-94196	NM_177914	331374	Mm.392752	NM_177914	ENSMUSG00000062393	Dgkk	Gm360	diacylglycerol kinase kappa	protein-coding
mm_160215.1	chr7	98836261	98836261	+	1	NA	intron (NM_001285792, intron 2 of 6)	CpG	1149	NM_001285792	22411	Mm.22182	NM_009519	ENSMUSG00000015957	Wnt11	-	wingless-type MMTV integration site family, member 11	protein-coding
mm_70662.1	chr8	14881620	14881626	+	1	NA	Intergenic	Intergenic	-6913	NM_012000	26889	Mm.254027	NM_012000	ENSMUSG00000026317	Cln8	mnd	ceroid-lipofuscinosis, neuronal 8	protein-coding
mm_50050.1	chr6	41177442	41177468	+	1	NA	Intergenic	Intergenic	-124817	NM_011646	22074	Mm.383263	NM_011646	ENSMUSG00000054106	Try4	0910001B19Rik|Td	trypsin 4	protein-coding
mm_137278.1	chr17	24720252	24720262	+	1	NA	promoter-TSS (NR_028515)	promoter-TSS (NR_028515)	194	NM_008503	16898	Mm.157452	NM_008503	ENSMUSG00000044533	Rps2	Llrep3|S4	ribosomal protein S2	protein-coding
mm_87312.1	chr10	42767104	42767113	+	1	NA	intron (NM_153055, intron 1 of 20)	intron (NM_153055, intron 1 of 20)	5612	NM_153055	140740	Mm.214344	NM_153055	ENSMUSG00000019802	Sec63	5730478J10Rik|AI649014|AW319215	SEC63-like (S. cerevisiae)	protein-coding
mm_151500.1	chr19	58728965	58728981	+	1	NA	promoter-TSS (NM_018874)	promoter-TSS (NM_018874)	86	NM_018874	18946	Mm.10753	NM_018874	ENSMUSG00000042179	Pnliprp1	Plrp1	pancreatic lipase related protein 1	protein-coding
mm_10123.1	chr2	3749303	3749320	+	1	NA	intron (NM_025626, intron 1 of 3)	intron (NM_025626, intron 1 of 3)	35853	NM_025626	66540	Mm.277864	NM_025626	ENSMUSG00000026655	Fam107b	3110001A13Rik|AA589595|AA959793|AI132312	family with sequence similarity 107, member B	protein-coding
mm_152829.1	chr19	23142057	23142076	-	1	NA	exon (NM_010638, exon 1 of 2)	exon (NM_010638, exon 1 of 2)	840	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_64835.1	chr7	12991622	12991625	-	1	NA	intron (NM_009512, intron 4 of 9)	B4|SINE|B4	6569	NM_009512	26459	Mm.10984	NM_009512	ENSMUSG00000030382	Slc27a5	FACVL3|FATP5|VLCS-H2|VLCSH2|Vlacsr	solute carrier family 27 (fatty acid transporter), member 5	protein-coding
mm_162486.1	chr1	135746771	135746798	+	1	NA	exon (NM_007791, exon 4 of 6)	exon (NM_007791, exon 4 of 6)	17587	NM_007791	13007	Mm.196484	NM_007791	ENSMUSG00000026421	Csrp1	AA408841|AA959891|AW545626|CRP1|Csrp	cysteine and glycine-rich protein 1	protein-coding
mm_140521.1	chr17	6106490	6106539	-	1	NA	promoter-TSS (NM_001103181)	promoter-TSS (NM_001103181)	-316	NM_001103181	68842	Mm.449307	NM_054040	ENSMUSG00000034377	Tulp4	1110057P05Rik|2210038L17Rik|Tusp	tubby like protein 4	protein-coding
mm_70300.1	chr8	4087464	4087525	+	1	NA	Intergenic	CpG	18270	NM_026956	69142	Mm.171061	NM_026956	ENSMUSG00000051906	Cd209f	1810029C22Rik|AI647041|SIGNR8	CD209f antigen	protein-coding
mm_78962.1	chr9	45246319	45246342	+	1	NA	intron (NM_001198971, intron 4 of 4)	intron (NM_001198971, intron 4 of 4)	20377	NR_106054	102466803		NR_106054	ENSMUSG00000098361	Mir7086	Gm27643|mmu-mir-7086	microRNA 7086	ncRNA
mm_125371.1	chr15	39962625	39962636	+	1	NA	promoter-TSS (NR_045719)	promoter-TSS (NR_045719)	-19	NR_045719	105976	Mm.394885	NR_045719		AU022793	-	expressed sequence AU022793	ncRNA
mm_153933.1	chr19	47432626	47432642	-	1	NA	intron (NM_001164717, intron 1 of 13)	intron (NM_001164717, intron 1 of 13)	31777	NM_001164717	14218	Mm.127560	NM_008018	ENSMUSG00000053617	Sh3pxd2a	2310014D11Rik|AA589508|AI256723|AI413738|C230050L11|EG329070|Fish|Gm5098|Sh3md1|TSK5|Tks5	SH3 and PX domains 2A	protein-coding
mm_68079.1	chr7	101870607	101870612	-	1	NA	5' UTR (NM_008034, exon 1 of 7)	5' UTR (NM_008034, exon 1 of 7)	179	NM_001252554	14275	Mm.2135	NM_008034	ENSMUSG00000001827	Folr1	FBP1|Folbp-1|Folbp1	folate receptor 1 (adult)	protein-coding
mm_106350.1	chr11	118393521	118393537	-	1	NA	exon (NM_011150, exon 6 of 6)	exon (NM_011150, exon 6 of 6)	8402	NM_011150	19039	Mm.3152	NM_011150	ENSMUSG00000033880	Lgals3bp	90K|CyCAP|MAC-2BP|Ppicap|Tango10b	lectin, galactoside-binding, soluble, 3 binding protein	protein-coding
mm_121157.1	chr14	102981368	102981392	+	1	NA	3' UTR (NM_177715, exon 1 of 1)	3' UTR (NM_177715, exon 1 of 1)	1252	NR_039592	100628599		NR_039592	ENSMUSG00000092901	Mir5130	mir-5130|mmu-mir-5130|mu-mir-5130	microRNA 5130	ncRNA
mm_104515.1	chr11	96006158	96006173	-	1	NA	promoter-TSS (NM_009951)	promoter-TSS (NM_009951)	-221	NM_009951	140486	Mm.294769	NM_009951	ENSMUSG00000013415	Igf2bp1	AL024068|AW549074|CRD-BP|Crdbp|D030026A21Rik|D11Moh40e|D11Moh45|IMP-1|IMP1|Neilsen|ZBP-1|Zbp1|mir-3063	insulin-like growth factor 2 mRNA binding protein 1	protein-coding
mm_46424.1	chr5	104133978	104133979	-	1	NA	Intergenic	Intergenic	-19890	NM_010097	13602	Mm.29027	NM_010097	ENSMUSG00000029309	Sparcl1	Ecm2|Sc1|hevin|mast9	SPARC-like 1	protein-coding
mm_1598.1	chr1	74375278	74375289	+	1	NA	promoter-TSS (NM_013612)	promoter-TSS (NM_013612)	80	NM_013612	18173	Mm.2913	NM_013612	ENSMUSG00000026177	Slc11a1	Bcg|Ity|Ity1|Lsh|Nramp|Nramp1|ity	solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1	protein-coding
mm_66771.1	chr7	46795662	46795722	-	1	NA	promoter-TSS (NM_001291075)	promoter-TSS (NM_001291075)	189	NM_001005248	246694	Mm.379442	NM_178742	ENSMUSG00000014418	Hps5	AI646796|AL022647|C85120|haze|hz|maroon|mr|ru-2|ru2	Hermansky-Pudlak syndrome 5	protein-coding
mm_131990.1	chr16	25042372	25042382	+	1	NA	Intergenic	Intergenic	-17262	NR_040374	319487	Mm.137341	NR_040374	ENSMUSG00000096960	A230028O05Rik	-	RIKEN cDNA A230028O05 gene	ncRNA
mm_77429.1	chr8	121125636	121125640	-	1	NA	Intergenic	CpG	-2047	NM_008024	14241	Mm.5111	NM_008024	ENSMUSG00000097084	Foxl1	FREAC7|Fkh6|fkh-6	forkhead box L1	protein-coding
mm_131552.1	chr16	17922042	17922076	+	1	NA	Intergenic	CpG	6160	NM_153150	13358	Mm.229291	NM_153150	ENSMUSG00000003528	Slc25a1	1300019P08Rik|2610100G11Rik|AI194714|Ctp|Dgsj|Slc20a3	solute carrier family 25 (mitochondrial carrier, citrate transporter), member 1	protein-coding
mm_865.1	chr1	52150849	52150858	+	1	NA	intron (NM_001205313, intron 19 of 24)	intron (NM_001205313, intron 19 of 24)	31231	NM_001205313	20846	Mm.277406	NM_009283	ENSMUSG00000026104	Stat1	2010005J02Rik|AA408197	signal transducer and activator of transcription 1	protein-coding
mm_90603.1	chr10	128322576	128322595	+	1	NA	5' UTR (NM_019953, exon 1 of 6)	5' UTR (NM_019953, exon 1 of 6)	126	NM_019953	56530	Mm.44220	NM_019953	ENSMUSG00000025381	Cnpy2	5330432A10Rik|AW229003|D10Bwg1546e|Tmem4|Zsig9	canopy FGF signaling regulator 2	protein-coding
mm_23877.1	chr3	83030831	83030845	+	1	NA	exon (NM_010196, exon 5 of 5)	exon (NM_010196, exon 5 of 5)	4685	NM_001111048	14161	Mm.88793	NM_010196	ENSMUSG00000028001	Fga	ENSMUSG00000059807|Fib	fibrinogen alpha chain	protein-coding
mm_140383.1	chr17	87119253	87119263	+	1	NA	intron (NM_019654, intron 1 of 2)	L1M5|LINE|L1	11579	NM_019654	56468	Mm.126885	NM_019654	ENSMUSG00000037104	Socs5	1810018L08Rik|Cish5|mKIAA0671	suppressor of cytokine signaling 5	protein-coding
mm_119549.1	chr14	48538348	48538367	+	1	NA	Intergenic	Intergenic	92005	NR_132324	218989	Mm.85211	NM_172600	ENSMUSG00000036339	Tmem260	5930435P15|6720456H20Rik	transmembrane protein 260	protein-coding
mm_121059.1	chr14	87416727	87416745	+	1	NA	5' UTR (NM_001253755, exon 1 of 12)	5' UTR (NM_001253755, exon 1 of 12)	153	NM_001253755	219249	Mm.35168	NM_172605	ENSMUSG00000022019	Tdrd3	4732418C03Rik|6720468N18	tudor domain containing 3	protein-coding
mm_58499.1	chr7	3705026	3705042	+	1	NA	intron (NM_029767, intron 3 of 4)	Lx2|LINE|L1	993	NM_029767	76846	Mm.13944	NM_029767	ENSMUSG00000006333	Rps9	3010033P07Rik|AL022771|AL022885	ribosomal protein S9	protein-coding
mm_92137.1	chr10	66911404	66911434	-	1	NA	TTS (NR_138560)	TTS (NR_138560)	8965	NR_138560	68488	Mm.338835	NR_138560		1110002J07Rik	-	RIKEN cDNA 1110002J07 gene	ncRNA
mm_109777.1	chr12	119136015	119136018	+	1	NA	Intergenic	Intergenic	102260	NM_177290	320910	Mm.217000	NM_177290	ENSMUSG00000025321	Itgb8	4832412O06Rik	integrin beta 8	protein-coding
mm_172607.1	chr8	15520047	15520060	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	462400	NM_008664	17930	Mm.272115	NM_008664	ENSMUSG00000031461	Myom2	AW146149	myomesin 2	protein-coding
mm_38008.1	chr4	133723160	133723163	-	1	NA	intron (NM_001080819, intron 1 of 19)	intron (NM_001080819, intron 1 of 19)	-6053	NR_106086	102465707		NR_106086	ENSMUSG00000104566	Mir7227	mmu-mir-7227	microRNA 7227	ncRNA
mm_94027.1	chr10	127751674	127751684	-	1	NA	5' UTR (NM_007412, exon 1 of 2)	5' UTR (NM_007412, exon 1 of 2)	119	NM_007412	11536	Mm.2857	NM_007412	ENSMUSG00000058396	Gpr182	AM-R|Admr|G10-D|Gpcr17|Gpcr22|MB10|NOW	G protein-coupled receptor 182	protein-coding
mm_115645.1	chr13	12278910	12278932	-	1	NA	exon (NM_033268, exon 15 of 21)	exon (NM_033268, exon 15 of 21)	-20808	NM_001081128	238505	Mm.40335	NM_001081128	ENSMUSG00000021311	Mtr	AI894170|D830038K18Rik|MS	5-methyltetrahydrofolate-homocysteine methyltransferase	protein-coding
mm_167462.1	chr8	123891792	123891799	-	1	NA	TTS (NM_009606)	TTS (NM_009606)	2980	NM_001272041	11459	Mm.214950	NM_009606	ENSMUSG00000031972	Acta1	AA959943|Acta-2|Acts|Actsk-1	actin, alpha 1, skeletal muscle	protein-coding
mm_93621.1	chr10	117277837	117277863	-	1	NA	3' UTR (NM_017372, exon 4 of 4)	3' UTR (NM_017372, exon 4 of 4)	4422	NM_017372	17105	Mm.45436	NM_017372	ENSMUSG00000069516	Lyz2	AI326280|Lys|Lysm|Lyzf2|Lyzs|Lzm|Lzm-s1|Lzp	lysozyme 2	protein-coding
mm_61304.1	chr7	67952005	67952065	+	1	NA	promoter-TSS (NM_010513)	promoter-TSS (NM_010513)	-222	NM_010513	16001	Mm.275742	NM_010513	ENSMUSG00000005533	Igf1r	A330103N21Rik|CD221|D930020L01|IGF-1R|hyft	insulin-like growth factor I receptor	protein-coding
mm_66040.1	chr7	30660251	30660263	-	1	NA	intron (NM_027999, intron 7 of 18)	intron (NM_027999, intron 7 of 18)	4737	NM_027999	71909	Mm.290410	NM_027999	ENSMUSG00000078762	Haus5	2310022K01Rik	HAUS augmin-like complex, subunit 5	protein-coding
mm_142853.1	chr17	51812046	51812057	-	1	NA	promoter-TSS (NM_001163630)	promoter-TSS (NM_001163630)	3	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_169818.1	chr16	21119234	21119239	-	1	NA	Intergenic	BGLII_B|LTR|ERVK	34708	NM_025634	66561	Mm.422867	NM_025634	ENSMUSG00000090356	Teddm3	2310042E22Rik	transmembrane epididymal family member 3	protein-coding
mm_73246.1	chr8	104250961	104250971	+	1	NA	non-coding (NR_104433, exon 1 of 5)	non-coding (NR_104433, exon 1 of 5)	105	NM_001286383	75458	Mm.269219	NM_029295	ENSMUSG00000054400	Cklf	1700001C14Rik|1810018M11Rik|A730028G07Rik|C32|CKLF1|CKLF3|CKLF4|CKLF5|Cklf2|Cklf6|HSPC224|UCK-1	chemokine-like factor	protein-coding
mm_124146.1	chr14	88350427	88350429	-	1	NA	Intergenic	Intergenic	120968	NM_178685	219257	Mm.128861	NM_178685	ENSMUSG00000050505	Pcdh20	C630015B17Rik|Pcdh13	protocadherin 20	protein-coding
mm_68552.1	chr7	114415038	114415061	-	1	NA	promoter-TSS (NM_011055)	promoter-TSS (NM_011055)	112	NR_029437	71045	Mm.235682	NR_029437	ENSMUSG00000087475	4933406I18Rik	4933403D24Rik	RIKEN cDNA 4933406I18 gene	ncRNA
mm_50263.1	chr6	43598215	43598220	+	1	NA	intron (NM_001311111, intron 3 of 7)	L1VL4|LINE|L1	68061	NM_001311111	29807	Mm.320979	NM_013861	ENSMUSG00000029735	Tpk1	-	thiamine pyrophosphokinase	protein-coding
mm_160600.1	chr9	76545722	76545722	-	1	NA	promoter-TSS (NM_001045518)	promoter-TSS (NM_001045518)	82	NM_001045518	208994	Mm.256929	NM_001045518	ENSMUSG00000032358	Fam83b	C530008M07Rik|Gm516	family with sequence similarity 83, member B	protein-coding
mm_166005.1	chr4	116686166	116686189	+	1	NA	promoter-TSS (NR_040442)	promoter-TSS (NR_040442)	-155	NR_040442	100502959	Mm.395400	NR_040442		AV051173	-	expressed sequence AV051173	ncRNA
mm_132466.1	chr16	36633294	36633331	+	1	NA	intron (NM_019388, intron 1 of 7)	intron (NM_019388, intron 1 of 7)	32765	NM_019388	12524	Mm.1452	NM_019388	ENSMUSG00000022901	Cd86	B7|B7-2|B7.2|B70|CLS1|Cd28l2|ETC-1|Ly-58|Ly58|MB7|MB7-2|TS/A-2	CD86 antigen	protein-coding
mm_70473.1	chr8	12385752	12385766	+	1	NA	promoter-TSS (NR_027975)	promoter-TSS (NR_027975)	-12	NR_027975	434280	Mm.447484	NM_001013812	ENSMUSG00000047935	Gm5607	EG434280	predicted gene 5607	ncRNA
mm_144349.1	chr18	15195267	15195277	+	1	NA	Intergenic	Intergenic	-43826	NM_134112	106931	Mm.329299	NM_134112	ENSMUSG00000036225	Kctd1	4933402K10Rik|AI661543|AW553000	potassium channel tetramerisation domain containing 1	protein-coding
mm_23052.1	chr3	35722086	35722096	+	1	NA	Intergenic	Intergenic	-32047	NM_029570	76295	Mm.239416	NM_029570	ENSMUSG00000037400	Atp11b	1110019I14Rik|ATPIF|ATPIR|mKIAA0956	ATPase, class VI, type 11B	protein-coding
mm_74311.1	chr8	126594794	126594822	+	1	NA	Intergenic	CpG-14677	-1372	NM_001164598	270110	Mm.334918	NM_001164598	ENSMUSG00000051495	Irf2bp2	E130305N23Rik|IRF-2BP2	interferon regulatory factor 2 binding protein 2	protein-coding
mm_68734.1	chr7	120880910	120880911	-	1	NA	intron (NM_007908, intron 6 of 17)	ORR1A2|LTR|ERVL-MaLR	29721	NM_001267711	13631	Mm.25997	NM_007908	ENSMUSG00000035064	Eef2k	C86191|eEF-2K	eukaryotic elongation factor-2 kinase	protein-coding
mm_11408.1	chr2	31518707	31518741	+	1	NA	intron (NR_002687, intron 14 of 15)	intron (NR_002687, intron 14 of 15)	48416	NR_002687	432466	Mm.333323	NR_002687	ENSMUSG00000046687	Gm5424	EG432466	argininosuccinate synthase pseudogene	pseudo
mm_154798.1	chrX	13284171	13284192	+	1	NA	exon (NM_010028, exon 2 of 17)	exon (NM_010028, exon 2 of 17)	3159	NM_010028	13205	Mm.289662	NM_010028	ENSMUSG00000000787	Ddx3x	D1Pas1-rs2|Ddx3|Fin14	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 3, X-linked	protein-coding
mm_60014.1	chr7	30751527	30751543	+	1	NA	promoter-TSS (NM_172205)	promoter-TSS (NM_172205)	64	NM_001083903	282619	Mm.250717	NM_172205	ENSMUSG00000046056	Sbsn	1110005D19Rik|AI747508	suprabasin	protein-coding
mm_142983.1	chr17	56276719	56276749	-	1	NA	promoter-TSS (NM_174989)	promoter-TSS (NM_174989)	33	NM_174989	106759	Mm.203952	NM_174989	ENSMUSG00000047123	Ticam1	AW046014|AW547018|TICAM-1|TRIF	toll-like receptor adaptor molecule 1	protein-coding
mm_72133.1	chr8	71882061	71882120	+	1	NA	promoter-TSS (NM_145624)	promoter-TSS (NM_145624)	22	NM_145624	236193	Mm.290790	NM_145624	ENSMUSG00000056019	Zfp709	BC021921|GIOT-4|HIT-40	zinc finger protein 709	protein-coding
mm_81444.1	chr9	109812220	109812230	+	1	NA	Intergenic	Intergenic	-4402	NM_183136	78709	Mm.99613	NM_183136	ENSMUSG00000050074	Spink8	C630041L24Rik	serine peptidase inhibitor, Kazal type 8	protein-coding
mm_106301.1	chr11	118248591	118248607	-	1	NA	promoter-TSS (NM_011180)	promoter-TSS (NM_011180)	-7	NM_011180	19157	Mm.86413	NM_011180	ENSMUSG00000017132	Cyth1	CLM1|CTH-1|CYTIP|Pscd1	cytohesin 1	protein-coding
mm_110189.1	chr12	27340185	27340197	-	1	NA	3' UTR (NM_009234, exon 1 of 1)	3' UTR (NM_009234, exon 1 of 1)	2527	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding
mm_55376.1	chr6	58780512	58780526	-	1	NA	Intergenic	MTD-int|LTR|ERVL-MaLR	-53181	NM_028705	73998	Mm.191892	NM_028705	ENSMUSG00000029804	Herc3	5730409F18Rik|AI646603|mKIAA0032	hect domain and RLD 3	protein-coding
mm_69177.1	chr7	127218468	127218478	-	1	NA	promoter-TSS (NM_017461)	promoter-TSS (NM_017461)	-28	NM_017461	54204	Mm.18	NM_017461	ENSMUSG00000000486	Sept1	Diff6|Pnutl3	septin 1	protein-coding
mm_11857.1	chr2	48627463	48627470	+	1	NA	Intergenic	Intergenic	-186643	NM_007396	11480	Mm.314338	NM_007396	ENSMUSG00000052155	Acvr2a	ActrIIa|Acvr2|TactrII	activin receptor IIA	protein-coding
mm_24572.1	chr3	93444593	93444602	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	2267	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_88390.1	chr10	76481051	76481094	+	1	NA	exon (NM_019434, exon 7 of 29)	exon (NM_019434, exon 7 of 29)	-11958	NM_172550	216119	Mm.344778	NM_172550	ENSMUSG00000033126	Ybey	1110068N23Rik|A130042E20Rik|C21orf57|ORF57|ORF66	ybeY metallopeptidase	protein-coding
mm_109822.1	chr12	3862205	3862220	-	1	NA	promoter-TSS (NR_045884)	promoter-TSS (NR_045884)	32	NR_045884	100038522	Mm.417270	NR_045884	ENSMUSG00000073242	Dnmt3aos	ENSMUSG00000073242|Gm10485	DNA methyltransferase 3A, opposite strand	ncRNA
mm_163807.1	chr14	19416100	19416122	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	186476	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_138235.1	chr17	34399534	34399538	+	1	NA	intron (NM_001001177, intron 1 of 19)	RMER21A|LTR|ERV1	716	NM_001163855	407788	Mm.73205	NM_001001177	ENSMUSG00000057246	BC051142	NG8|TSBP|Tesb|Tesbp	cDNA sequence BC051142	protein-coding
mm_70694.1	chr8	15027300	15027349	+	1	NA	5' UTR (NM_029116, exon 2 of 2)	5' UTR (NM_029116, exon 2 of 2)	16299	NM_029116	74901	Mm.46675	NM_029116	ENSMUSG00000055675	Kbtbd11	2900016B01Rik|4930465M17Rik|mKIAA0711	kelch repeat and BTB (POZ) domain containing 11	protein-coding
mm_18686.1	chr2	71389056	71389073	-	1	NA	promoter-TSS (NM_026115)	promoter-TSS (NM_026115)	-196	NM_026115	107435	Mm.272472	NM_026115	ENSMUSG00000027018	Hat1	2410071B14Rik|AA536933|Hat-1|KAT1	histone aminotransferase 1	protein-coding
mm_157032.1	chrX	7947665	7947674	-	1	NA	5' UTR (NM_010413, exon 1 of 29)	5' UTR (NM_010413, exon 1 of 29)	220	NM_001130416	15185	Mm.29854	NM_010413	ENSMUSG00000031161	Hdac6	Hd6|Hdac5|Sfc6|mHDA2	histone deacetylase 6	protein-coding
mm_62779.1	chr7	112427026	112427038	+	1	NA	promoter-TSS (NM_020606)	promoter-TSS (NM_020606)	-674	NM_020606	57342	Mm.143763	NM_020606	ENSMUSG00000030770	Parva	2010012A22Rik|5430400F08Rik|AI225929|AU042898|Actp|CH-ILKBP|Parvin	parvin, alpha	protein-coding
mm_137734.1	chr17	29319184	29319203	+	1	NA	5' UTR (NM_023734, exon 1 of 7)	5' UTR (NM_023734, exon 1 of 7)	311	NM_023734	74116	Mm.30950	NM_023734	ENSMUSG00000024011	Pi16	1200009H11Rik|Cripi|PI-16	peptidase inhibitor 16	protein-coding
mm_104440.1	chr11	94976333	94976339	-	1	NA	promoter-TSS (NM_009161)	promoter-TSS (NM_009161)	-9	NM_009161	20391	Mm.18709	NM_009161	ENSMUSG00000001508	Sgca	50DAG|Asg	sarcoglycan, alpha (dystrophin-associated glycoprotein)	protein-coding
mm_121963.1	chr14	25460326	25460341	-	1	NA	intron (NM_001310666, intron 1 of 23)	CpG	1148	NM_183208	328365	Mm.227484	NM_183208	ENSMUSG00000007817	Zmiz1	BC065120|E330020C23|ENSMUSG00000072684|Gm10397|I920194n01|Rai17|Zimp10	zinc finger, MIZ-type containing 1	protein-coding
mm_50798.1	chr6	54267152	54267180	+	1	NA	intron (NM_001311133, intron 1 of 7)	intron (NM_001311133, intron 1 of 7)	-1990	NM_001311134	69993	Mm.321147	NM_023543	ENSMUSG00000004633	Chn2	1700026N20Rik|4930557O16Rik|ARHGAP3|Bch	chimerin 2	protein-coding
mm_84158.1	chr9	59539920	59539988	-	1	NA	exon (NM_010421, exon 1 of 14)	exon (NM_010421, exon 1 of 14)	414	NM_010421	15211	Mm.2284	NM_010421	ENSMUSG00000025232	Hexa	Hex-1	hexosaminidase A	protein-coding
mm_118334.1	chr13	113881080	113881091	-	1	NA	intron (NM_172595, intron 1 of 4)	intron (NM_172595, intron 1 of 4)	86577	NM_172595	218639	Mm.79837	NM_172595	ENSMUSG00000042348	Arl15	A430036I03|Arfrp2|C230032K13Rik	ADP-ribosylation factor-like 15	protein-coding
mm_143001.1	chr17	56422703	56422737	-	1	NA	intron (NM_001252455, intron 14 of 27)	intron (NM_001252455, intron 14 of 27)	-3811	NR_105943	102465590		NR_105943	ENSMUSG00000098339	Mir6977	Gm27922|mmu-mir-6977	microRNA 6977	ncRNA
mm_34644.1	chr4	150710873	150710876	+	1	NA	Intergenic	Intergenic	-58700	NM_173774	242773	Mm.29280	NM_173774	ENSMUSG00000039838	Slc45a1	C230078B22|Dnb5	solute carrier family 45, member 1	protein-coding
mm_159626.1	chr4	136423505	136423505	+	1	NA	promoter-TSS (NM_001285482)	promoter-TSS (NM_001285482)	-19	NM_001285482	15552	Mm.40573	NM_008309	ENSMUSG00000070687	Htr1d	5-HT-1D|5-HT1D|AI853647|Gpcr14|Htr1db	5-hydroxytryptamine (serotonin) receptor 1D	protein-coding
mm_61393.1	chr7	73185767	73185775	+	1	NA	Intergenic	Intergenic	-83703	NR_046024	625243	Mm.261798	NR_046024	ENSMUSG00000108383	Gm6567	-	predicted gene 6567	ncRNA
mm_38544.1	chr4	141599869	141599906	-	1	NA	promoter-TSS (NM_001163256)	promoter-TSS (NM_001163256)	37	NM_001163256	74202	Mm.490327	NM_133754	ENSMUSG00000006219	Fblim1	2410043F08Rik|Cal|Fblp1|Gt10|migfilin|migfilin(s)	filamin binding LIM protein 1	protein-coding
mm_80780.1	chr9	95637653	95637656	+	1	NA	promoter-TSS (NM_029620)	promoter-TSS (NM_029620)	26	NM_029620	76477	Mm.46016	NM_029620	ENSMUSG00000015354	Pcolce2	2400001O18Rik|Pcpe2	procollagen C-endopeptidase enhancer 2	protein-coding
mm_14225.1	chr2	127365363	127365366	+	1	NA	3' UTR (NM_009633, exon 1 of 1)	3' UTR (NM_009633, exon 1 of 1)	2078	NM_009633	11552	Mm.347390	NM_009633	ENSMUSG00000058620	Adra2b	Adra-2b|[a]2B|a2b-AR|alpha2-C2|alpha2B	adrenergic receptor, alpha 2b	protein-coding
mm_171257.1	chr3	81712293	81712297	-	1	NA	Intergenic	L1Md_T|LINE|L1	-89730	NR_138586	320566	Mm.208417	NR_138586	ENSMUSG00000103695	A830029E22Rik	-	RIKEN cDNA A830029E22 gene	ncRNA
mm_95380.1	chr11	49098775	49098804	+	1	NA	intron (NM_010999, intron 2 of 5)	intron (NM_010999, intron 2 of 5)	11772	NM_008330	15953	Mm.24769	NM_008330	ENSMUSG00000078920	Ifi47	47kDa|IRG-47|Ifggc1|Igrd|Iigp4|Iipg4|Irgd	interferon gamma inducible protein 47	protein-coding
mm_59466.1	chr7	27258762	27258815	+	1	NA	promoter-TSS (NM_010950)	promoter-TSS (NM_010950)	27	NM_010950	18223	Mm.458153	NM_010950	ENSMUSG00000063160	Numbl	nbl	numb-like	protein-coding
mm_22645.1	chr3	14866802	14866844	+	1	NA	exon (NM_007606, exon 3 of 7)	exon (NM_007606, exon 3 of 7)	3285	NM_007606	12350	Mm.300	NM_007606	ENSMUSG00000027559	Car3	BB219044|Ca3|Car-3	carbonic anhydrase 3	protein-coding
mm_15228.1	chr2	154548890	154548932	+	1	NA	promoter-TSS (NM_029305)	promoter-TSS (NM_029305)	7	NM_029305	75480	Mm.440434	NM_029305	ENSMUSG00000038523	1700003F12Rik	-	RIKEN cDNA 1700003F12 gene	protein-coding
mm_70813.1	chr8	23085576	23085591	+	1	NA	exon (NM_031158, exon 5 of 45)	exon (NM_031158, exon 5 of 45)	27324	NR_102385	11733	Mm.334444	NM_031158	ENSMUSG00000031543	Ank1	Ank-1|nb|pale	ankyrin 1, erythroid	protein-coding
mm_152876.1	chr19	24518348	24518361	-	1	NA	intron (NM_008846, intron 1 of 14)	(TG)n|Simple_repeat|Simple_repeat	37473	NM_008846	18719	Mm.217214	NM_008846	ENSMUSG00000024867	Pip5k1b	PI4P5K-I[b]|PIP5K1-beta|PIP5KIbeta|Pipk5b|STM7	phosphatidylinositol-4-phosphate 5-kinase, type 1 beta	protein-coding
mm_135269.1	chr16	38394298	38394332	-	1	NA	Intergenic	Intergenic	32125	NM_022318	64082	Mm.390856	NM_022318	ENSMUSG00000022803	Popdc2	AV006127|Pop2	popeye domain containing 2	protein-coding
mm_103339.1	chr11	74699693	74699696	-	1	NA	intron (NM_013625, intron 1 of 10)	intron (NM_013625, intron 1 of 10)	24164	NR_037610	18472	Mm.397111	NM_013625	ENSMUSG00000020745	Pafah1b1	LIS-1|Lis1|MMS10-U|Mdsh|Ms10u|Pafaha	platelet-activating factor acetylhydrolase, isoform 1b, subunit 1	protein-coding
mm_92800.1	chr10	81358912	81358935	-	1	NA	intron (NM_028657, intron 1 of 9)	intron (NM_028657, intron 1 of 9)	1353	NM_028657	73822	Mm.182281	NM_028657	ENSMUSG00000034854	Mfsd12	C19orf28|F630110N24Rik|Wdt1	major facilitator superfamily domain containing 12	protein-coding
mm_168455.1	chr11	41380881	41380882	+	1	NA	Intergenic	Intergenic	619833	NM_177408	14406	Mm.5309	NM_008073	ENSMUSG00000020436	Gabrg2	GABAA-R|Gabrg-2|gamma2	gamma-aminobutyric acid (GABA) A receptor, subunit gamma 2	protein-coding
mm_135744.1	chr16	55895325	55895338	-	1	NA	promoter-TSS (NM_001134457)	promoter-TSS (NM_001134457)	-52	NM_001134457	385658	Mm.310635	NM_001134457	ENSMUSG00000075033	Nxpe3	Fam55c|Gm1752|Gm611	neurexophilin and PC-esterase domain family, member 3	protein-coding
mm_2618.1	chr1	120492034	120492067	+	1	NA	exon (NM_010766, exon 5 of 17)	exon (NM_010766, exon 5 of 17)	13034	NM_010766	17167	Mm.1856	NM_010766	ENSMUSG00000026390	Marco	AI323439|Ly112|Scara2	macrophage receptor with collagenous structure	protein-coding
mm_49709.1	chr6	34415417	34415425	+	1	NA	exon (NM_009731, exon 2 of 10)	exon (NM_009731, exon 2 of 10)	3059	NM_009731	11997	Mm.482073	NM_009731	ENSMUSG00000052131	Akr1b7	AR|Avdp|MVDP	aldo-keto reductase family 1, member B7	protein-coding
mm_11349.1	chr2	30845362	30845396	+	1	NA	promoter-TSS (NM_009116)	promoter-TSS (NM_009116)	12	NM_009116	20204	Mm.1802	NM_009116	ENSMUSG00000039476	Prrx2	Prx2|S8	paired related homeobox 2	protein-coding
mm_115480.1	chr13	3170798	3170804	-	1	NA	intron (NR_001581, intron 3 of 4)	Lx2A1|LINE|L1	21326	NR_001581	73266	Mm.335891	NR_001581		Speer6-ps1	1700039A02Rik|SPEER-6	spermatogenesis associated glutamate (E)-rich protein 6, pseudogene 1	pseudo
mm_37105.1	chr4	116637518	116637521	-	1	NA	intron (NM_021473, intron 8 of 8)	PB1D9|SINE|Alu	-9568	NM_016777	50927	Mm.257181	NM_016777	ENSMUSG00000028693	Nasp	5033430J04Rik|AI131596|AI317140|D4Ertd767e|Epcs32|Nasp-T	nuclear autoantigenic sperm protein (histone-binding)	protein-coding
mm_89388.1	chr10	89785838	89785841	+	1	NA	intron (NM_029166, intron 7 of 20)	MusHAL1|LINE|L1	40848	NM_029166	75089	Mm.268922	NM_029166	ENSMUSG00000019951	Uhrf1bp1l	2010319N22Rik|4930506D01Rik|AA589495|C80672|E030041M21Rik|mKIAA0701	UHRF1 (ICBP90) binding protein 1-like	protein-coding
mm_43025.1	chr5	123909091	123909108	+	1	NA	intron (NM_026603, intron 2 of 7)	B4A|SINE|B4	1824	NM_026603	68184	Mm.28549	NM_026603	ENSMUSG00000023106	Denr	1500003K04Rik	density-regulated protein	protein-coding
mm_32413.1	chr4	107036115	107036125	+	1	NA	intron (NM_023672, intron 9 of 17)	intron (NM_023672, intron 9 of 17)	30746	NM_025500	56280	Mm.29517	NM_025500	ENSMUSG00000028622	Mrpl37	2300004O14Rik|AI132596|MRP-L2|Rpml2	mitochondrial ribosomal protein L37	protein-coding
mm_85983.1	chr9	112179319	112179322	-	1	NA	TTS (NM_001177620)	TTS (NM_001177620)	6629	NM_001177618	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_80236.1	chr9	72686059	72686075	+	1	NA	exon (NM_010890, exon 6 of 29)	exon (NM_010890, exon 6 of 29)	23720	NM_010890	17999	Mm.279923	NM_010890	ENSMUSG00000032216	Nedd4	AA959633|AL023035|AU019897|E430025J12Rik|Nedd4-1|Nedd4a|mKIAA0093	neural precursor cell expressed, developmentally down-regulated 4	protein-coding
mm_20302.1	chr2	127141201	127141246	-	1	NA	exon (NM_001163528, exon 2 of 2)	exon (NM_001163528, exon 2 of 2)	1367	NM_001163528	73338	Mm.57559	NM_001163527	ENSMUSG00000074825	Itpripl1	1700041B20Rik	inositol 1,4,5-triphosphate receptor interacting protein-like 1	protein-coding
mm_3054.1	chr1	134061137	134061150	+	1	NA	Intergenic	Intergenic	18012	NM_007570	12227	Mm.392646	NM_007570	ENSMUSG00000020423	Btg2	AA959598|APRO1|Pc3|TIS21	B cell translocation gene 2, anti-proliferative	protein-coding
mm_127818.1	chr15	5108446	5108459	-	1	NA	promoter-TSS (NM_001163138)	promoter-TSS (NM_001163138)	81	NM_001163138	239319	Mm.31252	NM_001163138	ENSMUSG00000041849	Card6	D730008L15	caspase recruitment domain family, member 6	protein-coding
mm_81052.1	chr9	105658403	105658426	+	1	NA	intron (NM_001081309, intron 6 of 19)	intron (NM_001081309, intron 6 of 19)	15419	NM_001081309	75669	Mm.274830	NM_029380	ENSMUSG00000032571	Pik3r4	2210010O15Rik|C730038E05Rik|C85833|D9Ertd418e	phosphatidylinositol 3 kinase, regulatory subunit, polypeptide 4, p150	protein-coding
mm_59137.1	chr7	24112352	24112396	+	1	NA	promoter-TSS (NM_021307)	promoter-TSS (NM_021307)	54	NM_021307	57745	Mm.82678	NM_021307	ENSMUSG00000052675	Zfp112	Znf112|Znf228	zinc finger protein 112	protein-coding
mm_152731.1	chr19	18936392	18936428	-	1	NA	3' UTR (NM_001289921, exon 11 of 11)	3' UTR (NM_001289921, exon 11 of 11)	64707	NM_146095	225998	Mm.234641	NM_146095	ENSMUSG00000036192	Rorb	Nr1f2|RZR-beta|RZRB|Rorbeta|hstp	RAR-related orphan receptor beta	protein-coding
mm_34835.1	chr4	155250190	155250201	+	1	NA	non-coding (NR_033802, exon 1 of 3)	non-coding (NR_033802, exon 1 of 3)	229	NR_033802	67513	Mm.10374	NM_001190445	ENSMUSG00000073684	Faap20	2610002J02Rik	Fanconi anemia core complex associated protein 20	protein-coding
mm_79050.1	chr9	46229111	46229154	+	1	NA	exon (NM_009692, exon 3 of 4)	exon (NM_009692, exon 3 of 4)	502	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2|apo-AI|apoA-I	apolipoprotein A-I	protein-coding
mm_73332.1	chr8	105300396	105300446	+	1	NA	exon (NM_148952, exon 6 of 10)	exon (NM_148952, exon 6 of 10)	2758	NM_148952	104394	Mm.34554	NM_148952	ENSMUSG00000014859	E2f4	2010111M04Rik|AI427446	E2F transcription factor 4	protein-coding
mm_157619.1	chrX	56549597	56549605	-	1	NA	promoter-TSS (NM_001033372)	promoter-TSS (NM_001033372)	5	NM_001033372	270599	Mm.424438	NM_001033372	ENSMUSG00000064016	Gm648	-	predicted gene 648	protein-coding
mm_106567.1	chr11	120643290	120643302	-	1	NA	5' UTR (NM_144795, exon 1 of 8)	5' UTR (NM_144795, exon 1 of 8)	374	NM_144795	209027	Mm.127731	NM_144795	ENSMUSG00000025140	Pycr1	-	pyrroline-5-carboxylate reductase 1	protein-coding
mm_6329.1	chr1	71619478	71619497	-	1	NA	exon (NM_001276413, exon 22 of 44)	exon (NM_001276413, exon 22 of 44)	33747	NM_010233	14268	Mm.193099	NM_010233	ENSMUSG00000026193	Fn1	E330027I09|Fn|Fn-1	fibronectin 1	protein-coding
mm_100272.1	chr11	117762216	117762220	+	1	NA	3' UTR (NM_198022, exon 22 of 22)	3' UTR (NM_198022, exon 22 of 22)	18403	NM_181321	217353	Mm.286963	NM_145439	ENSMUSG00000025572	Tmc6	D11Ertd204e|EVER1	transmembrane channel-like gene family 6	protein-coding
mm_125710.1	chr15	68403754	68403755	+	1	NA	Intergenic	RMER19B|LTR|ERVK	-62465	NR_029718	387228		NR_029718	ENSMUSG00000065437	Mir30d	Mirn30d|mir-30d|mmu-mir-30d	microRNA 30d	ncRNA
mm_161611.1	chr16	45736783	45736783	-	1	NA	intron (NR_073572, intron 3 of 4)	intron (NR_073572, intron 3 of 4)	6172	NM_001272070	213012	Mm.247453	NM_172511	ENSMUSG00000033157	Abhd10	-	abhydrolase domain containing 10	protein-coding
mm_125996.1	chr15	76380493	76380542	+	1	NA	promoter-TSS (NM_175457)	promoter-TSS (NM_175457)	4	NM_175457	223658	Mm.123240	NM_175457	ENSMUSG00000022558	Mroh1	D330001F17Rik|Heatr7a	maestro heat-like repeat family member 1	protein-coding
mm_167695.1	chr9	88274073	88274109	-	1	NA	Intergenic	Intergenic	-53518	NM_011851	23959	Mm.244235	NM_011851	ENSMUSG00000032420	Nt5e	2210401F01Rik|5'-NT|AI447961|CD73|NT|Nt5|eNT	5' nucleotidase, ecto	protein-coding
mm_117168.1	chr13	62867366	62867385	-	1	NA	exon (NM_019395, exon 6 of 7)	exon (NM_019395, exon 6 of 7)	-9005	NM_007994	14120	Mm.391871	NM_007994	ENSMUSG00000021456	Fbp2	Fbp-1|Fbp1|Rae-30	fructose bisphosphatase 2	protein-coding
mm_150633.1	chr19	41482633	41482688	+	1	NA	Intergenic	GC_rich|Low_complexity|Low_complexity	-42592	NM_001326287	627352	Mm.395111	NM_001326287		Morf4l1b	EG627352|Gm6747	mortality factor 4 like 1B	protein-coding
mm_117912.1	chr13	99431036	99431053	-	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-18218	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_33865.1	chr4	135932352	135932355	+	1	NA	intron (NM_024243, intron 4 of 7)	intron (NM_024243, intron 4 of 7)	11627	NM_024243	71665	Mm.439940	NM_024243	ENSMUSG00000028673	Fuca1	0610006A03Rik|9530055J05Rik|Afuc|Fuca	fucosidase, alpha-L- 1, tissue	protein-coding
mm_26400.1	chr3	142603576	142603623	+	1	NA	exon (NM_010259, exon 5 of 11)	exon (NM_010259, exon 5 of 11)	8752	NM_010259	14468	Mm.457978	NM_010259	ENSMUSG00000040264	Gbp2b	Gbp-1|Gbp1|Mag-1|Mpa-1|Mpa1	guanylate binding protein 2b	protein-coding
mm_9493.1	chr1	173729570	173729582	-	1	NA	exon (NM_001204910, exon 5 of 8)	exon (NM_001204910, exon 5 of 8)	12233	NM_001204910	226691	Mm.440876	NM_001204910	ENSMUSG00000073490	Ifi207	AI607873|Pyhin-A	interferon activated gene 207	protein-coding
mm_153780.1	chr19	45783501	45783511	-	1	NA	promoter-TSS (NM_023799)	promoter-TSS (NM_023799)	-215	NM_023799	76055	Mm.122725	NM_023799	ENSMUSG00000025220	Mgea5	2810009A20Rik|4833427O07Rik|5830447M11Rik|AA408215|Hy5|Ncoat|OGA|mKIAA0679	meningioma expressed antigen 5 (hyaluronidase)	protein-coding
mm_151776.1	chr19	5307509	5307528	-	1	NA	exon (NM_001024717, exon 3 of 3)	exon (NM_001024717, exon 3 of 3)	9187	NM_001024717	545276	Mm.447174	NM_001024717	ENSMUSG00000047658	Gal3st3	-	galactose-3-O-sulfotransferase 3	protein-coding
mm_128843.1	chr15	70791381	70791384	-	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	867149	NR_045071	100503580	Mm.404646	NR_045071		Gm19782	-	predicted gene, 19782	ncRNA
mm_126562.1	chr15	82169964	82169976	+	1	NA	exon (NM_033218, exon 2 of 19)	exon (NM_033218, exon 2 of 19)	22701	NM_033218	20788	Mm.9002	NM_033218	ENSMUSG00000022463	Srebf2	AI608257|SREBP-2|SREBP2|SREBP2gc|bHLHd2|lop13|nuc	sterol regulatory element binding factor 2	protein-coding
mm_24332.1	chr3	89520153	89520175	+	1	NA	promoter-TSS (NM_080466)	promoter-TSS (NM_080466)	0	NM_080466	140493	Mm.120250	NM_080466	ENSMUSG00000000794	Kcnn3	KCa2.3|SK3|SKCA3	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3	protein-coding
mm_147982.1	chr18	67555310	67555315	-	1	NA	Intergenic	RMER5|LTR|ERV1	-2591	NM_194355	68166	Mm.208723	NM_176832	ENSMUSG00000024533	Spire1	6030430B19Rik|AI415299|AU022898|AW550622|Spir-1	spire homolog 1 (Drosophila)	protein-coding
mm_63232.1	chr7	126470386	126470396	+	1	NA	intron (NR_110346, intron 4 of 9)	intron (NR_110346, intron 4 of 9)	2703	NR_110346	20399	Mm.8538	NM_011363	ENSMUSG00000030733	Sh2b1	AI425885|C530001K22Rik|Irip|Psm|SH2-B|SH2-Bb|Sh2bpsm1|mKIAA1299	SH2B adaptor protein 1	protein-coding
mm_21773.1	chr2	164846619	164846628	-	1	NA	exon (NM_011125, exon 10 of 16)	exon (NM_011125, exon 10 of 16)	11085	NM_011125	18830	Mm.6105	NM_011125	ENSMUSG00000017754	Pltp	Bpife|OD107	phospholipid transfer protein	protein-coding
mm_119709.1	chr14	53845264	53845276	+	1	NA	Intergenic	Intergenic	408659	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_14184.1	chr2	127080193	127080211	+	1	NA	intron (NM_026678, intron 1 of 7)	intron (NM_026678, intron 1 of 7)	9545	NM_026678	109778	Mm.22028	NM_026678	ENSMUSG00000001999	Blvra	0610006A11Rik|2500001N03Rik|Blvr	biliverdin reductase A	protein-coding
mm_83962.1	chr9	57148218	57148240	-	1	NA	Intergenic	Intergenic	-1195	NM_028347	72774	Mm.35749	NM_028347	ENSMUSG00000032298	Neil1	2810450N13Rik|Nei1	nei endonuclease VIII-like 1 (E. coli)	protein-coding
mm_37412.1	chr4	122859492	122859523	-	1	NA	TTS (NM_008917)	TTS (NM_008917)	23280	NM_008917	19063	Mm.277719	NM_008917	ENSMUSG00000028657	Ppt1	9530043G02Rik|AA960502|C77813|CLN1|D4Ertd184e|INCL|PPT	palmitoyl-protein thioesterase 1	protein-coding
mm_113146.1	chr13	24722587	24722588	+	1	NA	intron (NM_001286100, intron 20 of 22)	intron (NM_001286100, intron 20 of 22)	39350	NM_020567	57441	Mm.12239	NM_020567	ENSMUSG00000006715	Gmnn	AW546347|Gem	geminin	protein-coding
mm_92906.1	chr10	83533384	83533406	-	1	NA	intron (NM_153543, intron 1 of 22)	intron (NM_153543, intron 1 of 22)	745	NM_153543	216188	Mm.263138	NM_153543	ENSMUSG00000020256	Aldh1l2	D330038I09Rik|mtFDH	aldehyde dehydrogenase 1 family, member L2	protein-coding
mm_153967.1	chr19	47855293	47855328	-	1	NA	exon (NM_010362, exon 2 of 6)	exon (NM_010362, exon 2 of 6)	337	NM_010362	14873	Mm.378931	NM_010362	ENSMUSG00000025068	Gsto1	AA407097|AI194287|AU018802|Gsto-1|Gstx|Spg-r|p28	glutathione S-transferase omega 1	protein-coding
mm_26610.1	chr3	152253609	152253641	+	1	NA	intron (NM_199465, intron 2 of 12)	intron (NM_199465, intron 2 of 12)	12695	NM_199465	68810	Mm.200188	NM_199465	ENSMUSG00000039103	Nexn	1110046H09Rik|AA553326|NELIN	nexilin	protein-coding
mm_112694.1	chr13	17695030	17695040	+	1	NA	promoter-TSS (NM_138654)	promoter-TSS (NM_138654)	-270	NM_138654	192136	Mm.364180	NM_138654	ENSMUSG00000055137	Sugct	5033411D12Rik|D17907	succinyl-CoA glutarate-CoA transferase	protein-coding
mm_25159.1	chr3	103043624	103043646	+	1	NA	exon (NM_001310693, exon 6 of 18)	exon (NM_001310693, exon 6 of 18)	-14650	NM_010937	18176	Mm.400954	NM_010937	ENSMUSG00000027852	Nras	AV095280|N-ras	neuroblastoma ras oncogene	protein-coding
mm_108331.1	chr12	79969606	79969655	+	1	NA	Intergenic	Intergenic	-33366	NR_131074	77290	Mm.395042	NR_131073		9430078K24Rik	-	RIKEN cDNA 9430078K24 gene	ncRNA
mm_7049.1	chr1	87127387	87127391	-	1	NA	exon (NM_007432, exon 10 of 11)	exon (NM_007432, exon 10 of 11)	2381	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_121043.1	chr14	80022161	80022180	+	1	NA	TTS (NM_001030294)	TTS (NM_001030294)	21868	NM_001030294	380924	Mm.26456	NM_001030294	ENSMUSG00000022026	Olfm4	GC1|GW112|Gm296|Gm913|OlfD|pPD4	olfactomedin 4	protein-coding
mm_41456.1	chr5	90905831	90905839	+	1	NA	3' UTR (NM_009140, exon 4 of 4)	3' UTR (NM_009140, exon 4 of 4)	1936	NM_009140	20310	Mm.4979	NM_009140	ENSMUSG00000058427	Cxcl2	CINC-2a|GROb|Gro2|MIP-2|MIP-2a|Mgsa-b|Mip2|Scyb|Scyb2	chemokine (C-X-C motif) ligand 2	protein-coding
mm_10358.1	chr2	11690947	11691024	+	1	NA	3' UTR (NM_008367, exon 8 of 8)	3' UTR (NM_008367, exon 8 of 8)	-14308	NM_001271498	16169	Mm.200196	NM_008358	ENSMUSG00000023206	Il15ra	AA690181|IL-15RA	interleukin 15 receptor, alpha chain	protein-coding
mm_87785.1	chr10	60296913	60296927	+	1	NA	intron (NM_011179, intron 8 of 14)	intron (NM_011179, intron 8 of 14)	12459	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_6322.1	chr1	71606817	71606850	-	1	NA	exon (NM_001276413, exon 29 of 44)	exon (NM_001276413, exon 29 of 44)	46401	NM_010233	14268	Mm.193099	NM_010233	ENSMUSG00000026193	Fn1	E330027I09|Fn|Fn-1	fibronectin 1	protein-coding
mm_85157.1	chr9	96333260	96333277	-	1	NA	3' UTR (NM_007502, exon 7 of 7)	3' UTR (NM_007502, exon 7 of 7)	31031	NM_007502	11933	Mm.424	NM_007502	ENSMUSG00000032412	Atp1b3	AA409958|AI664000|AW212096	ATPase, Na+/K+ transporting, beta 3 polypeptide	protein-coding
mm_45137.1	chr5	48934186	48934189	-	1	NA	intron (NM_001199244, intron 1 of 7)	Lx3A|LINE|L1	-44630	NM_030265	80334	Mm.160172	NM_030265	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding
mm_163226.1	chr11	102365174	102365178	-	1	NA	5' UTR (NM_011403, exon 1 of 20)	5' UTR (NM_011403, exon 1 of 20)	105	NM_011403	20533	Mm.7248	NM_011403	ENSMUSG00000006574	Slc4a1	Ae1|CD233|Empb3|l11Jus51	solute carrier family 4 (anion exchanger), member 1	protein-coding
mm_130749.1	chr15	101266521	101266529	-	1	NA	promoter-TSS (NM_010444)	promoter-TSS (NM_010444)	-321	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_141545.1	chr17	32021941	32021948	-	1	NA	intron (NM_028902, intron 3 of 7)	B2_Mm2|SINE|B2	12564	NM_028902	74377	Mm.75856	NM_028902	ENSMUSG00000002076	Hsf2bp	4932437G14Rik	heat shock transcription factor 2 binding protein	protein-coding
mm_135845.1	chr16	58718770	58718783	-	1	NA	promoter-TSS (NM_001162955)	promoter-TSS (NM_001162955)	-52	NM_001162955	71223	Mm.359970	NM_001162955	ENSMUSG00000047293	Gpr15	4933439K08Rik	G protein-coupled receptor 15	protein-coding
mm_138599.1	chr17	35552168	35552182	+	1	NA	promoter-TSS (NM_001008424)	promoter-TSS (NM_001008424)	47	NM_001008424	386463	Mm.426664	NM_001008424	ENSMUSG00000039518	Cdsn	AI747712	corneodesmosin	protein-coding
mm_100371.1	chr11	119089386	119089388	+	1	NA	Intergenic	Intergenic	-3150	NM_007625	12418	Mm.268070	NM_007625	ENSMUSG00000039989	Cbx4	MPc2|PC2	chromobox 4	protein-coding
mm_162909.1	chr10	118101962	118101970	+	1	NA	Intergenic	L2|LINE|L2	-39821	NM_001162904	17245	Mm.101191	NM_010785	ENSMUSG00000020212	Mdm1	Arrd2|Mdm-1	transformed mouse 3T3 cell double minute 1	protein-coding
mm_155235.1	chrX	57212045	57212055	+	1	NA	promoter-TSS (NM_011616)	promoter-TSS (NM_011616)	-93	NM_011616	21947	Mm.4861	NM_011616	ENSMUSG00000031132	Cd40lg	CD154|CD40-L|Cd40l|HIGM1|IGM|IMD3|Ly-62|Ly62|T-BAM|TRAP|Tnfsf5|Tnlg8b|gp39	CD40 ligand	protein-coding
mm_126587.1	chr15	82341200	82341213	+	1	NA	promoter-TSS (NM_177391)	promoter-TSS (NM_177391)	27	NM_177391	338368	Mm.444916	NM_177391	ENSMUSG00000049687	Fam109b	C920005C14Rik|IPIP27B|Ses2	family with sequence similarity 109, member B	protein-coding
mm_158238.1	chrX	106603457	106603485	-	1	NA	5' UTR (NM_001281859, exon 1 of 4)	5' UTR (NM_001281859, exon 1 of 4)	208	NM_001281862	58861	Mm.287166	NM_021476	ENSMUSG00000052821	Cysltr1	BB147369|CysLT1R|Cyslt1	cysteinyl leukotriene receptor 1	protein-coding
mm_70464.1	chr8	11913013	11913024	+	1	NA	Intergenic	Intergenic	72497	NM_029326	75528	Mm.440342	NM_029326	ENSMUSG00000031512	Tex29	1700018L24Rik	testis expressed 29	protein-coding
mm_29620.1	chr3	121343357	121343371	-	1	NA	intron (NM_024178, intron 3 of 3)	intron (NM_024178, intron 3 of 3)	51547	NM_024178	66789	Mm.269881	NM_024178	ENSMUSG00000039887	Alg14	5430428G01Rik|AI854024	asparagine-linked glycosylation 14	protein-coding
mm_96690.1	chr11	69591414	69591423	+	1	NA	exon (NM_011640, exon 11 of 11)	exon (NM_011640, exon 11 of 11)	11059	NM_001127233	22059	Mm.222	NM_011640	ENSMUSG00000059552	Trp53	Tp53|bbl|bfy|bhy|p44|p53	transformation related protein 53	protein-coding
mm_110308.1	chr12	33092884	33092902	-	1	NA	promoter-TSS (NM_001024478)	promoter-TSS (NM_001024478)	-18	NM_001024478	68764	Mm.60083	NM_001024478	ENSMUSG00000035860	Cdhr3	1110049B09Rik|BB172694|Cdh28	cadherin-related family member 3	protein-coding
mm_143920.1	chr17	85618379	85618402	-	1	NA	promoter-TSS (NR_015387)	promoter-TSS (NR_015387)	6	NR_038084	100043902	Mm.150838	NR_015385	ENSMUSG00000093460	Six3os1	D17Mgi26|E130112H22Rik|Rncr1|Six3os	SIX homeobox 3, opposite strand 1	ncRNA
mm_156551.1	chrX	151593963	151593966	+	1	NA	intron (NM_177201, intron 13 of 18)	PB1D11|SINE|Alu	73292	NM_001113354	320595	Mm.17156	NM_177201	ENSMUSG00000041229	Phf8	9830141C09Rik|mKIAA1111	PHD finger protein 8	protein-coding
mm_105956.1	chr11	115367688	115367734	-	1	NA	promoter-TSS (NM_175454)	promoter-TSS (NM_175454)	8	NM_175454	217310	Mm.205707	NM_175454	ENSMUSG00000034586	Hid1	C630004H02Rik	HID1 domain containing	protein-coding
mm_66942.1	chr7	61943625	61943640	-	1	NA	TTS (NR_015599)	TTS (NR_015599)	-3526	NR_030557	100124439		NR_030557	ENSMUSG00000093187	Mir344-2	Mirn344-2|mir-344-2	microRNA 344-2	ncRNA
mm_33010.1	chr4	120825319	120825369	+	1	NA	intron (NM_001048168, intron 1 of 9)	CpG	397	NM_001277095	18046	Mm.435590	NM_008692	ENSMUSG00000032897	Nfyc	-	nuclear transcription factor-Y gamma	protein-coding
mm_98799.1	chr11	97029926	97029997	+	1	NA	promoter-TSS (NM_146027)	promoter-TSS (NM_146027)	9	NM_146027	217140	Mm.46189	NM_146027	ENSMUSG00000020877	Scrn2	AV001119|D11Moh48|SES2	secernin 2	protein-coding
mm_156067.1	chrX	109161035	109161089	+	1	NA	3' UTR (NM_019989, exon 4 of 4)	3' UTR (NM_019989, exon 4 of 4)	-35694	NM_001037917	622976	Mm.482747	NM_001037917	ENSMUSG00000048621	Gm6377	EG622976	predicted gene 6377	protein-coding
mm_83300.1	chr9	43240377	43240391	-	1	NA	promoter-TSS (NM_178644)	promoter-TSS (NM_178644)	-568	NM_178644	102644	Mm.246479	NM_178644	ENSMUSG00000032014	Oaf	AL024221|D130038B21Rik|D9Ucla1	out at first homolog	protein-coding
mm_116662.1	chr13	49200527	49200531	-	1	NA	Intergenic	Intergenic	12982	NM_013610	18081	Mm.18503	NM_013610	ENSMUSG00000037966	Ninj1	AU024536	ninjurin 1	protein-coding
mm_169692.1	chr15	74955679	74955679	+	1	NA	5' UTR (NM_001164036, exon 1 of 4)	5' UTR (NM_001164036, exon 1 of 4)	573	NM_001164040	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_119733.1	chr14	54113436	54113446	+	1	NA	Intergenic	Intergenic	140488	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_159232.1	chr2	136890976	136890976	+	1	NA	promoter-TSS (NM_028201)	promoter-TSS (NM_028201)	-242	NM_028201	74243	Mm.330612	NM_028201	ENSMUSG00000027281	Slx4ip	2210009G21Rik|2410004I22Rik|C85661|Slxip	SLX4 interacting protein	protein-coding
mm_3777.1	chr1	156558845	156558869	+	1	NA	promoter-TSS (NM_009595)	promoter-TSS (NM_009595)	70	NM_001136104	11352	Mm.329515	NM_009595	ENSMUSG00000026596	Abl2	AA536808|Abll|Arg	v-abl Abelson murine leukemia viral oncogene 2 (arg, Abelson-related gene)	protein-coding
mm_143495.1	chr17	71475361	71475371	-	1	NA	promoter-TSS (NM_028887)	promoter-TSS (NM_028887)	-23	NM_028887	74355	Mm.194450	NM_028887	ENSMUSG00000024054	Smchd1	4931400A14Rik|AW554188|MommeD1|mKIAA0650	SMC hinge domain containing 1	protein-coding
mm_166480.1	chr5	145104652	145104656	+	1	NA	intron (NM_019767, intron 7 of 9)	intron (NM_019767, intron 7 of 9)	-9602	NM_023142	11867	Mm.30010	NM_023142	ENSMUSG00000029622	Arpc1b	41kDa|AA408064|AA408534|AA571392|AF007010|AW208418|L72|SOP2Hs|p41-ARC	actin related protein 2/3 complex, subunit 1B	protein-coding
mm_77806.1	chr9	3036071	3036098	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	2659	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_74785.1	chr8	22060311	22060336	-	1	NA	promoter-TSS (NM_001243161)	promoter-TSS (NM_001243161)	-249	NM_007511	11979	Mm.87854	NM_007511	ENSMUSG00000006567	Atp7b	Atp7a|WND|tx	ATPase, Cu++ transporting, beta polypeptide	protein-coding
mm_22131.1	chr2	170427838	170427852	-	1	NA	promoter-TSS (NM_001164369)	promoter-TSS (NM_001164369)	0	NM_001164369	76960	Mm.240850	NM_029815	ENSMUSG00000013523	Bcas1	2210416M21Rik|9030223A09Rik|AI841227|NABC1	breast carcinoma amplified sequence 1	protein-coding
mm_127969.1	chr15	12010872	12010882	-	1	NA	Intergenic	Intergenic	-14870	NM_011294	20024	Mm.41746	NM_011294	ENSMUSG00000022205	Sub1	AI842364|P15|P9|Pc4|Rpo2tc1	SUB1 homolog (S. cerevisiae)	protein-coding
mm_102687.1	chr11	65365781	65365819	-	1	NA	Intergenic	Intergenic	-77967	NR_040280	327946	Mm.383301	NR_040280	ENSMUSG00000085162	Gm12295	A730013G04|OTTMUSG00000005904	predicted gene 12295	ncRNA
mm_96324.1	chr11	64079614	64079624	+	1	NA	promoter-TSS (NM_178379)	promoter-TSS (NM_178379)	135	NR_033780	66456	Mm.124828	NR_033780	ENSMUSG00000087497	2810001G20Rik	AW045514	RIKEN cDNA 2810001G20 gene	ncRNA
mm_38345.1	chr4	137769949	137769955	-	1	NA	intron (NM_007431, intron 1 of 11)	intron (NM_007431, intron 1 of 11)	-3477	NM_001287172	11647	Mm.288186	NM_007431	ENSMUSG00000028766	Alpl	ALP|APTNAP|Akp-2|Akp2|TNAP|TNSALP	alkaline phosphatase, liver/bone/kidney	protein-coding
mm_165030.1	chr19	33965650	33965650	+	1	NA	exon (NM_026334, exon 4 of 10)	exon (NM_026334, exon 4 of 10)	4402	NM_026334	67717	Mm.329816	NM_026334	ENSMUSG00000024768	Lipf	2310051B21Rik|AV082900	lipase, gastric	protein-coding
mm_133396.1	chr16	84774429	84774439	+	1	NA	5' UTR (NM_023844, exon 1 of 10)	5' UTR (NM_023844, exon 1 of 10)	311	NM_023844	67374	Mm.41758	NM_023844	ENSMUSG00000053062	Jam2	1110002N23Rik|2410030G21Rik|2410167M24Rik|JAM-2|JAM-B|Jcam2|VE-JAM	junction adhesion molecule 2	protein-coding
mm_14047.1	chr2	122301132	122301150	+	1	NA	intron (NM_025777, intron 3 of 5)	intron (NM_025777, intron 3 of 5)	2241	NM_025777	66811	Mm.171333	NM_025777	ENSMUSG00000027225	Duoxa2	9030623N16Rik|Nip2	dual oxidase maturation factor 2	protein-coding
mm_162593.1	chr1	181285699	181285712	+	1	NA	Intergenic	Intergenic	-66923	NM_028408	72978	Mm.338083	NM_028408	ENSMUSG00000026514	Cnih3	2900075G08Rik|CNIH-3	cornichon family AMPA receptor auxiliary protein 3	protein-coding
mm_54258.1	chr6	28304810	28304858	-	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	-43233	NM_001081678	627049	Mm.84441	NM_001081678	ENSMUSG00000039841	Zfp800	AA407452|Znf800	zinc finger protein 800	protein-coding
mm_111168.1	chr12	83597191	83597245	-	1	NA	promoter-TSS (NM_183154)	promoter-TSS (NM_183154)	-71	NM_183154	217695	Mm.59257	NM_183154	ENSMUSG00000042628	Zfyve1	DFCP1|G630053K23|TAFF1|ZNFN2A1|mKIAA1589	zinc finger, FYVE domain containing 1	protein-coding
mm_112474.1	chr13	5868589	5868621	+	1	NA	3' UTR (NM_011803, exon 4 of 4)	3' UTR (NM_011803, exon 4 of 4)	7116	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_50925.1	chr6	57609803	57609826	+	1	NA	intron (NM_025992, intron 8 of 22)	intron (NM_025992, intron 8 of 22)	28822	NM_025992	67138	Mm.297393	NM_025992	ENSMUSG00000029798	Herc6	1700121D12Rik|2510038N07Rik|4930427L17Rik|AI451296|CEB1|Herc5	hect domain and RLD 6	protein-coding
mm_148475.1	chr19	4100001	4100083	+	1	NA	promoter-TSS (NM_008851)	promoter-TSS (NM_008851)	44	NR_075078	18739	Mm.1860	NM_008851	ENSMUSG00000024851	Pitpnm1	DRES9|Mpt-1|Nir-2|PITPnm 1|Pitpnm|R75447|Rd9|RdgB|RdgB1	phosphatidylinositol transfer protein, membrane-associated 1	protein-coding
mm_89647.1	chr10	97393473	97393496	+	1	NA	Intergenic	Intergenic	-29994	NR_039547	100628616		NR_039547	ENSMUSG00000105557	Mir3966	mmu-mir-3966|mu-mir-3966	microRNA 3966	ncRNA
mm_59665.1	chr7	28372931	28372971	+	1	NA	promoter-TSS (NM_001083912)	promoter-TSS (NM_001083912)	-289	NM_001083912	101497	Mm.235700	NM_138752	ENSMUSG00000037552	Plekhg2	AI194308|Clg|Cslg	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	protein-coding
mm_1619.1	chr1	74391741	74391760	+	1	NA	5' UTR (NM_153088, exon 1 of 7)	5' UTR (NM_153088, exon 1 of 7)	141	NM_153088	227292	Mm.165042	NM_153088	ENSMUSG00000026176	Ctdsp1	GIP|NLIIF|Nif3|SCP1	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 1	protein-coding
mm_15836.1	chr2	164687339	164687342	+	1	NA	3' UTR (NM_001012704, exon 2 of 2)	3' UTR (NM_001012704, exon 2 of 2)	2233	NM_001012704	408190	Mm.376205	NM_001012704	ENSMUSG00000067704	Wfdc13	Wfdc13l1	WAP four-disulfide core domain 13	protein-coding
mm_13754.1	chr2	118126665	118126678	+	1	NA	3' UTR (NM_011580, exon 22 of 22)	3' UTR (NM_011580, exon 22 of 22)	14795	NM_001313914	21825	Mm.4159	NM_011580	ENSMUSG00000040152	Thbs1	TSP-1|TSP1|Thbs-1|tbsp1	thrombospondin 1	protein-coding
mm_30575.1	chr4	3938905	3938932	+	1	NA	promoter-TSS (NM_019969)	promoter-TSS (NM_019969)	30	NM_001285804	66433	Mm.27406	NM_181391	ENSMUSG00000042198	Chchd7	1810049H20Rik	coiled-coil-helix-coiled-coil-helix domain containing 7	protein-coding
mm_97399.1	chr11	77838120	77838126	+	1	NA	intron (NM_001291214, intron 19 of 38)	intron (NM_001291214, intron 19 of 38)	36825	NM_001291215	360013	Mm.341248	NM_011586	ENSMUSG00000000631	Myo18a	MAJN|MyoPDZ|MysPDZ|SP-R210	myosin XVIIIA	protein-coding
mm_17180.1	chr2	25365157	25365183	-	1	NA	intron (NM_001033293, intron 1 of 8)	intron (NM_001033293, intron 1 of 8)	456	NM_001033293	227620	Mm.33797	NM_001033293	ENSMUSG00000026956	Uap1l1	5730445F03Rik	UDP-N-acteylglucosamine pyrophosphorylase 1-like 1	protein-coding
mm_89738.1	chr10	99023409	99023428	+	1	NA	3' UTR (NM_026482, exon 21 of 21)	3' UTR (NM_026482, exon 21 of 21)	-83753	NM_027740	382406	Mm.440656	NM_027740	ENSMUSG00000019952	Poc1b	4933430F16Rik|Wdr51b	POC1 centriolar protein B	protein-coding
mm_116734.1	chr13	51734696	51734747	-	1	NA	intron (NM_001281880, intron 2 of 16)	intron (NM_001281880, intron 2 of 16)	59026	NM_001281880	20354	Mm.33903	NM_013660	ENSMUSG00000021451	Sema4d	CD100|Semacl2|Semaj|Semcl2|coll-4	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D	protein-coding
mm_171728.1	chr4	89711603	89711614	+	1	NA	Intergenic	RLTR9D|LTR|ERVK	23410	NM_175647	242523	Mm.130167	NM_175647	ENSMUSG00000043753	Dmrta1	Dmrt4	doublesex and mab-3 related transcription factor like family A1	protein-coding
mm_168172.1	chr10	55574835	55574835	+	1	NA	Intergenic	Intergenic	-532082	NM_001163833	73390	Mm.181475	NM_133751	ENSMUSG00000047669	Msl3l2	1700060H10Rik	male-specific lethal 3-like 2 (Drosophila)	protein-coding
mm_102183.1	chr11	54069214	54069256	-	1	NA	promoter-TSS (NM_019417)	promoter-TSS (NM_019417)	-218	NM_019417	30794	Mm.21830	NM_019417	ENSMUSG00000020388	Pdlim4	Ril	PDZ and LIM domain 4	protein-coding
mm_122154.1	chr14	31323931	31323950	-	1	NA	promoter-TSS (NM_001033668)	promoter-TSS (NM_001033668)	-44	NM_001033668	110084	Mm.101811	NM_001033668	ENSMUSG00000019027	Dnah1	B230373P09Rik|Dnahc1|E030034C22Rik|MDHC7	dynein, axonemal, heavy chain 1	protein-coding
mm_84923.1	chr9	80465430	80465445	-	1	NA	promoter-TSS (NM_022016)	promoter-TSS (NM_022016)	1	NM_022016	63859	Mm.422780	NM_022016	ENSMUSG00000032343	Impg1	A930015H12Rik|IMP150|SPACR	interphotoreceptor matrix proteoglycan 1	protein-coding
mm_54772.1	chr6	41532819	41532829	-	1	NA	Intergenic	Intergenic	11048	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_21660.1	chr2	164424285	164424287	-	1	NA	TTS (NM_011521)	TTS (NM_011521)	18902	NM_011521	20971	Mm.3815	NM_011521	ENSMUSG00000017009	Sdc4	AA959608|AW108331|S4|Synd4|ryudocan|syndecan-4	syndecan 4	protein-coding
mm_4809.1	chr1	185356629	185356640	+	1	NA	3' UTR (NM_011794, exon 9 of 9)	3' UTR (NM_011794, exon 9 of 9)	-6461	NM_029735	107508	Mm.154511	NM_029735	ENSMUSG00000026615	Eprs	2410081F06Rik|3010002K18Rik|C79379|Qprs	glutamyl-prolyl-tRNA synthetase	protein-coding
mm_69834.1	chr7	141276730	141276791	-	1	NA	promoter-TSS (NM_028069)	promoter-TSS (NM_028069)	26	NM_028069	72040	Mm.29080	NM_028069	ENSMUSG00000025497	Cdhr5	1810074H01Rik|AI481143|Mucdhl|Mupcdh	cadherin-related family member 5	protein-coding
mm_55325.1	chr6	55679318	55679344	-	1	NA	exon (NM_009717, exon 2 of 2)	exon (NM_009717, exon 2 of 2)	1932	NM_009717	11922	Mm.5106	NM_009717	ENSMUSG00000037984	Neurod6	Atoh2|Math-2|Math2|Nex|Nex1m|bHLHa2	neurogenic differentiation 6	protein-coding
mm_69153.1	chr7	127144336	127144351	-	1	NA	Intergenic	MTE2b|LTR|ERVL-MaLR	-6520	NM_001037810	20737	Mm.283714	NM_009259	ENSMUSG00000051457	Spn	A630014B01Rik|Cd43|Galgp|Ly-48|Ly48	sialophorin	protein-coding
mm_54657.1	chr6	39089007	39089020	-	1	NA	exon (NM_172893, exon 11 of 12)	exon (NM_172893, exon 11 of 12)	-21427	NR_040523	69986	Mm.490941	NR_040523	ENSMUSG00000100121	1700025N23Rik	-	RIKEN cDNA 1700025N23 gene	ncRNA
mm_44601.1	chr5	25100580	25100586	-	1	NA	promoter-TSS (NM_145401)	promoter-TSS (NM_145401)	59	NM_145401	108099	Mm.33649	NM_145401	ENSMUSG00000028944	Prkag2	2410051C13Rik|AAKG|AAKG2|AI854673|H91620p|WPWS	protein kinase, AMP-activated, gamma 2 non-catalytic subunit	protein-coding
mm_102000.1	chr11	51263018	51263035	-	1	NA	promoter-TSS (NM_177567)	promoter-TSS (NM_177567)	-75	NM_177567	193286	Mm.80975	NM_177567	ENSMUSG00000045942	BC049762	4930503F14	cDNA sequence BC049762	protein-coding
mm_18846.1	chr2	75633545	75633557	-	1	NA	Intergenic	RMER20B|LTR|ERVK	-25708	NM_146130	229279	Mm.316306	NM_053263	ENSMUSG00000059005	Hnrnpa3	2410013L13Rik|2610209F03Rik|2610510D13Rik|Hnrpa3	heterogeneous nuclear ribonucleoprotein A3	protein-coding
mm_2822.1	chr1	131138397	131138426	+	1	NA	promoter-TSS (NM_145508)	promoter-TSS (NM_145508)	-177	NM_145508	226419	Mm.39299	NM_145508	ENSMUSG00000016526	Dyrk3	BC006704	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 3	protein-coding
mm_8089.1	chr1	135685338	135685372	-	1	NA	Intergenic	Intergenic	-43842	NM_007791	13007	Mm.196484	NM_007791	ENSMUSG00000026421	Csrp1	AA408841|AA959891|AW545626|CRP1|Csrp	cysteine and glycine-rich protein 1	protein-coding
mm_63469.1	chr7	127588715	127588725	+	1	NA	promoter-TSS (NM_001033040)	promoter-TSS (NM_001033040)	22	NM_172281	233900	Mm.41122	NM_172281	ENSMUSG00000030816	Rnf40	AI848422|mKIAA0661	ring finger protein 40	protein-coding
mm_58431.1	chr7	3297550	3297560	+	1	NA	exon (NM_016969, exon 3 of 3)	exon (NM_016969, exon 3 of 3)	4527	NM_001093766	50918	Mm.29874	NM_016969	ENSMUSG00000068566	Myadm	D7Wsu62e	myeloid-associated differentiation marker	protein-coding
mm_78706.1	chr9	41376467	41376485	+	1	NA	promoter-TSS (NR_040725)	promoter-TSS (NR_040725)	-50	NR_040725	73144	Mm.38166	NM_001033153	ENSMUSG00000074415	3110039I08Rik	2610203C20Rik|AI848448|D230004N17Rik|D3Mgi9|Mir100hg	RIKEN cDNA 3110039I08 gene	ncRNA
mm_40339.1	chr5	44226738	44226748	+	1	NA	promoter-TSS (NM_173764)	promoter-TSS (NM_173764)	-137	NM_173764	231225	Mm.30688	NM_173764	ENSMUSG00000046985	Tapt1	4932414K18Rik	transmembrane anterior posterior transformation 1	protein-coding
mm_3714.1	chr1	153909200	153909210	+	1	NA	3' UTR (NM_008131, exon 7 of 7)	3' UTR (NM_008131, exon 7 of 7)	9276	NM_008131	14645	Mm.210745	NM_008131	ENSMUSG00000026473	Glul	GS|Glns	glutamate-ammonia ligase (glutamine synthetase)	protein-coding
mm_119860.1	chr14	54467601	54467611	+	1	NA	exon (NM_022993, exon 4 of 7)	exon (NM_022993, exon 4 of 7)	3459	NM_022993	65107	Mm.472719	NM_022993	ENSMUSG00000022175	Lrp10	Lrp9	low-density lipoprotein receptor-related protein 10	protein-coding
mm_63019.1	chr7	121034417	121034421	+	1	NA	promoter-TSS (NM_021554)	promoter-TSS (NM_021554)	-26	NM_021554	59052	Mm.29122	NM_021554	ENSMUSG00000030876	Mettl9	0610012D09Rik|AA517660|Drev|MNCb-5680	methyltransferase like 9	protein-coding
mm_43570.1	chr5	137641277	137641335	+	1	NA	promoter-TSS (NM_001081962)	promoter-TSS (NM_001081962)	-167	NM_001081962	751865	Mm.200763	NM_001081962	ENSMUSG00000079165	Sap25	-	sin3 associated polypeptide	protein-coding
mm_159609.1	chr4	131957713	131957713	-	1	NA	exon (NM_001128607, exon 13 of 18)	exon (NM_001128607, exon 13 of 18)	35942	NM_001201367	623230	Mm.421179	NM_001201367	ENSMUSG00000070720	Tmem200b	EG623230	transmembrane protein 200B	protein-coding
mm_27039.1	chr3	26331855	26331901	-	1	NA	promoter-TSS (NM_138666)	promoter-TSS (NM_138666)	31	NM_138666	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_14086.1	chr2	125136749	125136769	+	1	NA	promoter-TSS (NM_001162934)	promoter-TSS (NM_001162934)	67	NM_001162934	381418	Mm.295608	NM_001162934	ENSMUSG00000074872	Ctxn2	BB181834|Gm1638	cortexin 2	protein-coding
mm_111093.1	chr12	80441488	80441518	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-4902	NM_177267	320808	Mm.220310	NM_177267	ENSMUSG00000049106	Dcaf5	9430020B07Rik|AI325023|AI430035|AI848110|AW124614|BCRG2|BCRP2|Wdr22	DDB1 and CUL4 associated factor 5	protein-coding
mm_170510.1	chr19	28155664	28155682	-	1	NA	Intergenic	L1Md_T|LINE|L1	-144507	NM_011265	19726	Mm.313321	NM_011265	ENSMUSG00000040929	Rfx3	C230093O12Rik|MRFX3	regulatory factor X, 3 (influences HLA class II expression)	protein-coding
mm_107646.1	chr12	52505142	52505145	+	1	NA	Intergenic	Intergenic	-10934	NM_009706	11855	Mm.35059	NM_009706	ENSMUSG00000035133	Arhgap5	p190-B|p190B	Rho GTPase activating protein 5	protein-coding
mm_132216.1	chr16	32630112	32630120	+	1	NA	exon (NM_011638, exon 19 of 19)	exon (NM_011638, exon 19 of 19)	-14527	NM_001110147	51789	Mm.251115	NM_016788	ENSMUSG00000022791	Tnk2	Ack|Ack-1|Ack1|Cdgip|Pyk1	tyrosine kinase, non-receptor, 2	protein-coding
mm_35158.1	chr4	12171971	12172024	-	1	NA	promoter-TSS (NM_001310743)	promoter-TSS (NM_001310743)	18	NM_001310743	68099	Mm.25340	NM_026558	ENSMUSG00000028218	Fam92a	6720467C03Rik|Fam92a1	family with sequence similarity 92, member A	protein-coding
mm_126894.1	chr15	89499599	89499653	+	1	NA	promoter-TSS (NM_021423)	promoter-TSS (NM_021423)	-231	NM_021423	58234	Mm.146855	NM_021423	ENSMUSG00000022623	Shank3	AI841104|SHANK3c-3|SHANK3c-4|Shank3b	SH3/ankyrin domain gene 3	protein-coding
mm_72897.1	chr8	90861955	90861957	+	1	NA	intron (NM_177224, intron 2 of 39)	intron (NM_177224, intron 2 of 39)	33121	NM_177224	109151	Mm.100615	NM_177224	ENSMUSG00000056608	Chd9	1810014J18Rik|9030205D12Rik|A330063D19Rik|AD013|PRIC320|mKIAA0308	chromodomain helicase DNA binding protein 9	protein-coding
mm_74412.1	chr8	3624922	3624926	-	1	NA	TTS (NM_001195244)	TTS (NM_001195244)	125	NM_001129804	18545	Mm.440882	NM_008790	ENSMUSG00000004630	Pcp2	L7|Pcp-2	Purkinje cell protein 2 (L7)	protein-coding
mm_66877.1	chr7	57509985	57509993	-	1	NA	promoter-TSS (NM_176942)	promoter-TSS (NM_176942)	20	NM_176942	110886	Mm.273114	NM_176942	ENSMUSG00000055078	Gabra5	A230018I05Rik	gamma-aminobutyric acid (GABA) A receptor, subunit alpha 5	protein-coding
mm_78603.1	chr9	37528072	37528148	+	1	NA	promoter-TSS (NM_027102)	promoter-TSS (NM_027102)	21	NM_027102	69524	Mm.41751	NM_027102	ENSMUSG00000001946	Esam	2310008D05Rik|Esam1|W117m	endothelial cell-specific adhesion molecule	protein-coding
mm_67739.1	chr7	90265378	90265395	-	1	NA	promoter-TSS (NM_183293)	promoter-TSS (NM_183293)	46	NM_029256	75338	Mm.487222	NM_029256	ENSMUSG00000030617	Ccdc83	4930549K11Rik|4930554C01Rik|4932423M01Rik	coiled-coil domain containing 83	protein-coding
mm_92562.1	chr10	79854286	79854317	-	1	NA	promoter-TSS (NM_008956)	promoter-TSS (NM_008956)	-131	NM_001077363	19205	Mm.265610	NM_008956	ENSMUSG00000006498	Ptbp1	AA407203|AL033359|HNRPI|PTB-1|PTB2|PTB3|PTB4|Ptb|pPTB	polypyrimidine tract binding protein 1	protein-coding
mm_157367.1	chrX	37210999	37211010	-	1	NA	promoter-TSS (NM_001033234)	promoter-TSS (NM_001033234)	37	NM_001033234	194854	Mm.296429	NM_001033234	ENSMUSG00000073243	Gm9	-	predicted gene 9	protein-coding
mm_111352.1	chr12	86950538	86950566	-	1	NA	intron (NM_001289432, intron 1 of 4)	intron (NM_001289432, intron 1 of 4)	3209	NM_001289432	217732	Mm.22337	NM_173735	ENSMUSG00000034157	Cipc	2310044G17Rik|AI842544|AI853744|Kiaa1737|mKIAA1737	CLOCK interacting protein, circadian	protein-coding
mm_57478.1	chr6	125236924	125236934	-	1	NA	promoter-TSS (NM_001042564)	promoter-TSS (NM_001042564)	98	NM_001033126	21940	Mm.367714	NM_001033126	ENSMUSG00000030336	Cd27	S152|Tnfrsf7|Tp55	CD27 antigen	protein-coding
mm_14033.1	chr2	122152932	122152943	+	1	NA	3' UTR (NM_009735, exon 4 of 4)	3' UTR (NM_009735, exon 4 of 4)	5250	NM_009735	12010	Mm.163	NM_009735	ENSMUSG00000060802	B2m	Ly-m11|beta2-m|beta2m	beta-2 microglobulin	protein-coding
mm_138833.1	chr17	39848249	39848268	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	5261	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_136563.1	chr17	3210507	3210510	+	1	NA	Intergenic	Intergenic	95536	NM_134123	106583	Mm.124373	NM_134123	ENSMUSG00000046201	Scaf8	A630086M08Rik|A930036P18Rik|AA408306|AI447644|AI448652|AU015035|Rbm16|mKIAA1116	SR-related CTD-associated factor 8	protein-coding
mm_141503.1	chr17	31636506	31636526	-	1	NA	intron (NM_178224, intron 1 of 15)	CpG	689	NM_144855	12411	Mm.206417	NM_144855	ENSMUSG00000024039	Cbs	AI047524|AI303044|HIP4	cystathionine beta-synthase	protein-coding
mm_48008.1	chr5	136162059	136162071	-	1	NA	intron (NM_178751, intron 1 of 2)	B4A|SINE|B4	8591	NM_178751	269717	Mm.308396	NM_178751	ENSMUSG00000039747	Orai2	A730041O15Rik|Tmem142b	ORAI calcium release-activated calcium modulator 2	protein-coding
mm_92645.1	chr10	80387587	80387630	-	1	NA	promoter-TSS (NM_198615)	promoter-TSS (NM_198615)	43	NM_198615	237400	Mm.268389	NM_198615	ENSMUSG00000048696	Mex3d	BC059858|Rkhd1	mex3 RNA binding family member D	protein-coding
mm_74458.1	chr8	4214614	4214624	-	1	NA	exon (NM_207203, exon 6 of 7)	exon (NM_207203, exon 6 of 7)	2693	NM_207203	73072	Mm.477379	NM_207203	ENSMUSG00000064125	Prr36	-	proline rich 36	protein-coding
mm_166531.1	chr6	29853962	29853969	+	1	NA	intron (NM_001347084, intron 1 of 17)	intron (NM_001347084, intron 1 of 17)	224	NM_001347084	74340	Mm.210899	NM_021414	ENSMUSG00000029772	Ahcyl2	4631427C17Rik|AI227036|Adohcyase3|mKIAA0828	S-adenosylhomocysteine hydrolase-like 2	protein-coding
mm_34094.1	chr4	138835069	138835073	+	1	NA	non-coding (NR_002926, exon 5 of 5)	non-coding (NR_002926, exon 5 of 5)	3195	NM_001082531	18780	Mm.4675	NM_011108	ENSMUSG00000058908	Pla2g2a	EF|Mom1|Pla2|sPLA2|sPla2-IIA	phospholipase A2, group IIA (platelets, synovial fluid)	protein-coding
mm_92756.1	chr10	81037259	81037295	-	1	NA	Intergenic	Intergenic	-3365	NM_134135	106947	Mm.5353	NM_134135	ENSMUSG00000046822	Slc39a3	AI845814|Zip3	solute carrier family 39 (zinc transporter), member 3	protein-coding
mm_161681.1	chr17	17579140	17579140	-	1	NA	exon (NM_172827, exon 2 of 18)	exon (NM_172827, exon 2 of 18)	45349	NM_172827	240028	Mm.328807	NM_172827	ENSMUSG00000023845	Lnpep	2010309L07Rik|4732490P18Rik|CAP|IRAP|PLAP|gp160|vp165	leucyl/cystinyl aminopeptidase	protein-coding
mm_119390.1	chr14	41137442	41137452	+	1	NA	Intergenic	Lx9|LINE|L1	5659	NM_023134	20387	Mm.46062	NM_023134	ENSMUSG00000021789	Sftpa1	SP-A|Sftp-1|Sftp1	surfactant associated protein A1	protein-coding
mm_79969.1	chr9	66448047	66448069	+	1	NA	exon (NM_145617, exon 37 of 78)	exon (NM_145617, exon 37 of 78)	66535	NM_175206	74165	Mm.297998	NM_175206	ENSMUSG00000050503	Fbxl22	1110004B15Rik	F-box and leucine-rich repeat protein 22	protein-coding
mm_83006.1	chr9	36757022	36757036	-	1	NA	intron (NM_008408, intron 5 of 17)	intron (NM_008408, intron 5 of 17)	10549	NM_008408	16430	Mm.2863	NM_008408	ENSMUSG00000032116	Stt3a	AA408947|BB081708|Itm1	STT3, subunit of the oligosaccharyltransferase complex, homolog A (S. cerevisiae)	protein-coding
mm_81677.1	chr9	111057355	111057376	+	1	NA	promoter-TSS (NM_017466)	promoter-TSS (NM_017466)	-95	NM_017466	54199	Mm.7336	NM_017466	ENSMUSG00000043953	Ccrl2	1810047I05Rik|Ackr5|CCR11|Cmkbr1l2|E01|L-CCR	chemokine (C-C motif) receptor-like 2	protein-coding
mm_77109.1	chr8	111081736	111081740	-	1	NA	promoter-TSS (NM_181549)	promoter-TSS (NM_181549)	-30	NM_181549	353287	Mm.135495	NM_181549	ENSMUSG00000033633	Clec18a	Mrcl	C-type lectin domain family 18, member A	protein-coding
mm_124407.1	chr14	115477586	115477600	-	1	NA	intron (NM_175500, intron 5 of 7)	intron (NM_175500, intron 5 of 7)	-68041	NR_045761	75088	Mm.444706	NR_045761	ENSMUSG00000093551	4930505G20Rik	-	RIKEN cDNA 4930505G20 gene	ncRNA
mm_61769.1	chr7	82867452	82867499	+	1	NA	5' UTR (NM_175366, exon 1 of 2)	5' UTR (NM_175366, exon 1 of 2)	142	NM_175366	108797	Mm.306789	NM_175366	ENSMUSG00000057706	Mex3b	4931439A04Rik|M-04814|Rkhd3|mKIAA2009	mex3 RNA binding family member B	protein-coding
mm_87917.1	chr10	62494780	62494813	+	1	NA	3' UTR (NM_011157, exon 3 of 3)	3' UTR (NM_011157, exon 3 of 3)	-7991	NM_133672	30930	Mm.260703	NM_133672	ENSMUSG00000020078	Vps26a	AA407240|HB58|Vps26	VPS26 retromer complex component A	protein-coding
mm_171520.1	chr4	146565232	146565246	-	1	NA	Intergenic	Intergenic	-18366	NR_045468	67524	Mm.444300	NR_045468	ENSMUSG00000086046	1700095A21Rik	-	RIKEN cDNA 1700095A21 gene	ncRNA
mm_25493.1	chr3	109340704	109340715	+	1	NA	promoter-TSS (NM_020505)	promoter-TSS (NM_020505)	26	NM_020505	57257	Mm.282257	NM_020505	ENSMUSG00000033721	Vav3	A530094I06Rik|AA986410|Idd18.1	vav 3 oncogene	protein-coding
mm_165895.1	chr4	45741951	45741952	+	1	NA	Intergenic	Intergenic	22272	NR_046068	100040567	Mm.490816	NR_046068	ENSMUSG00000085876	Gm12409	OTTMUSG00000006726	predicted gene 12409	ncRNA
mm_57569.1	chr6	127129290	127129318	-	1	NA	3' UTR (NM_009829, exon 5 of 5)	3' UTR (NM_009829, exon 5 of 5)	-19752	NM_177003	319801	Mm.101836	NM_177003	ENSMUSG00000038028	Tigar	9630033F20Rik|AA793651|AI595337|C79710|C85509	Trp53 induced glycolysis repulatory phosphatase	protein-coding
mm_71271.1	chr8	40919495	40919514	+	1	NA	3' UTR (NM_001044740, exon 12 of 12)	3' UTR (NM_001044740, exon 12 of 12)	-6729	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_11405.1	chr2	31511052	31511068	+	1	NA	intron (NR_002687, intron 13 of 15)	intron (NR_002687, intron 13 of 15)	40752	NR_002687	432466	Mm.333323	NR_002687	ENSMUSG00000046687	Gm5424	EG432466	argininosuccinate synthase pseudogene	pseudo
mm_147938.1	chr18	66059503	66059517	-	1	NA	3' UTR (NM_178793, exon 11 of 11)	3' UTR (NM_178793, exon 11 of 11)	-56875	NM_001172062	70361	Mm.290857	NM_027400	ENSMUSG00000041891	Lman1	2610020P13Rik|AI326273|AU043785|C730041J05|ERGIC53|F5F8D|MCFD1|MR60|P58|gp58	lectin, mannose-binding, 1	protein-coding
mm_166698.1	chr6	114315666	114315674	+	1	NA	3' UTR (NM_178703, exon 16 of 16)	3' UTR (NM_178703, exon 16 of 16)	33035	NM_178703	232333	Mm.5260	NM_178703	ENSMUSG00000030310	Slc6a1	A730043E01|GABATHG|GABATR|GAT-1|Gabt|Gabt1|Gat1|XT-1|Xtrp1	solute carrier family 6 (neurotransmitter transporter, GABA), member 1	protein-coding
mm_145480.1	chr18	60379174	60379200	+	1	NA	intron (NM_021792, intron 1 of 1)	L1Md_A|LINE|L1	3158	NM_001146275	60440	Mm.261140	NM_021792	ENSMUSG00000054072	Iigp1	2900074L10Rik|AI046432|AW111922|Ifgga1|Iigp|Irga6	interferon inducible GTPase 1	protein-coding
mm_59105.1	chr7	19749955	19749968	+	1	NA	promoter-TSS (NM_001159724)	promoter-TSS (NM_001159724)	-388	NM_001159724	19294	Mm.4341	NM_008990	ENSMUSG00000062300	Nectin2	AI325026|AI987993|Cd112|MPH|Pvr|Pvrl2|Pvs|nectin-2	nectin cell adhesion molecule 2	protein-coding
mm_78555.1	chr9	35424959	35424984	+	1	NA	Intergenic	Intergenic	-27105	NM_021339	57810	Mm.80509	NM_021339	ENSMUSG00000038119	Cdon	CDO|Cd0|Orcam	cell adhesion molecule-related/down-regulated by oncogenes	protein-coding
mm_116180.1	chr13	30897444	30897456	-	1	NA	intron (NM_025588, intron 11 of 27)	intron (NM_025588, intron 11 of 27)	50311	NM_153072	210554	Mm.450571	NM_153072	ENSMUSG00000076430	Hus1b	-	HUS1 checkpoint clamp component B	protein-coding
mm_118208.1	chr13	109903699	109903716	-	1	NA	promoter-TSS (NR_035442)	promoter-TSS (NR_035442)	-102	NR_035442	100316683		NR_035442	ENSMUSG00000084651	Mir1904	Mirn1904|mmu-mir-1904	microRNA 1904	ncRNA
mm_133969.1	chr16	4320653	4320663	-	1	NA	intron (NM_001291910, intron 4 of 11)	intron (NM_001291910, intron 4 of 11)	91429	NR_003628	436332	Mm.478141	NM_001013830	ENSMUSG00000089645	Gm5766	EG436332	ribosomal protein L7a pseudogene	pseudo
mm_149385.1	chr19	11382562	11382573	+	1	NA	intron (NM_001310331, intron 3 of 6)	intron (NM_001310331, intron 3 of 6)	7079	NM_001310331	666907		NM_001310331	ENSMUSG00000101389	Ms4a4a	EG666907	membrane-spanning 4-domains, subfamily A, member 4A	protein-coding
mm_52283.1	chr6	108660856	108660866	+	1	NA	promoter-TSS (NR_104577)	promoter-TSS (NR_104577)	73	NR_104577	75394	Mm.395061	NR_040757	ENSMUSG00000087341	0610040F04Rik	-	RIKEN cDNA 0610040F04 gene	ncRNA
mm_55753.1	chr6	78378837	78378850	-	1	NA	promoter-TSS (NM_001161741)	promoter-TSS (NM_001161741)	22	NM_001161741	30053	Mm.33691	NM_013893	ENSMUSG00000068341	Reg3d	INGAP|Ingaprp	regenerating islet-derived 3 delta	protein-coding
mm_119235.1	chr14	33337436	33337443	+	1	NA	intron (NM_153800, intron 4 of 10)	intron (NM_153800, intron 4 of 10)	73585	NM_001310452	26419	Mm.21495	NM_016700	ENSMUSG00000021936	Mapk8	AI849689|JNK|JNK1|Prkm8|SAPK1	mitogen-activated protein kinase 8	protein-coding
mm_150049.1	chr19	29380497	29380509	+	1	NA	exon (NM_021893, exon 4 of 7)	exon (NM_021893, exon 4 of 7)	13065	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_35706.1	chr4	44167989	44168008	-	1	NA	promoter-TSS (NM_175201)	promoter-TSS (NM_175201)	285	NM_001038993	73469	Mm.262859	NM_175201	ENSMUSG00000035696	Rnf38	1700065B19Rik|2610202O07Rik|AA673263|Oip1	ring finger protein 38	protein-coding
mm_173324.1	chrY	90737509	90737509	+	1	NA	Intergenic	IMPB_01|Satellite|Satellite	17541	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_5037.1	chr1	193332279	193332285	+	1	NA	exon (NM_001277928, exon 14 of 23)	exon (NM_001277928, exon 14 of 23)	30039	NM_001277928	16780	Mm.435441	NM_008484	ENSMUSG00000026639	Lamb3	-	laminin, beta 3	protein-coding
mm_101261.1	chr11	21046283	21046329	-	1	NA	Intergenic	Intergenic	-45018	NM_023324	67245	Mm.28957	NM_023324	ENSMUSG00000020134	Peli1	2810468L03Rik|A930031K15Rik|AA409794|AI586297|D11Ertd676e	pellino 1	protein-coding
mm_112825.1	chr13	20805171	20805180	+	1	NA	intron (NM_012054, intron 1 of 20)	Lx8b|LINE|L1	11062	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_160254.1	chr7	107814833	107814833	+	1	NA	exon (NM_001005488, exon 1 of 1)	exon (NM_001005488, exon 1 of 1)	247	NM_001005488	257919	Mm.377303	NM_001005488	ENSMUSG00000066242	Olfr467	GA_x5J8B7W6B6J-2556603-2556836|MOR204-33P	olfactory receptor 467	protein-coding
mm_103541.1	chr11	77513246	77513304	-	1	NA	promoter-TSS (NM_001024920)	promoter-TSS (NM_001024920)	-2	NM_001024920	216964	Mm.341211	NM_001024920	ENSMUSG00000044328	Trp53i13	2410019G02Rik|Tp53i13	transformation related protein 53 inducible protein 13	protein-coding
mm_132003.1	chr16	25684147	25684199	+	1	NA	5' UTR (NM_001127261, exon 1 of 11)	5' UTR (NM_001127261, exon 1 of 11)	408	NM_001127260	22061	Mm.20894	NM_011641	ENSMUSG00000022510	Trp63	AI462811|Ket|P51/P63|P63|P73l|Tp63|Trp53rp1	transformation related protein 63	protein-coding
mm_31811.1	chr4	66827638	66827644	+	1	NA	promoter-TSS (NM_021297)	promoter-TSS (NM_021297)	90	NM_021297	21898	Mm.38049	NM_021297	ENSMUSG00000039005	Tlr4	Lps|Ly87|Ran/M1|Rasl2-8	toll-like receptor 4	protein-coding
mm_77763.1	chr9	3002329	3002361	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	36398	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_98421.1	chr11	94644133	94644166	+	1	NA	TTS (NM_177752)	TTS (NM_177752)	9605	NM_177752	268465	Mm.358937	NM_177752	ENSMUSG00000039055	Eme1	6820428D13	essential meiotic structure-specific endonuclease 1	protein-coding
mm_49867.1	chr6	38557048	38557066	+	1	NA	5' UTR (NM_001331223, exon 1 of 13)	5' UTR (NM_001331223, exon 1 of 13)	1334	NM_001331223	192196	Mm.276133	NM_138680	ENSMUSG00000029823	Luc7l2	4930471C18Rik|AA522013|AU015269|CGI59|Cgi74	LUC7-like 2 (S. cerevisiae)	protein-coding
mm_149549.1	chr19	12599929	12599939	+	1	NA	promoter-TSS (NM_001167907)	promoter-TSS (NM_001167907)	-50	NM_001167907	240549	Mm.302458	NM_001013762	ENSMUSG00000071633	Gm4952	EG240549	predicted gene 4952	protein-coding
mm_38794.1	chr4	148148897	148148905	-	1	NA	intron (NM_015797, intron 2 of 5)	intron (NM_015797, intron 2 of 5)	-1905	NR_105989	102465619		NR_105989	ENSMUSG00000099043	Mir7022	Gm27291|mmu-mir-7022	microRNA 7022	ncRNA
mm_44748.1	chr5	31241216	31241243	-	1	NA	intron (NM_001347326, intron 1 of 18)	CpG	311	NM_147201	192292	Mm.292040	NM_147201	ENSMUSG00000029148	Nrbp1	B230344L17Rik|Nrbp	nuclear receptor binding protein 1	protein-coding
mm_103314.1	chr11	73138178	73138239	-	1	NA	promoter-TSS (NM_010353)	promoter-TSS (NM_010353)	86	NM_010353	14841	Mm.42045	NM_010353	ENSMUSG00000050107	Gsg2	Haspin	germ cell associated 2, haspin	protein-coding
mm_45160.1	chr5	49524988	49524998	-	1	NA	Intergenic	CpG	-239334	NM_001199244	80334	Mm.160172	NM_030265	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding
mm_47067.1	chr5	116422859	116422873	-	1	NA	promoter-TSS (NM_030704)	promoter-TSS (NM_030704)	-2	NM_030704	80888	Mm.21549	NM_030704	ENSMUSG00000041548	Hspb8	AU018630|AW413033|Cryac|D5Ucla4|E2IG1|H11|H11K|HSP20-like|HSP22	heat shock protein 8	protein-coding
mm_88946.1	chr10	81328720	81328739	+	1	NA	promoter-TSS (NM_009325)	promoter-TSS (NM_009325)	26	NM_001277265	21390	Mm.4545	NM_009325	ENSMUSG00000034881	Tbxa2r	TP|TXA2-R	thromboxane A2 receptor	protein-coding
mm_14201.1	chr2	127209079	127209103	+	1	NA	promoter-TSS (NM_198630)	promoter-TSS (NM_198630)	687	NM_177214	320632	Mm.215860	NM_177214	ENSMUSG00000003660	Snrnp200	A330064G03Rik|Ascc3l1|BC011390|HELIC2|U5-200-KD|U5-200KD	small nuclear ribonucleoprotein 200 (U5)	protein-coding
mm_40093.1	chr5	34549596	34549631	+	1	NA	promoter-TSS (NM_001145859)	promoter-TSS (NM_001145859)	37	NM_001145859	24055	Mm.5012	NM_011893	ENSMUSG00000054520	Sh3bp2	3BP2	SH3-domain binding protein 2	protein-coding
mm_45065.1	chr5	43749495	43749502	-	1	NA	intron (NM_001159963, intron 10 of 10)	AT_rich|Low_complexity|Low_complexity	32651	NM_001159963	242960	Mm.25794	NM_178729	ENSMUSG00000039753	Fbxl5	Fbl4|Fir4	F-box and leucine-rich repeat protein 5	protein-coding
mm_162953.1	chr11	4160426	4160427	+	1	NA	promoter-TSS (NM_177616)	promoter-TSS (NM_177616)	72	NM_026175	67465	Mm.156914	NM_026175	ENSMUSG00000002129	Sf3a1	1200014H24Rik|5930416L09Rik|AI159724	splicing factor 3a, subunit 1	protein-coding
mm_32994.1	chr4	120450002	120450006	+	1	NA	intron (NM_001159630, intron 2 of 17)	Lx5|LINE|L1	44723	NM_013883	29871	Mm.427014	NM_013883	ENSMUSG00000000085	Scmh1	AI315320|AI851618|Scml1|Scml3	sex comb on midleg homolog 1	protein-coding
mm_136681.1	chr17	6730224	6730261	+	1	NA	intron (NM_183368, intron 4 of 8)	intron (NM_183368, intron 4 of 8)	24412	NM_183368	83672	Mm.442201	NM_031395	ENSMUSG00000041831	Sytl3	A430092N21|Slp3|Slp3-a|Slp3-b|mFLJ00307	synaptotagmin-like 3	protein-coding
mm_1940.1	chr1	86234024	86234035	+	1	NA	intron (NM_030184, intron 19 of 24)	intron (NM_030184, intron 19 of 24)	-69192	NM_145222	227327	Mm.86467	NM_145222	ENSMUSG00000079445	B3gnt7	C330001H22Rik|beta-3GnT7	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 7	protein-coding
mm_2749.1	chr1	128705469	128705493	+	1	NA	Intergenic	Intergenic	-113182	NM_009911	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding
mm_14630.1	chr2	136781287	136781293	+	1	NA	3' UTR (NM_001291056, exon 8 of 8)	3' UTR (NM_001291056, exon 8 of 8)	67840	NM_001291056	20614	Mm.45953	NM_011428	ENSMUSG00000027273	Snap25	Bdr|GENA70|SNAP-25|SUP|sp	synaptosomal-associated protein 25	protein-coding
mm_9901.1	chr1	186749305	186749340	-	1	NA	promoter-TSS (NM_026041)	promoter-TSS (NM_026041)	36	NM_026041	67223	Mm.289841	NM_026041	ENSMUSG00000001305	Rrp15	2810430M08Rik|5430437H21Rik	ribosomal RNA processing 15 homolog (S. cerevisiae)	protein-coding
mm_100582.1	chr11	120784499	120784570	+	1	NA	promoter-TSS (NM_145370)	promoter-TSS (NM_145370)	19	NM_145370	209318	Mm.30195	NM_145370	ENSMUSG00000025156	Gps1	Cops1|Csn1|R75577|Sgn1	G protein pathway suppressor 1	protein-coding
mm_158278.1	chrX	111463479	111463520	-	1	NA	intron (NM_025949, intron 2 of 24)	CpG-15872	74460	NM_025949	67071	Mm.37617	NM_025949	ENSMUSG00000025665	Rps6ka6	2610524K04Rik|RSK4|S6K-alpha-6	ribosomal protein S6 kinase polypeptide 6	protein-coding
mm_111021.1	chr12	79068443	79068460	-	1	NA	exon (NM_181073, exon 16 of 29)	exon (NM_181073, exon 16 of 29)	21219	NM_029988	110417	Mm.268317	NM_029988	ENSMUSG00000021120	Pigh	2210416H01Rik|A930028P05Rik	phosphatidylinositol glycan anchor biosynthesis, class H	protein-coding
mm_63992.1	chr7	140097092	140097119	+	1	NA	TTS (NM_009475)	TTS (NM_009475)	3709	NM_009475	22264	Mm.439707	NM_009475	ENSMUSG00000025467	Prap1	Upa	proline-rich acidic protein 1	protein-coding
mm_4686.1	chr1	180598258	180598272	+	1	NA	exon (NM_007415, exon 19 of 23)	exon (NM_007415, exon 19 of 23)	11064	NR_105869	102466761		NR_105869	ENSMUSG00000098926	Mir6904	Gm27426|mmu-mir-6904	microRNA 6904	ncRNA
mm_137160.1	chr17	23790626	23790670	+	1	NA	Intergenic	CpG	-4571	NM_029798	76917	Mm.269613	NM_029798	ENSMUSG00000023911	Flywch2	2810417J12Rik|3010014L17Rik|AW548203	FLYWCH family member 2	protein-coding
mm_111880.1	chr12	108004087	108004097	-	1	NA	promoter-TSS (NM_021399)	promoter-TSS (NM_021399)	-678	NM_021399	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_155143.1	chrX	52788287	52788296	+	1	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	-2909	NM_001034059	434778	Mm.23411	NM_001034059	ENSMUSG00000073207	Ccdc160	6330534C20Rik	coiled-coil domain containing 160	protein-coding
mm_67119.1	chr7	70361598	70361611	-	1	NA	intron (NM_183261, intron 1 of 2)	intron (NM_183261, intron 1 of 2)	-1011	NM_009697	11819	Mm.158143	NM_009697	ENSMUSG00000030551	Nr2f2	2700033K02Rik|9430015G03Rik|ARP-1|Aporp1|COUP-TF2|COUP-TFII|COUPTFB|EAR3|SVP40|Tcfcoup2	nuclear receptor subfamily 2, group F, member 2	protein-coding
mm_90488.1	chr10	128015158	128015175	+	1	NA	promoter-TSS (NM_008921)	promoter-TSS (NM_008921)	-49	NM_008921	19075	Mm.2903	NM_008921	ENSMUSG00000025395	Prim1	AI324982	DNA primase, p49 subunit	protein-coding
mm_44892.1	chr5	35096019	35096029	-	1	NA	exon (NM_013587, exon 6 of 8)	exon (NM_013587, exon 6 of 8)	9673	NM_013587	16976	Mm.277661	NM_013587	ENSMUSG00000029103	Lrpap1	AA617339|AI790446|AU042172|C77774|HBP44|RAP	low density lipoprotein receptor-related protein associated protein 1	protein-coding
mm_78691.1	chr9	40804225	40804235	+	1	NA	exon (NM_031165, exon 7 of 9)	exon (NM_031165, exon 7 of 9)	2957	NM_031165	15481	Mm.290774	NM_031165	ENSMUSG00000015656	Hspa8	2410008N15Rik|Hsc70|Hsc71|Hsc73|Hsp73|Hspa10	heat shock protein 8	protein-coding
mm_39485.1	chr5	20882446	20882526	+	1	NA	promoter-TSS (NM_177601)	promoter-TSS (NM_177601)	33	NM_177601	212090	Mm.347525	NM_177601	ENSMUSG00000045435	Tmem60	BC027828	transmembrane protein 60	protein-coding
mm_97244.1	chr11	75733038	75733043	+	1	NA	exon (NM_009536, exon 1 of 6)	exon (NM_009536, exon 1 of 6)	153	NM_009536	22627	Mm.234700	NM_009536	ENSMUSG00000020849	Ywhae	AU019196	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide	protein-coding
mm_118347.1	chr13	114854445	114854449	-	1	NA	exon (NM_008396, exon 21 of 30)	exon (NM_008396, exon 21 of 30)	36210	NM_001113374	17434	Mm.19027	NM_013826	ENSMUSG00000015536	Mocs2	AI415403	molybdenum cofactor synthesis 2	protein-coding
mm_24494.1	chr3	92366037	92366046	+	1	NA	exon (NM_011472, exon 2 of 2)	exon (NM_011472, exon 2 of 2)	854	NM_011472	20760	Mm.10692	NM_011472	ENSMUSG00000050635	Sprr2f	-	small proline-rich protein 2F	protein-coding
mm_149991.1	chr19	29252430	29252442	+	1	NA	intron (NM_001048177, intron 1 of 23)	intron (NM_001048177, intron 1 of 23)	633	NM_008413	16452	Mm.275839	NM_008413	ENSMUSG00000024789	Jak2	Fd17	Janus kinase 2	protein-coding
mm_32587.1	chr4	111414960	111415036	+	1	NA	promoter-TSS (NM_026279)	promoter-TSS (NM_026279)	-8	NR_033793	67621	Mm.45533	NM_026279	ENSMUSG00000028545	Bend5	2310026E23Rik	BEN domain containing 5	protein-coding
mm_36739.1	chr4	99656036	99656040	-	1	NA	promoter-TSS (NM_010425)	promoter-TSS (NM_010425)	-261	NM_010425	15221	Mm.4758	NM_010425	ENSMUSG00000067261	Foxd3	CWH3|Genesis|Hfh2	forkhead box D3	protein-coding
mm_37377.1	chr4	120975181	120975189	-	1	NA	intron (NM_133716, intron 6 of 9)	intron (NM_133716, intron 6 of 9)	-1863	NR_105982	102465614		NR_105982	ENSMUSG00000106436	Mir7015	mmu-mir-7015	microRNA 7015	ncRNA
mm_14804.1	chr2	145886931	145886941	+	1	NA	3' UTR (NM_028724, exon 13 of 13)	3' UTR (NM_028724, exon 13 of 13)	-16305	NM_026425	67877	Mm.151168	NM_026425	ENSMUSG00000002728	Naa20	1500004D14Rik|2900026I01Rik|AU041458|D2Ertd186e|Nat5	N(alpha)-acetyltransferase 20, NatB catalytic subunit	protein-coding
mm_59417.1	chr7	27121687	27121716	+	1	NA	exon (NM_007817, exon 2 of 10)	exon (NM_007817, exon 2 of 10)	1746	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_110636.1	chr12	57546466	57546504	-	1	NA	promoter-TSS (NM_008259)	promoter-TSS (NM_008259)	-364	NM_008259	15375	Mm.4578	NM_008259	ENSMUSG00000035451	Foxa1	Hnf-3a|Hnf3a|Tcf-3a|Tcf3a	forkhead box A1	protein-coding
mm_144149.1	chr18	5125611	5125615	+	1	NA	Intergenic	Intergenic	79024	NM_001347449	225115	Mm.136791	NM_153153	ENSMUSG00000024236	Svil	AU024053|B430302E16Rik	supervillin	protein-coding
mm_9890.1	chr1	186704957	186704964	-	1	NA	5' UTR (NM_009367, exon 1 of 7)	5' UTR (NM_009367, exon 1 of 7)	1029	NM_009367	21808	Mm.18213	NM_009367	ENSMUSG00000039239	Tgfb2	BB105277|Tgf-beta2|Tgfb-2	transforming growth factor, beta 2	protein-coding
mm_27565.1	chr3	58577730	58577739	-	1	NA	intron (NM_001040396, intron 1 of 5)	intron (NM_001040396, intron 1 of 5)	1076	NM_001040396	69227	Mm.270950	NM_001040396	ENSMUSG00000075700	Selenot	2810407C02Rik|5730408P04Rik|Selt	selenoprotein T	protein-coding
mm_117378.1	chr13	72628591	72628607	-	1	NA	promoter-TSS (NR_030701)	promoter-TSS (NR_030701)	-35	NR_030701	328287	Mm.235072	NR_030701		Gm20554	D430050G20	predicted gene, 20554	ncRNA
mm_133362.1	chr16	84703568	84703578	+	1	NA	Intergenic	Intergenic	-9450	NR_132106	100653389	Mm.261808	NR_132106	ENSMUSG00000097418	Mir155hg	Bic|Gm26667	Mir155 host gene (non-protein coding)	ncRNA
mm_45519.1	chr5	72559615	72559691	-	1	NA	promoter-TSS (NM_133921)	promoter-TSS (NM_133921)	-8	NM_133921	100978	Mm.187453	NM_133921	ENSMUSG00000072889	Nfxl1	1700012H24Rik|AW538212|D430033A06Rik|DNABF|GCF|Gm1058|TCF9	nuclear transcription factor, X-box binding-like 1	protein-coding
mm_127227.1	chr15	99401812	99401826	+	1	NA	intron (NM_001171035, intron 2 of 9)	intron (NM_001171035, intron 2 of 9)	8600	NM_001171035	110213	Mm.16769	NM_026669	ENSMUSG00000023010	Tmbim6	5031406P05Rik|Bi1|Tegt	transmembrane BAX inhibitor motif containing 6	protein-coding
mm_5020.1	chr1	193153168	193153179	+	1	NA	promoter-TSS (NM_016851)	promoter-TSS (NM_016851)	61	NM_016851	54139	Mm.273695	NM_016851	ENSMUSG00000026638	Irf6	AI876454|E230028I05Rik|mirf6	interferon regulatory factor 6	protein-coding
mm_168614.1	chr11	76868368	76868373	-	1	NA	Intergenic	MT2_Mm|LTR|ERVL	-21362	NM_007754	12874	Mm.276736	NM_007754	ENSMUSG00000020841	Cpd	AA960140|AW322530|D830034L15Rik	carboxypeptidase D	protein-coding
mm_59780.1	chr7	28863832	28863835	+	1	NA	promoter-TSS (NM_008496)	promoter-TSS (NM_008496)	-553	NM_008496	16858	Mm.20973	NM_008496	ENSMUSG00000053522	Lgals7	Galectin-7|Pig1	lectin, galactose binding, soluble 7	protein-coding
mm_122735.1	chr14	53845831	53845844	-	1	NA	Intergenic	Intergenic	408092	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_4081.1	chr1	166379362	166379407	+	1	NA	5' UTR (NM_030245, exon 1 of 8)	5' UTR (NM_030245, exon 1 of 8)	217	NM_030245	27878	Mm.100665	NM_030245	ENSMUSG00000026563	Tada1	2900026B15Rik|D1Ertd251e|Staf42|Tada1l	transcriptional adaptor 1	protein-coding
mm_3534.1	chr1	150392795	150392849	+	1	NA	promoter-TSS (NM_133780)	promoter-TSS (NM_133780)	-16	NM_133780	108989	Mm.174256	NM_133780	ENSMUSG00000006005	Tpr	2610029M07Rik|C77892	translocated promoter region, nuclear basket protein	protein-coding
mm_151324.1	chr19	55893146	55893154	+	1	NA	intron (NR_138565, intron 4 of 15)	intron (NR_138565, intron 4 of 15)	-2171	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_54048.1	chr6	13838098	13838107	-	1	NA	5' UTR (NM_001330666, exon 3 of 4)	5' UTR (NM_001330666, exon 3 of 4)	1840	NM_001330666	64450	Mm.167625	NM_145066	ENSMUSG00000048216	Gpr85	2900026B03Rik	G protein-coupled receptor 85	protein-coding
mm_90963.1	chr10	13335506	13335514	-	1	NA	intron (NM_001195065, intron 1 of 12)	intron (NM_001195065, intron 1 of 12)	-11350	NM_001033257	215789	Mm.283359	NM_001033257	ENSMUSG00000062866	Phactr2	AV158170|BC012871	phosphatase and actin regulator 2	protein-coding
mm_80107.1	chr9	70399324	70399349	+	1	NA	3' UTR (NM_181072, exon 28 of 28)	3' UTR (NM_181072, exon 28 of 28)	6417	NR_049200	100885839		NR_049200	ENSMUSG00000093763	Mir5626	Gm25590|mir-5626|mmu-mir-5626	microRNA 5626	ncRNA
mm_13971.1	chr2	121433516	121433537	+	1	NA	exon (NM_007952, exon 8 of 13)	exon (NM_007952, exon 8 of 13)	9075	NM_145973	269344	Mm.330522	NM_145973	ENSMUSG00000027246	Ell3	A930015D22Rik	elongation factor RNA polymerase II-like 3	protein-coding
mm_44410.1	chr5	17849738	17849781	-	1	NA	promoter-TSS (NM_001159557)	promoter-TSS (NM_001159557)	33	NM_001159557	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_103927.1	chr11	83648096	83648199	-	1	NA	3' UTR (NM_011337, exon 3 of 3)	3' UTR (NM_011337, exon 3 of 3)	1231	NM_011337	20302	Mm.1282	NM_011337	ENSMUSG00000000982	Ccl3	AI323804|G0S19-1|LD78alpha|MIP-1alpha|MIP1-(a)|MIP1-alpha|Mip1a|Scya3	chemokine (C-C motif) ligand 3	protein-coding
mm_118367.1	chr13	115102139	115102141	-	1	NA	promoter-TSS (NM_001033228)	promoter-TSS (NM_001033228)	-176	NM_001033228	109700	Mm.317280	NM_001033228	ENSMUSG00000042284	Itga1	CD49A|E130012M19Rik|Vla1	integrin alpha 1	protein-coding
mm_145330.1	chr18	55939568	55939587	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	-492555	NM_026240	107022	Mm.24356	NM_026240	ENSMUSG00000001700	Gramd3	9030613F08Rik|9130427A09Rik|AW061306|NS3TP2	GRAM domain containing 3	protein-coding
mm_32593.1	chr4	111720174	111720182	+	1	NA	5' UTR (NM_026470, exon 1 of 13)	5' UTR (NM_026470, exon 1 of 13)	168	NM_026470	67946	Mm.275526	NM_026470	ENSMUSG00000034401	Spata6	1700062C23Rik|AI790763|Hash|KRP|Mash	spermatogenesis associated 6	protein-coding
mm_126857.1	chr15	89243332	89243366	+	1	NA	5' UTR (NM_026813, exon 3 of 25)	5' UTR (NM_026813, exon 3 of 25)	31790	NM_027805	71474	Mm.184055	NM_026813	ENSMUSG00000036561	Ppp6r2	1110033O10Rik|8430411H09Rik|B230107H12Rik|Pp6r2|Saps2	protein phosphatase 6, regulatory subunit 2	protein-coding
mm_128376.1	chr15	42676772	42676791	-	1	NA	5' UTR (NM_001286062, exon 1 of 9)	5' UTR (NM_001286062, exon 1 of 9)	196	NM_001286062	11600	Mm.309336	NM_009640	ENSMUSG00000022309	Angpt1	1110046O21Rik|Ang-1|Ang1	angiopoietin 1	protein-coding
mm_7216.1	chr1	93160268	93160285	-	1	NA	5' UTR (NM_001159940, exon 2 of 6)	5' UTR (NM_001159940, exon 2 of 6)	594	NM_001159940	71874	Mm.158766	NM_172411	ENSMUSG00000034159	2310007B03Rik	-	RIKEN cDNA 2310007B03 gene	protein-coding
mm_136205.1	chr16	89833144	89833154	-	1	NA	exon (NM_001145886, exon 15 of 28)	exon (NM_001145886, exon 15 of 28)	-14797	NM_001145887	21844	Mm.310902	NM_009384	ENSMUSG00000002489	Tiam1	AI847750|D16Ium10|D16Ium10e	T cell lymphoma invasion and metastasis 1	protein-coding
mm_103419.1	chr11	75573229	75573244	-	1	NA	3' UTR (NM_001199283, exon 14 of 14)	3' UTR (NM_001199283, exon 14 of 14)	-14843	NM_008850	18738	Mm.3128	NM_008850	ENSMUSG00000017781	Pitpna	Pitpn|vb|vibrator	phosphatidylinositol transfer protein, alpha	protein-coding
mm_122253.1	chr14	34102693	34102709	-	1	NA	promoter-TSS (NM_001251843)	promoter-TSS (NM_001251843)	53	NM_001251843	105518	Mm.246608	NM_001251843	ENSMUSG00000095493	A630023A22Rik	AI461879	RIKEN cDNA A630023A22 gene	protein-coding
mm_148003.1	chr18	67724561	67724599	-	1	NA	promoter-TSS (NM_001127177)	promoter-TSS (NM_001127177)	41	NM_001127177	19255	Mm.260433	NM_008977	ENSMUSG00000024539	Ptpn2	AI325124|Ptpt|TC-PTP	protein tyrosine phosphatase, non-receptor type 2	protein-coding
mm_166654.1	chr6	86765600	86765605	-	1	NA	intron (NM_013471, intron 2 of 12)	intron (NM_013471, intron 2 of 12)	9512	NM_001331120	11746	Mm.259702	NM_013471	ENSMUSG00000029994	Anxa4	AI265406|AIV|AW106930|Anx4|Xanx-4	annexin A4	protein-coding
mm_105005.1	chr11	100376885	100376903	-	1	NA	exon (NM_010593, exon 9 of 14)	exon (NM_010593, exon 9 of 14)	-20753	NM_010404	15114	Mm.281700	NM_010404	ENSMUSG00000006930	Hap1	HAP-1	huntingtin-associated protein 1	protein-coding
mm_70268.1	chr8	3587698	3587711	+	1	NA	5' UTR (NM_027171, exon 1 of 17)	5' UTR (NM_027171, exon 1 of 17)	254	NM_001347111	69697	Mm.390010	NM_027171	ENSMUSG00000044433	Camsap3	2310057J16Rik|Kiaa1543|Nezha	calmodulin regulated spectrin-associated protein family, member 3	protein-coding
mm_43191.1	chr5	128736169	128736187	+	1	NA	promoter-TSS (NM_021311)	promoter-TSS (NM_021311)	-68	NM_021311	57749	Mm.272720	NM_021311	ENSMUSG00000029423	Piwil1	MIWI	piwi-like RNA-mediated gene silencing 1	protein-coding
mm_32599.1	chr4	111827983	111827996	+	1	NA	intron (NM_026470, intron 12 of 12)	intron (NM_026470, intron 12 of 12)	74807	NM_145551	230612	Mm.26630	NM_145551	ENSMUSG00000028544	Slc5a9	AI159731|SGLT4	solute carrier family 5 (sodium/glucose cotransporter), member 9	protein-coding
mm_9963.1	chr1	191164816	191164818	-	1	NA	promoter-TSS (NM_001109759)	promoter-TSS (NM_001109759)	0	NM_001109759	619288	Mm.61148	NM_001109759	ENSMUSG00000091017	Fam71a	4933417M04Rik|GARI-L4	family with sequence similarity 71, member A	protein-coding
mm_28801.1	chr3	96209656	96209658	-	1	NA	Intergenic	Intergenic	-10259	NM_178213	621893		NM_178213	ENSMUSG00000063689	Hist2h2ab	EG621893|H2a-613a	histone cluster 2, H2ab	protein-coding
mm_61565.1	chr7	79686498	79686501	+	1	NA	intron (NM_029835, intron 15 of 21)	L1M4|LINE|L1	26303	NM_029835	77011	Mm.28132	NM_029835	ENSMUSG00000046591	Ticrr	5730590G19Rik|BC028450|Lrrk1	TOPBP1-interacting checkpoint and replication regulator	protein-coding
mm_35775.1	chr4	46404042	46404058	-	1	NA	5' UTR (NM_053149, exon 1 of 4)	5' UTR (NM_053149, exon 1 of 4)	133	NM_053149	93966	Mm.25793	NM_053149	ENSMUSG00000028332	Hemgn	4921524M03Rik|AI317176|EDAG|Hgn|mNDR	hemogen	protein-coding
mm_30897.1	chr4	32335933	32335935	+	1	NA	Intergenic	Intergenic	-81501	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_111592.1	chr12	101975936	101975946	-	1	NA	promoter-TSS (NM_016856)	promoter-TSS (NM_016856)	-33	NM_016856	51786	Mm.716	NM_016856	ENSMUSG00000041781	Cpsf2	100kDa|2610024B04Rik|AI662483|Cpsf|MCPSF|mKIAA1367	cleavage and polyadenylation specific factor 2	protein-coding
mm_109151.1	chr12	107691067	107691077	+	1	NA	Intergenic	Intergenic	44416	NR_045973	74968	Mm.359821	NR_045973	ENSMUSG00000085641	4930465M20Rik	4930431H15Rik	RIKEN cDNA 4930465M20 gene	ncRNA
mm_120844.1	chr14	75199274	75199351	+	1	NA	exon (NM_001247984, exon 3 of 16)	exon (NM_001247984, exon 3 of 16)	-42975	NM_019775	56373	Mm.24242	NM_019775	ENSMUSG00000021999	Cpb2	1110032P04Rik|4930405E17Rik|AI255929|CPR|Cpu|TAFI	carboxypeptidase B2 (plasma)	protein-coding
mm_83602.1	chr9	48495322	48495335	-	1	NA	promoter-TSS (NM_001004191)	promoter-TSS (NM_001004191)	2	NM_001326355	67010	Mm.76911	NM_144948	ENSMUSG00000042396	Rbm7	1200007M24Rik|1500011D06Rik|AU041934|AW554393	RNA binding motif protein 7	protein-coding
mm_118868.1	chr14	25855604	25855606	+	1	NA	intron (NM_013469, intron 1 of 14)	intron (NM_013469, intron 1 of 14)	13450	NM_013469	11744	Mm.294083	NM_013469	ENSMUSG00000021866	Anxa11	A830099O17Rik|Anx11	annexin A11	protein-coding
mm_132679.1	chr16	42925931	42925936	+	1	NA	intron (NM_001285805, intron 1 of 10)	AT_rich|Low_complexity|Low_complexity	-13863	NR_040402	100503040	Mm.490721	NR_040402		Gm19522	-	predicted gene, 19522	ncRNA
mm_39820.1	chr5	30778863	30778888	+	1	NA	exon (NM_023047, exon 5 of 13)	exon (NM_023047, exon 5 of 13)	-35766	NM_133350	100732	Mm.332295	NM_133350	ENSMUSG00000029166	Mapre3	AI790651|EB2|EB3|EBF3|RP3	microtubule-associated protein, RP/EB family, member 3	protein-coding
mm_127572.1	chr15	102279496	102279548	+	1	NA	promoter-TSS (NM_134100)	promoter-TSS (NM_134100)	66	NM_134100	106073	Mm.287740	NM_134100	ENSMUSG00000045665	Mfsd5	AA409375|AW556797|D15Mgi27	major facilitator superfamily domain containing 5	protein-coding
mm_156499.1	chrX	144364050	144364073	+	1	NA	non-coding (NR_037145, exon 24 of 27)	non-coding (NR_037145, exon 24 of 27)	46095	NM_026247	67574	Mm.249084	NM_026247	ENSMUSG00000041718	Alg13	2810046O15Rik|4833435D08Rik|Glt28d1|MDS031|OTTMUSG00000018917	asparagine-linked glycosylation 13	protein-coding
mm_134950.1	chr16	31300480	31300502	-	1	NA	intron (NM_001301353, intron 4 of 5)	intron (NM_001301353, intron 4 of 5)	14317	NM_001301353	11815	Mm.2082	NM_007470	ENSMUSG00000022548	Apod	-	apolipoprotein D	protein-coding
mm_88586.1	chr10	79710768	79710791	+	1	NA	exon (NM_001077184, exon 5 of 7)	exon (NM_001077184, exon 5 of 7)	-5855	NM_008226	15166	Mm.12956	NM_008226	ENSMUSG00000020331	Hcn2	BCNG2|HAC1|trls	hyperpolarization-activated, cyclic nucleotide-gated K+ 2	protein-coding
mm_3870.1	chr1	160989572	160989588	+	1	NA	exon (NM_080844, exon 3 of 8)	exon (NM_080844, exon 3 of 8)	10974	NM_080844	11905	Mm.260770	NM_080844	ENSMUSG00000026715	Serpinc1	AI114908|ATIII|At-3|At3	serine (or cysteine) peptidase inhibitor, clade C (antithrombin), member 1	protein-coding
mm_62063.1	chr7	92448963	92448966	+	1	NA	3' UTR (NM_001243047, exon 11 of 11)	3' UTR (NM_001243047, exon 11 of 11)	-112185	NM_025515	66365	Mm.21173	NM_025515	ENSMUSG00000030613	Ccdc90b	2310015N07Rik|C86558	coiled-coil domain containing 90B	protein-coding
mm_85016.1	chr9	88273337	88273345	-	1	NA	Intergenic	Intergenic	-54268	NM_011851	23959	Mm.244235	NM_011851	ENSMUSG00000032420	Nt5e	2210401F01Rik|5'-NT|AI447961|CD73|NT|Nt5|eNT	5' nucleotidase, ecto	protein-coding
mm_67885.1	chr7	99349122	99349152	-	1	NA	exon (NM_009825, exon 2 of 5)	exon (NM_009825, exon 2 of 5)	4102	NM_009825	12406	Mm.22708	NM_009825	ENSMUSG00000070436	Serpinh1	BERF-1|Cbp1|Cbp2|Hsp47|J6|Serpinh2|gp46	serine (or cysteine) peptidase inhibitor, clade H, member 1	protein-coding
mm_153701.1	chr19	44397682	44397741	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	9998	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_51461.1	chr6	82070713	82070725	+	1	NA	intron (NM_145570, intron 1 of 2)	intron (NM_145570, intron 1 of 2)	29091	NM_145570	232146	Mm.489683	NM_145570	ENSMUSG00000035104	Eva1a	BC014699|Fam176a|Tmem166	eva-1 homolog A (C. elegans)	protein-coding
mm_164988.1	chr19	11165598	11165604	-	1	NA	promoter-TSS (NM_027074)	promoter-TSS (NM_027074)	-281	NM_027074	69416	Mm.72491	NM_027074	ENSMUSG00000024728	1700025F22Rik	-	RIKEN cDNA 1700025F22 gene	protein-coding
mm_140400.1	chr17	87638411	87638415	+	1	NA	intron (NM_008532, intron 2 of 9)	intron (NM_008532, intron 2 of 9)	2434	NM_008532	17075	Mm.4259	NM_008532	ENSMUSG00000045394	Epcam	CD326|EGP|EGP-2|Egp314|Ep-CAM|EpCAM1|GA733-2|Ly74|TROP1|Tacsd1|Tacstd1|gp40	epithelial cell adhesion molecule	protein-coding
mm_93307.1	chr10	98690063	98690094	-	1	NA	Intergenic	Intergenic	-225074	NM_026482	67972	Mm.166944	NM_026482	ENSMUSG00000019943	Atp2b1	2810442I22Rik|E130111D10Rik|Pmca1	ATPase, Ca++ transporting, plasma membrane 1	protein-coding
mm_28140.1	chr3	87263519	87263591	-	1	NA	promoter-TSS (NM_030707)	promoter-TSS (NM_030707)	-31	NM_030707	80891	Mm.45173	NM_030707	ENSMUSG00000015852	Fcrls	2810439C17Rik|9330158F12|FcRH2sc|Fcrh2|IFGP2|IgSR|MMAN-g|Msr2|moFcRH2sc	Fc receptor-like S, scavenger receptor	protein-coding
mm_67471.1	chr7	80420009	80420021	-	1	NA	Intergenic	Intergenic	-14579	NM_001081454	18550	Mm.5241	NM_011046	ENSMUSG00000030530	Furin	9130404I01Rik|Fur|PACE|Pcsk3|SPC1	furin (paired basic amino acid cleaving enzyme)	protein-coding
mm_20831.1	chr2	147013786	147013799	-	1	NA	intron (NM_011917, intron 1 of 29)	CpG	732	NM_011917	24128	Mm.3065	NM_011917	ENSMUSG00000027433	Xrn2	-	5'-3' exoribonuclease 2	protein-coding
mm_40841.1	chr5	73284265	73284273	+	1	NA	promoter-TSS (NR_040689)	promoter-TSS (NR_040689)	-85	NR_040687	72276	Mm.271215	NR_040687	ENSMUSG00000100175	1700025M24Rik	-	RIKEN cDNA 1700025M24 gene	ncRNA
mm_46446.1	chr5	105109433	105109435	-	1	NA	intron (NM_172777, intron 1 of 10)	L1MB4|LINE|L1	858	NM_172777	236573	Mm.425261	NM_172777	ENSMUSG00000029298	Gbp9	-	guanylate-binding protein 9	protein-coding
mm_39120.1	chr4	154964344	154964361	-	1	NA	intron (NM_001305804, intron 1 of 19)	CpG	229	NR_131230	269614	Mm.30042	NM_172990	ENSMUSG00000029056	Pank4	D030031I12Rik|R75150	pantothenate kinase 4	protein-coding
mm_113948.1	chr13	50417926	50417932	+	1	NA	promoter-TSS (NM_175401)	promoter-TSS (NM_175401)	52	NM_175401	109082	Mm.18638	NM_175401	ENSMUSG00000037816	Fbxw17	1110064L07Rik|C85886	F-box and WD-40 domain protein 17	protein-coding
mm_160872.1	chr11	67771046	67771046	-	1	NA	5' UTR (NM_175681, exon 1 of 13)	5' UTR (NM_175681, exon 1 of 13)	107	NM_175681	93896	Mm.118883	NM_175681	ENSMUSG00000049928	Glp2r	9530092J08Rik|GLP-2	glucagon-like peptide 2 receptor	protein-coding
mm_30869.1	chr4	32149459	32149486	+	1	NA	Intergenic	Intergenic	185365	NM_172688	26409	Mm.258589	NM_009316	ENSMUSG00000028284	Map3k7	B430101B05|C87327|Tak1	mitogen-activated protein kinase kinase kinase 7	protein-coding
mm_165544.1	chr2	181887984	181887987	+	1	NA	Intergenic	Intergenic	23625	NM_025901	67005	Mm.271986	NM_025901	ENSMUSG00000038628	Polr3k	12.3kDa|1500004O14Rik|AI196849|AU014893|C11|RPC10|RPC11	polymerase (RNA) III (DNA directed) polypeptide K	protein-coding
mm_50778.1	chr6	53681075	53681110	+	1	NA	exon (NM_172728, exon 4 of 7)	exon (NM_172728, exon 4 of 7)	107718	NM_172728	231991	Mm.227444	NM_172728	ENSMUSG00000053007	Creb5	9430076C15Rik|CRE-BPa|Crebpa|D430026C09Rik	cAMP responsive element binding protein 5	protein-coding
mm_39567.1	chr5	23387301	23387317	+	1	NA	Intergenic	Intergenic	47044	NR_040469	269630	Mm.425231	NR_040469	ENSMUSG00000073147	5031425E22Rik	-	RIKEN cDNA 5031425E22 gene	ncRNA
mm_30977.1	chr4	34588506	34588508	+	1	NA	intron (NM_001159563, intron 9 of 19)	intron (NM_001159563, intron 9 of 19)	26435	NM_001159563	50793	Mm.399624	NM_015824	ENSMUSG00000040044	Orc3	Orc3l	origin recognition complex, subunit 3	protein-coding
mm_22846.1	chr3	28034669	28034672	+	1	NA	intron (NM_008875, intron 6 of 25)	intron (NM_008875, intron 6 of 25)	50499	NM_008875	18805	Mm.212039	NM_008875	ENSMUSG00000027695	Pld1	AA536939|C85393|Pld1a|Pld1b|mPLD1	phospholipase D1	protein-coding
mm_19305.1	chr2	90491081	90491088	-	1	NA	intron (NM_008982, intron 1 of 23)	intron (NM_008982, intron 1 of 23)	-11910	NM_001135657	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_106467.1	chr11	120070670	120070686	-	1	NA	intron (NM_009734, intron 14 of 25)	intron (NM_009734, intron 14 of 25)	16149	NM_009734	12009	Mm.2556	NM_009734	ENSMUSG00000039781	Cep131	AZ1|Azi|Azi1	centrosomal protein 131	protein-coding
mm_41881.1	chr5	105400409	105400418	+	1	NA	Intergenic	Intergenic	-15362	NM_001033550	433926	Mm.439781	NM_001033550	ENSMUSG00000070639	Lrrc8b	R75581|Ta-lrrp|mKIAA0231	leucine rich repeat containing 8 family, member B	protein-coding
mm_87821.1	chr10	60346897	60346916	+	1	NA	promoter-TSS (NM_001159572)	promoter-TSS (NM_001159572)	55	NM_028732	74048	Mm.273584	NM_028732	ENSMUSG00000020101	Vsir	4632428N05Rik|Dies1|PD-1H|VISTA	V-set immunoregulatory receptor	protein-coding
mm_9703.1	chr1	179156265	179156307	-	1	NA	intron (NM_027188, intron 5 of 11)	RSINE1|SINE|B4	361717	NM_027188	69726	Mm.222338	NM_027188	ENSMUSG00000055067	Smyd3	2410008A19Rik|Zmynd1	SET and MYND domain containing 3	protein-coding
mm_164674.1	chr17	45747120	45747129	+	1	NA	Intergenic	Intergenic	-13280	NM_028164	72240	Mm.482897	NM_028164	ENSMUSG00000094690	1600014C23Rik	-	RIKEN cDNA 1600014C23 gene	protein-coding
mm_148736.1	chr19	5912953	5912954	+	1	NA	promoter-TSS (NM_001291078)	promoter-TSS (NM_001291078)	-82	NM_001291078	19708	Mm.2651	NM_011262	ENSMUSG00000024826	Dpf2	2210010M07Rik|BAF45D|Req|ubi-d4	D4, zinc and double PHD fingers family 2	protein-coding
mm_101160.1	chr11	16972924	16973000	-	1	NA	3' UTR (NM_019549, exon 10 of 10)	3' UTR (NM_019549, exon 10 of 10)	21552	NM_176982	319701	Mm.120672	NM_176982	ENSMUSG00000044966	Fbxo48	A630050E13Rik	F-box protein 48	protein-coding
mm_122600.1	chr14	51039364	51039369	-	1	NA	exon (NM_183032, exon 2 of 2)	exon (NM_183032, exon 2 of 2)	2501	NM_183032	328401	Mm.99528	NM_183032	ENSMUSG00000052382	Rnase9	ESRL|Rak1	ribonuclease, RNase A family, 9 (non-active)	protein-coding
mm_94987.1	chr11	31870869	31870900	+	1	NA	promoter-TSS (NM_026252)	promoter-TSS (NM_026252)	-56	NM_001290676	67579	Mm.339792	NM_026252	ENSMUSG00000020300	Cpeb4	Cpe-bp4|Cpeb-4|mCPEB-4	cytoplasmic polyadenylation element binding protein 4	protein-coding
mm_146729.1	chr18	15207791	15207797	-	1	NA	Intergenic	ID_B1|SINE|B4	-56348	NM_134112	106931	Mm.329299	NM_134112	ENSMUSG00000036225	Kctd1	4933402K10Rik|AI661543|AW553000	potassium channel tetramerisation domain containing 1	protein-coding
mm_114602.1	chr13	75771049	75771070	+	1	NA	3' UTR (NM_138953, exon 12 of 12)	3' UTR (NM_138953, exon 12 of 12)	63575	NM_138953	192657	Mm.21288	NM_138953	ENSMUSG00000001542	Ell2	-	elongation factor RNA polymerase II 2	protein-coding
mm_122481.1	chr14	45658146	45658183	-	1	NA	promoter-TSS (NM_001042719)	promoter-TSS (NM_001042719)	-21	NM_001042719	114874	Mm.121918	NM_176845	ENSMUSG00000037697	Ddhd1	Mir5131|PA-PLA1	DDHD domain containing 1	protein-coding
mm_83342.1	chr9	44288313	44288323	-	1	NA	promoter-TSS (NM_138955)	promoter-TSS (NM_138955)	-74	NM_138955	192663	Mm.101876	NM_138955	ENSMUSG00000032131	Abcg4	6430517O04Rik	ATP-binding cassette, sub-family G (WHITE), member 4	protein-coding
mm_113629.1	chr13	41865932	41865945	+	1	NA	promoter-TSS (NR_033545)	promoter-TSS (NR_033545)	23	NR_033545	100038577	Mm.387093	NR_033545		Gm10790	ENSMUSG00000074927	predicted gene 10790	ncRNA
mm_39821.1	chr5	30796888	30796914	+	1	NA	3' UTR (NM_023047, exon 13 of 13)	3' UTR (NM_023047, exon 13 of 13)	-17740	NM_133350	100732	Mm.332295	NM_133350	ENSMUSG00000029166	Mapre3	AI790651|EB2|EB3|EBF3|RP3	microtubule-associated protein, RP/EB family, member 3	protein-coding
mm_110721.1	chr12	69607308	69607316	-	1	NA	exon (NM_001135559, exon 14 of 23)	exon (NM_001135559, exon 14 of 23)	-24284	NM_001033236	207965	Mm.102487	NM_001033236	ENSMUSG00000049882	Vcpkmt	Gm71|Mettl21d|Mettl221d|VCP-KMT	valosin containing protein lysine (K) methyltransferase	protein-coding
mm_57265.1	chr6	123286305	123286367	-	1	NA	exon (NM_019948, exon 4 of 6)	exon (NM_019948, exon 4 of 6)	3535	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_10268.1	chr2	9879748	9879764	+	1	NA	Intergenic	Intergenic	-1156	NM_008091	14462	Mm.313866	NM_008091	ENSMUSG00000015619	Gata3	Gata-3|jal	GATA binding protein 3	protein-coding
mm_112226.1	chr12	113430450	113430486	-	1	NA	Intergenic	Intergenic	-59097	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_139828.1	chr17	69075673	69075691	+	1	NA	Intergenic	CpG	-81128	NM_013813	13823	Mm.131135	NM_013813	ENSMUSG00000024044	Epb41l3	4.1B|DAL1P|Dal1|Epb4.1l3|NBL3	erythrocyte membrane protein band 4.1 like 3	protein-coding
mm_122320.1	chr14	36935561	36935578	-	1	NA	promoter-TSS (NM_028407)	promoter-TSS (NM_028407)	-1	NM_028407	72972	Mm.27621	NM_027045	ENSMUSG00000058690	Ccser2	1700012P13Rik|2900054P12Rik|AI035535|AW108503|Fam190b|Gcap14	coiled-coil serine rich 2	protein-coding
mm_101985.1	chr11	50718842	50718853	-	1	NA	intron (NM_175643, intron 3 of 21)	intron (NM_175643, intron 3 of 21)	108884	NM_013922	30944	Mm.103674	NM_013922	ENSMUSG00000044807	Zfp354c	5330421P20Rik|AJ18|AW743325|Kid3|Tcf17l2|Znf354c|mKIAA4218	zinc finger protein 354C	protein-coding
mm_4595.1	chr1	178337871	178337902	+	1	NA	promoter-TSS (NM_016805)	promoter-TSS (NM_016805)	-102	NM_016805	51810	Mm.86589	NM_016805	ENSMUSG00000039630	Hnrnpu	AA408410|AI256620|AL024194|AL024437|AW557595|C86794|Hnrpu|SAFA|Sp120|hnRNP U	heterogeneous nuclear ribonucleoprotein U	protein-coding
mm_4435.1	chr1	172506768	172506785	+	1	NA	3' UTR (NM_178598, exon 5 of 5)	3' UTR (NM_178598, exon 5 of 5)	6530	NM_178598	21346	Mm.271711	NM_178598	ENSMUSG00000026547	Tagln2	2700094C18Rik|SM22beta|Sm22B|Sm22a	transgelin 2	protein-coding
mm_28949.1	chr3	100365779	100365783	-	1	NA	Intergenic	Intergenic	-60624	NR_040543	73806	Mm.396549	NR_040543	ENSMUSG00000086923	4930406D18Rik	-	RIKEN cDNA 4930406D18 gene	ncRNA
mm_152905.1	chr19	26046442	26046452	-	1	NA	Intergenic	ID4|SINE|ID	374036	NM_145831	226049	Mm.275572	NM_145831	ENSMUSG00000048138	Dmrt2	Terra	doublesex and mab-3 related transcription factor 2	protein-coding
mm_58186.1	chr6	142964405	142964438	-	1	NA	promoter-TSS (NM_011374)	promoter-TSS (NM_011374)	31	NM_011374	20449	Mm.260838	NM_011374	ENSMUSG00000030283	St8sia1	9330109E03Rik|GD3S|Sia-T|Siat8|Siat8a	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 1	protein-coding
mm_171618.1	chr4	151921747	151921748	-	1	NA	Intergenic	LTRIS2|LTR|ERV1	-11973	NM_172704	230935	Mm.21353	NM_172704	ENSMUSG00000039768	Dnajc11	E030019A03Rik	DnaJ heat shock protein family (Hsp40) member C11	protein-coding
mm_96366.1	chr11	67200092	67200107	+	1	NA	promoter-TSS (NM_030679)	promoter-TSS (NM_030679)	-15	NM_030679	17879	Mm.477065	NM_030679	ENSMUSG00000056328	Myh1	A530084A17Rik|IId|IId/x|MHC-2X/D|MHC2X/D|MYHC-IIX|MdMs|MyHC-IId/x|MyHC-IIx/d|Myhs-f|Myhs-f2|Myhsf2	myosin, heavy polypeptide 1, skeletal muscle, adult	protein-coding
mm_96425.1	chr11	67257195	67257211	+	1	NA	exon (NM_010855, exon 35 of 40)	exon (NM_010855, exon 35 of 40)	19391	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_153546.1	chr19	42086269	42086279	-	1	NA	promoter-TSS (NM_198108)	promoter-TSS (NM_198108)	96	NM_198108	226123	Mm.259441	NM_198108	ENSMUSG00000049670	Morn4	-	MORN repeat containing 4	protein-coding
mm_66538.1	chr7	45154520	45154572	-	1	NA	promoter-TSS (NM_145954)	promoter-TSS (NM_145954)	-8	NM_145954	69748	Mm.82139	NM_145954	ENSMUSG00000007833	Aldh16a1	2410004H02Rik|AI452234|mFLJ00209	aldehyde dehydrogenase 16 family, member A1	protein-coding
mm_138203.1	chr17	34293922	34293934	+	1	NA	Intergenic	Intergenic	-6157	NM_010378	14960	Mm.235338	NM_010378	ENSMUSG00000036594	H2-Aa	Aalpha|H-2Aa|H2Aa|I-Aalpha|IAalpha|Ia-1|Ia1	histocompatibility 2, class II antigen A, alpha	protein-coding
mm_165634.1	chr3	69127028	69127034	-	1	NA	promoter-TSS (NM_008467)	promoter-TSS (NM_008467)	61	NM_008467	16649	Mm.30601	NM_008467	ENSMUSG00000027782	Kpna4	1110058D08Rik|IPOA3	karyopherin (importin) alpha 4	protein-coding
mm_1787.1	chr1	78657857	78657868	+	1	NA	promoter-TSS (NM_001136222)	promoter-TSS (NM_001136222)	37	NM_001001981	195434	Mm.276016	NM_001001981	ENSMUSG00000079470	Utp14b	4932411L21Rik|jsd	UTP14B small subunit processome component	protein-coding
mm_102022.1	chr11	51644394	51644403	-	1	NA	exon (NM_145974, exon 4 of 5)	exon (NM_145974, exon 4 of 5)	-6556	NR_027958	97775	Mm.220299	NM_175289	ENSMUSG00000052563	D930048N14Rik	AI315703|R75254	RIKEN cDNA D930048N14 gene	ncRNA
mm_131238.1	chr16	10488176	10488204	+	1	NA	promoter-TSS (NM_007575)	promoter-TSS (NM_007575)	12	NM_007575	12265	Mm.249560	NM_007575	ENSMUSG00000022504	Ciita	C2ta|EG669998|Gm9475|Mhc2ta	class II transactivator	protein-coding
mm_31333.1	chr4	46454796	46454802	+	1	NA	intron (NM_130889, intron 1 of 6)	intron (NM_130889, intron 1 of 6)	3873	NM_130889	67628	Mm.263913	NM_130889	ENSMUSG00000028333	Anp32b	2410015B15Rik|PAL31|PHAPI2a|Ssp29	acidic (leucine-rich) nuclear phosphoprotein 32 family, member B	protein-coding
mm_7315.1	chr1	98095575	98095592	-	1	NA	promoter-TSS (NM_013626)	promoter-TSS (NM_013626)	49	NM_013626	18484	Mm.5121	NM_013626	ENSMUSG00000026335	Pam	PHM	peptidylglycine alpha-amidating monooxygenase	protein-coding
mm_46978.1	chr5	115272382	115272441	-	1	NA	exon (NM_016698, exon 1 of 17)	exon (NM_016698, exon 1 of 17)	484	NM_001302448	50849	Mm.30051	NM_016698	ENSMUSG00000041740	Rnf10	AA675014|RIE2|mKIAA0262	ring finger protein 10	protein-coding
mm_108143.1	chr12	76255333	76255337	+	1	NA	5' UTR (NM_138745, exon 1 of 28)	5' UTR (NM_138745, exon 1 of 28)	103	NM_138745	108156	Mm.29584	NM_138745	ENSMUSG00000021048	Mthfd1	Dcs|E430024A07Rik|Mthfd	methylenetetrahydrofolate dehydrogenase (NADP+ dependent), methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthase	protein-coding
mm_133205.1	chr16	73497318	73497328	+	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	834174	NM_019413	19876	Mm.310772	NM_019413	ENSMUSG00000022883	Robo1	AW494633|AW742721|DUTT1|Gm310	roundabout guidance receptor 1	protein-coding
mm_124067.1	chr14	78536855	78536879	-	1	NA	promoter-TSS (NM_001164503)	promoter-TSS (NM_001164503)	-7	NM_001164503	219181	Mm.89413	NM_001164503	ENSMUSG00000022016	Akap11	6330501D17Rik|AKAP220|Gm80|PRKA11|mKIAA0629	A kinase (PRKA) anchor protein 11	protein-coding
mm_14019.1	chr2	122150935	122150948	+	1	NA	exon (NM_009735, exon 2 of 4)	exon (NM_009735, exon 2 of 4)	3254	NM_009735	12010	Mm.163	NM_009735	ENSMUSG00000060802	B2m	Ly-m11|beta2-m|beta2m	beta-2 microglobulin	protein-coding
mm_102327.1	chr11	57801437	57801453	-	1	NA	promoter-TSS (NM_001081168)	promoter-TSS (NM_001081168)	22	NR_131042	76516	Mm.28485	NR_131042	ENSMUSG00000087165	2010001A14Rik	-	RIKEN cDNA 2010001A14 gene	ncRNA
mm_62864.1	chr7	114718644	114718661	+	1	NA	promoter-TSS (NM_054084)	promoter-TSS (NM_054084)	9	NM_054084	116903	Mm.273838	NM_054084	ENSMUSG00000030666	Calcb	CGRP2|Calc2	calcitonin-related polypeptide, beta	protein-coding
mm_161881.1	chr18	37496996	37496996	+	1	NA	promoter-TSS (NM_053144)	promoter-TSS (NM_053144)	-2	NM_053144	93890	Mm.118311	NM_053144	ENSMUSG00000043313	Pcdhb19	Pcdhb11|PcdhbS	protocadherin beta 19	protein-coding
mm_140884.1	chr17	23844135	23844177	-	1	NA	promoter-TSS (NM_027644)	promoter-TSS (NM_027644)	0	NM_027644	71003	Mm.328839	NM_027644	ENSMUSG00000024114	Prss41	4931440B09Rik|Tessp-1|Tessp1	protease, serine 41	protein-coding
mm_169642.1	chr1	55088259	55088260	+	1	NA	promoter-TSS (NM_010477)	promoter-TSS (NM_010477)	111	NM_008303	15528	Mm.215667	NM_008303	ENSMUSG00000073676	Hspe1	10kDa|Hsp10|mt-cpn10	heat shock protein 1 (chaperonin 10)	protein-coding
mm_64817.1	chr7	7278071	7278086	-	1	NA	intron (NR_003555, intron 1 of 6)	CpG	211	NR_003555	76229	Mm.387947	NM_001113468	ENSMUSG00000095730	Vmn2r29	6430701C03Rik	vomeronasal 2, receptor 29	protein-coding
mm_119857.1	chr14	54464142	54464222	+	1	NA	promoter-TSS (NM_022993)	promoter-TSS (NM_022993)	35	NM_022993	65107	Mm.472719	NM_022993	ENSMUSG00000022175	Lrp10	Lrp9	low-density lipoprotein receptor-related protein 10	protein-coding
mm_153083.1	chr19	32388085	32388093	-	1	NA	intron (NM_144792, intron 1 of 9)	CpG	365	NM_144792	208449	Mm.329810	NM_144792	ENSMUSG00000040451	Sgms1	9530058O11Rik|AI841905|C80702|Mob|Sms1|Sor1|Tmem23	sphingomyelin synthase 1	protein-coding
mm_15871.1	chr2	164834864	164834884	+	1	NA	exon (NM_008906, exon 5 of 15)	exon (NM_008906, exon 5 of 15)	1101	NM_008906	19025	Mm.359633	NM_008906	ENSMUSG00000017760	Ctsa	AU019505|PPCA|Ppgb	cathepsin A	protein-coding
mm_43769.1	chr5	140956552	140956572	+	1	NA	intron (NM_175362, intron 1 of 24)	intron (NM_175362, intron 1 of 24)	44034	NM_175362	108723	Mm.46187	NM_175362	ENSMUSG00000036526	Card11	0610008L17Rik|2410011D02Rik|BIMP3|CARMA1	caspase recruitment domain family, member 11	protein-coding
mm_106486.1	chr11	120231629	120231639	-	1	NA	Intergenic	Intergenic	-1313	NM_001347621	268515	Mm.309498	NM_198423	ENSMUSG00000039741	Bahcc1	B930044J06|BC060615	BAH domain and coiled-coil containing 1	protein-coding
mm_312.1	chr1	24210375	24210387	+	1	NA	exon (NM_001290691, exon 12 of 32)	exon (NM_001290691, exon 12 of 32)	15178	NM_001290691	12839	Mm.154662	NM_007740	ENSMUSG00000026147	Col9a1	Col9a-1	collagen, type IX, alpha 1	protein-coding
mm_5657.1	chr1	42651325	42651328	-	1	NA	intron (NR_027826, intron 3 of 3)	intron (NR_027826, intron 3 of 3)	43499	NR_027826	66297	Mm.45203	NM_183252	ENSMUSG00000060424	Pantr1	2610017I09Rik|Pou3f3os|linc-Brn1a	POU domain, class 3, transcription factor 3 adjacent noncoding transcript 1	ncRNA
mm_60310.1	chr7	44137265	44137289	+	1	NA	promoter-TSS (NM_008454)	promoter-TSS (NM_008454)	-13	NM_008454	16615	Mm.440887	NM_008454	ENSMUSG00000038968	Klk1b16	Klk16|mGk-16	kallikrein 1-related peptidase b16	protein-coding
mm_47980.1	chr5	135911347	135911360	-	1	NA	exon (NM_018871, exon 2 of 2)	exon (NM_018871, exon 2 of 2)	23288	NM_018871	22628	Mm.233813	NM_018871	ENSMUSG00000051391	Ywhag	14-3-3gamma|D7Bwg1348e	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, gamma polypeptide	protein-coding
mm_93531.1	chr10	115362153	115362163	-	1	NA	5' UTR (NM_133683, exon 1 of 7)	5' UTR (NM_133683, exon 1 of 7)	104	NM_133683	67226	Mm.29647	NM_133683	ENSMUSG00000069520	Tmem19	2810428F02Rik|AW125171	transmembrane protein 19	protein-coding
mm_22871.1	chr3	29082540	29082590	+	1	NA	promoter-TSS (NM_001167748)	promoter-TSS (NM_001167748)	-12	NM_001167748	75740	Mm.330948	NM_029412	ENSMUSG00000063600	Egfem1	6130401L20Rik|Efcab11	EGF-like and EMI domain containing 1	protein-coding
mm_107300.1	chr12	30911660	30911733	+	1	NA	promoter-TSS (NM_013709)	promoter-TSS (NM_013709)	27	NM_013709	24057	Mm.218624	NM_013709	ENSMUSG00000020669	Sh3yl1	AI314953|Ray|YSC84	Sh3 domain YSC-like 1	protein-coding
mm_88704.1	chr10	80148264	80148279	+	1	NA	promoter-TSS (NM_001305798)	promoter-TSS (NM_001305798)	-1	NM_001305798	59090	Mm.143813	NM_021565	ENSMUSG00000035621	Midn	3000003C15Rik	midnolin	protein-coding
mm_47304.1	chr5	122372231	122372390	-	1	NA	promoter-TSS (NM_026883)	promoter-TSS (NM_026883)	-198	NM_024216	68080	Mm.266328	NM_024216	ENSMUSG00000029464	Gpn3	A930018B01Rik|Atpbd1c|D5Ertd708e	GPN-loop GTPase 3	protein-coding
mm_104443.1	chr11	94976403	94976423	-	1	NA	promoter-TSS (NM_009161)	promoter-TSS (NM_009161)	-86	NM_009161	20391	Mm.18709	NM_009161	ENSMUSG00000001508	Sgca	50DAG|Asg	sarcoglycan, alpha (dystrophin-associated glycoprotein)	protein-coding
mm_104657.1	chr11	97576442	97576449	-	1	NA	Intergenic	Intergenic	-1319	NM_018873	56013	Mm.342665	NM_018873	ENSMUSG00000038453	Srcin1	P140|SNIP|mKIAA1684|p140Cap	SRC kinase signaling inhibitor 1	protein-coding
mm_88318.1	chr10	75564087	75564165	+	1	NA	Intergenic	Intergenic	-3796	NM_198860	192734	Mm.259320	NM_198860	ENSMUSG00000046807	Lrrc75b	AI646023|Fam211b	leucine rich repeat containing 75B	protein-coding
mm_122167.1	chr14	31434320	31434326	-	1	NA	intron (NM_011894, intron 1 of 8)	intron (NM_011894, intron 1 of 8)	1777	NM_011894	24056	Mm.383198	NM_011894	ENSMUSG00000021892	Sh3bp5	AI606498|SH3BP-5|Sab	SH3-domain binding protein 5 (BTK-associated)	protein-coding
mm_120892.1	chr14	75845138	75845165	+	1	NA	promoter-TSS (NM_009429)	promoter-TSS (NM_009429)	-105	NM_009429	22070	Mm.297482	NM_009429	ENSMUSG00000060126	Tpt1	TCTP|Trt|p21|p23	tumor protein, translationally-controlled 1	protein-coding
mm_106356.1	chr11	118393636	118393642	-	1	NA	exon (NM_011150, exon 6 of 6)	exon (NM_011150, exon 6 of 6)	8292	NM_011150	19039	Mm.3152	NM_011150	ENSMUSG00000033880	Lgals3bp	90K|CyCAP|MAC-2BP|Ppicap|Tango10b	lectin, galactoside-binding, soluble, 3 binding protein	protein-coding
mm_24790.1	chr3	95545369	95545387	+	1	NA	exon (NM_021281, exon 5 of 8)	exon (NM_021281, exon 5 of 8)	-14299	NM_026489	67981	Mm.179050	NM_026489	ENSMUSG00000028109	Hormad1	4921522K05Rik|Nohma	HORMA domain containing 1	protein-coding
mm_108867.1	chr12	99341016	99341056	+	1	NA	intron (NM_183186, intron 3 of 5)	intron (NM_183186, intron 3 of 5)	109038	NM_183186	71375	Mm.341972	NM_183186	ENSMUSG00000033713	Foxn3	5430426H20Rik|AA589593|AW556347|Ches1|Ches1l|HTLFL1	forkhead box N3	protein-coding
mm_126750.1	chr15	85736800	85736818	+	1	NA	5' UTR (NM_011144, exon 2 of 8)	5' UTR (NM_011144, exon 2 of 8)	1033	NM_011144	19013	Mm.212789	NM_011144	ENSMUSG00000022383	Ppara	4933429D07Rik|AW742785|Nr1c1|PPAR-alpha|PPARalpha|Ppar	peroxisome proliferator activated receptor alpha	protein-coding
mm_13196.1	chr2	93219211	93219224	+	1	NA	intron (NM_183180, intron 5 of 9)	intron (NM_183180, intron 5 of 9)	31633	NM_001025246	277414	Mm.41033	NM_001025246	ENSMUSG00000068735	Trp53i11	Tp53i11	transformation related protein 53 inducible protein 11	protein-coding
mm_57405.1	chr6	124865300	124865308	-	1	NA	3' UTR (NM_013488, exon 10 of 10)	3' UTR (NM_013488, exon 10 of 10)	-1387	NM_013533	14788	Mm.2514	NM_013533	ENSMUSG00000038390	Gpr162	A-2|BC031437|Grca	G protein-coupled receptor 162	protein-coding
mm_107641.1	chr12	52503993	52504028	+	1	NA	Intergenic	CpG	-12067	NM_009706	11855	Mm.35059	NM_009706	ENSMUSG00000035133	Arhgap5	p190-B|p190B	Rho GTPase activating protein 5	protein-coding
mm_61220.1	chr7	64392767	64392790	+	1	NA	promoter-TSS (NM_026483)	promoter-TSS (NM_026483)	7	NM_028626	73724	Mm.10093	NM_028626	ENSMUSG00000033429	Mcee	1110007A04Rik	methylmalonyl CoA epimerase	protein-coding
mm_30491.1	chr3	156380650	156380656	-	1	NA	Intergenic	Intergenic	181034	NR_040398	329782	Mm.183459	NR_040398	ENSMUSG00000085084	4930570G19Rik	C630015G22	RIKEN cDNA 4930570G19 gene	ncRNA
mm_2691.1	chr1	127729406	127729418	+	1	NA	promoter-TSS (NM_001033041)	promoter-TSS (NM_001033041)	-1	NM_001033041	266645	Mm.25735	NM_001033041	ENSMUSG00000026348	Acmsd	-	amino carboxymuconate semialdehyde decarboxylase	protein-coding
mm_48582.1	chr5	143527978	143528010	-	1	NA	promoter-TSS (NM_009007)	promoter-TSS (NM_009007)	-1	NM_009007	19353	Mm.292510	NM_009007	ENSMUSG00000001847	Rac1	AL023026|D5Ertd559e	RAS-related C3 botulinum substrate 1	protein-coding
mm_23559.1	chr3	62340047	62340058	+	1	NA	exon (NM_001081295, exon 1 of 14)	exon (NM_001081295, exon 1 of 14)	1275	NM_001081295	622434	Mm.153974	NM_001081295	ENSMUSG00000036885	Arhgef26	4631416L12Rik|8430436L14Rik|AI303572|AW491953|SGEF	Rho guanine nucleotide exchange factor (GEF) 26	protein-coding
mm_132392.1	chr16	35000573	35000579	+	1	NA	3' UTR (NM_139300, exon 32 of 32)	3' UTR (NM_139300, exon 32 of 32)	-21845	NM_023587	70757	Mm.27286	NM_023587	ENSMUSG00000035376	Hacd2	6330408J20Rik|AI255777|AI481689|Hcad2|Ptplb	3-hydroxyacyl-CoA dehydratase 2	protein-coding
mm_84431.1	chr9	65908780	65908798	-	1	NA	promoter-TSS (NM_019797)	promoter-TSS (NM_019797)	5	NM_019797	56404	Mm.208379	NM_019797	ENSMUSG00000032386	Trip4	4930558E03Rik|ASC-1|Asc1|BB191711	thyroid hormone receptor interactor 4	protein-coding
mm_20330.1	chr2	127521274	127521282	-	1	NA	exon (NM_001291005, exon 1 of 9)	exon (NM_001291005, exon 1 of 9)	114	NM_001291005	56461	Mm.315292	NM_019789	ENSMUSG00000079056	Kcnip3	4933407H12Rik|AI413860|Csen|DREAM|KChIP3|R74849	Kv channel interacting protein 3, calsenilin	protein-coding
mm_8859.1	chr1	162724765	162724780	-	1	NA	exon (NM_001081290, exon 2 of 35)	exon (NM_001081290, exon 2 of 35)	15784	NM_001081290	226562	Mm.245446	NM_001081290	ENSMUSG00000040225	Prrc2c	1810043M20Rik|9630039I18Rik|A630006J20|Bat2d|Bat2d1|Bat2l2|E130112L15Rik|Prrc3|mKIAA1096	proline-rich coiled-coil 2C	protein-coding
mm_96467.1	chr11	67617169	67617192	+	1	NA	intron (NM_001109657, intron 2 of 13)	intron (NM_001109657, intron 2 of 13)	20625	NM_001277079	14457	Mm.40338	NM_008088	ENSMUSG00000033066	Gas7	AW124766|B230343A10Rik|Gas7-cb	growth arrest specific 7	protein-coding
mm_70414.1	chr8	11448970	11449001	+	1	NA	3' UTR (NM_009932, exon 48 of 48)	3' UTR (NM_009932, exon 48 of 48)	-28944	NR_126558	102132	Mm.37632	NR_126558	ENSMUSG00000096957	E230013L22Rik	AI645545	RIKEN cDNA E230013L22 gene	ncRNA
mm_159100.1	chr2	36890720	36890720	-	1	NA	exon (NM_146941, exon 1 of 1)	exon (NM_146941, exon 1 of 1)	126	NM_146941	258943	Mm.377762	NM_146941	ENSMUSG00000075382	Olfr353	MOR127-3	olfactory receptor 353	protein-coding
mm_166335.1	chr5	114380052	114380070	+	1	NA	promoter-TSS (NM_054093)	promoter-TSS (NM_054093)	444	NM_001159941	330171	Mm.238285	NM_026145	ENSMUSG00000001098	Kctd10	AW536343|C87062|mBACURD3	potassium channel tetramerisation domain containing 10	protein-coding
mm_162.1	chr1	12725374	12725374	+	1	NA	intron (NM_172294, intron 1 of 21)	intron (NM_172294, intron 1 of 21)	6829	NM_172294	240725	Mm.45563	NM_172294	ENSMUSG00000016918	Sulf1	AI467640|AW121680|mKIAA1077	sulfatase 1	protein-coding
mm_137766.1	chr17	29490689	29490700	+	1	NA	promoter-TSS (NM_008842)	promoter-TSS (NM_008842)	-351	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_67805.1	chr7	98112619	98112636	-	1	NA	intron (NM_001256081, intron 2 of 48)	intron (NM_001256081, intron 2 of 48)	-3379	NM_001256083	17921	Mm.1403	NM_008663	ENSMUSG00000030761	Myo7a	Hdb|Myo7|USH1B|nmf371|polka|sh-1|sh1	myosin VIIA	protein-coding
mm_2376.1	chr1	93373797	93373807	+	1	NA	promoter-TSS (NM_207031)	promoter-TSS (NM_207031)	-94	NM_207031	404545	Mm.297411	NM_207031	ENSMUSG00000034107	Ano7	Ngep|Ngep-L|Pcanap5|Tmem16g	anoctamin 7	protein-coding
mm_35963.1	chr4	53142779	53142789	-	1	NA	intron (NM_013454, intron 2 of 49)	Charlie29a|DNA|hAT-Charlie	17111	NM_013454	11303	Mm.277376	NM_013454	ENSMUSG00000015243	Abca1	ABC-1|Abc1	ATP-binding cassette, sub-family A (ABC1), member 1	protein-coding
mm_146697.1	chr18	12941778	12941800	-	1	NA	promoter-TSS (NM_207530)	promoter-TSS (NM_207530)	52	NM_207530	64291	Mm.259470	NM_020573	ENSMUSG00000044252	Osbpl1a	G430090F17Rik|Gm753|ORP-1|Osbpl1b	oxysterol binding protein-like 1A	protein-coding
mm_71771.1	chr8	66444142	66444145	+	1	NA	intron (NM_175188, intron 6 of 7)	intron (NM_175188, intron 6 of 7)	42364	NM_025465	66282	Mm.294985	NM_025465	ENSMUSG00000025591	Tma16	1810029B16Rik	translation machinery associated 16	protein-coding
mm_112269.1	chr12	114153715	114153724	-	1	NA	Intergenic	Intergenic	315747	NR_106062	102465663		NR_106062	ENSMUSG00000105438	Mir7094-1	mmu-mir-7094-1	microRNA 7094-1	ncRNA
mm_135479.1	chr16	45991359	45991359	-	1	NA	intron (NM_001134480, intron 1 of 3)	intron (NM_001134480, intron 1 of 3)	19054	NM_001134480	433022	Mm.380993	NM_001134480	ENSMUSG00000087141	Plcxd2	AW494639|EG433022	phosphatidylinositol-specific phospholipase C, X domain containing 2	protein-coding
mm_31004.1	chr4	40183573	40183592	+	1	NA	exon (NM_007386, exon 13 of 21)	exon (NM_007386, exon 13 of 21)	40317	NM_007386	11428	Mm.331547	NM_007386	ENSMUSG00000028405	Aco1	Aco-1|Irebp|Irp1	aconitase 1	protein-coding
mm_146178.1	chr18	75370527	75370539	+	1	NA	intron (NM_001042660, intron 1 of 3)	intron (NM_001042660, intron 1 of 3)	3168	NM_001042660	17131	Mm.34407	NM_008543	ENSMUSG00000025880	Smad7	Madh7	SMAD family member 7	protein-coding
mm_60042.1	chr7	31059389	31059410	+	1	NA	promoter-TSS (NM_144556)	promoter-TSS (NM_144556)	-536	NM_144556	243914	Mm.389870	NM_144556	ENSMUSG00000036560	Lgi4	Lgil3|clp	leucine-rich repeat LGI family, member 4	protein-coding
mm_63726.1	chr7	130865687	130865688	+	1	NA	promoter-TSS (NM_133942)	promoter-TSS (NM_133942)	-37	NM_001346515	101476	Mm.323554	NM_133942	ENSMUSG00000040268	Plekha1	AA960558|C920009D07Rik|TAPP1	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 1	protein-coding
mm_69829.1	chr7	141271727	141271738	-	1	NA	exon (NM_001114322, exon 13 of 15)	exon (NM_001114322, exon 13 of 15)	5054	NM_028069	72040	Mm.29080	NM_028069	ENSMUSG00000025497	Cdhr5	1810074H01Rik|AI481143|Mucdhl|Mupcdh	cadherin-related family member 5	protein-coding
mm_133614.1	chr16	91547233	91547273	+	1	NA	intron (NM_008338, intron 1 of 6)	CpG	159	NM_008338	15980	Mm.249364	NM_008338	ENSMUSG00000022965	Ifngr2	Ifgr2|Ifgt	interferon gamma receptor 2	protein-coding
mm_9438.1	chr1	172550653	172550717	-	1	NA	non-coding (NR_040558, exon 1 of 3)	non-coding (NR_040558, exon 1 of 3)	121	NR_040558	71319	Mm.123774	NR_040558	ENSMUSG00000085184	4933439K11Rik	-	RIKEN cDNA 4933439K11 gene	ncRNA
mm_151501.1	chr19	58729301	58729335	+	1	NA	intron (NM_018874, intron 2 of 12)	Lx7|LINE|L1	431	NM_018874	18946	Mm.10753	NM_018874	ENSMUSG00000042179	Pnliprp1	Plrp1	pancreatic lipase related protein 1	protein-coding
mm_104191.1	chr11	87826024	87826039	-	1	NA	promoter-TSS (NM_080420)	promoter-TSS (NM_080420)	83	NM_080420	76113	Mm.41236	NM_080420	ENSMUSG00000009356	Lpo	5830499B15Rik	lactoperoxidase	protein-coding
mm_155713.1	chrX	96096118	96096128	+	1	NA	promoter-TSS (NM_010833)	promoter-TSS (NM_010833)	78	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_45251.1	chr5	62677446	62677468	-	1	NA	intron (NM_178407, intron 12 of 32)	intron (NM_178407, intron 12 of 32)	88720	NM_178407	212285	Mm.244403	NM_178407	ENSMUSG00000037999	Arap2	Centd1|Gm148|mKIAA0580	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2	protein-coding
mm_111360.1	chr12	86990604	86990612	-	1	NA	Intergenic	Intergenic	-1932	NM_001080943	238331	Mm.185890	NM_001080943	ENSMUSG00000048483	Zdhhc22	Gm262	zinc finger, DHHC-type containing 22	protein-coding
mm_80089.1	chr9	70220747	70220766	+	1	NA	intron (NM_181072, intron 1 of 27)	B4|SINE|B4	13406	NM_181072	71602	Mm.249311	NM_181072	ENSMUSG00000032220	Myo1e	2310020N23Rik|9130023P14Rik|AA407778|myosin-1e|myr 3	myosin IE	protein-coding
mm_103918.1	chr11	83589776	83589803	-	1	NA	exon (NM_009139, exon 2 of 4)	exon (NM_009139, exon 2 of 4)	3298	NM_009139	20305	Mm.137	NM_009139	ENSMUSG00000018927	Ccl6	MRP-1|Scya6|c10	chemokine (C-C motif) ligand 6	protein-coding
mm_108029.1	chr12	73725663	73725666	+	1	NA	intron (NM_001313977, intron 11 of 14)	intron (NM_001313977, intron 11 of 14)	140868	NM_008856	18755	Mm.341677	NM_008856	ENSMUSG00000021108	Prkch	Pkch	protein kinase C, eta	protein-coding
mm_103960.1	chr11	84164477	84164493	-	1	NA	exon (NM_001037932, exon 3 of 7)	exon (NM_001037932, exon 3 of 7)	2991	NM_001037932	628813	Mm.390389	NM_001037932	ENSMUSG00000051452	Gm11437	AI463690|OTTMUSG00000000997	predicted gene 11437	protein-coding
mm_134633.1	chr16	21668342	21668358	-	1	NA	intron (NM_001001881, intron 1 of 1)	intron (NM_001001881, intron 1 of 1)	26315	NM_001001881	72190	Mm.131606	NM_001001881	ENSMUSG00000043391	2510009E07Rik	AI194952	RIKEN cDNA 2510009E07 gene	protein-coding
mm_57613.1	chr6	128138014	128138025	-	1	NA	intron (NM_175414, intron 1 of 8)	B3A|SINE|B2	5559	NM_175414	109246	Mm.21814	NM_175414	ENSMUSG00000030352	Tspan9	6720474K14Rik|9430079M16Rik|AU018597	tetraspanin 9	protein-coding
mm_124367.1	chr14	105892593	105892596	-	1	NA	3' UTR (NM_011897, exon 2 of 2)	3' UTR (NM_011897, exon 2 of 2)	4225	NM_011897	24064	Mm.89982	NM_011897	ENSMUSG00000022114	Spry2	sprouty2	sprouty homolog 2 (Drosophila)	protein-coding
mm_38655.1	chr4	143299499	143299511	-	1	NA	promoter-TSS (NM_010329)	promoter-TSS (NM_010329)	59	NM_010329	14726	Mm.2976	NM_010329	ENSMUSG00000028583	Pdpn	Gp38|OTS-8|RANDAM-2|T1-alpha|T1a|T1alpha	podoplanin	protein-coding
mm_83459.1	chr9	45262890	45262939	-	1	NA	intron (NR_136903, intron 4 of 5)	intron (NR_136903, intron 4 of 5)	3793	NR_106054	102466803		NR_106054	ENSMUSG00000098361	Mir7086	Gm27643|mmu-mir-7086	microRNA 7086	ncRNA
mm_71394.1	chr8	46163676	46163729	+	1	NA	Intergenic	CpG	-5854	NM_025747	66756	Mm.133623	NM_025747	ENSMUSG00000031631	Cfap97	1110068E21Rik|4933411K20Rik|AW049273|Kiaa1430|mKIAA1430	cilia and flagella associated protein 97	protein-coding
mm_73225.1	chr8	103235876	103235901	+	1	NA	Intergenic	Intergenic	111646	NR_036588	69794	Mm.396139	NR_036588	ENSMUSG00000110340	1600027J07Rik	-	RIKEN cDNA 1600027J07 gene	ncRNA
mm_141877.1	chr17	34850330	34850349	-	1	NA	promoter-TSS (NM_021337)	promoter-TSS (NM_021337)	-52	NM_138580	27632	Mm.653	NM_138580	ENSMUSG00000024369	Nelfe	D17H6S45|NELF-E|RD|Rdbp	negative elongation factor complex member E, Rdbp	protein-coding
mm_106381.1	chr11	118494210	118494235	-	1	NA	exon (NM_001039167, exon 14 of 15)	exon (NM_001039167, exon 14 of 15)	17262	NM_172573	217364	Mm.473963	NM_172573	ENSMUSG00000033857	Engase	C130099A03|D230014K01Rik	endo-beta-N-acetylglucosaminidase	protein-coding
mm_2724.1	chr1	128190389	128190403	+	1	NA	intron (NM_181750, intron 16 of 26)	intron (NM_181750, intron 16 of 26)	-11965	NR_029543	387147		NR_029543	ENSMUSG00000065520	Mir128-1	Mirn128|Mirn128-1|Mirn128a|mir-128-1	microRNA 128-1	ncRNA
mm_101509.1	chr11	32265425	32265428	-	1	NA	intron (NR_104306, intron 1 of 13)	intron (NR_104306, intron 1 of 13)	2281	NM_181569	17168	Mm.263161	NM_181569	ENSMUSG00000020289	Nprl3	Aag|CGTHBA|HS-26|HS-40|Mare|Phg|Prox1|m(alpha)RE	nitrogen permease regulator-like 3	protein-coding
mm_30522.1	chr3	158561740	158561798	-	1	NA	5' UTR (NM_001291453, exon 1 of 26)	5' UTR (NM_001291453, exon 1 of 26)	452	NM_001291453	242274	Mm.132162	NM_001081358	ENSMUSG00000028176	Lrrc7	AK122498|densin|mKIAA1365	leucine rich repeat containing 7	protein-coding
mm_136.1	chr1	10284901	10284926	+	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-52243	NM_001102430	211673	Mm.229141	NM_001102430	ENSMUSG00000067851	Arfgef1	ARFGEP1|BIG1|D130059B05Rik|D730028O18Rik|P200	ADP-ribosylation factor guanine nucleotide-exchange factor 1(brefeldin A-inhibited)	protein-coding
mm_49478.1	chr6	29529278	29529296	+	1	NA	promoter-TSS (NM_001252382)	promoter-TSS (NM_001252382)	5	NM_001252382	27056	Mm.6479	NM_012057	ENSMUSG00000029771	Irf5	AW491843|mirf5	interferon regulatory factor 5	protein-coding
mm_107009.1	chr12	11456053	11456058	+	1	NA	promoter-TSS (NM_001111118)	promoter-TSS (NM_001111118)	-24	NM_001111118	209550	Mm.341257	NM_001111118	ENSMUSG00000086022	Rad51ap2	EG209550	RAD51 associated protein 2	protein-coding
mm_42208.1	chr5	112476354	112476399	+	1	NA	intron (NM_001253917, intron 1 of 15)	intron (NM_001253917, intron 1 of 15)	26950	NM_001177504	625464	Mm.389676	NM_001177504	ENSMUSG00000072722	Gm6588	EG625464	predicted gene 6588	protein-coding
mm_31513.1	chr4	53826015	53826107	+	1	NA	promoter-TSS (NM_028053)	promoter-TSS (NM_028053)	16	NM_028053	52076	Mm.27184	NM_028053	ENSMUSG00000028420	Tmem38b	1600017F22Rik|AA437809|AV051057|D4Ertd89e|TRIC-B|mg33b	transmembrane protein 38B	protein-coding
mm_82071.1	chr9	122903239	122903263	+	1	NA	Intergenic	Intergenic	14780	NM_001177505	382118	Mm.86999	NM_001177505	ENSMUSG00000063488	Zkscan7	BC042569|Zfp167	zinc finger with KRAB and SCAN domains 7	protein-coding
mm_170237.1	chr17	89440576	89440577	+	1	NA	Intergenic	L1_Mm|LINE|L1	61335	NR_045952	100043904	Mm.396198	NR_045952		Gm4719	-	predicted gene 4719	ncRNA
mm_103862.1	chr11	83302615	83302637	-	1	NA	promoter-TSS (NM_001035854)	promoter-TSS (NM_001035854)	-71	NM_027915	71770	Mm.39053	NM_027915	ENSMUSG00000035152	Ap2b1	1300012O03Rik|AI788979	adaptor-related protein complex 2, beta 1 subunit	protein-coding
mm_130114.1	chr15	89476405	89476407	-	1	NA	5' UTR (NM_009713, exon 2 of 9)	5' UTR (NM_009713, exon 2 of 9)	154	NR_077233	100532730	Mm.461541	NR_077233		C230037L18Rik	-	RIKEN cDNA C230037L18 gene	ncRNA
mm_63151.1	chr7	123370303	123370321	+	1	NA	promoter-TSS (NM_001122643)	promoter-TSS (NM_001122643)	-397	NM_001316713	70497	Mm.403318	NM_144529	ENSMUSG00000030766	Arhgap17	5730403H17Rik|Nadrin|Nadrin2|Rich1|Wbp15	Rho GTPase activating protein 17	protein-coding
mm_121660.1	chr14	12344839	12344846	-	1	NA	exon (NM_080433, exon 2 of 5)	exon (NM_080433, exon 2 of 5)	1023	NM_080433	54713	Mm.34644	NM_080433	ENSMUSG00000021743	Fezf2	AI451466|AI852056|Fez|Fezl|Zfp312	Fez family zinc finger 2	protein-coding
mm_172183.1	chr6	4923996	4924003	-	1	NA	intron (NM_181595, intron 2 of 15)	(CCCTAA)n|Simple_repeat|Simple_repeat	20679	NM_181595	243725	Mm.332901	NM_181595	ENSMUSG00000032827	Ppp1r9a	2810430P21Rik|4930518N04Rik|5330407E15|A230094E16Rik|BB181831|NRB|mKIAA1222|neurabin-I	protein phosphatase 1, regulatory (inhibitor) subunit 9A	protein-coding
mm_161125.1	chr12	111274707	111274707	+	1	NA	intron (NM_033603, intron 5 of 11)	CpG-3529	3611	NM_033603	93835	Mm.197639	NM_033603	ENSMUSG00000021278	Amn	-	amnionless	protein-coding
mm_147566.1	chr18	54990358	54990405	-	1	NA	promoter-TSS (NM_175751)	promoter-TSS (NM_175751)	-201	NM_175751	269023	Mm.192984	NM_175751	ENSMUSG00000052713	Zfp608	4932417D18Rik|D430007A19Rik|Znf608	zinc finger protein 608	protein-coding
mm_167903.1	chrX	77534283	77534284	+	1	NA	intron (NM_020601, intron 1 of 15)	intron (NM_020601, intron 1 of 15)	23056	NM_020601	21372	Mm.258476	NM_020601	ENSMUSG00000025246	Tbl1x	5330429M20|Tbl1	transducin (beta)-like 1 X-linked	protein-coding
mm_86418.1	chr10	3540266	3540282	+	1	NA	promoter-TSS (NM_027391)	promoter-TSS (NM_027391)	-5	NM_027391	70337	Mm.24153	NM_027391	ENSMUSG00000019762	Iyd	0610009A07Rik|AI265638|Dehal1	iodotyrosine deiodinase	protein-coding
mm_71701.1	chr8	61909533	61909558	+	1	NA	Intergenic	Intergenic	-6851	NM_001293772	72333	Mm.29933	NM_001081390	ENSMUSG00000058056	Palld	2410003B16Rik|6030492A02	palladin, cytoskeletal associated protein	protein-coding
mm_170580.1	chr19	57239536	57239539	-	1	NA	Intergenic	Intergenic	-23505	NM_178688	226251	Mm.217161	NM_178688	ENSMUSG00000025085	Ablim1	2210411C18Rik|2610209L21Rik|4833406P10Rik|9330196J19Rik|AV079770|AW060987|AW215784|Limab1|mKIAA0059	actin-binding LIM protein 1	protein-coding
mm_168884.1	chr12	4552558	4552558	-	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	28445	NR_136891	102634330	Mm.402324	NR_136891		Gm31938	-	predicted gene, 31938	ncRNA
mm_43311.1	chr5	134932352	134932382	+	1	NA	promoter-TSS (NM_024479)	promoter-TSS (NM_024479)	-6	NM_024479	79565	Mm.34235	NM_024479	ENSMUSG00000040557	Wbscr27	AW492986|BC002286	Williams Beuren syndrome chromosome region 27 (human)	protein-coding
mm_90466.1	chr10	127776375	127776407	+	1	NA	promoter-TSS (NM_153133)	promoter-TSS (NM_153133)	-14	NM_153133	103142	Mm.235814	NM_153133	ENSMUSG00000056148	Rdh9	AI121090|Crad3	retinol dehydrogenase 9	protein-coding
mm_20692.1	chr2	132792813	132792881	-	1	NA	exon (NM_007694, exon 4 of 5)	exon (NM_007694, exon 4 of 5)	11569	NM_007694	12653	Mm.255241	NM_007694	ENSMUSG00000027350	Chgb	Scg-1	chromogranin B	protein-coding
mm_86393.1	chr9	123968442	123968455	-	1	NA	5' UTR (NM_009912, exon 1 of 2)	5' UTR (NM_009912, exon 1 of 2)	244	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_43753.1	chr5	140437181	140437191	+	1	NA	intron (NM_133916, intron 11 of 18)	intron (NM_133916, intron 11 of 18)	9847	NR_106005	102466792		NR_106005	ENSMUSG00000098319	Mir7038	Gm27955|mmu-mir-7038	microRNA 7038	ncRNA
mm_78377.1	chr9	27790974	27790976	+	1	NA	promoter-TSS (NM_177906)	promoter-TSS (NM_177906)	-294	NM_177906	330908	Mm.379474	NM_177906	ENSMUSG00000062257	Opcml	2900075O15Rik|3732419F12|AI844366|B930023M13Rik|C230027C17|Gm181|Obcam	opioid binding protein/cell adhesion molecule-like	protein-coding
mm_33949.1	chr4	137424779	137424797	+	1	NA	exon (NM_026419, exon 4 of 8)	exon (NM_026419, exon 4 of 8)	5732	NM_026419	67868	Mm.297477	NM_026419	ENSMUSG00000023433	Cela3b	0910001F22Rik|2310074F01Rik|AI504000|Ela3|Ela3b	chymotrypsin-like elastase family, member 3B	protein-coding
mm_14727.1	chr2	144116179	144116189	+	1	NA	Intergenic	Intergenic	73106	NR_136884	433481	Mm.330630	NR_136884	ENSMUSG00000074758	Gm5535	EG433481	predicted gene 5535	ncRNA
mm_163373.1	chr12	42346719	42346719	+	1	NA	Intergenic	Intergenic	-860662	NM_010733	16981	Mm.404786	NM_010733	ENSMUSG00000036295	Lrrn3	NLRR-3	leucine rich repeat protein 3, neuronal	protein-coding
mm_75846.1	chr8	70632420	70632461	-	1	NA	promoter-TSS (NM_011819)	promoter-TSS (NM_011819)	16	NM_001330687	23886	Mm.31325	NM_011819	ENSMUSG00000038508	Gdf15	MIC-1|NAG-1|SBF	growth differentiation factor 15	protein-coding
mm_23164.1	chr3	40744230	40744234	+	1	NA	Intergenic	Intergenic	-1381	NM_011020	18415	Mm.39330	NM_011020	ENSMUSG00000025757	Hspa4l	94kDa|AI461691|APG-1|Osp94	heat shock protein 4 like	protein-coding
mm_100390.1	chr11	119389940	119389959	+	1	NA	promoter-TSS (NR_035453)	promoter-TSS (NR_035453)	-523	NR_035453	100316690		NR_035453	ENSMUSG00000088015	Mir1932	mir-1932|mmu-mir-1932	microRNA 1932	ncRNA
mm_154575.1	chrX	7429742	7429790	+	1	NA	Intergenic	Intergenic	-6778	NR_027924	68355	Mm.45111	NR_027924		2010204K13Rik	0610010M13Rik|Cip7	RIKEN cDNA 2010204K13 gene	ncRNA
mm_104310.1	chr11	93614940	93614944	-	1	NA	Intergenic	Intergenic	270824	NM_001013375	217109	Mm.379350	NM_001013375	ENSMUSG00000054079	Utp18	6230425C22Rik|6430513M13|Wdr50	UTP18 small subunit processome component	protein-coding
mm_71376.1	chr8	45827261	45827283	+	1	NA	3' UTR (NM_001205219, exon 24 of 24)	3' UTR (NM_001205219, exon 24 of 24)	-7975	NR_045739	319940	Mm.441720	NR_045739	ENSMUSG00000085440	Sorbs2os	D330022K07Rik	sorbin and SH3 domain containing 2, opposite strand	ncRNA
mm_23631.1	chr3	66219970	66219988	+	1	NA	promoter-TSS (NM_008987)	promoter-TSS (NM_008987)	92	NM_008987	19288	Mm.276776	NM_008987	ENSMUSG00000027832	Ptx3	AI607804|TSG-14	pentraxin related gene	protein-coding
mm_172364.1	chr7	120754227	120754240	-	1	NA	intron (NM_177697, intron 3 of 33)	LSU-rRNA_Hsa|rRNA|rRNA	14676	NM_177697	233813	Mm.389939	NM_177697	ENSMUSG00000030889	Vwa3a	E030013G06Rik	von Willebrand factor A domain containing 3A	protein-coding
mm_156643.1	chrX	157699070	157699076	+	1	NA	promoter-TSS (NM_001252591)	promoter-TSS (NM_001252591)	100	NR_103722	66106	Mm.140340	NM_025357	ENSMUSG00000041476	Smpx	1010001C09Rik|Csl	small muscle protein, X-linked	protein-coding
mm_143831.1	chr17	84073753	84073765	-	1	NA	Intergenic	Intergenic	-4901	NR_045458	74473	Mm.399575	NR_045458		4933433H22Rik	-	RIKEN cDNA 4933433H22 gene	ncRNA
mm_58577.1	chr7	4912532	4912558	+	1	NA	Intergenic	ORR1B2|LTR|ERVL-MaLR	-2672	NM_170759	232816	Mm.27442	NM_170759	ENSMUSG00000074406	Zfp628	Zec|Znf628	zinc finger protein 628	protein-coding
mm_48912.1	chr6	3994024	3994027	+	1	NA	promoter-TSS (NM_010314)	promoter-TSS (NM_010314)	13	NM_010314	14699	Mm.95398	NM_010314	ENSMUSG00000029663	Gngt1	G(y)1|Gng1	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1	protein-coding
mm_10057.1	chr1	193263994	193264004	-	1	NA	promoter-TSS (NM_008288)	promoter-TSS (NM_008288)	46	NM_008288	15483	Mm.28328	NM_008288	ENSMUSG00000016194	Hsd11b1	-	hydroxysteroid 11-beta dehydrogenase 1	protein-coding
mm_35959.1	chr4	53131092	53131103	-	1	NA	intron (NM_013454, intron 3 of 49)	intron (NM_013454, intron 3 of 49)	28798	NM_013454	11303	Mm.277376	NM_013454	ENSMUSG00000015243	Abca1	ABC-1|Abc1	ATP-binding cassette, sub-family A (ABC1), member 1	protein-coding
mm_42600.1	chr5	117509801	117509807	+	1	NA	intron (NM_001312914, intron 3 of 19)	intron (NM_001312914, intron 3 of 19)	95802	NM_001312914	333050	Mm.437947	NM_001034873	ENSMUSG00000061578	Ksr2	-	kinase suppressor of ras 2	protein-coding
mm_1.1	chr1	3674609	3674612	+	1	NA	Intergenic	Intergenic	-3112	NM_001011874	497097	Mm.454496	NM_001011874	ENSMUSG00000051951	Xkr4	AY534250|Gm210|XRG4|mKIAA1889	X-linked Kx blood group related 4	protein-coding
mm_160934.1	chr11	93099419	93099419	+	1	NA	5' UTR (NM_028296, exon 1 of 9)	5' UTR (NM_028296, exon 1 of 9)	129	NM_028296	72605	Mm.342160	NM_028296	ENSMUSG00000056158	Car10	2700029L05Rik|BB085816|Ca10	carbonic anhydrase 10	protein-coding
mm_62955.1	chr7	119617805	119617819	+	1	NA	promoter-TSS (NM_054094)	promoter-TSS (NM_054094)	-16	NM_054094	117147	Mm.427560	NM_054094	ENSMUSG00000033533	Acsm1	Acas3|Bucs1|Macs	acyl-CoA synthetase medium-chain family member 1	protein-coding
mm_24779.1	chr3	95540029	95540041	+	1	NA	intron (NM_001267695, intron 3 of 7)	intron (NM_001267695, intron 3 of 7)	13249	NM_001267695	13040	Mm.3619	NM_021281	ENSMUSG00000038642	Ctss	Cats	cathepsin S	protein-coding
mm_104077.1	chr11	86586955	86586979	-	1	NA	intron (NM_029478, intron 10 of 11)	intron (NM_029478, intron 10 of 11)	-2809	NR_029738	387140		NR_029738	ENSMUSG00000065455	Mir21a	Mir21|Mirn21|mmu-mir-21|mmu-mir-21a	microRNA 21a	ncRNA
mm_58720.1	chr7	13024121	13024188	+	1	NA	promoter-TSS (NM_011588)	promoter-TSS (NM_011588)	2	NM_011588	21849	Mm.15701	NM_011588	ENSMUSG00000005566	Trim28	AA408787|KAP-1|KRIP-1|MommeD9|Tif1b|Tif1beta	tripartite motif-containing 28	protein-coding
mm_147908.1	chr18	65393981	65393991	-	1	NA	promoter-TSS (NM_001037294)	promoter-TSS (NM_001037294)	-98	NM_001037294	225638	Mm.296528	NM_001037294	ENSMUSG00000032845	Alpk2	Gm549|Hak	alpha-kinase 2	protein-coding
mm_19464.1	chr2	92401156	92401180	-	1	NA	promoter-TSS (NM_011162)	promoter-TSS (NM_011162)	95	NM_011162	19099	Mm.2720	NM_011162	ENSMUSG00000027223	Mapk8ip1	IB1|JIP-1|Jip1|Prkm8ip|Skip|mjip-2a	mitogen-activated protein kinase 8 interacting protein 1	protein-coding
mm_160802.1	chr11	6000614	6000614	-	1	NA	intron (NM_007595, intron 4 of 20)	intron (NM_007595, intron 4 of 20)	44856	NM_019661	56418	Mm.294821	NM_019661	ENSMUSG00000002741	Ykt6	0610042I15Rik|1810013M05Rik|AW105923	YKT6 v-SNARE homolog (S. cerevisiae)	protein-coding
mm_98410.1	chr11	94363938	94363946	+	1	NA	intron (NM_029600, intron 15 of 30)	intron (NM_029600, intron 15 of 30)	29034	NM_029600	76408	Mm.23942	NM_029600	ENSMUSG00000020865	Abcc3	1700019L09Rik|ABC31|MLP2|MOAT-D|MRP3	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	protein-coding
mm_89022.1	chr10	82354279	82354296	+	1	NA	Intergenic	Intergenic	-113012	NM_001105557	237411		NM_172789	ENSMUSG00000062931	Zfp938	B230315N10Rik	zinc finger protein 938	protein-coding
mm_68569.1	chr7	115698185	115698206	-	1	NA	intron (NM_001025560, intron 5 of 15)	B3|SINE|B2	103414	NM_001277328	20679	Mm.323365	NM_011445	ENSMUSG00000051910	Sox6	AI987981|SOX-LZ	SRY (sex determining region Y)-box 6	protein-coding
mm_116512.1	chr13	45654701	45654717	-	1	NA	intron (NM_001199304, intron 5 of 6)	intron (NM_001199304, intron 5 of 6)	147265	NM_025508	66355	Mm.290802	NM_025508	ENSMUSG00000000253	Gmpr	2310004P21Rik|AV028449|GMPR 1	guanosine monophosphate reductase	protein-coding
mm_27610.1	chr3	59210849	59210855	-	1	NA	promoter-TSS (NM_028808)	promoter-TSS (NM_028808)	30	NM_028808	74191	Mm.90067	NM_028808	ENSMUSG00000036362	P2ry13	2010001L06Rik|GPCR1|GPR94|Gpr86|P2Y13|P2yr13|SP174	purinergic receptor P2Y, G-protein coupled 13	protein-coding
mm_110969.1	chr12	76940073	76940100	-	1	NA	exon (NM_001146176, exon 3 of 4)	exon (NM_001146176, exon 3 of 4)	22162	NM_008558	17187	Mm.268548	NM_008558	ENSMUSG00000059436	Max	AA960152|AI875693|bHLHd4|bHLHd5|bHLHd6|bHLHd7|bHLHd8	Max protein	protein-coding
mm_114873.1	chr13	94130754	94130766	+	1	NA	intron (NM_172589, intron 2 of 3)	intron (NM_172589, intron 2 of 3)	72964	NM_172589	218454	Mm.316553	NM_172589	ENSMUSG00000045312	Lhfpl2	6030465B15|AI447312|AW050335|mKIAA0206|vgim	lipoma HMGIC fusion partner-like 2	protein-coding
mm_107594.1	chr12	49377822	49377851	+	1	NA	Intergenic	Intergenic	-5047	NM_001160112	15228	Mm.4704	NM_008241	ENSMUSG00000020950	Foxg1	2900064B05Rik|BF-1|Bf1|Hfh9|Hfhbf1	forkhead box G1	protein-coding
mm_135963.1	chr16	74815198	74815206	-	1	NA	Intergenic	(CAAAAA)n|Simple_repeat|Simple_repeat	-404290	NM_175549	268902	Mm.171736	NM_175549	ENSMUSG00000052516	Robo2	2600013A04Rik|9430089E08Rik|BB097918|D230004I22Rik|mKIAA1568	roundabout guidance receptor 2	protein-coding
mm_45925.1	chr5	89443515	89443535	-	1	NA	exon (NM_008096, exon 4 of 13)	exon (NM_008096, exon 4 of 13)	14373	NM_008096	14473	Mm.196595	NM_008096	ENSMUSG00000035540	Gc	DBP|VDB	group specific component	protein-coding
mm_145695.1	chr18	62323826	62323844	+	1	NA	promoter-TSS (NM_008313)	promoter-TSS (NM_008313)	-369	NM_008313	15562	Mm.20440	NM_008313	ENSMUSG00000026322	Htr4	5-HT-4|5-HT4|5-HT<4L>|5HTR4	5 hydroxytryptamine (serotonin) receptor 4	protein-coding
mm_153267.1	chr19	37077505	37077523	-	1	NA	intron (NM_001290826, intron 7 of 10)	intron (NM_001290826, intron 7 of 10)	-96329	NR_045329	319931	Mm.446730	NR_045329	ENSMUSG00000097591	A330032B11Rik	-	RIKEN cDNA A330032B11 gene	ncRNA
mm_172743.1	chr8	79816298	79816301	+	1	NA	Intergenic	RLTR27|LTR|ERVK	104479	NM_026904	68999	Mm.257445	NM_026904	ENSMUSG00000036977	Anapc10	1500026N15Rik|A830003M23Rik|APC10	anaphase promoting complex subunit 10	protein-coding
mm_154453.1	chrM	2259	2280	-	1	NA	NA	Intergenic	NA	NA								
mm_10169.1	chr2	4559646	4559656	+	1	NA	promoter-TSS (NM_001177844)	promoter-TSS (NM_001177844)	-103	NM_001177844	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding
mm_123656.1	chr14	69243130	69243143	-	1	NA	3' UTR (NM_026331, exon 4 of 4)	3' UTR (NM_026331, exon 4 of 4)	41967	NM_026331	67712	Mm.293635	NM_026331	ENSMUSG00000034248	Slc25a37	1700020E22Rik|4930513O14Rik|4930526G11Rik|AI848481|C330015G08Rik|Mfrn|Mfrn1|Mscp|frascati|mitoferrin	solute carrier family 25, member 37	protein-coding
mm_68329.1	chr7	106504074	106504101	-	1	NA	Intergenic	Intergenic	-63014	NR_003967	209380	Mm.461779	NM_001001318		Gm4759	EG209380	GTPase, very large interferon inducible 1 pseudogene	pseudo
mm_164135.1	chr15	50194773	50194777	+	1	NA	Intergenic	Intergenic	694274	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_42905.1	chr5	122501709	122501735	+	1	NA	non-coding (NR_027838, exon 1 of 21)	non-coding (NR_027838, exon 1 of 21)	503	NM_001110140	11938	Mm.227583	NM_009722	ENSMUSG00000029467	Atp2a2	9530097L16Rik|D5Wsu150e|SERCA2|SERCA2B|Serca2a|mKIAA4195	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	protein-coding
mm_10744.1	chr2	23098090	23098093	+	1	NA	intron (NM_001102436, intron 9 of 12)	B2_Mm2|SINE|B2	29019	NM_001102438	74159	Mm.181973	NM_028793	ENSMUSG00000026781	Acbd5	1300014E15Rik	acyl-Coenzyme A binding domain containing 5	protein-coding
mm_1030.1	chr1	58755116	58755127	+	1	NA	3' UTR (NM_207653, exon 10 of 10)	3' UTR (NM_207653, exon 10 of 10)	24569	NM_001293805	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_152231.1	chr19	8708300	8708303	-	1	NA	intron (NM_001161413, intron 8 of 9)	intron (NM_001161413, intron 8 of 9)	5596	NM_008577	17254	Mm.4114	NM_008577	ENSMUSG00000010095	Slc3a2	4F2|4F2HC|AI314110|Cd98|Ly-10|Ly-m10|Ly10|Mdu1|Mgp-2hc|NACAE	solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2	protein-coding
mm_62084.1	chr7	92934911	92934928	+	1	NA	TTS (NM_028243)	TTS (NM_028243)	59666	NM_028243	72461	Mm.389969	NM_028243	ENSMUSG00000061119	Prcp	2510048K03Rik|2610104A14Rik|AI451719|HUMPCP|PCP	prolylcarboxypeptidase (angiotensinase C)	protein-coding
mm_147310.1	chr18	40923806	40923818	-	1	NA	Intergenic	Lx9|LINE|L1	665451	NM_026135	383348	Mm.76366	NM_026135	ENSMUSG00000051401	Kctd16	4930434H12Rik|Gm1267	potassium channel tetramerisation domain containing 16	protein-coding
mm_79029.1	chr9	46012823	46012860	+	1	NA	promoter-TSS (NM_027498)	promoter-TSS (NM_027498)	21	NM_027498	70661	Mm.219459	NM_027498	ENSMUSG00000034135	Sik3	5730525O22Rik|9030204A07Rik|AI447252|AI846254|AI849445|Qsk|SIK-3|mKIAA0999	SIK family kinase 3	protein-coding
mm_71051.1	chr8	33697292	33697330	+	1	NA	3' UTR (NM_010344, exon 13 of 13)	3' UTR (NM_010344, exon 13 of 13)	-34603	NM_001167921	68153	Mm.286104	NM_026584	ENSMUSG00000031585	Gtf2e2	34kDa|AI462509|C330006J08Rik	general transcription factor II E, polypeptide 2 (beta subunit)	protein-coding
mm_70590.1	chr8	13173870	13173895	+	1	NA	exon (NM_010684, exon 8 of 9)	exon (NM_010684, exon 8 of 9)	14721	NM_010684	16783	Mm.16716	NM_010684	ENSMUSG00000031447	Lamp1	CD107a|LGP-120|LGP-A|Lamp-1|P2B	lysosomal-associated membrane protein 1	protein-coding
mm_50551.1	chr6	49047325	49047342	+	1	NA	exon (NM_053110, exon 5 of 11)	exon (NM_053110, exon 5 of 11)	10815	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_31044.1	chr4	41135643	41135653	+	1	NA	promoter-TSS (NM_026275)	promoter-TSS (NM_026275)	-373	NM_026275	67615	Mm.389540	NM_026275	ENSMUSG00000036241	Ube2r2	1200003M11Rik|Cdc34b|Ubc3b	ubiquitin-conjugating enzyme E2R 2	protein-coding
mm_154460.1	chrM	3112	3126	-	1	NA	NA	Intergenic	NA	NA								
mm_40035.1	chr5	33720823	33720832	+	1	NA	promoter-TSS (NM_001163215)	promoter-TSS (NM_001163215)	-897	NM_001205270	14184	Mm.6904	NM_008010	ENSMUSG00000054252	Fgfr3	CD333|FR3|Fgfr-3|Flg-2|HBGFR|Mfr3|sam3	fibroblast growth factor receptor 3	protein-coding
mm_25571.1	chr3	116808263	116808285	+	1	NA	promoter-TSS (NM_001081326)	promoter-TSS (NM_001081326)	-108	NM_001081326	77559	Mm.237099	NM_001081326	ENSMUSG00000033400	Agl	1110061O17Rik|9430004C13Rik|9630046L06Rik|AI850929|C77197	amylo-1,6-glucosidase, 4-alpha-glucanotransferase	protein-coding
mm_103890.1	chr11	83575058	83575068	-	1	NA	3' UTR (NM_011338, exon 4 of 4)	3' UTR (NM_011338, exon 4 of 4)	3573	NM_011338	20308	Mm.416125	NM_011338	ENSMUSG00000019122	Ccl9	CCF18|MRP-2|Scya10|Scya9	chemokine (C-C motif) ligand 9	protein-coding
mm_125449.1	chr15	49229486	49229498	+	1	NA	Intergenic	RLTR41A2|LTR|ERV1	-437503	NM_001081391	239420	Mm.309363	NM_001081391	ENSMUSG00000022311	Csmd3	4930500N14Rik|mKIAA1894	CUB and Sushi multiple domains 3	protein-coding
mm_113444.1	chr13	35189261	35189267	+	1	NA	Intergenic	Intergenic	7641	NR_045616	100503727	Mm.32214	NR_045616	ENSMUSG00000102099	1700011B04Rik	-	RIKEN cDNA 1700011B04 gene	ncRNA
mm_124200.1	chr14	98169543	98169595	-	1	NA	5' UTR (NM_001038610, exon 1 of 11)	5' UTR (NM_001038610, exon 1 of 11)	196	NM_001038610	13134	Mm.320593	NM_007826	ENSMUSG00000055639	Dach1	Dac|Dach	dachshund 1 (Drosophila)	protein-coding
mm_59554.1	chr7	28075225	28075242	+	1	NA	exon (NM_001122603, exon 3 of 20)	exon (NM_001122603, exon 3 of 20)	3997	NM_001122603	215384	Mm.292276	NM_175444	ENSMUSG00000047730	Fcgbp	A430096B05Rik	Fc fragment of IgG binding protein	protein-coding
mm_149046.1	chr19	8826703	8826724	+	1	NA	exon (NM_001081196, exon 10 of 14)	exon (NM_001081196, exon 10 of 14)	7312	NM_001081196	68693	Mm.476519	NM_001081196	ENSMUSG00000071659	Hnrnpul2	1110031M08Rik|AI465155|Hnrpul2	heterogeneous nuclear ribonucleoprotein U-like 2	protein-coding
mm_82616.1	chr9	21770030	21770046	-	1	NA	exon (NM_145611, exon 10 of 12)	exon (NM_145611, exon 10 of 12)	-9752	NM_026282	67629	Mm.295642	NM_026282	ENSMUSG00000074476	Spc24	2410030K01Rik|AV109292|Spbc24	SPC24, NDC80 kinetochore complex component, homolog (S. cerevisiae)	protein-coding
mm_169893.1	chr16	48283744	48283744	+	1	NA	promoter-TSS (NM_028610)	promoter-TSS (NM_028610)	9	NM_001018002	73693	Mm.35597	NM_028610	ENSMUSG00000058550	Dppa4	2410091M23Rik|C76608|ECAT15-1	developmental pluripotency associated 4	protein-coding
mm_10138.1	chr2	4141271	4141281	+	1	NA	promoter-TSS (NR_040500)	promoter-TSS (NR_040500)	-135	NR_040500	73489	Mm.488103	NR_040500	ENSMUSG00000084859	1700080N15Rik	4933408D14Rik	RIKEN cDNA 1700080N15 gene	ncRNA
mm_96611.1	chr11	69097732	69097744	+	1	NA	Intergenic	Intergenic	-1218	NM_011065	18626	Mm.7373	NM_011065	ENSMUSG00000020893	Per1	Hftm|Per|m-rigui|mPer1	period circadian clock 1	protein-coding
mm_57102.1	chr6	122591117	122591131	-	1	NA	5' UTR (NM_031159, exon 4 of 8)	5' UTR (NM_031159, exon 4 of 8)	11320	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_132702.1	chr16	43363900	43363917	+	1	NA	intron (NM_181058, intron 2 of 6)	intron (NM_181058, intron 2 of 6)	56288	NR_046026	626693	Mm.447083	NR_046026	ENSMUSG00000085499	Gm15713	OTTMUSG00000025617	predicted gene 15713	ncRNA
mm_35568.1	chr4	41640323	41640344	-	1	NA	promoter-TSS (NM_027147)	promoter-TSS (NM_027147)	-31	NM_027147	69638	Mm.372459	NM_027147	ENSMUSG00000028445	Enho	1110065P19Rik|2310040A07Rik	energy homeostasis associated	protein-coding
mm_146401.1	chr18	82911327	82911333	+	1	NA	intron (NM_183033, intron 1 of 5)	CpG-7144	451	NM_183033	329003	Mm.326526	NM_183033	ENSMUSG00000058881	Zfp516	C330029B10Rik|D230016L03|Zfp26l|Znf516|mKIAA0222	zinc finger protein 516	protein-coding
mm_67098.1	chr7	69908088	69908098	-	1	NA	Intergenic	Intergenic	411999	NR_045940	73796	Mm.410832	NR_045940	ENSMUSG00000108885	4930402F11Rik	-	RIKEN cDNA 4930402F11 gene	ncRNA
mm_164616.1	chr17	31161537	31161543	-	1	NA	3' UTR (NM_009362, exon 3 of 3)	3' UTR (NM_009362, exon 3 of 3)	3513	NM_009362	21784	Mm.2854	NM_009362	ENSMUSG00000024032	Tff1	Bcei|PS2	trefoil factor 1	protein-coding
mm_63463.1	chr7	127573547	127573611	+	1	NA	intron (NM_026888, intron 1 of 9)	intron (NM_026888, intron 1 of 9)	231	NM_026888	68961	Mm.274473	NM_026888	ENSMUSG00000030815	Phkg2	1500017I02Rik	phosphorylase kinase, gamma 2 (testis)	protein-coding
mm_56679.1	chr6	113747122	113747125	-	1	NA	3' UTR (NM_001036684, exon 20 of 20)	3' UTR (NM_001036684, exon 20 of 20)	-6442	NM_024206	110379	Mm.29296	NM_024206	ENSMUSG00000030298	Sec13	1110003H02Rik|Sec13l1|Sec13r	SEC13 homolog, nuclear pore and COPII coat complex component	protein-coding
mm_95339.1	chr11	46817573	46817590	+	1	NA	exon (NM_178759, exon 3 of 9)	exon (NM_178759, exon 3 of 9)	6782	NM_178759	276891	Mm.69002	NM_178759	ENSMUSG00000055546	Timd4	B430010N18Rik|TIM-4|Tim4	T cell immunoglobulin and mucin domain containing 4	protein-coding
mm_41522.1	chr5	92532920	92532921	+	1	NA	Intergenic	ERVB3_1-I_MM-int|LTR|ERVK	-27263	NM_007644	12492	Mm.297964	NM_007644	ENSMUSG00000029426	Scarb2	9330185J12Rik|Cd36l2|LGP85|LIMP II|LIMP-2|MLGP85	scavenger receptor class B, member 2	protein-coding
mm_17770.1	chr2	32796080	32796091	-	1	NA	exon (NM_001113569, exon 18 of 20)	exon (NM_001113569, exon 18 of 20)	-11680	NM_025619	227736	Mm.441499	NM_025619	ENSMUSG00000038987	Cfap157	1700019L03Rik	cilia and flagella associated protein 157	protein-coding
mm_48462.1	chr5	140826775	140826818	-	1	NA	intron (NM_010302, intron 1 of 3)	intron (NM_010302, intron 1 of 3)	3635	NM_010302	14673	Mm.370185	NM_010302	ENSMUSG00000000149	Gna12	AI414047|AI504261|Galpha12	guanine nucleotide binding protein, alpha 12	protein-coding
mm_38638.1	chr4	143136641	143136644	-	1	NA	promoter-TSS (NR_105988)	promoter-TSS (NR_105988)	-480	NR_105988	102465618		NR_105988	ENSMUSG00000106597	Mir7021	mmu-mir-7021	microRNA 7021	ncRNA
mm_140023.1	chr17	73870766	73870780	+	1	NA	Intergenic	Intergenic	65932	NM_020578	57440	Mm.18526	NM_020578	ENSMUSG00000024065	Ehd3	Ehd2	EH-domain containing 3	protein-coding
mm_101230.1	chr11	20332571	20332603	-	1	NA	5' UTR (NM_018861, exon 1 of 8)	5' UTR (NM_018861, exon 1 of 8)	126	NM_018861	55963	Mm.6379	NM_018861	ENSMUSG00000020142	Slc1a4	ASCT-1|ASCT1|AW045657|SATT	solute carrier family 1 (glutamate/neutral amino acid transporter), member 4	protein-coding
mm_27415.1	chr3	51400693	51400720	-	1	NA	Intergenic	B1_Mur4|SINE|Alu	-4159	NR_028121	67749	Mm.273339	NM_026358	ENSMUSG00000037161	Mgarp	4930583H14Rik|AI195347|CESP-1|HUMMR|Osap|Qsap	mitochondria localized glutamic acid rich protein	protein-coding
mm_74541.1	chr8	9976295	9976335	-	1	NA	promoter-TSS (NM_176953)	promoter-TSS (NM_176953)	8	NM_176953	319583	Mm.80584	NM_176953	ENSMUSG00000049717	Lig4	5830471N16Rik|tiny	ligase IV, DNA, ATP-dependent	protein-coding
mm_167921.1	chrX	102037269	102037277	+	1	NA	intron (NM_001163610, intron 1 of 7)	intron (NM_001163610, intron 1 of 7)	34034	NM_001278534	331474	Mm.23297	NM_183318	ENSMUSG00000049191	Rgag4	6430402L03Rik|Mar5|Mart5|mKIAA2001	retrotransposon gag domain containing 4	protein-coding
mm_23389.1	chr3	57425435	57425452	+	1	NA	promoter-TSS (NM_145539)	promoter-TSS (NM_145539)	33	NM_145539	229302	Mm.26618	NM_145539	ENSMUSG00000027801	Tm4sf4	Iltmp	transmembrane 4 superfamily member 4	protein-coding
mm_52303.1	chr6	108821614	108821643	+	1	NA	3' UTR (NM_026011, exon 7 of 7)	3' UTR (NM_026011, exon 7 of 7)	-7013	NM_138677	192193	Mm.21596	NM_138677	ENSMUSG00000030104	Edem1	A130059K23Rik|EDEM|mKIAA0212	ER degradation enhancer, mannosidase alpha-like 1	protein-coding
mm_37314.1	chr4	119333620	119333632	-	1	NA	exon (NM_001270435, exon 11 of 15)	exon (NM_001270435, exon 11 of 15)	-13103	NM_001110130	66101	Mm.304080	NM_028677	ENSMUSG00000060288	Ppih	1100001J08Rik|2010111B15Rik|4833408F11Rik|AI464484|CYP-20|CYPH|D4Wsu43e	peptidyl prolyl isomerase H	protein-coding
mm_159022.1	chr1	172261618	172261618	+	1	NA	Intergenic	Intergenic	-3194	NM_013734	27222	Mm.482392	NM_013734	ENSMUSG00000007107	Atp1a4	-	ATPase, Na+/K+ transporting, alpha 4 polypeptide	protein-coding
mm_7470.1	chr1	120488184	120488195	-	1	NA	exon (NM_010766, exon 8 of 17)	exon (NM_010766, exon 8 of 17)	16895	NM_010766	17167	Mm.1856	NM_010766	ENSMUSG00000026390	Marco	AI323439|Ly112|Scara2	macrophage receptor with collagenous structure	protein-coding
mm_111629.1	chr12	102439659	102439737	-	1	NA	5' UTR (NM_011175, exon 1 of 14)	5' UTR (NM_011175, exon 1 of 14)	115	NM_011175	19141	Mm.17185	NM_011175	ENSMUSG00000021190	Lgmn	AEP|AI746452|AU022324|Prsc1	legumain	protein-coding
mm_14795.1	chr2	145860917	145860925	+	1	NA	exon (NM_028724, exon 9 of 13)	exon (NM_028724, exon 9 of 13)	-42320	NM_026425	67877	Mm.151168	NM_026425	ENSMUSG00000002728	Naa20	1500004D14Rik|2900026I01Rik|AU041458|D2Ertd186e|Nat5	N(alpha)-acetyltransferase 20, NatB catalytic subunit	protein-coding
mm_69099.1	chr7	127019885	127019917	-	1	NA	exon (NM_001102563, exon 2 of 4)	exon (NM_001102563, exon 2 of 4)	1310	NM_001102563	69017	Mm.392047	NM_001102563	ENSMUSG00000045114	Prrt2	1500031I19Rik|AI195361|DSPB3	proline-rich transmembrane protein 2	protein-coding
mm_148945.1	chr19	7221870	7221877	+	1	NA	Intergenic	RMER17A|LTR|ERVK	-4257	NM_007750	12868	Mm.14022	NM_007750	ENSMUSG00000035885	Cox8a	COX8L	cytochrome c oxidase subunit VIIIa	protein-coding
mm_14769.1	chr2	145731061	145731064	+	1	NA	intron (NR_033220, intron 2 of 3)	intron (NR_033220, intron 2 of 3)	29867	NR_033220	408057	Mm.486711	NR_033220	ENSMUSG00000087594	BC039771	-	cDNA sequence BC039771	ncRNA
mm_108068.1	chr12	73941755	73941782	+	1	NA	exon (NM_010431, exon 11 of 15)	exon (NM_010431, exon 11 of 15)	-22762	NM_178392	75627	Mm.25937	NM_178392	ENSMUSG00000021113	Snapc1	2700033G17Rik|AU015787	small nuclear RNA activating complex, polypeptide 1	protein-coding
mm_125675.1	chr15	66577537	66577637	+	1	NA	promoter-TSS (NM_001081409)	promoter-TSS (NM_001081409)	15	NM_001081409	239510	Mm.267473	NM_178718	ENSMUSG00000072501	Phf20l1	CGI-72|E130113K22Rik	PHD finger protein 20-like 1	protein-coding
mm_80830.1	chr9	97015941	97015952	+	1	NA	intron (NM_145134, intron 1 of 2)	intron (NM_145134, intron 1 of 2)	2409	NM_145134	211949	Mm.491271	NM_145134	ENSMUSG00000046997	Spsb4	D030068E18Rik|SSB-4|Ssb4	splA/ryanodine receptor domain and SOCS box containing 4	protein-coding
mm_47895.1	chr5	134723213	134723225	-	1	NA	intron (NM_007925, intron 13 of 36)	intron (NM_007925, intron 13 of 36)	24104	NM_007925	13717	Mm.275320	NM_007925	ENSMUSG00000029675	Eln	AI385707|AI480567|E030024M20Rik	elastin	protein-coding
mm_156594.1	chrX	152233229	152233260	+	1	NA	promoter-TSS (NM_013668)	promoter-TSS (NM_013668)	17	NM_013668	20591	Mm.142655	NM_013668	ENSMUSG00000025332	Kdm5c	D930009K15Rik|Jarid1c|Smcx|mKIAA0234	lysine (K)-specific demethylase 5C	protein-coding
mm_111803.1	chr12	105010024	105010059	-	1	NA	promoter-TSS (NM_172500)	promoter-TSS (NM_172500)	-232	NM_172500	212073	Mm.212688	NM_172500	ENSMUSG00000054150	Syne3	nesprin-3	spectrin repeat containing, nuclear envelope family member 3	protein-coding
mm_120563.1	chr14	68123719	68123766	+	1	NA	promoter-TSS (NR_045897)	promoter-TSS (NR_045897)	-10	NR_045897	100043072	Mm.242832	NR_045897		A230070E04Rik	Gm4210	RIKEN cDNA A230070E04 gene	ncRNA
mm_115718.1	chr13	15914356	15914363	-	1	NA	Intergenic	ORR1B2|LTR|ERVL-MaLR	-97492	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_19760.1	chr2	105399209	105399243	-	1	NA	promoter-TSS (NM_009037)	promoter-TSS (NM_009037)	93	NM_009037	19672	Mm.4876	NM_009037	ENSMUSG00000005973	Rcn1	Rcn	reticulocalbin 1	protein-coding
mm_5720.1	chr1	44101983	44101996	-	1	NA	intron (NM_029368, intron 1 of 7)	CpG	399	NM_029368	75623	Mm.348017	NM_029368	ENSMUSG00000026049	Tex30	1700029F09Rik|3110030D08Rik	testis expressed 30	protein-coding
mm_3217.1	chr1	135845579	135845602	+	1	NA	exon (NM_001130176, exon 3 of 13)	exon (NM_001130176, exon 3 of 13)	4729	NM_001130176	21956	Mm.247470	NM_011619	ENSMUSG00000026414	Tnnt2	Tnt|cTnT	troponin T2, cardiac	protein-coding
mm_37731.1	chr4	129573571	129573598	-	1	NA	promoter-TSS (NM_001162433)	promoter-TSS (NM_001162433)	57	NM_001162433	16818	Mm.293753	NM_010693	ENSMUSG00000000409	Lck	Hck-3|Lsk|Lskt|p56<lck>|p56Lck	lymphocyte protein tyrosine kinase	protein-coding
mm_78628.1	chr9	38731002	38731015	+	1	NA	intron (NM_172767, intron 11 of 19)	intron (NM_172767, intron 11 of 19)	12740	NM_172767	67776	Mm.290950	NM_172767	ENSMUSG00000023186	Vwa5a	5830475I06Rik|AW552491|BCSC-1|E130119J22|Loh11cr2a	von Willebrand factor A domain containing 5A	protein-coding
mm_151839.1	chr19	5726215	5726227	-	1	NA	promoter-TSS (NM_001114597)	promoter-TSS (NM_001114597)	96	NM_001114595	114601	Mm.210447	NM_053252	ENSMUSG00000024937	Ehbp1l1	G430002G23Rik	EH domain binding protein 1-like 1	protein-coding
mm_62254.1	chr7	99269072	99269086	+	1	NA	exon (NM_001043355, exon 1 of 3)	exon (NM_001043355, exon 1 of 3)	733	NM_001043355	17760	Mm.154087	NM_010837	ENSMUSG00000055407	Map6	2810411E12Rik|Map-6|Mtap6|STOP	microtubule-associated protein 6	protein-coding
mm_70451.1	chr8	11779276	11779294	+	1	NA	intron (NM_001113517, intron 2 of 18)	intron (NM_001113517, intron 2 of 18)	20955	NM_001113518	54126	Mm.244068	NM_017402	ENSMUSG00000031511	Arhgef7	Cool|PIX|Pak3bp|betaPix|betaPix-b|betaPix-c|cool-1|mKIAA0142|p85Cool1|p85SPR	Rho guanine nucleotide exchange factor (GEF7)	protein-coding
mm_137545.1	chr17	27556921	27556932	+	1	NA	5' UTR (NM_016660, exon 1 of 5)	5' UTR (NM_016660, exon 1 of 5)	273	NM_001166477	111241	Mm.426212	NM_001166476	ENSMUSG00000078249	Hmga1-rs1	ENSMUSG00000041059|Hmgi-rs1	high mobility group AT-hook I, related sequence 1	protein-coding
mm_138411.1	chr17	35068722	35068750	+	1	NA	intron (NM_023463, intron 1 of 2)	intron (NM_023463, intron 1 of 2)	1411	NM_023463	68468	Mm.215096	NM_023463	ENSMUSG00000092586	Ly6g6c	1110003M04Rik|AU016360|G6c|NG24	lymphocyte antigen 6 complex, locus G6C	protein-coding
mm_77437.1	chr8	121578756	121578817	-	1	NA	promoter-TSS (NM_133765)	promoter-TSS (NM_133765)	20	NM_133765	76454	Mm.24829	NM_133765	ENSMUSG00000052934	Fbxo31	1110003O08Rik|2310046N15Rik|Fbx14|Fbxo14	F-box protein 31	protein-coding
mm_100321.1	chr11	118014545	118014577	+	1	NA	intron (NM_133757, intron 7 of 9)	intron (NM_133757, intron 7 of 9)	12291	NR_105898	102466768		NR_105898	ENSMUSG00000098958	Mir6933	Gm27856|mmu-mir-6933	microRNA 6933	ncRNA
mm_62715.1	chr7	110770627	110770633	+	1	NA	intron (NM_001276301, intron 1 of 14)	MIR|SINE|MIR	-1974	NM_009667	11717	Mm.3238	NM_009667	ENSMUSG00000005686	Ampd3	-	adenosine monophosphate deaminase 3	protein-coding
mm_75566.1	chr8	60452627	60452628	-	1	NA	Intergenic	Intergenic	-53497	NM_011834	23923	Mm.35020	NM_011834	ENSMUSG00000057228	Aadat	AI875679|Aadt|KATII|Kat2|Kyat2|mKat-2	aminoadipate aminotransferase	protein-coding
mm_119877.1	chr14	54883321	54883391	+	1	NA	promoter-TSS (NM_007537)	promoter-TSS (NM_007537)	-69	NM_007537	12050	Mm.6967	NM_007537	ENSMUSG00000089682	Bcl2l2	AW048834|Bcl-w|Gtrgal2|Gtrosa41|bclw|c98	BCL2-like 2	protein-coding
mm_136795.1	chr17	12119252	12119265	+	1	NA	promoter-TSS (NM_026644)	promoter-TSS (NM_026644)	-26	NM_026644	68262	Mm.258300	NM_026644	ENSMUSG00000023827	Agpat4	1500003P24Rik	1-acylglycerol-3-phosphate O-acyltransferase 4 (lysophosphatidic acid acyltransferase, delta)	protein-coding
mm_161837.1	chr17	84974009	84974009	+	1	NA	promoter-TSS (NM_001159498)	promoter-TSS (NM_001159498)	-43	NM_001159498	19043	Mm.249695	NM_011151	ENSMUSG00000061130	Ppm1b	PP2CB	protein phosphatase 1B, magnesium dependent, beta isoform	protein-coding
mm_24383.1	chr3	90248963	90248971	+	1	NA	5' UTR (NM_013901, exon 2 of 4)	5' UTR (NM_013901, exon 2 of 4)	775	NM_013901	30791	Mm.294709	NM_013901	ENSMUSG00000052310	Slc39a1	Zip1|Zirtl	solute carrier family 39 (zinc transporter), member 1	protein-coding
mm_11432.1	chr2	31962202	31962242	+	1	NA	exon (NM_145144, exon 3 of 6)	exon (NM_145144, exon 3 of 6)	11919	NM_145144	108897	Mm.24838	NM_145144	ENSMUSG00000001864	Aif1l	2810003C17Rik|AI043124|C87647|Iba2	allograft inflammatory factor 1-like	protein-coding
mm_88741.1	chr10	80280407	80280409	+	1	NA	intron (NM_001122604, intron 6 of 11)	L1MEd|LINE|L1	2244	NR_105876	102466207		NR_105876	ENSMUSG00000098672	Mir6911	Gm27822|mmu-mir-6911	microRNA 6911	ncRNA
mm_67296.1	chr7	79145296	79145315	-	1	NA	exon (NM_008594, exon 3 of 10)	exon (NM_008594, exon 3 of 10)	3755	NM_001045489	17304	Mm.1451	NM_008594	ENSMUSG00000030605	Mfge8	AA408458|AI325141|MFG-E8|MP47|Mfgm|P47|SED1|lactadherin	milk fat globule-EGF factor 8 protein	protein-coding
mm_20656.1	chr2	132103455	132103465	-	1	NA	intron (NM_018824, intron 1 of 15)	intron (NM_018824, intron 1 of 15)	41648	NM_018824	54338	Mm.103581	NM_018824	ENSMUSG00000027340	Slc23a2	AI844736|NBTL1|SVCT2|Slc23a1|YSPL2|YSPL3|mKIAA0238	solute carrier family 23 (nucleobase transporters), member 2	protein-coding
mm_74668.1	chr8	13677576	13677592	-	1	NA	promoter-TSS (NM_009025)	promoter-TSS (NM_009025)	3	NM_009025	19414	Mm.18517	NM_009025	ENSMUSG00000031453	Rasa3	AI326412|C86362|E130011G04|GAPIII|hlb381|scat	RAS p21 protein activator 3	protein-coding
mm_110194.1	chr12	27340322	27340332	-	1	NA	3' UTR (NM_009234, exon 1 of 1)	3' UTR (NM_009234, exon 1 of 1)	2391	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding
mm_101503.1	chr11	32199370	32199380	-	1	NA	intron (NM_001134458, intron 1 of 8)	intron (NM_001134458, intron 1 of 8)	904	NM_001134458	16199	Mm.384	NM_008374	ENSMUSG00000020279	Il9r	-	interleukin 9 receptor	protein-coding
mm_163839.1	chr14	19417909	19417926	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	184670	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_147986.1	chr18	67610803	67610808	-	1	NA	Intergenic	CpG	30531	NM_001081073	225659	Mm.111928	NM_001081073	ENSMUSG00000073542	Cep76	6230425F05Rik|9630013E05	centrosomal protein 76	protein-coding
mm_138796.1	chr17	37532140	37532150	+	1	NA	Intergenic	Intergenic	2188	NM_001005485	545205	Mm.383371	NM_001005485	ENSMUSG00000090675	Olfr111	-	olfactory receptor 111	protein-coding
mm_84834.1	chr9	78347141	78347157	-	1	NA	promoter-TSS (NM_008182)	promoter-TSS (NM_008182)	-4	NM_008182	14858	Mm.422778	NM_008182	ENSMUSG00000057933	Gsta2	Gst2-2|Gstc-2|Gstc2	glutathione S-transferase, alpha 2 (Yc2)	protein-coding
mm_41257.1	chr5	88934213	88934239	+	1	NA	intron (NM_001197147, intron 1 of 25)	intron (NM_001197147, intron 1 of 25)	46966	NM_018760	54403	Mm.41044	NM_018760	ENSMUSG00000060961	Slc4a4	AI835705|NBC|NBC1	solute carrier family 4 (anion exchanger), member 4	protein-coding
mm_102566.1	chr11	61493882	61493890	-	1	NA	5' UTR (NM_001291037, exon 1 of 6)	5' UTR (NM_001291037, exon 1 of 6)	380	NM_001291037	23939	Mm.38172	NM_011841	ENSMUSG00000001034	Mapk7	BMK-1|BMK1|ERK-5|ERK5|Erk5-T|PRKM7	mitogen-activated protein kinase 7	protein-coding
mm_125173.1	chr15	31565366	31565406	+	1	NA	Intergenic	Intergenic	-3526	NM_181588	69574	Mm.28108	NM_181588	ENSMUSG00000022235	Cmbl	2310016A09Rik	carboxymethylenebutenolidase-like (Pseudomonas)	protein-coding
mm_74482.1	chr8	4325000	4325091	-	1	NA	promoter-TSS (NM_010485)	promoter-TSS (NM_010485)	55	NM_010485	15568	Mm.119162	NM_010485	ENSMUSG00000040028	Elavl1	2410055N02Rik|HUR|Hua|W91709	ELAV (embryonic lethal, abnormal vision)-like 1 (Hu antigen R)	protein-coding
mm_41462.1	chr5	90931210	90931311	+	1	NA	promoter-TSS (NM_026788)	promoter-TSS (NM_026788)	64	NM_026788	665563	Mm.153030	NM_026788	ENSMUSG00000029376	Mthfd2l	1110019K23Rik|C630010D07Rik	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2-like	protein-coding
mm_171652.1	chr4	40723745	40723748	+	1	NA	promoter-TSS (NR_077226)	promoter-TSS (NR_077226)	816	NM_001164672	15502	Mm.27897	NM_008298	ENSMUSG00000028410	Dnaja1	HSJ-2|Hsj2|Nedd7	DnaJ heat shock protein family (Hsp40) member A1	protein-coding
mm_30735.1	chr4	13854805	13854808	+	1	NA	intron (NM_001111026, intron 5 of 10)	intron (NM_001111026, intron 5 of 10)	70024	NM_009822	12395	Mm.4909	NM_009822	ENSMUSG00000006586	Runx1t1	Cbfa2t1h|ETO|MTG8	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	protein-coding
mm_78514.1	chr9	32915972	32916003	+	1	NA	intron (NR_131058, intron 1 of 3)	intron (NR_131058, intron 1 of 3)	12979	NR_131058	330917	Mm.488283	NR_131058		Gm27162	A430016B06	predicted gene 27162	ncRNA
mm_54287.1	chr6	29245790	29245801	-	1	NA	Intergenic	Intergenic	-26693	NM_001190461	69573	Mm.45161	NM_023516	ENSMUSG00000043421	Hilpda	2310016C08Rik|AW049004|Hig2	hypoxia inducible lipid droplet associated	protein-coding
mm_59799.1	chr7	29043594	29043680	+	1	NA	intron (NM_009109, intron 84 of 105)	intron (NM_009109, intron 84 of 105)	40057	NR_035489	100316710		NR_035489	ENSMUSG00000089219	Mir1963	mir-1963|mmu-mir-1963	microRNA 1963	ncRNA
mm_30438.1	chr3	153633466	153633483	-	1	NA	intron (NM_011372, intron 1 of 4)	intron (NM_011372, intron 1 of 4)	91659	NM_011372	20447	Mm.296453	NM_011372	ENSMUSG00000052544	St6galnac3	Siat7c	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 3	protein-coding
mm_101809.1	chr11	46372404	46372443	-	1	NA	intron (NM_010583, intron 1 of 16)	intron (NM_010583, intron 1 of 16)	17092	NM_001281968	16428	Mm.339927	NM_010583	ENSMUSG00000020395	Itk	Emt|Tcsk|Tsk	IL2 inducible T cell kinase	protein-coding
mm_72667.1	chr8	84901956	84901992	+	1	NA	promoter-TSS (NM_010635)	promoter-TSS (NM_010635)	46	NM_010635	16596	Mm.4847	NM_010635	ENSMUSG00000054191	Klf1	Eklf|Nan	Kruppel-like factor 1 (erythroid)	protein-coding
mm_161392.1	chr14	93888826	93888826	-	1	NA	promoter-TSS (NM_001271800)	promoter-TSS (NM_001271800)	62	NM_001271800	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding
mm_109122.1	chr12	105706005	105706012	+	1	NA	promoter-TSS (NM_030187)	promoter-TSS (NM_030187)	26	NM_030187	78801	Mm.36006	NM_030187	ENSMUSG00000041323	Ak7	4930502N02Rik|AK 7	adenylate kinase 7	protein-coding
mm_57375.1	chr6	124812964	124813033	-	1	NA	intron (NM_009415, intron 1 of 6)	intron (NM_009415, intron 1 of 6)	1298	NM_009415	21991	Mm.4222	NM_009415	ENSMUSG00000023456	Tpi1	AI255506|Tpi|Tpi-1	triosephosphate isomerase 1	protein-coding
mm_64058.1	chr7	140847817	140847829	+	1	NA	promoter-TSS (NM_027019)	promoter-TSS (NM_027019)	-93	NM_027019	69287	Mm.56404	NM_027019	ENSMUSG00000025482	Odf3	1700011O04Rik|SHIPPO1	outer dense fiber of sperm tails 3	protein-coding
mm_86699.1	chr10	18508840	18508849	+	1	NA	intron (NM_173390, intron 3 of 6)	intron (NM_173390, intron 3 of 6)	37232	NM_019487	56016	Mm.35551	NM_019487	ENSMUSG00000019853	Hebp2	SOUL	heme binding protein 2	protein-coding
mm_5952.1	chr1	56969865	56969875	-	1	NA	5' UTR (NM_139146, exon 2 of 11)	5' UTR (NM_139146, exon 2 of 11)	1464	NM_139146	212712	Mm.145599	NM_139146	ENSMUSG00000038331	Satb2	mKIAA1034	special AT-rich sequence binding protein 2	protein-coding
mm_139494.1	chr17	56162553	56162567	+	1	NA	promoter-TSS (NM_025566)	promoter-TSS (NM_025566)	69	NM_025566	66443	Mm.2312	NM_025566	ENSMUSG00000044469	Tnfaip8l1	2600017J23Rik|TIPE1	tumor necrosis factor, alpha-induced protein 8-like 1	protein-coding
mm_15181.1	chr2	154190834	154190857	+	1	NA	promoter-TSS (NM_001012392)	promoter-TSS (NM_001012392)	27	NM_001012392	228801	Mm.3783	NM_153418	ENSMUSG00000027485	Bpifb1	Lplunc1	BPI fold containing family B, member 1	protein-coding
mm_31625.1	chr4	59214157	59214176	+	1	NA	intron (NM_011673, intron 5 of 8)	intron (NM_011673, intron 5 of 8)	24616	NM_011673	22234	Mm.198803	NM_011673	ENSMUSG00000028381	Ugcg	AU043821|C80537|Epcs21|GlcT-1|Ugcgl	UDP-glucose ceramide glucosyltransferase	protein-coding
mm_30896.1	chr4	32313076	32313082	+	1	NA	Intergenic	Intergenic	-104356	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_94735.1	chr11	21048901	21048937	+	1	NA	Intergenic	Intergenic	-42405	NM_023324	67245	Mm.28957	NM_023324	ENSMUSG00000020134	Peli1	2810468L03Rik|A930031K15Rik|AA409794|AI586297|D11Ertd676e	pellino 1	protein-coding
mm_54928.1	chr6	48048940	48048956	-	1	NA	promoter-TSS (NM_001081382)	promoter-TSS (NM_001081382)	-834	NM_001081382	72306	Mm.381553	NM_001081382	ENSMUSG00000071477	Zfp777	2500002G23Rik	zinc finger protein 777	protein-coding
mm_9040.1	chr1	167243608	167243616	-	1	NA	intron (NM_030724, intron 1 of 6)	intron (NM_030724, intron 1 of 6)	41515	NM_030724	80914	Mm.280895	NM_030724	ENSMUSG00000026558	Uck2	AA407809|AI481316|AU018180|AU020720|TSA903|UK|UMK|Umpk	uridine-cytidine kinase 2	protein-coding
mm_60078.1	chr7	34021747	34021760	+	1	NA	exon (NM_009596, exon 2 of 3)	exon (NM_009596, exon 2 of 3)	186	NM_009596	11354	Mm.8025	NM_009596	ENSMUSG00000066583	Scgb1b27	Abp|Abpa|Abpa27|Sal-1|Tcp	secretoglobin, family 1B, member 27	protein-coding
mm_46545.1	chr5	106458410	106458418	-	1	NA	promoter-TSS (NM_001005477)	promoter-TSS (NM_001005477)	-248	NM_001005477	104382	Mm.271593	NM_001005477	ENSMUSG00000034384	Barhl2	E130309B19Rik|MBH1	BarH-like 2 (Drosophila)	protein-coding
mm_10601.1	chr2	18698988	18698997	+	1	NA	promoter-TSS (NM_001001334)	promoter-TSS (NM_001001334)	-30	NM_001001334	381350	Mm.330024	NM_001001334	ENSMUSG00000037708	Spag6	Spag6l	sperm associated antigen 6	protein-coding
mm_13800.1	chr2	118926577	118926608	+	1	NA	promoter-TSS (NM_028117)	promoter-TSS (NM_028117)	95	NM_028117	72136	Mm.486238	NM_028117	ENSMUSG00000074916	Chst14	2600016L03Rik|D4ST-1|D4st1	carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 14	protein-coding
mm_1016.1	chr1	58738433	58738452	+	1	NA	intron (NM_001293805, intron 4 of 7)	intron (NM_001293805, intron 4 of 7)	7890	NM_001293805	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_70391.1	chr8	10902047	10902061	+	1	NA	non-coding (NR_102285, exon 3 of 3)	non-coding (NR_102285, exon 3 of 3)	2132	NR_102285	71624	Mm.139075	NR_102285	ENSMUSG00000109089	4833411C07Rik	-	RIKEN cDNA 4833411C07 gene	ncRNA
mm_7061.1	chr1	87510307	87510373	-	1	NA	promoter-TSS (NM_019867)	promoter-TSS (NM_019867)	22	NM_019867	53972	Mm.435439	NM_019867	ENSMUSG00000026259	Ngef	Tims2|ephexin	neuronal guanine nucleotide exchange factor	protein-coding
mm_159309.1	chr2	180642588	180642588	-	1	NA	exon (NM_178254, exon 1 of 6)	exon (NM_178254, exon 1 of 6)	103	NM_178254	277353	Mm.473700	NM_178254	ENSMUSG00000038932	Tcfl5	AV260129|Figlb|Sosf1	transcription factor-like 5 (basic helix-loop-helix)	protein-coding
mm_17185.1	chr2	25460971	25460983	-	1	NA	5' UTR (NM_153557, exon 1 of 7)	5' UTR (NM_153557, exon 1 of 7)	117	NM_153557	227622	Mm.261780	NM_153557	ENSMUSG00000047617	BC029214	D930050G13Rik|Paxx	cDNA sequence BC029214	protein-coding
mm_86585.1	chr10	13060530	13060538	+	1	NA	Intergenic	Intergenic	-30254	NM_009538	22634	Mm.287857	NM_009538	ENSMUSG00000019817	Plagl1	Lot1|Zac1	pleiomorphic adenoma gene-like 1	protein-coding
mm_144719.1	chr18	35119807	35119818	+	1	NA	intron (NM_009818, intron 1 of 17)	intron (NM_009818, intron 1 of 17)	900	NM_009818	12385	Mm.18962	NM_009818	ENSMUSG00000037815	Ctnna1	2010010M04Rik|AA517462|AI988031|Catna1	catenin (cadherin associated protein), alpha 1	protein-coding
mm_56015.1	chr6	86525931	86525941	-	1	NA	5' UTR (NM_011865, exon 1 of 1)	5' UTR (NM_011865, exon 1 of 1)	229	NM_011865	23983	Mm.274146	NM_011865	ENSMUSG00000051695	Pcbp1	WBP17|[a]CP-1|alphaCP-1|hnRNP E1	poly(rC) binding protein 1	protein-coding
mm_149412.1	chr19	11414448	11414454	+	1	NA	intron (NM_029499, intron 1 of 6)	intron (NM_029499, intron 1 of 6)	6790	NM_029499	64380	Mm.440715	NM_029499	ENSMUSG00000024675	Ms4a4c	5830413L19Rik|AI449185|Ms4a9	membrane-spanning 4-domains, subfamily A, member 4C	protein-coding
mm_167937.1	chrX	111768407	111768415	-	1	NA	Intergenic	Intergenic	-71332	NM_001290459	245596	Mm.246623	NM_001080549	ENSMUSG00000034551	Hdx	D030011N01Rik|Gm380	highly divergent homeobox	protein-coding
mm_15831.1	chr2	164653978	164653982	+	1	NA	intron (NM_001160414, intron 1 of 3)	PB1D10|SINE|Alu	986	NM_001160414	629754	Mm.190489	NM_001160414	ENSMUSG00000074594	Wfdc9	OTTMUSG00000001088	WAP four-disulfide core domain 9	protein-coding
mm_1904.1	chr1	85849211	85849242	+	1	NA	3' UTR (NM_133781, exon 9 of 9)	3' UTR (NM_133781, exon 9 of 9)	-45284	NM_022417	64294	Mm.29870	NM_022417	ENSMUSG00000026223	Itm2c	3110038L02Rik|BRI3|Bricd2c|E25|E25C|ITM3	integral membrane protein 2C	protein-coding
mm_115446.1	chr13	118047294	118047302	+	1	NA	Intergenic	Intergenic	-327287	NR_045508	71100	Mm.414841	NR_045508	ENSMUSG00000079048	4933413L06Rik	-	RIKEN cDNA 4933413L06 gene	ncRNA
mm_155709.1	chrX	96096008	96096016	+	1	NA	promoter-TSS (NM_010833)	promoter-TSS (NM_010833)	-33	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_129484.1	chr15	78771880	78771892	-	1	NA	intron (NM_008595, intron 1 of 7)	intron (NM_008595, intron 1 of 7)	1559	NM_008595	17305	Mm.149235	NM_008595	ENSMUSG00000018169	Mfng	AW546563	MFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	protein-coding
mm_104262.1	chr11	88954885	88954910	-	1	NA	intron (NM_029023, intron 1 of 12)	intron (NM_029023, intron 1 of 12)	545	NM_029023	74617	Mm.34126	NM_029023	ENSMUSG00000000278	Scpep1	2410018F01Rik|4833411K15Rik|AI957256|Risc	serine carboxypeptidase 1	protein-coding
mm_124207.1	chr14	99046111	99046141	-	1	NA	promoter-TSS (NM_175245)	promoter-TSS (NM_175245)	10	NM_175245	76789	Mm.38912	NM_175245	ENSMUSG00000033186	Mzt1	2410129H14Rik|AI120158|Mozart1	mitotic spindle organizing protein 1	protein-coding
mm_119760.1	chr14	54168656	54168683	+	1	NA	Intergenic	Intergenic	85260	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_149959.1	chr19	28963893	28963969	+	1	NA	promoter-TSS (NM_028922)	promoter-TSS (NM_028922)	11	NM_028922	74411	Mm.441887	NM_028922	ENSMUSG00000040105	Plpp6	4932443D16Rik|Ppapdc2	phospholipid phosphatase 6	protein-coding
mm_168581.1	chr1	171903039	171903052	-	1	NA	Intergenic	RLTR4_Mm|LTR|ERV1	-14417	NM_001347187	30925	Mm.486404	NM_030710	ENSMUSG00000015314	Slamf6	KAL1|KAL1b|Ly108|NTB-A|NTBA|SF2000	SLAM family member 6	protein-coding
mm_77195.1	chr8	112011321	112011372	-	1	NA	promoter-TSS (NM_001286384)	promoter-TSS (NM_001286384)	8	NM_001286384	85305	Mm.196544	NM_053092	ENSMUSG00000031948	Kars	AA589550|AL024334|AL033315|AL033367|D8Ertd698e|D8Wsu108e|LysRS|mKIAA0070	lysyl-tRNA synthetase	protein-coding
mm_62777.1	chr7	112391196	112391210	+	1	NA	intron (NM_027587, intron 4 of 9)	intron (NM_027587, intron 4 of 9)	22895	NM_027587	100504195	Mm.291129	NM_027587	ENSMUSG00000030771	Micalcl	4921517J23Rik	MICAL C-terminal like	protein-coding
mm_13587.1	chr2	112446914	112446923	+	1	NA	Intergenic	B1F|SINE|Alu	-8107	NM_133749	73024	Mm.268027	NM_133749	ENSMUSG00000055943	Emc7	2900064A13Rik|AI451465|ORF3|c11orf3	ER membrane protein complex subunit 7	protein-coding
mm_85676.1	chr9	107769623	107769626	-	1	NA	5' UTR (NM_148930, exon 2 of 25)	5' UTR (NM_148930, exon 2 of 25)	1378	NM_148930	83486	Mm.259197	NM_148930	ENSMUSG00000032580	Rbm5	D030069N10Rik	RNA binding motif protein 5	protein-coding
mm_85457.1	chr9	105412493	105412495	-	1	NA	3' UTR (NM_175025, exon 28 of 28)	3' UTR (NM_175025, exon 28 of 28)	11706	NM_001164828	66595	Mm.84941	NM_025651	ENSMUSG00000032567	Aste1	1100001A21Rik|AV006403	asteroid homolog 1 (Drosophila)	protein-coding
mm_673.1	chr1	40465966	40465975	+	1	NA	promoter-TSS (NM_008365)	promoter-TSS (NM_008365)	-36	NM_008365	16182	Mm.253664	NM_008365	ENSMUSG00000026070	Il18r1	Il18ralpha|Il1rrp	interleukin 18 receptor 1	protein-coding
mm_157096.1	chrX	9437345	9437355	-	1	NA	3' UTR (NM_007807, exon 13 of 13)	3' UTR (NM_007807, exon 13 of 13)	31974	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_154514.1	chrM	12442	12477	-	1	NA	NA	Intergenic	NA	NA								
mm_134170.1	chr16	10796512	10796524	-	1	NA	exon (NM_013637, exon 2 of 2)	exon (NM_013637, exon 2 of 2)	305	NM_013637	19118	Mm.42733	NM_013637	ENSMUSG00000022501	Prm1	Prm-1	protamine 1	protein-coding
mm_151803.1	chr19	5424879	5424890	-	1	NA	promoter-TSS (NM_024176)	promoter-TSS (NM_024176)	95	NM_024176	66556	Mm.275446	NM_024176	ENSMUSG00000024914	Drap1	2310074H19Rik|NC2-alpha	Dr1 associated protein 1 (negative cofactor 2 alpha)	protein-coding
mm_124299.1	chr14	103055585	103055604	-	1	NA	3' UTR (NM_008392, exon 5 of 5)	3' UTR (NM_008392, exon 5 of 5)	8582	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_52158.1	chr6	98018703	98018730	+	1	NA	3' UTR (NM_001178049, exon 10 of 10)	3' UTR (NM_001178049, exon 10 of 10)	26933	NM_008601	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_16491.1	chr2	181013435	181013445	+	1	NA	exon (NM_028518, exon 29 of 36)	exon (NM_028518, exon 29 of 36)	25737	NM_015730	11438	Mm.252369	NM_015730	ENSMUSG00000027577	Chrna4	Acra-4|Acra4|EBN1|ENFL1	cholinergic receptor, nicotinic, alpha polypeptide 4	protein-coding
mm_127562.1	chr15	102203640	102203693	+	1	NA	promoter-TSS (NM_001289690)	promoter-TSS (NM_001289690)	21	NM_001289691	68744	Mm.352945	NM_153194	ENSMUSG00000046897	Zfp740	1110034O07Rik|AW548228|Znf740	zinc finger protein 740	protein-coding
mm_172741.1	chr8	79028663	79028678	+	1	NA	5' UTR (NM_178267, exon 1 of 15)	5' UTR (NM_178267, exon 1 of 15)	233	NM_178267	622675	Mm.48724	NM_178267	ENSMUSG00000071064	Zfp827	2810449M09Rik|D630040G17Rik|Znf827	zinc finger protein 827	protein-coding
mm_155184.1	chrX	56317516	56317540	+	1	NA	promoter-TSS (NR_038168)	promoter-TSS (NR_038168)	-80	NR_038168	72030	Mm.426148	NR_038168	ENSMUSG00000085114	1600025M17Rik	Gm394	RIKEN cDNA 1600025M17 gene	ncRNA
mm_11084.1	chr2	27736036	27736039	+	1	NA	intron (NM_001290482, intron 1 of 9)	PB1D9|SINE|Alu	25454	NM_001290482	20181	Mm.24624	NM_011305	ENSMUSG00000015846	Rxra	9530071D11Rik|Nr2b1|RXRalpha1	retinoid X receptor alpha	protein-coding
mm_243.1	chr1	19209113	19209126	+	1	NA	5' UTR (NM_009334, exon 1 of 7)	5' UTR (NM_009334, exon 1 of 7)	205	NM_001286340	21419	Mm.137021	NM_009334	ENSMUSG00000025927	Tfap2b	AI606113|AP-2(beta)|E130018K07Rik|Tcfap2b	transcription factor AP-2 beta	protein-coding
mm_57814.1	chr6	129462608	129462616	-	1	NA	non-coding (NR_132130, exon 6 of 6)	non-coding (NR_132130, exon 6 of 6)	10167	NM_001309637	56644	Mm.239516	NM_020008	ENSMUSG00000079293	Clec7a	BGR|Clecsf12|beta-GR	C-type lectin domain family 7, member a	protein-coding
mm_10166.1	chr2	4416288	4416319	+	1	NA	intron (NM_001177843, intron 1 of 23)	L3|LINE|CR1	15327	NM_001177843	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding
mm_98667.1	chr11	96282530	96282554	+	1	NA	5' UTR (NM_010461, exon 1 of 2)	5' UTR (NM_010461, exon 1 of 2)	637	NM_010461	15416	Mm.4822	NM_010461	ENSMUSG00000056648	Hoxb8	Hox-2.4	homeobox B8	protein-coding
mm_9201.1	chr1	171226402	171226424	-	1	NA	TTS (NM_013474)	TTS (NM_013474)	1359	NM_013474	11807	Mm.389209	NM_013474	ENSMUSG00000005681	Apoa2	Alp-2|Apo-AII|ApoA-II|ApoAII|Apoa-2|Hdl-1	apolipoprotein A-II	protein-coding
mm_163515.1	chr12	113427524	113427531	-	1	NA	Intergenic	Intergenic	-62038	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_24180.1	chr3	88579858	88579864	+	1	NA	5' UTR (NM_025448, exon 1 of 5)	5' UTR (NM_025448, exon 1 of 5)	190	NM_025448	66256	Mm.7091	NM_025448	ENSMUSG00000041355	Ssr2	1500032E05Rik|AI315033|AU020133|TLAP|TRAPB|TRAPbeta	signal sequence receptor, beta	protein-coding
mm_71975.1	chr8	70594362	70594372	+	1	NA	promoter-TSS (NM_023627)	promoter-TSS (NM_023627)	-114	NM_023627	71780	Mm.29357	NM_023627	ENSMUSG00000019139	Isyna1	1300017C10Rik|AU018670	myo-inositol 1-phosphate synthase A1	protein-coding
mm_1792.1	chr1	78816910	78816913	+	1	NA	promoter-TSS (NM_021342)	promoter-TSS (NM_021342)	-38	NM_021342	57814	Mm.24386	NM_021342	ENSMUSG00000047330	Kcne4	AW487937|MiRP3	potassium voltage-gated channel, Isk-related subfamily, gene 4	protein-coding
mm_94376.1	chr11	5105215	5105221	+	1	NA	exon (NM_177370, exon 7 of 9)	exon (NM_177370, exon 7 of 9)	5053	NM_001290493	279766	Mm.260866	NM_177370	ENSMUSG00000034175	Rhbdd3	Ptag	rhomboid domain containing 3	protein-coding
mm_112984.1	chr13	21362827	21362883	+	1	NA	promoter-TSS (NM_016684)	promoter-TSS (NM_016684)	35	NM_016684	22758	Mm.24124	NM_016684	ENSMUSG00000036721	Zscan12	2510038J07Rik|FPM315|Zfp96|mKIAA0426|zfp-96	zinc finger and SCAN domain containing 12	protein-coding
mm_172490.1	chr7	55086419	55086421	-	1	NA	intron (NM_178705, intron 5 of 11)	intron (NM_178705, intron 5 of 11)	251175	NM_178705	233271	Mm.387344	NM_178705	ENSMUSG00000063297	Luzp2	9330154K17Rik|D130073E01	leucine zipper protein 2	protein-coding
mm_101425.1	chr11	29548495	29548512	-	1	NA	promoter-TSS (NM_024277)	promoter-TSS (NM_024277)	-463	NM_001033865	78294	Mm.180003	NM_024277	ENSMUSG00000020460	Rps27a	0610006J14Rik|Uba52|Ubb|Ubc	ribosomal protein S27A	protein-coding
mm_77229.1	chr8	115703959	115703970	-	1	NA	3' UTR (NM_001025577, exon 1 of 1)	3' UTR (NM_001025577, exon 1 of 1)	2930	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_164083.1	chr15	4164961	4164964	+	1	NA	Intergenic	LTRIS2|LTR|ERV1	-137556	NR_028266	414066	Mm.394461	NR_028266		BC037032	-	cDNA Sequence BC037032	ncRNA
mm_167691.1	chr9	87731238	87731244	-	1	NA	promoter-TSS (NM_023814)	promoter-TSS (NM_023814)	19	NM_023814	76365	Mm.158789	NM_023814	ENSMUSG00000032419	Tbx18	2810012F10Rik|2810404D13Rik	T-box18	protein-coding
mm_54766.1	chr6	41314701	41314715	-	1	NA	promoter-TSS (NM_001003405)	promoter-TSS (NM_001003405)	2	NM_001003405	103964	Mm.333022	NM_001003405	ENSMUSG00000036938	Try5	1810049H19Rik|Tc|Tesp4	trypsin 5	protein-coding
mm_24570.1	chr3	93444506	93444514	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	2180	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_115313.1	chr13	112344740	112344745	+	1	NA	TTS (NM_001168405)	TTS (NM_001168405)	56224	NM_001168404	77318	Mm.159895	NM_029898	ENSMUSG00000049985	Ankrd55	C030011J08Rik	ankyrin repeat domain 55	protein-coding
mm_34471.1	chr4	148160632	148160652	+	1	NA	promoter-TSS (NM_001161852)	promoter-TSS (NM_001161852)	-26	NM_176848	230904	Mm.262287	NM_176848	ENSMUSG00000041556	Fbxo2	FBG1|FBX2|Fbs1|Fbs2|NFB42|Prpl4	F-box protein 2	protein-coding
mm_126202.1	chr15	78877298	78877315	+	1	NA	5' UTR (NM_145929, exon 1 of 17)	5' UTR (NM_145929, exon 1 of 17)	116	NM_145929	106039	Mm.251331	NM_145929	ENSMUSG00000033128	Gga1	4930406E12Rik|AU016030|AW209092	golgi associated, gamma adaptin ear containing, ARF binding protein 1	protein-coding
mm_1916.1	chr1	86021960	86021972	+	1	NA	promoter-TSS (NM_001122732)	promoter-TSS (NM_001122732)	24	NM_027029	70060	Mm.196313	NM_027029	ENSMUSG00000026226	Spata3	1700011N12Rik|1700029H01Rik|4930424D10Rik|Mtsarg1|Tsarg1	spermatogenesis associated 3	protein-coding
mm_86209.1	chr9	119984665	119984684	-	1	NA	promoter-TSS (NM_153287)	promoter-TSS (NM_153287)	-16	NM_153287	215418	Mm.491094	NM_153287	ENSMUSG00000032515	Csrnp1	4931429D10Rik|Axud1|CSRNP-1|URAX1|taip-3	cysteine-serine-rich nuclear protein 1	protein-coding
mm_99706.1	chr11	106216429	106216477	+	1	NA	promoter-TSS (NM_026009)	promoter-TSS (NM_026009)	-86	NM_026009	67163	Mm.22109	NM_026009	ENSMUSG00000078622	Ccdc47	2610204L23Rik|C88307|asp4|calumin	coiled-coil domain containing 47	protein-coding
mm_56030.1	chr6	86609316	86609326	-	1	NA	Intergenic	RSINE1|SINE|B4	-18853	NM_026414	67855	Mm.183043	NM_026414	ENSMUSG00000033508	Asprv1	2300003P22Rik|AA986851|SASP|SASPase|Taps	aspartic peptidase, retroviral-like 1	protein-coding
mm_37901.1	chr4	132731711	132731721	-	1	NA	intron (NM_201368, intron 1 of 2)	intron (NM_201368, intron 1 of 2)	830	NM_201368	381560	Mm.44558	NM_201368	ENSMUSG00000037752	Xkr8	4931440N07Rik|AI597014|Gm1031|XRG8|mXkr8	X-linked Kx blood group related 8	protein-coding
mm_161119.1	chr12	108306515	108306515	+	1	NA	exon (NM_001044380, exon 1 of 9)	exon (NM_001044380, exon 1 of 9)	245	NM_001044380	214305	Mm.36423	NM_001044380	ENSMUSG00000021260	Hhipl1	1600002O04Rik|AK129450|mKIAA1822	hedgehog interacting protein-like 1	protein-coding
mm_139439.1	chr17	53769858	53769873	+	1	NA	Intergenic	Intergenic	53356	NR_073205	211496	Mm.251553	NM_177599	ENSMUSG00000062036	4932415M13Rik	-	RIKEN cDNA 4932415M13 gene	ncRNA
mm_127422.1	chr15	101267129	101267143	+	1	NA	intron (NM_010444, intron 1 of 6)	intron (NM_010444, intron 1 of 6)	290	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_83773.1	chr9	52110966	52110969	-	1	NA	Intergenic	Intergenic	-4656	NR_105750	102465150		NR_105750	ENSMUSG00000099311	Mir6244	Gm27368|mmu-mir-6244	microRNA 6244	ncRNA
mm_34884.1	chr4	155587351	155587364	+	1	NA	exon (NM_001159637, exon 8 of 12)	exon (NM_001159637, exon 8 of 12)	-14059	NM_177186	320541	Mm.306018	NM_177186	ENSMUSG00000042202	Slc35e2	A530082C11Rik|AI957035	solute carrier family 35, member E2	protein-coding
mm_23196.1	chr3	41107921	41107933	+	1	NA	Intergenic	Intergenic	-24881	NM_027558	70804	Mm.40321	NM_027558	ENSMUSG00000049940	Pgrmc2	4631434O19Rik|5730409G06Rik|DG6|PMBP	progesterone receptor membrane component 2	protein-coding
mm_152502.1	chr19	11165342	11165350	-	1	NA	promoter-TSS (NM_027074)	promoter-TSS (NM_027074)	-26	NM_027074	69416	Mm.72491	NM_027074	ENSMUSG00000024728	1700025F22Rik	-	RIKEN cDNA 1700025F22 gene	protein-coding
mm_28089.1	chr3	85887306	85887316	-	1	NA	5' UTR (NM_177130, exon 1 of 2)	5' UTR (NM_177130, exon 1 of 2)	207	NM_177130	320302	Mm.482978	NM_177130	ENSMUSG00000031286	Glt28d2	4732486J07Rik|Glt28d1l	glycosyltransferase 28 domain containing 2	protein-coding
mm_46976.1	chr5	115194284	115194327	-	1	NA	promoter-TSS (NM_001310712)	promoter-TSS (NM_001310712)	76	NM_001310712	29867	Mm.38551	NM_013879	ENSMUSG00000029544	Cabp1	caldendrin	calcium binding protein 1	protein-coding
mm_45468.1	chr5	69341553	69341568	-	1	NA	5' UTR (NM_175519, exon 1 of 2)	5' UTR (NM_175519, exon 1 of 2)	149	NM_175519	243043	Mm.234821	NM_175519	ENSMUSG00000037653	Kctd8	A730087N02Rik	potassium channel tetramerisation domain containing 8	protein-coding
mm_152750.1	chr19	19111208	19111221	-	1	NA	promoter-TSS (NM_001043354)	promoter-TSS (NM_001043354)	-18	NM_001043354	225998	Mm.234641	NM_146095	ENSMUSG00000036192	Rorb	Nr1f2|RZR-beta|RZRB|Rorbeta|hstp	RAR-related orphan receptor beta	protein-coding
mm_132855.1	chr16	48289029	48289032	+	1	NA	intron (NM_001018002, intron 2 of 5)	intron (NM_001018002, intron 2 of 5)	5295	NM_001018002	73693	Mm.35597	NM_028610	ENSMUSG00000058550	Dppa4	2410091M23Rik|C76608|ECAT15-1	developmental pluripotency associated 4	protein-coding
mm_20357.1	chr2	128128025	128128032	-	1	NA	intron (NM_001284410, intron 1 of 3)	CpG-8520	453	NM_001284410	12125	Mm.141083	NM_009754	ENSMUSG00000027381	Bcl2l11	1500006F24Rik|Bim|Bod|bcl2-L-11	BCL2-like 11 (apoptosis facilitator)	protein-coding
mm_166582.1	chr6	52902681	52902688	+	1	NA	intron (NM_173406, intron 1 of 4)	intron (NM_173406, intron 1 of 4)	6936	NM_001168277	231986	Mm.386865	NM_173406	ENSMUSG00000063568	Jazf1	AI591476|C820002C15|Jaz1|Tip27	JAZF zinc finger 1	protein-coding
mm_28354.1	chr3	89730552	89730562	-	1	NA	promoter-TSS (NM_001146296)	promoter-TSS (NM_001146296)	-161	NM_001146296	56417	Mm.316628	NM_019655	ENSMUSG00000027951	Adar	AV242451|Adar1|Adar1p110|Adar1p150|mZaADAR	adenosine deaminase, RNA-specific	protein-coding
mm_107282.1	chr12	29732908	29732910	+	1	NA	intron (NM_001093778, intron 4 of 24)	L1MB3|LINE|L1	-46464	NR_046080	328075	Mm.447832	NR_046080		C630031E19Rik	C630031E19	RIKEN cDNA C630031E19 gene	ncRNA
mm_109166.1	chr12	108306185	108306203	+	1	NA	promoter-TSS (NM_001044380)	promoter-TSS (NM_001044380)	-76	NM_001044380	214305	Mm.36423	NM_001044380	ENSMUSG00000021260	Hhipl1	1600002O04Rik|AK129450|mKIAA1822	hedgehog interacting protein-like 1	protein-coding
mm_96745.1	chr11	69846851	69846947	+	1	NA	non-coding (NR_033133, exon 1 of 7)	non-coding (NR_033133, exon 1 of 7)	255	NR_033133	70310	Mm.28874	NM_023564	ENSMUSG00000019461	Plscr3	2210403O21Rik|2610037N06Rik|ESTM3|X83310	phospholipid scramblase 3	protein-coding
mm_63250.1	chr7	126595224	126595236	+	1	NA	promoter-TSS (NM_145636)	promoter-TSS (NM_145636)	-320	NM_145636	246779	Mm.222632	NM_145636	ENSMUSG00000044701	Il27	IL-27|IL-27p28|Il30|p28	interleukin 27	protein-coding
mm_172380.1	chr7	13034800	13034800	-	1	NA	promoter-TSS (NM_026885)	promoter-TSS (NM_026885)	-23	NM_026885	68953	Mm.295670	NM_026885	ENSMUSG00000033916	Chmp2a	1500016L11Rik	charged multivesicular body protein 2A	protein-coding
mm_18867.1	chr2	75768024	75768028	-	1	NA	Intergenic	ID_B1|SINE|B4	-63363	NM_010902	18024	Mm.1025	NM_010902	ENSMUSG00000015839	Nfe2l2	Nrf2	nuclear factor, erythroid derived 2, like 2	protein-coding
mm_25881.1	chr3	130817879	130817889	+	1	NA	Intergenic	Intergenic	-87486	NM_001005859	68436	Mm.140568	NM_026724	ENSMUSG00000062006	Rpl34	1100001I22Rik	ribosomal protein L34	protein-coding
mm_141944.1	chr17	35058718	35058720	-	1	NA	promoter-TSS (NM_016765)	promoter-TSS (NM_016765)	-316	NM_001190449	51793	Mm.1457	NM_016765	ENSMUSG00000007039	Ddah2	1110003M04Rik|AU019324|AW413173|DDAH-2|DDAHII|Ddah|G6a|NG30	dimethylarginine dimethylaminohydrolase 2	protein-coding
mm_152815.1	chr19	23093747	23093791	-	1	NA	Intergenic	MTC|LTR|ERVL-MaLR	-47457	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_21847.1	chr2	165852609	165852624	-	1	NA	intron (NM_001252584, intron 2 of 22)	ORR1E|LTR|ERVL-MaLR	5557	NM_001252585	228880	Mm.227598	NM_027230	ENSMUSG00000039671	Zmynd8	1110013E22Rik|2010005I16Rik|3632413B07Rik|AI316811|AL024039|Prkcbp1|RACK7	zinc finger, MYND-type containing 8	protein-coding
mm_111230.1	chr12	84760786	84760849	-	1	NA	exon (NM_023409, exon 3 of 4)	exon (NM_023409, exon 3 of 4)	12295	NM_023409	67963	Mm.282556	NM_023409	ENSMUSG00000021242	Npc2	2700012J19Rik|AA408070|AU045843|HE1	Niemann-Pick type C2	protein-coding
mm_40910.1	chr5	75600311	75600349	+	1	NA	intron (NM_021099, intron 1 of 20)	intron (NM_021099, intron 1 of 20)	25339	NM_021099	16590	Mm.247073	NM_021099	ENSMUSG00000005672	Kit	Bs|CD117|Fdc|Gsfsco1|Gsfsco5|Gsfsow3|SCO1|SCO5|SOW3|Ssm|Tr-kit|W|c-KIT	KIT proto-oncogene receptor tyrosine kinase	protein-coding
mm_112602.1	chr13	14164277	14164302	+	1	NA	exon (NM_194262, exon 15 of 24)	exon (NM_194262, exon 15 of 24)	100505	NM_198122	94246	Mm.439784	NM_194262	ENSMUSG00000039219	Arid4b	BCAA|BRCAA1|RBBP1L1|Rbp1l1|SAP180	AT rich interactive domain 4B (RBP1-like)	protein-coding
mm_47132.1	chr5	120485069	120485086	-	1	NA	3' UTR (NM_023625, exon 12 of 12)	3' UTR (NM_023625, exon 12 of 12)	8530	NM_145565	231691	Mm.28685	NM_145565	ENSMUSG00000029597	Sds	4432411H13Rik|SDH	serine dehydratase	protein-coding
mm_112936.1	chr13	20986163	20986177	+	1	NA	intron (NM_012054, intron 13 of 20)	MT2B|LTR|ERVL	87129	NM_146535	258528	Mm.377554	NM_146535	ENSMUSG00000042869	Olfr1370	MOR256-14	olfactory receptor 1370	protein-coding
mm_122610.1	chr14	51057612	51057628	-	1	NA	promoter-TSS (NM_001011875)	promoter-TSS (NM_001011875)	-378	NM_001011875	497106	Mm.379740	NM_001011875	ENSMUSG00000068407	Rnase12	Rai1	ribonuclease, RNase A family, 12 (non-active)	protein-coding
mm_40012.1	chr5	33018991	33019015	+	1	NA	5' UTR (NM_011738, exon 1 of 2)	5' UTR (NM_011738, exon 1 of 2)	187	NM_011738	22629	Mm.332314	NM_011738	ENSMUSG00000018965	Ywhah	-	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta polypeptide	protein-coding
mm_168451.1	chr1	141189690	141189690	+	1	NA	Intergenic	L1Md_T|LINE|L1	-533288	NR_040604	75910	Mm.483845	NR_040604	ENSMUSG00000102368	4930590L20Rik	-	RIKEN cDNA 4930590L20 gene	ncRNA
mm_51714.1	chr6	86790722	86790734	+	1	NA	intron (NM_013471, intron 1 of 12)	ID4_|SINE|ID	2856	NM_013471	11746	Mm.259702	NM_013471	ENSMUSG00000029994	Anxa4	AI265406|AIV|AW106930|Anx4|Xanx-4	annexin A4	protein-coding
mm_36978.1	chr4	109531227	109531232	-	1	NA	promoter-TSS (NM_026291)	promoter-TSS (NM_026291)	-25	NM_001199090	67646	Mm.45820	NM_026291	ENSMUSG00000060491	4930522H14Rik	1700007J23Rik	RIKEN cDNA 4930522H14 gene	protein-coding
mm_135742.1	chr16	55865567	55865570	-	1	NA	intron (NM_001134457, intron 3 of 5)	intron (NM_001134457, intron 3 of 5)	-26927	NM_001159395	80859	Mm.247272	NM_030612	ENSMUSG00000035356	Nfkbiz	AA408868|INAP|Mail	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, zeta	protein-coding
mm_62335.1	chr7	100494270	100494330	+	1	NA	5' UTR (NM_011671, exon 2 of 8)	5' UTR (NM_011671, exon 2 of 8)	942	NM_011671	22228	Mm.171378	NM_011671	ENSMUSG00000033685	Ucp2	Slc25a8	uncoupling protein 2 (mitochondrial, proton carrier)	protein-coding
mm_88716.1	chr10	80157950	80157957	+	1	NA	3' UTR (NM_001305798, exon 8 of 8)	3' UTR (NM_001305798, exon 8 of 8)	8271	NM_001305799	59090	Mm.143813	NM_021565	ENSMUSG00000035621	Midn	3000003C15Rik	midnolin	protein-coding
mm_56185.1	chr6	88504981	88504984	-	1	NA	3' UTR (NM_016906, exon 12 of 12)	3' UTR (NM_016906, exon 12 of 12)	13818	NM_016906	53421	Mm.28375	NM_016906	ENSMUSG00000030082	Sec61a1	AA408394|AA410007|Sec61a	Sec61 alpha 1 subunit (S. cerevisiae)	protein-coding
mm_124124.1	chr14	79662108	79662112	-	1	NA	promoter-TSS (NM_001310655)	promoter-TSS (NM_001310655)	73	NM_001310655	16840	Mm.46561	NM_010701	ENSMUSG00000022025	Cnmd	Bricd3|ChM-I|Chmd|Lect1	chondromodulin	protein-coding
mm_34280.1	chr4	141424635	141424645	+	1	NA	3' UTR (NM_013868, exon 3 of 3)	3' UTR (NM_013868, exon 3 of 3)	3861	NM_013868	29818	Mm.46181	NM_013868	ENSMUSG00000006221	Hspb7	27kDa|Hsp25-2|cvHsp	heat shock protein family, member 7 (cardiovascular)	protein-coding
mm_110812.1	chr12	72236693	72236708	-	1	NA	promoter-TSS (NR_104446)	promoter-TSS (NR_104446)	27	NM_001007596	104001	Mm.221275	NM_153457	ENSMUSG00000021087	Rtn1	Nsp	reticulon 1	protein-coding
mm_19095.1	chr2	79409601	79409602	-	1	NA	intron (NM_001048176, intron 1 of 12)	intron (NM_001048176, intron 1 of 12)	19387	NM_001048176	228094	Mm.440704	NM_001033295	ENSMUSG00000075256	Cerkl	Gm1958|Rp26	ceramide kinase-like	protein-coding
mm_124635.1	chr15	4069349	4069357	+	1	NA	intron (NM_024188, intron 7 of 16)	intron (NM_024188, intron 7 of 16)	-41947	NR_028266	414066	Mm.394461	NR_028266		BC037032	-	cDNA Sequence BC037032	ncRNA
mm_118395.1	chr13	119339915	119339938	-	1	NA	exon (NM_008710, exon 15 of 17)	exon (NM_008710, exon 15 of 17)	69085	NM_008710	18115	Mm.132584	NM_008710	ENSMUSG00000025453	Nnt	4930423F13Rik|AI323702|BB168308	nicotinamide nucleotide transhydrogenase	protein-coding
mm_41194.1	chr5	88328051	88328088	+	1	NA	exon (NM_008644, exon 3 of 3)	exon (NM_008644, exon 3 of 3)	10757	NM_008644	17830	Mm.200411	NM_008644	ENSMUSG00000064156	Prol1	Muc10	proline rich, lacrimal 1	protein-coding
mm_152700.1	chr19	17326960	17326963	-	1	NA	3' UTR (NM_001136484, exon 3 of 3)	3' UTR (NM_001136484, exon 3 of 3)	12544	NM_001136484	14537	Mm.244825	NM_010265	ENSMUSG00000038843	Gcnt1	5630400D21Rik|B130048E03|C2 GlcNAcT|C2GNT|IGnT	glucosaminyl (N-acetyl) transferase 1, core 2	protein-coding
mm_136917.1	chr17	13760293	13760335	+	1	NA	promoter-TSS (NM_010806)	promoter-TSS (NM_010806)	-227	NM_010806	17356	Mm.59167	NM_010806	ENSMUSG00000068036	Afdn	5033403D15Rik|AF6|Af-6|Afadin|Gm314|I-afadin|Mllt4|S-afadin	afadin, adherens junction formation factor	protein-coding
mm_128537.1	chr15	54906861	54906901	-	1	NA	exon (NM_001285995, exon 4 of 26)	exon (NM_001285995, exon 4 of 26)	13265	NM_015744	18606	Mm.250256	NM_015744	ENSMUSG00000022425	Enpp2	ATX|E-NPP 2|Npps2|PD-Ialpha|Pdnp2|lysoPLD	ectonucleotide pyrophosphatase/phosphodiesterase 2	protein-coding
mm_25483.1	chr3	109123105	109123167	+	1	NA	promoter-TSS (NM_172685)	promoter-TSS (NM_172685)	-13	NM_172685	229731	Mm.33574	NM_172685	ENSMUSG00000040322	Slc25a24	2610016M12Rik	solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 24	protein-coding
mm_149709.1	chr19	21653177	21653192	+	1	NA	promoter-TSS (NM_025423)	promoter-TSS (NM_025423)	-125	NM_146096	226016	Mm.28796	NM_146096	ENSMUSG00000047368	Abhd17b	5730446C15Rik|Cgi67|Fam108b|Fam108b1	abhydrolase domain containing 17B	protein-coding
mm_45477.1	chr5	69592246	69592256	-	1	NA	promoter-TSS (NM_001038015)	promoter-TSS (NM_001038015)	34	NM_001038015	67980	Mm.33830	NM_027681	ENSMUSG00000029209	Gnpda2	4921523I18Rik|4933412A11Rik|BB189630|GNPDA|Gnp2|Sb52|mKIAA4008	glucosamine-6-phosphate deaminase 2	protein-coding
mm_172674.1	chr8	48070558	48070558	-	1	NA	Intergenic	Intergenic	-28534	NM_001161516	320685	Mm.121549	NM_178788	ENSMUSG00000031562	Dctd	6030466N05Rik	dCMP deaminase	protein-coding
mm_55181.1	chr6	52164449	52164464	-	1	NA	exon (NM_010451, exon 1 of 2)	exon (NM_010451, exon 1 of 2)	375	NM_010451	15399	Mm.131	NM_010451	ENSMUSG00000014704	Hoxa2	AI324701|HOX1.11|Hox-1.11	homeobox A2	protein-coding
mm_32574.1	chr4	110152654	110152674	+	1	NA	Intergenic	Intergenic	134170	NM_010488	15572	Mm.3970	NM_010488	ENSMUSG00000028546	Elavl4	Elav|Hud|PNEM	ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4 (Hu antigen D)	protein-coding
mm_33334.1	chr4	129136949	129136973	+	1	NA	promoter-TSS (NM_027402)	promoter-TSS (NM_027402)	-38	NM_027402	384061	Mm.44075	NM_027402	ENSMUSG00000001334	Fndc5	1500001L03Rik|AI836596|C87088|PeP|Pxp	fibronectin type III domain containing 5	protein-coding
mm_152359.1	chr19	10066590	10066603	-	1	NA	exon (NM_019699, exon 8 of 12)	exon (NM_019699, exon 8 of 12)	25048	NM_021890	60527	Mm.253875	NM_021890	ENSMUSG00000024664	Fads3	AI464531	fatty acid desaturase 3	protein-coding
mm_95107.1	chr11	34071014	34071018	+	1	NA	exon (NM_010696, exon 7 of 21)	exon (NM_010696, exon 7 of 21)	23815	NM_010696	16822	Mm.265350	NM_010696	ENSMUSG00000002699	Lcp2	AI323664|BB161688|SLP-76|SLP76|m1Khoe|twm	lymphocyte cytosolic protein 2	protein-coding
mm_148046.1	chr18	70530220	70530284	-	1	NA	promoter-TSS (NM_001136090)	promoter-TSS (NM_001136090)	69	NM_001136090	26447	Mm.244352	NM_011972	ENSMUSG00000038425	Poli	Rad30b	polymerase (DNA directed), iota	protein-coding
mm_169938.1	chr16	62587227	62587239	+	1	NA	Intergenic	L1Md_T|LINE|L1	199483	NM_178925	106338	Mm.26321	NM_178925	ENSMUSG00000050312	Nsun3	6720484A09Rik|AU022521	NOL1/NOP2/Sun domain family member 3	protein-coding
mm_79965.1	chr9	66373249	66373252	+	1	NA	intron (NM_145617, intron 2 of 77)	intron (NM_145617, intron 2 of 77)	22800	NM_145617	235439	Mm.244179	NM_145617	ENSMUSG00000038664	Herc1	2810449H11Rik|B230218H07|D130015N03Rik|tbl	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	protein-coding
mm_69386.1	chr7	131329508	131329522	-	1	NA	promoter-TSS (NM_027037)	promoter-TSS (NM_027037)	-16	NM_027037	69318	Mm.233840	NM_027037	ENSMUSG00000030858	1700007K09Rik	-	RIKEN cDNA 1700007K09 gene	protein-coding
mm_173163.1	chrX	40955651	40955652	-	1	NA	Intergenic	Intergenic	-445650	NM_016886	53623	Mm.327681	NM_016886	ENSMUSG00000001986	Gria3	2900064I19Rik|GluA3|GluR-C|GluR-K3|Glur-3|Glur3|Gluralpha3	glutamate receptor, ionotropic, AMPA3 (alpha 3)	protein-coding
mm_113166.1	chr13	24813337	24813352	+	1	NA	TTS (NM_024473)	TTS (NM_024473)	11687	NM_024473	79555	Mm.266668	NM_024473	ENSMUSG00000019132	BC005537	8030460C05Rik|C78201	cDNA sequence BC005537	protein-coding
mm_46141.1	chr5	93150710	93150723	-	1	NA	intron (NM_001347377, intron 3 of 10)	intron (NM_001347377, intron 3 of 10)	55779	NM_017367	12453	Mm.250419	NM_017367	ENSMUSG00000063015	Ccni	-	cyclin I	protein-coding
mm_21787.1	chr2	164856725	164856806	-	1	NA	exon (NM_011125, exon 3 of 16)	exon (NM_011125, exon 3 of 16)	943	NM_011125	18830	Mm.6105	NM_011125	ENSMUSG00000017754	Pltp	Bpife|OD107	phospholipid transfer protein	protein-coding
mm_94661.1	chr11	17198557	17198579	+	1	NA	3' UTR (NM_024459, exon 6 of 6)	3' UTR (NM_024459, exon 6 of 6)	13021	NM_025443	66249	Mm.27831	NM_025443	ENSMUSG00000020116	Pno1	1810003N24Rik|AA407421|AU015468|AU019495|AU042323|Emi3|Imi3	partner of NOB1 homolog	protein-coding
mm_123640.1	chr14	68582173	68582183	-	1	NA	promoter-TSS (NM_021475)	promoter-TSS (NM_021475)	-106	NM_021475	58860	Mm.36742	NM_021475	ENSMUSG00000022057	Adamdec1	2210414L24Rik|AI574231|Dcsn	ADAM-like, decysin 1	protein-coding
mm_79943.1	chr9	65924179	65924198	+	1	NA	intron (NM_173185, intron 1 of 13)	intron (NM_173185, intron 1 of 13)	15178	NM_173185	214897	Mm.325816	NM_173185	ENSMUSG00000032384	Csnk1g1	9130020E21Rik	casein kinase 1, gamma 1	protein-coding
mm_2436.1	chr1	97563717	97563730	+	1	NA	Intergenic	Intergenic	98295	NM_133825	52392	Mm.12309	NM_133825	ENSMUSG00000044768	D1Ertd622e	AI987691|AW047450	DNA segment, Chr 1, ERATO Doi 622, expressed	protein-coding
mm_50078.1	chr6	41392372	41392380	+	1	NA	promoter-TSS (NM_001038997)	promoter-TSS (NM_001038997)	20	NM_001038997	436523	Mm.449428	NM_001038997	ENSMUSG00000058119	Gm5771	EG436523	predicted gene 5771	protein-coding
mm_105304.1	chr11	102666008	102666017	-	1	NA	intron (NM_001127576, intron 1 of 7)	CpG	427	NM_001127576	268491	Mm.447643	NM_001127576	ENSMUSG00000051455	Meioc	Gm1564|Gm663	meiosis specific with coiled-coil domain	protein-coding
mm_116104.1	chr13	28885617	28885633	-	1	NA	promoter-TSS (NR_045054)	promoter-TSS (NR_045054)	-203	NR_045053	72518	Mm.37454	NR_045053		2610307P16Rik	AI666457	RIKEN cDNA 2610307P16 gene	ncRNA
mm_66558.1	chr7	45238795	45238864	-	1	NA	promoter-TSS (NM_007645)	promoter-TSS (NM_007645)	10	NM_007645	12493	Mm.3689	NM_007645	ENSMUSG00000030798	Cd37	Tspan26	CD37 antigen	protein-coding
mm_57844.1	chr6	129467590	129467599	-	1	NA	exon (NM_020008, exon 4 of 6)	exon (NM_020008, exon 4 of 6)	5185	NM_001309637	56644	Mm.239516	NM_020008	ENSMUSG00000079293	Clec7a	BGR|Clecsf12|beta-GR	C-type lectin domain family 7, member a	protein-coding
mm_121630.1	chr14	8360340	8360362	-	1	NA	intron (NM_146050, intron 4 of 9)	intron (NM_146050, intron 4 of 9)	18412	NM_146050	18300	Mm.25351	NM_146050	ENSMUSG00000021749	Oit1	2310076N21Rik|AV067083|EF-7|Fam3d	oncoprotein induced transcript 1	protein-coding
mm_169336.1	chr14	12107543	12107552	-	1	NA	intron (NM_008981, intron 6 of 29)	RLTR9E|LTR|ERVK	-82396	NM_001347593	19270	Mm.431266	NM_008981	ENSMUSG00000021745	Ptprg	5430405N12Rik|AW046354|AW549872|RPTPgamma	protein tyrosine phosphatase, receptor type, G	protein-coding
mm_123146.1	chr14	57099160	57099178	-	1	NA	3' UTR (NM_008125, exon 2 of 2)	3' UTR (NM_008125, exon 2 of 2)	5533	NM_008125	14619	Mm.390683	NM_008125	ENSMUSG00000046352	Gjb2	AI325222|Cnx26|Cx26|Gjb-2	gap junction protein, beta 2	protein-coding
mm_584.1	chr1	39368103	39368128	+	1	NA	5' UTR (NM_001252218, exon 1 of 4)	5' UTR (NM_001252218, exon 1 of 4)	264	NM_001252218	114641	Mm.379302	NM_053257	ENSMUSG00000073702	Rpl31	Dts	ribosomal protein L31	protein-coding
mm_10343.1	chr2	11654255	11654267	+	1	NA	intron (NM_008367, intron 1 of 7)	intron (NM_008367, intron 1 of 7)	11469	NM_008367	16184	Mm.915	NM_008367	ENSMUSG00000026770	Il2ra	CD25|Il2r|Ly-43	interleukin 2 receptor, alpha chain	protein-coding
mm_156855.1	chrX	164401732	164401741	+	1	NA	TTS (NM_001308489)	TTS (NM_001308489)	-18051	NM_011081	18700	Mm.3781	NM_011081	ENSMUSG00000031381	Piga	AI194334|Pig-a	phosphatidylinositol glycan anchor biosynthesis, class A	protein-coding
mm_32218.1	chr4	101647764	101647797	+	1	NA	promoter-TSS (NM_175036)	promoter-TSS (NM_175036)	-3	NM_175036	230514	Mm.4756	NM_175036	ENSMUSG00000035212	Leprot	LEPR|OB-RGRP|Obrgrp|VPS55	leptin receptor overlapping transcript	protein-coding
mm_54651.1	chr6	38876533	38876541	-	1	NA	promoter-TSS (NM_010433)	promoter-TSS (NM_010433)	-347	NM_001294143	15258	Mm.23790	NM_010433	ENSMUSG00000061436	Hipk2	1110014O20Rik|B230339E18Rik|Stank	homeodomain interacting protein kinase 2	protein-coding
mm_153720.1	chr19	44406626	44406630	-	1	NA	exon (NM_009127, exon 2 of 6)	exon (NM_009127, exon 2 of 6)	1081	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_154385.1	chrM	11460	11470	+	1	NA	NA	Intergenic	NA	NA								
mm_45447.1	chr5	67428039	67428053	-	1	NA	promoter-TSS (NM_001164806)	promoter-TSS (NM_001164806)	-247	NM_001164806	666938	Mm.101339	NM_001164806	ENSMUSG00000092060	Bend4	D330027G24Rik|EG666938	BEN domain containing 4	protein-coding
mm_59603.1	chr7	28140170	28140179	+	1	NA	exon (NM_001164655, exon 5 of 20)	exon (NM_001164655, exon 5 of 20)	10708	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_104964.1	chr11	100145942	100145946	-	1	NA	promoter-TSS (NM_008471)	promoter-TSS (NM_008471)	-18	NM_008471	16669	Mm.439699	NM_008471	ENSMUSG00000020911	Krt19	AI663979|CK-19|EndoC|K19|Krt-1.19|Krt1-19	keratin 19	protein-coding
mm_133650.1	chr16	91799212	91799231	+	1	NA	intron (NM_001110275, intron 5 of 28)	intron (NM_001110275, intron 5 of 28)	69850	NM_010587	16443	Mm.40546	NM_010587	ENSMUSG00000022957	Itsn1	AA517634|AA545208|AI316805|AI839402|AI848451|Ehsh1|Ese1|Itsn|Sh3p17	intersectin 1 (SH3 domain protein 1A)	protein-coding
mm_32908.1	chr4	119126214	119126223	+	1	NA	intron (NM_011400, intron 2 of 9)	intron (NM_011400, intron 2 of 9)	17473	NM_011400	20525	Mm.21002	NM_011400	ENSMUSG00000028645	Slc2a1	Glut-1|Glut1	solute carrier family 2 (facilitated glucose transporter), member 1	protein-coding
mm_168448.1	chr1	140722908	140722925	+	1	NA	Intergenic	L1Md_F3|LINE|L1	-66514	NR_040604	75910	Mm.483845	NR_040604	ENSMUSG00000102368	4930590L20Rik	-	RIKEN cDNA 4930590L20 gene	ncRNA
mm_60199.1	chr7	43409297	43409301	+	1	NA	exon (NM_172900, exon 4 of 12)	exon (NM_172900, exon 4 of 12)	1019	NM_172900	243958	Mm.24444	NM_172900	ENSMUSG00000030468	Siglecg	9830164H23|A630096C01Rik|Siglec-G|Siglec10|mSiglec-G	sialic acid binding Ig-like lectin G	protein-coding
mm_26972.1	chr3	24858198	24858209	-	1	NA	Intergenic	Intergenic	-74197	NM_001326288	635702	Mm.448351	NM_001326288	ENSMUSG00000102758	Naaladl2	2810043G22Rik|EG635702|Gm1021	N-acetylated alpha-linked acidic dipeptidase-like 2	protein-coding
mm_72354.1	chr8	79711793	79711827	+	1	NA	promoter-TSS (NM_026904)	promoter-TSS (NM_026904)	-10	NM_026904	68999	Mm.257445	NM_026904	ENSMUSG00000036977	Anapc10	1500026N15Rik|A830003M23Rik|APC10	anaphase promoting complex subunit 10	protein-coding
mm_149095.1	chr19	8929842	8929866	+	1	NA	promoter-TSS (NM_009073)	promoter-TSS (NM_009073)	160	NM_144872	225898	Mm.31008	NM_144872	ENSMUSG00000071647	Eml3	BC022146	echinoderm microtubule associated protein like 3	protein-coding
mm_115893.1	chr13	22009758	22009771	-	1	NA	promoter-TSS (NM_019429)	promoter-TSS (NM_019429)	-23	NM_019429	54373	Mm.32043	NM_019429	ENSMUSG00000006179	Prss16	AI448615|TSSP	protease, serine 16 (thymus)	protein-coding
mm_76036.1	chr8	77387400	77387417	-	1	NA	intron (NM_030113, intron 11 of 22)	B3A|SINE|B2	-129648	NR_028125	70345	Mm.411813	NR_028125	ENSMUSG00000097882	0610038B21Rik	-	RIKEN cDNA 0610038B21 gene	ncRNA
mm_16124.1	chr2	170155125	170155129	+	1	NA	Intergenic	Intergenic	-12452	NM_001159683	228913	Mm.22858	NM_001033299	ENSMUSG00000052056	Zfp217	4933431C08Rik|AW987152|Gm562|ZABC1|Znf217	zinc finger protein 217	protein-coding
mm_833.1	chr1	51478515	51478522	+	1	NA	promoter-TSS (NM_001310549)	promoter-TSS (NM_001310549)	-119	NM_001310549	109019	Mm.196290	NM_028696	ENSMUSG00000026107	Nabp1	4930434H03Rik|4930442A21Rik|4930488J04Rik|4933440J18Rik|5830411E10Rik|AI852561|Nbp1|Obfc2a|Ssb2	nucleic acid binding protein 1	protein-coding
mm_98198.1	chr11	87795308	87795318	+	1	NA	exon (NM_010824, exon 4 of 14)	exon (NM_010824, exon 4 of 14)	1529	NM_010824	17523	Mm.4668	NM_010824	ENSMUSG00000009350	Mpo	mKIAA4033	myeloperoxidase	protein-coding
mm_18172.1	chr2	45110074	45110104	-	1	NA	5' UTR (NM_015753, exon 2 of 10)	5' UTR (NM_015753, exon 2 of 10)	188	NM_001289521	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_72737.1	chr8	85084699	85084767	+	1	NA	exon (NM_010764, exon 3 of 24)	exon (NM_010764, exon 3 of 24)	1464	NM_010764	17159	Mm.4219	NM_010764	ENSMUSG00000005142	Man2b1	AW107687|LAMAN	mannosidase 2, alpha B1	protein-coding
mm_31719.1	chr4	62663621	62663664	+	1	NA	intron (NM_134257, intron 10 of 15)	intron (NM_134257, intron 10 of 15)	-10332	NM_001310706	50780	Mm.286753	NM_019492	ENSMUSG00000059810	Rgs3	4930506N09Rik|C2PA-RGS3|C2pa|PDZ-RGS3|RGS3S	regulator of G-protein signaling 3	protein-coding
mm_32207.1	chr4	101507932	101507941	+	1	NA	promoter-TSS (NM_001164585)	promoter-TSS (NM_001164585)	-40	NM_001164585	72685	Mm.76494	NM_198412	ENSMUSG00000028528	Dnajc6	2810027M23Rik|mKIAA0473	DnaJ heat shock protein family (Hsp40) member C6	protein-coding
mm_28981.1	chr3	101250617	101250619	-	1	NA	Intergenic	Intergenic	37321	NM_013486	12481	Mm.22842	NM_013486	ENSMUSG00000027863	Cd2	LFA-2|Ly-37|Ly37	CD2 antigen	protein-coding
mm_23244.1	chr3	51223839	51223855	+	1	NA	promoter-TSS (NM_009834)	promoter-TSS (NM_009834)	-600	NM_009834	12457	Mm.86541	NM_009834	ENSMUSG00000023087	Noct	AU043840|Ccr4|Ccrn4l	nocturnin	protein-coding
mm_94940.1	chr11	29710814	29710829	+	1	NA	intron (NM_194054, intron 3 of 8)	ID|SINE|ID	-7742	NM_024226	68585	Mm.192580	NM_024226	ENSMUSG00000020458	Rtn4	1110020G17Rik|AA407876|AA409940|AA960376|ASY|C130026I10Rik|NOGO|NSP-CL|NgA|Nogo-A|Nogo-B|Nogo-C|mKIAA0886|mKIAA4153	reticulon 4	protein-coding
mm_19324.1	chr2	90572088	90572110	-	1	NA	intron (NM_008982, intron 1 of 23)	L1ME4b|LINE|L1	8548	NM_008982	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_124701.1	chr15	6522790	6522867	+	1	NA	Intergenic	Intergenic	-57019	NM_001278269	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_85567.1	chr9	107231817	107231894	-	1	NA	promoter-TSS (NM_153413)	promoter-TSS (NM_153413)	54	NM_153413	208869	Mm.150259	NM_153413	ENSMUSG00000039716	Dock3	MOCA|PBP|mKIAA0299	dedicator of cyto-kinesis 3	protein-coding
mm_83332.1	chr9	44234156	44234164	-	1	NA	promoter-TSS (NM_007619)	promoter-TSS (NM_007619)	-114	NM_007619	12402	Mm.266871	NM_007619	ENSMUSG00000034342	Cbl	4732447J05Rik|Cbl-2|c-Cbl|cbl	Casitas B-lineage lymphoma	protein-coding
mm_9510.1	chr1	173741008	173741027	-	1	NA	intron (NM_001204910, intron 1 of 7)	intron (NM_001204910, intron 1 of 7)	792	NM_001204910	226691	Mm.440876	NM_001204910	ENSMUSG00000073490	Ifi207	AI607873|Pyhin-A	interferon activated gene 207	protein-coding
mm_92640.1	chr10	80348406	80348418	-	1	NA	promoter-TSS (NM_001285435)	promoter-TSS (NM_001285435)	36	NM_001285435	66548	Mm.71891	NM_025629	ENSMUSG00000043822	Adamtsl5	2010109H09Rik|Thsd6	ADAMTS-like 5	protein-coding
mm_61549.1	chr7	79364750	79364762	+	1	NA	Intergenic	Intergenic	22271	NM_020599	19771	Mm.41653	NM_020599	ENSMUSG00000039194	Rlbp1	3110056M11Rik|CRALBP	retinaldehyde binding protein 1	protein-coding
mm_90064.1	chr10	116301456	116301475	+	1	NA	promoter-TSS (NM_029928)	promoter-TSS (NM_029928)	91	NM_029928	19263	Mm.37213	NM_029928	ENSMUSG00000020154	Ptprb	3230402H02Rik|C130094E24|Ptpz|Rptpb|VE-PTP|Veptp	protein tyrosine phosphatase, receptor type, B	protein-coding
mm_68204.1	chr7	104395169	104395177	-	1	NA	Intergenic	MYSERV6-int|LTR|ERVK	-36527	NM_175648	244183	Mm.347647	NM_175648	ENSMUSG00000052749	Trim30b	A530023O14Rik|Trim30-1	tripartite motif-containing 30B	protein-coding
mm_42088.1	chr5	110231118	110231133	+	1	NA	5' UTR (NM_001253814, exon 1 of 13)	5' UTR (NM_001253814, exon 1 of 13)	121	NM_027922	71782	Mm.288442	NM_027922	ENSMUSG00000029501	Ankle2	1110001J12Rik|AI661024|D5Ertd585e	ankyrin repeat and LEM domain containing 2	protein-coding
mm_149186.1	chr19	9899948	9899977	+	1	NA	promoter-TSS (NM_016692)	promoter-TSS (NM_016692)	-429	NM_016692	16319	Mm.29755	NM_016692	ENSMUSG00000024660	Incenp	2700067E22Rik|AU019509|C130081E20|C77457	inner centromere protein	protein-coding
mm_3887.1	chr1	161142707	161142744	+	1	NA	promoter-TSS (NM_028664)	promoter-TSS (NM_028664)	13	NM_028664	73844	Mm.38830	NM_028664	ENSMUSG00000044835	Ankrd45	4933409K03Rik	ankyrin repeat domain 45	protein-coding
mm_77084.1	chr8	110522171	110522188	-	1	NA	intron (NM_172916, intron 42 of 86)	L2a|LINE|L2	-19823	NR_105058	100861869	Mm.84499	NR_105058		Gm21283	-	predicted gene, 21283	ncRNA
mm_94528.1	chr11	9117953	9117990	+	1	NA	promoter-TSS (NM_009477)	promoter-TSS (NM_009477)	-37	NM_001159401	22271	Mm.4610	NM_009477	ENSMUSG00000020407	Upp1	AI325217|UPase|UdRPase|Up|Upp	uridine phosphorylase 1	protein-coding
mm_30712.1	chr4	12140264	12140272	+	1	NA	5' UTR (NM_028226, exon 1 of 3)	5' UTR (NM_028226, exon 1 of 3)	151	NM_028226	72397	Mm.430709	NM_028226	ENSMUSG00000046667	Rbm12b1	3000004N20Rik|Rbm12b|Rbm12ba	RNA binding motif protein 12 B1	protein-coding
mm_33105.1	chr4	124707888	124707916	+	1	NA	exon (NM_010213, exon 6 of 6)	exon (NM_010213, exon 6 of 6)	-6959	NM_029157	75062	Mm.25779	NM_029157	ENSMUSG00000028902	Sf3a3	4930512K19Rik|60kDa	splicing factor 3a, subunit 3	protein-coding
mm_76198.1	chr8	82660857	82660876	-	1	NA	Intergenic	Intergenic	113260	NM_145600	30932	Mm.269248	NM_145600	ENSMUSG00000031711	Zfp330	BC008086|Noa36|Znf330	zinc finger protein 330	protein-coding
mm_66983.1	chr7	63938863	63938933	-	1	NA	promoter-TSS (NM_021366)	promoter-TSS (NM_021366)	17	NM_021366	50794	Mm.240473	NM_021366	ENSMUSG00000052040	Klf13	0610043C13Rik|9430029L20Rik|Bteb3|FKLF-2|FKLF2|NSLP1|RFLAT-1|RFLAT1	Kruppel-like factor 13	protein-coding
mm_164061.1	chr14	114946060	114946063	+	1	NA	promoter-TSS (NR_126551)	promoter-TSS (NR_126551)	-113	NR_126548	74982		NR_126548		1700100I10Rik	1700085D13Rik|4930481K08Rik	RIKEN cDNA 1700100I10 gene	ncRNA
mm_52865.1	chr6	122308924	122308934	+	1	NA	promoter-TSS (NM_010749)	promoter-TSS (NM_010749)	-81	NM_010749	17113	Mm.249225	NM_010749	ENSMUSG00000007458	M6pr	CD-MPR|Mpr46	mannose-6-phosphate receptor, cation dependent	protein-coding
mm_171269.1	chr3	88771463	88771474	+	1	NA	intron (NM_018804, intron 1 of 3)	intron (NM_018804, intron 1 of 3)	1131	NM_018804	229521	Mm.379376	NM_018804	ENSMUSG00000068923	Syt11	1500004A13Rik|3632445O20Rik|5430404N14Rik|6530420C11Rik|AI851970	synaptotagmin XI	protein-coding
mm_99554.1	chr11	103638979	103638985	+	1	NA	promoter-TSS (NM_027083)	promoter-TSS (NM_027083)	46	NR_131143	78629	Mm.398236	NR_131109		1700072I22Rik	-	RIKEN cDNA 1700072I22 gene	ncRNA
mm_144866.1	chr18	36726298	36726334	+	1	NA	exon (NM_009841, exon 2 of 2)	exon (NM_009841, exon 2 of 2)	499	NM_009841	12475	Mm.3460	NM_009841	ENSMUSG00000051439	Cd14	-	CD14 antigen	protein-coding
mm_6201.1	chr1	65186457	65186504	-	1	NA	promoter-TSS (NM_001310624)	promoter-TSS (NM_001310624)	-1	NM_001111320	15926	Mm.9925	NM_010497	ENSMUSG00000025950	Idh1	AI314845|AI788952|E030024J03Rik|Id-1|Idh-1|Idpc	isocitrate dehydrogenase 1 (NADP+), soluble	protein-coding
mm_120480.1	chr14	65975697	65975703	+	1	NA	exon (NM_013492, exon 5 of 9)	exon (NM_013492, exon 5 of 9)	7217	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_125062.1	chr15	25940847	25940934	+	1	NA	promoter-TSS (NM_001277316)	promoter-TSS (NM_001277316)	64	NM_025459	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_172439.1	chr7	29965580	29965581	-	1	NA	Intergenic	CpG	-13687	NM_178384	72723	Mm.371648	NM_178384	ENSMUSG00000059975	Zfp74	2810054M15Rik|KRAB8|Zfp66|Znf569|mszf21|mszf77	zinc finger protein 74	protein-coding
mm_52676.1	chr6	117916993	117917006	+	1	NA	promoter-TSS (NM_001166427)	promoter-TSS (NM_001166427)	-295	NM_001166427	98758	Mm.422979	NM_133834	ENSMUSG00000042079	Hnrnpf	4833420I20Rik|AA407306|Hnrpf	heterogeneous nuclear ribonucleoprotein F	protein-coding
mm_42218.1	chr5	113138673	113138683	+	1	NA	promoter-TSS (NM_001347397)	promoter-TSS (NM_001347397)	-93	NM_001347397	243219	Mm.160131	NM_172884	ENSMUSG00000051339	2900026A02Rik	8430408O14Rik|A530094D01|AW539426|Gm449|Kiaa1671|mKIAA1671	RIKEN cDNA 2900026A02 gene	protein-coding
mm_67418.1	chr7	80324100	80324112	-	1	NA	5' UTR (NM_173445, exon 1 of 9)	5' UTR (NM_173445, exon 1 of 9)	348	NM_173445	269955	Mm.474502	NM_173445	ENSMUSG00000038930	Rccd1	5830436H09|E430018M08Rik	RCC1 domain containing 1	protein-coding
mm_154825.1	chrX	17251546	17251558	+	1	NA	intron (NM_028916, intron 2 of 14)	intron (NM_028916, intron 2 of 14)	67816	NM_028916	74405	Mm.248531	NM_028916	ENSMUSG00000025038	Efhc2	4933407D04Rik|mRib72-2	EF-hand domain (C-terminal) containing 2	protein-coding
mm_14854.1	chr2	148681135	148681150	+	1	NA	promoter-TSS (NM_028986)	promoter-TSS (NM_028986)	22	NM_028986	74533	Mm.136913	NM_028986	ENSMUSG00000027439	Gzf1	8430437G08Rik|Zfp336|mGZF1	GDNF-inducible zinc finger protein 1	protein-coding
mm_2419.1	chr1	94077024	94077027	+	1	NA	Intergenic	Intergenic	-24472	NM_008798	18566	Mm.5024	NM_008798	ENSMUSG00000026285	Pdcd1	Ly101|PD-1|Pdc1	programmed cell death 1	protein-coding
mm_27656.1	chr3	64233578	64233580	-	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	53838	NM_001104614	637004	Mm.469887	NM_001104614	ENSMUSG00000091572	Vmn2r3	EG637004	vomeronasal 2, receptor 3	protein-coding
mm_80705.1	chr9	92250040	92250060	+	1	NA	promoter-TSS (NM_011636)	promoter-TSS (NM_011636)	-144	NM_011636	22038	Mm.421956	NM_011636	ENSMUSG00000032369	Plscr1	MmTRA1a|MmTRA1b|Nor1|Tra1|Tra1a|Tra1b|Tras1|Tras2	phospholipid scramblase 1	protein-coding
mm_79647.1	chr9	59566507	59566508	+	1	NA	Intergenic	PB1D9|SINE|Alu	-11830	NM_175235	76183	Mm.265415	NM_175235	ENSMUSG00000032297	Celf6	6330569O16Rik|Brunol6	CUGBP, Elav-like family member 6	protein-coding
mm_49886.1	chr6	38674654	38674655	+	1	NA	intron (NM_001101507, intron 2 of 4)	intron (NM_001101507, intron 2 of 4)	11585	NM_001101507	665180	Mm.349066	NM_001101507	ENSMUSG00000079598	Clec2l	AI414054|AW122724|Gm1064	C-type lectin domain family 2, member L	protein-coding
mm_87476.1	chr10	51492727	51492741	+	1	NA	intron (NM_001291894, intron 4 of 8)	MTD|LTR|ERVL-MaLR	1836	NM_013532	14728	Mm.34408	NM_013532	ENSMUSG00000062593	Lilrb4a	CD85K|Gp49b|HM18|ILT3|LIR-5|Lilrb4|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4A	protein-coding
mm_80981.1	chr9	103217360	103217388	+	1	NA	exon (NM_133977, exon 12 of 17)	exon (NM_133977, exon 12 of 17)	12912	NM_133977	22041	Mm.37214	NM_133977	ENSMUSG00000032554	Trf	AI266983|Cd176|HP|Tf|Tfn|hpx	transferrin	protein-coding
mm_88829.1	chr10	80804721	80804740	+	1	NA	promoter-TSS (NM_007445)	promoter-TSS (NM_007445)	-518	NM_007445	11705	Mm.376094	NM_007445	ENSMUSG00000035262	Amh	MIS	anti-Mullerian hormone	protein-coding
mm_69192.1	chr7	127274082	127274089	-	1	NA	promoter-TSS (NM_009266)	promoter-TSS (NM_009266)	-26	NM_009266	20768	Mm.20294	NM_009266	ENSMUSG00000049091	Sephs2	Sps2|Ysg3	selenophosphate synthetase 2	protein-coding
mm_90652.1	chr10	128748502	128748538	+	1	NA	promoter-TSS (NM_001170869)	promoter-TSS (NM_001170869)	65	NM_001253704	78428	Mm.27358	NM_030100	ENSMUSG00000064030	Pym1	A030010B05Rik|Pym|Wibg	PYM homolog 1, exon junction complex associated factor	protein-coding
mm_152999.1	chr19	30100903	30100920	-	1	NA	exon (NM_138595, exon 23 of 25)	exon (NM_138595, exon 23 of 25)	70398	NM_144873	109113	Mm.313364	NM_144873	ENSMUSG00000024817	Uhrf2	2310065A22Rik|AI426270|AW214556|D130071B19Rik|Nirf	ubiquitin-like, containing PHD and RING finger domains 2	protein-coding
mm_74170.1	chr8	123420866	123420879	+	1	NA	exon (NM_023279, exon 4 of 4)	exon (NM_023279, exon 4 of 4)	9308	NM_023279	22152	Mm.40068	NM_023279	ENSMUSG00000062380	Tubb3	3200002H15Rik|M(beta)3|M(beta)6	tubulin, beta 3 class III	protein-coding
mm_20089.1	chr2	120850390	120850417	-	1	NA	promoter-TSS (NM_001024856)	promoter-TSS (NM_001024856)	15	NM_001024857	140810	Mm.275698	NM_080788	ENSMUSG00000090100	Ttbk2	2610507N02Rik|AI326283|B930008N24Rik|TTK|Ttbk|Ttbk1|mKIAA0847	tau tubulin kinase 2	protein-coding
mm_148177.1	chr18	78142138	78142154	-	1	NA	promoter-TSS (NM_001171011)	promoter-TSS (NM_001171011)	-27	NM_001171011	108052	Mm.33832	NM_028122	ENSMUSG00000059336	Slc14a1	2610507K20Rik|3021401A05Rik|UT-B|Utb1	solute carrier family 14 (urea transporter), member 1	protein-coding
mm_91167.1	chr10	20692002	20692018	-	1	NA	intron (NM_013875, intron 1 of 12)	intron (NM_013875, intron 1 of 12)	33068	NM_013875	29863	Mm.425617	NM_013875	ENSMUSG00000019990	Pde7b	-	phosphodiesterase 7B	protein-coding
mm_113032.1	chr13	23531084	23531088	+	1	NA	promoter-TSS (NM_153173)	promoter-TSS (NM_153173)	42	NM_153173	69386	Mm.158272	NM_153173	ENSMUSG00000060981	Hist1h4h	1700024H08Rik	histone cluster 1, H4h	protein-coding
mm_70709.1	chr8	15059059	15059081	+	1	NA	intron (NM_008664, intron 1 of 36)	intron (NM_008664, intron 1 of 36)	1417	NM_008664	17930	Mm.272115	NM_008664	ENSMUSG00000031461	Myom2	AW146149	myomesin 2	protein-coding
mm_146056.1	chr18	69649577	69649579	+	1	NA	intron (NM_013685, intron 11 of 19)	intron (NM_013685, intron 11 of 19)	-275981	NM_201362	381175	Mm.266831	NM_201362	ENSMUSG00000038903	Ccdc68	BC046343	coiled-coil domain containing 68	protein-coding
mm_77394.1	chr8	120293609	120293622	-	1	NA	Intergenic	Intergenic	-65385	NR_110496	434353	Mm.411793	NR_110496	ENSMUSG00000097960	A330074K22Rik	-	RIKEN cDNA A330074K22 gene	ncRNA
mm_120359.1	chr14	64104317	64104328	+	1	NA	promoter-TSS (NM_028525)	promoter-TSS (NM_028525)	-1	NM_028525	73382	Mm.481055	NM_028525	ENSMUSG00000021966	Prss52	1700049K14Rik|Tesp3	protease, serine 52	protein-coding
mm_57146.1	chr6	122657775	122657786	-	1	NA	Intergenic	Intergenic	31356	NM_139218	73708	Mm.27982	NM_139218	ENSMUSG00000046323	Dppa3	2410075G02Rik|PCG7|PGC7|Stella	developmental pluripotency-associated 3	protein-coding
mm_158109.1	chrX	102071326	102071341	-	1	NA	promoter-TSS (NM_001278534)	promoter-TSS (NM_001278534)	-26	NM_001278534	331474	Mm.23297	NM_183318	ENSMUSG00000049191	Rgag4	6430402L03Rik|Mar5|Mart5|mKIAA2001	retrotransposon gag domain containing 4	protein-coding
mm_84228.1	chr9	61965153	61965166	-	1	NA	intron (NM_028748, intron 5 of 7)	intron (NM_028748, intron 5 of 7)	-18360	NM_024245	71819	Mm.259374	NM_024245	ENSMUSG00000032254	Kif23	3110001D19Rik|C87313|CHO1|Knsl5|MKLP-1|MKLP1	kinesin family member 23	protein-coding
mm_61796.1	chr7	83970262	83970276	+	1	NA	intron (NM_030728, intron 13 of 28)	intron (NM_030728, intron 13 of 28)	78269	NM_023403	67943	Mm.117365	NM_023403	ENSMUSG00000038503	Mesdc2	2210015O11Rik|AW537813|mKIAA0081|mesd|msd	mesoderm development candidate 2	protein-coding
mm_110080.1	chr12	24651056	24651097	-	1	NA	promoter-TSS (NM_178357)	promoter-TSS (NM_178357)	-295	NM_178357	194655	Mm.9616	NM_178357	ENSMUSG00000020653	Klf11	9830142A17|D12Ertd427e|Tieg2|Tieg2b|Tieg3	Kruppel-like factor 11	protein-coding
mm_88573.1	chr10	79681785	79681813	+	1	NA	promoter-TSS (NM_177613)	promoter-TSS (NM_177613)	-396	NM_177613	216150	Mm.21981	NM_177613	ENSMUSG00000020307	Cdc34	AI327276|UBE2R1	cell division cycle 34	protein-coding
mm_8319.1	chr1	144775420	144775438	-	1	NA	promoter-TSS (NM_022881)	promoter-TSS (NM_022881)	-8	NM_022881	64214	Mm.253927	NM_022881	ENSMUSG00000026357	Rgs18	-	regulator of G-protein signaling 18	protein-coding
mm_24693.1	chr3	95015761	95015785	+	1	NA	promoter-TSS (NM_030074)	promoter-TSS (NM_030074)	-535	NM_030074	78266	Mm.389478	NM_030074	ENSMUSG00000019338	Zfp687	4931408L03Rik|Znf687|mKIAA1441	zinc finger protein 687	protein-coding
mm_69232.1	chr7	127708586	127708602	-	1	NA	TTS (NR_030428)	TTS (NR_030428)	107	NR_030428	791073		NR_030428	ENSMUSG00000076454	Mir762	Mirn762|mir-762|mmu-mir-762	microRNA 762	ncRNA
mm_8961.1	chr1	165091899	165091930	-	1	NA	promoter-TSS (NR_040480)	promoter-TSS (NR_040480)	16	NR_040480	75857	Mm.109021	NR_040480	ENSMUSG00000102408	4930568G15Rik	-	RIKEN cDNA 4930568G15 gene	ncRNA
mm_70269.1	chr8	3587785	3587802	+	1	NA	5' UTR (NM_027171, exon 1 of 17)	5' UTR (NM_027171, exon 1 of 17)	343	NM_001347111	69697	Mm.390010	NM_027171	ENSMUSG00000044433	Camsap3	2310057J16Rik|Kiaa1543|Nezha	calmodulin regulated spectrin-associated protein family, member 3	protein-coding
mm_55796.1	chr6	82752736	82752739	-	1	NA	intron (NM_013820, intron 2 of 17)	intron (NM_013820, intron 2 of 17)	21717	NM_013820	15277	Mm.255848	NM_013820	ENSMUSG00000000628	Hk2	AI642394|HKII	hexokinase 2	protein-coding
mm_8199.1	chr1	138121508	138121519	-	1	NA	intron (NM_001111316, intron 3 of 31)	intron (NM_001111316, intron 3 of 31)	53613	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_168247.1	chr10	81997059	81997061	+	1	NA	Intergenic	Intergenic	-51063	NM_001319203	408062	Mm.391409	NM_001024626	ENSMUSG00000061371	Zfp873	-	zinc finger protein 873	protein-coding
mm_117598.1	chr13	89742685	89742695	-	1	NA	promoter-TSS (NM_001134474)	promoter-TSS (NM_001134474)	-178	NM_001134475	13003	Mm.158700	NM_019389	ENSMUSG00000021614	Vcan	5430420N07Rik|9430051N09|Cspg2|DPEAAE|NG2|PG-M|PG-M(V0)|PG-M(V1)|hdf	versican	protein-coding
mm_68339.1	chr7	106506041	106506048	-	1	NA	Intergenic	Intergenic	-64971	NR_003967	209380	Mm.461779	NM_001001318		Gm4759	EG209380	GTPase, very large interferon inducible 1 pseudogene	pseudo
mm_20064.1	chr2	120355489	120355491	-	1	NA	3' UTR (NM_173734, exon 20 of 20)	3' UTR (NM_173734, exon 20 of 20)	-2357	NR_027618	269338	Mm.246131	NM_147153	ENSMUSG00000027291	Vps39	A230065P22Rik|AW743070|Vam6|Vam6P|mVam6	VPS39 HOPS complex subunit	protein-coding
mm_84486.1	chr9	66845691	66845704	-	1	NA	3' UTR (NM_173413, exon 8 of 8)	3' UTR (NM_173413, exon 8 of 8)	-10991	NM_026674	68318	Mm.284229	NM_026674	ENSMUSG00000053040	Aph1c	0610008A10Rik|APH-1b|Aph1b	aph1 homolog C, gamma secretase subunit	protein-coding
mm_41846.1	chr5	104436369	104436387	+	1	NA	exon (NM_001204201, exon 2 of 7)	exon (NM_001204201, exon 2 of 7)	186	NM_001204233	20750	Mm.288474	NM_009263	ENSMUSG00000029304	Spp1	2AR|Apl-1|BNSP|BSPI|Bsp|ETA-1|Eta|OP|Opn|Opnl|Ric|Spp-1	secreted phosphoprotein 1	protein-coding
mm_33198.1	chr4	126286776	126286778	+	1	NA	promoter-TSS (NM_199473)	promoter-TSS (NM_199473)	-17	NM_199473	329941	Mm.296327	NM_199473	ENSMUSG00000056174	Col8a2	AI429819	collagen, type VIII, alpha 2	protein-coding
mm_116249.1	chr13	33947692	33947695	-	1	NA	intron (NR_040707, intron 1 of 4)	RMER12|LTR|ERVK	-11610	NM_001164117	20719	Mm.252210	NM_009254	ENSMUSG00000060147	Serpinb6a	4930482L21Rik|D330015H01Rik|PI-6|Serpinb6|Spi3|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 6a	protein-coding
mm_64600.1	chr7	3212141	3212154	-	1	NA	Intergenic	Intergenic	-6479	NR_029640	100049710		NR_029640	ENSMUSG00000077815	Mir290a	Mir290|Mirn290|mir-290a|mmu-miR-290|mmu-mir-290a	microRNA 290a	ncRNA
mm_91145.1	chr10	19907646	19907689	-	1	NA	promoter-TSS (NM_008822)	promoter-TSS (NM_008822)	7	NM_008822	18634	Mm.338363	NM_008822	ENSMUSG00000020003	Pex7	MmPEX7	peroxisomal biogenesis factor 7	protein-coding
mm_38441.1	chr4	139833566	139833577	-	1	NA	promoter-TSS (NM_011039)	promoter-TSS (NM_011039)	-603	NM_011039	18509	Mm.218760	NM_011039	ENSMUSG00000028736	Pax7	Pax-7	paired box 7	protein-coding
mm_129654.1	chr15	81018078	81018117	-	1	NA	exon (NM_153049, exon 9 of 13)	exon (NM_153049, exon 9 of 13)	40332	NM_134091	105835	Mm.274943	NM_134091	ENSMUSG00000042303	Sgsm3	1810012I01Rik|AI428557|BB175482|Cip85|R75178|RUSC3|Rutbc3	small G protein signaling modulator 3	protein-coding
mm_172201.1	chr6	51470705	51470706	+	1	NA	promoter-TSS (NM_007624)	promoter-TSS (NM_007624)	89	NM_007624	12417	Mm.280968	NM_007624	ENSMUSG00000029836	Cbx3	HP1g|M32	chromobox 3	protein-coding
mm_38573.1	chr4	141815790	141815791	-	1	NA	3' UTR (NM_015733, exon 9 of 9)	3' UTR (NM_015733, exon 9 of 9)	10215	NM_007919	13706	Mm.45316	NM_007919	ENSMUSG00000058579	Cela2a	Ela-2|Ela2|Ela2a	chymotrypsin-like elastase family, member 2A	protein-coding
mm_18148.1	chr2	45067097	45067109	-	1	NA	intron (NM_001289521, intron 1 of 8)	intron (NM_001289521, intron 1 of 8)	43174	NM_001289521	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_167146.1	chr7	128461193	128461195	-	1	NA	5' UTR (NM_009383, exon 1 of 12)	5' UTR (NM_009383, exon 1 of 12)	319	NM_009383	21843	Mm.242072	NM_009383	ENSMUSG00000030846	Tial1	5330433G13Rik|AL033329|TIAR|mTIAR	Tia1 cytotoxic granule-associated RNA binding protein-like 1	protein-coding
mm_39736.1	chr5	29223949	29223949	+	1	NA	intron (NM_001289757, intron 8 of 9)	intron (NM_001289757, intron 8 of 9)	27956	NR_110371	56874	Mm.87352	NM_021470	ENSMUSG00000029130	Rnf32	1700009J01Rik|2700025B22Rik|4930542N22Rik|Lmbr2	ring finger protein 32	protein-coding
mm_15101.1	chr2	153346172	153346195	+	1	NA	promoter-TSS (NM_001039939)	promoter-TSS (NM_001039939)	44	NM_001039939	228790	Mm.330677	NM_001039939	ENSMUSG00000042548	Asxl1	mKIAA0978	additional sex combs like 1	protein-coding
mm_6798.1	chr1	84150835	84150845	-	1	NA	intron (NM_001003948, intron 2 of 2)	intron (NM_001003948, intron 2 of 2)	68121	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_11153.1	chr2	28534344	28534354	+	1	NA	intron (NM_001145836, intron 1 of 17)	intron (NM_001145836, intron 1 of 17)	885	NM_001145836	19730	Mm.5236	NM_009058	ENSMUSG00000026821	Ralgds	Gnds|Rgds|mKIAA1308	ral guanine nucleotide dissociation stimulator	protein-coding
mm_36197.1	chr4	62337118	62337143	-	1	NA	intron (NM_001045528, intron 7 of 27)	intron (NM_001045528, intron 7 of 27)	23418	NM_001045528	338355	Mm.357792	NM_001045528	ENSMUSG00000066151	Fkbp15	BB131447|C430014M02Rik|FKBO133|FKBP-133|FKBP-15|FKBP133|mKIAA0674	FK506 binding protein 15	protein-coding
mm_122456.1	chr14	45318728	45318770	-	1	NA	promoter-TSS (NM_015774)	promoter-TSS (NM_015774)	-177	NM_015774	50527	Mm.387108	NM_015774	ENSMUSG00000021831	Ero1l	ERO1-L|Ero1a	ERO1-like (S. cerevisiae)	protein-coding
mm_37384.1	chr4	120985248	120985260	-	1	NA	exon (NM_133716, exon 2 of 10)	exon (NM_133716, exon 2 of 10)	-11932	NR_105982	102465614		NR_105982	ENSMUSG00000106436	Mir7015	mmu-mir-7015	microRNA 7015	ncRNA
mm_171451.1	chr4	145432492	145432492	+	1	NA	Intergenic	Intergenic	-31718	NR_002888	545700	Mm.389595	NR_002888	ENSMUSG00000052912	Smarca5-ps	9230115A19Rik|OTTMUSG00000011029	SWI/SNF related, matrix associated, actin depenent ragulator of chromatin, subfamily a, member 5, pseudogene	pseudo
mm_77204.1	chr8	113848852	113848870	-	1	NA	promoter-TSS (NM_172466)	promoter-TSS (NM_172466)	-22	NM_172466	208936	Mm.167471	NM_172466	ENSMUSG00000053399	Adamts18	9630038L21|ADAMTS21|E130314N14Rik	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 18	protein-coding
mm_140155.1	chr17	80127872	80127874	+	1	NA	exon (NM_176963, exon 1 of 7)	exon (NM_176963, exon 1 of 7)	402	NM_176963	319625	Mm.29098	NM_176963	ENSMUSG00000035473	Galm	A530057M15Rik|AU015645|AU020959	galactose mutarotase	protein-coding
mm_110715.1	chr12	69475568	69475588	-	1	NA	promoter-TSS (NR_038060)	promoter-TSS (NR_038060)	-28	NR_038060	76062	Mm.380755	NR_038060		5830428M24Rik	100040862|Gm3007	RIKEN cDNA 5830428M24 gene	ncRNA
mm_92512.1	chr10	78439205	78439226	-	1	NA	3' UTR (NM_172134, exon 11 of 11)	3' UTR (NM_172134, exon 11 of 11)	4416	NR_105837	102465221		NR_105837	ENSMUSG00000098932	Mir6410	Gm27916|mmu-mir-6410	microRNA 6410	ncRNA
mm_114255.1	chr13	56703450	56703460	+	1	NA	promoter-TSS (NM_001164042)	promoter-TSS (NM_001164042)	-213	NM_001164042	17129	Mm.272920	NM_008541	ENSMUSG00000021540	Smad5	1110051M15Rik|AI451355|Dwf-C|Madh5|MusMLP	SMAD family member 5	protein-coding
mm_118462.1	chr14	11122755	11122756	+	1	NA	intron (NM_001308285, intron 2 of 9)	RSINE1|SINE|B4	39280	NM_010210	14198	Mm.397619	NM_010210	ENSMUSG00000060579	Fhit	AW045638|Fra14A2	fragile histidine triad gene	protein-coding
mm_147849.1	chr18	63692218	63692228	-	1	NA	5' UTR (NM_016792, exon 1 of 8)	5' UTR (NM_016792, exon 1 of 8)	136	NM_016792	53382	Mm.19169	NM_016792	ENSMUSG00000024583	Txnl1	32kDa|TRP32|Txnl	thioredoxin-like 1	protein-coding
mm_4838.1	chr1	186705895	186705919	+	1	NA	promoter-TSS (NM_009367)	promoter-TSS (NM_009367)	82	NM_009367	21808	Mm.18213	NM_009367	ENSMUSG00000039239	Tgfb2	BB105277|Tgf-beta2|Tgfb-2	transforming growth factor, beta 2	protein-coding
mm_101565.1	chr11	34103731	34103743	-	1	NA	Intergenic	Intergenic	56536	NM_010696	16822	Mm.265350	NM_010696	ENSMUSG00000002699	Lcp2	AI323664|BB161688|SLP-76|SLP76|m1Khoe|twm	lymphocyte cytosolic protein 2	protein-coding
mm_487.1	chr1	36767071	36767095	+	1	NA	5' UTR (NM_001289765, exon 1 of 13)	5' UTR (NM_001289765, exon 1 of 13)	149	NM_001289765	22637	Mm.8038	NM_009539	ENSMUSG00000026117	Zap70	Srk|ZAP-70|mrtle|mur	zeta-chain (TCR) associated protein kinase	protein-coding
mm_111014.1	chr12	78983472	78983472	-	1	NA	promoter-TSS (NM_001170401)	promoter-TSS (NM_001170401)	6	NM_001170401	268567	Mm.341747	NM_178745	ENSMUSG00000046157	Tmem229b	6330442E10Rik|9830138K24|AU019070	transmembrane protein 229B	protein-coding
mm_164453.1	chr16	54166297	54166298	-	1	NA	Intergenic	Intergenic	1116940	NM_178720	239852	Mm.245045	NM_178720	ENSMUSG00000064310	Zpld1	9430016A21Rik	zona pellucida like domain containing 1	protein-coding
mm_10135.1	chr2	4057909	4057919	+	1	NA	intron (NM_001347086, intron 2 of 24)	intron (NM_001347086, intron 2 of 24)	40231	NM_001347086	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding
mm_85866.1	chr9	110878899	110878902	-	1	NA	intron (NM_146260, intron 1 of 5)	B4|SINE|B4	1183	NM_146260	20776	Mm.390229	NM_146260	ENSMUSG00000049555	Tmie	5131400L21Rik|Mm.87012|sr	transmembrane inner ear	protein-coding
mm_165445.1	chr2	155357860	155357862	+	1	NA	promoter-TSS (NM_001004721)	promoter-TSS (NM_001004721)	-437	NM_001004721	228812	Mm.5434	NM_001004721	ENSMUSG00000038383	Pigu	5430426F17Rik|BC028278|Cdc91l1	phosphatidylinositol glycan anchor biosynthesis, class U	protein-coding
mm_4895.1	chr1	189728265	189728326	+	1	NA	promoter-TSS (NM_008976)	promoter-TSS (NM_008976)	27	NM_008976	19250	Mm.4498	NM_008976	ENSMUSG00000026604	Ptpn14	C130080N23Rik|OTTMUSG00000022087|PTP36	protein tyrosine phosphatase, non-receptor type 14	protein-coding
mm_87125.1	chr10	33412028	33412041	+	1	NA	intron (NM_029726, intron 23 of 37)	intron (NM_029726, intron 23 of 37)	-155677	NR_040657	442820	Mm.490725	NR_040657		D830005E20Rik	-	RIKEN cDNA D830005E20 gene	ncRNA
mm_62935.1	chr7	118731868	118731871	+	1	NA	intron (NM_182995, intron 13 of 15)	intron (NM_182995, intron 13 of 15)	-8402	NM_027815	71517	Mm.213298	NM_027815	ENSMUSG00000030982	9030624J02Rik	2610029J22Rik	RIKEN cDNA 9030624J02 gene	protein-coding
mm_170460.1	chr1	89133541	89133550	+	1	NA	intron (NM_133816, intron 2 of 5)	intron (NM_133816, intron 2 of 5)	63083	NM_133816	98402	Mm.170983	NM_133816	ENSMUSG00000036206	Sh3bp4	AI594717|AW227605|BOG25	SH3-domain binding protein 4	protein-coding
mm_132776.1	chr16	44775140	44775170	+	1	NA	intron (NM_021325, intron 1 of 6)	T-rich|Low_complexity|Low_complexity	9419	NM_021325	57781	Mm.416152	NM_021325	ENSMUSG00000022667	Cd200r1	CD200R|Mox2r|OX2R	CD200 receptor 1	protein-coding
mm_152201.1	chr19	7597970	7597987	-	1	NA	3' UTR (NM_019516, exon 9 of 9)	3' UTR (NM_019516, exon 9 of 9)	9198	NM_019516	56072	Mm.298242	NM_019516	ENSMUSG00000024972	Lgals12	AW987437|Grip1	lectin, galactose binding, soluble 12	protein-coding
mm_98392.1	chr11	94214807	94214817	+	1	NA	3' UTR (NM_009427, exon 2 of 2)	3' UTR (NM_009427, exon 2 of 2)	3358	NM_009427	22057	Mm.259673	NM_009427	ENSMUSG00000037573	Tob1	Tob|Trob	transducer of ErbB-2.1	protein-coding
mm_7149.1	chr1	91403283	91403286	-	1	NA	Intergenic	Intergenic	2745	NR_026924	67086	Mm.396158	NR_026924	ENSMUSG00000100253	1700020N18Rik	-	RIKEN cDNA 1700020N18 gene	ncRNA
mm_119868.1	chr14	54603586	54603618	+	1	NA	intron (NM_028890, intron 1 of 6)	intron (NM_028890, intron 1 of 6)	2306	NM_028890	74359	Mm.79815	NM_028890	ENSMUSG00000022179	4931414P19Rik	-	RIKEN cDNA 4931414P19 gene	protein-coding
mm_132538.1	chr16	37868820	37868845	+	1	NA	exon (NM_177093, exon 1 of 4)	exon (NM_177093, exon 1 of 4)	432	NM_177093	320184	Mm.390882	NM_177093	ENSMUSG00000034158	Lrrc58	1810012N18Rik|C330018J07Rik	leucine rich repeat containing 58	protein-coding
mm_91378.1	chr10	30600663	30600701	-	1	NA	promoter-TSS (NM_028604)	promoter-TSS (NM_028604)	67	NM_028604	73681	Mm.294503	NM_028604	ENSMUSG00000019792	Trmt11	2410075D05Rik|3110045I18Rik|AW213713	tRNA methyltransferase 11	protein-coding
mm_114400.1	chr13	63563398	63563402	+	1	NA	intron (NM_001328514, intron 2 of 23)	CpG	2335	NM_008957	19206	Mm.228798	NM_008957	ENSMUSG00000021466	Ptch1	A230106A15Rik|Ptc|Ptc1|Ptch|mes	patched 1	protein-coding
mm_131719.1	chr16	21527459	21527471	+	1	NA	intron (NM_001285893, intron 29 of 46)	intron (NM_001285893, intron 29 of 46)	104347	NM_001285894	209018	Mm.235683	NM_145948	ENSMUSG00000033653	Vps8	AI315068|AU040738|mKIAA0804	VPS8 CORVET complex subunit	protein-coding
mm_135114.1	chr16	35832843	35832846	-	1	NA	TTS (NM_001039530)	TTS (NM_001039530)	38538	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_16001.1	chr2	167349721	167349735	+	1	NA	promoter-TSS (NM_019835)	promoter-TSS (NM_019835)	-550	NM_019835	56336	Mm.200886	NM_019835	ENSMUSG00000017929	B4galt5	9430078I07Rik|AW049941|AW539721	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 5	protein-coding
mm_170094.1	chr17	37995836	37995847	+	1	NA	Intergenic	Intergenic	-42819	NM_001011829	258094	Mm.377348	NM_001011829	ENSMUSG00000109376	Olfr761	MOR218-12|MOR218-5P|MOR218-6P|Olfr1552-ps1	olfactory receptor 761	protein-coding
mm_77480.1	chr8	122475710	122475729	-	1	NA	promoter-TSS (NM_153775)	promoter-TSS (NM_153775)	345	NM_001033142	68718	Mm.34356	NM_001033142	ENSMUSG00000014470	Rnf166	1110031E24Rik|AW555115|Zfp313l	ring finger protein 166	protein-coding
mm_110496.1	chr12	54203274	54203297	-	1	NA	exon (NM_028133, exon 1 of 5)	exon (NM_028133, exon 1 of 5)	589	NM_028133	112407	Mm.133037	NM_028133	ENSMUSG00000035105	Egln3	2610021G09Rik|AI505553|AI648162|Hif-p4h-3|Phd3|SM-20	egl-9 family hypoxia-inducible factor 3	protein-coding
mm_120326.1	chr14	63143645	63143660	+	1	NA	3' UTR (NM_007798, exon 10 of 10)	3' UTR (NM_007798, exon 10 of 10)	21190	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_39364.1	chr5	9118839	9118843	+	1	NA	TTS (NM_001110327)	TTS (NM_001110327)	18104	NM_001081029	652925	Mm.439954	NM_001081029	ENSMUSG00000079659	Tmem243	4930420K17Rik|E030031F02Rik	transmembrane protein 243, mitochondrial	protein-coding
mm_163705.1	chr13	107744254	107744254	+	1	NA	intron (NM_145456, intron 6 of 14)	intron (NM_145456, intron 6 of 14)	16833	NR_029759	723929		NR_029759	ENSMUSG00000065425	Mir325	Mirn325|mmu-mir-325	microRNA 325	ncRNA
mm_132456.1	chr16	36072069	36072090	+	1	NA	promoter-TSS (NM_027342)	promoter-TSS (NM_027342)	419	NM_001159421	381045	Mm.310434	NM_198645	ENSMUSG00000075229	Ccdc58	A930007B11Rik|AI413631	coiled-coil domain containing 58	protein-coding
mm_69768.1	chr7	141010760	141010772	-	1	NA	promoter-TSS (NM_025378)	promoter-TSS (NM_025378)	-22	NM_025378	66141	Mm.141021	NM_025378	ENSMUSG00000025492	Ifitm3	1110004C05Rik|Cd225|Cdw217|DSPA2b|Fgls|IP15|mil-1	interferon induced transmembrane protein 3	protein-coding
mm_2736.1	chr1	128244757	128244761	+	1	NA	intron (NM_026390, intron 1 of 12)	CpG	578	NM_026390	67812	Mm.293321	NM_026390	ENSMUSG00000026353	Ubxn4	1300013G12Rik|Ubxd2|mKIAA0242	UBX domain protein 4	protein-coding
mm_108956.1	chr12	102368347	102368372	+	1	NA	intron (NM_177620, intron 5 of 9)	intron (NM_177620, intron 5 of 9)	71454	NM_011175	19141	Mm.17185	NM_011175	ENSMUSG00000021190	Lgmn	AEP|AI746452|AU022324|Prsc1	legumain	protein-coding
mm_84660.1	chr9	71724544	71724556	-	1	NA	exon (NM_026599, exon 2 of 19)	exon (NM_026599, exon 2 of 19)	47052	NM_026599	68178	Mm.99961	NM_026599	ENSMUSG00000032232	Cgnl1	4933421H10Rik|9930020M10Rik|AI503810|Jacop	cingulin-like 1	protein-coding
mm_162187.1	chrX	105499823	105499823	+	1	NA	promoter-TSS (NM_173436)	promoter-TSS (NM_173436)	51	NM_173436	245566	Mm.250428	NM_173436	ENSMUSG00000090132	Cypt2	Ckt1|Cypt2-ps	cysteine-rich perinuclear theca 2	protein-coding
mm_60326.1	chr7	44236138	44236142	+	1	NA	promoter-TSS (NR_029436)	promoter-TSS (NR_029436)	-18	NR_029436	70004	Mm.158317	NR_029436	ENSMUSG00000038782	1700028J19Rik	-	RIKEN cDNA 1700028J19 gene	ncRNA
mm_71688.1	chr8	61239392	61239394	+	1	NA	intron (NM_021506, intron 2 of 11)	intron (NM_021506, intron 2 of 11)	15222	NM_021506	59009	Mm.27949	NM_021506	ENSMUSG00000031642	Sh3rf1	2200003J05Rik|Posh|R75531|Sh3md2	SH3 domain containing ring finger 1	protein-coding
mm_81415.1	chr9	109054904	109054990	+	1	NA	promoter-TSS (NM_026381)	promoter-TSS (NM_026381)	81	NM_026381	66940	Mm.196533	NM_025858	ENSMUSG00000025647	Shisa5	2310008D10Rik|6430628I05Rik|Scotin|mShisa5	shisa family member 5	protein-coding
mm_13819.1	chr2	119237483	119237508	+	1	NA	intron (NM_016907, intron 1 of 10)	CpG	135	NM_016907	20732	Mm.104955	NM_016907	ENSMUSG00000027315	Spint1	HAI-1	serine protease inhibitor, Kunitz type 1	protein-coding
mm_131596.1	chr16	18877214	18877241	+	1	NA	promoter-TSS (NM_010922)	promoter-TSS (NM_010922)	477	NM_010435	15260	Mm.15694	NM_010435	ENSMUSG00000022702	Hira	AA138857|D16Ertd95e|Gm15797|N28177|OTTMUSG00000026264|Tuple1	histone cell cycle regulator	protein-coding
mm_50046.1	chr6	41151676	41151685	+	1	NA	Intergenic	Intergenic	-116171	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_114922.1	chr13	95325196	95325229	+	1	NA	5' UTR (NM_028106, exon 1 of 2)	5' UTR (NM_028106, exon 1 of 2)	387	NM_028106	72114	Mm.3774	NM_028106	ENSMUSG00000041995	Zbed3	0610037K01Rik|2610005H11Rik|AU018975|AU024588	zinc finger, BED type containing 3	protein-coding
mm_98791.1	chr11	96931509	96931516	+	1	NA	5' UTR (NM_146026, exon 2 of 3)	5' UTR (NM_146026, exon 2 of 3)	2188	NM_146026	217138	Mm.342551	NM_146026	ENSMUSG00000047040	Prr15l	Atad4|BC022765|E230006A12Rik	proline rich 15-like	protein-coding
mm_83621.1	chr9	48835909	48835922	-	1	NA	promoter-TSS (NM_001033324)	promoter-TSS (NM_001033324)	30	NM_001033324	235320	Mm.457803	NM_001033324	ENSMUSG00000066687	Zbtb16	AI467657|PLZF|Zfp145|lu	zinc finger and BTB domain containing 16	protein-coding
mm_90079.1	chr10	116509028	116509034	+	1	NA	TTS (NM_001037848)	TTS (NM_001037848)	-35508	NM_021452	58802	Mm.440652	NM_021452	ENSMUSG00000054934	Kcnmb4	1700058G18Rik|2900045G12Rik	potassium large conductance calcium-activated channel, subfamily M, beta member 4	protein-coding
mm_173318.1	chrY	90736727	90736730	+	1	NA	Intergenic	(CAGAGA)n|Simple_repeat|Simple_repeat	18322	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_70762.1	chr8	21722025	21722025	+	1	NA	Intergenic	Intergenic	-12469	NM_001024225	503491	Mm.443396	NM_001024225	ENSMUSG00000064213	Defa24	Defcr24	defensin, alpha, 24	protein-coding
mm_10478.1	chr2	14604201	14604203	+	1	NA	promoter-TSS (NM_023116)	promoter-TSS (NM_023116)	-104	NM_023116	12296	Mm.313930	NM_023116	ENSMUSG00000057914	Cacnb2	AW060387|CAB2|Cavbeta2|Cchb2	calcium channel, voltage-dependent, beta 2 subunit	protein-coding
mm_76404.1	chr8	84846614	84846622	-	1	NA	intron (NM_007591, intron 1 of 8)	CpG	313	NM_007591	12317	Mm.1971	NM_007591	ENSMUSG00000003814	Calr	CRT|Calregulin	calreticulin	protein-coding
mm_163938.1	chr14	51145254	51145256	-	1	NA	3' UTR (NM_011271, exon 2 of 2)	3' UTR (NM_011271, exon 2 of 2)	1512	NM_011271	19752	Mm.235538	NM_011271	ENSMUSG00000035896	Rnase1	AI574248|Rib-1|Rib1	ribonuclease, RNase A family, 1 (pancreatic)	protein-coding
mm_22809.1	chr3	27182974	27182986	+	1	NA	promoter-TSS (NM_178772)	promoter-TSS (NM_178772)	-24	NM_178772	320024	Mm.24576	NM_178772	ENSMUSG00000027698	Nceh1	Aadacl1|B230106I24Rik|CPO-BP|Nceh	neutral cholesterol ester hydrolase 1	protein-coding
mm_152575.1	chr19	11600410	11600437	-	1	NA	intron (NM_026835, intron 3 of 6)	intron (NM_026835, intron 3 of 6)	4381	NM_026835	68774	Mm.290390	NM_026835	ENSMUSG00000024679	Ms4a6d	1110058E16Rik|AI447446|Ms4a11	membrane-spanning 4-domains, subfamily A, member 6D	protein-coding
mm_82822.1	chr9	31106131	31106145	-	1	NA	exon (NM_011176, exon 7 of 19)	exon (NM_011176, exon 7 of 19)	25661	NM_011176	19143	Mm.243926	NM_011176	ENSMUSG00000031995	St14	Epithin|MT-SP1|Prss14|Tmprss14|mCAP3|matriptase	suppression of tumorigenicity 14 (colon carcinoma)	protein-coding
mm_24610.1	chr3	93447374	93447381	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	5047	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_133804.1	chr16	95455138	95455145	+	1	NA	intron (NM_001302152, intron 3 of 10)	intron (NM_001302152, intron 3 of 10)	4207	NM_001302154	13876	Mm.164531	NM_133659	ENSMUSG00000040732	Erg	D030036I24Rik	avian erythroblastosis virus E-26 (v-ets) oncogene related	protein-coding
mm_4035.1	chr1	165774301	165774315	+	1	NA	3' UTR (NM_011804, exon 4 of 4)	3' UTR (NM_011804, exon 4 of 4)	10528	NM_011804	433375	Mm.294885	NM_011804	ENSMUSG00000040713	Creg1	AA755314|Creg	cellular repressor of E1A-stimulated genes 1	protein-coding
mm_76986.1	chr8	107048199	107048209	-	1	NA	TTS (NM_139229)	TTS (NM_139229)	410	NM_026513	68023	Mm.482335	NM_026513	ENSMUSG00000078931	Pdf	2610019N19Rik	peptide deformylase (mitochondrial)	protein-coding
mm_123048.1	chr14	55591541	55591574	-	1	NA	promoter-TSS (NM_011190)	promoter-TSS (NM_011190)	-233	NM_194346	268749	Mm.23748	NM_194346	ENSMUSG00000047098	Rnf31	AL033293|BC031509|Flj10111|HOIP|Paul|mFLJ00217	ring finger protein 31	protein-coding
mm_68785.1	chr7	123294520	123294539	-	1	NA	exon (NM_144529, exon 17 of 20)	exon (NM_144529, exon 17 of 20)	75386	NM_001122643	70497	Mm.403318	NM_144529	ENSMUSG00000030766	Arhgap17	5730403H17Rik|Nadrin|Nadrin2|Rich1|Wbp15	Rho GTPase activating protein 17	protein-coding
mm_170919.1	chr2	37261839	37261840	-	1	NA	Intergenic	MMERVK9C_I-int|LTR|ERVK	-5112	NM_001081010	545417	Mm.379955	NM_001081010		Olfr367-ps	EG545417|MOR128-1|ORL1283|OTTMUSG00000012147|Olfr367	olfactory receptor 367, pseudogene	protein-coding
mm_169695.1	chr15	74998097	74998099	+	1	NA	promoter-TSS (NM_001271446)	promoter-TSS (NM_001271446)	-67	NM_010738	110454	Mm.425949	NM_010738	ENSMUSG00000075602	Ly6a	Ly-6A.2|Ly-6A/E|Ly-6E.1|Sca-1|Sca1|TAP	lymphocyte antigen 6 complex, locus A	protein-coding
mm_30007.1	chr3	135650317	135650358	-	1	NA	intron (NM_008689, intron 6 of 24)	PB1D10|SINE|Alu	41210	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_89823.1	chr10	105573275	105573277	+	1	NA	intron (NM_177368, intron 1 of 11)	intron (NM_177368, intron 1 of 11)	1203	NM_177368	278279	Mm.25225	NM_177368	ENSMUSG00000036019	Tmtc2	8430438D04Rik|D330034A10Rik	transmembrane and tetratricopeptide repeat containing 2	protein-coding
mm_42545.1	chr5	116006832	116006835	+	1	NA	TTS (NM_007708)	TTS (NM_007708)	17595	NM_031869	19079	Mm.458152	NM_031869	ENSMUSG00000029513	Prkab1	1300015D22Rik|AU021155|E430008F22	protein kinase, AMP-activated, beta 1 non-catalytic subunit	protein-coding
mm_21575.1	chr2	164237149	164237162	-	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	1186	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_10935.1	chr2	25468122	25468140	+	1	NA	exon (NM_008963, exon 4 of 7)	exon (NM_008963, exon 4 of 7)	1618	NM_008963	19215	Mm.1008	NM_008963	ENSMUSG00000015090	Ptgds	21kDa|L-PGDS|PGD2|PGDS|PGDS2|Ptgs3	prostaglandin D2 synthase (brain)	protein-coding
mm_161832.1	chr17	83846602	83846602	-	1	NA	intron (NM_025325, intron 1 of 9)	intron (NM_025325, intron 1 of 9)	188	NM_025325	107766	Mm.30100	NM_025325	ENSMUSG00000000673	Haao	0610007K21Rik|0610012J07Rik|3-HAO|3-HAOxase|3HAO	3-hydroxyanthranilate 3,4-dioxygenase	protein-coding
mm_121311.1	chr14	106120907	106120912	+	1	NA	intron (NR_073203, intron 1 of 1)	intron (NR_073203, intron 1 of 1)	14711	NR_073203	212085	Mm.78128	NM_198601	ENSMUSG00000022113	Trim52	4921513B05Rik	tripartite motif-containing 52	protein-coding
mm_162119.1	chrX	57089371	57089371	+	1	NA	5' UTR (NM_133251, exon 2 of 8)	5' UTR (NM_133251, exon 2 of 8)	1265	NM_133251	170828	Mm.190616	NM_133251	ENSMUSG00000031131	Vgll1	Tondu	vestigial like family member 1	protein-coding
mm_141680.1	chr17	33930734	33930757	-	1	NA	intron (NM_009059, intron 2 of 17)	intron (NM_009059, intron 2 of 17)	851	NM_009059	19732	Mm.43777	NM_009059	ENSMUSG00000041354	Rgl2	KE1.5|Rab2l|Rgt2|Rlf	ral guanine nucleotide dissociation stimulator-like 2	protein-coding
mm_156468.1	chrX	143518577	143518599	+	1	NA	promoter-TSS (NM_001195048)	promoter-TSS (NM_001195048)	-3	NM_001195048	18481	Mm.40035	NM_008778	ENSMUSG00000031284	Pak3	PAK-3|Pak65alpha|Pak65beta|Stk4	p21 protein (Cdc42/Rac)-activated kinase 3	protein-coding
mm_9663.1	chr1	177796638	177796648	-	1	NA	promoter-TSS (NM_007422)	promoter-TSS (NM_007422)	-134	NM_007422	11566	Mm.338021	NM_007422	ENSMUSG00000015961	Adss	AI314886|AS|Adss2	adenylosuccinate synthetase, non muscle	protein-coding
mm_102281.1	chr11	55395903	55395940	-	1	NA	exon (NM_009242, exon 9 of 10)	exon (NM_009242, exon 9 of 10)	24159	NM_009242	20692	Mm.291442	NM_009242	ENSMUSG00000018593	Sparc	BM-40|ON	secreted acidic cysteine rich glycoprotein	protein-coding
mm_3655.1	chr1	153115909	153115931	+	1	NA	3' UTR (NM_175460, exon 11 of 11)	3' UTR (NM_175460, exon 11 of 11)	70527	NM_008485	16782	Mm.329272	NM_008485	ENSMUSG00000026479	Lamc2	AA589349	laminin, gamma 2	protein-coding
mm_109414.1	chr12	110484051	110484077	+	1	NA	intron (NM_001135001, intron 3 of 13)	intron (NM_001135001, intron 3 of 13)	-1675	NM_001081457	26931	Mm.240396	NM_012023	ENSMUSG00000017843	Ppp2r5c	2610043M05Rik|2700063L20Rik|AI060890|AW545884|C85228|D12Bwg0916e|mKIAA0044	protein phosphatase 2, regulatory subunit B', gamma	protein-coding
mm_58419.1	chr7	3293001	3293016	+	1	NA	promoter-TSS (NM_001093766)	promoter-TSS (NM_001093766)	-20	NM_001093766	50918	Mm.29874	NM_016969	ENSMUSG00000068566	Myadm	D7Wsu62e	myeloid-associated differentiation marker	protein-coding
mm_7073.1	chr1	88205675	88205746	-	1	NA	promoter-TSS (NM_008299)	promoter-TSS (NM_008299)	38	NM_008299	15504	Mm.439983	NM_008299	ENSMUSG00000081984	Dnajb3	Hsj3|MSJ-1|Msj1	DnaJ heat shock protein family (Hsp40) member B3	protein-coding
mm_90331.1	chr10	127079007	127079024	+	1	NA	5' UTR (NM_001301014, exon 1 of 18)	5' UTR (NM_001301014, exon 1 of 18)	108	NM_001033263	216439	Mm.336761	NM_001033263	ENSMUSG00000025422	Agap2	AGAP-2|Centg1|PIKE|cnt-g1|mKIAA0167	ArfGAP with GTPase domain, ankyrin repeat and PH domain 2	protein-coding
mm_168383.1	chr11	23306949	23306952	+	1	NA	promoter-TSS (NM_001190401)	promoter-TSS (NM_001190401)	55	NM_001190401	17847	Mm.119155	NM_001190401	ENSMUSG00000056342	Usp34	A530081C03Rik|Murr2	ubiquitin specific peptidase 34	protein-coding
mm_112111.1	chr12	112795931	112795961	-	1	NA	Intergenic	Intergenic	-13029	NM_145450	217887	Mm.186678	NM_145450	ENSMUSG00000037594	BC022687	AW050009|C130001I08Rik|Flj20080	cDNA sequence BC022687	protein-coding
mm_166786.1	chr6	144902099	144902106	+	1	NA	Intergenic	Intergenic	146710	NM_001024468	12035	Mm.4606	NM_007532	ENSMUSG00000030268	Bcat1	BCATc|Eca39	branched chain aminotransferase 1, cytosolic	protein-coding
mm_109924.1	chr12	8640671	8640682	-	1	NA	Intergenic	(A)n|Simple_repeat|Simple_repeat	-33458	NM_001160221	80913	Mm.341243	NM_030723	ENSMUSG00000020594	Pum2	5730503J23Rik|Pumm2	pumilio RNA-binding family member 2	protein-coding
mm_25864.1	chr3	129878572	129878704	+	1	NA	promoter-TSS (NR_104611)	promoter-TSS (NR_104611)	32	NR_104611	66350	Mm.151951	NM_023196	ENSMUSG00000027999	Pla2g12a	2310004B05Rik|GXII|GXII-1|GXII-1-PLA2|Pla2g12|Rossy|mGXII-1	phospholipase A2, group XIIA	protein-coding
mm_170601.1	chr19	5802597	5802597	-	1	NA	promoter-TSS (NR_002847)	promoter-TSS (NR_002847)	75	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_151939.1	chr19	5800835	5800845	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	1832	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_25770.1	chr3	126447721	126447721	+	1	NA	Intergenic	Intergenic	83869	NM_173451	271970	Mm.317021	NM_173451	ENSMUSG00000046561	Arsj	9330196J05Rik|D830047F08	arylsulfatase J	protein-coding
mm_24926.1	chr3	96557951	96557968	+	1	NA	promoter-TSS (NM_023719)	promoter-TSS (NM_023719)	2	NM_023719	56338	Mm.410189	NM_023719	ENSMUSG00000038393	Txnip	1200008J08Rik|AA682105|Hyplip1|THIF|Tbp-2|VDUP1	thioredoxin interacting protein	protein-coding
mm_149307.1	chr19	10739118	10739126	+	1	NA	promoter-TSS (NM_007650)	promoter-TSS (NM_007650)	-148	NM_007650	12507	Mm.779	NM_007650	ENSMUSG00000024669	Cd5	Ly-1|Ly-12|Ly-A|Lyt-1	CD5 antigen	protein-coding
mm_98570.1	chr11	95414079	95414130	+	1	NA	promoter-TSS (NM_025287)	promoter-TSS (NM_025287)	21	NM_025287	20747	Mm.285454	NM_025287	ENSMUSG00000057522	Spop	AI315626|Pcif1|TEF2	speckle-type POZ protein	protein-coding
mm_150556.1	chr19	39330258	39330262	+	1	NA	exon (NM_007815, exon 9 of 9)	exon (NM_007815, exon 9 of 9)	43175	NM_007815	13095	Mm.20764	NM_007815	ENSMUSG00000003053	Cyp2c29	AHOH|AHOHase|AI159681|AI196010|Ah-2|Ahh-1|Cyp2c|P450-2C	cytochrome P450, family 2, subfamily c, polypeptide 29	protein-coding
mm_146290.1	chr18	78494890	78494891	+	1	NA	intron (NM_030683, intron 2 of 11)	intron (NM_030683, intron 2 of 11)	102060	NM_207651	27411	Mm.44158	NM_030683	ENSMUSG00000024552	Slc14a2	UT-A1|UT-A3	solute carrier family 14 (urea transporter), member 2	protein-coding
mm_59695.1	chr7	28540895	28540906	+	1	NA	promoter-TSS (NM_026716)	promoter-TSS (NM_026716)	15	NM_026716	68416	Mm.25210	NM_026716	ENSMUSG00000084174	Sycn	0910001K16Rik|1810038B08Rik|SYL	syncollin	protein-coding
mm_138135.1	chr17	34196846	34196858	+	1	NA	3' UTR (NM_001161730, exon 12 of 12)	3' UTR (NM_001161730, exon 12 of 12)	-1343	NM_010724	16913	Mm.180191	NM_010724	ENSMUSG00000024338	Psmb8	Lmp-7|Lmp7	proteasome (prosome, macropain) subunit, beta type 8 (large multifunctional peptidase 7)	protein-coding
mm_10622.1	chr2	19452450	19452456	+	1	NA	Intergenic	Intergenic	-5779	NR_131924	102637107	Mm.406835	NR_131924	ENSMUSG00000085388	Ptf1aos	Gm13336|OTTMUSG00000011493	pancreas specific transcription factor 1a, opposite strand	ncRNA
mm_38729.1	chr4	145238660	145238675	-	1	NA	intron (NM_011610, intron 1 of 9)	B3|SINE|B2	8203	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_151221.1	chr19	53677396	53677425	+	1	NA	exon (NM_001170847, exon 1 of 14)	exon (NM_001170847, exon 1 of 14)	104	NM_001170847	73713	Mm.313695	NM_001170847	ENSMUSG00000043639	Rbm20	1110018J23Rik|2010003H22Rik|AI646761	RNA binding motif protein 20	protein-coding
mm_140681.1	chr17	12992604	12992648	-	1	NA	promoter-TSS (NM_175394)	promoter-TSS (NM_175394)	-87	NM_175394	60532	Mm.275521	NM_175394	ENSMUSG00000060475	Wtap	2810408K05Rik|9430038B09Rik	Wilms tumour 1-associating protein	protein-coding
mm_88907.1	chr10	81179395	81179418	+	1	NA	TTS (NR_028549)	TTS (NR_028549)	445	NR_028549	100217454		NR_028549	ENSMUSG00000064441	Snord37	MBII-376	small nucleolar RNA, C/D box 37	snoRNA
mm_63299.1	chr7	126823182	126823214	+	1	NA	promoter-TSS (NM_029978)	promoter-TSS (NM_029978)	-105	NM_029978	68952	Mm.440393	NM_026884	ENSMUSG00000058966	Fam57b	1500016O10Rik|A330104J06Rik|AI413816|AW060769	family with sequence similarity 57, member B	protein-coding
mm_45719.1	chr5	84417479	84417489	-	1	NA	promoter-TSS (NM_007937)	promoter-TSS (NM_007937)	-102	NM_007937	13839	Mm.137991	NM_007937	ENSMUSG00000029245	Epha5	AI854630|AW125296|Cek7|Ehk1|Els1|Hek7|Rek7|bsk	Eph receptor A5	protein-coding
mm_141001.1	chr17	24895461	24895485	-	1	NA	promoter-TSS (NM_001163102)	promoter-TSS (NM_001163102)	353	NM_023260	79044	Mm.328851	NM_023260	ENSMUSG00000038880	Mrps34	0610007F04Rik|5330430D13Rik|AV001970|Tce2	mitochondrial ribosomal protein S34	protein-coding
mm_69224.1	chr7	127604455	127604465	-	1	NA	promoter-TSS (NR_027915)	promoter-TSS (NR_027915)	-15	NR_027915	68232	Mm.347960	NM_026628	ENSMUSG00000099579	1700120K04Rik	-	RIKEN cDNA 1700120K04 gene	ncRNA
mm_93652.1	chr10	117380039	117380051	-	1	NA	Intergenic	MT2B1|LTR|ERVL	-3072	NM_001310609	432508	Mm.478881	NM_001013391	ENSMUSG00000055531	Cpsf6	4733401N12Rik|AI256641|CFIM|CFIM68|HPBRII-4|HPBRII-7	cleavage and polyadenylation specific factor 6	protein-coding
mm_149488.1	chr19	11813430	11813441	+	1	NA	intron (NM_001025307, intron 1 of 10)	intron (NM_001025307, intron 1 of 10)	5968	NM_001286543	20908	Mm.272264	NM_011502	ENSMUSG00000041488	Stx3	Syn-3	syntaxin 3	protein-coding
mm_17540.1	chr2	29787251	29787254	-	1	NA	intron (NM_145520, intron 1 of 7)	ID_B1|SINE|B4	419	NM_001290496	227682	Mm.245739	NM_145520	ENSMUSG00000039826	Trub2	G430055L02Rik	TruB pseudouridine (psi) synthase family member 2	protein-coding
mm_104619.1	chr11	97282308	97282316	-	1	NA	Intergenic	Intergenic	-1736	NM_008942	19155	Mm.29824	NM_008942	ENSMUSG00000001441	Npepps	AAP-S|MP100|Psa|R74825|goku	aminopeptidase puromycin sensitive	protein-coding
mm_171334.1	chr3	99253408	99253408	+	1	NA	promoter-TSS (NM_009323)	promoter-TSS (NM_009323)	-352	NM_009323	21384	Mm.88761	NM_009323	ENSMUSG00000027868	Tbx15	Tbx14|Tbx8|de	T-box 15	protein-coding
mm_44098.1	chr5	149289020	149289043	+	1	NA	TTS (NM_009663)	TTS (NM_009663)	24027	NM_009663	11690	Mm.19844	NM_009663	ENSMUSG00000060063	Alox5ap	Flap	arachidonate 5-lipoxygenase activating protein	protein-coding
mm_162515.1	chr1	156476196	156476234	-	1	NA	Intergenic	Intergenic	-1887	NM_009230	20652	Mm.28099	NM_009230	ENSMUSG00000026600	Soat1	8430426K15Rik|ACAT-1|AW550831|Acact|ald|hid	sterol O-acyltransferase 1	protein-coding
mm_139846.1	chr17	69383025	69383065	+	1	NA	promoter-TSS (NM_009547)	promoter-TSS (NM_009547)	-933	NM_009547	22666	Mm.29434	NM_009547	ENSMUSG00000049672	Zbtb14	ZF5|Zfp161|b2b1982Clo	zinc finger and BTB domain containing 14	protein-coding
mm_30440.1	chr3	153650127	153650143	-	1	NA	intron (NM_011372, intron 1 of 4)	(TG)n|Simple_repeat|Simple_repeat	74998	NM_011372	20447	Mm.296453	NM_011372	ENSMUSG00000052544	St6galnac3	Siat7c	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 3	protein-coding
mm_82737.1	chr9	25252398	25252415	-	1	NA	promoter-TSS (NM_001205367)	promoter-TSS (NM_001205367)	-33	NM_009859	235072	Mm.270259	NM_009859	ENSMUSG00000001833	Sept7	Cdc10|E430034N22	septin 7	protein-coding
mm_7619.1	chr1	126830734	126830778	-	1	NA	promoter-TSS (NM_176957)	promoter-TSS (NM_176957)	-124	NM_176957	210356	Mm.377234	NM_172484	ENSMUSG00000049690	Nckap5	8430408F21|D130011D22Rik|E030049G20Rik|Erih1|Erih2|Gm1548|Nap5	NCK-associated protein 5	protein-coding
mm_94882.1	chr11	26167714	26167716	+	1	NA	intron (NR_027973, intron 1 of 5)	RLTR13D4|LTR|ERVK	-34525	NR_105791	102466154		NR_105791	ENSMUSG00000099015	Mir6372	Gm27358|mmu-mir-6372	microRNA 6372	ncRNA
mm_83336.1	chr9	44268052	44268111	-	1	NA	5' UTR (NM_001163743, exon 1 of 10)	5' UTR (NM_001163743, exon 1 of 10)	106	NM_001163743	270151	Mm.3957	NM_178420	ENSMUSG00000032109	Nlrx1	BC034204|NOD9	NLR family member X1	protein-coding
mm_88351.1	chr10	75893404	75893429	+	1	NA	promoter-TSS (NM_024440)	promoter-TSS (NM_024440)	18	NM_024440	70377	Mm.275878	NM_024440	ENSMUSG00000009092	Derl3	1810006I20Rik|1810063P04Rik|IZP6|derlin-3	Der1-like domain family, member 3	protein-coding
mm_95864.1	chr11	58009576	58009584	+	1	NA	intron (NM_028451, intron 1 of 18)	CpG	516	NM_028451	73158	Mm.248843	NM_028451	ENSMUSG00000037331	Larp1	1810024J12Rik|3110040D16Rik|Larp|mKIAA0731	La ribonucleoprotein domain family, member 1	protein-coding
mm_115783.1	chr13	19311683	19311715	-	1	NA	Intergenic	Intergenic	84114	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_170359.1	chr1	85270151	85270151	-	1	NA	5' UTR (NM_001037909, exon 1 of 7)	5' UTR (NM_001037909, exon 1 of 7)	415	NM_175219	620078	Mm.386456	NM_175219	ENSMUSG00000052477	C130026I21Rik	4930565N07Rik|OTTMUSG00000029174	RIKEN cDNA C130026I21 gene	protein-coding
mm_51637.1	chr6	85915710	85915770	+	1	NA	promoter-TSS (NM_001170488)	promoter-TSS (NM_001170488)	21	NM_001170488	69786	Mm.218434	NM_176842	ENSMUSG00000054226	Tprkb	0610033G21Rik|1810034M08Rik|Cgi-121|DRWMS1|mDRWMS1	Tp53rk binding protein	protein-coding
mm_88751.1	chr10	80299133	80299162	+	1	NA	intron (NR_038088, intron 1 of 4)	intron (NR_038088, intron 1 of 4)	-2673	NM_011789	23805	Mm.57247	NM_011789	ENSMUSG00000020135	Apc2	AI852447|APCL|R75424	adenomatosis polyposis coli 2	protein-coding
mm_104795.1	chr11	98772121	98772132	-	1	NA	exon (NM_145434, exon 2 of 8)	exon (NM_145434, exon 2 of 8)	3251	NM_145434	217166	Mm.390397	NM_145434	ENSMUSG00000020889	Nr1d1	A530070C09Rik|R75201	nuclear receptor subfamily 1, group D, member 1	protein-coding
mm_50135.1	chr6	41542721	41542777	+	1	NA	Intergenic	Intergenic	20973	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_118793.1	chr14	24216266	24216268	+	1	NA	intron (NM_001163513, intron 1 of 31)	intron (NM_001163513, intron 1 of 31)	29653	NM_001163513	71228	Mm.68971	NM_027726	ENSMUSG00000021782	Dlg5	4933429D20Rik|T25557|mKIAA0583	discs, large homolog 5 (Drosophila)	protein-coding
mm_150060.1	chr19	29384092	29384122	+	1	NA	exon (NM_021893, exon 6 of 7)	exon (NM_021893, exon 6 of 7)	16669	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_141314.1	chr17	28358732	28358748	-	1	NA	intron (NM_021478, intron 10 of 14)	intron (NM_021478, intron 10 of 14)	6403	NM_021478	22157	Mm.42102	NM_021478	ENSMUSG00000037446	Tulp1	Tulp1l	tubby like protein 1	protein-coding
mm_32407.1	chr4	106947235	106947250	+	1	NA	intron (NM_023672, intron 4 of 17)	intron (NM_023672, intron 4 of 17)	35772	NM_023672	72475	Mm.195635	NM_023672	ENSMUSG00000061887	Ssbp3	2610021L12Rik|2610200M23Rik|5730488C10Rik|AI854733|AW551939|LAST|SSDP1	single-stranded DNA binding protein 3	protein-coding
mm_10955.1	chr2	25657945	25657963	+	1	NA	promoter-TSS (NM_007947)	promoter-TSS (NM_007947)	2	NM_001042630	13863	Mm.12867	NM_007947	ENSMUSG00000026937	Lcn5	E-RABP|Erabp|MEP10	lipocalin 5	protein-coding
mm_69863.1	chr7	141437830	141437853	-	1	NA	promoter-TSS (NM_026646)	promoter-TSS (NM_026646)	33	NM_026646	68267	Mm.33729	NM_026646	ENSMUSG00000019082	Slc25a22	1300006L01Rik|AI060884|Gc1	solute carrier family 25 (mitochondrial carrier, glutamate), member 22	protein-coding
mm_67276.1	chr7	78192566	78192577	-	1	NA	exon (NM_008746, exon 17 of 17)	exon (NM_008746, exon 17 of 17)	385267	NM_008746	18213	Mm.33496	NM_008746	ENSMUSG00000059146	Ntrk3	AW125844|Ntrk3_tv3|TrkC	neurotrophic tyrosine kinase, receptor, type 3	protein-coding
mm_20636.1	chr2	132019469	132019476	-	1	NA	intron (NM_175445, intron 1 of 10)	intron (NM_175445, intron 1 of 10)	10516	NM_175445	215653	Mm.204737	NM_175445	ENSMUSG00000027339	Rassf2	3830431H01Rik|9030412M04Rik|AI852669|AW495050	Ras association (RalGDS/AF-6) domain family member 2	protein-coding
mm_12805.1	chr2	80292794	80292803	+	1	NA	5' UTR (NM_177256, exon 1 of 1)	5' UTR (NM_177256, exon 1 of 1)	328	NM_177256	320769	Mm.60992	NM_177256	ENSMUSG00000050114	Prdx6b	1-cysPrx-P1|4930414C22Rik|Aop2-rs1|Prdx5-rs1|Prdx6-ps1|Prdx6-rs1|Prdx6-rs1-ps	peroxiredoxin 6B	protein-coding
mm_25851.1	chr3	129533654	129533657	+	1	NA	intron (NM_130450, intron 2 of 4)	CpG	1269	NM_130450	170439	Mm.314113	NM_130450	ENSMUSG00000041220	Elovl6	C77826|FAE|LCE	ELOVL family member 6, elongation of long chain fatty acids (yeast)	protein-coding
mm_2984.1	chr1	133131370	133131382	+	1	NA	5' UTR (NM_133819, exon 1 of 2)	5' UTR (NM_133819, exon 1 of 2)	210	NM_133819	108954	Mm.293628	NM_133819	ENSMUSG00000046062	Ppp1r15b	1810033K10Rik|AI606441|C530022L24Rik|CReP	protein phosphatase 1, regulatory (inhibitor) subunit 15b	protein-coding
mm_39896.1	chr5	31202467	31202506	+	1	NA	promoter-TSS (NM_001177901)	promoter-TSS (NM_001177901)	-183	NM_175311	101023	Mm.45033	NM_175311	ENSMUSG00000043059	Zfp513	AW990386|D430028M17Rik|Znf513	zinc finger protein 513	protein-coding
mm_134299.1	chr16	15564711	15564716	-	1	NA	intron (NM_001159351, intron 2 of 2)	Lx4B|LINE|L1	29805	NM_001159351	70620	Mm.235407	NM_023585	ENSMUSG00000022674	Ube2v2	1110021H13Rik|4632410D19Rik|5730524P06Rik|6820402M05|AI848315|C81524|MMS2	ubiquitin-conjugating enzyme E2 variant 2	protein-coding
mm_40263.1	chr5	38277446	38277464	+	1	NA	promoter-TSS (NM_172709)	promoter-TSS (NM_172709)	51	NM_172709	21906	Mm.204765	NM_172709	ENSMUSG00000051596	Otop1	A530025J20Rik|Otp1|tlt	otopetrin 1	protein-coding
mm_101349.1	chr11	23665863	23665937	-	1	NA	promoter-TSS (NM_023651)	promoter-TSS (NM_023651)	35	NM_023651	72129	Mm.29536	NM_023651	ENSMUSG00000020283	Pex13	2610008O20Rik	peroxisomal biogenesis factor 13	protein-coding
mm_23616.1	chr3	65659220	65659242	+	1	NA	promoter-TSS (NR_106200)	promoter-TSS (NR_106200)	-57	NR_106200	102465905		NR_106200	ENSMUSG00000098944	Mir8120	Gm27637|mmu-mir-8120	microRNA 8120	ncRNA
mm_109311.1	chr12	109560945	109560955	+	1	NA	non-coding (NR_003633, exon 5 of 5)	non-coding (NR_003633, exon 5 of 5)	-2742	NR_030427	791079		NR_030427	ENSMUSG00000076451	Mir770	Mirn770|mir-770|mmu-mir-770	microRNA 770	ncRNA
mm_70816.1	chr8	23095627	23095638	+	1	NA	intron (NR_102385, intron 11 of 45)	GSAT_MM|Satellite|Satellite	37373	NR_102385	11733	Mm.334444	NM_031158	ENSMUSG00000031543	Ank1	Ank-1|nb|pale	ankyrin 1, erythroid	protein-coding
mm_52067.1	chr6	97625003	97625007	+	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	-7348	NM_145148	232288	Mm.27789	NM_145148	ENSMUSG00000030064	Frmd4b	6030440G05Rik|C87375|GOBLIN|GRSP1|R74720	FERM domain containing 4B	protein-coding
mm_142410.1	chr17	45488665	45488702	-	1	NA	Intergenic	Intergenic	-13745	NM_027649	71020	Mm.44257	NM_027649	ENSMUSG00000023935	Spats1	1700011H05Rik|4933400B06Rik|Daip2|Ddip|Srsp1	spermatogenesis associated, serine-rich 1	protein-coding
mm_7011.1	chr1	86503404	86503416	-	1	NA	Intergenic	Intergenic	-23326	NM_008972	19231	Mm.19187	NM_008972	ENSMUSG00000026238	Ptma	Thym	prothymosin alpha	protein-coding
mm_39207.1	chr4	156050499	156050506	-	1	NA	intron (NM_029264, intron 1 of 14)	intron (NM_029264, intron 1 of 14)	315	NM_029264	330010	Mm.440232	NM_029264	ENSMUSG00000029074	Ttll10	4833412E22Rik|4930595O22Rik|AU022799|BC042775|Ttll5	tubulin tyrosine ligase-like family, member 10	protein-coding
mm_63040.1	chr7	121083415	121083434	+	1	NA	promoter-TSS (NM_139310)	promoter-TSS (NM_139310)	-14	NM_139310	246190	Mm.221073	NM_139310	ENSMUSG00000034990	Otoa	-	otoancorin	protein-coding
mm_36065.1	chr4	57916284	57916306	-	1	NA	promoter-TSS (NM_178727)	promoter-TSS (NM_178727)	-31	NM_178727	242484	Mm.23214	NM_178727	ENSMUSG00000052117	D630039A03Rik	-	RIKEN cDNA D630039A03 gene	protein-coding
mm_44484.1	chr5	23518726	23518757	-	1	NA	intron (NM_009274, intron 10 of 14)	intron (NM_009274, intron 10 of 14)	84312	NM_026984	69188	Mm.205190	NM_026984	ENSMUSG00000029004	Kmt2e	1810033J14Rik|9530077A04Rik|D230038D11Rik|Mll5|NKp44L	lysine (K)-specific methyltransferase 2E	protein-coding
mm_88771.1	chr10	80336063	80336093	+	1	NA	3' UTR (NM_139292, exon 6 of 6)	3' UTR (NM_139292, exon 6 of 6)	5933	NM_139292	70335	Mm.28147	NM_139292	ENSMUSG00000035504	Reep6	0610011M24Rik|Dp1l1	receptor accessory protein 6	protein-coding
mm_110406.1	chr12	45074360	45074388	-	1	NA	5' UTR (NM_144552, exon 1 of 6)	5' UTR (NM_144552, exon 1 of 6)	109	NM_144552	217517	Mm.285400	NM_144552	ENSMUSG00000046314	Stxbp6	BC024598|C85317	syntaxin binding protein 6 (amisyn)	protein-coding
mm_84482.1	chr9	66845319	66845327	-	1	NA	3' UTR (NM_173413, exon 8 of 8)	3' UTR (NM_173413, exon 8 of 8)	-10617	NM_026674	68318	Mm.284229	NM_026674	ENSMUSG00000053040	Aph1c	0610008A10Rik|APH-1b|Aph1b	aph1 homolog C, gamma secretase subunit	protein-coding
mm_41842.1	chr5	104434411	104434422	+	1	NA	promoter-TSS (NM_001204203)	promoter-TSS (NM_001204203)	-695	NM_001204201	20750	Mm.288474	NM_009263	ENSMUSG00000029304	Spp1	2AR|Apl-1|BNSP|BSPI|Bsp|ETA-1|Eta|OP|Opn|Opnl|Ric|Spp-1	secreted phosphoprotein 1	protein-coding
mm_83552.1	chr9	46242529	46242535	-	1	NA	exon (NM_007468, exon 3 of 3)	exon (NM_007468, exon 3 of 3)	1688	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_119742.1	chr14	54122162	54122184	+	1	NA	Intergenic	Intergenic	131756	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_111050.1	chr12	80109534	80109579	-	1	NA	3' UTR (NM_007564, exon 2 of 2)	3' UTR (NM_007564, exon 2 of 2)	3457	NM_007564	12192	Mm.235132	NM_007564	ENSMUSG00000021127	Zfp36l1	AW742437|AW743212|Berg36|Brf1|D530020L18Rik|ERF1|TIS11b|cMG1	zinc finger protein 36, C3H type-like 1	protein-coding
mm_51144.1	chr6	70532943	70532944	+	1	NA	Intergenic	Intergenic	259232	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_171350.1	chr4	109118016	109118027	-	1	NA	promoter-TSS (NM_173350)	promoter-TSS (NM_173350)	15	NM_173350	100273	Mm.366315	NM_133885	ENSMUSG00000028559	Osbpl9	2600011I06Rik|AU015843|Orp-9	oxysterol binding protein-like 9	protein-coding
mm_75737.1	chr8	69716416	69716424	-	1	NA	promoter-TSS (NM_181274)	promoter-TSS (NM_181274)	66	NM_181274	66869	Mm.334581	NM_181274	ENSMUSG00000054648	Zfp869	1200003I07Rik	zinc finger protein 869	protein-coding
mm_46339.1	chr5	101851524	101851537	-	1	NA	intron (NM_172882, intron 59 of 66)	intron (NM_172882, intron 59 of 66)	86400	NM_173370	74596	Mm.46764	NM_173370	ENSMUSG00000029330	Cds1	4833409J18Rik|AI314024|AW125888	CDP-diacylglycerol synthase 1	protein-coding
mm_9303.1	chr1	171639167	171639177	-	1	NA	exon (NM_144539, exon 4 of 8)	exon (NM_144539, exon 4 of 8)	2728	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_157530.1	chrX	51018041	51018064	-	1	NA	promoter-TSS (NM_172413)	promoter-TSS (NM_172413)	-34	NM_172413	72065	Mm.43152	NM_172413	ENSMUSG00000050029	Rap2c	2010200P20Rik|AI194294|AL022976	RAP2C, member of RAS oncogene family	protein-coding
mm_168111.1	chr10	14746495	14746500	-	1	NA	intron (NR_045824, intron 3 of 5)	intron (NR_045824, intron 3 of 5)	-13792	NM_008703	18101	Mm.487342	NM_008703	ENSMUSG00000019865	Nmbr	BB182387	neuromedin B receptor	protein-coding
mm_119316.1	chr14	36970021	36970030	+	1	NA	Intergenic	Intergenic	-1261	NM_027045	72972	Mm.27621	NM_027045	ENSMUSG00000058690	Ccser2	1700012P13Rik|2900054P12Rik|AI035535|AW108503|Fam190b|Gcap14	coiled-coil serine rich 2	protein-coding
mm_132306.1	chr16	33684461	33684472	+	1	NA	promoter-TSS (NM_175256)	promoter-TSS (NM_175256)	0	NM_175256	77446	Mm.245741	NM_172934	ENSMUSG00000075254	Heg1	4632417D23Rik|5530401I02Rik|9530025L16Rik|BC038614|Gm629|OTTMUSG00000027315	heart development protein with EGF-like domains 1	protein-coding
mm_5109.1	chr1	6214437	6214447	-	1	NA	promoter-TSS (NM_009826)	promoter-TSS (NM_009826)	-220	NM_009826	12421	Mm.293811	NM_009826	ENSMUSG00000025907	Rb1cc1	2900055E04Rik|5930404L04Rik|Cc1|FIP200|LaXp180	RB1-inducible coiled-coil 1	protein-coding
mm_161286.1	chr14	26066972	26066972	-	1	NA	promoter-TSS (NM_025311).2	promoter-TSS (NM_025311).2	20	NM_001270499	100039192	Mm.33344	NM_001270498	ENSMUSG00000072680	Tmem254c	ENSMUSG00000072676|Gm10395	transmembrane protein 254c	protein-coding
mm_98759.1	chr11	96547028	96547031	+	1	NA	intron (NM_001033186, intron 4 of 12)	intron (NM_001033186, intron 4 of 12)	82438	NM_001177898	78473	Mm.395840	NM_001033186	ENSMUSG00000057058	Skap1	1700091G21Rik|Scap1|Skap-55	src family associated phosphoprotein 1	protein-coding
mm_94423.1	chr11	5955755	5955821	+	1	NA	promoter-TSS (NM_019661)	promoter-TSS (NM_019661)	30	NM_019661	56418	Mm.294821	NM_019661	ENSMUSG00000002741	Ykt6	0610042I15Rik|1810013M05Rik|AW105923	YKT6 v-SNARE homolog (S. cerevisiae)	protein-coding
mm_146076.1	chr18	70568900	70568942	+	1	NA	exon (NM_010773, exon 1 of 7)	exon (NM_010773, exon 1 of 7)	629	NM_010773	17191	Mm.322	NM_010773	ENSMUSG00000024513	Mbd2	MBD2a	methyl-CpG binding domain protein 2	protein-coding
mm_80743.1	chr9	94770210	94770210	+	1	NA	intron (NM_177909, intron 4 of 15)	intron (NM_177909, intron 4 of 15)	18381	NR_106116	102465763		NR_106116	ENSMUSG00000098251	Mir7656	Gm27614|mmu-mir-7656	microRNA 7656	ncRNA
mm_51429.1	chr6	78466266	78466271	+	1	NA	TTS (NM_011260)	TTS (NM_011260)	2606	NM_011260	19695	Mm.252385	NM_011260	ENSMUSG00000030017	Reg3g	AI449515|REG-3-gamma|reg III-gamma	regenerating islet-derived 3 gamma	protein-coding
mm_117513.1	chr13	80885510	80885532	-	1	NA	intron (NM_001042591, intron 1 of 7)	CpG	2099	NM_001042591	105171	Mm.423137	NM_001042591	ENSMUSG00000074794	Arrdc3	AI450344|mKIAA1376	arrestin domain containing 3	protein-coding
mm_74243.1	chr8	124793062	124793070	+	1	NA	promoter-TSS (NM_198632)	promoter-TSS (NM_198632)	47	NM_198632	330863	Mm.422769	NM_198632	ENSMUSG00000036913	Trim67	D130049O21Rik|TNL	tripartite motif-containing 67	protein-coding
mm_2388.1	chr1	93507881	93507895	+	1	NA	3' UTR (NM_010891, exon 13 of 13)	3' UTR (NM_010891, exon 13 of 13)	-4216	NM_145519	227377	Mm.243091	NM_145519	ENSMUSG00000034066	Farp2	AI465173|BC009153|D030026M03Rik|Fir|mKIAA0793	FERM, RhoGEF and pleckstrin domain protein 2	protein-coding
mm_61956.1	chr7	90208770	90208783	+	1	NA	3' UTR (NM_001252521, exon 20 of 20)	3' UTR (NM_001252521, exon 20 of 20)	56656	NM_029256	75338	Mm.487222	NM_029256	ENSMUSG00000030617	Ccdc83	4930549K11Rik|4930554C01Rik|4932423M01Rik	coiled-coil domain containing 83	protein-coding
mm_114578.1	chr13	75644864	75644867	+	1	NA	promoter-TSS (NR_030451)	promoter-TSS (NR_030451)	-181	NR_030451	751556		NR_030451	ENSMUSG00000076236	Mir682	Mirn682|mir-682|mmu-mir-682	microRNA 682	ncRNA
mm_48637.1	chr5	145191535	145191548	-	1	NA	promoter-TSS (NM_020582)	promoter-TSS (NM_020582)	51	NM_020582	57423	Mm.133551	NM_020582	ENSMUSG00000038690	Atp5j2	1110019H14Rik	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit F2	protein-coding
mm_68611.1	chr7	116402986	116403020	-	1	NA	intron (NM_011083, intron 3 of 32)	Tigger7|DNA|TcMar-Tigger	40455	NM_011083	18704	Mm.3810	NM_011083	ENSMUSG00000030660	Pik3c2a	Cpk-m|PI3KC2	phosphatidylinositol 3-kinase, C2 domain containing, alpha polypeptide	protein-coding
mm_171307.1	chr3	94093596	94093603	-	1	NA	Intergenic	MT2B1|LTR|ERVL	-20955	NM_001163731	100042761	Mm.484910	NM_001163731	ENSMUSG00000095251	Gm10697	ENSMUSG00000074425	predicted gene 10697	protein-coding
mm_12787.1	chr2	79587793	79587799	+	1	NA	Intergenic	Intergenic	-47629	NM_080558	70599	Mm.272881	NM_080558	ENSMUSG00000027007	Ssfa2	5730488C15Rik|CS-1|CS1|KRAP|SPAG13|mKIAA1927	sperm specific antigen 2	protein-coding
mm_121481.1	chr14	121035760	121035802	+	1	NA	5' UTR (NM_134082, exon 1 of 27)	5' UTR (NM_134082, exon 1 of 27)	207	NM_134082	223254	Mm.223980	NM_134082	ENSMUSG00000025555	Farp1	AW228844|BC030329|Cdep	FERM, RhoGEF (Arhgef) and pleckstrin domain protein 1 (chondrocyte-derived)	protein-coding
mm_69045.1	chr7	126809135	126809231	-	1	NA	Intergenic	CpG	-7702	NM_026884	68952	Mm.440393	NM_026884	ENSMUSG00000058966	Fam57b	1500016O10Rik|A330104J06Rik|AI413816|AW060769	family with sequence similarity 57, member B	protein-coding
mm_58488.1	chr7	3645510	3645567	+	1	NA	5' UTR (NM_146176, exon 1 of 18)	5' UTR (NM_146176, exon 1 of 18)	269	NM_146176	232791	Mm.358731	NM_146176	ENSMUSG00000035632	Cnot3	A930039N10Rik	CCR4-NOT transcription complex, subunit 3	protein-coding
mm_24552.1	chr3	93442408	93442414	+	1	NA	promoter-TSS (NM_001163098)	promoter-TSS (NM_001163098)	81	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_109057.1	chr12	104340587	104340638	+	1	NA	exon (NM_011458, exon 2 of 5)	exon (NM_011458, exon 2 of 5)	2126	NM_011458	20714	Mm.291569	NM_011458	ENSMUSG00000058207	Serpina3k	1300001I07Rik|D12Rp54|MMCM2|MMSpi2|RP54|Spi-2|Spi2|contrapsin	serine (or cysteine) peptidase inhibitor, clade A, member 3K	protein-coding
mm_129938.1	chr15	84856044	84856057	-	1	NA	promoter-TSS (NM_001081166)	promoter-TSS (NM_001081166)	79	NM_001081166	271305	Mm.101022	NM_001081166	ENSMUSG00000016624	Phf21b	A730032D07Rik	PHD finger protein 21B	protein-coding
mm_130449.1	chr15	98534232	98534305	-	1	NA	promoter-TSS (NM_001289439)	promoter-TSS (NM_001289439)	1	NM_001289438	69612	Mm.229107	NM_133714	ENSMUSG00000022992	Kansl2	2310037I24Rik|B930009D17	KAT8 regulatory NSL complex subunit 2	protein-coding
mm_131061.1	chr16	4558108	4558142	+	1	NA	intron (NM_031182, intron 1 of 6)	intron (NM_031182, intron 1 of 6)	1595	NM_031182	83383	Mm.273210	NM_031182	ENSMUSG00000005718	Tfap4	AI642933|AP-4|D930048N17Rik|Tcfap4|bHLHc41	transcription factor AP4	protein-coding
mm_71221.1	chr8	40899157	40899174	+	1	NA	exon (NM_001044740, exon 2 of 12)	exon (NM_001044740, exon 2 of 12)	-27068	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_10272.1	chr2	9882145	9882153	+	1	NA	TTS (NR_040511)	TTS (NR_040511)	903	NR_024257	381347	Mm.441450	NR_024257		4930412O13Rik	ENSMUSG00000075535|Gm10853	RIKEN cDNA 4930412O13 gene	ncRNA
mm_24327.1	chr3	89459168	89459178	+	1	NA	promoter-TSS (NM_026784)	promoter-TSS (NM_026784)	55	NM_026784	68603	Mm.34242	NM_026784	ENSMUSG00000027952	Pmvk	1110011E12Rik|2900002L22Rik|AV001327|PMK|PMKA|PMKASE	phosphomevalonate kinase	protein-coding
mm_155084.1	chrX	48106786	48106794	+	1	NA	Intergenic	Intergenic	-1935	NM_001289729	170745	Mm.129279	NM_133213	ENSMUSG00000037005	Xpnpep2	9030008G12Rik|mAPP	X-prolyl aminopeptidase (aminopeptidase P) 2, membrane-bound	protein-coding
mm_58436.1	chr7	3297809	3297838	+	1	NA	3' UTR (NM_016969, exon 3 of 3)	3' UTR (NM_016969, exon 3 of 3)	4795	NM_001093766	50918	Mm.29874	NM_016969	ENSMUSG00000068566	Myadm	D7Wsu62e	myeloid-associated differentiation marker	protein-coding
mm_60673.1	chr7	45061822	45061823	+	1	NA	promoter-TSS (NM_025533)	promoter-TSS (NM_025533)	-170	NM_022999	65116	Mm.379098	NM_022999	ENSMUSG00000007837	Prrg2	1600014G02Rik|2510041M06Rik|N4WBP1	proline-rich Gla (G-carboxyglutamic acid) polypeptide 2	protein-coding
mm_43584.1	chr5	137747067	137747089	+	1	NA	5' UTR (NM_023910, exon 2 of 5)	5' UTR (NM_023910, exon 2 of 5)	1109	NM_029805	78829	Mm.286399	NM_023910	ENSMUSG00000029723	Tsc22d4	0610009M14Rik|1700023B23Rik|AI415410|Thg-1pit|Tilz2	TSC22 domain family, member 4	protein-coding
mm_76844.1	chr8	105289876	105289886	-	1	NA	promoter-TSS (NM_028888)	promoter-TSS (NM_028888)	-353	NM_028888	74356	Mm.204876	NM_028888	ENSMUSG00000014837	4931428F04Rik	AI426165|Kiaa0895l	RIKEN cDNA 4931428F04 gene	protein-coding
mm_159696.1	chr5	24526632	24526632	-	1	NA	exon (NM_015739, exon 1 of 2)	exon (NM_015739, exon 1 of 2)	216	NM_015739	231044	Mm.246596	NM_015739	ENSMUSG00000067724	Gbx1	Gbx-1	gastrulation brain homeobox 1	protein-coding
mm_42453.1	chr5	115435128	115435144	+	1	NA	intron (NM_008629, intron 5 of 14)	intron (NM_008629, intron 5 of 14)	5451	NM_008629	17690	Mm.5077	NM_008629	ENSMUSG00000054256	Msi1	Msi1h|Musahi1|m-Msi-1	musashi RNA-binding protein 1	protein-coding
mm_166449.1	chr5	137268641	137268684	-	1	NA	Intergenic	Intergenic	-19592	NM_009599	11423	Mm.255464	NM_009599	ENSMUSG00000023328	Ache	-	acetylcholinesterase	protein-coding
mm_169247.1	chr13	74865110	74865113	+	1	NA	Intergenic	(TGG)n|Simple_repeat|Simple_repeat	-56351	NM_001301153	12380	Mm.29163	NM_009817	ENSMUSG00000021585	Cast	-	calpastatin	protein-coding
mm_58521.1	chr7	4142090	4142109	+	1	NA	exon (NM_172736, exon 6 of 15)	exon (NM_172736, exon 6 of 15)	5043	NM_172736	232798	Mm.22831	NM_172736	ENSMUSG00000035545	Leng8	AW049671	leukocyte receptor cluster (LRC) member 8	protein-coding
mm_21962.1	chr2	167240535	167240577	-	1	NA	promoter-TSS (NM_008968)	promoter-TSS (NM_008968)	-19	NM_008968	19223	Mm.2339	NM_008968	ENSMUSG00000017969	Ptgis	Cyp8|Cyp8a1|Pgis	prostaglandin I2 (prostacyclin) synthase	protein-coding
mm_67249.1	chr7	75372141	75372143	-	1	NA	Intergenic	Intergenic	-62880	NM_153579	64176	Mm.273082	NM_153579	ENSMUSG00000053025	Sv2b	A830038F04Rik|AI850768|mKIAA0735	synaptic vesicle glycoprotein 2 b	protein-coding
mm_20609.1	chr2	131562756	131562773	-	1	NA	promoter-TSS (NM_013460)	promoter-TSS (NM_013460)	-479	NM_013460	11550	Mm.389380	NM_013460	ENSMUSG00000027335	Adra1d	Adra-1|Adra1|Adra1a|Gpcr8|Spr8|[a]1d|alpha1D-AR	adrenergic receptor, alpha 1d	protein-coding
mm_133813.1	chr16	95703700	95703745	+	1	NA	intron (NM_011809, intron 1 of 9)	intron (NM_011809, intron 1 of 9)	1315	NM_011809	23872	Mm.290207	NM_011809	ENSMUSG00000022895	Ets2	AU022856|Ets-2	E26 avian leukemia oncogene 2, 3' domain	protein-coding
mm_72210.1	chr8	72646501	72646518	+	1	NA	promoter-TSS (NM_176940)	promoter-TSS (NM_176940)	-202	NM_176940	319555	Mm.212927	NM_176940	ENSMUSG00000048148	Nwd1	A230063L24Rik	NACHT and WD repeat domain containing 1	protein-coding
mm_150884.1	chr19	45149834	45149878	+	1	NA	promoter-TSS (NM_021901)	promoter-TSS (NM_021901)	-859	NM_021901	21908	Mm.391203	NM_021901	ENSMUSG00000025215	Tlx1	Hox-11|Hox11|Tlx-1	T cell leukemia, homeobox 1	protein-coding
mm_92676.1	chr10	80561529	80561557	-	1	NA	promoter-TSS (NM_025852)	promoter-TSS (NM_025852)	17	NM_025852	66932	Mm.1116	NM_025852	ENSMUSG00000047417	Rexo1	1700021P10Rik|2610511M11Rik|AW050347|EloA-BP1|Rex1|Tceb3bp1	REX1, RNA exonuclease 1	protein-coding
mm_134929.1	chr16	30933498	30933508	-	1	NA	intron (NR_035427, intron 1 of 2)	intron (NR_035427, intron 1 of 2)	147929	NM_198626	268880	Mm.286693	NM_198626	ENSMUSG00000047434	Xxylt1	AI480653	xyloside xylosyltransferase 1	protein-coding
mm_77076.1	chr8	110168205	110168221	-	1	NA	promoter-TSS (NM_007586)	promoter-TSS (NM_007586)	-7	NM_007586	12308	Mm.2755	NM_007586	ENSMUSG00000003657	Calb2	CR	calbindin 2	protein-coding
mm_48469.1	chr5	140830456	140830467	-	1	NA	promoter-TSS (NM_010302)	promoter-TSS (NM_010302)	-30	NM_010302	14673	Mm.370185	NM_010302	ENSMUSG00000000149	Gna12	AI414047|AI504261|Galpha12	guanine nucleotide binding protein, alpha 12	protein-coding
mm_141180.1	chr17	26886236	26886248	-	1	NA	Intergenic	CpG	-30849	NM_053173	16580	Mm.491138	NM_016761	ENSMUSG00000024301	Kifc5b	Hset|KNSL2|Kifc5a	kinesin family member C5B	protein-coding
mm_165340.1	chr2	118008038	118008044	-	1	NA	intron (NR_126479, intron 8 of 9)	intron (NR_126479, intron 8 of 9)	103161	NR_126479	329496	Mm.235844	NR_126479	ENSMUSG00000087203	Gm13986	C230060E24|OTTMUSG00000015236	predicted gene 13986	ncRNA
mm_101072.1	chr11	11519451	11519457	-	1	NA	Intergenic	Intergenic	30188	NM_028669	73862	Mm.159077	NM_028669	ENSMUSG00000020191	4930415F15Rik	-	RIKEN cDNA 4930415F15 gene	protein-coding
mm_82081.1	chr9	123021120	123021132	+	1	NA	promoter-TSS (NM_025339)	promoter-TSS (NM_025339)	-200	NM_025339	66079	Mm.482265	NM_025339	ENSMUSG00000066233	Tmem42	0610027O18Rik|4933429E06Rik|AV003444|D9Ertd662e	transmembrane protein 42	protein-coding
mm_19174.1	chr2	84356397	84356412	-	1	NA	intron (NM_018782, intron 9 of 15)	intron (NM_018782, intron 9 of 15)	68862	NM_018782	54598	Mm.75467	NM_018782	ENSMUSG00000059588	Calcrl	AV071593|CRLR	calcitonin receptor-like	protein-coding
mm_111598.1	chr12	101976878	101976887	-	1	NA	intron (NM_016856, intron 1 of 14)	intron (NM_016856, intron 1 of 14)	908	NM_016856	51786	Mm.716	NM_016856	ENSMUSG00000041781	Cpsf2	100kDa|2610024B04Rik|AI662483|Cpsf|MCPSF|mKIAA1367	cleavage and polyadenylation specific factor 2	protein-coding
mm_143121.1	chr17	57210219	57210253	-	1	NA	exon (NM_009778, exon 30 of 41)	exon (NM_009778, exon 30 of 41)	6992	NR_105944	102465591		NR_105944	ENSMUSG00000099066	Mir6978	Gm27858|mmu-mir-6978	microRNA 6978	ncRNA
mm_156616.1	chrX	153500299	153500310	+	1	NA	exon (NM_018798, exon 1 of 1)	exon (NM_018798, exon 1 of 1)	2072	NM_018798	54609	Mm.430772	NM_018798	ENSMUSG00000050148	Ubqln2	Chap1|Dsk2|HRIHFB2157|Plic-2|Plic2	ubiquilin 2	protein-coding
mm_29943.1	chr3	132904866	132904983	-	1	NA	exon (NM_001287103, exon 8 of 12)	exon (NM_001287103, exon 8 of 12)	-26328	NR_102298	101243624	Mm.306256	NR_102297	ENSMUSG00000106230	Gm29811	-	predicted gene, 29811	ncRNA
mm_62932.1	chr7	118712517	118712572	+	1	NA	promoter-TSS (NM_182995)	promoter-TSS (NM_182995)	-67	NM_182995	101565	Mm.23279	NM_182995	ENSMUSG00000033904	Ccp110	6330503K22Rik|AA415922|AI427129|AW557948|CP110	centriolar coiled coil protein 110	protein-coding
mm_51406.1	chr6	78373395	78373404	+	1	NA	TTS (NM_011036)	TTS (NM_011036)	2514	NM_011036	18489	Mm.2553	NM_011036	ENSMUSG00000071356	Reg3b	HIP|PAP1|Pap|REG-III	regenerating islet-derived 3 beta	protein-coding
mm_134184.1	chr16	10963290	10963305	-	1	NA	exon (NM_019980, exon 3 of 4)	exon (NM_019980, exon 3 of 4)	29824	NM_019980	56722	Mm.294753	NM_019980	ENSMUSG00000022500	Litaf	3222402J11Rik|C85531|N4WBP3|TBX1	LPS-induced TN factor	protein-coding
mm_80090.1	chr9	70221036	70221044	+	1	NA	intron (NM_181072, intron 1 of 27)	intron (NM_181072, intron 1 of 27)	13690	NM_181072	71602	Mm.249311	NM_181072	ENSMUSG00000032220	Myo1e	2310020N23Rik|9130023P14Rik|AA407778|myosin-1e|myr 3	myosin IE	protein-coding
mm_136009.1	chr16	75905514	75905516	-	1	NA	intron (NM_023380, intron 1 of 7)	intron (NM_023380, intron 1 of 7)	3751	NM_023380	67742	Mm.131406	NM_023380	ENSMUSG00000022876	Samsn1	4930571B16Rik|930571B16Rik|Hacs1|SLy2	SAM domain, SH3 domain and nuclear localization signals, 1	protein-coding
mm_2845.1	chr1	131638441	131638484	+	1	NA	5' UTR (NM_007799, exon 1 of 10)	5' UTR (NM_007799, exon 1 of 10)	148	NM_007799	13034	Mm.230249	NM_007799	ENSMUSG00000004552	Ctse	A430072O03Rik|C920004C08Rik|CE|CatE	cathepsin E	protein-coding
mm_80016.1	chr9	67862290	67862298	+	1	NA	intron (NM_177184, intron 5 of 84)	intron (NM_177184, intron 5 of 84)	21898	NM_177184	320528	Mm.241454	NM_177184	ENSMUSG00000035284	Vps13c	AI552542|AV026040|C230055H22Rik|W51662|chorein	vacuolar protein sorting 13C	protein-coding
mm_40129.1	chr5	35041540	35041595	+	1	NA	promoter-TSS (NM_019447)	promoter-TSS (NM_019447)	58	NM_019447	54426	Mm.27369	NM_019447	ENSMUSG00000029102	Hgfac	HGFA	hepatocyte growth factor activator	protein-coding
mm_22193.1	chr2	173276470	173276499	-	1	NA	promoter-TSS (NM_022995)	promoter-TSS (NM_022995)	49	NM_022995	65112	Mm.73682	NM_022995	ENSMUSG00000038400	Pmepa1	2210418I02Rik|AW455466|Erg1.2|N4wbp4|Stag1|Tmepai	prostate transmembrane protein, androgen induced 1	protein-coding
mm_154298.1	chr19	61224737	61224754	-	1	NA	3' UTR (NM_009970, exon 12 of 12)	3' UTR (NM_009970, exon 12 of 12)	3673	NM_009970	12982	Mm.287228	NM_009970	ENSMUSG00000059326	Csf2ra	CD116|Csfgmra|GM-CSF-Ra|GM-CSFR	colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)	protein-coding
mm_149668.1	chr19	18776173	18776182	+	1	NA	intron (NM_153417, intron 2 of 38)	MTEb|LTR|ERVL-MaLR	26194	NM_153417	225997	Mm.215171	NM_153417	ENSMUSG00000024727	Trpm6	CHAK2|TRPM6/CHAK2	transient receptor potential cation channel, subfamily M, member 6	protein-coding
mm_121296.1	chr14	105500000	105500046	+	1	NA	intron (NR_045921, intron 1 of 2)	intron (NR_045921, intron 1 of 2)	1235	NR_045921	74864	Mm.159344	NR_045921	ENSMUSG00000022116	4930449E01Rik	-	RIKEN cDNA 4930449E01 gene	ncRNA
mm_125569.1	chr15	59315031	59315087	+	1	NA	promoter-TSS (NM_009270)	promoter-TSS (NM_009270)	-33	NM_009270	20775	Mm.296169	NM_009270	ENSMUSG00000022351	Sqle	AI323792	squalene epoxidase	protein-coding
mm_31250.1	chr4	44981390	44981461	+	1	NA	promoter-TSS (NM_001312880)	promoter-TSS (NM_001312880)	31	NM_001312880	76238	Mm.196574	NM_080289	ENSMUSG00000035637	Grhpr	1110059D05Rik|6430629L09Rik|Glxr	glyoxylate reductase/hydroxypyruvate reductase	protein-coding
mm_53363.1	chr6	129377427	129377431	+	1	NA	intron (NM_001204223, intron 6 of 6)	intron (NM_001204223, intron 6 of 6)	8074	NM_027709	71183	Mm.79402	NM_027709	ENSMUSG00000030158	Clec12b	4933425B16Rik	C-type lectin domain family 12, member B	protein-coding
mm_7215.1	chr1	93160235	93160245	-	1	NA	5' UTR (NM_001159940, exon 2 of 6)	5' UTR (NM_001159940, exon 2 of 6)	630	NM_001159940	71874	Mm.158766	NM_172411	ENSMUSG00000034159	2310007B03Rik	-	RIKEN cDNA 2310007B03 gene	protein-coding
mm_29034.1	chr3	102167672	102167695	-	1	NA	intron (NM_177545, intron 4 of 7)	intron (NM_177545, intron 4 of 7)	37010	NM_177545	229658	Mm.118004	NM_177545	ENSMUSG00000027860	Vangl1	Kitenin|Lpp2|Stb2|Stbm	vang-like 1 (van gogh, Drosophila)	protein-coding
mm_33100.1	chr4	124701386	124701418	+	1	NA	intron (NM_010213, intron 1 of 5)	intron (NM_010213, intron 1 of 5)	703	NM_010213	14201	Mm.331856	NM_010213	ENSMUSG00000032643	Fhl3	SLIM2	four and a half LIM domains 3	protein-coding
mm_120836.1	chr14	75177849	75177866	+	1	NA	intron (NM_008879, intron 2 of 16)	intron (NM_008879, intron 2 of 16)	41432	NM_008879	18826	Mm.153911	NM_008879	ENSMUSG00000021998	Lcp1	AW536232|D14Ertd310e|LCP-1|Pls2|pp65	lymphocyte cytosolic protein 1	protein-coding
mm_11259.1	chr2	29963425	29963428	+	1	NA	Intergenic	Intergenic	-2134	NM_001177668	20740	Mm.204969	NM_001076554	ENSMUSG00000057738	Sptan1	2610027H02Rik|Spna-2|Spna2	spectrin alpha, non-erythrocytic 1	protein-coding
mm_53217.1	chr6	126853140	126853154	+	1	NA	promoter-TSS (NM_009650)	promoter-TSS (NM_009650)	49	NM_009650	11642	Mm.87748	NM_009650	ENSMUSG00000030344	Akap3	Prka3	A kinase (PRKA) anchor protein 3	protein-coding
mm_68252.1	chr7	105574325	105574329	-	1	NA	exon (NM_001253886, exon 2 of 14)	exon (NM_001253886, exon 2 of 14)	-5009	NM_001253887	11785	Mm.38469	NM_009685	ENSMUSG00000037032	Apbb1	Fe65|Rir	amyloid beta (A4) precursor protein-binding, family B, member 1	protein-coding
mm_59001.1	chr7	19178204	19178239	+	1	NA	intron (NM_001347582, intron 1 of 21)	intron (NM_001347582, intron 1 of 21)	1800	NM_001347582	72205	Mm.154121	NM_028153	ENSMUSG00000040811	Eml2	1600029N02Rik|EMAP-2	echinoderm microtubule associated protein like 2	protein-coding
mm_88632.1	chr10	79887665	79887685	+	1	NA	exon (NM_015779, exon 4 of 5)	exon (NM_015779, exon 4 of 5)	1363	NM_015779	50701	Mm.262194	NM_015779	ENSMUSG00000020125	Elane	Ela2|F430011M15Rik|NE	elastase, neutrophil expressed	protein-coding
mm_114114.1	chr13	54949389	54949481	+	1	NA	promoter-TSS (NM_153131)	promoter-TSS (NM_153131)	3	NM_153131	107448	Mm.23573	NM_153131	ENSMUSG00000025876	Unc5a	Unc5h1|mKIAA1976	unc-5 netrin receptor A	protein-coding
mm_151304.1	chr19	55742057	55742066	+	1	NA	non-coding (NR_138565, exon 1 of 16)	non-coding (NR_138565, exon 1 of 16)	251	NM_001142923	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_110694.1	chr12	69197099	69197117	-	1	NA	promoter-TSS (NR_033222)	promoter-TSS (NR_033222)	-103	NR_033222	414085	Mm.256223	NR_033222	ENSMUSG00000097061	9330151L19Rik	-	RIKEN cDNA 9330151L19 gene	ncRNA
mm_104811.1	chr11	98939650	98939679	-	1	NA	promoter-TSS (NM_001177303)	promoter-TSS (NM_001177303)	-47	NM_001177303	19401	Mm.439744	NM_009024	ENSMUSG00000037992	Rara	Nr1b1|RAR|RARalpha1	retinoic acid receptor, alpha	protein-coding
mm_42082.1	chr5	110176851	110176864	+	1	NA	promoter-TSS (NR_040431)	promoter-TSS (NR_040431)	156	NM_008146	269682	Mm.9392	NM_008146	ENSMUSG00000029502	Golga3	5330413L04|5430416E01Rik|AI449376|AW490576|G1-499-14|Mea-2|Mea2|repro27	golgi autoantigen, golgin subfamily a, 3	protein-coding
mm_8914.1	chr1	163313461	163313494	-	1	NA	5' UTR (NM_175686, exon 1 of 5)	5' UTR (NM_175686, exon 1 of 5)	173	NM_011127	18933	Mm.288642	NM_011127	ENSMUSG00000026586	Prrx1	A230024N07Rik|AA755424|AI385634|AI843499|K-2|Pmx|Pmx1|Prx1|mHox	paired related homeobox 1	protein-coding
mm_171880.1	chr5	32854265	32854265	-	1	NA	promoter-TSS (NM_194340)	promoter-TSS (NM_194340)	-35	NM_194340	215476	Mm.248721	NM_194340	ENSMUSG00000054280	Prr14l	6030436E02Rik|C330019G07Rik|Prl14l	proline rich 14-like	protein-coding
mm_31379.1	chr4	47474716	47474726	+	1	NA	promoter-TSS (NM_024171)	promoter-TSS (NM_024171)	60	NM_024171	66212	Mm.20188	NM_024171	ENSMUSG00000053317	Sec61b	1190006C12Rik|AI326121|AW122942	Sec61 beta subunit	protein-coding
mm_67913.1	chr7	99823384	99823424	-	1	NA	exon (NM_016720, exon 2 of 3)	exon (NM_016720, exon 2 of 3)	5013	NM_016720	50877	Mm.103703	NM_016720	ENSMUSG00000035239	Neu3	-	neuraminidase 3	protein-coding
mm_61208.1	chr7	64185407	64185422	+	1	NA	promoter-TSS (NM_018752)	promoter-TSS (NM_018752)	-45	NM_018752	17364	Mm.38875	NM_018752	ENSMUSG00000030523	Trpm1	4732499L03Rik|AI606771|Ltrpc1|Mlsn1	transient receptor potential cation channel, subfamily M, member 1	protein-coding
mm_63466.1	chr7	127573721	127573737	+	1	NA	intron (NM_026888, intron 1 of 9)	intron (NM_026888, intron 1 of 9)	381	NM_026888	68961	Mm.274473	NM_026888	ENSMUSG00000030815	Phkg2	1500017I02Rik	phosphorylase kinase, gamma 2 (testis)	protein-coding
mm_44034.1	chr5	147439333	147439340	+	1	NA	intron (NM_028291, intron 1 of 18)	intron (NM_028291, intron 1 of 18)	8756	NM_028291	72587	Mm.320469	NM_028291	ENSMUSG00000029647	Pan3	2700050F09Rik|A430027N15Rik|AU014670	PAN3 poly(A) specific ribonuclease subunit	protein-coding
mm_137231.1	chr17	24398608	24398611	+	1	NA	intron (NM_013855, intron 22 of 32)	intron (NM_013855, intron 22 of 32)	15904	NR_033554	654822	Mm.489806	NM_001039561	ENSMUSG00000073437	D330041H03Rik	-	RIKEN cDNA D330041H03 gene	ncRNA
mm_73310.1	chr8	105171551	105171569	+	1	NA	intron (NM_001161456, intron 2 of 4)	CpG-14413	886	NM_001161458	12400	Mm.2018	NM_022309	ENSMUSG00000031885	Cbfb	AI893578|PEA2|PEBP2b|Pebp2|Pebpb2	core binding factor beta	protein-coding
mm_66105.1	chr7	31041486	31041497	-	1	NA	5' UTR (NM_001111073, exon 1 of 8)	5' UTR (NM_001111073, exon 1 of 8)	348	NM_001111073	18301	Mm.1870	NM_008761	ENSMUSG00000009687	Fxyd5	EF-8|Oit2|RIC	FXYD domain-containing ion transport regulator 5	protein-coding
mm_23219.1	chr3	47704570	47704572	+	1	NA	Intergenic	Intergenic	322188	NR_040408	666202	Mm.465057	NR_040408	ENSMUSG00000103257	Gm7977	EG666202	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide pseudogene	pseudo
mm_127400.1	chr15	101174097	101174148	+	1	NA	promoter-TSS (NM_007395)	promoter-TSS (NM_007395)	-3	NM_007395	11479	Mm.308467	NM_007395	ENSMUSG00000000532	Acvr1b	6820432J04|ActR-IB|ActRIB|Acvrlk4|Alk4|SKR2	activin A receptor, type 1B	protein-coding
mm_160638.1	chr9	108494598	108494598	+	1	NA	intron (NM_145407, intron 8 of 25)	intron (NM_145407, intron 8 of 25)	3922	NM_027804	71472	Mm.289706	NM_027804	ENSMUSG00000006676	Usp19	8430421I07Rik|AI047774|Zmynd9	ubiquitin specific peptidase 19	protein-coding
mm_40368.1	chr5	50821437	50821439	+	1	NA	Intergenic	Intergenic	568676	NR_106197	102465903		NR_106197	ENSMUSG00000099124	Mir8117	Gm27323|mmu-mir-8117	microRNA 8117	ncRNA
mm_165455.1	chr2	157914674	157914680	+	1	NA	promoter-TSS (NM_198627)	promoter-TSS (NM_198627)	24	NM_198627	277432	Mm.441156	NM_198627	ENSMUSG00000037843	Vstm2l	Gm691	V-set and transmembrane domain containing 2-like	protein-coding
mm_97805.1	chr11	82960896	82960906	+	1	NA	promoter-TSS (NR_045932)	promoter-TSS (NR_045932)	-220	NR_045932	76392	Mm.295205	NR_045932	ENSMUSG00000086327	Slfn5os	1700003F17Rik	schlafen 5, opposite strand	ncRNA
mm_92644.1	chr10	80349000	80349031	-	1	NA	promoter-TSS (NM_001285435)	promoter-TSS (NM_001285435)	-567	NR_104340	66548	Mm.71891	NM_025629	ENSMUSG00000043822	Adamtsl5	2010109H09Rik|Thsd6	ADAMTS-like 5	protein-coding
mm_49484.1	chr6	29535373	29535383	+	1	NA	exon (NM_001252382, exon 6 of 9)	exon (NM_001252382, exon 6 of 9)	6096	NM_001252382	27056	Mm.6479	NM_012057	ENSMUSG00000029771	Irf5	AW491843|mirf5	interferon regulatory factor 5	protein-coding
mm_30695.1	chr4	11604485	11604488	+	1	NA	intron (NM_001039556, intron 8 of 14)	intron (NM_001039556, intron 8 of 14)	24824	NM_001256142	100503583	Mm.249437	NM_001256142	ENSMUSG00000094595	Fsbp	-	fibrinogen silencer binding protein	protein-coding
mm_157948.1	chrX	86746565	86746566	-	1	NA	TTS (NM_001160403)	TTS (NM_001160403)	-391571	NR_036689	245502	Mm.490821	NR_036689		Gm41	-	melanoma antigen, family B, 4 pseudogene	pseudo
mm_143946.1	chr17	86753419	86753451	-	1	NA	promoter-TSS (NM_010137)	promoter-TSS (NM_010137)	-429	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_59072.1	chr7	19508761	19508771	+	1	NA	promoter-TSS (NM_177692)	promoter-TSS (NM_177692)	96	NM_025960	67091	Mm.44213	NM_025960	ENSMUSG00000002043	Trappc6a	1810073E21Rik|4930519D19Rik|AI480686|TRS33|mhyp	trafficking protein particle complex 6A	protein-coding
mm_114858.1	chr13	93304941	93304955	+	1	NA	5' UTR (NM_011982, exon 1 of 5)	5' UTR (NM_011982, exon 1 of 5)	1191	NM_011982	26556	Mm.37533	NM_011982	ENSMUSG00000007617	Homer1	PSD-Zip45|SYN47|Ves-1|homer-1|vesl-1	homer scaffolding protein 1	protein-coding
mm_34134.1	chr4	139291031	139291073	+	1	NA	exon (NM_001271405, exon 9 of 9)	exon (NM_001271405, exon 9 of 9)	19648	NM_145384	212555	Mm.45131	NM_145384	ENSMUSG00000028744	Pqlc2	BC019216	PQ loop repeat containing 2	protein-coding
mm_6234.1	chr1	66945006	66945017	-	1	NA	promoter-TSS (NM_021285)	promoter-TSS (NM_021285)	45	NM_021285	17901	Mm.1000	NM_021285	ENSMUSG00000061816	Myl1	AI325107|MLC1f|MLC3f|Mylf	myosin, light polypeptide 1	protein-coding
mm_129012.1	chr15	74920777	74920804	-	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-34261	NM_001164039	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_83396.1	chr9	44721290	44721341	-	1	NA	intron (NM_153537, intron 4 of 21)	CpG	13883	NM_153537	102693	Mm.28639	NM_153537	ENSMUSG00000048537	Phldb1	AU041016|D330037A14Rik|Ll5a	pleckstrin homology like domain, family B, member 1	protein-coding
mm_130088.1	chr15	89379247	89379262	-	1	NA	promoter-TSS (NM_001013022)	promoter-TSS (NM_001013022)	0	NM_001013022	70113	Mm.247273	NM_001013022	ENSMUSG00000047394	Odf3b	2010001J22Rik	outer dense fiber of sperm tails 3B	protein-coding
mm_66925.1	chr7	61311680	61311690	-	1	NA	Intergenic	Intergenic	303642	NR_045727	319752	Mm.294476	NR_045727		B230209E15Rik	-	RIKEN cDNA B230209E15 gene	ncRNA
mm_3864.1	chr1	160988932	160988942	+	1	NA	intron (NM_080844, intron 2 of 7)	intron (NM_080844, intron 2 of 7)	10331	NM_080844	11905	Mm.260770	NM_080844	ENSMUSG00000026715	Serpinc1	AI114908|ATIII|At-3|At3	serine (or cysteine) peptidase inhibitor, clade C (antithrombin), member 1	protein-coding
mm_89709.1	chr10	97693054	97693061	+	1	NA	promoter-TSS (NM_025724)	promoter-TSS (NM_025724)	-2	NM_025724	66716	Mm.56430	NM_025724	ENSMUSG00000047025	Ccer1	4921510H08Rik|AV259683	coiled-coil glutamate-rich protein 1	protein-coding
mm_4388.1	chr1	172312379	172312437	+	1	NA	promoter-TSS (NM_080419)	promoter-TSS (NM_080419)	41	NM_080419	140559	Mm.271717	NM_080419	ENSMUSG00000038034	Igsf8	ESTM34|EWI-2|KCT-4|PGRL	immunoglobulin superfamily, member 8	protein-coding
mm_22409.1	chr2	181314259	181314269	-	1	NA	5' UTR (NM_009133, exon 1 of 5)	5' UTR (NM_009133, exon 1 of 5)	236	NM_009133	20262	Mm.2319	NM_009133	ENSMUSG00000027581	Stmn3	9330161A03Rik|AI604839|R75323|Sclip	stathmin-like 3	protein-coding
mm_141267.1	chr17	27635239	27635267	-	1	NA	promoter-TSS (NM_025963)	promoter-TSS (NM_025963)	-11	NM_025963	67097	Mm.275810	NM_025963	ENSMUSG00000052146	Rps10	2210402A09Rik	ribosomal protein S10	protein-coding
mm_126895.1	chr15	89499919	89499922	+	1	NA	promoter-TSS (NM_021423)	promoter-TSS (NM_021423)	63	NM_021423	58234	Mm.146855	NM_021423	ENSMUSG00000022623	Shank3	AI841104|SHANK3c-3|SHANK3c-4|Shank3b	SH3/ankyrin domain gene 3	protein-coding
mm_57539.1	chr6	126644735	126644772	-	1	NA	5' UTR (NM_010595, exon 1 of 2)	5' UTR (NM_010595, exon 1 of 2)	1048	NM_010595	16485	Mm.40424	NM_010595	ENSMUSG00000047976	Kcna1	AI840627|Kca1-1|Kv1.1|MBK1|Mk-1|Shak|mceph	potassium voltage-gated channel, shaker-related subfamily, member 1	protein-coding
mm_26890.1	chr3	18243290	18243349	-	1	NA	promoter-TSS (NM_007825)	promoter-TSS (NM_007825)	19	NM_007825	13123	Mm.316000	NM_007825	ENSMUSG00000039519	Cyp7b1	AW261589|D3Ertd552e|hct-1	cytochrome P450, family 7, subfamily b, polypeptide 1	protein-coding
mm_101173.1	chr11	16985348	16985387	-	1	NA	intron (NM_019549, intron 7 of 9)	intron (NM_019549, intron 7 of 9)	23351	NM_019549	56193	Mm.98232	NM_019549	ENSMUSG00000020120	Plek	2010300B13Rik	pleckstrin	protein-coding
mm_137106.1	chr17	21733728	21733749	+	1	NA	promoter-TSS (NM_001164676)	promoter-TSS (NM_001164676)	14	NM_001164676	381067	Mm.482723	NM_001164676	ENSMUSG00000061544	Zfp229	-	zinc finger protein 229	protein-coding
mm_110487.1	chr12	51971290	51971326	-	1	NA	promoter-TSS (NM_177171)	promoter-TSS (NM_177171)	13	NM_177171	320487	Mm.131941	NM_177171	ENSMUSG00000035181	Heatr5a	C230081H03Rik|D930036F22Rik|mKIAA1316	HEAT repeat containing 5A	protein-coding
mm_5773.1	chr1	51475336	51475349	-	1	NA	intron (NM_001310548, intron 2 of 5)	PB1D11|SINE|Alu	3057	NM_028696	109019	Mm.196290	NM_028696	ENSMUSG00000026107	Nabp1	4930434H03Rik|4930442A21Rik|4930488J04Rik|4933440J18Rik|5830411E10Rik|AI852561|Nbp1|Obfc2a|Ssb2	nucleic acid binding protein 1	protein-coding
mm_56898.1	chr6	119137317	119137325	-	1	NA	intron (NM_001255998, intron 1 of 47)	intron (NM_001255998, intron 1 of 47)	-28826	NM_001256002	12288	Mm.41628	NM_009781	ENSMUSG00000051331	Cacna1c	Cav1.2|Cchl1a1|D930026N18Rik|MBC|MELC-CC	calcium channel, voltage-dependent, L type, alpha 1C subunit	protein-coding
mm_107623.1	chr12	51593316	51593357	+	1	NA	promoter-TSS (NM_001198835)	promoter-TSS (NM_001198835)	-5	NM_007728	12810	Mm.21325	NM_007728	ENSMUSG00000020953	Coch	AW122937|Coch-5B2|D12H14S564E	cochlin	protein-coding
mm_91628.1	chr10	41933760	41933770	-	1	NA	intron (NM_001034858, intron 12 of 17)	intron (NM_001034858, intron 12 of 17)	46326	NM_001013370	140742	Mm.139418	NM_001013370	ENSMUSG00000038332	Sesn1	1110002G11Rik|AU044290|Pa26|Sest1	sestrin 1	protein-coding
mm_98857.1	chr11	97663367	97663386	+	1	NA	promoter-TSS (NM_139311)	promoter-TSS (NM_139311)	-36	NM_139311	246198	Mm.23685	NM_139311	ENSMUSG00000038437	Mllt6	AI315037|Af17	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 6	protein-coding
mm_156623.1	chrX	155154868	155154871	+	1	NA	Intergenic	Intergenic	-7020	NM_001081671	73347	Mm.63848	NM_001081671	ENSMUSG00000057402	Cldn34b2	1700042B14Rik	claudin 34B2	protein-coding
mm_116482.1	chr13	43789077	43789093	-	1	NA	intron (NM_001289915, intron 2 of 4)	intron (NM_001289915, intron 2 of 4)	3973	NM_001289915	12522	Mm.57175	NM_009856	ENSMUSG00000015396	Cd83	-	CD83 antigen	protein-coding
mm_97058.1	chr11	72689984	72689994	+	1	NA	promoter-TSS (NM_009671)	promoter-TSS (NM_009671)	-13	NM_009671	11736	Mm.10313	NM_009671	ENSMUSG00000020790	Ankfy1	Ankhzn|ZFYVE14|mKIAA1255	ankyrin repeat and FYVE domain containing 1	protein-coding
mm_116989.1	chr13	56482154	56482197	-	1	NA	promoter-TSS (NM_008373)	promoter-TSS (NM_008373)	71	NM_008373	16198	Mm.3006	NM_008373	ENSMUSG00000021538	Il9	Il-9|P40	interleukin 9	protein-coding
mm_93686.1	chr10	117815668	117815685	-	1	NA	3' UTR (NM_024457, exon 8 of 8)	3' UTR (NM_024457, exon 8 of 8)	-22971	NM_134010	103468	Mm.12568	NM_134010	ENSMUSG00000052798	Nup107	AW541137|C76801	nucleoporin 107	protein-coding
mm_51403.1	chr6	78372868	78372895	+	1	NA	exon (NM_011036, exon 5 of 6)	exon (NM_011036, exon 5 of 6)	1996	NM_011036	18489	Mm.2553	NM_011036	ENSMUSG00000071356	Reg3b	HIP|PAP1|Pap|REG-III	regenerating islet-derived 3 beta	protein-coding
mm_25655.1	chr3	121531604	121531634	+	1	NA	intron (NM_145394, intron 2 of 14)	intron (NM_145394, intron 2 of 14)	725	NM_145394	213603	Mm.33062	NM_145394	ENSMUSG00000039865	Slc44a3	BC010552	solute carrier family 44, member 3	protein-coding
mm_98938.1	chr11	98371793	98371811	+	1	NA	intron (NM_021547, intron 1 of 14)	LTR105_Mam|LTR|ERVL	-12009	NM_011540	21393	Mm.10762	NM_011540	ENSMUSG00000007877	Tcap	AI503981|AJ223855	titin-cap	protein-coding
mm_49449.1	chr6	29348164	29348165	+	1	NA	promoter-TSS (NM_184053)	promoter-TSS (NM_184053)	58	NM_184053	12321	Mm.392075	NM_007594	ENSMUSG00000029767	Calu	9530075H20Rik	calumenin	protein-coding
mm_63103.1	chr7	122628814	122628825	+	1	NA	3' UTR (NM_008855, exon 17 of 17)	3' UTR (NM_008855, exon 17 of 17)	-42925	NM_019430	54376	Mm.444212	NM_019430	ENSMUSG00000066189	Cacng3	-	calcium channel, voltage-dependent, gamma subunit 3	protein-coding
mm_94278.1	chr11	3963952	3963964	+	1	NA	promoter-TSS (NM_022889)	promoter-TSS (NM_022889)	-17	NM_022889	64934	Mm.28659	NM_022889	ENSMUSG00000020430	Pes1	-	pescadillo ribosomal biogenesis factor 1	protein-coding
mm_62559.1	chr7	103814069	103814094	+	1	NA	promoter-TSS (NM_016956)	promoter-TSS (NM_016956)	-158	NM_008220	101488143	Mm.467412	NM_008220	ENSMUSG00000073940	Hbb-bt	Beta-t	hemoglobin, beta adult t chain	protein-coding
mm_128752.1	chr15	64920985	64920995	-	1	NA	exon (NM_009623, exon 1 of 18)	exon (NM_009623, exon 1 of 18)	1306	NM_001331075	11514	Mm.1425	NM_009623	ENSMUSG00000022376	Adcy8	AC8|AW060868	adenylate cyclase 8	protein-coding
mm_106703.1	chr12	3732187	3732189	+	1	NA	intron (NR_027869, intron 10 of 20)	intron (NR_027869, intron 10 of 20)	-74792	NM_007872	13435	Mm.5001	NM_007872	ENSMUSG00000020661	Dnmt3a	MmuIIIA	DNA methyltransferase 3A	protein-coding
mm_40728.1	chr5	66053126	66053136	+	1	NA	intron (NM_178446, intron 2 of 6)	intron (NM_178446, intron 2 of 6)	45048	NM_139065	245945	Mm.36863	NM_139065	ENSMUSG00000070780	Rbm47	9530077J19Rik	RNA binding motif protein 47	protein-coding
mm_87019.1	chr10	28013493	28013502	+	1	NA	Intergenic	Intergenic	-61323	NM_008983	19272	Mm.332303	NM_008983	ENSMUSG00000019889	Ptprk	AI853699|PTPk|RPTPkappa	protein tyrosine phosphatase, receptor type, K	protein-coding
mm_43984.1	chr5	146384948	146384994	+	1	NA	promoter-TSS (NM_145155)	promoter-TSS (NM_145155)	-35	NM_145155	245880	Mm.472750	NM_145155	ENSMUSG00000029636	Wasf3	Scar3|Wave3	WAS protein family, member 3	protein-coding
mm_127841.1	chr15	6874302	6874306	-	1	NA	promoter-TSS (NM_011019)	promoter-TSS (NM_011019)	9	NM_011019	18414	Mm.10760	NM_011019	ENSMUSG00000022146	Osmr	OSMRB	oncostatin M receptor	protein-coding
mm_63381.1	chr7	127213132	127213148	+	1	NA	intron (NM_001347655, intron 2 of 6)	intron (NM_001347655, intron 2 of 6)	1532	NM_016754	17907	Mm.14526	NM_016754	ENSMUSG00000030672	Mylpf	2410014J02Rik|MLC-2|Mlc2	myosin light chain, phosphorylatable, fast skeletal muscle	protein-coding
mm_12294.1	chr2	69057775	69057790	+	1	NA	intron (NM_172856, intron 6 of 9)	L1_Mus3|LINE|L1	-78018	NM_181547	329416	Mm.90047	NM_181547	ENSMUSG00000034738	Nostrin	Daip2|mDaIP2	nitric oxide synthase trafficker	protein-coding
mm_54890.1	chr6	44083329	44083345	-	1	NA	Intergenic	Intergenic	-417059	NM_013861	29807	Mm.320979	NM_013861	ENSMUSG00000029735	Tpk1	-	thiamine pyrophosphokinase	protein-coding
mm_24704.1	chr3	95131436	95131440	+	1	NA	intron (NM_027013, intron 5 of 6)	MT2B2|LTR|ERVL	2574	NM_027013	69269	Mm.182944	NM_027013	ENSMUSG00000092607	Scnm1	3110001I17Rik|Scnm1-ps	sodium channel modifier 1	protein-coding
mm_166931.1	chr7	34881586	34881589	-	1	NA	Intergenic	Intergenic	-30820	NM_008820	18624	Mm.69751	NM_008820	ENSMUSG00000063931	Pepd	Pep-4|Pep4|dal	peptidase D	protein-coding
mm_69000.1	chr7	126695715	126695728	-	1	NA	promoter-TSS (NM_029420)	promoter-TSS (NM_029420)	62	NM_029420	75764	Mm.280573	NM_029420	ENSMUSG00000059772	Slx1b	1110030E23Rik|2410170E21Rik|4833422P03Rik|AI853643|Giyd1|Giyd2	SLX1 structure-specific endonuclease subunit homolog B (S. cerevisiae)	protein-coding
mm_92308.1	chr10	75185175	75185184	-	1	NA	TTS (NM_001081412)	TTS (NM_001081412)	-26894	NM_153406	74392	Mm.27716	NM_153406	ENSMUSG00000033444	Specc1l	4930470P14Rik|4932439K10Rik|9530057A13Rik|AI317249|Cytsa|mKIAA0376	sperm antigen with calponin homology and coiled-coil domains 1-like	protein-coding
mm_130799.1	chr15	101694300	101694318	-	1	NA	promoter-TSS (NM_008476)	promoter-TSS (NM_008476)	-4	NM_008476	16687	Mm.302399	NM_008476	ENSMUSG00000058354	Krt6a	2310016L08Rik|Krt2-6a|Krt2-6c|MK6a|mK6[a]	keratin 6A	protein-coding
mm_143603.1	chr17	78417643	78417646	-	1	NA	intron (NM_001285949, intron 1 of 7)	intron (NM_001285949, intron 1 of 7)	508	NM_001285949	225020	Mm.236835	NM_199448	ENSMUSG00000056121	Fez2	9030616F16|D17Ertd315e	fasciculation and elongation protein zeta 2 (zygin II)	protein-coding
mm_108763.1	chr12	89450187	89450191	+	1	NA	intron (NM_172544, intron 8 of 19)	intron (NM_172544, intron 8 of 19)	-362294	NM_001252074	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding
mm_28627.1	chr3	95133990	95134017	-	1	NA	promoter-TSS (NM_001163573)	promoter-TSS (NM_001163573)	9	NM_027013	69269	Mm.182944	NM_027013	ENSMUSG00000092607	Scnm1	3110001I17Rik|Scnm1-ps	sodium channel modifier 1	protein-coding
mm_113194.1	chr13	24943213	24943222	+	1	NA	promoter-TSS (NM_008156)	promoter-TSS (NM_008156)	65	NM_008156	14756	Mm.291831	NM_008156	ENSMUSG00000021340	Gpld1	6330541J12Rik|AW546131	glycosylphosphatidylinositol specific phospholipase D1	protein-coding
mm_92816.1	chr10	81430967	81431039	-	1	NA	Intergenic	CpG	-3830	NM_026756	18029	Mm.426936	NM_008688	ENSMUSG00000055053	Nfic	1110019L22Rik|1500041O16Rik|AA589446|AI746521|NF1-C	nuclear factor I/C	protein-coding
mm_76915.1	chr8	105933018	105933024	-	1	NA	exon (NM_023182, exon 3 of 7)	exon (NM_023182, exon 3 of 7)	841	NM_023182	109660	Mm.2745	NM_023182	ENSMUSG00000031896	Ctrl	0910001G08Rik|1810004D15Rik|AV005227|Ctra-1|Ctra1|chymopasin|mFLJ00366	chymotrypsin-like	protein-coding
mm_60220.1	chr7	43562260	43562282	+	1	NA	promoter-TSS (NM_001008549)	promoter-TSS (NM_001008549)	-99	NM_001008549	210104	Mm.333821	NM_001008549	ENSMUSG00000056592	Zfp658	-	zinc finger protein 658	protein-coding
mm_19896.1	chr2	114052078	114052087	-	1	NA	intron (NM_009608, intron 1 of 6)	intron (NM_009608, intron 1 of 6)	793	NM_009608	11464	Mm.686	NM_009608	ENSMUSG00000068614	Actc1	Actc-1	actin, alpha, cardiac muscle 1	protein-coding
mm_119888.1	chr14	54936240	54936303	+	1	NA	promoter-TSS (NM_026066)	promoter-TSS (NM_026066)	-199	NM_026066	67272	Mm.41614	NM_026066	ENSMUSG00000040759	Cmtm5	1500005P16Rik|2900052H21Rik|Cklfsf5	CKLF-like MARVEL transmembrane domain containing 5	protein-coding
mm_83660.1	chr9	49554576	49554596	-	1	NA	intron (NM_001081445, intron 8 of 17)	intron (NM_001081445, intron 8 of 17)	36298	NR_029465	100036537	Mm.437541	NR_029465	ENSMUSG00000079564	Gm11149	ENSMUSG00000060603|ENSMUSG00000079564	predicted gene 11149	ncRNA
mm_53736.1	chr6	145121868	145121878	+	1	NA	5' UTR (NM_008511, exon 1 of 19)	5' UTR (NM_008511, exon 1 of 19)	134	NM_008511	16970	Mm.843	NM_008511	ENSMUSG00000030263	Lrmp	D6Int3|D6Int4|D6Int5|D6Int7|D6Int8|Jaw1	lymphoid-restricted membrane protein	protein-coding
mm_114566.1	chr13	74617812	74617834	+	1	NA	Intergenic	Intergenic	-22049	NM_030711	80898	Mm.83526	NM_030711	ENSMUSG00000021583	Erap1	Arts1|ERAAP|PILSA|PILSAP	endoplasmic reticulum aminopeptidase 1	protein-coding
mm_4278.1	chr1	171619229	171619232	+	1	NA	Intergenic	RMER19B|LTR|ERVK	-11820	NM_008534	17085	Mm.560	NM_008534	ENSMUSG00000004707	Ly9	AI893573|CD229|Lgp100|Ly-9|SLAMF3|T100	lymphocyte antigen 9	protein-coding
mm_65523.1	chr7	25772227	25772320	-	1	NA	intron (NM_001190974, intron 9 of 18)	intron (NM_001190974, intron 9 of 18)	16460	NM_001190974	26362	Mm.4128	NM_009465	ENSMUSG00000002602	Axl	AI323647|Ark|Tyro7|Ufo	AXL receptor tyrosine kinase	protein-coding
mm_134586.1	chr16	20425882	20425971	-	1	NA	intron (NM_176839, intron 1 of 6)	CpG	468	NM_013790	27416	Mm.20845	NM_013790	ENSMUSG00000022822	Abcc5	2900011L11Rik|AI132311|Abcc5a|Abcc5b|Mrp5	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	protein-coding
mm_103926.1	chr11	83648076	83648086	-	1	NA	3' UTR (NM_011337, exon 3 of 3)	3' UTR (NM_011337, exon 3 of 3)	1297	NM_011337	20302	Mm.1282	NM_011337	ENSMUSG00000000982	Ccl3	AI323804|G0S19-1|LD78alpha|MIP-1alpha|MIP1-(a)|MIP1-alpha|Mip1a|Scya3	chemokine (C-C motif) ligand 3	protein-coding
mm_55250.1	chr6	52866313	52866333	-	1	NA	intron (NM_173406, intron 2 of 4)	intron (NM_173406, intron 2 of 4)	43297	NM_001168277	231986	Mm.386865	NM_173406	ENSMUSG00000063568	Jazf1	AI591476|C820002C15|Jaz1|Tip27	JAZF zinc finger 1	protein-coding
mm_44977.1	chr5	36827308	36827319	-	1	NA	intron (NM_008550, intron 3 of 18)	intron (NM_008550, intron 3 of 18)	3336	NM_008550	17160	Mm.761	NM_008550	ENSMUSG00000029119	Man2b2	mKIAA0935	mannosidase 2, alpha B2	protein-coding
mm_9761.1	chr1	180885491	180885520	-	1	NA	Intergenic	GA-rich|Low_complexity|Low_complexity	-7603	NM_177099	320202	Mm.87078	NM_177099	ENSMUSG00000066652	Lefty2	6030463A22Rik|Ebaf|Lefta|Leftb|lefty-2|lefty-B	left-right determination factor 2	protein-coding
mm_7989.1	chr1	134234983	134235001	-	1	NA	promoter-TSS (NM_001291928)	promoter-TSS (NM_001291928)	-136	NM_001291928	11539	Mm.298908	NM_009629	ENSMUSG00000042429	Adora1	A1-AR|A1AR|A1R|AA1R|AI848715|BB176431|Ri	adenosine A1 receptor	protein-coding
mm_38266.1	chr4	136880576	136880594	-	1	NA	exon (NM_009777, exon 3 of 3)	exon (NM_009777, exon 3 of 3)	5592	NM_009777	12260	Mm.2570	NM_009777	ENSMUSG00000036905	C1qb	-	complement component 1, q subcomponent, beta polypeptide	protein-coding
mm_58616.1	chr7	5065065	5065075	+	1	NA	intron (NM_133671, intron 1 of 11)	intron (NM_133671, intron 1 of 11)	2927	NM_001205231	22185	Mm.360389	NM_133671	ENSMUSG00000030435	U2af2	65kDa	U2 small nuclear ribonucleoprotein auxiliary factor (U2AF) 2	protein-coding
mm_35397.1	chr4	34587049	34587088	-	1	NA	exon (NM_015824, exon 10 of 20)	exon (NM_015824, exon 10 of 20)	27874	NM_001159563	50793	Mm.399624	NM_015824	ENSMUSG00000040044	Orc3	Orc3l	origin recognition complex, subunit 3	protein-coding
mm_133797.1	chr16	95279355	95279367	+	1	NA	intron (NM_001271687, intron 3 of 4)	intron (NM_001271687, intron 3 of 4)	21803	NM_001271690	16516	Mm.272239	NM_019664	ENSMUSG00000062609	Kcnj15	4930414N08Rik|AI182284|AI267127|IRKK|Kir4.2	potassium inwardly-rectifying channel, subfamily J, member 15	protein-coding
mm_65920.1	chr7	30231706	30231716	-	1	NA	promoter-TSS (NM_027259)	promoter-TSS (NM_027259)	318	NM_025548	66411	Mm.27947	NM_025548	ENSMUSG00000006095	Tbcb	2410007D12Rik|AU041393|CG22|CKAPI|Ckap1	tubulin folding cofactor B	protein-coding
mm_14559.1	chr2	134786199	134786218	+	1	NA	promoter-TSS (NM_001145830)	promoter-TSS (NM_001145830)	44	NM_001145830	18795	Mm.330607	NM_019677	ENSMUSG00000051177	Plcb1	3110043I21Rik|AI132408|Plcb|mKIAA0581	phospholipase C, beta 1	protein-coding
mm_86240.1	chr9	120919327	120919337	-	1	NA	Intergenic	LTR16A2|LTR|ERVL	-4082	NR_040742	76402	Mm.436588	NR_040742	ENSMUSG00000100146	1700020M21Rik	-	RIKEN cDNA 1700020M21 gene	ncRNA
mm_51696.1	chr6	86571137	86571152	+	1	NA	Intergenic	Intergenic	43743	NR_037961	72012	Mm.349174	NR_037960	ENSMUSG00000097048	1600020E01Rik	-	RIKEN cDNA 1600020E01 gene	ncRNA
mm_43600.1	chr5	137831230	137831244	+	1	NA	exon (NM_153510, exon 3 of 7)	exon (NM_153510, exon 3 of 7)	5041	NM_153510	231805	Mm.379385	NM_153510	ENSMUSG00000046245	Pilra	AV021745|FDF03	paired immunoglobin-like type 2 receptor alpha	protein-coding
mm_142513.1	chr17	46202577	46202673	-	1	NA	promoter-TSS (NM_028198)	promoter-TSS (NM_028198)	0	NM_030715	80905	Mm.311585	NM_030715	ENSMUSG00000023953	Polh	RAD30A|XPV	polymerase (DNA directed), eta (RAD 30 related)	protein-coding
mm_117193.1	chr13	63566250	63566278	-	1	NA	promoter-TSS (NM_008957)	promoter-TSS (NM_008957)	-529	NM_008957	19206	Mm.228798	NM_008957	ENSMUSG00000021466	Ptch1	A230106A15Rik|Ptc|Ptc1|Ptch|mes	patched 1	protein-coding
mm_114751.1	chr13	84290291	84290300	+	1	NA	intron (NM_175187, intron 9 of 11)	intron (NM_175187, intron 9 of 11)	67999	NM_175187	72745	Mm.295063	NM_175187	ENSMUSG00000035762	Tmem161b	2810446P07Rik|AI843389	transmembrane protein 161B	protein-coding
mm_9375.1	chr1	172210194	172210204	-	1	NA	3' UTR (NM_009813, exon 11 of 11)	3' UTR (NM_009813, exon 11 of 11)	-3395	NM_011063	18611	Mm.544	NM_011063	ENSMUSG00000013698	Pea15a	Mat1|PEA-15|Pea15|Pkcs15	phosphoprotein enriched in astrocytes 15A	protein-coding
mm_133671.1	chr16	92082493	92082514	+	1	NA	3' UTR (NM_017391, exon 2 of 2)	3' UTR (NM_017391, exon 2 of 2)	24167	NM_080456	121022	Mm.217354	NM_080456	ENSMUSG00000039680	Mrps6	AW046321	mitochondrial ribosomal protein S6	protein-coding
mm_115882.1	chr13	21783392	21783406	-	1	NA	promoter-TSS (NM_178207)	promoter-TSS (NM_178207)	-2	NM_178207	319153	Mm.390558	NM_178207	ENSMUSG00000101972	Hist1h3i	H3-H	histone cluster 1, H3i	protein-coding
mm_167287.1	chr8	41100775	41100778	+	1	NA	intron (NM_001005863, intron 1 of 13)	intron (NM_001005863, intron 1 of 13)	13891	NM_001286413	102103	Mm.149438	NM_001005863	ENSMUSG00000045636	Mtus1	AI481402|ATBP135|Atip1|B430010I23Rik|B430305I03Rik|C85752|Cctsg1-440|MD44|MTSG1|mKIAA1288	mitochondrial tumor suppressor 1	protein-coding
mm_57896.1	chr6	131376088	131376103	-	1	NA	exon (NM_139117, exon 6 of 10)	exon (NM_139117, exon 6 of 10)	12355	NM_139117	56449	Mm.458000	NM_011733	ENSMUSG00000030189	Ybx3	Csda|Dpba|MSY3|MSY4|Yb2|dbpA|oxyR	Y box protein 3	protein-coding
mm_55345.1	chr6	56715453	56715468	-	1	NA	intron (NM_030235, intron 1 of 15)	CpG	555	NM_030235	78937	Mm.105343	NM_030235	ENSMUSG00000029787	Avl9	5830411G16Rik|D730049P16Rik|mKIAA0241	AVL9 cell migration associated	protein-coding
mm_54249.1	chr6	28261121	28261133	-	1	NA	intron (NM_001081678, intron 1 of 5)	CpG	474	NM_001081678	627049	Mm.84441	NM_001081678	ENSMUSG00000039841	Zfp800	AA407452|Znf800	zinc finger protein 800	protein-coding
mm_13250.1	chr2	98663801	98663805	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	1196146	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_31070.1	chr4	41352610	41352615	+	1	NA	intron (NM_023305, intron 1 of 6)	B1_Mus2|SINE|Alu	3616	NM_023305	67123	Mm.289795	NM_023305	ENSMUSG00000028437	Ubap1	2700092A01Rik|NAG20|UBAP-1|Ubap	ubiquitin-associated protein 1	protein-coding
mm_63310.1	chr7	126862573	126862586	+	1	NA	intron (NM_172746, intron 1 of 6)	CpG	607	NM_172746	233876	Mm.363427	NM_172746	ENSMUSG00000042606	Hirip3	B130036O03|C86302	HIRA interacting protein 3	protein-coding
mm_124380.1	chr14	108813926	108813936	-	1	NA	Intergenic	Lx7|LINE|L1	100308	NM_199065	76965	Mm.257268	NM_199065	ENSMUSG00000075478	Slitrk1	3200001I04Rik	SLIT and NTRK-like family, member 1	protein-coding
mm_122210.1	chr14	32085596	32085639	-	1	NA	promoter-TSS (NM_001284346)	promoter-TSS (NM_001284346)	75	NR_104303	105638	Mm.2519	NM_172254	ENSMUSG00000021905	Dph3	DELGIP1|DelgipP1|Desr1|KTI11|Zcsl2	diphthamine biosynthesis 3	protein-coding
mm_10705.1	chr2	22774082	22774096	+	1	NA	promoter-TSS (NM_019456)	promoter-TSS (NM_019456)	-238	NM_019456	54519	Mm.14255	NM_019456	ENSMUSG00000026786	Apbb1ip	9930118P07Rik|Prp48	amyloid beta (A4) precursor protein-binding, family B, member 1 interacting protein	protein-coding
mm_19329.1	chr2	90577395	90577402	-	1	NA	intron (NM_008982, intron 1 of 23)	B1_Mur1|SINE|Alu	3249	NM_008982	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_51267.1	chr6	72098815	72098823	+	1	NA	intron (NM_011375, intron 1 of 6)	intron (NM_011375, intron 1 of 6)	1211	NM_011375	20454	Mm.38248	NM_011375	ENSMUSG00000056091	St3gal5	3S-T|Siat9|[a]2	ST3 beta-galactoside alpha-2,3-sialyltransferase 5	protein-coding
mm_10035.1	chr1	192834558	192834558	-	1	NA	Intergenic	Intergenic	-7147	NR_040468	73455	Mm.414869	NR_040468		1700065J18Rik	-	RIKEN cDNA 1700065J18 gene	ncRNA
mm_49984.1	chr6	41033071	41033088	+	1	NA	exon (NM_023333, exon 3 of 5)	exon (NM_023333, exon 3 of 5)	2430	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_87739.1	chr10	60219029	60219034	+	1	NA	5' UTR (NM_016803, exon 1 of 4)	5' UTR (NM_016803, exon 1 of 4)	229	NM_016803	53374	Mm.12866	NM_016803	ENSMUSG00000057337	Chst3	C6ST|C6ST-1|GST-0	carbohydrate (chondroitin 6/keratan) sulfotransferase 3	protein-coding
mm_45514.1	chr5	72504336	72504346	-	1	NA	promoter-TSS (NM_016869)	promoter-TSS (NM_016869)	-133	NM_016869	53419	Mm.332425	NM_016869	ENSMUSG00000005220	Corin	AV273130|Lrp4	corin	protein-coding
mm_52445.1	chr6	113654371	113654394	+	1	NA	intron (NM_001113553, intron 2 of 11)	intron (NM_001113553, intron 2 of 11)	15915	NM_001113553	108960	Mm.152142	NM_172161	ENSMUSG00000060477	Irak2	6330415L08Rik|AI649099|IRAK-2	interleukin-1 receptor-associated kinase 2	protein-coding
mm_40552.1	chr5	58226618	58226628	+	1	NA	Intergenic	MERV1_LTR|LTR|ERV1	226375	NR_046190	78163	Mm.243828	NR_046190	ENSMUSG00000105234	4930459L07Rik	-	RIKEN cDNA 4930459L07 gene	ncRNA
mm_166169.1	chr5	23501592	23501608	+	1	NA	exon (NM_026984, exon 26 of 26)	exon (NM_026984, exon 26 of 26)	67171	NM_026984	69188	Mm.205190	NM_026984	ENSMUSG00000029004	Kmt2e	1810033J14Rik|9530077A04Rik|D230038D11Rik|Mll5|NKp44L	lysine (K)-specific methyltransferase 2E	protein-coding
mm_7056.1	chr1	87156128	87156145	-	1	NA	promoter-TSS (NM_001277925)	promoter-TSS (NM_001277925)	0	NM_001277925	13599	Mm.140765	NM_021306	ENSMUSG00000026247	Ecel1	DINE|xce	endothelin converting enzyme-like 1	protein-coding
mm_67333.1	chr7	79743016	79743033	-	1	NA	promoter-TSS (NM_001037927)	promoter-TSS (NM_001037927)	1	NM_011068	18631	Mm.20615	NM_011068	ENSMUSG00000030545	Pex11a	PEX11alpha	peroxisomal biogenesis factor 11 alpha	protein-coding
mm_51258.1	chr6	72097345	72097357	+	1	NA	promoter-TSS (NM_011375)	promoter-TSS (NM_011375)	-257	NM_001035228	20454	Mm.38248	NM_011375	ENSMUSG00000056091	St3gal5	3S-T|Siat9|[a]2	ST3 beta-galactoside alpha-2,3-sialyltransferase 5	protein-coding
mm_121674.1	chr14	12616128	12616146	-	1	NA	exon (NM_001042617, exon 4 of 31)	exon (NM_001042617, exon 4 of 31)	206942	NM_001042617	27062	Mm.260881	NM_012061	ENSMUSG00000054423	Cadps	AU067781|CAPS|CAPS1|mKIAA1121	Ca2+-dependent secretion activator	protein-coding
mm_37536.1	chr4	125065604	125065672	-	1	NA	promoter-TSS (NM_175223)	promoter-TSS (NM_175223)	19	NM_175223	75563	Mm.50304	NM_175223	ENSMUSG00000042707	Dnali1	1700023A09Rik|AW049135	dynein, axonemal, light intermediate polypeptide 1	protein-coding
mm_36488.1	chr4	83052230	83052241	-	1	NA	promoter-TSS (NM_001198811)	promoter-TSS (NM_001198811)	-68	NM_001198811	329872	Mm.242337	NM_177863	ENSMUSG00000059049	Frem1	BC037594|D430009N09|D630008K06|crf11|eye<m02Jus>|eyes2|heb|qbrick	Fras1 related extracellular matrix protein 1	protein-coding
mm_27645.1	chr3	63893828	63893855	-	1	NA	Intergenic	Intergenic	35544	NM_177856	329659	Mm.39342	NM_177856	ENSMUSG00000048581	E130311K13Rik	-	RIKEN cDNA E130311K13 gene	protein-coding
mm_8487.1	chr1	153620728	153620736	-	1	NA	Intergenic	AT_rich|Low_complexity|Low_complexity	-32305	NM_026380	67792	Mm.379143	NM_026380	ENSMUSG00000042671	Rgs8	6530413N01Rik	regulator of G-protein signaling 8	protein-coding
mm_123341.1	chr14	63136516	63136531	-	1	NA	exon (NM_007798, exon 5 of 10)	exon (NM_007798, exon 5 of 10)	14061	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_46024.1	chr5	91014499	91014504	-	1	NA	intron (NM_026788, intron 7 of 7)	intron (NM_026788, intron 7 of 7)	-13016	NM_053087	71920	Mm.197319	NM_053087	ENSMUSG00000035020	Epgn	2310069M11Rik|epigen	epithelial mitogen	protein-coding
mm_137150.1	chr17	23679673	23679736	+	1	NA	intron (NM_018777, intron 1 of 2)	CpG	339	NM_018777	54419	Mm.86421	NM_018777	ENSMUSG00000023906	Cldn6	AL024037	claudin 6	protein-coding
mm_93945.1	chr10	127230685	127230690	-	1	NA	intron (NM_008447, intron 25 of 27)	intron (NM_008447, intron 25 of 27)	-19065	NM_054097	117150	Mm.22682	NM_054097	ENSMUSG00000025417	Pip4k2c	Pip5k2c	phosphatidylinositol-5-phosphate 4-kinase, type II, gamma	protein-coding
mm_162348.1	chr1	53825178	53825186	+	1	NA	intron (NM_001001883, intron 28 of 28)	intron (NM_001001883, intron 28 of 28)	-24242	NR_106149	102465783		NR_106149	ENSMUSG00000098443	Mir7681	Gm27806|mmu-mir-7681	microRNA 7681	ncRNA
mm_53963.1	chr6	5496297	5496316	-	1	NA	promoter-TSS (NM_013743)	promoter-TSS (NM_013743)	-28	NM_013743	27273	Mm.235547	NM_013743	ENSMUSG00000019577	Pdk4	AV005916	pyruvate dehydrogenase kinase, isoenzyme 4	protein-coding
mm_20413.1	chr2	129300338	129300340	-	1	NA	3' UTR (NM_010554, exon 7 of 7)	3' UTR (NM_010554, exon 7 of 7)	2969	NR_040371	100503468	Mm.446943	NR_040371	ENSMUSG00000085498	Gm14023	OTTMUSG00000015408	predicted gene 14023	ncRNA
mm_106511.1	chr11	120492541	120492551	-	1	NA	intron (NM_013770, intron 1 of 10)	intron (NM_013770, intron 1 of 10)	709	NM_013770	27376	Mm.3991	NM_013770	ENSMUSG00000025792	Slc25a10	Dic	solute carrier family 25 (mitochondrial carrier, dicarboxylate transporter), member 10	protein-coding
mm_2580.1	chr1	118569905	118569908	+	1	NA	intron (NM_001293300, intron 34 of 40)	intron (NM_001293300, intron 34 of 40)	-58039	NM_023755	81879	Mm.24621	NM_023755	ENSMUSG00000026380	Tfcp2l1	1810030F05Rik|4932442M07Rik|AA575098|Cp2l1|Crtr-1|D930018N21Rik|LBP-9|Tcfcp2l1	transcription factor CP2-like 1	protein-coding
mm_103227.1	chr11	70670005	70670023	-	1	NA	promoter-TSS (NM_001167669)	promoter-TSS (NM_001167669)	-598	NM_001167669	216873	Mm.432524	NM_172561	ENSMUSG00000018287	Spag7	5730443G10|ACRP|FSA-1|Fsa1l	sperm associated antigen 7	protein-coding
mm_110146.1	chr12	26448683	26448713	-	1	NA	exon (NM_021384, exon 4 of 6)	exon (NM_021384, exon 4 of 6)	7754	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_44912.1	chr5	35664059	35664072	-	1	NA	exon (NM_001042615, exon 6 of 7)	exon (NM_001042615, exon 6 of 7)	15715	NM_001042615	78558	Mm.274255	NM_030127	ENSMUSG00000029096	Htra3	2210021K23Rik|9530081K03Rik|Prsp|Tasp	HtrA serine peptidase 3	protein-coding
mm_143508.1	chr17	71752921	71752925	-	1	NA	promoter-TSS (NM_146082)	promoter-TSS (NM_146082)	-38	NM_146082	225004	Mm.134151	NM_146082	ENSMUSG00000044375	BC027072	-	cDNA sequence BC027072	protein-coding
mm_92354.1	chr10	75920203	75920206	-	1	NA	intron (NM_011418, intron 1 of 8)	intron (NM_011418, intron 1 of 8)	1410	NM_011418	20587	Mm.279751	NM_011418	ENSMUSG00000000902	Smarcb1	AU020204|Baf47|Ini1|SNF5/INI1|Snf5	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1	protein-coding
mm_7487.1	chr1	121327735	121327768	-	1	NA	promoter-TSS (NM_001271531)	promoter-TSS (NM_001271531)	-73	NM_001271531	72999	Mm.27136	NM_133748	ENSMUSG00000003721	Insig2	2900053I11Rik|C730043J18Rik|Insig-2	insulin induced gene 2	protein-coding
mm_113717.1	chr13	43615999	43616016	+	1	NA	5' UTR (NM_183204, exon 1 of 2)	5' UTR (NM_183204, exon 1 of 2)	210	NM_183204	328234	Mm.40588	NM_183204	ENSMUSG00000044164	Rnf182	C630023L15Rik	ring finger protein 182	protein-coding
mm_16084.1	chr2	168670202	168670210	+	1	NA	intron (NM_001289446, intron 13 of 27)	intron (NM_001289446, intron 13 of 27)	-29447	NR_105971	102466784		NR_105971	ENSMUSG00000105496	Mir7004	mmu-mir-7004	microRNA 7004	ncRNA
mm_34601.1	chr4	150237203	150237208	+	1	NA	promoter-TSS (NM_001025388).2	promoter-TSS (NM_001025388).2	8	NM_023119	13806	Mm.70666	NM_023119	ENSMUSG00000063524	Eno1	0610008I15|AL022784|Eno-1|MBP-1	enolase 1, alpha non-neuron	protein-coding
mm_95834.1	chr11	57011560	57011587	+	1	NA	promoter-TSS (NM_001113325)	promoter-TSS (NM_001113325)	-45	NM_001113325	14799	Mm.4920	NM_008165	ENSMUSG00000020524	Gria1	2900051M01Rik|Glr-1|Glr1|GluA1|GluR-A|GluRA|Glur-1|Glur1|HIPA1|gluR-K1	glutamate receptor, ionotropic, AMPA1 (alpha 1)	protein-coding
mm_7726.1	chr1	130716006	130716032	-	1	NA	promoter-TSS (NM_008825)	promoter-TSS (NM_008825)	-198	NM_008825	18640	Mm.249861	NM_008825	ENSMUSG00000026409	Pfkfb2	4930568D07Rik	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2	protein-coding
mm_54079.1	chr6	15683451	15683456	-	1	NA	Intergenic	Intergenic	-37208	NM_175088	16543	Mm.1314	NM_175088	ENSMUSG00000041390	Mdfic	Kdt1|Mdfid	MyoD family inhibitor domain containing	protein-coding
mm_16810.1	chr2	11170068	11170087	-	1	NA	Intergenic	Intergenic	-2305	NM_008859	18761	Mm.329993	NM_008859	ENSMUSG00000026778	Prkcq	A130035A12Rik|AW494342|PKC-0|PKC-theta|PKCtheta|Pkcq	protein kinase C, theta	protein-coding
mm_16075.1	chr2	168230598	168230639	+	1	NA	promoter-TSS (NM_010072)	promoter-TSS (NM_010072)	-4	NM_001160330	69372	Mm.482182	NM_001160330	ENSMUSG00000074576	Mocs3	1700020H17Rik|Uba4	molybdenum cofactor synthesis 3	protein-coding
mm_21436.1	chr2	158610567	158610580	-	1	NA	promoter-TSS (NM_009508)	promoter-TSS (NM_009508)	150	NR_040358	100045469	Mm.143404	NR_040358	ENSMUSG00000086496	Gm14204	OTTMUSG00000015935	predicted gene 14204	ncRNA
mm_19197.1	chr2	84443157	84443177	-	1	NA	intron (NM_001177320, intron 7 of 7)	intron (NM_001177320, intron 7 of 7)	-17901	NM_018782	54598	Mm.75467	NM_018782	ENSMUSG00000059588	Calcrl	AV071593|CRLR	calcitonin receptor-like	protein-coding
mm_154655.1	chrX	7841942	7841966	+	1	NA	promoter-TSS (NM_001290537)	promoter-TSS (NM_001290537)	123	NM_138604	54644	Mm.142827	NM_138604	ENSMUSG00000031154	Otud5	AA407879|AI553596|BB114028|DUBA|DXImx46e|Sfc7	OTU domain containing 5	protein-coding
mm_166506.1	chr6	4759829	4759835	+	1	NA	3' UTR (NM_130877, exon 2 of 2)	3' UTR (NM_130877, exon 2 of 2)	12526	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_28708.1	chr3	95650507	95650526	-	1	NA	Intergenic	ID_B1|SINE|B4	-8205	NM_008562	17210	Mm.1639	NM_008562	ENSMUSG00000038612	Mcl1	AW556805|Mcl-1	myeloid cell leukemia sequence 1	protein-coding
mm_6806.1	chr1	84156072	84156093	-	1	NA	intron (NM_001003948, intron 2 of 2)	intron (NM_001003948, intron 2 of 2)	62879	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_167472.1	chr8	127063993	127064006	+	1	NA	promoter-TSS (NM_033620)	promoter-TSS (NM_033620)	-57	NM_033620	93742	Mm.299254	NM_033620	ENSMUSG00000025812	Pard3	AA960621|AI256638|Asip|D8Ertd580e|Par-3|Par3|Pard-3|Pard3a|Phip	par-3 family cell polarity regulator	protein-coding
mm_22831.1	chr3	27317020	27317026	+	1	NA	promoter-TSS (NM_009425)	promoter-TSS (NM_009425)	-54	NM_009425	22035	Mm.1062	NM_009425	ENSMUSG00000039304	Tnfsf10	A330042I21Rik|AI448571|APO-2L|Ly81|TL2|Tnlg6a|Trail	tumor necrosis factor (ligand) superfamily, member 10	protein-coding
mm_129678.1	chr15	81399657	81399732	-	1	NA	promoter-TSS (NM_133726)	promoter-TSS (NM_133726)	0	NM_133726	70356	Mm.180337	NM_133726	ENSMUSG00000022403	St13	1110007I03Rik|3110002K08Rik|AW555194|HIP|HOP|HSPABP|HSPABP1|PRO0786|SNC6|p48	suppression of tumorigenicity 13	protein-coding
mm_71973.1	chr8	70583535	70583537	+	1	NA	intron (NM_007924, intron 5 of 11)	intron (NM_007924, intron 5 of 11)	-10945	NM_023627	71780	Mm.29357	NM_023627	ENSMUSG00000019139	Isyna1	1300017C10Rik|AU018670	myo-inositol 1-phosphate synthase A1	protein-coding
mm_80653.1	chr9	90054346	90054379	+	1	NA	promoter-TSS (NM_007801)	promoter-TSS (NM_007801)	95	NM_001312649	13036	Mm.2277	NM_007801	ENSMUSG00000032359	Ctsh	AL022844	cathepsin H	protein-coding
mm_172355.1	chr7	11478031	11478043	+	1	NA	Intergenic	Intergenic	80122	NM_001110316	665902	Mm.425380	NM_001110316	ENSMUSG00000070828	Zscan4f	C330039H09Rik	zinc finger and SCAN domain containing 4F	protein-coding
mm_45665.1	chr5	77211145	77211154	-	1	NA	promoter-TSS (NM_001289767)	promoter-TSS (NM_001289767)	56	NM_001289767	69982	Mm.46106	NM_183284	ENSMUSG00000053030	Spink2	1700007F22Rik|AV038945|HUSI-II	serine peptidase inhibitor, Kazal type 2	protein-coding
mm_18410.1	chr2	60553278	60553302	-	1	NA	promoter-TSS (NM_008867)	promoter-TSS (NM_008867)	18	NM_008867	18779	Mm.5092	NM_008867	ENSMUSG00000054580	Pla2r1	Pla2-r|Pla2g1br|Pla2r	phospholipase A2 receptor 1	protein-coding
mm_154742.1	chrX	10319842	10319873	+	1	NA	exon (NM_008769, exon 10 of 10)	exon (NM_008769, exon 10 of 10)	67552	NM_008769	18416	Mm.2611	NM_008769	ENSMUSG00000031173	Otc	AI265390|Sf|spf	ornithine transcarbamylase	protein-coding
mm_39822.1	chr5	30797188	30797205	+	1	NA	3' UTR (NM_023047, exon 13 of 13)	3' UTR (NM_023047, exon 13 of 13)	-17445	NM_133350	100732	Mm.332295	NM_133350	ENSMUSG00000029166	Mapre3	AI790651|EB2|EB3|EBF3|RP3	microtubule-associated protein, RP/EB family, member 3	protein-coding
mm_146801.1	chr18	20738638	20738641	-	1	NA	intron (NM_019737, intron 1 of 8)	intron (NM_019737, intron 1 of 8)	7765	NM_019737	56386	Mm.393827	NM_019737	ENSMUSG00000056124	B4galt6	AA536803|AU022389	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 6	protein-coding
mm_119731.1	chr14	54075733	54075746	+	1	NA	Intergenic	Intergenic	178190	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_94153.1	chr10	128744241	128744252	-	1	NA	promoter-TSS (NM_016811)	promoter-TSS (NM_016811)	-190	NM_016811	13139	Mm.291235	NM_016811	ENSMUSG00000025357	Dgka	80kDa|AW146112|Dagk1	diacylglycerol kinase, alpha	protein-coding
mm_127155.1	chr15	98571050	98571059	+	1	NA	promoter-TSS (NM_001201322)	promoter-TSS (NM_001201322)	50	NM_001201322	73863	Mm.66894	NM_001201322	ENSMUSG00000022993	4930415O20Rik	-	RIKEN cDNA 4930415O20 gene	protein-coding
mm_123906.1	chr14	73322227	73322242	-	1	NA	intron (NM_009029, intron 1 of 26)	intron (NM_009029, intron 1 of 26)	3557	NM_009029	19645	Mm.273862	NM_009029	ENSMUSG00000022105	Rb1	Rb|Rb-1|pRb	retinoblastoma 1	protein-coding
mm_100855.1	chr11	5837761	5837835	-	1	NA	5' UTR (NM_017401, exon 1 of 11)	5' UTR (NM_017401, exon 1 of 11)	218	NM_017401	54125	Mm.260194	NM_017401	ENSMUSG00000020474	Polm	AI462166|B230309I03Rik|Tdt-N	polymerase (DNA directed), mu	protein-coding
mm_88053.1	chr10	67540748	67540751	+	1	NA	exon (NM_010118, exon 2 of 2)	exon (NM_010118, exon 2 of 2)	2819	NM_001347458	13654	Mm.290421	NM_010118	ENSMUSG00000037868	Egr2	Egr-2|Krox-20|Krox20|NGF1-B|Zfp-25|Zfp-6	early growth response 2	protein-coding
mm_95794.1	chr11	55098043	55098102	+	1	NA	promoter-TSS (NM_010299)	promoter-TSS (NM_010299)	87	NM_010299	14667	Mm.287807	NM_010299	ENSMUSG00000000594	Gm2a	AA408702|AW215435|GM2-AP|SAP-3	GM2 ganglioside activator protein	protein-coding
mm_107273.1	chr12	29533452	29533467	+	1	NA	intron (NM_001093778, intron 1 of 24)	intron (NM_001093778, intron 1 of 24)	-1446	NM_001093776	17933	Mm.253067	NM_008666	ENSMUSG00000061911	Myt1l	2900046C06Rik|2900093J19Rik|C630034G21Rik|Nztf1|Pmng1|Png-1|mKIAA1106	myelin transcription factor 1-like	protein-coding
mm_10005.1	chr1	191575491	191575526	-	1	NA	promoter-TSS (NM_178632)	promoter-TSS (NM_178632)	36	NM_001305233	76843	Mm.189102	NM_029766	ENSMUSG00000037474	Dtl	2810047L02Rik|5730564G15Rik|L2dtl|Ramp	denticleless E3 ubiquitin protein ligase	protein-coding
mm_162635.1	chr1	190170264	190170268	+	1	NA	intron (NM_008937, intron 1 of 4)	intron (NM_008937, intron 1 of 4)	414	NM_008937	19130	Mm.132579	NM_008937	ENSMUSG00000010175	Prox1	A230003G05Rik	prospero homeobox 1	protein-coding
mm_75807.1	chr8	70234098	70234160	-	1	NA	promoter-TSS (NM_001168290)	promoter-TSS (NM_001168290)	-97	NM_001168290	234373	Mm.284505	NM_172755	ENSMUSG00000036054	Sugp2	Sfrs14|Srsf14|mKIAA0365	SURP and G patch domain containing 2	protein-coding
mm_45413.1	chr5	66337648	66337677	-	1	NA	promoter-TSS (NM_001201416)	promoter-TSS (NM_001201416)	3	NM_001201416	11787	Mm.5159	NM_009686	ENSMUSG00000029207	Apbb2	2310007D03Rik|FE65L1|Rirl1|TR2L|Zfra	amyloid beta (A4) precursor protein-binding, family B, member 2	protein-coding
mm_35134.1	chr4	11385427	11385437	-	1	NA	intron (NM_001347052, intron 2 of 13)	CpG	1346	NM_001347052	207920	Mm.387719	NM_194055	ENSMUSG00000040728	Esrp1	2210008M09Rik|A630065D16|BC031468|Rbm35a	epithelial splicing regulatory protein 1	protein-coding
mm_18817.1	chr2	74579408	74579417	-	1	NA	promoter-TSS (NM_027133)	promoter-TSS (NM_027133)	-464	NM_027133	69605	Mm.156113	NM_027133	ENSMUSG00000009207	Lnpk	2310011O18Rik|4921514L11Rik|9530051D01Rik|AI666268|Lnp|Lnpk1|Ul|ulnaless	lunapark, ER junction formation factor	protein-coding
mm_144884.1	chr18	36796521	36796536	+	1	NA	exon (NM_025594, exon 5 of 6)	exon (NM_025594, exon 5 of 6)	2605	NM_025594	66492	Mm.251155	NM_025594	ENSMUSG00000001383	Zmat2	2610510D14Rik|2900082I05Rik	zinc finger, matrin type 2	protein-coding
mm_120318.1	chr14	63142815	63142834	+	1	NA	3' UTR (NM_007798, exon 10 of 10)	3' UTR (NM_007798, exon 10 of 10)	20362	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_71127.1	chr8	36458162	36458206	+	1	NA	Intergenic	CpG	-31007	NM_176952	319582	Mm.180924	NM_176952	ENSMUSG00000039620	6430573F11Rik	Kiaa1456|TRM9L	RIKEN cDNA 6430573F11 gene	protein-coding
mm_51810.1	chr6	88827395	88827402	+	1	NA	3' UTR (NM_001166251, exon 8 of 8)	3' UTR (NM_001166251, exon 8 of 8)	14537	NM_030251	80283	Mm.166858	NM_030251	ENSMUSG00000030083	Abtb1	AI847549|BC003234|BPOZ|EF1ABP	ankyrin repeat and BTB (POZ) domain containing 1	protein-coding
mm_95292.1	chr11	45981233	45981242	+	1	NA	exon (NM_173384, exon 1 of 5)	exon (NM_173384, exon 1 of 5)	927	NM_173384	214105	Mm.66708	NM_173384	ENSMUSG00000040489	Sox30	-	SRY (sex determining region Y)-box 30	protein-coding
mm_75535.1	chr8	57320432	57320471	-	1	NA	promoter-TSS (NM_010402)	promoter-TSS (NM_010402)	408	NR_110474	102636514		NR_110474	ENSMUSG00000100510	Uph	-	upperhand	ncRNA
mm_73989.1	chr8	120668313	120668318	+	1	NA	promoter-TSS (NM_009941)	promoter-TSS (NM_009941)	-5	NM_001293559	12857	Mm.386758	NM_009941	ENSMUSG00000031818	Cox4i1	AL024441|COX|COX IV-1|COXIV|Cox4|Cox4a|IV-1	cytochrome c oxidase subunit IV isoform 1	protein-coding
mm_130818.1	chr15	101786555	101786568	-	1	NA	promoter-TSS (NM_213728)	promoter-TSS (NM_213728)	-103	NM_213728	105866	Mm.298210	NM_213728	ENSMUSG00000056605	Krt72	AI507495|K6irs2|Krt2-35|Krt72-ps	keratin 72	protein-coding
mm_155682.1	chrX	93675089	93675161	+	1	NA	promoter-TSS (NM_211138)	promoter-TSS (NM_211138)	13	NM_211138	236899	Mm.166467	NM_177546	ENSMUSG00000035246	Pcyt1b	AW045697|CTTbeta	phosphate cytidylyltransferase 1, choline, beta isoform	protein-coding
mm_154600.1	chrX	7593504	7593511	+	1	NA	TTS (NM_138603)	TTS (NM_138603)	11913	NM_138603	54638	Mm.288192	NM_138603	ENSMUSG00000031143	Ccdc22	AI481216|DXImx40e|Ppp1r3f|Sfc22	coiled-coil domain containing 22	protein-coding
mm_166660.1	chr6	88075032	88075043	-	1	NA	Intergenic	Intergenic	-9436	NM_133933	103963	Mm.188544	NM_133933	ENSMUSG00000030062	Rpn1	AU018702|D6Wsu137e|Rpn-1	ribophorin I	protein-coding
mm_146244.1	chr18	77564142	77564149	+	1	NA	intron (NM_001164504, intron 1 of 7)	intron (NM_001164504, intron 1 of 7)	991	NM_001164504	225743	Mm.23293	NM_001164504	ENSMUSG00000025427	Rnf165	2900024M11Rik|AI427432|Akd2|Ark2c|G630064H08Rik|Gm96	ring finger protein 165	protein-coding
mm_27476.1	chr3	53463235	53463306	-	1	NA	promoter-TSS (NM_172501)	promoter-TSS (NM_172501)	-12	NM_172501	212114	Mm.85744	NM_172501	ENSMUSG00000042997	Nhlrc3	4833441N19|8030451K01Rik|mKIAA4083	NHL repeat containing 3	protein-coding
mm_140696.1	chr17	13899205	13899211	-	1	NA	exon (NM_010806, exon 31 of 33)	exon (NM_010806, exon 31 of 33)	-49165	NM_001122977	635895	Mm.388844	NM_001122977	ENSMUSG00000067941	Gm7168	EG635895	predicted gene 7168	protein-coding
mm_21099.1	chr2	153232118	153232129	-	1	NA	exon (NM_018807, exon 3 of 3)	exon (NM_018807, exon 3 of 3)	-6682	NM_198617	241732	Mm.277243	NM_198617	ENSMUSG00000074671	Tspyl3	AW212607|Gm36	TSPY-like 3	protein-coding
mm_112854.1	chr13	20837219	20837240	+	1	NA	intron (NM_012054, intron 2 of 20)	Lx7|LINE|L1	43116	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_73253.1	chr8	104339348	104339396	+	1	NA	Intergenic	Intergenic	-1222	NM_024217	68119	Mm.390108	NM_024217	ENSMUSG00000031875	Cmtm3	9430096L06Rik|AI413895|BNAS2|Cklfsf3	CKLF-like MARVEL transmembrane domain containing 3	protein-coding
mm_7045.1	chr1	87125734	87125740	-	1	NA	exon (NM_007432, exon 4 of 11)	exon (NM_007432, exon 4 of 11)	729	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_98027.1	chr11	85194334	85194352	+	1	NA	intron (NM_025825, intron 12 of 12)	intron (NM_025825, intron 12 of 12)	23247	NM_028589	73634	Mm.48850	NM_028589	ENSMUSG00000018479	1700125H20Rik	-	RIKEN cDNA 1700125H20 gene	protein-coding
mm_8108.1	chr1	135852238	135852261	-	1	NA	TTS (NM_001130176)	TTS (NM_001130176)	11388	NM_001130176	21956	Mm.247470	NM_011619	ENSMUSG00000026414	Tnnt2	Tnt|cTnT	troponin T2, cardiac	protein-coding
mm_41165.1	chr5	87956274	87956315	+	1	NA	intron (NR_045924, intron 1 of 4)	intron (NR_045924, intron 1 of 4)	23057	NR_045924	73471	Mm.396240	NR_045924	ENSMUSG00000099605	1700066N21Rik	-	RIKEN cDNA 1700066N21 gene	ncRNA
mm_13323.1	chr2	102778270	102778274	+	1	NA	TTS (NM_011393)	TTS (NM_011393)	71834	NM_001077515	20511	Mm.267547	NM_011393	ENSMUSG00000005089	Slc1a2	1700091C19Rik|2900019G14Rik|AI159670|Eaat2|GLT-1|GLT1|MGLT1	solute carrier family 1 (glial high affinity glutamate transporter), member 2	protein-coding
mm_9667.1	chr1	177796717	177796725	-	1	NA	promoter-TSS (NM_007422)	promoter-TSS (NM_007422)	-212	NM_007422	11566	Mm.338021	NM_007422	ENSMUSG00000015961	Adss	AI314886|AS|Adss2	adenylosuccinate synthetase, non muscle	protein-coding
mm_165920.1	chr4	59402046	59402050	+	1	NA	intron (NM_001163288, intron 5 of 16)	intron (NM_001163288, intron 5 of 16)	36585	NM_001163288	634731	Mm.483589	NM_001163288	ENSMUSG00000038578	Susd1	A530080P10|Gm12528|OTTMUSG00000007332	sushi domain containing 1	protein-coding
mm_154929.1	chrX	35888624	35888634	+	1	NA	promoter-TSS (NM_001009947)	promoter-TSS (NM_001009947)	-203	NM_001009947	75974	Mm.32873	NM_177745	ENSMUSG00000031093	Dock11	5033414A21Rik|8030476J24|Zizimin2|sph238	dedicator of cytokinesis 11	protein-coding
mm_77513.1	chr8	122893983	122894013	-	1	NA	non-coding (NR_037865, exon 10 of 14)	non-coding (NR_037865, exon 10 of 14)	45624	NM_007662	12555	Mm.1976	NM_007662	ENSMUSG00000031962	Cdh15	AI323380|Cdh14|Mcad	cadherin 15	protein-coding
mm_10625.1	chr2	19657721	19657784	+	1	NA	promoter-TSS (NM_027715)	promoter-TSS (NM_027715)	145	NR_033642	100041244	Mm.407223	NR_033642		Gm3230	-	predicted gene 3230	ncRNA
mm_10056.1	chr1	193242427	193242433	-	1	NA	promoter-TSS (NM_001044751)	promoter-TSS (NM_001044751)	-70	NM_001044751	15483	Mm.28328	NM_008288	ENSMUSG00000016194	Hsd11b1	-	hydroxysteroid 11-beta dehydrogenase 1	protein-coding
mm_106619.1	chr11	120820617	120820636	-	1	NA	exon (NM_007988, exon 5 of 43)	exon (NM_007988, exon 5 of 43)	3921	NM_007988	14104	Mm.236443	NM_007988	ENSMUSG00000025153	Fasn	A630082H08Rik|FAS	fatty acid synthase	protein-coding
mm_48577.1	chr5	143505940	143505943	-	1	NA	3' UTR (NM_009007, exon 6 of 6)	3' UTR (NM_009007, exon 6 of 6)	22052	NM_009007	19353	Mm.292510	NM_009007	ENSMUSG00000001847	Rac1	AL023026|D5Ertd559e	RAS-related C3 botulinum substrate 1	protein-coding
mm_91917.1	chr10	60299212	60299239	-	1	NA	exon (NM_011179, exon 9 of 15)	exon (NM_011179, exon 9 of 15)	14764	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_33461.1	chr4	130792695	130792720	+	1	NA	exon (NM_011520, exon 1 of 5)	exon (NM_011520, exon 1 of 5)	170	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_96863.1	chr11	70130144	70130163	+	1	NA	promoter-TSS (NM_145137)	promoter-TSS (NM_145137)	-204	NM_145137	216864	Mm.222465	NM_145137	ENSMUSG00000040950	Mgl2	CD301b	macrophage galactose N-acetyl-galactosamine specific lectin 2	protein-coding
mm_81049.1	chr9	105495233	105495249	+	1	NA	promoter-TSS (NM_175025)	promoter-TSS (NM_175025)	-108	NM_001253836	235574	Mm.326247	NM_175025	ENSMUSG00000032570	Atp2c1	1700121J11Rik|ATP2C1A|AW061228|BCPM|D930003G21Rik|HHD|SPCA|pmr1	ATPase, Ca++-sequestering	protein-coding
mm_43859.1	chr5	143464526	143464536	+	1	NA	promoter-TSS (NM_144915)	promoter-TSS (NM_144915)	38	NM_144915	231871	Mm.469963	NM_144915	ENSMUSG00000039206	Daglb	E330036I19Rik	diacylglycerol lipase, beta	protein-coding
mm_96724.1	chr11	69671367	69671400	+	1	NA	intron (NM_001159375, intron 1 of 10)	CpG	1040	NM_144958	13681	Mm.26680	NM_144958	ENSMUSG00000059796	Eif4a1	BM-010|Ddx2a|Eif4	eukaryotic translation initiation factor 4A1	protein-coding
mm_111964.1	chr12	109615511	109615526	-	1	NA	intron (NR_028261, intron 2 of 20)	intron (NR_028261, intron 2 of 20)	-2740	NR_029918	723854		NR_029918	ENSMUSG00000065433	Mir370	Mirn370|mir-370|mmu-mir-370	microRNA 370	ncRNA
mm_126941.1	chr15	91906534	91906570	+	1	NA	exon (NM_207243, exon 33 of 44)	exon (NM_207243, exon 33 of 44)	68224	NM_198927	223809	Mm.486225	NM_198927	ENSMUSG00000047295	Smgc	2310010P21Rik|DXImx49e|Muc19|Muc19/Smgc|Sfc21	submandibular gland protein C	protein-coding
mm_13303.1	chr2	102550139	102550168	+	1	NA	5' UTR (NM_173749, exon 1 of 11)	5' UTR (NM_173749, exon 1 of 11)	132	NM_173749	210622	Mm.28649	NM_173749	ENSMUSG00000027188	Pamr1	5930437L24|E430002G05Rik|Ramp	peptidase domain containing associated with muscle regeneration 1	protein-coding
mm_126376.1	chr15	80171588	80171611	+	1	NA	Intergenic	Intergenic	-2122	NM_010795	17309	Mm.299693	NM_010795	ENSMUSG00000042428	Mgat3	1110038J12Rik|AI848272|GnT-III	mannoside acetylglucosaminyltransferase 3	protein-coding
mm_39983.1	chr5	32459252	32459291	+	1	NA	5' UTR (NM_172707, exon 1 of 8)	5' UTR (NM_172707, exon 1 of 8)	301	NM_172707	19046	Mm.241931	NM_172707	ENSMUSG00000014956	Ppp1cb	1200010B19	protein phosphatase 1, catalytic subunit, beta isoform	protein-coding
mm_76065.1	chr8	78355051	78355054	-	1	NA	intron (NM_183096, intron 12 of 13)	intron (NM_183096, intron 12 of 13)	81600	NM_138944	18997	Mm.234261	NM_138944	ENSMUSG00000031688	Pou4f2	Brn-3.2|Brn-3b|Brn3b|Pou4f-rs1|mBrn3-3R	POU domain, class 4, transcription factor 2	protein-coding
mm_147109.1	chr18	35703109	35703133	-	1	NA	promoter-TSS (NM_029669)	promoter-TSS (NM_029669)	23	NM_029669	76594	Mm.108596	NM_029669	ENSMUSG00000024350	Dnajc18	2700075B01Rik|AU041129	DnaJ heat shock protein family (Hsp40) member C18	protein-coding
mm_57507.1	chr6	125462156	125462179	-	1	NA	exon (NM_007657, exon 6 of 8)	exon (NM_007657, exon 6 of 8)	32588	NM_007657	12527	Mm.210676	NM_007657	ENSMUSG00000030342	Cd9	Tspan29	CD9 antigen	protein-coding
mm_143954.1	chr17	86831346	86831369	-	1	NA	3' UTR (NM_010137, exon 16 of 16)	3' UTR (NM_010137, exon 16 of 16)	77493	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_105636.1	chr11	106998466	106998482	-	1	NA	intron (NM_010655, intron 1 of 10)	intron (NM_010655, intron 1 of 10)	1051	NM_010655	16647	Mm.12508	NM_010655	ENSMUSG00000018362	Kpna2	2410044B12Rik|IPOA1|PTAC58|Rch1	karyopherin (importin) alpha 2	protein-coding
mm_29368.1	chr3	108711398	108711406	-	1	NA	5' UTR (NM_029522, exon 2 of 15)	5' UTR (NM_029522, exon 2 of 15)	10897	NM_029522	76123	Mm.226941	NM_029522	ENSMUSG00000027883	Gpsm2	6230410J09Rik|LGN|Pins	G-protein signalling modulator 2 (AGS3-like, C. elegans)	protein-coding
mm_69254.1	chr7	127874968	127874971	-	1	NA	intron (NM_146259, intron 1 of 2)	intron (NM_146259, intron 1 of 2)	1854	NM_146259	244219	Mm.207872	NM_146259	ENSMUSG00000049728	Zfp668	BC030314|E130018B19Rik|Znf668	zinc finger protein 668	protein-coding
mm_26115.1	chr3	137780410	137780450	+	1	NA	Intergenic	Intergenic	-84057	NM_001316995	51788	Mm.117541	NM_016750	ENSMUSG00000037894	H2afz	H2A.Z|H2a.z-1	H2A histone family, member Z	protein-coding
mm_25518.1	chr3	114030533	114030571	+	1	NA	promoter-TSS (NM_007729)	promoter-TSS (NM_007729)	12	NM_007729	12814	Mm.209715	NM_007729	ENSMUSG00000027966	Col11a1	C530001D20Rik|cho	collagen, type XI, alpha 1	protein-coding
mm_101413.1	chr11	28584261	28584309	-	1	NA	promoter-TSS (NM_181577)	promoter-TSS (NM_181577)	39	NM_001166661	216613	Mm.93759	NM_181577	ENSMUSG00000032878	Ccdc85a	-	coiled-coil domain containing 85A	protein-coding
mm_159175.1	chr2	109709597	109709597	+	1	NA	5' UTR (NM_001285421, exon 1 of 2)	5' UTR (NM_001285421, exon 1 of 2)	214	NM_001285421	12064	Mm.1442	NM_007540	ENSMUSG00000048482	Bdnf	-	brain derived neurotrophic factor	protein-coding
mm_134927.1	chr16	30693947	30693961	-	1	NA	Intergenic	RMER10B|LTR|ERVL	94231	NM_177632	224093	Mm.28244	NM_177632	ENSMUSG00000046546	Fam43a	Tuf1	family with sequence similarity 43, member A	protein-coding
mm_2530.1	chr1	106934503	106934524	+	1	NA	promoter-TSS (NM_027971)	promoter-TSS (NM_027971)	64	NM_027971	71869	Mm.321740	NM_027971	ENSMUSG00000059956	Serpinb12	2300003F07Rik|4833409F13Rik	serine (or cysteine) peptidase inhibitor, clade B (ovalbumin), member 12	protein-coding
mm_78657.1	chr9	40457656	40457658	+	1	NA	Intergenic	Intergenic	-1893	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_108732.1	chr12	87514316	87514319	+	1	NA	promoter-TSS (NM_001177565)	promoter-TSS (NM_001177565)	1	NM_001177565	666806	Mm.379796	NM_001177565	ENSMUSG00000079034	Gm8300	EG666806	predicted gene 8300	protein-coding
mm_118326.1	chr13	113618550	113618565	-	1	NA	promoter-TSS (NM_130796)	promoter-TSS (NM_130796)	7	NM_130796	170625	Mm.33721	NM_130796	ENSMUSG00000042364	Snx18	Snag1	sorting nexin 18	protein-coding
mm_50439.1	chr6	48860380	48860405	+	1	NA	Intergenic	Intergenic	18736	NM_001098271	66058	Mm.27061	NM_025326	ENSMUSG00000023367	Tmem176a	0610011I04Rik|AU040201|AU041743|Keg2	transmembrane protein 176A	protein-coding
mm_56618.1	chr6	112694646	112694649	-	1	NA	intron (NM_001167730, intron 1 of 13)	B1F2|SINE|Alu	2023	NM_021385	58186	Mm.103812	NM_021385	ENSMUSG00000030254	Rad18	2810024C04Rik|Rad18sc	RAD18 E3 ubiquitin protein ligase	protein-coding
mm_63041.1	chr7	121089937	121089939	+	1	NA	intron (NM_139310, intron 1 of 28)	L1MEc|LINE|L1	6500	NM_139310	246190	Mm.221073	NM_139310	ENSMUSG00000034990	Otoa	-	otoancorin	protein-coding
mm_65917.1	chr7	30198820	30198843	-	1	NA	Intergenic	Intergenic	-3783	NM_009795	12336	Mm.439782	NM_009795	ENSMUSG00000001794	Capns1	Capa-4|Capa4|Capn4|D7Ertd146e	calpain, small subunit 1	protein-coding
mm_108625.1	chr12	85599351	85599362	+	1	NA	promoter-TSS (NM_001205053)	promoter-TSS (NM_001205053)	-60	NM_030887	81703	Mm.103560	NM_030887	ENSMUSG00000034271	Jdp2	Jundm2|Jundp2|TIF	Jun dimerization protein 2	protein-coding
mm_70484.1	chr8	12396117	12396127	+	1	NA	5' UTR (NM_009233, exon 1 of 1)	5' UTR (NM_009233, exon 1 of 1)	603	NM_009233	20664	Mm.39088	NM_009233	ENSMUSG00000096014	Sox1	BB176347|Sox-1	SRY (sex determining region Y)-box 1	protein-coding
mm_122874.1	chr14	54925811	54925852	-	1	NA	5' UTR (NM_010112, exon 1 of 6)	5' UTR (NM_010112, exon 1 of 6)	957	NM_010112	13644	Mm.236438	NM_010112	ENSMUSG00000022203	Efs	-	embryonal Fyn-associated substrate	protein-coding
mm_171236.1	chr3	68902880	68902891	-	1	NA	intron (NM_026641, intron 18 of 19)	intron (NM_026641, intron 18 of 19)	33299	NM_001167996	68725	Mm.45741	NM_001167996	ENSMUSG00000046999	1110032F04Rik	AI115547	RIKEN cDNA 1110032F04 gene	protein-coding
mm_113011.1	chr13	21910967	21910975	+	1	NA	Intergenic	B1_Mur1|SINE|Alu	-13922	NR_035500	100316716		NR_035500	ENSMUSG00000088148	Mir1983	mmu-mir-1983	microRNA 1983	ncRNA
mm_159828.1	chr5	124414421	124414421	-	1	NA	exon (NM_001081203, exon 2 of 32)	exon (NM_001081203, exon 2 of 32)	11493	NM_001081203	243272	Mm.23879	NM_001081203	ENSMUSG00000038095	Sbno1	9330180L10Rik|AI849128|AW557836|BC021875|Sbno|mSno1|sno	strawberry notch homolog 1 (Drosophila)	protein-coding
mm_80341.1	chr9	75071580	75071584	+	1	NA	5' UTR (NM_010864, exon 1 of 41)	5' UTR (NM_010864, exon 1 of 41)	376	NM_010864	17918	Mm.3645	NM_010864	ENSMUSG00000034593	Myo5a	9630007J19Rik|AI413174|AI661011|Dbv|MVa|Myo5|MyoVA|Sev-1|d|d-120J|flail|flr	myosin VA	protein-coding
mm_159647.1	chr4	144686359	144686359	-	1	NA	promoter-TSS (NM_001085504)	promoter-TSS (NM_001085504)	9	NM_001085504	230890	Mm.457843	NM_001085504	ENSMUSG00000078505	Gm436	-	predicted gene 436	protein-coding
mm_143055.1	chr17	57004691	57004713	-	1	NA	exon (NM_133801, exon 7 of 13)	exon (NM_133801, exon 7 of 13)	-4597	NM_008954	19197	Mm.86487	NM_008954	ENSMUSG00000002664	Pspn	PSP	persephin	protein-coding
mm_57331.1	chr6	124741120	124741128	-	1	NA	promoter-TSS (NM_013535)	promoter-TSS (NM_013535)	-45	NM_013535	14790	Mm.439877	NM_013535	ENSMUSG00000072772	Grcc10	2310033H05Rik|C10	gene rich cluster, C10 gene	protein-coding
mm_17640.1	chr2	31153167	31153172	-	1	NA	promoter-TSS (NR_040334)	promoter-TSS (NR_040334)	853	NM_178760	277463	Mm.236074	NM_178760	ENSMUSG00000000194	Gpr107	9930033D15Rik|AI790205|C530034M11|mKIAA1624	G protein-coupled receptor 107	protein-coding
mm_92248.1	chr10	70559222	70559256	-	1	NA	TTS (NM_001143777)	TTS (NM_001143777)	33573	NM_001162846	70911	Mm.19825	NM_178621	ENSMUSG00000037747	Phyhipl	4921522K17Rik|AI267048	phytanoyl-CoA hydroxylase interacting protein-like	protein-coding
mm_126199.1	chr15	78877162	78877170	+	1	NA	promoter-TSS (NM_145929)	promoter-TSS (NM_145929)	-24	NM_145929	106039	Mm.251331	NM_145929	ENSMUSG00000033128	Gga1	4930406E12Rik|AU016030|AW209092	golgi associated, gamma adaptin ear containing, ARF binding protein 1	protein-coding
mm_130757.1	chr15	101270724	101270769	-	1	NA	exon (NM_010444, exon 2 of 7)	exon (NM_010444, exon 2 of 7)	3900	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_158525.1	chrX	143860975	143861006	-	1	NA	3' UTR (NM_010025, exon 7 of 7)	3' UTR (NM_010025, exon 7 of 7)	-33578	NM_007603	12338	Mm.30290	NM_007603	ENSMUSG00000067276	Capn6	-	calpain 6	protein-coding
mm_51991.1	chr6	92092329	92092334	+	1	NA	promoter-TSS (NM_001347342)	promoter-TSS (NM_001347342)	-102	NM_001347342	22026	Mm.87062	NM_011630	ENSMUSG00000005893	Nr2c2	TAK1|Tr4|mKIAA4145	nuclear receptor subfamily 2, group C, member 2	protein-coding
mm_46577.1	chr5	107403621	107403638	-	1	NA	exon (NM_001001804, exon 1 of 7)	exon (NM_001001804, exon 1 of 7)	116	NM_001001804	384214	Mm.489863	NM_001001804	ENSMUSG00000033805	Ephx4	Abhd7|Ephxrp|Gm1382	epoxide hydrolase 4	protein-coding
mm_145501.1	chr18	60391154	60391186	+	1	NA	3' UTR (NM_001146275, exon 3 of 3)	3' UTR (NM_001146275, exon 3 of 3)	15141	NM_001146275	60440	Mm.261140	NM_021792	ENSMUSG00000054072	Iigp1	2900074L10Rik|AI046432|AW111922|Ifgga1|Iigp|Irga6	interferon inducible GTPase 1	protein-coding
mm_88330.1	chr10	75571523	75571532	+	1	NA	intron (NM_001305992, intron 1 of 13)	intron (NM_001305992, intron 1 of 13)	-1968	NM_008116	14598	Mm.4559	NM_008116	ENSMUSG00000006345	Ggt1	CD224|GGT|GGT 1|GGT-1|Ggtp|dwg	gamma-glutamyltransferase 1	protein-coding
mm_162728.1	chr10	41490108	41490151	-	1	NA	promoter-TSS (NM_028430)	promoter-TSS (NM_028430)	211	NM_009213	20598	Mm.953	NM_009213	ENSMUSG00000019822	Smpd2	AW108287|nSMase|nSMase1	sphingomyelin phosphodiesterase 2, neutral	protein-coding
mm_13283.1	chr2	101624770	101624780	+	1	NA	promoter-TSS (NM_009020)	promoter-TSS (NM_009020)	27	NM_009020	19374	Mm.4988	NM_009020	ENSMUSG00000032864	Rag2	Rag-2	recombination activating gene 2	protein-coding
mm_150911.1	chr19	46057287	46057311	+	1	NA	intron (NM_001346801, intron 1 of 13)	CpG	760	NM_001081214	226169	Mm.2415	NM_145504	ENSMUSG00000055491	Pprc1	A930018M19|BC013720|PRC|mKIAA0595	peroxisome proliferative activated receptor, gamma, coactivator-related 1	protein-coding
mm_25949.1	chr3	131637738	131637781	+	1	NA	intron (NM_001289477, intron 12 of 12)	intron (NM_001289477, intron 12 of 12)	71727	NM_001289477	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_141797.1	chr17	34344558	34344594	-	1	NA	promoter-TSS (NM_010381)	promoter-TSS (NM_010381)	69	NM_010381	100504404	Mm.15680	NM_010381		H2-Ea-ps	AI323765|E-alpha-f|H-2Ea|H2-Ea|I-Ealpha|Ia-3|Ia3|MHC-H2-Ea	histocompatibility 2, class II antigen E alpha, pseudogene	protein-coding
mm_136946.1	chr17	14399261	14399272	+	1	NA	promoter-TSS (NR_027986)	promoter-TSS (NR_027986)	-324	NR_027986	74917	Mm.32228	NM_183107		4930474M22Rik	-	RIKEN cDNA 4930474M22 gene	ncRNA
mm_83499.1	chr9	45953674	45953684	-	1	NA	intron (NM_172257, intron 1 of 25)	intron (NM_172257, intron 1 of 25)	1570	NM_172257	214597	Mm.379345	NM_172257	ENSMUSG00000034908	Sidt2	B930096O19|BC023957|CGI-40	SID1 transmembrane family, member 2	protein-coding
mm_121001.1	chr14	79481524	79481608	+	1	NA	promoter-TSS (NM_018765)	promoter-TSS (NM_018765)	-298	NM_018765	22380	Mm.476813	NM_018765	ENSMUSG00000022023	Wbp4	AW545037|BB101031|FBP21	WW domain binding protein 4	protein-coding
mm_114585.1	chr13	75711840	75711847	+	1	NA	intron (NM_138953, intron 1 of 11)	BC1_Mm|scRNA|scRNA	4359	NM_138953	192657	Mm.21288	NM_138953	ENSMUSG00000001542	Ell2	-	elongation factor RNA polymerase II 2	protein-coding
mm_90448.1	chr10	127677044	127677059	+	1	NA	promoter-TSS (NM_001113211)	promoter-TSS (NM_001113211)	-14	NM_173732	210035	Mm.251075	NM_173732	ENSMUSG00000040195	Nemp1	Tmem194|Tmem194a	nuclear envelope integral membrane protein 1	protein-coding
mm_146922.1	chr18	31634770	31634811	-	1	NA	intron (NM_172965, intron 1 of 20)	CpG	407	NM_172965	269003	Mm.194538	NM_172965	ENSMUSG00000024260	Sap130	2610304F09Rik|6720406D06	Sin3A associated protein	protein-coding
mm_138533.1	chr17	35243206	35243227	+	1	NA	promoter-TSS (NR_105941)	promoter-TSS (NR_105941)	399	NM_001252457	53817	Mm.439827	NM_019693	ENSMUSG00000019432	Ddx39b	0610030D10Rik|AI428441|Bat-1|Bat1|Bat1a|D17H6S81E|D17H6S81E-1|D6S81Eh	DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B	protein-coding
mm_118515.1	chr14	14347106	14347128	+	1	NA	5' UTR (NM_008369, exon 2 of 12)	5' UTR (NM_008369, exon 2 of 12)	622	NM_008369	16188	Mm.425857	NM_008369	ENSMUSG00000068758	Il3ra	CD123|CDw123|SUT-1	interleukin 3 receptor, alpha chain	protein-coding
mm_85484.1	chr9	106096740	106096744	-	1	NA	promoter-TSS (NM_026763)	promoter-TSS (NM_026763)	-51	NM_026763	68553	Mm.28854	NM_026763	ENSMUSG00000032572	Col6a4	1110001D15Rik|AI413310|AU023415|Dvwa|EG235580|Vwa6	collagen, type VI, alpha 4	protein-coding
mm_43295.1	chr5	134314947	134314992	+	1	NA	promoter-TSS (NM_010365)	promoter-TSS (NM_010365)	-209	NM_010365	14886	Mm.261570	NM_010365	ENSMUSG00000060261	Gtf2i	6030441I21Rik|BAP-135|Diws1t|GtfII-I|Spin|TFII-I|WBSCR6	general transcription factor II I	protein-coding
mm_63120.1	chr7	122965637	122965647	+	1	NA	Intergenic	MT2B1|LTR|ERVL	4817	NR_045614	73951	Mm.389936	NR_045614		4930413G21Rik	-	RIKEN cDNA 4930413G21 gene	ncRNA
mm_142397.1	chr17	45433507	45433530	-	1	NA	promoter-TSS (NR_130961)	promoter-TSS (NR_130961)	189	NM_152810	71702	Mm.28270	NM_152810	ENSMUSG00000023932	Cdc5l	1200002I02Rik|AA408004|PCDC5RP	cell division cycle 5-like (S. pombe)	protein-coding
mm_140952.1	chr17	24599179	24599215	-	1	NA	intron (NM_001286718, intron 33 of 39)	intron (NM_001286718, intron 33 of 39)	33430	NM_011647	22084	Mm.30435	NM_011647	ENSMUSG00000002496	Tsc2	Nafld|Tcs2	tuberous sclerosis 2	protein-coding
mm_159580.1	chr4	118734536	118734536	+	1	NA	promoter-TSS (NM_146852)	promoter-TSS (NM_146852)	5	NM_146852	258851	Mm.377719	NM_146852	ENSMUSG00000070820	Olfr1339	MOR258-2	olfactory receptor 1339	protein-coding
mm_119926.1	chr14	54968782	54968800	+	1	NA	promoter-TSS (NR_033497)	promoter-TSS (NR_033497)	4	NR_033497	791403	Mm.319176	NR_033497	ENSMUSG00000097652	Mhrt	D830015G02Rik|ENSMUSG00000053118|Myheart	myosin heavy chain associated RNA transcript	ncRNA
mm_74266.1	chr8	124898477	124898483	+	1	NA	promoter-TSS (NM_198103)	promoter-TSS (NM_198103)	594	NM_001111141	244666	Mm.482915	NM_001111141	ENSMUSG00000031986	Sprtn	Gm505	SprT-like N-terminal domain	protein-coding
mm_74129.1	chr8	123193944	123193989	+	1	NA	intron (NM_007876, intron 1 of 10)	intron (NM_007876, intron 1 of 10)	7731	NM_007876	13479	Mm.20388	NM_007876	ENSMUSG00000019278	Dpep1	AI327012|MBD	dipeptidase 1 (renal)	protein-coding
mm_76100.1	chr8	80392303	80392306	-	1	NA	Intergenic	Intergenic	-101741	NM_010369	14934	Mm.13123	NM_010369	ENSMUSG00000051839	Gypa	AI853584|CD235a|GPA	glycophorin A	protein-coding
mm_163787.1	chr14	8099600	8099614	-	1	NA	intron (NM_178279, intron 1 of 18)	intron (NM_178279, intron 1 of 18)	1394	NM_178279	218699	Mm.29515	NM_145458	ENSMUSG00000033885	Pxk	C230080L11Rik|D14Ertd813e|MONaKA	PX domain containing serine/threonine kinase	protein-coding
mm_38069.1	chr4	134095079	134095090	-	1	NA	promoter-TSS (NM_013706)	promoter-TSS (NM_013706)	-11	NM_013706	23833	Mm.24130	NM_013706	ENSMUSG00000000682	Cd52	AI463198|B7|B7-Ag|CAMPATH-1|CLS1|MB7	CD52 antigen	protein-coding
mm_52490.1	chr6	114648907	114648920	+	1	NA	intron (NM_001253718, intron 2 of 19)	intron (NM_001253718, intron 2 of 19)	5816	NM_001253717	74244	Mm.275332	NM_028835	ENSMUSG00000030314	Atg7	1810013K23Rik|Agp7|Apg7l|Atg7l|Gm21553	autophagy related 7	protein-coding
mm_26186.1	chr3	138374147	138374163	+	1	NA	promoter-TSS (NR_033581)	promoter-TSS (NR_033581)	34	NR_033581	639769	Mm.484043	NR_033581	ENSMUSG00000090306	Adh6-ps1	1300002P07Rik|Adh5ps|Gm7277	alcohol dehydrogenase 6 (class V), pseudogene 1	pseudo
mm_10275.1	chr2	9882503	9882546	+	1	NA	TTS (NR_040511)	TTS (NR_040511)	1278	NR_024257	381347	Mm.441450	NR_024257		4930412O13Rik	ENSMUSG00000075535|Gm10853	RIKEN cDNA 4930412O13 gene	ncRNA
mm_125902.1	chr15	75969205	75969215	+	1	NA	promoter-TSS (NM_001081065)	promoter-TSS (NM_001081065)	25	NM_001081065	69020	Mm.294295	NM_001081065	ENSMUSG00000034429	Zfp707	1500031N24Rik|AI451708|AW495315	zinc finger protein 707	protein-coding
mm_31773.1	chr4	63558459	63558503	+	1	NA	Intergenic	CpG	-1879	NM_144905	230279	Mm.41523	NM_144905	ENSMUSG00000045917	Tmem268	6330416G13Rik|AW492431|bM230C2.2	transmembrane protein 268	protein-coding
mm_62773.1	chr7	112354824	112354840	+	1	NA	TTS (NM_001193305)	TTS (NM_001193305)	-13476	NM_027587	100504195	Mm.291129	NM_027587	ENSMUSG00000030771	Micalcl	4921517J23Rik	MICAL C-terminal like	protein-coding
mm_81982.1	chr9	121367021	121367042	+	1	NA	promoter-TSS (NM_175114)	promoter-TSS (NM_175114)	73	NM_175114	67095	Mm.491112	NM_175114	ENSMUSG00000032536	Trak1	2310001H13Rik|AI413908|AI467545|hyrt|mKIAA1042	trafficking protein, kinesin binding 1	protein-coding
mm_104473.1	chr11	95356710	95356722	-	1	NA	intron (NM_172543, intron 1 of 7)	intron (NM_172543, intron 1 of 7)	19698	NM_172543	215512	Mm.262113	NM_172543	ENSMUSG00000038893	Fam117a	5730593F17Rik|AW548096	family with sequence similarity 117, member A	protein-coding
mm_54757.1	chr6	41034395	41034415	-	1	NA	exon (NM_023333, exon 2 of 5)	exon (NM_023333, exon 2 of 5)	1104	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_62913.1	chr7	117604469	117604472	+	1	NA	intron (NM_175645, intron 5 of 11)	intron (NM_175645, intron 5 of 11)	223491	NM_175645	233781	Mm.461427	NM_175645	ENSMUSG00000030657	Xylt1	8030490L12	xylosyltransferase 1	protein-coding
mm_114546.1	chr13	73937800	73937880	+	1	NA	promoter-TSS (NM_027182)	promoter-TSS (NM_027182)	29	NM_001308041	105246	Mm.278509	NM_001024508	ENSMUSG00000057649	Brd9	AL022779	bromodomain containing 9	protein-coding
mm_47998.1	chr5	136160747	136160771	-	1	NA	intron (NM_178751, intron 2 of 2)	B4A|SINE|B4	9897	NM_178751	269717	Mm.308396	NM_178751	ENSMUSG00000039747	Orai2	A730041O15Rik|Tmem142b	ORAI calcium release-activated calcium modulator 2	protein-coding
mm_23144.1	chr3	39009827	39009838	+	1	NA	exon (NM_183221, exon 17 of 17)	exon (NM_183221, exon 17 of 17)	122892	NM_183221	329628	Mm.316210	NM_183221	ENSMUSG00000046743	Fat4	6030410K14Rik|9430004M15	FAT atypical cadherin 4	protein-coding
mm_26833.1	chr3	11015193	11015193	-	1	NA	Intergenic	Intergenic	-575063	NM_001127191	74718	Mm.440548	NM_029068	ENSMUSG00000027534	Snx16	4930522N22Rik|AI117577|AI747675	sorting nexin 16	protein-coding
mm_16844.1	chr2	11513175	11513196	-	1	NA	intron (NM_001177758, intron 1 of 14)	intron (NM_001177758, intron 1 of 14)	-11095	NM_001177757	170768	Mm.19669	NM_133232	ENSMUSG00000026773	Pfkfb3	E330010H22Rik|iPFK-2|uPFK-2	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	protein-coding
mm_96835.1	chr11	70017200	70017208	+	1	NA	Intergenic	Intergenic	-1401	NM_001109752	13385	Mm.27256	NM_007864	ENSMUSG00000020886	Dlg4	Dlgh4|PSD-95|PSD95|SAP90|SAP90A	discs, large homolog 4 (Drosophila)	protein-coding
mm_55768.1	chr6	78467517	78467526	-	1	NA	exon (NM_011260, exon 4 of 6)	exon (NM_011260, exon 4 of 6)	1353	NM_011260	19695	Mm.252385	NM_011260	ENSMUSG00000030017	Reg3g	AI449515|REG-3-gamma|reg III-gamma	regenerating islet-derived 3 gamma	protein-coding
mm_64726.1	chr7	4674505	4674533	-	1	NA	intron (NM_024172, intron 4 of 7)	intron (NM_024172, intron 4 of 7)	10444	NM_024172	66245	Mm.6803	NM_024172	ENSMUSG00000063802	Hspbp1	1500019G21Rik	HSPA (heat shock 70kDa) binding protein, cytoplasmic cochaperone 1	protein-coding
mm_98927.1	chr11	98350444	98350453	+	1	NA	TTS (NR_045477)	TTS (NR_045477)	452	NM_001313970	19049	Mm.45372	NM_144828	ENSMUSG00000061718	Ppp1r1b	AU040756|DARPP-32|Darpp32	protein phosphatase 1, regulatory (inhibitor) subunit 1B	protein-coding
mm_128122.1	chr15	31268192	31268218	-	1	NA	intron (NM_146057, intron 2 of 3)	intron (NM_146057, intron 2 of 3)	43820	NM_146057	223453	Mm.222867	NM_146057	ENSMUSG00000039168	Dap	4921531N22Rik|AI789753|AU040360	death-associated protein	protein-coding
mm_54947.1	chr6	48613739	48613741	-	1	NA	intron (NM_173429, intron 1 of 1)	intron (NM_173429, intron 1 of 1)	560	NM_173429	243372	Mm.435190	NM_173429	ENSMUSG00000007216	Zfp775	C130032F08Rik|Znf775	zinc finger protein 775	protein-coding
mm_150467.1	chr19	38396026	38396083	+	1	NA	promoter-TSS (NM_175507)	promoter-TSS (NM_175507)	74	NM_175507	240660	Mm.262085	NM_175507	ENSMUSG00000044026	Slc35g1	AA590464|D330039I19Rik|Tmem20	solute carrier family 35, member G1	protein-coding
mm_116436.1	chr13	42244436	42244442	-	1	NA	Intergenic	Intergenic	-57037	NM_010104	13614	Mm.14543	NM_010104	ENSMUSG00000021367	Edn1	ET-1|PPET1|preproET	endothelin 1	protein-coding
mm_136250.1	chr16	90938156	90938175	-	1	NA	3' UTR (NM_001045515, exon 33 of 33)	3' UTR (NM_001045515, exon 33 of 33)	-3316	NM_026502	68001	Mm.45374	NM_026502	ENSMUSG00000022972	1110004E09Rik	-	RIKEN cDNA 1110004E09 gene	protein-coding
mm_40694.1	chr5	65781413	65781443	+	1	NA	intron (NM_001024917, intron 3 of 19)	ORR1F|LTR|ERVL-MaLR	17907	NM_001024917	333789	Mm.332398	NM_001024917	ENSMUSG00000037795	N4bp2	B3bp|E430014I16|Gm1791|Gm868	NEDD4 binding protein 2	protein-coding
mm_77774.1	chr9	3016321	3016336	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	22415	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_60577.1	chr7	44482116	44482153	+	1	NA	Intergenic	B1_Mus2|SINE|Alu	-2383	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_68467.1	chr7	110614889	110614928	-	1	NA	promoter-TSS (NM_177324)	promoter-TSS (NM_177324)	12	NM_177324	319934	Mm.102970	NM_177324	ENSMUSG00000038371	Sbf2	4833411B01Rik|AA414977|AI317167|B430219L04Rik|Mtmr13|mMTMH1	SET binding factor 2	protein-coding
mm_38237.1	chr4	136173039	136173047	-	1	NA	intron (NM_177733, intron 1 of 6)	CpG	769	NM_177733	242705	Mm.307932	NM_177733	ENSMUSG00000018983	E2f2	E2F-2	E2F transcription factor 2	protein-coding
mm_95656.1	chr11	53770043	53770057	+	1	NA	promoter-TSS (NM_001159396)	promoter-TSS (NM_001159396)	36	NM_008390	16362	Mm.105218	NM_008390	ENSMUSG00000018899	Irf1	AU020929|Irf-1	interferon regulatory factor 1	protein-coding
mm_89627.1	chr10	96371211	96371241	+	1	NA	Intergenic	Intergenic	145019	NR_110448	74881	Mm.410819	NR_110448		4930459C07Rik	-	RIKEN cDNA 4930459C07 gene	ncRNA
mm_106818.1	chr12	7983028	7983038	+	1	NA	exon (NM_009693, exon 5 of 29)	exon (NM_009693, exon 5 of 29)	5356	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_26.1	chr1	6214628	6214683	+	1	NA	promoter-TSS (NM_009826)	promoter-TSS (NM_009826)	-7	NM_009826	12421	Mm.293811	NM_009826	ENSMUSG00000025907	Rb1cc1	2900055E04Rik|5930404L04Rik|Cc1|FIP200|LaXp180	RB1-inducible coiled-coil 1	protein-coding
mm_133770.1	chr16	94629711	94629713	+	1	NA	intron (NM_001347731, intron 1 of 10)	intron (NM_001347731, intron 1 of 10)	18293	NM_001347731	13548	Mm.310973	NM_007890	ENSMUSG00000022897	Dyrk1a	2310043O08Rik|D16Ertd272e|D16Ertd493e|Dyrk|ENSMUSG00000074897|Gm10783|Mnbh|Mp86|mmb	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1a	protein-coding
mm_64832.1	chr7	12922071	12922096	-	1	NA	promoter-TSS (NM_009095)	promoter-TSS (NM_009095)	-228	NM_009095	20103	Mm.5291	NM_009095	ENSMUSG00000012848	Rps5	AA617411	ribosomal protein S5	protein-coding
mm_140914.1	chr17	24169415	24169450	-	1	NA	promoter-TSS (NM_009729)	promoter-TSS (NM_009729)	-3	NM_009729	11984	Mm.30155	NM_009729	ENSMUSG00000024121	Atp6v0c	Atp6c|Atp6c2|Atp6l|Atpl|Atpl-rs1|PL16|VATL|Vma3	ATPase, H+ transporting, lysosomal V0 subunit C	protein-coding
mm_143559.1	chr17	74173937	74173943	-	1	NA	Intergenic	Intergenic	120923	NM_133771	76890	Mm.311874	NM_133771	ENSMUSG00000058704	Memo1	0610016J10Rik|D930048L02Rik	mediator of cell motility 1	protein-coding
mm_111198.1	chr12	84218813	84218828	-	1	NA	promoter-TSS (NM_001163501)	promoter-TSS (NM_001163501)	61	NM_001163501	238317	Mm.31256	NM_001163501	ENSMUSG00000042507	Elmsan1	9430029N19Rik|C130039O16Rik|Gm260	ELM2 and Myb/SANT-like domain containing 1	protein-coding
mm_84302.1	chr9	63399217	63399262	-	1	NA	promoter-TSS (NM_027090)	promoter-TSS (NM_027090)	5	NM_027090	69478	Mm.113942	NM_027090	ENSMUSG00000032403	2300009A05Rik	-	RIKEN cDNA 2300009A05 gene	protein-coding
mm_133524.1	chr16	90832772	90832777	+	1	NA	intron (NM_001316761, intron 1 of 5)	intron (NM_001316761, intron 1 of 5)	1915	NM_001316761	70967	Mm.253077	NM_027627	ENSMUSG00000039903	Eva1c	1700092M14Rik|4931408A02Rik|Fam176c	eva-1 homolog C (C. elegans)	protein-coding
mm_74398.1	chr8	3252663	3252668	-	1	NA	intron (NM_010568, intron 2 of 20)	PB1D7|SINE|Alu	26952	NM_010568	16337	Mm.268003	NM_010568	ENSMUSG00000005534	Insr	4932439J01Rik|CD220|D630014A15Rik|IR|IR-A|IR-B	insulin receptor	protein-coding
mm_159767.1	chr5	97392367	97392367	-	1	NA	promoter-TSS (NM_001033191)	promoter-TSS (NM_001033191)	-37	NM_001033191	97243	Mm.11746	NM_001033191	ENSMUSG00000046000	Naa11	Ard1b|Ard2|C80008	N(alpha)-acetyltransferase 11, NatA catalytic subunit	protein-coding
mm_45676.1	chr5	77246263	77246273	-	1	NA	Intergenic	Intergenic	-19226	NM_011263	19712	Mm.28840	NM_011263	ENSMUSG00000029249	Rest	2610008J04Rik|AA407358|NRSF|REST4	RE1-silencing transcription factor	protein-coding
mm_37533.1	chr4	124862264	124862300	-	1	NA	promoter-TSS (NM_001007573)	promoter-TSS (NM_001007573)	-111	NM_001007573	215090	Mm.472762	NM_001007573	ENSMUSG00000042763	Maneal	Gm50	mannosidase, endo-alpha-like	protein-coding
mm_98306.1	chr11	90033489	90033497	+	1	NA	intron (NM_026433, intron 1 of 2)	intron (NM_026433, intron 1 of 2)	3145	NM_026433	67888	Mm.212428	NM_026433	ENSMUSG00000069763	Tmem100	1810057C19Rik|AV011897	transmembrane protein 100	protein-coding
mm_40090.1	chr5	34547845	34547845	+	1	NA	intron (NM_001145858, intron 1 of 12)	L1M4|LINE|L1	-1731	NM_001145859	24055	Mm.5012	NM_011893	ENSMUSG00000054520	Sh3bp2	3BP2	SH3-domain binding protein 2	protein-coding
mm_5913.1	chr1	55023817	55023820	-	1	NA	intron (NM_031179, intron 1 of 24)	B1_Mur3|SINE|Alu	3660	NM_031179	81898	Mm.279736	NM_031179	ENSMUSG00000025982	Sf3b1	155kDa|2810001M05Rik|AA409119|Prp10|SAP155|SF3b155|TA-8|Targ4	splicing factor 3b, subunit 1	protein-coding
mm_34250.1	chr4	141282918	141282936	+	1	NA	Intergenic	Intergenic	-18294	NM_010139	13836	Mm.2581	NM_010139	ENSMUSG00000006445	Epha2	AW545284|Eck|Myk2|Sek-2|Sek2	Eph receptor A2	protein-coding
mm_56690.1	chr6	114042021	114042097	-	1	NA	promoter-TSS (NM_009723)	promoter-TSS (NM_009723)	21	NM_009723	11941	Mm.321755	NM_009723	ENSMUSG00000030302	Atp2b2	D6Abb2e|Gena300|PMCA2|Tmy|dfw|jog|wms|wri	ATPase, Ca++ transporting, plasma membrane 2	protein-coding
mm_35873.1	chr4	49536683	49536694	-	1	NA	3' UTR (NM_144903, exon 9 of 9)	3' UTR (NM_144903, exon 9 of 9)	12858	NM_144903	230163	Mm.482116	NM_144903	ENSMUSG00000028307	Aldob	Aldo-2|Aldo2|BC016435	aldolase B, fructose-bisphosphate	protein-coding
mm_85185.1	chr9	96691750	96691776	-	1	NA	intron (NM_175537, intron 2 of 2)	B1_Mur4|SINE|Alu	39912	NM_175537	245007	Mm.485954	NM_175537	ENSMUSG00000040433	Zbtb38	A930014K01Rik|CIBZ	zinc finger and BTB domain containing 38	protein-coding
mm_58077.1	chr6	136941463	136941492	-	1	NA	promoter-TSS (NM_001301305)	promoter-TSS (NM_001301305)	26	NM_001301305	11857	Mm.2241	NM_007486	ENSMUSG00000030220	Arhgdib	D4|Gdid4|Ly-GDI	Rho, GDP dissociation inhibitor (GDI) beta	protein-coding
mm_89718.1	chr10	98914414	98914418	+	1	NA	promoter-TSS (NM_026482)	promoter-TSS (NM_026482)	-736	NM_026482	67972	Mm.166944	NM_026482	ENSMUSG00000019943	Atp2b1	2810442I22Rik|E130111D10Rik|Pmca1	ATPase, Ca++ transporting, plasma membrane 1	protein-coding
mm_96858.1	chr11	70092635	70092643	+	1	NA	promoter-TSS (NM_007493)	promoter-TSS (NM_007493)	-5	NM_007493	11890	Mm.1357	NM_007493	ENSMUSG00000040963	Asgr2	ASGPR2|Asgr|Asgr-2|HL-2	asialoglycoprotein receptor 2	protein-coding
mm_154114.1	chr19	57155415	57155461	-	1	NA	intron (NM_001290813, intron 2 of 20)	intron (NM_001290813, intron 2 of 20)	-36414	NM_001103178	226251	Mm.217161	NM_178688	ENSMUSG00000025085	Ablim1	2210411C18Rik|2610209L21Rik|4833406P10Rik|9330196J19Rik|AV079770|AW060987|AW215784|Limab1|mKIAA0059	actin-binding LIM protein 1	protein-coding
mm_139341.1	chr17	50181231	50181238	+	1	NA	intron (NM_181397, intron 1 of 9)	intron (NM_181397, intron 1 of 9)	9263	NM_181397	76438	Mm.41854	NM_181397	ENSMUSG00000039316	Rftn1	2310015N21Rik|AI853526	raftlin lipid raft linker 1	protein-coding
mm_44051.1	chr5	147873264	147873287	+	1	NA	intron (NM_025624, intron 5 of 5)	intron (NM_025624, intron 5 of 5)	12647	NM_025624	66537	Mm.332855	NM_025624	ENSMUSG00000029649	Pomp	2510048O06Rik|Ump1	proteasome maturation protein	protein-coding
mm_110222.1	chr12	28635844	28635865	-	1	NA	promoter-TSS (NM_011300)	promoter-TSS (NM_011300)	99	NM_011300	20115	Mm.279839	NM_011300	ENSMUSG00000061477	Rps7	Mtu|Rps7A|S7	ribosomal protein S7	protein-coding
mm_66160.1	chr7	31155870	31155896	-	1	NA	Intergenic	Intergenic	-4833	NM_027898	52857	Mm.27366	NM_027898	ENSMUSG00000001248	Gramd1a	1300003M23Rik|AI415002|AW547240|D7Bwg0611e	GRAM domain containing 1A	protein-coding
mm_143150.1	chr17	57222892	57222900	-	1	NA	exon (NM_009778, exon 13 of 41)	exon (NM_009778, exon 13 of 41)	5240	NM_009778	12266	Mm.19131	NM_009778	ENSMUSG00000024164	C3	AI255234|ASP|HSE-MSF|Plp	complement component 3	protein-coding
mm_110747.1	chr12	69976127	69976139	-	1	NA	exon (NM_022028, exon 3 of 5)	exon (NM_022028, exon 3 of 5)	10869	NM_022028	64010	Mm.390480	NM_022028	ENSMUSG00000021067	Sav1	1700040G09Rik|Salv|Sav|WW45|Wwp3|Wwp4	salvador family WW domain containing 1	protein-coding
mm_48019.1	chr5	136171180	136171190	-	1	NA	promoter-TSS (NM_178751)	promoter-TSS (NM_178751)	-529	NM_178751	269717	Mm.308396	NM_178751	ENSMUSG00000039747	Orai2	A730041O15Rik|Tmem142b	ORAI calcium release-activated calcium modulator 2	protein-coding
mm_170217.1	chr17	75555163	75555166	-	1	NA	Intergenic	ERVB7_1-LTR_MM|LTR|ERVK	-3218	NM_133747	72722	Mm.24641	NM_133747	ENSMUSG00000002017	Fam98a	2810405J04Rik|AL024114	family with sequence similarity 98, member A	protein-coding
mm_1548.1	chr1	72862365	72862379	+	1	NA	3' UTR (NM_010518, exon 4 of 4)	3' UTR (NM_010518, exon 4 of 4)	12493	NM_010518	16011	Mm.405761	NM_010518	ENSMUSG00000026185	Igfbp5	AI256729|AW208790|IGFBP-5|IGFBP-5P	insulin-like growth factor binding protein 5	protein-coding
mm_35714.1	chr4	44233883	44233949	-	1	NA	Intergenic	CpG	-12649	NR_039565	100628618		NR_039565	ENSMUSG00000092677	Mir5106	mir-5106|mmu-mir-5106|mu-mir-5106	microRNA 5106	ncRNA
mm_47890.1	chr5	134711202	134711249	-	1	NA	intron (NM_007925, intron 26 of 36)	intron (NM_007925, intron 26 of 36)	-22635	NM_010717	16885	Mm.15409	NM_010717	ENSMUSG00000029674	Limk1	KIZ-1|LIMK-1|Limk	LIM-domain containing, protein kinase	protein-coding
mm_68792.1	chr7	123369871	123369920	-	1	NA	promoter-TSS (NM_001122643)	promoter-TSS (NM_001122643)	20	NM_001122643	70497	Mm.403318	NM_144529	ENSMUSG00000030766	Arhgap17	5730403H17Rik|Nadrin|Nadrin2|Rich1|Wbp15	Rho GTPase activating protein 17	protein-coding
mm_41284.1	chr5	90462692	90462744	+	1	NA	exon (NM_009654, exon 3 of 15)	exon (NM_009654, exon 3 of 15)	1848	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_129463.1	chr15	78581564	78581621	-	1	NA	Intergenic	Intergenic	-8809	NM_009008	19354	Mm.1972	NM_009008	ENSMUSG00000033220	Rac2	AI323801|AI452260	RAS-related C3 botulinum substrate 2	protein-coding
mm_131117.1	chr16	5378143	5378153	+	1	NA	Intergenic	Intergenic	-122192	NM_027446	70511	Mm.45780	NM_027446	ENSMUSG00000022544	Eef2kmt	5730409G15Rik|Fam86|Fam86a|eEF2-KMT	eukaryotic elongation factor 2 lysine methyltransferase	protein-coding
mm_71199.1	chr8	40885601	40885643	+	1	NA	intron (NM_007514, intron 1 of 11)	L1MEd|LINE|L1	23255	NM_001044740	11988	Mm.4676	NM_007514	ENSMUSG00000031596	Slc7a2	20.5|AI158848|Atrc2|CAT-2|Cat2|Tea	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	protein-coding
mm_47437.1	chr5	123181468	123181479	-	1	NA	exon (NM_008277, exon 4 of 14)	exon (NM_008277, exon 4 of 14)	1213	NM_008277	15445	Mm.439709	NM_008277	ENSMUSG00000029445	Hpd	Fla|Flp|Hppd|Laf	4-hydroxyphenylpyruvic acid dioxygenase	protein-coding
mm_157598.1	chrX	53269023	53269068	-	1	NA	5' UTR (NM_030167, exon 1 of 9)	5' UTR (NM_030167, exon 1 of 9)	760	NM_030167	78755	Mm.28559	NM_030167	ENSMUSG00000036022	Fam122b	4632404H22Rik|AI256344|SPACIA2	family with sequence similarity 122, member B	protein-coding
mm_151650.1	chr19	4069090	4069112	-	1	NA	Intergenic	RLTR19-int|LTR|ERVK	-9807	NM_144869	225884	Mm.440201	NM_144869	ENSMUSG00000058216	Gstp3	-	glutathione S-transferase pi 3	protein-coding
mm_115353.1	chr13	112800777	112800781	+	1	NA	promoter-TSS (NM_008903)	promoter-TSS (NM_008903)	2	NM_008247	19012	Mm.291029	NM_008247	ENSMUSG00000021759	Plpp1	Hic53|Hpic53|LPP-1|LPP1|PAP-2a|PAP2-alpha|PAP2a|Ppap2a|mPAP	phospholipid phosphatase 1	protein-coding
mm_130251.1	chr15	96641565	96641575	-	1	NA	5' UTR (NM_134086, exon 1 of 16)	5' UTR (NM_134086, exon 1 of 16)	392	NM_134086	105727	Mm.103568	NM_134086	ENSMUSG00000023169	Slc38a1	AA408026|AA409865|AL022800|AU015942|NAT2	solute carrier family 38, member 1	protein-coding
mm_130819.1	chr15	101802351	101802367	-	1	NA	promoter-TSS (NM_212485)	promoter-TSS (NM_212485)	-27	NM_212485	223915	Mm.291498	NM_212485	ENSMUSG00000063661	Krt73	BC067067|Kb36	keratin 73	protein-coding
mm_173284.1	chrY	1641681	1641681	+	1	NA	Intergenic	L1Md_T|LINE|L1	-181899	NM_148943	107868	Mm.347376	NM_148943	ENSMUSG00000069044	Usp9y	Dffry|Fafl2	ubiquitin specific peptidase 9, Y chromosome	protein-coding
mm_27505.1	chr3	55780685	55780698	-	1	NA	intron (NM_030595, intron 41 of 57)	intron (NM_030595, intron 41 of 57)	-1819	NM_010750	17116	Mm.440209	NM_010750	ENSMUSG00000056947	Mab21l1	AW047968	mab-21-like 1 (C. elegans)	protein-coding
mm_103963.1	chr11	84442681	84442703	-	1	NA	intron (NM_019816, intron 11 of 12)	intron (NM_019816, intron 11 of 12)	70809	NM_019816	56321	Mm.257482	NM_019816	ENSMUSG00000018697	Aatf	4933415H02Rik|5830465M17Rik|Che-1|Trb	apoptosis antagonizing transcription factor	protein-coding
mm_314.1	chr1	24338533	24338539	+	1	NA	intron (NM_007733, intron 17 of 50)	intron (NM_007733, intron 17 of 50)	143333	NM_001290691	12839	Mm.154662	NM_007740	ENSMUSG00000026147	Col9a1	Col9a-1	collagen, type IX, alpha 1	protein-coding
mm_55167.1	chr6	51895580	51895583	-	1	NA	intron (NM_018773, intron 9 of 12)	intron (NM_018773, intron 9 of 12)	116968	NM_018773	54353	Mm.221479	NM_018773	ENSMUSG00000059182	Skap2	2610021A10Rik|AA960083|BB137539|RA70|SKAP-HOM|Saps|Scap2|mSKAP55R	src family associated phosphoprotein 2	protein-coding
mm_1168.1	chr1	60911926	60911932	+	1	NA	intron (NM_001281976, intron 1 of 2)	intron (NM_001281976, intron 1 of 2)	2904	NM_001281976	12477	Mm.390	NM_009843	ENSMUSG00000026011	Ctla4	Cd152|Ctla-4|Ly-56	cytotoxic T-lymphocyte-associated protein 4	protein-coding
mm_69283.1	chr7	128150652	128150658	-	1	NA	TTS (NM_021334)	TTS (NM_021334)	21087	NM_021334	16411	Mm.22378	NM_021334	ENSMUSG00000030789	Itgax	AI449405|Cd11c|Cr4|N418	integrin alpha X	protein-coding
mm_167860.1	chrX	18162722	18162730	+	1	NA	5' UTR (NM_009483, exon 1 of 29)	5' UTR (NM_009483, exon 1 of 29)	151	NM_001310444	22289	Mm.257498	NM_009483	ENSMUSG00000037369	Kdm6a	Utx	lysine (K)-specific demethylase 6A	protein-coding
mm_44189.1	chr5	3342404	3342410	-	1	NA	Intergenic	CpG	-1486	NM_009873	12571	Mm.31672	NM_009873	ENSMUSG00000040274	Cdk6	AI504062|Crk2	cyclin-dependent kinase 6	protein-coding
mm_3916.1	chr1	162217689	162217717	+	1	NA	promoter-TSS (NR_029810)	promoter-TSS (NR_029810)	80	NR_002870	474332	Mm.479755	NR_002870	ENSMUSG00000078190	Dnm3os	6030416H16Rik|Hag2|Npn1|P/L01	dynamin 3, opposite strand	ncRNA
mm_117767.1	chr13	96471215	96471224	-	1	NA	promoter-TSS (NM_001042714)	promoter-TSS (NM_001042714)	-59	NM_001042714	271144	Mm.470057	NM_001042714	ENSMUSG00000047117	Ankdd1b	9330128J19Rik	ankyrin repeat and death domain containing 1B	protein-coding
mm_165173.1	chr2	26974008	26974024	-	1	NA	intron (NM_001001322, intron 2 of 28)	intron (NM_001001322, intron 2 of 28)	600	NM_001290465	279028	Mm.330084	NM_001001322	ENSMUSG00000014852	Adamts13	ADAM-TS13|ADAMTS-13|Gm710|vWF-CP	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 13	protein-coding
mm_97873.1	chr11	83176675	83176679	+	1	NA	5' UTR (NM_011410, exon 4 of 8)	5' UTR (NM_011410, exon 4 of 8)	1491	NM_001302559	20558	Mm.38192	NM_011410	ENSMUSG00000000204	Slfn4	AI450778	schlafen 4	protein-coding
mm_7935.1	chr1	133912536	133912547	-	1	NA	3' UTR (NM_054077, exon 3 of 3)	3' UTR (NM_054077, exon 3 of 3)	-4542	NM_001160420	269120	Mm.59985	NM_054076	ENSMUSG00000010311	Optc	-	opticin	protein-coding
mm_52981.1	chr6	123262657	123262711	+	1	NA	intron (NM_001163161, intron 1 of 5)	ID_B1|SINE|B4	577	NM_010819	17474	Mm.441101	NM_010819	ENSMUSG00000030144	Clec4d	Clecsf8|Mpcl|mcl	C-type lectin domain family 4, member d	protein-coding
mm_103756.1	chr11	80858211	80858213	-	1	NA	promoter-TSS (NM_029367)	promoter-TSS (NM_029367)	88	NR_110449	75043	Mm.410815	NR_110449	ENSMUSG00000086703	4930507D10Rik	-	RIKEN cDNA 4930507D10 gene	ncRNA
mm_117045.1	chr13	58359023	58359066	-	1	NA	Intergenic	CpG	-4182	NM_175214	75050	Mm.446094	NM_175214	ENSMUSG00000060176	Kif27	4930517I18Rik	kinesin family member 27	protein-coding
mm_69722.1	chr7	140759826	140759828	-	1	NA	Intergenic	Lx5|LINE|L1	-4005	NM_021282	13106	Mm.21758	NM_021282	ENSMUSG00000025479	Cyp2e1	Cyp2e	cytochrome P450, family 2, subfamily e, polypeptide 1	protein-coding
mm_137235.1	chr17	24424471	24424476	+	1	NA	exon (NM_001080128, exon 6 of 7)	exon (NM_001080128, exon 6 of 7)	-2210	NM_010023	13177	Mm.291743	NM_010023	ENSMUSG00000024132	Eci1	Dci|eci	enoyl-Coenzyme A delta isomerase 1	protein-coding
mm_87885.1	chr10	61726148	61726159	+	1	NA	intron (NM_001284300, intron 2 of 9)	intron (NM_001284300, intron 2 of 9)	5504	NM_153779	71361	Mm.286309	NM_153779	ENSMUSG00000020085	Aifm2	5430437E11Rik|Amid|D730001I10Rik|PRG3	apoptosis-inducing factor, mitochondrion-associated 2	protein-coding
mm_98722.1	chr11	96332542	96332546	+	1	NA	intron (NM_001079869, intron 1 of 3)	intron (NM_001079869, intron 1 of 3)	9418	NM_001079869	15410	Mm.342481	NM_010458	ENSMUSG00000048763	Hoxb3	Hox-2.7	homeobox B3	protein-coding
mm_108374.1	chr12	80847146	80847158	+	1	NA	intron (NM_178682, intron 2 of 5)	intron (NM_178682, intron 2 of 5)	56620	NM_001242419	217684	Mm.341776	NM_178682	ENSMUSG00000021133	Susd6	4933426M11Rik|mKIAA0247	sushi domain containing 6	protein-coding
mm_149341.1	chr19	10850386	10850411	+	1	NA	intron (NM_023044, intron 2 of 7)	MTD|LTR|ERVL-MaLR	7854	NM_023044	65221	Mm.27387	NM_023044	ENSMUSG00000024737	Slc15a3	Ci1|cI-1	solute carrier family 15, member 3	protein-coding
mm_50409.1	chr6	48739007	48739019	+	1	NA	promoter-TSS (NM_008376)	promoter-TSS (NM_008376)	-34	NM_175860	16205	Mm.252599	NM_008376	ENSMUSG00000090019	Gimap1	IAP38|Imap38|imap	GTPase, IMAP family member 1	protein-coding
mm_99229.1	chr11	101062408	101062450	+	1	NA	3' UTR (NM_001243049, exon 21 of 21)	3' UTR (NM_001243049, exon 21 of 21)	-7665	NM_013792	27419	Mm.95452	NM_013792	ENSMUSG00000001751	Naglu	-	alpha-N-acetylglucosaminidase (Sanfilippo disease IIIB)	protein-coding
mm_390.1	chr1	34089284	34089296	+	1	NA	intron (NM_001276764, intron 5 of 102)	intron (NM_001276764, intron 5 of 102)	-28069	NR_105861	102466987		NR_105861	ENSMUSG00000105982	Mir6896	mmu-mir-6896	microRNA 6896	ncRNA
mm_68487.1	chr7	111072731	111072765	-	1	NA	exon (NM_013507, exon 22 of 22)	exon (NM_013507, exon 22 of 22)	10282	NM_001040131	13690	Mm.185453	NM_013507	ENSMUSG00000005610	Eif4g2	DAP-5|E130105L11Rik|Nat1|Natm1|p97	eukaryotic translation initiation factor 4, gamma 2	protein-coding
mm_55498.1	chr6	69727181	69727184	-	1	NA	Intergenic	Intergenic	-400008	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_105996.1	chr11	115663807	115663810	-	1	NA	intron (NM_001313937, intron 1 of 4)	intron (NM_001313937, intron 1 of 4)	-35513	NM_001252395	67283	Mm.383426	NM_026071	ENSMUSG00000020744	Slc25a19	2900089E13Rik|DNC|MUP1|TPC	solute carrier family 25 (mitochondrial thiamine pyrophosphate carrier), member 19	protein-coding
mm_2726.1	chr1	128196991	128197006	+	1	NA	exon (NM_181750, exon 19 of 27)	exon (NM_181750, exon 19 of 27)	-5363	NR_029543	387147		NR_029543	ENSMUSG00000065520	Mir128-1	Mirn128|Mirn128-1|Mirn128a|mir-128-1	microRNA 128-1	ncRNA
mm_80381.1	chr9	75434438	75434442	+	1	NA	Intergenic	PB1D10|SINE|Alu	-7084	NM_001039522	235497	Mm.41508	NM_001006122	ENSMUSG00000042487	Leo1	Gm185	Leo1, Paf1/RNA polymerase II complex component	protein-coding
mm_78981.1	chr9	45389878	45389882	+	1	NA	intron (NM_022004, intron 1 of 7)	intron (NM_022004, intron 1 of 7)	-9829	NR_028499	11936	Mm.22742	NM_007503	ENSMUSG00000059412	Fxyd2	Atp1g1	FXYD domain-containing ion transport regulator 2	protein-coding
mm_8981.1	chr1	165657880	165657892	-	1	NA	intron (NM_178593, intron 4 of 6)	intron (NM_178593, intron 4 of 6)	-23345	NM_001083897	68481	Mm.46438	NM_001001880	ENSMUSG00000026566	Mpzl1	1110007A10Rik|PZR	myelin protein zero-like 1	protein-coding
mm_94243.1	chr11	3310057	3310061	+	1	NA	TTS (NM_001253691)	TTS (NM_001253691)	1059	NR_045708	100302648	Mm.458664	NR_045708	ENSMUSG00000084941	Gm11944	OTTMUSG00000005017	predicted gene 11944	ncRNA
mm_142269.1	chr17	39846655	39846683	-	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	3672	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_21782.1	chr2	164848533	164848538	-	1	NA	intron (NM_011125, intron 8 of 15)	B1_Mur1|SINE|Alu	9173	NM_011125	18830	Mm.6105	NM_011125	ENSMUSG00000017754	Pltp	Bpife|OD107	phospholipid transfer protein	protein-coding
mm_71874.1	chr8	69654483	69654497	+	1	NA	promoter-TSS (NM_001177527)	promoter-TSS (NM_001177527)	-66	NM_001177527	636741	Mm.480188	NM_001177527	ENSMUSG00000091764	Zfp964	4732490P12|EG636741|Gm7187	zinc finger protein 964	protein-coding
mm_40067.1	chr5	34196804	34196817	+	1	NA	intron (NM_001015039, intron 11 of 12)	intron (NM_001015039, intron 11 of 12)	-9100	NM_010753	17122	Mm.259260	NM_010753	ENSMUSG00000037235	Mxd4	2810410A03Rik|Mad4|bHLHc12	Max dimerization protein 4	protein-coding
mm_37232.1	chr4	118005893	118005935	-	1	NA	intron (NM_009176, intron 5 of 11)	ORR1D1|LTR|ERVL-MaLR	-76151	NM_001284192	11876	Mm.56897	NM_009711	ENSMUSG00000028539	Artn	neublastin	artemin	protein-coding
mm_62488.1	chr7	101896853	101896869	+	1	NA	intron (NM_001291349, intron 1 of 4)	intron (NM_001291349, intron 1 of 4)	530	NM_001291349	75430	Mm.284491	NM_027532	ENSMUSG00000030649	Anapc15	3200002M19Rik|6330414C15Rik|APC15	anaphase prompoting complex C subunit 15	protein-coding
mm_48571.1	chr5	143315316	143315358	-	1	NA	promoter-TSS (NM_172726)	promoter-TSS (NM_172726)	23	NM_172726	231868	Mm.440105	NM_172726	ENSMUSG00000039244	E130309D02Rik	A630028N22	RIKEN cDNA E130309D02 gene	protein-coding
mm_97263.1	chr11	75764764	75764800	+	1	NA	3' UTR (NM_009536, exon 6 of 6)	3' UTR (NM_009536, exon 6 of 6)	-31027	NR_136933	102641247	Mm.411386	NR_136932		Gm12339	OTTMUSG00000006218	predicted gene 12339	ncRNA
mm_18826.1	chr2	74661195	74661201	-	1	NA	Intergenic	Intergenic	-1641	NM_007967	14029	Mm.25365	NM_007967	ENSMUSG00000001815	Evx2	Evx-2	even-skipped homeobox 2	protein-coding
mm_128262.1	chr15	36771456	36771475	-	1	NA	3' UTR (NM_001253807, exon 5 of 5)	3' UTR (NM_001253807, exon 5 of 5)	19467	NM_001253807	22631	Mm.3360	NM_011740	ENSMUSG00000022285	Ywhaz	1110013I11Rik|14-3-3zeta|AI596267|AL022924|AU020854	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide	protein-coding
mm_146600.1	chr18	9450164	9450174	-	1	NA	promoter-TSS (NM_026484)	promoter-TSS (NM_026484)	-19	NM_026484	67974	Mm.86523	NM_026484	ENSMUSG00000024286	Ccny	1700025H17Rik|3110050L10Rik|4631402G10Rik|5730405I09Rik	cyclin Y	protein-coding
mm_88802.1	chr10	80712757	80712792	+	1	NA	exon (NM_007460, exon 21 of 31)	exon (NM_007460, exon 21 of 31)	10081	NM_027829	71564	Mm.35802	NM_027829	ENSMUSG00000055862	Izumo4	9030607L17Rik|AI550407	IZUMO family member 4	protein-coding
mm_86557.1	chr10	11149407	11149417	+	1	NA	promoter-TSS (NM_001077707)	promoter-TSS (NM_001077707)	-18	NM_001077707	268281	Mm.133101	NM_172937	ENSMUSG00000090112	Shprh	2610103K11Rik|AA450458|AU024614|BC006883|D230017O13Rik|E130018M05	SNF2 histone linker PHD RING helicase	protein-coding
mm_134553.1	chr16	19983053	19983067	-	1	NA	promoter-TSS (NM_183390)	promoter-TSS (NM_183390)	-11	NM_183390	239743	Mm.86699	NM_183390	ENSMUSG00000043008	Klhl6	-	kelch-like 6	protein-coding
mm_50790.1	chr6	54039710	54039733	+	1	NA	promoter-TSS (NM_001163640)	promoter-TSS (NM_001163640)	-211	NM_001163640	69993	Mm.321147	NM_023543	ENSMUSG00000004633	Chn2	1700026N20Rik|4930557O16Rik|ARHGAP3|Bch	chimerin 2	protein-coding
mm_29697.1	chr3	123116986	123116996	-	1	NA	exon (NM_080451, exon 3 of 5)	exon (NM_080451, exon 3 of 5)	-82004	NM_021503	59006	Mm.141157	NM_021503	ENSMUSG00000028116	Myoz2	1110012I24Rik|Fatz-2|Myozl2	myozenin 2	protein-coding
mm_36873.1	chr4	107177714	107177723	-	1	NA	promoter-TSS (NM_029565)	promoter-TSS (NM_029565)	648	NM_025617	66526	Mm.246956	NM_025617	ENSMUSG00000028619	Tceanc2	2210010B22Rik|2210012G02Rik|6330404A07Rik|AU015593|Tdeanc2	transcription elongation factor A (SII) N-terminal and central domain containing 2	protein-coding
mm_147211.1	chr18	37954937	37954952	-	1	NA	promoter-TSS (NM_010411)	promoter-TSS (NM_010411)	44	NM_010411	15183	Mm.20521	NM_010411	ENSMUSG00000024454	Hdac3	AW537363	histone deacetylase 3	protein-coding
mm_80244.1	chr9	72742668	72742688	+	1	NA	exon (NM_010890, exon 26 of 29)	exon (NM_010890, exon 26 of 29)	-64596	NM_175485	235472	Mm.31696	NM_175485	ENSMUSG00000036030	Prtg	A230098A12Rik|Igdcc5	protogenin	protein-coding
mm_166022.1	chr4	123947978	123947985	+	1	NA	Intergenic	Intergenic	30548	NM_017475	54170	Mm.220922	NM_017475	ENSMUSG00000028646	Rragc	AU041672|Gtr2|RAGC|TIB929|YGR163W	Ras-related GTP binding C	protein-coding
mm_121229.1	chr14	103055706	103055716	+	1	NA	3' UTR (NM_008392, exon 5 of 5)	3' UTR (NM_008392, exon 5 of 5)	8699	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_31854.1	chr4	76451454	76451463	+	1	NA	intron (NM_011211, intron 10 of 39)	intron (NM_011211, intron 10 of 39)	-1173172	NM_025849	66928	Mm.24332	NM_025849	ENSMUSG00000028398	Tmem261	1700027K24Rik|3110001D03Rik	transmembrane protein 261	protein-coding
mm_12753.1	chr2	79255218	79255243	+	1	NA	promoter-TSS (NM_010576)	promoter-TSS (NM_010576)	-196	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D|Itga4B	integrin alpha 4	protein-coding
mm_29293.1	chr3	107783467	107783470	-	1	NA	Intergenic	Intergenic	-22999	NM_001113529	12977	Mm.795	NM_007778	ENSMUSG00000014599	Csf1	C87615|Csfm|MCSF|op	colony stimulating factor 1 (macrophage)	protein-coding
mm_101086.1	chr11	11822947	11822963	-	1	NA	intron (NM_001190448, intron 11 of 14)	intron (NM_001190448, intron 11 of 14)	-13993	NM_001163360	60530	Mm.236114	NM_021891	ENSMUSG00000035455	Fignl1	-	fidgetin-like 1	protein-coding
mm_40170.1	chr5	35814456	35814482	+	1	NA	intron (NM_001177696, intron 6 of 21)	intron (NM_001177696, intron 6 of 21)	56589	NM_001177698	231148	Mm.254446	NM_177678	ENSMUSG00000029095	Ablim2	AI606905|C230091L11	actin-binding LIM protein 2	protein-coding
mm_32508.1	chr4	108478968	108478980	+	1	NA	exon (NM_175472, exon 3 of 31)	exon (NM_175472, exon 3 of 31)	19548	NM_175472	230594	Mm.25181	NM_175472	ENSMUSG00000034610	Zcchc11	6030404K05Rik|9230115F04Rik|PPAPD3|mKIAA0191	zinc finger, CCHC domain containing 11	protein-coding
mm_116370.1	chr13	40731662	40731670	-	1	NA	intron (NM_001301674, intron 2 of 7)	CpG	-1209	NM_001122948	21418	Mm.85544	NM_011547	ENSMUSG00000021359	Tfap2a	AP-2|AP2alpha|Ap-2 (a)|Ap2|Ap2tf|Tcfap2a	transcription factor AP-2, alpha	protein-coding
mm_149226.1	chr19	10034673	10034689	+	1	NA	3' UTR (NM_144538, exon 10 of 10)	3' UTR (NM_144538, exon 10 of 10)	-6867	NM_021890	60527	Mm.253875	NM_021890	ENSMUSG00000024664	Fads3	AI464531	fatty acid desaturase 3	protein-coding
mm_55506.1	chr6	69858903	69858932	-	1	NA	Intergenic	Intergenic	-531743	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_33884.1	chr4	136173168	136173178	+	1	NA	intron (NM_177733, intron 1 of 6)	CpG	899	NM_177733	242705	Mm.307932	NM_177733	ENSMUSG00000018983	E2f2	E2F-2	E2F transcription factor 2	protein-coding
mm_164854.1	chr18	48586404	48586406	+	1	NA	Intergenic	RLTR13D5|LTR|ERVK	541070	NM_001025388	433182	Mm.70666	NM_001025388	ENSMUSG00000059040	Eno1b	EG433182|Eno1|Gm5506	enolase 1B, retrotransposed	protein-coding
mm_112859.1	chr13	20842231	20842251	+	1	NA	intron (NM_012054, intron 3 of 20)	L2|LINE|L2	48128	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_166229.1	chr5	66069968	66069984	-	1	NA	intron (NM_178446, intron 2 of 6)	intron (NM_178446, intron 2 of 6)	28203	NM_139065	245945	Mm.36863	NM_139065	ENSMUSG00000070780	Rbm47	9530077J19Rik	RNA binding motif protein 47	protein-coding
mm_151565.1	chr19	60755948	60755979	+	1	NA	promoter-TSS (NM_178421)	promoter-TSS (NM_178421)	-24	NM_178421	332397	Mm.186390	NM_178421	ENSMUSG00000072437	Nanos1	NOS-1	nanos homolog 1 (Drosophila)	protein-coding
mm_123708.1	chr14	69805525	69805552	-	1	NA	promoter-TSS (NM_153514)	promoter-TSS (NM_153514)	7	NM_153514	246710	Mm.102367	NM_153514	ENSMUSG00000022075	Rhobtb2	Dbc2|E130206H14Rik|mKIAA0717	Rho-related BTB domain containing 2	protein-coding
mm_158641.1	chrX	155216445	155216456	-	1	NA	promoter-TSS (NM_009121)	promoter-TSS (NM_009121)	-1	NM_001291865	20229	Mm.2734	NM_009121	ENSMUSG00000025283	Sat1	AA617398|SSAT|Sat	spermidine/spermine N1-acetyl transferase 1	protein-coding
mm_78770.1	chr9	43320517	43320536	+	1	NA	exon (NM_023655, exon 3 of 9)	exon (NM_023655, exon 3 of 9)	9763	NM_023655	72169	Mm.273277	NM_023655	ENSMUSG00000032013	Trim29	1110047J21Rik|2810431N19Rik|4732461M22Rik|AI119726	tripartite motif-containing 29	protein-coding
mm_35867.1	chr4	49506529	49506533	-	1	NA	promoter-TSS (NM_007519)	promoter-TSS (NM_007519)	27	NM_007519	12012	Mm.2859	NM_007519	ENSMUSG00000039653	Baat	AI118337|AI158864|BAT	bile acid-Coenzyme A: amino acid N-acyltransferase	protein-coding
mm_106091.1	chr11	116198255	116198269	-	1	NA	promoter-TSS (NM_027107)	promoter-TSS (NM_027107)	-593	NM_027107	69535	Mm.390347	NM_027107	ENSMUSG00000020778	Ten1	2310004N24Rik	TEN1 telomerase capping complex subunit	protein-coding
mm_21388.1	chr2	157557607	157557609	-	1	NA	3' UTR (NM_016916, exon 2 of 2)	3' UTR (NM_016916, exon 2 of 2)	-2470	NM_001291129	18111	Mm.34330	NM_010923	ENSMUSG00000067786	Nnat	5730414I02Rik|AW107673|Peg5	neuronatin	protein-coding
mm_80068.1	chr9	69467281	69467305	+	1	NA	exon (NM_007585, exon 3 of 13)	exon (NM_007585, exon 3 of 13)	10349	NR_037296	100526560		NR_037296	ENSMUSG00000093042	Mir3109	mir-3109|mmu-mir-3109	microRNA 3109	ncRNA
mm_91869.1	chr10	59469491	59469497	-	1	NA	intron (NM_001033259, intron 2 of 7)	L1MEf|LINE|L1	-27715	NM_010959	18302	Mm.123013	NM_010959	ENSMUSG00000009654	Oit3	EF-9|LZP	oncoprotein induced transcript 3	protein-coding
mm_172212.1	chr6	59199919	59199927	+	1	NA	Intergenic	L1Md_Gf|LINE|L1	-8947	NM_001081145	68140	Mm.25843	NM_001081145	ENSMUSG00000049232	Tigd2	3632410O17Rik	tigger transposable element derived 2	protein-coding
mm_65104.1	chr7	19304429	19304446	-	1	NA	3' UTR (NM_008036, exon 4 of 4)	3' UTR (NM_008036, exon 4 of 4)	5608	NM_008036	14282	Mm.248335	NM_008036	ENSMUSG00000003545	Fosb	-	FBJ osteosarcoma oncogene B	protein-coding
mm_94071.1	chr10	128401832	128401853	-	1	NA	promoter-TSS (NM_001136237)	promoter-TSS (NM_001136237)	-618	NM_001136237	72002	Mm.22983	NM_028051	ENSMUSG00000039878	Slc39a5	1810013D05Rik|2010205A06Rik|Zip5	solute carrier family 39 (metal ion transporter), member 5	protein-coding
mm_98635.1	chr11	96124514	96124541	+	1	NA	Intergenic	CpG	-9259	NM_172799	237930	Mm.249912	NM_172799	ENSMUSG00000038756	Ttll6	4932418K24Rik|D11Moh43e|D11Moh44e|t8130b59	tubulin tyrosine ligase-like family, member 6	protein-coding
mm_159461.1	chr3	158023207	158023207	-	1	NA	intron (NM_001093752, intron 3 of 12)	intron (NM_001093752, intron 3 of 12)	8547	NM_001093753	69207	Mm.223946	NM_026989	ENSMUSG00000055436	Srsf11	0610009J05Rik|2610019N13Rik|BF642805|Sfrs11	serine/arginine-rich splicing factor 11	protein-coding
mm_105378.1	chr11	103267365	103267391	-	1	NA	promoter-TSS (NM_016896)	promoter-TSS (NM_016896)	23	NM_016896	53859	Mm.158981	NM_016896	ENSMUSG00000020941	Map3k14	Nik|aly	mitogen-activated protein kinase kinase kinase 14	protein-coding
mm_153861.1	chr19	46573060	46573082	-	1	NA	promoter-TSS (NM_053196)	promoter-TSS (NM_053196)	14	NM_019718	56350	Mm.22085	NM_019718	ENSMUSG00000025035	Arl3	-	ADP-ribosylation factor-like 3	protein-coding
mm_87530.1	chr10	53344204	53344215	+	1	NA	3' UTR (NM_001141927, exon 3 of 3)	3' UTR (NM_001141927, exon 3 of 3)	6523	NM_001141927	18821	Mm.34145	NM_023129	ENSMUSG00000038583	Pln	Plb	phospholamban	protein-coding
mm_105716.1	chr11	108344091	108344104	-	1	NA	promoter-TSS (NM_011101)	promoter-TSS (NM_011101)	-209	NM_011101	18750	Mm.222178	NM_011101	ENSMUSG00000050965	Prkca	AI875142|Pkca	protein kinase C, alpha	protein-coding
mm_116454.1	chr13	43268960	43268969	-	1	NA	intron (NM_001033399, intron 1 of 1)	intron (NM_001033399, intron 1 of 1)	35208	NM_001033399	328232	Mm.441399	NM_001033399	ENSMUSG00000051335	Gfod1	9630032O13|AI850995	glucose-fructose oxidoreductase domain containing 1	protein-coding
mm_89246.1	chr10	87858817	87858832	+	1	NA	promoter-TSS (NM_010512)	promoter-TSS (NM_010512)	-228	NM_001111275	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_57827.1	chr6	129463154	129463165	-	1	NA	exon (NM_020008, exon 6 of 6)	exon (NM_020008, exon 6 of 6)	9620	NM_001309637	56644	Mm.239516	NM_020008	ENSMUSG00000079293	Clec7a	BGR|Clecsf12|beta-GR	C-type lectin domain family 7, member a	protein-coding
mm_126742.1	chr15	85723826	85723849	+	1	NA	Intergenic	L2c|LINE|L2	-11727	NM_001113418	19013	Mm.212789	NM_011144	ENSMUSG00000022383	Ppara	4933429D07Rik|AW742785|Nr1c1|PPAR-alpha|PPARalpha|Ppar	peroxisome proliferator activated receptor alpha	protein-coding
mm_13048.1	chr2	91098421	91098466	+	1	NA	intron (NM_011355, intron 1 of 4)	intron (NM_011355, intron 1 of 4)	1765	NM_011355	20375	Mm.1302	NM_011355	ENSMUSG00000002111	Spi1	Dis-1|Dis1|PU.1|Sfpi-1|Sfpi1|Spi-1|Tcfpu1|Tfpu.1	spleen focus forming virus (SFFV) proviral integration oncogene	protein-coding
mm_147872.1	chr18	64488978	64488982	-	1	NA	promoter-TSS (NM_007998)	promoter-TSS (NM_007998)	86	NM_007998	14151	Mm.1070	NM_007998	ENSMUSG00000024588	Fech	AI894116|Fcl|fch	ferrochelatase	protein-coding
mm_29751.1	chr3	127027664	127027675	-	1	NA	intron (NM_001327938, intron 13 of 47)	B4A|SINE|B4	-29217	NM_178655	109676	Mm.220242	NM_178655	ENSMUSG00000032826	Ank2	100043364|AI835472|AW491075|Ank-2|Gm4392	ankyrin 2, brain	protein-coding
mm_3126.1	chr1	134709362	134709369	+	1	NA	intron (NM_009307, intron 2 of 9)	CpG	62684	NM_009307	20980	Mm.5102	NM_009307	ENSMUSG00000026452	Syt2	IP4BP|R74640|mKIAA4194	synaptotagmin II	protein-coding
mm_139200.1	chr17	47662989	47662991	+	1	NA	intron (NM_198421, intron 2 of 6)	B2_Mm1t|SINE|B2	-24620	NR_045945	100415787	Mm.392206	NR_045945	ENSMUSG00000084880	Tomm6os	Gm14872|OTTMUSG00000018355|Prickle4os	translocase of outer mitochondrial membrane 6, opposite strand	ncRNA
mm_60638.1	chr7	44828526	44828537	+	1	NA	5' UTR (NM_053074, exon 2 of 2)	5' UTR (NM_053074, exon 2 of 2)	-7757	NM_010215	14204	Mm.2565	NM_010215	ENSMUSG00000074141	Il4i1	Fig1|Fig1-ps|LAAO|LAO	interleukin 4 induced 1	protein-coding
mm_163551.1	chr13	23706099	23706114	-	1	NA	exon (NM_001347493, exon 3 of 5)	exon (NM_001347493, exon 3 of 5)	4748	NM_001347493	15216	Mm.2681	NM_010424	ENSMUSG00000006611	Hfe	MR2	hemochromatosis	protein-coding
mm_32294.1	chr4	103117220	103117251	+	1	NA	intron (NM_001286223, intron 1 of 12)	intron (NM_001286223, intron 1 of 12)	1675	NM_001286223	71148	Mm.288721	NM_027696	ENSMUSG00000028522	Mier1	4933425I22Rik|5830411K19Rik|er1	MEIR1 treanscription regulator	protein-coding
mm_38492.1	chr4	140906779	140906785	-	1	NA	intron (NM_008812, intron 1 of 15)	intron (NM_008812, intron 1 of 15)	422	NM_008812	18600	Mm.2296	NM_008812	ENSMUSG00000028927	Padi2	Pdi|Pdi2|mKIAA0994	peptidyl arginine deiminase, type II	protein-coding
mm_26599.1	chr3	151988441	151988447	+	1	NA	Intergenic	Intergenic	-150916	NM_008966	19220	Mm.331442	NM_008966	ENSMUSG00000028036	Ptgfr	AI957154|PGF|fp	prostaglandin F receptor	protein-coding
mm_125778.1	chr15	74709370	74709398	+	1	NA	promoter-TSS (NM_008415)	promoter-TSS (NM_008415)	-62	NM_008415	16469	Mm.87052	NM_008415	ENSMUSG00000046380	Jrk	-	jerky	protein-coding
mm_91454.1	chr10	34019562	34019626	-	1	NA	promoter-TSS (NM_025614)	promoter-TSS (NM_025614)	22	NM_025614	66521	Mm.28528	NM_025614	ENSMUSG00000019782	Rwdd1	0710001K08Rik|2610002D06Rik|2700069A07Rik|IH1	RWD domain containing 1	protein-coding
mm_1262.1	chr1	63177092	63177096	+	1	NA	promoter-TSS (NM_001160039)	promoter-TSS (NM_001160039)	263	NM_018796	55949	Mm.2718	NM_018796	ENSMUSG00000025967	Eef1b2	2810017J07Rik|Eef1b	eukaryotic translation elongation factor 1 beta 2	protein-coding
mm_6347.1	chr1	71642023	71642038	-	1	NA	exon (NM_001276413, exon 8 of 44)	exon (NM_001276413, exon 8 of 44)	11204	NM_010233	14268	Mm.193099	NM_010233	ENSMUSG00000026193	Fn1	E330027I09|Fn|Fn-1	fibronectin 1	protein-coding
mm_21875.1	chr2	166081028	166081064	-	1	NA	intron (NM_001252579, intron 13 of 20)	intron (NM_001252579, intron 13 of 20)	74239	NM_001252578	72043	Mm.1011	NM_028072	ENSMUSG00000006800	Sulf2	2010004N24Rik|AU020235|MSulf-2|mKIAA1247	sulfatase 2	protein-coding
mm_117911.1	chr13	99430818	99430826	-	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-17996	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_138945.1	chr17	44078913	44078950	+	1	NA	5' UTR (NM_001329620, exon 1 of 4)	5' UTR (NM_001329620, exon 1 of 4)	129	NM_001329619	83965	Mm.30145	NM_032003	ENSMUSG00000023960	Enpp5	AW061004|D17Abb1e|E-NPP 5	ectonucleotide pyrophosphatase/phosphodiesterase 5	protein-coding
mm_124926.1	chr15	12146276	12146286	+	1	NA	exon (NM_011767, exon 6 of 20)	exon (NM_011767, exon 6 of 20)	-25211	NR_035443	100316684		NR_035443	ENSMUSG00000084592	Mir1898	Mirn1898|mmu-mir-1898	microRNA 1898	ncRNA
mm_126658.1	chr15	84232051	84232076	+	1	NA	promoter-TSS (NM_133167)	promoter-TSS (NM_133167)	20	NM_133167	170736	Mm.323892	NM_133167	ENSMUSG00000022438	Parvb	AI595373|AW742462|D15Gsk1|affixin	parvin, beta	protein-coding
mm_92679.1	chr10	80577286	80577327	-	1	NA	promoter-TSS (NM_078477)	promoter-TSS (NM_078477)	-10	NM_078477	118445	Mm.41513	NM_078477	ENSMUSG00000035397	Klf16	AI843742|BTEB4|DRRF	Kruppel-like factor 16	protein-coding
mm_18122.1	chr2	44997298	44997310	-	1	NA	exon (NM_015753, exon 8 of 10)	exon (NM_015753, exon 8 of 10)	25873	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_122214.1	chr14	32160069	32160070	-	1	NA	intron (NM_001033988, intron 1 of 9)	CpG	182	NM_001033988	27057	Mm.371598	NM_019744	ENSMUSG00000056234	Ncoa4	ARA70|Rfg	nuclear receptor coactivator 4	protein-coding
mm_158078.1	chrX	101264954	101264965	-	1	NA	promoter-TSS (NM_001317221)	promoter-TSS (NM_001317221)	-967	NM_001317221	245536	Mm.212463	NM_001033362	ENSMUSG00000090141	Gm614	-	predicted gene 614	protein-coding
mm_63514.1	chr7	127875926	127875948	+	1	NA	intron (NM_146259, intron 1 of 2)	CpG	886	NM_146259	244219	Mm.207872	NM_146259	ENSMUSG00000049728	Zfp668	BC030314|E130018B19Rik|Znf668	zinc finger protein 668	protein-coding
mm_89794.1	chr10	102511774	102511778	+	1	NA	promoter-TSS (NM_146240)	promoter-TSS (NM_146240)	-446	NM_146240	237504	Mm.282672	NM_146240	ENSMUSG00000044921	Rassf9	AW322107|Pamci	Ras association (RalGDS/AF-6) domain family (N-terminal) member 9	protein-coding
mm_125384.1	chr15	40655338	40655357	+	1	NA	5' UTR (NM_011766, exon 1 of 8)	5' UTR (NM_011766, exon 1 of 8)	305	NM_011766	22762	Mm.39496	NM_011766	ENSMUSG00000022306	Zfpm2	B330005D23Rik|FOG-2|FOG2	zinc finger protein, multitype 2	protein-coding
mm_85512.1	chr9	106251017	106251031	-	1	NA	Intergenic	Intergenic	-3070	NM_020559	11655	Mm.290578	NM_020559	ENSMUSG00000032786	Alas1	ALAS|ALAS-N|Alas-1|Alas-h	aminolevulinic acid synthase 1	protein-coding
mm_14908.1	chr2	150570373	150570381	+	1	NA	promoter-TSS (NM_009977)	promoter-TSS (NM_009977)	-38	NM_009977	13011	Mm.12965	NM_009977	ENSMUSG00000068129	Cst7	Cmap	cystatin F (leukocystatin)	protein-coding
mm_145718.1	chr18	62994890	62994923	+	1	NA	intron (NM_028017, intron 10 of 11)	intron (NM_028017, intron 10 of 11)	16990	NM_028017	108123	Mm.292687	NM_028017	ENSMUSG00000024581	Napg	2400003O04Rik|SNARE	N-ethylmaleimide sensitive fusion protein attachment protein gamma	protein-coding
mm_83494.1	chr9	45946002	45946011	-	1	NA	intron (NM_172257, intron 12 of 25)	intron (NM_172257, intron 12 of 25)	-6416	NR_106055	102465659		NR_106055	ENSMUSG00000098327	Mir7087	Gm27273|mmu-mir-7087	microRNA 7087	ncRNA
mm_45483.1	chr5	70960465	70960466	-	1	NA	TTS (NM_008066)	TTS (NM_008066)	-117848	NM_010252	14405	Mm.255292	NM_010252	ENSMUSG00000001260	Gabrg1	GabaA|GabaA/BZ	gamma-aminobutyric acid (GABA) A receptor, subunit gamma 1	protein-coding
mm_84151.1	chr9	59486438	59486480	-	1	NA	promoter-TSS (NM_019927)	promoter-TSS (NM_019927)	-85	NM_019927	23806	Mm.305925	NM_019927	ENSMUSG00000025234	Arih1	AU021774|Ari|Ari1|Hari|Hhari|Ubch7bp|Uip77	ariadne RBR E3 ubiquitin protein ligase 1	protein-coding
mm_165280.1	chr2	82053063	82053091	+	1	NA	promoter-TSS (NM_175513)	promoter-TSS (NM_175513)	-581	NM_175513	241514	Mm.119383	NM_175513	ENSMUSG00000070866	Zfp804a	C630007C17Rik|Znf804a	zinc finger protein 804A	protein-coding
mm_52091.1	chr6	97833005	97833019	+	1	NA	intron (NM_001113198, intron 1 of 9)	intron (NM_001113198, intron 1 of 9)	25954	NM_001113198	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_155880.1	chrX	101449165	101449170	+	1	NA	promoter-TSS (NM_013712)	promoter-TSS (NM_013712)	58	NM_013712	26549	Mm.46232	NM_013712	ENSMUSG00000031312	Itgb1bp2	Chordc3	integrin beta 1 binding protein 2	protein-coding
mm_50631.1	chr6	50891298	50891305	+	1	NA	Intergenic	Intergenic	115186	NR_045984	319981	Mm.131454	NR_045984	ENSMUSG00000107667	C530044C16Rik	-	RIKEN cDNA C530044C16 gene	ncRNA
mm_34394.1	chr4	145017949	145017966	+	1	NA	intron (NM_001276502, intron 65 of 68)	intron (NM_001276502, intron 65 of 68)	124820	NM_011303	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding
mm_75735.1	chr8	69625147	69625193	-	1	NA	promoter-TSS (NM_001045553)	promoter-TSS (NM_001045553)	5	NM_001045553	234362	Mm.458487	NM_172754	ENSMUSG00000060427	Zfp868	AI449175|AW108241|C530032E20|mszf62	zinc finger protein 868	protein-coding
mm_68361.1	chr7	106513751	106513761	-	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	-72683	NR_003967	209380	Mm.461779	NM_001001318		Gm4759	EG209380	GTPase, very large interferon inducible 1 pseudogene	pseudo
mm_141709.1	chr17	34000277	34000290	-	1	NA	promoter-TSS (NM_001001892)	promoter-TSS (NM_001001892)	50	NM_001001892	14972	Mm.422886	NM_001001892	ENSMUSG00000061232	H2-K1	H-2K|H-2K(d)|H2-K|K-f	histocompatibility 2, K1, K region	protein-coding
mm_5060.1	chr1	194986616	194986641	+	1	NA	Intergenic	Intergenic	-9669	NR_033564	320400	Mm.417608	NR_033564	ENSMUSG00000097325	Gm16897	C030002c11rik	predicted gene, 16897	ncRNA
mm_56657.1	chr6	113434801	113434807	-	1	NA	intron (NM_178373, intron 1 of 5)	intron (NM_178373, intron 1 of 5)	951	NM_178373	14311	Mm.10026	NM_178373	ENSMUSG00000030278	Cidec	CIDE-3|Fsp27	cell death-inducing DFFA-like effector c	protein-coding
mm_160594.1	chr9	71869924	71869924	-	1	NA	intron (NM_001253863, intron 7 of 13)	intron (NM_001253863, intron 7 of 13)	26172	NM_001253864	21406	Mm.171615	NM_011544	ENSMUSG00000032228	Tcf12	A130037E08Rik|ALF1|HEB|HEBAlt|HTF-4|HTF4|ME1|REB|bHLHb20	transcription factor 12	protein-coding
mm_75052.1	chr8	33234932	33234951	-	1	NA	3' UTR (NM_001122822, exon 34 of 34)	3' UTR (NM_001122822, exon 34 of 34)	150586	NM_001122822	22427	Mm.228805	NM_011721	ENSMUSG00000031583	Wrn	AI846146	Werner syndrome homolog (human)	protein-coding
mm_167591.1	chr9	46241091	46241100	+	1	NA	5' UTR (NM_007468, exon 1 of 3)	5' UTR (NM_007468, exon 1 of 3)	251	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_155998.1	chrX	106157435	106157449	+	1	NA	exon (NM_205820, exon 3 of 3)	exon (NM_205820, exon 3 of 3)	14167	NM_205820	279572	Mm.336203	NM_205820	ENSMUSG00000033777	Tlr13	AI666735|Gm713	toll-like receptor 13	protein-coding
mm_67297.1	chr7	79145362	79145384	-	1	NA	exon (NM_008594, exon 3 of 10)	exon (NM_008594, exon 3 of 10)	3687	NM_001045489	17304	Mm.1451	NM_008594	ENSMUSG00000030605	Mfge8	AA408458|AI325141|MFG-E8|MP47|Mfgm|P47|SED1|lactadherin	milk fat globule-EGF factor 8 protein	protein-coding
mm_20657.1	chr2	132111441	132111465	-	1	NA	intron (NM_018824, intron 1 of 15)	intron (NM_018824, intron 1 of 15)	33655	NM_018824	54338	Mm.103581	NM_018824	ENSMUSG00000027340	Slc23a2	AI844736|NBTL1|SVCT2|Slc23a1|YSPL2|YSPL3|mKIAA0238	solute carrier family 23 (nucleobase transporters), member 2	protein-coding
mm_83325.1	chr9	44196524	44196556	-	1	NA	intron (NM_007619, intron 2 of 15)	L1MB5|LINE|L1	37506	NM_007619	12402	Mm.266871	NM_007619	ENSMUSG00000034342	Cbl	4732447J05Rik|Cbl-2|c-Cbl|cbl	Casitas B-lineage lymphoma	protein-coding
mm_92738.1	chr10	80918213	80918256	-	1	NA	promoter-TSS (NM_010722)	promoter-TSS (NM_010722)	11	NM_010722	16907	Mm.7362	NM_010722	ENSMUSG00000062075	Lmnb2	-	lamin B2	protein-coding
mm_106523.1	chr11	120562697	120562714	-	1	NA	exon (NM_011032, exon 8 of 11)	exon (NM_011032, exon 8 of 11)	10231	NM_011032	18453	Mm.16660	NM_011032	ENSMUSG00000025130	P4hb	ERp59|PDI|Pdia1|Thbp	prolyl 4-hydroxylase, beta polypeptide	protein-coding
mm_99712.1	chr11	106230666	106230666	+	1	NA	intron (NM_028074, intron 5 of 17)	intron (NM_028074, intron 5 of 17)	13740	NM_028074	72047	Mm.41367	NM_028074	ENSMUSG00000020705	Ddx42	1810047H21Rik|AW319508|AW556242|B430002H05Rik|RHELP|RNAHP|SF3b125	DEAD (Asp-Glu-Ala-Asp) box polypeptide 42	protein-coding
mm_141139.1	chr17	26252856	26252875	-	1	NA	promoter-TSS (NM_025881)	promoter-TSS (NM_025881)	-45	NM_025881	66978	Mm.440216	NM_025881	ENSMUSG00000024188	Luc7l	1810045C04Rik|2410018D03Rik	Luc7-like	protein-coding
mm_11814.1	chr2	43997302	43997312	+	1	NA	intron (NM_001301832, intron 7 of 14)	intron (NM_001301832, intron 7 of 14)	68017	NR_040622	320872	Mm.445023	NR_040622	ENSMUSG00000085089	Arhgap15os	A430092G05Rik	Rho GTPase activating protein 15, opposite strand	ncRNA
mm_105799.1	chr11	110097545	110097586	-	1	NA	Intergenic	Intergenic	-1628	NM_153145	217258	Mm.344148	NM_153145	ENSMUSG00000041828	Abca8a	-	ATP-binding cassette, sub-family A (ABC1), member 8a	protein-coding
mm_118775.1	chr14	22937444	22937454	+	1	NA	intron (NM_028275, intron 6 of 6)	intron (NM_028275, intron 6 of 6)	157122	NR_033550	791307	Mm.364384	NR_033550	ENSMUSG00000068680	Gm10248	ENSMUSG00000068680	predicted gene 10248	ncRNA
mm_98237.1	chr11	88105373	88105376	+	1	NA	intron (NM_198013, intron 1 of 10)	B1F|SINE|Alu	6228	NM_198013	103841	Mm.374846	NM_198013	ENSMUSG00000018378	Cuedc1	AI841487|C330016O16Rik	CUE domain containing 1	protein-coding
mm_99371.1	chr11	101984239	101984248	+	1	NA	intron (NM_028207, intron 1 of 2)	intron (NM_028207, intron 1 of 2)	548	NM_028207	72349	Mm.196295	NM_028207	ENSMUSG00000003518	Dusp3	2210015O03Rik|5031436O03Rik|T-DSP11|VHR	dual specificity phosphatase 3 (vaccinia virus phosphatase VH1-related)	protein-coding
mm_97018.1	chr11	71516516	71516541	+	1	NA	Intergenic	Intergenic	-231296	NR_027858	627984	Mm.390378	NM_001039234	ENSMUSG00000092528	Nlrp1c-ps	Nalp1c|Nlrp1c|OTTMUSG00000006090	NLR family, pyrin domain containing 1C, pseudogene	pseudo
mm_32577.1	chr4	110397711	110397763	+	1	NA	promoter-TSS (NM_001284190)	promoter-TSS (NM_001284190)	39	NM_030231	78933	Mm.435620	NM_030231	ENSMUSG00000061298	Agbl4	4930578N11Rik|4931433A01Rik	ATP/GTP binding protein-like 4	protein-coding
mm_132644.1	chr16	40495713	40495715	+	1	NA	Intergenic	Intergenic	-1037112	NM_001347236	268890	Mm.310524	NM_175548	ENSMUSG00000061080	Lsamp	5430428I19|AW046674|B130007O04Rik|D930023J12Rik|Lam|Lamp	limbic system-associated membrane protein	protein-coding
mm_79424.1	chr9	55430346	55430364	+	1	NA	exon (NM_172923, exon 9 of 11)	exon (NM_172923, exon 9 of 11)	81888	NM_145615	110842	Mm.290853	NM_145615	ENSMUSG00000032314	Etfa	2010200I21Rik|D9Ertd394e	electron transferring flavoprotein, alpha polypeptide	protein-coding
mm_37176.1	chr4	117251811	117251831	-	1	NA	promoter-TSS (NM_001033774)	promoter-TSS (NM_001033774)	96	NM_001145637	381544	Mm.23504	NM_001033774	ENSMUSG00000060268	Gm1661	Gm1662|Ncrna00082	predicted gene 1661	protein-coding
mm_165419.1	chr2	148397560	148397565	+	1	NA	TTS (NM_009219)	TTS (NM_009219)	2185	NM_009219	20608	Mm.35324	NM_009219	ENSMUSG00000037014	Sstr4	Smstr4|sst4	somatostatin receptor 4	protein-coding
mm_19557.1	chr2	98667015	98667031	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	1199366	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_77140.1	chr8	111522074	111522112	-	1	NA	promoter-TSS (NM_176923)	promoter-TSS (NM_176923)	14	NM_001170742	319481	Mm.247294	NM_176923	ENSMUSG00000031959	Wdr59	5430401O09Rik|Cdw12	WD repeat domain 59	protein-coding
mm_81230.1	chr9	107676043	107676051	+	1	NA	exon (NM_008140, exon 8 of 9)	exon (NM_008140, exon 8 of 9)	3545	NM_008140	14685	Mm.284853	NM_008140	ENSMUSG00000034837	Gnat1	Gnat-1|Ird1|Ird2|Tralpha|irdc|irdr|transducin	guanine nucleotide binding protein, alpha transducing 1	protein-coding
mm_76443.1	chr8	85025269	85025296	-	1	NA	promoter-TSS (NM_019652)	promoter-TSS (NM_019652)	-4	NM_019652	56495	Mm.41475	NM_019652	ENSMUSG00000052456	Asna1	1810048H22Rik|ArsA	arsA arsenite transporter, ATP-binding, homolog 1 (bacterial)	protein-coding
mm_164151.1	chr15	63814340	63814360	-	1	NA	Intergenic	MT2B|LTR|ERVL	-2838	NR_108057	78462	Mm.82775	NR_040315	ENSMUSG00000099435	1700065I16Rik	1700084L08Rik	gasdermin pseudogene	pseudo
mm_24118.1	chr3	88167573	88167588	+	1	NA	exon (NM_001310593, exon 9 of 11)	exon (NM_001310593, exon 9 of 11)	10205	NR_045997	76642	Mm.424420	NR_045997	ENSMUSG00000096935	1700113A16Rik	2210408E11Rik|AA408983	RIKEN cDNA 1700113A16 gene	ncRNA
mm_1360.1	chr1	66323948	66323985	+	1	NA	intron (NM_001310634, intron 2 of 14)	intron (NM_001310634, intron 2 of 14)	2242	NM_001310634	17756	Mm.256966	NM_008632	ENSMUSG00000015222	Map2	G1-397-34|MAP-2|Mtap-2|Mtap2|repro4	microtubule-associated protein 2	protein-coding
mm_28480.1	chr3	92438772	92438786	-	1	NA	promoter-TSS (NM_009265)	promoter-TSS (NM_009265)	0	NM_009265	20754	Mm.140151	NM_009265	ENSMUSG00000048455	Sprr1b	-	small proline-rich protein 1B	protein-coding
mm_45458.1	chr5	67783730	67783754	-	1	NA	intron (NM_001284345, intron 6 of 36)	intron (NM_001284345, intron 6 of 36)	63689	NM_009727	11980	Mm.153230	NM_009727	ENSMUSG00000037685	Atp8a1	AI481521|AI853962|APLT|AW743152|AW822227|Atp3a2|B230107D19Rik|ClassI	ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1	protein-coding
mm_20293.1	chr2	126933154	126933164	-	1	NA	promoter-TSS (NM_023220)	promoter-TSS (NM_023220)	76	NM_023220	66552	Mm.269928	NM_023220	ENSMUSG00000027366	Sppl2a	2010106G01Rik|C130089K23Rik	signal peptide peptidase like 2A	protein-coding
mm_87204.1	chr10	39641112	39641124	+	1	NA	intron (NM_134000, intron 4 of 8)	intron (NM_134000, intron 4 of 8)	28184	NM_134000	103213	Mm.436686	NM_134000	ENSMUSG00000019842	Traf3ip2	AI429613|Act1|CIKS	TRAF3 interacting protein 2	protein-coding
mm_1298.1	chr1	64532867	64532877	+	1	NA	promoter-TSS (NM_009952)	promoter-TSS (NM_009952)	68	NM_001037726	12912	Mm.422634	NM_009952	ENSMUSG00000025958	Creb1	2310001E10Rik|3526402H21Rik|AV083133|Creb|Creb-1	cAMP responsive element binding protein 1	protein-coding
mm_56058.1	chr6	86772344	86772385	-	1	NA	intron (NM_013471, intron 1 of 12)	intron (NM_013471, intron 1 of 12)	2750	NM_001331120	11746	Mm.259702	NM_013471	ENSMUSG00000029994	Anxa4	AI265406|AIV|AW106930|Anx4|Xanx-4	annexin A4	protein-coding
mm_45478.1	chr5	69592279	69592308	-	1	NA	promoter-TSS (NM_001038015)	promoter-TSS (NM_001038015)	-8	NM_001038015	67980	Mm.33830	NM_027681	ENSMUSG00000029209	Gnpda2	4921523I18Rik|4933412A11Rik|BB189630|GNPDA|Gnp2|Sb52|mKIAA4008	glucosamine-6-phosphate deaminase 2	protein-coding
mm_90022.1	chr10	115385046	115385057	+	1	NA	promoter-TSS (NM_025780)	promoter-TSS (NM_025780)	92	NM_001033261	216345	Mm.207621	NM_001033261	ENSMUSG00000034163	Zfc3h1	BC033596|Ccdc131|Psrc2	zinc finger, C3H1-type containing	protein-coding
mm_6926.1	chr1	84850037	84850045	-	1	NA	intron (NM_025386, intron 1 of 3)	ORR1D1|LTR|ERVL-MaLR	10200	NM_025386	66153	Mm.381192	NM_025386	ENSMUSG00000073633	Fbxo36	0610008D19Rik|1110020F21Rik|2410002G19Rik|D1Ertd757e	F-box protein 36	protein-coding
mm_121061.1	chr14	87417032	87417066	+	1	NA	intron (NM_172605, intron 1 of 13)	CpG	466	NM_001253755	219249	Mm.35168	NM_172605	ENSMUSG00000022019	Tdrd3	4732418C03Rik|6720468N18	tudor domain containing 3	protein-coding
mm_10986.1	chr2	26267333	26267333	+	1	NA	Intergenic	Intergenic	27224	NM_177841	329366	Mm.77712	NM_177841	ENSMUSG00000048038	Ccdc187	4932418E24Rik	coiled-coil domain containing 187	protein-coding
mm_28206.1	chr3	88296980	88296988	-	1	NA	promoter-TSS (NM_009836)	promoter-TSS (NM_009836)	-146	NM_029801	76927	Mm.273330	NM_029801	ENSMUSG00000010538	Tsacc	1700021C14Rik|SIP	TSSK6 activating co-chaperone	protein-coding
mm_161007.1	chr11	117860796	117860796	+	1	NA	promoter-TSS (NM_001085535)	promoter-TSS (NM_001085535)	44	NM_001085535	546519	Mm.385578	NM_001085535	ENSMUSG00000070330	Tmem235	Cldn27|Gm12581|OTTMUSG00000007589	transmembrane protein 235	protein-coding
mm_134684.1	chr16	22412960	22412981	-	1	NA	exon (NM_023794, exon 6 of 13)	exon (NM_023794, exon 6 of 13)	26600	NM_023794	104156	Mm.155708	NM_023794	ENSMUSG00000013089	Etv5	1110005E01Rik|8430401F14Rik|ERM	ets variant 5	protein-coding
mm_9672.1	chr1	178329057	178329068	-	1	NA	3' UTR (NM_016805, exon 14 of 14)	3' UTR (NM_016805, exon 14 of 14)	8722	NM_016805	51810	Mm.86589	NM_016805	ENSMUSG00000039630	Hnrnpu	AA408410|AI256620|AL024194|AL024437|AW557595|C86794|Hnrpu|SAFA|Sp120|hnRNP U	heterogeneous nuclear ribonucleoprotein U	protein-coding
mm_14852.1	chr2	148522558	148522586	+	1	NA	Intergenic	Intergenic	-79037	NM_010740	17064	Mm.681	NM_010740	ENSMUSG00000027435	Cd93	6030404G09Rik|AA145088|AA4.1|AW555904|C1qr1|C1qrp|Ly68	CD93 antigen	protein-coding
mm_87703.1	chr10	59899036	59899039	+	1	NA	Intergenic	Intergenic	19446	NM_019965	56709	Mm.103610	NM_019965	ENSMUSG00000020109	Dnajb12	Dj10|mDj10	DnaJ heat shock protein family (Hsp40) member B12	protein-coding
mm_21023.1	chr2	152398146	152398197	-	1	NA	promoter-TSS (NM_011438)	promoter-TSS (NM_011438)	-125	NM_011438	20667	Mm.28424	NM_011438	ENSMUSG00000051817	Sox12	2010205A02Rik	SRY (sex determining region Y)-box 12	protein-coding
mm_47638.1	chr5	125326336	125326385	-	1	NA	intron (NM_001205083, intron 1 of 10)	intron (NM_001205083, intron 1 of 10)	14734	NM_016741	20778	Mm.282242	NM_016741	ENSMUSG00000037936	Scarb1	AI120173|CD36|Cd36l1|Chohd1|Cla-1|Cla1|D5Ertd460e|Hdlq1|Hlb398|SR-B1|SR-BI|SRBI|Srb1|mSR-BI	scavenger receptor class B, member 1	protein-coding
mm_48987.1	chr6	4755793	4755809	+	1	NA	exon (NM_130877, exon 2 of 2)	exon (NM_130877, exon 2 of 2)	8495	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_33934.1	chr4	136890359	136890403	+	1	NA	exon (NM_007574, exon 3 of 3)	exon (NM_007574, exon 3 of 3)	2533	NM_007574	12262	Mm.439732	NM_007574	ENSMUSG00000036896	C1qc	AI385742|C1qg|Ciqc	complement component 1, q subcomponent, C chain	protein-coding
mm_119589.1	chr14	50944500	50944514	+	1	NA	5' UTR (NM_013632, exon 1 of 6)	5' UTR (NM_013632, exon 1 of 6)	204	NM_013632	18950	Mm.17932	NM_013632	ENSMUSG00000021871	Pnp	AL024301|AU015798|Np|Np-1|Np-2|Pnp1	purine-nucleoside phosphorylase	protein-coding
mm_91733.1	chr10	45486443	45486461	-	1	NA	Intergenic	CpG	-16251	NM_001031772	380669	Mm.440328	NM_001031772	ENSMUSG00000063804	Lin28b	2810403D23Rik|D030047M17Rik|Lin-28.2	lin-28 homolog B (C. elegans)	protein-coding
mm_132248.1	chr16	32751364	32751373	+	1	NA	exon (NM_080457, exon 2 of 27)	exon (NM_080457, exon 2 of 27)	15482	NM_080457	140474	Mm.214599	NM_080457	ENSMUSG00000079620	Muc4	4933405I11Rik|Asgp	mucin 4	protein-coding
mm_91730.1	chr10	45470250	45470260	-	1	NA	promoter-TSS (NM_001031772)	promoter-TSS (NM_001031772)	-54	NM_001031772	380669	Mm.440328	NM_001031772	ENSMUSG00000063804	Lin28b	2810403D23Rik|D030047M17Rik|Lin-28.2	lin-28 homolog B (C. elegans)	protein-coding
mm_156926.1	chrX	169302991	169303003	+	1	NA	exon (NM_001287530, exon 13 of 13)	exon (NM_001287530, exon 13 of 13)	17375	NM_001331050	15159	Mm.284033	NM_008222	ENSMUSG00000031352	Hccs	-	holocytochrome c synthetase	protein-coding
mm_137029.1	chr17	17887827	17887837	+	1	NA	promoter-TSS (NM_008039)	promoter-TSS (NM_008039)	8	NM_008039	14289	Mm.378918	NM_008039	ENSMUSG00000052270	Fpr2	E330010I07Rik|Fpr-rs2	formyl peptide receptor 2	protein-coding
mm_92180.1	chr10	67912476	67912492	-	1	NA	5' UTR (NM_178679, exon 1 of 5)	5' UTR (NM_178679, exon 1 of 5)	178	NM_178679	216049	Mm.268346	NM_178679	ENSMUSG00000037855	Zfp365	AI839779|AV340892|DBZ|Su48|Znf365|talanin	zinc finger protein 365	protein-coding
mm_122545.1	chr14	47757495	47757501	-	1	NA	Intergenic	Intergenic	93742	NM_001347522	16709	Mm.3110	NM_008477	ENSMUSG00000021843	Ktn1	-	kinectin 1	protein-coding
mm_147059.1	chr18	34953931	34953939	-	1	NA	intron (NM_010481, intron 1 of 16)	intron (NM_010481, intron 1 of 16)	416	NM_010481	15526	Mm.209419	NM_010481	ENSMUSG00000024359	Hspa9	74kDa|Csa|Grp75|Hsc74|Hsp74|Hsp74a|Hspa9a|Mortalin|Mot-2|Mot2|Mthsp70|Pbp74	heat shock protein 9	protein-coding
mm_86966.1	chr10	25359851	25359887	+	1	NA	promoter-TSS (NM_001199265)	promoter-TSS (NM_001199265)	71	NM_001199265	13822	Mm.306026	NM_013511	ENSMUSG00000019978	Epb41l2	4.1G|AW555191|D10Ertd398e|Epb4.1l2|NBL2	erythrocyte membrane protein band 4.1 like 2	protein-coding
mm_80873.1	chr9	98955274	98955291	+	1	NA	promoter-TSS (NR_003248)	promoter-TSS (NR_003248)	28	NR_003248	768252	Mm.129645	NR_003248	ENSMUSG00000097072	Foxl2os	ENSMUSG00000074122	forkhead box L2, opposite strand	ncRNA
mm_83174.1	chr9	40783056	40783105	-	1	NA	3' UTR (NM_133733, exon 7 of 7)	3' UTR (NM_133733, exon 7 of 7)	-18193	NM_031165	15481	Mm.290774	NM_031165	ENSMUSG00000015656	Hspa8	2410008N15Rik|Hsc70|Hsc71|Hsc73|Hsp73|Hspa10	heat shock protein 8	protein-coding
mm_21859.1	chr2	165884637	165884686	-	1	NA	5' UTR (NM_001252584, exon 1 of 23)	5' UTR (NM_001252584, exon 1 of 23)	177	NM_001252584	228880	Mm.227598	NM_027230	ENSMUSG00000039671	Zmynd8	1110013E22Rik|2010005I16Rik|3632413B07Rik|AI316811|AL024039|Prkcbp1|RACK7	zinc finger, MYND-type containing 8	protein-coding
mm_9862.1	chr1	184827222	184827243	-	1	NA	intron (NM_133684, intron 4 of 7)	intron (NM_133684, intron 4 of 7)	-4744	NR_035502	100316821		NR_035502	ENSMUSG00000088559	Mir1981	mir-1981|mmu-mir-1981	microRNA 1981	ncRNA
mm_71012.1	chr8	31168812	31168884	+	1	NA	promoter-TSS (NM_026453)	promoter-TSS (NM_026453)	-124	NM_026453	67920	Mm.289818	NM_026453	ENSMUSG00000031578	Mak16	2600016B03Rik|AI314911|Rbm13	MAK16 homolog	protein-coding
mm_47027.1	chr5	115631781	115631829	-	1	NA	promoter-TSS (NR_027810)	promoter-TSS (NR_027810)	11	NR_027810	66123	Mm.133063	NM_021417	ENSMUSG00000107121	1110006O24Rik	-	RIKEN cDNA 1110006O24 gene	ncRNA
mm_156365.1	chrX	139563696	139563746	+	1	NA	exon (NM_001254761, exon 1 of 7)	exon (NM_001254761, exon 1 of 7)	381	NM_001254761	66889	Mm.27764	NM_023270	ENSMUSG00000031438	Rnf128	1300002C13Rik|AI987883|GRAIL|Greul1	ring finger protein 128	protein-coding
mm_156360.1	chrX	139480465	139480468	+	1	NA	promoter-TSS (NM_175326)	promoter-TSS (NM_175326)	99	NM_001346522	102871	Mm.26565	NM_175326	ENSMUSG00000042498	D330045A20Rik	AI132325	RIKEN cDNA D330045A20 gene	protein-coding
mm_30102.1	chr3	138493768	138493787	-	1	NA	Intergenic	Intergenic	-4395	NM_175224	75624	Mm.26833	NM_175224	ENSMUSG00000005813	Metap1	1700029C17Rik|AW047992|mKIAA0094	methionyl aminopeptidase 1	protein-coding
mm_89863.1	chr10	108162181	108162216	+	1	NA	promoter-TSS (NM_027892)	promoter-TSS (NM_027892)	-202	NM_027892	17931	Mm.422959	NM_027892	ENSMUSG00000019907	Ppp1r12a	1200015F06Rik|5730577I22Rik|AA792106|AV099298|D10Ertd625e|Mypt1	protein phosphatase 1, regulatory (inhibitor) subunit 12A	protein-coding
mm_140891.1	chr17	23980563	23980582	-	1	NA	Intergenic	Intergenic	-5342	NM_013921	30943	Mm.142568	NM_013921	ENSMUSG00000024124	Prss30	2010015P21Rik|Disp|Disp1|Tmprss8	protease, serine 30	protein-coding
mm_8251.1	chr1	138619688	138619759	-	1	NA	promoter-TSS (NM_021605)	promoter-TSS (NM_021605)	34	NM_021605	59125	Mm.143817	NM_021605	ENSMUSG00000026393	Nek7	2810460C19Rik|AU020186	NIMA (never in mitosis gene a)-related expressed kinase 7	protein-coding
mm_155025.1	chrX	42067840	42067872	+	1	NA	promoter-TSS (NR_125870)	promoter-TSS (NR_125870)	20	NM_009688	11798	Mm.259879	NM_009688	ENSMUSG00000025860	Xiap	1110015C02Rik|Aipa|Api3|Birc4|IAP3|ILP-1|MIHA	X-linked inhibitor of apoptosis	protein-coding
mm_116.1	chr1	9788410	9788420	+	1	NA	Intergenic	Intergenic	-9715	NM_133220	170755	Mm.336410	NM_133220	ENSMUSG00000025915	Sgk3	2510015P22Rik|A330005P07Rik|Cisk|fy|fz	serum/glucocorticoid regulated kinase 3	protein-coding
mm_97430.1	chr11	78094683	78094696	+	1	NA	promoter-TSS (NM_145430)	promoter-TSS (NM_145430)	16	NM_145430	216971	Mm.119387	NM_145430	ENSMUSG00000037750	Fam222b	9630020I17Rik	family with sequence similarity 222, member B	protein-coding
mm_55634.1	chr6	72333244	72333256	-	1	NA	intron (NM_138592, intron 6 of 12)	intron (NM_138592, intron 6 of 12)	11925	NM_138592	28035	Mm.281900	NM_138592	ENSMUSG00000056305	Usp39	AA408960|AI894154|CGI-21|D6Wsu157e|SAD1	ubiquitin specific peptidase 39	protein-coding
mm_120857.1	chr14	75228646	75228672	+	1	NA	intron (NM_008879, intron 16 of 16)	intron (NM_008879, intron 16 of 16)	-13628	NM_019775	56373	Mm.24242	NM_019775	ENSMUSG00000021999	Cpb2	1110032P04Rik|4930405E17Rik|AI255929|CPR|Cpu|TAFI	carboxypeptidase B2 (plasma)	protein-coding
mm_168063.1	chr10	101880676	101880680	-	1	NA	intron (NM_001205098, intron 2 of 7)	MT2_Mm|LTR|ERVL	107986	NR_037211	100526516		NR_037211	ENSMUSG00000092952	Mir3059	mir-3059|mmu-mir-3059	microRNA 3059	ncRNA
mm_17681.1	chr2	32288713	32288729	-	1	NA	promoter-TSS (NR_110965)	promoter-TSS (NR_110965)	468	NM_001080968	99412	Mm.106376	NM_133852	ENSMUSG00000002546	Golga2	AW555139|GM130|mKIAA4150	golgi autoantigen, golgin subfamily a, 2	protein-coding
mm_109666.1	chr12	113049967	113049975	+	1	NA	intron (NM_001291444, intron 5 of 23)	intron (NM_001291444, intron 5 of 23)	-24531	NM_029381	75671	Mm.23377	NM_029381	ENSMUSG00000012211	Tex22	1700028O09Rik|AV210422|Tep22	testis expressed gene 22	protein-coding
mm_75776.1	chr8	69996223	69996236	-	1	NA	5' UTR (NM_001286450, exon 1 of 13)	5' UTR (NM_001286450, exon 1 of 13)	155	NM_001286450	234366	Mm.270044	NM_145596	ENSMUSG00000036180	Gatad2a	1110066C11Rik|BC031407|C80248	GATA zinc finger domain containing 2A	protein-coding
mm_138841.1	chr17	40294309	40294321	+	1	NA	3' UTR (NM_009638, exon 8 of 8)	3' UTR (NM_009638, exon 8 of 8)	24892	NM_009638	11571	Mm.16781	NM_009638	ENSMUSG00000025431	Crisp1	AW324342|Aeg1|CRISP-1	cysteine-rich secretory protein 1	protein-coding
mm_71197.1	chr8	40884654	40884665	+	1	NA	intron (NM_007514, intron 1 of 11)	intron (NM_007514, intron 1 of 11)	22292	NM_001044740	11988	Mm.4676	NM_007514	ENSMUSG00000031596	Slc7a2	20.5|AI158848|Atrc2|CAT-2|Cat2|Tea	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	protein-coding
mm_23513.1	chr3	60546819	60546822	+	1	NA	intron (NM_001310514, intron 2 of 8)	intron (NM_001310514, intron 2 of 8)	45641	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_35840.1	chr4	48047136	48047150	-	1	NA	intron (NM_015743, intron 1 of 7)	intron (NM_015743, intron 1 of 7)	1838	NM_015743	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_55410.1	chr6	63328437	63328449	-	1	NA	intron (NM_008167, intron 1 of 15)	intron (NM_008167, intron 1 of 15)	71586	NM_008167	14804	Mm.439651	NM_008167	ENSMUSG00000071424	Grid2	B230104L07Rik|GluD2|GluRdelta2|Lc|Lc<J>|MMS10-AC|Ms10ac|cpr|ho|nmf408|tpr	glutamate receptor, ionotropic, delta 2	protein-coding
mm_25311.1	chr3	106131861	106131869	+	1	NA	exon (NM_023186, exon 11 of 11)	exon (NM_023186, exon 11 of 11)	18483	NM_023186	81600	Mm.46418	NM_023186	ENSMUSG00000062778	Chia1	2200003E03Rik|AMCase|Chia|YNL	chitinase, acidic 1	protein-coding
mm_28334.1	chr3	89387083	89387100	-	1	NA	intron (NM_009565, intron 1 of 2)	intron (NM_009565, intron 1 of 2)	-4773	NR_040403	545539	Mm.393389	NR_040403	ENSMUSG00000074466	Gm15417	ENSMUSG00000074466|OTTMUSG00000021274	predicted gene 15417	ncRNA
mm_137485.1	chr17	26941231	26941270	+	1	NA	promoter-TSS (NM_001281491)	promoter-TSS (NM_001281491)	-202	NM_001281491	240057	Mm.328888	NM_001281491	ENSMUSG00000067629	Syngap1	Gm1963|Syngap	synaptic Ras GTPase activating protein 1 homolog (rat)	protein-coding
mm_130742.1	chr15	101256050	101256058	-	1	NA	Intergenic	Intergenic	-10792	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_77139.1	chr8	111421676	111421682	-	1	NA	Intergenic	L1M4|LINE|L1	-27858	NM_178086	338521	Mm.41083	NM_178086	ENSMUSG00000033579	Fa2h	FAAH|Faxdc1|G630055L08Rik	fatty acid 2-hydroxylase	protein-coding
mm_75635.1	chr8	64733571	64733584	-	1	NA	promoter-TSS (NM_025436)	promoter-TSS (NM_025436)	1	NM_025436	66234	Mm.30119	NM_025436	ENSMUSG00000031604	Msmo1	1500001G16Rik|C78600|DESP4|ERG25|Sc4mol	methylsterol monoxygenase 1	protein-coding
mm_172406.1	chr7	15806300	15806304	-	1	NA	Intergenic	MT2_Mm|LTR|ERVL	33377	NM_145710	252830	Mm.25863	NM_145710	ENSMUSG00000041583	Obox6	D17Ertd599e	oocyte specific homeobox 6	protein-coding
mm_39791.1	chr5	30588041	30588051	+	1	NA	promoter-TSS (NM_010608)	promoter-TSS (NM_010608)	-124	NM_010608	16527	Mm.439936	NM_010608	ENSMUSG00000049265	Kcnk3	TASK|Task-1|cTBAK-1	potassium channel, subfamily K, member 3	protein-coding
mm_36660.1	chr4	95049806	95049810	-	1	NA	3' UTR (NM_010591, exon 1 of 1)	3' UTR (NM_010591, exon 1 of 1)	2414	NM_010591	16476	Mm.275071	NM_010591	ENSMUSG00000052684	Jun	AP-1|Junc|c-jun	jun proto-oncogene	protein-coding
mm_81989.1	chr9	121452833	121452863	+	1	NA	intron (NM_175114, intron 11 of 15)	intron (NM_175114, intron 11 of 15)	42846	NM_001284508	12424	Mm.2619	NM_031161	ENSMUSG00000032532	Cck	-	cholecystokinin	protein-coding
mm_75524.1	chr8	56625186	56625191	-	1	NA	Intergenic	Intergenic	74054	NM_015791	50753	Mm.251174	NM_015791	ENSMUSG00000038206	Fbxo8	Fbx8	F-box protein 8	protein-coding
mm_141156.1	chr17	26507154	26507172	-	1	NA	exon (NM_013642, exon 3 of 4)	exon (NM_013642, exon 3 of 4)	1309	NM_013642	19252	Mm.239041	NM_013642	ENSMUSG00000024190	Dusp1	3CH134|MKP1|Ptpn16|U19515|erp|mkp-1	dual specificity phosphatase 1	protein-coding
mm_69337.1	chr7	129592424	129592437	-	1	NA	intron (NM_172255, intron 1 of 28)	intron (NM_172255, intron 1 of 28)	567	NM_172255	207425	Mm.229323	NM_172255	ENSMUSG00000042055	Wdr11	2900055P10Rik|AW489876|Brwd2|mKIAA1351	WD repeat domain 11	protein-coding
mm_107031.1	chr12	13303274	13303286	+	1	NA	intron (NM_027706, intron 10 of 51)	intron (NM_027706, intron 10 of 51)	34153	NM_027706	71169	Mm.177520	NM_027706	ENSMUSG00000020576	Nbas	4933425L03Rik|Nag	neuroblastoma amplified sequence	protein-coding
mm_152276.1	chr19	8821311	8821331	-	1	NA	intron (NM_001081196, intron 1 of 13)	intron (NM_001081196, intron 1 of 13)	1920	NM_001081196	68693	Mm.476519	NM_001081196	ENSMUSG00000071659	Hnrnpul2	1110031M08Rik|AI465155|Hnrpul2	heterogeneous nuclear ribonucleoprotein U-like 2	protein-coding
mm_94908.1	chr11	29374291	29374325	+	1	NA	5' UTR (NM_176841, exon 1 of 32)	5' UTR (NM_176841, exon 1 of 32)	136	NM_176841	108686	Mm.338284	NM_176841	ENSMUSG00000032740	Ccdc88a	A430106J12Rik|AI848406|Ape|C130096N06Rik|C330012F17Rik|D130005J21Rik|Girdin|Giv|Grdn|Hkrp1	coiled coil domain containing 88A	protein-coding
mm_83053.1	chr9	37545082	37545094	-	1	NA	TTS (NM_020518)	TTS (NM_020518)	5833	NM_020518	57276	Mm.27478	NM_020518	ENSMUSG00000001943	Vsig2	1190004B15Rik|2210413P10Rik|AU040484|CTX|Ctm	V-set and immunoglobulin domain containing 2	protein-coding
mm_26846.1	chr3	14767496	14767497	-	1	NA	exon (NM_001083957, exon 6 of 7)	exon (NM_001083957, exon 6 of 7)	10964	NM_001083957	12346	Mm.273195	NM_009799	ENSMUSG00000027556	Car1	AW555628|Ca1|Car-1	carbonic anhydrase 1	protein-coding
mm_154396.1	chrM	13424	13435	+	1	NA	NA	Intergenic	NA	NA								
mm_144909.1	chr18	37421429	37421455	+	1	NA	promoter-TSS (NM_053136)	promoter-TSS (NM_053136)	24	NM_053136	93882	Mm.196702	NM_053136	ENSMUSG00000051486	Pcdhb11	Pcdhb5E|PcdhbK	protocadherin beta 11	protein-coding
mm_134992.1	chr16	32163250	32163297	-	1	NA	5' UTR (NM_146069, exon 2 of 4)	5' UTR (NM_146069, exon 2 of 4)	2203	NM_146069	224109	Mm.33498	NM_146069	ENSMUSG00000052384	Nrros	E430025L02Rik|Lrcc33|Lrrc33	negative regulator of reactive oxygen species	protein-coding
mm_41960.1	chr5	106351508	106351521	+	1	NA	Intergenic	Intergenic	30174	NR_136913	102635633	Mm.383511	NR_136913	ENSMUSG00000105508	Gm32921	-	predicted gene, 32921	ncRNA
mm_33175.1	chr4	126047158	126047168	+	1	NA	exon (NM_025544, exon 1 of 8)	exon (NM_025544, exon 1 of 8)	235	NM_025544	66407	Mm.195628	NM_025544	ENSMUSG00000028861	Mrps15	1500003E24Rik|2410002B11Rik|Mprs15	mitochondrial ribosomal protein S15	protein-coding
mm_169191.1	chr13	66077858	66077874	+	1	NA	Intergenic	RLTR27|LTR|ERVK	-35587	NM_001177832	628709	Mm.390595	NM_001177832	ENSMUSG00000095909	Gm10324	ENSMUSG00000071302	predicted gene 10324	protein-coding
mm_164775.1	chr17	93711919	93711919	-	1	NA	Intergenic	Intergenic	512751	NM_009625	11516	Mm.3407	NM_009625	ENSMUSG00000024256	Adcyap1	PACAP	adenylate cyclase activating polypeptide 1	protein-coding
mm_171324.1	chr3	96450441	96450443	+	1	NA	intron (NM_001256181, intron 1 of 3)	intron (NM_001256181, intron 1 of 3)	1864	NM_001256181	329716	Mm.275223	NM_183223	ENSMUSG00000046317	BC107364	D730018G16	cDNA sequence BC107364	protein-coding
mm_104750.1	chr11	98463601	98463605	-	1	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	16769	NM_010346	14786	Mm.276702	NM_010346	ENSMUSG00000019312	Grb7	mKIAA4028	growth factor receptor bound protein 7	protein-coding
mm_79122.1	chr9	46913554	46913554	+	1	NA	promoter-TSS (NR_015605)	promoter-TSS (NR_015605)	-49	NR_015605	73040	Mm.265384	NR_015605	ENSMUSG00000099696	2900052N01Rik	AU067665	RIKEN cDNA 2900052N01 gene	ncRNA
mm_112358.1	chr12	118966396	118966411	-	1	NA	promoter-TSS (NM_029961)	promoter-TSS (NM_029961)	18	NM_029961	77706	Mm.261496	NM_029961	ENSMUSG00000072791	Abcb5	9230106F14Rik	ATP-binding cassette, sub-family B (MDR/TAP), member 5	protein-coding
mm_34803.1	chr4	154864411	154864425	+	1	NA	intron (NM_172878, intron 6 of 6)	intron (NM_172878, intron 6 of 6)	-5167	NM_013783	27390	Mm.116944	NM_013783	ENSMUSG00000058183	Mmel1	Mell1|NEP2|NEPII|Nl1|SEP	membrane metallo-endopeptidase-like 1	protein-coding
mm_32915.1	chr4	119136551	119136573	+	1	NA	3' UTR (NM_011400, exon 10 of 10)	3' UTR (NM_011400, exon 10 of 10)	27817	NM_011400	20525	Mm.21002	NM_011400	ENSMUSG00000028645	Slc2a1	Glut-1|Glut1	solute carrier family 2 (facilitated glucose transporter), member 1	protein-coding
mm_49931.1	chr6	39431029	39431053	+	1	NA	Intergenic	RLTR45|LTR|ERVK	-10672	NM_018810	54484	Mm.270484	NM_018810	ENSMUSG00000029922	Mkrn1	RFP	makorin, ring finger protein, 1	protein-coding
mm_10428.1	chr2	13878953	13878958	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-85435	NM_145838	241230	Mm.330004	NM_145838	ENSMUSG00000003418	St8sia6	1700007J08Rik|AI314453|AI875066|ST8SiaVI|Siat8f	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 6	protein-coding
mm_155448.1	chrX	73495146	73495303	+	1	NA	3' UTR (NM_007542, exon 8 of 8)	3' UTR (NM_007542, exon 8 of 8)	-7862	NM_001310537	320707	Mm.210095	NM_177236	ENSMUSG00000031376	Atp2b3	6430519O13Rik|Pmca3	ATPase, Ca++ transporting, plasma membrane 3	protein-coding
mm_35172.1	chr4	14826583	14826589	-	1	NA	promoter-TSS (NM_152812)	promoter-TSS (NM_152812)	1	NM_152812	72201	Mm.387724	NM_152812	ENSMUSG00000040550	Otud6b	2600013N14Rik|AU015433	OTU domain containing 6B	protein-coding
mm_172752.1	chr8	85037259	85037261	+	1	NA	promoter-TSS (NM_001122843)	promoter-TSS (NM_001122843)	92	NM_001122843	212999	Mm.220357	NM_145390	ENSMUSG00000031691	Tnpo2	1110034O24Rik|AA414969|AI464345|AI852433|IPO3|Knpb2b|Kpnb2b|TRN2	transportin 2 (importin 3, karyopherin beta 2b)	protein-coding
mm_138105.1	chr17	34119540	34119542	+	1	NA	non-coding (NR_037970, exon 1 of 13)	non-coding (NR_037970, exon 1 of 13)	359	NR_037970	14312	Mm.3444	NM_010238	ENSMUSG00000024335	Brd2	AW228947|D17H6S113E|Frg-1|Fsrg-1|Fsrg1|Nat|Ring3|Rnf3|mKIAA4005	bromodomain containing 2	protein-coding
mm_76016.1	chr8	73313407	73313431	-	1	NA	intron (NM_010687, intron 1 of 14)	intron (NM_010687, intron 1 of 14)	40121	NM_001317391	16795	Mm.324371	NM_010687	ENSMUSG00000004383	Large1	BPFD#36|Gyltl1a|Large|Mbp-1|Mbp1|enr|fg|froggy|myd	LARGE xylosyl- and glucuronyltransferase 1	protein-coding
mm_169110.1	chr13	44869942	44869944	-	1	NA	intron (NM_001205044, intron 4 of 18)	LSU-rRNA_Hsa|rRNA|rRNA	132153	NM_025772	94245	Mm.352311	NM_025772	ENSMUSG00000057531	Dtnbp1	5430437B18Rik|AW048963|Bloc1s8|dysbindin|sdy	dystrobrevin binding protein 1	protein-coding
mm_64615.1	chr7	3502618	3502629	-	1	NA	promoter-TSS (NM_177363)	promoter-TSS (NM_177363)	-71	NM_177363	245126	Mm.245747	NM_177363	ENSMUSG00000053338	Tarm1	9930022N03Rik|ENSMUSG00000053338|Gm9904|OLT-2	T cell-interacting, activating receptor on myeloid cells 1	protein-coding
mm_86502.1	chr10	7212294	7212331	+	1	NA	promoter-TSS (NM_172546)	promoter-TSS (NM_172546)	-75	NM_172546	215748	Mm.37984	NM_172546	ENSMUSG00000015202	Cnksr3	6820402C05|BC024086|Magi1	Cnksr family member 3	protein-coding
mm_56815.1	chr6	116673791	116673853	-	1	NA	promoter-TSS (NM_178045)	promoter-TSS (NM_178045)	14	NM_178045	213391	Mm.257931	NM_178045	ENSMUSG00000042129	Rassf4	3830411C14Rik|AD037|AI586137	Ras association (RalGDS/AF-6) domain family member 4	protein-coding
mm_17606.1	chr2	30903256	30903269	-	1	NA	promoter-TSS (NM_022415)	promoter-TSS (NM_022415)	35	NM_022415	64292	Mm.28768	NM_022415	ENSMUSG00000050737	Ptges	2410099E23Rik|D2Ertd369e|Pges|mPGES|mPGES-1	prostaglandin E synthase	protein-coding
mm_116666.1	chr13	49205429	49205442	-	1	NA	intron (NM_026738, intron 2 of 5)	intron (NM_026738, intron 2 of 5)	10591	NM_026738	68480	Mm.3336	NM_026738	ENSMUSG00000037960	Card19	1110007C09Rik|AI851695|Bincard	caspase recruitment domain family, member 19	protein-coding
mm_42027.1	chr5	108279484	108279498	+	1	NA	3' UTR (NM_026106, exon 3 of 3)	3' UTR (NM_026106, exon 3 of 3)	10594	NM_026106	13486	Mm.303534	NM_026106	ENSMUSG00000029265	Dr1	1700121L09Rik|Dr1l|NC2|NC2beta	down-regulator of transcription 1	protein-coding
mm_46360.1	chr5	103211252	103211321	-	1	NA	promoter-TSS (NM_001081567)	promoter-TSS (NM_001081567)	48	NM_001081567	26414	Mm.39253	NM_009158	ENSMUSG00000046709	Mapk10	C230008H04Rik|JNK3|JNK3B1|JNK3B2|SAPK(beta)|Serk2|p493F12|p54bSAPK	mitogen-activated protein kinase 10	protein-coding
mm_159658.1	chr4	148932730	148932730	+	1	NA	intron (NM_027195, intron 5 of 15)	intron (NM_027195, intron 5 of 15)	128338	NM_027195	69743	Mm.233879	NM_027195	ENSMUSG00000028977	Casz1	2410019P08Rik|AV096627|BC040081|Cst|D4Ertd432e	castor zinc finger 1	protein-coding
mm_117389.1	chr13	73347341	73347365	-	1	NA	promoter-TSS (NR_045293)	promoter-TSS (NR_045293)	31	NR_045293	432777	Mm.415319	NR_045293		D630045M09Rik	AU019512	RIKEN cDNA D630045M09 gene	ncRNA
mm_63617.1	chr7	128238093	128238123	+	1	NA	promoter-TSS (NM_177001)	promoter-TSS (NM_177001)	-77	NM_177001	100043133	Mm.183647	NM_177001	ENSMUSG00000062944	9130023H24Rik	GLI4	RIKEN cDNA 9130023H24 gene	protein-coding
mm_167883.1	chrX	48884901	48884921	+	1	NA	Intergenic	Intergenic	-7198	NM_001085499	209005	Mm.336054	NM_001085499	ENSMUSG00000079606	Gm595	-	predicted gene 595	protein-coding
mm_64057.1	chr7	140847802	140847813	+	1	NA	promoter-TSS (NM_027019)	promoter-TSS (NM_027019)	-109	NM_027019	69287	Mm.56404	NM_027019	ENSMUSG00000025482	Odf3	1700011O04Rik|SHIPPO1	outer dense fiber of sperm tails 3	protein-coding
mm_36120.1	chr4	58912204	58912238	-	1	NA	intron (NM_172381, intron 1 of 48)	CpG	504	NM_172381	230249	Mm.234801	NM_172381	ENSMUSG00000050812	AI314180	AW558785|BB181316|mKIAA0368	expressed sequence AI314180	protein-coding
mm_128364.1	chr15	41869693	41869701	-	1	NA	promoter-TSS (NM_175456)	promoter-TSS (NM_175456)	23	NM_175456	223513	Mm.148913	NM_175456	ENSMUSG00000042895	Abra	C130068O12Rik|STARS	actin-binding Rho activating protein	protein-coding
mm_151525.1	chr19	58741211	58741224	+	1	NA	exon (NM_018874, exon 12 of 13)	exon (NM_018874, exon 12 of 13)	12330	NM_018874	18946	Mm.10753	NM_018874	ENSMUSG00000042179	Pnliprp1	Plrp1	pancreatic lipase related protein 1	protein-coding
mm_89666.1	chr10	97495012	97495041	+	1	NA	exon (NM_007833, exon 3 of 8)	exon (NM_007833, exon 3 of 8)	12695	NM_007833	13179	Mm.56769	NM_007833	ENSMUSG00000019929	Dcn	DC|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding
mm_152038.1	chr19	6118492	6118554	-	1	NA	promoter-TSS (NM_133678)	promoter-TSS (NM_133678)	63	NM_133678	66406	Mm.303924	NM_133678	ENSMUSG00000024790	Sac3d1	2410004C24Rik|AU015683|shd1	SAC3 domain containing 1	protein-coding
mm_124693.1	chr15	6438245	6438269	+	1	NA	intron (NM_001310446, intron 13 of 13)	intron (NM_001310446, intron 13 of 13)	-7076	NM_013485	12279	Mm.29095	NM_013485	ENSMUSG00000022149	C9	-	complement component 9	protein-coding
mm_162203.1	chrX	135302345	135302345	+	1	NA	promoter-TSS (NM_031390)	promoter-TSS (NM_031390)	29	NM_031390	83565	Mm.108239	NM_031390	ENSMUSG00000067360	Pramel3	-	preferentially expressed antigen in melanoma-like 3	protein-coding
mm_104872.1	chr11	99418391	99418427	-	1	NA	intron (NM_010661, intron 4 of 7)	intron (NM_010661, intron 4 of 7)	3850	NM_010661	268482	Mm.436651	NM_010661	ENSMUSG00000020912	Krt12	AI835216|K12|Krt-12|Krt1-12	keratin 12	protein-coding
mm_25651.1	chr3	121449748	121449764	+	1	NA	intron (NM_028044, intron 1 of 6)	intron (NM_028044, intron 1 of 6)	23215	NM_028044	71994	Mm.275555	NM_028044	ENSMUSG00000053931	Cnn3	1600014M03Rik|C85854|Calpo3	calponin 3, acidic	protein-coding
mm_68684.1	chr7	119184549	119184572	-	1	NA	promoter-TSS (NM_001024138)	promoter-TSS (NM_001024138)	-186	NM_001024138	209776	Mm.300632	NM_001024138	ENSMUSG00000066197	Gpr139	GPRg1|Gm495|PGR3	G protein-coupled receptor 139	protein-coding
mm_166895.1	chr7	28379357	28379400	-	1	NA	promoter-TSS (NM_011756)	promoter-TSS (NM_011756)	-150	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_164718.1	chr17	56472877	56472922	-	1	NA	intron (NM_001252455, intron 1 of 27)	intron (NM_001252455, intron 1 of 27)	3581	NM_001252455	19280	Mm.258771	NM_011218	ENSMUSG00000013236	Ptprs	AL022616|PTP|PTP-NU3|PTPNU-3|PTPsigma|Ptpt9|R-PTP-S|RPTPsigma	protein tyrosine phosphatase, receptor type, S	protein-coding
mm_165319.1	chr2	104919855	104919859	+	1	NA	intron (NM_177600, intron 3 of 17)	intron (NM_177600, intron 3 of 17)	33533	NM_177600	211936	Mm.416538	NM_177600	ENSMUSG00000045106	Ccdc73	2210415I11Rik|4931417A20|AV080665|BC095976	coiled-coil domain containing 73	protein-coding
mm_133268.1	chr16	77368377	77368397	+	1	NA	intron (NR_015543, intron 2 of 4)	intron (NR_015543, intron 2 of 4)	39059	NR_015543	77994	Mm.394688	NR_015543	ENSMUSG00000090386	Mir99ahg	2810055G20Rik|D730043B02Rik	Mir99a and Mirlet7c-1 host gene (non-protein coding)	ncRNA
mm_51168.1	chr6	70726541	70726549	+	1	NA	Intergenic	Intergenic	65630	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_58074.1	chr6	136924271	136924283	-	1	NA	exon (NM_007486, exon 6 of 6)	exon (NM_007486, exon 6 of 6)	-2097	NM_026983	69187	Mm.33692	NM_026983	ENSMUSG00000030219	Erp27	1810033M07Rik|1810047B09Rik	endoplasmic reticulum protein 27	protein-coding
mm_32280.1	chr4	102969074	102969076	+	1	NA	intron (NR_040444, intron 3 of 3)	intron (NR_040444, intron 3 of 3)	-17304	NM_001163767	67344	Mm.111346	NM_026100	ENSMUSG00000028523	Tctex1d1	1700055O19Rik	Tctex1 domain containing 1	protein-coding
mm_101342.1	chr11	23627234	23627236	-	1	NA	intron (NM_027860, intron 3 of 21)	intron (NM_027860, intron 3 of 21)	6396	NM_001347242	71675	Mm.48031	NM_027860	ENSMUSG00000042208	0610010F05Rik	Kiaa1841|mKIAA1841	RIKEN cDNA 0610010F05 gene	protein-coding
mm_120231.1	chr14	62865639	62865664	+	1	NA	TTS (NR_105860)	TTS (NR_105860)	109	NR_105860	102465311		NR_105860	ENSMUSG00000098858	Mir6541	Gm27311|mmu-mir-6541	microRNA 6541	ncRNA
mm_1202.1	chr1	62718983	62719007	+	1	NA	exon (NM_001077407, exon 2 of 16)	exon (NM_001077407, exon 2 of 16)	15678	NM_001077405	18187	Mm.266341	NM_010939	ENSMUSG00000025969	Nrp2	1110048P06Rik|Np-2|Np2|Npn-2|Npn2	neuropilin 2	protein-coding
mm_102662.1	chr11	64079445	64079480	-	1	NA	promoter-TSS (NM_178379)	promoter-TSS (NM_178379)	10	NM_178379	70383	Mm.340211	NM_178379	ENSMUSG00000042148	Cox10	2410004F01Rik|AU042636	cytochrome c oxidase assembly protein 10	protein-coding
mm_101459.1	chr11	30268117	30268123	-	1	NA	Intergenic	CpG	-48348	NM_175836	20742	Mm.123110	NM_009260	ENSMUSG00000020315	Sptbn1	9930031C03Rik|AL033301|SPTB2|Spnb-2|Spnb2|elf1|elf3|mKIAA4049	spectrin beta, non-erythrocytic 1	protein-coding
mm_161271.1	chr14	7332409	7332409	-	1	NA	promoter-TSS (NM_001025085)	promoter-TSS (NM_001025085)	-14	NM_001025085	545013	Mm.422841	NM_001025085	ENSMUSG00000072726	Gm5797	EG545013	predicted gene 5797	protein-coding
mm_37622.1	chr4	127313981	127313998	-	1	NA	promoter-TSS (NM_008120)	promoter-TSS (NM_008120)	50	NM_008120	14612	Mm.24615	NM_008120	ENSMUSG00000050234	Gja4	AU020209|AW558810|Cnx37|Cx37|Gja-4	gap junction protein, alpha 4	protein-coding
mm_147922.1	chr18	65873873	65873885	-	1	NA	intron (NM_175012, intron 1 of 2)	intron (NM_175012, intron 1 of 2)	393	NM_175012	225642	Mm.20298	NM_175012	ENSMUSG00000024517	Grp	BLP	gastrin releasing peptide	protein-coding
mm_8993.1	chr1	165709669	165709694	-	1	NA	Intergenic	ID_B1|SINE|B4	-1587	NM_001038846	226594	Mm.265552	NM_178593	ENSMUSG00000040723	Rcsd1	A430105K13Rik|BC025872|CapZIP	RCSD domain containing 1	protein-coding
mm_98737.1	chr11	96353325	96353342	+	1	NA	exon (NM_134032, exon 2 of 2)	exon (NM_134032, exon 2 of 2)	1701	NM_134032	103889	Mm.281153	NM_134032	ENSMUSG00000075588	Hoxb2	AI894218|Hox-2.8|Hoxbes2	homeobox B2	protein-coding
mm_14550.1	chr2	132870018	132870021	+	1	NA	exon (NM_177303, exon 5 of 5)	exon (NM_177303, exon 5 of 5)	10843	NM_177303	320974	Mm.357342	NM_177303	ENSMUSG00000043110	Lrrn4	B430119L13Rik|Nlrr4	leucine rich repeat neuronal 4	protein-coding
mm_16975.1	chr2	17996918	17996919	-	1	NA	promoter-TSS (NM_026627)	promoter-TSS (NM_026627)	40	NM_026627	68231	Mm.23887	NM_026627	ENSMUSG00000062651	H2afb1	1700113O17Rik|H2A.Bbd|H2al2|TSEG-1|Tseg1	H2A histone family, member B1	protein-coding
mm_135489.1	chr16	46049240	46049263	-	1	NA	intron (NM_032465, intron 11 of 14)	intron (NM_032465, intron 11 of 14)	-38838	NM_001134480	433022	Mm.380993	NM_001134480	ENSMUSG00000087141	Plcxd2	AW494639|EG433022	phosphatidylinositol-specific phospholipase C, X domain containing 2	protein-coding
mm_64116.1	chr7	141079126	141079167	+	1	NA	promoter-TSS (NM_019762)	promoter-TSS (NM_019762)	-623	NM_019762	56460	Mm.350037	NM_019762	ENSMUSG00000054065	Pkp3	2310056L12Rik	plakophilin 3	protein-coding
mm_33943.1	chr4	137129377	137129380	+	1	NA	Intergenic	Intergenic	35688	NR_040443	100503595	Mm.421314	NR_040443	ENSMUSG00000085833	Gm13003	OTTMUSG00000009822	predicted gene 13003	ncRNA
mm_18852.1	chr2	75676391	75676402	-	1	NA	exon (NM_010902, exon 5 of 5)	exon (NM_010902, exon 5 of 5)	17106	NR_033513	627828	Mm.459502	NR_033513	ENSMUSG00000092086	Gm6793	EG627828	heterogeneous nuclear ribonucleoprotein A3 pseudogene	pseudo
mm_137975.1	chr17	33576608	33576640	+	1	NA	exon (NM_053214, exon 4 of 28)	exon (NM_053214, exon 4 of 28)	20917	NM_053214	17916	Mm.42019	NM_053214	ENSMUSG00000024300	Myo1f	C330006B10Rik	myosin IF	protein-coding
mm_125847.1	chr15	74959092	74959102	+	1	NA	3' UTR (NM_001164036, exon 4 of 4)	3' UTR (NM_001164036, exon 4 of 4)	3991	NM_001164040	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_137804.1	chr17	29848221	29848223	+	1	NA	intron (NM_001081160, intron 6 of 15)	ID_B1|SINE|B4	39660	NM_001081160	74762	Mm.40901	NM_001081160	ENSMUSG00000043557	Mdga1	1200011I03Rik|GPIM|Mamdc3	MAM domain containing glycosylphosphatidylinositol anchor 1	protein-coding
mm_120900.1	chr14	75955012	75955016	+	1	NA	promoter-TSS (NM_026214)	promoter-TSS (NM_026214)	11	NM_026214	67516	Mm.390712	NM_026214	ENSMUSG00000046523	Kctd4	2210017A09Rik|AU017169	potassium channel tetramerisation domain containing 4	protein-coding
mm_73865.1	chr8	118470654	118470680	+	1	NA	intron (NM_019707, intron 1 of 13)	intron (NM_019707, intron 1 of 13)	187056	NM_019707	12554	Mm.334841	NM_019707	ENSMUSG00000031841	Cdh13	4932416G01Rik|Cdht|Tcad	cadherin 13	protein-coding
mm_134375.1	chr16	17144392	17144401	-	1	NA	promoter-TSS (NM_029779)	promoter-TSS (NM_029779)	27	NM_029779	76872	Mm.101656	NM_029779	ENSMUSG00000022768	Ccdc116	4930432J16Rik	coiled-coil domain containing 116	protein-coding
mm_27498.1	chr3	55055039	55055051	-	1	NA	promoter-TSS (NM_007628)	promoter-TSS (NM_007628)	10	NM_007628	12427	Mm.4815	NM_007628	ENSMUSG00000027793	Ccna1	-	cyclin A1	protein-coding
mm_3108.1	chr1	134540823	134540839	+	1	NA	TTS (NM_001145300)	TTS (NM_001145300)	8851	NM_001145300	71001	Mm.158529	NM_183292	ENSMUSG00000046367	Mgat4e	4931440L10Rik	MGAT4 family, member E	protein-coding
mm_109958.1	chr12	12492014	12492022	-	1	NA	Intergenic	Intergenic	-99543	NR_045829	70858	Mm.410838	NR_045829		4921511I17Rik	-	RIKEN cDNA 4921511I17 gene	ncRNA
mm_168903.1	chr12	55124469	55124473	+	1	NA	promoter-TSS (NM_028527)	promoter-TSS (NM_028527)	-57	NM_001100116	100101807	Mm.439875	NM_001100116	ENSMUSG00000094103	1700047I17Rik2	-	RIKEN cDNA 1700047I17 gene 2	protein-coding
mm_118242.1	chr13	111797147	111797165	-	1	NA	intron (NM_011945, intron 1 of 19)	intron (NM_011945, intron 1 of 19)	11827	NM_011945	26401	Mm.15918	NM_011945	ENSMUSG00000021754	Map3k1	MAPKKK1|MEKK1|Mekk	mitogen-activated protein kinase kinase kinase 1	protein-coding
mm_125827.1	chr15	74957248	74957263	+	1	NA	intron (NM_001164039, intron 2 of 4)	intron (NM_001164039, intron 2 of 4)	2149	NM_001164040	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_47779.1	chr5	131963909	131963912	-	1	NA	intron (NM_177047, intron 4 of 18)	intron (NM_177047, intron 4 of 18)	83641	NR_040704	75369	Mm.389696	NR_040704	ENSMUSG00000105773	4930563F08Rik	-	RIKEN cDNA 4930563F08 gene	ncRNA
mm_18987.1	chr2	76857183	76857200	-	1	NA	exon (NM_011652, exon 122 of 313)	exon (NM_011652, exon 122 of 313)	125356	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_152755.1	chr19	20123911	20123919	-	1	NA	Intergenic	Intergenic	266756	NM_010730	16952	Mm.248360	NM_010730	ENSMUSG00000024659	Anxa1	Anx-1|Anx-A1|C430014K04Rik|Lpc-1|Lpc1	annexin A1	protein-coding
mm_143260.1	chr17	65613487	65613514	-	1	NA	promoter-TSS (NM_013933)	promoter-TSS (NM_013933)	55	NM_013933	30960	Mm.266767	NM_013933	ENSMUSG00000024091	Vapa	33kDa|VAP33	vesicle-associated membrane protein, associated protein A	protein-coding
mm_86232.1	chr9	120571362	120571375	-	1	NA	promoter-TSS (NM_025974)	promoter-TSS (NM_025974)	-149	NM_025974	67115	Mm.289810	NM_025974	ENSMUSG00000025794	Rpl14	3100001N19Rik|AA407502|AL022816|CAG-ISL-7|CTG-B33|L14	ribosomal protein L14	protein-coding
mm_89250.1	chr10	87859159	87859178	+	1	NA	5' UTR (NM_010512, exon 1 of 5)	5' UTR (NM_010512, exon 1 of 5)	116	NM_010512	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_59206.1	chr7	24507702	24507704	+	1	NA	intron (NR_110958, intron 1 of 2)	CpG	616	NR_110958	232969	Mm.181332	NM_146183	ENSMUSG00000064264	Zfp428	2410005H09Rik|AV271806|AW047854|Znf428	zinc finger protein 428	protein-coding
mm_138715.1	chr17	36191436	36191455	+	1	NA	Intergenic	Intergenic	-1294	NM_008208	15043	Mm.426002	NM_008208	ENSMUSG00000054128	H2-T3	H-2T3|H2-Tw3|MumuTL|TL	histocompatibility 2, T region locus 3	protein-coding
mm_67886.1	chr7	99349166	99349177	-	1	NA	exon (NM_009825, exon 2 of 5)	exon (NM_009825, exon 2 of 5)	4068	NM_009825	12406	Mm.22708	NM_009825	ENSMUSG00000070436	Serpinh1	BERF-1|Cbp1|Cbp2|Hsp47|J6|Serpinh2|gp46	serine (or cysteine) peptidase inhibitor, clade H, member 1	protein-coding
mm_43885.1	chr5	143890645	143890649	+	1	NA	TTS (NM_001310772)	TTS (NM_001310772)	4420	NM_025732	66729	Mm.439817	NM_025732	ENSMUSG00000029607	Ankrd61	4921520G13Rik	ankyrin repeat domain 61	protein-coding
mm_161467.1	chr15	78395862	78395862	-	1	NA	promoter-TSS (NM_028522)	promoter-TSS (NM_028522)	50	NM_028522	73376	Mm.73222	NM_028522	ENSMUSG00000062154	Tex33	1700061J05Rik|Ean57	testis expressed 33	protein-coding
mm_44412.1	chr5	17854092	17854097	-	1	NA	intron (NM_001159558, intron 1 of 15)	intron (NM_001159558, intron 1 of 15)	-4302	NM_001159556	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_21197.1	chr2	155473741	155473751	-	1	NA	Intergenic	(TCCG)n|Simple_repeat|Simple_repeat	-32963	NM_019825	56406	Mm.27592	NM_019825	ENSMUSG00000038369	Ncoa6	AIB3|ASC-2|ASC2|NRC|Ncoa7|PRIP|RAP250|mKIAA0181	nuclear receptor coactivator 6	protein-coding
mm_154675.1	chrX	7899335	7899341	+	1	NA	promoter-TSS (NM_001252528)	promoter-TSS (NM_001252528)	2	NR_132589	21855	Mm.27393	NM_011591	ENSMUSG00000031158	Timm17b	17kDa|Sfc3|mTim17b	translocase of inner mitochondrial membrane 17b	protein-coding
mm_55196.1	chr6	52200947	52200973	-	1	NA	promoter-TSS (NR_015611)	promoter-TSS (NR_015611)	-164	NR_015611	72628	Mm.348030	NR_015611	ENSMUSG00000085696	Hoxaas3	2700086A05Rik	Hoxa cluster antisense RNA 3	ncRNA
mm_154720.1	chrX	9272672	9272693	+	1	NA	promoter-TSS (NM_023500)	promoter-TSS (NM_023500)	-102	NM_023500	22439	Mm.56468	NM_023500	ENSMUSG00000015342	Xk	1810038K19Rik|XRG1|Xkh	X-linked Kx blood group	protein-coding
mm_71337.1	chr8	45507821	45507825	+	1	NA	promoter-TSS (NM_001205219)	promoter-TSS (NM_001205219)	35	NM_001205219	234214	Mm.211096	NM_172752	ENSMUSG00000031626	Sorbs2	2010203O03Rik|9430041O17Rik|A530071H08|Argbp2|mKIAA0777|nArgBP2	sorbin and SH3 domain containing 2	protein-coding
mm_59676.1	chr7	28383420	28383437	+	1	NA	Intergenic	B1F|SINE|Alu	-4200	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_108832.1	chr12	95760412	95760417	+	1	NA	intron (NM_201518, intron 1 of 1)	B4A|SINE|B4	68188	NM_201518	399558	Mm.341948	NM_201518	ENSMUSG00000047414	Flrt2	-	fibronectin leucine rich transmembrane protein 2	protein-coding
mm_28077.1	chr3	84479419	84479476	-	1	NA	promoter-TSS (NM_001205355)	promoter-TSS (NM_001205355)	44	NM_001205355	229474	Mm.331107	NM_001033301	ENSMUSG00000041842	Fhdc1	6330505N24Rik|Gm126	FH2 domain containing 1	protein-coding
mm_12689.1	chr2	76344464	76344464	+	1	NA	Intergenic	Intergenic	-5811	NM_001081033	241489	Mm.246613	NM_001081033	ENSMUSG00000075270	Pde11a	6330414F14Rik|A630086N24Rik|Gm350|PDE11A1	phosphodiesterase 11A	protein-coding
mm_65184.1	chr7	19696465	19696483	-	1	NA	exon (NM_009696, exon 4 of 4)	exon (NM_009696, exon 4 of 4)	1924	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_105798.1	chr11	110095975	110096043	-	1	NA	promoter-TSS (NM_153145)	promoter-TSS (NM_153145)	-72	NM_153145	217258	Mm.344148	NM_153145	ENSMUSG00000041828	Abca8a	-	ATP-binding cassette, sub-family A (ABC1), member 8a	protein-coding
mm_128555.1	chr15	55906743	55906796	-	1	NA	5' UTR (NM_016667, exon 1 of 7)	5' UTR (NM_016667, exon 1 of 7)	180	NM_016667	20649	Mm.309425	NM_016667	ENSMUSG00000060429	Sntb1	-	syntrophin, basic 1	protein-coding
mm_139684.1	chr17	57419305	57419375	+	1	NA	exon (NM_010130, exon 11 of 22)	exon (NM_010130, exon 11 of 22)	60654	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_53590.1	chr6	137754603	137754608	+	1	NA	promoter-TSS (NM_172733)	promoter-TSS (NM_172733)	28	NM_172733	232449	Mm.29181	NM_172733	ENSMUSG00000030225	Dera	2010002D22Rik|2500002K03Rik|DEOC	deoxyribose-phosphate aldolase (putative)	protein-coding
mm_129458.1	chr15	78572687	78572690	-	1	NA	promoter-TSS (NM_009008)	promoter-TSS (NM_009008)	95	NM_009008	19354	Mm.1972	NM_009008	ENSMUSG00000033220	Rac2	AI323801|AI452260	RAS-related C3 botulinum substrate 2	protein-coding
mm_16062.1	chr2	167932337	167932379	+	1	NA	promoter-TSS (NM_011201)	promoter-TSS (NM_011201)	31	NM_011201	19246	Mm.277916	NM_011201	ENSMUSG00000027540	Ptpn1	PTP-1B|PTP-HA2|PTP1B	protein tyrosine phosphatase, non-receptor type 1	protein-coding
mm_53602.1	chr6	138150804	138150834	+	1	NA	exon (NM_019946, exon 3 of 4)	exon (NM_019946, exon 3 of 4)	9225	NM_001347489	56615	Mm.14796	NM_019946	ENSMUSG00000008540	Mgst1	1500002K10Rik|Gst	microsomal glutathione S-transferase 1	protein-coding
mm_92981.1	chr10	86693952	86693971	-	1	NA	exon (NM_011631, exon 13 of 18)	exon (NM_011631, exon 13 of 18)	8434	NR_015572	66263	Mm.392261	NR_015572		1810014B01Rik	-	RIKEN cDNA 1810014B01 gene	pseudo
mm_6594.1	chr1	75278346	75278440	-	1	NA	promoter-TSS (NR_138251)	promoter-TSS (NR_138251)	22	NR_138251	19711	Mm.4032	NM_009049	ENSMUSG00000033061	Resp18	AI851012	regulated endocrine-specific protein 18	protein-coding
mm_119136.1	chr14	31167951	31167958	+	1	NA	intron (NM_138672, intron 1 of 68)	intron (NM_138672, intron 1 of 68)	687	NM_138672	192187	Mm.220821	NM_138672	ENSMUSG00000042286	Stab1	FEEL-1|FELE-1|MFEEL-1|MS-1|STAB-1|mKIAA0246	stabilin 1	protein-coding
mm_84839.1	chr9	78368192	78368196	-	1	NA	promoter-TSS (NM_025274)	promoter-TSS (NM_025274)	5	NM_025274	434423	Mm.139314	NM_025274	ENSMUSG00000060461	Dppa5a	AA536857|Dppa5|Esg1|ecat2	developmental pluripotency associated 5A	protein-coding
mm_130560.1	chr15	99251930	99251968	-	1	NA	promoter-TSS (NM_016766)	promoter-TSS (NM_016766)	12	NM_001164156	51812	Mm.383472	NM_016766	ENSMUSG00000037570	Mcrs1	C78274|ICP22BP|MSP58|P78	microspherule protein 1	protein-coding
mm_18734.1	chr2	72980922	72980940	-	1	NA	promoter-TSS (NM_001018042)	promoter-TSS (NM_001018042)	-485	NM_001018042	20687	Mm.124328	NM_011450	ENSMUSG00000027109	Sp3	D130027J01Rik	trans-acting transcription factor 3	protein-coding
mm_99578.1	chr11	104191001	104191004	+	1	NA	3' UTR (NM_001082535, exon 2 of 2)	3' UTR (NM_001082535, exon 2 of 2)	4675	NM_199019	237958	Mm.117063	NM_199019	ENSMUSG00000049506	Sppl2c	4933407P14Rik|IMP5	signal peptide peptidase 2C	protein-coding
mm_167120.1	chr7	119878683	119878686	-	1	NA	intron (NM_001163703, intron 1 of 2)	intron (NM_001163703, intron 1 of 2)	16774	NM_173408	233805	Mm.31539	NM_173408	ENSMUSG00000048787	Dcun1d3	1700020A13Rik|BC030335	DCN1, defective in cullin neddylation 1, domain containing 3 (S. cerevisiae)	protein-coding
mm_36469.1	chr4	82705641	82705659	-	1	NA	Intergenic	Intergenic	154011	NM_026647	68268	Mm.32047	NM_026647	ENSMUSG00000028403	Zdhhc21	9130404H11Rik|AL024349|D130004H04Rik|dep	zinc finger, DHHC domain containing 21	protein-coding
mm_168062.1	chr10	101567407	101567407	+	1	NA	Intergenic	L1Md_A|LINE|L1	-114080	NM_001205098	67569	Mm.25252	NM_026243	ENSMUSG00000019888	Mgat4c	9130411I17Rik|GntIVh	MGAT4 family, member C	protein-coding
mm_33905.1	chr4	136286179	136286190	+	1	NA	5' UTR (NM_009557, exon 1 of 3)	5' UTR (NM_009557, exon 1 of 3)	115	NM_009557	22704	Mm.1504	NM_009557	ENSMUSG00000051351	Zfp46	AI426962|Mlz-4|Zfp-46|Znf436	zinc finger protein 46	protein-coding
mm_108898.1	chr12	100187677	100187718	+	1	NA	promoter-TSS (NR_045282)	promoter-TSS (NR_045282)	-271	NR_045282	100038378	Mm.387075	NR_045282	ENSMUSG00000072884	Gm10433	ENSMUSG00000072884	predicted gene 10433	ncRNA
mm_13403.1	chr2	103977697	103977699	+	1	NA	intron (NM_001142335, intron 3 of 3)	intron (NM_001142335, intron 3 of 3)	7411	NM_001142335	16909	Mm.29266	NM_008505	ENSMUSG00000032698	Lmo2	Rbtn-2|Rbtn2|Rhom-2|Ttg2	LIM domain only 2	protein-coding
mm_144931.1	chr18	37714740	37714820	+	1	NA	promoter-TSS (NM_033590)	promoter-TSS (NM_033590)	-54	NM_033590	93715	Mm.247203	NM_033590	ENSMUSG00000103472	Pcdhga7	-	protocadherin gamma subfamily A, 7	protein-coding
mm_43880.1	chr5	143758370	143758384	+	1	NA	promoter-TSS (NR_015486)	promoter-TSS (NR_015486)	23	NR_015486	320064	Mm.332820	NR_015486		D130017N08Rik	1700012G11Rik	RIKEN cDNA D130017N08 gene	ncRNA
mm_87755.1	chr10	60278478	60278527	+	1	NA	intron (NM_001146120, intron 1 of 13)	B1F|SINE|Alu	874	NM_001146121	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_106701.1	chr12	3572529	3572548	+	1	NA	promoter-TSS (NM_007886)	promoter-TSS (NM_007886)	147	NR_027870	13528	Mm.286202	NM_007886	ENSMUSG00000071454	Dtnb	-	dystrobrevin, beta	protein-coding
mm_132691.1	chr16	43235976	43235986	+	1	NA	intron (NM_001285805, intron 3 of 10)	intron (NM_001285805, intron 3 of 10)	-11303	NM_181058	56490	Mm.136238	NM_019778	ENSMUSG00000022708	Zbtb20	1300017A20Rik|7330412A13Rik|A930017C21Rik|D16Wsu73e|DPZF|HOF|ODA-8S|Oda8|Zfp288	zinc finger and BTB domain containing 20	protein-coding
mm_40679.1	chr5	65537345	65537357	+	1	NA	non-coding (NR_144566, exon 1 of 6)	non-coding (NR_144566, exon 1 of 6)	106	NM_001310619	53323	Mm.319512	NM_016786	ENSMUSG00000029203	Ube2k	AW492011|D5Ertd601e|E2-25k|HIP-2|Hip2|Hypg|Lig	ubiquitin-conjugating enzyme E2K	protein-coding
mm_88816.1	chr10	80798653	80798757	+	1	NA	promoter-TSS (NM_013651)	promoter-TSS (NM_013651)	-30	NM_013651	20222	Mm.358633	NM_013651	ENSMUSG00000020211	Sf3a2	66kDa|AW047242|PRP11|SFA66|Sap62	splicing factor 3a, subunit 2	protein-coding
mm_21226.1	chr2	155930191	155930211	-	1	NA	non-coding (NR_024487, exon 1 of 10)	non-coding (NR_024487, exon 1 of 10)	109	NM_018888	56046	Mm.158827	NM_018888	ENSMUSG00000005882	Uqcc1	2310079L17Rik|2410003P15Rik|3110038N19Rik|Bfzb|Bfzp|Cbp3|Uqcc	ubiquinol-cytochrome c reductase complex assembly factor 1	protein-coding
mm_130078.1	chr15	89374009	89374030	-	1	NA	promoter-TSS (NM_001111288)	promoter-TSS (NM_001111288)	-201	NM_001111288	100126824	Mm.287977	NM_001111288	ENSMUSG00000091780	Sco2	-	SCO2 cytochrome c oxidase assembly protein	protein-coding
mm_9944.1	chr1	190911709	190911719	-	1	NA	promoter-TSS (NM_178775)	promoter-TSS (NM_178775)	56	NM_178775	320119	Mm.220912	NM_178775	ENSMUSG00000089872	Rps6kc1	AA682037|B130003F20Rik|C80612|Rpk118	ribosomal protein S6 kinase polypeptide 1	protein-coding
mm_101484.1	chr11	31369863	31369882	-	1	NA	5' UTR (NM_011491, exon 1 of 4)	5' UTR (NM_011491, exon 1 of 4)	189	NM_011491	20856	Mm.32506	NM_011491	ENSMUSG00000020303	Stc2	AW125853|Stc2l|mustc2	stanniocalcin 2	protein-coding
mm_133844.1	chr16	96200629	96200655	+	1	NA	5' UTR (NM_015825, exon 1 of 8)	5' UTR (NM_015825, exon 1 of 8)	172	NM_015825	50795	Mm.28638	NM_015825	ENSMUSG00000040666	Sh3bgr	5430437A18Rik	SH3-binding domain glutamic acid-rich protein	protein-coding
mm_149958.1	chr19	28963852	28963877	+	1	NA	promoter-TSS (NM_028922)	promoter-TSS (NM_028922)	-56	NM_028922	74411	Mm.441887	NM_028922	ENSMUSG00000040105	Plpp6	4932443D16Rik|Ppapdc2	phospholipid phosphatase 6	protein-coding
mm_124646.1	chr15	5116590	5116629	+	1	NA	promoter-TSS (NM_026069)	promoter-TSS (NM_026069)	-4	NM_026069	67281	Mm.10474	NM_026069	ENSMUSG00000041841	Rpl37	3110005M08Rik	ribosomal protein L37	protein-coding
mm_73434.1	chr8	106150021	106150063	+	1	NA	promoter-TSS (NM_133792)	promoter-TSS (NM_133792)	-357	NM_133792	192654	Mm.284770	NM_133792	ENSMUSG00000031903	Pla2g15	ACS|C87498|LLPL|Lpla2|Lypla3	phospholipase A2, group XV	protein-coding
mm_136399.1	chr16	93365320	93365343	-	1	NA	Intergenic	Intergenic	-4389	NR_030429	791074		NR_030429	ENSMUSG00000076457	Mir802	Mirn802|mir-802|mmu-mir-802	microRNA 802	ncRNA
mm_171056.1	chr3	104864381	104864402	-	1	NA	promoter-TSS (NM_001253703)	promoter-TSS (NM_001253703)	114	NM_009797	12340	Mm.19142	NM_009797	ENSMUSG00000070372	Capza1	CAPZ|CAZ1|Cappa1	capping protein (actin filament) muscle Z-line, alpha 1	protein-coding
mm_154226.1	chr19	59943569	59943579	-	1	NA	promoter-TSS (NM_001164367)	promoter-TSS (NM_001164367)	80	NM_001164367	74998	Mm.24167	NM_001033172	ENSMUSG00000040022	Rab11fip2	4930470G04Rik|A830046J09Rik|AW558126|Nrip11	RAB11 family interacting protein 2 (class I)	protein-coding
mm_121216.1	chr14	103054758	103054799	+	1	NA	exon (NM_008392, exon 5 of 5)	exon (NM_008392, exon 5 of 5)	7766	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_59290.1	chr7	24990515	24990531	+	1	NA	exon (NM_001290469, exon 12 of 23)	exon (NM_001290469, exon 12 of 23)	-2856	NR_106014	102465634		NR_106014	ENSMUSG00000099258	Mir7047	Gm27270|mmu-mir-7047	microRNA 7047	ncRNA
mm_47143.1	chr5	120560246	120560295	-	1	NA	exon (NM_145853, exon 3 of 28)	exon (NM_145853, exon 3 of 28)	28343	NM_145853	252972	Mm.114054	NM_145853	ENSMUSG00000032741	Tpcn1	5730403B01Rik|Tpc1|mKIAA1169	two pore channel 1	protein-coding
mm_149974.1	chr19	29067308	29067327	+	1	NA	promoter-TSS (NR_045687)	promoter-TSS (NR_045687)	16	NR_045687	100503337	Mm.103412	NR_045687		Gm9895	ENSMUSG00000052976	predicted gene 9895	ncRNA
mm_124178.1	chr14	93867241	93867251	-	1	NA	intron (NM_001346722, intron 2 of 4)	intron (NM_001346722, intron 2 of 4)	21642	NM_001271800	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding
mm_53795.1	chr6	146725006	146725027	+	1	NA	promoter-TSS (NM_172734)	promoter-TSS (NM_172734)	86	NM_172734	232533	Mm.322121	NM_172734	ENSMUSG00000001630	Stk38l	4930473A22Rik|Ndr2|Ndr54	serine/threonine kinase 38 like	protein-coding
mm_24067.1	chr3	87915790	87915805	+	1	NA	3' UTR (NM_008231, exon 6 of 6)	3' UTR (NM_008231, exon 6 of 6)	-3747	NM_026591	67707	Mm.393802	NM_026591	ENSMUSG00000019710	Mrpl24	2010005E08Rik|2810470K06Rik|6720473G22Rik|AA407670	mitochondrial ribosomal protein L24	protein-coding
mm_4373.1	chr1	172126751	172126779	+	1	NA	promoter-TSS (NM_001159525)	promoter-TSS (NM_001159525)	10	NM_023041	19298	Mm.247764	NM_023041	ENSMUSG00000003464	Pex19	Pxf	peroxisomal biogenesis factor 19	protein-coding
mm_8637.1	chr1	156421147	156421157	-	1	NA	promoter-TSS (NM_001346967)	promoter-TSS (NM_001346967)	-237	NM_001346967	77352	Mm.428709	NM_001033180	ENSMUSG00000026601	Axdnd1	9430070O13Rik|Gm979	axonemal dynein light chain domain containing 1	protein-coding
mm_169499.1	chr1	47658016	47658020	+	1	NA	Intergenic	Intergenic	-190893	NR_105768	102466969		NR_105768	ENSMUSG00000098876	Mir6350	Gm27958|mmu-mir-6350	microRNA 6350	ncRNA
mm_90688.1	chr10	128933783	128933828	+	1	NA	promoter-TSS (NM_008398)	promoter-TSS (NM_008398)	-8	NM_008398	16404	Mm.179747	NM_008398	ENSMUSG00000025348	Itga7	[a]7|alpha7	integrin alpha 7	protein-coding
mm_117166.1	chr13	62858416	62858425	-	1	NA	promoter-TSS (NM_007994)	promoter-TSS (NM_007994)	-50	NM_007994	14120	Mm.391871	NM_007994	ENSMUSG00000021456	Fbp2	Fbp-1|Fbp1|Rae-30	fructose bisphosphatase 2	protein-coding
mm_104546.1	chr11	96773360	96773366	-	1	NA	intron (NM_001163389, intron 3 of 7)	B1F2|SINE|Alu	4192	NM_028965	74479	Mm.270781	NM_028965	ENSMUSG00000020876	Snx11	4933439F10Rik|A930041K09Rik|AI117694	sorting nexin 11	protein-coding
mm_71781.1	chr8	66511733	66511743	+	1	NA	promoter-TSS (NM_028927)	promoter-TSS (NM_028927)	-2	NM_001271574	74419	Mm.159193	NM_028927	ENSMUSG00000025519	Tktl2	4933401I19Rik	transketolase-like 2	protein-coding
mm_40267.1	chr5	38508058	38508075	+	1	NA	Intergenic	BGLII_Mur|LTR|ERVK	-5914	NM_145559	117591	Mm.260137	NM_145559	ENSMUSG00000005107	Slc2a9	Glut9|SLC2A9B|SLC2a9A	solute carrier family 2 (facilitated glucose transporter), member 9	protein-coding
mm_48709.1	chr5	147221837	147221854	-	1	NA	Intergenic	Intergenic	33149	NM_008178	14842	Mm.4797	NM_008178	ENSMUSG00000053129	Gsx1	Gsh-1|Gsh1	GS homeobox 1	protein-coding
mm_52144.1	chr6	97977956	97977969	+	1	NA	intron (NM_001113198, intron 2 of 9)	intron (NM_001113198, intron 2 of 9)	-13821	NM_008601	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_71114.1	chr8	36025668	36025678	+	1	NA	Intergenic	Intergenic	-69155	NM_172911	244418	Mm.244971	NM_172911	ENSMUSG00000050271	Prag1	9830148H23|D8Ertd82e|NACK|Sgk223|mFLJ00269	PEAK1 related kinase activating pseudokinase 1	protein-coding
mm_22663.1	chr3	14871834	14871834	+	1	NA	3' UTR (NM_007606, exon 7 of 7)	3' UTR (NM_007606, exon 7 of 7)	8296	NM_007606	12350	Mm.300	NM_007606	ENSMUSG00000027559	Car3	BB219044|Ca3|Car-3	carbonic anhydrase 3	protein-coding
mm_49219.1	chr6	15779157	15779168	+	1	NA	intron (NM_175088, intron 4 of 4)	intron (NM_175088, intron 4 of 4)	58501	NM_175088	16543	Mm.1314	NM_175088	ENSMUSG00000041390	Mdfic	Kdt1|Mdfid	MyoD family inhibitor domain containing	protein-coding
mm_161118.1	chr12	105646739	105646739	-	1	NA	intron (NM_029654, intron 22 of 41)	intron (NM_029654, intron 22 of 41)	38502	NM_029654	76559	Mm.114362	NM_029654	ENSMUSG00000041341	Atg2b	2410024A21Rik|AI047755|AI503411|AW558123|C030004M05Rik|C630028L02Rik|mKIAA4067	autophagy related 2B	protein-coding
mm_27190.1	chr3	34757854	34757860	-	1	NA	Intergenic	Intergenic	-14218	NR_110488	102638436	Mm.261793	NR_110488	ENSMUSG00000106519	Gm38509	Peril	predicted gene, 38509	ncRNA
mm_94201.1	chr11	3101952	3101961	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	-22065	NR_003517	236604	Mm.247625	NM_001004146		Pisd-ps1	-	phosphatidylserine decarboxylase, pseudogene 1	pseudo
mm_111867.1	chr12	107996217	107996218	-	1	NA	intron (NM_001079883, intron 1 of 3)	intron (NM_001079883, intron 1 of 3)	7197	NM_001079883	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_48152.1	chr5	137151127	137151137	-	1	NA	Intergenic	Intergenic	-34925	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_109287.1	chr12	109559099	109559112	+	1	NA	non-coding (NR_003633, exon 5 of 5)	non-coding (NR_003633, exon 5 of 5)	-4587	NR_030427	791079		NR_030427	ENSMUSG00000076451	Mir770	Mirn770|mir-770|mmu-mir-770	microRNA 770	ncRNA
mm_15269.1	chr2	155133502	155133552	+	1	NA	promoter-TSS (NM_001243712)	promoter-TSS (NM_001243712)	46	NM_008395	16396	Mm.208286	NM_008395	ENSMUSG00000027598	Itch	6720481N21Rik|8030492O04Rik|A130065M08|AIP4|C230047C07Rik	itchy, E3 ubiquitin protein ligase	protein-coding
mm_104712.1	chr11	98051721	98051732	-	1	NA	intron (NM_146028, intron 1 of 10)	intron (NM_146028, intron 1 of 10)	1736	NM_146028	217154	Mm.181008	NM_146028	ENSMUSG00000017400	Stac2	24b2|24b2/STAC2|AW240854	SH3 and cysteine rich domain 2	protein-coding
mm_122010.1	chr14	27234408	27234418	-	1	NA	intron (NM_001289686, intron 3 of 12)	intron (NM_001289686, intron 3 of 12)	-3597	NM_027871	71704	Mm.248606	NM_027871	ENSMUSG00000021895	Arhgef3	1200004I24Rik|9830169H03Rik|C76747|Xpln	Rho guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_28641.1	chr3	95220128	95220187	-	1	NA	3' UTR (NM_019914, exon 2 of 2)	3' UTR (NM_019914, exon 2 of 2)	-2215	NM_029885	213054	Mm.224820	NM_029885	ENSMUSG00000038766	Gabpb2	1810015F01Rik|5830427M07|9430006E19Rik|A430024B14Rik|AV050852|Gabpb2-1	GA repeat binding protein, beta 2	protein-coding
mm_15083.1	chr2	153161959	153161976	+	1	NA	intron (NM_133847, intron 1 of 17)	intron (NM_133847, intron 1 of 17)	666	NM_133847	99237	Mm.330674	NM_133847	ENSMUSG00000068040	Tm9sf4	AA986553|AU045326|B930079E06|mKIAA0255	transmembrane 9 superfamily protein member 4	protein-coding
mm_12380.1	chr2	69861586	69861635	+	1	NA	promoter-TSS (NM_001110145)	promoter-TSS (NM_001110145)	48	NM_009278	20823	Mm.10508	NM_009278	ENSMUSG00000068882	Ssb	SS-B	Sjogren syndrome antigen B	protein-coding
mm_89958.1	chr10	111296058	111296064	+	1	NA	3' UTR (NM_001003717, exon 23 of 23)	3' UTR (NM_001003717, exon 23 of 23)	-2618	NM_027914	71769	Mm.45256	NM_027914	ENSMUSG00000035759	Bbs10	1300007O09Rik|AI452285	Bardet-Biedl syndrome 10 (human)	protein-coding
mm_3906.1	chr1	161877854	161877865	+	1	NA	Intergenic	RMER10A|LTR|ERVL	-1198	NM_172645	226551	Mm.170002	NM_172645	ENSMUSG00000040297	Suco	4732491B11|AI848100|AU016931|Opt	SUN domain containing ossification factor	protein-coding
mm_21815.1	chr2	165283649	165283655	-	1	NA	intron (NM_144893, intron 1 of 9)	intron (NM_144893, intron 1 of 9)	4135	NM_001252574	228875	Mm.21184	NM_144893	ENSMUSG00000017664	Slc35c2	C85957|CGI-15|D2Wsu58e|Ovcov1	solute carrier family 35, member C2	protein-coding
mm_145915.1	chr18	66509873	66509877	+	1	NA	non-coding (NR_040528, exon 3 of 3)	non-coding (NR_040528, exon 3 of 3)	5697	NR_040528	100503565	Mm.98256	NR_040528		Gm9926	ENSMUSG00000053891	predicted gene 9926	ncRNA
mm_66574.1	chr7	45333755	45333800	-	1	NA	promoter-TSS (NM_175130)	promoter-TSS (NM_175130)	3	NM_175130	68667	Mm.439890	NM_175130	ENSMUSG00000038260	Trpm4	1110030C19Rik|AW047689|LTRPC4|LTrpC-4|TRPM4B	transient receptor potential cation channel, subfamily M, member 4	protein-coding
mm_36670.1	chr4	95741237	95741240	-	1	NA	intron (NM_001113412, intron 7 of 15)	intron (NM_001113412, intron 7 of 15)	161817	NM_029347	75578	Mm.276098	NM_029347	ENSMUSG00000028573	Fggy	2310009E04Rik	FGGY carbohydrate kinase domain containing	protein-coding
mm_142434.1	chr17	45570700	45570714	-	1	NA	exon (NM_008302, exon 5 of 11)	exon (NM_008302, exon 5 of 11)	2554	NM_008302	15516	Mm.2180	NM_008302	ENSMUSG00000023944	Hsp90ab1	90kDa|AL022974|C81438|Hsp84|Hsp84-1|Hsp90|Hspcb	heat shock protein 90 alpha (cytosolic), class B member 1	protein-coding
mm_21693.1	chr2	164473702	164473712	-	1	NA	promoter-TSS (NM_001271575)	promoter-TSS (NM_001271575)	17	NM_001271575	73603	Mm.472883	NM_001271575	ENSMUSG00000017720	Trp53tg5	1700126L10Rik	transformation related protein 53 target 5	protein-coding
mm_101717.1	chr11	42182208	42182222	-	1	NA	5' UTR (NM_010250, exon 1 of 10)	5' UTR (NM_010250, exon 1 of 10)	715	NM_010250	14394	Mm.439668	NM_010250	ENSMUSG00000010803	Gabra1	Gabra-1	gamma-aminobutyric acid (GABA) A receptor, subunit alpha 1	protein-coding
mm_73054.1	chr8	94377853	94377864	+	1	NA	Intergenic	Intergenic	-8642	NM_022331	64209	Mm.29151	NM_022331	ENSMUSG00000031770	Herpud1	Herp|Mifl|SUP	homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1	protein-coding
mm_141695.1	chr17	33978783	33978841	-	1	NA	promoter-TSS (NR_004446)	promoter-TSS (NR_004446)	-21	NR_004446	630499	Mm.440940	NM_001081015		H2-K2	EG630499|Gm7035|H-2K1|H-2K1K|H-2K2|H2-K1	histocompatibility 2, K region locus 2	pseudo
mm_112051.1	chr12	111713059	111713116	-	1	NA	promoter-TSS (NM_026511)	promoter-TSS (NM_026511)	-134	NM_001324482	70369	Mm.44239	NM_027404	ENSMUSG00000049792	Bag5	1600025G07Rik|4930405J06Rik|Bag-5	BCL2-associated athanogene 5	protein-coding
mm_80766.1	chr9	95559572	95559583	+	1	NA	promoter-TSS (NM_198414)	promoter-TSS (NM_198414)	-240	NM_198414	75552	Mm.151485	NM_198414	ENSMUSG00000064225	Paqr9	1700020G04Rik	progestin and adipoQ receptor family member IX	protein-coding
mm_42556.1	chr5	117120121	117120180	+	1	NA	promoter-TSS (NM_001199685)	promoter-TSS (NM_001199685)	21	NM_001199685	330177	Mm.24343	NM_183306	ENSMUSG00000061288	Taok3	2900006A08Rik|A130052D22|A430105I05Rik	TAO kinase 3	protein-coding
mm_15808.1	chr2	164488198	164488200	+	1	NA	promoter-TSS (NM_001048229)	promoter-TSS (NM_001048229)	88	NM_001048229	52840	Mm.256927	NM_026797	ENSMUSG00000017734	Dbndd2	1110017A21Rik|2900022J10Rik|AU041050|AW048677|D2Bwg0891e|Nkip|R74724	dysbindin (dystrobrevin binding protein 1) domain containing 2	protein-coding
mm_25823.1	chr3	127930612	127930637	+	1	NA	intron (NR_040552, intron 3 of 4)	intron (NR_040552, intron 3 of 4)	14453	NR_040552	329753	Mm.119720	NR_040552	ENSMUSG00000104763	9830132P13Rik	9830132P13	RIKEN cDNA 9830132P13 gene	ncRNA
mm_79625.1	chr9	59291566	59291577	+	1	NA	promoter-TSS (NM_028121)	promoter-TSS (NM_028121)	-1	NM_028121	72141	Mm.22456	NM_028121	ENSMUSG00000025236	Adpgk	2610017G09Rik|Adp-gk|C77577	ADP-dependent glucokinase	protein-coding
mm_123467.1	chr14	65973361	65973398	-	1	NA	exon (NM_013492, exon 3 of 9)	exon (NM_013492, exon 3 of 9)	4896	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_33742.1	chr4	134127619	134127715	+	1	NA	TTS (NM_026257)	TTS (NM_026257)	1086	NM_080559	73723	Mm.22240	NM_080559	ENSMUSG00000028843	Sh3bgrl3	1110004L05Rik|AU022188	SH3 domain binding glutamic acid-rich protein-like 3	protein-coding
mm_71134.1	chr8	39005828	39005866	+	1	NA	promoter-TSS (NM_030254)	promoter-TSS (NM_030254)	-20	NM_030254	80286	Mm.272722	NM_030254	ENSMUSG00000039530	Tusc3	AU022242|BC003311|N33	tumor suppressor candidate 3	protein-coding
mm_139100.1	chr17	46924623	46924628	+	1	NA	3' UTR (NM_008938, exon 3 of 3)	3' UTR (NM_008938, exon 3 of 3)	14140	NM_008938	19133	Mm.291370	NM_008938	ENSMUSG00000023978	Prph2	AOFMD|AVMD|Nmf193|PRPH|RP7|Rd-2|Rd2|Rds|Tspan22|rds	peripherin 2	protein-coding
mm_32430.1	chr4	107178687	107178723	+	1	NA	promoter-TSS (NM_029565)	promoter-TSS (NM_029565)	75	NM_029565	56374	Mm.291192	NM_029565	ENSMUSG00000028618	Tmem59	1110001M20Rik|3110046P06Rik|AI256529|D4Ertd20e|MTDCF1|ORF18	transmembrane protein 59	protein-coding
mm_71153.1	chr8	39933358	39933397	+	1	NA	intron (NR_035426, intron 3 of 5)	intron (NR_035426, intron 3 of 5)	-290699	NM_001113326	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_31138.1	chr4	43267166	43267204	+	1	NA	promoter-TSS (NM_177195)	promoter-TSS (NM_177195)	26	NM_177195	320571	Mm.74465	NM_177195	ENSMUSG00000028457	Atp8b5	4930417M19Rik|Feta	ATPase, class I, type 8B, member 5	protein-coding
mm_72827.1	chr8	88250792	88250832	+	1	NA	exon (NM_001164497, exon 8 of 13)	exon (NM_001164497, exon 8 of 13)	-21591	NM_007406	11513	Mm.288206	NM_007406	ENSMUSG00000031659	Adcy7	AA407758	adenylate cyclase 7	protein-coding
mm_77955.1	chr9	7567757	7567771	+	1	NA	3' UTR (NM_008611, exon 10 of 10)	3' UTR (NM_008611, exon 10 of 10)	-3632	NM_001310717	234911	Mm.334940	NM_001030289	ENSMUSG00000070323	Mmp27	Gm180	matrix metallopeptidase 27	protein-coding
mm_119418.1	chr14	45299880	45299927	+	1	NA	exon (NM_015774, exon 7 of 16)	exon (NM_015774, exon 7 of 16)	18669	NM_015774	50527	Mm.387108	NM_015774	ENSMUSG00000021831	Ero1l	ERO1-L|Ero1a	ERO1-like (S. cerevisiae)	protein-coding
mm_88175.1	chr10	69787514	69787537	+	1	NA	intron (NM_170730, intron 1 of 17)	intron (NM_170730, intron 1 of 17)	-138007	NM_170687	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_4229.1	chr1	171358056	171358091	+	1	NA	TTS (NM_001033039)	TTS (NM_001033039)	2725	NM_001033039	68874	Mm.10756	NM_001033039	ENSMUSG00000045259	Klhdc9	1190002J23Rik|AA087357|ESTM31	kelch domain containing 9	protein-coding
mm_13291.1	chr2	101965158	101965159	+	1	NA	intron (NM_001290784, intron 4 of 5)	RLTR27|LTR|ERVK	78896	NM_029635	76501	Mm.330424	NM_029635	ENSMUSG00000027163	Commd9	1810029F08Rik|AA409293	COMM domain containing 9	protein-coding
mm_52142.1	chr6	97977729	97977739	+	1	NA	intron (NM_001113198, intron 2 of 9)	Lx8|LINE|L1	-14049	NM_008601	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_100147.1	chr11	116006550	116006564	+	1	NA	exon (NM_133663, exon 34 of 39)	exon (NM_133663, exon 34 of 39)	6162	NM_016905	14635	Mm.2820	NM_016905	ENSMUSG00000020766	Galk1	AA409894|GALK|Gk|Glk|Glk1	galactokinase 1	protein-coding
mm_112442.1	chr13	5845317	5845334	+	1	NA	Intergenic	Intergenic	12767	NR_045891	71867	Mm.179181	NR_045891	ENSMUSG00000100625	1700016G22Rik	-	RIKEN cDNA 1700016G22 gene	ncRNA
mm_54373.1	chr6	31184720	31184732	-	1	NA	intron (NR_110470, intron 1 of 2)	L4_C_Mam|LINE|RTE-X	33748	NR_110470	232685	Mm.443019	NM_144555	ENSMUSG00000044471	Lncpint	Lincpint|MNCb-1768|Pint|linc-Pint	long non-protein coding RNA, Trp53 induced transcript	ncRNA
mm_69090.1	chr7	127017302	127017343	-	1	NA	promoter-TSS (NM_030240)	promoter-TSS (NM_030240)	30	NM_030240	67278	Mm.345385	NM_030240	ENSMUSG00000030680	Pagr1a	2900092E17Rik|C77040|PA1|PAGR1	PAXIP1 associated glutamate rich protein 1A	protein-coding
mm_37051.1	chr4	116018043	116018063	-	1	NA	promoter-TSS (NM_010173)	promoter-TSS (NM_010173)	-151	NM_010173	14073	Mm.256025	NM_010173	ENSMUSG00000034171	Faah	AW412498	fatty acid amide hydrolase	protein-coding
mm_145323.1	chr18	54971039	54971072	+	1	NA	intron (NM_175751, intron 2 of 9)	intron (NM_175751, intron 2 of 9)	19125	NM_175751	269023	Mm.192984	NM_175751	ENSMUSG00000052713	Zfp608	4932417D18Rik|D430007A19Rik|Znf608	zinc finger protein 608	protein-coding
mm_40274.1	chr5	41250607	41250607	+	1	NA	Intergenic	Intergenic	457084	NM_001310592	100972	Mm.41555	NM_027295	ENSMUSG00000029128	Rab28	2700023P08Rik|AW496496	RAB28, member RAS oncogene family	protein-coding
mm_30307.1	chr3	149445254	149445265	-	1	NA	Intergenic	Intergenic	170522	NR_040591	381482	Mm.393866	NR_040591		Gm1653	-	predicted gene 1653	ncRNA
mm_66849.1	chr7	49637102	49637111	-	1	NA	promoter-TSS (NM_001005232)	promoter-TSS (NM_001005232)	-271	NM_001005232	13172	Mm.307176	NM_001005232	ENSMUSG00000030507	Dbx1	AI426026|Dbx	developing brain homeobox 1	protein-coding
mm_22.1	chr1	5098062	5098109	+	1	NA	exon (NM_133826, exon 6 of 14)	exon (NM_133826, exon 6 of 14)	14999	NM_001310442	108664	Mm.27082	NM_133826	ENSMUSG00000033793	Atp6v1h	0710001F19Rik|AU022349|CGI-11|SFD|SFDalpha|SFDbeta|VMA13	ATPase, H+ transporting, lysosomal V1 subunit H	protein-coding
mm_27260.1	chr3	37672420	37672425	-	1	NA	Intergenic	Intergenic	32475	NM_001305442	24063	Mm.330986	NM_011896	ENSMUSG00000037211	Spry1	sprouty1|spry-1	sprouty homolog 1 (Drosophila)	protein-coding
mm_133018.1	chr16	56477822	56477835	+	1	NA	promoter-TSS (NM_178790)	promoter-TSS (NM_178790)	-18	NM_001014422	320712	Mm.209236	NM_178790	ENSMUSG00000035258	Abi3bp	5033411B22Rik|AI506287|BG172926|D930038M13Rik|TARSH|eratin	ABI gene family, member 3 (NESH) binding protein	protein-coding
mm_82789.1	chr9	28996501	28996515	-	1	NA	3' UTR (NM_172290, exon 8 of 8)	3' UTR (NM_172290, exon 8 of 8)	966621	NM_172290	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding
mm_6486.1	chr1	74108357	74108370	-	1	NA	intron (NM_027884, intron 1 of 34)	intron (NM_027884, intron 1 of 34)	16084	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_53435.1	chr6	134106264	134106275	+	1	NA	intron (NM_001303102, intron 2 of 8)	intron (NM_001303102, intron 2 of 8)	70569	NM_007961	14011	Mm.269995	NM_007961	ENSMUSG00000030199	Etv6	AW123102|AW557856|Tel	ets variant 6	protein-coding
mm_151858.1	chr19	5797062	5797104	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	-1102	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_81785.1	chr9	114731178	114731234	+	1	NA	promoter-TSS (NM_026036)	promoter-TSS (NM_026036)	3	NM_026036	67213	Mm.28858	NM_026036	ENSMUSG00000032434	Cmtm6	2810051A14Rik|AA536733|Cklfsf6	CKLF-like MARVEL transmembrane domain containing 6	protein-coding
mm_72321.1	chr8	78508622	78508632	+	1	NA	promoter-TSS (NM_001282108)	promoter-TSS (NM_001282108)	301	NM_001252089	19656	Mm.24718	NM_009033	ENSMUSG00000037070	Rbmxl1	Hnrpg|Rbmx|Rbmxrt	RNA binding motif protein, X-linked like-1	protein-coding
mm_51345.1	chr6	72549431	72549478	+	1	NA	promoter-TSS (NM_001271395)	promoter-TSS (NM_001271395)	181	NM_001042534	12332	Mm.18626	NM_007599	ENSMUSG00000056737	Capg	gCap39|mbh1	capping protein (actin filament), gelsolin-like	protein-coding
mm_159873.1	chr5	149053014	149053014	-	1	NA	promoter-TSS (NM_010439)	promoter-TSS (NM_010439)	43	NM_010439	15289	Mm.207047	NM_010439	ENSMUSG00000066551	Hmgb1	HMG-1|Hmg1|SBP-1|p30	high mobility group box 1	protein-coding
mm_25075.1	chr3	99968921	99968923	+	1	NA	intron (NM_028892, intron 4 of 48)	intron (NM_028892, intron 4 of 48)	83505	NM_028892	74362	Mm.55847	NM_028892	ENSMUSG00000027867	Spag17	4931427F14Rik|PF6|Spag17-ps	sperm associated antigen 17	protein-coding
mm_141075.1	chr17	25844489	25844503	-	1	NA	TTS (NM_001163766)	TTS (NM_001163766)	355	NM_145999	214952	Mm.40907	NM_145999	ENSMUSG00000025733	Rhot2	Arht2|Miro2	ras homolog family member T2	protein-coding
mm_96640.1	chr11	69326669	69326681	+	1	NA	TTS (NM_001024206)	TTS (NM_001024206)	417	NM_010599	16499	Mm.232472	NM_010599	ENSMUSG00000018470	Kcnab3	C330022D06Rik|Kcnab4|mKv(beta)4	potassium voltage-gated channel, shaker-related subfamily, beta member 3	protein-coding
mm_39237.1	chr4	156255654	156255666	-	1	NA	promoter-TSS (NM_001110516)	promoter-TSS (NM_001110516)	-322	NM_001110516	231004	Mm.406833	NM_173736	ENSMUSG00000096351	Samd11	BC026991|mr-s	sterile alpha motif domain containing 11	protein-coding
mm_102446.1	chr11	59787211	59787231	-	1	NA	promoter-TSS (NR_110894)	promoter-TSS (NR_110894)	1	NR_110894	194908	Mm.344651	NM_183139	ENSMUSG00000043648	Pld6	4933433K01Rik|Gm10|Zuc|mZuc|mitoPLD	phospholipase D family, member 6	protein-coding
mm_163828.1	chr14	19417482	19417508	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	185092	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_146715.1	chr18	14899366	14899383	-	1	NA	3' UTR (NM_001100449, exon 15 of 15)	3' UTR (NM_001100449, exon 15 of 15)	-89621	NR_045372	74456	Mm.391075	NR_045372		4933424G05Rik	-	RIKEN cDNA 4933424G05 gene	ncRNA
mm_115588.1	chr13	11826870	11826886	-	1	NA	intron (NM_023868, intron 15 of 104)	(TG)n|Simple_repeat|Simple_repeat	280067	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding
mm_165680.1	chr3	90687109	90687115	+	1	NA	Intergenic	Intergenic	8609	NM_001281852	20202	Mm.2128	NM_009114	ENSMUSG00000056071	S100a9	60B8Ag|AW546964|BEE22|Cagb|GAGB|L1Ag|MRP14|p14	S100 calcium binding protein A9 (calgranulin B)	protein-coding
mm_148644.1	chr19	5490476	5490487	+	1	NA	promoter-TSS (NM_007687)	promoter-TSS (NM_007687)	26	NM_007687	12631	Mm.329655	NM_007687	ENSMUSG00000056201	Cfl1	AA959946|Cof	cofilin 1, non-muscle	protein-coding
mm_45029.1	chr5	38876709	38876757	-	1	NA	promoter-TSS (NM_013748)	promoter-TSS (NM_013748)	-40	NM_013748	27278	Mm.440845	NM_013748	ENSMUSG00000039315	Clnk	MIST	cytokine-dependent hematopoietic cell linker	protein-coding
mm_43001.1	chr5	123442291	123442304	+	1	NA	exon (NM_177582, exon 4 of 9)	exon (NM_177582, exon 4 of 9)	39804	NM_029594	76399	Mm.75049	NM_029594	ENSMUSG00000029437	Il31	1700013B14Rik	interleukin 31	protein-coding
mm_97975.1	chr11	83862810	83862820	+	1	NA	intron (NM_001291269, intron 3 of 8)	intron (NM_001291269, intron 3 of 8)	9855	NM_001291269	21410	Mm.7226	NM_009330	ENSMUSG00000020679	Hnf1b	HNF-1-beta|HNF-1B|HNF-1Beta|Hnf1beta|LFB3|Tcf-2|Tcf2|vHNF1	HNF1 homeobox B	protein-coding
mm_168156.1	chr10	42055433	42055434	-	1	NA	Intergenic	Intergenic	-37051	NM_001034858	213402	Mm.211320	NM_001034858	ENSMUSG00000071324	Armc2	2610018I05Rik	armadillo repeat containing 2	protein-coding
mm_141908.1	chr17	34959585	34959592	-	1	NA	promoter-TSS (NM_010478)	promoter-TSS (NM_010478)	-350	NM_010478	15511	Mm.372314	NM_010478	ENSMUSG00000090877	Hspa1b	Hsp70|Hsp70-1|Hsp70.1|hsp68	heat shock protein 1B	protein-coding
mm_69681.1	chr7	139986949	139986961	-	1	NA	promoter-TSS (NR_106029)	promoter-TSS (NR_106029)	-81	NR_106029	102465643		NR_106029	ENSMUSG00000099092	Mir7062	Gm27339|mmu-mir-7062	microRNA 7062	ncRNA
mm_111272.1	chr12	85339317	85339327	-	1	NA	promoter-TSS (NM_145138)	promoter-TSS (NM_145138)	40	NM_145138	217718	Mm.29071	NM_145138	ENSMUSG00000034290	Nek9	C130021H08Rik	NIMA (never in mitosis gene a)-related expressed kinase 9	protein-coding
mm_138415.1	chr17	35069326	35069343	+	1	NA	exon (NM_023463, exon 3 of 3)	exon (NM_023463, exon 3 of 3)	2009	NM_023463	68468	Mm.215096	NM_023463	ENSMUSG00000092586	Ly6g6c	1110003M04Rik|AU016360|G6c|NG24	lymphocyte antigen 6 complex, locus G6C	protein-coding
mm_12316.1	chr2	69380432	69380458	+	1	NA	promoter-TSS (NM_175512)	promoter-TSS (NM_175512)	-17	NM_175512	241452	Mm.211655	NM_175512	ENSMUSG00000027068	Dhrs9	C730025I08Rik|Rdh15	dehydrogenase/reductase (SDR family) member 9	protein-coding
mm_148005.1	chr18	67774711	67774759	-	1	NA	promoter-TSS (NM_001039088)	promoter-TSS (NM_001039088)	-141	NM_028112	72124	Mm.307315	NM_028112	ENSMUSG00000079614	Seh1l	2610007A16Rik|AW540070|SEC13L|SEH1A|SEH1B|Seh1	SEH1-like (S. cerevisiae	protein-coding
mm_18292.1	chr2	52676120	52676146	-	1	NA	promoter-TSS (NM_001285428)	promoter-TSS (NM_001285428)	10	NM_001285426	12298	Mm.330223	NM_146123	ENSMUSG00000017412	Cacnb4	3110038O15Rik|Cchb4|lh	calcium channel, voltage-dependent, beta 4 subunit	protein-coding
mm_18820.1	chr2	74591892	74591908	-	1	NA	Intergenic	Intergenic	-12952	NM_027133	69605	Mm.156113	NM_027133	ENSMUSG00000009207	Lnpk	2310011O18Rik|4921514L11Rik|9530051D01Rik|AI666268|Lnp|Lnpk1|Ul|ulnaless	lunapark, ER junction formation factor	protein-coding
mm_129399.1	chr15	78284121	78284151	-	1	NA	TTS (NR_106137).2	TTS (NR_106137).2	713	NR_106138	102466845		NR_106138	ENSMUSG00000099059	Mir7676-2	Gm27790|mmu-mir-7676-2	microRNA 7676-2	ncRNA
mm_126178.1	chr15	78598060	78598117	+	1	NA	intron (NM_028195, intron 1 of 12)	intron (NM_028195, intron 1 of 12)	1041	NM_028195	72318	Mm.32911	NM_028195	ENSMUSG00000018008	Cyth4	2510004M07Rik|5830469K17Rik|AI467541|Pscd4|mFLJ00017	cytohesin 4	protein-coding
mm_56351.1	chr6	93675916	93675919	-	1	NA	3' UTR (NM_010367, exon 22 of 22)	3' UTR (NM_010367, exon 22 of 22)	237046	NR_104594	14924	Mm.217216	NM_010367	ENSMUSG00000045095	Magi1	AIP3|BAP1|Baiap1|Gukmi1|MAGI1c|Magi-1|TNRC19|WWP3|mKIAA4129	membrane associated guanylate kinase, WW and PDZ domain containing 1	protein-coding
mm_163649.1	chr13	64066085	64066091	-	1	NA	intron (NM_008291, intron 6 of 10)	B4A|SINE|B4	23113	NM_008291	15487	Mm.5109	NM_008291	ENSMUSG00000033122	Hsd17b3	-	hydroxysteroid (17-beta) dehydrogenase 3	protein-coding
mm_24427.1	chr3	90537334	90537386	+	1	NA	Intergenic	Intergenic	-3863	NM_026416	67860	Mm.331185	NM_026416	ENSMUSG00000074457	S100a16	2300002L21Rik|AI325039|AI663996|DT1P1A7|S100F	S100 calcium binding protein A16	protein-coding
mm_88793.1	chr10	80629672	80629687	+	1	NA	promoter-TSS (NM_001159591)	promoter-TSS (NM_001159591)	23	NM_001159591	103236	Mm.29873	NM_134002	ENSMUSG00000003345	Csnk1g2	2810429I12Rik|AI463719	casein kinase 1, gamma 2	protein-coding
mm_114139.1	chr13	55265199	55265205	+	1	NA	intron (NM_008739, intron 8 of 22)	Lx8b|LINE|L1	55420	NM_008739	18193	Mm.12964	NM_008739	ENSMUSG00000021488	Nsd1	AI528500|KMT3B	nuclear receptor-binding SET-domain protein 1	protein-coding
mm_30278.1	chr3	148819829	148819849	-	1	NA	intron (NM_001081298, intron 23 of 23)	CpG	134796	NM_001081298	99633	Mm.9776	NM_001081298	ENSMUSG00000028184	Adgrl2	AI450192|CIRL-2|Gm619|Lec1|Lphh1|Lphn2|mKIAA0786	adhesion G protein-coupled receptor L2	protein-coding
mm_121333.1	chr14	115040962	115040978	+	1	NA	Intergenic	CpG	-2701	NR_029785	723905		NR_029785	ENSMUSG00000065508	Mir17	Mirn17|mir-17|mmu-mir-17	microRNA 17	ncRNA
mm_126454.1	chr15	80902393	80902407	+	1	NA	intron (NM_144812, intron 16 of 24)	intron (NM_144812, intron 16 of 24)	-37639	NR_039573	100628612		NR_039573	ENSMUSG00000092868	Mir5113	mir-5113|mmu-mir-5113|mu-mir-5113	microRNA 5113	ncRNA
mm_44143.1	chr5	150259737	150259748	+	1	NA	promoter-TSS (NM_172887)	promoter-TSS (NM_172887)	-188	NM_172887	320365	Mm.216590	NM_172887	ENSMUSG00000056602	Fry	13CDNA73|9330186A19Rik|AF346502|AI462658|C87180|D930046M03|cg003|mKIAA4143	FRY microtubule binding protein	protein-coding
mm_100912.1	chr11	6230175	6230242	-	1	NA	promoter-TSS (NM_207242)	promoter-TSS (NM_207242)	37	NM_207242	237636	Mm.212492	NM_207242	ENSMUSG00000020447	Npc1l1	9130221N23Rik|Gm243	NPC1-like 1	protein-coding
mm_68674.1	chr7	118976699	118976729	-	1	NA	intron (NM_022420, intron 2 of 3)	G-rich|Low_complexity|Low_complexity	18497	NM_022420	64297	Mm.103439	NM_022420	ENSMUSG00000008734	Gprc5b	AW125761|Raig2	G protein-coupled receptor, family C, group 5, member B	protein-coding
mm_67544.1	chr7	81493687	81493697	-	1	NA	TTS (NM_183143)	TTS (NM_183143)	233	NM_021492	11775	Mm.322894	NM_021492	ENSMUSG00000062444	Ap3b2	AI549966|AU042881|Naptb|[b]-NAP|beta-NAP|beta3B	adaptor-related protein complex 3, beta 2 subunit	protein-coding
mm_20904.1	chr2	150136642	150136687	-	1	NA	promoter-TSS (NM_023266)	promoter-TSS (NM_023266)	14	NM_023266	104348	Mm.485851	NM_023266	ENSMUSG00000068134	Zfp120	AI315103|E030042N05Rik|F80|MZF31|Zfp844	zinc finger protein 120	protein-coding
mm_128765.1	chr15	66286597	66286661	-	1	NA	promoter-TSS (NM_152923)	promoter-TSS (NM_152923)	-405	NM_152923	110862	Mm.255585	NM_152923	ENSMUSG00000056258	Kcnq3	-	potassium voltage-gated channel, subfamily Q, member 3	protein-coding
mm_165357.1	chr2	121985678	121985682	+	1	NA	intron (NM_212450, intron 5 of 12)	B1_Mur4|SINE|Alu	-29588	NM_008545	17147	Mm.389349	NM_008545	ENSMUSG00000074881	Mageb3	Mage-b3|Mage-ps1|Mage-rs3|Smage3	melanoma antigen, family B, 3	protein-coding
mm_34791.1	chr4	154299639	154299650	+	1	NA	intron (NM_001112744, intron 1 of 14)	intron (NM_001112744, intron 1 of 14)	251	NM_001112744	230972	Mm.38481	NM_001112744	ENSMUSG00000029032	Arhgef16	-	Rho guanine nucleotide exchange factor (GEF) 16	protein-coding
mm_99840.1	chr11	109344282	109344297	+	1	NA	Intergenic	Intergenic	-2578	NR_027883	67927	Mm.394490	NR_027883	ENSMUSG00000099630	1700096J18Rik	-	RIKEN cDNA 1700096J18 gene	ncRNA
mm_132565.1	chr16	38089962	38089982	+	1	NA	promoter-TSS (NR_033221)	promoter-TSS (NR_033221)	-712	NR_033221	414072	Mm.483602	NR_033221		BC031361	-	cDNA sequence BC031361	ncRNA
mm_65567.1	chr7	27178836	27178888	-	1	NA	promoter-TSS (NM_029391)	promoter-TSS (NM_029391)	21	NM_029391	19342	Mm.482114	NM_029391	ENSMUSG00000053291	Rab4b	1500031G17Rik	RAB4B, member RAS oncogene family	protein-coding
mm_45546.1	chr5	72914099	72914113	-	1	NA	promoter-TSS (NM_001113423)	promoter-TSS (NM_001113423)	-256	NM_001113423	75991	Mm.121285	NM_153567	ENSMUSG00000036087	Slain2	5033405K12Rik|8030444K12Rik|AI596370	SLAIN motif family, member 2	protein-coding
mm_94291.1	chr11	4046319	4046319	+	1	NA	exon (NM_146013, exon 12 of 12)	exon (NM_146013, exon 12 of 12)	14537	NM_146013	103655	Mm.337476	NM_146013	ENSMUSG00000019368	Sec14l4	AI256582|AW536553|SPF|TAP	SEC14-like lipid binding 4	protein-coding
mm_130630.1	chr15	100423046	100423056	-	1	NA	promoter-TSS (NM_001146161)	promoter-TSS (NM_001146161)	4	NM_001146161	18174	Mm.234608	NM_008732	ENSMUSG00000023030	Slc11a2	DCT1|DMT1|Nramp2|mk|van	solute carrier family 11 (proton-coupled divalent metal ion transporters), member 2	protein-coding
mm_165320.1	chr2	105683567	105683594	+	1	NA	intron (NM_001310146, intron 1 of 9)	intron (NM_001310146, intron 1 of 9)	1117	NM_001310145	18508	Mm.3608	NM_013627	ENSMUSG00000027168	Pax6	1500038E17Rik|AEY11|Dey|Gsfaey11|Pax-6|Sey	paired box 6	protein-coding
mm_45350.1	chr5	65910521	65910544	-	1	NA	Intergenic	Intergenic	46963	NM_001081105	74734	Mm.20323	NM_001081105	ENSMUSG00000029204	Rhoh	5830400A04Rik|AU019774|Arhh	ras homolog family member H	protein-coding
mm_132992.1	chr16	53576460	53576466	+	1	NA	Intergenic	IAPLTR1_Mm|LTR|ERVK	-760719	NR_040495	73820	Mm.60493	NR_040495		4930404A05Rik	-	RIKEN cDNA 4930404A05 gene	ncRNA
mm_123297.1	chr14	61626923	61626923	-	1	NA	intron (NR_028264, intron 4 of 6)	intron (NR_028264, intron 4 of 6)	5049	NR_029734	387134		NR_029734	ENSMUSG00000092995	Mir16-1	Mirn16|Mirn16-1|miR-16|mir-16-1	microRNA 16-1	ncRNA
mm_146901.1	chr18	30975269	30975279	-	1	NA	3' UTR (NM_009065, exon 5 of 5)	3' UTR (NM_009065, exon 5 of 5)	341854	NM_009065	19762	Mm.5163	NM_009065	ENSMUSG00000057455	Rit2	RIBA|Rin|Roc2	Ras-like without CAAX 2	protein-coding
mm_102963.1	chr11	69665576	69665586	-	1	NA	exon (NM_001291058, exon 2 of 6)	exon (NM_001291058, exon 2 of 6)	589	NM_001291058	12514	Mm.15819	NM_009853	ENSMUSG00000018774	Cd68	Lamp4|Scard1|gp110	CD68 antigen	protein-coding
mm_26606.1	chr3	152215438	152215449	+	1	NA	intron (NM_057172, intron 2 of 19)	intron (NM_057172, intron 2 of 19)	4985	NM_057172	51886	Mm.278922	NM_057172	ENSMUSG00000028034	Fubp1	9530027K12Rik|D3Ertd330e|FBP|Fubp|Fubp4	far upstream element (FUSE) binding protein 1	protein-coding
mm_143171.1	chr17	57226797	57226812	-	1	NA	exon (NM_009778, exon 2 of 41)	exon (NM_009778, exon 2 of 41)	1332	NM_009778	12266	Mm.19131	NM_009778	ENSMUSG00000024164	C3	AI255234|ASP|HSE-MSF|Plp	complement component 3	protein-coding
mm_95468.1	chr11	50603370	50603380	+	1	NA	exon (NM_175643, exon 2 of 22)	exon (NM_175643, exon 2 of 22)	1290	NM_175643	216725	Mm.110597	NM_175643	ENSMUSG00000036545	Adamts2	ADAM-TS 2|ADAM-TS2|ADAMTS-2|PC I-NP|PCINP|pNPI	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 2	protein-coding
mm_63082.1	chr7	122288723	122288734	+	1	NA	promoter-TSS (NM_008855)	promoter-TSS (NM_008855)	-397	NM_001316672	18751	Mm.207496	NM_008855	ENSMUSG00000052889	Prkcb	PKC-B|PKC-Beta|Pkcb|Prkcb1|Prkcb2	protein kinase C, beta	protein-coding
mm_116041.1	chr13	27243824	27243843	-	1	NA	exon (NM_008865, exon 2 of 5)	exon (NM_008865, exon 2 of 5)	1403	NM_008865	18776	Mm.37203	NM_008865	ENSMUSG00000038891	Prl3b1	Csh2|Ghd8|PL|Pl-2|Pl2|mPL-II|mplII	prolactin family 3, subfamily b, member 1	protein-coding
mm_155322.1	chrX	62382958	62382959	+	1	NA	Intergenic	B1_Mus1|SINE|Alu	95816	NM_001199996	74437	Mm.85792	NM_001199996	ENSMUSG00000045330	4933402E13Rik	-	RIKEN cDNA 4933402E13 gene	protein-coding
mm_40798.1	chr5	67611334	67611341	+	1	NA	exon (NM_001033415, exon 2 of 2)	exon (NM_001033415, exon 2 of 2)	3454	NM_001033415	330096	Mm.442747	NM_001033415	ENSMUSG00000050010	Shisa3	D830007B15Rik	shisa family member 3	protein-coding
mm_1519.1	chr1	72824514	72824522	+	1	NA	promoter-TSS (NM_008342)	promoter-TSS (NM_008342)	38	NM_008342	16008	Mm.141936	NM_008342	ENSMUSG00000039323	Igfbp2	AI255832|IBP-2|Igfbp-2|mIGFBP-2	insulin-like growth factor binding protein 2	protein-coding
mm_48682.1	chr5	146584828	146584880	-	1	NA	promoter-TSS (NM_008151)	promoter-TSS (NM_008151)	385	NM_001010941	14738	Mm.153539	NM_008151	ENSMUSG00000041468	Gpr12	Gpcr01|Gpcr12|Gpcr20|Gpcr21	G-protein coupled receptor 12	protein-coding
mm_128931.1	chr15	74636349	74636356	-	1	NA	promoter-TSS (NM_001177437)	promoter-TSS (NM_001177437)	-34	NM_001177437	69439	Mm.263708	NM_001177437	ENSMUSG00000022603	Mroh4	1700016M24Rik	maestro heat-like repeat family member 4	protein-coding
mm_106295.1	chr11	118212850	118212852	-	1	NA	promoter-TSS (NM_001112700)	promoter-TSS (NM_001112700)	-109	NM_001112700	19157	Mm.86413	NM_011180	ENSMUSG00000017132	Cyth1	CLM1|CTH-1|CYTIP|Pscd1	cytohesin 1	protein-coding
mm_49483.1	chr6	29534063	29534088	+	1	NA	exon (NM_001252382, exon 3 of 9)	exon (NM_001252382, exon 3 of 9)	4793	NM_001252382	27056	Mm.6479	NM_012057	ENSMUSG00000029771	Irf5	AW491843|mirf5	interferon regulatory factor 5	protein-coding
mm_24934.1	chr3	96559938	96559974	+	1	NA	exon (NM_023719, exon 6 of 8)	exon (NM_023719, exon 6 of 8)	1999	NM_023719	56338	Mm.410189	NM_023719	ENSMUSG00000038393	Txnip	1200008J08Rik|AA682105|Hyplip1|THIF|Tbp-2|VDUP1	thioredoxin interacting protein	protein-coding
mm_167372.1	chr8	90348127	90348160	-	1	NA	5' UTR (NM_172913, exon 1 of 7)	5' UTR (NM_172913, exon 1 of 7)	109	NM_172913	244579	Mm.302755	NM_172913	ENSMUSG00000043668	Tox3	500-9|BC052044|C230068E13|CAGF9|Tnrc9	TOX high mobility group box family member 3	protein-coding
mm_19208.1	chr2	84531347	84531357	-	1	NA	Intergenic	MTEa|LTR|ERVL-MaLR	-24479	NR_046046	672763	Mm.491046	NR_046046	ENSMUSG00000087362	Gm13710	OTTMUSG00000013441	predicted gene 13710	ncRNA
mm_165676.1	chr3	90487934	90487937	+	1	NA	TTS (NM_133854)	TTS (NM_133854)	3078	NM_133854	20615	Mm.331182	NM_133854	ENSMUSG00000001018	Snapin	25kDa|AA407989|AV026596|Bloc1s7|Snap25bp|Snapap	SNAP-associated protein	protein-coding
mm_139300.1	chr17	48346434	48346445	+	1	NA	promoter-TSS (NM_031254)	promoter-TSS (NM_031254)	38	NM_001272078	83433	Mm.261623	NM_031254	ENSMUSG00000023992	Trem2	TREM-2|Trem2a|Trem2b|Trem2c	triggering receptor expressed on myeloid cells 2	protein-coding
mm_161352.1	chr14	55115533	55115533	-	1	NA	intron (NM_177049, intron 1 of 5)	intron (NM_177049, intron 1 of 5)	1402	NM_177049	319984	Mm.19047	NM_177049	ENSMUSG00000022208	Jph4	9330157P13Rik|JP-4|JPHL1	junctophilin 4	protein-coding
mm_153108.1	chr19	32956543	32956543	-	1	NA	Intergenic	Intergenic	198966	NM_008960	19211	Mm.245395	NM_008960	ENSMUSG00000013663	Pten	2310035O07Rik|A130070J02Rik|AI463227|B430203M17Rik|MMAC1|TEP1	phosphatase and tensin homolog	protein-coding
mm_38334.1	chr4	137594818	137594842	-	1	NA	intron (NM_001347227, intron 1 of 26)	intron (NM_001347227, intron 1 of 26)	641	NM_130879	170707	Mm.218478	NM_130879	ENSMUSG00000043411	Usp48	2810449C13Rik|AI115503|BC021769|D330022K21Rik|Usp31	ubiquitin specific peptidase 48	protein-coding
mm_38313.1	chr4	137118136	137118165	-	1	NA	Intergenic	Intergenic	46916	NR_040443	100503595	Mm.421314	NR_040443	ENSMUSG00000085833	Gm13003	OTTMUSG00000009822	predicted gene 13003	ncRNA
mm_85906.1	chr9	111056485	111056499	-	1	NA	intron (NM_001302377, intron 2 of 2)	intron (NM_001302377, intron 2 of 2)	752	NM_001302377	54199	Mm.7336	NM_017466	ENSMUSG00000043953	Ccrl2	1810047I05Rik|Ackr5|CCR11|Cmkbr1l2|E01|L-CCR	chemokine (C-C motif) receptor-like 2	protein-coding
mm_70611.1	chr8	13414290	13414295	+	1	NA	intron (NM_011881, intron 5 of 6)	intron (NM_011881, intron 5 of 6)	9211	NM_011881	24013	Mm.257501	NM_011881	ENSMUSG00000031450	Grk1	Gprk1|Rhok|Rk	G protein-coupled receptor kinase 1	protein-coding
mm_49155.1	chr6	12911082	12911085	+	1	NA	Intergenic	Intergenic	-158676	NM_027992	71900	Mm.27742	NM_027992	ENSMUSG00000029571	Tmem106b	2310036D22Rik|5830455K21Rik|6430519M21Rik|AI428776|AI661344	transmembrane protein 106B	protein-coding
mm_36299.1	chr4	68240915	68240919	-	1	NA	Intergenic	Tigger17a|DNA|TcMar-Tigger	713480	NM_019967	56710	Mm.248788	NM_019967	ENSMUSG00000028351	Brinp1	BRINP|Dbc1|Dbccr1|Fam5a	bone morphogenic protein/retinoic acid inducible neural specific 1	protein-coding
mm_18956.1	chr2	76790010	76790022	-	1	NA	exon (NM_011652, exon 214 of 313)	exon (NM_011652, exon 214 of 313)	114701	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_146394.1	chr18	82902089	82902100	+	1	NA	Intergenic	Intergenic	-8785	NM_183033	329003	Mm.326526	NM_183033	ENSMUSG00000058881	Zfp516	C330029B10Rik|D230016L03|Zfp26l|Znf516|mKIAA0222	zinc finger protein 516	protein-coding
mm_52266.1	chr6	108386728	108386742	+	1	NA	exon (NM_010585, exon 21 of 62)	exon (NM_010585, exon 21 of 62)	-103008	NR_106121	102465766		NR_106121	ENSMUSG00000105697	Mir7661	mmu-mir-7661	microRNA 7661	ncRNA
mm_74574.1	chr8	11202992	11203009	-	1	NA	exon (NM_009931, exon 50 of 52)	exon (NM_009931, exon 50 of 52)	-109805	NM_009932	12827	Mm.181021	NM_009932	ENSMUSG00000031503	Col4a2	Col4a-2	collagen, type IV, alpha 2	protein-coding
mm_116525.1	chr13	45790511	45790522	-	1	NA	intron (NM_001199304, intron 4 of 6)	MER44B|DNA|TcMar-Tigger	174475	NM_001199304	20238	Mm.342683	NM_009124	ENSMUSG00000046876	Atxn1	2900016G23Rik|Atx1|C85907|ENSMUSG00000074917|Gm10786|Sca1	ataxin 1	protein-coding
mm_60892.1	chr7	46397292	46397320	+	1	NA	5' UTR (NM_001112739, exon 1 of 4)	5' UTR (NM_001112739, exon 1 of 4)	838	NM_001112739	16502	Mm.249386	NM_008421	ENSMUSG00000058975	Kcnc1	C230009H10Rik|KShIIIB|KV4|Kcr2-1|Kv3.1|NGK2|Shaw	potassium voltage gated channel, Shaw-related subfamily, member 1	protein-coding
mm_59987.1	chr7	30553294	30553309	+	1	NA	promoter-TSS (NM_001012401)	promoter-TSS (NM_001012401)	-1	NM_001012401	243912	Mm.34885	NM_001012401	ENSMUSG00000036854	Hspb6	AA387366|Gm479|Hsp20	heat shock protein, alpha-crystallin-related, B6	protein-coding
mm_169688.1	chr15	74094455	74094466	-	1	NA	Intergenic	Intergenic	-254789	NM_001033365	268816	Mm.440635	NM_001033365	ENSMUSG00000072487	Mroh5	Gm628	maestro heat-like repeat family member 5	protein-coding
mm_26456.1	chr3	142731528	142731531	+	1	NA	intron (NM_173763, intron 10 of 13)	intron (NM_173763, intron 10 of 13)	30481	NM_001293560	229905	Mm.289643	NM_173763	ENSMUSG00000040213	Kyat3	Ccbl2|KATIII|Kat3	kynurenine aminotransferase 3	protein-coding
mm_16344.1	chr2	174345489	174345516	+	1	NA	non-coding (NR_003258, exon 10 of 13)	non-coding (NR_003258, exon 10 of 13)	15413	NM_001077510	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_99459.1	chr11	102435079	102435113	+	1	NA	exon (NM_008175, exon 9 of 13)	exon (NM_008175, exon 9 of 13)	4774	NM_008175	14824	Mm.1568	NM_008175	ENSMUSG00000034708	Grn	Pgrn|epithelin	granulin	protein-coding
mm_6832.1	chr1	84224637	84224642	-	1	NA	intron (NM_001003948, intron 1 of 2)	intron (NM_001003948, intron 1 of 2)	-5678	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_117962.1	chr13	99513616	99513619	-	1	NA	intron (NM_008634, intron 1 of 6)	intron (NM_008634, intron 1 of 6)	2985	NM_008634	17755	Mm.4173	NM_008634	ENSMUSG00000052727	Map1b	A230055D22|AI843217|LC1|MAP5|Mtap-5|Mtap1b|Mtap5	microtubule-associated protein 1B	protein-coding
mm_14788.1	chr2	145860486	145860521	+	1	NA	exon (NM_028724, exon 9 of 13)	exon (NM_028724, exon 9 of 13)	-42738	NM_026425	67877	Mm.151168	NM_026425	ENSMUSG00000002728	Naa20	1500004D14Rik|2900026I01Rik|AU041458|D2Ertd186e|Nat5	N(alpha)-acetyltransferase 20, NatB catalytic subunit	protein-coding
mm_170197.1	chr17	6655831	6655840	-	1	NA	promoter-TSS (NM_001166630).2	promoter-TSS (NM_001166630).2	-4	NM_001166630	100040563	Mm.457381	NM_001166630	ENSMUSG00000000579	Dynlt1c	100040603|Dynlt1d	dynein light chain Tctex-type 1C	protein-coding
mm_3223.1	chr1	135847990	135848026	+	1	NA	exon (NM_001130176, exon 7 of 13)	exon (NM_001130176, exon 7 of 13)	7147	NM_001130176	21956	Mm.247470	NM_011619	ENSMUSG00000026414	Tnnt2	Tnt|cTnT	troponin T2, cardiac	protein-coding
mm_62924.1	chr7	118600153	118600173	+	1	NA	intron (NM_001105252, intron 1 of 21)	intron (NM_001105252, intron 1 of 21)	2866	NM_001105252	74424	Mm.11068	NM_028930	ENSMUSG00000030650	Tmc5	4932443L08Rik|AU016085	transmembrane channel-like gene family 5	protein-coding
mm_13086.1	chr2	91210772	91210796	+	1	NA	TTS (NM_028119)	TTS (NM_028119)	7872	NM_007387	11432	Mm.45570	NM_007387	ENSMUSG00000002103	Acp2	Acp-2|LAP	acid phosphatase 2, lysosomal	protein-coding
mm_122056.1	chr14	30297300	30297306	-	1	NA	intron (NM_001302637, intron 3 of 48)	intron (NM_001302637, intron 3 of 48)	56183	NM_001302637	12289	Mm.9772	NM_028981	ENSMUSG00000015968	Cacna1d	8430418G19Rik|C79217|Cach3|Cacn4|Cacnl1a2|Cav1.3|Cchl1a|Cchl1a2|D-LTCC	calcium channel, voltage-dependent, L type, alpha 1D subunit	protein-coding
mm_108852.1	chr12	98445527	98445530	+	1	NA	intron (NM_029911, intron 4 of 6)	intron (NM_029911, intron 4 of 6)	-78316	NR_136759	105245437	Mm.446375	NR_136759		Gm40893	-	predicted gene, 40893	ncRNA
mm_52319.1	chr6	108836346	108836356	+	1	NA	intron (NM_138677, intron 1 of 11)	intron (NM_138677, intron 1 of 11)	7710	NM_138677	192193	Mm.21596	NM_138677	ENSMUSG00000030104	Edem1	A130059K23Rik|EDEM|mKIAA0212	ER degradation enhancer, mannosidase alpha-like 1	protein-coding
mm_128097.1	chr15	27856428	27856463	-	1	NA	intron (NM_001081302, intron 11 of 56)	intron (NM_001081302, intron 11 of 56)	169403	NM_001081302	223435	Mm.485422	NM_001081302	ENSMUSG00000022263	Trio	6720464I07Rik|AA408740|Solo	triple functional domain (PTPRF interacting)	protein-coding
mm_74881.1	chr8	25091342	25091351	-	1	NA	intron (NM_031257, intron 1 of 11)	intron (NM_031257, intron 1 of 11)	10465	NM_031257	83436	Mm.261122	NM_031257	ENSMUSG00000031557	Plekha2	6430512N22Rik|AI851530|AU041791|TAPP2|W91773	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 2	protein-coding
mm_96785.1	chr11	69964759	69964811	+	1	NA	promoter-TSS (NM_001193619)	promoter-TSS (NM_001193619)	6	NM_001193619	53624	Mm.281896	NM_016887	ENSMUSG00000018569	Cldn7	-	claudin 7	protein-coding
mm_135609.1	chr16	52250136	52250152	-	1	NA	3' UTR (NM_001331110, exon 15 of 15)	3' UTR (NM_001331110, exon 15 of 15)	202937	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_68429.1	chr7	109808241	109808251	-	1	NA	intron (NM_020052, intron 18 of 21)	intron (NM_020052, intron 18 of 21)	-26701	NM_020610	78593	Mm.275374	NM_020610	ENSMUSG00000034825	Nrip3	A330103B05Rik|D7H11orf14|ICRFP703B1614Q5.2	nuclear receptor interacting protein 3	protein-coding
mm_50829.1	chr6	54679454	54679472	+	1	NA	Intergenic	RMER19C|LTR|ERVK	-2161	NM_001289741	68235	Mm.233860	NM_026629	ENSMUSG00000038065	Mturn	2410066E13Rik|AI448550|B230212L03Rik	maturin, neural progenitor differentiation regulator homolog (Xenopus)	protein-coding
mm_40920.1	chr5	75830442	75830452	+	1	NA	Intergenic	L2a|LINE|L2	147981	NM_010612	16542	Mm.285	NM_010612	ENSMUSG00000062960	Kdr	6130401C07|Flk-1|Flk1|Krd-1|Ly73|VEGFR-2|VEGFR2|sVEGFR-2	kinase insert domain protein receptor	protein-coding
mm_131109.1	chr16	5080948	5080952	+	1	NA	intron (NM_026666, intron 16 of 18)	B1_Mur4|SINE|Alu	30882	NM_026666	170644	Mm.66356	NM_026666	ENSMUSG00000039473	Ubn1	1110029L11Rik|2610108L02Rik|AA673476|AW124741	ubinuclein 1	protein-coding
mm_58659.1	chr7	6460223	6460227	+	1	NA	promoter-TSS (NM_146915)	promoter-TSS (NM_146915)	-286	NM_146915	258917	Mm.223322	NM_146915	ENSMUSG00000048620	Olfr1336	MOR103-7	olfactory receptor 1336	protein-coding
mm_8000.1	chr1	134415252	134415287	-	1	NA	promoter-TSS (NM_001306069)	promoter-TSS (NM_001306069)	-109	NM_028320	72674	Mm.259976	NM_028320	ENSMUSG00000026457	Adipor1	2810031L11Rik|ACDCR1|CGI-45|Paqr1	adiponectin receptor 1	protein-coding
mm_24916.1	chr3	96268672	96268683	+	1	NA	promoter-TSS (NM_178215)	promoter-TSS (NM_178215)	23	NM_178215	319154	Mm.383293	NM_178215	ENSMUSG00000074403	Hist2h3b	H3-615|H3-616	histone cluster 2, H3b	protein-coding
mm_28858.1	chr3	97204475	97204483	-	1	NA	3' UTR (NM_029933, exon 10 of 10)	3' UTR (NM_029933, exon 10 of 10)	22885	NM_029933	77578	Mm.226175	NM_029933	ENSMUSG00000038256	Bcl9	2610202E01Rik|8030475K17Rik|A330041G23Rik|Gm130	B cell CLL/lymphoma 9	protein-coding
mm_155790.1	chrX	97526987	97526987	+	1	NA	Intergenic	Intergenic	-149778	NM_001161433	245527	Mm.189270	NM_175540	ENSMUSG00000034457	Eda2r	9430060M22Rik|TNFRSF27|Xedar	ectodysplasin A2 receptor	protein-coding
mm_89419.1	chr10	90875640	90875643	+	1	NA	intron (NM_001347053, intron 1 of 8)	intron (NM_001347053, intron 1 of 8)	45798	NM_001347053	77531	Mm.440605	NM_181398	ENSMUSG00000058589	Anks1b	AIDA-1b|C030032C09Rik|E530015N03Rik|ENSMUSG00000078431|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding
mm_13886.1	chr2	120027482	120027509	+	1	NA	promoter-TSS (NM_001114637)	promoter-TSS (NM_001114637)	12	NM_001114637	433466	Mm.482417	NM_001114637	ENSMUSG00000098789	Jmjd7	-	jumonji domain containing 7	protein-coding
mm_110053.1	chr12	20815719	20815733	-	1	NA	promoter-TSS (NR_015521)	promoter-TSS (NR_015521)	53	NR_015521	69513	Mm.273972	NR_015521	ENSMUSG00000099759	1700030C10Rik	-	RIKEN cDNA 1700030C10 gene	ncRNA
mm_102825.1	chr11	69061049	69061063	-	1	NA	3' UTR (NM_028005, exon 1 of 1)	3' UTR (NM_028005, exon 1 of 1)	1281	NM_028005	71923	Mm.340257	NM_028005	ENSMUSG00000045176	Borcs6	2310047M10Rik	BLOC-1 related complex subunit 6	protein-coding
mm_150189.1	chr19	32665614	32665643	+	1	NA	3' UTR (NM_011864, exon 13 of 13)	3' UTR (NM_011864, exon 13 of 13)	45623	NM_011864	23972	Mm.203916	NM_011864	ENSMUSG00000024899	Papss2	1810018P12Rik|AI159688|AtpsU2|Atpsk2|Sk2|bm	3'-phosphoadenosine 5'-phosphosulfate synthase 2	protein-coding
mm_36656.1	chr4	94928790	94928815	-	1	NA	promoter-TSS (NM_001290623)	promoter-TSS (NM_001290623)	41	NM_027089	67753	Mm.25097	NM_027089	ENSMUSG00000028575	Eqtn	1700028B15Rik|4930579C15Rik|Afaf|C81058|Eqtl|Eqts	equatorin, sperm acrosome associated	protein-coding
mm_9709.1	chr1	179518029	179518045	-	1	NA	promoter-TSS (NM_027188)	promoter-TSS (NM_027188)	-34	NM_027188	69726	Mm.222338	NM_027188	ENSMUSG00000055067	Smyd3	2410008A19Rik|Zmynd1	SET and MYND domain containing 3	protein-coding
mm_161494.1	chr15	86057681	86057681	+	1	NA	promoter-TSS (NM_172611)	promoter-TSS (NM_172611)	-14	NM_172611	223752	Mm.24442	NM_172611	ENSMUSG00000035900	Gramd4	9930016O13	GRAM domain containing 4	protein-coding
mm_44483.1	chr5	23507238	23507240	-	1	NA	3' UTR (NM_009274, exon 15 of 15)	3' UTR (NM_009274, exon 15 of 15)	72810	NM_026984	69188	Mm.205190	NM_026984	ENSMUSG00000029004	Kmt2e	1810033J14Rik|9530077A04Rik|D230038D11Rik|Mll5|NKp44L	lysine (K)-specific methyltransferase 2E	protein-coding
mm_162772.1	chr10	68136726	68136736	-	1	NA	intron (NM_023598, intron 4 of 9)	intron (NM_023598, intron 4 of 9)	141995	NM_023598	71371	Mm.440357	NM_023598	ENSMUSG00000019947	Arid5b	4930580B11|5430435G07Rik|AI467247|Desrt|Mrf2|Mrf2alpha|Mrf2beta	AT rich interactive domain 5B (MRF1-like)	protein-coding
mm_13092.1	chr2	91256095	91256105	+	1	NA	promoter-TSS (NM_030880)	promoter-TSS (NM_030880)	-65	NM_001289677	80708	Mm.236650	NM_028733	ENSMUSG00000027257	Pacsin3	4921507A02Rik|6330413E15Rik|AW413130	protein kinase C and casein kinase substrate in neurons 3	protein-coding
mm_370.1	chr1	33974745	33974748	+	1	NA	intron (NM_001276764, intron 3 of 102)	intron (NM_001276764, intron 3 of 102)	-37079	NM_133833	13518	Mm.336625	NM_010081	ENSMUSG00000026131	Dst	2310001O04Rik|A830042E19Rik|AW554249|BP230|BPAG1-n|Bpag|Bpag1|Macf2|ah|athetoid|dt|mKIAA0728|nmf203|nmf339	dystonin	protein-coding
mm_7778.1	chr1	131276798	131276813	-	1	NA	intron (NM_019777, intron 2 of 21)	intron (NM_019777, intron 2 of 21)	2758	NM_019777	56489	Mm.386783	NM_019777	ENSMUSG00000042349	Ikbke	AW558201|IKK-i|IKKepsilon|Ikki	inhibitor of kappaB kinase epsilon	protein-coding
mm_50788.1	chr6	54039591	54039605	+	1	NA	promoter-TSS (NM_001163640)	promoter-TSS (NM_001163640)	-334	NM_001163640	69993	Mm.321147	NM_023543	ENSMUSG00000004633	Chn2	1700026N20Rik|4930557O16Rik|ARHGAP3|Bch	chimerin 2	protein-coding
mm_172983.1	chr9	97275787	97275789	+	1	NA	Intergenic	RLTR44A|LTR|ERVK	94170	NM_030219	78911	Mm.108347	NM_030219	ENSMUSG00000032451	Trim42	4930486B16Rik	tripartite motif-containing 42	protein-coding
mm_121159.1	chr14	102982928	102982931	+	1	NA	promoter-TSS (NR_039592)	promoter-TSS (NR_039592)	-292	NM_177715	239217	Mm.246466	NM_177715	ENSMUSG00000098557	Kctd12	AU046135|AW538430|Pfet1|Pfetin	potassium channel tetramerisation domain containing 12	protein-coding
mm_158239.1	chrX	106603539	106603551	-	1	NA	5' UTR (NM_001281859, exon 1 of 4)	5' UTR (NM_001281859, exon 1 of 4)	134	NM_001281862	58861	Mm.287166	NM_021476	ENSMUSG00000052821	Cysltr1	BB147369|CysLT1R|Cyslt1	cysteinyl leukotriene receptor 1	protein-coding
mm_86099.1	chr9	115310058	115310065	-	1	NA	5' UTR (NM_024222, exon 1 of 16)	5' UTR (NM_024222, exon 1 of 16)	360	NM_024222	68292	Mm.296158	NM_024222	ENSMUSG00000032437	Stt3b	1300006C19Rik|Simp	STT3, subunit of the oligosaccharyltransferase complex, homolog B (S. cerevisiae)	protein-coding
mm_43459.1	chr5	136247474	136247505	+	1	NA	TTS (NM_198602)	TTS (NM_198602)	-2549	NM_018825	23921	Mm.425294	NM_018825	ENSMUSG00000005057	Sh2b2	Aps	SH2B adaptor protein 2	protein-coding
mm_143447.1	chr17	70892865	70892881	-	1	NA	Intergenic	Intergenic	-39341	NM_001164074	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_144975.1	chr18	37955127	37955135	+	1	NA	promoter-TSS (NM_010411)	promoter-TSS (NM_010411)	-143	NM_010411	15183	Mm.20521	NM_010411	ENSMUSG00000024454	Hdac3	AW537363	histone deacetylase 3	protein-coding
mm_94814.1	chr11	23152100	23152106	+	1	NA	promoter-TSS (NR_131065)	promoter-TSS (NR_131065)	-37	NR_131065	76993	Mm.59224	NR_131065	ENSMUSG00000086366	1700061J23Rik	-	RIKEN cDNA 1700061J23 gene	ncRNA
mm_156436.1	chrX	141981579	141981597	+	1	NA	Intergenic	Intergenic	215348	NM_001007576	245650	Mm.208511	NM_001007576	ENSMUSG00000042282	Gucy2f	A930002I06|GC-F|GC2	guanylate cyclase 2f	protein-coding
mm_165537.1	chr2	180510284	180510284	+	1	NA	intron (NM_018766, intron 1 of 3)	intron (NM_018766, intron 1 of 3)	10308	NM_018766	18216	Mm.301712	NM_018766	ENSMUSG00000027568	Ntsr1	NT-1R|NTR-1|NTR1	neurotensin receptor 1	protein-coding
mm_17631.1	chr2	31051182	31051198	-	1	NA	intron (NM_001177648, intron 10 of 16)	intron (NM_001177648, intron 10 of 16)	45310	NM_001177650	14269	Mm.52297	NM_019406	ENSMUSG00000075415	Fnbp1	1110057E06Rik|2210010H06Rik|FBP1|Fbp17	formin binding protein 1	protein-coding
mm_112864.1	chr13	20847713	20847726	+	1	NA	intron (NM_012054, intron 3 of 20)	L1M2|LINE|L1	53606	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_134336.1	chr16	16527272	16527298	-	1	NA	5' UTR (NM_001301818, exon 1 of 17)	5' UTR (NM_001301818, exon 1 of 17)	126	NM_001301818	224014	Mm.256131	NM_139232	ENSMUSG00000022788	Fgd4	9030023J02Rik|9330209B17Rik|Frabp|ZFYVE6	FYVE, RhoGEF and PH domain containing 4	protein-coding
mm_123919.1	chr14	73364569	73364578	-	1	NA	exon (NM_008410, exon 5 of 6)	exon (NM_008410, exon 5 of 6)	20698	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_19438.1	chr2	91963747	91963760	-	1	NA	promoter-TSS (NM_138306)	promoter-TSS (NM_138306)	-190	NM_138306	104418	Mm.314923	NM_138306	ENSMUSG00000040479	Dgkz	E130307B02Rik|ENSMUSG00000075035|F730209L11Rik|mDGK[z]	diacylglycerol kinase zeta	protein-coding
mm_94072.1	chr10	128401859	128401880	-	1	NA	promoter-TSS (NM_001136237)	promoter-TSS (NM_001136237)	-645	NM_001136237	72002	Mm.22983	NM_028051	ENSMUSG00000039878	Slc39a5	1810013D05Rik|2010205A06Rik|Zip5	solute carrier family 39 (metal ion transporter), member 5	protein-coding
mm_56421.1	chr6	97252780	97252790	-	1	NA	promoter-TSS (NM_001081157)	promoter-TSS (NM_001081157)	-5	NM_001081157	320502	Mm.68163	NM_001081157	ENSMUSG00000044086	Lmod3	5430424A14Rik	leiomodin 3 (fetal)	protein-coding
mm_72998.1	chr8	93810553	93810563	+	1	NA	promoter-TSS (NM_010308)	promoter-TSS (NM_010308)	-280	NM_010308	14681	Mm.251445	NM_010308	ENSMUSG00000031748	Gnao1	AW050213|Galphao|Gnao|alphaO	guanine nucleotide binding protein, alpha O	protein-coding
mm_92231.1	chr10	69125038	69125045	-	1	NA	Intergenic	Intergenic	-83511	NM_001252636	69288	Mm.26659	NM_001081347	ENSMUSG00000019944	Rhobtb1	1700008H16Rik|3110048G13Rik|AI173445|AI573858|AV350930	Rho-related BTB domain containing 1	protein-coding
mm_6302.1	chr1	71414819	71414829	-	1	NA	promoter-TSS (NM_175210)	promoter-TSS (NM_175210)	86	NM_175210	74591	Mm.159251	NM_175210	ENSMUSG00000050296	Abca12	4832428G11Rik|4833417A11Rik	ATP-binding cassette, sub-family A (ABC1), member 12	protein-coding
mm_95528.1	chr11	52232238	52232256	+	1	NA	intron (NM_011543, intron 1 of 5)	CpG	252	NM_011543	21402	Mm.42944	NM_011543	ENSMUSG00000036309	Skp1a	15kDa|2610043E24Rik|2610206H23Rik|EMC19|OCP-II|OCP2|SKP1|Tceb1l|p19A|p19Skp1	S-phase kinase-associated protein 1A	protein-coding
mm_76428.1	chr8	84978123	84978143	-	1	NA	exon (NM_008416, exon 1 of 1)	exon (NM_008416, exon 1 of 1)	615	NM_008416	16477	Mm.1167	NM_008416	ENSMUSG00000052837	Junb	-	jun B proto-oncogene	protein-coding
mm_22392.1	chr2	181213123	181213133	-	1	NA	promoter-TSS (NM_011481)	promoter-TSS (NM_011481)	43	NM_011481	20811	Mm.4752	NM_011481	ENSMUSG00000027579	Srms	A230069J08Rik|srm	src-related kinase lacking C-terminal regulatory tyrosine and N-terminal myristylation sites	protein-coding
mm_56600.1	chr6	108731366	108731404	-	1	NA	Intergenic	L2c|LINE|L2	-51674	NM_026011	67166	Mm.271178	NM_026011	ENSMUSG00000030105	Arl8b	2610313E07Rik|3100002J04Rik|Arl10c|gie1	ADP-ribosylation factor-like 8B	protein-coding
mm_150783.1	chr19	44295088	44295127	+	1	NA	exon (NM_009128, exon 2 of 6)	exon (NM_009128, exon 2 of 6)	1431	NM_009128	20250	Mm.487021	NM_009128	ENSMUSG00000025203	Scd2	Mir5114|Scd-2|mir-5114|swty	stearoyl-Coenzyme A desaturase 2	protein-coding
mm_21406.1	chr2	158091742	158091756	-	1	NA	promoter-TSS (NR_040609)	promoter-TSS (NR_040609)	48	NR_040609	72340	Mm.443395	NR_040609	ENSMUSG00000100860	2010009K17Rik	-	RIKEN cDNA 2010009K17 gene	ncRNA
mm_75326.1	chr8	43141510	43141530	-	1	NA	promoter-TSS (NM_177742)	promoter-TSS (NM_177742)	-34	NM_177742	244448	Mm.64542	NM_177742	ENSMUSG00000031651	Triml1	4933403D14|BC050188	tripartite motif family-like 1	protein-coding
mm_109724.1	chr12	116281245	116281261	+	1	NA	promoter-TSS (NM_028731)	promoter-TSS (NM_028731)	31	NM_028731	52635	Mm.273755	NM_028731	ENSMUSG00000021171	Esyt2	2410017M09Rik|4921504I16Rik|CHR2SYT|D12Ertd551e|Fam62b	extended synaptotagmin-like protein 2	protein-coding
mm_127677.1	chr15	102921138	102921142	+	1	NA	promoter-TSS (NM_010464)	promoter-TSS (NM_010464)	9	NM_010464	15422	Mm.207062	NM_010464	ENSMUSG00000001655	Hoxc13	-	homeobox C13	protein-coding
mm_151449.1	chr19	57658962	57658969	+	1	NA	intron (NM_181415, intron 9 of 28)	intron (NM_181415, intron 9 of 28)	47931	NM_181415	226255	Mm.245340	NM_181415	ENSMUSG00000054843	Atrnl1	AI504415|AW555641|Alp|Atrnl|Atrnlp	attractin like 1	protein-coding
mm_50250.1	chr6	42397326	42397335	+	1	NA	Intergenic	Intergenic	-2908	NM_001001452	387514	Mm.377921	NM_001001452	ENSMUSG00000046652	Tas2r143	Gm1404|Tas2r43|mt2r36	taste receptor, type 2, member 143	protein-coding
mm_47563.1	chr5	124425950	124426001	-	1	NA	promoter-TSS (NM_001081203)	promoter-TSS (NM_001081203)	-61	NM_001081203	243272	Mm.23879	NM_001081203	ENSMUSG00000038095	Sbno1	9330180L10Rik|AI849128|AW557836|BC021875|Sbno|mSno1|sno	strawberry notch homolog 1 (Drosophila)	protein-coding
mm_89257.1	chr10	87859311	87859334	+	1	NA	5' UTR (NM_010512, exon 1 of 5)	5' UTR (NM_010512, exon 1 of 5)	270	NM_010512	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_111856.1	chr12	107939271	107939311	-	1	NA	intron (NM_001286343, intron 1 of 1)	intron (NM_001286343, intron 1 of 1)	64123	NM_001079883	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_67187.1	chr7	73940319	73940331	-	1	NA	3' UTR (NM_009181, exon 6 of 6)	3' UTR (NM_009181, exon 6 of 6)	73357	NM_009181	20450	Mm.4954	NM_009181	ENSMUSG00000025789	St8sia2	AI323367|ST8SiaII|STX|Siat8b	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 2	protein-coding
mm_20547.1	chr2	131068877	131068890	-	1	NA	TTS (NM_011426)	TTS (NM_011426)	-5069	NM_001163529	110751	Mm.108550	NM_033615	ENSMUSG00000027318	Adam33	Adaml	a disintegrin and metallopeptidase domain 33	protein-coding
mm_158480.1	chrX	142196945	142196949	-	1	NA	promoter-TSS (NM_001007576)	promoter-TSS (NM_001007576)	-11	NM_001007576	245650	Mm.208511	NM_001007576	ENSMUSG00000042282	Gucy2f	A930002I06|GC-F|GC2	guanylate cyclase 2f	protein-coding
mm_75553.1	chr8	57653631	57653677	-	1	NA	promoter-TSS (NM_144731)	promoter-TSS (NM_144731)	-599	NM_144731	108150	Mm.62886	NM_144731	ENSMUSG00000031608	Galnt7	AI225872	UDP-N-acetyl-alpha-D-galactosamine: polypeptide N-acetylgalactosaminyltransferase 7	protein-coding
mm_140271.1	chr17	84683191	84683193	+	1	NA	promoter-TSS (NM_031884)	promoter-TSS (NM_031884)	71	NM_026180	67470	Mm.26581	NM_026180	ENSMUSG00000024254	Abcg8	1300003C16Rik|AI114946|sterolin-2	ATP-binding cassette, sub-family G (WHITE), member 8	protein-coding
mm_17274.1	chr2	26091962	26091988	-	1	NA	5' UTR (NM_001037098, exon 1 of 6)	5' UTR (NM_001037098, exon 1 of 6)	421	NM_001037098	67991	Mm.131074	NM_026495	ENSMUSG00000026932	Nacc2	0610020I02Rik|AI448087|Btbd14a|C030048H19Rik	nucleus accumbens associated 2, BEN and BTB (POZ) domain containing	protein-coding
mm_126660.1	chr15	84257128	84257151	+	1	NA	intron (NM_133167, intron 1 of 12)	intron (NM_133167, intron 1 of 12)	25096	NM_133167	170736	Mm.323892	NM_133167	ENSMUSG00000022438	Parvb	AI595373|AW742462|D15Gsk1|affixin	parvin, beta	protein-coding
mm_94176.1	chr10	128891864	128891878	-	1	NA	promoter-TSS (NM_010272)	promoter-TSS (NM_010272)	-153	NM_010272	14561	Mm.299218	NM_010272	ENSMUSG00000025352	Gdf11	BMP-11|Bmp11	growth differentiation factor 11	protein-coding
mm_52008.1	chr6	93034960	93034964	+	1	NA	intron (NR_015530, intron 1 of 2)	intron (NR_015530, intron 1 of 2)	94380	NR_015530	330385	Mm.483472	NR_015530	ENSMUSG00000097462	9530026P05Rik	B430306B02	RIKEN cDNA 9530026P05 gene	ncRNA
mm_94795.1	chr11	22972272	22972291	+	1	NA	5' UTR (NM_011663, exon 1 of 1)	5' UTR (NM_011663, exon 1 of 1)	276	NM_011663	22183	Mm.29542	NM_011663	ENSMUSG00000044068	Zrsr1	D11Ncvs75|Irlgs2|SP2|U2af1-rs1|U2afbp-rs	zinc finger (CCCH type), RNA binding motif and serine/arginine rich 1	protein-coding
mm_126713.1	chr15	85336222	85336232	+	1	NA	promoter-TSS (NM_016843)	promoter-TSS (NM_016843)	-154	NM_016843	54138	Mm.248906	NM_016843	ENSMUSG00000016541	Atxn10	AI325283|C77170|E46|Sca10|TEG-169|Tex169	ataxin 10	protein-coding
mm_64248.1	chr7	141704343	141704355	+	1	NA	intron (NM_023566, intron 27 of 45)	intron (NM_023566, intron 27 of 45)	14009	NM_023566	17831	Mm.2041	NM_023566		Muc2	2010015E03Rik|MCM|wnn	mucin 2	protein-coding
mm_43927.1	chr5	144919084	144919089	+	1	NA	intron (NM_001038627, intron 1 of 17)	intron (NM_001038627, intron 1 of 17)	-22270	NR_106006	102465629		NR_106006	ENSMUSG00000098822	Mir7039	Gm27824|mmu-mir-7039	microRNA 7039	ncRNA
mm_122358.1	chr14	39208765	39208798	-	1	NA	intron (NM_001190187, intron 1 of 9)	B3|SINE|B2	-263648	NR_131973	432842	Mm.352566	NR_131973		LOC432842	-	uncharacterized LOC432842	ncRNA
mm_111405.1	chr12	91099711	91099715	-	1	NA	intron (NM_181815, intron 20 of 25)	intron (NM_181815, intron 20 of 25)	-10516	NR_030473	735273		NR_030473	ENSMUSG00000076118	Mir669c	Mirn669c|Mirn669c-1	microRNA 669c	ncRNA
mm_126738.1	chr15	85671520	85671533	+	1	NA	Intergenic	CpG	-32247	NR_110483	102800312	Mm.33117	NR_110483		Lncppara	Lincppara|Mirlet7bhg|linc-Ppara	long noncoding RNA near Ppara	ncRNA
mm_166521.1	chr6	24597686	24597694	+	1	NA	promoter-TSS (NM_053098)	promoter-TSS (NM_053098)	-81	NM_053098	93677	Mm.332941	NM_053098	ENSMUSG00000029683	Lmod2	C-Lmod	leiomodin 2 (cardiac)	protein-coding
mm_58638.1	chr7	6045169	6045197	+	1	NA	promoter-TSS (NM_031389)	promoter-TSS (NM_031389)	22	NM_031389	83564	Mm.247765	NM_031389	ENSMUSG00000034690	Nlrp4c	Nalp-alpha|Nalp4c|Rnh2	NLR family, pyrin domain containing 4C	protein-coding
mm_159776.1	chr5	104077609	104077609	-	1	NA	promoter-TSS (NM_001163772)	promoter-TSS (NM_001163772)	-1	NM_001163772	100271704	Mm.366664	NM_001163772	ENSMUSG00000091034	Gm17660	Scpppq1	predicted gene, 17660	protein-coding
mm_7321.1	chr1	100180208	100180245	-	1	NA	intron (NM_172851, intron 10 of 23)	L1Md_F2|LINE|L1	407461	NM_172851	241175	Mm.251301	NM_172851	ENSMUSG00000067028	Cntnap5b	C230078M14Rik|Caspr5-2	contactin associated protein-like 5B	protein-coding
mm_131065.1	chr16	4594741	4594759	+	1	NA	promoter-TSS (NM_031184)	promoter-TSS (NM_031184)	37	NM_031184	83396	Mm.134072	NM_031184	ENSMUSG00000014303	Glis2	Gli5|Klf16|Nkl	GLIS family zinc finger 2	protein-coding
mm_12505.1	chr2	71873347	71873349	+	1	NA	5' UTR (NM_172665, exon 1 of 11)	5' UTR (NM_172665, exon 1 of 11)	124	NM_172665	228026	Mm.34411	NM_172665	ENSMUSG00000006494	Pdk1	B830012B01|D530020C15Rik	pyruvate dehydrogenase kinase, isoenzyme 1	protein-coding
mm_91363.1	chr10	28986332	28986344	-	1	NA	promoter-TSS (NM_026336)	promoter-TSS (NM_026336)	-32	NM_026336	67719	Mm.440480	NM_026336	ENSMUSG00000015519	2310057J18Rik	2210414P04Rik|Leg1	RIKEN cDNA 2310057J18 gene	protein-coding
mm_55895.1	chr6	83536550	83536552	-	1	NA	promoter-TSS (NM_009610)	promoter-TSS (NM_009610)	-300	NM_009610	11468	Mm.292865	NM_009610	ENSMUSG00000059430	Actg2	ACTA3|Act-4|Act4|SMGA	actin, gamma 2, smooth muscle, enteric	protein-coding
mm_42873.1	chr5	122240765	122240826	+	1	NA	non-coding (NR_104441, exon 13 of 13)	non-coding (NR_104441, exon 13 of 13)	23665	NR_104441	654470	Mm.28804	NM_001039153	ENSMUSG00000038593	Tctn1	G730031O11Rik|Tect1	tectonic family member 1	protein-coding
mm_35838.1	chr4	48044952	48044981	-	1	NA	promoter-TSS (NM_015743)	promoter-TSS (NM_015743)	-339	NM_015743	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_50143.1	chr6	41543446	41543473	+	1	NA	Intergenic	Intergenic	21683	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_48453.1	chr5	140760265	140760286	-	1	NA	3' UTR (NM_010302, exon 4 of 4)	3' UTR (NM_010302, exon 4 of 4)	36148	NM_173405	231842	Mm.491298	NM_173405	ENSMUSG00000050022	Amz1	5330426I05|6530401C20Rik	archaelysin family metallopeptidase 1	protein-coding
mm_62650.1	chr7	107685563	107685575	+	1	NA	intron (NM_001163557, intron 4 of 25)	intron (NM_001163557, intron 4 of 25)	72463	NM_001205227	320635	Mm.132828	NM_177216	ENSMUSG00000048065	Cyb5r2	D630003K02Rik|b5R.2	cytochrome b5 reductase 2	protein-coding
mm_123882.1	chr14	72709797	72709805	-	1	NA	5' UTR (NM_207636, exon 1 of 26)	5' UTR (NM_207636, exon 1 of 26)	202	NM_207636	319448	Mm.205421	NM_207636	ENSMUSG00000033487	Fndc3a	1700094E19Rik|D14Ertd453e|F730017H24Rik|Fndc3|sys	fibronectin type III domain containing 3A	protein-coding
mm_70849.1	chr8	23446943	23446969	+	1	NA	3' UTR (NM_013834, exon 3 of 3)	3' UTR (NM_013834, exon 3 of 3)	35454	NM_013834	20377	Mm.281691	NM_013834	ENSMUSG00000031548	Sfrp1	2210415K03Rik|AW011917|AW107218|AW742929|sFRP-1	secreted frizzled-related protein 1	protein-coding
mm_21327.1	chr2	157101314	157101322	-	1	NA	intron (NM_018851, intron 15 of 15)	B3|SINE|B2	14263	NM_001177439	383766	Mm.480305	NM_001177439	ENSMUSG00000074628	Tldc2	Gm1332	TBC/LysM associated domain containing 2	protein-coding
mm_133426.1	chr16	87454993	87455057	+	1	NA	promoter-TSS (NM_024258)	promoter-TSS (NM_024258)	40	NM_024258	74112	Mm.152941	NM_024258	ENSMUSG00000025616	Usp16	1200004E02Rik|2810483I07Rik|6330514E22Rik|UBPM	ubiquitin specific peptidase 16	protein-coding
mm_87892.1	chr10	61959602	61959608	+	1	NA	intron (NM_001304757, intron 2 of 37)	intron (NM_001304757, intron 2 of 37)	19503	NM_001304757	12817	Mm.300931	NM_007731	ENSMUSG00000058806	Col13a1	-	collagen, type XIII, alpha 1	protein-coding
mm_91188.1	chr10	21125969	21125972	-	1	NA	3' UTR (NM_001198914, exon 16 of 16)	3' UTR (NM_001198914, exon 16 of 16)	35014	NM_001198914	17863	Mm.52109	NM_010848	ENSMUSG00000019982	Myb	AI550390|M16449|c-myb	myeloblastosis oncogene	protein-coding
mm_131030.1	chr16	3744090	3744145	+	1	NA	promoter-TSS (NM_148924)	promoter-TSS (NM_148924)	18	NM_148924	74120	Mm.29081	NM_148924	ENSMUSG00000022529	Zfp263	1200014J04Rik|AI326880|AU020888|NT2|mFPM315	zinc finger protein 263	protein-coding
mm_23918.1	chr3	83046690	83046716	+	1	NA	exon (NM_181849, exon 2 of 8)	exon (NM_181849, exon 2 of 8)	3160	NM_181849	110135	Mm.30063	NM_181849	ENSMUSG00000033831	Fgb	2510049G14Rik	fibrinogen beta chain	protein-coding
mm_164593.1	chr17	27354801	27354803	+	1	NA	promoter-TSS (NR_106076)	promoter-TSS (NR_106076)	-936	NR_106076	102465701		NR_106076	ENSMUSG00000106578	Mir7217	mmu-mir-7217	microRNA 7217	ncRNA
mm_147783.1	chr18	61626435	61626445	-	1	NA	Intergenic	Intergenic	-13213	NR_045420	545261	Mm.426593	NR_045420	ENSMUSG00000098098	Bvht	Braveheart|Gm20748	braveheart long non-coding RNA	ncRNA
mm_3830.1	chr1	159608764	159608766	+	1	NA	intron (NM_022312, intron 1 of 22)	intron (NM_022312, intron 1 of 22)	84996	NM_022312	21960	Mm.44701	NM_022312	ENSMUSG00000015829	Tnr	J1-tenascin|TN-R|janusin|restrictin	tenascin R	protein-coding
mm_86373.1	chr9	123807747	123807761	-	1	NA	intron (NM_030712, intron 1 of 1)	intron (NM_030712, intron 1 of 1)	1277	NM_030712	80901	Mm.124289	NM_030712	ENSMUSG00000048521	Cxcr6	BB217514|BONZO|STRL33	chemokine (C-X-C motif) receptor 6	protein-coding
mm_81398.1	chr9	109007545	109007587	+	1	NA	intron (NM_173019, intron 5 of 13)	intron (NM_173019, intron 5 of 13)	15664	NM_173019	270198	Mm.132391	NM_173019	ENSMUSG00000025648	Pfkfb4	C230090D14	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4	protein-coding
mm_43733.1	chr5	139791523	139791539	+	1	NA	promoter-TSS (NM_010757)	promoter-TSS (NM_010757)	-5	NM_010757	17135	Mm.157313	NM_010757	ENSMUSG00000018143	Mafk	AW061068|NF-E2|Nfe2u	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein K (avian)	protein-coding
mm_160763.1	chr10	93890203	93890203	-	1	NA	5' UTR (NM_019648, exon 2 of 12)	5' UTR (NM_019648, exon 2 of 12)	999	NM_019648	56307	Mm.289329	NM_019648	ENSMUSG00000036112	Metap2	4930584B20Rik|A930035J23Rik|AI047573|AL024412|AU014659|Amp2|Mnpep|p67|p67eIF2	methionine aminopeptidase 2	protein-coding
mm_44661.1	chr5	28458943	28458958	-	1	NA	intron (NM_009170, intron 2 of 2)	CpG	-8034	NR_015562	654796	Mm.57202	NR_015562	ENSMUSG00000097726	9530036O11Rik	-	RIKEN cDNA 9530036O11Rik	ncRNA
mm_86247.1	chr9	121314796	121314817	-	1	NA	Intergenic	Intergenic	-37634	NM_177589	209012	Mm.371804	NM_177589	ENSMUSG00000040936	Ulk4	4932415A06Rik|A730098P15	unc-51-like kinase 4	protein-coding
mm_53859.1	chr6	149309546	149309558	+	1	NA	5' UTR (NM_001289662, exon 1 of 5)	5' UTR (NM_001289662, exon 1 of 5)	138	NM_001289662	67246	Mm.333515	NM_026054	ENSMUSG00000032712	2810474O19Rik	6720435I21Rik|AA536804|AU020969|GET|Kiaa1551	RIKEN cDNA 2810474O19 gene	protein-coding
mm_43607.1	chr5	137928295	137928307	+	1	NA	Intergenic	Intergenic	-6682	NM_007819	13113	Mm.289886	NM_007819	ENSMUSG00000029727	Cyp3a13	IIIAm2	cytochrome P450, family 3, subfamily a, polypeptide 13	protein-coding
mm_30080.1	chr3	138091040	138091070	-	1	NA	exon (NM_001163457, exon 20 of 20)	exon (NM_001163457, exon 20 of 20)	-23667	NR_037975	329763	Mm.169710	NM_177860	ENSMUSG00000049349	Gm5105	D830013H12|EG329763	predicted gene 5105	ncRNA
mm_102704.1	chr11	66526572	66526582	-	1	NA	promoter-TSS (NM_001034874)	promoter-TSS (NM_001034874)	-451	NM_001034874	380702	Mm.351764	NM_001034874	ENSMUSG00000053930	Shisa6	Gm879|ckamp52	shisa family member 6	protein-coding
mm_169184.1	chr13	65896906	65896925	-	1	NA	Intergenic	Intergenic	-216538	NM_001177832	628709	Mm.390595	NM_001177832	ENSMUSG00000095909	Gm10324	ENSMUSG00000071302	predicted gene 10324	protein-coding
mm_38486.1	chr4	140774197	140774212	-	1	NA	promoter-TSS (NM_011061)	promoter-TSS (NM_011061)	-1	NM_011061	18602	Mm.250358	NM_011061	ENSMUSG00000025330	Padi4	Pad4|Pdi4	peptidyl arginine deiminase, type IV	protein-coding
mm_20369.1	chr2	128429074	128429091	-	1	NA	intron (NR_028591, intron 1 of 1)	intron (NR_028591, intron 1 of 1)	269	NR_028591	100043424	Mm.297222	NR_028589		Gm14005	OTTMUSG00000015351	predicted gene 14005	ncRNA
mm_145509.1	chr18	60392042	60392086	+	1	NA	3' UTR (NM_001146275, exon 3 of 3)	3' UTR (NM_001146275, exon 3 of 3)	16035	NM_001146275	60440	Mm.261140	NM_021792	ENSMUSG00000054072	Iigp1	2900074L10Rik|AI046432|AW111922|Ifgga1|Iigp|Irga6	interferon inducible GTPase 1	protein-coding
mm_99639.1	chr11	105244172	105244179	+	1	NA	intron (NM_001294329, intron 7 of 19)	intron (NM_001294329, intron 7 of 19)	-48471	NM_008626	17534	Mm.235616	NM_008626	ENSMUSG00000020695	Mrc2	Endo180|mKIAA0709|uPARAP	mannose receptor, C type 2	protein-coding
mm_105132.1	chr11	101424631	101424675	-	1	NA	promoter-TSS (NM_172566)	promoter-TSS (NM_172566)	-432	NM_172566	217201	Mm.305941	NM_172566	ENSMUSG00000035007	Rundc1	AW125546|D930024B17	RUN domain containing 1	protein-coding
mm_76705.1	chr8	94588080	94588093	-	1	NA	exon (NM_028221, exon 4 of 8)	exon (NM_028221, exon 4 of 8)	13640	NM_028221	102122	Mm.250425	NM_028221	ENSMUSG00000031774	Fam192a	1700001O11Rik|2310065K24Rik|AI596259|Nip30	family with sequence similarity 192, member A	protein-coding
mm_21688.1	chr2	164443178	164443194	-	1	NA	promoter-TSS (NM_011521)	promoter-TSS (NM_011521)	2	NM_011521	20971	Mm.3815	NM_011521	ENSMUSG00000017009	Sdc4	AA959608|AW108331|S4|Synd4|ryudocan|syndecan-4	syndecan 4	protein-coding
mm_14897.1	chr2	149830814	149830831	+	1	NA	promoter-TSS (NM_001085521)	promoter-TSS (NM_001085521)	39	NM_001085521	433485	Mm.330649	NM_001085521	ENSMUSG00000074736	Syndig1	AW123113|DSPC2|Gm14134|H2C20orf39|OTTMUSG00000015750|Tmem90b	synapse differentiation inducing 1	protein-coding
mm_94518.1	chr11	8722634	8722677	+	1	NA	Intergenic	Intergenic	-58120	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_11358.1	chr2	30925464	30925474	+	1	NA	Intergenic	Intergenic	-22172	NM_022415	64292	Mm.28768	NM_022415	ENSMUSG00000050737	Ptges	2410099E23Rik|D2Ertd369e|Pges|mPGES|mPGES-1	prostaglandin E synthase	protein-coding
mm_91499.1	chr10	37136064	37136077	-	1	NA	3' UTR (NM_008538, exon 2 of 2)	3' UTR (NM_008538, exon 2 of 2)	2856	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_138759.1	chr17	37050797	37050806	+	1	NA	intron (NM_019439, intron 5 of 22)	CpG	4835	NM_019439	54393	Mm.32191	NM_019439	ENSMUSG00000024462	Gabbr1	GABAB1|GABAbR1|bM573K1.1	gamma-aminobutyric acid (GABA) B receptor, 1	protein-coding
mm_40964.1	chr5	76995771	76995789	+	1	NA	exon (NM_025691, exon 16 of 19)	exon (NM_025691, exon 16 of 19)	-8275	NM_206935	384185	Mm.451858	NM_206935	ENSMUSG00000063820	Arl9	1700110A09Rik	ADP-ribosylation factor-like 9	protein-coding
mm_76539.1	chr8	87960647	87960661	-	1	NA	Intergenic	CpG-14330	-1059	NM_033327	94187	Mm.23452	NM_033327	ENSMUSG00000045333	Zfp423	Ebfaz|Roaz|Zfp104|Znf423|ataxia1|mKIAA0760|nur12	zinc finger protein 423	protein-coding
mm_152027.1	chr19	6067796	6067865	-	1	NA	promoter-TSS (NM_028454)	promoter-TSS (NM_028454)	20	NM_028454	73166	Mm.489613	NM_028454	ENSMUSG00000024799	Tm7sf2	3110041O18Rik|ANG1|C14SR|Dhcr14	transmembrane 7 superfamily member 2	protein-coding
mm_126276.1	chr15	79208978	79209012	+	1	NA	intron (NR_029470, intron 2 of 4)	intron (NR_029470, intron 2 of 4)	-20178	NM_008837	18693	Mm.259464	NM_008837	ENSMUSG00000068206	Pick1	Prkcabp	protein interacting with C kinase 1	protein-coding
mm_9434.1	chr1	172513934	172513980	-	1	NA	Intergenic	Intergenic	-7173	NM_027972	71870	Mm.78373	NM_027972	ENSMUSG00000026546	Cfap45	1700028D05Rik|Ccdc19|Nesg1	cilia and flagella associated protein 45	protein-coding
mm_122461.1	chr14	45477853	45477855	-	1	NA	intron (NM_146054, intron 4 of 14)	intron (NM_146054, intron 4 of 14)	52211	NM_146054	218952	Mm.210018	NM_146054	ENSMUSG00000037712	Fermt2	AA960555|Kindlin-2|Mig2|Plekhc1	fermitin family member 2	protein-coding
mm_164868.1	chr18	56546833	56546835	-	1	NA	intron (NM_138600, intron 7 of 17)	intron (NM_138600, intron 7 of 17)	8695	NR_106160	102465790		NR_106160	ENSMUSG00000099196	Mir1258	Gm27371|mmu-mir-1258	microRNA 1258	ncRNA
mm_147586.1	chr18	56505637	56505637	-	1	NA	Intergenic	Intergenic	-32502	NR_106160	102465790		NR_106160	ENSMUSG00000099196	Mir1258	Gm27371|mmu-mir-1258	microRNA 1258	ncRNA
mm_109964.1	chr12	12493120	12493128	-	1	NA	Intergenic	MLT1F|LTR|ERVL-MaLR	-100649	NR_045829	70858	Mm.410838	NR_045829		4921511I17Rik	-	RIKEN cDNA 4921511I17 gene	ncRNA
mm_22815.1	chr3	27188448	27188458	+	1	NA	intron (NM_178772, intron 1 of 4)	intron (NM_178772, intron 1 of 4)	5449	NM_178772	320024	Mm.24576	NM_178772	ENSMUSG00000027698	Nceh1	Aadacl1|B230106I24Rik|CPO-BP|Nceh	neutral cholesterol ester hydrolase 1	protein-coding
mm_117276.1	chr13	65112880	65112897	-	1	NA	promoter-TSS (NM_001083901)	promoter-TSS (NM_001083901)	94	NM_001083901	66631	Mm.239196	NM_133680	ENSMUSG00000038212	Mfsd14b	5730414C17Rik|AU045608|AW539692|Hiatl1	major facilitator superfamily domain containing 14B	protein-coding
mm_125314.1	chr15	38199019	38199068	+	1	NA	Intergenic	Intergenic	-20160	NM_008757	18285	Mm.252830	NM_008757	ENSMUSG00000061923	Odf1	-	outer dense fiber of sperm tails 1	protein-coding
mm_4130.1	chr1	170308891	170308893	+	1	NA	promoter-TSS (NM_001039593)	promoter-TSS (NM_001039593)	31	NM_001039593	76925	Mm.33631	NM_001039593	ENSMUSG00000042800	1700015E13Rik	-	RIKEN cDNA 1700015E13 gene	protein-coding
mm_102068.1	chr11	52257794	52257809	-	1	NA	exon (NM_009331, exon 6 of 10)	exon (NM_009331, exon 6 of 10)	24794	NM_009331	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_23294.1	chr3	52186584	52186602	+	1	NA	Intergenic	Intergenic	-81587	NM_001004176	433586	Mm.234972	NM_001004176	ENSMUSG00000061143	Maml3	AV234550|BC049812|Mam-2|mKIAA1816	mastermind like 3 (Drosophila)	protein-coding
mm_51746.1	chr6	87378128	87378141	+	1	NA	exon (NM_025467, exon 5 of 6)	exon (NM_025467, exon 5 of 6)	4769	NM_025467	66284	Mm.46446	NM_025467	ENSMUSG00000030049	Gkn2	1810036H07Rik|Bricd1b	gastrokine 2	protein-coding
mm_13372.1	chr2	103583594	103583602	+	1	NA	intron (NM_178890, intron 1 of 16)	intron (NM_178890, intron 1 of 16)	17288	NM_178890	99382	Mm.35850	NM_178890	ENSMUSG00000032724	Abtb2	AW539457|BPOZ-2	ankyrin repeat and BTB (POZ) domain containing 2	protein-coding
mm_154024.1	chr19	53390560	53390581	-	1	NA	promoter-TSS (NM_172429)	promoter-TSS (NM_172429)	3	NM_172429	76479	Mm.313687	NM_172429	ENSMUSG00000025024	Smndc1	2410004J23Rik|4933440I19Rik	survival motor neuron domain containing 1	protein-coding
mm_65339.1	chr7	24980105	24980127	-	1	NA	exon (NM_001290469, exon 20 of 23)	exon (NM_001290469, exon 20 of 23)	-7388	NM_010261	14470	Mm.22473	NM_010261	ENSMUSG00000003380	Rabac1	2310040I06Rik|Gbpap1|PRA1|prenylin	Rab acceptor 1 (prenylated)	protein-coding
mm_132913.1	chr16	48994198	48994239	+	1	NA	promoter-TSS (NM_001110017)	promoter-TSS (NM_001110017)	30	NM_172616	224171	Mm.24491	NM_172616	ENSMUSG00000033031	C330027C09Rik	AA408511|AU018569|Cip2a|Kiaa1524	RIKEN cDNA C330027C09 gene	protein-coding
mm_151282.1	chr19	55264467	55264506	+	1	NA	intron (NM_027976, intron 1 of 21)	intron (NM_027976, intron 1 of 21)	11117	NM_027976	433256	Mm.292056	NM_027976	ENSMUSG00000024981	Acsl5	1700030F05Rik|ACS2|ACS5|Facl5	acyl-CoA synthetase long-chain family member 5	protein-coding
mm_57643.1	chr6	128430564	128430605	-	1	NA	3' UTR (NM_010219, exon 10 of 10)	3' UTR (NM_010219, exon 10 of 10)	-5674	NM_133927	101142	Mm.31345	NM_133927	ENSMUSG00000001518	Itfg2	2700050P07Rik|AI646725	integrin alpha FG-GAP repeat containing 2	protein-coding
mm_74848.1	chr8	24595603	24595610	-	1	NA	promoter-TSS (NM_001293690)	promoter-TSS (NM_001293690)	60	NM_001293690	15930	Mm.392	NM_008324	ENSMUSG00000031551	Ido1	Ido|Indo	indoleamine 2,3-dioxygenase 1	protein-coding
mm_6215.1	chr1	66839249	66839252	-	1	NA	intron (NM_007381, intron 8 of 10)	B1_Mur3|SINE|Alu	-21655	NM_001122738	68691	Mm.240912	NM_177645	ENSMUSG00000026004	Kansl1l	1110028C15Rik|1190030G24|AI427598|C430010P07Rik|mKIAA4189	KAT8 regulatory NSL complex subunit 1-like	protein-coding
mm_146842.1	chr18	23041612	23041622	-	1	NA	promoter-TSS (NM_199024)	promoter-TSS (NM_199024)	36	NM_199024	319211	Mm.209896	NM_199024	ENSMUSG00000041923	Nol4	1700013J13Rik|4930568N03Rik|Gm1262	nucleolar protein 4	protein-coding
mm_140690.1	chr17	13741665	13741686	-	1	NA	intron (NM_022311, intron 1 of 2)	intron (NM_022311, intron 1 of 2)	-18866	NM_010806	17356	Mm.59167	NM_010806	ENSMUSG00000068036	Afdn	5033403D15Rik|AF6|Af-6|Afadin|Gm314|I-afadin|Mllt4|S-afadin	afadin, adherens junction formation factor	protein-coding
mm_7490.1	chr1	121332516	121332538	-	1	NA	promoter-TSS (NM_178082)	promoter-TSS (NM_178082)	62	NM_178082	72999	Mm.27136	NM_133748	ENSMUSG00000003721	Insig2	2900053I11Rik|C730043J18Rik|Insig-2	insulin induced gene 2	protein-coding
mm_107950.1	chr12	72434642	72434651	+	1	NA	Intergenic	MLT1A0|LTR|ERVL-MaLR	-7220	NM_001142728	78257	Mm.266280	NM_030070	ENSMUSG00000021090	Lrrc9	4921529O18Rik|4930432K16Rik	leucine rich repeat containing 9	protein-coding
mm_118653.1	chr14	21750543	21750608	+	1	NA	promoter-TSS (NM_026283)	promoter-TSS (NM_026283)	44	NM_026283	67630	Mm.102765	NM_026283	ENSMUSG00000021770	Samd8	1110053F04Rik|1700010P07Rik|SMSr	sterile alpha motif domain containing 8	protein-coding
mm_96773.1	chr11	69935866	69935883	+	1	NA	promoter-TSS (NM_016875)	promoter-TSS (NM_016875)	-25	NM_016875	53422	Mm.29286	NM_016875	ENSMUSG00000018554	Ybx2	Msy2	Y box protein 2	protein-coding
mm_169185.1	chr13	65950323	65950330	-	1	NA	Intergenic	Intergenic	-163127	NM_001177832	628709	Mm.390595	NM_001177832	ENSMUSG00000095909	Gm10324	ENSMUSG00000071302	predicted gene 10324	protein-coding
mm_69245.1	chr7	127807300	127807330	-	1	NA	exon (NM_024414, exon 10 of 10)	exon (NM_024414, exon 10 of 10)	6706	NM_001040684	101502	Mm.157103	NM_133943	ENSMUSG00000042289	Hsd3b7	AI195443|BB098564	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 7	protein-coding
mm_87526.1	chr10	53337727	53337758	+	1	NA	promoter-TSS (NM_001141927)	promoter-TSS (NM_001141927)	56	NM_001141927	18821	Mm.34145	NM_023129	ENSMUSG00000038583	Pln	Plb	phospholamban	protein-coding
mm_58767.1	chr7	15881697	15881715	+	1	NA	promoter-TSS (NR_038092)	promoter-TSS (NR_038092)	-911	NR_038092	546024	Mm.259041	NM_001033638	ENSMUSG00000074365	Crxos	AA606869|AY590891|Crxos1|Egam1	cone-rod homeobox, opposite strand	protein-coding
mm_75354.1	chr8	45024753	45024769	-	1	NA	exon (NM_001081286, exon 9 of 26)	exon (NM_001081286, exon 9 of 26)	40657	NR_033588	434310	Mm.334512	NR_033588	ENSMUSG00000066158	AY512931	-	cDNA sequence AY512931	ncRNA
mm_124260.1	chr14	102977946	102977971	-	1	NA	3' UTR (NM_177715, exon 1 of 1)	3' UTR (NM_177715, exon 1 of 1)	4674	NR_039592	100628599		NR_039592	ENSMUSG00000092901	Mir5130	mir-5130|mmu-mir-5130|mu-mir-5130	microRNA 5130	ncRNA
mm_84549.1	chr9	67573191	67573224	-	1	NA	Intergenic	Intergenic	-13504	NM_001081242	70549	Mm.33645	NM_027458	ENSMUSG00000052698	Tln2	5730421P04Rik|AI507121|AI787438|AL118320|mKIAA0320	talin 2	protein-coding
mm_41909.1	chr5	105591216	105591240	+	1	NA	intron (NM_133897, intron 3 of 3)	B4|SINE|B4	71757	NM_133897	100604	Mm.319847	NM_133897	ENSMUSG00000054720	Lrrc8c	AD158|AI326115|E430036I04Rik|fad158	leucine rich repeat containing 8 family, member C	protein-coding
mm_121505.1	chr14	121938999	121939036	+	1	NA	intron (NM_026861, intron 4 of 8)	intron (NM_026861, intron 4 of 8)	-23243	NM_182806	110168	Mm.37405	NM_182806	ENSMUSG00000050350	Gpr18	-	G protein-coupled receptor 18	protein-coding
mm_27601.1	chr3	59153490	59153501	-	1	NA	promoter-TSS (NM_001287119)	promoter-TSS (NM_001287119)	-3	NM_001287119	140795	Mm.439021	NM_133200	ENSMUSG00000036381	P2ry14	A330108O13Rik|Gpr105|P2Y14	purinergic receptor P2Y, G-protein coupled, 14	protein-coding
mm_19933.1	chr2	116065674	116065689	-	1	NA	promoter-TSS (NM_010825)	promoter-TSS (NM_010825)	-623	NM_010825	17536	Mm.247566	NM_010825	ENSMUSG00000027210	Meis2	A430109D20Rik|Mrg1|Stra10	Meis homeobox 2	protein-coding
mm_79986.1	chr9	66978319	66978342	+	1	NA	Intergenic	L1M5|LINE|L1	-2846	NM_030717	80907	Mm.157882	NM_030717	ENSMUSG00000032370	Lactb	LACT-1|Lact1|Mrpl56	lactamase, beta	protein-coding
mm_51045.1	chr6	65625157	65625203	+	1	NA	intron (NM_001001495, intron 7 of 7)	(TAGA)n|Simple_repeat|Simple_repeat	34782	NM_001001495	414084	Mm.117558	NM_001001495	ENSMUSG00000044162	Tnip3	9030611K07Rik|ABIN-3|LIND	TNFAIP3 interacting protein 3	protein-coding
mm_157266.1	chrX	19206373	19206392	-	1	NA	Intergenic	Intergenic	-59411	NR_029807	723828		NR_029807	ENSMUSG00000065471	Mir222	Mirn222|mir-222|mmu-mir-222	microRNA 222	ncRNA
mm_43465.1	chr5	136693020	136693030	+	1	NA	promoter-TSS (NM_021611)	promoter-TSS (NM_021611)	-121	NM_001303019	59310	Mm.5178	NM_021611	ENSMUSG00000005474	Myl10	1700027I08Rik|Mylc2pl|PLRLC	myosin, light chain 10, regulatory	protein-coding
mm_18238.1	chr2	52151431	52151435	-	1	NA	exon (NM_010889, exon 149 of 157)	exon (NM_010889, exon 149 of 157)	78596	NM_175238	51869	Mm.254530	NM_175238	ENSMUSG00000036202	Rif1	5730435J01Rik|6530403D07Rik|AU016181|AW549474|D2Ertd145e	replication timing regulatory factor 1	protein-coding
mm_133609.1	chr16	91506182	91506225	+	1	NA	3' UTR (NM_010508, exon 11 of 11)	3' UTR (NM_010508, exon 11 of 11)	20988	NM_010508	15975	Mm.502	NM_010508	ENSMUSG00000022967	Ifnar1	CD118|Ifar|Ifnar|Ifrc|Infar	interferon (alpha and beta) receptor 1	protein-coding
mm_73351.1	chr8	105427649	105427672	+	1	NA	promoter-TSS (NM_001170789)	promoter-TSS (NM_001170789)	20	NM_001170789	270091	Mm.212709	NM_001033371	ENSMUSG00000054320	Lrrc36	BC036564	leucine rich repeat containing 36	protein-coding
mm_66638.1	chr7	45571072	45571078	-	1	NA	promoter-TSS (NM_001243052)	promoter-TSS (NM_001243052)	-204	NM_001243052	12036	Mm.24210	NM_009737	ENSMUSG00000030826	Bcat2	Bcat-2|Eca40	branched chain aminotransferase 2, mitochondrial	protein-coding
mm_446.1	chr1	34866180	34866200	+	1	NA	exon (NM_145516, exon 6 of 8)	exon (NM_145516, exon 6 of 8)	16231	NM_145516	226971	Mm.292751	NM_145516	ENSMUSG00000026123	Plekhb2	2310009M15Rik|AU018239|Evt2|Phdc|evt-2	pleckstrin homology domain containing, family B (evectins) member 2	protein-coding
mm_171717.1	chr4	82744501	82744519	-	1	NA	Intergenic	Intergenic	115151	NM_026647	68268	Mm.32047	NM_026647	ENSMUSG00000028403	Zdhhc21	9130404H11Rik|AL024349|D130004H04Rik|dep	zinc finger, DHHC domain containing 21	protein-coding
mm_4033.1	chr1	165774273	165774285	+	1	NA	3' UTR (NM_011804, exon 4 of 4)	3' UTR (NM_011804, exon 4 of 4)	10499	NM_011804	433375	Mm.294885	NM_011804	ENSMUSG00000040713	Creg1	AA755314|Creg	cellular repressor of E1A-stimulated genes 1	protein-coding
mm_121070.1	chr14	96205694	96205696	+	1	NA	intron (NM_053105, intron 6 of 10)	MLTR31A_MM|LTR|ERVK	313339	NM_053105	93688	Mm.308735	NM_053105	ENSMUSG00000022076	Klhl1	mKIAA1490	kelch-like 1	protein-coding
mm_21243.1	chr2	156173177	156173190	-	1	NA	intron (NM_133242, intron 3 of 16)	intron (NM_133242, intron 3 of 16)	6397	NM_001291115	170791	Mm.392436	NM_133242	ENSMUSG00000027620	Rbm39	1500012C14Rik|2310040E03Rik|B330012G18Rik|C79248|R75070|Rnpc2|caper	RNA binding motif protein 39	protein-coding
mm_72362.1	chr8	80496295	80496311	+	1	NA	exon (NM_010369, exon 2 of 8)	exon (NM_010369, exon 2 of 8)	2258	NM_010369	14934	Mm.13123	NM_010369	ENSMUSG00000051839	Gypa	AI853584|CD235a|GPA	glycophorin A	protein-coding
mm_62872.1	chr7	114745675	114745683	+	1	NA	promoter-TSS (NM_173767)	promoter-TSS (NM_173767)	-87	NM_173767	233752	Mm.83037	NM_173767	ENSMUSG00000048782	Insc	3830422K02Rik|C730020D23	inscuteable homolog (Drosophila)	protein-coding
mm_43063.1	chr5	124328084	124328094	+	1	NA	promoter-TSS (NM_001134717)	promoter-TSS (NM_001134717)	0	NM_028310	72650	Mm.121658	NM_028310	ENSMUSG00000047635	2810006K23Rik	-	RIKEN cDNA 2810006K23 gene	protein-coding
mm_142887.1	chr17	51832636	51832654	-	1	NA	promoter-TSS (NM_009122)	promoter-TSS (NM_009122)	2	NM_009122	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_95511.1	chr11	52004221	52004311	+	1	NA	promoter-TSS (NM_001166657)	promoter-TSS (NM_001166657)	45	NM_001166653	213084	Mm.280557	NM_153785	ENSMUSG00000020389	Cdkl3	AI852479|B230379H01Rik	cyclin-dependent kinase-like 3	protein-coding
mm_26576.1	chr3	146894329	146894333	+	1	NA	intron (NM_001302957, intron 2 of 21)	intron (NM_001302957, intron 2 of 21)	41964	NM_001302958	70892	Mm.187793	NM_027594	ENSMUSG00000036745	Ttll7	1110049N09Rik|4921517B04Rik|C630030B20|mTTLL7	tubulin tyrosine ligase-like family, member 7	protein-coding
mm_139234.1	chr17	47732420	47732453	+	1	NA	exon (NM_025973, exon 6 of 9)	exon (NM_025973, exon 6 of 9)	-4601	NM_001161722	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_6396.1	chr1	72860296	72860309	-	1	NA	3' UTR (NM_010518, exon 4 of 4)	3' UTR (NM_010518, exon 4 of 4)	14563	NM_010518	16011	Mm.405761	NM_010518	ENSMUSG00000026185	Igfbp5	AI256729|AW208790|IGFBP-5|IGFBP-5P	insulin-like growth factor binding protein 5	protein-coding
mm_43775.1	chr5	141848021	141848023	+	1	NA	intron (NM_177879, intron 5 of 44)	intron (NM_177879, intron 5 of 44)	-553475	NM_199068	17425	Mm.24214	NM_010812	ENSMUSG00000056493	Foxk1	A630048H08Rik|AI463295|ENSMUSG00000075577|Gm10868|Mnf	forkhead box K1	protein-coding
mm_87577.1	chr10	56388979	56388996	+	1	NA	3' UTR (NM_010288, exon 2 of 2)	3' UTR (NM_010288, exon 2 of 2)	11687	NM_010288	14609	Mm.378921	NM_010288	ENSMUSG00000050953	Gja1	AU042049|AW546267|Cnx43|Cx43|Cx43alpha1|Gja-1|Npm1|connexin43	gap junction protein, alpha 1	protein-coding
mm_34498.1	chr4	148601981	148601997	+	1	NA	promoter-TSS (NM_010767)	promoter-TSS (NM_010767)	-555	NM_010767	17175	Mm.378962	NM_010767	ENSMUSG00000028979	Masp2	MASP-2|MAp19	mannan-binding lectin serine peptidase 2	protein-coding
mm_111847.1	chr12	107938794	107938801	-	1	NA	intron (NM_001286343, intron 1 of 1)	intron (NM_001286343, intron 1 of 1)	64617	NM_001079883	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_84179.1	chr9	59950069	59950122	-	1	NA	promoter-TSS (NM_013708)	promoter-TSS (NM_013708)	-16	NM_013708	23958	Mm.103641	NM_013708	ENSMUSG00000032292	Nr2e3	A930035N01Rik|PNR|RNR|rd7	nuclear receptor subfamily 2, group E, member 3	protein-coding
mm_57510.1	chr6	125481716	125481725	-	1	NA	intron (NM_007657, intron 1 of 7)	intron (NM_007657, intron 1 of 7)	13035	NM_007657	12527	Mm.210676	NM_007657	ENSMUSG00000030342	Cd9	Tspan29	CD9 antigen	protein-coding
mm_166827.1	chr7	18567550	18567561	-	1	NA	promoter-TSS (NM_001037168)	promoter-TSS (NM_001037168)	-250	NM_001037168	545925	Mm.440302	NM_001037168	ENSMUSG00000070797	Psg27	EG545925|cea15	pregnancy-specific glycoprotein 27	protein-coding
mm_36372.1	chr4	76536412	76536415	-	1	NA	intron (NM_011211, intron 10 of 39)	intron (NM_011211, intron 10 of 39)	-1258127	NM_025849	66928	Mm.24332	NM_025849	ENSMUSG00000028398	Tmem261	1700027K24Rik|3110001D03Rik	transmembrane protein 261	protein-coding
mm_95508.1	chr11	52000913	52000928	+	1	NA	promoter-TSS (NM_009458)	promoter-TSS (NM_009458)	-454	NM_009458	22210	Mm.384918	NM_009458	ENSMUSG00000020390	Ube2b	2610301N02Rik|E2-14k|HR6B|Rad6b|mHR6B	ubiquitin-conjugating enzyme E2B	protein-coding
mm_159432.1	chr3	113356520	113356520	-	1	NA	promoter-TSS (NM_001042711).4	promoter-TSS (NM_001042711).4	0	NM_001042711	109959	Mm.275426	NM_001042711	ENSMUSG00000074268	Amy2a5	1810008N23Rik|Amy-2|Amy2|mAmy2-2	amylase 2a5	protein-coding
mm_95986.1	chr11	58982163	58982189	+	1	NA	exon (NM_053168, exon 3 of 6)	exon (NM_053168, exon 3 of 6)	4083	NM_053168	94091	Mm.248049	NM_053168	ENSMUSG00000020455	Trim11	-	tripartite motif-containing 11	protein-coding
mm_60541.1	chr7	44480494	44480499	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-4021	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_157347.1	chrX	36989459	36989479	-	1	NA	5' UTR (NM_001253706, exon 1 of 11)	5' UTR (NM_001253706, exon 1 of 11)	226	NM_001177324	56526	Mm.260036	NM_019942	ENSMUSG00000050379	Sept6	2810035H17Rik|C920001C06Rik|Sep6|mKIAA0128	septin 6	protein-coding
mm_52129.1	chr6	97944246	97944294	+	1	NA	intron (NM_001113198, intron 2 of 9)	intron (NM_001113198, intron 2 of 9)	14453	NM_001178049	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_132963.1	chr16	50529064	50529071	+	1	NA	intron (NR_040379, intron 1 of 5)	CpG	565	NR_040379	619312	Mm.427671	NR_040379		G730013B05Rik	linc-Cblb|linc1610	RIKEN cDNA G730013B05 gene	ncRNA
mm_119660.1	chr14	52140988	52141008	+	1	NA	intron (NM_023879, intron 13 of 24)	intron (NM_023879, intron 13 of 24)	30095	NM_023879	77945	Mm.21662	NM_023879	ENSMUSG00000057132	Rpgrip1	0610005A07Rik|4930401L23Rik|4930505G06Rik|A930002K18Rik|AA415034|nmf247	retinitis pigmentosa GTPase regulator interacting protein 1	protein-coding
mm_94339.1	chr11	4729859	4729867	+	1	NA	intron (NM_026015, intron 3 of 5)	intron (NM_026015, intron 3 of 5)	16915	NM_138948	192650	Mm.207056	NM_138948	ENSMUSG00000009075	Cabp7	-	calcium binding protein 7	protein-coding
mm_55976.1	chr6	85869057	85869067	-	1	NA	promoter-TSS (NM_053096)	promoter-TSS (NM_053096)	75	NM_053096	93673	Mm.24251	NM_053096	ENSMUSG00000033634	Nat8f2	Cml2	N-acetyltransferase 8 (GCN5-related) family member 2	protein-coding
mm_150178.1	chr19	32619980	32619996	+	1	NA	promoter-TSS (NM_011864)	promoter-TSS (NM_011864)	-17	NM_011864	23972	Mm.203916	NM_011864	ENSMUSG00000024899	Papss2	1810018P12Rik|AI159688|AtpsU2|Atpsk2|Sk2|bm	3'-phosphoadenosine 5'-phosphosulfate synthase 2	protein-coding
mm_12686.1	chr2	75900697	75900700	+	1	NA	intron (NM_172666, intron 15 of 19)	intron (NM_172666, intron 15 of 19)	37764	NM_028235	72421	Mm.275109	NM_028235	ENSMUSG00000075273	Ttc30b	2510042P03Rik|Tcc30b	tetratricopeptide repeat domain 30B	protein-coding
mm_85861.1	chr9	110747180	110747191	-	1	NA	promoter-TSS (NM_011199)	promoter-TSS (NM_011199)	-40	NM_011199	19228	Mm.3542	NM_011199	ENSMUSG00000032492	Pth1r	PPR|Pthr|Pthr1	parathyroid hormone 1 receptor	protein-coding
mm_142710.1	chr17	47888191	47888217	-	1	NA	exon (NM_028767, exon 3 of 17)	exon (NM_028767, exon 3 of 17)	36428	NM_028767	74123	Mm.240062	NM_028767	ENSMUSG00000023991	Foxp4	1200010K03Rik|2310007G05Rik|mFKHLA	forkhead box P4	protein-coding
mm_119976.1	chr14	55560905	55560974	+	1	NA	promoter-TSS (NM_001199009)	promoter-TSS (NM_001199009)	16	NM_001199009	28199	Mm.11535	NM_133734	ENSMUSG00000022214	Dcaf11	0710008A13Rik|C76035|D14Ucla1|Dacf11|GLO14|Wdr23	DDB1 and CUL4 associated factor 11	protein-coding
mm_116254.1	chr13	34002785	34002812	-	1	NA	promoter-TSS (NM_009068)	promoter-TSS (NM_009068)	-4	NM_001243192	20719	Mm.252210	NM_009254	ENSMUSG00000060147	Serpinb6a	4930482L21Rik|D330015H01Rik|PI-6|Serpinb6|Spi3|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 6a	protein-coding
mm_142909.1	chr17	52350051	52350061	-	1	NA	Intergenic	Intergenic	-252653	NM_001031811	211468	Mm.399068	NM_001031811	ENSMUSG00000035580	Kcnh8	C130090D05Rik|ELK|ELK1|ELK3|Kv12.1	potassium voltage-gated channel, subfamily H (eag-related), member 8	protein-coding
mm_19235.1	chr2	84715025	84715103	-	1	NA	promoter-TSS (NM_144887)	promoter-TSS (NM_144887)	100	NM_144887	228136	Mm.288508	NM_144887	ENSMUSG00000034075	Zdhhc5	1110032A17Rik|AI451382|Zisp	zinc finger, DHHC domain containing 5	protein-coding
mm_155256.1	chrX	57224115	57224133	+	1	NA	TTS (NM_011616)	TTS (NM_011616)	11981	NM_011616	21947	Mm.4861	NM_011616	ENSMUSG00000031132	Cd40lg	CD154|CD40-L|Cd40l|HIGM1|IGM|IMD3|Ly-62|Ly62|T-BAM|TRAP|Tnfsf5|Tnlg8b|gp39	CD40 ligand	protein-coding
mm_87336.1	chr10	43319309	43319314	+	1	NA	intron (NM_027772, intron 2 of 7)	intron (NM_027772, intron 2 of 7)	97825	NM_001168289	71365	Mm.490430	NM_027772	ENSMUSG00000038240	Pdss2	5430420P03Rik|Gm60|Plmp|kd|mDLP1	prenyl (solanesyl) diphosphate synthase, subunit 2	protein-coding
mm_28969.1	chr3	101012112	101012128	-	1	NA	exon (NM_001167906, exon 6 of 9)	exon (NM_001167906, exon 6 of 9)	17375	NM_001167906	630146	Mm.190915	NM_001099332	ENSMUSG00000086564	Cd101	EWI-101|Gm1016|Gm734|Igsf2	CD101 antigen	protein-coding
mm_48925.1	chr6	4508572	4508592	+	1	NA	intron (NM_007743, intron 2 of 51)	intron (NM_007743, intron 2 of 51)	2964	NM_007743	12843	Mm.277792	NM_007743	ENSMUSG00000029661	Col1a2	AA960264|AI325291|Col1a-2|Cola-2|Cola2|oim	collagen, type I, alpha 2	protein-coding
mm_121589.1	chr14	7843108	7843120	-	1	NA	intron (NM_134080, intron 1 of 45)	intron (NM_134080, intron 1 of 45)	25157	NM_134080	286940	Mm.489652	NM_134080	ENSMUSG00000025278	Flnb	AL024016|Fln-b	filamin, beta	protein-coding
mm_56543.1	chr6	99726335	99726360	-	1	NA	promoter-TSS (NM_001170419)	promoter-TSS (NM_001170419)	45	NM_001037539	50501	Mm.87365	NM_015768	ENSMUSG00000030069	Prok2	Bv8|PK2|Prok1	prokineticin 2	protein-coding
mm_22538.1	chr3	8671344	8671345	+	1	NA	Intergenic	MT2B1|LTR|ERVL	-4306	NM_010423	15213	Mm.29581	NM_010423	ENSMUSG00000040289	Hey1	AI316788|AI414254|CHF2|HRT1|Herp2|Hesr1|bHLHb31|hesr-1	hairy/enhancer-of-split related with YRPW motif 1	protein-coding
mm_33987.1	chr4	137719686	137719725	+	1	NA	intron (NM_001256218, intron 15 of 24)	intron (NM_001256218, intron 15 of 24)	-4756	NR_138592	110351	Mm.180763	NM_029563	ENSMUSG00000041351	Rap1gap	1300019I11Rik|2310004O14Rik|AI427470|ARPP-90|Gap|Rap1GAP1|Rap1ga1	Rap1 GTPase-activating protein	protein-coding
mm_36133.1	chr4	59331772	59331786	-	1	NA	intron (NM_001163288, intron 13 of 16)	intron (NM_001163288, intron 13 of 16)	71728	NR_105031	101055769	Mm.421401	NR_105031		Gm12596	OTTMUSG00000007649	predicted gene 12596	ncRNA
mm_150664.1	chr19	42019391	42019411	+	1	NA	intron (NM_145500, intron 1 of 2)	intron (NM_145500, intron 1 of 2)	-16637	NM_020033	56642	Mm.143737	NM_020033	ENSMUSG00000025172	Ankrd2	Arpp|mArpp	ankyrin repeat domain 2 (stretch responsive muscle)	protein-coding
mm_123394.1	chr14	63417074	63417084	-	1	NA	5' UTR (NM_007549, exon 1 of 13)	5' UTR (NM_007549, exon 1 of 13)	108	NM_007549	12143	Mm.3962	NM_007549	ENSMUSG00000014453	Blk	-	B lymphoid kinase	protein-coding
mm_65504.1	chr7	25733093	25733112	-	1	NA	exon (NM_144922, exon 10 of 15)	exon (NM_144922, exon 10 of 15)	-14049	NM_028771	52132	Mm.278798	NM_028771	ENSMUSG00000002608	Ccdc97	1200014H14Rik|2810446P04Rik|AA545218|D7Ertd462e	coiled-coil domain containing 97	protein-coding
mm_103516.1	chr11	76778989	76779008	-	1	NA	3' UTR (NM_007754, exon 21 of 21)	3' UTR (NM_007754, exon 21 of 21)	-15443	NM_016810	53334	Mm.20931	NM_016810	ENSMUSG00000010392	Gosr1	AI414660|AI426320|BB145494|GOS-28|GOSRI|GS28	golgi SNAP receptor complex member 1	protein-coding
mm_4118.1	chr1	168430402	168430414	+	1	NA	intron (NM_008783, intron 1 of 7)	intron (NM_008783, intron 1 of 7)	1761	NM_001291508	18514	Mm.43358	NM_008783	ENSMUSG00000052534	Pbx1	2310056B04Rik|D230003C07Rik|Pbx-1	pre B cell leukemia homeobox 1	protein-coding
mm_166893.1	chr7	28157019	28157026	+	1	NA	exon (NM_001164655, exon 15 of 20)	exon (NM_001164655, exon 15 of 20)	-12726	NM_007991	14113	Mm.4595	NM_007991	ENSMUSG00000046865	Fbl	AL022665|FIB|FLRN|RNU3IP1	fibrillarin	protein-coding
mm_3073.1	chr1	134270356	134270366	+	1	NA	Intergenic	RLTR16B_MM|LTR|ERVK	-19643	NM_031189	17928	Mm.16528	NM_031189	ENSMUSG00000026459	Myog	MYF4|bHLHc3|myo	myogenin	protein-coding
mm_63659.1	chr7	129591525	129591552	+	1	NA	promoter-TSS (NM_172255)	promoter-TSS (NM_172255)	-325	NM_172255	207425	Mm.229323	NM_172255	ENSMUSG00000042055	Wdr11	2900055P10Rik|AW489876|Brwd2|mKIAA1351	WD repeat domain 11	protein-coding
mm_67313.1	chr7	79477363	79477390	-	1	NA	Intergenic	Intergenic	-11103	NM_017462	18975	Mm.3616	NM_017462	ENSMUSG00000039176	Polg	AA409516|PolgA	polymerase (DNA directed), gamma	protein-coding
mm_54276.1	chr6	29164985	29164999	-	1	NA	promoter-TSS (NM_133925)	promoter-TSS (NM_133925)	-268	NM_133925	68272	Mm.40802	NM_026650	ENSMUSG00000029701	Rbm28	2810480G15Rik|AI503051	RNA binding motif protein 28	protein-coding
mm_138399.1	chr17	35058346	35058360	+	1	NA	promoter-TSS (NM_016765)	promoter-TSS (NM_016765)	-682	NM_001190449	51793	Mm.1457	NM_016765	ENSMUSG00000007039	Ddah2	1110003M04Rik|AU019324|AW413173|DDAH-2|DDAHII|Ddah|G6a|NG30	dimethylarginine dimethylaminohydrolase 2	protein-coding
mm_138087.1	chr17	33997495	33997537	+	1	NA	exon (NM_001001892, exon 4 of 8)	exon (NM_001001892, exon 4 of 8)	2817	NM_001001892	14972	Mm.422886	NM_001001892	ENSMUSG00000061232	H2-K1	H-2K|H-2K(d)|H2-K|K-f	histocompatibility 2, K1, K region	protein-coding
mm_101626.1	chr11	35980592	35980608	-	1	NA	promoter-TSS (NM_170779)	promoter-TSS (NM_170779)	-511	NM_170779	211652	Mm.31267	NM_170779	ENSMUSG00000018849	Wwc1	AA408228|AU017197|BC037006|Kibra|mKIAA0869	WW, C2 and coiled-coil domain containing 1	protein-coding
mm_27595.1	chr3	59131084	59131094	-	1	NA	promoter-TSS (NM_001287124)	promoter-TSS (NM_001287124)	29	NM_001287122	140795	Mm.439021	NM_133200	ENSMUSG00000036381	P2ry14	A330108O13Rik|Gpr105|P2Y14	purinergic receptor P2Y, G-protein coupled, 14	protein-coding
mm_81204.1	chr9	107569139	107569155	+	1	NA	promoter-TSS (NM_010489)	promoter-TSS (NM_010489)	-16	NM_010489	15587	Mm.4834	NM_010489	ENSMUSG00000010047	Hyal2	AI256841|AU020858|AW555733	hyaluronoglucosaminidase 2	protein-coding
mm_28652.1	chr3	95228881	95228908	-	1	NA	promoter-TSS (NM_019914)	promoter-TSS (NM_019914)	-49	NM_001038708	57912	Mm.28189	NM_172395	ENSMUSG00000046722	Cdc42se1	1300002M12Rik|AW558204|Cdcse1|SCIP1|Spec1	CDC42 small effector 1	protein-coding
mm_163159.1	chr11	83885776	83885811	+	1	NA	intron (NM_001291269, intron 5 of 8)	(CA)n|Simple_repeat|Simple_repeat	32833	NM_001291269	21410	Mm.7226	NM_009330	ENSMUSG00000020679	Hnf1b	HNF-1-beta|HNF-1B|HNF-1Beta|Hnf1beta|LFB3|Tcf-2|Tcf2|vHNF1	HNF1 homeobox B	protein-coding
mm_277.1	chr1	21249742	21249751	+	1	NA	intron (NM_001077353, intron 2 of 7)	intron (NM_001077353, intron 2 of 7)	9161	NM_010356	14859	Mm.394593	NM_010356	ENSMUSG00000025934	Gsta3	Gst2-3	glutathione S-transferase, alpha 3	protein-coding
mm_113081.1	chr13	23839402	23839442	+	1	NA	promoter-TSS (NM_001164743)	promoter-TSS (NM_001164743)	-12	NM_001164743	105355	Mm.27038	NM_134069	ENSMUSG00000036083	Slc17a3	AW261723|Npt4	solute carrier family 17 (sodium phosphate), member 3	protein-coding
mm_126109.1	chr15	78250889	78250902	+	1	NA	exon (NM_008677, exon 3 of 10)	exon (NM_008677, exon 3 of 10)	6084	NM_008677	17972	Mm.2068	NM_008677	ENSMUSG00000071715	Ncf4	AI451400|p40phox	neutrophil cytosolic factor 4	protein-coding
mm_130337.1	chr15	97731215	97731226	-	1	NA	exon (NM_001168693, exon 1 of 10)	exon (NM_001168693, exon 1 of 10)	185	NM_001168693	19011	Mm.1001	NM_008902	ENSMUSG00000022468	Endou	Pp11r|Tcl-30	endonuclease, polyU-specific	protein-coding
mm_109947.1	chr12	11326498	11326509	-	1	NA	exon (NM_012038, exon 4 of 4)	exon (NM_012038, exon 4 of 4)	26616	NR_106136	102465775		NR_106136	ENSMUSG00000098879	Mir7675	Gm27965|mmu-mir-7675	microRNA 7675	ncRNA
mm_67771.1	chr7	96947034	96947042	-	1	NA	Intergenic	RMER17B|LTR|ERVK	-4489	NM_153591	244141	Mm.274864	NM_153591	ENSMUSG00000018995	Nars2	AI875199	asparaginyl-tRNA synthetase 2 (mitochondrial)(putative)	protein-coding
mm_103322.1	chr11	73324617	73324641	-	1	NA	promoter-TSS (NM_023113)	promoter-TSS (NM_023113)	8	NM_023113	11484	Mm.293574	NM_023113	ENSMUSG00000020774	Aspa	Acy-2|Acy2|nur7	aspartoacylase	protein-coding
mm_133752.1	chr16	94420302	94420320	+	1	NA	exon (NM_009441, exon 20 of 46)	exon (NM_009441, exon 20 of 46)	-49296	NM_001159617	56176	Mm.474449	NM_019543	ENSMUSG00000022940	Pigp	Dcrc|Dscr5	phosphatidylinositol glycan anchor biosynthesis, class P	protein-coding
mm_25168.1	chr3	103074010	103074033	+	1	NA	promoter-TSS (NM_001033303)	promoter-TSS (NM_001033303)	7	NM_001033303	229665	Mm.331272	NM_001033303	ENSMUSG00000070385	Ampd1	AI553520|Ampd-1	adenosine monophosphate deaminase 1	protein-coding
mm_103355.1	chr11	74832220	74832235	-	1	NA	intron (NM_010813, intron 1 of 5)	CpG-2219	1303	NM_010813	17428	Mm.3759	NM_010813	ENSMUSG00000000282	Mnt	Rox|bHLHd3	max binding protein	protein-coding
mm_113494.1	chr13	37415493	37415521	+	1	NA	exon (NM_010745, exon 4 of 5)	exon (NM_010745, exon 4 of 5)	70162	NM_010745	17084	Mm.2639	NM_010745	ENSMUSG00000021423	Ly86	MD-1|MD1|ly86_tv2	lymphocyte antigen 86	protein-coding
mm_155531.1	chrX	74299957	74299960	+	1	NA	intron (NM_018794, intron 2 of 9)	intron (NM_018794, intron 2 of 9)	2861	NM_018794	54411	Mm.21961	NM_018794	ENSMUSG00000019087	Atp6ap1	16A|AC45|AI316502|AW108110|Atp6ip1|Atp6s1|C7-1|CF2|VATPS1|XAP-3|mFLJ00383	ATPase, H+ transporting, lysosomal accessory protein 1	protein-coding
mm_131841.1	chr16	22961130	22961144	+	1	NA	exon (NM_053176, exon 7 of 7)	exon (NM_053176, exon 7 of 7)	10065	NM_053176	94175	Mm.358794	NM_053176	ENSMUSG00000022877	Hrg	AI265597|AW413091|D16jh2|D18020|Hprg|Hrgp	histidine-rich glycoprotein	protein-coding
mm_34512.1	chr4	148889396	148889444	+	1	NA	intron (NM_027195, intron 2 of 15)	intron (NM_027195, intron 2 of 15)	85028	NM_027195	69743	Mm.233879	NM_027195	ENSMUSG00000028977	Casz1	2410019P08Rik|AV096627|BC040081|Cst|D4Ertd432e	castor zinc finger 1	protein-coding
mm_168181.1	chr10	58464462	58464468	+	1	NA	exon (NM_011240, exon 12 of 29)	exon (NM_011240, exon 12 of 29)	17613	NM_011240	19386	Mm.431695	NM_011240	ENSMUSG00000003226	Ranbp2	A430087B05Rik|AI256741|NUP358	RAN binding protein 2	protein-coding
mm_162432.1	chr1	96507108	96507111	+	1	NA	Intergenic	Lx8b|LINE|L1	155464	NR_040478	75159	Mm.243854	NR_040478	ENSMUSG00000100589	4930533P14Rik	-	RIKEN cDNA 4930533P14 gene	ncRNA
mm_60270.1	chr7	43842232	43842263	+	1	NA	promoter-TSS (NM_026806)	promoter-TSS (NM_026806)	-22	NM_026806	68668	Mm.458122	NM_026806	ENSMUSG00000074155	Klk5	1110030O19Rik	kallikrein related-peptidase 5	protein-coding
mm_165336.1	chr2	116925470	116925471	+	1	NA	Intergenic	RSINE1|SINE|B4	25318	NR_040335	320975	Mm.132509	NR_040335	ENSMUSG00000085316	D330050G23Rik	-	RIKEN cDNA D330050G23 gene	ncRNA
mm_150111.1	chr19	29605752	29605766	+	1	NA	3' UTR (NM_001081319, exon 26 of 26)	3' UTR (NM_001081319, exon 26 of 26)	42661	NM_001081213	226090	Mm.267131	NM_146098	ENSMUSG00000046324	Ermp1	D19Ertd410e|D19Wsu12e|Fxna|mKIAA1815	endoplasmic reticulum metallopeptidase 1	protein-coding
mm_88754.1	chr10	80308280	80308283	+	1	NA	exon (NM_011789, exon 12 of 14)	exon (NM_011789, exon 12 of 14)	6461	NM_011789	23805	Mm.57247	NM_011789	ENSMUSG00000020135	Apc2	AI852447|APCL|R75424	adenomatosis polyposis coli 2	protein-coding
mm_30335.1	chr3	151732296	151732300	-	1	NA	3' UTR (NM_133871, exon 8 of 8)	3' UTR (NM_133871, exon 8 of 8)	17661	NM_133871	99899	Mm.30756	NM_133871	ENSMUSG00000028037	Ifi44	A430056A10Rik|AW261460|MTAP44|p44	interferon-induced protein 44	protein-coding
mm_158144.1	chrX	103460404	103460429	-	1	NA	TTS (NR_001570)	TTS (NR_001570)	22817	NR_001570	213742	Mm.274770	NR_001463	ENSMUSG00000086503	Xist	A430022B11|AI314753	inactive X specific transcripts	ncRNA
mm_8560.1	chr1	155276377	155276381	-	1	NA	3' UTR (NM_011273, exon 15 of 15)	3' UTR (NM_011273, exon 15 of 15)	117676	NM_021433	58244	Mm.66264	NM_021433	ENSMUSG00000026470	Stx6	2310039E05Rik|2410005I16Rik|AA437559|AI415714|AI845861	syntaxin 6	protein-coding
mm_64630.1	chr7	3693140	3693194	-	1	NA	promoter-TSS (NM_001164205)	promoter-TSS (NM_001164205)	358	NM_029934	77582	Mm.397541	NM_029934	ENSMUSG00000035596	Mboat7	5730589L02Rik|BB1|Leng4|Lpiat|Lpiat1|mBB1	membrane bound O-acyltransferase domain containing 7	protein-coding
mm_4477.1	chr1	173420629	173420639	+	1	NA	promoter-TSS (NM_001013779)	promoter-TSS (NM_001013779)	30	NM_001013779	383619	Mm.131453	NM_001013779	ENSMUSG00000037860	Aim2	Gm1313|Ifi210	absent in melanoma 2	protein-coding
mm_157634.1	chrX	57176871	57176878	-	1	NA	Intergenic	Intergenic	-23763	NR_038463	100502842	Mm.164733	NR_038463	ENSMUSG00000085808	Gm14718	OTTMUSG00000017790	predicted gene 14718	ncRNA
mm_133732.1	chr16	93832222	93832308	+	1	NA	5' UTR (NM_001045529, exon 1 of 17)	5' UTR (NM_001045529, exon 1 of 17)	144	NM_001045529	338467	Mm.287329	NM_001045529	ENSMUSG00000039456	Morc3	1110051N18Rik|AI452146|BF318192|D16Jhu32e|NXP2|Zcwcc3	microrchidia 3	protein-coding
mm_70293.1	chr8	3665959	3665968	+	1	NA	intron (NM_026985, intron 1 of 6)	intron (NM_026985, intron 1 of 6)	201	NM_026985	69189	Mm.175176	NM_026985	ENSMUSG00000013974	Mcemp1	1810033B17Rik	mast cell expressed membrane protein 1	protein-coding
mm_150907.1	chr19	45998132	45998142	+	1	NA	intron (NM_198296, intron 1 of 25)	CpG	351	NM_198296	71617	Mm.210949	NM_198296	ENSMUSG00000039901	9130011E15Rik	AI431055|AW050122	RIKEN cDNA 9130011E15 gene	protein-coding
mm_94031.1	chr10	127885232	127885234	-	1	NA	intron (NM_017473, intron 3 of 3)	B1_Mus1|SINE|Alu	3466	NM_017473	54150	Mm.6696	NM_017473	ENSMUSG00000040134	Rdh7	AI194929|CRAD2	retinol dehydrogenase 7	protein-coding
mm_90743.1	chr10	5368451	5368462	-	1	NA	intron (NM_001347732, intron 13 of 145)	intron (NM_001347732, intron 13 of 145)	119858	NM_001347711	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_171008.1	chr2	82412338	82412344	+	1	NA	Intergenic	IAPLTR2b|LTR|ERVK	358683	NM_175513	241514	Mm.119383	NM_175513	ENSMUSG00000070866	Zfp804a	C630007C17Rik|Znf804a	zinc finger protein 804A	protein-coding
mm_133735.1	chr16	93883896	93883954	+	1	NA	promoter-TSS (NM_028083)	promoter-TSS (NM_028083)	24	NM_028083	110749	Mm.274222	NM_028083	ENSMUSG00000022945	Chaf1b	2600017H24Rik|C76145|CAF-I p60|CAF-Ip60|CAF1|CAF1A|CAF1P60|MPHOSPH7	chromatin assembly factor 1, subunit B (p60)	protein-coding
mm_10205.1	chr2	4994470	4994474	+	1	NA	intron (NM_001305259, intron 16 of 19)	intron (NM_001305259, intron 16 of 19)	17872	NM_001305259	70024	Mm.23828	NM_027290	ENSMUSG00000026669	Mcm10	2410041F14Rik|AU018508|C330019M07Rik|C79164	minichromosome maintenance 10 replication initiation factor	protein-coding
mm_21599.1	chr2	164237867	164237877	-	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	469	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_158138.1	chrX	103186683	103186691	-	1	NA	promoter-TSS (NM_008671)	promoter-TSS (NM_008671)	-23	NM_008671	17954	Mm.388694	NM_008671	ENSMUSG00000082229	Nap1l2	Bpx	nucleosome assembly protein 1-like 2	protein-coding
mm_30347.1	chr3	151745540	151745574	-	1	NA	exon (NM_133871, exon 5 of 8)	exon (NM_133871, exon 5 of 8)	4402	NM_133871	99899	Mm.30756	NM_133871	ENSMUSG00000028037	Ifi44	A430056A10Rik|AW261460|MTAP44|p44	interferon-induced protein 44	protein-coding
mm_52895.1	chr6	122628381	122628396	+	1	NA	intron (NM_139218, intron 1 of 3)	intron (NM_139218, intron 1 of 3)	1964	NM_139218	73708	Mm.27982	NM_139218	ENSMUSG00000046323	Dppa3	2410075G02Rik|PCG7|PGC7|Stella	developmental pluripotency-associated 3	protein-coding
mm_44658.1	chr5	28413814	28413821	-	1	NA	3' UTR (NM_028234, exon 19 of 19)	3' UTR (NM_028234, exon 19 of 19)	-53167	NR_015562	654796	Mm.57202	NR_015562	ENSMUSG00000097726	9530036O11Rik	-	RIKEN cDNA 9530036O11Rik	ncRNA
mm_28358.1	chr3	89764582	89764646	-	1	NA	promoter-TSS (NM_009602)	promoter-TSS (NM_009602)	18	NM_009602	11444	Mm.35088	NM_009602	ENSMUSG00000027950	Chrnb2	Acrb-2|Acrb2|C030030P04Rik|[b]2-nAchR	cholinergic receptor, nicotinic, beta polypeptide 2 (neuronal)	protein-coding
mm_22666.1	chr3	14872152	14872154	+	1	NA	3' UTR (NM_007606, exon 7 of 7)	3' UTR (NM_007606, exon 7 of 7)	8615	NM_007606	12350	Mm.300	NM_007606	ENSMUSG00000027559	Car3	BB219044|Ca3|Car-3	carbonic anhydrase 3	protein-coding
mm_29701.1	chr3	123117258	123117266	-	1	NA	exon (NM_080451, exon 3 of 5)	exon (NM_080451, exon 3 of 5)	-82275	NM_021503	59006	Mm.141157	NM_021503	ENSMUSG00000028116	Myoz2	1110012I24Rik|Fatz-2|Myozl2	myozenin 2	protein-coding
mm_45928.1	chr5	89445347	89445366	-	1	NA	exon (NM_008096, exon 3 of 13)	exon (NM_008096, exon 3 of 13)	12542	NM_008096	14473	Mm.196595	NM_008096	ENSMUSG00000035540	Gc	DBP|VDB	group specific component	protein-coding
mm_95329.1	chr11	46750507	46750543	+	1	NA	promoter-TSS (NM_001166631)	promoter-TSS (NM_001166631)	14	NM_001166631	171283	Mm.17771	NM_134248	ENSMUSG00000040405	Havcr1	AI503787|KIM-1|TIM-1|Tim1|Timd1	hepatitis A virus cellular receptor 1	protein-coding
mm_22406.1	chr2	181288017	181288041	-	1	NA	promoter-TSS (NM_198169)	promoter-TSS (NM_198169)	-63	NM_198169	229004	Mm.220423	NM_198169	ENSMUSG00000038705	Gmeb2	AI839884	glucocorticoid modulatory element binding protein 2	protein-coding
mm_45414.1	chr5	66416860	66416865	-	1	NA	intron (NM_001201414, intron 5 of 15)	intron (NM_001201414, intron 5 of 15)	-79197	NM_001201416	11787	Mm.5159	NM_009686	ENSMUSG00000029207	Apbb2	2310007D03Rik|FE65L1|Rirl1|TR2L|Zfra	amyloid beta (A4) precursor protein-binding, family B, member 2	protein-coding
mm_16330.1	chr2	174327748	174327763	+	1	NA	promoter-TSS (NR_003258)	promoter-TSS (NR_003258)	-13	NM_001310083	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_32390.1	chr4	106615872	106615904	+	1	NA	intron (NM_183182, intron 2 of 9)	intron (NM_183182, intron 2 of 9)	1350	NM_183182	242602	Mm.235591	NM_183182	ENSMUSG00000054362	Lexm	-	lymphocyte expansion molecule	protein-coding
mm_19439.1	chr2	91965507	91965525	-	1	NA	Intergenic	CpG	-1953	NM_138306	104418	Mm.314923	NM_138306	ENSMUSG00000040479	Dgkz	E130307B02Rik|ENSMUSG00000075035|F730209L11Rik|mDGK[z]	diacylglycerol kinase zeta	protein-coding
mm_130637.1	chr15	100491853	100491853	-	1	NA	intron (NM_153407, intron 1 of 4)	intron (NM_153407, intron 1 of 4)	3386	NM_153407	207785	Mm.294969	NM_153407	ENSMUSG00000044636	Csrnp2	CSRNP-2|Csnrp2|taip-12	cysteine-serine-rich nuclear protein 2	protein-coding
mm_154948.1	chrX	36346205	36346210	+	1	NA	intron (NM_028894, intron 5 of 10)	intron (NM_028894, intron 5 of 10)	17798	NM_028894	74365	Mm.327654	NM_028894	ENSMUSG00000016239	Lonrf3	4932412G04Rik|5730439E01Rik|A830039N02Rik|AU023707|Rnf127	LON peptidase N-terminal domain and ring finger 3	protein-coding
mm_149889.1	chr19	25406662	25406692	+	1	NA	intron (NM_181404, intron 4 of 13)	intron (NM_181404, intron 4 of 13)	-99029	NM_015826	50796	Mm.391208	NM_015826	ENSMUSG00000024837	Dmrt1	-	doublesex and mab-3 related transcription factor 1	protein-coding
mm_71401.1	chr8	46310740	46310743	+	1	NA	Intergenic	Intergenic	-16070	NM_173789	234219	Mm.145631	NM_173789	ENSMUSG00000047171	Helt	A830086M02|Hesl|Heslike|Mgn|megane	helt bHLH transcription factor	protein-coding
mm_8694.1	chr1	157332396	157332400	-	1	NA	intron (NM_177644, intron 1 of 17)	B1_Mur4|SINE|Alu	-79954	NR_027984	69953	Mm.286863	NM_027274	ENSMUSG00000049881	2810025M15Rik	AI429618	RIKEN cDNA 2810025M15 gene	ncRNA
mm_59910.1	chr7	30414341	30414371	+	1	NA	exon (NM_011662, exon 2 of 5)	exon (NM_011662, exon 2 of 5)	568	NM_011662	22177	Mm.46301	NM_011662	ENSMUSG00000030579	Tyrobp	DAP12|KARAP|Ly83	TYRO protein tyrosine kinase binding protein	protein-coding
mm_38614.1	chr4	141933054	141933065	-	1	NA	intron (NM_177868, intron 15 of 31)	intron (NM_177868, intron 15 of 31)	-49933	NR_040672	545691	Mm.332015	NR_040672	ENSMUSG00000085424	Fhad1os1	Gm13037|OTTMUSG00000010113	forkhead-associated (FHA) phosphopeptide binding domain 1, opposite strand 1	ncRNA
mm_31839.1	chr4	74013595	74013674	+	1	NA	promoter-TSS (NM_001163732)	promoter-TSS (NM_001163732)	31	NM_172869	242506	Mm.221597	NM_172869	ENSMUSG00000049122	Frmd3	4.1O|9430066I12Rik|EPB41L4O|P410	FERM domain containing 3	protein-coding
mm_110634.1	chr12	57546128	57546141	-	1	NA	promoter-TSS (NM_008259)	promoter-TSS (NM_008259)	-13	NM_008259	15375	Mm.4578	NM_008259	ENSMUSG00000035451	Foxa1	Hnf-3a|Hnf3a|Tcf-3a|Tcf3a	forkhead box A1	protein-coding
mm_4367.1	chr1	172082797	172082855	+	1	NA	promoter-TSS (NM_021607)	promoter-TSS (NM_021607)	-77	NM_021607	59287	Mm.218203	NM_021607	ENSMUSG00000003458	Ncstn	9430068N19Rik|AA727311|Aph2|D1Dau13e|Kiaa0253|Nct|mKIAA0253	nicastrin	protein-coding
mm_16060.1	chr2	167871761	167871794	+	1	NA	Intergenic	Intergenic	-60550	NM_011201	19246	Mm.277916	NM_011201	ENSMUSG00000027540	Ptpn1	PTP-1B|PTP-HA2|PTP1B	protein tyrosine phosphatase, non-receptor type 1	protein-coding
mm_7866.1	chr1	132627045	132627048	-	1	NA	intron (NM_001160318, intron 7 of 26)	intron (NM_001160318, intron 7 of 26)	15812	NM_001160316	269116	Mm.326702	NM_182716	ENSMUSG00000026442	Nfasc	AA387016|D430023G06Rik|NF|mKIAA0756	neurofascin	protein-coding
mm_135611.1	chr16	52258466	52258471	-	1	NA	intron (NM_009655, intron 14 of 15)	URR1A|DNA|hAT-Charlie	194613	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_54217.1	chr6	25809190	25809207	-	1	NA	promoter-TSS (NM_133931)	promoter-TSS (NM_133931)	28	NM_133931	101185	Mm.274589	NM_133931	ENSMUSG00000029676	Pot1a	1500031H18Rik|AI851169|Pot1	protection of telomeres 1A	protein-coding
mm_7909.1	chr1	133689948	133689962	-	1	NA	promoter-TSS (NM_172842)	promoter-TSS (NM_172842)	61	NM_172842	240754	Mm.36534	NM_172842	ENSMUSG00000051998	Lax1	A530029E09|E430019B13Rik	lymphocyte transmembrane adaptor 1	protein-coding
mm_42893.1	chr5	122396839	122396895	+	1	NA	exon (NM_019824, exon 2 of 7)	exon (NM_019824, exon 2 of 7)	4989	NM_019824	56378	Mm.275942	NM_019824	ENSMUSG00000029465	Arpc3	1110006A04Rik|p21-ARC|p21-Ar|p21Arc	actin related protein 2/3 complex, subunit 3	protein-coding
mm_91383.1	chr10	30623533	30623537	-	1	NA	Intergenic	Intergenic	-5169	NM_025798	66847	Mm.46218	NM_025798	ENSMUSG00000019791	Hint3	0610010I17Rik|AV009015|HINT-3|HINT-4|HINT4	histidine triad nucleotide binding protein 3	protein-coding
mm_137146.1	chr17	23673582	23673652	+	1	NA	promoter-TSS (NM_181821)	promoter-TSS (NM_181821)	9	NM_181821	353502	Mm.359030	NM_181821	ENSMUSG00000023904	Hcfc1r1	HPIP	host cell factor C1 regulator 1 (XPO1-dependent)	protein-coding
mm_117284.1	chr13	65991077	65991111	-	1	NA	Intergenic	Intergenic	-122359	NM_001177832	628709	Mm.390595	NM_001177832	ENSMUSG00000095909	Gm10324	ENSMUSG00000071302	predicted gene 10324	protein-coding
mm_17732.1	chr2	32495301	32495324	-	1	NA	Intergenic	Intergenic	-40047	NM_153560	98952	Mm.4065	NM_153560	ENSMUSG00000039157	Fam102a	AI426465|C230093N12Rik|Eeig1	family with sequence similarity 102, member A	protein-coding
mm_142165.1	chr17	36145940	36145956	-	1	NA	intron (NR_033517, intron 1 of 3)	CpG	930	NR_033517	675325	Mm.75890	NR_033517	ENSMUSG00000038311	2410017I17Rik	-	RIKEN cDNA 2410017I17 gene	ncRNA
mm_167564.1	chr9	41206187	41206189	+	1	NA	promoter-TSS (NR_040392)	promoter-TSS (NR_040392)	33	NR_040392	78500	Mm.275715	NR_040392	ENSMUSG00000100837	1700063D05Rik	-	RIKEN cDNA 1700063D05 gene	ncRNA
mm_5403.1	chr1	33757687	33757695	-	1	NA	promoter-TSS (NM_145392)	promoter-TSS (NM_145392)	59	NM_145392	213539	Mm.247037	NM_145392	ENSMUSG00000042215	Bag2	2610042A13Rik|BC016230	BCL2-associated athanogene 2	protein-coding
mm_75565.1	chr8	60329547	60329549	-	1	NA	Intergenic	Intergenic	-176576	NM_011834	23923	Mm.35020	NM_011834	ENSMUSG00000057228	Aadat	AI875679|Aadt|KATII|Kat2|Kyat2|mKat-2	aminoadipate aminotransferase	protein-coding
mm_89054.1	chr10	82879808	82879838	+	1	NA	exon (NM_001042523, exon 7 of 15)	exon (NM_001042523, exon 7 of 15)	13197	NM_025499	66341	Mm.443284	NM_025499	ENSMUSG00000109864	Eid3	1700027M21Rik|NS4EB	EP300 interacting inhibitor of differentiation 3	protein-coding
mm_131001.1	chr15	103537929	103538019	-	1	NA	promoter-TSS (NM_021391)	promoter-TSS (NM_021391)	18	NM_021391	58200	Mm.143788	NM_021391	ENSMUSG00000022490	Ppp1r1a	0610038N18Rik|I-1	protein phosphatase 1, regulatory (inhibitor) subunit 1A	protein-coding
mm_109639.1	chr12	112796015	112796036	+	1	NA	Intergenic	Intergenic	-12950	NM_145450	217887	Mm.186678	NM_145450	ENSMUSG00000037594	BC022687	AW050009|C130001I08Rik|Flj20080	cDNA sequence BC022687	protein-coding
mm_76030.1	chr8	76902010	76902023	-	1	NA	promoter-TSS (NM_001083906)	promoter-TSS (NM_001083906)	-492	NM_001083906	110784	Mm.324393	NM_001083906	ENSMUSG00000031618	Nr3c2	MR|Mlr	nuclear receptor subfamily 3, group C, member 2	protein-coding
mm_140481.1	chr17	3114553	3114563	-	1	NA	promoter-TSS (NM_134123)	promoter-TSS (NM_134123)	-414	NM_134123	106583	Mm.124373	NM_134123	ENSMUSG00000046201	Scaf8	A630086M08Rik|A930036P18Rik|AA408306|AI447644|AI448652|AU015035|Rbm16|mKIAA1116	SR-related CTD-associated factor 8	protein-coding
mm_85196.1	chr9	96731402	96731415	-	1	NA	TTS (NR_015511)	TTS (NR_015511)	267	NM_175537	245007	Mm.485954	NM_175537	ENSMUSG00000040433	Zbtb38	A930014K01Rik|CIBZ	zinc finger and BTB domain containing 38	protein-coding
mm_105871.1	chr11	114795889	114795903	-	1	NA	promoter-TSS (NM_028055)	promoter-TSS (NM_028055)	-4	NM_028055	72014	Mm.38347	NM_028055	ENSMUSG00000000202	Btbd17	1500005I02Rik|Tango10a	BTB (POZ) domain containing 17	protein-coding
mm_78018.1	chr9	13707276	13707279	+	1	NA	3' UTR (NM_173776, exon 4 of 4)	3' UTR (NM_173776, exon 4 of 4)	-41904	NM_023858	77116	Mm.210405	NM_023858	ENSMUSG00000031918	Mtmr2	6030445P13Rik	myotubularin related protein 2	protein-coding
mm_41184.1	chr5	88318574	88318590	+	1	NA	exon (NM_008644, exon 2 of 3)	exon (NM_008644, exon 2 of 3)	1270	NM_008644	17830	Mm.200411	NM_008644	ENSMUSG00000064156	Prol1	Muc10	proline rich, lacrimal 1	protein-coding
mm_162898.1	chr10	112837749	112837755	+	1	NA	Intergenic	Intergenic	91274	NM_001033474	382423	Mm.431239	NM_001033474	ENSMUSG00000074748	Atxn7l3b	4921506J03Rik|6230409E21Rik|AI315132|ENSMUSG00000074747	ataxin 7-like 3B	protein-coding
mm_73414.1	chr8	106054603	106054611	+	1	NA	TTS (NM_025518)	TTS (NM_025518)	-4996	NM_010901	18021	Mm.383185	NM_010901	ENSMUSG00000031902	Nfatc3	C80703|D8Ertd281e|NFAT4|NFATx	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 3	protein-coding
mm_458.1	chr1	36274573	36274617	+	1	NA	Intergenic	Intergenic	-1170	NM_153408	214854	Mm.389110	NM_153408	ENSMUSG00000047180	Neurl3	2010300P06Rik|Lincr	neuralized E3 ubiquitin protein ligase 3	protein-coding
mm_112191.1	chr12	113425362	113425390	-	1	NA	Intergenic	(CAGCT)n|Simple_repeat|Simple_repeat	-64189	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_88618.1	chr10	79854659	79854674	+	1	NA	non-coding (NR_029447, exon 1 of 1)	non-coding (NR_029447, exon 1 of 1)	234	NM_001283013	19205	Mm.265610	NM_008956	ENSMUSG00000006498	Ptbp1	AA407203|AL033359|HNRPI|PTB-1|PTB2|PTB3|PTB4|Ptb|pPTB	polypyrimidine tract binding protein 1	protein-coding
mm_62356.1	chr7	100499267	100499283	+	1	NA	exon (NM_011671, exon 8 of 8)	exon (NM_011671, exon 8 of 8)	5917	NM_011671	22228	Mm.171378	NM_011671	ENSMUSG00000033685	Ucp2	Slc25a8	uncoupling protein 2 (mitochondrial, proton carrier)	protein-coding
mm_70866.1	chr8	24818970	24818971	+	1	NA	intron (NM_001272059, intron 1 of 18)	CT-rich|Low_complexity|Low_complexity	5399	NM_001272058	11499	Mm.143889	NM_007401	ENSMUSG00000031554	Adam5	tMDC II|tMDCII	a disintegrin and metallopeptidase domain 5	protein-coding
mm_22214.1	chr2	174294159	174294161	-	1	NA	intron (NR_002846, intron 1 of 4)	AT_rich|Low_complexity|Low_complexity	1276	NR_002846	56802	Mm.125770	NR_002846	ENSMUSG00000086537	Nespas	Gnas-as|Nespos	neuroendocrine secretory protein antisense	ncRNA
mm_64457.1	chr7	142660481	142660497	+	1	NA	non-coding (NR_002855, exon 1 of 4)	non-coding (NR_002855, exon 1 of 4)	782	NM_001122736	16002	Mm.3862	NM_010514	ENSMUSG00000048583	Igf2	AL033362|Igf-2|Igf-II|M6pr|Mpr|Peg2	insulin-like growth factor 2	protein-coding
mm_88185.1	chr10	69993290	69993300	+	1	NA	intron (NM_146005, intron 36 of 42)	intron (NM_146005, intron 36 of 42)	67763	NM_009670	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_6104.1	chr1	64030290	64030302	-	1	NA	Intergenic	Intergenic	12205	NR_105864	102466760		NR_105864	ENSMUSG00000098487	Mir6899	Gm27384|mmu-mir-6899	microRNA 6899	ncRNA
mm_116306.1	chr13	36734405	36734415	-	1	NA	promoter-TSS (NM_153529)	promoter-TSS (NM_153529)	67	NM_153529	68404	Mm.232930	NM_153529	ENSMUSG00000039114	Nrn1	0710008J23Rik|Cpg15|Nrn	neuritin 1	protein-coding
mm_58518.1	chr7	4137476	4137484	+	1	NA	promoter-TSS (NR_033548)	promoter-TSS (NR_033548)	424	NM_172736	232798	Mm.22831	NM_172736	ENSMUSG00000035545	Leng8	AW049671	leukocyte receptor cluster (LRC) member 8	protein-coding
mm_4279.1	chr1	171628276	171628288	+	1	NA	Intergenic	RLTR18B|LTR|ERVK	13618	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_70977.1	chr8	27172717	27172763	+	1	NA	intron (NM_029423, intron 1 of 4)	intron (NM_029423, intron 1 of 4)	1906	NM_029423	75767	Mm.205335	NM_029423	ENSMUSG00000031488	Rab11fip1	2010200K21Rik|4833414G05Rik|Rcp	RAB11 family interacting protein 1 (class I)	protein-coding
mm_49149.1	chr6	11926759	11926790	+	1	NA	exon (NM_001168382, exon 2 of 18)	exon (NM_001168382, exon 2 of 18)	893	NM_001168382	75725	Mm.212411	NM_029404	ENSMUSG00000029629	Phf14	1110001C23Rik|4932409F11Rik|5730446A07Rik|AA623952|AV297001|mKIAA0783	PHD finger protein 14	protein-coding
mm_12152.1	chr2	61812557	61812575	+	1	NA	3' UTR (NM_009322, exon 6 of 6)	3' UTR (NM_009322, exon 6 of 6)	8113	NM_009322	21375	Mm.308525	NM_009322	ENSMUSG00000035033	Tbr1	-	T-box brain gene 1	protein-coding
mm_122955.1	chr14	54968064	54968074	-	1	NA	promoter-TSS (NR_033497)	promoter-TSS (NR_033497)	-718	NR_033497	791403	Mm.319176	NR_033497	ENSMUSG00000097652	Mhrt	D830015G02Rik|ENSMUSG00000053118|Myheart	myosin heavy chain associated RNA transcript	ncRNA
mm_30179.1	chr3	144205944	144205985	-	1	NA	promoter-TSS (NM_010723)	promoter-TSS (NM_010723)	-709	NM_010723	16911	Mm.29187	NM_010723	ENSMUSG00000028266	Lmo4	A730077C12Rik|Crp3|Etohi4	LIM domain only 4	protein-coding
mm_91732.1	chr10	45486421	45486436	-	1	NA	Intergenic	CpG	-16227	NM_001031772	380669	Mm.440328	NM_001031772	ENSMUSG00000063804	Lin28b	2810403D23Rik|D030047M17Rik|Lin-28.2	lin-28 homolog B (C. elegans)	protein-coding
mm_1552.1	chr1	72942440	72942449	+	1	NA	Intergenic	RMER19B|LTR|ERVK	-67579	NM_010518	16011	Mm.405761	NM_010518	ENSMUSG00000026185	Igfbp5	AI256729|AW208790|IGFBP-5|IGFBP-5P	insulin-like growth factor binding protein 5	protein-coding
mm_13823.1	chr2	119237647	119237649	+	1	NA	intron (NM_016907, intron 1 of 10)	CpG	288	NM_016907	20732	Mm.104955	NM_016907	ENSMUSG00000027315	Spint1	HAI-1	serine protease inhibitor, Kunitz type 1	protein-coding
mm_24106.1	chr3	88141974	88142024	+	1	NA	promoter-TSS (NM_001310593)	promoter-TSS (NM_001310593)	-373	NM_001310587	17261	Mm.28184	NM_133665	ENSMUSG00000001419	Mef2d	C80750	myocyte enhancer factor 2D	protein-coding
mm_6639.1	chr1	79436253	79436265	-	1	NA	exon (NM_009129, exon 2 of 2)	exon (NM_009129, exon 2 of 2)	3831	NM_009129	20254	Mm.5038	NM_009129	ENSMUSG00000050711	Scg2	Chgc|SgII	secretogranin II	protein-coding
mm_125233.1	chr15	34142961	34142965	+	1	NA	TTS (NM_026002)	TTS (NM_026002)	60244	NM_026002	67154	Mm.130883	NM_026002	ENSMUSG00000022255	Mtdh	2610103J23Rik|3D3|3D3/Lyric|AEG-1|AV353288|D8Bwg1112e|Lyric	metadherin	protein-coding
mm_136710.1	chr17	7926942	7926949	+	1	NA	intron (NM_145968, intron 2 of 9)	intron (NM_145968, intron 2 of 9)	945	NM_145968	72536	Mm.119680	NM_145968	ENSMUSG00000033450	Tagap	2610315E15Rik	T cell activation Rho GTPase activating protein	protein-coding
mm_82419.1	chr9	14903753	14903772	-	1	NA	5' UTR (NM_176807, exon 1 of 5)	5' UTR (NM_176807, exon 1 of 5)	189	NM_176807	64931	Mm.86738	NM_022888	ENSMUSG00000031933	Izumo1r	0910001L11Rik|C86255|Folbp3|Folr4|Juno	IZUMO1 receptor, JUNO	protein-coding
mm_54547.1	chr6	36810072	36810091	-	1	NA	5' UTR (NM_008973, exon 1 of 5)	5' UTR (NM_008973, exon 1 of 5)	1280	NM_008973	19242	Mm.279690	NM_008973	ENSMUSG00000029838	Ptn	HARP|HB-GAM|HBBN|HBGF-8|HBNF|OSF|Osf-1|Osf1	pleiotrophin	protein-coding
mm_144158.1	chr18	5603740	5603761	+	1	NA	intron (NM_011546, intron 1 of 7)	intron (NM_011546, intron 1 of 7)	-11313	NR_033552	791318	Mm.84339	NR_033552	ENSMUSG00000063087	Gm10125	ENSMUSG00000063087|Zeb1os	predicted gene 10125	ncRNA
mm_96755.1	chr11	69909021	69909032	+	1	NA	exon (NM_001291119, exon 18 of 28)	exon (NM_001291119, exon 18 of 28)	-5166	NM_019726	56310	Mm.477738	NM_019726	ENSMUSG00000023170	Gps2	AI505953	G protein pathway suppressor 2	protein-coding
mm_125278.1	chr15	36226216	36226219	+	1	NA	intron (NM_012031, intron 15 of 18)	intron (NM_012031, intron 15 of 18)	13947	NR_106173	102465888		NR_106173	ENSMUSG00000098457	Mir8097	Gm27497|mmu-mir-8097	microRNA 8097	ncRNA
mm_42118.1	chr5	110867887	110867914	+	1	NA	intron (NM_016681, intron 12 of 14)	intron (NM_016681, intron 12 of 14)	-11903	NM_001267622	209683	Mm.295660	NM_024477	ENSMUSG00000033209	Ttc28	2310015L07Rik|6030435N04|AI428795|AI851761|BC002262|TPRBK	tetratricopeptide repeat domain 28	protein-coding
mm_56398.1	chr6	96166196	96166208	-	1	NA	promoter-TSS (NR_003643)	promoter-TSS (NR_003643)	3	NR_003643	78482	Mm.391486	NM_030107	ENSMUSG00000072878	1700123L14Rik	-	nucleoporin 50 pseudogene	pseudo
mm_172165.1	chr6	44793110	44793115	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-266949	NM_001004357	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding
mm_103801.1	chr11	82908361	82908400	-	1	NA	promoter-TSS (NM_145431)	promoter-TSS (NM_145431)	15	NM_145431	217011	Mm.29176	NM_145431	ENSMUSG00000020692	Nle1	AL022765|BC018399|Nle|l11Jus1|l11Jus4	notchless homolog 1 (Drosophila)	protein-coding
mm_107242.1	chr12	26479178	26479191	+	1	NA	3' UTR (NM_020557, exon 5 of 5)	3' UTR (NM_020557, exon 5 of 5)	9969	NM_020557	22169	Mm.271839	NM_020557	ENSMUSG00000020638	Cmpk2	1200004E04Rik|TDKI|Tyki	cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial	protein-coding
mm_99106.1	chr11	100129300	100129305	+	1	NA	Intergenic	Intergenic	6647	NM_008469	16665	Mm.440010	NM_008469	ENSMUSG00000054146	Krt15	AI528832|K15|Krt1-15	keratin 15	protein-coding
mm_121493.1	chr14	121830986	121830999	+	1	NA	Intergenic	Intergenic	-33258	NM_134074	105445	Mm.378591	NM_134074	ENSMUSG00000025558	Dock9	AA959601|AW538057|B230309H04Rik|D14Wsu89e|Zizimin1|mKIAA1058	dedicator of cytokinesis 9	protein-coding
mm_63213.1	chr7	126272507	126272524	+	1	NA	promoter-TSS (NM_145587)	promoter-TSS (NM_145587)	-104	NM_145587	104175	Mm.29660	NM_145587	ENSMUSG00000042978	Sbk1	Sbk	SH3-binding kinase 1	protein-coding
mm_166390.1	chr5	134394836	134394876	+	1	NA	intron (NM_001347488, intron 9 of 27)	intron (NM_001347488, intron 9 of 27)	61406	NM_001081465	57080	Mm.332735	NM_020331	ENSMUSG00000023079	Gtf2ird1	1700012P16Rik|BEN|Cream1|ESTM9|GTF3|Gtf2il|MusTRD1|Tg(Alb1-Myc)166.8Sst|WBSCR11|X83320	general transcription factor II I repeat domain-containing 1	protein-coding
mm_145417.1	chr18	58555959	58556009	+	1	NA	promoter-TSS (NM_001081072)	promoter-TSS (NM_001081072)	-256	NM_001081072	225579	Mm.258517	NM_001081072	ENSMUSG00000024600	Slc27a6	4732438L20Rik|FACVL2|FATP6|VLCS-H1	solute carrier family 27 (fatty acid transporter), member 6	protein-coding
mm_84891.1	chr9	79792851	79792883	-	1	NA	promoter-TSS (NR_040734)	promoter-TSS (NR_040734)	563	NM_133718	69981	Mm.486324	NM_133718	ENSMUSG00000032328	Tmem30a	2010200I23Rik|AW540225|Cdc50a|D9Wsu20e	transmembrane protein 30A	protein-coding
mm_106771.1	chr12	4599745	4599774	+	1	NA	intron (NM_011365, intron 1 of 38)	PB1D9|SINE|Alu	6751	NM_001198968	20403	Mm.341204	NM_011365	ENSMUSG00000020640	Itsn2	AI327390|Ese2|Sh3d1B|Sh3p18|mKIAA1256	intersectin 2	protein-coding
mm_74769.1	chr8	20944753	20944756	-	1	NA	promoter-TSS (NM_001012640)	promoter-TSS (NM_001012640)	-6	NM_001012640	100503970	Mm.490241	NM_001012640	ENSMUSG00000079120	AY761185	-	cDNA sequence AY761185	protein-coding
mm_135441.1	chr16	45408956	45409048	-	1	NA	promoter-TSS (NM_010818)	promoter-TSS (NM_010818)	51	NM_010818	17470	Mm.245851	NM_010818	ENSMUSG00000022661	Cd200	Mox2|OX2	CD200 antigen	protein-coding
mm_12212.1	chr2	67318567	67318569	+	1	NA	Intergenic	Intergenic	-127434	NM_001083919	241431	Mm.261043	NM_001024618	ENSMUSG00000027022	Xirp2	2310003D02Rik|2310008C07Rik|A530024P18Rik|AI452089|Cmya3|Gm352|Xin2	xin actin-binding repeat containing 2	protein-coding
mm_158960.1	chr1	91366517	91366517	+	1	NA	promoter-TSS (NM_173395)	promoter-TSS (NM_173395)	87	NM_173395	227358	Mm.389157	NM_173395	ENSMUSG00000047443	Erfe	4832406C22|Fam132b|myonectin	erythroferrone	protein-coding
mm_133076.1	chr16	58726370	58726375	+	1	NA	Intergenic	Intergenic	-1538	NR_045518	224250	Mm.29482	NM_171826	ENSMUSG00000022744	Cldnd1	1110019C08Rik|AA407103|AI849195|AW489850|Cldn25	claudin domain containing 1	protein-coding
mm_135908.1	chr16	67519507	67519522	-	1	NA	intron (NM_178721, intron 1 of 9)	intron (NM_178721, intron 1 of 9)	101394	NM_001347247	239857	Mm.394300	NM_178721	ENSMUSG00000064115	Cadm2	2900078E11Rik|9330131D06|A830029E02Rik|Igdf4d|Igsf4d|NECL3|SynCAM 2|SynCAM2	cell adhesion molecule 2	protein-coding
mm_88873.1	chr10	81070139	81070153	+	1	NA	promoter-TSS (NM_022653)	promoter-TSS (NM_022653)	63	NM_022653	50492	Mm.26995	NM_022653	ENSMUSG00000004929	Thop1	AI131655|AI327041|EP24.15	thimet oligopeptidase 1	protein-coding
mm_69132.1	chr7	127027028	127027055	-	1	NA	promoter-TSS (NM_010772)	promoter-TSS (NM_010772)	-562	NM_010772	17188	Mm.378964	NM_010772	ENSMUSG00000030678	Maz	MAZI|PUR1|Pur-1|SAF-1|SAF-2	MYC-associated zinc finger protein (purine-binding transcription factor)	protein-coding
mm_66170.1	chr7	33944301	33944304	-	1	NA	exon (NM_178308, exon 2 of 3)	exon (NM_178308, exon 2 of 3)	683	NM_178308	110187	Mm.155750	NM_178308	ENSMUSG00000066586	Scgb2b26	Abpbg26|Abpbg4|Abpg|C2d|Scgb2b4	secretoglobin, family 2B, member 26	protein-coding
mm_130041.1	chr15	89074124	89074145	-	1	NA	non-coding (NR_040417, exon 2 of 4)	non-coding (NR_040417, exon 2 of 4)	1720	NR_040417	69120	Mm.276391	NR_040417	ENSMUSG00000087331	1810021B22Rik	-	RIKEN cDNA 1810021B22 gene	ncRNA
mm_166389.1	chr5	134314957	134314958	-	1	NA	promoter-TSS (NM_010365)	promoter-TSS (NM_010365)	-197	NM_010365	14886	Mm.261570	NM_010365	ENSMUSG00000060261	Gtf2i	6030441I21Rik|BAP-135|Diws1t|GtfII-I|Spin|TFII-I|WBSCR6	general transcription factor II I	protein-coding
mm_170472.1	chr19	11121320	11121321	+	1	NA	intron (NM_027058, intron 1 of 6)	intron (NM_027058, intron 1 of 6)	9558	NM_027058	69369	Mm.391200	NM_027058	ENSMUSG00000024729	1700017D01Rik	-	RIKEN cDNA 1700017D01 gene	protein-coding
mm_128749.1	chr15	64383040	64383069	-	1	NA	promoter-TSS (NM_001276467)	promoter-TSS (NM_001276467)	-135	NM_010026	13196	Mm.277236	NM_010026	ENSMUSG00000022377	Asap1	AV239055|DEF-1|Ddef1|PAP|mKIAA1249|s19	ArfGAP with SH3 domain, ankyrin repeat and PH domain1	protein-coding
mm_76425.1	chr8	84978011	84978025	-	1	NA	exon (NM_008416, exon 1 of 1)	exon (NM_008416, exon 1 of 1)	730	NM_008416	16477	Mm.1167	NM_008416	ENSMUSG00000052837	Junb	-	jun B proto-oncogene	protein-coding
mm_143567.1	chr17	74294835	74294854	-	1	NA	promoter-TSS (NM_133771)	promoter-TSS (NM_133771)	19	NM_133771	76890	Mm.311874	NM_133771	ENSMUSG00000058704	Memo1	0610016J10Rik|D930048L02Rik	mediator of cell motility 1	protein-coding
mm_5576.1	chr1	39551883	39551893	-	1	NA	3' UTR (NM_001033135, exon 7 of 7)	3' UTR (NM_001033135, exon 7 of 7)	-3048	NR_028555	100217461		NR_028555	ENSMUSG00000077704	Snord89	MBII-289	small nucleolar RNA, C/D box 89	snoRNA
mm_3920.1	chr1	162223460	162223461	+	1	NA	promoter-TSS (NR_029796)	promoter-TSS (NR_029796)	92	NR_029796	387210		NR_029796	ENSMUSG00000065516	Mir214	Mirn214|mir-214|mmu-mir-214	microRNA 214	ncRNA
mm_160366.1	chr8	23058279	23058279	+	1	NA	promoter-TSS (NM_031158)	promoter-TSS (NM_031158)	20	NR_102385	11733	Mm.334444	NM_031158	ENSMUSG00000031543	Ank1	Ank-1|nb|pale	ankyrin 1, erythroid	protein-coding
mm_81647.1	chr9	110953438	110953439	+	1	NA	intron (NM_028838, intron 1 of 8)	intron (NM_028838, intron 1 of 8)	1893	NM_028838	74249	Mm.307615	NM_028838	ENSMUSG00000032495	Lrrc2	2400002D05Rik|4933431K03Rik	leucine rich repeat containing 2	protein-coding
mm_66943.1	chr7	61982275	61982285	-	1	NA	promoter-TSS (NR_037287)	promoter-TSS (NR_037287)	23	NR_015599	320026	Mm.131850	NR_015599	ENSMUSG00000109321	A330076H08Rik	Mirh1	RIKEN cDNA A330076H08 gene	ncRNA
mm_41004.1	chr5	80684291	80684292	+	1	NA	Intergenic	RMER15|LTR|ERVL	-336280	NM_001347367	319387	Mm.273631	NM_198702	ENSMUSG00000037605	Adgrl3	5430402I23Rik|CIRL-3|D130075K09Rik|Gm1379|LEC3|Lphn3|mKIAA0768	adhesion G protein-coupled receptor L3	protein-coding
mm_144053.1	chr17	90603559	90603566	-	1	NA	intron (NM_001346957, intron 9 of 18)	intron (NM_001346957, intron 9 of 18)	-147682	NM_001346959	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_6368.1	chr1	72242730	72242739	-	1	NA	Intergenic	ORR1C2|LTR|ERVL-MaLR	-30427	NM_001005423	381269	Mm.422636	NM_001005423	ENSMUSG00000039395	Mreg	Gm974|Wdt2|dsu	melanoregulin	protein-coding
mm_120571.1	chr14	69040778	69040791	+	1	NA	3' UTR (NM_009285, exon 4 of 4)	3' UTR (NM_009285, exon 4 of 4)	11495	NM_009285	20855	Mm.20911	NM_009285	ENSMUSG00000014813	Stc1	Stc	stanniocalcin 1	protein-coding
mm_40490.1	chr5	57716926	57716939	+	1	NA	intron (NR_015588, intron 1 of 4)	intron (NR_015588, intron 1 of 4)	987	NR_015588	319216	Mm.332387	NR_015588	ENSMUSG00000097216	4932441J04Rik	-	RIKEN cDNA 4932441J04 gene	ncRNA
mm_141118.1	chr17	26090188	26090208	-	1	NA	promoter-TSS (NM_011933)	promoter-TSS (NM_011933)	-34	NM_011933	26378	Mm.292869	NM_011933	ENSMUSG00000036775	Decr2	-	2-4-dienoyl-Coenzyme A reductase 2, peroxisomal	protein-coding
mm_49126.1	chr6	8544574	8544587	+	1	NA	intron (NM_133236, intron 2 of 7)	intron (NM_133236, intron 2 of 7)	24522	NM_001286729	170772	Mm.210787	NM_133236	ENSMUSG00000029638	Glcci1	2310047L21Rik|A130036A18Rik|Fam117c|Gig18|Tssn1	glucocorticoid induced transcript 1	protein-coding
mm_107022.1	chr12	12828036	12828069	+	1	NA	Intergenic	Intergenic	113784	NM_008709	18109	Mm.16469	NM_008709	ENSMUSG00000037169	Mycn	N-myc|Nmyc|Nmyc-1|Nmyc1|bHLHe37|c-nmyc	v-myc avian myelocytomatosis viral related oncogene, neuroblastoma derived	protein-coding
mm_65843.1	chr7	29247927	29247939	-	1	NA	TTS (NM_001110201)	TTS (NM_001110201)	534	NM_028179	72275	Mm.441142	NM_028179	ENSMUSG00000030587	2200002D01Rik	2010005J02Rik|H2RSP|IMUP|IMUP-1|IMUP-2	RIKEN cDNA 2200002D01 gene	protein-coding
mm_39389.1	chr5	13399326	13399382	+	1	NA	promoter-TSS (NM_009152)	promoter-TSS (NM_009152)	45	NM_009152	20346	Mm.372039	NM_009152	ENSMUSG00000028883	Sema3a	Hsema-I|SEMA1|SemD|Semad|coll-1	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	protein-coding
mm_79612.1	chr9	58629103	58629110	+	1	NA	intron (NM_001293673, intron 3 of 7)	intron (NM_001293673, intron 3 of 7)	46866	NM_009145	20320	Mm.15125	NM_009145	ENSMUSG00000032336	Nptn	AW554172|SDR-1|Sdfr1	neuroplastin	protein-coding
mm_60303.1	chr7	44071817	44071826	+	1	NA	Intergenic	Intergenic	19531	NM_020268	16619	Mm.445911	NM_020268	ENSMUSG00000063177	Klk1b27	Gk27|Klk21l|Klk27|mGK-27	kallikrein 1-related peptidase b27	protein-coding
mm_26921.1	chr3	20249546	20249555	-	1	NA	TTS (NM_029706)	TTS (NM_029706)	-7369	NM_007753	12873	Mm.1135	NM_007753	ENSMUSG00000001865	Cpa3	MC-CPA	carboxypeptidase A3, mast cell	protein-coding
mm_103792.1	chr11	82867350	82867351	-	1	NA	intron (NM_001164569, intron 1 of 7)	B1_Mur4|SINE|Alu	3394	NM_001164570	67338	Mm.341608	NM_026097	ENSMUSG00000020696	Rffl	1700051E09Rik|4930516L10Rik|BG080975|Carp2	ring finger and FYVE like domain containing protein	protein-coding
mm_71649.1	chr8	59825662	59825681	+	1	NA	promoter-TSS (NR_126087)	promoter-TSS (NR_126087)	22	NR_126087	75017	Mm.60775	NR_126087	ENSMUSG00000110406	4930470O06Rik	-	RIKEN cDNA 4930470O06 gene	ncRNA
mm_8152.1	chr1	136674769	136674830	-	1	NA	Intergenic	Intergenic	-8597	NR_045324	100503460	Mm.30630	NR_045324	ENSMUSG00000097113	Gm19705	-	predicted gene, 19705	ncRNA
mm_113198.1	chr13	24943568	24943576	+	1	NA	5' UTR (NM_008156, exon 2 of 26)	5' UTR (NM_008156, exon 2 of 26)	420	NM_008156	14756	Mm.291831	NM_008156	ENSMUSG00000021340	Gpld1	6330541J12Rik|AW546131	glycosylphosphatidylinositol specific phospholipase D1	protein-coding
mm_90362.1	chr10	127165826	127165900	+	1	NA	promoter-TSS (NM_027739)	promoter-TSS (NM_027739)	32	NM_001244618	14421	Mm.386762	NM_008080	ENSMUSG00000006731	B4galnt1	4933429D13Rik|Gal-NAc-T|GalNAc-T|GalNAcT|Galgt1|Ggm-2|Ggm2	beta-1,4-N-acetyl-galactosaminyl transferase 1	protein-coding
mm_127962.1	chr15	11907185	11907227	-	1	NA	non-coding (NR_131059, exon 2 of 2)	non-coding (NR_131059, exon 2 of 2)	165	NM_001286395	18162	Mm.25259	NM_008728	ENSMUSG00000022206	Npr3	ANP-C|ANPR-C|EF-2|NPR-C|lgj|stri	natriuretic peptide receptor 3	protein-coding
mm_48523.1	chr5	142903392	142903419	-	1	NA	3' UTR (NM_007393, exon 6 of 6)	3' UTR (NM_007393, exon 6 of 6)	3349	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_127850.1	chr15	7398414	7398420	-	1	NA	promoter-TSS (NM_001289498)	promoter-TSS (NM_001289498)	-22	NM_001289498	268780	Mm.203208	NM_178748	ENSMUSG00000042961	Egflam	5930412K08|AU040377	EGF-like, fibronectin type III and laminin G domains	protein-coding
mm_108009.1	chr12	73584817	73584823	+	1	NA	promoter-TSS (NM_008856)	promoter-TSS (NM_008856)	24	NM_008856	18755	Mm.341677	NM_008856	ENSMUSG00000021108	Prkch	Pkch	protein kinase C, eta	protein-coding
mm_149286.1	chr19	10634301	10634312	+	1	NA	promoter-TSS (NM_027913)	promoter-TSS (NM_027913)	73	NM_027913	71768	Mm.169261	NM_027913	ENSMUSG00000043789	Vwce	1300015B04Rik	von Willebrand factor C and EGF domains	protein-coding
mm_169076.1	chr13	3110437	3110441	+	1	NA	Intergenic	L1Md_T|LINE|L1	-39036	NR_001581	73266	Mm.335891	NR_001581		Speer6-ps1	1700039A02Rik|SPEER-6	spermatogenesis associated glutamate (E)-rich protein 6, pseudogene 1	pseudo
mm_56760.1	chr6	116107562	116107577	-	1	NA	intron (NM_177412, intron 3 of 5)	intron (NM_177412, intron 3 of 5)	85805	NM_177412	330401	Mm.425352	NM_177412	ENSMUSG00000030126	Tmcc1	3632431M01Rik|mKIAA0779	transmembrane and coiled coil domains 1	protein-coding
mm_24607.1	chr3	93446097	93446105	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	3771	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_83348.1	chr9	44338273	44338281	-	1	NA	intron (NM_013551, intron 8 of 13)	A-rich|Low_complexity|Low_complexity	3562	NM_010436	15270	Mm.245931	NM_010436	ENSMUSG00000049932	H2afx	AW228881|H2A.X|H2ax|Hist5-2ax|gammaH2ax	H2A histone family, member X	protein-coding
mm_127233.1	chr15	99406192	99406200	+	1	NA	exon (NM_026669, exon 7 of 10)	exon (NM_026669, exon 7 of 10)	12977	NM_001171035	110213	Mm.16769	NM_026669	ENSMUSG00000023010	Tmbim6	5031406P05Rik|Bi1|Tegt	transmembrane BAX inhibitor motif containing 6	protein-coding
mm_74646.1	chr8	13387476	13387494	-	1	NA	exon (NM_009724, exon 6 of 7)	exon (NM_009724, exon 6 of 7)	9293	NM_009724	11945	Mm.154039	NM_009724	ENSMUSG00000031449	Atp4b	AV080843	ATPase, H+/K+ exchanging, beta polypeptide	protein-coding
mm_158162.1	chrX	103482833	103482849	-	1	NA	non-coding (NR_002844, exon 4 of 4)	non-coding (NR_002844, exon 4 of 4)	392	NR_001570	213742	Mm.274770	NR_001463	ENSMUSG00000086503	Xist	A430022B11|AI314753	inactive X specific transcripts	ncRNA
mm_118962.1	chr14	27431342	27431346	+	1	NA	intron (NM_028945, intron 1 of 23)	PB1D9|SINE|Alu	2497	NM_001114879	218850	Mm.247767	NM_028945	ENSMUSG00000040651	Fam208a	4732418E12|4933409E02Rik|D14Abb1e|MommeD6	family with sequence similarity 208, member A	protein-coding
mm_102551.1	chr11	61366604	61366614	-	1	NA	intron (NM_026183, intron 6 of 16)	intron (NM_026183, intron 6 of 16)	11466	NM_026183	67473	Mm.100741	NM_026183	ENSMUSG00000010122	Slc47a1	1300013J15Rik|AI036982|MATE1|mMATE1	solute carrier family 47, member 1	protein-coding
mm_158827.1	chrX	168051288	168051290	-	1	NA	intron (NM_001033330, intron 3 of 19)	intron (NM_001033330, intron 3 of 19)	71708	NM_001290427	333605	Mm.426168	NM_001033330	ENSMUSG00000049176	Frmpd4	Gm196|PKAP1|Pdzd10|Pdzk10|Preso1|preso	FERM and PDZ domain containing 4	protein-coding
mm_37399.1	chr4	121109240	121109253	-	1	NA	promoter-TSS (NM_001081312)	promoter-TSS (NM_001081312)	-20	NM_001081312	69469	Mm.481120	NM_001081312	ENSMUSG00000078577	Tmco2	1700028F16Rik	transmembrane and coiled-coil domains 2	protein-coding
mm_89763.1	chr10	100050851	100050855	+	1	NA	intron (NM_001347156, intron 1 of 8)	intron (NM_001347156, intron 1 of 8)	35032	NM_013598	17311	Mm.45124	NM_013598	ENSMUSG00000019966	Kitl	Clo|Con|Gb|Kitlg|Mgf|SCF|SF|SLF|Sl|blz|contrasted	kit ligand	protein-coding
mm_113462.1	chr13	36096861	36096865	+	1	NA	intron (NM_201358, intron 1 of 2)	intron (NM_201358, intron 1 of 2)	20494	NM_201358	380840	Mm.390576	NM_201358	ENSMUSG00000046573	Lyrm4	BC034664|Gm903	LYR motif containing 4	protein-coding
mm_159443.1	chr3	127633184	127633184	+	1	NA	promoter-TSS (NM_009718)	promoter-TSS (NM_009718)	39	NM_009718	11924	Mm.42017	NM_009718	ENSMUSG00000027967	Neurog2	Atoh4|Math4A|bHLHa8|ngn-2|ngn2	neurogenin 2	protein-coding
mm_172423.1	chr7	28050088	28050089	-	1	NA	promoter-TSS (NM_011874)	promoter-TSS (NM_011874)	4	NM_011874	23996	Mm.29582	NM_011874	ENSMUSG00000030603	Psmc4	CIP21|MIP224	proteasome (prosome, macropain) 26S subunit, ATPase, 4	protein-coding
mm_122816.1	chr14	54617994	54618017	-	1	NA	promoter-TSS (NM_011186)	promoter-TSS (NM_011186)	-10	NM_011186	19173	Mm.8911	NM_011186	ENSMUSG00000022193	Psmb5	-	proteasome (prosome, macropain) subunit, beta type 5	protein-coding
mm_100486.1	chr11	120348683	120348782	+	1	NA	promoter-TSS (NM_009609)	promoter-TSS (NM_009609)	54	NR_038126	66838	Mm.375010	NR_038126	ENSMUSG00000043644	0610009L18Rik	-	RIKEN cDNA 0610009L18 gene	ncRNA
mm_155704.1	chrX	95558194	95558196	+	1	NA	promoter-TSS (NM_001313743)	promoter-TSS (NM_001313743)	-208	NM_001313743	70392	Mm.79122	NM_080858	ENSMUSG00000031204	Asb12	2310036C05Rik|Asb-12	ankyrin repeat and SOCS box-containing 12	protein-coding
mm_141224.1	chr17	27323321	27323361	-	1	NA	Intergenic	RMER4A|LTR|ERVK	-5044	NR_106075	102466818		NR_106075	ENSMUSG00000099237	Mir7216	Gm27555|mmu-mir-7216	microRNA 7216	ncRNA
mm_6908.1	chr1	84838986	84839022	-	1	NA	promoter-TSS (NM_025386)	promoter-TSS (NM_025386)	300	NM_133975	14897	Mm.209265	NM_133975	ENSMUSG00000026219	Trip12	1110036I07Rik|6720416K24Rik|AA410158|Gtl6|TRIP-12	thyroid hormone receptor interactor 12	protein-coding
mm_75940.1	chr8	71566616	71566626	-	1	NA	promoter-TSS (NM_145598)	promoter-TSS (NM_145598)	28	NM_145598	234404	Mm.213208	NM_145598	ENSMUSG00000034829	Nxnl1	A930031O08Rik|RdCVF|Txnl6	nucleoredoxin-like 1	protein-coding
mm_19404.1	chr2	91643591	91643594	-	1	NA	TTS (NM_001033451)	TTS (NM_001033451)	6186	NM_001347175	381410	Mm.330401	NM_001033451	ENSMUSG00000075040	Zfp408	Gm1011	zinc finger protein 408	protein-coding
mm_63960.1	chr7	139943782	139943794	+	1	NA	promoter-TSS (NM_009482)	promoter-TSS (NM_009482)	-68	NM_009482	22286	Mm.10205	NM_009482	ENSMUSG00000047751	Utf1	AI505934	undifferentiated embryonic cell transcription factor 1	protein-coding
mm_71086.1	chr8	34807288	34807310	+	1	NA	promoter-TSS (NM_176933)	promoter-TSS (NM_176933)	-311	NM_176933	319520	Mm.170276	NM_176933	ENSMUSG00000031530	Dusp4	2700078F24Rik|AI844617|BB104621|E130306H24Rik|MKP2	dual specificity phosphatase 4	protein-coding
mm_99834.1	chr11	109011816	109011826	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	91472	NM_015732	12006	Mm.71710	NM_015732	ENSMUSG00000000142	Axin2	Axi1|Axil|Conductin	axin 2	protein-coding
mm_129799.1	chr15	82899742	82899776	-	1	NA	intron (NR_045068, intron 1 of 3)	CpG	679	NR_045068	100504637	Mm.440928	NR_045068	ENSMUSG00000100199	Gm20324	-	predicted gene, 20324	ncRNA
mm_31724.1	chr4	62685392	62685416	+	1	NA	intron (NM_001310706, intron 1 of 6)	intron (NM_001310706, intron 1 of 6)	11430	NM_001310706	50780	Mm.286753	NM_019492	ENSMUSG00000059810	Rgs3	4930506N09Rik|C2PA-RGS3|C2pa|PDZ-RGS3|RGS3S	regulator of G-protein signaling 3	protein-coding
mm_3275.1	chr1	136570614	136570624	+	1	NA	Intergenic	Intergenic	-54282	NM_177643	226442	Mm.62521	NM_177643	ENSMUSG00000041483	Zfp281	Znf281	zinc finger protein 281	protein-coding
mm_82456.1	chr9	15627841	15627851	-	1	NA	promoter-TSS (NM_181816)	promoter-TSS (NM_181816)	87	NM_181816	234964	Mm.32237	NM_181816	ENSMUSG00000039977	Ccdc67	4933401K09Rik|Deup1	coiled-coil domain containing 67	protein-coding
mm_64354.1	chr7	142388171	142388207	+	1	NA	promoter-TSS (NM_009983)	promoter-TSS (NM_009983)	-319	NM_009983	13033	Mm.231395	NM_009983	ENSMUSG00000007891	Ctsd	CD|CatD	cathepsin D	protein-coding
mm_31620.1	chr4	59189441	59189555	+	1	NA	promoter-TSS (NM_011673)	promoter-TSS (NM_011673)	-52	NM_011673	22234	Mm.198803	NM_011673	ENSMUSG00000028381	Ugcg	AU043821|C80537|Epcs21|GlcT-1|Ugcgl	UDP-glucose ceramide glucosyltransferase	protein-coding
mm_173291.1	chrY	2383256	2383259	-	1	NA	Intergenic	IAPLTR4|LTR|ERVK	-212848	NM_009571	22768	Mm.411381	NM_009571	ENSMUSG00000000103	Zfy2	Zfy-2	zinc finger protein 2, Y-linked	protein-coding
mm_83145.1	chr9	40455782	40455812	-	1	NA	promoter-TSS (NM_172768)	promoter-TSS (NM_172768)	-33	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_142078.1	chr17	35702041	35702068	-	1	NA	promoter-TSS (NM_001198831)	promoter-TSS (NM_001198831)	-10	NM_001198831	12305	Mm.5021	NM_007584	ENSMUSG00000003534	Ddr1	6030432F18|AI323681|CD167a|Cak|Nep|PTK3A	discoidin domain receptor family, member 1	protein-coding
mm_106231.1	chr11	117360477	117360492	-	1	NA	exon (NM_001113486, exon 12 of 12)	exon (NM_001113486, exon 12 of 12)	28171	NM_001113488	53860	Mm.38450	NM_017380	ENSMUSG00000059248	Sept9	MSF1|Msf|PNUTL4|Sint1	septin 9	protein-coding
mm_151111.1	chr19	47864389	47864403	+	1	NA	exon (NM_010362, exon 6 of 6)	exon (NM_010362, exon 6 of 6)	-1149	NM_030051	68214	Mm.63791	NM_026619	ENSMUSG00000025069	Gsto2	1700020F09Rik|4930425C18Rik|GSTO 2-2	glutathione S-transferase omega 2	protein-coding
mm_133811.1	chr16	95702449	95702470	+	1	NA	promoter-TSS (NM_011809)	promoter-TSS (NM_011809)	52	NM_011809	23872	Mm.290207	NM_011809	ENSMUSG00000022895	Ets2	AU022856|Ets-2	E26 avian leukemia oncogene 2, 3' domain	protein-coding
mm_108693.1	chr12	86902581	86902593	+	1	NA	Intergenic	B1_Mur2|SINE|Alu	-17773	NM_145836	238330	Mm.248358	NM_145836	ENSMUSG00000034168	Irf2bpl	6430527G18Rik|Eap1	interferon regulatory factor 2 binding protein-like	protein-coding
mm_12285.1	chr2	69008581	69008595	+	1	NA	intron (NM_172856, intron 4 of 9)	intron (NM_172856, intron 4 of 9)	-127212	NM_181547	329416	Mm.90047	NM_181547	ENSMUSG00000034738	Nostrin	Daip2|mDaIP2	nitric oxide synthase trafficker	protein-coding
mm_59438.1	chr7	27131321	27131331	+	1	NA	exon (NM_007817, exon 8 of 10)	exon (NM_007817, exon 8 of 10)	11371	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_25887.1	chr3	130936586	130936601	+	1	NA	Intergenic	Intergenic	-173704	NM_010703	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_1663.1	chr1	74732026	74732042	+	1	NA	exon (NM_024264, exon 2 of 9)	exon (NM_024264, exon 2 of 9)	16921	NM_153744	241113	Mm.166501	NM_153744	ENSMUSG00000006542	Prkag3	AMPKg3L|AMPKg3S|Amkg3|Ampkg3	protein kinase, AMP-activated, gamma 3 non-catatlytic subunit	protein-coding
mm_24670.1	chr3	94693563	94693568	+	1	NA	promoter-TSS (NM_019414)	promoter-TSS (NM_019414)	-8	NM_019414	20342	Mm.225405	NM_019414	ENSMUSG00000068877	Selenbp2	AP56|Lpsb2	selenium binding protein 2	protein-coding
mm_125030.1	chr15	25753231	25753241	+	1	NA	intron (NM_019472, intron 19 of 40)	intron (NM_019472, intron 19 of 40)	-90062	NM_001034851	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_163774.1	chr13	120018339	120018373	+	1	NA	Intergenic	Intergenic	33848	NM_001302966	100861753	Mm.165042	NM_001302966	ENSMUSG00000095609	Gm21188	-	predicted gene, 21188	protein-coding
mm_9930.1	chr1	189901706	189901709	-	1	NA	intron (NM_026796, intron 2 of 11)	B4|SINE|B4	20581	NM_026796	226830	Mm.156895	NM_026796	ENSMUSG00000026603	Smyd2	1110020E07Rik|4930402C15|KMT3C|Zmynd14	SET and MYND domain containing 2	protein-coding
mm_53532.1	chr6	136587534	136587555	+	1	NA	exon (NM_019426, exon 9 of 15)	exon (NM_019426, exon 9 of 15)	68693	NM_019426	54343	Mm.173271	NM_019426	ENSMUSG00000030213	Atf7ip	2610204M12Rik|AM|Mcaf1	activating transcription factor 7 interacting protein	protein-coding
mm_77347.1	chr8	119574915	119574927	-	1	NA	promoter-TSS (NM_026648)	promoter-TSS (NM_026648)	279	NM_175185	72552	Mm.36756	NM_175185	ENSMUSG00000034189	Hsdl1	2700067E09Rik	hydroxysteroid dehydrogenase like 1	protein-coding
mm_32887.1	chr4	118961985	118962001	+	1	NA	promoter-TSS (NM_133892)	promoter-TSS (NM_133892)	26	NM_133892	100470	Mm.26698	NM_133892	ENSMUSG00000024903	Lao1	AW990848	L-amino acid oxidase 1	protein-coding
mm_169840.1	chr16	3083303	3083307	-	1	NA	Intergenic	IAPLTR4|LTR|ERVK	-509093	NM_146860	258859	Mm.377723	NM_146860	ENSMUSG00000051003	Olfr161	MOR131-1|OR912-47M6	olfactory receptor 161	protein-coding
mm_62131.1	chr7	97081643	97081675	+	1	NA	promoter-TSS (NM_010248)	promoter-TSS (NM_010248)	-92	NM_001162477	14389	Mm.42033	NM_010248	ENSMUSG00000004508	Gab2	AI463667|D130058I17Rik|p97	growth factor receptor bound protein 2-associated protein 2	protein-coding
mm_61003.1	chr7	49343450	49343514	+	1	NA	intron (NM_175272, intron 1 of 37)	intron (NM_175272, intron 1 of 37)	97293	NM_175272	78286	Mm.333881	NM_175272	ENSMUSG00000052512	Nav2	5330421F07Rik|AU067780|BQ960892|HELAD1|POMFIL2|RAINB1|RAINB2|Unc53H2|mKIAA3015	neuron navigator 2	protein-coding
mm_25781.1	chr3	126597416	126597435	+	1	NA	5' UTR (NM_001293663, exon 1 of 20)	5' UTR (NM_001293663, exon 1 of 20)	474	NM_023813	108058	Mm.255822	NM_023813	ENSMUSG00000053819	Camk2d	2810011D23Rik|8030469K03Rik|CaMK II|[d]-CaMKII	calcium/calmodulin-dependent protein kinase II, delta	protein-coding
mm_96251.1	chr11	62575982	62575992	+	1	NA	5' UTR (NM_011706, exon 2 of 16)	5' UTR (NM_011706, exon 2 of 16)	1501	NM_011706	22368	Mm.288064	NM_011706	ENSMUSG00000018507	Trpv2	GRC|OTRPC2|VRL-1|Vrl1	transient receptor potential cation channel, subfamily V, member 2	protein-coding
mm_121113.1	chr14	101838502	101838515	+	1	NA	intron (NM_201529, intron 3 of 30)	intron (NM_201529, intron 3 of 30)	-2115	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_128310.1	chr15	37792167	37792188	-	1	NA	promoter-TSS (NM_001170866)	promoter-TSS (NM_001170866)	-177	NM_001170866	52589	Mm.283370	NM_134094	ENSMUSG00000051359	Ncald	AI848120|D030020D09Rik|D15Ertd412e	neurocalcin delta	protein-coding
mm_53856.1	chr6	149309314	149309318	+	1	NA	promoter-TSS (NM_001289662)	promoter-TSS (NM_001289662)	-98	NM_001289661	67246	Mm.333515	NM_026054	ENSMUSG00000032712	2810474O19Rik	6720435I21Rik|AA536804|AU020969|GET|Kiaa1551	RIKEN cDNA 2810474O19 gene	protein-coding
mm_132949.1	chr16	49911875	49911894	+	1	NA	TTS (NM_010581)	TTS (NM_010581)	56230	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_149200.1	chr19	9978000	9978038	+	1	NA	Intergenic	Intergenic	-2581	NR_073181	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
mm_104847.1	chr11	99230999	99231019	-	1	NA	promoter-TSS (NM_020618)	promoter-TSS (NM_020618)	8	NM_020618	57376	Mm.379086	NM_020618	ENSMUSG00000037935	Smarce1	2810417B20Rik|5830412H02Rik|9030408N19Rik|Baf27	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1	protein-coding
mm_112333.1	chr12	115952985	115953000	-	1	NA	Intergenic	Intergenic	-94732	NM_001004066	56220	Mm.254997	NM_019565	ENSMUSG00000042063	Zfp386	Kzf1|mKIAA4205	zinc finger protein 386 (Kruppel-like)	protein-coding
mm_26832.1	chr3	10971969	10971973	-	1	NA	Intergenic	Intergenic	-531841	NM_001127191	74718	Mm.440548	NM_029068	ENSMUSG00000027534	Snx16	4930522N22Rik|AI117577|AI747675	sorting nexin 16	protein-coding
mm_71704.1	chr8	61928114	61928127	+	1	NA	promoter-TSS (NM_001293783)	promoter-TSS (NM_001293783)	33	NM_001293783	234311	Mm.275233	NM_144928	ENSMUSG00000037921	Ddx60	9830118M07	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	protein-coding
mm_130603.1	chr15	99819701	99819715	-	1	NA	exon (NM_001113545, exon 4 of 11)	exon (NM_001113545, exon 4 of 11)	441	NM_023063	65970	Mm.33207	NM_023063	ENSMUSG00000023022	Lima1	Eplin	LIM domain and actin binding 1	protein-coding
mm_160690.1	chr10	23920358	23920358	+	1	NA	promoter-TSS (NM_053205)	promoter-TSS (NM_053205)	-48	NM_053205	111174	Mm.377141	NM_053205	ENSMUSG00000056379	Taar1	Tar1|Trar1|taR-1	trace amine-associated receptor 1	protein-coding
mm_144527.1	chr18	25065806	25065820	+	1	NA	intron (NM_175276, intron 15 of 26)	intron (NM_175276, intron 15 of 26)	100152	NM_001142697	66648	Mm.263189	NM_001004361	ENSMUSG00000024269	Tpgs2	5730437P09Rik|5730494M16Rik|AI666318|Pgs2	tubulin polyglutamylase complex subunit 2	protein-coding
mm_59272.1	chr7	24902954	24902963	+	1	NA	promoter-TSS (NM_008488)	promoter-TSS (NM_008488)	-28	NM_001130150	16801	Mm.3181	NM_008488	ENSMUSG00000040940	Arhgef1	Lbcl2|Lsc	Rho guanine nucleotide exchange factor (GEF) 1	protein-coding
mm_55981.1	chr6	85902529	85902538	-	1	NA	promoter-TSS (NM_001145895)	promoter-TSS (NM_001145895)	0	NM_001145895	75541	Mm.24454	NM_029331	ENSMUSG00000068299	Nat8f4	1700019G17Rik	N-acetyltransferase 8 (GCN5-related) family member 4	protein-coding
mm_25170.1	chr3	103090184	103090197	+	1	NA	intron (NM_001033303, intron 7 of 15)	intron (NM_001033303, intron 7 of 15)	16176	NM_001033303	229665	Mm.331272	NM_001033303	ENSMUSG00000070385	Ampd1	AI553520|Ampd-1	adenosine monophosphate deaminase 1	protein-coding
mm_17253.1	chr2	25815840	25815858	-	1	NA	promoter-TSS (NM_001039095)	promoter-TSS (NM_001039095)	-13	NM_001039095	71103	Mm.236431	NM_001039095	ENSMUSG00000036401	Glt6d1	4933411C14Rik|GT6m7	glycosyltransferase 6 domain containing 1	protein-coding
mm_126698.1	chr15	85042504	85042522	+	1	NA	intron (NM_133750, intron 1 of 8)	intron (NM_133750, intron 1 of 8)	5451	NM_133750	73225	Mm.247535	NM_133750	ENSMUSG00000022434	Fam118a	-	family with sequence similarity 118, member A	protein-coding
mm_4324.1	chr1	171852015	171852023	+	1	NA	exon (NM_013489, exon 3 of 9)	exon (NM_013489, exon 3 of 9)	12322	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_138034.1	chr17	33919646	33919676	+	1	NA	TTS (NM_020625)	TTS (NM_020625)	183	NM_009318	21356	Mm.154457	NM_009318	ENSMUSG00000024308	Tapbp	D17Wsu91e|TPN	TAP binding protein	protein-coding
mm_112053.1	chr12	111804136	111804161	-	1	NA	3' UTR (NM_028875, exon 8 of 8)	3' UTR (NM_028875, exon 8 of 8)	9731	NM_028875	74335	Mm.19082	NM_028875	ENSMUSG00000021287	Xrcc3	-	X-ray repair complementing defective repair in Chinese hamster cells 3	protein-coding
mm_120922.1	chr14	76436257	76436305	+	1	NA	intron (NM_001310646, intron 3 of 4)	intron (NM_001310646, intron 3 of 4)	20460	NM_207652	21807	Mm.153272	NM_009366	ENSMUSG00000022010	Tsc22d1	AA589566|AW105905|Egr5|TSC-22|Tgfb1i4|Tsc|Tsc22	TSC22 domain family, member 1	protein-coding
mm_163069.1	chr11	67250874	67250877	-	1	NA	exon (NM_010855, exon 22 of 40)	exon (NM_010855, exon 22 of 40)	13063	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_91430.1	chr10	33211354	33211357	-	1	NA	intron (NM_029726, intron 9 of 37)	B1_Mm|SINE|Alu	45002	NR_040657	442820	Mm.490725	NR_040657		D830005E20Rik	-	RIKEN cDNA D830005E20 gene	ncRNA
mm_164105.1	chr15	25828819	25828835	+	1	NA	Intergenic	Intergenic	-14471	NM_001034851	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_98267.1	chr11	88994727	88994749	+	1	NA	Intergenic	RSINE1|SINE|B4	-4665	NM_009546	217069	Mm.248445	NM_009546	ENSMUSG00000000275	Trim25	AA960166|AL022677|EFP|Zfp147	tripartite motif-containing 25	protein-coding
mm_89127.1	chr10	84917658	84917692	+	1	NA	promoter-TSS (NM_183172)	promoter-TSS (NM_183172)	62	NM_183172	237422	Mm.18936	NM_183172	ENSMUSG00000035620	Ric8b	BC051080|Ric-8|Ric-8b	RIC8 guanine nucleotide exchange factor B	protein-coding
mm_112178.1	chr12	113421999	113422012	-	1	NA	Intergenic	Intergenic	-67560	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_74372.1	chr8	128503269	128503336	+	1	NA	3' UTR (NM_008737, exon 17 of 17)	3' UTR (NM_008737, exon 17 of 17)	144061	NR_035436	100316680		NR_035436	ENSMUSG00000084523	Mir1903	Mirn1903|mmu-mir-1903	microRNA 1903	ncRNA
mm_145609.1	chr18	61096812	61096818	+	1	NA	Intergenic	Intergenic	-8757	NM_001037859	12978	Mm.22574	NM_007779	ENSMUSG00000024621	Csf1r	AI323359|CD115|CSF-1R|Csfmr|Fim-2|Fim2|Fms|M-CSF-R|M-CSFR	colony stimulating factor 1 receptor	protein-coding
mm_90602.1	chr10	128322545	128322574	+	1	NA	promoter-TSS (NM_019953)	promoter-TSS (NM_019953)	100	NM_019953	56530	Mm.44220	NM_019953	ENSMUSG00000025381	Cnpy2	5330432A10Rik|AW229003|D10Bwg1546e|Tmem4|Zsig9	canopy FGF signaling regulator 2	protein-coding
mm_88383.1	chr10	76449075	76449093	+	1	NA	promoter-TSS (NM_029816)	promoter-TSS (NM_029816)	3	NM_029816	76964	Mm.472489	NM_029816	ENSMUSG00000009114	2610028H24Rik	ORF67	RIKEN cDNA 2610028H24 gene	protein-coding
mm_39475.1	chr5	20117556	20117557	+	1	NA	intron (NM_001170746, intron 3 of 22)	intron (NM_001170746, intron 3 of 22)	210038	NM_015823	50791	Mm.332231	NM_015823	ENSMUSG00000040003	Magi2	AIP-1|Acvri1|Acvrinp1|Acvrip1|Magi-2|S-SCAM|mKIAA0705	membrane associated guanylate kinase, WW and PDZ domain containing 2	protein-coding
mm_126381.1	chr15	80173271	80173300	+	1	NA	promoter-TSS (NM_010795)	promoter-TSS (NM_010795)	-436	NM_010795	17309	Mm.299693	NM_010795	ENSMUSG00000042428	Mgat3	1110038J12Rik|AI848272|GnT-III	mannoside acetylglucosaminyltransferase 3	protein-coding
mm_100280.1	chr11	117792456	117792466	+	1	NA	intron (NM_001195089, intron 15 of 15)	intron (NM_001195089, intron 15 of 15)	-5199	NM_029964	77727	Mm.159981	NM_029964	ENSMUSG00000025573	6030468B19Rik	-	RIKEN cDNA 6030468B19 gene	protein-coding
mm_95887.1	chr11	58104139	58104191	+	1	NA	promoter-TSS (NM_026949)	promoter-TSS (NM_026949)	12	NM_026949	69125	Mm.28910	NM_026949	ENSMUSG00000020515	Cnot8	1500015I04Rik|1810022F04Rik|AA536816|AU015770|AU043059	CCR4-NOT transcription complex, subunit 8	protein-coding
mm_32028.1	chr4	95215433	95215446	+	1	NA	Intergenic	RMER19C|LTR|ERVK	-163217	NM_010591	16476	Mm.275071	NM_010591	ENSMUSG00000052684	Jun	AP-1|Junc|c-jun	jun proto-oncogene	protein-coding
mm_151620.1	chr19	3905236	3905261	-	1	NA	promoter-TSS (NM_016921)	promoter-TSS (NM_016921)	-18	NM_016921	27060	Mm.271689	NM_016921	ENSMUSG00000001750	Tcirg1	ATP6N1C|ATP6a3|Atp6i|OC-116|OPTB1|Stv1|TIRC7|Vph1|oc	T cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 protein A3	protein-coding
mm_146036.1	chr18	69522156	69522190	+	1	NA	intron (NM_013685, intron 6 of 19)	intron (NM_013685, intron 6 of 19)	176452	NM_001083967	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding
mm_146962.1	chr18	33438305	33438319	-	1	NA	3' UTR (NM_001267717, exon 5 of 5)	3' UTR (NM_001267717, exon 5 of 5)	25322	NM_001267717	27528	Mm.407415	NM_053078	ENSMUSG00000042834	Nrep	AI325076|D0H4S114|Harp|P311|PTZ17|SEZ17	neuronal regeneration related protein	protein-coding
mm_18917.1	chr2	76737460	76737471	-	1	NA	exon (NM_011652, exon 275 of 313)	exon (NM_011652, exon 275 of 313)	62150	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_83683.1	chr9	50479583	50479592	-	1	NA	Intergenic	Intergenic	-14938	NM_029639	76509	Mm.29959	NM_029639	ENSMUSG00000032068	Plet1	0610037B23Rik|1600029D21Rik|AA407923|AU043048	placenta expressed transcript 1	protein-coding
mm_95159.1	chr11	35945511	35945516	+	1	NA	intron (NM_170779, intron 1 of 22)	intron (NM_170779, intron 1 of 22)	34576	NM_170779	211652	Mm.31267	NM_170779	ENSMUSG00000018849	Wwc1	AA408228|AU017197|BC037006|Kibra|mKIAA0869	WW, C2 and coiled-coil domain containing 1	protein-coding
mm_78071.1	chr9	15315521	15315536	+	1	NA	intron (NR_028401, intron 11 of 11)	intron (NR_028401, intron 11 of 11)	2917	NR_106108	102465758		NR_106108	ENSMUSG00000105847	Gm25500	Mir7650|mmu-mir-7650	predicted gene, 25500	ncRNA
mm_134551.1	chr16	19983006	19983029	-	1	NA	promoter-TSS (NM_183390)	promoter-TSS (NM_183390)	32	NM_183390	239743	Mm.86699	NM_183390	ENSMUSG00000043008	Klhl6	-	kelch-like 6	protein-coding
mm_155140.1	chrX	51020871	51020880	+	1	NA	Intergenic	Intergenic	-2857	NM_172413	72065	Mm.43152	NM_172413	ENSMUSG00000050029	Rap2c	2010200P20Rik|AI194294|AL022976	RAP2C, member of RAS oncogene family	protein-coding
mm_2671.1	chr1	127209745	127209748	+	1	NA	intron (NM_145128, intron 1 of 17)	ID_B1|SINE|B4	4760	NM_145128	107895	Mm.214682	NM_145128	ENSMUSG00000036155	Mgat5	4930471A21Rik|5330407H02Rik|AI480971|GlcNAc-TV	mannoside acetylglucosaminyltransferase 5	protein-coding
mm_4783.1	chr1	184034376	184034386	+	1	NA	promoter-TSS (NM_028516)	promoter-TSS (NM_028516)	-80	NM_022019	63953	Mm.404024	NM_022019	ENSMUSG00000039384	Dusp10	2610306G15Rik|AI158871|MKP-5|MKP5	dual specificity phosphatase 10	protein-coding
mm_15930.1	chr2	165081758	165081773	+	1	NA	intron (NR_033448, intron 2 of 2)	T-rich|Low_complexity|Low_complexity	8985	NR_033448	72211	Mm.482899	NR_033448	ENSMUSG00000078935	1700025C18Rik	-	RIKEN cDNA 1700025C18 gene	ncRNA
mm_101136.1	chr11	12464882	12464997	-	1	NA	promoter-TSS (NM_001282993)	promoter-TSS (NM_001282993)	21	NM_172496	12808	Mm.22847	NM_172496	ENSMUSG00000020173	Cobl	-	cordon-bleu WH2 repeat	protein-coding
mm_97553.1	chr11	78929821	78929832	+	1	NA	exon (NM_010927, exon 4 of 27)	exon (NM_010927, exon 4 of 27)	4535	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_27874.1	chr3	79169568	79169578	-	1	NA	Intergenic	Intergenic	-23698	NM_001099624	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_38409.1	chr4	139092994	139093000	-	1	NA	promoter-TSS (NM_008675)	promoter-TSS (NM_008675)	-27	NM_008675	17965	Mm.9404	NM_008675	ENSMUSG00000041120	Nbl1	D4H1S1733E|DAN|Dana|NO3	neuroblastoma, suppression of tumorigenicity 1	protein-coding
mm_125216.1	chr15	34083003	34083010	+	1	NA	5' UTR (NM_026002, exon 1 of 12)	5' UTR (NM_026002, exon 1 of 12)	287	NM_026002	67154	Mm.130883	NM_026002	ENSMUSG00000022255	Mtdh	2610103J23Rik|3D3|3D3/Lyric|AEG-1|AV353288|D8Bwg1112e|Lyric	metadherin	protein-coding
mm_12452.1	chr2	71211942	71211996	+	1	NA	promoter-TSS (NM_001198877)	promoter-TSS (NM_001198877)	23	NM_010064	13427	Mm.249479	NM_010064	ENSMUSG00000027012	Dync1i2	3110079H08Rik|AW554389|Dncic2	dynein cytoplasmic 1 intermediate chain 2	protein-coding
mm_106203.1	chr11	116843313	116843386	-	1	NA	promoter-TSS (NM_028865)	promoter-TSS (NM_028865)	100	NM_033398	107817	Mm.481684	NM_033398	ENSMUSG00000056962	Jmjd6	5730436I23Rik|D11Ertd195e|PSR|PtdSerR|Ptdsr|mKIAA0585	jumonji domain containing 6	protein-coding
mm_107463.1	chr12	37241805	37241897	+	1	NA	5' UTR (NM_178767, exon 1 of 13)	5' UTR (NM_178767, exon 1 of 13)	212	NM_178767	319660	Mm.485540	NM_178767	ENSMUSG00000050103	Agmo	A530016O06Rik|AI790538|Tmem195	alkylglycerol monooxygenase	protein-coding
mm_71210.1	chr8	40890681	40890692	+	1	NA	intron (NM_007514, intron 1 of 11)	intron (NM_007514, intron 1 of 11)	28319	NM_001044740	11988	Mm.4676	NM_007514	ENSMUSG00000031596	Slc7a2	20.5|AI158848|Atrc2|CAT-2|Cat2|Tea	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	protein-coding
mm_125177.1	chr15	31572161	31572175	+	1	NA	intron (NM_181588, intron 1 of 5)	intron (NM_181588, intron 1 of 5)	3256	NM_181588	69574	Mm.28108	NM_181588	ENSMUSG00000022235	Cmbl	2310016A09Rik	carboxymethylenebutenolidase-like (Pseudomonas)	protein-coding
mm_48277.1	chr5	137989974	137989995	-	1	NA	3' UTR (NM_013478, exon 4 of 4)	3' UTR (NM_013478, exon 4 of 4)	8463	NM_013478	12007	Mm.30061	NM_013478	ENSMUSG00000037053	Azgp1	Zag	alpha-2-glycoprotein 1, zinc	protein-coding
mm_137501.1	chr17	26973162	26973219	+	1	NA	promoter-TSS (NM_001005916)	promoter-TSS (NM_001005916)	11	NM_001005916	474156	Mm.328890	NM_001005916	ENSMUSG00000079605	Zbtb9	3930402F13Rik	zinc finger and BTB domain containing 9	protein-coding
mm_71255.1	chr8	40917526	40917532	+	1	NA	3' UTR (NM_001044740, exon 12 of 12)	3' UTR (NM_001044740, exon 12 of 12)	-8704	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_62806.1	chr7	112904902	112904906	+	1	NA	3' UTR (NM_001166585, exon 11 of 11)	3' UTR (NM_001166585, exon 11 of 11)	-49058	NM_175279	78748	Mm.349943	NM_175279	ENSMUSG00000098132	Rassf10	4632411J06Rik	Ras association (RalGDS/AF-6) domain family (N-terminal) member 10	protein-coding
mm_14200.1	chr2	127208465	127208475	+	1	NA	promoter-TSS (NM_177214)	promoter-TSS (NM_177214)	66	NM_177214	320632	Mm.215860	NM_177214	ENSMUSG00000003660	Snrnp200	A330064G03Rik|Ascc3l1|BC011390|HELIC2|U5-200-KD|U5-200KD	small nuclear ribonucleoprotein 200 (U5)	protein-coding
mm_89170.1	chr10	86311229	86311255	+	1	NA	intron (NM_011595, intron 1 of 4)	B4A|SINE|B4	10830	NM_011595	21859	Mm.4871	NM_011595	ENSMUSG00000020044	Timp3	Timp-3	tissue inhibitor of metalloproteinase 3	protein-coding
mm_10552.1	chr2	16729284	16729295	+	1	NA	exon (NM_026162, exon 13 of 14)	exon (NM_026162, exon 13 of 14)	284437	NR_040632	75069	Mm.50378	NR_040632		4930515L03Rik	-	RIKEN cDNA 4930515L03 gene	ncRNA
mm_11124.1	chr2	28229345	28229380	+	1	NA	exon (NM_001038613, exon 6 of 6)	exon (NM_001038613, exon 6 of 6)	23673	NM_019498	56177	Mm.43278	NM_019498	ENSMUSG00000026833	Olfm1	AMY|AW742568|Noe1|OlfA|Pancortin|Pancortin3	olfactomedin 1	protein-coding
mm_101558.1	chr11	33933014	33933018	-	1	NA	intron (NM_001190886, intron 1 of 7)	MTD|LTR|ERVL-MaLR	-29997	NM_031169	16533	Mm.6206	NM_031169	ENSMUSG00000020155	Kcnmb1	BKbeta1	potassium large conductance calcium-activated channel, subfamily M, beta member 1	protein-coding
mm_135092.1	chr16	34943270	34943287	-	1	NA	intron (NR_045723, intron 3 of 3)	intron (NR_045723, intron 3 of 3)	-3949	NR_040536	76649	Mm.420532	NR_040536	ENSMUSG00000100593	1700119H24Rik	-	RIKEN cDNA 1700119H24 gene	ncRNA
mm_151223.1	chr19	53700744	53700750	+	1	NA	intron (NM_001170847, intron 1 of 13)	RCHARR1|DNA|hAT-Charlie	23441	NM_001170847	73713	Mm.313695	NM_001170847	ENSMUSG00000043639	Rbm20	1110018J23Rik|2010003H22Rik|AI646761	RNA binding motif protein 20	protein-coding
mm_56873.1	chr6	118748280	118748283	-	1	NA	intron (NM_001255998, intron 7 of 47)	intron (NM_001255998, intron 7 of 47)	9693	NM_001290335	12288	Mm.41628	NM_009781	ENSMUSG00000051331	Cacna1c	Cav1.2|Cchl1a1|D930026N18Rik|MBC|MELC-CC	calcium channel, voltage-dependent, L type, alpha 1C subunit	protein-coding
mm_4515.1	chr1	174501797	174501843	+	1	NA	promoter-TSS (NM_019445)	promoter-TSS (NM_019445)	-5	NM_019445	54418	Mm.330620	NM_019445	ENSMUSG00000028354	Fmn2	AU024104	formin 2	protein-coding
mm_159039.1	chr1	180696968	180696968	-	1	NA	promoter-TSS (NM_013729)	promoter-TSS (NM_013729)	66	NM_013729	27217	Mm.103647	NM_013729	ENSMUSG00000026497	Mixl1	Mm1|Mml	Mix1 homeobox-like 1 (Xenopus laevis)	protein-coding
mm_73740.1	chr8	114147990	114148005	+	1	NA	exon (NM_024437, exon 3 of 4)	exon (NM_024437, exon 3 of 4)	14423	NM_024437	67528	Mm.27889	NM_024437	ENSMUSG00000031767	Nudt7	1300007B24Rik|2210404C19Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 7	protein-coding
mm_10336.1	chr2	11642800	11642812	+	1	NA	promoter-TSS (NM_008367)	promoter-TSS (NM_008367)	14	NM_008367	16184	Mm.915	NM_008367	ENSMUSG00000026770	Il2ra	CD25|Il2r|Ly-43	interleukin 2 receptor, alpha chain	protein-coding
mm_46547.1	chr5	106458478	106458496	-	1	NA	promoter-TSS (NM_001005477)	promoter-TSS (NM_001005477)	-321	NM_001005477	104382	Mm.271593	NM_001005477	ENSMUSG00000034384	Barhl2	E130309B19Rik|MBH1	BarH-like 2 (Drosophila)	protein-coding
mm_29870.1	chr3	130730311	130730352	-	1	NA	promoter-TSS (NM_001287581)	promoter-TSS (NM_001287581)	-2	NM_001199350	619547	Mm.391636	NM_001199350		Rpl34-ps1	EG619547|ENSMUSG00000068396|Gm10239	ribosomal protein L34, pseudogene 1	protein-coding
mm_64062.1	chr7	140856472	140856513	+	1	NA	promoter-TSS (NM_053194)	promoter-TSS (NM_053194)	-109	NM_018742	54399	Mm.155696	NM_018742	ENSMUSG00000025484	Bet1l	2610021K23Rik|Gs15	Bet1 golgi vesicular membrane trafficking protein like	protein-coding
mm_98247.1	chr11	88204381	88204391	+	1	NA	promoter-TSS (NM_024174)	promoter-TSS (NM_024174)	-2	NM_024174	64656	Mm.168680	NM_024174	ENSMUSG00000023723	Mrps23	D11Bwg1153e|MRP-S23|Rpms23|S23mt	mitochondrial ribosomal protein S23	protein-coding
mm_64446.1	chr7	142654314	142654353	+	1	NA	TTS (NR_030251)	TTS (NR_030251)	663	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_55661.1	chr6	72394551	72394575	-	1	NA	Intergenic	Intergenic	-3896	NM_016794	22320	Mm.1838	NM_016794	ENSMUSG00000050732	Vamp8	AU041171|Edb|endobrevin	vesicle-associated membrane protein 8	protein-coding
mm_137673.1	chr17	28786061	28786064	+	1	NA	Intergenic	B4|SINE|B4	-15064	NM_001081315	268936	Mm.291877	NM_199061	ENSMUSG00000063952	Brpf3	AI413466|AW493400|mKIAA1286	bromodomain and PHD finger containing, 3	protein-coding
mm_57982.1	chr6	135733588	135733601	-	1	NA	exon (NM_008171, exon 15 of 15)	exon (NM_008171, exon 15 of 15)	74681	NR_126088	75024	Mm.399147	NR_126088	ENSMUSG00000107396	4930425L21Rik	4930473P14Rik	RIKEN cDNA 4930425L21 gene	ncRNA
mm_20401.1	chr2	129288903	129288903	-	1	NA	intron (NM_181589, intron 3 of 8)	intron (NM_181589, intron 3 of 8)	8309	NM_181589	70466	Mm.45785	NM_181589	ENSMUSG00000048327	Ckap2l	2010016H04Rik|2610318C08Rik|AV070319|radmis|rdm	cytoskeleton associated protein 2-like	protein-coding
mm_58849.1	chr7	16844139	16844143	+	1	NA	intron (NM_001252458, intron 2 of 18)	intron (NM_001252458, intron 2 of 18)	1076	NM_178900	101540	Mm.1881	NM_178900	ENSMUSG00000041187	Prkd2	AI325941|PKD2	protein kinase D2	protein-coding
mm_63657.1	chr7	129432432	129432433	+	1	NA	Intergenic	Intergenic	-159431	NM_172255	207425	Mm.229323	NM_172255	ENSMUSG00000042055	Wdr11	2900055P10Rik|AW489876|Brwd2|mKIAA1351	WD repeat domain 11	protein-coding
mm_171908.1	chr5	49498849	49498850	-	1	NA	Intergenic	L2|LINE|L2	-213190	NM_001199244	80334	Mm.160172	NM_030265	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding
mm_129045.1	chr15	75216166	75216180	-	1	NA	Intergenic	Intergenic	-52248	NM_008530	17071	Mm.377095	NM_008530	ENSMUSG00000022583	Ly6f	-	lymphocyte antigen 6 complex, locus F	protein-coding
mm_19523.1	chr2	94155387	94155401	-	1	NA	intron (NM_019657, intron 1 of 10)	MTC|LTR|ERVL-MaLR	2515	NM_019657	56348	Mm.22505	NM_019657	ENSMUSG00000027195	Hsd17b12	2610510O05Rik|AI172963|KIK-I|Kik1	hydroxysteroid (17-beta) dehydrogenase 12	protein-coding
mm_151609.1	chr19	3768695	3768709	-	1	NA	intron (NM_001167887, intron 2 of 11)	CpG-7172	1281	NM_001167885	225888	Mm.278578	NM_144871	ENSMUSG00000045098	Kmt5b	AA117471|C630029K18Rik|Suv4-20h1|Suv420h1	lysine methyltransferase 5B	protein-coding
mm_170762.1	chr2	16017101	16017103	-	1	NA	intron (NM_001310455, intron 29 of 38)	RLTR9E|LTR|ERVK	-339202	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding
mm_148248.1	chr18	80708116	80708180	-	1	NA	promoter-TSS (NM_016791)	promoter-TSS (NM_016791)	25	NM_001164111	18018	Mm.329560	NM_016791	ENSMUSG00000033016	Nfatc1	2210017P03Rik|AI449492|AV076380|NF-ATc|NFAT2|NFATc|Nfatcb	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 1	protein-coding
mm_137912.1	chr17	32113805	32113844	+	1	NA	Intergenic	CpG	-22401	NR_027316	435518	Mm.328944	NR_027316	ENSMUSG00000002791	Pdxk-ps	ENSMUSG00000002791|Gm9743	pyridoxal (pyridoxine, vitamin B6) kinase, pseudogene	pseudo
mm_122004.1	chr14	26928613	26928624	-	1	NA	exon (NM_145221, exon 17 of 22)	exon (NM_145221, exon 17 of 22)	34014	NM_080856	142687	Mm.138259	NM_080856	ENSMUSG00000021898	Asb14	Asb-14	ankyrin repeat and SOCS box-containing 14	protein-coding
mm_16282.1	chr2	174019256	174019270	+	1	NA	Intergenic	Intergenic	-57788	NM_172675	228960	Mm.277977	NM_172675	ENSMUSG00000027522	Stx16	4930401D03|5430410K23Rik|6330500A18Rik|AI648908|AW553605|Syn16	syntaxin 16	protein-coding
mm_4169.1	chr1	171114197	171114200	+	1	NA	Intergenic	Intergenic	-7463	NM_001081275	75472	Mm.32760	NM_029301	ENSMUSG00000026649	Cfap126	1700009P17Rik|AV282292|Flattop|Fltp	cilia and flagella associated protein 126	protein-coding
mm_104986.1	chr11	100265914	100265927	-	1	NA	intron (NM_212483, intron 3 of 7)	intron (NM_212483, intron 3 of 7)	3951	NM_212483	68239	Mm.158190	NM_212483	ENSMUSG00000053654	Krt42	2410039E07Rik|K17n|Ka22|ecat6	keratin 42	protein-coding
mm_59126.1	chr7	19940452	19940465	+	1	NA	intron (NM_027308, intron 3 of 4)	RMER15|LTR|ERVL	10285	NM_027308	70080	Mm.98583	NM_027308	ENSMUSG00000040498	Igsf23	2210010C17Rik	immunoglobulin superfamily, member 23	protein-coding
mm_128545.1	chr15	55072170	55072177	-	1	NA	promoter-TSS (NM_001081288)	promoter-TSS (NM_001081288)	-21	NM_001081288	319944	Mm.380957	NM_001081288	ENSMUSG00000037343	Taf2	150kDa|4732460C16Rik|AI425886|CIF150|TAF2B|TAFII-150|TAFII150	TATA-box binding protein associated factor 2	protein-coding
mm_118273.1	chr13	112620713	112620720	-	1	NA	exon (NM_010029, exon 14 of 21)	exon (NM_010029, exon 14 of 21)	31594	NM_010029	13206	Mm.12818	NM_010029	ENSMUSG00000021758	Ddx4	AV206478|Mvh|VASA	DEAD (Asp-Glu-Ala-Asp) box polypeptide 4	protein-coding
mm_112035.1	chr12	111538580	111538606	-	1	NA	intron (NM_178041, intron 2 of 11)	CpG-3539	492	NM_173363	217869	Mm.271222	NM_173363	ENSMUSG00000021282	Eif5	2810011H21Rik|D12Ertd549e	eukaryotic translation initiation factor 5	protein-coding
mm_125192.1	chr15	32691318	32691341	+	1	NA	3' UTR (NM_009154, exon 23 of 23)	3' UTR (NM_009154, exon 23 of 23)	-229394	NM_008304	15529	Mm.234266	NM_008304	ENSMUSG00000022261	Sdc2	4833414L08Rik|AA960457|Hspg1|Synd2|syndecan-2	syndecan 2	protein-coding
mm_3880.1	chr1	161035400	161035437	+	1	NA	non-coding (NR_002840, exon 1 of 4)	non-coding (NR_002840, exon 1 of 4)	252	NR_002840	14455	Mm.270065	NR_002840	ENSMUSG00000053332	Gas5	Gas-5|Mir5117|Snhg2	growth arrest specific 5	ncRNA
mm_7653.1	chr1	128327750	128327755	-	1	NA	exon (NM_001081078, exon 1 of 17)	exon (NM_001081078, exon 1 of 17)	566	NM_001081078	226413	Mm.26930	NM_001081078	ENSMUSG00000026354	Lct	Gm100|LAC|LPH|Lphl	lactase	protein-coding
mm_125940.1	chr15	76247995	76248018	+	1	NA	promoter-TSS (NR_105918)	promoter-TSS (NR_105918)	-185	NR_105918	102465575		NR_105918	ENSMUSG00000098625	Mir6953	Gm27738|mmu-mir-6953	microRNA 6953	ncRNA
mm_139704.1	chr17	57451613	57451627	+	1	NA	intron (NM_010130, intron 17 of 21)	intron (NM_010130, intron 17 of 21)	92934	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_27793.1	chr3	75556904	75556919	-	1	NA	promoter-TSS (NM_009250)	promoter-TSS (NM_009250)	-59	NM_019745	56426	Mm.316473	NM_019745	ENSMUSG00000027835	Pdcd10	2410003B13Rik|Ccm3|Tfa15|Tfar15	programmed cell death 10	protein-coding
mm_83276.1	chr9	43071185	43071197	-	1	NA	intron (NM_027144, intron 1 of 40)	intron (NM_027144, intron 1 of 40)	34527	NM_027144	69632	Mm.275266	NM_027144	ENSMUSG00000059495	Arhgef12	2310014B11Rik|AU019857|Larg|mKIAA0382	Rho guanine nucleotide exchange factor (GEF) 12	protein-coding
mm_68932.1	chr7	126495431	126495478	-	1	NA	exon (NM_183020, exon 14 of 23)	exon (NM_183020, exon 14 of 23)	6971	NM_001347658	233871	Mm.231450	NM_183020	ENSMUSG00000032637	Atxn2l	A2D|A2LG|A2RP|A2lp|Atxnl2	ataxin 2-like	protein-coding
mm_6916.1	chr1	84839580	84839591	-	1	NA	promoter-TSS (NM_025386)	promoter-TSS (NM_025386)	-256	NM_025386	66153	Mm.381192	NM_025386	ENSMUSG00000073633	Fbxo36	0610008D19Rik|1110020F21Rik|2410002G19Rik|D1Ertd757e	F-box protein 36	protein-coding
mm_123093.1	chr14	55784028	55784073	-	1	NA	promoter-TSS (NM_080435)	promoter-TSS (NM_080435)	-31	NM_080435	104110	Mm.287010	NM_080435	ENSMUSG00000022220	Adcy4	mKIAA4004	adenylate cyclase 4	protein-coding
mm_170207.1	chr17	69879881	69879891	-	1	NA	Intergenic	RLTR44C|LTR|ERVK	-89187	NM_001347412	224997	Mm.311840	NM_027712	ENSMUSG00000003279	Dlgap1	4933422O14Rik|9630002F18|AI845682|AI848168|BB075781|D17Bwg0511e|GKAP/SAPAP|GKPA/SAPAP|Gkap|Sapap1|mKIAA4162	discs, large (Drosophila) homolog-associated protein 1	protein-coding
mm_104158.1	chr11	87281197	87281200	-	1	NA	intron (NR_106195, intron 6 of 8)	intron (NR_106195, intron 6 of 8)	77796	NM_177167	320472	Mm.341988	NM_177167	ENSMUSG00000046442	Ppm1e	AW049266|B930008A12Rik|POPX1|PP2CH|mKIAA1072	protein phosphatase 1E (PP2C domain containing)	protein-coding
mm_127167.1	chr15	98738418	98738443	+	1	NA	3' UTR (NM_007478, exon 5 of 5)	3' UTR (NM_007478, exon 5 of 5)	-10232	NM_024169	66120	Mm.30729	NM_024169	ENSMUSG00000003355	Fkbp11	1110002O23Rik|FKBP-11	FK506 binding protein 11	protein-coding
mm_30013.1	chr3	135665114	135665125	-	1	NA	intron (NM_008689, intron 3 of 24)	(TG)n|Simple_repeat|Simple_repeat	26428	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_18840.1	chr2	75133709	75133722	-	1	NA	Intergenic	Intergenic	307903	NM_016804	53375	Mm.292613	NM_016804	ENSMUSG00000027099	Mtx2	1500012G02Rik	metaxin 2	protein-coding
mm_76282.1	chr8	84197580	84197593	-	1	NA	Intergenic	CpG	-10932	NR_029740	387216		NR_029740	ENSMUSG00000065611	Mir23a	Mirn23a|mir-23a|mmu-mir-23a	microRNA 23a	ncRNA
mm_69078.1	chr7	127001942	127001948	-	1	NA	exon (NM_080638, exon 2 of 15)	exon (NM_080638, exon 2 of 15)	12649	NM_080638	78388	Mm.228797	NM_080638	ENSMUSG00000030681	Mvp	2310009M24Rik|LRP|VAULT1	major vault protein	protein-coding
mm_40370.1	chr5	51052338	51052342	+	1	NA	Intergenic	Intergenic	501581	NR_027710	19017	Mm.259072	NM_008904	ENSMUSG00000029167	Ppargc1a	A830037N07Rik|ENSMUSG00000079510|Gm11133|PGC-1|PPARGC-1-alpha|Pgc-1alpha|Pgc1|Pgco1|Ppargc1	peroxisome proliferative activated receptor, gamma, coactivator 1 alpha	protein-coding
mm_25931.1	chr3	131223939	131223951	+	1	NA	3' UTR (NM_001276402, exon 10 of 10)	3' UTR (NM_001276402, exon 10 of 10)	48156	NM_008212	15107	Mm.260164	NM_008212	ENSMUSG00000027984	Hadh	AA409008|AU019341|AW742602|HCDH|Hadhsc|Schad	hydroxyacyl-Coenzyme A dehydrogenase	protein-coding
mm_122888.1	chr14	54947194	54947206	-	1	NA	exon (NM_010856, exon 33 of 39)	exon (NM_010856, exon 33 of 39)	1942	NR_029724	387204		NR_029724	ENSMUSG00000065432	Mir208a	Mirn208|Mirn208a|mir-208|mir-208a|mmu-mir-208	microRNA 208a	ncRNA
mm_145084.1	chr18	42398383	42398386	+	1	NA	Intergenic	Intergenic	3787	NM_138945	18998	Mm.488204	NM_138945	ENSMUSG00000024497	Pou4f3	Brn3.1|Brn3c|ddl|dreidel	POU domain, class 4, transcription factor 3	protein-coding
mm_136306.1	chr16	91638020	91638030	-	1	NA	exon (NM_010256, exon 7 of 22)	exon (NM_010256, exon 7 of 22)	8947	NM_010256	14450	Mm.4505	NM_010256	ENSMUSG00000022962	Gart	Gaps|Prgs	phosphoribosylglycinamide formyltransferase	protein-coding
mm_42482.1	chr5	115470837	115470841	+	1	NA	exon (NM_011107, exon 2 of 4)	exon (NM_011107, exon 2 of 4)	4573	NM_011107	18778	Mm.20190	NM_011107	ENSMUSG00000029522	Pla2g1b	Pla2a|sPLA2IB	phospholipase A2, group IB, pancreas	protein-coding
mm_41699.1	chr5	100846418	100846449	+	1	NA	intron (NM_172715, intron 1 of 12)	CpG	204	NM_172715	231510	Mm.271911	NM_172715	ENSMUSG00000029314	Agpat9	1-AGPAT|1-AGPAT 9|4933407I02Rik|4933408F15|A230097K15Rik|GPAT-3|Gpat3|mGPAT3	1-acylglycerol-3-phosphate O-acyltransferase 9	protein-coding
mm_37579.1	chr4	126321670	126321704	-	1	NA	promoter-TSS (NM_133883)	promoter-TSS (NM_133883)	16	NM_133883	100206	Mm.11285	NM_133883	ENSMUSG00000042558	Adprhl2	AI836109|Arh3	ADP-ribosylhydrolase like 2	protein-coding
mm_73278.1	chr8	104624567	104624576	+	1	NA	promoter-TSS (NM_001252627)	promoter-TSS (NM_001252627)	-175	NM_001252628	12556	Mm.19423	NM_007663	ENSMUSG00000031881	Cdh16	-	cadherin 16	protein-coding
mm_66362.1	chr7	43530381	43530392	-	1	NA	intron (NM_021293, intron 3 of 5)	intron (NM_021293, intron 3 of 5)	2785	NM_001111058	12489	Mm.140157	NM_021293	ENSMUSG00000004609	Cd33	Siglec-3|gp67	CD33 antigen	protein-coding
mm_13878.1	chr2	119948100	119948106	+	1	NA	exon (NM_013720, exon 17 of 24)	exon (NM_013720, exon 17 of 24)	-24596	NM_011941	26390	Mm.330501	NM_011941	ENSMUSG00000033902	Mapkbp1	2810483F24Rik|AW123212|JNKBP-1|Jnkbp1|mKIAA0596	mitogen-activated protein kinase binding protein 1	protein-coding
mm_77016.1	chr8	107966917	107966919	-	1	NA	Intergenic	Intergenic	-378436	NM_010817	17463	Mm.18347	NM_010817	ENSMUSG00000039067	Psmd7	AW107203|Mov-34|Mov34	proteasome (prosome, macropain) 26S subunit, non-ATPase, 7	protein-coding
mm_160135.1	chr7	30739407	30739407	-	1	NA	promoter-TSS (NM_008085)	promoter-TSS (NM_008085)	0	NM_008085	14447	Mm.436562	NM_008085	ENSMUSG00000061099	Gapdhs	Gapd-s|Gapds	glyceraldehyde-3-phosphate dehydrogenase, spermatogenic	protein-coding
mm_59863.1	chr7	30121916	30122001	+	1	NA	promoter-TSS (NM_001081007)	promoter-TSS (NM_001081007)	10	NM_001081007	233060	Mm.443484	NM_001081007	ENSMUSG00000074220	Zfp382	5930415A09Rik|Znf382	zinc finger protein 382	protein-coding
mm_58655.1	chr7	6398699	6398729	+	1	NA	Intergenic	Intergenic	15396	NM_175247	22690	Mm.127014	NM_175247	ENSMUSG00000062861	Zfp28	2810438M17Rik|Zfp-28|mkr-5	zinc finger protein 28	protein-coding
mm_150099.1	chr19	29470798	29470819	+	1	NA	3' UTR (NM_021396, exon 6 of 6)	3' UTR (NM_021396, exon 6 of 6)	51179	NR_015567	77779	Mm.458738	NR_015567	ENSMUSG00000097855	A930007I19Rik	-	RIKEN cDNA A930007I19 gene	ncRNA
mm_71955.1	chr8	70510527	70510548	+	1	NA	promoter-TSS (NM_019883)	promoter-TSS (NM_019883)	-170	NM_019883	22186	Mm.297372	NM_019883	ENSMUSG00000090137	Uba52	D8Ertd21e|Gm1863|Rps27a|Ubb|Ubc	ubiquitin A-52 residue ribosomal protein fusion product 1	protein-coding
mm_166423.1	chr5	137151899	137151908	-	1	NA	Intergenic	Intergenic	-35696	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_30711.1	chr4	12124398	12124404	+	1	NA	Intergenic	Intergenic	-15716	NM_028226	72397	Mm.430709	NM_028226	ENSMUSG00000046667	Rbm12b1	3000004N20Rik|Rbm12b|Rbm12ba	RNA binding motif protein 12 B1	protein-coding
mm_78129.1	chr9	20818491	20818506	+	1	NA	promoter-TSS (NM_001030290)	promoter-TSS (NM_001030290)	-6	NM_001030290	235033	Mm.297661	NM_001030290	ENSMUSG00000053773	Rdh8	Gm182|prRDH	retinol dehydrogenase 8	protein-coding
mm_1204.1	chr1	62725797	62725810	+	1	NA	intron (NM_001077405, intron 2 of 15)	intron (NM_001077405, intron 2 of 15)	22486	NM_001077405	18187	Mm.266341	NM_010939	ENSMUSG00000025969	Nrp2	1110048P06Rik|Np-2|Np2|Npn-2|Npn2	neuropilin 2	protein-coding
mm_169060.1	chr13	24416706	24416711	+	1	NA	intron (NM_007717, intron 1 of 15)	intron (NM_007717, intron 1 of 15)	1586	NM_001284520	12763	Mm.8396	NM_007717	ENSMUSG00000016756	Cmah	-	cytidine monophospho-N-acetylneuraminic acid hydroxylase	protein-coding
mm_17340.1	chr2	26601926	26601928	-	1	NA	intron (NM_026212, intron 1 of 5)	intron (NM_026212, intron 1 of 5)	2490	NM_026212	67512	Mm.24244	NM_026212	ENSMUSG00000026922	Agpat2	2510002J07Rik|AV000834|BSCL|BSCL1|LPAAB|LPAAT-beta	1-acylglycerol-3-phosphate O-acyltransferase 2 (lysophosphatidic acid acyltransferase, beta)	protein-coding
mm_1777.1	chr1	78511744	78511762	+	1	NA	intron (NM_026713, intron 1 of 6)	intron (NM_026713, intron 1 of 6)	693	NM_026713	68393	Mm.41325	NM_026713	ENSMUSG00000012187	Mogat1	0610030A14Rik|1110064N14Rik|Dgat2l|Dgat2l1|MGAT1|WI1-2612I11.1|mDC2	monoacylglycerol O-acyltransferase 1	protein-coding
mm_38229.1	chr4	136021630	136021665	-	1	NA	promoter-TSS (NM_013736)	promoter-TSS (NM_013736)	2	NM_013736	27224	Mm.27663	NM_013736	ENSMUSG00000028668	Eloa	110kDa|AA408125|Tceb3|Tceb3a	elongin A	protein-coding
mm_156494.1	chrX	144336165	144336169	+	1	NA	non-coding (NR_037145, exon 4 of 27)	non-coding (NR_037145, exon 4 of 27)	18201	NM_026247	67574	Mm.249084	NM_026247	ENSMUSG00000041718	Alg13	2810046O15Rik|4833435D08Rik|Glt28d1|MDS031|OTTMUSG00000018917	asparagine-linked glycosylation 13	protein-coding
mm_135903.1	chr16	67112637	67112644	-	1	NA	intron (NM_178721, intron 1 of 9)	intron (NM_178721, intron 1 of 9)	455522	NR_040512	75501	Mm.394300	NR_040512	ENSMUSG00000092599	1700010K23Rik	-	RIKEN cDNA 1700010K23 gene	ncRNA
mm_83949.1	chr9	56925925	56925930	-	1	NA	exon (NM_175483, exon 1 of 2)	exon (NM_175483, exon 1 of 2)	2444	NM_175483	235406	Mm.191459	NM_175483	ENSMUSG00000032733	Snx33	E130307J07Rik|Sh3px3	sorting nexin 33	protein-coding
mm_61394.1	chr7	73185799	73185809	+	1	NA	Intergenic	Intergenic	-83736	NR_046024	625243	Mm.261798	NR_046024	ENSMUSG00000108383	Gm6567	-	predicted gene 6567	ncRNA
mm_162711.1	chr10	27127466	27127495	-	1	NA	intron (NM_008481, intron 34 of 63)	intron (NM_008481, intron 34 of 63)	-262386	NR_131034	75855	Mm.402080	NR_131034	ENSMUSG00000101636	4930579H20Rik	-	RIKEN cDNA 4930579H20 gene	ncRNA
mm_158406.1	chrX	136838028	136838043	-	1	NA	3' UTR (NM_011123, exon 7 of 7)	3' UTR (NM_011123, exon 7 of 7)	15289	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_122763.1	chr14	54253711	54253721	-	1	NA	promoter-TSS (NM_001205181)	promoter-TSS (NM_001205181)	213	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_85059.1	chr9	90243020	90243033	-	1	NA	intron (NM_194334, intron 2 of 12)	intron (NM_194334, intron 2 of 12)	27743	NM_194334	67016	Mm.335347	NM_194334	ENSMUSG00000037410	Tbc1d2b	1810061M12Rik|AI480956|AV021536|AV023399|AW491493|mKIAA1055	TBC1 domain family, member 2B	protein-coding
mm_171088.1	chr3	124385798	124385809	+	1	NA	Intergenic	Intergenic	40225	NM_027939	71824	Mm.331353	NM_027939	ENSMUSG00000027973	1700006A11Rik	-	RIKEN cDNA 1700006A11 gene	protein-coding
mm_48667.1	chr5	145981457	145981484	-	1	NA	exon (NM_019792, exon 12 of 13)	exon (NM_019792, exon 12 of 13)	28147	NM_019792	56388	Mm.301900	NM_019792	ENSMUSG00000029630	Cyp3a25	AI327008	cytochrome P450, family 3, subfamily a, polypeptide 25	protein-coding
mm_78397.1	chr9	28920457	28920459	+	1	NA	3' UTR (NM_177906, exon 8 of 8)	3' UTR (NM_177906, exon 8 of 8)	1042671	NM_172290	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding
mm_124334.1	chr14	103844167	103844179	-	1	NA	promoter-TSS (NM_001276296)	promoter-TSS (NM_001276296)	303	NM_001136061	13618	Mm.229532	NM_007904	ENSMUSG00000022122	Ednrb	ET-B|ET-BR|ETR-b|ETb|Sox10m1	endothelin receptor type B	protein-coding
mm_172193.1	chr6	51466148	51466151	-	1	NA	exon (NM_182650, exon 6 of 10)	exon (NM_182650, exon 6 of 10)	3745	NM_182650	53379	Mm.155896	NM_016806	ENSMUSG00000004980	Hnrnpa2b1	9130414A06Rik|Hnrpa2|Hnrpa2b1|hnrnp-A	heterogeneous nuclear ribonucleoprotein A2/B1	protein-coding
mm_148440.1	chr19	3948774	3948785	+	1	NA	exon (NM_019449, exon 11 of 11)	exon (NM_019449, exon 11 of 11)	-10029	NM_028545	73458	Mm.482922	NM_028545	ENSMUSG00000037263	Aldh3b3	1700055N04Rik	aldehyde dehydrogenase 3 family, member B3	protein-coding
mm_137341.1	chr17	25136609	25136617	+	1	NA	promoter-TSS (NM_001317404)	promoter-TSS (NM_001317404)	-18	NM_001317404	26373	Mm.270587	NM_011930	ENSMUSG00000036636	Clcn7	ClC-7|D17Wsu51e	chloride channel, voltage-sensitive 7	protein-coding
mm_109530.1	chr12	111538786	111538804	+	1	NA	intron (NM_178041, intron 2 of 11)	CpG-3539	694	NM_173363	217869	Mm.271222	NM_173363	ENSMUSG00000021282	Eif5	2810011H21Rik|D12Ertd549e	eukaryotic translation initiation factor 5	protein-coding
mm_148524.1	chr19	4439512	4439539	+	1	NA	promoter-TSS (NM_001329989)	promoter-TSS (NM_001329989)	-34	NR_045989	319314	Mm.393810	NR_045989	ENSMUSG00000087132	A930001C03Rik	-	RIKEN cDNA A930001C03 gene	ncRNA
mm_100910.1	chr11	6229262	6229272	-	1	NA	exon (NM_207242, exon 2 of 19)	exon (NM_207242, exon 2 of 19)	978	NM_207242	237636	Mm.212492	NM_207242	ENSMUSG00000020447	Npc1l1	9130221N23Rik|Gm243	NPC1-like 1	protein-coding
mm_27151.1	chr3	33082846	33082868	-	1	NA	5' UTR (NM_021483, exon 1 of 15)	5' UTR (NM_021483, exon 1 of 15)	203	NM_021483	58869	Mm.151332	NM_021483	ENSMUSG00000027674	Pex5l	1700016J08Rik|PXR2|Pex2|TRIP8b|pex5Rp	peroxisomal biogenesis factor 5-like	protein-coding
mm_80908.1	chr9	100643573	100643601	+	1	NA	promoter-TSS (NM_009282)	promoter-TSS (NM_009282)	-36	NM_009282	20842	Mm.42135	NM_009282	ENSMUSG00000037286	Stag1	AU045003|SA-1|Scc3	stromal antigen 1	protein-coding
mm_93809.1	chr10	121297370	121297385	-	1	NA	intron (NM_029057, intron 5 of 11)	intron (NM_029057, intron 5 of 11)	13812	NM_029057	74694	Mm.233833	NM_029057	ENSMUSG00000052302	Tbc1d30	4930505D03Rik	TBC1 domain family, member 30	protein-coding
mm_144029.1	chr17	90037142	90037164	-	1	NA	exon (NM_001347419, exon 3 of 3)	exon (NM_001347419, exon 3 of 3)	51215	NM_001346962	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_56424.1	chr6	97253176	97253214	-	1	NA	promoter-TSS (NM_001081157)	promoter-TSS (NM_001081157)	-415	NM_001081157	320502	Mm.68163	NM_001081157	ENSMUSG00000044086	Lmod3	5430424A14Rik	leiomodin 3 (fetal)	protein-coding
mm_16907.1	chr2	13491954	13491958	-	1	NA	promoter-TSS (NM_001081084)	promoter-TSS (NM_001081084)	-80	NM_001081084	65969	Mm.313915	NM_001081084	ENSMUSG00000026726	Cubn	AA408369|AL022750|D2Wsu88e	cubilin (intrinsic factor-cobalamin receptor)	protein-coding
mm_117572.1	chr13	85289325	85289406	-	1	NA	5' UTR (NM_145452, exon 1 of 25)	5' UTR (NM_145452, exon 1 of 25)	121	NM_145452	218397	Mm.259653	NM_145452	ENSMUSG00000021549	Rasa1	Gap|RasGAP|Rasa	RAS p21 protein activator 1	protein-coding
mm_156143.1	chrX	129753568	129753580	+	1	NA	intron (NM_172493, intron 1 of 26)	B4|SINE|B4	3832	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diaph2	Dia3|Diap2|Drf2|E430022I22Rik	diaphanous related formin 2	protein-coding
mm_162638.1	chr1	191396092	191396127	-	1	NA	intron (NM_144880, intron 1 of 12)	CpG	932	NM_144880	226849	Mm.205569	NM_144880	ENSMUSG00000026626	Ppp2r5a	PR61alpha	protein phosphatase 2, regulatory subunit B', alpha	protein-coding
mm_123731.1	chr14	70173908	70173910	-	1	NA	intron (NM_145978, intron 3 of 9)	intron (NM_145978, intron 3 of 9)	2906	NM_001253736	213019	Mm.283968	NM_145978	ENSMUSG00000022090	Pdlim2	4732462F18Rik|Slim	PDZ and LIM domain 2	protein-coding
mm_165465.1	chr2	162392392	162392393	+	1	NA	intron (NR_040617, intron 2 of 2)	intron (NR_040617, intron 2 of 2)	1579	NR_040617	77645	Mm.447752	NR_040617	ENSMUSG00000084919	Ptprtos	C330008G21Rik	protein tyrosine phosphatase, receptor type T, opposite strand	ncRNA
mm_161905.1	chr18	60501952	60501952	-	1	NA	promoter-TSS (NM_134133)	promoter-TSS (NM_134133)	31	NM_134133	106878	Mm.273197	NM_134133	ENSMUSG00000038059	Smim3	2010002N04Rik|AI195350|AW561905|Nid67|cI-41	small integral membrane protein 3	protein-coding
mm_8567.1	chr1	155417367	155417386	-	1	NA	promoter-TSS (NM_011273)	promoter-TSS (NM_011273)	68	NM_011273	19775	Mm.266215	NM_011273	ENSMUSG00000026469	Xpr1	Rmc-1|Rmc1|Sxv|Syg1|XR	xenotropic and polytropic retrovirus receptor 1	protein-coding
mm_168883.1	chr12	44483084	44483086	+	1	NA	intron (NM_001146031, intron 3 of 27)	intron (NM_001146031, intron 3 of 27)	154200	NM_001146031	319504	Mm.208439	NM_176930	ENSMUSG00000020598	Nrcam	Bravo|C030017F07Rik|C130076O07Rik|mKIAA0343	neuronal cell adhesion molecule	protein-coding
mm_68631.1	chr7	118150617	118150620	-	1	NA	intron (NM_001031814, intron 50 of 62)	MYSERV16_I-int|LTR|ERVK	-20993	NM_019419	54208	Mm.29924	NM_019419	ENSMUSG00000030654	Arl6ip1	AIP-6|AL022945|ARMER|AU042858|Aip-1|Arl6ip|C85138|mKIAA0069	ADP-ribosylation factor-like 6 interacting protein 1	protein-coding
mm_4681.1	chr1	180568965	180569010	+	1	NA	promoter-TSS (NM_007415)	promoter-TSS (NM_007415)	12	NM_007415	11545	Mm.277779	NM_007415	ENSMUSG00000026496	Parp1	5830444G22Rik|AI893648|ARTD1|Adprp|Adprt1|C80510|PARP|PPOL|parp-1|sPARP-1	poly (ADP-ribose) polymerase family, member 1	protein-coding
mm_74182.1	chr8	123478145	123478181	+	1	NA	intron (NM_054070, intron 1 of 16)	CpG	301	NR_028260	114896	Mm.287475	NM_054070	ENSMUSG00000031967	Afg3l1	1700047G05Rik|3110061K15Rik	AFG3-like AAA ATPase 1	protein-coding
mm_27599.1	chr3	59146023	59146032	-	1	NA	TTS (NR_045641)	TTS (NR_045641)	7465	NM_001287119	140795	Mm.439021	NM_133200	ENSMUSG00000036381	P2ry14	A330108O13Rik|Gpr105|P2Y14	purinergic receptor P2Y, G-protein coupled, 14	protein-coding
mm_69410.1	chr7	132570159	132570174	-	1	NA	intron (NM_016978, intron 1 of 9)	intron (NM_016978, intron 1 of 9)	6232	NM_016978	18242	Mm.13694	NM_016978	ENSMUSG00000030934	Oat	AI194874|rhg	ornithine aminotransferase	protein-coding
mm_30002.1	chr3	135599000	135599018	-	1	NA	intron (NM_008689, intron 17 of 24)	C-rich|Low_complexity|Low_complexity	92538	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_124515.1	chr14	121963049	121963069	-	1	NA	intron (NM_183031, intron 1 of 1)	ID_B1|SINE|B4	2134	NM_183031	321019	Mm.265618	NM_183031	ENSMUSG00000051212	Gpr183	Ebi2	G protein-coupled receptor 183	protein-coding
mm_158804.1	chrX	167262852	167262865	-	1	NA	intron (NM_001313761, intron 1 of 2)	intron (NM_001313761, intron 1 of 2)	1471	NM_001313761	170744	Mm.196676	NM_133212	ENSMUSG00000040522	Tlr8	-	toll-like receptor 8	protein-coding
mm_123329.1	chr14	63034827	63034833	-	1	NA	intron (NM_001039566, intron 2 of 2)	intron (NM_001039566, intron 2 of 2)	3016	NM_001039566	73670	Mm.82875	NM_001039566	ENSMUSG00000075571	Defb30	2410125J01Rik|4930449O14Rik|BD-30|mBD-30	defensin beta 30	protein-coding
mm_98713.1	chr11	96314780	96314790	+	1	NA	Intergenic	CpG	-2380	NR_029784	723893		NR_029784	ENSMUSG00000065519	Mir10a	Mirn10a|miR-10a|mmu-mir-10a	microRNA 10a	ncRNA
mm_126446.1	chr15	80722519	80722522	+	1	NA	intron (NM_144812, intron 1 of 24)	intron (NM_144812, intron 1 of 24)	11207	NM_144812	213988	Mm.131328	NM_144812	ENSMUSG00000047888	Tnrc6b	2700090M07Rik|A730065C02Rik|AI848765|D230019K20Rik	trinucleotide repeat containing 6b	protein-coding
mm_95438.1	chr11	50225309	50225311	+	1	NA	promoter-TSS (NM_145926)	promoter-TSS (NM_145926)	-25	NM_145926	103534	Mm.86759	NM_145926	ENSMUSG00000036620	Mgat4b	AA407995|GnTIVb	mannoside acetylglucosaminyltransferase 4, isoenzyme B	protein-coding
mm_90156.1	chr10	118633749	118633775	+	1	NA	Intergenic	Intergenic	-77237	NR_104123	103214	Mm.30529	NR_104123		Tmevpg1	AI447422	Theiler's murine encephalomyelitis virus persistence candidate gene 1	ncRNA
mm_55306.1	chr6	54972397	54972424	-	1	NA	promoter-TSS (NM_001171007)	promoter-TSS (NM_001171007)	202	NM_172729	107607	Mm.28498	NM_172729	ENSMUSG00000038058	Nod1	C230079P11|Card4|F830007N14Rik|Nlrc1	nucleotide-binding oligomerization domain containing 1	protein-coding
mm_156351.1	chrX	139333838	139333870	+	1	NA	5' UTR (NM_011635, exon 1 of 3)	5' UTR (NM_011635, exon 1 of 3)	171	NM_011635	22037	Mm.1297	NM_011635	ENSMUSG00000051257	Trap1a	Tra-P1A	tumor rejection antigen P1A	protein-coding
mm_114018.1	chr13	52618193	52618208	+	1	NA	intron (NM_001198977, intron 3 of 13)	intron (NM_001198977, intron 3 of 13)	21318	NM_011518	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_90250.1	chr10	121586254	121586263	+	1	NA	intron (NM_019786, intron 1 of 20)	CpG	536	NM_019786	56480	Mm.34580	NM_019786	ENSMUSG00000020115	Tbk1	1200008B05Rik|AI462036|AW048562	TANK-binding kinase 1	protein-coding
mm_7957.1	chr1	133928695	133928701	-	1	NA	Intergenic	PB1D11|SINE|Alu	-7297	NM_054077	116847	Mm.214514	NM_054077	ENSMUSG00000041577	Prelp	7330409J17Rik|SLRR2A	proline arginine-rich end leucine-rich repeat	protein-coding
mm_58454.1	chr7	3331999	3332076	+	1	NA	TTS (NM_011102)	TTS (NM_011102)	-4548	NM_133189	81904	Mm.214994	NM_133189	ENSMUSG00000069806	Cacng7	-	calcium channel, voltage-dependent, gamma subunit 7	protein-coding
mm_19116.1	chr2	79985724	79985727	-	1	NA	intron (NM_001159582, intron 2 of 15)	intron (NM_001159582, intron 2 of 15)	-77326	NM_001009978	18573	Mm.40678	NM_016744	ENSMUSG00000059173	Pde1a	AI987702|AW125737	phosphodiesterase 1A, calmodulin-dependent	protein-coding
mm_32926.1	chr4	119195354	119195395	+	1	NA	promoter-TSS (NM_024462)	promoter-TSS (NM_024462)	64	NM_024462	69216	Mm.36697	NM_024462	ENSMUSG00000028643	Svbp	2410005K17Rik|AI851162|Ccdc23	small vasohibin binding protein	protein-coding
mm_79261.1	chr9	50753121	50753129	+	1	NA	promoter-TSS (NM_024441)	promoter-TSS (NM_024441)	154	NM_009964	12955	Mm.178	NM_009964	ENSMUSG00000032060	Cryab	Crya-2|Crya2|HspB5|P23	crystallin, alpha B	protein-coding
mm_100654.1	chr11	3172796	3172797	-	1	NA	intron (NM_030207, intron 6 of 32)	intron (NM_030207, intron 6 of 32)	20667	NM_030207	78887	Mm.394071	NM_030207	ENSMUSG00000023764	Sfi1	-	Sfi1 homolog, spindle assembly associated (yeast)	protein-coding
mm_92528.1	chr10	79097561	79097614	-	1	NA	promoter-TSS (NM_001004362)	promoter-TSS (NM_001004362)	13	NM_001004362	72128	Mm.297854	NM_001004362	ENSMUSG00000060301	2610008E11Rik	-	RIKEN cDNA 2610008E11 gene	protein-coding
mm_82051.1	chr9	122422121	122422128	+	1	NA	Intergenic	Intergenic	-23323	NR_045967	654800	Mm.393956	NR_045967		A730085K08Rik	-	RIKEN cDNA A730085K08 gene	ncRNA
mm_165608.1	chr3	52009207	52009221	-	1	NA	intron (NM_001004176, intron 1 of 4)	intron (NM_001004176, intron 1 of 4)	95792	NM_001004176	433586	Mm.234972	NM_001004176	ENSMUSG00000061143	Maml3	AV234550|BC049812|Mam-2|mKIAA1816	mastermind like 3 (Drosophila)	protein-coding
mm_90287.1	chr10	123360181	123360192	+	1	NA	intron (NR_045514, intron 1 of 5)	intron (NR_045514, intron 1 of 5)	96110	NM_001252387	268354	Mm.51939	NM_182807	ENSMUSG00000044071	Fam19a2	6330575M02|FAM19A2 TAFA-2|TAFA2|Tafa-2	family with sequence similarity 19, member A2	protein-coding
mm_4598.1	chr1	178406018	178406020	+	1	NA	5' UTR (NM_026626, exon 1 of 7)	5' UTR (NM_026626, exon 1 of 7)	138	NM_026626	68226	Mm.252132	NM_026626	ENSMUSG00000026495	Efcab2	1700073K01Rik|D830011E08Rik	EF-hand calcium binding domain 2	protein-coding
mm_10347.1	chr2	11678189	11678207	+	1	NA	intron (NM_008367, intron 3 of 7)	(T)n|Simple_repeat|Simple_repeat	-27095	NM_001271498	16169	Mm.200196	NM_008358	ENSMUSG00000023206	Il15ra	AA690181|IL-15RA	interleukin 15 receptor, alpha chain	protein-coding
mm_123266.1	chr14	61360305	61360319	-	1	NA	exon (NM_026598, exon 1 of 4)	exon (NM_026598, exon 1 of 4)	133	NM_026598	68177	Mm.22758	NM_026598	ENSMUSG00000021928	Ebpl	5730442K12Rik|EBRP	emopamil binding protein-like	protein-coding
mm_16410.1	chr2	180042716	180042727	+	1	NA	promoter-TSS (NM_001289476)	promoter-TSS (NM_001289476)	238	NM_178750	269397	Mm.63068	NM_178750	ENSMUSG00000039086	Ss18l1	A230053O16Rik|CREST	SS18, nBAF chromatin remodeling complex subunit like 1	protein-coding
mm_32816.1	chr4	117252011	117252057	+	1	NA	promoter-TSS (NM_001033774)	promoter-TSS (NM_001033774)	83	NM_001285815	68777	Mm.331805	NM_026837	ENSMUSG00000048772	Tmem53	1110038M16Rik|1500001P22Rik|1700012A05Rik	transmembrane protein 53	protein-coding
mm_68618.1	chr7	117470269	117470287	-	1	NA	intron (NM_175645, intron 1 of 11)	intron (NM_175645, intron 1 of 11)	89299	NM_175645	233781	Mm.461427	NM_175645	ENSMUSG00000030657	Xylt1	8030490L12	xylosyltransferase 1	protein-coding
mm_167082.1	chr7	101144498	101144502	+	1	NA	intron (NM_199012, intron 3 of 20)	intron (NM_199012, intron 3 of 20)	35725	NM_199012	207278	Mm.263041	NM_199012	ENSMUSG00000030691	Fchsd2	BC034086|R74866|Sh3md3|mKIAA0769	FCH and double SH3 domains 2	protein-coding
mm_45901.1	chr5	88676193	88676209	-	1	NA	promoter-TSS (NM_178700)	promoter-TSS (NM_178700)	-30	NM_178700	231413	Mm.332474	NM_178700	ENSMUSG00000044221	Grsf1	BB232551|C80280|D5Wsu31e	G-rich RNA sequence binding factor 1	protein-coding
mm_16409.1	chr2	180042699	180042707	+	1	NA	promoter-TSS (NM_001289476)	promoter-TSS (NM_001289476)	220	NM_178750	269397	Mm.63068	NM_178750	ENSMUSG00000039086	Ss18l1	A230053O16Rik|CREST	SS18, nBAF chromatin remodeling complex subunit like 1	protein-coding
mm_119502.1	chr14	47380315	47380331	+	1	NA	exon (NM_010705, exon 3 of 6)	exon (NM_010705, exon 3 of 6)	6463	NM_001145953	16854	Mm.248615	NM_010705	ENSMUSG00000050335	Lgals3	GBP|L-34|Mac-2|gal3	lectin, galactose binding, soluble 3	protein-coding
mm_1509.1	chr1	72346257	72346270	+	1	NA	exon (NM_009533, exon 14 of 21)	exon (NM_009533, exon 14 of 21)	38842	NM_009533	22596	Mm.246952	NM_009533	ENSMUSG00000026187	Xrcc5	AI314015|Ku80|Ku86	X-ray repair complementing defective repair in Chinese hamster cells 5	protein-coding
mm_45193.1	chr5	52190042	52190086	-	1	NA	promoter-TSS (NR_015537)	promoter-TSS (NR_015537)	482	NR_104311	13204	Mm.993	NM_007839	ENSMUSG00000029169	Dhx15	DBP1|DEAH9|Ddx15|HRH2|mDEAH9	DEAH (Asp-Glu-Ala-His) box polypeptide 15	protein-coding
mm_152747.1	chr19	19100271	19100273	-	1	NA	intron (NM_001043354, intron 1 of 9)	intron (NM_001043354, intron 1 of 9)	10924	NM_001043354	225998	Mm.234641	NM_146095	ENSMUSG00000036192	Rorb	Nr1f2|RZR-beta|RZRB|Rorbeta|hstp	RAR-related orphan receptor beta	protein-coding
mm_114309.1	chr13	59731886	59731911	+	1	NA	promoter-TSS (NM_177711)	promoter-TSS (NM_177711)	-146	NM_177711	238663	Mm.444776	NM_177711	ENSMUSG00000043986	Spata31d1d	4932411G14Rik|Fam75d1d	spermatogenesis associated 31 subfamily D, member 1D	protein-coding
mm_144726.1	chr18	35220850	35220852	+	1	NA	intron (NM_009818, intron 7 of 17)	PB1D9|SINE|Alu	-5827	NM_178005	107065	Mm.39900	NM_178005	ENSMUSG00000071862	Lrrtm2	AI851755|BB129880|C630011A14Rik|mKIAA0416	leucine rich repeat transmembrane neuronal 2	protein-coding
mm_108651.1	chr12	86241849	86241936	+	1	NA	promoter-TSS (NM_027405)	promoter-TSS (NM_027405)	34	NM_001324488	70373	Mm.252967	NM_027405	ENSMUSG00000021254	Gpatch2l	1700020O03Rik|4732487G21Rik|A630090I05Rik|Kiaa1152	G patch domain containing 2 like	protein-coding
mm_38849.1	chr4	149307715	149307738	-	1	NA	promoter-TSS (NM_001290995)	promoter-TSS (NM_001290995)	7	NM_001290995	16561	Mm.402393	NM_008441	ENSMUSG00000063077	Kif1b	A530096N05Rik|AI448212|AI506502|D4Mil1e|KIF1Bp130|KIF1Bp204	kinesin family member 1B	protein-coding
mm_669.1	chr1	40462301	40462333	+	1	NA	3' UTR (NM_001025602, exon 11 of 11)	3' UTR (NM_001025602, exon 11 of 11)	-3235	NM_001161842	16182	Mm.253664	NM_008365	ENSMUSG00000026070	Il18r1	Il18ralpha|Il1rrp	interleukin 18 receptor 1	protein-coding
mm_156854.1	chrX	164401407	164401432	+	1	NA	TTS (NM_001308489)	TTS (NM_001308489)	-18368	NM_011081	18700	Mm.3781	NM_011081	ENSMUSG00000031381	Piga	AI194334|Pig-a	phosphatidylinositol glycan anchor biosynthesis, class A	protein-coding
mm_9063.1	chr1	167466980	167466987	-	1	NA	promoter-TSS (NM_001013382)	promoter-TSS (NM_001013382)	-203	NM_001013382	240899	Mm.159799	NM_001013382	ENSMUSG00000040485	Lrrc52	4930413P14Rik	leucine rich repeat containing 52	protein-coding
mm_165573.1	chr3	20155057	20155072	-	1	NA	promoter-TSS (NM_013755)	promoter-TSS (NM_013755)	52	NM_013755	27357	Mm.6375	NM_013755	ENSMUSG00000019528	Gyg	AU017667|Gyg1	glycogenin	protein-coding
mm_139387.1	chr17	52163222	52163232	+	1	NA	Intergenic	Intergenic	280500	NR_045095	100504169	Mm.417731	NR_045095		Gm20098	-	predicted gene, 20098	ncRNA
mm_82208.1	chr9	124103747	124103783	+	1	NA	intron (NM_009915, intron 1 of 2)	intron (NM_009915, intron 1 of 2)	1582	NM_009915	12772	Mm.6272	NM_009915	ENSMUSG00000049103	Ccr2	Cc-ckr-2|Ccr2a|Ccr2b|Ckr2|Ckr2a|Ckr2b|Cmkbr2|mJe-r	chemokine (C-C motif) receptor 2	protein-coding
mm_129362.1	chr15	77967593	77967599	-	1	NA	intron (NM_018749, intron 3 of 14)	MER5A1|DNA|hAT-Charlie	3228	NM_018749	55944	Mm.3955	NM_018749	ENSMUSG00000016554	Eif3d	66/67kDa|AA407891|Eif3s7|eIF3p66	eukaryotic translation initiation factor 3, subunit D	protein-coding
mm_60828.1	chr7	45707813	45707829	+	1	NA	intron (NM_016974, intron 2 of 3)	intron (NM_016974, intron 2 of 3)	2574	NM_016974	13170	Mm.24222	NM_016974	ENSMUSG00000059824	Dbp	-	D site albumin promoter binding protein	protein-coding
mm_31207.1	chr4	43875568	43875582	+	1	NA	promoter-TSS (NM_016678)	promoter-TSS (NM_016678)	45	NM_016678	53614	Mm.331573	NM_016678	ENSMUSG00000028476	Reck	St15|mRECK	reversion-inducing-cysteine-rich protein with kazal motifs	protein-coding
mm_159117.1	chr2	60357589	60357589	-	1	NA	intron (NM_013825, intron 5 of 34)	intron (NM_013825, intron 5 of 34)	25642	NM_013825	17076	Mm.2074	NM_013825	ENSMUSG00000026980	Ly75	CD205|DEC-205|DEC205	lymphocyte antigen 75	protein-coding
mm_94055.1	chr10	128211767	128211775	-	1	NA	promoter-TSS (NM_025716)	promoter-TSS (NM_025716)	23	NM_025716	66701	Mm.29694	NM_025716	ENSMUSG00000051346	Spryd4	4633402N23Rik|AA114801	SPRY domain containing 4	protein-coding
mm_92120.1	chr10	63339024	63339042	-	1	NA	promoter-TSS (NM_001159589)	promoter-TSS (NM_001159589)	2	NM_019812	93759	Mm.351459	NM_019812	ENSMUSG00000020063	Sirt1	AA673258|SIR2L1|Sir2|Sir2a|Sir2alpha	sirtuin 1	protein-coding
mm_121178.1	chr14	103048881	103048905	+	1	NA	intron (NM_008392, intron 1 of 4)	intron (NM_008392, intron 1 of 4)	1881	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_137987.1	chr17	33629334	33629344	+	1	NA	intron (NM_026712, intron 1 of 5)	intron (NM_026712, intron 1 of 5)	247	NM_026712	328801	Mm.181488	NM_026712	ENSMUSG00000073423	Zfp414	0610030H11Rik|Znf414	zinc finger protein 414	protein-coding
mm_99425.1	chr11	102393552	102393562	+	1	NA	5' UTR (NM_001252347, exon 1 of 11)	5' UTR (NM_001252347, exon 1 of 11)	154	NM_001252347	51799	Mm.2560	NM_016759	ENSMUSG00000006575	Rundc3a	RPIP-8|Rap2ip|Rpip8	RUN domain containing 3A	protein-coding
mm_11991.1	chr2	55451700	55451703	+	1	NA	intron (NM_008426, intron 3 of 3)	intron (NM_008426, intron 3 of 3)	15731	NM_008426	16519	Mm.5127	NM_008426	ENSMUSG00000026824	Kcnj3	GIRK-1|GIRK1|Kcnf3|Kir3.1	potassium inwardly-rectifying channel, subfamily J, member 3	protein-coding
mm_51776.1	chr6	88095650	88095663	+	1	NA	exon (NM_133933, exon 5 of 10)	exon (NM_133933, exon 5 of 10)	8602	NR_105795	102465196		NR_105795	ENSMUSG00000099095	Mir6376	Gm27778|mmu-mir-6376	microRNA 6376	ncRNA
mm_139413.1	chr17	52757092	52757093	+	1	NA	intron (NM_001031811, intron 3 of 15)	intron (NM_001031811, intron 3 of 15)	154383	NM_001031811	211468	Mm.399068	NM_001031811	ENSMUSG00000035580	Kcnh8	C130090D05Rik|ELK|ELK1|ELK3|Kv12.1	potassium voltage-gated channel, subfamily H (eag-related), member 8	protein-coding
mm_67916.1	chr7	99828345	99828384	-	1	NA	promoter-TSS (NM_016720)	promoter-TSS (NM_016720)	53	NM_016720	50877	Mm.103703	NM_016720	ENSMUSG00000035239	Neu3	-	neuraminidase 3	protein-coding
mm_105776.1	chr11	109722019	109722057	-	1	NA	5' UTR (NM_153782, exon 1 of 11)	5' UTR (NM_153782, exon 1 of 11)	218	NM_153782	208659	Mm.208662	NM_153782	ENSMUSG00000020614	Fam20a	AI606893	family with sequence similarity 20, member A	protein-coding
mm_165797.1	chr3	141464696	141464702	+	1	NA	promoter-TSS (NM_009472)	promoter-TSS (NM_009472)	-865	NM_009472	22253	Mm.24430	NM_009472	ENSMUSG00000059921	Unc5c	B130051O18Rik|Unc5h3|rcm	unc-5 netrin receptor C	protein-coding
mm_161233.1	chr13	93186414	93186414	-	1	NA	exon (NM_133905, exon 2 of 15)	exon (NM_133905, exon 2 of 15)	5869	NM_133905	100715	Mm.242865	NM_133905	ENSMUSG00000042167	Papd4	8030446C20Rik|AI649009|GLD-2|Gld2	PAP associated domain containing 4	protein-coding
mm_135564.1	chr16	50070879	50070904	-	1	NA	intron (NR_045935, intron 1 of 3)	intron (NR_045935, intron 1 of 3)	1961	NR_045935	224180	Mm.146439	NM_175010		Gm4827	B130050K08|EG224180	predicted gene 4827	ncRNA
mm_146712.1	chr18	14683313	14683331	-	1	NA	promoter-TSS (NM_001161371)	promoter-TSS (NM_001161371)	-408	NM_001161370	268996	Mm.31761	NM_009280	ENSMUSG00000037013	Ss18	D130059H17|Ssxt|Syt	SS18, nBAF chromatin remodeling complex subunit	protein-coding
mm_5600.1	chr1	39567618	39567623	-	1	NA	intron (NM_001033135, intron 1 of 6)	intron (NM_001033135, intron 1 of 6)	9727	NM_001033135	67702	Mm.28614	NM_001033135	ENSMUSG00000048234	Rnf149	1600023E10Rik|AV037261|C76763|Gm15832|Greul4|OTTMUSG00000026591	ring finger protein 149	protein-coding
mm_157456.1	chrX	43428971	43428985	-	1	NA	Intergenic	Intergenic	-154194	NM_011855	23963	Mm.327698	NM_011855	ENSMUSG00000016150	Tenm1	Odz1|Odz2|TCAP-1|Ten-m1|ten-1	teneurin transmembrane protein 1	protein-coding
mm_153015.1	chr19	30625486	30625496	-	1	NA	intron (NM_011160, intron 9 of 17)	intron (NM_011160, intron 9 of 17)	-75995	NM_010051	13380	Mm.214717	NM_010051	ENSMUSG00000024868	Dkk1	mdkk-1	dickkopf WNT signaling pathway inhibitor 1	protein-coding
mm_98292.1	chr11	89066434	89066451	+	1	NA	intron (NR_110336, intron 2 of 3)	intron (NR_110336, intron 2 of 3)	5691	NR_110336	414094	Mm.124287	NM_001001497		Dgkeos	A930013B10Rik	diacylglycerol kinase, epsilon, opposite strand	ncRNA
mm_40648.1	chr5	65107552	65107582	+	1	NA	promoter-TSS (NM_001347355)	promoter-TSS (NM_001347355)	-1	NM_001347355	71778	Mm.10281	NM_175174	ENSMUSG00000054920	Klhl5	1300013C10Rik	kelch-like 5	protein-coding
mm_6340.1	chr1	71632106	71632145	-	1	NA	exon (NM_001276413, exon 13 of 44)	exon (NM_001276413, exon 13 of 44)	21109	NM_010233	14268	Mm.193099	NM_010233	ENSMUSG00000026193	Fn1	E330027I09|Fn|Fn-1	fibronectin 1	protein-coding
mm_11439.1	chr2	32017512	32017530	+	1	NA	intron (NM_172268, intron 22 of 35)	intron (NM_172268, intron 22 of 35)	-33425	NR_106135	102466844		NR_106135	ENSMUSG00000099075	Mir7674	Gm27563|mmu-mir-7674	microRNA 7674	ncRNA
mm_122621.1	chr14	51145548	51145563	-	1	NA	exon (NM_011271, exon 2 of 2)	exon (NM_011271, exon 2 of 2)	1212	NM_011271	19752	Mm.235538	NM_011271	ENSMUSG00000035896	Rnase1	AI574248|Rib-1|Rib1	ribonuclease, RNase A family, 1 (pancreatic)	protein-coding
mm_143312.1	chr17	66101467	66101534	-	1	NA	promoter-TSS (NM_028388)	promoter-TSS (NM_028388)	59	NM_001278415	72900	Mm.2206	NM_028388	ENSMUSG00000024099	Ndufv2	2900010C23Rik	NADH dehydrogenase (ubiquinone) flavoprotein 2	protein-coding
mm_71121.1	chr8	36188586	36188635	+	1	NA	Intergenic	Intergenic	60906	NM_001081150	244421	Mm.324032	NM_001081150	ENSMUSG00000039633	Lonrf1	-	LON peptidase N-terminal domain and ring finger 1	protein-coding
mm_129427.1	chr15	78468659	78468681	-	1	NA	promoter-TSS (NM_027902)	promoter-TSS (NM_027902)	-36	NM_027902	71753	Mm.34056	NM_027902	ENSMUSG00000016942	Tmprss6	1300008A22Rik	transmembrane serine protease 6	protein-coding
mm_78030.1	chr9	13806697	13806699	+	1	NA	TTS (NM_023858)	TTS (NM_023858)	20355	NR_037622	74360	Mm.157212	NM_026665	ENSMUSG00000031922	Cep57	3110002L15Rik|4921510P06Rik|4931428M20Rik|AI467480|Tsp57|mKIAA0092	centrosomal protein 57	protein-coding
mm_55047.1	chr6	49038375	49038379	-	1	NA	intron (NM_053110, intron 1 of 10)	B1_Mur2|SINE|Alu	1859	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_101333.1	chr11	23306303	23306316	-	1	NA	promoter-TSS (NM_001190401)	promoter-TSS (NM_001190401)	-586	NM_001190401	17847	Mm.119155	NM_001190401	ENSMUSG00000056342	Usp34	A530081C03Rik|Murr2	ubiquitin specific peptidase 34	protein-coding
mm_62132.1	chr7	97081679	97081699	+	1	NA	promoter-TSS (NM_010248)	promoter-TSS (NM_010248)	-62	NM_001162477	14389	Mm.42033	NM_010248	ENSMUSG00000004508	Gab2	AI463667|D130058I17Rik|p97	growth factor receptor bound protein 2-associated protein 2	protein-coding
mm_91493.1	chr10	37135857	37135874	-	1	NA	3' UTR (NM_008538, exon 2 of 2)	3' UTR (NM_008538, exon 2 of 2)	3061	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_127305.1	chr15	100227872	100227878	+	1	NA	promoter-TSS (NM_007497)	promoter-TSS (NM_007497)	16	NM_007497	11908	Mm.676	NM_007497	ENSMUSG00000023027	Atf1	-	activating transcription factor 1	protein-coding
mm_151210.1	chr19	53618892	53618896	+	1	NA	intron (NM_007790, intron 7 of 28)	intron (NM_007790, intron 7 of 28)	18498	NM_007790	13006	Mm.14910	NM_007790	ENSMUSG00000024974	Smc3	Bamacan|Cspg6|HCAP|Mmip1|SMC-3|SmcD	structural maintenance of chromosomes 3	protein-coding
mm_12765.1	chr2	79266039	79266044	+	1	NA	intron (NM_010576, intron 2 of 27)	(T)n|Simple_repeat|Simple_repeat	10615	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D|Itga4B	integrin alpha 4	protein-coding
mm_138175.1	chr17	34264906	34264930	+	1	NA	exon (NM_207105, exon 2 of 6)	exon (NM_207105, exon 2 of 6)	1691	NM_207105	14961	Mm.254067	NM_207105	ENSMUSG00000073421	H2-Ab1	AI845868|Abeta|H-2Ab|H2-Ab|I-Abeta|IAb|Ia-2|Ia2|Rmcs1	histocompatibility 2, class II antigen A, beta 1	protein-coding
mm_156698.1	chrX	159488813	159488815	+	1	NA	intron (NM_001313753, intron 6 of 12)	intron (NM_001313753, intron 6 of 12)	29689	NM_001313753	78283	Mm.160079	NM_001081124	ENSMUSG00000041020	Map7d2	1600028E09Rik|2900002G04Rik|5330432J06Rik|C030036K04Rik|Mtap7d2	MAP7 domain containing 2	protein-coding
mm_97387.1	chr11	77765653	77765665	+	1	NA	Intergenic	Intergenic	-11576	NM_001291213	360013	Mm.341248	NM_011586	ENSMUSG00000000631	Myo18a	MAJN|MyoPDZ|MysPDZ|SP-R210	myosin XVIIIA	protein-coding
mm_86035.1	chr9	113955907	113955929	-	1	NA	intron (NM_013699, intron 4 of 15)	intron (NM_013699, intron 4 of 15)	24984	NM_013699	22221	Mm.28052	NM_013699	ENSMUSG00000009741	Ubp1	Cp2b|LBP-1a|LBP-1b|NF2d9	upstream binding protein 1	protein-coding
mm_142652.1	chr17	47611175	47611178	-	1	NA	promoter-TSS (NM_020048)	promoter-TSS (NM_020048)	316	NM_016859	53414	Mm.472101	NM_016859	ENSMUSG00000023988	Bysl	Bys|Enp1	bystin-like	protein-coding
mm_116276.1	chr13	34874457	34874469	-	1	NA	Intergenic	CpG	-1031	NM_013830	19134	Mm.10027	NM_013830	ENSMUSG00000021413	Prpf4b	2610037H07|Prp4|Prp4k|Prpk|cbp143	pre-mRNA processing factor 4B	protein-coding
mm_70501.1	chr8	12866647	12866661	+	1	NA	non-coding (NR_121603, exon 30 of 30)	non-coding (NR_121603, exon 30 of 30)	-34735	NR_045775	100504249	Mm.441494	NR_045775	ENSMUSG00000084780	Gm15350	OTTMUSG00000020611	predicted gene 15350	ncRNA
mm_40713.1	chr5	65910661	65910677	+	1	NA	Intergenic	Intergenic	47100	NM_001081105	74734	Mm.20323	NM_001081105	ENSMUSG00000029204	Rhoh	5830400A04Rik|AU019774|Arhh	ras homolog family member H	protein-coding
mm_36484.1	chr4	83003062	83003065	-	1	NA	intron (NM_177863, intron 6 of 35)	intron (NM_177863, intron 6 of 35)	18039	NM_177863	329872	Mm.242337	NM_177863	ENSMUSG00000059049	Frem1	BC037594|D430009N09|D630008K06|crf11|eye<m02Jus>|eyes2|heb|qbrick	Fras1 related extracellular matrix protein 1	protein-coding
mm_18520.1	chr2	62800729	62800733	-	1	NA	intron (NM_133207, intron 6 of 15)	intron (NM_133207, intron 6 of 15)	136404	NM_145523	227960	Mm.219877	NM_145523	ENSMUSG00000026893	Gca	5133401E04Rik|AI573844	grancalcin	protein-coding
mm_5609.1	chr1	39621198	39621209	-	1	NA	3' UTR (NM_170597, exon 4 of 4)	3' UTR (NM_170597, exon 4 of 4)	29979	NM_170597	263764	Mm.122091	NM_170597	ENSMUSG00000050967	Creg2	A830098L22Rik	cellular repressor of E1A-stimulated genes 2	protein-coding
mm_119007.1	chr14	29021435	29021444	+	1	NA	intron (NM_176920, intron 1 of 2)	intron (NM_176920, intron 1 of 2)	3231	NM_176920	319476	Mm.95780	NM_176920	ENSMUSG00000045776	Lrtm1	A930016D02Rik	leucine-rich repeats and transmembrane domains 1	protein-coding
mm_61635.1	chr7	80269633	80269726	+	1	NA	promoter-TSS (NM_178070)	promoter-TSS (NM_178070)	24	NM_178070	233405	Mm.322870	NM_178070	ENSMUSG00000030534	Vps33b	-	vacuolar protein sorting 33B	protein-coding
mm_24871.1	chr3	95972458	95972479	+	1	NA	Intergenic	Intergenic	-13042	NR_045872	668224	Mm.357766	NR_045872		Gm9054	EG668224	predicted gene 9054	ncRNA
mm_163942.1	chr14	51145539	51145544	-	1	NA	exon (NM_011271, exon 2 of 2)	exon (NM_011271, exon 2 of 2)	1226	NM_011271	19752	Mm.235538	NM_011271	ENSMUSG00000035896	Rnase1	AI574248|Rib-1|Rib1	ribonuclease, RNase A family, 1 (pancreatic)	protein-coding
mm_55416.1	chr6	65125560	65125582	-	1	NA	intron (NM_019455, intron 4 of 5)	intron (NM_019455, intron 4 of 5)	19159	NM_019455	54486	Mm.410688	NM_019455	ENSMUSG00000029919	Hpgds	H-PGDS|Ptgds2	hematopoietic prostaglandin D synthase	protein-coding
mm_9054.1	chr1	167331260	167331306	-	1	NA	3' UTR (NM_001039483, exon 7 of 7)	3' UTR (NM_001039483, exon 7 of 7)	-18708	NM_019993	56752	Mm.292539	NM_019993	ENSMUSG00000026687	Aldh9a1	AA139417|Abaldh|ESTM40|TMABA-DH|Tmabadh	aldehyde dehydrogenase 9, subfamily A1	protein-coding
mm_109301.1	chr12	109560446	109560464	+	1	NA	non-coding (NR_003633, exon 5 of 5)	non-coding (NR_003633, exon 5 of 5)	-3237	NR_030427	791079		NR_030427	ENSMUSG00000076451	Mir770	Mirn770|mir-770|mmu-mir-770	microRNA 770	ncRNA
mm_158661.1	chrX	157415306	157415318	-	1	NA	promoter-TSS (NM_011077)	promoter-TSS (NM_011077)	-26	NM_011077	18675	Mm.2529	NM_011077	ENSMUSG00000057457	Phex	Gy|HPDR|HPDR1|Hyp|PEX	phosphate regulating endopeptidase homolog, X-linked	protein-coding
mm_102715.1	chr11	67114789	67114793	-	1	NA	non-coding (NR_038055, exon 4 of 5)	non-coding (NR_038055, exon 4 of 5)	5289	NR_038055	74184	Mm.162554	NR_038055	ENSMUSG00000087410	2310065F04Rik	linc-Myh	RIKEN cDNA 2310065F04 gene	ncRNA
mm_126256.1	chr15	79081580	79081625	+	1	NA	exon (NM_145139, exon 6 of 13)	exon (NM_145139, exon 6 of 13)	6379	NM_145139	223691	Mm.206404	NM_145139	ENSMUSG00000033047	Eif3l	0610011H21Rik|D15N1e|Eif3eip|Eif3ip|Eif3s6ip|HSP-66Y|PAF67	eukaryotic translation initiation factor 3, subunit L	protein-coding
mm_16578.1	chr2	3511213	3511243	-	1	NA	non-coding (NR_103465, exon 2 of 5)	non-coding (NR_103465, exon 2 of 5)	1586	NR_103465	50497	Mm.89341	NM_015765	ENSMUSG00000051396	Hspa14	70kDa|HSP70L1|Hsp70-4|NST-1|hsr.1	heat shock protein 14	protein-coding
mm_127261.1	chr15	99710469	99710480	+	1	NA	intron (NM_031842, intron 10 of 12)	intron (NM_031842, intron 10 of 12)	-7119	NM_010271	14555	Mm.252391	NM_010271	ENSMUSG00000023019	Gpd1	AI747587|Gdc-1|Gdc1|mKIAA4010	glycerol-3-phosphate dehydrogenase 1 (soluble)	protein-coding
mm_161988.1	chr19	31909001	31909001	+	1	NA	intron (NM_001081074, intron 3 of 11)	intron (NM_001081074, intron 3 of 11)	40240	NM_001081074	69865	Mm.87538	NM_001081074	ENSMUSG00000052595	A1cf	1810073H04Rik|ACF64|ACF65|ASP|Acf|MCM|MerCreMer|Tg(Myh6-cre/Esr1*)1Jmk|mer	APOBEC1 complementation factor	protein-coding
mm_93395.1	chr10	107494784	107494795	-	1	NA	promoter-TSS (NM_008657)	promoter-TSS (NM_008657)	-60	NM_008657	17878	Mm.11	NM_008657	ENSMUSG00000035923	Myf6	MRF4|bHLHc4|herculin	myogenic factor 6	protein-coding
mm_3818.1	chr1	159232300	159232320	+	1	NA	promoter-TSS (NM_011931)	promoter-TSS (NM_011931)	-16	NM_011931	26374	Mm.328135	NM_011931	ENSMUSG00000040782	Rfwd2	AI316802|C80879|Cop1	ring finger and WD repeat domain 2	protein-coding
mm_151071.1	chr19	47513279	47513287	+	1	NA	non-coding (NR_045322, exon 2 of 3)	non-coding (NR_045322, exon 2 of 3)	301	NR_045322	100503104	Mm.442735	NR_045322	ENSMUSG00000097990	Gm19557	-	predicted gene, 19557	ncRNA
mm_2555.1	chr1	110238623	110238652	+	1	NA	Intergenic	RMER17A|LTR|ERVK	254914	NM_172853	241201	Mm.213407	NM_172853	ENSMUSG00000026312	Cdh7	9330156F07Rik|CDH7L1	cadherin 7, type 2	protein-coding
mm_131754.1	chr16	22546955	22546990	+	1	NA	intron (NM_001346673, intron 19 of 23)	intron (NM_001346673, intron 19 of 23)	-14788	NR_106170	102465887		NR_106170	ENSMUSG00000099071	Mir8095	Gm27566|mmu-mir-8095	microRNA 8095	ncRNA
mm_42070.1	chr5	110099790	110099801	+	1	NA	promoter-TSS (NM_001281812)	promoter-TSS (NM_001281812)	-174	NM_207279	403178	Mm.297057	NM_207279	ENSMUSG00000064247	Plcxd1	A330045H12Rik|Gm576	phosphatidylinositol-specific phospholipase C, X domain containing 1	protein-coding
mm_122184.1	chr14	31619035	31619043	-	1	NA	exon (NM_019975, exon 12 of 17)	exon (NM_019975, exon 12 of 17)	21926	NM_019975	56794	Mm.38887	NM_019975	ENSMUSG00000021884	Hacl1	1600020H07Rik|Hpcl|Phyh2	2-hydroxyacyl-CoA lyase 1	protein-coding
mm_4430.1	chr1	172506573	172506584	+	1	NA	exon (NM_178598, exon 5 of 5)	exon (NM_178598, exon 5 of 5)	6332	NM_178598	21346	Mm.271711	NM_178598	ENSMUSG00000026547	Tagln2	2700094C18Rik|SM22beta|Sm22B|Sm22a	transgelin 2	protein-coding
mm_59383.1	chr7	26187726	26187730	+	1	NA	exon (NM_010000, exon 4 of 9)	exon (NM_010000, exon 4 of 9)	14319	NM_010000	13094	Mm.14413	NM_010000	ENSMUSG00000040660	Cyp2b9	Cyp2b	cytochrome P450, family 2, subfamily b, polypeptide 9	protein-coding
mm_137943.1	chr17	32686094	32686106	+	1	NA	exon (NM_134127, exon 2 of 13)	exon (NM_134127, exon 2 of 13)	441	NM_134127	106648	Mm.26539	NM_134127	ENSMUSG00000073424	Cyp4f15	AI787289|Cyp4f-15	cytochrome P450, family 4, subfamily f, polypeptide 15	protein-coding
mm_21728.1	chr2	164743100	164743108	-	1	NA	5' UTR (NM_027961, exon 1 of 4)	5' UTR (NM_027961, exon 1 of 4)	163	NM_027961	71856	Mm.330770	NM_027961	ENSMUSG00000076434	Wfdc3	1700015L13Rik|1700127F16Rik	WAP four-disulfide core domain 3	protein-coding
mm_130454.1	chr15	98567510	98567516	-	1	NA	exon (NM_009833, exon 1 of 9)	exon (NM_009833, exon 1 of 9)	123	NM_009833	12455	Mm.29941	NM_009833	ENSMUSG00000011960	Ccnt1	2810478G24Rik|AI115585|CycT1	cyclin T1	protein-coding
mm_86422.1	chr10	3740454	3740486	+	1	NA	promoter-TSS (NM_001159942)	promoter-TSS (NM_001159942)	93	NM_001159942	213783	Mm.150831	NM_001033253	ENSMUSG00000040624	Plekhg1	D10Ertd733e|Gm521|mKIAA1209	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	protein-coding
mm_72879.1	chr8	88950235	88950249	+	1	NA	Intergenic	Intergenic	-74493	NR_106190	102465899		NR_106190	ENSMUSG00000099078	Mir8110	Gm27571|mmu-mir-8110	microRNA 8110	ncRNA
mm_38112.1	chr4	134535199	134535267	-	1	NA	promoter-TSS (NM_001256112)	promoter-TSS (NM_001256112)	35	NM_001256112	76824	Mm.30153	NM_029759	ENSMUSG00000046671	Mtfr1l	2410166I05Rik|AI480750|Fam54b	mitochondrial fission regulator 1-like	protein-coding
mm_114283.1	chr13	58402234	58402261	+	1	NA	promoter-TSS (NR_031761)	promoter-TSS (NR_031761)	-1	NR_031761	74386	Mm.85289	NM_028904	ENSMUSG00000035367	Rmi1	4932432N11Rik|C79893	RecQ mediated genome instability 1	protein-coding
mm_127002.1	chr15	95790923	95790933	+	1	NA	promoter-TSS (NM_001253813)	promoter-TSS (NM_001253813)	85	NM_001253813	105722	Mm.38087	NM_175344	ENSMUSG00000064210	Ano6	2900059G15Rik|AA407480|AW554778|F730003B03Rik|Tmem16f	anoctamin 6	protein-coding
mm_43561.1	chr5	137629170	137629202	+	1	NA	promoter-TSS (NM_146164)	promoter-TSS (NM_146164)	63	NR_033148	100316903	Mm.200763	NR_033148		Gm20605	Lrch4-sap25	predicted gene 20605	ncRNA
mm_143184.1	chr17	57483522	57483525	-	1	NA	TTS (NM_010130)	TTS (NM_010130)	61791	NM_001104591	224916	Mm.469889	NM_001104591	ENSMUSG00000090655	Vmn2r120	EG224916	vomeronasal 2, receptor 120	protein-coding
mm_74703.1	chr8	16815687	16815689	-	1	NA	intron (NM_053171, intron 3 of 69)	B4A|SINE|B4	-646850	NR_037214	100526464		NR_037214	ENSMUSG00000093142	Mir3106	mir-3106|mmu-mir-3106	microRNA 3106	ncRNA
mm_8949.1	chr1	164441559	164441576	-	1	NA	exon (NM_009721, exon 4 of 6)	exon (NM_009721, exon 4 of 6)	16788	NM_009721	11931	Mm.4550	NM_009721	ENSMUSG00000026576	Atp1b1	Atp4b|Atpb|Atpb-1|NKbeta1	ATPase, Na+/K+ transporting, beta 1 polypeptide	protein-coding
mm_160243.1	chr7	104596962	104596962	-	1	NA	exon (NM_146820, exon 1 of 1)	exon (NM_146820, exon 1 of 1)	217	NM_146820	258817	Mm.377706	NM_146820	ENSMUSG00000051182	Olfr655	MOR38-1	olfactory receptor 655	protein-coding
mm_168443.1	chr11	40570289	40570308	-	1	NA	Intergenic	Intergenic	122384	NM_134017	108645	Mm.293771	NM_134017	ENSMUSG00000042032	Mat2b	1110064C04Rik|2410018D16Rik|AI182287|AU022853|MAT-II|MATIIbeta|TGR	methionine adenosyltransferase II, beta	protein-coding
mm_50251.1	chr6	42416987	42416989	+	1	NA	Intergenic	Intergenic	11459	NM_199159	387512	Mm.377919	NM_199159	ENSMUSG00000056203	Tas2r135	Tas2r35|mt2r38	taste receptor, type 2, member 135	protein-coding
mm_68234.1	chr7	104507813	104507836	-	1	NA	promoter-TSS (NM_001167828)	promoter-TSS (NM_001167828)	25	NM_199146	209387	Mm.277377	NM_199146	ENSMUSG00000057596	Trim30d	AI451617|TRIM30-3|Trim79	tripartite motif-containing 30D	protein-coding
mm_65785.1	chr7	28809060	28809081	-	1	NA	Intergenic	CpG	-1820	NM_177301	15388	Mm.9043	NM_177301	ENSMUSG00000015165	Hnrnpl	C79783|D830027H13Rik|Hnrpl	heterogeneous nuclear ribonucleoprotein L	protein-coding
mm_16680.1	chr2	6872589	6872615	-	1	NA	promoter-TSS (NM_001347094)	promoter-TSS (NM_001347094)	-567	NM_001347094	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_139161.1	chr17	47551161	47551164	+	1	NA	intron (NM_001081635, intron 1 of 6)	intron (NM_001081635, intron 1 of 6)	-42305	NM_007632	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_123807.1	chr14	70521886	70521928	-	1	NA	exon (NM_011359, exon 4 of 6)	exon (NM_011359, exon 4 of 6)	-1647	NR_033241	12153	Mm.27757	NM_009755	ENSMUSG00000022098	Bmp1	Pcp|Tld	bone morphogenetic protein 1	protein-coding
mm_101316.1	chr11	22853112	22853122	-	1	NA	intron (NM_001169114, intron 1 of 1)	intron (NM_001169114, intron 1 of 1)	6618	NM_016888	53625	Mm.395495	NM_016888	ENSMUSG00000051650	B3gnt2	AA408337|AA409404|AW260308|B3Galt6|B3gnt1|BGnT-1|BGnT-2|BGnT1|BGnT2|Beta3gnt	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 2	protein-coding
mm_150102.1	chr19	29486950	29486967	+	1	NA	Intergenic	Intergenic	35029	NR_015567	77779	Mm.458738	NR_015567	ENSMUSG00000097855	A930007I19Rik	-	RIKEN cDNA A930007I19 gene	ncRNA
mm_85187.1	chr9	96713144	96713147	-	1	NA	intron (NM_175537, intron 2 of 2)	intron (NM_175537, intron 2 of 2)	18530	NM_175537	245007	Mm.485954	NM_175537	ENSMUSG00000040433	Zbtb38	A930014K01Rik|CIBZ	zinc finger and BTB domain containing 38	protein-coding
mm_37880.1	chr4	132422470	132422480	-	1	NA	promoter-TSS (NM_175306)	promoter-TSS (NM_175306)	-29	NM_175306	100169	Mm.158361	NM_175306	ENSMUSG00000066043	Phactr4	3110001B12Rik|AI527228|AW495572|C330013F19Rik|N28169|mKIAA4120	phosphatase and actin regulator 4	protein-coding
mm_59852.1	chr7	29941450	29941454	+	1	NA	intron (NM_178384, intron 2 of 4)	RMER1C|Other|Other	10441	NM_178384	72723	Mm.371648	NM_178384	ENSMUSG00000059975	Zfp74	2810054M15Rik|KRAB8|Zfp66|Znf569|mszf21|mszf77	zinc finger protein 74	protein-coding
mm_134313.1	chr16	15887132	15887161	-	1	NA	promoter-TSS (NM_007679)	promoter-TSS (NM_007679)	-140	NM_007679	12609	Mm.347407	NM_007679	ENSMUSG00000071637	Cebpd	c/EBPdelta	CCAAT/enhancer binding protein (C/EBP), delta	protein-coding
mm_116779.1	chr13	52982898	52982927	-	1	NA	Intergenic	Intergenic	-1873	NM_017373	18030	Mm.136604	NM_017373	ENSMUSG00000056749	Nfil3	AV225605|E4BP4	nuclear factor, interleukin 3, regulated	protein-coding
mm_29286.1	chr3	107696463	107696574	-	1	NA	promoter-TSS (NM_145542)	promoter-TSS (NM_145542)	30	NM_145542	229709	Mm.220328	NM_145542	ENSMUSG00000027893	Ahcyl1	1110034F20Rik|AA409031|AA414901|Ahcy-rs3|DCAL|Irbit	S-adenosylhomocysteine hydrolase-like 1	protein-coding
mm_51363.1	chr6	72636269	72636281	+	1	NA	intron (NM_009332, intron 4 of 11)	intron (NM_009332, intron 4 of 11)	6444	NR_040421	100038714	Mm.321330	NR_040421		Gm15401	ENSMUSG00000072999|OTTMUSG00000021199	predicted gene 15401	ncRNA
mm_34162.1	chr4	139574698	139574725	+	1	NA	promoter-TSS (NM_001205173)	promoter-TSS (NM_001205173)	-9	NM_001205173	212632	Mm.30464	NM_183148	ENSMUSG00000041025	Iffo2	C79267	intermediate filament family orphan 2	protein-coding
mm_139477.1	chr17	56008566	56008590	+	1	NA	promoter-TSS (NM_026530)	promoter-TSS (NM_026530)	-623	NM_026530	68047	Mm.358710	NM_026530	ENSMUSG00000003199	Mpnd	E130307M08Rik	MPN domain containing	protein-coding
mm_155107.1	chrX	48400526	48400541	+	1	NA	intron (NM_178782, intron 12 of 14)	intron (NM_178782, intron 12 of 14)	59175	NM_178782	320376	Mm.210146	NM_178782	ENSMUSG00000036959	Bcorl1	6720425J07Rik|B930011H20Rik	BCL6 co-repressor-like 1	protein-coding
mm_165230.1	chr2	55726989	55726995	+	1	NA	Intergenic	IAPLTR2a|LTR|ERVK	291022	NM_008426	16519	Mm.5127	NM_008426	ENSMUSG00000026824	Kcnj3	GIRK-1|GIRK1|Kcnf3|Kir3.1	potassium inwardly-rectifying channel, subfamily J, member 3	protein-coding
mm_163289.1	chr11	118146694	118146737	+	1	NA	Intergenic	MLT1H|LTR|ERVL-MaLR	-17496	NM_001167746	69926	Mm.473893	NM_001167746	ENSMUSG00000033987	Dnah17	2810003K23Rik|Dnahc17|Dnahcl1|Gm1178|mKIAA3028	dynein, axonemal, heavy chain 17	protein-coding
mm_57836.1	chr6	129465471	129465487	-	1	NA	exon (NM_020008, exon 5 of 6)	exon (NM_020008, exon 5 of 6)	7300	NM_001309637	56644	Mm.239516	NM_020008	ENSMUSG00000079293	Clec7a	BGR|Clecsf12|beta-GR	C-type lectin domain family 7, member a	protein-coding
mm_100117.1	chr11	115882891	115882901	+	1	NA	Intergenic	Intergenic	-17243	NM_183259	66528	Mm.275740	NM_183259	ENSMUSG00000048442	Smim5	2210020M01Rik	small integral membrane protein 5	protein-coding
mm_37652.1	chr4	128806179	128806186	-	1	NA	promoter-TSS (NM_001081098)	promoter-TSS (NM_001081098)	-70	NM_001081098	230761	Mm.22616	NM_001081098	ENSMUSG00000028799	Zfp362	-	zinc finger protein 362	protein-coding
mm_76874.1	chr8	105565922	105565947	-	1	NA	TTS (NM_001271806)	TTS (NM_001271806)	106	NM_013477	11972	Mm.17708	NM_013477	ENSMUSG00000013160	Atp6v0d1	AI267038|Ac39|Atp6d|P39|VATX|Vma6	ATPase, H+ transporting, lysosomal V0 subunit D1	protein-coding
mm_23528.1	chr3	60626571	60626601	+	1	NA	3' UTR (NM_001253711, exon 8 of 8)	3' UTR (NM_001253711, exon 8 of 8)	125407	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_114038.1	chr13	53393590	53393678	+	1	NA	promoter-TSS (NR_037991)	promoter-TSS (NR_037991)	-55	NR_037991	100040421	Mm.83967	NR_037991	ENSMUSG00000107008	Gm2762	1700025I17Rik	predicted gene 2762	ncRNA
mm_28007.1	chr3	83031448	83031486	-	1	NA	exon (NM_010196, exon 5 of 5)	exon (NM_010196, exon 5 of 5)	5314	NM_001111048	14161	Mm.88793	NM_010196	ENSMUSG00000028001	Fga	ENSMUSG00000059807|Fib	fibrinogen alpha chain	protein-coding
mm_103121.1	chr11	70191324	70191326	-	1	NA	Intergenic	Intergenic	-22585	NM_153081	216867	Mm.289238	NM_153081	ENSMUSG00000040938	Slc16a11	AB041591|MCT 11|MNCb-2717	solute carrier family 16 (monocarboxylic acid transporters), member 11	protein-coding
mm_92038.1	chr10	62494796	62494806	-	1	NA	3' UTR (NM_011157, exon 3 of 3)	3' UTR (NM_011157, exon 3 of 3)	-7996	NM_133672	30930	Mm.260703	NM_133672	ENSMUSG00000020078	Vps26a	AA407240|HB58|Vps26	VPS26 retromer complex component A	protein-coding
mm_19922.1	chr2	116018261	116018265	-	1	NA	intron (NM_001346047, intron 8 of 13)	intron (NM_001346047, intron 8 of 13)	46356	NM_001346044	17536	Mm.247566	NM_010825	ENSMUSG00000027210	Meis2	A430109D20Rik|Mrg1|Stra10	Meis homeobox 2	protein-coding
mm_18621.1	chr2	68472139	68472145	-	1	NA	promoter-TSS (NM_016866)	promoter-TSS (NM_016866)	-161	NM_016866	53416	Mm.198414	NM_016866	ENSMUSG00000027030	Stk39	AW227544|AW556857|DCHT|RF005|Rnl5|SPAK	serine/threonine kinase 39	protein-coding
mm_66652.1	chr7	45711538	45711566	-	1	NA	exon (NM_001172561, exon 6 of 6)	exon (NM_001172561, exon 6 of 6)	3655	NM_020011	56632	Mm.24222	NM_020011	ENSMUSG00000057342	Sphk2	C76851	sphingosine kinase 2	protein-coding
mm_52433.1	chr6	113531676	113531721	+	1	NA	promoter-TSS (NM_001033244)	promoter-TSS (NM_001033244)	16	NM_001347350	211651	Mm.160061	NM_001033244	ENSMUSG00000034023	Fancd2	2410150O07Rik|AU015151|BB137857|FA-D2|FA4|FACD|FAD|FANCD	Fanconi anemia, complementation group D2	protein-coding
mm_145376.1	chr18	56737645	56737692	+	1	NA	intron (NM_010721, intron 5 of 10)	intron (NM_010721, intron 5 of 10)	29855	NM_010721	16906	Mm.4105	NM_010721	ENSMUSG00000024590	Lmnb1	-	lamin B1	protein-coding
mm_100587.1	chr11	120949101	120949114	+	1	NA	promoter-TSS (NM_001038654)	promoter-TSS (NM_001038654)	40	NM_001038654	80879	Mm.28632	NM_030696	ENSMUSG00000025161	Slc16a3	Mct3|Mct4	solute carrier family 16 (monocarboxylic acid transporters), member 3	protein-coding
mm_1872.1	chr1	85600831	85600865	+	1	NA	5' UTR (NM_001013817, exon 1 of 17)	5' UTR (NM_001013817, exon 1 of 17)	145	NM_001013817	434484	Mm.445821	NM_001013817	ENSMUSG00000070031	Sp140	-	Sp140 nuclear body protein	protein-coding
mm_28748.1	chr3	95761882	95761886	-	1	NA	3' UTR (NM_001081293, exon 11 of 11)	3' UTR (NM_001081293, exon 11 of 11)	-6907	NM_001163618	71807	Mm.271754	NM_027931	ENSMUSG00000028107	Tars2	2610024N01Rik|AI429208|Tarsl1	threonyl-tRNA synthetase 2, mitochondrial (putative)	protein-coding
mm_27636.1	chr3	62480195	62480204	-	1	NA	intron (NM_028136, intron 16 of 24)	MLTR31D_MM|LTR|ERVK	26789	NM_028136	72162	Mm.224233	NM_028136	ENSMUSG00000027770	Dhx36	2810407E23Rik|AI452301|AU022184|Ddx36|mKIAA1488	DEAH (Asp-Glu-Ala-His) box polypeptide 36	protein-coding
mm_95546.1	chr11	52306973	52306988	+	1	NA	Intergenic	Intergenic	-23966	NM_001313981	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_149333.1	chr19	10848516	10848528	+	1	NA	exon (NM_023044, exon 2 of 8)	exon (NM_023044, exon 2 of 8)	5978	NM_023044	65221	Mm.27387	NM_023044	ENSMUSG00000024737	Slc15a3	Ci1|cI-1	solute carrier family 15, member 3	protein-coding
mm_88629.1	chr10	79886812	79886819	+	1	NA	exon (NM_015779, exon 2 of 5)	exon (NM_015779, exon 2 of 5)	503	NM_015779	50701	Mm.262194	NM_015779	ENSMUSG00000020125	Elane	Ela2|F430011M15Rik|NE	elastase, neutrophil expressed	protein-coding
mm_90792.1	chr10	7064252	7064266	-	1	NA	Intergenic	Intergenic	-41074	NM_001033391	320495	Mm.331674	NM_001033391	ENSMUSG00000064065	Ipcef1	A130090K04Rik	interaction protein for cytohesin exchange factors 1	protein-coding
mm_101938.1	chr11	50207566	50207576	-	1	NA	exon (NM_011018, exon 3 of 8)	exon (NM_011018, exon 3 of 8)	3249	NM_001290769	18412	Mm.40828	NM_011018	ENSMUSG00000015837	Sqstm1	A170|OSF-6|Osi|STAP|STONE14|p62	sequestosome 1	protein-coding
mm_117374.1	chr13	71963731	71963755	-	1	NA	promoter-TSS (NM_010573)	promoter-TSS (NM_010573)	-20	NM_010573	16371	Mm.316056	NM_010573	ENSMUSG00000060969	Irx1	-	Iroquois related homeobox 1 (Drosophila)	protein-coding
mm_28257.1	chr3	88570465	88570481	-	1	NA	TTS (NM_033526)	TTS (NM_033526)	-9198	NM_025448	66256	Mm.7091	NM_025448	ENSMUSG00000041355	Ssr2	1500032E05Rik|AI315033|AU020133|TLAP|TRAPB|TRAPbeta	signal sequence receptor, beta	protein-coding
mm_45076.1	chr5	43869461	43869492	-	1	NA	intron (NM_007646, intron 1 of 7)	intron (NM_007646, intron 1 of 7)	667	NM_007646	12494	Mm.249873	NM_007646	ENSMUSG00000029084	Cd38	ADPRC 1|Cd38-rs1|I-19	CD38 antigen	protein-coding
mm_116046.1	chr13	27249491	27249497	-	1	NA	exon (NM_008865, exon 5 of 5)	exon (NM_008865, exon 5 of 5)	7064	NM_008865	18776	Mm.37203	NM_008865	ENSMUSG00000038891	Prl3b1	Csh2|Ghd8|PL|Pl-2|Pl2|mPL-II|mplII	prolactin family 3, subfamily b, member 1	protein-coding
mm_168117.1	chr10	15896778	15896778	-	1	NA	Intergenic	L1Md_T|LINE|L1	105001	NR_131087	77538	Mm.128235	NR_131087		C330004P14Rik	-	RIKEN cDNA C330004P14 gene	ncRNA
mm_41487.1	chr5	92127294	92127316	+	1	NA	Intergenic	Intergenic	-10633	NM_019490	56041	Mm.15868	NM_019490	ENSMUSG00000029407	Uso1	115kDa|TAP|Vdp	USO1 vesicle docking factor	protein-coding
mm_144028.1	chr17	90036808	90036818	-	1	NA	3' UTR (NM_001347419, exon 3 of 3)	3' UTR (NM_001347419, exon 3 of 3)	51555	NM_001346962	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_157066.1	chrX	8190236	8190257	-	1	NA	exon (NM_007898, exon 2 of 5)	exon (NM_007898, exon 2 of 5)	3266	NM_007898	13595	Mm.27183	NM_007898	ENSMUSG00000031168	Ebp	AI255399|Pabp|SI|Td|mSI	phenylalkylamine Ca2+ antagonist (emopamil) binding protein	protein-coding
mm_3292.1	chr1	136678159	136678181	+	1	NA	Intergenic	Intergenic	-5226	NR_045324	100503460	Mm.30630	NR_045324	ENSMUSG00000097113	Gm19705	-	predicted gene, 19705	ncRNA
mm_46495.1	chr5	105132482	105132490	-	1	NA	intron (NM_008620, intron 3 of 10)	L1M2|LINE|L1	7066	NM_008620	17472	Mm.440525	NM_008620	ENSMUSG00000079363	Gbp4	AW228052|Mag-2|Mpa-2|Mpa2	guanylate binding protein 4	protein-coding
mm_31317.1	chr4	46138578	46138594	+	1	NA	promoter-TSS (NM_173033)	promoter-TSS (NM_173033)	75	NM_001033201	433702	Mm.389536	NM_001033201	ENSMUSG00000028330	Ncbp1	AU014645|AW538051|CBP80	nuclear cap binding protein subunit 1	protein-coding
mm_103222.1	chr11	70656516	70656534	-	1	NA	promoter-TSS (NM_007933)	promoter-TSS (NM_007933)	-651	NM_001136062	13808	Mm.251322	NM_007933	ENSMUSG00000060600	Eno3	Eno-3|MSE	enolase 3, beta muscle	protein-coding
mm_151928.1	chr19	5800156	5800162	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	2513	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_60643.1	chr7	44849583	44849629	+	1	NA	promoter-TSS (NM_001290694)	promoter-TSS (NM_001290694)	-29	NM_001290694	67605	Mm.148007	NM_026270	ENSMUSG00000011096	Akt1s1	1110012J22Rik|AI227026|Lobe|Lobel|PRAS40	AKT1 substrate 1 (proline-rich)	protein-coding
mm_117179.1	chr13	63398253	63398261	-	1	NA	intron (NM_001347514, intron 3 of 15)	intron (NM_001347514, intron 3 of 15)	33488	NM_001347515	14088	Mm.126106	NM_007985	ENSMUSG00000021461	Fancc	Facc	Fanconi anemia, complementation group C	protein-coding
mm_30807.1	chr4	20042015	20042032	+	1	NA	promoter-TSS (NM_010281)	promoter-TSS (NM_010281)	-29	NM_010281	14590	Mm.20461	NM_010281	ENSMUSG00000073987	Ggh	gamma-GH	gamma-glutamyl hydrolase	protein-coding
mm_76357.1	chr8	84772191	84772203	-	1	NA	exon (NM_010906, exon 2 of 9)	exon (NM_010906, exon 2 of 9)	2172	NM_001081981	18032	Mm.9394	NM_010906	ENSMUSG00000001911	Nfix	CTF|NF-I/X|NF1-X|NFI-X	nuclear factor I/X	protein-coding
mm_154241.1	chr19	60764169	60764232	-	1	NA	exon (NM_010123, exon 20 of 22)	exon (NM_010123, exon 20 of 22)	8213	NM_178421	332397	Mm.186390	NM_178421	ENSMUSG00000072437	Nanos1	NOS-1	nanos homolog 1 (Drosophila)	protein-coding
mm_20141.1	chr2	121442575	121442614	-	1	NA	promoter-TSS (NM_145973)	promoter-TSS (NM_145973)	7	NM_145973	269344	Mm.330522	NM_145973	ENSMUSG00000027246	Ell3	A930015D22Rik	elongation factor RNA polymerase II-like 3	protein-coding
mm_152368.1	chr19	10101833	10101839	-	1	NA	promoter-TSS (NM_019699)	promoter-TSS (NM_019699)	-333	NM_019699	56473	Mm.38901	NM_019699	ENSMUSG00000024665	Fads2	2900042M13Rik|Fadsd2	fatty acid desaturase 2	protein-coding
mm_71533.1	chr8	46934478	46934514	+	1	NA	Intergenic	Intergenic	-52391	NM_177304	320981	Mm.211429	NM_177304	ENSMUSG00000038173	Enpp6	4833421B01Rik|B830047L21Rik|D8Ertd514e|E-NPP 6|GPC-Cpde|Npp6	ectonucleotide pyrophosphatase/phosphodiesterase 6	protein-coding
mm_148226.1	chr18	80346070	80346089	-	1	NA	intron (NM_001190373, intron 1 of 3)	B4A|SINE|B4	18175	NM_001190373	240444	Mm.279568	NM_001190373	ENSMUSG00000059852	Kcng2	AA591524	potassium voltage-gated channel, subfamily G, member 2	protein-coding
mm_54433.1	chr6	34176942	34177014	-	1	NA	promoter-TSS (NM_021435)	promoter-TSS (NM_021435)	76	NM_021435	58246	Mm.245527	NM_021435	ENSMUSG00000018999	Slc35b4	4930474D06Rik|AB041549|AW494345	solute carrier family 35, member B4	protein-coding
mm_34942.1	chr4	155847500	155847516	+	1	NA	5' UTR (NM_010091, exon 1 of 15)	5' UTR (NM_010091, exon 1 of 15)	191	NM_010091	13542	Mm.3400	NM_010091	ENSMUSG00000029071	Dvl1	Dvl|mKIAA4029	dishevelled segment polarity protein 1	protein-coding
mm_56786.1	chr6	116637873	116637894	-	1	NA	3' UTR (NM_178045, exon 11 of 11)	3' UTR (NM_178045, exon 11 of 11)	8164	NR_106010	102466793		NR_106010	ENSMUSG00000098334	Mir7043	Gm27776|mmu-mir-7043	microRNA 7043	ncRNA
mm_136784.1	chr17	10496435	10496441	+	1	NA	intron (NM_027032, intron 4 of 4)	intron (NM_027032, intron 4 of 4)	40222	NR_077238	319750	Mm.383485	NR_077237	ENSMUSG00000089633	A230009B12Rik	-	RIKEN cDNA A230009B12 gene	ncRNA
mm_148905.1	chr19	6942544	6942584	+	1	NA	promoter-TSS (NM_001285453)	promoter-TSS (NM_001285453)	2	NM_001285453	12015	Mm.4387	NM_007522	ENSMUSG00000024959	Bad	AI325008|Bbc2	BCL2-associated agonist of cell death	protein-coding
mm_7005.1	chr1	86467467	86467492	-	1	NA	Intergenic	Intergenic	41150	NM_027966	71863	Mm.179627	NM_027966	ENSMUSG00000036574	1700019O17Rik	-	RIKEN cDNA 1700019O17 gene	protein-coding
mm_123626.1	chr14	68122887	68122913	-	1	NA	promoter-TSS (NR_045897)	promoter-TSS (NR_045897)	-852	NR_045897	100043072	Mm.242832	NR_045897		A230070E04Rik	Gm4210	RIKEN cDNA A230070E04 gene	ncRNA
mm_61376.1	chr7	70365376	70365399	+	1	NA	promoter-TSS (NR_045850)	promoter-TSS (NR_045850)	4	NR_045850	434198	Mm.389911	NR_045850	ENSMUSG00000100005	B130024G19Rik	-	RIKEN cDNA B130024G19 gene	ncRNA
mm_77410.1	chr8	120589072	120589080	-	1	NA	promoter-TSS (NM_178856)	promoter-TSS (NM_178856)	-1	NM_178856	272551	Mm.275910	NM_178856	ENSMUSG00000031821	Gins2	2210013I18Rik|4833427B12Rik|AI323585|Pfs2	GINS complex subunit 2 (Psf2 homolog)	protein-coding
mm_106104.1	chr11	116274198	116274208	-	1	NA	promoter-TSS (NM_146032)	promoter-TSS (NM_146032)	14	NM_146032	217337	Mm.29655	NM_146032	ENSMUSG00000020780	Srp68	2610024I03Rik	signal recognition particle 68	protein-coding
mm_27434.1	chr3	51560817	51560875	-	1	NA	promoter-TSS (NM_080793)	promoter-TSS (NM_080793)	-23	NM_080793	73251	Mm.192111	NM_080793	ENSMUSG00000037111	Setd7	1600028F23Rik|H3K4MT|KMT7|Set7|Set7/9|mKIAA1717	SET domain containing (lysine methyltransferase) 7	protein-coding
mm_49129.1	chr6	8580635	8580635	+	1	NA	intron (NM_133236, intron 5 of 7)	L1MB8|LINE|L1	60577	NM_001286729	170772	Mm.210787	NM_133236	ENSMUSG00000029638	Glcci1	2310047L21Rik|A130036A18Rik|Fam117c|Gig18|Tssn1	glucocorticoid induced transcript 1	protein-coding
mm_110118.1	chr12	26443937	26443945	-	1	NA	3' UTR (NM_021384, exon 6 of 6)	3' UTR (NM_021384, exon 6 of 6)	12511	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_137917.1	chr17	32321377	32321422	+	1	NA	promoter-TSS (NM_019774)	promoter-TSS (NM_019774)	-161	NR_131218	56399	Mm.328945	NM_019774	ENSMUSG00000024045	Akap8	1200016A02Rik|AA673585|AKAP-8|AKAP95|AU015639	A kinase (PRKA) anchor protein 8	protein-coding
mm_152149.1	chr19	7217524	7217528	-	1	NA	promoter-TSS (NM_007750)	promoter-TSS (NM_007750)	90	NM_007750	12868	Mm.14022	NM_007750	ENSMUSG00000035885	Cox8a	COX8L	cytochrome c oxidase subunit VIIIa	protein-coding
mm_66430.1	chr7	44668378	44668390	-	1	NA	intron (NM_001271540, intron 1 of 41)	intron (NM_001271540, intron 1 of 41)	2459	NM_001271540	71960	Mm.158289	NM_028021	ENSMUSG00000030739	Myh14	2400004E04Rik|II-C|NHMCII|NMHC II-C	myosin, heavy polypeptide 14	protein-coding
mm_92872.1	chr10	82316541	82316561	-	1	NA	Intergenic	(CTAAA)n|Simple_repeat|Simple_repeat	-75276	NM_001105557	237411		NM_172789	ENSMUSG00000062931	Zfp938	B230315N10Rik	zinc finger protein 938	protein-coding
mm_14046.1	chr2	122298899	122298903	+	1	NA	promoter-TSS (NM_177610)	promoter-TSS (NM_177610)	1	NM_025777	66811	Mm.171333	NM_025777	ENSMUSG00000027225	Duoxa2	9030623N16Rik|Nip2	dual oxidase maturation factor 2	protein-coding
mm_85592.1	chr9	107334571	107334583	-	1	NA	intron (NM_133984, intron 4 of 10)	intron (NM_133984, intron 4 of 10)	3773	NM_133984	69536	Mm.259467	NM_133984	ENSMUSG00000032579	Hemk1	2310008M14Rik|AW049265	HemK methyltransferase family member 1	protein-coding
mm_6641.1	chr1	79440004	79440014	-	1	NA	promoter-TSS (NM_009129)	promoter-TSS (NM_009129)	81	NM_009129	20254	Mm.5038	NM_009129	ENSMUSG00000050711	Scg2	Chgc|SgII	secretogranin II	protein-coding
mm_169481.1	chr14	73194410	73194425	-	1	NA	Intergenic	ETnERV-int|LTR|ERVK	12434	NR_030459	751541		NR_030459	ENSMUSG00000076121	Mir687	Mirn687|mir-687|mmu-mir-687	microRNA 687	ncRNA
mm_72817.1	chr8	88118748	88118777	+	1	NA	promoter-TSS (NM_029074)	promoter-TSS (NM_029074)	3	NM_029074	382030	Mm.216574	NM_029074	ENSMUSG00000036810	Cnep1r1	5033428A16Rik|NEP1-R1|Tmem188	CTD nuclear envelope phosphatase 1 regulatory subunit 1	protein-coding
mm_18661.1	chr2	70726132	70726136	-	1	NA	intron (NM_172664, intron 12 of 19)	intron (NM_172664, intron 12 of 19)	64625	NM_027352	70231	Mm.271950	NM_027352	ENSMUSG00000014959	Gorasp2	0610011A07Rik|2410043M02Rik|5730520M13Rik|9430094F20Rik|AW552058|ENSMUSG00000075299|GOLPH2|GRASP55|GRS2|p59	golgi reassembly stacking protein 2	protein-coding
mm_64725.1	chr7	4660576	4660625	-	1	NA	TTS (NM_024172)	TTS (NM_024172)	-1650	NM_172894	243819	Mm.258670	NM_172894	ENSMUSG00000052296	Ppp6r1	2010309P17Rik|AI836219|B430201G11Rik|D030074N20Rik|Pp6r1|Saps1|mKIAA1115	protein phosphatase 6, regulatory subunit 1	protein-coding
mm_91834.1	chr10	57516487	57516515	-	1	NA	3' UTR (NM_019760, exon 9 of 9)	3' UTR (NM_019760, exon 9 of 9)	16028	NM_019760	56442	Mm.29344	NM_019760	ENSMUSG00000019877	Serinc1	1500011D18Rik|AI315070|AIGP-2|TMS-2|Tde1l|Tde2|Tms2|mKIAA1253	serine incorporator 1	protein-coding
mm_30486.1	chr3	155055342	155055370	-	1	NA	promoter-TSS (NM_177066)	promoter-TSS (NM_177066)	51	NM_177066	435766	Mm.210428	NM_177066	ENSMUSG00000040086	Tnni3k	Cark|D830019J24Rik	TNNI3 interacting kinase	protein-coding
mm_1781.1	chr1	78511905	78511921	+	1	NA	5' UTR (NM_026713, exon 2 of 7)	5' UTR (NM_026713, exon 2 of 7)	853	NM_026713	68393	Mm.41325	NM_026713	ENSMUSG00000012187	Mogat1	0610030A14Rik|1110064N14Rik|Dgat2l|Dgat2l1|MGAT1|WI1-2612I11.1|mDC2	monoacylglycerol O-acyltransferase 1	protein-coding
mm_96152.1	chr11	61208735	61208747	+	1	NA	promoter-TSS (NM_007436)	promoter-TSS (NM_007436)	-1	NM_007436	11670	Mm.4257	NM_007436	ENSMUSG00000019102	Aldh3a1	Ahd-4|Ahd4|Aldh|Aldh3	aldehyde dehydrogenase family 3, subfamily A1	protein-coding
mm_3792.1	chr1	157412668	157412677	+	1	NA	promoter-TSS (NM_177644)	promoter-TSS (NM_177644)	-77	NM_177644	226525	Mm.235028	NM_177644	ENSMUSG00000070565	Rasal2	6530401P13|A330066M24Rik	RAS protein activator like 2	protein-coding
mm_126606.1	chr15	82642152	82642168	+	1	NA	promoter-TSS (NR_003552)	promoter-TSS (NR_003552)	-115	NR_003552	68444	Mm.443212	NR_003552		Cyp2d13	1300007K12Rik	cytochrome P450, family 2, subfamily d, polypeptide 13	pseudo
mm_94182.1	chr10	128923440	128923545	-	1	NA	promoter-TSS (NM_015740)	promoter-TSS (NM_015740)	32	NM_015740	14533	Mm.30118	NM_015740	ENSMUSG00000090247	Bloc1s1	AI839753|BLOS1|Gcn5l1	biogenesis of lysosomal organelles complex-1, subunit 1	protein-coding
mm_158958.1	chr1	91250595	91250595	+	1	NA	intron (NM_026454, intron 1 of 9)	CpG	276	NM_026454	67921	Mm.337238	NM_026454	ENSMUSG00000034343	Ube2f	2510010F15Rik|AI851109	ubiquitin-conjugating enzyme E2F (putative)	protein-coding
mm_53745.1	chr6	145182318	145182328	+	1	NA	intron (NM_177222, intron 11 of 15)	intron (NM_177222, intron 11 of 15)	28647	NM_177222	320662	Mm.207779	NM_177222	ENSMUSG00000043541	Casc1	A230084G12Rik|Las1	cancer susceptibility candidate 1	protein-coding
mm_99297.1	chr11	101337763	101337777	+	1	NA	3' UTR (NM_009675, exon 4 of 4)	3' UTR (NM_009675, exon 4 of 4)	7164	NM_009675	11754	Mm.67281	NM_009675	ENSMUSG00000019326	Aoc3	SSAO|VAP1	amine oxidase, copper containing 3	protein-coding
mm_65527.1	chr7	25788494	25788513	-	1	NA	5' UTR (NM_001190974, exon 1 of 19)	5' UTR (NM_001190974, exon 1 of 19)	230	NM_001190974	26362	Mm.4128	NM_009465	ENSMUSG00000002602	Axl	AI323647|Ark|Tyro7|Ufo	AXL receptor tyrosine kinase	protein-coding
mm_169244.1	chr13	74768157	74768160	-	1	NA	intron (NM_001301153, intron 3 of 31)	(CCA)n|Simple_repeat|Simple_repeat	2578	NM_001301156	12380	Mm.29163	NM_009817	ENSMUSG00000021585	Cast	-	calpastatin	protein-coding
mm_91538.1	chr10	39369561	39369595	-	1	NA	promoter-TSS (NM_008054)	promoter-TSS (NM_008054)	-221	NM_001122892	14360	Mm.4848	NM_008054	ENSMUSG00000019843	Fyn	AI448320|AW552119	Fyn proto-oncogene	protein-coding
mm_129492.1	chr15	78802886	78802920	-	1	NA	exon (NM_130859, exon 1 of 21)	exon (NM_130859, exon 1 of 21)	139	NM_130859	105844	Mm.17629	NM_130859	ENSMUSG00000033170	Card10	AI449026|Bimp1|Carma3	caspase recruitment domain family, member 10	protein-coding
mm_134206.1	chr16	11151732	11151765	-	1	NA	intron (NM_145931, intron 11 of 22)	intron (NM_145931, intron 11 of 22)	-17216	NM_029582	106200	Mm.291015	NM_029582	ENSMUSG00000022498	Txndc11	2810408E11Rik|AI427833|EFP1|Txdc11	thioredoxin domain containing 11	protein-coding
mm_52649.1	chr6	117179972	117179983	+	1	NA	3' UTR (NM_001012477, exon 4 of 4)	3' UTR (NM_001012477, exon 4 of 4)	11442	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_23150.1	chr3	40410162	40410163	+	1	NA	Intergenic	Intergenic	112750	NR_040445	100040882	Mm.272869	NR_040445	ENSMUSG00000037884	1700017G19Rik	-	RIKEN cDNA 1700017G19 gene	ncRNA
mm_133078.1	chr16	58733771	58733788	+	1	NA	non-coding (NR_045518, exon 4 of 4)	non-coding (NR_045518, exon 4 of 4)	5869	NM_001252451	224250	Mm.29482	NM_171826	ENSMUSG00000022744	Cldnd1	1110019C08Rik|AA407103|AI849195|AW489850|Cldn25	claudin domain containing 1	protein-coding
mm_165886.1	chr4	42952826	42952828	+	1	NA	promoter-TSS (NM_019874)	promoter-TSS (NM_019874)	-267	NM_019874	56323	Mm.20437	NM_019874	ENSMUSG00000036052	Dnajb5	1110058L06Rik|AI462558|Hsc40|Hsp40-3	DnaJ heat shock protein family (Hsp40) member B5	protein-coding
mm_142843.1	chr17	51796281	51796319	-	1	NA	intron (NM_009122, intron 5 of 10)	intron (NM_009122, intron 5 of 10)	15754	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_118586.1	chr14	20348304	20348325	+	1	NA	promoter-TSS (NM_027475)	promoter-TSS (NM_027475)	152	NM_001177633	105428	Mm.206990	NM_172379	ENSMUSG00000039599	Fam149b	AA536717|AI428773|Fam149b1|mKIAA0974	family with sequence similarity 149, member B	protein-coding
mm_121321.1	chr14	111676009	111676039	+	1	NA	intron (NM_198865, intron 1 of 1)	CpG	909	NM_198865	75409	Mm.235097	NM_029273	ENSMUSG00000033214	Slitrk5	2610019D03Rik	SLIT and NTRK-like family, member 5	protein-coding
mm_34834.1	chr4	155250089	155250123	+	1	NA	non-coding (NR_033802, exon 1 of 3)	non-coding (NR_033802, exon 1 of 3)	140	NR_033802	67513	Mm.10374	NM_001190445	ENSMUSG00000073684	Faap20	2610002J02Rik	Fanconi anemia core complex associated protein 20	protein-coding
mm_163458.1	chr12	98650763	98650771	+	1	NA	intron (NM_001289573, intron 5 of 9)	intron (NM_001289573, intron 5 of 9)	22625	NM_001289574	104871	Mm.210053	NM_178914	ENSMUSG00000021007	Spata7	AI661438|B230306G18Rik|HSD3	spermatogenesis associated 7	protein-coding
mm_136789.1	chr17	10865100	10865103	+	1	NA	intron (NM_001317726, intron 1 of 6)	intron (NM_001317726, intron 1 of 6)	24742	NM_016694	50873	Mm.311110	NM_016694	ENSMUSG00000023826	Park2	PRKN	Parkinson disease (autosomal recessive, juvenile) 2, parkin	protein-coding
mm_40260.1	chr5	38260373	38260386	+	1	NA	promoter-TSS (NM_025480)	promoter-TSS (NM_025480)	4	NM_025480	66309	Mm.256185	NM_025480	ENSMUSG00000067365	Tmem128	2810021O14Rik	transmembrane protein 128	protein-coding
mm_118598.1	chr14	20694990	20695000	+	1	NA	promoter-TSS (NM_028428)	promoter-TSS (NM_028428)	27	NM_028428	73068	Mm.277552	NM_028428	ENSMUSG00000039357	Fut11	3110009G03Rik|AI317183	fucosyltransferase 11	protein-coding
mm_86211.1	chr9	120011192	120011233	-	1	NA	Intergenic	CpG	12386	NM_011724	22437	Mm.10117	NM_011724	ENSMUSG00000079243	Xirp1	AI415219|Cmya1	xin actin-binding repeat containing 1	protein-coding
mm_31544.1	chr4	55480253	55480263	+	1	NA	Intergenic	Intergenic	52217	NM_010637	16600	Mm.4325	NM_010637	ENSMUSG00000003032	Klf4	EZF|Gklf|Zie	Kruppel-like factor 4 (gut)	protein-coding
mm_76659.1	chr8	93229629	93229639	-	1	NA	promoter-TSS (NM_133660)	promoter-TSS (NM_133660)	-15	NM_133660	13897	Mm.63490	NM_133660	ENSMUSG00000061959	Ces1e	Eg|Es-22|Es22|egasyn	carboxylesterase 1E	protein-coding
mm_27120.1	chr3	31310219	31310231	-	1	NA	promoter-TSS (NM_172861)	promoter-TSS (NM_172861)	94	NM_172861	241919	Mm.285366	NM_172861	ENSMUSG00000069072	Slc7a14	A930013N06|BC061928	solute carrier family 7 (cationic amino acid transporter, y+ system), member 14	protein-coding
mm_150701.1	chr19	42255873	42255889	+	1	NA	5' UTR (NM_027694, exon 1 of 5)	5' UTR (NM_027694, exon 1 of 5)	142	NM_027694	71146	Mm.329851	NM_027694	ENSMUSG00000042532	Golga7b	4933417O08Rik|AI839934	golgi autoantigen, golgin subfamily a, 7B	protein-coding
mm_116269.1	chr13	34652674	34652688	-	1	NA	promoter-TSS (NR_105041)	promoter-TSS (NR_105041)	0	NM_025831	66895	Mm.28943	NM_025831	ENSMUSG00000021411	Pxdc1	1300014I06Rik	PX domain containing 1	protein-coding
mm_41684.1	chr5	100210690	100210698	+	1	NA	promoter-TSS (NR_040679)	promoter-TSS (NR_040679)	2	NR_040679	69571	Mm.396412	NR_040679	ENSMUSG00000100157	2310034O05Rik	-	RIKEN cDNA 2310034O05 gene	ncRNA
mm_105764.1	chr11	109607721	109607724	-	1	NA	intron (NM_145940, intron 1 of 12)	intron (NM_145940, intron 1 of 12)	3667	NM_145940	52639	Mm.35817	NM_145940	ENSMUSG00000041895	Wipi1	4930533H01Rik|AW411817|D11Ertd498e	WD repeat domain, phosphoinositide interacting 1	protein-coding
mm_99477.1	chr11	102604455	102604478	+	1	NA	promoter-TSS (NM_020510)	promoter-TSS (NM_020510)	35	NM_020510	57265	Mm.36416	NM_020510	ENSMUSG00000050288	Fzd2	AL033370|AW456835|Fz10|Fzd10|Mfz10|Mfz10a	frizzled class receptor 2	protein-coding
mm_50868.1	chr6	55451829	55451872	+	1	NA	promoter-TSS (NM_001025372)	promoter-TSS (NM_001025372)	-128	NM_001025372	11517	Mm.44245	NM_007407	ENSMUSG00000029778	Adcyap1r1	2900024I10Rik|AI846590|PAC1|PAC1R|PACAP1-R	adenylate cyclase activating polypeptide 1 receptor 1	protein-coding
mm_22945.1	chr3	32067277	32067309	+	1	NA	intron (NM_028231, intron 2 of 5)	intron (NM_028231, intron 2 of 5)	164590	NM_028231	72413	Mm.64790	NM_028231	ENSMUSG00000037610	Kcnmb2	2700049B16Rik|3110031N04Rik	potassium large conductance calcium-activated channel, subfamily M, beta member 2	protein-coding
mm_10079.1	chr1	195131506	195131534	-	1	NA	promoter-TSS (NM_013499)	promoter-TSS (NM_013499)	50	NM_013499	12946	Mm.301652	NM_013499	ENSMUSG00000016481	Cr1l	Crry|Mcp|mCRY	complement component (3b/4b) receptor 1-like	protein-coding
mm_146996.1	chr18	34371843	34371845	-	1	NA	intron (NM_007874, intron 2 of 4)	RSINE1|SINE|B4	1571	NM_007874	13476	Mm.280075	NM_007874	ENSMUSG00000005873	Reep5	AI324241|AU022809|AW495741|DP1/TB2|Dp1|R74856|TB2/DP1	receptor accessory protein 5	protein-coding
mm_59031.1	chr7	19304784	19304799	+	1	NA	3' UTR (NM_008036, exon 4 of 4)	3' UTR (NM_008036, exon 4 of 4)	5254	NM_008036	14282	Mm.248335	NM_008036	ENSMUSG00000003545	Fosb	-	FBJ osteosarcoma oncogene B	protein-coding
mm_89517.1	chr10	94312150	94312162	+	1	NA	Intergenic	CpG	-13453	NR_033209	215472	Mm.255656	NM_174999	ENSMUSG00000053420	Gm4792	E130012K09|EG215472	predicted gene 4792	ncRNA
mm_105035.1	chr11	100545580	100545593	-	1	NA	promoter-TSS (NM_028918)	promoter-TSS (NM_028918)	-46	NM_028918	74407	Mm.31590	NM_028918	ENSMUSG00000006784	Ttc25	4933404O19Rik	tetratricopeptide repeat domain 25	protein-coding
mm_8377.1	chr1	151250723	151250727	-	1	NA	Intergenic	Intergenic	-93773	NM_001039512	117198	Mm.33764	NM_028582	ENSMUSG00000023150	Ivns1abp	1190004M08Rik|1700126I16Rik|AA960440|HSPC068|ND1|NS-1|NS1-BP|Nd1-L|Nd1-S|mKIAA0850	influenza virus NS1A binding protein	protein-coding
mm_92429.1	chr10	77113110	77113120	-	1	NA	exon (NM_001109991, exon 1 of 41)	exon (NM_001109991, exon 1 of 41)	590	NM_001109991	12822	Mm.4352	NM_009929	ENSMUSG00000001435	Col18a1	-	collagen, type XVIII, alpha 1	protein-coding
mm_21994.1	chr2	167654914	167654963	-	1	NA	intron (NM_145538, intron 1 of 5)	intron (NM_145538, intron 1 of 5)	6606	NM_145538	407243	Mm.4863	NM_145538	ENSMUSG00000090213	Tmem189	AI840826|Kua	transmembrane protein 189	protein-coding
mm_112955.1	chr13	21179468	21179481	+	1	NA	promoter-TSS (NM_009054)	promoter-TSS (NM_009054)	-457	NM_009054	19720	Mm.314056	NM_009054	ENSMUSG00000021326	Trim27	AW538890|Gm19403|Rfp	tripartite motif-containing 27	protein-coding
mm_39661.1	chr5	25100924	25100988	+	1	NA	promoter-TSS (NM_145401)	promoter-TSS (NM_145401)	-19	NR_027851	67261	Mm.461781	NM_026059	ENSMUSG00000043833	2900005J15Rik	-	RIKEN cDNA 2900005J15 gene	ncRNA
mm_74800.1	chr8	22476624	22476686	-	1	NA	promoter-TSS (NM_011394)	promoter-TSS (NM_011394)	-45	NM_011394	20516	Mm.323901	NM_011394	ENSMUSG00000037656	Slc20a2	MolPit2|Pit-2|Pit2|Ram-1|Ram1	solute carrier family 20, member 2	protein-coding
mm_106641.1	chr11	120991306	120991339	-	1	NA	promoter-TSS (NM_139059)	promoter-TSS (NM_139059)	11	NM_139059	104318	Mm.216227	NM_027874	ENSMUSG00000025162	Csnk1d	1200006A05Rik|AA409348|D930010H05Rik	casein kinase 1, delta	protein-coding
mm_25633.1	chr3	119903350	119903362	+	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-119968	NM_019550	56195	Mm.29966	NM_019550	ENSMUSG00000028134	Ptbp2	Ptb2|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding
mm_91153.1	chr10	20505520	20505562	-	1	NA	intron (NM_013875, intron 2 of 12)	intron (NM_013875, intron 2 of 12)	42787	NM_001347366	29863	Mm.425617	NM_013875	ENSMUSG00000019990	Pde7b	-	phosphodiesterase 7B	protein-coding
mm_17671.1	chr2	32167931	32167978	-	1	NA	intron (NM_172661, intron 1 of 29)	intron (NM_172661, intron 1 of 29)	16806	NM_001159634	227723	Mm.25504	NM_172661	ENSMUSG00000039262	Prrc2b	5830434P21Rik|AI173903|Bat2l|Bat2l1|D430039P21|mKIAA0515	proline-rich coiled-coil 2B	protein-coding
mm_169172.1	chr13	65639780	65639783	+	1	NA	Intergenic	Intergenic	360927	NM_178364	170936	Mm.151546	NM_178364	ENSMUSG00000021514	Zfp369	B930030B22Rik|D230020H11Rik|NRIF2	zinc finger protein 369	protein-coding
mm_4709.1	chr1	180942326	180942352	+	1	NA	promoter-TSS (NM_144794)	promoter-TSS (NM_144794)	-179	NM_144794	208795	Mm.185518	NM_144794	ENSMUSG00000026519	Tmem63a	BC014795|Tmem64a	transmembrane protein 63a	protein-coding
mm_105401.1	chr11	103412669	103412711	-	1	NA	promoter-TSS (NM_183034)	promoter-TSS (NM_183034)	-26	NM_183034	353047	Mm.18556	NM_183034	ENSMUSG00000034247	Plekhm1	AP162|B2|BC038943|D330036J23Rik	pleckstrin homology domain containing, family M (with RUN domain) member 1	protein-coding
mm_98637.1	chr11	96177364	96177366	+	1	NA	Intergenic	Intergenic	-16996	NM_008267	15408	Mm.57221	NM_008267	ENSMUSG00000049604	Hoxb13	-	homeobox B13	protein-coding
mm_109700.1	chr12	113185878	113185937	+	1	NA	promoter-TSS (NM_153776)	promoter-TSS (NM_153776)	4	NM_153776	69195	Mm.313244	NM_153776	ENSMUSG00000049036	Tmem121	2410008J05Rik|Hole	transmembrane protein 121	protein-coding
mm_151301.1	chr19	55741811	55741842	+	1	NA	promoter-TSS (NM_001142918)	promoter-TSS (NM_001142918)	16	NM_001142923	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_81329.1	chr9	108516956	108516968	+	1	NA	promoter-TSS (NM_175143)	promoter-TSS (NM_175143)	-125	NM_001114119	69232	Mm.335449	NM_175143	ENSMUSG00000006673	Qrich1	2610028H07Rik	glutamine-rich 1	protein-coding
mm_168184.1	chr10	59395631	59395648	+	1	NA	Intergenic	CpG	-8046	NM_023530	69836	Mm.30268	NM_023530	ENSMUSG00000009646	Pla2g12b	2010002E04Rik|Fksg71|Pla2g13|hlb218	phospholipase A2, group XIIB	protein-coding
mm_36757.1	chr4	101346943	101346957	-	1	NA	promoter-TSS (NR_029537)	promoter-TSS (NR_029537)	77	NR_029537	387143		NR_029537	ENSMUSG00000065451	Mir101a	Mirn101|Mirn101a|miR-101|mir-101a	microRNA 101a	ncRNA
mm_86194.1	chr9	119579041	119579051	-	1	NA	promoter-TSS (NM_021544)	promoter-TSS (NM_021544)	-30	NM_021544	20271	Mm.103584	NM_021544	ENSMUSG00000032511	Scn5a	Nav1.5|Nav1.5c|SkM1|SkM2|mH1	sodium channel, voltage-gated, type V, alpha	protein-coding
mm_43554.1	chr5	137601354	137601363	+	1	NA	promoter-TSS (NM_030037)	promoter-TSS (NM_030037)	-299	NM_030037	68929	Mm.41355	NM_030037	ENSMUSG00000037221	Mospd3	1190005J19Rik|5133401H10Rik|Gtig2|R124	motile sperm domain containing 3	protein-coding
mm_156600.1	chrX	152434151	152434173	+	1	NA	Intergenic	Intergenic	65134	NR_045452	75693	Mm.287381	NR_045451	ENSMUSG00000084885	3010001F23Rik	-	RIKEN cDNA 3010001F23 gene	ncRNA
mm_151792.1	chr19	5402461	5402484	-	1	NA	Intergenic	Intergenic	-4343	NR_015545	74931	Mm.388511	NR_015545	ENSMUSG00000086938	4930481A15Rik	-	RIKEN cDNA 4930481A15 gene	ncRNA
mm_126946.1	chr15	92051278	92051288	+	1	NA	5' UTR (NM_001159648, exon 1 of 24)	5' UTR (NM_001159648, exon 1 of 24)	118	NM_001159648	12805	Mm.4911	NM_007727	ENSMUSG00000055022	Cntn1	AW495098|CNTN|F3cam|usl	contactin 1	protein-coding
mm_73034.1	chr8	94180218	94180256	+	1	NA	TTS (NM_013602)	TTS (NM_013602)	1148	NM_013602	17748	Mm.192991	NM_013602	ENSMUSG00000031765	Mt1	MT-I|Mt-1	metallothionein 1	protein-coding
mm_137575.1	chr17	27857241	27857247	+	1	NA	intron (NM_001080769, intron 1 of 20)	intron (NM_001080769, intron 1 of 20)	737	NM_001080769	224648	Mm.291291	NM_001080769	ENSMUSG00000039512	Uhrf1bp1	1110020K19Rik|AA408674|F830021D11Rik|mKIAA4127	UHRF1 (ICBP90) binding protein 1	protein-coding
mm_73438.1	chr8	106161273	106161283	+	1	NA	exon (NM_133792, exon 5 of 6)	exon (NM_133792, exon 5 of 6)	-7597	NM_178798	330836	Mm.46749	NM_178798	ENSMUSG00000031904	Slc7a6	AI643885|LAT-2|LAT3	solute carrier family 7 (cationic amino acid transporter, y+ system), member 6	protein-coding
mm_139122.1	chr17	47468338	47468378	+	1	NA	exon (NM_145489, exon 4 of 5)	exon (NM_145489, exon 4 of 5)	-30983	NM_029296	75462	Mm.46129	NM_029296	ENSMUSG00000047150	1700001C19Rik	-	RIKEN cDNA 1700001C19 gene	protein-coding
mm_134215.1	chr16	11227562	11227567	-	1	NA	intron (NM_146066, intron 11 of 14)	intron (NM_146066, intron 11 of 14)	24181	NR_038156	69918	Mm.440400	NR_038154		2610020C07Rik	-	RIKEN cDNA 2610020C07 gene	ncRNA
mm_4908.1	chr1	190170282	190170301	+	1	NA	5' UTR (NM_008937, exon 1 of 5)	5' UTR (NM_008937, exon 1 of 5)	389	NM_008937	19130	Mm.132579	NM_008937	ENSMUSG00000010175	Prox1	A230003G05Rik	prospero homeobox 1	protein-coding
mm_75793.1	chr8	70096068	70096078	-	1	NA	3' UTR (NM_007789, exon 15 of 15)	3' UTR (NM_007789, exon 15 of 15)	6513	NR_106033	102465646		NR_106033	ENSMUSG00000099042	Mir7066	Gm27290|mmu-mir-7066	microRNA 7066	ncRNA
mm_126047.1	chr15	76904994	76905004	+	1	NA	exon (NM_012053, exon 4 of 6)	exon (NM_012053, exon 4 of 6)	928	NM_012053	26961	Mm.30066	NM_012053	ENSMUSG00000003970	Rpl8	-	ribosomal protein L8	protein-coding
mm_24511.1	chr3	92584426	92584439	+	1	NA	exon (NM_008574, exon 2 of 2)	exon (NM_008574, exon 2 of 2)	4592	NM_008574	17235	Mm.331192	NM_008574		Smcp	Mcs|Mcsp	sperm mitochondria-associated cysteine-rich protein	protein-coding
mm_4439.1	chr1	172506927	172506959	+	1	NA	3' UTR (NM_178598, exon 5 of 5)	3' UTR (NM_178598, exon 5 of 5)	6697	NM_178598	21346	Mm.271711	NM_178598	ENSMUSG00000026547	Tagln2	2700094C18Rik|SM22beta|Sm22B|Sm22a	transgelin 2	protein-coding
mm_121856.1	chr14	20664583	20664588	-	1	NA	promoter-TSS (NM_001310432)	promoter-TSS (NM_001310432)	-11	NM_001310432	68760	Mm.35789	NM_175132	ENSMUSG00000039376	Synpo2l	1110054M18Rik|Chap	synaptopodin 2-like	protein-coding
mm_165310.1	chr2	102781987	102782006	+	1	NA	3' UTR (NM_001077514, exon 11 of 11)	3' UTR (NM_001077514, exon 11 of 11)	75558	NM_001077515	20511	Mm.267547	NM_011393	ENSMUSG00000005089	Slc1a2	1700091C19Rik|2900019G14Rik|AI159670|Eaat2|GLT-1|GLT1|MGLT1	solute carrier family 1 (glial high affinity glutamate transporter), member 2	protein-coding
mm_23800.1	chr3	79877262	79877283	+	1	NA	Intergenic	Intergenic	-8658	NM_133187	68659	Mm.427274	NM_133187	ENSMUSG00000027955	Fam198b	1110032E23Rik|2210419I08Rik|AV011458|Ened	family with sequence similarity 198, member B	protein-coding
mm_138861.1	chr17	42645314	42645320	+	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-34004	NM_181753	353344	Mm.184937	NM_181753	ENSMUSG00000043972	Opn5	Gpr136|Neuropsin|PGR12|TMEM13	opsin 5	protein-coding
mm_251.1	chr1	19235770	19235782	+	1	NA	3' UTR (NM_009334, exon 7 of 7)	3' UTR (NM_009334, exon 7 of 7)	23722	NM_001025305	21419	Mm.137021	NM_009334	ENSMUSG00000025927	Tfap2b	AI606113|AP-2(beta)|E130018K07Rik|Tcfap2b	transcription factor AP-2 beta	protein-coding
mm_108844.1	chr12	98268627	98268654	+	1	NA	promoter-TSS (NM_008152)	promoter-TSS (NM_008152)	5	NM_008152	14744	Mm.378924	NM_008152	ENSMUSG00000021886	Gpr65	Dig1|Gpcr25|TDAG8	G-protein coupled receptor 65	protein-coding
mm_69853.1	chr7	141429355	141429429	-	1	NA	promoter-TSS (NM_021316)	promoter-TSS (NM_021316)	28	NM_021316	57754	Mm.87027	NM_021316	ENSMUSG00000060240	Cend1	1500001H12Rik|AI415214|BM88	cell cycle exit and neuronal differentiation 1	protein-coding
mm_111238.1	chr12	84772955	84772961	-	1	NA	promoter-TSS (NM_028863)	promoter-TSS (NM_028863)	154	NM_023409	67963	Mm.282556	NM_023409	ENSMUSG00000021242	Npc2	2700012J19Rik|AA408070|AU045843|HE1	Niemann-Pick type C2	protein-coding
mm_70678.1	chr8	14974967	14974976	+	1	NA	intron (NM_172751, intron 18 of 28)	intron (NM_172751, intron 18 of 28)	-36054	NM_029116	74901	Mm.46675	NM_029116	ENSMUSG00000055675	Kbtbd11	2900016B01Rik|4930465M17Rik|mKIAA0711	kelch repeat and BTB (POZ) domain containing 11	protein-coding
mm_171126.1	chr3	144828386	144828390	+	1	NA	intron (NM_139148, intron 9 of 13)	intron (NM_139148, intron 9 of 13)	-8894	NM_030601	80797	Mm.20897	NM_030601	ENSMUSG00000028262	Clca3a2	Clca2	chloride channel accessory 3A2	protein-coding
mm_23068.1	chr3	36066112	36066118	+	1	NA	exon (NM_172678, exon 1 of 18)	exon (NM_172678, exon 1 of 18)	115	NM_172678	229211	Mm.260997	NM_172678	ENSMUSG00000027710	Acad9	2600017P15Rik|4732402K02|C630012L17Rik|NPD002	acyl-Coenzyme A dehydrogenase family, member 9	protein-coding
mm_167262.1	chr8	27031298	27031337	+	1	NA	intron (NM_153592, intron 6 of 11)	intron (NM_153592, intron 6 of 11)	7518	NM_153592	244373	Mm.277699	NM_153592	ENSMUSG00000031483	Erlin2	BC036333|C87251|Spfh2	ER lipid raft associated 2	protein-coding
mm_61909.1	chr7	90137695	90137723	+	1	NA	intron (NM_001252520, intron 1 of 20)	B3A|SINE|B2	7477	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_137091.1	chr17	21516999	21517018	+	1	NA	Intergenic	Intergenic	-18531	NM_144515	22710	Mm.296100	NM_144515	ENSMUSG00000051341	Zfp52	KRAB11|Zfp-52|Zfp76|mszf23-2|mszf24|mszf34|mszf75|zfec29	zinc finger protein 52	protein-coding
mm_90184.1	chr10	120113084	120113100	+	1	NA	promoter-TSS (NM_080446)	promoter-TSS (NM_080446)	-127	NM_080446	117599	Mm.214703	NM_080446	ENSMUSG00000020228	Helb	AI447783|D10Ertd664e	helicase (DNA) B	protein-coding
mm_157936.1	chrX	83772602	83772618	-	1	NA	exon (NM_007868, exon 19 of 79)	exon (NM_007868, exon 19 of 79)	-284686	NM_021898	100502723	Mm.383210	NM_021898	ENSMUSG00000035522	Tsga8	Halap-X|Halapx	testis specific gene A8	protein-coding
mm_107577.1	chr12	44525558	44525562	+	1	NA	intron (NM_001146031, intron 3 of 27)	intron (NM_001146031, intron 3 of 27)	196675	NM_001146031	319504	Mm.208439	NM_176930	ENSMUSG00000020598	Nrcam	Bravo|C030017F07Rik|C130076O07Rik|mKIAA0343	neuronal cell adhesion molecule	protein-coding
mm_27501.1	chr3	55055502	55055519	-	1	NA	promoter-TSS (NM_007628)	promoter-TSS (NM_007628)	268	NR_040593	70970	Mm.251485	NR_040593	ENSMUSG00000106589	4931419H13Rik	-	RIKEN cDNA 4931419H13 gene	ncRNA
mm_79962.1	chr9	66350446	66350454	+	1	NA	promoter-TSS (NM_145617)	promoter-TSS (NM_145617)	0	NM_145617	235439	Mm.244179	NM_145617	ENSMUSG00000038664	Herc1	2810449H11Rik|B230218H07|D130015N03Rik|tbl	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	protein-coding
mm_4623.1	chr1	179546304	179546363	+	1	NA	promoter-TSS (NM_146105)	promoter-TSS (NM_146105)	-57	NM_001331054	15278	Mm.293529	NM_008249	ENSMUSG00000026492	Tfb2m	Hkp1	transcription factor B2, mitochondrial	protein-coding
mm_129464.1	chr15	78597769	78597787	-	1	NA	intron (NM_028195, intron 1 of 12)	intron (NM_028195, intron 1 of 12)	731	NM_028195	72318	Mm.32911	NM_028195	ENSMUSG00000018008	Cyth4	2510004M07Rik|5830469K17Rik|AI467541|Pscd4|mFLJ00017	cytohesin 4	protein-coding
mm_157167.1	chrX	9467896	9467919	-	1	NA	intron (NM_007807, intron 1 of 12)	intron (NM_007807, intron 1 of 12)	1417	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_4208.1	chr1	171250556	171250557	+	1	NA	5' UTR (NM_172845, exon 1 of 9)	5' UTR (NM_172845, exon 1 of 9)	427	NM_172845	240913	Mm.491147	NM_172845	ENSMUSG00000006403	Adamts4	ADAM-TS4|ADAMTS-2|ADMP-1	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 4	protein-coding
mm_153272.1	chr19	37176026	37176034	-	1	NA	promoter-TSS (NM_001290826)	promoter-TSS (NM_001290826)	33	NM_001290826	208922	Mm.391176	NM_198300	ENSMUSG00000039652	Cpeb3	4831444O18Rik|CPE-BP3|mKIAA0940	cytoplasmic polyadenylation element binding protein 3	protein-coding
mm_37987.1	chr4	133625601	133625629	-	1	NA	intron (NM_001017968, intron 2 of 7)	intron (NM_001017968, intron 2 of 7)	7814	NM_001017968	503610	Mm.331948	NM_001017968	ENSMUSG00000037553	Zdhhc18	-	zinc finger, DHHC domain containing 18	protein-coding
mm_164846.1	chr18	44174982	44175001	-	1	NA	promoter-TSS (NM_183123)	promoter-TSS (NM_183123)	82	NM_183123	77424	Mm.99224	NM_183123	ENSMUSG00000053729	Spinkl	9530002K18Rik	serine protease inhibitor, Kazal type-like	protein-coding
mm_63184.1	chr7	125552236	125552257	+	1	NA	promoter-TSS (NM_001008700)	promoter-TSS (NM_001008700)	-36	NM_001008700	16190	Mm.233802	NM_010557	ENSMUSG00000030748	Il4ra	CD124|Il4r	interleukin 4 receptor, alpha	protein-coding
mm_35524.1	chr4	41275092	41275118	-	1	NA	promoter-TSS (NM_026872)	promoter-TSS (NM_026872)	30	NM_026872	68926	Mm.41864	NM_026872	ENSMUSG00000028433	Ubap2	1190005K07Rik|AA408600|AU045235|UBAP-2|mKIAA1491	ubiquitin-associated protein 2	protein-coding
mm_131357.1	chr16	13729805	13729848	+	1	NA	promoter-TSS (NR_040574)	promoter-TSS (NR_040574)	-10	NR_040574	76684	Mm.491043	NR_040574		Pla2g10os	1810007I06Rik	phospholipase A2, group X, opposite strand	ncRNA
mm_50822.1	chr6	54460275	54460275	+	1	NA	intron (NM_001167860, intron 1 of 7)	intron (NM_001167860, intron 1 of 7)	7392	NM_001167861	330319	Mm.434326	NM_001167860	ENSMUSG00000086040	Wipf3	9030621G03|BQ952480	WAS/WASL interacting protein family, member 3	protein-coding
mm_40293.1	chr5	43515477	43515485	+	1	NA	promoter-TSS (NM_001135172)	promoter-TSS (NM_001135172)	-88	NM_001135172	109323	Mm.275553	NM_175425	ENSMUSG00000061535	C1qtnf7	5530401N20Rik|8430425G24Rik|Ctrp7	C1q and tumor necrosis factor related protein 7	protein-coding
mm_146443.1	chr18	84952086	84952128	+	1	NA	promoter-TSS (NM_025969)	promoter-TSS (NM_025969)	-583	NM_025969	67105	Mm.250617	NM_025969	ENSMUSG00000024645	Timm21	1700034H14Rik|2700002I20Rik	tranlocase of inner mitochondrial membrane 21	protein-coding
mm_109727.1	chr12	116373958	116373965	+	1	NA	TTS (NM_028731)	TTS (NM_028731)	31200	NR_028421	319545	Mm.390543	NR_028421		D430020J02Rik	-	RIKEN cDNA D430020J02 gene	ncRNA
mm_121087.1	chr14	99298653	99298715	+	1	NA	promoter-TSS (NM_009769)	promoter-TSS (NM_009769)	-7	NM_009769	12224	Mm.30262	NM_009769	ENSMUSG00000005148	Klf5	4930520J07Rik|Bteb2|CKLF|IKLF	Kruppel-like factor 5	protein-coding
mm_162004.1	chr19	40451344	40451344	-	1	NA	promoter-TSS (NM_001034962)	promoter-TSS (NM_001034962)	54	NM_001034962	20411	Mm.210815	NM_009166	ENSMUSG00000025006	Sorbs1	2310065E01Rik|9530001P15Rik|CAP|SH3P12|Sh3d5|mKIAA1296	sorbin and SH3 domain containing 1	protein-coding
mm_90699.1	chr10	130330983	130331031	+	1	NA	intron (NM_183264, intron 1 of 8)	intron (NM_183264, intron 1 of 8)	8155	NM_183264	67596	Mm.131264	NM_183264	ENSMUSG00000034833	Tespa1	5830405N20Rik|A430001F24Rik|AI450549	thymocyte expressed, positive selection associated 1	protein-coding
mm_143360.1	chr17	67308369	67308372	-	1	NA	intron (NM_008984, intron 1 of 30)	intron (NM_008984, intron 1 of 30)	46089	NM_008984	19274	Mm.311809	NM_008984	ENSMUSG00000033278	Ptprm	RPTPmu|mKIAA4044	protein tyrosine phosphatase, receptor type, M	protein-coding
mm_143103.1	chr17	57087558	57087612	-	1	NA	5' UTR (NM_009451, exon 1 of 4)	5' UTR (NM_009451, exon 1 of 4)	197	NM_009451	22153	Mm.7420	NM_009451	ENSMUSG00000062591	Tubb4a	AI325297|M(beta)4|Tubb|Tubb4	tubulin, beta 4A class IVA	protein-coding
mm_104949.1	chr11	100135502	100135528	-	1	NA	exon (NM_008469, exon 1 of 8)	exon (NM_008469, exon 1 of 8)	434	NM_008469	16665	Mm.440010	NM_008469	ENSMUSG00000054146	Krt15	AI528832|K15|Krt1-15	keratin 15	protein-coding
mm_118327.1	chr13	113663612	113663634	-	1	NA	promoter-TSS (NM_019960)	promoter-TSS (NM_019960)	53	NM_019960	56534	Mm.41410	NM_019960	ENSMUSG00000051456	Hspb3	2310035K17Rik|AI844863|Hsbp3|spb3	heat shock protein 3	protein-coding
mm_27923.1	chr3	79539734	79539776	-	1	NA	intron (NM_001162999, intron 1 of 16)	intron (NM_001162999, intron 1 of 16)	27924	NM_001162999	329679	Mm.244005	NM_001162999	ENSMUSG00000061175	Fnip2	D630023B12Rik|mKIAA1450	folliculin interacting protein 2	protein-coding
mm_138920.1	chr17	43611342	43611396	+	1	NA	exon (NM_013737, exon 11 of 12)	exon (NM_013737, exon 11 of 12)	18930	NM_001161366	210510	Mm.329058	NM_198418	ENSMUSG00000040140	Tdrd6	AB097085|Tdr2	tudor domain containing 6	protein-coding
mm_98493.1	chr11	94951605	94951624	+	1	NA	exon (NM_007742, exon 51 of 51)	exon (NM_007742, exon 51 of 51)	15390	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_116816.1	chr13	54504310	54504326	-	1	NA	intron (NM_176987, intron 1 of 9)	CpG	513	NM_176987	319719	Mm.376151	NM_176987	ENSMUSG00000043183	Simc1	4732471D19Rik	SUMO-interacting motifs containing 1	protein-coding
mm_131572.1	chr16	18248962	18249041	+	1	NA	promoter-TSS (NM_011239)	promoter-TSS (NM_011239)	118	NM_001081000	15547	Mm.271798	NM_008307	ENSMUSG00000022721	Trmt2a	Htf9c	TRM2 tRNA methyltransferase 2A	protein-coding
mm_161501.1	chr15	89454116	89454116	+	1	NA	5' UTR (NM_021921, exon 1 of 12)	5' UTR (NM_021921, exon 1 of 12)	205	NM_021921	60597	Mm.173337	NM_021921	ENSMUSG00000022619	Mapk8ip2	3230402N03Rik|AI847694|AW049958|IB2|Jip2|R75148	mitogen-activated protein kinase 8 interacting protein 2	protein-coding
mm_159825.1	chr5	123703588	123703588	-	1	NA	intron (NM_027494, intron 11 of 13)	B1_Mm|SINE|Alu	17456	NM_027494	70650	Mm.279427	NM_027494	ENSMUSG00000029427	Zcchc8	5730565F05Rik	zinc finger, CCHC domain containing 8	protein-coding
mm_161329.1	chr14	50360710	50360710	+	1	NA	exon (NM_205819, exon 2 of 2)	exon (NM_205819, exon 2 of 2)	2796	NM_205819	239081	Mm.291512	NM_205819	ENSMUSG00000051969	Tlr11	Gm287	toll-like receptor 11	protein-coding
mm_115537.1	chr13	6636654	6636686	-	1	NA	intron (NM_019703, intron 1 of 21)	intron (NM_019703, intron 1 of 21)	12101	NM_019703	56421	Mm.273874	NM_019703	ENSMUSG00000021196	Pfkp	1200015H23Rik|9330125N24Rik|ATP-PFK|PFK-C|PFK-P	phosphofructokinase, platelet	protein-coding
mm_9833.1	chr1	184033715	184033721	-	1	NA	promoter-TSS (NM_022019)	promoter-TSS (NM_022019)	280	NM_028516	73363	Mm.50115	NM_028516	ENSMUSG00000044854	1700056E22Rik	-	RIKEN cDNA 1700056E22 gene	protein-coding
mm_24796.1	chr3	95546796	95546804	+	1	NA	exon (NM_021281, exon 6 of 8)	exon (NM_021281, exon 6 of 8)	-12877	NM_026489	67981	Mm.179050	NM_026489	ENSMUSG00000028109	Hormad1	4921522K05Rik|Nohma	HORMA domain containing 1	protein-coding
mm_5794.1	chr1	51941290	51941302	-	1	NA	Intergenic	Intergenic	-25318	NM_001161817	17912	Mm.3390	NM_010863	ENSMUSG00000018417	Myo1b	AA406997|MIH-L|MMIa	myosin IB	protein-coding
mm_150204.1	chr19	32776034	32776053	+	1	NA	exon (NM_008960, exon 2 of 9)	exon (NM_008960, exon 2 of 9)	18466	NM_008960	19211	Mm.245395	NM_008960	ENSMUSG00000013663	Pten	2310035O07Rik|A130070J02Rik|AI463227|B430203M17Rik|MMAC1|TEP1	phosphatase and tensin homolog	protein-coding
mm_63325.1	chr7	126942109	126942119	+	1	NA	intron (NM_172747, intron 4 of 5)	intron (NM_172747, intron 4 of 5)	7467	NM_001347657	233879	Mm.444143	NM_001039645	ENSMUSG00000046378	Asphd1	A830007L07Rik|Gm168	aspartate beta-hydroxylase domain containing 1	protein-coding
mm_15399.1	chr2	156721846	156721870	+	1	NA	promoter-TSS (NR_040505)	promoter-TSS (NR_040505)	579	NM_001042487	228836	Mm.22094	NM_146128	ENSMUSG00000061689	Dlgap4	AI225853|BC024558|DAP-4|DAP4|SAPAP-4|Sapap4|WBP16	discs, large homolog-associated protein 4 (Drosophila)	protein-coding
mm_67585.1	chr7	83631803	83631819	-	1	NA	promoter-TSS (NM_023377)	promoter-TSS (NM_023377)	-206	NM_023377	170460	Mm.357953	NM_023377	ENSMUSG00000046027	Stard5	2310058G22Rik|AI607880|D7Ertd152e	StAR-related lipid transfer (START) domain containing 5	protein-coding
mm_20945.1	chr2	151563613	151563619	-	1	NA	Intergenic	Intergenic	-9007	NM_145535	228765	Mm.32068	NM_145535	ENSMUSG00000027456	Sdcbp2	-	syndecan binding protein (syntenin) 2	protein-coding
mm_139501.1	chr17	56303332	56303349	+	1	NA	promoter-TSS (NM_001111080)	promoter-TSS (NM_001111080)	3	NM_001111079	18140	Mm.42196	NM_010931	ENSMUSG00000001228	Uhrf1	AL022808|ICBP90|Np95|RNF106	ubiquitin-like, containing PHD and RING finger domains, 1	protein-coding
mm_141830.1	chr17	34628053	34628059	-	1	NA	promoter-TSS (NM_019441)	promoter-TSS (NM_019441)	-40	NM_001302394	54397	Mm.373627	NM_019441	ENSMUSG00000015474	Ppt2	0610007M19Rik|AA672937	palmitoyl-protein thioesterase 2	protein-coding
mm_37427.1	chr4	122886045	122886068	-	1	NA	promoter-TSS (NM_007598)	promoter-TSS (NM_007598)	1	NM_007598	12331	Mm.8687	NM_007598	ENSMUSG00000028656	Cap1	-	CAP, adenylate cyclase-associated protein 1 (yeast)	protein-coding
mm_83429.1	chr9	44986531	44986548	-	1	NA	3' UTR (NM_013487, exon 5 of 5)	3' UTR (NM_013487, exon 5 of 5)	4753	NM_013487	12500	Mm.4527	NM_013487	ENSMUSG00000032094	Cd3d	T3d	CD3 antigen, delta polypeptide	protein-coding
mm_117423.1	chr13	74363938	74363948	-	1	NA	promoter-TSS (NM_001033042)	promoter-TSS (NM_001033042)	57	NM_001033042	432779	Mm.324679	NM_001033042	ENSMUSG00000021579	Lrrc14b	AI595366	leucine rich repeat containing 14B	protein-coding
mm_166311.1	chr5	106926558	106926567	-	1	NA	promoter-TSS (NM_177873)	promoter-TSS (NM_177873)	-672	NM_001252516	330149	Mm.121664	NM_177873	ENSMUSG00000043410	Hfm1	A330009G12Rik|Gm1046|Mer3|Sec63d1	HFM1, ATP-dependent DNA helicase homolog	protein-coding
mm_51928.1	chr6	91440965	91441028	+	1	NA	promoter-TSS (NR_045980)	promoter-TSS (NR_045980)	9	NR_038153	69798	Mm.229265	NR_038153	ENSMUSG00000100680	1810044D09Rik	-	RIKEN cDNA 1810044D09 gene	ncRNA
mm_139511.1	chr17	56425660	56425662	+	1	NA	exon (NM_011218, exon 14 of 33)	exon (NM_011218, exon 14 of 33)	-6752	NR_105943	102465590		NR_105943	ENSMUSG00000098339	Mir6977	Gm27922|mmu-mir-6977	microRNA 6977	ncRNA
mm_147341.1	chr18	43059528	43059538	-	1	NA	promoter-TSS (NM_028392)	promoter-TSS (NM_028392)	-62	NM_028392	72930	Mm.26134	NM_027531	ENSMUSG00000024500	Ppp2r2b	2900026H06Rik|6330404L05Rik|E130009M08Rik|PP2A-PR55B|PR55-BETA|SCA12	protein phosphatase 2, regulatory subunit B, beta	protein-coding
mm_40142.1	chr5	35166435	35166445	+	1	NA	Intergenic	Intergenic	-60743	NM_013587	16976	Mm.277661	NM_013587	ENSMUSG00000029103	Lrpap1	AA617339|AI790446|AU042172|C77774|HBP44|RAP	low density lipoprotein receptor-related protein associated protein 1	protein-coding
mm_79217.1	chr9	49340354	49340363	+	1	NA	promoter-TSS (NM_010077)	promoter-TSS (NM_010077)	-304	NM_010077	13489	Mm.41970	NM_010077	ENSMUSG00000032259	Drd2	D2R|Drd-2	dopamine receptor D2	protein-coding
mm_114535.1	chr13	73627186	73627197	+	1	NA	exon (NM_009354, exon 1 of 16)	exon (NM_009354, exon 1 of 16)	190	NM_009354	21752	Mm.10109	NM_009354	ENSMUSG00000021611	Tert	EST2|TCS1|TP2|TR|TRT	telomerase reverse transcriptase	protein-coding
mm_28946.1	chr3	99981318	99981327	-	1	NA	intron (NM_028892, intron 4 of 48)	GSAT_MM|Satellite|Satellite	95905	NM_028892	74362	Mm.55847	NM_028892	ENSMUSG00000027867	Spag17	4931427F14Rik|PF6|Spag17-ps	sperm associated antigen 17	protein-coding
mm_7122.1	chr1	90780360	90780361	-	1	NA	intron (NM_001243008, intron 36 of 43)	intron (NM_001243008, intron 36 of 43)	63611	NM_001243009	12835	Mm.7562	NM_009935	ENSMUSG00000048126	Col6a3	AI507288|Col6a-3	collagen, type VI, alpha 3	protein-coding
mm_113028.1	chr13	23492275	23492284	+	1	NA	Intergenic	Intergenic	-3422	NM_001289614	238555	Mm.129668	NM_175938	ENSMUSG00000053216	Btn2a2	Btn2|D030063K05	butyrophilin, subfamily 2, member A2	protein-coding
mm_170609.1	chr19	5845432	5845433	-	1	NA	promoter-TSS (NR_003513)	promoter-TSS (NR_003513)	46	NR_131212	66961	Mm.281895	NR_003513	ENSMUSG00000092274	Neat1	2310043N10Rik|VINC	nuclear paraspeckle assembly transcript 1 (non-protein coding)	ncRNA
mm_111024.1	chr12	79089699	79089719	-	1	NA	promoter-TSS (NM_029988)	promoter-TSS (NM_029988)	-39	NM_029988	110417	Mm.268317	NM_029988	ENSMUSG00000021120	Pigh	2210416H01Rik|A930028P05Rik	phosphatidylinositol glycan anchor biosynthesis, class H	protein-coding
mm_74780.1	chr8	22006584	22006584	-	1	NA	intron (NM_007511, intron 12 of 20)	intron (NM_007511, intron 12 of 20)	35988	NM_026459	67929	Mm.60688	NM_026459	ENSMUSG00000017049	Ccdc70	1700112P19Rik	coiled-coil domain containing 70	protein-coding
mm_76386.1	chr8	84842609	84842619	-	1	NA	3' UTR (NM_007591, exon 9 of 9)	3' UTR (NM_007591, exon 9 of 9)	-1949	NM_009010	19358	Mm.255539	NM_009010	ENSMUSG00000003813	Rad23a	2310040P19Rik|AL024030|HR23A|mHR23A	RAD23 homolog A, nucleotide excision repair protein	protein-coding
mm_53729.1	chr6	145121135	145121146	+	1	NA	promoter-TSS (NM_008511)	promoter-TSS (NM_008511)	-599	NM_008511	16970	Mm.843	NM_008511	ENSMUSG00000030263	Lrmp	D6Int3|D6Int4|D6Int5|D6Int7|D6Int8|Jaw1	lymphoid-restricted membrane protein	protein-coding
mm_38848.1	chr4	149307686	149307703	-	1	NA	promoter-TSS (NM_001290995)	promoter-TSS (NM_001290995)	4	NM_207682	16561	Mm.402393	NM_008441	ENSMUSG00000063077	Kif1b	A530096N05Rik|AI448212|AI506502|D4Mil1e|KIF1Bp130|KIF1Bp204	kinesin family member 1B	protein-coding
mm_154978.1	chrX	37827014	37827019	+	1	NA	promoter-TSS (NM_008955)	promoter-TSS (NM_008955)	-39	NM_008955	19202	Mm.10105	NM_008955	ENSMUSG00000006200	Rhox6	AV213605|AW548842|Psx1	reproductive homeobox 6	protein-coding
mm_106362.1	chr11	118393942	118393950	-	1	NA	exon (NM_011150, exon 6 of 6)	exon (NM_011150, exon 6 of 6)	7985	NM_011150	19039	Mm.3152	NM_011150	ENSMUSG00000033880	Lgals3bp	90K|CyCAP|MAC-2BP|Ppicap|Tango10b	lectin, galactoside-binding, soluble, 3 binding protein	protein-coding
mm_162883.1	chr10	102388994	102388998	+	1	NA	exon (NM_001162369, exon 6 of 6)	exon (NM_001162369, exon 6 of 6)	14559	NM_026243	67569	Mm.25252	NM_026243	ENSMUSG00000019888	Mgat4c	9130411I17Rik|GntIVh	MGAT4 family, member C	protein-coding
mm_41562.1	chr5	93120188	93120190	+	1	NA	intron (NM_001347377, intron 1 of 10)	L1MD|LINE|L1	26773	NM_001347377	52398	Mm.394184	NM_001009818	ENSMUSG00000058013	Sept11	6230410I01Rik|AW548875|D5Ertd606e	septin 11	protein-coding
mm_74779.1	chr8	21993406	21993410	-	1	NA	TTS (NM_007511)	TTS (NM_007511)	22812	NM_026459	67929	Mm.60688	NM_026459	ENSMUSG00000017049	Ccdc70	1700112P19Rik	coiled-coil domain containing 70	protein-coding
mm_85209.1	chr9	96787882	96787912	-	1	NA	Intergenic	Intergenic	22335	NR_102296	319707	Mm.392191	NR_102293	ENSMUSG00000101581	C430002N11Rik	-	RIKEN cDNA C430002N11 gene	ncRNA
mm_16229.1	chr2	173156061	173156071	+	1	NA	exon (NM_011044, exon 6 of 10)	exon (NM_011044, exon 6 of 10)	2993	NM_011044	18534	Mm.266867	NM_011044	ENSMUSG00000027513	Pck1	AI265463|PEPCK|Pck-1	phosphoenolpyruvate carboxykinase 1, cytosolic	protein-coding
mm_155481.1	chrX	73675532	73675538	+	1	NA	intron (NM_001142810, intron 1 of 12)	intron (NM_001142810, intron 1 of 12)	2402	NM_001142809	102857	Mm.274553	NM_133987	ENSMUSG00000019558	Slc6a8	AA589632|CRT|CRTR|CT1|CTR5|Creat	solute carrier family 6 (neurotransmitter transporter, creatine), member 8	protein-coding
mm_158719.1	chrX	162829380	162829402	-	1	NA	promoter-TSS (NM_001290778)	promoter-TSS (NM_001290778)	63	NM_001290776	353170	Mm.270186	NM_178935	ENSMUSG00000038344	Txlng	4932441K18Rik|Fiat|Lrp	taxilin gamma	protein-coding
mm_43012.1	chr5	123893817	123893827	+	1	NA	Intergenic	RLTR17B_Mm|LTR|ERVK	-13453	NM_026603	68184	Mm.28549	NM_026603	ENSMUSG00000023106	Denr	1500003K04Rik	density-regulated protein	protein-coding
mm_4034.1	chr1	165774291	165774299	+	1	NA	3' UTR (NM_011804, exon 4 of 4)	3' UTR (NM_011804, exon 4 of 4)	10515	NM_011804	433375	Mm.294885	NM_011804	ENSMUSG00000040713	Creg1	AA755314|Creg	cellular repressor of E1A-stimulated genes 1	protein-coding
mm_149612.1	chr19	16385866	16385875	+	1	NA	3' UTR (NM_008139, exon 7 of 7)	3' UTR (NM_008139, exon 7 of 7)	-49797	NM_008137	14675	Mm.313181	NM_008137	ENSMUSG00000024697	Gna14	AU023208	guanine nucleotide binding protein, alpha 14	protein-coding
mm_124924.1	chr15	12136570	12136588	+	1	NA	exon (NM_011767, exon 3 of 20)	exon (NM_011767, exon 3 of 20)	18728	NM_011767	22763	Mm.273496	NM_011767	ENSMUSG00000022201	Zfr	C920030H05Rik	zinc finger RNA binding protein	protein-coding
mm_83432.1	chr9	44998940	44998950	-	1	NA	3' UTR (NM_007648, exon 8 of 8)	3' UTR (NM_007648, exon 8 of 8)	10645	NM_007648	12501	Mm.210361	NM_007648	ENSMUSG00000032093	Cd3e	AI504783|CD3|CD3epsilon|T3e	CD3 antigen, epsilon polypeptide	protein-coding
mm_140454.1	chr17	88627439	88627484	+	1	NA	intron (NM_029858, intron 1 of 3)	intron (NM_029858, intron 1 of 3)	906	NM_029858	77057	Mm.482203	NM_029858	ENSMUSG00000033855	Ston1	4921524J06Rik|C86231|Salf|Sblf	stonin 1	protein-coding
mm_93884.1	chr10	125328372	125328412	-	1	NA	5' UTR (NM_011391, exon 1 of 7)	5' UTR (NM_011391, exon 1 of 7)	143	NM_011391	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|Mct2	solute carrier family 16 (monocarboxylic acid transporters), member 7	protein-coding
mm_111320.1	chr12	86078904	86078941	-	1	NA	5' UTR (NM_009368, exon 1 of 7)	5' UTR (NM_009368, exon 1 of 7)	119	NM_009368	21809	Mm.3992	NM_009368	ENSMUSG00000021253	Tgfb3	TGF-beta-3|Tgfb-3	transforming growth factor, beta 3	protein-coding
mm_57743.1	chr6	129049831	129049851	-	1	NA	intron (NR_024262, intron 1 of 5)	intron (NR_024262, intron 1 of 5)	3940	NR_024263	232408	Mm.259262	NM_153094	ENSMUSG00000030154	Klrb1f	A630024B12Rik|Nkr-p1f|Nkrp1-f|Nkrp1f	killer cell lectin-like receptor subfamily B member 1F	protein-coding
mm_151577.1	chr19	61151839	61151871	+	1	NA	Intergenic	Intergenic	-11015	NR_131954	414758	Mm.100056	NM_001001737	ENSMUSG00000074733	Zfp950	5830428H23Rik|AU016073|BC055757|Gm34518|Zfp826|mszf84	zinc finger protein 950	protein-coding
mm_30794.1	chr4	19737364	19737382	+	1	NA	Intergenic	Intergenic	-28369	NR_074090	107568	Mm.78312	NM_177327	ENSMUSG00000041058	Wwp1	8030445B08Rik|AIP5|SDRP1|Tiul1	WW domain containing E3 ubiquitin protein ligase 1	protein-coding
mm_37439.1	chr4	123138730	123138748	-	1	NA	intron (NM_019489, intron 2 of 9)	intron (NM_019489, intron 2 of 9)	1202	NM_019489	56031	Mm.126873	NM_019489	ENSMUSG00000028651	Ppie	2010010D16Rik|Cyp33	peptidylprolyl isomerase E (cyclophilin E)	protein-coding
mm_23418.1	chr3	58548894	58548912	+	1	NA	exon (NM_001005509, exon 10 of 14)	exon (NM_001005509, exon 10 of 14)	-23019	NM_030685	28146	Mm.29702	NM_030685	ENSMUSG00000027808	Serp1	D3Ucla1|Ramp4	stress-associated endoplasmic reticulum protein 1	protein-coding
mm_156322.1	chrX	137374644	137374653	+	1	NA	Intergenic	RMER13B|LTR|ERVK	-196106	NM_030688	60367	Mm.328321	NM_030688	ENSMUSG00000059203	Il1rapl2	-	interleukin 1 receptor accessory protein-like 2	protein-coding
mm_46990.1	chr5	115334069	115334095	-	1	NA	3' UTR (NM_029645, exon 3 of 3)	3' UTR (NM_029645, exon 3 of 3)	6905	NR_036616	108014	Mm.287826	NM_025573	ENSMUSG00000029538	Srsf9	25kDa|2610029M16Rik|SRp30c|Sfrs9	serine/arginine-rich splicing factor 9	protein-coding
mm_7306.1	chr1	97977303	97977332	-	1	NA	intron (NM_013626, intron 1 of 25)	intron (NM_013626, intron 1 of 25)	70476	NR_037993	78603	Mm.442597	NR_037993	ENSMUSG00000089706	B230216N24Rik	-	RIKEN cDNA B230216N24 gene	ncRNA
mm_122482.1	chr14	45664419	45664425	-	1	NA	Intergenic	Intergenic	-6279	NM_001042719	114874	Mm.121918	NM_176845	ENSMUSG00000037697	Ddhd1	Mir5131|PA-PLA1	DDHD domain containing 1	protein-coding
mm_161992.1	chr19	34601973	34601973	-	1	NA	promoter-TSS (NM_001101605)	promoter-TSS (NM_001101605)	-5	NM_001101605	667373	Mm.371956	NM_001101605	ENSMUSG00000079339	Ifit1bl1	Gm14446|Ifit1c|OTTMUSG00000016644	interferon induced protein with tetratricpeptide repeats 1B like 1	protein-coding
mm_110999.1	chr12	78845271	78845310	-	1	NA	exon (NM_023721, exon 8 of 9)	exon (NM_023721, exon 8 of 9)	16348	NM_023721	73834	Mm.311549	NM_023721	ENSMUSG00000021114	Atp6v1d	1110004P10Rik|Atp6m|VATD|Vma8	ATPase, H+ transporting, lysosomal V1 subunit D	protein-coding
mm_117604.1	chr13	90089557	90089616	-	1	NA	promoter-TSS (NM_025335)	promoter-TSS (NM_025335)	22	NM_028012	108138	Mm.37531	NM_028012	ENSMUSG00000021615	Xrcc4	2310057B22Rik|AW413319|AW545101	X-ray repair complementing defective repair in Chinese hamster cells 4	protein-coding
mm_133108.1	chr16	65473925	65473939	+	1	NA	Intergenic	(CAG)n|Simple_repeat|Simple_repeat	-46697	NM_008849	18736	Mm.355440	NM_008849	ENSMUSG00000004842	Pou1f1	GHF-1|Hmp1|Pit-1|Pit1|Pit1-rs1|dw|dwarf	POU domain, class 1, transcription factor 1	protein-coding
mm_72770.1	chr8	85824295	85824330	+	1	NA	intron (NM_028007, intron 5 of 17)	intron (NM_028007, intron 5 of 17)	16637	NM_028007	71927	Mm.61018	NM_028007	ENSMUSG00000031703	Itfg1	2310047C21Rik|AI314457|Cda08|D8Wsu49e	integrin alpha FG-GAP repeat containing 1	protein-coding
mm_140483.1	chr17	3114836	3114892	-	1	NA	promoter-TSS (NM_134123)	promoter-TSS (NM_134123)	-108	NM_134123	106583	Mm.124373	NM_134123	ENSMUSG00000046201	Scaf8	A630086M08Rik|A930036P18Rik|AA408306|AI447644|AI448652|AU015035|Rbm16|mKIAA1116	SR-related CTD-associated factor 8	protein-coding
mm_3090.1	chr1	134408087	134408129	+	1	NA	intron (NM_028057, intron 5 of 8)	intron (NM_028057, intron 5 of 8)	2118	NM_028057	72017	Mm.280230	NM_028057	ENSMUSG00000026456	Cyb5r1	1500005G05Rik|B5R.1|C80155|Nqo3a2	cytochrome b5 reductase 1	protein-coding
mm_122585.1	chr14	50869351	50869355	-	1	NA	intron (NM_009351, intron 1 of 54)	ID_B1|SINE|B4	1201	NM_009351	21745	Mm.318736	NM_009351	ENSMUSG00000006281	Tep1	Tp1	telomerase associated protein 1	protein-coding
mm_82855.1	chr9	31455427	31455430	-	1	NA	intron (NM_144936, intron 1 of 5)	L1_Mur3|LINE|L1	8810	NM_144936	235135	Mm.390134	NM_144936	ENSMUSG00000041737	Tmem45b	BC018222	transmembrane protein 45b	protein-coding
mm_28586.1	chr3	94377255	94377281	-	1	NA	promoter-TSS (NM_001293734)	promoter-TSS (NM_001293734)	-164	NM_001293734	19885	Mm.4372	NM_011281	ENSMUSG00000028150	Rorc	Nr1f3|RORgamma|TOR|Thor	RAR-related orphan receptor gamma	protein-coding
mm_20360.1	chr2	128295000	128295008	-	1	NA	Intergenic	Intergenic	134347	NR_028591	100043424	Mm.297222	NR_028589		Gm14005	OTTMUSG00000015351	predicted gene 14005	ncRNA
mm_142102.1	chr17	35835535	35835567	-	1	NA	exon (NM_011655, exon 4 of 4)	exon (NM_011655, exon 4 of 4)	2750	NM_011655	22154	Mm.273538	NM_011655	ENSMUSG00000001525	Tubb5	AA408537|AI596182|B130022C14Rik|M(beta)5	tubulin, beta 5 class I	protein-coding
mm_13148.1	chr2	92344584	92344595	+	1	NA	exon (NM_001109690, exon 8 of 16)	exon (NM_001109690, exon 8 of 16)	26468	NM_001290774	228366	Mm.31158	NM_172670	ENSMUSG00000040434	Large2	5730485C17Rik|AI891893|Gyltl1b|Largel|mKIAA4105	LARGE xylosyl- and glucuronyltransferase 2	protein-coding
mm_45057.1	chr5	41819384	41819391	-	1	NA	exon (NM_001081422, exon 10 of 27)	exon (NM_001081422, exon 10 of 27)	24928	NM_001310601	665775	Mm.158726	NM_001081422	ENSMUSG00000061755	Bod1l	A230054D04Rik|AI853319|FAM44A|mKIAA1327	biorientation of chromosomes in cell division 1-like	protein-coding
mm_126598.1	chr15	82362911	82362913	+	1	NA	Intergenic	RLTR6_Mm|LTR|ERV1	-8621	NM_025987	67130	Mm.27570	NM_025987	ENSMUSG00000022450	Ndufa6	14kDa|2700038D15Rik|B230217P19Rik	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 6 (B14)	protein-coding
mm_127770.1	chr15	3279262	3279268	-	1	NA	exon (NM_009155, exon 5 of 5)	exon (NM_009155, exon 5 of 5)	8288	NM_009155	20363	Mm.392203	NM_009155	ENSMUSG00000064373	Selenop	AU018766|D15Ucla1|Se-P|Sepp1|selp	selenoprotein P	protein-coding
mm_20789.1	chr2	144009203	144009218	-	1	NA	intron (NM_024281, intron 1 of 23)	intron (NM_024281, intron 1 of 23)	2053	NM_133626	81910	Mm.13705	NM_024281	ENSMUSG00000027422	Rrbp1	1700087N07Rik|5730465C04Rik|ES/130|mKIAA1398|mRRp0|mRRp1.8|mRRp10|mRRp15a|mRRp15b|mRRp16.8|mRRp2|mRRp41|mRRp47|mRRp5.4|p180	ribosome binding protein 1	protein-coding
mm_119974.1	chr14	55560011	55560037	+	1	NA	promoter-TSS (NM_001199009)	promoter-TSS (NM_001199009)	-5	NR_037572	28199	Mm.11535	NM_133734	ENSMUSG00000022214	Dcaf11	0710008A13Rik|C76035|D14Ucla1|Dacf11|GLO14|Wdr23	DDB1 and CUL4 associated factor 11	protein-coding
mm_52035.1	chr6	96126650	96126663	+	1	NA	intron (NM_182808, intron 2 of 4)	intron (NM_182808, intron 2 of 4)	13502	NM_182808	320265	Mm.489890	NM_182808	ENSMUSG00000059187	Fam19a1	C630007B19Rik|FAM19A1 TAFA-1|TAFA1|Tafa-1	family with sequence similarity 19, member A1	protein-coding
mm_6463.1	chr1	74030863	74030878	-	1	NA	intron (NM_027884, intron 3 of 34)	L2c|LINE|L2	93577	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_154205.1	chr19	59075502	59075522	-	1	NA	exon (NM_001114312, exon 1 of 17)	exon (NM_001114312, exon 1 of 17)	557	NM_175172	71653	Mm.37338	NM_175172	ENSMUSG00000041362	Shtn1	4930506M07Rik|Kiaa1598|Shootin1|mKIAA1598	shootin 1	protein-coding
mm_83258.1	chr9	42428199	42428209	-	1	NA	intron (NM_173038, intron 7 of 7)	L2a|LINE|L2	-28275	NM_001324548	21683	Mm.42209	NM_009347	ENSMUSG00000037705	Tecta	Tctna	tectorin alpha	protein-coding
mm_89981.1	chr10	111608604	111608635	+	1	NA	Intergenic	Intergenic	-14346	NR_045344	71321	Mm.410785	NR_045344	ENSMUSG00000097082	4933440J02Rik	-	RIKEN cDNA 4933440J02 gene	ncRNA
mm_163336.1	chr12	12170539	12170540	-	1	NA	Intergenic	Intergenic	-91600	NM_029758	76820	Mm.440802	NM_029758	ENSMUSG00000020589	Fam49a	2410157M17Rik|9630047E15|D12Ertd553e	family with sequence similarity 49, member A	protein-coding
mm_131262.1	chr16	10791825	10791832	+	1	NA	promoter-TSS (NM_013638)	promoter-TSS (NM_013638)	277	NM_008933	19119	Mm.325769	NM_008933	ENSMUSG00000038015	Prm2	AI528784|Prm-2	protamine 2	protein-coding
mm_62804.1	chr7	112899010	112899013	+	1	NA	3' UTR (NM_001166585, exon 11 of 11)	3' UTR (NM_001166585, exon 11 of 11)	-54951	NM_175279	78748	Mm.349943	NM_175279	ENSMUSG00000098132	Rassf10	4632411J06Rik	Ras association (RalGDS/AF-6) domain family (N-terminal) member 10	protein-coding
mm_60377.1	chr7	44468075	44468084	+	1	NA	promoter-TSS (NM_001205073)	promoter-TSS (NM_001205073)	99	NM_001205070	66124	Mm.358691	NM_025368	ENSMUSG00000038695	Josd2	1110007C05Rik	Josephin domain containing 2	protein-coding
mm_20030.1	chr2	119618456	119618510	-	1	NA	promoter-TSS (NM_001042653)	promoter-TSS (NM_001042653)	22	NM_001042653	70645	Mm.246412	NM_001042653	ENSMUSG00000072980	Oip5	5730547N13Rik|Lint-25|Ms18b	Opa interacting protein 5	protein-coding
mm_38795.1	chr4	148149646	148149650	-	1	NA	5' UTR (NM_001163707, exon 2 of 6)	5' UTR (NM_001163707, exon 2 of 6)	2277	NM_001163705	50762	Mm.27445	NM_015797	ENSMUSG00000055401	Fbxo6	AA408845|FBG2|Fbs2|Fbx6b|Fbxo6b	F-box protein 6	protein-coding
mm_9710.1	chr1	179546228	179546260	-	1	NA	promoter-TSS (NM_146105)	promoter-TSS (NM_146105)	32	NM_001331055	15278	Mm.293529	NM_008249	ENSMUSG00000026492	Tfb2m	Hkp1	transcription factor B2, mitochondrial	protein-coding
mm_100042.1	chr11	115091838	115091857	+	1	NA	5' UTR (NM_001163753, exon 1 of 9)	5' UTR (NM_001163753, exon 1 of 9)	416	NM_001163753	58222	Mm.143789	NM_021411	ENSMUSG00000020732	Rab37	B230331O03Rik|B230354I04Rik	RAB37, member RAS oncogene family	protein-coding
mm_157600.1	chrX	53370443	53370466	-	1	NA	non-coding (NR_110964, exon 1 of 7)	non-coding (NR_110964, exon 1 of 7)	105	NM_027409	70380	Mm.491083	NM_027409	ENSMUSG00000023074	Mospd1	1810018L05Rik	motile sperm domain containing 1	protein-coding
mm_35801.1	chr4	46591864	46591867	-	1	NA	intron (NM_001164804, intron 1 of 11)	B1_Mur1|SINE|Alu	10064	NM_001164804	107684	Mm.416311	NM_178893	ENSMUSG00000028337	Coro2a	9030208C03Rik|AI563590|IR10	coronin, actin binding protein 2A	protein-coding
mm_148592.1	chr19	5069691	5069705	+	1	NA	exon (NM_054042, exon 1 of 1)	exon (NM_054042, exon 1 of 1)	1620	NM_054042	70445	Mm.29597	NM_054042	ENSMUSG00000056481	Cd248	2610111G01Rik|AI842296|Cd164l1|Tem1	CD248 antigen, endosialin	protein-coding
mm_134451.1	chr16	18407944	18407957	-	1	NA	TTS (NM_001272032)	TTS (NM_001272032)	5544	NM_001111063	12846	Mm.100940	NM_007744	ENSMUSG00000000326	Comt	Comt1|D16Wsu103e|D330014B15Rik	catechol-O-methyltransferase	protein-coding
mm_161703.1	chr17	24364531	24364531	+	1	NA	5' UTR (NM_001039581, exon 3 of 32)	5' UTR (NM_001039581, exon 3 of 32)	12508	NM_001039581	27410	Mm.239470	NM_013855	ENSMUSG00000024130	Abca3	1810036E22Rik|ABC-C|Abc3	ATP-binding cassette, sub-family A (ABC1), member 3	protein-coding
mm_144351.1	chr18	15195389	15195410	+	1	NA	Intergenic	Intergenic	-43953	NM_134112	106931	Mm.329299	NM_134112	ENSMUSG00000036225	Kctd1	4933402K10Rik|AI661543|AW553000	potassium channel tetramerisation domain containing 1	protein-coding
mm_73046.1	chr8	94354997	94355003	+	1	NA	intron (NM_019415, intron 21 of 24)	intron (NM_019415, intron 21 of 24)	25792	NM_001205311	20497	Mm.25804	NM_019415	ENSMUSG00000031766	Slc12a3	AI035291|NCC|NCCT|TSC	solute carrier family 12, member 3	protein-coding
mm_117106.1	chr13	60176548	60176564	-	1	NA	exon (NM_008086, exon 1 of 1)	exon (NM_008086, exon 1 of 1)	979	NM_008086	14451	Mm.22701	NM_008086	ENSMUSG00000052957	Gas1	AW554192|Gas-1	growth arrest specific 1	protein-coding
mm_137273.1	chr17	24719954	24719956	+	1	NA	promoter-TSS (NR_028515)	promoter-TSS (NR_028515)	10	NR_027900	73474	Mm.443320	NR_027900	ENSMUSG00000090101	Snhg9	1700072N11Rik	small nucleolar RNA host gene 9	ncRNA
mm_100525.1	chr11	120581662	120581700	+	1	NA	promoter-TSS (NM_133796)	promoter-TSS (NM_133796)	-61	NM_133796	192662	Mm.30016	NM_133796	ENSMUSG00000025132	Arhgdia	5330430M07Rik|Gdi-1|Rho-GDI|RhoDGI|RhoGDI-1	Rho GDP dissociation inhibitor (GDI) alpha	protein-coding
mm_58376.1	chr6	149100376	149100379	-	1	NA	intron (NM_177192, intron 1 of 20)	intron (NM_177192, intron 1 of 20)	1303	NM_177192	320560	Mm.426874	NM_177192	ENSMUSG00000030313	Dennd5b	9330160C06Rik|AI852444|D030011O10Rik|ENSMUSG00000072657|Gm17524	DENN/MADD domain containing 5B	protein-coding
mm_122620.1	chr14	51145480	51145490	-	1	NA	exon (NM_011271, exon 2 of 2)	exon (NM_011271, exon 2 of 2)	1282	NM_011271	19752	Mm.235538	NM_011271	ENSMUSG00000035896	Rnase1	AI574248|Rib-1|Rib1	ribonuclease, RNase A family, 1 (pancreatic)	protein-coding
mm_96477.1	chr11	67656046	67656065	+	1	NA	intron (NM_001109657, intron 5 of 13)	intron (NM_001109657, intron 5 of 13)	-39271	NM_009038	19674	Mm.439726	NM_009038	ENSMUSG00000020907	Rcvrn	CAR|S-modulin	recoverin	protein-coding
mm_136635.1	chr17	5713140	5713143	+	1	NA	intron (NM_146073, intron 4 of 8)	intron (NM_146073, intron 4 of 8)	-85516	NR_045081	78512	Mm.23696	NR_045079	ENSMUSG00000096965	3300005D01Rik	-	RIKEN cDNA 3300005D01 gene	ncRNA
mm_127906.1	chr15	9524130	9524135	-	1	NA	intron (NM_008372, intron 2 of 7)	intron (NM_008372, intron 2 of 7)	5744	NM_008372	16197	Mm.389	NM_008372	ENSMUSG00000003882	Il7r	CD127|IL-7Ralpha	interleukin 7 receptor	protein-coding
mm_122640.1	chr14	51219225	51219249	-	1	NA	Intergenic	MLTR25A|LTR|ERVK	15542	NM_017389	503847	Mm.377124	NM_017389	ENSMUSG00000050766	Ear14	-	eosinophil-associated, ribonuclease A family, member 14	protein-coding
mm_140617.1	chr17	10840566	10840585	-	1	NA	promoter-TSS (NM_027032)	promoter-TSS (NM_027032)	216	NM_016694	50873	Mm.311110	NM_016694	ENSMUSG00000023826	Park2	PRKN	Parkinson disease (autosomal recessive, juvenile) 2, parkin	protein-coding
mm_56350.1	chr6	92988267	92988270	-	1	NA	intron (NR_015530, intron 1 of 2)	intron (NR_015530, intron 1 of 2)	47686	NR_015530	330385	Mm.483472	NR_015530	ENSMUSG00000097462	9530026P05Rik	B430306B02	RIKEN cDNA 9530026P05 gene	ncRNA
mm_95966.1	chr11	58917890	58917915	+	1	NA	promoter-TSS (NM_138678)	promoter-TSS (NM_138678)	-155	NM_138678	192194	Mm.22540	NM_138678	ENSMUSG00000020490	Btnl10	BUTR-1|Butr1	butyrophilin-like 10	protein-coding
mm_79521.1	chr9	57561002	57561012	+	1	NA	promoter-TSS (NM_022813)	promoter-TSS (NM_022813)	63	NM_022813	24044	Mm.286069	NM_022813	ENSMUSG00000040188	Scamp2	AI875466|Sc2	secretory carrier membrane protein 2	protein-coding
mm_17961.1	chr2	37423007	37423055	-	1	NA	promoter-TSS (NM_001100591)	promoter-TSS (NM_001100591)	-128	NM_001290642	319817	Mm.288785	NM_001100591	ENSMUSG00000075376	Rc3h2	2900024N03Rik|9430019J22Rik|D930043C02Rik|Mnab|Rnf164	ring finger and CCCH-type zinc finger domains 2	protein-coding
mm_60464.1	chr7	44477861	44477880	+	1	NA	Intergenic	Intergenic	-6647	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_2771.1	chr1	130731964	130731991	+	1	NA	promoter-TSS (NM_177604)	promoter-TSS (NM_177604)	1	NM_177604	212439	Mm.268547	NM_177604	ENSMUSG00000042510	AA986860	E030025M07|Sarg	expressed sequence AA986860	protein-coding
mm_7686.1	chr1	128591168	128591183	-	1	NA	intron (NM_009911, intron 1 of 1)	CpG	1124	NM_009911	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding
mm_116912.1	chr13	55488028	55488032	-	1	NA	promoter-TSS (NM_019813)	promoter-TSS (NM_019813)	46	NM_001177371	56320	Mm.19016	NM_019813	ENSMUSG00000034675	Dbn1	-	drebrin 1	protein-coding
mm_172358.1	chr7	11609282	11609294	+	1	NA	Intergenic	Intergenic	61231	NM_145843	252905	Mm.377264	NM_145843	ENSMUSG00000095430	Vmn1r72	V1rg1	vomeronasal 1 receptor 72	protein-coding
mm_56366.1	chr6	93913271	93913281	-	1	NA	promoter-TSS (NR_104594)	promoter-TSS (NR_104594)	-313	NR_104594	14924	Mm.217216	NM_010367	ENSMUSG00000045095	Magi1	AIP3|BAP1|Baiap1|Gukmi1|MAGI1c|Magi-1|TNRC19|WWP3|mKIAA4129	membrane associated guanylate kinase, WW and PDZ domain containing 1	protein-coding
mm_116617.1	chr13	48871755	48871770	-	1	NA	promoter-TSS (NM_011078)	promoter-TSS (NM_011078)	-877	NM_011078	18676	Mm.486213	NM_011078	ENSMUSG00000038025	Phf2	GRC5	PHD finger protein 2	protein-coding
mm_335.1	chr1	29841835	29841839	+	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	420349	NR_105760	102465174		NR_105760	ENSMUSG00000099257	Mir6342	Gm27268|mmu-mir-6342	microRNA 6342	ncRNA
mm_146070.1	chr18	70472661	70472675	+	1	NA	promoter-TSS (NM_001289649)	promoter-TSS (NM_001289649)	2	NM_001289650	170461	Mm.83623	NM_029019	ENSMUSG00000079608	Stard6	1700011K09Rik|4833424I06Rik|4933429L05Rik|AI644424	StAR-related lipid transfer (START) domain containing 6	protein-coding
mm_100100.1	chr11	115708063	115708087	+	1	NA	intron (NM_008163, intron 1 of 5)	CpG	522	NM_008163	14784	Mm.439649	NM_008163	ENSMUSG00000059923	Grb2	AA408164|Ash	growth factor receptor bound protein 2	protein-coding
mm_130731.1	chr15	101247192	101247221	-	1	NA	Intergenic	Intergenic	-19640	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_109579.1	chr12	112490741	112490754	+	1	NA	intron (NM_177039, intron 1 of 4)	intron (NM_177039, intron 1 of 4)	1299	NM_177039	319942	Mm.185209	NM_177039	ENSMUSG00000043122	A530016L24Rik	Nrac	RIKEN cDNA A530016L24 gene	protein-coding
mm_131278.1	chr16	11060936	11060949	+	1	NA	Intergenic	Intergenic	-5356	NM_009223	20621	Mm.325800	NM_009223	ENSMUSG00000037972	Snn	2810407J07Rik|AI848521|AW547286	stannin	protein-coding
mm_59929.1	chr7	30423413	30423423	+	1	NA	5' UTR (NM_172142, exon 1 of 11)	5' UTR (NM_172142, exon 1 of 11)	114	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_14453.1	chr2	131186943	131186971	+	1	NA	promoter-TSS (NM_001111075)	promoter-TSS (NM_001111075)	9	NM_001111075	12531	Mm.38444	NM_023117	ENSMUSG00000027330	Cdc25b	AI604853	cell division cycle 25B	protein-coding
mm_4306.1	chr1	171840816	171840834	+	1	NA	intron (NM_001289470, intron 2 of 8)	intron (NM_001289470, intron 2 of 8)	1128	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_28709.1	chr3	95651338	95651341	-	1	NA	Intergenic	Intergenic	-7382	NM_008562	17210	Mm.1639	NM_008562	ENSMUSG00000038612	Mcl1	AW556805|Mcl-1	myeloid cell leukemia sequence 1	protein-coding
mm_87621.1	chr10	57794730	57794750	+	1	NA	exon (NM_020561, exon 1 of 8)	exon (NM_020561, exon 1 of 8)	196	NM_020561	57319	Mm.2379	NM_020561	ENSMUSG00000019872	Smpdl3a	0610010C24Rik|AI529588|ASM3A|ASML3|ASML3A	sphingomyelin phosphodiesterase, acid-like 3A	protein-coding
mm_144729.1	chr18	35553402	35553421	+	1	NA	promoter-TSS (NR_038073)	promoter-TSS (NR_038073)	1	NR_038073	100503380	Mm.482118	NR_038073	ENSMUSG00000097769	Snhg4	Gm17457	small nucleolar RNA host gene 4	ncRNA
mm_686.1	chr1	40529601	40529611	+	1	NA	intron (NM_010553, intron 6 of 12)	intron (NM_010553, intron 6 of 12)	14244	NM_010553	16174	Mm.20466	NM_010553	ENSMUSG00000026068	Il18rap	AcPL|IL-18R-beta|IL-18RAcP|IL-18Rbeta|IL-1RAcPL	interleukin 18 receptor accessory protein	protein-coding
mm_29572.1	chr3	116968791	116968815	-	1	NA	5' UTR (NM_023245, exon 1 of 8)	5' UTR (NM_023245, exon 1 of 8)	149	NM_023245	114301	Mm.253736	NM_023245	ENSMUSG00000033377	Palmd	4631423C22Rik|PALML	palmdelphin	protein-coding
mm_109480.1	chr12	111429030	111429110	+	1	NA	intron (NM_001289487, intron 12 of 13)	intron (NM_001289487, intron 12 of 13)	11625	NM_001289488	74190	Mm.248640	NM_028807	ENSMUSG00000021280	Exoc3l4	1200009I06Rik|1600013K19Rik	exocyst complex component 3-like 4	protein-coding
mm_92234.1	chr10	69210094	69210120	-	1	NA	3' UTR (NM_001331193, exon 2 of 2)	3' UTR (NM_001331193, exon 2 of 2)	1555	NM_001252636	69288	Mm.26659	NM_001081347	ENSMUSG00000019944	Rhobtb1	1700008H16Rik|3110048G13Rik|AI173445|AI573858|AV350930	Rho-related BTB domain containing 1	protein-coding
mm_198.1	chr1	16053300	16053300	+	1	NA	Intergenic	Intergenic	40025	NM_001305227	75799	Mm.78557	NM_001243238	ENSMUSG00000067795	4930444P10Rik	-	RIKEN cDNA 4930444P10 gene	protein-coding
mm_47965.1	chr5	135744197	135744204	-	1	NA	promoter-TSS (NM_172541)	promoter-TSS (NM_172541)	-28	NM_172541	215210	Mm.11688	NM_172541	ENSMUSG00000039886	Tmem120a	2010310D06Rik|Tmpit	transmembrane protein 120A	protein-coding
mm_47045.1	chr5	116024453	116024468	-	1	NA	promoter-TSS (NM_031869)	promoter-TSS (NM_031869)	-32	NM_031869	19079	Mm.458152	NM_031869	ENSMUSG00000029513	Prkab1	1300015D22Rik|AU021155|E430008F22	protein kinase, AMP-activated, beta 1 non-catalytic subunit	protein-coding
mm_122997.1	chr14	54992428	54992438	-	1	NA	intron (NM_080728, intron 4 of 40)	intron (NM_080728, intron 4 of 40)	2116	NM_080728	140781	Mm.457983	NM_080728	ENSMUSG00000053093	Myh7	B-MHC|MyHC-I|Myhc-b|Myhcb|beta-MHC	myosin, heavy polypeptide 7, cardiac muscle, beta	protein-coding
mm_11641.1	chr2	34879443	34879446	+	1	NA	intron (NM_001308024, intron 1 of 4)	B4A|SINE|B4	5048	NM_030021	77996	Mm.215255	NM_030021	ENSMUSG00000026870	Cutal	D730039F16Rik	cutA divalent cation tolerance homolog-like	protein-coding
mm_108359.1	chr12	80721728	80721757	+	1	NA	intron (NM_001177503, intron 11 of 12)	intron (NM_001177503, intron 11 of 12)	29141	NM_001177503	217682	Mm.154541	NM_001177503	ENSMUSG00000066438	Plekhd1	3830431G21Rik	pleckstrin homology domain containing, family D (with coiled-coil domains) member 1	protein-coding
mm_119573.1	chr14	50466031	50466033	+	1	NA	Intergenic	Intergenic	-7025	NM_207133	258233	Mm.377278	NM_207133	ENSMUSG00000095765	Olfr741	GA_x5J8B7TYL6J-3-280|GA_x5J8B7U07Q4-325-757|GA_x6K02T2PMLR-6197851-6198786|MOR106-10|MOR106-15	olfactory receptor 741	protein-coding
mm_47472.1	chr5	123700065	123700072	-	1	NA	3' UTR (NM_027494, exon 14 of 14)	3' UTR (NM_027494, exon 14 of 14)	-15707	NM_001347468	56430	Mm.241109	NM_019765	ENSMUSG00000049550	Clip1	1110007I12Rik|4631429H07Rik|AV017631|C81039|CLIP-170|CLIP170|CYLN1|Clip50|Rsn|mKIAA4046|restin	CAP-GLY domain containing linker protein 1	protein-coding
mm_32592.1	chr4	111720085	111720095	+	1	NA	promoter-TSS (NM_026470)	promoter-TSS (NM_026470)	80	NM_026470	67946	Mm.275526	NM_026470	ENSMUSG00000034401	Spata6	1700062C23Rik|AI790763|Hash|KRP|Mash	spermatogenesis associated 6	protein-coding
mm_123933.1	chr14	73366715	73366722	-	1	NA	intron (NM_008410, intron 2 of 5)	intron (NM_008410, intron 2 of 5)	18553	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_154974.1	chrX	37190441	37190444	+	1	NA	promoter-TSS (NM_153503)	promoter-TSS (NM_153503)	-780	NM_153503	69942	Mm.307182	NM_153503	ENSMUSG00000036537	Rnf113a1	2810428C21Rik|Rnf113a	ring finger protein 113A1	protein-coding
mm_13970.1	chr2	121432312	121432349	+	1	NA	exon (NM_007952, exon 7 of 13)	exon (NM_007952, exon 7 of 13)	10271	NM_145973	269344	Mm.330522	NM_145973	ENSMUSG00000027246	Ell3	A930015D22Rik	elongation factor RNA polymerase II-like 3	protein-coding
mm_17531.1	chr2	29623553	29623583	-	1	NA	intron (NM_001039087, intron 1 of 25)	intron (NM_001039087, intron 1 of 25)	3848	NM_001039086	107746	Mm.298274	NM_054050	ENSMUSG00000039844	Rapgef1	4932418O06Rik|C3G|Grf2	Rap guanine nucleotide exchange factor (GEF) 1	protein-coding
mm_119994.1	chr14	55591820	55591859	+	1	NA	promoter-TSS (NM_011190)	promoter-TSS (NM_011190)	49	NM_194346	268749	Mm.23748	NM_194346	ENSMUSG00000047098	Rnf31	AL033293|BC031509|Flj10111|HOIP|Paul|mFLJ00217	ring finger protein 31	protein-coding
mm_168400.1	chr11	29547892	29547892	-	1	NA	promoter-TSS (NM_028504)	promoter-TSS (NM_028504)	-58	NM_028504	73324	Mm.69388	NM_028504	ENSMUSG00000020461	Clhc1	1700034F02Rik	clathrin heavy chain linker domain containing 1	protein-coding
mm_16279.1	chr2	173779214	173779226	+	1	NA	3' UTR (NM_019806, exon 6 of 6)	3' UTR (NM_019806, exon 6 of 6)	41649	NM_019806	56491	Mm.260456	NM_019806	ENSMUSG00000054455	Vapb	AI225786|AI840687|AI848259|D2Abb2e|R75548|VAP33b|Vamp33b	vesicle-associated membrane protein, associated protein B and C	protein-coding
mm_169953.1	chr16	84834990	84834994	+	1	NA	promoter-TSS (NM_001302216)	promoter-TSS (NM_001302216)	6	NM_001302216	11957	Mm.353	NM_016755	ENSMUSG00000022890	Atp5j	CF6	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit F	protein-coding
mm_14666.1	chr2	138365623	138365631	+	1	NA	Intergenic	Intergenic	87134	NM_145534	228662	Mm.153405	NM_145534	ENSMUSG00000062098	Btbd3	mKIAA0952	BTB (POZ) domain containing 3	protein-coding
mm_64696.1	chr7	4528097	4528139	-	1	NA	intron (NM_001033548, intron 4 of 11)	intron (NM_001033548, intron 4 of 11)	4324	NM_001033548	436022	Mm.425359	NM_001033548	ENSMUSG00000055809	Dnaaf3	6030429G01Rik|b2b1739Clo	dynein, axonemal assembly factor 3	protein-coding
mm_58416.1	chr7	3290589	3290614	+	1	NA	promoter-TSS (NM_016969)	promoter-TSS (NM_016969)	45	NM_001093765	50918	Mm.29874	NM_016969	ENSMUSG00000068566	Myadm	D7Wsu62e	myeloid-associated differentiation marker	protein-coding
mm_149012.1	chr19	8735809	8735864	+	1	NA	promoter-TSS (NM_134139)	promoter-TSS (NM_134139)	-3	NM_134139	107071	Mm.29627	NM_134139	ENSMUSG00000042729	Wdr74	5730436H21Rik|AA407588	WD repeat domain 74	protein-coding
mm_128723.1	chr15	64060219	64060278	-	1	NA	5' UTR (NM_144846, exon 1 of 12)	5' UTR (NM_144846, exon 1 of 12)	200	NM_144846	223601	Mm.246108	NM_144846	ENSMUSG00000022378	Fam49b	0910001A06Rik|AW122079	family with sequence similarity 49, member B	protein-coding
mm_36245.1	chr4	63387074	63387083	-	1	NA	exon (NM_001045514, exon 5 of 22)	exon (NM_001045514, exon 5 of 22)	11162	NM_001305432	100182	Mm.387725	NM_001045514	ENSMUSG00000039158	Akna	AI597013	AT-hook transcription factor	protein-coding
mm_134590.1	chr16	20426323	20426372	-	1	NA	promoter-TSS (NM_013790)	promoter-TSS (NM_013790)	47	NM_013790	27416	Mm.20845	NM_013790	ENSMUSG00000022822	Abcc5	2900011L11Rik|AI132311|Abcc5a|Abcc5b|Mrp5	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	protein-coding
mm_80571.1	chr9	83939069	83939083	+	1	NA	intron (NM_001305935, intron 1 of 10)	RMER6D|LTR|ERVK	-9705	NM_199195	12040	Mm.12819	NM_199195	ENSMUSG00000032263	Bckdhb	BCKDE1B|BCKDH E1-beta	branched chain ketoacid dehydrogenase E1, beta polypeptide	protein-coding
mm_37850.1	chr4	132212000	132212010	-	1	NA	5' UTR (NM_145393, exon 1 of 5)	5' UTR (NM_145393, exon 1 of 5)	251	NM_145393	213541	Mm.23998	NM_145393	ENSMUSG00000040025	Ythdf2	9430020E02Rik|HGRG8|NY-REN-2	YTH domain family 2	protein-coding
mm_123001.1	chr14	54992834	54992847	-	1	NA	exon (NM_080728, exon 4 of 41)	exon (NM_080728, exon 4 of 41)	1709	NM_080728	140781	Mm.457983	NM_080728	ENSMUSG00000053093	Myh7	B-MHC|MyHC-I|Myhc-b|Myhcb|beta-MHC	myosin, heavy polypeptide 7, cardiac muscle, beta	protein-coding
mm_39591.1	chr5	23496423	23496435	+	1	NA	exon (NM_026984, exon 18 of 26)	exon (NM_026984, exon 18 of 26)	62000	NM_026984	69188	Mm.205190	NM_026984	ENSMUSG00000029004	Kmt2e	1810033J14Rik|9530077A04Rik|D230038D11Rik|Mll5|NKp44L	lysine (K)-specific methyltransferase 2E	protein-coding
mm_160519.1	chr9	24300338	24300338	+	1	NA	intron (NM_175678, intron 6 of 9)	intron (NM_175678, intron 6 of 9)	202320	NM_175678	319239	Mm.130824	NM_175678	ENSMUSG00000043659	Npsr1	9330128H10Rik|GPRA|Gpr154|MVTR|PGR14|VRR1	neuropeptide S receptor 1	protein-coding
mm_57482.1	chr6	125241668	125241673	-	1	NA	Intergenic	Intergenic	-4643	NM_001286753	21940	Mm.367714	NM_001033126	ENSMUSG00000030336	Cd27	S152|Tnfrsf7|Tp55	CD27 antigen	protein-coding
mm_39616.1	chr5	24383548	24383561	+	1	NA	TTS (NM_001002897)	TTS (NM_001002897)	8589	NM_001002897	213948	Mm.332252	NM_001002897	ENSMUSG00000038295	Atg9b	Apg912|Apg9l2|Apgdc2|Gm574|Nos3as|eONE|sONE	autophagy related 9B	protein-coding
mm_1878.1	chr1	85649998	85650004	+	1	NA	promoter-TSS (NM_013673)	promoter-TSS (NM_013673)	13	NM_001313714	20684	Mm.290906	NM_013673	ENSMUSG00000026222	Sp100	A430075G10Rik	nuclear antigen Sp100	protein-coding
mm_155118.1	chrX	48695021	48695029	+	1	NA	promoter-TSS (NM_173376)	promoter-TSS (NM_173376)	21	NM_173376	209003	Mm.32561	NM_173376	ENSMUSG00000031107	Rbmx2	2700089A17Rik|2810411A03Rik|CGI-79	RNA binding motif protein, X-linked 2	protein-coding
mm_7486.1	chr1	121327673	121327690	-	1	NA	promoter-TSS (NM_001271531)	promoter-TSS (NM_001271531)	-3	NM_001271531	72999	Mm.27136	NM_133748	ENSMUSG00000003721	Insig2	2900053I11Rik|C730043J18Rik|Insig-2	insulin induced gene 2	protein-coding
mm_126528.1	chr15	81987836	81987848	+	1	NA	Intergenic	Intergenic	7302	NM_025503	66346	Mm.54292	NM_025503	ENSMUSG00000061633	1700029P11Rik	-	RIKEN cDNA 1700029P11 gene	protein-coding
mm_65301.1	chr7	24672033	24672048	-	1	NA	promoter-TSS (NM_019981)	promoter-TSS (NM_019981)	10	NM_019981	56746	Mm.23385	NM_019981	ENSMUSG00000062773	Tex101	1700008H15Rik|AI429076|TES101RP	testis expressed gene 101	protein-coding
mm_48693.1	chr5	146795003	146795009	-	1	NA	promoter-TSS (NM_011669)	promoter-TSS (NM_011669)	-50	NM_011669	22217	Mm.167971	NM_011669	ENSMUSG00000029640	Usp12	Ubh1	ubiquitin specific peptidase 12	protein-coding
mm_32219.1	chr4	101656141	101656158	+	1	NA	exon (NM_175036, exon 3 of 4)	exon (NM_175036, exon 3 of 4)	8366	NM_175036	230514	Mm.4756	NM_175036	ENSMUSG00000035212	Leprot	LEPR|OB-RGRP|Obrgrp|VPS55	leptin receptor overlapping transcript	protein-coding
mm_34933.1	chr4	155839770	155839824	+	1	NA	5' UTR (NM_024263, exon 1 of 10)	5' UTR (NM_024263, exon 1 of 10)	117	NM_024263	74761	Mm.159028	NM_024263	ENSMUSG00000029070	Mxra8	1200013A08Rik|1700095D18Rik|AI131686|Asp3|Dicam	matrix-remodelling associated 8	protein-coding
mm_17049.1	chr2	20968944	20968957	-	1	NA	promoter-TSS (NR_033225)	promoter-TSS (NR_033225)	76	NR_033225	433408	Mm.386941	NR_033225		Gm13375	OTTMUSG00000011664	predicted gene 13375	ncRNA
mm_116991.1	chr13	56488102	56488131	-	1	NA	Intergenic	Intergenic	-5870	NM_008373	16198	Mm.3006	NM_008373	ENSMUSG00000021538	Il9	Il-9|P40	interleukin 9	protein-coding
mm_98373.1	chr11	94044195	94044238	+	1	NA	promoter-TSS (NM_001199205)	promoter-TSS (NM_001199205)	11	NM_001025429	70834	Mm.260737	NM_027569	ENSMUSG00000020859	Spag9	3110018C07Rik|4733401I23Rik|4831406C20Rik|AW552012|JLP|JSAP2|JSAP2a|Jip4|Mapk8ip4|syd1	sperm associated antigen 9	protein-coding
mm_92941.1	chr10	84794743	84794753	-	1	NA	intron (NM_001024918, intron 2 of 17)	intron (NM_001024918, intron 2 of 17)	38700	NM_001024918	71137	Mm.79070	NM_027689	ENSMUSG00000020037	Rfx4	4933412G19Rik|NYD-sp10	regulatory factor X, 4 (influences HLA class II expression)	protein-coding
mm_88274.1	chr10	75037078	75037100	+	1	NA	promoter-TSS (NM_029781)	promoter-TSS (NM_029781)	0	NM_029781	76877	Mm.133593	NM_029781	ENSMUSG00000020175	Rab36	6330593L16Rik|AW047545	RAB36, member RAS oncogene family	protein-coding
mm_135460.1	chr16	45742811	45742821	-	1	NA	exon (NM_001272070, exon 1 of 6)	exon (NM_001272070, exon 1 of 6)	139	NM_001272070	213012	Mm.247453	NM_172511	ENSMUSG00000033157	Abhd10	-	abhydrolase domain containing 10	protein-coding
mm_16573.1	chr2	3423988	3424024	-	1	NA	promoter-TSS (NM_175683)	promoter-TSS (NM_175683)	-125	NM_146114	227525	Mm.23483	NM_146114	ENSMUSG00000026648	Dclre1c	9930121L06Rik|AI661365|Art|Snm1l	DNA cross-link repair 1C	protein-coding
mm_125803.1	chr15	74918706	74918729	+	1	NA	Intergenic	Intergenic	-36334	NM_001164039	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_3446.1	chr1	150102835	150102841	+	1	NA	intron (NM_011198, intron 5 of 9)	intron (NM_011198, intron 5 of 9)	2807	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_124043.1	chr14	77036899	77036923	-	1	NA	promoter-TSS (NM_172488)	promoter-TSS (NM_172488)	139	NM_001310649	108811	Mm.102168	NM_175369	ENSMUSG00000034795	Ccdc122	4933415L06Rik	coiled-coil domain containing 122	protein-coding
mm_89385.1	chr10	89744989	89745022	+	1	NA	promoter-TSS (NM_029166)	promoter-TSS (NM_029166)	14	NM_029166	75089	Mm.268922	NM_029166	ENSMUSG00000019951	Uhrf1bp1l	2010319N22Rik|4930506D01Rik|AA589495|C80672|E030041M21Rik|mKIAA0701	UHRF1 (ICBP90) binding protein 1-like	protein-coding
mm_71293.1	chr8	41154090	41154106	+	1	NA	Intergenic	Intergenic	-20372	NM_001005863	102103	Mm.149438	NM_001005863	ENSMUSG00000045636	Mtus1	AI481402|ATBP135|Atip1|B430010I23Rik|B430305I03Rik|C85752|Cctsg1-440|MD44|MTSG1|mKIAA1288	mitochondrial tumor suppressor 1	protein-coding
mm_67535.1	chr7	81345276	81345331	-	1	NA	promoter-TSS (NM_009092)	promoter-TSS (NM_009092)	-69	NM_009092	20068	Mm.42767	NM_009092	ENSMUSG00000061787	Rps17	-	ribosomal protein S17	protein-coding
mm_131519.1	chr16	17581187	17581188	+	1	NA	Intergenic	Intergenic	-4516	NM_144852	224022	Mm.298878	NM_144852	ENSMUSG00000022756	Slc7a4	AI853530	solute carrier family 7 (cationic amino acid transporter, y+ system), member 4	protein-coding
mm_62185.1	chr7	97480929	97480966	+	1	NA	promoter-TSS (NM_027256)	promoter-TSS (NM_027256)	-9	NM_027256	101861	Mm.27383	NM_027256	ENSMUSG00000025133	Ints4	2610034N24Rik|AA692684|AW493223	integrator complex subunit 4	protein-coding
mm_29666.1	chr3	122619664	122619680	-	1	NA	promoter-TSS (NM_001114665)	promoter-TSS (NM_001114665)	42	NM_001114665	214459	Mm.209491	NM_153118	ENSMUSG00000039735	Fnbp1l	2610318I01Rik|AW548221|TOCA1|toca-1	formin binding protein 1-like	protein-coding
mm_118026.1	chr13	100946929	100946930	-	1	NA	Intergenic	Intergenic	-113502	NM_022885	69048	Mm.402215	NM_022885	ENSMUSG00000021629	Slc30a5	1810010K08Rik|AF233321|ZNT5|ZTL1|ZnT-5|Zntl1	solute carrier family 30 (zinc transporter), member 5	protein-coding
mm_54119.1	chr6	18109039	18109062	-	1	NA	promoter-TSS (NM_023729)	promoter-TSS (NM_023729)	11	NM_023729	74068	Mm.73091	NM_023729	ENSMUSG00000010796	Asz1	4933400N19Rik|Gasz|ORF3	ankyrin repeat, SAM and basic leucine zipper domain containing 1	protein-coding
mm_76334.1	chr8	84713794	84713804	-	1	NA	exon (NM_010906, exon 8 of 9)	exon (NM_010906, exon 8 of 9)	12342	NM_008535	17095	Mm.4925	NM_008535	ENSMUSG00000034041	Lyl1	Lyl-1|bHLHa18	lymphoblastomic leukemia 1	protein-coding
mm_48500.1	chr5	142815407	142815477	-	1	NA	5' UTR (NM_001122730, exon 2 of 28)	5' UTR (NM_001122730, exon 2 of 28)	1945	NM_178242	231861	Mm.354649	NM_178242	ENSMUSG00000039477	Tnrc18	BC025631|EG381742|Zfp469	trinucleotide repeat containing 18	protein-coding
mm_61247.1	chr7	65803995	65804003	+	1	NA	promoter-TSS (NR_045301)	promoter-TSS (NR_045301)	-53	NR_045301	100503969	Mm.383527	NR_045301		1810008I18Rik	-	RIKEN cDNA 1810008I18 gene	ncRNA
mm_143351.1	chr17	67120421	67120423	-	1	NA	intron (NM_008984, intron 2 of 30)	intron (NM_008984, intron 2 of 30)	-94187	NR_049205	100885844		NR_049205	ENSMUSG00000093508	Mir5709	Gm22041|mir-5709|mmu-mir-5709	microRNA 5709	ncRNA
mm_35886.1	chr4	49541274	49541295	-	1	NA	exon (NM_144903, exon 5 of 9)	exon (NM_144903, exon 5 of 9)	8262	NM_144903	230163	Mm.482116	NM_144903	ENSMUSG00000028307	Aldob	Aldo-2|Aldo2|BC016435	aldolase B, fructose-bisphosphate	protein-coding
mm_3436.1	chr1	150101978	150102113	+	1	NA	exon (NM_011198, exon 4 of 10)	exon (NM_011198, exon 4 of 10)	2014	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_34772.1	chr4	153957248	153957275	+	1	NA	promoter-TSS (NM_001163019)	promoter-TSS (NM_001163019)	24	NM_001163019	97159	Mm.7066	NM_175287	ENSMUSG00000047613	A430005L14Rik	C79672	RIKEN cDNA A430005L14 gene	protein-coding
mm_50171.1	chr6	41557679	41557733	+	1	NA	Intergenic	Intergenic	35930	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_94791.1	chr11	22859862	22859873	+	1	NA	promoter-TSS (NM_016888)	promoter-TSS (NM_016888)	-132	NM_016888	53625	Mm.395495	NM_016888	ENSMUSG00000051650	B3gnt2	AA408337|AA409404|AW260308|B3Galt6|B3gnt1|BGnT-1|BGnT-2|BGnT1|BGnT2|Beta3gnt	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 2	protein-coding
mm_112113.1	chr12	112797647	112797657	-	1	NA	Intergenic	Intergenic	-11323	NM_145450	217887	Mm.186678	NM_145450	ENSMUSG00000037594	BC022687	AW050009|C130001I08Rik|Flj20080	cDNA sequence BC022687	protein-coding
mm_169833.1	chr16	25517581	25517588	+	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-166181	NM_001127259	22061	Mm.20894	NM_011641	ENSMUSG00000022510	Trp63	AI462811|Ket|P51/P63|P63|P73l|Tp63|Trp53rp1	transformation related protein 63	protein-coding
mm_86048.1	chr9	114512440	114512443	-	1	NA	3' UTR (NM_001042503, exon 4 of 4)	3' UTR (NM_001042503, exon 4 of 4)	-15897	NM_009916	12773	Mm.1337	NM_009916	ENSMUSG00000047898	Ccr4	C-C CKR-4|CHEMR1|Cmkbr4|LESTR|Sdf1r	chemokine (C-C motif) receptor 4	protein-coding
mm_59640.1	chr7	28157842	28157849	+	1	NA	exon (NM_001164655, exon 16 of 20)	exon (NM_001164655, exon 16 of 20)	-11903	NM_007991	14113	Mm.4595	NM_007991	ENSMUSG00000046865	Fbl	AL022665|FIB|FLRN|RNU3IP1	fibrillarin	protein-coding
mm_43408.1	chr5	135887976	135887986	+	1	NA	promoter-TSS (NM_013560)	promoter-TSS (NM_013560)	62	NM_013560	15507	Mm.13849	NM_013560	ENSMUSG00000004951	Hspb1	27kDa|Hsp25	heat shock protein 1	protein-coding
mm_114943.1	chr13	96542603	96542626	+	1	NA	promoter-TSS (NM_001164222)	promoter-TSS (NM_001164222)	-35	NM_012048	27015	Mm.89926	NM_012048	ENSMUSG00000021668	Polk	DINP|Dinb1	polymerase (DNA directed), kappa	protein-coding
mm_20431.1	chr2	129306459	129306464	-	1	NA	intron (NR_040371, intron 4 of 4)	intron (NR_040371, intron 4 of 4)	3511	NM_010554	16175	Mm.15534	NM_010554	ENSMUSG00000027399	Il1a	Il-1a	interleukin 1 alpha	protein-coding
mm_145495.1	chr18	60390462	60390483	+	1	NA	exon (NM_001146275, exon 3 of 3)	exon (NM_001146275, exon 3 of 3)	14443	NM_001146275	60440	Mm.261140	NM_021792	ENSMUSG00000054072	Iigp1	2900074L10Rik|AI046432|AW111922|Ifgga1|Iigp|Irga6	interferon inducible GTPase 1	protein-coding
mm_162430.1	chr1	93511914	93511920	-	1	NA	promoter-TSS (NM_145519)	promoter-TSS (NM_145519)	-187	NM_145519	227377	Mm.243091	NM_145519	ENSMUSG00000034066	Farp2	AI465173|BC009153|D030026M03Rik|Fir|mKIAA0793	FERM, RhoGEF and pleckstrin domain protein 2	protein-coding
mm_164329.1	chr16	7767871	7767879	+	1	NA	Intergenic	Intergenic	657261	NM_029070	74720	Mm.159318	NM_029070	ENSMUSG00000022715	Tmem114	4930511J11Rik|Cldn26	transmembrane protein 114	protein-coding
mm_19367.1	chr2	91182869	91182933	-	1	NA	5' UTR (NM_145527, exon 1 of 34)	5' UTR (NM_145527, exon 1 of 34)	146	NM_001177719	228355	Mm.36410	NM_145527	ENSMUSG00000040687	Madd	9630059K23Rik|IG20	MAP-kinase activating death domain	protein-coding
mm_169020.1	chr13	112578245	112578253	-	1	NA	intron (NM_139299, intron 1 of 16)	LSU-rRNA_Hsa|rRNA|rRNA	2413	NM_139299	218624	Mm.380801	NM_139299	ENSMUSG00000050377	Il31ra	CRL3|GLM-R|GPL|Glmr|NR10	interleukin 31 receptor A	protein-coding
mm_126055.1	chr15	76949558	76949568	+	1	NA	exon (NM_054099, exon 3 of 4)	exon (NM_054099, exon 3 of 4)	1019	NM_054099	117171	Mm.322968	NM_054099	ENSMUSG00000063236	1110038F14Rik	-	RIKEN cDNA 1110038F14 gene	protein-coding
mm_13553.1	chr2	112242594	112242628	+	1	NA	intron (NM_207206, intron 4 of 13)	intron (NM_207206, intron 4 of 13)	2770	NM_207206	99010	Mm.33438	NM_207206	ENSMUSG00000027134	Lpcat4	AI505034|Agpat7|Aytl3|LPEAT2	lysophosphatidylcholine acyltransferase 4	protein-coding
mm_72773.1	chr8	86209031	86209034	+	1	NA	Intergenic	RMER19B|LTR|ERVK	357558	NM_172912	244562	Mm.67485	NM_172912	ENSMUSG00000036872	Abcc12	4930467B22Rik|MRP9	ATP-binding cassette, sub-family C (CFTR/MRP), member 12	protein-coding
mm_15315.1	chr2	155611176	155611216	+	1	NA	promoter-TSS (NM_001085378)	promoter-TSS (NM_001085378)	-47	NM_001085378	668940	Mm.469980	NM_001085378	ENSMUSG00000074652	Myh7b	Myh14	myosin, heavy chain 7B, cardiac muscle, beta	protein-coding
mm_148133.1	chr18	75697634	75697638	-	1	NA	promoter-TSS (NM_201354)	promoter-TSS (NM_201354)	60	NM_201354	269037	Mm.36745	NM_201354	ENSMUSG00000052928	Ctif	Gm672	CBP80/20-dependent translation initiation factor	protein-coding
mm_161696.1	chr17	23763264	23763264	-	1	NA	5' UTR (NM_153791, exon 2 of 7)	5' UTR (NM_153791, exon 2 of 7)	8327	NM_153791	224613	Mm.328835	NM_153791	ENSMUSG00000040097	Flywch1	E030034P13Rik|mKIAA1552	FLYWCH-type zinc finger 1	protein-coding
mm_131261.1	chr16	10791802	10791818	+	1	NA	promoter-TSS (NM_013638)	promoter-TSS (NM_013638)	295	NM_008933	19119	Mm.325769	NM_008933	ENSMUSG00000038015	Prm2	AI528784|Prm-2	protamine 2	protein-coding
mm_165523.1	chr2	174339331	174339354	+	1	NA	intron (NM_001310085, intron 4 of 12)	intron (NM_001310085, intron 4 of 12)	9253	NM_001077510	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_66670.1	chr7	45725788	45725813	-	1	NA	promoter-TSS (NM_027055)	promoter-TSS (NM_027055)	16	NM_027055	69363	Mm.45607	NM_027055	ENSMUSG00000070563	Spaca4	1700008E09Rik|AV043694|Samp14	sperm acrosome associated 4	protein-coding
mm_44905.1	chr5	35654164	35654180	-	1	NA	intron (NM_030127, intron 7 of 8)	intron (NM_030127, intron 7 of 8)	25608	NM_001042615	78558	Mm.274255	NM_030127	ENSMUSG00000029096	Htra3	2210021K23Rik|9530081K03Rik|Prsp|Tasp	HtrA serine peptidase 3	protein-coding
mm_138122.1	chr17	34145312	34145331	+	1	NA	promoter-TSS (NM_010388)	promoter-TSS (NM_010388)	-95	NM_010388	15000	Mm.195060	NM_010388	ENSMUSG00000037548	H2-DMb2	H-2Mb2|H2-Mb2	histocompatibility 2, class II, locus Mb2	protein-coding
mm_98286.1	chr11	89065875	89065886	+	1	NA	intron (NR_110336, intron 1 of 3)	intron (NR_110336, intron 1 of 3)	5129	NR_110336	414094	Mm.124287	NM_001001497		Dgkeos	A930013B10Rik	diacylglycerol kinase, epsilon, opposite strand	ncRNA
mm_12556.1	chr2	72445629	72445647	+	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	-30581	NM_025866	66953	Mm.270676	NM_025866	ENSMUSG00000055612	Cdca7	2310021G01Rik|AU044109|JPO1	cell division cycle associated 7	protein-coding
mm_77933.1	chr9	7354711	7354798	+	1	NA	exon (NM_008605, exon 7 of 10)	exon (NM_008605, exon 7 of 10)	7380	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_98695.1	chr11	96303508	96303551	+	1	NA	promoter-TSS (NM_008268)	promoter-TSS (NM_008268)	17	NM_008268	15413	Mm.207	NM_008268	ENSMUSG00000038700	Hoxb5	AI385717|Hox-2.1	homeobox B5	protein-coding
mm_76747.1	chr8	95423322	95423325	-	1	NA	intron (NM_008187, intron 2 of 5)	intron (NM_008187, intron 2 of 5)	11546	NM_008187	14894	Mm.2080	NM_008187	ENSMUSG00000031796	Cfap20	2600014O15Rik|AL024127|Gtl3|T10-2A2	cilia and flagella associated protein 20	protein-coding
mm_27041.1	chr3	26331935	26331943	-	1	NA	promoter-TSS (NM_138666)	promoter-TSS (NM_138666)	-30	NM_138666	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_168514.1	chr11	5699863	5699865	-	1	NA	Intergenic	RLTR9D|LTR|ERVK	7835	NM_026080	64660	Mm.7328	NM_026080	ENSMUSG00000020477	Mrps24	3110030K20Rik|AI414579|Rpms24	mitochondrial ribosomal protein S24	protein-coding
mm_45145.1	chr5	49174705	49174742	-	1	NA	intron (NM_001199244, intron 1 of 7)	intron (NM_001199244, intron 1 of 7)	110936	NM_001199244	80334	Mm.160172	NM_030265	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding
mm_118314.1	chr13	113110646	113110648	-	1	NA	Intergenic	Intergenic	-9666	NM_010370	14938	Mm.15510	NM_010370	ENSMUSG00000023132	Gzma	AW494114|Ctla-3|Ctla3|Hf|Hf1|SE1|TSP-1|TSP1	granzyme A	protein-coding
mm_104636.1	chr11	97523226	97523241	-	1	NA	exon (NM_018873, exon 18 of 20)	exon (NM_018873, exon 18 of 20)	-22893	NM_001289118	100141474	Mm.482426	NM_001289118	ENSMUSG00000047988	4933428G20Rik	-	RIKEN cDNA 4933428G20 gene	protein-coding
mm_94651.1	chr11	17051655	17051674	+	1	NA	promoter-TSS (NM_029861)	promoter-TSS (NM_029861)	-270	NM_029861	380686	Mm.425666	NM_029861	ENSMUSG00000044629	Cnrip1	1500041B16Rik|3110054C06Rik|5330437A18Rik|AI854501|C2orf32	cannabinoid receptor interacting protein 1	protein-coding
mm_132281.1	chr16	33056516	33056531	+	1	NA	promoter-TSS (NM_021338)	promoter-TSS (NM_021338)	9	NM_021338	57808	Mm.19355	NM_021338	ENSMUSG00000060636	Rpl35a	2810431L15Rik|Rpl35	ribosomal protein L35A	protein-coding
mm_26740.1	chr3	6620442	6620444	-	1	NA	promoter-TSS (NM_027048)	promoter-TSS (NM_027048)	0	NM_027048	69347	Mm.45822	NM_027048	ENSMUSG00000069118	1700008P02Rik	-	RIKEN cDNA 1700008P02 gene	protein-coding
mm_95370.1	chr11	49086978	49086984	+	1	NA	promoter-TSS (NM_008330)	promoter-TSS (NM_008330)	-36	NM_001271676	15953	Mm.24769	NM_008330	ENSMUSG00000078920	Ifi47	47kDa|IRG-47|Ifggc1|Igrd|Iigp4|Iipg4|Irgd	interferon gamma inducible protein 47	protein-coding
mm_116099.1	chr13	28884220	28884244	-	1	NA	intron (NR_045053, intron 1 of 8)	intron (NR_045053, intron 1 of 8)	1190	NR_045054	72518	Mm.37454	NR_045053		2610307P16Rik	AI666457	RIKEN cDNA 2610307P16 gene	ncRNA
mm_84308.1	chr9	63666803	63666813	-	1	NA	intron (NM_016769, intron 3 of 8)	intron (NM_016769, intron 3 of 8)	64153	NM_025857	66939	Mm.34338	NM_025857	ENSMUSG00000037257	Aagab	2310007F21Rik|p34	alpha- and gamma-adaptin binding protein	protein-coding
mm_139728.1	chr17	57476796	57476816	+	1	NA	intron (NM_010130, intron 19 of 21)	RLTR17B_Mm|LTR|ERVK	68508	NM_001104591	224916	Mm.469889	NM_001104591	ENSMUSG00000090655	Vmn2r120	EG224916	vomeronasal 2, receptor 120	protein-coding
mm_72403.1	chr8	81770572	81770576	+	1	NA	intron (NM_001024617, intron 6 of 24)	intron (NM_001024617, intron 6 of 24)	428012	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_37988.1	chr4	133631131	133631158	-	1	NA	intron (NM_001017968, intron 1 of 7)	intron (NM_001017968, intron 1 of 7)	2285	NM_001017968	503610	Mm.331948	NM_001017968	ENSMUSG00000037553	Zdhhc18	-	zinc finger, DHHC domain containing 18	protein-coding
mm_45359.1	chr5	65990158	65990182	-	1	NA	intron (NR_027961, intron 5 of 6)	intron (NR_027961, intron 5 of 6)	14115	NR_027961	231253	Mm.436542	NM_177679	ENSMUSG00000054598	9130230L23Rik	-	RIKEN cDNA 9130230L23 gene	ncRNA
mm_46140.1	chr5	93136972	93136985	-	1	NA	intron (NM_001347377, intron 1 of 10)	intron (NM_001347377, intron 1 of 10)	43562	NM_001347377	52398	Mm.394184	NM_001009818	ENSMUSG00000058013	Sept11	6230410I01Rik|AW548875|D5Ertd606e	septin 11	protein-coding
mm_65535.1	chr7	25816549	25816563	-	1	NA	promoter-TSS (NM_028775)	promoter-TSS (NM_028775)	-26	NM_028775	74134	Mm.275188	NM_028775	ENSMUSG00000040703	Cyp2s1	1200011C15Rik|AU041727|C79779	cytochrome P450, family 2, subfamily s, polypeptide 1	protein-coding
mm_71755.1	chr8	65966660	65966664	+	1	NA	intron (NM_001166372, intron 2 of 7)	intron (NM_001166372, intron 2 of 7)	348137	NM_175188	72925	Mm.380457	NM_175188	ENSMUSG00000036469	March1	2900024D24Rik|BB085186	membrane-associated ring finger (C3HC4) 1	protein-coding
mm_899.1	chr1	53360390	53360397	+	1	NA	Intergenic	Intergenic	-7641	NM_133728	70396	Mm.285783	NM_133728	ENSMUSG00000026095	Asnsd1	2210409M21Rik	asparagine synthetase domain containing 1	protein-coding
mm_147339.1	chr18	42938239	42938258	-	1	NA	intron (NM_028392, intron 1 of 8)	intron (NM_028392, intron 1 of 8)	-38742	NR_073583	72930	Mm.26134	NM_027531	ENSMUSG00000024500	Ppp2r2b	2900026H06Rik|6330404L05Rik|E130009M08Rik|PP2A-PR55B|PR55-BETA|SCA12	protein phosphatase 2, regulatory subunit B, beta	protein-coding
mm_78310.1	chr9	22678752	22678767	+	1	NA	intron (NM_178415, intron 18 of 22)	intron (NM_178415, intron 18 of 22)	203044	NM_178415	319845	Mm.176725	NM_178415	ENSMUSG00000035919	Bbs9	E130103I17Rik	Bardet-Biedl syndrome 9 (human)	protein-coding
mm_107506.1	chr12	40038094	40038107	+	1	NA	promoter-TSS (NM_007487)	promoter-TSS (NM_007487)	-113	NM_001039515	11861	Mm.12723	NM_007487	ENSMUSG00000047446	Arl4a	AI467555|Arl4	ADP-ribosylation factor-like 4A	protein-coding
mm_145838.1	chr18	65444899	65444915	+	1	NA	exon (NM_172833, exon 3 of 16)	exon (NM_172833, exon 3 of 16)	13910	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_138117.1	chr17	34143223	34143255	+	1	NA	Intergenic	Intergenic	-2177	NM_010388	15000	Mm.195060	NM_010388	ENSMUSG00000037548	H2-DMb2	H-2Mb2|H2-Mb2	histocompatibility 2, class II, locus Mb2	protein-coding
mm_168694.1	chr11	97187985	97187989	-	1	NA	promoter-TSS (NM_008379)	promoter-TSS (NM_008379)	-95	NM_008379	16211	Mm.251013	NM_008379	ENSMUSG00000001440	Kpnb1	AA409963|IPOB|Impnb	karyopherin (importin) beta 1	protein-coding
mm_82136.1	chr9	123757044	123757049	+	1	NA	Intergenic	Intergenic	-10165	NM_009913	12769	Mm.440604	NM_009913	ENSMUSG00000029530	Ccr9	A130091K22Rik|Cmkbr10|GPR-9-6	chemokine (C-C motif) receptor 9	protein-coding
mm_90618.1	chr10	128411681	128411720	+	1	NA	promoter-TSS (NM_026259)	promoter-TSS (NM_026259)	84	NM_026259	67588	Mm.294120	NM_026259	ENSMUSG00000025373	Rnf41	2210404G21Rik|4930511A05Rik|4933415P08Rik|D10Ertd722e|FLRF|Nrdp1	ring finger protein 41	protein-coding
mm_25056.1	chr3	98600887	98600899	+	1	NA	Intergenic	RLTR48A|LTR|ERV1	-36855	NM_008294	15495	Mm.14309	NM_008294	ENSMUSG00000095143	Hsd3b4	-	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 4	protein-coding
mm_73563.1	chr8	109566028	109566031	+	1	NA	promoter-TSS (NM_178380)	promoter-TSS (NM_178380)	137	NM_175646	234723	Mm.37667	NM_175646	ENSMUSG00000031723	Txnl4b	AI595343|D530025J19Rik|DLP|Dim2	thioredoxin-like 4B	protein-coding
mm_165550.1	chr3	9890839	9890880	-	1	NA	Intergenic	Lx2|LINE|L1	-57180	NM_001195031	94212	Mm.23897	NM_053182	ENSMUSG00000027508	Pag1	Cbp|F730007C19Rik|Pag	phosphoprotein associated with glycosphingolipid microdomains 1	protein-coding
mm_65094.1	chr7	19271577	19271589	-	1	NA	non-coding (NR_104069, exon 1 of 11)	non-coding (NR_104069, exon 1 of 11)	271	NM_001282021	22323	Mm.9684	NM_009499	ENSMUSG00000030403	Vasp	-	vasodilator-stimulated phosphoprotein	protein-coding
mm_12633.1	chr2	74705146	74705156	+	1	NA	promoter-TSS (NM_001290730)	promoter-TSS (NM_001290730)	-338	NM_001290730	15437	Mm.280673	NM_008276	ENSMUSG00000027102	Hoxd8	4921540P06Rik|AI047735|Hox-4.3|Hox-5.4	homeobox D8	protein-coding
mm_25461.1	chr3	108537587	108537592	+	1	NA	promoter-TSS (NM_029314)	promoter-TSS (NM_029314)	5	NM_029314	75504	Mm.271255	NM_029314	ENSMUSG00000027886	1700013F07Rik	-	RIKEN cDNA 1700013F07 gene	protein-coding
mm_128786.1	chr15	66804044	66804054	-	1	NA	intron (NM_001029841, intron 1 of 7)	intron (NM_001029841, intron 1 of 7)	27780	NM_001029841	20491	Mm.7601	NM_009192	ENSMUSG00000022372	Sla	Slap|Slap-1	src-like adaptor	protein-coding
mm_105559.1	chr11	106488311	106488329	-	1	NA	promoter-TSS (NM_023913)	promoter-TSS (NM_023913)	-524	NM_023913	78943	Mm.340943	NM_023913	ENSMUSG00000020715	Ern1	9030414B18Rik|AI225830|C85377|Ire1a|Ire1alpha|Ire1p	endoplasmic reticulum (ER) to nucleus signalling 1	protein-coding
mm_145171.1	chr18	46921798	46921836	+	1	NA	promoter-TSS (NM_001033446)	promoter-TSS (NM_001033446)	2	NM_001033446	381142	Mm.329423	NM_001033446	ENSMUSG00000073568	Arl14epl	Gm949	ADP-ribosylation factor-like 14 effector protein-like	protein-coding
mm_45683.1	chr5	77351284	77351301	-	1	NA	exon (NM_008048, exon 4 of 5)	exon (NM_008048, exon 4 of 5)	40808	NM_153798	231329	Mm.273217	NM_153798	ENSMUSG00000029250	Polr2b	Pol2rb|Rpb140|Rpb2	polymerase (RNA) II (DNA directed) polypeptide B	protein-coding
mm_26054.1	chr3	135825606	135825620	+	1	NA	promoter-TSS (NM_001135150)	promoter-TSS (NM_001135150)	-44	NM_001135149	67547	Mm.30239	NM_026228	ENSMUSG00000053897	Slc39a8	4933419D20Rik|AA986696|BIGM103|ZIP-8|Zip8	solute carrier family 39 (metal ion transporter), member 8	protein-coding
mm_80671.1	chr9	90164883	90164886	+	1	NA	intron (NM_001326294, intron 1 of 22)	intron (NM_001326294, intron 1 of 22)	1906	NM_001311115	108153	Mm.102141	NM_001003911	ENSMUSG00000032363	Adamts7	ADAM-TS7|ADAMTS7B	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 7	protein-coding
mm_150515.1	chr19	39031302	39031306	+	1	NA	exon (NM_028089, exon 5 of 9)	exon (NM_028089, exon 5 of 9)	24285	NM_028089	72082	Mm.142581	NM_028089	ENSMUSG00000025002	Cyp2c55	2010318C06Rik	cytochrome P450, family 2, subfamily c, polypeptide 55	protein-coding
mm_48138.1	chr5	137150285	137150293	-	1	NA	Intergenic	(TGG)n|Simple_repeat|Simple_repeat	-34082	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_20020.1	chr2	119325592	119325628	-	1	NA	promoter-TSS (NM_019454)	promoter-TSS (NM_019454)	-174	NM_019454	54485	Mm.143719	NM_019454	ENSMUSG00000027314	Dll4	Delta4	delta-like 4 (Drosophila)	protein-coding
mm_29982.1	chr3	135408719	135408738	-	1	NA	3' UTR (NM_025902, exon 3 of 3)	3' UTR (NM_025902, exon 3 of 3)	14705	NM_025902	67006	Mm.269993	NM_025902	ENSMUSG00000028165	Cisd2	1500009M05Rik|1500026J14Rik|1500031D15Rik|AI848398|B630006A20Rik|Miner1|Naf-1|Noxp70|Zcd2	CDGSH iron sulfur domain 2	protein-coding
mm_13615.1	chr2	113405198	113405201	+	1	NA	intron (NM_001285458, intron 2 of 16)	intron (NM_001285458, intron 2 of 16)	-35865	NM_001285459	14260	Mm.4938	NM_010230	ENSMUSG00000044042	Fmn1	Fmn|formin-1|ld	formin 1	protein-coding
mm_37939.1	chr4	133056171	133056182	-	1	NA	intron (NM_146155, intron 3 of 6)	intron (NM_146155, intron 3 of 6)	44670	NM_146155	230793	Mm.31816	NM_146155	ENSMUSG00000037692	Ahdc1	D030015G18Rik	AT hook, DNA binding motif, containing 1	protein-coding
mm_72876.1	chr8	88697085	88697108	+	1	NA	promoter-TSS (NM_001128171)	promoter-TSS (NM_001128171)	68	NM_001128171	74256	Mm.490395	NM_173369	ENSMUSG00000036712	Cyld	2010013M14Rik|2900009M21Rik|C130039D01Rik|CDMT|CYLD1|EAC|mKIAA0849	CYLD lysine 63 deubiquitinase	protein-coding
mm_101584.1	chr11	34497163	34497173	-	1	NA	intron (NM_033374, intron 25 of 51)	intron (NM_033374, intron 25 of 51)	182346	NM_001025382	574403	Mm.444796	NM_001025382	ENSMUSG00000069911	Fam196b	EG574403|Gm6041	family with sequence similarity 196, member B	protein-coding
mm_158844.1	chrX	169779610	169779621	-	1	NA	promoter-TSS (NR_003635)	promoter-TSS (NR_003635)	20	NR_003635	66747	Mm.34441	NM_025743	ENSMUSG00000055357	4933400A11Rik	-	capping protein (actin filament) muscle Z-line, alpha 1 pseudogene	pseudo
mm_148616.1	chr19	5388839	5388885	+	1	NA	promoter-TSS (NM_016882)	promoter-TSS (NM_016882)	-159	NM_016882	20227	Mm.34562	NM_016882	ENSMUSG00000039148	Sart1	U5-110K	squamous cell carcinoma antigen recognized by T cells 1	protein-coding
mm_21607.1	chr2	164254610	164254618	-	1	NA	3' UTR (NM_173377, exon 3 of 3)	3' UTR (NM_173377, exon 3 of 3)	2029	NM_173377	329557	Mm.118769	NM_173377	ENSMUSG00000050383	Svs3b	9530004A22Rik	seminal vesicle secretory protein 3B	protein-coding
mm_100526.1	chr11	120598455	120598518	+	1	NA	promoter-TSS (NM_011568)	promoter-TSS (NM_011568)	-46	NM_001038230	66156	Mm.21645	NM_025389	ENSMUSG00000025135	Anapc11	1110011I19Rik|R75218	anaphase promoting complex subunit 11	protein-coding
mm_44064.1	chr5	148399993	148400009	+	1	NA	promoter-TSS (NM_007513)	promoter-TSS (NM_007513)	-97	NM_007513	11987	Mm.275489	NM_007513	ENSMUSG00000041313	Slc7a1	4831426K01Rik|AI447493|Atrc-1|Atrc1|Cat1|Rec-1|Rev-1|mCAT-1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 1	protein-coding
mm_154703.1	chrX	8272220	8272230	+	1	NA	intron (NM_172479, intron 3 of 15)	intron (NM_172479, intron 3 of 15)	844	NM_172479	209837	Mm.6055	NM_172479	ENSMUSG00000031170	Slc38a5	C81234|E330031E14|JM24|SN2	solute carrier family 38, member 5	protein-coding
mm_27552.1	chr3	58163787	58163832	-	1	NA	promoter-TSS (NR_040538)	promoter-TSS (NR_040538)	-2	NR_040538	67850	Mm.416968	NR_040538	ENSMUSG00000100666	1700007F19Rik	-	RIKEN cDNA 1700007F19 gene	ncRNA
mm_114477.1	chr13	68597426	68597473	+	1	NA	promoter-TSS (NM_027035)	promoter-TSS (NM_027035)	10	NM_027035	69315	Mm.272795	NM_027035	ENSMUSG00000021534	1700001L19Rik	-	RIKEN cDNA 1700001L19 gene	protein-coding
mm_132770.1	chr16	44765899	44765920	+	1	NA	5' UTR (NM_021325, exon 1 of 7)	5' UTR (NM_021325, exon 1 of 7)	173	NM_021325	57781	Mm.416152	NM_021325	ENSMUSG00000022667	Cd200r1	CD200R|Mox2r|OX2R	CD200 receptor 1	protein-coding
mm_45045.1	chr5	41707418	41707429	-	1	NA	intron (NR_132325, intron 1 of 5)	intron (NR_132325, intron 1 of 5)	268	NM_001310592	100972	Mm.41555	NM_027295	ENSMUSG00000029128	Rab28	2700023P08Rik|AW496496	RAB28, member RAS oncogene family	protein-coding
mm_100461.1	chr11	119856258	119856268	+	1	NA	intron (NM_028898, intron 17 of 33)	intron (NM_028898, intron 17 of 33)	-21898	NR_045312	319454	Mm.442144	NR_045312	ENSMUSG00000085081	Rptoros	A430071A18Rik	regulatory associated protein of MTOR, complex 1, opposite strand	ncRNA
mm_79483.1	chr9	56995078	56995117	+	1	NA	5' UTR (NM_019651, exon 1 of 13)	5' UTR (NM_019651, exon 1 of 13)	129	NM_019651	56294	Mm.325643	NM_019651	ENSMUSG00000032290	Ptpn9	MEG2	protein tyrosine phosphatase, non-receptor type 9	protein-coding
mm_149768.1	chr19	23061450	23061464	+	1	NA	Intergenic	Intergenic	-79769	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_22664.1	chr3	14872021	14872031	+	1	NA	3' UTR (NM_007606, exon 7 of 7)	3' UTR (NM_007606, exon 7 of 7)	8488	NM_007606	12350	Mm.300	NM_007606	ENSMUSG00000027559	Car3	BB219044|Ca3|Car-3	carbonic anhydrase 3	protein-coding
mm_118492.1	chr14	12867519	12867540	+	1	NA	Intergenic	Intergenic	-44450	NM_012061	27062	Mm.260881	NM_012061	ENSMUSG00000054423	Cadps	AU067781|CAPS|CAPS1|mKIAA1121	Ca2+-dependent secretion activator	protein-coding
mm_106094.1	chr11	116198674	116198677	-	1	NA	promoter-TSS (NM_027107)	promoter-TSS (NM_027107)	-180	NM_027107	69535	Mm.390347	NM_027107	ENSMUSG00000020778	Ten1	2310004N24Rik	TEN1 telomerase capping complex subunit	protein-coding
mm_129475.1	chr15	78718463	78718510	-	1	NA	promoter-TSS (NM_183141)	promoter-TSS (NM_183141)	-373	NM_183141	207393	Mm.323188	NM_183141	ENSMUSG00000043460	Elfn2	6330514E13|AW048948|BC094219|Lrrc62|Ppp1r29	leucine rich repeat and fibronectin type III, extracellular 2	protein-coding
mm_30499.1	chr3	157906272	157906303	-	1	NA	exon (NM_145953, exon 9 of 12)	exon (NM_145953, exon 9 of 12)	18776	NM_145953	107869	Mm.28301	NM_145953	ENSMUSG00000028179	Cth	0610010I13Rik|AI314617|BC019483|CSE|Cys3	cystathionase (cystathionine gamma-lyase)	protein-coding
mm_95183.1	chr11	42420438	42420443	+	1	NA	promoter-TSS (NM_001347314)	promoter-TSS (NM_001347314)	683	NM_008070	14401	Mm.338723	NM_008070	ENSMUSG00000007653	Gabrb2	AI834970|C030002O17Rik|C030021G16Rik|Gabrab2|Gabrb-2	gamma-aminobutyric acid (GABA) A receptor, subunit beta 2	protein-coding
mm_76249.1	chr8	83607920	83607981	-	1	NA	promoter-TSS (NM_018808)	promoter-TSS (NM_018808)	-225	NM_018808	81489	Mm.282092	NM_018808	ENSMUSG00000005483	Dnajb1	0610007I11Rik|DjB1|HSPF1|Hdj1|Hsp40	DnaJ heat shock protein family (Hsp40) member B1	protein-coding
mm_66238.1	chr7	35528639	35528641	-	1	NA	intron (NM_028034, intron 2 of 11)	RLTR1B|LTR|ERV1	9104	NM_028034	71981	Mm.47904	NM_028034	ENSMUSG00000030491	Tdrd12	2410004F06Rik|2410070K17Rik|ECAT8|EG434165|G1-476-14|repro23	tudor domain containing 12	protein-coding
mm_104032.1	chr11	86257533	86257547	-	1	NA	promoter-TSS (NM_027421)	promoter-TSS (NM_027421)	28	NM_027421	70422	Mm.171304	NM_027421	ENSMUSG00000018068	Ints2	2810417D08Rik|AA408260|AI987735|mKIAA1287	integrator complex subunit 2	protein-coding
mm_92108.1	chr10	63023882	63023907	-	1	NA	promoter-TSS (NM_001079824)	promoter-TSS (NM_001079824)	-45	NM_001079824	432467	Mm.274784	NM_001079824	ENSMUSG00000020069	Hnrnph3	AA693301|AI666703|Hnrph3	heterogeneous nuclear ribonucleoprotein H3	protein-coding
mm_68539.1	chr7	113564973	113564986	-	1	NA	promoter-TSS (NR_126544)	promoter-TSS (NR_126544)	8	NR_126544	69295	Mm.396150	NR_126544	ENSMUSG00000084984	Far1os	1700006P19Rik	fatty acyl CoA reductase 1, opposite strand	ncRNA
mm_31262.1	chr4	45203885	45203889	+	1	NA	intron (NM_001081172, intron 1 of 15)	intron (NM_001081172, intron 1 of 15)	18981	NM_001081172	666060	Mm.24783	NM_001081172	ENSMUSG00000035615	Frmpd1	BC031840|mKIAA0967	FERM and PDZ domain containing 1	protein-coding
mm_102027.1	chr11	51651032	51651046	-	1	NA	promoter-TSS (NM_145974)	promoter-TSS (NM_145974)	34	NM_145974	212706	Mm.41760	NM_145974	ENSMUSG00000001053	N4bp3	C330016O10Rik	NEDD4 binding protein 3	protein-coding
mm_6957.1	chr1	85991478	85991496	-	1	NA	Intergenic	L1MCb|LINE|L1	-30432	NM_001033290	227326	Mm.244158	NM_001033290	ENSMUSG00000049608	Gpr55	CTFL|Gm218|Lpir1	G protein-coupled receptor 55	protein-coding
mm_98515.1	chr11	94952477	94952498	+	1	NA	3' UTR (NM_007742, exon 51 of 51)	3' UTR (NM_007742, exon 51 of 51)	-15106	NM_018792	54388	Mm.30482	NM_018792	ENSMUSG00000038994	Hils1	H1.9|TISP64	histone H1-like protein in spermatids 1	protein-coding
mm_122149.1	chr14	31240374	31240386	-	1	NA	exon (NM_027949, exon 7 of 11)	exon (NM_027949, exon 7 of 11)	10838	NM_027949	71838	Mm.5348	NM_027949	ENSMUSG00000021902	Phf7	1700006H01Rik|1700010P14Rik|AI427892|AW555949	PHD finger protein 7	protein-coding
mm_166763.1	chr6	132314752	132314757	-	1	NA	promoter-TSS (NM_001024705)	promoter-TSS (NM_001024705)	-11	NM_001024705	381832	Mm.441627	NM_001024705	ENSMUSG00000107874	Prpmp5	MP5	proline-rich protein MP5	protein-coding
mm_88244.1	chr10	72654874	72654920	+	1	NA	promoter-TSS (NM_025635)	promoter-TSS (NM_025635)	51	NM_001293683	52696	Mm.62876	NM_025635	ENSMUSG00000019923	Zwint	2010007E07Rik|2600001N01Rik|D10Ertd749e|Zwint-1	ZW10 interactor	protein-coding
mm_103583.1	chr11	78178524	78178596	-	1	NA	promoter-TSS (NM_001291236)	promoter-TSS (NM_001291236)	-98	NM_001291236	68385	Mm.390375	NM_026708	ENSMUSG00000019437	Tlcd1	-	TLC domain containing 1	protein-coding
mm_2222.1	chr1	90252722	90252726	+	1	NA	Intergenic	MIRb|SINE|MIR	48744	NM_007722	12778	Mm.6522	NM_007722	ENSMUSG00000044337	Ackr3	AW541270|CXC-R7|CXCR-7|Cmkor1|Cxcr7|RDC-1|Rdc1	atypical chemokine receptor 3	protein-coding
mm_39544.1	chr5	21543594	21543612	+	1	NA	promoter-TSS (NM_028977)	promoter-TSS (NM_028977)	76	NM_028977	74511	Mm.439963	NM_028977	ENSMUSG00000039883	Lrrc17	37kDa|4833425M04Rik|6130400C22Rik|P37nb	leucine rich repeat containing 17	protein-coding
mm_27370.1	chr3	50438832	50438843	-	1	NA	exon (NM_011990, exon 2 of 12)	exon (NM_011990, exon 2 of 12)	4776	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_14276.1	chr2	128761815	128761818	+	1	NA	intron (NM_008587, intron 7 of 18)	PB1D10|SINE|Alu	-56487	NM_028248	72477	Mm.259688	NM_028248	ENSMUSG00000014353	Tmem87b	2610301K12Rik|2810431I02Rik|AU014804	transmembrane protein 87B	protein-coding
mm_112343.1	chr12	116405190	116405217	-	1	NA	promoter-TSS (NR_028421)	promoter-TSS (NR_028421)	-42	NR_028421	319545	Mm.390543	NR_028421		D430020J02Rik	-	RIKEN cDNA D430020J02 gene	ncRNA
mm_81758.1	chr9	113969237	113969252	+	1	NA	intron (NM_013699, intron 11 of 15)	intron (NM_013699, intron 11 of 15)	24556	NR_039590	100628597		NR_039590	ENSMUSG00000092958	Mir5128	mir-5128|mmu-mir-5128|mu-mir-5128	microRNA 5128	ncRNA
mm_27502.1	chr3	55403192	55403210	-	1	NA	intron (NM_019978, intron 4 of 16)	intron (NM_019978, intron 4 of 16)	-58557	NM_001195539	13175	Mm.393242	NM_019978	ENSMUSG00000027797	Dclk1	1700113D08Rik|2810480F11Rik|AI836758|Click-I|Cpg16|Dcamkl1|Dcl|Dclk|mKIAA0369	doublecortin-like kinase 1	protein-coding
mm_104891.1	chr11	99580704	99580739	-	1	NA	exon (NM_027157, exon 1 of 1)	exon (NM_027157, exon 1 of 1)	295	NM_027157	69664	Mm.38303	NM_027157	ENSMUSG00000047253	Krtap1-5	2310043L02Rik|AI592983	keratin associated protein 1-5	protein-coding
mm_57268.1	chr6	123287387	123287397	-	1	NA	intron (NM_019948, intron 2 of 5)	RMER20B|LTR|ERVK	2479	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_111184.1	chr12	83984850	83984856	-	1	NA	Intergenic	Intergenic	-3008	NM_134188	171210	Mm.371675	NM_134188	ENSMUSG00000021226	Acot2	AA571646|MTE-I|Mte1	acyl-CoA thioesterase 2	protein-coding
mm_8165.1	chr1	136953601	136953605	-	1	NA	promoter-TSS (NM_001159769)	promoter-TSS (NM_001159769)	27	NM_001159769	26424	Mm.16794	NM_030676	ENSMUSG00000026398	Nr5a2	AU020803|D1Ertd308e|Ftf|LRH-1|UF2-H3B	nuclear receptor subfamily 5, group A, member 2	protein-coding
mm_129714.1	chr15	81865622	81865634	-	1	NA	3' UTR (NM_026737, exon 4 of 4)	3' UTR (NM_026737, exon 4 of 4)	6264	NM_026737	68479	Mm.271715	NM_026737	ENSMUSG00000061360	Phf5a	1110007B08Rik	PHD finger protein 5A	protein-coding
mm_115910.1	chr13	23462794	23462795	-	1	NA	intron (NM_013483, intron 3 of 7)	B1_Mur1|SINE|Alu	3107	NM_013483	12231	Mm.1420	NM_013483	ENSMUSG00000000706	Btn1a1	Btn	butyrophilin, subfamily 1, member A1	protein-coding
mm_22048.1	chr2	168231122	168231132	-	1	NA	promoter-TSS (NM_010072)	promoter-TSS (NM_010072)	505	NM_001160330	69372	Mm.482182	NM_001160330	ENSMUSG00000074576	Mocs3	1700020H17Rik|Uba4	molybdenum cofactor synthesis 3	protein-coding
mm_106157.1	chr11	116624263	116624273	-	1	NA	promoter-TSS (NM_001167680)	promoter-TSS (NM_001167680)	-16	NM_001167680	217344	Mm.89695	NM_172572	ENSMUSG00000020806	Rhbdf2	4732465I17Rik|Rhbdl6|cub	rhomboid 5 homolog 2	protein-coding
mm_150948.1	chr19	46310303	46310317	+	1	NA	exon (NM_001177370, exon 16 of 22)	exon (NM_001177370, exon 16 of 22)	4380	NM_001177370	18034	Mm.102365	NM_019408	ENSMUSG00000025225	Nfkb2	NF-kappaB2|lyt|p49|p49/p100|p50B|p52	nuclear factor of kappa light polypeptide gene enhancer in B cells 2, p49/p100	protein-coding
mm_137894.1	chr17	31681296	31681299	+	1	NA	3' UTR (NM_001278570, exon 3 of 3)	3' UTR (NM_001278570, exon 3 of 3)	3366	NM_001278570	12954	Mm.1228	NM_013501	ENSMUSG00000024041	Cryaa	Acry-1|Crya-1|Crya1|DAcry-1|lop18	crystallin, alpha A	protein-coding
mm_91272.1	chr10	24588782	24588784	-	1	NA	Intergenic	Intergenic	-6659	NM_010217	14219	Mm.390287	NM_010217	ENSMUSG00000019997	Ctgf	Ccn2|Fisp12|Hcs24|fisp-12	connective tissue growth factor	protein-coding
mm_106691.1	chr12	3365291	3365359	+	1	NA	5' UTR (NM_008445, exon 1 of 8)	5' UTR (NM_008445, exon 1 of 8)	193	NM_008445	16570	Mm.7688	NM_008445	ENSMUSG00000020668	Kif3c	mKIAA4058	kinesin family member 3C	protein-coding
mm_120716.1	chr14	72788643	72788660	+	1	NA	Intergenic	MERVL_2A-int|LTR|ERVL	-78648	NM_207636	319448	Mm.205421	NM_207636	ENSMUSG00000033487	Fndc3a	1700094E19Rik|D14Ertd453e|F730017H24Rik|Fndc3|sys	fibronectin type III domain containing 3A	protein-coding
mm_26224.1	chr3	138903095	138903114	+	1	NA	non-coding (NR_121195, exon 8 of 8)	non-coding (NR_121195, exon 8 of 8)	160896	NM_019571	56224	Mm.31927	NM_019571	ENSMUSG00000028152	Tspan5	2810455A09Rik|4930505M03Rik|NET-4|Tm4sf9	tetraspanin 5	protein-coding
mm_95225.1	chr11	44470580	44470606	+	1	NA	promoter-TSS (NM_024475)	promoter-TSS (NM_024475)	-45	NM_024475	79560	Mm.338784	NM_024475	ENSMUSG00000041231	Ublcp1	4930527B16Rik|8430435I17Rik|BC002236	ubiquitin-like domain containing CTD phosphatase 1	protein-coding
mm_89239.1	chr10	87830944	87830955	+	1	NA	Intergenic	Intergenic	-27316	NM_001314010	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_21462.1	chr2	160874399	160874424	-	1	NA	Intergenic	L2a|LINE|L2	-1421	NM_177263	320799	Mm.436734	NM_177263	ENSMUSG00000035877	Zhx3	1810059C13Rik|4932418O04Rik|9530010N21Rik|Tix1|mKIAA0395	zinc fingers and homeoboxes 3	protein-coding
mm_43126.1	chr5	125249628	125249630	+	1	NA	Intergenic	Intergenic	-70415	NM_001253904	20602	Mm.278646	NM_011424	ENSMUSG00000029478	Ncor2	N-CoR|SMRT|SMRTe	nuclear receptor co-repressor 2	protein-coding
mm_68925.1	chr7	126472415	126472437	-	1	NA	exon (NM_001289538, exon 2 of 9)	exon (NM_001289538, exon 2 of 9)	668	NR_110346	20399	Mm.8538	NM_011363	ENSMUSG00000030733	Sh2b1	AI425885|C530001K22Rik|Irip|Psm|SH2-B|SH2-Bb|Sh2bpsm1|mKIAA1299	SH2B adaptor protein 1	protein-coding
mm_33357.1	chr4	129474069	129474084	+	1	NA	exon (NM_133889, exon 9 of 11)	exon (NM_133889, exon 9 of 11)	12397	NM_133889	100383	Mm.17918	NM_133889	ENSMUSG00000040859	Bsdc1	1110063F24Rik|AW011758	BSD domain containing 1	protein-coding
mm_95999.1	chr11	59228393	59228397	+	1	NA	promoter-TSS (NM_007476)	promoter-TSS (NM_007476)	-128	NM_007476	11840	Mm.371546	NM_007476	ENSMUSG00000048076	Arf1	-	ADP-ribosylation factor 1	protein-coding
mm_64999.1	chr7	17018622	17018625	-	1	NA	intron (NM_011155, intron 2 of 12)	intron (NM_011155, intron 2 of 12)	9291	NM_011155	19060	Mm.3294	NM_011155	ENSMUSG00000003099	Ppp5c	AU020526|PP5	protein phosphatase 5, catalytic subunit	protein-coding
mm_10117.1	chr2	3727175	3727185	+	1	NA	intron (NM_025626, intron 1 of 3)	intron (NM_025626, intron 1 of 3)	13722	NM_025626	66540	Mm.277864	NM_025626	ENSMUSG00000026655	Fam107b	3110001A13Rik|AA589595|AA959793|AI132312	family with sequence similarity 107, member B	protein-coding
mm_74562.1	chr8	11006712	11006725	-	1	NA	exon (NM_001081212, exon 1 of 2)	exon (NM_001081212, exon 1 of 2)	-1132	NR_046017	619321	Mm.403007	NR_046017	ENSMUSG00000096938	9530052E02Rik	-	RIKEN cDNA 9530052E02 gene	ncRNA
mm_129442.1	chr15	78529618	78529636	-	1	NA	promoter-TSS (NM_001204153)	promoter-TSS (NM_001204153)	24	NM_001204153	72709	Mm.34776	NM_028331	ENSMUSG00000022440	C1qtnf6	2810036M19Rik|CTRP6	C1q and tumor necrosis factor related protein 6	protein-coding
mm_140254.1	chr17	84313844	84313846	+	1	NA	intron (NM_183021, intron 28 of 37)	intron (NM_183021, intron 28 of 37)	-125898	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_165574.1	chr3	22073327	22073328	+	1	NA	Intergenic	RMER15|LTR|ERVL	-3325	NM_030732	81004	Mm.202966	NM_030732	ENSMUSG00000027630	Tbl1xr1	8030499H02Rik|A630076E03Rik|AW539987|C21|C230089I12Rik|DC42|Ira1|TBLR1	transducin (beta)-like 1X-linked receptor 1	protein-coding
mm_144937.1	chr18	37742089	37742137	+	1	NA	promoter-TSS (NM_033578)	promoter-TSS (NM_033578)	19	NM_033578	93703	Mm.247203	NM_033578	ENSMUSG00000103088	Pcdhgb6	-	protocadherin gamma subfamily B, 6	protein-coding
mm_25121.1	chr3	102012402	102012425	+	1	NA	intron (NM_178777, intron 2 of 2)	CpG	2268	NM_178777	18072	Mm.137286	NM_178777	ENSMUSG00000048540	Nhlh2	6230401I09Rik|Hen2|NSCL2|Nscl-2|bHLHa34	nescient helix loop helix 2	protein-coding
mm_28953.1	chr3	100487942	100487975	-	1	NA	intron (NM_001142952, intron 1 of 1)	intron (NM_001142952, intron 1 of 1)	1234	NM_001142952	74645	Mm.226900	NM_001142952	ENSMUSG00000044468	Fam46c	4930431B09Rik|AI449797	family with sequence similarity 46, member C	protein-coding
mm_159496.1	chr4	43267117	43267117	+	1	NA	promoter-TSS (NM_177195)	promoter-TSS (NM_177195)	-42	NM_177195	320571	Mm.74465	NM_177195	ENSMUSG00000028457	Atp8b5	4930417M19Rik|Feta	ATPase, class I, type 8B, member 5	protein-coding
mm_146797.1	chr18	20673696	20673770	-	1	NA	exon (NM_013697, exon 4 of 4)	exon (NM_013697, exon 4 of 4)	8483	NM_013697	22139	Mm.2108	NM_013697	ENSMUSG00000061808	Ttr	AA408768|AI787086|D17860|prealbumin	transthyretin	protein-coding
mm_47300.1	chr5	122354162	122354237	-	1	NA	promoter-TSS (NM_019780)	promoter-TSS (NM_019780)	-4	NM_144912	231724	Mm.255587	NM_144912	ENSMUSG00000038569	Rad9b	A630082N15Rik|BC021784	RAD9 checkpoint clamp component B	protein-coding
mm_107698.1	chr12	55410282	55410286	+	1	NA	intron (NM_011968, intron 4 of 6)	intron (NM_011968, intron 4 of 6)	11459	NM_011968	26443	Mm.30210	NM_011968	ENSMUSG00000021024	Psma6	IOTA	proteasome (prosome, macropain) subunit, alpha type 6	protein-coding
mm_60949.1	chr7	47021290	47021301	+	1	NA	Intergenic	Intergenic	-12881	NM_175318	101685	Mm.155687	NM_175318	ENSMUSG00000049516	Spty2d1	5830435K17Rik|AI852426|P16H6	SPT2, Suppressor of Ty, domain containing 1 (S. cerevisiae)	protein-coding
mm_120741.1	chr14	73178262	73178289	+	1	NA	intron (NR_033185, intron 14 of 15)	intron (NR_033185, intron 14 of 15)	28576	NR_030459	751541		NR_030459	ENSMUSG00000076121	Mir687	Mirn687|mir-687|mmu-mir-687	microRNA 687	ncRNA
mm_152321.1	chr19	9931251	9931253	-	1	NA	Intergenic	Intergenic	-31719	NM_016692	16319	Mm.29755	NM_016692	ENSMUSG00000024660	Incenp	2700067E22Rik|AU019509|C130081E20|C77457	inner centromere protein	protein-coding
mm_47834.1	chr5	134312546	134312549	-	1	NA	intron (NM_001080746, intron 1 of 34)	intron (NM_001080746, intron 1 of 34)	2213	NM_001080746	14886	Mm.261570	NM_010365	ENSMUSG00000060261	Gtf2i	6030441I21Rik|BAP-135|Diws1t|GtfII-I|Spin|TFII-I|WBSCR6	general transcription factor II I	protein-coding
mm_114291.1	chr13	58807820	58807838	+	1	NA	5' UTR (NM_001025074, exon 1 of 18)	5' UTR (NM_001025074, exon 1 of 18)	132	NM_001025074	18212	Mm.130054	NM_008745	ENSMUSG00000055254	Ntrk2	GP145-TrkB/GP95-TrkB|Tkrb|trk-B|trkB	neurotrophic tyrosine kinase, receptor, type 2	protein-coding
mm_87902.1	chr10	62072212	62072233	+	1	NA	Intergenic	Intergenic	38791	NM_027251	69894	Mm.294126	NM_027251	ENSMUSG00000020083	2010107G23Rik	AA545165	RIKEN cDNA 2010107G23 gene	protein-coding
mm_168418.1	chr11	3265790	3265803	+	1	NA	intron (NM_007879, intron 1 of 8)	intron (NM_007879, intron 1 of 8)	590	NM_007879	13494	Mm.3250	NM_007879	ENSMUSG00000020457	Drg1	AA408859|AI132520|Nedd3	developmentally regulated GTP binding protein 1	protein-coding
mm_35282.1	chr4	20778853	20778876	-	1	NA	promoter-TSS (NM_172987)	promoter-TSS (NM_172987)	-196	NM_172987	269513	Mm.317473	NM_172987	ENSMUSG00000055761	Nkain3	C530048M05|E130310K16Rik	Na+/K+ transporting ATPase interacting 3	protein-coding
mm_140623.1	chr17	12276390	12276391	-	1	NA	intron (NM_011948, intron 2 of 26)	intron (NM_011948, intron 2 of 26)	42270	NM_011948	26407	Mm.28587	NM_011948	ENSMUSG00000014426	Map3k4	D17Rp17|D17Rp17e|MAPKKK4|MEKK 4|MTK1|Mek4b|Mekk4|RP17|Rp17a|Tas|mKIAA0213	mitogen-activated protein kinase kinase kinase 4	protein-coding
mm_157660.1	chrX	57392972	57392988	-	1	NA	promoter-TSS (NM_001166623)	promoter-TSS (NM_001166623)	56	NM_011252	19655	Mm.28275	NM_011252	ENSMUSG00000031134	Rbmx	hnRNP G	RNA binding motif protein, X chromosome	protein-coding
mm_138799.1	chr17	37995858	37995888	+	1	NA	Intergenic	Intergenic	-42851	NM_001011829	258094	Mm.377348	NM_001011829	ENSMUSG00000109376	Olfr761	MOR218-12|MOR218-5P|MOR218-6P|Olfr1552-ps1	olfactory receptor 761	protein-coding
mm_140208.1	chr17	83775629	83775637	+	1	NA	exon (NM_001171052, exon 9 of 16)	exon (NM_001171052, exon 9 of 16)	69470	NM_001171052	116871	Mm.277668	NM_054082	ENSMUSG00000055817	Mta3	1110002J22Rik|mKIAA1266	metastasis associated 3	protein-coding
mm_93536.1	chr10	115384327	115384336	-	1	NA	promoter-TSS (NM_001033261)	promoter-TSS (NM_001033261)	104	NM_025780	66816	Mm.32314	NM_025780	ENSMUSG00000020137	Thap2	2900040O07Rik|9030625G08Rik|AI450385|AI649097	THAP domain containing, apoptosis associated protein 2	protein-coding
mm_67977.1	chr7	100656960	100656985	-	1	NA	promoter-TSS (NM_001163187)	promoter-TSS (NM_001163187)	-7	NM_001163186	27276	Mm.491216	NM_013746	ENSMUSG00000030701	Plekhb1	AI315628|PHR1|Phret1|evt-1	pleckstrin homology domain containing, family B (evectins) member 1	protein-coding
mm_161620.1	chr16	58460245	58460245	+	1	NA	intron (NM_028523, intron 12 of 15)	RMER17A2|LTR|ERVK	51710	NM_028523	73379	Mm.373589	NM_028523	ENSMUSG00000035107	Dcbld2	1700055P21Rik|AW146002|CLCP1|Esdn	discoidin, CUB and LCCL domain containing 2	protein-coding
mm_50414.1	chr6	48746189	48746212	+	1	NA	promoter-TSS (NM_175035)	promoter-TSS (NM_175035)	3	NM_175035	317757	Mm.455917	NM_175035	ENSMUSG00000043505	Gimap5	D630024P16|E230026N22Rik	GTPase, IMAP family member 5	protein-coding
mm_111251.1	chr12	84881443	84881445	-	1	NA	Intergenic	Intergenic	-4949	NM_013589	16997	Mm.3900	NM_013589	ENSMUSG00000002020	Ltbp2	AW208642	latent transforming growth factor beta binding protein 2	protein-coding
mm_65792.1	chr7	28894346	28894361	-	1	NA	TTS (NM_001110807)	TTS (NM_001110807)	12697	NM_001110807	60594	Mm.476990	NM_021894	ENSMUSG00000054083	Capn12	CANP 12	calpain 12	protein-coding
mm_139171.1	chr17	47587268	47587270	+	1	NA	intron (NM_001081635, intron 2 of 6)	B1_Mur3|SINE|Alu	-6198	NM_007632	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_165817.1	chr3	146404955	146404966	+	1	NA	intron (NM_001253769, intron 1 of 13)	CpG	318	NM_138744	99167	Mm.200783	NM_138744	ENSMUSG00000036825	Ssx2ip	AU014939|AU042321|Adip	synovial sarcoma, X 2 interacting protein	protein-coding
mm_169064.1	chr13	26492524	26492542	+	1	NA	Intergenic	Intergenic	-180127	NR_045933	73576	Mm.45473	NR_045933		1700092E19Rik	-	RIKEN cDNA 1700092E19 gene	ncRNA
mm_153404.1	chr19	40512082	40512086	-	1	NA	intron (NM_009166, intron 1 of 23)	intron (NM_009166, intron 1 of 23)	1652	NM_178362	20411	Mm.210815	NM_009166	ENSMUSG00000025006	Sorbs1	2310065E01Rik|9530001P15Rik|CAP|SH3P12|Sh3d5|mKIAA1296	sorbin and SH3 domain containing 1	protein-coding
mm_134130.1	chr16	10447341	10447369	-	1	NA	promoter-TSS (NM_001013778)	promoter-TSS (NM_001013778)	-5	NM_001013778	383103	Mm.325732	NM_001013778	ENSMUSG00000050908	Tvp23a	Fam18a	trans-golgi network vesicle protein 23A	protein-coding
mm_94652.1	chr11	17051793	17051808	+	1	NA	promoter-TSS (NM_029861)	promoter-TSS (NM_029861)	-134	NM_029861	380686	Mm.425666	NM_029861	ENSMUSG00000044629	Cnrip1	1500041B16Rik|3110054C06Rik|5330437A18Rik|AI854501|C2orf32	cannabinoid receptor interacting protein 1	protein-coding
mm_129667.1	chr15	81302233	81302247	-	1	NA	Intergenic	Intergenic	-50378	NR_077230	78102	Mm.296832	NR_077229		8430426J06Rik	-	RIKEN cDNA 8430426J06 gene	ncRNA
mm_8907.1	chr1	163312596	163312645	-	1	NA	exon (NM_175686, exon 1 of 5)	exon (NM_175686, exon 1 of 5)	1030	NM_011127	18933	Mm.288642	NM_011127	ENSMUSG00000026586	Prrx1	A230024N07Rik|AA755424|AI385634|AI843499|K-2|Pmx|Pmx1|Prx1|mHox	paired related homeobox 1	protein-coding
mm_52834.1	chr6	121365927	121365937	+	1	NA	TTS (NM_133661)	TTS (NM_133661)	19235	NM_133661	14411	Mm.274506	NM_133661	ENSMUSG00000030109	Slc6a12	BGT1|GAT-2|GAT2|Gabt2	solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12	protein-coding
mm_161255.1	chr13	107733880	107733880	-	1	NA	exon (NM_145456, exon 11 of 15)	exon (NM_145456, exon 11 of 15)	27207	NR_029759	723929		NR_029759	ENSMUSG00000065425	Mir325	Mirn325|mmu-mir-325	microRNA 325	ncRNA
mm_168605.1	chr11	75348331	75348331	-	1	NA	promoter-TSS (NM_026653)	promoter-TSS (NM_026653)	52	NM_001164223	68275	Mm.102574	NM_026653	ENSMUSG00000000751	Rpa1	5031405K23Rik|70kDa|AA589576|AW557552|RF-A|RP-A|Rpa	replication protein A1	protein-coding
mm_110087.1	chr12	24831301	24831323	-	1	NA	promoter-TSS (NM_026037)	promoter-TSS (NM_026037)	-287	NM_026037	67216	Mm.167671	NM_026037	ENSMUSG00000020646	Mboat2	2810049G06Rik|AU022889|AW547221|LPCAT4|Moact2|Oact2	membrane bound O-acyltransferase domain containing 2	protein-coding
mm_67526.1	chr7	81161745	81161755	-	1	NA	intron (NM_001004184, intron 12 of 17)	intron (NM_001004184, intron 12 of 17)	46951	NM_001004184	434203	Mm.389909	NM_001004184	ENSMUSG00000025726	Slc28a1	Cnt1	solute carrier family 28 (sodium-coupled nucleoside transporter), member 1	protein-coding
mm_2540.1	chr1	107511417	107511431	+	1	NA	promoter-TSS (NM_001174170)	promoter-TSS (NM_001174170)	1	NM_001174170	18788	Mm.271870	NM_011111	ENSMUSG00000062345	Serpinb2	PAI-2|Planh2|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 2	protein-coding
mm_66803.1	chr7	47185058	47185061	-	1	NA	TTS (NM_001308537)	TTS (NM_001308537)	4357	NM_001308537	381886	Mm.377894	NM_205821		Mrgpra6	MrgA6	MAS-related GPR, member A6	protein-coding
mm_45275.1	chr5	64806264	64806278	-	1	NA	intron (NM_008453, intron 1 of 5)	intron (NM_008453, intron 1 of 5)	2748	NM_008453	16599	Mm.392759	NM_008453	ENSMUSG00000029178	Klf3	9930027G08Rik|AL024007|Bklf|Tef-2	Kruppel-like factor 3 (basic)	protein-coding
mm_52450.1	chr6	113673020	113673051	+	1	NA	exon (NM_172161, exon 6 of 13)	exon (NM_172161, exon 6 of 13)	-24015	NM_001347356	381801	Mm.333322	NM_001033463	ENSMUSG00000056952	Tatdn2	AI646012|mKIAA0218	TatD DNase domain containing 2	protein-coding
mm_105221.1	chr11	102218924	102218935	-	1	NA	intron (NM_001284248, intron 4 of 28)	intron (NM_001284248, intron 4 of 28)	11221	NR_106179	102465892		NR_106179	ENSMUSG00000098863	Mir8101	Gm27705|mmu-mir-8101	microRNA 8101	ncRNA
mm_134411.1	chr16	17691628	17691631	-	1	NA	intron (NM_033609, intron 2 of 17)	intron (NM_033609, intron 2 of 17)	31271	NM_001285886	94112	Mm.208970	NM_033609	ENSMUSG00000012114	Med15	A230074L19Rik|AW536074|Pcqap|mPcqap	mediator complex subunit 15	protein-coding
mm_92830.1	chr10	81482334	81482353	-	1	NA	intron (NM_001311124, intron 1 of 11)	intron (NM_001311124, intron 1 of 11)	366	NM_176954	319586	Mm.152689	NM_176954	ENSMUSG00000034818	Celf5	4930565A21Rik|Brunol5	CUGBP, Elav-like family member 5	protein-coding
mm_63684.1	chr7	130553031	130553062	+	1	NA	Intergenic	Intergenic	-5665	NM_001162855	67872	Mm.21714	NM_001162855	ENSMUSG00000040331	Nsmce4a	2410003A14Rik	NSE4 homolog A, SMC5-SMC6 complex component	protein-coding
mm_118164.1	chr13	105294382	105294419	-	1	NA	Intergenic	CpG	-1386	NM_027934	71816	Mm.317015	NM_027934	ENSMUSG00000021720	Rnf180	3110001E11Rik|Rines	ring finger protein 180	protein-coding
mm_130403.1	chr15	97976157	97976172	-	1	NA	exon (NM_001113515, exon 53 of 53)	exon (NM_001113515, exon 53 of 53)	11935	NM_001252153	380967	Mm.196630	NM_201359	ENSMUSG00000052369	Tmem106c	AI046681|BC046621|D15Ertd405e	transmembrane protein 106C	protein-coding
mm_95092.1	chr11	33940266	33940276	+	1	NA	intron (NM_001190886, intron 1 of 7)	intron (NM_001190886, intron 1 of 7)	-22742	NM_031169	16533	Mm.6206	NM_031169	ENSMUSG00000020155	Kcnmb1	BKbeta1	potassium large conductance calcium-activated channel, subfamily M, beta member 1	protein-coding
mm_156080.1	chrX	109196823	109196829	+	1	NA	promoter-TSS (NM_001037917)	promoter-TSS (NM_001037917)	70	NM_001037917	622976	Mm.482747	NM_001037917	ENSMUSG00000048621	Gm6377	EG622976	predicted gene 6377	protein-coding
mm_73569.1	chr8	109693445	109693460	+	1	NA	promoter-TSS (NM_028018)	promoter-TSS (NM_028018)	-158	NM_028018	71955	Mm.290036	NM_028018	ENSMUSG00000031729	Ist1	2400003C14Rik|AW536298|mKIAA0174	increased sodium tolerance 1 homolog (yeast)	protein-coding
mm_35922.1	chr4	53031797	53031806	-	1	NA	3' UTR (NM_013454, exon 50 of 50)	3' UTR (NM_013454, exon 50 of 50)	19921	NM_025623	66536	Mm.38244	NM_025623	ENSMUSG00000015247	Nipsnap3b	2700063N13Rik|Nipsnap3a	nipsnap homolog 3B (C. elegans)	protein-coding
mm_137976.1	chr17	33577908	33577909	+	1	NA	intron (NM_053214, intron 4 of 27)	intron (NM_053214, intron 4 of 27)	22201	NM_053214	17916	Mm.42019	NM_053214	ENSMUSG00000024300	Myo1f	C330006B10Rik	myosin IF	protein-coding
mm_166472.1	chr5	142907966	142907982	-	1	NA	Intergenic	Intergenic	-1220	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_6498.1	chr1	74284353	74284361	-	1	NA	promoter-TSS (NM_025580)	promoter-TSS (NM_025580)	381	NM_146110	227290	Mm.379371	NM_146110	ENSMUSG00000006299	Aamp	AU040907|Aamp-rs	angio-associated migratory protein	protein-coding
mm_121971.1	chr14	25593932	25593943	-	1	NA	intron (NM_001310666, intron 6 of 23)	intron (NM_001310666, intron 6 of 23)	7133	NR_033492	77592	Mm.444871	NM_175264		4931406H21Rik	-	RIKEN cDNA 4931406H21 gene	ncRNA
mm_22524.1	chr3	7646942	7646953	+	1	NA	Intergenic	Intergenic	-33187	NM_001313888	16196	Mm.3825	NM_008371	ENSMUSG00000040329	Il7	A630026I06Rik|Il-7|hlb368	interleukin 7	protein-coding
mm_10349.1	chr2	11689845	11689855	+	1	NA	3' UTR (NM_008367, exon 8 of 8)	3' UTR (NM_008367, exon 8 of 8)	-15443	NM_001271498	16169	Mm.200196	NM_008358	ENSMUSG00000023206	Il15ra	AA690181|IL-15RA	interleukin 15 receptor, alpha chain	protein-coding
mm_172321.1	chr7	106441073	106441079	-	1	NA	promoter-TSS (NR_003967)	promoter-TSS (NR_003967)	-3	NR_003967	209380	Mm.461779	NM_001001318		Gm4759	EG209380	GTPase, very large interferon inducible 1 pseudogene	pseudo
mm_6107.1	chr1	64033848	64033863	-	1	NA	Intergenic	Intergenic	8646	NR_105864	102466760		NR_105864	ENSMUSG00000098487	Mir6899	Gm27384|mmu-mir-6899	microRNA 6899	ncRNA
mm_137667.1	chr17	28746015	28746030	+	1	NA	intron (NM_001168513, intron 11 of 11)	intron (NM_001168513, intron 11 of 11)	-23295	NM_011950	26415	Mm.27970	NM_011950	ENSMUSG00000004864	Mapk13	SAPK4|Serk4	mitogen-activated protein kinase 13	protein-coding
mm_43485.1	chr5	136908230	136908232	+	1	NA	promoter-TSS (NM_026073)	promoter-TSS (NM_026073)	81	NM_026073	67286	Mm.41779	NM_026073	ENSMUSG00000007987	Ift22	3110017O03Rik|AI835745|AI847427|Rabl5	intraflagellar transport 22	protein-coding
mm_162374.1	chr1	69685761	69685771	-	1	NA	5' UTR (NM_011770, exon 1 of 8)	5' UTR (NM_011770, exon 1 of 8)	194	NM_011770	22779	Mm.106343	NM_011770	ENSMUSG00000025997	Ikzf2	A730095J18Rik|Helios|Zfpn1a2|Znfn1a2	IKAROS family zinc finger 2	protein-coding
mm_89026.1	chr10	82697355	82697362	+	1	NA	Intergenic	Intergenic	-1649	NM_001081218	67933	Mm.127405	NM_026462	ENSMUSG00000020246	Hcfc2	1700129L13Rik|AU019838	host cell factor C2	protein-coding
mm_162846.1	chr10	86347243	86347257	+	1	NA	3' UTR (NM_011595, exon 5 of 5)	3' UTR (NM_011595, exon 5 of 5)	46838	NM_011595	21859	Mm.4871	NM_011595	ENSMUSG00000020044	Timp3	Timp-3	tissue inhibitor of metalloproteinase 3	protein-coding
mm_28114.1	chr3	86551305	86551316	-	1	NA	intron (NM_001077687, intron 40 of 50)	intron (NM_001077687, intron 40 of 50)	-3027	NM_011839	23937	Mm.389466	NM_011839	ENSMUSG00000057777	Mab21l2	-	mab-21-like 2 (C. elegans)	protein-coding
mm_3133.1	chr1	135108956	135108967	+	1	NA	exon (NM_007955, exon 37 of 38)	exon (NM_007955, exon 37 of 38)	-3685	NM_001033409	329252	Mm.279594	NM_001033409	ENSMUSG00000042793	Lgr6	A530037C04Rik|D830026M09	leucine-rich repeat-containing G protein-coupled receptor 6	protein-coding
mm_158616.1	chrX	152644473	152644486	-	1	NA	promoter-TSS (NM_001290687)	promoter-TSS (NM_001290687)	69	NM_001290686	110380	Mm.40796	NM_172441	ENSMUSG00000045180	Shroom2	4832440C16|Apxl|C630003H05Rik|Shrm2	shroom family member 2	protein-coding
mm_69223.1	chr7	127604417	127604450	-	1	NA	promoter-TSS (NR_027915)	promoter-TSS (NR_027915)	12	NR_027915	68232	Mm.347960	NM_026628	ENSMUSG00000099579	1700120K04Rik	-	RIKEN cDNA 1700120K04 gene	ncRNA
mm_52951.1	chr6	122990351	122990365	+	1	NA	promoter-TSS (NM_001005860)	promoter-TSS (NM_001005860)	-9	NM_001005860	474145	Mm.263483	NM_001005860	ENSMUSG00000059639	Clec4a4	Dcir2	C-type lectin domain family 4, member a4	protein-coding
mm_1701.1	chr1	75168632	75168656	+	1	NA	promoter-TSS (NM_001159905)	promoter-TSS (NM_001159905)	-2	NM_001159905	68818	Mm.32646	NM_026846	ENSMUSG00000026197	Zfand2b	1110060O18Rik|C81256	zinc finger, AN1 type domain 2B	protein-coding
mm_158314.1	chrX	127736543	127736553	-	1	NA	promoter-TSS (NM_001281537)	promoter-TSS (NM_001281537)	6	NM_001281537	73934	Mm.159093	NM_001281537	ENSMUSG00000043569	Cldn34c4	4930412D23Rik	claudin 34C4	protein-coding
mm_102970.1	chr11	69667226	69667255	-	1	NA	3' UTR (NM_144958, exon 11 of 11)	3' UTR (NM_144958, exon 11 of 11)	-1070	NR_110993	12514	Mm.15819	NM_009853	ENSMUSG00000018774	Cd68	Lamp4|Scard1|gp110	CD68 antigen	protein-coding
mm_160160.1	chr7	44257166	44257166	-	1	NA	promoter-TSS (NM_001195034)	promoter-TSS (NM_001195034)	38	NM_001195034	100503991	Mm.367353	NM_001195034	ENSMUSG00000012777	Acpt	EG546967|Gm1432	acid phosphatase, testicular	protein-coding
mm_92820.1	chr10	81461030	81461058	-	1	NA	3' UTR (NM_176954, exon 12 of 12)	3' UTR (NM_176954, exon 12 of 12)	12087	NM_001311127	319586	Mm.152689	NM_176954	ENSMUSG00000034818	Celf5	4930565A21Rik|Brunol5	CUGBP, Elav-like family member 5	protein-coding
mm_57451.1	chr6	125164090	125164106	-	1	NA	intron (NM_001289726, intron 2 of 6)	intron (NM_001289726, intron 2 of 6)	1675	NM_008084	14433	Mm.304088	NM_008084	ENSMUSG00000057666	Gapdh	Gapd	glyceraldehyde-3-phosphate dehydrogenase	protein-coding
mm_83256.1	chr9	42428154	42428163	-	1	NA	intron (NM_173038, intron 7 of 7)	L2a|LINE|L2	-28229	NM_001324548	21683	Mm.42209	NM_009347	ENSMUSG00000037705	Tecta	Tctna	tectorin alpha	protein-coding
mm_98288.1	chr11	89066032	89066043	+	1	NA	intron (NR_110336, intron 1 of 3)	intron (NR_110336, intron 1 of 3)	5286	NR_110336	414094	Mm.124287	NM_001001497		Dgkeos	A930013B10Rik	diacylglycerol kinase, epsilon, opposite strand	ncRNA
mm_95912.1	chr11	58206968	58206976	+	1	NA	exon (NM_018738, exon 3 of 3)	exon (NM_018738, exon 3 of 3)	7416	NM_018738	16145	Mm.33902	NM_018738	ENSMUSG00000078853	Igtp	AW558444|Irgm3	interferon gamma induced GTPase	protein-coding
mm_42886.1	chr5	122372516	122372604	+	1	NA	promoter-TSS (NM_026883)	promoter-TSS (NM_026883)	52	NM_024216	68080	Mm.266328	NM_024216	ENSMUSG00000029464	Gpn3	A930018B01Rik|Atpbd1c|D5Ertd708e	GPN-loop GTPase 3	protein-coding
mm_116507.1	chr13	45079184	45079191	-	1	NA	Intergenic	Intergenic	-77091	NM_025772	94245	Mm.352311	NM_025772	ENSMUSG00000057531	Dtnbp1	5430437B18Rik|AW048963|Bloc1s8|dysbindin|sdy	dystrobrevin binding protein 1	protein-coding
mm_134148.1	chr16	10785036	10785057	-	1	NA	intron (NM_001271603, intron 1 of 1)	CpG	490	NM_009896	12703	Mm.130	NM_009896	ENSMUSG00000038037	Socs1	Cish1|Cish7|JAB|SOCS-1|SSI-1	suppressor of cytokine signaling 1	protein-coding
mm_2849.1	chr1	131661949	131661974	+	1	NA	5' UTR (NM_007799, exon 2 of 10)	5' UTR (NM_007799, exon 2 of 10)	23647	NM_007799	13034	Mm.230249	NM_007799	ENSMUSG00000004552	Ctse	A430072O03Rik|C920004C08Rik|CE|CatE	cathepsin E	protein-coding
mm_68864.1	chr7	126414856	126414895	-	1	NA	promoter-TSS (NM_009844)	promoter-TSS (NM_009844)	-5	NM_009844	12478	Mm.4360	NM_009844	ENSMUSG00000030724	Cd19	AW495831	CD19 antigen	protein-coding
mm_139291.1	chr17	48300473	48300479	+	1	NA	5' UTR (NM_001033405, exon 1 of 5)	5' UTR (NM_001033405, exon 1 of 5)	438	NM_001033405	328833	Mm.329104	NM_001033405	ENSMUSG00000071068	Treml2	AW049306|Gm750|Tlt2	triggering receptor expressed on myeloid cells-like 2	protein-coding
mm_167640.1	chr9	64704846	64704846	+	1	NA	intron (NM_001134399, intron 23 of 24)	intron (NM_001134399, intron 23 of 24)	32910	NM_017382	53869	Mm.1387	NM_017382	ENSMUSG00000004771	Rab11a	-	RAB11A, member RAS oncogene family	protein-coding
mm_149752.1	chr19	22692614	22692630	+	1	NA	promoter-TSS (NM_001035246)	promoter-TSS (NM_001035246)	3	NM_001035244	226025	Mm.131943	NM_177341	ENSMUSG00000052387	Trpm3	6330504P12Rik|9330180E14|AU018608|B930001P07Rik|LTRPC3|MLSN2	transient receptor potential cation channel, subfamily M, member 3	protein-coding
mm_22996.1	chr3	34020076	34020082	+	1	NA	promoter-TSS (NM_001113188)	promoter-TSS (NM_001113188)	0	NM_001113189	14359	Mm.259021	NM_008053	ENSMUSG00000027680	Fxr1	1110050J02Rik|9530073J07Rik|AI851072|Fxr1h|Fxr1p	fragile X mental retardation gene 1, autosomal homolog	protein-coding
mm_63508.1	chr7	127841905	127841933	+	1	NA	5' UTR (NM_009294, exon 1 of 11)	5' UTR (NM_009294, exon 1 of 11)	111	NM_009294	20909	Mm.24867	NM_009294	ENSMUSG00000030805	Stx4a	Stx4|Syn-4|Syn4	syntaxin 4A (placental)	protein-coding
mm_21553.1	chr2	164077846	164077874	-	1	NA	intron (NM_021420, intron 1 of 10)	intron (NM_021420, intron 1 of 10)	3682	NM_021420	58231	Mm.234472	NM_021420	ENSMUSG00000018209	Stk4	AI447339|AU020804|Kas-2|Mst1|Ysk3	serine/threonine kinase 4	protein-coding
mm_69308.1	chr7	128412255	128412275	-	1	NA	intron (NM_026418, intron 1 of 4)	intron (NM_026418, intron 1 of 4)	5907	NM_026418	67865	Mm.18635	NM_026418	ENSMUSG00000030844	Rgs10	2310010N19Rik	regulator of G-protein signalling 10	protein-coding
mm_113842.1	chr13	47194012	47194014	+	1	NA	promoter-TSS (NM_001170643)	promoter-TSS (NM_001170643)	10	NM_001170643	218215	Mm.287609	NM_146042	ENSMUSG00000038068	Rnf144b	BC025007|E130105P19Rik|Ibrdc2|Pir2	ring finger protein 144B	protein-coding
mm_81486.1	chr9	109999764	109999813	+	1	NA	exon (NM_008633, exon 3 of 19)	exon (NM_008633, exon 3 of 19)	-52233	NM_001311163	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_118696.1	chr14	22140334	22140344	+	1	NA	intron (NM_028275, intron 2 of 6)	ORR1C1|LTR|ERVL-MaLR	120627	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_17601.1	chr2	30828202	30828219	-	1	NA	promoter-TSS (NM_133346)	promoter-TSS (NM_133346)	90	NM_133346	72323	Mm.27656	NM_133346	ENSMUSG00000039483	Asb6	2510004M11Rik|AA409356	ankyrin repeat and SOCS box-containing 6	protein-coding
mm_134425.1	chr16	17911304	17911354	-	1	NA	promoter-TSS (NM_022408)	promoter-TSS (NM_022408)	19	NM_022408	27886	Mm.256480	NM_022408	ENSMUSG00000003527	Dgcr14	AI462402|D16H22S1269E|Dgcr1|Dgsi|ES2|Es2el	DiGeorge syndrome critical region gene 14	protein-coding
mm_53575.1	chr6	137410747	137410772	+	1	NA	promoter-TSS (NM_001164403)	promoter-TSS (NM_001164403)	38	NM_001164403	19277	Mm.186361	NM_011216	ENSMUSG00000030223	Ptpro	D28|GLEPP1|PTPBK|PTPROt|PTPU2|PTPoc|PTPphi|Ptpn15|R-PTP-O	protein tyrosine phosphatase, receptor type, O	protein-coding
mm_10194.1	chr2	4922821	4922856	+	1	NA	exon (NM_010726, exon 2 of 9)	exon (NM_010726, exon 2 of 9)	3842	NM_010726	16922	Mm.391704	NM_010726	ENSMUSG00000026664	Phyh	AI256161|AI265699|Lnap1|PAHX	phytanoyl-CoA hydroxylase	protein-coding
mm_123801.1	chr14	70520255	70520268	-	1	NA	promoter-TSS (NM_009755)	promoter-TSS (NM_009755)	-1	NR_033241	12153	Mm.27757	NM_009755	ENSMUSG00000022098	Bmp1	Pcp|Tld	bone morphogenetic protein 1	protein-coding
mm_154851.1	chrX	20548224	20548235	+	1	NA	Intergenic	Intergenic	-1589	NM_009060	19733	Mm.2118	NM_009060	ENSMUSG00000023070	Rgn	AI265316|GNL|SMP30	regucalcin	protein-coding
mm_48877.1	chr5	151127477	151127491	-	1	NA	intron (NM_146258, intron 1 of 13)	intron (NM_146258, intron 1 of 13)	62709	NM_001163493	243362	Mm.209272	NM_146258	ENSMUSG00000016128	Stard13	DLC2|GT650	StAR-related lipid transfer (START) domain containing 13	protein-coding
mm_63591.1	chr7	128134855	128134859	+	1	NA	intron (NM_021334, intron 8 of 29)	intron (NM_021334, intron 8 of 29)	5289	NM_021334	16411	Mm.22378	NM_021334	ENSMUSG00000030789	Itgax	AI449405|Cd11c|Cr4|N418	integrin alpha X	protein-coding
mm_146365.1	chr18	82584500	82584516	+	1	NA	3' UTR (NM_010777, exon 7 of 7)	3' UTR (NM_010777, exon 7 of 7)	30000	NM_001025254	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_80675.1	chr9	90245442	90245453	+	1	NA	intron (NM_194334, intron 2 of 12)	intron (NM_194334, intron 2 of 12)	25322	NM_194334	67016	Mm.335347	NM_194334	ENSMUSG00000037410	Tbc1d2b	1810061M12Rik|AI480956|AV021536|AV023399|AW491493|mKIAA1055	TBC1 domain family, member 2B	protein-coding
mm_87160.1	chr10	36641084	36641087	+	1	NA	intron (NM_001081208, intron 2 of 3)	L1Md_A|LINE|L1	134278	NM_001253356	319415	Mm.332442	NM_001081208	ENSMUSG00000044499	Hs3st5	D930005L05Rik|Gm1151|Hs3ost5	heparan sulfate (glucosamine) 3-O-sulfotransferase 5	protein-coding
mm_156851.1	chrX	164401081	164401091	+	1	NA	TTS (NM_001308489)	TTS (NM_001308489)	-18701	NM_011081	18700	Mm.3781	NM_011081	ENSMUSG00000031381	Piga	AI194334|Pig-a	phosphatidylinositol glycan anchor biosynthesis, class A	protein-coding
mm_21233.1	chr2	156052968	156053009	-	1	NA	promoter-TSS (NM_001136556)	promoter-TSS (NM_001136556)	-41	NM_001136556	74562	Mm.159241	NM_001136556	ENSMUSG00000013338	Fer1l4	9130402C12Rik	fer-1-like 4 (C. elegans)	protein-coding
mm_13090.1	chr2	91237111	91237145	+	1	NA	promoter-TSS (NM_028119)	promoter-TSS (NM_028119)	-18	NR_015464	606735	Mm.246808	NR_015464	ENSMUSG00000097868	A330069E16Rik	-	RIKEN cDNA A330069E16 gene	ncRNA
mm_156331.1	chrX	138985492	138985502	+	1	NA	exon (NM_013724, exon 18 of 28)	exon (NM_013724, exon 18 of 28)	71067	NM_013724	27206	Mm.482319	NM_013724	ENSMUSG00000052854	Nrk	AA407323|AA409510|AI225895|AV168563|AW538185|Nesk	Nik related kinase	protein-coding
mm_163844.1	chr14	19418042	19418052	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	184540	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_91083.1	chr10	19014536	19014548	-	1	NA	intron (NM_009397, intron 1 of 8)	intron (NM_009397, intron 1 of 8)	868	NM_009397	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_11777.1	chr2	38932016	38932031	+	1	NA	promoter-TSS (NM_172854)	promoter-TSS (NM_172854)	43	NM_172854	241327	Mm.103491	NM_172854	ENSMUSG00000046618	Olfml2a	4932431K08Rik|mFLJ00237	olfactomedin-like 2A	protein-coding
mm_106929.1	chr12	8500254	8500278	+	1	NA	promoter-TSS (NM_007483)	promoter-TSS (NM_007483)	-281	NM_007483	11852	Mm.687	NM_007483	ENSMUSG00000054364	Rhob	AA017882|Arh6|Arhb	ras homolog family member B	protein-coding
mm_110163.1	chr12	27160448	27160476	-	1	NA	promoter-TSS (NR_045869)	promoter-TSS (NR_045869)	54	NR_045868	636791	Mm.423496	NM_001039248	ENSMUSG00000094002	Gm9866	EG636791|ENSMUSG00000052076	predicted gene 9866	ncRNA
mm_14938.1	chr2	151543957	151544009	+	1	NA	exon (NM_001302078, exon 3 of 6)	exon (NM_001302078, exon 3 of 6)	1500	NM_001302078	14225	Mm.278458	NM_008019	ENSMUSG00000032966	Fkbp1a	FKBP12|Fkbp|Fkbp1	FK506 binding protein 1a	protein-coding
mm_111531.1	chr12	100636582	100636584	-	1	NA	intron (NM_153587, intron 3 of 17)	ORR1F|LTR|ERVL-MaLR	88537	NM_001330702	73086	Mm.220417	NM_153587	ENSMUSG00000021180	Rps6ka5	3110005L17Rik|6330404E13Rik|AI854034|MSK1|MSPK1|RLPK|RLSK|S6K-alpha-5	ribosomal protein S6 kinase, polypeptide 5	protein-coding
mm_29259.1	chr3	107221723	107221738	-	1	NA	promoter-TSS (NM_001111143)	promoter-TSS (NM_001111143)	2	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_145398.1	chr18	57142838	57142858	+	1	NA	intron (NM_001001979, intron 1 of 24)	intron (NM_001001979, intron 1 of 24)	9758	NM_001001979	70417	Mm.297863	NM_001001979	ENSMUSG00000024593	Megf10	3000002B06Rik|Gm331	multiple EGF-like-domains 10	protein-coding
mm_167171.1	chr7	139070517	139070517	+	1	NA	intron (NM_028708, intron 19 of 19)	MTC-int|LTR|ERVL-MaLR	-15484	NM_011993	26757	Mm.250414	NM_011993	ENSMUSG00000025478	Dpysl4	AI173505|CRMP-3|Crmp3|DPY4|Drp-4|Ulip4	dihydropyrimidinase-like 4	protein-coding
mm_74479.1	chr8	4289596	4289652	-	1	NA	exon (NM_010485, exon 6 of 6)	exon (NM_010485, exon 6 of 6)	-13719	NM_011592	21856	Mm.195249	NM_011592	ENSMUSG00000002949	Timm44	0710005E20Rik|D8Ertd118e|Mimt44|Tim44	translocase of inner mitochondrial membrane 44	protein-coding
mm_99964.1	chr11	113684488	113684506	+	1	NA	promoter-TSS (NM_138598)	promoter-TSS (NM_138598)	85	NM_177777	276852	Mm.239566	NM_177777	ENSMUSG00000041623	D11Wsu47e	-	DNA segment, Chr 11, Wayne State University 47, expressed	protein-coding
mm_158758.1	chrX	166479634	166479707	-	1	NA	5' UTR (NM_019773, exon 1 of 3)	5' UTR (NM_019773, exon 1 of 3)	197	NM_019773	56382	Mm.25306	NM_019773	ENSMUSG00000079316	Rab9	2410064E05Rik|AI195561|Rab9a|Sid6061p	RAB9, member RAS oncogene family	protein-coding
mm_26358.1	chr3	142549366	142549377	+	1	NA	3' UTR (NM_001083312, exon 11 of 11)	3' UTR (NM_001083312, exon 11 of 11)	-10681	NM_018734	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_117998.1	chr13	100497898	100497899	-	1	NA	3' UTR (NM_008756, exon 9 of 9)	3' UTR (NM_008756, exon 9 of 9)	-5289	NM_022011	23894	Mm.272533	NM_022011	ENSMUSG00000021639	Gtf2h2	44kDa|BTF2 p44|BTF2-p44|Btf2p44|p44	general transcription factor II H, polypeptide 2	protein-coding
mm_10507.1	chr2	16356081	16356083	+	1	NA	promoter-TSS (NM_026162)	promoter-TSS (NM_026162)	-222	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding
mm_145325.1	chr18	54990281	54990315	+	1	NA	promoter-TSS (NM_175751)	promoter-TSS (NM_175751)	-118	NM_175751	269023	Mm.192984	NM_175751	ENSMUSG00000052713	Zfp608	4932417D18Rik|D430007A19Rik|Znf608	zinc finger protein 608	protein-coding
mm_170103.1	chr17	39844584	39844586	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	1588	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_43302.1	chr5	134613944	134613956	+	1	NA	intron (NM_020044, intron 1 of 12)	intron (NM_020044, intron 1 of 12)	1075	NM_022964	56743	Mm.391375	NM_020044	ENSMUSG00000040751	Lat2	AW125574|LAB|NTAL|WSCR5|Wbscr15|Wbscr5	linker for activation of T cells family, member 2	protein-coding
mm_162015.1	chr19	44941498	44941498	+	1	NA	exon (NM_001081225, exon 5 of 20)	exon (NM_001081225, exon 5 of 20)	10379	NM_001081225	226151	Mm.212609	NM_172638	ENSMUSG00000036097	Fam178a	3632432H19|6030443O07Rik|AU014917|Slf2	family with sequence similarity 178, member A	protein-coding
mm_42247.1	chr5	113907211	113907216	+	1	NA	intron (NM_011779, intron 1 of 10)	MTC|LTR|ERVL-MaLR	1493	NM_011779	23790	Mm.260158	NM_011779	ENSMUSG00000004530	Coro1c	AL022675|AW455561|AW548837	coronin, actin binding protein 1C	protein-coding
mm_77357.1	chr8	119635492	119635505	-	1	NA	5' UTR (NM_025734, exon 1 of 3)	5' UTR (NM_025734, exon 1 of 3)	182	NM_025734	66733	Mm.358699	NM_025734	ENSMUSG00000045246	Kcng4	4921535I01Rik|AW049024|KV6.3|KV6.4	potassium voltage-gated channel, subfamily G, member 4	protein-coding
mm_164424.1	chr16	45093764	45093771	+	1	NA	promoter-TSS (NM_026439)	promoter-TSS (NM_026439)	-286	NM_026439	67896	Mm.181074	NM_026439	ENSMUSG00000022665	Ccdc80	2610001E17Rik|DRO1|Ssg1|Urb	coiled-coil domain containing 80	protein-coding
mm_85738.1	chr9	108566867	108566877	-	1	NA	exon (NM_023247, exon 1 of 5)	exon (NM_023247, exon 1 of 5)	470	NM_023247	66706	Mm.29471	NM_023247	ENSMUSG00000070283	Ndufaf3	4733401H18Rik	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, assembly factor 3	protein-coding
mm_116082.1	chr13	28519681	28519684	-	1	NA	intron (NR_045053, intron 7 of 8)	intron (NR_045053, intron 7 of 8)	191191	NR_105787	102466635		NR_105787	ENSMUSG00000099158	Mir6368	Gm27800|mmu-mir-6368	microRNA 6368	ncRNA
mm_150153.1	chr19	31950776	31950803	+	1	NA	Intergenic	Intergenic	82028	NM_001081074	69865	Mm.87538	NM_001081074	ENSMUSG00000052595	A1cf	1810073H04Rik|ACF64|ACF65|ASP|Acf|MCM|MerCreMer|Tg(Myh6-cre/Esr1*)1Jmk|mer	APOBEC1 complementation factor	protein-coding
mm_83796.1	chr9	52679397	52679426	-	1	NA	promoter-TSS (NM_178906)	promoter-TSS (NM_178906)	26	NM_178906	330941	Mm.335160	NM_177907	ENSMUSG00000078307	AI593442	E130102D23	expressed sequence AI593442	protein-coding
mm_152228.1	chr19	8707880	8707897	-	1	NA	exon (NM_008577, exon 9 of 9)	exon (NM_008577, exon 9 of 9)	6009	NM_008577	17254	Mm.4114	NM_008577	ENSMUSG00000010095	Slc3a2	4F2|4F2HC|AI314110|Cd98|Ly-10|Ly-m10|Ly10|Mdu1|Mgp-2hc|NACAE	solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2	protein-coding
mm_105016.1	chr11	100415192	100415202	-	1	NA	promoter-TSS (NM_010221)	promoter-TSS (NM_010221)	-378	NM_176830	66180	Mm.4940	NM_176830	ENSMUSG00000006931	P3h4	1110036O03Rik|AI413214|Leprel4|Sc65	prolyl 3-hydroxylase family member 4 (non-enzymatic)	protein-coding
mm_67197.1	chr7	74065546	74065556	-	1	NA	Intergenic	MER5A|DNA|hAT-Charlie	-51869	NM_009181	20450	Mm.4954	NM_009181	ENSMUSG00000025789	St8sia2	AI323367|ST8SiaII|STX|Siat8b	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 2	protein-coding
mm_50113.1	chr6	41533906	41533910	+	1	NA	Intergenic	Intergenic	12132	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_20557.1	chr2	131072654	131072673	-	1	NA	exon (NM_011426, exon 17 of 21)	exon (NM_011426, exon 17 of 21)	-8849	NM_001163529	110751	Mm.108550	NM_033615	ENSMUSG00000027318	Adam33	Adaml	a disintegrin and metallopeptidase domain 33	protein-coding
mm_8964.1	chr1	165160790	165160793	-	1	NA	promoter-TSS (NM_032005)	promoter-TSS (NM_032005)	-18	NM_032005	83993	Mm.190649	NM_032005	ENSMUSG00000026572	Tbx19	AU019250|D1Ertd754e|Tpit	T-box 19	protein-coding
mm_91891.1	chr10	59951548	59951559	-	1	NA	5' UTR (NM_029083, exon 2 of 3)	5' UTR (NM_029083, exon 2 of 3)	217	NM_029083	74747	Mm.21697	NM_029083	ENSMUSG00000020108	Ddit4	5830413E08Rik|AA415483|REDD1|Rtp801|dig2	DNA-damage-inducible transcript 4	protein-coding
mm_111899.1	chr12	108702323	108702331	-	1	NA	promoter-TSS (NM_027299)	promoter-TSS (NM_027299)	-21	NM_027299	70059	Mm.207605	NM_027299	ENSMUSG00000021263	Degs2	2210008A03Rik|AI852933|DES2	delta(4)-desaturase, sphingolipid 2	protein-coding
mm_37287.1	chr4	119169966	119169969	-	1	NA	3' UTR (NM_001145936, exon 2 of 2)	3' UTR (NM_001145936, exon 2 of 2)	3889	NM_001145935	195522	Mm.169620	NM_183140	ENSMUSG00000045268	Zfp691	6430544H17Rik|Znf691	zinc finger protein 691	protein-coding
mm_172558.1	chr8	106573385	106573389	-	1	NA	Intergenic	Intergenic	-13756	NR_045470	68692	Mm.416843	NR_045470	ENSMUSG00000099139	1110028F18Rik	-	RIKEN cDNA 1110028F18 gene	ncRNA
mm_148742.1	chr19	5964268	5964306	+	1	NA	promoter-TSS (NM_008893)	promoter-TSS (NM_008893)	-81	NM_008893	18969	Mm.209931	NM_008893	ENSMUSG00000024833	Pola2	AI573378	polymerase (DNA directed), alpha 2	protein-coding
mm_83022.1	chr9	37019826	37019849	-	1	NA	intron (NM_001029838, intron 2 of 12)	intron (NM_001029838, intron 2 of 12)	127485	NM_148950	208076	Mm.260335	NM_148950	ENSMUSG00000035934	Pknox2	D230005H23Rik|Prep2	Pbx/knotted 1 homeobox 2	protein-coding
mm_18131.1	chr2	45005076	45005115	-	1	NA	intron (NM_001289521, intron 3 of 8)	intron (NM_001289521, intron 3 of 8)	18082	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_89599.1	chr10	95980323	95980334	+	1	NA	intron (NM_001001932, intron 2 of 28)	intron (NM_001001932, intron 2 of 28)	39665	NM_001001932	216238	Mm.210035	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding
mm_58409.1	chr7	3289064	3289099	+	1	NA	promoter-TSS (NM_001093764)	promoter-TSS (NM_001093764)	43	NM_001093764	50918	Mm.29874	NM_016969	ENSMUSG00000068566	Myadm	D7Wsu62e	myeloid-associated differentiation marker	protein-coding
mm_90122.1	chr10	117285200	117285229	+	1	NA	Intergenic	Intergenic	-2942	NM_017372	17105	Mm.45436	NM_017372	ENSMUSG00000069516	Lyz2	AI326280|Lys|Lysm|Lyzf2|Lyzs|Lzm|Lzm-s1|Lzp	lysozyme 2	protein-coding
mm_7472.1	chr1	120490083	120490100	-	1	NA	intron (NM_010766, intron 6 of 16)	intron (NM_010766, intron 6 of 16)	14993	NM_010766	17167	Mm.1856	NM_010766	ENSMUSG00000026390	Marco	AI323439|Ly112|Scara2	macrophage receptor with collagenous structure	protein-coding
mm_60273.1	chr7	43881155	43881159	+	1	NA	promoter-TSS (NM_019928)	promoter-TSS (NM_019928)	-15	NM_019928	56640	Mm.42080	NM_019928	ENSMUSG00000006948	Klk4	ESMP1|KLK-L1|PSTS|Prss17	kallikrein related-peptidase 4 (prostase, enamel matrix, prostate)	protein-coding
mm_32522.1	chr4	108834803	108834807	+	1	NA	exon (NM_025334, exon 1 of 7)	exon (NM_025334, exon 1 of 7)	127	NM_025334	66073	Mm.159965	NM_025334	ENSMUSG00000028567	Txndc12	0610040B21Rik|ERp16|ERp19	thioredoxin domain containing 12 (endoplasmic reticulum)	protein-coding
mm_118741.1	chr14	22318436	22318454	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	224353	NR_046307	74896	Mm.444661	NR_046307		4930405A10Rik	4930456G20Rik	RIKEN cDNA 4930405A10 gene	ncRNA
mm_157438.1	chrX	38635067	38635093	-	1	NA	promoter-TSS (NM_021550)	promoter-TSS (NM_021550)	63	NM_021550	59048	Mm.441410	NM_021550	ENSMUSG00000048970	C1galt1c1	1500002I11Rik|AB030184|C1GalT2|C81205|Cosmc	C1GALT1-specific chaperone 1	protein-coding
mm_9823.1	chr1	182517356	182517364	-	1	NA	5' UTR (NM_009794, exon 1 of 21)	5' UTR (NM_009794, exon 1 of 21)	123	NM_009794	12334	Mm.19306	NM_009794	ENSMUSG00000026509	Capn2	AI326419|Capa-2|Capa2|m-calpain|m-calpin	calpain 2	protein-coding
mm_13948.1	chr2	121299484	121299501	+	1	NA	exon (NM_001173506, exon 4 of 6)	exon (NM_001173506, exon 4 of 6)	4038	NM_001173506	17754	Mm.36501	NM_032393	ENSMUSG00000027254	Map1a	6330416M19Rik|AI853608|Mtap-1|Mtap1|Mtap1a|moth1	microtubule-associated protein 1 A	protein-coding
mm_106706.1	chr12	3806514	3806527	+	1	NA	promoter-TSS (NM_001271753)	promoter-TSS (NM_001271753)	-460	NM_007872	13435	Mm.5001	NM_007872	ENSMUSG00000020661	Dnmt3a	MmuIIIA	DNA methyltransferase 3A	protein-coding
mm_159183.1	chr2	111913031	111913031	-	1	NA	promoter-TSS (NM_001011803)	promoter-TSS (NM_001011803)	-103	NM_001011803	258023	Mm.377331	NM_001011803	ENSMUSG00000096566	Olfr1306	MOR245-15	olfactory receptor 1306	protein-coding
mm_48378.1	chr5	139736267	139736287	-	1	NA	promoter-TSS (NM_174850)	promoter-TSS (NM_174850)	56	NM_174850	231830	Mm.240510	NM_174850	ENSMUSG00000036718	Micall2	A930021H16Rik|JRAB|MICAL-L2|mFLJ00139	MICAL-like 2	protein-coding
mm_28106.1	chr3	86548333	86548338	-	1	NA	promoter-TSS (NM_011839)	promoter-TSS (NM_011839)	-52	NM_011839	23937	Mm.389466	NM_011839	ENSMUSG00000057777	Mab21l2	-	mab-21-like 2 (C. elegans)	protein-coding
mm_120946.1	chr14	76694195	76694210	+	1	NA	Intergenic	Intergenic	16634	NR_015485	73272	Mm.116804	NR_015485	ENSMUSG00000101009	1700108F19Rik	1700020I02Rik|BB065030	RIKEN cDNA 1700108F19 gene	ncRNA
mm_47280.1	chr5	122084901	122084906	-	1	NA	Intergenic	Intergenic	-16077	NM_010861	17906	Mm.1529	NM_010861	ENSMUSG00000013936	Myl2	MLC-2|MLC-2s/v|MLC-2v|Mlc2v|Mylpc	myosin, light polypeptide 2, regulatory, cardiac, slow	protein-coding
mm_145809.1	chr18	65412904	65412910	+	1	NA	intron (NR_105742, intron 3 of 6)	B1_Mur2|SINE|Alu	-18090	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_101474.1	chr11	30749071	30749118	-	1	NA	Intergenic	Intergenic	-22681	NM_134013	103554	Mm.240066	NM_134013	ENSMUSG00000040850	Psme4	AA409398|AU041366|TEMO|mKIAA0077	proteasome (prosome, macropain) activator subunit 4	protein-coding
mm_53131.1	chr6	125145296	125145298	+	1	NA	promoter-TSS (NM_001039669)	promoter-TSS (NM_001039669)	73	NM_001302779	320678	Mm.129415	NM_178787	ENSMUSG00000038271	Iffo1	4733401N06Rik|A930037G23Rik|HOM-TES-103|Iffo	intermediate filament family orphan 1	protein-coding
mm_69452.1	chr7	133112707	133112718	-	1	NA	intron (NM_009980, intron 1 of 10)	intron (NM_009980, intron 1 of 10)	10771	NM_009980	13017	Mm.246240	NM_009980	ENSMUSG00000030970	Ctbp2	AA407280|D7Ertd45e|Gtrgeo6|Ribeye	C-terminal binding protein 2	protein-coding
mm_115978.1	chr13	24206282	24206295	-	1	NA	intron (NM_001311122, intron 2 of 37)	intron (NM_001311122, intron 2 of 37)	74502	NM_001311122	68732	Mm.211047	NM_026825	ENSMUSG00000021338	Carmil1	1110037D04Rik|AI425970|CARMIL|CARML1|D130057M20|Lrrc16|Lrrc16a	capping protein regulator and myosin 1 linker 1	protein-coding
mm_132600.1	chr16	38555745	38555759	+	1	NA	Intergenic	MERV1_I-int|LTR|ERV1	-2946	NM_001205286	67846	Mm.310476	NM_026407	ENSMUSG00000002845	Tmem39a	2610033C09Rik	transmembrane protein 39a	protein-coding
mm_33706.1	chr4	133658957	133658978	+	1	NA	Intergenic	B3A|SINE|B2	13680	NM_001145955	230801	Mm.217004	NM_178698	ENSMUSG00000043257	Pigv	B330013B03|D430024F16Rik	phosphatidylinositol glycan anchor biosynthesis, class V	protein-coding
mm_111772.1	chr12	104044289	104044299	-	1	NA	5' UTR (NM_026535, exon 1 of 5)	5' UTR (NM_026535, exon 1 of 5)	149	NM_026535	68054	Mm.20286	NM_026535	ENSMUSG00000041567	Serpina12	4632419J12Rik	serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 12	protein-coding
mm_131125.1	chr16	5855768	5855779	+	1	NA	Intergenic	Intergenic	-29020	NM_021477	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_62749.1	chr7	111122836	111122870	+	1	NA	promoter-TSS (NR_015573)	promoter-TSS (NR_015573)	-178	NR_015573	75479	Mm.381620	NR_015573	ENSMUSG00000110424	1700012D14Rik	-	RIKEN cDNA 1700012D14 gene	ncRNA
mm_26806.1	chr3	10183924	10183927	-	1	NA	promoter-TSS (NM_001030305)	promoter-TSS (NM_001030305)	-40	NM_001030305	18857	Mm.371777	NM_001030305	ENSMUSG00000052468	Pmp2	P2	peripheral myelin protein 2	protein-coding
mm_76694.1	chr8	94180155	94180165	-	1	NA	exon (NM_013602, exon 3 of 3)	exon (NM_013602, exon 3 of 3)	1071	NM_013602	17748	Mm.192991	NM_013602	ENSMUSG00000031765	Mt1	MT-I|Mt-1	metallothionein 1	protein-coding
mm_54399.1	chr6	31528633	31528639	-	1	NA	exon (NM_013723, exon 2 of 8)	exon (NM_013723, exon 2 of 8)	35301	NM_013723	27205	Mm.89918	NM_013723	ENSMUSG00000025608	Podxl	AW121214|Ly102|PC|PCLP-1|Pclp1	podocalyxin-like	protein-coding
mm_163179.1	chr11	89078208	89078211	+	1	NA	intron (NM_001033266, intron 2 of 3)	B1_Mur3|SINE|Alu	4368	NM_001033266	217071	Mm.342127	NM_001033266	ENSMUSG00000072553	Gm525	-	predicted gene 525	protein-coding
mm_48812.1	chr5	148995209	148995233	-	1	NA	promoter-TSS (NR_102383)	promoter-TSS (NR_102383)	-6	NR_102384	319982	Mm.33303	NR_102383	ENSMUSG00000106951	5930430L01Rik	-	RIKEN cDNA 5930430L01 gene	ncRNA
mm_1636.1	chr1	74506703	74506718	+	1	NA	promoter-TSS (NM_001310662)	promoter-TSS (NM_001310662)	650	NM_021383	58184	Mm.291708	NM_021383	ENSMUSG00000026174	Cnot9	2610007F23Rik|AI593551|Fl10|Rqcd1	CCR4-NOT transcription complex, subunit 9	protein-coding
mm_90260.1	chr10	122615884	122615909	+	1	NA	Intergenic	ORR1D2|LTR|ERVL-MaLR	-46005	NR_040616	319272	Mm.411763	NR_040616		A130077B15Rik	-	RIKEN cDNA A130077B15 gene	ncRNA
mm_161500.1	chr15	89387136	89387136	+	1	NA	exon (NM_001160178, exon 1 of 1)	exon (NM_001160178, exon 1 of 1)	245	NM_001160178	546648	Mm.478787	NM_001160178	ENSMUSG00000091680	Klhdc7b	EG546648|Gm306	kelch domain containing 7B	protein-coding
mm_48405.1	chr5	140246837	140246838	-	1	NA	intron (NM_010752, intron 10 of 17)	B1_Mur1|SINE|Alu	74715	NM_010752	17120	Mm.27250	NM_010752	ENSMUSG00000029554	Mad1l1	AI173502|AW550425|Mad1	MAD1 mitotic arrest deficient 1-like 1	protein-coding
mm_115578.1	chr13	11581576	11581579	-	1	NA	intron (NM_023868, intron 96 of 104)	Lx|LINE|L1	59525	NR_027813	664793	Mm.410565	NR_027813		Zp4-ps	EG664793|Zp4|Zpb	zona pellucida glycoprotein 4, pseudogene	pseudo
mm_163438.1	chr12	85474611	85474634	+	1	NA	intron (NM_010234, intron 1 of 3)	CpG	721	NM_010234	14281	Mm.246513	NM_010234	ENSMUSG00000021250	Fos	D12Rfj1|c-fos|cFos	FBJ osteosarcoma oncogene	protein-coding
mm_128337.1	chr15	38518192	38518212	-	1	NA	intron (NR_125913, intron 1 of 11)	intron (NR_125913, intron 1 of 11)	1064	NM_001301688	54375	Mm.250214	NM_018745	ENSMUSG00000037458	Azin1	1700085L02Rik|AZI|Oazi|Oazin	antizyme inhibitor 1	protein-coding
mm_148031.1	chr18	70053335	70053427	-	1	NA	5' UTR (NM_030554, exon 1 of 6)	5' UTR (NM_030554, exon 1 of 6)	207	NM_001302798	80718	Mm.246753	NM_030554	ENSMUSG00000024511	Rab27b	2310021G14Rik|B130064M09Rik	RAB27B, member RAS oncogene family	protein-coding
mm_76714.1	chr8	94667204	94667216	-	1	NA	5' UTR (NM_024269, exon 1 of 6)	5' UTR (NM_024269, exon 1 of 6)	119	NM_024269	107566	Mm.393247	NM_024191	ENSMUSG00000031776	Arl2bp	1700010P10Rik|1700027H16Rik|6330544B05Rik|AI482273|AI849834|BART|Bart1	ADP-ribosylation factor-like 2 binding protein	protein-coding
mm_157073.1	chrX	8252305	8252333	-	1	NA	promoter-TSS (NM_001290430)	promoter-TSS (NM_001290430)	87	NM_133991	54632	Mm.327529	NM_133991	ENSMUSG00000031171	Ftsj1	AI931847|Ftsj|Ftsjl|Sfc12	FtsJ RNA methyltransferase homolog 1 (E. coli)	protein-coding
mm_166744.1	chr6	124865697	124865701	-	1	NA	3' UTR (NM_013488, exon 10 of 10)	3' UTR (NM_013488, exon 10 of 10)	-1782	NM_013533	14788	Mm.2514	NM_013533	ENSMUSG00000038390	Gpr162	A-2|BC031437|Grca	G protein-coupled receptor 162	protein-coding
mm_49217.1	chr6	15755770	15755775	+	1	NA	intron (NM_175088, intron 3 of 4)	intron (NM_175088, intron 3 of 4)	35111	NM_175088	16543	Mm.1314	NM_175088	ENSMUSG00000041390	Mdfic	Kdt1|Mdfid	MyoD family inhibitor domain containing	protein-coding
mm_100659.1	chr11	3203334	3203360	-	1	NA	intron (NM_001166549, intron 1 of 17)	intron (NM_001166549, intron 1 of 17)	328	NM_001166549	74203	Mm.255649	NM_023743	ENSMUSG00000020454	Eif4enif1	2610509L04Rik|A930019J01Rik|AA410001|AU021239|Clast4|D11Ertd166e	eukaryotic translation initiation factor 4E nuclear import factor 1	protein-coding
mm_157268.1	chrX	19236027	19236035	-	1	NA	Intergenic	B1F|SINE|Alu	-89060	NR_029807	723828		NR_029807	ENSMUSG00000065471	Mir222	Mirn222|mir-222|mmu-mir-222	microRNA 222	ncRNA
mm_113641.1	chr13	42103157	42103196	+	1	NA	intron (NM_007772, intron 2 of 8)	intron (NM_007772, intron 2 of 8)	51155	NM_007772	110521	Mm.4808	NM_007772	ENSMUSG00000021366	Hivep1	Cryabp1	human immunodeficiency virus type I enhancer binding protein 1	protein-coding
mm_53004.1	chr6	123270596	123270609	+	1	NA	intron (NM_001163161, intron 5 of 5)	intron (NM_001163161, intron 5 of 5)	8495	NM_010819	17474	Mm.441101	NM_010819	ENSMUSG00000030144	Clec4d	Clecsf8|Mpcl|mcl	C-type lectin domain family 4, member d	protein-coding
mm_52545.1	chr6	115934350	115934378	+	1	NA	intron (NM_145383, intron 2 of 4)	(TC)n|Simple_repeat|Simple_repeat	2437	NM_145383	212541	Mm.2965	NM_145383	ENSMUSG00000030324	Rho	Noerg1|Opn2|Ops|RP4	rhodopsin	protein-coding
mm_104491.1	chr11	95834136	95834149	-	1	NA	intron (NM_025659, intron 4 of 7)	intron (NM_025659, intron 4 of 7)	-8153	NM_023121	14710	Mm.46299	NM_023121	ENSMUSG00000038811	Gngt2	AV096488	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 2	protein-coding
mm_146399.1	chr18	82910887	82910901	+	1	NA	promoter-TSS (NM_183033)	promoter-TSS (NM_183033)	15	NM_183033	329003	Mm.326526	NM_183033	ENSMUSG00000058881	Zfp516	C330029B10Rik|D230016L03|Zfp26l|Znf516|mKIAA0222	zinc finger protein 516	protein-coding
mm_77284.1	chr8	116733256	116733314	-	1	NA	promoter-TSS (NM_029441)	promoter-TSS (NM_029441)	-294	NM_029441	75796	Mm.159575	NM_029441	ENSMUSG00000031758	Cdyl2	1700029M19Rik|4930453I21Rik|Gm20194	chromodomain protein, Y chromosome-like 2	protein-coding
mm_8467.1	chr1	153332886	153332894	-	1	NA	promoter-TSS (NM_010683)	promoter-TSS (NM_010683)	-104	NM_010683	226519	Mm.1249	NM_010683	ENSMUSG00000026478	Lamc1	Lamb2	laminin, gamma 1	protein-coding
mm_159554.1	chr4	106727926	106727926	-	1	NA	promoter-TSS (NM_001126487)	promoter-TSS (NM_001126487)	4	NM_001126487	381538	Mm.318201	NM_001126487	ENSMUSG00000047502	Mroh7	Gm1027|Heatr8	maestro heat-like repeat family member 7	protein-coding
mm_136662.1	chr17	6079900	6079908	+	1	NA	promoter-TSS (NM_001111017)	promoter-TSS (NM_001111017)	76	NM_181392	66467	Mm.303441	NM_181392	ENSMUSG00000034345	Gtf2h5	2700017P07Rik|2810432H05Rik|D17Wsu155e	general transcription factor IIH, polypeptide 5	protein-coding
mm_61717.1	chr7	81762928	81762943	+	1	NA	promoter-TSS (NM_025997)	promoter-TSS (NM_025997)	-18	NM_025997	67148	Mm.241472	NM_025997	ENSMUSG00000038646	Fam103a1	2410047I02Rik|2610204K14Rik|RAM	family with sequence similarity 103, member A1	protein-coding
mm_32642.1	chr4	115057117	115057127	+	1	NA	promoter-TSS (NM_001287388)	promoter-TSS (NM_001287388)	-689	NM_001287388	21349	Mm.239869	NM_011527	ENSMUSG00000028717	Tal1	Hpt|SCL/tal-1|Scl|bHLHa17|tal-1	T cell acute lymphocytic leukemia 1	protein-coding
mm_167045.1	chr7	80751841	80751847	+	1	NA	intron (NM_016721, intron 13 of 37)	intron (NM_016721, intron 13 of 37)	51487	NM_016721	29875	Mm.207619	NM_016721	ENSMUSG00000030536	Iqgap1	AA682088|D7Ertd237e|D7Ertd257e|mKIAA0051	IQ motif containing GTPase activating protein 1	protein-coding
mm_73975.1	chr8	120535724	120535734	+	1	NA	promoter-TSS (NM_001145897)	promoter-TSS (NM_001145897)	-128	NM_001145897	382034	Mm.334856	NM_198671	ENSMUSG00000031822	Gse1	2210013I18Rik|mKIAA0182	genetic suppressor element 1, coiled-coil protein	protein-coding
mm_34241.1	chr4	141210613	141210635	+	1	NA	Intergenic	RSINE1|SINE|B4	-3332	NM_001081174	76166	Mm.271064	NM_001081174	ENSMUSG00000073733	Rsg1	6330545A04Rik|Gm723	REM2 and RAB-like small GTPase 1	protein-coding
mm_51221.1	chr6	71370056	71370064	+	1	NA	Intergenic	Intergenic	-3367	NM_009857	12525	Mm.1858	NM_009857	ENSMUSG00000053977	Cd8a	BB154331|Ly-2|Ly-35|Ly-B|Lyt-2	CD8 antigen, alpha chain	protein-coding
mm_32312.1	chr4	103314494	103314504	+	1	NA	intron (NM_025909, intron 1 of 8)	(T)n|Simple_repeat|Simple_repeat	653	NM_025909	67013	Mm.30021	NM_025909	ENSMUSG00000035069	Oma1	2010001O09Rik|MPRP-1|ZMPOMA1	OMA1 zinc metallopeptidase	protein-coding
mm_162151.1	chrX	78245960	78245960	-	1	NA	promoter-TSS (NM_001126321)	promoter-TSS (NM_001126321)	-39	NM_001126321	236874	Mm.371699	NM_001126321	ENSMUSG00000079519	Gm14743	OTTMUSG00000017864	predicted gene 14743	protein-coding
mm_153274.1	chr19	37176056	37176078	-	1	NA	promoter-TSS (NM_001290826)	promoter-TSS (NM_001290826)	-4	NM_001290826	208922	Mm.391176	NM_198300	ENSMUSG00000039652	Cpeb3	4831444O18Rik|CPE-BP3|mKIAA0940	cytoplasmic polyadenylation element binding protein 3	protein-coding
mm_123149.1	chr14	57099673	57099697	-	1	NA	3' UTR (NM_008125, exon 2 of 2)	3' UTR (NM_008125, exon 2 of 2)	5017	NM_008125	14619	Mm.390683	NM_008125	ENSMUSG00000046352	Gjb2	AI325222|Cnx26|Cx26|Gjb-2	gap junction protein, beta 2	protein-coding
mm_160705.1	chr10	51677889	51677889	+	1	NA	exon (NM_001159389, exon 1 of 19)	exon (NM_001159389, exon 1 of 19)	129	NM_001159389	320995	Mm.109190	NM_177306	ENSMUSG00000019900	Rfx6	4930572O07Rik|Rfxdc1	regulatory factor X, 6	protein-coding
mm_49011.1	chr6	4758452	4758464	+	1	NA	3' UTR (NM_130877, exon 2 of 2)	3' UTR (NM_130877, exon 2 of 2)	11152	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_29597.1	chr3	119783251	119783261	-	1	NA	5' UTR (NM_019550, exon 1 of 14)	5' UTR (NM_019550, exon 1 of 14)	132	NM_001310711	56195	Mm.29966	NM_019550	ENSMUSG00000028134	Ptbp2	Ptb2|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding
mm_30839.1	chr4	22519589	22519601	+	1	NA	Intergenic	Intergenic	29047	NR_131335	105500046		NR_131335	ENSMUSG00000107859	Gm30731	Pnky|lnc-pou3f2	predicted gene, 30731	ncRNA
mm_21025.1	chr2	152413269	152413311	-	1	NA	3' UTR (NM_175126, exon 1 of 1)	3' UTR (NM_175126, exon 1 of 1)	1754	NM_175126	67917	Mm.391810	NM_175126	ENSMUSG00000074682	Zcchc3	2810406K24Rik	zinc finger, CCHC domain containing 3	protein-coding
mm_121446.1	chr14	120430604	120430666	+	1	NA	3' UTR (NM_207515, exon 8 of 8)	3' UTR (NM_207515, exon 8 of 8)	-47826	NM_029519	76108	Mm.261448	NM_029519	ENSMUSG00000051615	Rap2a	5830461H18Rik	RAS related protein 2a	protein-coding
mm_17269.1	chr2	26072677	26072677	-	1	NA	intron (NM_026495, intron 2 of 5)	intron (NM_026495, intron 2 of 5)	19719	NM_001037098	67991	Mm.131074	NM_026495	ENSMUSG00000026932	Nacc2	0610020I02Rik|AI448087|Btbd14a|C030048H19Rik	nucleus accumbens associated 2, BEN and BTB (POZ) domain containing	protein-coding
mm_115617.1	chr13	12063544	12063554	-	1	NA	intron (NM_023868, intron 1 of 104)	intron (NM_023868, intron 1 of 104)	43396	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding
mm_91034.1	chr10	18227519	18227525	-	1	NA	intron (NM_001346751, intron 2 of 4)	MTD|LTR|ERVL-MaLR	7459	NM_001346751	215814	Mm.296565	NM_144820	ENSMUSG00000059554	Ccdc28a	1700009P13Rik|AI480677	coiled-coil domain containing 28A	protein-coding
mm_133622.1	chr16	91563008	91563025	+	1	NA	3' UTR (NM_008338, exon 7 of 7)	3' UTR (NM_008338, exon 7 of 7)	15922	NM_008338	15980	Mm.249364	NM_008338	ENSMUSG00000022965	Ifngr2	Ifgr2|Ifgt	interferon gamma receptor 2	protein-coding
mm_45333.1	chr5	65679872	65679875	-	1	NA	intron (NM_001081321, intron 2 of 31)	intron (NM_001081321, intron 2 of 31)	17983	NM_001081321	71521	Mm.278974	NM_027818	ENSMUSG00000029202	Pds5a	9030416H16Rik|E230024D05Rik|mKIAA0648	PDS5 cohesin associated factor A	protein-coding
mm_101557.1	chr11	33880121	33880123	-	1	NA	intron (NM_001190886, intron 1 of 7)	intron (NM_001190886, intron 1 of 7)	-36537	NM_001290690	70357	Mm.252514	NM_027398	ENSMUSG00000053519	Kcnip1	KCHIP1|Kchip1.2	Kv channel-interacting protein 1	protein-coding
mm_120882.1	chr14	75327370	75327383	+	1	NA	intron (NM_026083, intron 11 of 18)	intron (NM_026083, intron 11 of 18)	43003	NM_026083	67302	Mm.74704	NM_026083	ENSMUSG00000022000	Zc3h13	2600010B19Rik|3110050K21Rik|4930570G11Rik|C87618	zinc finger CCCH type containing 13	protein-coding
mm_82041.1	chr9	122128970	122128986	+	1	NA	intron (NM_001164572, intron 1 of 5)	intron (NM_001164572, intron 1 of 5)	11712	NM_133741	20623	Mm.257989	NM_133741	ENSMUSG00000038145	Snrk	2010012F07Rik|AI448042|AW547029|E030034B15|R74830|mKIAA0096	SNF related kinase	protein-coding
mm_35545.1	chr4	41496320	41496333	-	1	NA	3' UTR (NM_001085515, exon 2 of 2)	3' UTR (NM_001085515, exon 2 of 2)	6749	NM_001085515	329828	Mm.27054	NM_001085515	ENSMUSG00000046312	AI464131	AA408153|AI604836|Gm762|Kiaa1161|NET37	expressed sequence AI464131	protein-coding
mm_19669.1	chr2	103372712	103372720	-	1	NA	promoter-TSS (NR_040332)	promoter-TSS (NR_040332)	48	NR_040332	319854	Mm.403818	NR_040332	ENSMUSG00000087278	A930006I01Rik	-	RIKEN cDNA A930006I01 gene	ncRNA
mm_147684.1	chr18	60718717	60718726	-	1	NA	Intergenic	Intergenic	-5332	NM_008306	15531	Mm.181862	NM_008306	ENSMUSG00000054008	Ndst1	1200015G06Rik|HSNST|HSNST 1|Hsst|N-HSST|N-HSST 1|NDST-1|b2b2230Clo	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 1	protein-coding
mm_131662.1	chr16	20611676	20611686	+	1	NA	promoter-TSS (NM_025462)	promoter-TSS (NM_025462)	80	NM_025462	107522	Mm.263319	NM_025462	ENSMUSG00000022842	Ece2	1810009K13Rik|6330509A19Rik|9630025D12Rik|BB127715|Ece-2	endothelin converting enzyme 2	protein-coding
mm_167352.1	chr8	83741277	83741297	+	1	NA	promoter-TSS (NM_001163029)	promoter-TSS (NM_001163029)	24	NM_001163029	26364	Mm.334648	NM_011925	ENSMUSG00000002885	Adgre5	AA409984|Cd97|TM7LN1	adhesion G protein-coupled receptor E5	protein-coding
mm_66826.1	chr7	48691825	48691829	-	1	NA	Intergenic	Intergenic	-48026	NM_207537	404238	Mm.377926	NM_207537	ENSMUSG00000070546	Mrgprb3	MrgB3	MAS-related GPR, member B3	protein-coding
mm_65196.1	chr7	19696807	19696824	-	1	NA	exon (NM_009696, exon 4 of 4)	exon (NM_009696, exon 4 of 4)	1583	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_34411.1	chr4	145245783	145245827	+	1	NA	intron (NM_011610, intron 1 of 9)	intron (NM_011610, intron 1 of 9)	1065	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_64500.1	chr7	143475167	143475192	+	1	NA	promoter-TSS (NM_001042760)	promoter-TSS (NM_001042760)	63	NM_001042760	18400	Mm.271740	NM_008767	ENSMUSG00000000154	Slc22a18	AW260131|BWR1A|BWSCR1A|HET|ITM|Impt1|Orctl2|Slc22a1l|TSSC5|p45-BWR1A	solute carrier family 22 (organic cation transporter), member 18	protein-coding
mm_169724.1	chr15	7975055	7975070	+	1	NA	intron (NM_001081402, intron 10 of 17)	intron (NM_001081402, intron 10 of 17)	124147	NM_001081402	545085	Mm.321312	NM_198413	ENSMUSG00000039828	Wdr70	4833422F06Rik	WD repeat domain 70	protein-coding
mm_166809.1	chr7	6952214	6952221	+	1	NA	intron (NM_021323, intron 5 of 7)	intron (NM_021323, intron 5 of 7)	24445	NR_036631	116811	Mm.381671	NR_036631	ENSMUSG00000108043	Zim3	1700128I23Rik	zinc finger, imprinted 3	ncRNA
mm_5599.1	chr1	39567015	39567048	-	1	NA	intron (NM_001033135, intron 1 of 6)	intron (NM_001033135, intron 1 of 6)	10316	NM_001033135	67702	Mm.28614	NM_001033135	ENSMUSG00000048234	Rnf149	1600023E10Rik|AV037261|C76763|Gm15832|Greul4|OTTMUSG00000026591	ring finger protein 149	protein-coding
mm_82171.1	chr9	123850287	123850302	+	1	NA	intron (NM_148925, intron 1 of 18)	intron (NM_148925, intron 1 of 18)	1367	NM_148925	17281	Mm.252941	NM_148925	ENSMUSG00000025241	Fyco1	2810409M01Rik|Mem2|RUFY3|ZFYVE7	FYVE and coiled-coil domain containing 1	protein-coding
mm_80868.1	chr9	98563697	98563698	+	1	NA	promoter-TSS (NM_015827)	promoter-TSS (NM_015827)	-34	NM_015827	50797	Mm.400464	NM_015827	ENSMUSG00000032458	Copb2	AI256832	coatomer protein complex, subunit beta 2 (beta prime)	protein-coding
mm_14814.1	chr2	146200652	146200660	+	1	NA	Intergenic	Intergenic	-21341	NM_016889	53626	Mm.379070	NM_016889	ENSMUSG00000068154	Insm1	IA-1	insulinoma-associated 1	protein-coding
mm_152470.1	chr19	10968761	10968772	-	1	NA	5' UTR (NM_023529, exon 2 of 9)	5' UTR (NM_023529, exon 2 of 9)	5904	NM_023529	69826	Mm.273404	NM_023529	ENSMUSG00000024731	Ms4a10	2010001N17Rik	membrane-spanning 4-domains, subfamily A, member 10	protein-coding
mm_117916.1	chr13	99432809	99432823	-	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-19990	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_520.1	chr1	37494598	37494604	+	1	NA	intron (NM_001290801, intron 3 of 14)	ID4_|SINE|ID	-5996	NR_024017	77633	Mm.483177	NR_024017	ENSMUSG00000103948	4930594C11Rik	-	G1 to S phase transition pseudogene	pseudo
mm_96218.1	chr11	62458617	62458629	+	1	NA	exon (NM_001039536, exon 1 of 7)	exon (NM_001039536, exon 1 of 7)	163	NM_001039536	327942	Mm.390358	NM_199026	ENSMUSG00000014245	Pigl	Gm737	phosphatidylinositol glycan anchor biosynthesis, class L	protein-coding
mm_85583.1	chr9	107298216	107298227	-	1	NA	intron (NM_001317354, intron 1 of 1)	intron (NM_001317354, intron 1 of 1)	1562	NM_009895	12700	Mm.4592	NM_009895	ENSMUSG00000032578	Cish	CIS-1|CIS1|Cis|F17|F23|SOCS	cytokine inducible SH2-containing protein	protein-coding
mm_39320.1	chr5	8068444	8068463	+	1	NA	3' UTR (NM_025618, exon 8 of 8)	3' UTR (NM_025618, exon 8 of 8)	11911	NM_001080974	109552	Mm.96211	NM_025618	ENSMUSG00000003161	Sri	2210417O06Rik|2900070H08Rik|Sor	sorcin	protein-coding
mm_2043.1	chr1	87281758	87281762	+	1	NA	intron (NM_028889, intron 1 of 3)	intron (NM_028889, intron 1 of 3)	17396	NM_028889	98363	Mm.247951	NM_028889	ENSMUSG00000026255	Efhd1	4931430I01Rik|AI452351|PP3051|mitocalcin	EF hand domain containing 1	protein-coding
mm_7029.1	chr1	87099420	87099428	-	1	NA	exon (NM_001081082, exon 9 of 11)	exon (NM_001081082, exon 9 of 11)	2182	NM_001081082	76768	Mm.58068	NM_001081082	ENSMUSG00000079440	Alpi	2010001C14Rik|Akp6|gIAP	alkaline phosphatase, intestinal	protein-coding
mm_165836.1	chr3	156642175	156642181	+	1	NA	intron (NM_177274, intron 1 of 6)	intron (NM_177274, intron 1 of 6)	80384	NM_001039094	320840	Mm.317293	NM_177274	ENSMUSG00000040037	Negr1	5330422G01Rik|KILON|Ntra	neuronal growth regulator 1	protein-coding
mm_129751.1	chr15	82338858	82338864	-	1	NA	promoter-TSS (NM_008669)	promoter-TSS (NM_008669)	-35	NM_008669	17939	Mm.20325	NM_008669	ENSMUSG00000022453	Naga	-	N-acetyl galactosaminidase, alpha	protein-coding
mm_99409.1	chr11	102268733	102268761	+	1	NA	promoter-TSS (NM_148953)	promoter-TSS (NM_148953)	-76	NM_148953	217217	Mm.216432	NM_148953	ENSMUSG00000034768	Asb16	-	ankyrin repeat and SOCS box-containing 16	protein-coding
mm_133062.1	chr16	58466279	58466281	+	1	NA	3' UTR (NM_028523, exon 16 of 16)	3' UTR (NM_028523, exon 16 of 16)	57032	NM_018784	54613	Mm.212742	NM_018784	ENSMUSG00000022747	St3gal6	1700023B24Rik|AI930218|AW552396|Siat10|St3galVI	ST3 beta-galactoside alpha-2,3-sialyltransferase 6	protein-coding
mm_97177.1	chr11	75532197	75532220	+	1	NA	promoter-TSS (NM_001199283)	promoter-TSS (NM_001199283)	96	NM_001199283	215113	Mm.11186	NM_173388	ENSMUSG00000038178	Slc43a2	7630402D21Rik|BC042513|Lat4	solute carrier family 43, member 2	protein-coding
mm_115654.1	chr13	12340511	12340545	-	1	NA	5' UTR (NM_033268, exon 1 of 21)	5' UTR (NM_033268, exon 1 of 21)	204	NM_033268	11472	Mm.37638	NM_033268	ENSMUSG00000052374	Actn2	1110008F24Rik	actinin alpha 2	protein-coding
mm_17203.1	chr2	25469124	25469193	-	1	NA	intron (NM_008963, intron 1 of 6)	intron (NM_008963, intron 1 of 6)	591	NM_008963	19215	Mm.1008	NM_008963	ENSMUSG00000015090	Ptgds	21kDa|L-PGDS|PGD2|PGDS|PGDS2|Ptgs3	prostaglandin D2 synthase (brain)	protein-coding
mm_75649.1	chr8	65129335	65129343	-	1	NA	non-coding (NR_033217, exon 1 of 3)	non-coding (NR_033217, exon 1 of 3)	198	NR_033217	407795	Mm.387876	NR_033217	ENSMUSG00000074300	BC030870	-	cDNA sequence BC030870	ncRNA
mm_139505.1	chr17	56304205	56304221	+	1	NA	promoter-TSS (NM_001111080)	promoter-TSS (NM_001111080)	-100	NM_001111078	18140	Mm.42196	NM_010931	ENSMUSG00000001228	Uhrf1	AL022808|ICBP90|Np95|RNF106	ubiquitin-like, containing PHD and RING finger domains, 1	protein-coding
mm_1734.1	chr1	75400071	75400163	+	1	NA	promoter-TSS (NM_001173477)	promoter-TSS (NM_001173477)	32	NM_001173477	11790	Mm.275397	NM_007463	ENSMUSG00000026207	Speg	AW125581|Apeg1|BPEG|D1Bwg1450e|SPEGalpha|SPEGbeta|mKIAA1297	SPEG complex locus	protein-coding
mm_31608.1	chr4	58645186	58645226	+	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	-91715	NM_010336	14745	Mm.4772	NM_010336	ENSMUSG00000038668	Lpar1	AI326300|Edg2|Gpcr26|Kdt2|lpA1|vzg-1	lysophosphatidic acid receptor 1	protein-coding
mm_132146.1	chr16	32099905	32099973	+	1	NA	promoter-TSS (NM_001111025)	promoter-TSS (NM_001111025)	137	NM_025892	66994	Mm.22990	NM_025892	ENSMUSG00000035790	Cep19	1500031L02Rik|AI428934|AL022620	centrosomal protein 19	protein-coding
mm_54506.1	chr6	35510766	35510789	-	1	NA	3' UTR (NM_008098, exon 4 of 4)	3' UTR (NM_008098, exon 4 of 4)	29111	NM_008098	14489	Mm.182746	NM_008098	ENSMUSG00000029840	Mtpn	5033418D15Rik|Gcdp|V1	myotrophin	protein-coding
mm_104086.1	chr11	86614283	86614286	-	1	NA	intron (NM_029478, intron 7 of 11)	intron (NM_029478, intron 7 of 11)	-30126	NR_029738	387140		NR_029738	ENSMUSG00000065455	Mir21a	Mir21|Mirn21|mmu-mir-21|mmu-mir-21a	microRNA 21a	ncRNA
mm_26548.1	chr3	146220956	146221009	+	1	NA	promoter-TSS (NM_022983)	promoter-TSS (NM_022983)	21	NM_022983	65086	Mm.155520	NM_022983	ENSMUSG00000036832	Lpar3	Edg7|lpA3	lysophosphatidic acid receptor 3	protein-coding
mm_126347.1	chr15	79906545	79906556	+	1	NA	exon (NM_001160415, exon 7 of 9)	exon (NM_001160415, exon 7 of 9)	11527	NM_001347041	80287	Mm.284059	NM_030255	ENSMUSG00000009585	Apobec3	Apobec|Arp3|BC003314|Cem15|Rfv3	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 3	protein-coding
mm_158668.1	chrX	157568984	157568991	-	1	NA	promoter-TSS (NM_001098723)	promoter-TSS (NM_001098723)	-2	NM_001098723	100073351	Mm.491276	NM_001098723	ENSMUSG00000046873	Yy2	-	Yy2 transcription factor	protein-coding
mm_133405.1	chr16	84835326	84835339	+	1	NA	promoter-TSS (NM_001302216)	promoter-TSS (NM_001302216)	208	NM_008065	14390	Mm.18974	NM_008065	ENSMUSG00000008976	Gabpa	GABPalpha	GA repeat binding protein, alpha	protein-coding
mm_153816.1	chr19	46148370	46148386	-	1	NA	promoter-TSS (NM_008852)	promoter-TSS (NM_008852)	-53	NM_008852	18742	Mm.6255	NM_008852	ENSMUSG00000025229	Pitx3	Ptx3|ak	paired-like homeodomain transcription factor 3	protein-coding
mm_44226.1	chr5	4875681	4875691	-	1	NA	intron (NM_011074, intron 14 of 14)	(A)n|Simple_repeat|Simple_repeat	-117470	NM_021457	14362	Mm.246003	NM_021457	ENSMUSG00000044674	Fzd1	AW227548|FZ-1|Fz1	frizzled class receptor 1	protein-coding
mm_82961.1	chr9	35611916	35611918	-	1	NA	promoter-TSS (NM_020264)	promoter-TSS (NM_020264)	-32	NM_020264	56872	Mm.390143	NM_020264	ENSMUSG00000032099	Pate4	9530004K16Rik|Pate-B|Svs7	prostate and testis expressed 4	protein-coding
mm_67553.1	chr7	81572242	81572261	-	1	NA	intron (NM_001004185, intron 1 of 9)	intron (NM_001004185, intron 1 of 9)	959	NM_001004185	434204	Mm.181641	NM_001004185	ENSMUSG00000045795	Whamm	BB081391|Whdc1|mKIAA1971	WAS protein homolog associated with actin, golgi membranes and microtubules	protein-coding
mm_20913.1	chr2	150600416	150600463	-	1	NA	intron (NM_027977, intron 1 of 8)	intron (NM_027977, intron 1 of 8)	8084	NM_027977	71881	Mm.26599	NM_027977	ENSMUSG00000033096	Apmap	2310001A20Rik|AI314817	adipocyte plasma membrane associated protein	protein-coding
mm_166321.1	chr5	111380209	111380231	+	1	NA	exon (NM_019640, exon 9 of 12)	exon (NM_019640, exon 9 of 12)	-37946	NM_001081235	433938	Mm.332576	NM_001081235	ENSMUSG00000070576	Mn1	AA003644|AA009236	meningioma 1	protein-coding
mm_89606.1	chr10	96002903	96002922	+	1	NA	exon (NM_001001932, exon 10 of 29)	exon (NM_001001932, exon 10 of 29)	62249	NM_001001932	216238	Mm.210035	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding
mm_124621.1	chr15	3280097	3280108	+	1	NA	TTS (NM_001166063)	TTS (NM_001166063)	9125	NM_009155	20363	Mm.392203	NM_009155	ENSMUSG00000064373	Selenop	AU018766|D15Ucla1|Se-P|Sepp1|selp	selenoprotein P	protein-coding
mm_139900.1	chr17	70853101	70853133	+	1	NA	intron (NM_001164074, intron 1 of 2)	CpG	415	NM_001164074	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_62257.1	chr7	99296522	99296523	+	1	NA	intron (NM_001048167, intron 1 of 2)	intron (NM_001048167, intron 1 of 2)	28176	NM_001043355	17760	Mm.154087	NM_010837	ENSMUSG00000055407	Map6	2810411E12Rik|Map-6|Mtap6|STOP	microtubule-associated protein 6	protein-coding
mm_18960.1	chr2	76796465	76796476	-	1	NA	exon (NM_011652, exon 200 of 313)	exon (NM_011652, exon 200 of 313)	121155	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_99973.1	chr11	113786160	113786204	+	1	NA	intron (NM_172800, intron 44 of 44)	intron (NM_172800, intron 44 of 44)	-34367	NM_001163346	56699	Mm.293378	NM_020006	ENSMUSG00000041598	Cdc42ep4	1500041M20Rik|Borg4|CEP4	CDC42 effector protein (Rho GTPase binding) 4	protein-coding
mm_74863.1	chr8	24903369	24903373	-	1	NA	intron (NM_153397, intron 9 of 21)	intron (NM_153397, intron 9 of 21)	45433	NM_001293693	353188	Mm.269223	NM_153397	ENSMUSG00000037437	Adam32	-	a disintegrin and metallopeptidase domain 32	protein-coding
mm_51756.1	chr6	87776130	87776149	+	1	NA	Intergenic	Intergenic	-1997	NM_018762	54368	Mm.12897	NM_018762	ENSMUSG00000030054	Gp9	Cd42|GPIX	glycoprotein 9 (platelet)	protein-coding
mm_84541.1	chr9	67299237	67299281	-	1	NA	intron (NM_001081242, intron 36 of 57)	intron (NM_001081242, intron 36 of 57)	-62533	NR_029576	387185		NR_029576	ENSMUSG00000076379	Mir190a	Mir190|Mirn190|mir-190|mir-190a|mmu-mir-190|mmu-mir-190a	microRNA 190a	ncRNA
mm_41901.1	chr5	105558860	105558891	+	1	NA	intron (NM_133897, intron 2 of 3)	ID_B1|SINE|B4	39404	NM_133897	100604	Mm.319847	NM_133897	ENSMUSG00000054720	Lrrc8c	AD158|AI326115|E430036I04Rik|fad158	leucine rich repeat containing 8 family, member C	protein-coding
mm_61114.1	chr7	54835615	54835623	+	1	NA	5' UTR (NM_178705, exon 1 of 12)	5' UTR (NM_178705, exon 1 of 12)	374	NM_178705	233271	Mm.387344	NM_178705	ENSMUSG00000063297	Luzp2	9330154K17Rik|D130073E01	leucine zipper protein 2	protein-coding
mm_63435.1	chr7	127479049	127479091	+	1	NA	Intergenic	CpG	-6151	NM_010183	14123	Mm.323505	NM_010183	ENSMUSG00000042423	Fbrs	Fbs|Fbs1	fibrosin	protein-coding
mm_7266.1	chr1	95667491	95667505	-	1	NA	promoter-TSS (NM_001159745)	promoter-TSS (NM_001159745)	96	NM_009183	20452	Mm.306228	NM_009183	ENSMUSG00000040710	St8sia4	PST|PST-1|SIAT8-D|ST8SiaIV|Siat8d	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4	protein-coding
mm_39660.1	chr5	25100701	25100759	+	1	NA	promoter-TSS (NM_145401)	promoter-TSS (NM_145401)	-88	NM_145401	108099	Mm.33649	NM_145401	ENSMUSG00000028944	Prkag2	2410051C13Rik|AAKG|AAKG2|AI854673|H91620p|WPWS	protein kinase, AMP-activated, gamma 2 non-catalytic subunit	protein-coding
mm_155697.1	chrX	94481886	94481886	+	1	NA	Intergenic	Intergenic	39154	NR_045323	100503393	Mm.402891	NR_045323	ENSMUSG00000084904	Gm14827	OTTMUSG00000018126	predicted gene 14827	ncRNA
mm_2516.1	chr1	106317215	106317243	+	1	NA	intron (NM_133821, intron 3 of 16)	intron (NM_133821, intron 3 of 16)	145360	NM_133821	98432	Mm.24115	NM_133821	ENSMUSG00000044340	Phlpp1	AI836256|Phlpp|Plekhe1|SCOP|mKIAA0606	PH domain and leucine rich repeat protein phosphatase 1	protein-coding
mm_102096.1	chr11	52306712	52306723	-	1	NA	Intergenic	Intergenic	-23703	NM_001313981	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_21425.1	chr2	158228699	158228702	-	1	NA	intron (NM_001131021, intron 1 of 15)	intron (NM_001131021, intron 1 of 15)	524	NM_001131021	228846	Mm.187574	NM_177657	ENSMUSG00000037813	D630003M21Rik	-	RIKEN cDNA D630003M21 gene	protein-coding
mm_74033.1	chr8	121806419	121806432	+	1	NA	intron (NM_145605, intron 6 of 11)	intron (NM_145605, intron 6 of 11)	23144	NM_145605	234825	Mm.209329	NM_145605	ENSMUSG00000040263	Klhdc4	AA408426|AV352552|BC012312|G430025P05Rik	kelch domain containing 4	protein-coding
mm_164929.1	chr18	81087519	81087524	+	1	NA	Intergenic	MTC|LTR|ERVL-MaLR	-100943	NM_178280	20689	Mm.215917	NM_178280	ENSMUSG00000024565	Sall3	B130022O04Rik|Msal|Msal-1|Sal|Salt|Spalt	sal-like 3 (Drosophila)	protein-coding
mm_92312.1	chr10	75303335	75303374	-	1	NA	intron (NM_153406, intron 13 of 15)	intron (NM_153406, intron 13 of 15)	-13523	NM_009630	11540	Mm.333734	NM_009630	ENSMUSG00000020178	Adora2a	A2AAR|A2aR|AA2AR	adenosine A2a receptor	protein-coding
mm_118051.1	chr13	101711809	101711810	-	1	NA	intron (NM_001077495, intron 2 of 15)	intron (NM_001077495, intron 2 of 15)	-19179	NM_001024955	18708	Mm.259333	NM_001024955	ENSMUSG00000041417	Pik3r1	PI3K|p50alpha|p55alpha|p85alpha	phosphatidylinositol 3-kinase, regulatory subunit, polypeptide 1 (p85 alpha)	protein-coding
mm_30700.1	chr4	11758175	11758220	+	1	NA	promoter-TSS (NM_019753)	promoter-TSS (NM_019753)	40	NM_019753	12557	Mm.33402	NM_019753	ENSMUSG00000028217	Cdh17	HPT-1|HPT-1/LI	cadherin 17	protein-coding
mm_101911.1	chr11	49712623	49712631	-	1	NA	promoter-TSS (NM_212484)	promoter-TSS (NM_212484)	95	NM_212484	104625	Mm.247113	NM_212484	ENSMUSG00000020362	Cnot6	CCR4	CCR4-NOT transcription complex, subunit 6	protein-coding
mm_20070.1	chr2	120404689	120404703	-	1	NA	promoter-TSS (NM_173734)	promoter-TSS (NM_173734)	-580	NM_001110496	211499	Mm.260712	NM_173734	ENSMUSG00000033808	Tmem87a	A930025J12Rik	transmembrane protein 87A	protein-coding
mm_95174.1	chr11	40755446	40755466	+	1	NA	promoter-TSS (NM_009831)	promoter-TSS (NM_009831)	-170	NM_009831	12450	Mm.2103	NM_009831	ENSMUSG00000020326	Ccng1	AI314029	cyclin G1	protein-coding
mm_142320.1	chr17	43158280	43158306	-	1	NA	promoter-TSS (NR_045155)	promoter-TSS (NR_045155)	-2	NR_045153	545207	Mm.329050	NR_045153		E130008D07Rik	-	RIKEN cDNA E130008D07 gene	ncRNA
mm_54307.1	chr6	29609795	29609805	-	1	NA	promoter-TSS (NM_177296)	promoter-TSS (NM_177296)	-193	NM_177296	320938	Mm.276381	NM_177296	ENSMUSG00000012535	Tnpo3	5730544L10Rik|C430013M08Rik|C81142|D6Ertd313e|Trn-SR|mKIAA4133	transportin 3	protein-coding
mm_5203.1	chr1	13374433	13374475	-	1	NA	promoter-TSS (NM_008678)	promoter-TSS (NM_008678)	-371	NM_008678	17978	Mm.2537	NM_008678	ENSMUSG00000005886	Ncoa2	D1Ertd433e|GRIP-1|Grip1|KAT13C|NCoA-2|SRC-2|TIF2|bHLHe75	nuclear receptor coactivator 2	protein-coding
mm_148846.1	chr19	6376013	6376017	+	1	NA	non-coding (NR_122118, exon 12 of 12)	non-coding (NR_122118, exon 12 of 12)	-8393	NM_011224	19309	Mm.27806	NM_011224	ENSMUSG00000032648	Pygm	AI115133|PG	muscle glycogen phosphorylase	protein-coding
mm_56277.1	chr6	91116786	91116832	-	1	NA	promoter-TSS (NM_018815)	promoter-TSS (NM_018815)	17	NM_018815	54563	Mm.28162	NM_018815	ENSMUSG00000030091	Nup210	9830001L10|AI836801|Pom210|gp190|gp210	nucleoporin 210	protein-coding
mm_40558.1	chr5	60744684	60744691	+	1	NA	Intergenic	Intergenic	-758685	NR_040682	71057	Mm.50817	NR_040682	ENSMUSG00000106013	4933402J10Rik	-	RIKEN cDNA 4933402J10 gene	ncRNA
mm_33745.1	chr4	134243755	134243768	+	1	NA	promoter-TSS (NR_040436)	promoter-TSS (NR_040436)	-2	NR_040435	77490	Mm.426238	NR_040435	ENSMUSG00000086322	E130218I03Rik	E130106C14Rik	RIKEN cDNA E130218I03 gene	ncRNA
mm_44041.1	chr5	147546517	147546535	+	1	NA	3' UTR (NM_028291, exon 19 of 19)	3' UTR (NM_028291, exon 19 of 19)	115946	NM_028291	72587	Mm.320469	NM_028291	ENSMUSG00000029647	Pan3	2700050F09Rik|A430027N15Rik|AU014670	PAN3 poly(A) specific ribonuclease subunit	protein-coding
mm_153219.1	chr19	34747484	34747494	-	1	NA	promoter-TSS (NM_172838)	promoter-TSS (NM_172838)	-378	NM_172838	240638	Mm.74636	NM_172838	ENSMUSG00000009378	Slc16a12	3230401A21|AW210596	solute carrier family 16 (monocarboxylic acid transporters), member 12	protein-coding
mm_110874.1	chr12	73880474	73880477	-	1	NA	Intergenic	Intergenic	-20849	NM_001313920	15251	Mm.3879	NM_010431	ENSMUSG00000021109	Hif1a	AA959795|HIF-1-alpha|HIF1-alpha|HIF1alpha|MOP1|bHLHe78	hypoxia inducible factor 1, alpha subunit	protein-coding
mm_17362.1	chr2	26668772	26668780	-	1	NA	intron (NM_010695, intron 4 of 6)	intron (NM_010695, intron 4 of 6)	2506	NM_010695	16821	Mm.123925	NM_010695	ENSMUSG00000026919	Lcn4	A630045M08Rik|Vnsp2	lipocalin 4	protein-coding
mm_149997.1	chr19	29271520	29271525	+	1	NA	intron (NM_001048177, intron 3 of 23)	intron (NM_001048177, intron 3 of 23)	19719	NM_008413	16452	Mm.275839	NM_008413	ENSMUSG00000024789	Jak2	Fd17	Janus kinase 2	protein-coding
mm_148652.1	chr19	5493757	5493782	+	1	NA	3' UTR (NM_007687, exon 4 of 4)	3' UTR (NM_007687, exon 4 of 4)	3314	NM_007687	12631	Mm.329655	NM_007687	ENSMUSG00000056201	Cfl1	AA959946|Cof	cofilin 1, non-muscle	protein-coding
mm_105326.1	chr11	102895971	102895982	-	1	NA	intron (NM_001131020, intron 1 of 7)	intron (NM_001131020, intron 1 of 7)	1224	NM_001131020	14580	Mm.1239	NM_010277	ENSMUSG00000020932	Gfap	AI836096	glial fibrillary acidic protein	protein-coding
mm_22959.1	chr3	32510539	32510561	+	1	NA	promoter-TSS (NM_144519)	promoter-TSS (NM_144519)	0	NM_001161818	67778	Mm.285620	NM_144519	ENSMUSG00000027667	Zfp639	6230400O18Rik|ANC-2H01|ZASC1|Znf639	zinc finger protein 639	protein-coding
mm_52399.1	chr6	113307868	113307885	+	1	NA	intron (NM_001282128, intron 1 of 13)	intron (NM_001282128, intron 1 of 13)	739	NM_001282126	78783	Mm.356059	NM_030178	ENSMUSG00000001632	Brpf1	4833438B11Rik|4930540D11Rik|Brpf2	bromodomain and PHD finger containing, 1	protein-coding
mm_33344.1	chr4	129308414	129308418	+	1	NA	3' UTR (NM_009030, exon 12 of 12)	3' UTR (NM_009030, exon 12 of 12)	20795	NM_023485	68828	Mm.132243	NM_023485	ENSMUSG00000001333	Sync	1110057H03Rik|SNIP4	syncoilin	protein-coding
mm_20260.1	chr2	126607605	126607612	-	1	NA	intron (NM_008230, intron 2 of 11)	intron (NM_008230, intron 2 of 11)	11070	NM_008230	15186	Mm.18603	NM_008230	ENSMUSG00000027360	Hdc	AW108189|Hdc-a|Hdc-c|Hdc-e|Hdc-s	histidine decarboxylase	protein-coding
mm_55449.1	chr6	67271967	67271983	-	1	NA	exon (NM_025814, exon 3 of 8)	exon (NM_025814, exon 3 of 8)	4996	NM_025814	66870	Mm.240490	NM_025814	ENSMUSG00000036371	Serbp1	1200009K13Rik|9330147J08Rik|AL022786|Pairbp1	serpine1 mRNA binding protein 1	protein-coding
mm_25797.1	chr3	127633135	127633140	+	1	NA	promoter-TSS (NM_009718)	promoter-TSS (NM_009718)	-8	NM_009718	11924	Mm.42017	NM_009718	ENSMUSG00000027967	Neurog2	Atoh4|Math4A|bHLHa8|ngn-2|ngn2	neurogenin 2	protein-coding
mm_147145.1	chr18	36559888	36559912	-	1	NA	promoter-TSS (NM_175375)	promoter-TSS (NM_175375)	-703	NM_175375	108857	Mm.482287	NM_175375	ENSMUSG00000024483	Ankhd1	1110004O12Rik|4933432B13Rik|9130019P20Rik|A530027J04Rik|A630021B20Rik|AA571404|Mask|mFLJ00246|mKIAA1085	ankyrin repeat and KH domain containing 1	protein-coding
mm_171563.1	chr4	147234349	147234352	+	1	NA	intron (NM_001039209, intron 1 of 2)	intron (NM_001039209, intron 1 of 2)	58484	NM_001039209	195531	Mm.270762	NM_001039209	ENSMUSG00000078496	Zfp982	Gm13152|OTTMUSG00000010671	zinc finger protein 982	protein-coding
mm_129514.1	chr15	79062720	79062756	-	1	NA	exon (NM_144849, exon 1 of 8)	exon (NM_144849, exon 1 of 8)	121	NM_144849	223690	Mm.24262	NM_144849	ENSMUSG00000033055	Ankrd54	C730048E16Rik|EST1068184|EST475269|Liar	ankyrin repeat domain 54	protein-coding
mm_120638.1	chr14	70467870	70467883	+	1	NA	3' UTR (NM_145981, exon 5 of 5)	3' UTR (NM_145981, exon 5 of 5)	10359	NM_145981	105653	Mm.192598	NM_145981	ENSMUSG00000003469	Phyhip	AW049870|C630010D02Rik|Lnap1ip|PAHX-AP#1|PAHX-AP1	phytanoyl-CoA hydroxylase interacting protein	protein-coding
mm_69024.1	chr7	126792447	126792455	-	1	NA	promoter-TSS (NM_019674)	promoter-TSS (NM_019674)	20	NM_019674	56420	Mm.41998	NM_019674	ENSMUSG00000030697	Ppp4c	1110002D08Rik|AU016079|Ppx	protein phosphatase 4, catalytic subunit	protein-coding
mm_125024.1	chr15	25726628	25726630	+	1	NA	intron (NM_019472, intron 9 of 40)	intron (NM_019472, intron 9 of 40)	104079	NM_019472	17909	Mm.60590	NM_019472	ENSMUSG00000022272	Myo10	AW048724|D15Ertd600e|mKIAA0799|myosin-X	myosin X	protein-coding
mm_146660.1	chr18	12061422	12061432	-	1	NA	intron (NM_178801, intron 10 of 14)	ID4|SINE|ID	60110	NR_110356	338363	Mm.271567	NM_178801	ENSMUSG00000049411	Tmem241	6030446N20Rik	transmembrane protein 241	protein-coding
mm_92176.1	chr10	67648321	67648324	-	1	NA	Intergenic	Intergenic	-99367	NM_001005419	211488	Mm.297250	NM_001005419	ENSMUSG00000057134	Ado	Gm237	2-aminoethanethiol (cysteamine) dioxygenase	protein-coding
mm_15725.1	chr2	164084178	164084202	+	1	NA	intron (NM_021420, intron 3 of 10)	intron (NM_021420, intron 3 of 10)	10012	NM_021420	58231	Mm.234472	NM_021420	ENSMUSG00000018209	Stk4	AI447339|AU020804|Kas-2|Mst1|Ysk3	serine/threonine kinase 4	protein-coding
mm_69843.1	chr7	141328182	141328209	-	1	NA	promoter-TSS (NM_001282076)	promoter-TSS (NM_001282076)	65	NM_027797	71448	Mm.248960	NM_027797	ENSMUSG00000025505	Tmem80	5530601I19Rik	transmembrane protein 80	protein-coding
mm_11774.1	chr2	38931932	38931948	+	1	NA	promoter-TSS (NM_172854)	promoter-TSS (NM_172854)	-40	NM_172854	241327	Mm.103491	NM_172854	ENSMUSG00000046618	Olfml2a	4932431K08Rik|mFLJ00237	olfactomedin-like 2A	protein-coding
mm_3308.1	chr1	137898678	137898701	+	1	NA	Intergenic	Intergenic	-67766	NR_029795	735252		NR_029795	ENSMUSG00000065565	Mir181a-1	Mirn181a-1|Mirn213|miR-213|mir-181a-1|mmu-mir-213	microRNA 181a-1	ncRNA
mm_63020.1	chr7	121034521	121034529	+	1	NA	promoter-TSS (NM_021554)	promoter-TSS (NM_021554)	80	NM_021554	59052	Mm.29122	NM_021554	ENSMUSG00000030876	Mettl9	0610012D09Rik|AA517660|Drev|MNCb-5680	methyltransferase like 9	protein-coding
mm_17840.1	chr2	34371754	34371772	-	1	NA	exon (NM_001290576, exon 1 of 8)	exon (NM_001290576, exon 1 of 8)	282	NM_001290576	18516	Mm.239941	NM_016768	ENSMUSG00000038718	Pbx3	-	pre B cell leukemia homeobox 3	protein-coding
mm_101518.1	chr11	32534117	32534123	-	1	NA	intron (NM_009288, intron 1 of 18)	intron (NM_009288, intron 1 of 18)	854	NM_009288	20868	Mm.8235	NM_009288	ENSMUSG00000020272	Stk10	Gek1|Lok|mKIAA4026	serine/threonine kinase 10	protein-coding
mm_126579.1	chr15	82275198	82275281	+	1	NA	intron (NM_011889, intron 1 of 9)	G-rich|Low_complexity|Low_complexity	304	NM_011889	24050	Mm.309707	NM_011889	ENSMUSG00000022456	Sept3	3110018K01Rik|AV154067|B530002E20Rik|Sep3	septin 3	protein-coding
mm_61297.1	chr7	67679054	67679070	+	1	NA	exon (NM_025905, exon 6 of 12)	exon (NM_025905, exon 6 of 12)	31652	NM_025905	67009	Mm.249356	NM_025905	ENSMUSG00000030555	Ttc23	1600012K10Rik	tetratricopeptide repeat domain 23	protein-coding
mm_54623.1	chr6	38637174	38637214	-	1	NA	promoter-TSS (NM_001033171)	promoter-TSS (NM_001033171)	45	NM_001033171	74253	Mm.121859	NM_001033171	ENSMUSG00000071537	Klrg2	2310020F24Rik	killer cell lectin-like receptor subfamily G, member 2	protein-coding
mm_70393.1	chr8	11009178	11009197	+	1	NA	promoter-TSS (NM_001081212)	promoter-TSS (NM_001081212)	-757	NM_001081212	384783	Mm.407207	NM_001081212	ENSMUSG00000038894	Irs2	Irs-2	insulin receptor substrate 2	protein-coding
mm_64850.1	chr7	13034124	13034146	-	1	NA	TTS (NM_145578)	TTS (NM_145578)	642	NM_026885	68953	Mm.295670	NM_026885	ENSMUSG00000033916	Chmp2a	1500016L11Rik	charged multivesicular body protein 2A	protein-coding
mm_52778.1	chr6	121245930	121245946	+	1	NA	promoter-TSS (NM_011909)	promoter-TSS (NM_011909)	32	NM_011909	24110	Mm.326911	NM_011909	ENSMUSG00000030107	Usp18	1110058H21Rik|AW047653|UBP43|Ubp15	ubiquitin specific peptidase 18	protein-coding
mm_53881.1	chr6	3340768	3340803	-	1	NA	Intergenic	IAPEY4_I-int|LTR|ERVK	52266	NR_036696	667335	Mm.380219	NR_036696	ENSMUSG00000106779	Gm8579	EG667335	spermatogenesis associated glutamate (E)-rich protein 4a pseudogene	pseudo
mm_95701.1	chr11	54437769	54437773	+	1	NA	promoter-TSS (NM_173753)	promoter-TSS (NM_173753)	-408	NM_173753	216742	Mm.34087	NM_173753	ENSMUSG00000035992	Fnip1	A730024A03Rik|AI838773|AW557298	folliculin interacting protein 1	protein-coding
mm_72979.1	chr8	92901439	92901447	+	1	NA	promoter-TSS (NM_027112)	promoter-TSS (NM_027112)	48	NM_027112	69543	Mm.440514	NM_027112	ENSMUSG00000078144	Capns2	2310005G05Rik|30K-2	calpain, small subunit 2	protein-coding
mm_160189.1	chr7	55806256	55806256	+	1	NA	intron (NM_146190, intron 9 of 22)	intron (NM_146190, intron 9 of 22)	12108	NM_146190	233276	Mm.284306	NM_146190	ENSMUSG00000033790	Tubgcp5	B130010C12Rik|GCP5|mKIAA1899	tubulin, gamma complex associated protein 5	protein-coding
mm_32961.1	chr4	119814376	119814388	+	1	NA	promoter-TSS (NM_010657)	promoter-TSS (NM_010657)	-296	NM_010657	16656	Mm.302758	NM_010657	ENSMUSG00000028634	Hivep3	2900056N03Rik|A130075N07|AI848000|E030045D18Rik|KBP-1|KBP1|Krc|Rc|Schnurri-3|Shn3|Zas3	human immunodeficiency virus type I enhancer binding protein 3	protein-coding
mm_81304.1	chr9	108339929	108339987	+	1	NA	exon (NM_008160, exon 2 of 2)	exon (NM_008160, exon 2 of 2)	878	NM_001329528	14775	Mm.1090	NM_008160	ENSMUSG00000063856	Gpx1	AI195024|AL033363|CGPx|GPx-1|GSHPx-1|Gpx	glutathione peroxidase 1	protein-coding
mm_34660.1	chr4	150866808	150866832	+	1	NA	exon (NM_133753, exon 4 of 4)	exon (NM_133753, exon 4 of 4)	11729	NM_133753	74155	Mm.318841	NM_133753	ENSMUSG00000028967	Errfi1	1300002F13Rik|AI788755|Mig-6|Mig6|RALT	ERBB receptor feedback inhibitor 1	protein-coding
mm_160311.1	chr7	141214098	141214098	-	1	NA	promoter-TSS (NM_028050)	promoter-TSS (NM_028050)	-18	NM_028050	72000	Mm.334314	NM_028050	ENSMUSG00000025500	Lmntd2	1600016N20Rik	lamin tail domain containing 2	protein-coding
mm_122953.1	chr14	54967982	54967999	-	1	NA	promoter-TSS (NR_033497)	promoter-TSS (NR_033497)	-797	NR_033497	791403	Mm.319176	NR_033497	ENSMUSG00000097652	Mhrt	D830015G02Rik|ENSMUSG00000053118|Myheart	myosin heavy chain associated RNA transcript	ncRNA
mm_68955.1	chr7	126564762	126564779	-	1	NA	intron (NM_146200, intron 2 of 20)	intron (NM_146200, intron 2 of 20)	1596	NM_146200	56347	Mm.22776	NM_146200	ENSMUSG00000030738	Eif3c	110kDa|3230401O13Rik|Eif3s8|NIPIL(A3)|NipilA3|Xs|Xsl	eukaryotic translation initiation factor 3, subunit C	protein-coding
mm_160633.1	chr9	107607062	107607062	-	1	NA	promoter-TSS (NM_001291538)	promoter-TSS (NM_001291538)	30	NM_001291538	20347	Mm.4083	NM_009153	ENSMUSG00000057969	Sema3b	SemA|Semaa|sema5|semaV	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B	protein-coding
mm_147649.1	chr18	60501632	60501646	-	1	NA	5' UTR (NM_134133, exon 1 of 2)	5' UTR (NM_134133, exon 1 of 2)	344	NM_134133	106878	Mm.273197	NM_134133	ENSMUSG00000038059	Smim3	2010002N04Rik|AI195350|AW561905|Nid67|cI-41	small integral membrane protein 3	protein-coding
mm_44619.1	chr5	25532553	25532586	-	1	NA	Intergenic	Intergenic	2551	NR_027388	73571	Mm.105263	NR_027388	ENSMUSG00000101856	1700096K18Rik	-	RIKEN cDNA 1700096K18 gene	ncRNA
mm_82235.1	chr9	3038045	3038070	-	1	NA	TTS (NR_039546)	TTS (NR_039546)	686	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_139531.1	chr17	56673357	56673392	+	1	NA	non-coding (NR_045519, exon 1 of 17)	non-coding (NR_045519, exon 1 of 17)	149	NM_027933	71810	Mm.29608	NM_027933	ENSMUSG00000002372	Ranbp3	2610024N24Rik|AA408221	RAN binding protein 3	protein-coding
mm_48199.1	chr5	137531962	137531984	-	1	NA	intron (NM_010312, intron 1 of 9)	CpG	1256	NM_010312	14693	Mm.30141	NM_010312	ENSMUSG00000029713	Gnb2	Gnb-2	guanine nucleotide binding protein (G protein), beta 2	protein-coding
mm_137442.1	chr17	26509727	26509741	+	1	NA	Intergenic	Intergenic	-1262	NM_013642	19252	Mm.239041	NM_013642	ENSMUSG00000024190	Dusp1	3CH134|MKP1|Ptpn16|U19515|erp|mkp-1	dual specificity phosphatase 1	protein-coding
mm_158291.1	chrX	112698415	112698485	-	1	NA	exon (NM_181579, exon 2 of 17)	exon (NM_181579, exon 2 of 17)	201	NM_181579	69693	Mm.34964	NM_181579	ENSMUSG00000034607	Pof1b	2310066B14Rik	premature ovarian failure 1B	protein-coding
mm_136324.1	chr16	92321407	92321422	-	1	NA	promoter-TSS (NM_029252)	promoter-TSS (NM_029252)	27	NM_029252	75328	Mm.72970	NM_029252	ENSMUSG00000051728	4930563D23Rik	-	RIKEN cDNA 4930563D23 gene	protein-coding
mm_85099.1	chr9	94533825	94533833	-	1	NA	intron (NM_001033145, intron 1 of 2)	intron (NM_001033145, intron 1 of 2)	4252	NM_001033145	68861	Mm.258746	NM_001033145	ENSMUSG00000045414	1190002N15Rik	GoPro49|HASF	RIKEN cDNA 1190002N15 gene	protein-coding
mm_101037.1	chr11	8601132	8601144	-	1	NA	intron (NM_001083587, intron 2 of 30)	intron (NM_001083587, intron 2 of 30)	63397	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_63129.1	chr7	123001657	123001678	+	1	NA	exon (NM_011247, exon 18 of 18)	exon (NM_011247, exon 18 of 18)	31103	NM_175023	19647	Mm.4480	NM_011247	ENSMUSG00000030779	Rbbp6	4933422O15Rik|AI316869|BB233631|C030034J04Rik|C77662|P2P-R|PACT	retinoblastoma binding protein 6	protein-coding
mm_50688.1	chr6	51584627	51584637	+	1	NA	intron (NM_028035, intron 5 of 6)	intron (NM_028035, intron 5 of 6)	40109	NM_001127348	71982	Mm.294166	NM_028035	ENSMUSG00000038301	Snx10	2410004M09Rik	sorting nexin 10	protein-coding
mm_107895.1	chr12	70650014	70650031	+	1	NA	intron (NR_037248, intron 4 of 4)	intron (NR_037248, intron 4 of 4)	-175492	NM_028127	319710	Mm.2962	NM_028127	ENSMUSG00000048285	Frmd6	2610019M19Rik|4930488L10Rik|AW212977|Willin	FERM domain containing 6	protein-coding
mm_12660.1	chr2	75634012	75634042	+	1	NA	Intergenic	RMER20B|LTR|ERVK	-25232	NM_146130	229279	Mm.316306	NM_053263	ENSMUSG00000059005	Hnrnpa3	2410013L13Rik|2610209F03Rik|2610510D13Rik|Hnrpa3	heterogeneous nuclear ribonucleoprotein A3	protein-coding
mm_121359.1	chr14	117068521	117068528	+	1	NA	intron (NM_001079844, intron 1 of 9)	intron (NM_001079844, intron 1 of 9)	143227	NM_011821	23888	Mm.440025	NM_011821	ENSMUSG00000058571	Gpc6	-	glypican 6	protein-coding
mm_52489.1	chr6	114648812	114648889	+	1	NA	intron (NM_001253718, intron 2 of 19)	intron (NM_001253718, intron 2 of 19)	5753	NM_001253717	74244	Mm.275332	NM_028835	ENSMUSG00000030314	Atg7	1810013K23Rik|Agp7|Apg7l|Atg7l|Gm21553	autophagy related 7	protein-coding
mm_172329.1	chr7	108026448	108026465	-	1	NA	Intergenic	L1Md_T|LINE|L1	5885	NM_146734	258729	Mm.223162	NM_146734	ENSMUSG00000094426	Olfr478	MOR204-13	olfactory receptor 478	protein-coding
mm_18538.1	chr2	64393854	64393862	-	1	NA	Intergenic	Intergenic	-295820	NM_001267847	60344	Mm.130769	NM_021716	ENSMUSG00000075324	Fign	fi|fidget	fidgetin	protein-coding
mm_51553.1	chr6	83326072	83326085	+	1	NA	promoter-TSS (NM_145571)	promoter-TSS (NM_145571)	39	NM_145571	232157	Mm.29500	NM_145571	ENSMUSG00000043131	Mob1a	4022402H07Rik|MOB1|MOB4B|Mobk1b|Mobkl1b	MOB kinase activator 1A	protein-coding
mm_55177.1	chr6	52012477	52012551	-	1	NA	promoter-TSS (NM_018773)	promoter-TSS (NM_018773)	35	NM_018773	54353	Mm.221479	NM_018773	ENSMUSG00000059182	Skap2	2610021A10Rik|AA960083|BB137539|RA70|SKAP-HOM|Saps|Scap2|mSKAP55R	src family associated phosphoprotein 2	protein-coding
mm_12484.1	chr2	71529923	71529936	+	1	NA	TTS (NR_002854)	TTS (NR_002854)	484	NM_010053	13390	Mm.475101	NM_010053	ENSMUSG00000041911	Dlx1	Dlx|Dlx-1	distal-less homeobox 1	protein-coding
mm_129471.1	chr15	78673231	78673259	-	1	NA	exon (NM_183141, exon 2 of 2)	exon (NM_183141, exon 2 of 2)	44868	NM_183141	207393	Mm.323188	NM_183141	ENSMUSG00000043460	Elfn2	6330514E13|AW048948|BC094219|Lrrc62|Ppp1r29	leucine rich repeat and fibronectin type III, extracellular 2	protein-coding
mm_98406.1	chr11	94329643	94329650	+	1	NA	intron (NM_146024, intron 1 of 4)	intron (NM_146024, intron 1 of 4)	1645	NM_146024	71452	Mm.141054	NM_027799	ENSMUSG00000020864	Ankrd40	1110011C06Rik|5530600A18Rik|Gcap15	ankyrin repeat domain 40	protein-coding
mm_6172.1	chr1	65080277	65080287	-	1	NA	TTS (NM_144761)	TTS (NM_144761)	2008	NM_144761	12965	Mm.440053	NM_144761	ENSMUSG00000073658	Crygb	Cryg-3|DGcry-3|Nop	crystallin, gamma B	protein-coding
mm_140574.1	chr17	9669713	9669721	-	1	NA	promoter-TSS (NM_001163836)	promoter-TSS (NM_001163836)	-13	NM_001163836	67543	Mm.26987	NM_026226	ENSMUSG00000046173	Pabpc6	4932702K14Rik|AI428050|Pabpc3	poly(A) binding protein, cytoplasmic 6	protein-coding
mm_110403.1	chr12	44269026	44269053	-	1	NA	promoter-TSS (NM_026164)	promoter-TSS (NM_026164)	-115	NM_026164	67452	Mm.54126	NM_026164	ENSMUSG00000036257	Pnpla8	1200006O19Rik|AI467579|Ipla2(gamma)	patatin-like phospholipase domain containing 8	protein-coding
mm_80189.1	chr9	72394114	72394127	+	1	NA	Intergenic	Intergenic	-44409	NM_008613	17427	Mm.387671	NM_008613	ENSMUSG00000032221	Mns1	AW546487	meiosis-specific nuclear structural protein 1	protein-coding
mm_170033.1	chr17	22364202	22364215	+	1	NA	intron (NM_001347330, intron 1 of 2)	RLTR9D|LTR|ERVK	2755	NM_145484	224598	Mm.390945	NM_145484	ENSMUSG00000044501	Zfp758	BC021442	zinc finger protein 758	protein-coding
mm_118835.1	chr14	25607834	25607846	+	1	NA	intron (NM_001310666, intron 6 of 23)	CpG	4327	NM_001309430	100188919	Mm.473810	NM_001309430		Israa	-	immune system released activating agent	protein-coding
mm_140899.1	chr17	24097115	24097124	-	1	NA	intron (NM_001080773, intron 7 of 13)	intron (NM_001080773, intron 7 of 13)	-23634	NM_027008	69259	Mm.28171	NM_027008	ENSMUSG00000016946	Kctd5	2610030N08Rik|mKIAA0176	potassium channel tetramerisation domain containing 5	protein-coding
mm_156355.1	chrX	139335492	139335494	+	1	NA	intron (NM_011635, intron 1 of 2)	intron (NM_011635, intron 1 of 2)	1810	NM_011635	22037	Mm.1297	NM_011635	ENSMUSG00000051257	Trap1a	Tra-P1A	tumor rejection antigen P1A	protein-coding
mm_128261.1	chr15	36771395	36771417	-	1	NA	3' UTR (NM_001253807, exon 5 of 5)	3' UTR (NM_001253807, exon 5 of 5)	19526	NM_001253807	22631	Mm.3360	NM_011740	ENSMUSG00000022285	Ywhaz	1110013I11Rik|14-3-3zeta|AI596267|AL022924|AU020854	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide	protein-coding
mm_132779.1	chr16	44787285	44787311	+	1	NA	intron (NM_021325, intron 1 of 6)	intron (NM_021325, intron 1 of 6)	21562	NM_021325	57781	Mm.416152	NM_021325	ENSMUSG00000022667	Cd200r1	CD200R|Mox2r|OX2R	CD200 receptor 1	protein-coding
mm_39471.1	chr5	19907712	19907762	+	1	NA	5' UTR (NM_001170745, exon 1 of 21)	5' UTR (NM_001170745, exon 1 of 21)	219	NM_015823	50791	Mm.332231	NM_015823	ENSMUSG00000040003	Magi2	AIP-1|Acvri1|Acvrinp1|Acvrip1|Magi-2|S-SCAM|mKIAA0705	membrane associated guanylate kinase, WW and PDZ domain containing 2	protein-coding
mm_40898.1	chr5	75155893	75155919	+	1	NA	promoter-TSS (NM_001083316)	promoter-TSS (NM_001083316)	-260	NM_001083316	18595	Mm.221403	NM_011058	ENSMUSG00000029231	Pdgfra	AI115593|CD140a|Pdgfr-2	platelet derived growth factor receptor, alpha polypeptide	protein-coding
mm_4024.1	chr1	165765847	165765851	+	1	NA	intron (NM_011804, intron 1 of 3)	MIRb|SINE|MIR	2069	NM_011804	433375	Mm.294885	NM_011804	ENSMUSG00000040713	Creg1	AA755314|Creg	cellular repressor of E1A-stimulated genes 1	protein-coding
mm_96654.1	chr11	69368879	69368901	+	1	NA	intron (NM_146019, intron 1 of 39)	CpG	536	NM_146019	216848	Mm.178246	NM_146019	ENSMUSG00000018474	Chd3	2600010P09Rik|AF020312|Chd7|Prp7|Prp9-1	chromodomain helicase DNA binding protein 3	protein-coding
mm_149330.1	chr19	10843261	10843269	+	1	NA	exon (NM_023044, exon 1 of 8)	exon (NM_023044, exon 1 of 8)	721	NM_023044	65221	Mm.27387	NM_023044	ENSMUSG00000024737	Slc15a3	Ci1|cI-1	solute carrier family 15, member 3	protein-coding
mm_7541.1	chr1	124490884	124490886	-	1	NA	Intergenic	U6|snRNA|snRNA	-445326	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_11573.1	chr2	32916410	32916419	+	1	NA	intron (NM_146119, intron 5 of 13)	B3|SINE|B2	40280	NM_146119	227737	Mm.301646	NM_146119	ENSMUSG00000026796	Fam129b	9130404D14Rik	family with sequence similarity 129, member B	protein-coding
mm_16971.1	chr2	17731393	17731411	-	1	NA	promoter-TSS (NM_028757)	promoter-TSS (NM_028757)	-334	NM_028757	74103	Mm.120298	NM_028757	ENSMUSG00000053702	Nebl	1200007O21Rik|A630080F05Rik|BB140644|D830029A09Rik|Lnebl	nebulette	protein-coding
mm_132980.1	chr16	52129735	52129743	+	1	NA	intron (NM_001033238, intron 4 of 17)	intron (NM_001033238, intron 4 of 17)	98190	NM_001033238	208650	Mm.328206	NM_001033238	ENSMUSG00000022637	Cblb	AI429560|AI851073|Cbl-b	Casitas B-lineage lymphoma b	protein-coding
mm_74950.1	chr8	25976737	25976741	-	1	NA	promoter-TSS (NM_029884)	promoter-TSS (NM_029884)	5	NM_029884	52120	Mm.28326	NM_029884	ENSMUSG00000037260	Hgsnat	9430010M12Rik|AW208455|D8Ertd354e|Tmem76	heparan-alpha-glucosaminide N-acetyltransferase	protein-coding
mm_13251.1	chr2	98663819	98663845	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	1196175	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_478.1	chr1	36691531	36691554	+	1	NA	promoter-TSS (NM_009942)	promoter-TSS (NM_009942)	55	NM_009942	12859	Mm.180182	NM_009942	ENSMUSG00000061518	Cox5b	-	cytochrome c oxidase subunit Vb	protein-coding
mm_81640.1	chr9	110895742	110895750	+	1	NA	exon (NM_001146059, exon 22 of 27)	exon (NM_001146059, exon 22 of 27)	15424	NM_001146060	235633	Mm.86338	NM_146228	ENSMUSG00000044037	Als2cl	79H19D|79H19E|BC022645|D930044G19Rik|mRn.49018	ALS2 C-terminal like	protein-coding
mm_65125.1	chr7	19458729	19458739	-	1	NA	promoter-TSS (NM_172279)	promoter-TSS (NM_172279)	-240	NM_172279	232944	Mm.260504	NM_172279	ENSMUSG00000030397	Mark4	2410090P21Rik|C79806|Markl1	MAP/microtubule affinity regulating kinase 4	protein-coding
mm_39353.1	chr5	9100657	9100667	+	1	NA	promoter-TSS (NM_001081029)	promoter-TSS (NM_001081029)	-75	NM_001081029	652925	Mm.439954	NM_001081029	ENSMUSG00000079659	Tmem243	4930420K17Rik|E030031F02Rik	transmembrane protein 243, mitochondrial	protein-coding
mm_29550.1	chr3	116807734	116807755	-	1	NA	intron (NM_001081326, intron 1 of 33)	intron (NM_001081326, intron 1 of 33)	422	NM_001081326	77559	Mm.237099	NM_001081326	ENSMUSG00000033400	Agl	1110061O17Rik|9430004C13Rik|9630046L06Rik|AI850929|C77197	amylo-1,6-glucosidase, 4-alpha-glucanotransferase	protein-coding
mm_151095.1	chr19	47854104	47854115	+	1	NA	promoter-TSS (NM_010362)	promoter-TSS (NM_010362)	-864	NM_010362	14873	Mm.378931	NM_010362	ENSMUSG00000025068	Gsto1	AA407097|AI194287|AU018802|Gsto-1|Gstx|Spg-r|p28	glutathione S-transferase omega 1	protein-coding
mm_143002.1	chr17	56423228	56423249	-	1	NA	exon (NM_001252453, exon 14 of 29)	exon (NM_001252453, exon 14 of 29)	-4329	NR_105943	102465590		NR_105943	ENSMUSG00000098339	Mir6977	Gm27922|mmu-mir-6977	microRNA 6977	ncRNA
mm_11050.1	chr2	27180980	27180983	+	1	NA	exon (NM_138942, exon 10 of 12)	exon (NM_138942, exon 10 of 12)	15474	NM_138942	13166	Mm.167781	NM_138942	ENSMUSG00000000889	Dbh	-	dopamine beta hydroxylase	protein-coding
mm_30152.1	chr3	142606852	142606874	-	1	NA	exon (NM_010259, exon 7 of 11)	exon (NM_010259, exon 7 of 11)	12016	NM_010259	14468	Mm.457978	NM_010259	ENSMUSG00000040264	Gbp2b	Gbp-1|Gbp1|Mag-1|Mpa-1|Mpa1	guanylate binding protein 2b	protein-coding
mm_17245.1	chr2	25621924	25622031	-	1	NA	promoter-TSS (NM_001040130)	promoter-TSS (NM_001040130)	25	NM_001040130	51875	Mm.271147	NM_001040130	ENSMUSG00000026939	Tmem141	1110065P14Rik|AI663999|D2Ertd217e	transmembrane protein 141	protein-coding
mm_68576.1	chr7	115846119	115846154	-	1	NA	promoter-TSS (NM_001277326)	promoter-TSS (NM_001277326)	4	NM_001277326	20679	Mm.323365	NM_011445	ENSMUSG00000051910	Sox6	AI987981|SOX-LZ	SRY (sex determining region Y)-box 6	protein-coding
mm_51589.1	chr6	83841644	83841649	+	1	NA	Intergenic	Intergenic	-9905	NM_146169	232164	Mm.404420	NM_146169	ENSMUSG00000045896	Paip2b	-	poly(A) binding protein interacting protein 2B	protein-coding
mm_159836.1	chr5	131475105	131475105	-	1	NA	exon (NM_177047, exon 8 of 19)	exon (NM_177047, exon 8 of 19)	-167583	NM_145218	212996	Mm.299204	NM_145218	ENSMUSG00000034040	Wbscr17	AA388321|E330012B09Rik	Williams-Beuren syndrome chromosome region 17 homolog (human)	protein-coding
mm_161085.1	chr12	85140012	85140012	-	1	NA	intron (NM_146244, intron 6 of 10)	intron (NM_146244, intron 6 of 10)	11252	NM_146244	238323	Mm.44829	NM_146244	ENSMUSG00000019235	Rps6kl1	A830084F09Rik|AW046440	ribosomal protein S6 kinase-like 1	protein-coding
mm_83080.1	chr9	39604260	39604276	-	1	NA	promoter-TSS (NM_001199556)	promoter-TSS (NM_001199556)	-144	NM_178737	244810	Mm.208855	NM_178737	ENSMUSG00000038112	AW551984	3222402N16	expressed sequence AW551984	protein-coding
mm_68856.1	chr7	126369552	126369578	-	1	NA	promoter-TSS (NM_010689)	promoter-TSS (NM_010689)	3	NM_010689	16797	Mm.10280	NM_010689	ENSMUSG00000030742	Lat	p36-38|pp36	linker for activation of T cells	protein-coding
mm_126250.1	chr15	79028531	79028543	+	1	NA	5' UTR (NM_008197, exon 1 of 1)	5' UTR (NM_008197, exon 1 of 1)	325	NM_008197	14958	Mm.24350	NM_008197	ENSMUSG00000096210	H1f0	D130017D06Rik|H1(0)|H1fv	H1 histone family, member 0	protein-coding
mm_45168.1	chr5	51458118	51458135	-	1	NA	non-coding (NR_027710, exon 13 of 13)	non-coding (NR_027710, exon 13 of 13)	95795	NR_027710	19017	Mm.259072	NM_008904	ENSMUSG00000029167	Ppargc1a	A830037N07Rik|ENSMUSG00000079510|Gm11133|PGC-1|PPARGC-1-alpha|Pgc-1alpha|Pgc1|Pgco1|Ppargc1	peroxisome proliferative activated receptor, gamma, coactivator 1 alpha	protein-coding
mm_15214.1	chr2	154220181	154220210	+	1	NA	exon (NM_153418, exon 16 of 16)	exon (NM_153418, exon 16 of 16)	-3547	NM_144890	228802	Mm.167411	NM_144890	ENSMUSG00000038572	Bpifb5	Lplunc5	BPI fold containing family B, member 5	protein-coding
mm_153472.1	chr19	41273266	41273278	-	1	NA	TTS (NM_031376)	TTS (NM_031376)	-9268	NM_133352	107358	Mm.246440	NM_133352	ENSMUSG00000025016	Tm9sf3	1810073M23Rik|2810031D16Rik|AI115521|AI413748|AW146116|AW549777|Smbp|mKIAA4036	transmembrane 9 superfamily member 3	protein-coding
mm_148464.1	chr19	4082474	4082517	+	1	NA	promoter-TSS (NM_001160253)	promoter-TSS (NM_001160253)	7	NM_001160253	29866	Mm.46268	NM_013878	ENSMUSG00000024857	Cabp2	-	calcium binding protein 2	protein-coding
mm_52582.1	chr6	116650662	116650666	+	1	NA	promoter-TSS (NM_001166580)	promoter-TSS (NM_001166580)	-20	NM_145980	213393	Mm.38231	NM_145980	ENSMUSG00000048489	8430408G22Rik	Depp|Fseg	RIKEN cDNA 8430408G22 gene	protein-coding
mm_25370.1	chr3	107101767	107101803	+	1	NA	intron (NM_008417, intron 1 of 2)	CpG	218	NM_008417	16490	Mm.39285	NM_008417	ENSMUSG00000040724	Kcna2	Akr6a4|ENSMUSG00000074335|Gm10672|Kca1-2|Kv1.2|Mk-2	potassium voltage-gated channel, shaker-related subfamily, member 2	protein-coding
mm_131979.1	chr16	25011410	25011415	+	1	NA	Intergenic	Intergenic	-48227	NR_040374	319487	Mm.137341	NR_040374	ENSMUSG00000096960	A230028O05Rik	-	RIKEN cDNA A230028O05 gene	ncRNA
mm_153001.1	chr19	30115244	30115247	-	1	NA	exon (NM_138595, exon 19 of 25)	exon (NM_138595, exon 19 of 25)	60196	NM_138595	104174	Mm.274852	NM_138595	ENSMUSG00000024827	Gldc	D030049L12Rik|D19Wsu57e	glycine decarboxylase	protein-coding
mm_147606.1	chr18	56919233	56919255	-	1	NA	intron (NM_177115, intron 1 of 4)	intron (NM_177115, intron 1 of 4)	6304	NM_177115	320253	Mm.312623	NM_177115	ENSMUSG00000032656	March3	6330411I15Rik|A530081L18Rik|AI843639|MARCH-III	membrane-associated ring finger (C3HC4) 3	protein-coding
mm_128635.1	chr15	59082110	59082122	-	1	NA	promoter-TSS (NM_144800)	promoter-TSS (NM_144800)	-90	NM_144800	211401	Mm.215481	NM_144800	ENSMUSG00000022353	Mtss1	2310003N14Rik|BC024131|D130001D01Rik|Mim|mKIAA0429	metastasis suppressor 1	protein-coding
mm_55115.1	chr6	50394007	50394030	-	1	NA	intron (NM_001347213, intron 2 of 23)	intron (NM_001347213, intron 2 of 23)	-11181	NM_027881	71720	Mm.44153	NM_027881	ENSMUSG00000029822	Osbpl3	1200014M06Rik|6720421I08Rik|A530055M08|ORP-3|ORP3|OSBP3	oxysterol binding protein-like 3	protein-coding
mm_21090.1	chr2	153182473	153182492	-	1	NA	exon (NM_133847, exon 3 of 18)	exon (NM_133847, exon 3 of 18)	21181	NM_133847	99237	Mm.330674	NM_133847	ENSMUSG00000068040	Tm9sf4	AA986553|AU045326|B930079E06|mKIAA0255	transmembrane 9 superfamily protein member 4	protein-coding
mm_46957.1	chr5	114973317	114973335	-	1	NA	Intergenic	Intergenic	-2264	NM_009327	21405	Mm.332607	NM_009327	ENSMUSG00000029556	Hnf1a	AI323641|HNF1|HNF1-alpha|HNF1[a]|Hnf-1|Hnf1alpha|LFB1|Tcf-1|Tcf1	HNF1 homeobox A	protein-coding
mm_90770.1	chr10	5823820	5823873	-	1	NA	promoter-TSS (NM_175374)	promoter-TSS (NM_175374)	97	NM_175374	108853	Mm.55082	NM_175374	ENSMUSG00000019774	Mtrf1l	9130004K12Rik	mitochondrial translational release factor 1-like	protein-coding
mm_99079.1	chr11	99388986	99389009	+	1	NA	exon (NM_010660, exon 1 of 8)	exon (NM_010660, exon 1 of 8)	367	NM_010660	16661	Mm.22662	NM_010660	ENSMUSG00000019761	Krt10	D130054E02Rik|K10|K1C1|Krt-1.10|Krt1-10	keratin 10	protein-coding
mm_115176.1	chr13	108316341	108316358	+	1	NA	promoter-TSS (NM_178683)	promoter-TSS (NM_178683)	12	NM_178683	218581	Mm.32318	NM_178683	ENSMUSG00000021697	Depdc1b	9830132O03|AW260467|XTP1	DEP domain containing 1B	protein-coding
mm_17510.1	chr2	29121105	29121108	-	1	NA	Intergenic	Intergenic	-3886	NM_198033	269254	Mm.41867	NM_198033	ENSMUSG00000043535	Setx	A130090N03|A930037J23Rik|AOA2|AW060766|Als4|SCAR1|Sen1|mKIAA0625	senataxin	protein-coding
mm_2232.1	chr1	91044421	91044437	+	1	NA	intron (NM_001111312, intron 1 of 12)	intron (NM_001111312, intron 1 of 12)	-9015	NM_001310732	16978	Mm.45039	NM_008515	ENSMUSG00000026305	Lrrfip1	AU024550|Fliiap1	leucine rich repeat (in FLII) interacting protein 1	protein-coding
mm_16951.1	chr2	17365308	17365321	-	1	NA	intron (NM_028757, intron 5 of 6)	ORR1E|LTR|ERVL-MaLR	-198200	NR_105847	102465964		NR_105847	ENSMUSG00000099161	Mir6419	Gm27713|mmu-mir-6419	microRNA 6419	ncRNA
mm_128762.1	chr15	65976801	65976805	-	1	NA	promoter-TSS (NM_001145096)	promoter-TSS (NM_001145096)	1	NM_001145096	654498	Mm.364550	NM_001145096	ENSMUSG00000072511	Hhla1	F930104E18Rik	HERV-H LTR-associating 1	protein-coding
mm_40078.1	chr5	34363380	34363380	+	1	NA	Intergenic	RMER19B|LTR|ERVK	-6553	NM_001243123	231128	Mm.286885	NM_001030306	ENSMUSG00000037210	Fam193a	-	family with sequence similarity 193, member A	protein-coding
mm_117574.1	chr13	85538315	85538316	-	1	NA	Intergenic	L1MA4|LINE|L1	-248829	NM_145452	218397	Mm.259653	NM_145452	ENSMUSG00000021549	Rasa1	Gap|RasGAP|Rasa	RAS p21 protein activator 1	protein-coding
mm_102552.1	chr11	61366689	61366713	-	1	NA	intron (NM_026183, intron 6 of 16)	intron (NM_026183, intron 6 of 16)	11374	NM_026183	67473	Mm.100741	NM_026183	ENSMUSG00000010122	Slc47a1	1300013J15Rik|AI036982|MATE1|mMATE1	solute carrier family 47, member 1	protein-coding
mm_26277.1	chr3	142505524	142505534	+	1	NA	exon (NM_153564, exon 7 of 11)	exon (NM_153564, exon 7 of 11)	8595	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_91817.1	chr10	54076582	54076620	-	1	NA	promoter-TSS (NM_008548)	promoter-TSS (NM_008548)	679	NR_038016	100502920	Mm.403982	NR_038016	ENSMUSG00000097069	Gm16998	-	predicted gene, 16998	ncRNA
mm_3354.1	chr1	138166678	138166681	+	1	NA	intron (NM_001111316, intron 1 of 31)	intron (NM_001111316, intron 1 of 31)	8447	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_148469.1	chr19	4097370	4097386	+	1	NA	promoter-TSS (NM_026373)	promoter-TSS (NM_026373)	27	NM_026373	52004	Mm.29609	NM_026373	ENSMUSG00000024856	Cdk2ap2	5830466O21Rik|D19Ertd144e|Doc-1r	CDK2-associated protein 2	protein-coding
mm_141258.1	chr17	27597198	27597226	-	1	NA	intron (NM_019837, intron 1 of 4)	intron (NM_019837, intron 1 of 4)	25752	NM_001291046	56409	Mm.144699	NM_019837	ENSMUSG00000024213	Nudt3	1110011B09Rik|AA960325|Dipp|Dipp1	nudix (nucleotide diphosphate linked moiety X)-type motif 3	protein-coding
mm_158075.1	chrX	101264891	101264907	-	1	NA	promoter-TSS (NM_001317221)	promoter-TSS (NM_001317221)	-907	NM_001317221	245536	Mm.212463	NM_001033362	ENSMUSG00000090141	Gm614	-	predicted gene 614	protein-coding
mm_31447.1	chr4	48586992	48587000	+	1	NA	intron (NM_021436, intron 1 of 9)	intron (NM_021436, intron 1 of 9)	1803	NM_021436	230157	Mm.422686	NM_021436	ENSMUSG00000028347	Tmeff1	A830033E11|M7365|Tr1	transmembrane protein with EGF-like and two follistatin-like domains 1	protein-coding
mm_106976.1	chr12	9485404	9485407	+	1	NA	Intergenic	Intergenic	85180	NR_045488	69420	Mm.396193	NR_045488	ENSMUSG00000099360	1700022H16Rik	-	RIKEN cDNA 1700022H16 gene	ncRNA
mm_40840.1	chr5	73284240	73284248	+	1	NA	promoter-TSS (NR_040689)	promoter-TSS (NR_040689)	-60	NR_040687	72276	Mm.271215	NR_040687	ENSMUSG00000100175	1700025M24Rik	-	RIKEN cDNA 1700025M24 gene	ncRNA
mm_45489.1	chr5	71548191	71548260	-	1	NA	promoter-TSS (NM_030052)	promoter-TSS (NM_030052)	-20	NM_030052	78174	Mm.60690	NM_030052	ENSMUSG00000049387	Cox7b2	4930503B16Rik	cytochrome c oxidase subunit VIIb2	protein-coding
mm_61473.1	chr7	75612332	75612343	+	1	NA	intron (NM_029332, intron 7 of 36)	intron (NM_029332, intron 7 of 36)	156803	NM_029332	75547	Mm.216107	NM_029332	ENSMUSG00000066406	Akap13	1700026G02Rik|5730522G15Rik|5830460E08Rik|AKAP-13|AKAP-Lbc|BRX|Ht31|LBC|PROTO-LB|PROTO-LBC	A kinase (PRKA) anchor protein 13	protein-coding
mm_74994.1	chr8	27202543	27202557	-	1	NA	promoter-TSS (NM_029674)	promoter-TSS (NM_029674)	-3	NM_029674	76615	Mm.272794	NM_029674	ENSMUSG00000039720	Got1l1	1700083M11Rik	glutamic-oxaloacetic transaminase 1-like 1	protein-coding
mm_19532.1	chr2	94332901	94332911	-	1	NA	exon (NM_183106, exon 18 of 25)	exon (NM_183106, exon 18 of 25)	-71507	NR_030431	735259		NR_030431	ENSMUSG00000076335	Mir670	Mirn670|mir-670|mmu-mir-670	microRNA 670	ncRNA
mm_123127.1	chr14	56211424	56211430	-	1	NA	promoter-TSS (NM_010374)	promoter-TSS (NM_010374)	-20	NM_010374	14943	Mm.457976	NM_010374	ENSMUSG00000015441	Gzmf	CCP4|Ctla-7|Ctla7|MCSP-3	granzyme F	protein-coding
mm_171681.1	chr4	5693940	5693947	-	1	NA	intron (NM_173426, intron 1 of 2)	RLTR9E|LTR|ERVK	49764	NM_173426	242297	Mm.331470	NM_173426	ENSMUSG00000049119	Fam110b	1700012H17Rik|5031405P22|AW049855	family with sequence similarity 110, member B	protein-coding
mm_168650.1	chr11	8605365	8605365	-	1	NA	intron (NM_001083587, intron 2 of 30)	RLTR11A2|LTR|ERVK	59170	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_6537.1	chr1	74935550	74935613	-	1	NA	promoter-TSS (NM_001039495)	promoter-TSS (NM_001039495)	18	NM_001039495	241116	Mm.186404	NM_172848	ENSMUSG00000047021	Ccdc108	A230051F10|B230363K08Rik|Cfap65	coiled-coil domain containing 108	protein-coding
mm_144146.1	chr18	4994973	4994983	+	1	NA	Intergenic	Intergenic	-51611	NM_153153	225115	Mm.136791	NM_153153	ENSMUSG00000024236	Svil	AU024053|B430302E16Rik	supervillin	protein-coding
mm_70026.1	chr7	142576267	142576314	-	1	NA	TTS (NR_030416)	TTS (NR_030416)	857	NR_030416	735280		NR_030416	ENSMUSG00000076275	Mir675	Mirn675|mir-675|mmu-mir-675	microRNA 675	ncRNA
mm_141560.1	chr17	32221191	32221220	-	1	NA	exon (NM_001286630, exon 7 of 20)	exon (NM_001286630, exon 7 of 20)	-20715	NR_102329	100043434		NR_102329		Gm4432	-	predicted gene 4432	pseudo
mm_155385.1	chrX	71816752	71816760	+	1	NA	promoter-TSS (NM_001081356)	promoter-TSS (NM_001081356)	-2	NM_001081356	67048	Mm.41102	NM_001081356	ENSMUSG00000073131	Vma21	2610030H06Rik|AI840175	VMA21 vacuolar H+-ATPase homolog (S. cerevisiae)	protein-coding
mm_24996.1	chr3	97162990	97163002	+	1	NA	intron (NM_019800, intron 1 of 9)	intron (NM_019800, intron 1 of 9)	4219	NM_019800	66659	Mm.101368	NM_019800	ENSMUSG00000028093	Acp6	5730559A09Rik|ACPL1|AU022842|mPACPL1	acid phosphatase 6, lysophosphatidic	protein-coding
mm_90070.1	chr10	116347387	116347389	+	1	NA	intron (NM_029928, intron 15 of 31)	intron (NM_029928, intron 15 of 31)	46014	NM_029928	19263	Mm.37213	NM_029928	ENSMUSG00000020154	Ptprb	3230402H02Rik|C130094E24|Ptpz|Rptpb|VE-PTP|Veptp	protein tyrosine phosphatase, receptor type, B	protein-coding
mm_73807.1	chr8	117340197	117340199	+	1	NA	intron (NM_001163262, intron 1 of 20)	intron (NM_001163262, intron 1 of 20)	-8972	NM_028941	74440	Mm.233181	NM_028941	ENSMUSG00000034390	Cmip	4933407C03Rik|5830471E12Rik|AI314065|AI464126	c-Maf inducing protein	protein-coding
mm_11057.1	chr2	27496898	27496938	+	1	NA	Intergenic	MURVY-int|LTR|ERV1	-18229	NM_080848	140858	Mm.28265	NM_080848	ENSMUSG00000026917	Wdr5	2410008O07Rik|AA408785|AA960360|Big|Big-3	WD repeat domain 5	protein-coding
mm_164588.1	chr17	26509517	26509521	-	1	NA	Intergenic	Intergenic	-1047	NM_013642	19252	Mm.239041	NM_013642	ENSMUSG00000024190	Dusp1	3CH134|MKP1|Ptpn16|U19515|erp|mkp-1	dual specificity phosphatase 1	protein-coding
mm_26255.1	chr3	142496816	142496830	+	1	NA	promoter-TSS (NM_153564)	promoter-TSS (NM_153564)	-111	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_69265.1	chr7	127895579	127895647	-	1	NA	promoter-TSS (NM_178600)	promoter-TSS (NM_178600)	4	NM_178600	27973	Mm.29703	NM_178600	ENSMUSG00000096145	Vkorc1	D7Wsu86e	vitamin K epoxide reductase complex, subunit 1	protein-coding
mm_82937.1	chr9	35267747	35267786	-	1	NA	promoter-TSS (NM_001286604)	promoter-TSS (NM_001286604)	39	NM_175411	109229	Mm.24197	NM_175411	ENSMUSG00000050471	Fam118b	2310022O21Rik|2700018L24Rik|C030004A17Rik|Ppp4r1l	family with sequence similarity 118, member B	protein-coding
mm_88783.1	chr10	80603202	80603259	+	1	NA	intron (NM_019575, intron 1 of 6)	intron (NM_019575, intron 1 of 6)	348	NM_019575	56214	Mm.273170	NM_019575	ENSMUSG00000078441	Scamp4	2410022D05Rik|AI448940|AU022392|AW742369|Sc4	secretory carrier membrane protein 4	protein-coding
mm_104660.1	chr11	97628903	97628918	-	1	NA	exon (NM_175332, exon 1 of 1)	exon (NM_175332, exon 1 of 1)	806	NM_175332	103551	Mm.24506	NM_175332	ENSMUSG00000043439	Epop	AA409164|AI413509|AW539173|E13|E130012A19Rik|esPRC2p48	elongin BC and polycomb repressive complex 2 associated protein	protein-coding
mm_162263.1	chrY	2796225	2796225	-	1	NA	Intergenic	Intergenic	-34455	NM_001270516	100862398	Mm.4711	NM_001270516	ENSMUSG00000095948	Gm21708	-	predicted gene, 21708	protein-coding
mm_71980.1	chr8	70594614	70594649	+	1	NA	exon (NM_023627, exon 2 of 11)	exon (NM_023627, exon 2 of 11)	150	NM_023627	71780	Mm.29357	NM_023627	ENSMUSG00000019139	Isyna1	1300017C10Rik|AU018670	myo-inositol 1-phosphate synthase A1	protein-coding
mm_144887.1	chr18	36801857	36801882	+	1	NA	non-coding (NR_027885, exon 1 of 1)	non-coding (NR_027885, exon 1 of 1)	106	NR_027885	378472	Mm.482379	NR_027885		Vaultrc5	Gm22653|Mvg1	vault RNA component 5	ncRNA
mm_72808.1	chr8	87473154	87473163	+	1	NA	promoter-TSS (NM_019626)	promoter-TSS (NM_019626)	42	NR_125722	100040294	Mm.213632	NR_033430	ENSMUSG00000097248	Gm2694	C230036H16Rik|linc1582	predicted gene 2694	ncRNA
mm_89435.1	chr10	91123398	91123414	+	1	NA	intron (NM_133668, intron 2 of 7)	intron (NM_133668, intron 2 of 7)	557	NM_133668	18674	Mm.298	NM_133668	ENSMUSG00000061904	Slc25a3	5730556H19Rik|PTP|Phc	solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 3	protein-coding
mm_97657.1	chr11	79528204	79528215	+	1	NA	5' UTR (NM_001033711, exon 2 of 2)	5' UTR (NM_001033711, exon 2 of 2)	2400	NM_146023	101488212	Mm.439665	NM_146023	ENSMUSG00000070354	Gm21975	Evi2a-evi2b	predicted gene 21975	protein-coding
mm_84737.1	chr9	75254757	75254772	-	1	NA	intron (NM_001081322, intron 8 of 40)	CT-rich|Low_complexity|Low_complexity	22750	NM_001081322	208943	Mm.41339	NM_001081322	ENSMUSG00000033590	Myo5c	9130003O20Rik|BB085560|C330029I24	myosin VC	protein-coding
mm_117426.1	chr13	74390781	74390866	-	1	NA	Intergenic	Intergenic	-14257	NM_001081680	238722	Mm.461254	NM_001081680	ENSMUSG00000069184	Zfp72	Zfp74	zinc finger protein 72	protein-coding
mm_130473.1	chr15	98727531	98727551	-	1	NA	intron (NM_024169, intron 2 of 5)	intron (NM_024169, intron 2 of 5)	657	NM_024169	66120	Mm.30729	NM_024169	ENSMUSG00000003355	Fkbp11	1110002O23Rik|FKBP-11	FK506 binding protein 11	protein-coding
mm_42808.1	chr5	121787320	121787342	+	1	NA	intron (NM_009125, intron 14 of 24)	intron (NM_009125, intron 14 of 24)	31942	NR_105998	102465624		NR_105998	ENSMUSG00000099063	Mir7031	Gm27859|mmu-mir-7031	microRNA 7031	ncRNA
mm_164402.1	chr16	34994971	34994975	+	1	NA	intron (NM_139300, intron 29 of 31)	intron (NM_139300, intron 29 of 31)	-27448	NM_023587	70757	Mm.27286	NM_023587	ENSMUSG00000035376	Hacd2	6330408J20Rik|AI255777|AI481689|Hcad2|Ptplb	3-hydroxyacyl-CoA dehydratase 2	protein-coding
mm_143010.1	chr17	56454962	56454973	-	1	NA	exon (NM_001252453, exon 3 of 29)	exon (NM_001252453, exon 3 of 29)	7254	NM_001252456	19280	Mm.258771	NM_011218	ENSMUSG00000013236	Ptprs	AL022616|PTP|PTP-NU3|PTPNU-3|PTPsigma|Ptpt9|R-PTP-S|RPTPsigma	protein tyrosine phosphatase, receptor type, S	protein-coding
mm_61253.1	chr7	65861896	65861905	+	1	NA	promoter-TSS (NM_001291184)	promoter-TSS (NM_001291184)	-236	NM_001291184	18553	Mm.294007	NM_011048	ENSMUSG00000030513	Pcsk6	C86343|Pace4|SPC4	proprotein convertase subtilisin/kexin type 6	protein-coding
mm_1856.1	chr1	84839460	84839475	+	1	NA	promoter-TSS (NM_025386)	promoter-TSS (NM_025386)	-163	NM_133975	14897	Mm.209265	NM_133975	ENSMUSG00000026219	Trip12	1110036I07Rik|6720416K24Rik|AA410158|Gtl6|TRIP-12	thyroid hormone receptor interactor 12	protein-coding
mm_9219.1	chr1	171234291	171234324	-	1	NA	promoter-TSS (NM_010185)	promoter-TSS (NM_010185)	42	NM_010185	14127	Mm.22673	NM_010185	ENSMUSG00000058715	Fcer1g	AI573376|CD23|FcR-gamma|FcR[g]|FcRgamma|Fce1g|FcepsilonRI|Ly-50	Fc receptor, IgE, high affinity I, gamma polypeptide	protein-coding
mm_85146.1	chr9	95857560	95857570	-	1	NA	promoter-TSS (NM_019864)	promoter-TSS (NM_019864)	-32	NM_019864	245000	Mm.212462	NM_019864	ENSMUSG00000032409	Atr	-	ataxia telangiectasia and Rad3 related	protein-coding
mm_76802.1	chr8	104248500	104248569	-	1	NA	promoter-TSS (NR_045642)	promoter-TSS (NR_045642)	24	NR_045642	57813	Mm.183110	NM_021028	ENSMUSG00000035824	Tk2	AU024611|mt-TK	thymidine kinase 2, mitochondrial	protein-coding
mm_21102.1	chr2	153241359	153241394	-	1	NA	promoter-TSS (NM_080463)	promoter-TSS (NM_080463)	-18	NM_018807	54711	Mm.103199	NM_018807	ENSMUSG00000051413	Plagl2	AU018672|AW552839|mKIAA0198	pleiomorphic adenoma gene-like 2	protein-coding
mm_57025.1	chr6	122282811	122282821	-	1	NA	promoter-TSS (NM_016970)	promoter-TSS (NM_016970)	17	NM_016970	50928	Mm.20434	NM_016970	ENSMUSG00000030114	Klrg1	2F1-Ag|MAFA|MAFA-L	killer cell lectin-like receptor subfamily G, member 1	protein-coding
mm_145568.1	chr18	60911728	60911755	+	1	NA	promoter-TSS (NM_001038499)	promoter-TSS (NM_001038499)	-499	NM_001038499	545260	Mm.20147	NM_001038499	ENSMUSG00000036412	Arsi	BC020108	arylsulfatase i	protein-coding
mm_3015.1	chr1	133363746	133363755	+	1	NA	5' UTR (NM_175443, exon 1 of 8)	5' UTR (NM_175443, exon 1 of 8)	178	NM_175443	214253	Mm.52111	NM_175443	ENSMUSG00000070644	Etnk2	4933417N20Rik|AI197444|EKI 2|Eki2|Tuc1	ethanolamine kinase 2	protein-coding
mm_32958.1	chr4	119733808	119733834	+	1	NA	Intergenic	CpG	-74876	NM_008191	14916	Mm.278	NM_008191	ENSMUSG00000032978	Guca2b	AV066530|Gcap2|Ugn	guanylate cyclase activator 2b (retina)	protein-coding
mm_93587.1	chr10	117063034	117063058	-	1	NA	exon (NM_007636, exon 2 of 16)	exon (NM_007636, exon 2 of 16)	768	NM_007636	12461	Mm.247788	NM_007636	ENSMUSG00000034024	Cct2	Cctb	chaperonin containing Tcp1, subunit 2 (beta)	protein-coding
mm_44239.1	chr5	5266039	5266083	-	1	NA	promoter-TSS (NM_001310448)	promoter-TSS (NM_001310448)	7	NM_001310448	18647	Mm.389061	NM_011074	ENSMUSG00000028926	Cdk14	Pftk1|mKIAA0834	cyclin-dependent kinase 14	protein-coding
mm_104943.1	chr11	100118834	100118843	-	1	NA	exon (NM_010662, exon 6 of 8)	exon (NM_010662, exon 6 of 8)	1739	NM_001313949	16663	Mm.4646	NM_010662	ENSMUSG00000044041	Krt13	CK13|K13|Krt-1.13|Krt1-13	keratin 13	protein-coding
mm_2294.1	chr1	91458558	91458563	+	1	NA	intron (NM_011066, intron 1 of 22)	intron (NM_011066, intron 1 of 22)	768	NM_011066	18627	Mm.482463	NM_011066	ENSMUSG00000055866	Per2	mKIAA0347|mPer2	period circadian clock 2	protein-coding
mm_111898.1	chr12	108702266	108702320	-	1	NA	promoter-TSS (NM_027299)	promoter-TSS (NM_027299)	13	NM_001171002	70059	Mm.207605	NM_027299	ENSMUSG00000021263	Degs2	2210008A03Rik|AI852933|DES2	delta(4)-desaturase, sphingolipid 2	protein-coding
mm_55137.1	chr6	51320918	51320925	-	1	NA	Intergenic	Intergenic	-51011	NR_029719	387166		NR_029719	ENSMUSG00000065505	Mir148a	Mirn148|Mirn148a|mir-148a	microRNA 148a	ncRNA
mm_138934.1	chr17	43804045	43804088	+	1	NA	promoter-TSS (NM_001286653)	promoter-TSS (NM_001286653)	63	NM_001286653	53901	Mm.251242	NM_030598	ENSMUSG00000039601	Rcan2	Csp2|Dscr1l1|MCIP2|ZAKI-4	regulator of calcineurin 2	protein-coding
mm_118950.1	chr14	27362805	27362816	+	1	NA	exon (NM_027871, exon 3 of 11)	exon (NM_027871, exon 3 of 11)	1421	NM_001289688	71704	Mm.248606	NM_027871	ENSMUSG00000021895	Arhgef3	1200004I24Rik|9830169H03Rik|C76747|Xpln	Rho guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_129756.1	chr15	82371937	82371961	-	1	NA	exon (NM_019823, exon 9 of 10)	exon (NM_019823, exon 9 of 10)	8311	NM_019823	56448	Mm.474216	NM_019823	ENSMUSG00000061740	Cyp2d22	2D22	cytochrome P450, family 2, subfamily d, polypeptide 22	protein-coding
mm_86648.1	chr10	17476994	17477004	+	1	NA	Intergenic	L2b|LINE|L2	-246229	NM_010828	17684	Mm.272321	NM_010828	ENSMUSG00000039910	Cited2	AI835299|ER154-like|Mrg1|Msg2|p35srj	Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 2	protein-coding
mm_32871.1	chr4	118526987	118527024	+	1	NA	promoter-TSS (NM_025572)	promoter-TSS (NM_025572)	-270	NM_025572	66451	Mm.34431	NM_025572	ENSMUSG00000028536	2610528J11Rik	TEMP	RIKEN cDNA 2610528J11 gene	protein-coding
mm_106038.1	chr11	116079147	116079157	-	1	NA	3' UTR (NM_016852, exon 8 of 8)	3' UTR (NM_016852, exon 8 of 8)	-1191	NM_001009573	70450	Mm.259460	NM_001009573	ENSMUSG00000057948	Unc13d	2610108D09Rik|Jinx|Munc13-4|mFLJ00067	unc-13 homolog D (C. elegans)	protein-coding
mm_104856.1	chr11	99351087	99351113	-	1	NA	promoter-TSS (NM_010666)	promoter-TSS (NM_010666)	18	NM_010666	16675	Mm.440476	NM_010666	ENSMUSG00000017588	Krt27	CK-27|Krt1-c29|mIRSa3.1|stpm	keratin 27	protein-coding
mm_126237.1	chr15	78987084	78987103	+	1	NA	intron (NM_001024716, intron 1 of 13)	intron (NM_001024716, intron 1 of 13)	4037	NM_001024716	110253	Mm.123714	NM_138579	ENSMUSG00000033088	Triobp	AI428493|EST478828|Tara|mKIAA1662	TRIO and F-actin binding protein	protein-coding
mm_61690.1	chr7	81057584	81057588	+	1	NA	promoter-TSS (NM_054085)	promoter-TSS (NM_054085)	-14	NM_054085	116904	Mm.475768	NM_054085	ENSMUSG00000038763	Alpk3	AW319487|D330016D04|MAK|Midori|mKIAA1330	alpha-kinase 3	protein-coding
mm_60311.1	chr7	44140590	44140610	+	1	NA	exon (NM_008454, exon 3 of 5)	exon (NM_008454, exon 3 of 5)	3310	NM_008454	16615	Mm.440887	NM_008454	ENSMUSG00000038968	Klk1b16	Klk16|mGk-16	kallikrein 1-related peptidase b16	protein-coding
mm_12424.1	chr2	70563374	70563433	+	1	NA	promoter-TSS (NR_040496)	promoter-TSS (NR_040496)	-46	NR_040496	68986	Mm.437697	NR_040496	ENSMUSG00000087264	Gad1os	1500002O10Rik	glutamate decarboxylase 1, opposite strand	ncRNA
mm_134312.1	chr16	15885622	15885629	-	1	NA	Intergenic	Intergenic	-1661	NM_007679	12609	Mm.347407	NM_007679	ENSMUSG00000071637	Cebpd	c/EBPdelta	CCAAT/enhancer binding protein (C/EBP), delta	protein-coding
mm_154881.1	chrX	20698715	20698732	+	1	NA	3' UTR (NM_011049, exon 16 of 16)	3' UTR (NM_011049, exon 16 of 16)	-5186	NM_145628	236733	Mm.34489	NM_145628	ENSMUSG00000031066	Usp11	6230415D12Rik|mKIAA4085	ubiquitin specific peptidase 11	protein-coding
mm_57665.1	chr6	128487937	128487959	-	1	NA	exon (NM_007376, exon 30 of 36)	exon (NM_007376, exon 30 of 36)	38772	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_92999.1	chr10	86778496	86778540	-	1	NA	promoter-TSS (NM_175331)	promoter-TSS (NM_175331)	-487	NM_175331	103466	Mm.200446	NM_175331	ENSMUSG00000054027	Nt5dc3	AU040402|AW540062|C630002B14Rik|TU12B1-TY	5'-nucleotidase domain containing 3	protein-coding
mm_18307.1	chr2	53191215	53191260	-	1	NA	promoter-TSS (NM_018785)	promoter-TSS (NM_018785)	-50	NM_018785	56194	Mm.257474	NM_018785	ENSMUSG00000061136	Prpf40a	2810012K09Rik|FBP-11|FBP11|Fnbp11|Fnbp3	pre-mRNA processing factor 40A	protein-coding
mm_139747.1	chr17	63533431	63533441	+	1	NA	Intergenic	Intergenic	-32856	NM_015794	50758	Mm.136366	NM_015794	ENSMUSG00000023965	Fbxl17	6330576B01Rik|AI452053|BB073797|C130023C01Rik|Fbx13|Fbxo13	F-box and leucine-rich repeat protein 17	protein-coding
mm_17488.1	chr2	28583148	28583174	-	1	NA	5' UTR (NM_001290484, exon 1 of 12)	5' UTR (NM_001290484, exon 1 of 12)	118	NM_148928	70239	Mm.274120	NM_148928	ENSMUSG00000026816	Gtf3c5	2700084A09Rik|TFIIIC63|TFiiiC2-63	general transcription factor IIIC, polypeptide 5	protein-coding
mm_3055.1	chr1	134063454	134063460	+	1	NA	Intergenic	Intergenic	15698	NM_007570	12227	Mm.392646	NM_007570	ENSMUSG00000020423	Btg2	AA959598|APRO1|Pc3|TIS21	B cell translocation gene 2, anti-proliferative	protein-coding
mm_115246.1	chr13	110396081	110396100	+	1	NA	exon (NM_152804, exon 2 of 14)	exon (NM_152804, exon 2 of 14)	1046	NM_152804	20620	Mm.380	NM_152804	ENSMUSG00000021701	Plk2	Snk	polo-like kinase 2	protein-coding
mm_112313.1	chr12	114915081	114915086	-	1	NA	Intergenic	Intergenic	-401389	NR_106063	102465664		NR_106063	ENSMUSG00000098357	Mir7094-2	Gm27508|mmu-mir-7094-2	microRNA 7094-2	ncRNA
mm_134615.1	chr16	20822888	20822893	-	1	NA	Intergenic	Intergenic	-88379	NM_009379	21832	Mm.3943	NM_009379	ENSMUSG00000022847	Thpo	Mgdf|Ml|Mpllg|Tpo	thrombopoietin	protein-coding
mm_73920.1	chr8	119754243	119754266	+	1	NA	exon (NM_026922, exon 24 of 27)	exon (NM_026922, exon 24 of 27)	24162	NM_028883	74347	Mm.358759	NM_028883	ENSMUSG00000034105	Tldc1	4632415K11Rik|Kiaa1609	TBC/LysM associated domain containing 1	protein-coding
mm_137862.1	chr17	31247324	31247334	+	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	30027	NM_025290	22092	Mm.12743	NM_025290	ENSMUSG00000024033	Rsph1	MCA|Tsga2	radial spoke head 1 homolog (Chlamydomonas)	protein-coding
mm_117823.1	chr13	98016238	98016242	-	1	NA	intron (NM_012026, intron 9 of 35)	intron (NM_012026, intron 9 of 35)	189925	NM_012026	110596	Mm.252718	NM_012026	ENSMUSG00000021662	Arhgef28	9230110L08Rik|AI323540|D13Bwg1089e|RIP2|Rgnef|RhoGEF|Rhoip2|p190RhoGEF	Rho guanine nucleotide exchange factor (GEF) 28	protein-coding
mm_167300.1	chr8	55401677	55401682	-	1	NA	Intergenic	RLTR48A|LTR|ERV1	446951	NM_001253756	234267	Mm.241700	NM_153581	ENSMUSG00000031517	Gpm6a	Gpm6|M6A	glycoprotein m6a	protein-coding
mm_166378.1	chr5	129704951	129704953	-	1	NA	5' UTR (NM_028826, exon 2 of 11)	5' UTR (NM_028826, exon 2 of 11)	3559	NM_028826	74222	Mm.159143	NM_028826	ENSMUSG00000034219	Sept14	1700016K13Rik	septin 14	protein-coding
mm_12906.1	chr2	84827080	84827098	+	1	NA	promoter-TSS (NM_013899)	promoter-TSS (NM_013899)	68	NM_013899	30059	Mm.21826	NM_013899	ENSMUSG00000027076	Timm10	Tim13|Timm13a	translocase of inner mitochondrial membrane 10	protein-coding
mm_152674.1	chr19	14960782	14960784	-	1	NA	Intergenic	Intergenic	-362600	NM_001302947	21888	Mm.103638	NM_011600	ENSMUSG00000024642	Tle4	5730411M05Rik|AA792082|Bce-1|Bce1|ESTM13|ESTM14|Grg4|X83332|X83333|grg-4	transducin-like enhancer of split 4	protein-coding
mm_145902.1	chr18	65698254	65698277	+	1	NA	promoter-TSS (NM_177028)	promoter-TSS (NM_177028)	-3	NM_177028	319888	Mm.183576	NM_177028	ENSMUSG00000046610	Oacyl	5330437I02Rik|Acyl3	O-acyltransferase like	protein-coding
mm_137920.1	chr17	32452746	32452757	+	1	NA	promoter-TSS (NM_177307)	promoter-TSS (NM_177307)	28	NM_177307	320997	Mm.130900	NM_177307	ENSMUSG00000061126	Cyp4f39	4732474A20Rik	cytochrome P450, family 4, subfamily f, polypeptide 39	protein-coding
mm_68416.1	chr7	109672230	109672248	-	1	NA	Intergenic	Intergenic	-31498	NM_020616	57373	Mm.334138	NM_020616	ENSMUSG00000031023	Akip1	BCA3|C11orf17|D7H11orf17|D930014E17Rik|ICRFP703B1614Q5.6|ORF27	A kinase (PRKA) interacting protein 1	protein-coding
mm_142044.1	chr17	35503925	35503936	-	1	NA	Intergenic	Intergenic	-2102	NM_013633	18999	Mm.17031	NM_013633	ENSMUSG00000024406	Pou5f1	NF-A3|Oct-3|Oct-3/4|Oct-4|Oct3|Oct3/4|Oct4|Otf-3|Otf-4|Otf3|Otf3-rs7|Otf3g|Otf4	POU domain, class 5, transcription factor 1	protein-coding
mm_7540.1	chr1	124490319	124490333	-	1	NA	Intergenic	Intergenic	-444767	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_52684.1	chr6	118011449	118011496	+	1	NA	promoter-TSS (NM_001316749)	promoter-TSS (NM_001316749)	-65	NM_001316749	70727	Mm.87660	NM_027526	ENSMUSG00000030134	Rasgef1a	6330404M18Rik|AI835194	RasGEF domain family, member 1A	protein-coding
mm_46374.1	chr5	103692065	103692065	-	1	NA	Intergenic	Intergenic	-36333	NM_001163550	74218	Mm.159141	NM_028824	ENSMUSG00000029320	1700016H13Rik	-	RIKEN cDNA 1700016H13 gene	protein-coding
mm_90084.1	chr10	116914002	116914020	+	1	NA	intron (NM_001003950, intron 7 of 9)	intron (NM_001003950, intron 7 of 9)	-17132	NM_001033333	237558	Mm.336386	NM_001033333	ENSMUSG00000034057	Myrfl	Gm239	myelin regulatory factor-like	protein-coding
mm_32395.1	chr4	106733884	106733898	+	1	NA	promoter-TSS (NM_146149)	promoter-TSS (NM_146149)	-24	NM_146149	230579	Mm.222956	NM_146149	ENSMUSG00000034871	Fam151a	2010309H15Rik	family with sequence simliarity 151, member A	protein-coding
mm_61147.1	chr7	57591194	57591203	+	1	NA	promoter-TSS (NM_008071)	promoter-TSS (NM_008071)	25	NM_008071	14402	Mm.8004	NM_008071	ENSMUSG00000033676	Gabrb3	A230092K12Rik|AW049585|Cp1|Gabrb-3|beta3	gamma-aminobutyric acid (GABA) A receptor, subunit beta 3	protein-coding
mm_116808.1	chr13	54219952	54219962	-	1	NA	intron (NM_001010973, intron 2 of 2)	intron (NM_001010973, intron 2 of 2)	27828	NM_008286	15466	Mm.57243	NM_008286	ENSMUSG00000034987	Hrh2	-	histamine receptor H2	protein-coding
mm_26273.1	chr3	142504829	142504838	+	1	NA	intron (NM_153564, intron 6 of 10)	intron (NM_153564, intron 6 of 10)	7899	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_110085.1	chr12	24767600	24767609	-	1	NA	Intergenic	RMER1C|Other|Other	59350	NM_009104	20135	Mm.99	NM_009104	ENSMUSG00000020649	Rrm2	AA407299|R2	ribonucleotide reductase M2	protein-coding
mm_125296.1	chr15	37007598	37007615	+	1	NA	promoter-TSS (NM_026521)	promoter-TSS (NM_026521)	-204	NM_026521	68036	Mm.371631	NM_026521	ENSMUSG00000062397	Zfp706	3110006P09Rik|AA793007|AW536850|C77232|Znf706	zinc finger protein 706	protein-coding
mm_172390.1	chr7	136810844	136810846	+	1	NA	Intergenic	Intergenic	-83766	NM_008598	17314	Mm.440219	NM_008598	ENSMUSG00000054612	Mgmt	AGT|AI267024|Agat	O-6-methylguanine-DNA methyltransferase	protein-coding
mm_100938.1	chr11	6522783	6522786	-	1	NA	Intergenic	Intergenic	-1826	NM_178440	246177	Mm.239554	NM_178440	ENSMUSG00000020437	Myo1g	E430002D17Rik	myosin IG	protein-coding
mm_121826.1	chr14	20479930	20479968	-	1	NA	5' UTR (NM_001110794, exon 1 of 13)	5' UTR (NM_001110794, exon 1 of 13)	184	NM_001110794	11750	Mm.280231	NM_009674	ENSMUSG00000021814	Anxa7	AI265384|AI316497|Anx7|synexin	annexin A7	protein-coding
mm_158632.1	chrX	153696164	153696182	-	1	NA	5' UTR (NM_175429, exon 1 of 3)	5' UTR (NM_175429, exon 1 of 3)	107	NM_175429	207474	Mm.271572	NM_175429	ENSMUSG00000041633	Kctd12b	9530071H11Rik|B430319H24Rik	potassium channel tetramerisation domain containing 12b	protein-coding
mm_73815.1	chr8	117401371	117401384	+	1	NA	intron (NM_028941, intron 3 of 20)	MTD|LTR|ERVL-MaLR	-51646	NR_106045	102466801		NR_106045	ENSMUSG00000099062	Mir7077	Gm27774|mmu-mir-7077	microRNA 7077	ncRNA
mm_152540.1	chr19	11330373	11330387	-	1	NA	intron (NM_001025610, intron 2 of 5)	intron (NM_001025610, intron 2 of 5)	4315	NM_001276398	109225	Mm.491251	NM_027836	ENSMUSG00000024672	Ms4a7	9130422I10Rik|A430103C15Rik|CD20l4|CFFMA	membrane-spanning 4-domains, subfamily A, member 7	protein-coding
mm_22863.1	chr3	28728830	28728841	+	1	NA	TTS (NM_031197)	TTS (NM_031197)	30932	NM_031197	20526	Mm.18443	NM_031197	ENSMUSG00000027690	Slc2a2	AI266973|Glut-2|Glut2	solute carrier family 2 (facilitated glucose transporter), member 2	protein-coding
mm_105823.1	chr11	113063200	113063208	-	1	NA	intron (NR_015556, intron 2 of 2)	intron (NR_015556, intron 2 of 2)	138634	NR_015556	72386	Mm.266961	NR_015556	ENSMUSG00000087259	2610035D17Rik	-	RIKEN cDNA 2610035D17 gene	ncRNA
mm_44687.1	chr5	30148017	30148025	-	1	NA	exon (NM_178878, exon 2 of 20)	exon (NM_178878, exon 2 of 20)	6959	NM_178878	97212	Mm.200497	NM_178878	ENSMUSG00000025745	Hadha	C77020|Mtpa	hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), alpha subunit	protein-coding
mm_86381.1	chr9	123851856	123851912	-	1	NA	promoter-TSS (NM_001110253)	promoter-TSS (NM_001110253)	15	NM_001110253	17281	Mm.252941	NM_148925	ENSMUSG00000025241	Fyco1	2810409M01Rik|Mem2|RUFY3|ZFYVE7	FYVE and coiled-coil domain containing 1	protein-coding
mm_43741.1	chr5	139912576	139912594	+	1	NA	intron (NM_175522, intron 1 of 1)	CpG	4642	NM_175522	243312	Mm.237102	NM_175522	ENSMUSG00000048988	Elfn1	A930017N06Rik|AI197272|Ppp1r28	leucine rich repeat and fibronectin type III, extracellular 1	protein-coding
mm_28838.1	chr3	96580188	96580203	-	1	NA	intron (NM_001293701, intron 4 of 6)	(TG)n|Simple_repeat|Simple_repeat	-13394	NR_040409	100038464	Mm.475126	NR_040409	ENSMUSG00000074398	Gm15441	ENSMUSG00000074398|OTTMUSG00000021867	predicted gene 15441	ncRNA
mm_86386.1	chr9	123931685	123931712	-	1	NA	Intergenic	L1M2|LINE|L1	36994	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_43746.1	chr5	140331899	140331939	+	1	NA	promoter-TSS (NM_026510)	promoter-TSS (NM_026510)	-3	NM_008637	17766	Mm.118846	NM_008637	ENSMUSG00000036639	Nudt1	Mth1	nudix (nucleoside diphosphate linked moiety X)-type motif 1	protein-coding
mm_147797.1	chr18	61657957	61657972	-	1	NA	intron (NR_045402, intron 1 of 4)	(TG)n|Simple_repeat|Simple_repeat	7574	NR_045402	328968	Mm.392305	NR_045402		Carmn	Carmen|E330013P06|Gm16908|Mir143hg	cardiac mesoderm enhancer-associated non-coding RNA	ncRNA
mm_159495.1	chr4	43000433	43000433	-	1	NA	promoter-TSS (NM_009503)	promoter-TSS (NM_009503)	74	NM_009503	269523	Mm.245976	NM_009503	ENSMUSG00000028452	Vcp	3110001E05|CDC48|p97|p97/VCP	valosin containing protein	protein-coding
mm_132797.1	chr16	45094037	45094041	+	1	NA	promoter-TSS (NM_026439)	promoter-TSS (NM_026439)	-14	NM_026439	67896	Mm.181074	NM_026439	ENSMUSG00000022665	Ccdc80	2610001E17Rik|DRO1|Ssg1|Urb	coiled-coil domain containing 80	protein-coding
mm_124956.1	chr15	12924006	12924015	+	1	NA	intron (NM_001130149, intron 29 of 34)	intron (NM_001130149, intron 29 of 34)	99195	NM_001130149	14000	Mm.293142	NM_026799	ENSMUSG00000022191	Drosha	1110013A17Rik|AI874853|Etohi2|Rn3|Rnasen	drosha, ribonuclease type III	protein-coding
mm_98434.1	chr11	94937904	94937946	+	1	NA	exon (NM_007742, exon 2 of 51)	exon (NM_007742, exon 2 of 51)	1701	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_127341.1	chr15	100599751	100599767	+	1	NA	intron (NM_001304965, intron 1 of 10)	CpG	225	NM_001304965	19009	Mm.28825	NM_010127	ENSMUSG00000009739	Pou6f1	2310038G18Rik|C79593|Emb|cns-1	POU domain, class 6, transcription factor 1	protein-coding
mm_39824.1	chr5	30797893	30797899	+	1	NA	3' UTR (NM_023047, exon 13 of 13)	3' UTR (NM_023047, exon 13 of 13)	-16745	NM_133350	100732	Mm.332295	NM_133350	ENSMUSG00000029166	Mapre3	AI790651|EB2|EB3|EBF3|RP3	microtubule-associated protein, RP/EB family, member 3	protein-coding
mm_153470.1	chr19	41273158	41273171	-	1	NA	Intergenic	Intergenic	-9160	NM_133352	107358	Mm.246440	NM_133352	ENSMUSG00000025016	Tm9sf3	1810073M23Rik|2810031D16Rik|AI115521|AI413748|AW146116|AW549777|Smbp|mKIAA4036	transmembrane 9 superfamily member 3	protein-coding
mm_156959.1	chrX	169989378	169989396	+	1	NA	3' UTR (NM_001290504, exon 10 of 10)	3' UTR (NM_001290504, exon 10 of 10)	-10470	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_77853.1	chr9	5309659	5309679	+	1	NA	intron (NM_007609, intron 1 of 8)	intron (NM_007609, intron 1 of 8)	820	NM_007609	12363	Mm.1569	NM_007609	ENSMUSG00000033538	Casp4	CASP-11|CASP-4|Casp11|Caspl|ich-3	caspase 4, apoptosis-related cysteine peptidase	protein-coding
mm_56749.1	chr6	115994829	115994857	-	1	NA	5' UTR (NM_026376, exon 1 of 36)	5' UTR (NM_026376, exon 1 of 36)	162	NM_026376	67784	Mm.3085	NM_026376	ENSMUSG00000030123	Plxnd1	6230425C21Rik|b2b1863Clo|b2b553Clo	plexin D1	protein-coding
mm_13402.1	chr2	103971560	103971562	+	1	NA	intron (NM_001142335, intron 2 of 3)	intron (NM_001142335, intron 2 of 3)	1274	NM_001142335	16909	Mm.29266	NM_008505	ENSMUSG00000032698	Lmo2	Rbtn-2|Rbtn2|Rhom-2|Ttg2	LIM domain only 2	protein-coding
mm_93350.1	chr10	100590414	100590426	-	1	NA	Intergenic	Intergenic	-1161	NM_175128	68281	Mm.268474	NM_175128	ENSMUSG00000046567	4930430F08Rik	4930571E09Rik|A730088G13Rik|AW551239|C430008C19Rik	RIKEN cDNA 4930430F08 gene	protein-coding
mm_162594.1	chr1	181446267	181446267	-	1	NA	intron (NM_028408, intron 3 of 5)	(TG)n|Simple_repeat|Simple_repeat	65184	NM_207280	403180	Mm.220754	NM_207280	ENSMUSG00000050625	Ccdc121	6530421E24Rik|Gm755	coiled-coil domain containing 121	protein-coding
mm_112125.1	chr12	112917640	112917647	-	1	NA	intron (NM_010588, intron 5 of 25)	intron (NM_010588, intron 5 of 25)	2898	NR_105906	102465567		NR_105906	ENSMUSG00000098338	Mir6941	Gm27923|mmu-mir-6941	microRNA 6941	ncRNA
mm_134280.1	chr16	14202102	14202110	-	1	NA	exon (NM_013607, exon 38 of 42)	exon (NM_013607, exon 38 of 42)	38831	NM_001114085	67203	Mm.24105	NM_023317	ENSMUSG00000022678	Nde1	2810027M15Rik|AU042936|AW822251|Nude|mNudE	nudE neurodevelopment protein 1	protein-coding
mm_15624.1	chr2	162661245	162661260	+	1	NA	promoter-TSS (NM_021464)	promoter-TSS (NM_021464)	89	NR_033569	77288	Mm.376571	NR_033569		9430021M05Rik	-	RIKEN cDNA 9430021M05 gene	ncRNA
mm_130393.1	chr15	97910623	97910641	-	1	NA	Intergenic	Intergenic	-2336	NM_009504	22337	Mm.245084	NM_009504	ENSMUSG00000022479	Vdr	Nr1i1	vitamin D receptor	protein-coding
mm_64139.1	chr7	141196851	141196858	+	1	NA	intron (NM_001172064, intron 2 of 12)	intron (NM_001172064, intron 2 of 12)	1711	NM_153777	70552	Mm.45104	NM_153777	ENSMUSG00000038637	Lrrc56	5730427C23Rik|BB110509|mFLJ00101	leucine rich repeat containing 56	protein-coding
mm_132073.1	chr16	30065643	30065653	+	1	NA	exon (NM_008235, exon 1 of 4)	exon (NM_008235, exon 1 of 4)	291	NM_008235	15205	Mm.390859	NM_008235	ENSMUSG00000022528	Hes1	Hry|bHLHb39	hairy and enhancer of split 1 (Drosophila)	protein-coding
mm_117803.1	chr13	97435922	97435959	-	1	NA	intron (NR_110432, intron 1 of 1)	intron (NR_110432, intron 1 of 1)	970	NR_110432	100039691	Mm.219358	NR_110430	ENSMUSG00000078952	Lncenc1	ENSMUSG00000078952|Gm11019|Gm2373|Lincenc1|Platr18|linc-Enc1	long non-coding RNA, embryonic stem cells expressed 1	ncRNA
mm_162650.1	chr1	195241650	195241655	+	1	NA	Intergenic	CpG	-64937	NM_007758	12902	Mm.235387	NM_007758	ENSMUSG00000026616	Cr2	C3DR|CD21|CD35|Cr-1|Cr-2|Cr1	complement receptor 2	protein-coding
mm_33944.1	chr4	137146699	137146702	+	1	NA	Intergenic	Intergenic	18366	NR_040443	100503595	Mm.421314	NR_040443	ENSMUSG00000085833	Gm13003	OTTMUSG00000009822	predicted gene 13003	ncRNA
mm_156895.1	chrX	167201585	167201620	+	1	NA	Intergenic	Intergenic	7616	NM_021278	19241	Mm.142729	NM_021278	ENSMUSG00000049775	Tmsb4x	Ptmb4|Tb4	thymosin, beta 4, X chromosome	protein-coding
mm_138697.1	chr17	35980447	35980455	+	1	NA	promoter-TSS (NM_001282025)	promoter-TSS (NM_001282025)	496	NM_008136	14670	Mm.335754	NM_008136	ENSMUSG00000024429	Gnl1	Gna-rs1|Gnal1	guanine nucleotide binding protein-like 1	protein-coding
mm_87579.1	chr10	56389791	56389798	+	1	NA	3' UTR (NM_010288, exon 2 of 2)	3' UTR (NM_010288, exon 2 of 2)	12494	NM_010288	14609	Mm.378921	NM_010288	ENSMUSG00000050953	Gja1	AU042049|AW546267|Cnx43|Cx43|Cx43alpha1|Gja-1|Npm1|connexin43	gap junction protein, alpha 1	protein-coding
mm_119954.1	chr14	55055850	55055875	+	1	NA	Intergenic	Intergenic	-17229	NR_004444	432855	Mm.490799	NR_004444	ENSMUSG00000093452	Zfhx2os	Zfhx2as	zinc finger homeobox 2, opposite strand	ncRNA
mm_22277.1	chr2	179806688	179806696	-	1	NA	intron (NM_001316723, intron 4 of 5)	intron (NM_001316723, intron 4 of 5)	169954	NM_001081092	228980	Mm.235542	NM_001081092	ENSMUSG00000039117	Taf4	135kDa|AI450312|TAFII130|TAFII135|Taf2c1|Taf4a	TATA-box binding protein associated factor 4	protein-coding
mm_43026.1	chr5	123909125	123909133	+	1	NA	intron (NM_026603, intron 2 of 7)	B4A|SINE|B4	1854	NM_026603	68184	Mm.28549	NM_026603	ENSMUSG00000023106	Denr	1500003K04Rik	density-regulated protein	protein-coding
mm_37938.1	chr4	132922628	132922631	-	1	NA	promoter-TSS (NM_145553)	promoter-TSS (NM_145553)	-78	NM_001163792	230789	Mm.11473	NM_145553	ENSMUSG00000028878	Fam76a	-	family with sequence similarity 76, member A	protein-coding
mm_54836.1	chr6	42586270	42586280	-	1	NA	TTS (NM_203396)	TTS (NM_203396)	11097	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_159551.1	chr4	102587574	102587574	+	1	NA	promoter-TSS (NM_001177982)	promoter-TSS (NM_001177982)	16	NM_001177982	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_122708.1	chr14	52197217	52197267	-	1	NA	promoter-TSS (NM_033618)	promoter-TSS (NM_033618)	-3	NM_033618	114741	Mm.21662	NM_033618	ENSMUSG00000035726	Supt16	Cdc68|Fact140|Spt16|Supt16h	suppressor of Ty 16	protein-coding
mm_101667.1	chr11	36831694	36831712	-	1	NA	intron (NM_011856, intron 2 of 28)	intron (NM_011856, intron 2 of 28)	112538	NM_001290702	23964	Mm.439889	NM_011856	ENSMUSG00000049336	Tenm2	Odz2|Odz3|Ten-2|Ten-m2	teneurin transmembrane protein 2	protein-coding
mm_80504.1	chr9	78615739	78615743	+	1	NA	5' UTR (NM_153098, exon 1 of 33)	5' UTR (NM_153098, exon 1 of 33)	195	NM_153098	235505	Mm.32955	NM_153098	ENSMUSG00000046186	Cd109	9930012E15Rik|AI480638|GARP	CD109 antigen	protein-coding
mm_34490.1	chr4	148591483	148591546	+	1	NA	promoter-TSS (NM_009272)	promoter-TSS (NM_009272)	1	NM_009272	20810	Mm.10	NM_009272	ENSMUSG00000006442	Srm	AA407669|SpdST|SpdSy	spermidine synthase	protein-coding
mm_107220.1	chr12	26469907	26469981	+	1	NA	exon (NM_020557, exon 1 of 5)	exon (NM_020557, exon 1 of 5)	729	NM_020557	22169	Mm.271839	NM_020557	ENSMUSG00000020638	Cmpk2	1200004E04Rik|TDKI|Tyki	cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial	protein-coding
mm_78295.1	chr9	22409009	22409019	+	1	NA	Intergenic	Intergenic	-2563	NM_026739	68283	Mm.280669	NM_026739	ENSMUSG00000036411	9530077C05Rik	1110003N12Rik|Kiaa0895|mKIAA0895	RIKEN cDNA 9530077C05 gene	protein-coding
mm_49152.1	chr6	12019832	12019834	+	1	NA	intron (NM_001168382, intron 16 of 17)	B4|SINE|B4	89747	NR_003631	625347	Mm.389084	NM_001039041	ENSMUSG00000057223	Gm6578	EG625347	mitochondrial ribosomal protein L32 pseudogene	pseudo
mm_117652.1	chr13	93093756	93093777	-	1	NA	exon (NM_023821, exon 2 of 13)	exon (NM_023821, exon 2 of 13)	-1067	NR_046182	408254	Mm.474857	NR_046182		A630019I02Rik	-	RIKEN cDNA A630019I02 gene	ncRNA
mm_130986.1	chr15	103366528	103366579	-	1	NA	5' UTR (NM_010577, exon 1 of 30)	5' UTR (NM_010577, exon 1 of 30)	238	NM_010577	16402	Mm.16234	NM_010577	ENSMUSG00000000555	Itga5	Cd49e|Fnra|VLA5	integrin alpha 5 (fibronectin receptor alpha)	protein-coding
mm_163900.1	chr14	29479436	29479437	+	1	NA	intron (NM_009785, intron 3 of 37)	intron (NM_009785, intron 3 of 37)	242428	NM_009785	12294	Mm.386754	NM_009785	ENSMUSG00000021991	Cacna2d3	Cacnad3|alapha2delta3	calcium channel, voltage-dependent, alpha2/delta subunit 3	protein-coding
mm_95283.1	chr11	45890693	45890702	+	1	NA	exon (NM_001045520, exon 6 of 12)	exon (NM_001045520, exon 6 of 12)	38733	NM_001045520	216705	Mm.169673	NM_001045520	ENSMUSG00000006169	Clint1	AI642036|AW537616|C530049I24Rik|Enth|Epn4|F630206G17Rik|mKIAA0171	clathrin interactor 1	protein-coding
mm_37836.1	chr4	132049059	132049156	-	1	NA	promoter-TSS (NM_001128606)	promoter-TSS (NM_001128606)	-29	NM_001128606	269587	Mm.30038	NM_183428	ENSMUSG00000028906	Epb41	4.1R|AI415518|D4Ertd442e|Elp-1|Elp1|Epb4.1|mKIAA4056	erythrocyte membrane protein band 4.1	protein-coding
mm_20111.1	chr2	121140623	121140632	-	1	NA	promoter-TSS (NM_177846)	promoter-TSS (NM_177846)	71	NM_177846	329504	Mm.219449	NM_177846	ENSMUSG00000074890	Lcmt2	D330024M17|Tyw4	leucine carboxyl methyltransferase 2	protein-coding
mm_75413.1	chr8	46502843	46502849	-	1	NA	intron (NM_001302163, intron 2 of 20)	intron (NM_001302163, intron 2 of 20)	11880	NM_001302163	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_164292.1	chr15	103895913	103895934	-	1	NA	TTS (NM_009267)	TTS (NM_009267)	3377	NM_009268	20771	Mm.30276	NM_009268		Mucl1	Spt-2|Spt2	mucin-like 1	protein-coding
mm_62129.1	chr7	96958121	96958148	+	1	NA	exon (NM_153591, exon 3 of 14)	exon (NM_153591, exon 3 of 14)	6607	NM_153591	244141	Mm.274864	NM_153591	ENSMUSG00000018995	Nars2	AI875199	asparaginyl-tRNA synthetase 2 (mitochondrial)(putative)	protein-coding
mm_58893.1	chr7	17093696	17093698	+	1	NA	exon (NM_007676, exon 3 of 5)	exon (NM_007676, exon 3 of 5)	19657	NM_007676	26436	Mm.143686	NM_007676	ENSMUSG00000066760	Psg16	Cea11|PSG|bCEA	pregnancy specific glycoprotein 16	protein-coding
mm_160803.1	chr11	6395145	6395145	+	1	NA	promoter-TSS (NM_028601)	promoter-TSS (NM_028601)	20	NM_028601	52915	Mm.1144	NM_028601	ENSMUSG00000041164	Zmiz2	Zimp7	zinc finger, MIZ-type containing 2	protein-coding
mm_89729.1	chr10	98945680	98945684	+	1	NA	intron (NM_026482, intron 1 of 20)	T-rich|Low_complexity|Low_complexity	30530	NM_026482	67972	Mm.166944	NM_026482	ENSMUSG00000019943	Atp2b1	2810442I22Rik|E130111D10Rik|Pmca1	ATPase, Ca++ transporting, plasma membrane 1	protein-coding
mm_36127.1	chr4	58987096	58987116	-	1	NA	promoter-TSS (NM_025968)	promoter-TSS (NM_025968)	-28	NM_025968	67103	Mm.34497	NM_025968	ENSMUSG00000028378	Ptgr1	2510002C21Rik|Ltb4dh|Zadh3	prostaglandin reductase 1	protein-coding
mm_43202.1	chr5	129096717	129096726	+	1	NA	promoter-TSS (NM_001081342)	promoter-TSS (NM_001081342)	-29	NM_001081342	243277	Mm.440501	NM_177734	ENSMUSG00000044017	Adgrd1	E230012M21Rik|Gpr133	adhesion G protein-coupled receptor D1	protein-coding
mm_97995.1	chr11	84129726	84129732	+	1	NA	promoter-TSS (NM_172562)	promoter-TSS (NM_172562)	-161	NM_172562	217031	Mm.45159	NM_172562	ENSMUSG00000018651	Tada2a	AV319371|D030022J10Rik|Tada2l	transcriptional adaptor 2A	protein-coding
mm_76693.1	chr8	94178766	94178803	-	1	NA	promoter-TSS (NM_013602)	promoter-TSS (NM_013602)	-305	NM_013602	17748	Mm.192991	NM_013602	ENSMUSG00000031765	Mt1	MT-I|Mt-1	metallothionein 1	protein-coding
mm_164898.1	chr18	65970228	65970232	-	1	NA	promoter-TSS (NM_145493)	promoter-TSS (NM_145493)	-52	NM_145493	225644	Mm.192285	NM_145493	ENSMUSG00000024519	Cplx4	A930004D23Rik|CPXIV|Gm957	complexin 4	protein-coding
mm_9508.1	chr1	173738187	173738200	-	1	NA	intron (NM_001204910, intron 1 of 7)	intron (NM_001204910, intron 1 of 7)	3616	NM_001204910	226691	Mm.440876	NM_001204910	ENSMUSG00000073490	Ifi207	AI607873|Pyhin-A	interferon activated gene 207	protein-coding
mm_145796.1	chr18	65247183	65247194	+	1	NA	intron (NR_105742, intron 4 of 6)	intron (NR_105742, intron 4 of 6)	-1673	NR_029600	387231		NR_029600	ENSMUSG00000065402	Mir122	Mir122a|Mirn122a|mir-122|mmu-mir-122	microRNA 122	ncRNA
mm_108051.1	chr12	73910086	73910119	+	1	NA	intron (NM_010431, intron 1 of 14)	intron (NM_010431, intron 1 of 14)	2235	NM_001313919	15251	Mm.3879	NM_010431	ENSMUSG00000021109	Hif1a	AA959795|HIF-1-alpha|HIF1-alpha|HIF1alpha|MOP1|bHLHe78	hypoxia inducible factor 1, alpha subunit	protein-coding
mm_28637.1	chr3	95217932	95217989	-	1	NA	promoter-TSS (NM_172512)	promoter-TSS (NM_172512)	-18	NM_029885	213054	Mm.224820	NM_029885	ENSMUSG00000038766	Gabpb2	1810015F01Rik|5830427M07|9430006E19Rik|A430024B14Rik|AV050852|Gabpb2-1	GA repeat binding protein, beta 2	protein-coding
mm_19009.1	chr2	76894731	76894743	-	1	NA	exon (NM_011652, exon 65 of 313)	exon (NM_011652, exon 65 of 313)	87810	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_101486.1	chr11	31370067	31370080	-	1	NA	promoter-TSS (NM_011491)	promoter-TSS (NM_011491)	-12	NM_011491	20856	Mm.32506	NM_011491	ENSMUSG00000020303	Stc2	AW125853|Stc2l|mustc2	stanniocalcin 2	protein-coding
mm_93471.1	chr10	111164631	111164678	-	1	NA	promoter-TSS (NM_001003717)	promoter-TSS (NM_001003717)	-148	NM_001003717	237542	Mm.220204	NM_175489	ENSMUSG00000020189	Osbpl8	AA536976|AA536995|C730029P18Rik|D330025H14Rik|ORP-8	oxysterol binding protein-like 8	protein-coding
mm_40244.1	chr5	38039225	38039299	+	1	NA	promoter-TSS (NM_026959)	promoter-TSS (NM_026959)	32	NM_026959	71116	Mm.18959	NM_026959	ENSMUSG00000029125	Stx18	1810035L21Rik|4933425D03Rik|AU041562	syntaxin 18	protein-coding
mm_88865.1	chr10	80940216	80940226	+	1	NA	Intergenic	Intergenic	10130	NM_008655	17873	Mm.1360	NM_008655	ENSMUSG00000015312	Gadd45b	AI323528|Myd118	growth arrest and DNA-damage-inducible 45 beta	protein-coding
mm_66321.1	chr7	41560813	41560836	-	1	NA	Intergenic	Intergenic	-60934	NM_001033530	101835	Mm.370336	NM_001033530	ENSMUSG00000074166	AW146154	AI451288	expressed sequence AW146154	protein-coding
mm_87670.1	chr10	58812476	58812495	+	1	NA	promoter-TSS (NM_172788)	promoter-TSS (NM_172788)	-874	NM_172788	237353	Mm.333078	NM_172788	ENSMUSG00000037990	Sh3rf3	4831416G18Rik|Igfbp5-ip|Sh3md4|Sh3rf31	SH3 domain containing ring finger 3	protein-coding
mm_43229.1	chr5	129908539	129908593	+	1	NA	promoter-TSS (NM_026916)	promoter-TSS (NM_026916)	26	NM_026916	69034	Mm.211372	NM_026916	ENSMUSG00000095789	Nupr1l	1810010E01Rik|4930579G22Rik|Nupr2	nuclear protein transcriptional regulator 1 like	protein-coding
mm_12113.1	chr2	61593424	61593444	+	1	NA	intron (NM_001164072, intron 1 of 7)	CpG	337	NM_001164071	21353	Mm.244393	NM_011529	ENSMUSG00000064289	Tank	C86182|E430026L09Rik|I-TRAF	TRAF family member-associated Nf-kappa B activator	protein-coding
mm_28154.1	chr3	87748578	87748598	-	1	NA	promoter-TSS (NM_028971)	promoter-TSS (NM_028971)	35	NM_028971	74485	Mm.474494	NM_028971	ENSMUSG00000023084	Lrrc71	4933430H15Rik	leucine rich repeat containing 71	protein-coding
mm_108210.1	chr12	76920745	76920757	+	1	NA	3' UTR (NM_145927, exon 12 of 12)	3' UTR (NM_145927, exon 12 of 12)	41497	NM_008558	17187	Mm.268548	NM_008558	ENSMUSG00000059436	Max	AA960152|AI875693|bHLHd4|bHLHd5|bHLHd6|bHLHd7|bHLHd8	Max protein	protein-coding
mm_123166.1	chr14	57306221	57306225	-	1	NA	intron (NM_030004, intron 4 of 7)	B1_Mur1|SINE|Alu	92260	NM_030004	68631	Mm.25539	NM_030004	ENSMUSG00000021947	Cryl1	1110025H08Rik|A230106J09Rik|C85932|gul3dh	crystallin, lambda 1	protein-coding
mm_84176.1	chr9	59949697	59949706	-	1	NA	intron (NM_013708, intron 1 of 7)	intron (NM_013708, intron 1 of 7)	378	NM_013708	23958	Mm.103641	NM_013708	ENSMUSG00000032292	Nr2e3	A930035N01Rik|PNR|RNR|rd7	nuclear receptor subfamily 2, group E, member 3	protein-coding
mm_152116.1	chr19	6980421	6980481	-	1	NA	promoter-TSS (NM_001166368)	promoter-TSS (NM_001166368)	10	NM_001166368	14227	Mm.4234	NM_008020	ENSMUSG00000056629	Fkbp2	13kDa|FKBP-2|mFKBP13|mFKBP2	FK506 binding protein 2	protein-coding
mm_110858.1	chr12	73409544	73409588	-	1	NA	promoter-TSS (NR_046013)	promoter-TSS (NR_046013)	-3	NR_046013	380765	Mm.490476	NR_046013		D830013O20Rik	Gm891	RIKEN cDNA D830013O20 gene	ncRNA
mm_80842.1	chr9	98032885	98032901	+	1	NA	exon (NM_022319, exon 1 of 18)	exon (NM_022319, exon 1 of 18)	274	NM_022319	64085	Mm.440903	NM_022319	ENSMUSG00000032452	Clstn2	2900042C18Rik|AI448973|CSTN2|Cs2|Cst-2|mKIAA4134	calsyntenin 2	protein-coding
mm_129908.1	chr15	84090644	84090672	-	1	NA	exon (NM_013873, exon 3 of 7)	exon (NM_013873, exon 3 of 7)	15096	NM_013873	29859	Mm.248796	NM_013873	ENSMUSG00000018865	Sult4a1	2400007A17Rik|AI853543|BR-STL-1|ST4A1|Sultx3	sulfotransferase family 4A, member 1	protein-coding
mm_65847.1	chr7	29248512	29248533	-	1	NA	promoter-TSS (NM_028179)	promoter-TSS (NM_028179)	-55	NM_028179	72275	Mm.441142	NM_028179	ENSMUSG00000030587	2200002D01Rik	2010005J02Rik|H2RSP|IMUP|IMUP-1|IMUP-2	RIKEN cDNA 2200002D01 gene	protein-coding
mm_96358.1	chr11	67052711	67052721	+	1	NA	promoter-TSS (NM_025510)	promoter-TSS (NM_025510)	46	NM_001040026	52892	Mm.129731	NM_001040026	ENSMUSG00000069844	Sco1	2610001C07Rik|D11Bwg1310e	SCO1 cytochrome c oxidase assembly protein	protein-coding
mm_143836.1	chr17	84115368	84115374	-	1	NA	Intergenic	Intergenic	36711	NR_045458	74473	Mm.399575	NR_045458		4933433H22Rik	-	RIKEN cDNA 4933433H22 gene	ncRNA
mm_136927.1	chr17	13874479	13874500	+	1	NA	intron (NM_010806, intron 22 of 32)	intron (NM_010806, intron 22 of 32)	-73884	NM_001122977	635895	Mm.388844	NM_001122977	ENSMUSG00000067941	Gm7168	EG635895	predicted gene 7168	protein-coding
mm_16296.1	chr2	174285298	174285319	+	1	NA	exon (NM_022000, exon 2 of 13)	exon (NM_022000, exon 2 of 13)	988	NM_022000	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_117488.1	chr13	78183146	78183176	-	1	NA	Intergenic	Intergenic	13288	NM_001347538	13865	Mm.439653	NM_010151	ENSMUSG00000069171	Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR-3|EAR3|Erbal3|SVP44|Tcfcoup1	nuclear receptor subfamily 2, group F, member 1	protein-coding
mm_53758.1	chr6	145616037	145616041	+	1	NA	promoter-TSS (NM_009449)	promoter-TSS (NM_009449)	76	NM_009449	22147	Mm.270295	NM_009449	ENSMUSG00000067338	Tuba3b	M[a]7|Tuba7	tubulin, alpha 3B	protein-coding
mm_112711.1	chr13	19177906	19177930	+	1	NA	Intergenic	Intergenic	217895	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_127740.1	chr15	103299355	103299388	+	1	NA	3' UTR (NM_019817, exon 9 of 9)	3' UTR (NM_019817, exon 9 of 9)	11067	NM_030720	80910	Mm.160369	NM_030720	ENSMUSG00000063234	Gpr84	EX33	G protein-coupled receptor 84	protein-coding
mm_56795.1	chr6	116647866	116647868	-	1	NA	intron (NM_178045, intron 3 of 10)	intron (NM_178045, intron 3 of 10)	-1820	NR_106010	102466793		NR_106010	ENSMUSG00000098334	Mir7043	Gm27776|mmu-mir-7043	microRNA 7043	ncRNA
mm_102104.1	chr11	52997397	52997418	-	1	NA	intron (NM_177059, intron 3 of 15)	intron (NM_177059, intron 3 of 15)	122649	NR_046047	790909	Mm.404626	NR_046047	ENSMUSG00000087668	Gm11186	OTTMUSG00000000039	predicted gene 11186	ncRNA
mm_13223.1	chr2	97467477	97467505	+	1	NA	promoter-TSS (NM_178725)	promoter-TSS (NM_178725)	-166	NM_001289744	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_165809.1	chr3	145160155	145160157	+	1	NA	Intergenic	RMER15|LTR|ERVL	41556	NM_025714	52184	Mm.259105	NM_025714	ENSMUSG00000028256	Odf2l	4733401D09Rik|9630045K08Rik|D3Ertd250e	outer dense fiber of sperm tails 2-like	protein-coding
mm_100362.1	chr11	118490119	118490120	+	1	NA	TTS (NM_172573)	TTS (NM_172573)	13159	NM_172573	217364	Mm.473963	NM_172573	ENSMUSG00000033857	Engase	C130099A03|D230014K01Rik	endo-beta-N-acetylglucosaminidase	protein-coding
mm_114061.1	chr13	54371528	54371532	+	1	NA	5' UTR (NM_009946, exon 1 of 4)	5' UTR (NM_009946, exon 1 of 4)	181	NM_009946	12890	Mm.268902	NM_009946	ENSMUSG00000025867	Cplx2	921-L|AI413745|AW492120	complexin 2	protein-coding
mm_72299.1	chr8	75770903	75770904	+	1	NA	intron (NM_001164235, intron 12 of 13)	intron (NM_001164235, intron 12 of 13)	322209	NM_001164235	71831	Mm.443238	NM_027944	ENSMUSG00000031620	1700007B14Rik	-	RIKEN cDNA 1700007B14 gene	protein-coding
mm_32865.1	chr4	118428797	118428816	+	1	NA	promoter-TSS (NM_001039176)	promoter-TSS (NM_001039176)	713	NM_019422	54325	Mm.282096	NM_019422	ENSMUSG00000006390	Elovl1	AA407424|BB151133|Ssc1	elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 1	protein-coding
mm_153480.1	chr19	41276809	41276852	-	1	NA	intron (NM_031376, intron 16 of 16)	intron (NM_031376, intron 16 of 16)	-12826	NM_133352	107358	Mm.246440	NM_133352	ENSMUSG00000025016	Tm9sf3	1810073M23Rik|2810031D16Rik|AI115521|AI413748|AW146116|AW549777|Smbp|mKIAA4036	transmembrane 9 superfamily member 3	protein-coding
mm_57578.1	chr6	127149638	127149650	-	1	NA	promoter-TSS (NR_040275)	promoter-TSS (NR_040275)	18	NR_040273	77558	Mm.358918	NR_040273	ENSMUSG00000097166	9330179D12Rik	-	RIKEN cDNA 9330179D12 gene	ncRNA
mm_109612.1	chr12	112731210	112731218	+	1	NA	intron (NM_001024602, intron 2 of 18)	intron (NM_001024602, intron 2 of 18)	-2108	NR_105905	102466989		NR_105905	ENSMUSG00000099165	Mir6940	Gm27655|mmu-mir-6940	microRNA 6940	ncRNA
mm_91006.1	chr10	14545645	14545677	-	1	NA	promoter-TSS (NM_001002268)	promoter-TSS (NM_001002268)	-625	NM_001002268	215798	Mm.440142	NM_001002268	ENSMUSG00000039116	Adgrg6	1190004A11Rik|AI449247|AW045736|DREG|Gm222|Gpr126	adhesion G protein-coupled receptor G6	protein-coding
mm_72579.1	chr8	84200861	84200875	+	1	NA	Intergenic	GC_rich|Low_complexity|Low_complexity	-7650	NR_029740	387216		NR_029740	ENSMUSG00000065611	Mir23a	Mirn23a|mir-23a|mmu-mir-23a	microRNA 23a	ncRNA
mm_34545.1	chr4	149539865	149539878	+	1	NA	5' UTR (NM_023465, exon 2 of 5)	5' UTR (NM_023465, exon 2 of 5)	2008	NR_049189	100885828		NR_049189	ENSMUSG00000093403	Mir5616	Gm25191|mir-5616|mmu-mir-5616	microRNA 5616	ncRNA
mm_1950.1	chr1	86356394	86356427	+	1	NA	promoter-TSS (NR_002851)	promoter-TSS (NR_002851)	-83	NR_002851	80828		NR_002851	ENSMUSG00000064823	Snord82	Rnu82|U82|Z25	small nucleolar RNA, C/D box 82	snoRNA
mm_41035.1	chr5	86071735	86071756	+	1	NA	promoter-TSS (NM_019992)	promoter-TSS (NM_019992)	-1	NM_019992	56792	Mm.131237	NM_019992	ENSMUSG00000029254	Stap1	AI586015|Brdg1|STAP-1	signal transducing adaptor family member 1	protein-coding
mm_13571.1	chr2	112284562	112284610	+	1	NA	promoter-TSS (NM_133648)	promoter-TSS (NM_133648)	-102	NM_133648	107723	Mm.491155	NM_133648	ENSMUSG00000027130	Slc12a6	9530023I19Rik|KCC3|gaxp	solute carrier family 12, member 6	protein-coding
mm_75280.1	chr8	41016296	41016321	-	1	NA	intron (NM_001005863, intron 6 of 13)	intron (NM_001005863, intron 6 of 13)	-1160	NR_015457	78849	Mm.440930	NR_015457	ENSMUSG00000084960	B430010I23Rik	-	RIKEN cDNA B430010I23 gene	ncRNA
mm_5242.1	chr1	16294893	16294897	-	1	NA	intron (NM_001111272, intron 11 of 12)	intron (NM_001111272, intron 11 of 12)	189013	NM_133832	98711	Mm.274376	NM_133832	ENSMUSG00000025921	Rdh10	3110069K09Rik|4921506A21Rik|AI875664|AW549993|D1Ertd762e|m366Asp	retinol dehydrogenase 10 (all-trans)	protein-coding
mm_128960.1	chr15	74799890	74799900	-	1	NA	promoter-TSS (NM_029627)	promoter-TSS (NM_029627)	73	NM_029627	76486	Mm.273319	NM_029627	ENSMUSG00000044678	Ly6k	2410015A16Rik|3110035B01Rik|mLy-6K	lymphocyte antigen 6 complex, locus K	protein-coding
mm_135407.1	chr16	44746311	44746319	-	1	NA	promoter-TSS (NM_025332)	promoter-TSS (NM_025332)	48	NM_001159329	66067	Mm.34520	NM_025332	ENSMUSG00000022668	Gtpbp8	0610037H22Rik	GTP-binding protein 8 (putative)	protein-coding
mm_25756.1	chr3	123447119	123447155	+	1	NA	5' UTR (NM_008939, exon 1 of 11)	5' UTR (NM_008939, exon 1 of 11)	224	NM_008939	19142	Mm.9431	NM_008939	ENSMUSG00000027978	Prss12	Bssp-3|motopsin	protease, serine 12 neurotrypsin (motopsin)	protein-coding
mm_28184.1	chr3	88027466	88027500	-	1	NA	promoter-TSS (NM_022031)	promoter-TSS (NM_022031)	28	NM_022031	73940	Mm.294467	NM_022031	ENSMUSG00000004894	Hapln2	4930401E20Rik|Bral1	hyaluronan and proteoglycan link protein 2	protein-coding
mm_123511.1	chr14	66236365	66236377	-	1	NA	intron (NM_001162365, intron 1 of 30)	RMER5|LTR|ERV1	-22819	NM_001162366	19229	Mm.21613	NM_172498	ENSMUSG00000059456	Ptk2b	CADTK|CAKB|CAKbeta|E430023O05Rik|FADK2|FAK2|PYK2|Raftk	PTK2 protein tyrosine kinase 2 beta	protein-coding
mm_142525.1	chr17	46407498	46407524	-	1	NA	intron (NM_207671, intron 6 of 9)	intron (NM_207671, intron 6 of 9)	-21431	NM_053250	114570	Mm.25168	NM_053250	ENSMUSG00000023968	Crip3	TLP|TLP-A|TLP-B|Tlmp	cysteine-rich protein 3	protein-coding
mm_72900.1	chr8	90876567	90876579	+	1	NA	intron (NM_177224, intron 2 of 39)	intron (NM_177224, intron 2 of 39)	47738	NM_177224	109151	Mm.100615	NM_177224	ENSMUSG00000056608	Chd9	1810014J18Rik|9030205D12Rik|A330063D19Rik|AD013|PRIC320|mKIAA0308	chromodomain helicase DNA binding protein 9	protein-coding
mm_108698.1	chr12	86947432	86947481	+	1	NA	5' UTR (NM_173735, exon 1 of 4)	5' UTR (NM_173735, exon 1 of 4)	113	NM_001289432	217732	Mm.22337	NM_173735	ENSMUSG00000034157	Cipc	2310044G17Rik|AI842544|AI853744|Kiaa1737|mKIAA1737	CLOCK interacting protein, circadian	protein-coding
mm_50136.1	chr6	41542950	41542972	+	1	NA	Intergenic	Intergenic	21185	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_165316.1	chr2	103566286	103566286	+	1	NA	promoter-TSS (NM_178890)	promoter-TSS (NM_178890)	-24	NM_178890	99382	Mm.35850	NM_178890	ENSMUSG00000032724	Abtb2	AW539457|BPOZ-2	ankyrin repeat and BTB (POZ) domain containing 2	protein-coding
mm_153724.1	chr19	44407554	44407569	-	1	NA	5' UTR (NM_009127, exon 1 of 6)	5' UTR (NM_009127, exon 1 of 6)	148	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_6266.1	chr1	69547878	69547890	-	1	NA	intron (NM_011770, intron 6 of 7)	intron (NM_011770, intron 6 of 7)	138076	NM_011770	22779	Mm.106343	NM_011770	ENSMUSG00000025997	Ikzf2	A730095J18Rik|Helios|Zfpn1a2|Znfn1a2	IKAROS family zinc finger 2	protein-coding
mm_155412.1	chrX	73483626	73483644	+	1	NA	promoter-TSS (NM_007542)	promoter-TSS (NM_007542)	34	NM_007542	12111	Mm.2608	NM_007542	ENSMUSG00000031375	Bgn	BG|DSPG1|PG-S1|PGI|SLRR1A	biglycan	protein-coding
mm_156944.1	chrX	169979101	169979124	+	1	NA	promoter-TSS (NR_029457)	promoter-TSS (NR_029457)	-195	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_137512.1	chr17	27057341	27057356	+	1	NA	promoter-TSS (NM_080553)	promoter-TSS (NM_080553)	44	NM_080553	16440	Mm.458106	NM_080553	ENSMUSG00000042644	Itpr3	IP3R 3|Ip3r3|Itpr-3|tf	inositol 1,4,5-triphosphate receptor 3	protein-coding
mm_72064.1	chr8	71469227	71469258	+	1	NA	promoter-TSS (NM_025600)	promoter-TSS (NM_025600)	48	NR_122114	66498	Mm.260360	NM_025600	ENSMUSG00000074247	Dda1	1500034J01Rik|1700095J19Rik|R74921	DET1 and DDB1 associated 1	protein-coding
mm_72724.1	chr8	85057223	85057268	+	1	NA	3' UTR (NM_145390, exon 25 of 25)	3' UTR (NM_145390, exon 25 of 25)	-2874	NM_026791	68628	Mm.374815	NM_026791	ENSMUSG00000008167	Fbxw9	1110017H11Rik|Fbw9	F-box and WD-40 domain protein 9	protein-coding
mm_100196.1	chr11	116752651	116752669	+	1	NA	intron (NR_003364, intron 1 of 3)	intron (NR_003364, intron 1 of 3)	493	NR_003364	193217	Mm.100084	NR_003364		BC018473	-	cDNA sequence BC018473	ncRNA
mm_86462.1	chr10	4387182	4387205	+	1	NA	intron (NM_001033466, intron 1 of 2)	CpG	915	NM_001033466	381990	Mm.262466	NM_001033466	ENSMUSG00000075327	Zbtb2	Gm1103	zinc finger and BTB domain containing 2	protein-coding
mm_44418.1	chr5	18360385	18360473	-	1	NA	promoter-TSS (NM_010305)	promoter-TSS (NM_010305)	-16	NM_010305	14677	Mm.254629	NM_010305	ENSMUSG00000057614	Gnai1	AU046200|Gialpha1|Gnai-1	guanine nucleotide binding protein (G protein), alpha inhibiting 1	protein-coding
mm_159169.1	chr2	93462930	93462930	-	1	NA	promoter-TSS (NM_007656)	promoter-TSS (NM_007656)	20	NM_001271431	12521	Mm.4261	NM_007656	ENSMUSG00000027215	Cd82	AA682076|AL023070|C33|IA4|Kai1|Tspan27	CD82 antigen	protein-coding
mm_84519.1	chr9	67043744	67043820	-	1	NA	promoter-TSS (NM_001164256)	promoter-TSS (NM_001164256)	89	NM_001164252	22003	Mm.121878	NM_024427	ENSMUSG00000032366	Tpm1	AA986836|AI854628|TM2|Tm3|Tmpa|Tpm-1|alpha-TM	tropomyosin 1, alpha	protein-coding
mm_170447.1	chr18	83700885	83700885	+	1	NA	Intergenic	IAPLTR1_Mm|LTR|ERVK	-375001	NR_045361	70960	Mm.410834	NR_045361		4921531P14Rik	1700108N05Rik	RIKEN cDNA 4921531P14 gene	ncRNA
mm_83778.1	chr9	52141731	52141747	-	1	NA	intron (NM_001162921, intron 2 of 5)	intron (NM_001162921, intron 2 of 5)	26116	NR_105750	102465150		NR_105750	ENSMUSG00000099311	Mir6244	Gm27368|mmu-mir-6244	microRNA 6244	ncRNA
mm_127081.1	chr15	97471740	97471748	+	1	NA	Intergenic	RMER17C|LTR|ERVK	-224457	NM_001164602	105827	Mm.24005	NM_178114	ENSMUSG00000048218	Amigo2	AI415330|AMIGO-2|AW208913|Ali1	adhesion molecule with Ig like domain 2	protein-coding
mm_94017.1	chr10	127661654	127661667	-	1	NA	TTS (NM_009284)	TTS (NM_009284)	5043	NM_001122895	17937	Mm.336898	NM_008668	ENSMUSG00000025402	Nab2	AI451907	Ngfi-A binding protein 2	protein-coding
mm_123990.1	chr14	75760964	75760971	-	1	NA	Intergenic	A-rich|Low_complexity|Low_complexity	-6474	NM_177381	338337	Mm.86507	NM_177381	ENSMUSG00000034893	Cog3	E430004N23	component of oligomeric golgi complex 3	protein-coding
mm_144792.1	chr18	35965010	35965023	+	1	NA	non-coding (NR_110349, exon 1 of 15)	non-coding (NR_110349, exon 1 of 15)	186	NR_110349	74002	Mm.196944	NM_028707	ENSMUSG00000024347	Psd2	6330404E20Rik|AW125584|EFA6C	pleckstrin and Sec7 domain containing 2	protein-coding
mm_10396.1	chr2	13574095	13574114	+	1	NA	promoter-TSS (NM_011701)	promoter-TSS (NM_011701)	-207	NM_011701	22352	Mm.268000	NM_011701	ENSMUSG00000026728	Vim	-	vimentin	protein-coding
mm_17475.1	chr2	28560588	28560607	-	1	NA	exon (NM_009885, exon 4 of 11)	exon (NM_009885, exon 4 of 11)	2806	NM_009885	12613	Mm.236017	NM_009885	ENSMUSG00000026818	Cel	1810036E18Rik|BAL	carboxyl ester lipase	protein-coding
mm_87864.1	chr10	61297729	61297739	+	1	NA	promoter-TSS (NM_011073)	promoter-TSS (NM_011073)	-102	NM_011073	18646	Mm.240313	NM_011073	ENSMUSG00000037202	Prf1	Pfn|Pfp|Prf-1	perforin 1 (pore forming protein)	protein-coding
mm_162899.1	chr10	114301985	114301987	-	1	NA	Intergenic	MTC|LTR|ERVL-MaLR	499384	NM_146241	237553	Mm.445550	NM_146241	ENSMUSG00000050663	Trhde	9330155P21Rik	TRH-degrading enzyme	protein-coding
mm_65622.1	chr7	27541201	27541243	-	1	NA	exon (NM_011116, exon 7 of 14)	exon (NM_011116, exon 7 of 14)	11996	NM_011116	18807	Mm.6483	NM_011116	ENSMUSG00000003363	Pld3	Sam-9	phospholipase D family, member 3	protein-coding
mm_55258.1	chr6	53452531	53452538	-	1	NA	intron (NM_001327821, intron 5 of 10)	intron (NM_001327821, intron 5 of 10)	-120840	NM_172728	231991	Mm.227444	NM_172728	ENSMUSG00000053007	Creb5	9430076C15Rik|CRE-BPa|Crebpa|D430026C09Rik	cAMP responsive element binding protein 5	protein-coding
mm_53103.1	chr6	125067914	125067942	+	1	NA	promoter-TSS (NM_001163269)	promoter-TSS (NM_001163269)	8	NM_001163269	381810	Mm.333386	NM_001163268	ENSMUSG00000067714	Lpar5	GPR93|Gm1072|Gpr92|LPA5	lysophosphatidic acid receptor 5	protein-coding
mm_46129.1	chr5	92505502	92505516	-	1	NA	5' UTR (NM_007644, exon 1 of 12)	5' UTR (NM_007644, exon 1 of 12)	148	NM_007644	12492	Mm.297964	NM_007644	ENSMUSG00000029426	Scarb2	9330185J12Rik|Cd36l2|LGP85|LIMP II|LIMP-2|MLGP85	scavenger receptor class B, member 2	protein-coding
mm_28427.1	chr3	90464631	90464640	-	1	NA	intron (NM_008727, intron 1 of 21)	intron (NM_008727, intron 1 of 21)	1231	NM_008727	18160	Mm.4627	NM_008727	ENSMUSG00000027931	Npr1	AI893888|GC-A|NPR-A|NPRA|Pndr	natriuretic peptide receptor 1	protein-coding
mm_157364.1	chrX	37191105	37191148	-	1	NA	promoter-TSS (NM_153503)	promoter-TSS (NM_153503)	-96	NM_153503	69942	Mm.307182	NM_153503	ENSMUSG00000036537	Rnf113a1	2810428C21Rik|Rnf113a	ring finger protein 113A1	protein-coding
mm_165827.1	chr3	151386374	151386380	+	1	NA	Intergenic	Intergenic	-51505	NM_133222	170757	Mm.317261	NM_133222	ENSMUSG00000039167	Adgrl4	1110033N21Rik|ETL1|Eltd1|Etl	adhesion G protein-coupled receptor L4	protein-coding
mm_96487.1	chr11	67687133	67687139	+	1	NA	3' UTR (NM_001277080, exon 13 of 13)	3' UTR (NM_001277080, exon 13 of 13)	-8190	NM_009038	19674	Mm.439726	NM_009038	ENSMUSG00000020907	Rcvrn	CAR|S-modulin	recoverin	protein-coding
mm_39095.1	chr4	154899038	154899073	-	1	NA	promoter-TSS (NM_025582)	promoter-TSS (NM_025582)	-12	NM_025582	66469	Mm.41868	NM_025582	ENSMUSG00000029059	Fam213b	2810405K02Rik|AI836168|PM/PGFS	family with sequence similarity 213, member B	protein-coding
mm_31587.1	chr4	57845220	57845238	+	1	NA	promoter-TSS (NM_001035532)	promoter-TSS (NM_001035532)	-19	NM_009649	11641	Mm.467752	NM_009649	ENSMUSG00000038729	Akap2	AA959716|AI649048|Akap-2|Akap-kl|B230340M18Rik|Prka2	A kinase (PRKA) anchor protein 2	protein-coding
mm_144226.1	chr18	9958188	9958192	+	1	NA	promoter-TSS (NM_153552)	promoter-TSS (NM_153552)	10	NM_153552	225160	Mm.219648	NM_153552	ENSMUSG00000024287	Thoc1	3110002N20Rik|AW107452|NMP-84	THO complex 1	protein-coding
mm_53348.1	chr6	129350238	129350249	+	1	NA	promoter-TSS (NM_177686)	promoter-TSS (NM_177686)	-1	NM_177686	232413	Mm.90241	NM_177686	ENSMUSG00000053063	Clec12a	CLL-1|D230024O04|KLRL1|Micl	C-type lectin domain family 12, member a	protein-coding
mm_11510.1	chr2	32572337	32572362	+	1	NA	exon (NM_010073, exon 3 of 4)	exon (NM_010073, exon 3 of 4)	1491	NM_010073	13481	Mm.22001	NM_010073	ENSMUSG00000026810	Dpm2	AW557993|R75484	dolichol-phosphate (beta-D) mannosyltransferase 2	protein-coding
mm_77426.1	chr8	121083950	121083972	-	1	NA	promoter-TSS (NM_010426)	promoter-TSS (NM_010426)	-425	NM_010426	15227	Mm.33897	NM_010426	ENSMUSG00000042812	Foxf1	AI450827|FREAC1|Foxf1a|Freac-1|HFH-8|Hfh8	forkhead box F1	protein-coding
mm_142357.1	chr17	43649698	43649719	-	1	NA	exon (NM_028711, exon 6 of 9)	exon (NM_028711, exon 6 of 9)	17307	NM_028711	74011	Mm.288697	NM_028711	ENSMUSG00000023912	Slc25a27	3632410G24Rik|9430092A03Rik|D530043E16Rik|Ucp4	solute carrier family 25, member 27	protein-coding
mm_48211.1	chr5	137608928	137608950	-	1	NA	exon (NM_008788, exon 3 of 9)	exon (NM_008788, exon 3 of 9)	2465	NM_008788	18542	Mm.262345	NM_008788	ENSMUSG00000029718	Pcolce	Astt-2|Astt2|P14|PCPE-1	procollagen C-endopeptidase enhancer protein	protein-coding
mm_151190.1	chr19	53460611	53460654	+	1	NA	intron (NR_028427, intron 2 of 9)	intron (NR_028427, intron 2 of 9)	4164	NR_028427	381232	Mm.248624	NR_028427	ENSMUSG00000097636	Mirt1	4833407H14Rik|5430437C04Rik|5830416P10Rik|ENSMUSG00000074788|Gm10758	myocardial infarction associated transcript 1	ncRNA
mm_79229.1	chr9	50494140	50494146	+	1	NA	promoter-TSS (NM_029639)	promoter-TSS (NM_029639)	-382	NM_029639	76509	Mm.29959	NM_029639	ENSMUSG00000032068	Plet1	0610037B23Rik|1600029D21Rik|AA407923|AU043048	placenta expressed transcript 1	protein-coding
mm_132177.1	chr16	32388778	32388781	+	1	NA	3' UTR (NM_177633, exon 11 of 11)	3' UTR (NM_177633, exon 11 of 11)	-11727	NM_001160402	277203	Mm.484240	NM_001160402	ENSMUSG00000079625	Tm4sf19	EG277203	transmembrane 4 L six family member 19	protein-coding
mm_101871.1	chr11	48891991	48892001	-	1	NA	intron (NM_001024230, intron 4 of 4)	intron (NM_001024230, intron 4 of 4)	10156	NM_001024230	432555	Mm.338931	NM_001024230	ENSMUSG00000058163	Gm5431	EG432555|Irgb9b8	predicted gene 5431	protein-coding
mm_93063.1	chr10	88826738	88826742	-	1	NA	promoter-TSS (NM_175158)	promoter-TSS (NM_175158)	74	NM_175158	70683	Mm.29631	NM_175158	ENSMUSG00000004356	Utp20	3830408P06Rik|AA617408|Drim|mDRIM|mDRIN	UTP20 small subunit processome component	protein-coding
mm_8678.1	chr1	156807422	156807425	-	1	NA	non-coding (NR_027640, exon 20 of 20)	non-coding (NR_027640, exon 20 of 20)	-31600	NM_028333	72713	Mm.389206	NM_028333	ENSMUSG00000033544	Angptl1	2810039D03Rik|ANG3|ANGPT3|ANGY|ARP1	angiopoietin-like 1	protein-coding
mm_66814.1	chr7	48137575	48137602	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	31397	NM_207538	404239	Mm.377927	NM_207538	ENSMUSG00000070551	Mrgprb5	Mgrg11|MrgB5	MAS-related GPR, member B5	protein-coding
mm_99153.1	chr11	100580790	100580814	+	1	NA	3' UTR (NM_009923, exon 4 of 4)	3' UTR (NM_009923, exon 4 of 4)	4911	NM_001146318	12799	Mm.15711	NM_009923	ENSMUSG00000006782	Cnp	CNPase|Cnp-1|Cnp1	2',3'-cyclic nucleotide 3' phosphodiesterase	protein-coding
mm_114731.1	chr13	83727348	83727358	+	1	NA	promoter-TSS (NR_015561)	promoter-TSS (NR_015561)	-753	NR_015561	320203	Mm.245636	NM_177100	ENSMUSG00000050334	C130071C03Rik	2810449C10Rik	RIKEN cDNA C130071C03 gene	ncRNA
mm_153216.1	chr19	34747322	34747335	-	1	NA	promoter-TSS (NM_172838)	promoter-TSS (NM_172838)	-217	NM_172838	240638	Mm.74636	NM_172838	ENSMUSG00000009378	Slc16a12	3230401A21|AW210596	solute carrier family 16 (monocarboxylic acid transporters), member 12	protein-coding
mm_160555.1	chr9	49106053	49106053	+	1	NA	intron (NM_030709, intron 1 of 12)	intron (NM_030709, intron 1 of 12)	3274	NM_030709	80893	Mm.72799	NM_030709	ENSMUSG00000032268	Tmprss5	spinesin	transmembrane protease, serine 5 (spinesin)	protein-coding
mm_99870.1	chr11	109399038	109399057	+	1	NA	3' UTR (NM_010303, exon 4 of 4)	3' UTR (NM_010303, exon 4 of 4)	-26899	NM_025275	13929	Mm.211850	NM_025275	ENSMUSG00000020610	Amz2	AA408420|ESTM12|X83328	archaelysin family metallopeptidase 2	protein-coding
mm_155916.1	chrX	102037250	102037260	+	1	NA	intron (NM_001163610, intron 1 of 7)	intron (NM_001163610, intron 1 of 7)	34052	NM_001278534	331474	Mm.23297	NM_183318	ENSMUSG00000049191	Rgag4	6430402L03Rik|Mar5|Mart5|mKIAA2001	retrotransposon gag domain containing 4	protein-coding
mm_99523.1	chr11	103170494	103170496	+	1	NA	promoter-TSS (NM_001077698)	promoter-TSS (NM_001077698)	-643	NM_001077698	57778	Mm.138913	NM_019679	ENSMUSG00000055805	Fmnl1	8030453N10Rik|AI553564|Fmnl|Fnrl|Frls	formin-like 1	protein-coding
mm_8515.1	chr1	154726719	154726741	-	1	NA	promoter-TSS (NM_009782)	promoter-TSS (NM_009782)	-810	NM_009782	12290	Mm.267517	NM_009782	ENSMUSG00000004110	Cacna1e	A430040I15|BII|Cach6|Cacnl1a6|Cav2.3|Cchra1|alpha1E	calcium channel, voltage-dependent, R type, alpha 1E subunit	protein-coding
mm_83177.1	chr9	40784141	40784156	-	1	NA	TTS (NM_133733)	TTS (NM_133733)	-17125	NM_031165	15481	Mm.290774	NM_031165	ENSMUSG00000015656	Hspa8	2410008N15Rik|Hsc70|Hsc71|Hsc73|Hsp73|Hspa10	heat shock protein 8	protein-coding
mm_69585.1	chr7	135704735	135704746	-	1	NA	exon (NM_001081117, exon 8 of 14)	exon (NM_001081117, exon 8 of 14)	11639	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_107887.1	chr12	70453122	70453165	+	1	NA	promoter-TSS (NM_028339)	promoter-TSS (NM_028339)	-11	NM_028339	72736	Mm.204670	NM_028339	ENSMUSG00000021072	Tmx1	2810425A04Rik|AI465319|Txndc1	thioredoxin-related transmembrane protein 1	protein-coding
mm_151930.1	chr19	5800240	5800245	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	2430	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_93626.1	chr10	117278100	117278120	-	1	NA	3' UTR (NM_017372, exon 4 of 4)	3' UTR (NM_017372, exon 4 of 4)	4162	NM_017372	17105	Mm.45436	NM_017372	ENSMUSG00000069516	Lyz2	AI326280|Lys|Lysm|Lyzf2|Lyzs|Lzm|Lzm-s1|Lzp	lysozyme 2	protein-coding
mm_126651.1	chr15	84167762	84167772	+	1	NA	promoter-TSS (NR_105816)	promoter-TSS (NR_105816)	-49	NM_054088	116939	Mm.390817	NM_054088	ENSMUSG00000041653	Pnpla3	Adpn	patatin-like phospholipase domain containing 3	protein-coding
mm_65563.1	chr7	27168729	27168746	-	1	NA	3' UTR (NM_029391, exon 8 of 8)	3' UTR (NM_029391, exon 8 of 8)	-1935	NM_053208	112406	Mm.29978	NM_053208	ENSMUSG00000058709	Egln2	0610011A13Rik|C85656|Hif-p4h-1|Ier4|Phd1|SM-20	egl-9 family hypoxia-inducible factor 2	protein-coding
mm_130428.1	chr15	98145699	98145711	-	1	NA	promoter-TSS (NM_030121)	promoter-TSS (NM_030121)	-3	NM_001170710	78541	Mm.200766	NM_030121	ENSMUSG00000048175	Asb8	4930539L19Rik|AI788835|C430011H06Rik	ankyrin repeat and SOCS box-containing 8	protein-coding
mm_149181.1	chr19	9847557	9847560	+	1	NA	Intergenic	Intergenic	51975	NM_016692	16319	Mm.29755	NM_016692	ENSMUSG00000024660	Incenp	2700067E22Rik|AU019509|C130081E20|C77457	inner centromere protein	protein-coding
mm_41080.1	chr5	87677030	87677031	+	1	NA	intron (NM_001286015, intron 25 of 32)	intron (NM_001286015, intron 25 of 32)	10822	NM_001286016	12990	Mm.427467	NM_007784	ENSMUSG00000070702	Csn1s1	AA959832|AW212882|Csna	casein alpha s1	protein-coding
mm_11062.1	chr2	27515219	27515229	+	1	NA	promoter-TSS (NM_080848)	promoter-TSS (NM_080848)	77	NM_080848	140858	Mm.28265	NM_080848	ENSMUSG00000026917	Wdr5	2410008O07Rik|AA408785|AA960360|Big|Big-3	WD repeat domain 5	protein-coding
mm_17962.1	chr2	37428252	37428284	-	1	NA	3' UTR (NM_146253, exon 2 of 2)	3' UTR (NM_146253, exon 2 of 2)	2651	NM_146253	241322	Mm.330182	NM_146253	ENSMUSG00000066798	Zbtb6	A830092L04Rik|ZID|Zfp482	zinc finger and BTB domain containing 6	protein-coding
mm_34998.1	chr4	156130513	156130517	+	1	NA	5' UTR (NM_001220499, exon 1 of 2)	5' UTR (NM_001220499, exon 1 of 2)	3027	NM_001220499	100045778		NM_001220499	ENSMUSG00000110404	Rnf223	9930005F22Rik	ring finger 223	protein-coding
mm_29175.1	chr3	106516272	106516283	-	1	NA	intron (NM_133869, intron 4 of 8)	PB1D10|SINE|Alu	30237	NM_028110	72121	Mm.14816	NM_028110	ENSMUSG00000027901	Dennd2d	2010308M01Rik|AI451421	DENN/MADD domain containing 2D	protein-coding
mm_122738.1	chr14	54075622	54075636	-	1	NA	Intergenic	Intergenic	178300	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_90748.1	chr10	5488189	5488195	-	1	NA	5' UTR (NM_001347711, exon 1 of 146)	5' UTR (NM_001347711, exon 1 of 146)	122	NM_001347711	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_113726.1	chr13	43797885	43797897	+	1	NA	intron (NM_009856, intron 3 of 4)	intron (NM_009856, intron 3 of 4)	12779	NM_001289915	12522	Mm.57175	NM_009856	ENSMUSG00000015396	Cd83	-	CD83 antigen	protein-coding
mm_127104.1	chr15	97831628	97831674	+	1	NA	5' UTR (NM_019572, exon 1 of 24)	5' UTR (NM_019572, exon 1 of 24)	116	NM_019572	56233	Mm.384027	NM_019572	ENSMUSG00000022475	Hdac7	5830434K02Rik|HD7|HD7a|Hdac7a|mFLJ00062	histone deacetylase 7	protein-coding
mm_127169.1	chr15	98789840	98789850	+	1	NA	promoter-TSS (NM_021279)	promoter-TSS (NM_021279)	-12	NM_021279	22408	Mm.1123	NM_021279	ENSMUSG00000022997	Wnt1	Int-1|Wnt-1|sw|swaying	wingless-type MMTV integration site family, member 1	protein-coding
mm_148320.1	chr18	83828052	83828081	-	1	NA	Intergenic	Intergenic	258496	NM_001081300	110796	Mm.102136	NM_001081300	ENSMUSG00000046982	Tshz1	5730407I04Rik|D18Bwg1409e|Mtsh1|NY-CO-33|Sdccag33|Tsh1|mKIAA4206|teashirt1	teashirt zinc finger family member 1	protein-coding
mm_85409.1	chr9	103365860	103365901	-	1	NA	promoter-TSS (NM_001134427)	promoter-TSS (NM_001134427)	-100	NM_001134426	321022	Mm.261025	NM_175565	ENSMUSG00000032803	Cdv3	2510010F10Rik|C230084J24Rik|C79446|TPP36	carnitine deficiency-associated gene expressed in ventricle 3	protein-coding
mm_155087.1	chrX	48108913	48108964	+	1	NA	5' UTR (NM_001289729, exon 1 of 21)	5' UTR (NM_001289729, exon 1 of 21)	213	NM_133213	170745	Mm.129279	NM_133213	ENSMUSG00000037005	Xpnpep2	9030008G12Rik|mAPP	X-prolyl aminopeptidase (aminopeptidase P) 2, membrane-bound	protein-coding
mm_46838.1	chr5	113332797	113332801	-	1	NA	Intergenic	Intergenic	4846	NR_106089	102466821		NR_106089	ENSMUSG00000104840	Mir7230	mmu-mir-7230	microRNA 7230	ncRNA
mm_126572.1	chr15	82256153	82256155	+	1	NA	non-coding (NR_037698, exon 1 of 2)	non-coding (NR_037698, exon 1 of 2)	131	NR_037698	76505	Mm.23023	NR_037697	ENSMUSG00000068099	1500009C09Rik	-	RIKEN cDNA 1500009C09 gene	ncRNA
mm_48943.1	chr6	4539539	4539545	+	1	NA	exon (NM_007743, exon 51 of 52)	exon (NM_007743, exon 51 of 52)	33924	NM_007743	12843	Mm.277792	NM_007743	ENSMUSG00000029661	Col1a2	AA960264|AI325291|Col1a-2|Cola-2|Cola2|oim	collagen, type I, alpha 2	protein-coding
mm_83584.1	chr9	48340815	48340842	-	1	NA	promoter-TSS (NM_030069)	promoter-TSS (NM_030069)	70	NM_030069	78252	Mm.31626	NM_030069	ENSMUSG00000032028	Nxpe2	4432416J03Rik|AI323362|Fam55b	neurexophilin and PC-esterase domain family, member 2	protein-coding
mm_49393.1	chr6	28262044	28262100	+	1	NA	promoter-TSS (NM_001081678)	promoter-TSS (NM_001081678)	-471	NM_001081678	627049	Mm.84441	NM_001081678	ENSMUSG00000039841	Zfp800	AA407452|Znf800	zinc finger protein 800	protein-coding
mm_173158.1	chrX	36668183	36668200	+	1	NA	Intergenic	Intergenic	-22777	NM_001081956	338351	Mm.116704	NM_001081956	ENSMUSG00000059708	Akap17b	AA407619|AKAP-17B|B230333C21Rik|C230056F04Rik|PRKA17B|Sfrs17b|Srsf17b|Talia	A kinase (PRKA) anchor protein 17B	protein-coding
mm_145546.1	chr18	60808908	60808920	+	1	NA	intron (NM_001042605, intron 3 of 8)	intron (NM_001042605, intron 3 of 8)	-3162	NR_039567	100628611		NR_039567	ENSMUSG00000093327	Mir5107	mir-5107|mmu-mir-5107|mu-mir-5107	microRNA 5107	ncRNA
mm_122778.1	chr14	54410111	54410117	-	1	NA	promoter-TSS (NM_001253680)	promoter-TSS (NM_001253680)	-642	NM_001253680	20540	Mm.142455	NM_011405	ENSMUSG00000000958	Slc7a7	AI790233|my+lat1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 7	protein-coding
mm_65752.1	chr7	28561684	28561694	-	1	NA	promoter-TSS (NR_106016)	promoter-TSS (NR_106016)	-705	NR_106016	102466795		NR_106016	ENSMUSG00000098558	Mir7049	Gm27277|mmu-mir-7049	microRNA 7049	ncRNA
mm_94281.1	chr11	3967733	3967735	+	1	NA	intron (NM_022889, intron 1 of 14)	B3|SINE|B2	3759	NM_022889	64934	Mm.28659	NM_022889	ENSMUSG00000020430	Pes1	-	pescadillo ribosomal biogenesis factor 1	protein-coding
mm_90058.1	chr10	116252899	116252913	+	1	NA	exon (NM_001161837, exon 11 of 13)	exon (NM_001161837, exon 11 of 13)	-48468	NM_029928	19263	Mm.37213	NM_029928	ENSMUSG00000020154	Ptprb	3230402H02Rik|C130094E24|Ptpz|Rptpb|VE-PTP|Veptp	protein tyrosine phosphatase, receptor type, B	protein-coding
mm_18414.1	chr2	60673655	60673731	-	1	NA	promoter-TSS (NM_021359)	promoter-TSS (NM_021359)	0	NM_021359	16420	Mm.98193	NM_021359	ENSMUSG00000026971	Itgb6	2210409C20Rik|4831415H04Rik	integrin beta 6	protein-coding
mm_12389.1	chr2	69897195	69897206	+	1	NA	promoter-TSS (NM_177783)	promoter-TSS (NM_177783)	-46	NM_001303033	68795	Mm.314576	NM_177783	ENSMUSG00000044308	Ubr3	1110059H15Rik|4833421P10Rik|A130030D10Rik|AA409735|AA414972|AA422631|AI646861|AU016126|Zfp650|Znf650	ubiquitin protein ligase E3 component n-recognin 3	protein-coding
mm_118920.1	chr14	26894600	26894604	+	1	NA	promoter-TSS (NM_080856)	promoter-TSS (NM_080856)	-2	NM_001170748	142687	Mm.138259	NM_080856	ENSMUSG00000021898	Asb14	Asb-14	ankyrin repeat and SOCS box-containing 14	protein-coding
mm_71524.1	chr8	46852668	46852678	+	1	NA	Intergenic	LTR67B|LTR|ERVL	112928	NM_008391	16363	Mm.1149	NM_008391	ENSMUSG00000031627	Irf2	9830146E22Rik|AI646973|Irf-2	interferon regulatory factor 2	protein-coding
mm_154478.1	chrM	4330	4352	-	1	NA	NA	Intergenic	NA	NA								
mm_55082.1	chr6	49214726	49214748	-	1	NA	5' UTR (NM_023670, exon 1 of 15)	5' UTR (NM_023670, exon 1 of 15)	217	NM_023670	140488	Mm.281018	NM_023670	ENSMUSG00000029814	Igf2bp3	2610101N11Rik|AA522010|AL022933|AU045931|IMP-3|IMP3|Koc13|Neilsen|mimp3	insulin-like growth factor 2 mRNA binding protein 3	protein-coding
mm_71055.1	chr8	33732050	33732137	+	1	NA	promoter-TSS (NM_001167922)	promoter-TSS (NM_001167922)	26	NM_026584	68153	Mm.286104	NM_026584	ENSMUSG00000031585	Gtf2e2	34kDa|AI462509|C330006J08Rik	general transcription factor II E, polypeptide 2 (beta subunit)	protein-coding
mm_7961.1	chr1	133930051	133930072	-	1	NA	Intergenic	Intergenic	-8660	NM_054077	116847	Mm.214514	NM_054077	ENSMUSG00000041577	Prelp	7330409J17Rik|SLRR2A	proline arginine-rich end leucine-rich repeat	protein-coding
mm_68514.1	chr7	111594232	111594245	-	1	NA	intron (NM_173739, intron 3 of 10)	intron (NM_173739, intron 3 of 10)	185739	NM_173739	233733	Mm.323322	NM_173739	ENSMUSG00000038296	Galnt18	2900011G21Rik|BC024988|Galntl4	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 18	protein-coding
mm_111955.1	chr12	109560089	109560114	-	1	NA	non-coding (NR_003633, exon 5 of 5)	non-coding (NR_003633, exon 5 of 5)	-3591	NR_030427	791079		NR_030427	ENSMUSG00000076451	Mir770	Mirn770|mir-770|mmu-mir-770	microRNA 770	ncRNA
mm_49896.1	chr6	38919062	38919074	+	1	NA	promoter-TSS (NM_011539)	promoter-TSS (NM_011539)	82	NM_011539	21391	Mm.4054	NM_011539	ENSMUSG00000029925	Tbxas1	CYP5|CYP5A1|THAS|TS|TXAS|TXS	thromboxane A synthase 1, platelet	protein-coding
mm_119827.1	chr14	54259243	54259300	+	1	NA	promoter-TSS (NM_134076)	promoter-TSS (NM_134076)	39	NM_134076	105501	Mm.28771	NM_134076	ENSMUSG00000040997	Abhd4	1110035H23Rik|AI429574|Abh4	abhydrolase domain containing 4	protein-coding
mm_106423.1	chr11	119299130	119299132	-	1	NA	intron (NM_138669, intron 1 of 11)	intron (NM_138669, intron 1 of 11)	912	NM_138669	192170	Mm.197555	NM_138669	ENSMUSG00000025580	Eif4a3	2400003O03Rik|Ddx48|eIF4A-III|mKIAA0111	eukaryotic translation initiation factor 4A3	protein-coding
mm_62219.1	chr7	98455107	98455140	+	1	NA	intron (NM_001130693, intron 7 of 18)	intron (NM_001130693, intron 7 of 18)	14707	NM_001130693	14918	Mm.389928	NM_001034890	ENSMUSG00000074003	Gucy2d	-	guanylate cyclase 2d	protein-coding
mm_63192.1	chr7	125603482	125603496	+	1	NA	promoter-TSS (NM_021887)	promoter-TSS (NM_021887)	60	NM_021887	60504	Mm.155643	NM_021887	ENSMUSG00000030745	Il21r	NILR	interleukin 21 receptor	protein-coding
mm_38760.1	chr4	147902987	147903005	-	1	NA	5' UTR (NM_001285920, exon 3 of 20)	5' UTR (NM_001285920, exon 3 of 20)	1702	NM_001285923	170731	Mm.154312	NM_133201	ENSMUSG00000029020	Mfn2	D630023P19Rik|Fzo	mitofusin 2	protein-coding
mm_74123.1	chr8	123186109	123186117	+	1	NA	promoter-TSS (NM_007876)	promoter-TSS (NM_007876)	-122	NM_007876	13479	Mm.20388	NM_007876	ENSMUSG00000019278	Dpep1	AI327012|MBD	dipeptidase 1 (renal)	protein-coding
mm_73717.1	chr8	111940747	111940756	+	1	NA	promoter-TSS (NM_026693)	promoter-TSS (NM_026693)	48	NM_026693	93739	Mm.371666	NM_026693	ENSMUSG00000031950	Gabarapl2	0610012F20Rik|2900019O08Rik|AI173605|GATE-16|Gef2	gamma-aminobutyric acid (GABA) A receptor-associated protein-like 2	protein-coding
mm_102409.1	chr11	59182811	59182833	-	1	NA	promoter-TSS (NM_175452)	promoter-TSS (NM_175452)	4	NM_175452	118454	Mm.40016	NM_080454	ENSMUSG00000043448	Gjc2	B230382L12Rik|Cx47|Gja12	gap junction protein, gamma 2	protein-coding
mm_149118.1	chr19	8970561	8970565	+	1	NA	intron (NM_026007, intron 5 of 9)	AT_rich|Low_complexity|Low_complexity	3522	NM_026007	67160	Mm.247762	NM_026007	ENSMUSG00000071644	Eef1g	2610301D06Rik|AA407312|EF1G	eukaryotic translation elongation factor 1 gamma	protein-coding
mm_109461.1	chr12	111166537	111166547	+	1	NA	5' UTR (NM_011632, exon 1 of 12)	5' UTR (NM_011632, exon 1 of 12)	172	NM_011632	22031	Mm.27431	NM_011632	ENSMUSG00000021277	Traf3	AI528849|CAP-1|CD40bp|CRAF1|LAP1|T-BAM|amn	TNF receptor-associated factor 3	protein-coding
mm_61866.1	chr7	89392051	89392091	+	1	NA	Intergenic	Intergenic	-12295	NM_008055	14366	Mm.86755	NM_008055	ENSMUSG00000049791	Fzd4	Fz4	frizzled class receptor 4	protein-coding
mm_87854.1	chr10	61171955	61171970	+	1	NA	promoter-TSS (NM_001017419)	promoter-TSS (NM_001017419)	-2	NM_001017419	65971	Mm.30227	NM_023064	ENSMUSG00000020096	Tbata	1700021K02Rik|AI428928|Spatial|Titest	thymus, brain and testes associated	protein-coding
mm_97197.1	chr11	75588065	75588151	+	1	NA	promoter-TSS (NM_008850)	promoter-TSS (NM_008850)	29	NM_008850	18738	Mm.3128	NM_008850	ENSMUSG00000017781	Pitpna	Pitpn|vb|vibrator	phosphatidylinositol transfer protein, alpha	protein-coding
mm_103597.1	chr11	78386395	78386413	-	1	NA	intron (NM_001277290, intron 1 of 8)	intron (NM_001277290, intron 1 of 8)	204	NM_008238	15218	Mm.4496	NM_008238	ENSMUSG00000002057	Foxn1	D11Bhm185e|Fkh19|HFH-11|Hfh11|Whn|nu|nude	forkhead box N1	protein-coding
mm_156976.1	chrX	7041651	7041658	-	1	NA	promoter-TSS (NM_183015)	promoter-TSS (NM_183015)	-35	NM_183015	209091	Mm.448624	NM_183015	ENSMUSG00000051592	Ccnb3	-	cyclin B3	protein-coding
mm_10451.1	chr2	14276297	14276317	+	1	NA	exon (NM_008625, exon 10 of 30)	exon (NM_008625, exon 10 of 30)	15304	NR_030609	100124488		NR_030609	ENSMUSG00000077897	Mir511	Mirn511|mir-511|mmu-mir-511	microRNA 511	ncRNA
mm_98100.1	chr11	86646808	86646852	+	1	NA	intron (NM_029478, intron 5 of 11)	intron (NM_029478, intron 5 of 11)	-9241	NR_106195	102465902		NR_106195	ENSMUSG00000099324	Mir8115	Gm28012|mmu-mir-8115	microRNA 8115	ncRNA
mm_21712.1	chr2	164593607	164593615	-	1	NA	promoter-TSS (NM_029325)	promoter-TSS (NM_029325)	-40	NM_029325	75526	Mm.159533	NM_029325	ENSMUSG00000017733	Eppin	1700024E17Rik|Spinlw1	epididymal peptidase inhibitor	protein-coding
mm_161511.1	chr15	98456388	98456388	+	1	NA	promoter-TSS (NM_146280)	promoter-TSS (NM_146280)	76	NM_146280	258277	Mm.222977	NM_146280	ENSMUSG00000032987	Olfr281	MOR160-5	olfactory receptor 281	protein-coding
mm_42095.1	chr5	110343117	110343119	+	1	NA	promoter-TSS (NM_153400)	promoter-TSS (NM_153400)	31	NM_001310701	231602	Mm.55948	NM_153400	ENSMUSG00000029503	P2rx2	P2X2a|P2x2	purinergic receptor P2X, ligand-gated ion channel, 2	protein-coding
mm_78196.1	chr9	21367891	21367970	+	1	NA	promoter-TSS (NM_001042707)	promoter-TSS (NM_001042707)	59	NM_001042709	16201	Mm.440026	NM_010561	ENSMUSG00000032178	Ilf3	MBII-26|MPHOSPH4|NF90|NFAR	interleukin enhancer binding factor 3	protein-coding
mm_16560.1	chr2	3291516	3291517	-	1	NA	intron (NM_001290368, intron 1 of 13)	U4|snRNA|snRNA	7304	NM_001290370	18108	Mm.65021	NM_008708	ENSMUSG00000026643	Nmt2	A930001K02Rik|AI605445|AU044698|hNMT-2	N-myristoyltransferase 2	protein-coding
mm_152156.1	chr19	7241217	7241226	-	1	NA	promoter-TSS (NM_027643)	promoter-TSS (NM_027643)	1	NM_027643	70999	Mm.329605	NM_027643	ENSMUSG00000024764	Naa40	4931433E08Rik|AU023197|Nat11	N(alpha)-acetyltransferase 40, NatD catalytic subunit	protein-coding
mm_6713.1	chr1	82291115	82291174	-	1	NA	5' UTR (NM_010570, exon 1 of 2)	5' UTR (NM_010570, exon 1 of 2)	295	NM_010570	16367	Mm.4952	NM_010570	ENSMUSG00000055980	Irs1	G972R|IRS-1	insulin receptor substrate 1	protein-coding
mm_30642.1	chr4	8822783	8822804	+	1	NA	intron (NM_001277149, intron 8 of 37)	intron (NM_001277149, intron 8 of 37)	132387	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_155551.1	chrX	74425458	74425477	+	1	NA	intron (NM_001136067, intron 1 of 10)	intron (NM_001136067, intron 1 of 10)	855	NM_001136067	16151	Mm.12967	NM_010547	ENSMUSG00000004221	Ikbkg	1110037D23Rik|AI848108|AI851264|AW124339|IKK[g]|NEMO	inhibitor of kappaB kinase gamma	protein-coding
mm_62582.1	chr7	105425935	105426002	+	1	NA	5' UTR (NM_007627, exon 1 of 5)	5' UTR (NM_007627, exon 1 of 5)	237	NM_007627	12426	Mm.44513	NM_007627	ENSMUSG00000030898	Cckbr	CCK-BR|CCK2-R|CCK2R|CCKR-2	cholecystokinin B receptor	protein-coding
mm_87884.1	chr10	61720593	61720621	+	1	NA	promoter-TSS (NM_153779)	promoter-TSS (NM_153779)	-42	NM_153779	71361	Mm.286309	NM_153779	ENSMUSG00000020085	Aifm2	5430437E11Rik|Amid|D730001I10Rik|PRG3	apoptosis-inducing factor, mitochondrion-associated 2	protein-coding
mm_105067.1	chr11	100724225	100724256	-	1	NA	intron (NM_024456, intron 1 of 5)	intron (NM_024456, intron 1 of 5)	10390	NM_029307	75482	Mm.46175	NM_029307	ENSMUSG00000017832	Hspb9	1700007H20Rik	heat shock protein, alpha-crystallin-related, B9	protein-coding
mm_22566.1	chr3	10012612	10012622	+	1	NA	promoter-TSS (NM_010634)	promoter-TSS (NM_010634)	32	NM_001272098	16592	Mm.741	NM_010634	ENSMUSG00000027533	Fabp5	E-FABP|Fabpe|Klbp|PA-FABP|mal1	fatty acid binding protein 5, epidermal	protein-coding
mm_132024.1	chr16	26641077	26641080	+	1	NA	intron (NM_001159318, intron 2 of 10)	B1F|SINE|Alu	59373	NM_008364	16180	Mm.253424	NM_008364	ENSMUSG00000022514	Il1rap	6430709H04Rik|AI255955|AV239853|IL-1RAcP	interleukin 1 receptor accessory protein	protein-coding
mm_147161.1	chr18	36720022	36720026	-	1	NA	Intergenic	Intergenic	6791	NM_009841	12475	Mm.3460	NM_009841	ENSMUSG00000051439	Cd14	-	CD14 antigen	protein-coding
mm_154756.1	chrX	10717503	10717514	+	1	NA	5' UTR (NM_001166635, exon 1 of 2)	5' UTR (NM_001166635, exon 1 of 2)	143	NM_001166635	68041	Mm.29429	NM_026524	ENSMUSG00000008035	Mid1ip1	3110038L01Rik|Mig12|S14R	Mid1 interacting protein 1 (gastrulation specific G12-like (zebrafish))	protein-coding
mm_116265.1	chr13	34345980	34346012	-	1	NA	promoter-TSS (NM_001033167)	promoter-TSS (NM_001033167)	-814	NM_001033167	73102	Mm.23932	NM_001033167	ENSMUSG00000038267	Slc22a23	3110004L20Rik	solute carrier family 22, member 23	protein-coding
mm_87153.1	chr10	36506835	36506846	+	1	NA	promoter-TSS (NM_001253356)	promoter-TSS (NM_001253356)	33	NM_001253356	319415	Mm.332442	NM_001081208	ENSMUSG00000044499	Hs3st5	D930005L05Rik|Gm1151|Hs3ost5	heparan sulfate (glucosamine) 3-O-sulfotransferase 5	protein-coding
mm_32800.1	chr4	117096050	117096083	+	1	NA	promoter-TSS (NM_008958)	promoter-TSS (NM_008958)	10	NM_008958	19207	Mm.287037	NM_008958	ENSMUSG00000028681	Ptch2	ptc2	patched 2	protein-coding
mm_6795.1	chr1	84148369	84148372	-	1	NA	intron (NM_001003948, intron 2 of 2)	intron (NM_001003948, intron 2 of 2)	70591	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_79812.1	chr9	64178401	64178416	+	1	NA	promoter-TSS (NM_183316)	promoter-TSS (NM_183316)	-889	NM_183316	330959	Mm.24082	NM_183316	ENSMUSG00000032398	Snapc5	2010103A03Rik	small nuclear RNA activating complex, polypeptide 5	protein-coding
mm_160244.1	chr7	104647288	104647288	-	1	NA	promoter-TSS (NM_147049)	promoter-TSS (NM_147049)	17	NM_147049	259051	Mm.223432	NM_147049	ENSMUSG00000070421	Olfr658	MOR34-5	olfactory receptor 658	protein-coding
mm_104337.1	chr11	94053538	94053551	-	1	NA	intron (NM_001025429, intron 2 of 26)	intron (NM_001025429, intron 2 of 26)	9339	NM_001025429	70834	Mm.260737	NM_027569	ENSMUSG00000020859	Spag9	3110018C07Rik|4733401I23Rik|4831406C20Rik|AW552012|JLP|JSAP2|JSAP2a|Jip4|Mapk8ip4|syd1	sperm associated antigen 9	protein-coding
mm_90818.1	chr10	7919935	7919961	-	1	NA	exon (NM_138667, exon 3 of 7)	exon (NM_138667, exon 3 of 7)	36175	NM_138667	68652	Mm.193041	NM_138667	ENSMUSG00000015755	Tab2	1110030N06Rik|A530078N03Rik|Map3k7ip2|mKIAA0733	TGF-beta activated kinase 1/MAP3K7 binding protein 2	protein-coding
mm_122109.1	chr14	30923755	30923765	-	1	NA	promoter-TSS (NM_008407)	promoter-TSS (NM_008407)	-173	NM_008407	16426	Mm.4517	NM_008407	ENSMUSG00000006522	Itih3	AW108094|ITI-HC3|Intin3|Itih-3	inter-alpha trypsin inhibitor, heavy chain 3	protein-coding
mm_39788.1	chr5	30281378	30281447	+	1	NA	Intergenic	Intergenic	48831	NR_137634	28042	Mm.168854	NM_027652	ENSMUSG00000075703	Selenoi	4933402G07Rik|AI448296|AI452230|C79563|D5Wsu178e|Ept1|SELI|mKIAA1724	selenoprotein I	protein-coding
mm_35538.1	chr4	41316694	41316708	-	1	NA	Intergenic	Intergenic	-1800	NM_026893	68970	Mm.28891	NM_026893	ENSMUSG00000028436	Dcaf12	1500001L20Rik|5830424K06Rik|AA420338|AI851081|Wdr40a	DDB1 and CUL4 associated factor 12	protein-coding
mm_5948.1	chr1	56871361	56871364	-	1	NA	exon (NM_139146, exon 7 of 11)	exon (NM_139146, exon 7 of 11)	99972	NM_139146	212712	Mm.145599	NM_139146	ENSMUSG00000038331	Satb2	mKIAA1034	special AT-rich sequence binding protein 2	protein-coding
mm_150200.1	chr19	32757648	32757659	+	1	NA	promoter-TSS (NM_008960)	promoter-TSS (NM_008960)	76	NM_008960	19211	Mm.245395	NM_008960	ENSMUSG00000013663	Pten	2310035O07Rik|A130070J02Rik|AI463227|B430203M17Rik|MMAC1|TEP1	phosphatase and tensin homolog	protein-coding
mm_90705.1	chr10	130379134	130379137	+	1	NA	Intergenic	L1VL4|LINE|L1	15106	NM_001081448	625068	Mm.359168	NM_001081448	ENSMUSG00000070601	Vmn2r84	EG625068	vomeronasal 2, receptor 84	protein-coding
mm_34910.1	chr4	155705047	155705057	+	1	NA	5' UTR (NM_026899, exon 1 of 5)	5' UTR (NM_026899, exon 1 of 5)	237	NM_026899	68991	Mm.294770	NM_026899	ENSMUSG00000029038	Ssu72	1190002E22Rik|1500011L16Rik|2610101M12Rik	Ssu72 RNA polymerase II CTD phosphatase homolog (yeast)	protein-coding
mm_88479.1	chr10	77616212	77616236	+	1	NA	exon (NM_019929, exon 4 of 4)	exon (NM_019929, exon 4 of 4)	2515	NR_125903	20610	Mm.24433	NM_019929	ENSMUSG00000020265	Sumo3	2810014B19Rik|D10Ertd345e|SMT3A|SUMO-3|Smt3h1	small ubiquitin-like modifier 3	protein-coding
mm_101504.1	chr11	32200249	32200271	-	1	NA	promoter-TSS (NM_008374)	promoter-TSS (NM_008374)	19	NM_001134458	16199	Mm.384	NM_008374	ENSMUSG00000020279	Il9r	-	interleukin 9 receptor	protein-coding
mm_147278.1	chr18	39466085	39466096	-	1	NA	intron (NM_008173, intron 1 of 7)	intron (NM_008173, intron 1 of 7)	21155	NM_008173	14815	Mm.129481	NM_008173	ENSMUSG00000024431	Nr3c1	GR|Grl-1|Grl1	nuclear receptor subfamily 3, group C, member 1	protein-coding
mm_54292.1	chr6	29272553	29272563	-	1	NA	promoter-TSS (NM_001190461)	promoter-TSS (NM_001190461)	-68	NM_023516	69573	Mm.45161	NM_023516	ENSMUSG00000043421	Hilpda	2310016C08Rik|AW049004|Hig2	hypoxia inducible lipid droplet associated	protein-coding
mm_89632.1	chr10	96398811	96398823	+	1	NA	Intergenic	Intergenic	172610	NR_110448	74881	Mm.410819	NR_110448		4930459C07Rik	-	RIKEN cDNA 4930459C07 gene	ncRNA
mm_126838.1	chr15	89020398	89020420	+	1	NA	exon (NM_031260, exon 17 of 27)	exon (NM_031260, exon 17 of 27)	37415	NM_031260	83456	Mm.358791	NM_031260	ENSMUSG00000015365	Mov10l1	CHAMP|Csm	Moloney leukemia virus 10-like 1	protein-coding
mm_128003.1	chr15	12824585	12824604	-	1	NA	promoter-TSS (NM_029998)	promoter-TSS (NM_029998)	63	NM_029998	77877	Mm.207311	NM_029998	ENSMUSG00000022195	6030458C11Rik	-	RIKEN cDNA 6030458C11 gene	protein-coding
mm_130852.1	chr15	101954277	101954294	-	1	NA	promoter-TSS (NM_212487)	promoter-TSS (NM_212487)	2	NM_212487	332131	Mm.325105	NM_212487	ENSMUSG00000050463	Krt78	2310030B04Rik|Kb40	keratin 78	protein-coding
mm_63245.1	chr7	126585930	126585943	+	1	NA	promoter-TSS (NM_001146311)	promoter-TSS (NM_001146311)	-119	NM_001146311	12752	Mm.268930	NM_009907	ENSMUSG00000030720	Cln3	AI323623	ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease)	protein-coding
mm_72112.1	chr8	71629460	71629509	+	1	NA	exon (NM_001029873, exon 42 of 42)	exon (NM_001029873, exon 42 of 42)	1622	NR_106035	102466799		NR_106035	ENSMUSG00000098976	Mir6769b	Gm27546|mmu-mir-6769b	microRNA 6769b	ncRNA
mm_70472.1	chr8	12385740	12385750	+	1	NA	promoter-TSS (NR_027975)	promoter-TSS (NR_027975)	-26	NR_027975	434280	Mm.447484	NM_001013812	ENSMUSG00000047935	Gm5607	EG434280	predicted gene 5607	ncRNA
mm_60561.1	chr7	44481336	44481351	+	1	NA	Intergenic	Intergenic	-3174	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_79269.1	chr9	50753351	50753353	+	1	NA	promoter-TSS (NM_024441)	promoter-TSS (NM_024441)	381	NM_009964	12955	Mm.178	NM_009964	ENSMUSG00000032060	Cryab	Crya-2|Crya2|HspB5|P23	crystallin, alpha B	protein-coding
mm_104525.1	chr11	96075597	96075636	-	1	NA	promoter-TSS (NM_001161419)	promoter-TSS (NM_001161419)	15	NM_001161419	11951	Mm.258	NM_007506	ENSMUSG00000006057	Atp5g1	-	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit C1 (subunit 9)	protein-coding
mm_140423.1	chr17	87975087	87975107	+	1	NA	promoter-TSS (NM_010830)	promoter-TSS (NM_010830)	47	NM_010830	17688	Mm.18210	NM_010830	ENSMUSG00000005370	Msh6	AU044881|AW550279|GTBP|Gtmbp	mutS homolog 6	protein-coding
mm_2532.1	chr1	106938954	106938958	+	1	NA	promoter-TSS (NM_001199213)	promoter-TSS (NM_001199213)	-1	NM_001199213	71869	Mm.321740	NM_027971	ENSMUSG00000059956	Serpinb12	2300003F07Rik|4833409F13Rik	serine (or cysteine) peptidase inhibitor, clade B (ovalbumin), member 12	protein-coding
mm_152936.1	chr19	28680133	28680143	-	1	NA	promoter-TSS (NM_175459)	promoter-TSS (NM_175459)	-61	NM_175459	226075	Mm.223508	NM_175459	ENSMUSG00000052942	Glis3	4833409N03Rik|E330013K21Rik	GLIS family zinc finger 3	protein-coding
mm_40464.1	chr5	53635433	53635435	+	1	NA	intron (NM_001080928, intron 2 of 10)	intron (NM_001080928, intron 2 of 10)	44948	NM_001080927	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_70566.1	chr8	13140063	13140081	+	1	NA	intron (NM_146207, intron 15 of 19)	intron (NM_146207, intron 15 of 19)	4000	NR_106032	102465645		NR_106032	ENSMUSG00000098532	Mir7065	Gm27871|mmu-mir-7065	microRNA 7065	ncRNA
mm_47535.1	chr5	124248079	124248126	-	1	NA	intron (NM_011256, intron 1 of 24)	intron (NM_011256, intron 1 of 24)	1658	NM_011256	19679	Mm.44261	NM_011256	ENSMUSG00000029406	Pitpnm2	NIR3|RDGBA2|Rdgb2|mKIAA1457	phosphatidylinositol transfer protein, membrane-associated 2	protein-coding
mm_26153.1	chr3	138143847	138143886	+	1	NA	promoter-TSS (NM_001163457)	promoter-TSS (NM_001163457)	328	NM_175389	108943	Mm.471692	NM_175389	ENSMUSG00000004127	Trmt10a	3110023L08Rik|AA794508|Rg9mtd2|Rnmtd2	tRNA methyltransferase 10A	protein-coding
mm_63930.1	chr7	139469715	139469725	+	1	NA	intron (NM_183144, intron 2 of 15)	intron (NM_183144, intron 2 of 15)	80611	NM_001127363	212111	Mm.28308	NM_183144	ENSMUSG00000025477	Inpp5a	-	inositol polyphosphate-5-phosphatase A	protein-coding
mm_17411.1	chr2	27247185	27247193	-	1	NA	5' UTR (NM_138665, exon 1 of 21)	5' UTR (NM_138665, exon 1 of 21)	114	NM_138665	192166	Mm.278467	NM_138665	ENSMUSG00000009614	Sardh	-	sarcosine dehydrogenase	protein-coding
mm_16894.1	chr2	13224708	13224723	-	1	NA	intron (NM_009105, intron 3 of 8)	intron (NM_009105, intron 3 of 8)	46700	NM_009105	20163	Mm.905	NM_009105	ENSMUSG00000026727	Rsu1	RsuI|rsp-1	Ras suppressor protein 1	protein-coding
mm_75406.1	chr8	46211021	46211036	-	1	NA	promoter-TSS (NM_007450)	promoter-TSS (NM_007450)	-19	NM_007450	11739	Mm.16228	NM_007450	ENSMUSG00000031633	Slc25a4	AU019225|Ant1	solute carrier family 25 (mitochondrial carrier, adenine nucleotide translocator), member 4	protein-coding
mm_147539.1	chr18	53723177	53723197	-	1	NA	exon (NM_178686, exon 9 of 21)	exon (NM_178686, exon 9 of 21)	21360	NM_178686	225523	Mm.193678	NM_178686	ENSMUSG00000048799	Cep120	A230075C01|AU016693|Ccdc100	centrosomal protein 120	protein-coding
mm_33033.1	chr4	122689384	122689391	+	1	NA	exon (NM_023865, exon 1 of 5)	exon (NM_023865, exon 1 of 5)	128	NM_023865	77432	Mm.491436	NM_023865	ENSMUSG00000023263	9530002B09Rik	Aump|Vpp1|Vppl	RIKEN cDNA 9530002B09 gene	protein-coding
mm_62987.1	chr7	120328661	120328691	+	1	NA	promoter-TSS (NM_177213)	promoter-TSS (NM_177213)	-8	NM_177213	320631	Mm.78330	NM_177213	ENSMUSG00000054746	Abca15	4930500I12Rik	ATP-binding cassette, sub-family A (ABC1), member 15	protein-coding
mm_46718.1	chr5	110471298	110471324	-	1	NA	Intergenic	RMER10A|LTR|ERVL	-22808	NM_001142642	381668	Mm.348782	NM_028596	ENSMUSG00000043323	Fbrsl1	2410025L10Rik|AI467568|Gm1049|Gm29766|mKIAA1545	fibrosin-like 1	protein-coding
mm_88059.1	chr10	67554577	67554581	+	1	NA	Intergenic	Intergenic	-5624	NM_001005419	211488	Mm.297250	NM_001005419	ENSMUSG00000057134	Ado	Gm237	2-aminoethanethiol (cysteamine) dioxygenase	protein-coding
mm_85445.1	chr9	104262424	104262431	-	1	NA	intron (NM_001163026, intron 1 of 55)	CpG	503	NM_001163026	235567	Mm.217256	NM_001163026	ENSMUSG00000032560	Dnajc13	D030002L11Rik|Gm1124|RME-8|Rme8|mKIAA0678	DnaJ heat shock protein family (Hsp40) member C13	protein-coding
mm_123084.1	chr14	55745648	55745658	-	1	NA	promoter-TSS (NM_026403)	promoter-TSS (NM_026403)	31	NM_026819	52585	Mm.21623	NM_026819	ENSMUSG00000002332	Dhrs1	1110029G07Rik|AW112170|D14Ertd484e	dehydrogenase/reductase (SDR family) member 1	protein-coding
mm_33156.1	chr4	125504635	125504653	+	1	NA	promoter-TSS (NR_109835)	promoter-TSS (NR_109835)	-105	NR_109835	735288		NR_109835	ENSMUSG00000094403	Mir692-2	Mir692-2a|Mir692-3|Mirn692-2|Mirn692-2a|mir-692-2|mmu-mir-692-2	microRNA 692-2	ncRNA
mm_101508.1	chr11	32222234	32222315	-	1	NA	promoter-TSS (NM_001291818)	promoter-TSS (NM_001291818)	19	NM_010117	13650	Mm.11545	NM_010117	ENSMUSG00000020282	Rhbdf1	C16ORF8|Dist|Dist1|Egfr-rs|mKIAA4242	rhomboid 5 homolog 1	protein-coding
mm_161438.1	chr15	63878558	63878558	-	1	NA	promoter-TSS (NM_183194)	promoter-TSS (NM_183194)	0	NM_183194	270328	Mm.483471	NM_183194	ENSMUSG00000055827	Gsdmc3	9930109F21Rik	gasdermin C3	protein-coding
mm_35476.1	chr4	40851654	40851668	-	1	NA	intron (NM_022305, intron 1 of 5)	intron (NM_022305, intron 1 of 5)	-1523	NR_039584	100628614		NR_039584	ENSMUSG00000096377	Mir5123	mmu-mir-5123|mu-mir-5123	microRNA 5123	ncRNA
mm_22856.1	chr3	28313306	28313309	+	1	NA	intron (NM_026910, intron 1 of 32)	intron (NM_026910, intron 1 of 32)	50093	NM_001163009	665113	Mm.126193	NM_026910	ENSMUSG00000027692	Tnik	1500031A17Rik|4831440I19Rik|AI451411|C530008O15Rik|C630040K21Rik	TRAF2 and NCK interacting kinase	protein-coding
mm_85864.1	chr9	110874019	110874029	-	1	NA	5' UTR (NM_146260, exon 3 of 6)	5' UTR (NM_146260, exon 3 of 6)	6059	NM_146260	20776	Mm.390229	NM_146260	ENSMUSG00000049555	Tmie	5131400L21Rik|Mm.87012|sr	transmembrane inner ear	protein-coding
mm_85291.1	chr9	100466818	100466828	-	1	NA	intron (NM_001033543, intron 4 of 6)	intron (NM_001033543, intron 4 of 6)	19650	NM_001033543	213208	Mm.242896	NM_001033543	ENSMUSG00000044244	Il20rb	AV228068|Fndc6|Gm186|Il20R2	interleukin 20 receptor beta	protein-coding
mm_38381.1	chr4	138757492	138757496	-	1	NA	5' UTR (NM_012045, exon 1 of 5)	5' UTR (NM_012045, exon 1 of 5)	104	NM_012045	26971	Mm.331989	NM_012045	ENSMUSG00000028749	Pla2g2f	-	phospholipase A2, group IIF	protein-coding
mm_135668.1	chr16	52407813	52407820	-	1	NA	intron (NM_009655, intron 1 of 15)	B4A|SINE|B4	45265	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_148191.1	chr18	79015181	79015194	-	1	NA	intron (NM_053099, intron 2 of 5)	intron (NM_053099, intron 2 of 5)	94204	NM_053099	240427	Mm.312871	NM_053099	ENSMUSG00000024548	Setbp1	C130092E12|Seb|mKIAA0437	SET binding protein 1	protein-coding
mm_5228.1	chr1	14309939	14309947	-	1	NA	5' UTR (NM_001252192, exon 1 of 17)	5' UTR (NM_001252192, exon 1 of 17)	256	NM_001310459	14048	Mm.250185	NM_010164	ENSMUSG00000025932	Eya1	bor	EYA transcriptional coactivator and phosphatase 1	protein-coding
mm_80470.1	chr9	78167303	78167348	+	1	NA	intron (NM_019987, intron 13 of 13)	intron (NM_019987, intron 13 of 13)	-8589	NR_040401	320295	Mm.131285	NR_040401	ENSMUSG00000097574	C920006O11Rik	-	RIKEN cDNA C920006O11 gene	ncRNA
mm_152532.1	chr19	11326838	11326873	-	1	NA	intron (NM_027836, intron 3 of 6)	intron (NM_027836, intron 3 of 6)	7840	NM_001276398	109225	Mm.491251	NM_027836	ENSMUSG00000024672	Ms4a7	9130422I10Rik|A430103C15Rik|CD20l4|CFFMA	membrane-spanning 4-domains, subfamily A, member 7	protein-coding
mm_78589.1	chr9	37367678	37367682	+	1	NA	promoter-TSS (NM_175189)	promoter-TSS (NM_175189)	74	NM_175189	72927	Mm.266133	NM_175189	ENSMUSG00000046240	Hepacam	2900042E01Rik|Glialcam|Hepn1	hepatocyte cell adhesion molecule	protein-coding
mm_47463.1	chr5	123670997	123671034	-	1	NA	intron (NM_001347468, intron 1 of 24)	intron (NM_001347468, intron 1 of 24)	13346	NM_019765	56430	Mm.241109	NM_019765	ENSMUSG00000049550	Clip1	1110007I12Rik|4631429H07Rik|AV017631|C81039|CLIP-170|CLIP170|CYLN1|Clip50|Rsn|mKIAA4046|restin	CAP-GLY domain containing linker protein 1	protein-coding
mm_25639.1	chr3	121070985	121070985	+	1	NA	Intergenic	Intergenic	100710	NM_028456	66568	Mm.263163	NM_025637	ENSMUSG00000028133	Rwdd3	2510027J23Rik|3110037C01Rik|AI035684|AI662458|Rsume|X2CR1	RWD domain containing 3	protein-coding
mm_141799.1	chr17	34416516	34416522	-	1	NA	5' UTR (NM_001163855, exon 2 of 24)	5' UTR (NM_001163855, exon 2 of 24)	17699	NM_001163855	407788	Mm.73205	NM_001001177	ENSMUSG00000057246	BC051142	NG8|TSBP|Tesb|Tesbp	cDNA sequence BC051142	protein-coding
mm_170893.1	chr2	27886412	27886413	+	1	NA	promoter-TSS (NM_015734)	promoter-TSS (NM_015734)	-13	NM_015734	12831	Mm.7281	NM_015734	ENSMUSG00000026837	Col5a1	AI413331	collagen, type V, alpha 1	protein-coding
mm_146728.1	chr18	15151428	15151431	-	1	NA	promoter-TSS (NM_134112)	promoter-TSS (NM_134112)	17	NM_134112	106931	Mm.329299	NM_134112	ENSMUSG00000036225	Kctd1	4933402K10Rik|AI661543|AW553000	potassium channel tetramerisation domain containing 1	protein-coding
mm_69732.1	chr7	140874089	140874109	-	1	NA	intron (NM_022433, intron 4 of 6)	MTEa|LTR|ERVL-MaLR	7770	NM_001127351	64384	Mm.29760	NM_022433	ENSMUSG00000025486	Sirt3	2310003L23Rik|AI848213|Sir2l3	sirtuin 3	protein-coding
mm_3504.1	chr1	150107053	150107063	+	1	NA	3' UTR (NM_011198, exon 10 of 10)	3' UTR (NM_011198, exon 10 of 10)	7027	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_32504.1	chr4	108460922	108460932	+	1	NA	intron (NM_175472, intron 2 of 30)	AmnSINE1|SINE|Deu	1501	NM_175472	230594	Mm.25181	NM_175472	ENSMUSG00000034610	Zcchc11	6030404K05Rik|9230115F04Rik|PPAPD3|mKIAA0191	zinc finger, CCHC domain containing 11	protein-coding
mm_13278.1	chr2	101621782	101621792	+	1	NA	intron (NM_026592, intron 1 of 6)	intron (NM_026592, intron 1 of 6)	-2961	NM_009020	19374	Mm.4988	NM_009020	ENSMUSG00000032864	Rag2	Rag-2	recombination activating gene 2	protein-coding
mm_147538.1	chr18	53536216	53536223	-	1	NA	intron (NM_001033281, intron 2 of 6)	intron (NM_001033281, intron 2 of 6)	71673	NM_001033281	225518	Mm.297645	NM_001033281	ENSMUSG00000069378	Prdm6	Gm92|PRISM	PR domain containing 6	protein-coding
mm_122603.1	chr14	51042051	51042072	-	1	NA	promoter-TSS (NM_183032)	promoter-TSS (NM_183032)	-194	NM_183032	328401	Mm.99528	NM_183032	ENSMUSG00000052382	Rnase9	ESRL|Rak1	ribonuclease, RNase A family, 9 (non-active)	protein-coding
mm_27866.1	chr3	79159476	79159502	-	1	NA	Intergenic	B3|SINE|B2	-13614	NM_001099624	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_105837.1	chr11	113676116	113676123	-	1	NA	intron (NM_138598, intron 2 of 2)	intron (NM_138598, intron 2 of 2)	8032	NM_138598	28081	Mm.351688	NM_138598	ENSMUSG00000041629	Fam104a	D11Wsu99e	family with sequence similarity 104, member A	protein-coding
mm_52973.1	chr6	123253081	123253113	+	1	NA	Intergenic	Intergenic	-9010	NM_001163161	17474	Mm.441101	NM_010819	ENSMUSG00000030144	Clec4d	Clecsf8|Mpcl|mcl	C-type lectin domain family 4, member d	protein-coding
mm_160023.1	chr6	130193071	130193071	-	1	NA	promoter-TSS (NM_010651)	promoter-TSS (NM_010651)	41	NM_010651	16640	Mm.457996	NM_010651	ENSMUSG00000033024	Klra9	LY49I1|Ly49I	killer cell lectin-like receptor subfamily A, member 9	protein-coding
mm_9889.1	chr1	186704512	186704583	-	1	NA	exon (NM_009367, exon 1 of 7)	exon (NM_009367, exon 1 of 7)	1442	NM_009367	21808	Mm.18213	NM_009367	ENSMUSG00000039239	Tgfb2	BB105277|Tgf-beta2|Tgfb-2	transforming growth factor, beta 2	protein-coding
mm_105674.1	chr11	107470714	107470726	-	1	NA	promoter-TSS (NM_145823)	promoter-TSS (NM_145823)	0	NM_145823	71795	Mm.397413	NM_145823	ENSMUSG00000040430	Pitpnc1	1110020B03Rik|5830436L09Rik|AI662802|AI851387|C330017I21Rik|Dnr411|RDGBB|RDGBB1|rdgB-beta	phosphatidylinositol transfer protein, cytoplasmic 1	protein-coding
mm_128395.1	chr15	43265779	43265794	-	1	NA	intron (NM_008388, intron 6 of 12)	intron (NM_008388, intron 6 of 12)	16950	NM_008388	16341	Mm.289992	NM_008388	ENSMUSG00000022336	Eif3e	48kDa|Eif3s6|Int6|eIF3-p46|eIF3-p48	eukaryotic translation initiation factor 3, subunit E	protein-coding
mm_6481.1	chr1	74091330	74091336	-	1	NA	intron (NM_027884, intron 1 of 34)	intron (NM_027884, intron 1 of 34)	33114	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_164208.1	chr15	82197601	82197611	+	1	NA	promoter-TSS (NR_029804)	promoter-TSS (NR_029804)	-516	NR_029804	723897		NR_029804	ENSMUSG00000065465	Mir33	Mirn33|mir-33|mmu-mir-33	microRNA 33	ncRNA
mm_141932.1	chr17	35029878	35029889	-	1	NA	non-coding (NR_130641, exon 21 of 24)	non-coding (NR_130641, exon 21 of 24)	-1867	NM_023893	78376	Mm.390966	NM_023893	ENSMUSG00000036185	Sapcd1	2810436B06Rik|G7d|Ng23	suppressor APC domain containing 1	protein-coding
mm_129059.1	chr15	75567016	75567053	-	1	NA	promoter-TSS (NM_001135689)	promoter-TSS (NM_001135689)	148	NM_011837	23934	Mm.22154	NM_011837	ENSMUSG00000022577	Ly6h	-	lymphocyte antigen 6 complex, locus H	protein-coding
mm_72490.1	chr8	83715192	83715204	+	1	NA	promoter-TSS (NM_197982)	promoter-TSS (NM_197982)	21	NM_197982	68278	Mm.28222	NM_197982	ENSMUSG00000005481	Ddx39	2610307C23Rik|BAT1|DDXL|Ddx39a|URH49	DEAD (Asp-Glu-Ala-Asp) box polypeptide 39	protein-coding
mm_133463.1	chr16	89169434	89169437	+	1	NA	Intergenic	Intergenic	-36426	NM_001163615	622935	Mm.459837	NM_001163615	ENSMUSG00000091039	Krtap20-2	1190004K03Rik|EG622935|Gm6371	keratin associated protein 20-2	protein-coding
mm_78520.1	chr9	33728158	33728159	+	1	NA	Intergenic	(CGG)n|Simple_repeat|Simple_repeat	-314213	NR_040744	77119	Mm.367930	NR_040744	ENSMUSG00000098758	7630403G23Rik	-	RIKEN cDNA 7630403G23 gene	ncRNA
mm_141688.1	chr17	33951773	33951786	-	1	NA	promoter-TSS (NM_019420)	promoter-TSS (NM_019420)	-291	NM_019420	54218	Mm.11132	NM_019420	ENSMUSG00000067370	B3galt4	Gal-T2|Galt2	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 4	protein-coding
mm_67339.1	chr7	79793253	79793259	-	1	NA	exon (NM_008588, exon 1 of 2)	exon (NM_008588, exon 1 of 2)	334	NM_008588	17292	Mm.1404	NM_008588	ENSMUSG00000030544	Mesp1	bHLHc5	mesoderm posterior 1	protein-coding
mm_71280.1	chr8	40919810	40919821	+	1	NA	3' UTR (NM_001044740, exon 12 of 12)	3' UTR (NM_001044740, exon 12 of 12)	-6418	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_26263.1	chr3	142501253	142501276	+	1	NA	exon (NM_153564, exon 3 of 11)	exon (NM_153564, exon 3 of 11)	4330	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_13319.1	chr2	102686097	102686130	+	1	NA	intron (NM_001077514, intron 1 of 10)	intron (NM_001077514, intron 1 of 10)	-20325	NM_011393	20511	Mm.267547	NM_011393	ENSMUSG00000005089	Slc1a2	1700091C19Rik|2900019G14Rik|AI159670|Eaat2|GLT-1|GLT1|MGLT1	solute carrier family 1 (glial high affinity glutamate transporter), member 2	protein-coding
mm_141651.1	chr17	33677438	33677442	-	1	NA	exon (NM_001109913, exon 2 of 17)	exon (NM_001109913, exon 2 of 17)	8018	NM_001109913	76936	Mm.311439	NM_029804	ENSMUSG00000059208	Hnrnpm	2610023M21Rik|AA409009|Hnrpm|mKIAA4193	heterogeneous nuclear ribonucleoprotein M	protein-coding
mm_105113.1	chr11	101009315	101009349	-	1	NA	promoter-TSS (NM_001243049)	promoter-TSS (NM_001243049)	-120	NM_016920	11975	Mm.340818	NM_016920	ENSMUSG00000019302	Atp6v0a1	AA959968|ATP6a1|Atp6n1|Atp6n1a|Atpv0a1|Vpp-1|Vpp1	ATPase, H+ transporting, lysosomal V0 subunit A1	protein-coding
mm_60165.1	chr7	40898185	40898213	+	1	NA	non-coding (NR_040329, exon 1 of 5)	non-coding (NR_040329, exon 1 of 5)	125	NR_040329	320210	Mm.126237	NR_040329	ENSMUSG00000100600	A230077H06Rik	-	RIKEN cDNA A230077H06 gene	ncRNA
mm_39650.1	chr5	24685834	24685853	+	1	NA	promoter-TSS (NM_001305264)	promoter-TSS (NM_001305264)	28	NM_001305264	53312	Mm.5856	NM_016736	ENSMUSG00000028954	Nub1	4931404D21Rik|6330412F12Rik|BS4|NY-REN-18	negative regulator of ubiquitin-like proteins 1	protein-coding
mm_127028.1	chr15	96287767	96287769	+	1	NA	exon (NM_175251, exon 1 of 21)	exon (NM_175251, exon 1 of 21)	246	NM_175251	77044	Mm.17166	NM_175251	ENSMUSG00000033237	Arid2	1700124K17Rik|4432409D24Rik|zipzap/p200	AT rich interactive domain 2 (ARID, RFX-like)	protein-coding
mm_132533.1	chr16	37868338	37868375	+	1	NA	promoter-TSS (NM_177093)	promoter-TSS (NM_177093)	-44	NM_177093	320184	Mm.390882	NM_177093	ENSMUSG00000034158	Lrrc58	1810012N18Rik|C330018J07Rik	leucine rich repeat containing 58	protein-coding
mm_160595.1	chr9	72111250	72111250	-	1	NA	promoter-TSS (NM_001253862)	promoter-TSS (NM_001253862)	-49	NM_001253862	21406	Mm.171615	NM_011544	ENSMUSG00000032228	Tcf12	A130037E08Rik|ALF1|HEB|HEBAlt|HTF-4|HTF4|ME1|REB|bHLHb20	transcription factor 12	protein-coding
mm_59077.1	chr7	19577315	19577329	+	1	NA	promoter-TSS (NM_022409)	promoter-TSS (NM_022409)	35	NM_022409	63872	Mm.23310	NM_022409	ENSMUSG00000011267	Zfp296	2210018A16Rik|Znf296	zinc finger protein 296	protein-coding
mm_123736.1	chr14	70177669	70177696	-	1	NA	promoter-TSS (NM_001253736)	promoter-TSS (NM_001253736)	-10	NM_145978	213019	Mm.283968	NM_145978	ENSMUSG00000022090	Pdlim2	4732462F18Rik|Slim	PDZ and LIM domain 2	protein-coding
mm_170632.1	chr19	8257305	8257323	+	1	NA	Intergenic	Intergenic	-38414	NM_001347426	236293	Mm.440581	NM_172776	ENSMUSG00000075044	Slc22a29	D630002G06Rik	solute carrier family 22. member 29	protein-coding
mm_152991.1	chr19	29672722	29672728	-	1	NA	Intergenic	RLTR27|LTR|ERVK	-24305	NM_001081213	226090	Mm.267131	NM_146098	ENSMUSG00000046324	Ermp1	D19Ertd410e|D19Wsu12e|Fxna|mKIAA1815	endoplasmic reticulum metallopeptidase 1	protein-coding
mm_149105.1	chr19	8943560	8943564	+	1	NA	intron (NM_011842, intron 2 of 17)	B1F2|SINE|Alu	1642	NM_011842	23942	Mm.25339	NM_011842	ENSMUSG00000071646	Mta2	AW550797|Mata1l1|Mta1l1|mmta2	metastasis-associated gene family, member 2	protein-coding
mm_31749.1	chr4	63344614	63344627	+	1	NA	promoter-TSS (NM_008768)	promoter-TSS (NM_008768)	64	NM_008768	18405	Mm.4777	NM_008768	ENSMUSG00000039196	Orm1	Agp-1|Agp-2|Orm-1	orosomucoid 1	protein-coding
mm_68226.1	chr7	104435717	104435735	-	1	NA	exon (NM_009099, exon 2 of 8)	exon (NM_009099, exon 2 of 8)	29467	NM_009099	20128	Mm.295578	NM_009099	ENSMUSG00000030921	Trim30a	Rpt-1|Rpt1|Trim30	tripartite motif-containing 30A	protein-coding
mm_40766.1	chr5	66998618	66998640	+	1	NA	intron (NM_001256122, intron 5 of 20)	(TC)n|Simple_repeat|Simple_repeat	30213	NM_001256122	77569	Mm.374778	NM_001001980	ENSMUSG00000037736	Limch1	3732412D22Rik|mKIAA1102	LIM and calponin homology domains 1	protein-coding
mm_97316.1	chr11	76891193	76891203	+	1	NA	Intergenic	Intergenic	-13347	NM_025655	66601	Mm.25138	NM_025655	ENSMUSG00000020839	Tmigd1	2010002A20Rik|Tmigd	transmembrane and immunoglobulin domain containing 1	protein-coding
mm_164182.1	chr15	76270004	76270013	+	1	NA	promoter-TSS (NR_045747)	promoter-TSS (NR_045747)	-169	NR_045747	100038659	Mm.448549	NR_045747		Mirt2	ENSMUSG00000075583|Gm10872|Gm24562	myocardial infraction associated transcript 2	ncRNA
mm_28776.1	chr3	95951018	95951036	-	1	NA	Intergenic	CpG	21770	NM_023210	66471	Mm.218657	NM_023210	ENSMUSG00000015749	Anp32e	2810018A15Rik|AI047746|AI326868|CPD1|LANP-L|LANPL|mLANP-L	acidic (leucine-rich) nuclear phosphoprotein 32 family, member E	protein-coding
mm_87457.1	chr10	51484349	51484377	+	1	NA	intron (NM_001291892, intron 6 of 8)	intron (NM_001291892, intron 6 of 8)	3751	NM_001291892	14727	Mm.439661	NM_008147	ENSMUSG00000062593	Lilr4b	Gp49a|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4B	protein-coding
mm_144943.1	chr18	37768381	37768394	+	1	NA	exon (NM_033595, exon 1 of 4)	exon (NM_033595, exon 1 of 4)	2807	NM_033595	93724	Mm.247203	NM_033595	ENSMUSG00000102428	Pcdhga12	Pcdh13|pc2c	protocadherin gamma subfamily A, 12	protein-coding
mm_64162.1	chr7	141392165	141392213	+	1	NA	promoter-TSS (NM_011528)	promoter-TSS (NM_011528)	29	NM_011528	21351	Mm.29182	NM_011528	ENSMUSG00000025503	Taldo1	-	transaldolase 1	protein-coding
mm_36045.1	chr4	57278931	57278934	-	1	NA	intron (NM_011207, intron 1 of 25)	intron (NM_011207, intron 1 of 25)	22905	NM_011207	545622	Mm.246552	NM_011207	ENSMUSG00000038764	Ptpn3	9530011I20Rik|PTP-H1|PTPCL	protein tyrosine phosphatase, non-receptor type 3	protein-coding
mm_215.1	chr1	16688460	16688471	+	1	NA	promoter-TSS (NM_001159711)	promoter-TSS (NM_001159711)	9	NM_016923	17087	Mm.116844	NM_016923	ENSMUSG00000025779	Ly96	ESOP-1|MD-2|MD2	lymphocyte antigen 96	protein-coding
mm_151363.1	chr19	55917368	55917377	+	1	NA	exon (NM_001142918, exon 8 of 15)	exon (NM_001142918, exon 8 of 15)	22051	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_84456.1	chr9	66520384	66520414	-	1	NA	intron (NM_001302122, intron 10 of 12)	intron (NM_001302122, intron 10 of 12)	-5806	NM_175206	74165	Mm.297998	NM_175206	ENSMUSG00000050503	Fbxl22	1110004B15Rik	F-box and leucine-rich repeat protein 22	protein-coding
mm_56910.1	chr6	119330594	119330607	-	1	NA	5' UTR (NM_172492, exon 1 of 5)	5' UTR (NM_172492, exon 1 of 5)	166	NM_172492	211187	Mm.121498	NM_172492	ENSMUSG00000055003	Lrtm2	A230084J22|AI841794	leucine-rich repeats and transmembrane domains 2	protein-coding
mm_41816.1	chr5	103804795	103804808	+	1	NA	intron (NM_001080798, intron 3 of 19)	intron (NM_001080798, intron 3 of 19)	50228	NM_001080798	17355	Mm.6949	NM_133919	ENSMUSG00000029313	Aff1	9630032B01Rik|AW319193|Af4|Mllt2h|Rob	AF4/FMR2 family, member 1	protein-coding
mm_139777.1	chr17	65724507	65724509	+	1	NA	intron (NM_133685, intron 1 of 6)	intron (NM_133685, intron 1 of 6)	48244	NM_133685	106572	Mm.29274	NM_133685	ENSMUSG00000056515	Rab31	1700093E07Rik|AI415285|Rab22B	RAB31, member RAS oncogene family	protein-coding
mm_129424.1	chr15	78468450	78468460	-	1	NA	5' UTR (NM_027902, exon 1 of 18)	5' UTR (NM_027902, exon 1 of 18)	179	NM_027902	71753	Mm.34056	NM_027902	ENSMUSG00000016942	Tmprss6	1300008A22Rik	transmembrane serine protease 6	protein-coding
mm_60123.1	chr7	36698003	36698059	+	1	NA	promoter-TSS (NM_172298)	promoter-TSS (NM_172298)	-87	NM_172298	243931	Mm.44141	NM_172298	ENSMUSG00000021217	Tshz3	A630038G13Rik|Tsh3|Zfp537|mKIAA1474|teashirt3	teashirt zinc finger family member 3	protein-coding
mm_131236.1	chr16	10480149	10480153	+	1	NA	promoter-TSS (NM_001243760)	promoter-TSS (NM_001243760)	79	NM_001302618	12265	Mm.249560	NM_007575	ENSMUSG00000022504	Ciita	C2ta|EG669998|Gm9475|Mhc2ta	class II transactivator	protein-coding
mm_74730.1	chr8	17535662	17535677	-	1	NA	promoter-TSS (NM_053171)	promoter-TSS (NM_053171)	-284	NM_053171	94109	Mm.436988	NM_053171	ENSMUSG00000060924	Csmd1	B930082H09|mKIAA1890	CUB and Sushi multiple domains 1	protein-coding
mm_10765.1	chr2	24186470	24186484	+	1	NA	promoter-TSS (NM_153511)	promoter-TSS (NM_153511)	1	NM_153511	215257	Mm.249379	NM_153511	ENSMUSG00000044103	Il1f9	Il36g	interleukin 1 family, member 9	protein-coding
mm_162096.1	chrX	37581479	37581479	+	1	NA	exon (NM_001040089, exon 1 of 4)	exon (NM_001040089, exon 1 of 4)	127	NM_001040089	621852	Mm.490237	NM_001040089	ENSMUSG00000095510	Rhox3f	OTTMUSG00000017155|Rhox3.6|Rhox3e	reproductive homeobox 3F	protein-coding
mm_53078.1	chr6	124935738	124935762	+	1	NA	3' UTR (NM_001170341, exon 9 of 9)	3' UTR (NM_001170341, exon 9 of 9)	4362	NM_001170341	30853	Mm.29737	NM_145385	ENSMUSG00000030120	Mlf2	AI256856|AU018944|C77284	myeloid leukemia factor 2	protein-coding
mm_65619.1	chr7	27535879	27535909	-	1	NA	exon (NM_011116, exon 11 of 14)	exon (NM_011116, exon 11 of 14)	12633	NM_001033315	233020	Mm.429716	NM_001033315	ENSMUSG00000040424	Hipk4	Gm162	homeodomain interacting protein kinase 4	protein-coding
mm_147100.1	chr18	35654939	35654950	-	1	NA	exon (NM_001270646, exon 1 of 1)	exon (NM_001270646, exon 1 of 1)	255	NM_001270646	381148	Mm.297784	NM_001270646	ENSMUSG00000073600	Prob1	Gm1614	proline rich basic protein 1	protein-coding
mm_19930.1	chr2	116065129	116065133	-	1	NA	promoter-TSS (NM_010825)	promoter-TSS (NM_010825)	-73	NM_010825	17536	Mm.247566	NM_010825	ENSMUSG00000027210	Meis2	A430109D20Rik|Mrg1|Stra10	Meis homeobox 2	protein-coding
mm_136468.1	chr16	95585626	95585643	-	1	NA	intron (NM_001302152, intron 1 of 10)	CpG	959	NM_001302152	13876	Mm.164531	NM_133659	ENSMUSG00000040732	Erg	D030036I24Rik	avian erythroblastosis virus E-26 (v-ets) oncogene related	protein-coding
mm_10527.1	chr2	16401679	16401706	+	1	NA	intron (NM_026162, intron 1 of 13)	RSINE1|SINE|B4	45388	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding
mm_61928.1	chr7	90164092	90164095	+	1	NA	intron (NM_001252520, intron 3 of 20)	intron (NM_001252520, intron 3 of 20)	33861	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_85929.1	chr9	112087748	112087765	-	1	NA	intron (NM_001177618, intron 17 of 18)	intron (NM_001177618, intron 17 of 18)	30955	NR_029823	723815		NR_029823	ENSMUSG00000065441	Mir128-2	Mirn128-2|Mirn128b|mir-128-2|mir-128b	microRNA 128-2	ncRNA
mm_38461.1	chr4	140587842	140587858	-	1	NA	intron (NM_001290803, intron 7 of 28)	RMER12C|LTR|ERVK	60906	NM_001112723	72754	Mm.29329	NM_172415	ENSMUSG00000040964	Arhgef10l	2810441C07Rik	Rho guanine nucleotide exchange factor (GEF) 10-like	protein-coding
mm_65167.1	chr7	19677021	19677032	-	1	NA	intron (NM_001277944, intron 1 of 4)	PB1|SINE|Alu	915	NM_001277944	11813	Mm.28394	NM_001277944	ENSMUSG00000002992	Apoc2	apo-CII|apoC-II	apolipoprotein C-II	protein-coding
mm_53686.1	chr6	142387278	142387291	+	1	NA	promoter-TSS (NM_001204907)	promoter-TSS (NM_001204907)	41	NM_025872	66964	Mm.3676	NM_025872	ENSMUSG00000030245	Golt1b	2310061A22Rik|AA407874|AU024291|CGI-141	golgi transport 1B	protein-coding
mm_44851.1	chr5	34220161	34220162	-	1	NA	intron (NM_001015039, intron 7 of 12)	MTD|LTR|ERVL-MaLR	-32451	NM_010753	17122	Mm.259260	NM_010753	ENSMUSG00000037235	Mxd4	2810410A03Rik|Mad4|bHLHc12	Max dimerization protein 4	protein-coding
mm_105785.1	chr11	109797399	109797401	-	1	NA	exon (NM_001162428, exon 3 of 6)	exon (NM_001162428, exon 3 of 6)	30646	NM_027038	69324	Mm.31700	NM_027038	ENSMUSG00000020617	1700012B07Rik	1700069D21Rik	RIKEN cDNA 1700012B07 gene	protein-coding
mm_101473.1	chr11	30649511	30649523	-	1	NA	promoter-TSS (NM_029344)	promoter-TSS (NM_029344)	-121	NM_029344	75572	Mm.390319	NM_029344	ENSMUSG00000060923	Acyp2	2310004B09Rik	acylphosphatase 2, muscle type	protein-coding
mm_131713.1	chr16	21204772	21204787	+	1	NA	promoter-TSS (NM_010143)	promoter-TSS (NM_010143)	-16	NM_010143	13845	Mm.6972	NM_010143	ENSMUSG00000005958	Ephb3	AW456895|Cek10|Etk2|HEK2|MDK5|Sek4|Tyro6	Eph receptor B3	protein-coding
mm_32835.1	chr4	117787269	117787284	+	1	NA	Intergenic	Intergenic	-21610	NM_029416	75753	Mm.3848	NM_029416	ENSMUSG00000048626	Klf17	7420700M05Rik|AA420409|AU043468|C85123|D4Ertd561e|Gzf|Zfp393	Kruppel-like factor 17	protein-coding
mm_82850.1	chr9	31209610	31209614	-	1	NA	intron (NM_001102455, intron 1 of 16)	intron (NM_001102455, intron 1 of 16)	2203	NM_001102455	11804	Mm.19133	NM_009691	ENSMUSG00000031996	Aplp2	AI790698|APLP-2	amyloid beta (A4) precursor-like protein 2	protein-coding
mm_97091.1	chr11	73160383	73160395	+	1	NA	promoter-TSS (NM_033321)	promoter-TSS (NM_033321)	-141	NM_033321	94045	Mm.156893	NM_033321	ENSMUSG00000005950	P2rx5	P2X5	purinergic receptor P2X, ligand-gated ion channel, 5	protein-coding
mm_149524.1	chr19	12457900	12457917	+	1	NA	Intergenic	Intergenic	-2871	NM_010821	17476	Mm.3999	NM_010821	ENSMUSG00000046805	Mpeg1	MPS1|Mpg-1	macrophage expressed gene 1	protein-coding
mm_76627.1	chr8	91801588	91801611	-	1	NA	promoter-TSS (NM_001253822)	promoter-TSS (NM_001253822)	55	NM_001253822	16373	Mm.238044	NM_008393	ENSMUSG00000031734	Irx3	AI894186	Iroquois related homeobox 3	protein-coding
mm_108728.1	chr12	87387501	87387503	+	1	NA	intron (NM_011479, intron 1 of 11)	intron (NM_011479, intron 1 of 11)	853	NM_011479	20773	Mm.565	NM_011479	ENSMUSG00000021036	Sptlc2	LCB2|LCB2a|Spt2	serine palmitoyltransferase, long chain base subunit 2	protein-coding
mm_66346.1	chr7	43490181	43490224	-	1	NA	promoter-TSS (NM_001164518)	promoter-TSS (NM_001164518)	-179	NM_001164518	210094	Mm.228087	NM_001164518	ENSMUSG00000013367	Iglon5	A230106M20Rik|Gm1431	IgLON family member 5	protein-coding
mm_77508.1	chr8	122752340	122752378	-	1	NA	Intergenic	Intergenic	-23127	NM_144932	257633	Mm.334875	NM_144932	ENSMUSG00000015016	Acsf3	BB101783	acyl-CoA synthetase family member 3	protein-coding
mm_153255.1	chr19	36736657	36736670	-	1	NA	promoter-TSS (NM_016854)	promoter-TSS (NM_016854)	-59	NM_016854	53412	Mm.24724	NM_016854	ENSMUSG00000067279	Ppp1r3c	PTG|Ppp1r5	protein phosphatase 1, regulatory (inhibitor) subunit 3C	protein-coding
mm_71290.1	chr8	41017731	41017744	+	1	NA	non-coding (NR_015457, exon 1 of 3)	non-coding (NR_015457, exon 1 of 3)	269	NR_015457	78849	Mm.440930	NR_015457	ENSMUSG00000084960	B430010I23Rik	-	RIKEN cDNA B430010I23 gene	ncRNA
mm_97604.1	chr11	78949965	78949981	+	1	NA	exon (NM_010927, exon 20 of 27)	exon (NM_010927, exon 20 of 27)	24682	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_63569.1	chr7	128117343	128117394	+	1	NA	exon (NM_008401, exon 30 of 30)	exon (NM_008401, exon 30 of 30)	-12200	NM_021334	16411	Mm.22378	NM_021334	ENSMUSG00000030789	Itgax	AI449405|Cd11c|Cr4|N418	integrin alpha X	protein-coding
mm_120816.1	chr14	75131585	75131607	+	1	NA	promoter-TSS (NM_027581)	promoter-TSS (NM_027581)	473	NM_001247984	18826	Mm.153911	NM_008879	ENSMUSG00000021998	Lcp1	AW536232|D14Ertd310e|LCP-1|Pls2|pp65	lymphocyte cytosolic protein 1	protein-coding
mm_73115.1	chr8	94749890	94749896	+	1	NA	3' UTR (NM_009137, exon 3 of 3)	3' UTR (NM_009137, exon 3 of 3)	4209	NM_009137	20299	Mm.12895	NM_009137	ENSMUSG00000031779	Ccl22	ABCD-1|DCBCK|MDC|Scya22	chemokine (C-C motif) ligand 22	protein-coding
mm_150544.1	chr19	39315515	39315521	+	1	NA	intron (NM_007815, intron 5 of 8)	MurERV4-int|LTR|ERVK	28433	NM_007815	13095	Mm.20764	NM_007815	ENSMUSG00000003053	Cyp2c29	AHOH|AHOHase|AI159681|AI196010|Ah-2|Ahh-1|Cyp2c|P450-2C	cytochrome P450, family 2, subfamily c, polypeptide 29	protein-coding
mm_12381.1	chr2	69861639	69861653	+	1	NA	promoter-TSS (NM_001110145)	promoter-TSS (NM_001110145)	84	NM_009278	20823	Mm.10508	NM_009278	ENSMUSG00000068882	Ssb	SS-B	Sjogren syndrome antigen B	protein-coding
mm_58216.1	chr6	144209350	144209356	-	1	NA	exon (NM_011444, exon 1 of 15)	exon (NM_011444, exon 1 of 15)	215	NM_001113559	20678	Mm.1752	NM_011444	ENSMUSG00000041540	Sox5	A730017D01Rik|AI528773	SRY (sex determining region Y)-box 5	protein-coding
mm_29456.1	chr3	113532289	113532291	-	1	NA	Intergenic	Intergenic	42472	NM_007446	11722	Mm.439727	NM_007446	ENSMUSG00000074264	Amy1	Amy-1|Amy1a|C030014B17Rik	amylase 1, salivary	protein-coding
mm_146000.1	chr18	68398129	68398136	+	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	29708	NM_001271717	17200	Mm.426053	NM_008560	ENSMUSG00000045569	Mc2r	ACTH-R|ACTHR|MC2-R	melanocortin 2 receptor	protein-coding
mm_73227.1	chr8	103603790	103603810	+	1	NA	promoter-TSS (NR_045730)	promoter-TSS (NR_045730)	1	NR_045730	71058	Mm.67707	NR_045730	ENSMUSG00000110336	4933400L20Rik	-	RIKEN cDNA 4933400L20 gene	ncRNA
mm_30830.1	chr4	21931101	21931164	+	1	NA	promoter-TSS (NM_175234)	promoter-TSS (NM_175234)	-194	NM_175234	76132	Mm.159689	NM_175234	ENSMUSG00000028246	Faxc	6230409E13Rik|AW742931	failed axon connections homolog	protein-coding
mm_39877.1	chr5	31077114	31077128	+	1	NA	exon (NM_001289522, exon 39 of 43)	exon (NM_001289522, exon 39 of 43)	16406	NM_011773	22784	Mm.1396	NM_011773	ENSMUSG00000029151	Slc30a3	Znt3	solute carrier family 30 (zinc transporter), member 3	protein-coding
mm_15759.1	chr2	164289198	164289207	+	1	NA	promoter-TSS (NM_021363)	promoter-TSS (NM_021363)	-65	NM_001311114	64335	Mm.389393	NM_021363	ENSMUSG00000017003	Svs3a	9530026M05Rik|BB121242|Semg2|Svp-3|Svp3|Svs3	seminal vesicle secretory protein 3A	protein-coding
mm_72952.1	chr8	92357835	92357891	+	1	NA	promoter-TSS (NM_018826)	promoter-TSS (NM_018826)	67	NM_018826	54352	Mm.101153	NM_018826	ENSMUSG00000031737	Irx5	-	Iroquois related homeobox 5 (Drosophila)	protein-coding
mm_54066.1	chr6	13872320	13872345	-	1	NA	promoter-TSS (NR_024619)	promoter-TSS (NR_024619)	763	NR_045995	76311	Mm.367129	NR_045995	ENSMUSG00000097616	1110019D14Rik	-	RIKEN cDNA 1110019D14 gene	ncRNA
mm_57008.1	chr6	121130994	121131004	-	1	NA	promoter-TSS (NM_001270475)	promoter-TSS (NM_001270475)	23	NM_001270475	194401	Mm.122399	NM_153396	ENSMUSG00000051586	Mical3	C130040D16Rik|Mical-3|mKIAA1364	microtubule associated monooxygenase, calponin and LIM domain containing 3	protein-coding
mm_60974.1	chr7	48881333	48881365	+	1	NA	promoter-TSS (NM_001013368)	promoter-TSS (NM_001013368)	-308	NM_001013368	108961	Mm.240566	NM_001013368	ENSMUSG00000046179	E2f8	4432406C08Rik|AA410048	E2F transcription factor 8	protein-coding
mm_119475.1	chr14	47319400	47319412	+	1	NA	intron (NM_178684, intron 3 of 3)	intron (NM_178684, intron 3 of 3)	21092	NM_178684	218975	Mm.212297	NM_178684	ENSMUSG00000021840	Mapk1ip1l	9130202B12|C130032J12Rik	mitogen-activated protein kinase 1 interacting protein 1-like	protein-coding
mm_131874.1	chr16	23192069	23192075	+	1	NA	Intergenic	Lx8|LINE|L1	-32668	NM_145933	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_67971.1	chr7	100653397	100653401	-	1	NA	intron (NM_013746, intron 6 of 8)	intron (NM_013746, intron 6 of 8)	3566	NM_001163187	27276	Mm.491216	NM_013746	ENSMUSG00000030701	Plekhb1	AI315628|PHR1|Phret1|evt-1	pleckstrin homology domain containing, family B (evectins) member 1	protein-coding
mm_165873.1	chr4	40721020	40721054	-	1	NA	non-coding (NR_077226, exon 3 of 3)	non-coding (NR_077226, exon 3 of 3)	1280	NR_077221	622208	Mm.471544	NR_077221		Gm6297	-	predicted gene 6297	ncRNA
mm_126491.1	chr15	81627152	81627253	+	1	NA	exon (NM_177821, exon 14 of 31)	exon (NM_177821, exon 14 of 31)	-36687	NM_001289712	214669	Mm.280768	NM_145993	ENSMUSG00000022394	L3mbtl2	4732493N06Rik|M4mbt	l(3)mbt-like 2 (Drosophila)	protein-coding
mm_139741.1	chr17	62883394	62883399	+	1	NA	Intergenic	Intergenic	-2079	NM_010109	13640	Mm.7978	NM_010109	ENSMUSG00000048915	Efna5	AL-1|AV158822|EFL-5|Ephrin-A5|Epl7|LERK-7|RAGS	ephrin A5	protein-coding
mm_40606.1	chr5	64421433	64421455	+	1	NA	Intergenic	L1MC1|LINE|L1	46498	NR_040681	69999	Mm.261413	NR_040681	ENSMUSG00000100911	1700027F09Rik	-	RIKEN cDNA 1700027F09 gene	ncRNA
mm_33685.1	chr4	133403943	133403945	+	1	NA	intron (NM_016981, intron 1 of 11)	intron (NM_016981, intron 1 of 11)	34168	NR_039582	100628620		NR_039582	ENSMUSG00000092745	Mir5122	mmu-mir-5122|mu-mir-5122	microRNA 5122	ncRNA
mm_43036.1	chr5	123997363	123997374	+	1	NA	TTS (NR_105999)	TTS (NR_105999)	516	NR_105999	102465625		NR_105999	ENSMUSG00000098454	Mir7032	Gm27309|mmu-mir-7032	microRNA 7032	ncRNA
mm_97853.1	chr11	83069747	83069750	+	1	NA	exon (NM_011408, exon 2 of 2)	exon (NM_011408, exon 2 of 2)	4636	NM_011408	20556	Mm.278689	NM_011408	ENSMUSG00000072620	Slfn2	Shlf2	schlafen 2	protein-coding
mm_77468.1	chr8	122426215	122426234	-	1	NA	exon (NM_007806, exon 5 of 6)	exon (NM_007806, exon 5 of 6)	4139	NM_145834	234836	Mm.222808	NM_145834	ENSMUSG00000046108	Il17c	IL-17C	interleukin 17C	protein-coding
mm_129674.1	chr15	81380732	81380742	-	1	NA	intron (NM_133726, intron 5 of 11)	AT_rich|Low_complexity|Low_complexity	18957	NM_133726	70356	Mm.180337	NM_133726	ENSMUSG00000022403	St13	1110007I03Rik|3110002K08Rik|AW555194|HIP|HOP|HSPABP|HSPABP1|PRO0786|SNC6|p48	suppression of tumorigenicity 13	protein-coding
mm_112060.1	chr12	111909167	111909182	-	1	NA	Intergenic	Intergenic	-1119	NM_011625	21981	Mm.313076	NM_011625	ENSMUSG00000021285	Ppp1r13b	AI449786|ASPP1|AW545810|Tp53bp2|Trp53bp2|p85	protein phosphatase 1, regulatory (inhibitor) subunit 13B	protein-coding
mm_68737.1	chr7	121034424	121034450	-	1	NA	promoter-TSS (NM_021554)	promoter-TSS (NM_021554)	-8	NM_021554	59052	Mm.29122	NM_021554	ENSMUSG00000030876	Mettl9	0610012D09Rik|AA517660|Drev|MNCb-5680	methyltransferase like 9	protein-coding
mm_112990.1	chr13	21716386	21716401	+	1	NA	promoter-TSS (NM_178199)	promoter-TSS (NM_178199)	-19	NM_178182	319191	Mm.14767	NM_178182	ENSMUSG00000071516	Hist1h2ai	H2a-291A	histone cluster 1, H2ai	protein-coding
mm_56557.1	chr6	101199080	101199090	-	1	NA	intron (NM_018884, intron 3 of 9)	IMPB_01|Satellite|Satellite	178812	NM_018884	55983	Mm.321654	NM_018884	ENSMUSG00000035357	Pdzrn3	1110020C07Rik|AI429718|AL023082|LNX3|SEMACAP3|Semcap3	PDZ domain containing RING finger 3	protein-coding
mm_23762.1	chr3	73066333	73066344	+	1	NA	promoter-TSS (NR_040557)	promoter-TSS (NR_040557)	-13	NR_040557	626082	Mm.428099	NR_040557	ENSMUSG00000103428	Gm20754	-	predicted gene, 20754	ncRNA
mm_89188.1	chr10	86346534	86346543	+	1	NA	3' UTR (NM_011595, exon 5 of 5)	3' UTR (NM_011595, exon 5 of 5)	46126	NM_011595	21859	Mm.4871	NM_011595	ENSMUSG00000020044	Timp3	Timp-3	tissue inhibitor of metalloproteinase 3	protein-coding
mm_119570.1	chr14	50062281	50062293	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	22392	NM_146316	258313	Mm.463727	NM_146316	ENSMUSG00000060523	Olfr726	MOR246-4	olfactory receptor 726	protein-coding
mm_81899.1	chr9	119937613	119937651	+	1	NA	promoter-TSS (NM_028735)	promoter-TSS (NM_028735)	26	NM_028735	74052	Mm.189573	NM_028735	ENSMUSG00000032514	Ttc21a	4921538N17Rik|AA387572|Thm2	tetratricopeptide repeat domain 21A	protein-coding
mm_35064.1	chr4	6454069	6454075	-	1	NA	5' UTR (NM_010945, exon 1 of 31)	5' UTR (NM_010945, exon 1 of 31)	199	NM_010945	18201	Mm.3059	NM_010945	ENSMUSG00000028245	Nsmaf	AA959567|C630007J05|Fan	neutral sphingomyelinase (N-SMase) activation associated factor	protein-coding
mm_98351.1	chr11	93421426	93421430	+	1	NA	intron (NM_028296, intron 3 of 8)	intron (NM_028296, intron 3 of 8)	322138	NM_028296	72605	Mm.342160	NM_028296	ENSMUSG00000056158	Car10	2700029L05Rik|BB085816|Ca10	carbonic anhydrase 10	protein-coding
mm_56208.1	chr6	89273207	89273248	-	1	NA	intron (NR_131021, intron 3 of 3)	intron (NR_131021, intron 3 of 3)	12498	NR_131021	75131	Mm.391482	NR_131021	ENSMUSG00000107622	4930512J16Rik	-	RIKEN cDNA 4930512J16 gene	ncRNA
mm_683.1	chr1	40515378	40515431	+	1	NA	promoter-TSS (NM_010553)	promoter-TSS (NM_010553)	42	NM_010553	16174	Mm.20466	NM_010553	ENSMUSG00000026068	Il18rap	AcPL|IL-18R-beta|IL-18RAcP|IL-18Rbeta|IL-1RAcPL	interleukin 18 receptor accessory protein	protein-coding
mm_24457.1	chr3	90613776	90613853	+	1	NA	exon (NM_011313, exon 2 of 3)	exon (NM_011313, exon 2 of 3)	920	NM_011313	20200	Mm.100144	NM_011313	ENSMUSG00000001025	S100a6	2A9|5B10|CALCYCLIN|Cacy|PRA	S100 calcium binding protein A6 (calcyclin)	protein-coding
mm_21042.1	chr2	152540017	152540031	-	1	NA	promoter-TSS (NM_001001444)	promoter-TSS (NM_001001444)	17	NM_001001444	75400	Mm.45560	NM_001001444	ENSMUSG00000044249	Defb29	0610030I09Rik|BD-29|mBD-29	defensin beta 29	protein-coding
mm_96545.1	chr11	68853296	68853340	+	1	NA	promoter-TSS (NM_023668)	promoter-TSS (NM_023668)	-187	NM_023668	83431	Mm.31979	NM_023668	ENSMUSG00000018736	Ndel1	2600006O07Rik|MITAP1|NUDEL|mNudel	nudE neurodevelopment protein 1 like 1	protein-coding
mm_79422.1	chr9	55396436	55396436	+	1	NA	intron (NM_172923, intron 3 of 10)	intron (NM_172923, intron 3 of 10)	69487	NM_172923	244886	Mm.24361	NM_172923	ENSMUSG00000032313	Tmem266	9630029F15|AI118078|HVRP1	transmembrane protein 266	protein-coding
mm_167779.1	chr9	114363956	114364002	-	1	NA	intron (NR_040738, intron 1 of 5)	intron (NR_040738, intron 1 of 5)	648	NR_040738	75100	Mm.78599	NR_040738		4930525D18Rik	-	RIKEN cDNA 4930525D18 gene	ncRNA
mm_82272.1	chr9	7350113	7350123	-	1	NA	exon (NM_008605, exon 4 of 10)	exon (NM_008605, exon 4 of 10)	2744	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_152226.1	chr19	8707842	8707852	-	1	NA	exon (NM_008577, exon 9 of 9)	exon (NM_008577, exon 9 of 9)	6050	NM_008577	17254	Mm.4114	NM_008577	ENSMUSG00000010095	Slc3a2	4F2|4F2HC|AI314110|Cd98|Ly-10|Ly-m10|Ly10|Mdu1|Mgp-2hc|NACAE	solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2	protein-coding
mm_34022.1	chr4	138035889	138035897	+	1	NA	intron (NM_172703, intron 2 of 34)	intron (NM_172703, intron 2 of 34)	42437	NM_172703	230861	Mm.268903	NM_172703	ENSMUSG00000028760	Eif4g3	1500002J22Rik|4930523M17Rik|G1-419-52|eIF4GII|repro8	eukaryotic translation initiation factor 4 gamma, 3	protein-coding
mm_108985.1	chr12	102757766	102757776	+	1	NA	promoter-TSS (NM_001142939)	promoter-TSS (NM_001142939)	39	NM_001142939	100859931	Mm.291222	NM_001142939	ENSMUSG00000041716	Gm20604	AK010878-Moap1	predicted gene 20604	protein-coding
mm_66741.1	chr7	46672555	46672559	-	1	NA	promoter-TSS (NM_009414)	promoter-TSS (NM_009414)	-20	NM_009414	21990	Mm.248684	NM_009414	ENSMUSG00000040046	Tph1	Tph	tryptophan hydroxylase 1	protein-coding
mm_33336.1	chr4	129231709	129231713	+	1	NA	intron (NM_001285867, intron 1 of 6)	intron (NM_001285867, intron 1 of 6)	-3800	NM_001285866	97130	Mm.331907	NM_001033189	ENSMUSG00000050390	C77080	Kiaa1522|mKIAA1522	expressed sequence C77080	protein-coding
mm_139969.1	chr17	71769652	71769660	+	1	NA	promoter-TSS (NM_001271484)	promoter-TSS (NM_001271484)	-35	NR_073185	78785	Mm.196382	NM_030179	ENSMUSG00000024059	Clip4	1700024K14Rik|1700074B05Rik|4833417L20Rik|5830409B12Rik|Rsnl2	CAP-GLY domain containing linker protein family, member 4	protein-coding
mm_112134.1	chr12	113000227	113000238	-	1	NA	exon (NM_028193, exon 1 of 18)	exon (NM_028193, exon 1 of 18)	389	NM_028193	72308	Mm.196721	NM_028193	ENSMUSG00000011158	Brf1	2510002F24Rik|GTF3B|TAF3C|TAFIII90|TFIIIB90|mTFIIIB90	BRF1, RNA polymerase III transcription initiation factor 90 kDa subunit	protein-coding
mm_105631.1	chr11	106928031	106928051	-	1	NA	Intergenic	Intergenic	-7326	NM_025481	66313	Mm.340955	NM_025481	ENSMUSG00000018363	Smurf2	2810411E22Rik|AI558114|AI649275	SMAD specific E3 ubiquitin protein ligase 2	protein-coding
mm_35471.1	chr4	40806564	40806581	-	1	NA	3' UTR (NM_022305, exon 6 of 6)	3' UTR (NM_022305, exon 6 of 6)	43566	NR_039584	100628614		NR_039584	ENSMUSG00000096377	Mir5123	mmu-mir-5123|mu-mir-5123	microRNA 5123	ncRNA
mm_83148.1	chr9	40456138	40456148	-	1	NA	promoter-TSS (NM_172768)	promoter-TSS (NM_172768)	-379	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_153900.1	chr19	47068413	47068423	-	1	NA	intron (NM_177342, intron 1 of 10)	CpG	670	NM_177342	226182	Mm.301522	NM_177342	ENSMUSG00000025049	Taf5	6330528C20Rik|AV117817	TATA-box binding protein associated factor 5	protein-coding
mm_96.1	chr1	8936385	8936402	+	1	NA	intron (NM_027671, intron 3 of 20)	RLTR9E|LTR|ERVK	363484	NM_001290390	71096	Mm.336395	NM_027671	ENSMUSG00000025909	Sntg1	4933426D16Rik|G1SYN|SYN4	syntrophin, gamma 1	protein-coding
mm_32755.1	chr4	116687195	116687218	+	1	NA	intron (NM_011034, intron 1 of 5)	intron (NM_011034, intron 1 of 5)	-1184	NR_040442	100502959	Mm.395400	NR_040442		AV051173	-	expressed sequence AV051173	ncRNA
mm_132245.1	chr16	32751143	32751165	+	1	NA	exon (NM_080457, exon 2 of 27)	exon (NM_080457, exon 2 of 27)	15268	NM_080457	140474	Mm.214599	NM_080457	ENSMUSG00000079620	Muc4	4933405I11Rik|Asgp	mucin 4	protein-coding
mm_74599.1	chr8	11635730	11635743	-	1	NA	promoter-TSS (NM_001167967)	promoter-TSS (NM_001167967)	0	NR_106097	102465714		NR_106097	ENSMUSG00000104958	Mir7238	mmu-mir-7238	microRNA 7238	ncRNA
mm_92746.1	chr10	80998175	80998192	-	1	NA	intron (NM_010319, intron 1 of 3)	intron (NM_010319, intron 1 of 3)	3182	NM_001038655	14708	Mm.222496	NM_010319	ENSMUSG00000048240	Gng7	AI840417	guanine nucleotide binding protein (G protein), gamma 7	protein-coding
mm_128342.1	chr15	39112643	39112699	-	1	NA	promoter-TSS (NM_198606)	promoter-TSS (NM_198606)	45	NM_172402	69906	Mm.17875	NM_172402	ENSMUSG00000022299	Slc25a32	2610043O12Rik|Mftc	solute carrier family 25, member 32	protein-coding
mm_146163.1	chr18	75106193	75106196	+	1	NA	intron (NM_027727, intron 8 of 16)	intron (NM_027727, intron 8 of 16)	87422	NM_027727	69190	Mm.173826	NM_027727	ENSMUSG00000035765	Dym	1810041M12Rik|4933427L07Rik|C030019K18Rik	dymeclin	protein-coding
mm_8599.1	chr1	156034791	156034797	-	1	NA	promoter-TSS (NM_001160180)	promoter-TSS (NM_001160180)	23	NM_001160019	208263	Mm.211654	NM_144791	ENSMUSG00000026466	Tor1aip1	LAP1|Lap1B	torsin A interacting protein 1	protein-coding
mm_30317.1	chr3	151731579	151731626	-	1	NA	3' UTR (NM_133871, exon 8 of 8)	3' UTR (NM_133871, exon 8 of 8)	18357	NM_133871	99899	Mm.30756	NM_133871	ENSMUSG00000028037	Ifi44	A430056A10Rik|AW261460|MTAP44|p44	interferon-induced protein 44	protein-coding
mm_125679.1	chr15	66615764	66615799	+	1	NA	exon (NM_001081409, exon 12 of 21)	exon (NM_001081409, exon 12 of 21)	38209	NM_001081409	239510	Mm.267473	NM_178718	ENSMUSG00000072501	Phf20l1	CGI-72|E130113K22Rik	PHD finger protein 20-like 1	protein-coding
mm_144996.1	chr18	38297211	38297231	+	1	NA	intron (NM_001164621, intron 1 of 9)	intron (NM_001164621, intron 1 of 9)	416	NM_001164621	56736	Mm.228903	NM_020012	ENSMUSG00000060450	Rnf14	2310075C09Rik|2610005D23Rik|AA986456|AU041447|D18Ertd188e|D7Bwg0165e|Triad2	ring finger protein 14	protein-coding
mm_123832.1	chr14	70627444	70627466	-	1	NA	promoter-TSS (NM_001252663)	promoter-TSS (NM_001252663)	-390	NM_001252663	13829	Mm.210863	NM_013514	ENSMUSG00000022099	Dmtn	AI325486|Epb4.9|Epb49|dematin	dematin actin binding protein	protein-coding
mm_36039.1	chr4	57241180	57241192	-	1	NA	intron (NM_011207, intron 10 of 25)	intron (NM_011207, intron 10 of 25)	60651	NM_011207	545622	Mm.246552	NM_011207	ENSMUSG00000038764	Ptpn3	9530011I20Rik|PTP-H1|PTPCL	protein tyrosine phosphatase, non-receptor type 3	protein-coding
mm_1533.1	chr1	72849275	72849290	+	1	NA	exon (NM_008342, exon 2 of 4)	exon (NM_008342, exon 2 of 4)	23895	NM_001310659	16008	Mm.141936	NM_008342	ENSMUSG00000039323	Igfbp2	AI255832|IBP-2|Igfbp-2|mIGFBP-2	insulin-like growth factor binding protein 2	protein-coding
mm_15827.1	chr2	164643952	164643957	+	1	NA	Intergenic	Intergenic	-5152	NM_001012723	277345	Mm.247244	NM_001012723	ENSMUSG00000070530	Wfdc16	BC043944|WAP16	WAP four-disulfide core domain 16	protein-coding
mm_111983.1	chr12	110471405	110471425	-	1	NA	intron (NM_001135001, intron 3 of 13)	ORR1C1|LTR|ERVL-MaLR	-14324	NM_001081457	26931	Mm.240396	NM_012023	ENSMUSG00000017843	Ppp2r5c	2610043M05Rik|2700063L20Rik|AI060890|AW545884|C85228|D12Bwg0916e|mKIAA0044	protein phosphatase 2, regulatory subunit B', gamma	protein-coding
mm_164783.1	chr18	7585700	7585706	+	1	NA	intron (NM_001081287, intron 1 of 16)	ID_B1|SINE|B4	41160	NM_001081287	75739	Mm.133293	NM_001081287	ENSMUSG00000057440	Mpp7	1110068J02Rik|2810038M04Rik|5430426E14Rik|AI415104|Gm955	membrane protein, palmitoylated 7 (MAGUK p55 subfamily member 7)	protein-coding
mm_66097.1	chr7	31036458	31036499	-	1	NA	exon (NM_001111073, exon 5 of 8)	exon (NM_001111073, exon 5 of 8)	3839	NR_106017	102465635		NR_106017	ENSMUSG00000098783	Mir7050	Gm27578|mmu-mir-7050	microRNA 7050	ncRNA
mm_163274.1	chr11	115466669	115466673	+	1	NA	intron (NM_001080934, intron 2 of 3)	B4|SINE|B4	4198	NM_001080934	217316	Mm.25773	NM_001080934	ENSMUSG00000045775	Slc16a5	A130015N09Rik|MCT 5|MCT 6|MCT5	solute carrier family 16 (monocarboxylic acid transporters), member 5	protein-coding
mm_104609.1	chr11	97188071	97188072	-	1	NA	promoter-TSS (NM_008379)	promoter-TSS (NM_008379)	-179	NM_008379	16211	Mm.251013	NM_008379	ENSMUSG00000001440	Kpnb1	AA409963|IPOB|Impnb	karyopherin (importin) beta 1	protein-coding
mm_72046.1	chr8	71310681	71310710	+	1	NA	intron (NM_015742, intron 2 of 39)	RLTR17|LTR|ERVK	37981	NM_001142323	17925	Mm.33779	NM_015742	ENSMUSG00000004677	Myo9b	-	myosin IXb	protein-coding
mm_76645.1	chr8	93100410	93100421	-	1	NA	intron (NM_007954, intron 12 of 12)	intron (NM_007954, intron 12 of 12)	-20398	NM_001081372	382044	Mm.482549	NM_001081372	ENSMUSG00000078964	Ces1b	Gm5158	carboxylesterase 1B	protein-coding
mm_141796.1	chr17	34344187	34344191	-	1	NA	intron (NM_010381, intron 1 of 3)	intron (NM_010381, intron 1 of 3)	456	NM_010381	100504404	Mm.15680	NM_010381		H2-Ea-ps	AI323765|E-alpha-f|H-2Ea|H2-Ea|I-Ealpha|Ia-3|Ia3|MHC-H2-Ea	histocompatibility 2, class II antigen E alpha, pseudogene	protein-coding
mm_101984.1	chr11	50557088	50557103	-	1	NA	Intergenic	Lx8|LINE|L1	-44990	NM_175643	216725	Mm.110597	NM_175643	ENSMUSG00000036545	Adamts2	ADAM-TS 2|ADAM-TS2|ADAMTS-2|PC I-NP|PCINP|pNPI	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 2	protein-coding
mm_160195.1	chr7	63924762	63924762	-	1	NA	intron (NM_021366, intron 1 of 1)	intron (NM_021366, intron 1 of 1)	7905	NM_001256311	381994	Mm.425466	NM_001256311	ENSMUSG00000095061	E030018B13Rik	Gm1697	RIKEN cDNA E030018B13 gene	protein-coding
mm_148288.1	chr18	82575202	82575213	-	1	NA	exon (NM_010777, exon 6 of 7)	exon (NM_010777, exon 6 of 7)	20699	NM_001025254	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_165638.1	chr3	73708361	73708363	-	1	NA	promoter-TSS (NM_009738)	promoter-TSS (NM_009738)	53	NM_009738	12038	Mm.250719	NM_009738	ENSMUSG00000027792	Bche	C730038G20Rik	butyrylcholinesterase	protein-coding
mm_12911.1	chr2	84840650	84840662	+	1	NA	promoter-TSS (NM_001083809)	promoter-TSS (NM_001083809)	30	NM_001083809	72401	Mm.22716	NM_024497	ENSMUSG00000027075	Slc43a1	2610016F07Rik|AA986141|Lat3|PB39|Pov1|R00504	solute carrier family 43, member 1	protein-coding
mm_11066.1	chr2	27676241	27676252	+	1	NA	promoter-TSS (NM_011305)	promoter-TSS (NM_011305)	-955	NM_011305	20181	Mm.24624	NM_011305	ENSMUSG00000015846	Rxra	9530071D11Rik|Nr2b1|RXRalpha1	retinoid X receptor alpha	protein-coding
mm_164870.1	chr18	56733874	56733881	-	1	NA	intron (NM_010721, intron 5 of 10)	PB1D9|SINE|Alu	26064	NM_010721	16906	Mm.4105	NM_010721	ENSMUSG00000024590	Lmnb1	-	lamin B1	protein-coding
mm_89182.1	chr10	86345896	86345947	+	1	NA	3' UTR (NM_011595, exon 5 of 5)	3' UTR (NM_011595, exon 5 of 5)	45509	NM_011595	21859	Mm.4871	NM_011595	ENSMUSG00000020044	Timp3	Timp-3	tissue inhibitor of metalloproteinase 3	protein-coding
mm_34376.1	chr4	144893863	144893875	+	1	NA	intron (NM_011303, intron 1 of 5)	intron (NM_011303, intron 1 of 5)	732	NM_011303	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding
mm_79290.1	chr9	51213720	51213725	+	1	NA	promoter-TSS (NM_011136)	promoter-TSS (NM_011136)	32	NM_011136	18985	Mm.897	NM_011136	ENSMUSG00000032053	Pou2af1	BOB.1|Bob-1|Bob1|OBF-1|OBF.1|OCA-B|OCAB	POU domain, class 2, associating factor 1	protein-coding
mm_71132.1	chr8	36745112	36745135	+	1	NA	intron (NM_001194940, intron 5 of 17)	intron (NM_001194940, intron 5 of 17)	-12069	NM_001194941	50768	Mm.125155	NM_015802	ENSMUSG00000031523	Dlc1	A730069N07Rik|Arhgap7|HP|STARD12|dlc-1	deleted in liver cancer 1	protein-coding
mm_62832.1	chr7	113765838	113765847	+	1	NA	promoter-TSS (NM_145584)	promoter-TSS (NM_145584)	-156	NM_145584	233744	Mm.334160	NM_145584	ENSMUSG00000038156	Spon1	AI666765|AW455831|BC020531|D330035F22Rik|FSP	spondin 1, (f-spondin) extracellular matrix protein	protein-coding
mm_138050.1	chr17	33926266	33926279	+	1	NA	exon (NM_009318, exon 5 of 8)	exon (NM_009318, exon 5 of 8)	-3622	NM_009059	19732	Mm.43777	NM_009059	ENSMUSG00000041354	Rgl2	KE1.5|Rab2l|Rgt2|Rlf	ral guanine nucleotide dissociation stimulator-like 2	protein-coding
mm_84681.1	chr9	72110835	72110870	-	1	NA	intron (NM_001253865, intron 1 of 14)	intron (NM_001253865, intron 1 of 14)	349	NM_001253862	21406	Mm.171615	NM_011544	ENSMUSG00000032228	Tcf12	A130037E08Rik|ALF1|HEB|HEBAlt|HTF-4|HTF4|ME1|REB|bHLHb20	transcription factor 12	protein-coding
mm_146989.1	chr18	34007255	34007361	-	1	NA	promoter-TSS (NM_013512)	promoter-TSS (NM_013512)	-102	NM_013512	13824	Mm.3465	NM_013512	ENSMUSG00000024376	Epb41l4a	Epb4.1l4|Epb4.1l4a|NBL4	erythrocyte membrane protein band 4.1 like 4a	protein-coding
mm_101020.1	chr11	8575614	8575633	-	1	NA	intron (NM_001083587, intron 4 of 30)	intron (NM_001083587, intron 4 of 30)	88912	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_124844.1	chr15	9436086	9436103	+	1	NA	promoter-TSS (NM_029341)	promoter-TSS (NM_029341)	66	NM_029341	75568	Mm.82143	NM_029341	ENSMUSG00000039676	Capsl	1700028N11Rik|AW125205	calcyphosine-like	protein-coding
mm_120063.1	chr14	56903915	56903939	+	1	NA	intron (NM_029498, intron 2 of 23)	intron (NM_029498, intron 2 of 23)	16132	NM_029498	76007	Mm.31417	NM_029498	ENSMUSG00000021945	Zmym2	5830413P05Rik|FIM|MYM|RAMP|SCLL|Zfp198|Znf198	zinc finger, MYM-type 2	protein-coding
mm_102030.1	chr11	51693099	51693142	-	1	NA	3' UTR (NM_175255, exon 23 of 23)	3' UTR (NM_175255, exon 23 of 23)	-4486	NM_025319	66050	Mm.35693	NM_025319	ENSMUSG00000007777	0610009B22Rik	-	RIKEN cDNA 0610009B22 gene	protein-coding
mm_74169.1	chr8	123420795	123420840	+	1	NA	exon (NM_023279, exon 4 of 4)	exon (NM_023279, exon 4 of 4)	9253	NM_023279	22152	Mm.40068	NM_023279	ENSMUSG00000062380	Tubb3	3200002H15Rik|M(beta)3|M(beta)6	tubulin, beta 3 class III	protein-coding
mm_68042.1	chr7	101362771	101362780	-	1	NA	intron (NM_001040111, intron 1 of 33)	intron (NM_001040111, intron 1 of 33)	14706	NM_001040111	69710	Mm.277687	NM_027180	ENSMUSG00000032812	Arap1	2410002L19Rik|Centd2|mKIAA0782	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	protein-coding
mm_17803.1	chr2	33371383	33371389	-	1	NA	5' UTR (NM_175211, exon 1 of 20)	5' UTR (NM_175211, exon 1 of 20)	108	NM_001290570	241308	Mm.274249	NM_175211	ENSMUSG00000038831	Ralgps1	5830418G11Rik|AI853783|AI854138|RALGEF2|RALGPS1A|RalGEF 2|mKIAA0351	Ral GEF with PH domain and SH3 binding motif 1	protein-coding
mm_157973.1	chrX	93832021	93832031	-	1	NA	promoter-TSS (NM_145630)	promoter-TSS (NM_145630)	69	NM_145630	236900	Mm.12775	NM_145630	ENSMUSG00000035232	Pdk3	2610001M10Rik|AI035637	pyruvate dehydrogenase kinase, isoenzyme 3	protein-coding
mm_17034.1	chr2	20654683	20654692	-	1	NA	intron (NM_029895, intron 3 of 18)	intron (NM_029895, intron 3 of 18)	135174	NM_001177631	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding
mm_148444.1	chr19	3964331	3964344	+	1	NA	intron (NM_028545, intron 2 of 9)	MIR|SINE|MIR	5529	NM_028545	73458	Mm.482922	NM_028545	ENSMUSG00000037263	Aldh3b3	1700055N04Rik	aldehyde dehydrogenase 3 family, member B3	protein-coding
mm_165211.1	chr2	35341561	35341565	+	1	NA	Intergenic	Intergenic	-4554	NM_013515	13830	Mm.295284	NM_013515	ENSMUSG00000026880	Stom	Epb7.2	stomatin	protein-coding
mm_144090.1	chr18	3281235	3281249	+	1	NA	promoter-TSS (NM_001311067)	promoter-TSS (NM_001311067)	-110	NM_001311067	12916	Mm.5244	NM_013498	ENSMUSG00000063889	Crem	ICER|ICERI	cAMP responsive element modulator	protein-coding
mm_148186.1	chr18	78859872	78859874	-	1	NA	exon (NM_053099, exon 4 of 6)	exon (NM_053099, exon 4 of 6)	249518	NM_053099	240427	Mm.312871	NM_053099	ENSMUSG00000024548	Setbp1	C130092E12|Seb|mKIAA0437	SET binding protein 1	protein-coding
mm_134609.1	chr16	20717723	20717751	-	1	NA	promoter-TSS (NM_145632)	promoter-TSS (NM_145632)	-89	NM_145632	245841	Mm.288730	NM_145632	ENSMUSG00000021018	Polr2h	-	polymerase (RNA) II (DNA directed) polypeptide H	protein-coding
mm_118450.1	chr14	8332447	8332453	+	1	NA	Intergenic	URR1A|DNA|hAT-Charlie	-22674	NM_183187	268709	Mm.256058	NM_183187	ENSMUSG00000021750	Fam107a	DRR1	family with sequence similarity 107, member A	protein-coding
mm_134273.1	chr16	13986914	13986933	-	1	NA	promoter-TSS (NM_001270718)	promoter-TSS (NM_001270718)	-56	NM_001270718	74482	Mm.484026	NM_028968	ENSMUSG00000065968	Ifitm7	4933438K12Rik|Mil4	interferon induced transmembrane protein 7	protein-coding
mm_6414.1	chr1	73015885	73015901	-	1	NA	promoter-TSS (NR_038001)	promoter-TSS (NR_038001)	6	NM_009407	21958	Mm.425024	NM_009407	ENSMUSG00000026182	Tnp1	Stp-1|TP1|Tp-1	transition protein 1	protein-coding
mm_80125.1	chr9	70579373	70579386	+	1	NA	exon (NM_025690, exon 10 of 21)	exon (NM_025690, exon 10 of 21)	36509	NM_025690	66660	Mm.22379	NM_025690	ENSMUSG00000032212	Sltm	5730455C01Rik|5730555F13Rik|9130215G10Rik|Met	SAFB-like, transcription modulator	protein-coding
mm_104014.1	chr11	85311073	85311103	-	1	NA	promoter-TSS (NM_016910)	promoter-TSS (NM_016910)	-166	NM_016910	53892	Mm.45609	NM_016910	ENSMUSG00000020525	Ppm1d	AV338790|Wip1	protein phosphatase 1D magnesium-dependent, delta isoform	protein-coding
mm_103107.1	chr11	69980234	69980271	-	1	NA	promoter-TSS (NM_026017)	promoter-TSS (NM_026017)	78	NM_001253700	54351	Mm.13430	NM_018740	ENSMUSG00000018565	Elp5	Derp6|Rai12	elongator acetyltransferase complex subunit 5	protein-coding
mm_161870.1	chr18	36946010	36946010	+	1	NA	promoter-TSS (NM_138662)	promoter-TSS (NM_138662)	-197	NM_138662	192163	Mm.308500	NM_138662	ENSMUSG00000102312	Pcdha3	mKIAA0345	protocadherin alpha 3	protein-coding
mm_120691.1	chr14	70774974	70774984	+	1	NA	intron (NM_010071, intron 1 of 4)	intron (NM_010071, intron 1 of 4)	598	NM_010071	13449	Mm.243323	NM_010071	ENSMUSG00000022102	Dok2	DokR|Frip	docking protein 2	protein-coding
mm_57241.1	chr6	123283079	123283090	-	1	NA	3' UTR (NM_019948, exon 6 of 6)	3' UTR (NM_019948, exon 6 of 6)	6787	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_4859.1	chr1	187616359	187616364	+	1	NA	intron (NM_001243792, intron 1 of 7)	intron (NM_001243792, intron 1 of 7)	7355	NM_001243792	26381	Mm.89989	NM_011935	ENSMUSG00000026610	Esrrg	ERR3|Errg|NR3B3|mKIAA0832	estrogen-related receptor gamma	protein-coding
mm_86904.1	chr10	22343427	22343441	+	1	NA	intron (NM_009018, intron 5 of 5)	intron (NM_009018, intron 5 of 5)	-18460	NM_020030	56554	Mm.458004	NM_020030	ENSMUSG00000078452	Raet1d	RAE-1delta	retinoic acid early transcript delta	protein-coding
mm_95133.1	chr11	34783255	34783291	+	1	NA	intron (NM_033374, intron 1 of 51)	intron (NM_033374, intron 1 of 51)	632	NM_033374	94176	Mm.380679	NM_033374	ENSMUSG00000020143	Dock2	AI662014|AW122239|CED-5|Hch|MBC	dedicator of cyto-kinesis 2	protein-coding
mm_149809.1	chr19	23845607	23845609	+	1	NA	intron (NM_177034, intron 1 of 12)	intron (NM_177034, intron 1 of 12)	86732	NM_177034	319924	Mm.22879	NM_177034	ENSMUSG00000024897	Apba1	6430513E09Rik|Lin-10|Mint|Mint1|Urop11|X11|X11alpha	amyloid beta (A4) precursor protein binding, family A, member 1	protein-coding
mm_124242.1	chr14	101514027	101514031	-	1	NA	intron (NM_001081278, intron 1 of 18)	AT_rich|Low_complexity|Low_complexity	95162	NM_001081278	210789	Mm.320639	NM_173380	ENSMUSG00000033083	Tbc1d4	5930406J04Rik|A930035N22|AV295684|As160	TBC1 domain family, member 4	protein-coding
mm_112814.1	chr13	20794921	20794942	+	1	NA	intron (NM_012054, intron 1 of 20)	intron (NM_012054, intron 1 of 20)	818	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_6315.1	chr1	71600338	71600367	-	1	NA	exon (NM_001276413, exon 34 of 44)	exon (NM_001276413, exon 34 of 44)	43196	NM_026195	108147	Mm.38010	NM_026195	ENSMUSG00000026192	Atic	2610509C24Rik|AA536954|AW212393	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	protein-coding
mm_30326.1	chr3	151732015	151732027	-	1	NA	3' UTR (NM_133871, exon 8 of 8)	3' UTR (NM_133871, exon 8 of 8)	17938	NM_133871	99899	Mm.30756	NM_133871	ENSMUSG00000028037	Ifi44	A430056A10Rik|AW261460|MTAP44|p44	interferon-induced protein 44	protein-coding
mm_95466.1	chr11	50602073	50602094	+	1	NA	promoter-TSS (NM_175643)	promoter-TSS (NM_175643)	-2	NM_175643	216725	Mm.110597	NM_175643	ENSMUSG00000036545	Adamts2	ADAM-TS 2|ADAM-TS2|ADAMTS-2|PC I-NP|PCINP|pNPI	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 2	protein-coding
mm_106582.1	chr11	120729596	120729623	-	1	NA	3' UTR (NM_007621, exon 8 of 8)	3' UTR (NM_007621, exon 8 of 8)	-2325	NM_001347608	67880	Mm.231091	NM_026428	ENSMUSG00000039450	Dcxr	0610038K04Rik|1810027P18Rik|XR	dicarbonyl L-xylulose reductase	protein-coding
mm_69476.1	chr7	133738948	133738961	-	1	NA	intron (NM_133941, intron 4 of 11)	intron (NM_133941, intron 4 of 11)	21315	NM_001286030	101437	Mm.199223	NM_133941	ENSMUSG00000030986	Dhx32	3110079L04Rik|4732469F02Rik|AA408140|Ddx32	DEAH (Asp-Glu-Ala-His) box polypeptide 32	protein-coding
mm_144737.1	chr18	35562435	35562490	+	1	NA	intron (NM_010771, intron 1 of 14)	CpG	304	NM_010771	17184	Mm.215034	NM_010771	ENSMUSG00000037236	Matr3	1110061A14Rik|2810017I02Rik|AI841759|AW555618|D030046F20Rik|mKIAA0723	matrin 3	protein-coding
mm_167524.1	chr9	21287695	21287720	+	1	NA	TTS (NM_009878)	TTS (NM_009878)	262	NM_145416	215194	Mm.290690	NM_145416	ENSMUSG00000035047	Kri1	-	KRI1 homolog	protein-coding
mm_60624.1	chr7	44708761	44708778	+	1	NA	promoter-TSS (NM_029317)	promoter-TSS (NM_029317)	26	NM_029317	75510	Mm.273301	NM_029317	ENSMUSG00000066500	Izumo2	1700023D19Rik	IZUMO family member 2	protein-coding
mm_96362.1	chr11	67097895	67097948	+	1	NA	exon (NM_001099635, exon 32 of 41)	exon (NM_001099635, exon 32 of 41)	-1883	NR_105888	102466766		NR_105888	ENSMUSG00000098855	Mir6923	Gm27312|mmu-mir-6923	microRNA 6923	ncRNA
mm_107806.1	chr12	65036320	65036358	+	1	NA	promoter-TSS (NM_177806)	promoter-TSS (NM_177806)	5	NM_177806	328110	Mm.283339	NM_177806	ENSMUSG00000035597	Prpf39	Srcs1	pre-mRNA processing factor 39	protein-coding
mm_126654.1	chr15	84192224	84192260	+	1	NA	promoter-TSS (NM_178614)	promoter-TSS (NM_178614)	9	NM_178614	68653	Mm.290725	NM_178614	ENSMUSG00000022437	Samm50	1110030L07Rik	SAMM50 sorting and assembly machinery component	protein-coding
mm_51551.1	chr6	83317253	83317264	+	1	NA	intron (NM_008638, intron 1 of 7)	intron (NM_008638, intron 1 of 7)	346	NM_008638	17768	Mm.443	NM_008638	ENSMUSG00000005667	Mthfd2	AW558851|NMDMC	methylenetetrahydrofolate dehydrogenase (NAD+ dependent), methenyltetrahydrofolate cyclohydrolase	protein-coding
mm_82408.1	chr9	14771206	14771221	-	1	NA	promoter-TSS (NM_029306)	promoter-TSS (NM_029306)	-183	NM_029306	69325	Mm.440453	NM_029306	ENSMUSG00000031927	1700012B09Rik	1700007P19Rik	RIKEN cDNA 1700012B09 gene	protein-coding
mm_144057.1	chr17	90611928	90611969	-	1	NA	intron (NM_001346957, intron 9 of 18)	intron (NM_001346957, intron 9 of 18)	-156068	NM_001346959	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_126765.1	chr15	85860015	85860057	+	1	NA	promoter-TSS (NM_013882)	promoter-TSS (NM_013882)	90	NM_013882	29870	Mm.20858	NM_013882	ENSMUSG00000022385	Gtse1	B99|Gtse-1	G two S phase expressed protein 1	protein-coding
mm_47612.1	chr5	125140870	125140889	-	1	NA	intron (NM_011424, intron 1 of 46)	intron (NM_011424, intron 1 of 46)	38335	NM_001253905	20602	Mm.278646	NM_011424	ENSMUSG00000029478	Ncor2	N-CoR|SMRT|SMRTe	nuclear receptor co-repressor 2	protein-coding
mm_94264.1	chr11	3514931	3514952	+	1	NA	5' UTR (NM_053267, exon 1 of 5)	5' UTR (NM_053267, exon 1 of 5)	257	NM_053267	114679	Mm.34046	NM_053267	ENSMUSG00000075702	Selenom	1500040L08Rik|A230103K18|Selm|Sepm	selenoprotein M	protein-coding
mm_41384.1	chr5	90759350	90759367	+	1	NA	promoter-TSS (NM_009141)	promoter-TSS (NM_009141)	60	NM_009141	20311	Mm.4660	NM_009141	ENSMUSG00000029371	Cxcl5	AMCF-II|Cxcl6|ENA-78|GCP-2|LIX|Scyb5|Scyb6	chemokine (C-X-C motif) ligand 5	protein-coding
mm_39619.1	chr5	24413383	24413398	+	1	NA	promoter-TSS (NM_183000)	promoter-TSS (NM_183000)	-61	NM_183000	171209	Mm.299636	NM_183000	ENSMUSG00000038276	Asic3	AW742291|Accn3|DRASIC|SLNAC1|TNAC1	acid-sensing (proton-gated) ion channel 3	protein-coding
mm_92433.1	chr10	77166502	77166524	-	1	NA	promoter-TSS (NM_009929)	promoter-TSS (NM_009929)	17	NM_009929	12822	Mm.4352	NM_009929	ENSMUSG00000001435	Col18a1	-	collagen, type XVIII, alpha 1	protein-coding
mm_91453.1	chr10	34019498	34019559	-	1	NA	promoter-TSS (NM_025614)	promoter-TSS (NM_025614)	88	NM_025614	66521	Mm.28528	NM_025614	ENSMUSG00000019782	Rwdd1	0710001K08Rik|2610002D06Rik|2700069A07Rik|IH1	RWD domain containing 1	protein-coding
mm_109076.1	chr12	104387760	104387791	+	1	NA	intron (NM_009253, intron 1 of 4)	intron (NM_009253, intron 1 of 4)	611	NM_009253	20717	Mm.395085	NM_009253	ENSMUSG00000079012	Serpina3m	3e46|AI195004|MMCM7|MMSPi2.4|Spi-2l|Spi-2rs1|Spi2-rs1|Spi2.4|spi2	serine (or cysteine) peptidase inhibitor, clade A, member 3M	protein-coding
mm_13937.1	chr2	121140740	121140767	+	1	NA	promoter-TSS (NM_177846)	promoter-TSS (NM_177846)	-55	NM_177846	329504	Mm.219449	NM_177846	ENSMUSG00000074890	Lcmt2	D330024M17|Tyw4	leucine carboxyl methyltransferase 2	protein-coding
mm_49689.1	chr6	33457002	33457018	+	1	NA	intron (NM_009148, intron 9 of 17)	intron (NM_009148, intron 9 of 17)	207860	NM_009148	20336	Mm.265512	NM_009148	ENSMUSG00000029763	Exoc4	C78892|Sec8|Sec8l1	exocyst complex component 4	protein-coding
mm_45362.1	chr5	66001357	66001390	-	1	NA	non-coding (NR_027961, exon 2 of 7)	non-coding (NR_027961, exon 2 of 7)	2912	NR_027961	231253	Mm.436542	NM_177679	ENSMUSG00000054598	9130230L23Rik	-	RIKEN cDNA 9130230L23 gene	ncRNA
mm_89154.1	chr10	86032995	86033006	+	1	NA	intron (NM_001347151, intron 4 of 8)	intron (NM_001347151, intron 4 of 8)	10846	NM_001347151	69754	Mm.44236	NM_153195	ENSMUSG00000001786	Fbxo7	2410015K21Rik|A230052G17Rik|AI117679|AW260462|C85118	F-box protein 7	protein-coding
mm_15355.1	chr2	156312420	156312426	+	1	NA	promoter-TSS (NM_027585)	promoter-TSS (NM_027585)	-50	NM_027585	70873	Mm.475234	NM_027585	ENSMUSG00000038085	Cnbd2	4921517L17Rik|5430421B09Rik|Cris	cyclic nucleotide binding domain containing 2	protein-coding
mm_33523.1	chr4	130932013	130932025	+	1	NA	exon (NM_010686, exon 7 of 8)	exon (NM_010686, exon 7 of 8)	-12366	NM_010769	17180	Mm.271796	NM_010769	ENSMUSG00000040533	Matn1	CMP|Crtm|Mat1|matrilin-1	matrilin 1, cartilage matrix protein	protein-coding
mm_119274.1	chr14	34218210	34218241	+	1	NA	Intergenic	Intergenic	-1821	NM_176931	319508	Mm.228006	NM_176931	ENSMUSG00000041479	Syt15	CHR10SYT|E230025K04Rik|sytXV	synaptotagmin XV	protein-coding
mm_18001.1	chr2	38214444	38214459	-	1	NA	intron (NM_146122, intron 2 of 21)	intron (NM_146122, intron 2 of 21)	72933	NM_146122	227801	Mm.314245	NM_146122	ENSMUSG00000035392	Dennd1a	6030446I19Rik|connecdenn	DENN/MADD domain containing 1A	protein-coding
mm_7588.1	chr1	125435433	125435444	-	1	NA	5' UTR (NM_023735, exon 1 of 12)	5' UTR (NM_023735, exon 1 of 12)	289	NM_023735	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding
mm_17916.1	chr2	35432553	35432623	-	1	NA	5' UTR (NM_001145821, exon 2 of 8)	5' UTR (NM_001145821, exon 2 of 8)	28861	NM_001308299	14594	Mm.281124	NM_010283	ENSMUSG00000035778	Ggta1	AW108479|GALT|Gal|Ggta|Ggta-1|alpha Gal|alpha3GalT	glycoprotein galactosyltransferase alpha 1, 3	protein-coding
mm_82773.1	chr9	26977904	26977909	-	1	NA	intron (NM_025862, intron 9 of 10)	intron (NM_025862, intron 9 of 10)	21643	NM_025862	66948	Mm.289244	NM_025862	ENSMUSG00000031969	Acad8	2310016C19Rik|AI786953	acyl-Coenzyme A dehydrogenase family, member 8	protein-coding
mm_149601.1	chr19	16328627	16328637	+	1	NA	intron (NM_008139, intron 3 of 6)	intron (NM_008139, intron 3 of 6)	-13628	NR_105832	102465218		NR_105832	ENSMUSG00000098718	Mir496b	Gm28028|mmu-mir-496b	microRNA 496b	ncRNA
mm_51104.1	chr6	67277759	67277807	+	1	NA	exon (NM_025814, exon 6 of 8)	exon (NM_025814, exon 6 of 8)	10804	NM_025814	66870	Mm.240490	NM_025814	ENSMUSG00000036371	Serbp1	1200009K13Rik|9330147J08Rik|AL022786|Pairbp1	serpine1 mRNA binding protein 1	protein-coding
mm_83370.1	chr9	44479725	44479743	-	1	NA	Intergenic	Intergenic	-19402	NM_030256	80288	Mm.370270	NM_030256	ENSMUSG00000063382	Bcl9l	B9L|BC003321|BCL9-2|DLNB11	B cell CLL/lymphoma 9-like	protein-coding
mm_51466.1	chr6	82737367	82737367	+	1	NA	intron (NM_013820, intron 9 of 17)	intron (NM_013820, intron 9 of 17)	37087	NM_013820	15277	Mm.255848	NM_013820	ENSMUSG00000000628	Hk2	AI642394|HKII	hexokinase 2	protein-coding
mm_1276.1	chr1	63445949	63445980	+	1	NA	promoter-TSS (NM_011780)	promoter-TSS (NM_011780)	73	NM_011780	23792	Mm.124892	NM_011780	ENSMUSG00000025964	Adam23	AW046396|MDC3	a disintegrin and metallopeptidase domain 23	protein-coding
mm_15479.1	chr2	157561476	157561485	+	1	NA	intron (NM_010923, intron 2 of 2)	(CAG)n|Simple_repeat|Simple_repeat	1402	NM_180960	18111	Mm.34330	NM_010923	ENSMUSG00000067786	Nnat	5730414I02Rik|AW107673|Peg5	neuronatin	protein-coding
mm_127707.1	chr15	102998228	102998247	+	1	NA	Intergenic	Intergenic	7698	NM_010466	15426	Mm.6167	NM_010466	ENSMUSG00000001657	Hoxc8	D130011F21Rik|Hox-3.1	homeobox C8	protein-coding
mm_117625.1	chr13	91876877	91876890	-	1	NA	promoter-TSS (NM_198415)	promoter-TSS (NM_198415)	2	NM_198415	76722	Mm.316438	NM_198415	ENSMUSG00000021622	Ckmt2	2300008A19Rik|ScCKmit	creatine kinase, mitochondrial 2	protein-coding
mm_100103.1	chr11	115766677	115766738	+	1	NA	intron (NM_028014, intron 1 of 31)	intron (NM_028014, intron 1 of 31)	1274	NM_028014	71947	Mm.23168	NM_028014	ENSMUSG00000020747	Tmem94	2310067B10Rik|Kiaa0195|mKIAA0195	transmembrane protein 94	protein-coding
mm_3894.1	chr1	161396864	161396865	+	1	NA	intron (NM_009452, intron 1 of 2)	intron (NM_009452, intron 1 of 2)	1426	NM_009452	22164	Mm.4994	NM_009452	ENSMUSG00000026700	Tnfsf4	Ath-1|Ath1|CD134L|OX-40L|Ox40l|TXGP1|Tnlg2b|Txgp1l|gp34	tumor necrosis factor (ligand) superfamily, member 4	protein-coding
mm_7143.1	chr1	91216952	91216959	-	1	NA	intron (NM_016894, intron 2 of 2)	intron (NM_016894, intron 2 of 2)	-33364	NM_026454	67921	Mm.337238	NM_026454	ENSMUSG00000034343	Ube2f	2510010F15Rik|AI851109	ubiquitin-conjugating enzyme E2F (putative)	protein-coding
mm_89064.1	chr10	82897063	82897073	+	1	NA	3' UTR (NM_001042523, exon 15 of 15)	3' UTR (NM_001042523, exon 15 of 15)	30442	NM_025499	66341	Mm.443284	NM_025499	ENSMUSG00000109864	Eid3	1700027M21Rik|NS4EB	EP300 interacting inhibitor of differentiation 3	protein-coding
mm_120120.1	chr14	59625279	59625291	+	1	NA	promoter-TSS (NM_145463)	promoter-TSS (NM_145463)	4	NM_145463	219134	Mm.275409	NM_145463	ENSMUSG00000044461	Shisa2	9430059P22Rik|MAd2|Tmem46|mShisa|shisa	shisa family member 2	protein-coding
mm_7841.1	chr1	132357625	132357660	-	1	NA	exon (NM_178874, exon 5 of 5)	exon (NM_178874, exon 5 of 5)	10306	NM_001311108	68875	Mm.273785	NM_178874	ENSMUSG00000042066	Tmcc2	1110063G11Rik	transmembrane and coiled-coil domains 2	protein-coding
mm_162088.1	chrX	37432503	37432503	+	1	NA	promoter-TSS (NM_021300)	promoter-TSS (NM_021300)	9	NM_021300	57737	Mm.327419	NM_021300	ENSMUSG00000071771	Rhox4b	5430432L21Rik|Ehox|Rhox4.2|Rhox4a	reproductive homeobox 4B	protein-coding
mm_48418.1	chr5	140360379	140360428	-	1	NA	intron (NM_172277, intron 1 of 10)	intron (NM_172277, intron 1 of 10)	28481	NM_008637	17766	Mm.118846	NM_008637	ENSMUSG00000036639	Nudt1	Mth1	nudix (nucleoside diphosphate linked moiety X)-type motif 1	protein-coding
mm_64011.1	chr7	140218089	140218099	+	1	NA	promoter-TSS (NM_172909)	promoter-TSS (NM_172909)	-173	NM_172909	244233	Mm.19283	NM_172909	ENSMUSG00000025461	Cd163l1	B430307C05|E430002D04Rik|Scart1	CD163 molecule-like 1	protein-coding
mm_125415.1	chr15	41789496	41789527	+	1	NA	promoter-TSS (NM_001130163)	promoter-TSS (NM_001130163)	-4	NM_001130163	170719	Mm.254267	NM_130885	ENSMUSG00000022307	Oxr1	2210416C20Rik|C7|C7B	oxidation resistance 1	protein-coding
mm_16217.1	chr2	173082774	173082780	+	1	NA	Intergenic	Intergenic	36748	NM_001081387	664799	Mm.389396	NM_001081387	ENSMUSG00000070495	Ctcfl	Boris|OTTMUSG00000016680	CCCTC-binding factor (zinc finger protein)-like	protein-coding
mm_21811.1	chr2	165135446	165135454	-	1	NA	intron (NM_174988, intron 7 of 11)	intron (NM_174988, intron 7 of 11)	-44700	NR_033448	72211	Mm.482899	NR_033448	ENSMUSG00000078935	1700025C18Rik	-	RIKEN cDNA 1700025C18 gene	ncRNA
mm_131904.1	chr16	23268496	23268539	+	1	NA	intron (NM_001252505, intron 2 of 7)	intron (NM_001252505, intron 2 of 7)	-21953	NM_001252506	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_83143.1	chr9	40455507	40455520	-	1	NA	exon (NM_172768, exon 1 of 20)	exon (NM_172768, exon 1 of 20)	251	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_76354.1	chr8	84771986	84772002	-	1	NA	exon (NM_010906, exon 2 of 9)	exon (NM_010906, exon 2 of 9)	2375	NM_001081981	18032	Mm.9394	NM_010906	ENSMUSG00000001911	Nfix	CTF|NF-I/X|NF1-X|NFI-X	nuclear factor I/X	protein-coding
mm_132764.1	chr16	44724570	44724617	+	1	NA	intron (NM_145972, intron 1 of 8)	CpG	292	NM_145972	212547	Mm.310573	NM_145972	ENSMUSG00000036208	Nepro	-	nucleolus and neural progenitor protein	protein-coding
mm_32246.1	chr4	102570066	102570124	+	1	NA	promoter-TSS (NM_001177980)	promoter-TSS (NM_001177980)	35	NM_001177980	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_24873.1	chr3	95982386	95982402	+	1	NA	Intergenic	Intergenic	-3116	NR_045872	668224	Mm.357766	NR_045872		Gm9054	EG668224	predicted gene 9054	ncRNA
mm_128518.1	chr15	53902394	53902450	-	1	NA	promoter-TSS (NM_177225)	promoter-TSS (NM_177225)	14	NM_177225	320679	Mm.442455	NM_177225	ENSMUSG00000058656	Samd12	A830094I09Rik	sterile alpha motif domain containing 12	protein-coding
mm_165996.1	chr4	112232392	112232408	+	1	NA	promoter-TSS (NM_001102474)	promoter-TSS (NM_001102474)	-21	NM_001102474	195564	Mm.259652	NM_177578	ENSMUSG00000070868	Skint3	A430090E18Rik|Skint-3	selection and upkeep of intraepithelial T cells 3	protein-coding
mm_77421.1	chr8	121083024	121083050	-	1	NA	promoter-TSS (NR_045471)	promoter-TSS (NR_045471)	73	NR_045471	68790	Mm.246916	NR_045471	ENSMUSG00000097336	Fendrr	1110050K14Rik|LL66|linc-Foxf1a|lincFoxf1	Foxf1 adjacent non-coding developmental regulatory RNA	ncRNA
mm_155499.1	chrX	73774424	73774434	+	1	NA	promoter-TSS (NM_019684)	promoter-TSS (NM_019684)	24	NM_019684	56504	Mm.111904	NM_019684	ENSMUSG00000002007	Srpk3	Mssk1|Stk23	serine/arginine-rich protein specific kinase 3	protein-coding
mm_136023.1	chr16	76347951	76347954	-	1	NA	intron (NM_173440, intron 2 of 3)	intron (NM_173440, intron 2 of 3)	25097	NM_173440	268903	Mm.74711	NM_173440	ENSMUSG00000048490	Nrip1	6030458L20Rik|8430438I05Rik|9630050P12|AA959574|AW456757|RIP140	nuclear receptor interacting protein 1	protein-coding
mm_68184.1	chr7	104143244	104143246	-	1	NA	promoter-TSS (NM_198623)	promoter-TSS (NM_198623)	27	NM_198623	244178	Mm.334092	NM_198623	ENSMUSG00000051618	Ubqln3	4933400K24Rik	ubiquilin 3	protein-coding
mm_115961.1	chr13	23763520	23763543	-	1	NA	promoter-TSS (NM_030609)	promoter-TSS (NM_030609)	-137	NM_030609	80838	Mm.480242	NM_030609	ENSMUSG00000049539	Hist1h1a	H1.1|H1a|H1f1|H1var3	histone cluster 1, H1a	protein-coding
mm_17307.1	chr2	26360844	26360872	-	1	NA	Intergenic	Intergenic	-1311	NM_001037747	332579	Mm.330064	NM_001037747	ENSMUSG00000026928	Card9	Gm782	caspase recruitment domain family, member 9	protein-coding
mm_27507.1	chr3	55783471	55783492	-	1	NA	exon (NM_010750, exon 1 of 1)	exon (NM_010750, exon 1 of 1)	971	NM_010750	17116	Mm.440209	NM_010750	ENSMUSG00000056947	Mab21l1	AW047968	mab-21-like 1 (C. elegans)	protein-coding
mm_107065.1	chr12	16810980	16810990	+	1	NA	promoter-TSS (NM_033270)	promoter-TSS (NM_033270)	20	NM_033270	50496	Mm.23296	NM_033270	ENSMUSG00000057469	E2f6	AI462434|E2F6a|E2F6b|EMA	E2F transcription factor 6	protein-coding
mm_171939.1	chr5	66595040	66595058	-	1	NA	intron (NM_001310626, intron 1 of 15)	intron (NM_001310626, intron 1 of 15)	23768	NM_009686	11787	Mm.5159	NM_009686	ENSMUSG00000029207	Apbb2	2310007D03Rik|FE65L1|Rirl1|TR2L|Zfra	amyloid beta (A4) precursor protein-binding, family B, member 2	protein-coding
mm_105801.1	chr11	110168074	110168182	-	1	NA	promoter-TSS (NM_147220)	promoter-TSS (NM_147220)	25	NM_147220	217262	Mm.291459	NM_147220	ENSMUSG00000041797	Abca9	D630040K07Rik	ATP-binding cassette, sub-family A (ABC1), member 9	protein-coding
mm_127996.1	chr15	12681727	12681729	-	1	NA	Intergenic	MTC|LTR|ERVL-MaLR	-89172	NM_001081064	68070	Mm.423205	NM_001081064	ENSMUSG00000022197	Pdzd2	4930537L06Rik|A930022H17Rik|Gm21706|Gm82|Pdzk3|mKIAA0300	PDZ domain containing 2	protein-coding
mm_77197.1	chr8	112030876	112030914	-	1	NA	Intergenic	Lx3B|LINE|L1	19536	NM_020584	57321	Mm.213064	NM_020584	ENSMUSG00000033430	Terf2ip	Rap1	telomeric repeat binding factor 2, interacting protein	protein-coding
mm_58229.1	chr6	144779354	144779374	-	1	NA	Intergenic	Intergenic	106496	NR_040519	66760	Mm.233631	NR_040519	ENSMUSG00000085785	Sox5os3	4933425H06Rik	SRY (sex determining region Y)-box 5, opposite strand 3	ncRNA
mm_98588.1	chr11	95768317	95768357	+	1	NA	Intergenic	Intergenic	19270	NM_201609	268469	Mm.389038	NM_201609	ENSMUSG00000075595	Zfp652	9530033F24Rik|ZNF652	zinc finger protein 652	protein-coding
mm_97806.1	chr11	82961261	82961272	+	1	NA	promoter-TSS (NR_045932)	promoter-TSS (NR_045932)	-585	NR_045932	76392	Mm.295205	NR_045932	ENSMUSG00000086327	Slfn5os	1700003F17Rik	schlafen 5, opposite strand	ncRNA
mm_98707.1	chr11	96306540	96306543	+	1	NA	TTS (NM_008268)	TTS (NM_008268)	369	NR_131758	75395	Mm.440014	NR_131758	ENSMUSG00000085645	Hoxb5os	0610040B09Rik|AV302770|Hoxb5/6as	homeobox B5 and homeobox B6, opposite strand	ncRNA
mm_153253.1	chr19	36689270	36689306	-	1	NA	non-coding (NR_033510, exon 1 of 5)	non-coding (NR_033510, exon 1 of 5)	191	NR_033510	668215	Mm.394223	NR_033510	ENSMUSG00000087579	1500017E21Rik	-	RIKEN cDNA 1500017E21 gene	ncRNA
mm_77787.1	chr9	3025854	3025873	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	12880	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_126731.1	chr15	85645690	85645713	+	1	NA	Intergenic	Intergenic	-58072	NR_110483	102800312	Mm.33117	NR_110483		Lncppara	Lincppara|Mirlet7bhg|linc-Ppara	long noncoding RNA near Ppara	ncRNA
mm_108288.1	chr12	79140002	79140028	+	1	NA	intron (NM_009705, intron 2 of 7)	B1_Mus2|SINE|Alu	9227	NM_009705	11847	Mm.3506	NM_009705	ENSMUSG00000021125	Arg2	AII|AU022422	arginase type II	protein-coding
mm_54671.1	chr6	39207469	39207479	-	1	NA	promoter-TSS (NM_001033430)	promoter-TSS (NM_001033430)	-701	NM_001033430	338523	Mm.293175	NM_001033430	ENSMUSG00000042599	Kdm7a	A630082K20Rik|BB041802|ENSMUSG00000073143|Jhdm1d|mKIAA1718	lysine (K)-specific demethylase 7A	protein-coding
mm_116760.1	chr13	52568018	52568031	-	1	NA	Intergenic	L1M5|LINE|L1	5201	NR_046069	100040572	Mm.278873	NR_046069		Gm2848	-	predicted gene 2848	ncRNA
mm_122722.1	chr14	52305057	52305130	-	1	NA	promoter-TSS (NM_019721)	promoter-TSS (NM_019721)	31	NM_019721	56335	Mm.271759	NM_019721	ENSMUSG00000022160	Mettl3	2310024F18Rik|M6A|Spo8	methyltransferase like 3	protein-coding
mm_105948.1	chr11	115285446	115285469	-	1	NA	exon (NM_178035, exon 4 of 6)	exon (NM_178035, exon 4 of 6)	-8488	NM_007997	14149	Mm.4719	NM_007997	ENSMUSG00000018861	Fdxr	-	ferredoxin reductase	protein-coding
mm_30905.1	chr4	32376260	32376283	+	1	NA	Intergenic	Intergenic	-41164	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_100998.1	chr11	8468489	8468511	-	1	NA	intron (NM_001083587, intron 20 of 30)	intron (NM_001083587, intron 20 of 30)	196035	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_118632.1	chr14	21280744	21280749	+	1	NA	intron (NM_001243041, intron 6 of 10)	intron (NM_001243041, intron 6 of 10)	204594	NM_001243041	11534	Mm.188734	NM_134079	ENSMUSG00000039197	Adk	2310026J05Rik|5033405D03Rik|AI255373|AI987814|Ak	adenosine kinase	protein-coding
mm_104411.1	chr11	94601884	94601895	-	1	NA	promoter-TSS (NM_153807)	promoter-TSS (NM_153807)	-103	NM_153807	264895	Mm.386885	NM_153807	ENSMUSG00000076435	Acsf2	-	acyl-CoA synthetase family member 2	protein-coding
mm_56256.1	chr6	90782038	90782066	-	1	NA	intron (NM_001134384, intron 1 of 13)	intron (NM_001134384, intron 1 of 13)	28071	NM_001134384	232227	Mm.196943	NM_182784	ENSMUSG00000034312	Iqsec1	AW561907|BC026481|BRAG2|D6Ertd349e|cI-43	IQ motif and Sec7 domain 1	protein-coding
mm_1537.1	chr1	72851996	72852004	+	1	NA	exon (NM_008342, exon 4 of 4)	exon (NM_008342, exon 4 of 4)	22865	NM_010518	16011	Mm.405761	NM_010518	ENSMUSG00000026185	Igfbp5	AI256729|AW208790|IGFBP-5|IGFBP-5P	insulin-like growth factor binding protein 5	protein-coding
mm_17027.1	chr2	19547302	19547302	-	1	NA	intron (NM_027600, intron 1 of 16)	L2a|LINE|L2	6608	NM_027600	70909	Mm.158488	NM_027600	ENSMUSG00000026734	4921504E06Rik	4921522E24Rik	RIKEN cDNA 4921504E06 gene	protein-coding
mm_96986.1	chr11	70656946	70656956	+	1	NA	promoter-TSS (NM_007933)	promoter-TSS (NM_007933)	-225	NM_001136062	13808	Mm.251322	NM_007933	ENSMUSG00000060600	Eno3	Eno-3|MSE	enolase 3, beta muscle	protein-coding
mm_94255.1	chr11	3332427	3332460	+	1	NA	intron (NM_178149, intron 3 of 5)	CpG-1656	1712	NM_178149	216505	Mm.390323	NM_178149	ENSMUSG00000034614	Pik3ip1	1500004A08Rik|5830455E04Rik|Crkd|Hgfl	phosphoinositide-3-kinase interacting protein 1	protein-coding
mm_158062.1	chrX	101212809	101212814	-	1	NA	3' UTR (NM_001110310, exon 4 of 4)	3' UTR (NM_001110310, exon 4 of 4)	9752	NM_001110311	55988	Mm.206949	NM_018875	ENSMUSG00000046032	Snx12	2610001F05Rik|AW045757|SDP8	sorting nexin 12	protein-coding
mm_106696.1	chr12	3463373	3463386	+	1	NA	intron (NM_001270988, intron 4 of 11)	intron (NM_001270988, intron 4 of 11)	36522	NM_172421	75302	Mm.120475	NM_172421	ENSMUSG00000037486	Asxl2	4930556B16Rik|mKIAA1685	additional sex combs like 2 (Drosophila)	protein-coding
mm_114621.1	chr13	75967757	75967789	+	1	NA	promoter-TSS (NM_029343)	promoter-TSS (NM_029343)	34	NM_029343	75571	Mm.443291	NM_029343	ENSMUSG00000021590	Spata9	1700030K01Rik|4930599C08Rik|A930023H06Rik	spermatogenesis associated 9	protein-coding
mm_150746.1	chr19	43786972	43786981	+	1	NA	intron (NM_013806, intron 2 of 31)	intron (NM_013806, intron 2 of 31)	4668	NM_013806	12780	Mm.39054	NM_013806	ENSMUSG00000025194	Abcc2	AI173996|Abc30|Cmoat|Mrp2|cMRP	ATP-binding cassette, sub-family C (CFTR/MRP), member 2	protein-coding
mm_171434.1	chr4	140701274	140701276	-	1	NA	promoter-TSS (NM_173867)	promoter-TSS (NM_173867)	-198	NM_173867	108911	Mm.253	NM_173867	ENSMUSG00000040945	Rcc2	2610510H01Rik|2610529N02Rik|AA536646|AA675016|Td60|mKIAA1470	regulator of chromosome condensation 2	protein-coding
mm_159830.1	chr5	125387611	125387611	-	1	NA	exon (NM_019639, exon 2 of 2)	exon (NM_019639, exon 2 of 2)	2406	NM_019639	22190	Mm.331	NM_019639	ENSMUSG00000008348	Ubc	2700054O04Rik|AI194771|Rps27a|TI-225|Uba52|Ubb	ubiquitin C	protein-coding
mm_62866.1	chr7	114722192	114722208	+	1	NA	intron (NM_054084, intron 4 of 4)	intron (NM_054084, intron 4 of 4)	3557	NM_054084	116903	Mm.273838	NM_054084	ENSMUSG00000030666	Calcb	CGRP2|Calc2	calcitonin-related polypeptide, beta	protein-coding
mm_97888.1	chr11	83298911	83298925	+	1	NA	promoter-TSS (NM_134025)	promoter-TSS (NM_134025)	59	NM_134025	103737	Mm.102205	NM_134025	ENSMUSG00000018733	Pex12	AI451906	peroxisomal biogenesis factor 12	protein-coding
mm_33590.1	chr4	132563600	132563628	+	1	NA	promoter-TSS (NM_001081211)	promoter-TSS (NM_001081211)	-453	NM_001081211	19204	Mm.89389	NM_001081211	ENSMUSG00000056529	Ptafr	PAFR	platelet-activating factor receptor	protein-coding
mm_131068.1	chr16	4639957	4639978	+	1	NA	promoter-TSS (NM_139307)	promoter-TSS (NM_139307)	22	NM_139307	246154	Mm.482140	NM_139307	ENSMUSG00000039646	Vasn	2610528G05Rik|Atia|Slitl2	vasorin	protein-coding
mm_91123.1	chr10	19584237	19584253	-	1	NA	Intergenic	Intergenic	-7704	NM_010511	15979	Mm.549	NM_010511	ENSMUSG00000020009	Ifngr1	CD119|IFN-gammaR|Ifgr|Ifngr|Nktar	interferon gamma receptor 1	protein-coding
mm_172810.1	chr9	123689424	123689427	-	1	NA	Intergenic	RLTR19-int|LTR|ERVK	-10593	NM_139142	102680	Mm.440867	NM_139142	ENSMUSG00000036814	Slc6a20a	A730081N20Rik|AU022428|Xt3s1|Xtrp3s1	solute carrier family 6 (neurotransmitter transporter), member 20A	protein-coding
mm_116127.1	chr13	28952880	28952897	-	1	NA	exon (NM_009238, exon 1 of 1)	exon (NM_009238, exon 1 of 1)	794	NM_009238	20677	Mm.240627	NM_009238	ENSMUSG00000076431	Sox4	AA682046|Sox-4	SRY (sex determining region Y)-box 4	protein-coding
mm_118035.1	chr13	101692314	101692329	-	1	NA	5' UTR (NM_001024955, exon 1 of 10)	5' UTR (NM_001024955, exon 1 of 10)	309	NM_001024955	18708	Mm.259333	NM_001024955	ENSMUSG00000041417	Pik3r1	PI3K|p50alpha|p55alpha|p85alpha	phosphatidylinositol 3-kinase, regulatory subunit, polypeptide 1 (p85 alpha)	protein-coding
mm_148050.1	chr18	71506108	71506109	-	1	NA	intron (NM_007831, intron 12 of 28)	intron (NM_007831, intron 12 of 28)	844961	NM_007831	13176	Mm.167882	NM_007831	ENSMUSG00000060534	Dcc	C030036D22Rik|Igdcc1	deleted in colorectal carcinoma	protein-coding
mm_97792.1	chr11	82892117	82892128	+	1	NA	promoter-TSS (NM_030224)	promoter-TSS (NM_030224)	-23	NM_030224	78919	Mm.286733	NM_030224	ENSMUSG00000018844	Fndc8	4930466G16Rik	fibronectin type III domain containing 8	protein-coding
mm_42215.1	chr5	113060472	113060489	+	1	NA	intron (NM_007773, intron 6 of 6)	intron (NM_007773, intron 6 of 6)	9637	NM_007773	12961	Mm.1215	NM_007773	ENSMUSG00000042240	Crybb2	Cryb-2	crystallin, beta B2	protein-coding
mm_46332.1	chr5	101239678	101239709	-	1	NA	Intergenic	Intergenic	393464	NM_172715	231510	Mm.271911	NM_172715	ENSMUSG00000029314	Agpat9	1-AGPAT|1-AGPAT 9|4933407I02Rik|4933408F15|A230097K15Rik|GPAT-3|Gpat3|mGPAT3	1-acylglycerol-3-phosphate O-acyltransferase 9	protein-coding
mm_5223.1	chr1	14304595	14304609	-	1	NA	intron (NM_001310459, intron 1 of 17)	intron (NM_001310459, intron 1 of 17)	5597	NM_001310459	14048	Mm.250185	NM_010164	ENSMUSG00000025932	Eya1	bor	EYA transcriptional coactivator and phosphatase 1	protein-coding
mm_5077.1	chr1	3671771	3671808	-	1	NA	promoter-TSS (NM_001011874)	promoter-TSS (NM_001011874)	-291	NM_001011874	497097	Mm.454496	NM_001011874	ENSMUSG00000051951	Xkr4	AY534250|Gm210|XRG4|mKIAA1889	X-linked Kx blood group related 4	protein-coding
mm_76992.1	chr8	107065633	107065650	-	1	NA	promoter-TSS (NM_025458)	promoter-TSS (NM_025458)	3	NM_025458	66269	Mm.23032	NM_025458	ENSMUSG00000031919	Tmed6	1810015P03Rik|1810018I24Rik	transmembrane p24 trafficking protein 6	protein-coding
mm_134823.1	chr16	26064750	26064755	-	1	NA	intron (NM_173379, intron 1 of 14)	intron (NM_173379, intron 1 of 14)	41032	NM_173379	210530	Mm.326869	NM_173379	ENSMUSG00000038168	P3h2	4832416N06|AW553532|Leprel1|Mlat4	prolyl 3-hydroxylase 2	protein-coding
mm_141942.1	chr17	35051826	35051847	-	1	NA	intron (NM_033444, intron 1 of 5)	intron (NM_033444, intron 1 of 5)	1593	NM_033444	114584	Mm.29524	NM_033444	ENSMUSG00000007041	Clic1	Clcp|G6	chloride intracellular channel 1	protein-coding
mm_105719.1	chr11	108533655	108533679	-	1	NA	intron (NM_029606, intron 18 of 27)	intron (NM_029606, intron 18 of 27)	108401	NM_029606	76380	Mm.344071	NM_029586	ENSMUSG00000020728	Cep112	1700001M19Rik|1700029K01Rik|8430407H02Rik|AV043680|AV207351|Ccdc46|Macoco	centrosomal protein 112	protein-coding
mm_6265.1	chr1	69541371	69541382	-	1	NA	intron (NM_011770, intron 7 of 7)	intron (NM_011770, intron 7 of 7)	144584	NM_011770	22779	Mm.106343	NM_011770	ENSMUSG00000025997	Ikzf2	A730095J18Rik|Helios|Zfpn1a2|Znfn1a2	IKAROS family zinc finger 2	protein-coding
mm_106992.1	chr12	11265868	11265883	+	1	NA	promoter-TSS (NM_177331)	promoter-TSS (NM_177331)	-11	NM_001324476	67241	Mm.173953	NM_025695	ENSMUSG00000020608	Smc6	2810489L22Rik|3830418C19Rik|AA990493|AU018782|AW742439|SMC-6|Smc6l1|mKIAA4103	structural maintenance of chromosomes 6	protein-coding
mm_23649.1	chr3	67504209	67504219	+	1	NA	intron (NM_001164763, intron 1 of 5)	MER5A|DNA|hAT-Charlie	11309	NM_001164763	109222	Mm.38002	NM_001164763	ENSMUSG00000049404	Rarres1	5430417P09Rik|AI662122	retinoic acid receptor responder (tazarotene induced) 1	protein-coding
mm_25241.1	chr3	103914413	103914430	+	1	NA	5' UTR (NM_172684, exon 1 of 7)	5' UTR (NM_172684, exon 1 of 7)	301	NM_172684	229675	Mm.29366	NM_172684	ENSMUSG00000044098	Rsbn1	C230004D03Rik|E330004N01|Rosbin|Rsbn|Rsbp|mKIAA3002	rosbin, round spermatid basic protein 1	protein-coding
mm_72087.1	chr8	71579330	71579347	+	1	NA	intron (NM_011977, intron 3 of 13)	intron (NM_011977, intron 3 of 13)	10411	NM_011977	26457	Mm.38165	NM_011977	ENSMUSG00000031808	Slc27a1	FATP1|Fatp	solute carrier family 27 (fatty acid transporter), member 1	protein-coding
mm_45691.1	chr5	81556064	81556076	-	1	NA	intron (NM_001347371, intron 7 of 23)	RLTR17|LTR|ERVK	534477	NM_198702	319387	Mm.273631	NM_198702	ENSMUSG00000037605	Adgrl3	5430402I23Rik|CIRL-3|D130075K09Rik|Gm1379|LEC3|Lphn3|mKIAA0768	adhesion G protein-coupled receptor L3	protein-coding
mm_61707.1	chr7	81213778	81213876	+	1	NA	promoter-TSS (NM_008803)	promoter-TSS (NM_008803)	23	NM_008803	18584	Mm.371577	NM_008803	ENSMUSG00000025584	Pde8a	AI551852|Pde8	phosphodiesterase 8A	protein-coding
mm_91004.1	chr10	14545387	14545418	-	1	NA	promoter-TSS (NM_001002268)	promoter-TSS (NM_001002268)	-366	NM_001002268	215798	Mm.440142	NM_001002268	ENSMUSG00000039116	Adgrg6	1190004A11Rik|AI449247|AW045736|DREG|Gm222|Gpr126	adhesion G protein-coupled receptor G6	protein-coding
mm_63134.1	chr7	123031265	123031284	+	1	NA	Intergenic	Intergenic	60710	NM_175023	19647	Mm.4480	NM_011247	ENSMUSG00000030779	Rbbp6	4933422O15Rik|AI316869|BB233631|C030034J04Rik|C77662|P2P-R|PACT	retinoblastoma binding protein 6	protein-coding
mm_81277.1	chr9	108290434	108290497	+	1	NA	promoter-TSS (NM_025449)	promoter-TSS (NM_025449)	8	NM_025449	66257	Mm.10407	NM_025449	ENSMUSG00000032606	Nicn1	1500032A17Rik	nicolin 1	protein-coding
mm_130372.1	chr15	97823629	97823640	-	1	NA	intron (NM_001204275, intron 1 of 24)	intron (NM_001204275, intron 1 of 24)	8133	NM_019572	56233	Mm.384027	NM_019572	ENSMUSG00000022475	Hdac7	5830434K02Rik|HD7|HD7a|Hdac7a|mFLJ00062	histone deacetylase 7	protein-coding
mm_71967.1	chr8	70531615	70531625	+	1	NA	exon (NM_001199631, exon 5 of 9)	exon (NM_001199631, exon 5 of 9)	3774	NM_001199631	14232	Mm.141864	NM_010223	ENSMUSG00000019428	Fkbp8	38kDa|FKBP-38|FKBP-8|Fkbp38	FK506 binding protein 8	protein-coding
mm_125501.1	chr15	55258399	55258404	+	1	NA	3' UTR (NM_145470, exon 9 of 9)	3' UTR (NM_145470, exon 9 of 9)	-49349	NM_181277	12818	Mm.297859	NM_181277	ENSMUSG00000022371	Col14a1	5730412L22Rik|AW108078	collagen, type XIV, alpha 1	protein-coding
mm_77591.1	chr8	123891864	123891897	-	1	NA	3' UTR (NM_009606, exon 7 of 7)	3' UTR (NM_009606, exon 7 of 7)	2895	NM_001272041	11459	Mm.214950	NM_009606	ENSMUSG00000031972	Acta1	AA959943|Acta-2|Acts|Actsk-1	actin, alpha 1, skeletal muscle	protein-coding
mm_162576.1	chr1	177447160	177447178	+	1	NA	exon (NM_013915, exon 1 of 1)	exon (NM_013915, exon 1 of 1)	1348	NM_013915	30928	Mm.330700	NM_013915	ENSMUSG00000063659	Zbtb18	RP58|Zfp238|Znf238	zinc finger and BTB domain containing 18	protein-coding
mm_56539.1	chr6	99669581	99669595	-	1	NA	Intergenic	Intergenic	-2817	NM_025829	66892	Mm.32889	NM_025829	ENSMUSG00000093661	Eif4e3	1300018P11Rik|AI451927|eIF4E-3	eukaryotic translation initiation factor 4E member 3	protein-coding
mm_54374.1	chr6	31190675	31190676	-	1	NA	intron (NR_110470, intron 1 of 2)	intron (NR_110470, intron 1 of 2)	27799	NR_110470	232685	Mm.443019	NM_144555	ENSMUSG00000044471	Lncpint	Lincpint|MNCb-1768|Pint|linc-Pint	long non-protein coding RNA, Trp53 induced transcript	ncRNA
mm_64240.1	chr7	141701402	141701412	+	1	NA	exon (NM_023566, exon 24 of 46)	exon (NM_023566, exon 24 of 46)	11067	NM_023566	17831	Mm.2041	NM_023566		Muc2	2010015E03Rik|MCM|wnn	mucin 2	protein-coding
mm_60531.1	chr7	44480261	44480300	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-4237	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_95013.1	chr11	31935110	31935132	+	1	NA	3' UTR (NM_026252, exon 10 of 10)	3' UTR (NM_026252, exon 10 of 10)	-30512	NM_026262	67592	Mm.78654	NM_026262	ENSMUSG00000020299	4930524B15Rik	-	RIKEN cDNA 4930524B15 gene	protein-coding
mm_41366.1	chr5	90508748	90508787	+	1	NA	3' UTR (NM_007423, exon 15 of 15)	3' UTR (NM_007423, exon 15 of 15)	-10182	NM_145146	280662	Mm.348786	NM_145146	ENSMUSG00000029369	Afm	Alf|alpha-Alb	afamin	protein-coding
mm_163259.1	chr11	112469204	112469204	-	1	NA	Intergenic	RSINE1|SINE|B4	242152	NR_024085	217294	Mm.297761	NM_146031	ENSMUSG00000041674	BC006965	-	cDNA sequence BC006965	ncRNA
mm_81021.1	chr9	104361830	104361833	+	1	NA	Intergenic	Intergenic	-24109	NM_207668	56318	Mm.19941	NM_019807	ENSMUSG00000032561	Acpp	5'-NT|A030005E02Rik|FRAP|Lap|PAP|Ppal	acid phosphatase, prostate	protein-coding
mm_136126.1	chr16	85901057	85901071	-	1	NA	promoter-TSS (NM_011782)	promoter-TSS (NM_011782)	61	NM_011782	23794	Mm.112933	NM_011782	ENSMUSG00000022894	Adamts5	9530092O11Rik|ADAM-TS5|ADAMTS1|ADAMTS11|ADMP-2|AI481094|ASMP-2	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)	protein-coding
mm_45867.1	chr5	87930089	87930108	-	1	NA	exon (NM_007786, exon 4 of 5)	exon (NM_007786, exon 4 of 5)	4465	NM_007786	12994	Mm.296303	NM_007786	ENSMUSG00000001622	Csn3	AW208918|CSN10|Csnk	casein kappa	protein-coding
mm_149804.1	chr19	23730205	23730208	+	1	NA	Intergenic	Intergenic	-28670	NM_177034	319924	Mm.22879	NM_177034	ENSMUSG00000024897	Apba1	6430513E09Rik|Lin-10|Mint|Mint1|Urop11|X11|X11alpha	amyloid beta (A4) precursor protein binding, family A, member 1	protein-coding
mm_57597.1	chr6	127794667	127794677	-	1	NA	Intergenic	Intergenic	-6529	NR_106092	102466996		NR_106092	ENSMUSG00000104804	Mir7233	mmu-mir-7233	microRNA 7233	ncRNA
mm_159535.1	chr4	73790782	73790782	-	1	NA	promoter-TSS (NR_046042)	promoter-TSS (NR_046042)	-180	NM_001017427	242505	Mm.389582	NM_001017427	ENSMUSG00000043003	Rasef	BC030882|RAB45	RAS and EF hand domain containing	protein-coding
mm_171869.1	chr5	25025927	25025930	-	1	NA	intron (NM_145401, intron 2 of 15)	intron (NM_145401, intron 2 of 15)	-30175	NM_001310480	108099	Mm.33649	NM_145401	ENSMUSG00000028944	Prkag2	2410051C13Rik|AAKG|AAKG2|AI854673|H91620p|WPWS	protein kinase, AMP-activated, gamma 2 non-catalytic subunit	protein-coding
mm_828.1	chr1	51289107	51289142	+	1	NA	promoter-TSS (NM_138741)	promoter-TSS (NM_138741)	-2	NM_138741	20324	Mm.398690	NM_138741	ENSMUSG00000045954	Sdpr	-	serum deprivation response	protein-coding
mm_46375.1	chr5	103753845	103753848	-	1	NA	promoter-TSS (NM_133919)	promoter-TSS (NM_133919)	-316	NM_133919	17355	Mm.6949	NM_133919	ENSMUSG00000029313	Aff1	9630032B01Rik|AW319193|Af4|Mllt2h|Rob	AF4/FMR2 family, member 1	protein-coding
mm_75887.1	chr8	70839652	70839666	-	1	NA	promoter-TSS (NM_027560)	promoter-TSS (NM_027560)	61	NM_027560	70807	Mm.24215	NM_027560	ENSMUSG00000002910	Arrdc2	4632416I05Rik|Ilad1	arrestin domain containing 2	protein-coding
mm_48197.1	chr5	137531141	137531157	-	1	NA	intron (NM_010312, intron 1 of 9)	CpG	-1555	NR_105846	102465227		NR_105846	ENSMUSG00000098597	Mir6418	Gm27629|mir-6418|mmu-mir-6418	microRNA 6418	ncRNA
mm_27753.1	chr3	69596273	69596279	-	1	NA	intron (NM_020026, intron 1 of 2)	ORR1A4|LTR|ERVL-MaLR	2684	NM_020026	26879	Mm.153710	NM_020026	ENSMUSG00000043300	B3galnt1	B3galt3|b3GT3	UDP-GalNAc:betaGlcNAc beta 1,3-galactosaminyltransferase, polypeptide 1	protein-coding
mm_99814.1	chr11	108407281	108407307	+	1	NA	exon (NM_013475, exon 5 of 8)	exon (NM_013475, exon 5 of 8)	11997	NM_013475	11818	Mm.2266	NM_013475	ENSMUSG00000000049	Apoh	B2GPI|beta-2-GPI|beta2-GPI	apolipoprotein H	protein-coding
mm_1165.1	chr1	60911068	60911072	+	1	NA	intron (NM_001281976, intron 1 of 2)	intron (NM_001281976, intron 1 of 2)	2045	NM_001281976	12477	Mm.390	NM_009843	ENSMUSG00000026011	Ctla4	Cd152|Ctla-4|Ly-56	cytotoxic T-lymphocyte-associated protein 4	protein-coding
mm_4775.1	chr1	182861169	182861171	+	1	NA	intron (NM_144796, intron 4 of 7)	B3A|SINE|B2	-93618	NM_016928	53791	Mm.116894	NM_016928	ENSMUSG00000079164	Tlr5	-	toll-like receptor 5	protein-coding
mm_93897.1	chr10	125389432	125389553	-	1	NA	Intergenic	G-rich|Low_complexity|Low_complexity	-60957	NM_011391	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|Mct2	solute carrier family 16 (monocarboxylic acid transporters), member 7	protein-coding
mm_110220.1	chr12	28635234	28635240	-	1	NA	intron (NM_011300, intron 3 of 6)	intron (NM_011300, intron 3 of 6)	716	NM_011300	20115	Mm.279839	NM_011300	ENSMUSG00000061477	Rps7	Mtu|Rps7A|S7	ribosomal protein S7	protein-coding
mm_38083.1	chr4	134129605	134129611	-	1	NA	promoter-TSS (NM_080559)	promoter-TSS (NM_080559)	-855	NM_080559	73723	Mm.22240	NM_080559	ENSMUSG00000028843	Sh3bgrl3	1110004L05Rik|AU022188	SH3 domain binding glutamic acid-rich protein-like 3	protein-coding
mm_76129.1	chr8	80880275	80880306	-	1	NA	5' UTR (NM_001301298, exon 1 of 11)	5' UTR (NM_001301298, exon 1 of 11)	189	NM_021356	14388	Mm.277409	NM_021356	ENSMUSG00000031714	Gab1	AA408973|AW107238	growth factor receptor bound protein 2-associated protein 1	protein-coding
mm_148505.1	chr19	4204212	4204221	+	1	NA	Intergenic	Intergenic	-2613	NM_011237	19367	Mm.277629	NM_011237	ENSMUSG00000024824	Rad9a	Rad9	RAD9 checkpoint clamp component A	protein-coding
mm_144383.1	chr18	20666553	20666567	+	1	NA	exon (NM_013697, exon 2 of 4)	exon (NM_013697, exon 2 of 4)	1310	NM_013697	22139	Mm.2108	NM_013697	ENSMUSG00000061808	Ttr	AA408768|AI787086|D17860|prealbumin	transthyretin	protein-coding
mm_153748.1	chr19	45006112	45006122	-	1	NA	promoter-TSS (NM_153796)	promoter-TSS (NM_153796)	325	NM_053164	94067	Mm.44174	NM_053164	ENSMUSG00000025208	Mrpl43	4930442D21Rik|bMRP36a	mitochondrial ribosomal protein L43	protein-coding
mm_32625.1	chr4	114680770	114680782	+	1	NA	Intergenic	Intergenic	-140944	NR_033617	433746	Mm.388908	NR_033617	ENSMUSG00000055198	Gm12830	OTTMUSG00000008584	predicted gene 12830	ncRNA
mm_108145.1	chr12	76255372	76255436	+	1	NA	5' UTR (NM_138745, exon 1 of 28)	5' UTR (NM_138745, exon 1 of 28)	172	NM_138745	108156	Mm.29584	NM_138745	ENSMUSG00000021048	Mthfd1	Dcs|E430024A07Rik|Mthfd	methylenetetrahydrofolate dehydrogenase (NADP+ dependent), methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthase	protein-coding
mm_56315.1	chr6	92242673	92242708	-	1	NA	exon (NM_009426, exon 3 of 3)	exon (NM_009426, exon 3 of 3)	1960	NM_009426	22044	Mm.1363	NM_009426	ENSMUSG00000005892	Trh	Pro-TRH|Trf	thyrotropin releasing hormone	protein-coding
mm_87861.1	chr10	61175683	61175693	+	1	NA	intron (NM_001017409, intron 1 of 3)	intron (NM_001017409, intron 1 of 3)	426	NM_023064	65971	Mm.30227	NM_023064	ENSMUSG00000020096	Tbata	1700021K02Rik|AI428928|Spatial|Titest	thymus, brain and testes associated	protein-coding
mm_71546.1	chr8	47824531	47824542	+	1	NA	promoter-TSS (NM_029383)	promoter-TSS (NM_029383)	54	NM_029383	75677	Mm.390033	NM_029383	ENSMUSG00000038064	Cldn22	2210404A22Rik|5330431C14Rik|9530051B05Rik	claudin 22	protein-coding
mm_32401.1	chr4	106910429	106910434	+	1	NA	Intergenic	Intergenic	-1039	NM_198438	72475	Mm.195635	NM_023672	ENSMUSG00000061887	Ssbp3	2610021L12Rik|2610200M23Rik|5730488C10Rik|AI854733|AW551939|LAST|SSDP1	single-stranded DNA binding protein 3	protein-coding
mm_138148.1	chr17	34205557	34205574	+	1	NA	exon (NM_011530, exon 2 of 12)	exon (NM_011530, exon 2 of 12)	1086	NM_011530	21355	Mm.14814	NM_011530	ENSMUSG00000024339	Tap2	ABC18|AI462429|APT2|Abcb3|Ham-2|Ham2|MTP2|PSF2|RING11|Tap-2|Y1|jas	transporter 2, ATP-binding cassette, sub-family B (MDR/TAP)	protein-coding
mm_64934.1	chr7	16295439	16295452	-	1	NA	Intergenic	Intergenic	-8650	NM_001136471	243846	Mm.482401	NM_172297	ENSMUSG00000041375	Ccdc9	2600011L02Rik	coiled-coil domain containing 9	protein-coding
mm_149380.1	chr19	11379154	11379166	+	1	NA	intron (NM_001310331, intron 2 of 6)	intron (NM_001310331, intron 2 of 6)	3672	NM_001310331	666907		NM_001310331	ENSMUSG00000101389	Ms4a4a	EG666907	membrane-spanning 4-domains, subfamily A, member 4A	protein-coding
mm_138173.1	chr17	34264848	34264860	+	1	NA	exon (NM_207105, exon 2 of 6)	exon (NM_207105, exon 2 of 6)	1627	NM_207105	14961	Mm.254067	NM_207105	ENSMUSG00000073421	H2-Ab1	AI845868|Abeta|H-2Ab|H2-Ab|I-Abeta|IAb|Ia-2|Ia2|Rmcs1	histocompatibility 2, class II antigen A, beta 1	protein-coding
mm_97503.1	chr11	78465584	78465596	+	1	NA	promoter-TSS (NM_026740)	promoter-TSS (NM_026740)	-111	NM_026740	52466	Mm.131618	NM_026740	ENSMUSG00000020829	Slc46a1	1110002C08Rik|D11Ertd18e|HCP1|Pcft	solute carrier family 46, member 1	protein-coding
mm_73101.1	chr8	94570171	94570183	+	1	NA	3' UTR (NM_153507, exon 16 of 16)	3' UTR (NM_153507, exon 16 of 16)	31549	NM_028221	102122	Mm.250425	NM_028221	ENSMUSG00000031774	Fam192a	1700001O11Rik|2310065K24Rik|AI596259|Nip30	family with sequence similarity 192, member A	protein-coding
mm_64980.1	chr7	16915461	16915476	-	1	NA	TTS (NM_007590)	TTS (NM_007590)	8564	NM_007590	12315	Mm.288630	NM_007590	ENSMUSG00000019370	Calm3	CaMA|R75142	calmodulin 3	protein-coding
mm_92364.1	chr10	75940567	75940578	-	1	NA	promoter-TSS (NM_001277132)	promoter-TSS (NM_001277132)	100	NM_001277132	333670	Mm.291320	NM_001037714	ENSMUSG00000050157	Gm867	Gm736	predicted gene 867	protein-coding
mm_110213.1	chr12	28623283	28623296	-	1	NA	promoter-TSS (NM_027866)	promoter-TSS (NM_027866)	41	NM_001313978	71693	Mm.30724	NM_027866	ENSMUSG00000036655	Colec11	CL-K1	collectin sub-family member 11	protein-coding
mm_25036.1	chr3	98280031	98280036	+	1	NA	promoter-TSS (NM_008256)	promoter-TSS (NM_008256)	-398	NM_008256	15360	Mm.289131	NM_008256	ENSMUSG00000027875	Hmgcs2	1300002P16|mHS	3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2	protein-coding
mm_57905.1	chr6	132364130	132364135	-	1	NA	promoter-TSS (NM_001177588)	promoter-TSS (NM_001177588)	2	NM_001177588	667929	Mm.428480	NM_001177588	ENSMUSG00000030143	Gm8882	EG667929	predicted gene 8882	protein-coding
mm_104522.1	chr11	96065351	96065369	-	1	NA	promoter-TSS (NM_172300)	promoter-TSS (NM_172300)	4	NM_172300	268470	Mm.38802	NM_172300	ENSMUSG00000014349	Ube2z	AW049199|C030047H17Rik|D11Moh35	ubiquitin-conjugating enzyme E2Z	protein-coding
mm_94781.1	chr11	21572274	21572334	+	1	NA	promoter-TSS (NM_001316675)	promoter-TSS (NM_001316675)	23	NM_145425	216560	Mm.138090	NM_145425	ENSMUSG00000020319	Wdpcp	AV249152	WD repeat containing planar cell polarity effector	protein-coding
mm_14696.1	chr2	142217580	142217593	+	1	NA	exon (NM_001013802, exon 11 of 19)	exon (NM_001013802, exon 11 of 19)	683878	NM_001081133	16558	Mm.251934	NM_001081133	ENSMUSG00000038844	Kif16b	8430434E15Rik|AA623607|AI789011|C80253|C80902|mKIAA1590	kinesin family member 16B	protein-coding
mm_23344.1	chr3	54717565	54717596	+	1	NA	TTS (NM_019995)	TTS (NM_019995)	17784	NM_027148	69639	Mm.29253	NM_027148	ENSMUSG00000027752	Exosc8	2310032N20Rik|CIP3|mKIAA4013	exosome component 8	protein-coding
mm_22714.1	chr3	19188227	19188273	+	1	NA	promoter-TSS (NM_026182)	promoter-TSS (NM_026182)	29	NR_045575	67472	Mm.45125	NM_026182	ENSMUSG00000027601	Mtfr1	1300002C08Rik|1700080D04Rik|2810026O10Rik|4930579E05Rik|Chppr|Fam54a2	mitochondrial fission regulator 1	protein-coding
mm_166753.1	chr6	125425444	125425475	-	1	NA	Intergenic	Intergenic	-44955	NM_198604	213522	Mm.333396	NM_198604	ENSMUSG00000038167	Plekhg6	BC026778|Gm155	pleckstrin homology domain containing, family G (with RhoGef domain) member 6	protein-coding
mm_41372.1	chr5	90561103	90561111	+	1	NA	promoter-TSS (NM_001252661)	promoter-TSS (NM_001252661)	-102	NM_001252661	622307	Mm.389654	NM_001252661	ENSMUSG00000070690	5830473C10Rik	Arg|Gm17754	RIKEN cDNA 5830473C10 gene	protein-coding
mm_148020.1	chr18	68429316	68429320	-	1	NA	promoter-TSS (NM_001271716)	promoter-TSS (NM_001271716)	2	NM_001301372	17200	Mm.426053	NM_008560	ENSMUSG00000045569	Mc2r	ACTH-R|ACTHR|MC2-R	melanocortin 2 receptor	protein-coding
mm_70498.1	chr8	12762646	12762657	+	1	NA	intron (NR_121603, intron 1 of 29)	GA-rich|Low_complexity|Low_complexity	5635	NM_001293667	50770	Mm.257837	NM_015804	ENSMUSG00000031441	Atp11a	4930558F19Rik|AU040868|Atpc1h|Ih	ATPase, class VI, type 11A	protein-coding
mm_67477.1	chr7	80535127	80535158	-	1	NA	promoter-TSS (NM_007550)	promoter-TSS (NM_007550)	-23	NM_001042527	12144	Mm.12932	NM_007550	ENSMUSG00000030528	Blm	-	Bloom syndrome, RecQ helicase-like	protein-coding
mm_20837.1	chr2	147281122	147281125	-	1	NA	intron (NR_030769, intron 1 of 5)	intron (NR_030769, intron 1 of 5)	81670	NR_040330	99041	Mm.373081	NR_040330		AI646519	Aspax1|OTTMUSG00000015701	expressed sequence AI646519	ncRNA
mm_65989.1	chr7	30534793	30534815	-	1	NA	intron (NM_178252, intron 1 of 21)	(CGGGG)n|Simple_repeat|Simple_repeat	256	NM_001289670	233071	Mm.190704	NM_178252	ENSMUSG00000036882	Arhgap33	AW324378|NOMA-GAP|Snx26|TCGAP	Rho GTPase activating protein 33	protein-coding
mm_148690.1	chr19	5727212	5727225	+	1	NA	promoter-TSS (NM_001114597)	promoter-TSS (NM_001114597)	-901	NM_053252	114601	Mm.210447	NM_053252	ENSMUSG00000024937	Ehbp1l1	G430002G23Rik	EH domain binding protein 1-like 1	protein-coding
mm_99056.1	chr11	99052110	99052135	+	1	NA	3' UTR (NM_010517, exon 4 of 4)	3' UTR (NM_010517, exon 4 of 4)	10862	NM_010517	16010	Mm.233799	NM_010517	ENSMUSG00000017493	Igfbp4	AI875747|Deb2|IGFBP-4	insulin-like growth factor binding protein 4	protein-coding
mm_104248.1	chr11	88863802	88863810	-	1	NA	intron (NR_126433, intron 3 of 4)	intron (NR_126433, intron 3 of 4)	780	NM_001042541	11640	Mm.2969	NM_009648	ENSMUSG00000018428	Akap1	AKAP121|AKAP84|Akap|C76494|C81186|DAKAP1|S-AKAP84	A kinase (PRKA) anchor protein 1	protein-coding
mm_170593.1	chr19	5802172	5802172	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	500	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_73831.1	chr8	117460527	117460540	+	1	NA	3' UTR (NM_001163262, exon 21 of 21)	3' UTR (NM_001163262, exon 21 of 21)	1268	NR_106046	102465653		NR_106046	ENSMUSG00000098483	Mir7078	Gm27386|mmu-mir-7078	microRNA 7078	ncRNA
mm_112304.1	chr12	114764896	114764911	-	1	NA	Intergenic	Intergenic	-251209	NR_106063	102465664		NR_106063	ENSMUSG00000098357	Mir7094-2	Gm27508|mmu-mir-7094-2	microRNA 7094-2	ncRNA
mm_79274.1	chr9	50756427	50756442	+	1	NA	exon (NM_001289784, exon 4 of 4)	exon (NM_001289784, exon 4 of 4)	3463	NM_009964	12955	Mm.178	NM_009964	ENSMUSG00000032060	Cryab	Crya-2|Crya2|HspB5|P23	crystallin, alpha B	protein-coding
mm_56515.1	chr6	99435347	99435368	-	1	NA	promoter-TSS (NM_053202)	promoter-TSS (NM_053202)	-12	NM_053202	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_98633.1	chr11	96124083	96124111	+	1	NA	Intergenic	Intergenic	-9689	NM_172799	237930	Mm.249912	NM_172799	ENSMUSG00000038756	Ttll6	4932418K24Rik|D11Moh43e|D11Moh44e|t8130b59	tubulin tyrosine ligase-like family, member 6	protein-coding
mm_89443.1	chr10	92680377	92680382	+	1	NA	Intergenic	PB1D11|SINE|Alu	42039	NM_008682	17997	Mm.2998	NM_008682	ENSMUSG00000019988	Nedd1	-	neural precursor cell expressed, developmentally down-regulated gene 1	protein-coding
mm_86546.1	chr10	9882209	9882210	+	1	NA	intron (NM_001081344, intron 2 of 25)	B1_Mm|SINE|Alu	18831	NM_001081344	78808	Mm.331751	NM_030191	ENSMUSG00000019790	Stxbp5	0710001E20Rik|4930565N16Rik|AW742610|LGL3|mKIAA1006	syntaxin binding protein 5 (tomosyn)	protein-coding
mm_111724.1	chr12	103764816	103764826	-	1	NA	intron (NM_009246, intron 3 of 4)	intron (NM_009246, intron 3 of 4)	8812	NM_009246	20703	Mm.439695	NM_009246	ENSMUSG00000071177	Serpina1d	AI118301|Dom4|PI4|Spi1-4	serine (or cysteine) peptidase inhibitor, clade A, member 1D	protein-coding
mm_12896.1	chr2	84798874	84798888	+	1	NA	promoter-TSS (NM_019949)	promoter-TSS (NM_019949)	53	NM_019949	56791	Mm.38261	NM_019949	ENSMUSG00000027078	Ube2l6	2810489I21Rik|RIG-B|UBCH8|Ubce8|Ubcm8	ubiquitin-conjugating enzyme E2L 6	protein-coding
mm_141244.1	chr17	27467873	27467892	-	1	NA	intron (NM_001013385, intron 2 of 8)	intron (NM_001013385, intron 2 of 8)	35651	NM_001013385	268934	Mm.358940	NM_001013385	ENSMUSG00000063239	Grm4	Gprc1d|mGluR4	glutamate receptor, metabotropic 4	protein-coding
mm_130652.1	chr15	100636854	100636900	-	1	NA	promoter-TSS (NM_174992)	promoter-TSS (NM_174992)	63	NR_104338	207818	Mm.26282	NM_174992	ENSMUSG00000053559	Smagp	-	small cell adhesion glycoprotein	protein-coding
mm_2933.1	chr1	132298633	132298649	+	1	NA	promoter-TSS (NM_144810)	promoter-TSS (NM_144810)	15	NM_144810	213417	Mm.39723	NM_144810	ENSMUSG00000042115	Klhdc8a	A630065K24Rik	kelch domain containing 8A	protein-coding
mm_172169.1	chr6	44793154	44793165	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-266902	NM_001004357	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding
mm_13922.1	chr2	120629114	120629127	+	1	NA	Intergenic	CpG	19525	NM_001290807	66296	Mm.221900	NM_025475	ENSMUSG00000027285	Haus2	1700101G24Rik|2410007P03Rik|AU020217|Cep27	HAUS augmin-like complex, subunit 2	protein-coding
mm_139509.1	chr17	56326046	56326097	+	1	NA	promoter-TSS (NM_172132)	promoter-TSS (NM_172132)	21	NM_172132	193796	Mm.45047	NM_172132	ENSMUSG00000024201	Kdm4b	4732474L06Rik|Jmjd2b|mKIAA0876	lysine (K)-specific demethylase 4B	protein-coding
mm_157431.1	chrX	38576167	38576187	-	1	NA	promoter-TSS (NM_028288)	promoter-TSS (NM_028288)	19	NM_028288	72584	Mm.327675	NM_028288	ENSMUSG00000031095	Cul4b	2700050M05Rik|AA409770|CUL-4B|mKIAA0695	cullin 4B	protein-coding
mm_141524.1	chr17	31790636	31790656	-	1	NA	Intergenic	Intergenic	65146	NM_010831	17691	Mm.290941	NM_010831	ENSMUSG00000024042	Sik1	Msk|Sik|Snf1lk	salt inducible kinase 1	protein-coding
mm_92591.1	chr10	80075379	80075407	-	1	NA	intron (NM_183426, intron 4 of 31)	intron (NM_183426, intron 4 of 31)	21374	NM_001037741	625249	Mm.332810	NM_008162	ENSMUSG00000075706	Gpx4	GPx-4|GSHPx-4|PHGPx|mtPHGPx|snGPx	glutathione peroxidase 4	protein-coding
mm_168052.1	chrY	90812393	90812405	+	1	NA	intron (NM_133362, intron 2 of 3)	IMPB_01|Satellite|Satellite	26957	NM_133362	170942	Mm.76062	NM_133362	ENSMUSG00000096768	Erdr1	edr	erythroid differentiation regulator 1	protein-coding
mm_21648.1	chr2	164333562	164333566	-	1	NA	exon (NM_009301, exon 2 of 3)	exon (NM_009301, exon 2 of 3)	799	NM_009301	20944	Mm.140154	NM_009301	ENSMUSG00000017004	Svs5	BB115186|Semg1|Svp-1|Svp1|Svp5	seminal vesicle secretory protein 5	protein-coding
mm_128770.1	chr15	66560937	66560984	-	1	NA	promoter-TSS (NM_172514)	promoter-TSS (NM_172514)	86	NM_172514	213068	Mm.132299	NM_172514	ENSMUSG00000036944	Tmem71	AI661017|E430024D12	transmembrane protein 71	protein-coding
mm_108929.1	chr12	101082940	101082973	+	1	NA	non-coding (NR_038049, exon 1 of 2)	non-coding (NR_038049, exon 1 of 2)	505	NR_038049	319760	Mm.440198	NM_176997	ENSMUSG00000097121	D130020L05Rik	9430007L23Rik	RIKEN cDNA D130020L05 gene	ncRNA
mm_128188.1	chr15	34876211	34876228	-	1	NA	3' UTR (NM_019635, exon 11 of 11)	3' UTR (NM_019635, exon 11 of 11)	38170	NM_001271704	16539	Mm.71045	NM_181317	ENSMUSG00000050963	Kcns2	E130006J24Rik|Kv9.2	K+ voltage-gated channel, subfamily S, 2	protein-coding
mm_125333.1	chr15	38686465	38686469	+	1	NA	intron (NM_025494, intron 8 of 12)	intron (NM_025494, intron 8 of 12)	24563	NM_025494	66335	Mm.276618	NM_025494	ENSMUSG00000022295	Atp6v1c1	1700025B18Rik|U13839	ATPase, H+ transporting, lysosomal V1 subunit C1	protein-coding
mm_37707.1	chr4	129440801	129440823	-	1	NA	promoter-TSS (NM_153541)	promoter-TSS (NM_153541)	6	NM_153541	215627	Mm.428660	NM_153541	ENSMUSG00000048485	Zbtb8b	AV220464|BC023839|BOZF1|Zbtb8	zinc finger and BTB domain containing 8b	protein-coding
mm_110297.1	chr12	32487443	32487449	-	1	NA	Intergenic	Intergenic	108657	NM_001162903	72123	Mm.341352	NM_028111	ENSMUSG00000090946	Ccdc71l	2010109K11Rik|AV375874	coiled-coil domain containing 71 like	protein-coding
mm_109424.1	chr12	110591734	110591791	+	1	NA	non-coding (NR_033340, exon 1 of 1)	non-coding (NR_033340, exon 1 of 1)	388	NR_033340	319786	Mm.129691	NR_033340		B930059L03Rik	-	RIKEN cDNA B930059L03 gene	ncRNA
mm_90858.1	chr10	8852188	8852190	-	1	NA	intron (NM_175155, intron 1 of 19)	intron (NM_175155, intron 1 of 19)	33881	NM_175155	70097	Mm.338275	NM_175155	ENSMUSG00000015305	Sash1	1100001C18Rik|2500002E12Rik|A330076K04Rik|mKIAA0790	SAM and SH3 domain containing 1	protein-coding
mm_62460.1	chr7	101547866	101547872	+	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	7933	NM_007490	11871	Mm.439746	NM_007490	ENSMUSG00000092517	Art2a-ps	ARTC2|Art2a|Ly92a|Rt-6|Rt6|Rt6-1	ADP-ribosyltransferase 2a, pseudogene	protein-coding
mm_46482.1	chr5	105131945	105131972	-	1	NA	intron (NM_008620, intron 3 of 10)	L1MA6|LINE|L1	7594	NM_008620	17472	Mm.440525	NM_008620	ENSMUSG00000079363	Gbp4	AW228052|Mag-2|Mpa-2|Mpa2	guanylate binding protein 4	protein-coding
mm_77224.1	chr8	115703140	115703159	-	1	NA	TTS (NM_001025577)	TTS (NM_001025577)	3745	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_73144.1	chr8	94984410	94984477	+	1	NA	promoter-TSS (NM_018882)	promoter-TSS (NM_018882)	44	NM_018882	14766	Mm.290834	NM_018882	ENSMUSG00000031785	Adgrg1	Cyt28|Gpr56|TM7LN4|TM7XN1	adhesion G protein-coupled receptor G1	protein-coding
mm_14504.1	chr2	132247844	132247863	+	1	NA	promoter-TSS (NM_027478)	promoter-TSS (NM_027478)	-65	NM_001141971	70612	Mm.30116	NM_027478	ENSMUSG00000027341	Tmem230	5730494N06Rik|AA407821	transmembrane protein 230	protein-coding
mm_157751.1	chrX	73492051	73492063	-	1	NA	exon (NM_007542, exon 4 of 8)	exon (NM_007542, exon 4 of 8)	8456	NM_007542	12111	Mm.2608	NM_007542	ENSMUSG00000031375	Bgn	BG|DSPG1|PG-S1|PGI|SLRR1A	biglycan	protein-coding
mm_18440.1	chr2	60881361	60881491	-	1	NA	promoter-TSS (NM_001141932)	promoter-TSS (NM_001141932)	12	NM_001141932	56878	Mm.259667	NM_020296	ENSMUSG00000026970	Rbms1	2600014B10Rik|AI255215|MSSP-1|MSSP-2|MSSP-3|YC1	RNA binding motif, single stranded interacting protein 1	protein-coding
mm_64425.1	chr7	142577413	142577445	+	1	NA	promoter-TSS (NR_030416)	promoter-TSS (NR_030416)	-282	NR_030416	735280		NR_030416	ENSMUSG00000076275	Mir675	Mirn675|mir-675|mmu-mir-675	microRNA 675	ncRNA
mm_102766.1	chr11	67965632	67965663	-	1	NA	promoter-TSS (NM_018768)	promoter-TSS (NM_018768)	-5	NM_027963	71860	Mm.441823	NM_027963	ENSMUSG00000020904	Cfap52	1700019F09Rik|4933417B11Rik|WDRPUH|Wdr16	cilia and flagella associated protein 52	protein-coding
mm_78038.1	chr9	14276321	14276347	+	1	NA	promoter-TSS (NM_030261)	promoter-TSS (NM_030261)	33	NM_030261	75747	Mm.325126	NM_030261	ENSMUSG00000032009	Sesn3	5630400E15Rik|BC003348|SEST3	sestrin 3	protein-coding
mm_120577.1	chr14	69190703	69190712	+	1	NA	promoter-TSS (NM_010921)	promoter-TSS (NM_010921)	15	NM_010921	18095	Mm.3520	NM_010921	ENSMUSG00000022061	Nkx3-1	Bax|NKX3.1|NKX3A|Nkx-3.1|bagpipe	NK-3 transcription factor, locus 1 (Drosophila)	protein-coding
mm_45365.1	chr5	66017619	66017622	-	1	NA	3' UTR (NM_139065, exon 7 of 7)	3' UTR (NM_139065, exon 7 of 7)	-13335	NR_027961	231253	Mm.436542	NM_177679	ENSMUSG00000054598	9130230L23Rik	-	RIKEN cDNA 9130230L23 gene	ncRNA
mm_78192.1	chr9	21337833	21337859	+	1	NA	promoter-TSS (NM_152808)	promoter-TSS (NM_152808)	18	NM_152808	68682	Mm.148425	NM_152808	ENSMUSG00000057193	Slc44a2	1110028E10Rik|CTL2	solute carrier family 44, member 2	protein-coding
mm_40579.1	chr5	64092990	64093007	+	1	NA	promoter-TSS (NM_025700)	promoter-TSS (NM_025700)	48	NM_025700	66681	Mm.2325	NM_025700	ENSMUSG00000029171	Pgm1	3230402E02Rik|Pgm-1|Pgm2	phosphoglucomutase 1	protein-coding
mm_114987.1	chr13	97495074	97495089	+	1	NA	non-coding (NR_110432, exon 2 of 2)	non-coding (NR_110432, exon 2 of 2)	12380	NR_110431	100039691	Mm.219358	NR_110430	ENSMUSG00000078952	Lncenc1	ENSMUSG00000078952|Gm11019|Gm2373|Lincenc1|Platr18|linc-Enc1	long non-coding RNA, embryonic stem cells expressed 1	ncRNA
mm_55243.1	chr6	52620211	52620217	-	1	NA	intron (NM_145567, intron 3 of 7)	intron (NM_145567, intron 3 of 7)	20086	NM_145567	58875	Mm.286458	NM_145567	ENSMUSG00000029776	Hibadh	6430402H10Rik|AI265272	3-hydroxyisobutyrate dehydrogenase	protein-coding
mm_148126.1	chr18	75562195	75562202	-	1	NA	intron (NM_201354, intron 7 of 11)	B3A|SINE|B2	47553	NR_045879	100038353	Mm.440724	NR_045879	ENSMUSG00000097712	Gm10532	ENSMUSG00000073534	predicted gene 10532	ncRNA
mm_71254.1	chr8	40917391	40917401	+	1	NA	3' UTR (NM_001044740, exon 12 of 12)	3' UTR (NM_001044740, exon 12 of 12)	-8837	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_73572.1	chr8	109705641	109705666	+	1	NA	promoter-TSS (NM_029468)	promoter-TSS (NM_029468)	107	NM_001167946	75871	Mm.180410	NM_029468	ENSMUSG00000031728	Zfp821	4930566A11Rik|Znf821	zinc finger protein 821	protein-coding
mm_12814.1	chr2	80315536	80315546	+	1	NA	promoter-TSS (NM_024181)	promoter-TSS (NM_024181)	75	NM_024181	66861	Mm.21762	NM_024181	ENSMUSG00000027006	Dnajc10	1200006L06Rik|D2Ertd706e|ERdj5|JPDI	DnaJ heat shock protein family (Hsp40) member C10	protein-coding
mm_105389.1	chr11	103363672	103363685	-	1	NA	promoter-TSS (NM_183288)	promoter-TSS (NM_183288)	14	NM_183288	544817	Mm.259113	NM_133715	ENSMUSG00000034255	Arhgap27	2310069I04Rik|5730442P18Rik|Gm21552|Sh3d20	Rho GTPase activating protein 27	protein-coding
mm_16727.1	chr2	7396013	7396031	-	1	NA	promoter-TSS (NM_001110232)	promoter-TSS (NM_001110232)	-22	NM_001110232	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_136360.1	chr16	92776839	92776847	-	1	NA	intron (NM_001111022, intron 2 of 6)	intron (NM_001111022, intron 2 of 6)	49231	NM_001111021	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_77256.1	chr8	115706948	115706956	-	1	NA	promoter-TSS (NM_001025577)	promoter-TSS (NM_001025577)	-58	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_145138.1	chr18	45559431	45559482	+	1	NA	promoter-TSS (NM_080465)	promoter-TSS (NM_080465)	-698	NM_080465	140492	Mm.411614	NM_080465	ENSMUSG00000054477	Kcnn2	KCa2.2|SK2|SKCA2|bc|fri	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2	protein-coding
mm_167943.1	chrX	128399965	128399970	-	1	NA	Intergenic	Lx8b|LINE|L1	-651557	NR_045441	75274	Mm.108718	NR_045441	ENSMUSG00000086244	4930558G05Rik	-	RIKEN cDNA 4930558G05 gene	ncRNA
mm_58012.1	chr6	136532581	136532595	-	1	NA	intron (NM_019426, intron 1 of 14)	intron (NM_019426, intron 1 of 14)	13737	NM_019426	54343	Mm.173271	NM_019426	ENSMUSG00000030213	Atf7ip	2610204M12Rik|AM|Mcaf1	activating transcription factor 7 interacting protein	protein-coding
mm_48563.1	chr5	143180722	143180795	-	1	NA	promoter-TSS (NM_177880)	promoter-TSS (NM_177880)	17	NM_021326	57782	Mm.320419	NM_021326	ENSMUSG00000061898	Rbak	-	RB-associated KRAB zinc finger	protein-coding
mm_42693.1	chr5	119836698	119836727	+	1	NA	intron (NM_011537, intron 1 of 8)	intron (NM_011537, intron 1 of 8)	2049	NM_011537	21388	Mm.103636	NM_011537	ENSMUSG00000018263	Tbx5	-	T-box 5	protein-coding
mm_1737.1	chr1	75436003	75436013	+	1	NA	promoter-TSS (NM_133708)	promoter-TSS (NM_133708)	65	NM_133708	69080	Mm.23951	NM_133708	ENSMUSG00000033021	Gmppa	1810012N01Rik	GDP-mannose pyrophosphorylase A	protein-coding
mm_59591.1	chr7	28135056	28135058	+	1	NA	intron (NM_001164655, intron 3 of 19)	B3A|SINE|B2	5591	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_132444.1	chr16	35972186	35972219	+	1	NA	exon (NM_030253, exon 11 of 11)	exon (NM_030253, exon 11 of 11)	-11161	NM_008465	16646	Mm.3991	NM_008465	ENSMUSG00000022905	Kpna1	AW494490|IPOA5|NPI1|Rch2|mSRP1	karyopherin (importin) alpha 1	protein-coding
mm_27900.1	chr3	79458813	79458829	-	1	NA	3' UTR (NM_001162999, exon 17 of 17)	3' UTR (NM_001162999, exon 17 of 17)	108858	NM_001162999	329679	Mm.244005	NM_001162999	ENSMUSG00000061175	Fnip2	D630023B12Rik|mKIAA1450	folliculin interacting protein 2	protein-coding
mm_122088.1	chr14	30625127	30625137	-	1	NA	intron (NM_011103, intron 1 of 17)	intron (NM_011103, intron 1 of 17)	1076	NM_011103	18753	Mm.2314	NM_011103	ENSMUSG00000021948	Prkcd	AI385711|D14Ertd420e|PKC[d]|PKCdelta|Pkcd	protein kinase C, delta	protein-coding
mm_117364.1	chr13	70841704	70841716	-	1	NA	non-coding (NR_137640, exon 1 of 23)	non-coding (NR_137640, exon 1 of 23)	101	NM_172053	271127	Mm.115970	NM_172053	ENSMUSG00000049538	Adamts16	-	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 16	protein-coding
mm_161190.1	chr13	50643240	50643240	+	1	NA	promoter-TSS (NM_001033770)	promoter-TSS (NM_001033770)	12	NM_001033770	380845	Mm.379403	NM_001033770	ENSMUSG00000096641	Gm904	Gm1135	predicted gene 904	protein-coding
mm_147248.1	chr18	38419355	38419365	-	1	NA	intron (NM_022996, intron 1 of 7)	CpG	385	NM_022996	65113	Mm.102496	NM_022996	ENSMUSG00000024425	Ndfip1	0610010M22Rik|N4wbp5	Nedd4 family interacting protein 1	protein-coding
mm_98153.1	chr11	87617152	87617164	+	1	NA	promoter-TSS (NM_001045527)	promoter-TSS (NM_001045527)	-6	NM_001045527	327992	Mm.390371	NM_001045527	ENSMUSG00000070345	Hsf5	Gm739|MLZ-220	heat shock transcription factor family member 5	protein-coding
mm_90401.1	chr10	127325762	127325782	+	1	NA	intron (NM_146011, intron 3 of 14)	intron (NM_146011, intron 3 of 14)	2045	NM_146011	216445	Mm.227198	NM_146011	ENSMUSG00000040345	Arhgap9	AU043488	Rho GTPase activating protein 9	protein-coding
mm_61782.1	chr7	83755842	83755872	+	1	NA	Intergenic	Intergenic	-20367	NM_010551	16170	Mm.10137	NM_010551	ENSMUSG00000001741	Il16	mKIAA4048	interleukin 16	protein-coding
mm_164502.1	chr16	91946662	91946662	+	1	NA	Intergenic	Intergenic	-15032	NM_138597	28080	Mm.41	NM_138597	ENSMUSG00000022956	Atp5o	ATPO|D12Wsu28e|OSCP	ATP synthase, H+ transporting, mitochondrial F1 complex, O subunit	protein-coding
mm_36098.1	chr4	58553172	58553180	-	1	NA	5' UTR (NM_172989, exon 1 of 4)	5' UTR (NM_172989, exon 1 of 4)	117	NM_172989	14745	Mm.4772	NM_010336	ENSMUSG00000038668	Lpar1	AI326300|Edg2|Gpcr26|Kdt2|lpA1|vzg-1	lysophosphatidic acid receptor 1	protein-coding
mm_133398.1	chr16	84793547	84793556	+	1	NA	intron (NM_023844, intron 1 of 9)	intron (NM_023844, intron 1 of 9)	19428	NM_023844	67374	Mm.41758	NM_023844	ENSMUSG00000053062	Jam2	1110002N23Rik|2410030G21Rik|2410167M24Rik|JAM-2|JAM-B|Jcam2|VE-JAM	junction adhesion molecule 2	protein-coding
mm_142622.1	chr17	47017036	47017040	-	1	NA	Intergenic	MYSERV-int|LTR|ERVK	-6506	NM_001177374	224826	Mm.28234	NM_146078	ENSMUSG00000023977	Ubr2	9930021A08Rik|AI462103|AW540746|E130209G04Rik|ENSMUSG00000043296|mKIAA0349	ubiquitin protein ligase E3 component n-recognin 2	protein-coding
mm_93191.1	chr10	94035729	94035769	-	1	NA	promoter-TSS (NM_053072)	promoter-TSS (NM_053072)	-7	NM_001304720	215008	Mm.124177	NM_172538	ENSMUSG00000036099	Vezt	A630071D13Rik|AI848282	vezatin, adherens junctions transmembrane protein	protein-coding
mm_58379.1	chr6	149130929	149130971	-	1	NA	Intergenic	RLTR23|LTR|ERV1	-10563	NM_001252096	320204	Mm.274099	NM_177101	ENSMUSG00000039958	Etfbkmt	4833442J19Rik|AI256744|ETFB-KMT|Mettl20	electron transfer flavoprotein beta subunit lysine methyltransferase	protein-coding
mm_78211.1	chr9	21499400	21499414	+	1	NA	intron (NM_007871, intron 15 of 19)	intron (NM_007871, intron 15 of 19)	-2843	NR_029585	387194		NR_029585	ENSMUSG00000065547	Mir199a-1	Mirn199|Mirn199a-1|mir-199a-1	microRNA 199a-1	ncRNA
mm_159670.1	chr4	154667749	154667749	-	1	NA	5' UTR (NM_028513, exon 1 of 1)	5' UTR (NM_028513, exon 1 of 1)	118	NM_028513	73353	Mm.30958	NM_028513	ENSMUSG00000051276	Actrt2	1700052K15Rik|Arp-T2|Arpm2	actin-related protein T2	protein-coding
mm_124864.1	chr15	10177371	10177392	+	1	NA	5' UTR (NM_011169, exon 1 of 10)	5' UTR (NM_011169, exon 1 of 10)	143	NM_011169	19116	Mm.10516	NM_011169	ENSMUSG00000005268	Prlr	AI987712|Pr-1|Pr-3|Prlr-rs1	prolactin receptor	protein-coding
mm_53966.1	chr6	5977348	5977393	-	1	NA	promoter-TSS (NR_040255)	promoter-TSS (NR_040255)	23	NR_040255	72249	Mm.443268	NR_040255	ENSMUSG00000085416	1700019G24Rik	-	RIKEN cDNA 1700019G24 gene	ncRNA
mm_108151.1	chr12	76307144	76307157	+	1	NA	intron (NM_138745, intron 21 of 27)	intron (NM_138745, intron 21 of 27)	-17741	NM_001101471	238276	Mm.311452	NM_001101471	ENSMUSG00000021057	Akap5	3526401B18Rik|AKAP 150|AKAP-5|AKAP150|BB098886|Gm258|P150	A kinase (PRKA) anchor protein 5	protein-coding
mm_81565.1	chr9	110417750	110417753	+	1	NA	Intergenic	RLTR24|LTR|ERV1	-2057	NM_008694	18054	Mm.236225	NM_008694	ENSMUSG00000032484	Ngp	bectenecin	neutrophilic granule protein	protein-coding
mm_167355.1	chr8	84197468	84197478	-	1	NA	Intergenic	CpG	-11045	NR_029740	387216		NR_029740	ENSMUSG00000065611	Mir23a	Mirn23a|mir-23a|mmu-mir-23a	microRNA 23a	ncRNA
mm_78320.1	chr9	24503498	24503512	+	1	NA	promoter-TSS (NM_172920)	promoter-TSS (NM_172920)	-365	NM_172920	244745	Mm.38526	NM_172920	ENSMUSG00000043067	Dpy19l1	1100001I19Rik|6030402K12|AI225861|AW558481	dpy-19-like 1 (C. elegans)	protein-coding
mm_87723.1	chr10	60106335	60106364	+	1	NA	promoter-TSS (NM_052994)	promoter-TSS (NM_052994)	92	NM_052994	94214	Mm.153429	NM_052994	ENSMUSG00000058297	Spock2	AA407235|Gcap26|mKIAA0275	sparc/osteonectin, cwcv and kazal-like domains proteoglycan 2	protein-coding
mm_57586.1	chr6	127458626	127458638	-	1	NA	intron (NM_001346512, intron 1 of 5)	intron (NM_001346512, intron 1 of 5)	4909	NM_181402	101187	Mm.110818	NM_181402	ENSMUSG00000037997	Parp11	5330431N24Rik|AI851877|ARTD11|HIN1L|PARP-11	poly (ADP-ribose) polymerase family, member 11	protein-coding
mm_153301.1	chr19	37959760	37959777	-	1	NA	exon (NM_001099634, exon 20 of 53)	exon (NM_001099634, exon 20 of 53)	83809	NM_001099634	226101	Mm.34674	NM_177035	ENSMUSG00000048612	Myof	2310004N10Rik|2310051D19Rik|E030042N20Rik|Fer1l3	myoferlin	protein-coding
mm_103100.1	chr11	69936234	69936279	-	1	NA	promoter-TSS (NM_001347634)	promoter-TSS (NM_001347634)	-72	NM_001347634	53422	Mm.29286	NM_016875	ENSMUSG00000018554	Ybx2	Msy2	Y box protein 2	protein-coding
mm_109882.1	chr12	4996804	4996809	-	1	NA	intron (NM_001099628, intron 21 of 30)	intron (NM_001099628, intron 21 of 30)	79453	NM_001099628	320817	Mm.210966	NM_001099628	ENSMUSG00000052812	Atad2b	1110014E10Rik|BC032887|C79189|D530031C13Rik	ATPase family, AAA domain containing 2B	protein-coding
mm_84982.1	chr9	85710414	85710439	-	1	NA	exon (NM_001081282, exon 21 of 29)	exon (NM_001081282, exon 21 of 29)	38908	NM_001081282	108837	Mm.22315	NM_175371	ENSMUSG00000035941	Ibtk	5430411K16Rik|AA409502|BTKI|mKIAA1417	inhibitor of Bruton agammaglobulinemia tyrosine kinase	protein-coding
mm_98666.1	chr11	96282415	96282431	+	1	NA	5' UTR (NM_010461, exon 1 of 2)	5' UTR (NM_010461, exon 1 of 2)	518	NM_010461	15416	Mm.4822	NM_010461	ENSMUSG00000056648	Hoxb8	Hox-2.4	homeobox B8	protein-coding
mm_34184.1	chr4	140701427	140701437	+	1	NA	promoter-TSS (NM_173867)	promoter-TSS (NM_173867)	-41	NM_173867	108911	Mm.253	NM_173867	ENSMUSG00000040945	Rcc2	2610510H01Rik|2610529N02Rik|AA536646|AA675016|Td60|mKIAA1470	regulator of chromosome condensation 2	protein-coding
mm_33118.1	chr4	124751596	124751604	+	1	NA	exon (NM_008385, exon 7 of 24)	exon (NM_008385, exon 7 of 24)	7819	NR_030480	735263		NR_030480	ENSMUSG00000076119	Mir698	Mirn698|mir-698|mmu-mir-698	microRNA 698	ncRNA
mm_171430.1	chr4	135716679	135716703	-	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-11468	NM_178257	230828	Mm.261647	NM_178257	ENSMUSG00000037157	Il22ra1	9130219A07Rik|ENSMUSG00000073746|IL-22R|Il22r	interleukin 22 receptor, alpha 1	protein-coding
mm_10840.1	chr2	24962419	24962473	+	1	NA	promoter-TSS (NM_026044)	promoter-TSS (NM_026044)	24	NM_026044	67228	Mm.389248	NM_026044	ENSMUSG00000026975	Dph7	2810443J12Rik|AW060693|Wdr85	diphthamine biosynethesis 7	protein-coding
mm_77872.1	chr9	6168554	6168567	+	1	NA	promoter-TSS (NM_027924)	promoter-TSS (NM_027924)	-52	NM_027924	71785	Mm.390122	NM_027924	ENSMUSG00000032006	Pdgfd	1110003I09Rik	platelet-derived growth factor, D polypeptide	protein-coding
mm_138888.1	chr17	43455632	43455656	+	1	NA	3' UTR (NM_001081178, exon 21 of 21)	3' UTR (NM_001081178, exon 21 of 21)	47129	NM_008585	17287	Mm.5346	NM_008585	ENSMUSG00000023914	Mep1a	AI098089|AW107200|Mep-1|Mep-1a|Mep1	meprin 1 alpha	protein-coding
mm_105909.1	chr11	114983353	114983363	-	1	NA	3' UTR (NM_145437, exon 4 of 4)	3' UTR (NM_145437, exon 4 of 4)	6528	NM_145437	217305	Mm.275986	NM_145437	ENSMUSG00000034641	Cd300ld	4732429D16Rik|CLM5|Cd300ld1|LMIR4|MAIR-IV|clm-5	CD300 molecule like family member d	protein-coding
mm_102355.1	chr11	58231435	58231445	-	1	NA	Intergenic	Intergenic	16463	NM_019440	54396	Mm.458517	NM_019440	ENSMUSG00000069874	Irgm2	AI481100|GTPI|Ifggd2|Iigp2	immunity-related GTPase family M member 2	protein-coding
mm_124943.1	chr15	12321535	12321547	+	1	NA	promoter-TSS (NM_025673)	promoter-TSS (NM_025673)	45	NM_025673	66629	Mm.157655	NM_025673	ENSMUSG00000022200	Golph3	4733401N08Rik|5730410D03Rik|AW413496	golgi phosphoprotein 3	protein-coding
mm_130772.1	chr15	101427785	101427807	-	1	NA	TTS (NM_033073)	TTS (NM_033073)	11008	NM_001003668	406219	Mm.347934	NM_001003668	ENSMUSG00000047641	Krt87	K83|K87|Krt2-25|Krt83	keratin 87	protein-coding
mm_72155.1	chr8	72161102	72161147	+	1	NA	promoter-TSS (NM_023126)	promoter-TSS (NM_023126)	-76	NM_023126	17274	Mm.162811	NM_023126	ENSMUSG00000003037	Rab8a	AA409338|Mel	RAB8A, member RAS oncogene family	protein-coding
mm_26436.1	chr3	142620723	142620733	+	1	NA	promoter-TSS (NM_010260)	promoter-TSS (NM_010260)	65	NM_010260	14469	Mm.24038	NM_010260	ENSMUSG00000028270	Gbp2	-	guanylate binding protein 2	protein-coding
mm_96232.1	chr11	62551235	62551246	+	1	NA	promoter-TSS (NR_002875).2	promoter-TSS (NR_002875).2	69	NM_011664	22187	Mm.371592	NM_011664	ENSMUSG00000019505	Ubb	AL033289|Rps27a|Uba52|Ubb2|Ubc	ubiquitin B	protein-coding
mm_139952.1	chr17	71220203	71220211	+	1	NA	intron (NM_001164885, intron 2 of 19)	intron (NM_001164885, intron 2 of 19)	15553	NM_001164885	64898	Mm.227924	NM_022882	ENSMUSG00000024052	Lpin2	2610511G02Rik|AI481352|AW742896	lipin 2	protein-coding
mm_147261.1	chr18	38866703	38866748	-	1	NA	intron (NM_010197, intron 1 of 3)	L2b|LINE|L2	-25731	NM_001033789	545253	Mm.244585	NM_001033789	ENSMUSG00000036452	Gm5820	EG545253	predicted gene 5820	protein-coding
mm_82870.1	chr9	32423818	32423838	-	1	NA	exon (NM_008026, exon 9 of 9)	exon (NM_008026, exon 9 of 9)	29843	NM_001168354	56379	Mm.390168	NM_019659	ENSMUSG00000041248	Kcnj1	Kir1.1|ROMK|Romk2	potassium inwardly-rectifying channel, subfamily J, member 1	protein-coding
mm_115323.1	chr13	112438149	112438178	+	1	NA	Intergenic	RCHARR1|DNA|hAT-Charlie	-25907	NM_010560	16195	Mm.4364	NM_010560	ENSMUSG00000021756	Il6st	5133400A03Rik|AA389424|BB405851|CD130|D13Ertd699e|gp130	interleukin 6 signal transducer	protein-coding
mm_141153.1	chr17	26506527	26506537	-	1	NA	exon (NM_013642, exon 4 of 4)	exon (NM_013642, exon 4 of 4)	1940	NM_013642	19252	Mm.239041	NM_013642	ENSMUSG00000024190	Dusp1	3CH134|MKP1|Ptpn16|U19515|erp|mkp-1	dual specificity phosphatase 1	protein-coding
mm_72529.1	chr8	83989466	83989479	+	1	NA	intron (NM_001277898, intron 5 of 9)	intron (NM_001277898, intron 5 of 9)	-8200	NM_001081415	666704	Mm.298091	NM_001081415	ENSMUSG00000079003	Samd1	AA589507	sterile alpha motif domain containing 1	protein-coding
mm_24027.1	chr3	87535758	87535772	+	1	NA	exon (NM_012051, exon 5 of 5)	exon (NM_012051, exon 5 of 5)	10187	NM_012051	27049	Mm.219460	NM_012051	ENSMUSG00000003382	Etv3	AI414410|METS|Pe1	ets variant 3	protein-coding
mm_110703.1	chr12	69318136	69318148	-	1	NA	exon (NM_025441, exon 26 of 33)	exon (NM_025441, exon 26 of 33)	21461	NM_027117	69554	Mm.234368	NM_027117	ENSMUSG00000020978	Klhdc2	2310022K15Rik|D12Ertd522e|HCLP-1|LCP	kelch domain containing 2	protein-coding
mm_125918.1	chr15	76172094	76172109	+	1	NA	3' UTR (NM_201393, exon 32 of 32)	3' UTR (NM_201393, exon 32 of 32)	23609	NM_201394	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
mm_7403.1	chr1	119053522	119053555	-	1	NA	promoter-TSS (NM_001081125)	promoter-TSS (NM_001081125)	81	NM_001081125	14633	Mm.273292	NM_001081125	ENSMUSG00000048402	Gli2	-	GLI-Kruppel family member GLI2	protein-coding
mm_7268.1	chr1	95667556	95667597	-	1	NA	promoter-TSS (NM_001159745)	promoter-TSS (NM_001159745)	18	NM_009183	20452	Mm.306228	NM_009183	ENSMUSG00000040710	St8sia4	PST|PST-1|SIAT8-D|ST8SiaIV|Siat8d	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4	protein-coding
mm_19714.1	chr2	104028288	104028337	-	1	NA	intron (NM_020593, intron 1 of 9)	CpG	513	NM_212433	57443	Mm.143768	NM_020593	ENSMUSG00000027180	Fbxo3	1200002G09Rik|1700026K02Rik|AI046358|Fba	F-box protein 3	protein-coding
mm_35168.1	chr4	14796034	14796045	-	1	NA	promoter-TSS (NM_028499)	promoter-TSS (NM_028499)	13	NM_028499	73314	Mm.52613	NM_028499	ENSMUSG00000023151	Lrrc69	1700034K16Rik	leucine rich repeat containing 69	protein-coding
mm_91417.1	chr10	32051204	32051209	-	1	NA	intron (NM_001013411, intron 3 of 6)	intron (NM_001013411, intron 3 of 6)	-441481	NM_001146349	268291	Mm.295212	NM_001146349	ENSMUSG00000063760	Rnf217	AU016819|Ibrdc1	ring finger protein 217	protein-coding
mm_24568.1	chr3	93444292	93444300	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	1966	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_99953.1	chr11	112806599	112806602	+	1	NA	Intergenic	Intergenic	-7592	NR_126071	100038732	Mm.65345	NR_126070	ENSMUSG00000075437	Gm11681	-	predicted gene 11681	ncRNA
mm_91479.1	chr10	34233594	34233596	-	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	-26044	NM_172508	212898	Mm.34557	NM_172508	ENSMUSG00000039497	Dse	6030499O08|AI480506|B130024B19Rik|DS-epi1|Sart2	dermatan sulfate epimerase	protein-coding
mm_70495.1	chr8	12757003	12757027	+	1	NA	promoter-TSS (NM_001293667)	promoter-TSS (NM_001293667)	-1	NM_015804	50770	Mm.257837	NM_015804	ENSMUSG00000031441	Atp11a	4930558F19Rik|AU040868|Atpc1h|Ih	ATPase, class VI, type 11A	protein-coding
mm_104106.1	chr11	86710926	86710955	-	1	NA	intron (NM_001003908, intron 17 of 31)	intron (NM_001003908, intron 17 of 31)	26859	NM_001098810	217057	Mm.24868	NM_175004	ENSMUSG00000072582	Ptrh2	A230072I16Rik|Bit1|CGI-147	peptidyl-tRNA hydrolase 2	protein-coding
mm_87912.1	chr10	62340229	62340242	+	1	NA	promoter-TSS (NR_038038)	promoter-TSS (NR_038038)	186	NM_001146100	15275	Mm.196605	NM_010438	ENSMUSG00000037012	Hk1	BB404130|Hk-1|Hk1-s|dea|mHk1-s	hexokinase 1	protein-coding
mm_157333.1	chrX	36025842	36025860	-	1	NA	intron (NM_001009947, intron 35 of 52)	CpG	-86257	NM_133990	16164	Mm.24208	NM_133990	ENSMUSG00000017057	Il13ra1	AI882074|CD213a1|IL-13R-alpha-1|IL-13r[a]|Il13ra|NR4	interleukin 13 receptor, alpha 1	protein-coding
mm_115933.1	chr13	23585984	23585995	-	1	NA	promoter-TSS (NM_001290530)	promoter-TSS (NM_001290530)	-19	NM_001290530	319179	Mm.440391	NM_178194	ENSMUSG00000047246	Hist1h2be	-	histone cluster 1, H2be	protein-coding
mm_51840.1	chr6	90302160	90302168	+	1	NA	intron (NM_177738, intron 2 of 4)	intron (NM_177738, intron 2 of 4)	894	NM_177738	243535	Mm.233854	NM_177738	ENSMUSG00000049694	BC048671	-	cDNA sequence BC048671	protein-coding
mm_60677.1	chr7	45077626	45077680	+	1	NA	3' UTR (NM_025533, exon 9 of 9)	3' UTR (NM_025533, exon 9 of 9)	14560	NM_026555	52377	Mm.29997	NM_026555	ENSMUSG00000019539	Rcn3	6030455P07Rik|D530026G20Rik|D7Ertd671e|RLP49	reticulocalbin 3, EF-hand calcium binding domain	protein-coding
mm_155739.1	chrX	96166566	96166574	+	1	NA	exon (NM_010833, exon 13 of 13)	exon (NM_010833, exon 13 of 13)	70525	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_37994.1	chr4	133660746	133660783	-	1	NA	TTS (NM_178698)	TTS (NM_178698)	11883	NM_001145955	230801	Mm.217004	NM_178698	ENSMUSG00000043257	Pigv	B330013B03|D430024F16Rik	phosphatidylinositol glycan anchor biosynthesis, class V	protein-coding
mm_7320.1	chr1	100180148	100180185	-	1	NA	intron (NM_172851, intron 10 of 23)	L1Md_F2|LINE|L1	407401	NM_172851	241175	Mm.251301	NM_172851	ENSMUSG00000067028	Cntnap5b	C230078M14Rik|Caspr5-2	contactin associated protein-like 5B	protein-coding
mm_42465.1	chr5	115450908	115450923	+	1	NA	exon (NM_008629, exon 13 of 15)	exon (NM_008629, exon 13 of 15)	-15351	NM_011107	18778	Mm.20190	NM_011107	ENSMUSG00000029522	Pla2g1b	Pla2a|sPLA2IB	phospholipase A2, group IB, pancreas	protein-coding
mm_3856.1	chr1	160972610	160972613	+	1	NA	3' UTR (NM_001024952, exon 20 of 20)	3' UTR (NM_001024952, exon 20 of 20)	-5995	NM_080844	11905	Mm.260770	NM_080844	ENSMUSG00000026715	Serpinc1	AI114908|ATIII|At-3|At3	serine (or cysteine) peptidase inhibitor, clade C (antithrombin), member 1	protein-coding
mm_165123.1	chr2	4822622	4822629	+	1	NA	Intergenic	Intergenic	-58939	NM_175400	109079	Mm.34329	NM_175400	ENSMUSG00000026662	Sephs1	1110046B24Rik|AA589574|AI505014|AW111620|SELD|SPS|SPS1	selenophosphate synthetase 1	protein-coding
mm_67364.1	chr7	79839191	79839204	-	1	NA	exon (NM_008486, exon 5 of 20)	exon (NM_008486, exon 5 of 20)	3155	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_20724.1	chr2	136387930	136387985	-	1	NA	promoter-TSS (NM_172858)	promoter-TSS (NM_172858)	10	NM_172858	241656	Mm.131572	NM_172858	ENSMUSG00000039913	Pak7	2900083L08Rik|6430627N20|Pak5	p21 protein (Cdc42/Rac)-activated kinase 7	protein-coding
mm_77638.1	chr8	124274473	124274487	-	1	NA	intron (NM_139272, intron 1 of 15)	intron (NM_139272, intron 1 of 15)	43086	NM_139272	108148	Mm.33808	NM_139272	ENSMUSG00000089704	Galnt2	AI480629	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2	protein-coding
mm_15096.1	chr2	153336404	153336421	+	1	NA	Intergenic	Intergenic	9398	NR_040318	72326	Mm.400102	NR_040318	ENSMUSG00000073236	2500004C02Rik	-	RIKEN cDNA 2500004C02 gene	ncRNA
mm_161840.1	chr17	86947965	86947965	-	1	NA	promoter-TSS (NM_029121)	promoter-TSS (NM_029121)	-78	NM_029121	74915	Mm.159369	NM_029121	ENSMUSG00000053375	Atp6v1e2	4930500C14Rik|Atp6e1|E1	ATPase, H+ transporting, lysosomal V1 subunit E2	protein-coding
mm_102317.1	chr11	57199390	57199392	-	1	NA	intron (NM_001252403, intron 4 of 15)	intron (NM_001252403, intron 4 of 15)	186345	NM_001252403	14799	Mm.4920	NM_008165	ENSMUSG00000020524	Gria1	2900051M01Rik|Glr-1|Glr1|GluA1|GluR-A|GluRA|Glur-1|Glur1|HIPA1|gluR-K1	glutamate receptor, ionotropic, AMPA1 (alpha 1)	protein-coding
mm_16475.1	chr2	180732276	180732286	+	1	NA	intron (NM_183161, intron 2 of 12)	intron (NM_183161, intron 2 of 12)	6942	NM_183161	228993	Mm.87189	NM_183161	ENSMUSG00000023393	Slc17a9	1700019H03Rik|BC019537|Vnut	solute carrier family 17, member 9	protein-coding
mm_2825.1	chr1	131143005	131143013	+	1	NA	Intergenic	RMER17C|LTR|ERVK	-4775	NM_145508	226419	Mm.39299	NM_145508	ENSMUSG00000016526	Dyrk3	BC006704	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 3	protein-coding
mm_88875.1	chr10	81075514	81075541	+	1	NA	exon (NM_022653, exon 3 of 13)	exon (NM_022653, exon 3 of 13)	5444	NM_022653	50492	Mm.26995	NM_022653	ENSMUSG00000004929	Thop1	AI131655|AI327041|EP24.15	thimet oligopeptidase 1	protein-coding
mm_100144.1	chr11	115993063	115993072	+	1	NA	exon (NM_133663, exon 24 of 39)	exon (NM_133663, exon 24 of 39)	18342	NM_133663	192897	Mm.213873	NM_133663	ENSMUSG00000020758	Itgb4	AA407042|C230078O20|CD104	integrin beta 4	protein-coding
mm_4199.1	chr1	171229574	171229584	+	1	NA	TTS (NM_010185)	TTS (NM_010185)	4525	NM_013474	11807	Mm.389209	NM_013474	ENSMUSG00000005681	Apoa2	Alp-2|Apo-AII|ApoA-II|ApoAII|Apoa-2|Hdl-1	apolipoprotein A-II	protein-coding
mm_19180.1	chr2	84389797	84389813	-	1	NA	intron (NM_018782, intron 2 of 15)	intron (NM_018782, intron 2 of 15)	35461	NM_018782	54598	Mm.75467	NM_018782	ENSMUSG00000059588	Calcrl	AV071593|CRLR	calcitonin receptor-like	protein-coding
mm_109854.1	chr12	4738412	4738444	-	1	NA	promoter-TSS (NM_029107)	promoter-TSS (NM_029107)	-45	NM_029107	74855	Mm.269534	NM_029107	ENSMUSG00000079177	Fam228a	4930417G10Rik	family with sequence similarity 228, member A	protein-coding
mm_14286.1	chr2	128802381	128802398	+	1	NA	TTS (NM_008587)	TTS (NM_008587)	-15914	NM_028248	72477	Mm.259688	NM_028248	ENSMUSG00000014353	Tmem87b	2610301K12Rik|2810431I02Rik|AU014804	transmembrane protein 87B	protein-coding
mm_47796.1	chr5	132479068	132479071	-	1	NA	intron (NM_177047, intron 1 of 18)	intron (NM_177047, intron 1 of 18)	63274	NM_177047	319974	Mm.409595	NM_177047	ENSMUSG00000029673	Auts2	2700063G02Rik|A730011F23Rik|D830032G16Rik	autism susceptibility candidate 2	protein-coding
mm_104109.1	chr11	86715721	86715757	-	1	NA	intron (NM_001003908, intron 14 of 31)	intron (NM_001003908, intron 14 of 31)	31658	NM_001098810	217057	Mm.24868	NM_175004	ENSMUSG00000072582	Ptrh2	A230072I16Rik|Bit1|CGI-147	peptidyl-tRNA hydrolase 2	protein-coding
mm_153155.1	chr19	34252559	34252574	-	1	NA	5' UTR (NM_007392, exon 2 of 9)	5' UTR (NM_007392, exon 2 of 9)	2807	NM_007392	11475	Mm.213025	NM_007392	ENSMUSG00000035783	Acta2	0610041G09Rik|Actvs|SMalphaA|a-SMA|alphaSMA	actin, alpha 2, smooth muscle, aorta	protein-coding
mm_36609.1	chr4	89128218	89128237	-	1	NA	Intergenic	Intergenic	-9143	NM_024433	66902	Mm.28500	NM_024433	ENSMUSG00000062937	Mtap	1300019I21Rik|MSAP	methylthioadenosine phosphorylase	protein-coding
mm_123415.1	chr14	64174611	64174633	-	1	NA	intron (NM_001347639, intron 5 of 5)	intron (NM_001347639, intron 5 of 5)	70299	NM_028525	73382	Mm.481055	NM_028525	ENSMUSG00000021966	Prss52	1700049K14Rik|Tesp3	protease, serine 52	protein-coding
mm_159401.1	chr3	97216447	97216447	-	1	NA	5' UTR (NM_029933, exon 4 of 10)	5' UTR (NM_029933, exon 4 of 10)	10917	NM_029933	77578	Mm.226175	NM_029933	ENSMUSG00000038256	Bcl9	2610202E01Rik|8030475K17Rik|A330041G23Rik|Gm130	B cell CLL/lymphoma 9	protein-coding
mm_74652.1	chr8	13471068	13471068	-	1	NA	intron (NM_019521, intron 11 of 14)	intron (NM_019521, intron 11 of 14)	23467	NM_019521	14456	Mm.3982	NM_019521	ENSMUSG00000031451	Gas6	Gas-6	growth arrest specific 6	protein-coding
mm_108666.1	chr12	86493778	86493778	+	1	NA	intron (NM_001159500, intron 3 of 6)	intron (NM_001159500, intron 3 of 6)	72134	NM_011934	26380	Mm.235550	NM_011934	ENSMUSG00000021255	Esrrb	Err2|Errb|Estrrb|Nr3b2	estrogen related receptor, beta	protein-coding
mm_115689.1	chr13	13954333	13954370	-	1	NA	promoter-TSS (NM_178640)	promoter-TSS (NM_178640)	-323	NM_178640	97884	Mm.21686	NM_178640	ENSMUSG00000039242	B3galnt2	A930105D20Rik|C80633|D230016N13Rik	UDP-GalNAc:betaGlcNAc beta 1,3-galactosaminyltransferase, polypeptide 2	protein-coding
mm_128237.1	chr15	36608552	36608619	-	1	NA	5' UTR (NM_008774, exon 1 of 15)	5' UTR (NM_008774, exon 1 of 15)	388	NM_008774	18458	Mm.371570	NM_008774	ENSMUSG00000022283	Pabpc1	PABP|Pabp1|PabpI|Pabpl1|ePAB	poly(A) binding protein, cytoplasmic 1	protein-coding
mm_29622.1	chr3	121478779	121478789	-	1	NA	intron (NM_145394, intron 12 of 14)	intron (NM_145394, intron 12 of 14)	52243	NM_028044	71994	Mm.275555	NM_028044	ENSMUSG00000053931	Cnn3	1600014M03Rik|C85854|Calpo3	calponin 3, acidic	protein-coding
mm_172872.1	chr9	4266849	4266854	+	1	NA	Intergenic	RLTR46A2|LTR|ERVK	42643	NR_136941	67618	Mm.33970	NM_026276	ENSMUSG00000025894	Aasdhppt	2010309J24Rik|2810407B07Rik|AASD-PPT|CGI-80|LYS2|LYS5	aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase	protein-coding
mm_35965.1	chr4	53144061	53144088	-	1	NA	5' UTR (NM_013454, exon 2 of 50)	5' UTR (NM_013454, exon 2 of 50)	15821	NM_013454	11303	Mm.277376	NM_013454	ENSMUSG00000015243	Abca1	ABC-1|Abc1	ATP-binding cassette, sub-family A (ABC1), member 1	protein-coding
mm_5506.1	chr1	37430017	37430057	-	1	NA	promoter-TSS (NM_026123)	promoter-TSS (NM_026123)	66	NM_198006	76178	Mm.28085	NM_198006	ENSMUSG00000026112	Coa5	1700001A24Rik|6330578E17Rik|Pet191	cytochrome C oxidase assembly factor 5	protein-coding
mm_171179.1	chr3	35754222	35754230	+	1	NA	promoter-TSS (NM_029570)	promoter-TSS (NM_029570)	88	NM_029570	76295	Mm.239416	NM_029570	ENSMUSG00000037400	Atp11b	1110019I14Rik|ATPIF|ATPIR|mKIAA0956	ATPase, class VI, type 11B	protein-coding
mm_168586.1	chr1	173535758	173535777	-	1	NA	5' UTR (NM_001024721, exon 1 of 5)	5' UTR (NM_001024721, exon 1 of 5)	190	NM_001024721	545384	Mm.371698	NM_001024721	ENSMUSG00000070501	Ifi214	Pyhin-B|p214	interferon activated gene 214	protein-coding
mm_47587.1	chr5	124861946	124861956	-	1	NA	promoter-TSS (NM_001081750)	promoter-TSS (NM_001081750)	270	NM_144819	215707	Mm.389693	NM_144819	ENSMUSG00000037979	Ccdc92	AW050178|D5Bwg0834e	coiled-coil domain containing 92	protein-coding
mm_16517.1	chr2	181385761	181385762	+	1	NA	non-coding (NR_045164, exon 2 of 3)	non-coding (NR_045164, exon 2 of 3)	1511	NR_045164	329584	Mm.386906	NR_045164	ENSMUSG00000085028	Slc2a4rg-ps	C430010C01|Gm14462|OTTMUSG00000016710	Slc2a4 regulator, pseudogene	pseudo
mm_111995.1	chr12	110696249	110696262	-	1	NA	5' UTR (NM_010480, exon 1 of 11)	5' UTR (NM_010480, exon 1 of 11)	140	NM_010480	15519	Mm.1843	NM_010480	ENSMUSG00000021270	Hsp90aa1	86kDa|89kDa|AL024080|AL024147|Hsp86-1|Hsp89|Hsp90|Hspca|hsp4	heat shock protein 90, alpha (cytosolic), class A member 1	protein-coding
mm_120752.1	chr14	73306171	73306175	+	1	NA	intron (NM_009029, intron 2 of 26)	Lx7|LINE|L1	19618	NM_009029	19645	Mm.273862	NM_009029	ENSMUSG00000022105	Rb1	Rb|Rb-1|pRb	retinoblastoma 1	protein-coding
mm_125436.1	chr15	44457523	44457534	+	1	NA	promoter-TSS (NM_138674)	promoter-TSS (NM_138674)	-25	NM_138674	192190	Mm.211494	NM_138674	ENSMUSG00000038725	Pkhd1l1	AB055648|PKHDL1	polycystic kidney and hepatic disease 1-like 1	protein-coding
mm_169700.1	chr15	75086815	75086816	+	1	NA	Intergenic	Intergenic	25134	NM_001099217	100041546	Mm.482110	NM_001099217	ENSMUSG00000022584	Ly6c2	Ly-6C.2|Ly-6C2	lymphocyte antigen 6 complex, locus C2	protein-coding
mm_44310.1	chr5	9160909	9160912	-	1	NA	intron (NM_011806, intron 1 of 17)	intron (NM_011806, intron 1 of 17)	866	NM_001110327	23857	Mm.22480	NM_011806	ENSMUSG00000042508	Dmtf1	Dimp|Dmp1	cyclin D binding myb-like transcription factor 1	protein-coding
mm_152814.1	chr19	23093673	23093684	-	1	NA	Intergenic	MTC|LTR|ERVL-MaLR	-47548	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_37498.1	chr4	123687238	123687307	-	1	NA	Intergenic	CpG	-2912	NM_001199136	11426	Mm.402299	NM_009600	ENSMUSG00000028649	Macf1	ABP620|Acf7|Aclp7|MACF|R74989|mKIAA0465	microtubule-actin crosslinking factor 1	protein-coding
mm_31345.1	chr4	46538867	46538867	+	1	NA	3' UTR (NM_001164804, exon 12 of 12)	3' UTR (NM_001164804, exon 12 of 12)	-2726	NM_029077	74735	Mm.240252	NM_029077	ENSMUSG00000039853	Trim14	5830400N10Rik|pub	tripartite motif-containing 14	protein-coding
mm_12241.1	chr2	68861434	68861510	+	1	NA	promoter-TSS (NM_001347161)	promoter-TSS (NM_001347161)	31	NM_001347161	241447	Mm.222222	NM_172856	ENSMUSG00000027035	Cers6	4732462C07Rik|AW544719|Lass6|T1L	ceramide synthase 6	protein-coding
mm_73568.1	chr8	109614418	109614421	+	1	NA	promoter-TSS (NM_001286454)	promoter-TSS (NM_001286454)	-98	NM_001286454	244646	Mm.436810	NM_181544	ENSMUSG00000048827	Pkd1l3	-	polycystic kidney disease 1 like 3	protein-coding
mm_162051.1	chrX	7376019	7376019	-	1	NA	promoter-TSS (NM_019461)	promoter-TSS (NM_019461)	94	NR_026741	100270707	Mm.117112	NR_026741	ENSMUSG00000087252	Gm14379	OTTMUSG00000016482	predicted gene 14379	ncRNA
mm_24188.1	chr3	88607219	88607235	+	1	NA	Intergenic	Intergenic	-8980	NM_001198911	16800	Mm.239329	NM_008487	ENSMUSG00000028059	Arhgef2	AA408978|GEF|GEF-H1|GEFH1|LFP40|Lbcl1|Lfc|P40|mKIAA0651	rho/rac guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_21634.1	chr2	164278301	164278312	-	1	NA	promoter-TSS (NM_009300)	promoter-TSS (NM_009300)	1	NM_009300	20941	Mm.1286	NM_009300	ENSMUSG00000016998	Svs4	SVS-IV|Svp-2|Svp-4|Svp2|Svp4	seminal vesicle secretory protein 4	protein-coding
mm_30196.1	chr3	144712660	144712711	-	1	NA	exon (NM_019464, exon 2 of 9)	exon (NM_019464, exon 2 of 9)	7650	NM_001282042	54673	Mm.271775	NM_019464	ENSMUSG00000037062	Sh3glb1	AA409932|AI314629|AU015566|Bif-1|mKIAA0491	SH3-domain GRB2-like B1 (endophilin)	protein-coding
mm_109445.1	chr12	110889232	110889305	+	1	NA	promoter-TSS (NM_026048)	promoter-TSS (NM_026048)	4	NM_001081057	104859	Mm.35583	NM_175336	ENSMUSG00000021275	Tecpr2	4930573I19Rik|AI604920|mKIAA0297	tectonin beta-propeller repeat containing 2	protein-coding
mm_17401.1	chr2	27209929	27209953	-	1	NA	intron (NM_138665, intron 17 of 20)	intron (NM_138665, intron 17 of 20)	37362	NM_138665	192166	Mm.278467	NM_138665	ENSMUSG00000009614	Sardh	-	sarcosine dehydrogenase	protein-coding
mm_71208.1	chr8	40890486	40890528	+	1	NA	intron (NM_007514, intron 1 of 11)	MLT1B|LTR|ERVL-MaLR	28140	NM_001044740	11988	Mm.4676	NM_007514	ENSMUSG00000031596	Slc7a2	20.5|AI158848|Atrc2|CAT-2|Cat2|Tea	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	protein-coding
mm_44105.1	chr5	149368386	149368401	+	1	NA	Intergenic	Intergenic	-43413	NM_027519	70717	Mm.252139	NM_027519	ENSMUSG00000029659	Medag	6330406I15Rik|Awms3|MEDA-4|Meda4|mAWMS3	mesenteric estrogen dependent adipogenesis	protein-coding
mm_39112.1	chr4	154928408	154928414	-	1	NA	promoter-TSS (NM_178931)	promoter-TSS (NM_178931)	-334	NM_178931	230979	Mm.215147	NM_178931	ENSMUSG00000042333	Tnfrsf14	Atar|HveA|Hvem|Tnfrs14	tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)	protein-coding
mm_159668.1	chr4	154139963	154139963	-	1	NA	5' UTR (NM_011642, exon 1 of 14)	5' UTR (NM_011642, exon 1 of 14)	245	NM_011642	22062	Mm.78015	NM_011642	ENSMUSG00000029026	Trp73	TAp73|Tp73|deltaNp73|p73	transformation related protein 73	protein-coding
mm_30177.1	chr3	144205166	144205208	-	1	NA	promoter-TSS (NM_010723)	promoter-TSS (NM_010723)	68	NM_010723	16911	Mm.29187	NM_010723	ENSMUSG00000028266	Lmo4	A730077C12Rik|Crp3|Etohi4	LIM domain only 4	protein-coding
mm_128811.1	chr15	67083066	67083072	-	1	NA	Intergenic	Intergenic	93813	NM_009177	20442	Mm.248334	NM_009177	ENSMUSG00000013846	St3gal1	5330418N22Rik|AI467004|ST3GalI|Siat4|Siat4a|St3gal-1	ST3 beta-galactoside alpha-2,3-sialyltransferase 1	protein-coding
mm_29887.1	chr3	131234028	131234034	-	1	NA	3' UTR (NM_008212, exon 8 of 8)	3' UTR (NM_008212, exon 8 of 8)	38070	NM_008212	15107	Mm.260164	NM_008212	ENSMUSG00000027984	Hadh	AA409008|AU019341|AW742602|HCDH|Hadhsc|Schad	hydroxyacyl-Coenzyme A dehydrogenase	protein-coding
mm_159125.1	chr2	71018301	71018301	-	1	NA	promoter-TSS (NM_001110512)	promoter-TSS (NM_001110512)	73	NM_001110512	228019	Mm.490343	NM_145524	ENSMUSG00000041975	Mettl8	BC004636|Tip	methyltransferase like 8	protein-coding
mm_42301.1	chr5	114676322	114676337	+	1	NA	exon (NM_019821, exon 3 of 5)	exon (NM_019821, exon 3 of 5)	14606	NM_019821	56356	Mm.275766	NM_019821	ENSMUSG00000011884	Gltp	1110001F24Rik|C76925|C77564	glycolipid transfer protein	protein-coding
mm_163718.1	chr13	111809518	111809534	-	1	NA	promoter-TSS (NM_011945)	promoter-TSS (NM_011945)	-543	NM_011945	26401	Mm.15918	NM_011945	ENSMUSG00000021754	Map3k1	MAPKKK1|MEKK1|Mekk	mitogen-activated protein kinase kinase kinase 1	protein-coding
mm_85149.1	chr9	95954659	95954698	-	1	NA	promoter-TSS (NM_001311130)	promoter-TSS (NM_001311130)	-82	NM_011916	24127	Mm.291179	NM_011916	ENSMUSG00000032410	Xrn1	Dhm2|exo|mXrn1	5'-3' exoribonuclease 1	protein-coding
mm_78968.1	chr9	45318983	45319019	+	1	NA	promoter-TSS (NM_001013373)	promoter-TSS (NM_001013373)	-99	NM_001013373	214531	Mm.394987	NM_001013373	ENSMUSG00000037129	Tmprss13	BC010843|Tpmrss13	transmembrane protease, serine 13	protein-coding
mm_65630.1	chr7	27545125	27545160	-	1	NA	intron (NM_001317355, intron 2 of 13)	intron (NM_001317355, intron 2 of 13)	8076	NM_011116	18807	Mm.6483	NM_011116	ENSMUSG00000003363	Pld3	Sam-9	phospholipase D family, member 3	protein-coding
mm_8023.1	chr1	135105211	135105225	-	1	NA	promoter-TSS (NM_001033409)	promoter-TSS (NM_001033409)	58	NM_001033409	329252	Mm.279594	NM_001033409	ENSMUSG00000042793	Lgr6	A530037C04Rik|D830026M09	leucine-rich repeat-containing G protein-coupled receptor 6	protein-coding
mm_168721.1	chr12	109544429	109544440	+	1	NA	promoter-TSS (NR_035440).2	promoter-TSS (NR_035440).2	-107	NR_035440	100316809		NR_035440	ENSMUSG00000084535	Mir1906-1	Mir1906|Mirn1906|mmu-mir-1906|mmu-mir-1906-1	microRNA 1906-1	ncRNA
mm_14458.1	chr2	131193269	131193276	+	1	NA	exon (NM_001111075, exon 9 of 15)	exon (NM_001111075, exon 9 of 15)	6324	NM_001111075	12531	Mm.38444	NM_023117	ENSMUSG00000027330	Cdc25b	AI604853	cell division cycle 25B	protein-coding
mm_90839.1	chr10	8518802	8518851	-	1	NA	promoter-TSS (NM_177387)	promoter-TSS (NM_177387)	-1	NM_177387	338362	Mm.41163	NM_177387	ENSMUSG00000047712	Ust	D930010O20Rik|UA2OST	uronyl-2-sulfotransferase	protein-coding
mm_60375.1	chr7	44468021	44468043	+	1	NA	promoter-TSS (NM_001205073)	promoter-TSS (NM_001205073)	52	NM_001205070	66124	Mm.358691	NM_025368	ENSMUSG00000038695	Josd2	1110007C05Rik	Josephin domain containing 2	protein-coding
mm_248.1	chr1	19212446	19212468	+	1	NA	intron (NM_001025305, intron 1 of 6)	intron (NM_001025305, intron 1 of 6)	403	NM_001025305	21419	Mm.137021	NM_009334	ENSMUSG00000025927	Tfap2b	AI606113|AP-2(beta)|E130018K07Rik|Tcfap2b	transcription factor AP-2 beta	protein-coding
mm_108622.1	chr12	85598601	85598607	+	1	NA	promoter-TSS (NM_030887)	promoter-TSS (NM_030887)	-501	NM_001205052	81703	Mm.103560	NM_030887	ENSMUSG00000034271	Jdp2	Jundm2|Jundp2|TIF	Jun dimerization protein 2	protein-coding
mm_37157.1	chr4	117126055	117126074	-	1	NA	promoter-TSS (NM_175030)	promoter-TSS (NM_175030)	-339	NR_024078	78611	Mm.446227	NM_001033187		Btbd19	9530048O09Rik|BB115071	BTB (POZ) domain containing 19	ncRNA
mm_114429.1	chr13	64917432	64917466	+	1	NA	promoter-TSS (NM_030047)	promoter-TSS (NM_030047)	43	NM_030047	78124	Mm.342895	NM_030047	ENSMUSG00000056223	Spata31	4930458L03Rik|Aep1|Fam75a|Spata31a|Vad1.3	spermatogenesis associated 31	protein-coding
mm_157140.1	chrX	9459393	9459406	-	1	NA	intron (NM_007807, intron 3 of 12)	intron (NM_007807, intron 3 of 12)	9925	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_119092.1	chr14	30892575	30892588	+	1	NA	exon (NM_001289633, exon 11 of 22)	exon (NM_001289633, exon 11 of 22)	6105	NM_001289632	16427	Mm.34819	NM_018746	ENSMUSG00000021922	Itih4	ITI-HC4|Itih-4|PK-120	inter alpha-trypsin inhibitor, heavy chain 4	protein-coding
mm_91616.1	chr10	41633865	41633875	-	1	NA	Intergenic	Intergenic	-27275	NM_001303469	75973	Mm.228517	NM_029493	ENSMUSG00000075225	Ccdc162	5033413D22Rik|Ccdc162p|Gm29096|Gm61|Gm6976	coiled-coil domain containing 162	protein-coding
mm_156399.1	chrX	139808596	139808628	+	1	NA	5' UTR (NM_016675, exon 2 of 2)	5' UTR (NM_016675, exon 2 of 2)	7804	NM_016675	12738	Mm.117068	NM_016675	ENSMUSG00000047230	Cldn2	AL022813	claudin 2	protein-coding
mm_18477.1	chr2	62412317	62412335	-	1	NA	promoter-TSS (NM_010074)	promoter-TSS (NM_010074)	-95	NM_001159543	13482	Mm.1151	NM_010074	ENSMUSG00000035000	Dpp4	Cd26|Dpp-4|THAM	dipeptidylpeptidase 4	protein-coding
mm_163501.1	chr12	112795808	112795835	-	1	NA	Intergenic	Intergenic	-13154	NM_145450	217887	Mm.186678	NM_145450	ENSMUSG00000037594	BC022687	AW050009|C130001I08Rik|Flj20080	cDNA sequence BC022687	protein-coding
mm_50363.1	chr6	48647425	48647437	+	1	NA	promoter-TSS (NM_001286629)	promoter-TSS (NM_001286629)	70	NM_212486	243374	Mm.86514	NM_212486	ENSMUSG00000064262	Gimap8	Gm457|IAN9|IMAP8	GTPase, IMAP family member 8	protein-coding
mm_47983.1	chr5	135911547	135911558	-	1	NA	exon (NM_018871, exon 2 of 2)	exon (NM_018871, exon 2 of 2)	23089	NM_018871	22628	Mm.233813	NM_018871	ENSMUSG00000051391	Ywhag	14-3-3gamma|D7Bwg1348e	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, gamma polypeptide	protein-coding
mm_129245.1	chr15	76659692	76659743	-	1	NA	promoter-TSS (NM_001276335)	promoter-TSS (NM_001276335)	19	NM_001276333	54151	Mm.247752	NM_019396	ENSMUSG00000053929	Cyhr1	1110031M01Rik|AU042374|Chrp	cysteine and histidine rich 1	protein-coding
mm_104942.1	chr11	100117632	100117646	-	1	NA	exon (NM_010662, exon 8 of 8)	exon (NM_010662, exon 8 of 8)	2938	NM_001313949	16663	Mm.4646	NM_010662	ENSMUSG00000044041	Krt13	CK13|K13|Krt-1.13|Krt1-13	keratin 13	protein-coding
mm_98696.1	chr11	96303555	96303561	+	1	NA	promoter-TSS (NM_008268)	promoter-TSS (NM_008268)	46	NM_008268	15413	Mm.207	NM_008268	ENSMUSG00000038700	Hoxb5	AI385717|Hox-2.1	homeobox B5	protein-coding
mm_84910.1	chr9	79977685	79977702	-	1	NA	5' UTR (NM_001081243, exon 1 of 6)	5' UTR (NM_001081243, exon 1 of 6)	189	NM_001081243	70598	Mm.23049	NM_001081243	ENSMUSG00000034898	Filip1	5730485H21Rik|AI843021	filamin A interacting protein 1	protein-coding
mm_31270.1	chr4	45342064	45342134	+	1	NA	promoter-TSS (NM_153167)	promoter-TSS (NM_153167)	-2	NM_153167	242418	Mm.317668	NM_153167	ENSMUSG00000035572	Dcaf10	AA959934|Wdr32	DDB1 and CUL4 associated factor 10	protein-coding
mm_72043.1	chr8	71227133	71227134	+	1	NA	Intergenic	ORR1B1-int|LTR|ERVL-MaLR	-20185	NR_131056	330796	Mm.258257	NR_131056		Gm38415	E230016D10	predicted gene, 38415	ncRNA
mm_111568.1	chr12	101809895	101809907	-	1	NA	exon (NM_011812, exon 4 of 11)	exon (NM_011812, exon 4 of 11)	9218	NM_011812	23876	Mm.288381	NM_011812	ENSMUSG00000021186	Fbln5	A55|DANCE|EVEC	fibulin 5	protein-coding
mm_46437.1	chr5	104989350	104989371	-	1	NA	Intergenic	Intergenic	-6643	NM_030239	27405	Mm.389663	NM_030239	ENSMUSG00000029299	Abcg3	Abcp2|Mxr2	ATP-binding cassette, sub-family G (WHITE), member 3	protein-coding
mm_32112.1	chr4	98923846	98923893	+	1	NA	promoter-TSS (NM_146144)	promoter-TSS (NM_146144)	59	NM_146144	230484	Mm.371692	NM_146144	ENSMUSG00000028560	Usp1	-	ubiquitin specific peptidase 1	protein-coding
mm_14254.1	chr2	128132619	128132622	+	1	NA	intron (NM_207680, intron 2 of 3)	ID_B1|SINE|B4	5045	NM_001284410	12125	Mm.141083	NM_009754	ENSMUSG00000027381	Bcl2l11	1500006F24Rik|Bim|Bod|bcl2-L-11	BCL2-like 11 (apoptosis facilitator)	protein-coding
mm_75246.1	chr8	39643647	39643688	-	1	NA	promoter-TSS (NM_031195)	promoter-TSS (NM_031195)	-989	NM_001113326	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_124532.1	chr14	122451081	122451093	-	1	NA	promoter-TSS (NR_033325)	promoter-TSS (NR_033325)	28	NR_033325	328479	Mm.86095	NR_033325	ENSMUSG00000064052	Gm5089	6530402A20|C030005G22Rik|EG328479	predicted gene 5089	ncRNA
mm_20069.1	chr2	120404608	120404653	-	1	NA	promoter-TSS (NM_173734)	promoter-TSS (NM_173734)	-514	NM_001110496	211499	Mm.260712	NM_173734	ENSMUSG00000033808	Tmem87a	A930025J12Rik	transmembrane protein 87A	protein-coding
mm_39187.1	chr4	155841095	155841104	-	1	NA	exon (NM_024263, exon 3 of 10)	exon (NM_024263, exon 3 of 10)	1419	NM_024263	74761	Mm.159028	NM_024263	ENSMUSG00000029070	Mxra8	1200013A08Rik|1700095D18Rik|AI131686|Asp3|Dicam	matrix-remodelling associated 8	protein-coding
mm_93965.1	chr10	127288820	127288846	-	1	NA	5' UTR (NM_001347171, exon 1 of 13)	5' UTR (NM_001347171, exon 1 of 13)	185	NM_001347171	110962	Mm.372826	NM_033072	ENSMUSG00000025409	Mbd6	D10Wsu93e	methyl-CpG binding domain protein 6	protein-coding
mm_128589.1	chr15	58113273	58113277	-	1	NA	intron (NM_027435, intron 13 of 27)	intron (NM_027435, intron 13 of 27)	21807	NM_027435	70472	Mm.221758	NM_027435	ENSMUSG00000022360	Atad2	2610509G12Rik	ATPase family, AAA domain containing 2	protein-coding
mm_9809.1	chr1	181937216	181937238	-	1	NA	intron (NM_010135, intron 3 of 14)	intron (NM_010135, intron 3 of 14)	82753	NM_008680	13800	Mm.87759	NM_008680	ENSMUSG00000022995	Enah	Mena|NDPP-1|Ndpp1|WBP8	enabled homolog (Drosophila)	protein-coding
mm_75693.1	chr8	68212030	68212050	-	1	NA	Intergenic	L2b|LINE|L2	-64488	NM_028182	72281	Mm.40974	NM_028182	ENSMUSG00000053886	Sh2d4a	2210402M20Rik|SH2A	SH2 domain containing 4A	protein-coding
mm_56834.1	chr6	117174822	117174839	-	1	NA	3' UTR (NM_021704, exon 3 of 3)	3' UTR (NM_021704, exon 3 of 3)	6295	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_161101.1	chr12	101404617	101404617	+	1	NA	promoter-TSS (NM_173023)	promoter-TSS (NM_173023)	-56	NM_173023	271036	Mm.84218	NM_173023	ENSMUSG00000047014	Catsperb	4931410B03|4932415G16Rik	catsper channel auxiliary subunit beta	protein-coding
mm_113765.1	chr13	44807757	44807768	+	1	NA	intron (NM_001205044, intron 2 of 18)	B4A|SINE|B4	76491	NM_001205043	16468	Mm.25059	NM_021878	ENSMUSG00000038518	Jarid2	Jmj|jumonji	jumonji, AT rich interactive domain 2	protein-coding
mm_63336.1	chr7	126950838	126950848	+	1	NA	5' UTR (NM_001252566, exon 1 of 17)	5' UTR (NM_001252566, exon 1 of 17)	308	NM_001252566	233878	Mm.283926	NM_144926	ENSMUSG00000030683	Sez6l2	AI835913|AW121566|BSRP-A|Psk1	seizure related 6 homolog like 2	protein-coding
mm_91009.1	chr10	14718192	14718228	-	1	NA	promoter-TSS (NM_029722)	promoter-TSS (NM_029722)	4	NM_029722	76743	Mm.136985	NM_029722	ENSMUSG00000019867	Gje1	AEY12|Cx23|D230044M03Rik|Gjf1|Gsfaey12	gap junction protein, epsilon 1	protein-coding
mm_36714.1	chr4	98235368	98235387	-	1	NA	Intergenic	Intergenic	147888	NM_053157	94043	Mm.331719	NM_053157	ENSMUSG00000028563	Tm2d1	2310026L18Rik|AA990549|Bbp	TM2 domain containing 1	protein-coding
mm_144753.1	chr18	35726863	35726888	+	1	NA	promoter-TSS (NM_001033168)	promoter-TSS (NM_001033168)	-114	NM_001033168	73449	Mm.379225	NM_001033168	ENSMUSG00000073598	1700066B19Rik	-	RIKEN cDNA 1700066B19 gene	protein-coding
mm_67424.1	chr7	80340215	80340231	-	1	NA	promoter-TSS (NM_133952)	promoter-TSS (NM_133952)	-4	NM_133952	101869	Mm.243024	NM_133952	ENSMUSG00000030533	Unc45a	AW538196	unc-45 myosin chaperone A	protein-coding
mm_25581.1	chr3	116865622	116865638	+	1	NA	intron (NM_009146, intron 1 of 16)	intron (NM_009146, intron 1 of 16)	3950	NM_009146	20321	Mm.66293	NM_009146	ENSMUSG00000033386	Frrs1	AI131732|Sdfr2	ferric-chelate reductase 1	protein-coding
mm_153885.1	chr19	46961877	46961895	-	1	NA	intron (NM_001164363, intron 1 of 17)	CpG	465	NM_029810	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_90226.1	chr10	121096589	121096618	+	1	NA	intron (NM_011915, intron 8 of 9)	intron (NM_011915, intron 8 of 9)	62599	NM_011915	24117	Mm.32831	NM_011915	ENSMUSG00000020218	Wif1	AW107799|WIF-1	Wnt inhibitory factor 1	protein-coding
mm_167332.1	chr8	70699155	70699161	+	1	NA	exon (NM_010592, exon 1 of 1)	exon (NM_010592, exon 1 of 1)	1419	NM_001286944	16478	Mm.419851	NM_010592	ENSMUSG00000071076	Jund	Jund1	jun D proto-oncogene	protein-coding
mm_97992.1	chr11	84033033	84033038	+	1	NA	intron (NM_194341, intron 18 of 19)	MLT1D|LTR|ERVL-MaLR	35322	NM_019819	56405	Mm.240885	NM_019819	ENSMUSG00000018648	Dusp14	1110014C10Rik|2310042C07Rik|D11Ertd395e|MKP-L|Mkp6	dual specificity phosphatase 14	protein-coding
mm_73743.1	chr8	114205591	114205642	+	1	NA	promoter-TSS (NM_173016)	promoter-TSS (NM_173016)	-24	NM_173016	270097	Mm.334825	NM_173016	ENSMUSG00000046844	Vat1l	9430073I07|AI427515|mKIAA1576	vesicle amine transport protein 1 like	protein-coding
mm_149400.1	chr19	11390283	11390322	+	1	NA	exon (NM_001310331, exon 6 of 7)	exon (NM_001310331, exon 6 of 7)	14814	NM_001310331	666907		NM_001310331	ENSMUSG00000101389	Ms4a4a	EG666907	membrane-spanning 4-domains, subfamily A, member 4A	protein-coding
mm_98380.1	chr11	94111624	94111632	+	1	NA	intron (NM_001025429, intron 23 of 26)	intron (NM_001025429, intron 23 of 26)	67423	NM_001025429	70834	Mm.260737	NM_027569	ENSMUSG00000020859	Spag9	3110018C07Rik|4733401I23Rik|4831406C20Rik|AW552012|JLP|JSAP2|JSAP2a|Jip4|Mapk8ip4|syd1	sperm associated antigen 9	protein-coding
mm_145461.1	chr18	60246046	60246064	+	1	NA	exon (NM_001033767, exon 3 of 3)	exon (NM_001033767, exon 3 of 3)	27212	NM_001034859	225594	Mm.329460	NM_001034859	ENSMUSG00000068606	Gm4841	EG225594|Ifgga3	predicted gene 4841	protein-coding
mm_104327.1	chr11	93968243	93968281	-	1	NA	5' UTR (NM_008704, exon 1 of 5)	5' UTR (NM_008704, exon 1 of 5)	259	NM_008704	18102	Mm.439702	NM_008704	ENSMUSG00000037601	Nme1	AL024257|NDPK-A|NM23-M1|NM23A	NME/NM23 nucleoside diphosphate kinase 1	protein-coding
mm_157313.1	chrX	20962006	20962025	-	1	NA	promoter-TSS (NM_013840)	promoter-TSS (NM_013840)	-37	NM_013840	22294	Mm.34779	NM_013840	ENSMUSG00000001134	Uxt	0910002B17Rik	ubiquitously expressed transcript	protein-coding
mm_72823.1	chr8	88199237	88199247	+	1	NA	promoter-TSS (NM_001164497)	promoter-TSS (NM_001164497)	29	NM_001164498	214627	Mm.491211	NM_001164497	ENSMUSG00000036779	Papd5	5730445M16Rik|5830428A09	PAP associated domain containing 5	protein-coding
mm_11257.1	chr2	29920769	29920797	+	1	NA	exon (NM_001113213, exon 15 of 21)	exon (NM_001113213, exon 15 of 21)	-14626	NM_028923	74412	Mm.275121	NM_028923	ENSMUSG00000019715	Gle1	4933405K21Rik|AA553313|Gle1l	GLE1 RNA export mediator (yeast)	protein-coding
mm_43261.1	chr5	130255591	130255630	+	1	NA	promoter-TSS (NM_178897)	promoter-TSS (NM_178897)	-9	NM_178897	100929	Mm.271296	NM_178897	ENSMUSG00000056310	Tyw1	AW125391|Rsafd1	tRNA-yW synthesizing protein 1 homolog (S. cerevisiae)	protein-coding
mm_34111.1	chr4	139193310	139193330	+	1	NA	promoter-TSS (NM_001271405)	promoter-TSS (NM_001271405)	421	NM_001037761	12345	Mm.2945	NM_009798	ENSMUSG00000028745	Capzb	1700120C01Rik|AI325129|CPB1|CPB2|CPbeat2|CPbeta1|CPbeta2|Cappb1	capping protein (actin filament) muscle Z-line, beta	protein-coding
mm_34720.1	chr4	152159575	152159589	+	1	NA	intron (NM_001301805, intron 1 of 4)	intron (NM_001301805, intron 1 of 4)	715	NM_008236	15206	Mm.57038	NM_008236	ENSMUSG00000028940	Hes2	HES-2	hairy and enhancer of split 2 (Drosophila)	protein-coding
mm_114461.1	chr13	67586371	67586389	+	1	NA	Intergenic	Intergenic	23327	NM_001163246	100416706	Mm.478045	NM_001163246	ENSMUSG00000058093	Zfp729b	AA987127	zinc finger protein 729b	protein-coding
mm_97522.1	chr11	78501080	78501091	+	1	NA	intron (NM_011707, intron 6 of 7)	intron (NM_011707, intron 6 of 7)	1965	NM_011707	22370	Mm.3667	NM_011707	ENSMUSG00000017344	Vtn	AI256434|Vn	vitronectin	protein-coding
mm_96211.1	chr11	62281504	62281521	+	1	NA	promoter-TSS (NM_028360)	promoter-TSS (NM_028360)	39	NM_029704	72795	Mm.489722	NM_028360	ENSMUSG00000042298	Ttc19	2010204O13Rik|2810460C24Rik|AI505442	tetratricopeptide repeat domain 19	protein-coding
mm_122511.1	chr14	47167823	47167835	-	1	NA	intron (NM_008102, intron 2 of 5)	intron (NM_008102, intron 2 of 5)	21573	NM_008102	14528	Mm.10651	NM_008102	ENSMUSG00000037580	Gch1	GTP-CH|GTPCH|Gch	GTP cyclohydrolase 1	protein-coding
mm_113244.1	chr13	27348873	27348881	+	1	NA	exon (NM_010088, exon 2 of 6)	exon (NM_010088, exon 2 of 6)	3204	NM_001289919	13529	Mm.291450	NM_010088	ENSMUSG00000018259	Prl8a2	D/tPRP|DPRP|Dtprp|Ghd11|mdPRP	prolactin family 8, subfamily a, member 2	protein-coding
mm_156783.1	chrX	161717499	161717519	+	1	NA	promoter-TSS (NM_198409)	promoter-TSS (NM_198409)	-44	NM_198409	24004	Mm.328503	NM_198409	ENSMUSG00000043518	Rai2	3f8	retinoic acid induced 2	protein-coding
mm_136757.1	chr17	8770784	8770789	+	1	NA	intron (NM_001290707, intron 2 of 22)	L1MB2|LINE|L1	-30959	NM_011866	23984	Mm.87161	NM_011866	ENSMUSG00000023868	Pde10a	-	phosphodiesterase 10A	protein-coding
mm_16171.1	chr2	172546230	172546232	+	1	NA	Intergenic	Intergenic	-3362	NM_009335	21420	Mm.3629	NM_009335	ENSMUSG00000028640	Tfap2c	AA409384|AP2gamma|Ap-2.2|Stra2|Tcfap2c	transcription factor AP-2, gamma	protein-coding
mm_39224.1	chr4	156200035	156200037	-	1	NA	exon (NM_015783, exon 2 of 2)	exon (NM_015783, exon 2 of 2)	782	NM_015783	100038882	Mm.4950	NM_015783	ENSMUSG00000035692	Isg15	G1p2|IGI15|IP17|Irfp|UCRP	ISG15 ubiquitin-like modifier	protein-coding
mm_25878.1	chr3	130617565	130617583	+	1	NA	promoter-TSS (NM_027907)	promoter-TSS (NM_027907)	-1	NM_027907	71760	Mm.29125	NM_027907	ENSMUSG00000019232	Etnppl	1300019H02Rik|AI195447|Agxt2l1	ethanolamine phosphate phospholyase	protein-coding
mm_25208.1	chr3	103832696	103832727	+	1	NA	promoter-TSS (NM_001142960)	promoter-TSS (NM_001142960)	15	NM_001142960	229672	Mm.297245	NM_001142959	ENSMUSG00000044165	Bcl2l15	Bfk|Gm566	BCLl2-like 15	protein-coding
mm_59358.1	chr7	25686995	25687012	+	1	NA	promoter-TSS (NM_011577)	promoter-TSS (NM_011577)	1	NM_011577	21803	Mm.248380	NM_011577	ENSMUSG00000002603	Tgfb1	TGF-beta1|TGFbeta1|Tgfb|Tgfb-1	transforming growth factor, beta 1	protein-coding
mm_171265.1	chr3	85287574	85287576	+	1	NA	Intergenic	MTA_Mm|LTR|ERVL-MaLR	-29944	NR_040542	73283	Mm.489084	NR_040542	ENSMUSG00000099995	1700036G14Rik	-	RIKEN cDNA 1700036G14 gene	ncRNA
mm_171082.1	chr3	121594280	121594288	+	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	49201	NR_036456	100503044	Mm.65320	NM_176992	ENSMUSG00000044522	A730020M07Rik	-	RIKEN cDNA A730020M07 gene	ncRNA
mm_65216.1	chr7	19698351	19698381	-	1	NA	promoter-TSS (NM_001305819)	promoter-TSS (NM_001305819)	32	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_148107.1	chr18	74207737	74207759	-	1	NA	promoter-TSS (NM_001164355)	promoter-TSS (NM_001164355)	70	NM_001164355	66468	Mm.283406	NM_025581	ENSMUSG00000036223	Ska1	2810433K01Rik|AV117428	spindle and kinetochore associated complex subunit 1	protein-coding
mm_53838.1	chr6	148354684	148354694	+	1	NA	promoter-TSS (NR_003634)	promoter-TSS (NR_003634)	33	NR_003634	66184	Mm.391542	NM_025405	ENSMUSG00000063171	Rps4l	1110033J19Rik|AA407494|Rps4y2	ribosomal protein S4-like	pseudo
mm_27778.1	chr3	73706660	73706670	-	1	NA	intron (NM_009738, intron 1 of 3)	MLTR14|LTR|ERV1	1750	NM_009738	12038	Mm.250719	NM_009738	ENSMUSG00000027792	Bche	C730038G20Rik	butyrylcholinesterase	protein-coding
mm_98701.1	chr11	96303726	96303759	+	1	NA	exon (NM_008268, exon 1 of 2)	exon (NM_008268, exon 1 of 2)	230	NM_008268	15413	Mm.207	NM_008268	ENSMUSG00000038700	Hoxb5	AI385717|Hox-2.1	homeobox B5	protein-coding
mm_9557.1	chr1	173963905	173963924	-	1	NA	exon (NM_011940, exon 6 of 7)	exon (NM_011940, exon 6 of 7)	18930	NM_008327	26388	Mm.218770	NM_008327	ENSMUSG00000026535	Ifi202b	Ifbip-1|Ifi202|Ifi202a|p202	interferon activated gene 202B	protein-coding
mm_169945.1	chr1	66948980	66948981	-	1	NA	Intergenic	Intergenic	-3924	NM_021285	17901	Mm.1000	NM_021285	ENSMUSG00000061816	Myl1	AI325107|MLC1f|MLC3f|Mylf	myosin, light polypeptide 1	protein-coding
mm_88841.1	chr10	80871837	80871852	+	1	NA	Intergenic	Intergenic	-7972	NM_001081688	432478	Mm.235302	NM_001081688	ENSMUSG00000059406	Tmprss9	Serase-1B	transmembrane protease, serine 9	protein-coding
mm_19606.1	chr2	102568923	102568927	-	1	NA	intron (NM_173749, intron 1 of 10)	intron (NM_173749, intron 1 of 10)	18904	NM_173749	210622	Mm.28649	NM_173749	ENSMUSG00000027188	Pamr1	5930437L24|E430002G05Rik|Ramp	peptidase domain containing associated with muscle regeneration 1	protein-coding
mm_6569.1	chr1	75191683	75191735	-	1	NA	promoter-TSS (NM_026187)	promoter-TSS (NM_026187)	301	NM_001003917	245860	Mm.238266	NM_001003917	ENSMUSG00000033124	Atg9a	AU019532|Apg9l1|Atg9|Atg9l1	autophagy related 9A	protein-coding
mm_98250.1	chr11	88253354	88253379	+	1	NA	Intergenic	Intergenic	-40677	NM_028859	74297	Mm.207320	NM_028859	ENSMUSG00000034031	Ccdc182	1700106J16Rik	coiled-coil domain containing 182	protein-coding
mm_137672.1	chr17	28769742	28769783	+	1	NA	intron (NM_011950, intron 1 of 11)	intron (NM_011950, intron 1 of 11)	445	NM_011950	26415	Mm.27970	NM_011950	ENSMUSG00000004864	Mapk13	SAPK4|Serk4	mitogen-activated protein kinase 13	protein-coding
mm_125651.1	chr15	62886370	62886375	+	1	NA	Intergenic	Intergenic	593236	NR_045279	432958	Mm.255105	NR_045279		Gm20740	-	predicted gene, 20740	ncRNA
mm_115365.1	chr13	112993794	112993820	+	1	NA	promoter-TSS (NM_001037914)	promoter-TSS (NM_001037914)	-61	NM_001037914	622408	Mm.360976	NM_001037914	ENSMUSG00000074651	Mcidas	EG622408|Gm6320|Idas|Mci|Mcin	multiciliate differentiation and DNA synthesis associated cell cycle protein	protein-coding
mm_45042.1	chr5	41684157	41684161	-	1	NA	intron (NR_132325, intron 3 of 5)	Lx7|LINE|L1	23532	NM_001310592	100972	Mm.41555	NM_027295	ENSMUSG00000029128	Rab28	2700023P08Rik|AW496496	RAB28, member RAS oncogene family	protein-coding
mm_59323.1	chr7	25306086	25306157	+	1	NA	promoter-TSS (NM_183311)	promoter-TSS (NM_183311)	13	NM_183311	330485	Mm.260740	NM_183311	ENSMUSG00000043843	Tmem145	B930076A02Rik	transmembrane protein 145	protein-coding
mm_94156.1	chr10	128745047	128745058	-	1	NA	promoter-TSS (NM_016811)	promoter-TSS (NM_016811)	-996	NM_016811	13139	Mm.291235	NM_016811	ENSMUSG00000025357	Dgka	80kDa|AW146112|Dagk1	diacylglycerol kinase, alpha	protein-coding
mm_166794.1	chr6	149188355	149188368	+	1	NA	intron (NM_001113424, intron 1 of 6)	intron (NM_001113424, intron 1 of 6)	351	NM_001113424	232566	Mm.209147	NM_001113424	ENSMUSG00000068250	Amn1	5830467E07Rik|A230083D09|C730024G19Rik	antagonist of mitotic exit network 1	protein-coding
mm_91104.1	chr10	19117076	19117078	-	1	NA	Intergenic	Intergenic	-24672	NR_038021	100504265	Mm.383417	NR_038021		Gm20139	-	predicted gene, 20139	ncRNA
mm_12735.1	chr2	78869483	78869511	+	1	NA	intron (NM_009454, intron 1 of 5)	CpG	450	NM_009454	22193	Mm.1485	NM_009454	ENSMUSG00000027011	Ube2e3	Ubce4|ubcM2	ubiquitin-conjugating enzyme E2E 3	protein-coding
mm_32982.1	chr4	120136149	120136177	+	1	NA	TTS (NM_010657)	TTS (NM_010657)	-25043	NM_007902	13615	Mm.284855	NM_007902	ENSMUSG00000028635	Edn2	ET-2|PPET2|VIC	endothelin 2	protein-coding
mm_68617.1	chr7	116825843	116825847	-	1	NA	Intergenic	Intergenic	321476	NM_001130479	53322	Mm.9901	NM_016773	ENSMUSG00000030659	Nucb2	AI607786|Calnuc|Nefa|Nesfatin-1	nucleobindin 2	protein-coding
mm_59051.1	chr7	19403910	19403924	+	1	NA	intron (NM_001286039, intron 1 of 12)	CpG	187	NM_001286039	232943	Mm.213403	NM_146182	ENSMUSG00000040714	Klc3	BC017147|Klct	kinesin light chain 3	protein-coding
mm_154666.1	chrX	7878707	7878717	+	1	NA	exon (NM_138606, exon 2 of 6)	exon (NM_138606, exon 2 of 6)	406	NM_138606	18715	Mm.347478	NM_138606	ENSMUSG00000031155	Pim2	DXCch3|Pim-2	proviral integration site 2	protein-coding
mm_16789.1	chr2	10063535	10063549	-	1	NA	exon (NM_001112738, exon 5 of 10)	exon (NM_001112738, exon 5 of 10)	-14933	NM_027748	209361	Mm.86343	NM_027748	ENSMUSG00000025782	Taf3	140kDa|4933439M23Rik|AW539625|TAF140|TAFII-140|TAFII140|mTAFII140	TATA-box binding protein associated factor 3	protein-coding
mm_59737.1	chr7	28813992	28814002	+	1	NA	exon (NM_177301, exon 3 of 13)	exon (NM_177301, exon 3 of 13)	3107	NM_177301	15388	Mm.9043	NM_177301	ENSMUSG00000015165	Hnrnpl	C79783|D830027H13Rik|Hnrpl	heterogeneous nuclear ribonucleoprotein L	protein-coding
mm_137490.1	chr17	26948647	26948686	+	1	NA	promoter-TSS (NR_037244)	promoter-TSS (NR_037244)	-547	NR_037244	100526534		NR_037244	ENSMUSG00000093118	Mir3083	mir-3083|mmu-mir-3083	microRNA 3083	ncRNA
mm_16766.1	chr2	9878439	9878449	-	1	NA	5' UTR (NM_008091, exon 1 of 6)	5' UTR (NM_008091, exon 1 of 6)	156	NM_008091	14462	Mm.313866	NM_008091	ENSMUSG00000015619	Gata3	Gata-3|jal	GATA binding protein 3	protein-coding
mm_33418.1	chr4	129984810	129984821	+	1	NA	promoter-TSS (NM_173071)	promoter-TSS (NM_173071)	-55	NM_001290714	230775	Mm.262241	NM_173071	ENSMUSG00000028782	Adgrb2	Bai2	adhesion G protein-coupled receptor B2	protein-coding
mm_128854.1	chr15	71954396	71954424	-	1	NA	intron (NM_027174, intron 12 of 63)	intron (NM_027174, intron 12 of 63)	79817	NM_027174	69700	Mm.322500	NM_027174	ENSMUSG00000079022	Col22a1	2310067L16Rik|C80743	collagen, type XXII, alpha 1	protein-coding
mm_69359.1	chr7	130513806	130513829	-	1	NA	exon (NM_001136054, exon 3 of 12)	exon (NM_001136054, exon 3 of 12)	5763	NM_001136054	11907	Mm.216321	NM_013799	ENSMUSG00000030850	Ate1	AI225793|AW547406	arginyltransferase 1	protein-coding
mm_33023.1	chr4	121094003	121094008	+	1	NA	intron (NM_172700, intron 2 of 9)	intron (NM_172700, intron 2 of 9)	4238	NM_172700	230709	Mm.34399	NM_172700	ENSMUSG00000043207	Zmpste24	A530043O15Rik|D030046F19|FACE1|Face-1|MADB|STE24|Ste24p	zinc metallopeptidase, STE24	protein-coding
mm_105602.1	chr11	106778815	106778819	-	1	NA	intron (NR_027785, intron 1 of 7)	intron (NR_027785, intron 1 of 7)	698	NR_027785	50776	Mm.859	NM_015810	ENSMUSG00000020718	Polg2	-	polymerase (DNA directed), gamma 2, accessory subunit	protein-coding
mm_168260.1	chr10	8762506	8762509	-	1	NA	intron (NM_175155, intron 8 of 19)	intron (NM_175155, intron 8 of 19)	123563	NM_175155	70097	Mm.338275	NM_175155	ENSMUSG00000015305	Sash1	1100001C18Rik|2500002E12Rik|A330076K04Rik|mKIAA0790	SAM and SH3 domain containing 1	protein-coding
mm_169543.1	chr15	101589952	101589955	-	1	NA	Intergenic	MMERGLN_LTR|LTR|ERV1	-1381	NR_002868	432985	Mm.491078	NR_002868		Gm5476	EG432985|Kb17P	type II keratin Kb17P pseudogene	pseudo
mm_67281.1	chr7	78578309	78578400	-	1	NA	promoter-TSS (NM_182809)	promoter-TSS (NM_182809)	-516	NM_182809	18213	Mm.33496	NM_008746	ENSMUSG00000059146	Ntrk3	AW125844|Ntrk3_tv3|TrkC	neurotrophic tyrosine kinase, receptor, type 3	protein-coding
mm_20641.1	chr2	132021229	132021238	-	1	NA	intron (NM_175445, intron 1 of 10)	intron (NM_175445, intron 1 of 10)	8755	NM_175445	215653	Mm.204737	NM_175445	ENSMUSG00000027339	Rassf2	3830431H01Rik|9030412M04Rik|AI852669|AW495050	Ras association (RalGDS/AF-6) domain family member 2	protein-coding
mm_92997.1	chr10	86705486	86705492	-	1	NA	promoter-TSS (NM_011631)	promoter-TSS (NM_011631)	-45	NM_011631	22027	Mm.87773	NM_011631	ENSMUSG00000020048	Hsp90b1	ERp99|GRP94|TA-3|Targ2|Tra-1|Tra1|endoplasmin|gp96	heat shock protein 90, beta (Grp94), member 1	protein-coding
mm_93078.1	chr10	89443889	89443962	-	1	NA	promoter-TSS (NM_001284344)	promoter-TSS (NM_001284344)	42	NM_001284344	237436	Mm.11982	NM_001033331	ENSMUSG00000074802	Gas2l3	8430435B07Rik|Gm240	growth arrest-specific 2 like 3	protein-coding
mm_164167.1	chr15	74563552	74563561	+	1	NA	intron (NM_174991, intron 17 of 30)	intron (NM_174991, intron 17 of 30)	47360	NM_174991	107831	Mm.43133	NM_174991	ENSMUSG00000034730	Adgrb1	B830018M07Rik|Bai1|R75078|mKIAA4089	adhesion G protein-coupled receptor B1	protein-coding
mm_103894.1	chr11	83575262	83575273	-	1	NA	3' UTR (NM_011338, exon 4 of 4)	3' UTR (NM_011338, exon 4 of 4)	3369	NM_011338	20308	Mm.416125	NM_011338	ENSMUSG00000019122	Ccl9	CCF18|MRP-2|Scya10|Scya9	chemokine (C-C motif) ligand 9	protein-coding
mm_134002.1	chr16	4789985	4789995	-	1	NA	promoter-TSS (NM_025670)	promoter-TSS (NM_025670)	-55	NM_025670	66626	Mm.157648	NM_025670	ENSMUSG00000004071	Cdip1	2700048O17Rik|5730403B10Rik|AU018521|AW742692|CDIP	cell death inducing Trp53 target 1	protein-coding
mm_166356.1	chr5	121660443	121660476	-	1	NA	promoter-TSS (NM_001289543)	promoter-TSS (NM_001289543)	51	NM_028037	71985	Mm.45423	NM_028037	ENSMUSG00000029456	Acad10	2410021P16Rik	acyl-Coenzyme A dehydrogenase family, member 10	protein-coding
mm_118176.1	chr13	106936908	106936952	-	1	NA	promoter-TSS (NM_029665)	promoter-TSS (NM_029665)	-15	NM_029665	76582	Mm.132208	NM_029665	ENSMUSG00000042590	Ipo11	1700081H05Rik|2510001A17Rik|AI314624|AW555235|E330021B14Rik|Ranbp11	importin 11	protein-coding
mm_87681.1	chr10	59226010	59226056	+	1	NA	3' UTR (NM_172939, exon 1 of 1)	3' UTR (NM_172939, exon 1 of 1)	4111	NM_172939	268301	Mm.3036	NM_172939	ENSMUSG00000098188	Sowahc	4921515A04Rik|9430099J10Rik|Ankrd57|C820004L04Rik	sosondowah ankyrin repeat domain family member C	protein-coding
mm_55933.1	chr6	84588652	84588687	-	1	NA	intron (NM_175475, intron 1 of 6)	G-rich|Low_complexity|Low_complexity	5141	NM_175475	232174	Mm.255246	NM_175475	ENSMUSG00000063415	Cyp26b1	CP26|P450RAI-2	cytochrome P450, family 26, subfamily b, polypeptide 1	protein-coding
mm_108668.1	chr12	86504769	86504791	+	1	NA	intron (NM_001159500, intron 3 of 6)	intron (NM_001159500, intron 3 of 6)	83136	NM_011934	26380	Mm.235550	NM_011934	ENSMUSG00000021255	Esrrb	Err2|Errb|Estrrb|Nr3b2	estrogen related receptor, beta	protein-coding
mm_44870.1	chr5	34513704	34513714	-	1	NA	exon (NM_139064, exon 1 of 6)	exon (NM_139064, exon 1 of 6)	270	NM_139064	231130	Mm.28615	NM_139064	ENSMUSG00000059866	Tnip2	1810020H16Rik|ABIN-2|AI428870	TNFAIP3 interacting protein 2	protein-coding
mm_21004.1	chr2	152344010	152344033	-	1	NA	promoter-TSS (NM_175093)	promoter-TSS (NM_175093)	39	NM_175093	228775	Mm.276018	NM_144554	ENSMUSG00000032715	Trib3	Ifld2|Nipk|SINK|SKIP3|TRB-3|Trb3	tribbles pseudokinase 3	protein-coding
mm_44623.1	chr5	25705792	25705829	-	1	NA	promoter-TSS (NM_020570)	promoter-TSS (NM_020570)	-13	NM_020570	57434	Mm.143767	NM_020570	ENSMUSG00000028933	Xrcc2	4921524O04Rik|8030409M04Rik|RAD51|RecA	X-ray repair complementing defective repair in Chinese hamster cells 2	protein-coding
mm_103715.1	chr11	79524335	79524381	-	1	NA	promoter-TSS (NM_001077496)	promoter-TSS (NM_001077496)	-596	NM_001077496	216984	Mm.439665	NM_001077496	ENSMUSG00000093938	Evi2b	Evi-2|Evi2	ecotropic viral integration site 2b	protein-coding
mm_38119.1	chr4	134548152	134548162	-	1	NA	intron (NM_029100, intron 2 of 11)	intron (NM_029100, intron 2 of 11)	4009	NM_029100	74777	Mm.29773	NM_029100	ENSMUSG00000050989	Selenon	1110019I12Rik|AI414492|SelN|Sepn1	selenoprotein N	protein-coding
mm_95475.1	chr11	50850792	50850808	+	1	NA	5' UTR (NM_173372, exon 1 of 11)	5' UTR (NM_173372, exon 1 of 11)	115	NM_173372	108072	Mm.134265	NM_173372	ENSMUSG00000000617	Grm6	BC021919|Gm3|Gprc1f|mGluR6|nerg1|nob2|nob3|nob4	glutamate receptor, metabotropic 6	protein-coding
mm_5526.1	chr1	37890334	37890416	-	1	NA	promoter-TSS (NM_027098)	promoter-TSS (NM_027098)	36	NM_026913	69028	Mm.63984	NM_026913	ENSMUSG00000026088	Mitd1	1500032H18Rik	MIT, microtubule interacting and transport, domain containing 1	protein-coding
mm_34587.1	chr4	150187426	150187441	+	1	NA	exon (NM_009802, exon 8 of 8)	exon (NM_009802, exon 8 of 8)	13702	NM_009802	12353	Mm.232523	NM_009802	ENSMUSG00000028972	Car6	Ca6|DOC1	carbonic anhydrase 6	protein-coding
mm_98731.1	chr11	96352121	96352138	+	1	NA	exon (NM_134032, exon 1 of 2)	exon (NM_134032, exon 1 of 2)	497	NM_134032	103889	Mm.281153	NM_134032	ENSMUSG00000075588	Hoxb2	AI894218|Hox-2.8|Hoxbes2	homeobox B2	protein-coding
mm_131681.1	chr16	20675390	20675430	+	1	NA	exon (NM_145941, exon 5 of 33)	exon (NM_145941, exon 5 of 33)	2683	NM_001304432	208643	Mm.260256	NM_145941	ENSMUSG00000045983	Eif4g1	E030015G23Rik|eIF-4-gamma 1|eIF-4G 1|eIF-4G1|eIF4GI	eukaryotic translation initiation factor 4, gamma 1	protein-coding
mm_32690.1	chr4	115878923	115878940	+	1	NA	3' UTR (NM_001285488, exon 14 of 14)	3' UTR (NM_001285488, exon 14 of 14)	-5469	NM_001039124	654462	Mm.388913	NM_001039124	ENSMUSG00000073774	Kncn	Kino|L5	kinocilin	protein-coding
mm_138077.1	chr17	33955824	33955901	+	1	NA	promoter-TSS (NM_011296)	promoter-TSS (NM_011296)	-20	NM_172620	224705	Mm.448614	NM_172620	ENSMUSG00000024319	Vps52	ARE1|D130068D18|D430041K17Rik|SAC2|Sacm2l|tclw5	VPS52 GARP complex subunit	protein-coding
mm_167121.1	chr7	121589410	121589427	-	1	NA	promoter-TSS (NR_131051)	promoter-TSS (NR_131051)	418	NR_102286	75793	Mm.23397	NR_102286		4933432K03Rik	1700001C18Rik|4930433G11Rik|AI428127	RIKEN cDNA 4933432K03 gene	ncRNA
mm_9879.1	chr1	185451602	185451620	-	1	NA	intron (NR_040305, intron 2 of 2)	intron (NR_040305, intron 2 of 2)	-3237	NM_001033286	226781	Mm.227117	NM_001033286	ENSMUSG00000026614	Slc30a10	E130106K10Rik|Gm212	solute carrier family 30, member 10	protein-coding
mm_65661.1	chr7	28140128	28140136	-	1	NA	exon (NM_001164655, exon 5 of 20)	exon (NM_001164655, exon 5 of 20)	10666	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_23675.1	chr3	68584155	68584181	+	1	NA	intron (NM_013928, intron 1 of 6)	intron (NM_013928, intron 1 of 6)	11800	NM_013928	30953	Mm.331064	NM_013928	ENSMUSG00000027777	Schip1	Nf2ip|Schip-1	schwannomin interacting protein 1	protein-coding
mm_158944.1	chr1	82729236	82729236	+	1	NA	5' UTR (NM_029409, exon 3 of 9)	5' UTR (NM_029409, exon 3 of 9)	4346	NM_001310699	75734	Mm.396863	NM_029409	ENSMUSG00000026150	Mff	5230400G24Rik|AI314724	mitochondrial fission factor	protein-coding
mm_66061.1	chr7	30744218	30744230	-	1	NA	promoter-TSS (NM_001290631)	promoter-TSS (NM_001290631)	-543	NM_001290631	14447	Mm.436562	NM_008085	ENSMUSG00000061099	Gapdhs	Gapd-s|Gapds	glyceraldehyde-3-phosphate dehydrogenase, spermatogenic	protein-coding
mm_36529.1	chr4	86581797	86581800	-	1	NA	3' UTR (NM_173400, exon 17 of 17)	3' UTR (NM_173400, exon 17 of 17)	4772	NR_028545	100217448	Mm.453533	NR_028545	ENSMUSG00000088958	Scarna8	MBI-57	small Cajal body-specific RNA 8	ncRNA
mm_26344.1	chr3	142547371	142547383	+	1	NA	3' UTR (NM_001083312, exon 11 of 11)	3' UTR (NM_001083312, exon 11 of 11)	-12675	NM_018734	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_59291.1	chr7	24998684	24998737	+	1	NA	exon (NM_001290469, exon 6 of 23)	exon (NM_001290469, exon 6 of 23)	7227	NM_001290469	232975	Mm.44101	NM_144921	ENSMUSG00000040907	Atp1a3	Atpa-2	ATPase, Na+/K+ transporting, alpha 3 polypeptide	protein-coding
mm_31386.1	chr4	48043002	48043023	+	1	NA	Intergenic	CpG	-2293	NM_015743	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_132814.1	chr16	45171720	45171736	+	1	NA	exon (NM_026402, exon 5 of 12)	exon (NM_026402, exon 5 of 12)	12899	NM_026402	67841	Mm.41775	NM_026402	ENSMUSG00000022663	Atg3	2610016C12Rik|APG3|Apg3l|Atg3l|PC3-96	autophagy related 3	protein-coding
mm_83248.1	chr9	42400042	42400048	-	1	NA	promoter-TSS (NM_001324548)	promoter-TSS (NM_001324548)	-116	NM_001324548	21683	Mm.42209	NM_009347	ENSMUSG00000037705	Tecta	Tctna	tectorin alpha	protein-coding
mm_70943.1	chr8	26119612	26119682	+	1	NA	promoter-TSS (NM_207659)	promoter-TSS (NM_207659)	267	NM_029965	77733	Mm.291906	NM_029965	ENSMUSG00000013878	Rnf170	6720407G21Rik|AI481227	ring finger protein 170	protein-coding
mm_62294.1	chr7	99979756	99979771	+	1	NA	intron (NM_175388, intron 1 of 5)	CpG	695	NM_175388	108937	Mm.323087	NM_175388	ENSMUSG00000058761	Rnf169	2900057K09Rik	ring finger protein 169	protein-coding
mm_66203.1	chr7	34234068	34234099	-	1	NA	Intergenic	CpG	-3747	NM_008155	14751	Mm.589	NM_008155	ENSMUSG00000036427	Gpi1	Amf|Gpi|Gpi-1|Gpi-1r|Gpi-1s|Gpi-1t|Gpi1-r|Gpi1-s|Gpi1-t|Gpi1s|MF|NK|NK/GPI|Nlk|Org|Pgi|Phi	glucose phosphate isomerase 1	protein-coding
mm_7102.1	chr1	89069996	89070004	-	1	NA	promoter-TSS (NM_133816)	promoter-TSS (NM_133816)	-462	NM_133816	98402	Mm.170983	NM_133816	ENSMUSG00000036206	Sh3bp4	AI594717|AW227605|BOG25	SH3-domain binding protein 4	protein-coding
mm_137124.1	chr17	22674391	22674423	+	1	NA	Intergenic	Intergenic	73259	NM_001104575	628185	Mm.390947	NM_001104575	ENSMUSG00000094921	Vmn2r112	EG628185|V2rp1	vomeronasal 2, receptor 112	protein-coding
mm_64610.1	chr7	3296789	3296801	-	1	NA	exon (NM_016969, exon 3 of 3)	exon (NM_016969, exon 3 of 3)	3767	NM_001093766	50918	Mm.29874	NM_016969	ENSMUSG00000068566	Myadm	D7Wsu62e	myeloid-associated differentiation marker	protein-coding
mm_22565.1	chr3	10012565	10012598	+	1	NA	promoter-TSS (NM_010634)	promoter-TSS (NM_010634)	-4	NM_001272097	16592	Mm.741	NM_010634	ENSMUSG00000027533	Fabp5	E-FABP|Fabpe|Klbp|PA-FABP|mal1	fatty acid binding protein 5, epidermal	protein-coding
mm_78471.1	chr9	32652466	32652485	+	1	NA	Intergenic	B3A|SINE|B2	-43567	NM_011808	23871	Mm.292415	NM_011808	ENSMUSG00000032035	Ets1	AI196000|AI448617|D230050P06|Ets-1|Tpl1|vs	E26 avian leukemia oncogene 1, 5' domain	protein-coding
mm_87417.1	chr10	50592671	50592739	+	1	NA	promoter-TSS (NM_198007)	promoter-TSS (NM_198007)	36	NM_198007	77987	Mm.222497	NM_198007	ENSMUSG00000038774	Ascc3	ASC1p200|B630009I04Rik|BC023451|D430001L07Rik|D630041L21|Helic1|RNAH	activating signal cointegrator 1 complex subunit 3	protein-coding
mm_82447.1	chr9	15306117	15306159	-	1	NA	promoter-TSS (NM_001199485)	promoter-TSS (NM_001199485)	29	NM_001199485	70984	Mm.261842	NM_133732	ENSMUSG00000031938	4931406C07Rik	-	RIKEN cDNA 4931406C07 gene	protein-coding
mm_13180.1	chr2	93030364	93030372	+	1	NA	intron (NR_110333, intron 2 of 5)	intron (NR_110333, intron 2 of 5)	1020	NR_110333	433456	Mm.235231	NM_001002794	ENSMUSG00000075027	4631405J19Rik	-	RIKEN cDNA 4631405J19 gene	ncRNA
mm_131621.1	chr16	19761964	19761969	+	1	NA	intron (NM_054052, intron 2 of 3)	intron (NM_054052, intron 2 of 3)	1732	NM_001159407	108105	Mm.33935	NM_054052	ENSMUSG00000022686	B3gnt5	beta3GnT5	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5	protein-coding
mm_160732.1	chr10	77836088	77836088	+	1	NA	exon (NM_001024709, exon 1 of 1)	exon (NM_001024709, exon 1 of 1)	141	NM_001024709	544710	Mm.441890	NM_001024709		Krtap10-10	EG544710	keratin associated protein 10-10	protein-coding
mm_6180.1	chr1	65103083	65103100	-	1	NA	exon (NM_007774, exon 2 of 3)	exon (NM_007774, exon 2 of 3)	272	NM_007774	12964	Mm.26904	NM_007774	ENSMUSG00000044429	Cryga	Cryg-4|DGcry-4	crystallin, gamma A	protein-coding
mm_5306.1	chr1	22315824	22315834	-	1	NA	intron (NM_001012623, intron 10 of 14)	intron (NM_001012623, intron 10 of 14)	117014	NM_053270	116837	Mm.60061	NM_053270	ENSMUSG00000041670	Rims1	C030033M19Rik|RIM1|RIM1a|RIM1alpha|Rab3ip1|Rim|Serg1|mKIAA0340	regulating synaptic membrane exocytosis 1	protein-coding
mm_90640.1	chr10	128501293	128501295	+	1	NA	intron (NR_131151, intron 1 of 1)	intron (NR_131151, intron 1 of 1)	2047	NR_131151	654440	Mm.441262	NR_131150	ENSMUSG00000097353	A430046D13Rik	-	Riken cDNA A430046D13 gene	ncRNA
mm_111367.1	chr12	87200307	87200344	-	1	NA	promoter-TSS (NM_001290288)	promoter-TSS (NM_001290288)	-96	NM_001033475	382620	Mm.374912	NM_001033475	ENSMUSG00000034111	Tmed8	6430595O10Rik|AI447224|Gm1184|Mem1	transmembrane p24 trafficking protein 8	protein-coding
mm_28954.1	chr3	100489164	100489215	-	1	NA	promoter-TSS (NM_001142952)	promoter-TSS (NM_001142952)	3	NM_001142952	74645	Mm.226900	NM_001142952	ENSMUSG00000044468	Fam46c	4930431B09Rik|AI449797	family with sequence similarity 46, member C	protein-coding
mm_152676.1	chr19	15920180	15920182	-	1	NA	intron (NM_177420, intron 2 of 8)	B1_Mur3|SINE|Alu	4441	NM_001205339	107272	Mm.289936	NM_177420	ENSMUSG00000024640	Psat1	D8Ertd814e|EPIP|PSA|Psat	phosphoserine aminotransferase 1	protein-coding
mm_167271.1	chr8	33411169	33411172	+	1	NA	intron (NM_001098233, intron 1 of 1)	intron (NM_001098233, intron 1 of 1)	24845	NM_001098233	75029	Mm.159402	NM_152821	ENSMUSG00000049184	Purg	4930486B15Rik	purine-rich element binding protein G	protein-coding
mm_50218.1	chr6	42349666	42349681	+	1	NA	promoter-TSS (NM_001289618)	promoter-TSS (NM_001289618)	-155	NM_011777	22793	Mm.282303	NM_011777	ENSMUSG00000029860	Zyx	9530098H06Rik|R75157	zyxin	protein-coding
mm_65190.1	chr7	19696584	19696639	-	1	NA	exon (NM_009696, exon 4 of 4)	exon (NM_009696, exon 4 of 4)	1787	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_115001.1	chr13	98263188	98263221	+	1	NA	promoter-TSS (NM_178918)	promoter-TSS (NM_178918)	128	NM_001271388	68558	Mm.209642	NM_023472	ENSMUSG00000021661	Ankra2	1110004M18Rik|Ankra	ankyrin repeat, family A (RFXANK-like), 2	protein-coding
mm_12752.1	chr2	79254920	79254926	+	1	NA	promoter-TSS (NM_010576)	promoter-TSS (NM_010576)	-503	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D|Itga4B	integrin alpha 4	protein-coding
mm_127066.1	chr15	97373410	97373422	+	1	NA	intron (NM_172293, intron 4 of 5)	intron (NM_172293, intron 4 of 5)	-126129	NM_001164602	105827	Mm.24005	NM_178114	ENSMUSG00000048218	Amigo2	AI415330|AMIGO-2|AW208913|Ali1	adhesion molecule with Ig like domain 2	protein-coding
mm_47252.1	chr5	121593774	121593789	-	1	NA	promoter-TSS (NM_001308450)	promoter-TSS (NM_001308450)	43	NM_009656	11669	Mm.284446	NM_009656	ENSMUSG00000029455	Aldh2	AHD-M1|ALDH-E2|ALDHI|Ahd-5|Ahd5	aldehyde dehydrogenase 2, mitochondrial	protein-coding
mm_111660.1	chr12	103314758	103314773	-	1	NA	promoter-TSS (NM_001195726)	promoter-TSS (NM_001195726)	4	NR_136894	102632488	Mm.109435	NR_136894	ENSMUSG00000100789	Gm29508	-	predicted gene 29508	ncRNA
mm_144075.1	chr17	91088986	91089014	-	1	NA	5' UTR (NM_020252, exon 2 of 23)	5' UTR (NM_020252, exon 2 of 23)	605	NM_001346957	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_110398.1	chr12	44210096	44210104	-	1	NA	promoter-TSS (NM_013760)	promoter-TSS (NM_013760)	-32	NM_013760	27362	Mm.27432	NM_013760	ENSMUSG00000014905	Dnajb9	AA408011|AA673251|AA673481|AW556981|ERdj4|Mdg1|mDj7	DnaJ heat shock protein family (Hsp40) member B9	protein-coding
mm_50531.1	chr6	49045600	49045611	+	1	NA	intron (NM_053110, intron 4 of 10)	intron (NM_053110, intron 4 of 10)	9087	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_18999.1	chr2	76870384	76870392	-	1	NA	exon (NM_011652, exon 103 of 313)	exon (NM_011652, exon 103 of 313)	112159	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_11339.1	chr2	30717481	30717509	+	1	NA	Intergenic	MER115|DNA|hAT-Tip100	-3715	NR_037272	100526499		NR_037272	ENSMUSG00000093091	Mir3089	mir-3089|mmu-mir-3089	microRNA 3089	ncRNA
mm_86307.1	chr9	122805422	122805432	-	1	NA	promoter-TSS (NM_001013405)	promoter-TSS (NM_001013405)	-120	NM_001013405	382117	Mm.215892	NM_001013405	ENSMUSG00000046603	Tcaim	D9Ertd402e|Gm1129|TOAG-1	T cell activation inhibitor, mitochondrial	protein-coding
mm_130776.1	chr15	101488114	101488121	-	1	NA	intron (NM_001201323, intron 4 of 8)	intron (NM_001201323, intron 4 of 8)	3186	NM_016879	53622	Mm.347934	NM_016879		Krt85	AA589597|BB007925|Hb5|Krt2-18	keratin 85	protein-coding
mm_158455.1	chrX	140598587	140598590	-	1	NA	intron (NM_001077364, intron 1 of 3)	CpG	1934	NM_001077364	14605	Mm.22216	NM_010286	ENSMUSG00000031431	Tsc22d3	DIP|Dsip1|Gilz|TSC-22R|Tilz3	TSC22 domain family, member 3	protein-coding
mm_6557.1	chr1	75141519	75141530	-	1	NA	intron (NM_026977, intron 1 of 8)	CpG	844	NM_026977	69171	Mm.28193	NM_026977	ENSMUSG00000033159	Cnppd1	1810031K17Rik|AU043960	cyclin Pas1/PHO80 domain containing 1	protein-coding
mm_87509.1	chr10	52417590	52417611	+	1	NA	promoter-TSS (NM_030250)	promoter-TSS (NM_030250)	53	NM_030250	52014	Mm.199964	NM_030250	ENSMUSG00000023068	Nus1	1600027K07Rik|AU019165|AW538011|BC003223|D10Ertd438e	NUS1 dehydrodolichyl diphosphate synthase subunit	protein-coding
mm_163331.1	chr12	8500326	8500332	+	1	NA	promoter-TSS (NM_007483)	promoter-TSS (NM_007483)	-344	NM_007483	11852	Mm.687	NM_007483	ENSMUSG00000054364	Rhob	AA017882|Arh6|Arhb	ras homolog family member B	protein-coding
mm_122753.1	chr14	54197909	54197918	-	1	NA	Intergenic	Intergenic	56016	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_149972.1	chr19	29067235	29067245	+	1	NA	promoter-TSS (NR_045687)	promoter-TSS (NR_045687)	-61	NR_045687	100503337	Mm.103412	NR_045687		Gm9895	ENSMUSG00000052976	predicted gene 9895	ncRNA
mm_9653.1	chr1	177744639	177744643	-	1	NA	intron (NM_027077, intron 4 of 5)	MERV1_LTR|LTR|ERV1	14827	NM_027077	69428	Mm.84467	NM_027077	ENSMUSG00000015962	1700016C15Rik	-	RIKEN cDNA 1700016C15 gene	protein-coding
mm_46662.1	chr5	108675659	108675671	-	1	NA	promoter-TSS (NM_001310692)	promoter-TSS (NM_001310692)	-300	NM_174870	231583	Mm.440571	NM_174870	ENSMUSG00000046959	Slc26a1	Sat1	solute carrier family 26 (sulfate transporter), member 1	protein-coding
mm_13646.1	chr2	114054297	114054303	+	1	NA	promoter-TSS (NR_028422)	promoter-TSS (NR_028422)	-96	NR_028422	100303644	Mm.330469	NR_028422	ENSMUSG00000092397	C130080G10Rik	-	RIKEN cDNA C130080G10 gene	ncRNA
mm_11919.1	chr2	52072318	52072328	+	1	NA	promoter-TSS (NM_175238)	promoter-TSS (NM_175238)	-514	NM_175238	51869	Mm.254530	NM_175238	ENSMUSG00000036202	Rif1	5730435J01Rik|6530403D07Rik|AU016181|AW549474|D2Ertd145e	replication timing regulatory factor 1	protein-coding
mm_111248.1	chr12	84876447	84876467	-	1	NA	promoter-TSS (NM_013589)	promoter-TSS (NM_013589)	38	NM_013589	16997	Mm.3900	NM_013589	ENSMUSG00000002020	Ltbp2	AW208642	latent transforming growth factor beta binding protein 2	protein-coding
mm_88552.1	chr10	78595511	78595583	+	1	NA	Intergenic	Intergenic	-3583	NM_027875	71709	Mm.86439	NM_027875	ENSMUSG00000032714	Syde1	1200008N06Rik|BB043000|mSYD1A	synapse defective 1, Rho GTPase, homolog 1 (C. elegans)	protein-coding
mm_60501.1	chr7	44479233	44479235	+	1	NA	Intergenic	L1MC4|LINE|L1	-5283	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_110374.1	chr12	40199584	40199596	-	1	NA	promoter-TSS (NM_001033437)	promoter-TSS (NM_001033437)	-275	NM_001033437	380755	Mm.390463	NM_001033437	ENSMUSG00000071342	Lsmem1	Gm889	leucine-rich single-pass membrane protein 1	protein-coding
mm_109191.1	chr12	108554735	108554752	+	1	NA	promoter-TSS (NM_007965)	promoter-TSS (NM_007965)	23	NM_007965	14026	Mm.238841	NM_007965	ENSMUSG00000021262	Evl	AI528774	Ena-vasodilator stimulated phosphoprotein	protein-coding
mm_158752.1	chrX	165327428	165327459	-	1	NA	promoter-TSS (NM_183427)	promoter-TSS (NM_183427)	-462	NM_183427	237213	Mm.113877	NM_183427	ENSMUSG00000018589	Glra2	-	glycine receptor, alpha 2 subunit	protein-coding
mm_45803.1	chr5	87568983	87569002	-	1	NA	promoter-TSS (NM_016771)	promoter-TSS (NM_016771)	14	NM_016771	53315	Mm.6824	NM_016771	ENSMUSG00000029273	Sult1d1	5033411P13Rik|AI987815|ST1d1|SULT-N|Sultn	sulfotransferase family 1D, member 1	protein-coding
mm_58634.1	chr7	5095891	5095908	+	1	NA	exon (NM_001252454, exon 9 of 11)	exon (NM_001252454, exon 9 of 11)	15664	NM_001252454	13854	Mm.3091	NM_010147	ENSMUSG00000035203	Epn1	AA269831|Ibp1	epsin 1	protein-coding
mm_50288.1	chr6	47454007	47454017	+	1	NA	promoter-TSS (NM_012042)	promoter-TSS (NM_012042)	-312	NM_012042	26965	Mm.87611	NM_012042	ENSMUSG00000029686	Cul1	-	cullin 1	protein-coding
mm_107821.1	chr12	68424502	68424507	+	1	NA	Intergenic	Intergenic	734682	NM_009093	20090	Mm.379006	NM_009093	ENSMUSG00000034892	Rps29	-	ribosomal protein S29	protein-coding
mm_158067.1	chrX	101213487	101213530	-	1	NA	3' UTR (NM_001110310, exon 4 of 4)	3' UTR (NM_001110310, exon 4 of 4)	9055	NM_001110311	55988	Mm.206949	NM_018875	ENSMUSG00000046032	Snx12	2610001F05Rik|AW045757|SDP8	sorting nexin 12	protein-coding
mm_34629.1	chr4	150571886	150571891	+	1	NA	intron (NM_001085492, intron 12 of 22)	L1MEd|LINE|L1	80286	NM_173774	242773	Mm.29280	NM_173774	ENSMUSG00000039838	Slc45a1	C230078B22|Dnb5	solute carrier family 45, member 1	protein-coding
mm_46497.1	chr5	105132929	105132939	-	1	NA	intron (NM_008620, intron 3 of 10)	MTEa|LTR|ERVL-MaLR	6618	NM_008620	17472	Mm.440525	NM_008620	ENSMUSG00000079363	Gbp4	AW228052|Mag-2|Mpa-2|Mpa2	guanylate binding protein 4	protein-coding
mm_122333.1	chr14	37114013	37114027	-	1	NA	Intergenic	Intergenic	-3919	NM_001206684	70045	Mm.271619	NM_001206684	ENSMUSG00000096001	2610528A11Rik	AW494830	RIKEN cDNA 2610528A11 gene	protein-coding
mm_72656.1	chr8	84847224	84847234	+	1	NA	promoter-TSS (NM_007591)	promoter-TSS (NM_007591)	-298	NM_007591	12317	Mm.1971	NM_007591	ENSMUSG00000003814	Calr	CRT|Calregulin	calreticulin	protein-coding
mm_166193.1	chr5	35679390	35679414	-	1	NA	5' UTR (NM_001042615, exon 1 of 7)	5' UTR (NM_001042615, exon 1 of 7)	378	NM_001042615	78558	Mm.274255	NM_030127	ENSMUSG00000029096	Htra3	2210021K23Rik|9530081K03Rik|Prsp|Tasp	HtrA serine peptidase 3	protein-coding
mm_107731.1	chr12	57501246	57501252	+	1	NA	Intergenic	Intergenic	44872	NM_008259	15375	Mm.4578	NM_008259	ENSMUSG00000035451	Foxa1	Hnf-3a|Hnf3a|Tcf-3a|Tcf3a	forkhead box A1	protein-coding
mm_86683.1	chr10	18407627	18407650	+	1	NA	promoter-TSS (NM_173390)	promoter-TSS (NM_173390)	-37	NM_173390	215819	Mm.297971	NM_173390	ENSMUSG00000039835	Nhsl1	5730409E15Rik|A630035H13Rik|A730096F01|BC013565|D10Bwg0940e|mKIAA1357	NHS-like 1	protein-coding
mm_86374.1	chr9	123809043	123809056	-	1	NA	intron (NM_030712, intron 1 of 1)	MTD|LTR|ERVL-MaLR	2572	NM_030712	80901	Mm.124289	NM_030712	ENSMUSG00000048521	Cxcr6	BB217514|BONZO|STRL33	chemokine (C-X-C motif) receptor 6	protein-coding
mm_43734.1	chr5	139791557	139791601	+	1	NA	promoter-TSS (NM_010757)	promoter-TSS (NM_010757)	43	NM_010757	17135	Mm.157313	NM_010757	ENSMUSG00000018143	Mafk	AW061068|NF-E2|Nfe2u	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein K (avian)	protein-coding
mm_63676.1	chr7	130531309	130531313	+	1	NA	Intergenic	RLTR1B|LTR|ERV1	-10942	NM_001271343	11907	Mm.216321	NM_013799	ENSMUSG00000030850	Ate1	AI225793|AW547406	arginyltransferase 1	protein-coding
mm_60539.1	chr7	44480473	44480482	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-4040	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_65198.1	chr7	19696860	19696866	-	1	NA	exon (NM_009696, exon 4 of 4)	exon (NM_009696, exon 4 of 4)	1535	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_45742.1	chr5	86518617	86518627	-	1	NA	promoter-TSS (NM_177162)	promoter-TSS (NM_177162)	-22	NM_177162	320454	Mm.184522	NM_177162	ENSMUSG00000079451	Tmprss11g	9930032O22Rik|Desc4	transmembrane protease, serine 11g	protein-coding
mm_149480.1	chr19	11755855	11755865	+	1	NA	intron (NM_008118, intron 5 of 8)	intron (NM_008118, intron 5 of 8)	8301	NM_008118	14603	Mm.456	NM_008118	ENSMUSG00000024682	Gif	AV073125	gastric intrinsic factor	protein-coding
mm_75093.1	chr8	34094350	34094378	-	1	NA	intron (NM_001293759, intron 5 of 7)	intron (NM_001293759, intron 5 of 7)	13450	NM_001293758	22428	Mm.150373	NM_011722	ENSMUSG00000031516	Dctn6	AU044699|WS-3|p27	dynactin 6	protein-coding
mm_23703.1	chr3	68762047	68762081	+	1	NA	Intergenic	Intergenic	70640	NM_008351	16159	Mm.103783	NM_008351	ENSMUSG00000027776	Il12a	IL-12p35|Il-12a|Ll12a|p35	interleukin 12a	protein-coding
mm_149894.1	chr19	25407095	25407108	+	1	NA	intron (NM_181404, intron 4 of 13)	intron (NM_181404, intron 4 of 13)	-98605	NM_015826	50796	Mm.391208	NM_015826	ENSMUSG00000024837	Dmrt1	-	doublesex and mab-3 related transcription factor 1	protein-coding
mm_163981.1	chr14	56450534	56450552	+	1	NA	intron (NM_001033043, intron 11 of 36)	L1VL2|LINE|L1	47846	NM_001033043	30054	Mm.287783	NM_001033043	ENSMUSG00000000365	Rnf17	MMIP-2|Mmip2|TDRD4	ring finger protein 17	protein-coding
mm_138684.1	chr17	35916978	35916993	+	1	NA	promoter-TSS (NM_025878)	promoter-TSS (NM_025878)	-211	NM_001163818	52040	Mm.29385	NM_175934	ENSMUSG00000039220	Ppp1r10	2610025H06Rik|Cat53|D17Ertd808e|Fb19|Pnuts	protein phosphatase 1, regulatory subunit 10	protein-coding
mm_28636.1	chr3	95217878	95217918	-	1	NA	promoter-TSS (NM_172512)	promoter-TSS (NM_172512)	44	NM_172512	213054	Mm.224820	NM_029885	ENSMUSG00000038766	Gabpb2	1810015F01Rik|5830427M07|9430006E19Rik|A430024B14Rik|AV050852|Gabpb2-1	GA repeat binding protein, beta 2	protein-coding
mm_151397.1	chr19	56461566	56461572	+	1	NA	promoter-TSS (NM_001164263)	promoter-TSS (NM_001164263)	-68	NM_001164263	226245	Mm.156742	NM_172641	ENSMUSG00000035818	Plekhs1	9930023K05Rik	pleckstrin homology domain containing, family S member 1	protein-coding
mm_132193.1	chr16	32467181	32467184	+	1	NA	exon (NM_009981, exon 7 of 9)	exon (NM_009981, exon 7 of 9)	20697	NM_145932	106407	Mm.476915	NM_145932	ENSMUSG00000035699	Slc51a	AV001382|AW261577|D630035O19Rik|OSTalpha|Osta	solute carrier family 51, alpha subunit	protein-coding
mm_135942.1	chr16	74303686	74303688	-	1	NA	intron (NM_175549, intron 2 of 27)	intron (NM_175549, intron 2 of 27)	38380	NR_030464	751561		NR_030464	ENSMUSG00000104758	Mir691	Mirn691|mir-691|mmu-mir-691	microRNA 691	ncRNA
mm_58072.1	chr6	136924185	136924199	-	1	NA	exon (NM_007486, exon 6 of 6)	exon (NM_007486, exon 6 of 6)	-2012	NM_026983	69187	Mm.33692	NM_026983	ENSMUSG00000030219	Erp27	1810033M07Rik|1810047B09Rik	endoplasmic reticulum protein 27	protein-coding
mm_119022.1	chr14	30009116	30009146	+	1	NA	promoter-TSS (NM_019583)	promoter-TSS (NM_019583)	131	NM_001136240	218865	Mm.259916	NM_172264	ENSMUSG00000015970	Chdh	AU041472|D630034H06Rik	choline dehydrogenase	protein-coding
mm_164954.1	chr19	5460660	5460666	+	1	NA	promoter-TSS (NM_021438)	promoter-TSS (NM_021438)	56	NM_021438	58249	Mm.329656	NM_021438	ENSMUSG00000024911	Fibp	2010004G08Rik|2010005N21Rik|3010027N18Rik	fibroblast growth factor (acidic) intracellular binding protein	protein-coding
mm_86230.1	chr9	120180422	120180464	-	1	NA	Intergenic	Intergenic	30701	NM_001039364	17433	Mm.486167	NM_008614	ENSMUSG00000032517	Mobp	AI835053|AI839848|MOBP155|MOBP170|MOBP69|MOBP73|MOBP81|R74645	myelin-associated oligodendrocytic basic protein	protein-coding
mm_36695.1	chr4	96658723	96658757	-	1	NA	exon (NM_010007, exon 4 of 9)	exon (NM_010007, exon 4 of 9)	5379	NM_010007	13109	Mm.12838	NM_010007	ENSMUSG00000052520	Cyp2j5	-	cytochrome P450, family 2, subfamily j, polypeptide 5	protein-coding
mm_61183.1	chr7	62348336	62348351	+	1	NA	promoter-TSS (NM_010882)	promoter-TSS (NM_010882)	66	NM_010882	17984	Mm.400253	NM_010882	ENSMUSG00000033585	Ndn	AI528698|Peg6	necdin	protein-coding
mm_56053.1	chr6	86761166	86761171	-	1	NA	intron (NM_013471, intron 2 of 12)	intron (NM_013471, intron 2 of 12)	13946	NM_001331120	11746	Mm.259702	NM_013471	ENSMUSG00000029994	Anxa4	AI265406|AIV|AW106930|Anx4|Xanx-4	annexin A4	protein-coding
mm_172434.1	chr7	29648548	29648570	-	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	78456	NM_029714	76718	Mm.69030	NM_029714	ENSMUSG00000049123	Catsperg2	1700067C01Rik|CATSPERG	catsper channel auxiliary subunit gamma 2	protein-coding
mm_99981.1	chr11	114668571	114668607	+	1	NA	promoter-TSS (NM_001048058)	promoter-TSS (NM_001048058)	46	NM_001048057	67671	Mm.238817	NM_023372	ENSMUSG00000057322	Rpl38	0610025G13Rik|Rbt|Ts|Tss	ribosomal protein L38	protein-coding
mm_148439.1	chr19	3948621	3948680	+	1	NA	exon (NM_019449, exon 11 of 11)	exon (NM_019449, exon 11 of 11)	-10158	NM_028545	73458	Mm.482922	NM_028545	ENSMUSG00000037263	Aldh3b3	1700055N04Rik	aldehyde dehydrogenase 3 family, member B3	protein-coding
mm_122836.1	chr14	54723762	54723782	-	1	NA	3' UTR (NM_016972, exon 11 of 11)	3' UTR (NM_016972, exon 11 of 11)	-11598	NM_207131	110794	Mm.236223	NM_207131	ENSMUSG00000052435	Cebpe	C/EBPe|CRP1|Gm294	CCAAT/enhancer binding protein (C/EBP), epsilon	protein-coding
mm_136754.1	chr17	8582393	8582411	+	1	NA	intron (NM_001290707, intron 1 of 22)	Tigger17a|DNA|TcMar-Tigger	55601	NM_001290707	23984	Mm.87161	NM_011866	ENSMUSG00000023868	Pde10a	-	phosphodiesterase 10A	protein-coding
mm_30477.1	chr3	154711334	154711350	-	1	NA	intron (NM_175176, intron 1 of 6)	MamRep605|LTR?|LTR?	209	NM_175176	209601	Mm.331454	NM_175176	ENSMUSG00000078161	Erich3	1700013E18Rik|4922501L14Rik|5031409G23Rik|AI596448|Gm133	glutamate rich 3	protein-coding
mm_152853.1	chr19	24142908	24142914	-	1	NA	intron (NM_011597, intron 1 of 22)	intron (NM_011597, intron 1 of 22)	31229	NM_001198985	21873	Mm.104744	NM_011597	ENSMUSG00000024812	Tjp2	ZO-2	tight junction protein 2	protein-coding
mm_42560.1	chr5	117133653	117133663	+	1	NA	promoter-TSS (NM_183306)	promoter-TSS (NM_183306)	70	NM_183306	330177	Mm.24343	NM_183306	ENSMUSG00000061288	Taok3	2900006A08Rik|A130052D22|A430105I05Rik	TAO kinase 3	protein-coding
mm_96097.1	chr11	60417608	60417625	+	1	NA	promoter-TSS (NM_145427)	promoter-TSS (NM_145427)	471	NM_025757	66771	Mm.29950	NM_025757	ENSMUSG00000018415	Gid4	4933439F18Rik	GID complex subunit 4, VID24 homolog	protein-coding
mm_47086.1	chr5	117119877	117119897	-	1	NA	promoter-TSS (NM_001199685)	promoter-TSS (NM_001199685)	-242	NM_001199685	330177	Mm.24343	NM_183306	ENSMUSG00000061288	Taok3	2900006A08Rik|A130052D22|A430105I05Rik	TAO kinase 3	protein-coding
mm_107918.1	chr12	71048339	71048356	+	1	NA	intron (NM_001081195, intron 11 of 23)	intron (NM_001081195, intron 11 of 23)	32380	NM_001081195	238247	Mm.241601	NM_001081195	ENSMUSG00000048118	Arid4a	A630009N03|A630067N03Rik|MmRBBP1|Rbbp1	AT rich interactive domain 4A (RBP1-like)	protein-coding
mm_119796.1	chr14	54199973	54199983	+	1	NA	Intergenic	Intergenic	53951	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_167571.1	chr9	43142423	43142424	+	1	NA	intron (NM_011139, intron 6 of 12)	intron (NM_011139, intron 6 of 12)	-25853	NM_001034863	235300	Mm.261326	NM_001034863	ENSMUSG00000048503	Tmem136	AA396355|Gm184	transmembrane protein 136	protein-coding
mm_68607.1	chr7	116290561	116290602	-	1	NA	intron (NM_001305185, intron 3 of 26)	intron (NM_001305185, intron 3 of 26)	17795	NM_001305185	233765	Mm.3741	NM_172743	ENSMUSG00000045659	Plekha7	A430081P20Rik|AI414265	pleckstrin homology domain containing, family A member 7	protein-coding
mm_163052.1	chr11	58421125	58421151	+	1	NA	promoter-TSS (NM_027239)	promoter-TSS (NM_027239)	27	NM_027239	69864	Mm.45641	NM_027239	ENSMUSG00000013653	1810065E05Rik	AV047390	RIKEN cDNA 1810065E05 gene	protein-coding
mm_171231.1	chr3	66914549	66914549	+	1	NA	Intergenic	L1Md_T|LINE|L1	64262	NM_001302358	20429	Mm.39093	NM_013665	ENSMUSG00000027833	Shox2	6330543G17Rik|OG12|Og12x|Prx3|SHOT	short stature homeobox 2	protein-coding
mm_70348.1	chr8	4777800	4777817	+	1	NA	intron (NM_011369, intron 1 of 12)	intron (NM_011369, intron 1 of 12)	1726	NM_011369	20419	Mm.37801	NM_011369	ENSMUSG00000022322	Shcbp1	mPAL	Shc SH2-domain binding protein 1	protein-coding
mm_30352.1	chr3	151749878	151749919	-	1	NA	promoter-TSS (NM_133871)	promoter-TSS (NM_133871)	61	NM_133871	99899	Mm.30756	NM_133871	ENSMUSG00000028037	Ifi44	A430056A10Rik|AW261460|MTAP44|p44	interferon-induced protein 44	protein-coding
mm_21527.1	chr2	163644691	163644770	-	1	NA	promoter-TSS (NR_028113)	promoter-TSS (NR_028113)	-120	NR_028113	68386	Mm.410649	NR_028113	ENSMUSG00000058812	0610039K10Rik	-	RIKEN cDNA 0610039K10 gene	ncRNA
mm_117001.1	chr13	57426364	57426367	-	1	NA	3' UTR (NM_001166463, exon 11 of 11)	3' UTR (NM_001166463, exon 11 of 11)	481967	NM_009262	20745	Mm.379020	NM_009262	ENSMUSG00000056222	Spock1	Spock|Ticn1|testican	sparc/osteonectin, cwcv and kazal-like domains proteoglycan 1	protein-coding
mm_138686.1	chr17	35926428	35926433	+	1	NA	exon (NM_001163818, exon 7 of 19)	exon (NM_001163818, exon 7 of 19)	8541	NR_035445	100316810		NR_035445	ENSMUSG00000084751	Mir1894	Mirn1894|mmu-mir-1894	microRNA 1894	ncRNA
mm_96758.1	chr11	69914009	69914078	+	1	NA	promoter-TSS (NM_019726)	promoter-TSS (NM_019726)	-149	NM_019726	56310	Mm.477738	NM_019726	ENSMUSG00000023170	Gps2	AI505953	G protein pathway suppressor 2	protein-coding
mm_114997.1	chr13	97844774	97844782	+	1	NA	Intergenic	Intergenic	284778	NR_046157	328314	Mm.138047	NR_046157	ENSMUSG00000110235	Gm5086	B230311A21|EG328314	predicted gene 5086	ncRNA
mm_130450.1	chr15	98542622	98542625	-	1	NA	TTS (NM_009833)	TTS (NM_009833)	-8354	NM_001289440	69612	Mm.229107	NM_133714	ENSMUSG00000022992	Kansl2	2310037I24Rik|B930009D17	KAT8 regulatory NSL complex subunit 2	protein-coding
mm_144553.1	chr18	31619499	31619509	+	1	NA	Intergenic	Intergenic	-9602	NM_026165	67453	Mm.23896	NM_026165	ENSMUSG00000024259	Slc25a46	1200007B05Rik|AI325987	solute carrier family 25, member 46	protein-coding
mm_60308.1	chr7	44122249	44122258	+	1	NA	Intergenic	Intergenic	9580	NM_010114	13646	Mm.5193	NM_010114	ENSMUSG00000060177	Klk1b22	EGF-BP A|Egfbp-1|Egfbp1|Klk22|mGk-22	kallikrein 1-related peptidase b22	protein-coding
mm_26422.1	chr3	142618175	142618185	+	1	NA	exon (NM_010259, exon 11 of 11)	exon (NM_010259, exon 11 of 11)	-2483	NM_010260	14469	Mm.24038	NM_010260	ENSMUSG00000028270	Gbp2	-	guanylate binding protein 2	protein-coding
mm_45643.1	chr5	76951179	76951198	-	1	NA	promoter-TSS (NM_025939)	promoter-TSS (NM_025939)	-223	NM_025939	67054	Mm.182931	NM_025939	ENSMUSG00000029247	Paics	2610511I09Rik|ADE2H1|AIRC|PAIS	phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoribosylaminoimidazole, succinocarboxamide synthetase	protein-coding
mm_62042.1	chr7	92235136	92235144	+	1	NA	5' UTR (NM_001243047, exon 1 of 11)	5' UTR (NM_001243047, exon 1 of 11)	170	NM_001243047	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_155993.1	chrX	106156744	106156755	+	1	NA	exon (NM_205820, exon 3 of 3)	exon (NM_205820, exon 3 of 3)	13474	NM_205820	279572	Mm.336203	NM_205820	ENSMUSG00000033777	Tlr13	AI666735|Gm713	toll-like receptor 13	protein-coding
mm_49609.1	chr6	30747168	30747209	+	1	NA	TTS (NM_017478)	TTS (NM_017478)	5889	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_118377.1	chr13	117024570	117024570	-	1	NA	intron (NM_001081009, intron 2 of 26)	CpG	946	NM_001081009	52552	Mm.274466	NM_027272	ENSMUSG00000021725	Parp8	2810430O08Rik|ARTD16|D13Ertd275e	poly (ADP-ribose) polymerase family, member 8	protein-coding
mm_87766.1	chr10	60293345	60293359	+	1	NA	exon (NM_011179, exon 4 of 15)	exon (NM_011179, exon 4 of 15)	8891	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_135646.1	chr16	52376428	52376438	-	1	NA	intron (NM_009655, intron 1 of 15)	MTE2b|LTR|ERVL-MaLR	76648	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_94099.1	chr10	128559301	128559328	-	1	NA	exon (NM_011119, exon 10 of 12)	exon (NM_011119, exon 10 of 12)	6620	NM_011119	18813	Mm.4742	NM_011119	ENSMUSG00000025364	Pa2g4	38kDa|AA672939|Ebp1|Plfap	proliferation-associated 2G4	protein-coding
mm_133606.1	chr16	91485296	91485309	+	1	NA	promoter-TSS (NM_010508)	promoter-TSS (NM_010508)	87	NM_010508	15975	Mm.502	NM_010508	ENSMUSG00000022967	Ifnar1	CD118|Ifar|Ifnar|Ifrc|Infar	interferon (alpha and beta) receptor 1	protein-coding
mm_120095.1	chr14	57999349	57999362	+	1	NA	promoter-TSS (NM_028643)	promoter-TSS (NM_028643)	-93	NM_028643	68514	Mm.26834	NM_028643	ENSMUSG00000021973	Micu2	1110008L20Rik|4833427E09Rik|AU041871|Efha1|Smhs2	mitochondrial calcium uptake 2	protein-coding
mm_143168.1	chr17	57226201	57226225	-	1	NA	exon (NM_009778, exon 3 of 41)	exon (NM_009778, exon 3 of 41)	1923	NM_009778	12266	Mm.19131	NM_009778	ENSMUSG00000024164	C3	AI255234|ASP|HSE-MSF|Plp	complement component 3	protein-coding
mm_97112.1	chr11	74662004	74662023	+	1	NA	exon (NM_001081158, exon 10 of 26)	exon (NM_001081158, exon 10 of 26)	12518	NM_001081158	74148	Mm.214574	NM_001081158	ENSMUSG00000020741	Cluh	1300001I01Rik|Kiaa0664|mKIAA0664	clustered mitochondria (cluA/CLU1) homolog	protein-coding
mm_35943.1	chr4	53104519	53104565	-	1	NA	intron (NM_013454, intron 7 of 49)	MIRb|SINE|MIR	55353	NM_013454	11303	Mm.277376	NM_013454	ENSMUSG00000015243	Abca1	ABC-1|Abc1	ATP-binding cassette, sub-family A (ABC1), member 1	protein-coding
mm_41410.1	chr5	90787503	90787563	+	1	NA	3' UTR (NM_203320, exon 4 of 4)	3' UTR (NM_203320, exon 4 of 4)	1432	NM_203320	330122	Mm.244289	NM_203320	ENSMUSG00000029379	Cxcl3	Dcip1|Gm1960	chemokine (C-X-C motif) ligand 3	protein-coding
mm_154466.1	chrM	3435	3653	-	1	NA	NA	Intergenic	NA	NA								
mm_18971.1	chr2	76814355	76814371	-	1	NA	exon (NM_011652, exon 175 of 313)	exon (NM_011652, exon 175 of 313)	139048	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_78742.1	chr9	41885233	41885237	+	1	NA	Intergenic	Intergenic	239054	NM_011436	20660	Mm.121920	NM_011436	ENSMUSG00000049313	Sorl1	2900010L19Rik|AI596264|AW261561|LR11|SorLA|gp250|mSorLA	sortilin-related receptor, LDLR class A repeats-containing	protein-coding
mm_42124.1	chr5	110898567	110898571	+	1	NA	intron (NM_001267622, intron 2 of 22)	AT_rich|Low_complexity|Low_complexity	18766	NM_001267622	209683	Mm.295660	NM_024477	ENSMUSG00000033209	Ttc28	2310015L07Rik|6030435N04|AI428795|AI851761|BC002262|TPRBK	tetratricopeptide repeat domain 28	protein-coding
mm_156533.1	chrX	151047311	151047327	+	1	NA	5' UTR (NM_008001, exon 1 of 18)	5' UTR (NM_008001, exon 1 of 18)	149	NM_008001	14163	Mm.8142	NM_008001	ENSMUSG00000025265	Fgd1	ZFYVE3	FYVE, RhoGEF and PH domain containing 1	protein-coding
mm_8017.1	chr1	134955848	134955852	-	1	NA	promoter-TSS (NM_001081307)	promoter-TSS (NM_001081307)	90	NM_001081307	329251	Mm.188709	NM_001081307	ENSMUSG00000073557	Ppp1r12b	1810037O03Rik|9530009M10Rik|AI132431|Mypt2	protein phosphatase 1, regulatory (inhibitor) subunit 12B	protein-coding
mm_85708.1	chr9	108139453	108139455	-	1	NA	TTS (NR_126078)	TTS (NR_126078)	2599	NR_126077	76873	Mm.436935	NR_126077	ENSMUSG00000102224	4930447F24Rik	-	RIKEN cDNA 4930447F24 gene	ncRNA
mm_88028.1	chr10	67224970	67224994	+	1	NA	exon (NM_001242396, exon 9 of 25)	exon (NM_001242396, exon 9 of 25)	39232	NM_001242396	108829	Mm.23846	NM_207221	ENSMUSG00000037876	Jmjd1c	5430433L24Rik|D630035I23Rik|Jmjdic|TRIP8	jumonji domain containing 1C	protein-coding
mm_152098.1	chr19	6910068	6910082	-	1	NA	promoter-TSS (NM_012021)	promoter-TSS (NM_012021)	377	NM_026306	67674	Mm.318804	NM_026306	ENSMUSG00000038812	Trmt112	0610038D11Rik|Trm112p	tRNA methyltransferase 11-2	protein-coding
mm_44018.1	chr5	147343140	147343175	+	1	NA	intron (NM_010229, intron 19 of 23)	MT2A|LTR|ERVL	-20717	NM_001039678	231903	Mm.291286	NM_001039678	ENSMUSG00000075543	Urad	EG231903|Prhoxnb	ureidoimidazoline (2-oxo-4-hydroxy-4-carboxy-5) decarboxylase	protein-coding
mm_21727.1	chr2	164674114	164674114	-	1	NA	promoter-TSS (NM_001161806)	promoter-TSS (NM_001161806)	-27	NM_001161806	629761	Mm.389336	NM_001161806	ENSMUSG00000078940	Wfdc11	-	WAP four-disulfide core domain 11	protein-coding
mm_48941.1	chr6	4539493	4539502	+	1	NA	exon (NM_007743, exon 51 of 52)	exon (NM_007743, exon 51 of 52)	33879	NM_007743	12843	Mm.277792	NM_007743	ENSMUSG00000029661	Col1a2	AA960264|AI325291|Col1a-2|Cola-2|Cola2|oim	collagen, type I, alpha 2	protein-coding
mm_152861.1	chr19	24201975	24201975	-	1	NA	intron (NM_011597, intron 1 of 22)	intron (NM_011597, intron 1 of 22)	23051	NM_011597	21873	Mm.104744	NM_011597	ENSMUSG00000024812	Tjp2	ZO-2	tight junction protein 2	protein-coding
mm_55417.1	chr6	65125767	65125779	-	1	NA	intron (NM_019455, intron 4 of 5)	intron (NM_019455, intron 4 of 5)	18957	NM_019455	54486	Mm.410688	NM_019455	ENSMUSG00000029919	Hpgds	H-PGDS|Ptgds2	hematopoietic prostaglandin D synthase	protein-coding
mm_123226.1	chr14	59629401	59629437	-	1	NA	intron (NM_145463, intron 1 of 1)	intron (NM_145463, intron 1 of 1)	4138	NM_145463	219134	Mm.275409	NM_145463	ENSMUSG00000044461	Shisa2	9430059P22Rik|MAd2|Tmem46|mShisa|shisa	shisa family member 2	protein-coding
mm_82402.1	chr9	14770980	14771000	-	1	NA	promoter-TSS (NM_029306)	promoter-TSS (NM_029306)	40	NM_029306	69325	Mm.440453	NM_029306	ENSMUSG00000031927	1700012B09Rik	1700007P19Rik	RIKEN cDNA 1700012B09 gene	protein-coding
mm_52050.1	chr6	97210781	97210818	+	1	NA	promoter-TSS (NM_022992)	promoter-TSS (NM_022992)	7	NM_022992	65106	Mm.291014	NM_022992	ENSMUSG00000035199	Arl6ip5	5930404D22Rik|AV001879|Aip-5|Gtrap3-18|addiscin	ADP-ribosylation factor-like 6 interacting protein 5	protein-coding
mm_84856.1	chr9	78489142	78489166	-	1	NA	Intergenic	Intergenic	-7430	NM_010106	13627	Mm.138471	NM_010106	ENSMUSG00000037742	Eef1a1	-	eukaryotic translation elongation factor 1 alpha 1	protein-coding
mm_50564.1	chr6	49047976	49047986	+	1	NA	exon (NM_053110, exon 6 of 11)	exon (NM_053110, exon 6 of 11)	11463	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_109318.1	chr12	109561599	109561610	+	1	NA	non-coding (NR_003633, exon 5 of 5)	non-coding (NR_003633, exon 5 of 5)	-2088	NR_030427	791079		NR_030427	ENSMUSG00000076451	Mir770	Mirn770|mir-770|mmu-mir-770	microRNA 770	ncRNA
mm_145997.1	chr18	68344483	68344518	+	1	NA	Intergenic	MTC-int|LTR|ERVL-MaLR	6897	NM_013596	17203	Mm.8003	NM_013596	ENSMUSG00000007480	Mc5r	-	melanocortin 5 receptor	protein-coding
mm_161316.1	chr14	43957079	43957079	+	1	NA	promoter-TSS (NM_001123394)	promoter-TSS (NM_001123394)	10	NM_007448	503844	Mm.24663	NM_007448	ENSMUSG00000053961	Ang5	-	angiogenin, ribonuclease A family, member 5	protein-coding
mm_171089.1	chr3	124589173	124589175	-	1	NA	Intergenic	Intergenic	-8083	NR_015460	384775	Mm.489851	NR_015460	ENSMUSG00000039174	1700003H04Rik	4930538K10Rik|4933400D22Rik	RIKEN cDNA 1700003H04 gene	ncRNA
mm_8704.1	chr1	158822817	158822820	-	1	NA	intron (NM_001085376, intron 11 of 21)	intron (NM_001085376, intron 11 of 21)	134620	NM_001085376	23850	Mm.458621	NM_001085376	ENSMUSG00000073530	Pappa2	PAPP-A2|PLAC3|Pappe	pappalysin 2	protein-coding
mm_54244.1	chr6	28256566	28256576	-	1	NA	intron (NM_001081678, intron 2 of 5)	intron (NM_001081678, intron 2 of 5)	5030	NM_001081678	627049	Mm.84441	NM_001081678	ENSMUSG00000039841	Zfp800	AA407452|Znf800	zinc finger protein 800	protein-coding
mm_167482.1	chr8	129234363	129234377	-	1	NA	promoter-TSS (NM_153780)	promoter-TSS (NM_153780)	-324	NM_153780	72139	Mm.426514	NM_153780	ENSMUSG00000071302	2610044O15Rik8	2610044O15Rik	RIKEN cDNA 2610044O15 gene	protein-coding
mm_53335.1	chr6	129236163	129236188	+	1	NA	intron (NR_040265, intron 1 of 2)	intron (NR_040265, intron 1 of 2)	1870	NR_040265	76432	Mm.261738	NR_040265	ENSMUSG00000097354	2310001H17Rik	AI646108	RIKEN cDNA 2310001H17 gene	ncRNA
mm_78731.1	chr9	41581301	41581316	+	1	NA	promoter-TSS (NR_029822)	promoter-TSS (NR_029822)	55	NR_015483	73144	Mm.38166	NM_001033153	ENSMUSG00000074415	3110039I08Rik	2610203C20Rik|AI848448|D230004N17Rik|D3Mgi9|Mir100hg	RIKEN cDNA 3110039I08 gene	ncRNA
mm_70932.1	chr8	25815208	25815214	+	1	NA	TTS (NM_001080793)	TTS (NM_001080793)	6737	NM_011485	20845	Mm.293314	NM_011485	ENSMUSG00000031574	Star	AV363654|D8Ertd419e|stARD1	steroidogenic acute regulatory protein	protein-coding
mm_140908.1	chr17	24163669	24163771	-	1	NA	promoter-TSS (NM_172935)	promoter-TSS (NM_172935)	13	NM_172935	245847	Mm.87319	NM_172935	ENSMUSG00000036820	Amdhd2	5730457F11Rik	amidohydrolase domain containing 2	protein-coding
mm_31962.1	chr4	86930705	86930713	+	1	NA	intron (NM_001290543, intron 5 of 5)	RLTR51A_Mm|LTR|ERVK?	56295	NM_139306	230379	Mm.45019	NM_139306	ENSMUSG00000038007	Acer2	2410116I05Rik|Asah3l|CRG-L1|maCER2	alkaline ceramidase 2	protein-coding
mm_136184.1	chr16	88932262	88932267	-	1	NA	promoter-TSS (NM_133359)	promoter-TSS (NM_133359)	0	NM_133359	170939	Mm.188445	NM_133359	ENSMUSG00000057174	Krtap19-9b	Krtap16-10b|Krtap16.10L	keratin associated protein 19-9B	protein-coding
mm_15638.1	chr2	163054592	163054649	+	1	NA	promoter-TSS (NM_008652)	promoter-TSS (NM_008652)	-15	NM_008652	17865	Mm.4594	NM_008652	ENSMUSG00000017861	Mybl2	B-Myb|Bmyb	myeloblastosis oncogene-like 2	protein-coding
mm_121136.1	chr14	101884315	101884327	+	1	NA	exon (NM_201529, exon 8 of 31)	exon (NM_201529, exon 8 of 31)	43698	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_29059.1	chr3	103778189	103778201	-	1	NA	non-coding (NR_125731, exon 2 of 16)	non-coding (NR_125731, exon 2 of 16)	13080	NM_001301306	15257	Mm.20827	NM_010432	ENSMUSG00000008730	Hipk1	1110062K04Rik|Myak	homeodomain interacting protein kinase 1	protein-coding
mm_130442.1	chr15	98482208	98482231	-	1	NA	exon (NM_010679, exon 2 of 4)	exon (NM_010679, exon 2 of 4)	464	NM_010679	16770	Mm.5074	NM_010679	ENSMUSG00000022991	Lalba	AW208827|Lyzg	lactalbumin, alpha	protein-coding
mm_4202.1	chr1	171229841	171229856	+	1	NA	3' UTR (NM_010185, exon 5 of 5)	3' UTR (NM_010185, exon 5 of 5)	4501	NM_010185	14127	Mm.22673	NM_010185	ENSMUSG00000058715	Fcer1g	AI573376|CD23|FcR-gamma|FcR[g]|FcRgamma|Fce1g|FcepsilonRI|Ly-50	Fc receptor, IgE, high affinity I, gamma polypeptide	protein-coding
mm_85442.1	chr9	104186585	104186597	-	1	NA	intron (NM_001163026, intron 35 of 55)	intron (NM_001163026, intron 35 of 55)	-59948	NM_145700	252837	Mm.269254	NM_145700	ENSMUSG00000079355	Ackr4	A630091E18Rik|CCBP2|CCR11|CCX-CKR|CCX-CKR1|Ccrl1|Cmkbrl1|PPR1|VSHK1	atypical chemokine receptor 4	protein-coding
mm_52115.1	chr6	97915236	97915244	+	1	NA	intron (NM_001113198, intron 1 of 9)	intron (NM_001113198, intron 1 of 9)	-14577	NM_001178049	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_102219.1	chr11	54909786	54909788	-	1	NA	TTS (NM_021327)	TTS (NM_021327)	6933	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_148860.1	chr19	6400524	6400559	+	1	NA	promoter-TSS (NM_011242)	promoter-TSS (NM_011242)	-42	NM_011242	19395	Mm.77017	NM_011242	ENSMUSG00000032946	Rasgrp2	CDC25L|Caldaggef1	RAS, guanyl releasing protein 2	protein-coding
mm_65004.1	chr7	17053128	17053131	-	1	NA	intron (NM_001162950, intron 3 of 14)	B1_Mur1|SINE|Alu	3550	NM_016868	53417	Mm.135110	NM_016868	ENSMUSG00000004328	Hif3a	Ipas|MOP7|NEPAS|bHLHe17	hypoxia inducible factor 3, alpha subunit	protein-coding
mm_170576.1	chr19	54520593	54520610	-	1	NA	Intergenic	BGLII|LTR|ERVK	475419	NM_007417	11551	Mm.235195	NM_007417	ENSMUSG00000033717	Adra2a	AW122659|Adra-2|Adra-2a|alpha(2A)AR|alpha2-C10|alpha2A|alpha2A-AR	adrenergic receptor, alpha 2a	protein-coding
mm_6931.1	chr1	84935191	84935241	-	1	NA	promoter-TSS (NM_027921)	promoter-TSS (NM_027921)	-133	NM_027921	71781	Mm.158754	NM_027921	ENSMUSG00000026220	Slc16a14	1110004H10Rik	solute carrier family 16 (monocarboxylic acid transporters), member 14	protein-coding
mm_10841.1	chr2	24975192	24975219	+	1	NA	promoter-TSS (NM_001031808)	promoter-TSS (NM_001031808)	-107	NM_001031808	107733	Mm.23010	NM_001031808	ENSMUSG00000036850	Mrpl41	MRP-L27|Rpml27	mitochondrial ribosomal protein L41	protein-coding
mm_37152.1	chr4	117121242	117121248	-	1	NA	non-coding (NR_024078, exon 6 of 7)	non-coding (NR_024078, exon 6 of 7)	4480	NR_024078	78611	Mm.446227	NM_001033187		Btbd19	9530048O09Rik|BB115071	BTB (POZ) domain containing 19	ncRNA
mm_167470.1	chr8	126574748	126574750	-	1	NA	Intergenic	Intergenic	18687	NM_001164598	270110	Mm.334918	NM_001164598	ENSMUSG00000051495	Irf2bp2	E130305N23Rik|IRF-2BP2	interferon regulatory factor 2 binding protein 2	protein-coding
mm_80529.1	chr9	80165014	80165055	+	1	NA	promoter-TSS (NM_001039546)	promoter-TSS (NM_001039546)	0	NM_001039546	17920	Mm.4040	NM_008662	ENSMUSG00000033577	Myo6	BC029719|Tlc|sv	myosin VI	protein-coding
mm_140469.1	chr17	93199349	93199408	+	1	NA	5' UTR (NM_009625, exon 1 of 5)	5' UTR (NM_009625, exon 1 of 5)	210	NM_009625	11516	Mm.3407	NM_009625	ENSMUSG00000024256	Adcyap1	PACAP	adenylate cyclase activating polypeptide 1	protein-coding
mm_110789.1	chr12	72071094	72071106	-	1	NA	promoter-TSS (NM_181752)	promoter-TSS (NM_181752)	-109	NM_181752	238252	Mm.390508	NM_181752	ENSMUSG00000043398	Gpr135	PAFR	G protein-coupled receptor 135	protein-coding
mm_26295.1	chr3	142507733	142507746	+	1	NA	exon (NM_153564, exon 9 of 11)	exon (NM_153564, exon 9 of 11)	10805	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_170719.1	chr2	14739169	14739173	+	1	NA	intron (NM_023116, intron 2 of 13)	intron (NM_023116, intron 2 of 13)	18529	NR_028497	625342	Mm.484784	NR_028497		Gm13315	OTTMUSG00000011384	lactate dehydrogenase A pseudogene	pseudo
mm_145766.1	chr18	65023701	65023713	+	1	NA	5' UTR (NM_031881, exon 1 of 30)	5' UTR (NM_031881, exon 1 of 30)	180	NM_031881	83814	Mm.98668	NM_031881	ENSMUSG00000024589	Nedd4l	1300012C07Rik|Nedd4-2|Nedd4b	neural precursor cell expressed, developmentally down-regulated gene 4-like	protein-coding
mm_113098.1	chr13	24376035	24376045	+	1	NA	intron (NM_001284519, intron 2 of 17)	intron (NM_001284519, intron 2 of 17)	-39082	NM_007717	12763	Mm.8396	NM_007717	ENSMUSG00000016756	Cmah	-	cytidine monophospho-N-acetylneuraminic acid hydroxylase	protein-coding
mm_108531.1	chr12	84206907	84206925	+	1	NA	intron (NM_001163501, intron 1 of 12)	intron (NM_001163501, intron 1 of 12)	11965	NM_001163501	238317	Mm.31256	NM_001163501	ENSMUSG00000042507	Elmsan1	9430029N19Rik|C130039O16Rik|Gm260	ELM2 and Myb/SANT-like domain containing 1	protein-coding
mm_60444.1	chr7	44477103	44477109	+	1	NA	Intergenic	Intergenic	6759	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_100852.1	chr11	5803736	5803759	-	1	NA	promoter-TSS (NM_018870)	promoter-TSS (NM_018870)	49	NM_018870	56012	Mm.219627	NM_018870	ENSMUSG00000020475	Pgam2	-	phosphoglycerate mutase 2	protein-coding
mm_53924.1	chr6	4540722	4540735	-	1	NA	3' UTR (NM_007743, exon 52 of 52)	3' UTR (NM_007743, exon 52 of 52)	35110	NM_007743	12843	Mm.277792	NM_007743	ENSMUSG00000029661	Col1a2	AA960264|AI325291|Col1a-2|Cola-2|Cola2|oim	collagen, type I, alpha 2	protein-coding
mm_96019.1	chr11	59543041	59543058	+	1	NA	intron (NM_145827, intron 1 of 9)	intron (NM_145827, intron 1 of 9)	363	NM_145827	216799	Mm.54174	NM_145827	ENSMUSG00000032691	Nlrp3	AGTAVPRL|AII/AVP|Cias1|FCAS|FCU|MWS|Mmig1|NALP3|Pypaf1	NLR family, pyrin domain containing 3	protein-coding
mm_68438.1	chr7	109960386	109960433	-	1	NA	promoter-TSS (NM_021494)	promoter-TSS (NM_021494)	13	NM_021494	19347	Mm.21904	NM_021494	ENSMUSG00000035901	Dennd5a	1500012B19Rik|AJ245569|AW496491|ORF37|Rab6ip1|mKIAA1091	DENN/MADD domain containing 5A	protein-coding
mm_139918.1	chr17	70967873	70967894	+	1	NA	Intergenic	Intergenic	22633	NM_023402	67938	Mm.261329	NM_023402	ENSMUSG00000034868	Myl12b	1500001M02Rik|C77744|Mylc2b|RLC-B	myosin, light chain 12B, regulatory	protein-coding
mm_129562.1	chr15	79546448	79546458	-	1	NA	5' UTR (NM_001040187, exon 1 of 13)	5' UTR (NM_001040187, exon 1 of 13)	106	NM_199079	67040	Mm.29644	NM_152806	ENSMUSG00000055065	Ddx17	2610007K22Rik|A430025E01Rik|AI047725|C80929|Gm926|p72	DEAD (Asp-Glu-Ala-Asp) box polypeptide 17	protein-coding
mm_110701.1	chr12	69241960	69242004	-	1	NA	exon (NM_178253, exon 1 of 13)	exon (NM_178253, exon 1 of 13)	150	NM_178253	271005	Mm.180969	NM_178253	ENSMUSG00000051890	Klhdc1	-	kelch domain containing 1	protein-coding
mm_41348.1	chr5	90501533	90501545	+	1	NA	exon (NM_007423, exon 8 of 15)	exon (NM_007423, exon 8 of 15)	10825	NM_007423	11576	Mm.358570	NM_007423	ENSMUSG00000054932	Afp	-	alpha fetoprotein	protein-coding
mm_62904.1	chr7	117380019	117380030	+	1	NA	promoter-TSS (NM_175645)	promoter-TSS (NM_175645)	-955	NM_175645	233781	Mm.461427	NM_175645	ENSMUSG00000030657	Xylt1	8030490L12	xylosyltransferase 1	protein-coding
mm_43127.1	chr5	125294063	125294068	+	1	NA	exon (NM_001205082, exon 7 of 12)	exon (NM_001205082, exon 7 of 12)	47029	NM_016741	20778	Mm.282242	NM_016741	ENSMUSG00000037936	Scarb1	AI120173|CD36|Cd36l1|Chohd1|Cla-1|Cla1|D5Ertd460e|Hdlq1|Hlb398|SR-B1|SR-BI|SRBI|Srb1|mSR-BI	scavenger receptor class B, member 1	protein-coding
mm_158785.1	chrX	167207751	167207771	-	1	NA	intron (NM_021278, intron 2 of 2)	intron (NM_021278, intron 2 of 2)	1457	NM_021278	19241	Mm.142729	NM_021278	ENSMUSG00000049775	Tmsb4x	Ptmb4|Tb4	thymosin, beta 4, X chromosome	protein-coding
mm_35337.1	chr4	31970561	31970571	-	1	NA	intron (NM_172688, intron 1 of 15)	RMER10B|LTR|ERVL	6459	NM_172688	26409	Mm.258589	NM_009316	ENSMUSG00000028284	Map3k7	B430101B05|C87327|Tak1	mitogen-activated protein kinase kinase kinase 7	protein-coding
mm_74559.1	chr8	10947822	10947845	-	1	NA	Intergenic	Intergenic	-19376	NR_135302	665306	Mm.358758	NR_030715	ENSMUSG00000038917	3930402G23Rik	-	RIKEN cDNA 3930402G23 gene	ncRNA
mm_35167.1	chr4	14621809	14621819	-	1	NA	promoter-TSS (NM_145947)	promoter-TSS (NM_145947)	-36	NM_145947	208890	Mm.483839	NM_145947	ENSMUSG00000040569	Slc26a7	-	solute carrier family 26, member 7	protein-coding
mm_134044.1	chr16	5196492	5196493	-	1	NA	intron (NR_027804, intron 8 of 8)	intron (NR_027804, intron 8 of 8)	7520	NM_013796	27426	Mm.215641	NM_013796	ENSMUSG00000023143	Nagpa	AI596180|UCE	N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase	protein-coding
mm_146943.1	chr18	32448410	32448422	-	1	NA	Intergenic	Intergenic	-70132	NR_045403	402767	Mm.385109	NR_045403	ENSMUSG00000097413	A830052D11Rik	-	RIKEN cDNA A830052D11 gene	ncRNA
mm_81246.1	chr9	107975530	107975601	+	1	NA	promoter-TSS (NM_023738)	promoter-TSS (NM_023738)	-2	NM_023738	74153	Mm.277125	NM_023738	ENSMUSG00000032596	Uba7	1300004C08Rik|Ube1l	ubiquitin-like modifier activating enzyme 7	protein-coding
mm_101411.1	chr11	28584075	28584105	-	1	NA	5' UTR (NM_181577, exon 1 of 5)	5' UTR (NM_181577, exon 1 of 5)	234	NM_001166661	216613	Mm.93759	NM_181577	ENSMUSG00000032878	Ccdc85a	-	coiled-coil domain containing 85A	protein-coding
mm_78332.1	chr9	25252879	25252900	+	1	NA	intron (NM_001205367, intron 1 of 12)	CpG	450	NM_001205367	235072	Mm.270259	NM_009859	ENSMUSG00000001833	Sept7	Cdc10|E430034N22	septin 7	protein-coding
mm_98946.1	chr11	98446827	98446869	+	1	NA	promoter-TSS (NM_010346)	promoter-TSS (NM_010346)	14	NM_010346	14786	Mm.276702	NM_010346	ENSMUSG00000019312	Grb7	mKIAA4028	growth factor receptor bound protein 7	protein-coding
mm_158492.1	chrX	142338918	142338932	-	1	NA	exon (NM_207625, exon 11 of 16)	exon (NM_207625, exon 11 of 16)	-32727	NM_021487	66240	Mm.58507	NM_021487	ENSMUSG00000090122	Kcne1l	1500015C14Rik|Kcne5|Mink	potassium voltage-gated channel, Isk-related family, member 1-like, pseudogene	protein-coding
mm_27764.1	chr3	69859876	69859901	-	1	NA	promoter-TSS (NM_133675)	promoter-TSS (NM_133675)	6	NM_001164210	66183	Mm.45481	NM_133675	ENSMUSG00000043461	Sptssb	1110032A04Rik|ADMP|Sssptb	serine palmitoyltransferase, small subunit B	protein-coding
mm_32341.1	chr4	104741703	104741713	+	1	NA	non-coding (NR_104385, exon 16 of 16)	non-coding (NR_104385, exon 16 of 16)	-24609	NM_133882	110382	Mm.87072	NM_133882	ENSMUSG00000029656	C8b	4930439B20Rik|AI595927	complement component 8, beta polypeptide	protein-coding
mm_18607.1	chr2	68251349	68251356	-	1	NA	intron (NM_016866, intron 16 of 17)	intron (NM_016866, intron 16 of 17)	146680	NM_020283	26877	Mm.226435	NM_020283	ENSMUSG00000034780	B3galt1	beta3Gal-T1	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 1	protein-coding
mm_94236.1	chr11	3292287	3292340	+	1	NA	intron (NM_019574, intron 1 of 3)	intron (NM_019574, intron 1 of 3)	1856	NM_019574	56218	Mm.275563	NM_019574	ENSMUSG00000020453	Patz1	8430401L15Rik|AI447519|Mazr|Patz|Zfp278	POZ (BTB) and AT hook containing zinc finger 1	protein-coding
mm_33589.1	chr4	132563571	132563593	+	1	NA	promoter-TSS (NM_001081211)	promoter-TSS (NM_001081211)	-485	NM_001081211	19204	Mm.89389	NM_001081211	ENSMUSG00000056529	Ptafr	PAFR	platelet-activating factor receptor	protein-coding
mm_15326.1	chr2	155751341	155751370	+	1	NA	5' UTR (NM_011171, exon 1 of 4)	5' UTR (NM_011171, exon 1 of 4)	138	NM_011171	19124	Mm.3243	NM_011171	ENSMUSG00000027611	Procr	AI325044|Ccca|Ccd41|Epcr	protein C receptor, endothelial	protein-coding
mm_62882.1	chr7	114768768	114768781	+	1	NA	intron (NM_173767, intron 1 of 12)	intron (NM_173767, intron 1 of 12)	23008	NM_173767	233752	Mm.83037	NM_173767	ENSMUSG00000048782	Insc	3830422K02Rik|C730020D23	inscuteable homolog (Drosophila)	protein-coding
mm_40051.1	chr5	33983742	33983750	+	1	NA	intron (NM_001310547, intron 1 of 3)	CpG	313	NM_001310546	381633	Mm.4923	NM_001033458	ENSMUSG00000070858	Gm1673	-	predicted gene 1673	protein-coding
mm_137565.1	chr17	27704501	27704505	+	1	NA	intron (NM_011861, intron 3 of 9)	intron (NM_011861, intron 3 of 9)	19264	NM_178365	23969	Mm.4926	NM_011861	ENSMUSG00000040276	Pacsin1	A830061D09Rik|H74|mKIAA1379|syndapin	protein kinase C and casein kinase substrate in neurons 1	protein-coding
mm_3759.1	chr1	156051434	156051454	+	1	NA	5' UTR (NM_001160182, exon 3 of 3)	5' UTR (NM_001160182, exon 3 of 3)	10583	NM_022329	240832	Mm.253335	NM_022329	ENSMUSG00000050565	Tor1aip2	1110020D10Rik|15kDa|A130072J07|AA103493|AW060462|AW610675|C77739|Ifrg15|Lull1	torsin A interacting protein 2	protein-coding
mm_167787.1	chr9	122438112	122438136	-	1	NA	Intergenic	RLTR10B|LTR|ERVK	-39323	NR_045967	654800	Mm.393956	NR_045967		A730085K08Rik	-	RIKEN cDNA A730085K08 gene	ncRNA
mm_77403.1	chr8	120537573	120537579	-	1	NA	intron (NM_001145896, intron 1 of 15)	CpG-14578	167	NM_001145896	382034	Mm.334856	NM_198671	ENSMUSG00000031822	Gse1	2210013I18Rik|mKIAA0182	genetic suppressor element 1, coiled-coil protein	protein-coding
mm_163690.1	chr13	99206177	99206179	+	1	NA	intron (NM_001004149, intron 1 of 4)	intron (NM_001004149, intron 1 of 4)	21355	NM_001004149	238803	Mm.343207	NM_001004149	ENSMUSG00000050919	Zfp366	DC-SCRIPT|Znf366	zinc finger protein 366	protein-coding
mm_64894.1	chr7	15946071	15946105	-	1	NA	promoter-TSS (NM_133831)	promoter-TSS (NM_133831)	20	NM_133831	68077	Mm.277634	NM_133831	ENSMUSG00000041560	Gltscr2	5330430H08Rik|9430097C02Rik|AU041936|AW536441|PICT-1|R74911	glioma tumor suppressor candidate region gene 2	protein-coding
mm_8602.1	chr1	156034827	156034839	-	1	NA	promoter-TSS (NM_001160180)	promoter-TSS (NM_001160180)	-16	NM_001160019	208263	Mm.211654	NM_144791	ENSMUSG00000026466	Tor1aip1	LAP1|Lap1B	torsin A interacting protein 1	protein-coding
mm_1797.1	chr1	79857504	79857506	+	1	NA	intron (NM_009255, intron 1 of 8)	intron (NM_009255, intron 1 of 8)	1160	NM_009255	20720	Mm.3093	NM_009255	ENSMUSG00000026249	Serpine2	B230326M24Rik|PAI-1|PI-7|PI7|PN-1|Spi4	serine (or cysteine) peptidase inhibitor, clade E, member 2	protein-coding
mm_47348.1	chr5	122560806	122560812	-	1	NA	intron (NM_009879, intron 14 of 18)	intron (NM_009879, intron 14 of 18)	53709	NM_009879	12589	Mm.10125	NM_009879	ENSMUSG00000029469	Ift81	AW060663|Cdv-1|Cdv-1r|Cdv1	intraflagellar transport 81	protein-coding
mm_83951.1	chr9	56927480	56927492	-	1	NA	5' UTR (NM_175483, exon 1 of 2)	5' UTR (NM_175483, exon 1 of 2)	885	NM_175483	235406	Mm.191459	NM_175483	ENSMUSG00000032733	Snx33	E130307J07Rik|Sh3px3	sorting nexin 33	protein-coding
mm_13787.1	chr2	118814196	118814235	+	1	NA	exon (NM_026412, exon 1 of 9)	exon (NM_026412, exon 1 of 9)	212	NM_026412	51944	Mm.252695	NM_026412	ENSMUSG00000027331	Knstrn	1700025D04Rik|C15orf23|D2Ertd750e|SKAP|Traf4af1	kinetochore-localized astrin/SPAG5 binding	protein-coding
mm_140875.1	chr17	23810007	23810053	-	1	NA	exon (NM_175229, exon 4 of 14)	exon (NM_175229, exon 4 of 14)	6843	NM_175229	75956	Mm.5222	NM_175229	ENSMUSG00000039218	Srrm2	5033413A03Rik|AA410130|SRm300|mKIAA0324	serine/arginine repetitive matrix 2	protein-coding
mm_95244.1	chr11	44617690	44617703	+	1	NA	promoter-TSS (NM_001290711)	promoter-TSS (NM_001290711)	-404	NM_001290711	13591	Mm.439662	NM_007897	ENSMUSG00000057098	Ebf1	Ebf|O/E-1|OE-1|Olf-1|Olf1	early B cell factor 1	protein-coding
mm_120556.1	chr14	68086689	68086697	+	1	NA	exon (NM_010910, exon 3 of 4)	exon (NM_010910, exon 3 of 4)	2809	NM_010910	18039	Mm.1956	NM_010910	ENSMUSG00000022055	Nefl	AI847934|CMT2E|NF-L|NF68|Nfl	neurofilament, light polypeptide	protein-coding
mm_35375.1	chr4	33072937	33072949	-	1	NA	intron (NM_008076, intron 2 of 8)	intron (NM_008076, intron 2 of 8)	9831	NM_008076	14409	Mm.6227	NM_008076	ENSMUSG00000023267	Gabrr2	-	gamma-aminobutyric acid (GABA) C receptor, subunit rho 2	protein-coding
mm_122121.1	chr14	31019056	31019069	-	1	NA	promoter-TSS (NM_001081251)	promoter-TSS (NM_001081251)	69	NM_153547	30877	Mm.88512	NM_153547	ENSMUSG00000042354	Gnl3	Ns	guanine nucleotide binding protein-like 3 (nucleolar)	protein-coding
mm_75455.1	chr8	47713921	47713938	-	1	NA	promoter-TSS (NM_172407)	promoter-TSS (NM_172407)	2	NM_172407	70925	Mm.393807	NM_172407	ENSMUSG00000038069	Cdkn2aip	4921511I16Rik|AW208986|CARF	CDKN2A interacting protein	protein-coding
mm_56286.1	chr6	91473362	91473470	-	1	NA	promoter-TSS (NM_133928)	promoter-TSS (NM_133928)	7	NM_133928	72170	Mm.41622	NM_133928	ENSMUSG00000034203	Chchd4	2410012P20Rik|2810014D17Rik|AI838740	coiled-coil-helix-coiled-coil-helix domain containing 4	protein-coding
mm_53091.1	chr6	125002848	125002888	+	1	NA	3' UTR (NM_001145926, exon 6 of 6)	3' UTR (NM_001145926, exon 6 of 6)	4258	NM_001145926	319352	Mm.295327	NM_175696	ENSMUSG00000030329	Pianp	AI255183|AU067746|C530028O21Rik|Panp	PILR alpha associated neural protein	protein-coding
mm_57619.1	chr6	128200599	128200635	-	1	NA	Intergenic	CpG	-16814	NR_077223	330427	Mm.426356	NR_077223	ENSMUSG00000107879	9330102E08Rik	-	RIKEN cDNA 9330102E08 gene	ncRNA
mm_16392.1	chr2	178964209	178964210	+	1	NA	Intergenic	Intergenic	-450727	NM_026596	68175	Mm.158187	NM_026596		4930591A17Rik	-	RIKEN cDNA 4930591A17 gene	protein-coding
mm_49028.1	chr6	4759675	4759695	+	1	NA	3' UTR (NM_130877, exon 2 of 2)	3' UTR (NM_130877, exon 2 of 2)	12379	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_57385.1	chr6	124819437	124819453	-	1	NA	exon (NM_001326594, exon 14 of 20)	exon (NM_001326594, exon 14 of 20)	-5149	NM_009415	21991	Mm.4222	NM_009415	ENSMUSG00000023456	Tpi1	AI255506|Tpi|Tpi-1	triosephosphate isomerase 1	protein-coding
mm_29552.1	chr3	116807783	116807789	-	1	NA	intron (NM_001081326, intron 1 of 33)	intron (NM_001081326, intron 1 of 33)	380	NM_001081326	77559	Mm.237099	NM_001081326	ENSMUSG00000033400	Agl	1110061O17Rik|9430004C13Rik|9630046L06Rik|AI850929|C77197	amylo-1,6-glucosidase, 4-alpha-glucanotransferase	protein-coding
mm_135855.1	chr16	59600980	59601059	-	1	NA	Intergenic	CpG	-35926	NR_040564	75145	Mm.399348	NR_040564		4930547E14Rik	-	RIKEN cDNA 4930547E14 gene	ncRNA
mm_56940.1	chr6	119926296	119926300	-	1	NA	3' UTR (NM_001185020, exon 26 of 26)	3' UTR (NM_001185020, exon 26 of 26)	23600	NM_001166381	19365	Mm.149	NM_011236	ENSMUSG00000030166	Rad52	Rad52yh	RAD52 homolog, DNA repair protein	protein-coding
mm_87327.1	chr10	42897868	42897888	+	1	NA	intron (NM_172938, intron 1 of 8)	intron (NM_172938, intron 1 of 8)	37366	NM_172938	268297	Mm.98731	NM_172938	ENSMUSG00000044770	Scml4	9330161D17|mFLJ00197	sex comb on midleg-like 4 (Drosophila)	protein-coding
mm_82586.1	chr9	21237175	21237208	-	1	NA	exon (NM_016679, exon 1 of 5)	exon (NM_016679, exon 1 of 5)	2141	NM_016679	50868	Mm.248266	NM_016679	ENSMUSG00000003308	Keap1	INRF2|mKIAA0132	kelch-like ECH-associated protein 1	protein-coding
mm_90772.1	chr10	5828021	5828034	-	1	NA	3' UTR (NM_019958, exon 5 of 5)	3' UTR (NM_019958, exon 5 of 5)	-4084	NM_175374	108853	Mm.55082	NM_175374	ENSMUSG00000019774	Mtrf1l	9130004K12Rik	mitochondrial translational release factor 1-like	protein-coding
mm_81140.1	chr9	106814145	106814156	+	1	NA	Intergenic	Intergenic	-7826	NM_001015507	321006	Mm.440089	NM_001015507	ENSMUSG00000040325	Vprbp	AI447437|B930007L02Rik|mKIAA0800	Vpr (HIV-1) binding protein	protein-coding
mm_93842.1	chr10	121626348	121626380	-	1	NA	promoter-TSS (NM_001081056)	promoter-TSS (NM_001081056)	-48	NM_001081056	73192	Mm.25042	NM_001081056	ENSMUSG00000034667	Xpot	1110004L07Rik|3110065H13Rik|AI452076|C79645|EXPORTIN-T	exportin, tRNA (nuclear export receptor for tRNAs)	protein-coding
mm_291.1	chr1	23256242	23256262	+	1	NA	Intergenic	CpG	-16017	NR_029533	387225		NR_029533	ENSMUSG00000065405	Mir30a	Mirn30a|mir-30a|mmu-mir-30a	microRNA 30a	ncRNA
mm_118383.1	chr13	117025933	117025963	-	1	NA	promoter-TSS (NM_001081009)	promoter-TSS (NM_001081009)	-432	NM_001081009	52552	Mm.274466	NM_027272	ENSMUSG00000021725	Parp8	2810430O08Rik|ARTD16|D13Ertd275e	poly (ADP-ribose) polymerase family, member 8	protein-coding
mm_134055.1	chr16	5949956	5949969	-	1	NA	intron (NM_021477, intron 1 of 16)	intron (NM_021477, intron 1 of 16)	-25625	NR_045799	68238	Mm.434605	NR_045799	ENSMUSG00000101481	1700123O21Rik	-	RIKEN cDNA 1700123O21 gene	ncRNA
mm_111644.1	chr12	102673593	102673601	-	1	NA	intron (NM_172584, intron 2 of 9)	intron (NM_172584, intron 2 of 9)	11423	NR_035457	100316812		NR_035457	ENSMUSG00000089324	Mir1936	mir-1936|mmu-mir-1936	microRNA 1936	ncRNA
mm_142153.1	chr17	36032517	36032562	-	1	NA	intron (NM_010398, intron 1 of 6)	intron (NM_010398, intron 1 of 6)	162	NM_010398	15040	Mm.439648	NM_010398	ENSMUSG00000067212	H2-T23	37b|37c|H-2T23|H2-Qa1|Qa-1|Qa-1(b)|Qa1|Qed-1|T18c|T18c(37)|T23b|T23d	histocompatibility 2, T region locus 23	protein-coding
mm_78852.1	chr9	44335596	44335609	+	1	NA	TTS (NM_001110251)	TTS (NM_001110251)	887	NM_010436	15270	Mm.245931	NM_010436	ENSMUSG00000049932	H2afx	AW228881|H2A.X|H2ax|Hist5-2ax|gammaH2ax	H2A histone family, member X	protein-coding
mm_23734.1	chr3	69030247	69030303	+	1	NA	exon (NM_133786, exon 18 of 24)	exon (NM_133786, exon 18 of 24)	14467	NM_025863	66949	Mm.176695	NM_025863	ENSMUSG00000034317	Trim59	2310035M22Rik|2700022F13Rik|Mrf1|TSBF1	tripartite motif-containing 59	protein-coding
mm_113732.1	chr13	44121295	44121322	+	1	NA	non-coding (NR_045285, exon 1 of 5)	non-coding (NR_045285, exon 1 of 5)	141	NR_045285	328235	Mm.188356	NR_045285	ENSMUSG00000089815	Gm5083	A730030A06	predicted gene 5083	ncRNA
mm_130131.1	chr15	90678519	90678524	-	1	NA	intron (NM_001033851, intron 1 of 3)	intron (NM_001033851, intron 1 of 3)	867	NM_025815	66871	Mm.290991	NM_025815	ENSMUSG00000052560	Cpne8	1200003E11Rik|1500031E20Rik	copine VIII	protein-coding
mm_33553.1	chr4	130935493	130935513	+	1	NA	3' UTR (NM_010686, exon 8 of 8)	3' UTR (NM_010686, exon 8 of 8)	-8882	NM_010769	17180	Mm.271796	NM_010769	ENSMUSG00000040533	Matn1	CMP|Crtm|Mat1|matrilin-1	matrilin 1, cartilage matrix protein	protein-coding
mm_152891.1	chr19	24861829	24861844	-	1	NA	promoter-TSS (NM_175013)	promoter-TSS (NM_175013)	6	NM_175013	226041	Mm.105222	NM_175013	ENSMUSG00000041731	Pgm5	4833423B07|9530034F03Rik|D830025G17|aciculin	phosphoglucomutase 5	protein-coding
mm_19230.1	chr2	84678052	84678083	-	1	NA	promoter-TSS (NM_025885)	promoter-TSS (NM_025885)	107	NM_001290751	66958	Mm.371621	NM_025868	ENSMUSG00000050043	Tmx2	2310042M24Rik|AA589631|Txndc14	thioredoxin-related transmembrane protein 2	protein-coding
mm_138352.1	chr17	34972688	34972705	+	1	NA	promoter-TSS (NM_013558)	promoter-TSS (NM_013558)	-7	NM_013558	15482	Mm.14287	NM_013558	ENSMUSG00000007033	Hspa1l	Hsc70t|Msh5	heat shock protein 1-like	protein-coding
mm_113566.1	chr13	38320619	38320628	+	1	NA	Intergenic	Intergenic	-25093	NM_007556	12161	Mm.385759	NM_007556	ENSMUSG00000039004	Bmp6	D13Wsu115e|Vgr1	bone morphogenetic protein 6	protein-coding
mm_23754.1	chr3	69740164	69740167	+	1	NA	intron (NM_133787, intron 10 of 15)	ID_B1|SINE|B4	18110	NM_133787	97112	Mm.21062	NM_133787	ENSMUSG00000027787	Nmd3	C87860	NMD3 ribosome export adaptor	protein-coding
mm_44179.1	chr5	151252423	151252432	+	1	NA	Intergenic	Intergenic	-62234	NM_146258	243362	Mm.209272	NM_146258	ENSMUSG00000016128	Stard13	DLC2|GT650	StAR-related lipid transfer (START) domain containing 13	protein-coding
mm_160375.1	chr8	40287019	40287019	-	1	NA	promoter-TSS (NM_030610)	promoter-TSS (NM_030610)	-66	NM_030610	80857	Mm.425526	NM_030610	ENSMUSG00000031603	Fgf20	-	fibroblast growth factor 20	protein-coding
mm_86450.1	chr10	4320700	4320703	+	1	NA	intron (NM_031185, intron 2 of 3)	intron (NM_031185, intron 2 of 3)	54372	NM_031185	83397	Mm.27481	NM_031185	ENSMUSG00000038587	Akap12	AI317366|SSeCKS|Srcs5|Tsga12	A kinase (PRKA) anchor protein (gravin) 12	protein-coding
mm_154379.1	chrM	11242	11283	+	1	NA	NA	Intergenic	NA	NA								
mm_6778.1	chr1	84137468	84137478	-	1	NA	intron (NM_001003948, intron 2 of 2)	Lx7|LINE|L1	81488	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_49636.1	chr6	30805032	30805044	+	1	NA	intron (NM_017478, intron 20 of 23)	intron (NM_017478, intron 20 of 23)	63739	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_33071.1	chr4	123664809	123664832	+	1	NA	intron (NM_001199136, intron 1 of 97)	CpG	-1061	NR_136925	102633214	Mm.399387	NR_136925		Gm12925	OTTMUSG00000009214	predicted gene 12925	ncRNA
mm_26626.1	chr3	152785439	152785457	+	1	NA	exon (NM_025662, exon 11 of 11)	exon (NM_025662, exon 11 of 11)	71348	NM_025662	329777	Mm.331447	NM_025662	ENSMUSG00000039047	Pigk	3000001O05Rik	phosphatidylinositol glycan anchor biosynthesis, class K	protein-coding
mm_58367.1	chr6	148831449	148831494	-	1	NA	promoter-TSS (NM_001081113)	promoter-TSS (NM_001081113)	-4	NM_001081113	320727	Mm.260105	NM_001081113	ENSMUSG00000040029	Ipo8	6230418K12Rik|Abcc10|C130009K11Rik|MRP7|OM-1|Om1|Ranbp8	importin 8	protein-coding
mm_54664.1	chr6	39206632	39206662	-	1	NA	5' UTR (NM_001033430, exon 1 of 20)	5' UTR (NM_001033430, exon 1 of 20)	126	NM_001033430	338523	Mm.293175	NM_001033430	ENSMUSG00000042599	Kdm7a	A630082K20Rik|BB041802|ENSMUSG00000073143|Jhdm1d|mKIAA1718	lysine (K)-specific demethylase 7A	protein-coding
mm_46678.1	chr5	109555557	109555584	-	1	NA	exon (NM_001164735, exon 6 of 8)	exon (NM_001164735, exon 6 of 8)	3423	NM_016715	57914	Mm.35771	NM_016715	ENSMUSG00000033467	Crlf2	CRLM2|Ly114|Tpte2|Tslpr	cytokine receptor-like factor 2	protein-coding
mm_140339.1	chr17	86809712	86809740	+	1	NA	exon (NM_010137, exon 6 of 16)	exon (NM_010137, exon 6 of 16)	55862	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_137970.1	chr17	33556366	33556378	+	1	NA	intron (NM_053214, intron 1 of 27)	ID4_|SINE|ID	665	NM_053214	17916	Mm.42019	NM_053214	ENSMUSG00000024300	Myo1f	C330006B10Rik	myosin IF	protein-coding
mm_86456.1	chr10	4347763	4347796	+	1	NA	intron (NM_031185, intron 2 of 3)	intron (NM_031185, intron 2 of 3)	40329	NM_001033466	381990	Mm.262466	NM_001033466	ENSMUSG00000075327	Zbtb2	Gm1103	zinc finger and BTB domain containing 2	protein-coding
mm_138102.1	chr17	34092850	34092858	+	1	NA	intron (NR_046183, intron 2 of 4)	intron (NR_046183, intron 2 of 4)	475	NM_008206	15001	Mm.116	NM_008206	ENSMUSG00000024334	H2-Oa	H-2Oa	histocompatibility 2, O region alpha locus	protein-coding
mm_96032.1	chr11	59555918	59555922	+	1	NA	intron (NM_145827, intron 6 of 9)	intron (NM_145827, intron 6 of 9)	13234	NM_145827	216799	Mm.54174	NM_145827	ENSMUSG00000032691	Nlrp3	AGTAVPRL|AII/AVP|Cias1|FCAS|FCU|MWS|Mmig1|NALP3|Pypaf1	NLR family, pyrin domain containing 3	protein-coding
mm_84638.1	chr9	71163354	71163364	-	1	NA	promoter-TSS (NM_001271843)	promoter-TSS (NM_001271843)	-70	NM_022026	64008	Mm.449427	NM_022026	ENSMUSG00000032204	Aqp9	1700020I22Rik|AI266899|AQP-9	aquaporin 9	protein-coding
mm_15194.1	chr2	154204778	154204786	+	1	NA	exon (NM_153418, exon 3 of 16)	exon (NM_153418, exon 3 of 16)	4402	NM_153418	228801	Mm.3783	NM_153418	ENSMUSG00000027485	Bpifb1	Lplunc1	BPI fold containing family B, member 1	protein-coding
mm_142062.1	chr17	35673676	35673700	-	1	NA	promoter-TSS (NM_010364)	promoter-TSS (NM_010364)	55	NM_010364	14885	Mm.10182	NM_010364	ENSMUSG00000001524	Gtf2h4	AW545633|BTF2 p52|p52	general transcription factor II H, polypeptide 4	protein-coding
mm_69642.1	chr7	138885978	138885982	-	1	NA	Intergenic	B1_Mur2|SINE|Alu	23526	NM_009760	12176	Mm.378890	NM_009760	ENSMUSG00000078566	Bnip3	Nip3	BCL2/adenovirus E1B interacting protein 3	protein-coding
mm_50880.1	chr6	55681209	55681239	+	1	NA	promoter-TSS (NM_009717)	promoter-TSS (NM_009717)	39	NM_009717	11922	Mm.5106	NM_009717	ENSMUSG00000037984	Neurod6	Atoh2|Math-2|Math2|Nex|Nex1m|bHLHa2	neurogenic differentiation 6	protein-coding
mm_155129.1	chrX	49470533	49470548	+	1	NA	promoter-TSS (NM_001081123)	promoter-TSS (NM_001081123)	90	NM_001081123	75404	Mm.44305	NM_001081123	ENSMUSG00000036198	Arhgap36	1100001E04Rik|rho-gap	Rho GTPase activating protein 36	protein-coding
mm_149470.1	chr19	11603167	11603197	+	1	NA	exon (NM_026835, exon 2 of 7)	exon (NM_026835, exon 2 of 7)	1622	NM_026835	68774	Mm.290390	NM_026835	ENSMUSG00000024679	Ms4a6d	1110058E16Rik|AI447446|Ms4a11	membrane-spanning 4-domains, subfamily A, member 6D	protein-coding
mm_6478.1	chr1	74070160	74070172	-	1	NA	intron (NM_027884, intron 2 of 34)	RMER1A|Other|Other	54281	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_119445.1	chr14	46832211	46832274	+	1	NA	promoter-TSS (NM_026832)	promoter-TSS (NM_026832)	-2	NM_026832	68755	Mm.343809	NM_026832	ENSMUSG00000055128	Cgrrf1	1110038G02Rik|1810009H17Rik|CGR19	cell growth regulator with ring finger domain 1	protein-coding
mm_30986.1	chr4	34905150	34905158	+	1	NA	exon (NM_009889, exon 3 of 4)	exon (NM_009889, exon 3 of 4)	6327	NR_040652	73696	Mm.1361	NR_040652	ENSMUSG00000085824	Platr9	2410114N07Rik	pluripotency associated transcript 9	ncRNA
mm_19597.1	chr2	102400406	102400420	-	1	NA	exon (NM_020267, exon 1 of 5)	exon (NM_020267, exon 1 of 5)	487	NM_020267	80985	Mm.315002	NM_020267	ENSMUSG00000027189	Trim44	Dipb|Mc7	tripartite motif-containing 44	protein-coding
mm_126905.1	chr15	89573906	89573915	+	1	NA	exon (NM_013455, exon 5 of 5)	exon (NM_013455, exon 5 of 5)	5584	NM_001277246	11434	Mm.57	NM_013455	ENSMUSG00000022622	Acr	-	acrosin prepropeptide	protein-coding
mm_132672.1	chr16	42907442	42907478	+	1	NA	promoter-TSS (NM_001285805)	promoter-TSS (NM_001285805)	-185	NM_001285805	56490	Mm.136238	NM_019778	ENSMUSG00000022708	Zbtb20	1300017A20Rik|7330412A13Rik|A930017C21Rik|D16Wsu73e|DPZF|HOF|ODA-8S|Oda8|Zfp288	zinc finger and BTB domain containing 20	protein-coding
mm_115755.1	chr13	19192738	19192749	-	1	NA	Intergenic	Intergenic	203070	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_21355.1	chr2	157123365	157123429	-	1	NA	exon (NM_001139520, exon 4 of 17)	exon (NM_001139520, exon 4 of 17)	11825	NM_001139520	56045	Mm.248478	NM_018851	ENSMUSG00000027639	Samhd1	E330031J07Rik|Mg11	SAM domain and HD domain, 1	protein-coding
mm_10775.1	chr2	24305086	24305101	+	1	NA	Intergenic	Intergenic	13897	NM_153077	215274	Mm.218750	NM_153077	ENSMUSG00000046845	Il1f10	-	interleukin 1 family, member 10	protein-coding
mm_62660.1	chr7	107862961	107862967	+	1	NA	Intergenic	Intergenic	-17233	NM_146425	258417	Mm.377488	NM_146425	ENSMUSG00000109542	Olfr470	MOR204-22	olfactory receptor 470	protein-coding
mm_110583.1	chr12	56529378	56529386	-	1	NA	promoter-TSS (NR_045082)	promoter-TSS (NR_045082)	38	NR_045082	104798	Mm.310950	NR_045082		E030019B13Rik	AI413669	RIKEN cDNA E030019B13 gene	ncRNA
mm_71786.1	chr8	66697405	66697428	+	1	NA	promoter-TSS (NM_010934)	promoter-TSS (NM_010934)	-6	NM_010934	18166	Mm.5112	NM_010934	ENSMUSG00000036437	Npy1r	Npyr|Y1-R	neuropeptide Y receptor Y1	protein-coding
mm_11848.1	chr2	45201603	45201636	+	1	NA	Intergenic	B1_Mur4|SINE|Alu	-88340	NM_015753	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_125095.1	chr15	27571399	27571417	+	1	NA	promoter-TSS (NR_106065)	promoter-TSS (NR_106065)	-86	NR_106065	102466808		NR_106065	ENSMUSG00000098416	Mir7117	Gm27729|mmu-mir-7117	microRNA 7117	ncRNA
mm_172412.1	chr7	19707262	19707262	-	1	NA	intron (NM_016871, intron 6 of 9)	B1_Mus1|SINE|Alu	-8074	NM_009696	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_10374.1	chr2	11725096	11725108	+	1	NA	intron (NR_073191, intron 4 of 5)	B3A|SINE|B2	19390	NM_001271500	16169	Mm.200196	NM_008358	ENSMUSG00000023206	Il15ra	AA690181|IL-15RA	interleukin 15 receptor, alpha chain	protein-coding
mm_103778.1	chr11	82764228	82764240	-	1	NA	promoter-TSS (NM_025884)	promoter-TSS (NM_025884)	87	NM_009839	12467	Mm.4126	NM_009839	ENSMUSG00000020698	Cct6b	CCT-zeta-2|CCTzeta-2|Cctz-2|TCP-1-zeta-2	chaperonin containing Tcp1, subunit 6b (zeta)	protein-coding
mm_170220.1	chr17	78736590	78736598	-	1	NA	promoter-TSS (NM_011500)	promoter-TSS (NM_011500)	-34	NM_011500	268980	Mm.311915	NM_011500	ENSMUSG00000024077	Strn	AU022939|D130055P19	striatin, calmodulin binding protein	protein-coding
mm_143533.1	chr17	73936567	73936576	-	1	NA	intron (NM_011723, intron 4 of 35)	intron (NM_011723, intron 4 of 35)	13625	NM_011723	22436	Mm.11223	NM_011723	ENSMUSG00000024066	Xdh	XO|Xor|Xox-1|Xox1	xanthine dehydrogenase	protein-coding
mm_9718.1	chr1	179803626	179803702	-	1	NA	5' UTR (NM_026375, exon 1 of 36)	5' UTR (NM_026375, exon 1 of 36)	351	NM_026375	226747	Mm.128165	NM_026375	ENSMUSG00000026491	Ahctf1	6230412P20Rik|AV011447|Elys	AT hook containing transcription factor 1	protein-coding
mm_78447.1	chr9	32224286	32224292	+	1	NA	promoter-TSS (NM_177379)	promoter-TSS (NM_177379)	40	NM_177379	330914	Mm.46683	NM_177379	ENSMUSG00000041444	Arhgap32	3426406O18Rik|Gc-gap|Grit|Px-rics|Rics|mKIAA0712|p200Rhogap|p250Gap	Rho GTPase activating protein 32	protein-coding
mm_84645.1	chr9	71485501	71485570	-	1	NA	promoter-TSS (NM_001164793)	promoter-TSS (NM_001164793)	448	NM_178602	28015	Mm.21094	NM_178602	ENSMUSG00000032199	Polr2m	AA407243|AA408799|AI303746|AW553238|D9Wsu138e|Grinl1a|mKIAA4185	polymerase (RNA) II (DNA directed) polypeptide M	protein-coding
mm_150991.1	chr19	46595124	46595126	+	1	NA	3' UTR (NM_053196, exon 12 of 12)	3' UTR (NM_053196, exon 12 of 12)	-3981	NM_001177812	226178	Mm.329895	NM_146099	ENSMUSG00000047731	Wbp1l	D19Wsu162e|Opal1	WW domain binding protein 1 like	protein-coding
mm_146177.1	chr18	75368513	75368516	+	1	NA	5' UTR (NM_001042660, exon 1 of 4)	5' UTR (NM_001042660, exon 1 of 4)	1149	NM_001042660	17131	Mm.34407	NM_008543	ENSMUSG00000025880	Smad7	Madh7	SMAD family member 7	protein-coding
mm_12986.1	chr2	90847540	90847550	+	1	NA	intron (NM_001317242, intron 1 of 12)	CpG	390	NM_001317242	56428	Mm.28023	NM_019758	ENSMUSG00000027282	Mtch2	2310034D24Rik|4930539J07Rik|HSPC032	mitochondrial carrier 2	protein-coding
mm_103159.1	chr11	70454463	70454473	-	1	NA	TTS (NM_025397)	TTS (NM_025397)	2537	NM_025397	66172	Mm.46424	NM_025397	ENSMUSG00000018923	Med11	1110030J09Rik|AI465144|AW545069	mediator complex subunit 11	protein-coding
mm_118033.1	chr13	101692111	101692114	-	1	NA	intron (NM_001077495, intron 7 of 15)	intron (NM_001077495, intron 7 of 15)	518	NM_001024955	18708	Mm.259333	NM_001024955	ENSMUSG00000041417	Pik3r1	PI3K|p50alpha|p55alpha|p85alpha	phosphatidylinositol 3-kinase, regulatory subunit, polypeptide 1 (p85 alpha)	protein-coding
mm_169108.1	chr13	44869816	44869821	-	1	NA	intron (NM_001205044, intron 4 of 18)	LSU-rRNA_Hsa|rRNA|rRNA	132278	NM_025772	94245	Mm.352311	NM_025772	ENSMUSG00000057531	Dtnbp1	5430437B18Rik|AW048963|Bloc1s8|dysbindin|sdy	dystrobrevin binding protein 1	protein-coding
mm_57456.1	chr6	125166464	125166499	-	1	NA	promoter-TSS (NM_008084)	promoter-TSS (NM_008084)	-14	NM_001289726	14433	Mm.304088	NM_008084	ENSMUSG00000057666	Gapdh	Gapd	glyceraldehyde-3-phosphate dehydrogenase	protein-coding
mm_36661.1	chr4	95049827	95049841	-	1	NA	3' UTR (NM_010591, exon 1 of 1)	3' UTR (NM_010591, exon 1 of 1)	2388	NM_010591	16476	Mm.275071	NM_010591	ENSMUSG00000052684	Jun	AP-1|Junc|c-jun	jun proto-oncogene	protein-coding
mm_129251.1	chr15	76669833	76669851	-	1	NA	exon (NM_007989, exon 1 of 3)	exon (NM_007989, exon 1 of 3)	106	NM_007989	14106	Mm.42011	NM_007989	ENSMUSG00000033837	Foxh1	Fast1|Fast2|fast-1|fast-2	forkhead box H1	protein-coding
mm_88435.1	chr10	77530608	77530617	+	1	NA	intron (NM_008404, intron 1 of 15)	intron (NM_008404, intron 1 of 15)	264	NM_008404	16414	Mm.1137	NM_008404	ENSMUSG00000000290	Itgb2	2E6|AI528527|Cd18|LAD|LCAMB|Lfa1|MF17	integrin beta 2	protein-coding
mm_99493.1	chr11	102835906	102835959	+	1	NA	promoter-TSS (NM_080846)	promoter-TSS (NM_080846)	-364	NM_080846	75689	Mm.44408	NM_080846	ENSMUSG00000020928	Higd1b	2310056K19Rik	HIG1 domain family, member 1B	protein-coding
mm_170592.1	chr19	5802152	5802155	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	519	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_141095.1	chr17	26004714	26004752	-	1	NA	intron (NM_153140, intron 4 of 11)	intron (NM_153140, intron 4 of 11)	17127	NM_153140	215445	Mm.41191	NM_153140	ENSMUSG00000037098	Rab11fip3	Cart1|D030060O14Rik|Rab11-FIP3|mKIAA0665	RAB11 family interacting protein 3 (class II)	protein-coding
mm_162106.1	chrX	48591945	48591945	-	1	NA	promoter-TSS (NM_001166650)	promoter-TSS (NM_001166650)	-184	NM_001166650	208968	Mm.293819	NM_153532	ENSMUSG00000036916	Zfp280c	BC028839|Suhw3|Zfp633|Znf280c|mKIAA1584	zinc finger protein 280C	protein-coding
mm_77211.1	chr8	114090761	114090766	-	1	NA	Intergenic	Intergenic	-42811	NM_024446	67528	Mm.27889	NM_024437	ENSMUSG00000031767	Nudt7	1300007B24Rik|2210404C19Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 7	protein-coding
mm_991.1	chr1	58711463	58711473	+	1	NA	promoter-TSS (NM_001289704)	promoter-TSS (NM_001289704)	-23	NM_001289704	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_57880.1	chr6	131293158	131293168	-	1	NA	promoter-TSS (NM_025564)	promoter-TSS (NM_025564)	81	NM_001327860	66441	Mm.46623	NM_025564	ENSMUSG00000030188	Magohb	2010012C16Rik|Mago|Magoh|Magoh-rs1	mago homolog B, exon junction complex core component	protein-coding
mm_140035.1	chr17	74338944	74338953	+	1	NA	promoter-TSS (NM_001162870)	promoter-TSS (NM_001162870)	-39	NM_001162870	50850	Mm.19804	NM_016962	ENSMUSG00000024068	Spast	Spg4|mKIAA1083	spastin	protein-coding
mm_144976.1	chr18	37955529	37955537	+	1	NA	promoter-TSS (NM_010411)	promoter-TSS (NM_010411)	-26	NM_153793	225392	Mm.233516	NM_153793	ENSMUSG00000044024	Rell2	4631403P03Rik|ependolin	RELT-like 2	protein-coding
mm_138311.1	chr17	34647650	34647679	+	1	NA	exon (NM_017406, exon 2 of 18)	exon (NM_017406, exon 2 of 18)	518	NM_017406	12915	Mm.4068	NM_017406	ENSMUSG00000015461	Atf6b	AA617266|ATF6beta|Creb-rp|Crebl1	activating transcription factor 6 beta	protein-coding
mm_95522.1	chr11	52122418	52122432	+	1	NA	3' UTR (NM_019411, exon 7 of 7)	3' UTR (NM_019411, exon 7 of 7)	-4321	NR_037221	100526467		NR_037221	ENSMUSG00000092870	Mir3061	mir-3061|mmu-mir-3061	microRNA 3061	ncRNA
mm_103468.1	chr11	76479117	76479127	-	1	NA	exon (NM_198018, exon 3 of 22)	exon (NM_198018, exon 3 of 22)	-10657	NM_001291186	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_84851.1	chr9	78480737	78480782	-	1	NA	intron (NM_010106, intron 1 of 7)	intron (NM_010106, intron 1 of 7)	965	NM_010106	13627	Mm.138471	NM_010106	ENSMUSG00000037742	Eef1a1	-	eukaryotic translation elongation factor 1 alpha 1	protein-coding
mm_88149.1	chr10	69534026	69534038	+	1	NA	5' UTR (NM_170688, exon 1 of 43)	5' UTR (NM_170688, exon 1 of 43)	324	NM_146005	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_70333.1	chr8	4493476	4493491	+	1	NA	promoter-TSS (NM_026058)	promoter-TSS (NM_026058)	78	NM_026058	67260	Mm.35511	NM_026058	ENSMUSG00000008206	Cers4	2900019C14Rik|Lass4|Trh1	ceramide synthase 4	protein-coding
mm_58335.1	chr6	146634528	146634580	-	1	NA	promoter-TSS (NM_026281)	promoter-TSS (NM_026281)	38	NM_026281	67623	Mm.278037	NM_026281	ENSMUSG00000040234	Tm7sf3	2010003B14Rik|NARP1	transmembrane 7 superfamily member 3	protein-coding
mm_136650.1	chr17	5898102	5898105	+	1	NA	intron (NM_025664, intron 4 of 17)	intron (NM_025664, intron 4 of 17)	-43177	NM_001113353	20975	Mm.236068	NM_011523	ENSMUSG00000023805	Synj2	AI481647|SJ2|mKIAA0348	synaptojanin 2	protein-coding
mm_126015.1	chr15	76660329	76660361	+	1	NA	promoter-TSS (NM_019396)	promoter-TSS (NM_019396)	-137	NM_019396	54151	Mm.247752	NM_019396	ENSMUSG00000053929	Cyhr1	1110031M01Rik|AU042374|Chrp	cysteine and histidine rich 1	protein-coding
mm_19626.1	chr2	102813572	102813585	-	1	NA	3' UTR (NM_009851, exon 19 of 19)	3' UTR (NM_009851, exon 19 of 19)	88087	NM_001177785	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_64520.1	chr7	143841221	143841235	+	1	NA	exon (NM_007856, exon 6 of 9)	exon (NM_007856, exon 6 of 9)	18061	NM_007856	13360	Mm.249342	NM_007856	ENSMUSG00000058454	Dhcr7	AA409147	7-dehydrocholesterol reductase	protein-coding
mm_69969.1	chr7	142376892	142376915	-	1	NA	exon (NM_009983, exon 8 of 9)	exon (NM_009983, exon 8 of 9)	-3157	NM_001347541	320802	Mm.154486	NM_177265	ENSMUSG00000045777	Ifitm10	6330512M04Rik|AI848576|DSPA3	interferon induced transmembrane protein 10	protein-coding
mm_35342.1	chr4	32239954	32239964	-	1	NA	Intergenic	CpG	-177476	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_60680.1	chr7	45128983	45129005	+	1	NA	promoter-TSS (NM_009438)	promoter-TSS (NM_009438)	-249	NM_009438	22121	Mm.180458	NM_009438	ENSMUSG00000074129	Rpl13a	1810026N22Rik|Tstap198-7|tum-antigen	ribosomal protein L13A	protein-coding
mm_149690.1	chr19	21271829	21271848	+	1	NA	promoter-TSS (NM_009551)	promoter-TSS (NM_009551)	-440	NM_009551	22682	Mm.292405	NM_009551	ENSMUSG00000024750	Zfand5	2310057A04Rik|5830475F03Rik|AA415485|Za20d2|Zfp216	zinc finger, AN1-type domain 5	protein-coding
mm_166859.1	chr7	24435583	24435585	-	1	NA	intron (NM_199013, intron 2 of 2)	intron (NM_199013, intron 2 of 2)	10098	NM_199013	210145	Mm.33811	NM_199013	ENSMUSG00000062028	Irgc1	F630044M05Rik|Gm1102|Gm474|Ifgge|Iigp5|Irgc	immunity-related GTPase family, cinema 1	protein-coding
mm_125112.1	chr15	28081469	28081473	+	1	NA	Intergenic	Intergenic	-55623	NM_001081302	223435	Mm.485422	NM_001081302	ENSMUSG00000022263	Trio	6720464I07Rik|AA408740|Solo	triple functional domain (PTPRF interacting)	protein-coding
mm_151634.1	chr19	3930803	3930814	-	1	NA	Intergenic	Intergenic	-1092	NM_026316	67689	Mm.109341	NM_026316	ENSMUSG00000024885	Aldh3b1	1700001N19Rik|ALDH4|ALDH7	aldehyde dehydrogenase 3 family, member B1	protein-coding
mm_44702.1	chr5	30588739	30588751	-	1	NA	promoter-TSS (NR_040427)	promoter-TSS (NR_040427)	-126	NR_040427	100502829	Mm.39944	NR_040427	ENSMUSG00000053214	Gm9899	ENSMUSG00000053214	predicted gene 9899	ncRNA
mm_119337.1	chr14	40557169	40557170	+	1	NA	Intergenic	Intergenic	335796	NM_177816	328381	Mm.235694	NM_177816	ENSMUSG00000037833	Sh2d4b	A430109M18Rik|D030001E08	SH2 domain containing 4B	protein-coding
mm_64937.1	chr7	16309379	16309390	-	1	NA	promoter-TSS (NM_133234)	promoter-TSS (NM_133234)	-199	NM_133234	170770	Mm.7660	NM_133234	ENSMUSG00000002083	Bbc3	PUMA|PUMA/JFY1	BCL2 binding component 3	protein-coding
mm_149321.1	chr19	10842509	10842524	+	1	NA	promoter-TSS (NM_023044)	promoter-TSS (NM_023044)	-28	NM_023044	65221	Mm.27387	NM_023044	ENSMUSG00000024737	Slc15a3	Ci1|cI-1	solute carrier family 15, member 3	protein-coding
mm_55595.1	chr6	71632652	71632694	-	1	NA	promoter-TSS (NM_173001)	promoter-TSS (NM_173001)	13	NM_173001	104263	Mm.260479	NM_173001	ENSMUSG00000053470	Kdm3a	1700105C21Rik|C230043E16Rik|JHDM2a|Jmjd1|Jmjd1a|KDM2A|TGSA|Tsga	lysine (K)-specific demethylase 3A	protein-coding
mm_102511.1	chr11	60777242	60777284	-	1	NA	promoter-TSS (NM_001085440)	promoter-TSS (NM_001085440)	102	NM_009410	21975	Mm.10708	NM_009410	ENSMUSG00000002814	Top3a	-	topoisomerase (DNA) III alpha	protein-coding
mm_88164.1	chr10	69706467	69706493	+	1	NA	intron (NM_170730, intron 1 of 17)	intron (NM_170730, intron 1 of 17)	172772	NM_146005	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_51052.1	chr6	65631316	65631345	+	1	NA	3' UTR (NM_001001495, exon 8 of 8)	3' UTR (NM_001001495, exon 8 of 8)	-40281	NM_172399	68169	Mm.52392	NM_172399	ENSMUSG00000049001	Ndnf	A930038C07Rik|epidermacan	neuron-derived neurotrophic factor	protein-coding
mm_40635.1	chr5	64899056	64899066	+	1	NA	Intergenic	Intergenic	33638	NM_030682	21897	Mm.273024	NM_030682	ENSMUSG00000044827	Tlr1	-	toll-like receptor 1	protein-coding
mm_114882.1	chr13	94223605	94223615	+	1	NA	intron (NM_001346609, intron 6 of 8)	L1MC|LINE|L1	61671	NM_029153	107767	Mm.201455	NM_029153	ENSMUSG00000021687	Scamp1	4930505M11Rik|AI415563|AW122395	secretory carrier membrane protein 1	protein-coding
mm_16139.1	chr2	170731878	170731920	+	1	NA	promoter-TSS (NM_029761)	promoter-TSS (NM_029761)	92	NM_001163686	76829	Mm.41633	NM_029761	ENSMUSG00000027560	Dok5	2700055C10Rik	docking protein 5	protein-coding
mm_80118.1	chr9	70543213	70543226	+	1	NA	intron (NM_026337, intron 1 of 20)	CpG	349	NM_025690	66660	Mm.22379	NM_025690	ENSMUSG00000032212	Sltm	5730455C01Rik|5730555F13Rik|9130215G10Rik|Met	SAFB-like, transcription modulator	protein-coding
mm_151811.1	chr19	5488272	5488396	-	1	NA	promoter-TSS (NM_027877)	promoter-TSS (NM_027877)	2	NM_027877	71711	Mm.27697	NM_027877	ENSMUSG00000024906	Mus81	1200008A18Rik|AI182501|AW045863	MUS81 structure-specific endonuclease subunit	protein-coding
mm_19968.1	chr2	118008051	118008069	-	1	NA	intron (NR_126479, intron 8 of 9)	intron (NR_126479, intron 8 of 9)	103142	NR_126479	329496	Mm.235844	NR_126479	ENSMUSG00000087203	Gm13986	C230060E24|OTTMUSG00000015236	predicted gene 13986	ncRNA
mm_79941.1	chr9	65909091	65909101	+	1	NA	promoter-TSS (NM_019797)	promoter-TSS (NM_019797)	86	NM_173185	214897	Mm.325816	NM_173185	ENSMUSG00000032384	Csnk1g1	9130020E21Rik	casein kinase 1, gamma 1	protein-coding
mm_112883.1	chr13	20858343	20858360	+	1	NA	intron (NM_012054, intron 4 of 20)	L1Md_F2|LINE|L1	64238	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_115214.1	chr13	109441135	109441145	+	1	NA	intron (NM_011056, intron 3 of 16)	intron (NM_011056, intron 3 of 16)	116396	NR_030644	100124489		NR_030644	ENSMUSG00000076946	Mir582	Mirn582|mir-582|mmu-mir-582	microRNA 582	ncRNA
mm_119941.1	chr14	54983367	54983376	+	1	NA	exon (NM_080728, exon 25 of 41)	exon (NM_080728, exon 25 of 41)	-7595	NR_030607	100124433		NR_030607	ENSMUSG00000077928	Mir208b	Mirn208b|mir-208b	microRNA 208b	ncRNA
mm_79743.1	chr9	62366916	62366934	+	1	NA	intron (NM_009672, intron 1 of 6)	intron (NM_009672, intron 1 of 6)	25582	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	protein-coding
mm_122262.1	chr14	34275346	34275348	-	1	NA	intron (NM_029389, intron 2 of 10)	intron (NM_029389, intron 2 of 10)	35156	NM_029389	75698	Mm.45406	NM_029389	ENSMUSG00000041471	Fam35a	3110001K24Rik	family with sequence similarity 35, member A	protein-coding
mm_14829.1	chr2	147046970	147046973	+	1	NA	intron (NM_011917, intron 20 of 29)	intron (NM_011917, intron 20 of 29)	33911	NM_011917	24128	Mm.3065	NM_011917	ENSMUSG00000027433	Xrn2	-	5'-3' exoribonuclease 2	protein-coding
mm_126589.1	chr15	82346009	82346035	+	1	NA	promoter-TSS (NM_026914)	promoter-TSS (NM_026914)	-24	NM_026914	69029	Mm.260042	NM_026914	ENSMUSG00000022452	Smdt1	1500032L24Rik|Emre	single-pass membrane protein with aspartate rich tail 1	protein-coding
mm_57130.1	chr6	122602346	122602400	-	1	NA	promoter-TSS (NM_031159)	promoter-TSS (NM_031159)	71	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_47414.1	chr5	123137719	123137740	-	1	NA	Intergenic	Intergenic	-4464	NM_001040398	208043	Mm.250391	NM_177581	ENSMUSG00000038384	Setd1b	AA516740|BC035291|KMT2G|mKIAA1076	SET domain containing 1B	protein-coding
mm_130807.1	chr15	101712638	101712649	-	1	NA	exon (NM_027011, exon 1 of 9)	exon (NM_027011, exon 1 of 9)	248	NM_027011	110308	Mm.451847	NM_027011	ENSMUSG00000061527	Krt5	3300001P10Rik|AW146334|CK5|K5|Krt2-5|Tfip8	keratin 5	protein-coding
mm_66589.1	chr7	45406971	45406984	-	1	NA	exon (NM_010596, exon 1 of 2)	exon (NM_010596, exon 1 of 2)	1017	NM_010596	16495	Mm.12955	NM_010596	ENSMUSG00000038201	Kcna7	Kv1.7	potassium voltage-gated channel, shaker-related subfamily, member 7	protein-coding
mm_163617.1	chr13	54991435	54991435	+	1	NA	intron (NM_001311128, intron 2 of 14)	intron (NM_001311128, intron 2 of 14)	29384	NM_001206390	212032	Mm.267479	NM_001033245	ENSMUSG00000025877	Hk3	HK III|HK-III	hexokinase 3	protein-coding
mm_147026.1	chr18	34651746	34651759	-	1	NA	promoter-TSS (NM_178347)	promoter-TSS (NM_178347)	-16	NM_178347	52563	Mm.196638	NM_178347	ENSMUSG00000024370	Cdc23	6030435O18|D18Ertd243e	CDC23 cell division cycle 23	protein-coding
mm_15504.1	chr2	158028688	158028729	+	1	NA	5' UTR (NM_027434, exon 1 of 7)	5' UTR (NM_027434, exon 1 of 7)	211	NM_001291135	70470	Mm.290810	NM_027434	ENSMUSG00000027651	Rprd1b	2610304G08Rik|2810446G03Rik|Crept	regulation of nuclear pre-mRNA domain containing 1B	protein-coding
mm_10402.1	chr2	13575564	13575580	+	1	NA	exon (NM_011701, exon 2 of 9)	exon (NM_011701, exon 2 of 9)	1261	NM_011701	22352	Mm.268000	NM_011701	ENSMUSG00000026728	Vim	-	vimentin	protein-coding
mm_30872.1	chr4	32220137	32220140	+	1	NA	Intergenic	Intergenic	-197297	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_86365.1	chr9	123792078	123792096	-	1	NA	3' UTR (NM_001110253, exon 18 of 18)	3' UTR (NM_001110253, exon 18 of 18)	-14390	NM_030712	80901	Mm.124289	NM_030712	ENSMUSG00000048521	Cxcr6	BB217514|BONZO|STRL33	chemokine (C-X-C motif) receptor 6	protein-coding
mm_68126.1	chr7	102209161	102209164	-	1	NA	intron (NM_022979, intron 1 of 22)	ID_B1|SINE|B4	705	NM_001287167	269966	Mm.439800	NM_022979	ENSMUSG00000063550	Nup98	4732457F17|AI849286|Nup96	nucleoporin 98	protein-coding
mm_43725.1	chr5	139543912	139543932	+	1	NA	promoter-TSS (NM_013702)	promoter-TSS (NM_013702)	24	NM_013702	22255	Mm.42190	NM_013702	ENSMUSG00000029546	Uncx	Chx4|Uncx4.1	UNC homeobox	protein-coding
mm_36756.1	chr4	101293123	101293170	-	1	NA	Intergenic	CpG	-27864	NM_146145	16451	Mm.289657	NM_146145	ENSMUSG00000028530	Jak1	AA960307|BAP004|C130039L05Rik	Janus kinase 1	protein-coding
mm_76460.1	chr8	85336399	85336442	-	1	NA	exon (NM_175441, exon 10 of 13)	exon (NM_175441, exon 10 of 13)	28904	NM_175441	213435	Mm.32804	NM_175441	ENSMUSG00000031698	Mylk3	D830007F02Rik|MLCK	myosin light chain kinase 3	protein-coding
mm_80296.1	chr9	73113448	73113454	+	1	NA	promoter-TSS (NM_198609)	promoter-TSS (NM_198609)	-18	NM_198609	225215	Mm.379366	NM_198609	ENSMUSG00000032215	Rsl24d1	2410159K22Rik	ribosomal L24 domain containing 1	protein-coding
mm_164452.1	chr16	52468561	52468565	-	1	NA	Intergenic	Intergenic	-15482	NM_001331110	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_40576.1	chr5	63945618	63945618	+	1	NA	intron (NM_145923, intron 1 of 6)	MIR|SINE|MIR	23279	NM_145923	100532	Mm.243632	NM_145923	ENSMUSG00000047881	Rell1	AA536743	RELT-like 1	protein-coding
mm_166182.1	chr5	31614878	31614913	+	1	NA	intron (NM_025796, intron 2 of 3)	intron (NM_025796, intron 2 of 3)	944	NM_025796	66845	Mm.120763	NM_025796	ENSMUSG00000106918	Mrpl33	0610009M10Rik|L33mt|MRP-L33	mitochondrial ribosomal protein L33	protein-coding
mm_64146.1	chr7	141259741	141259766	+	1	NA	exon (NM_001081118, exon 14 of 18)	exon (NM_001081118, exon 14 of 18)	6671	NM_001252601	54123	Mm.3233	NM_016850	ENSMUSG00000025498	Irf7	-	interferon regulatory factor 7	protein-coding
mm_112093.1	chr12	112721731	112721753	-	1	NA	promoter-TSS (NM_001024602)	promoter-TSS (NM_001024602)	-432	NM_001024602	217882	Mm.23689	NM_001024602	ENSMUSG00000072825	Cep170b	AI466840|AW555464|Kiaa0284|mKIAA0284	centrosomal protein 170B	protein-coding
mm_164805.1	chr18	27705573	27705573	+	1	NA	Intergenic	Intergenic	-854591	NR_045398	320624	Mm.50107	NR_045398		4930474G06Rik	-	RIKEN cDNA 4930474G06 gene	ncRNA
mm_60582.1	chr7	44482651	44482683	+	1	NA	Intergenic	Intergenic	-1850	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_120242.1	chr14	62992306	62992311	+	1	NA	Intergenic	Intergenic	-5769	NM_001039125	654465	Mm.424929	NM_001039125	ENSMUSG00000075573	Defb47	Defb41|EG654465	defensin beta 47	protein-coding
mm_149041.1	chr19	8820217	8820249	+	1	NA	promoter-TSS (NM_027412)	promoter-TSS (NM_027412)	832	NM_001081196	68693	Mm.476519	NM_001081196	ENSMUSG00000071659	Hnrnpul2	1110031M08Rik|AI465155|Hnrpul2	heterogeneous nuclear ribonucleoprotein U-like 2	protein-coding
mm_53746.1	chr6	145211142	145211222	+	1	NA	promoter-TSS (NM_001163628)	promoter-TSS (NM_001163628)	35	NM_133688	67636	Mm.486359	NM_133688	ENSMUSG00000040370	Lyrm5	4930469P12Rik|AL022899|Etfrf1|Ghiso	LYR motif containing 5	protein-coding
mm_4510.1	chr1	174173808	174173813	+	1	NA	intron (NM_011465, intron 1 of 51)	intron (NM_011465, intron 1 of 51)	1034	NM_011465	20739	Mm.200611	NM_011465	ENSMUSG00000026532	Spta1	AF093576|AI451697|Spna-1|Spna1|ha|ihj|nmf4|sph	spectrin alpha, erythrocytic 1	protein-coding
mm_107226.1	chr12	26474033	26474067	+	1	NA	exon (NM_020557, exon 3 of 5)	exon (NM_020557, exon 3 of 5)	4835	NM_020557	22169	Mm.271839	NM_020557	ENSMUSG00000020638	Cmpk2	1200004E04Rik|TDKI|Tyki	cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial	protein-coding
mm_14540.1	chr2	132793368	132793379	+	1	NA	exon (NM_007694, exon 4 of 5)	exon (NM_007694, exon 4 of 5)	12095	NM_007694	12653	Mm.255241	NM_007694	ENSMUSG00000027350	Chgb	Scg-1	chromogranin B	protein-coding
mm_21335.1	chr2	157104342	157104373	-	1	NA	intron (NM_018851, intron 14 of 15)	Lx6|LINE|L1	17302	NM_001177439	383766	Mm.480305	NM_001177439	ENSMUSG00000074628	Tldc2	Gm1332	TBC/LysM associated domain containing 2	protein-coding
mm_141879.1	chr17	34857080	34857093	-	1	NA	TTS (NM_138580)	TTS (NM_138580)	546	NR_105938	102465587		NR_105938	ENSMUSG00000098445	Mir6972	Gm27810|mmu-mir-6972	microRNA 6972	ncRNA
mm_103054.1	chr11	69817907	69817926	-	1	NA	exon (NM_175368, exon 3 of 3)	exon (NM_175368, exon 3 of 3)	524	NM_175368	108803	Mm.73263	NM_175368	ENSMUSG00000044084	4933402P03Rik	-	RIKEN cDNA 4933402P03 gene	protein-coding
mm_38239.1	chr4	136180530	136180540	-	1	NA	promoter-TSS (NM_001305399)	promoter-TSS (NM_001305399)	-247	NM_001305399	242705	Mm.307932	NM_177733	ENSMUSG00000018983	E2f2	E2F-2	E2F transcription factor 2	protein-coding
mm_33446.1	chr4	130663278	130663294	+	1	NA	promoter-TSS (NM_001159603)	promoter-TSS (NM_001159603)	-73	NM_030722	80912	Mm.440206	NM_030722	ENSMUSG00000028580	Pum1	AA517475|Pumm|mKIAA0099	pumilio RNA-binding family member 1	protein-coding
mm_148271.1	chr18	81927207	81927241	-	1	NA	Intergenic	ID_B1|SINE|B4	64856	NR_039589	100628596		NR_039589	ENSMUSG00000093036	Mir5127	mmu-mir-5127|mu-mir-5127	microRNA 5127	ncRNA
mm_85876.1	chr9	110989713	110989728	-	1	NA	promoter-TSS (NM_153100)	promoter-TSS (NM_153100)	-7	NM_153100	235636	Mm.441138	NM_153100	ENSMUSG00000066319	Rtp3	Tmem7	receptor transporter protein 3	protein-coding
mm_119318.1	chr14	36970102	36970112	+	1	NA	Intergenic	Intergenic	-1343	NM_027045	72972	Mm.27621	NM_027045	ENSMUSG00000058690	Ccser2	1700012P13Rik|2900054P12Rik|AI035535|AW108503|Fam190b|Gcap14	coiled-coil serine rich 2	protein-coding
mm_130792.1	chr15	101689957	101689989	-	1	NA	TTS (NM_008476)	TTS (NM_008476)	4332	NM_008476	16687	Mm.302399	NM_008476	ENSMUSG00000058354	Krt6a	2310016L08Rik|Krt2-6a|Krt2-6c|MK6a|mK6[a]	keratin 6A	protein-coding
mm_132907.1	chr16	48872819	48872825	+	1	NA	intron (NM_181596, intron 1 of 3)	intron (NM_181596, intron 1 of 3)	214	NM_181596	245195	Mm.231288	NM_181596	ENSMUSG00000022651	Retnlg	Fizz3|Relmg|Xcp1	resistin like gamma	protein-coding
mm_76290.1	chr8	84201625	84201668	-	1	NA	Intergenic	Intergenic	-6872	NR_029740	387216		NR_029740	ENSMUSG00000065611	Mir23a	Mirn23a|mir-23a|mmu-mir-23a	microRNA 23a	ncRNA
mm_70622.1	chr8	13595119	13595130	+	1	NA	intron (NM_009025, intron 7 of 23)	intron (NM_009025, intron 7 of 23)	-32663	NM_001080781	66501	Mm.46136	NM_025601	ENSMUSG00000031452	1700029H14Rik	-	RIKEN cDNA 1700029H14 gene	protein-coding
mm_37148.1	chr4	117003007	117003035	-	1	NA	intron (NM_175244, intron 19 of 20)	intron (NM_175244, intron 19 of 20)	7673	NM_175244	76608	Mm.251420	NM_175244	ENSMUSG00000046861	Hectd3	1700064K09Rik|AI467540|AW743312	HECT domain containing 3	protein-coding
mm_100903.1	chr11	6200146	6200210	-	1	NA	5' UTR (NM_173748, exon 1 of 6)	5' UTR (NM_173748, exon 1 of 6)	273	NM_173748	209586	Mm.25321	NM_173748	ENSMUSG00000053838	Nudcd3	AI427847|BC024322|mKIAA1068	NudC domain containing 3	protein-coding
mm_159043.1	chr1	181051123	181051123	+	1	NA	promoter-TSS (NM_001033819)	promoter-TSS (NM_001033819)	-114	NM_001033819	619326	Mm.355174	NM_001033819	ENSMUSG00000038768	9130409I23Rik	-	RIKEN cDNA 9130409I23 gene	protein-coding
mm_99311.1	chr11	101377204	101377211	+	1	NA	3' UTR (NM_008061, exon 5 of 5)	3' UTR (NM_008061, exon 5 of 5)	9491	NM_008061	14377	Mm.18064	NM_008061	ENSMUSG00000078650	G6pc	AW107337|G6Pase|G6pt|Glc-6-Pase	glucose-6-phosphatase, catalytic	protein-coding
mm_166780.1	chr6	139321957	139321959	+	1	NA	intron (NR_045149, intron 1 of 3)	intron (NR_045149, intron 1 of 3)	618	NR_045149	70962	Mm.410833	NR_045149	ENSMUSG00000108128	4922502N22Rik	-	RIKEN cDNA 4922502N22 gene	ncRNA
mm_38548.1	chr4	141601669	141601675	-	1	NA	intron (NM_133754, intron 1 of 8)	intron (NM_133754, intron 1 of 8)	-1748	NM_001163256	74202	Mm.490327	NM_133754	ENSMUSG00000006219	Fblim1	2410043F08Rik|Cal|Fblp1|Gt10|migfilin|migfilin(s)	filamin binding LIM protein 1	protein-coding
mm_84491.1	chr9	66847596	66847621	-	1	NA	3' UTR (NM_173413, exon 8 of 8)	3' UTR (NM_173413, exon 8 of 8)	-12902	NM_026674	68318	Mm.284229	NM_026674	ENSMUSG00000053040	Aph1c	0610008A10Rik|APH-1b|Aph1b	aph1 homolog C, gamma secretase subunit	protein-coding
mm_41851.1	chr5	104439313	104439377	+	1	NA	exon (NM_001204203, exon 6 of 7)	exon (NM_001204203, exon 6 of 7)	3153	NM_001204233	20750	Mm.288474	NM_009263	ENSMUSG00000029304	Spp1	2AR|Apl-1|BNSP|BSPI|Bsp|ETA-1|Eta|OP|Opn|Opnl|Ric|Spp-1	secreted phosphoprotein 1	protein-coding
mm_34051.1	chr4	138250463	138250485	+	1	NA	promoter-TSS (NM_001099631)	promoter-TSS (NM_001099631)	63	NM_001099631	230863	Mm.482408	NM_001099631	ENSMUSG00000045349	Sh2d5	BC036961	SH2 domain containing 5	protein-coding
mm_5009.1	chr1	192745569	192745573	+	1	NA	intron (NM_144881, intron 3 of 11)	U5|snRNA|snRNA	25648	NM_144881	226861	Mm.145857	NM_144881	ENSMUSG00000037375	Hhat	2810432O22Rik|AI462858|AP-2CRE|Skn|Tg(TFAP2A-cre)1Will	hedgehog acyltransferase	protein-coding
mm_131297.1	chr16	11401173	11401193	+	1	NA	intron (NM_028964, intron 7 of 20)	intron (NM_028964, intron 7 of 20)	-4465	NM_001290148	74478	Mm.325831	NM_028964	ENSMUSG00000071669	Snx29	4933437K13Rik|ENSMUSG00000079738|Gm11170|Gm1737|Gm930|Rundc2a	sorting nexin 29	protein-coding
mm_83629.1	chr9	49055487	49055497	-	1	NA	promoter-TSS (NM_012039)	promoter-TSS (NM_012039)	-89	NM_012039	26951	Mm.24791	NM_012039	ENSMUSG00000032264	Zw10	6330566F14Rik|MmZw10	zw10 kinetochore protein	protein-coding
mm_20198.1	chr2	124490182	124490183	-	1	NA	intron (NM_001290997, intron 5 of 20)	intron (NM_001290997, intron 5 of 20)	-120114	NM_199238	214968	Mm.330536	NM_172537	ENSMUSG00000027200	Sema6d	1110067B02Rik|AA409156|D330011G23|mKIAA1479	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	protein-coding
mm_74515.1	chr8	8690482	8690492	-	1	NA	promoter-TSS (NR_106114)	promoter-TSS (NR_106114)	50	NM_176849	234023	Mm.251655	NM_176849	ENSMUSG00000040459	Arglu1	9430010O03Rik|C130008N12	arginine and glutamate rich 1	protein-coding
mm_60812.1	chr7	45684370	45684393	+	1	NA	5' UTR (NM_001289693, exon 1 of 7)	5' UTR (NM_001289693, exon 1 of 7)	359	NM_001033356	243967	Mm.291240	NM_001033356	ENSMUSG00000070564	Ntn5	Gm484	netrin 5	protein-coding
mm_121377.1	chr14	118787895	118787942	+	1	NA	promoter-TSS (NM_001160098)	promoter-TSS (NM_001160098)	47	NM_001160097	58187	Mm.390755	NM_021386	ENSMUSG00000022132	Cldn10	6720456I16Rik|Cldn10a|Cldn10b|D14Ertd728e	claudin 10	protein-coding
mm_98297.1	chr11	90029656	90029664	+	1	NA	promoter-TSS (NM_026433)	promoter-TSS (NM_026433)	-688	NM_026433	67888	Mm.212428	NM_026433	ENSMUSG00000069763	Tmem100	1810057C19Rik|AV011897	transmembrane protein 100	protein-coding
mm_123447.1	chr14	65149855	65149897	-	1	NA	Intergenic	CpG	-51770	NM_018788	54616	Mm.103748	NM_018788	ENSMUSG00000021978	Extl3	2900009G18Rik|AU040105|Ext1l|mKIAA0519	exostoses (multiple)-like 3	protein-coding
mm_50879.1	chr6	55681188	55681201	+	1	NA	promoter-TSS (NM_009717)	promoter-TSS (NM_009717)	69	NM_009717	11922	Mm.5106	NM_009717	ENSMUSG00000037984	Neurod6	Atoh2|Math-2|Math2|Nex|Nex1m|bHLHa2	neurogenic differentiation 6	protein-coding
mm_17520.1	chr2	29252812	29252826	-	1	NA	non-coding (NR_029460, exon 1 of 2)	non-coding (NR_029460, exon 1 of 2)	174	NR_029460	76220	Mm.330108	NR_029460	ENSMUSG00000079499	6530402F18Rik	mKIAA1857	RIKEN cDNA 6530402F18 gene	ncRNA
mm_17726.1	chr2	32424058	32424079	-	1	NA	promoter-TSS (NM_001290558)	promoter-TSS (NM_001290558)	-2	NM_001290558	227731	Mm.37395	NM_146118	ENSMUSG00000026819	Slc25a25	1110030N17Rik|MCSC|mKIAA1896	solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 25	protein-coding
mm_142581.1	chr17	46704903	46705000	-	1	NA	promoter-TSS (NM_009358)	promoter-TSS (NM_009358)	51	NM_009358	21770	Mm.295009	NM_009358	ENSMUSG00000059409	Ppp2r5d	B'delta|TEG-271|Tex271	protein phosphatase 2, regulatory subunit B', delta	protein-coding
mm_2894.1	chr1	131910680	131910702	+	1	NA	5' UTR (NM_001145804, exon 1 of 7)	5' UTR (NM_001145804, exon 1 of 7)	233	NM_001145804	98415	Mm.246869	NM_175294	ENSMUSG00000026434	Nucks1	2700010L10Rik|8430423A01Rik|AI647518|C78391|Nucks	nuclear casein kinase and cyclin-dependent kinase substrate 1	protein-coding
mm_35078.1	chr4	6990775	6990823	-	1	NA	promoter-TSS (NM_145711)	promoter-TSS (NM_145711)	-76	NM_145711	252838	Mm.435828	NM_145711	ENSMUSG00000041272	Tox	1700007F02Rik	thymocyte selection-associated high mobility group box	protein-coding
mm_148938.1	chr19	7039593	7039608	+	1	NA	intron (NM_016737, intron 1 of 13)	CpG	426	NM_016737	20867	Mm.258633	NM_016737	ENSMUSG00000024966	Stip1	Hop|Sti1|p60	stress-induced phosphoprotein 1	protein-coding
mm_58028.1	chr6	136661988	136661994	-	1	NA	promoter-TSS (NM_025806)	promoter-TSS (NM_025806)	-98	NM_025806	66857	Mm.3311	NM_025806	ENSMUSG00000030214	Plbd1	1100001H23Rik	phospholipase B domain containing 1	protein-coding
mm_22987.1	chr3	33799792	33799809	+	1	NA	promoter-TSS (NM_025978)	promoter-TSS (NM_025978)	-383	NM_027619	67120	Mm.275710	NM_025978	ENSMUSG00000027677	Ttc14	2700016E08Rik|4930434D01Rik|4931403I22Rik|4933402I15Rik|AI662468|AU014779|AW561908|cI-44|mKIAA1980	tetratricopeptide repeat domain 14	protein-coding
mm_90336.1	chr10	127084582	127084586	+	1	NA	intron (NM_001033263, intron 5 of 18)	intron (NM_001033263, intron 5 of 18)	5677	NM_001033263	216439	Mm.336761	NM_001033263	ENSMUSG00000025422	Agap2	AGAP-2|Centg1|PIKE|cnt-g1|mKIAA0167	ArfGAP with GTPase domain, ankyrin repeat and PH domain 2	protein-coding
mm_156553.1	chrX	151800778	151800812	+	1	NA	Intergenic	Intergenic	-2487	NM_021523	59026	Mm.27372	NM_021523	ENSMUSG00000025261	Huwe1	5430439H10Rik|AU041296|Arf-bp1|C430014N20Rik|C80292|Gm1718|Ib772|LASU1|Mule|Ureb1	HECT, UBA and WWE domain containing 1	protein-coding
mm_150961.1	chr19	46454694	46454705	+	1	NA	intron (NM_001025391, intron 7 of 11)	intron (NM_001025391, intron 7 of 11)	-46949	NM_053100	93679	Mm.392177	NM_053100	ENSMUSG00000025034	Trim8	AA408830|BB006755|GERP|Rnf27	tripartite motif-containing 8	protein-coding
mm_112312.1	chr12	114910492	114910499	-	1	NA	Intergenic	Intergenic	-396801	NR_106063	102465664		NR_106063	ENSMUSG00000098357	Mir7094-2	Gm27508|mmu-mir-7094-2	microRNA 7094-2	ncRNA
mm_47385.1	chr5	122990519	122990529	-	1	NA	intron (NR_045820, intron 1 of 2)	intron (NR_045820, intron 1 of 2)	1170	NR_045820	109202	Mm.30769	NM_175405	ENSMUSG00000056735	A930024E05Rik	-	RIKEN cDNA A930024E05 gene	ncRNA
mm_152117.1	chr19	6985440	6985466	-	1	NA	exon (NM_011697, exon 6 of 7)	exon (NM_011697, exon 6 of 7)	2198	NM_001185164	22340	Mm.15607	NM_011697	ENSMUSG00000024962	Vegfb	VEGF-B|Vrf	vascular endothelial growth factor B	protein-coding
mm_167141.1	chr7	127890969	127890972	-	1	NA	promoter-TSS (NM_001081268)	promoter-TSS (NM_001081268)	0	NM_001081268	330657	Mm.425491	NM_001081268	ENSMUSG00000044139	Prss53	Pol3s|mFLJ00289	protease, serine 53	protein-coding
mm_64275.1	chr7	141808538	141808549	+	1	NA	intron (NM_010844, intron 31 of 49)	intron (NM_010844, intron 31 of 49)	19532	NM_010844	17833	Mm.334332	NM_010844	ENSMUSG00000037974	Muc5ac	2210005L13Rik|MGM	mucin 5, subtypes A and C, tracheobronchial/gastric	protein-coding
mm_154104.1	chr19	57079690	57079691	-	1	NA	intron (NM_001103178, intron 3 of 19)	(A)n|Simple_repeat|Simple_repeat	39334	NM_001347459	226251	Mm.217161	NM_178688	ENSMUSG00000025085	Ablim1	2210411C18Rik|2610209L21Rik|4833406P10Rik|9330196J19Rik|AV079770|AW060987|AW215784|Limab1|mKIAA0059	actin-binding LIM protein 1	protein-coding
mm_142993.1	chr17	56300253	56300270	-	1	NA	promoter-TSS (NM_029799)	promoter-TSS (NM_029799)	25	NM_029799	76920	Mm.329132	NM_029799	ENSMUSG00000073380	Arrdc5	1700013E09Rik	arrestin domain containing 5	protein-coding
mm_20498.1	chr2	130393264	130393279	-	1	NA	intron (NM_019696, intron 11 of 13)	intron (NM_019696, intron 11 of 13)	4358	NM_019696	56264	Mm.112701	NM_019696	ENSMUSG00000027408	Cpxm1	AA986902|Cpx-1|Cpx1|Cpxm	carboxypeptidase X 1 (M14 family)	protein-coding
mm_59455.1	chr7	27195149	27195159	+	1	NA	promoter-TSS (NM_001290511)	promoter-TSS (NM_001290511)	606	NM_001046637	53607	Mm.386890	NM_015782	ENSMUSG00000061479	Snrpa	C430021M15Rik|Rnu1a-1|Rnu1a1|U1-A|U1A	small nuclear ribonucleoprotein polypeptide A	protein-coding
mm_10346.1	chr2	11667568	11667570	+	1	NA	intron (NM_008367, intron 1 of 7)	intron (NM_008367, intron 1 of 7)	24777	NM_008367	16184	Mm.915	NM_008367	ENSMUSG00000026770	Il2ra	CD25|Il2r|Ly-43	interleukin 2 receptor, alpha chain	protein-coding
mm_86865.1	chr10	21993947	21993955	+	1	NA	promoter-TSS (NM_011361)	promoter-TSS (NM_011361)	61	NM_001161850	20393	Mm.28405	NM_011361	ENSMUSG00000019970	Sgk1	Sgk	serum/glucocorticoid regulated kinase 1	protein-coding
mm_60990.1	chr7	49160777	49160788	+	1	NA	intron (NM_001111016, intron 2 of 38)	intron (NM_001111016, intron 2 of 38)	-85407	NM_175272	78286	Mm.333881	NM_175272	ENSMUSG00000052512	Nav2	5330421F07Rik|AU067780|BQ960892|HELAD1|POMFIL2|RAINB1|RAINB2|Unc53H2|mKIAA3015	neuron navigator 2	protein-coding
mm_150558.1	chr19	39330291	39330306	+	1	NA	exon (NM_007815, exon 9 of 9)	exon (NM_007815, exon 9 of 9)	43213	NM_007815	13095	Mm.20764	NM_007815	ENSMUSG00000003053	Cyp2c29	AHOH|AHOHase|AI159681|AI196010|Ah-2|Ahh-1|Cyp2c|P450-2C	cytochrome P450, family 2, subfamily c, polypeptide 29	protein-coding
mm_41175.1	chr5	88008046	88008054	+	1	NA	exon (NM_011422, exon 3 of 3)	exon (NM_011422, exon 3 of 3)	5525	NM_011422	20599	Mm.261199	NM_011422	ENSMUSG00000029280	Smr3a	AA589601|MSG1|MSG3|Smr1|Smr3	submaxillary gland androgen regulated protein 3A	protein-coding
mm_90789.1	chr10	7063101	7063109	-	1	NA	Intergenic	Intergenic	-39920	NM_001033391	320495	Mm.331674	NM_001033391	ENSMUSG00000064065	Ipcef1	A130090K04Rik	interaction protein for cytohesin exchange factors 1	protein-coding
mm_106698.1	chr12	3496349	3496395	+	1	NA	exon (NM_172421, exon 10 of 11)	exon (NM_172421, exon 10 of 11)	69515	NM_172421	75302	Mm.120475	NM_172421	ENSMUSG00000037486	Asxl2	4930556B16Rik|mKIAA1685	additional sex combs like 2 (Drosophila)	protein-coding
mm_164408.1	chr16	36277072	36277073	+	1	NA	promoter-TSS (NM_001082543)	promoter-TSS (NM_001082543)	-76	NM_001082543	20861	Mm.327618	NM_001082543	ENSMUSG00000071562	Stfa1	Stefin-3|Stf-3|Stf1|Stf3|Stfa3	stefin A1	protein-coding
mm_164076.1	chr14	121787490	121787498	-	1	NA	intron (NM_134074, intron 1 of 52)	intron (NM_134074, intron 1 of 52)	10240	NM_134074	105445	Mm.378591	NM_134074	ENSMUSG00000025558	Dock9	AA959601|AW538057|B230309H04Rik|D14Wsu89e|Zizimin1|mKIAA1058	dedicator of cytokinesis 9	protein-coding
mm_115331.1	chr13	112467505	112467521	+	1	NA	intron (NM_010560, intron 1 of 16)	intron (NM_010560, intron 1 of 16)	3443	NM_010560	16195	Mm.4364	NM_010560	ENSMUSG00000021756	Il6st	5133400A03Rik|AA389424|BB405851|CD130|D13Ertd699e|gp130	interleukin 6 signal transducer	protein-coding
mm_124419.1	chr14	118052146	118052154	-	1	NA	promoter-TSS (NM_010024)	promoter-TSS (NM_010024)	96	NM_010024	13190	Mm.19987	NM_010024	ENSMUSG00000022129	Dct	DT|TRP-2|TRP2|Tyrp-2|Tyrp2|slaty|slt	dopachrome tautomerase	protein-coding
mm_106868.1	chr12	8010052	8010061	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	32379	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_108311.1	chr12	79547760	79547777	+	1	NA	intron (NM_009014, intron 7 of 10)	intron (NM_009014, intron 7 of 10)	250417	NM_001252562	19363	Mm.341756	NM_009014	ENSMUSG00000059060	Rad51b	AI553500|R51H2|Rad51l1|mREC2	RAD51 paralog B	protein-coding
mm_45454.1	chr5	67754987	67754990	-	1	NA	intron (NM_009727, intron 14 of 35)	intron (NM_009727, intron 14 of 35)	92443	NM_009727	11980	Mm.153230	NM_009727	ENSMUSG00000037685	Atp8a1	AI481521|AI853962|APLT|AW743152|AW822227|Atp3a2|B230107D19Rik|ClassI	ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1	protein-coding
mm_33265.1	chr4	127243789	127243856	+	1	NA	promoter-TSS (NM_030252)	promoter-TSS (NM_030252)	38	NM_030252	80284	Mm.139607	NM_030252	ENSMUSG00000042380	Smim12	BC003266	small integral membrane protein 12	protein-coding
mm_157702.1	chrX	60892677	60892690	-	1	NA	exon (NM_009237, exon 1 of 1)	exon (NM_009237, exon 1 of 1)	747	NM_009237	20675	Mm.35784	NM_009237	ENSMUSG00000045179	Sox3	Sox-3	SRY (sex determining region Y)-box 3	protein-coding
mm_120739.1	chr14	73173799	73173808	+	1	NA	exon (NM_001170694, exon 11 of 15)	exon (NM_001170694, exon 11 of 15)	31018	NR_033185	105670	Mm.280068	NM_134083	ENSMUSG00000022106	Rcbtb2	2610028E02Rik|2810420M18Rik|AI448345|AW240694|Chc1l|RC/BTB2	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 2	protein-coding
mm_71052.1	chr8	33697460	33697488	+	1	NA	3' UTR (NM_010344, exon 13 of 13)	3' UTR (NM_010344, exon 13 of 13)	-34440	NM_001167921	68153	Mm.286104	NM_026584	ENSMUSG00000031585	Gtf2e2	34kDa|AI462509|C330006J08Rik	general transcription factor II E, polypeptide 2 (beta subunit)	protein-coding
mm_171988.1	chr5	93804302	93804320	+	1	NA	Intergenic	L1Md_T|LINE|L1	-132848	NM_001164285	381654	Mm.326591	NM_001164284	ENSMUSG00000070686	C87414	-	expressed sequence C87414	protein-coding
mm_169494.1	chr14	75845393	75845395	+	1	NA	promoter-TSS (NR_045294)	promoter-TSS (NR_045294)	138	NM_009429	22070	Mm.297482	NM_009429	ENSMUSG00000060126	Tpt1	TCTP|Trt|p21|p23	tumor protein, translationally-controlled 1	protein-coding
mm_79238.1	chr9	50504287	50504297	+	1	NA	exon (NM_029639, exon 4 of 4)	exon (NM_029639, exon 4 of 4)	513	NR_040714	69631	Mm.414996	NR_040714	ENSMUSG00000101304	Plet1os	2310014F07Rik	placenta expressed transcript 1, opposite strand	ncRNA
mm_1985.1	chr1	87099077	87099100	+	1	NA	exon (NM_001081082, exon 10 of 11)	exon (NM_001081082, exon 10 of 11)	2518	NM_001081082	76768	Mm.58068	NM_001081082	ENSMUSG00000079440	Alpi	2010001C14Rik|Akp6|gIAP	alkaline phosphatase, intestinal	protein-coding
mm_102447.1	chr11	59787236	59787244	-	1	NA	promoter-TSS (NR_110894)	promoter-TSS (NR_110894)	-18	NR_110894	194908	Mm.344651	NM_183139	ENSMUSG00000043648	Pld6	4933433K01Rik|Gm10|Zuc|mZuc|mitoPLD	phospholipase D family, member 6	protein-coding
mm_36020.1	chr4	56990088	56990112	-	1	NA	exon (NM_001142965, exon 1 of 5)	exon (NM_001142965, exon 1 of 5)	291	NM_001142965	230235	Mm.207654	NM_001142965	ENSMUSG00000045589	Frrs1l	6430704M03Rik	ferric-chelate reductase 1 like	protein-coding
mm_154256.1	chr19	60766958	60766975	-	1	NA	exon (NM_010123, exon 19 of 22)	exon (NM_010123, exon 19 of 22)	7419	NR_034047	100217439		NR_034047		Snora19	MBI-51	small nucleolar RNA, H/ACA box 19	snoRNA
mm_7422.1	chr1	119648623	119648653	-	1	NA	intron (NM_145506, intron 1 of 24)	CpG	362	NM_001113416	226352	Mm.253156	NM_145506	ENSMUSG00000026383	Epb41l5	1700030C16Rik|AL022914|BE37|E230025E14Rik|Epb4.1l5|Lulu1|NBL5	erythrocyte membrane protein band 4.1 like 5	protein-coding
mm_142377.1	chr17	44735613	44735666	-	1	NA	non-coding (NR_073425, exon 1 of 6)	intron (NM_001271627, intron 1 of 7)	537	NR_073425	12393	Mm.391013	NM_009820	ENSMUSG00000039153	Runx2	AML3|Cbf|Cbfa-1|Cbfa1|LS3|Osf2|PEBP2aA|Pebp2a1|Pebpa2a	runt related transcription factor 2	protein-coding
mm_98784.1	chr11	96855255	96855272	+	1	NA	exon (NM_019877, exon 6 of 9)	exon (NM_019877, exon 6 of 9)	4870	NR_029562	387170		NR_029562	ENSMUSG00000065515	Mir152	Mirn152|mir-152|mmu-mir-152	microRNA 152	ncRNA
mm_91578.1	chr10	40129576	40129604	-	1	NA	intron (NM_001114332, intron 1 of 5)	B2_Mm2|SINE|B2	12664	NM_028247	72472	Mm.186778	NM_028247	ENSMUSG00000019838	Slc16a10	2610103N14Rik|9830169E08|Mct10|PRO0813|TAT1	solute carrier family 16 (monocarboxylic acid transporters), member 10	protein-coding
mm_9245.1	chr1	171345601	171345628	-	1	NA	promoter-TSS (NM_012049)	promoter-TSS (NM_012049)	31	NM_001242580	27045	Mm.12915	NM_012049	ENSMUSG00000013997	Nit1	AI255805|ESTM30|W57327	nitrilase 1	protein-coding
mm_16275.1	chr2	173737493	173737503	+	1	NA	promoter-TSS (NM_019806)	promoter-TSS (NM_019806)	-73	NM_019806	56491	Mm.260456	NM_019806	ENSMUSG00000054455	Vapb	AI225786|AI840687|AI848259|D2Abb2e|R75548|VAP33b|Vamp33b	vesicle-associated membrane protein, associated protein B and C	protein-coding
mm_135154.1	chr16	35858000	35858011	-	1	NA	exon (NM_001039530, exon 6 of 17)	exon (NM_001039530, exon 6 of 17)	13377	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_15505.1	chr2	158028734	158028821	+	1	NA	5' UTR (NM_027434, exon 1 of 7)	5' UTR (NM_027434, exon 1 of 7)	280	NM_001291135	70470	Mm.290810	NM_027434	ENSMUSG00000027651	Rprd1b	2610304G08Rik|2810446G03Rik|Crept	regulation of nuclear pre-mRNA domain containing 1B	protein-coding
mm_109450.1	chr12	111039335	111039400	+	1	NA	promoter-TSS (NM_198023)	promoter-TSS (NM_198023)	-431	NM_198023	217864	Mm.23808	NM_198023	ENSMUSG00000037896	Rcor1	5730409O11|6720480E22Rik|AU042633|D12Wsu95e|Rocr1|mKIAA0071	REST corepressor 1	protein-coding
mm_107674.1	chr12	54135159	54135170	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	68710	NM_028133	112407	Mm.133037	NM_028133	ENSMUSG00000035105	Egln3	2610021G09Rik|AI505553|AI648162|Hif-p4h-3|Phd3|SM-20	egl-9 family hypoxia-inducible factor 3	protein-coding
mm_140512.1	chr17	5591644	5591675	-	1	NA	intron (NM_146073, intron 1 of 8)	intron (NM_146073, intron 1 of 8)	99059	NM_146073	224454	Mm.487663	NM_146073	ENSMUSG00000034265	Zdhhc14	B530001K09Rik|New1cp	zinc finger, DHHC domain containing 14	protein-coding
mm_21898.1	chr2	166156140	166156152	-	1	NA	promoter-TSS (NM_028072)	promoter-TSS (NM_028072)	-463	NM_028072	72043	Mm.1011	NM_028072	ENSMUSG00000006800	Sulf2	2010004N24Rik|AU020235|MSulf-2|mKIAA1247	sulfatase 2	protein-coding
mm_133160.1	chr16	70407855	70407862	+	1	NA	intron (NM_028803, intron 3 of 15)	intron (NM_028803, intron 3 of 15)	93909	NM_028803	74185	Mm.396102	NM_028803	ENSMUSG00000022707	Gbe1	2310045H19Rik|2810426P10Rik|D16Ertd536e	glucan (1,4-alpha-), branching enzyme 1	protein-coding
mm_62373.1	chr7	100706607	100706619	+	1	NA	promoter-TSS (NM_178764)	promoter-TSS (NM_178764)	-89	NM_178764	319604	Mm.260362	NM_178764	ENSMUSG00000029461	Fam168a	2610030B18Rik|B930006L02Rik|mKIAA0280	family with sequence similarity 168, member A	protein-coding
mm_168790.1	chr12	19288554	19288561	+	1	NA	Intergenic	CpG	774047	NM_001201330	236366	Mm.352227	NM_001033157	ENSMUSG00000073197	5730507C01Rik	-	RIKEN cDNA 5730507C01 gene	protein-coding
mm_80246.1	chr9	72747996	72748025	+	1	NA	3' UTR (NM_010890, exon 29 of 29)	3' UTR (NM_010890, exon 29 of 29)	-59264	NM_175485	235472	Mm.31696	NM_175485	ENSMUSG00000036030	Prtg	A230098A12Rik|Igdcc5	protogenin	protein-coding
mm_151060.1	chr19	47228805	47228815	+	1	NA	promoter-TSS (NM_001163480)	promoter-TSS (NM_001163480)	-33	NM_001163480	18011	Mm.313651	NM_021360	ENSMUSG00000006435	Neurl1a	2410129E16Rik|AI450910|AI481072|Neu1|Neur1|Neurl|Neurl1|Nlz|Rnf67	neuralized E3 ubiquitin protein ligase 1A	protein-coding
mm_97626.1	chr11	78958702	78958711	+	1	NA	intron (NM_001313921, intron 25 of 25)	L2a|LINE|L2	26218	NM_001159301	16859	Mm.341434	NM_010708	ENSMUSG00000001123	Lgals9	AA407335|AI194909|AI265545|LGALS35|Lgals5|gal-9|galectin-9	lectin, galactose binding, soluble 9	protein-coding
mm_112502.1	chr13	8279128	8279141	+	1	NA	intron (NR_110345, intron 1 of 10)	intron (NR_110345, intron 1 of 10)	76268	NM_052977	94191	Mm.425794	NM_052977	ENSMUSG00000052551	Adarb2	Adar3|RED2	adenosine deaminase, RNA-specific, B2	protein-coding
mm_3884.1	chr1	161037603	161037613	+	1	NA	promoter-TSS (NR_028543)	promoter-TSS (NR_028543)	-484	NR_028543	100217446		NR_028543	ENSMUSG00000064968	Snord47	MBII-96	small nucleolar RNA, C/D box 47	snoRNA
mm_110869.1	chr12	73715799	73715808	-	1	NA	intron (NM_001313977, intron 10 of 14)	intron (NM_001313977, intron 10 of 14)	131007	NM_008856	18755	Mm.341677	NM_008856	ENSMUSG00000021108	Prkch	Pkch	protein kinase C, eta	protein-coding
mm_74087.1	chr8	122557847	122557895	+	1	NA	Intergenic	Intergenic	-6542	NM_001037298	234839	Mm.37324	NM_001037298	ENSMUSG00000014444	Piezo1	9630020g22|Fam38a|mKIAA0233	piezo-type mechanosensitive ion channel component 1	protein-coding
mm_65702.1	chr7	28377618	28377631	-	1	NA	exon (NM_011756, exon 2 of 2)	exon (NM_011756, exon 2 of 2)	1604	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_56688.1	chr6	113980006	113980006	-	1	NA	intron (NM_009723, intron 2 of 21)	intron (NM_009723, intron 2 of 21)	-45325	NM_001347365	11941	Mm.321755	NM_009723	ENSMUSG00000030302	Atp2b2	D6Abb2e|Gena300|PMCA2|Tmy|dfw|jog|wms|wri	ATPase, Ca++ transporting, plasma membrane 2	protein-coding
mm_142655.1	chr17	47611450	47611544	-	1	NA	promoter-TSS (NM_020048)	promoter-TSS (NM_020048)	-5	NM_016859	53414	Mm.472101	NM_016859	ENSMUSG00000023988	Bysl	Bys|Enp1	bystin-like	protein-coding
mm_96261.1	chr11	62648657	62648685	+	1	NA	promoter-TSS (NM_175002)	promoter-TSS (NM_175002)	7	NM_175002	216829	Mm.295306	NM_175002	ENSMUSG00000048497	Mmgt2	AI852046	membrane magnesium transporter 2	protein-coding
mm_95695.1	chr11	54327045	54327053	+	1	NA	intron (NM_001033597, intron 6 of 20)	intron (NM_001033597, intron 6 of 20)	12146	NM_001033599	216739	Mm.267478	NM_144823	ENSMUSG00000020333	Acsl6	A330035H04Rik|AW050338|Facl6|LACS|Lacsl|mKIAA0837	acyl-CoA synthetase long-chain family member 6	protein-coding
mm_66197.1	chr7	34229446	34229461	-	1	NA	intron (NM_008155, intron 1 of 17)	intron (NM_008155, intron 1 of 17)	883	NM_008155	14751	Mm.589	NM_008155	ENSMUSG00000036427	Gpi1	Amf|Gpi|Gpi-1|Gpi-1r|Gpi-1s|Gpi-1t|Gpi1-r|Gpi1-s|Gpi1-t|Gpi1s|MF|NK|NK/GPI|Nlk|Org|Pgi|Phi	glucose phosphate isomerase 1	protein-coding
mm_95734.1	chr11	54626661	54626685	+	1	NA	exon (NM_001252494, exon 11 of 29)	exon (NM_001252494, exon 11 of 29)	30527	NM_001252497	192786	Mm.254404	NM_175258	ENSMUSG00000037533	Rapgef6	A530068K01|AI844632|BB085664|C030018K18Rik|PDZ-GEF2|Pdzgef2|RA-GEF-2|Ragef2|mKIAA4052	Rap guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_96691.1	chr11	69591441	69591474	+	1	NA	3' UTR (NM_011640, exon 11 of 11)	3' UTR (NM_011640, exon 11 of 11)	11098	NM_001127233	22059	Mm.222	NM_011640	ENSMUSG00000059552	Trp53	Tp53|bbl|bfy|bhy|p44|p53	transformation related protein 53	protein-coding
mm_105160.1	chr11	101591783	101591786	-	1	NA	TTS (NM_144830)	TTS (NM_144830)	9542	NM_144830	217203	Mm.280559	NM_144830	ENSMUSG00000034947	Tmem106a	0610008L10Rik|AI043106|BC022145	transmembrane protein 106A	protein-coding
mm_142164.1	chr17	36145928	36145938	-	1	NA	intron (NR_033517, intron 1 of 3)	CpG	915	NR_033517	675325	Mm.75890	NR_033517	ENSMUSG00000038311	2410017I17Rik	-	RIKEN cDNA 2410017I17 gene	ncRNA
mm_86826.1	chr10	21152839	21152844	+	1	NA	intron (NM_010848, intron 4 of 14)	intron (NM_010848, intron 4 of 14)	8143	NM_001198914	17863	Mm.52109	NM_010848	ENSMUSG00000019982	Myb	AI550390|M16449|c-myb	myeloblastosis oncogene	protein-coding
mm_77798.1	chr9	3031099	3031114	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	7637	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_116362.1	chr13	40730732	40730739	-	1	NA	promoter-TSS (NM_001122948)	promoter-TSS (NM_001122948)	-278	NM_001122948	21418	Mm.85544	NM_011547	ENSMUSG00000021359	Tfap2a	AP-2|AP2alpha|Ap-2 (a)|Ap2|Ap2tf|Tcfap2a	transcription factor AP-2, alpha	protein-coding
mm_64223.1	chr7	141613839	141613845	+	1	NA	promoter-TSS (NR_040337)	promoter-TSS (NR_040337)	-95	NR_040337	100036523	Mm.398994	NR_040337	ENSMUSG00000097170	Gm16982	-	predicted gene, 16982	ncRNA
mm_4221.1	chr1	171331123	171331129	+	1	NA	intron (NM_011615, intron 1 of 4)	intron (NM_011615, intron 1 of 4)	1981	NM_011615	21945	Mm.270139	NM_011615	ENSMUSG00000013973	Dedd	CASP8IP1|DEFT|Dedpro1|FLDED1|KE05	death effector domain-containing	protein-coding
mm_22170.1	chr2	173148044	173148060	-	1	NA	Intergenic	Intergenic	-5021	NM_011044	18534	Mm.266867	NM_011044	ENSMUSG00000027513	Pck1	AI265463|PEPCK|Pck-1	phosphoenolpyruvate carboxykinase 1, cytosolic	protein-coding
mm_89101.1	chr10	84556413	84556434	+	1	NA	Intergenic	Intergenic	-3085	NR_040658	442847	Mm.128292	NR_040658	ENSMUSG00000097076	Platr7	C330046G13Rik	pluripotency associated transcript 7	ncRNA
mm_2164.1	chr1	88259111	88259125	+	1	NA	3' UTR (NM_198652, exon 8 of 8)	3' UTR (NM_198652, exon 8 of 8)	10290	NR_040291	78605	Mm.384762	NR_040291		6430706D22Rik	-	RIKEN cDNA 6430706D22 gene	ncRNA
mm_38590.1	chr4	141822258	141822262	-	1	NA	exon (NM_007919, exon 3 of 8)	exon (NM_007919, exon 3 of 8)	3745	NM_007919	13706	Mm.45316	NM_007919	ENSMUSG00000058579	Cela2a	Ela-2|Ela2|Ela2a	chymotrypsin-like elastase family, member 2A	protein-coding
mm_107522.1	chr12	40465179	40465202	+	1	NA	intron (NM_172803, intron 1 of 52)	intron (NM_172803, intron 1 of 52)	19137	NM_172803	238130	Mm.341423	NM_172803	ENSMUSG00000035954	Dock4	5330406C03|6330411N01Rik|AF263288|C030023J22|mKIAA0716	dedicator of cytokinesis 4	protein-coding
mm_119578.1	chr14	50839793	50839830	+	1	NA	intron (NM_009351, intron 33 of 54)	B1_Mus1|SINE|Alu	30743	NM_009351	21745	Mm.318736	NM_009351	ENSMUSG00000006281	Tep1	Tp1	telomerase associated protein 1	protein-coding
mm_43312.1	chr5	134932396	134932422	+	1	NA	promoter-TSS (NM_024479)	promoter-TSS (NM_024479)	36	NM_001347490	79565	Mm.34235	NM_024479	ENSMUSG00000040557	Wbscr27	AW492986|BC002286	Williams Beuren syndrome chromosome region 27 (human)	protein-coding
mm_103093.1	chr11	69921058	69921077	-	1	NA	promoter-TSS (NM_001166592)	promoter-TSS (NM_001166592)	18	NM_001166596	276770	Mm.18026	NM_181582	ENSMUSG00000078812	Eif5a	AA410058|D19Wsu54e|Eif4d|Eif5a1|eIF-4D|eIF-5A|eIF-5A-1|eIF-5A1	eukaryotic translation initiation factor 5A	protein-coding
mm_9321.1	chr1	171652874	171652884	-	1	NA	5' UTR (NM_144539, exon 1 of 8)	5' UTR (NM_144539, exon 1 of 8)	158	NM_144539	75345	Mm.164642	NM_144539	ENSMUSG00000038179	Slamf7	19A|19A24|4930560D03Rik|CRACC|CS1	SLAM family member 7	protein-coding
mm_110684.1	chr12	67193941	67193983	-	1	NA	intron (NM_001193266, intron 1 of 16)	B3A|SINE|B2	28587	NM_001193266	320772	Mm.227680	NM_207010	ENSMUSG00000034912	Mdga2	6720489L24Rik|9330209L04Rik|Adp|Mamdc1	MAM domain containing glycosylphosphatidylinositol anchor 2	protein-coding
mm_3544.1	chr1	150407325	150407336	+	1	NA	exon (NM_133780, exon 9 of 52)	exon (NM_133780, exon 9 of 52)	-14275	NM_145511	226499	Mm.222093	NM_145511	ENSMUSG00000006010	BC003331	1810053E15Rik|Odr4|odr-4	cDNA sequence BC003331	protein-coding
mm_57654.1	chr6	128485612	128485628	-	1	NA	exon (NM_007376, exon 34 of 36)	exon (NM_007376, exon 34 of 36)	41100	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_24286.1	chr3	89231817	89231826	+	1	NA	exon (NM_013605, exon 5 of 7)	exon (NM_013605, exon 5 of 7)	2765	NM_013605	17829	Mm.16193	NM_013605	ENSMUSG00000042784	Muc1	CD227|EMA|Muc-1	mucin 1, transmembrane	protein-coding
mm_22615.1	chr3	14578742	14578759	+	1	NA	promoter-TSS (NM_007892)	promoter-TSS (NM_007892)	79	NM_007892	13559	Mm.153415	NM_007892	ENSMUSG00000027552	E2f5	AU024671|E2F-5	E2F transcription factor 5	protein-coding
mm_171857.1	chr5	20694727	20694727	-	1	NA	intron (NM_001170746, intron 22 of 22)	LTRIS2|LTR|ERV1	187397	NM_172992	68770	Mm.86410	NM_172992	ENSMUSG00000039987	Phtf2	1110054G21Rik|9530062N20Rik|AI447096|C77923	putative homeodomain transcription factor 2	protein-coding
mm_42286.1	chr5	114374794	114374798	+	1	NA	intron (NM_026145, intron 2 of 6)	intron (NM_026145, intron 2 of 6)	5709	NM_001159941	330171	Mm.238285	NM_026145	ENSMUSG00000001098	Kctd10	AW536343|C87062|mBACURD3	potassium channel tetramerisation domain containing 10	protein-coding
mm_22682.1	chr3	16183865	16183877	+	1	NA	intron (NR_027375, intron 1 of 5)	intron (NR_027375, intron 1 of 5)	688	NM_001145919	229096	Mm.23834	NM_172677	ENSMUSG00000047213	Ythdf3	9130022A11Rik	YTH domain family 3	protein-coding
mm_106312.1	chr11	118302408	118302423	-	1	NA	3' UTR (NM_011594, exon 5 of 5)	3' UTR (NM_011594, exon 5 of 5)	-12171	NM_001033528	72344	Mm.232293	NM_001033528	ENSMUSG00000033909	Usp36	2700002L06Rik|mKIAA1453	ubiquitin specific peptidase 36	protein-coding
mm_72035.1	chr8	70776848	70776897	+	1	NA	promoter-TSS (NR_029440)	promoter-TSS (NR_029440)	10	NR_029440	72093	Mm.271208	NR_029440		2010320M18Rik	-	RIKEN cDNA 2010320M18 gene	ncRNA
mm_51394.1	chr6	78371171	78371183	+	1	NA	intron (NM_011036, intron 1 of 5)	intron (NM_011036, intron 1 of 5)	292	NM_011036	18489	Mm.2553	NM_011036	ENSMUSG00000071356	Reg3b	HIP|PAP1|Pap|REG-III	regenerating islet-derived 3 beta	protein-coding
mm_100353.1	chr11	118428494	118428509	+	1	NA	promoter-TSS (NM_001204129)	promoter-TSS (NM_001204129)	44	NM_001204129	56745	Mm.23845	NM_019959	ENSMUSG00000017446	C1qtnf1	1600017K21Rik|CTRP1|Zsig37	C1q and tumor necrosis factor related protein 1	protein-coding
mm_112205.1	chr12	113426917	113426947	-	1	NA	Intergenic	Intergenic	-62633	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_173238.1	chrX	84443099	84443108	-	1	NA	intron (NM_007868, intron 50 of 78)	RLTR11A|LTR|ERVK	-605192	NM_001314038	13405	Mm.275608	NM_007868	ENSMUSG00000045103	Dmd	DXSmh7|DXSmh9|Dp427|Dp71|dys|mdx|pke	dystrophin, muscular dystrophy	protein-coding
mm_91304.1	chr10	24916833	24916847	-	1	NA	exon (NM_007482, exon 5 of 8)	exon (NM_007482, exon 5 of 8)	6176	NR_105870	102465545		NR_105870	ENSMUSG00000099181	Mir6905	Gm27879|mmu-mir-6905	microRNA 6905	ncRNA
mm_71385.1	chr8	45999298	45999313	+	1	NA	exon (NM_001039562, exon 2 of 5)	exon (NM_001039562, exon 2 of 5)	545	NM_001039562	654824	Mm.334517	NM_001039562	ENSMUSG00000050914	Ankrd37	-	ankyrin repeat domain 37	protein-coding
mm_128528.1	chr15	54847348	54847356	-	1	NA	intron (NM_001136077, intron 22 of 25)	intron (NM_001136077, intron 22 of 25)	72794	NM_015744	18606	Mm.250256	NM_015744	ENSMUSG00000022425	Enpp2	ATX|E-NPP 2|Npps2|PD-Ialpha|Pdnp2|lysoPLD	ectonucleotide pyrophosphatase/phosphodiesterase 2	protein-coding
mm_52793.1	chr6	121264120	121264137	+	1	NA	intron (NM_011909, intron 8 of 10)	intron (NM_011909, intron 8 of 10)	18222	NM_011909	24110	Mm.326911	NM_011909	ENSMUSG00000030107	Usp18	1110058H21Rik|AW047653|UBP43|Ubp15	ubiquitin specific peptidase 18	protein-coding
mm_104144.1	chr11	87034409	87034411	-	1	NA	3' UTR (NM_025638, exon 10 of 10)	3' UTR (NM_025638, exon 10 of 10)	39727	NM_025638	66569	Mm.281887	NM_025638	ENSMUSG00000061666	Gdpd1	2610020H15Rik	glycerophosphodiester phosphodiesterase domain containing 1	protein-coding
mm_128938.1	chr15	74716636	74716668	-	1	NA	3' UTR (NM_028216, exon 3 of 3)	3' UTR (NM_028216, exon 3 of 3)	1813	NM_028216	72373	Mm.46395	NM_028216	ENSMUSG00000022598	Psca	2210408B04Rik	prostate stem cell antigen	protein-coding
mm_111884.1	chr12	108203959	108203963	-	1	NA	TTS (NM_009832)	TTS (NM_009832)	24223	NM_009832	12454	Mm.474441	NM_009832	ENSMUSG00000021258	Ccnk	AW123198|AW413594|CPR4|CycK	cyclin K	protein-coding
mm_103439.1	chr11	75937678	75937722	-	1	NA	Intergenic	Intergenic	-11809	NM_001291159	380714	Mm.425697	NM_029548	ENSMUSG00000020847	Rph3al	Gm1753|Noc2	rabphilin 3A-like (without C2 domains)	protein-coding
mm_129218.1	chr15	76538703	76538721	-	1	NA	promoter-TSS (NM_013909)	promoter-TSS (NM_013909)	34	NM_013909	30840	Mm.275279	NM_013909	ENSMUSG00000022559	Fbxl6	AU021795|Fbl6	F-box and leucine-rich repeat protein 6	protein-coding
mm_169529.1	chr14	91805726	91805726	-	1	NA	Intergenic	L1Md_A|LINE|L1	1678835	NR_045712	74967	Mm.390704	NR_045712		4930474H20Rik	-	RIKEN cDNA 4930474H20 gene	ncRNA
mm_22928.1	chr3	31149751	31149765	+	1	NA	promoter-TSS (NM_008770)	promoter-TSS (NM_008770)	-162	NM_008770	18417	Mm.4425	NM_008770	ENSMUSG00000037625	Cldn11	Claudin-11|Claudin11|Osp|Otm	claudin 11	protein-coding
mm_111111.1	chr12	80960505	80960505	-	1	NA	exon (NM_001177561, exon 2 of 5)	exon (NM_001177561, exon 2 of 5)	7574	NM_011387	20493	Mm.486361	NM_011387	ENSMUSG00000021135	Slc10a1	Ntcp	solute carrier family 10 (sodium/bile acid cotransporter family), member 1	protein-coding
mm_135066.1	chr16	34199428	34199458	-	1	NA	intron (NM_001164268, intron 23 of 33)	intron (NM_001164268, intron 23 of 33)	-232440	NM_009471	22247	Mm.13145	NM_009471	ENSMUSG00000022814	Umps	1700095D23Rik|AA408257|AL033308|BB164745	uridine monophosphate synthetase	protein-coding
mm_133302.1	chr16	77594192	77594213	+	1	NA	Intergenic	Intergenic	-4734	NR_029535	387229		NR_029535	ENSMUSG00000065530	Mir99a	Mirn99a|mir-99a|mmu-mir-99a	microRNA 99a	ncRNA
mm_110109.1	chr12	26443190	26443200	-	1	NA	3' UTR (NM_021384, exon 6 of 6)	3' UTR (NM_021384, exon 6 of 6)	13257	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_87645.1	chr10	58394362	58394380	+	1	NA	promoter-TSS (NM_001193303)	promoter-TSS (NM_001193303)	-2	NM_001193303	110829	Mm.57734	NM_026148	ENSMUSG00000019920	Lims1	2310016J22Rik|4921524A02Rik|AI507642|AU021743|AW551584|C430041B13Rik|Lims1l|PINCH|PINCH1	LIM and senescent cell antigen-like domains 1	protein-coding
mm_7820.1	chr1	132007920	132007943	-	1	NA	5' UTR (NM_007923, exon 1 of 5)	5' UTR (NM_007923, exon 1 of 5)	326	NM_007923	13714	Mm.254233	NM_007923	ENSMUSG00000026436	Elk4	2310011G17Rik|A130026I01Rik|BB162516|SAP-1|Sap1	ELK4, member of ETS oncogene family	protein-coding
mm_90403.1	chr10	127326114	127326120	+	1	NA	exon (NM_001285785, exon 6 of 16)	exon (NM_001285785, exon 6 of 16)	2390	NM_146011	216445	Mm.227198	NM_146011	ENSMUSG00000040345	Arhgap9	AU043488	Rho GTPase activating protein 9	protein-coding
mm_126831.1	chr15	88864201	88864208	+	1	NA	intron (NM_145478, intron 4 of 5)	intron (NM_145478, intron 4 of 5)	2010	NM_145478	223775	Mm.400129	NM_145478	ENSMUSG00000035828	Pim3	BC026639|Kid1	proviral integration site 3	protein-coding
mm_25681.1	chr3	122173739	122173756	+	1	NA	intron (NM_007378, intron 47 of 49)	intron (NM_007378, intron 47 of 49)	-71810	NM_008129	14630	Mm.292676	NM_008129	ENSMUSG00000028124	Gclm	AI649393|Gcmc|Glclr	glutamate-cysteine ligase, modifier subunit	protein-coding
mm_9350.1	chr1	172068768	172068772	-	1	NA	exon (NM_021607, exon 12 of 17)	exon (NM_021607, exon 12 of 17)	-11174	NM_010916	18071	Mm.2474	NM_010916	ENSMUSG00000051251	Nhlh1	Hen1|Nscl|Tal2|bHLHa35	nescient helix loop helix 1	protein-coding
mm_169964.1	chr1	69969129	69969133	-	1	NA	intron (NM_025728, intron 1 of 7)	L1Md_F3|LINE|L1	17516	NM_025728	66722	Mm.440554	NM_025728	ENSMUSG00000053153	Spag16	4921511D23Rik|4930524F24Rik|4930585K05Rik|AV261009|Pf20|Wdr29	sperm associated antigen 16	protein-coding
mm_75286.1	chr8	41041606	41041610	-	1	NA	5' UTR (NM_001005865, exon 1 of 10)	5' UTR (NM_001005865, exon 1 of 10)	323	NM_001005865	102103	Mm.149438	NM_001005863	ENSMUSG00000045636	Mtus1	AI481402|ATBP135|Atip1|B430010I23Rik|B430305I03Rik|C85752|Cctsg1-440|MD44|MTSG1|mKIAA1288	mitochondrial tumor suppressor 1	protein-coding
mm_62076.1	chr7	92839872	92839878	+	1	NA	Intergenic	B1F|SINE|Alu	34357	NM_001080995	74041	Mm.26468	NM_028729	ENSMUSG00000030641	Ddias	4632434I11Rik|noxin	DNA damage-induced apoptosis suppressor	protein-coding
mm_166191.1	chr5	34000924	34000945	+	1	NA	exon (NM_001001985, exon 3 of 3)	exon (NM_001001985, exon 3 of 3)	4950	NM_001001985	269642	Mm.274610	NM_001001985	ENSMUSG00000048142	Nat8l	1110038O08Rik|Shati	N-acetyltransferase 8-like	protein-coding
mm_172444.1	chr7	29965640	29965643	-	1	NA	Intergenic	Intergenic	-13748	NM_178384	72723	Mm.371648	NM_178384	ENSMUSG00000059975	Zfp74	2810054M15Rik|KRAB8|Zfp66|Znf569|mszf21|mszf77	zinc finger protein 74	protein-coding
mm_58847.1	chr7	16843087	16843103	+	1	NA	promoter-TSS (NM_178900)	promoter-TSS (NM_178900)	30	NM_178900	101540	Mm.1881	NM_178900	ENSMUSG00000041187	Prkd2	AI325941|PKD2	protein kinase D2	protein-coding
mm_164610.1	chr17	31152793	31152829	+	1	NA	promoter-TSS (NR_110503)	promoter-TSS (NR_110503)	59	NR_110502	102631757	Mm.373036	NR_110502	ENSMUSG00000086010	LOC102631757	-	uncharacterized LOC102631757	ncRNA
mm_64308.1	chr7	141863743	141863756	+	1	NA	exon (NM_028801, exon 31 of 49)	exon (NM_028801, exon 31 of 49)	24677	NM_028801	74180	Mm.200752	NM_028801	ENSMUSG00000066108	Muc5b	2300002I04Rik|A130042M24|AV085033|MUC5|MUC9|mucin 5b	mucin 5, subtype B, tracheobronchial	protein-coding
mm_86501.1	chr10	6851720	6851721	+	1	NA	intron (NM_001302796, intron 3 of 4)	intron (NM_001302796, intron 3 of 4)	63144	NM_001039652	18390	Mm.438000	NM_011013	ENSMUSG00000000766	Oprm1	M-OR-1|MOP-R|MOR-1|MOR-1O|Oprm|mor|muOR	opioid receptor, mu 1	protein-coding
mm_25021.1	chr3	98037440	98037443	+	1	NA	intron (NM_010928, intron 1 of 33)	intron (NM_010928, intron 1 of 33)	23903	NM_010928	18129	Mm.485843	NM_010928	ENSMUSG00000027878	Notch2	AI853703|N2	notch 2	protein-coding
mm_158255.1	chrX	108765421	108765423	-	1	NA	intron (NM_001081477, intron 24 of 40)	intron (NM_001081477, intron 24 of 40)	68933	NM_001081477	382236	Mm.100112	NM_001081477	ENSMUSG00000063663	Brwd3	Brodl|D030064D06Rik|Gm596	bromodomain and WD repeat domain containing 3	protein-coding
mm_9312.1	chr1	171643349	171643375	-	1	NA	intron (NM_001347184, intron 1 of 5)	intron (NM_001347184, intron 1 of 5)	-1462	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_40706.1	chr5	65862651	65862653	+	1	NA	promoter-TSS (NM_001081105)	promoter-TSS (NM_001081105)	-917	NM_001081105	74734	Mm.20323	NM_001081105	ENSMUSG00000029204	Rhoh	5830400A04Rik|AU019774|Arhh	ras homolog family member H	protein-coding
mm_125310.1	chr15	37754439	37754445	+	1	NA	intron (NM_134094, intron 1 of 6)	RLTR41|LTR|ERV1	37558	NM_001170866	52589	Mm.283370	NM_134094	ENSMUSG00000051359	Ncald	AI848120|D030020D09Rik|D15Ertd412e	neurocalcin delta	protein-coding
mm_119975.1	chr14	55560481	55560528	+	1	NA	promoter-TSS (NM_001199009)	promoter-TSS (NM_001199009)	-419	NM_001199009	28199	Mm.11535	NM_133734	ENSMUSG00000022214	Dcaf11	0710008A13Rik|C76035|D14Ucla1|Dacf11|GLO14|Wdr23	DDB1 and CUL4 associated factor 11	protein-coding
mm_167386.1	chr8	94749930	94749930	+	1	NA	3' UTR (NM_009137, exon 3 of 3)	3' UTR (NM_009137, exon 3 of 3)	4246	NM_009137	20299	Mm.12895	NM_009137	ENSMUSG00000031779	Ccl22	ABCD-1|DCBCK|MDC|Scya22	chemokine (C-C motif) ligand 22	protein-coding
mm_76496.1	chr8	86686735	86686747	-	1	NA	intron (NM_001168591, intron 5 of 8)	intron (NM_001168591, intron 5 of 8)	35172	NM_001168591	66887	Mm.324550	NM_025827	ENSMUSG00000047866	Lonp2	1300002A08Rik|AU015403|Lonp	lon peptidase 2, peroxisomal	protein-coding
mm_121376.1	chr14	118594416	118594421	+	1	NA	intron (NM_001033336, intron 19 of 30)	intron (NM_001033336, intron 19 of 30)	-1946	NR_105815	102465208		NR_105815	ENSMUSG00000098433	Mir6391	Gm27914|mmu-mir-6391	microRNA 6391	ncRNA
mm_148147.1	chr18	77462192	77462193	-	1	NA	3' UTR (NM_001164504, exon 8 of 8)	3' UTR (NM_001164504, exon 8 of 8)	102944	NM_001164504	225743	Mm.23293	NM_001164504	ENSMUSG00000025427	Rnf165	2900024M11Rik|AI427432|Akd2|Ark2c|G630064H08Rik|Gm96	ring finger protein 165	protein-coding
mm_86349.1	chr9	123632470	123632491	-	1	NA	promoter-TSS (NM_011731)	promoter-TSS (NM_011731)	85	NM_011731	22599	Mm.41963	NM_011731	ENSMUSG00000025243	Slc6a20b	AA986306|Sit1|Slc6a20|XT3|Xtrp3	solute carrier family 6 (neurotransmitter transporter), member 20B	protein-coding
mm_43709.1	chr5	139377689	139377710	+	1	NA	promoter-TSS (NR_033147)	promoter-TSS (NR_033147)	2	NR_033147	320197	Mm.474295	NM_177097	ENSMUSG00000044197	D830046C22Rik	-	RIKEN cDNA D830046C22 gene	ncRNA
mm_46523.1	chr5	105346480	105346489	-	1	NA	promoter-TSS (NM_001039647)	promoter-TSS (NM_001039647)	-8	NR_132129	634650	Mm.458435	NM_001039647	ENSMUSG00000092021	Gbp11	EG634650|Gm7141	guanylate binding protein 11	protein-coding
mm_12981.1	chr2	90783229	90783263	+	1	NA	intron (NM_178755, intron 1 of 17)	CpG	502	NM_178755	271813	Mm.61146	NM_178755	ENSMUSG00000040812	Agbl2	4930524K04|A430081C19Rik|CCP2	ATP/GTP binding protein-like 2	protein-coding
mm_132187.1	chr16	32430986	32430990	+	1	NA	promoter-TSS (NM_009981)	promoter-TSS (NM_009981)	-32	NM_001163159	13026	Mm.98775	NM_009981	ENSMUSG00000005615	Pcyt1a	CTalpha|Cctalpha|Ctpct|Cttalpha	phosphate cytidylyltransferase 1, choline, alpha isoform	protein-coding
mm_43289.1	chr5	134176341	134176376	+	1	NA	intron (NM_033572, intron 1 of 10)	CpG	409	NM_033572	94254	Mm.29508	NM_033572	ENSMUSG00000061979	Rcc1l	5730496C04Rik|AU019812|Wbscr16	reculator of chromosome condensation 1 like	protein-coding
mm_119041.1	chr14	30570959	30570975	+	1	NA	exon (NM_009388, exon 11 of 14)	exon (NM_009388, exon 11 of 14)	-1182	NR_037237	100526475		NR_037237	ENSMUSG00000093156	Mir3076	mir-3076|mmu-mir-3076	microRNA 3076	ncRNA
mm_81370.1	chr9	108826027	108826074	+	1	NA	promoter-TSS (NM_080437)	promoter-TSS (NM_080437)	-270	NM_080437	107934	Mm.39945	NM_080437	ENSMUSG00000023473	Celsr3	Adgrc3|Fmi1|flamingo|mKIAA0812	cadherin, EGF LAG seven-pass G-type receptor 3	protein-coding
mm_106946.1	chr12	8771346	8771361	+	1	NA	promoter-TSS (NM_011519)	promoter-TSS (NM_011519)	-43	NM_011519	20969	Mm.2580	NM_011519	ENSMUSG00000020592	Sdc1	AA408134|AA409076|CD138|Sstn|Synd|Synd1|syn-1	syndecan 1	protein-coding
mm_74825.1	chr8	23162962	23162972	-	1	NA	Intergenic	L1MA9|LINE|L1	9696	NM_029002	74561	Mm.290028	NM_029002	ENSMUSG00000063672	Nkx6-3	9130417I07Rik|Nkx6.3	NK6 homeobox 3	protein-coding
mm_63315.1	chr7	126872360	126872361	+	1	NA	exon (NM_001163775, exon 14 of 16)	exon (NM_001163775, exon 14 of 16)	10388	NM_172746	233876	Mm.363427	NM_172746	ENSMUSG00000042606	Hirip3	B130036O03|C86302	HIRA interacting protein 3	protein-coding
mm_153151.1	chr19	34252449	34252467	-	1	NA	exon (NM_007392, exon 2 of 9)	exon (NM_007392, exon 2 of 9)	2915	NM_007392	11475	Mm.213025	NM_007392	ENSMUSG00000035783	Acta2	0610041G09Rik|Actvs|SMalphaA|a-SMA|alphaSMA	actin, alpha 2, smooth muscle, aorta	protein-coding
mm_134789.1	chr16	24013400	24013409	-	1	NA	Intergenic	Intergenic	-24792	NM_009744	12053	Mm.347398	NM_009744	ENSMUSG00000022508	Bcl6	Bcl5	B cell leukemia/lymphoma 6	protein-coding
mm_71089.1	chr8	34809533	34809535	+	1	NA	intron (NM_176933, intron 1 of 3)	CpG-13950	1924	NM_176933	319520	Mm.170276	NM_176933	ENSMUSG00000031530	Dusp4	2700078F24Rik|AI844617|BB104621|E130306H24Rik|MKP2	dual specificity phosphatase 4	protein-coding
mm_37166.1	chr4	117156186	117156197	-	1	NA	promoter-TSS (NR_030704)	promoter-TSS (NR_030704)	-59	NM_009098	20116	Mm.260904	NM_009098	ENSMUSG00000047675	Rps8	-	ribosomal protein S8	protein-coding
mm_112840.1	chr13	20829355	20829367	+	1	NA	intron (NM_012054, intron 2 of 20)	RMER17B2|LTR|ERVK	35248	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_119246.1	chr14	33923331	33923353	+	1	NA	promoter-TSS (NM_145741)	promoter-TSS (NM_145741)	-245	NM_145741	14560	Mm.432071	NM_145741	ENSMUSG00000021943	Gdf10	Bmp3b	growth differentiation factor 10	protein-coding
mm_41873.1	chr5	104508573	104508575	+	1	NA	intron (NM_001166581, intron 1 of 1)	CpG	222	NM_001166581	100042165	Mm.482189	NM_001166581	ENSMUSG00000079065	BC005561	-	cDNA sequence BC005561	protein-coding
mm_68101.1	chr7	102016123	102016144	-	1	NA	exon (NM_010531, exon 6 of 7)	exon (NM_010531, exon 6 of 7)	2022	NM_010531	16068	Mm.422756	NM_010531	ENSMUSG00000070427	Il18bp	IL-18BP|Igifbp|MC54L	interleukin 18 binding protein	protein-coding
mm_142662.1	chr17	47694734	47694755	-	1	NA	promoter-TSS (NM_144939)	promoter-TSS (NM_144939)	-8	NM_001290337	381104	Mm.392206	NM_001290337	ENSMUSG00000079444	Prickle4	Gm939	prickle planar cell polarity protein 4	protein-coding
mm_82770.1	chr9	26923134	26923148	-	1	NA	promoter-TSS (NM_001281475)	promoter-TSS (NM_001281475)	-60	NM_001281475	382064	Mm.335028	NM_001177509	ENSMUSG00000079644	Gm1110	-	predicted gene 1110	protein-coding
mm_106745.1	chr12	3913161	3913183	+	1	NA	3' UTR (NM_153743, exon 18 of 18)	3' UTR (NM_153743, exon 18 of 18)	21428	NM_153743	13435	Mm.5001	NM_007872	ENSMUSG00000020661	Dnmt3a	MmuIIIA	DNA methyltransferase 3A	protein-coding
mm_1465.1	chr1	69759846	69759860	+	1	NA	Intergenic	Intergenic	-67117	NM_029160	66722	Mm.440554	NM_025728	ENSMUSG00000053153	Spag16	4921511D23Rik|4930524F24Rik|4930585K05Rik|AV261009|Pf20|Wdr29	sperm associated antigen 16	protein-coding
mm_67262.1	chr7	75776607	75776625	-	1	NA	Intergenic	Intergenic	-71722	NM_001122780	207952	Mm.206223	NM_029652	ENSMUSG00000055652	Klhl25	2810402K13Rik|BC027373|Enc-1	kelch-like 25	protein-coding
mm_20622.1	chr2	131859740	131859755	-	1	NA	promoter-TSS (NM_001166206)	promoter-TSS (NM_001166206)	0	NM_001166206	71995	Mm.22	NM_028045	ENSMUSG00000037482	Erv3	1600014E20Rik|AA389086|AI426069|AI448024|D19349	endogenous retroviral sequence 3	protein-coding
mm_44841.1	chr5	34187053	34187065	-	1	NA	intron (NM_010753, intron 2 of 5)	CpG	651	NM_010753	17122	Mm.259260	NM_010753	ENSMUSG00000037235	Mxd4	2810410A03Rik|Mad4|bHLHc12	Max dimerization protein 4	protein-coding
mm_46221.1	chr5	98943787	98943805	-	1	NA	intron (NM_008926, intron 15 of 18)	intron (NM_008926, intron 15 of 18)	89381	NM_001310677	110075	Mm.136461	NM_173404	ENSMUSG00000029335	Bmp3	9530029I04Rik	bone morphogenetic protein 3	protein-coding
mm_76620.1	chr8	91708500	91708505	-	1	NA	Intergenic	Intergenic	93152	NM_001253822	16373	Mm.238044	NM_008393	ENSMUSG00000031734	Irx3	AI894186	Iroquois related homeobox 3	protein-coding
mm_3156.1	chr1	135155311	135155335	+	1	NA	3' UTR (NM_026823, exon 7 of 7)	3' UTR (NM_026823, exon 7 of 7)	8489	NM_026823	68724	Mm.174998	NM_026823	ENSMUSG00000026426	Arl8a	1110033P22Rik|Arl10b|gie2	ADP-ribosylation factor-like 8A	protein-coding
mm_15755.1	chr2	164275953	164275958	+	1	NA	TTS (NM_009300)	TTS (NM_009300)	2352	NM_009300	20941	Mm.1286	NM_009300	ENSMUSG00000016998	Svs4	SVS-IV|Svp-2|Svp-4|Svp2|Svp4	seminal vesicle secretory protein 4	protein-coding
mm_72923.1	chr8	91082460	91082486	+	1	NA	intron (NM_001282000, intron 4 of 20)	intron (NM_001282000, intron 4 of 20)	12416	NM_001282000	19651	Mm.235580	NM_011250	ENSMUSG00000031666	Rbl2	PRB2|RBR-2|Rb2|p130	retinoblastoma-like 2	protein-coding
mm_37592.1	chr4	126533398	126533423	-	1	NA	promoter-TSS (NM_153177)	promoter-TSS (NM_153177)	48	NM_153177	76850	Mm.86705	NM_153177	ENSMUSG00000042500	Ago4	5730550L01Rik|AI481660|Eif2c4	argonaute RISC catalytic subunit 4	protein-coding
mm_96325.1	chr11	64435316	64435339	+	1	NA	promoter-TSS (NM_178870)	promoter-TSS (NM_178870)	-5	NM_178870	15478	Mm.340214	NM_178870	ENSMUSG00000047759	Hs3st3a1	3Ost3a|Hs3st3a	heparan sulfate (glucosamine) 3-O-sulfotransferase 3A1	protein-coding
mm_9029.1	chr1	166503781	166503792	-	1	NA	Intergenic	Intergenic	-6198	NM_001164306	226601	Mm.475593	NM_001164306	ENSMUSG00000086056	Gm4846	EG226601|Fmo13	predicted gene 4846	protein-coding
mm_170891.1	chr2	26640279	26640282	-	1	NA	promoter-TSS (NR_028571)	promoter-TSS (NR_028571)	-36	NR_024068	72091	Mm.27103	NR_024068		Snhg7	2610002F03Rik|AI427062	small nucleolar RNA host gene 7	ncRNA
mm_70193.1	chr7	144406930	144406948	-	1	NA	intron (NM_001113373, intron 12 of 15)	intron (NM_001113373, intron 12 of 15)	36494	NR_037302	100499519		NR_037302	ENSMUSG00000093912	Mir3470b	mmu-mir-3470b	microRNA 3470b	ncRNA
mm_7326.1	chr1	102189078	102189084	-	1	NA	Intergenic	Intergenic	1033313	NR_037989	100504525	Mm.87065	NR_037989	ENSMUSG00000100684	Gm20268	-	predicted gene, 20268	ncRNA
mm_167337.1	chr8	71676277	71676315	+	1	NA	promoter-TSS (NM_001190830)	promoter-TSS (NM_001190830)	-87	NM_001190830	16453	Mm.249645	NM_010589	ENSMUSG00000031805	Jak3	fae|wil	Janus kinase 3	protein-coding
mm_100410.1	chr11	119423395	119423398	+	1	NA	Intergenic	Intergenic	32924	NR_035453	100316690		NR_035453	ENSMUSG00000088015	Mir1932	mir-1932|mmu-mir-1932	microRNA 1932	ncRNA
mm_150451.1	chr19	38118316	38118334	+	1	NA	exon (NM_011255, exon 5 of 6)	exon (NM_011255, exon 5 of 6)	6486	NM_011255	19662	Mm.2605	NM_011255	ENSMUSG00000024990	Rbp4	Rbp-4	retinol binding protein 4, plasma	protein-coding
mm_34681.1	chr4	151405002	151405011	+	1	NA	intron (NM_001081557, intron 5 of 23)	intron (NM_001081557, intron 5 of 23)	315436	NM_001308446	105704528	Mm.415128	NM_001308446	ENSMUSG00000078491	Gm13090	OTTMUSG00000010356	predicted gene 13090	protein-coding
mm_83627.1	chr9	48911068	48911078	-	1	NA	promoter-TSS (NM_013561)	promoter-TSS (NM_013561)	26	NM_013561	15561	Mm.4831	NM_013561	ENSMUSG00000032269	Htr3a	5-HT3	5-hydroxytryptamine (serotonin) receptor 3A	protein-coding
mm_13268.1	chr2	98666885	98666900	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	1199235	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_102149.1	chr11	53633209	53633218	-	1	NA	exon (NM_008355, exon 2 of 4)	exon (NM_008355, exon 2 of 4)	1489	NM_008355	16163	Mm.1284	NM_008355	ENSMUSG00000020383	Il13	Il-13	interleukin 13	protein-coding
mm_28908.1	chr3	98723894	98723925	-	1	NA	intron (NM_153193, intron 1 of 5)	ORR1D1|LTR|ERVL-MaLR	634	NM_153193	15493	Mm.482364	NM_153193	ENSMUSG00000063730	Hsd3b2	-	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 2	protein-coding
mm_121275.1	chr14	103513439	103513443	+	1	NA	promoter-TSS (NM_022886)	promoter-TSS (NM_022886)	100	NM_022886	64929	Mm.244003	NM_022886	ENSMUSG00000022123	Scel	9230114I02Rik	sciellin	protein-coding
mm_133269.1	chr16	77368877	77368902	+	1	NA	intron (NR_015543, intron 2 of 4)	intron (NR_015543, intron 2 of 4)	39561	NR_015543	77994	Mm.394688	NR_015543	ENSMUSG00000090386	Mir99ahg	2810055G20Rik|D730043B02Rik	Mir99a and Mirlet7c-1 host gene (non-protein coding)	ncRNA
mm_106436.1	chr11	119541134	119541152	-	1	NA	3' UTR (NM_008730, exon 5 of 5)	3' UTR (NM_008730, exon 5 of 5)	6677	NM_008730	18164	Mm.5142	NM_008730	ENSMUSG00000025582	Nptx1	D11Bwg1004e|Np1	neuronal pentraxin 1	protein-coding
mm_75456.1	chr8	47714106	47714110	-	1	NA	promoter-TSS (NM_172407)	promoter-TSS (NM_172407)	-177	NM_172407	70925	Mm.393807	NM_172407	ENSMUSG00000038069	Cdkn2aip	4921511I16Rik|AW208986|CARF	CDKN2A interacting protein	protein-coding
mm_8889.1	chr1	162886513	162886537	-	1	NA	intron (NM_018881, intron 4 of 8)	intron (NM_018881, intron 4 of 8)	12187	NM_018881	55990	Mm.10929	NM_018881	ENSMUSG00000040170	Fmo2	2310008D08Rik|2310042I22Rik|AW107733	flavin containing monooxygenase 2	protein-coding
mm_58684.1	chr7	12603726	12603730	+	1	NA	intron (NM_001104644, intron 1 of 4)	intron (NM_001104644, intron 1 of 4)	2816	NM_001104644	637908	Mm.469871	NM_001104644	ENSMUSG00000096002	Vmn2r53	EG637908|Gm471	vomeronasal 2, receptor 53	protein-coding
mm_49099.1	chr6	7845319	7845329	+	1	NA	promoter-TSS (NM_052993)	promoter-TSS (NM_052993)	100	NM_052993	94192	Mm.102752	NM_052993	ENSMUSG00000042460	C1galt1	2210410E06Rik|AV284120|T-synthase	core 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase, 1	protein-coding
mm_127336.1	chr15	100469082	100469126	+	1	NA	promoter-TSS (NM_134093)	promoter-TSS (NM_134093)	70	NM_134093	68614	Mm.275272	NM_134093	ENSMUSG00000037353	Letmd1	1110019O13Rik|AI593524|BB130465|BB235638|HCCR-2|HCCR1|MCC-32|Mccr	LETM1 domain containing 1	protein-coding
mm_114320.1	chr13	60601744	60601754	+	1	NA	promoter-TSS (NM_134062)	promoter-TSS (NM_134062)	-198	NM_001285917	69635	Mm.24103	NM_029653	ENSMUSG00000021559	Dapk1	D13Ucla1|DAP-Kinase	death associated protein kinase 1	protein-coding
mm_137882.1	chr17	31586371	31586374	+	1	NA	intron (NR_027493, intron 3 of 11)	intron (NR_027493, intron 3 of 11)	21599	NM_016670	18771	Mm.259295	NM_016670	ENSMUSG00000006705	Pknox1	D17Wsu76e|PREP1	Pbx/knotted 1 homeobox	protein-coding
mm_73976.1	chr8	120535790	120535867	+	1	NA	promoter-TSS (NM_001145897)	promoter-TSS (NM_001145897)	-29	NM_001145897	382034	Mm.334856	NM_198671	ENSMUSG00000031822	Gse1	2210013I18Rik|mKIAA0182	genetic suppressor element 1, coiled-coil protein	protein-coding
mm_86795.1	chr10	20229780	20229802	+	1	NA	intron (NM_001198635, intron 1 of 17)	intron (NM_001198635, intron 1 of 17)	21352	NM_001101561	621697	Mm.440587	NM_001101561		Rpl32l	EG621697|Gm6251	ribosomal protein L32-like	protein-coding
mm_60420.1	chr7	44476363	44476372	+	1	NA	Intergenic	L1MEd|LINE|L1	6020	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_95581.1	chr11	52820215	52820216	+	1	NA	intron (NM_177059, intron 3 of 15)	intron (NM_177059, intron 3 of 15)	55509	NM_177059	320027	Mm.44518	NM_177059	ENSMUSG00000036264	Fstl4	B230374F23Rik|SPIG1|mKIAA1061	follistatin-like 4	protein-coding
mm_107720.1	chr12	56289228	56289234	+	1	NA	Intergenic	Intergenic	35988	NR_045048	100503961	Mm.136732	NR_045048		Gm19990	-	predicted gene, 19990	ncRNA
mm_108248.1	chr12	78226628	78226652	+	1	NA	promoter-TSS (NM_172952)	promoter-TSS (NM_172952)	-15	NM_172952	268566	Mm.341742	NM_145965	ENSMUSG00000047454	Gphn	5730552E08Rik|AI662856|BC027112|C230040D23|GPH|GPHRYN|geph	gephyrin	protein-coding
mm_88231.1	chr10	70868634	70868652	+	1	NA	Intergenic	Intergenic	-212680	NR_045292	319646	Mm.483039	NR_045291	ENSMUSG00000037747	D630013N20Rik	-	RIKEN cDNA D630013N20 gene	ncRNA
mm_71485.1	chr8	46739850	46739871	+	1	NA	promoter-TSS (NR_045750)	promoter-TSS (NR_045750)	115	NM_008391	16363	Mm.1149	NM_008391	ENSMUSG00000031627	Irf2	9830146E22Rik|AI646973|Irf-2	interferon regulatory factor 2	protein-coding
mm_93314.1	chr10	98913767	98913770	-	1	NA	Intergenic	Intergenic	-1384	NM_026482	67972	Mm.166944	NM_026482	ENSMUSG00000019943	Atp2b1	2810442I22Rik|E130111D10Rik|Pmca1	ATPase, Ca++ transporting, plasma membrane 1	protein-coding
mm_455.1	chr1	36262418	36262427	+	1	NA	Intergenic	HAL1|LINE|L1	11003	NM_153408	214854	Mm.389110	NM_153408	ENSMUSG00000047180	Neurl3	2010300P06Rik|Lincr	neuralized E3 ubiquitin protein ligase 3	protein-coding
mm_31161.1	chr4	43442515	43442527	+	1	NA	5' UTR (NM_011571, exon 1 of 10)	5' UTR (NM_011571, exon 1 of 10)	244	NM_011571	21754	Mm.485441	NM_011571	ENSMUSG00000028458	Tesk1	AI326901	testis specific protein kinase 1	protein-coding
mm_90677.1	chr10	128908997	128909027	+	1	NA	promoter-TSS (NM_007653)	promoter-TSS (NM_007653)	93	NM_001042580	12512	Mm.371552	NM_007653	ENSMUSG00000025351	Cd63	C75951|ME491|Tspan30	CD63 antigen	protein-coding
mm_51.1	chr1	6527955	6527987	+	1	NA	intron (NM_001244693, intron 2 of 22)	intron (NM_001244693, intron 2 of 22)	40740	NM_001244692	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding
mm_80278.1	chr9	73012113	73012133	+	1	NA	exon (NM_001286546, exon 8 of 8)	exon (NM_001286546, exon 8 of 8)	26619	NM_028181	72278	Mm.268475	NM_028181	ENSMUSG00000034563	Ccpg1	1700030B06Rik|1810073J13Rik|9430028F23Rik|AI426686|AI875170|CPR8|D9Ertd392e	cell cycle progression 1	protein-coding
mm_42414.1	chr5	115235523	115235533	+	1	NA	promoter-TSS (NM_026398)	promoter-TSS (NM_026398)	-323	NM_026398	117109	Mm.24636	NM_026398	ENSMUSG00000060152	Pop5	1500019J17Rik|2700077E03Rik|AW049989|Rnasep3	processing of precursor 5, ribonuclease P/MRP family (S. cerevisiae)	protein-coding
mm_44383.1	chr5	17828813	17828831	-	1	NA	exon (NM_001159558, exon 4 of 16)	exon (NM_001159558, exon 4 of 16)	7074	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_172979.1	chr9	96530462	96530469	-	1	NA	Intergenic	BGLII|LTR|ERVK	-51790	NM_001311135	19823	Mm.28235	NM_011279	ENSMUSG00000051234	Rnf7	Rbx2|SAG	ring finger protein 7	protein-coding
mm_150610.1	chr19	40846561	40846563	+	1	NA	3' UTR (NM_172839, exon 6 of 6)	3' UTR (NM_172839, exon 6 of 6)	15283	NM_172839	240665	Mm.309	NM_172839	ENSMUSG00000025010	Ccnj	D430039C20Rik	cyclin J	protein-coding
mm_153400.1	chr19	40497014	40497024	-	1	NA	intron (NM_178362, intron 1 of 28)	intron (NM_178362, intron 1 of 28)	16717	NM_178362	20411	Mm.210815	NM_009166	ENSMUSG00000025006	Sorbs1	2310065E01Rik|9530001P15Rik|CAP|SH3P12|Sh3d5|mKIAA1296	sorbin and SH3 domain containing 1	protein-coding
mm_142352.1	chr17	43630281	43630289	-	1	NA	promoter-TSS (NM_198418)	promoter-TSS (NM_198418)	14	NM_001161366	210510	Mm.329058	NM_198418	ENSMUSG00000040140	Tdrd6	AB097085|Tdr2	tudor domain containing 6	protein-coding
mm_117622.1	chr13	91861341	91861351	-	1	NA	exon (NM_198415, exon 5 of 10)	exon (NM_198415, exon 5 of 10)	15539	NM_198415	76722	Mm.316438	NM_198415	ENSMUSG00000021622	Ckmt2	2300008A19Rik|ScCKmit	creatine kinase, mitochondrial 2	protein-coding
mm_42956.1	chr5	123047101	123047122	+	1	NA	promoter-TSS (NM_029112)	promoter-TSS (NM_029112)	-95	NM_001347456	74890	Mm.141383	NM_029112	ENSMUSG00000029477	Morn3	4930438O03Rik	MORN repeat containing 3	protein-coding
mm_145409.1	chr18	57468722	57468730	+	1	NA	5' UTR (NM_001134697, exon 1 of 2)	5' UTR (NM_001134697, exon 1 of 2)	240	NM_001134697	629147	Mm.57415	NM_001134697	ENSMUSG00000069372	Ctxn3	ENSMUSG00000069372	cortexin 3	protein-coding
mm_65868.1	chr7	29505564	29505579	-	1	NA	promoter-TSS (NM_001081028)	promoter-TSS (NM_001081028)	-111	NM_001081028	74206	Mm.447042	NM_001081028	ENSMUSG00000030583	Sipa1l3	2610511M17Rik	signal-induced proliferation-associated 1 like 3	protein-coding
mm_173131.1	chrX	18049056	18049059	+	1	NA	Intergenic	RLTR9E|LTR|ERVK	-96813	NM_028568	73547	Mm.159027	NM_028568	ENSMUSG00000025043	Dusp21	1700094E07Rik|DSP21	dual specificity phosphatase 21	protein-coding
mm_25307.1	chr3	106001579	106001621	+	1	NA	promoter-TSS (NM_029604)	promoter-TSS (NM_029604)	-103	NM_029604	100503311	Mm.386825	NM_029604	ENSMUSG00000010136	Pifo	1700027A23Rik	primary cilia formation	protein-coding
mm_98081.1	chr11	86545069	86545080	+	1	NA	promoter-TSS (NM_001199045)	promoter-TSS (NM_001199045)	83	NM_001199046	56427	Mm.383207	NM_019756	ENSMUSG00000020513	Tubd1	4930550G19Rik|Tubd	tubulin, delta 1	protein-coding
mm_104584.1	chr11	96977346	96977384	-	1	NA	intron (NM_030220, intron 1 of 6)	CpG	323	NM_030220	78912	Mm.491183	NM_030220	ENSMUSG00000018678	Sp2	4930480I16Rik|mKIAA0048	Sp2 transcription factor	protein-coding
mm_145721.1	chr18	63708733	63708741	+	1	NA	promoter-TSS (NM_001014981)	promoter-TSS (NM_001014981)	42	NM_001014981	104082	Mm.30850	NM_001014981	ENSMUSG00000040560	Wdr7	AI462727|TRAG|mKIAA0541	WD repeat domain 7	protein-coding
mm_138565.1	chr17	35345663	35345668	+	1	NA	TTS (NM_010392)	TTS (NM_010392)	3332	NM_010392	15013	Mm.427969	NM_010392	ENSMUSG00000091705	H2-Q2	BE136769|ENSMUSG00000079507|Gm11132|H-2Q2|gs14-2	histocompatibility 2, Q region locus 2	protein-coding
mm_171101.1	chr3	133517541	133517545	-	1	NA	intron (NM_001040400, intron 1 of 10)	intron (NM_001040400, intron 1 of 10)	26847	NM_001346736	214133	Mm.347816	NM_145989	ENSMUSG00000040943	Tet2	Ayu17-449|E130014J05Rik|mKIAA1546	tet methylcytosine dioxygenase 2	protein-coding
mm_50811.1	chr6	54326892	54326914	+	1	NA	promoter-TSS (NM_030024)	promoter-TSS (NM_030024)	-109	NM_030024	78004	Mm.41984	NM_030024	ENSMUSG00000045725	Prr15	E130201N16Rik|G90	proline rich 15	protein-coding
mm_22692.1	chr3	17793990	17793992	+	1	NA	intron (NR_033490, intron 1 of 2)	intron (NR_033490, intron 1 of 2)	-1671	NR_029814	723950		NR_029814	ENSMUSG00000093073	Mir124a-2	Mirn124a-2|mir-124-2|mir-124a-2	microRNA 124a-2	ncRNA
mm_136006.1	chr16	75767074	75767075	-	1	NA	promoter-TSS (NM_030201)	promoter-TSS (NM_030201)	-256	NM_030201	110920	Mm.26704	NM_030201	ENSMUSG00000032932	Hspa13	1600002I10Rik|AV006182|B230217N24Rik|Stch	heat shock protein 70 family, member 13	protein-coding
mm_19825.1	chr2	110950223	110950303	-	1	NA	promoter-TSS (NM_001128103)	promoter-TSS (NM_001128103)	-19	NM_001128103	228432	Mm.483325	NM_001081556	ENSMUSG00000074968	Ano3	AI838058|B230324K02Rik|Tmem16c	anoctamin 3	protein-coding
mm_150889.1	chr19	45363745	45363831	+	1	NA	promoter-TSS (NM_001286466)	promoter-TSS (NM_001286466)	54	NM_001037758	12234	Mm.119717	NM_009771	ENSMUSG00000025217	Btrc	Beta-Trcp1|E3RS-IkappaB|E3RSIkappaB|FWD1|Fbw1a|HOS|Slimb|b-TrCP|beta-TrCP	beta-transducin repeat containing protein	protein-coding
mm_37187.1	chr4	117375472	117375485	-	1	NA	promoter-TSS (NM_001310729)	promoter-TSS (NM_001310729)	-17	NM_001310729	66743	Mm.318331	NM_025739	ENSMUSG00000028677	Rnf220	4732477A13|4931406I20Rik|5730503K05Rik|AV302541	ring finger protein 220	protein-coding
mm_62390.1	chr7	100943610	100943621	+	1	NA	intron (NM_183168, intron 1 of 2)	intron (NM_183168, intron 1 of 2)	-11454	NM_001081116	207212	Mm.29954	NM_001081116	ENSMUSG00000032875	Arhgef17	8030463K16|AI428794|AW558066|BC035332|mKIAA0337	Rho guanine nucleotide exchange factor (GEF) 17	protein-coding
mm_106004.1	chr11	115708526	115708534	-	1	NA	promoter-TSS (NM_008163)	promoter-TSS (NM_008163)	67	NM_008163	14784	Mm.439649	NM_008163	ENSMUSG00000059923	Grb2	AA408164|Ash	growth factor receptor bound protein 2	protein-coding
mm_49056.1	chr6	5048329	5048338	+	1	NA	intron (NM_181595, intron 3 of 15)	intron (NM_181595, intron 3 of 15)	145013	NM_181595	243725	Mm.332901	NM_181595	ENSMUSG00000032827	Ppp1r9a	2810430P21Rik|4930518N04Rik|5330407E15|A230094E16Rik|BB181831|NRB|mKIAA1222|neurabin-I	protein phosphatase 1, regulatory (inhibitor) subunit 9A	protein-coding
mm_148854.1	chr19	6393710	6393729	+	1	NA	exon (NM_011224, exon 17 of 20)	exon (NM_011224, exon 17 of 20)	-6864	NM_011242	19395	Mm.77017	NM_011242	ENSMUSG00000032946	Rasgrp2	CDC25L|Caldaggef1	RAS, guanyl releasing protein 2	protein-coding
mm_66732.1	chr7	46639779	46639817	-	1	NA	promoter-TSS (NM_013789)	promoter-TSS (NM_013789)	9	NM_013789	27414	Mm.76659	NM_013789	ENSMUSG00000030839	Sergef	DelGEF|Gef|Gnef|Gnefr	secretion regulating guanine nucleotide exchange factor	protein-coding
mm_47594.1	chr5	124862278	124862293	-	1	NA	promoter-TSS (NM_001081750)	promoter-TSS (NM_001081750)	-64	NM_144819	215707	Mm.389693	NM_144819	ENSMUSG00000037979	Ccdc92	AW050178|D5Bwg0834e	coiled-coil domain containing 92	protein-coding
mm_8285.1	chr1	140183284	140183332	-	1	NA	5' UTR (NM_009888, exon 1 of 22)	5' UTR (NM_009888, exon 1 of 22)	103	NM_009888	12628	Mm.8655	NM_009888	ENSMUSG00000026365	Cfh	Mud-1|NOM|Sas-1|Sas1	complement component factor h	protein-coding
mm_104510.1	chr11	95982631	95982646	-	1	NA	intron (NM_009951, intron 2 of 14)	intron (NM_009951, intron 2 of 14)	-19255	NR_037223	100526468		NR_037223	ENSMUSG00000093358	Mir3063	mmu-mir-3063	microRNA 3063	ncRNA
mm_66526.1	chr7	45127458	45127463	-	1	NA	promoter-TSS (NR_039581)	promoter-TSS (NR_039581)	3	NR_000002	27209		NR_000002	ENSMUSG00000065219	Snord32a	Rnu32|Rnu32a|U32|U32A	small nucleolar RNA, C/D box 32A	snoRNA
mm_93000.1	chr10	86885747	86885768	-	1	NA	intron (NM_138673, intron 42 of 68)	intron (NM_138673, intron 42 of 68)	106752	NM_175331	103466	Mm.200446	NM_175331	ENSMUSG00000054027	Nt5dc3	AU040402|AW540062|C630002B14Rik|TU12B1-TY	5'-nucleotidase domain containing 3	protein-coding
mm_139971.1	chr17	71769685	71769725	+	1	NA	promoter-TSS (NM_001271484)	promoter-TSS (NM_001271484)	14	NM_001271484	78785	Mm.196382	NM_030179	ENSMUSG00000024059	Clip4	1700024K14Rik|1700074B05Rik|4833417L20Rik|5830409B12Rik|Rsnl2	CAP-GLY domain containing linker protein family, member 4	protein-coding
mm_61501.1	chr7	76229856	76229866	+	1	NA	promoter-TSS (NM_001199224)	promoter-TSS (NM_001199224)	-26	NM_001199224	244071	Mm.322829	NM_172902	ENSMUSG00000025754	Agbl1	Ccp4|D430020F16|EG244071|Nna1-l1	ATP/GTP binding protein-like 1	protein-coding
mm_166842.1	chr7	19414963	19414977	+	1	NA	exon (NM_007710, exon 3 of 8)	exon (NM_007710, exon 3 of 8)	3876	NM_007710	12715	Mm.2375	NM_007710	ENSMUSG00000030399	Ckm	Ckmm|M-CK|MCK	creatine kinase, muscle	protein-coding
mm_105255.1	chr11	102356115	102356142	-	1	NA	exon (NM_011403, exon 13 of 20)	exon (NM_011403, exon 13 of 20)	9153	NM_011403	20533	Mm.7248	NM_011403	ENSMUSG00000006574	Slc4a1	Ae1|CD233|Empb3|l11Jus51	solute carrier family 4 (anion exchanger), member 1	protein-coding
mm_98593.1	chr11	95808753	95808765	+	1	NA	Intergenic	Intergenic	-15741	NM_153104	237928	Mm.133075	NM_153104	ENSMUSG00000050860	Phospho1	D11Moh36|Phospo1	phosphatase, orphan 1	protein-coding
mm_58925.1	chr7	17972118	17972128	+	1	NA	promoter-TSS (NM_023289)	promoter-TSS (NM_023289)	-44	NM_023289	66996	Mm.36666	NM_023289	ENSMUSG00000030368	Ceacam11	1600015D01Rik	carcinoembryonic antigen-related cell adhesion molecule 11	protein-coding
mm_81460.1	chr9	109848616	109848624	+	1	NA	exon (NM_009921, exon 2 of 4)	exon (NM_009921, exon 2 of 4)	836	NM_009921	12796	Mm.3834	NM_009921	ENSMUSG00000038357	Camp	CAP18|Cnlp|Cramp|FALL39|MCLP	cathelicidin antimicrobial peptide	protein-coding
mm_110985.1	chr12	77113620	77113628	-	1	NA	Intergenic	Intergenic	-124480	NM_001252614	53618	Mm.35628	NM_016893	ENSMUSG00000021065	Fut8	-	fucosyltransferase 8	protein-coding
mm_169408.1	chr14	51860820	51860840	+	1	NA	Intergenic	Intergenic	6832	NM_017385	53873	Mm.221324	NM_017385		Ear7	mR7	eosinophil-associated, ribonuclease A family, member 7	protein-coding
mm_90366.1	chr10	127167359	127167376	+	1	NA	intron (NR_045166, intron 4 of 9)	intron (NR_045166, intron 4 of 9)	1536	NM_001244618	14421	Mm.386762	NM_008080	ENSMUSG00000006731	B4galnt1	4933429D13Rik|Gal-NAc-T|GalNAc-T|GalNAcT|Galgt1|Ggm-2|Ggm2	beta-1,4-N-acetyl-galactosaminyl transferase 1	protein-coding
mm_115181.1	chr13	108449585	108449606	+	1	NA	Intergenic	Intergenic	133258	NM_178683	218581	Mm.32318	NM_178683	ENSMUSG00000021697	Depdc1b	9830132O03|AW260467|XTP1	DEP domain containing 1B	protein-coding
mm_121356.1	chr14	116925804	116925872	+	1	NA	5' UTR (NM_011821, exon 1 of 9)	5' UTR (NM_011821, exon 1 of 9)	541	NM_011821	23888	Mm.440025	NM_011821	ENSMUSG00000058571	Gpc6	-	glypican 6	protein-coding
mm_50540.1	chr6	49046168	49046171	+	1	NA	intron (NM_053110, intron 4 of 10)	intron (NM_053110, intron 4 of 10)	9651	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_145709.1	chr18	62922423	62922458	+	1	NA	5' UTR (NM_133237, exon 1 of 5)	5' UTR (NM_133237, exon 1 of 5)	113	NM_133237	494504	Mm.391102	NM_133237	ENSMUSG00000071847	Apcdd1	AB023957|AU041258|Drapc1|EIG180	adenomatosis polyposis coli down-regulated 1	protein-coding
mm_139242.1	chr17	47733760	47733784	+	1	NA	exon (NM_025973, exon 8 of 9)	exon (NM_025973, exon 8 of 9)	-3265	NM_001161722	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_173334.1	chrY	90792048	90792061	+	1	NA	intron (NM_133362, intron 1 of 3)	B2_Mm1t|SINE|B2	6612	NM_133362	170942	Mm.76062	NM_133362	ENSMUSG00000096768	Erdr1	edr	erythroid differentiation regulator 1	protein-coding
mm_89453.1	chr10	93160788	93160815	+	1	NA	promoter-TSS (NM_146239)	promoter-TSS (NM_146239)	-75	NM_146239	237459	Mm.217404	NM_146239	ENSMUSG00000020015	Cdk17	6430598J10Rik|Pctk2	cyclin-dependent kinase 17	protein-coding
mm_21159.1	chr2	154569817	154569825	-	1	NA	promoter-TSS (NM_001291105)	promoter-TSS (NM_001291105)	71	NM_007891	13555	Mm.18036	NM_007891	ENSMUSG00000027490	E2f1	E2F-1|mKIAA4009	E2F transcription factor 1	protein-coding
mm_113987.1	chr13	52582766	52582780	+	1	NA	promoter-TSS (NM_001198977)	promoter-TSS (NM_001198977)	-664	NM_001198977	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_111704.1	chr12	103694658	103694673	-	1	NA	promoter-TSS (NM_001164742)	promoter-TSS (NM_001164742)	24	NM_001164742	68348	Mm.20149	NM_026687	ENSMUSG00000021081	Serpina1f	0610012A11Rik|AI327419|Serpina2|epserin	serine (or cysteine) peptidase inhibitor, clade A, member 1F	protein-coding
mm_147939.1	chr18	66059562	66059592	-	1	NA	3' UTR (NM_178793, exon 11 of 11)	3' UTR (NM_178793, exon 11 of 11)	-56942	NM_001172062	70361	Mm.290857	NM_027400	ENSMUSG00000041891	Lman1	2610020P13Rik|AI326273|AU043785|C730041J05|ERGIC53|F5F8D|MCFD1|MR60|P58|gp58	lectin, mannose-binding, 1	protein-coding
mm_102783.1	chr11	68400783	68400808	-	1	NA	Intergenic	Intergenic	-13969	NM_008744	18208	Mm.39095	NM_008744	ENSMUSG00000020902	Ntn1	AI561871|BC019633|Netrin-1	netrin 1	protein-coding
mm_92139.1	chr10	66921270	66921309	-	1	NA	promoter-TSS (NR_138560)	promoter-TSS (NR_138560)	-905	NR_138561	68488	Mm.338835	NR_138560		1110002J07Rik	-	RIKEN cDNA 1110002J07 gene	ncRNA
mm_135122.1	chr16	35841557	35841567	-	1	NA	exon (NM_001039530, exon 13 of 17)	exon (NM_001039530, exon 13 of 17)	29820	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_52891.1	chr6	122600322	122600332	+	1	NA	intron (NM_001134391, intron 1 of 7)	MRLTR33|LTR|ERVK	2117	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_96053.1	chr11	59565989	59565997	+	1	NA	exon (NM_145827, exon 9 of 10)	exon (NM_145827, exon 9 of 10)	5745	NM_001011789	257962	Mm.377316	NM_001011789	ENSMUSG00000059610	Olfr222	MOR256-45P	olfactory receptor 222	protein-coding
mm_15452.1	chr2	157423891	157423912	+	1	NA	promoter-TSS (NM_001025395)	promoter-TSS (NM_001025395)	-392	NM_009271	20779	Mm.22845	NM_009271	ENSMUSG00000027646	Src	AW259666|pp60c-src	Rous sarcoma oncogene	protein-coding
mm_38530.1	chr4	141547040	141547057	-	1	NA	non-coding (NR_030695, exon 1 of 1)	non-coding (NR_030695, exon 1 of 1)	886	NR_030695	320456	Mm.32859	NM_177163		B330016D10Rik	-	RIKEN cDNA B330016D10 gene	ncRNA
mm_138763.1	chr17	37051050	37051062	+	1	NA	exon (NM_019439, exon 6 of 23)	exon (NM_019439, exon 6 of 23)	5090	NM_019439	54393	Mm.32191	NM_019439	ENSMUSG00000024462	Gabbr1	GABAB1|GABAbR1|bM573K1.1	gamma-aminobutyric acid (GABA) B receptor, 1	protein-coding
mm_151108.1	chr19	47864292	47864306	+	1	NA	exon (NM_010362, exon 6 of 6)	exon (NM_010362, exon 6 of 6)	-1246	NM_030051	68214	Mm.63791	NM_026619	ENSMUSG00000025069	Gsto2	1700020F09Rik|4930425C18Rik|GSTO 2-2	glutathione S-transferase omega 2	protein-coding
mm_16693.1	chr2	6884959	6884969	-	1	NA	promoter-TSS (NM_001110228)	promoter-TSS (NM_001110228)	32	NM_010160	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_88781.1	chr10	80602866	80602904	+	1	NA	promoter-TSS (NM_019575)	promoter-TSS (NM_019575)	3	NM_019575	56214	Mm.273170	NM_019575	ENSMUSG00000078441	Scamp4	2410022D05Rik|AI448940|AU022392|AW742369|Sc4	secretory carrier membrane protein 4	protein-coding
mm_36092.1	chr4	58499378	58499388	-	1	NA	promoter-TSS (NM_001290486)	promoter-TSS (NM_001290486)	20	NM_001290486	14745	Mm.4772	NM_010336	ENSMUSG00000038668	Lpar1	AI326300|Edg2|Gpcr26|Kdt2|lpA1|vzg-1	lysophosphatidic acid receptor 1	protein-coding
mm_152920.1	chr19	28010996	28011054	-	1	NA	5' UTR (NM_011265, exon 1 of 17)	5' UTR (NM_011265, exon 1 of 17)	141	NM_011265	19726	Mm.313321	NM_011265	ENSMUSG00000040929	Rfx3	C230093O12Rik|MRFX3	regulatory factor X, 3 (influences HLA class II expression)	protein-coding
mm_127920.1	chr15	9580623	9580633	-	1	NA	intron (NM_001305042, intron 36 of 36)	intron (NM_001305042, intron 36 of 36)	-50752	NM_008372	16197	Mm.389	NM_008372	ENSMUSG00000003882	Il7r	CD127|IL-7Ralpha	interleukin 7 receptor	protein-coding
mm_125759.1	chr15	73836140	73836163	+	1	NA	intron (NM_001033365, intron 1 of 10)	intron (NM_001033365, intron 1 of 10)	3520	NM_001033365	268816	Mm.440635	NM_001033365	ENSMUSG00000072487	Mroh5	Gm628	maestro heat-like repeat family member 5	protein-coding
mm_158445.1	chrX	140542613	140542688	-	1	NA	promoter-TSS (NR_122039)	promoter-TSS (NR_122039)	18	NR_122039	14605	Mm.22216	NM_010286	ENSMUSG00000031431	Tsc22d3	DIP|Dsip1|Gilz|TSC-22R|Tilz3	TSC22 domain family, member 3	protein-coding
mm_85162.1	chr9	96364300	96364322	-	1	NA	promoter-TSS (NM_007502)	promoter-TSS (NM_007502)	-12	NM_007502	11933	Mm.424	NM_007502	ENSMUSG00000032412	Atp1b3	AA409958|AI664000|AW212096	ATPase, Na+/K+ transporting, beta 3 polypeptide	protein-coding
mm_19979.1	chr2	118373986	118374007	-	1	NA	promoter-TSS (NM_201367)	promoter-TSS (NM_201367)	-577	NM_201367	381413	Mm.70979	NM_201367	ENSMUSG00000040133	Gpr176	Gm1012	G protein-coupled receptor 176	protein-coding
mm_111278.1	chr12	85344468	85344495	-	1	NA	intron (NM_026775, intron 3 of 4)	intron (NM_026775, intron 3 of 4)	-5119	NM_145138	217718	Mm.29071	NM_145138	ENSMUSG00000034290	Nek9	C130021H08Rik	NIMA (never in mitosis gene a)-related expressed kinase 9	protein-coding
mm_92434.1	chr10	77166546	77166556	-	1	NA	promoter-TSS (NM_009929)	promoter-TSS (NM_009929)	-21	NM_009929	12822	Mm.4352	NM_009929	ENSMUSG00000001435	Col18a1	-	collagen, type XVIII, alpha 1	protein-coding
mm_154517.1	chrM	12845	12881	-	1	NA	NA	Intergenic	NA	NA								
mm_75130.1	chr8	34965426	34965436	-	1	NA	exon (NM_175091, exon 1 of 27)	exon (NM_175091, exon 1 of 27)	259	NM_175091	21951	Mm.88364	NM_175091	ENSMUSG00000031529	Tnks	4930554K12Rik|AI662855|ARTD5|C86528|D130072O21Rik|TANK1|mTNKS1	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase	protein-coding
mm_107353.1	chr12	32820812	32820828	+	1	NA	intron (NM_021524, intron 1 of 10)	CpG	485	NM_021524	59027	Mm.202727	NM_021524	ENSMUSG00000020572	Nampt	1110035O14Rik|AI314458|AI480535|NAmPRTase|Pbef|Pbef1|Visfatin	nicotinamide phosphoribosyltransferase	protein-coding
mm_60204.1	chr7	43430093	43430114	+	1	NA	promoter-TSS (NM_177693)	promoter-TSS (NM_177693)	2	NM_177693	233187	Mm.267027	NM_177693	ENSMUSG00000004613	Lim2	19kDa|4833403J20|MP19|To3	lens intrinsic membrane protein 2	protein-coding
mm_151232.1	chr19	53771829	53771838	+	1	NA	intron (NM_001170847, intron 1 of 13)	B1_Mus1|SINE|Alu	94527	NM_001170847	73713	Mm.313695	NM_001170847	ENSMUSG00000043639	Rbm20	1110018J23Rik|2010003H22Rik|AI646761	RNA binding motif protein 20	protein-coding
mm_117145.1	chr13	61040602	61040608	-	1	NA	promoter-TSS (NM_029636)	promoter-TSS (NM_029636)	-8	NM_029636	104002	Mm.46088	NM_029636	ENSMUSG00000021439	Ctsq	1600010J02Rik	cathepsin Q	protein-coding
mm_297.1	chr1	23272654	23272657	+	1	NA	TTS (NR_029533)	TTS (NR_029533)	386	NR_029533	387225		NR_029533	ENSMUSG00000065405	Mir30a	Mirn30a|mir-30a|mmu-mir-30a	microRNA 30a	ncRNA
mm_133337.1	chr16	80372254	80372258	+	1	NA	Intergenic	L1ME3A|LINE|L1	-828441	NM_001113208	17968	Mm.433941	NM_010954	ENSMUSG00000022762	Ncam2	Ncam-2|Ocam|RNCAM	neural cell adhesion molecule 2	protein-coding
mm_52935.1	chr6	122933965	122933976	+	1	NA	3' UTR (NM_199311, exon 6 of 6)	3' UTR (NM_199311, exon 6 of 6)	12122	NM_199311	269799	Mm.297275	NM_199311	ENSMUSG00000049037	Clec4a1	BC049354|Dcir4	C-type lectin domain family 4, member a1	protein-coding
mm_24240.1	chr3	89088769	89088804	+	1	NA	intron (NM_028188, intron 8 of 10)	intron (NM_028188, intron 8 of 10)	1245	NM_001083808	72296	Mm.27687	NM_028188	ENSMUSG00000041263	Rusc1	2210403N08Rik|AA408288|NESCA	RUN and SH3 domain containing 1	protein-coding
mm_4395.1	chr1	172343179	172343198	+	1	NA	intron (NM_001039484, intron 1 of 1)	intron (NM_001039484, intron 1 of 1)	1978	NM_001039484	16513	Mm.254563	NM_020269	ENSMUSG00000044708	Kcnj10	BIR10|BIRK-1|Kir1.2|Kir4.1	potassium inwardly-rectifying channel, subfamily J, member 10	protein-coding
mm_149038.1	chr19	8820050	8820060	+	1	NA	promoter-TSS (NM_027412)	promoter-TSS (NM_027412)	654	NM_001081196	68693	Mm.476519	NM_001081196	ENSMUSG00000071659	Hnrnpul2	1110031M08Rik|AI465155|Hnrpul2	heterogeneous nuclear ribonucleoprotein U-like 2	protein-coding
mm_105118.1	chr11	101119815	101119849	-	1	NA	promoter-TSS (NM_134024)	promoter-TSS (NM_134024)	-8	NM_026501	67998	Mm.33881	NM_026501	ENSMUSG00000017802	Fam134c	1300010M03Rik|4933404C01Rik|AI551748	family with sequence similarity 134, member C	protein-coding
mm_146624.1	chr18	10172447	10172451	-	1	NA	intron (NM_009071, intron 1 of 32)	L1MC5|LINE|L1	9343	NM_009071	19877	Mm.6710	NM_009071	ENSMUSG00000024290	Rock1	1110055K06Rik|Rock-I	Rho-associated coiled-coil containing protein kinase 1	protein-coding
mm_98404.1	chr11	94328243	94328261	+	1	NA	5' UTR (NM_027799, exon 1 of 5)	5' UTR (NM_027799, exon 1 of 5)	251	NM_146024	71452	Mm.141054	NM_027799	ENSMUSG00000020864	Ankrd40	1110011C06Rik|5530600A18Rik|Gcap15	ankyrin repeat domain 40	protein-coding
mm_32437.1	chr4	107209139	107209159	+	1	NA	promoter-TSS (NM_001081272)	promoter-TSS (NM_001081272)	-31	NM_001081272	546840	Mm.331755	NM_001081272	ENSMUSG00000070877	Ldlrad1	OTTMUSG00000008594	low density lipoprotein receptor class A domain containing 1	protein-coding
mm_23575.1	chr3	63331665	63331670	+	1	NA	intron (NM_001289462, intron 8 of 22)	L1M3|LINE|L1	35572	NM_001289463	17380	Mm.296022	NM_008604	ENSMUSG00000027820	Mme	6030454K05Rik|C85356|CALLA|CD10|NEP|SFE	membrane metallo endopeptidase	protein-coding
mm_4700.1	chr1	180849160	180849170	+	1	NA	Intergenic	Intergenic	-1986	NM_145943	208768	Mm.272625	NM_145943	ENSMUSG00000038806	Sde2	-	SDE2 telomere maintenance homolog (S. pombe)	protein-coding
mm_127293.1	chr15	100154380	100154411	+	1	NA	promoter-TSS (NM_172819)	promoter-TSS (NM_172819)	-1	NM_172819	239667	Mm.243658	NM_172819	ENSMUSG00000023026	Dip2b	4932422C22|AI317237|AI854602|mKIAA1463	disco interacting protein 2 homolog B	protein-coding
mm_96329.1	chr11	64979026	64979110	+	1	NA	promoter-TSS (NM_023479)	promoter-TSS (NM_023479)	33	NM_023479	68626	Mm.157711	NM_023479	ENSMUSG00000020549	Elac2	1110017O07Rik|D11Wsu80e|Hpc2	elaC ribonuclease Z 2	protein-coding
mm_109494.1	chr12	111449540	111449565	+	1	NA	intron (NM_009396, intron 7 of 11)	intron (NM_009396, intron 7 of 11)	6891	NM_009396	21928	Mm.255332	NM_009396	ENSMUSG00000021281	Tnfaip2	B94|Exoc3l3|M-sec|Tnfip2|tnfb94	tumor necrosis factor, alpha-induced protein 2	protein-coding
mm_119056.1	chr14	30715647	30715664	+	1	NA	promoter-TSS (NM_001166532)	promoter-TSS (NM_001166532)	40	NM_001166532	54650	Mm.294662	NM_019460	ENSMUSG00000006527	Sfmbt1	4930442N21Rik|9330180L21Rik|AA536974|Sfmbt|Smr	Scm-like with four mbt domains 1	protein-coding
mm_63677.1	chr7	130546964	130546980	+	1	NA	intron (NM_001162855, intron 1 of 10)	CpG	409	NM_001162855	67872	Mm.21714	NM_001162855	ENSMUSG00000040331	Nsmce4a	2410003A14Rik	NSE4 homolog A, SMC5-SMC6 complex component	protein-coding
mm_126967.1	chr15	93002205	93002218	+	1	NA	Intergenic	Intergenic	272873	NM_001033275	223827	Mm.22819	NM_001033275	ENSMUSG00000036197	Gxylt1	Glt8d3|Gm1228|Gm87	glucoside xylosyltransferase 1	protein-coding
mm_44943.1	chr5	36530611	36530629	-	1	NA	promoter-TSS (NM_001113364)	promoter-TSS (NM_001113364)	3	NM_001113364	100855	Mm.486203	NM_133910	ENSMUSG00000029192	Tbc1d14	2810413P16Rik|AU043625|C86258|D5Ertd110e|mKIAA1322	TBC1 domain family, member 14	protein-coding
mm_120621.1	chr14	70457227	70457274	+	1	NA	promoter-TSS (NM_145981)	promoter-TSS (NM_145981)	-267	NM_145981	105653	Mm.192598	NM_145981	ENSMUSG00000003469	Phyhip	AW049870|C630010D02Rik|Lnap1ip|PAHX-AP#1|PAHX-AP1	phytanoyl-CoA hydroxylase interacting protein	protein-coding
mm_67942.1	chr7	100355039	100355076	-	1	NA	intron (NM_028292, intron 2 of 13)	intron (NM_028292, intron 2 of 13)	16839	NM_028292	72590	Mm.177502	NM_028292	ENSMUSG00000030718	Ppme1	1110069N17Rik|2700017M01Rik|PME-1|Pme1	protein phosphatase methylesterase 1	protein-coding
mm_115523.1	chr13	5861189	5861204	-	1	NA	promoter-TSS (NM_011803)	promoter-TSS (NM_011803)	-293	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_163418.1	chr12	79611240	79611243	+	1	NA	intron (NM_009014, intron 7 of 10)	intron (NM_009014, intron 7 of 10)	313492	NR_131075	77290	Mm.395042	NR_131073		9430078K24Rik	-	RIKEN cDNA 9430078K24 gene	ncRNA
mm_168688.1	chr11	96081144	96081163	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-5459	NM_007506	11951	Mm.258	NM_007506	ENSMUSG00000006057	Atp5g1	-	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit C1 (subunit 9)	protein-coding
mm_18779.1	chr2	73625693	73625725	-	1	NA	promoter-TSS (NM_029716)	promoter-TSS (NM_029716)	31	NM_029716	108699	Mm.257073	NM_029716	ENSMUSG00000056486	Chn1	0610007I19Rik|0710001E19Rik|1700112L09Rik|2900046J01Rik|AI413815|ARHGAP2	chimerin 1	protein-coding
mm_93931.1	chr10	127166344	127166358	-	1	NA	intron (NR_045166, intron 2 of 9)	intron (NR_045166, intron 2 of 9)	520	NM_001244618	14421	Mm.386762	NM_008080	ENSMUSG00000006731	B4galnt1	4933429D13Rik|Gal-NAc-T|GalNAc-T|GalNAcT|Galgt1|Ggm-2|Ggm2	beta-1,4-N-acetyl-galactosaminyl transferase 1	protein-coding
mm_61276.1	chr7	66743637	66743646	+	1	NA	5' UTR (NM_001164201, exon 1 of 11)	5' UTR (NM_001164201, exon 1 of 11)	137	NM_001164201	545975	Mm.380104	NM_001164201	ENSMUSG00000030510	Cers3	4930550L11Rik|Gm488|Lass3|T3L	ceramide synthase 3	protein-coding
mm_121064.1	chr14	91891250	91891252	+	1	NA	Intergenic	Intergenic	1764360	NR_045712	74967	Mm.390704	NR_045712		4930474H20Rik	-	RIKEN cDNA 4930474H20 gene	ncRNA
mm_132449.1	chr16	36026827	36026867	+	1	NA	intron (NM_008465, intron 10 of 13)	intron (NM_008465, intron 10 of 13)	-14343	NM_027113	69544	Mm.37802	NM_027113	ENSMUSG00000034379	Wdr5b	2310009C03Rik|AI606931	WD repeat domain 5B	protein-coding
mm_14229.1	chr2	127514744	127514756	+	1	NA	intron (NR_110989, intron 1 of 8)	L1MD2|LINE|L1	6642	NM_001291005	56461	Mm.315292	NM_019789	ENSMUSG00000079056	Kcnip3	4933407H12Rik|AI413860|Csen|DREAM|KChIP3|R74849	Kv channel interacting protein 3, calsenilin	protein-coding
mm_113450.1	chr13	35741409	35741516	+	1	NA	promoter-TSS (NM_001123386)	promoter-TSS (NM_001123386)	60	NM_001123386	12593	Mm.29002	NM_009881	ENSMUSG00000059288	Cdyl	AI325931	chromodomain protein, Y chromosome-like	protein-coding
mm_82019.1	chr9	121746524	121746552	+	1	NA	exon (NM_010918, exon 12 of 17)	exon (NM_010918, exon 12 of 17)	13405	NR_033503	320301	Mm.373883	NR_033503		E530011L22Rik	-	RIKEN cDNA E530011L22 gene	ncRNA
mm_11293.1	chr2	30133850	30133865	+	1	NA	5' UTR (NM_146252, exon 1 of 12)	5' UTR (NM_146252, exon 1 of 12)	111	NM_146252	70296	Mm.19172	NM_146252	ENSMUSG00000039678	Tbc1d13	2600014A06Rik|BC025586	TBC1 domain family, member 13	protein-coding
mm_46072.1	chr5	92323100	92323106	-	1	NA	3' UTR (NM_008599, exon 4 of 4)	3' UTR (NM_008599, exon 4 of 4)	4976	NM_008599	17329	Mm.766	NM_008599	ENSMUSG00000029417	Cxcl9	BB139920|CMK|Mig|MuMIG|Scyb9|crg-10	chemokine (C-X-C motif) ligand 9	protein-coding
mm_83940.1	chr9	56796221	56796243	-	1	NA	Intergenic	CpG	55731	NM_198673	382075	Mm.335177	NM_198673	ENSMUSG00000045620	Odf3l1	BC049697|Gm1116	outer dense fiber of sperm tails 3-like 1	protein-coding
mm_44210.1	chr5	4104599	4104624	-	1	NA	promoter-TSS (NM_020010)	promoter-TSS (NM_020010)	86	NM_020010	13121	Mm.140158	NM_020010	ENSMUSG00000001467	Cyp51	AI426508|CYPLI|Cyp51a1|Ldm|P450-14DM|P450LI	cytochrome P450, family 51	protein-coding
mm_151335.1	chr19	55894915	55894927	+	1	NA	promoter-TSS (NM_001142924)	promoter-TSS (NM_001142924)	-400	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_121100.1	chr14	99584484	99584484	+	1	NA	Intergenic	Intergenic	285793	NM_009769	12224	Mm.30262	NM_009769	ENSMUSG00000005148	Klf5	4930520J07Rik|Bteb2|CKLF|IKLF	Kruppel-like factor 5	protein-coding
mm_107977.1	chr12	72945633	72945643	+	1	NA	TTS (NM_011384)	TTS (NM_011384)	5756	NM_011384	20476	Mm.57138	NM_011384	ENSMUSG00000021099	Six6	Optx2|Six9	sine oculis-related homeobox 6	protein-coding
mm_166167.1	chr5	21256876	21256894	+	1	NA	intron (NM_175437, intron 18 of 30)	B1_Mur4|SINE|Alu	70618	NM_175437	212167	Mm.121705	NM_175437	ENSMUSG00000039934	Gsap	A530088I07Rik|Pion	gamma-secretase activating protein	protein-coding
mm_95463.1	chr11	50383017	50383028	+	1	NA	exon (NM_021510, exon 8 of 14)	exon (NM_021510, exon 8 of 14)	5303	NM_001347487	59013	Mm.21740	NM_021510	ENSMUSG00000007850	Hnrnph1	AI642080|E430005G16Rik|Hnrnph|Hnrph1	heterogeneous nuclear ribonucleoprotein H1	protein-coding
mm_120243.1	chr14	62992347	62992347	+	1	NA	Intergenic	Intergenic	-5730	NM_001039125	654465	Mm.424929	NM_001039125	ENSMUSG00000075573	Defb47	Defb41|EG654465	defensin beta 47	protein-coding
mm_6245.1	chr1	67038876	67038889	-	1	NA	promoter-TSS (NM_001190985)	promoter-TSS (NM_001190985)	-10	NM_021295	14768	Mm.20522	NM_021295	ENSMUSG00000026000	Lancl1	AW124738|Gpr69|Gpr69a|p40	LanC (bacterial lantibiotic synthetase component C)-like 1	protein-coding
mm_28468.1	chr3	90695757	90695764	-	1	NA	promoter-TSS (NM_001281852)	promoter-TSS (NM_001281852)	-39	NM_009114	20202	Mm.2128	NM_009114	ENSMUSG00000056071	S100a9	60B8Ag|AW546964|BEE22|Cagb|GAGB|L1Ag|MRP14|p14	S100 calcium binding protein A9 (calgranulin B)	protein-coding
mm_47877.1	chr5	134688640	134688650	-	1	NA	promoter-TSS (NM_010717)	promoter-TSS (NM_010717)	-55	NM_010717	16885	Mm.15409	NM_010717	ENSMUSG00000029674	Limk1	KIZ-1|LIMK-1|Limk	LIM-domain containing, protein kinase	protein-coding
mm_127877.1	chr15	8602009	8602009	-	1	NA	Intergenic	Intergenic	108798	NM_148938	20512	Mm.204834	NM_148938	ENSMUSG00000005360	Slc1a3	AI504299|B430115D02Rik|Eaat1|GLAST|GLAST-1|GLU-T|GluT-1|Gmt1|MGluT1	solute carrier family 1 (glial high affinity glutamate transporter), member 3	protein-coding
mm_19220.1	chr2	84650680	84650687	-	1	NA	promoter-TSS (NM_001085449)	promoter-TSS (NM_001085449)	57	NM_001085449	12388	Mm.35738	NM_007615	ENSMUSG00000034101	Ctnnd1	AA409437|AU019353|Catns|Ctnnd|P120|mKIAA0384	catenin (cadherin associated protein), delta 1	protein-coding
mm_131781.1	chr16	22895321	22895330	+	1	NA	promoter-TSS (NR_110508)	promoter-TSS (NR_110508)	-939	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_76478.1	chr8	85541876	85541879	-	1	NA	intron (NM_019794, intron 6 of 8)	intron (NM_019794, intron 6 of 8)	13394	NM_019794	56445	Mm.475573	NM_019794	ENSMUSG00000031701	Dnaja2	1500017M13Rik|2010206B19Rik|DNAJ|DNJ3|Dnaj3|HIRIP4|PRO3015|mDj3	DnaJ heat shock protein family (Hsp40) member A2	protein-coding
mm_170542.1	chr19	39902614	39902617	+	1	NA	Intergenic	RLTR9D|LTR|ERVK	-15846	NM_001104525	100043108	Mm.482331	NM_001104525	ENSMUSG00000092008	Cyp2c69	AI098658	cytochrome P450, family 2, subfamily c, polypeptide 69	protein-coding
mm_153462.1	chr19	41263918	41263922	-	1	NA	promoter-TSS (NM_133352)	promoter-TSS (NM_133352)	84	NM_133352	107358	Mm.246440	NM_133352	ENSMUSG00000025016	Tm9sf3	1810073M23Rik|2810031D16Rik|AI115521|AI413748|AW146116|AW549777|Smbp|mKIAA4036	transmembrane 9 superfamily member 3	protein-coding
mm_131188.1	chr16	7217753	7217760	+	1	NA	intron (NM_183188, intron 1 of 12)	intron (NM_183188, intron 1 of 12)	147921	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_128792.1	chr15	66812113	66812135	-	1	NA	intron (NM_001029841, intron 1 of 7)	MIRb|SINE|MIR	19705	NM_001029841	20491	Mm.7601	NM_009192	ENSMUSG00000022372	Sla	Slap|Slap-1	src-like adaptor	protein-coding
mm_99122.1	chr11	100164648	100164654	+	1	NA	Intergenic	Intergenic	-18725	NM_008471	16669	Mm.439699	NM_008471	ENSMUSG00000020911	Krt19	AI663979|CK-19|EndoC|K19|Krt-1.19|Krt1-19	keratin 19	protein-coding
mm_138938.1	chr17	43953241	43953276	+	1	NA	promoter-TSS (NM_030598)	promoter-TSS (NM_030598)	67	NM_030598	53901	Mm.251242	NM_030598	ENSMUSG00000039601	Rcan2	Csp2|Dscr1l1|MCIP2|ZAKI-4	regulator of calcineurin 2	protein-coding
mm_57832.1	chr6	129464878	129464884	-	1	NA	intron (NR_132130, intron 5 of 5)	intron (NR_132130, intron 5 of 5)	7898	NM_001309637	56644	Mm.239516	NM_020008	ENSMUSG00000079293	Clec7a	BGR|Clecsf12|beta-GR	C-type lectin domain family 7, member a	protein-coding
mm_154045.1	chr19	53944622	53944632	-	1	NA	promoter-TSS (NM_019658)	promoter-TSS (NM_019658)	0	NM_001195348	100503572	Mm.375091	NM_001195338	ENSMUSG00000084957	Bbip1	2310002J21Rik|2610002B11Rik|4930560M04Rik|Ncrna00081	BBSome interacting protein 1	protein-coding
mm_115609.1	chr13	11991986	11992006	-	1	NA	intron (NM_023868, intron 1 of 104)	B4A|SINE|B4	114949	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding
mm_163681.1	chr13	92576225	92576231	-	1	NA	promoter-TSS (NM_030237)	promoter-TSS (NM_030237)	4	NM_030237	79401	Mm.23520	NM_030237	ENSMUSG00000046957	Spz1	1700027M20Rik|AI429130	spermatogenic leucine zipper 1	protein-coding
mm_58816.1	chr7	16401269	16401283	+	1	NA	promoter-TSS (NM_198631)	promoter-TSS (NM_198631)	80	NM_198631	330474	Mm.333594	NM_198631	ENSMUSG00000059273	Zc3h4	Bwq1|Gm768|Kiaa1064-hp|mKIAA1064	zinc finger CCCH-type containing 4	protein-coding
mm_81545.1	chr9	110247261	110247272	+	1	NA	exon (NM_013884, exon 2 of 5)	exon (NM_013884, exon 2 of 5)	3483	NM_001166273	29873	Mm.38496	NM_013884	ENSMUSG00000032482	Cspg5	Caleb|Ngc	chondroitin sulfate proteoglycan 5	protein-coding
mm_126931.1	chr15	91677017	91677020	+	1	NA	intron (NM_025730, intron 2 of 50)	intron (NM_025730, intron 2 of 50)	3794	NM_025730	66725	Mm.37558	NM_025730	ENSMUSG00000036273	Lrrk2	4921513O20Rik|9330188B09Rik|AW561911|D630001M17Rik|Gm927|cI-46	leucine-rich repeat kinase 2	protein-coding
mm_60195.1	chr7	43408483	43408518	+	1	NA	intron (NM_172900, intron 1 of 11)	intron (NM_172900, intron 1 of 11)	220	NM_172900	243958	Mm.24444	NM_172900	ENSMUSG00000030468	Siglecg	9830164H23|A630096C01Rik|Siglec-G|Siglec10|mSiglec-G	sialic acid binding Ig-like lectin G	protein-coding
mm_8276.1	chr1	139858685	139858729	-	1	NA	promoter-TSS (NM_001025575)	promoter-TSS (NM_001025575)	-8	NM_001025575	545366	Mm.439660	NM_001025575	ENSMUSG00000033898	Cfhr2	Cfhrb_4/2	complement factor H-related 2	protein-coding
mm_21758.1	chr2	164839802	164839815	-	1	NA	exon (NM_011125, exon 16 of 16)	exon (NM_011125, exon 16 of 16)	6035	NM_008906	19025	Mm.359633	NM_008906	ENSMUSG00000017760	Ctsa	AU019505|PPCA|Ppgb	cathepsin A	protein-coding
mm_30505.1	chr3	158021401	158021430	-	1	NA	exon (NM_001093753, exon 5 of 12)	exon (NM_001093753, exon 5 of 12)	10339	NM_001093753	69207	Mm.223946	NM_026989	ENSMUSG00000055436	Srsf11	0610009J05Rik|2610019N13Rik|BF642805|Sfrs11	serine/arginine-rich splicing factor 11	protein-coding
mm_116490.1	chr13	44679280	44679284	-	1	NA	Intergenic	RLTR45|LTR|ERVK	-51492	NM_021878	16468	Mm.25059	NM_021878	ENSMUSG00000038518	Jarid2	Jmj|jumonji	jumonji, AT rich interactive domain 2	protein-coding
mm_110821.1	chr12	72408742	72408759	-	1	NA	5' UTR (NM_001286448, exon 1 of 7)	5' UTR (NM_001286448, exon 1 of 7)	304	NM_001286448	104001	Mm.221275	NM_153457	ENSMUSG00000021087	Rtn1	Nsp	reticulon 1	protein-coding
mm_56359.1	chr6	93811091	93811093	-	1	NA	intron (NM_001083321, intron 2 of 21)	L1_Mur3|LINE|L1	101871	NR_104594	14924	Mm.217216	NM_010367	ENSMUSG00000045095	Magi1	AIP3|BAP1|Baiap1|Gukmi1|MAGI1c|Magi-1|TNRC19|WWP3|mKIAA4129	membrane associated guanylate kinase, WW and PDZ domain containing 1	protein-coding
mm_104246.1	chr11	88844435	88844454	-	1	NA	exon (NM_009648, exon 2 of 11)	exon (NM_009648, exon 2 of 11)	7059	NM_009648	11640	Mm.2969	NM_009648	ENSMUSG00000018428	Akap1	AKAP121|AKAP84|Akap|C76494|C81186|DAKAP1|S-AKAP84	A kinase (PRKA) anchor protein 1	protein-coding
mm_9398.1	chr1	172220025	172220102	-	1	NA	promoter-TSS (NM_009813)	promoter-TSS (NM_009813)	-168	NM_009813	12372	Mm.12829	NM_009813	ENSMUSG00000007122	Casq1	CSQ|CSQ-1|CSQ1|sCSQ	calsequestrin 1	protein-coding
mm_98044.1	chr11	85614821	85614824	+	1	NA	intron (NM_138681, intron 24 of 25)	intron (NM_138681, intron 24 of 25)	104922	NR_045875	71489	Mm.442482	NR_045875	ENSMUSG00000086199	Bcas3os1	8430403D17Rik	breast carcinoma amplified sequence 3, opposite strand 1	ncRNA
mm_59476.1	chr7	27459325	27459344	+	1	NA	exon (NM_144923, exon 2 of 5)	exon (NM_144923, exon 2 of 5)	6916	NM_001290525	233016	Mm.24021	NM_144923	ENSMUSG00000040466	Blvrb	-	biliverdin reductase B (flavin reductase (NADPH))	protein-coding
mm_110075.1	chr12	21481720	21481727	-	1	NA	Intergenic	Intergenic	-64287	NM_011739	22630	Mm.289630	NM_011739	ENSMUSG00000076432	Ywhaq	2700028P07Rik|AA409740|AU021156|R74690	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide	protein-coding
mm_101666.1	chr11	36823560	36823562	-	1	NA	intron (NM_011856, intron 2 of 28)	intron (NM_011856, intron 2 of 28)	120680	NM_001290702	23964	Mm.439889	NM_011856	ENSMUSG00000049336	Tenm2	Odz2|Odz3|Ten-2|Ten-m2	teneurin transmembrane protein 2	protein-coding
mm_101773.1	chr11	44470465	44470513	-	1	NA	promoter-TSS (NM_024475)	promoter-TSS (NM_024475)	59	NM_024475	79560	Mm.338784	NM_024475	ENSMUSG00000041231	Ublcp1	4930527B16Rik|8430435I17Rik|BC002236	ubiquitin-like domain containing CTD phosphatase 1	protein-coding
mm_144575.1	chr18	31860611	31860625	+	1	NA	intron (NM_028866, intron 7 of 21)	intron (NM_028866, intron 7 of 21)	51285	NM_026006	67158	Mm.31537	NM_026006	ENSMUSG00000044982	Sft2d3	2610206C24Rik|AI847965|AW046173	SFT2 domain containing 3	protein-coding
mm_115567.1	chr13	9765241	9765257	-	1	NA	promoter-TSS (NM_001347480)	promoter-TSS (NM_001347480)	72	NM_001347474	66505	Mm.397307	NM_144516	ENSMUSG00000021156	Zmynd11	2210402G22Rik|BS69	zinc finger, MYND domain containing 11	protein-coding
mm_116745.1	chr13	51788407	51788411	-	1	NA	intron (NM_013660, intron 1 of 15)	intron (NM_013660, intron 1 of 15)	5338	NM_001281880	20354	Mm.33903	NM_013660	ENSMUSG00000021451	Sema4d	CD100|Semacl2|Semaj|Semcl2|coll-4	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D	protein-coding
mm_18080.1	chr2	43739017	43739029	-	1	NA	Intergenic	Intergenic	-9801	NM_001301832	76117	Mm.217350	NM_153820	ENSMUSG00000049744	Arhgap15	5830480G12Rik	Rho GTPase activating protein 15	protein-coding
mm_48651.1	chr5	145860142	145860158	-	1	NA	intron (NM_007818, intron 11 of 12)	intron (NM_007818, intron 11 of 12)	19704	NM_007818	13112	Mm.332844	NM_007818	ENSMUSG00000056035	Cyp3a11	AI256190|Cyp3a|IIIAm1|Pcn	cytochrome P450, family 3, subfamily a, polypeptide 11	protein-coding
mm_142273.1	chr17	39847916	39847961	-	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	4941	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_153208.1	chr19	34691542	34691565	-	1	NA	intron (NM_172838, intron 1 of 6)	intron (NM_172838, intron 1 of 6)	50664	NM_008331	15957	Mm.439751	NM_008331	ENSMUSG00000034459	Ifit1	ISG56|Ifi56|P56	interferon-induced protein with tetratricopeptide repeats 1	protein-coding
mm_137192.1	chr17	23822491	23822504	+	1	NA	exon (NM_175229, exon 11 of 14)	exon (NM_175229, exon 11 of 14)	6612	NM_026305	67673	Mm.153758	NM_026305	ENSMUSG00000055839	Elob	0610040H15Rik|Tceb2	elongin B	protein-coding
mm_9544.1	chr1	173912949	173912961	-	1	NA	promoter-TSS (NM_001301745)	promoter-TSS (NM_001301745)	91	NM_001301745	381308	Mm.490248	NM_001033450	ENSMUSG00000026536	Ifi211	A730048F03|Ifi205b|Mnda|ifi-205-B	interferon activated gene 211	protein-coding
mm_16764.1	chr2	9878156	9878194	-	1	NA	intron (NM_008091, intron 1 of 5)	intron (NM_008091, intron 1 of 5)	425	NM_008091	14462	Mm.313866	NM_008091	ENSMUSG00000015619	Gata3	Gata-3|jal	GATA binding protein 3	protein-coding
mm_91712.1	chr10	44148963	44148969	-	1	NA	Intergenic	CpG	-21481	NR_001582	70365	Mm.87073	NR_001582	ENSMUSG00000091358	Speer5-ps1	1700007C10Rik|SPEER-5|Speer5-ps	spermatogenesis associated glutamate (E)-rich protein 5, pseudogene 1	pseudo
mm_66483.1	chr7	45017268	45017279	-	1	NA	promoter-TSS (NM_009101)	promoter-TSS (NM_009101)	-734	NM_009101	20130	Mm.389894	NM_009101	ENSMUSG00000038387	Rras	AI573426	related RAS viral (r-ras) oncogene	protein-coding
mm_135290.1	chr16	38522663	38522683	-	1	NA	promoter-TSS (NM_024273)	promoter-TSS (NM_024273)	-10	NM_024273	76916	Mm.132231	NM_024273	ENSMUSG00000002846	Timmdc1	2810021C21Rik|4930455C21Rik|AV135763	translocase of inner mitochondrial membrane domain containing 1	protein-coding
mm_121427.1	chr14	120326558	120326578	+	1	NA	intron (NM_175341, intron 2 of 8)	B4|SINE|B4	50899	NM_175341	105559	Mm.238266	NM_175341	ENSMUSG00000022139	Mbnl2	1110002M11Rik|AI047808|AI837313|AI849185|AL118326|MBLL|R75232|mKIAA4072	muscleblind-like 2	protein-coding
mm_117614.1	chr13	91591419	91591419	-	1	NA	intron (NM_024186, intron 4 of 15)	MTC|LTR|ERVL-MaLR	130322	NM_024186	66970	Mm.343095	NM_024186	ENSMUSG00000003992	Ssbp2	1500004K09Rik|2310079I02Rik|9330163K02Rik|A830008M03Rik|AU067692|AW558684|Hspc116|SSDP2	single-stranded DNA binding protein 2	protein-coding
mm_134077.1	chr16	8682744	8682751	-	1	NA	intron (NM_001324517, intron 1 of 3)	MIRc|SINE|MIR	1977	NM_001324517	436336	Mm.357666	NM_001324517		Gm5767	EG436336	predicted gene 5767	protein-coding
mm_103759.1	chr11	80858313	80858321	-	1	NA	promoter-TSS (NM_029367)	promoter-TSS (NM_029367)	-17	NR_110449	75043	Mm.410815	NR_110449	ENSMUSG00000086703	4930507D10Rik	-	RIKEN cDNA 4930507D10 gene	ncRNA
mm_115945.1	chr13	23710786	23710829	-	1	NA	promoter-TSS (NM_001347493)	promoter-TSS (NM_001347493)	47	NM_001347493	15216	Mm.2681	NM_010424	ENSMUSG00000006611	Hfe	MR2	hemochromatosis	protein-coding
mm_141846.1	chr17	34801374	34801391	-	1	NA	TTS (NM_009995)	TTS (NM_009995)	3044	NM_009995	13079	Mm.440407	NM_009995	ENSMUSG00000024365	Cyp21a1	21-OH|21OH|21OHA|21OHB|CYP21OH-A|Cyp21|Cyp21-ps1|Cyp21B|Cyp21a2-ps|Cyp21a2ps|Oh21-1|Oh21-2	cytochrome P450, family 21, subfamily a, polypeptide 1	protein-coding
mm_128330.1	chr15	38299691	38299693	-	1	NA	intron (NM_001289471, intron 1 of 4)	CpG	1019	NM_013692	21847	Mm.4292	NM_013692	ENSMUSG00000037465	Klf10	AI115143|EGR[a]|Egral|Gdnfif|TIEG-1|Tieg|Tieg1|mGIF	Kruppel-like factor 10	protein-coding
mm_34656.1	chr4	150865374	150865408	+	1	NA	exon (NM_133753, exon 3 of 4)	exon (NM_133753, exon 3 of 4)	10300	NM_133753	74155	Mm.318841	NM_133753	ENSMUSG00000028967	Errfi1	1300002F13Rik|AI788755|Mig-6|Mig6|RALT	ERBB receptor feedback inhibitor 1	protein-coding
mm_19598.1	chr2	102400457	102400469	-	1	NA	exon (NM_020267, exon 1 of 5)	exon (NM_020267, exon 1 of 5)	437	NM_020267	80985	Mm.315002	NM_020267	ENSMUSG00000027189	Trim44	Dipb|Mc7	tripartite motif-containing 44	protein-coding
mm_155773.1	chrX	96255713	96255721	+	1	NA	intron (NM_177789, intron 4 of 6)	MTEa|LTR|ERVL-MaLR	12900	NR_029801	723814		NR_029801	ENSMUSG00000076066	Mir223	Mirn223|miR-223|mmu-mir-223	microRNA 223	ncRNA
mm_152361.1	chr19	10091798	10091822	-	1	NA	exon (NM_019699, exon 2 of 12)	exon (NM_019699, exon 2 of 12)	9693	NM_019699	56473	Mm.38901	NM_019699	ENSMUSG00000024665	Fads2	2900042M13Rik|Fadsd2	fatty acid desaturase 2	protein-coding
mm_110795.1	chr12	72116260	72116264	-	1	NA	intron (NM_028687, intron 14 of 20)	intron (NM_028687, intron 14 of 20)	30423	NM_024205	104771	Mm.258935	NM_024205	ENSMUSG00000005078	Jkamp	1200003C05Rik|2310047L11Rik|Jamp	JNK1/MAPK8-associated membrane protein	protein-coding
mm_106987.1	chr12	10390757	10390836	+	1	NA	promoter-TSS (NM_023697)	promoter-TSS (NM_023697)	16	NM_023697	105014	Mm.119343	NM_023697	ENSMUSG00000020621	Rdh14	3110030G19Rik|AW215439|PAN2	retinol dehydrogenase 14 (all-trans and 9-cis)	protein-coding
mm_140305.1	chr17	85629110	85629133	+	1	NA	Intergenic	Intergenic	8287	NM_011381	20473	Mm.370208	NM_011381	ENSMUSG00000038805	Six3	E130112M24Rik|Six3a|Six3alpha|Six3b|Six3beta	sine oculis-related homeobox 3	protein-coding
mm_28814.1	chr3	96259792	96259796	-	1	NA	Intergenic	Intergenic	3523	NM_033596	97122	Mm.227295	NM_033596	ENSMUSG00000091405	Hist2h4	H4|X04652	histone cluster 2, H4	protein-coding
mm_5471.1	chr1	36558215	36558266	-	1	NA	promoter-TSS (NM_001304329)	promoter-TSS (NM_001304329)	141	NM_001126047	20353	Mm.29558	NM_001126047	ENSMUSG00000026121	Sema4c	AI426163|M-Sema F|Semacl1|Semaf|Semai|sema I	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4C	protein-coding
mm_1931.1	chr1	86110977	86110983	+	1	NA	5' UTR (NM_008311, exon 2 of 4)	5' UTR (NM_008311, exon 2 of 4)	990	NM_008311	15559	Mm.439747	NM_008311	ENSMUSG00000026228	Htr2b	5-HT2B|AJ012488|AV377389	5-hydroxytryptamine (serotonin) receptor 2B	protein-coding
mm_52690.1	chr6	118163091	118163103	+	1	NA	intron (NM_001080780, intron 18 of 18)	intron (NM_001080780, intron 18 of 18)	-23957	NM_030165	78752	Mm.300317	NM_030165	ENSMUSG00000042042	Csgalnact2	4632415D10Rik|Galnact2	chondroitin sulfate N-acetylgalactosaminyltransferase 2	protein-coding
mm_13312.1	chr2	102658844	102658852	+	1	NA	5' UTR (NM_001077514, exon 1 of 11)	5' UTR (NM_001077514, exon 1 of 11)	165	NM_001077514	20511	Mm.267547	NM_011393	ENSMUSG00000005089	Slc1a2	1700091C19Rik|2900019G14Rik|AI159670|Eaat2|GLT-1|GLT1|MGLT1	solute carrier family 1 (glial high affinity glutamate transporter), member 2	protein-coding
mm_96016.1	chr11	59542984	59543001	+	1	NA	intron (NM_145827, intron 1 of 9)	intron (NM_145827, intron 1 of 9)	306	NM_145827	216799	Mm.54174	NM_145827	ENSMUSG00000032691	Nlrp3	AGTAVPRL|AII/AVP|Cias1|FCAS|FCU|MWS|Mmig1|NALP3|Pypaf1	NLR family, pyrin domain containing 3	protein-coding
mm_29662.1	chr3	122569711	122569749	-	1	NA	exon (NM_001114665, exon 4 of 16)	exon (NM_001114665, exon 4 of 16)	-28049	NR_106117	102465764		NR_106117	ENSMUSG00000104773	Mir7657	mmu-mir-7657	microRNA 7657	ncRNA
mm_25135.1	chr3	102469899	102469912	+	1	NA	promoter-TSS (NM_013609)	promoter-TSS (NM_013609)	-14	NM_001112698	18049	Mm.1259	NM_013609	ENSMUSG00000027859	Ngf	Ngfb	nerve growth factor	protein-coding
mm_163196.1	chr11	95830523	95830544	+	1	NA	3' UTR (NM_001163464, exon 8 of 8)	3' UTR (NM_001163464, exon 8 of 8)	6033	NM_153104	237928	Mm.133075	NM_153104	ENSMUSG00000050860	Phospho1	D11Moh36|Phospo1	phosphatase, orphan 1	protein-coding
mm_113314.1	chr13	30764126	30764132	+	1	NA	3' UTR (NM_013674, exon 9 of 9)	3' UTR (NM_013674, exon 9 of 9)	14896	NM_013674	16364	Mm.4677	NM_013674	ENSMUSG00000021356	Irf4	AI385587|IRF-4|LSIRF|NF-EM5|Spip	interferon regulatory factor 4	protein-coding
mm_34087.1	chr4	138832882	138832896	+	1	NA	intron (NM_001082531, intron 2 of 5)	intron (NM_001082531, intron 2 of 5)	1013	NM_001082531	18780	Mm.4675	NM_011108	ENSMUSG00000058908	Pla2g2a	EF|Mom1|Pla2|sPLA2|sPla2-IIA	phospholipase A2, group IIA (platelets, synovial fluid)	protein-coding
mm_27580.1	chr3	59098377	59098382	-	1	NA	5' UTR (NM_173398, exon 2 of 2)	5' UTR (NM_173398, exon 2 of 2)	3442	NM_173398	229323	Mm.123648	NM_173398	ENSMUSG00000050075	Gpr171	A630006E05|F730001G15Rik|H963	G protein-coupled receptor 171	protein-coding
mm_71364.1	chr8	45695470	45695483	+	1	NA	intron (NM_001310708, intron 1 of 19)	intron (NM_001310708, intron 1 of 19)	33483	NM_001310708	234214	Mm.211096	NM_172752	ENSMUSG00000031626	Sorbs2	2010203O03Rik|9430041O17Rik|A530071H08|Argbp2|mKIAA0777|nArgBP2	sorbin and SH3 domain containing 2	protein-coding
mm_25266.1	chr3	104794022	104794041	+	1	NA	TTS (NM_008619)	TTS (NM_008619)	4997	NM_007484	11853	Mm.262	NM_007484	ENSMUSG00000002233	Rhoc	AI324259|Arh9|Arhc	ras homolog family member C	protein-coding
mm_158921.1	chr1	59120442	59120442	-	1	NA	promoter-TSS (NM_001037812)	promoter-TSS (NM_001037812)	-346	NM_001033449	381259	Mm.261275	NM_001033449	ENSMUSG00000038079	Tmem237	AI853305|Als2cr4|Gm972	transmembrane protein 237	protein-coding
mm_4512.1	chr1	174211655	174211658	+	1	NA	intron (NM_011465, intron 25 of 51)	intron (NM_011465, intron 25 of 51)	38880	NM_011465	20739	Mm.200611	NM_011465	ENSMUSG00000026532	Spta1	AF093576|AI451697|Spna-1|Spna1|ha|ihj|nmf4|sph	spectrin alpha, erythrocytic 1	protein-coding
mm_98430.1	chr11	94681811	94681815	+	1	NA	Intergenic	ID_B1|SINE|B4	-4320	NM_145828	217119	Mm.100638	NM_145828	ENSMUSG00000020868	Xylt2	E030002B02Rik|XT-II|XT2|xylT-II	xylosyltransferase II	protein-coding
mm_161228.1	chr13	76825477	76825477	+	1	NA	intron (NM_030174, intron 13 of 20)	intron (NM_030174, intron 13 of 20)	309991	NM_134071	105377	Mm.209730	NM_134071	ENSMUSG00000021597	Slf1	2700017A04Rik|AW545819|Ankrd32|Brctd1|Brctx|C730024G01Rik	SMC5-SMC6 complex localization factor 1	protein-coding
mm_118818.1	chr14	25517505	25517524	+	1	NA	intron (NM_001310666, intron 2 of 23)	intron (NM_001310666, intron 2 of 23)	-16925	NR_037236	100526533		NR_037236	ENSMUSG00000093081	Mir3075	mir-3075|mmu-mir-3075	microRNA 3075	ncRNA
mm_165405.1	chr2	140671381	140671387	-	1	NA	promoter-TSS (NM_178382)	promoter-TSS (NM_178382)	92	NM_001172160	71436	Mm.426781	NM_178382	ENSMUSG00000051379	Flrt3	5530600M07Rik|C430047I10Rik|mKIAA1469	fibronectin leucine rich transmembrane protein 3	protein-coding
mm_152193.1	chr19	7483086	7483123	-	1	NA	5' UTR (NM_053076, exon 1 of 7)	5' UTR (NM_053076, exon 1 of 7)	187	NM_001271486	20168	Mm.246990	NM_053076	ENSMUSG00000024758	Rtn3	RTN3-A1	reticulon 3	protein-coding
mm_55724.1	chr6	73608668	73608675	-	1	NA	Intergenic	RMER17A|LTR|ERVK	-137650	NR_108032	73408	Mm.233629	NR_108032	ENSMUSG00000107408	1700065L07Rik	-	RIKEN cDNA 1700065L07 gene	ncRNA
mm_144698.1	chr18	34862597	34862616	+	1	NA	exon (NM_007913, exon 2 of 2)	exon (NM_007913, exon 2 of 2)	1399	NM_007913	13653	Mm.181959	NM_007913	ENSMUSG00000038418	Egr1	A530045N19Rik|ETR103|Egr-1|Krox-1|Krox-24|Krox24|NGF1-A|NGFI-A|NGFIA|TIS8|Zenk|Zfp-6|Zif268|egr	early growth response 1	protein-coding
mm_138870.1	chr17	43077312	43077318	+	1	NA	intron (NM_178589, intron 4 of 5)	intron (NM_178589, intron 4 of 5)	60760	NM_178589	94185	Mm.200792	NM_178589	ENSMUSG00000023915	Tnfrsf21	AA959878|DR6|R74815|TR7	tumor necrosis factor receptor superfamily, member 21	protein-coding
mm_109529.1	chr12	111538470	111538482	+	1	NA	5' UTR (NM_178041, exon 2 of 12)	5' UTR (NM_178041, exon 2 of 12)	375	NM_173363	217869	Mm.271222	NM_173363	ENSMUSG00000021282	Eif5	2810011H21Rik|D12Ertd549e	eukaryotic translation initiation factor 5	protein-coding
mm_6371.1	chr1	72284249	72284266	-	1	NA	promoter-TSS (NM_175564)	promoter-TSS (NM_175564)	57	NM_023523	111175	Mm.281738	NM_023523	ENSMUSG00000026189	Pecr	2400003B18Rik|TERP	peroxisomal trans-2-enoyl-CoA reductase	protein-coding
mm_26771.1	chr3	8937982	8937985	-	1	NA	intron (NM_001025263, intron 4 of 6)	intron (NM_001025263, intron 4 of 6)	-14126	NM_025434	66230	Mm.38460	NM_025434	ENSMUSG00000040269	Mrps28	1500012D08Rik|AW061224	mitochondrial ribosomal protein S28	protein-coding
mm_147814.1	chr18	61726303	61726336	-	1	NA	promoter-TSS (NM_021296)	promoter-TSS (NM_021296)	12	NM_021296	17714	Mm.269657	NM_021296	ENSMUSG00000024580	Grpel2	mt-GrpE#2|mt-Grpel2	GrpE-like 2, mitochondrial	protein-coding
mm_46516.1	chr5	105293689	105293705	-	1	NA	promoter-TSS (NM_194336)	promoter-TSS (NM_194336)	2	NM_194336	100702	Mm.491210	NM_194336	ENSMUSG00000079362	Gbp6	AI595338|Mpa2l	guanylate binding protein 6	protein-coding
mm_81942.1	chr9	120490157	120490166	+	1	NA	Intergenic	Intergenic	-2445	NM_026892	68969	Mm.28753	NM_026892	ENSMUSG00000006941	Eif1b	1500010M16Rik|3110001N14Rik|Gc20	eukaryotic translation initiation factor 1B	protein-coding
mm_21016.1	chr2	152397706	152397729	-	1	NA	5' UTR (NM_011438, exon 1 of 1)	5' UTR (NM_011438, exon 1 of 1)	329	NM_011438	20667	Mm.28424	NM_011438	ENSMUSG00000051817	Sox12	2010205A02Rik	SRY (sex determining region Y)-box 12	protein-coding
mm_89834.1	chr10	106632687	106632698	+	1	NA	intron (NM_001205341, intron 3 of 31)	intron (NM_001205341, intron 3 of 31)	-30212	NR_131026	75833	Mm.159596	NR_131026		4930532I03Rik	-	RIKEN cDNA 4930532I03 gene	ncRNA
mm_169039.1	chr13	13892250	13892264	-	1	NA	Intergenic	Intergenic	-62417	NM_178640	97884	Mm.21686	NM_178640	ENSMUSG00000039242	B3galnt2	A930105D20Rik|C80633|D230016N13Rik	UDP-GalNAc:betaGlcNAc beta 1,3-galactosaminyltransferase, polypeptide 2	protein-coding
mm_86613.1	chr10	13965240	13965248	+	1	NA	Intergenic	CpG	-1135	NM_010437	15273	Mm.42157	NM_010437	ENSMUSG00000015501	Hivep2	Gm20114|MIBP1|Schnurri-2|Shn-2	human immunodeficiency virus type I enhancer binding protein 2	protein-coding
mm_133994.1	chr16	4719044	4719054	-	1	NA	5' UTR (NM_001290761, exon 1 of 5)	5' UTR (NM_001290761, exon 1 of 5)	307	NM_001290763	67824	Mm.28451	NM_026393	ENSMUSG00000063445	Nmral1	1110025F24Rik|AI256624	NmrA-like family domain containing 1	protein-coding
mm_99354.1	chr11	101586233	101586322	+	1	NA	exon (NM_144830, exon 5 of 9)	exon (NM_144830, exon 5 of 9)	4035	NM_144830	217203	Mm.280559	NM_144830	ENSMUSG00000034947	Tmem106a	0610008L10Rik|AI043106|BC022145	transmembrane protein 106A	protein-coding
mm_64919.1	chr7	16247476	16247479	-	1	NA	3' UTR (NM_001173550, exon 2 of 2)	3' UTR (NM_001173550, exon 2 of 2)	-3323	NM_176912	319430	Mm.239570	NM_176912	ENSMUSG00000074361	C5ar2	C5L2|E030029A11Rik|Gpr77	complement component 5a receptor 2	protein-coding
mm_95000.1	chr11	31872787	31872797	+	1	NA	exon (NM_026252, exon 1 of 10)	exon (NM_026252, exon 1 of 10)	1852	NM_026252	67579	Mm.339792	NM_026252	ENSMUSG00000020300	Cpeb4	Cpe-bp4|Cpeb-4|mCPEB-4	cytoplasmic polyadenylation element binding protein 4	protein-coding
mm_4095.1	chr1	167331347	167331379	+	1	NA	3' UTR (NM_001039483, exon 7 of 7)	3' UTR (NM_001039483, exon 7 of 7)	-18628	NM_019993	56752	Mm.292539	NM_019993	ENSMUSG00000026687	Aldh9a1	AA139417|Abaldh|ESTM40|TMABA-DH|Tmabadh	aldehyde dehydrogenase 9, subfamily A1	protein-coding
mm_110657.1	chr12	59061481	59061483	-	1	NA	promoter-TSS (NM_001306218)	promoter-TSS (NM_001306218)	-10	NM_001306217	78232	Mm.290070	NM_030057	ENSMUSG00000020993	Trappc6b	5830498C14Rik|C79212	trafficking protein particle complex 6B	protein-coding
mm_44927.1	chr5	36037030	36037041	-	1	NA	intron (NM_030889, intron 17 of 26)	intron (NM_030889, intron 17 of 26)	143716	NM_027373	70292	Mm.125167	NM_027373	ENSMUSG00000029094	Afap1	2600003E23Rik|9630044L16Rik|AI848729|Afap|mKIAA3018	actin filament associated protein 1	protein-coding
mm_50313.1	chr6	47877549	47877569	+	1	NA	promoter-TSS (NM_146175)	promoter-TSS (NM_146175)	4	NM_146175	101095	Mm.440186	NM_146175	ENSMUSG00000025821	Zfp282	AI449432|C81429|E430019K09Rik|HUB1	zinc finger protein 282	protein-coding
mm_66488.1	chr7	45050911	45050939	-	1	NA	intron (NM_175022, intron 2 of 13)	intron (NM_175022, intron 2 of 13)	1956	NM_175022	233210	Mm.219137	NM_175022	ENSMUSG00000046574	Prr12	6720469B10|BC058674	proline rich 12	protein-coding
mm_138440.1	chr17	35122785	35122795	+	1	NA	promoter-TSS (NM_032460)	promoter-TSS (NM_032460)	-162	NM_032460	81845	Mm.7405	NM_032460	ENSMUSG00000092417	Gpank1	Bat-4|Bat4|D17H6S54E|G5	G patch domain and ankyrin repeats 1	protein-coding
mm_108723.1	chr12	87200337	87200345	+	1	NA	promoter-TSS (NM_001290288)	promoter-TSS (NM_001290288)	-112	NM_001033475	382620	Mm.374912	NM_001033475	ENSMUSG00000034111	Tmed8	6430595O10Rik|AI447224|Gm1184|Mem1	transmembrane p24 trafficking protein 8	protein-coding
mm_51192.1	chr6	71204901	71204932	+	1	NA	exon (NM_017399, exon 4 of 4)	exon (NM_017399, exon 4 of 4)	5028	NM_017399	14080	Mm.22126	NM_017399	ENSMUSG00000054422	Fabp1	Fabpl|L-FABP	fatty acid binding protein 1, liver	protein-coding
mm_121467.1	chr14	120910608	120910620	+	1	NA	promoter-TSS (NM_023579)	promoter-TSS (NM_023579)	-580	NM_023579	70572	Mm.221452	NM_023579	ENSMUSG00000030662	Ipo5	1110011C18Rik|5730478E03Rik|AA409333|C76941|IMB3|Kpnb3|Ranbp5	importin 5	protein-coding
mm_44959.1	chr5	36696746	36696758	-	1	NA	promoter-TSS (NM_001081232)	promoter-TSS (NM_001081232)	-731	NM_001081232	320661	Mm.26480	NM_177221	ENSMUSG00000029190	D5Ertd579e	9030221A05Rik|A930018H20Rik|Kiaa0232	DNA segment, Chr 5, ERATO Doi 579, expressed	protein-coding
mm_51579.1	chr6	83762666	83762692	+	1	NA	promoter-TSS (NR_105027)	promoter-TSS (NR_105027)	33	NM_029245	75305	Mm.391478	NM_029245	ENSMUSG00000014747	Ankrd53	4930564N15Rik	ankyrin repeat domain 53	protein-coding
mm_119835.1	chr14	54414105	54414127	+	1	NA	intron (NM_011405, intron 2 of 11)	intron (NM_011405, intron 2 of 11)	3563	NM_001253679	20540	Mm.142455	NM_011405	ENSMUSG00000000958	Slc7a7	AI790233|my+lat1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 7	protein-coding
mm_53158.1	chr6	125320634	125320639	+	1	NA	promoter-TSS (NM_011324)	promoter-TSS (NM_011324)	-704	NM_011324	20276	Mm.144114	NM_011324	ENSMUSG00000030340	Scnn1a	ENaC|SCNEA|Scnn1|mENaC	sodium channel, nonvoltage-gated 1 alpha	protein-coding
mm_40949.1	chr5	76840598	76840637	+	1	NA	promoter-TSS (NM_001163793)	promoter-TSS (NM_001163793)	18	NM_001163793	320827	Mm.101504	NM_001163793	ENSMUSG00000036377	C530008M17Rik	2810489J07Rik|4930529A19Rik|4931405B09Rik|Kiaa1211|mKIAA1211	RIKEN cDNA C530008M17 gene	protein-coding
mm_100951.1	chr11	6605662	6605670	-	1	NA	exon (NM_001081652, exon 1 of 8)	exon (NM_001081652, exon 1 of 8)	388	NM_001081652	192950	Mm.337771	NM_001081652	ENSMUSG00000041073	Nacad	D230024G13Rik|mKIAA0363	NAC alpha domain containing	protein-coding
mm_170655.1	chr2	104826211	104826222	-	1	NA	Intergenic	RLTR31B2|LTR|ERVK	-9520	NM_001123327	99003	Mm.274314	NM_001123327	ENSMUSG00000074994	Qser1	4732486I23Rik|AI502974	glutamine and serine rich 1	protein-coding
mm_28517.1	chr3	92584479	92584481	-	1	NA	exon (NM_008574, exon 2 of 2)	exon (NM_008574, exon 2 of 2)	4544	NM_008574	17235	Mm.331192	NM_008574		Smcp	Mcs|Mcsp	sperm mitochondria-associated cysteine-rich protein	protein-coding
mm_171197.1	chr3	47051785	47051804	-	1	NA	Intergenic	Intergenic	-151012	NR_105800	102465199		NR_105800	ENSMUSG00000098417	Mir6379	Gm27730|mmu-mir-6379	microRNA 6379	ncRNA
mm_146395.1	chr18	82910590	82910645	+	1	NA	promoter-TSS (NM_183033)	promoter-TSS (NM_183033)	-262	NM_183033	329003	Mm.326526	NM_183033	ENSMUSG00000058881	Zfp516	C330029B10Rik|D230016L03|Zfp26l|Znf516|mKIAA0222	zinc finger protein 516	protein-coding
mm_136261.1	chr16	91011417	91011431	-	1	NA	promoter-TSS (NM_001045515)	promoter-TSS (NM_001045515)	-116	NM_001164483	104015	Mm.187079	NM_001045515	ENSMUSG00000022973	Synj1	A930006D20Rik|AA675315|mKIAA0910	synaptojanin 1	protein-coding
mm_7222.1	chr1	93342583	93342597	-	1	NA	5' UTR (NM_080850, exon 1 of 18)	5' UTR (NM_080850, exon 1 of 18)	198	NM_080850	269224	Mm.379454	NM_080850	ENSMUSG00000026274	Pask	mKIAA0135	PAS domain containing serine/threonine kinase	protein-coding
mm_24333.1	chr3	89586372	89586373	+	1	NA	intron (NM_080466, intron 2 of 7)	intron (NM_080466, intron 2 of 7)	66208	NM_080466	140493	Mm.120250	NM_080466	ENSMUSG00000000794	Kcnn3	KCa2.3|SK3|SKCA3	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3	protein-coding
mm_157701.1	chrX	60892026	60892057	-	1	NA	3' UTR (NM_009237, exon 1 of 1)	3' UTR (NM_009237, exon 1 of 1)	1389	NM_009237	20675	Mm.35784	NM_009237	ENSMUSG00000045179	Sox3	Sox-3	SRY (sex determining region Y)-box 3	protein-coding
mm_76034.1	chr8	77376220	77376223	-	1	NA	intron (NM_030113, intron 13 of 22)	intron (NM_030113, intron 13 of 22)	-140835	NR_028125	70345	Mm.411813	NR_028125	ENSMUSG00000097882	0610038B21Rik	-	RIKEN cDNA 0610038B21 gene	ncRNA
mm_172215.1	chr6	62042185	62042187	-	1	NA	intron (NM_001164316, intron 10 of 10)	intron (NM_001164316, intron 10 of 10)	-861376	NR_040287	100504262	Mm.438066	NR_040287		A730020E08Rik	-	RIKEN cDNA A730020E08 gene	ncRNA
mm_153005.1	chr19	30175396	30175406	-	1	NA	promoter-TSS (NM_138595)	promoter-TSS (NM_138595)	40	NM_138595	104174	Mm.274852	NM_138595	ENSMUSG00000024827	Gldc	D030049L12Rik|D19Wsu57e	glycine decarboxylase	protein-coding
mm_36449.1	chr4	82498423	82498433	-	1	NA	exon (NM_001113209, exon 2 of 12)	exon (NM_001113209, exon 2 of 12)	7351	NM_001286127	18028	Mm.317947	NM_008687	ENSMUSG00000008575	Nfib	6720429L07Rik|CTF|E030026I10Rik|NF-I/B|NF1-B|NFI-B	nuclear factor I/B	protein-coding
mm_25095.1	chr3	101011015	101011048	+	1	NA	intron (NM_001167906, intron 6 of 8)	ORR1B1|LTR|ERVL-MaLR	18464	NM_001167906	630146	Mm.190915	NM_001099332	ENSMUSG00000086564	Cd101	EWI-101|Gm1016|Gm734|Igsf2	CD101 antigen	protein-coding
mm_161948.1	chr19	4625589	4625589	-	1	NA	promoter-TSS (NM_023131)	promoter-TSS (NM_023131)	28	NM_023131	19671	Mm.391143	NM_023131	ENSMUSG00000024889	Rce1	D19Ertd283e|D19Ertd98e	Ras converting CAAX endopeptidase 1	protein-coding
mm_86409.1	chr10	3366126	3366160	+	1	NA	promoter-TSS (NM_133485)	promoter-TSS (NM_133485)	-7	NM_133485	76142	Mm.308126	NM_133485	ENSMUSG00000040653	Ppp1r14c	6330514J04Rik|KEPI	protein phosphatase 1, regulatory (inhibitor) subunit 14c	protein-coding
mm_79439.1	chr9	56089989	56090007	+	1	NA	promoter-TSS (NM_011193)	promoter-TSS (NM_011193)	22	NM_011193	19200	Mm.2534	NM_011193	ENSMUSG00000032322	Pstpip1	CD2BP1|def-2	proline-serine-threonine phosphatase-interacting protein 1	protein-coding
mm_74109.1	chr8	122937854	122937883	+	1	NA	intron (NM_001081379, intron 2 of 12)	intron (NM_001081379, intron 2 of 12)	89494	NM_007662	12555	Mm.1976	NM_007662	ENSMUSG00000031962	Cdh15	AI323380|Cdh14|Mcad	cadherin 15	protein-coding
mm_81511.1	chr9	110034939	110034955	+	1	NA	exon (NM_008633, exon 7 of 19)	exon (NM_008633, exon 7 of 19)	-17074	NM_001311163	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_71043.1	chr8	33668448	33668461	+	1	NA	intron (NM_010344, intron 1 of 12)	intron (NM_010344, intron 1 of 12)	15216	NM_010344	14782	Mm.283573	NM_010344	ENSMUSG00000031584	Gsr	AI325518|D8Ertd238e|Gr-1|Gr1	glutathione reductase	protein-coding
mm_14766.1	chr2	145675343	145675358	+	1	NA	Intergenic	CpG	-25845	NR_033220	408057	Mm.486711	NR_033220	ENSMUSG00000087594	BC039771	-	cDNA sequence BC039771	ncRNA
mm_98935.1	chr11	98358385	98358400	+	1	NA	promoter-TSS (NR_045477)	promoter-TSS (NR_045477)	24	NM_021547	59045	Mm.265546	NM_021547	ENSMUSG00000018167	Stard3	Mln64|es64	START domain containing 3	protein-coding
mm_119297.1	chr14	34692531	34692543	+	1	NA	exon (NM_001301330, exon 3 of 19)	exon (NM_001301330, exon 3 of 19)	18609	NM_001301330	218914	Mm.27957	NM_001004436	ENSMUSG00000041408	Wapl	A530089A20Rik|BC037674|DIF-2|FOE|Wapal	WAPL cohesin release factor	protein-coding
mm_123091.1	chr14	55783601	55783645	-	1	NA	exon (NM_080435, exon 2 of 26)	exon (NM_080435, exon 2 of 26)	396	NM_080435	104110	Mm.287010	NM_080435	ENSMUSG00000022220	Adcy4	mKIAA4004	adenylate cyclase 4	protein-coding
mm_37070.1	chr4	116144611	116144626	-	1	NA	promoter-TSS (NM_026547)	promoter-TSS (NM_026547)	-2	NM_026547	68075	Mm.132803	NM_026547	ENSMUSG00000028701	Lurap1	1520402A15Rik|Lrp35a	leucine rich adaptor protein 1	protein-coding
mm_82845.1	chr9	31170521	31170524	-	1	NA	exon (NM_009691, exon 5 of 16)	exon (NM_009691, exon 5 of 16)	-38723	NM_011176	19143	Mm.243926	NM_011176	ENSMUSG00000031995	St14	Epithin|MT-SP1|Prss14|Tmprss14|mCAP3|matriptase	suppression of tumorigenicity 14 (colon carcinoma)	protein-coding
mm_149.1	chr1	11185255	11185258	+	1	NA	intron (NM_029525, intron 28 of 39)	intron (NM_029525, intron 28 of 39)	-78707	NM_001033636	109294	Mm.123247	NM_029525	ENSMUSG00000048960	Prex2	6230420N16Rik|AI316880|AI553603|C030045D06Rik|D430013K02|Depdc2|P-Rex2	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	protein-coding
mm_130111.1	chr15	89476318	89476328	-	1	NA	promoter-TSS (NR_077233)	promoter-TSS (NR_077233)	71	NR_077233	100532730	Mm.461541	NR_077233		C230037L18Rik	-	RIKEN cDNA C230037L18 gene	ncRNA
mm_130020.1	chr15	88734218	88734240	-	1	NA	promoter-TSS (NM_001033274)	promoter-TSS (NM_001033274)	-10	NM_001033274	223770	Mm.254438	NM_001033274	ENSMUSG00000022387	Brd1	1110059H06Rik|AI316859|mKIAA4191	bromodomain containing 1	protein-coding
mm_110777.1	chr12	70514011	70514015	-	1	NA	intron (NR_037248, intron 2 of 4)	Lx6|LINE|L1	60859	NM_028339	72736	Mm.204670	NM_028339	ENSMUSG00000021072	Tmx1	2810425A04Rik|AI465319|Txndc1	thioredoxin-related transmembrane protein 1	protein-coding
mm_19162.1	chr2	83917363	83917378	-	1	NA	intron (NM_027964, intron 7 of 8)	intron (NM_027964, intron 7 of 8)	23856	NM_027964	71861	Mm.116957	NM_027964	ENSMUSG00000034552	Zswim2	1700025P14Rik|4933437F18Rik|MEX	zinc finger SWIM-type containing 2	protein-coding
mm_7603.1	chr1	126173790	126173791	-	1	NA	intron (NM_001081756, intron 7 of 16)	RLTR44B|LTR|ERVK	-260862	NM_001311089	72585	Mm.490405	NM_145100	ENSMUSG00000026344	Lypd1	2700050C12Rik|AI853408|C530008O16Rik|Lynx2|Lypdc1	Ly6/Plaur domain containing 1	protein-coding
mm_141261.1	chr17	27623380	27623390	-	1	NA	promoter-TSS (NM_001291046)	promoter-TSS (NM_001291046)	67	NM_019837	56409	Mm.144699	NM_019837	ENSMUSG00000024213	Nudt3	1110011B09Rik|AA960325|Dipp|Dipp1	nudix (nucleotide diphosphate linked moiety X)-type motif 3	protein-coding
mm_36402.1	chr4	77856777	77856782	-	1	NA	intron (NM_011211, intron 2 of 39)	Lx3B|LINE|L1	355116	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding
mm_15470.1	chr2	157471167	157471183	+	1	NA	3' UTR (NM_001025395, exon 14 of 14)	3' UTR (NM_001025395, exon 14 of 14)	46882	NM_001025395	20779	Mm.22845	NM_009271	ENSMUSG00000027646	Src	AW259666|pp60c-src	Rous sarcoma oncogene	protein-coding
mm_8989.1	chr1	165707993	165708008	-	1	NA	promoter-TSS (NM_001038846)	promoter-TSS (NM_001038846)	94	NM_178593	226594	Mm.265552	NM_178593	ENSMUSG00000040723	Rcsd1	A430105K13Rik|BC025872|CapZIP	RCSD domain containing 1	protein-coding
mm_5559.1	chr1	38795085	38795087	-	1	NA	3' UTR (NM_001029878, exon 11 of 11)	3' UTR (NM_001029878, exon 11 of 11)	26129	NM_001029878	381338	Mm.487137	NM_028403	ENSMUSG00000048814	Lonrf2	2900060P06Rik|AI851349	LON peptidase N-terminal domain and ring finger 2	protein-coding
mm_4370.1	chr1	172102133	172102147	+	1	NA	intron (NM_009938, intron 9 of 32)	intron (NM_009938, intron 9 of 32)	-19391	NM_021607	59287	Mm.218203	NM_021607	ENSMUSG00000003458	Ncstn	9430068N19Rik|AA727311|Aph2|D1Dau13e|Kiaa0253|Nct|mKIAA0253	nicastrin	protein-coding
mm_8634.1	chr1	156420873	156420897	-	1	NA	promoter-TSS (NM_001346967)	promoter-TSS (NM_001346967)	30	NM_001346967	77352	Mm.428709	NM_001033180	ENSMUSG00000026601	Axdnd1	9430070O13Rik|Gm979	axonemal dynein light chain domain containing 1	protein-coding
mm_146495.1	chr18	3280998	3281015	-	1	NA	5' UTR (NM_001311067, exon 1 of 4)	5' UTR (NM_001311067, exon 1 of 4)	126	NM_001311066	12916	Mm.5244	NM_013498	ENSMUSG00000063889	Crem	ICER|ICERI	cAMP responsive element modulator	protein-coding
mm_100845.1	chr11	5762359	5762404	-	1	NA	promoter-TSS (NM_001077661)	promoter-TSS (NM_001077661)	-5	NM_001077661	72046	Mm.271657	NM_178623	ENSMUSG00000049680	Urgcp	2010005J08Rik|9130001I21Rik|AW060359|Urg4|mKIAA1507	upregulator of cell proliferation	protein-coding
mm_18641.1	chr2	69453225	69453230	-	1	NA	intron (NM_001081088, intron 61 of 78)	intron (NM_001081088, intron 61 of 78)	72765	NM_175512	241452	Mm.211655	NM_175512	ENSMUSG00000027068	Dhrs9	C730025I08Rik|Rdh15	dehydrogenase/reductase (SDR family) member 9	protein-coding
mm_169139.1	chr13	61804250	61804270	+	1	NA	Intergenic	Intergenic	32680	NR_028430	432812	Mm.317358	NR_028430		BC052688	-	cDNA sequence BC052688	pseudo
mm_99753.1	chr11	106723254	106723268	+	1	NA	Intergenic	Intergenic	-7980	NM_001305157	18613	Mm.343951	NM_008816	ENSMUSG00000020717	Pecam1	C85791|Cd31|PECAM-1|Pecam	platelet/endothelial cell adhesion molecule 1	protein-coding
mm_166368.1	chr5	125267244	125267244	+	1	NA	Intergenic	Intergenic	73850	NM_016741	20778	Mm.282242	NM_016741	ENSMUSG00000037936	Scarb1	AI120173|CD36|Cd36l1|Chohd1|Cla-1|Cla1|D5Ertd460e|Hdlq1|Hlb398|SR-B1|SR-BI|SRBI|Srb1|mSR-BI	scavenger receptor class B, member 1	protein-coding
mm_24499.1	chr3	92407984	92407997	+	1	NA	promoter-TSS (NM_011475)	promoter-TSS (NM_011475)	-1	NM_011475	20763	Mm.196439	NM_011475	ENSMUSG00000042157	Sprr2i	-	small proline-rich protein 2I	protein-coding
mm_63600.1	chr7	128144843	128144857	+	1	NA	exon (NM_021334, exon 22 of 30)	exon (NM_021334, exon 22 of 30)	15282	NM_021334	16411	Mm.22378	NM_021334	ENSMUSG00000030789	Itgax	AI449405|Cd11c|Cr4|N418	integrin alpha X	protein-coding
mm_68445.1	chr7	109986446	109986480	-	1	NA	promoter-TSS (NM_153525)	promoter-TSS (NM_153525)	-233	NM_153525	233724	Mm.43212	NM_153525	ENSMUSG00000047554	Tmem41b	1500015G02Rik|1500031M19Rik|AU018901|D7Ertd70e|D7Ertd743e	transmembrane protein 41B	protein-coding
mm_151081.1	chr19	47619823	47619837	+	1	NA	exon (NM_001164639, exon 9 of 18)	exon (NM_001164639, exon 9 of 18)	39811	NM_001164639	20874	Mm.281011	NM_009289	ENSMUSG00000025060	Slk	9A2|AV021402|AW411554|Etk4|SMAK|Stk2|mKIAA0204|mSLK	STE20-like kinase	protein-coding
mm_155147.1	chrX	52791161	52791173	+	1	NA	promoter-TSS (NM_001034059)	promoter-TSS (NM_001034059)	-33	NM_001034059	434778	Mm.23411	NM_001034059	ENSMUSG00000073207	Ccdc160	6330534C20Rik	coiled-coil domain containing 160	protein-coding
mm_143765.1	chr17	81629025	81629028	-	1	NA	intron (NR_104580, intron 2 of 8)	intron (NR_104580, intron 2 of 8)	109361	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_144445.1	chr18	22344914	22344925	+	1	NA	promoter-TSS (NM_001167777)	promoter-TSS (NM_001167777)	-170	NM_001167777	211961	Mm.392310	NM_001167777	ENSMUSG00000045215	Asxl3	C230079D11Rik|D430002O22Rik|D930044O18Rik|Gm329|Gm945	additional sex combs like 3 (Drosophila)	protein-coding
mm_60052.1	chr7	31149946	31149959	+	1	NA	intron (NM_027898, intron 1 of 18)	intron (NM_027898, intron 1 of 18)	1098	NM_027898	52857	Mm.27366	NM_027898	ENSMUSG00000001248	Gramd1a	1300003M23Rik|AI415002|AW547240|D7Bwg0611e	GRAM domain containing 1A	protein-coding
mm_123818.1	chr14	70540777	70540787	-	1	NA	Intergenic	ID_B1|SINE|B4	-4469	NM_180588	72549	Mm.46742	NM_180588	ENSMUSG00000033589	Reep4	2700029E10Rik	receptor accessory protein 4	protein-coding
mm_96659.1	chr11	69396108	69396180	+	1	NA	promoter-TSS (NM_001045525)	promoter-TSS (NM_001045525)	353	NM_030083	78304	Mm.45683	NM_030083	ENSMUSG00000059278	Naa38	1500034E06Rik|Lsmd1	N(alpha)-acetyltransferase 38, NatC auxiliary subunit	protein-coding
mm_19317.1	chr2	90556358	90556368	-	1	NA	intron (NM_008982, intron 1 of 23)	B4A|SINE|B4	24284	NM_008982	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_172450.1	chr7	32641236	32641242	-	1	NA	Intergenic	L1Md_T|LINE|L1	188414	NM_001281523	624439	Mm.326965	NM_001281523	ENSMUSG00000097972	Scgb2b15	Abpb15|EG624439|Gm6504	secretoglobin, family 2B, member 15	protein-coding
mm_7546.1	chr1	124504236	124504264	-	1	NA	Intergenic	RSINE1|SINE|B4	-458691	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_37283.1	chr4	119072925	119072941	-	1	NA	Intergenic	Intergenic	-3822	NR_131914	433751	Mm.224312	NR_131914	ENSMUSG00000066060	Gm12866	OTTMUSG00000008833	predicted gene 12866	ncRNA
mm_172457.1	chr7	40190905	40190925	+	1	NA	Intergenic	Intergenic	-483822	NR_045504	71029	Mm.399496	NR_045504	ENSMUSG00000102004	4933402C06Rik	-	RIKEN cDNA 4933402C06 gene	ncRNA
mm_115575.1	chr13	11572981	11572997	-	1	NA	intron (NM_023868, intron 97 of 104)	RSINE1|SINE|B4	50937	NR_027813	664793	Mm.410565	NR_027813		Zp4-ps	EG664793|Zp4|Zpb	zona pellucida glycoprotein 4, pseudogene	pseudo
mm_84558.1	chr9	67733739	67733749	-	1	NA	Intergenic	Intergenic	-4167	NR_106101	102465716		NR_106101	ENSMUSG00000098446	Mir7242	Gm27809|mmu-mir-7242	microRNA 7242	ncRNA
mm_41918.1	chr5	105606577	105606591	+	1	NA	exon (NM_133897, exon 4 of 4)	exon (NM_133897, exon 4 of 4)	87113	NM_133897	100604	Mm.319847	NM_133897	ENSMUSG00000054720	Lrrc8c	AD158|AI326115|E430036I04Rik|fad158	leucine rich repeat containing 8 family, member C	protein-coding
mm_140633.1	chr17	12507362	12507379	-	1	NA	5' UTR (NM_011395, exon 1 of 11)	5' UTR (NM_011395, exon 1 of 11)	334	NM_011395	20519	Mm.99252	NM_011395	ENSMUSG00000023828	Slc22a3	EMT|Oct3|Orct3|Slca22a3	solute carrier family 22 (organic cation transporter), member 3	protein-coding
mm_75339.1	chr8	43306691	43306701	-	1	NA	intron (NM_009556, intron 1 of 3)	intron (NM_009556, intron 1 of 3)	313	NM_009556	22702	Mm.285848	NM_009556	ENSMUSG00000051176	Zfp42	Rex-1|Rex1|Zfp-42	zinc finger protein 42	protein-coding
mm_150698.1	chr19	42255242	42255245	+	1	NA	promoter-TSS (NM_027694)	promoter-TSS (NM_027694)	-496	NM_027694	71146	Mm.329851	NM_027694	ENSMUSG00000042532	Golga7b	4933417O08Rik|AI839934	golgi autoantigen, golgin subfamily a, 7B	protein-coding
mm_7680.1	chr1	128589332	128589346	-	1	NA	exon (NM_009911, exon 2 of 2)	exon (NM_009911, exon 2 of 2)	2960	NM_009911	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding
mm_133460.1	chr16	89140885	89140889	+	1	NA	Intergenic	Intergenic	-64974	NM_001163615	622935	Mm.459837	NM_001163615	ENSMUSG00000091039	Krtap20-2	1190004K03Rik|EG622935|Gm6371	keratin associated protein 20-2	protein-coding
mm_36763.1	chr4	101356706	101356729	-	1	NA	promoter-TSS (NR_040708)	promoter-TSS (NR_040708)	-469	NR_040708	77866	Mm.137053	NR_040708	ENSMUSG00000086782	E130102H24Rik	-	RIKEN cDNA E130102H24 gene	ncRNA
mm_4175.1	chr1	171122034	171122053	+	1	NA	intron (NM_001081275, intron 1 of 5)	Lx8|LINE|L1	382	NM_001081275	75472	Mm.32760	NM_029301	ENSMUSG00000026649	Cfap126	1700009P17Rik|AV282292|Flattop|Fltp	cilia and flagella associated protein 126	protein-coding
mm_8439.1	chr1	152766357	152766367	-	1	NA	promoter-TSS (NM_026369)	promoter-TSS (NM_026369)	-57	NM_001346117	19731	Mm.245270	NM_016846	ENSMUSG00000026482	Rgl1	Rgl|mKIAA0959	ral guanine nucleotide dissociation stimulator,-like 1	protein-coding
mm_32793.1	chr4	116995307	116995342	+	1	NA	promoter-TSS (NM_009478)	promoter-TSS (NM_009478)	-24	NM_175244	76608	Mm.251420	NM_175244	ENSMUSG00000046861	Hectd3	1700064K09Rik|AI467540|AW743312	HECT domain containing 3	protein-coding
mm_112522.1	chr13	9175417	9175450	+	1	NA	TTS (NM_172585)	TTS (NM_172585)	81552	NM_172585	217980	Mm.234944	NM_172585	ENSMUSG00000033499	Larp4b	A630096F19|AI256361|D13Wsu64e|Larp5	La ribonucleoprotein domain family, member 4B	protein-coding
mm_77604.1	chr8	123893171	123893184	-	1	NA	exon (NM_009606, exon 3 of 7)	exon (NM_009606, exon 3 of 7)	1598	NM_001272041	11459	Mm.214950	NM_009606	ENSMUSG00000031972	Acta1	AA959943|Acta-2|Acts|Actsk-1	actin, alpha 1, skeletal muscle	protein-coding
mm_116770.1	chr13	52929485	52929497	-	1	NA	exon (NM_016709, exon 1 of 10)	exon (NM_016709, exon 1 of 10)	186	NM_016709	11992	Mm.252034	NM_016709	ENSMUSG00000021460	Auh	C77140|W91705	AU RNA binding protein/enoyl-coenzyme A hydratase	protein-coding
mm_145566.1	chr18	60812510	60812520	+	1	NA	TTS (NR_039567)	TTS (NR_039567)	439	NR_039567	100628611		NR_039567	ENSMUSG00000093327	Mir5107	mir-5107|mmu-mir-5107|mu-mir-5107	microRNA 5107	ncRNA
mm_57276.1	chr6	123290588	123290596	-	1	NA	promoter-TSS (NM_019948)	promoter-TSS (NM_019948)	-721	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_37299.1	chr4	119219206	119219228	-	1	NA	promoter-TSS (NM_029198)	promoter-TSS (NM_029198)	-1000	NM_029198	75180	Mm.179335	NM_029198	ENSMUSG00000028642	Tmem269	4930538K18Rik	transmembrane protein 269	protein-coding
mm_26419.1	chr3	142611482	142611490	+	1	NA	exon (NM_010259, exon 10 of 11)	exon (NM_010259, exon 10 of 11)	-9177	NM_010260	14469	Mm.24038	NM_010260	ENSMUSG00000028270	Gbp2	-	guanylate binding protein 2	protein-coding
mm_15317.1	chr2	155629367	155629385	+	1	NA	exon (NM_001085378, exon 29 of 42)	exon (NM_001085378, exon 29 of 42)	6496	NR_030757	735275		NR_030757	ENSMUSG00000076312	Mir499	Mirn499|mir-499|mmu-mir-499	microRNA 499	ncRNA
mm_106683.1	chr12	3235735	3235801	+	1	NA	promoter-TSS (NR_015551)	promoter-TSS (NR_015551)	-23	NR_015551	74173	Mm.309774	NM_028796	ENSMUSG00000079179	Rab10os	1700012B15Rik|1810036A22Rik	RAB10, member RAS oncogene family, opposite strand	ncRNA
mm_77043.1	chr8	109575671	109575753	-	1	NA	exon (NM_017370, exon 5 of 5)	exon (NM_017370, exon 5 of 5)	3460	NM_017370	15439	Mm.26730	NM_017370	ENSMUSG00000031722	Hp	HP-1|preHP2	haptoglobin	protein-coding
mm_47819.1	chr5	134231489	134231528	-	1	NA	Intergenic	Intergenic	-1883	NR_104383	17969	Mm.425296	NM_010876	ENSMUSG00000015950	Ncf1	NCF-47K|NOXO2|Ncf-1|p47-phox|p47<phox>|p47phox	neutrophil cytosolic factor 1	protein-coding
mm_85402.1	chr9	103365372	103365408	-	1	NA	promoter-TSS (NM_001134427)	promoter-TSS (NM_001134427)	390	NM_175833	321022	Mm.261025	NM_175565	ENSMUSG00000032803	Cdv3	2510010F10Rik|C230084J24Rik|C79446|TPP36	carnitine deficiency-associated gene expressed in ventricle 3	protein-coding
mm_159409.1	chr3	102203884	102203884	-	1	NA	intron (NM_177545, intron 1 of 7)	CpG	809	NM_177545	229658	Mm.118004	NM_177545	ENSMUSG00000027860	Vangl1	Kitenin|Lpp2|Stb2|Stbm	vang-like 1 (van gogh, Drosophila)	protein-coding
mm_82345.1	chr9	13821689	13821693	-	1	NA	intron (NM_026665, intron 1 of 10)	intron (NM_026665, intron 1 of 10)	5362	NR_037622	74360	Mm.157212	NM_026665	ENSMUSG00000031922	Cep57	3110002L15Rik|4921510P06Rik|4931428M20Rik|AI467480|Tsp57|mKIAA0092	centrosomal protein 57	protein-coding
mm_2378.1	chr1	93373845	93373860	+	1	NA	promoter-TSS (NM_207031)	promoter-TSS (NM_207031)	-44	NM_207031	404545	Mm.297411	NM_207031	ENSMUSG00000034107	Ano7	Ngep|Ngep-L|Pcanap5|Tmem16g	anoctamin 7	protein-coding
mm_100416.1	chr11	119430259	119430277	+	1	NA	Intergenic	Intergenic	39796	NR_035453	100316690		NR_035453	ENSMUSG00000088015	Mir1932	mir-1932|mmu-mir-1932	microRNA 1932	ncRNA
mm_97961.1	chr11	83740707	83740741	+	1	NA	Intergenic	Intergenic	-6216	NM_183249	66107	Mm.902	NM_183249	ENSMUSG00000051748	Wfdc21	1100001G20Rik|Wdnm1-like	WAP four-disulfide core domain 21	protein-coding
mm_57758.1	chr6	129232898	129232904	-	1	NA	non-coding (NR_040268, exon 4 of 4)	non-coding (NR_040268, exon 4 of 4)	5144	NR_040265	76432	Mm.261738	NR_040265	ENSMUSG00000097354	2310001H17Rik	AI646108	RIKEN cDNA 2310001H17 gene	ncRNA
mm_4733.1	chr1	181576586	181576616	+	1	NA	Intergenic	Intergenic	-65150	NM_207280	403180	Mm.220754	NM_207280	ENSMUSG00000050625	Ccdc121	6530421E24Rik|Gm755	coiled-coil domain containing 121	protein-coding
mm_47336.1	chr5	122501778	122501788	-	1	NA	non-coding (NR_027838, exon 1 of 21)	non-coding (NR_027838, exon 1 of 21)	442	NM_001110140	11938	Mm.227583	NM_009722	ENSMUSG00000029467	Atp2a2	9530097L16Rik|D5Wsu150e|SERCA2|SERCA2B|Serca2a|mKIAA4195	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	protein-coding
mm_158387.1	chrX	136170986	136171008	-	1	NA	exon (NM_025703, exon 3 of 3)	exon (NM_025703, exon 3 of 3)	1254	NM_001168578	66684	Mm.182094	NM_025703	ENSMUSG00000051579	Tceal8	3930402F23Rik	transcription elongation factor A (SII)-like 8	protein-coding
mm_96269.1	chr11	62761028	62761051	+	1	NA	Intergenic	RMER15-int|LTR|ERVL	28378	NM_138949	192651	Mm.168530	NM_138949	ENSMUSG00000047342	Zfp286	BC027023	zinc finger protein 286	protein-coding
mm_94957.1	chr11	30268296	30268336	+	1	NA	Intergenic	CpG	-48544	NM_175836	20742	Mm.123110	NM_009260	ENSMUSG00000020315	Sptbn1	9930031C03Rik|AL033301|SPTB2|Spnb-2|Spnb2|elf1|elf3|mKIAA4049	spectrin beta, non-erythrocytic 1	protein-coding
mm_93452.1	chr10	110084541	110084545	-	1	NA	Intergenic	Intergenic	-84324	NM_001081035	260315	Mm.225050	NM_177797	ENSMUSG00000020181	Nav3	4732483H20Rik|9630020C08Rik|POMFIL1|Pomfil1p|mKIAA0938|unc53H3	neuron navigator 3	protein-coding
mm_161614.1	chr16	49057423	49057423	+	1	NA	promoter-TSS (NM_001166210)	promoter-TSS (NM_001166210)	-63	NM_001166210	667772	Mm.301387	NM_001166210	ENSMUSG00000092009	Myh15	EG667772	myosin, heavy chain 15	protein-coding
mm_125012.1	chr15	25622748	25622754	+	1	NA	5' UTR (NM_019472, exon 1 of 41)	5' UTR (NM_019472, exon 1 of 41)	201	NM_019472	17909	Mm.60590	NM_019472	ENSMUSG00000022272	Myo10	AW048724|D15Ertd600e|mKIAA0799|myosin-X	myosin X	protein-coding
mm_144955.1	chr18	37813071	37813088	+	1	NA	intron (NM_033581, intron 1 of 3)	(CA)n|Simple_repeat|Simple_repeat	-2000	NM_033582	93707	Mm.247203	NM_033582	ENSMUSG00000023036	Pcdhgc4	-	protocadherin gamma subfamily C, 4	protein-coding
mm_31843.1	chr4	74251929	74251990	+	1	NA	promoter-TSS (NM_144787)	promoter-TSS (NM_144787)	80	NM_144787	76804	Mm.209059	NM_144787	ENSMUSG00000028397	Kdm4c	2410141F18Rik|AA517467|Gasc1|Jmjd2c	lysine (K)-specific demethylase 4C	protein-coding
mm_4366.1	chr1	172082781	172082793	+	1	NA	promoter-TSS (NM_021607)	promoter-TSS (NM_021607)	-38	NM_021607	59287	Mm.218203	NM_021607	ENSMUSG00000003458	Ncstn	9430068N19Rik|AA727311|Aph2|D1Dau13e|Kiaa0253|Nct|mKIAA0253	nicastrin	protein-coding
mm_63380.1	chr7	127213092	127213129	+	1	NA	intron (NM_001347655, intron 2 of 6)	intron (NM_001347655, intron 2 of 6)	1502	NM_016754	17907	Mm.14526	NM_016754	ENSMUSG00000030672	Mylpf	2410014J02Rik|MLC-2|Mlc2	myosin light chain, phosphorylatable, fast skeletal muscle	protein-coding
mm_23347.1	chr3	54755542	54755571	+	1	NA	promoter-TSS (NM_019483)	promoter-TSS (NM_019483)	-26	NM_019483	55994	Mm.244353	NM_019483	ENSMUSG00000027796	Smad9	MADH6|Madh8|Madh9|Smad8	SMAD family member 9	protein-coding
mm_44191.1	chr5	3480864	3480884	-	1	NA	intron (NM_009873, intron 5 of 7)	intron (NM_009873, intron 5 of 7)	-62959	NM_001042501	68152	Mm.240265	NM_026583	ENSMUSG00000058503	Fam133b	2900022K02Rik|5830415L20Rik	family with sequence similarity 133, member B	protein-coding
mm_82904.1	chr9	32915634	32915639	-	1	NA	intron (NR_131058, intron 1 of 3)	intron (NR_131058, intron 1 of 3)	13330	NR_131058	330917	Mm.488283	NR_131058		Gm27162	A430016B06	predicted gene 27162	ncRNA
mm_102615.1	chr11	62457936	62457946	-	1	NA	promoter-TSS (NM_177229)	promoter-TSS (NM_177229)	-519	NM_001039536	327942	Mm.390358	NM_199026	ENSMUSG00000014245	Pigl	Gm737	phosphatidylinositol glycan anchor biosynthesis, class L	protein-coding
mm_69762.1	chr7	141009739	141009750	-	1	NA	exon (NM_025378, exon 2 of 2)	exon (NM_025378, exon 2 of 2)	1000	NM_025378	66141	Mm.141021	NM_025378	ENSMUSG00000025492	Ifitm3	1110004C05Rik|Cd225|Cdw217|DSPA2b|Fgls|IP15|mil-1	interferon induced transmembrane protein 3	protein-coding
mm_92491.1	chr10	78298293	78298327	-	1	NA	intron (NM_053014, intron 2 of 9)	intron (NM_053014, intron 2 of 9)	41897	NR_106119	102465765		NR_106119	ENSMUSG00000098885	Mir7659	Gm27433|mmu-mir-7659	microRNA 7659	ncRNA
mm_67430.1	chr7	80370844	80370869	-	1	NA	5' UTR (NM_172903, exon 2 of 24)	5' UTR (NM_172903, exon 2 of 24)	519	NM_172903	140481	Mm.269245	NM_172903	ENSMUSG00000038886	Man2a2	1700052O22Rik|4931438M07Rik|AI480988|MX|Man IIx	mannosidase 2, alpha 2	protein-coding
mm_137484.1	chr17	26937972	26937979	+	1	NA	TTS (NM_026307)	TTS (NM_026307)	1483	NR_104458	67675	Mm.439919	NM_026307	ENSMUSG00000024194	Cuta	0610039D01Rik|1810022E02Rik|1810060C03Rik|2700094G22Rik|AI326454	cutA divalent cation tolerance homolog	protein-coding
mm_126447.1	chr15	80743794	80743838	+	1	NA	intron (NM_144812, intron 1 of 24)	intron (NM_144812, intron 1 of 24)	32503	NM_144812	213988	Mm.131328	NM_144812	ENSMUSG00000047888	Tnrc6b	2700090M07Rik|A730065C02Rik|AI848765|D230019K20Rik	trinucleotide repeat containing 6b	protein-coding
mm_57549.1	chr6	126740614	126740623	-	1	NA	promoter-TSS (NM_013568)	promoter-TSS (NM_013568)	56	NM_013568	16494	Mm.62535	NM_013568	ENSMUSG00000038077	Kcna6	Kv1.6|MK1.6	potassium voltage-gated channel, shaker-related, subfamily, member 6	protein-coding
mm_11417.1	chr2	31680277	31680280	+	1	NA	intron (NM_144886, intron 8 of 8)	intron (NM_144886, intron 8 of 8)	-8259	NM_001283047	11350	Mm.1318	NM_009594	ENSMUSG00000026842	Abl1	AI325092|Abl|E430008G22Rik|c-Abl	c-abl oncogene 1, non-receptor tyrosine kinase	protein-coding
mm_116405.1	chr13	41425128	41425146	-	1	NA	intron (NM_001111324, intron 2 of 7)	(TG)n|Simple_repeat|Simple_repeat	62223	NM_001111324	18003	Mm.288980	NM_017464	ENSMUSG00000021365	Nedd9	Cas-L|CasL|HEF1|MEF1|Nedd-9|p105	neural precursor cell expressed, developmentally down-regulated gene 9	protein-coding
mm_64367.1	chr7	142434981	142434991	+	1	NA	promoter-TSS (NM_001285857)	promoter-TSS (NM_001285857)	9	NM_018802	55925	Mm.213002	NM_018802	ENSMUSG00000031098	Syt8	-	synaptotagmin VIII	protein-coding
mm_23860.1	chr3	83011380	83011421	+	1	NA	exon (NM_133862, exon 7 of 10)	exon (NM_133862, exon 7 of 10)	3676	NM_001317105	99571	Mm.16422	NM_133862	ENSMUSG00000033860	Fgg	3010002H13Rik|AI256424	fibrinogen gamma chain	protein-coding
mm_24484.1	chr3	92024547	92024561	+	1	NA	intron (NM_207247, intron 2 of 6)	CpG	9971	NM_207247	242100	Mm.297406	NM_207247	ENSMUSG00000042244	Pglyrp3	Gm420	peptidoglycan recognition protein 3	protein-coding
mm_54703.1	chr6	39592522	39592554	-	1	NA	promoter-TSS (NM_026612)	promoter-TSS (NM_026612)	-45	NM_026612	68198	Mm.29415	NM_026612	ENSMUSG00000002416	Ndufb2	1810011O01Rik|8kDa|AGGG|AI325567|CI-AGGG	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 2	protein-coding
mm_19632.1	chr2	102813922	102813928	-	1	NA	3' UTR (NM_009851, exon 19 of 19)	3' UTR (NM_009851, exon 19 of 19)	87740	NM_001177785	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_36921.1	chr4	108118734	108118779	-	1	NA	promoter-TSS (NM_011327)	promoter-TSS (NM_011327)	-209	NM_011327	20280	Mm.379011	NM_011327	ENSMUSG00000028603	Scp2	AA409774|AA409893|C76618|C79031|NSL-TP|SCP-2|SCP-X|SCPX|ns-LTP	sterol carrier protein 2, liver	protein-coding
mm_15034.1	chr2	152754157	152754186	+	1	NA	promoter-TSS (NM_053091)	promoter-TSS (NM_053091)	-2	NM_053091	84682	Mm.196668	NM_053091	ENSMUSG00000009876	Cox4i2	Cox4b|CoxIV-2	cytochrome c oxidase subunit IV isoform 2	protein-coding
mm_103829.1	chr11	83020087	83020113	-	1	NA	intron (NM_181545, intron 1 of 5)	intron (NM_181545, intron 1 of 5)	622	NM_001167743	276950	Mm.491599	NM_181545	ENSMUSG00000035208	Slfn8	-	schlafen 8	protein-coding
mm_125933.1	chr15	76247665	76247676	+	1	NA	promoter-TSS (NR_105918)	promoter-TSS (NR_105918)	-521	NR_105918	102465575		NR_105918	ENSMUSG00000098625	Mir6953	Gm27738|mmu-mir-6953	microRNA 6953	ncRNA
mm_90540.1	chr10	128091160	128091168	+	1	NA	TTS (NM_016774)	TTS (NM_016774)	-1619	NM_054078	116848	Mm.252213	NM_054078	ENSMUSG00000040054	Baz2a	AA415431|C030005G16Rik|C78388|Tip5|Walp3|mKIAA0314	bromodomain adjacent to zinc finger domain, 2A	protein-coding
mm_30203.1	chr3	144720370	144720384	-	1	NA	promoter-TSS (NM_019464)	promoter-TSS (NM_019464)	-42	NM_001282037	54673	Mm.271775	NM_019464	ENSMUSG00000037062	Sh3glb1	AA409932|AI314629|AU015566|Bif-1|mKIAA0491	SH3-domain GRB2-like B1 (endophilin)	protein-coding
mm_90429.1	chr10	127515161	127515168	+	1	NA	intron (NM_001098789, intron 1 of 3)	intron (NM_001098789, intron 1 of 3)	225	NM_001098789	407790	Mm.336856	NM_001098789	ENSMUSG00000040280	Ndufa4l2	BC064011	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 4-like 2	protein-coding
mm_62323.1	chr7	100372225	100372383	+	1	NA	promoter-TSS (NM_001017985)	promoter-TSS (NM_001017985)	71	NM_001017985	277939	Mm.276374	NM_001017985	ENSMUSG00000047248	C2cd3	AU020772	C2 calcium-dependent domain containing 3	protein-coding
mm_86579.1	chr10	12975704	12975714	+	1	NA	Intergenic	ID_B1|SINE|B4	-11450	NM_001163591	74732	Mm.248648	NM_029075	ENSMUSG00000039232	Stx11	5830405C08Rik	syntaxin 11	protein-coding
mm_18947.1	chr2	76770548	76770560	-	1	NA	exon (NM_011652, exon 248 of 313)	exon (NM_011652, exon 248 of 313)	95239	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_122804.1	chr14	54554407	54554413	-	1	NA	promoter-TSS (NM_145462)	promoter-TSS (NM_145462)	-49	NM_145462	219072	Mm.202152	NM_145462	ENSMUSG00000022177	Haus4	9430093H08Rik|AU016300|D14Ertd500e	HAUS augmin-like complex, subunit 4	protein-coding
mm_172509.1	chr7	7098031	7098049	-	1	NA	Intergenic	Intergenic	23436	NM_172738	232853	Mm.23838	NM_172738	ENSMUSG00000062116	Zfp954	5730403M16Rik|8030437F07|AA123315	zinc finger protein 954	protein-coding
mm_79741.1	chr9	62351167	62351170	+	1	NA	intron (NM_009672, intron 1 of 6)	intron (NM_009672, intron 1 of 6)	9825	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	protein-coding
mm_111161.1	chr12	83562428	83562440	-	1	NA	intron (NM_183154, intron 4 of 11)	intron (NM_183154, intron 4 of 11)	34713	NM_183154	217695	Mm.59257	NM_183154	ENSMUSG00000042628	Zfyve1	DFCP1|G630053K23|TAFF1|ZNFN2A1|mKIAA1589	zinc finger, FYVE domain containing 1	protein-coding
mm_67869.1	chr7	99164662	99164692	-	1	NA	exon (NM_026384, exon 4 of 8)	exon (NM_026384, exon 4 of 8)	18036	NM_026384	67800	Mm.180189	NM_026384	ENSMUSG00000030747	Dgat2	0610010B06Rik|ARAT|DGAT-2	diacylglycerol O-acyltransferase 2	protein-coding
mm_132502.1	chr16	36952528	36952541	+	1	NA	intron (NM_008225, intron 6 of 13)	L1MD|LINE|L1	17551	NM_008225	15163	Mm.4091	NM_008225	ENSMUSG00000022831	Hcls1	AW213261|HS1	hematopoietic cell specific Lyn substrate 1	protein-coding
mm_73122.1	chr8	94780458	94780470	+	1	NA	exon (NM_009142, exon 3 of 3)	exon (NM_009142, exon 3 of 3)	8284	NM_009142	20312	Mm.103711	NM_009142	ENSMUSG00000031778	Cx3cl1	AB030188|ABCD-3|AI848747|CX3C|Cxc3|D8Bwg0439e|Scyd1	chemokine (C-X3-C motif) ligand 1	protein-coding
mm_138743.1	chr17	37002575	37002586	+	1	NA	promoter-TSS (NM_001013745)	promoter-TSS (NM_001013745)	55	NM_001013745	22715	Mm.305561	NM_009559	ENSMUSG00000036036	Zfp57	G19|Zfp-57	zinc finger protein 57	protein-coding
mm_114178.1	chr13	55623000	55623084	+	1	NA	promoter-TSS (NM_007596)	promoter-TSS (NM_007596)	37	NM_007596	12328	Mm.2313	NM_007596	ENSMUSG00000021501	Caml	AI385748|Camlg	calcium modulating ligand	protein-coding
mm_154857.1	chrX	20641883	20641919	+	1	NA	intron (NM_001167775, intron 6 of 23)	intron (NM_001167775, intron 6 of 23)	-16401	NM_001276316	22201	Mm.1104	NM_009457	ENSMUSG00000001924	Uba1	A1S9|Sbx|Ube-1|Ube1x	ubiquitin-like modifier activating enzyme 1	protein-coding
mm_78146.1	chr9	21002894	21002909	+	1	NA	5' UTR (NM_023167, exon 1 of 9)	5' UTR (NM_023167, exon 1 of 9)	164	NM_023167	66163	Mm.427576	NM_023167	ENSMUSG00000003299	Mrpl4	1110017G11Rik	mitochondrial ribosomal protein L4	protein-coding
mm_17342.1	chr2	26604164	26604174	-	1	NA	exon (NM_026212, exon 1 of 6)	exon (NM_026212, exon 1 of 6)	248	NM_026212	67512	Mm.24244	NM_026212	ENSMUSG00000026922	Agpat2	2510002J07Rik|AV000834|BSCL|BSCL1|LPAAB|LPAAT-beta	1-acylglycerol-3-phosphate O-acyltransferase 2 (lysophosphatidic acid acyltransferase, beta)	protein-coding
mm_59860.1	chr7	30054063	30054066	+	1	NA	Intergenic	ID_B1|SINE|B4	-2668	NM_178733	243906	Mm.347644	NM_011748	ENSMUSG00000053985	Zfp14	4732429I09Rik|Krox-9|Zfp-14|mKIAA1559	zinc finger protein 14	protein-coding
mm_107018.1	chr12	12580918	12580951	+	1	NA	Intergenic	Intergenic	88983	NR_136889	102637952	Mm.421393	NR_136889		Gm34637	-	predicted gene, 34637	ncRNA
mm_48484.1	chr5	142424816	142424829	-	1	NA	intron (NM_199068, intron 1 of 8)	intron (NM_199068, intron 1 of 8)	23325	NM_199068	17425	Mm.24214	NM_010812	ENSMUSG00000056493	Foxk1	A630048H08Rik|AI463295|ENSMUSG00000075577|Gm10868|Mnf	forkhead box K1	protein-coding
mm_162431.1	chr1	96313242	96313242	+	1	NA	Intergenic	Lx5|LINE|L1	-291484	NR_040467	73454	Mm.396229	NR_040467	ENSMUSG00000100062	1700063A18Rik	-	RIKEN cDNA 1700063A18 gene	ncRNA
mm_47853.1	chr5	134552242	134552282	-	1	NA	5' UTR (NM_001039162, exon 1 of 16)	5' UTR (NM_001039162, exon 1 of 16)	172	NM_001039162	269713	Mm.255138	NM_009990	ENSMUSG00000063146	Clip2	B230327O20|CLIP-115|Clip1|Cyln2|WSCR4|mKIAA0291|wbscr4	CAP-GLY domain containing linker protein 2	protein-coding
mm_24811.1	chr3	95588992	95589009	+	1	NA	promoter-TSS (NM_001177669)	promoter-TSS (NM_001177669)	66	NM_001177670	229593	Mm.245830	NM_146133	ENSMUSG00000046519	Golph3l	2010204I15Rik|AU015439|AW549227|C77637|Gpp34r	golgi phosphoprotein 3-like	protein-coding
mm_110421.1	chr12	46818136	46818155	-	1	NA	intron (NM_021361, intron 1 of 4)	intron (NM_021361, intron 1 of 4)	630	NM_021361	664883	Mm.247195	NM_021361	ENSMUSG00000021047	Nova1	9430099M15Rik|G630039L02|Nova-1	neuro-oncological ventral antigen 1	protein-coding
mm_149022.1	chr19	8757100	8757126	+	1	NA	promoter-TSS (NM_001276704)	promoter-TSS (NM_001276704)	-4	NM_001276704	53319	Mm.7271	NM_016813	ENSMUSG00000010097	Nxf1	Mex67|Mvb1|Tap	nuclear RNA export factor 1	protein-coding
mm_88899.1	chr10	81168023	81168040	+	1	NA	promoter-TSS (NM_021501)	promoter-TSS (NM_021501)	-311	NM_021501	59004	Mm.34428	NM_021501	ENSMUSG00000004934	Pias4	PIASY|Pias-gamma|Piasg	protein inhibitor of activated STAT 4	protein-coding
mm_63390.1	chr7	127233228	127233317	+	1	NA	promoter-TSS (NM_146201)	promoter-TSS (NM_146201)	-142	NR_030674	100043580	Mm.482209	NR_030674	ENSMUSG00000000486	Gm4532	-	predicted gene 4532	ncRNA
mm_102674.1	chr11	65243571	65243603	-	1	NA	intron (NM_146386, intron 1 of 12)	intron (NM_146386, intron 1 of 12)	26402	NM_145136	214384	Mm.32257	NM_145136	ENSMUSG00000020542	Myocd	BSAC2A|Srfcp	myocardin	protein-coding
mm_154247.1	chr19	60766554	60766594	-	1	NA	exon (NM_010123, exon 19 of 22)	exon (NM_010123, exon 19 of 22)	7811	NR_034047	100217439		NR_034047		Snora19	MBI-51	small nucleolar RNA, H/ACA box 19	snoRNA
mm_122879.1	chr14	54926588	54926606	-	1	NA	5' UTR (NM_010112, exon 1 of 6)	5' UTR (NM_010112, exon 1 of 6)	191	NM_010112	13644	Mm.236438	NM_010112	ENSMUSG00000022203	Efs	-	embryonal Fyn-associated substrate	protein-coding
mm_167006.1	chr7	51879191	51879201	+	1	NA	5' UTR (NM_001330607, exon 1 of 8)	5' UTR (NM_001330607, exon 1 of 8)	229	NM_001330607	14453	Mm.207360	NM_008087	ENSMUSG00000030498	Gas2	Gas-2	growth arrest specific 2	protein-coding
mm_17428.1	chr2	27475601	27475611	-	1	NA	promoter-TSS (NM_001113574)	promoter-TSS (NM_001113574)	67	NM_001113573	67382	Mm.28721	NM_023336	ENSMUSG00000026918	Brd3	2410084F24Rik|AW060456|Fsrg2|ORFX|RINGL3	bromodomain containing 3	protein-coding
mm_71723.1	chr8	61976252	61976266	+	1	NA	intron (NM_001293783, intron 17 of 37)	B1_Mus1|SINE|Alu	48172	NM_001293783	234311	Mm.275233	NM_144928	ENSMUSG00000037921	Ddx60	9830118M07	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	protein-coding
mm_166061.1	chr4	133973775	133973778	+	1	NA	intron (NM_026144, intron 8 of 8)	B3A|SINE|B2	-5785	NM_016957	15331	Mm.319660	NM_016957	ENSMUSG00000003038	Hmgn2	HMG-17|Hmg17	high mobility group nucleosomal binding domain 2	protein-coding
mm_45334.1	chr5	65693254	65693257	-	1	NA	intron (NM_001081321, intron 2 of 31)	ID_B1|SINE|B4	4601	NM_001081321	71521	Mm.278974	NM_027818	ENSMUSG00000029202	Pds5a	9030416H16Rik|E230024D05Rik|mKIAA0648	PDS5 cohesin associated factor A	protein-coding
mm_135438.1	chr16	45383263	45383269	-	1	NA	3' UTR (NM_010818, exon 6 of 6)	3' UTR (NM_010818, exon 6 of 6)	25787	NM_010818	17470	Mm.245851	NM_010818	ENSMUSG00000022661	Cd200	Mox2|OX2	CD200 antigen	protein-coding
mm_23136.1	chr3	38885313	38885331	+	1	NA	Intergenic	CpG	-1618	NM_183221	329628	Mm.316210	NM_183221	ENSMUSG00000046743	Fat4	6030410K14Rik|9430004M15	FAT atypical cadherin 4	protein-coding
mm_97034.1	chr11	72267252	72267267	+	1	NA	promoter-TSS (NM_001004148)	promoter-TSS (NM_001004148)	415	NR_045922	73366	Mm.396157	NR_045922	ENSMUSG00000086951	1700051A21Rik	-	RIKEN cDNA 1700051A21 gene	ncRNA
mm_8803.1	chr1	161855551	161855561	-	1	NA	intron (NM_172645, intron 6 of 23)	intron (NM_172645, intron 6 of 23)	21105	NM_172645	226551	Mm.170002	NM_172645	ENSMUSG00000040297	Suco	4732491B11|AI848100|AU016931|Opt	SUN domain containing ossification factor	protein-coding
mm_53665.1	chr6	141524659	141524672	+	1	NA	5' UTR (NM_001177772, exon 1 of 15)	5' UTR (NM_001177772, exon 1 of 15)	279	NM_021471	58807	Mm.284495	NM_021471	ENSMUSG00000030235	Slco1c1	OATP-14|OATP-F|Oatp2|Oatpf|Slc21a14	solute carrier organic anion transporter family, member 1c1	protein-coding
mm_147559.1	chr18	54988014	54988092	-	1	NA	exon (NM_175751, exon 2 of 10)	exon (NM_175751, exon 2 of 10)	2127	NM_175751	269023	Mm.192984	NM_175751	ENSMUSG00000052713	Zfp608	4932417D18Rik|D430007A19Rik|Znf608	zinc finger protein 608	protein-coding
mm_147000.1	chr18	34372492	34372500	-	1	NA	exon (NM_007874, exon 2 of 5)	exon (NM_007874, exon 2 of 5)	919	NM_007874	13476	Mm.280075	NM_007874	ENSMUSG00000005873	Reep5	AI324241|AU022809|AW495741|DP1/TB2|Dp1|R74856|TB2/DP1	receptor accessory protein 5	protein-coding
mm_155573.1	chrX	77511102	77511137	+	1	NA	promoter-TSS (NM_020601)	promoter-TSS (NM_020601)	-108	NM_020601	21372	Mm.258476	NM_020601	ENSMUSG00000025246	Tbl1x	5330429M20|Tbl1	transducin (beta)-like 1 X-linked	protein-coding
mm_1195.1	chr1	62703947	62703982	+	1	NA	5' UTR (NM_001077407, exon 1 of 16)	5' UTR (NM_001077407, exon 1 of 16)	647	NM_001077405	18187	Mm.266341	NM_010939	ENSMUSG00000025969	Nrp2	1110048P06Rik|Np-2|Np2|Npn-2|Npn2	neuropilin 2	protein-coding
mm_125495.1	chr15	55112421	55112451	+	1	NA	non-coding (NR_045093, exon 2 of 5)	non-coding (NR_045093, exon 2 of 5)	119	NM_145470	97998	Mm.295397	NM_145470	ENSMUSG00000022419	Deptor	Depdc6	DEP domain containing MTOR-interacting protein	protein-coding
mm_138083.1	chr17	33996176	33996331	+	1	NA	3' UTR (NM_001001892, exon 8 of 8)	3' UTR (NM_001001892, exon 8 of 8)	4080	NM_001001892	14972	Mm.422886	NM_001001892	ENSMUSG00000061232	H2-K1	H-2K|H-2K(d)|H2-K|K-f	histocompatibility 2, K1, K region	protein-coding
mm_162740.1	chr10	56389016	56389025	+	1	NA	3' UTR (NM_010288, exon 2 of 2)	3' UTR (NM_010288, exon 2 of 2)	11720	NM_010288	14609	Mm.378921	NM_010288	ENSMUSG00000050953	Gja1	AU042049|AW546267|Cnx43|Cx43|Cx43alpha1|Gja-1|Npm1|connexin43	gap junction protein, alpha 1	protein-coding
mm_153221.1	chr19	34812024	34812031	-	1	NA	3' UTR (NM_023792, exon 7 of 7)	3' UTR (NM_023792, exon 7 of 7)	8746	NR_029783	723826		NR_029783	ENSMUSG00000065594	Mir107	Mirn107|mir-107|mmu-mir-107	microRNA 107	ncRNA
mm_172143.1	chr6	37686742	37686744	-	1	NA	Intergenic	Intergenic	156570	NM_145364	208665	Mm.262635	NM_145364	ENSMUSG00000038641	Akr1d1	-	aldo-keto reductase family 1, member D1	protein-coding
mm_97616.1	chr11	78952920	78952932	+	1	NA	exon (NM_010927, exon 22 of 27)	exon (NM_010927, exon 22 of 27)	27635	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_125265.1	chr15	35491994	35492008	+	1	NA	intron (NM_177151, intron 17 of 61)	intron (NM_177151, intron 17 of 61)	120455	NM_177151	666173	Mm.309250	NM_177151	ENSMUSG00000037646	Vps13b	1810042B05Rik|2310042E16Rik|4732488H20|C330002D13Rik|C87206|Coh1|D230005K13|mKIAA0532|mKIAA5032	vacuolar protein sorting 13B	protein-coding
mm_84495.1	chr9	66881547	66881548	-	1	NA	intron (NM_173413, intron 1 of 7)	PB1D10|SINE|Alu	38158	NM_173413	235442	Mm.260376	NM_173413	ENSMUSG00000036943	Rab8b	5930437D16|D330025I23Rik	RAB8B, member RAS oncogene family	protein-coding
mm_41855.1	chr5	104440264	104440318	+	1	NA	exon (NM_001204203, exon 7 of 7)	exon (NM_001204203, exon 7 of 7)	4099	NM_001204233	20750	Mm.288474	NM_009263	ENSMUSG00000029304	Spp1	2AR|Apl-1|BNSP|BSPI|Bsp|ETA-1|Eta|OP|Opn|Opnl|Ric|Spp-1	secreted phosphoprotein 1	protein-coding
mm_32571.1	chr4	109977973	109977995	+	1	NA	promoter-TSS (NM_172296)	promoter-TSS (NM_172296)	-41	NM_172296	242620	Mm.32825	NM_172296	ENSMUSG00000047143	Dmrta2	Dmrt5	doublesex and mab-3 related transcription factor like family A2	protein-coding
mm_84421.1	chr9	65629895	65629898	-	1	NA	promoter-TSS (NM_028030)	promoter-TSS (NM_028030)	-686	NM_028030	71973	Mm.29148	NM_028030	ENSMUSG00000032387	Rbpms2	2400008B06Rik|AI316523	RNA binding protein with multiple splicing 2	protein-coding
mm_167346.1	chr8	80493971	80493979	+	1	NA	promoter-TSS (NM_010369)	promoter-TSS (NM_010369)	-70	NM_010369	14934	Mm.13123	NM_010369	ENSMUSG00000051839	Gypa	AI853584|CD235a|GPA	glycophorin A	protein-coding
mm_63597.1	chr7	128141920	128141960	+	1	NA	exon (NM_021334, exon 19 of 30)	exon (NM_021334, exon 19 of 30)	12372	NM_021334	16411	Mm.22378	NM_021334	ENSMUSG00000030789	Itgax	AI449405|Cd11c|Cr4|N418	integrin alpha X	protein-coding
mm_166883.1	chr7	26222808	26222813	+	1	NA	Intergenic	L1_Mus3|LINE|L1	-44021	NM_001167540	100312477	Mm.480246	NM_001167540	ENSMUSG00000046130	Vmn1r184	-	vomeronasal 1 receptor, 184	protein-coding
mm_140976.1	chr17	24696542	24696553	-	1	NA	promoter-TSS (NM_023040)	promoter-TSS (NM_023040)	313	NM_027988	71893	Mm.390971	NM_027988	ENSMUSG00000019320	Noxo1	2310034C04Rik|P41NOX|P41NOXA|P41NOXB|P41NOXC|Snx28|hslt	NADPH oxidase organizer 1	protein-coding
mm_115298.1	chr13	112001416	112001426	+	1	NA	Intergenic	Intergenic	133485	NR_130345	102636620	Mm.402328	NR_130345	ENSMUSG00000086111	Gm15326	OTTMUSG00000020187	predicted gene 15326	ncRNA
mm_112885.1	chr13	20859587	20859598	+	1	NA	intron (NM_012054, intron 4 of 20)	intron (NM_012054, intron 4 of 20)	65479	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_144211.1	chr18	9724735	9724745	+	1	NA	intron (NM_130449, intron 2 of 9)	intron (NM_130449, intron 2 of 9)	17092	NM_130449	140792	Mm.218571	NM_130449	ENSMUSG00000036103	Colec12	CL-P1|SRCL|Scara4	collectin sub-family member 12	protein-coding
mm_54501.1	chr6	35510398	35510408	-	1	NA	3' UTR (NM_008098, exon 4 of 4)	3' UTR (NM_008098, exon 4 of 4)	29485	NM_008098	14489	Mm.182746	NM_008098	ENSMUSG00000029840	Mtpn	5033418D15Rik|Gcdp|V1	myotrophin	protein-coding
mm_97161.1	chr11	75486794	75486808	+	1	NA	promoter-TSS (NM_138659)	promoter-TSS (NM_138659)	24	NM_138659	192159	Mm.3757	NM_138659	ENSMUSG00000020850	Prpf8	AU019467|D11Bwg0410e|DBF3/PRP8|Prp8|Sfprp8l	pre-mRNA processing factor 8	protein-coding
mm_141816.1	chr17	34606346	34606359	-	1	NA	intron (NM_001163379, intron 1 of 6)	intron (NM_001163379, intron 1 of 6)	491	NM_001163379	55979	Mm.8684	NM_018862	ENSMUSG00000034254	Agpat1	1-AGP|1-AGPAT|AW047140	1-acylglycerol-3-phosphate O-acyltransferase 1 (lysophosphatidic acid acyltransferase, alpha)	protein-coding
mm_97707.1	chr11	80178551	80178567	+	1	NA	3' UTR (NM_172133, exon 11 of 11)	3' UTR (NM_172133, exon 11 of 11)	-5313	NM_028019	71956	Mm.22985	NM_028019	ENSMUSG00000020707	Rnf135	0610037N03Rik|2410006N06Rik	ring finger protein 135	protein-coding
mm_49086.1	chr6	6863770	6863781	+	1	NA	TTS (NR_002839)	TTS (NR_002839)	441	NM_010057	13396	Mm.439763	NM_010057	ENSMUSG00000029754	Dlx6	-	distal-less homeobox 6	protein-coding
mm_114189.1	chr13	55714763	55714773	+	1	NA	5' UTR (NM_175150, exon 1 of 5)	5' UTR (NM_175150, exon 1 of 5)	118	NM_175150	69672	Mm.294457	NM_175150	ENSMUSG00000021497	Txndc15	2310047H23Rik|AI854086|C5orf14|UNQ335	thioredoxin domain containing 15	protein-coding
mm_79559.1	chr9	58026952	58026962	+	1	NA	TTS (NM_001346787)	TTS (NM_001346787)	-5317	NM_001243265	330951	Mm.406992	NM_001243265		Gm16130	E330033L03|OTTMUSG00000030814	predicted gene 16130	protein-coding
mm_171825.1	chr5	142904137	142904141	-	1	NA	exon (NM_007393, exon 5 of 6)	exon (NM_007393, exon 5 of 6)	2615	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_116524.1	chr13	45790450	45790469	-	1	NA	intron (NM_001199304, intron 4 of 6)	intron (NM_001199304, intron 4 of 6)	174532	NM_001199304	20238	Mm.342683	NM_009124	ENSMUSG00000046876	Atxn1	2900016G23Rik|Atx1|C85907|ENSMUSG00000074917|Gm10786|Sca1	ataxin 1	protein-coding
mm_45308.1	chr5	65427524	65427552	-	1	NA	exon (NM_009466, exon 2 of 12)	exon (NM_009466, exon 2 of 12)	8304	NM_009466	22235	Mm.344831	NM_009466	ENSMUSG00000029201	Ugdh	Udpgdh	UDP-glucose dehydrogenase	protein-coding
mm_144718.1	chr18	35119422	35119429	+	1	NA	intron (NM_009818, intron 1 of 17)	CpG	513	NM_009818	12385	Mm.18962	NM_009818	ENSMUSG00000037815	Ctnna1	2010010M04Rik|AA517462|AI988031|Catna1	catenin (cadherin associated protein), alpha 1	protein-coding
mm_120736.1	chr14	73168967	73168976	+	1	NA	intron (NR_033185, intron 11 of 15)	intron (NR_033185, intron 11 of 15)	26186	NR_033185	105670	Mm.280068	NM_134083	ENSMUSG00000022106	Rcbtb2	2610028E02Rik|2810420M18Rik|AI448345|AW240694|Chc1l|RC/BTB2	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 2	protein-coding
mm_79209.1	chr9	49028129	49028140	+	1	NA	exon (NM_175482, exon 16 of 24)	exon (NM_175482, exon 16 of 24)	-27447	NM_012039	26951	Mm.24791	NM_012039	ENSMUSG00000032264	Zw10	6330566F14Rik|MmZw10	zw10 kinetochore protein	protein-coding
mm_12057.1	chr2	59338694	59338704	+	1	NA	intron (NM_175464, intron 13 of 20)	intron (NM_175464, intron 13 of 20)	47983	NR_040510	76676	Mm.110038	NR_040510	ENSMUSG00000087455	5330411J11Rik	-	RIKEN cDNA 5330411J11 gene	ncRNA
mm_117286.1	chr13	66062984	66063005	-	1	NA	Intergenic	Intergenic	-50459	NM_001177832	628709	Mm.390595	NM_001177832	ENSMUSG00000095909	Gm10324	ENSMUSG00000071302	predicted gene 10324	protein-coding
mm_128297.1	chr15	37433045	37433060	-	1	NA	promoter-TSS (NR_045283)	promoter-TSS (NR_045283)	-388	NR_045283	100503538	Mm.445166	NR_045283	ENSMUSG00000086992	Gm15941	OTTMUSG00000028027	predicted gene 15941	ncRNA
mm_84562.1	chr9	67817987	67818024	-	1	NA	Intergenic	Intergenic	14325	NM_001163143	244911	Mm.325849	NM_001163143	ENSMUSG00000047990	C2cd4a	EG244911|Fam148a	C2 calcium-dependent domain containing 4A	protein-coding
mm_41922.1	chr5	105610319	105610323	+	1	NA	Intergenic	Intergenic	-89648	NM_001122768	231549	Mm.23837	NM_178701	ENSMUSG00000046079	Lrrc8d	2810473G09Rik|4930525N13Rik|A930019F03|Lrrc5	leucine rich repeat containing 8D	protein-coding
mm_148747.1	chr19	6047056	6047080	+	1	NA	promoter-TSS (NM_001164709)	promoter-TSS (NM_001164709)	-77	NM_001164709	74126	Mm.149870	NM_028769	ENSMUSG00000024807	Syvn1	1200010C09Rik|AW211966|C85322|D530017H19Rik|Hrd1	synovial apoptosis inhibitor 1, synoviolin	protein-coding
mm_96350.1	chr11	66956698	66956704	+	1	NA	promoter-TSS (NR_130315)	promoter-TSS (NR_130315)	63	NR_130315	71576	Mm.340077	NR_130315	ENSMUSG00000085683	9130409J20Rik	-	RIKEN cDNA 9130409J20 gene	ncRNA
mm_126667.1	chr15	84324717	84324723	+	1	NA	promoter-TSS (NM_022321)	promoter-TSS (NM_022321)	0	NM_022321	64099	Mm.251356	NM_022321	ENSMUSG00000022439	Parvg	AI413459	parvin, gamma	protein-coding
mm_26232.1	chr3	139205921	139205936	+	1	NA	promoter-TSS (NM_198659)	promoter-TSS (NM_198659)	35	NM_198659	381476	Mm.188334	NM_198659	ENSMUSG00000047940	Stpg2	B930007M17Rik|Gm1017	sperm tail PG rich repeat containing 2	protein-coding
mm_162977.1	chr11	19009080	19009098	+	1	NA	intron (NM_001193271, intron 6 of 12)	intron (NM_001193271, intron 6 of 12)	9880	NM_001193271	17268	Mm.356578	NM_010789	ENSMUSG00000020160	Meis1	C530044H18Rik|Evi8	Meis homeobox 1	protein-coding
mm_87596.1	chr10	57632109	57632120	+	1	NA	5' UTR (NM_008863, exon 1 of 6)	5' UTR (NM_008863, exon 1 of 6)	133	NM_001039051	18768	Mm.262135	NM_008863	ENSMUSG00000019876	Pkib	Pkibeta|Prkacn2	protein kinase inhibitor beta, cAMP dependent, testis specific	protein-coding
mm_168720.1	chr12	109453455	109453457	+	1	NA	promoter-TSS (NM_010052)	promoter-TSS (NM_010052)	1	NM_010052	13386	Mm.157069	NM_010052	ENSMUSG00000040856	Dlk1	AW742678|DLK-1|DlkI|FA1|Ly107|Peg9|SCP1|ZOG|pG2|pref-1	delta-like 1 homolog (Drosophila)	protein-coding
mm_113413.1	chr13	34002431	34002441	+	1	NA	promoter-TSS (NM_009068)	promoter-TSS (NM_009068)	358	NM_001243192	20719	Mm.252210	NM_009254	ENSMUSG00000060147	Serpinb6a	4930482L21Rik|D330015H01Rik|PI-6|Serpinb6|Spi3|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 6a	protein-coding
mm_55373.1	chr6	57825283	57825305	-	1	NA	promoter-TSS (NM_146168)	promoter-TSS (NM_146168)	-169	NM_146168	232023	Mm.24642	NM_146168	ENSMUSG00000037788	Vopp1	AW146242|Ecop	vesicular, overexpressed in cancer, prosurvival protein 1	protein-coding
mm_144141.1	chr18	4994641	4994669	+	1	NA	Intergenic	Intergenic	-51934	NM_153153	225115	Mm.136791	NM_153153	ENSMUSG00000024236	Svil	AU024053|B430302E16Rik	supervillin	protein-coding
mm_9164.1	chr1	170968205	170968225	-	1	NA	exon (NM_001077189, exon 3 of 8)	exon (NM_001077189, exon 3 of 8)	7856	NM_001077189	14130	Mm.425062	NM_010187	ENSMUSG00000026656	Fcgr2b	AI528646|CD32|F630109E10Rik|Fc[g]RII|FcgRII|Fcgr2|Fcgr2a|Fcr-2|Fcr-3|Ly-17|Ly-m20|LyM-1|Lym-1|fcRII	Fc receptor, IgG, low affinity IIb	protein-coding
mm_119854.1	chr14	54442170	54442180	+	1	NA	3' UTR (NM_008608, exon 10 of 10)	3' UTR (NM_008608, exon 10 of 10)	10577	NM_008608	17387	Mm.280175	NM_008608	ENSMUSG00000000957	Mmp14	AI325305|MMP-X1|MT-MMP-1|MT1-MMP|sabe	matrix metallopeptidase 14 (membrane-inserted)	protein-coding
mm_43666.1	chr5	138754809	138754819	+	1	NA	promoter-TSS (NM_030565)	promoter-TSS (NM_030565)	-267	NM_030565	80752	Mm.320355	NM_030565	ENSMUSG00000025854	Fam20c	C76981|DMP-4|DMP4|GEF-CK|mKIAA4081	family with sequence similarity 20, member C	protein-coding
mm_159241.1	chr2	150218103	150218103	+	1	NA	promoter-TSS (NM_001142411)	promoter-TSS (NM_001142411)	4	NM_001142411	245174	Mm.378428	NM_001142411	ENSMUSG00000060336	Zfp937	EG245174|Gm4979|ZIPO-I	zinc finger protein 937	protein-coding
mm_101272.1	chr11	21370648	21370656	-	1	NA	promoter-TSS (NM_139297)	promoter-TSS (NM_139297)	-23	NM_139297	216558	Mm.28877	NM_139297	ENSMUSG00000001891	Ugp2	UDPGP|UGPase	UDP-glucose pyrophosphorylase 2	protein-coding
mm_101248.1	chr11	20741934	20741944	-	1	NA	promoter-TSS (NM_001252503)	promoter-TSS (NM_001252503)	-383	NM_181411	216549	Mm.356580	NM_181411	ENSMUSG00000049659	Aftph	-	aftiphilin	protein-coding
mm_108125.1	chr12	75983669	75983680	+	1	NA	intron (NM_001005510, intron 53 of 115)	intron (NM_001005510, intron 53 of 115)	74571	NR_039560	100628610		NR_039560	ENSMUSG00000092922	Mir5101	mmu-mir-5101|mu-mir-5101	microRNA 5101	ncRNA
mm_125016.1	chr15	25626418	25626440	+	1	NA	intron (NM_019472, intron 1 of 40)	intron (NM_019472, intron 1 of 40)	3879	NM_019472	17909	Mm.60590	NM_019472	ENSMUSG00000022272	Myo10	AW048724|D15Ertd600e|mKIAA0799|myosin-X	myosin X	protein-coding
mm_81348.1	chr9	108567527	108567540	+	1	NA	promoter-TSS (NR_029577)	promoter-TSS (NR_029577)	-191	NM_023247	66706	Mm.29471	NM_023247	ENSMUSG00000070283	Ndufaf3	4733401H18Rik	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, assembly factor 3	protein-coding
mm_24803.1	chr3	95556083	95556114	+	1	NA	exon (NM_021281, exon 8 of 8)	exon (NM_021281, exon 8 of 8)	-3579	NM_026489	67981	Mm.179050	NM_026489	ENSMUSG00000028109	Hormad1	4921522K05Rik|Nohma	HORMA domain containing 1	protein-coding
mm_100201.1	chr11	116813222	116813238	+	1	NA	intron (NM_001347633, intron 2 of 4)	intron (NM_001347633, intron 2 of 4)	14816	NM_026280	67622	Mm.64962	NM_026280	ENSMUSG00000020814	Mxra7	1810057P16Rik|E130302J09Rik	matrix-remodelling associated 7	protein-coding
mm_9126.1	chr1	170589752	170589769	-	1	NA	promoter-TSS (NM_001109985)	promoter-TSS (NM_001109985)	89	NM_001109985	70729	Mm.487078	NM_027528	ENSMUSG00000038473	Nos1ap	6330408P19Rik|Capon	nitric oxide synthase 1 (neuronal) adaptor protein	protein-coding
mm_100304.1	chr11	117952462	117952480	+	1	NA	Intergenic	Intergenic	16895	NM_007707	12702	Mm.3468	NM_007707	ENSMUSG00000053113	Socs3	Cis3|Cish3|EF-10|Ef10|SSI-3|Ssi3	suppressor of cytokine signaling 3	protein-coding
mm_132341.1	chr16	33829791	33829802	+	1	NA	5' UTR (NM_001145884, exon 1 of 15)	5' UTR (NM_001145884, exon 1 of 15)	131	NM_001145884	16419	Mm.6424	NM_010580	ENSMUSG00000022817	Itgb5	AA475909|AI874634|ESTM23|[b]-5|[b]5|[b]5A|[b]5B|beta-5|beta5	integrin beta 5	protein-coding
mm_115536.1	chr13	6605029	6605063	-	1	NA	exon (NM_001291071, exon 10 of 22)	exon (NM_001291071, exon 10 of 22)	43725	NM_019703	56421	Mm.273874	NM_019703	ENSMUSG00000021196	Pfkp	1200015H23Rik|9330125N24Rik|ATP-PFK|PFK-C|PFK-P	phosphofructokinase, platelet	protein-coding
mm_143112.1	chr17	57198295	57198319	-	1	NA	Intergenic	RMER15|LTR|ERVL	-4126	NM_019418	50930	Mm.483369	NM_019418	ENSMUSG00000005824	Tnfsf14	HVEM-L|HVEML|LIGHT|LTg|Ly113|Tnlg1d	tumor necrosis factor (ligand) superfamily, member 14	protein-coding
mm_108644.1	chr12	85956406	85956415	+	1	NA	intron (NM_001347395, intron 28 of 32)	intron (NM_001347395, intron 28 of 32)	122631	NM_009368	21809	Mm.3992	NM_009368	ENSMUSG00000021253	Tgfb3	TGF-beta-3|Tgfb-3	transforming growth factor, beta 3	protein-coding
mm_74208.1	chr8	123893624	123893661	+	1	NA	exon (NM_009606, exon 2 of 7)	exon (NM_009606, exon 2 of 7)	1133	NM_001272041	11459	Mm.214950	NM_009606	ENSMUSG00000031972	Acta1	AA959943|Acta-2|Acts|Actsk-1	actin, alpha 1, skeletal muscle	protein-coding
mm_99629.1	chr11	105126468	105126519	+	1	NA	promoter-TSS (NM_172567)	promoter-TSS (NM_172567)	68	NM_172567	52686	Mm.270091	NM_172567	ENSMUSG00000020691	Mettl2	2810438F06Rik|AW493404|C130031G21Rik|D11Ertd768e|METL|PSENIP1	methyltransferase like 2	protein-coding
mm_53801.1	chr6	146850101	146850109	+	1	NA	promoter-TSS (NM_027059)	promoter-TSS (NM_027059)	-5	NM_027059	69371	Mm.252733	NM_027059	ENSMUSG00000030292	Smco2	1700023A16Rik	single-pass membrane protein with coiled-coil domains 2	protein-coding
mm_148055.1	chr18	72141702	72141715	-	1	NA	intron (NM_007831, intron 1 of 28)	(CA)n|Simple_repeat|Simple_repeat	209361	NM_007831	13176	Mm.167882	NM_007831	ENSMUSG00000060534	Dcc	C030036D22Rik|Igdcc1	deleted in colorectal carcinoma	protein-coding
mm_25201.1	chr3	103787528	103787532	+	1	NA	intron (NM_001301304, intron 1 of 15)	intron (NM_001301304, intron 1 of 15)	3745	NM_001301306	15257	Mm.20827	NM_010432	ENSMUSG00000008730	Hipk1	1110062K04Rik|Myak	homeodomain interacting protein kinase 1	protein-coding
mm_154360.1	chrM	6344	6355	+	1	NA	NA	Intergenic	NA	NA								
mm_27717.1	chr3	68780425	68780434	-	1	NA	Intergenic	RLTR41A2|LTR|ERV1	89005	NM_008351	16159	Mm.103783	NM_008351	ENSMUSG00000027776	Il12a	IL-12p35|Il-12a|Ll12a|p35	interleukin 12a	protein-coding
mm_13651.1	chr2	114054417	114054461	+	1	NA	promoter-TSS (NR_028422)	promoter-TSS (NR_028422)	43	NR_028422	100303644	Mm.330469	NR_028422	ENSMUSG00000092397	C130080G10Rik	-	RIKEN cDNA C130080G10 gene	ncRNA
mm_42100.1	chr5	110344777	110344782	+	1	NA	promoter-TSS (NM_001310709)	promoter-TSS (NM_001310709)	49	NM_001310709	381667	Mm.332572	NM_001033459	ENSMUSG00000072754	Lrcol1	Clpsl3|Gm1679	leucine rich colipase-like 1	protein-coding
mm_27032.1	chr3	26153996	26154006	-	1	NA	promoter-TSS (NM_001163387)	promoter-TSS (NM_001163387)	-694	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_107807.1	chr12	65036828	65036833	+	1	NA	intron (NM_177806, intron 1 of 13)	intron (NM_177806, intron 1 of 13)	496	NM_177806	328110	Mm.283339	NM_177806	ENSMUSG00000035597	Prpf39	Srcs1	pre-mRNA processing factor 39	protein-coding
mm_120213.1	chr14	62555643	62555699	+	1	NA	promoter-TSS (NM_001243857)	promoter-TSS (NM_001243857)	-66	NM_001243857	629059	Mm.291864	NM_001243857	ENSMUSG00000035184	Fam124a	EG629059	family with sequence similarity 124, member A	protein-coding
mm_43594.1	chr5	137761681	137761714	+	1	NA	intron (NM_029805, intron 4 of 5)	intron (NM_029805, intron 4 of 5)	15728	NM_029805	78829	Mm.286399	NM_023910	ENSMUSG00000029723	Tsc22d4	0610009M14Rik|1700023B23Rik|AI415410|Thg-1pit|Tilz2	TSC22 domain family, member 4	protein-coding
mm_99774.1	chr11	107137795	107137840	+	1	NA	Intergenic	Intergenic	-5895	NM_176850	207165	Mm.343986	NM_176850	ENSMUSG00000040481	Bptf	9430093H17Rik|Falz	bromodomain PHD finger transcription factor	protein-coding
mm_131692.1	chr16	20691806	20691810	+	1	NA	intron (NM_001304432, intron 31 of 31)	intron (NM_001304432, intron 31 of 31)	-3249	NM_133778	78408	Mm.196512	NM_133778	ENSMUSG00000050821	Fam131a	2900046G09Rik	family with sequence similarity 131, member A	protein-coding
mm_91200.1	chr10	21160824	21160877	-	1	NA	5' UTR (NM_001198914, exon 1 of 16)	5' UTR (NM_001198914, exon 1 of 16)	134	NM_001198914	17863	Mm.52109	NM_010848	ENSMUSG00000019982	Myb	AI550390|M16449|c-myb	myeloblastosis oncogene	protein-coding
mm_28098.1	chr3	86142594	86142636	-	1	NA	promoter-TSS (NM_016959)	promoter-TSS (NM_016959)	53	NM_016959	20091	Mm.391785	NM_016959	ENSMUSG00000028081	Rps3a1	Rps3a	ribosomal protein S3A1	protein-coding
mm_29393.1	chr3	108904353	108904360	-	1	NA	exon (NM_025845, exon 6 of 6)	exon (NM_025845, exon 6 of 6)	7348	NM_025845	66921	Mm.51049	NM_025845	ENSMUSG00000027881	Prpf38b	1110021E09Rik|AU018955	PRP38 pre-mRNA processing factor 38 (yeast) domain containing B	protein-coding
mm_130320.1	chr15	97469268	97469276	-	1	NA	Intergenic	Intergenic	-221985	NM_001164602	105827	Mm.24005	NM_178114	ENSMUSG00000048218	Amigo2	AI415330|AMIGO-2|AW208913|Ali1	adhesion molecule with Ig like domain 2	protein-coding
mm_74407.1	chr8	3467708	3467714	-	1	NA	promoter-TSS (NM_026951)	promoter-TSS (NM_026951)	-63	NM_026951	69129	Mm.45279	NM_026951	ENSMUSG00000069633	Pex11g	1810022F11Rik|1810049N02Rik|Pex11c|Pex11gamma	peroxisomal biogenesis factor 11 gamma	protein-coding
mm_85282.1	chr9	99692488	99692503	-	1	NA	3' UTR (NM_001194922, exon 5 of 5)	3' UTR (NM_001194922, exon 5 of 5)	17568	NM_019815	56492	Mm.386784	NM_019815	ENSMUSG00000032473	Cldn18	-	claudin 18	protein-coding
mm_91965.1	chr10	61383333	61383372	-	1	NA	5' UTR (NM_013753, exon 1 of 20)	5' UTR (NM_013753, exon 1 of 20)	171	NM_013753	27355	Mm.269699	NM_013753	ENSMUSG00000020092	Pald1	MMPAL|Pald|mKIAA1274	phosphatase domain containing, paladin 1	protein-coding
mm_104343.1	chr11	94242702	94242729	-	1	NA	promoter-TSS (NM_181819)	promoter-TSS (NM_181819)	-136	NM_181819	278507	Mm.342216	NM_181819	ENSMUSG00000044177	Wfikkn2	2610304F08Rik|AY100450|Gasp1|WFIKKNRP	WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 2	protein-coding
mm_56610.1	chr6	112489820	112489828	-	1	NA	promoter-TSS (NM_001081147)	promoter-TSS (NM_001081147)	-16	NM_001081147	18430	Mm.333310	NM_001081147	ENSMUSG00000049112	Oxtr	OTR	oxytocin receptor	protein-coding
mm_24974.1	chr3	96757953	96757989	+	1	NA	intron (NM_026406, intron 2 of 8)	intron (NM_026406, intron 2 of 8)	30360	NM_026406	67845	Mm.386792	NM_026406	ENSMUSG00000028098	Rnf115	2610028E05Rik|AU042696|Zfp364	ring finger protein 115	protein-coding
mm_14533.1	chr2	132781606	132781629	+	1	NA	5' UTR (NM_007694, exon 1 of 5)	5' UTR (NM_007694, exon 1 of 5)	339	NM_007694	12653	Mm.255241	NM_007694	ENSMUSG00000027350	Chgb	Scg-1	chromogranin B	protein-coding
mm_12372.1	chr2	69822026	69822034	+	1	NA	promoter-TSS (NM_177784)	promoter-TSS (NM_177784)	-340	NM_177784	277396	Mm.138073	NM_177784	ENSMUSG00000042155	Klhl23	C130068N17Rik	kelch-like 23	protein-coding
mm_84717.1	chr9	73967812	73967822	-	1	NA	Intergenic	Intergenic	-34250	NM_001081153	208898	Mm.41035	NM_001081153	ENSMUSG00000062151	Unc13c	1500037O19Rik|AU019458|D9Ertd414e|Munc13-3|Unc13h3	unc-13 homolog C (C. elegans)	protein-coding
mm_22771.1	chr3	20251957	20251993	+	1	NA	exon (NM_029706, exon 10 of 11)	exon (NM_029706, exon 10 of 11)	-9794	NM_007753	12873	Mm.1135	NM_007753	ENSMUSG00000001865	Cpa3	MC-CPA	carboxypeptidase A3, mast cell	protein-coding
mm_162026.1	chr19	47143938	47143938	-	1	NA	exon (NM_001081271, exon 1 of 2)	exon (NM_001081271, exon 1 of 2)	236	NM_001081271	546729	Mm.439624	NM_001081271	ENSMUSG00000079258	Calhm1	EG546729	calcium homeostasis modulator 1	protein-coding
mm_111624.1	chr12	102421516	102421526	-	1	NA	intron (NM_011175, intron 2 of 13)	ORR1C2|LTR|ERVL-MaLR	18292	NM_011175	19141	Mm.17185	NM_011175	ENSMUSG00000021190	Lgmn	AEP|AI746452|AU022324|Prsc1	legumain	protein-coding
mm_162122.1	chrX	69945098	69945098	+	1	NA	promoter-TSS (NM_029316)	promoter-TSS (NM_029316)	-183	NM_029316	75509	Mm.233475	NM_029316	ENSMUSG00000059690	1700020N15Rik	-	RIKEN cDNA 1700020N15 gene	protein-coding
mm_15112.1	chr2	153649475	153649516	+	1	NA	promoter-TSS (NM_010068)	promoter-TSS (NM_010068)	46	NM_001271747	13436	Mm.89772	NM_010068	ENSMUSG00000027478	Dnmt3b	MmuIIIB	DNA methyltransferase 3B	protein-coding
mm_156233.1	chrX	135885904	135885943	+	1	NA	promoter-TSS (NM_198161)	promoter-TSS (NM_198161)	72	NM_198161	70237	Mm.440847	NM_198161	ENSMUSG00000072964	Bhlhb9	2700087I09Rik	basic helix-loop-helix domain containing, class B9	protein-coding
mm_19384.1	chr2	91236878	91236921	-	1	NA	promoter-TSS (NR_015464)	promoter-TSS (NR_015464)	167	NM_028119	107986	Mm.389334	NM_028119	ENSMUSG00000002109	Ddb2	2610043A19Rik	damage specific DNA binding protein 2	protein-coding
mm_148424.1	chr19	3941523	3941533	+	1	NA	exon (NM_019449, exon 4 of 11)	exon (NM_019449, exon 4 of 11)	6342	NM_001161428	54445	Mm.262094	NM_019449	ENSMUSG00000036908	Unc93b1	Unc-93B1|Unc93b	unc-93 homolog B1 (C. elegans)	protein-coding
mm_96241.1	chr11	62551849	62551859	+	1	NA	intron (NM_001313984, intron 1 of 1)	intron (NM_001313984, intron 1 of 1)	123	NM_001313984	22187	Mm.371592	NM_011664	ENSMUSG00000019505	Ubb	AL033289|Rps27a|Uba52|Ubb2|Ubc	ubiquitin B	protein-coding
mm_114569.1	chr13	74692221	74692237	+	1	NA	TTS (NM_030711)	TTS (NM_030711)	42032	NM_001301158	12380	Mm.29163	NM_009817	ENSMUSG00000021585	Cast	-	calpastatin	protein-coding
mm_20323.1	chr2	127337769	127337793	-	1	NA	promoter-TSS (NM_172539)	promoter-TSS (NM_172539)	-858	NM_172539	215095	Mm.31313	NM_172539	ENSMUSG00000050468	Astl	7420700F21|C87576|Sas1b	astacin-like metalloendopeptidase (M12 family)	protein-coding
mm_79807.1	chr9	64177375	64177398	+	1	NA	exon (NM_024212, exon 7 of 10)	exon (NM_024212, exon 7 of 10)	-1911	NM_183316	330959	Mm.24082	NM_183316	ENSMUSG00000032398	Snapc5	2010103A03Rik	small nuclear RNA activating complex, polypeptide 5	protein-coding
mm_44475.1	chr5	23433306	23433344	-	1	NA	non-coding (NR_040469, exon 1 of 1)	non-coding (NR_040469, exon 1 of 1)	1028	NR_040469	269630	Mm.425231	NR_040469	ENSMUSG00000073147	5031425E22Rik	-	RIKEN cDNA 5031425E22 gene	ncRNA
mm_170852.1	chr2	177925650	177925663	-	1	NA	promoter-TSS (NM_183135)	promoter-TSS (NM_183135)	-6	NM_183135	78703		NM_183135	ENSMUSG00000074529	Zfp972	C330013J21Rik	zinc finger protein 972	protein-coding
mm_109426.1	chr12	110601440	110601450	+	1	NA	promoter-TSS (NM_030238)	promoter-TSS (NM_030238)	50	NM_030238	13424	Mm.181430	NM_030238	ENSMUSG00000018707	Dync1h1	9930018I23Rik|AI894280|DHC1|DHC1a|DNCL|Dnchc1|Dnec1|Dnecl|Loa|MAP1C|P22|Swl|mKIAA0325	dynein cytoplasmic 1 heavy chain 1	protein-coding
mm_48162.1	chr5	137152820	137152830	-	1	NA	Intergenic	Intergenic	-36618	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_80555.1	chr9	83112583	83112593	+	1	NA	intron (NM_175074, intron 3 of 5)	intron (NM_175074, intron 3 of 5)	34019	NM_175074	94353	Mm.244426	NM_026122	ENSMUSG00000066456	Hmgn3	1110002A15Rik|6330514M13Rik|BB071015|TRIP7	high mobility group nucleosomal binding domain 3	protein-coding
mm_51319.1	chr6	72314734	72314749	+	1	NA	TTS (NM_001282071)	TTS (NM_001282071)	10131	NM_147779	20388	Mm.46033	NM_147779	ENSMUSG00000056370	Sftpb	AI562151|SF-B|SP-B|Sftp-3|Sftp3	surfactant associated protein B	protein-coding
mm_7150.1	chr1	91406022	91406040	-	1	NA	promoter-TSS (NR_026924)	promoter-TSS (NR_026924)	-2	NR_026924	67086	Mm.396158	NR_026924	ENSMUSG00000100253	1700020N18Rik	-	RIKEN cDNA 1700020N18 gene	ncRNA
mm_116857.1	chr13	54765594	54765615	-	1	NA	exon (NM_033610, exon 2 of 6)	exon (NM_033610, exon 2 of 6)	836	NM_033610	104069	Mm.200843	NM_033610	ENSMUSG00000034891	Sncb	AI838531|betaSYN	synuclein, beta	protein-coding
mm_97297.1	chr11	76493987	76494001	+	1	NA	intron (NM_198895, intron 2 of 22)	intron (NM_198895, intron 2 of 22)	501	NM_001346670	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_127888.1	chr15	9140317	9140369	-	1	NA	promoter-TSS (NM_177178)	promoter-TSS (NM_177178)	111	NM_013787	27401	Mm.35584	NM_013787	ENSMUSG00000054115	Skp2	4930500A04Rik|FBXL1|FWD1|p45	S-phase kinase-associated protein 2 (p45)	protein-coding
mm_46952.1	chr5	114952719	114952721	-	1	NA	exon (NM_009327, exon 7 of 10)	exon (NM_009327, exon 7 of 10)	10518	NM_028211	72357	Mm.292672	NM_028211	ENSMUSG00000029559	2210016L21Rik	-	RIKEN cDNA 2210016L21 gene	protein-coding
mm_81369.1	chr9	108808357	108808441	+	1	NA	promoter-TSS (NM_030729)	promoter-TSS (NM_030729)	19	NM_030729	80987	Mm.192416	NM_030729	ENSMUSG00000032598	Nckipsd	AF3P21|DIP1|ORF1|SPIN90|WASLBP|WISH|Wasbp	NCK interacting protein with SH3 domain	protein-coding
mm_16121.1	chr2	170131345	170131362	+	1	NA	promoter-TSS (NM_001033299)	promoter-TSS (NM_001033299)	-133	NM_001033299	228913	Mm.22858	NM_001033299	ENSMUSG00000052056	Zfp217	4933431C08Rik|AW987152|Gm562|ZABC1|Znf217	zinc finger protein 217	protein-coding
mm_85893.1	chr9	111055433	111055441	-	1	NA	exon (NM_017466, exon 2 of 2)	exon (NM_017466, exon 2 of 2)	1807	NM_001302377	54199	Mm.7336	NM_017466	ENSMUSG00000043953	Ccrl2	1810047I05Rik|Ackr5|CCR11|Cmkbr1l2|E01|L-CCR	chemokine (C-C motif) receptor-like 2	protein-coding
mm_45263.1	chr5	64093538	64093547	-	1	NA	intron (NM_025700, intron 1 of 13)	intron (NM_025700, intron 1 of 13)	592	NM_025700	66681	Mm.2325	NM_025700	ENSMUSG00000029171	Pgm1	3230402E02Rik|Pgm-1|Pgm2	phosphoglucomutase 1	protein-coding
mm_149870.1	chr19	25155778	25155787	+	1	NA	intron (NM_028785, intron 27 of 47)	intron (NM_028785, intron 27 of 47)	-81420	NM_181404	107351	Mm.260722	NM_181404	ENSMUSG00000032702	Kank1	A930031B09Rik|AU015049|AW121052|Ankrd15|D330024H06Rik|mKIAA0172	KN motif and ankyrin repeat domains 1	protein-coding
mm_149234.1	chr19	10182995	10183005	+	1	NA	5' UTR (NM_146094, exon 1 of 12)	5' UTR (NM_146094, exon 1 of 12)	112	NM_146094	76267	Mm.30158	NM_146094	ENSMUSG00000010663	Fads1	0710001O03Rik|A930006B21Rik|AI317215|DSD	fatty acid desaturase 1	protein-coding
mm_9442.1	chr1	172588570	172588613	-	1	NA	intron (NM_029084, intron 1 of 4)	L2b|LINE|L2	1977	NM_029084	74748	Mm.179812	NM_029084	ENSMUSG00000053318	Slamf8	5830408F06Rik|Blame|SBBI42	SLAM family member 8	protein-coding
mm_133517.1	chr16	90826743	90826757	+	1	NA	promoter-TSS (NM_001316760)	promoter-TSS (NM_001316760)	31	NM_001316760	70967	Mm.253077	NM_027627	ENSMUSG00000039903	Eva1c	1700092M14Rik|4931408A02Rik|Fam176c	eva-1 homolog C (C. elegans)	protein-coding
mm_5213.1	chr1	13660455	13660469	-	1	NA	promoter-TSS (NM_145381)	promoter-TSS (NM_145381)	47	NM_145381	212442	Mm.89572	NM_145381	ENSMUSG00000025937	Lactb2	Cgi-83|E430032H21Rik	lactamase, beta 2	protein-coding
mm_59616.1	chr7	28147026	28147032	+	1	NA	exon (NM_001164655, exon 8 of 20)	exon (NM_001164655, exon 8 of 20)	17563	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_162284.1	chr1	22469261	22469261	-	1	NA	intron (NM_001012623, intron 14 of 14).2	intron (NM_001012623, intron 14 of 14).2	-36418	NM_183018	116837	Mm.60061	NM_053270	ENSMUSG00000041670	Rims1	C030033M19Rik|RIM1|RIM1a|RIM1alpha|Rab3ip1|Rim|Serg1|mKIAA0340	regulating synaptic membrane exocytosis 1	protein-coding
mm_10122.1	chr2	3749274	3749290	+	1	NA	intron (NM_025626, intron 1 of 3)	intron (NM_025626, intron 1 of 3)	35824	NM_025626	66540	Mm.277864	NM_025626	ENSMUSG00000026655	Fam107b	3110001A13Rik|AA589595|AA959793|AI132312	family with sequence similarity 107, member B	protein-coding
mm_101128.1	chr11	12309761	12309771	-	1	NA	intron (NM_172496, intron 7 of 14)	intron (NM_172496, intron 7 of 14)	102374	NM_001282994	12808	Mm.22847	NM_172496	ENSMUSG00000020173	Cobl	-	cordon-bleu WH2 repeat	protein-coding
mm_83510.1	chr9	45984778	45984808	-	1	NA	promoter-TSS (NM_008775)	promoter-TSS (NM_008775)	78	NM_008775	18475	Mm.200859	NM_008775	ENSMUSG00000003131	Pafah1b2	AI747451|AU021353|Pafahb|mus[b]	platelet-activating factor acetylhydrolase, isoform 1b, subunit 2	protein-coding
mm_11527.1	chr2	32625445	32625495	+	1	NA	promoter-TSS (NM_001198791)	promoter-TSS (NM_001198791)	33	NM_001198791	11636	Mm.29189	NM_021515	ENSMUSG00000026817	Ak1	Ak-1|B430205N08Rik	adenylate kinase 1	protein-coding
mm_107136.1	chr12	21316386	21316400	+	1	NA	promoter-TSS (NM_026347)	promoter-TSS (NM_026347)	1	NM_026347	67732	Mm.335830	NM_026347	ENSMUSG00000062054	Iah1	1500019E20Rik|4833421E05Rik	isoamyl acetate-hydrolyzing esterase 1 homolog	protein-coding
mm_54367.1	chr6	31126545	31126561	-	1	NA	intron (NR_110471, intron 3 of 3)	intron (NR_110471, intron 3 of 3)	-63460	NR_029532	387223		NR_029532	ENSMUSG00000065604	Mir29b-1	Mirn29b|Mirn29b-1|mir-29b-1	microRNA 29b-1	ncRNA
mm_126090.1	chr15	77905622	77905634	+	1	NA	Intergenic	Intergenic	23366	NM_019913	56551	Mm.291917	NM_019913	ENSMUSG00000005354	Txn2	2510006J11Rik|AI788873|Trx2	thioredoxin 2	protein-coding
mm_40190.1	chr5	36484579	36484620	+	1	NA	promoter-TSS (NM_001170454)	promoter-TSS (NM_001170454)	11	NM_025725	66717	Mm.42368	NM_025725	ENSMUSG00000050677	Ccdc96	4921513E08Rik	coiled-coil domain containing 96	protein-coding
mm_120091.1	chr14	57889781	57889792	+	1	NA	intron (NM_029492, intron 1 of 12)	intron (NM_029492, intron 1 of 12)	476	NM_029492	75965	Mm.29044	NM_029492	ENSMUSG00000021969	Zdhhc20	4930542A17Rik|5033406L14Rik|AI448102|B230110O18Rik|ENSMUSG00000055956|HK11	zinc finger, DHHC domain containing 20	protein-coding
mm_133393.1	chr16	84774302	84774314	+	1	NA	5' UTR (NM_023844, exon 1 of 10)	5' UTR (NM_023844, exon 1 of 10)	185	NM_023844	67374	Mm.41758	NM_023844	ENSMUSG00000053062	Jam2	1110002N23Rik|2410030G21Rik|2410167M24Rik|JAM-2|JAM-B|Jcam2|VE-JAM	junction adhesion molecule 2	protein-coding
mm_72427.1	chr8	82863352	82863397	+	1	NA	promoter-TSS (NM_177378)	promoter-TSS (NM_177378)	18	NM_177378	330812	Mm.491438	NM_177378	ENSMUSG00000047747	Rnf150	A630007N06Rik|C030044C12Rik|Greul5|mKIAA1214	ring finger protein 150	protein-coding
mm_63923.1	chr7	139360283	139360288	+	1	NA	Intergenic	Intergenic	-28824	NM_183144	212111	Mm.28308	NM_183144	ENSMUSG00000025477	Inpp5a	-	inositol polyphosphate-5-phosphatase A	protein-coding
mm_116218.1	chr13	32845806	32845816	-	1	NA	exon (NM_025429, exon 5 of 7)	exon (NM_025429, exon 5 of 7)	5374	NM_025429	66222	Mm.20144	NM_025429	ENSMUSG00000044734	Serpinb1a	1190005M04Rik|AI325983|EI|EIA|ELANH2|LEI|M/NEI|MNEI|PI2	serine (or cysteine) peptidase inhibitor, clade B, member 1a	protein-coding
mm_51633.1	chr6	85587592	85587630	+	1	NA	promoter-TSS (NM_145223)	promoter-TSS (NM_145223)	80	NM_145223	236266	Mm.246967	NM_145223	ENSMUSG00000063810	Alms1	bbb	Alstrom syndrome 1	protein-coding
mm_155793.1	chrX	98936315	98936318	+	1	NA	Intergenic	Intergenic	-1465	NM_207633	77929	Mm.212290	NM_207633	ENSMUSG00000047694	Yipf6	A430107J06Rik	Yip1 domain family, member 6	protein-coding
mm_101071.1	chr11	11462437	11462446	-	1	NA	promoter-TSS (NM_015785)	promoter-TSS (NM_015785)	-22	NM_001185153	53604	Mm.9500	NM_015785	ENSMUSG00000020193	Zpbp	4930486K01Rik|Iam38|Sp38	zona pellucida binding protein	protein-coding
mm_106724.1	chr12	3871356	3871364	+	1	NA	intron (NM_007872, intron 4 of 22)	intron (NM_007872, intron 4 of 22)	-9116	NR_045884	100038522	Mm.417270	NR_045884	ENSMUSG00000073242	Dnmt3aos	ENSMUSG00000073242|Gm10485	DNA methyltransferase 3A, opposite strand	ncRNA
mm_152745.1	chr19	19079543	19079545	-	1	NA	intron (NM_001043354, intron 1 of 9)	intron (NM_001043354, intron 1 of 9)	31652	NM_001043354	225998	Mm.234641	NM_146095	ENSMUSG00000036192	Rorb	Nr1f2|RZR-beta|RZRB|Rorbeta|hstp	RAR-related orphan receptor beta	protein-coding
mm_123876.1	chr14	72669363	72669373	-	1	NA	intron (NM_207636, intron 2 of 25)	intron (NM_207636, intron 2 of 25)	40635	NM_207636	319448	Mm.205421	NM_207636	ENSMUSG00000033487	Fndc3a	1700094E19Rik|D14Ertd453e|F730017H24Rik|Fndc3|sys	fibronectin type III domain containing 3A	protein-coding
mm_16149.1	chr2	172288146	172288159	+	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	39660	NM_008561	17201	Mm.57183	NM_008561	ENSMUSG00000038537	Mc3r	MC3-R	melanocortin 3 receptor	protein-coding
mm_65997.1	chr7	30558743	30558747	-	1	NA	intron (NM_001290569, intron 1 of 8)	intron (NM_001290569, intron 1 of 8)	901	NM_029377	75660	Mm.379242	NM_029377	ENSMUSG00000036845	Lin37	1810054G18Rik	lin-37 homolog (C. elegans)	protein-coding
mm_21378.1	chr2	157407611	157407618	-	1	NA	Intergenic	Intergenic	-16679	NM_009271	20779	Mm.22845	NM_009271	ENSMUSG00000027646	Src	AW259666|pp60c-src	Rous sarcoma oncogene	protein-coding
mm_19370.1	chr2	91183824	91183840	-	1	NA	promoter-TSS (NM_145527)	promoter-TSS (NM_145527)	-785	NM_145527	228355	Mm.36410	NM_145527	ENSMUSG00000040687	Madd	9630059K23Rik|IG20	MAP-kinase activating death domain	protein-coding
mm_6742.1	chr1	83277149	83277164	-	1	NA	exon (NM_172430, exon 7 of 11)	exon (NM_172430, exon 7 of 11)	117394	NM_027725	71227	Mm.256482	NM_027725	ENSMUSG00000053161	Daw1	4930563E19Rik|4933429D11Rik|Wdr69|b2b1116Clo|b2b1584Clo	dynein assembly factor with WDR repeat domains 1	protein-coding
mm_62069.1	chr7	92638300	92638302	+	1	NA	Intergenic	Intergenic	-1159	NM_028665	73845	Mm.73248	NM_028665	ENSMUSG00000041343	Ankrd42	4931426M20|4933417L02Rik|Ikbn	ankyrin repeat domain 42	protein-coding
mm_12574.1	chr2	73267998	73268005	+	1	NA	Intergenic	Intergenic	-3925	NM_001005343	381373	Mm.330293	NM_001005343	ENSMUSG00000068859	Sp9	-	trans-acting transcription factor 9	protein-coding
mm_109432.1	chr12	110628772	110628791	+	1	NA	exon (NM_030238, exon 19 of 77)	exon (NM_030238, exon 19 of 77)	27386	NM_030238	13424	Mm.181430	NM_030238	ENSMUSG00000018707	Dync1h1	9930018I23Rik|AI894280|DHC1|DHC1a|DNCL|Dnchc1|Dnec1|Dnecl|Loa|MAP1C|P22|Swl|mKIAA0325	dynein cytoplasmic 1 heavy chain 1	protein-coding
mm_33513.1	chr4	130926766	130926779	+	1	NA	exon (NM_010686, exon 3 of 8)	exon (NM_010686, exon 3 of 8)	13438	NM_010686	16792	Mm.271868	NM_010686	ENSMUSG00000028581	Laptm5	E3	lysosomal-associated protein transmembrane 5	protein-coding
mm_86920.1	chr10	23851523	23851533	+	1	NA	promoter-TSS (NM_011979)	promoter-TSS (NM_011979)	66	NM_011979	26464	Mm.27334	NM_011979	ENSMUSG00000020010	Vnn3	-	vanin 3	protein-coding
mm_90817.1	chr10	7919873	7919891	-	1	NA	exon (NM_138667, exon 3 of 7)	exon (NM_138667, exon 3 of 7)	36241	NM_138667	68652	Mm.193041	NM_138667	ENSMUSG00000015755	Tab2	1110030N06Rik|A530078N03Rik|Map3k7ip2|mKIAA0733	TGF-beta activated kinase 1/MAP3K7 binding protein 2	protein-coding
mm_108901.1	chr12	100199548	100199552	+	1	NA	promoter-TSS (NM_001313934)	promoter-TSS (NM_001313934)	115	NM_009790	12313	Mm.285993	NM_009790	ENSMUSG00000001175	Calm1	AI256814|AI327027|AI461935|AL024000|CaM|Calm	calmodulin 1	protein-coding
mm_24950.1	chr3	96630169	96630200	+	1	NA	promoter-TSS (NR_003619)	promoter-TSS (NR_003619)	256	NM_001102407	60365	Mm.261972	NM_025875	ENSMUSG00000038374	Rbm8a	2310057C03Rik|AA673428|Rbm8	RNA binding motif protein 8a	protein-coding
mm_66276.1	chr7	37591148	37591150	-	1	NA	intron (NM_172385, intron 3 of 5)	intron (NM_172385, intron 3 of 5)	178603	NM_172385	243937	Mm.322505	NM_172385	ENSMUSG00000043456	Zfp536	9630010P11Rik|Znf536|mKIAA0390	zinc finger protein 536	protein-coding
mm_134048.1	chr16	5227826	5227830	-	1	NA	Intergenic	ERVB4_1B-LTR_MM|LTR|ERVK	-5529	NM_001033220	239691	Mm.325639	NM_001033220	ENSMUSG00000051669	AU021092	-	expressed sequence AU021092	protein-coding
mm_11585.1	chr2	33177889	33177917	+	1	NA	intron (NM_001290572, intron 8 of 17)	intron (NM_001290572, intron 8 of 17)	-38058	NM_011923	26360	Mm.208919	NM_011923	ENSMUSG00000004105	Angptl2	AI593246|AW260363|Arp2	angiopoietin-like 2	protein-coding
mm_19596.1	chr2	102400386	102400396	-	1	NA	exon (NM_020267, exon 1 of 5)	exon (NM_020267, exon 1 of 5)	509	NM_020267	80985	Mm.315002	NM_020267	ENSMUSG00000027189	Trim44	Dipb|Mc7	tripartite motif-containing 44	protein-coding
mm_134390.1	chr16	17356170	17356204	-	1	NA	exon (NM_001001983, exon 14 of 55)	exon (NM_001001983, exon 14 of 55)	24816	NM_001331047	15160	Mm.6609	NM_008223	ENSMUSG00000022766	Serpind1	AA985900|AI303446|HC-II|HCII|Hcf2	serine (or cysteine) peptidase inhibitor, clade D, member 1	protein-coding
mm_16982.1	chr2	18047786	18047801	-	1	NA	exon (NM_028317, exon 1 of 1)	exon (NM_028317, exon 1 of 1)	656	NM_028317	72668	Mm.102183	NM_028317	ENSMUSG00000054074	Skida1	2810030E01Rik|5730507N06Rik|BB088113	SKI/DACH domain containing 1	protein-coding
mm_126254.1	chr15	79030946	79030952	+	1	NA	promoter-TSS (NM_001161712)	promoter-TSS (NM_001161712)	75	NM_001161712	26912	Mm.237085	NM_013847	ENSMUSG00000006378	Gcat	AI526977|Kbl	glycine C-acetyltransferase (2-amino-3-ketobutyrate-coenzyme A ligase)	protein-coding
mm_12939.1	chr2	85136375	85136439	+	1	NA	promoter-TSS (NM_011784)	promoter-TSS (NM_011784)	47	NM_011784	23796	Mm.29368	NM_011784	ENSMUSG00000044338	Aplnr	APJ|Agtrl1|msr/apj	apelin receptor	protein-coding
mm_48664.1	chr5	145981256	145981281	-	1	NA	intron (NR_030782, intron 11 of 11)	ORR1D1|LTR|ERVL-MaLR	28349	NM_019792	56388	Mm.301900	NM_019792	ENSMUSG00000029630	Cyp3a25	AI327008	cytochrome P450, family 3, subfamily a, polypeptide 25	protein-coding
mm_16684.1	chr2	6884519	6884530	-	1	NA	intron (NM_001110229, intron 2 of 14)	intron (NM_001110229, intron 2 of 14)	472	NM_010160	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_152354.1	chr19	10001626	10001632	-	1	NA	promoter-TSS (NM_011913)	promoter-TSS (NM_011913)	4	NM_011913	24115	Mm.31577	NM_011913	ENSMUSG00000037418	Best1	Bmd|Vmd2|mBest1	bestrophin 1	protein-coding
mm_62341.1	chr7	100498100	100498113	+	1	NA	exon (NM_011671, exon 5 of 8)	exon (NM_011671, exon 5 of 8)	4748	NM_011671	22228	Mm.171378	NM_011671	ENSMUSG00000033685	Ucp2	Slc25a8	uncoupling protein 2 (mitochondrial, proton carrier)	protein-coding
mm_151478.1	chr19	58675068	58675081	+	1	NA	exon (NM_026925, exon 6 of 13)	exon (NM_026925, exon 6 of 13)	4709	NM_026925	69060	Mm.20407	NM_026925	ENSMUSG00000046008	Pnlip	1810007A24Rik|PL|PTL	pancreatic lipase	protein-coding
mm_129270.1	chr15	77016060	77016078	-	1	NA	exon (NM_013593, exon 4 of 4)	exon (NM_013593, exon 4 of 4)	6658	NM_001164048	17189	Mm.404074	NM_013593	ENSMUSG00000018893	Mb	AI325109	myoglobin	protein-coding
mm_158087.1	chrX	101268219	101268229	-	1	NA	promoter-TSS (NM_001308535)	promoter-TSS (NM_001308535)	31	NM_001308535	16186	Mm.2923	NM_013563	ENSMUSG00000031304	Il2rg	CD132|[g]c|gamma(c)|gc|p64	interleukin 2 receptor, gamma chain	protein-coding
mm_123182.1	chr14	57744651	57744655	-	1	NA	intron (NM_015771, intron 1 of 7)	intron (NM_015771, intron 1 of 7)	1470	NM_015771	50523	Mm.347899	NM_015771	ENSMUSG00000021959	Lats2	4932411G09Rik|AV277261|AW228608	large tumor suppressor 2	protein-coding
mm_102496.1	chr11	60352928	60352932	-	1	NA	promoter-TSS (NM_001039093)	promoter-TSS (NM_001039093)	-25	NM_001039092	216810	Mm.218875	NM_153080	ENSMUSG00000000538	Tom1l2	2900016I08Rik|A730055F12Rik|AU042072|Srebf1	target of myb1-like 2 (chicken)	protein-coding
mm_95936.1	chr11	58382311	58382325	+	1	NA	5' UTR (NM_001083884, exon 3 of 7)	5' UTR (NM_001083884, exon 3 of 7)	1672	NM_001330197	70163	Mm.24119	NM_027339	ENSMUSG00000013643	Lypd8	2210415F13Rik	LY6/PLAUR domain containing 8	protein-coding
mm_91222.1	chr10	22058590	22058604	-	1	NA	Intergenic	CpG	9482	NM_053264	114671	Mm.288194	NM_053264	ENSMUSG00000069712	4930444G20Rik	-	RIKEN cDNA 4930444G20 gene	protein-coding
mm_46229.1	chr5	99037370	99037384	-	1	NA	promoter-TSS (NM_008926)	promoter-TSS (NM_008926)	-298	NM_008926	19092	Mm.263002	NM_008926	ENSMUSG00000029334	Prkg2	AW212535|CGKII|Prkgr2|cGK-II	protein kinase, cGMP-dependent, type II	protein-coding
mm_132442.1	chr16	35948307	35948320	+	1	NA	exon (NM_030253, exon 4 of 11)	exon (NM_030253, exon 4 of 11)	-9286	NM_001013371	209200	Mm.390852	NM_001013371	ENSMUSG00000049502	Dtx3l	AU042200|BC023741	deltex 3-like, E3 ubiquitin ligase	protein-coding
mm_159404.1	chr3	98563389	98563389	-	1	NA	exon (NM_001111336, exon 2 of 4).3	exon (NM_001111336, exon 2 of 4).3	554	NM_001111336	15495	Mm.14309	NM_008294	ENSMUSG00000095143	Hsd3b4	-	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 4	protein-coding
mm_36932.1	chr4	108460703	108460713	-	1	NA	intron (NM_175472, intron 2 of 30)	CpG	1282	NM_175472	230594	Mm.25181	NM_175472	ENSMUSG00000034610	Zcchc11	6030404K05Rik|9230115F04Rik|PPAPD3|mKIAA0191	zinc finger, CCHC domain containing 11	protein-coding
mm_20217.1	chr2	125737886	125737890	-	1	NA	3' UTR (NM_177608, exon 18 of 18)	3' UTR (NM_177608, exon 18 of 18)	-13740	NM_199022	271849	Mm.425101	NM_199022	ENSMUSG00000035109	Shc4	6230417E10Rik|9930029B02Rik|Gm685|RaLP	SHC (Src homology 2 domain containing) family, member 4	protein-coding
mm_67022.1	chr7	66332539	66332554	-	1	NA	intron (NM_146191, intron 4 of 33)	intron (NM_146191, intron 4 of 33)	49178	NR_106024	102465640		NR_106024	ENSMUSG00000098353	Mir7057	Gm27550|mmu-mir-7057	microRNA 7057	ncRNA
mm_1922.1	chr1	86039664	86039674	+	1	NA	Intergenic	Intergenic	-6194	NM_001144993	72792	Mm.54981	NM_001144992	ENSMUSG00000026227	2810459M11Rik	-	RIKEN cDNA 2810459M11 gene	protein-coding
mm_45800.1	chr5	87568914	87568924	-	1	NA	promoter-TSS (NM_016771)	promoter-TSS (NM_016771)	87	NM_016771	53315	Mm.6824	NM_016771	ENSMUSG00000029273	Sult1d1	5033411P13Rik|AI987815|ST1d1|SULT-N|Sultn	sulfotransferase family 1D, member 1	protein-coding
mm_99470.1	chr11	102436100	102436150	+	1	NA	TTS (NM_199200)	TTS (NM_199200)	5803	NM_008175	14824	Mm.1568	NM_008175	ENSMUSG00000034708	Grn	Pgrn|epithelin	granulin	protein-coding
mm_3633.1	chr1	152807906	152807916	+	1	NA	5' UTR (NM_010877, exon 2 of 16)	5' UTR (NM_010877, exon 2 of 16)	7758	NM_010877	17970	Mm.270307	NM_010877	ENSMUSG00000026480	Ncf2	NOXA2|Ncf-2|p67phox	neutrophil cytosolic factor 2	protein-coding
mm_72838.1	chr8	88290553	88290575	+	1	NA	intron (NM_001037723, intron 1 of 27)	intron (NM_001037723, intron 1 of 27)	1498	NM_001037723	11513	Mm.288206	NM_007406	ENSMUSG00000031659	Adcy7	AA407758	adenylate cyclase 7	protein-coding
mm_22182.1	chr2	173217670	173217715	-	1	NA	intron (NM_001139519, intron 1 of 3)	PB1D7|SINE|Alu	1230	NM_021394	58203	Mm.116687	NM_021394	ENSMUSG00000027514	Zbp1	2010010H03Rik|Dai|Dlm1|mZaDLM	Z-DNA binding protein 1	protein-coding
mm_56110.1	chr6	87503735	87503761	-	1	NA	intron (NM_001037727, intron 1 of 10)	intron (NM_001037727, intron 1 of 10)	-7421	NM_175476	232201	Mm.119564	NM_175476	ENSMUSG00000030047	Arhgap25	A130039I20Rik	Rho GTPase activating protein 25	protein-coding
mm_116657.1	chr13	49190199	49190208	-	1	NA	intron (NM_013610, intron 1 of 3)	intron (NM_013610, intron 1 of 3)	2656	NM_013610	18081	Mm.18503	NM_013610	ENSMUSG00000037966	Ninj1	AU024536	ninjurin 1	protein-coding
mm_140858.1	chr17	23740278	23740298	-	1	NA	promoter-TSS (NM_023824)	promoter-TSS (NM_023824)	42	NM_023824	76498	Mm.491253	NM_023824	ENSMUSG00000023909	Paqr4	1500004C10Rik	progestin and adipoQ receptor family member IV	protein-coding
mm_39682.1	chr5	25768503	25768515	+	1	NA	intron (NM_001310504, intron 1 of 10)	L1MB1|LINE|L1	8536	NM_001004365	242894	Mm.150319	NM_001004365	ENSMUSG00000056367	Actr3b	9630005C02|ARP11|AW047569|Arp3b|Arp3beta	ARP3 actin-related protein 3B	protein-coding
mm_152314.1	chr19	9899451	9899501	-	1	NA	promoter-TSS (NM_016692)	promoter-TSS (NM_016692)	57	NM_016692	16319	Mm.29755	NM_016692	ENSMUSG00000024660	Incenp	2700067E22Rik|AU019509|C130081E20|C77457	inner centromere protein	protein-coding
mm_9917.1	chr1	189277763	189277801	-	1	NA	intron (NM_001281848, intron 2 of 5)	intron (NM_001281848, intron 2 of 5)	65571	NM_001159850	16526	Mm.33304	NM_010607	ENSMUSG00000037624	Kcnk2	A430027H14Rik|AI848635|TREK-1	potassium channel, subfamily K, member 2	protein-coding
mm_90385.1	chr10	127290004	127290014	+	1	NA	promoter-TSS (NM_001290183)	promoter-TSS (NM_001290183)	-784	NM_007837	13198	Mm.110220	NM_007837	ENSMUSG00000025408	Ddit3	CHOP-10|CHOP10|chop|gadd153	DNA-damage inducible transcript 3	protein-coding
mm_56012.1	chr6	86516284	86516296	-	1	NA	Intergenic	Intergenic	9875	NM_011865	23983	Mm.274146	NM_011865	ENSMUSG00000051695	Pcbp1	WBP17|[a]CP-1|alphaCP-1|hnRNP E1	poly(rC) binding protein 1	protein-coding
mm_48889.1	chr5	151368441	151368474	-	1	NA	promoter-TSS (NR_045700)	promoter-TSS (NR_045700)	-218	NR_045700	625175	Mm.443286	NR_045699	ENSMUSG00000097321	1700028E10Rik	A630054D14|Gm6561	RIKEN cDNA 1700028E10 gene	ncRNA
mm_148452.1	chr19	3988340	3988347	+	1	NA	intron (NM_001302479, intron 5 of 7)	intron (NM_001302479, intron 5 of 7)	1773	NM_001302482	71670	Mm.29735	NM_027857	ENSMUSG00000024866	Acy3	0610006H10Rik|AA3|AAIII|AW107362|Acy-3|HCBP1	aspartoacylase (aminoacylase) 3	protein-coding
mm_133167.1	chr16	70504409	70504420	+	1	NA	intron (NM_028803, intron 12 of 15)	B1_Mur2|SINE|Alu	-112011	NR_040474	52645	Mm.188475	NR_040474		D16Ertd519e	-	DNA segment, Chr 16, ERATO Doi 519, expressed	ncRNA
mm_24209.1	chr3	88621835	88621874	+	1	NA	intron (NM_001198912, intron 1 of 21)	intron (NM_001198912, intron 1 of 21)	460	NM_001198912	16800	Mm.239329	NM_008487	ENSMUSG00000028059	Arhgef2	AA408978|GEF|GEF-H1|GEFH1|LFP40|Lbcl1|Lfc|P40|mKIAA0651	rho/rac guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_97867.1	chr11	83121737	83121745	+	1	NA	exon (NM_011407, exon 2 of 2)	exon (NM_011407, exon 2 of 2)	4896	NM_011407	20555	Mm.10948	NM_011407	ENSMUSG00000078763	Slfn1	AV316259	schlafen 1	protein-coding
mm_15844.1	chr2	164769922	164769954	+	1	NA	promoter-TSS (NM_026785)	promoter-TSS (NM_026785)	9	NM_026785	68612	Mm.89830	NM_026785	ENSMUSG00000001403	Ube2c	1110015A16Rik|D2Ertd695e	ubiquitin-conjugating enzyme E2C	protein-coding
mm_38217.1	chr4	135972549	135972567	-	1	NA	promoter-TSS (NM_011942)	promoter-TSS (NM_011942)	36	NM_011942	26394	Mm.34302	NM_011942	ENSMUSG00000028670	Lypla2	LysoII	lysophospholipase 2	protein-coding
mm_137400.1	chr17	25861706	25861715	+	1	NA	promoter-TSS (NM_001163766)	promoter-TSS (NM_001163766)	-195	NM_001163766	106618	Mm.35470	NM_134124	ENSMUSG00000073434	Wdr90	3230401M21Rik|AI551153|mKIAA1924	WD repeat domain 90	protein-coding
mm_164656.1	chr17	36190221	36190262	-	1	NA	promoter-TSS (NM_008208)	promoter-TSS (NM_008208)	-90	NM_008208	15043	Mm.426002	NM_008208	ENSMUSG00000054128	H2-T3	H-2T3|H2-Tw3|MumuTL|TL	histocompatibility 2, T region locus 3	protein-coding
mm_155093.1	chrX	48166591	48166596	+	1	NA	Intergenic	MIRb|SINE|MIR	20157	NM_028773	74131	Mm.276131	NM_028773	ENSMUSG00000031101	Sash3	1200013B08Rik|AW413946|SLY1	SAM and SH3 domain containing 3	protein-coding
mm_70985.1	chr8	27260430	27260462	+	1	NA	exon (NM_007918, exon 1 of 3)	exon (NM_007918, exon 1 of 3)	119	NM_007918	13685	Mm.6700	NM_007918	ENSMUSG00000031490	Eif4ebp1	4e-bp1|AA959816|PHAS-I	eukaryotic translation initiation factor 4E binding protein 1	protein-coding
mm_64974.1	chr7	16815473	16815481	-	1	NA	promoter-TSS (NM_001039878)	promoter-TSS (NM_001039878)	-412	NM_133789	97387	Mm.21612	NM_133789	ENSMUSG00000030374	Strn4	C80611|ZIN|zinedin	striatin, calmodulin binding protein 4	protein-coding
mm_165715.1	chr3	100489378	100489386	-	1	NA	promoter-TSS (NM_001142952)	promoter-TSS (NM_001142952)	-190	NM_001142952	74645	Mm.226900	NM_001142952	ENSMUSG00000044468	Fam46c	4930431B09Rik|AI449797	family with sequence similarity 46, member C	protein-coding
mm_94267.1	chr11	3530909	3530927	+	1	NA	intron (NM_001159284, intron 9 of 21)	intron (NM_001159284, intron 9 of 21)	8374	NM_013870	29856	Mm.188516	NM_013870	ENSMUSG00000020439	Smtn	smsmo	smoothelin	protein-coding
mm_66596.1	chr7	45458184	45458202	-	1	NA	exon (NM_010240, exon 4 of 4)	exon (NM_010240, exon 4 of 4)	1693	NM_010240	14325	Mm.30357	NM_010240	ENSMUSG00000050708	Ftl1	Ftl|Ftl-1|L-ferritin	ferritin light polypeptide 1	protein-coding
mm_114228.1	chr13	56522498	56522516	+	1	NA	promoter-TSS (NM_178674)	promoter-TSS (NM_178674)	-1	NM_178674	213311	Mm.233904	NM_178674	ENSMUSG00000035509	Fbxl21	D630045D17Rik|FBL3B|FBXL3B|Psttm	F-box and leucine-rich repeat protein 21	protein-coding
mm_59372.1	chr7	25704778	25704802	+	1	NA	exon (NM_011577, exon 7 of 7)	exon (NM_011577, exon 7 of 7)	14263	NM_028771	52132	Mm.278798	NM_028771	ENSMUSG00000002608	Ccdc97	1200014H14Rik|2810446P04Rik|AA545218|D7Ertd462e	coiled-coil domain containing 97	protein-coding
mm_143369.1	chr17	67354923	67354965	-	1	NA	promoter-TSS (NM_008984)	promoter-TSS (NM_008984)	-485	NM_008984	19274	Mm.311809	NM_008984	ENSMUSG00000033278	Ptprm	RPTPmu|mKIAA4044	protein tyrosine phosphatase, receptor type, M	protein-coding
mm_40509.1	chr5	57755322	57755365	+	1	NA	intron (NM_001310608, intron 1 of 3)	ORR1D1|LTR|ERVL-MaLR	37262	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_9604.1	chr1	175625581	175625613	-	1	NA	promoter-TSS (NM_010209)	promoter-TSS (NM_010209)	38	NM_010209	14194	Mm.41502	NM_010209	ENSMUSG00000026526	Fh1	Fh|Fh-1	fumarate hydratase 1	protein-coding
mm_106880.1	chr12	8011647	8011657	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	33975	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_159558.1	chr4	107823135	107823135	+	1	NA	intron (NR_033496, intron 2 of 20)	intron (NR_033496, intron 2 of 20)	20876	NM_001080926	16975	Mm.442134	NM_053073	ENSMUSG00000028613	Lrp8	4932703M08Rik|AA921429|AI848122|ApoER2|Lr8b	low density lipoprotein receptor-related protein 8, apolipoprotein e receptor	protein-coding
mm_23793.1	chr3	79591438	79591448	+	1	NA	promoter-TSS (NM_026352)	promoter-TSS (NM_026352)	54	NM_026352	67738	Mm.295252	NM_026352	ENSMUSG00000027804	Ppid	4930564J03Rik|CYP-40|Ppidl|Ppif	peptidylprolyl isomerase D (cyclophilin D)	protein-coding
mm_112385.1	chr12	119238151	119238159	-	1	NA	5' UTR (NM_177290, exon 1 of 14)	5' UTR (NM_177290, exon 1 of 14)	121	NM_177290	320910	Mm.217000	NM_177290	ENSMUSG00000025321	Itgb8	4832412O06Rik	integrin beta 8	protein-coding
mm_63932.1	chr7	139525728	139525730	+	1	NA	exon (NM_001127363, exon 8 of 16)	exon (NM_001127363, exon 8 of 16)	57068	NM_183248	14912	Mm.28308	NM_183248	ENSMUSG00000041309	Nkx6-2	Gtx|Nkx6.2	NK6 homeobox 2	protein-coding
mm_99917.1	chr11	110180217	110180229	+	1	NA	intron (NM_147218, intron 36 of 38)	intron (NM_147218, intron 36 of 38)	-12070	NM_147220	217262	Mm.291459	NM_147220	ENSMUSG00000041797	Abca9	D630040K07Rik	ATP-binding cassette, sub-family A (ABC1), member 9	protein-coding
mm_94798.1	chr11	22973264	22973272	+	1	NA	exon (NM_011663, exon 1 of 1)	exon (NM_011663, exon 1 of 1)	1263	NM_011663	22183	Mm.29542	NM_011663	ENSMUSG00000044068	Zrsr1	D11Ncvs75|Irlgs2|SP2|U2af1-rs1|U2afbp-rs	zinc finger (CCCH type), RNA binding motif and serine/arginine rich 1	protein-coding
mm_93886.1	chr10	125328484	125328496	-	1	NA	promoter-TSS (NM_011391)	promoter-TSS (NM_011391)	45	NM_011391	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|Mct2	solute carrier family 16 (monocarboxylic acid transporters), member 7	protein-coding
mm_131097.1	chr16	4939100	4939142	+	1	NA	promoter-TSS (NM_001316715)	promoter-TSS (NM_001316715)	10	NM_025839	66911	Mm.428698	NM_025839	ENSMUSG00000022516	Nudt16l1	1110001K21Rik|5330437I08Rik|Sdos	nudix (nucleoside diphosphate linked moiety X)-type motif 16-like 1	protein-coding
mm_99195.1	chr11	101011749	101011765	+	1	NA	5' UTR (NM_016920, exon 2 of 22)	5' UTR (NM_016920, exon 2 of 22)	2305	NM_001243051	11975	Mm.340818	NM_016920	ENSMUSG00000019302	Atp6v0a1	AA959968|ATP6a1|Atp6n1|Atp6n1a|Atpv0a1|Vpp-1|Vpp1	ATPase, H+ transporting, lysosomal V0 subunit A1	protein-coding
mm_46682.1	chr5	109558958	109559014	-	1	NA	promoter-TSS (NM_001164735)	promoter-TSS (NM_001164735)	7	NM_016715	57914	Mm.35771	NM_016715	ENSMUSG00000033467	Crlf2	CRLM2|Ly114|Tpte2|Tslpr	cytokine receptor-like factor 2	protein-coding
mm_21970.1	chr2	167309297	167309306	-	1	NA	exon (NM_019835, exon 3 of 9)	exon (NM_019835, exon 3 of 9)	39877	NM_019835	56336	Mm.200886	NM_019835	ENSMUSG00000017929	B4galt5	9430078I07Rik|AW049941|AW539721	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 5	protein-coding
mm_72163.1	chr8	72219798	72219808	+	1	NA	promoter-TSS (NM_026455)	promoter-TSS (NM_026455)	73	NM_026455	67922	Mm.28327	NM_026455	ENSMUSG00000003039	Fam32a	2510049I19Rik|AW822030|OTAG-12|Otag12	family with sequence similarity 32, member A	protein-coding
mm_137936.1	chr17	32659045	32659058	+	1	NA	promoter-TSS (NM_001101588)	promoter-TSS (NM_001101588)	-432	NM_001101588	631304	Mm.328950	NM_001101588	ENSMUSG00000090700	Cyp4f40	EG631304	cytochrome P450, family 4, subfamily f, polypeptide 40	protein-coding
mm_113215.1	chr13	25191882	25191886	+	1	NA	intron (NM_177577, intron 8 of 9)	B4A|SINE|B4	78112	NM_009513	22360	Mm.4766	NM_009513	ENSMUSG00000048978	Nrsn1	Neurensin-1|Neuro-p24|Vmp	neurensin 1	protein-coding
mm_24395.1	chr3	90293164	90293253	+	1	NA	Intergenic	(CCG)n|Simple_repeat|Simple_repeat	23059	NR_105979	102465612		NR_105979	ENSMUSG00000099199	Mir7012	Gm27370|mmu-mir-7012	microRNA 7012	ncRNA
mm_134646.1	chr16	21787797	21787813	-	1	NA	promoter-TSS (NM_023737)	promoter-TSS (NM_023737)	29	NM_023737	74147	Mm.28100	NM_023737	ENSMUSG00000022853	Ehhadh	1300002P22Rik|HD|L-PBE|LBFP|LBP|MFP|MFP1|PBFE	enoyl-Coenzyme A, hydratase/3-hydroxyacyl Coenzyme A dehydrogenase	protein-coding
mm_52397.1	chr6	113307240	113307246	+	1	NA	5' UTR (NM_001282127, exon 1 of 14)	5' UTR (NM_001282127, exon 1 of 14)	106	NM_001282126	78783	Mm.356059	NM_030178	ENSMUSG00000001632	Brpf1	4833438B11Rik|4930540D11Rik|Brpf2	bromodomain and PHD finger containing, 1	protein-coding
mm_65480.1	chr7	25615808	25615814	-	1	NA	promoter-TSS (NM_001039243)	promoter-TSS (NM_001039243)	81	NM_001039243	632778	Mm.423112	NM_001039243	ENSMUSG00000074261	Erich4	EG632778|Gm7092|Kseg1	glutamate rich 4	protein-coding
mm_106630.1	chr11	120866642	120866674	-	1	NA	exon (NM_027745, exon 16 of 19)	exon (NM_027745, exon 16 of 19)	-42111	NM_007988	14104	Mm.236443	NM_007988	ENSMUSG00000025153	Fasn	A630082H08Rik|FAS	fatty acid synthase	protein-coding
mm_43902.1	chr5	144244433	144244457	+	1	NA	promoter-TSS (NM_001163709)	promoter-TSS (NM_001163709)	8	NM_001163709	55950	Mm.38011	NM_018772	ENSMUSG00000047843	Bri3	I3	brain protein I3	protein-coding
mm_26708.1	chr3	157947214	157947244	+	1	NA	promoter-TSS (NM_001013806)	promoter-TSS (NM_001013806)	-237	NM_001013806	433667	Mm.265806	NM_001013806	ENSMUSG00000039988	Ankrd13c	AI505652|AU022220	ankyrin repeat domain 13c	protein-coding
mm_83689.1	chr9	50561262	50561268	-	1	NA	promoter-TSS (NM_025687)	promoter-TSS (NM_025687)	3	NM_025687	66654	Mm.442255	NM_025687	ENSMUSG00000032065	Tex12	5730518K06Rik	testis expressed gene 12	protein-coding
mm_96231.1	chr11	62551168	62551191	+	1	NA	promoter-TSS (NR_002875).2	promoter-TSS (NR_002875).2	8	NM_011664	22187	Mm.371592	NM_011664	ENSMUSG00000019505	Ubb	AL033289|Rps27a|Uba52|Ubb2|Ubc	ubiquitin B	protein-coding
mm_106136.1	chr11	116488332	116488336	-	1	NA	intron (NM_026364, intron 1 of 9)	B1F1|SINE|Alu	2012	NM_026364	67763	Mm.25125	NM_026364	ENSMUSG00000015869	Prpsap1	5730409F23Rik|PAP39	phosphoribosyl pyrophosphate synthetase-associated protein 1	protein-coding
mm_131988.1	chr16	25042304	25042334	+	1	NA	Intergenic	Intergenic	-17320	NR_040374	319487	Mm.137341	NR_040374	ENSMUSG00000096960	A230028O05Rik	-	RIKEN cDNA A230028O05 gene	ncRNA
mm_146295.1	chr18	80046907	80046963	+	1	NA	promoter-TSS (NM_053117)	promoter-TSS (NM_053117)	40	NM_053117	93737	Mm.24678	NM_053117	ENSMUSG00000056214	Pard6g	2410049N21Rik|Par6a	par-6 family cell polarity regulator gamma	protein-coding
mm_117877.1	chr13	98926375	98926389	-	1	NA	promoter-TSS (NM_178716)	promoter-TSS (NM_178716)	2	NM_178716	238799	Mm.173286	NM_178716	ENSMUSG00000009470	Tnpo1	AU021749|D13Ertd688e|IPO2|Kpnb2|MIP|MIP1|TRN	transportin 1	protein-coding
mm_120307.1	chr14	63141761	63141781	+	1	NA	exon (NM_007798, exon 9 of 10)	exon (NM_007798, exon 9 of 10)	19309	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_82573.1	chr9	21121652	21121660	-	1	NA	exon (NM_018793, exon 7 of 25)	exon (NM_018793, exon 7 of 25)	9619	NM_018793	54721	Mm.20249	NM_018793	ENSMUSG00000032175	Tyk2	JTK1	tyrosine kinase 2	protein-coding
mm_15434.1	chr2	157278999	157279025	+	1	NA	promoter-TSS (NM_019642)	promoter-TSS (NM_019642)	-86	NM_019642	20014	Mm.22130	NM_019642	ENSMUSG00000027642	Rpn2	1300012C06Rik|AV261018|Rpn-2	ribophorin II	protein-coding
mm_152137.1	chr19	7039932	7039980	-	1	NA	promoter-TSS (NM_016737)	promoter-TSS (NM_016737)	70	NM_016737	20867	Mm.258633	NM_016737	ENSMUSG00000024966	Stip1	Hop|Sti1|p60	stress-induced phosphoprotein 1	protein-coding
mm_100517.1	chr11	120530708	120530733	+	1	NA	promoter-TSS (NM_008101)	promoter-TSS (NM_008101)	-7	NM_008101	14527	Mm.22329	NM_008101	ENSMUSG00000025127	Gcgr	GR	glucagon receptor	protein-coding
mm_72262.1	chr8	75097161	75097172	+	1	NA	exon (NM_010442, exon 3 of 5)	exon (NM_010442, exon 3 of 5)	3548	NM_010442	15368	Mm.276389	NM_010442	ENSMUSG00000005413	Hmox1	D8Wsu38e|HO-1|HO1|Hemox|Hmox|Hsp32	heme oxygenase 1	protein-coding
mm_25006.1	chr3	97658384	97658392	+	1	NA	intron (NM_182997, intron 1 of 7)	CpG	176	NM_182997	108097	Mm.31175	NM_182997	ENSMUSG00000038205	Prkab2	5730553K21Rik|AW049591|BB124140	protein kinase, AMP-activated, beta 2 non-catalytic subunit	protein-coding
mm_51330.1	chr6	72356210	72356221	+	1	NA	5' UTR (NM_144916, exon 2 of 8)	5' UTR (NM_144916, exon 2 of 8)	732	NM_144916	232086	Mm.491165	NM_144916	ENSMUSG00000055912	Tmem150a	BC014685|Tmem150	transmembrane protein 150A	protein-coding
mm_71911.1	chr8	70083510	70083547	+	1	NA	promoter-TSS (NM_177900)	promoter-TSS (NM_177900)	-1	NM_177900	330790	Mm.152048	NM_177900	ENSMUSG00000007594	Hapln4	9330174O11|Bral2|Lpr4	hyaluronan and proteoglycan link protein 4	protein-coding
mm_7185.1	chr1	92774941	92774952	-	1	NA	Intergenic	Intergenic	-56740	NM_016696	14733	Mm.297976	NM_016696	ENSMUSG00000034220	Gpc1	AI462976	glypican 1	protein-coding
mm_154910.1	chrX	21360905	21360930	+	1	NA	promoter-TSS (NR_045668)	promoter-TSS (NR_045668)	52	NR_045668	331392	Mm.23126	NM_198633	ENSMUSG00000051537	Gm5124	EG331392	nucleolar and coiled-body phosphoprotein 1 pseudogene	pseudo
mm_117581.1	chr13	89278357	89278357	-	1	NA	intron (NM_010103, intron 8 of 9)	intron (NM_010103, intron 8 of 9)	-262279	NM_013500	12950	Mm.266790	NM_013500	ENSMUSG00000021613	Hapln1	BB099155|CLP|Crtl1|Crtl1l|LP|LP-1	hyaluronan and proteoglycan link protein 1	protein-coding
mm_50998.1	chr6	63516213	63516239	+	1	NA	intron (NM_008167, intron 2 of 15)	intron (NM_008167, intron 2 of 15)	259369	NM_008167	14804	Mm.439651	NM_008167	ENSMUSG00000071424	Grid2	B230104L07Rik|GluD2|GluRdelta2|Lc|Lc<J>|MMS10-AC|Ms10ac|cpr|ho|nmf408|tpr	glutamate receptor, ionotropic, delta 2	protein-coding
mm_118410.1	chr14	3545881	3545898	+	1	NA	intron (NM_001270806, intron 4 of 4).2	intron (NM_001270806, intron 4 of 4).2	41789	NR_038059	73549	Mm.398741	NR_038059	ENSMUSG00000079407	1700110I01Rik	100040740|1700016F01Rik|Gm2938	RIKEN cDNA 1700110I01 gene	ncRNA
mm_22094.1	chr2	168955258	168955305	-	1	NA	5' UTR (NM_009564, exon 1 of 6)	5' UTR (NM_009564, exon 1 of 6)	306	NM_009564	22722	Mm.2095	NM_009564	ENSMUSG00000027551	Zfp64	-	zinc finger protein 64	protein-coding
mm_119283.1	chr14	34375518	34375582	+	1	NA	promoter-TSS (NM_011430)	promoter-TSS (NM_011430)	46	NM_153127	105450	Mm.272673	NM_153127	ENSMUSG00000041445	Mmrn2	AA986839|ENDOGLYX1|Emilin3|EndoGlyx-1	multimerin 2	protein-coding
mm_112444.1	chr13	5861504	5861526	+	1	NA	promoter-TSS (NM_011803)	promoter-TSS (NM_011803)	26	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_109196.1	chr12	108635744	108635839	+	1	NA	promoter-TSS (NM_001163396)	promoter-TSS (NM_001163396)	38	NM_001163396	14026	Mm.238841	NM_007965	ENSMUSG00000021262	Evl	AI528774	Ena-vasodilator stimulated phosphoprotein	protein-coding
mm_46901.1	chr5	114130706	114130726	-	1	NA	promoter-TSS (NM_011677)	promoter-TSS (NM_011677)	281	NM_001040691	22256	Mm.1393	NM_011677	ENSMUSG00000029591	Ung	UNG1|UNG2	uracil DNA glycosylase	protein-coding
mm_167778.1	chr9	114118086	114118089	+	1	NA	Intergenic	Intergenic	60733	NM_001101510	382111	Mm.376140	NM_001101510	ENSMUSG00000086596	Susd5	Gm1126	sushi domain containing 5	protein-coding
mm_79333.1	chr9	53341210	53341226	+	1	NA	intron (NM_176846, intron 3 of 5)	intron (NM_176846, intron 3 of 5)	39548	NM_176846	320051	Mm.277540	NM_176846	ENSMUSG00000034584	Exph5	AC079869.22gm5|B130009M24Rik|E030050P12|Kiaa0624|Slac2b|slac2-b	exophilin 5	protein-coding
mm_117046.1	chr13	58359078	58359122	-	1	NA	Intergenic	CpG	-4238	NM_175214	75050	Mm.446094	NM_175214	ENSMUSG00000060176	Kif27	4930517I18Rik	kinesin family member 27	protein-coding
mm_69752.1	chr7	140956176	140956182	-	1	NA	promoter-TSS (NM_030694)	promoter-TSS (NM_030694)	-218	NM_030694	80876	Mm.379266	NM_030694	ENSMUSG00000060591	Ifitm2	DSPA2c|Ifitm3l|fragilis3|mil-3	interferon induced transmembrane protein 2	protein-coding
mm_106015.1	chr11	116012679	116012711	-	1	NA	promoter-TSS (NM_016905)	promoter-TSS (NM_016905)	24	NM_016905	14635	Mm.2820	NM_016905	ENSMUSG00000020766	Galk1	AA409894|GALK|Gk|Glk|Glk1	galactokinase 1	protein-coding
mm_111354.1	chr12	86990452	86990467	-	1	NA	Intergenic	CpG	-1783	NM_001080943	238331	Mm.185890	NM_001080943	ENSMUSG00000048483	Zdhhc22	Gm262	zinc finger, DHHC-type containing 22	protein-coding
mm_7017.1	chr1	86526549	86526559	-	1	NA	promoter-TSS (NM_008972)	promoter-TSS (NM_008972)	-182	NM_008972	19231	Mm.19187	NM_008972	ENSMUSG00000026238	Ptma	Thym	prothymosin alpha	protein-coding
mm_85360.1	chr9	103217391	103217440	-	1	NA	exon (NM_133977, exon 12 of 17)	exon (NM_133977, exon 12 of 17)	12871	NM_133977	22041	Mm.37214	NM_133977	ENSMUSG00000032554	Trf	AI266983|Cd176|HP|Tf|Tfn|hpx	transferrin	protein-coding
mm_57558.1	chr6	126939525	126939604	-	1	NA	promoter-TSS (NM_001347455)	promoter-TSS (NM_001347455)	23	NM_009013	19362	Mm.204634	NM_009013	ENSMUSG00000030346	Rad51ap1	2510006L10Rik|RAB22	RAD51 associated protein 1	protein-coding
mm_31968.1	chr4	88094600	88094653	+	1	NA	promoter-TSS (NM_001081184)	promoter-TSS (NM_001081184)	-4	NM_001081184	230393	Mm.287210	NM_001081184	ENSMUSG00000038368	Focad	-	focadhesin	protein-coding
mm_28604.1	chr3	94582721	94582741	-	1	NA	promoter-TSS (NM_029721)	promoter-TSS (NM_029721)	-15	NM_029721	76742	Mm.28160	NM_029721	ENSMUSG00000028136	Snx27	5730552M22Rik|ESTM45|ESTM47|R75405	sorting nexin family member 27	protein-coding
mm_123586.1	chr14	67072394	67072402	-	1	NA	promoter-TSS (NM_028032)	promoter-TSS (NM_028032)	73	NM_028032	71978	Mm.273997	NM_028032	ENSMUSG00000022052	Ppp2r2a	2410004D02Rik|mKIAA1541	protein phosphatase 2, regulatory subunit B, alpha	protein-coding
mm_142405.1	chr17	45458980	45459008	-	1	NA	intron (NM_027649, intron 3 of 7)	intron (NM_027649, intron 3 of 7)	15944	NM_027649	71020	Mm.44257	NM_027649	ENSMUSG00000023935	Spats1	1700011H05Rik|4933400B06Rik|Daip2|Ddip|Srsp1	spermatogenesis associated, serine-rich 1	protein-coding
mm_57231.1	chr6	123282799	123282806	-	1	NA	3' UTR (NM_019948, exon 6 of 6)	3' UTR (NM_019948, exon 6 of 6)	7069	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_34106.1	chr4	139192918	139192941	+	1	NA	promoter-TSS (NM_009798)	promoter-TSS (NM_009798)	30	NM_001037761	12345	Mm.2945	NM_009798	ENSMUSG00000028745	Capzb	1700120C01Rik|AI325129|CPB1|CPB2|CPbeat2|CPbeta1|CPbeta2|Cappb1	capping protein (actin filament) muscle Z-line, beta	protein-coding
mm_103998.1	chr11	84870697	84870711	-	1	NA	promoter-TSS (NM_153144)	promoter-TSS (NM_153144)	34	NM_153144	217039	Mm.356653	NM_153144	ENSMUSG00000020530	Ggnbp2	AI451896|C75939|D330017P12Rik|DIF-3|Zfp403	gametogenetin binding protein 2	protein-coding
mm_100609.1	chr11	121421389	121421469	+	1	NA	promoter-TSS (NM_181420)	promoter-TSS (NM_181420)	56	NM_181420	238024	Mm.117394	NM_181420	ENSMUSG00000039253	Fn3krp	FN3K-RP	fructosamine 3 kinase related protein	protein-coding
mm_84538.1	chr9	67266901	67266910	-	1	NA	exon (NM_001081242, exon 45 of 58)	exon (NM_001081242, exon 45 of 58)	-30179	NR_029576	387185		NR_029576	ENSMUSG00000076379	Mir190a	Mir190|Mirn190|mir-190|mir-190a|mmu-mir-190|mmu-mir-190a	microRNA 190a	ncRNA
mm_74870.1	chr8	25016744	25016877	-	1	NA	promoter-TSS (NM_027194)	promoter-TSS (NM_027194)	112	NM_001270996	11502	Mm.28908	NM_007404	ENSMUSG00000031555	Adam9	AU020942|MDC9|Mltng|mKIAA0021	a disintegrin and metallopeptidase domain 9 (meltrin gamma)	protein-coding
mm_54454.1	chr6	34746399	34746444	-	1	NA	intron (NM_001347100, intron 5 of 13)	GA-rich|Low_complexity|Low_complexity	-34011	NM_001289657	76223	Mm.150047	NM_178630	ENSMUSG00000038836	Agbl3	2900053G10Rik|4930431N21Rik|6530406M24Rik|CCP3	ATP/GTP binding protein-like 3	protein-coding
mm_30014.1	chr3	135665155	135665166	-	1	NA	intron (NM_008689, intron 3 of 24)	(TG)n|Simple_repeat|Simple_repeat	26387	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_142386.1	chr17	44814509	44814515	-	1	NA	non-coding (NR_073392, exon 1 of 8)	non-coding (NR_073392, exon 1 of 8)	115	NM_009820	12393	Mm.391013	NM_009820	ENSMUSG00000039153	Runx2	AML3|Cbf|Cbfa-1|Cbfa1|LS3|Osf2|PEBP2aA|Pebp2a1|Pebpa2a	runt related transcription factor 2	protein-coding
mm_162006.1	chr19	40831525	40831525	+	1	NA	intron (NM_172839, intron 1 of 5)	CpG	246	NM_172839	240665	Mm.309	NM_172839	ENSMUSG00000025010	Ccnj	D430039C20Rik	cyclin J	protein-coding
mm_45872.1	chr5	88008281	88008283	-	1	NA	exon (NM_011422, exon 3 of 3)	exon (NM_011422, exon 3 of 3)	5757	NM_011422	20599	Mm.261199	NM_011422	ENSMUSG00000029280	Smr3a	AA589601|MSG1|MSG3|Smr1|Smr3	submaxillary gland androgen regulated protein 3A	protein-coding
mm_18868.1	chr2	75782005	75782021	-	1	NA	Intergenic	Intergenic	-50164	NM_172666	228061	Mm.31227	NM_172666	ENSMUSG00000042410	Agps	5832437L22|9930035G10Rik|AW123847|Adaps|Adas|Adhaps|Adps|Aldhpsy|bs2	alkylglycerone phosphate synthase	protein-coding
mm_76244.1	chr8	83588546	83588550	-	1	NA	intron (NM_134118, intron 1 of 12)	intron (NM_134118, intron 1 of 12)	5943	NM_027179	106529	Mm.352239	NM_027179	ENSMUSG00000031708	Tecr	2410016D23Rik|A230102P12Rik|AI173355|D17Ertd178e|Gpsn2|SC2	trans-2,3-enoyl-CoA reductase	protein-coding
mm_61057.1	chr7	49910353	49910358	+	1	NA	promoter-TSS (NM_001146013)	promoter-TSS (NM_001146013)	56	NM_001146013	104245	Mm.207053	NM_148931	ENSMUSG00000039728	Slc6a5	Glyt2|prestin	solute carrier family 6 (neurotransmitter transporter, glycine), member 5	protein-coding
mm_73429.1	chr8	106135542	106135570	+	1	NA	non-coding (NR_040346, exon 1 of 4)	non-coding (NR_040346, exon 1 of 4)	156	NR_040346	69771	Mm.393274	NR_040344		1810019D21Rik	-	RIKEN cDNA 1810019D21 gene	ncRNA
mm_114588.1	chr13	75751809	75751822	+	1	NA	intron (NM_138953, intron 4 of 11)	intron (NM_138953, intron 4 of 11)	44331	NM_138953	192657	Mm.21288	NM_138953	ENSMUSG00000001542	Ell2	-	elongation factor RNA polymerase II 2	protein-coding
mm_53682.1	chr6	142345649	142345693	+	1	NA	promoter-TSS (NM_183165)	promoter-TSS (NM_183165)	-26	NM_183165	232491	Mm.490474	NM_183165	ENSMUSG00000041671	Pyroxd1	-	pyridine nucleotide-disulphide oxidoreductase domain 1	protein-coding
mm_77565.1	chr8	123428966	123428972	-	1	NA	Intergenic	MuLV-int|LTR|ERV1	-13987	NM_001253784	23854	Mm.275127	NM_054046	ENSMUSG00000001482	Def8	AI449518|D8Ertd713e|DEF-8	differentially expressed in FDCP 8	protein-coding
mm_99788.1	chr11	107428232	107428241	+	1	NA	intron (NM_145823, intron 1 of 9)	intron (NM_145823, intron 1 of 9)	42484	NM_145823	71795	Mm.397413	NM_145823	ENSMUSG00000040430	Pitpnc1	1110020B03Rik|5830436L09Rik|AI662802|AI851387|C330017I21Rik|Dnr411|RDGBB|RDGBB1|rdgB-beta	phosphatidylinositol transfer protein, cytoplasmic 1	protein-coding
mm_135429.1	chr16	45382757	45382767	-	1	NA	3' UTR (NM_010818, exon 6 of 6)	3' UTR (NM_010818, exon 6 of 6)	26291	NM_010818	17470	Mm.245851	NM_010818	ENSMUSG00000022661	Cd200	Mox2|OX2	CD200 antigen	protein-coding
mm_79160.1	chr9	47813790	47813813	+	1	NA	exon (NM_018770, exon 7 of 10)	exon (NM_018770, exon 7 of 10)	4407	NR_046048	100038460	Mm.447649	NR_046048		Gm10677	ENSMUSG00000074363	predicted gene 10677	ncRNA
mm_68202.1	chr7	104380720	104380733	-	1	NA	Intergenic	Intergenic	-22080	NM_175648	244183	Mm.347647	NM_175648	ENSMUSG00000052749	Trim30b	A530023O14Rik|Trim30-1	tripartite motif-containing 30B	protein-coding
mm_169482.1	chr14	73525217	73525236	-	1	NA	5' UTR (NM_172527, exon 3 of 5)	5' UTR (NM_172527, exon 3 of 5)	15177	NM_026119	67381	Mm.282888	NM_026119	ENSMUSG00000022109	Med4	2410046H15Rik|DRIP36|HSPC126|TRAP36|Vdirp|Vdrip	mediator complex subunit 4	protein-coding
mm_149732.1	chr19	21858076	21858081	+	1	NA	3' UTR (NM_031997, exon 25 of 25)	3' UTR (NM_031997, exon 25 of 25)	79738	NM_031997	83921	Mm.329776	NM_031997	ENSMUSG00000024754	Tmem2	-	transmembrane protein 2	protein-coding
mm_78712.1	chr9	41446690	41446717	+	1	NA	intron (NR_131928, intron 3 of 4)	intron (NR_131928, intron 3 of 4)	-28190	NR_131931	73144	Mm.38166	NM_001033153	ENSMUSG00000074415	3110039I08Rik	2610203C20Rik|AI848448|D230004N17Rik|D3Mgi9|Mir100hg	RIKEN cDNA 3110039I08 gene	ncRNA
mm_121250.1	chr14	103057502	103057506	+	1	NA	TTS (NM_008392)	TTS (NM_008392)	10492	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_71559.1	chr8	49485446	49485487	+	1	NA	Intergenic	Intergenic	-810776	NM_011857	23965	Mm.42191	NM_011857	ENSMUSG00000031561	Tenm3	2610100B16Rik|Odz1|Odz3|Ten-m3|mKIAA1455	teneurin transmembrane protein 3	protein-coding
mm_22166.1	chr2	173033530	173033571	-	1	NA	exon (NM_019547, exon 4 of 4)	exon (NM_019547, exon 4 of 4)	11648	NM_019547	56190	Mm.485782	NM_019547	ENSMUSG00000027510	Rbm38	Rnpc1|Seb4|Seb4l	RNA binding motif protein 38	protein-coding
mm_156129.1	chrX	120160638	120160638	+	1	NA	Intergenic	Intergenic	-129689	NM_001271809	245578	Mm.39691	NM_001081385	ENSMUSG00000034755	Pcdh11x	PCDHX|PCDHX11|Pcdh11	protocadherin 11 X-linked	protein-coding
mm_62784.1	chr7	112452937	112452959	+	1	NA	intron (NM_020606, intron 1 of 12)	intron (NM_020606, intron 1 of 12)	25242	NM_020606	57342	Mm.143763	NM_020606	ENSMUSG00000030770	Parva	2010012A22Rik|5430400F08Rik|AI225929|AU042898|Actp|CH-ILKBP|Parvin	parvin, alpha	protein-coding
mm_141266.1	chr17	27623821	27623831	-	1	NA	promoter-TSS (NM_001291046)	promoter-TSS (NM_001291046)	-374	NM_019837	56409	Mm.144699	NM_019837	ENSMUSG00000024213	Nudt3	1110011B09Rik|AA960325|Dipp|Dipp1	nudix (nucleotide diphosphate linked moiety X)-type motif 3	protein-coding
mm_163236.1	chr11	104160607	104160608	+	1	NA	intron (NM_001313929, intron 3 of 13)	intron (NM_001313929, intron 3 of 13)	-25720	NM_001082535	237958	Mm.117063	NM_199019	ENSMUSG00000049506	Sppl2c	4933407P14Rik|IMP5	signal peptide peptidase 2C	protein-coding
mm_165947.1	chr4	82882648	82882650	-	1	NA	exon (NM_009887, exon 2 of 2)	exon (NM_009887, exon 2 of 2)	2502	NM_009887	12622	Mm.6780	NM_009887	ENSMUSG00000038192	Cer1	Cerl|Cerl1|Cerr1|cer-1	cerberus 1, DAN family BMP antagonist	protein-coding
mm_157324.1	chrX	23285446	23285454	-	1	NA	5' UTR (NM_001290476, exon 1 of 7)	5' UTR (NM_001290476, exon 1 of 7)	109	NM_001290476	67455	Mm.224306	NM_026167	ENSMUSG00000036782	Klhl13	1200009K10Rik|AI451128|Bklhd2|D130072F20Rik	kelch-like 13	protein-coding
mm_154866.1	chrX	20672988	20672999	+	1	NA	intron (NM_001276316, intron 15 of 26)	intron (NM_001276316, intron 15 of 26)	10097	NM_001136085	22201	Mm.1104	NM_009457	ENSMUSG00000001924	Uba1	A1S9|Sbx|Ube-1|Ube1x	ubiquitin-like modifier activating enzyme 1	protein-coding
mm_126355.1	chr15	79933955	79934002	+	1	NA	Intergenic	Intergenic	-1332	NM_144811	52609	Mm.323442	NM_144811	ENSMUSG00000053411	Cbx7	1600014J01Rik|AI851678|D15Ertd417e	chromobox 7	protein-coding
mm_95032.1	chr11	32057763	32057784	+	1	NA	3' UTR (NM_008741, exon 5 of 5)	3' UTR (NM_008741, exon 5 of 5)	43455	NR_130637	104692	Mm.414035	NR_130637	ENSMUSG00000086386	Gm12108	BB052462|OTTMUSG00000005365	predicted gene 12108	ncRNA
mm_90242.1	chr10	121474236	121474247	+	1	NA	intron (NM_138956, intron 1 of 4)	intron (NM_138956, intron 1 of 4)	2009	NM_138956	192678	Mm.41265	NM_138956	ENSMUSG00000025795	Rassf3	AW212023|AW322379	Ras association (RalGDS/AF-6) domain family member 3	protein-coding
mm_5169.1	chr1	10214246	10214258	-	1	NA	exon (NM_001102430, exon 4 of 38)	exon (NM_001102430, exon 4 of 38)	18418	NM_001102430	211673	Mm.229141	NM_001102430	ENSMUSG00000067851	Arfgef1	ARFGEP1|BIG1|D130059B05Rik|D730028O18Rik|P200	ADP-ribosylation factor guanine nucleotide-exchange factor 1(brefeldin A-inhibited)	protein-coding
mm_163200.1	chr11	96299254	96299265	+	1	NA	promoter-TSS (NM_008269)	promoter-TSS (NM_008269)	88	NM_008269	15414	Mm.215	NM_008269	ENSMUSG00000000690	Hoxb6	Hox-2.2	homeobox B6	protein-coding
mm_92739.1	chr10	80939704	80939708	-	1	NA	Intergenic	Intergenic	9615	NM_008655	17873	Mm.1360	NM_008655	ENSMUSG00000015312	Gadd45b	AI323528|Myd118	growth arrest and DNA-damage-inducible 45 beta	protein-coding
mm_137229.1	chr17	24352018	24352028	+	1	NA	promoter-TSS (NM_001039581)	promoter-TSS (NM_001039581)	0	NM_013855	27410	Mm.239470	NM_013855	ENSMUSG00000024130	Abca3	1810036E22Rik|ABC-C|Abc3	ATP-binding cassette, sub-family A (ABC1), member 3	protein-coding
mm_100652.1	chr11	3151427	3151459	-	1	NA	intron (NM_030207, intron 14 of 32)	B1F|SINE|Alu	27422	NR_003517	236604	Mm.247625	NM_001004146		Pisd-ps1	-	phosphatidylserine decarboxylase, pseudogene 1	pseudo
mm_104710.1	chr11	98043055	98043059	-	1	NA	intron (NM_146028, intron 2 of 10)	B1_Mus2|SINE|Alu	10405	NM_146028	217154	Mm.181008	NM_146028	ENSMUSG00000017400	Stac2	24b2|24b2/STAC2|AW240854	SH3 and cysteine rich domain 2	protein-coding
mm_8393.1	chr1	151428325	151428401	-	1	NA	promoter-TSS (NM_025819)	promoter-TSS (NM_025819)	72	NM_025819	66875	Mm.290905	NM_025819	ENSMUSG00000052748	Swt1	1200016B10Rik|C1orf26	SWT1 RNA endoribonuclease homolog (S. cerevisiae)	protein-coding
mm_163809.1	chr14	19416145	19416179	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	186425	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_112132.1	chr12	112959509	112959528	-	1	NA	TTS (NM_028193)	TTS (NM_028193)	-16964	NM_001145900	399566	Mm.440140	NM_201646	ENSMUSG00000002803	Btbd6	-	BTB (POZ) domain containing 6	protein-coding
mm_150165.1	chr19	32485726	32485735	+	1	NA	promoter-TSS (NM_010799)	promoter-TSS (NM_010799)	-39	NM_010799	17330	Mm.255116	NM_010799	ENSMUSG00000024896	Minpp1	AA408516	multiple inositol polyphosphate histidine phosphatase 1	protein-coding
mm_89288.1	chr10	87892466	87892487	+	1	NA	intron (NM_001314010, intron 3 of 4)	B4A|SINE|B4	31365	NM_001111276	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_122116.1	chr14	31001533	31001587	-	1	NA	5' UTR (NM_029626, exon 1 of 10)	5' UTR (NM_029626, exon 1 of 10)	106	NM_026911	69019	Mm.28852	NM_026911	ENSMUSG00000021917	Spcs1	1810004F21Rik	signal peptidase complex subunit 1 homolog (S. cerevisiae)	protein-coding
mm_27221.1	chr3	36000663	36000682	-	1	NA	promoter-TSS (NM_023644)	promoter-TSS (NM_023644)	6	NM_023644	72039	Mm.249016	NM_023644	ENSMUSG00000027709	Mccc1	1810045E08Rik|2310058B18Rik|MCCalpha|Mcca|R75106	methylcrotonoyl-Coenzyme A carboxylase 1 (alpha)	protein-coding
mm_120532.1	chr14	67189251	67189254	+	1	NA	Intergenic	MER20B|DNA|hAT-Charlie	-44040	NM_010095	13592	Mm.319947	NM_010095	ENSMUSG00000022053	Ebf2	D14Ggc1e|EBF-2|Mmot1|O/E-3|OE-3	early B cell factor 2	protein-coding
mm_54100.1	chr6	16852356	16852367	-	1	NA	intron (NM_031198, intron 2 of 6)	L1M3|LINE|L1	46080	NM_031198	21426	Mm.36217	NM_031198	ENSMUSG00000029553	Tfec	BB107417|Tcfec|bHLHe34	transcription factor EC	protein-coding
mm_44825.1	chr5	33782710	33782749	-	1	NA	promoter-TSS (NM_019694)	promoter-TSS (NM_019694)	-25	NM_019694	56384	Mm.260538	NM_019694	ENSMUSG00000005299	Letm1	-	leucine zipper-EF-hand containing transmembrane protein 1	protein-coding
mm_114940.1	chr13	96388388	96388401	+	1	NA	promoter-TSS (NM_026173)	promoter-TSS (NM_026173)	100	NM_026173	67463	Mm.86472	NM_026173	ENSMUSG00000021671	Poc5	1200014M14Rik|AV144706	POC5 centriolar protein	protein-coding
mm_44733.1	chr5	31108226	31108237	-	1	NA	promoter-TSS (NM_177677)	promoter-TSS (NM_177677)	13	NM_001347323	22784	Mm.1396	NM_011773	ENSMUSG00000029151	Slc30a3	Znt3	solute carrier family 30 (zinc transporter), member 3	protein-coding
mm_112092.1	chr12	112721693	112721710	-	1	NA	promoter-TSS (NM_001024602)	promoter-TSS (NM_001024602)	-473	NM_001024602	217882	Mm.23689	NM_001024602	ENSMUSG00000072825	Cep170b	AI466840|AW555464|Kiaa0284|mKIAA0284	centrosomal protein 170B	protein-coding
mm_16559.1	chr2	181864443	181864464	+	1	NA	promoter-TSS (NM_025901)	promoter-TSS (NM_025901)	93	NM_025901	67005	Mm.271986	NM_025901	ENSMUSG00000038628	Polr3k	12.3kDa|1500004O14Rik|AI196849|AU014893|C11|RPC10|RPC11	polymerase (RNA) III (DNA directed) polypeptide K	protein-coding
mm_61818.1	chr7	87584118	87584130	+	1	NA	promoter-TSS (NM_001081414)	promoter-TSS (NM_001081414)	-44	NM_001081414	108071	Mm.235018	NM_001033224	ENSMUSG00000049583	Grm5	6430542K11Rik|AI850523|Glu5R|Gprc1e|mGluR5|mGluR5b	glutamate receptor, metabotropic 5	protein-coding
mm_120826.1	chr14	75151485	75151495	+	1	NA	intron (NM_008879, intron 1 of 16)	intron (NM_008879, intron 1 of 16)	15065	NM_008879	18826	Mm.153911	NM_008879	ENSMUSG00000021998	Lcp1	AW536232|D14Ertd310e|LCP-1|Pls2|pp65	lymphocyte cytosolic protein 1	protein-coding
mm_126764.1	chr15	85859962	85860013	+	1	NA	promoter-TSS (NM_013882)	promoter-TSS (NM_013882)	41	NM_013882	29870	Mm.20858	NM_013882	ENSMUSG00000022385	Gtse1	B99|Gtse-1	G two S phase expressed protein 1	protein-coding
mm_76786.1	chr8	101783851	101783884	-	1	NA	Intergenic	RMER17B|LTR|ERVK	1001244	NM_009866	12552	Mm.1571	NM_009866	ENSMUSG00000031673	Cdh11	Cad11|OSF-4	cadherin 11	protein-coding
mm_118127.1	chr13	104431404	104431404	-	1	NA	intron (NR_136938, intron 18 of 26)	intron (NR_136938, intron 18 of 26)	143569	NM_001081020	108154	Mm.208125	NM_175496	ENSMUSG00000046169	Adamts6	A930019D11Rik|ADAM-TS6|b2b1879.1Clo|b2b2029Clo|b2b2182Clo|b2b2187.1Clo|b2b2228Clo	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 6	protein-coding
mm_102992.1	chr11	69686748	69686797	-	1	NA	3' UTR (NM_011614, exon 7 of 7)	3' UTR (NM_011614, exon 7 of 7)	-1218	NM_023517	69583	Mm.8983	NM_023517	ENSMUSG00000089669	Tnfsf13	2310026N09Rik|April|Tall2|Tnlg7b|Trdl1	tumor necrosis factor (ligand) superfamily, member 13	protein-coding
mm_97791.1	chr11	82870411	82870433	+	1	NA	intron (NM_001164569, intron 1 of 7)	intron (NM_001164569, intron 1 of 7)	322	NM_001164570	67338	Mm.341608	NM_026097	ENSMUSG00000020696	Rffl	1700051E09Rik|4930516L10Rik|BG080975|Carp2	ring finger and FYVE like domain containing protein	protein-coding
mm_86466.1	chr10	4432587	4432661	+	1	NA	promoter-TSS (NM_024261)	promoter-TSS (NM_024261)	19	NM_024261	73419	Mm.346733	NM_024261	ENSMUSG00000061759	Armt1	1700052N19Rik|AW320013|AW536799	acidic residue methyltransferase 1	protein-coding
mm_65081.1	chr7	19169660	19169682	-	1	NA	Intergenic	Intergenic	-3544	NM_001080815	381853	Mm.333633	NM_001080815	ENSMUSG00000030406	Gipr	GIP-R|Gm1081|Gm160	gastric inhibitory polypeptide receptor	protein-coding
mm_115852.1	chr13	21288770	21288789	-	1	NA	exon (NM_010343, exon 4 of 5)	exon (NM_010343, exon 4 of 5)	3907	NM_010343	14780	Mm.1332	NM_010343	ENSMUSG00000004344	Gpx5	AV379049|Arep	glutathione peroxidase 5	protein-coding
mm_122896.1	chr14	54950101	54950151	-	1	NA	promoter-TSS (NR_029724)	promoter-TSS (NR_029724)	-984	NR_029724	387204		NR_029724	ENSMUSG00000065432	Mir208a	Mirn208|Mirn208a|mir-208|mir-208a|mmu-mir-208	microRNA 208a	ncRNA
mm_134248.1	chr16	13541232	13541267	-	1	NA	intron (NM_028761, intron 22 of 23)	intron (NM_028761, intron 22 of 23)	-20830	NR_037997	70100	Mm.158330	NR_037997	ENSMUSG00000099411	2310015D24Rik	-	RIKEN cDNA 2310015D24 gene	ncRNA
mm_80861.1	chr9	98490523	98490536	+	1	NA	promoter-TSS (NM_009034)	promoter-TSS (NM_009034)	-8	NM_009034	19660	Mm.12825	NM_009034	ENSMUSG00000032454	Rbp2	Crbp-2|CrbpII|Rbp-2	retinol binding protein 2, cellular	protein-coding
mm_145696.1	chr18	62324237	62324248	+	1	NA	promoter-TSS (NM_008313)	promoter-TSS (NM_008313)	38	NM_008313	15562	Mm.20440	NM_008313	ENSMUSG00000026322	Htr4	5-HT-4|5-HT4|5-HT<4L>|5HTR4	5 hydroxytryptamine (serotonin) receptor 4	protein-coding
mm_471.1	chr1	36384492	36384494	+	1	NA	intron (NM_001277076, intron 10 of 52)	ID_B1|SINE|B4	12202	NM_001277076	100534273	Mm.389112	NM_001277076	ENSMUSG00000037432	Fer1l5	4930533C12Rik	fer-1-like 5 (C. elegans)	protein-coding
mm_41106.1	chr5	87775767	87775782	+	1	NA	intron (NM_007785, intron 1 of 13)	intron (NM_007785, intron 1 of 13)	1324	NM_007785	12993	Mm.4908	NM_007785	ENSMUSG00000061937	Csn1s2a	Csng|PP22	casein alpha s2-like A	protein-coding
mm_155933.1	chrX	103493616	103493625	+	1	NA	promoter-TSS (NR_015508)	promoter-TSS (NR_015508)	62	NR_015508	70252	Mm.380486	NR_015508	ENSMUSG00000097571	Jpx	2010000I03Rik|2510040I06Rik|Enox	Jpx transcript, Xist activator (non-protein coding)	ncRNA
mm_40677.1	chr5	65537256	65537266	+	1	NA	promoter-TSS (NM_016786)	promoter-TSS (NM_016786)	16	NM_001310619	53323	Mm.319512	NM_016786	ENSMUSG00000029203	Ube2k	AW492011|D5Ertd601e|E2-25k|HIP-2|Hip2|Hypg|Lig	ubiquitin-conjugating enzyme E2K	protein-coding
mm_34927.1	chr4	155831310	155831341	+	1	NA	promoter-TSS (NM_025338)	promoter-TSS (NM_025338)	56	NM_025338	66077	Mm.28999	NM_025338	ENSMUSG00000065990	Aurkaip1	0610033H09Rik|Aip|Akip|MRP-S38	aurora kinase A interacting protein 1	protein-coding
mm_129439.1	chr15	78529560	78529570	-	1	NA	promoter-TSS (NM_001204153)	promoter-TSS (NM_001204153)	86	NM_001204153	72709	Mm.34776	NM_028331	ENSMUSG00000022440	C1qtnf6	2810036M19Rik|CTRP6	C1q and tumor necrosis factor related protein 6	protein-coding
mm_93380.1	chr10	105574169	105574243	-	1	NA	promoter-TSS (NR_038032)	promoter-TSS (NR_038032)	273	NM_177368	278279	Mm.25225	NM_177368	ENSMUSG00000036019	Tmtc2	8430438D04Rik|D330034A10Rik	transmembrane and tetratricopeptide repeat containing 2	protein-coding
mm_148842.1	chr19	6372583	6372598	+	1	NA	non-coding (NR_122118, exon 7 of 12)	non-coding (NR_122118, exon 7 of 12)	8900	NR_122118	22668	Mm.256422	NM_011750	ENSMUSG00000024949	Sf1	BBP|MZFM|WBP4|Zfp162	splicing factor 1	protein-coding
mm_122192.1	chr14	31742828	31742838	-	1	NA	intron (NM_001024604, intron 8 of 27)	L1ME2z|LINE|L1	87582	NM_001024604	105522	Mm.37660	NM_001024604	ENSMUSG00000014496	Ankrd28	AI465466|AI604979|E430019N21Rik|mKIAA0379	ankyrin repeat domain 28	protein-coding
mm_36447.1	chr4	82492818	82492851	-	1	NA	intron (NM_001113210, intron 2 of 11)	intron (NM_001113210, intron 2 of 11)	12945	NM_001286127	18028	Mm.317947	NM_008687	ENSMUSG00000008575	Nfib	6720429L07Rik|CTF|E030026I10Rik|NF-I/B|NF1-B|NFI-B	nuclear factor I/B	protein-coding
mm_97682.1	chr11	79999242	79999245	+	1	NA	intron (NM_199196, intron 4 of 15)	AT_rich|Low_complexity|Low_complexity	6137	NM_199196	52615	Mm.283410	NM_199196	ENSMUSG00000017548	Suz12	2610028O16Rik|AI195385|AU016842|AW536442|D11Ertd530e|mKIAA0160	suppressor of zeste 12 homolog (Drosophila)	protein-coding
mm_43095.1	chr5	124459887	124459901	+	1	NA	exon (NM_001310723, exon 6 of 7)	exon (NM_001310723, exon 6 of 7)	13190	NM_001310727	67956	Mm.137966	NM_030241	ENSMUSG00000049327	Kmt5a	2410195B05Rik|AA617402|AW536475|PR-SET7|PR/SET07|Setd8	lysine methyltransferase 5A	protein-coding
mm_151110.1	chr19	47864346	47864350	+	1	NA	exon (NM_010362, exon 6 of 6)	exon (NM_010362, exon 6 of 6)	-1197	NM_030051	68214	Mm.63791	NM_026619	ENSMUSG00000025069	Gsto2	1700020F09Rik|4930425C18Rik|GSTO 2-2	glutathione S-transferase omega 2	protein-coding
mm_93229.1	chr10	95322980	95322985	-	1	NA	intron (NM_001330175, intron 1 of 2)	intron (NM_001330175, intron 1 of 2)	727	NM_001330138	12905	Mm.473739	NM_009950	ENSMUSG00000045867	Cradd	RAIDD	CASP2 and RIPK1 domain containing adaptor with death domain	protein-coding
mm_171989.1	chr5	95974835	95974835	+	1	NA	Intergenic	Intergenic	17896	NM_018866	55985	Mm.10116	NM_018866	ENSMUSG00000023078	Cxcl13	4631412M08Rik|ANGIE2|Angie|BCA-1|BLC|BLR1L|Scyb13	chemokine (C-X-C motif) ligand 13	protein-coding
mm_81233.1	chr9	107888137	107888211	+	1	NA	promoter-TSS (NM_028369)	promoter-TSS (NM_028369)	45	NM_028369	72825	Mm.38037	NM_028369	ENSMUSG00000032583	Mon1a	2810468K17Rik	MON1 homolog A, secretory traffciking associated	protein-coding
mm_94945.1	chr11	29718786	29718791	+	1	NA	5' UTR (NM_024226, exon 1 of 7)	5' UTR (NM_024226, exon 1 of 7)	225	NM_024226	68585	Mm.192580	NM_024226	ENSMUSG00000020458	Rtn4	1110020G17Rik|AA407876|AA409940|AA960376|ASY|C130026I10Rik|NOGO|NSP-CL|NgA|Nogo-A|Nogo-B|Nogo-C|mKIAA0886|mKIAA4153	reticulon 4	protein-coding
mm_12528.1	chr2	72180223	72180228	+	1	NA	intron (NM_001204165, intron 10 of 30)	intron (NM_001204165, intron 10 of 30)	-105412	NM_023057	65964	Mm.304143	NM_023057	ENSMUSG00000004085	Map3k20	AV006891|B230120H23Rik|MLTK|MLTKalpha|MLTKbeta|Zak	mitogen-activated protein kinase kinase kinase 20	protein-coding
mm_141702.1	chr17	33998976	33998996	-	1	NA	intron (NM_001347346, intron 3 of 7)	intron (NM_001347346, intron 3 of 7)	1347	NM_001001892	14972	Mm.422886	NM_001001892	ENSMUSG00000061232	H2-K1	H-2K|H-2K(d)|H2-K|K-f	histocompatibility 2, K1, K region	protein-coding
mm_3338.1	chr1	137966530	137966532	+	1	NA	promoter-TSS (NR_029820)	promoter-TSS (NR_029820)	76	NR_029795	735252		NR_029795	ENSMUSG00000065565	Mir181a-1	Mirn181a-1|Mirn213|miR-213|mir-181a-1|mmu-mir-213	microRNA 181a-1	ncRNA
mm_58858.1	chr7	16893803	16893846	+	1	NA	intron (NM_010320, intron 2 of 3)	intron (NM_010320, intron 2 of 3)	2038	NM_010320	14709	Mm.103770	NM_010320	ENSMUSG00000063594	Gng8	G(y)8	guanine nucleotide binding protein (G protein), gamma 8	protein-coding
mm_139426.1	chr17	53492889	53492892	+	1	NA	intron (NM_025887, intron 2 of 5)	intron (NM_025887, intron 2 of 5)	13656	NM_025887	271457	Mm.329123	NM_025887	ENSMUSG00000017831	Rab5a	2410015H04Rik|AI663973|AU021172|nnyRab5a	RAB5A, member RAS oncogene family	protein-coding
mm_125799.1	chr15	74876645	74876647	+	1	NA	Intergenic	Intergenic	5058	NM_025929	67038	Mm.154566	NM_025929	ENSMUSG00000063522	2010109I03Rik	Ly6m	RIKEN cDNA 2010109I03 gene	protein-coding
mm_53560.1	chr6	137102489	137102490	+	1	NA	intron (NM_181988, intron 2 of 4)	intron (NM_181988, intron 2 of 4)	67229	NM_001164214	232441	Mm.46233	NM_181988	ENSMUSG00000030222	Rerg	-	RAS-like, estrogen-regulated, growth-inhibitor	protein-coding
mm_111687.1	chr12	103457189	103457192	-	1	NA	promoter-TSS (NM_145449)	promoter-TSS (NM_145449)	33	NM_145449	217845	Mm.298416	NM_145449	ENSMUSG00000021208	Ifi27l2b	1810023F06Rik|ISG12(b2)	interferon, alpha-inducible protein 27 like 2B	protein-coding
mm_55011.1	chr6	48840539	48840550	-	1	NA	promoter-TSS (NM_025326)	promoter-TSS (NM_025326)	444	NM_023056	65963	Mm.28385	NM_023056	ENSMUSG00000029810	Tmem176b	1810009M01Rik|Clast1|Lr8	transmembrane protein 176B	protein-coding
mm_54795.1	chr6	41680786	41680796	-	1	NA	promoter-TSS (NM_001007572)	promoter-TSS (NM_001007572)	-68	NM_001007572	194352	Mm.135734	NM_001007572	ENSMUSG00000036899	Trpv5	CAT2|D630033B11|ECAC1	transient receptor potential cation channel, subfamily V, member 5	protein-coding
mm_26128.1	chr3	137867959	137867964	+	1	NA	exon (NM_001033155, exon 1 of 8)	exon (NM_001033155, exon 1 of 8)	286	NM_001033155	70604	Mm.256488	NM_001033155	ENSMUSG00000074212	Dnajb14	5730496F10Rik	DnaJ heat shock protein family (Hsp40) member B14	protein-coding
mm_124954.1	chr15	12833604	12833621	+	1	NA	intron (NM_001130149, intron 3 of 34)	(CGTG)n|Simple_repeat|Simple_repeat	8797	NM_001130149	14000	Mm.293142	NM_026799	ENSMUSG00000022191	Drosha	1110013A17Rik|AI874853|Etohi2|Rn3|Rnasen	drosha, ribonuclease type III	protein-coding
mm_38304.1	chr4	136898233	136898257	-	1	NA	intron (NM_007572, intron 1 of 2)	intron (NM_007572, intron 1 of 2)	599	NM_007572	12259	Mm.439957	NM_007572	ENSMUSG00000036887	C1qa	AI255395|C1q	complement component 1, q subcomponent, alpha polypeptide	protein-coding
mm_128836.1	chr15	68341211	68341215	-	1	NA	promoter-TSS (NR_029718)	promoter-TSS (NR_029718)	76	NR_029718	387228		NR_029718	ENSMUSG00000065437	Mir30d	Mirn30d|mir-30d|mmu-mir-30d	microRNA 30d	ncRNA
mm_58371.1	chr6	148945427	148945445	-	1	NA	non-coding (NR_144294, exon 1 of 2)	non-coding (NR_144294, exon 1 of 2)	579	NR_144294	109163	Mm.440359	NM_175404		3010003L21Rik	-	RIKEN cDNA 3010003L21 gene	ncRNA
mm_27492.1	chr3	54807817	54807827	-	1	NA	promoter-TSS (NM_133231)	promoter-TSS (NM_133231)	-31	NM_133231	170767	Mm.185735	NM_133231	ENSMUSG00000036615	Rfxap	5730495K23Rik	regulatory factor X-associated protein	protein-coding
mm_139260.1	chr17	47759242	47759245	+	1	NA	intron (NM_001161723, intron 1 of 8)	intron (NM_001161723, intron 1 of 8)	21312	NM_001161723	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_125519.1	chr15	57694840	57694849	+	1	NA	5' UTR (NM_199449, exon 1 of 4)	5' UTR (NM_199449, exon 1 of 4)	177	NM_199449	387609	Mm.36557	NM_199449	ENSMUSG00000071757	Zhx2	Afr-1|Afr1|Raf|mKIAA0854	zinc fingers and homeoboxes 2	protein-coding
mm_48795.1	chr5	148928620	148928659	-	1	NA	promoter-TSS (NM_153572)	promoter-TSS (NM_153572)	8	NM_153572	231912	Mm.397405	NM_153572	ENSMUSG00000041298	Katnal1	-	katanin p60 subunit A-like 1	protein-coding
mm_98456.1	chr11	94947110	94947145	+	1	NA	exon (NM_007742, exon 36 of 51)	exon (NM_007742, exon 36 of 51)	10903	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_101729.1	chr11	42321046	42321056	-	1	NA	promoter-TSS (NM_008068)	promoter-TSS (NM_008068)	21	NM_008068	14399	Mm.4915	NM_008068	ENSMUSG00000020428	Gabra6	GABA-ARalpha6|Gabra-6|alpha6	gamma-aminobutyric acid (GABA) A receptor, subunit alpha 6	protein-coding
mm_136240.1	chr16	90934677	90934688	-	1	NA	exon (NM_026502, exon 1 of 7)	exon (NM_026502, exon 1 of 7)	167	NM_026502	68001	Mm.45374	NM_026502	ENSMUSG00000022972	1110004E09Rik	-	RIKEN cDNA 1110004E09 gene	protein-coding
mm_79482.1	chr9	56994933	56994986	+	1	NA	promoter-TSS (NM_019651)	promoter-TSS (NM_019651)	-9	NM_019651	56294	Mm.325643	NM_019651	ENSMUSG00000032290	Ptpn9	MEG2	protein tyrosine phosphatase, non-receptor type 9	protein-coding
mm_117993.1	chr13	100452850	100452860	-	1	NA	promoter-TSS (NM_008670)	promoter-TSS (NM_008670)	9	NM_008670	17940	Mm.6898	NM_008670	ENSMUSG00000021640	Naip1	AV364616|Birc1a|D13Lsd1|Naip|Naip-rs1	NLR family, apoptosis inhibitory protein 1	protein-coding
mm_105379.1	chr11	103267394	103267404	-	1	NA	promoter-TSS (NM_016896)	promoter-TSS (NM_016896)	2	NM_016896	53859	Mm.158981	NM_016896	ENSMUSG00000020941	Map3k14	Nik|aly	mitogen-activated protein kinase kinase kinase 14	protein-coding
mm_41382.1	chr5	90739202	90739214	+	1	NA	Intergenic	Intergenic	-20090	NM_009141	20311	Mm.4660	NM_009141	ENSMUSG00000029371	Cxcl5	AMCF-II|Cxcl6|ENA-78|GCP-2|LIX|Scyb5|Scyb6	chemokine (C-X-C motif) ligand 5	protein-coding
mm_45219.1	chr5	53213298	53213349	-	1	NA	5' UTR (NM_172710, exon 1 of 24)	5' UTR (NM_172710, exon 1 of 24)	129	NM_172710	231238	Mm.235020	NM_172710	ENSMUSG00000029189	Sel1l3	2310045A20Rik|AI429585|mKIAA0746	sel-1 suppressor of lin-12-like 3 (C. elegans)	protein-coding
mm_101110.1	chr11	11933459	11933498	-	1	NA	exon (NM_010345, exon 17 of 17)	exon (NM_010345, exon 17 of 17)	-35334	NM_001190448	13195	Mm.12906	NM_016672	ENSMUSG00000020182	Ddc	Aadc	dopa decarboxylase	protein-coding
mm_90874.1	chr10	9027296	9027335	-	1	NA	Intergenic	Intergenic	-141245	NM_175155	70097	Mm.338275	NM_175155	ENSMUSG00000015305	Sash1	1100001C18Rik|2500002E12Rik|A330076K04Rik|mKIAA0790	SAM and SH3 domain containing 1	protein-coding
mm_12420.1	chr2	70562133	70562143	+	1	NA	promoter-TSS (NM_008077)	promoter-TSS (NM_008077)	9	NM_008077	14415	Mm.272120	NM_008077	ENSMUSG00000070880	Gad1	EP10|Gad-1	glutamate decarboxylase 1	protein-coding
mm_103205.1	chr11	70652823	70652868	-	1	NA	exon (NM_011072, exon 2 of 3)	exon (NM_011072, exon 2 of 3)	1805	NM_011072	18643	Mm.2647	NM_011072	ENSMUSG00000018293	Pfn1	Pfn	profilin 1	protein-coding
mm_90826.1	chr10	7955899	7955942	-	1	NA	5' UTR (NM_138667, exon 1 of 7)	5' UTR (NM_138667, exon 1 of 7)	203	NM_138667	68652	Mm.193041	NM_138667	ENSMUSG00000015755	Tab2	1110030N06Rik|A530078N03Rik|Map3k7ip2|mKIAA0733	TGF-beta activated kinase 1/MAP3K7 binding protein 2	protein-coding
mm_21372.1	chr2	157279520	157279555	-	1	NA	promoter-TSS (NM_001039557)	promoter-TSS (NM_001039557)	12	NM_001039557	629499	Mm.384235	NM_001039557	ENSMUSG00000074627	Mroh8	4922505G16Rik	maestro heat-like repeat family member 8	protein-coding
mm_85516.1	chr9	106438170	106438198	-	1	NA	promoter-TSS (NM_001276442)	promoter-TSS (NM_001276442)	52	NM_025371	109652	Mm.7165	NM_025371	ENSMUSG00000023262	Acy1	1110014J22Rik|Acy-1	aminoacylase 1	protein-coding
mm_27977.1	chr3	80802790	80802840	-	1	NA	promoter-TSS (NM_013540)	promoter-TSS (NM_013540)	-24	NM_001039195	14800	Mm.220224	NM_013540	ENSMUSG00000033981	Gria2	GluA2|GluR-B|Glur-2|Glur2	glutamate receptor, ionotropic, AMPA2 (alpha 2)	protein-coding
mm_16790.1	chr2	10064428	10064453	-	1	NA	intron (NM_020615, intron 3 of 9)	intron (NM_020615, intron 3 of 9)	-15831	NM_027748	209361	Mm.86343	NM_027748	ENSMUSG00000025782	Taf3	140kDa|4933439M23Rik|AW539625|TAF140|TAFII-140|TAFII140|mTAFII140	TATA-box binding protein associated factor 3	protein-coding
mm_77914.1	chr9	7350087	7350094	+	1	NA	exon (NM_008605, exon 4 of 10)	exon (NM_008605, exon 4 of 10)	2716	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_16547.1	chr2	181715087	181715102	+	1	NA	promoter-TSS (NM_011012)	promoter-TSS (NM_011012)	78	NM_001318923	18389	Mm.285075	NM_011012	ENSMUSG00000027584	Oprl1	KOR-3|KOR3|LC132|MOR-C|NOP|ORGC|ORL1|Oprl|XOR1|morc	opioid receptor-like 1	protein-coding
mm_158195.1	chrX	104857207	104857220	-	1	NA	promoter-TSS (NM_053206)	promoter-TSS (NM_053206)	54	NM_053206	272790	Mm.165776	NM_053206	ENSMUSG00000031224	Magee2	9630059J11Rik|BB131182|Mage-e2	melanoma antigen, family E, 2	protein-coding
mm_39212.1	chr4	156059430	156059435	-	1	NA	intron (NR_132444, intron 1 of 1)	intron (NR_132444, intron 1 of 1)	370	NR_132444	100415901	Mm.437006	NR_132444	ENSMUSG00000086549	Gm13648	OTTMUSG00000013217	predicted gene 13648	ncRNA
mm_27367.1	chr3	50438043	50438055	-	1	NA	intron (NM_011990, intron 2 of 11)	intron (NM_011990, intron 2 of 11)	5564	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_37975.1	chr4	133598766	133598788	-	1	NA	Intergenic	Intergenic	3391	NM_018754	55948	Mm.44482	NM_018754	ENSMUSG00000047281	Sfn	Er|Mme1|Ywhas	stratifin	protein-coding
mm_160287.1	chr7	126429410	126429410	+	1	NA	intron (NM_030566, intron 1 of 12)	intron (NM_030566, intron 1 of 12)	643	NM_030566	70314	Mm.35467	NM_030566	ENSMUSG00000030727	Rabep2	2610011A08Rik|AI462746|Fra	rabaptin, RAB GTPase binding effector protein 2	protein-coding
mm_75174.1	chr8	36816173	36816175	-	1	NA	intron (NM_001194940, intron 4 of 17)	intron (NM_001194940, intron 4 of 17)	-83120	NM_001194941	50768	Mm.125155	NM_015802	ENSMUSG00000031523	Dlc1	A730069N07Rik|Arhgap7|HP|STARD12|dlc-1	deleted in liver cancer 1	protein-coding
mm_22100.1	chr2	169233231	169233232	-	1	NA	Intergenic	RMER21B|LTR|ERV1	254962	NR_040326	75508	Mm.271256	NR_040326	ENSMUSG00000086348	1700017J07Rik	-	RIKEN cDNA 1700017J07 gene	ncRNA
mm_19047.1	chr2	77170593	77170645	-	1	NA	promoter-TSS (NM_001025576)	promoter-TSS (NM_001025576)	16	NM_001025576	545428	Mm.26579	NM_001025576	ENSMUSG00000044033	Ccdc141	2610301F02Rik|CAMDI|ENSMUSG00000075261	coiled-coil domain containing 141	protein-coding
mm_119583.1	chr14	50925017	50925027	+	1	NA	promoter-TSS (NM_009687)	promoter-TSS (NM_009687)	73	NM_009687	11792	Mm.203	NM_009687	ENSMUSG00000035960	Apex1	APE|Apex|HAP1|Ref-1	apurinic/apyrimidinic endonuclease 1	protein-coding
mm_137024.1	chr17	17871964	17871972	+	1	NA	Intergenic	Intergenic	11971	NM_013521	14293	Mm.56951	NM_013521	ENSMUSG00000045551	Fpr1	FPR|LXA4R|fMLF-R	formyl peptide receptor 1	protein-coding
mm_26723.1	chr3	159839691	159839717	+	1	NA	promoter-TSS (NR_037590)	promoter-TSS (NR_037590)	9	NM_026582	68151	Mm.6766	NM_026582	ENSMUSG00000028173	Wls	5031439A09Rik|AI173978|AI987742|Gpr177	wntless homolog (Drosophila)	protein-coding
mm_109224.1	chr12	108793269	108793275	+	1	NA	promoter-TSS (NM_009537)	promoter-TSS (NM_009537)	-39	NM_009537	22632	Mm.3868	NM_009537	ENSMUSG00000021264	Yy1	AW488674|NF-E1	YY1 transcription factor	protein-coding
mm_81242.1	chr9	107950953	107950991	+	1	NA	promoter-TSS (NM_011634)	promoter-TSS (NM_011634)	9	NM_011634	22036	Mm.297870	NM_011634	ENSMUSG00000032586	Traip	Trip	TRAF-interacting protein	protein-coding
mm_53933.1	chr6	4747067	4747132	-	1	NA	promoter-TSS (NM_130877)	promoter-TSS (NM_130877)	105	NM_001130188	20392	Mm.8739	NM_011360	ENSMUSG00000004631	Sgce	e-SG	sarcoglycan, epsilon	protein-coding
mm_4659.1	chr1	180364000	180364012	+	1	NA	intron (NM_001081175, intron 2 of 7)	intron (NM_001081175, intron 2 of 7)	-33457	NR_003623	277333	Mm.389223	NM_199472		Gm5069	EG277333	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_16198.1	chr2	173006093	173006099	+	1	NA	intron (NM_175112, intron 4 of 11)	intron (NM_175112, intron 4 of 11)	5979	NM_175112	66679	Mm.4113	NM_175112	ENSMUSG00000027509	Rae1	3230401I12Rik|D2Ertd342e|MNRP|MNRP41	ribonucleic acid export 1	protein-coding
mm_126702.1	chr15	85132139	85132143	+	1	NA	promoter-TSS (NM_080470)	promoter-TSS (NM_080470)	42	NM_026357	67747	Mm.158173	NM_026357	ENSMUSG00000022431	Ribc2	4930579A10Rik|Trib	RIB43A domain with coiled-coils 2	protein-coding
mm_55527.1	chr6	70726483	70726509	-	1	NA	Intergenic	Intergenic	65679	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_149217.1	chr19	9991590	9991590	+	1	NA	intron (NM_011913, intron 6 of 11)	intron (NM_011913, intron 6 of 11)	8944	NM_010239	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
mm_92109.1	chr10	63023914	63023918	-	1	NA	promoter-TSS (NM_001079824)	promoter-TSS (NM_001079824)	-67	NM_001079824	432467	Mm.274784	NM_001079824	ENSMUSG00000020069	Hnrnph3	AA693301|AI666703|Hnrph3	heterogeneous nuclear ribonucleoprotein H3	protein-coding
mm_162493.1	chr1	136220385	136220392	-	1	NA	intron (NM_028872, intron 6 of 9)	intron (NM_028872, intron 6 of 9)	-7560	NM_001329610	76422	Mm.159735	NM_001329610		Mroh3	2310006M14Rik	maestro heat-like repeat family member 3	protein-coding
mm_89123.1	chr10	84839068	84839068	+	1	NA	intron (NM_027689, intron 1 of 13)	intron (NM_027689, intron 1 of 13)	920	NM_027689	71137	Mm.79070	NM_027689	ENSMUSG00000020037	Rfx4	4933412G19Rik|NYD-sp10	regulatory factor X, 4 (influences HLA class II expression)	protein-coding
mm_38624.1	chr4	142049006	142049012	-	1	NA	intron (NM_145402, intron 1 of 2)	intron (NM_145402, intron 1 of 2)	31111	NR_131014	78917	Mm.139995	NR_131014	ENSMUSG00000085761	4930455G09Rik	-	RIKEN cDNA 4930455G09 gene	ncRNA
mm_127684.1	chr15	102966753	102966774	+	1	NA	promoter-TSS (NM_010462)	promoter-TSS (NM_010462)	-33	NM_010462	209448	Mm.31665	NM_010462	ENSMUSG00000022484	Hoxc10	AI506621|Hox-3.6	homeobox C10	protein-coding
mm_145332.1	chr18	56387461	56387489	+	1	NA	Intergenic	Intergenic	-44657	NM_026240	107022	Mm.24356	NM_026240	ENSMUSG00000001700	Gramd3	9030613F08Rik|9130427A09Rik|AW061306|NS3TP2	GRAM domain containing 3	protein-coding
mm_22638.1	chr3	14863477	14863483	+	1	NA	promoter-TSS (NM_007606)	promoter-TSS (NM_007606)	-58	NM_007606	12350	Mm.300	NM_007606	ENSMUSG00000027559	Car3	BB219044|Ca3|Car-3	carbonic anhydrase 3	protein-coding
mm_8754.1	chr1	160309087	160309115	-	1	NA	intron (NM_001038621, intron 2 of 8)	intron (NM_001038621, intron 2 of 8)	-13129	NR_035448	100316784		NR_035448	ENSMUSG00000089204	Mir1927	mmu-mir-1927	microRNA 1927	ncRNA
mm_29740.1	chr3	126922895	126922919	-	1	NA	3' UTR (NM_178655, exon 25 of 25)	3' UTR (NM_178655, exon 25 of 25)	20479	NM_001034168	109676	Mm.220242	NM_178655	ENSMUSG00000032826	Ank2	100043364|AI835472|AW491075|Ank-2|Gm4392	ankyrin 2, brain	protein-coding
mm_9938.1	chr1	190169507	190169526	-	1	NA	intron (NM_008937, intron 1 of 4)	CpG	1164	NM_008937	19130	Mm.132579	NM_008937	ENSMUSG00000010175	Prox1	A230003G05Rik	prospero homeobox 1	protein-coding
mm_126241.1	chr15	79002281	79002296	+	1	NA	promoter-TSS (NR_105921)	promoter-TSS (NR_105921)	65	NR_105921	102465577		NR_105921	ENSMUSG00000099180	Mir6956	Gm27880|mmu-mir-6956	microRNA 6956	ncRNA
mm_41104.1	chr5	87774928	87774936	+	1	NA	intron (NM_007785, intron 1 of 13)	MIRb|SINE|MIR	482	NM_007785	12993	Mm.4908	NM_007785	ENSMUSG00000061937	Csn1s2a	Csng|PP22	casein alpha s2-like A	protein-coding
mm_81525.1	chr9	110062609	110062620	+	1	NA	intron (NM_001311163, intron 1 of 10)	intron (NM_001311163, intron 1 of 10)	10593	NM_001311164	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_67635.1	chr7	84372657	84372684	-	1	NA	intron (NM_007488, intron 1 of 18)	intron (NM_007488, intron 1 of 18)	37368	NM_007488	11864	Mm.38594	NM_007488	ENSMUSG00000015709	Arnt2	Hif-2b|bHLHe1|mKIAA0307	aryl hydrocarbon receptor nuclear translocator 2	protein-coding
mm_137390.1	chr17	25817920	25817938	+	1	NA	exon (NM_001164225, exon 3 of 6)	exon (NM_001164225, exon 3 of 6)	-5698	NM_173741	268933	Mm.95512	NM_173741	ENSMUSG00000025737	Wdr24	BC037651	WD repeat domain 24	protein-coding
mm_85570.1	chr9	107280665	107280673	-	1	NA	intron (NM_001316691, intron 1 of 7)	intron (NM_001316691, intron 1 of 7)	8727	NM_001316691	102626	Mm.222612	NM_178907	ENSMUSG00000032577	Mapkapk3	3PK|AI874665|MAPKAP-K3|MAPKAP3|MK-3|MK3|MapkKapk3	mitogen-activated protein kinase-activated protein kinase 3	protein-coding
mm_172058.1	chr6	130639224	130639230	+	1	NA	Intergenic	L1Md_T|LINE|L1	-252353	NM_016659	16627	Mm.24399	NM_016659	ENSMUSG00000079853	Klra1	A1|CH29-493D4.3|Klra22|Ly49a|Ly49o<129>|Ly49v	killer cell lectin-like receptor, subfamily A, member 1	protein-coding
mm_26904.1	chr3	19311334	19311344	-	1	NA	promoter-TSS (NM_001122759)	promoter-TSS (NM_001122759)	-17	NM_001122759	18583	Mm.355614	NM_008802	ENSMUSG00000069094	Pde7a	AU015378|AW047537	phosphodiesterase 7A	protein-coding
mm_82544.1	chr9	20888128	20888155	-	1	NA	promoter-TSS (NM_145610)	promoter-TSS (NM_145610)	-34	NM_145610	235036	Mm.2930	NM_145610	ENSMUSG00000004100	Ppan	A230087P06Rik|SSF1	peter pan homolog (Drosophila)	protein-coding
mm_28489.1	chr3	92484207	92484215	-	1	NA	3' UTR (NM_009264, exon 2 of 2)	3' UTR (NM_009264, exon 2 of 2)	1670	NM_009264	20753	Mm.331191	NM_009264	ENSMUSG00000050359	Sprr1a	AI528815|SPR1a|mSPRR1A	small proline-rich protein 1A	protein-coding
mm_6686.1	chr1	80665208	80665219	-	1	NA	5' UTR (NM_001285927, exon 1 of 56)	5' UTR (NM_001285927, exon 1 of 56)	139	NM_001285927	210293	Mm.133473	NM_175291	ENSMUSG00000038608	Dock10	9330153B10Rik|A630054M16Rik|Jr4|Jr5|R75174|ZIZ3|Zizimin3|mKIAA0694	dedicator of cytokinesis 10	protein-coding
mm_165757.1	chr3	113155621	113155629	-	1	NA	intron (NM_001190403, intron 2 of 9)	intron (NM_001190403, intron 2 of 9)	1102	NM_001190404	545562	Mm.462977	NM_001190403		Amy2b	Amy-X|Amy2-2|OTTMUSG00000022462|mAmy2-1	amylase 2b	protein-coding
mm_12652.1	chr2	74825803	74825858	+	1	NA	promoter-TSS (NM_016804)	promoter-TSS (NM_016804)	18	NM_016804	53375	Mm.292613	NM_016804	ENSMUSG00000027099	Mtx2	1500012G02Rik	metaxin 2	protein-coding
mm_155361.1	chrX	71050066	71050125	+	1	NA	promoter-TSS (NM_001256048)	promoter-TSS (NM_001256048)	-161	NM_001256048	333639	Mm.371730	NM_001081354	ENSMUSG00000059401	Mamld1	G630014P10Rik	mastermind-like domain containing 1	protein-coding
mm_153718.1	chr19	44403583	44403595	-	1	NA	intron (NM_009127, intron 2 of 5)	intron (NM_009127, intron 2 of 5)	4120	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_109124.1	chr12	105734067	105734105	+	1	NA	intron (NM_030187, intron 6 of 17)	intron (NM_030187, intron 6 of 17)	28104	NM_030187	78801	Mm.36006	NM_030187	ENSMUSG00000041323	Ak7	4930502N02Rik|AK 7	adenylate kinase 7	protein-coding
mm_49712.1	chr6	34423029	34423046	+	1	NA	TTS (NM_009731)	TTS (NM_009731)	10675	NM_009731	11997	Mm.482073	NM_009731	ENSMUSG00000052131	Akr1b7	AR|Avdp|MVDP	aldo-keto reductase family 1, member B7	protein-coding
mm_30614.1	chr4	7669956	7669958	+	1	NA	Intergenic	Intergenic	109269	NR_040645	71510	Mm.410775	NR_040645	ENSMUSG00000086070	8430436N08Rik	-	RIKEN cDNA 8430436N08 gene	ncRNA
mm_152735.1	chr19	18936692	18936709	-	1	NA	3' UTR (NM_001289921, exon 11 of 11)	3' UTR (NM_001289921, exon 11 of 11)	64417	NM_146095	225998	Mm.234641	NM_146095	ENSMUSG00000036192	Rorb	Nr1f2|RZR-beta|RZRB|Rorbeta|hstp	RAR-related orphan receptor beta	protein-coding
mm_69111.1	chr7	127024900	127024927	-	1	NA	exon (NM_010772, exon 3 of 5)	exon (NM_010772, exon 3 of 5)	1566	NM_010772	17188	Mm.378964	NM_010772	ENSMUSG00000030678	Maz	MAZI|PUR1|Pur-1|SAF-1|SAF-2	MYC-associated zinc finger protein (purine-binding transcription factor)	protein-coding
mm_106994.1	chr12	11266180	11266188	+	1	NA	promoter-TSS (NM_177331)	promoter-TSS (NM_177331)	298	NM_025695	67241	Mm.173953	NM_025695	ENSMUSG00000020608	Smc6	2810489L22Rik|3830418C19Rik|AA990493|AU018782|AW742439|SMC-6|Smc6l1|mKIAA4103	structural maintenance of chromosomes 6	protein-coding
mm_135335.1	chr16	42249060	42249072	-	1	NA	exon (NM_008083, exon 3 of 3)	exon (NM_008083, exon 3 of 3)	54403	NR_105858	102466172		NR_105858	ENSMUSG00000098300	Mir6540	Gm27780|mir-6540|mmu-mir-6540	microRNA 6540	ncRNA
mm_108550.1	chr12	84409167	84409176	+	1	NA	promoter-TSS (NM_007647)	promoter-TSS (NM_007647)	103	NM_028377	72873	Mm.440428	NM_028377	ENSMUSG00000057265	Bbof1	2900006K08Rik|AI427784|Ccdc176	basal body orientation factor 1	protein-coding
mm_9138.1	chr1	170867746	170867756	-	1	NA	promoter-TSS (NM_001081304)	promoter-TSS (NM_001081304)	20	NM_001081304	226641	Mm.377046	NM_001081304	ENSMUSG00000026663	Atf6	9130025P16Rik|9630036G24|AA789574|Atf6alpha|ESTM49	activating transcription factor 6	protein-coding
mm_108961.1	chr12	102391350	102391351	+	1	NA	TTS (NM_001161365)	TTS (NM_001161365)	48463	NM_011175	19141	Mm.17185	NM_011175	ENSMUSG00000021190	Lgmn	AEP|AI746452|AU022324|Prsc1	legumain	protein-coding
mm_134937.1	chr16	31151920	31151923	-	1	NA	intron (NM_030138, intron 4 of 22)	B1_Mus1|SINE|Alu	49317	NM_030138	78618	Mm.274646	NM_030138	ENSMUSG00000049076	Acap2	4832442G16|9530039J15Rik|CNT-B2|Centb2|mKIAA0041	ArfGAP with coiled-coil, ankyrin repeat and PH domains 2	protein-coding
mm_78721.1	chr9	41579936	41579967	+	1	NA	intron (NR_131930, intron 3 of 3)	intron (NR_131930, intron 3 of 3)	-1302	NR_015483	73144	Mm.38166	NM_001033153	ENSMUSG00000074415	3110039I08Rik	2610203C20Rik|AI848448|D230004N17Rik|D3Mgi9|Mir100hg	RIKEN cDNA 3110039I08 gene	ncRNA
mm_75291.1	chr8	41041918	41041928	-	1	NA	promoter-TSS (NM_001005865)	promoter-TSS (NM_001005865)	8	NM_001005865	102103	Mm.149438	NM_001005863	ENSMUSG00000045636	Mtus1	AI481402|ATBP135|Atip1|B430010I23Rik|B430305I03Rik|C85752|Cctsg1-440|MD44|MTSG1|mKIAA1288	mitochondrial tumor suppressor 1	protein-coding
mm_60786.1	chr7	45566911	45566921	+	1	NA	TTS (NR_038166)	TTS (NR_038166)	-3237	NM_009737	12036	Mm.24210	NM_009737	ENSMUSG00000030826	Bcat2	Bcat-2|Eca40	branched chain aminotransferase 2, mitochondrial	protein-coding
mm_36117.1	chr4	58911914	58911945	-	1	NA	intron (NM_172381, intron 1 of 48)	CpG	796	NM_172381	230249	Mm.234801	NM_172381	ENSMUSG00000050812	AI314180	AW558785|BB181316|mKIAA0368	expressed sequence AI314180	protein-coding
mm_82953.1	chr9	35570020	35570073	-	1	NA	promoter-TSS (NM_029762)	promoter-TSS (NM_029762)	23	NM_029762	76832	Mm.482285	NM_029762	ENSMUSG00000050555	Hyls1	3010015K02Rik	hydrolethalus syndrome 1	protein-coding
mm_34133.1	chr4	139290993	139291026	+	1	NA	exon (NM_001271405, exon 9 of 9)	exon (NM_001271405, exon 9 of 9)	19691	NM_145384	212555	Mm.45131	NM_145384	ENSMUSG00000028744	Pqlc2	BC019216	PQ loop repeat containing 2	protein-coding
mm_12810.1	chr2	80302345	80302355	+	1	NA	Intergenic	Intergenic	9880	NM_177256	320769	Mm.60992	NM_177256	ENSMUSG00000050114	Prdx6b	1-cysPrx-P1|4930414C22Rik|Aop2-rs1|Prdx5-rs1|Prdx6-ps1|Prdx6-rs1|Prdx6-rs1-ps	peroxiredoxin 6B	protein-coding
mm_146844.1	chr18	23805772	23805779	-	1	NA	intron (NM_153058, intron 1 of 6)	intron (NM_153058, intron 1 of 6)	1805	NM_153058	212307	Mm.132237	NM_153058	ENSMUSG00000024277	Mapre2	AI314113|C820009F03Rik|D18Abb1e|EB1|EB2|RP1	microtubule-associated protein, RP/EB family, member 2	protein-coding
mm_29651.1	chr3	122372814	122372853	-	1	NA	Intergenic	Intergenic	-46947	NM_013867	29815	Mm.45815	NM_013867	ENSMUSG00000028121	Bcar3	AI131758|AND-34	breast cancer anti-estrogen resistance 3	protein-coding
mm_169240.1	chr13	73347367	73347367	-	1	NA	promoter-TSS (NR_045293)	promoter-TSS (NR_045293)	17	NR_045293	432777	Mm.415319	NR_045293		D630045M09Rik	AU019512	RIKEN cDNA D630045M09 gene	ncRNA
mm_45664.1	chr5	77205298	77205304	-	1	NA	3' UTR (NM_001289764, exon 4 of 4)	3' UTR (NM_001289764, exon 4 of 4)	5904	NM_001289767	69982	Mm.46106	NM_183284	ENSMUSG00000053030	Spink2	1700007F22Rik|AV038945|HUSI-II	serine peptidase inhibitor, Kazal type 2	protein-coding
mm_99009.1	chr11	98836776	98836831	+	1	NA	promoter-TSS (NM_001080925)	promoter-TSS (NM_001080925)	18	NM_001080925	268480	Mm.340766	NM_001080925	ENSMUSG00000038020	Rapgefl1	B230105J10	Rap guanine nucleotide exchange factor (GEF)-like 1	protein-coding
mm_163719.1	chr13	112733685	112733689	+	1	NA	3' UTR (NM_178746, exon 15 of 15)	3' UTR (NM_178746, exon 15 of 15)	-67090	NM_008903	19012	Mm.291029	NM_008247	ENSMUSG00000021759	Plpp1	Hic53|Hpic53|LPP-1|LPP1|PAP-2a|PAP2-alpha|PAP2a|Ppap2a|mPAP	phospholipid phosphatase 1	protein-coding
mm_71544.1	chr8	47788843	47788848	+	1	NA	Intergenic	B1_Mur4|SINE|Alu	-33298	NM_001111318	100039801	Mm.471595	NM_001111318	ENSMUSG00000061974	Cldn24	ENSMUSG00000061974|Gm10107	claudin 24	protein-coding
mm_64359.1	chr7	142390296	142390329	+	1	NA	Intergenic	L2a|LINE|L2	-2442	NM_009983	13033	Mm.231395	NM_009983	ENSMUSG00000007891	Ctsd	CD|CatD	cathepsin D	protein-coding
mm_161219.1	chr13	67399775	67399775	-	1	NA	promoter-TSS (NM_001080941)	promoter-TSS (NM_001080941)	-8	NM_001080941	72807	Mm.303790	NM_001080941	ENSMUSG00000078994	Zfp429	2810487A22Rik|AI929863|Rsl2	zinc finger protein 429	protein-coding
mm_77228.1	chr8	115703829	115703839	-	1	NA	3' UTR (NM_001025577, exon 1 of 1)	3' UTR (NM_001025577, exon 1 of 1)	3060	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_43125.1	chr5	125158439	125158444	+	1	NA	intron (NM_001253905, intron 1 of 42)	intron (NM_001253905, intron 1 of 42)	20773	NM_001253905	20602	Mm.278646	NM_011424	ENSMUSG00000029478	Ncor2	N-CoR|SMRT|SMRTe	nuclear receptor co-repressor 2	protein-coding
mm_101279.1	chr11	21569098	21569100	-	1	NA	intron (NM_008618, intron 1 of 8)	intron (NM_008618, intron 1 of 8)	2835	NM_008618	17449	Mm.212703	NM_008618	ENSMUSG00000020321	Mdh1	B230377B03Rik|D17921|MDH-s|MDHA|Mor-2|Mor2	malate dehydrogenase 1, NAD (soluble)	protein-coding
mm_40259.1	chr5	38230662	38230678	+	1	NA	exon (NM_025281, exon 6 of 9)	exon (NM_025281, exon 6 of 9)	10188	NM_025281	17089	Mm.28560	NM_025281	ENSMUSG00000067367	Lyar	MLZ-264	Ly1 antibody reactive clone	protein-coding
mm_58936.1	chr7	18065998	18066008	+	1	NA	promoter-TSS (NM_001162524)	promoter-TSS (NM_001162524)	74	NM_001162523	67315	Mm.46089	NM_026087	ENSMUSG00000030366	Ceacam12	1600031J20Rik|Ceacam12-C1|Ceacam12-C3|Ceacam12C1|Ceacam12C3	carcinoembryonic antigen-related cell adhesion molecule 12	protein-coding
mm_43209.1	chr5	129234183	129234186	+	1	NA	Intergenic	RMER21A|LTR|ERV1	137434	NM_001347486	243277	Mm.440501	NM_177734	ENSMUSG00000044017	Adgrd1	E230012M21Rik|Gpr133	adhesion G protein-coupled receptor D1	protein-coding
mm_16289.1	chr2	174111110	174111135	+	1	NA	exon (NM_213733, exon 2 of 12)	exon (NM_213733, exon 2 of 12)	771	NM_213733	228961	Mm.295629	NM_213733	ENSMUSG00000039263	Npepl1	BC023239|C85514|mKIAA1974	aminopeptidase-like 1	protein-coding
mm_18614.1	chr2	68415859	68415864	-	1	NA	intron (NM_016866, intron 1 of 17)	intron (NM_016866, intron 1 of 17)	56120	NM_016866	53416	Mm.198414	NM_016866	ENSMUSG00000027030	Stk39	AW227544|AW556857|DCHT|RF005|Rnl5|SPAK	serine/threonine kinase 39	protein-coding
mm_131076.1	chr16	4726358	4726370	+	1	NA	promoter-TSS (NM_001136066)	promoter-TSS (NM_001136066)	3	NM_001136066	15369	Mm.272866	NM_010443	ENSMUSG00000004070	Hmox2	HO-2|HO2	heme oxygenase 2	protein-coding
mm_105862.1	chr11	113803643	113803692	-	1	NA	intron (NM_172800, intron 38 of 44)	intron (NM_172800, intron 38 of 44)	-51852	NM_001163346	56699	Mm.293378	NM_020006	ENSMUSG00000041598	Cdc42ep4	1500041M20Rik|Borg4|CEP4	CDC42 effector protein (Rho GTPase binding) 4	protein-coding
mm_34893.1	chr4	155624854	155624929	+	1	NA	promoter-TSS (NM_007661)	promoter-TSS (NM_007661)	22	NM_007661	12537	Mm.267410	NM_007661	ENSMUSG00000029062	Cdk11b	AA989746|CDK11-p110|CDK11-p46|CDK11-p58|Cdc11b|Cdc2l1|Cdc2l2|Cdk11|p58	cyclin-dependent kinase 11B	protein-coding
mm_26212.1	chr3	138745878	138745889	+	1	NA	intron (NM_019571, intron 1 of 7)	intron (NM_019571, intron 1 of 7)	3675	NM_019571	56224	Mm.31927	NM_019571	ENSMUSG00000028152	Tspan5	2810455A09Rik|4930505M03Rik|NET-4|Tm4sf9	tetraspanin 5	protein-coding
mm_94382.1	chr11	5498677	5498689	+	1	NA	Intergenic	Intergenic	-21958	NM_013842	22433	Mm.469937	NM_013842	ENSMUSG00000020484	Xbp1	D11Ertd39e|TREB-5|TREB5|XBP-1	X-box binding protein 1	protein-coding
mm_29094.1	chr3	104777484	104777493	-	1	NA	promoter-TSS (NM_183224)	promoter-TSS (NM_183224)	59	NM_183224	329731	Mm.389494	NM_183224	ENSMUSG00000055865	Fam19a3	7530404M11Rik|TAFA3|Tafa-3	family with sequence similarity 19, member A3	protein-coding
mm_17445.1	chr2	28533109	28533119	-	1	NA	promoter-TSS (NM_001145835)	promoter-TSS (NM_001145835)	-350	NM_001145835	19730	Mm.5236	NM_009058	ENSMUSG00000026821	Ralgds	Gnds|Rgds|mKIAA1308	ral guanine nucleotide dissociation stimulator	protein-coding
mm_12973.1	chr2	90768423	90768426	+	1	NA	intron (NM_018828, intron 11 of 16)	intron (NM_018828, intron 11 of 16)	-14320	NM_178755	271813	Mm.61146	NM_178755	ENSMUSG00000040812	Agbl2	4930524K04|A430081C19Rik|CCP2	ATP/GTP binding protein-like 2	protein-coding
mm_39560.1	chr5	22991076	22991076	+	1	NA	intron (NM_001081231, intron 1 of 3)	intron (NM_001081231, intron 1 of 3)	-244192	NR_027362	330052	Mm.459265	NR_027362	ENSMUSG00000105076	A930003O13Rik	-	RIKEN cDNA A930003O13 gene	ncRNA
mm_13887.1	chr2	120027583	120027587	+	1	NA	TTS (NM_011941)	TTS (NM_011941)	102	NM_001114637	433466	Mm.482417	NM_001114637	ENSMUSG00000098789	Jmjd7	-	jumonji domain containing 7	protein-coding
mm_121790.1	chr14	19977252	19977253	-	1	NA	promoter-TSS (NM_001285911)	promoter-TSS (NM_001285911)	-3	NM_001285909	14702	Mm.41737	NM_010315	ENSMUSG00000043004	Gng2	-	guanine nucleotide binding protein (G protein), gamma 2	protein-coding
mm_84601.1	chr9	70040681	70040715	-	1	NA	Intergenic	Intergenic	-2610	NM_028087	72077	Mm.195555	NM_028087	ENSMUSG00000032226	Gcnt3	2010013H22Rik|2210021I22Rik|2210401J11Rik	glucosaminyl (N-acetyl) transferase 3, mucin type	protein-coding
mm_10301.1	chr2	10594862	10594869	+	1	NA	3' UTR (NM_177386, exon 23 of 23)	3' UTR (NM_177386, exon 23 of 23)	77261	NR_035417	100316668		NR_035417	ENSMUSG00000080657	Mir669i	Mirn669i|mir-669i|mmu-mir-669i	microRNA 669i	ncRNA
mm_52520.1	chr6	115441524	115441534	+	1	NA	exon (NM_001127330, exon 4 of 8)	exon (NM_001127330, exon 4 of 8)	19463	NM_011146	19016	Mm.3020	NM_011146	ENSMUSG00000000440	Pparg	Nr1c3|PPAR-gamma|PPAR-gamma2|PPARgamma|PPARgamma2	peroxisome proliferator activated receptor gamma	protein-coding
mm_12894.1	chr2	84798798	84798805	+	1	NA	promoter-TSS (NM_019949)	promoter-TSS (NM_019949)	-27	NM_019949	56791	Mm.38261	NM_019949	ENSMUSG00000027078	Ube2l6	2810489I21Rik|RIG-B|UBCH8|Ubce8|Ubcm8	ubiquitin-conjugating enzyme E2L 6	protein-coding
mm_50769.1	chr6	53620531	53620566	+	1	NA	intron (NM_001327821, intron 7 of 10)	intron (NM_001327821, intron 7 of 10)	47174	NM_172728	231991	Mm.227444	NM_172728	ENSMUSG00000053007	Creb5	9430076C15Rik|CRE-BPa|Crebpa|D430026C09Rik	cAMP responsive element binding protein 5	protein-coding
mm_59256.1	chr7	24870048	24870061	+	1	NA	promoter-TSS (NM_027732)	promoter-TSS (NM_027732)	-3	NM_027732	71241	Mm.66855	NM_027732	ENSMUSG00000011349	Dmrtc2	4933432E21Rik|Dmrt7	doublesex and mab-3 related transcription factor like family C2	protein-coding
mm_34531.1	chr4	149347880	149347889	+	1	NA	intron (NM_022022, intron 20 of 26)	intron (NM_022022, intron 20 of 26)	13245	NR_131918	74310	Mm.440455	NR_131918	ENSMUSG00000085286	Ube4bos3	1700121F15Rik	ubiquitination factor E4B, opposite strand 3	ncRNA
mm_81459.1	chr9	109848595	109848610	+	1	NA	exon (NM_009921, exon 2 of 4)	exon (NM_009921, exon 2 of 4)	854	NM_009921	12796	Mm.3834	NM_009921	ENSMUSG00000038357	Camp	CAP18|Cnlp|Cramp|FALL39|MCLP	cathelicidin antimicrobial peptide	protein-coding
mm_57981.1	chr6	135732763	135732767	-	1	NA	exon (NM_008171, exon 15 of 15)	exon (NM_008171, exon 15 of 15)	73852	NR_126088	75024	Mm.399147	NR_126088	ENSMUSG00000107396	4930425L21Rik	4930473P14Rik	RIKEN cDNA 4930425L21 gene	ncRNA
mm_30469.1	chr3	154330544	154330576	-	1	NA	promoter-TSS (NM_010713)	promoter-TSS (NM_010713)	0	NM_010713	16875	Mm.15530	NM_010713	ENSMUSG00000096225	Lhx8	L3|Lhx7	LIM homeobox protein 8	protein-coding
mm_123222.1	chr14	59571994	59572000	-	1	NA	intron (NM_001168535, intron 8 of 10)	B4A|SINE|B4	25962	NM_001168537	71891	Mm.439850	NM_027986	ENSMUSG00000021982	Cdadc1	2310010M10Rik|AI449174|AI463398|BB130816|NYD-SP15	cytidine and dCMP deaminase domain containing 1	protein-coding
mm_145202.1	chr18	49979554	49979556	+	1	NA	5' UTR (NM_001177760, exon 1 of 3)	5' UTR (NM_001177760, exon 1 of 3)	128	NM_001177759	106869	Mm.27740	NM_134131	ENSMUSG00000062210	Tnfaip8	AA987150|E130304C20Rik|ENSMUSG00000073567|Gg2-1|Gm10539|Nded|Ssc-2|Tipe	tumor necrosis factor, alpha-induced protein 8	protein-coding
mm_72081.1	chr8	71570668	71570725	+	1	NA	intron (NM_011977, intron 2 of 13)	CpG	1769	NM_011977	26457	Mm.38165	NM_011977	ENSMUSG00000031808	Slc27a1	FATP1|Fatp	solute carrier family 27 (fatty acid transporter), member 1	protein-coding
mm_20041.1	chr2	120091009	120091022	-	1	NA	3' UTR (NM_133838, exon 6 of 6)	3' UTR (NM_133838, exon 6 of 6)	57582	NM_145378	211429	Mm.41467	NM_145378	ENSMUSG00000098488	Pla2g4b	A030011C02Rik|Gm1013|cPLA2-beta	phospholipase A2, group IVB (cytosolic)	protein-coding
mm_71178.1	chr8	40793273	40793297	+	1	NA	promoter-TSS (NM_001009548)	promoter-TSS (NM_001009548)	12	NM_001009548	384806	Mm.444736	NM_001009548	ENSMUSG00000046282	Adam20	4930529F22Rik|Adam38	a disintegrin and metallopeptidase domain 20	protein-coding
mm_100102.1	chr11	115765501	115765533	+	1	NA	promoter-TSS (NM_028014)	promoter-TSS (NM_028014)	84	NM_028014	71947	Mm.23168	NM_028014	ENSMUSG00000020747	Tmem94	2310067B10Rik|Kiaa0195|mKIAA0195	transmembrane protein 94	protein-coding
mm_164264.1	chr15	100784348	100784348	+	1	NA	intron (NM_001347102, intron 3 of 23)	B3|SINE|B2	3094	NM_001347102	59033	Mm.209856	NM_021530	ENSMUSG00000023032	Slc4a8	AW493845|C230026C11|NDCBE|kNBC-3	solute carrier family 4 (anion exchanger), member 8	protein-coding
mm_78294.1	chr9	22389269	22389316	+	1	NA	promoter-TSS (NM_028390)	promoter-TSS (NM_028390)	-86	NM_028390	68743	Mm.282751	NM_028390	ENSMUSG00000036777	Anln	1110037A17Rik|2900037I21Rik|C78101|Scraps	anillin, actin binding protein	protein-coding
mm_59721.1	chr7	28784354	28784365	+	1	NA	intron (NM_001122765, intron 8 of 14)	intron (NM_001122765, intron 8 of 14)	-2845	NR_040339	100503790	Mm.446894	NR_040339		Gm19897	-	predicted gene, 19897	ncRNA
mm_33152.1	chr4	125490409	125490456	+	1	NA	promoter-TSS (NM_001081097)	promoter-TSS (NM_001081097)	-399	NM_001081097	14807	Mm.40896	NM_001081097	ENSMUSG00000001985	Grik3	9630027E11|GluK3|GluR7-3|Glur-7|Glur7	glutamate receptor, ionotropic, kainate 3	protein-coding
mm_44338.1	chr5	17397868	17397877	-	1	NA	Intergenic	Intergenic	-78250	NM_027609	70935	Mm.332225	NM_027609	ENSMUSG00000058643	Speer4f1	4922502J04Rik|SPEER-4F|Speer4f	spermatogenesis associated glutamate (E)-rich protein 4F1	protein-coding
mm_35383.1	chr4	33247574	33247599	-	1	NA	intron (NM_001033225, intron 1 of 1)	CpG	1201	NM_001033225	108767	Mm.27769	NM_001033225	ENSMUSG00000040128	Pnrc1	5730463C12Rik|B4-2|PRR2|Prol2	proline-rich nuclear receptor coactivator 1	protein-coding
mm_27393.1	chr3	50887054	50887064	-	1	NA	Intergenic	Intergenic	-337388	NM_009834	12457	Mm.86541	NM_009834	ENSMUSG00000023087	Noct	AU043840|Ccr4|Ccrn4l	nocturnin	protein-coding
mm_46579.1	chr5	107431875	107431880	-	1	NA	5' UTR (NM_027599, exon 1 of 2)	5' UTR (NM_027599, exon 1 of 2)	328	NM_027599	70902	Mm.55870	NM_027599	ENSMUSG00000033794	Lpcat2b	4921521K07Rik|Aytl1b	lysophosphatidylcholine acyltransferase 2B	protein-coding
mm_126979.1	chr15	93435969	93435974	+	1	NA	intron (NM_175363, intron 3 of 8)	intron (NM_175363, intron 3 of 8)	37507	NM_001285863	223828	Mm.74208	NM_146062	ENSMUSG00000036167	Pphln1	CR|HSPC206|HSPC232	periphilin 1	protein-coding
mm_92062.1	chr10	62514359	62514370	-	1	NA	Intergenic	Intergenic	-6609	NM_011157	19073	Mm.338790	NM_011157	ENSMUSG00000020077	Srgn	Prg|Prg1|Sgc	serglycin	protein-coding
mm_166222.1	chr5	64960810	64960829	-	1	NA	promoter-TSS (NM_011604)	promoter-TSS (NM_011604)	-785	NM_011604	21899	Mm.42146	NM_011604	ENSMUSG00000051498	Tlr6	-	toll-like receptor 6	protein-coding
mm_55153.1	chr6	51469837	51469854	-	1	NA	promoter-TSS (NM_007624)	promoter-TSS (NM_007624)	49	NM_182650	53379	Mm.155896	NM_016806	ENSMUSG00000004980	Hnrnpa2b1	9130414A06Rik|Hnrpa2|Hnrpa2b1|hnrnp-A	heterogeneous nuclear ribonucleoprotein A2/B1	protein-coding
mm_9133.1	chr1	170841772	170841790	-	1	NA	exon (NM_001081304, exon 5 of 16)	exon (NM_001081304, exon 5 of 16)	25990	NM_001081304	226641	Mm.377046	NM_001081304	ENSMUSG00000026663	Atf6	9130025P16Rik|9630036G24|AA789574|Atf6alpha|ESTM49	activating transcription factor 6	protein-coding
mm_64186.1	chr7	141459889	141459920	+	1	NA	non-coding (NR_028142, exon 10 of 10)	non-coding (NR_028142, exon 10 of 10)	-1190	NM_001025103	213573	Mm.386851	NM_001025103	ENSMUSG00000048200	Cracr2b	6330520A15Rik|BC026645|Cracr2a|Efcab4|Efcab4a	calcium release activated channel regulator 2B	protein-coding
mm_45353.1	chr5	65912369	65912392	-	1	NA	Intergenic	Intergenic	48811	NM_001081105	74734	Mm.20323	NM_001081105	ENSMUSG00000029204	Rhoh	5830400A04Rik|AU019774|Arhh	ras homolog family member H	protein-coding
mm_138362.1	chr17	34985534	34985567	+	1	NA	3' UTR (NM_001110101, exon 5 of 5)	3' UTR (NM_001110101, exon 5 of 5)	3420	NM_030597	27756	Mm.165735	NM_030597	ENSMUSG00000007050	Lsm2	D17H6S56E-2|D17H6S56E2|Dmapl|Dmpkap|G7b|Sm-X5|SmX5|snRNP	LSM2 homolog, U6 small nuclear RNA and mRNA degradation associated	protein-coding
mm_83261.1	chr9	42457595	42457606	-	1	NA	intron (NM_173038, intron 1 of 7)	intron (NM_173038, intron 1 of 7)	14626	NM_173038	272589	Mm.34483	NM_173038	ENSMUSG00000037287	Tbcel	D330014K23|E130107N23Rik|Lrrc35	tubulin folding cofactor E-like	protein-coding
mm_69776.1	chr7	141017553	141017569	-	1	NA	promoter-TSS (NM_001033632)	promoter-TSS (NM_001033632)	-669	NM_001033632	213002	Mm.276440	NM_001033632	ENSMUSG00000059108	Ifitm6	A330075D07|Dspa2f|Fgls5|fragilis5	interferon induced transmembrane protein 6	protein-coding
mm_97004.1	chr11	70877096	70877124	+	1	NA	intron (NM_001291143, intron 3 of 18)	B3|SINE|B2	32349	NM_001291142	54189	Mm.7087	NM_019400	ENSMUSG00000020817	Rabep1	Rab5ep|rabaptin-5|rabaptin-5alpha	rabaptin, RAB GTPase binding effector protein 1	protein-coding
mm_96153.1	chr11	61484886	61484910	+	1	NA	promoter-TSS (NM_029568)	promoter-TSS (NM_029568)	-533	NM_001347545	76293	Mm.272278	NM_029568	ENSMUSG00000042436	Mfap4	1110007F23Rik	microfibrillar-associated protein 4	protein-coding
mm_67046.1	chr7	67280639	67280666	-	1	NA	intron (NM_001033713, intron 4 of 11)	intron (NM_001033713, intron 4 of 11)	58036	NM_001191051	75099	Mm.121691	NM_175215	ENSMUSG00000043831	Lysmd4	4930506D23Rik	LysM, putative peptidoglycan-binding, domain containing 4	protein-coding
mm_5990.1	chr1	58504947	58504965	-	1	NA	5' UTR (NM_001271526, exon 1 of 18)	5' UTR (NM_001271526, exon 1 of 18)	153	NM_001271526	18393	Mm.3411	NM_008765	ENSMUSG00000026037	Orc2	AU041563|Orc2l	origin recognition complex, subunit 2	protein-coding
mm_62894.1	chr7	116093297	116093329	+	1	NA	promoter-TSS (NM_019772)	promoter-TSS (NM_019772)	-67	NM_019772	56372	Mm.24231	NM_019772	ENSMUSG00000030663	1110004F10Rik	Smacp|Smap|sid2057|sid2057p	RIKEN cDNA 1110004F10 gene	protein-coding
mm_31916.1	chr4	85205504	85205516	+	1	NA	promoter-TSS (NM_019535)	promoter-TSS (NM_019535)	54	NM_019535	20404	Mm.143603	NM_019535	ENSMUSG00000028488	Sh3gl2	9530001L19Rik|AI120490|AW555077|B930049H17Rik|EEN-B1|SH3PA|Sh3d2a	SH3-domain GRB2-like 2	protein-coding
mm_113523.1	chr13	37825995	37826003	+	1	NA	promoter-TSS (NM_001177868)	promoter-TSS (NM_001177868)	-39	NM_026830	68750	Mm.491109	NM_026830	ENSMUSG00000039087	Rreb1	1110037N09Rik|AA414966|B930013M22Rik	ras responsive element binding protein 1	protein-coding
mm_40870.1	chr5	74014212	74014226	+	1	NA	intron (NM_177561, intron 5 of 8)	intron (NM_177561, intron 5 of 8)	54192	NM_177561	69727	Mm.48795	NM_177561	ENSMUSG00000054814	Usp46	1190009E20Rik|2410018I08Rik|AI451644	ubiquitin specific peptidase 46	protein-coding
mm_94189.1	chr10	128960949	128960959	-	1	NA	promoter-TSS (NM_027853)	promoter-TSS (NM_027853)	34	NM_027853	71664	Mm.337232	NM_027853	ENSMUSG00000025347	Mettl7b	0610006F02Rik|AI266817	methyltransferase like 7B	protein-coding
mm_33227.1	chr4	126756984	126757004	+	1	NA	exon (NM_001035526, exon 2 of 24)	exon (NM_001035526, exon 2 of 24)	3224	NM_001035526	100317	Mm.206206	NM_133886	ENSMUSG00000028830	AU040320	A730047D20Rik|AAVR|Kiaa0319l	expressed sequence AU040320	protein-coding
mm_58088.1	chr6	137169711	137169723	-	1	NA	promoter-TSS (NM_001164214)	promoter-TSS (NM_001164214)	1	NM_001164214	232441	Mm.46233	NM_181988	ENSMUSG00000030222	Rerg	-	RAS-like, estrogen-regulated, growth-inhibitor	protein-coding
mm_75600.1	chr8	61760039	61760061	-	1	NA	promoter-TSS (NM_001293773)	promoter-TSS (NM_001293773)	48	NM_001293773	72333	Mm.29933	NM_001081390	ENSMUSG00000058056	Palld	2410003B16Rik|6030492A02	palladin, cytoskeletal associated protein	protein-coding
mm_147036.1	chr18	34856223	34856241	-	1	NA	Intergenic	Intergenic	-4975	NM_007913	13653	Mm.181959	NM_007913	ENSMUSG00000038418	Egr1	A530045N19Rik|ETR103|Egr-1|Krox-1|Krox-24|Krox24|NGF1-A|NGFI-A|NGFIA|TIS8|Zenk|Zfp-6|Zif268|egr	early growth response 1	protein-coding
mm_156912.1	chrX	169076772	169076793	+	1	NA	intron (NR_109847, intron 1 of 14)	Lx8|LINE|L1	-36096	NM_001287530	11856	Mm.441810	NM_009707	ENSMUSG00000031355	Arhgap6	AI504284|RhoGAPX-1	Rho GTPase activating protein 6	protein-coding
mm_30567.1	chr4	3790340	3790360	+	1	NA	3' UTR (NM_001111096, exon 13 of 13)	3' UTR (NM_001111096, exon 13 of 13)	45305	NM_026147	67427	Mm.21938	NM_026147	ENSMUSG00000028234	Rps20	4632426K06Rik|Dsk4	ribosomal protein S20	protein-coding
mm_138914.1	chr17	43604562	43604580	+	1	NA	exon (NM_013737, exon 9 of 12)	exon (NM_013737, exon 9 of 12)	-13062	NR_045444	73504	Mm.9277	NR_045444	ENSMUSG00000090307	1700071M16Rik	-	RIKEN cDNA 1700071M16 gene	ncRNA
mm_152278.1	chr19	8838636	8838649	-	1	NA	promoter-TSS (NM_008144)	promoter-TSS (NM_008144)	604	NM_010316	14704	Mm.329700	NM_010316	ENSMUSG00000071658	Gng3	-	guanine nucleotide binding protein (G protein), gamma 3	protein-coding
mm_101410.1	chr11	28574672	28574675	-	1	NA	intron (NM_001346759, intron 2 of 5)	L1MA7|LINE|L1	9651	NM_001166661	216613	Mm.93759	NM_181577	ENSMUSG00000032878	Ccdc85a	-	coiled-coil domain containing 85A	protein-coding
mm_32751.1	chr4	116686383	116686424	+	1	NA	promoter-TSS (NR_040442)	promoter-TSS (NR_040442)	-381	NR_040442	100502959	Mm.395400	NR_040442		AV051173	-	expressed sequence AV051173	ncRNA
mm_119268.1	chr14	34053467	34053473	+	1	NA	promoter-TSS (NM_172808)	promoter-TSS (NM_172808)	0	NM_172808	239029	Mm.477093	NM_172808	ENSMUSG00000047441	Antxrl	1700112N15Rik|4933430J11	anthrax toxin receptor-like	protein-coding
mm_23984.1	chr3	86104025	86104063	+	1	NA	intron (NM_001082414, intron 4 of 14)	RLTR20A4|LTR|ERVK	19610	NM_001082414	27059	Mm.2454	NM_012059	ENSMUSG00000028082	Sh3d19	AW011754|Kryn	SH3 domain protein D19	protein-coding
mm_95850.1	chr11	57801576	57801649	+	1	NA	promoter-TSS (NM_001081168)	promoter-TSS (NM_001081168)	-25	NM_001081168	50724	Mm.340083	NM_001081168	ENSMUSG00000020519	Sap30l	2310079P12Rik|AF006998|L55	SAP30-like	protein-coding
mm_65835.1	chr7	29180700	29180710	-	1	NA	promoter-TSS (NM_026545)	promoter-TSS (NM_026545)	-32	NM_026545	57296	Mm.273152	NM_026545	ENSMUSG00000030591	Psmd8	6720456J22Rik|AA407360|AL033291|AL033322|AL033323|C76433	proteasome (prosome, macropain) 26S subunit, non-ATPase, 8	protein-coding
mm_125826.1	chr15	74957232	74957246	+	1	NA	intron (NM_001164039, intron 2 of 4)	intron (NM_001164039, intron 2 of 4)	2133	NM_001164040	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_149281.1	chr19	10608248	10608270	+	1	NA	exon (NM_015735, exon 4 of 27)	exon (NM_015735, exon 4 of 27)	2634	NM_015735	13194	Mm.289915	NM_015735	ENSMUSG00000024740	Ddb1	127kDa|AA408517|p127-Ddb1	damage specific DNA binding protein 1	protein-coding
mm_90142.1	chr10	118098271	118098281	+	1	NA	Intergenic	Intergenic	-43511	NM_001162904	17245	Mm.101191	NM_010785	ENSMUSG00000020212	Mdm1	Arrd2|Mdm-1	transformed mouse 3T3 cell double minute 1	protein-coding
mm_106299.1	chr11	118248490	118248504	-	1	NA	promoter-TSS (NM_011180)	promoter-TSS (NM_011180)	95	NM_001112699	19157	Mm.86413	NM_011180	ENSMUSG00000017132	Cyth1	CLM1|CTH-1|CYTIP|Pscd1	cytohesin 1	protein-coding
mm_120267.1	chr14	63122507	63122525	+	1	NA	promoter-TSS (NM_007798)	promoter-TSS (NM_007798)	54	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_35145.1	chr4	11615006	11615012	-	1	NA	intron (NM_001039556, intron 14 of 14)	intron (NM_001039556, intron 14 of 14)	35347	NM_001256142	100503583	Mm.249437	NM_001256142	ENSMUSG00000094595	Fsbp	-	fibrinogen silencer binding protein	protein-coding
mm_97081.1	chr11	73018987	73019047	+	1	NA	promoter-TSS (NM_018883)	promoter-TSS (NM_018883)	9	NM_018883	55984	Mm.9998	NM_018883	ENSMUSG00000020785	Camkk1	AI846603|CaMKKalpha|Camkk	calcium/calmodulin-dependent protein kinase kinase 1, alpha	protein-coding
mm_81266.1	chr9	108049860	108049894	+	1	NA	intron (NM_177910, intron 2 of 8)	intron (NM_177910, intron 2 of 8)	587	NM_177910	331026	Mm.22554	NM_177910	ENSMUSG00000070284	Gmppb	AI317178|E430010H19	GDP-mannose pyrophosphorylase B	protein-coding
mm_103680.1	chr11	79254664	79254685	-	1	NA	promoter-TSS (NM_019653)	promoter-TSS (NM_019653)	21	NM_019653	78889	Mm.307022	NM_019653	ENSMUSG00000017677	Wsb1	1110056B13Rik|2700038M07Rik	WD repeat and SOCS box-containing 1	protein-coding
mm_1236.1	chr1	62795970	62795984	+	1	NA	exon (NM_001077407, exon 16 of 16)	exon (NM_001077407, exon 16 of 16)	-1245	NR_040601	74992	Mm.401979	NR_040601		4930487H11Rik	-	RIKEN cDNA 4930487H11 gene	ncRNA
mm_19586.1	chr2	101883011	101883023	-	1	NA	Intergenic	Intergenic	-3245	NM_029635	76501	Mm.330424	NM_029635	ENSMUSG00000027163	Commd9	1810029F08Rik|AA409293	COMM domain containing 9	protein-coding
mm_161003.1	chr11	116581424	116581424	-	1	NA	promoter-TSS (NM_173755)	promoter-TSS (NM_173755)	23	NM_173755	217342	Mm.243950	NM_173755	ENSMUSG00000020802	Ube2o	9630022H21|B230113M03Rik|E2-230K|mKIAA1734	ubiquitin-conjugating enzyme E2O	protein-coding
mm_86297.1	chr9	122294410	122294431	-	1	NA	promoter-TSS (NM_133979)	promoter-TSS (NM_133979)	3	NM_001271873	102566	Mm.87676	NM_133979	ENSMUSG00000037949	Ano10	AI604832|Tmem16k	anoctamin 10	protein-coding
mm_43657.1	chr5	138619302	138619326	+	1	NA	intron (NM_013844, intron 1 of 5)	intron (NM_013844, intron 1 of 5)	429	NM_001163797	24135	Mm.27575	NM_013844	ENSMUSG00000058291	Zfp68	KRAB3|KRAZ2|Zfp70|mszf22|mszf49	zinc finger protein 68	protein-coding
mm_149610.1	chr19	16385739	16385752	+	1	NA	3' UTR (NM_008139, exon 7 of 7)	3' UTR (NM_008139, exon 7 of 7)	-49922	NM_008137	14675	Mm.313181	NM_008137	ENSMUSG00000024697	Gna14	AU023208	guanine nucleotide binding protein, alpha 14	protein-coding
mm_53194.1	chr6	125532553	125532559	+	1	NA	Intergenic	Intergenic	-20392	NM_011708	22371	Mm.22339	NM_011708	ENSMUSG00000001930	Vwf	6820430P06Rik|AI551257|B130011O06Rik|C630030D09|F8VWF|VWD	Von Willebrand factor	protein-coding
mm_168154.1	chr10	41415437	41415439	-	1	NA	Intergenic	RLTR9D|LTR|ERVK	-34920	NM_001277229	268294	Mm.258475	NM_153398	ENSMUSG00000019826	Zbtb24	BC055367|Bif1|Bsg1|ZNF450	zinc finger and BTB domain containing 24	protein-coding
mm_121339.1	chr14	115092290	115092296	+	1	NA	promoter-TSS (NM_175500)	promoter-TSS (NM_175500)	78	NM_175500	103978	Mm.320791	NM_175500	ENSMUSG00000022112	Gpc5	A230034F01Rik	glypican 5	protein-coding
mm_14060.1	chr2	122637845	122637864	+	1	NA	promoter-TSS (NM_001004174)	promoter-TSS (NM_001004174)	-33	NM_001004174	433470	Mm.36783	NM_001004174	ENSMUSG00000033213	AA467197	Nmes1|mir-147	expressed sequence AA467197	protein-coding
mm_57325.1	chr6	124738597	124738630	-	1	NA	promoter-TSS (NM_001077705)	promoter-TSS (NM_001077705)	96	NM_001077705	15170	Mm.271799	NM_013545	ENSMUSG00000004266	Ptpn6	70Z-SHP|Hcph|PTPTY-42|Ptp1C|SH-PTP1|SHP-1|hcp|me	protein tyrosine phosphatase, non-receptor type 6	protein-coding
mm_27462.1	chr3	52179987	52179997	-	1	NA	Intergenic	Intergenic	-74986	NM_001004176	433586	Mm.234972	NM_001004176	ENSMUSG00000061143	Maml3	AV234550|BC049812|Mam-2|mKIAA1816	mastermind like 3 (Drosophila)	protein-coding
mm_94113.1	chr10	128626465	128626520	-	1	NA	promoter-TSS (NM_013765)	promoter-TSS (NM_013765)	14	NM_013765	27370	Mm.32118	NM_013765	ENSMUSG00000025362	Rps26	-	ribosomal protein S26	protein-coding
mm_67763.1	chr7	92874155	92874165	-	1	NA	promoter-TSS (NM_001080995)	promoter-TSS (NM_001080995)	72	NM_001080995	74041	Mm.26468	NM_028729	ENSMUSG00000030641	Ddias	4632434I11Rik|noxin	DNA damage-induced apoptosis suppressor	protein-coding
mm_160507.1	chr9	20212453	20212453	+	1	NA	exon (NM_146903, exon 1 of 1)	exon (NM_146903, exon 1 of 1)	246	NM_146903	258905	Mm.103798	NM_146903	ENSMUSG00000061457	Olfr871	MOR141-2	olfactory receptor 871	protein-coding
mm_78937.1	chr9	45121166	45121177	+	1	NA	intron (NM_001014761, intron 1 of 3)	intron (NM_001014761, intron 1 of 3)	3295	NM_001014761	72821	Mm.229373	NM_001014761	ENSMUSG00000070304	Scn2b	2810451E09Rik|AI840361|Gm183	sodium channel, voltage-gated, type II, beta	protein-coding
mm_60396.1	chr7	44475472	44475485	+	1	NA	Intergenic	Intergenic	5131	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_72606.1	chr8	84468673	84468677	+	1	NA	intron (NM_001252059, intron 2 of 45)	intron (NM_001252059, intron 2 of 45)	53311	NM_001252061	12286	Mm.334658	NM_007578	ENSMUSG00000034656	Cacna1a	APCA|BI|Caca1a|Cacnl1a4|Cav2.1|Ccha1a|EA2|FHM|HPCA|MHP|MHP1|SCA6|alpha1A|la|nmf352|rkr|smrl|tg	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	protein-coding
mm_161436.1	chr15	63845176	63845176	-	1	NA	promoter-TSS (NM_177912)	promoter-TSS (NM_177912)	0	NM_001168274	331063	Mm.273185	NM_177912	ENSMUSG00000056293	Gsdmc2	9130023H10|AI987692	gasdermin C2	protein-coding
mm_69745.1	chr7	140955439	140955493	-	1	NA	intron (NM_030694, intron 1 of 1)	intron (NM_030694, intron 1 of 1)	495	NM_030694	80876	Mm.379266	NM_030694	ENSMUSG00000060591	Ifitm2	DSPA2c|Ifitm3l|fragilis3|mil-3	interferon induced transmembrane protein 2	protein-coding
mm_142972.1	chr17	56133888	56133911	-	1	NA	promoter-TSS (NM_013662)	promoter-TSS (NM_013662)	-47	NM_013662	20359	Mm.8029	NM_013662	ENSMUSG00000001227	Sema6b	Sema|Seman|VIb|semaZ	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B	protein-coding
mm_60657.1	chr7	44929737	44929760	+	1	NA	promoter-TSS (NM_001077264)	promoter-TSS (NM_001077264)	-258	NM_001077264	11771	Mm.6877	NM_007458	ENSMUSG00000060279	Ap2a1	Adtaa	adaptor-related protein complex 2, alpha 1 subunit	protein-coding
mm_160653.1	chr9	114330058	114330058	+	1	NA	promoter-TSS (NM_007535)	promoter-TSS (NM_007535)	-77	NM_007535	12046	Mm.378887	NM_007535	ENSMUSG00000053820	Bcl2a1c	A1-c	B cell leukemia/lymphoma 2 related protein A1c	protein-coding
mm_120500.1	chr14	66140920	66140962	+	1	NA	promoter-TSS (NM_144803)	promoter-TSS (NM_144803)	-19	NM_144803	110902	Mm.57350	NM_144803	ENSMUSG00000022041	Chrna2	Acra-2|Acra2|BC011490	cholinergic receptor, nicotinic, alpha polypeptide 2 (neuronal)	protein-coding
mm_50869.1	chr6	55451996	55452051	+	1	NA	promoter-TSS (NM_001025372)	promoter-TSS (NM_001025372)	45	NM_007407	11517	Mm.44245	NM_007407	ENSMUSG00000029778	Adcyap1r1	2900024I10Rik|AI846590|PAC1|PAC1R|PACAP1-R	adenylate cyclase activating polypeptide 1 receptor 1	protein-coding
mm_160774.1	chr10	120227083	120227083	+	1	NA	promoter-TSS (NM_025431)	promoter-TSS (NM_025431)	23	NM_025431	66225	Mm.291755	NM_025431	ENSMUSG00000020224	Llph	1190005P17Rik	LLP homolog, long-term synaptic facilitation (Aplysia)	protein-coding
mm_122043.1	chr14	30009359	30009367	-	1	NA	promoter-TSS (NM_019583)	promoter-TSS (NM_019583)	363	NM_001136240	218865	Mm.259916	NM_172264	ENSMUSG00000015970	Chdh	AU041472|D630034H06Rik	choline dehydrogenase	protein-coding
mm_135954.1	chr16	74621231	74621236	-	1	NA	Intergenic	Intergenic	-210321	NM_175549	268902	Mm.171736	NM_175549	ENSMUSG00000052516	Robo2	2600013A04Rik|9430089E08Rik|BB097918|D230004I22Rik|mKIAA1568	roundabout guidance receptor 2	protein-coding
mm_98030.1	chr11	85311233	85311286	+	1	NA	promoter-TSS (NM_016910)	promoter-TSS (NM_016910)	5	NM_016910	53892	Mm.45609	NM_016910	ENSMUSG00000020525	Ppm1d	AV338790|Wip1	protein phosphatase 1D magnesium-dependent, delta isoform	protein-coding
mm_44909.1	chr5	35663605	35663658	-	1	NA	intron (NM_001042615, intron 6 of 6)	(TGGG)n|Simple_repeat|Simple_repeat	16149	NM_001042615	78558	Mm.274255	NM_030127	ENSMUSG00000029096	Htra3	2210021K23Rik|9530081K03Rik|Prsp|Tasp	HtrA serine peptidase 3	protein-coding
mm_47458.1	chr5	123661652	123661663	-	1	NA	intron (NM_001347468, intron 1 of 24)	intron (NM_001347468, intron 1 of 24)	22704	NM_019765	56430	Mm.241109	NM_019765	ENSMUSG00000049550	Clip1	1110007I12Rik|4631429H07Rik|AV017631|C81039|CLIP-170|CLIP170|CYLN1|Clip50|Rsn|mKIAA4046|restin	CAP-GLY domain containing linker protein 1	protein-coding
mm_78134.1	chr9	20888235	20888239	+	1	NA	promoter-TSS (NM_145610)	promoter-TSS (NM_145610)	62	NM_145610	235036	Mm.2930	NM_145610	ENSMUSG00000004100	Ppan	A230087P06Rik|SSF1	peter pan homolog (Drosophila)	protein-coding
mm_86780.1	chr10	20170804	20170821	+	1	NA	intron (NM_001198635, intron 1 of 17)	intron (NM_001198635, intron 1 of 17)	21892	NM_001198635	17761	Mm.20928	NM_008635	ENSMUSG00000019996	Map7	E-MAP-115|MAP-7|Mtap7|R75000|mshi|mste|ste	microtubule-associated protein 7	protein-coding
mm_166905.1	chr7	28811073	28811077	+	1	NA	exon (NM_177301, exon 1 of 13)	exon (NM_177301, exon 1 of 13)	185	NM_177301	15388	Mm.9043	NM_177301	ENSMUSG00000015165	Hnrnpl	C79783|D830027H13Rik|Hnrpl	heterogeneous nuclear ribonucleoprotein L	protein-coding
mm_54109.1	chr6	17065465	17065509	-	1	NA	intron (NM_207176, intron 1 of 6)	CpG	338	NM_207176	21753	Mm.436548	NM_011570	ENSMUSG00000029552	Tes	D6Ertd352e|TESS|Tes1|Tes2|testin2	testis derived transcript	protein-coding
mm_11315.1	chr2	30364228	30364260	+	1	NA	promoter-TSS (NM_001242407)	promoter-TSS (NM_001242407)	11	NM_001242407	108958	Mm.254974	NM_175392	ENSMUSG00000026858	Miga2	5730472N09Rik|AA408683|AI790341|C9orf54|Fam73b|R74766	mitoguardin 2	protein-coding
mm_97787.1	chr11	82783332	82783342	+	1	NA	intron (NM_001291247, intron 1 of 19)	intron (NM_001291247, intron 1 of 19)	2228	NM_010716	16882	Mm.277136	NM_010716	ENSMUSG00000020697	Lig3	D11Wsu78e	ligase III, DNA, ATP-dependent	protein-coding
mm_67171.1	chr7	73557904	73557940	-	1	NA	intron (NR_037569, intron 1 of 4)	CpG	473	NR_037569	69170	Mm.34539	NR_037569	ENSMUSG00000101970	1810026B05Rik	-	RIKEN cDNA 1810026B05 gene	ncRNA
mm_20531.1	chr2	131025148	131025159	-	1	NA	intron (NM_009730, intron 28 of 28)	intron (NM_009730, intron 28 of 28)	15245	NR_105969	102465606		NR_105969	ENSMUSG00000098686	Mir6973b	Gm27815|mmu-mir-6973b	microRNA 6973b	ncRNA
mm_125782.1	chr15	74716462	74716471	+	1	NA	exon (NM_028216, exon 3 of 3)	exon (NM_028216, exon 3 of 3)	1627	NM_028216	72373	Mm.46395	NM_028216	ENSMUSG00000022598	Psca	2210408B04Rik	prostate stem cell antigen	protein-coding
mm_86116.1	chr9	115609743	115609746	-	1	NA	Intergenic	MTE2a|LTR|ERVL-MaLR	227925	NR_130329	100316675		NR_130329	ENSMUSG00000080409	Mir467h	Mirn467h|mmu-mir-467h	microRNA 467h	ncRNA
mm_28562.1	chr3	93444706	93444719	-	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	2382	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_121729.1	chr14	18021889	18021914	-	1	NA	intron (NM_009380, intron 4 of 6)	ORR1E|LTR|ERVL-MaLR	40257	NM_009380	21834	Mm.32563	NM_009380	ENSMUSG00000021779	Thrb	Nr1a2|T3R[b]|T3Rbeta|Thrb1|Thrb2|c-erbAbeta	thyroid hormone receptor beta	protein-coding
mm_53087.1	chr6	124997091	124997112	+	1	NA	intron (NM_175696, intron 1 of 5)	intron (NM_175696, intron 1 of 5)	381	NM_175696	319352	Mm.295327	NM_175696	ENSMUSG00000030329	Pianp	AI255183|AU067746|C530028O21Rik|Panp	PILR alpha associated neural protein	protein-coding
mm_35845.1	chr4	48435005	48435017	-	1	NA	exon (NM_172304, exon 14 of 16)	exon (NM_172304, exon 14 of 16)	38411	NM_172304	269536	Mm.272025	NM_172304	ENSMUSG00000028345	Tex10	2610206N19Rik|2810462N03Rik|BC006867	testis expressed gene 10	protein-coding
mm_172180.1	chr6	49236555	49236555	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-21601	NM_023670	140488	Mm.281018	NM_023670	ENSMUSG00000029814	Igf2bp3	2610101N11Rik|AA522010|AL022933|AU045931|IMP-3|IMP3|Koc13|Neilsen|mimp3	insulin-like growth factor 2 mRNA binding protein 3	protein-coding
mm_96043.1	chr11	59557362	59557372	+	1	NA	intron (NM_145827, intron 6 of 9)	L1MB3|LINE|L1	14371	NM_001011789	257962	Mm.377316	NM_001011789	ENSMUSG00000059610	Olfr222	MOR256-45P	olfactory receptor 222	protein-coding
mm_166467.1	chr5	142734067	142734073	+	1	NA	intron (NM_001122730, intron 22 of 27)	intron (NM_001122730, intron 22 of 27)	31969	NM_146257	243328	Mm.125942	NM_146257	ENSMUSG00000050822	Slc29a4	ENT4|mPMAT	solute carrier family 29 (nucleoside transporters), member 4	protein-coding
mm_59773.1	chr7	28834169	28834171	+	1	NA	promoter-TSS (NM_010707)	promoter-TSS (NM_010707)	0	NM_010707	16857	Mm.210336	NM_010707		Lgals6	galectin-6	lectin, galactose binding, soluble 6	protein-coding
mm_51277.1	chr6	72142135	72142141	+	1	NA	intron (NM_001035228, intron 3 of 6)	intron (NM_001035228, intron 3 of 6)	-18941	NR_045165	71265	Mm.442035	NR_045163	ENSMUSG00000108709	4933431G14Rik	4930565C19Rik	RIKEN cDNA 4933431G14 gene	ncRNA
mm_48.1	chr1	6518663	6518683	+	1	NA	intron (NM_001244693, intron 2 of 22)	intron (NM_001244693, intron 2 of 22)	31442	NM_001244692	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding
mm_65609.1	chr7	27465869	27465896	-	1	NA	TTS (NM_144923)	TTS (NM_144923)	-7958	NM_133210	170742	Mm.200120	NM_133210	ENSMUSG00000055200	Sertad3	AW124805|D1Mgi51|Rbt1|Sei3	SERTA domain containing 3	protein-coding
mm_35614.1	chr4	43429072	43429088	-	1	NA	promoter-TSS (NM_177377)	promoter-TSS (NM_177377)	54	NM_177377	329831	Mm.454466	NM_177377	ENSMUSG00000042788	Fam166b	4833436C18Rik	family with sequence similarity 166, member B	protein-coding
mm_17623.1	chr2	31030789	31030803	-	1	NA	intron (NM_001038700, intron 14 of 14)	intron (NM_001038700, intron 14 of 14)	48517	NM_028846	74270	Mm.346654	NM_028846	ENSMUSG00000026854	Usp20	1700055M05Rik|AI467231|Vdu2	ubiquitin specific peptidase 20	protein-coding
mm_52178.1	chr6	99265023	99265042	+	1	NA	intron (NM_001347345, intron 3 of 19)	intron (NM_001347345, intron 3 of 19)	1483	NM_001197321	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_136965.1	chr17	15705098	15705142	+	1	NA	5' UTR (NM_007690, exon 1 of 36)	5' UTR (NM_007690, exon 1 of 36)	153	NM_007690	12648	Mm.8137	NM_007690	ENSMUSG00000023852	Chd1	4930525N21Rik|AI851787|AW555109	chromodomain helicase DNA binding protein 1	protein-coding
mm_72292.1	chr8	75213357	75213369	+	1	NA	promoter-TSS (NM_029182)	promoter-TSS (NM_029182)	-581	NM_029182	75141	Mm.179267	NM_029182	ENSMUSG00000034472	Rasd2	4930526B11Rik|AU045414|Rhes|TEM-2|TEM2	RASD family, member 2	protein-coding
mm_172874.1	chr9	42761785	42761786	-	1	NA	intron (NM_175481, intron 3 of 20)	L2a|LINE|L2	182586	NM_175481	110637	Mm.370291	NM_175481	ENSMUSG00000032017	Grik4	6330551K01Rik|GluK4|GluRgamma1|KA-1|KA1	glutamate receptor, ionotropic, kainate 4	protein-coding
mm_95282.1	chr11	45890648	45890662	+	1	NA	exon (NM_001045520, exon 6 of 12)	exon (NM_001045520, exon 6 of 12)	38691	NM_001045520	216705	Mm.169673	NM_001045520	ENSMUSG00000006169	Clint1	AI642036|AW537616|C530049I24Rik|Enth|Epn4|F630206G17Rik|mKIAA0171	clathrin interactor 1	protein-coding
mm_43596.1	chr5	137778977	137778988	+	1	NA	promoter-TSS (NM_027242)	promoter-TSS (NM_027242)	64	NM_027242	69871	Mm.276058	NM_027242	ENSMUSG00000029725	Ppp1r35	2010007H12Rik|2010011D20Rik|AL024004	protein phosphatase 1, regulatory subunit 35	protein-coding
mm_78924.1	chr9	45042664	45042669	+	1	NA	5' UTR (NM_007962, exon 1 of 6)	5' UTR (NM_007962, exon 1 of 6)	322	NM_007962	14012	Mm.33240	NM_007962	ENSMUSG00000032092	Mpzl2	Eva|Eva1	myelin protein zero-like 2	protein-coding
mm_172839.1	chr9	30872592	30872592	-	1	NA	Intergenic	Intergenic	48358	NM_001329420	235130	Mm.65867	NM_001024139	ENSMUSG00000033453	Adamts15	-	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 15	protein-coding
mm_76689.1	chr8	94153952	94153992	-	1	NA	exon (NM_013603, exon 3 of 3)	exon (NM_013603, exon 3 of 3)	1365	NM_013603	17751	Mm.2064	NM_013603	ENSMUSG00000031760	Mt3	Mt-3	metallothionein 3	protein-coding
mm_64379.1	chr7	142466933	142466941	+	1	NA	intron (NM_001271510, intron 1 of 10)	(TGGA)n|Simple_repeat|Simple_repeat	-4906	NM_001271508	16985	Mm.234003	NM_019391	ENSMUSG00000018819	Lsp1	Lsp-1|WP34|p50|pp52	lymphocyte specific 1	protein-coding
mm_121512.1	chr14	121977838	121977839	+	1	NA	intron (NM_026861, intron 5 of 8)	MYSERV6-int|LTR|ERVK	-12645	NM_183031	321019	Mm.265618	NM_183031	ENSMUSG00000051212	Gpr183	Ebi2	G protein-coupled receptor 183	protein-coding
mm_71900.1	chr8	70043019	70043062	+	1	NA	promoter-TSS (NM_001167939)	promoter-TSS (NM_001167939)	227	NM_027481	70616	Mm.17665	NM_027481	ENSMUSG00000011306	Sugp1	5730496N02Rik|Sf4	SURP and G patch domain containing 1	protein-coding
mm_141780.1	chr17	34296072	34296074	-	1	NA	Intergenic	Intergenic	-8302	NM_010378	14960	Mm.235338	NM_010378	ENSMUSG00000036594	H2-Aa	Aalpha|H-2Aa|H2Aa|I-Aalpha|IAalpha|Ia-1|Ia1	histocompatibility 2, class II antigen A, alpha	protein-coding
mm_92685.1	chr10	80623608	80623648	-	1	NA	intron (NM_134002, intron 1 of 10)	intron (NM_134002, intron 1 of 10)	848	NM_134002	103236	Mm.29873	NM_134002	ENSMUSG00000003345	Csnk1g2	2810429I12Rik|AI463719	casein kinase 1, gamma 2	protein-coding
mm_9088.1	chr1	168432205	168432225	-	1	NA	promoter-TSS (NM_001291509)	promoter-TSS (NM_001291509)	-46	NM_008783	18514	Mm.43358	NM_008783	ENSMUSG00000052534	Pbx1	2310056B04Rik|D230003C07Rik|Pbx-1	pre B cell leukemia homeobox 1	protein-coding
mm_23176.1	chr3	40785998	40786004	+	1	NA	intron (NM_011020, intron 17 of 18)	AT_rich|Low_complexity|Low_complexity	-13950	NM_173169	20873	Mm.3794	NM_011495	ENSMUSG00000025758	Plk4	1700028H20|AI385771|Sak|Stk18	polo-like kinase 4	protein-coding
mm_72881.1	chr8	88951730	88951779	+	1	NA	Intergenic	Intergenic	-72981	NR_106190	102465899		NR_106190	ENSMUSG00000099078	Mir8110	Gm27571|mmu-mir-8110	microRNA 8110	ncRNA
mm_109038.1	chr12	104127996	104128002	+	1	NA	promoter-TSS (NM_173024)	promoter-TSS (NM_173024)	3	NM_173024	271047	Mm.120265	NM_173024	ENSMUSG00000066364	Serpina3b	6A1|A030003A19Rik	serine (or cysteine) peptidase inhibitor, clade A, member 3B	protein-coding
mm_50011.1	chr6	41062292	41062302	+	1	NA	Intergenic	Intergenic	-26788	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_45843.1	chr5	87697279	87697298	-	1	NA	intron (NM_009972, intron 2 of 8)	intron (NM_009972, intron 2 of 8)	2137	NM_001286020	12991	Mm.268737	NM_009972	ENSMUSG00000063157	Csn2	Csnb	casein beta	protein-coding
mm_76662.1	chr8	93279718	93279747	-	1	NA	promoter-TSS (NM_144930)	promoter-TSS (NM_144930)	4	NM_144930	234564	Mm.29110	NM_144930	ENSMUSG00000031725	Ces1f	AU018778|CesML1|TGH-2	carboxylesterase 1F	protein-coding
mm_62363.1	chr7	100537193	100537221	+	1	NA	intron (NM_183270, intron 1 of 1)	CpG	107	NM_183270	68185	Mm.228995	NM_183270	ENSMUSG00000044881	Coa4	5330414O08Rik|AI115477|AW047259|Chchd8|E2ig2	cytochrome c oxidase assembly factor 4	protein-coding
mm_135043.1	chr16	33056175	33056211	-	1	NA	promoter-TSS (NM_021338)	promoter-TSS (NM_021338)	-7	NM_178378	69707	Mm.227918	NM_178378	ENSMUSG00000035578	Iqcg	2400003L07Rik|G1-374-12|esgd12d|repro1|stubby12d	IQ motif containing G	protein-coding
mm_8969.1	chr1	165219119	165219126	-	1	NA	intron (NM_145513, intron 5 of 6)	B1_Mur2|SINE|Alu	17836	NM_145513	226591	Mm.21520	NM_145513	ENSMUSG00000040843	Tiprl	1810011K17Rik	TIP41, TOR signalling pathway regulator-like (S. cerevisiae)	protein-coding
mm_63084.1	chr7	122289077	122289225	+	1	NA	promoter-TSS (NM_008855)	promoter-TSS (NM_008855)	26	NM_008855	18751	Mm.207496	NM_008855	ENSMUSG00000052889	Prkcb	PKC-B|PKC-Beta|Pkcb|Prkcb1|Prkcb2	protein kinase C, beta	protein-coding
mm_105592.1	chr11	106736449	106736466	-	1	NA	Intergenic	Intergenic	-14769	NM_001271375	380732	Mm.343952	NM_001033435	ENSMUSG00000040528	Milr1	Allergin-1|Gm885|Mca32	mast cell immunoglobulin like receptor 1	protein-coding
mm_4883.1	chr1	187997836	187997882	+	1	NA	promoter-TSS (NM_011935)	promoter-TSS (NM_011935)	32	NM_011935	26381	Mm.89989	NM_011935	ENSMUSG00000026610	Esrrg	ERR3|Errg|NR3B3|mKIAA0832	estrogen-related receptor gamma	protein-coding
mm_60427.1	chr7	44476668	44476670	+	1	NA	Intergenic	L1MEd|LINE|L1	6322	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_76630.1	chr8	91801916	91801940	-	1	NA	promoter-TSS (NM_001253822)	promoter-TSS (NM_001253822)	-274	NM_008393	16373	Mm.238044	NM_008393	ENSMUSG00000031734	Irx3	AI894186	Iroquois related homeobox 3	protein-coding
mm_137486.1	chr17	26941278	26941316	+	1	NA	promoter-TSS (NM_001281491)	promoter-TSS (NM_001281491)	-155	NM_001281491	240057	Mm.328888	NM_001281491	ENSMUSG00000067629	Syngap1	Gm1963|Syngap	synaptic Ras GTPase activating protein 1 homolog (rat)	protein-coding
mm_7774.1	chr1	131271863	131271878	-	1	NA	exon (NM_019777, exon 9 of 22)	exon (NM_019777, exon 9 of 22)	7693	NM_019777	56489	Mm.386783	NM_019777	ENSMUSG00000042349	Ikbke	AW558201|IKK-i|IKKepsilon|Ikki	inhibitor of kappaB kinase epsilon	protein-coding
mm_112001.1	chr12	110839079	110839096	-	1	NA	intron (NM_011973, intron 1 of 11)	intron (NM_011973, intron 1 of 11)	1852	NM_011973	26448	Mm.140948	NM_011973	ENSMUSG00000056458	Mok	RAGE1|Rage|Stk30	MOK protein kinase	protein-coding
mm_58939.1	chr7	18176471	18176475	+	1	NA	promoter-TSS (NM_001003393)	promoter-TSS (NM_001003393)	-21	NM_001003393	232925	Mm.37237	NM_001003393	ENSMUSG00000066756	Igfl3	Gm580|Igfl|Rprc483	IGF-like family member 3	protein-coding
mm_171144.1	chr3	152214038	152214039	+	1	NA	exon (NM_057172, exon 2 of 20)	exon (NM_057172, exon 2 of 20)	3580	NM_057172	51886	Mm.278922	NM_057172	ENSMUSG00000028034	Fubp1	9530027K12Rik|D3Ertd330e|FBP|Fubp|Fubp4	far upstream element (FUSE) binding protein 1	protein-coding
mm_23376.1	chr3	55533993	55533995	+	1	NA	3' UTR (NM_001111052, exon 14 of 14)	3' UTR (NM_001111052, exon 14 of 14)	72236	NM_001195540	13175	Mm.393242	NM_019978	ENSMUSG00000027797	Dclk1	1700113D08Rik|2810480F11Rik|AI836758|Click-I|Cpg16|Dcamkl1|Dcl|Dclk|mKIAA0369	doublecortin-like kinase 1	protein-coding
mm_78166.1	chr9	21029426	21029442	+	1	NA	promoter-TSS (NM_023892)	promoter-TSS (NM_023892)	61	NM_023892	78369	Mm.30220	NM_023892	ENSMUSG00000001014	Icam4	1810015M19Rik|Cd242|ICAM-4	intercellular adhesion molecule 4, Landsteiner-Wiener blood group	protein-coding
mm_155831.1	chrX	100730179	100730189	+	1	NA	promoter-TSS (NM_001305941)	promoter-TSS (NM_001305941)	-2	NM_001305941	71584	Mm.283495	NM_023608	ENSMUSG00000019359	Gdpd2	9130017L10Rik|Gde3|Obdpf	glycerophosphodiester phosphodiesterase domain containing 2	protein-coding
mm_38048.1	chr4	133968612	133968621	-	1	NA	promoter-TSS (NM_016957)	promoter-TSS (NM_016957)	-625	NM_016957	15331	Mm.319660	NM_016957	ENSMUSG00000003038	Hmgn2	HMG-17|Hmg17	high mobility group nucleosomal binding domain 2	protein-coding
mm_161388.1	chr14	78725150	78725150	-	1	NA	promoter-TSS (NM_001081336)	promoter-TSS (NM_001081336)	-61	NM_001081336	380921	Mm.89591	NM_001081336	ENSMUSG00000034731	Dgkh	5930402B05Rik|D130015C16|DGK	diacylglycerol kinase, eta	protein-coding
mm_62544.1	chr7	102335770	102335772	+	1	NA	intron (NM_009287, intron 1 of 11)	intron (NM_009287, intron 1 of 11)	67947	NM_009287	20866	Mm.645	NM_009287	ENSMUSG00000030987	Stim1	SIM	stromal interaction molecule 1	protein-coding
mm_133471.1	chr16	89274452	89274457	+	1	NA	Intergenic	Intergenic	68593	NM_001163615	622935	Mm.459837	NM_001163615	ENSMUSG00000091039	Krtap20-2	1190004K03Rik|EG622935|Gm6371	keratin associated protein 20-2	protein-coding
mm_80754.1	chr9	95511268	95511289	+	1	NA	intron (NM_026476, intron 1 of 26)	intron (NM_026476, intron 1 of 26)	718	NM_026476	67958	Mm.292742	NM_026476	ENSMUSG00000032407	U2surp	2610101N10Rik|AU023006|Sr140	U2 snRNP-associated SURP domain containing	protein-coding
mm_114664.1	chr13	78199134	78199170	+	1	NA	promoter-TSS (NM_010151)	promoter-TSS (NM_010151)	-279	NM_010151	13865	Mm.439653	NM_010151	ENSMUSG00000069171	Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR-3|EAR3|Erbal3|SVP44|Tcfcoup1	nuclear receptor subfamily 2, group F, member 1	protein-coding
mm_70084.1	chr7	142654319	142654335	-	1	NA	TTS (NR_030251)	TTS (NR_030251)	669	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_66147.1	chr7	31137124	31137148	-	1	NA	intron (NM_027898, intron 11 of 18)	(TG)n|Simple_repeat|Simple_repeat	-10113	NM_011322	20266	Mm.1418	NM_011322	ENSMUSG00000019194	Scn1b	-	sodium channel, voltage-gated, type I, beta	protein-coding
mm_44982.1	chr5	37336838	37336864	-	1	NA	promoter-TSS (NM_021292)	promoter-TSS (NM_021292)	30	NM_021292	59056	Mm.479678	NM_021292	ENSMUSG00000029122	Evc	-	Ellis van Creveld gene syndrome	protein-coding
mm_4702.1	chr1	180851088	180851110	+	1	NA	promoter-TSS (NM_145943)	promoter-TSS (NM_145943)	-52	NM_145943	208768	Mm.272625	NM_145943	ENSMUSG00000038806	Sde2	-	SDE2 telomere maintenance homolog (S. pombe)	protein-coding
mm_97230.1	chr11	75651620	75651637	+	1	NA	promoter-TSS (NM_001080774)	promoter-TSS (NM_001080774)	119	NM_008659	17913	Mm.234502	NM_008659	ENSMUSG00000017774	Myo1c	C80397|MMIb|MYO1E|NMI|mm1beta|myr2	myosin IC	protein-coding
mm_77827.1	chr9	3904163	3904180	+	1	NA	3' UTR (NM_001033322, exon 8 of 8)	3' UTR (NM_001033322, exon 8 of 8)	371822	NM_001033322	234889	Mm.91240	NM_001033322	ENSMUSG00000041624	Gucy1a2	6330407I18Rik|A230060L24Rik	guanylate cyclase 1, soluble, alpha 2	protein-coding
mm_36474.1	chr4	82850643	82850659	-	1	NA	intron (NM_026647, intron 2 of 8)	intron (NM_026647, intron 2 of 8)	9010	NM_026647	68268	Mm.32047	NM_026647	ENSMUSG00000028403	Zdhhc21	9130404H11Rik|AL024349|D130004H04Rik|dep	zinc finger, DHHC domain containing 21	protein-coding
mm_97594.1	chr11	78948295	78948306	+	1	NA	exon (NM_010927, exon 17 of 27)	exon (NM_010927, exon 17 of 27)	23009	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_74023.1	chr8	121729963	121729999	+	1	NA	promoter-TSS (NM_020605)	promoter-TSS (NM_020605)	-578	NM_020605	57340	Mm.306870	NM_020605	ENSMUSG00000025318	Jph3	JP-3|Jp3	junctophilin 3	protein-coding
mm_172748.1	chr8	83594438	83594438	-	1	NA	promoter-TSS (NM_027179)	promoter-TSS (NM_027179)	53	NM_027179	106529	Mm.352239	NM_027179	ENSMUSG00000031708	Tecr	2410016D23Rik|A230102P12Rik|AI173355|D17Ertd178e|Gpsn2|SC2	trans-2,3-enoyl-CoA reductase	protein-coding
mm_163806.1	chr14	19416046	19416057	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	186536	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_51235.1	chr6	71494056	71494073	+	1	NA	5' UTR (NM_009543, exon 1 of 4)	5' UTR (NM_009543, exon 1 of 4)	187	NM_001308303	22644	Mm.422969	NM_009543	ENSMUSG00000052656	Rnf103	AW146237|AW212918|Zfp103|kf-1	ring finger protein 103	protein-coding
mm_111694.1	chr12	103655053	103655078	-	1	NA	intron (NM_007618, intron 1 of 4)	intron (NM_007618, intron 1 of 4)	2153	NM_007618	12401	Mm.290079	NM_007618	ENSMUSG00000060807	Serpina6	Cbg	serine (or cysteine) peptidase inhibitor, clade A, member 6	protein-coding
mm_47435.1	chr5	123180687	123180698	-	1	NA	exon (NM_008277, exon 6 of 14)	exon (NM_008277, exon 6 of 14)	1994	NM_008277	15445	Mm.439709	NM_008277	ENSMUSG00000029445	Hpd	Fla|Flp|Hppd|Laf	4-hydroxyphenylpyruvic acid dioxygenase	protein-coding
mm_150526.1	chr19	39061053	39061083	+	1	NA	promoter-TSS (NM_028191)	promoter-TSS (NM_028191)	62	NM_028191	72303	Mm.482578	NM_028191	ENSMUSG00000067231	Cyp2c65	2210009K14Rik	cytochrome P450, family 2, subfamily c, polypeptide 65	protein-coding
mm_41029.1	chr5	84123213	84123217	+	1	NA	intron (NM_007937, intron 6 of 15)	intron (NM_007937, intron 6 of 15)	294167	NM_007937	13839	Mm.137991	NM_007937	ENSMUSG00000029245	Epha5	AI854630|AW125296|Cek7|Ehk1|Els1|Hek7|Rek7|bsk	Eph receptor A5	protein-coding
mm_39050.1	chr4	153482769	153482787	-	1	NA	promoter-TSS (NM_001099299)	promoter-TSS (NM_001099299)	52	NM_001099299	230959	Mm.318874	NM_001099299	ENSMUSG00000039546	Ajap1	Gm573	adherens junction associated protein 1	protein-coding
mm_123477.1	chr14	65975764	65975794	-	1	NA	exon (NM_013492, exon 5 of 9)	exon (NM_013492, exon 5 of 9)	7296	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_74888.1	chr8	25102370	25102388	-	1	NA	promoter-TSS (NM_031257)	promoter-TSS (NM_031257)	-568	NM_031257	83436	Mm.261122	NM_031257	ENSMUSG00000031557	Plekha2	6430512N22Rik|AI851530|AU041791|TAPP2|W91773	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 2	protein-coding
mm_13766.1	chr2	118559552	118559556	+	1	NA	Intergenic	Intergenic	-9868	NM_138313	171543	Mm.210125	NM_138313	ENSMUSG00000040093	Bmf	AW260063|AW411872	BCL2 modifying factor	protein-coding
mm_74288.1	chr8	125743712	125743794	+	1	NA	intron (NM_025636, intron 3 of 4)	intron (NM_025636, intron 3 of 4)	9550	NM_001310688	66566	Mm.25296	NM_025636	ENSMUSG00000031851	Ntpcr	2310079N02Rik|AI449709	nucleoside-triphosphatase, cancer-related	protein-coding
mm_144821.1	chr18	36342929	36342933	+	1	NA	Intergenic	Intergenic	-5693	NM_001081365	66060	Mm.272527	NM_001081365	ENSMUSG00000046727	Cystm1	0610010O12Rik	cysteine-rich transmembrane module containing 1	protein-coding
mm_123864.1	chr14	72539504	72539546	-	1	NA	3' UTR (NM_207636, exon 26 of 26)	3' UTR (NM_207636, exon 26 of 26)	170478	NM_207636	319448	Mm.205421	NM_207636	ENSMUSG00000033487	Fndc3a	1700094E19Rik|D14Ertd453e|F730017H24Rik|Fndc3|sys	fibronectin type III domain containing 3A	protein-coding
mm_113350.1	chr13	31806996	31807005	+	1	NA	5' UTR (NM_008592, exon 1 of 1)	5' UTR (NM_008592, exon 1 of 1)	354	NM_008592	17300	Mm.12949	NM_008592	ENSMUSG00000050295	Foxc1	FREAC3|Fkh1|Mf1|Mf4|ch|fkh-1|frkhda	forkhead box C1	protein-coding
mm_26205.1	chr3	138550572	138550616	+	1	NA	intron (NM_001313980, intron 5 of 7)	intron (NM_001313980, intron 5 of 7)	23326	NM_001313980	13684	Mm.3941	NM_007917	ENSMUSG00000028156	Eif4e	EG668879|Eif4e-ps|If4e|eIF-4E	eukaryotic translation initiation factor 4E	protein-coding
mm_59462.1	chr7	27243367	27243369	+	1	NA	exon (NM_133770, exon 10 of 15)	exon (NM_133770, exon 10 of 15)	10355	NM_133770	76889	Mm.124728	NM_133770	ENSMUSG00000003762	Coq8b	0610012P18Rik|Adck4	coenzyme Q8B	protein-coding
mm_3624.1	chr1	152766541	152766551	+	1	NA	promoter-TSS (NM_026369)	promoter-TSS (NM_026369)	4	NM_026369	67771	Mm.288974	NM_026369	ENSMUSG00000008475	Arpc5	5830443F10Rik|p16-Arc	actin related protein 2/3 complex, subunit 5	protein-coding
mm_36708.1	chr4	97584606	97584610	-	1	NA	promoter-TSS (NR_015513)	promoter-TSS (NR_015513)	-17	NR_015513	319865	Mm.373807	NM_177023		E130114P18Rik	-	RIKEN cDNA E130114P18 gene	ncRNA
mm_117972.1	chr13	100015563	100015647	-	1	NA	promoter-TSS (NM_030026)	promoter-TSS (NM_030026)	34	NM_030026	78038	Mm.137327	NM_030026	ENSMUSG00000021646	Mccc2	4930552N12Rik|MCCB	methylcrotonoyl-Coenzyme A carboxylase 2 (beta)	protein-coding
mm_153169.1	chr19	34493460	34493476	-	1	NA	3' UTR (NM_021460, exon 10 of 10)	3' UTR (NM_021460, exon 10 of 10)	-18333	NM_009890	12642	Mm.30824	NM_009890	ENSMUSG00000050370	Ch25h	AI462618|m25OH	cholesterol 25-hydroxylase	protein-coding
mm_146744.1	chr18	15760150	15760162	-	1	NA	Intergenic	CpG	-42110	NM_199055	71367	Mm.329304	NM_199055	ENSMUSG00000047161	Chst9	5430438D01Rik	carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 9	protein-coding
mm_120993.1	chr14	79397949	79397991	+	1	NA	5' UTR (NM_145960, exon 1 of 11)	5' UTR (NM_145960, exon 1 of 11)	198	NM_145960	211253	Mm.35306	NM_145960	ENSMUSG00000022022	Mtrf1	A830062K05Rik|MtRF-1	mitochondrial translational release factor 1	protein-coding
mm_80404.1	chr9	77636620	77636620	+	1	NA	promoter-TSS (NM_172925)	promoter-TSS (NM_172925)	-112	NM_172925	244923	Mm.138238	NM_172925	ENSMUSG00000044938	Klhl31	9830147P19Rik|D930047P17Rik|Kbtbd1	kelch-like 31	protein-coding
mm_117950.1	chr13	99435532	99435542	-	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-22711	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_122076.1	chr14	30604937	30604983	-	1	NA	intron (NM_011103, intron 8 of 17)	intron (NM_011103, intron 8 of 17)	5350	NM_001310682	18753	Mm.2314	NM_011103	ENSMUSG00000021948	Prkcd	AI385711|D14Ertd420e|PKC[d]|PKCdelta|Pkcd	protein kinase C, delta	protein-coding
mm_111267.1	chr12	85270613	85270643	-	1	NA	promoter-TSS (NM_001304475)	promoter-TSS (NM_001304475)	-29	NM_175337	217716	Mm.311981	NM_145446	ENSMUSG00000021245	Mlh3	AV125803|BB126472	mutL homolog 3	protein-coding
mm_145748.1	chr18	64386649	64386659	+	1	NA	3' UTR (NM_194268, exon 2 of 2)	3' UTR (NM_194268, exon 2 of 2)	46290	NM_194268	225631	Mm.234723	NM_194268	ENSMUSG00000045991	Onecut2	C730009D12|OC-2|Oc2	one cut domain, family member 2	protein-coding
mm_172654.1	chr8	36094831	36094833	+	1	NA	promoter-TSS (NM_172911)	promoter-TSS (NM_172911)	4	NM_172911	244418	Mm.244971	NM_172911	ENSMUSG00000050271	Prag1	9830148H23|D8Ertd82e|NACK|Sgk223|mFLJ00269	PEAK1 related kinase activating pseudokinase 1	protein-coding
mm_128975.1	chr15	74832499	74832506	-	1	NA	Intergenic	B1_Mus1|SINE|Alu	9141	NM_001033229	110115	Mm.322606	NM_001033229	ENSMUSG00000075604	Cyp11b1	AA389061|CPN1|Cyp11b|Cyp11b-1|FHI	cytochrome P450, family 11, subfamily b, polypeptide 1	protein-coding
mm_152362.1	chr19	10092196	10092204	-	1	NA	intron (NM_019699, intron 1 of 11)	intron (NM_019699, intron 1 of 11)	9303	NM_019699	56473	Mm.38901	NM_019699	ENSMUSG00000024665	Fads2	2900042M13Rik|Fadsd2	fatty acid desaturase 2	protein-coding
mm_117945.1	chr13	99435010	99435016	-	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-22187	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_7693.1	chr1	128747539	128747551	-	1	NA	Intergenic	RMER19B|LTR|ERVK	-155246	NM_009911	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding
mm_77467.1	chr8	122425062	122425087	-	1	NA	exon (NM_007806, exon 6 of 6)	exon (NM_007806, exon 6 of 6)	2989	NM_145834	234836	Mm.222808	NM_145834	ENSMUSG00000046108	Il17c	IL-17C	interleukin 17C	protein-coding
mm_84640.1	chr9	71168672	71168683	-	1	NA	promoter-TSS (NR_110517)	promoter-TSS (NR_110517)	-99	NR_110517	102635087	Mm.444536	NR_110517	ENSMUSG00000111429	Gm32511	-	predicted gene, 32511	ncRNA
mm_128039.1	chr15	25364827	25364838	-	1	NA	exon (NM_027395, exon 2 of 2)	exon (NM_027395, exon 2 of 2)	48932	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	brain abundant, membrane attached signal protein 1	protein-coding
mm_127091.1	chr15	97784464	97784466	+	1	NA	promoter-TSS (NM_026353)	promoter-TSS (NM_026353)	100	NM_026353	67739	Mm.28955	NM_026353	ENSMUSG00000081534	Slc48a1	4930570C03Rik	solute carrier family 48 (heme transporter), member 1	protein-coding
mm_70416.1	chr8	11458499	11458521	+	1	NA	intron (NM_011227, intron 1 of 1)	intron (NM_011227, intron 1 of 1)	-19419	NR_126558	102132	Mm.37632	NR_126558	ENSMUSG00000096957	E230013L22Rik	AI645545	RIKEN cDNA E230013L22 gene	ncRNA
mm_68813.1	chr7	125636520	125636523	-	1	NA	Intergenic	Intergenic	33092	NM_021887	60504	Mm.155643	NM_021887	ENSMUSG00000030745	Il21r	NILR	interleukin 21 receptor	protein-coding
mm_41361.1	chr5	90506640	90506665	+	1	NA	exon (NM_007423, exon 12 of 15)	exon (NM_007423, exon 12 of 15)	-12297	NM_145146	280662	Mm.348786	NM_145146	ENSMUSG00000029369	Afm	Alf|alpha-Alb	afamin	protein-coding
mm_57728.1	chr6	128945531	128945552	-	1	NA	intron (NM_027562, intron 1 of 6)	intron (NM_027562, intron 1 of 6)	11160	NM_027562	70809	Mm.439891	NM_027562	ENSMUSG00000000248	Clec2g	4632413B12Rik|Clr-c|Clr-d|Clrc|Clrd|Clrx|Ddv10|Ocilrp1	C-type lectin domain family 2, member g	protein-coding
mm_144805.1	chr18	36281390	36281402	+	1	NA	5' UTR (NM_008989, exon 1 of 2)	5' UTR (NM_008989, exon 1 of 2)	234	NM_008989	19290	Mm.231802	NM_008989	ENSMUSG00000043991	Pura	CAGER-1|Pur-alpha|ssCRE-BP	purine rich element binding protein A	protein-coding
mm_106174.1	chr11	116680076	116680086	-	1	NA	intron (NM_009180, intron 6 of 8)	intron (NM_009180, intron 6 of 8)	5484	NR_028570	100216538		NR_028570	ENSMUSG00000065094	Snord1a	snR38	small nucleolar RNA, C/D box 1A	snoRNA
mm_53097.1	chr6	125039831	125039859	+	1	NA	promoter-TSS (NM_133345)	promoter-TSS (NM_133345)	-3	NM_133345	28019	Mm.262547	NM_133345	ENSMUSG00000030330	Ing4	D6Wsu147e|D6Xrf92|p29ING4	inhibitor of growth family, member 4	protein-coding
mm_128116.1	chr15	28058920	28058922	-	1	NA	Intergenic	Intergenic	-33073	NM_001081302	223435	Mm.485422	NM_001081302	ENSMUSG00000022263	Trio	6720464I07Rik|AA408740|Solo	triple functional domain (PTPRF interacting)	protein-coding
mm_145351.1	chr18	56504701	56504708	+	1	NA	TTS (NM_026240)	TTS (NM_026240)	-33435	NR_106160	102465790		NR_106160	ENSMUSG00000099196	Mir1258	Gm27371|mmu-mir-1258	microRNA 1258	ncRNA
mm_23492.1	chr3	60505035	60505038	+	1	NA	intron (NM_001253710, intron 1 of 7)	intron (NM_001253710, intron 1 of 7)	3857	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_15825.1	chr2	164613520	164613529	+	1	NA	promoter-TSS (NM_001276432)	promoter-TSS (NM_001276432)	102	NM_001080550	277343	Mm.383292	NM_001080550	ENSMUSG00000070533	Wfdc8	Gm706	WAP four-disulfide core domain 8	protein-coding
mm_16219.1	chr2	173089902	173089904	+	1	NA	Intergenic	ID_B1|SINE|B4	29622	NM_001081387	664799	Mm.389396	NM_001081387	ENSMUSG00000070495	Ctcfl	Boris|OTTMUSG00000016680	CCCTC-binding factor (zinc finger protein)-like	protein-coding
mm_100298.1	chr11	117832240	117832267	+	1	NA	intron (NM_027827, intron 2 of 10)	intron (NM_027827, intron 2 of 10)	-6239	NM_009387	21877	Mm.2661	NM_009387	ENSMUSG00000025574	Tk1	D530002A18Rik|Tk-1|Tk1a|Tk1b	thymidine kinase 1	protein-coding
mm_130280.1	chr15	96709628	96709643	-	1	NA	Intergenic	CpG	-9937	NM_175121	67760	Mm.46754	NM_175121	ENSMUSG00000022462	Slc38a2	5033402L14Rik|AI316867|ATA2|SAT2|mKIAA1382	solute carrier family 38, member 2	protein-coding
mm_49813.1	chr6	36389409	36389419	+	1	NA	intron (NM_203491, intron 2 of 2)	intron (NM_203491, intron 2 of 2)	-1180	NR_015589	319472	Mm.226434	NR_015589	ENSMUSG00000073154	9330158H04Rik	-	RIKEN cDNA 9330158H04 gene	ncRNA
mm_97606.1	chr11	78950015	78950047	+	1	NA	exon (NM_010927, exon 20 of 27)	exon (NM_010927, exon 20 of 27)	24740	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_126027.1	chr15	76701456	76701496	+	1	NA	promoter-TSS (NM_027122)	promoter-TSS (NM_027122)	-66	NM_027122	69572	Mm.34920	NM_027122	ENSMUSG00000019080	Mfsd3	2310010G13Rik	major facilitator superfamily domain containing 3	protein-coding
mm_82869.1	chr9	32423131	32423162	-	1	NA	3' UTR (NM_008026, exon 9 of 9)	3' UTR (NM_008026, exon 9 of 9)	29161	NM_001168354	56379	Mm.390168	NM_019659	ENSMUSG00000041248	Kcnj1	Kir1.1|ROMK|Romk2	potassium inwardly-rectifying channel, subfamily J, member 1	protein-coding
mm_139169.1	chr17	47557908	47557926	+	1	NA	intron (NM_001081635, intron 1 of 6)	(TCCA)n|Simple_repeat|Simple_repeat	-35550	NM_007632	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_2276.1	chr1	91298335	91298353	+	1	NA	promoter-TSS (NM_016717)	promoter-TSS (NM_016717)	6	NM_016717	50880	Mm.25724	NM_016717	ENSMUSG00000026307	Scly	9830169H08|A930015N15Rik|SCL|Scly1|Scly2	selenocysteine lyase	protein-coding
mm_85063.1	chr9	90255933	90255943	-	1	NA	intron (NM_194334, intron 1 of 12)	intron (NM_194334, intron 1 of 12)	14831	NM_194334	67016	Mm.335347	NM_194334	ENSMUSG00000037410	Tbc1d2b	1810061M12Rik|AI480956|AV021536|AV023399|AW491493|mKIAA1055	TBC1 domain family, member 2B	protein-coding
mm_37889.1	chr4	132530785	132530828	-	1	NA	exon (NM_007512, exon 4 of 4)	exon (NM_007512, exon 4 of 4)	4608	NM_007512	11983	Mm.2171	NM_007512	ENSMUSG00000054428	Atpif1	Atpi|IF(1)|If1	ATPase inhibitory factor 1	protein-coding
mm_93371.1	chr10	105315703	105315709	-	1	NA	intron (NM_177368, intron 7 of 11)	intron (NM_177368, intron 7 of 11)	258773	NM_177368	278279	Mm.25225	NM_177368	ENSMUSG00000036019	Tmtc2	8430438D04Rik|D330034A10Rik	transmembrane and tetratricopeptide repeat containing 2	protein-coding
mm_157092.1	chrX	9437175	9437175	-	1	NA	3' UTR (NM_007807, exon 13 of 13)	3' UTR (NM_007807, exon 13 of 13)	32149	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_131387.1	chr16	14207687	14207728	+	1	NA	exon (NM_013607, exon 31 of 42)	exon (NM_013607, exon 31 of 42)	44432	NM_001114085	67203	Mm.24105	NM_023317	ENSMUSG00000022678	Nde1	2810027M15Rik|AU042936|AW822251|Nude|mNudE	nudE neurodevelopment protein 1	protein-coding
mm_49641.1	chr6	30805428	30805442	+	1	NA	intron (NM_017478, intron 20 of 23)	intron (NM_017478, intron 20 of 23)	64136	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_47214.1	chr5	121009511	121009521	-	1	NA	promoter-TSS (NM_011286)	promoter-TSS (NM_011286)	22	NM_011286	19894	Mm.181166	NM_011286	ENSMUSG00000029608	Rph3a	2900002P20Rik|AU022689|AW108370	rabphilin 3A	protein-coding
mm_68316.1	chr7	106117301	106117324	-	1	NA	Intergenic	Intergenic	-38164	NR_030719	668108	Mm.429088	NR_030719		Gm8979	EG668108|Gm21884	very large inducible GTPase 1 pseudogene	pseudo
mm_30953.1	chr4	33248664	33248683	+	1	NA	5' UTR (NM_001033225, exon 1 of 2)	5' UTR (NM_001033225, exon 1 of 2)	114	NM_001033225	108767	Mm.27769	NM_001033225	ENSMUSG00000040128	Pnrc1	5730463C12Rik|B4-2|PRR2|Prol2	proline-rich nuclear receptor coactivator 1	protein-coding
mm_151682.1	chr19	4269141	4269200	-	1	NA	promoter-TSS (NM_198113)	promoter-TSS (NM_198113)	2	NM_198113	245857	Mm.248388	NM_198113	ENSMUSG00000034616	Ssh3	BC028922|SSH-3|mSSH-3L	slingshot homolog 3 (Drosophila)	protein-coding
mm_67138.1	chr7	73105161	73105170	-	1	NA	Intergenic	Intergenic	-3097	NR_046024	625243	Mm.261798	NR_046024	ENSMUSG00000108383	Gm6567	-	predicted gene 6567	ncRNA
mm_105694.1	chr11	107794742	107794755	-	1	NA	promoter-TSS (NM_019431)	promoter-TSS (NM_019431)	-284	NM_019431	54377	Mm.103724	NM_019431	ENSMUSG00000020723	Cacng4	AI413107|AW491861	calcium channel, voltage-dependent, gamma subunit 4	protein-coding
mm_165311.1	chr2	102948025	102948060	+	1	NA	Intergenic	ERV3-16A3_LTR|LTR|ERVL	-46377	NM_001039150	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_62616.1	chr7	107209385	107209404	+	1	NA	promoter-TSS (NM_029660)	promoter-TSS (NM_029660)	-51	NM_029660	76572	Mm.128134	NM_029660	ENSMUSG00000073894	Rbmxl2	1700012H05Rik|Hnrnpg-t	RNA binding motif protein, X-linked-like 2	protein-coding
mm_146527.1	chr18	5273258	5273276	-	1	NA	intron (NM_178722, intron 2 of 4)	intron (NM_178722, intron 2 of 4)	61172	NM_178722	240186	Mm.118257	NM_178722	ENSMUSG00000050945	Zfp438	9430031G09|9430091M14Rik|B830013J05Rik	zinc finger protein 438	protein-coding
mm_97030.1	chr11	72266410	72266423	+	1	NA	promoter-TSS (NR_045922)	promoter-TSS (NR_045922)	188	NM_001004148	237831	Mm.340778	NM_001004148	ENSMUSG00000020805	Slc13a5	Indy|NaC2/NaCT|Nact|mINDY	solute carrier family 13 (sodium-dependent citrate transporter), member 5	protein-coding
mm_158771.1	chrX	166618677	166618683	-	1	NA	Intergenic	MLTR25A|LTR|ERVK	-32964	NM_019397	54156	Mm.37707	NM_019397	ENSMUSG00000000402	Egfl6	Maeg	EGF-like-domain, multiple 6	protein-coding
mm_116707.1	chr13	51015180	51015184	-	1	NA	Intergenic	Intergenic	85545	NR_029463	77428	Mm.405630	NR_029463		9430083A17Rik	-	RIKEN cDNA 9430083A17 gene	ncRNA
mm_69950.1	chr7	142371102	142371110	-	1	NA	exon (NM_001347541, exon 2 of 3)	exon (NM_001347541, exon 2 of 3)	1153	NM_177265	320802	Mm.154486	NM_177265	ENSMUSG00000045777	Ifitm10	6330512M04Rik|AI848576|DSPA3	interferon induced transmembrane protein 10	protein-coding
mm_142528.1	chr17	46438416	46438424	-	1	NA	promoter-TSS (NM_144856)	promoter-TSS (NM_144856)	57	NM_144856	108114	Mm.387538	NM_144856	ENSMUSG00000067144	Slc22a7	NLT|OAT2	solute carrier family 22 (organic anion transporter), member 7	protein-coding
mm_121885.1	chr14	21740396	21740420	-	1	NA	intron (NM_001007268, intron 5 of 7)	intron (NM_001007268, intron 5 of 7)	2471	NM_013849	27389	Mm.390674	NM_013849	ENSMUSG00000021768	Dusp13	DUSP13A|DUSP13B|Gm1203|LMW-DSP6|MDSP|TMDP|TS-DSP6	dual specificity phosphatase 13	protein-coding
mm_148873.1	chr19	6497773	6497845	+	1	NA	intron (NM_001205234, intron 17 of 22)	CpG	45261	NM_009203	20521	Mm.391146	NM_009203	ENSMUSG00000061742	Slc22a12	AI987855|OAT4L|Rst|Slc22al2|URAT1	solute carrier family 22 (organic anion/cation transporter), member 12	protein-coding
mm_50500.1	chr6	49036014	49036038	+	1	NA	promoter-TSS (NM_053110)	promoter-TSS (NM_053110)	-492	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_20673.1	chr2	132253078	132253103	-	1	NA	promoter-TSS (NM_011045)	promoter-TSS (NM_011045)	90	NM_011045	18538	Mm.7141	NM_011045	ENSMUSG00000027342	Pcna	-	proliferating cell nuclear antigen	protein-coding
mm_68173.1	chr7	103826589	103826707	-	1	NA	3' UTR (NM_001278161, exon 3 of 3)	3' UTR (NM_001278161, exon 3 of 3)	1280	NM_001201391	100503605	Mm.288567	NM_001201391	ENSMUSG00000052305	Hbb-bs	Beta-s|Hbbt1|Hbbt2	hemoglobin, beta adult s chain	protein-coding
mm_127407.1	chr15	101247402	101247412	+	1	NA	Intergenic	Intergenic	-19439	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_60331.1	chr7	44310191	44310205	+	1	NA	promoter-TSS (NM_001034115)	promoter-TSS (NM_001034115)	-66	NM_001034115	243961	Mm.360368	NM_001034115	ENSMUSG00000038738	Shank1	-	SH3/ankyrin domain gene 1	protein-coding
mm_41090.1	chr5	87694515	87694526	+	1	NA	exon (NM_001286023, exon 5 of 7)	exon (NM_001286023, exon 5 of 7)	4905	NM_001286020	12991	Mm.268737	NM_009972	ENSMUSG00000063157	Csn2	Csnb	casein beta	protein-coding
mm_103168.1	chr11	70459502	70459514	-	1	NA	promoter-TSS (NM_001029929)	promoter-TSS (NM_001029929)	-114	NM_001029929	574428	Mm.472771	NM_001029929	ENSMUSG00000040829	Zmynd15	-	zinc finger, MYND-type containing 15	protein-coding
mm_3389.1	chr1	140381532	140381534	+	1	NA	intron (NM_001081027, intron 7 of 27)	intron (NM_001081027, intron 7 of 27)	135276	NM_001081027	240776	Mm.483845	NM_001081027	ENSMUSG00000052726	Kcnt2	E330038N15Rik|Slick	potassium channel, subfamily T, member 2	protein-coding
mm_75411.1	chr8	46471640	46471651	-	1	NA	intron (NM_007981, intron 1 of 20)	CpG	608	NM_007981	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_60299.1	chr7	44016283	44016305	+	1	NA	exon (NM_010644, exon 4 of 5)	exon (NM_010644, exon 4 of 5)	3597	NM_010115	13647	Mm.439663	NM_010115		Egfbp2	Egfbp-2|Klk1b26|mGk-13	epidermal growth factor binding protein type B	protein-coding
mm_70253.1	chr8	3500452	3500524	+	1	NA	promoter-TSS (NM_053177)	promoter-TSS (NM_053177)	-31	NM_053177	94178	Mm.8356	NM_053177	ENSMUSG00000004567	Mcoln1	2210015I05Rik|TRPML1|mucolipidin	mucolipin 1	protein-coding
mm_37705.1	chr4	129377934	129377950	-	1	NA	promoter-TSS (NM_028603)	promoter-TSS (NM_028603)	86	NM_028603	73680	Mm.32997	NM_028603	ENSMUSG00000028807	Zbtb8a	2410081M15Rik|AI480941	zinc finger and BTB domain containing 8a	protein-coding
mm_83369.1	chr9	44454758	44454773	-	1	NA	promoter-TSS (NM_009476)	promoter-TSS (NM_009476)	2	NM_009476	22269	Mm.4453	NM_009476	ENSMUSG00000041523	Upk2	AW491716|UPII	uroplakin 2	protein-coding
mm_142787.1	chr17	50164092	50164111	-	1	NA	intron (NM_181397, intron 2 of 9)	RLTR17B_Mm|LTR|ERVK	26396	NM_181397	76438	Mm.41854	NM_181397	ENSMUSG00000039316	Rftn1	2310015N21Rik|AI853526	raftlin lipid raft linker 1	protein-coding
mm_4562.1	chr1	177447278	177447291	+	1	NA	exon (NM_013915, exon 1 of 1)	exon (NM_013915, exon 1 of 1)	1463	NM_013915	30928	Mm.330700	NM_013915	ENSMUSG00000063659	Zbtb18	RP58|Zfp238|Znf238	zinc finger and BTB domain containing 18	protein-coding
mm_38346.1	chr4	137769963	137769967	-	1	NA	intron (NM_007431, intron 1 of 11)	intron (NM_007431, intron 1 of 11)	-3490	NM_001287172	11647	Mm.288186	NM_007431	ENSMUSG00000028766	Alpl	ALP|APTNAP|Akp-2|Akp2|TNAP|TNSALP	alkaline phosphatase, liver/bone/kidney	protein-coding
mm_112500.1	chr13	8202923	8202935	+	1	NA	promoter-TSS (NM_001289530)	promoter-TSS (NM_001289530)	63	NM_052977	94191	Mm.425794	NM_052977	ENSMUSG00000052551	Adarb2	Adar3|RED2	adenosine deaminase, RNA-specific, B2	protein-coding
mm_171836.1	chr5	149052902	149052905	-	1	NA	5' UTR (NM_010439, exon 1 of 5)	5' UTR (NM_010439, exon 1 of 5)	154	NM_010439	15289	Mm.207047	NM_010439	ENSMUSG00000066551	Hmgb1	HMG-1|Hmg1|SBP-1|p30	high mobility group box 1	protein-coding
mm_141526.1	chr17	31811455	31811465	-	1	NA	Intergenic	Intergenic	44332	NM_010831	17691	Mm.290941	NM_010831	ENSMUSG00000024042	Sik1	Msk|Sik|Snf1lk	salt inducible kinase 1	protein-coding
mm_123295.1	chr14	61609868	61609870	-	1	NA	intron (NM_206974, intron 1 of 1)	AT_rich|Low_complexity|Low_complexity	2412	NM_001039105	328424	Mm.224464	NM_206974	ENSMUSG00000046168	Kcnrg	Clld4|E030012H22Rik|Gm745	potassium channel regulator	protein-coding
mm_55541.1	chr6	70792037	70792049	-	1	NA	exon (NM_009075, exon 1 of 9)	exon (NM_009075, exon 1 of 9)	132	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_142373.1	chr17	44658585	44658590	-	1	NA	exon (NM_009820, exon 6 of 9)	exon (NM_009820, exon 6 of 9)	77589	NR_073425	12393	Mm.391013	NM_009820	ENSMUSG00000039153	Runx2	AML3|Cbf|Cbfa-1|Cbfa1|LS3|Osf2|PEBP2aA|Pebp2a1|Pebpa2a	runt related transcription factor 2	protein-coding
mm_167879.1	chrX	42227567	42227570	+	1	NA	intron (NM_001077712, intron 9 of 32)	AT_rich|Low_complexity|Low_complexity	25713	NM_001290713	20843	Mm.290422	NM_021465	ENSMUSG00000025862	Stag2	9230105L23Rik|B230112I07Rik|SA-2|SAP2	stromal antigen 2	protein-coding
mm_8348.1	chr1	150197510	150197527	-	1	NA	Intergenic	Intergenic	-32570	NR_110420	102639566	Mm.417208	NR_110420	ENSMUSG00000097754	Ptgs2os2	Gm26687|Linc-cox2|Lincrna-cox2	prostaglandin-endoperoxide synthase 2, opposite strand 2	ncRNA
mm_144101.1	chr18	3507918	3507943	+	1	NA	promoter-TSS (NM_026505)	promoter-TSS (NM_026505)	-27	NM_026505	68010	Mm.284863	NM_026505	ENSMUSG00000024232	Bambi	2610003H06Rik	BMP and activin membrane-bound inhibitor	protein-coding
mm_73448.1	chr8	106282241	106282247	+	1	NA	promoter-TSS (NR_126090)	promoter-TSS (NR_126090)	15	NR_126090	75044	Mm.445896	NR_126090		4930506A18Rik	-	RIKEN cDNA 4930506A18 gene	ncRNA
mm_162074.1	chrX	20617567	20617567	-	1	NA	promoter-TSS (NM_145627)	promoter-TSS (NM_145627)	-3	NM_019435	104130	Mm.30084	NM_019435	ENSMUSG00000031059	Ndufb11	D5Bwg0566e|D5Bwg0577e|NP15.6|Np15	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 11	protein-coding
mm_41597.1	chr5	95973921	95973924	+	1	NA	Intergenic	Intergenic	16983	NM_018866	55985	Mm.10116	NM_018866	ENSMUSG00000023078	Cxcl13	4631412M08Rik|ANGIE2|Angie|BCA-1|BLC|BLR1L|Scyb13	chemokine (C-X-C motif) ligand 13	protein-coding
mm_163039.1	chr11	53350976	53350984	+	1	NA	5' UTR (NM_033565, exon 1 of 21)	5' UTR (NM_033565, exon 1 of 21)	213	NM_033565	93736	Mm.395281	NM_033565	ENSMUSG00000049470	Aff4	AF5Q31|Alf4|Laf4l|MCEF	AF4/FMR2 family, member 4	protein-coding
mm_18962.1	chr2	76798430	76798442	-	1	NA	exon (NM_011652, exon 196 of 313)	exon (NM_011652, exon 196 of 313)	123121	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_7232.1	chr1	93429401	93429418	-	1	NA	exon (NM_133808, exon 9 of 28)	exon (NM_133808, exon 9 of 28)	16292	NM_001301364	110611	Mm.30012	NM_133808	ENSMUSG00000034088	Hdlbp	1110005P14Rik|AA960365|AI118566|D1Ertd101e	high density lipoprotein (HDL) binding protein	protein-coding
mm_7190.1	chr1	92906861	92906887	-	1	NA	promoter-TSS (NM_175118)	promoter-TSS (NM_175118)	-115	NM_175118	67446	Mm.46179	NM_175118	ENSMUSG00000047067	Dusp28	0710001B24Rik|AV005521	dual specificity phosphatase 28	protein-coding
mm_166397.1	chr5	135053406	135053428	-	1	NA	exon (NM_025375, exon 13 of 13)	exon (NM_025375, exon 13 of 13)	-10789	NM_025362	66114	Mm.178012	NM_025362	ENSMUSG00000061118	Dnajc30	1300007M11Rik|Wbscr18	DnaJ heat shock protein family (Hsp40) member C30	protein-coding
mm_29628.1	chr3	121548143	121548144	-	1	NA	Intergenic	Intergenic	-15799	NM_145394	213603	Mm.33062	NM_145394	ENSMUSG00000039865	Slc44a3	BC010552	solute carrier family 44, member 3	protein-coding
mm_107458.1	chr12	37241621	37241631	+	1	NA	promoter-TSS (NM_178767)	promoter-TSS (NM_178767)	-13	NM_178767	319660	Mm.485540	NM_178767	ENSMUSG00000050103	Agmo	A530016O06Rik|AI790538|Tmem195	alkylglycerol monooxygenase	protein-coding
mm_105663.1	chr11	107387801	107387822	-	1	NA	intron (NM_145823, intron 1 of 9)	B3|SINE|B2	82909	NM_145823	71795	Mm.397413	NM_145823	ENSMUSG00000040430	Pitpnc1	1110020B03Rik|5830436L09Rik|AI662802|AI851387|C330017I21Rik|Dnr411|RDGBB|RDGBB1|rdgB-beta	phosphatidylinositol transfer protein, cytoplasmic 1	protein-coding
mm_69713.1	chr7	140137533	140137561	-	1	NA	promoter-TSS (NM_199301)	promoter-TSS (NM_199301)	-17	NM_199301	212508	Mm.296088	NM_199301	ENSMUSG00000039018	Mtg1	Gm169|Gtpbp7	mitochondrial ribosome-associated GTPase 1	protein-coding
mm_46657.1	chr5	108674788	108674802	-	1	NA	promoter-TSS (NM_001310692)	promoter-TSS (NM_001310692)	1	NM_001310692	231583	Mm.440571	NM_174870	ENSMUSG00000046959	Slc26a1	Sat1	solute carrier family 26 (sulfate transporter), member 1	protein-coding
mm_12355.1	chr2	69749592	69749605	+	1	NA	exon (NM_001081086, exon 14 of 14)	exon (NM_001081086, exon 14 of 14)	26510	NM_001081086	228005	Mm.11815	NM_001081086	ENSMUSG00000042133	Ppig	AU019516|AU022200|B230312B02Rik|CYP|SRCyp	peptidyl-prolyl isomerase G (cyclophilin G)	protein-coding
mm_9371.1	chr1	172206685	172206755	-	1	NA	promoter-TSS (NM_001329871)	promoter-TSS (NM_001329871)	84	NM_001329871	18611	Mm.544	NM_011063	ENSMUSG00000013698	Pea15a	Mat1|PEA-15|Pea15|Pkcs15	phosphoprotein enriched in astrocytes 15A	protein-coding
mm_39302.1	chr5	7179300	7179302	+	1	NA	intron (NM_001163223, intron 1 of 3)	intron (NM_001163223, intron 1 of 3)	-124863	NM_027603	70920	Mm.158494	NM_027603	ENSMUSG00000040514	4921511H03Rik	-	RIKEN cDNA 4921511H03 gene	protein-coding
mm_81320.1	chr9	108479924	108479935	+	1	NA	promoter-TSS (NM_008483)	promoter-TSS (NM_008483)	67	NM_008483	16779	Mm.27560	NM_008483	ENSMUSG00000052911	Lamb2	AW211941|Lamb-2|Lams|npht	laminin, beta 2	protein-coding
mm_7260.1	chr1	93825464	93825490	-	1	NA	5' UTR (NM_001310767, exon 1 of 10)	5' UTR (NM_001310767, exon 1 of 10)	237	NM_001310767	98314	Mm.383401	NM_178882	ENSMUSG00000073609	D2hgdh	AA408776|AA408778|AI325464	D-2-hydroxyglutarate dehydrogenase	protein-coding
mm_127192.1	chr15	99030857	99030868	+	1	NA	intron (NM_009448, intron 1 of 3)	intron (NM_009448, intron 1 of 3)	971	NM_009448	22146	Mm.88212	NM_009448	ENSMUSG00000043091	Tuba1c	M[a]6|Tuba6	tubulin, alpha 1C	protein-coding
mm_51772.1	chr6	88075366	88075397	+	1	NA	Intergenic	Intergenic	-9092	NM_133933	103963	Mm.188544	NM_133933	ENSMUSG00000030062	Rpn1	AU018702|D6Wsu137e|Rpn-1	ribophorin I	protein-coding
mm_39009.1	chr4	152033754	152033760	-	1	NA	intron (NM_031867, intron 2 of 5)	intron (NM_031867, intron 2 of 5)	4733	NM_031867	110326	Mm.29232	NM_031867	ENSMUSG00000028950	Tas1r1	Gpr70|T1r1|TR1	taste receptor, type 1, member 1	protein-coding
mm_157447.1	chrX	41843274	41843277	-	1	NA	intron (NM_001033422, intron 15 of 38)	intron (NM_001033422, intron 15 of 38)	68626	NM_001033422	331401	Mm.259498	NM_001033422	ENSMUSG00000037475	Thoc2	6330441O12Rik|D130005M13Rik|Gm1139|Gm1793|Tho2	THO complex 2	protein-coding
mm_156717.1	chrX	159701350	159701354	+	1	NA	intron (NM_001135727, intron 2 of 17)	intron (NM_001135727, intron 2 of 17)	-7249	NM_021389	58194	Mm.286495	NM_021389	ENSMUSG00000040990	Sh3kbp1	1200007H22Rik|1700125L08Rik|5830464D22Rik|AI447724|Cin85|IN85|Ruk|Seta	SH3-domain kinase binding protein 1	protein-coding
mm_76710.1	chr8	94601633	94601708	-	1	NA	promoter-TSS (NM_028221)	promoter-TSS (NM_028221)	56	NM_028221	102122	Mm.250425	NM_028221	ENSMUSG00000031774	Fam192a	1700001O11Rik|2310065K24Rik|AI596259|Nip30	family with sequence similarity 192, member A	protein-coding
mm_102548.1	chr11	61342810	61342814	-	1	NA	promoter-TSS (NM_001033542)	promoter-TSS (NM_001033542)	48	NM_001033542	380701	Mm.340166	NM_001033542	ENSMUSG00000069855	Slc47a2	4933429E10Rik	solute carrier family 47, member 2	protein-coding
mm_93398.1	chr10	107643563	107643571	-	1	NA	exon (NM_001081432, exon 22 of 45)	exon (NM_001081432, exon 22 of 45)	76460	NM_001081432	237523	Mm.391418	NM_001081432	ENSMUSG00000035916	Ptprq	-	protein tyrosine phosphatase, receptor type, Q	protein-coding
mm_88470.1	chr10	77582388	77582431	+	1	NA	intron (NM_145925, intron 1 of 5)	intron (NM_145925, intron 1 of 5)	642	NM_145925	108705	Mm.28853	NM_145925	ENSMUSG00000009291	Pttg1ip	1810010L20Rik|AI314311|AU018448|C79540	pituitary tumor-transforming 1 interacting protein	protein-coding
mm_37296.1	chr4	119189984	119190003	-	1	NA	promoter-TSS (NM_013848)	promoter-TSS (NM_013848)	18	NM_013848	27028	Mm.290753	NM_013848	ENSMUSG00000028644	Ermap	AA409279|AI666418	erythroblast membrane-associated protein	protein-coding
mm_15642.1	chr2	163059209	163059219	+	1	NA	intron (NM_008652, intron 1 of 13)	B1_Mur3|SINE|Alu	4579	NM_008652	17865	Mm.4594	NM_008652	ENSMUSG00000017861	Mybl2	B-Myb|Bmyb	myeloblastosis oncogene-like 2	protein-coding
mm_101948.1	chr11	50238452	50238469	-	1	NA	promoter-TSS (NM_001313968)	promoter-TSS (NM_001313968)	72	NM_001313968	17001	Mm.245151	NM_008521	ENSMUSG00000020377	Ltc4s	-	leukotriene C4 synthase	protein-coding
mm_160809.1	chr11	17151139	17151139	+	1	NA	Intergenic	Intergenic	-8159	NM_024459	19058	Mm.41840	NM_024459	ENSMUSG00000033953	Ppp3r1	CaNB1|Cnb1|MCIP1	protein phosphatase 3, regulatory subunit B, alpha isoform (calcineurin B, type I)	protein-coding
mm_9514.1	chr1	173741796	173741817	-	1	NA	promoter-TSS (NM_001204910)	promoter-TSS (NM_001204910)	3	NM_001204910	226691	Mm.440876	NM_001204910	ENSMUSG00000073490	Ifi207	AI607873|Pyhin-A	interferon activated gene 207	protein-coding
mm_154342.1	chrM	4871	4907	+	1	NA	NA	Intergenic	NA	NA								
mm_11556.1	chr2	32741453	32741499	+	1	NA	promoter-TSS (NM_027529)	promoter-TSS (NM_027529)	-460	NM_027529	70730	Mm.401360	NM_027529	ENSMUSG00000009551	6330409D20Rik	AA517851	RIKEN cDNA 6330409D20 gene	protein-coding
mm_137771.1	chr17	29490905	29490915	+	1	NA	promoter-TSS (NM_008842)	promoter-TSS (NM_008842)	-135	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_117157.1	chr13	61570098	61570109	-	1	NA	promoter-TSS (NM_054092)	promoter-TSS (NM_054092)	24	NM_026906	117066	Mm.485905	NM_026906	ENSMUSG00000074870	Cts3	1600000I23Rik	cathepsin 3	protein-coding
mm_14726.1	chr2	144033128	144033134	+	1	NA	promoter-TSS (NM_207275)	promoter-TSS (NM_207275)	29	NM_207275	403171	Mm.389362	NM_207275	ENSMUSG00000037307	Banf2	4930517K23Rik|Baf-L|Baf-like|Gm115	barrier to autointegration factor 2	protein-coding
mm_172701.1	chr8	63933338	63933338	-	1	NA	intron (NM_001195687, intron 5 of 7)	intron (NM_001195687, intron 5 of 7)	18832	NM_001195687	244495	Mm.485331	NM_001195687	ENSMUSG00000094443	Sgol2b	EG244495|Gm4975|Sgo2B	shugoshin like 2b (S. pombe)	protein-coding
mm_172399.1	chr7	142141014	142141033	+	1	NA	Intergenic	BGLII|LTR|ERVK	-4940	NM_001347556	105243089		NM_001347556	ENSMUSG00000110091	Gm39115	-	predicted gene, 39115	protein-coding
mm_167788.1	chr9	123043058	123043087	+	1	NA	intron (NM_177911, intron 3 of 13)	intron (NM_177911, intron 3 of 13)	8331	NM_177911	331046	Mm.195309	NM_177911	ENSMUSG00000025787	Tgm4	9530008N10Rik|Eapa1|TGP	transglutaminase 4 (prostate)	protein-coding
mm_125056.1	chr15	25910353	25910383	+	1	NA	intron (NM_001034851, intron 3 of 8)	intron (NM_001034851, intron 3 of 8)	-23184	NM_001277318	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_42450.1	chr5	115435041	115435064	+	1	NA	intron (NM_008629, intron 5 of 14)	intron (NM_008629, intron 5 of 14)	5367	NM_008629	17690	Mm.5077	NM_008629	ENSMUSG00000054256	Msi1	Msi1h|Musahi1|m-Msi-1	musashi RNA-binding protein 1	protein-coding
mm_143492.1	chr17	71455669	71455685	-	1	NA	exon (NM_028887, exon 5 of 48)	exon (NM_028887, exon 5 of 48)	19666	NM_028887	74355	Mm.194450	NM_028887	ENSMUSG00000024054	Smchd1	4931400A14Rik|AW554188|MommeD1|mKIAA0650	SMC hinge domain containing 1	protein-coding
mm_4537.1	chr1	176779226	176779227	+	1	NA	intron (NM_001099637, intron 7 of 19)	intron (NM_001099637, intron 7 of 19)	-6803	NR_029775	723921		NR_029775	ENSMUSG00000065573	Mir350	Mirn350|mir-350|mmu-mir-350	microRNA 350	ncRNA
mm_100183.1	chr11	116657107	116657117	+	1	NA	promoter-TSS (NM_001163318)	promoter-TSS (NM_001163318)	4	NM_001163318	100038570	Mm.390349	NM_001163318	ENSMUSG00000075410	Prcd	Gm11744|OTTMUSG00000003947	progressive rod cone degeneration protein	protein-coding
mm_37229.1	chr4	117964722	117964739	-	1	NA	intron (NM_009176, intron 5 of 11)	intron (NM_009176, intron 5 of 11)	-34967	NM_001284192	11876	Mm.56897	NM_009711	ENSMUSG00000028539	Artn	neublastin	artemin	protein-coding
mm_143321.1	chr17	66345417	66345425	-	1	NA	intron (NM_001114098, intron 12 of 14)	intron (NM_001114098, intron 12 of 14)	104329	NM_172963	68617	Mm.33421	NM_172963	ENSMUSG00000052105	Mtcl1	1110012J17Rik|Ccdc165|D130071O13|Kiaa0802|Soga2|mKIAA0802|t8219b25	microtubule crosslinking factor 1	protein-coding
mm_123038.1	chr14	55578824	55578841	-	1	NA	intron (NM_011189, intron 1 of 10)	intron (NM_011189, intron 1 of 10)	338	NM_011189	19186	Mm.830	NM_011189	ENSMUSG00000022216	Psme1	AW413925|PA28a	proteasome (prosome, macropain) activator subunit 1 (PA28 alpha)	protein-coding
mm_133662.1	chr16	91867903	91867944	+	1	NA	intron (NM_001110275, intron 26 of 28)	intron (NM_001110275, intron 26 of 28)	63707	NM_138597	28080	Mm.41	NM_138597	ENSMUSG00000022956	Atp5o	ATPO|D12Wsu28e|OSCP	ATP synthase, H+ transporting, mitochondrial F1 complex, O subunit	protein-coding
mm_11577.1	chr2	32916640	32916659	+	1	NA	intron (NM_146119, intron 5 of 13)	intron (NM_146119, intron 5 of 13)	40515	NM_146119	227737	Mm.301646	NM_146119	ENSMUSG00000026796	Fam129b	9130404D14Rik	family with sequence similarity 129, member B	protein-coding
mm_1728.1	chr1	75381632	75381650	+	1	NA	promoter-TSS (NM_001085371)	promoter-TSS (NM_001085371)	-473	NM_001085371	11790	Mm.275397	NM_007463	ENSMUSG00000026207	Speg	AW125581|Apeg1|BPEG|D1Bwg1450e|SPEGalpha|SPEGbeta|mKIAA1297	SPEG complex locus	protein-coding
mm_76380.1	chr8	84838627	84838687	-	1	NA	intron (NM_009010, intron 2 of 8)	intron (NM_009010, intron 2 of 8)	2008	NM_001297607	19358	Mm.255539	NM_009010	ENSMUSG00000003813	Rad23a	2310040P19Rik|AL024030|HR23A|mHR23A	RAD23 homolog A, nucleotide excision repair protein	protein-coding
mm_169273.1	chr13	8937987	8937989	+	1	NA	Intergenic	RLTR9E|LTR|ERVK	-14875	NM_177197	320581	Mm.313743	NM_177197	ENSMUSG00000033520	Idi2	4833405L16Rik|IPPI2	isopentenyl-diphosphate delta isomerase 2	protein-coding
mm_58362.1	chr6	148444292	148444303	-	1	NA	promoter-TSS (NM_198967)	promoter-TSS (NM_198967)	55	NM_001347518	387314	Mm.137858	NM_198967	ENSMUSG00000030306	Tmtc1	Arg99|BC023818	transmembrane and tetratricopeptide repeat containing 1	protein-coding
mm_30353.1	chr3	151762459	151762470	-	1	NA	intron (NM_031367, intron 1 of 4)	intron (NM_031367, intron 1 of 4)	427	NM_031367	15061	Mm.219544	NM_031367	ENSMUSG00000039146	Ifi44l	H-28|H28|H28-1|NS1178	interferon-induced protein 44 like	protein-coding
mm_112317.1	chr12	114991577	114991582	-	1	NA	Intergenic	Intergenic	-477885	NR_106063	102465664		NR_106063	ENSMUSG00000098357	Mir7094-2	Gm27508|mmu-mir-7094-2	microRNA 7094-2	ncRNA
mm_76098.1	chr8	80292278	80292279	-	1	NA	Intergenic	Intergenic	-201767	NM_010369	14934	Mm.13123	NM_010369	ENSMUSG00000051839	Gypa	AI853584|CD235a|GPA	glycophorin A	protein-coding
mm_146326.1	chr18	80707273	80707286	+	1	NA	intron (NM_198429, intron 1 of 9)	intron (NM_198429, intron 1 of 9)	894	NM_001164111	18018	Mm.329560	NM_016791	ENSMUSG00000033016	Nfatc1	2210017P03Rik|AI449492|AV076380|NF-ATc|NFAT2|NFATc|Nfatcb	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 1	protein-coding
mm_130911.1	chr15	102524616	102524619	-	1	NA	promoter-TSS (NM_018787)	promoter-TSS (NM_018787)	4	NM_018787	54615	Mm.445915	NM_018787	ENSMUSG00000023052	Npff	-	neuropeptide FF-amide peptide precursor	protein-coding
mm_119394.1	chr14	41137837	41137851	+	1	NA	Intergenic	Intergenic	6056	NM_023134	20387	Mm.46062	NM_023134	ENSMUSG00000021789	Sftpa1	SP-A|Sftp-1|Sftp1	surfactant associated protein A1	protein-coding
mm_153782.1	chr19	45783792	45783813	-	1	NA	promoter-TSS (NM_023799)	promoter-TSS (NM_023799)	-511	NM_023799	76055	Mm.122725	NM_023799	ENSMUSG00000025220	Mgea5	2810009A20Rik|4833427O07Rik|5830447M11Rik|AA408215|Hy5|Ncoat|OGA|mKIAA0679	meningioma expressed antigen 5 (hyaluronidase)	protein-coding
mm_110803.1	chr12	72212413	72212422	-	1	NA	non-coding (NR_104446, exon 7 of 7)	non-coding (NR_104446, exon 7 of 7)	23329	NR_104446	104001	Mm.221275	NM_153457	ENSMUSG00000021087	Rtn1	Nsp	reticulon 1	protein-coding
mm_169611.1	chr15	37344744	37344744	+	1	NA	exon (NM_026496, exon 13 of 16)	exon (NM_026496, exon 13 of 16)	-80810	NM_029113	74892	Mm.107630	NM_029113	ENSMUSG00000022288	4930447A16Rik	-	RIKEN cDNA 4930447A16 gene	protein-coding
mm_48890.1	chr5	151368477	151368489	-	1	NA	promoter-TSS (NR_045700)	promoter-TSS (NR_045700)	-192	NR_045700	625175	Mm.443286	NR_045699	ENSMUSG00000097321	1700028E10Rik	A630054D14|Gm6561	RIKEN cDNA 1700028E10 gene	ncRNA
mm_85448.1	chr9	104300084	104300096	-	1	NA	3' UTR (NM_019807, exon 11 of 11)	3' UTR (NM_019807, exon 11 of 11)	-37160	NM_001163026	235567	Mm.217256	NM_001163026	ENSMUSG00000032560	Dnajc13	D030002L11Rik|Gm1124|RME-8|Rme8|mKIAA0678	DnaJ heat shock protein family (Hsp40) member C13	protein-coding
mm_157874.1	chrX	75578189	75578247	-	1	NA	promoter-TSS (NM_175122)	promoter-TSS (NM_175122)	13	NM_175122	67790	Mm.45148	NM_175122	ENSMUSG00000031202	Rab39b	6330580M05Rik	RAB39B, member RAS oncogene family	protein-coding
mm_74418.1	chr8	3625275	3625288	-	1	NA	promoter-TSS (NM_001129804)	promoter-TSS (NM_001129804)	1	NM_008790	18545	Mm.440882	NM_008790	ENSMUSG00000004630	Pcp2	L7|Pcp-2	Purkinje cell protein 2 (L7)	protein-coding
mm_171313.1	chr3	95357109	95357110	-	1	NA	promoter-TSS (NM_001163642)	promoter-TSS (NM_001163642)	93	NM_001163641	84505	Mm.490259	NM_018877	ENSMUSG00000015697	Setdb1	AU022152|ESET|KMT1E|mKIAA0067	SET domain, bifurcated 1	protein-coding
mm_54320.1	chr6	30302615	30302619	-	1	NA	intron (NM_001169576, intron 1 of 4)	intron (NM_001169576, intron 1 of 4)	1922	NM_009459	22214	Mm.332967	NM_009459	ENSMUSG00000039159	Ube2h	1500009C23Rik|AI181839|AI326965|AI462483|AW227540|E2-20K|Gid3|N28148|Ubc8	ubiquitin-conjugating enzyme E2H	protein-coding
mm_48496.1	chr5	142794721	142794782	-	1	NA	intron (NM_178242, intron 2 of 15)	intron (NM_178242, intron 2 of 15)	22636	NM_178242	231861	Mm.354649	NM_178242	ENSMUSG00000039477	Tnrc18	BC025631|EG381742|Zfp469	trinucleotide repeat containing 18	protein-coding
mm_45358.1	chr5	65975649	65975688	-	1	NA	intron (NM_001081104, intron 4 of 4)	PB1|SINE|Alu	8544	NM_001081104	231252	Mm.140015	NM_001081104	ENSMUSG00000029205	Chrna9	2410015I05Rik|Acra9|EG666827|Gm8311	cholinergic receptor, nicotinic, alpha polypeptide 9	protein-coding
mm_25867.1	chr3	129901420	129901430	+	1	NA	promoter-TSS (NM_009811)	promoter-TSS (NM_009811)	10	NM_009811	12368	Mm.281379	NM_009811	ENSMUSG00000027997	Casp6	CASP-6|Mch2	caspase 6	protein-coding
mm_6906.1	chr1	84837830	84837840	-	1	NA	intron (NM_133975, intron 1 of 40)	intron (NM_133975, intron 1 of 40)	1469	NM_133975	14897	Mm.209265	NM_133975	ENSMUSG00000026219	Trip12	1110036I07Rik|6720416K24Rik|AA410158|Gtl6|TRIP-12	thyroid hormone receptor interactor 12	protein-coding
mm_99626.1	chr11	105091861	105091884	+	1	NA	promoter-TSS (NM_001081046)	promoter-TSS (NM_001081046)	-347	NM_001081046	70894	Mm.87320	NM_001081046	ENSMUSG00000020690	Efcab3	4921510J17Rik	EF-hand calcium binding domain 3	protein-coding
mm_113577.1	chr13	40734132	40734137	+	1	NA	promoter-TSS (NM_011547)	promoter-TSS (NM_011547)	-311	NM_011547	21418	Mm.85544	NM_011547	ENSMUSG00000021359	Tfap2a	AP-2|AP2alpha|Ap-2 (a)|Ap2|Ap2tf|Tcfap2a	transcription factor AP-2, alpha	protein-coding
mm_48528.1	chr5	142903706	142903730	-	1	NA	3' UTR (NM_007393, exon 6 of 6)	3' UTR (NM_007393, exon 6 of 6)	3036	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_154130.1	chr19	57314727	57314743	-	1	NA	Intergenic	CpG	40775	NR_045319	78120	Mm.445892	NR_045319		4930449E18Rik	-	RIKEN cDNA 4930449E18 gene	ncRNA
mm_15441.1	chr2	157367034	157367039	+	1	NA	promoter-TSS (NM_026968)	promoter-TSS (NM_026968)	-558	NM_026968	69161	Mm.228619	NM_026968	ENSMUSG00000063019	Manbal	1810024K12Rik|AI836500	mannosidase, beta A, lysosomal-like	protein-coding
mm_105775.1	chr11	109721724	109721798	-	1	NA	5' UTR (NM_153782, exon 1 of 11)	5' UTR (NM_153782, exon 1 of 11)	495	NM_153782	208659	Mm.208662	NM_153782	ENSMUSG00000020614	Fam20a	AI606893	family with sequence similarity 20, member A	protein-coding
mm_86663.1	chr10	17919277	17919285	+	1	NA	intron (NM_001033432, intron 1 of 3)	intron (NM_001033432, intron 1 of 3)	28786	NM_001033432	380629	Mm.276430	NM_001033432	ENSMUSG00000039879	Heca	Gm869|HDC|HDCL	hdc homolog, cell cycle regulator	protein-coding
mm_11132.1	chr2	28446832	28446878	+	1	NA	Intergenic	CpG	-1086	NM_001005420	241289	Mm.330095	NM_001005420	ENSMUSG00000035829	Ppp1r26	Gm347|Kiaa0649|mKIAA0649	protein phosphatase 1, regulatory subunit 26	protein-coding
mm_6657.1	chr1	80033654	80033662	-	1	NA	Intergenic	Intergenic	-174993	NM_009255	20720	Mm.3093	NM_009255	ENSMUSG00000026249	Serpine2	B230326M24Rik|PAI-1|PI-7|PI7|PN-1|Spi4	serine (or cysteine) peptidase inhibitor, clade E, member 2	protein-coding
mm_65478.1	chr7	25539916	25539933	-	1	NA	promoter-TSS (NM_001113369)	promoter-TSS (NM_001113369)	80	NM_001113368	26367	Mm.439731	NM_007543	ENSMUSG00000054385	Ceacam2	AI267129|Bgp2|Ceacam2-L	carcinoembryonic antigen-related cell adhesion molecule 2	protein-coding
mm_131482.1	chr16	17208604	17208628	+	1	NA	5' UTR (NM_001033338, exon 1 of 1)	5' UTR (NM_001033338, exon 1 of 1)	481	NM_001033338	239731	Mm.86671	NM_001033338	ENSMUSG00000071636	Rimbp3	Gm1759|Gm603|RIM-BP3|mKIAA1666	RIMS binding protein 3	protein-coding
mm_51613.1	chr6	85076361	85076386	+	1	NA	non-coding (NR_002702, exon 1 of 1)	non-coding (NR_002702, exon 1 of 1)	232	NR_002702	108176	Mm.431982	NR_002702		Npm3-ps1	-	nucleoplasmin 3, pseudogene 1	pseudo
mm_105243.1	chr11	102320266	102320278	-	1	NA	Intergenic	Intergenic	-1176	NM_011551	21429	Mm.2845	NM_011551	ENSMUSG00000020923	Ubtf	A930005G04Rik|NOR-90|Tcfubf|UBF|UBF-1|UBF1	upstream binding transcription factor, RNA polymerase I	protein-coding
mm_107181.1	chr12	24989758	24989769	+	1	NA	exon (NM_001081378, exon 5 of 32)	exon (NM_001081378, exon 5 of 32)	14831	NM_001081378	77480	Mm.250641	NM_001081378	ENSMUSG00000036333	Kidins220	3110039L19Rik|AI194387|AI316525|C330002I19Rik|mKIAA1250	kinase D-interacting substrate 220	protein-coding
mm_54605.1	chr6	38319746	38319758	-	1	NA	exon (NM_028421, exon 8 of 12)	exon (NM_028421, exon 8 of 12)	-20493	NM_172467	209032	Mm.101389	NM_172467	ENSMUSG00000047749	Zc3hav1l	B130055L09Rik|E430016P22Rik	zinc finger CCCH-type, antiviral 1-like	protein-coding
mm_45866.1	chr5	87930030	87930058	-	1	NA	exon (NM_007786, exon 4 of 5)	exon (NM_007786, exon 4 of 5)	4411	NM_007786	12994	Mm.296303	NM_007786	ENSMUSG00000001622	Csn3	AW208918|CSN10|Csnk	casein kappa	protein-coding
mm_158125.1	chrX	102515178	102515181	-	1	NA	3' UTR (NM_008832, exon 33 of 33)	3' UTR (NM_008832, exon 33 of 33)	-10021	NM_027382	70315	Mm.328128	NM_027382	ENSMUSG00000067567	Hdac8	2610007D20Rik	histone deacetylase 8	protein-coding
mm_43341.1	chr5	135106882	135106918	+	1	NA	promoter-TSS (NM_021455)	promoter-TSS (NM_021455)	9	NM_021455	58805	Mm.34213	NM_021455	ENSMUSG00000005373	Mlxipl	ChREBP|Mlx|WS-bHLH|Wbscr14|bHLHd14	MLX interacting protein-like	protein-coding
mm_126102.1	chr15	78244949	78245006	+	1	NA	5' UTR (NM_008677, exon 1 of 10)	5' UTR (NM_008677, exon 1 of 10)	166	NM_008677	17972	Mm.2068	NM_008677	ENSMUSG00000071715	Ncf4	AI451400|p40phox	neutrophil cytosolic factor 4	protein-coding
mm_42854.1	chr5	122210284	122210295	+	1	NA	promoter-TSS (NM_028752)	promoter-TSS (NM_028752)	2	NM_028752	74096	Mm.28804	NM_028752	ENSMUSG00000064267	Hvcn1	0610039P13Rik|AI450555|BTS|HV1|Vsop.|mVSOP	hydrogen voltage-gated channel 1	protein-coding
mm_159795.1	chr5	110703706	110703706	-	1	NA	intron (NM_173066, intron 19 of 50)	intron (NM_173066, intron 19 of 50)	-37565	NR_105993	102466216		NR_105993	ENSMUSG00000099284	Mir7026	Gm27988|mmu-mir-7026	microRNA 7026	ncRNA
mm_103316.1	chr11	73176543	73176593	-	1	NA	promoter-TSS (NM_029564)	promoter-TSS (NM_029564)	440	NM_001168470	66048	Mm.73608	NM_025318	ENSMUSG00000047260	Emc6	0610009E20Rik|0610025L18Rik|Tmem93	ER membrane protein complex subunit 6	protein-coding
mm_77518.1	chr8	122895202	122895222	-	1	NA	non-coding (NR_037865, exon 10 of 14)	non-coding (NR_037865, exon 10 of 14)	46838	NM_007662	12555	Mm.1976	NM_007662	ENSMUSG00000031962	Cdh15	AI323380|Cdh14|Mcad	cadherin 15	protein-coding
mm_57070.1	chr6	122578011	122578021	-	1	NA	3' UTR (NM_031159, exon 8 of 8)	3' UTR (NM_031159, exon 8 of 8)	24207	NM_009645	11628	Mm.391503	NM_009645	ENSMUSG00000040627	Aicda	Aid|Arp2	activation-induced cytidine deaminase	protein-coding
mm_77275.1	chr8	116616347	116616350	-	1	NA	intron (NM_029441, intron 2 of 6)	intron (NM_029441, intron 2 of 6)	111333	NM_029297	75465	Mm.23114	NM_029297	ENSMUSG00000034467	Dynlrb2	1700009A04Rik|DNLC2B|Dncl2b	dynein light chain roadblock-type 2	protein-coding
mm_68904.1	chr7	126456532	126456546	-	1	NA	exon (NM_007504, exon 9 of 23)	exon (NM_007504, exon 9 of 23)	6534	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_13753.1	chr2	118126590	118126600	+	1	NA	3' UTR (NM_011580, exon 22 of 22)	3' UTR (NM_011580, exon 22 of 22)	14719	NM_001313914	21825	Mm.4159	NM_011580	ENSMUSG00000040152	Thbs1	TSP-1|TSP1|Thbs-1|tbsp1	thrombospondin 1	protein-coding
mm_149692.1	chr19	21272258	21272263	+	1	NA	promoter-TSS (NM_009551)	promoter-TSS (NM_009551)	-18	NM_009551	22682	Mm.292405	NM_009551	ENSMUSG00000024750	Zfand5	2310057A04Rik|5830475F03Rik|AA415485|Za20d2|Zfp216	zinc finger, AN1-type domain 5	protein-coding
mm_162664.1	chr10	5593542	5593550	-	1	NA	promoter-TSS (NM_026793)	promoter-TSS (NM_026793)	-182	NM_026793	68632	Mm.338242	NM_026793	ENSMUSG00000046916	Myct1	1110020B04Rik|AI225941|AI642973|Mtmc1	myc target 1	protein-coding
mm_122259.1	chr14	34252575	34252581	-	1	NA	intron (NM_029389, intron 5 of 10)	L2a|LINE|L2	32532	NM_181529	319508	Mm.228006	NM_176931	ENSMUSG00000041479	Syt15	CHR10SYT|E230025K04Rik|sytXV	synaptotagmin XV	protein-coding
mm_140876.1	chr17	23815242	23815270	-	1	NA	exon (NM_175229, exon 10 of 14)	exon (NM_175229, exon 10 of 14)	12069	NM_175229	75956	Mm.5222	NM_175229	ENSMUSG00000039218	Srrm2	5033413A03Rik|AA410130|SRm300|mKIAA0324	serine/arginine repetitive matrix 2	protein-coding
mm_83787.1	chr9	52168741	52168768	-	1	NA	promoter-TSS (NM_001162921)	promoter-TSS (NM_001162921)	-643	NM_001162921	244871	Mm.295686	NM_001162921	ENSMUSG00000035164	Zc3h12c	A230108E06|C230027N18Rik|mKIAA1726	zinc finger CCCH type containing 12C	protein-coding
mm_120954.1	chr14	77156734	77156823	+	1	NA	promoter-TSS (NM_172813)	promoter-TSS (NM_172813)	15	NM_172813	239188	Mm.441158	NM_172813	ENSMUSG00000022012	Enox1	B230207J08|D230005D02Rik	ecto-NOX disulfide-thiol exchanger 1	protein-coding
mm_124777.1	chr15	7195068	7195071	+	1	NA	3' UTR (NM_013584, exon 20 of 20)	3' UTR (NM_013584, exon 20 of 20)	54527	NM_013584	16880	Mm.149720	NM_013584	ENSMUSG00000054263	Lifr	A230075M04Rik|AW061234|LIF	leukemia inhibitory factor receptor	protein-coding
mm_17102.1	chr2	23572039	23572112	-	1	NA	promoter-TSS (NM_001165997)	promoter-TSS (NM_001165997)	29	NM_029773	76857	Mm.276415	NM_029773	ENSMUSG00000026771	Spopl	4921517N04Rik|AU014935|BB233739|E430033K04Rik	speckle-type POZ protein-like	protein-coding
mm_97310.1	chr11	76679962	76679990	+	1	NA	5' UTR (NM_177709, exon 1 of 3)	5' UTR (NM_177709, exon 1 of 3)	103	NM_177709	237858	Mm.127006	NM_177709	ENSMUSG00000046275	Tusc5	C130069F04Rik|DSPB1|Lost1	tumor suppressor candidate 5	protein-coding
mm_89469.1	chr10	93488767	93488774	+	1	NA	promoter-TSS (NM_010401)	promoter-TSS (NM_010401)	2	NM_010401	15109	Mm.13000	NM_010401	ENSMUSG00000020017	Hal	Hsd|his|histidase	histidine ammonia lyase	protein-coding
mm_131686.1	chr16	20678406	20678434	+	1	NA	intron (NM_001304432, intron 6 of 31)	intron (NM_001304432, intron 6 of 31)	5693	NM_001304432	208643	Mm.260256	NM_145941	ENSMUSG00000045983	Eif4g1	E030015G23Rik|eIF-4-gamma 1|eIF-4G 1|eIF-4G1|eIF4GI	eukaryotic translation initiation factor 4, gamma 1	protein-coding
mm_166934.1	chr7	35333787	35333819	-	1	NA	promoter-TSS (NM_027897)	promoter-TSS (NM_027897)	-434	NM_027897	52428	Mm.286600	NM_027897	ENSMUSG00000030494	Rhpn2	1300002E07Rik|AA536890|C85860|D7Ertd784e	rhophilin, Rho GTPase binding protein 2	protein-coding
mm_61112.1	chr7	54835578	54835586	+	1	NA	5' UTR (NM_178705, exon 1 of 12)	5' UTR (NM_178705, exon 1 of 12)	337	NM_178705	233271	Mm.387344	NM_178705	ENSMUSG00000063297	Luzp2	9330154K17Rik|D130073E01	leucine zipper protein 2	protein-coding
mm_78406.1	chr9	29442373	29442389	+	1	NA	intron (NM_172290, intron 1 of 7)	MLT2D|LTR|ERVL	520748	NM_172290	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding
mm_20247.1	chr2	126499732	126499742	-	1	NA	Intergenic	Intergenic	-8184	NM_001080944	241633	Mm.222235	NM_001080944	ENSMUSG00000060131	Atp8b4	A530043E15|Im	ATPase, class I, type 8B, member 4	protein-coding
mm_16286.1	chr2	174110341	174110394	+	1	NA	promoter-TSS (NM_213733)	promoter-TSS (NM_213733)	16	NM_213733	228961	Mm.295629	NM_213733	ENSMUSG00000039263	Npepl1	BC023239|C85514|mKIAA1974	aminopeptidase-like 1	protein-coding
mm_64113.1	chr7	141078171	141078181	+	1	NA	promoter-TSS (NM_001162924)	promoter-TSS (NM_001162924)	-53	NM_001162924	56460	Mm.350037	NM_019762	ENSMUSG00000054065	Pkp3	2310056L12Rik	plakophilin 3	protein-coding
mm_120832.1	chr14	75176808	75176822	+	1	NA	5' UTR (NM_008879, exon 2 of 17)	5' UTR (NM_008879, exon 2 of 17)	40390	NM_008879	18826	Mm.153911	NM_008879	ENSMUSG00000021998	Lcp1	AW536232|D14Ertd310e|LCP-1|Pls2|pp65	lymphocyte cytosolic protein 1	protein-coding
mm_37381.1	chr4	120975520	120975584	-	1	NA	intron (NM_133716, intron 5 of 9)	intron (NM_133716, intron 5 of 9)	-2230	NR_105982	102465614		NR_105982	ENSMUSG00000106436	Mir7015	mmu-mir-7015	microRNA 7015	ncRNA
mm_15952.1	chr2	165977142	165977160	+	1	NA	Intergenic	Intergenic	-15486	NM_008679	17979	Mm.469663	NM_008679	ENSMUSG00000027678	Ncoa3	2010305B15Rik|AW321064|Actr|Aib1|KAT13B|Rac3|Src3|Tram-1|Tram1|bHLHe42|p/Cip|pCip	nuclear receptor coactivator 3	protein-coding
mm_133531.1	chr16	91011346	91011356	+	1	NA	promoter-TSS (NM_001045515)	promoter-TSS (NM_001045515)	-43	NM_001164483	104015	Mm.187079	NM_001045515	ENSMUSG00000022973	Synj1	A930006D20Rik|AA675315|mKIAA0910	synaptojanin 1	protein-coding
mm_170068.1	chr17	32051833	32051838	+	1	NA	exon (NM_028244, exon 8 of 16)	exon (NM_028244, exon 8 of 16)	3550	NM_001163734	72462	Mm.102761	NM_028244	ENSMUSG00000058392	Rrp1b	2600005C20Rik|D030064A17|Kiaa0179|mKIAA0179	ribosomal RNA processing 1 homolog B (S. cerevisiae)	protein-coding
mm_35814.1	chr4	46991517	46991527	-	1	NA	5' UTR (NM_001081141, exon 1 of 19)	5' UTR (NM_001081141, exon 1 of 19)	192	NM_001081141	242425	Mm.101909	NM_001081141	ENSMUSG00000039809	Gabbr2	GABABR2|Gb2|Gm425|Gpr51	gamma-aminobutyric acid (GABA) B receptor, 2	protein-coding
mm_70129.1	chr7	143230271	143230282	-	1	NA	non-coding (NR_001461, exon 1 of 1)	non-coding (NR_001461, exon 1 of 1)	66271	NR_001461	63830	Mm.356096	NR_001461	ENSMUSG00000101609	Kcnq1ot1	Kvlqt1-as|Lit1|Tssc8	KCNQ1 overlapping transcript 1	ncRNA
mm_67867.1	chr7	99159049	99159062	-	1	NA	intron (NM_026384, intron 4 of 7)	intron (NM_026384, intron 4 of 7)	-17911	NM_178635	78610	Mm.323072	NM_178635	ENSMUSG00000035354	Uvrag	9530039D02Rik|AI648770|BB124205|Uvrag1|Uvragl	UV radiation resistance associated gene	protein-coding
mm_130400.1	chr15	97976109	97976119	-	1	NA	exon (NM_001113515, exon 53 of 53)	exon (NM_001113515, exon 53 of 53)	11885	NM_001252153	380967	Mm.196630	NM_201359	ENSMUSG00000052369	Tmem106c	AI046681|BC046621|D15Ertd405e	transmembrane protein 106C	protein-coding
mm_158343.1	chrX	134162949	134162966	-	1	NA	Intergenic	Intergenic	-1029	NM_183319	331524	Mm.235055	NM_183319	ENSMUSG00000031258	Xkrx	A630026F04	X-linked Kx blood group related, X-linked	protein-coding
mm_33408.1	chr4	129848506	129848515	+	1	NA	3' UTR (NM_001164745, exon 6 of 6)	3' UTR (NM_001164745, exon 6 of 6)	27802	NM_001164745	19244	Mm.193688	NM_008974	ENSMUSG00000028788	Ptp4a2	Prl-2	protein tyrosine phosphatase 4a2	protein-coding
mm_124961.1	chr15	13155243	13155247	+	1	NA	intron (NM_007666, intron 1 of 11)	intron (NM_007666, intron 1 of 11)	18430	NM_007666	12563	Mm.57048	NM_007666	ENSMUSG00000039385	Cdh6	cad6	cadherin 6	protein-coding
mm_53731.1	chr6	145121712	145121722	+	1	NA	promoter-TSS (NM_008511)	promoter-TSS (NM_008511)	-22	NM_008511	16970	Mm.843	NM_008511	ENSMUSG00000030263	Lrmp	D6Int3|D6Int4|D6Int5|D6Int7|D6Int8|Jaw1	lymphoid-restricted membrane protein	protein-coding
mm_71801.1	chr8	68276714	68276752	+	1	NA	5' UTR (NM_028182, exon 1 of 9)	5' UTR (NM_028182, exon 1 of 9)	205	NM_028182	72281	Mm.40974	NM_028182	ENSMUSG00000053886	Sh2d4a	2210402M20Rik|SH2A	SH2 domain containing 4A	protein-coding
mm_169759.1	chr15	9357165	9357177	-	1	NA	intron (NM_144845, intron 3 of 6)	RLTRETN_Mm|LTR|ERVK	21573	NM_144845	223337	Mm.422853	NM_144845	ENSMUSG00000049152	Ugt3a2	AI313915	UDP glycosyltransferases 3 family, polypeptide A2	protein-coding
mm_107223.1	chr12	26470508	26470511	+	1	NA	intron (NM_020557, intron 1 of 4)	intron (NM_020557, intron 1 of 4)	1294	NM_020557	22169	Mm.271839	NM_020557	ENSMUSG00000020638	Cmpk2	1200004E04Rik|TDKI|Tyki	cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial	protein-coding
mm_129509.1	chr15	79028790	79028854	-	1	NA	exon (NM_008197, exon 1 of 1)	exon (NM_008197, exon 1 of 1)	610	NM_008197	14958	Mm.24350	NM_008197	ENSMUSG00000096210	H1f0	D130017D06Rik|H1(0)|H1fv	H1 histone family, member 0	protein-coding
mm_12224.1	chr2	67970659	67970665	+	1	NA	Intergenic	Intergenic	-134010	NM_020283	26877	Mm.226435	NM_020283	ENSMUSG00000034780	B3galt1	beta3Gal-T1	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 1	protein-coding
mm_155855.1	chrX	101299208	101299218	+	1	NA	promoter-TSS (NM_172932)	promoter-TSS (NM_172932)	34	NM_172932	245537	Mm.121508	NM_172932	ENSMUSG00000031302	Nlgn3	A230085M13Rik|HNL3|NL3	neuroligin 3	protein-coding
mm_1933.1	chr1	86111005	86111011	+	1	NA	5' UTR (NM_008311, exon 2 of 4)	5' UTR (NM_008311, exon 2 of 4)	962	NM_008311	15559	Mm.439747	NM_008311	ENSMUSG00000026228	Htr2b	5-HT2B|AJ012488|AV377389	5-hydroxytryptamine (serotonin) receptor 2B	protein-coding
mm_122211.1	chr14	32124404	32124410	-	1	NA	Intergenic	RLTR9A|LTR|ERVK	-17616	NM_020597	17695	Mm.2540	NM_020597	ENSMUSG00000021907	Msmb	PIP|PSP94|beta-MSP	beta-microseminoprotein	protein-coding
mm_105607.1	chr11	106782855	106782865	-	1	NA	promoter-TSS (NR_037224)	promoter-TSS (NR_037224)	-101	NR_037224	100526469		NR_037224	ENSMUSG00000093273	Mir3064	mir-3064|mmu-mir-3064	microRNA 3064	ncRNA
mm_59827.1	chr7	29289328	29289338	+	1	NA	promoter-TSS (NM_026731)	promoter-TSS (NM_026731)	13	NM_026731	68458	Mm.2343	NM_026731	ENSMUSG00000037166	Ppp1r14a	1110001M11Rik|Cpi17	protein phosphatase 1, regulatory (inhibitor) subunit 14A	protein-coding
mm_81753.1	chr9	113956223	113956233	+	1	NA	intron (NM_013699, intron 5 of 15)	intron (NM_013699, intron 5 of 15)	25294	NM_013699	22221	Mm.28052	NM_013699	ENSMUSG00000009741	Ubp1	Cp2b|LBP-1a|LBP-1b|NF2d9	upstream binding protein 1	protein-coding
mm_38235.1	chr4	136172319	136172323	-	1	NA	promoter-TSS (NM_177733)	promoter-TSS (NM_177733)	47	NM_177733	242705	Mm.307932	NM_177733	ENSMUSG00000018983	E2f2	E2F-2	E2F transcription factor 2	protein-coding
mm_81436.1	chr9	109095569	109095600	+	1	NA	5' UTR (NM_172775, exon 1 of 38)	5' UTR (NM_172775, exon 1 of 38)	148	NM_172775	235611	Mm.53862	NM_172775	ENSMUSG00000053646	Plxnb1	2900002G15Rik|AU042020|mKIAA0407	plexin B1	protein-coding
mm_102297.1	chr11	55461132	55461156	-	1	NA	promoter-TSS (NM_009720)	promoter-TSS (NM_009720)	-6	NM_009720	11927	Mm.217759	NM_009720	ENSMUSG00000018585	Atox1	AI256639|Atx1	antioxidant 1 copper chaperone	protein-coding
mm_128883.1	chr15	73140170	73140179	-	1	NA	intron (NM_153178, intron 2 of 18)	intron (NM_153178, intron 2 of 18)	44773	NM_153178	239528	Mm.23095	NM_153178	ENSMUSG00000036698	Ago2	1110029L17Rik|2310051F07Rik|AI225898|AL022874|AW546247|ENSMUSG00000072493|Eif2c2|Gerp95|Gm10365|mKIAA4215	argonaute RISC catalytic subunit 2	protein-coding
mm_58540.1	chr7	4519391	4519411	+	1	NA	exon (NM_009406, exon 7 of 8)	exon (NM_009406, exon 7 of 8)	3042	NM_009406	21954	Mm.27674	NM_009406	ENSMUSG00000035458	Tnni3	Tn1|cTnI	troponin I, cardiac 3	protein-coding
mm_84699.1	chr9	72510938	72510946	-	1	NA	Intergenic	L1MCa|LINE|L1	-18983	NM_009359	21778	Mm.14485	NM_009359	ENSMUSG00000090626	Tex9	Gm19407|tsec-1	testis expressed gene 9	protein-coding
mm_60507.1	chr7	44479534	44479544	+	1	NA	Intergenic	L1MC4|LINE|L1	-4978	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_156716.1	chrX	159697344	159697350	+	1	NA	intron (NM_001135727, intron 2 of 17)	intron (NM_001135727, intron 2 of 17)	-11254	NM_021389	58194	Mm.286495	NM_021389	ENSMUSG00000040990	Sh3kbp1	1200007H22Rik|1700125L08Rik|5830464D22Rik|AI447724|Cin85|IN85|Ruk|Seta	SH3-domain kinase binding protein 1	protein-coding
mm_154060.1	chr19	55127181	55127243	-	1	NA	Intergenic	Intergenic	-27765	NM_008149	14732	Mm.210196	NM_008149	ENSMUSG00000024978	Gpam	GPAT|GPAT1	glycerol-3-phosphate acyltransferase, mitochondrial	protein-coding
mm_120849.1	chr14	75210484	75210511	+	1	NA	exon (NM_001247984, exon 9 of 16)	exon (NM_001247984, exon 9 of 16)	-31790	NM_019775	56373	Mm.24242	NM_019775	ENSMUSG00000021999	Cpb2	1110032P04Rik|4930405E17Rik|AI255929|CPR|Cpu|TAFI	carboxypeptidase B2 (plasma)	protein-coding
mm_151334.1	chr19	55894607	55894615	+	1	NA	promoter-TSS (NM_001142924)	promoter-TSS (NM_001142924)	-710	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_63553.1	chr7	128076160	128076182	+	1	NA	intron (NM_001082960, intron 6 of 29)	intron (NM_001082960, intron 6 of 29)	13531	NM_008401	16409	Mm.262106	NM_008401	ENSMUSG00000030786	Itgam	CD11b/CD18|CR3|CR3A|Cd11b|F730045J24Rik|Ly-40|MAC1|Mac-1|Mac-1a	integrin alpha M	protein-coding
mm_88042.1	chr10	67538187	67538195	+	1	NA	5' UTR (NM_010118, exon 1 of 2)	5' UTR (NM_010118, exon 1 of 2)	261	NM_001347458	13654	Mm.290421	NM_010118	ENSMUSG00000037868	Egr2	Egr-2|Krox-20|Krox20|NGF1-B|Zfp-25|Zfp-6	early growth response 2	protein-coding
mm_91750.1	chr10	49783674	49783727	-	1	NA	intron (NM_001111268, intron 1 of 16)	intron (NM_001111268, intron 1 of 16)	5054	NM_010349	14806	Mm.332838	NM_010349	ENSMUSG00000056073	Grik2	AW124492|GluK2|Glur-6|Glur6|Glurbeta2	glutamate receptor, ionotropic, kainate 2 (beta 2)	protein-coding
mm_75422.1	chr8	46828481	46828493	-	1	NA	intron (NM_008391, intron 6 of 8)	intron (NM_008391, intron 6 of 8)	88742	NM_008391	16363	Mm.1149	NM_008391	ENSMUSG00000031627	Irf2	9830146E22Rik|AI646973|Irf-2	interferon regulatory factor 2	protein-coding
mm_146061.1	chr18	69684145	69684166	+	1	NA	3' UTR (NM_001083967, exon 20 of 20)	3' UTR (NM_001083967, exon 20 of 20)	-241404	NM_201362	381175	Mm.266831	NM_201362	ENSMUSG00000038903	Ccdc68	BC046343	coiled-coil domain containing 68	protein-coding
mm_132261.1	chr16	32756108	32756119	+	1	NA	exon (NM_080457, exon 4 of 27)	exon (NM_080457, exon 4 of 27)	20227	NM_080457	140474	Mm.214599	NM_080457	ENSMUSG00000079620	Muc4	4933405I11Rik|Asgp	mucin 4	protein-coding
mm_16777.1	chr2	9887731	9887744	-	1	NA	TTS (NR_024257)	TTS (NR_024257)	1803	NR_040511	77682	Mm.488621	NR_040511	ENSMUSG00000079602	9230102O04Rik	-	RIKEN cDNA 9230102O04 gene	ncRNA
mm_30303.1	chr3	149219425	149219433	-	1	NA	Intergenic	Intergenic	-55308	NR_040591	381482	Mm.393866	NR_040591		Gm1653	-	predicted gene 1653	ncRNA
mm_100601.1	chr11	121237217	121237289	+	1	NA	promoter-TSS (NM_026272)	promoter-TSS (NM_026272)	17	NM_026272	67608	Mm.291832	NM_026272	ENSMUSG00000000056	Narf	4430402O11Rik	nuclear prelamin A recognition factor	protein-coding
mm_54346.1	chr6	30804882	30804893	-	1	NA	intron (NM_017478, intron 20 of 23)	intron (NM_017478, intron 20 of 23)	63588	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_25998.1	chr3	134259340	134259355	+	1	NA	3' UTR (NM_001004367, exon 4 of 4)	3' UTR (NM_001004367, exon 4 of 4)	-18764	NR_035435	100316832		NR_035435	ENSMUSG00000084564	Mir1895	Mirn1895|mmu-mir-1895	microRNA 1895	ncRNA
mm_22420.1	chr2	181581901	181581911	-	1	NA	promoter-TSS (NM_026765)	promoter-TSS (NM_026765)	67	NM_026765	68556	Mm.232400	NM_026765	ENSMUSG00000089917	Uckl1	1110007H10Rik|Urkl1	uridine-cytidine kinase 1-like 1	protein-coding
mm_113537.1	chr13	37853470	37853473	+	1	NA	intron (NM_001039188, intron 1 of 9)	intron (NM_001039188, intron 1 of 9)	26078	NM_001039188	68750	Mm.491109	NM_026830	ENSMUSG00000039087	Rreb1	1110037N09Rik|AA414966|B930013M22Rik	ras responsive element binding protein 1	protein-coding
mm_53605.1	chr6	138156705	138156716	+	1	NA	TTS (NM_019946)	TTS (NM_019946)	15116	NM_001347489	56615	Mm.14796	NM_019946	ENSMUSG00000008540	Mgst1	1500002K10Rik|Gst	microsomal glutathione S-transferase 1	protein-coding
mm_4693.1	chr1	180731839	180731844	+	1	NA	intron (NM_133225, intron 1 of 7)	B2_Mm2|SINE|B2	5798	NM_133225	170760	Mm.272981	NM_133225	ENSMUSG00000026499	Acbd3	60kDa|8430407O11Rik|D1Ertd10e|GCP60|GOLPH1|Gocap1|Pap7	acyl-Coenzyme A binding domain containing 3	protein-coding
mm_95002.1	chr11	31873090	31873127	+	1	NA	exon (NM_026252, exon 1 of 10)	exon (NM_026252, exon 1 of 10)	2168	NM_026252	67579	Mm.339792	NM_026252	ENSMUSG00000020300	Cpeb4	Cpe-bp4|Cpeb-4|mCPEB-4	cytoplasmic polyadenylation element binding protein 4	protein-coding
mm_66965.1	chr7	62464506	62464548	-	1	NA	promoter-TSS (NM_013788)	promoter-TSS (NM_013788)	-17	NM_013788	27412	Mm.422745	NM_013788	ENSMUSG00000070526	Peg12	Frat3	paternally expressed 12	protein-coding
mm_52644.1	chr6	117178961	117178968	+	1	NA	3' UTR (NM_001012477, exon 4 of 4)	3' UTR (NM_001012477, exon 4 of 4)	10429	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_22829.1	chr3	27242784	27242794	+	1	NA	3' UTR (NM_178772, exon 5 of 5)	3' UTR (NM_178772, exon 5 of 5)	59785	NM_178772	320024	Mm.24576	NM_178772	ENSMUSG00000027698	Nceh1	Aadacl1|B230106I24Rik|CPO-BP|Nceh	neutral cholesterol ester hydrolase 1	protein-coding
mm_113140.1	chr13	24638637	24638736	+	1	NA	promoter-TSS (NM_001080381)	promoter-TSS (NM_001080381)	38	NM_029679	193385	Mm.217319	NM_029679	ENSMUSG00000036006	Fam65b	-	family with sequence similarity 65, member B	protein-coding
mm_75971.1	chr8	72002624	72002633	-	1	NA	intron (NM_024444, intron 2 of 12)	intron (NM_024444, intron 2 of 12)	6998	NM_024444	72054	Mm.160020	NM_024444	ENSMUSG00000003484	Cyp4f18	1810054N16Rik|Cyp4f3|Cypf18	cytochrome P450, family 4, subfamily f, polypeptide 18	protein-coding
mm_46273.1	chr5	100037643	100037663	-	1	NA	exon (NM_016690, exon 3 of 8)	exon (NM_016690, exon 3 of 8)	1569	NM_016690	50926	Mm.389579	NM_016690	ENSMUSG00000029328	Hnrnpdl	AA407431|AA959857|D5Ertd650e|D5Wsu145e|Hnrnpdl1|Hnrpdl|JKTBP|hnRNP DL|hnRNP-DL	heterogeneous nuclear ribonucleoprotein D-like	protein-coding
mm_99648.1	chr11	105589734	105589748	+	1	NA	promoter-TSS (NM_181071)	promoter-TSS (NM_181071)	-245	NM_181071	77097	Mm.22501	NM_175492	ENSMUSG00000053580	Tanc2	3526402J09Rik|5730590C14Rik	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2	protein-coding
mm_144765.1	chr18	35771898	35771954	+	1	NA	5' UTR (NM_019912, exon 1 of 7)	5' UTR (NM_019912, exon 1 of 7)	367	NM_019912	56550	Mm.180052	NM_019912	ENSMUSG00000091896	Ube2d2a	1500034D03Rik|Ubc2e|Ube2d2|ubc4	ubiquitin-conjugating enzyme E2D 2A	protein-coding
mm_45558.1	chr5	73182646	73182650	-	1	NA	intron (NM_028194, intron 3 of 62)	intron (NM_028194, intron 3 of 62)	73970	NM_028194	72313	Mm.260594	NM_028194	ENSMUSG00000070733	Fryl	2010313D22Rik|2310004H21Rik|2510002A14Rik|9030227G01Rik|mKIAA0826	FRY like transcription coactivator	protein-coding
mm_145742.1	chr18	64289003	64289052	+	1	NA	Intergenic	Intergenic	-11847	NR_045366	73588	Mm.65475	NR_045366	ENSMUSG00000086128	St8sia3os	1700091E21Rik	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3, opposite strand	ncRNA
mm_59236.1	chr7	24778169	24778186	+	1	NA	exon (NM_007675, exon 2 of 4)	exon (NM_007675, exon 2 of 4)	973	NM_007675	26366	Mm.30300	NM_007675	ENSMUSG00000054169	Ceacam10	Bgp3|Cea10	carcinoembryonic antigen-related cell adhesion molecule 10	protein-coding
mm_97099.1	chr11	73279758	73279791	+	1	NA	exon (NM_145099, exon 6 of 18)	exon (NM_145099, exon 6 of 18)	12154	NM_145099	246788	Mm.75196	NM_145099	ENSMUSG00000043029	Trpv3	1110036I10Rik|AI644701|Nh|VRL3	transient receptor potential cation channel, subfamily V, member 3	protein-coding
mm_118665.1	chr14	21848445	21848456	+	1	NA	5' UTR (NM_176925, exon 1 of 3)	5' UTR (NM_176925, exon 1 of 3)	460	NM_026965	69156	Mm.11827	NM_026965	ENSMUSG00000021773	Comtd1	1810030M08Rik|MT773	catechol-O-methyltransferase domain containing 1	protein-coding
mm_7210.1	chr1	93083972	93083974	-	1	NA	intron (NM_001294149, intron 1 of 47)	intron (NM_001294149, intron 1 of 47)	-1493	NM_001294150	16560	Mm.276408	NM_008440	ENSMUSG00000014602	Kif1a	ATSV|C630002N23Rik|Gm1626|Kns1	kinesin family member 1A	protein-coding
mm_90302.1	chr10	126371971	126371998	+	1	NA	Intergenic	Intergenic	338407	NR_105841	102465224		NR_105841	ENSMUSG00000098756	Mir378d	Gm27650|mmu-mir-378d	microRNA 378d	ncRNA
mm_27036.1	chr3	26331501	26331514	-	1	NA	5' UTR (NM_138666, exon 1 of 8)	5' UTR (NM_138666, exon 1 of 8)	402	NM_138666	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_64762.1	chr7	4912395	4912429	-	1	NA	Intergenic	ORR1B2|LTR|ERVL-MaLR	-2805	NM_170759	232816	Mm.27442	NM_170759	ENSMUSG00000074406	Zfp628	Zec|Znf628	zinc finger protein 628	protein-coding
mm_172522.1	chr7	81829418	81829420	-	1	NA	promoter-TSS (NM_146193)	promoter-TSS (NM_146193)	12	NM_146193	83962	Mm.439893	NM_146193	ENSMUSG00000025103	Btbd1	1190005H08Rik	BTB (POZ) domain containing 1	protein-coding
mm_50161.1	chr6	41547454	41547464	+	1	NA	Intergenic	Intergenic	25683	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_74281.1	chr8	125584627	125584643	+	1	NA	promoter-TSS (NR_015535)	promoter-TSS (NR_015535)	-3	NR_015535	75930	Mm.195663	NR_015535	ENSMUSG00000110629	4930567H12Rik	4930579P07Rik	RIKEN cDNA 4930567H12 gene	ncRNA
mm_33748.1	chr4	134246934	134246934	+	1	NA	Intergenic	Intergenic	-1343	NM_024215	68040	Mm.300404	NM_024215	ENSMUSG00000028840	Zfp593	3110024A21Rik|AV062409|E130106C14Rik|ZNF593	zinc finger protein 593	protein-coding
mm_145540.1	chr18	60807900	60807908	+	1	NA	intron (NM_001042605, intron 1 of 8)	intron (NM_001042605, intron 1 of 8)	4055	NM_010545	16149	Mm.439737	NM_010545	ENSMUSG00000024610	Cd74	CLIP|DHLAG|HLADG|Ia-GAMMA|Ii	CD74 antigen (invariant polypeptide of major histocompatibility complex, class II antigen-associated)	protein-coding
mm_38296.1	chr4	136893093	136893098	-	1	NA	promoter-TSS (NM_007574)	promoter-TSS (NM_007574)	-181	NM_007574	12262	Mm.439732	NM_007574	ENSMUSG00000036896	C1qc	AI385742|C1qg|Ciqc	complement component 1, q subcomponent, C chain	protein-coding
mm_55552.1	chr6	71262485	71262496	-	1	NA	promoter-TSS (NM_001160127)	promoter-TSS (NM_001160127)	-209	NM_009762	12180	Mm.234274	NM_009762	ENSMUSG00000055027	Smyd1	4632404M21Rik|Bop|C78565|Zmynd18	SET and MYND domain containing 1	protein-coding
mm_150938.1	chr19	46306024	46306032	+	1	NA	promoter-TSS (NM_001177370)	promoter-TSS (NM_001177370)	98	NM_001177370	18034	Mm.102365	NM_019408	ENSMUSG00000025225	Nfkb2	NF-kappaB2|lyt|p49|p49/p100|p50B|p52	nuclear factor of kappa light polypeptide gene enhancer in B cells 2, p49/p100	protein-coding
mm_6623.1	chr1	77488698	77488701	-	1	NA	intron (NM_007936, intron 3 of 17)	intron (NM_007936, intron 3 of 17)	8069	NR_105770	102465180		NR_105770	ENSMUSG00000099141	Mir6352	Gm27481|mmu-mir-6352	microRNA 6352	ncRNA
mm_166752.1	chr6	125350550	125350570	-	1	NA	intron (NM_011609, intron 1 of 9)	intron (NM_011609, intron 1 of 9)	837	NM_011609	21937	Mm.1258	NM_011609	ENSMUSG00000030341	Tnfrsf1a	CD120a|FPF|TNF-R|TNF-R-I|TNF-R1|TNF-R55|TNF-alphaR1|TNFAR|TNFR60|TNFRI|TNFRp55|TNFalpha-R1|Tnfr-2|Tnfr1|p55|p55-R	tumor necrosis factor receptor superfamily, member 1a	protein-coding
mm_120666.1	chr14	70546476	70546486	+	1	NA	exon (NM_180588, exon 2 of 8)	exon (NM_180588, exon 2 of 8)	1230	NM_180588	72549	Mm.46742	NM_180588	ENSMUSG00000033589	Reep4	2700029E10Rik	receptor accessory protein 4	protein-coding
mm_86120.1	chr9	116090168	116090178	-	1	NA	3' UTR (NM_029575, exon 7 of 7)	3' UTR (NM_029575, exon 7 of 7)	85190	NM_029575	21813	Mm.172346	NM_009371	ENSMUSG00000032440	Tgfbr2	1110020H15Rik|AU042018|DNIIR|RIIDN|TBR-II|TbetaR-II|TbetaRII	transforming growth factor, beta receptor II	protein-coding
mm_6377.1	chr1	72578961	72578983	-	1	NA	Intergenic	Intergenic	-4279	NM_018817	54380	Mm.274232	NM_018817	ENSMUSG00000039354	Smarcal1	6030401P21Rik|AI851716|Mharp	SWI/SNF related matrix associated, actin dependent regulator of chromatin, subfamily a-like 1	protein-coding
mm_167587.1	chr9	46240820	46240829	+	1	NA	promoter-TSS (NM_007468)	promoter-TSS (NM_007468)	-20	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_57864.1	chr6	129622603	129622613	-	1	NA	promoter-TSS (NM_033078)	promoter-TSS (NM_033078)	75	NM_033078	27007	Mm.8217	NM_033078	ENSMUSG00000030149	Klrk1	D6H12S2489E|NKG2-D|Nkg2d	killer cell lectin-like receptor subfamily K, member 1	protein-coding
mm_143148.1	chr17	57222832	57222846	-	1	NA	exon (NM_009778, exon 13 of 41)	exon (NM_009778, exon 13 of 41)	5297	NM_009778	12266	Mm.19131	NM_009778	ENSMUSG00000024164	C3	AI255234|ASP|HSE-MSF|Plp	complement component 3	protein-coding
mm_123729.1	chr14	70168012	70168020	-	1	NA	exon (NM_001253736, exon 7 of 10)	exon (NM_001253736, exon 7 of 10)	-8514	NM_001004155	268759	Mm.12148	NM_001004155	ENSMUSG00000044551	9930012K11Rik	-	RIKEN cDNA 9930012K11 gene	protein-coding
mm_53432.1	chr6	134056158	134056166	+	1	NA	intron (NM_007961, intron 1 of 7)	intron (NM_007961, intron 1 of 7)	20462	NM_007961	14011	Mm.269995	NM_007961	ENSMUSG00000030199	Etv6	AW123102|AW557856|Tel	ets variant 6	protein-coding
mm_55458.1	chr6	67376289	67376311	-	1	NA	promoter-TSS (NM_008354)	promoter-TSS (NM_008354)	-163	NM_008354	16162	Mm.188337	NM_008354	ENSMUSG00000018341	Il12rb2	A930027I18Rik|IL-12RB2|Ifnm	interleukin 12 receptor, beta 2	protein-coding
mm_147048.1	chr18	34931892	34931920	-	1	NA	promoter-TSS (NM_144866)	promoter-TSS (NM_144866)	97	NM_144866	225363	Mm.329353	NM_144866	ENSMUSG00000024360	Etf1	AI463371|D6Ertd109e|ERF|ERF1|SUP45L1|TB3-1	eukaryotic translation termination factor 1	protein-coding
mm_83611.1	chr9	48649606	48649624	-	1	NA	Intergenic	Intergenic	-44492	NM_010924	18113	Mm.8362	NM_010924	ENSMUSG00000032271	Nnmt	-	nicotinamide N-methyltransferase	protein-coding
mm_29145.1	chr3	105932626	105932630	-	1	NA	promoter-TSS (NM_001033780)	promoter-TSS (NM_001033780)	36	NM_001033780	433638	Mm.239081	NM_001033780	ENSMUSG00000074342	I830077J02Rik	-	RIKEN cDNA I830077J02 gene	protein-coding
mm_153337.1	chr19	38224706	38224719	-	1	NA	promoter-TSS (NM_001081075)	promoter-TSS (NM_001081075)	-580	NM_001081075	70567	Mm.30607	NM_001081075	ENSMUSG00000054237	Fra10ac1	5730455O13Rik|AI448293	FRA10AC1 homolog (human)	protein-coding
mm_24567.1	chr3	93444278	93444284	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	1951	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_160382.1	chr8	43576697	43576697	-	1	NA	promoter-TSS (NM_010085)	promoter-TSS (NM_010085)	10	NM_010085	13525	Mm.334510	NM_010085	ENSMUSG00000048516	Adam26a	Adam26|Dtgn4	a disintegrin and metallopeptidase domain 26A (testase 3)	protein-coding
mm_58238.1	chr6	145047606	145047614	-	1	NA	intron (NM_007532, intron 1 of 10)	intron (NM_007532, intron 1 of 10)	1202	NM_001024468	12035	Mm.4606	NM_007532	ENSMUSG00000030268	Bcat1	BCATc|Eca39	branched chain aminotransferase 1, cytosolic	protein-coding
mm_5481.1	chr1	36709905	36709978	-	1	NA	promoter-TSS (NM_146107)	promoter-TSS (NM_146107)	-16	NM_146107	226977	Mm.28521	NM_146107	ENSMUSG00000037351	Actr1b	2310066K23Rik|AA960180|AI851923|Arp1b	ARP1 actin-related protein 1B, centractin beta	protein-coding
mm_114715.1	chr13	83583095	83583118	+	1	NA	intron (NM_001347564, intron 3 of 11)	MusHAL1|LINE|L1	9499	NM_001347569	17260	Mm.24001	NM_025282	ENSMUSG00000005583	Mef2c	5430401D19Rik|9930028G15Rik|AV011172|Mef2	myocyte enhancer factor 2C	protein-coding
mm_90129.1	chr10	117710888	117710947	+	1	NA	promoter-TSS (NM_010786)	promoter-TSS (NM_010786)	-159	NM_001288586	17246	Mm.22670	NM_010786	ENSMUSG00000020184	Mdm2	1700007J15Rik|AA415488|Mdm-2	transformed mouse 3T3 cell double minute 2	protein-coding
mm_171491.1	chr4	146156772	146156773	+	1	NA	promoter-TSS (NM_001177545)	promoter-TSS (NM_001177545)	-55	NM_001177546	667666	Mm.459230	NM_001177545	ENSMUSG00000066007	Zfp600	Gm13164|OTTMUSG00000010694	zinc finger protein 600	protein-coding
mm_150166.1	chr19	32485752	32485774	+	1	NA	promoter-TSS (NM_010799)	promoter-TSS (NM_010799)	-6	NM_010799	17330	Mm.255116	NM_010799	ENSMUSG00000024896	Minpp1	AA408516	multiple inositol polyphosphate histidine phosphatase 1	protein-coding
mm_81167.1	chr9	107299913	107299921	+	1	NA	intron (NM_001317354, intron 1 of 1)	intron (NM_001317354, intron 1 of 1)	3258	NM_009895	12700	Mm.4592	NM_009895	ENSMUSG00000032578	Cish	CIS-1|CIS1|Cis|F17|F23|SOCS	cytokine inducible SH2-containing protein	protein-coding
mm_166589.1	chr6	55336201	55336207	+	1	NA	promoter-TSS (NM_007472)	promoter-TSS (NM_007472)	-95	NM_007472	11826	Mm.18625	NM_007472	ENSMUSG00000004655	Aqp1	CHIP28	aquaporin 1	protein-coding
mm_101377.1	chr11	23770954	23771028	-	1	NA	promoter-TSS (NM_009044)	promoter-TSS (NM_009044)	-21	NM_009044	19696	Mm.4869	NM_009044	ENSMUSG00000020275	Rel	c-Rel	reticuloendotheliosis oncogene	protein-coding
mm_12272.1	chr2	68979650	68979668	+	1	NA	intron (NM_172856, intron 3 of 9)	intron (NM_172856, intron 3 of 9)	118218	NM_001347161	241447	Mm.222222	NM_172856	ENSMUSG00000027035	Cers6	4732462C07Rik|AW544719|Lass6|T1L	ceramide synthase 6	protein-coding
mm_53149.1	chr6	125265471	125265481	+	1	NA	promoter-TSS (NR_015527)	promoter-TSS (NR_015527)	-49	NR_015527	73870	Mm.440681	NR_015527	ENSMUSG00000108129	4930417O13Rik	-	RIKEN cDNA 4930417O13 gene	ncRNA
mm_96063.1	chr11	59662472	59662543	+	1	NA	promoter-TSS (NM_201245)	promoter-TSS (NM_201245)	12	NM_012027	26936	Mm.2402	NM_012027	ENSMUSG00000005417	Mprip	9530046C02|AA536749|AI647711|C76423|RIP3|Rhoip3|mKIAA0864|p116Rip	myosin phosphatase Rho interacting protein	protein-coding
mm_62136.1	chr7	97083382	97083431	+	1	NA	intron (NM_001162477, intron 1 of 9)	PB1D10|SINE|Alu	1655	NM_010248	14389	Mm.42033	NM_010248	ENSMUSG00000004508	Gab2	AI463667|D130058I17Rik|p97	growth factor receptor bound protein 2-associated protein 2	protein-coding
mm_14572.1	chr2	135364772	135364784	+	1	NA	exon (NM_001145830, exon 26 of 32)	exon (NM_001145830, exon 26 of 32)	-41052	NR_039540	100628568		NR_039540	ENSMUSG00000092830	Mir3963	mmu-mir-3963|mu-mir-3963	microRNA 3963	ncRNA
mm_14111.1	chr2	125796853	125796869	+	1	NA	Intergenic	Intergenic	-13991	NM_177608	70354	Mm.138091	NM_133725	ENSMUSG00000035093	Secisbp2l	3110001I20Rik|AI504340|C630011I23	SECIS binding protein 2-like	protein-coding
mm_58589.1	chr7	5014439	5014454	+	1	NA	promoter-TSS (NM_011813)	promoter-TSS (NM_011813)	-193	NM_011813	23877	Mm.38911	NM_011813	ENSMUSG00000061374	Fiz1	AI790204|mFLJ00416	Flt3 interacting zinc finger protein 1	protein-coding
mm_115659.1	chr13	12461100	12461113	-	1	NA	intron (NM_018886, intron 1 of 9)	intron (NM_018886, intron 1 of 9)	632	NM_001291060	56048	Mm.474138	NM_018886	ENSMUSG00000057554	Lgals8	1200015E08Rik|AI326142|D13Ertd524e|Lgals-8	lectin, galactose binding, soluble 8	protein-coding
mm_126817.1	chr15	88710148	88710160	+	1	NA	intron (NM_001033274, intron 6 of 12)	ORR1A2-int|LTR|ERVL-MaLR	24065	NM_001033274	223770	Mm.254438	NM_001033274	ENSMUSG00000022387	Brd1	1110059H06Rik|AI316859|mKIAA4191	bromodomain containing 1	protein-coding
mm_102678.1	chr11	65261741	65261747	-	1	NA	intron (NM_146386, intron 1 of 12)	intron (NM_146386, intron 1 of 12)	8245	NM_145136	214384	Mm.32257	NM_145136	ENSMUSG00000020542	Myocd	BSAC2A|Srfcp	myocardin	protein-coding
mm_90052.1	chr10	116143943	116143952	+	1	NA	promoter-TSS (NM_001161837)	promoter-TSS (NM_001161837)	49	NM_001161837	19279	Mm.336316	NM_011217	ENSMUSG00000020151	Ptprr	Gmcp1|PTP-SL|PTPBR7|RPTPRR|mPTP213	protein tyrosine phosphatase, receptor type, R	protein-coding
mm_57642.1	chr6	128424884	128424935	-	1	NA	promoter-TSS (NM_133927)	promoter-TSS (NM_133927)	1	NM_133927	101142	Mm.31345	NM_133927	ENSMUSG00000001518	Itfg2	2700050P07Rik|AI646725	integrin alpha FG-GAP repeat containing 2	protein-coding
mm_163009.1	chr11	40451825	40451827	+	1	NA	Intergenic	Intergenic	240856	NM_134017	108645	Mm.293771	NM_134017	ENSMUSG00000042032	Mat2b	1110064C04Rik|2410018D16Rik|AI182287|AU022853|MAT-II|MATIIbeta|TGR	methionine adenosyltransferase II, beta	protein-coding
mm_99949.1	chr11	111276054	111276078	+	1	NA	Intergenic	Intergenic	209902	NM_008425	16518	Mm.4951	NM_008425	ENSMUSG00000041695	Kcnj2	IRK1|Kcnf1|Kir2.1	potassium inwardly-rectifying channel, subfamily J, member 2	protein-coding
mm_9619.1	chr1	176734210	176734213	-	1	NA	3' UTR (NM_001099637, exon 20 of 20)	3' UTR (NM_001099637, exon 20 of 20)	38212	NR_029775	723921		NR_029775	ENSMUSG00000065573	Mir350	Mirn350|mir-350|mmu-mir-350	microRNA 350	ncRNA
mm_23786.1	chr3	79345362	79345380	+	1	NA	promoter-TSS (NM_001142953)	promoter-TSS (NM_001142953)	-5	NM_001142953	100233207	Mm.373801	NM_001142953	ENSMUSG00000091685	Gm17359	-	predicted gene, 17359	protein-coding
mm_22588.1	chr3	13472872	13472927	+	1	NA	intron (NM_178631, intron 2 of 9)	CpG	1244	NM_001163328	76897	Mm.422625	NM_178631	ENSMUSG00000039717	Ralyl	0710005M24Rik	RALY RNA binding protein-like	protein-coding
mm_102701.1	chr11	66168468	66168480	-	1	NA	promoter-TSS (NM_001099633)	promoter-TSS (NM_001099633)	77	NM_001099633	237806	Mm.264210	NM_001099633	ENSMUSG00000056752	Dnah9	9030022M04|A230091C01|C230051G16|D11Ertd686e|Dnahc9|mKIAA0357	dynein, axonemal, heavy chain 9	protein-coding
mm_115196.1	chr13	108918098	108918101	+	1	NA	intron (NM_011056, intron 2 of 16)	(T)n|Simple_repeat|Simple_repeat	263922	NM_011056	238871	Mm.434429	NM_011056	ENSMUSG00000021699	Pde4d	9630011N22Rik|Dpde3	phosphodiesterase 4D, cAMP specific	protein-coding
mm_126230.1	chr15	78947912	78947934	+	1	NA	5' UTR (NM_001039155, exon 1 of 8)	5' UTR (NM_001039155, exon 1 of 8)	199	NM_001039155	110253	Mm.123714	NM_138579	ENSMUSG00000033088	Triobp	AI428493|EST478828|Tara|mKIAA1662	TRIO and F-actin binding protein	protein-coding
mm_110378.1	chr12	40205955	40205958	-	1	NA	intron (NM_013562, intron 9 of 11)	intron (NM_013562, intron 9 of 11)	-6641	NM_001033437	380755	Mm.390463	NM_001033437	ENSMUSG00000071342	Lsmem1	Gm889	leucine-rich single-pass membrane protein 1	protein-coding
mm_129571.1	chr15	79687745	79687756	-	1	NA	5' UTR (NM_028792, exon 1 of 4)	5' UTR (NM_028792, exon 1 of 4)	122	NM_028792	74158	Mm.323393	NM_028792	ENSMUSG00000022426	Josd1	1300006C06Rik|mKIAA0063	Josephin domain containing 1	protein-coding
mm_136277.1	chr16	91063848	91063868	-	1	NA	intron (NM_028905, intron 1 of 2)	RMER5|LTR|ERV1	5287	NM_001163695	74387	Mm.236220	NM_028905	ENSMUSG00000039851	4932438H23Rik	4931406G06Rik|AI550392	RIKEN cDNA 4932438H23 gene	protein-coding
mm_25941.1	chr3	131489738	131489753	+	1	NA	Intergenic	Intergenic	-75023	NM_001289479	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_133707.1	chr16	93153300	93153333	+	1	NA	Intergenic	Intergenic	199873	NR_040486	69857	Mm.81192	NR_040486	ENSMUSG00000100277	1810053B23Rik	1810008L18Rik|1810056K14Rik	RIKEN cDNA 1810053B23 gene	ncRNA
mm_95100.1	chr11	34047244	34047257	+	1	NA	promoter-TSS (NM_010696)	promoter-TSS (NM_010696)	49	NM_010696	16822	Mm.265350	NM_010696	ENSMUSG00000002699	Lcp2	AI323664|BB161688|SLP-76|SLP76|m1Khoe|twm	lymphocyte cytosolic protein 2	protein-coding
mm_62422.1	chr7	101321859	101321869	+	1	NA	exon (NM_019990, exon 2 of 7)	exon (NM_019990, exon 2 of 7)	545	NM_019990	56018	Mm.28896	NM_019990	ENSMUSG00000030688	Stard10	AV048538|CGI-52|NY-C0-28|PC-TP2|PCTP2|Pctpl|Sdccag28|SdccagG28|TISP-81	START domain containing 10	protein-coding
mm_117486.1	chr13	78183110	78183115	-	1	NA	Intergenic	Intergenic	13337	NM_001347538	13865	Mm.439653	NM_010151	ENSMUSG00000069171	Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR-3|EAR3|Erbal3|SVP44|Tcfcoup1	nuclear receptor subfamily 2, group F, member 1	protein-coding
mm_134290.1	chr16	14218937	14218960	-	1	NA	exon (NM_013607, exon 23 of 42)	exon (NM_013607, exon 23 of 42)	55673	NM_001114085	67203	Mm.24105	NM_023317	ENSMUSG00000022678	Nde1	2810027M15Rik|AU042936|AW822251|Nude|mNudE	nudE neurodevelopment protein 1	protein-coding
mm_141050.1	chr17	25566018	25566022	-	1	NA	3' UTR (NM_011447, exon 3 of 3)	3' UTR (NM_011447, exon 3 of 3)	4666	NM_011447	20681	Mm.258220	NM_011447	ENSMUSG00000024176	Sox8	-	SRY (sex determining region Y)-box 8	protein-coding
mm_45912.1	chr5	89435578	89435588	-	1	NA	exon (NM_008096, exon 9 of 13)	exon (NM_008096, exon 9 of 13)	22315	NM_008096	14473	Mm.196595	NM_008096	ENSMUSG00000035540	Gc	DBP|VDB	group specific component	protein-coding
mm_12500.1	chr2	71868508	71868513	+	1	NA	intron (NR_039557, intron 3 of 3).2	RLTR11C_MM|LTR|ERVK	-4714	NM_172665	228026	Mm.34411	NM_172665	ENSMUSG00000006494	Pdk1	B830012B01|D530020C15Rik	pyruvate dehydrogenase kinase, isoenzyme 1	protein-coding
mm_93864.1	chr10	122986470	122986498	-	1	NA	promoter-TSS (NR_029527)	promoter-TSS (NR_029527)	-760	NR_029527	387251		NR_029527	ENSMUSG00000065406	Mirlet7i	Mirnlet7i|let-7i|mmu-let-7i	microRNA let7i	ncRNA
mm_497.1	chr1	36939991	36940016	+	1	NA	promoter-TSS (NM_018872)	promoter-TSS (NM_018872)	-476	NM_018872	56030	Mm.186943	NM_018872	ENSMUSG00000026116	Tmem131	2610524E03Rik|CC28|D1Bwg0491e|Neg|RW1|YR-23|mKIAA0257	transmembrane protein 131	protein-coding
mm_131481.1	chr16	17200939	17200952	+	1	NA	intron (NM_009456, intron 1 of 3)	intron (NM_009456, intron 1 of 3)	547	NM_009456	22195	Mm.3074	NM_009456	ENSMUSG00000038965	Ube2l3	C79827|UbcM4|Ubce7	ubiquitin-conjugating enzyme E2L 3	protein-coding
mm_10865.1	chr2	25080498	25080530	+	1	NA	5' UTR (NM_028093, exon 1 of 10)	5' UTR (NM_028093, exon 1 of 10)	191	NM_028093	72090	Mm.33403	NM_028093	ENSMUSG00000036813	Entpd8	-	ectonucleoside triphosphate diphosphohydrolase 8	protein-coding
mm_99457.1	chr11	102434701	102434802	+	1	NA	exon (NM_008175, exon 8 of 13)	exon (NM_008175, exon 8 of 13)	4429	NM_008175	14824	Mm.1568	NM_008175	ENSMUSG00000034708	Grn	Pgrn|epithelin	granulin	protein-coding
mm_68315.1	chr7	105810948	105811095	-	1	NA	promoter-TSS (NM_025301)	promoter-TSS (NM_025301)	66	NM_025301	27397	Mm.44225	NM_025301	ENSMUSG00000030879	Mrpl17	MRP-L26|Rpml26	mitochondrial ribosomal protein L17	protein-coding
mm_148900.1	chr19	6910502	6910529	+	1	NA	promoter-TSS (NM_012021)	promoter-TSS (NM_012021)	817	NM_026306	67674	Mm.318804	NM_026306	ENSMUSG00000038812	Trmt112	0610038D11Rik|Trm112p	tRNA methyltransferase 11-2	protein-coding
mm_66600.1	chr7	45458526	45458559	-	1	NA	exon (NM_010240, exon 3 of 4)	exon (NM_010240, exon 3 of 4)	1344	NM_010240	14325	Mm.30357	NM_010240	ENSMUSG00000050708	Ftl1	Ftl|Ftl-1|L-ferritin	ferritin light polypeptide 1	protein-coding
mm_101244.1	chr11	20741355	20741365	-	1	NA	5' UTR (NM_001252503, exon 1 of 8)	5' UTR (NM_001252503, exon 1 of 8)	196	NM_001290545	216549	Mm.356580	NM_181411	ENSMUSG00000049659	Aftph	-	aftiphilin	protein-coding
mm_157930.1	chrX	79918456	79918484	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-247035	NM_028025	71967	Mm.379207	NM_028025	ENSMUSG00000046942	Mageb16	2410003J06Rik	melanoma antigen family B, 16	protein-coding
mm_101208.1	chr11	20063024	20063034	-	1	NA	3' UTR (NM_146243, exon 9 of 9)	3' UTR (NM_146243, exon 9 of 9)	49922	NM_146243	66713	Mm.259045	NM_146243	ENSMUSG00000020152	Actr2	4921510D23Rik|AA409782|Arp2|D6Ertd746e	ARP2 actin-related protein 2	protein-coding
mm_169595.1	chr15	31446819	31446837	-	1	NA	intron (NM_145852, intron 3 of 4)	intron (NM_145852, intron 3 of 4)	6861	NM_145852	252967	Mm.436668	NM_145852	ENSMUSG00000022236	Ropn1l	ASP|AV047578|Akapasp	ropporin 1-like	protein-coding
mm_26794.1	chr3	9801595	9801597	-	1	NA	intron (NM_001195031, intron 1 of 8)	intron (NM_001195031, intron 1 of 8)	32083	NM_053182	94212	Mm.23897	NM_053182	ENSMUSG00000027508	Pag1	Cbp|F730007C19Rik|Pag	phosphoprotein associated with glycosphingolipid microdomains 1	protein-coding
mm_59355.1	chr7	25680781	25680834	+	1	NA	promoter-TSS (NM_172148)	promoter-TSS (NM_172148)	-351	NM_172148	232987	Mm.22849	NM_172148	ENSMUSG00000063439	B9d2	stumpy	B9 protein domain 2	protein-coding
mm_168432.1	chr1	134533985	134533992	+	1	NA	Intergenic	RLTR1B|LTR|ERV1	15694	NM_001145300	71001	Mm.158529	NM_183292	ENSMUSG00000046367	Mgat4e	4931440L10Rik	MGAT4 family, member E	protein-coding
mm_153043.1	chr19	32061481	32061493	-	1	NA	intron (NM_018830, intron 2 of 23)	intron (NM_018830, intron 2 of 23)	41653	NM_018830	54447	Mm.491229	NM_018830	ENSMUSG00000024887	Asah2	AI585898	N-acylsphingosine amidohydrolase 2	protein-coding
mm_134843.1	chr16	26526745	26526774	-	1	NA	promoter-TSS (NM_001101640)	promoter-TSS (NM_001101640)	12	NM_001101640	100043057	Mm.295917	NM_001101640	ENSMUSG00000091972	Tmem207	Gm540	transmembrane protein 207	protein-coding
mm_50981.1	chr6	62119537	62119541	+	1	NA	intron (NM_001164316, intron 10 of 10)	Lx3A|LINE|L1	-938729	NR_040287	100504262	Mm.438066	NR_040287		A730020E08Rik	-	RIKEN cDNA A730020E08 gene	ncRNA
mm_125308.1	chr15	37346498	37346502	+	1	NA	intron (NM_026496, intron 13 of 15)	intron (NM_026496, intron 13 of 15)	-79054	NM_029113	74892	Mm.107630	NM_029113	ENSMUSG00000022288	4930447A16Rik	-	RIKEN cDNA 4930447A16 gene	protein-coding
mm_78353.1	chr9	25481624	25481634	+	1	NA	promoter-TSS (NM_026189)	promoter-TSS (NM_026189)	32	NM_026189	67484	Mm.112977	NM_026189	ENSMUSG00000036611	Eepd1	2310005P05Rik|AI481005	endonuclease/exonuclease/phosphatase family domain containing 1	protein-coding
mm_164993.1	chr19	14243430	14243433	-	1	NA	Intergenic	Intergenic	195075	NR_003027	19862		NR_003027	ENSMUSG00000095132	Rnu6	-	U6 small nuclear RNA	snRNA
mm_173173.1	chrX	49567517	49567521	-	1	NA	Intergenic	Lx9|LINE|L1	97069	NM_001081123	75404	Mm.44305	NM_001081123	ENSMUSG00000036198	Arhgap36	1100001E04Rik|rho-gap	Rho GTPase activating protein 36	protein-coding
mm_28876.1	chr3	97755491	97755494	-	1	NA	exon (NM_001289701, exon 13 of 47)	exon (NM_001289701, exon 13 of 47)	12522	NR_110360	83679	Mm.129840	NM_031401	ENSMUSG00000038170	Pde4dip	4732458A06Rik|9430063L05Rik|C87016|D130016K21Rik|D3Bwg1078e|Usmg4|mKIAA0454	phosphodiesterase 4D interacting protein (myomegalin)	protein-coding
mm_85868.1	chr9	110879512	110879524	-	1	NA	promoter-TSS (NM_001146059)	promoter-TSS (NM_001146059)	565	NM_146260	20776	Mm.390229	NM_146260	ENSMUSG00000049555	Tmie	5131400L21Rik|Mm.87012|sr	transmembrane inner ear	protein-coding
mm_74399.1	chr8	3269612	3269615	-	1	NA	intron (NM_010568, intron 1 of 20)	intron (NM_010568, intron 1 of 20)	10004	NM_010568	16337	Mm.268003	NM_010568	ENSMUSG00000005534	Insr	4932439J01Rik|CD220|D630014A15Rik|IR|IR-A|IR-B	insulin receptor	protein-coding
mm_18848.1	chr2	75633853	75633863	-	1	NA	Intergenic	RMER20B|LTR|ERVK	-25401	NM_146130	229279	Mm.316306	NM_053263	ENSMUSG00000059005	Hnrnpa3	2410013L13Rik|2610209F03Rik|2610510D13Rik|Hnrpa3	heterogeneous nuclear ribonucleoprotein A3	protein-coding
mm_69631.1	chr7	137410929	137410938	-	1	NA	promoter-TSS (NM_029886)	promoter-TSS (NM_029886)	-177	NM_029886	77252	Mm.29184	NM_029886	ENSMUSG00000040139	9430038I01Rik	-	RIKEN cDNA 9430038I01 gene	protein-coding
mm_98544.1	chr11	95010278	95010293	+	1	NA	5' UTR (NM_146025, exon 1 of 10)	5' UTR (NM_146025, exon 1 of 10)	406	NM_146025	217125	Mm.297199	NM_146025	ENSMUSG00000047181	Samd14	AI839049|AI854782|BC034054	sterile alpha motif domain containing 14	protein-coding
mm_17555.1	chr2	30124478	30124509	-	1	NA	5' UTR (NM_178694, exon 1 of 16)	5' UTR (NM_178694, exon 1 of 16)	118	NM_178694	227693	Mm.44526	NM_178694	ENSMUSG00000039686	Zer1	C230075L19Rik|Zyg11bl	zyg-11 related, cell cycle regulator	protein-coding
mm_115452.1	chr13	118714912	118714950	+	1	NA	5' UTR (NM_008002, exon 1 of 3)	5' UTR (NM_008002, exon 1 of 3)	232	NM_008002	14165	Mm.317323	NM_008002	ENSMUSG00000021732	Fgf10	AEY17|BB213776|Fgf-10|Gsfaey17	fibroblast growth factor 10	protein-coding
mm_130123.1	chr15	89568265	89568274	-	1	NA	promoter-TSS (NM_013455)	promoter-TSS (NM_013455)	-57	NM_013455	11434	Mm.57	NM_013455	ENSMUSG00000022622	Acr	-	acrosin prepropeptide	protein-coding
mm_162010.1	chr19	42752800	42752800	-	1	NA	promoter-TSS (NM_029011)	promoter-TSS (NM_029011)	-25	NM_029011	74580	Mm.329858	NM_029011	ENSMUSG00000060224	Pyroxd2	3830409H07Rik|4833409A17Rik	pyridine nucleotide-disulphide oxidoreductase domain 2	protein-coding
mm_155154.1	chrX	52913476	52913498	+	1	NA	intron (NM_001290546, intron 1 of 8)	intron (NM_001290546, intron 1 of 8)	1273	NM_001290546	70998	Mm.26870	NM_027642	ENSMUSG00000025626	Phf6	2700007B13Rik|4931428F02Rik|mKIAA1823	PHD finger protein 6	protein-coding
mm_83913.1	chr9	56418024	56418052	-	1	NA	promoter-TSS (NM_025812)	promoter-TSS (NM_025812)	12	NM_172924	244895	Mm.490331	NM_172924	ENSMUSG00000074305	Peak1	1110049L02Rik|9530046P14|AA690169|BE132841|C230081A13Rik|SGK269|mKIAA2002	pseudopodium-enriched atypical kinase 1	protein-coding
mm_149880.1	chr19	25237471	25237507	+	1	NA	intron (NM_181404, intron 1 of 13)	CpG	287	NM_181404	107351	Mm.260722	NM_181404	ENSMUSG00000032702	Kank1	A930031B09Rik|AU015049|AW121052|Ankrd15|D330024H06Rik|mKIAA0172	KN motif and ankyrin repeat domains 1	protein-coding
mm_69601.1	chr7	135716537	135716570	-	1	NA	promoter-TSS (NM_001081117)	promoter-TSS (NM_001081117)	-174	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_70624.1	chr8	13674490	13674526	+	1	NA	intron (NM_009025, intron 1 of 23)	intron (NM_009025, intron 1 of 23)	3079	NM_009025	19414	Mm.18517	NM_009025	ENSMUSG00000031453	Rasa3	AI326412|C86362|E130011G04|GAPIII|hlb381|scat	RAS p21 protein activator 3	protein-coding
mm_42279.1	chr5	114155472	114155515	+	1	NA	Intergenic	Intergenic	-10025	NM_133904	100705	Mm.81793	NM_133904	ENSMUSG00000042010	Acacb	AI597064|AW743042|Acc2|Accb	acetyl-Coenzyme A carboxylase beta	protein-coding
mm_38860.1	chr4	149426399	149426423	-	1	NA	5' UTR (NM_022022, exon 1 of 27)	5' UTR (NM_022022, exon 1 of 27)	220	NM_022022	63958	Mm.415260	NM_022022	ENSMUSG00000028960	Ube4b	4930551I19Rik|4933406G05Rik|AU014668|D4Bwg0973e|UFD2|UFD2a|Ufd2p|mKIAA0684	ubiquitination factor E4B	protein-coding
mm_142844.1	chr17	51796390	51796401	-	1	NA	intron (NM_009122, intron 5 of 10)	intron (NM_009122, intron 5 of 10)	15659	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_50317.1	chr6	47920585	47920636	+	1	NA	promoter-TSS (NM_001145881)	promoter-TSS (NM_001145881)	42	NM_001145881	232784	Mm.196782	NM_145576	ENSMUSG00000052763	Zfp212	Znf212|mKIAA3011	Zinc finger protein 212	protein-coding
mm_110067.1	chr12	21384473	21384497	-	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	-10853	NM_009615	11491	Mm.27681	NM_009615	ENSMUSG00000052593	Adam17	CD156b|Tace	a disintegrin and metallopeptidase domain 17	protein-coding
mm_142106.1	chr17	35835804	35835814	-	1	NA	exon (NM_011655, exon 4 of 4)	exon (NM_011655, exon 4 of 4)	2492	NM_011655	22154	Mm.273538	NM_011655	ENSMUSG00000001525	Tubb5	AA408537|AI596182|B130022C14Rik|M(beta)5	tubulin, beta 5 class I	protein-coding
mm_159774.1	chr5	103655670	103655670	-	1	NA	promoter-TSS (NM_001163550)	promoter-TSS (NM_001163550)	54	NM_028824	74218	Mm.159141	NM_028824	ENSMUSG00000029320	1700016H13Rik	-	RIKEN cDNA 1700016H13 gene	protein-coding
mm_52661.1	chr6	117900356	117900363	+	1	NA	promoter-TSS (NM_001166432)	promoter-TSS (NM_001166432)	19	NM_001166432	98758	Mm.422979	NM_133834	ENSMUSG00000042079	Hnrnpf	4833420I20Rik|AA407306|Hnrpf	heterogeneous nuclear ribonucleoprotein F	protein-coding
mm_17193.1	chr2	25467839	25467845	-	1	NA	exon (NM_008963, exon 5 of 7)	exon (NM_008963, exon 5 of 7)	1907	NM_008963	19215	Mm.1008	NM_008963	ENSMUSG00000015090	Ptgds	21kDa|L-PGDS|PGD2|PGDS|PGDS2|Ptgs3	prostaglandin D2 synthase (brain)	protein-coding
mm_73846.1	chr8	117595164	117595169	+	1	NA	intron (NM_172285, intron 19 of 32)	(T)n|Simple_repeat|Simple_repeat	76349	NM_028725	74032	Mm.296302	NM_028725	ENSMUSG00000034308	Sdr42e1	4632417N05Rik|AI117603	short chain dehydrogenase/reductase family 42E, member 1	protein-coding
mm_29337.1	chr3	108200808	108200858	-	1	NA	promoter-TSS (NM_028061)	promoter-TSS (NM_028061)	1	NM_028061	72023	Mm.246391	NM_028061	ENSMUSG00000048796	Cyb561d1	1600010M23Rik|AI605489|AW457162	cytochrome b-561 domain containing 1	protein-coding
mm_111388.1	chr12	87922440	87922445	-	1	NA	Intergenic	MTE2a|LTR|ERVL-MaLR	29608	NM_001177574	100039052	Mm.431321	NM_001177574		Gm2022	-	predicted pseudogene 2022	protein-coding
mm_134058.1	chr16	6842124	6842125	-	1	NA	intron (NM_021477, intron 5 of 16)	intron (NM_021477, intron 5 of 16)	-227711	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_161486.1	chr15	84719921	84719921	+	1	NA	promoter-TSS (NM_001164628)	promoter-TSS (NM_001164628)	-131	NM_001164628	73167	Mm.128411	NM_028455	ENSMUSG00000078954	Arhgap8	3110043J09Rik	Rho GTPase activating protein 8	protein-coding
mm_89304.1	chr10	87914525	87914539	+	1	NA	intron (NM_001314010, intron 4 of 4)	intron (NM_001314010, intron 4 of 4)	-52139	NR_000040	22172	Mm.391420	NR_000040		Tyms-ps	-	thymidylate synthase, pseudogene	pseudo
mm_32340.1	chr4	104741619	104741636	+	1	NA	non-coding (NR_104385, exon 16 of 16)	non-coding (NR_104385, exon 16 of 16)	-24690	NM_133882	110382	Mm.87072	NM_133882	ENSMUSG00000029656	C8b	4930439B20Rik|AI595927	complement component 8, beta polypeptide	protein-coding
mm_109235.1	chr12	108855333	108855362	+	1	NA	exon (NM_001012310, exon 5 of 6)	exon (NM_001012310, exon 5 of 6)	4218	NM_001012310	104910	Mm.202653	NM_001012310	ENSMUSG00000048856	Slc25a47	AI132487|AI876593|HDMCP	solute carrier family 25, member 47	protein-coding
mm_124035.1	chr14	77032504	77032516	-	1	NA	intron (NM_172488, intron 5 of 7)	L1MB3|LINE|L1	4107	NM_172488	210808	Mm.89278	NM_172488	ENSMUSG00000044350	Lacc1	9030625A04Rik	laccase (multicopper oxidoreductase) domain containing 1	protein-coding
mm_56373.1	chr6	94124871	94124873	-	1	NA	intron (NM_001029850, intron 1 of 23)	intron (NM_001029850, intron 1 of 23)	112570	NR_130996	78178	Mm.452749	NR_130996	ENSMUSG00000045095	4930511A08Rik	-	RIKEN cDNA 4930511A08 gene	ncRNA
mm_15329.1	chr2	155755001	155755014	+	1	NA	3' UTR (NM_011171, exon 4 of 4)	3' UTR (NM_011171, exon 4 of 4)	3790	NM_011171	19124	Mm.3243	NM_011171	ENSMUSG00000027611	Procr	AI325044|Ccca|Ccd41|Epcr	protein C receptor, endothelial	protein-coding
mm_75813.1	chr8	70303124	70303127	-	1	NA	promoter-TSS (NM_001024922)	promoter-TSS (NM_001024922)	340	NM_021538	59042	Mm.28668	NM_021538	ENSMUSG00000055681	Cope	1110005D17Rik|Cope1	coatomer protein complex, subunit epsilon	protein-coding
mm_66076.1	chr7	30924170	30924185	-	1	NA	promoter-TSS (NM_183257)	promoter-TSS (NM_183257)	4	NM_183257	66438	Mm.389860	NM_183257	ENSMUSG00000056978	Hamp2	1810073K19Rik|HEPC2	hepcidin antimicrobial peptide 2	protein-coding
mm_47776.1	chr5	131885916	131885919	-	1	NA	intron (NM_177047, intron 4 of 18)	B4A|SINE|B4	5648	NR_040704	75369	Mm.389696	NR_040704	ENSMUSG00000105773	4930563F08Rik	-	RIKEN cDNA 4930563F08 gene	ncRNA
mm_93052.1	chr10	88583568	88583577	-	1	NA	intron (NM_175418, intron 2 of 28)	RMER1A|Other|Other	21580	NM_001252372	109272	Mm.147208	NM_175418	ENSMUSG00000020061	Mybpc1	8030451F13Rik	myosin binding protein C, slow-type	protein-coding
mm_108617.1	chr12	85524716	85524742	+	1	NA	Intergenic	Intergenic	50828	NM_010234	14281	Mm.246513	NM_010234	ENSMUSG00000021250	Fos	D12Rfj1|c-fos|cFos	FBJ osteosarcoma oncogene	protein-coding
mm_167949.1	chrX	139610661	139610672	+	1	NA	promoter-TSS (NM_023270)	promoter-TSS (NM_023270)	46	NM_023270	66889	Mm.27764	NM_023270	ENSMUSG00000031438	Rnf128	1300002C13Rik|AI987883|GRAIL|Greul1	ring finger protein 128	protein-coding
mm_72030.1	chr8	70762935	70762979	+	1	NA	3' UTR (NM_023065, exon 8 of 8)	3' UTR (NM_023065, exon 8 of 8)	-2036	NM_183170	234384	Mm.213010	NM_183170	ENSMUSG00000035559	Mpv17l2	Fksg24	MPV17 mitochondrial membrane protein-like 2	protein-coding
mm_431.1	chr1	34473315	34473322	+	1	NA	intron (NM_011206, intron 13 of 14)	intron (NM_011206, intron 13 of 14)	13572	NM_011206	19253	Mm.361	NM_011206	ENSMUSG00000026126	Ptpn18	FLP1|HSCF|PTP-HSCF|PTP-K1|Ptpk1	protein tyrosine phosphatase, non-receptor type 18	protein-coding
mm_123854.1	chr14	70925825	70925858	-	1	NA	exon (NM_008115, exon 4 of 9)	exon (NM_008115, exon 4 of 9)	35734	NM_001302094	14586	Mm.32619	NM_008115	ENSMUSG00000022103	Gfra2	-	glial cell line derived neurotrophic factor family receptor alpha 2	protein-coding
mm_129408.1	chr15	78298081	78298092	-	1	NA	intron (NM_001287389, intron 2 of 11)	intron (NM_001287389, intron 2 of 11)	7635	NM_007781	12984	Mm.1940	NM_007781	ENSMUSG00000071714	Csf2rb2	AIC2A|BetaIl3|Bil3|Csfgmrb|Il3r|Il3rb|Il3rb2	colony stimulating factor 2 receptor, beta 2, low-affinity (granulocyte-macrophage)	protein-coding
mm_91670.1	chr10	43174578	43174580	-	1	NA	promoter-TSS (NR_102361)	promoter-TSS (NR_102361)	-49	NM_175407	109205	Mm.153750	NM_175407	ENSMUSG00000038248	Sobp	2900009C16Rik|5330439J01Rik|JXC1|jc	sine oculis-binding protein homolog (Drosophila)	protein-coding
mm_94357.1	chr11	4986884	4986894	+	1	NA	promoter-TSS (NM_001243044)	promoter-TSS (NM_001243044)	65	NM_007454	11764	Mm.274816	NM_007454	ENSMUSG00000009090	Ap1b1	Adtb1|b2b1660Clo	adaptor protein complex AP-1, beta 1 subunit	protein-coding
mm_168036.1	chrY	90742521	90742536	-	1	NA	Intergenic	CpG	12522	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_48565.1	chr5	143225877	143225892	-	1	NA	promoter-TSS (NM_029048)	promoter-TSS (NM_029048)	-2	NM_029048	74673	Mm.273303	NM_029048	ENSMUSG00000039296	Spdye4a	4930445A17Rik|4930451F05Rik|RINGO E4A|Spdy2|Spdyb|Spdye4|Spy/Ringo B	speedy/RINGO cell cycle regulator family, member E4A	protein-coding
mm_132276.1	chr16	32930942	32930950	+	1	NA	intron (NM_001310674, intron 1 of 21)	B1F|SINE|Alu	16846	NM_001310672	70144	Mm.491178	NM_001081255	ENSMUSG00000022801	Lrch3	2210409B11Rik|AW215594|Gm1742	leucine-rich repeats and calponin homology (CH) domain containing 3	protein-coding
mm_61761.1	chr7	82771769	82771803	+	1	NA	intron (NM_175317, intron 18 of 19)	intron (NM_175317, intron 18 of 19)	-16142	NR_046004	77800	Mm.444811	NR_046004	ENSMUSG00000086690	4933406J10Rik	A930009F24Rik	RIKEN cDNA 4933406J10 gene	ncRNA
mm_146156.1	chr18	75005840	75005945	+	1	NA	promoter-TSS (NM_001001181)	promoter-TSS (NM_001001181)	-8	NM_001001181	407819	Mm.29866	NM_001001181	ENSMUSG00000036299	BC031181	-	cDNA sequence BC031181	protein-coding
mm_66288.1	chr7	37774001	37774007	-	1	NA	Intergenic	Intergenic	-4252	NM_172385	243937	Mm.322505	NM_172385	ENSMUSG00000043456	Zfp536	9630010P11Rik|Znf536|mKIAA0390	zinc finger protein 536	protein-coding
mm_113779.1	chr13	45391781	45391794	+	1	NA	intron (NM_153789, intron 2 of 6)	intron (NM_153789, intron 2 of 6)	2045	NM_153789	218203	Mm.212855	NM_153789	ENSMUSG00000038175	Mylip	9430057C20Rik|Mir	myosin regulatory light chain interacting protein	protein-coding
mm_17695.1	chr2	32338074	32338085	-	1	NA	non-coding (NR_125959, exon 5 of 22)	non-coding (NR_125959, exon 5 of 22)	15250	NM_001301737	13429	Mm.44736	NM_010065	ENSMUSG00000026825	Dnm1	AI838169|Dnm|Ftfl|mKIAA4093	dynamin 1	protein-coding
mm_6447.1	chr1	74001939	74001942	-	1	NA	intron (NM_027884, intron 6 of 34)	intron (NM_027884, intron 6 of 34)	122507	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_133258.1	chr16	77329543	77329553	+	1	NA	non-coding (NR_015543, exon 1 of 5)	non-coding (NR_015543, exon 1 of 5)	220	NR_015543	77994	Mm.394688	NR_015543	ENSMUSG00000090386	Mir99ahg	2810055G20Rik|D730043B02Rik	Mir99a and Mirlet7c-1 host gene (non-protein coding)	ncRNA
mm_4500.1	chr1	173673784	173673808	+	1	NA	5' UTR (NM_001162938, exon 1 of 7)	5' UTR (NM_001162938, exon 1 of 7)	116	NM_001162938	100033459	Mm.303377	NM_001162938	ENSMUSG00000066677	Ifi208	9830148g24rik|E430029J22Rik|Pydc3|Pyr-rv1	interferon activated gene 208	protein-coding
mm_78767.1	chr9	43310808	43310818	+	1	NA	promoter-TSS (NM_023655)	promoter-TSS (NM_023655)	50	NM_023655	72169	Mm.273277	NM_023655	ENSMUSG00000032013	Trim29	1110047J21Rik|2810431N19Rik|4732461M22Rik|AI119726	tripartite motif-containing 29	protein-coding
mm_137516.1	chr17	27101535	27101563	+	1	NA	intron (NM_080553, intron 23 of 57)	intron (NM_080553, intron 23 of 57)	10304	NR_106142	102465779		NR_106142	ENSMUSG00000098826	Mir7677	Gm27400|mmu-mir-7677	microRNA 7677	ncRNA
mm_35065.1	chr4	6454159	6454226	-	1	NA	promoter-TSS (NM_010945)	promoter-TSS (NM_010945)	79	NM_010945	18201	Mm.3059	NM_010945	ENSMUSG00000028245	Nsmaf	AA959567|C630007J05|Fan	neutral sphingomyelinase (N-SMase) activation associated factor	protein-coding
mm_138783.1	chr17	37270609	37270620	+	1	NA	exon (NM_013819, exon 2 of 8)	exon (NM_013819, exon 2 of 8)	380	NM_013819	14991	Mm.14437	NM_013819	ENSMUSG00000016206	H2-M3	H-2M3|Hmt|M3a|MuprM3|MuprM301|MuprM302|R4B2	histocompatibility 2, M region locus 3	protein-coding
mm_63701.1	chr7	130645701	130645714	+	1	NA	intron (NM_001004468, intron 3 of 21)	intron (NM_001004468, intron 3 of 21)	-46849	NM_001347637	57752	Mm.86322	NM_021314	ENSMUSG00000030852	Tacc2	mKIAA4180	transforming, acidic coiled-coil containing protein 2	protein-coding
mm_160339.1	chr8	14888476	14888476	+	1	NA	promoter-TSS (NM_012000)	promoter-TSS (NM_012000)	-60	NM_012000	26889	Mm.254027	NM_012000	ENSMUSG00000026317	Cln8	mnd	ceroid-lipofuscinosis, neuronal 8	protein-coding
mm_70164.1	chr7	143592491	143592511	-	1	NA	exon (NM_013742, exon 2 of 23)	exon (NM_013742, exon 2 of 23)	7589	NM_001252593	27267	Mm.125659	NM_013742	ENSMUSG00000010755	Cars	CA3	cysteinyl-tRNA synthetase	protein-coding
mm_58414.1	chr7	3290541	3290549	+	1	NA	promoter-TSS (NM_016969)	promoter-TSS (NM_016969)	-10	NM_016969	50918	Mm.29874	NM_016969	ENSMUSG00000068566	Myadm	D7Wsu62e	myeloid-associated differentiation marker	protein-coding
mm_133580.1	chr16	91407086	91407132	+	1	NA	intron (NM_008349, intron 1 of 6)	intron (NM_008349, intron 1 of 6)	874	NM_008349	16155	Mm.4154	NM_008349	ENSMUSG00000022969	Il10rb	6620401D04Rik|AI528744|CRF2-4|Crfb4|D16H21S58|D21S58h|IL-10R2|Il10r2	interleukin 10 receptor, beta	protein-coding
mm_12478.1	chr2	71529086	71529110	+	1	NA	promoter-TSS (NM_010053)	promoter-TSS (NM_010053)	-347	NM_010053	13390	Mm.475101	NM_010053	ENSMUSG00000041911	Dlx1	Dlx|Dlx-1	distal-less homeobox 1	protein-coding
mm_119408.1	chr14	44988577	44988611	+	1	NA	5' UTR (NM_008964, exon 1 of 2)	5' UTR (NM_008964, exon 1 of 2)	483	NM_008964	19217	Mm.4630	NM_008964	ENSMUSG00000037759	Ptger2	EP2|Ptgerep2	prostaglandin E receptor 2 (subtype EP2)	protein-coding
mm_133320.1	chr16	77674603	77674628	+	1	NA	Intergenic	Intergenic	28342	NR_029540	723952		NR_029540	ENSMUSG00000065472	Mir125b-2	Mirn125b-2|mir-125b-2	microRNA 125b-2	ncRNA
mm_108208.1	chr12	76914637	76914655	+	1	NA	exon (NM_145927, exon 10 of 12)	exon (NM_145927, exon 10 of 12)	47602	NM_008558	17187	Mm.268548	NM_008558	ENSMUSG00000059436	Max	AA960152|AI875693|bHLHd4|bHLHd5|bHLHd6|bHLHd7|bHLHd8	Max protein	protein-coding
mm_132412.1	chr16	35063022	35063026	+	1	NA	intron (NM_023587, intron 3 of 6)	intron (NM_023587, intron 3 of 6)	40603	NM_023587	70757	Mm.27286	NM_023587	ENSMUSG00000035376	Hacd2	6330408J20Rik|AI255777|AI481689|Hcad2|Ptplb	3-hydroxyacyl-CoA dehydratase 2	protein-coding
mm_26566.1	chr3	146570393	146570424	+	1	NA	Intergenic	Intergenic	-26741	NM_009474	22262	Mm.10865	NM_009474	ENSMUSG00000028186	Uox	AI663847	urate oxidase	protein-coding
mm_143665.1	chr17	79871933	79871943	-	1	NA	intron (NM_001286647, intron 1 of 12)	intron (NM_001286647, intron 1 of 12)	24185	NM_178050	56298	Mm.175403	NM_019717	ENSMUSG00000059811	Atl2	2010110I21Rik|AA407293|AV334690|Aip-2|Arl6ip2	atlastin GTPase 2	protein-coding
mm_58516.1	chr7	4133646	4133651	+	1	NA	intron (NM_001305822, intron 12 of 13)	intron (NM_001305822, intron 12 of 13)	3278	NR_033548	100037396	Mm.447887	NR_033548	ENSMUSG00000085886	D030047H15Rik	Gm15924|OTTMUSG00000027889	RIKEN cDNA D030047H15 gene	ncRNA
mm_166402.1	chr5	136039059	136039072	+	1	NA	exon (NM_175309, exon 2 of 6)	exon (NM_175309, exon 2 of 6)	569	NM_175309	100647	Mm.3089	NM_175309	ENSMUSG00000042985	Upk3b	AI447729|AI957187|P35|PMS2L14|UpIIIb	uroplakin 3B	protein-coding
mm_22140.1	chr2	170775721	170775739	-	1	NA	intron (NM_001163686, intron 1 of 7)	intron (NM_001163686, intron 1 of 7)	43923	NM_001163686	76829	Mm.41633	NM_029761	ENSMUSG00000027560	Dok5	2700055C10Rik	docking protein 5	protein-coding
mm_145272.1	chr18	52768389	52768417	+	1	NA	5' UTR (NM_001199154, exon 1 of 11)	5' UTR (NM_001199154, exon 1 of 11)	259	NM_001199154	67847	Mm.292168	NM_026408	ENSMUSG00000024534	Sncaip	2810407O15Rik|4933427B05Rik|BB104594|SYPH1	synuclein, alpha interacting protein (synphilin)	protein-coding
mm_1699.1	chr1	75143244	75143271	+	1	NA	promoter-TSS (NM_026977)	promoter-TSS (NM_026977)	99	NM_001305232	227298	Mm.273062	NM_170755	ENSMUSG00000049339	Fam134a	-	family with sequence similarity 134, member A	protein-coding
mm_159273.1	chr2	164585174	164585174	-	1	NA	promoter-TSS (NM_001177848)	promoter-TSS (NM_001177848)	3	NM_001177848	209351	Mm.293365	NM_001033240	ENSMUSG00000074595	Wfdc6a	Gm122	WAP four-disulfide core domain 6A	protein-coding
mm_130086.1	chr15	89378997	89379028	-	1	NA	intron (NM_001013022, intron 1 of 4)	CpG-5245	242	NM_001013022	70113	Mm.247273	NM_001013022	ENSMUSG00000047394	Odf3b	2010001J22Rik	outer dense fiber of sperm tails 3B	protein-coding
mm_133886.1	chr16	96531287	96531314	+	1	NA	Intergenic	Intergenic	63694	NM_008791	18546	Mm.5023	NM_008791	ENSMUSG00000090223	Pcp4	P16Rimb19|Pcp-4|Pep19	Purkinje cell protein 4	protein-coding
mm_118189.1	chr13	107726376	107726401	-	1	NA	3' UTR (NM_145456, exon 15 of 15)	3' UTR (NM_145456, exon 15 of 15)	34699	NR_029759	723929		NR_029759	ENSMUSG00000065425	Mir325	Mirn325|mmu-mir-325	microRNA 325	ncRNA
mm_167606.1	chr9	53667408	53667418	-	1	NA	promoter-TSS (NM_001161618)	promoter-TSS (NM_001161618)	94	NM_001161618	75717	Mm.218910	NM_027807	ENSMUSG00000032030	Cul5	4921514I20Rik|8430423K24Rik|AI852817|C030032G03Rik|C330021I08Rik|VACM-1|VACM1	cullin 5	protein-coding
mm_49799.1	chr6	35510566	35510578	+	1	NA	3' UTR (NM_008098, exon 4 of 4)	3' UTR (NM_008098, exon 4 of 4)	29316	NM_008098	14489	Mm.182746	NM_008098	ENSMUSG00000029840	Mtpn	5033418D15Rik|Gcdp|V1	myotrophin	protein-coding
mm_86028.1	chr9	113662357	113662386	-	1	NA	exon (NM_001164677, exon 13 of 18)	exon (NM_001164677, exon 13 of 18)	45888	NM_001164678	18571	Mm.29816	NM_011052	ENSMUSG00000032504	Pdcd6ip	AI480591|AW544830|Aip1|Alix|C76364|Eig2|mKIAA1375	programmed cell death 6 interacting protein	protein-coding
mm_66183.1	chr7	34168517	34168582	-	1	NA	promoter-TSS (NM_016682)	promoter-TSS (NM_016682)	-20	NM_016682	50995	Mm.27560	NM_016682	ENSMUSG00000052997	Uba2	AA986091|Arx|Sae2|UBA1|Ubl1a2|Uble1b	ubiquitin-like modifier activating enzyme 2	protein-coding
mm_137234.1	chr17	24419464	24419467	+	1	NA	intron (NM_009070, intron 4 of 8)	B3|SINE|B2	4790	NM_001080128	19826	Mm.1951	NM_009070	ENSMUSG00000034681	Rnps1	-	ribonucleic acid binding protein S1	protein-coding
mm_134119.1	chr16	10313863	10313899	-	1	NA	promoter-TSS (NM_007929)	promoter-TSS (NM_007929)	87	NM_007929	13731	Mm.246009	NM_007929	ENSMUSG00000022505	Emp2	XMP	epithelial membrane protein 2	protein-coding
mm_6198.1	chr1	65184115	65184118	-	1	NA	intron (NM_001111320, intron 1 of 8)	intron (NM_001111320, intron 1 of 8)	2363	NM_001111320	15926	Mm.9925	NM_010497	ENSMUSG00000025950	Idh1	AI314845|AI788952|E030024J03Rik|Id-1|Idh-1|Idpc	isocitrate dehydrogenase 1 (NADP+), soluble	protein-coding
mm_131161.1	chr16	6986700	6986708	+	1	NA	intron (NM_021477, intron 5 of 16)	B3A|SINE|B2	-83131	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_172662.1	chr8	41936834	41936835	+	1	NA	intron (NR_045497, intron 3 of 5)	L1Md_F2|LINE|L1	109567	NR_045497	69966	Mm.416903	NR_045497	ENSMUSG00000102046	2810404M03Rik	-	RIKEN cDNA 2810404M03 gene	ncRNA
mm_166477.1	chr5	144295111	144295117	+	1	NA	intron (NM_025833, intron 3 of 13)	ID_B1|SINE|B4	18053	NR_040432	100504231	Mm.441035	NR_040432	ENSMUSG00000086894	Gm15708	OTTMUSG00000025583	predicted gene 15708	ncRNA
mm_152956.1	chr19	29325111	29325121	-	1	NA	exon (NM_013754, exon 1 of 2)	exon (NM_013754, exon 1 of 2)	202	NM_013754	27356	Mm.306511	NM_013754	ENSMUSG00000050957	Insl6	RIF1	insulin-like 6	protein-coding
mm_121536.1	chr14	122375491	122375506	+	1	NA	intron (NM_029556, intron 3 of 7)	intron (NM_029556, intron 3 of 7)	75617	NR_033325	328479	Mm.86095	NR_033325	ENSMUSG00000064052	Gm5089	6530402A20|C030005G22Rik|EG328479	predicted gene 5089	ncRNA
mm_118363.1	chr13	115101805	115101824	-	1	NA	5' UTR (NM_001033228, exon 1 of 29)	5' UTR (NM_001033228, exon 1 of 29)	150	NM_001033228	109700	Mm.317280	NM_001033228	ENSMUSG00000042284	Itga1	CD49A|E130012M19Rik|Vla1	integrin alpha 1	protein-coding
mm_52264.1	chr6	108277107	108277124	+	1	NA	intron (NM_010585, intron 4 of 61)	intron (NM_010585, intron 4 of 61)	64019	NM_010585	16438	Mm.227912	NM_010585	ENSMUSG00000030102	Itpr1	D6Pas2|ENSMUSG00000072853|Gm10429|IP3R 1|IP3R1|InsP3R|Ip3r|Itpr-1|P400|Pcp-1|Pcp1|insP3R1|opt|wblo	inositol 1,4,5-trisphosphate receptor 1	protein-coding
mm_11715.1	chr2	36237950	36237985	+	1	NA	exon (NM_008969, exon 5 of 11)	exon (NM_008969, exon 5 of 11)	7541	NM_008969	19224	Mm.275434	NM_008969	ENSMUSG00000047250	Ptgs1	COX1|Cox-1|Cox-3|PGHS-1|PHS 1|Pghs1	prostaglandin-endoperoxide synthase 1	protein-coding
mm_137678.1	chr17	28817679	28817692	+	1	NA	exon (NM_001081315, exon 6 of 13)	exon (NM_001081315, exon 6 of 13)	16559	NM_001081315	268936	Mm.291877	NM_199061	ENSMUSG00000063952	Brpf3	AI413466|AW493400|mKIAA1286	bromodomain and PHD finger containing, 3	protein-coding
mm_136297.1	chr16	91514807	91514810	-	1	NA	Intergenic	Intergenic	29593	NM_010508	15975	Mm.502	NM_010508	ENSMUSG00000022967	Ifnar1	CD118|Ifar|Ifnar|Ifrc|Infar	interferon (alpha and beta) receptor 1	protein-coding
mm_98273.1	chr11	89010970	89010977	+	1	NA	exon (NM_009546, exon 4 of 9)	exon (NM_009546, exon 4 of 9)	11570	NM_009546	217069	Mm.248445	NM_009546	ENSMUSG00000000275	Trim25	AA960166|AL022677|EFP|Zfp147	tripartite motif-containing 25	protein-coding
mm_111731.1	chr12	103773620	103773630	-	1	NA	promoter-TSS (NM_009246)	promoter-TSS (NM_009246)	8	NM_009246	20703	Mm.439695	NM_009246	ENSMUSG00000071177	Serpina1d	AI118301|Dom4|PI4|Spi1-4	serine (or cysteine) peptidase inhibitor, clade A, member 1D	protein-coding
mm_19549.1	chr2	98665156	98665171	-	1	NA	Intergenic	SYNREP_MM|Satellite|Satellite	1197506	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_19379.1	chr2	91195098	91195114	-	1	NA	promoter-TSS (NM_013839)	promoter-TSS (NM_013839)	10	NM_001177730	22259	Mm.22690	NM_013839	ENSMUSG00000002108	Nr1h3	AU018371|LXR|RLD1|Unr1	nuclear receptor subfamily 1, group H, member 3	protein-coding
mm_78666.1	chr9	40696118	40696120	+	1	NA	intron (NM_133733, intron 1 of 6)	intron (NM_133733, intron 1 of 6)	10155	NM_133733	71566	Mm.280560	NM_133733	ENSMUSG00000032024	Clmp	9030425E11Rik|ACAM|ASP5|AW557819	CXADR-like membrane protein	protein-coding
mm_75198.1	chr8	39006268	39006273	-	1	NA	intron (NM_030254, intron 1 of 7)	CpG	403	NM_030254	80286	Mm.272722	NM_030254	ENSMUSG00000039530	Tusc3	AU022242|BC003311|N33	tumor suppressor candidate 3	protein-coding
mm_85649.1	chr9	107657847	107657860	-	1	NA	exon (NM_001199218, exon 6 of 16)	exon (NM_001199218, exon 6 of 16)	9546	NM_023805	76257	Mm.296560	NM_023805	ENSMUSG00000010064	Slc38a3	0610012J02Rik|D9Ucla2|Nat1|Slc38-3|Sn1|Snat3|mNAT	solute carrier family 38, member 3	protein-coding
mm_65932.1	chr7	30323021	30323030	-	1	NA	promoter-TSS (NM_001033140)	promoter-TSS (NM_001033140)	-650	NM_001033140	68332	Mm.6844	NM_001033140	ENSMUSG00000074211	Sdhaf1	0610010E21Rik|AI430885|AW490662|Lyrm8	succinate dehydrogenase complex assembly factor 1	protein-coding
mm_20571.1	chr2	131085197	131085218	-	1	NA	exon (NM_011426, exon 3 of 21)	exon (NM_011426, exon 3 of 21)	1558	NM_011426	20612	Mm.1374	NM_011426	ENSMUSG00000027322	Siglec1	Cd169|Siglec-1|Sn	sialic acid binding Ig-like lectin 1, sialoadhesin	protein-coding
mm_41442.1	chr5	90905209	90905242	+	1	NA	3' UTR (NM_009140, exon 4 of 4)	3' UTR (NM_009140, exon 4 of 4)	1326	NM_009140	20310	Mm.4979	NM_009140	ENSMUSG00000058427	Cxcl2	CINC-2a|GROb|Gro2|MIP-2|MIP-2a|Mgsa-b|Mip2|Scyb|Scyb2	chemokine (C-X-C motif) ligand 2	protein-coding
mm_143244.1	chr17	64290046	64290047	-	1	NA	intron (NM_144859, intron 5 of 8)	intron (NM_144859, intron 5 of 8)	41837	NM_144859	224938	Mm.489681	NM_144859	ENSMUSG00000024083	Pja2	AI447901|AL022700|Neurodap1|mKIAA0438	praja 2, RING-H2 motif containing	protein-coding
mm_68452.1	chr7	110061354	110061364	-	1	NA	promoter-TSS (NM_009281)	promoter-TSS (NM_009281)	-343	NM_009281	20841	Mm.10815	NM_009281	ENSMUSG00000061079	Zfp143	AA959806|AU015869|D7Ertd805e|KRAB14|SBF|Staf|Zfp79|Zfp80-rs1|Znf143|pHZ-1	zinc finger protein 143	protein-coding
mm_86441.1	chr10	3973216	3973245	+	1	NA	5' UTR (NM_001170785, exon 1 of 28)	5' UTR (NM_001170785, exon 1 of 28)	155	NM_172308	270685	Mm.184752	NM_172308	ENSMUSG00000040675	Mthfd1l	2410004L15Rik|AI647056|Fthfsdc1	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1-like	protein-coding
mm_8771.1	chr1	161034795	161034832	-	1	NA	promoter-TSS (NM_173424)	promoter-TSS (NM_173424)	-353	NR_002840	14455	Mm.270065	NR_002840	ENSMUSG00000053332	Gas5	Gas-5|Mir5117|Snhg2	growth arrest specific 5	ncRNA
mm_63253.1	chr7	126623448	126623484	+	1	NA	3' UTR (NM_019738, exon 3 of 3)	3' UTR (NM_019738, exon 3 of 3)	2004	NM_019738	56312	Mm.18742	NM_019738	ENSMUSG00000030717	Nupr1	2310032H04Rik|Com1|p8	nuclear protein transcription regulator 1	protein-coding
mm_139053.1	chr17	46328084	46328136	+	1	NA	promoter-TSS (NM_170680)	promoter-TSS (NM_170680)	-87	NM_170680	224814	Mm.76543	NM_145140	ENSMUSG00000032842	Abcc10	Mrp7|mFLJ00002	ATP-binding cassette, sub-family C (CFTR/MRP), member 10	protein-coding
mm_12442.1	chr2	70931133	70931166	+	1	NA	Intergenic	Intergenic	87225	NM_001110512	228019	Mm.490343	NM_145524	ENSMUSG00000041975	Mettl8	BC004636|Tip	methyltransferase like 8	protein-coding
mm_39029.1	chr4	152152382	152152397	-	1	NA	promoter-TSS (NM_207687)	promoter-TSS (NM_207687)	-182	NM_207687	56226	Mm.264215	NM_019585	ENSMUSG00000028943	Espn	je	espin	protein-coding
mm_101003.1	chr11	8468708	8468757	-	1	NA	intron (NM_001083587, intron 20 of 30)	intron (NM_001083587, intron 20 of 30)	195803	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_75403.1	chr8	46209139	46209157	-	1	NA	exon (NM_007450, exon 2 of 4)	exon (NM_007450, exon 2 of 4)	1861	NM_007450	11739	Mm.16228	NM_007450	ENSMUSG00000031633	Slc25a4	AU019225|Ant1	solute carrier family 25 (mitochondrial carrier, adenine nucleotide translocator), member 4	protein-coding
mm_24239.1	chr3	89043242	89043278	+	1	NA	exon (NM_138679, exon 10 of 27)	exon (NM_138679, exon 10 of 27)	46771	NM_001083808	72296	Mm.27687	NM_028188	ENSMUSG00000041263	Rusc1	2210403N08Rik|AA408288|NESCA	RUN and SH3 domain containing 1	protein-coding
mm_141986.1	chr17	35165141	35165153	-	1	NA	promoter-TSS (NM_020027)	promoter-TSS (NM_020027)	-270	NM_020027	53761	Mm.272462	NM_020027	ENSMUSG00000024393	Prrc2a	3110039B05Rik|Bat-2|Bat2|D17H6S51E|G2|Wbp12|mKIAA4178	proline-rich coiled-coil 2A	protein-coding
mm_55091.1	chr6	49253073	49253085	-	1	NA	intron (NM_001347209, intron 1 of 7)	intron (NM_001347209, intron 1 of 7)	10973	NM_001347209	101214	Mm.196598	NM_198102	ENSMUSG00000029817	Tra2a	1500010G04Rik|AL022798|G430041M01Rik|mAWMS1	transformer 2 alpha homolog (Drosophila)	protein-coding
mm_40653.1	chr5	65114944	65114950	+	1	NA	intron (NM_001347355, intron 1 of 10)	intron (NM_001347355, intron 1 of 10)	7379	NM_001347355	71778	Mm.10281	NM_175174	ENSMUSG00000054920	Klhl5	1300013C10Rik	kelch-like 5	protein-coding
mm_56265.1	chr6	90947185	90947185	-	1	NA	Intergenic	Intergenic	-137062	NM_001134384	232227	Mm.196943	NM_182784	ENSMUSG00000034312	Iqsec1	AW561907|BC026481|BRAG2|D6Ertd349e|cI-43	IQ motif and Sec7 domain 1	protein-coding
mm_92060.1	chr10	62513524	62513527	-	1	NA	Intergenic	Intergenic	-5770	NM_011157	19073	Mm.338790	NM_011157	ENSMUSG00000020077	Srgn	Prg|Prg1|Sgc	serglycin	protein-coding
mm_60330.1	chr7	44261425	44261502	+	1	NA	Intergenic	Intergenic	-4259	NM_001195034	100503991	Mm.367353	NM_001195034	ENSMUSG00000012777	Acpt	EG546967|Gm1432	acid phosphatase, testicular	protein-coding
mm_124082.1	chr14	78656350	78656354	-	1	NA	intron (NM_001081336, intron 1 of 28)	intron (NM_001081336, intron 1 of 28)	-11901	NR_104044	380921	Mm.89591	NM_001081336	ENSMUSG00000034731	Dgkh	5930402B05Rik|D130015C16|DGK	diacylglycerol kinase, eta	protein-coding
mm_25440.1	chr3	108146201	108146223	+	1	NA	promoter-TSS (NM_010306)	promoter-TSS (NM_010306)	-60	NM_010306	14679	Mm.271703	NM_010306	ENSMUSG00000000001	Gnai3	AI158965|AW537698|Galphai3|Gnai-3	guanine nucleotide binding protein (G protein), alpha inhibiting 3	protein-coding
mm_162053.1	chrX	7671331	7671331	-	1	NA	promoter-TSS (NM_019755)	promoter-TSS (NM_019755)	59	NM_019755	18824	Mm.18565	NM_019755	ENSMUSG00000031146	Plp2	mIMA4	proteolipid protein 2	protein-coding
mm_51415.1	chr6	78381904	78381914	+	1	NA	exon (NM_011259, exon 3 of 6)	exon (NM_011259, exon 3 of 6)	1200	NM_011259	19694	Mm.2552	NM_011259	ENSMUSG00000079516	Reg3a	AV063448	regenerating islet-derived 3 alpha	protein-coding
mm_110953.1	chr12	76710030	76710054	-	1	NA	5' UTR (NM_013675, exon 1 of 36)	5' UTR (NM_013675, exon 1 of 36)	505	NM_013675	20741	Mm.32881	NM_013675	ENSMUSG00000021061	Sptb	AI842465|D330027P03Rik|Gm1301|Spnb-1|Spnb1|ja|jaundiced|mKIAA4219	spectrin beta, erythrocytic	protein-coding
mm_124448.1	chr14	118917553	118917569	-	1	NA	intron (NR_130725, intron 2 of 20)	intron (NR_130725, intron 2 of 20)	5606	NR_130725	66573	Mm.87456	NM_025943	ENSMUSG00000042156	Dzip1	2510025K24Rik|2810422M04Rik	DAZ interacting protein 1	protein-coding
mm_167420.1	chr8	111537547	111537572	+	1	NA	promoter-TSS (NM_001168623)	promoter-TSS (NM_001168623)	-784	NM_001168623	170737	Mm.271578	NM_133206	ENSMUSG00000033545	Znrf1	B830022L21Rik|Rnf42|Zrfp1|nin283	zinc and ring finger 1	protein-coding
mm_169974.1	chr17	14763917	14763921	-	1	NA	Intergenic	Intergenic	-69657	NM_011581	21826	Mm.26688	NM_011581	ENSMUSG00000023885	Thbs2	TSP2|Thbs-2	thrombospondin 2	protein-coding
mm_117351.1	chr13	69738982	69738990	-	1	NA	exon (NM_001145162, exon 1 of 2)	exon (NM_001145162, exon 1 of 2)	911	NM_001145162	76980	Mm.23960	NM_001145162	ENSMUSG00000052981	Ube2ql1	3110006E14Rik	ubiquitin-conjugating enzyme E2Q family-like 1	protein-coding
mm_121472.1	chr14	120946805	120946834	+	1	NA	3' UTR (NM_023579, exon 26 of 26)	3' UTR (NM_023579, exon 26 of 26)	35625	NM_023579	70572	Mm.221452	NM_023579	ENSMUSG00000030662	Ipo5	1110011C18Rik|5730478E03Rik|AA409333|C76941|IMB3|Kpnb3|Ranbp5	importin 5	protein-coding
mm_128776.1	chr15	66783071	66783108	-	1	NA	intron (NM_009192, intron 8 of 8)	intron (NM_009192, intron 8 of 8)	48740	NM_001029841	20491	Mm.7601	NM_009192	ENSMUSG00000022372	Sla	Slap|Slap-1	src-like adaptor	protein-coding
mm_30287.1	chr3	148989406	148989412	-	1	NA	Intergenic	CpG	-34774	NM_001081298	99633	Mm.9776	NM_001081298	ENSMUSG00000028184	Adgrl2	AI450192|CIRL-2|Gm619|Lec1|Lphh1|Lphn2|mKIAA0786	adhesion G protein-coupled receptor L2	protein-coding
mm_161908.1	chr18	62340843	62340843	+	1	NA	intron (NM_008313, intron 1 of 6)	intron (NM_008313, intron 1 of 6)	16639	NM_008313	15562	Mm.20440	NM_008313	ENSMUSG00000026322	Htr4	5-HT-4|5-HT4|5-HT<4L>|5HTR4	5 hydroxytryptamine (serotonin) receptor 4	protein-coding
mm_77030.1	chr8	109251479	109251491	-	1	NA	non-coding (NR_126329, exon 10 of 10)	non-coding (NR_126329, exon 10 of 10)	89423	NR_002928	384864	Mm.390083	NR_002928		Gm1943	-	WD repeat domain 70 pseudogene	pseudo
mm_86900.1	chr10	22306736	22306738	+	1	NA	promoter-TSS (NR_015465)	promoter-TSS (NR_015465)	17	NR_015465	606736	Mm.387042	NR_015465	ENSMUSG00000097352	C920009B18Rik	-	RIKEN cDNA C920009B18 gene	ncRNA
mm_144813.1	chr18	36287946	36287958	+	1	NA	exon (NM_008989, exon 2 of 2)	exon (NM_008989, exon 2 of 2)	6790	NM_008989	19290	Mm.231802	NM_008989	ENSMUSG00000043991	Pura	CAGER-1|Pur-alpha|ssCRE-BP	purine rich element binding protein A	protein-coding
mm_140612.1	chr17	10840126	10840197	-	1	NA	promoter-TSS (NM_016694)	promoter-TSS (NM_016694)	30	NM_027032	69310	Mm.18889	NM_027032	ENSMUSG00000037196	Pacrg	1700008H23Rik	PARK2 co-regulated	protein-coding
mm_145076.1	chr18	42275370	42275392	+	1	NA	promoter-TSS (NM_172626)	promoter-TSS (NM_172626)	28	NM_172626	225432	Mm.329400	NM_172626	ENSMUSG00000024491	Rbm27	A730010I06|AI043120|Psc1|mKIAA1311	RNA binding motif protein 27	protein-coding
mm_114381.1	chr13	63240387	63240400	+	1	NA	intron (NR_110520, intron 2 of 5)	intron (NR_110520, intron 2 of 5)	364	NR_110521	72061	Mm.188105	NM_028079	ENSMUSG00000021458	2010111I01Rik	2300006M17Rik|AP-O|AW742919|Aopep|ApO|mir-23b|mir-24-1|mir-27b	RIKEN cDNA 2010111I01 gene	protein-coding
mm_14416.1	chr2	130424322	130424393	+	1	NA	promoter-TSS (NM_178762)	promoter-TSS (NM_178762)	37	NM_030559	80743	Mm.276092	NM_030559	ENSMUSG00000027411	Vps16	1810074M16Rik	VSP16 CORVET/HOPS core subunit	protein-coding
mm_55701.1	chr6	72899953	72899985	-	1	NA	promoter-TSS (NM_019715)	promoter-TSS (NM_019715)	10	NM_019715	74287	Mm.29194	NM_019715	ENSMUSG00000055239	Kcmf1	1700094M07Rik|Debt91|Pmcf	potassium channel modulatory factor 1	protein-coding
mm_114304.1	chr13	59585349	59585441	+	1	NA	promoter-TSS (NM_030153)	promoter-TSS (NM_030153)	62	NM_030153	78689	Mm.253902	NM_030153	ENSMUSG00000021555	Naa35	A330021G12Rik|A330027C19Rik|AI158944|C030004C14Rik|Mak10	N(alpha)-acetyltransferase 35, NatC auxiliary subunit	protein-coding
mm_16518.1	chr2	181493186	181493220	+	1	NA	promoter-TSS (NM_183181)	promoter-TSS (NM_183181)	-3	NM_183181	241850	Mm.87455	NM_183181	ENSMUSG00000055882	Abhd16b	1700095H12	abhydrolase domain containing 16B	protein-coding
mm_152268.1	chr19	8809372	8809389	-	1	NA	3' UTR (NM_027412, exon 4 of 4)	3' UTR (NM_027412, exon 4 of 4)	6850	NM_001098237	75291	Mm.23423	NM_133759	ENSMUSG00000071661	Zbtb3	4930563M09Rik	zinc finger and BTB domain containing 3	protein-coding
mm_21828.1	chr2	165388217	165388232	-	1	NA	promoter-TSS (NM_178411)	promoter-TSS (NM_178411)	35	NM_178411	228876	Mm.26316	NM_178411	ENSMUSG00000017667	Zfp334	D2Ertd535e	zinc finger protein 334	protein-coding
mm_9008.1	chr1	165948536	165948537	-	1	NA	intron (NM_011137, intron 1 of 16)	intron (NM_011137, intron 1 of 16)	-13588	NM_198934	18986	Mm.245261	NM_011137	ENSMUSG00000026565	Pou2f1	2810482H01Rik|NF-A1|Oct-1|Oct1|Otf-1|Otf1	POU domain, class 2, transcription factor 1	protein-coding
mm_98052.1	chr11	85821844	85821852	+	1	NA	intron (NR_077059, intron 1 of 4)	intron (NR_077059, intron 1 of 4)	10540	NR_077059	69909	Mm.440214	NR_077059	ENSMUSG00000087013	2610027K06Rik	-	RIKEN cDNA 2610027K06 gene	ncRNA
mm_125.1	chr1	9848295	9848362	+	1	NA	promoter-TSS (NM_001037759)	promoter-TSS (NM_001037759)	47	NM_001037759	170755	Mm.336410	NM_133220	ENSMUSG00000025915	Sgk3	2510015P22Rik|A330005P07Rik|Cisk|fy|fz	serum/glucocorticoid regulated kinase 3	protein-coding
mm_107550.1	chr12	41024356	41024367	+	1	NA	intron (NM_053122, intron 1 of 6)	CpG	271	NM_053122	93757	Mm.363813	NM_053122	ENSMUSG00000056899	Immp2l	AI853880|IMP2	IMP2 inner mitochondrial membrane peptidase-like (S. cerevisiae)	protein-coding
mm_112701.1	chr13	17805529	17805540	+	1	NA	promoter-TSS (NM_001081058)	promoter-TSS (NM_001081058)	-437	NM_027118	69562	Mm.193924	NM_027118	ENSMUSG00000041297	Cdk13	2310015O17Rik|Cdc2l5	cyclin-dependent kinase 13	protein-coding
mm_163699.1	chr13	103978053	103978059	+	1	NA	Intergenic	Intergenic	-57470	NM_001005868	59079	Mm.277354	NM_021563	ENSMUSG00000021709	Erbin	1700028E05Rik|Erbb2ip|mKIAA1225	Erbb2 interacting protein	protein-coding
mm_73525.1	chr8	107545060	107545075	+	1	NA	intron (NM_025830, intron 10 of 23)	intron (NM_025830, intron 10 of 23)	-6177	NR_029553	387158		NR_029553	ENSMUSG00000065439	Mir140	Mirn140|mir-140|mmu-mir-140	microRNA 140	ncRNA
mm_38695.1	chr4	145213906	145213921	-	1	NA	3' UTR (NM_011610, exon 10 of 10)	3' UTR (NM_011610, exon 10 of 10)	-18908	NM_001276465	230895	Mm.240310	NM_001033190	ENSMUSG00000020220	Vps13d	-	vacuolar protein sorting 13D	protein-coding
mm_6655.1	chr1	79861295	79861303	-	1	NA	Intergenic	Intergenic	-2634	NM_009255	20720	Mm.3093	NM_009255	ENSMUSG00000026249	Serpine2	B230326M24Rik|PAI-1|PI-7|PI7|PN-1|Spi4	serine (or cysteine) peptidase inhibitor, clade E, member 2	protein-coding
mm_132706.1	chr16	43364146	43364157	+	1	NA	intron (NM_181058, intron 2 of 6)	intron (NM_181058, intron 2 of 6)	56045	NR_046026	626693	Mm.447083	NR_046026	ENSMUSG00000085499	Gm15713	OTTMUSG00000025617	predicted gene 15713	ncRNA
mm_66940.1	chr7	61916488	61916495	-	1	NA	intron (NR_015533, intron 3 of 8)	Lx7|LINE|L1	11083	NR_015533	319893	Mm.490625	NR_015533		A230057D06Rik	-	RIKEN cDNA A230057D06 gene	ncRNA
mm_152170.1	chr19	7333141	7333143	-	1	NA	intron (NM_007928, intron 1 of 17)	intron (NM_007928, intron 1 of 17)	8718	NM_001080389	13728	Mm.258986	NM_007928	ENSMUSG00000024969	Mark2	EMK-1|Emk|Par-1|Par-1b	MAP/microtubule affinity regulating kinase 2	protein-coding
mm_104206.1	chr11	88048285	88048345	-	1	NA	intron (NM_173374, intron 1 of 3)	CpG	942	NM_173374	110809	Mm.391719	NM_173374	ENSMUSG00000018379	Srsf1	1110054N12Rik|5730507C05Rik|6330415C05Rik|AI482334|AW491331|Asf|Sf2|Sfrs1	serine/arginine-rich splicing factor 1	protein-coding
mm_135519.1	chr16	48818719	48818733	-	1	NA	exon (NM_023881, exon 4 of 4)	exon (NM_023881, exon 4 of 4)	1870	NM_023881	57263	Mm.21123	NM_023881	ENSMUSG00000022650	Retnlb	9030012B21Rik|Fizz2|RELMbeta|Relmb|Xcp3	resistin like beta	protein-coding
mm_58910.1	chr7	17213338	17213345	+	1	NA	3' UTR (NM_054064, exon 5 of 5)	3' UTR (NM_054064, exon 5 of 5)	9864	NM_054064	114872	Mm.322280	NM_054064	ENSMUSG00000023159	Psg29	AA102956|AA409969|cea17	pregnancy-specific glycoprotein 29	protein-coding
mm_48392.1	chr5	139814232	139814279	-	1	NA	promoter-TSS (NM_001161548)	promoter-TSS (NM_001161548)	28	NM_001161548	231832	Mm.482655	NM_144914	ENSMUSG00000036687	Tmem184a	Sdmg1	transmembrane protein 184a	protein-coding
mm_66717.1	chr7	46099753	46099757	-	1	NA	exon (NM_010602, exon 1 of 1)	exon (NM_010602, exon 1 of 1)	482	NM_010602	16514	Mm.333863	NM_010602	ENSMUSG00000096146	Kcnj11	Kir6.2|mBIR	potassium inwardly rectifying channel, subfamily J, member 11	protein-coding
mm_138525.1	chr17	35241839	35241854	+	1	NA	promoter-TSS (NM_001252457)	promoter-TSS (NM_001252457)	100	NM_019693	53817	Mm.439827	NM_019693	ENSMUSG00000019432	Ddx39b	0610030D10Rik|AI428441|Bat-1|Bat1|Bat1a|D17H6S81E|D17H6S81E-1|D6S81Eh	DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B	protein-coding
mm_3474.1	chr1	150105002	150105068	+	1	NA	exon (NM_011198, exon 9 of 10)	exon (NM_011198, exon 9 of 10)	5004	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_155995.1	chrX	106156830	106156847	+	1	NA	exon (NM_205820, exon 3 of 3)	exon (NM_205820, exon 3 of 3)	13563	NM_205820	279572	Mm.336203	NM_205820	ENSMUSG00000033777	Tlr13	AI666735|Gm713	toll-like receptor 13	protein-coding
mm_58442.1	chr7	3298776	3298810	+	1	NA	3' UTR (NM_016969, exon 3 of 3)	3' UTR (NM_016969, exon 3 of 3)	-4739	NM_001291434	18752	Mm.7980	NM_011102	ENSMUSG00000078816	Prkcg	PKCgamma|Pkcc|Prkcc	protein kinase C, gamma	protein-coding
mm_143378.1	chr17	67924515	67924519	-	1	NA	intron (NM_172964, intron 1 of 17)	intron (NM_172964, intron 1 of 17)	26423	NM_001347410	268970	Mm.9935	NM_172964	ENSMUSG00000024043	Arhgap28	AU044757|AW550892|E130310N06	Rho GTPase activating protein 28	protein-coding
mm_167252.1	chr8	24779522	24779522	+	1	NA	intron (NM_001272059, intron 16 of 18)	Lx5|LINE|L1	44847	NM_001272058	11499	Mm.143889	NM_007401	ENSMUSG00000031554	Adam5	tMDC II|tMDCII	a disintegrin and metallopeptidase domain 5	protein-coding
mm_31453.1	chr4	48618928	48618933	+	1	NA	intron (NM_021436, intron 5 of 9)	intron (NM_021436, intron 5 of 9)	33737	NM_021436	230157	Mm.422686	NM_021436	ENSMUSG00000028347	Tmeff1	A830033E11|M7365|Tr1	transmembrane protein with EGF-like and two follistatin-like domains 1	protein-coding
mm_11225.1	chr2	29788238	29788302	+	1	NA	promoter-TSS (NM_178693)	promoter-TSS (NM_178693)	7	NM_178693	227683	Mm.245948	NM_178693	ENSMUSG00000026798	Coq4	A330041N06|D2Ertd97e	coenzyme Q4	protein-coding
mm_29657.1	chr3	122539545	122539549	-	1	NA	3' UTR (NM_001114665, exon 16 of 16)	3' UTR (NM_001114665, exon 16 of 16)	2134	NR_106117	102465764		NR_106117	ENSMUSG00000104773	Mir7657	mmu-mir-7657	microRNA 7657	ncRNA
mm_157677.1	chrX	59544046	59544048	-	1	NA	intron (NM_001290414, intron 2 of 6)	intron (NM_001290414, intron 2 of 6)	41525	NM_001290414	14168	Mm.7995	NM_010200	ENSMUSG00000031137	Fgf13	Fhf2	fibroblast growth factor 13	protein-coding
mm_13198.1	chr2	93452797	93452833	+	1	NA	promoter-TSS (NM_001271462)	promoter-TSS (NM_001271462)	-4	NR_040532	100038525	Mm.440596	NR_040532	ENSMUSG00000075025	Gm10804	ENSMUSG00000075025	predicted gene 10804	ncRNA
mm_75237.1	chr8	39630334	39630346	-	1	NA	intron (NM_001113326, intron 3 of 9)	intron (NM_001113326, intron 3 of 9)	12338	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_123121.1	chr14	56120624	56120627	-	1	NA	promoter-TSS (NM_010373)	promoter-TSS (NM_010373)	0	NM_010373	14942	Mm.14424	NM_010373	ENSMUSG00000022156	Gzme	CCP3|Ctla-6|Ctla6|MCSP-2	granzyme E	protein-coding
mm_65045.1	chr7	18616393	18616403	-	1	NA	5' UTR (NM_020261, exon 1 of 5)	5' UTR (NM_020261, exon 1 of 5)	103	NM_020261	56868	Mm.333617	NM_020261	ENSMUSG00000074359	Psg23	1620401C02Rik|cea11	pregnancy-specific glycoprotein 23	protein-coding
mm_27773.1	chr3	72967855	72967869	-	1	NA	promoter-TSS (NM_001081137)	promoter-TSS (NM_001081137)	-996	NM_001081137	69983	Mm.261054	NM_001081137	ENSMUSG00000027790	Sis	2010204N08Rik|SI|Si-s	sucrase isomaltase (alpha-glucosidase)	protein-coding
mm_107363.1	chr12	32841052	32841063	+	1	NA	exon (NM_021524, exon 7 of 11)	exon (NM_021524, exon 7 of 11)	16941	NR_045032	100504486	Mm.440246	NR_045032		Gdap10	Gdap-ps	ganglioside-induced differentiation-associated-protein 10	ncRNA
mm_118275.1	chr13	112651418	112651421	-	1	NA	intron (NM_001145885, intron 1 of 21)	intron (NM_001145885, intron 1 of 21)	891	NM_010029	13206	Mm.12818	NM_010029	ENSMUSG00000021758	Ddx4	AV206478|Mvh|VASA	DEAD (Asp-Glu-Ala-Asp) box polypeptide 4	protein-coding
mm_161533.1	chr15	102407885	102407885	+	1	NA	exon (NM_013672, exon 2 of 6)	exon (NM_013672, exon 2 of 6)	1569	NM_013672	20683	Mm.4618	NM_013672	ENSMUSG00000001280	Sp1	1110003E12Rik|AA450830|AI845540|Sp1-1	trans-acting transcription factor 1	protein-coding
mm_160735.1	chr10	79148815	79148815	+	1	NA	promoter-TSS (NM_001103368)	promoter-TSS (NM_001103368)	-1	NM_001103368	624765	Mm.469843	NM_001103368	ENSMUSG00000091888	Vmn2r80	EG624765	vomeronasal 2, receptor 80	protein-coding
mm_64415.1	chr7	142534584	142534598	+	1	NA	intron (NM_011288, intron 1 of 4)	intron (NM_011288, intron 1 of 4)	1474	NM_011288	19935	Mm.12144	NM_011288	ENSMUSG00000037772	Mrpl23	L23mrp|Rpl23|Rpl23l	mitochondrial ribosomal protein L23	protein-coding
mm_18828.1	chr2	74691759	74691779	-	1	NA	promoter-TSS (NM_013554)	promoter-TSS (NM_013554)	-122	NM_013554	15430	Mm.24420	NM_013554	ENSMUSG00000050368	Hoxd10	AI385591|AI874987|Hox-4.5|Hox-5.3	homeobox D10	protein-coding
mm_70668.1	chr8	14888997	14889013	+	1	NA	5' UTR (NM_012000, exon 1 of 3)	5' UTR (NM_012000, exon 1 of 3)	469	NM_012000	26889	Mm.254027	NM_012000	ENSMUSG00000026317	Cln8	mnd	ceroid-lipofuscinosis, neuronal 8	protein-coding
mm_153852.1	chr19	46377995	46378024	-	1	NA	3' UTR (NM_016860, exon 11 of 11)	3' UTR (NM_016860, exon 11 of 11)	17726	NM_016860	54130	Mm.3118	NM_016860	ENSMUSG00000025228	Actr1a	Arp1|alpha-Arp1	ARP1 actin-related protein 1A, centractin alpha	protein-coding
mm_4679.1	chr1	180541566	180541615	+	1	NA	Intergenic	Intergenic	-27385	NM_007415	11545	Mm.277779	NM_007415	ENSMUSG00000026496	Parp1	5830444G22Rik|AI893648|ARTD1|Adprp|Adprt1|C80510|PARP|PPOL|parp-1|sPARP-1	poly (ADP-ribose) polymerase family, member 1	protein-coding
mm_166041.1	chr4	130055352	130055379	+	1	NA	intron (NM_028266, intron 9 of 69)	intron (NM_028266, intron 9 of 69)	7525	NM_028266	107581	Mm.41860	NM_028266	ENSMUSG00000040690	Col16a1	2700007F12Rik|A530052M23Rik|AI838662|CA1F	collagen, type XVI, alpha 1	protein-coding
mm_84826.1	chr9	78108589	78108616	-	1	NA	promoter-TSS (NM_001163780)	promoter-TSS (NM_001163780)	54	NM_023605	71538	Mm.28584	NM_023605	ENSMUSG00000001366	Fbxo9	9030401P18Rik|AA986398	f-box protein 9	protein-coding
mm_67578.1	chr7	82541514	82541514	-	1	NA	intron (NM_001190374, intron 16 of 29)	ORR1A3-int|LTR|ERVL-MaLR	107014	NM_177894	330577	Mm.222812	NM_177894	ENSMUSG00000038570	Saxo2	1700129I04Rik|D030069K18|Fam154b	stabilizer of axonemal microtubules 2	protein-coding
mm_20938.1	chr2	151009341	151009356	-	1	NA	promoter-TSS (NM_207204)	promoter-TSS (NM_207204)	50	NM_207204	78177	Mm.120911	NM_207204	ENSMUSG00000068115	Ninl	4930519N13Rik|Gm1004|Gm1634|mKIAA0980	ninein-like	protein-coding
mm_136819.1	chr17	12409055	12409073	+	1	NA	exon (NM_008877, exon 14 of 19)	exon (NM_008877, exon 14 of 19)	30455	NM_008877	18815	Mm.971	NM_008877	ENSMUSG00000059481	Plg	AI649309|Pg	plasminogen	protein-coding
mm_169322.1	chr14	114349543	114349559	+	1	NA	Intergenic	ERVB7_3-LTR_MM|LTR|ERVK	-482414	NR_045661	75822	Mm.410813	NR_045661		4930524C18Rik	-	RIKEN cDNA 4930524C18 gene	ncRNA
mm_83832.1	chr9	54193520	54193523	-	1	NA	promoter-TSS (NM_007810)	promoter-TSS (NM_007810)	-79	NM_007810	13075	Mm.5199	NM_007810	ENSMUSG00000032274	Cyp19a1	Ar|ArKO|Cyp19|Int-5|Int5|p450arom	cytochrome P450, family 19, subfamily a, polypeptide 1	protein-coding
mm_117888.1	chr13	99422655	99422673	-	1	NA	3' UTR (NM_008634, exon 7 of 7)	3' UTR (NM_008634, exon 7 of 7)	-9838	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_94693.1	chr11	20021823	20021825	+	1	NA	3' UTR (NM_033523, exon 6 of 6)	3' UTR (NM_033523, exon 6 of 6)	91127	NM_146243	66713	Mm.259045	NM_146243	ENSMUSG00000020152	Actr2	4921510D23Rik|AA409782|Arp2|D6Ertd746e	ARP2 actin-related protein 2	protein-coding
mm_164160.1	chr15	72848882	72848882	+	1	NA	intron (NM_001164641, intron 17 of 17)	ORR1C2|LTR|ERVL-MaLR	-38558	NR_002864	353342	Mm.440245	NR_002864	ENSMUSG00000106847	Peg13	-	paternally expressed 13	ncRNA
mm_114592.1	chr13	75761916	75761927	+	1	NA	exon (NM_138953, exon 6 of 12)	exon (NM_138953, exon 6 of 12)	54437	NM_138953	192657	Mm.21288	NM_138953	ENSMUSG00000001542	Ell2	-	elongation factor RNA polymerase II 2	protein-coding
mm_84075.1	chr9	58201936	58201942	-	1	NA	promoter-TSS (NM_001161540)	promoter-TSS (NM_001161540)	-140	NM_001161540	320563	Mm.186499	NM_177193	ENSMUSG00000051243	Islr2	B930052A04Rik|Linx|Mbu-3|mKIAA1465	immunoglobulin superfamily containing leucine-rich repeat 2	protein-coding
mm_4600.1	chr1	178406039	178406045	+	1	NA	5' UTR (NM_026626, exon 1 of 7)	5' UTR (NM_026626, exon 1 of 7)	161	NM_026626	68226	Mm.252132	NM_026626	ENSMUSG00000026495	Efcab2	1700073K01Rik|D830011E08Rik	EF-hand calcium binding domain 2	protein-coding
mm_1003.1	chr1	58716843	58716845	+	1	NA	intron (NM_009805, intron 1 of 4)	intron (NM_009805, intron 1 of 4)	3558	NM_207653	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_135767.1	chr16	56721262	56721272	-	1	NA	Intergenic	(A)n|Simple_repeat|Simple_repeat	-3817	NM_019678	21787	Mm.425970	NM_019678	ENSMUSG00000022757	Tfg	AI173908	Trk-fused gene	protein-coding
mm_143342.1	chr17	66519735	66519746	-	1	NA	promoter-TSS (NM_024448)	promoter-TSS (NM_024448)	-70	NM_024448	19328	Mm.248313	NM_024448	ENSMUSG00000023460	Rab12	2900054P15Rik|AW555448|C77700	RAB12, member RAS oncogene family	protein-coding
mm_67888.1	chr7	99353105	99353121	-	1	NA	5' UTR (NM_009825, exon 1 of 5)	5' UTR (NM_009825, exon 1 of 5)	126	NM_009825	12406	Mm.22708	NM_009825	ENSMUSG00000070436	Serpinh1	BERF-1|Cbp1|Cbp2|Hsp47|J6|Serpinh2|gp46	serine (or cysteine) peptidase inhibitor, clade H, member 1	protein-coding
mm_144775.1	chr18	35829780	35829795	+	1	NA	promoter-TSS (NM_133687)	promoter-TSS (NM_133687)	-31	NM_133687	67393	Mm.94560	NM_133687	ENSMUSG00000046668	Cxxc5	4930415K17Rik	CXXC finger 5	protein-coding
mm_147494.1	chr18	47368909	47368933	-	1	NA	promoter-TSS (NM_018744)	promoter-TSS (NM_018744)	-51	NM_001311097	20358	Mm.40909	NM_018744	ENSMUSG00000019647	Sema6a	A730020P05Rik|AI851735|Sema6A-1|Semaq|VIa	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A	protein-coding
mm_975.1	chr1	58393194	58393241	+	1	NA	promoter-TSS (NM_025824)	promoter-TSS (NM_025824)	81	NM_025824	66882	Mm.21848	NM_025824	ENSMUSG00000051223	Bzw1	1200015E15Rik|mKIAA0005	basic leucine zipper and W2 domains 1	protein-coding
mm_155809.1	chrX	99147574	99147592	+	1	NA	3' UTR (NM_010110, exon 5 of 5)	3' UTR (NM_010110, exon 5 of 5)	11522	NM_010110	13641	Mm.3374	NM_010110	ENSMUSG00000031217	Efnb1	Cek5-L|EFL-3|Elk-L|Epl2|Eplg2|LERK-2|Lerk2|Stra1	ephrin B1	protein-coding
mm_57863.1	chr6	129615832	129615861	-	1	NA	intron (NM_001083322, intron 5 of 7)	Lx6|LINE|L1	6837	NM_033078	27007	Mm.8217	NM_033078	ENSMUSG00000030149	Klrk1	D6H12S2489E|NKG2-D|Nkg2d	killer cell lectin-like receptor subfamily K, member 1	protein-coding
mm_131145.1	chr16	6503178	6503183	+	1	NA	intron (NM_021477, intron 3 of 16)	intron (NM_021477, intron 3 of 16)	527593	NR_045799	68238	Mm.434605	NR_045799	ENSMUSG00000101481	1700123O21Rik	-	RIKEN cDNA 1700123O21 gene	ncRNA
mm_117054.1	chr13	58400489	58400492	-	1	NA	intron (NM_001301340, intron 1 of 15)	intron (NM_001301340, intron 1 of 15)	1679	NM_001301343	15387	Mm.142872	NM_025279	ENSMUSG00000021546	Hnrnpk	Hnrpk|KBBP|NOVA	heterogeneous nuclear ribonucleoprotein K	protein-coding
mm_58570.1	chr7	4793127	4793156	+	1	NA	intron (NM_009081, intron 1 of 4)	CpG	176	NM_009081	19943	Mm.379002	NM_009081	ENSMUSG00000030432	Rpl28	D7Wsu21e	ribosomal protein L28	protein-coding
mm_170915.1	chr2	36365374	36365377	-	1	NA	Intergenic	IAPLTR4|LTR|ERVK	-11403	NM_146947	258949	Mm.377765	NM_146947	ENSMUSG00000068950	Olfr338	MOR136-5	olfactory receptor 338	protein-coding
mm_152885.1	chr19	24676301	24676309	-	1	NA	intron (NM_183160, intron 1 of 1)	intron (NM_183160, intron 1 of 1)	2297	NM_183160	226040	Mm.391170	NM_183160	ENSMUSG00000048572	Tmem252	E030010A14Rik	transmembrane protein 252	protein-coding
mm_114230.1	chr13	56596325	56596355	+	1	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	-13263	NM_009369	21810	Mm.14455	NM_009369	ENSMUSG00000035493	Tgfbi	68kDa|AI181842|AI747162|Beta-ig|big-h3	transforming growth factor, beta induced	protein-coding
mm_60462.1	chr7	44477795	44477826	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-6707	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_54654.1	chr6	39078129	39078133	-	1	NA	intron (NM_011539, intron 10 of 12)	intron (NM_011539, intron 10 of 12)	-10545	NR_040523	69986	Mm.490941	NR_040523	ENSMUSG00000100121	1700025N23Rik	-	RIKEN cDNA 1700025N23 gene	ncRNA
mm_15729.1	chr2	164154623	164154645	+	1	NA	3' UTR (NM_021420, exon 11 of 11)	3' UTR (NM_021420, exon 11 of 11)	16479	NM_008435	16538	Mm.6217	NM_008435	ENSMUSG00000040164	Kcns1	Kv9.1	K+ voltage-gated channel, subfamily S, 1	protein-coding
mm_157814.1	chrX	73966974	73967008	-	1	NA	promoter-TSS (NM_008224)	promoter-TSS (NM_008224)	-634	NM_008224	15161	Mm.491126	NM_008224	ENSMUSG00000031386	Hcfc1	AW060991|HCF|HCF1	host cell factor C1	protein-coding
mm_151637.1	chr19	3942391	3942450	-	1	NA	exon (NM_019449, exon 6 of 11)	exon (NM_019449, exon 6 of 11)	7234	NM_001161428	54445	Mm.262094	NM_019449	ENSMUSG00000036908	Unc93b1	Unc-93B1|Unc93b	unc-93 homolog B1 (C. elegans)	protein-coding
mm_63903.1	chr7	139213004	139213016	+	1	NA	promoter-TSS (NM_027164)	promoter-TSS (NM_027164)	22	NM_027164	76612	Mm.17757	NM_027164	ENSMUSG00000015980	Lrrc27	1700071K18Rik|2310044E02Rik	leucine rich repeat containing 27	protein-coding
mm_91588.1	chr10	40257649	40257687	-	1	NA	promoter-TSS (NM_026113)	promoter-TSS (NM_026113)	-3	NM_026113	67371	Mm.64104	NM_026113	ENSMUSG00000019837	Gtf3c6	2410016F19Rik|AU019813	general transcription factor IIIC, polypeptide 6, alpha	protein-coding
mm_24267.1	chr3	89188321	89188328	+	1	NA	exon (NM_001014995, exon 11 of 12)	exon (NM_001014995, exon 11 of 12)	5099	NM_001014995	68521	Mm.274708	NM_001014995	ENSMUSG00000032657	Fam189b	1110013L07Rik	family with sequence similarity 189, member B	protein-coding
mm_142353.1	chr17	43630291	43630304	-	1	NA	promoter-TSS (NM_198418)	promoter-TSS (NM_198418)	2	NM_001161366	210510	Mm.329058	NM_198418	ENSMUSG00000040140	Tdrd6	AB097085|Tdr2	tudor domain containing 6	protein-coding
mm_171403.1	chr4	12431151	12431151	+	1	NA	Intergenic	Intergenic	-259136	NM_026558	68099	Mm.25340	NM_026558	ENSMUSG00000028218	Fam92a	6720467C03Rik|Fam92a1	family with sequence similarity 92, member A	protein-coding
mm_141360.1	chr17	28801587	28801600	-	1	NA	intron (NM_001081315, intron 1 of 12)	CpG	467	NM_001081315	268936	Mm.291877	NM_199061	ENSMUSG00000063952	Brpf3	AI413466|AW493400|mKIAA1286	bromodomain and PHD finger containing, 3	protein-coding
mm_113002.1	chr13	21811738	21811754	+	1	NA	promoter-TSS (NM_175657)	promoter-TSS (NM_175657)	0	NM_001195421	100041230	Mm.442307	NM_001195421	ENSMUSG00000069306	Hist1h4m	Gm11275|OTTMUSG00000000446	histone cluster 1, H4m	protein-coding
mm_71440.1	chr8	46512952	46512954	+	1	NA	intron (NM_001302163, intron 5 of 20)	intron (NM_001302163, intron 5 of 20)	21987	NM_001302163	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_152685.1	chr19	16267636	16267643	-	1	NA	intron (NM_008139, intron 2 of 6)	intron (NM_008139, intron 2 of 6)	47365	NR_105832	102465218		NR_105832	ENSMUSG00000098718	Mir496b	Gm28028|mmu-mir-496b	microRNA 496b	ncRNA
mm_23847.1	chr3	83008369	83008409	+	1	NA	exon (NM_133862, exon 3 of 10)	exon (NM_133862, exon 3 of 10)	665	NM_001317105	99571	Mm.16422	NM_133862	ENSMUSG00000033860	Fgg	3010002H13Rik|AI256424	fibrinogen gamma chain	protein-coding
mm_51710.1	chr6	86733642	86733664	+	1	NA	promoter-TSS (NM_011818)	promoter-TSS (NM_011818)	-275	NM_011818	23885	Mm.321452	NM_011818	ENSMUSG00000001157	Gmcl1	2810049L19Rik|Btbd13|DIP|Gcl|Gcl-1|glc-1|mglc-1	germ cell-less, spermatogenesis associated 1	protein-coding
mm_111980.1	chr12	110393573	110393613	-	1	NA	Intergenic	Lx8|LINE|L1	-53586	NM_001135001	26931	Mm.240396	NM_012023	ENSMUSG00000017843	Ppp2r5c	2610043M05Rik|2700063L20Rik|AI060890|AW545884|C85228|D12Bwg0916e|mKIAA0044	protein phosphatase 2, regulatory subunit B', gamma	protein-coding
mm_82307.1	chr9	7872585	7872603	-	1	NA	intron (NM_007464, intron 1 of 8)	CpG	576	NM_007464	11796	Mm.2026	NM_007464	ENSMUSG00000032000	Birc3	AW107670|Api1|Api2|Birc2|C-IAP2|HIAP2|IAP1|IAP2|MIAP1|MIAP2|MIHB|MIHC|RNF49|cIAP-1|cIAP-2|cIAP1|cIAP2	baculoviral IAP repeat-containing 3	protein-coding
mm_9646.1	chr1	177258316	177258438	-	1	NA	Intergenic	CpG	-9610	NM_011785	23797	Mm.235194	NM_011785	ENSMUSG00000019699	Akt3	AI851531|D930002M15Rik|Nmf350	thymoma viral proto-oncogene 3	protein-coding
mm_61102.1	chr7	51880313	51880356	+	1	NA	intron (NM_008087, intron 1 of 7)	intron (NM_008087, intron 1 of 7)	1367	NM_001330607	14453	Mm.207360	NM_008087	ENSMUSG00000030498	Gas2	Gas-2	growth arrest specific 2	protein-coding
mm_152809.1	chr19	23058164	23058171	-	1	NA	Intergenic	Intergenic	-83059	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_127546.1	chr15	102144468	102144486	+	1	NA	5' UTR (NM_008344, exon 1 of 4)	5' UTR (NM_008344, exon 1 of 4)	291	NM_008344	16012	Mm.358609	NM_008344	ENSMUSG00000023046	Igfbp6	IGFBP-6	insulin-like growth factor binding protein 6	protein-coding
mm_22383.1	chr2	181156900	181156905	-	1	NA	5' UTR (NM_007906, exon 1 of 8)	5' UTR (NM_007906, exon 1 of 8)	113	NM_007906	13628	Mm.2645	NM_007906	ENSMUSG00000016349	Eef1a2	Eef1a|S1|wasted|wst	eukaryotic translation elongation factor 1 alpha 2	protein-coding
mm_59590.1	chr7	28131697	28131707	+	1	NA	exon (NM_001164655, exon 3 of 20)	exon (NM_001164655, exon 3 of 20)	2236	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_81962.1	chr9	120933484	120933491	+	1	NA	promoter-TSS (NM_007614)	promoter-TSS (NM_007614)	87	NM_007614	12387	Mm.291928	NM_007614	ENSMUSG00000006932	Ctnnb1	Bfc|Catnb|Mesc	catenin (cadherin associated protein), beta 1	protein-coding
mm_21057.1	chr2	152654289	152654304	-	1	NA	Intergenic	Intergenic	-15165	NM_010376	14950	Mm.277327	NM_010376	ENSMUSG00000019188	H13	1200006O09Rik|4930443L17Rik|5031424B04Rik|AV020344|H-13|Hm13|PSL3|Spp	histocompatibility 13	protein-coding
mm_76581.1	chr8	89015616	89015630	-	1	NA	Intergenic	Intergenic	-9112	NR_106190	102465899		NR_106190	ENSMUSG00000099078	Mir8110	Gm27571|mmu-mir-8110	microRNA 8110	ncRNA
mm_153741.1	chr19	44696374	44696403	-	1	NA	Intergenic	Intergenic	-61006	NM_011037	18504	Mm.192158	NM_011037	ENSMUSG00000004231	Pax2	Opdc|Pax-2	paired box 2	protein-coding
mm_22623.1	chr3	14661870	14661888	+	1	NA	3' UTR (NM_024495, exon 7 of 7)	3' UTR (NM_024495, exon 7 of 7)	20152	NM_024495	71934	Mm.158776	NM_024495	ENSMUSG00000027555	Car13	2310075C21Rik|Ca13	carbonic anhydrase 13	protein-coding
mm_76587.1	chr8	89042448	89042469	-	1	NA	intron (NM_021390, intron 1 of 3)	CpG-14342	1704	NM_021390	58198	Mm.214361	NM_021390	ENSMUSG00000031665	Sall1	Msal-3	sal-like 1 (Drosophila)	protein-coding
mm_79307.1	chr9	52048002	52048030	+	1	NA	promoter-TSS (NM_009041)	promoter-TSS (NM_009041)	75	NM_001104617	19684	Mm.245746	NM_009041	ENSMUSG00000032050	Rdx	AA516625	radixin	protein-coding
mm_36116.1	chr4	58910144	58910154	-	1	NA	intron (NM_172381, intron 1 of 48)	L1MB3|LINE|L1	2576	NM_172381	230249	Mm.234801	NM_172381	ENSMUSG00000050812	AI314180	AW558785|BB181316|mKIAA0368	expressed sequence AI314180	protein-coding
mm_93592.1	chr10	117071971	117071984	-	1	NA	3' UTR (NM_177798, exon 10 of 10)	3' UTR (NM_177798, exon 10 of 10)	-8163	NM_007636	12461	Mm.247788	NM_007636	ENSMUSG00000034024	Cct2	Cctb	chaperonin containing Tcp1, subunit 2 (beta)	protein-coding
mm_5712.1	chr1	43827752	43827786	-	1	NA	promoter-TSS (NM_026430)	promoter-TSS (NM_026430)	-61	NM_026430	67883	Mm.387202	NM_026430	ENSMUSG00000057363	Uxs1	1600025I13Rik|AI451869|AI649125|AW550562	UDP-glucuronate decarboxylase 1	protein-coding
mm_158333.1	chrX	133961834	133961854	-	1	NA	exon (NM_001290718, exon 3 of 14)	exon (NM_001290718, exon 3 of 14)	19968	NM_001290718	27359	Mm.38674	NM_013757	ENSMUSG00000031255	Sytl4	Gph|Slp4	synaptotagmin-like 4	protein-coding
mm_70701.1	chr8	15036765	15036773	+	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	9309	NR_037972	434285	Mm.334425	NM_001007591	ENSMUSG00000049008	BB014433	-	expressed sequence BB014433	ncRNA
mm_114105.1	chr13	54783989	54783993	+	1	NA	promoter-TSS (NR_104407)	promoter-TSS (NR_104407)	-7	NM_001286179	218268	Mm.425821	NM_001033269	ENSMUSG00000074895	Eif4e1b	Eif4eloo|Gm273	eukaryotic translation initiation factor 4E family member 1B	protein-coding
mm_110582.1	chr12	56523255	56523266	-	1	NA	intron (NR_045082, intron 1 of 6)	intron (NR_045082, intron 1 of 6)	6160	NR_045082	104798	Mm.310950	NR_045082		E030019B13Rik	AI413669	RIKEN cDNA E030019B13 gene	ncRNA
mm_80408.1	chr9	77652689	77652694	+	1	NA	intron (NM_172925, intron 2 of 2)	intron (NM_172925, intron 2 of 2)	15959	NM_172925	244923	Mm.138238	NM_172925	ENSMUSG00000044938	Klhl31	9830147P19Rik|D930047P17Rik|Kbtbd1	kelch-like 31	protein-coding
mm_4593.1	chr1	178337083	178337178	+	1	NA	exon (NM_016805, exon 1 of 14)	exon (NM_016805, exon 1 of 14)	654	NM_016805	51810	Mm.86589	NM_016805	ENSMUSG00000039630	Hnrnpu	AA408410|AI256620|AL024194|AL024437|AW557595|C86794|Hnrpu|SAFA|Sp120|hnRNP U	heterogeneous nuclear ribonucleoprotein U	protein-coding
mm_17266.1	chr2	26021561	26021613	-	1	NA	5' UTR (NM_133835, exon 1 of 10)	5' UTR (NM_133835, exon 1 of 10)	173	NM_133835	98766	Mm.247824	NM_133835	ENSMUSG00000036352	Ubac1	1110033G07Rik|AA407978|GBDR1|Gdbr1|Kpc2|Ubadc1	ubiquitin associated domain containing 1	protein-coding
mm_141375.1	chr17	29052030	29052057	-	1	NA	Intergenic	Intergenic	19383	NR_036613	20383	Mm.6787	NM_013663	ENSMUSG00000071172	Srsf3	AL024116|Sfrs3|X16	serine/arginine-rich splicing factor 3	protein-coding
mm_110383.1	chr12	40223175	40223192	-	1	NA	promoter-TSS (NM_013562)	promoter-TSS (NM_013562)	6	NM_013562	15982	Mm.168	NM_013562	ENSMUSG00000001627	Ifrd1	Ifnl|PC4|Tis7	interferon-related developmental regulator 1	protein-coding
mm_122663.1	chr14	51913394	51913398	-	1	NA	promoter-TSS (NM_001145959)	promoter-TSS (NM_001145959)	92	NM_001145959	29811	Mm.26722	NM_013864	ENSMUSG00000004558	Ndrg2	AI182517|AU040374|Ndr2|SYLD	N-myc downstream regulated gene 2	protein-coding
mm_95907.1	chr11	58205103	58205124	+	1	NA	intron (NM_018738, intron 2 of 2)	intron (NM_018738, intron 2 of 2)	5557	NM_018738	16145	Mm.33902	NM_018738	ENSMUSG00000078853	Igtp	AW558444|Irgm3	interferon gamma induced GTPase	protein-coding
mm_147183.1	chr18	36783097	36783108	-	1	NA	promoter-TSS (NM_080636)	promoter-TSS (NM_080636)	103	NM_008214	15115	Mm.10528	NM_008214	ENSMUSG00000001380	Hars	MMHRS	histidyl-tRNA synthetase	protein-coding
mm_160900.1	chr11	75179554	75179554	-	1	NA	promoter-TSS (NM_027136)	promoter-TSS (NM_027136)	-746	NM_027136	246257	Mm.41496	NM_027136	ENSMUSG00000038268	Ovca2	9030414M07Rik	candidate tumor suppressor in ovarian cancer 2	protein-coding
mm_121676.1	chr14	12822865	12822875	-	1	NA	5' UTR (NM_001042617, exon 1 of 31)	5' UTR (NM_001042617, exon 1 of 31)	209	NM_001042617	27062	Mm.260881	NM_012061	ENSMUSG00000054423	Cadps	AU067781|CAPS|CAPS1|mKIAA1121	Ca2+-dependent secretion activator	protein-coding
mm_153161.1	chr19	34492936	34492946	-	1	NA	3' UTR (NM_021460, exon 10 of 10)	3' UTR (NM_021460, exon 10 of 10)	-17806	NM_009890	12642	Mm.30824	NM_009890	ENSMUSG00000050370	Ch25h	AI462618|m25OH	cholesterol 25-hydroxylase	protein-coding
mm_168653.1	chr11	87448622	87448642	+	1	NA	intron (NM_001199293, intron 2 of 30)	U3|snRNA|snRNA	21041	NM_001199293	83560	Mm.440758	NM_031386	ENSMUSG00000010342	Tex14	C85585	testis expressed gene 14	protein-coding
mm_10445.1	chr2	14266498	14266509	+	1	NA	exon (NM_008625, exon 7 of 30)	exon (NM_008625, exon 7 of 30)	5500	NR_030609	100124488		NR_030609	ENSMUSG00000077897	Mir511	Mirn511|mir-511|mmu-mir-511	microRNA 511	ncRNA
mm_84346.1	chr9	64253543	64253553	-	1	NA	promoter-TSS (NM_008927)	promoter-TSS (NM_008927)	57	NM_008927	26395	Mm.248907	NM_008927	ENSMUSG00000004936	Map2k1	MAPKK1|MEKK1|Mek1|Prkmk1	mitogen-activated protein kinase kinase 1	protein-coding
mm_41706.1	chr5	101765076	101765109	+	1	NA	promoter-TSS (NM_173370)	promoter-TSS (NM_173370)	-38	NM_173370	74596	Mm.46764	NM_173370	ENSMUSG00000029330	Cds1	4833409J18Rik|AI314024|AW125888	CDP-diacylglycerol synthase 1	protein-coding
mm_28783.1	chr3	95993703	95993719	-	1	NA	intron (NM_023320, intron 2 of 5)	intron (NM_023320, intron 2 of 5)	2128	NM_023320	67220	Mm.458147	NM_023320	ENSMUSG00000015745	Plekho1	2810052M02Rik|CKIP-1|Ckip1|JZA-20|Jza2	pleckstrin homology domain containing, family O member 1	protein-coding
mm_12992.1	chr2	90885765	90885771	+	1	NA	promoter-TSS (NM_026161)	promoter-TSS (NM_026161)	-18	NM_026161	67445	Mm.258993	NM_026161	ENSMUSG00000040794	C1qtnf4	0710001E10Rik|9430004J15Rik|CTRP4	C1q and tumor necrosis factor related protein 4	protein-coding
mm_151006.1	chr19	46668588	46668603	+	1	NA	intron (NM_007809, intron 6 of 7)	intron (NM_007809, intron 6 of 7)	4405	NM_007809	13074	Mm.1262	NM_007809	ENSMUSG00000003555	Cyp17a1	Cyp17|p450c17	cytochrome P450, family 17, subfamily a, polypeptide 1	protein-coding
mm_146506.1	chr18	3337252	3337276	-	1	NA	intron (NR_033457, intron 1 of 1)	CpG	325	NM_001110851	12916	Mm.5244	NM_013498	ENSMUSG00000063889	Crem	ICER|ICERI	cAMP responsive element modulator	protein-coding
mm_135738.1	chr16	55838667	55838675	-	1	NA	promoter-TSS (NM_030612)	promoter-TSS (NM_030612)	-30	NM_001159395	80859	Mm.247272	NM_030612	ENSMUSG00000035356	Nfkbiz	AA408868|INAP|Mail	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, zeta	protein-coding
mm_77901.1	chr9	7348789	7348813	+	1	NA	exon (NM_008605, exon 2 of 10)	exon (NM_008605, exon 2 of 10)	1427	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_169427.1	chr14	53544939	53544958	+	1	NA	Intergenic	Intergenic	708981	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_1970.1	chr1	86504512	86504542	+	1	NA	Intergenic	Intergenic	-22209	NM_008972	19231	Mm.19187	NM_008972	ENSMUSG00000026238	Ptma	Thym	prothymosin alpha	protein-coding
mm_139319.1	chr17	48410183	48410202	+	1	NA	promoter-TSS (NM_010913)	promoter-TSS (NM_010913)	192	NM_207219	106821	Mm.203943	NM_207219	ENSMUSG00000040771	Oard1	AI314976|AW558560	O-acyl-ADP-ribose deacylase 1	protein-coding
mm_100999.1	chr11	8468517	8468545	-	1	NA	intron (NM_001083587, intron 20 of 30)	intron (NM_001083587, intron 20 of 30)	196004	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_159758.1	chr5	89527379	89527379	+	1	NA	promoter-TSS (NM_133192)	promoter-TSS (NM_133192)	-50	NM_133192	104443	Mm.447881	NM_133192	ENSMUSG00000035528	Npffr2	Gpr74|HG31|NPFF2	neuropeptide FF receptor 2	protein-coding
mm_112922.1	chr13	20934592	20934612	+	1	NA	intron (NM_012054, intron 11 of 20)	intron (NM_012054, intron 11 of 20)	138697	NM_146535	258528	Mm.377554	NM_146535	ENSMUSG00000042869	Olfr1370	MOR256-14	olfactory receptor 1370	protein-coding
mm_64811.1	chr7	6709643	6709658	-	1	NA	exon (NM_008817, exon 9 of 9)	exon (NM_008817, exon 9 of 9)	2890	NR_023846	100169889	Mm.491213	NR_023846		Peg3os	Apeg3|Peg3as	Peg3 opposite strand	ncRNA
mm_3414.1	chr1	144317902	144317911	+	1	NA	Intergenic	Intergenic	-68802	NM_015811	50778	Mm.103701	NM_015811	ENSMUSG00000026358	Rgs1	BL34	regulator of G-protein signaling 1	protein-coding
mm_85579.1	chr9	107289848	107289866	-	1	NA	promoter-TSS (NM_178907)	promoter-TSS (NM_178907)	20	NM_178907	102626	Mm.222612	NM_178907	ENSMUSG00000032577	Mapkapk3	3PK|AI874665|MAPKAP-K3|MAPKAP3|MK-3|MK3|MapkKapk3	mitogen-activated protein kinase-activated protein kinase 3	protein-coding
mm_122867.1	chr14	54913065	54913084	-	1	NA	promoter-TSS (NM_021551)	promoter-TSS (NM_021551)	58	NM_021551	59049	Mm.27435	NM_021551	ENSMUSG00000022199	Slc22a17	1700094C23Rik|24p3R|AU041908|AW555662|BOIT|Boct	solute carrier family 22 (organic cation transporter), member 17	protein-coding
mm_144574.1	chr18	31860516	31860530	+	1	NA	intron (NM_028866, intron 7 of 21)	B3A|SINE|B2	51380	NM_026006	67158	Mm.31537	NM_026006	ENSMUSG00000044982	Sft2d3	2610206C24Rik|AI847965|AW046173	SFT2 domain containing 3	protein-coding
mm_76042.1	chr8	77517876	77517892	-	1	NA	promoter-TSS (NM_030113)	promoter-TSS (NM_030113)	23	NM_030113	78514	Mm.165974	NM_030113	ENSMUSG00000037148	Arhgap10	A930033B01Rik|PSGAP-m|PSGAP-s	Rho GTPase activating protein 10	protein-coding
mm_5606.1	chr1	39577341	39577427	-	1	NA	promoter-TSS (NM_001033135)	promoter-TSS (NM_001033135)	-37	NM_001033135	67702	Mm.28614	NM_001033135	ENSMUSG00000048234	Rnf149	1600023E10Rik|AV037261|C76763|Gm15832|Greul4|OTTMUSG00000026591	ring finger protein 149	protein-coding
mm_119747.1	chr14	54138493	54138537	+	1	NA	Intergenic	Intergenic	115414	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_64899.1	chr7	15959785	15959795	-	1	NA	intron (NM_153068, intron 3 of 5)	B3A|SINE|B2	7745	NM_153068	259300	Mm.138215	NM_153068	ENSMUSG00000074364	Ehd2	BC027084|C130052H20Rik	EH-domain containing 2	protein-coding
mm_150753.1	chr19	43839265	43839275	+	1	NA	non-coding (NR_033472, exon 1 of 1)	non-coding (NR_033472, exon 1 of 1)	467	NR_033472	100038628	Mm.212585	NR_033472	ENSMUSG00000025194	Gm10768	ENSMUSG00000074828	predicted gene 10768	ncRNA
mm_10439.1	chr2	14229391	14229404	+	1	NA	promoter-TSS (NM_008625)	promoter-TSS (NM_008625)	-17	NM_008625	17533	Mm.2019	NM_008625	ENSMUSG00000026712	Mrc1	AW259686|CD206|MR	mannose receptor, C type 1	protein-coding
mm_75116.1	chr8	34529104	34529111	-	1	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	111209	NR_040706	330734	Mm.149998	NR_040706	ENSMUSG00000109819	B930018H19Rik	B930018H19	RIKEN cDNA B930018H19 gene	ncRNA
mm_63239.1	chr7	126584949	126584953	+	1	NA	promoter-TSS (NM_138310)	promoter-TSS (NM_138310)	-57	NM_138310	171504	Mm.170665	NM_138310	ENSMUSG00000042759	Apobr	Apob-48r|Apob48r	apolipoprotein B receptor	protein-coding
mm_86234.1	chr9	120679842	120679846	-	1	NA	Intergenic	RLTR9A|LTR|ERVK	102513	NR_073359	76100	Mm.48212	NR_073359	ENSMUSG00000052658	5830454E08Rik	-	RIKEN cDNA 5830454E08 gene	ncRNA
mm_142468.1	chr17	45602071	45602086	-	1	NA	promoter-TSS (NM_001177468)	promoter-TSS (NM_001177468)	-11	NM_001177468	653016	Mm.45676	NM_001177468	ENSMUSG00000079471	Gm7325	EG653016|Esgp	predicted gene 7325	protein-coding
mm_156955.1	chrX	169988966	169988990	+	1	NA	exon (NM_001290504, exon 10 of 10)	exon (NM_001290504, exon 10 of 10)	-10061	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_31451.1	chr4	48615531	48615535	+	1	NA	intron (NM_021436, intron 4 of 9)	intron (NM_021436, intron 4 of 9)	30340	NM_021436	230157	Mm.422686	NM_021436	ENSMUSG00000028347	Tmeff1	A830033E11|M7365|Tr1	transmembrane protein with EGF-like and two follistatin-like domains 1	protein-coding
mm_155618.1	chrX	83222544	83222547	+	1	NA	intron (NM_007868, intron 2 of 78)	B1_Mur1|SINE|Alu	265379	NM_021898	100502723	Mm.383210	NM_021898	ENSMUSG00000035522	Tsga8	Halap-X|Halapx	testis specific gene A8	protein-coding
mm_94286.1	chr11	3992490	3992524	+	1	NA	intron (NM_001177691, intron 1 of 2)	intron (NM_001177691, intron 1 of 2)	2574	NM_001177691	53897	Mm.103414	NM_016922	ENSMUSG00000049721	Gal3st1	Cst|Gcst	galactose-3-O-sulfotransferase 1	protein-coding
mm_19354.1	chr2	91070181	91070249	-	1	NA	promoter-TSS (NR_110981)	promoter-TSS (NR_110981)	100	NM_026721	68427	Mm.192375	NM_026721	ENSMUSG00000002105	Slc39a13	1100001L14Rik|AA387663|ZIP-13|ZIP13	solute carrier family 39 (metal ion transporter), member 13	protein-coding
mm_103283.1	chr11	72215027	72215068	-	1	NA	promoter-TSS (NM_001163728)	promoter-TSS (NM_001163728)	-91	NM_001163728	75304	Mm.340776	NM_001163728		4930563E22Rik	-	RIKEN cDNA 4930563E22 gene	protein-coding
mm_74592.1	chr8	11555259	11555267	-	1	NA	promoter-TSS (NM_001302457)	promoter-TSS (NM_001302457)	-499	NM_001302458	26356	Mm.25709	NM_011919	ENSMUSG00000045969	Ing1	2610028J21Rik|AA407184|AI875420|mING1h|p33Ing1|p37Ing1b	inhibitor of growth family, member 1	protein-coding
mm_66963.1	chr7	62464469	62464477	-	1	NA	promoter-TSS (NM_013788)	promoter-TSS (NM_013788)	37	NM_013788	27412	Mm.422745	NM_013788	ENSMUSG00000070526	Peg12	Frat3	paternally expressed 12	protein-coding
mm_18316.1	chr2	57108077	57108085	-	1	NA	3' UTR (NM_013613, exon 8 of 8)	3' UTR (NM_013613, exon 8 of 8)	6957	NM_013613	18227	Mm.3507	NM_013613	ENSMUSG00000026826	Nr4a2	HZF-3|NOT|Nurr1|RNR-1|TINOR|TINUR	nuclear receptor subfamily 4, group A, member 2	protein-coding
mm_246.1	chr1	19212105	19212106	+	1	NA	promoter-TSS (NM_001025305)	promoter-TSS (NM_001025305)	51	NM_001025305	21419	Mm.137021	NM_009334	ENSMUSG00000025927	Tfap2b	AI606113|AP-2(beta)|E130018K07Rik|Tcfap2b	transcription factor AP-2 beta	protein-coding
mm_107372.1	chr12	32851434	32851444	+	1	NA	3' UTR (NM_021524, exon 11 of 11)	3' UTR (NM_021524, exon 11 of 11)	27323	NR_045032	100504486	Mm.440246	NR_045032		Gdap10	Gdap-ps	ganglioside-induced differentiation-associated-protein 10	ncRNA
mm_139708.1	chr17	57459919	57459949	+	1	NA	intron (NM_010130, intron 17 of 21)	RMER1B|Other|Other	85380	NM_001104591	224916	Mm.469889	NM_001104591	ENSMUSG00000090655	Vmn2r120	EG224916	vomeronasal 2, receptor 120	protein-coding
mm_148754.1	chr19	6058211	6058230	+	1	NA	promoter-TSS (NM_026246)	promoter-TSS (NM_026246)	253	NM_001190436	14109	Mm.329631	NM_007990	ENSMUSG00000038274	Fau	MNSFbeta	Finkel-Biskis-Reilly murine sarcoma virus (FBR-MuSV) ubiquitously expressed (fox derived)	protein-coding
mm_95899.1	chr11	58201470	58201501	+	1	NA	5' UTR (NM_018738, exon 2 of 3)	5' UTR (NM_018738, exon 2 of 3)	1929	NM_018738	16145	Mm.33902	NM_018738	ENSMUSG00000078853	Igtp	AW558444|Irgm3	interferon gamma induced GTPase	protein-coding
mm_65058.1	chr7	18798480	18798480	-	1	NA	promoter-TSS (NM_011964)	promoter-TSS (NM_011964)	30	NM_011964	26439	Mm.36878	NM_011964	ENSMUSG00000004542	Psg19	CGM7|Cea-4|Cea4	pregnancy specific glycoprotein 19	protein-coding
mm_1429.1	chr1	67177323	67177326	+	1	NA	intron (NM_001080809, intron 20 of 37)	AT_rich|Low_complexity|Low_complexity	54297	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_31953.1	chr4	86748852	86748862	+	1	NA	5' UTR (NM_184088, exon 1 of 32)	5' UTR (NM_184088, exon 1 of 32)	302	NM_184088	329877	Mm.273718	NM_184088	ENSMUSG00000038024	Dennd4c	1700065A05Rik|AA420392	DENN/MADD domain containing 4C	protein-coding
mm_112272.1	chr12	114223326	114223334	-	1	NA	Intergenic	Intergenic	246136	NR_106062	102465663		NR_106062	ENSMUSG00000105438	Mir7094-1	mmu-mir-7094-1	microRNA 7094-1	ncRNA
mm_4343.1	chr1	171856838	171856887	+	1	NA	intron (NM_001289470, intron 3 of 8)	L1_Mur3|LINE|L1	17165	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_8607.1	chr1	156035892	156035936	-	1	NA	promoter-TSS (NM_001160182)	promoter-TSS (NM_001160182)	-122	NM_001160182	240832	Mm.253335	NM_022329	ENSMUSG00000050565	Tor1aip2	1110020D10Rik|15kDa|A130072J07|AA103493|AW060462|AW610675|C77739|Ifrg15|Lull1	torsin A interacting protein 2	protein-coding
mm_82289.1	chr9	7661365	7661367	-	1	NA	intron (NM_013903, intron 8 of 9)	MERV1_LTR|LTR|ERV1	-30724	NM_010810	17393	Mm.4825	NM_010810	ENSMUSG00000018623	Mmp7	MAT|MMP-7	matrix metallopeptidase 7	protein-coding
mm_93767.1	chr10	120201465	120201483	-	1	NA	promoter-TSS (NM_028679)	promoter-TSS (NM_028679)	63	NM_028679	73914	Mm.146194	NM_028679	ENSMUSG00000020227	Irak3	4833428C18Rik|AI563835|IRAK-M	interleukin-1 receptor-associated kinase 3	protein-coding
mm_149237.1	chr19	10183148	10183156	+	1	NA	exon (NM_146094, exon 1 of 12)	exon (NM_146094, exon 1 of 12)	264	NM_146094	76267	Mm.30158	NM_146094	ENSMUSG00000010663	Fads1	0710001O03Rik|A930006B21Rik|AI317215|DSD	fatty acid desaturase 1	protein-coding
mm_6436.1	chr1	73997886	73997892	-	1	NA	intron (NM_027884, intron 6 of 34)	intron (NM_027884, intron 6 of 34)	126558	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_9395.1	chr1	172219584	172219589	-	1	NA	exon (NM_009813, exon 1 of 11)	exon (NM_009813, exon 1 of 11)	309	NM_009813	12372	Mm.12829	NM_009813	ENSMUSG00000007122	Casq1	CSQ|CSQ-1|CSQ1|sCSQ	calsequestrin 1	protein-coding
mm_132114.1	chr16	31663938	31663980	+	1	NA	promoter-TSS (NM_001252434)	promoter-TSS (NM_001252434)	24	NM_001252434	13383	Mm.382	NM_007862	ENSMUSG00000022770	Dlg1	B130052P05Rik|Dlgh1|E-dlg/SAP97|SAP-97|SAP97|mKIAA4187	discs, large homolog 1 (Drosophila)	protein-coding
mm_130085.1	chr15	89378972	89378994	-	1	NA	intron (NM_001013022, intron 1 of 4)	CpG-5245	271	NM_001013022	70113	Mm.247273	NM_001013022	ENSMUSG00000047394	Odf3b	2010001J22Rik	outer dense fiber of sperm tails 3B	protein-coding
mm_137846.1	chr17	31057741	31057749	+	1	NA	promoter-TSS (NM_009593)	promoter-TSS (NM_009593)	51	NM_009593	11307	Mm.15691	NM_009593	ENSMUSG00000024030	Abcg1	AW413978|Abc8|White	ATP-binding cassette, sub-family G (WHITE), member 1	protein-coding
mm_169691.1	chr15	74825199	74825213	-	1	NA	TTS (NM_010416)	TTS (NM_010416)	6130	NM_010416	15202	Mm.17336	NM_010416	ENSMUSG00000068600	Gml2	1700057K19Rik|HemT|Hemt1	glycosylphosphatidylinositol anchored molecule like 2	protein-coding
mm_77355.1	chr8	119625916	119625943	-	1	NA	exon (NM_025734, exon 3 of 3)	exon (NM_025734, exon 3 of 3)	9751	NM_025734	66733	Mm.358699	NM_025734	ENSMUSG00000045246	Kcng4	4921535I01Rik|AW049024|KV6.3|KV6.4	potassium voltage-gated channel, subfamily G, member 4	protein-coding
mm_103040.1	chr11	69761937	69761952	-	1	NA	promoter-TSS (NM_019871)	promoter-TSS (NM_019871)	-100	NM_019871	56293	Mm.6211	NM_019871	ENSMUSG00000018776	Slc35g3	Amac1	solute carrier family 35, member G3	protein-coding
mm_137023.1	chr17	17867340	17867350	+	1	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	-12157	NM_008215	15116	Mm.255701	NM_008215	ENSMUSG00000003665	Has1	HAS	hyaluronan synthase1	protein-coding
mm_109701.1	chr12	113259628	113259658	+	1	NA	Intergenic	Intergenic	73740	NM_153776	69195	Mm.313244	NM_153776	ENSMUSG00000049036	Tmem121	2410008J05Rik|Hole	transmembrane protein 121	protein-coding
mm_11901.1	chr2	50296895	50296910	+	1	NA	promoter-TSS (NM_133839)	promoter-TSS (NM_133839)	92	NR_040362	100502624	Mm.382825	NR_040361	ENSMUSG00000085862	Gm13483	OTTMUSG00000012382	predicted gene 13483	ncRNA
mm_52421.1	chr6	113471465	113471475	+	1	NA	promoter-TSS (NM_178942)	promoter-TSS (NM_178942)	15	NM_134159	171095	Mm.213397	NM_134159	ENSMUSG00000030281	Il17rc	1110025H02Rik|Gm19850|IL-17RC|IL17-RC|IL17-RL|Il17rl	interleukin 17 receptor C	protein-coding
mm_3426.1	chr1	146774187	146774196	+	1	NA	intron (NM_001145807, intron 6 of 7)	intron (NM_001145807, intron 6 of 7)	276504	NM_001145807	215378	Mm.441817	NM_153539	ENSMUSG00000035131	Brinp3	B830045N13Rik|Fam5c	bone morphogenetic protein/retinoic acid inducible neural specific 3	protein-coding
mm_107135.1	chr12	21286337	21286451	+	1	NA	promoter-TSS (NM_008403)	promoter-TSS (NM_008403)	97	NM_018813	54451	Mm.356778	NM_018813	ENSMUSG00000054309	Cpsf3	-	cleavage and polyadenylation specificity factor 3	protein-coding
mm_152988.1	chr19	29646482	29646486	-	1	NA	intron (NM_001081213, intron 1 of 14)	intron (NM_001081213, intron 1 of 14)	1936	NM_001081213	226090	Mm.267131	NM_146098	ENSMUSG00000046324	Ermp1	D19Ertd410e|D19Wsu12e|Fxna|mKIAA1815	endoplasmic reticulum metallopeptidase 1	protein-coding
mm_134578.1	chr16	20405516	20405537	-	1	NA	exon (NM_013790, exon 4 of 30)	exon (NM_013790, exon 4 of 30)	20868	NM_013790	27416	Mm.20845	NM_013790	ENSMUSG00000022822	Abcc5	2900011L11Rik|AI132311|Abcc5a|Abcc5b|Mrp5	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	protein-coding
mm_21675.1	chr2	164425976	164425986	-	1	NA	3' UTR (NM_011521, exon 5 of 5)	3' UTR (NM_011521, exon 5 of 5)	17207	NM_011521	20971	Mm.3815	NM_011521	ENSMUSG00000017009	Sdc4	AA959608|AW108331|S4|Synd4|ryudocan|syndecan-4	syndecan 4	protein-coding
mm_58836.1	chr7	16830841	16830861	+	1	NA	intron (NM_133789, intron 7 of 17)	intron (NM_133789, intron 7 of 17)	-12051	NM_001252458	101540	Mm.1881	NM_178900	ENSMUSG00000041187	Prkd2	AI325941|PKD2	protein kinase D2	protein-coding
mm_48293.1	chr5	138207270	138207301	-	1	NA	Intergenic	Intergenic	12971	NM_177878	330216	Mm.19719	NM_177878	ENSMUSG00000049285	Mblac1	-	metallo-beta-lactamase domain containing 1	protein-coding
mm_98834.1	chr11	97435370	97435379	+	1	NA	Intergenic	Intergenic	-14786	NM_021493	58996	Mm.394118	NM_021493	ENSMUSG00000049807	Arhgap23	A330041B18Rik	Rho GTPase activating protein 23	protein-coding
mm_115909.1	chr13	23458438	23458439	-	1	NA	3' UTR (NM_013483, exon 8 of 8)	3' UTR (NM_013483, exon 8 of 8)	7463	NM_013483	12231	Mm.1420	NM_013483	ENSMUSG00000000706	Btn1a1	Btn	butyrophilin, subfamily 1, member A1	protein-coding
mm_81544.1	chr9	110246216	110246236	+	1	NA	intron (NM_001166273, intron 1 of 4)	intron (NM_001166273, intron 1 of 4)	2443	NM_001166273	29873	Mm.38496	NM_013884	ENSMUSG00000032482	Cspg5	Caleb|Ngc	chondroitin sulfate proteoglycan 5	protein-coding
mm_147006.1	chr18	34491514	34491521	-	1	NA	intron (NM_146084, intron 6 of 20)	(A)n|Simple_repeat|Simple_repeat	15306	NM_146084	225358	Mm.226899	NM_146084	ENSMUSG00000036501	Fam13b	2610024E20Rik|AW060714|AW546153	family with sequence similarity 13, member B	protein-coding
mm_119280.1	chr14	34311259	34311272	+	1	NA	promoter-TSS (NM_029389)	promoter-TSS (NM_029389)	538	NM_008133	14661	Mm.10600	NM_008133	ENSMUSG00000021794	Glud1	AI118167|Gdh-X|Glud|Gludl	glutamate dehydrogenase 1	protein-coding
mm_149386.1	chr19	11383579	11383582	+	1	NA	intron (NM_001310331, intron 3 of 6)	Lx3A|LINE|L1	8092	NM_001310331	666907		NM_001310331	ENSMUSG00000101389	Ms4a4a	EG666907	membrane-spanning 4-domains, subfamily A, member 4A	protein-coding
mm_23172.1	chr3	40746668	40746670	+	1	NA	intron (NM_011020, intron 1 of 18)	intron (NM_011020, intron 1 of 18)	1056	NM_011020	18415	Mm.39330	NM_011020	ENSMUSG00000025757	Hspa4l	94kDa|AI461691|APG-1|Osp94	heat shock protein 4 like	protein-coding
mm_133610.1	chr16	91534069	91534076	+	1	NA	Intergenic	Intergenic	-13022	NM_008338	15980	Mm.249364	NM_008338	ENSMUSG00000022965	Ifngr2	Ifgr2|Ifgt	interferon gamma receptor 2	protein-coding
mm_75260.1	chr8	40595165	40595173	-	1	NA	intron (NM_001040699, intron 4 of 13)	intron (NM_001040699, intron 4 of 13)	39623	NM_001040699	54384	Mm.294871	NM_019433	ENSMUSG00000039431	Mtmr7	-	myotubularin related protein 7	protein-coding
mm_63448.1	chr7	127490419	127490428	+	1	NA	3' UTR (NM_010183, exon 11 of 11)	3' UTR (NM_010183, exon 11 of 11)	1172	NR_106027	102465642		NR_106027	ENSMUSG00000098267	Mir7060	Gm27515|mmu-mir-7060	microRNA 7060	ncRNA
mm_132140.1	chr16	31942493	31942496	+	1	NA	intron (NM_172822, intron 2 of 2)	B1_Mur2|SINE|Alu	6027	NR_027897	106264	Mm.347369	NM_025320	ENSMUSG00000107002	0610012G03Rik	AI839730	RIKEN cDNA 0610012G03 gene	ncRNA
mm_82707.1	chr9	24314820	24314822	-	1	NA	3' UTR (NM_175678, exon 10 of 10)	3' UTR (NM_175678, exon 10 of 10)	188319	NM_172920	244745	Mm.38526	NM_172920	ENSMUSG00000043067	Dpy19l1	1100001I19Rik|6030402K12|AI225861|AW558481	dpy-19-like 1 (C. elegans)	protein-coding
mm_60484.1	chr7	44478453	44478482	+	1	NA	Intergenic	Intergenic	-6050	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_77166.1	chr8	111689345	111689386	-	1	NA	TTS (NR_106044)	TTS (NR_106044)	309	NR_106044	102466993		NR_106044	ENSMUSG00000099129	Mir7076	Gm27318|mmu-mir-7076	microRNA 7076	ncRNA
mm_59421.1	chr7	27122134	27122144	+	1	NA	intron (NM_007817, intron 3 of 9)	intron (NM_007817, intron 3 of 9)	2184	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_42780.1	chr5	121399088	121399092	+	1	NA	intron (NM_172722, intron 1 of 23)	intron (NM_172722, intron 1 of 23)	1108	NM_172722	231713	Mm.33919	NM_172722	ENSMUSG00000042719	Naa25	4833422K13Rik|A630046C11|AI450868|C330023M02Rik|Mdm20	N(alpha)-acetyltransferase 25, NatB auxiliary subunit	protein-coding
mm_36363.1	chr4	76344163	76344221	-	1	NA	intron (NM_011211, intron 10 of 39)	intron (NM_011211, intron 10 of 39)	-1065906	NM_025849	66928	Mm.24332	NM_025849	ENSMUSG00000028398	Tmem261	1700027K24Rik|3110001D03Rik	transmembrane protein 261	protein-coding
mm_85058.1	chr9	90238000	90238022	-	1	NA	intron (NM_194334, intron 3 of 12)	intron (NM_194334, intron 3 of 12)	32758	NM_194334	67016	Mm.335347	NM_194334	ENSMUSG00000037410	Tbc1d2b	1810061M12Rik|AI480956|AV021536|AV023399|AW491493|mKIAA1055	TBC1 domain family, member 2B	protein-coding
mm_6009.1	chr1	58973477	58973486	-	1	NA	promoter-TSS (NM_172406)	promoter-TSS (NM_172406)	1	NM_172406	70827	Mm.222887	NM_172406	ENSMUSG00000026028	Trak2	2900022D04Rik|4733401O11Rik|AI480836|AW046271|Als2cr3|CALS-C|GRIF-1|GRIF1|OIP98|mKIAA0549	trafficking protein, kinesin binding 2	protein-coding
mm_74851.1	chr8	24596961	24596976	-	1	NA	promoter-TSS (NM_008324)	promoter-TSS (NM_008324)	-16	NM_008324	15930	Mm.392	NM_008324	ENSMUSG00000031551	Ido1	Ido|Indo	indoleamine 2,3-dioxygenase 1	protein-coding
mm_98663.1	chr11	96279381	96279406	+	1	NA	Intergenic	Intergenic	-2512	NM_010461	15416	Mm.4822	NM_010461	ENSMUSG00000056648	Hoxb8	Hox-2.4	homeobox B8	protein-coding
mm_97821.1	chr11	82964087	82964095	+	1	NA	3' UTR (NM_183201, exon 6 of 6)	3' UTR (NM_183201, exon 6 of 6)	-3410	NR_045932	76392	Mm.295205	NR_045932	ENSMUSG00000086327	Slfn5os	1700003F17Rik	schlafen 5, opposite strand	ncRNA
mm_115142.1	chr13	104817172	104817223	+	1	NA	promoter-TSS (NM_026072)	promoter-TSS (NM_026072)	27	NR_135272	67288	Mm.125465	NM_026075	ENSMUSG00000021716	Srek1ip1	3110031B13Rik|AI462702|AV348305|AW121048|Sfrs12ip1|Srsf12ip1	splicing regulatory glutamine/lysine-rich protein 1interacting protein 1	protein-coding
mm_88981.1	chr10	81559587	81559595	+	1	NA	non-coding (NR_074087, exon 1 of 7)	non-coding (NR_074087, exon 1 of 7)	147	NM_001276288	14797	Mm.180013	NM_010347	ENSMUSG00000054452	Aes	AL024115|Esp1|Grg|Grg-5|Grg5|Tle5	amino-terminal enhancer of split	protein-coding
mm_67991.1	chr7	100863374	100863426	-	1	NA	promoter-TSS (NM_177073)	promoter-TSS (NM_177073)	13	NM_177073	320100	Mm.40336	NM_177073	ENSMUSG00000008318	Relt	E430021K24Rik|Tnfrsf19l	RELT tumor necrosis factor receptor	protein-coding
mm_120193.1	chr14	61599494	61599548	+	1	NA	promoter-TSS (NM_023233)	promoter-TSS (NM_023233)	9	NM_023233	66597	Mm.491258	NM_023233	ENSMUSG00000035235	Trim13	3110001L12Rik|CAR|LEU5|RNF77|Rfp2	tripartite motif-containing 13	protein-coding
mm_15822.1	chr2	164564105	164564115	+	1	NA	exon (NM_026323, exon 3 of 5)	exon (NM_026323, exon 3 of 5)	1394	NM_026323	67701	Mm.27289	NM_026323	ENSMUSG00000017723	Wfdc2	1600023A02Rik|HE4|WAP5	WAP four-disulfide core domain 2	protein-coding
mm_29975.1	chr3	133545318	133545325	-	1	NA	promoter-TSS (NM_001346736)	promoter-TSS (NM_001346736)	-931	NM_001040400	214133	Mm.347816	NM_145989	ENSMUSG00000040943	Tet2	Ayu17-449|E130014J05Rik|mKIAA1546	tet methylcytosine dioxygenase 2	protein-coding
mm_8206.1	chr1	138123789	138123800	-	1	NA	intron (NM_001111316, intron 2 of 31)	intron (NM_001111316, intron 2 of 31)	51332	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_85206.1	chr9	96787757	96787763	-	1	NA	Intergenic	Intergenic	22198	NR_102296	319707	Mm.392191	NR_102293	ENSMUSG00000101581	C430002N11Rik	-	RIKEN cDNA C430002N11 gene	ncRNA
mm_159168.1	chr2	92370944	92370944	-	1	NA	intron (NM_172670, intron 1 of 14)	CpG-8292	113	NM_001290774	228366	Mm.31158	NM_172670	ENSMUSG00000040434	Large2	5730485C17Rik|AI891893|Gyltl1b|Largel|mKIAA4105	LARGE xylosyl- and glucuronyltransferase 2	protein-coding
mm_142773.1	chr17	49796284	49796286	-	1	NA	intron (NM_177052, intron 13 of 22)	MT2B|LTR|ERVL	181113	NM_177052	319991	Mm.441340	NM_177052	ENSMUSG00000023999	Kif6	D130004B10Rik|D130084M03Rik	kinesin family member 6	protein-coding
mm_115982.1	chr13	24280766	24280778	-	1	NA	promoter-TSS (NM_026825)	promoter-TSS (NM_026825)	18	NM_001311122	68732	Mm.211047	NM_026825	ENSMUSG00000021338	Carmil1	1110037D04Rik|AI425970|CARMIL|CARML1|D130057M20|Lrrc16|Lrrc16a	capping protein regulator and myosin 1 linker 1	protein-coding
mm_49899.1	chr6	38934072	38934084	+	1	NA	intron (NM_011539, intron 1 of 12)	intron (NM_011539, intron 1 of 12)	15092	NM_011539	21391	Mm.4054	NM_011539	ENSMUSG00000029925	Tbxas1	CYP5|CYP5A1|THAS|TS|TXAS|TXS	thromboxane A synthase 1, platelet	protein-coding
mm_135353.1	chr16	43699407	43699452	-	1	NA	Intergenic	Intergenic	-35245	NM_001146325	100043314	Mm.390896	NM_001146325	ENSMUSG00000071552	Tigit	ENSMUSG00000071552|Vstm3	T cell immunoreceptor with Ig and ITIM domains	protein-coding
mm_67935.1	chr7	100113848	100113850	-	1	NA	intron (NM_133692, intron 2 of 11)	intron (NM_133692, intron 2 of 11)	7651	NM_133692	67967	Mm.37562	NM_133692	ENSMUSG00000030726	Pold3	2410142G14Rik|C85233|P66|P68	polymerase (DNA-directed), delta 3, accessory subunit	protein-coding
mm_33659.1	chr4	133130614	133130636	+	1	NA	promoter-TSS (NM_153423)	promoter-TSS (NM_153423)	-8	NM_153423	242687	Mm.23566	NM_153423	ENSMUSG00000028868	Wasf2	AW742646|D4Ertd13e|WAVE2	WAS protein family, member 2	protein-coding
mm_51825.1	chr6	89294892	89294905	+	1	NA	Intergenic	Intergenic	-9173	NR_131021	75131	Mm.391482	NR_131021	ENSMUSG00000107622	4930512J16Rik	-	RIKEN cDNA 4930512J16 gene	ncRNA
mm_137753.1	chr17	29440129	29440137	+	1	NA	Intergenic	Intergenic	-50912	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_121619.1	chr14	8298096	8298105	-	1	NA	3' UTR (NM_183187, exon 4 of 4)	3' UTR (NM_183187, exon 4 of 4)	11676	NM_183187	268709	Mm.256058	NM_183187	ENSMUSG00000021750	Fam107a	DRR1	family with sequence similarity 107, member A	protein-coding
mm_46605.1	chr5	107869133	107869143	-	1	NA	intron (NM_007964, intron 1 of 17)	CpG	5969	NM_007964	14020	Mm.35796	NM_007964	ENSMUSG00000011831	Evi5	NB4S	ecotropic viral integration site 5	protein-coding
mm_71530.1	chr8	46890498	46890524	+	1	NA	Intergenic	Intergenic	-96376	NM_177304	320981	Mm.211429	NM_177304	ENSMUSG00000038173	Enpp6	4833421B01Rik|B830047L21Rik|D8Ertd514e|E-NPP 6|GPC-Cpde|Npp6	ectonucleotide pyrophosphatase/phosphodiesterase 6	protein-coding
mm_114650.1	chr13	77438907	77438909	+	1	NA	intron (NM_001145676, intron 19 of 19)	intron (NM_001145676, intron 19 of 19)	-269782	NM_001163420	68675	Mm.343005	NM_138312	ENSMUSG00000064138	Fam172a	1110033M05Rik|2610318O14Rik|53-E6|9430037D06Rik|AF064782|pEN87	family with sequence similarity 172, member A	protein-coding
mm_84497.1	chr9	66901534	66901574	-	1	NA	intron (NM_173413, intron 1 of 7)	ORR1D1|LTR|ERVL-MaLR	18151	NM_173413	235442	Mm.260376	NM_173413	ENSMUSG00000036943	Rab8b	5930437D16|D330025I23Rik	RAB8B, member RAS oncogene family	protein-coding
mm_41857.1	chr5	104440390	104440418	+	1	NA	exon (NM_001204203, exon 7 of 7)	exon (NM_001204203, exon 7 of 7)	4212	NM_001204233	20750	Mm.288474	NM_009263	ENSMUSG00000029304	Spp1	2AR|Apl-1|BNSP|BSPI|Bsp|ETA-1|Eta|OP|Opn|Opnl|Ric|Spp-1	secreted phosphoprotein 1	protein-coding
mm_18907.1	chr2	76723322	76723334	-	1	NA	exon (NM_011652, exon 292 of 313)	exon (NM_011652, exon 292 of 313)	48013	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_149658.1	chr19	18713193	18713212	+	1	NA	promoter-TSS (NM_177640)	promoter-TSS (NM_177640)	-34	NM_177640	225995	Mm.28101	NM_177640	ENSMUSG00000047044	D030056L22Rik	-	RIKEN cDNA D030056L22 gene	protein-coding
mm_163376.1	chr12	44439013	44439041	+	1	NA	intron (NM_001146031, intron 2 of 27)	intron (NM_001146031, intron 2 of 27)	110142	NM_001146031	319504	Mm.208439	NM_176930	ENSMUSG00000020598	Nrcam	Bravo|C030017F07Rik|C130076O07Rik|mKIAA0343	neuronal cell adhesion molecule	protein-coding
mm_60813.1	chr7	45684399	45684421	+	1	NA	5' UTR (NM_001289693, exon 1 of 7)	5' UTR (NM_001289693, exon 1 of 7)	388	NM_001033356	243967	Mm.291240	NM_001033356	ENSMUSG00000070564	Ntn5	Gm484	netrin 5	protein-coding
mm_25553.1	chr3	116007841	116007847	+	1	NA	promoter-TSS (NM_001163514)	promoter-TSS (NM_001163514)	395	NM_001163515	58193	Mm.41739	NM_021388	ENSMUSG00000027963	Extl2	3000001D04Rik|AW146439	exostoses (multiple)-like 2	protein-coding
mm_40134.1	chr5	35045264	35045271	+	1	NA	exon (NM_019447, exon 10 of 14)	exon (NM_019447, exon 10 of 14)	3758	NM_019447	54426	Mm.27369	NM_019447	ENSMUSG00000029102	Hgfac	HGFA	hepatocyte growth factor activator	protein-coding
mm_151297.1	chr19	55464790	55464816	+	1	NA	intron (NM_001293685, intron 6 of 8)	intron (NM_001293685, intron 6 of 8)	148746	NM_001293686	53611	Mm.258637	NM_016862	ENSMUSG00000024983	Vti1a	1110014F16Rik|1110018K19Rik|4921537J05Rik|MVti1|MVti1a|Vti1|Vti1-rp2	vesicle transport through interaction with t-SNAREs 1A	protein-coding
mm_69887.1	chr7	141637150	141637176	-	1	NA	intron (NM_001330001, intron 31 of 33)	intron (NM_001330001, intron 31 of 33)	16462	NR_106030	102466798		NR_106030	ENSMUSG00000098759	Mir7063	Gm27654|mmu-mir-7063	microRNA 7063	ncRNA
mm_94060.1	chr10	128368677	128368691	-	1	NA	intron (NM_001081040, intron 1 of 4)	CpG	1353	NM_001081040	210582	Mm.296876	NM_001081040	ENSMUSG00000039914	Coq10a	Gm1	coenzyme Q10A	protein-coding
mm_77550.1	chr8	123254148	123254168	-	1	NA	promoter-TSS (NM_020497)	promoter-TSS (NM_020497)	-37	NM_020497	57247	Mm.379084	NM_020497	ENSMUSG00000001065	Zfp276	AW048709|D8Ertd370e|D8Ertd377e|Znf276	zinc finger protein (C2H2 type) 276	protein-coding
mm_12407.1	chr2	70508814	70508824	+	1	NA	promoter-TSS (NM_025744)	promoter-TSS (NM_025744)	0	NM_025744	66748	Mm.423014	NM_025744	ENSMUSG00000075302	Erich2	4933404M02Rik	glutamate rich 2	protein-coding
mm_44557.1	chr5	24602176	24602218	-	1	NA	promoter-TSS (NM_025891)	promoter-TSS (NM_025891)	-195	NM_025891	66993	Mm.436539	NM_025891	ENSMUSG00000028949	Smarcd3	1500001J14Rik|2210409C08Rik|BAF60C	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3	protein-coding
mm_32079.1	chr4	98113708	98113724	+	1	NA	3' UTR (NM_001122953, exon 10 of 10)	3' UTR (NM_001122953, exon 10 of 10)	269549	NM_053157	94043	Mm.331719	NM_053157	ENSMUSG00000028563	Tm2d1	2310026L18Rik|AA990549|Bbp	TM2 domain containing 1	protein-coding
mm_143652.1	chr17	79462589	79462589	-	1	NA	Intergenic	Intergenic	15296	NR_033463	74622	Mm.311921	NR_033463		4930429F11Rik	-	RIKEN cDNA 4930429F11 gene	ncRNA
mm_155298.1	chrX	61185632	61185646	+	1	NA	promoter-TSS (NM_001166658)	promoter-TSS (NM_001166658)	-81	NM_001166658	631990	Mm.401324	NM_001166658	ENSMUSG00000090546	Cdr1	100039759|Cdr|Cdr34|EG631990|Gm2409|Gm7077	cerebellar degeneration related antigen 1	protein-coding
mm_44292.1	chr5	8422643	8422693	-	1	NA	promoter-TSS (NM_178766)	promoter-TSS (NM_178766)	48	NM_013726	27214	Mm.292470	NM_013726	ENSMUSG00000002297	Dbf4	AA545217|Ask	DBF4 zinc finger	protein-coding
mm_67931.1	chr7	99965709	99965728	-	1	NA	intron (NM_175388, intron 1 of 5)	intron (NM_175388, intron 1 of 5)	14740	NM_175388	108937	Mm.323087	NM_175388	ENSMUSG00000058761	Rnf169	2900057K09Rik	ring finger protein 169	protein-coding
mm_101943.1	chr11	50209455	50209482	-	1	NA	intron (NM_001290769, intron 1 of 7)	ID_B1|SINE|B4	1352	NM_001290769	18412	Mm.40828	NM_011018	ENSMUSG00000015837	Sqstm1	A170|OSF-6|Osi|STAP|STONE14|p62	sequestosome 1	protein-coding
mm_111663.1	chr12	103336144	103336156	-	1	NA	intron (NM_023049, intron 3 of 9)	intron (NM_023049, intron 3 of 9)	19851	NM_023049	65256	Mm.27159	NM_023049	ENSMUSG00000021200	Asb2	1110008E15Rik	ankyrin repeat and SOCS box-containing 2	protein-coding
mm_61616.1	chr7	80091331	80091343	+	1	NA	3' UTR (NM_175433, exon 5 of 5)	3' UTR (NM_175433, exon 5 of 5)	-16080	NR_045695	100859962	Mm.392575	NR_045695	ENSMUSG00000108714	Gm21057	-	predicted gene, 21057	ncRNA
mm_29707.1	chr3	123385995	123386010	-	1	NA	promoter-TSS (NM_201638)	promoter-TSS (NM_201638)	-12	NM_201638	210529	Mm.260039	NM_201638	ENSMUSG00000028114	Mettl14	G430022H21Rik|mKIAA1627	methyltransferase like 14	protein-coding
mm_109539.1	chr12	111574492	111574542	+	1	NA	promoter-TSS (NM_021516)	promoter-TSS (NM_021516)	7	NM_022801	17169	Mm.260504	NM_021516	ENSMUSG00000007411	Mark3	1600015G02Rik|A430080F22Rik|C-TAK1|ETK-1|ETK1|Emk2|MPK10	MAP/microtubule affinity regulating kinase 3	protein-coding
mm_138054.1	chr17	33926450	33926467	+	1	NA	exon (NM_009318, exon 6 of 8)	exon (NM_009318, exon 6 of 8)	-3436	NM_009059	19732	Mm.43777	NM_009059	ENSMUSG00000041354	Rgl2	KE1.5|Rab2l|Rgt2|Rlf	ral guanine nucleotide dissociation stimulator-like 2	protein-coding
mm_101061.1	chr11	9048474	9048489	-	1	NA	promoter-TSS (NM_001037928)	promoter-TSS (NM_001037928)	-111	NM_001037928	626870	Mm.369429	NM_001037928	ENSMUSG00000040978	Gm11992	OTTMUSG00000005148	predicted gene 11992	protein-coding
mm_84269.1	chr9	62666082	62666088	-	1	NA	Intergenic	Intergenic	-11770	NM_176922	319480	Mm.34883	NM_176922	ENSMUSG00000032243	Itga11	4732459H24Rik	integrin alpha 11	protein-coding
mm_41629.1	chr5	96997677	96997766	+	1	NA	promoter-TSS (NM_080708)	promoter-TSS (NM_080708)	32	NM_080708	140780	Mm.281490	NM_080708	ENSMUSG00000034663	Bmp2k	4933417M22Rik|AA673486|AV128808|BIKE	BMP2 inducible kinase	protein-coding
mm_165971.1	chr4	100776765	100776779	+	1	NA	promoter-TSS (NM_198037)	promoter-TSS (NM_198037)	93	NM_198037	320508	Mm.151962	NM_198037	ENSMUSG00000028532	Cachd1	1190007F10Rik|AI852726|B430218L07Rik|Vwcd1|mKIAA1573	cache domain containing 1	protein-coding
mm_144251.1	chr18	10816670	10816673	+	1	NA	Intergenic	Intergenic	-31119	NR_029781	723959		NR_029781	ENSMUSG00000106348	Mir1a-2	Mir1-2|Mirn1-2|mir-1a-2|mmu-mir-1-2|mmu-mir-1a-2	microRNA 1a-2	ncRNA
mm_92188.1	chr10	68102035	68102065	-	1	NA	exon (NM_023598, exon 9 of 10)	exon (NM_023598, exon 9 of 10)	122452	NM_001081346	170799	Mm.209844	NM_133244	ENSMUSG00000037846	Rtkn2	B130039D23Rik|Mbf|Plekhk1	rhotekin 2	protein-coding
mm_61109.1	chr7	52755402	52755415	+	1	NA	Intergenic	Intergenic	-739692	NM_001195601	100503036	Mm.279725	NM_001195601	ENSMUSG00000094445	1700015G11Rik	Ccdc179	RIKEN cDNA 1700015G11 gene	protein-coding
mm_32121.1	chr4	99031337	99031347	+	1	NA	exon (NM_013913, exon 1 of 7)	exon (NM_013913, exon 1 of 7)	388	NM_013913	30924	Mm.28341	NM_013913	ENSMUSG00000028553	Angptl3	hypl	angiopoietin-like 3	protein-coding
mm_162192.1	chrX	112238991	112238991	+	1	NA	promoter-TSS (NM_001177389)	promoter-TSS (NM_001177389)	-58	NM_001177389	71030	Mm.158538	NM_001177389	ENSMUSG00000079460	4933403O08Rik	-	RIKEN cDNA 4933403O08 gene	protein-coding
mm_95673.1	chr11	54083000	54083011	+	1	NA	Intergenic	Intergenic	-13988	NM_019417	30794	Mm.21830	NM_019417	ENSMUSG00000020388	Pdlim4	Ril	PDZ and LIM domain 4	protein-coding
mm_158999.1	chr1	153186222	153186222	-	1	NA	intron (NM_008485, intron 1 of 23)	CpG	225	NM_008485	16782	Mm.329272	NM_008485	ENSMUSG00000026479	Lamc2	AA589349	laminin, gamma 2	protein-coding
mm_171743.1	chr4	97203024	97203036	-	1	NA	Intergenic	RLTR9D|LTR|ERVK	-378913	NM_001122952	18027	Mm.31274	NM_010905	ENSMUSG00000028565	Nfia	1110047K16Rik|9430022M17Rik|CTF|NF1-A|NF1A	nuclear factor I/A	protein-coding
mm_71504.1	chr8	46814153	46814162	+	1	NA	intron (NM_008391, intron 5 of 8)	RMER5|LTR|ERV1	74412	NM_008391	16363	Mm.1149	NM_008391	ENSMUSG00000031627	Irf2	9830146E22Rik|AI646973|Irf-2	interferon regulatory factor 2	protein-coding
mm_172156.1	chr6	4282535	4282539	-	1	NA	Intergenic	L1Md_T|LINE|L1	-195610	NM_009748	12068	Mm.286457	NM_009748	ENSMUSG00000032757	Bet1	AW555236|Bet-1	Bet1 golgi vesicular membrane trafficking protein	protein-coding
mm_71035.1	chr8	33653553	33653623	+	1	NA	exon (NM_010344, exon 1 of 13)	exon (NM_010344, exon 1 of 13)	350	NM_010344	14782	Mm.283573	NM_010344	ENSMUSG00000031584	Gsr	AI325518|D8Ertd238e|Gr-1|Gr1	glutathione reductase	protein-coding
mm_70475.1	chr8	12395288	12395295	+	1	NA	promoter-TSS (NM_009233)	promoter-TSS (NM_009233)	-228	NM_009233	20664	Mm.39088	NM_009233	ENSMUSG00000096014	Sox1	BB176347|Sox-1	SRY (sex determining region Y)-box 1	protein-coding
mm_169012.1	chr13	107414768	107414768	-	1	NA	Intergenic	Intergenic	-55054	NR_045083	105120	Mm.417700	NR_045083		AI197445	-	expressed sequence AI197445	ncRNA
mm_23857.1	chr3	83010479	83010487	+	1	NA	exon (NM_133862, exon 6 of 10)	exon (NM_133862, exon 6 of 10)	2759	NM_001317105	99571	Mm.16422	NM_133862	ENSMUSG00000033860	Fgg	3010002H13Rik|AI256424	fibrinogen gamma chain	protein-coding
mm_88544.1	chr10	78575068	78575089	+	1	NA	intron (NM_173751, intron 1 of 15)	intron (NM_173751, intron 1 of 15)	578	NM_173751	216136	Mm.2644	NM_173751	ENSMUSG00000032763	Ilvbl	5830463I21|AI415009	ilvB (bacterial acetolactate synthase)-like	protein-coding
mm_35853.1	chr4	49383784	49383793	-	1	NA	intron (NM_145368, intron 2 of 4)	intron (NM_145368, intron 2 of 4)	24363	NM_145368	209186	Mm.35071	NM_145368	ENSMUSG00000060317	Acnat2	C730036D15Rik	acyl-coenzyme A amino acid N-acyltransferase 2	protein-coding
mm_15767.1	chr2	164317475	164317486	+	1	NA	exon (NM_013679, exon 3 of 4)	exon (NM_013679, exon 3 of 4)	729	NM_013679	20945	Mm.439686	NM_013679	ENSMUSG00000017000	Svs6	MSVSP99|Svp6	seminal vesicle secretory protein 6	protein-coding
mm_119141.1	chr14	31210678	31210685	+	1	NA	intron (NM_009393, intron 4 of 5)	intron (NM_009393, intron 4 of 5)	2369	NM_009393	21924	Mm.439921	NM_009393	ENSMUSG00000091898	Tnnc1	AI874626|TnC|cTnC|cTnI|tncc	troponin C, cardiac/slow skeletal	protein-coding
mm_33951.1	chr4	137424876	137424889	+	1	NA	exon (NM_026419, exon 4 of 8)	exon (NM_026419, exon 4 of 8)	5638	NM_026419	67868	Mm.297477	NM_026419	ENSMUSG00000023433	Cela3b	0910001F22Rik|2310074F01Rik|AI504000|Ela3|Ela3b	chymotrypsin-like elastase family, member 3B	protein-coding
mm_59367.1	chr7	25688095	25688123	+	1	NA	exon (NM_011577, exon 1 of 7)	exon (NM_011577, exon 1 of 7)	1107	NM_011577	21803	Mm.248380	NM_011577	ENSMUSG00000002603	Tgfb1	TGF-beta1|TGFbeta1|Tgfb|Tgfb-1	transforming growth factor, beta 1	protein-coding
mm_108509.1	chr12	83987801	83987827	+	1	NA	promoter-TSS (NM_134188)	promoter-TSS (NM_134188)	-47	NM_134188	171210	Mm.371675	NM_134188	ENSMUSG00000021226	Acot2	AA571646|MTE-I|Mte1	acyl-CoA thioesterase 2	protein-coding
mm_111137.1	chr12	81568257	81568265	-	1	NA	5' UTR (NM_020330, exon 1 of 2)	5' UTR (NM_020330, exon 1 of 2)	213	NM_020330	56622	Mm.117130	NM_020330	ENSMUSG00000008438	Adam21	Adam31	a disintegrin and metallopeptidase domain 21	protein-coding
mm_100945.1	chr11	6528783	6528807	-	1	NA	promoter-TSS (NR_045893)	promoter-TSS (NR_045893)	-35	NR_045893	100041286	Mm.459507	NR_045893	ENSMUSG00000085156	Snhg15	Gm11974|OTTMUSG00000005115	small nucleolar RNA host gene 15	ncRNA
mm_35850.1	chr4	48473383	48473401	-	1	NA	promoter-TSS (NM_172304)	promoter-TSS (NM_172304)	30	NM_172304	269536	Mm.272025	NM_172304	ENSMUSG00000028345	Tex10	2610206N19Rik|2810462N03Rik|BC006867	testis expressed gene 10	protein-coding
mm_57275.1	chr6	123290556	123290563	-	1	NA	promoter-TSS (NM_019948)	promoter-TSS (NM_019948)	-688	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_81507.1	chr9	110034722	110034741	+	1	NA	exon (NM_008633, exon 7 of 19)	exon (NM_008633, exon 7 of 19)	-17290	NM_001311163	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_88253.1	chr10	73201526	73201527	+	1	NA	Intergenic	Intergenic	-114821	NR_040646	327768	Mm.417745	NR_040646		A330049N07Rik	-	RIKEN cDNA A330049N07 gene	ncRNA
mm_1183.1	chr1	61874287	61874290	+	1	NA	intron (NM_001081050, intron 2 of 22)	intron (NM_001081050, intron 2 of 22)	235464	NM_001081050	72823	Mm.35153	NM_001081050	ENSMUSG00000052062	Pard3b	1810008K04Rik|2010002N16Rik|2810455B10Rik|Als2cr19|PAR3B|PAR3L|PAR3beta	par-3 family cell polarity regulator beta	protein-coding
mm_147513.1	chr18	52516606	52516631	-	1	NA	3' UTR (NM_010728, exon 7 of 7)	3' UTR (NM_010728, exon 7 of 7)	13103	NM_001286181	16948	Mm.172	NM_010728	ENSMUSG00000024529	Lox	AI893619|TSC-160|rrg	lysyl oxidase	protein-coding
mm_61890.1	chr7	89980721	89980759	+	1	NA	5' UTR (NM_021876, exon 1 of 12)	5' UTR (NM_021876, exon 1 of 12)	236	NM_021876	13626	Mm.380914	NM_021876	ENSMUSG00000030619	Eed	ENSMUSG00000039373|l(7)5Rn|l7Rn5|lusk	embryonic ectoderm development	protein-coding
mm_161990.1	chr19	33590222	33590222	-	1	NA	promoter-TSS (NM_001013770)	promoter-TSS (NM_001013770)	89	NM_001013770	381236	Mm.491242	NM_001013770	ENSMUSG00000024766	Lipo3	AI747699|Lipo1	lipase, member O3	protein-coding
mm_117458.1	chr13	75835493	75835497	-	1	NA	Intergenic	ORR1A2-int|LTR|ERVL-MaLR	-4391	NM_053108	93692	Mm.25844	NM_053108	ENSMUSG00000021591	Glrx	C86710|D13Wsu156e|Glrx1|Grx1|TTase	glutaredoxin	protein-coding
mm_102473.1	chr11	60031875	60031891	-	1	NA	intron (NM_001290012, intron 1 of 6)	intron (NM_001290012, intron 1 of 6)	5122	NM_008819	18618	Mm.2731	NM_008819	ENSMUSG00000000301	Pemt	PEAMT|PEMT2|PLMT|Pempt|Pempt2	phosphatidylethanolamine N-methyltransferase	protein-coding
mm_38722.1	chr4	145234826	145234854	-	1	NA	intron (NM_011610, intron 1 of 9)	intron (NM_011610, intron 1 of 9)	12030	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_48372.1	chr5	139478979	139478984	-	1	NA	intron (NM_133349, intron 3 of 6)	intron (NM_133349, intron 3 of 6)	5510	NM_133349	100494	Mm.24521	NM_133349	ENSMUSG00000053581	Zfand2a	AA407930|AU016206|Airap	zinc finger, AN1-type domain 2A	protein-coding
mm_34761.1	chr4	152341555	152341573	+	1	NA	intron (NM_029216, intron 1 of 40)	intron (NM_029216, intron 1 of 40)	2913	NM_001081376	269610	Mm.40192	NM_029216	ENSMUSG00000005045	Chd5	4930532L22Rik|AW060752|B230399N07Rik|CHD-5	chromodomain helicase DNA binding protein 5	protein-coding
mm_107854.1	chr12	69502538	69502588	+	1	NA	Intergenic	Intergenic	-27013	NR_038060	76062	Mm.380755	NR_038060		5830428M24Rik	100040862|Gm3007	RIKEN cDNA 5830428M24 gene	ncRNA
mm_117973.1	chr13	100032175	100032185	-	1	NA	intron (NM_001081061, intron 34 of 38)	B1_Mur2|SINE|Alu	-16541	NM_030026	78038	Mm.137327	NM_030026	ENSMUSG00000021646	Mccc2	4930552N12Rik|MCCB	methylcrotonoyl-Coenzyme A carboxylase 2 (beta)	protein-coding
mm_30963.1	chr4	33925033	33925047	+	1	NA	5' UTR (NM_007726, exon 1 of 2)	5' UTR (NM_007726, exon 1 of 2)	408	NM_007726	12801	Mm.7992	NM_007726	ENSMUSG00000044288	Cnr1	CB-R|CB1|CB1R	cannabinoid receptor 1 (brain)	protein-coding
mm_72222.1	chr8	72723282	72723293	+	1	NA	promoter-TSS (NM_009188)	promoter-TSS (NM_009188)	17	NM_009188	20467	Mm.2137	NM_009188	ENSMUSG00000031622	Sin3b	2810430C10Rik	transcriptional regulator, SIN3B (yeast)	protein-coding
mm_167813.1	chr9	123936722	123936726	-	1	NA	Intergenic	Intergenic	31968	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_84444.1	chr9	66126474	66126487	-	1	NA	promoter-TSS (NM_026635)	promoter-TSS (NM_026635)	-131	NM_026635	68250	Mm.27107	NM_026635	ENSMUSG00000032381	Fam96a	5730536A07Rik	family with sequence similarity 96, member A	protein-coding
mm_41804.1	chr5	103754155	103754188	+	1	NA	promoter-TSS (NM_133919)	promoter-TSS (NM_133919)	9	NM_133919	17355	Mm.6949	NM_133919	ENSMUSG00000029313	Aff1	9630032B01Rik|AW319193|Af4|Mllt2h|Rob	AF4/FMR2 family, member 1	protein-coding
mm_29416.1	chr3	108972762	108972772	-	1	NA	3' UTR (NM_001163567, exon 11 of 11)	3' UTR (NM_001163567, exon 11 of 11)	32210	NM_001078646	66715	Mm.158124	NM_025723	ENSMUSG00000045662	Henmt1	4921515J06Rik|Hen1|mHEN1	HEN1 methyltransferase homolog 1 (Arabidopsis)	protein-coding
mm_169815.1	chr16	20352870	20352879	+	1	NA	intron (NM_013790, intron 25 of 29)	MT2_Mm|LTR|ERVL	-27470	NM_183158	224044	Mm.276400	NM_183158	ENSMUSG00000022818	Cyp2ab1	EG224044|F730023N20	cytochrome P450, family 2, subfamily ab, polypeptide 1	protein-coding
mm_91502.1	chr10	37136141	37136183	-	1	NA	exon (NM_008538, exon 2 of 2)	exon (NM_008538, exon 2 of 2)	2764	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_168764.1	chr1	21202034	21202042	-	1	NA	Intergenic	L1Md_T|LINE|L1	-16537	NM_001290679	75712	Mm.304763	NM_029398	ENSMUSG00000025933	Tmem14a	5730496E24Rik|C85783|PTD011	transmembrane protein 14A	protein-coding
mm_163543.1	chr13	16910932	16910932	+	1	NA	intron (NM_138654, intron 13 of 13)	intron (NM_138654, intron 13 of 13)	783833	NM_138654	192136	Mm.364180	NM_138654	ENSMUSG00000055137	Sugct	5033411D12Rik|D17907	succinyl-CoA glutarate-CoA transferase	protein-coding
mm_133423.1	chr16	87354205	87354249	+	1	NA	promoter-TSS (NM_001159331)	promoter-TSS (NM_001159331)	42	NM_026366	67768	Mm.296532	NM_026366	ENSMUSG00000044442	N6amt1	5830445C04Rik|Hemk2|Pred28	N-6 adenine-specific DNA methyltransferase 1 (putative)	protein-coding
mm_37095.1	chr4	116611297	116611310	-	1	NA	exon (NM_016777, exon 7 of 16)	exon (NM_016777, exon 7 of 16)	-13673	NR_029450	654318	Mm.255685	NR_029450	ENSMUSG00000085408	C530005A16Rik	D930044c15rik	RIKEN cDNA C530005A16 gene	ncRNA
mm_13918.1	chr2	120594840	120594861	+	1	NA	exon (NM_001177793, exon 6 of 8)	exon (NM_001177793, exon 6 of 8)	14465	NM_025657	66606	Mm.428639	NM_025657	ENSMUSG00000027286	Lrrc57	2810002D13Rik|AA407405	leucine rich repeat containing 57	protein-coding
mm_100731.1	chr11	3931977	3931981	-	1	NA	promoter-TSS (NM_001130458)	promoter-TSS (NM_001130458)	-18	NM_001130459	21452	Mm.20948	NM_015749	ENSMUSG00000020432	Tcn2	AW208754|Tcn-2	transcobalamin 2	protein-coding
mm_114027.1	chr13	52637152	52637161	+	1	NA	intron (NM_001198977, intron 9 of 13)	intron (NM_001198977, intron 9 of 13)	40274	NM_011518	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_149920.1	chr19	26607376	26607410	+	1	NA	intron (NM_011416, intron 1 of 32)	CpG	2233	NM_011416	67155	Mm.342988	NM_011416	ENSMUSG00000024921	Smarca2	2610209L14Rik|SNF2alpha|Snf2l2|brahma|brm	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	protein-coding
mm_95280.1	chr11	45886424	45886448	+	1	NA	exon (NM_001045520, exon 4 of 12)	exon (NM_001045520, exon 4 of 12)	34472	NM_001045520	216705	Mm.169673	NM_001045520	ENSMUSG00000006169	Clint1	AI642036|AW537616|C530049I24Rik|Enth|Epn4|F630206G17Rik|mKIAA0171	clathrin interactor 1	protein-coding
mm_31804.1	chr4	65156465	65156497	+	1	NA	exon (NM_021362, exon 2 of 22)	exon (NM_021362, exon 2 of 22)	32307	NM_021362	18491	Mm.317854	NM_021362	ENSMUSG00000028370	Pappa	8430414N03Rik|IGFBP-4ase|PAG1|PAPP-A	pregnancy-associated plasma protein A	protein-coding
mm_25727.1	chr3	122730217	122730239	+	1	NA	intron (NM_153422, intron 1 of 20)	CpG	1070	NM_153422	242202	Mm.134911	NM_153422	ENSMUSG00000053965	Pde5a	Cgbpde|Cn5n|PDE5a2|Pde5|Pde5a1	phosphodiesterase 5A, cGMP-specific	protein-coding
mm_166558.1	chr6	42597495	42597503	-	1	NA	promoter-TSS (NM_203396)	promoter-TSS (NM_203396)	-127	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_44207.1	chr5	4104392	4104443	-	1	NA	5' UTR (NM_020010, exon 1 of 10)	5' UTR (NM_020010, exon 1 of 10)	280	NM_020010	13121	Mm.140158	NM_020010	ENSMUSG00000001467	Cyp51	AI426508|CYPLI|Cyp51a1|Ldm|P450-14DM|P450LI	cytochrome P450, family 51	protein-coding
mm_163107.1	chr11	69941090	69941099	+	1	NA	exon (NM_016875, exon 8 of 9)	exon (NM_016875, exon 8 of 9)	4766	NM_001347634	53422	Mm.29286	NM_016875	ENSMUSG00000018554	Ybx2	Msy2	Y box protein 2	protein-coding
mm_778.1	chr1	44551720	44551726	+	1	NA	promoter-TSS (NM_028450)	promoter-TSS (NM_028450)	52	NM_028450	70676	Mm.133132	NM_027506	ENSMUSG00000056870	Gulp1	3110030A04Rik|5730529O06Rik|CED-6|Ced6|GULP|Gulp-2	GULP, engulfment adaptor PTB domain containing 1	protein-coding
mm_157339.1	chrX	36839342	36839355	-	1	NA	Intergenic	Intergenic	-22148	NR_131979	69591	Mm.482947	NR_131979	ENSMUSG00000097468	Mdrl	2310010G23Rik	mitochondrial dynamic related lncRNA	ncRNA
mm_157765.1	chrX	73689582	73689623	-	1	NA	exon (NM_012060, exon 5 of 8)	exon (NM_012060, exon 5 of 8)	16469	NM_001142809	102857	Mm.274553	NM_133987	ENSMUSG00000019558	Slc6a8	AA589632|CRT|CRTR|CT1|CTR5|Creat	solute carrier family 6 (neurotransmitter transporter, creatine), member 8	protein-coding
mm_112709.1	chr13	18948345	18948417	+	1	NA	promoter-TSS (NM_001289546)	promoter-TSS (NM_001289546)	30	NM_001289546	218038	Mm.101650	NM_175007	ENSMUSG00000021314	Amph	-	amphiphysin	protein-coding
mm_36591.1	chr4	88438886	88438894	-	1	NA	promoter-TSS (NM_025760)	promoter-TSS (NM_025760)	36	NM_025760	66775	Mm.386788	NM_025760	ENSMUSG00000028497	Hacd4	4933428I03Rik|Hcad4|Ptplad2	3-hydroxyacyl-CoA dehydratase 4	protein-coding
mm_97725.1	chr11	80384043	80384048	+	1	NA	intron (NM_001130171, intron 1 of 10)	intron (NM_001130171, intron 1 of 10)	766	NM_001130171	22680	Mm.401332	NM_011751	ENSMUSG00000017421	Zfp207	8430401D15Rik|BuGZ|Zep|Znf207	zinc finger protein 207	protein-coding
mm_47223.1	chr5	121191410	121191420	-	1	NA	promoter-TSS (NM_001109992)	promoter-TSS (NM_001109992)	-18	NM_011202	19247	Mm.8681	NM_011202	ENSMUSG00000043733	Ptpn11	2700084A17Rik|AW536184|PTP1D|PTP2C|SAP-2|SH-PTP2|SH-PTP3|SHP-2|Shp2|Syp	protein tyrosine phosphatase, non-receptor type 11	protein-coding
mm_21006.1	chr2	152344077	152344085	-	1	NA	promoter-TSS (NM_175093)	promoter-TSS (NM_175093)	-21	NM_175093	228775	Mm.276018	NM_144554	ENSMUSG00000032715	Trib3	Ifld2|Nipk|SINK|SKIP3|TRB-3|Trb3	tribbles pseudokinase 3	protein-coding
mm_163281.1	chr11	116533973	116534004	-	1	NA	promoter-TSS (NM_011451)	promoter-TSS (NM_011451)	750	NM_025367	20698	Mm.20944	NM_011451	ENSMUSG00000061878	Sphk1	1110006G24Rik|Sk1|Spk1	sphingosine kinase 1	protein-coding
mm_57449.1	chr6	125131758	125131770	-	1	NA	promoter-TSS (NM_138747)	promoter-TSS (NM_138747)	-119	NM_138747	110109	Mm.29203	NM_138747	ENSMUSG00000038279	Nop2	120kDa|A530002O17|Nol1	NOP2 nucleolar protein	protein-coding
mm_7542.1	chr1	124504033	124504043	-	1	NA	Intergenic	(TATG)n|Simple_repeat|Simple_repeat	-458479	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_144723.1	chr18	35141935	35141936	+	1	NA	intron (NM_009818, intron 1 of 17)	MurERV4_19-int|LTR|ERVK	23023	NM_009818	12385	Mm.18962	NM_009818	ENSMUSG00000037815	Ctnna1	2010010M04Rik|AA517462|AI988031|Catna1	catenin (cadherin associated protein), alpha 1	protein-coding
mm_93903.1	chr10	126901316	126901396	-	1	NA	promoter-TSS (NM_026858)	promoter-TSS (NM_026858)	15	NM_026858	68876	Mm.276769	NM_026858	ENSMUSG00000025436	Xrcc6bp1	1110068E08Rik|2410012H02Rik|Atp23	XRCC6 binding protein 1	protein-coding
mm_108070.1	chr12	73941825	73941831	+	1	NA	exon (NM_010431, exon 11 of 15)	exon (NM_010431, exon 11 of 15)	-22702	NM_178392	75627	Mm.25937	NM_178392	ENSMUSG00000021113	Snapc1	2700033G17Rik|AU015787	small nuclear RNA activating complex, polypeptide 1	protein-coding
mm_300.1	chr1	23291776	23291778	+	1	NA	promoter-TSS (NR_029717)	promoter-TSS (NR_029717)	76	NR_029717	723964		NR_029717	ENSMUSG00000065567	Mir30c-2	Mirn30c-2|mir-30c-2	microRNA 30c-2	ncRNA
mm_147971.1	chr18	67245819	67245842	-	1	NA	promoter-TSS (NM_172630)	promoter-TSS (NM_172630)	0	NM_172630	225651	Mm.235792	NM_172630	ENSMUSG00000062526	Mppe1	A530095G11	metallophosphoesterase 1	protein-coding
mm_14124.1	chr2	125986765	125986798	+	1	NA	intron (NM_029455, intron 15 of 16)	intron (NM_029455, intron 15 of 16)	-47877	NM_008008	14178	Mm.330557	NM_008008	ENSMUSG00000027208	Fgf7	Kgf	fibroblast growth factor 7	protein-coding
mm_53172.1	chr6	125345200	125345208	+	1	NA	TTS (NM_011324)	TTS (NM_011324)	-4519	NM_011609	21937	Mm.1258	NM_011609	ENSMUSG00000030341	Tnfrsf1a	CD120a|FPF|TNF-R|TNF-R-I|TNF-R1|TNF-R55|TNF-alphaR1|TNFAR|TNFR60|TNFRI|TNFRp55|TNFalpha-R1|Tnfr-2|Tnfr1|p55|p55-R	tumor necrosis factor receptor superfamily, member 1a	protein-coding
mm_52068.1	chr6	97807015	97807067	+	1	NA	promoter-TSS (NM_001113198)	promoter-TSS (NM_001113198)	-17	NM_001113198	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_130475.1	chr15	98728029	98728033	-	1	NA	exon (NM_024169, exon 1 of 6)	exon (NM_024169, exon 1 of 6)	167	NM_024169	66120	Mm.30729	NM_024169	ENSMUSG00000003355	Fkbp11	1110002O23Rik|FKBP-11	FK506 binding protein 11	protein-coding
mm_75461.1	chr8	47750157	47750197	-	1	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	-36246	NM_172407	70925	Mm.393807	NM_172407	ENSMUSG00000038069	Cdkn2aip	4921511I16Rik|AW208986|CARF	CDKN2A interacting protein	protein-coding
mm_97843.1	chr11	83065280	83065286	+	1	NA	5' UTR (NM_011408, exon 1 of 2)	5' UTR (NM_011408, exon 1 of 2)	171	NM_011408	20556	Mm.278689	NM_011408	ENSMUSG00000072620	Slfn2	Shlf2	schlafen 2	protein-coding
mm_86772.1	chr10	20104865	20104883	+	1	NA	intron (NM_008580, intron 18 of 29)	intron (NM_008580, intron 18 of 29)	-44046	NM_008635	17761	Mm.20928	NM_008635	ENSMUSG00000019996	Map7	E-MAP-115|MAP-7|Mtap7|R75000|mshi|mste|ste	microtubule-associated protein 7	protein-coding
mm_95863.1	chr11	58009162	58009206	+	1	NA	5' UTR (NM_028451, exon 1 of 19)	5' UTR (NM_028451, exon 1 of 19)	120	NM_028451	73158	Mm.248843	NM_028451	ENSMUSG00000037331	Larp1	1810024J12Rik|3110040D16Rik|Larp|mKIAA0731	La ribonucleoprotein domain family, member 1	protein-coding
mm_19701.1	chr2	103768879	103768906	-	1	NA	exon (NM_016739, exon 17 of 19)	exon (NM_016739, exon 17 of 19)	-7642	NM_153126	98956	Mm.288005	NM_153126	ENSMUSG00000027185	Nat10	AI429152	N-acetyltransferase 10	protein-coding
mm_121207.1	chr14	103053584	103053596	+	1	NA	intron (NM_008392, intron 4 of 4)	Lx8|LINE|L1	6578	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_123377.1	chr14	63256598	63256632	-	1	NA	Intergenic	B1_Mus1|SINE|Alu	-11344	NM_001310610	14463	Mm.247669	NM_008092	ENSMUSG00000021944	Gata4	Gata-4	GATA binding protein 4	protein-coding
mm_33797.1	chr4	134925458	134925467	+	1	NA	intron (NM_023665, intron 3 of 4)	intron (NM_023665, intron 3 of 4)	1837	NM_023665	27981	Mm.331964	NM_023665	ENSMUSG00000037266	Rsrp1	2700043I21Rik|D4Ucla2|D4Wsu53e	arginine/serine rich protein 1	protein-coding
mm_19870.1	chr2	114047479	114047509	-	1	NA	exon (NM_009608, exon 7 of 7)	exon (NM_009608, exon 7 of 7)	5381	NM_009608	11464	Mm.686	NM_009608	ENSMUSG00000068614	Actc1	Actc-1	actin, alpha, cardiac muscle 1	protein-coding
mm_151728.1	chr19	4869406	4869449	-	1	NA	exon (NM_013456, exon 8 of 21)	exon (NM_013456, exon 8 of 21)	8482	NM_013456	11474	Mm.5316	NM_013456	ENSMUSG00000006457	Actn3	-	actinin alpha 3	protein-coding
mm_111875.1	chr12	108003623	108003633	-	1	NA	promoter-TSS (NM_021399)	promoter-TSS (NM_021399)	-214	NM_021399	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_98545.1	chr11	95010298	95010365	+	1	NA	5' UTR (NM_146025, exon 1 of 10)	5' UTR (NM_146025, exon 1 of 10)	452	NM_146025	217125	Mm.297199	NM_146025	ENSMUSG00000047181	Samd14	AI839049|AI854782|BC034054	sterile alpha motif domain containing 14	protein-coding
mm_158208.1	chrX	105856550	105856566	-	1	NA	exon (NM_009530, exon 11 of 35)	exon (NM_009530, exon 11 of 35)	72814	NM_009530	22589	Mm.10141	NM_009530	ENSMUSG00000031229	Atrx	4833408C14Rik|AI447451|ATR2|DXHXS6677E|HP1-BP38|Hp1bp2|Hp1bp38|MRXS3|RAD54L|Rad54|XH2|Xnp|ZNF-HX	alpha thalassemia/mental retardation syndrome X-linked	protein-coding
mm_40617.1	chr5	64803514	64803530	+	1	NA	promoter-TSS (NM_008453)	promoter-TSS (NM_008453)	-1	NM_008453	16599	Mm.392759	NM_008453	ENSMUSG00000029178	Klf3	9930027G08Rik|AL024007|Bklf|Tef-2	Kruppel-like factor 3 (basic)	protein-coding
mm_110475.1	chr12	51840718	51840739	-	1	NA	Intergenic	Intergenic	-11192	NM_144788	207304	Mm.249391	NM_144788	ENSMUSG00000035247	Hectd1	A630086P08Rik|AI844876|b2b327Clo|opm	HECT domain containing 1	protein-coding
mm_53259.1	chr6	127887764	127887777	+	1	NA	5' UTR (NM_026743, exon 1 of 8)	5' UTR (NM_026743, exon 1 of 8)	148	NM_026743	68498	Mm.174368	NM_026743	ENSMUSG00000030351	Tspan11	1110014F12Rik|AU067806	tetraspanin 11	protein-coding
mm_149029.1	chr19	8771059	8771069	+	1	NA	promoter-TSS (NM_025791)	promoter-TSS (NM_025791)	68	NM_025791	66836	Mm.440071	NM_025791	ENSMUSG00000010097	Tmem223	0610006I08Rik	transmembrane protein 223	protein-coding
mm_148327.1	chr18	84086258	84086269	-	1	NA	5' UTR (NM_001081300, exon 1 of 2)	5' UTR (NM_001081300, exon 1 of 2)	299	NM_001081300	110796	Mm.102136	NM_001081300	ENSMUSG00000046982	Tshz1	5730407I04Rik|D18Bwg1409e|Mtsh1|NY-CO-33|Sdccag33|Tsh1|mKIAA4206|teashirt1	teashirt zinc finger family member 1	protein-coding
mm_57794.1	chr6	129275361	129275376	-	1	NA	promoter-TSS (NM_001033122)	promoter-TSS (NM_001033122)	1	NM_001033122	12515	Mm.74745	NM_001033122	ENSMUSG00000030156	Cd69	5830438K24Rik|AI452015|AIM|VEA	CD69 antigen	protein-coding
mm_90446.1	chr10	127667156	127667174	+	1	NA	promoter-TSS (NM_008668)	promoter-TSS (NM_008668)	42	NR_045171	72243	Mm.482902	NR_045171	ENSMUSG00000040195	1700012D01Rik	-	RIKEN cDNA 1700012D01 gene	ncRNA
mm_48534.1	chr5	142904475	142904510	-	1	NA	exon (NM_007393, exon 4 of 6)	exon (NM_007393, exon 4 of 6)	2262	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_131658.1	chr16	20548638	20548672	+	1	NA	promoter-TSS (NR_030670)	promoter-TSS (NR_030670)	52	NM_013852	27406	Mm.27135	NM_013852	ENSMUSG00000003234	Abcf3	AI326318|AU016058|BB119416	ATP-binding cassette, sub-family F (GCN20), member 3	protein-coding
mm_90717.1	chr10	4429160	4429191	-	1	NA	promoter-TSS (NR_002891)	promoter-TSS (NR_002891)	-9	NR_002891	433224	Mm.153111	NR_002891		Gm5512	EG433224	required for meiotic nuclear division 1 pseudogene	pseudo
mm_151065.1	chr19	47451098	47451103	+	1	NA	intron (NM_001164717, intron 1 of 13)	intron (NM_001164717, intron 1 of 13)	13311	NM_001164717	14218	Mm.127560	NM_008018	ENSMUSG00000053617	Sh3pxd2a	2310014D11Rik|AA589508|AI256723|AI413738|C230050L11|EG329070|Fish|Gm5098|Sh3md1|TSK5|Tks5	SH3 and PX domains 2A	protein-coding
mm_47996.1	chr5	136136118	136136124	-	1	NA	promoter-TSS (NM_027891)	promoter-TSS (NM_027891)	-24	NM_001347492	72041	Mm.486605	NM_028070	ENSMUSG00000039754	Alkbh4	2010004B12Rik|Abj4	alkB homolog 4, lysine demethylase	protein-coding
mm_80654.1	chr9	90054388	90054423	+	1	NA	5' UTR (NM_007801, exon 1 of 12)	5' UTR (NM_007801, exon 1 of 12)	138	NM_001312649	13036	Mm.2277	NM_007801	ENSMUSG00000032359	Ctsh	AL022844	cathepsin H	protein-coding
mm_88991.1	chr10	81565789	81565799	+	1	NA	non-coding (NR_074087, exon 7 of 7)	non-coding (NR_074087, exon 7 of 7)	6350	NM_001276288	14797	Mm.180013	NM_010347	ENSMUSG00000054452	Aes	AL024115|Esp1|Grg|Grg-5|Grg5|Tle5	amino-terminal enhancer of split	protein-coding
mm_145753.1	chr18	64700012	64700015	+	1	NA	Intergenic	Intergenic	-39013	NM_001001488	54670	Mm.270043	NM_001001488	ENSMUSG00000039529	Atp8b1	AI451886|FIC1|Ic	ATPase, class I, type 8B, member 1	protein-coding
mm_100576.1	chr11	120767044	120767081	+	1	NA	Intergenic	Intergenic	17142	NM_009053	19719	Mm.871	NM_009053	ENSMUSG00000025158	Rfng	-	RFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	protein-coding
mm_72505.1	chr8	83748997	83749005	+	1	NA	Intergenic	Intergenic	-7690	NM_001163031	26364	Mm.334648	NM_011925	ENSMUSG00000002885	Adgre5	AA409984|Cd97|TM7LN1	adhesion G protein-coupled receptor E5	protein-coding
mm_86767.1	chr10	19934181	19934198	+	1	NA	promoter-TSS (NM_008580)	promoter-TSS (NM_008580)	-337	NM_008580	26408	Mm.6595	NM_008580	ENSMUSG00000071369	Map3k5	7420452D20Rik|ASK|ASK1|MAPKKK5|Mekk5	mitogen-activated protein kinase kinase kinase 5	protein-coding
mm_63615.1	chr7	128237392	128237401	+	1	NA	promoter-TSS (NM_146205)	promoter-TSS (NM_146205)	39	NM_146205	233912	Mm.475117	NM_146205	ENSMUSG00000042178	Armc5	AW049683|BC032200	armadillo repeat containing 5	protein-coding
mm_3744.1	chr1	155558320	155558402	+	1	NA	5' UTR (NM_026683, exon 1 of 4)	5' UTR (NM_026683, exon 1 of 4)	241	NM_026683	72482	Mm.288249	NM_026683	ENSMUSG00000033701	Acbd6	0610010G04Rik|2610100E10Rik	acyl-Coenzyme A binding domain containing 6	protein-coding
mm_5351.1	chr1	25228795	25228810	-	1	NA	intron (NM_175642, intron 16 of 30)	intron (NM_175642, intron 16 of 30)	49152	NM_001204913	100504323	Mm.484176	NM_001204913		Gm20172	-	predicted gene, 20172	protein-coding
mm_102605.1	chr11	62410900	62410926	-	1	NA	exon (NM_177229, exon 6 of 9)	exon (NM_177229, exon 6 of 9)	27602	NM_001252313	20185	Mm.271814	NM_011308	ENSMUSG00000018501	Ncor1	5730405M06Rik|A230020K14Rik|N-CoR|RIP13|Rxrip13|mKIAA1047	nuclear receptor co-repressor 1	protein-coding
mm_90150.1	chr10	118141904	118141912	+	1	NA	5' UTR (NM_010785, exon 1 of 13)	5' UTR (NM_010785, exon 1 of 13)	121	NM_010785	17245	Mm.101191	NM_010785	ENSMUSG00000020212	Mdm1	Arrd2|Mdm-1	transformed mouse 3T3 cell double minute 1	protein-coding
mm_44715.1	chr5	30945655	30945663	-	1	NA	promoter-TSS (NM_026770)	promoter-TSS (NM_026770)	-179	NM_026770	68567	Mm.45127	NM_026770	ENSMUSG00000029161	Cgref1	1110004G24Rik|AW045201|Cgr11	cell growth regulator with EF hand domain 1	protein-coding
mm_49678.1	chr6	32050282	32050307	+	1	NA	promoter-TSS (NM_029587)	promoter-TSS (NM_029587)	6	NM_029587	76382	Mm.23510	NM_029587	ENSMUSG00000029766	1700012A03Rik	AI429084	RIKEN cDNA 1700012A03 gene	protein-coding
mm_70151.1	chr7	143460708	143460753	-	1	NA	intron (NM_001161624, intron 1 of 3)	CpG-13764	320	NM_009876	12577	Mm.168789	NM_009876	ENSMUSG00000037664	Cdkn1c	AL024410|CDKI|Kip2|p57(kip2)|p57Kip2	cyclin-dependent kinase inhibitor 1C (P57)	protein-coding
mm_87694.1	chr10	59582344	59582360	+	1	NA	intron (NM_001033259, intron 1 of 7)	ID4_|SINE|ID	34340	NM_001033259	215999	Mm.296470	NM_001033259	ENSMUSG00000009647	Mcu	2010012O16Rik|AV064928|C10orf42|Ccdc109a|D130073L02Rik|Gm64	mitochondrial calcium uniporter	protein-coding
mm_80988.1	chr9	103227924	103227996	+	1	NA	exon (NM_133977, exon 2 of 17)	exon (NM_133977, exon 2 of 17)	2326	NM_133977	22041	Mm.37214	NM_133977	ENSMUSG00000032554	Trf	AI266983|Cd176|HP|Tf|Tfn|hpx	transferrin	protein-coding
mm_83603.1	chr9	48597442	48597446	-	1	NA	intron (NM_010924, intron 2 of 2)	intron (NM_010924, intron 2 of 2)	7679	NM_001311062	18113	Mm.8362	NM_010924	ENSMUSG00000032271	Nnmt	-	nicotinamide N-methyltransferase	protein-coding
mm_133533.1	chr16	91043528	91043590	+	1	NA	intron (NM_026110, intron 1 of 17)	intron (NM_026110, intron 1 of 17)	820	NM_026110	67367	Mm.347	NM_026110	ENSMUSG00000022974	Paxbp1	1810007M14Rik|C21orf66|Gcfc|Gcfc1|Pax3/7bp	PAX3 and PAX7 binding protein 1	protein-coding
mm_47941.1	chr5	135351437	135351438	-	1	NA	Intergenic	ID_B1|SINE|B4	-1393	NM_001277891	94244	Mm.26037	NM_033571	ENSMUSG00000040013	Fkbp6	1700008G22Rik|36kDa|AU017274|D5Ertd724e|FKBP-36|FKBP-6	FK506 binding protein 6	protein-coding
mm_163085.1	chr11	69408681	69408724	-	1	NA	5' UTR (NM_001017426, exon 2 of 23)	5' UTR (NM_001017426, exon 2 of 23)	4973	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_132703.1	chr16	43363924	43363934	+	1	NA	intron (NM_181058, intron 2 of 6)	intron (NM_181058, intron 2 of 6)	56267	NR_046026	626693	Mm.447083	NR_046026	ENSMUSG00000085499	Gm15713	OTTMUSG00000025617	predicted gene 15713	ncRNA
mm_165719.1	chr3	101424123	101424125	+	1	NA	intron (NM_207205, intron 2 of 10)	intron (NM_207205, intron 2 of 10)	46999	NM_207205	78908	Mm.257997	NM_207205	ENSMUSG00000042035	Igsf3	1700016K10Rik|2810035F16Rik|4833439O17Rik|mKIAA0466	immunoglobulin superfamily, member 3	protein-coding
mm_69165.1	chr7	127213467	127213478	-	1	NA	TTS (NM_017461)	TTS (NM_017461)	1864	NM_016754	17907	Mm.14526	NM_016754	ENSMUSG00000030672	Mylpf	2410014J02Rik|MLC-2|Mlc2	myosin light chain, phosphorylatable, fast skeletal muscle	protein-coding
mm_148504.1	chr19	4204195	4204207	+	1	NA	Intergenic	Intergenic	-2598	NM_011237	19367	Mm.277629	NM_011237	ENSMUSG00000024824	Rad9a	Rad9	RAD9 checkpoint clamp component A	protein-coding
mm_29440.1	chr3	110142997	110143010	-	1	NA	5' UTR (NM_001163350, exon 1 of 8)	5' UTR (NM_001163350, exon 1 of 8)	469	NM_001163348	80883	Mm.39262	NM_030699	ENSMUSG00000059857	Ntng1	A930010C08Rik|AI853992|Lmnt1	netrin G1	protein-coding
mm_131690.1	chr16	20681764	20681784	+	1	NA	exon (NM_145941, exon 15 of 33)	exon (NM_145941, exon 15 of 33)	-2482	NR_028530	100217430		NR_028530		Snord66	MBII-142|snoRNA142	small nucleolar RNA, C/D box 66	snoRNA
mm_2922.1	chr1	132114894	132114927	+	1	NA	3' UTR (NM_008795, exon 16 of 16)	3' UTR (NM_008795, exon 16 of 16)	24775	NM_008795	18557	Mm.28130	NM_008795	ENSMUSG00000026437	Cdk18	AA682070|Ctk18|Pctk3	cyclin-dependent kinase 18	protein-coding
mm_163941.1	chr14	51145527	51145531	-	1	NA	exon (NM_011271, exon 2 of 2)	exon (NM_011271, exon 2 of 2)	1238	NM_011271	19752	Mm.235538	NM_011271	ENSMUSG00000035896	Rnase1	AI574248|Rib-1|Rib1	ribonuclease, RNase A family, 1 (pancreatic)	protein-coding
mm_2972.1	chr1	133068500	133068513	+	1	NA	intron (NM_001099276, intron 2 of 32)	intron (NM_001099276, intron 2 of 32)	22494	NM_001099276	240752	Mm.387308	NM_001099276	ENSMUSG00000026447	Pik3c2b	C330011J12Rik|Gm199|PI3K-C2beta|PI3KC2beta	phosphoinositide-3-kinase, class 2, beta polypeptide	protein-coding
mm_121102.1	chr14	100213177	100213181	+	1	NA	Intergenic	MTEa|LTR|ERVL-MaLR	-63383	NM_010636	16597	Mm.396499	NM_010636	ENSMUSG00000072294	Klf12	2700063E05Rik|AI225908|AI315654|AP-2rep|B130052C06Rik|D530033K05Rik	Kruppel-like factor 12	protein-coding
mm_136742.1	chr17	8340998	8341018	+	1	NA	non-coding (NR_028280, exon 2 of 2)	non-coding (NR_028280, exon 2 of 2)	269	NM_178774	320111	Mm.442510	NM_178774	ENSMUSG00000055945	Prr18	9630019K15Rik	proline rich 18	protein-coding
mm_113583.1	chr13	40886798	40886818	+	1	NA	promoter-TSS (NM_008105)	promoter-TSS (NM_008105)	50	NM_008105	14538	Mm.314757	NM_008105	ENSMUSG00000021360	Gcnt2	5330430K10Rik|IGnT|IGnTA|IGnTB|IGnTC	glucosaminyl (N-acetyl) transferase 2, I-branching enzyme	protein-coding
mm_103925.1	chr11	83647977	83648002	-	1	NA	3' UTR (NM_011337, exon 3 of 3)	3' UTR (NM_011337, exon 3 of 3)	1389	NM_011337	20302	Mm.1282	NM_011337	ENSMUSG00000000982	Ccl3	AI323804|G0S19-1|LD78alpha|MIP-1alpha|MIP1-(a)|MIP1-alpha|Mip1a|Scya3	chemokine (C-C motif) ligand 3	protein-coding
mm_135167.1	chr16	35928845	35928865	-	1	NA	3' UTR (NM_001013371, exon 5 of 5)	3' UTR (NM_001013371, exon 5 of 5)	-9615	NM_030253	80285	Mm.49074	NM_030253	ENSMUSG00000022906	Parp9	ARTD9|AW214463|BC003281|Bagl|Bal|PARP-9	poly (ADP-ribose) polymerase family, member 9	protein-coding
mm_62687.1	chr7	110029747	110029761	+	1	NA	exon (NM_181517, exon 3 of 25)	exon (NM_181517, exon 3 of 25)	11329	NM_181517	233726	Mm.222328	NM_181517	ENSMUSG00000066232	Ipo7	A330055O14Rik|C330016G14|Imp7|Ranbp7	importin 7	protein-coding
mm_97514.1	chr11	78499704	78499719	+	1	NA	exon (NM_011707, exon 3 of 8)	exon (NM_011707, exon 3 of 8)	591	NM_011707	22370	Mm.3667	NM_011707	ENSMUSG00000017344	Vtn	AI256434|Vn	vitronectin	protein-coding
mm_91472.1	chr10	34207424	34207480	-	1	NA	promoter-TSS (NM_172508)	promoter-TSS (NM_172508)	99	NM_172508	212898	Mm.34557	NM_172508	ENSMUSG00000039497	Dse	6030499O08|AI480506|B130024B19Rik|DS-epi1|Sart2	dermatan sulfate epimerase	protein-coding
mm_3781.1	chr1	156634036	156634039	+	1	NA	intron (NM_001136104, intron 8 of 12)	PB1D11|SINE|Alu	40302	NM_023141	30935	Mm.206737	NM_023141	ENSMUSG00000060519	Tor3a	Adir	torsin family 3, member A	protein-coding
mm_58782.1	chr7	16098575	16098585	+	1	NA	promoter-TSS (NM_025898)	promoter-TSS (NM_025898)	-63	NM_025898	108124	Mm.104540	NM_025898	ENSMUSG00000006024	Napa	1500039N14Rik|AW209189|RA81|SNAPA|SNARE|a-SNAP|hyh	N-ethylmaleimide sensitive fusion protein attachment protein alpha	protein-coding
mm_61157.1	chr7	58709862	58709863	+	1	NA	intron (NM_009728, intron 1 of 20)	intron (NM_009728, intron 1 of 20)	51660	NM_009728	11982	Mm.135129	NM_009728	ENSMUSG00000025324	Atp10a	Atp10c|pfatp	ATPase, class V, type 10A	protein-coding
mm_41076.1	chr5	87673223	87673262	+	1	NA	intron (NM_001286015, intron 8 of 32)	intron (NM_001286015, intron 8 of 32)	7034	NM_001286016	12990	Mm.427467	NM_007784	ENSMUSG00000070702	Csn1s1	AA959832|AW212882|Csna	casein alpha s1	protein-coding
mm_171054.1	chr3	103833305	103833309	+	1	NA	intron (NM_001142959, intron 1 of 3)	intron (NM_001142959, intron 1 of 3)	611	NM_001142960	229672	Mm.297245	NM_001142959	ENSMUSG00000044165	Bcl2l15	Bfk|Gm566	BCLl2-like 15	protein-coding
mm_19524.1	chr2	94156191	94156193	-	1	NA	intron (NM_019657, intron 1 of 10)	intron (NM_019657, intron 1 of 10)	1717	NM_019657	56348	Mm.22505	NM_019657	ENSMUSG00000027195	Hsd17b12	2610510O05Rik|AI172963|KIK-I|Kik1	hydroxysteroid (17-beta) dehydrogenase 12	protein-coding
mm_18831.1	chr2	74715990	74716000	-	1	NA	non-coding (NR_027899, exon 1 of 3)	non-coding (NR_027899, exon 1 of 3)	135	NR_027899	73429	Mm.443313	NR_027899		Hoxd3os1	1700064D17Rik|1700109F18Rik	homeobox D3, opposite strand 1	ncRNA
mm_5784.1	chr1	51747055	51747070	-	1	NA	Intergenic	Intergenic	168916	NM_001290982	17912	Mm.3390	NM_010863	ENSMUSG00000018417	Myo1b	AA406997|MIH-L|MMIa	myosin IB	protein-coding
mm_91986.1	chr10	61784462	61784463	-	1	NA	promoter-TSS (NM_207000)	promoter-TSS (NM_207000)	-598	NM_207000	404634	Mm.272870	NM_207000	ENSMUSG00000020086	H2afy2	macroH2A2	H2A histone family, member Y2	protein-coding
mm_171570.1	chr4	147351955	147351957	+	1	NA	intron (NM_001039209, intron 1 of 2)	RLTR27|LTR|ERVK	176090	NM_001039209	195531	Mm.270762	NM_001039209	ENSMUSG00000078496	Zfp982	Gm13152|OTTMUSG00000010671	zinc finger protein 982	protein-coding
mm_27805.1	chr3	75956616	75956642	-	1	NA	5' UTR (NM_175193, exon 1 of 15)	5' UTR (NM_175193, exon 1 of 15)	320	NM_175193	73124	Mm.249232	NM_175193	ENSMUSG00000034109	Golim4	3110027H23Rik|GIMPC|GPP130|Golph4|P138	golgi integral membrane protein 4	protein-coding
mm_142664.1	chr17	47713341	47713351	-	1	NA	Intergenic	Intergenic	-11350	NR_045913	100126242	Mm.392746	NR_045912	ENSMUSG00000086930	Frs3os	4930417B13Rik|Gm14873|OTTMUSG00000018358	fibroblast growth factor receptor substrate 3, opposite strand	ncRNA
mm_117941.1	chr13	99434655	99434663	-	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-21833	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_69703.1	chr7	140082223	140082236	-	1	NA	promoter-TSS (NM_001190386)	promoter-TSS (NM_001190386)	72	NM_001190386	68566	Mm.44241	NM_026769	ENSMUSG00000025468	Caly	0710001P07Rik|1110004A22Rik|Calcyon|Drd1ip	calcyon neuron-specific vesicular protein	protein-coding
mm_38926.1	chr4	150187391	150187397	-	1	NA	3' UTR (NM_009802, exon 8 of 8)	3' UTR (NM_009802, exon 8 of 8)	13741	NM_009802	12353	Mm.232523	NM_009802	ENSMUSG00000028972	Car6	Ca6|DOC1	carbonic anhydrase 6	protein-coding
mm_163494.1	chr12	109723391	109723394	+	1	NA	promoter-TSS (NR_029651)	promoter-TSS (NR_029651)	-66	NR_029915	723934		NR_029915	ENSMUSG00000105853	Mir376b	Mirn376b|mir-376b	microRNA 376b	ncRNA
mm_153184.1	chr19	34499195	34499211	-	1	NA	intron (NM_001111100, intron 8 of 9)	intron (NM_001111100, intron 8 of 9)	-24068	NM_009890	12642	Mm.30824	NM_009890	ENSMUSG00000050370	Ch25h	AI462618|m25OH	cholesterol 25-hydroxylase	protein-coding
mm_122812.1	chr14	54577579	54577612	-	1	NA	promoter-TSS (NM_010590)	promoter-TSS (NM_010590)	66	NM_010590	16475	Mm.100253	NM_010590	ENSMUSG00000022178	Ajuba	Jub	ajuba LIM protein	protein-coding
mm_91027.1	chr10	17924418	17924419	-	1	NA	intron (NM_001033432, intron 1 of 3)	MTD|LTR|ERVL-MaLR	23649	NM_001033432	380629	Mm.276430	NM_001033432	ENSMUSG00000039879	Heca	Gm869|HDC|HDCL	hdc homolog, cell cycle regulator	protein-coding
mm_35049.1	chr4	6275630	6275634	-	1	NA	promoter-TSS (NM_007824)	promoter-TSS (NM_007824)	-1	NM_007824	13122	Mm.57029	NM_007824	ENSMUSG00000028240	Cyp7a1	-	cytochrome P450, family 7, subfamily a, polypeptide 1	protein-coding
mm_162519.1	chr1	156997151	156997155	-	1	NA	Intergenic	Intergenic	-57527	NM_023884	78255	Mm.28376	NM_023884	ENSMUSG00000026594	Ralgps2	1810020P17Rik|2210408F11Rik|4921528G01Rik|9130014M22Rik|AU043409|AW046161	Ral GEF with PH domain and SH3 binding motif 2	protein-coding
mm_10173.1	chr2	4559879	4559892	+	1	NA	5' UTR (NM_001177844, exon 1 of 12)	5' UTR (NM_001177844, exon 1 of 12)	131	NM_001177844	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding
mm_153105.1	chr19	32757323	32757338	-	1	NA	promoter-TSS (NM_008960)	promoter-TSS (NM_008960)	-247	NM_008960	19211	Mm.245395	NM_008960	ENSMUSG00000013663	Pten	2310035O07Rik|A130070J02Rik|AI463227|B430203M17Rik|MMAC1|TEP1	phosphatase and tensin homolog	protein-coding
mm_99491.1	chr11	102774073	102774122	+	1	NA	intron (NM_001110778, intron 14 of 25)	CpG	12662	NM_001110778	11488	Mm.89854	NM_009613	ENSMUSG00000020926	Adam11	AW060611|Mdc	a disintegrin and metallopeptidase domain 11	protein-coding
mm_123609.1	chr14	68120189	68120191	-	1	NA	exon (NM_008691, exon 3 of 3)	exon (NM_008691, exon 3 of 3)	-3562	NR_045897	100043072	Mm.242832	NR_045897		A230070E04Rik	Gm4210	RIKEN cDNA A230070E04 gene	ncRNA
mm_24052.1	chr3	87906609	87906637	+	1	NA	promoter-TSS (NM_001331051)	promoter-TSS (NM_001331051)	-227	NM_001331051	15191	Mm.292208	NM_008231	ENSMUSG00000004897	Hdgf	AI118077|D3Ertd299e	hepatoma-derived growth factor	protein-coding
mm_173350.1	chrY	90813537	90813538	+	1	NA	intron (NM_133362, intron 2 of 3)	IMPB_01|Satellite|Satellite	25869	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_88968.1	chr10	81396254	81396257	+	1	NA	TTS (NM_008688)	TTS (NM_008688)	3191	NM_001099917	72273	Mm.253147	NM_001099917	ENSMUSG00000078439	Smim24	2210404O07Rik	small integral membrane protein 24	protein-coding
mm_88034.1	chr10	67528370	67528398	+	1	NA	Intergenic	Intergenic	-9485	NM_010118	13654	Mm.290421	NM_010118	ENSMUSG00000037868	Egr2	Egr-2|Krox-20|Krox20|NGF1-B|Zfp-25|Zfp-6	early growth response 2	protein-coding
mm_117417.1	chr13	74317235	74317300	-	1	NA	promoter-TSS (NM_011051)	promoter-TSS (NM_011051)	59	NM_011051	18570	Mm.24254	NM_011051	ENSMUSG00000021576	Pdcd6	AV299538|Alg2|MA-3|PS2|alg-2	programmed cell death 6	protein-coding
mm_128318.1	chr15	37972687	37972693	-	1	NA	intron (NM_001112721, intron 56 of 58)	MER68B|LTR|ERVL	-11635	NM_199476	382985	Mm.24738	NM_199476	ENSMUSG00000022292	Rrm2b	p53R2	ribonucleotide reductase M2 B (TP53 inducible)	protein-coding
mm_19622.1	chr2	102812743	102812777	-	1	NA	3' UTR (NM_009851, exon 19 of 19)	3' UTR (NM_009851, exon 19 of 19)	88905	NM_001177785	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_25246.1	chr3	103968328	103968394	+	1	NA	promoter-TSS (NR_030676)	promoter-TSS (NR_030676)	-45	NR_030676	100125931	Mm.400392	NR_030676	ENSMUSG00000089998	Phtf1os	A130049A11Rik	putative homeodomain transcription factor 1, opposite strand	ncRNA
mm_94646.1	chr11	16917216	16917235	+	1	NA	Intergenic	Intergenic	34057	NR_110421	72735	Mm.268598	NR_015469		Eldr	2810442I21Rik|4930500E12Rik|Fabl	Egfr long non-coding downstream RNA	ncRNA
mm_23939.1	chr3	84473928	84473943	+	1	NA	intron (NM_001033301, intron 2 of 11)	intron (NM_001033301, intron 2 of 11)	5556	NM_001205355	229474	Mm.331107	NM_001033301	ENSMUSG00000041842	Fhdc1	6330505N24Rik|Gm126	FH2 domain containing 1	protein-coding
mm_6756.1	chr1	84053434	84053438	-	1	NA	intron (NM_001003948, intron 2 of 2)	intron (NM_001003948, intron 2 of 2)	165525	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_2092.1	chr1	87701197	87701197	+	1	NA	exon (NM_001110192, exon 16 of 27)	exon (NM_001110192, exon 16 of 27)	-54814	NM_029846	77040	Mm.272972	NM_029846	ENSMUSG00000026289	Atg16l1	1500009K01Rik|Apg16l|Atg16l|WDR30	autophagy related 16-like 1 (S. cerevisiae)	protein-coding
mm_130282.1	chr15	96953518	96953528	-	1	NA	Intergenic	Intergenic	102433	NM_027052	69354	Mm.250980	NM_027052	ENSMUSG00000022464	Slc38a4	1110012E16Rik|1700012A18Rik|Ata3|mATA3|mNAT3	solute carrier family 38, member 4	protein-coding
mm_46896.1	chr5	114091266	114091287	-	1	NA	5' UTR (NM_026805, exon 1 of 16)	5' UTR (NM_026805, exon 1 of 16)	104	NM_026805	68666	Mm.63584	NM_026805	ENSMUSG00000042078	Svop	1110030H18Rik|AI415691|msvop	SV2 related protein	protein-coding
mm_151157.1	chr19	53185796	53185814	+	1	NA	intron (NM_013758, intron 1 of 15)	intron (NM_013758, intron 1 of 15)	41808	NM_013758	27360	Mm.426080	NM_013758	ENSMUSG00000025026	Add3	AI463285|R75380	adducin 3 (gamma)	protein-coding
mm_14136.1	chr2	126035926	126035940	+	1	NA	exon (NM_008008, exon 2 of 4)	exon (NM_008008, exon 2 of 4)	1275	NM_008008	14178	Mm.330557	NM_008008	ENSMUSG00000027208	Fgf7	Kgf	fibroblast growth factor 7	protein-coding
mm_73111.1	chr8	94745678	94745693	+	1	NA	promoter-TSS (NM_009137)	promoter-TSS (NM_009137)	1	NM_009137	20299	Mm.12895	NM_009137	ENSMUSG00000031779	Ccl22	ABCD-1|DCBCK|MDC|Scya22	chemokine (C-C motif) ligand 22	protein-coding
mm_62545.1	chr7	102340705	102340718	+	1	NA	intron (NM_009287, intron 1 of 11)	B2_Mm2|SINE|B2	72887	NM_009287	20866	Mm.645	NM_009287	ENSMUSG00000030987	Stim1	SIM	stromal interaction molecule 1	protein-coding
mm_139906.1	chr17	70871929	70871930	+	1	NA	Intergenic	Intergenic	-18397	NM_001164074	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_88468.1	chr10	77581746	77581769	+	1	NA	promoter-TSS (NM_145925)	promoter-TSS (NM_145925)	-10	NM_145925	108705	Mm.28853	NM_145925	ENSMUSG00000009291	Pttg1ip	1810010L20Rik|AI314311|AU018448|C79540	pituitary tumor-transforming 1 interacting protein	protein-coding
mm_124678.1	chr15	6429436	6429463	+	1	NA	exon (NM_023118, exon 10 of 15)	exon (NM_023118, exon 10 of 15)	-15884	NM_013485	12279	Mm.29095	NM_013485	ENSMUSG00000022149	C9	-	complement component 9	protein-coding
mm_32739.1	chr4	116611327	116611348	+	1	NA	exon (NM_016777, exon 7 of 16)	exon (NM_016777, exon 7 of 16)	-13707	NR_029450	654318	Mm.255685	NR_029450	ENSMUSG00000085408	C530005A16Rik	D930044c15rik	RIKEN cDNA C530005A16 gene	ncRNA
mm_124064.1	chr14	78332060	78332066	-	1	NA	Intergenic	L2c|LINE|L2	-24020	NM_011613	21943	Mm.249221	NM_011613	ENSMUSG00000022015	Tnfsf11	Ly109l|ODF|OPGL|RANKL|Trance	tumor necrosis factor (ligand) superfamily, member 11	protein-coding
mm_47491.1	chr5	124006116	124006154	-	1	NA	3' UTR (NM_177876, exon 4 of 4)	3' UTR (NM_177876, exon 4 of 4)	9283	NR_105999	102465625		NR_105999	ENSMUSG00000098454	Mir7032	Gm27309|mmu-mir-7032	microRNA 7032	ncRNA
mm_1795.1	chr1	79776251	79776262	+	1	NA	exon (NM_001081210, exon 1 of 4)	exon (NM_001081210, exon 1 of 4)	238	NM_001081210	69163	Mm.238455	NM_001081210	ENSMUSG00000026248	Mrpl44	1810030E18Rik|5730593H20Rik|AI463302	mitochondrial ribosomal protein L44	protein-coding
mm_128655.1	chr15	59652903	59652914	-	1	NA	intron (NM_144549, intron 2 of 2)	intron (NM_144549, intron 2 of 2)	4254	NM_144549	211770	Mm.40298	NM_144549	ENSMUSG00000032501	Trib1	A530090O15Rik|TRB-1|Trb1	tribbles pseudokinase 1	protein-coding
mm_22541.1	chr3	8767141	8767152	+	1	NA	Intergenic	CpG	-100108	NM_010423	15213	Mm.29581	NM_010423	ENSMUSG00000040289	Hey1	AI316788|AI414254|CHF2|HRT1|Herp2|Hesr1|bHLHb31|hesr-1	hairy/enhancer-of-split related with YRPW motif 1	protein-coding
mm_153084.1	chr19	32388411	32388419	-	1	NA	promoter-TSS (NM_144792)	promoter-TSS (NM_144792)	39	NM_144792	208449	Mm.329810	NM_144792	ENSMUSG00000040451	Sgms1	9530058O11Rik|AI841905|C80702|Mob|Sms1|Sor1|Tmem23	sphingomyelin synthase 1	protein-coding
mm_166410.1	chr5	137150485	137150493	-	1	NA	Intergenic	Intergenic	-34282	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_75943.1	chr8	71566642	71566652	-	1	NA	promoter-TSS (NM_145598)	promoter-TSS (NM_145598)	2	NM_145598	234404	Mm.213208	NM_145598	ENSMUSG00000034829	Nxnl1	A930031O08Rik|RdCVF|Txnl6	nucleoredoxin-like 1	protein-coding
mm_131836.1	chr16	22960885	22960891	+	1	NA	exon (NM_053176, exon 7 of 7)	exon (NM_053176, exon 7 of 7)	9816	NM_053176	94175	Mm.358794	NM_053176	ENSMUSG00000022877	Hrg	AI265597|AW413091|D16jh2|D18020|Hprg|Hrgp	histidine-rich glycoprotein	protein-coding
mm_144416.1	chr18	20962682	20962686	+	1	NA	intron (NM_026301, intron 1 of 5)	intron (NM_026301, intron 1 of 5)	18059	NM_026301	67664	Mm.45980	NM_026301	ENSMUSG00000033107	Rnf125	4930553F04Rik	ring finger protein 125	protein-coding
mm_53761.1	chr6	145746780	145746808	+	1	NA	Intergenic	(CCCCG)n|Simple_repeat|Simple_repeat	-61589	NM_027760	71323	Mm.158669	NM_027760	ENSMUSG00000030259	Rassf8	5133400D11Rik|AA815821|AW123240|Hoj1|mHoj-1	Ras association (RalGDS/AF-6) domain family (N-terminal) member 8	protein-coding
mm_45225.1	chr5	53421294	53421330	-	1	NA	Intergenic	Intergenic	-134467	NM_001080928	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_136190.1	chr16	89122532	89122534	-	1	NA	Intergenic	Intergenic	-58531	NM_001276278	68637	Mm.384089	NM_001276278	ENSMUSG00000068073	1110025L11Rik	-	RIKEN cDNA 1110025L11 gene	protein-coding
mm_67094.1	chr7	68915990	68916016	-	1	NA	Intergenic	Intergenic	-166765	NM_025549	66412	Mm.251199	NM_025549	ENSMUSG00000042659	Arrdc4	2410003C09Rik|AV216361	arrestin domain containing 4	protein-coding
mm_101897.1	chr11	49173752	49173783	-	1	NA	intron (NM_172793, intron 6 of 9)	intron (NM_172793, intron 6 of 9)	13322	NM_172793	237754	Mm.130787	NM_172793	ENSMUSG00000040283	Btnl9	B430208I01|Btn3|D330012D11Rik	butyrophilin-like 9	protein-coding
mm_162854.1	chr10	88740173	88740180	+	1	NA	intron (NM_025859, intron 4 of 5)	ORR1D2|LTR|ERVL-MaLR	8762	NM_025859	104303	Mm.291247	NM_025859	ENSMUSG00000060904	Arl1	2310008D22Rik|AU019749	ADP-ribosylation factor-like 1	protein-coding
mm_126385.1	chr15	80173586	80173601	+	1	NA	promoter-TSS (NM_010795)	promoter-TSS (NM_010795)	-128	NM_010795	17309	Mm.299693	NM_010795	ENSMUSG00000042428	Mgat3	1110038J12Rik|AI848272|GnT-III	mannoside acetylglucosaminyltransferase 3	protein-coding
mm_59303.1	chr7	25219341	25219378	+	1	NA	intron (NM_207677, intron 1 of 4)	CpG	500	NM_207677	67379	Mm.280594	NM_026117	ENSMUSG00000054499	Dedd2	2410050E11Rik|FLAME-3	death effector domain-containing DNA binding protein 2	protein-coding
mm_24496.1	chr3	92373876	92373893	+	1	NA	promoter-TSS (NR_003548)	promoter-TSS (NR_003548)	-31	NR_003548	20761	Mm.57083	NR_003548	ENSMUSG00000046203	Sprr2g	-	small proline-rich protein 2G	pseudo
mm_165606.1	chr3	51122721	51122722	+	1	NA	Intergenic	Intergenic	-101726	NM_009834	12457	Mm.86541	NM_009834	ENSMUSG00000023087	Noct	AU043840|Ccr4|Ccrn4l	nocturnin	protein-coding
mm_6400.1	chr1	72861842	72861871	-	1	NA	3' UTR (NM_010518, exon 4 of 4)	3' UTR (NM_010518, exon 4 of 4)	13009	NM_010518	16011	Mm.405761	NM_010518	ENSMUSG00000026185	Igfbp5	AI256729|AW208790|IGFBP-5|IGFBP-5P	insulin-like growth factor binding protein 5	protein-coding
mm_133448.1	chr16	88225519	88225544	+	1	NA	intron (NM_146072, intron 1 of 16)	intron (NM_146072, intron 1 of 16)	64727	NM_146072	14805	Mm.5134	NM_010348	ENSMUSG00000022935	Grik1	A830007B11Rik|D16Ium24|D16Ium24e|GluK1|GluK5|Glur-5|Glur5|Glurbeta1	glutamate receptor, ionotropic, kainate 1	protein-coding
mm_143558.1	chr17	74173919	74173928	-	1	NA	Intergenic	Intergenic	120940	NM_133771	76890	Mm.311874	NM_133771	ENSMUSG00000058704	Memo1	0610016J10Rik|D930048L02Rik	mediator of cell motility 1	protein-coding
mm_32594.1	chr4	111720188	111720201	+	1	NA	5' UTR (NM_026470, exon 1 of 13)	5' UTR (NM_026470, exon 1 of 13)	184	NM_026470	67946	Mm.275526	NM_026470	ENSMUSG00000034401	Spata6	1700062C23Rik|AI790763|Hash|KRP|Mash	spermatogenesis associated 6	protein-coding
mm_17078.1	chr2	22875029	22875048	-	1	NA	exon (NM_019456, exon 14 of 14)	exon (NM_019456, exon 14 of 14)	-20484	NM_019501	56075	Mm.249752	NM_019501	ENSMUSG00000026784	Pdss1	2610203G20Rik|2700031G06Rik|TPT|TPT 1|Tprt|mDLP1|mSPS1	prenyl (solanesyl) diphosphate synthase, subunit 1	protein-coding
mm_157408.1	chrX	38440169	38440200	-	1	NA	exon (NM_001017959, exon 3 of 9)	exon (NM_001017959, exon 3 of 9)	16276	NM_010685	16784	Mm.486	NM_010685	ENSMUSG00000016534	Lamp2	CD107b|LGP-B|Lamp II|Lamp-2|Lamp-2a|Lamp-2b|Lamp-2c|Mac3	lysosomal-associated membrane protein 2	protein-coding
mm_39436.1	chr5	16553901	16553909	+	1	NA	promoter-TSS (NM_001289461)	promoter-TSS (NM_001289461)	4	NM_001289461	15234	Mm.267078	NM_010427	ENSMUSG00000028864	Hgf	C230052L06Rik|HGF/SF|NK1|NK2|SF|SF/HGF	hepatocyte growth factor	protein-coding
mm_72448.1	chr8	83165623	83165646	+	1	NA	5' UTR (NM_001111304, exon 1 of 21)	5' UTR (NM_001111304, exon 1 of 21)	282	NM_027758	71310	Mm.24031	NM_027758	ENSMUSG00000031709	Tbc1d9	4933431N12Rik|AI847101|AW490653|C76116	TBC1 domain family, member 9	protein-coding
mm_28873.1	chr3	97703666	97703704	-	1	NA	intron (NM_001039376, intron 35 of 46)	intron (NM_001039376, intron 35 of 46)	-13123	NR_106084	102466229		NR_106084	ENSMUSG00000098381	Mir7225	Gm27499|mmu-mir-7225	microRNA 7225	ncRNA
mm_162566.1	chr1	172514000	172514012	-	1	NA	Intergenic	Intergenic	-7124	NM_027972	71870	Mm.78373	NM_027972	ENSMUSG00000026546	Cfap45	1700028D05Rik|Ccdc19|Nesg1	cilia and flagella associated protein 45	protein-coding
mm_11987.1	chr2	55436389	55436399	+	1	NA	5' UTR (NM_001304810, exon 1 of 3)	5' UTR (NM_001304810, exon 1 of 3)	424	NM_008426	16519	Mm.5127	NM_008426	ENSMUSG00000026824	Kcnj3	GIRK-1|GIRK1|Kcnf3|Kir3.1	potassium inwardly-rectifying channel, subfamily J, member 3	protein-coding
mm_17570.1	chr2	30350863	30350878	-	1	NA	intron (NM_001346806, intron 3 of 12)	intron (NM_001346806, intron 3 of 12)	8446	NM_139302	227700	Mm.33343	NM_139302	ENSMUSG00000026860	Sh3glb2	SPAS-1	SH3-domain GRB2-like endophilin B2	protein-coding
mm_142744.1	chr17	48418177	48418179	-	1	NA	TTS (NM_001289491)	TTS (NM_001289491)	8178	NM_207219	106821	Mm.203943	NM_207219	ENSMUSG00000040771	Oard1	AI314976|AW558560	O-acyl-ADP-ribose deacylase 1	protein-coding
mm_132622.1	chr16	38828912	38828920	+	1	NA	promoter-TSS (NM_029042)	promoter-TSS (NM_029042)	-167	NM_029042	74663	Mm.50263	NM_029042	ENSMUSG00000022798	4930435E12Rik	TSCPA	RIKEN cDNA 4930435E12 gene	protein-coding
mm_153630.1	chr19	44021655	44021697	-	1	NA	exon (NM_001167905, exon 2 of 8)	exon (NM_001167905, exon 2 of 8)	7571	NM_001001446	226143	Mm.329866	NM_001001446	ENSMUSG00000025197	Cyp2c44	AW107714|BC034834|b2b386Clo	cytochrome P450, family 2, subfamily c, polypeptide 44	protein-coding
mm_36610.1	chr4	89274577	89274583	-	1	NA	3' UTR (NM_009877, exon 3 of 3)	3' UTR (NM_009877, exon 3 of 3)	7612	NM_001040654	12578	Mm.4733	NM_009877	ENSMUSG00000044303	Cdkn2a	ARF-INK4a|Arf|INK4a-ARF|Ink4a/Arf|MTS1|Pctr1|p16|p16(INK4a)|p16INK4a|p19<ARF>|p19ARF	cyclin-dependent kinase inhibitor 2A	protein-coding
mm_95278.1	chr11	45856241	45856252	+	1	NA	intron (NM_001346760, intron 1 of 11)	intron (NM_001346760, intron 1 of 11)	4282	NM_001045520	216705	Mm.169673	NM_001045520	ENSMUSG00000006169	Clint1	AI642036|AW537616|C530049I24Rik|Enth|Epn4|F630206G17Rik|mKIAA0171	clathrin interactor 1	protein-coding
mm_130665.1	chr15	100669513	100669529	-	1	NA	promoter-TSS (NM_001270537)	promoter-TSS (NM_001270537)	-21	NM_001270537	668218	Mm.451225	NM_001270537	ENSMUSG00000098112	Bin2	-	bridging integrator 2	protein-coding
mm_111066.1	chr12	80115295	80115307	-	1	NA	Intergenic	Intergenic	-2288	NM_007564	12192	Mm.235132	NM_007564	ENSMUSG00000021127	Zfp36l1	AW742437|AW743212|Berg36|Brf1|D530020L18Rik|ERF1|TIS11b|cMG1	zinc finger protein 36, C3H type-like 1	protein-coding
mm_10635.1	chr2	20339579	20339601	+	1	NA	intron (NM_001081006, intron 1 of 21)	intron (NM_001081006, intron 1 of 21)	49677	NM_001081006	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding
mm_6336.1	chr1	71628440	71628452	-	1	NA	exon (NM_001276413, exon 16 of 44)	exon (NM_001276413, exon 16 of 44)	24788	NM_010233	14268	Mm.193099	NM_010233	ENSMUSG00000026193	Fn1	E330027I09|Fn|Fn-1	fibronectin 1	protein-coding
mm_30734.1	chr4	13827941	13827949	+	1	NA	intron (NM_009822, intron 1 of 10)	intron (NM_009822, intron 1 of 10)	43163	NM_009822	12395	Mm.4909	NM_009822	ENSMUSG00000006586	Runx1t1	Cbfa2t1h|ETO|MTG8	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	protein-coding
mm_50992.1	chr6	63256360	63256381	+	1	NA	promoter-TSS (NM_008167)	promoter-TSS (NM_008167)	-487	NM_008167	14804	Mm.439651	NM_008167	ENSMUSG00000071424	Grid2	B230104L07Rik|GluD2|GluRdelta2|Lc|Lc<J>|MMS10-AC|Ms10ac|cpr|ho|nmf408|tpr	glutamate receptor, ionotropic, delta 2	protein-coding
mm_77941.1	chr9	7355847	7355857	+	1	NA	intron (NM_001320077, intron 9 of 10)	intron (NM_001320077, intron 9 of 10)	8478	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_36481.1	chr4	82882813	82882827	-	1	NA	exon (NM_009887, exon 2 of 2)	exon (NM_009887, exon 2 of 2)	2331	NM_009887	12622	Mm.6780	NM_009887	ENSMUSG00000038192	Cer1	Cerl|Cerl1|Cerr1|cer-1	cerberus 1, DAN family BMP antagonist	protein-coding
mm_157306.1	chrX	20931240	20931255	-	1	NA	exon (NM_008823, exon 2 of 9)	exon (NM_008823, exon 2 of 9)	308	NM_008823	18636	Mm.3064	NM_008823	ENSMUSG00000001128	Cfp	BCFG|Pfc	complement factor properdin	protein-coding
mm_53283.1	chr6	128887587	128887592	+	1	NA	promoter-TSS (NM_020257)	promoter-TSS (NM_020257)	2	NM_020257	93675	Mm.391513	NM_020257	ENSMUSG00000030365	Clec2i	Clr-g|Clrg|Dcl1|LCL-1|OCILrP2	C-type lectin domain family 2, member i	protein-coding
mm_171229.1	chr3	66233142	66233148	-	1	NA	intron (NM_145820, intron 4 of 13)	L1Md_T|LINE|L1	13258	NM_008987	19288	Mm.276776	NM_008987	ENSMUSG00000027832	Ptx3	AI607804|TSG-14	pentraxin related gene	protein-coding
mm_73212.1	chr8	95806970	95806986	+	1	NA	non-coding (NR_015574, exon 1 of 4)	non-coding (NR_015574, exon 1 of 4)	148	NR_015574	319960	Mm.386996	NR_015574	ENSMUSG00000074136	4930513N10Rik	-	RIKEN cDNA 4930513N10 gene	ncRNA
mm_97653.1	chr11	79512183	79512185	+	1	NA	intron (NM_010897, intron 36 of 57)	intron (NM_010897, intron 36 of 57)	-8102	NM_019409	18377	Mm.93335	NM_019409	ENSMUSG00000049612	Omg	-	oligodendrocyte myelin glycoprotein	protein-coding
mm_124476.1	chr14	121460130	121460134	-	1	NA	3' UTR (NM_053079, exon 23 of 23)	3' UTR (NM_053079, exon 23 of 23)	45122	NM_053079	56643	Mm.155618	NM_053079	ENSMUSG00000025557	Slc15a1	D630032F02|PECT1|PEPT1	solute carrier family 15 (oligopeptide transporter), member 1	protein-coding
mm_43843.1	chr5	143180922	143180962	+	1	NA	promoter-TSS (NM_177880)	promoter-TSS (NM_177880)	-75	NM_177880	330228	Mm.255752	NM_177880	ENSMUSG00000029586	Spdye4b	4933411G11Rik	speedy/RINGO cell cycle regulator family, member E4B	protein-coding
mm_76345.1	chr8	84726509	84726542	-	1	NA	exon (NM_010906, exon 6 of 9)	exon (NM_010906, exon 6 of 9)	25068	NM_008535	17095	Mm.4925	NM_008535	ENSMUSG00000034041	Lyl1	Lyl-1|bHLHa18	lymphoblastomic leukemia 1	protein-coding
mm_12782.1	chr2	79330832	79330836	+	1	NA	3' UTR (NM_010576, exon 28 of 28)	3' UTR (NM_010576, exon 28 of 28)	75408	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D|Itga4B	integrin alpha 4	protein-coding
mm_106017.1	chr11	116020560	116020563	-	1	NA	Intergenic	Intergenic	3943	NM_008211	15081	Mm.18516	NM_008211	ENSMUSG00000016559	H3f3b	9430068D06Rik|H3.3B	H3 histone, family 3B	protein-coding
mm_84032.1	chr9	57765094	57765148	-	1	NA	exon (NM_007713, exon 1 of 13)	exon (NM_007713, exon 1 of 13)	739	NM_007713	102414	Mm.25720	NM_007713	ENSMUSG00000032316	Clk3	AI256811	CDC-like kinase 3	protein-coding
mm_139665.1	chr17	57408608	57408650	+	1	NA	intron (NM_010130, intron 7 of 21)	intron (NM_010130, intron 7 of 21)	49943	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_72136.1	chr8	71922811	71922835	+	1	NA	promoter-TSS (NM_133358)	promoter-TSS (NM_133358)	-2	NM_133358	170938	Mm.480419	NM_133358	ENSMUSG00000066880	Zfp617	Zfps11-6	zinc finger protein 617	protein-coding
mm_75256.1	chr8	40511664	40511756	-	1	NA	promoter-TSS (NM_001271543)	promoter-TSS (NM_001271543)	44	NM_001271543	18983	Mm.272551	NM_011135	ENSMUSG00000031601	Cnot7	AU022737|CAF-1|Caf1|Pop2	CCR4-NOT transcription complex, subunit 7	protein-coding
mm_40052.1	chr5	33996010	33996030	+	1	NA	promoter-TSS (NM_001001985)	promoter-TSS (NM_001001985)	36	NM_001001985	269642	Mm.274610	NM_001001985	ENSMUSG00000048142	Nat8l	1110038O08Rik|Shati	N-acetyltransferase 8-like	protein-coding
mm_148395.1	chr19	3767868	3767921	+	1	NA	intron (NM_144871, intron 1 of 11)	CpG	473	NM_001167885	225888	Mm.278578	NM_144871	ENSMUSG00000045098	Kmt5b	AA117471|C630029K18Rik|Suv4-20h1|Suv420h1	lysine methyltransferase 5B	protein-coding
mm_52898.1	chr6	122654582	122654630	+	1	NA	Intergenic	Intergenic	28182	NM_139218	73708	Mm.27982	NM_139218	ENSMUSG00000046323	Dppa3	2410075G02Rik|PCG7|PGC7|Stella	developmental pluripotency-associated 3	protein-coding
mm_167934.1	chrX	106254198	106254198	+	1	NA	intron (NM_001033424, intron 1 of 19)	intron (NM_001033424, intron 1 of 19)	1174	NM_001033424	331491	Mm.426150	NM_001033424	ENSMUSG00000073012	Fnd3c2	5031408O05Rik|Gm775	fibronectin type III domain containing 3C2	protein-coding
mm_128144.1	chr15	31531000	31531069	-	1	NA	promoter-TSS (NM_172606)	promoter-TSS (NM_172606)	3	NM_172606	223455	Mm.272185	NM_172606	ENSMUSG00000039100	March6	3830408G03|F830029L24Rik|mKIAA0597	membrane-associated ring finger (C3HC4) 6	protein-coding
mm_135185.1	chr16	36071735	36071759	-	1	NA	promoter-TSS (NM_001159421)	promoter-TSS (NM_001159421)	87	NM_001159421	381045	Mm.310434	NM_198645	ENSMUSG00000075229	Ccdc58	A930007B11Rik|AI413631	coiled-coil domain containing 58	protein-coding
mm_29993.1	chr3	135546528	135546538	-	1	NA	intron (NM_027288, intron 9 of 16)	MLTR25A|LTR|ERVK	60922	NM_027288	110173	Mm.280536	NM_027288	ENSMUSG00000028164	Manba	2410030O07Rik|B930014J03Rik|Bmn	mannosidase, beta A, lysosomal	protein-coding
mm_69464.1	chr7	133602184	133602194	-	1	NA	promoter-TSS (NM_028654)	promoter-TSS (NM_028654)	-74	NM_028654	73808	Mm.159067	NM_028654	ENSMUSG00000030976	Tex36	4930404H21Rik	testis expressed 36	protein-coding
mm_26826.1	chr3	10346106	10346125	-	1	NA	exon (NM_001331013, exon 4 of 8)	exon (NM_001331013, exon 4 of 8)	5202	NM_001331015	66361	Mm.371617	NM_025512	ENSMUSG00000039795	Zfand1	2310008M20Rik|AW048890	zinc finger, AN1-type domain 1	protein-coding
mm_18728.1	chr2	72971375	72971386	-	1	NA	exon (NM_001098425, exon 2 of 5)	exon (NM_001098425, exon 2 of 5)	7901	NM_001098425	20687	Mm.124328	NM_011450	ENSMUSG00000027109	Sp3	D130027J01Rik	trans-acting transcription factor 3	protein-coding
mm_118356.1	chr13	115101536	115101544	-	1	NA	5' UTR (NM_001033228, exon 1 of 29)	5' UTR (NM_001033228, exon 1 of 29)	424	NM_001033228	109700	Mm.317280	NM_001033228	ENSMUSG00000042284	Itga1	CD49A|E130012M19Rik|Vla1	integrin alpha 1	protein-coding
mm_51032.1	chr6	65525360	65525371	+	1	NA	Intergenic	Intergenic	-65033	NM_001001495	414084	Mm.117558	NM_001001495	ENSMUSG00000044162	Tnip3	9030611K07Rik|ABIN-3|LIND	TNFAIP3 interacting protein 3	protein-coding
mm_29373.1	chr3	108722125	108722138	-	1	NA	5' UTR (NM_029522, exon 1 of 15)	5' UTR (NM_029522, exon 1 of 15)	168	NM_029522	76123	Mm.226941	NM_029522	ENSMUSG00000027883	Gpsm2	6230410J09Rik|LGN|Pins	G-protein signalling modulator 2 (AGS3-like, C. elegans)	protein-coding
mm_134812.1	chr16	25045208	25045222	-	1	NA	Intergenic	Intergenic	-14424	NR_040374	319487	Mm.137341	NR_040374	ENSMUSG00000096960	A230028O05Rik	-	RIKEN cDNA A230028O05 gene	ncRNA
mm_38259.1	chr4	136880274	136880285	-	1	NA	3' UTR (NM_009777, exon 3 of 3)	3' UTR (NM_009777, exon 3 of 3)	5898	NM_009777	12260	Mm.2570	NM_009777	ENSMUSG00000036905	C1qb	-	complement component 1, q subcomponent, beta polypeptide	protein-coding
mm_87686.1	chr10	59346163	59346178	+	1	NA	intron (NM_001316370, intron 5 of 13)	Lx7|LINE|L1	22874	NM_001316370	18451	Mm.2212	NM_011030	ENSMUSG00000019916	P4ha1	AL022634|P4ha	procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha 1 polypeptide	protein-coding
mm_86017.1	chr9	112235143	112235196	-	1	NA	promoter-TSS (NM_001177619)	promoter-TSS (NM_001177619)	-328	NM_001177619	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_29307.1	chr3	107943391	107943421	-	1	NA	intron (NM_008184, intron 1 of 7)	G-rich|Low_complexity|Low_complexity	343	NM_008184	14867	Mm.458154	NM_008184	ENSMUSG00000068762	Gstm6	-	glutathione S-transferase, mu 6	protein-coding
mm_156818.1	chrX	164139371	164139397	+	1	NA	promoter-TSS (NM_001130513)	promoter-TSS (NM_001130513)	42	NM_001130513	70008	Mm.13451	NM_027286	ENSMUSG00000015405	Ace2	2010305L05Rik	angiotensin I converting enzyme (peptidyl-dipeptidase A) 2	protein-coding
mm_170624.1	chr19	7268227	7268229	+	1	NA	promoter-TSS (NM_001320554)	promoter-TSS (NM_001320554)	-51	NM_001320554	104383	Mm.283859	NM_054048	ENSMUSG00000024968	Rcor2	1A13|AW122124|CoREST|Rcor|Rcor1	REST corepressor 2	protein-coding
mm_144583.1	chr18	31931471	31931520	+	1	NA	promoter-TSS (NM_144862)	promoter-TSS (NM_144862)	-12	NM_144862	225341	Mm.24551	NM_144862	ENSMUSG00000024395	Lims2	PINCH2	LIM and senescent cell antigen like domains 2	protein-coding
mm_132455.1	chr16	36071625	36071688	+	1	NA	promoter-TSS (NM_001159421)	promoter-TSS (NM_001159421)	-4	NM_198645	381045	Mm.310434	NM_198645	ENSMUSG00000075229	Ccdc58	A930007B11Rik|AI413631	coiled-coil domain containing 58	protein-coding
mm_32382.1	chr4	106561028	106561038	+	1	NA	promoter-TSS (NM_053272)	promoter-TSS (NM_053272)	-5	NM_053272	74754	Mm.133370	NM_053272	ENSMUSG00000034926	Dhcr24	2310076D10Rik|5830417J06Rik|mKIAA0018	24-dehydrocholesterol reductase	protein-coding
mm_162320.1	chr1	39238543	39238544	+	1	NA	intron (NM_008719, intron 1 of 20)	intron (NM_008719, intron 1 of 20)	44271	NM_008719	18143	Mm.2380	NM_008719	ENSMUSG00000026077	Npas2	MOP4|bHLHe9	neuronal PAS domain protein 2	protein-coding
mm_150055.1	chr19	29382515	29382533	+	1	NA	exon (NM_021893, exon 5 of 7)	exon (NM_021893, exon 5 of 7)	15086	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_141533.1	chr17	31850005	31850017	-	1	NA	exon (NM_010831, exon 8 of 14)	exon (NM_010831, exon 8 of 14)	5781	NM_010831	17691	Mm.290941	NM_010831	ENSMUSG00000024042	Sik1	Msk|Sik|Snf1lk	salt inducible kinase 1	protein-coding
mm_22229.1	chr2	174432430	174432441	-	1	NA	intron (NM_022325, intron 3 of 5)	B4A|SINE|B4	6604	NM_022325	64138	Mm.156919	NM_022325	ENSMUSG00000016256	Ctsz	AI787083|AU019819|CTSX|D2Wsu143e	cathepsin Z	protein-coding
mm_123220.1	chr14	59552522	59552530	-	1	NA	Intergenic	Intergenic	45433	NM_001168537	71891	Mm.439850	NM_027986	ENSMUSG00000021982	Cdadc1	2310010M10Rik|AI449174|AI463398|BB130816|NYD-SP15	cytidine and dCMP deaminase domain containing 1	protein-coding
mm_1222.1	chr1	62738404	62738418	+	1	NA	exon (NM_001077407, exon 3 of 16)	exon (NM_001077407, exon 3 of 16)	35094	NM_001077405	18187	Mm.266341	NM_010939	ENSMUSG00000025969	Nrp2	1110048P06Rik|Np-2|Np2|Npn-2|Npn2	neuropilin 2	protein-coding
mm_61400.1	chr7	73375815	73375833	+	1	NA	promoter-TSS (NR_040324)	promoter-TSS (NR_040324)	-50	NR_040324	319783	Mm.349813	NR_040324	ENSMUSG00000097756	A730056A06Rik	C76391	RIKEN cDNA A730056A06 gene	ncRNA
mm_79659.1	chr9	59656764	59656855	+	1	NA	intron (NM_001253883, intron 1 of 10)	CpG	441	NM_001253883	18746	Mm.326167	NM_011099	ENSMUSG00000032294	Pkm	AA414905|AL024370|AL024424|Pk-2|Pk-3|Pk3|Pkm2	pyruvate kinase, muscle	protein-coding
mm_152800.1	chr19	21652746	21652769	-	1	NA	promoter-TSS (NM_025423)	promoter-TSS (NM_025423)	34	NM_025423	66206	Mm.272430	NM_025423	ENSMUSG00000035171	1110059E24Rik	-	RIKEN cDNA 1110059E24 gene	protein-coding
mm_60840.1	chr7	45742031	45742051	+	1	NA	intron (NM_017465, intron 2 of 6)	intron (NM_017465, intron 2 of 6)	-16225	NM_027055	69363	Mm.45607	NM_027055	ENSMUSG00000070563	Spaca4	1700008E09Rik|AV043694|Samp14	sperm acrosome associated 4	protein-coding
mm_42940.1	chr5	122989576	122989612	+	1	NA	promoter-TSS (NM_001003953)	promoter-TSS (NM_001003953)	240	NR_045820	109202	Mm.30769	NM_175405	ENSMUSG00000056735	A930024E05Rik	-	RIKEN cDNA A930024E05 gene	ncRNA
mm_105904.1	chr11	114983107	114983114	-	1	NA	3' UTR (NM_145437, exon 4 of 4)	3' UTR (NM_145437, exon 4 of 4)	6776	NM_145437	217305	Mm.275986	NM_145437	ENSMUSG00000034641	Cd300ld	4732429D16Rik|CLM5|Cd300ld1|LMIR4|MAIR-IV|clm-5	CD300 molecule like family member d	protein-coding
mm_141231.1	chr17	27426502	27426512	-	1	NA	3' UTR (NM_001291045, exon 10 of 10)	3' UTR (NM_001291045, exon 10 of 10)	68410	NR_106077	102466228		NR_106077	ENSMUSG00000106215	Mir7218	mmu-mir-7218	microRNA 7218	ncRNA
mm_98967.1	chr11	98682579	98682612	+	1	NA	promoter-TSS (NM_009439)	promoter-TSS (NM_009439)	41	NM_009439	22123	Mm.12194	NM_009439	ENSMUSG00000017221	Psmd3	AI255837|AntP91a|D11Bwg1349e|Psd3|Tstap91a	proteasome (prosome, macropain) 26S subunit, non-ATPase, 3	protein-coding
mm_39608.1	chr5	24124829	24124834	+	1	NA	intron (NM_001161800, intron 1 of 9)	RLTR15|LTR|ERVK	5137	NR_037304	100499521		NR_037304	ENSMUSG00000092880	Mir3471-1	mmu-mir-3471-1	microRNA 3471-1	ncRNA
mm_117369.1	chr13	71960344	71960357	-	1	NA	intron (NM_010573, intron 1 of 3)	GA-rich|Low_complexity|Low_complexity	3373	NM_010573	16371	Mm.316056	NM_010573	ENSMUSG00000060969	Irx1	-	Iroquois related homeobox 1 (Drosophila)	protein-coding
mm_168232.1	chr10	8156550	8156555	-	1	NA	Intergenic	IAP1-MM_LTR|LTR|ERVK	-200429	NM_138667	68652	Mm.193041	NM_138667	ENSMUSG00000015755	Tab2	1110030N06Rik|A530078N03Rik|Map3k7ip2|mKIAA0733	TGF-beta activated kinase 1/MAP3K7 binding protein 2	protein-coding
mm_27560.1	chr3	58525894	58525897	-	1	NA	promoter-TSS (NM_030685)	promoter-TSS (NM_030685)	-11	NM_030685	28146	Mm.29702	NM_030685	ENSMUSG00000027808	Serp1	D3Ucla1|Ramp4	stress-associated endoplasmic reticulum protein 1	protein-coding
mm_104444.1	chr11	95010294	95010325	-	1	NA	5' UTR (NM_146025, exon 1 of 10)	5' UTR (NM_146025, exon 1 of 10)	430	NM_146025	217125	Mm.297199	NM_146025	ENSMUSG00000047181	Samd14	AI839049|AI854782|BC034054	sterile alpha motif domain containing 14	protein-coding
mm_48851.1	chr5	149619958	149619971	-	1	NA	exon (NM_013559, exon 14 of 18)	exon (NM_013559, exon 14 of 18)	16351	NM_013559	15505	Mm.270681	NM_013559	ENSMUSG00000029657	Hsph1	105kDa|AI790491|Hsp105|Hsp110|hsp-E7I|hsp110/105	heat shock 105kDa/110kDa protein 1	protein-coding
mm_27457.1	chr3	52104904	52104922	-	1	NA	promoter-TSS (NM_001004176)	promoter-TSS (NM_001004176)	93	NM_001004176	433586	Mm.234972	NM_001004176	ENSMUSG00000061143	Maml3	AV234550|BC049812|Mam-2|mKIAA1816	mastermind like 3 (Drosophila)	protein-coding
mm_105679.1	chr11	107716414	107716420	-	1	NA	promoter-TSS (NM_007582)	promoter-TSS (NM_007582)	59	NM_007582	12299	Mm.57093	NM_007582	ENSMUSG00000020722	Cacng1	-	calcium channel, voltage-dependent, gamma subunit 1	protein-coding
mm_139546.1	chr17	56764768	56764798	+	1	NA	promoter-TSS (NM_144858)	promoter-TSS (NM_144858)	32	NM_144858	224907	Mm.293973	NM_144858	ENSMUSG00000007603	Dus3l	AI662135|AW557805	dihydrouridine synthase 3-like (S. cerevisiae)	protein-coding
mm_173088.1	chrX	150020277	150020285	+	1	NA	Intergenic	L1Md_A|LINE|L1	78626	NM_001122735	382244	Mm.359506	NM_001122735	ENSMUSG00000095082	Gm15091	OTTMUSG00000018981	predicted gene 15091	protein-coding
mm_50455.1	chr6	48907666	48907668	+	1	NA	exon (NM_001161622, exon 3 of 5)	exon (NM_001161622, exon 3 of 5)	2681	NM_001161621	76507	Mm.213898	NM_029638	ENSMUSG00000029811	Aoc1	1600012D06Rik|Abp1|DAO	amine oxidase, copper-containing 1	protein-coding
mm_37186.1	chr4	117375454	117375467	-	1	NA	promoter-TSS (NM_001310729)	promoter-TSS (NM_001310729)	1	NM_001310729	66743	Mm.318331	NM_025739	ENSMUSG00000028677	Rnf220	4732477A13|4931406I20Rik|5730503K05Rik|AV302541	ring finger protein 220	protein-coding
mm_51526.1	chr6	83186083	83186151	+	1	NA	5' UTR (NM_001347310, exon 1 of 27)	5' UTR (NM_001347310, exon 1 of 27)	171	NM_001347310	13191	Mm.6919	NM_007835	ENSMUSG00000031865	Dctn1	AL022633|DAP-150|DP-150|Glued|p150|p150-glued|p150<glued>	dynactin 1	protein-coding
mm_12220.1	chr2	67648776	67648787	+	1	NA	Intergenic	Lx5c|LINE|L1	-26676	NR_106083	102465706		NR_106083	ENSMUSG00000098299	Mir7224	Gm27971|mmu-mir-7224	microRNA 7224	ncRNA
mm_111991.1	chr12	110682607	110682623	-	1	NA	promoter-TSS (NM_025488)	promoter-TSS (NM_025488)	4	NM_025488	66323	Mm.273316	NM_025488	ENSMUSG00000056508	1700001K19Rik	-	RIKEN cDNA 1700001K19 gene	protein-coding
mm_71610.1	chr8	56551104	56551143	+	1	NA	promoter-TSS (NM_015791)	promoter-TSS (NM_015791)	-11	NM_015791	50753	Mm.251174	NM_015791	ENSMUSG00000038206	Fbxo8	Fbx8	F-box protein 8	protein-coding
mm_51610.1	chr6	84551091	84551096	+	1	NA	Intergenic	RMER17C|LTR|ERVK	42717	NM_175475	232174	Mm.255246	NM_175475	ENSMUSG00000063415	Cyp26b1	CP26|P450RAI-2	cytochrome P450, family 26, subfamily b, polypeptide 1	protein-coding
mm_96256.1	chr11	62603062	62603078	+	1	NA	promoter-TSS (NR_028526)	promoter-TSS (NR_028526)	-16	NR_028526	100217426		NR_028526	ENSMUSG00000064437	Snord49b	MBII-252|MBII-366	small nucleolar RNA, C/D box 49B	snoRNA
mm_79688.1	chr9	60334187	60334195	+	1	NA	intron (NM_001040426, intron 6 of 17)	MTE2a|LTR|ERVL-MaLR	176844	NM_001040426	207596	Mm.28791	NM_172444	ENSMUSG00000032289	Thsd4	ADAMTSL-6|ADAMTSL6|AI585901|Adamtsl4|B230114P05Rik	thrombospondin, type I, domain containing 4	protein-coding
mm_14316.1	chr2	129297362	129297376	+	1	NA	promoter-TSS (NM_181589)	promoter-TSS (NM_181589)	-1	NR_040371	100503468	Mm.446943	NR_040371	ENSMUSG00000085498	Gm14023	OTTMUSG00000015408	predicted gene 14023	ncRNA
mm_116545.1	chr13	45963696	45963719	-	1	NA	intron (NM_001199304, intron 1 of 6)	CpG	1284	NM_001199304	20238	Mm.342683	NM_009124	ENSMUSG00000046876	Atxn1	2900016G23Rik|Atx1|C85907|ENSMUSG00000074917|Gm10786|Sca1	ataxin 1	protein-coding
mm_77991.1	chr9	8544200	8544225	+	1	NA	promoter-TSS (NM_001282087)	promoter-TSS (NM_001282087)	70	NM_001282087	22068	Mm.325086	NM_013838	ENSMUSG00000031997	Trpc6	AV025995|LLHWJM002|LLHWJM003|LLHWJM004|TRP-6|Trrp6|mtrp6	transient receptor potential cation channel, subfamily C, member 6	protein-coding
mm_98035.1	chr11	85312173	85312180	+	1	NA	intron (NM_016910, intron 1 of 5)	intron (NM_016910, intron 1 of 5)	922	NM_016910	53892	Mm.45609	NM_016910	ENSMUSG00000020525	Ppm1d	AV338790|Wip1	protein phosphatase 1D magnesium-dependent, delta isoform	protein-coding
mm_28166.1	chr3	87846885	87846905	-	1	NA	5' UTR (NM_021309, exon 1 of 7)	5' UTR (NM_021309, exon 1 of 7)	140	NM_021309	27371	Mm.86361	NM_021309	ENSMUSG00000028071	Sh2d2a	Lad|Ribp|Tsad	SH2 domain containing 2A	protein-coding
mm_154309.1	chr19	61227306	61227376	-	1	NA	exon (NM_009970, exon 2 of 12)	exon (NM_009970, exon 2 of 12)	1077	NM_009970	12982	Mm.287228	NM_009970	ENSMUSG00000059326	Csf2ra	CD116|Csfgmra|GM-CSF-Ra|GM-CSFR	colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)	protein-coding
mm_154285.1	chr19	60864202	60864205	-	1	NA	3' UTR (NM_007452, exon 7 of 7)	3' UTR (NM_007452, exon 7 of 7)	-2773	NM_053198	94281	Mm.48179	NM_053198	ENSMUSG00000063698	Sfxn4	-	sideroflexin 4	protein-coding
mm_92258.1	chr10	70644898	70644907	-	1	NA	intron (NR_045291, intron 1 of 5)	intron (NR_045291, intron 1 of 5)	7023	NR_045291	319646	Mm.483039	NR_045291	ENSMUSG00000037747	D630013N20Rik	-	RIKEN cDNA D630013N20 gene	ncRNA
mm_84342.1	chr9	64186102	64186119	-	1	NA	3' UTR (NM_008927, exon 11 of 11)	3' UTR (NM_008927, exon 11 of 11)	6813	NM_183316	330959	Mm.24082	NM_183316	ENSMUSG00000032398	Snapc5	2010103A03Rik	small nuclear RNA activating complex, polypeptide 5	protein-coding
mm_41702.1	chr5	100916755	100916784	+	1	NA	Intergenic	Intergenic	70540	NM_172715	231510	Mm.271911	NM_172715	ENSMUSG00000029314	Agpat9	1-AGPAT|1-AGPAT 9|4933407I02Rik|4933408F15|A230097K15Rik|GPAT-3|Gpat3|mGPAT3	1-acylglycerol-3-phosphate O-acyltransferase 9	protein-coding
mm_119453.1	chr14	47001337	47001343	+	1	NA	promoter-TSS (NM_001163433)	promoter-TSS (NM_001163433)	0	NM_001163433	74480	Mm.214454	NM_028966	ENSMUSG00000021838	Samd4	1700024G08Rik|1700111L17Rik|4933436G17Rik|Samd4a|Smaug|Smaug1|sunk	sterile alpha motif domain containing 4	protein-coding
mm_154433.1	chrM	748	752	-	1	NA	NA	Intergenic	NA	NA								
mm_111322.1	chr12	86241680	86241687	-	1	NA	promoter-TSS (NM_027405)	promoter-TSS (NM_027405)	-175	NM_027405	70373	Mm.252967	NM_027405	ENSMUSG00000021254	Gpatch2l	1700020O03Rik|4732487G21Rik|A630090I05Rik|Kiaa1152	G patch domain containing 2 like	protein-coding
mm_63350.1	chr7	126976408	126976422	+	1	NA	5' UTR (NM_026638, exon 1 of 6)	5' UTR (NM_026638, exon 1 of 6)	501	NM_001347656	52858	Mm.28219	NM_026638	ENSMUSG00000030682	Cdipt	9530042F15Rik|D7Bwg0575e|Pis|Pis1	CDP-diacylglycerol--inositol 3-phosphatidyltransferase (phosphatidylinositol synthase)	protein-coding
mm_85507.1	chr9	106243296	106243307	-	1	NA	exon (NM_020559, exon 3 of 11)	exon (NM_020559, exon 3 of 11)	4429	NM_001291835	11655	Mm.290578	NM_020559	ENSMUSG00000032786	Alas1	ALAS|ALAS-N|Alas-1|Alas-h	aminolevulinic acid synthase 1	protein-coding
mm_3529.1	chr1	150167454	150167462	+	1	NA	Intergenic	ORR1B2|LTR|ERVL-MaLR	-2510	NR_110420	102639566	Mm.417208	NR_110420	ENSMUSG00000097754	Ptgs2os2	Gm26687|Linc-cox2|Lincrna-cox2	prostaglandin-endoperoxide synthase 2, opposite strand 2	ncRNA
mm_9403.1	chr1	172258445	172258453	-	1	NA	promoter-TSS (NM_013734)	promoter-TSS (NM_013734)	-25	NM_013734	27222	Mm.482392	NM_013734	ENSMUSG00000007107	Atp1a4	-	ATPase, Na+/K+ transporting, alpha 4 polypeptide	protein-coding
mm_146341.1	chr18	82475236	82475255	+	1	NA	5' UTR (NM_010777, exon 1 of 7)	5' UTR (NM_010777, exon 1 of 7)	122	NM_001025245	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_96051.1	chr11	59565923	59565940	+	1	NA	exon (NM_145827, exon 9 of 10)	exon (NM_145827, exon 9 of 10)	5807	NM_001011789	257962	Mm.377316	NM_001011789	ENSMUSG00000059610	Olfr222	MOR256-45P	olfactory receptor 222	protein-coding
mm_123240.1	chr14	60178052	60178084	-	1	NA	Intergenic	Intergenic	50847	NR_030458	751526		NR_030458	ENSMUSG00000076270	Mir719	Mirn719|mmu-mir-719	microRNA 719	ncRNA
mm_52789.1	chr6	121261446	121261458	+	1	NA	exon (NM_011909, exon 6 of 11)	exon (NM_011909, exon 6 of 11)	15546	NM_011909	24110	Mm.326911	NM_011909	ENSMUSG00000030107	Usp18	1110058H21Rik|AW047653|UBP43|Ubp15	ubiquitin specific peptidase 18	protein-coding
mm_108236.1	chr12	77241032	77241035	+	1	NA	intron (NR_045554, intron 1 of 11)	intron (NR_045554, intron 1 of 11)	2294	NR_045554	53618	Mm.35628	NM_016893	ENSMUSG00000021065	Fut8	-	fucosyltransferase 8	protein-coding
mm_36908.1	chr4	108031895	108031905	-	1	NA	promoter-TSS (NM_001285956)	promoter-TSS (NM_001285956)	190	NM_001285958	242608	Mm.74710	NM_172874	ENSMUSG00000028600	Podn	9430070G18|Pcan|SLRR5A	podocan	protein-coding
mm_131100.1	chr16	4987450	4987465	+	1	NA	3' UTR (NM_029374, exon 9 of 9)	3' UTR (NM_029374, exon 9 of 9)	10395	NM_027669	71089	Mm.87382	NM_027669	ENSMUSG00000022542	Sept12	1700028G04Rik|4933413B09Rik|Septin12	septin 12	protein-coding
mm_34447.1	chr4	148001092	148001111	+	1	NA	exon (NM_008725, exon 2 of 3)	exon (NM_008725, exon 2 of 3)	379	NM_008725	230899	Mm.482123	NM_008725	ENSMUSG00000041616	Nppa	ANP|Anf|Pnd	natriuretic peptide type A	protein-coding
mm_32403.1	chr4	106911471	106911505	+	1	NA	promoter-TSS (NM_198438)	promoter-TSS (NM_198438)	18	NM_023672	72475	Mm.195635	NM_023672	ENSMUSG00000061887	Ssbp3	2610021L12Rik|2610200M23Rik|5730488C10Rik|AI854733|AW551939|LAST|SSDP1	single-stranded DNA binding protein 3	protein-coding
mm_121973.1	chr14	25687763	25687773	-	1	NA	Intergenic	Intergenic	-6402	NM_134084	105675	Mm.41656	NM_134084	ENSMUSG00000021868	Ppif	AW457192|CyP-D|CyP-F|CypD|PPIase	peptidylprolyl isomerase F (cyclophilin F)	protein-coding
mm_48561.1	chr5	143165720	143165733	-	1	NA	promoter-TSS (NR_040426)	promoter-TSS (NR_040426)	25	NR_040426	100042605	Mm.332809	NR_040424	ENSMUSG00000104529	Rbakdn	Gm3925	RB-associated KRAB zinc finger downstream neighbor (non-protein coding)	ncRNA
mm_164701.1	chr17	50891430	50891431	+	1	NA	intron (NM_028162, intron 13 of 21)	intron (NM_028162, intron 13 of 21)	192749	NM_001297747	12228	Mm.392910	NM_009770	ENSMUSG00000022863	Btg3	ANA|tob5	B cell translocation gene 3	protein-coding
mm_116948.1	chr13	56135519	56135538	-	1	NA	promoter-TSS (NM_001159515)	promoter-TSS (NM_001159515)	22	NM_012015	26914	Mm.283802	NM_012015	ENSMUSG00000015937	H2afy	H2AF12M|mH2a1|macroH2A1	H2A histone family, member Y	protein-coding
mm_147680.1	chr18	60660206	60660231	-	1	NA	Intergenic	Intergenic	-3192	NR_045401	328963	Mm.417203	NR_045401		G630071F17Rik	G630071F17	RIKEN cDNA G630071F17 gene	ncRNA
mm_97150.1	chr11	75461663	75461665	+	1	NA	non-coding (NR_030711, exon 1 of 3)	non-coding (NR_030711, exon 1 of 3)	125	NR_030711	100042498	Mm.482242	NR_030711	ENSMUSG00000085148	Mir22hg	2210403K04Rik|mir-22	Mir22 host gene (non-protein coding)	ncRNA
mm_115581.1	chr13	11669662	11669671	-	1	NA	intron (NM_023868, intron 64 of 104)	intron (NM_023868, intron 64 of 104)	147614	NR_027813	664793	Mm.410565	NR_027813		Zp4-ps	EG664793|Zp4|Zpb	zona pellucida glycoprotein 4, pseudogene	pseudo
mm_120883.1	chr14	75330422	75330439	+	1	NA	exon (NM_026083, exon 14 of 19)	exon (NM_026083, exon 14 of 19)	46057	NM_026083	67302	Mm.74704	NM_026083	ENSMUSG00000022000	Zc3h13	2600010B19Rik|3110050K21Rik|4930570G11Rik|C87618	zinc finger CCCH type containing 13	protein-coding
mm_56238.1	chr6	90663051	90663061	-	1	NA	intron (NM_001134384, intron 13 of 13)	intron (NM_001134384, intron 13 of 13)	43810	NM_001037493	71699	Mm.272633	NM_027868	ENSMUSG00000030089	Slc41a3	1010001P06Rik|AI480742|SLC41A1-L2	solute carrier family 41, member 3	protein-coding
mm_19450.1	chr2	91991958	91991982	-	1	NA	exon (NM_011957, exon 5 of 12)	exon (NM_011957, exon 5 of 12)	-28407	NM_138306	104418	Mm.314923	NM_138306	ENSMUSG00000040479	Dgkz	E130307B02Rik|ENSMUSG00000075035|F730209L11Rik|mDGK[z]	diacylglycerol kinase zeta	protein-coding
mm_113311.1	chr13	30757631	30757632	+	1	NA	exon (NM_013674, exon 7 of 9)	exon (NM_013674, exon 7 of 9)	8398	NM_013674	16364	Mm.4677	NM_013674	ENSMUSG00000021356	Irf4	AI385587|IRF-4|LSIRF|NF-EM5|Spip	interferon regulatory factor 4	protein-coding
mm_133823.1	chr16	95769987	95770010	+	1	NA	Intergenic	Intergenic	67591	NM_011809	23872	Mm.290207	NM_011809	ENSMUSG00000022895	Ets2	AU022856|Ets-2	E26 avian leukemia oncogene 2, 3' domain	protein-coding
mm_150881.1	chr19	45076708	45076727	+	1	NA	exon (NM_178929, exon 2 of 5)	exon (NM_178929, exon 2 of 5)	578	NM_178929	107250	Mm.24417	NM_178929	ENSMUSG00000025213	Kazald1	AI842353|Bono1|IGFBP-rP10	Kazal-type serine peptidase inhibitor domain 1	protein-coding
mm_124772.1	chr15	7129558	7129573	+	1	NA	promoter-TSS (NM_001113386)	promoter-TSS (NM_001113386)	-7	NM_001113386	16880	Mm.149720	NM_013584	ENSMUSG00000054263	Lifr	A230075M04Rik|AW061234|LIF	leukemia inhibitory factor receptor	protein-coding
mm_125950.1	chr15	76248844	76248861	+	1	NA	TTS (NR_105918)	TTS (NR_105918)	661	NR_105918	102465575		NR_105918	ENSMUSG00000098625	Mir6953	Gm27738|mmu-mir-6953	microRNA 6953	ncRNA
mm_168700.1	chr11	97781835	97781839	-	1	NA	promoter-TSS (NR_028078)	promoter-TSS (NR_028078)	-71	NR_028078	100302498	Mm.453536	NR_028078	ENSMUSG00000064901	Snora21	MBI-3	small nucleolar RNA, H/ACA box 21	snoRNA
mm_47177.1	chr5	120749660	120749672	-	1	NA	exon (NM_145227, exon 1 of 11)	exon (NM_145227, exon 1 of 11)	182	NM_145227	246728	Mm.260926	NM_145227	ENSMUSG00000032690	Oas2	Oasl11	2'-5' oligoadenylate synthetase 2	protein-coding
mm_142672.1	chr17	47730135	47730161	-	1	NA	exon (NM_025973, exon 4 of 9)	exon (NM_025973, exon 4 of 9)	3306	NM_025973	109820	Mm.22957	NM_025973	ENSMUSG00000023987	Pgc	2210410L06Rik|Upg-1|Upg1	progastricsin (pepsinogen C)	protein-coding
mm_52179.1	chr6	99305987	99305994	+	1	NA	intron (NM_001347345, intron 3 of 19)	intron (NM_001347345, intron 3 of 19)	-39475	NM_001197321	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_14013.1	chr2	122149165	122149184	+	1	NA	intron (NM_009735, intron 1 of 3)	intron (NM_009735, intron 1 of 3)	1487	NM_009735	12010	Mm.163	NM_009735	ENSMUSG00000060802	B2m	Ly-m11|beta2-m|beta2m	beta-2 microglobulin	protein-coding
mm_98475.1	chr11	94950473	94950475	+	1	NA	exon (NM_007742, exon 48 of 51)	exon (NM_007742, exon 48 of 51)	14250	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_45838.1	chr5	87695269	87695270	-	1	NA	intron (NM_001286024, intron 4 of 6)	intron (NM_001286024, intron 4 of 6)	4156	NM_001286020	12991	Mm.268737	NM_009972	ENSMUSG00000063157	Csn2	Csnb	casein beta	protein-coding
mm_26091.1	chr3	136755054	136755058	+	1	NA	intron (NM_008913, intron 1 of 13)	intron (NM_008913, intron 1 of 13)	84990	NM_001293622	19055	Mm.331389	NM_008913	ENSMUSG00000028161	Ppp3ca	2900074D19Rik|CN|Caln|Calna|CnA	protein phosphatase 3, catalytic subunit, alpha isoform	protein-coding
mm_11624.1	chr2	34774659	34774669	+	1	NA	exon (NM_001163434, exon 7 of 9)	exon (NM_001163434, exon 7 of 9)	2574	NM_022310	14828	Mm.330160	NM_022310	ENSMUSG00000026864	Hspa5	AL022860|AU019543|Bip|D2Wsu141e|D2Wsu17e|Grp78|Hsce70|SEZ-7|Sez7|baffled|mBiP	heat shock protein 5	protein-coding
mm_142703.1	chr17	47878697	47878740	-	1	NA	exon (NM_028767, exon 6 of 17)	exon (NM_028767, exon 6 of 17)	-44027	NM_001109973	17240	Mm.329100	NM_010783	ENSMUSG00000032717	Mdfi	I-mf|I-mfa	MyoD family inhibitor	protein-coding
mm_30162.1	chr3	144188818	144188828	-	1	NA	3' UTR (NM_010723, exon 5 of 5)	3' UTR (NM_010723, exon 5 of 5)	13509	NM_001161770	16911	Mm.29187	NM_010723	ENSMUSG00000028266	Lmo4	A730077C12Rik|Crp3|Etohi4	LIM domain only 4	protein-coding
mm_49329.1	chr6	21215359	21215387	+	1	NA	promoter-TSS (NM_019697)	promoter-TSS (NM_019697)	-736	NM_019697	16508	Mm.425316	NM_019697	ENSMUSG00000060882	Kcnd2	AI839615|AW555701|Kv4.2|R75121|mKIAA1044	potassium voltage-gated channel, Shal-related family, member 2	protein-coding
mm_123982.1	chr14	75591971	75591989	-	1	NA	promoter-TSS (NM_001164141)	promoter-TSS (NM_001164141)	5	NM_026457	67926	Mm.23361	NM_026457	ENSMUSG00000034913	Spert	1700086N05Rik|AI596460|Nurit	spermatid associated	protein-coding
mm_26820.1	chr3	10335410	10335441	-	1	NA	exon (NM_001010834, exon 1 of 1)	exon (NM_001010834, exon 1 of 1)	231	NM_001010834	241877	Mm.442146	NM_001010834	ENSMUSG00000058921	Slc10a5	Gm405|mP5	solute carrier family 10 (sodium/bile acid cotransporter family), member 5	protein-coding
mm_162156.1	chrX	86256228	86256228	-	1	NA	promoter-TSS (NM_001033492)	promoter-TSS (NM_001033492)	-9	NM_001033492	434903	Mm.213584	NM_001033492	ENSMUSG00000035427	Mageb4	CN716893|Mage-b4|mMage-b4	melanoma antigen, family B, 4	protein-coding
mm_60397.1	chr7	44475513	44475524	+	1	NA	Intergenic	Intergenic	5171	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_113449.1	chr13	35741375	35741385	+	1	NA	promoter-TSS (NM_001123386)	promoter-TSS (NM_001123386)	-22	NM_001123386	12593	Mm.29002	NM_009881	ENSMUSG00000059288	Cdyl	AI325931	chromodomain protein, Y chromosome-like	protein-coding
mm_71618.1	chr8	57323314	57323324	+	1	NA	intron (NM_010402, intron 1 of 1)	intron (NM_010402, intron 1 of 1)	2336	NM_010402	15111	Mm.430844	NM_010402	ENSMUSG00000038193	Hand2	AI225906|AI661148|Ehand2|Hed|Th2|Thing2|bHLHa26|dHAND	heart and neural crest derivatives expressed transcript 2	protein-coding
mm_141930.1	chr17	35027910	35027934	-	1	NA	promoter-TSS (NM_023893)	promoter-TSS (NM_023893)	94	NR_028258	78376	Mm.390966	NM_023893	ENSMUSG00000036185	Sapcd1	2810436B06Rik|G7d|Ng23	suppressor APC domain containing 1	protein-coding
mm_120934.1	chr14	76504550	76504560	+	1	NA	promoter-TSS (NM_009366)	promoter-TSS (NM_009366)	45	NM_009366	21807	Mm.153272	NM_009366	ENSMUSG00000022010	Tsc22d1	AA589566|AW105905|Egr5|TSC-22|Tgfb1i4|Tsc|Tsc22	TSC22 domain family, member 1	protein-coding
mm_125832.1	chr15	74957761	74957795	+	1	NA	5' UTR (NM_001164036, exon 2 of 4)	5' UTR (NM_001164036, exon 2 of 4)	2672	NM_001164040	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_306.1	chr1	23762004	23762018	+	1	NA	promoter-TSS (NM_172124)	promoter-TSS (NM_172124)	85	NM_172124	280645	Mm.471661	NM_172124	ENSMUSG00000026156	B3gat2	GlcAT-S|Glcats	beta-1,3-glucuronyltransferase 2 (glucuronosyltransferase S)	protein-coding
mm_26567.1	chr3	146597136	146597155	+	1	NA	promoter-TSS (NM_009474)	promoter-TSS (NM_009474)	-4	NM_009474	22262	Mm.10865	NM_009474	ENSMUSG00000028186	Uox	AI663847	urate oxidase	protein-coding
mm_130419.1	chr15	98085582	98085586	-	1	NA	intron (NM_144851, intron 2 of 17)	AT_rich|Low_complexity|Low_complexity	-7005	NM_001163488	18642	Mm.272582	NM_021514	ENSMUSG00000033065	Pfkm	AI131669|ATP-PFK|PFK-A|PFK-M|Pfk-4|Pfk4|Pfka|Pfkx	phosphofructokinase, muscle	protein-coding
mm_62859.1	chr7	114698499	114698501	+	1	NA	Intergenic	ORR1A3|LTR|ERVL-MaLR	-20143	NM_054084	116903	Mm.273838	NM_054084	ENSMUSG00000030666	Calcb	CGRP2|Calc2	calcitonin-related polypeptide, beta	protein-coding
mm_98370.1	chr11	94044112	94044121	+	1	NA	promoter-TSS (NM_001199205)	promoter-TSS (NM_001199205)	-89	NM_001025430	70834	Mm.260737	NM_027569	ENSMUSG00000020859	Spag9	3110018C07Rik|4733401I23Rik|4831406C20Rik|AW552012|JLP|JSAP2|JSAP2a|Jip4|Mapk8ip4|syd1	sperm associated antigen 9	protein-coding
mm_135007.1	chr16	32247104	32247148	-	1	NA	promoter-TSS (NM_026898)	promoter-TSS (NM_026898)	-101	NM_173439	268882	Mm.256137	NM_173439	ENSMUSG00000035764	Fbxo45	2610017J04Rik|AI463119|BC026799	F-box protein 45	protein-coding
mm_79518.1	chr9	57537584	57537634	+	1	NA	promoter-TSS (NM_001166364)	promoter-TSS (NM_001166364)	81	NM_001166364	78323	Mm.25814	NM_175273	ENSMUSG00000032305	Fam219b	2310046O06Rik|AI594866	family with sequence similarity 219, member B	protein-coding
mm_3586.1	chr1	151344532	151344584	+	1	NA	promoter-TSS (NM_001039512)	promoter-TSS (NM_001039512)	60	NM_001039511	117198	Mm.33764	NM_028582	ENSMUSG00000023150	Ivns1abp	1190004M08Rik|1700126I16Rik|AA960440|HSPC068|ND1|NS-1|NS1-BP|Nd1-L|Nd1-S|mKIAA0850	influenza virus NS1A binding protein	protein-coding
mm_22254.1	chr2	174853356	174853359	-	1	NA	Intergenic	Intergenic	92738	NM_007903	13616	Mm.9478	NM_007903	ENSMUSG00000027524	Edn3	ET-3|PPET3|ls|tmgc48	endothelin 3	protein-coding
mm_33484.1	chr4	130818972	130818981	+	1	NA	exon (NM_011520, exon 3 of 5)	exon (NM_011520, exon 3 of 5)	26439	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_173075.1	chrX	136215498	136215499	-	1	NA	promoter-TSS (NM_009052)	promoter-TSS (NM_009052)	15	NM_009052	19716	Mm.422943	NM_009052	ENSMUSG00000050071	Bex1	AA407839|AU018692|Bex4|Rex3	brain expressed X-linked 1	protein-coding
mm_150898.1	chr19	45528192	45528208	+	1	NA	intron (NM_001286465, intron 14 of 14)	intron (NM_001286465, intron 14 of 14)	32364	NM_001330506	56626	Mm.46509	NM_020032	ENSMUSG00000025218	Poll	1110003P06Rik|AV007317	polymerase (DNA directed), lambda	protein-coding
mm_17162.1	chr2	25246842	25246864	-	1	NA	3' UTR (NM_001082476, exon 14 of 14)	3' UTR (NM_001082476, exon 14 of 14)	3924	NM_176834	68846	Mm.24777	NM_176834	ENSMUSG00000044628	Rnf208	1110061N23Rik	ring finger protein 208	protein-coding
mm_149979.1	chr19	29101442	29101452	+	1	NA	promoter-TSS (NM_021525)	promoter-TSS (NM_021525)	72	NM_021525	59028	Mm.28630	NM_021525	ENSMUSG00000024785	Rcl1	2310040A02Rik|AI789745|C76567|RPCL1|Rnac	RNA terminal phosphate cyclase-like 1	protein-coding
mm_95544.1	chr11	52306764	52306776	+	1	NA	Intergenic	Intergenic	-23756	NM_001313981	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_155222.1	chrX	57053881	57053908	+	1	NA	promoter-TSS (NM_029371)	promoter-TSS (NM_029371)	60	NM_029371	72459	Mm.2152	NM_028242	ENSMUSG00000067873	Htatsf1	1600023H17Rik|2600017A12Rik|2700077B20Rik|TAT-SF1	HIV TAT specific factor 1	protein-coding
mm_50758.1	chr6	53503854	53503854	+	1	NA	intron (NM_001327821, intron 5 of 10)	intron (NM_001327821, intron 5 of 10)	-69520	NM_172728	231991	Mm.227444	NM_172728	ENSMUSG00000053007	Creb5	9430076C15Rik|CRE-BPa|Crebpa|D430026C09Rik	cAMP responsive element binding protein 5	protein-coding
mm_159603.1	chr4	128884148	128884148	+	1	NA	promoter-TSS (NM_178110)	promoter-TSS (NM_178110)	8	NM_178110	67525	Mm.30653	NM_178110	ENSMUSG00000041000	Trim62	6330414G21Rik|AI450348|Dear1	tripartite motif-containing 62	protein-coding
mm_104025.1	chr11	86087898	86087903	-	1	NA	intron (NM_178309, intron 16 of 19)	L1MA5A|LINE|L1	-63550	NR_046030	629393	Mm.372867	NR_046030		Gm20759	-	predicted gene, 20759	ncRNA
mm_103084.1	chr11	69916976	69917002	-	1	NA	TTS (NM_019726)	TTS (NM_019726)	2797	NM_019726	56310	Mm.477738	NM_019726	ENSMUSG00000023170	Gps2	AI505953	G protein pathway suppressor 2	protein-coding
mm_105395.1	chr11	103395257	103395268	-	1	NA	exon (NM_183034, exon 4 of 12)	exon (NM_183034, exon 4 of 12)	17402	NM_183034	353047	Mm.18556	NM_183034	ENSMUSG00000034247	Plekhm1	AP162|B2|BC038943|D330036J23Rik	pleckstrin homology domain containing, family M (with RUN domain) member 1	protein-coding
mm_146097.1	chr18	73869979	73869990	+	1	NA	exon (NM_001305882, exon 4 of 9)	exon (NM_001305882, exon 4 of 9)	10599	NM_001305882	71263	Mm.126220	NM_027741	ENSMUSG00000064036	Mro	4930507C04Rik|4933435E20Rik	maestro	protein-coding
mm_128380.1	chr15	42676939	42676952	-	1	NA	promoter-TSS (NM_001286062)	promoter-TSS (NM_001286062)	32	NM_001286062	11600	Mm.309336	NM_009640	ENSMUSG00000022309	Angpt1	1110046O21Rik|Ang-1|Ang1	angiopoietin 1	protein-coding
mm_97349.1	chr11	77470000	77470016	+	1	NA	TTS (NM_139129)	TTS (NM_139129)	6095	NM_139130	216961	Mm.33477	NM_139128	ENSMUSG00000020836	Coro6	-	coronin 6	protein-coding
mm_63145.1	chr7	123214809	123214853	+	1	NA	promoter-TSS (NM_146198)	promoter-TSS (NM_146198)	-35	NM_146198	233836	Mm.211838	NM_146198	ENSMUSG00000030769	Slc5a11	2010013B02Rik|Kst1|RKST2|SMIT2|Slc5a10	solute carrier family 5 (sodium/glucose cotransporter), member 11	protein-coding
mm_8310.1	chr1	144177260	144177281	-	1	NA	5' UTR (NM_153171, exon 1 of 6)	5' UTR (NM_153171, exon 1 of 6)	102	NM_153171	246709	Mm.38271	NM_153171	ENSMUSG00000051079	Rgs13	-	regulator of G-protein signaling 13	protein-coding
mm_138755.1	chr17	37050129	37050141	+	1	NA	intron (NM_019439, intron 5 of 22)	intron (NM_019439, intron 5 of 22)	4169	NM_019439	54393	Mm.32191	NM_019439	ENSMUSG00000024462	Gabbr1	GABAB1|GABAbR1|bM573K1.1	gamma-aminobutyric acid (GABA) B receptor, 1	protein-coding
mm_144078.1	chr17	91092861	91092877	-	1	NA	promoter-TSS (NM_020252)	promoter-TSS (NM_020252)	-67	NM_020252	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_74277.1	chr8	125292117	125292121	+	1	NA	Intergenic	Intergenic	200591	NM_001081337	244668	Mm.271668	NM_001081337	ENSMUSG00000001995	Sipa1l2	BC058408|mKIAA1389	signal-induced proliferation-associated 1 like 2	protein-coding
mm_64351.1	chr7	142385459	142385489	+	1	NA	exon (NM_009983, exon 2 of 9)	exon (NM_009983, exon 2 of 9)	2396	NM_009983	13033	Mm.231395	NM_009983	ENSMUSG00000007891	Ctsd	CD|CatD	cathepsin D	protein-coding
mm_157496.1	chrX	48454274	48454301	-	1	NA	intron (NM_019680, intron 1 of 8)	CpG	8845	NM_019680	56501	Mm.36808	NM_019680	ENSMUSG00000031103	Elf4	AV314029|BC042423|ENSMUSG00000053512|Gm9907|Mef	E74-like factor 4 (ets domain transcription factor)	protein-coding
mm_70596.1	chr8	13288238	13288263	+	1	NA	promoter-TSS (NM_001042649)	promoter-TSS (NM_001042649)	-124	NM_001042650	102323	Mm.368890	NM_001024504	ENSMUSG00000038506	Dcun1d2	AW495713|mFLJ10704	DCN1, defective in cullin neddylation 1, domain containing 2 (S. cerevisiae)	protein-coding
mm_101869.1	chr11	48891792	48891804	-	1	NA	intron (NM_001024230, intron 4 of 4)	intron (NM_001024230, intron 4 of 4)	10354	NM_001024230	432555	Mm.338931	NM_001024230	ENSMUSG00000058163	Gm5431	EG432555|Irgb9b8	predicted gene 5431	protein-coding
mm_75960.1	chr8	71719228	71719238	-	1	NA	intron (NR_131256, intron 3 of 25)	MIR|SINE|MIR	6448	NR_131256	74015	Mm.22025	NM_028715	ENSMUSG00000070000	Fcho1	3322402E17Rik|N28152	FCH domain only 1	protein-coding
mm_79182.1	chr9	48390049	48390059	+	1	NA	intron (NM_172921, intron 4 of 8)	intron (NM_172921, intron 4 of 8)	28013	NM_172921	244853	Mm.325522	NM_172921	ENSMUSG00000044229	Nxpe4	C130036J11|D930028F11Rik|Fam55d	neurexophilin and PC-esterase domain family, member 4	protein-coding
mm_66511.1	chr7	45103070	45103080	-	1	NA	5' UTR (NM_010189, exon 2 of 7)	5' UTR (NM_010189, exon 2 of 7)	747	NM_010189	14132	Mm.3303	NM_010189	ENSMUSG00000003420	Fcgrt	FcRn	Fc receptor, IgG, alpha chain transporter	protein-coding
mm_91146.1	chr10	20170850	20170854	-	1	NA	intron (NM_001198635, intron 1 of 17)	intron (NM_001198635, intron 1 of 17)	21932	NM_001198635	17761	Mm.20928	NM_008635	ENSMUSG00000019996	Map7	E-MAP-115|MAP-7|Mtap7|R75000|mshi|mste|ste	microtubule-associated protein 7	protein-coding
mm_60603.1	chr7	44572318	44572325	+	1	NA	promoter-TSS (NM_008437)	promoter-TSS (NM_008437)	-124	NM_008437	16541	Mm.383181	NM_008437	ENSMUSG00000002204	Napsa	KAP|Kdap|NAP1|SNAPA|pronapsin	napsin A aspartic peptidase	protein-coding
mm_56014.1	chr6	86525505	86525515	-	1	NA	exon (NM_011865, exon 1 of 1)	exon (NM_011865, exon 1 of 1)	655	NM_011865	23983	Mm.274146	NM_011865	ENSMUSG00000051695	Pcbp1	WBP17|[a]CP-1|alphaCP-1|hnRNP E1	poly(rC) binding protein 1	protein-coding
mm_94524.1	chr11	9048830	9048839	+	1	NA	5' UTR (NM_001037928, exon 1 of 7)	5' UTR (NM_001037928, exon 1 of 7)	157	NM_001290520	194974	Mm.79210	NM_177576	ENSMUSG00000040985	Sun3	Sunc1	Sad1 and UNC84 domain containing 3	protein-coding
mm_22263.1	chr2	178407450	178407470	-	1	NA	intron (NM_177191, intron 1 of 43)	CpG	198	NM_177191	320558	Mm.70781	NM_177191	ENSMUSG00000060445	Sycp2	3830402K23Rik|4930518F03Rik	synaptonemal complex protein 2	protein-coding
mm_167866.1	chrX	21475313	21475320	+	1	NA	Intergenic	Intergenic	-9308	NM_007429	11609	Mm.2679	NM_007429	ENSMUSG00000068122	Agtr2	AI316812|AW107640	angiotensin II receptor, type 2	protein-coding
mm_70068.1	chr7	142652993	142653008	-	1	NA	3' UTR (NM_010514, exon 4 of 4)	3' UTR (NM_010514, exon 4 of 4)	1996	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_144302.1	chr18	12410858	12410874	+	1	NA	intron (NM_010680, intron 6 of 74)	intron (NM_010680, intron 6 of 74)	76842	NM_010680	16774	Mm.42012	NM_010680	ENSMUSG00000024421	Lama3	Lama3B|[a]3B	laminin, alpha 3	protein-coding
mm_88132.1	chr10	69398771	69398788	+	1	NA	Intergenic	CpG	-45867	NM_007659	12534	Mm.281367	NM_007659	ENSMUSG00000019942	Cdk1	Cdc2|Cdc2a|p34<CDC2>	cyclin-dependent kinase 1	protein-coding
mm_42067.1	chr5	109866702	109866747	+	1	NA	Intergenic	Intergenic	-32582	NR_027964	667213	Mm.454429	NR_027964	ENSMUSG00000105044	Gm10416	EG667213|ENSMUSG00000072761	zinc finger protein pseudogene	pseudo
mm_124581.1	chr14	124669878	124669913	-	1	NA	intron (NM_207667, intron 1 of 4)	intron (NM_207667, intron 1 of 4)	7232	NM_207667	14169	Mm.206362	NM_010201	ENSMUSG00000025551	Fgf14	FHF-4|Fhf4|mFHF-4(1B)	fibroblast growth factor 14	protein-coding
mm_47869.1	chr5	134639487	134639522	-	1	NA	promoter-TSS (NM_033561)	promoter-TSS (NM_033561)	-95	NM_033561	22384	Mm.27955	NM_033561	ENSMUSG00000040731	Eif4h	AU018978|D5Ertd355e|E430026L18Rik|Ef4h|Wbscr1|Wscr1|eIF-4H	eukaryotic translation initiation factor 4H	protein-coding
mm_38833.1	chr4	149150624	149150643	-	1	NA	3' UTR (NM_001081274, exon 13 of 13)	3' UTR (NM_001081274, exon 13 of 13)	-13033	NM_027263	69928	Mm.260893	NM_027263	ENSMUSG00000073705	Apitd1	2610040C18Rik|2810407L01Rik|CENP-S	apoptosis-inducing, TAF9-like domain 1	protein-coding
mm_109551.1	chr12	111713002	111713031	+	1	NA	promoter-TSS (NM_026511)	promoter-TSS (NM_026511)	-63	NM_001324482	70369	Mm.44239	NM_027404	ENSMUSG00000049792	Bag5	1600025G07Rik|4930405J06Rik|Bag-5	BCL2-associated athanogene 5	protein-coding
mm_160213.1	chr7	98360139	98360139	-	1	NA	intron (NM_001168541, intron 1 of 3)	intron (NM_001168541, intron 1 of 3)	1149	NM_001168540	244152	Mm.25317	NM_001024619	ENSMUSG00000049580	Tsku	9530051K01Rik|E2ig4|Lrrc54|Tsk	tsukushi, small leucine rich proteoglycan	protein-coding
mm_87720.1	chr10	60106230	60106263	+	1	NA	promoter-TSS (NM_052994)	promoter-TSS (NM_052994)	-11	NM_052994	94214	Mm.153429	NM_052994	ENSMUSG00000058297	Spock2	AA407235|Gcap26|mKIAA0275	sparc/osteonectin, cwcv and kazal-like domains proteoglycan 2	protein-coding
mm_169911.1	chr16	54868297	54868309	-	1	NA	Intergenic	L1Md_T|LINE|L1	414934	NM_178720	239852	Mm.245045	NM_178720	ENSMUSG00000064310	Zpld1	9430016A21Rik	zona pellucida like domain containing 1	protein-coding
mm_41775.1	chr5	103692435	103692460	+	1	NA	Intergenic	CpG	-36715	NM_001163550	74218	Mm.159141	NM_028824	ENSMUSG00000029320	1700016H13Rik	-	RIKEN cDNA 1700016H13 gene	protein-coding
mm_105205.1	chr11	102097969	102097985	-	1	NA	Intergenic	Intergenic	3323	NM_008918	19064	Mm.1269	NM_008918	ENSMUSG00000017316	Ppy	AV061413|IGSPP|PP	pancreatic polypeptide	protein-coding
mm_31654.1	chr4	59806818	59806839	+	1	NA	intron (NM_172468, intron 1 of 8)	intron (NM_172468, intron 1 of 8)	1178	NM_172468	209131	Mm.259705	NM_172468	ENSMUSG00000028385	Snx30	4732481H14Rik|C030041J06Rik	sorting nexin family member 30	protein-coding
mm_114579.1	chr13	75704763	75704763	+	1	NA	Intergenic	Intergenic	-2721	NM_138953	192657	Mm.21288	NM_138953	ENSMUSG00000001542	Ell2	-	elongation factor RNA polymerase II 2	protein-coding
mm_153453.1	chr19	41032060	41032068	-	1	NA	intron (NM_009345, intron 1 of 11)	RSINE1|SINE|B4	2789	NM_009345	21673	Mm.25620	NM_009345	ENSMUSG00000025014	Dntt	Tdt	deoxynucleotidyltransferase, terminal	protein-coding
mm_90388.1	chr10	127321867	127321884	+	1	NA	promoter-TSS (NM_001285785)	promoter-TSS (NM_001285785)	-89	NM_001285785	216445	Mm.227198	NM_146011	ENSMUSG00000040345	Arhgap9	AU043488	Rho GTPase activating protein 9	protein-coding
mm_149493.1	chr19	11821482	11821495	+	1	NA	Intergenic	Intergenic	-2085	NM_001025307	20908	Mm.272264	NM_011502	ENSMUSG00000041488	Stx3	Syn-3	syntaxin 3	protein-coding
mm_3925.1	chr1	162581808	162581839	+	1	NA	exon (NM_016796, exon 4 of 8)	exon (NM_016796, exon 4 of 8)	10995	NM_001347125	53330	Mm.10699	NM_016796	ENSMUSG00000026696	Vamp4	D1Ertd147e	vesicle-associated membrane protein 4	protein-coding
mm_5613.1	chr1	39651166	39651196	-	1	NA	promoter-TSS (NM_170597)	promoter-TSS (NM_170597)	1	NM_170597	263764	Mm.122091	NM_170597	ENSMUSG00000050967	Creg2	A830098L22Rik	cellular repressor of E1A-stimulated genes 2	protein-coding
mm_97386.1	chr11	77765589	77765643	+	1	NA	Intergenic	Intergenic	-11619	NM_001291213	360013	Mm.341248	NM_011586	ENSMUSG00000000631	Myo18a	MAJN|MyoPDZ|MysPDZ|SP-R210	myosin XVIIIA	protein-coding
mm_149930.1	chr19	26753589	26753603	+	1	NA	intron (NM_001347439, intron 3 of 7)	intron (NM_001347439, intron 3 of 7)	5193	NM_026003	67155	Mm.342988	NM_011416	ENSMUSG00000024921	Smarca2	2610209L14Rik|SNF2alpha|Snf2l2|brahma|brm	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	protein-coding
mm_159326.1	chr3	30644498	30644498	+	1	NA	promoter-TSS (NM_026668)	promoter-TSS (NM_026668)	-9	NM_026668	68307	Mm.389425	NM_026668	ENSMUSG00000027703	Lrriq4	4930558O21Rik	leucine-rich repeats and IQ motif containing 4	protein-coding
mm_147146.1	chr18	36560154	36560178	-	1	NA	promoter-TSS (NM_175375)	promoter-TSS (NM_175375)	-437	NM_175375	108857	Mm.482287	NM_175375	ENSMUSG00000024483	Ankhd1	1110004O12Rik|4933432B13Rik|9130019P20Rik|A530027J04Rik|A630021B20Rik|AA571404|Mask|mFLJ00246|mKIAA1085	ankyrin repeat and KH domain containing 1	protein-coding
mm_27079.1	chr3	30012887	30012911	-	1	NA	5' UTR (NM_007963, exon 1 of 15)	5' UTR (NM_007963, exon 1 of 15)	305	NM_007963	14013	Mm.56965	NM_007963	ENSMUSG00000027684	Mecom	D630039M04Rik|Evi-1|Evi1|Jbo|Mds|Mds1|Mds1-Evi1|Prdm3|Znfpr1b1	MDS1 and EVI1 complex locus	protein-coding
mm_70132.1	chr7	143241423	143241441	-	1	NA	non-coding (NR_001461, exon 1 of 1)	non-coding (NR_001461, exon 1 of 1)	55115	NR_001461	63830	Mm.356096	NR_001461	ENSMUSG00000101609	Kcnq1ot1	Kvlqt1-as|Lit1|Tssc8	KCNQ1 overlapping transcript 1	ncRNA
mm_16277.1	chr2	173737603	173737632	+	1	NA	promoter-TSS (NM_019806)	promoter-TSS (NM_019806)	46	NM_019806	56491	Mm.260456	NM_019806	ENSMUSG00000054455	Vapb	AI225786|AI840687|AI848259|D2Abb2e|R75548|VAP33b|Vamp33b	vesicle-associated membrane protein, associated protein B and C	protein-coding
mm_3320.1	chr1	137912854	137912858	+	1	NA	Intergenic	Intergenic	-53599	NR_029795	735252		NR_029795	ENSMUSG00000065565	Mir181a-1	Mirn181a-1|Mirn213|miR-213|mir-181a-1|mmu-mir-213	microRNA 181a-1	ncRNA
mm_120875.1	chr14	75275007	75275023	+	1	NA	exon (NM_019775, exon 9 of 11)	exon (NM_019775, exon 9 of 11)	-9358	NM_026083	67302	Mm.74704	NM_026083	ENSMUSG00000022000	Zc3h13	2600010B19Rik|3110050K21Rik|4930570G11Rik|C87618	zinc finger CCCH type containing 13	protein-coding
mm_97028.1	chr11	72208268	72208284	+	1	NA	exon (NM_026559, exon 2 of 4)	exon (NM_026559, exon 2 of 4)	722	NM_026559	52700	Mm.27670	NM_026559	ENSMUSG00000020803	Txndc17	4831443O22Rik|D11Ertd672e|TRP14|Txnl5	thioredoxin domain containing 17	protein-coding
mm_134882.1	chr16	28951397	28951418	-	1	NA	Intergenic	Intergenic	-21709	NM_177718	239796	Mm.155887	NM_177718	ENSMUSG00000051065	Mb21d2	1600021P15Rik|A430031N04|C87006	Mab-21 domain containing 2	protein-coding
mm_158843.1	chrX	169320274	169320383	-	1	NA	promoter-TSS (NM_001331050)	promoter-TSS (NM_001331050)	44	NM_001331050	15159	Mm.284033	NM_008222	ENSMUSG00000031352	Hccs	-	holocytochrome c synthetase	protein-coding
mm_45752.1	chr5	86783108	86783118	-	1	NA	Intergenic	Intergenic	-21153	NM_001347375	231386	Mm.196325	NM_177680	ENSMUSG00000035851	Ythdc1	A730098D12Rik|C80342|mKIAA1966	YTH domain containing 1	protein-coding
mm_76432.1	chr8	84980998	84981036	-	1	NA	Intergenic	Intergenic	-2269	NM_008416	16477	Mm.1167	NM_008416	ENSMUSG00000052837	Junb	-	jun B proto-oncogene	protein-coding
mm_51586.1	chr6	83795183	83795204	+	1	NA	promoter-TSS (NM_001164187)	promoter-TSS (NM_001164187)	35	NM_001164187	56174	Mm.190650	NM_019542	ENSMUSG00000034744	Nagk	Gnk	N-acetylglucosamine kinase	protein-coding
mm_20983.1	chr2	151980098	151980130	-	1	NA	5' UTR (NM_146127, exon 1 of 2)	5' UTR (NM_146127, exon 1 of 2)	105	NM_146127	73847	Mm.272444	NM_028666	ENSMUSG00000027459	Fam110a	1700008J10Rik|5430432M24Rik|AI747080	family with sequence similarity 110, member A	protein-coding
mm_3627.1	chr1	152767990	152767994	+	1	NA	intron (NM_026369, intron 1 of 3)	intron (NM_026369, intron 1 of 3)	1450	NM_026369	67771	Mm.288974	NM_026369	ENSMUSG00000008475	Arpc5	5830443F10Rik|p16-Arc	actin related protein 2/3 complex, subunit 5	protein-coding
mm_88937.1	chr10	81293015	81293027	+	1	NA	promoter-TSS (NM_001146687)	promoter-TSS (NM_001146687)	58	NM_001146687	18717	Mm.24222	NM_008844	ENSMUSG00000034902	Pip5k1c	AI115456|AI835305|Pip5kIgamma	phosphatidylinositol-4-phosphate 5-kinase, type 1 gamma	protein-coding
mm_135336.1	chr16	42290973	42290977	-	1	NA	intron (NM_008083, intron 2 of 2)	intron (NM_008083, intron 2 of 2)	12494	NR_105858	102466172		NR_105858	ENSMUSG00000098300	Mir6540	Gm27780|mir-6540|mmu-mir-6540	microRNA 6540	ncRNA
mm_172430.1	chr7	28961153	28961154	-	1	NA	intron (NM_021895, intron 1 of 20)	intron (NM_021895, intron 1 of 20)	1127	NM_021895	60595	Mm.81144	NM_021895	ENSMUSG00000054808	Actn4	C77391	actinin alpha 4	protein-coding
mm_93185.1	chr10	93889610	93889619	-	1	NA	exon (NM_019648, exon 2 of 12)	exon (NM_019648, exon 2 of 12)	1588	NM_019648	56307	Mm.289329	NM_019648	ENSMUSG00000036112	Metap2	4930584B20Rik|A930035J23Rik|AI047573|AL024412|AU014659|Amp2|Mnpep|p67|p67eIF2	methionine aminopeptidase 2	protein-coding
mm_128580.1	chr15	58034209	58034224	-	1	NA	promoter-TSS (NM_029418)	promoter-TSS (NM_029418)	78	NM_029418	75758	Mm.455792	NM_029418	ENSMUSG00000101892	9130401M01Rik	AI849328	RIKEN cDNA 9130401M01 gene	protein-coding
mm_118853.1	chr14	25707365	25707399	+	1	NA	Intergenic	Intergenic	-6100	NR_028021	68173	Mm.444727	NM_026595		Ppifos	4930520F12Rik|Ppifs	peptidylprolyl isomerase F, opposite strand	ncRNA
mm_134053.1	chr16	5445868	5445877	-	1	NA	Intergenic	Intergenic	-189916	NM_027446	70511	Mm.45780	NM_027446	ENSMUSG00000022544	Eef2kmt	5730409G15Rik|Fam86|Fam86a|eEF2-KMT	eukaryotic elongation factor 2 lysine methyltransferase	protein-coding
mm_76531.1	chr8	87804412	87804463	-	1	NA	promoter-TSS (NM_001310520)	promoter-TSS (NM_001310520)	2	NM_001310520	94187	Mm.23452	NM_033327	ENSMUSG00000045333	Zfp423	Ebfaz|Roaz|Zfp104|Znf423|ataxia1|mKIAA0760|nur12	zinc finger protein 423	protein-coding
mm_141971.1	chr17	35135462	35135472	-	1	NA	promoter-TSS (NM_001252469)	promoter-TSS (NM_001252469)	-247	NM_001252469	224727	Mm.203962	NM_057171	ENSMUSG00000024392	Bag6	2410045D21Rik|AA408914|BAG-6|Bat3|D17H6S52E|G3|Scythe	BCL2-associated athanogene 6	protein-coding
mm_9678.1	chr1	178332122	178332140	-	1	NA	exon (NM_016805, exon 7 of 14)	exon (NM_016805, exon 7 of 14)	5653	NM_016805	51810	Mm.86589	NM_016805	ENSMUSG00000039630	Hnrnpu	AA408410|AI256620|AL024194|AL024437|AW557595|C86794|Hnrpu|SAFA|Sp120|hnRNP U	heterogeneous nuclear ribonucleoprotein U	protein-coding
mm_50938.1	chr6	57703379	57703445	+	1	NA	intron (NM_133737, intron 1 of 8)	intron (NM_133737, intron 1 of 8)	957	NM_133737	71835	Mm.274904	NM_133737	ENSMUSG00000062190	Lancl2	1700003F10Rik	LanC (bacterial lantibiotic synthetase component C)-like 2	protein-coding
mm_156414.1	chrX	140664832	140664850	+	1	NA	Intergenic	CpG	-13187	NM_011845	23947	Mm.131097	NM_011845	ENSMUSG00000000266	Mid2	FXY2|Trim1	midline 2	protein-coding
mm_60227.1	chr7	43580067	43580097	+	1	NA	intron (NM_172482, intron 1 of 3)	intron (NM_172482, intron 1 of 3)	496	NM_172482	210105	Mm.234422	NM_172482	ENSMUSG00000030469	Zfp719	8030458J18|9430094P17Rik|C630016O21Rik|mszf6	zinc finger protein 719	protein-coding
mm_24440.1	chr3	90600238	90600247	+	1	NA	promoter-TSS (NM_011310)	promoter-TSS (NM_011310)	27	NM_011310	20197	Mm.440044	NM_011310	ENSMUSG00000001021	S100a3	S100E	S100 calcium binding protein A3	protein-coding
mm_152863.1	chr19	24224925	24224946	-	1	NA	promoter-TSS (NM_011597)	promoter-TSS (NM_011597)	91	NM_011597	21873	Mm.104744	NM_011597	ENSMUSG00000024812	Tjp2	ZO-2	tight junction protein 2	protein-coding
mm_101117.1	chr11	12004319	12004322	-	1	NA	intron (NM_010345, intron 1 of 16)	intron (NM_010345, intron 1 of 16)	23651	NM_001177629	14783	Mm.273117	NM_010345	ENSMUSG00000020176	Grb10	5730571D09Rik|AI325020|Meg1|mKIAA0207	growth factor receptor bound protein 10	protein-coding
mm_31477.1	chr4	51229778	51229782	+	1	NA	exon (NM_001162865, exon 5 of 5)	exon (NM_001162865, exon 5 of 5)	13102	NM_001162865	74914	Mm.159368	NM_001162865	ENSMUSG00000039555	Cylc2	4930488P18Rik	cylicin, basic protein of sperm head cytoskeleton 2	protein-coding
mm_46423.1	chr5	104113778	104113788	-	1	NA	5' UTR (NM_010097, exon 1 of 11)	5' UTR (NM_010097, exon 1 of 11)	305	NM_010097	13602	Mm.29027	NM_010097	ENSMUSG00000029309	Sparcl1	Ecm2|Sc1|hevin|mast9	SPARC-like 1	protein-coding
mm_106588.1	chr11	120729733	120729750	-	1	NA	exon (NM_007621, exon 8 of 8)	exon (NM_007621, exon 8 of 8)	2280	NM_007621	12409	Mm.21454	NM_007621	ENSMUSG00000025150	Cbr2	MLCR	carbonyl reductase 2	protein-coding
mm_27917.1	chr3	79531794	79531804	-	1	NA	intron (NM_001162999, intron 1 of 16)	intron (NM_001162999, intron 1 of 16)	35880	NM_001162999	329679	Mm.244005	NM_001162999	ENSMUSG00000061175	Fnip2	D630023B12Rik|mKIAA1450	folliculin interacting protein 2	protein-coding
mm_101609.1	chr11	35798537	35798612	-	1	NA	5' UTR (NM_001004147, exon 1 of 1)	5' UTR (NM_001004147, exon 1 of 1)	310	NM_001004147	237730	Mm.189222	NM_001004147	ENSMUSG00000051062	Fbll1	AI595406	fibrillarin-like 1	protein-coding
mm_61923.1	chr7	90160491	90160515	+	1	NA	exon (NM_001252521, exon 2 of 20)	exon (NM_001252521, exon 2 of 20)	30271	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_54140.1	chr6	21858165	21858183	-	1	NA	Intergenic	Intergenic	-5659	NM_173007	269831	Mm.21950	NM_173007	ENSMUSG00000029669	Tspan12	9030619E17|AI426782|AI663988|AW111457|Tm4sf12	tetraspanin 12	protein-coding
mm_58357.1	chr6	148211997	148212059	-	1	NA	promoter-TSS (NR_015615)	promoter-TSS (NR_015615)	-260	NR_015615	320737	Mm.137858	NR_015615		4732416N19Rik	-	RIKEN cDNA 4732416N19 gene	ncRNA
mm_30965.1	chr4	33926376	33926384	+	1	NA	intron (NM_007726, intron 1 of 1)	intron (NM_007726, intron 1 of 1)	1748	NM_007726	12801	Mm.7992	NM_007726	ENSMUSG00000044288	Cnr1	CB-R|CB1|CB1R	cannabinoid receptor 1 (brain)	protein-coding
mm_144715.1	chr18	35118881	35118903	+	1	NA	promoter-TSS (NM_009818)	promoter-TSS (NM_009818)	-20	NM_009818	12385	Mm.18962	NM_009818	ENSMUSG00000037815	Ctnna1	2010010M04Rik|AA517462|AI988031|Catna1	catenin (cadherin associated protein), alpha 1	protein-coding
mm_142067.1	chr17	35688990	35689031	-	1	NA	intron (NM_001198831, intron 8 of 17)	intron (NM_001198831, intron 8 of 17)	11580	NM_001198833	12305	Mm.5021	NM_007584	ENSMUSG00000003534	Ddr1	6030432F18|AI323681|CD167a|Cak|Nep|PTK3A	discoidin domain receptor family, member 1	protein-coding
mm_167534.1	chr9	21291414	21291431	-	1	NA	promoter-TSS (NM_009878)	promoter-TSS (NM_009878)	-213	NM_009878	12581	Mm.29020	NM_009878	ENSMUSG00000096472	Cdkn2d	INK4d|p19|p19INK4d	cyclin-dependent kinase inhibitor 2D (p19, inhibits CDK4)	protein-coding
mm_146131.1	chr18	74625527	74625560	+	1	NA	intron (NM_201600, intron 5 of 38)	intron (NM_201600, intron 5 of 38)	-94419	NR_045368	73606	Mm.444734	NR_045368		1700120E14Rik	-	RIKEN cDNA 1700120E14 gene	ncRNA
mm_138754.1	chr17	37049967	37049985	+	1	NA	intron (NM_019439, intron 5 of 22)	intron (NM_019439, intron 5 of 22)	4010	NM_019439	54393	Mm.32191	NM_019439	ENSMUSG00000024462	Gabbr1	GABAB1|GABAbR1|bM573K1.1	gamma-aminobutyric acid (GABA) B receptor, 1	protein-coding
mm_12655.1	chr2	75138969	75138991	+	1	NA	Intergenic	Intergenic	305199	NR_040635	77269	Mm.389278	NR_040635		9430019J16Rik	-	RIKEN cDNA 9430019J16 gene	ncRNA
mm_183.1	chr1	15067004	15067042	+	1	NA	Intergenic	Lx|LINE|L1	-148161	NM_177781	277328	Mm.186329	NM_177781	ENSMUSG00000032769	Trpa1	Anktm1|TRPA1b	transient receptor potential cation channel, subfamily A, member 1	protein-coding
mm_19245.1	chr2	84743693	84743701	-	1	NA	Intergenic	Intergenic	-2519	NR_029544	387149		NR_029544	ENSMUSG00000065484	Mir130a	Mirn130|Mirn130a|mir-130a	microRNA 130a	ncRNA
mm_54574.1	chr6	38097032	38097041	-	1	NA	intron (NM_080467, intron 1 of 20)	intron (NM_080467, intron 1 of 20)	-12317	NM_029921	77522	Mm.387207	NM_029921	ENSMUSG00000029829	Tmem213	D630002J15Rik	transmembrane protein 213	protein-coding
mm_12668.1	chr2	75704852	75704880	+	1	NA	promoter-TSS (NM_010902)	promoter-TSS (NM_010902)	-203	NM_010902	18024	Mm.1025	NM_010902	ENSMUSG00000015839	Nfe2l2	Nrf2	nuclear factor, erythroid derived 2, like 2	protein-coding
mm_7748.1	chr1	131094974	131094985	-	1	NA	intron (NM_008551, intron 1 of 9)	B3A|SINE|B2	2864	NM_008551	17164	Mm.221235	NM_008551	ENSMUSG00000016528	Mapkapk2	AA960234|MAPKAP-K2|MK-2|MK2|Rps6kc1	MAP kinase-activated protein kinase 2	protein-coding
mm_19422.1	chr2	91931676	91931686	-	1	NA	promoter-TSS (NM_001291481)	promoter-TSS (NM_001291481)	21	NM_001291481	17242	Mm.906	NM_010784	ENSMUSG00000027239	Mdk	MK|Mek	midkine	protein-coding
mm_135484.1	chr16	46010263	46010284	-	1	NA	5' UTR (NM_001134480, exon 1 of 4)	5' UTR (NM_001134480, exon 1 of 4)	140	NM_001134480	433022	Mm.380993	NM_001134480	ENSMUSG00000087141	Plcxd2	AW494639|EG433022	phosphatidylinositol-specific phospholipase C, X domain containing 2	protein-coding
mm_71899.1	chr8	70042769	70042837	+	1	NA	promoter-TSS (NM_027481)	promoter-TSS (NM_027481)	-10	NM_027481	70616	Mm.17665	NM_027481	ENSMUSG00000011306	Sugp1	5730496N02Rik|Sf4	SURP and G patch domain containing 1	protein-coding
mm_37849.1	chr4	132206440	132206443	-	1	NA	intron (NM_145393, intron 3 of 4)	intron (NM_145393, intron 3 of 4)	5815	NM_145393	213541	Mm.23998	NM_145393	ENSMUSG00000040025	Ythdf2	9430020E02Rik|HGRG8|NY-REN-2	YTH domain family 2	protein-coding
mm_123268.1	chr14	61360375	61360385	-	1	NA	promoter-TSS (NM_026598)	promoter-TSS (NM_026598)	65	NM_026598	68177	Mm.22758	NM_026598	ENSMUSG00000021928	Ebpl	5730442K12Rik|EBRP	emopamil binding protein-like	protein-coding
mm_38467.1	chr4	140648717	140648729	-	1	NA	promoter-TSS (NM_172415)	promoter-TSS (NM_172415)	33	NM_001112723	72754	Mm.29329	NM_172415	ENSMUSG00000040964	Arhgef10l	2810441C07Rik	Rho guanine nucleotide exchange factor (GEF) 10-like	protein-coding
mm_107883.1	chr12	70154125	70154157	+	1	NA	promoter-TSS (NM_001195033)	promoter-TSS (NM_001195033)	-30	NM_001195033	100504285	Mm.291105	NM_001195033	ENSMUSG00000090121	Abhd12b	Gm804	abhydrolase domain containing 12B	protein-coding
mm_150254.1	chr19	34192271	34192290	+	1	NA	promoter-TSS (NM_029682)	promoter-TSS (NM_029682)	10	NM_029682	76630	Mm.130952	NM_029682	ENSMUSG00000024776	Stambpl1	1700095N21Rik|8230401J17Rik|ALMalpha|AMSH-FP	STAM binding protein like 1	protein-coding
mm_73922.1	chr8	119810046	119810073	+	1	NA	3' UTR (NM_028071, exon 4 of 4)	3' UTR (NM_028071, exon 4 of 4)	30520	NM_028071	72042	Mm.393405	NM_028071	ENSMUSG00000031827	Cotl1	1810074P22Rik|2010004C08Rik|Clp	coactosin-like 1 (Dictyostelium)	protein-coding
mm_130347.1	chr15	97748553	97748579	-	1	NA	intron (NM_144850, intron 24 of 27)	intron (NM_144850, intron 24 of 27)	-17161	NM_001168693	19011	Mm.1001	NM_008902	ENSMUSG00000022468	Endou	Pp11r|Tcl-30	endonuclease, polyU-specific	protein-coding
mm_72322.1	chr8	78509320	78509399	+	1	NA	promoter-TSS (NM_001282108)	promoter-TSS (NM_001282108)	31	NM_001282108	76775	Mm.334631	NM_029736	ENSMUSG00000031684	Slc10a7	2410193C02Rik|P7	solute carrier family 10 (sodium/bile acid cotransporter family), member 7	protein-coding
mm_103543.1	chr11	77519187	77519218	-	1	NA	3' UTR (NM_026185, exon 2 of 2)	3' UTR (NM_026185, exon 2 of 2)	4085	NM_026185	67477	Mm.432526	NM_026185	ENSMUSG00000000686	Abhd15	1300007F04Rik	abhydrolase domain containing 15	protein-coding
mm_167990.1	chrX	170009683	170009710	+	1	NA	Intergenic	CpG	-30779	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_164433.1	chr16	48872432	48872448	-	1	NA	promoter-TSS (NM_181596)	promoter-TSS (NM_181596)	-168	NM_181596	245195	Mm.231288	NM_181596	ENSMUSG00000022651	Retnlg	Fizz3|Relmg|Xcp1	resistin like gamma	protein-coding
mm_139483.1	chr17	56040425	56040445	+	1	NA	promoter-TSS (NM_013733)	promoter-TSS (NM_013733)	19	NM_013733	27221	Mm.391010	NM_013733	ENSMUSG00000002835	Chaf1a	AL023013|AL024058|CAF-1|Cac1p	chromatin assembly factor 1, subunit A (p150)	protein-coding
mm_156971.1	chrX	169997510	169997531	+	1	NA	Intergenic	CpG	-18603	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_96903.1	chr11	70455764	70455818	+	1	NA	exon (NM_023158, exon 4 of 5)	exon (NM_023158, exon 4 of 5)	-3831	NM_001029929	574428	Mm.472771	NM_001029929	ENSMUSG00000040829	Zmynd15	-	zinc finger, MYND-type containing 15	protein-coding
mm_170586.1	chr19	5799090	5799091	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	-3109	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_155927.1	chrX	103447713	103447735	+	1	NA	non-coding (NR_002844, exon 2 of 4)	non-coding (NR_002844, exon 2 of 4)	16207	NR_002844	22097	Mm.472939	NR_002844	ENSMUSG00000085715	Tsix	-	X (inactive)-specific transcript, opposite strand	ncRNA
mm_84875.1	chr9	79718613	79718620	-	1	NA	5' UTR (NM_001290308, exon 1 of 66)	5' UTR (NM_001290308, exon 1 of 66)	106	NM_001290308	12816	Mm.3819	NM_007730	ENSMUSG00000032332	Col12a1	-	collagen, type XII, alpha 1	protein-coding
mm_107321.1	chr12	31390844	31390850	+	1	NA	Intergenic	L2a|LINE|L2	-39376	NM_007861	13382	Mm.3131	NM_007861	ENSMUSG00000020664	Dld	-	dihydrolipoamide dehydrogenase	protein-coding
mm_115459.1	chr13	119428417	119428446	+	1	NA	promoter-TSS (NM_001079849)	promoter-TSS (NM_001079849)	-169	NM_001079849	218693	Mm.490243	NM_145457	ENSMUSG00000025451	Paip1	PAIP-1	polyadenylate binding protein-interacting protein 1	protein-coding
mm_141772.1	chr17	34283767	34283785	-	1	NA	exon (NM_010378, exon 3 of 5)	exon (NM_010378, exon 3 of 5)	3995	NM_010378	14960	Mm.235338	NM_010378	ENSMUSG00000036594	H2-Aa	Aalpha|H-2Aa|H2Aa|I-Aalpha|IAalpha|Ia-1|Ia1	histocompatibility 2, class II antigen A, alpha	protein-coding
mm_161544.1	chr16	3838922	3838922	+	1	NA	promoter-TSS (NM_008762)	promoter-TSS (NM_008762)	-53	NM_008762	18312	Mm.377102	NM_008762	ENSMUSG00000059043	Olfr15	MOR256-17|OR3	olfactory receptor 15	protein-coding
mm_80123.1	chr9	70576770	70576795	+	1	NA	exon (NM_025690, exon 9 of 21)	exon (NM_025690, exon 9 of 21)	33912	NM_025690	66660	Mm.22379	NM_025690	ENSMUSG00000032212	Sltm	5730455C01Rik|5730555F13Rik|9130215G10Rik|Met	SAFB-like, transcription modulator	protein-coding
mm_2077.1	chr1	87653314	87653326	+	1	NA	intron (NM_010566, intron 2 of 26)	intron (NM_010566, intron 2 of 26)	33008	NM_001110193	16331	Mm.15105	NM_010566	ENSMUSG00000026288	Inpp5d	SHIP|SHIP-1|SHIP1|SIP-145|p150Ship|s-SHIP	inositol polyphosphate-5-phosphatase D	protein-coding
mm_170865.1	chr2	18453654	18453655	+	1	NA	Intergenic	RLTR9E|LTR|ERVK	-60824	NM_007869	13418	Mm.246674	NM_007869	ENSMUSG00000026740	Dnajc1	4733401K02Rik|AA960110|D230036H06Rik|Dnajl1|ERdj1|ERj1p|MTJ1	DnaJ heat shock protein family (Hsp40) member C1	protein-coding
mm_146587.1	chr18	9282719	9282739	-	1	NA	promoter-TSS (NM_153086)	promoter-TSS (NM_153086)	80	NM_153086	225152	Mm.119273	NM_153086	ENSMUSG00000036855	Gjd4	9430022F06Rik|Cx39	gap junction protein, delta 4	protein-coding
mm_100197.1	chr11	116752934	116752938	+	1	NA	intron (NR_003364, intron 1 of 3)	intron (NR_003364, intron 1 of 3)	769	NR_003364	193217	Mm.100084	NR_003364		BC018473	-	cDNA sequence BC018473	ncRNA
mm_10559.1	chr2	17559055	17559065	+	1	NA	intron (NM_028757, intron 3 of 6)	intron (NM_028757, intron 3 of 6)	-4454	NR_105847	102465964		NR_105847	ENSMUSG00000099161	Mir6419	Gm27713|mmu-mir-6419	microRNA 6419	ncRNA
mm_73481.1	chr8	107031032	107031035	+	1	NA	promoter-TSS (NM_126165)	promoter-TSS (NM_126165)	-293	NM_126165	116733	Mm.236004	NM_126165	ENSMUSG00000031913	Vps4a	4930589C15Rik|AI325971|AW553189	vacuolar protein sorting 4A	protein-coding
mm_86878.1	chr10	21997122	21997135	+	1	NA	intron (NM_001161848, intron 8 of 11)	intron (NM_001161848, intron 8 of 11)	2462	NM_011361	20393	Mm.28405	NM_011361	ENSMUSG00000019970	Sgk1	Sgk	serum/glucocorticoid regulated kinase 1	protein-coding
mm_120625.1	chr14	70457590	70457596	+	1	NA	promoter-TSS (NM_145981)	promoter-TSS (NM_145981)	76	NM_145981	105653	Mm.192598	NM_145981	ENSMUSG00000003469	Phyhip	AW049870|C630010D02Rik|Lnap1ip|PAHX-AP#1|PAHX-AP1	phytanoyl-CoA hydroxylase interacting protein	protein-coding
mm_171055.1	chr3	104753289	104753302	-	1	NA	Intergenic	CpG	24252	NM_183224	329731	Mm.389494	NM_183224	ENSMUSG00000055865	Fam19a3	7530404M11Rik|TAFA3|Tafa-3	family with sequence similarity 19, member A3	protein-coding
mm_219.1	chr1	16814250	16814256	+	1	NA	Intergenic	B4A|SINE|B4	125797	NM_016923	17087	Mm.116844	NM_016923	ENSMUSG00000025779	Ly96	ESOP-1|MD-2|MD2	lymphocyte antigen 96	protein-coding
mm_110011.1	chr12	16589724	16589735	-	1	NA	promoter-TSS (NM_015763)	promoter-TSS (NM_015763)	41	NM_015763	14245	Mm.153625	NM_015763	ENSMUSG00000020593	Lpin1	4631420P06|Kiaa0188|Lipin1|fld|mKIAA0188	lipin 1	protein-coding
mm_109867.1	chr12	4907601	4907609	-	1	NA	promoter-TSS (NM_145441)	promoter-TSS (NM_145441)	-85	NM_145441	217379	Mm.259170	NM_145441	ENSMUSG00000020634	Ubxn2a	6330407P03Rik|Ubxd4	UBX domain protein 2A	protein-coding
mm_14376.1	chr2	129630576	129630586	+	1	NA	3' UTR (NM_001291022, exon 5 of 5)	3' UTR (NM_001291022, exon 5 of 5)	37412	NM_001291022	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_105065.1	chr11	100720145	100720155	-	1	NA	5' UTR (NM_001305003, exon 2 of 6)	5' UTR (NM_001305003, exon 2 of 6)	6300	NM_029307	75482	Mm.46175	NM_029307	ENSMUSG00000017832	Hspb9	1700007H20Rik	heat shock protein, alpha-crystallin-related, B9	protein-coding
mm_90104.1	chr10	116986652	116986695	+	1	NA	5' UTR (NM_001007583, exon 1 of 10)	5' UTR (NM_001007583, exon 1 of 10)	359	NM_001007583	382427	Mm.339322	NM_001007583	ENSMUSG00000020169	Best3	Vmd2l3|mBest4	bestrophin 3	protein-coding
mm_47091.1	chr5	117399385	117399392	-	1	NA	Intergenic	RMER17C|LTR|ERVK	-10365	NM_028128	72151	Mm.27997	NM_028128	ENSMUSG00000029363	Rfc5	2610020K06Rik|2610209F07Rik|36.5kDa|36kDa|Recc5	replication factor C (activator 1) 5	protein-coding
mm_42547.1	chr5	116058843	116058844	+	1	NA	intron (NM_001101546, intron 1 of 2)	intron (NM_001101546, intron 1 of 2)	24403	NM_001101546	545798	Mm.483995	NM_001101546	ENSMUSG00000079278	Tmem233	DSPB2|Gm13843|OTTMUSG00000014722	transmembrane protein 233	protein-coding
mm_62533.1	chr7	102247744	102247758	+	1	NA	intron (NM_019566, intron 1 of 1)	intron (NM_019566, intron 1 of 1)	2367	NM_019566	56212	Mm.259795	NM_019566	ENSMUSG00000073982	Rhog	2810426G09Rik|Arhg|Sid10750	ras homolog family member G	protein-coding
mm_143269.1	chr17	65642189	65642206	-	1	NA	promoter-TSS (NM_001146002)	promoter-TSS (NM_001146002)	7	NM_001146002	213272	Mm.255732	NM_153519	ENSMUSG00000050612	Txndc2	AU021712|Sptrx-1|Sptrx1|Trx4	thioredoxin domain containing 2 (spermatozoa)	protein-coding
mm_72648.1	chr8	84723004	84723022	+	1	NA	intron (NM_001297601, intron 6 of 8)	intron (NM_001297601, intron 6 of 8)	21556	NM_008535	17095	Mm.4925	NM_008535	ENSMUSG00000034041	Lyl1	Lyl-1|bHLHa18	lymphoblastomic leukemia 1	protein-coding
mm_93712.1	chr10	118869127	118869154	-	1	NA	promoter-TSS (NM_001014390)	promoter-TSS (NM_001014390)	-237	NM_001014390	69181	Mm.45565	NM_001014390	ENSMUSG00000028630	Dyrk2	1810038L18Rik	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 2	protein-coding
mm_157155.1	chrX	9463467	9463478	-	1	NA	intron (NM_007807, intron 3 of 12)	ID4|SINE|ID	5852	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_118701.1	chr14	22159084	22159095	+	1	NA	intron (NM_028275, intron 2 of 6)	B4|SINE|B4	139377	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_132249.1	chr16	32751379	32751391	+	1	NA	exon (NM_080457, exon 2 of 27)	exon (NM_080457, exon 2 of 27)	15499	NM_080457	140474	Mm.214599	NM_080457	ENSMUSG00000079620	Muc4	4933405I11Rik|Asgp	mucin 4	protein-coding
mm_77509.1	chr8	122892833	122892854	-	1	NA	non-coding (NR_037865, exon 10 of 14)	non-coding (NR_037865, exon 10 of 14)	44469	NM_007662	12555	Mm.1976	NM_007662	ENSMUSG00000031962	Cdh15	AI323380|Cdh14|Mcad	cadherin 15	protein-coding
mm_38111.1	chr4	134535048	134535107	-	1	NA	intron (NM_029759, intron 1 of 6)	CpG	191	NM_001256112	76824	Mm.30153	NM_029759	ENSMUSG00000046671	Mtfr1l	2410166I05Rik|AI480750|Fam54b	mitochondrial fission regulator 1-like	protein-coding
mm_54222.1	chr6	26766886	26766896	-	1	NA	Intergenic	Intergenic	835465	NR_040771	626904	Mm.126787	NR_040771	ENSMUSG00000106799	Gm20756	-	predicted gene, 20756	ncRNA
mm_45830.1	chr5	87694668	87694672	-	1	NA	exon (NM_001286023, exon 5 of 7)	exon (NM_001286023, exon 5 of 7)	4755	NM_001286020	12991	Mm.268737	NM_009972	ENSMUSG00000063157	Csn2	Csnb	casein beta	protein-coding
mm_159239.1	chr2	147085123	147085123	-	1	NA	exon (NM_023504, exon 1 of 2)	exon (NM_023504, exon 1 of 2)	222	NM_023504	228731	Mm.315498	NM_023504	ENSMUSG00000054160	Nkx2-4	1700001P03Rik|Nkx-2.4|tinman	NK2 homeobox 4	protein-coding
mm_170914.1	chr2	3550735	3550753	+	1	NA	Intergenic	Intergenic	27443	NR_030564	100124442		NR_030564	ENSMUSG00000076966	Mir466b-2	Mirn466b-2	microRNA 466b-2	ncRNA
mm_14154.1	chr2	126576800	126576810	+	1	NA	intron (NM_011978, intron 5 of 9)	intron (NM_011978, intron 5 of 9)	23781	NM_011978	26458	Mm.290044	NM_011978	ENSMUSG00000027359	Slc27a2	ACSVL1|FATP2|VLCS|Vlac|Vlacs	solute carrier family 27 (fatty acid transporter), member 2	protein-coding
mm_171184.1	chr3	37481706	37481725	+	1	NA	intron (NM_001310473, intron 14 of 16)	LSU-rRNA_Hsa|rRNA|rRNA	61765	NM_021343	57815	Mm.172679	NM_021343	ENSMUSG00000027722	Spata5	2510048F20Rik|C78064|Spaf	spermatogenesis associated 5	protein-coding
mm_95215.1	chr11	43682067	43682089	+	1	NA	promoter-TSS (NM_001164231)	promoter-TSS (NM_001164231)	80	NM_001164231	70802	Mm.397449	NM_027557	ENSMUSG00000044950	Pwwp2a	4631424J17Rik|AI891583|AU024105|D930040F23Rik	PWWP domain containing 2A	protein-coding
mm_163108.1	chr11	69966875	69966875	+	1	NA	intron (NM_016887, intron 1 of 3)	intron (NM_016887, intron 1 of 3)	1454	NM_016887	53624	Mm.281896	NM_016887	ENSMUSG00000018569	Cldn7	-	claudin 7	protein-coding
mm_134864.1	chr16	28500159	28500162	-	1	NA	intron (NM_010199, intron 2 of 5)	intron (NM_010199, intron 2 of 5)	-54085	NM_001276420	14167	Mm.7996	NM_010199	ENSMUSG00000022523	Fgf12	AV114868|B230343J05Rik|FGF-12|FHF-1|Fhf1	fibroblast growth factor 12	protein-coding
mm_33009.1	chr4	120667160	120667172	+	1	NA	exon (NM_019563, exon 1 of 1)	exon (NM_019563, exon 1 of 1)	603	NM_019563	56222	Mm.272646	NM_019563	ENSMUSG00000070803	Cited4	MRG-2|Mrg2	Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 4	protein-coding
mm_5360.1	chr1	25829648	25829651	-	1	NA	promoter-TSS (NM_175642)	promoter-TSS (NM_175642)	58	NM_175642	210933	Mm.336569	NM_175642	ENSMUSG00000033569	Adgrb3	A830096D10Rik|Bai3	adhesion G protein-coupled receptor B3	protein-coding
mm_52960.1	chr6	123123424	123123484	+	1	NA	5' UTR (NM_001170333, exon 1 of 7)	5' UTR (NM_001170333, exon 1 of 7)	138	NM_001170333	26888	Mm.47384	NM_011999	ENSMUSG00000030148	Clec4a2	Clec4a|Clecsf6|DCIR|Dcir1	C-type lectin domain family 4, member a2	protein-coding
mm_170306.1	chr18	34951382	34951401	-	1	NA	exon (NM_010481, exon 4 of 17)	exon (NM_010481, exon 4 of 17)	2960	NM_010481	15526	Mm.209419	NM_010481	ENSMUSG00000024359	Hspa9	74kDa|Csa|Grp75|Hsc74|Hsp74|Hsp74a|Hspa9a|Mortalin|Mot-2|Mot2|Mthsp70|Pbp74	heat shock protein 9	protein-coding
mm_112786.1	chr13	20184941	20184989	+	1	NA	intron (NM_080288, intron 1 of 21)	intron (NM_080288, intron 1 of 21)	94458	NM_080288	140580	Mm.342392	NM_080288	ENSMUSG00000041112	Elmo1	6330578D22Rik|C230095H21Rik|CED-12	engulfment and cell motility 1	protein-coding
mm_79475.1	chr9	56937813	56937840	+	1	NA	exon (NM_133976, exon 1 of 1)	exon (NM_133976, exon 1 of 1)	326	NM_133976	102462	Mm.12864	NM_133976	ENSMUSG00000032288	Imp3	1190002L16Rik|AI256594	IMP3, U3 small nucleolar ribonucleoprotein	protein-coding
mm_38629.1	chr4	142170999	142171038	-	1	NA	intron (NM_144531, intron 1 of 13)	intron (NM_144531, intron 1 of 13)	39190	NM_144531	71529	Mm.255986	NM_144531	ENSMUSG00000040606	Kazn	2310007B04Rik|9030409G11Rik|AI256607|AI666764|AW061099|Kaz|Kazrin	kazrin, periplakin interacting protein	protein-coding
mm_78960.1	chr9	45189988	45189991	+	1	NA	intron (NM_145403, intron 2 of 12)	intron (NM_145403, intron 2 of 12)	-5777	NM_001198971	408059	Mm.249297	NM_001198971	ENSMUSG00000091996	BC049352	-	cDNA sequence BC049352	protein-coding
mm_9005.1	chr1	165849040	165849050	-	1	NA	intron (NM_001113391, intron 1 of 7)	intron (NM_001113391, intron 1 of 7)	60364	NM_001113392	12503	Mm.217308	NM_031162	ENSMUSG00000005763	Cd247	4930549J05Rik|A430104F18Rik|AW552088|Cd3|Cd3-eta|Cd3-zeta|Cd3h|Cd3z|Cd3zeta|T3z|Tcrk|Tcrz	CD247 antigen	protein-coding
mm_95840.1	chr11	57011946	57011946	+	1	NA	5' UTR (NM_001113325, exon 1 of 16)	5' UTR (NM_001113325, exon 1 of 16)	328	NM_008165	14799	Mm.4920	NM_008165	ENSMUSG00000020524	Gria1	2900051M01Rik|Glr-1|Glr1|GluA1|GluR-A|GluRA|Glur-1|Glur1|HIPA1|gluR-K1	glutamate receptor, ionotropic, AMPA1 (alpha 1)	protein-coding
mm_155006.1	chrX	41400806	41400833	+	1	NA	promoter-TSS (NM_001290451)	promoter-TSS (NM_001290451)	-482	NM_016886	53623	Mm.327681	NM_016886	ENSMUSG00000001986	Gria3	2900064I19Rik|GluA3|GluR-C|GluR-K3|Glur-3|Glur3|Gluralpha3	glutamate receptor, ionotropic, AMPA3 (alpha 3)	protein-coding
mm_117894.1	chr13	99423571	99423593	-	1	NA	3' UTR (NM_008634, exon 7 of 7)	3' UTR (NM_008634, exon 7 of 7)	-10756	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_172884.1	chr9	50984126	50984141	-	1	NA	intron (NM_178710, intron 3 of 15)	MTB|LTR|ERVL-MaLR	24940	NM_178710	235344	Mm.104932	NM_178710	ENSMUSG00000037112	Sik2	G630080D20Rik|Snf1lk2	salt inducible kinase 2	protein-coding
mm_60319.1	chr7	44216333	44216382	+	1	NA	promoter-TSS (NM_008456)	promoter-TSS (NM_008456)	-117	NM_008456	16622	Mm.443373	NM_008456	ENSMUSG00000066512	Klk1b5	Klk5|kallikrein|mGK-5	kallikrein 1-related peptidase b5	protein-coding
mm_118168.1	chr13	105299289	105299291	-	1	NA	Intergenic	Intergenic	-6276	NM_027934	71816	Mm.317015	NM_027934	ENSMUSG00000021720	Rnf180	3110001E11Rik|Rines	ring finger protein 180	protein-coding
mm_71301.1	chr8	41265671	41265681	+	1	NA	intron (NM_023662, intron 5 of 37)	intron (NM_023662, intron 5 of 37)	25917	NM_023662	18536	Mm.117896	NM_023662	ENSMUSG00000031592	Pcm1	2600002H09Rik|9430077F19Rik|C030044G17Rik	pericentriolar material 1	protein-coding
mm_172484.1	chr7	5159295	5159296	+	1	NA	Intergenic	L1Md_T|LINE|L1	-11873	NM_001166706	384522	Mm.480286	NM_001166706	ENSMUSG00000074402	Vmn1r55	Gm1422|Gm403|V1rd5	vomeronasal 1 receptor 55	protein-coding
mm_112560.1	chr13	13275561	13275580	+	1	NA	Intergenic	Intergenic	92854	NM_001311129	107849	Mm.392548	NM_181852	ENSMUSG00000055360	Prl2c5	Ghd3|MRP-4|Mrpplf4|PLF-4	prolactin family 2, subfamily c, member 5	protein-coding
mm_41311.1	chr5	90468669	90468679	+	1	NA	exon (NM_009654, exon 8 of 15)	exon (NM_009654, exon 8 of 15)	7804	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_58562.1	chr7	4742523	4742538	+	1	NA	intron (NM_146177, intron 3 of 8)	MIR3|SINE|MIR	2403	NM_001115018	232811	Mm.247844	NM_146177	ENSMUSG00000059851	Kmt5c	BC024816|Suv4-20h2|Suv420h2	lysine methyltransferase 5C	protein-coding
mm_154044.1	chr19	53944437	53944487	-	1	NA	promoter-TSS (NM_019658)	promoter-TSS (NM_019658)	156	NM_001168505	56392	Mm.228669	NM_019658	ENSMUSG00000024976	Shoc2	AU017287|Sur8|mKIAA0862	soc-2 (suppressor of clear) homolog (C. elegans)	protein-coding
mm_143496.1	chr17	71475478	71475505	-	1	NA	promoter-TSS (NM_028887)	promoter-TSS (NM_028887)	-148	NM_028887	74355	Mm.194450	NM_028887	ENSMUSG00000024054	Smchd1	4931400A14Rik|AW554188|MommeD1|mKIAA0650	SMC hinge domain containing 1	protein-coding
mm_123237.1	chr14	60165931	60165942	-	1	NA	Intergenic	Intergenic	62979	NR_030458	751526		NR_030458	ENSMUSG00000076270	Mir719	Mirn719|mmu-mir-719	microRNA 719	ncRNA
mm_154647.1	chrX	7794331	7794344	+	1	NA	intron (NM_207670, intron 4 of 24)	intron (NM_207670, intron 4 of 24)	4344	NM_207670	54645	Mm.194811	NM_207670	ENSMUSG00000031153	Gripap1	AI854681|DXImx47e|GRASP-1|Sfc10|mKIAA1167	GRIP1 associated protein 1	protein-coding
mm_18349.1	chr2	58160484	58160492	-	1	NA	promoter-TSS (NM_139200)	promoter-TSS (NM_139200)	-366	NM_139200	227929	Mm.273905	NM_139200	ENSMUSG00000026832	Cytip	A130053M09Rik|AI462064|C80816|Cbp|Cybr|Pscdbp	cytohesin 1 interacting protein	protein-coding
mm_149142.1	chr19	9004040	9004052	+	1	NA	exon (NM_009643, exon 5 of 5)	exon (NM_009643, exon 5 of 5)	-13858	NR_105786	102465190		NR_105786	ENSMUSG00000099308	Mir6367	Gm27467|mmu-mir-6367	microRNA 6367	ncRNA
mm_62965.1	chr7	119794022	119794045	+	1	NA	promoter-TSS (NM_028129)	promoter-TSS (NM_028129)	25	NM_027698	71151	Mm.274160	NM_027698	ENSMUSG00000030929	Eri2	4933424N09Rik|Exod1|mKIAA1504	exoribonuclease 2	protein-coding
mm_75767.1	chr8	69974348	69974364	-	1	NA	promoter-TSS (NM_001113346)	promoter-TSS (NM_001113346)	27	NM_001113346	234366	Mm.270044	NM_145596	ENSMUSG00000036180	Gatad2a	1110066C11Rik|BC031407|C80248	GATA zinc finger domain containing 2A	protein-coding
mm_90376.1	chr10	127195241	127195298	+	1	NA	promoter-TSS (NR_045716)	promoter-TSS (NR_045716)	20	NR_045716	100038591	Mm.441071	NR_045715	ENSMUSG00000097331	F420014N23Rik	ENSMUSG00000074658	RIKEN cDNA F420014N23 gene	ncRNA
mm_166831.1	chr7	18727022	18727043	+	1	NA	3' UTR (NM_001004152, exon 5 of 5)	3' UTR (NM_001004152, exon 5 of 5)	8942	NM_001004152	243862	Mm.389833	NM_001004152	ENSMUSG00000044903	Psg22	AA408604|cea9	pregnancy-specific glycoprotein 22	protein-coding
mm_89433.1	chr10	91097130	91097140	+	1	NA	3' UTR (NM_026166, exon 3 of 3)	3' UTR (NM_026166, exon 3 of 3)	14096	NM_026166	67454	Mm.252843	NM_026166	ENSMUSG00000019975	Ikbip	1200009F10Rik|1700023M03Rik|D18354|Ikip	IKBKB interacting protein	protein-coding
mm_3575.1	chr1	150847354	150847354	+	1	NA	intron (NM_001024720, intron 4 of 106)	intron (NM_001024720, intron 4 of 106)	146081	NM_001024720	545370	Mm.379425	NM_001024720	ENSMUSG00000066842	Hmcn1	EG545370|FIBL-6|Gm201	hemicentin 1	protein-coding
mm_10639.1	chr2	20519777	20519835	+	1	NA	5' UTR (NM_178059, exon 2 of 19)	5' UTR (NM_178059, exon 2 of 19)	293	NM_001177631	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding
mm_126911.1	chr15	90303467	90303469	+	1	NA	Intergenic	Intergenic	79108	NR_106106	102466838		NR_106106	ENSMUSG00000099319	Mir7648	Gm27736|mmu-mir-7648	microRNA 7648	ncRNA
mm_125959.1	chr15	76266556	76266576	+	1	NA	TTS (NR_045747)	TTS (NR_045747)	-1523	NM_028852	74281	Mm.159156	NM_028852	ENSMUSG00000049653	Spatc1	1700084J23Rik|speriolin	spermatogenesis and centriole associated 1	protein-coding
mm_152826.1	chr19	23136782	23136785	-	1	NA	Intergenic	Intergenic	-4443	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_73800.1	chr8	117275118	117275132	+	1	NA	intron (NM_001163262, intron 1 of 20)	intron (NM_001163262, intron 1 of 20)	18106	NM_001163262	74440	Mm.233181	NM_028941	ENSMUSG00000034390	Cmip	4933407C03Rik|5830471E12Rik|AI314065|AI464126	c-Maf inducing protein	protein-coding
mm_107391.1	chr12	33314290	33314328	+	1	NA	intron (NM_001033436, intron 1 of 7)	intron (NM_001033436, intron 1 of 7)	11794	NM_001033436	380753	Mm.41540	NM_028139	ENSMUSG00000020564	Atxn7l1	2810423G08Rik|Atxn7l4	ataxin 7-like 1	protein-coding
mm_165526.1	chr2	177764031	177764032	+	1	NA	intron (NM_001243903, intron 2 of 4)	intron (NM_001243903, intron 2 of 4)	4743	NM_001324422	626802	Mm.386029	NM_001243903	ENSMUSG00000078864	Gm14322	OTTMUSG00000016321	predicted gene 14322	protein-coding
mm_134347.1	chr16	16571434	16571445	-	1	NA	intron (NM_001301817, intron 1 of 16)	intron (NM_001301817, intron 1 of 16)	-11220	NM_139232	224014	Mm.256131	NM_139232	ENSMUSG00000022788	Fgd4	9030023J02Rik|9330209B17Rik|Frabp|ZFYVE6	FYVE, RhoGEF and PH domain containing 4	protein-coding
mm_132579.1	chr16	38346987	38347050	+	1	NA	promoter-TSS (NM_001017429)	promoter-TSS (NM_001017429)	19	NM_001017429	12856	Mm.27396	NM_001017429	ENSMUSG00000046516	Cox17	AI037035	cytochrome c oxidase assembly protein 17	protein-coding
mm_4697.1	chr1	180749908	180749931	+	1	NA	intron (NM_133225, intron 7 of 7)	intron (NM_133225, intron 7 of 7)	23876	NM_133225	170760	Mm.272981	NM_133225	ENSMUSG00000026499	Acbd3	60kDa|8430407O11Rik|D1Ertd10e|GCP60|GOLPH1|Gocap1|Pap7	acyl-Coenzyme A binding domain containing 3	protein-coding
mm_30011.1	chr3	135665083	135665090	-	1	NA	intron (NM_008689, intron 3 of 24)	(TG)n|Simple_repeat|Simple_repeat	26461	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_171235.1	chr3	68902864	68902864	-	1	NA	intron (NM_026641, intron 18 of 19)	intron (NM_026641, intron 18 of 19)	33278	NM_001167996	68725	Mm.45741	NM_001167996	ENSMUSG00000046999	1110032F04Rik	AI115547	RIKEN cDNA 1110032F04 gene	protein-coding
mm_15122.1	chr2	153779228	153779235	+	1	NA	Intergenic	CpG	-1648	NR_036629	100504221	Mm.246778	NM_177849	ENSMUSG00000044083	Efcab8	A630008I04|EG329541	EF-hand calcium binding domain 8	ncRNA
mm_68930.1	chr7	126494201	126494274	-	1	NA	exon (NM_183020, exon 18 of 23)	exon (NM_183020, exon 18 of 23)	6882	NM_001163713	233870	Mm.197829	NM_172745	ENSMUSG00000073838	Tufm	2300002G02Rik|C76308|C76389|EF-TuMT|EFTU	Tu translation elongation factor, mitochondrial	protein-coding
mm_26848.1	chr3	14767552	14767562	-	1	NA	exon (NM_001083957, exon 6 of 7)	exon (NM_001083957, exon 6 of 7)	10903	NM_001083957	12346	Mm.273195	NM_009799	ENSMUSG00000027556	Car1	AW555628|Ca1|Car-1	carbonic anhydrase 1	protein-coding
mm_55114.1	chr6	50392958	50392978	-	1	NA	intron (NM_001347213, intron 2 of 23)	ORR1C2|LTR|ERVL-MaLR	-10131	NM_027881	71720	Mm.44153	NM_027881	ENSMUSG00000029822	Osbpl3	1200014M06Rik|6720421I08Rik|A530055M08|ORP-3|ORP3|OSBP3	oxysterol binding protein-like 3	protein-coding
mm_59203.1	chr7	24507228	24507240	+	1	NA	non-coding (NR_110958, exon 1 of 3)	non-coding (NR_110958, exon 1 of 3)	147	NR_110958	232969	Mm.181332	NM_146183	ENSMUSG00000064264	Zfp428	2410005H09Rik|AV271806|AW047854|Znf428	zinc finger protein 428	protein-coding
mm_162093.1	chrX	37530465	37530465	+	1	NA	promoter-TSS (NM_001085348)	promoter-TSS (NM_001085348)	-3	NM_001085348	100040016	Mm.455498	NM_001085348	ENSMUSG00000096788	Rhox2e	ENSMUSG00000063709|OTTMUSG00000017141|Rhox2.5|Rhox2d	reproductive homeobox 2E	protein-coding
mm_134372.1	chr16	17132303	17132313	-	1	NA	promoter-TSS (NM_022324)	promoter-TSS (NM_022324)	75	NM_022324	64136	Mm.30222	NM_022324	ENSMUSG00000022769	Sdf2l1	-	stromal cell-derived factor 2-like 1	protein-coding
mm_120497.1	chr14	65981416	65981426	+	1	NA	3' UTR (NM_013492, exon 9 of 9)	3' UTR (NM_013492, exon 9 of 9)	12938	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_149102.1	chr19	8942486	8942514	+	1	NA	TTS (NM_144872)	TTS (NM_144872)	580	NM_011842	23942	Mm.25339	NM_011842	ENSMUSG00000071646	Mta2	AW550797|Mata1l1|Mta1l1|mmta2	metastasis-associated gene family, member 2	protein-coding
mm_11183.1	chr2	28840766	28840778	+	1	NA	promoter-TSS (NM_001166033)	promoter-TSS (NM_001166033)	366	NM_001033294	227674	Mm.44179	NM_001033294	ENSMUSG00000026806	Ddx31	5830444G11Rik|Gm997	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 31	protein-coding
mm_32791.1	chr4	116877238	116877260	+	1	NA	promoter-TSS (NM_001029912)	promoter-TSS (NM_001029912)	-153	NM_001029912	74464	Mm.218946	NM_001029912	ENSMUSG00000033948	Zswim5	4933426E21Rik|AI503093|mKIAA1511	zinc finger SWIM-type containing 5	protein-coding
mm_82058.1	chr9	122682959	122682960	+	1	NA	promoter-TSS (NR_029819)	promoter-TSS (NR_029819)	83	NR_029819	387156		NR_029819	ENSMUSG00000065414	Mir138-1	Mirn138|Mirn138-1|mir-138-1	microRNA 138-1	ncRNA
mm_32435.1	chr4	107200757	107200778	+	1	NA	3' UTR (NM_029565, exon 8 of 8)	3' UTR (NM_029565, exon 8 of 8)	-8413	NM_001081272	546840	Mm.331755	NM_001081272	ENSMUSG00000070877	Ldlrad1	OTTMUSG00000008594	low density lipoprotein receptor class A domain containing 1	protein-coding
mm_35115.1	chr4	10797808	10797814	-	1	NA	promoter-TSS (NR_045185)	promoter-TSS (NR_045185)	-9	NR_045185	73624	Mm.67392	NR_045185	ENSMUSG00000086080	1700123O12Rik	-	RIKEN cDNA 1700123O12 gene	ncRNA
mm_72056.1	chr8	71371634	71371644	+	1	NA	non-coding (NR_122030, exon 1 of 3)	non-coding (NR_122030, exon 1 of 3)	341	NM_001293800	77090	Mm.440170	NM_029865	ENSMUSG00000002396	Ocel1	9430098E02Rik|AI326022|AI593544	occludin/ELL domain containing 1	protein-coding
mm_65310.1	chr7	24765967	24765989	-	1	NA	Intergenic	Intergenic	-5667	NM_026862	68891	Mm.292848	NM_026862	ENSMUSG00000052212	Cd177	1190003K14Rik|Pdp3	CD177 antigen	protein-coding
mm_51117.1	chr6	67861131	67861139	+	1	NA	Intergenic	Intergenic	-295436	NR_003100	75070	Mm.463364	NR_003100		4930515G16Rik	-	myc induced nuclear antigen pseudogene	pseudo
mm_54583.1	chr6	38124569	38124595	-	1	NA	promoter-TSS (NM_080467)	promoter-TSS (NM_080467)	4	NM_080467	140494	Mm.462308	NM_080467	ENSMUSG00000038600	Atp6v0a4	Atp6n1b|a4	ATPase, H+ transporting, lysosomal V0 subunit A4	protein-coding
mm_56717.1	chr6	115488852	115488861	-	1	NA	intron (NM_001308352, intron 7 of 7)	intron (NM_001308352, intron 7 of 7)	-55848	NM_199033	381802	Mm.291208	NM_199033	ENSMUSG00000042389	Tsen2	AU067695	tRNA splicing endonuclease subunit 2	protein-coding
mm_45698.1	chr5	82124703	82124723	-	1	NA	promoter-TSS (NR_138557)	promoter-TSS (NR_138557)	0	NR_138557	67327	Mm.87058	NR_138557		1700031L13Rik	-	RIKEN cDNA 1700031L13 gene	ncRNA
mm_14716.1	chr2	143915504	143915535	+	1	NA	5' UTR (NM_019771, exon 1 of 4)	5' UTR (NM_019771, exon 1 of 4)	188	NM_019771	56431	Mm.28919	NM_019771	ENSMUSG00000015932	Dstn	2610043P17Rik|ADF|AU042046|Dsn|corn1|sid23p	destrin	protein-coding
mm_164739.1	chr17	72836145	72836155	-	1	NA	promoter-TSS (NM_027166)	promoter-TSS (NM_027166)	-554	NM_027166	383295	Mm.277533	NM_027166	ENSMUSG00000039770	Ypel5	2310076K21Rik|CGI-127	yippee-like 5 (Drosophila)	protein-coding
mm_97233.1	chr11	75655846	75655856	+	1	NA	promoter-TSS (NM_001080775)	promoter-TSS (NM_001080775)	-164	NM_001080775	17913	Mm.234502	NM_008659	ENSMUSG00000017774	Myo1c	C80397|MMIb|MYO1E|NMI|mm1beta|myr2	myosin IC	protein-coding
mm_30050.1	chr3	136325954	136325961	-	1	NA	5' UTR (NM_001033350, exon 1 of 17)	5' UTR (NM_001033350, exon 1 of 17)	109	NM_001310749	242248	Mm.30832	NM_001033350	ENSMUSG00000037922	Bank1	A530094C12Rik|AI451642|AVIEF|BANK	B cell scaffold protein with ankyrin repeats 1	protein-coding
mm_165739.1	chr3	107213423	107213426	-	1	NA	exon (NM_001111143, exon 7 of 9)	exon (NM_001111143, exon 7 of 9)	8308	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_92888.1	chr10	82764134	82764157	-	1	NA	promoter-TSS (NM_010914)	promoter-TSS (NM_010914)	-4	NM_010914	18045	Mm.245998	NM_010914	ENSMUSG00000020248	Nfyb	AA985999|Cbf-A	nuclear transcription factor-Y beta	protein-coding
mm_65985.1	chr7	30485183	30485183	-	1	NA	intron (NM_019459, intron 28 of 29)	intron (NM_019459, intron 28 of 29)	-8475	NM_019546	56189	Mm.270525	NM_019546	ENSMUSG00000036892	Prodh2	2510028N04Rik|2510038B11Rik|MmPOX|MmPOX1|POX1	proline dehydrogenase (oxidase) 2	protein-coding
mm_38686.1	chr4	145122331	145122334	-	1	NA	intron (NM_001276502, intron 30 of 68)	PB1D9|SINE|Alu	68334	NM_001276502	230895	Mm.240310	NM_001033190	ENSMUSG00000020220	Vps13d	-	vacuolar protein sorting 13D	protein-coding
mm_948.1	chr1	57154588	57154588	+	1	NA	Intergenic	Intergenic	60408	NR_037990	407809	Mm.134505	NR_037990	ENSMUSG00000101429	BC055402	-	cDNA sequence BC055402	ncRNA
mm_76304.1	chr8	84257312	84257325	-	1	NA	promoter-TSS (NM_026423)	promoter-TSS (NM_026423)	6	NM_026423	67873	Mm.278085	NM_026423	ENSMUSG00000004996	Mri1	2410018C20Rik	methylthioribose-1-phosphate isomerase 1	protein-coding
mm_132925.1	chr16	49800521	49800547	+	1	NA	Intergenic	Intergenic	-55120	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_148826.1	chr19	6335016	6335070	+	1	NA	promoter-TSS (NM_001168489)	promoter-TSS (NM_001168489)	4	NM_008583	17283	Mm.12917	NM_008583	ENSMUSG00000024947	Men1	AW045611	multiple endocrine neoplasia 1	protein-coding
mm_141768.1	chr17	34283012	34283031	-	1	NA	3' UTR (NM_010378, exon 5 of 5)	3' UTR (NM_010378, exon 5 of 5)	4750	NM_010378	14960	Mm.235338	NM_010378	ENSMUSG00000036594	H2-Aa	Aalpha|H-2Aa|H2Aa|I-Aalpha|IAalpha|Ia-1|Ia1	histocompatibility 2, class II antigen A, alpha	protein-coding
mm_146004.1	chr18	68692098	68692130	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-47286	NR_105774	102465183		NR_105774	ENSMUSG00000099300	Mir6356	Gm27461|mmu-mir-6356	microRNA 6356	ncRNA
mm_17838.1	chr2	34350620	34350622	-	1	NA	intron (NM_016768, intron 2 of 8)	B1_Mur1|SINE|Alu	21424	NM_001290576	18516	Mm.239941	NM_016768	ENSMUSG00000038718	Pbx3	-	pre B cell leukemia homeobox 3	protein-coding
mm_9319.1	chr1	171648946	171648988	-	1	NA	promoter-TSS (NM_001347184)	promoter-TSS (NM_001347184)	32	NM_001347184	75345	Mm.164642	NM_144539	ENSMUSG00000038179	Slamf7	19A|19A24|4930560D03Rik|CRACC|CS1	SLAM family member 7	protein-coding
mm_109894.1	chr12	7381566	7381570	-	1	NA	Intergenic	Intergenic	-1238	NR_045045	73575	Mm.179463	NR_045045	ENSMUSG00000102096	1700101O22Rik	-	RIKEN cDNA 1700101O22 gene	ncRNA
mm_135206.1	chr16	36598352	36598373	-	1	NA	Intergenic	Intergenic	-36228	NM_013803	12374	Mm.103619	NM_013803	ENSMUSG00000051980	Casr	CaR|Gprc2a	calcium-sensing receptor	protein-coding
mm_165489.1	chr2	164608931	164608933	-	1	NA	5' UTR (NM_001080550, exon 2 of 8)	5' UTR (NM_001080550, exon 2 of 8)	4454	NM_001276432	277343	Mm.383292	NM_001080550	ENSMUSG00000070533	Wfdc8	Gm706	WAP four-disulfide core domain 8	protein-coding
mm_24152.1	chr3	88358283	88358295	+	1	NA	intron (NM_178246, intron 16 of 21)	intron (NM_178246, intron 16 of 21)	-6300	NM_198410	68957	Mm.441486	NM_198410	ENSMUSG00000041423	Paqr6	1500001B10Rik	progestin and adipoQ receptor family member VI	protein-coding
mm_134746.1	chr16	23107978	23108006	-	1	NA	promoter-TSS (NR_030705)	promoter-TSS (NR_030705)	524	NR_110335	13682	Mm.260084	NM_013506	ENSMUSG00000022884	Eif4a2	4833432N07Rik|BM-010|Ddx2b|Eif4|eIF-4A-II|eIF4A-II	eukaryotic translation initiation factor 4A2	protein-coding
mm_95978.1	chr11	58963791	58963807	+	1	NA	promoter-TSS (NM_031172)	promoter-TSS (NM_031172)	18	NM_031172	56631	Mm.179733	NM_031172	ENSMUSG00000036964	Trim17	Rnf16|terf	tripartite motif-containing 17	protein-coding
mm_45856.1	chr5	87786626	87786633	-	1	NA	exon (NM_001304768, exon 11 of 13)	exon (NM_001304768, exon 11 of 13)	12179	NM_007785	12993	Mm.4908	NM_007785	ENSMUSG00000061937	Csn1s2a	Csng|PP22	casein alpha s2-like A	protein-coding
mm_34123.1	chr4	139257063	139257077	+	1	NA	intron (NM_001037761, intron 2 of 9)	intron (NM_001037761, intron 2 of 9)	53630	NM_145384	212555	Mm.45131	NM_145384	ENSMUSG00000028744	Pqlc2	BC019216	PQ loop repeat containing 2	protein-coding
mm_56626.1	chr6	112758392	112758397	-	1	NA	intron (NM_080448, intron 11 of 21)	intron (NM_080448, intron 11 of 21)	-61724	NM_001167730	58186	Mm.103812	NM_021385	ENSMUSG00000030254	Rad18	2810024C04Rik|Rad18sc	RAD18 E3 ubiquitin protein ligase	protein-coding
mm_123308.1	chr14	62293178	62293213	-	1	NA	promoter-TSS (NM_173419)	promoter-TSS (NM_173419)	-216	NM_173419	239133	Mm.127330	NM_173419	ENSMUSG00000048281	Dleu7	BC038059	deleted in lymphocytic leukemia, 7	protein-coding
mm_64454.1	chr7	142659225	142659252	+	1	NA	promoter-TSS (NM_010514)	promoter-TSS (NM_010514)	-434	NM_010514	16002	Mm.3862	NM_010514	ENSMUSG00000048583	Igf2	AL033362|Igf-2|Igf-II|M6pr|Mpr|Peg2	insulin-like growth factor 2	protein-coding
mm_148207.1	chr18	80124566	80124595	-	1	NA	Intergenic	(A)n|Simple_repeat|Simple_repeat	26902	NM_175028	240442	Mm.26594	NM_175028	ENSMUSG00000053950	Adnp2	8430420L05Rik|BC024969|Kiaa0863|Zfp508|mKIAA0863	ADNP homeobox 2	protein-coding
mm_135628.1	chr16	52301359	52301384	-	1	NA	intron (NM_009655, intron 3 of 15)	intron (NM_009655, intron 3 of 15)	151710	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_69110.1	chr7	127021614	127021635	-	1	NA	promoter-TSS (NM_001102563)	promoter-TSS (NM_001102563)	-413	NM_001102563	69017	Mm.392047	NM_001102563	ENSMUSG00000045114	Prrt2	1500031I19Rik|AI195361|DSPB3	proline-rich transmembrane protein 2	protein-coding
mm_53204.1	chr6	125685708	125685736	+	1	NA	intron (NM_011708, intron 50 of 51)	intron (NM_011708, intron 50 of 51)	-4697	NM_153589	243634	Mm.333398	NM_153589	ENSMUSG00000038115	Ano2	BC033409|Tmem16b	anoctamin 2	protein-coding
mm_90551.1	chr10	128096916	128096926	+	1	NA	intron (NM_054078, intron 2 of 29)	CpG	4138	NM_054078	116848	Mm.252213	NM_054078	ENSMUSG00000040054	Baz2a	AA415431|C030005G16Rik|C78388|Tip5|Walp3|mKIAA0314	bromodomain adjacent to zinc finger domain, 2A	protein-coding
mm_152908.1	chr19	26623395	26623431	-	1	NA	intron (NM_011416, intron 2 of 32)	intron (NM_011416, intron 2 of 32)	18253	NM_011416	67155	Mm.342988	NM_011416	ENSMUSG00000024921	Smarca2	2610209L14Rik|SNF2alpha|Snf2l2|brahma|brm	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	protein-coding
mm_52806.1	chr6	121342561	121342585	+	1	NA	promoter-TSS (NM_001347433)	promoter-TSS (NM_001347433)	-503	NM_001347433	14411	Mm.274506	NM_133661	ENSMUSG00000030109	Slc6a12	BGT1|GAT-2|GAT2|Gabt2	solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12	protein-coding
mm_40033.1	chr5	33658551	33658563	+	1	NA	promoter-TSS (NM_026698)	promoter-TSS (NM_026698)	429	NM_001040435	21335	Mm.379024	NM_011524	ENSMUSG00000037313	Tacc3	Aint|C86661|Eric1	transforming, acidic coiled-coil containing protein 3	protein-coding
mm_104572.1	chr11	96943932	96943940	-	1	NA	promoter-TSS (NR_003293)	promoter-TSS (NR_003293)	83	NM_134021	103711	Mm.254704	NM_134021	ENSMUSG00000018659	Pnpo	AI415282	pyridoxine 5'-phosphate oxidase	protein-coding
mm_160359.1	chr8	21665752	21665752	+	1	NA	promoter-TSS (NM_001177528)	promoter-TSS (NM_001177528)	-45	NM_001177528	100041952	Mm.465152	NM_001177528	ENSMUSG00000063206	Defa34	ENSMUSG00000063206|Gm15315|OTTMUSG00000019924	defensin, alpha, 34	protein-coding
mm_36751.1	chr4	101185380	101185387	-	1	NA	intron (NM_146145, intron 4 of 24)	intron (NM_146145, intron 4 of 24)	79899	NM_146145	16451	Mm.289657	NM_146145	ENSMUSG00000028530	Jak1	AA960307|BAP004|C130039L05Rik	Janus kinase 1	protein-coding
mm_120042.1	chr14	56567730	56567745	+	1	NA	intron (NM_001014996, intron 1 of 16)	intron (NM_001014996, intron 1 of 16)	4109	NM_001014996	219103	Mm.212525	NM_001014996	ENSMUSG00000064128	Cenpj	4932437H03Rik|CPAP|Gm81|LAP|LIP1|Sas4	centromere protein J	protein-coding
mm_90229.1	chr10	121369128	121369133	+	1	NA	intron (NM_029364, intron 1 of 13)	intron (NM_029364, intron 1 of 13)	4040	NM_029364	75612	Mm.207683	NM_029364	ENSMUSG00000034707	Gns	2610016K11Rik|AU042285|C87209|G6S|N28088	glucosamine (N-acetyl)-6-sulfatase	protein-coding
mm_61676.1	chr7	80862230	80862243	+	1	NA	5' UTR (NM_009553, exon 1 of 3)	5' UTR (NM_009553, exon 1 of 3)	128	NM_009553	22691	Mm.358645	NM_009553	ENSMUSG00000038797	Zscan2	Zfp-29|Zfp29	zinc finger and SCAN domain containing 2	protein-coding
mm_100217.1	chr11	117076768	117076840	+	1	NA	promoter-TSS (NR_105853)	promoter-TSS (NR_105853)	21	NR_027059	76972	Mm.309167	NR_027059	ENSMUSG00000086859	Snhg20	2810008D09Rik	small nucleolar RNA host gene 20	ncRNA
mm_63529.1	chr7	127967483	127967496	+	1	NA	promoter-TSS (NM_139149)	promoter-TSS (NM_139149)	10	NM_139149	233908	Mm.277680	NM_139149	ENSMUSG00000030795	Fus	D430004D17Rik|D930039C12Rik|Fus1|Tls	fused in sarcoma	protein-coding
mm_64309.1	chr7	141864162	141864166	+	1	NA	exon (NM_028801, exon 31 of 49)	exon (NM_028801, exon 31 of 49)	25092	NM_028801	74180	Mm.200752	NM_028801	ENSMUSG00000066108	Muc5b	2300002I04Rik|A130042M24|AV085033|MUC5|MUC9|mucin 5b	mucin 5, subtype B, tracheobronchial	protein-coding
mm_55447.1	chr6	67267398	67267425	-	1	NA	intron (NM_001113564, intron 1 of 7)	CpG	432	NM_025814	66870	Mm.240490	NM_025814	ENSMUSG00000036371	Serbp1	1200009K13Rik|9330147J08Rik|AL022786|Pairbp1	serpine1 mRNA binding protein 1	protein-coding
mm_73035.1	chr8	94214548	94214558	+	1	NA	promoter-TSS (NM_172410)	promoter-TSS (NM_172410)	-48	NM_172410	71805	Mm.458170	NM_172410	ENSMUSG00000032939	Nup93	2410008G02Rik	nucleoporin 93	protein-coding
mm_38252.1	chr4	136688037	136688043	-	1	NA	intron (NM_001290753, intron 5 of 15)	intron (NM_001290753, intron 5 of 15)	65419	NM_001243262	242707	Mm.448979	NM_001243262	ENSMUSG00000070683	Lactbl1	-	lactamase, beta-like 1	protein-coding
mm_39737.1	chr5	29377775	29377810	+	1	NA	intron (NM_020295, intron 1 of 16)	intron (NM_020295, intron 1 of 16)	598	NM_020295	56873	Mm.41572	NM_020295	ENSMUSG00000010721	Lmbr1	1110048D14Rik|AU017641	limb region 1	protein-coding
mm_164317.1	chr16	3706813	3706818	-	1	NA	TTS (NM_001161791)	TTS (NM_001161791)	11309	NM_001161790	54483	Mm.143718	NM_019453	ENSMUSG00000022534	Mefv	FMF|TRIM20|pyrin	Mediterranean fever	protein-coding
mm_106396.1	chr11	118797765	118797774	-	1	NA	intron (NM_001039168, intron 2 of 14)	intron (NM_001039168, intron 2 of 14)	-36728	NM_001285438	52897	Mm.341103	NM_001024931	ENSMUSG00000025576	Rbfox3	Fox-3|Hrnbp3|NeuN|Neuna60	RNA binding protein, fox-1 homolog (C. elegans) 3	protein-coding
mm_115503.1	chr13	4150634	4150653	-	1	NA	promoter-TSS (NM_134066)	promoter-TSS (NM_134066)	3	NM_001346535	105349	Mm.41337	NM_134066	ENSMUSG00000021214	Akr1c18	AW146047	aldo-keto reductase family 1, member C18	protein-coding
mm_57908.1	chr6	132441746	132441752	-	1	NA	Intergenic	Intergenic	-77614	NM_053251	114600	Mm.428480	NM_053251		Gm4736	EG114600|Mp4|Mp6	predicted gene 4736	protein-coding
mm_118670.1	chr14	22019792	22019808	+	1	NA	promoter-TSS (NM_028275)	promoter-TSS (NM_028275)	88	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_111930.1	chr12	108888532	108888544	-	1	NA	5' UTR (NM_001164488, exon 2 of 10)	5' UTR (NM_001164488, exon 2 of 10)	4660	NM_001164488	22375	Mm.38433	NM_011710	ENSMUSG00000021266	Wars	TrpRS|WRS	tryptophanyl-tRNA synthetase	protein-coding
mm_17423.1	chr2	27447425	27447430	-	1	NA	3' UTR (NM_001113574, exon 13 of 13)	3' UTR (NM_001113574, exon 13 of 13)	3203	NR_106102	102466836		NR_106102	ENSMUSG00000098812	Mir7578	Gm27789|mmu-mir-7578	microRNA 7578	ncRNA
mm_155320.1	chrX	62287165	62287193	+	1	NA	promoter-TSS (NM_001199996)	promoter-TSS (NM_001199996)	37	NM_001199996	74437	Mm.85792	NM_001199996	ENSMUSG00000045330	4933402E13Rik	-	RIKEN cDNA 4933402E13 gene	protein-coding
mm_20473.1	chr2	129478124	129478155	-	1	NA	intron (NM_177653, intron 1 of 6)	intron (NM_177653, intron 1 of 6)	58463	NM_177653	228592	Mm.452175	NM_177653	ENSMUSG00000043727	F830045P16Rik	Sirpb3	RIKEN cDNA F830045P16 gene	protein-coding
mm_111588.1	chr12	101971851	101971863	-	1	NA	Intergenic	Intergenic	-4117	NM_016856	51786	Mm.716	NM_016856	ENSMUSG00000041781	Cpsf2	100kDa|2610024B04Rik|AI662483|Cpsf|MCPSF|mKIAA1367	cleavage and polyadenylation specific factor 2	protein-coding
mm_32424.1	chr4	107126699	107126716	+	1	NA	Intergenic	Intergenic	29816	NM_172873	242603	Mm.257231	NM_172873	ENSMUSG00000047636	Cdcp2	D030010E02Rik	CUB domain containing protein 2	protein-coding
mm_155198.1	chrX	56609752	56609797	+	1	NA	promoter-TSS (NM_172780)	promoter-TSS (NM_172780)	-61	NM_172780	236794	Mm.17815	NM_172780	ENSMUSG00000060681	Slc9a6	3732426M05|6430520C02Rik|NHE6|mKIAA0267	solute carrier family 9 (sodium/hydrogen exchanger), member 6	protein-coding
mm_87567.1	chr10	56377437	56377455	+	1	NA	5' UTR (NM_010288, exon 1 of 2)	5' UTR (NM_010288, exon 1 of 2)	146	NM_010288	14609	Mm.378921	NM_010288	ENSMUSG00000050953	Gja1	AU042049|AW546267|Cnx43|Cx43|Cx43alpha1|Gja-1|Npm1|connexin43	gap junction protein, alpha 1	protein-coding
mm_108209.1	chr12	76916418	76916442	+	1	NA	exon (NM_145927, exon 11 of 12)	exon (NM_145927, exon 11 of 12)	45818	NM_008558	17187	Mm.268548	NM_008558	ENSMUSG00000059436	Max	AA960152|AI875693|bHLHd4|bHLHd5|bHLHd6|bHLHd7|bHLHd8	Max protein	protein-coding
mm_28803.1	chr3	96220882	96220899	-	1	NA	promoter-TSS (NM_178214)	promoter-TSS (NM_178214)	-10	NM_175662	319176	Mm.358954	NM_175662	ENSMUSG00000068855	Hist2h2ac	H2a-613b	histone cluster 2, H2ac	protein-coding
mm_38904.1	chr4	149954992	149955027	-	1	NA	promoter-TSS (NM_029035)	promoter-TSS (NM_029035)	-3	NM_029035	74646	Mm.30	NM_029035	ENSMUSG00000039911	Spsb1	1110014L01Rik|4930422J18Rik|AI596360|AI854583|SSB-1|SSB1	splA/ryanodine receptor domain and SOCS box containing 1	protein-coding
mm_105163.1	chr11	101626942	101626943	-	1	NA	Intergenic	Intergenic	-1007	NM_025654	66599	Mm.41449	NM_025654	ENSMUSG00000010362	Rdm1	2410008M22Rik|AW212028|Rad52b	RAD52 motif 1	protein-coding
mm_54465.1	chr6	34906811	34906828	-	1	NA	intron (NM_001013366, intron 3 of 14)	intron (NM_001013366, intron 3 of 14)	4012	NM_001013366	101240	Mm.152120	NM_001013366	ENSMUSG00000058486	Wdr91	9530020G05Rik|AI987683|AU018665	WD repeat domain 91	protein-coding
mm_40984.1	chr5	77265455	77265549	+	1	NA	promoter-TSS (NM_011263)	promoter-TSS (NM_011263)	8	NM_011263	19712	Mm.28840	NM_011263	ENSMUSG00000029249	Rest	2610008J04Rik|AA407358|NRSF|REST4	RE1-silencing transcription factor	protein-coding
mm_164142.1	chr15	59275395	59275397	+	1	NA	Intergenic	Intergenic	-31552	NR_045613	100416830	Mm.490788	NR_045613	ENSMUSG00000098528	Zfp572	4930472F24Rik	zinc finger protein 572	pseudo
mm_39552.1	chr5	21786792	21786804	+	1	NA	exon (NM_011188, exon 2 of 13)	exon (NM_011188, exon 2 of 13)	1515	NM_011188	19181	Mm.2462	NM_011188	ENSMUSG00000028932	Psmc2	-	proteasome (prosome, macropain) 26S subunit, ATPase 2	protein-coding
mm_7376.1	chr1	106796688	106796713	-	1	NA	promoter-TSS (NM_009190)	promoter-TSS (NM_009190)	25	NM_009190	20479	Mm.18705	NM_009190	ENSMUSG00000009907	Vps4b	8030489C12Rik|Skd1	vacuolar protein sorting 4B	protein-coding
mm_5781.1	chr1	51584972	51584991	-	1	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	-106582	NM_001310549	109019	Mm.196290	NM_028696	ENSMUSG00000026107	Nabp1	4930434H03Rik|4930442A21Rik|4930488J04Rik|4933440J18Rik|5830411E10Rik|AI852561|Nbp1|Obfc2a|Ssb2	nucleic acid binding protein 1	protein-coding
mm_112801.1	chr13	20473065	20473089	+	1	NA	promoter-TSS (NM_198093)	promoter-TSS (NM_198093)	87	NM_198093	140580	Mm.342392	NM_080288	ENSMUSG00000041112	Elmo1	6330578D22Rik|C230095H21Rik|CED-12	engulfment and cell motility 1	protein-coding
mm_80900.1	chr9	100022318	100022327	+	1	NA	promoter-TSS (NR_040763)	promoter-TSS (NR_040763)	22	NR_040763	108970	Mm.390215	NR_040763	ENSMUSG00000101584	4930519F24Rik	-	RIKEN cDNA 4930519F24 gene	ncRNA
mm_110115.1	chr12	26443821	26443829	-	1	NA	3' UTR (NM_021384, exon 6 of 6)	3' UTR (NM_021384, exon 6 of 6)	12627	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_150873.1	chr19	45055564	45055575	+	1	NA	3' UTR (NM_053197, exon 11 of 11)	3' UTR (NM_053197, exon 11 of 11)	7993	NM_001178013	94280	Mm.36169	NM_053197	ENSMUSG00000025212	Sfxn3	-	sideroflexin 3	protein-coding
mm_84716.1	chr9	73831283	73831287	-	1	NA	intron (NM_001081153, intron 1 of 30)	intron (NM_001081153, intron 1 of 30)	102282	NM_001081153	208898	Mm.41035	NM_001081153	ENSMUSG00000062151	Unc13c	1500037O19Rik|AU019458|D9Ertd414e|Munc13-3|Unc13h3	unc-13 homolog C (C. elegans)	protein-coding
mm_148623.1	chr19	5425122	5425173	+	1	NA	promoter-TSS (NM_024176)	promoter-TSS (NM_024176)	3	NM_001256515	107242	Mm.329658	NM_134149	ENSMUSG00000047423	AI837181	Bles03|N28173	expressed sequence AI837181	protein-coding
mm_28388.1	chr3	90016820	90016831	-	1	NA	intron (NM_153489, intron 17 of 26)	intron (NM_153489, intron 17 of 26)	-5615	NR_106129	102465771		NR_106129	ENSMUSG00000098397	Mir7669	Gm27996|mmu-mir-7669	microRNA 7669	ncRNA
mm_117042.1	chr13	58358755	58358762	-	1	NA	Intergenic	CpG	-3896	NM_175214	75050	Mm.446094	NM_175214	ENSMUSG00000060176	Kif27	4930517I18Rik	kinesin family member 27	protein-coding
mm_169957.1	chr16	90416995	90416998	+	1	NA	intron (NM_015755, intron 1 of 10)	ORR1A2|LTR|ERVL-MaLR	30599	NM_015755	26559	Mm.125874	NM_015755	ENSMUSG00000053414	Hunk	Bstk1|Mak-v	hormonally upregulated Neu-associated kinase	protein-coding
mm_73560.1	chr8	109377843	109377868	+	1	NA	Intergenic	Intergenic	-36947	NR_002928	384864	Mm.390083	NR_002928		Gm1943	-	WD repeat domain 70 pseudogene	pseudo
mm_142403.1	chr17	45458873	45458881	-	1	NA	intron (NM_027649, intron 3 of 7)	intron (NM_027649, intron 3 of 7)	16061	NM_027649	71020	Mm.44257	NM_027649	ENSMUSG00000023935	Spats1	1700011H05Rik|4933400B06Rik|Daip2|Ddip|Srsp1	spermatogenesis associated, serine-rich 1	protein-coding
mm_144924.1	chr18	37685230	37685289	+	1	NA	promoter-TSS (NM_033587)	promoter-TSS (NM_033587)	-141	NM_033587	93712	Mm.247203	NM_033587	ENSMUSG00000103677	Pcdhga4	-	protocadherin gamma subfamily A, 4	protein-coding
mm_25815.1	chr3	127791158	127791184	+	1	NA	intron (NM_145133, intron 1 of 2)	intron (NM_145133, intron 1 of 2)	1258	NM_145133	211550	Mm.31852	NM_145133	ENSMUSG00000046688	Tifa	T2bp	TRAF-interacting protein with forkhead-associated domain	protein-coding
mm_8040.1	chr1	135265347	135265377	-	1	NA	exon (NM_145417, exon 9 of 11)	exon (NM_145417, exon 9 of 11)	-6890	NM_007921	13710	Mm.441439	NM_007921	ENSMUSG00000003051	Elf3	ESE-1|ESX|jen	E74-like factor 3	protein-coding
mm_132683.1	chr16	42955591	42955608	+	1	NA	promoter-TSS (NR_002445)	promoter-TSS (NR_002445)	19	NR_002445	170658	Mm.375824	NR_002445		BC002163	-	NADH dehydrogenase Fe-S protein 5 pseudogene	pseudo
mm_110440.1	chr12	50356032	50356034	-	1	NA	intron (NM_008858, intron 17 of 18)	intron (NM_008858, intron 17 of 18)	293190	NM_008858	18760	Mm.133719	NM_008858	ENSMUSG00000002688	Prkd1	PKD|PKD1|Pkcm|Prkcm	protein kinase D1	protein-coding
mm_67048.1	chr7	67293463	67293465	-	1	NA	intron (NM_001033713, intron 4 of 11)	intron (NM_001033713, intron 4 of 11)	70848	NM_001191051	75099	Mm.121691	NM_175215	ENSMUSG00000043831	Lysmd4	4930506D23Rik	LysM, putative peptidoglycan-binding, domain containing 4	protein-coding
mm_170437.1	chr18	80019259	80019266	+	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	-27633	NM_053117	93737	Mm.24678	NM_053117	ENSMUSG00000056214	Pard6g	2410049N21Rik|Par6a	par-6 family cell polarity regulator gamma	protein-coding
mm_101533.1	chr11	33203590	33203599	-	1	NA	promoter-TSS (NM_019916)	promoter-TSS (NM_019916)	-6	NM_019916	27140	Mm.25362	NM_019916	ENSMUSG00000040610	Tlx3	Hox11l2|Rnx|Tlx1l2	T cell leukemia, homeobox 3	protein-coding
mm_134345.1	chr16	16565638	16565639	-	1	NA	intron (NM_001301817, intron 1 of 16)	ORR1C2|LTR|ERVL-MaLR	-5419	NM_139232	224014	Mm.256131	NM_139232	ENSMUSG00000022788	Fgd4	9030023J02Rik|9330209B17Rik|Frabp|ZFYVE6	FYVE, RhoGEF and PH domain containing 4	protein-coding
mm_125775.1	chr15	74636379	74636393	+	1	NA	promoter-TSS (NM_001177437)	promoter-TSS (NM_001177437)	-68	NM_001177437	69439	Mm.263708	NM_001177437	ENSMUSG00000022603	Mroh4	1700016M24Rik	maestro heat-like repeat family member 4	protein-coding
mm_90146.1	chr10	118141549	118141559	+	1	NA	promoter-TSS (NM_010785)	promoter-TSS (NM_010785)	-233	NM_001162904	17245	Mm.101191	NM_010785	ENSMUSG00000020212	Mdm1	Arrd2|Mdm-1	transformed mouse 3T3 cell double minute 1	protein-coding
mm_134383.1	chr16	17201458	17201482	-	1	NA	promoter-TSS (NM_009456)	promoter-TSS (NM_009456)	22	NM_009456	22195	Mm.3074	NM_009456	ENSMUSG00000038965	Ube2l3	C79827|UbcM4|Ubce7	ubiquitin-conjugating enzyme E2L 3	protein-coding
mm_29689.1	chr3	123085927	123085947	-	1	NA	intron (NM_080451, intron 4 of 4)	intron (NM_080451, intron 4 of 4)	-50950	NM_021503	59006	Mm.141157	NM_021503	ENSMUSG00000028116	Myoz2	1110012I24Rik|Fatz-2|Myozl2	myozenin 2	protein-coding
mm_112233.1	chr12	113482327	113482340	-	1	NA	Intergenic	Intergenic	-7232	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_101064.1	chr11	9873738	9873754	-	1	NA	Intergenic	L1VL4|LINE|L1	681804	NM_178259	268379	Mm.39270	NM_178259	ENSMUSG00000004668	Abca13	9830132L24|A930002G16Rik|AI956815	ATP-binding cassette, sub-family A (ABC1), member 13	protein-coding
mm_155966.1	chrX	106045852	106045864	+	1	NA	intron (NM_001109757, intron 1 of 22)	Lx6|LINE|L1	18634	NM_009726	11977	Mm.254297	NM_009726	ENSMUSG00000033792	Atp7a	MNK	ATPase, Cu++ transporting, alpha polypeptide	protein-coding
mm_25087.1	chr3	100692442	100692470	+	1	NA	Intergenic	Intergenic	-6983	NM_010763	17156	Mm.271617	NM_010763	ENSMUSG00000008763	Man1a2	AI428775|AI528764|AI854422|Man1b|PCR2	mannosidase, alpha, class 1A, member 2	protein-coding
mm_134874.1	chr16	28911816	28911820	-	1	NA	intron (NM_177718, intron 1 of 1)	intron (NM_177718, intron 1 of 1)	17880	NM_177718	239796	Mm.155887	NM_177718	ENSMUSG00000051065	Mb21d2	1600021P15Rik|A430031N04|C87006	Mab-21 domain containing 2	protein-coding
mm_40583.1	chr5	64156536	64156553	+	1	NA	Intergenic	Intergenic	-3716	NM_019636	57915	Mm.286353	NM_019636	ENSMUSG00000029174	Tbc1d1	1110062G02Rik|AI385682|AW555803|Nob1|Nobq1|Tbc1|mKIAA1108	TBC1 domain family, member 1	protein-coding
mm_169407.1	chr14	5149031	5149037	+	1	NA	Intergenic	CpG	-14608	NM_001256885	100041735	Mm.464176	NM_001256885	ENSMUSG00000095295	Gm3488	100041747|Gm3494	predicted gene, 3488	protein-coding
mm_133041.1	chr16	57449139	57449141	+	1	NA	intron (NM_001040397, intron 1 of 4)	Lx8b|LINE|L1	95863	NM_001040397	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding
mm_39716.1	chr5	28032896	28032924	+	1	NA	Intergenic	Intergenic	-38502	NM_153526	231070	Mm.30221	NM_153526	ENSMUSG00000045294	Insig1	1810013C12Rik|Insig-1	insulin induced gene 1	protein-coding
mm_8493.1	chr1	153851037	153851044	-	1	NA	exon (NM_178243, exon 1 of 1)	exon (NM_178243, exon 1 of 1)	155	NM_178243	240817	Mm.439405	NM_178243	ENSMUSG00000045968	Teddm2	5830403L16Rik|AJ554213|Me9|e92	transmembrane epididymal family member 2	protein-coding
mm_156057.1	chrX	109150147	109150150	+	1	NA	intron (NM_019989, intron 2 of 3)	intron (NM_019989, intron 2 of 3)	-46608	NM_001037917	622976	Mm.482747	NM_001037917	ENSMUSG00000048621	Gm6377	EG622976	predicted gene 6377	protein-coding
mm_17381.1	chr2	27020069	27020077	-	1	NA	3' UTR (NM_029862, exon 6 of 6)	3' UTR (NM_029862, exon 6 of 6)	7925	NM_172659	227659	Mm.41203	NM_172659	ENSMUSG00000036067	Slc2a6	A330096C23|F630103L12Rik|Glut6|Glut9	solute carrier family 2 (facilitated glucose transporter), member 6	protein-coding
mm_103164.1	chr11	70455331	70455357	-	1	NA	3' UTR (NM_023158, exon 5 of 5)	3' UTR (NM_023158, exon 5 of 5)	3413	NM_025397	66172	Mm.46424	NM_025397	ENSMUSG00000018923	Med11	1110030J09Rik|AI465144|AW545069	mediator complex subunit 11	protein-coding
mm_31550.1	chr4	55744577	55744581	+	1	NA	Intergenic	Intergenic	-212104	NM_010637	16600	Mm.4325	NM_010637	ENSMUSG00000003032	Klf4	EZF|Gklf|Zie	Kruppel-like factor 4 (gut)	protein-coding
mm_45888.1	chr5	88527796	88527820	-	1	NA	promoter-TSS (NM_152839)	promoter-TSS (NM_152839)	89	NM_152839	16069	Mm.1192	NM_152839	ENSMUSG00000067149	Jchain	9530090F24Rik|AI323815|Igj|Jch	immunoglobulin joining chain	protein-coding
mm_19699.1	chr2	103761179	103761286	-	1	NA	promoter-TSS (NM_153126)	promoter-TSS (NM_153126)	18	NM_153126	98956	Mm.288005	NM_153126	ENSMUSG00000027185	Nat10	AI429152	N-acetyltransferase 10	protein-coding
mm_148290.1	chr18	82584242	82584284	-	1	NA	3' UTR (NM_010777, exon 7 of 7)	3' UTR (NM_010777, exon 7 of 7)	29755	NM_001025254	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_136975.1	chr17	15758575	15758585	+	1	NA	intron (NM_007690, intron 27 of 35)	intron (NM_007690, intron 27 of 35)	53613	NM_007690	12648	Mm.8137	NM_007690	ENSMUSG00000023852	Chd1	4930525N21Rik|AI851787|AW555109	chromodomain helicase DNA binding protein 1	protein-coding
mm_39482.1	chr5	20882111	20882122	+	1	NA	promoter-TSS (NM_177601)	promoter-TSS (NM_177601)	8	NM_172992	68770	Mm.86410	NM_172992	ENSMUSG00000039987	Phtf2	1110054G21Rik|9530062N20Rik|AI447096|C77923	putative homeodomain transcription factor 2	protein-coding
mm_102914.1	chr11	69579368	69579398	-	1	NA	promoter-TSS (NM_144824)	promoter-TSS (NM_144824)	-59	NM_144824	216853	Mm.31586	NM_144824	ENSMUSG00000041346	Wrap53	BC021790|Wdr79	WD repeat containing, antisense to Trp53	protein-coding
mm_33339.1	chr4	129287615	129287644	+	1	NA	promoter-TSS (NM_023485)	promoter-TSS (NM_023485)	8	NM_023485	68828	Mm.132243	NM_023485	ENSMUSG00000001333	Sync	1110057H03Rik|SNIP4	syncoilin	protein-coding
mm_561.1	chr1	38022274	38022293	+	1	NA	exon (NM_198303, exon 6 of 24)	exon (NM_198303, exon 6 of 24)	24273	NM_198303	226982	Mm.260943	NM_198303	ENSMUSG00000026083	Eif5b	A030003E17Rik|BC018347|IF2	eukaryotic translation initiation factor 5B	protein-coding
mm_116285.1	chr13	34994063	34994086	-	1	NA	promoter-TSS (NM_001110331)	promoter-TSS (NM_001110331)	70	NM_011868	23986	Mm.491141	NM_011868	ENSMUSG00000021417	Eci2	Acbd2|Drs1|Hca88|Peci	enoyl-Coenzyme A delta isomerase 2	protein-coding
mm_69618.1	chr7	137313648	137313658	-	1	NA	exon (NM_001113414, exon 2 of 16)	exon (NM_001113414, exon 2 of 16)	792	NM_001113415	13593	Mm.258708	NM_010096	ENSMUSG00000010476	Ebf3	3110018A08Rik|O/E-2|mKIAA4201	early B cell factor 3	protein-coding
mm_126460.1	chr15	80952473	80952480	+	1	NA	intron (NM_009634, intron 2 of 12)	intron (NM_009634, intron 2 of 12)	3986	NM_009634	11564	Mm.38151	NM_009634	ENSMUSG00000022407	Adsl	Adl|Asl	adenylosuccinate lyase	protein-coding
mm_117830.1	chr13	98316746	98316784	-	1	NA	promoter-TSS (NR_137279)	promoter-TSS (NR_137279)	202	NM_145455	218490	Mm.371688	NM_145455	ENSMUSG00000021660	Btf3	1700054E11Rik	basic transcription factor 3	protein-coding
mm_82655.1	chr9	22052022	22052026	-	1	NA	promoter-TSS (NM_010487)	promoter-TSS (NM_010487)	-1	NM_010487	15571	Mm.390167	NM_010487	ENSMUSG00000003410	Elavl3	2600009P04Rik|Huc|PLE21|mHuC	ELAV (embryonic lethal, abnormal vision, Drosophila)-like 3 (Hu antigen C)	protein-coding
mm_42951.1	chr5	123015281	123015299	+	1	NA	exon (NM_175423, exon 1 of 2)	exon (NM_175423, exon 1 of 2)	216	NM_175423	109305	Mm.218582	NM_175423	ENSMUSG00000049686	Orai1	D730049H07Rik|Tmem142a|orai-1	ORAI calcium release-activated calcium modulator 1	protein-coding
mm_108110.1	chr12	75308527	75308544	+	1	NA	5' UTR (NM_023275, exon 1 of 5)	5' UTR (NM_023275, exon 1 of 5)	222	NM_023275	80837	Mm.27467	NM_023275	ENSMUSG00000046768	Rhoj	1110005O19Rik|AW210585|Arhj|TC10L|TCL	ras homolog family member J	protein-coding
mm_130268.1	chr15	96691195	96691208	-	1	NA	exon (NM_175121, exon 15 of 16)	exon (NM_175121, exon 15 of 16)	8497	NM_175121	67760	Mm.46754	NM_175121	ENSMUSG00000022462	Slc38a2	5033402L14Rik|AI316867|ATA2|SAT2|mKIAA1382	solute carrier family 38, member 2	protein-coding
mm_171897.1	chr5	41832607	41832609	-	1	NA	exon (NM_001081422, exon 4 of 27)	exon (NM_001081422, exon 4 of 27)	11707	NM_001310601	665775	Mm.158726	NM_001081422	ENSMUSG00000061755	Bod1l	A230054D04Rik|AI853319|FAM44A|mKIAA1327	biorientation of chromosomes in cell division 1-like	protein-coding
mm_59806.1	chr7	29155672	29155691	+	1	NA	exon (NM_001146023, exon 3 of 8)	exon (NM_001146023, exon 3 of 8)	529	NM_001146023	73833	Mm.260890	NM_028661	ENSMUSG00000030590	Fam98c	1110006G06Rik|AI836081|AV026483|B230110F21Rik	family with sequence similarity 98, member C	protein-coding
mm_35233.1	chr4	19709103	19709120	-	1	NA	promoter-TSS (NM_177327)	promoter-TSS (NM_177327)	-107	NR_074090	107568	Mm.78312	NM_177327	ENSMUSG00000041058	Wwp1	8030445B08Rik|AIP5|SDRP1|Tiul1	WW domain containing E3 ubiquitin protein ligase 1	protein-coding
mm_167319.1	chr8	66386450	66386462	+	1	NA	exon (NM_001293784, exon 6 of 9)	exon (NM_001293784, exon 6 of 9)	155	NM_001166375	72925	Mm.380457	NM_175188	ENSMUSG00000036469	March1	2900024D24Rik|BB085186	membrane-associated ring finger (C3HC4) 1	protein-coding
mm_49493.1	chr6	29735472	29735547	+	1	NA	promoter-TSS (NM_176996)	promoter-TSS (NM_176996)	12	NM_176996	319757	Mm.29279	NM_176996	ENSMUSG00000001761	Smo	E130215L21Rik|Smoh|bnb|smoothened	smoothened, frizzled class receptor	protein-coding
mm_132353.1	chr16	34175797	34175806	+	1	NA	exon (NM_177357, exon 31 of 60)	exon (NM_177357, exon 31 of 60)	-208798	NM_009471	22247	Mm.13145	NM_009471	ENSMUSG00000022814	Umps	1700095D23Rik|AA408257|AL033308|BB164745	uridine monophosphate synthetase	protein-coding
mm_108470.1	chr12	83642634	83642675	+	1	NA	exon (NM_027349, exon 2 of 19)	exon (NM_027349, exon 2 of 19)	10420	NM_027349	67039	Mm.46005	NM_027349	ENSMUSG00000010608	Rbm25	2600011C06Rik|2610015J01Rik|A130095G20Rik|AI159652|AL023075|AU043498|RNPC7	RNA binding motif protein 25	protein-coding
mm_123543.1	chr14	66824623	66824628	-	1	NA	intron (NM_009955, intron 7 of 13)	intron (NM_009955, intron 7 of 13)	43975	NM_009955	12934	Mm.352648	NM_009955	ENSMUSG00000022048	Dpysl2	AI851130|Crmp2|DRP2|Musunc33|TOAD-64|Ulip2	dihydropyrimidinase-like 2	protein-coding
mm_38344.1	chr4	137769695	137769714	-	1	NA	intron (NM_007431, intron 1 of 11)	intron (NM_007431, intron 1 of 11)	-3229	NM_001287172	11647	Mm.288186	NM_007431	ENSMUSG00000028766	Alpl	ALP|APTNAP|Akp-2|Akp2|TNAP|TNSALP	alkaline phosphatase, liver/bone/kidney	protein-coding
mm_78107.1	chr9	20581297	20581333	+	1	NA	promoter-TSS (NM_172919)	promoter-TSS (NM_172919)	-13	NM_172919	244721	Mm.86627	NM_172919	ENSMUSG00000058192	Zfp846	2210010B09Rik|9130221F13|Znf846	zinc finger protein 846	protein-coding
mm_43807.1	chr5	142904131	142904174	+	1	NA	exon (NM_007393, exon 5 of 6)	exon (NM_007393, exon 5 of 6)	2602	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_63710.1	chr7	130692533	130692575	+	1	NA	promoter-TSS (NM_021314)	promoter-TSS (NM_021314)	-2	NM_001347637	57752	Mm.86322	NM_021314	ENSMUSG00000030852	Tacc2	mKIAA4180	transforming, acidic coiled-coil containing protein 2	protein-coding
mm_170291.1	chr18	3005270	3005270	+	1	NA	Intergenic	Intergenic	118142	NM_001167539	100312476	Mm.480293	NM_001167539	ENSMUSG00000091539	Vmn1r238	-	vomeronasal 1 receptor, 238	protein-coding
mm_80280.1	chr9	73039714	73039743	+	1	NA	promoter-TSS (NM_018889)	promoter-TSS (NM_018889)	10	NM_001308425	66364	Mm.392089	NM_001308425		2310009A05Rik	5031420N21Rik	RIKEN cDNA 2310009A05 gene	protein-coding
mm_115512.1	chr13	4756401	4756425	-	1	NA	Intergenic	L1M4|LINE|L1	-147249	NM_018859	56043	Mm.251908	NM_018859	ENSMUSG00000045410	Akr1e1	1810061I10Rik|Akr1e2	aldo-keto reductase family 1, member E1	protein-coding
mm_14595.1	chr2	136058208	136058212	+	1	NA	5' UTR (NM_029530, exon 1 of 6)	5' UTR (NM_029530, exon 1 of 6)	283	NM_029530	76161	Mm.41638	NM_029530	ENSMUSG00000027270	Lamp5	3110035N03Rik|6330527O06Rik|BAD-LAMP|LAMP-5	lysosomal-associated membrane protein family, member 5	protein-coding
mm_99698.1	chr11	106156213	106156219	+	1	NA	TTS (NM_172397)	TTS (NM_172397)	3926	NM_172397	67803	Mm.21687	NM_172397	ENSMUSG00000040699	Limd2	0610025L06Rik|AI413966	LIM domain containing 2	protein-coding
mm_72581.1	chr8	84201767	84201793	+	1	NA	Intergenic	Intergenic	-6738	NR_029740	387216		NR_029740	ENSMUSG00000065611	Mir23a	Mirn23a|mir-23a|mmu-mir-23a	microRNA 23a	ncRNA
mm_8904.1	chr1	163312421	163312423	-	1	NA	exon (NM_175686, exon 1 of 5)	exon (NM_175686, exon 1 of 5)	1228	NM_011127	18933	Mm.288642	NM_011127	ENSMUSG00000026586	Prrx1	A230024N07Rik|AA755424|AI385634|AI843499|K-2|Pmx|Pmx1|Prx1|mHox	paired related homeobox 1	protein-coding
mm_74348.1	chr8	127540716	127540718	+	1	NA	intron (NM_001309391, intron 22 of 24)	RCHARR1|DNA|hAT-Charlie	241065	NM_001013580	93742	Mm.299254	NM_033620	ENSMUSG00000025812	Pard3	AA960621|AI256638|Asip|D8Ertd580e|Par-3|Par3|Pard-3|Pard3a|Phip	par-3 family cell polarity regulator	protein-coding
mm_42650.1	chr5	118765003	118765021	+	1	NA	3' UTR (NM_172424, exon 31 of 31)	3' UTR (NM_172424, exon 31 of 31)	-187327	NR_040694	74627	Mm.410828	NR_040694	ENSMUSG00000107144	4930413E15Rik	-	RIKEN cDNA 4930413E15 gene	ncRNA
mm_48449.1	chr5	140702049	140702068	-	1	NA	intron (NM_001347517, intron 1 of 22)	CpG	320	NM_028833	74239	Mm.179704	NM_028833	ENSMUSG00000036555	Iqce	1700028P05Rik|mKIAA1023	IQ motif containing E	protein-coding
mm_72616.1	chr8	84623637	84623686	+	1	NA	intron (NM_001252059, intron 37 of 45)	intron (NM_001252059, intron 37 of 45)	39191	NM_010499	15936	Mm.399	NM_010499	ENSMUSG00000053560	Ier2	AI317238|Ch1|Pip92	immediate early response 2	protein-coding
mm_71060.1	chr8	33913366	33913409	+	1	NA	intron (NM_001042674, intron 1 of 7)	MTD|LTR|ERVL-MaLR	16476	NM_019733	19663	Mm.323997	NM_019733	ENSMUSG00000031586	Rbpms	2010300K22Rik|2700019M19Rik|AU017537|RBP-MS|hermes	RNA binding protein gene with multiple splicing	protein-coding
mm_12726.1	chr2	78845470	78845498	+	1	NA	Intergenic	Intergenic	-23563	NM_009454	22193	Mm.1485	NM_009454	ENSMUSG00000027011	Ube2e3	Ubce4|ubcM2	ubiquitin-conjugating enzyme E2E 3	protein-coding
mm_40990.1	chr5	77268738	77268757	+	1	NA	exon (NM_011263, exon 2 of 4)	exon (NM_011263, exon 2 of 4)	3253	NM_011263	19712	Mm.28840	NM_011263	ENSMUSG00000029249	Rest	2610008J04Rik|AA407358|NRSF|REST4	RE1-silencing transcription factor	protein-coding
mm_75574.1	chr8	60954869	60954877	-	1	NA	promoter-TSS (NM_173876)	promoter-TSS (NM_173876)	-74	NM_173876	12725	Mm.25263	NM_007711	ENSMUSG00000004319	Clcn3	Clc3	chloride channel, voltage-sensitive 3	protein-coding
mm_99699.1	chr11	106159654	106159678	+	1	NA	intron (NM_172397, intron 1 of 4)	intron (NM_172397, intron 1 of 4)	476	NM_172397	67803	Mm.21687	NM_172397	ENSMUSG00000040699	Limd2	0610025L06Rik|AI413966	LIM domain containing 2	protein-coding
mm_171963.1	chr5	85173776	85173777	-	1	NA	Intergenic	RLTR44C|LTR|ERVK	-756394	NM_007937	13839	Mm.137991	NM_007937	ENSMUSG00000029245	Epha5	AI854630|AW125296|Cek7|Ehk1|Els1|Hek7|Rek7|bsk	Eph receptor A5	protein-coding
mm_165736.1	chr3	107173797	107173800	+	1	NA	Intergenic	Intergenic	-9345	NM_001081140	242151	Mm.245155	NM_001081140	ENSMUSG00000042861	Kcna10	Gm1962|Kcna8|Kv1.8	potassium voltage-gated channel, shaker-related subfamily, member 10	protein-coding
mm_7837.1	chr1	132200311	132200315	-	1	NA	intron (NM_001311104, intron 1 of 4)	intron (NM_001311104, intron 1 of 4)	2225	NR_029777	723818		NR_029777	ENSMUSG00000065435	Mir135b	Mirn135b|mir-135b	microRNA 135b	ncRNA
mm_155102.1	chrX	48342058	48342073	+	1	NA	intron (NM_178782, intron 1 of 14)	CpG	707	NM_178782	320376	Mm.210146	NM_178782	ENSMUSG00000036959	Bcorl1	6720425J07Rik|B930011H20Rik	BCL6 co-repressor-like 1	protein-coding
mm_84115.1	chr9	58454817	58454846	-	1	NA	promoter-TSS (NR_040736)	promoter-TSS (NR_040736)	-342	NR_040736	74879	Mm.416924	NR_040736	ENSMUSG00000097651	4930461G14Rik	-	RIKEN cDNA 4930461G14 gene	ncRNA
mm_87874.1	chr10	61482273	61482285	+	1	NA	intron (NM_153542, intron 1 of 4)	intron (NM_153542, intron 1 of 4)	6446	NM_153542	216011	Mm.136116	NM_153542	ENSMUSG00000037151	Lrrc20	BC036304	leucine rich repeat containing 20	protein-coding
mm_70793.1	chr8	22593833	22593855	+	1	NA	promoter-TSS (NM_001198998)	promoter-TSS (NM_001198998)	-31	NM_011696	22335	Mm.227704	NM_011696	ENSMUSG00000008892	Vdac3	-	voltage-dependent anion channel 3	protein-coding
mm_48625.1	chr5	145132883	145132888	-	1	NA	exon (NM_001033313, exon 4 of 6)	exon (NM_001033313, exon 4 of 6)	7204	NM_001033313	231887	Mm.188851	NM_001033313	ENSMUSG00000029623	Pdap1	HASPP28|PAP|PAP1	PDGFA associated protein 1	protein-coding
mm_60628.1	chr7	44748641	44748651	+	1	NA	promoter-TSS (NM_178734)	promoter-TSS (NM_178734)	17	NM_133945	101568	Mm.28816	NM_133945	ENSMUSG00000002205	Vrk3	AI428238	vaccinia related kinase 3	protein-coding
mm_150939.1	chr19	46306094	46306109	+	1	NA	intron (NM_001177369, intron 2 of 22)	intron (NM_001177369, intron 2 of 22)	171	NM_001177370	18034	Mm.102365	NM_019408	ENSMUSG00000025225	Nfkb2	NF-kappaB2|lyt|p49|p49/p100|p50B|p52	nuclear factor of kappa light polypeptide gene enhancer in B cells 2, p49/p100	protein-coding
mm_167245.1	chr8	22506218	22506231	+	1	NA	intron (NM_011394, intron 1 of 10)	intron (NM_011394, intron 1 of 10)	-29345	NM_001146117	102032	Mm.378231	NM_001012667	ENSMUSG00000031534	Smim19	AI316807|BG694986|EST-c39	small integral membrane protein 19	protein-coding
mm_104668.1	chr11	97657991	97658001	-	1	NA	Intergenic	PB1D7|SINE|Alu	-5416	NM_139311	246198	Mm.23685	NM_139311	ENSMUSG00000038437	Mllt6	AI315037|Af17	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 6	protein-coding
mm_44.1	chr1	6489218	6489245	+	1	NA	intron (NM_001244693, intron 2 of 22)	intron (NM_001244693, intron 2 of 22)	2000	NM_001244692	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding
mm_158448.1	chrX	140543098	140543108	-	1	NA	promoter-TSS (NM_010286)	promoter-TSS (NM_010286)	84	NM_010286	14605	Mm.22216	NM_010286	ENSMUSG00000031431	Tsc22d3	DIP|Dsip1|Gilz|TSC-22R|Tilz3	TSC22 domain family, member 3	protein-coding
mm_102607.1	chr11	62433642	62433654	-	1	NA	exon (NM_177229, exon 3 of 9)	exon (NM_177229, exon 3 of 9)	4867	NM_001252313	20185	Mm.271814	NM_011308	ENSMUSG00000018501	Ncor1	5730405M06Rik|A230020K14Rik|N-CoR|RIP13|Rxrip13|mKIAA1047	nuclear receptor co-repressor 1	protein-coding
mm_44291.1	chr5	8368243	8368262	-	1	NA	promoter-TSS (NM_001007221)	promoter-TSS (NM_001007221)	-92	NM_001310439	11496	Mm.275895	NM_001007220	ENSMUSG00000040537	Adam22	2900022I03Rik|AI854032|MDC2	a disintegrin and metallopeptidase domain 22	protein-coding
mm_34428.1	chr4	145564615	145564646	+	1	NA	Intergenic	Intergenic	-20570	NM_001324416	433801	Mm.276881	NM_001013808	ENSMUSG00000078502	Gm13212	OTTMUSG00000010965	predicted gene 13212	protein-coding
mm_32479.1	chr4	107879806	107879823	+	1	NA	promoter-TSS (NM_001282737)	promoter-TSS (NM_001282737)	59	NM_001282737	17149	Mm.808	NM_001282737	ENSMUSG00000028609	Magoh	Mago-m|Mos2	mago homolog, exon junction complex core component	protein-coding
mm_95512.1	chr11	52004314	52004335	+	1	NA	5' UTR (NM_001166657, exon 1 of 8)	5' UTR (NM_001166657, exon 1 of 8)	103	NM_001166653	213084	Mm.280557	NM_153785	ENSMUSG00000020389	Cdkl3	AI852479|B230379H01Rik	cyclin-dependent kinase-like 3	protein-coding
mm_123267.1	chr14	61360335	61360351	-	1	NA	exon (NM_026598, exon 1 of 4)	exon (NM_026598, exon 1 of 4)	102	NM_026598	68177	Mm.22758	NM_026598	ENSMUSG00000021928	Ebpl	5730442K12Rik|EBRP	emopamil binding protein-like	protein-coding
mm_54316.1	chr6	30174729	30174746	-	1	NA	promoter-TSS (NR_126541)	promoter-TSS (NR_126541)	-612	NR_126541	101447999		NR_126540		Mirc35hg	-	microRNA cluster 35, host gene	ncRNA
mm_118063.1	chr13	102894997	102895031	-	1	NA	intron (NM_175171, intron 4 of 28)	intron (NM_175171, intron 4 of 28)	134759	NR_130171	76624	Mm.426384	NR_130171	ENSMUSG00000091906	1700099I09Rik	-	RIKEN cDNA 1700099I09 gene	ncRNA
mm_142445.1	chr17	45592416	45592452	-	1	NA	promoter-TSS (NM_022880)	promoter-TSS (NM_022880)	-41	NM_022880	63959	Mm.29744	NM_022880	ENSMUSG00000023942	Slc29a1	1200014D21Rik|AA407560|ENT1	solute carrier family 29 (nucleoside transporters), member 1	protein-coding
mm_48732.1	chr5	147431319	147431363	-	1	NA	intron (NM_028291, intron 1 of 18)	(TG)n|Simple_repeat|Simple_repeat	761	NM_028291	72587	Mm.320469	NM_028291	ENSMUSG00000029647	Pan3	2700050F09Rik|A430027N15Rik|AU014670	PAN3 poly(A) specific ribonuclease subunit	protein-coding
mm_111417.1	chr12	91571840	91571842	-	1	NA	intron (NM_175335, intron 4 of 8)	PB1D9|SINE|Alu	17808	NM_031391	83602	Mm.275728	NM_031391	ENSMUSG00000020962	Gtf2a1	6330549H03Rik|AA536742|AA959775|AW060250|TfIIAa/b|Tfiia1	general transcription factor II A, 1	protein-coding
mm_101560.1	chr11	33993147	33993159	-	1	NA	promoter-TSS (NM_001190886)	promoter-TSS (NM_001190886)	40	NM_001190886	70357	Mm.252514	NM_027398	ENSMUSG00000053519	Kcnip1	KCHIP1|Kchip1.2	Kv channel-interacting protein 1	protein-coding
mm_80773.1	chr9	95561092	95561107	+	1	NA	3' UTR (NM_198414, exon 1 of 1)	3' UTR (NM_198414, exon 1 of 1)	1282	NM_198414	75552	Mm.151485	NM_198414	ENSMUSG00000064225	Paqr9	1700020G04Rik	progestin and adipoQ receptor family member IX	protein-coding
mm_61858.1	chr7	88309686	88309692	+	1	NA	exon (NM_009982, exon 7 of 7)	exon (NM_009982, exon 7 of 7)	31604	NM_001311790	13032	Mm.89295	NM_009982	ENSMUSG00000030560	Ctsc	AI047818|CatC|DPP1|DPPI	cathepsin C	protein-coding
mm_6295.1	chr1	71030185	71030187	-	1	NA	3' UTR (NM_007525, exon 11 of 11)	3' UTR (NM_007525, exon 11 of 11)	72786	NM_007525	12021	Mm.10764	NM_007525	ENSMUSG00000026196	Bard1	ENSMUSG00000060893|ENSMUSG00000073653	BRCA1 associated RING domain 1	protein-coding
mm_1758.1	chr1	75521807	75521821	+	1	NA	exon (NM_027886, exon 2 of 25)	exon (NM_027886, exon 2 of 25)	285	NM_027886	71728	Mm.312650	NM_027886	ENSMUSG00000026213	Stk11ip	1200014D22Rik|BB131189|LIP1|LKB1IP	serine/threonine kinase 11 interacting protein	protein-coding
mm_113019.1	chr13	22006533	22006550	+	1	NA	intron (NM_019429, intron 7 of 11)	intron (NM_019429, intron 7 of 11)	3200	NM_019429	54373	Mm.32043	NM_019429	ENSMUSG00000006179	Prss16	AI448615|TSSP	protease, serine 16 (thymus)	protein-coding
mm_122893.1	chr14	54949901	54949909	-	1	NA	promoter-TSS (NR_029724)	promoter-TSS (NR_029724)	-763	NR_029724	387204		NR_029724	ENSMUSG00000065432	Mir208a	Mirn208|Mirn208a|mir-208|mir-208a|mmu-mir-208	microRNA 208a	ncRNA
mm_48939.1	chr6	4539468	4539474	+	1	NA	exon (NM_007743, exon 51 of 52)	exon (NM_007743, exon 51 of 52)	33853	NM_007743	12843	Mm.277792	NM_007743	ENSMUSG00000029661	Col1a2	AA960264|AI325291|Col1a-2|Cola-2|Cola2|oim	collagen, type I, alpha 2	protein-coding
mm_86816.1	chr10	20562244	20562265	+	1	NA	intron (NM_013875, intron 2 of 12)	B4|SINE|B4	-13926	NM_001347366	29863	Mm.425617	NM_013875	ENSMUSG00000019990	Pde7b	-	phosphodiesterase 7B	protein-coding
mm_115850.1	chr13	21287562	21287568	-	1	NA	exon (NM_010343, exon 5 of 5)	exon (NM_010343, exon 5 of 5)	5121	NM_010343	14780	Mm.1332	NM_010343	ENSMUSG00000004344	Gpx5	AV379049|Arep	glutathione peroxidase 5	protein-coding
mm_39204.1	chr4	156031656	156031674	-	1	NA	Intergenic	RLTR20B4_MM|LTR|ERVK	5323	NM_021985	21936	Mm.3180	NM_009400	ENSMUSG00000041954	Tnfrsf18	AITR|Gitr	tumor necrosis factor receptor superfamily, member 18	protein-coding
mm_140134.1	chr17	79626654	79626656	+	1	NA	intron (NM_201361, intron 2 of 10)	intron (NM_201361, intron 2 of 10)	11755	NM_201361	381110	Mm.209801	NM_201361	ENSMUSG00000036368	Rmdn2	AW061290|Fam82a1|RMD-2|mRMD-2	regulator of microtubule dynamics 2	protein-coding
mm_58754.1	chr7	13324655	13324661	+	1	NA	Intergenic	MER54B|LTR|ERVL	-1009	NM_001168504	232889	Mm.223639	NM_001004762	ENSMUSG00000033847	Pla2g4c	D7Ertd445e	phospholipase A2, group IVC (cytosolic, calcium-independent)	protein-coding
mm_170549.1	chr19	4064445	4064458	-	1	NA	Intergenic	MMVL30-int|LTR|ERV1	-5157	NM_144869	225884	Mm.440201	NM_144869	ENSMUSG00000058216	Gstp3	-	glutathione S-transferase pi 3	protein-coding
mm_37508.1	chr4	123842020	123842026	-	1	NA	Intergenic	Intergenic	54148	NM_183163	230726	Mm.37334	NM_183163	ENSMUSG00000043333	Rhbdl2	9130416B15|RRP2	rhomboid, veinlet-like 2 (Drosophila)	protein-coding
mm_30793.1	chr4	19709322	19709341	+	1	NA	promoter-TSS (NM_177327)	promoter-TSS (NM_177327)	-327	NR_074090	107568	Mm.78312	NM_177327	ENSMUSG00000041058	Wwp1	8030445B08Rik|AIP5|SDRP1|Tiul1	WW domain containing E3 ubiquitin protein ligase 1	protein-coding
mm_93782.1	chr10	120476737	120476764	-	1	NA	promoter-TSS (NM_010441)	promoter-TSS (NM_010441)	-281	NM_010441	15364	Mm.157190	NM_010441	ENSMUSG00000056758	Hmga2	9430083A20Rik|HMGI-C|Hmgic|pg|pygmy	high mobility group AT-hook 2	protein-coding
mm_48771.1	chr5	148489377	148489384	-	1	NA	Intergenic	Intergenic	63408	NM_011908	24109	Mm.21846	NM_011908	ENSMUSG00000001687	Ubl3	AW108023|HCG	ubiquitin-like 3	protein-coding
mm_154413.1	chrM	15461	15488	+	1	NA	NA	Intergenic	NA	NA								
mm_111720.1	chr12	103732534	103732565	-	1	NA	exon (NM_009244, exon 2 of 5)	exon (NM_009244, exon 2 of 5)	5640	NM_009244	20701	Mm.439692	NM_009244	ENSMUSG00000071178	Serpina1b	D12Ucla2|Dom2|PI2|Spi1-2	serine (or cysteine) preptidase inhibitor, clade A, member 1B	protein-coding
mm_65277.1	chr7	24333960	24333969	-	1	NA	promoter-TSS (NM_001163810)	promoter-TSS (NM_001163810)	1	NM_001163810	69301	Mm.144202	NM_027028	ENSMUSG00000055826	Tescl	1700008P20Rik	tescalcin-like	protein-coding
mm_59178.1	chr7	24460032	24460063	+	1	NA	Intergenic	Intergenic	-2436	NM_011113	18793	Mm.1359	NM_011113	ENSMUSG00000046223	Plaur	Cd87|u-PAR|uPAR	plasminogen activator, urokinase receptor	protein-coding
mm_56438.1	chr6	97431460	97431466	-	1	NA	intron (NM_145148, intron 2 of 23)	intron (NM_145148, intron 2 of 23)	27823	NM_001346639	232288	Mm.27789	NM_145148	ENSMUSG00000030064	Frmd4b	6030440G05Rik|C87375|GOBLIN|GRSP1|R74720	FERM domain containing 4B	protein-coding
mm_67221.1	chr7	74502157	74502160	-	1	NA	intron (NM_001038643, intron 2 of 10)	intron (NM_001038643, intron 2 of 10)	52622	NM_023908	108116	Mm.425467	NM_023908	ENSMUSG00000025790	Slco3a1	5830414C08Rik|Anr1|MJAM|OATP-D|R75096|Slc21a11	solute carrier organic anion transporter family, member 3a1	protein-coding
mm_170757.1	chr2	157135155	157135162	-	1	NA	promoter-TSS (NM_001139520)	promoter-TSS (NM_001139520)	64	NM_001139520	56045	Mm.248478	NM_018851	ENSMUSG00000027639	Samhd1	E330031J07Rik|Mg11	SAM domain and HD domain, 1	protein-coding
mm_157028.1	chrX	7899221	7899271	-	1	NA	promoter-TSS (NM_001252528)	promoter-TSS (NM_001252528)	23	NM_001252529	54633	Mm.14616	NM_019478	ENSMUSG00000031157	Pqbp1	PQBP-1|Sfc2|npw38	polyglutamine binding protein 1	protein-coding
mm_110919.1	chr12	76264885	76264885	-	1	NA	intron (NM_138745, intron 1 of 27)	intron (NM_138745, intron 1 of 27)	9653	NM_138745	108156	Mm.29584	NM_138745	ENSMUSG00000021048	Mthfd1	Dcs|E430024A07Rik|Mthfd	methylenetetrahydrofolate dehydrogenase (NADP+ dependent), methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthase	protein-coding
mm_54662.1	chr6	39196683	39196720	-	1	NA	intron (NM_001033430, intron 1 of 19)	B1_Mur4|SINE|Alu	10072	NM_001033430	338523	Mm.293175	NM_001033430	ENSMUSG00000042599	Kdm7a	A630082K20Rik|BB041802|ENSMUSG00000073143|Jhdm1d|mKIAA1718	lysine (K)-specific demethylase 7A	protein-coding
mm_2856.1	chr1	131675077	131675086	+	1	NA	3' UTR (NM_007799, exon 10 of 10)	3' UTR (NM_007799, exon 10 of 10)	-13614	NM_145509	226421	Mm.44508	NM_145509	ENSMUSG00000052688	Rab7b	5430435G22Rik	RAB7B, member RAS oncogene family	protein-coding
mm_164274.1	chr15	101743032	101743040	-	1	NA	promoter-TSS (NM_019956)	promoter-TSS (NM_019956)	61	NM_019956	56735	Mm.358677	NM_019956	ENSMUSG00000051879	Krt71	AA589543|Ca|Cal4|Cu|Krt2-6g|mK6irs|mK6irs1	keratin 71	protein-coding
mm_169231.1	chr13	6778403	6778403	+	1	NA	Intergenic	Intergenic	-129632	NM_001291071	56421	Mm.273874	NM_019703	ENSMUSG00000021196	Pfkp	1200015H23Rik|9330125N24Rik|ATP-PFK|PFK-C|PFK-P	phosphofructokinase, platelet	protein-coding
mm_165218.1	chr2	42823672	42823673	+	1	NA	Intergenic	MMERGLN-int|LTR|ERV1	-170074	NM_053011	94217	Mm.441398	NM_053011	ENSMUSG00000049252	Lrp1b	9630004P12Rik|LRP-DIT	low density lipoprotein-related protein 1B (deleted in tumors)	protein-coding
mm_147237.1	chr18	38284340	38284346	-	1	NA	promoter-TSS (NM_017378)	promoter-TSS (NM_017378)	58	NM_017378	53601	Mm.12862	NM_017378	ENSMUSG00000024440	Pcdh12	Pcdh14|VE-cad-2	protocadherin 12	protein-coding
mm_118116.1	chr13	104036504	104036514	-	1	NA	intron (NM_029447, intron 11 of 12)	intron (NM_029447, intron 11 of 12)	73105	NM_029447	75805	Mm.127692	NM_029447	ENSMUSG00000021710	Nln	4930472G13Rik|C79345	neurolysin (metallopeptidase M3 family)	protein-coding
mm_124728.1	chr15	6580394	6580404	+	1	NA	exon (NM_001278269, exon 1 of 17)	exon (NM_001278269, exon 1 of 17)	552	NM_011815	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_106984.1	chr12	9580852	9580872	+	1	NA	3' UTR (NM_011859, exon 3 of 3)	3' UTR (NM_011859, exon 3 of 3)	6420	NM_011859	23967	Mm.45055	NM_011859	ENSMUSG00000048387	Osr1	Odd1|Osr	odd-skipped related 1 (Drosophila)	protein-coding
mm_77288.1	chr8	116921379	116921392	-	1	NA	promoter-TSS (NM_028131)	promoter-TSS (NM_028131)	51	NM_026844	66531	Mm.4011	NM_026844	ENSMUSG00000014633	Cmc2	1110046L09Rik|2310061C15Rik|DC13	COX assembly mitochondrial protein 2	protein-coding
mm_53518.1	chr6	136470566	136470589	+	1	NA	Intergenic	Intergenic	-48274	NM_019426	54343	Mm.173271	NM_019426	ENSMUSG00000030213	Atf7ip	2610204M12Rik|AM|Mcaf1	activating transcription factor 7 interacting protein	protein-coding
mm_92391.1	chr10	76596659	76596675	-	1	NA	exon (NM_146007, exon 28 of 28)	exon (NM_146007, exon 28 of 28)	21019	NM_080845	14317	Mm.36278	NM_080845	ENSMUSG00000001155	Ftcd	-	formiminotransferase cyclodeaminase	protein-coding
mm_147838.1	chr18	62596321	62596326	-	1	NA	promoter-TSS (NM_001001803)	promoter-TSS (NM_001001803)	-59	NM_001001803	408198	Mm.478742	NM_001001803	ENSMUSG00000060201	Spink7	EG408198|Ecg2	serine peptidase inhibitor, Kazal type 7 (putative)	protein-coding
mm_51250.1	chr6	71831326	71831410	+	1	NA	promoter-TSS (NM_029673)	promoter-TSS (NM_029673)	48	NM_001253688	76614	Mm.235123	NM_029673	ENSMUSG00000052337	Immt	1700082C19Rik|D830041H16Rik|HMP|P87|P87/89|P89	inner membrane protein, mitochondrial	protein-coding
mm_57421.1	chr6	124913946	124913955	-	1	NA	3' UTR (NM_026988, exon 5 of 5)	3' UTR (NM_026988, exon 5 of 5)	-2245	NM_008479	16768	Mm.4528	NM_008479	ENSMUSG00000030124	Lag3	CD223|LAG-3|Ly66	lymphocyte-activation gene 3	protein-coding
mm_58369.1	chr6	148901170	148901170	-	1	NA	Intergenic	RMER6A|LTR|ERVK	-4933	NM_181541	232560	Mm.150568	NM_181541	ENSMUSG00000030309	Caprin2	C1qdc1|Eeg1|rng140	caprin family member 2	protein-coding
mm_18043.1	chr2	39005575	39005625	-	1	NA	promoter-TSS (NM_025592)	promoter-TSS (NM_025592)	-469	NM_025592	66489	Mm.345333	NM_025592	ENSMUSG00000062997	Rpl35	2410039E09Rik	ribosomal protein L35	protein-coding
mm_31922.1	chr4	85388225	85388239	+	1	NA	3' UTR (NM_019535, exon 9 of 9)	3' UTR (NM_019535, exon 9 of 9)	182776	NM_019535	20404	Mm.143603	NM_019535	ENSMUSG00000028488	Sh3gl2	9530001L19Rik|AI120490|AW555077|B930049H17Rik|EEN-B1|SH3PA|Sh3d2a	SH3-domain GRB2-like 2	protein-coding
mm_104621.1	chr11	97287749	97287752	-	1	NA	Intergenic	Intergenic	-7174	NM_008942	19155	Mm.29824	NM_008942	ENSMUSG00000001441	Npepps	AAP-S|MP100|Psa|R74825|goku	aminopeptidase puromycin sensitive	protein-coding
mm_162781.1	chr10	69872175	69872178	+	1	NA	intron (NM_146005, intron 10 of 42)	intron (NM_146005, intron 10 of 42)	-53356	NM_170687	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_18398.1	chr2	60253552	60253565	-	1	NA	intron (NM_025422, intron 4 of 4)	intron (NM_025422, intron 4 of 4)	30926	NM_025422	66205	Mm.227281	NM_025422	ENSMUSG00000060703	Cd302	1110055L24Rik|AI159627	CD302 antigen	protein-coding
mm_35437.1	chr4	38812859	38812868	-	1	NA	Intergenic	Intergenic	-637430	NM_001081095	75471	Mm.23522	NM_001081095	ENSMUSG00000028287	1700009N14Rik	AI429145	RIKEN cDNA 1700009N14 gene	protein-coding
mm_682.1	chr1	40504685	40504706	+	1	NA	Intergenic	Intergenic	-10667	NM_010553	16174	Mm.20466	NM_010553	ENSMUSG00000026068	Il18rap	AcPL|IL-18R-beta|IL-18RAcP|IL-18Rbeta|IL-1RAcPL	interleukin 18 receptor accessory protein	protein-coding
mm_12160.1	chr2	62147803	62147826	+	1	NA	intron (NM_001242378, intron 1 of 25)	intron (NM_001242378, intron 1 of 25)	101299	NM_033552	94229	Mm.314497	NM_033552	ENSMUSG00000026904	Slc4a10	NCBE|mKIAA4136	solute carrier family 4, sodium bicarbonate cotransporter-like, member 10	protein-coding
mm_168194.1	chr10	63421726	63421749	-	1	NA	Intergenic	Intergenic	-8361	NM_177612	216033	Mm.444692	NM_177612	ENSMUSG00000060843	Ctnna3	4930429L08Rik|4933408A16|Catna3|Vr22	catenin (cadherin associated protein), alpha 3	protein-coding
mm_108944.1	chr12	102283037	102283079	+	1	NA	promoter-TSS (NM_001161365)	promoter-TSS (NM_001161365)	-16	NM_177620	217835	Mm.24145	NM_177620	ENSMUSG00000044456	Rin3	6430500K07|C86933	Ras and Rab interactor 3	protein-coding
mm_46772.1	chr5	112326237	112326267	-	1	NA	promoter-TSS (NM_018783)	promoter-TSS (NM_018783)	-117	NM_018783	54723	Mm.172947	NM_018783	ENSMUSG00000029345	Tfip11	2810002G02Rik|AF097181|AW046167|Srr1|TIP33|Tip39	tuftelin interacting protein 11	protein-coding
mm_12645.1	chr2	74727191	74727201	+	1	NA	5' UTR (NM_010469, exon 5 of 6)	5' UTR (NM_010469, exon 5 of 6)	1126	NR_029566	387144		NR_029566	ENSMUSG00000065500	Mir10b	Mirn10b|mir-10b|mmu-mir-10b	microRNA 10b	ncRNA
mm_83255.1	chr9	42401677	42401697	-	1	NA	Intergenic	Intergenic	-1758	NM_001324548	21683	Mm.42209	NM_009347	ENSMUSG00000037705	Tecta	Tctna	tectorin alpha	protein-coding
mm_149093.1	chr19	8929555	8929581	+	1	NA	promoter-TSS (NM_144872)	promoter-TSS (NM_144872)	-126	NM_144872	225898	Mm.31008	NM_144872	ENSMUSG00000071647	Eml3	BC022146	echinoderm microtubule associated protein like 3	protein-coding
mm_49127.1	chr6	8545326	8545329	+	1	NA	intron (NM_133236, intron 2 of 7)	intron (NM_133236, intron 2 of 7)	25269	NM_001286729	170772	Mm.210787	NM_133236	ENSMUSG00000029638	Glcci1	2310047L21Rik|A130036A18Rik|Fam117c|Gig18|Tssn1	glucocorticoid induced transcript 1	protein-coding
mm_146651.1	chr18	11051439	11051453	-	1	NA	intron (NR_105022, intron 1 of 3)	intron (NR_105022, intron 1 of 3)	-1064	NM_010258	14465	Mm.329287	NM_010258	ENSMUSG00000005836	Gata6	AA410133|GATA-6	GATA binding protein 6	protein-coding
mm_121670.1	chr14	12466924	12466939	-	1	NA	intron (NM_012061, intron 19 of 28)	intron (NM_012061, intron 19 of 28)	-121066	NM_080433	54713	Mm.34644	NM_080433	ENSMUSG00000021743	Fezf2	AI451466|AI852056|Fez|Fezl|Zfp312	Fez family zinc finger 2	protein-coding
mm_3540.1	chr1	150395241	150395254	+	1	NA	exon (NM_133780, exon 3 of 52)	exon (NM_133780, exon 3 of 52)	-2192	NM_145511	226499	Mm.222093	NM_145511	ENSMUSG00000006010	BC003331	1810053E15Rik|Odr4|odr-4	cDNA sequence BC003331	protein-coding
mm_44030.1	chr5	147430731	147430743	+	1	NA	exon (NM_028291, exon 1 of 19)	exon (NM_028291, exon 1 of 19)	157	NM_028291	72587	Mm.320469	NM_028291	ENSMUSG00000029647	Pan3	2700050F09Rik|A430027N15Rik|AU014670	PAN3 poly(A) specific ribonuclease subunit	protein-coding
mm_164955.1	chr19	5569346	5569391	+	1	NA	exon (NM_001033448, exon 2 of 2)	exon (NM_001033448, exon 2 of 2)	1294	NM_001033448	381201	Mm.441906	NM_001033448	ENSMUSG00000049562	Ap5b1	Gm962	adaptor-related protein complex 5, beta 1 subunit	protein-coding
mm_94400.1	chr11	5628757	5628767	+	1	NA	exon (NM_023816, exon 16 of 27)	exon (NM_023816, exon 16 of 27)	59078	NM_023816	76389	Mm.67300	NM_023816	ENSMUSG00000020481	Ankrd36	1700008J08Rik|1700012M14Rik|Ankrd48	ankyrin repeat domain 36	protein-coding
mm_97585.1	chr11	78945670	78945679	+	1	NA	exon (NM_010927, exon 14 of 27)	exon (NM_010927, exon 14 of 27)	20383	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_90076.1	chr10	116418118	116418137	+	1	NA	promoter-TSS (NR_028107)	promoter-TSS (NR_028107)	6	NR_028107	67342	Mm.245800	NM_026098	ENSMUSG00000020164	Kcnmb4os1	1700058G18Rik	potassium large conductance calcium-activated channel, subfamily M, beta member 4, opposite strand 1	ncRNA
mm_81244.1	chr9	107972101	107972114	+	1	NA	3' UTR (NM_011634, exon 15 of 15)	3' UTR (NM_011634, exon 15 of 15)	-3460	NM_023738	74153	Mm.277125	NM_023738	ENSMUSG00000032596	Uba7	1300004C08Rik|Ube1l	ubiquitin-like modifier activating enzyme 7	protein-coding
mm_61031.1	chr7	49526382	49526385	+	1	NA	intron (NM_175272, intron 11 of 37)	intron (NM_175272, intron 11 of 37)	110452	NM_001005232	13172	Mm.307176	NM_001005232	ENSMUSG00000030507	Dbx1	AI426026|Dbx	developing brain homeobox 1	protein-coding
mm_103633.1	chr11	78949198	78949204	-	1	NA	exon (NM_010927, exon 18 of 27)	exon (NM_010927, exon 18 of 27)	23910	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_102883.1	chr11	69410697	69410707	-	1	NA	intron (NM_001017426, intron 1 of 22)	CpG	2973	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_95711.1	chr11	54507279	54507287	+	1	NA	intron (NM_173753, intron 15 of 17)	L1_Mus1|LINE|L1	-15562	NM_001252494	192786	Mm.254404	NM_175258	ENSMUSG00000037533	Rapgef6	A530068K01|AI844632|BB085664|C030018K18Rik|PDZ-GEF2|Pdzgef2|RA-GEF-2|Ragef2|mKIAA4052	Rap guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_62880.1	chr7	114753833	114753837	+	1	NA	intron (NM_173767, intron 1 of 12)	intron (NM_173767, intron 1 of 12)	8069	NM_173767	233752	Mm.83037	NM_173767	ENSMUSG00000048782	Insc	3830422K02Rik|C730020D23	inscuteable homolog (Drosophila)	protein-coding
mm_114970.1	chr13	97240448	97240465	+	1	NA	promoter-TSS (NM_007930)	promoter-TSS (NM_007930)	-649	NM_007930	13803	Mm.241073	NM_007930	ENSMUSG00000041773	Enc1	Nrpb|PIG10	ectodermal-neural cortex 1	protein-coding
mm_131994.1	chr16	25048367	25048387	+	1	NA	Intergenic	Intergenic	-11262	NR_040374	319487	Mm.137341	NR_040374	ENSMUSG00000096960	A230028O05Rik	-	RIKEN cDNA A230028O05 gene	ncRNA
mm_84762.1	chr9	75599109	75599118	-	1	NA	promoter-TSS (NM_001038710)	promoter-TSS (NM_001038710)	20	NM_001038710	50876	Mm.291880	NM_016711	ENSMUSG00000032186	Tmod2	N-Tmod|NTMOD	tropomodulin 2	protein-coding
mm_113207.1	chr13	25056156	25056205	+	1	NA	5' UTR (NM_177577, exon 1 of 10)	5' UTR (NM_177577, exon 1 of 10)	176	NM_177577	195208	Mm.284719	NM_177577	ENSMUSG00000035910	Dcdc2a	AW492955|Dcdc2|RU2	doublecortin domain containing 2a	protein-coding
mm_99903.1	chr11	109667604	109667627	+	1	NA	3' UTR (NM_001313974, exon 11 of 11)	3' UTR (NM_001313974, exon 11 of 11)	16694	NM_001313976	19084	Mm.30039	NM_021880	ENSMUSG00000020612	Prkar1a	1300018C22Rik|RIalpha|Tse-1|Tse1	protein kinase, cAMP dependent regulatory, type I, alpha	protein-coding
mm_28602.1	chr3	94582665	94582676	-	1	NA	promoter-TSS (NM_029721)	promoter-TSS (NM_029721)	46	NM_001082484	76742	Mm.28160	NM_029721	ENSMUSG00000028136	Snx27	5730552M22Rik|ESTM45|ESTM47|R75405	sorting nexin family member 27	protein-coding
mm_38343.1	chr4	137769664	137769675	-	1	NA	intron (NM_007431, intron 1 of 11)	intron (NM_007431, intron 1 of 11)	-3194	NM_001287172	11647	Mm.288186	NM_007431	ENSMUSG00000028766	Alpl	ALP|APTNAP|Akp-2|Akp2|TNAP|TNSALP	alkaline phosphatase, liver/bone/kidney	protein-coding
mm_146999.1	chr18	34372445	34372486	-	1	NA	exon (NM_007874, exon 2 of 5)	exon (NM_007874, exon 2 of 5)	950	NM_007874	13476	Mm.280075	NM_007874	ENSMUSG00000005873	Reep5	AI324241|AU022809|AW495741|DP1/TB2|Dp1|R74856|TB2/DP1	receptor accessory protein 5	protein-coding
mm_160582.1	chr9	63146995	63146995	-	1	NA	promoter-TSS (NM_001163757)	promoter-TSS (NM_001163757)	-15	NM_172446	207667	Mm.36349	NM_172446	ENSMUSG00000022245	Skor1	AV273001|C230094B15Rik|Corl1|Lbxcor1	SKI family transcriptional corepressor 1	protein-coding
mm_47939.1	chr5	135351270	135351280	-	1	NA	Intergenic	Intergenic	-1231	NM_001277891	94244	Mm.26037	NM_033571	ENSMUSG00000040013	Fkbp6	1700008G22Rik|36kDa|AU017274|D5Ertd724e|FKBP-36|FKBP-6	FK506 binding protein 6	protein-coding
mm_87079.1	chr10	29310989	29310995	+	1	NA	Intergenic	MT2B1|LTR|ERVL	-2174	NM_001110195	52665	Mm.28930	NM_025855	ENSMUSG00000019883	Echdc1	1700028A24Rik|AI314462|AI930038|D10Ertd667e|MMCD	enoyl Coenzyme A hydratase domain containing 1	protein-coding
mm_75979.1	chr8	72162950	72162960	-	1	NA	intron (NM_023126, intron 1 of 7)	intron (NM_023126, intron 1 of 7)	1755	NM_023126	17274	Mm.162811	NM_023126	ENSMUSG00000003037	Rab8a	AA409338|Mel	RAB8A, member RAS oncogene family	protein-coding
mm_171396.1	chr4	122474066	122474066	+	1	NA	Intergenic	RLTR10C|LTR|ERVK	-215193	NM_023865	77432	Mm.491436	NM_023865	ENSMUSG00000023263	9530002B09Rik	Aump|Vpp1|Vppl	RIKEN cDNA 9530002B09 gene	protein-coding
mm_66865.1	chr7	57165178	57165182	-	1	NA	intron (NM_008074, intron 3 of 9)	intron (NM_008074, intron 3 of 9)	221691	NM_008074	14407	Mm.434343	NM_008074	ENSMUSG00000055026	Gabrg3	B230362M20Rik|Gabrg-3	gamma-aminobutyric acid (GABA) A receptor, subunit gamma 3	protein-coding
mm_15775.1	chr2	164333296	164333326	+	1	NA	exon (NM_009301, exon 2 of 3)	exon (NM_009301, exon 2 of 3)	546	NM_009301	20944	Mm.140154	NM_009301	ENSMUSG00000017004	Svs5	BB115186|Semg1|Svp-1|Svp1|Svp5	seminal vesicle secretory protein 5	protein-coding
mm_98210.1	chr11	87797584	87797590	+	1	NA	exon (NM_010824, exon 8 of 14)	exon (NM_010824, exon 8 of 14)	3803	NM_010824	17523	Mm.4668	NM_010824	ENSMUSG00000009350	Mpo	mKIAA4033	myeloperoxidase	protein-coding
mm_37131.1	chr4	116708313	116708356	-	1	NA	promoter-TSS (NM_026714)	promoter-TSS (NM_026714)	51	NM_025962	67096	Mm.252785	NM_025962	ENSMUSG00000028690	Mmachc	1810037K07Rik|CblC	methylmalonic aciduria cblC type, with homocystinuria	protein-coding
mm_133699.1	chr16	92946800	92946823	+	1	NA	Intergenic	Intergenic	-120737	NM_001111022	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_82149.1	chr9	123774853	123774869	+	1	NA	intron (NM_009913, intron 2 of 2)	intron (NM_009913, intron 2 of 2)	7650	NM_001166625	12769	Mm.440604	NM_009913	ENSMUSG00000029530	Ccr9	A130091K22Rik|Cmkbr10|GPR-9-6	chemokine (C-C motif) receptor 9	protein-coding
mm_37895.1	chr4	132567492	132567502	-	1	NA	intron (NM_001081211, intron 1 of 1)	intron (NM_001081211, intron 1 of 1)	3430	NM_001081211	19204	Mm.89389	NM_001081211	ENSMUSG00000056529	Ptafr	PAFR	platelet-activating factor receptor	protein-coding
mm_150912.1	chr19	46064080	46064087	+	1	NA	exon (NM_001081214, exon 5 of 14)	exon (NM_001081214, exon 5 of 14)	7544	NM_001081214	226169	Mm.2415	NM_145504	ENSMUSG00000055491	Pprc1	A930018M19|BC013720|PRC|mKIAA0595	peroxisome proliferative activated receptor, gamma, coactivator-related 1	protein-coding
mm_154775.1	chrX	12762246	12762293	+	1	NA	promoter-TSS (NM_001048208)	promoter-TSS (NM_001048208)	-9	NR_045852	552913	Mm.216846	NR_045852	ENSMUSG00000085891	Gm14634	OTTMUSG00000017535	predicted gene 14634	ncRNA
mm_123887.1	chr14	72709970	72709978	-	1	NA	promoter-TSS (NM_207636)	promoter-TSS (NM_207636)	29	NM_207636	319448	Mm.205421	NM_207636	ENSMUSG00000033487	Fndc3a	1700094E19Rik|D14Ertd453e|F730017H24Rik|Fndc3|sys	fibronectin type III domain containing 3A	protein-coding
mm_71295.1	chr8	41218121	41218165	+	1	NA	Intergenic	RLTR20B3A_MM|LTR|ERVK	-2987	NM_145594	234199	Mm.277955	NM_145594	ENSMUSG00000031594	Fgl1	Mfire1	fibrinogen-like protein 1	protein-coding
mm_69087.1	chr7	127017036	127017064	-	1	NA	TTS (NM_001102563)	TTS (NM_001102563)	302	NM_030240	67278	Mm.345385	NM_030240	ENSMUSG00000030680	Pagr1a	2900092E17Rik|C77040|PA1|PAGR1	PAXIP1 associated glutamate rich protein 1A	protein-coding
mm_172171.1	chr6	44793241	44793253	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-266814	NM_001004357	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding
mm_41982.1	chr5	107534739	107534761	+	1	NA	promoter-TSS (NM_175241)	promoter-TSS (NM_175241)	39	NM_175241	76421	Mm.67037	NM_175241	ENSMUSG00000089798	1700028K03Rik	-	RIKEN cDNA 1700028K03 gene	protein-coding
mm_44221.1	chr5	4779937	4779937	-	1	NA	Intergenic	Intergenic	-21721	NM_021457	14362	Mm.246003	NM_021457	ENSMUSG00000044674	Fzd1	AW227548|FZ-1|Fz1	frizzled class receptor 1	protein-coding
mm_74474.1	chr8	4259174	4259185	-	1	NA	promoter-TSS (NM_183315)	promoter-TSS (NM_183315)	95	NM_183315	330695	Mm.34210	NM_183315	ENSMUSG00000048644	Ctxn1	BC028881|Ctxn	cortexin 1	protein-coding
mm_163957.1	chr14	54893978	54893998	+	1	NA	promoter-TSS (NM_019402)	promoter-TSS (NM_019402)	-155	NM_019402	54196	Mm.7723	NM_019402	ENSMUSG00000022194	Pabpn1	PAB2|Pabp3|mPABII	poly(A) binding protein, nuclear 1	protein-coding
mm_162651.1	chr10	3366272	3366283	+	1	NA	5' UTR (NM_133485, exon 1 of 4)	5' UTR (NM_133485, exon 1 of 4)	127	NM_133485	76142	Mm.308126	NM_133485	ENSMUSG00000040653	Ppp1r14c	6330514J04Rik|KEPI	protein phosphatase 1, regulatory (inhibitor) subunit 14c	protein-coding
mm_107908.1	chr12	70974715	70974726	+	1	NA	promoter-TSS (NM_011184)	promoter-TSS (NM_011184)	97	NM_011184	19167	Mm.296338	NM_011184	ENSMUSG00000060073	Psma3	Lmpc8	proteasome (prosome, macropain) subunit, alpha type 3	protein-coding
mm_119526.1	chr14	47621425	47621425	+	1	NA	Intergenic	MLT1E2|LTR|ERVL-MaLR	-27886	NM_001347527	16709	Mm.3110	NM_008477	ENSMUSG00000021843	Ktn1	-	kinectin 1	protein-coding
mm_46000.1	chr5	90640603	90640695	-	1	NA	promoter-TSS (NM_028478)	promoter-TSS (NM_028478)	-122	NM_001310656	73246	Mm.30172	NM_028478	ENSMUSG00000029370	Rassf6	1600016B17Rik	Ras association (RalGDS/AF-6) domain family member 6	protein-coding
mm_20049.1	chr2	120245078	120245105	-	1	NA	5' UTR (NM_177845, exon 1 of 20)	5' UTR (NM_177845, exon 1 of 20)	244	NM_177845	329502	Mm.330505	NM_177845	ENSMUSG00000050211	Pla2g4e	2310026J01Rik|C230096D22|Pla2epsilon	phospholipase A2, group IVE	protein-coding
mm_40359.1	chr5	48001659	48001692	+	1	NA	intron (NR_111900, intron 4 of 35)	intron (NR_111900, intron 4 of 35)	18520	NM_001291228	20563	Mm.289739	NM_178804	ENSMUSG00000031558	Slit2	Drad-1|E030015M03Rik|E130320P19Rik|Slil3|mKIAA4141|slit-2	slit homolog 2 (Drosophila)	protein-coding
mm_9452.1	chr1	172602584	172602590	-	1	NA	promoter-TSS (NM_001164725)	promoter-TSS (NM_001164725)	-36	NM_001164725	677296	Mm.439612	NM_001164725	ENSMUSG00000070504	Fcrl6	ENSMUSG00000070504|FcRH6|mIFGP6|moFcRH6	Fc receptor-like 6	protein-coding
mm_169585.1	chr15	25046417	25046417	+	1	NA	Intergenic	B1_Mus1|SINE|Alu	367347	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	brain abundant, membrane attached signal protein 1	protein-coding
mm_121504.1	chr14	121930917	121930927	+	1	NA	intron (NM_026861, intron 4 of 8)	L1ME3A|LINE|L1	-15148	NM_182806	110168	Mm.37405	NM_182806	ENSMUSG00000050350	Gpr18	-	G protein-coupled receptor 18	protein-coding
mm_103507.1	chr11	76611143	76611146	-	1	NA	Intergenic	Intergenic	-33405	NM_198894	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_128734.1	chr15	64242691	64242698	-	1	NA	intron (NM_010026, intron 3 of 30)	intron (NM_010026, intron 3 of 30)	69979	NM_001276462	13196	Mm.277236	NM_010026	ENSMUSG00000022377	Asap1	AV239055|DEF-1|Ddef1|PAP|mKIAA1249|s19	ArfGAP with SH3 domain, ankyrin repeat and PH domain1	protein-coding
mm_70575.1	chr8	13165893	13165907	+	1	NA	exon (NM_010684, exon 2 of 9)	exon (NM_010684, exon 2 of 9)	6739	NM_010684	16783	Mm.16716	NM_010684	ENSMUSG00000031447	Lamp1	CD107a|LGP-120|LGP-A|Lamp-1|P2B	lysosomal-associated membrane protein 1	protein-coding
mm_80541.1	chr9	80681902	80681913	+	1	NA	Intergenic	MLT1A1|LTR|ERVL-MaLR	-216469	NM_022016	63859	Mm.422780	NM_022016	ENSMUSG00000032343	Impg1	A930015H12Rik|IMP150|SPACR	interphotoreceptor matrix proteoglycan 1	protein-coding
mm_69164.1	chr7	127210327	127210329	-	1	NA	intron (NM_001347655, intron 1 of 6)	intron (NM_001347655, intron 1 of 6)	-1280	NM_016754	17907	Mm.14526	NM_016754	ENSMUSG00000030672	Mylpf	2410014J02Rik|MLC-2|Mlc2	myosin light chain, phosphorylatable, fast skeletal muscle	protein-coding
mm_33378.1	chr4	129515876	129515912	+	1	NA	TTS (NM_008228)	TTS (NM_008228)	2313	NM_010807	17357	Mm.424974	NM_010807	ENSMUSG00000047945	Marcksl1	AL022768|AW215397|AW536807|D4Bc1|F52|MacMARCKS|Macs2|Macs3|Mlp|Mrp	MARCKS-like 1	protein-coding
mm_76196.1	chr8	82403239	82403247	-	1	NA	promoter-TSS (NM_001254747)	promoter-TSS (NM_001254747)	-657	NM_008357	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_84637.1	chr9	71163296	71163315	-	1	NA	promoter-TSS (NM_001271843)	promoter-TSS (NM_001271843)	-16	NM_022026	64008	Mm.449427	NM_022026	ENSMUSG00000032204	Aqp9	1700020I22Rik|AI266899|AQP-9	aquaporin 9	protein-coding
mm_20405.1	chr2	129299808	129299817	-	1	NA	3' UTR (NM_010554, exon 7 of 7)	3' UTR (NM_010554, exon 7 of 7)	2442	NR_040371	100503468	Mm.446943	NR_040371	ENSMUSG00000085498	Gm14023	OTTMUSG00000015408	predicted gene 14023	ncRNA
mm_89174.1	chr10	86331653	86331660	+	1	NA	intron (NM_011595, intron 1 of 4)	intron (NM_011595, intron 1 of 4)	31244	NM_011595	21859	Mm.4871	NM_011595	ENSMUSG00000020044	Timp3	Timp-3	tissue inhibitor of metalloproteinase 3	protein-coding
mm_47907.1	chr5	134946022	134946031	-	1	NA	3' UTR (NM_009903, exon 1 of 1)	3' UTR (NM_009903, exon 1 of 1)	908	NM_009903	12740	Mm.7339	NM_009903	ENSMUSG00000047501	Cldn4	Cep-r|Cpetr|Cpetr1	claudin 4	protein-coding
mm_3754.1	chr1	156040885	156040898	+	1	NA	promoter-TSS (NM_001160181)	promoter-TSS (NM_001160181)	30	NM_022329	240832	Mm.253335	NM_022329	ENSMUSG00000050565	Tor1aip2	1110020D10Rik|15kDa|A130072J07|AA103493|AW060462|AW610675|C77739|Ifrg15|Lull1	torsin A interacting protein 2	protein-coding
mm_21576.1	chr2	164237166	164237166	-	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	1175	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_171243.1	chr3	75372532	75372550	+	1	NA	Intergenic	L1Md_T|LINE|L1	-102463	NM_026460	67931	Mm.259446	NM_026460	ENSMUSG00000034139	Serpini2	Spi14	serine (or cysteine) peptidase inhibitor, clade I, member 2	protein-coding
mm_65886.1	chr7	29906088	29906137	-	1	NA	promoter-TSS (NM_011754)	promoter-TSS (NM_011754)	-8	NM_001037707	22689	Mm.86747	NM_011754	ENSMUSG00000062040	Zfp27	Zfp-27|mkr-4|mszf76	zinc finger protein 27	protein-coding
mm_129622.1	chr15	80083375	80083420	-	1	NA	promoter-TSS (NM_013762)	promoter-TSS (NM_013762)	9	NM_013762	27367	Mm.290771	NM_013762	ENSMUSG00000060036	Rpl3	F2|J1	ribosomal protein L3	protein-coding
mm_20031.1	chr2	119662757	119662835	-	1	NA	promoter-TSS (NM_027175)	promoter-TSS (NM_027175)	2	NM_027175	69702	Mm.5390	NM_027175	ENSMUSG00000027305	Ndufaf1	2410001M24Rik|CGI-65|CIA30	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, assembly factor 1	protein-coding
mm_103288.1	chr11	72267142	72267164	-	1	NA	promoter-TSS (NM_001004148)	promoter-TSS (NM_001004148)	309	NR_045922	73366	Mm.396157	NR_045922	ENSMUSG00000086951	1700051A21Rik	-	RIKEN cDNA 1700051A21 gene	ncRNA
mm_13062.1	chr2	91115408	91115438	+	1	NA	3' UTR (NM_011355, exon 5 of 5)	3' UTR (NM_011355, exon 5 of 5)	-2721	NM_008653	17868	Mm.10728	NM_008653	ENSMUSG00000002100	Mybpc3	-	myosin binding protein C, cardiac	protein-coding
mm_74116.1	chr8	123065491	123065529	+	1	NA	promoter-TSS (NM_153176)	promoter-TSS (NM_153176)	2	NM_153176	234847	Mm.292075	NM_153176	ENSMUSG00000000738	Spg7	AI452278|AU015315|Cmar|PGN	spastic paraplegia 7 homolog (human)	protein-coding
mm_112309.1	chr12	114835696	114835710	-	1	NA	Intergenic	Intergenic	-322009	NR_106063	102465664		NR_106063	ENSMUSG00000098357	Mir7094-2	Gm27508|mmu-mir-7094-2	microRNA 7094-2	ncRNA
mm_34248.1	chr4	141278434	141278462	+	1	NA	Intergenic	Intergenic	-22773	NM_010139	13836	Mm.2581	NM_010139	ENSMUSG00000006445	Epha2	AW545284|Eck|Myk2|Sek-2|Sek2	Eph receptor A2	protein-coding
mm_91456.1	chr10	34044279	34044283	-	1	NA	promoter-TSS (NM_001081165)	promoter-TSS (NM_001081165)	32	NM_001081165	270711	Mm.303077	NM_001081165	ENSMUSG00000039508	Fam26d	4732454E20Rik|AI586164|Gm643	family with sequence similarity 26, member D	protein-coding
mm_333.1	chr1	27884018	27884028	+	1	NA	Intergenic	Intergenic	896229	NM_001013750	210962	Mm.214178	NM_001013750	ENSMUSG00000048411	Gm597	-	predicted gene 597	protein-coding
mm_113904.1	chr13	49247472	49247472	+	1	NA	intron (NM_028340, intron 1 of 4)	U2|snRNA|snRNA	691	NM_025491	66329	Mm.34308	NM_025491	ENSMUSG00000021384	Susd3	1700017I11Rik|2810440J20Rik	sushi domain containing 3	protein-coding
mm_47782.1	chr5	131982476	131982482	-	1	NA	intron (NM_177047, intron 4 of 18)	intron (NM_177047, intron 4 of 18)	102210	NR_040704	75369	Mm.389696	NR_040704	ENSMUSG00000105773	4930563F08Rik	-	RIKEN cDNA 4930563F08 gene	ncRNA
mm_144679.1	chr18	34758891	34758897	+	1	NA	promoter-TSS (NM_175104)	promoter-TSS (NM_175104)	-12	NM_175104	66306	Mm.29424	NM_175104	ENSMUSG00000034300	Fam53c	2810012G03Rik|Gm21179	family with sequence similarity 53, member C	protein-coding
mm_39007.1	chr4	152027633	152027684	-	1	NA	promoter-TSS (NM_133879)	promoter-TSS (NM_133879)	13	NM_133879	100090	Mm.24661	NM_133879	ENSMUSG00000028952	Zbtb48	0610011D15Rik|AI327031|Hkr3	zinc finger and BTB domain containing 48	protein-coding
mm_115374.1	chr13	113071463	113071477	+	1	NA	intron (NM_001281487, intron 5 of 11)	intron (NM_001281487, intron 5 of 11)	-25082	NM_027127	69590	Mm.12715	NM_027127	ENSMUSG00000021760	Gpx8	2310016C16Rik|AU017063	glutathione peroxidase 8 (putative)	protein-coding
mm_34038.1	chr4	138175875	138175887	+	1	NA	exon (NM_001256198, exon 22 of 33)	exon (NM_001256198, exon 22 of 33)	12672	NR_105825	102466907		NR_105825	ENSMUSG00000098513	Mir6399	Gm27667|mir-6399|mmu-mir-6399	microRNA 6399	ncRNA
mm_15171.1	chr2	154014934	154014941	+	1	NA	exon (NM_008953, exon 8 of 9)	exon (NM_008953, exon 8 of 9)	6661	NM_008953	19194	Mm.29197	NM_008953	ENSMUSG00000042459	Bpifa2	Bpifa2e|Psp	BPI fold containing family A, member 2	protein-coding
mm_137532.1	chr17	27555636	27555646	+	1	NA	promoter-TSS (NM_001166545)	promoter-TSS (NM_001166545)	-933	NM_001166536	15361	Mm.4438	NM_016660	ENSMUSG00000046711	Hmga1	AL023995|Hmga1a|Hmga1b|Hmgi|Hmgiy|Hmgy	high mobility group AT-hook 1	protein-coding
mm_57948.1	chr6	134898187	134898202	-	1	NA	promoter-TSS (NM_001167694)	promoter-TSS (NM_001167694)	233	NR_029441	72813	Mm.409034	NR_029441	ENSMUSG00000100876	2810454H06Rik	-	RIKEN cDNA 2810454H06 gene	ncRNA
mm_6023.1	chr1	59151680	59151686	-	1	NA	exon (NM_145143, exon 4 of 22)	exon (NM_145143, exon 4 of 22)	9953	NM_145143	227157	Mm.474049	NM_145143	ENSMUSG00000079550	Mpp4	Dlg6	membrane protein, palmitoylated 4 (MAGUK p55 subfamily member 4)	protein-coding
mm_60788.1	chr7	45567020	45567053	+	1	NA	TTS (NR_038166)	TTS (NR_038166)	-3117	NM_009737	12036	Mm.24210	NM_009737	ENSMUSG00000030826	Bcat2	Bcat-2|Eca40	branched chain aminotransferase 2, mitochondrial	protein-coding
mm_39308.1	chr5	7972471	7972501	+	1	NA	intron (NM_054098, intron 1 of 4)	LTR16E2|LTR|ERVL	12014	NM_054098	117167	Mm.31403	NM_054098	ENSMUSG00000012428	Steap4	1110021O17Rik|AI481214|Tiarp|Tnfaip9	STEAP family member 4	protein-coding
mm_152077.1	chr19	6853640	6853665	-	1	NA	exon (NM_001081291, exon 14 of 27)	exon (NM_001081291, exon 14 of 27)	4559	NM_001081291	78317	Mm.329596	NM_198008	ENSMUSG00000047810	Ccdc88b	2610041P08Rik|Ccdc88	coiled-coil domain containing 88B	protein-coding
mm_20175.1	chr2	122467725	122467750	-	1	NA	promoter-TSS (NR_027919)	promoter-TSS (NR_027919)	60	NR_027919	81913	Mm.122640	NR_027919		Bambi-ps1	-	BMP and activin membrane-bound inhibitor, pseudogene (Xenopus laevis)	pseudo
mm_41478.1	chr5	91962876	91962910	+	1	NA	promoter-TSS (NR_028429)	promoter-TSS (NR_028429)	11	NR_028429	381650	Mm.159453	NR_028429	ENSMUSG00000102644	Thap6	4930534K21Rik|AI448650	THAP domain containing 6	pseudo
mm_44821.1	chr5	33657638	33657666	-	1	NA	promoter-TSS (NM_001040435)	promoter-TSS (NM_001040435)	180	NM_026698	68366	Mm.491151	NM_026698	ENSMUSG00000019295	Tmem129	0610039G24Rik|2410015J15Rik|AA409575	transmembrane protein 129	protein-coding
mm_21856.1	chr2	165884183	165884232	-	1	NA	intron (NM_027230, intron 1 of 23)	intron (NM_027230, intron 1 of 23)	631	NM_001252584	228880	Mm.227598	NM_027230	ENSMUSG00000039671	Zmynd8	1110013E22Rik|2010005I16Rik|3632413B07Rik|AI316811|AL024039|Prkcbp1|RACK7	zinc finger, MYND-type containing 8	protein-coding
mm_152964.1	chr19	29367273	29367287	-	1	NA	promoter-TSS (NM_021893)	promoter-TSS (NM_021893)	-158	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_172852.1	chr9	37453714	37453717	+	1	NA	Intergenic	Intergenic	-20540	NM_001164767	19649	Mm.212826	NM_011248	ENSMUSG00000032128	Robo3	Rbig1|Rig-1|Rig1|Robo3a|Robo3b	roundabout guidance receptor 3	protein-coding
mm_147998.1	chr18	67677778	67677814	-	1	NA	exon (NM_001127177, exon 7 of 9)	exon (NM_001127177, exon 7 of 9)	36197	NM_134138	107047	Mm.150701	NM_134138	ENSMUSG00000024537	Psmg2	1700017I17Rik|AW545363|Clast3|Tnfsf5ip1	proteasome (prosome, macropain) assembly chaperone 2	protein-coding
mm_56796.1	chr6	116647872	116647890	-	1	NA	intron (NM_178045, intron 3 of 10)	intron (NM_178045, intron 3 of 10)	-1834	NR_106010	102466793		NR_106010	ENSMUSG00000098334	Mir7043	Gm27776|mmu-mir-7043	microRNA 7043	ncRNA
mm_130365.1	chr15	97791372	97791418	-	1	NA	3' UTR (NM_026353, exon 3 of 3)	3' UTR (NM_026353, exon 3 of 3)	7030	NM_026353	67739	Mm.28955	NM_026353	ENSMUSG00000081534	Slc48a1	4930570C03Rik	solute carrier family 48 (heme transporter), member 1	protein-coding
mm_2504.1	chr1	106201864	106201864	+	1	NA	intron (NM_133821, intron 1 of 16)	intron (NM_133821, intron 1 of 16)	29995	NM_133821	98432	Mm.24115	NM_133821	ENSMUSG00000044340	Phlpp1	AI836256|Phlpp|Plekhe1|SCOP|mKIAA0606	PH domain and leucine rich repeat protein phosphatase 1	protein-coding
mm_99279.1	chr11	101279113	101279147	+	1	NA	promoter-TSS (NM_026618)	promoter-TSS (NM_026618)	-73	NM_026562	68107	Mm.262369	NM_026562	ENSMUSG00000078653	Cntd1	1700051C09Rik|4921513J16Rik|5430417M23Rik|Cntd	cyclin N-terminal domain containing 1	protein-coding
mm_11684.1	chr2	35582830	35582851	+	1	NA	promoter-TSS (NM_001290637)	promoter-TSS (NM_001290637)	0	NM_001290637	69601	Mm.29629	NM_001001602	ENSMUSG00000026883	Dab2ip	2310011D08Rik|AI480459|Aip1|mKIAA1743	disabled 2 interacting protein	protein-coding
mm_163777.1	chr13	120044034	120044039	-	1	NA	intron (NM_001302966, intron 4 of 5)	B1_Mur2|SINE|Alu	8168	NM_001302966	100861753	Mm.165042	NM_001302966	ENSMUSG00000095609	Gm21188	-	predicted gene, 21188	protein-coding
mm_126273.1	chr15	79141365	79141390	+	1	NA	promoter-TSS (NM_001310576)	promoter-TSS (NM_001310576)	52	NM_027231	69833	Mm.279861	NM_027231	ENSMUSG00000033020	Polr2f	1810060D16Rik|RPB6	polymerase (RNA) II (DNA directed) polypeptide F	protein-coding
mm_18673.1	chr2	71055505	71055513	-	1	NA	promoter-TSS (NM_001165981)	promoter-TSS (NM_001165981)	97	NM_145524	228019	Mm.490343	NM_145524	ENSMUSG00000041975	Mettl8	BC004636|Tip	methyltransferase like 8	protein-coding
mm_145550.1	chr18	60809973	60810023	+	1	NA	exon (NM_010545, exon 5 of 8)	exon (NM_010545, exon 5 of 8)	-2078	NR_039567	100628611		NR_039567	ENSMUSG00000093327	Mir5107	mir-5107|mmu-mir-5107|mu-mir-5107	microRNA 5107	ncRNA
mm_132157.1	chr16	32179777	32179788	+	1	NA	promoter-TSS (NM_001033539)	promoter-TSS (NM_001033539)	-18	NM_001033539	328660	Mm.441006	NM_001033539	ENSMUSG00000075269	Bex6	B020003O03Rik	brain expressed family member 6	protein-coding
mm_72297.1	chr8	75448752	75448760	+	1	NA	promoter-TSS (NM_027944)	promoter-TSS (NM_027944)	62	NM_001164235	71831	Mm.443238	NM_027944	ENSMUSG00000031620	1700007B14Rik	-	RIKEN cDNA 1700007B14 gene	protein-coding
mm_135531.1	chr16	49768728	49768738	-	1	NA	Intergenic	ORR1D1|LTR|ERVL-MaLR	69439	NM_028680	73916	Mm.241276	NM_028680	ENSMUSG00000032965	Ift57	4833420A15Rik|Esrrbl1|Hippi|MHS4R2	intraflagellar transport 57	protein-coding
mm_134362.1	chr16	16863976	16864006	-	1	NA	promoter-TSS (NM_001190325)	promoter-TSS (NM_001190325)	-6	NM_001190325	16136	Mm.184441	NM_001190325	ENSMUSG00000075370	Igll1	BB139905|Igl-5|Igll|Lambda5	immunoglobulin lambda-like polypeptide 1	protein-coding
mm_120574.1	chr14	69171979	69171993	+	1	NA	promoter-TSS (NR_045931)	promoter-TSS (NR_045931)	-143	NR_045931	73554	Mm.320005	NR_045931	ENSMUSG00000092499	1700092C10Rik	-	RIKEN cDNA 1700092C10 gene	ncRNA
mm_130203.1	chr15	95527979	95528014	-	1	NA	intron (NM_001289653, intron 1 of 20)	CpG-5276	256	NM_001289653	54003	Mm.3959	NM_016743	ENSMUSG00000022454	Nell2	A330108N19Rik|R75516|mel91	NEL-like 2	protein-coding
mm_45377.1	chr5	66080972	66081009	-	1	NA	intron (NM_178446, intron 2 of 6)	intron (NM_178446, intron 2 of 6)	17189	NM_139065	245945	Mm.36863	NM_139065	ENSMUSG00000070780	Rbm47	9530077J19Rik	RNA binding motif protein 47	protein-coding
mm_100563.1	chr11	120730495	120730507	+	1	NA	exon (NM_007621, exon 5 of 8)	exon (NM_007621, exon 5 of 8)	1520	NM_007621	12409	Mm.21454	NM_007621	ENSMUSG00000025150	Cbr2	MLCR	carbonyl reductase 2	protein-coding
mm_111043.1	chr12	79493634	79493638	-	1	NA	intron (NM_009014, intron 7 of 10)	MLT1E3|LTR|ERVL-MaLR	196285	NM_001252562	19363	Mm.341756	NM_009014	ENSMUSG00000059060	Rad51b	AI553500|R51H2|Rad51l1|mREC2	RAD51 paralog B	protein-coding
mm_104938.1	chr11	100112013	100112052	-	1	NA	Intergenic	Intergenic	-6406	NM_001174099	16673	Mm.306829	NM_008472	ENSMUSG00000020916	Krt36	HRa-1|K36|Krt1-22|Krt1-5|MHRa-1	keratin 36	protein-coding
mm_90822.1	chr10	7920145	7920158	-	1	NA	exon (NM_138667, exon 3 of 7)	exon (NM_138667, exon 3 of 7)	35972	NM_138667	68652	Mm.193041	NM_138667	ENSMUSG00000015755	Tab2	1110030N06Rik|A530078N03Rik|Map3k7ip2|mKIAA0733	TGF-beta activated kinase 1/MAP3K7 binding protein 2	protein-coding
mm_92478.1	chr10	78244603	78244676	-	1	NA	promoter-TSS (NM_001081055)	promoter-TSS (NM_001081055)	3	NM_001081055	216131	Mm.27539	NM_001081055	ENSMUSG00000000374	Trappc10	B230307C21Rik|Gm870|Tmem1	trafficking protein particle complex 10	protein-coding
mm_30064.1	chr3	137878140	137878146	-	1	NA	intron (NM_001033155, intron 1 of 7)	HAL1M8|LINE|L1	10468	NM_001033155	70604	Mm.256488	NM_001033155	ENSMUSG00000074212	Dnajb14	5730496F10Rik	DnaJ heat shock protein family (Hsp40) member B14	protein-coding
mm_18142.1	chr2	45057513	45057515	-	1	NA	intron (NM_001289521, intron 1 of 8)	intron (NM_001289521, intron 1 of 8)	-34337	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_3411.1	chr1	144249384	144249390	+	1	NA	promoter-TSS (NM_015811)	promoter-TSS (NM_015811)	-283	NM_015811	50778	Mm.103701	NM_015811	ENSMUSG00000026358	Rgs1	BL34	regulator of G-protein signaling 1	protein-coding
mm_59623.1	chr7	28154629	28154638	+	1	NA	exon (NM_001164655, exon 13 of 20)	exon (NM_001164655, exon 13 of 20)	-15115	NM_007991	14113	Mm.4595	NM_007991	ENSMUSG00000046865	Fbl	AL022665|FIB|FLRN|RNU3IP1	fibrillarin	protein-coding
mm_4653.1	chr1	180342313	180342329	+	1	NA	intron (NM_001081175, intron 2 of 7)	intron (NM_001081175, intron 2 of 7)	-11772	NR_003623	277333	Mm.389223	NM_199472		Gm5069	EG277333	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_70173.1	chr7	143628398	143628411	-	1	NA	promoter-TSS (NM_175649)	promoter-TSS (NM_175649)	-559	NM_175649	244237	Mm.247498	NM_175649	ENSMUSG00000045362	Tnfrsf26	Tnfrh3|Tnfrsf24	tumor necrosis factor receptor superfamily, member 26	protein-coding
mm_77916.1	chr9	7350617	7350634	+	1	NA	intron (NM_001320077, intron 5 of 10)	intron (NM_001320077, intron 5 of 10)	3251	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_2677.1	chr1	127299971	127299999	+	1	NA	intron (NM_145128, intron 2 of 17)	Lx8|LINE|L1	94999	NM_145128	107895	Mm.214682	NM_145128	ENSMUSG00000036155	Mgat5	4930471A21Rik|5330407H02Rik|AI480971|GlcNAc-TV	mannoside acetylglucosaminyltransferase 5	protein-coding
mm_78978.1	chr9	45371639	45371655	+	1	NA	intron (NM_022004, intron 1 of 7)	intron (NM_022004, intron 1 of 7)	1462	NM_022004	59095	Mm.208287	NM_022004	ENSMUSG00000066705	Fxyd6	0610030I18Rik|Php	FXYD domain-containing ion transport regulator 6	protein-coding
mm_100078.1	chr11	115463768	115463784	+	1	NA	intron (NM_001080934, intron 1 of 3)	intron (NM_001080934, intron 1 of 3)	1303	NM_001080934	217316	Mm.25773	NM_001080934	ENSMUSG00000045775	Slc16a5	A130015N09Rik|MCT 5|MCT 6|MCT5	solute carrier family 16 (monocarboxylic acid transporters), member 5	protein-coding
mm_103841.1	chr11	83040484	83040518	-	1	NA	promoter-TSS (NR_073524)	promoter-TSS (NR_073524)	32	NR_073524	237887	Mm.341645	NM_181542	ENSMUSG00000072621	Slfn10-ps	Slfn10|mFLJ00257	schlafen 10, pseudogene	pseudo
mm_158927.1	chr1	60234919	60234919	+	1	NA	intron (NM_173444, intron 12 of 54)	intron (NM_173444, intron 12 of 54)	54320	NM_173444	269198	Mm.205224	NM_173444	ENSMUSG00000073664	Nbeal1	2310076G13Rik|A530050O19Rik|A530083I02Rik|AI662228|ALS2CR17	neurobeachin like 1	protein-coding
mm_156692.1	chrX	159459168	159459193	+	1	NA	promoter-TSS (NM_001313752)	promoter-TSS (NM_001313752)	55	NM_001313753	78283	Mm.160079	NM_001081124	ENSMUSG00000041020	Map7d2	1600028E09Rik|2900002G04Rik|5330432J06Rik|C030036K04Rik|Mtap7d2	MAP7 domain containing 2	protein-coding
mm_129319.1	chr15	77763832	77763843	-	1	NA	exon (NM_022410, exon 38 of 41)	exon (NM_022410, exon 38 of 41)	-8608	NM_001081970	239552	Mm.125650	NM_001081970	ENSMUSG00000056656	Apol8	9830006J20Rik|APOL-II|Apol2	apolipoprotein L 8	protein-coding
mm_65869.1	chr7	29505729	29505748	-	1	NA	promoter-TSS (NM_001081028)	promoter-TSS (NM_001081028)	-278	NM_001081028	74206	Mm.447042	NM_001081028	ENSMUSG00000030583	Sipa1l3	2610511M17Rik	signal-induced proliferation-associated 1 like 3	protein-coding
mm_17957.1	chr2	37367736	37367745	-	1	NA	Intergenic	L1MD2|LINE|L1	-8408	NM_026176	67466	Mm.30709	NM_026176	ENSMUSG00000009030	Pdcl	1200011E13Rik|AW108059|PhLP1	phosducin-like	protein-coding
mm_152017.1	chr19	6015153	6015198	-	1	NA	promoter-TSS (NM_007600)	promoter-TSS (NM_007600)	72	NM_007600	12333	Mm.6221	NM_007600	ENSMUSG00000024942	Capn1	Capa-1|Capa1|mu-calpin	calpain 1	protein-coding
mm_158490.1	chrX	142328033	142328047	-	1	NA	exon (NM_207625, exon 15 of 16)	exon (NM_207625, exon 15 of 16)	-21842	NM_021487	66240	Mm.58507	NM_021487	ENSMUSG00000090122	Kcne1l	1500015C14Rik|Kcne5|Mink	potassium voltage-gated channel, Isk-related family, member 1-like, pseudogene	protein-coding
mm_23023.1	chr3	34638322	34638342	+	1	NA	promoter-TSS (NR_035433)	promoter-TSS (NR_035433)	-132	NR_035433	100316679		NR_035433	ENSMUSG00000104797	Mir1897	Mirn1897|mmu-mir-1897	microRNA 1897	ncRNA
mm_14881.1	chr2	148835141	148835193	+	1	NA	promoter-TSS (NM_009979)	promoter-TSS (NM_009979)	20	NM_009979	13013	Mm.21005	NM_009979	ENSMUSG00000027445	Cst9	M12|cresp|testatin	cystatin 9	protein-coding
mm_36100.1	chr4	58553264	58553275	-	1	NA	promoter-TSS (NM_172989)	promoter-TSS (NM_172989)	24	NM_172989	14745	Mm.4772	NM_010336	ENSMUSG00000038668	Lpar1	AI326300|Edg2|Gpcr26|Kdt2|lpA1|vzg-1	lysophosphatidic acid receptor 1	protein-coding
mm_107531.1	chr12	40529622	40529626	+	1	NA	intron (NM_172803, intron 1 of 52)	(TTTTTG)n|Simple_repeat|Simple_repeat	83571	NM_172803	238130	Mm.341423	NM_172803	ENSMUSG00000035954	Dock4	5330406C03|6330411N01Rik|AF263288|C030023J22|mKIAA0716	dedicator of cytokinesis 4	protein-coding
mm_85454.1	chr9	105145012	105145014	-	1	NA	promoter-TSS (NM_028562)	promoter-TSS (NM_028562)	69	NM_028562	73532	Mm.23516	NM_028562	ENSMUSG00000032566	1700080E11Rik	AI429110|Tseg8	RIKEN cDNA 1700080E11 gene	protein-coding
mm_121958.1	chr14	24491752	24491756	-	1	NA	exon (NM_207634, exon 2 of 5)	exon (NM_207634, exon 2 of 5)	1073	NM_011297	20088	Mm.16775	NM_011297	ENSMUSG00000025290	Rps24	-	ribosomal protein S24	protein-coding
mm_53979.1	chr6	6861643	6861655	-	1	NA	intron (NR_015388, intron 1 of 1)	intron (NR_015388, intron 1 of 1)	-1685	NM_010057	13396	Mm.439763	NM_010057	ENSMUSG00000029754	Dlx6	-	distal-less homeobox 6	protein-coding
mm_34667.1	chr4	150914585	150914601	+	1	NA	Intergenic	CpG	-4672	NM_020569	57320	Mm.277349	NM_020569	ENSMUSG00000028964	Park7	DJ-1|Dj1	Parkinson disease (autosomal recessive, early onset) 7	protein-coding
mm_136645.1	chr17	5841253	5841271	+	1	NA	promoter-TSS (NM_025664)	promoter-TSS (NM_025664)	-118	NM_025664	66616	Mm.89515	NM_025664	ENSMUSG00000002365	Snx9	2700073N08Rik|SDP1|SH3PX1	sorting nexin 9	protein-coding
mm_102218.1	chr11	54909692	54909768	-	1	NA	3' UTR (NM_008161, exon 5 of 5)	3' UTR (NM_008161, exon 5 of 5)	6876	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_96436.1	chr11	67301768	67301779	+	1	NA	exon (NM_177369, exon 32 of 40)	exon (NM_177369, exon 32 of 40)	24649	NM_177369	17885	Mm.340163	NM_177369	ENSMUSG00000055775	Myh8	4832426G23Rik|AI327267|MHCp|MyHC-pn|Myhs-p|Myhsp	myosin, heavy polypeptide 8, skeletal muscle, perinatal	protein-coding
mm_47922.1	chr5	135008839	135008860	-	1	NA	promoter-TSS (NM_001190437)	promoter-TSS (NM_001190437)	-303	NM_001190437	68758	Mm.389700	NM_145215	ENSMUSG00000040532	Abhd11	1110054D16Rik|A630008N09Rik|Wbscr21	abhydrolase domain containing 11	protein-coding
mm_150161.1	chr19	32387556	32387562	+	1	NA	intron (NM_144792, intron 1 of 9)	CpG	895	NM_144792	208449	Mm.329810	NM_144792	ENSMUSG00000040451	Sgms1	9530058O11Rik|AI841905|C80702|Mob|Sms1|Sor1|Tmem23	sphingomyelin synthase 1	protein-coding
mm_128313.1	chr15	37960084	37960087	-	1	NA	intron (NM_199476, intron 1 of 8)	intron (NM_199476, intron 1 of 8)	970	NM_199476	382985	Mm.24738	NM_199476	ENSMUSG00000022292	Rrm2b	p53R2	ribonucleotide reductase M2 B (TP53 inducible)	protein-coding
mm_47340.1	chr5	122502268	122502278	-	1	NA	promoter-TSS (NM_009722)	promoter-TSS (NM_009722)	-48	NR_027838	11938	Mm.227583	NM_009722	ENSMUSG00000029467	Atp2a2	9530097L16Rik|D5Wsu150e|SERCA2|SERCA2B|Serca2a|mKIAA4195	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	protein-coding
mm_36450.1	chr4	82498519	82498535	-	1	NA	exon (NM_001113209, exon 2 of 12)	exon (NM_001113209, exon 2 of 12)	7252	NM_001286127	18028	Mm.317947	NM_008687	ENSMUSG00000008575	Nfib	6720429L07Rik|CTF|E030026I10Rik|NF-I/B|NF1-B|NFI-B	nuclear factor I/B	protein-coding
mm_76766.1	chr8	95807391	95807399	-	1	NA	promoter-TSS (NM_178078)	promoter-TSS (NM_178078)	67	NM_178078	234594	Mm.259220	NM_153164	ENSMUSG00000036550	Cnot1	6030411K04Rik|AA815922|D830048B13	CCR4-NOT transcription complex, subunit 1	protein-coding
mm_11460.1	chr2	32236580	32236595	+	1	NA	promoter-TSS (NM_145145)	promoter-TSS (NM_145145)	-96	NM_145145	99011	Mm.31192	NM_145145	ENSMUSG00000039254	Pomt1	AI505244	protein-O-mannosyltransferase 1	protein-coding
mm_15935.1	chr2	165601791	165601835	+	1	NA	intron (NM_001271963, intron 1 of 15)	intron (NM_001271963, intron 1 of 15)	6785	NM_001271963	14049	Mm.282719	NM_010165	ENSMUSG00000017897	Eya2	Eab1	EYA transcriptional coactivator and phosphatase 2	protein-coding
mm_154427.1	chrM	456	485	-	1	NA	NA	Intergenic	NA	NA								
mm_1007.1	chr1	58726065	58726075	+	1	NA	intron (NM_009805, intron 1 of 4)	intron (NM_009805, intron 1 of 4)	-4482	NM_001293805	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_40581.1	chr5	64103710	64103754	+	1	NA	exon (NM_025700, exon 6 of 14)	exon (NM_025700, exon 6 of 14)	10782	NM_025700	66681	Mm.2325	NM_025700	ENSMUSG00000029171	Pgm1	3230402E02Rik|Pgm-1|Pgm2	phosphoglucomutase 1	protein-coding
mm_108675.1	chr12	86678686	86678796	+	1	NA	promoter-TSS (NM_177354)	promoter-TSS (NM_177354)	41	NM_177354	238328	Mm.216101	NM_177354	ENSMUSG00000021256	Vash1	AI834978|D930046M13Rik|G630009D10Rik	vasohibin 1	protein-coding
mm_147563.1	chr18	54990082	54990122	-	1	NA	promoter-TSS (NM_175751)	promoter-TSS (NM_175751)	78	NM_175751	269023	Mm.192984	NM_175751	ENSMUSG00000052713	Zfp608	4932417D18Rik|D430007A19Rik|Znf608	zinc finger protein 608	protein-coding
mm_134358.1	chr16	16829259	16829261	-	1	NA	5' UTR (NM_015773, exon 1 of 11)	5' UTR (NM_015773, exon 1 of 11)	103	NM_015773	50525	Mm.31701	NM_015773	ENSMUSG00000022783	Spag6l	PF16|Spag6|Spag6l1	sperm associated antigen 6-like	protein-coding
mm_74847.1	chr8	24585351	24585374	-	1	NA	intron (NM_001293690, intron 8 of 9)	intron (NM_001293690, intron 8 of 9)	-9029	NM_145949	209176	Mm.219580	NM_145949	ENSMUSG00000031549	Ido2	AI265623|C230043N17Rik|Ido-2|Indol1	indoleamine 2,3-dioxygenase 2	protein-coding
mm_15911.1	chr2	165059923	165059931	+	1	NA	intron (NM_170702, intron 1 of 7)	intron (NM_170702, intron 1 of 7)	4291	NM_011611	21939	Mm.271833	NM_011611	ENSMUSG00000017652	Cd40	AI326936|Bp50|GP39|HIGM1|IGM|IMD3|T-BAM|TRAP|Tnfrsf5|p50	CD40 antigen	protein-coding
mm_104886.1	chr11	99556847	99556858	-	1	NA	promoter-TSS (NM_025720)	promoter-TSS (NM_025720)	1	NM_025720	66708	Mm.46389	NM_025720	ENSMUSG00000069721	Krtap3-2	2310020D06Rik|4733401L16Rik|KAP3.2|KRTAP3.2	keratin associated protein 3-2	protein-coding
mm_113975.1	chr13	51709956	51709985	+	1	NA	exon (NM_001281880, exon 13 of 17)	exon (NM_001281880, exon 13 of 17)	58262	NM_029279	75420	Mm.275981	NM_029279	ENSMUSG00000035139	Secisbp2	2210413N07Rik|2810012K13Rik|SBP2	SECIS binding protein 2	protein-coding
mm_108527.1	chr12	84126242	84126246	+	1	NA	intron (NM_001346528, intron 3 of 7)	intron (NM_001346528, intron 3 of 7)	11916	NM_001346528	105000	Mm.101525	NM_028821	ENSMUSG00000042523	Dnal1	1700010H15Rik|AW121714|Dnalc1|E330027P08Rik	dynein, axonemal, light chain 1	protein-coding
mm_107956.1	chr12	72442353	72442367	+	1	NA	5' UTR (NM_001142729, exon 1 of 16)	5' UTR (NM_001142729, exon 1 of 16)	111	NM_001142729	78257	Mm.266280	NM_030070	ENSMUSG00000021090	Lrrc9	4921529O18Rik|4930432K16Rik	leucine rich repeat containing 9	protein-coding
mm_56360.1	chr6	93815805	93815812	-	1	NA	exon (NM_010367, exon 3 of 22)	exon (NM_010367, exon 3 of 22)	97155	NR_104594	14924	Mm.217216	NM_010367	ENSMUSG00000045095	Magi1	AIP3|BAP1|Baiap1|Gukmi1|MAGI1c|Magi-1|TNRC19|WWP3|mKIAA4129	membrane associated guanylate kinase, WW and PDZ domain containing 1	protein-coding
mm_80354.1	chr9	75186058	75186073	+	1	NA	exon (NM_010864, exon 28 of 41)	exon (NM_010864, exon 28 of 41)	-45949	NM_001081322	208943	Mm.41339	NM_001081322	ENSMUSG00000033590	Myo5c	9130003O20Rik|BB085560|C330029I24	myosin VC	protein-coding
mm_29950.1	chr3	133091737	133091762	-	1	NA	promoter-TSS (NM_026231)	promoter-TSS (NM_026231)	-9	NM_026231	67553	Mm.304899	NM_026231	ENSMUSG00000028018	Gstcd	4933434L15Rik	glutathione S-transferase, C-terminal domain containing	protein-coding
mm_82422.1	chr9	14903867	14903882	-	1	NA	promoter-TSS (NM_176807)	promoter-TSS (NM_176807)	77	NM_176807	64931	Mm.86738	NM_022888	ENSMUSG00000031933	Izumo1r	0910001L11Rik|C86255|Folbp3|Folr4|Juno	IZUMO1 receptor, JUNO	protein-coding
mm_67798.1	chr7	98085444	98085454	-	1	NA	exon (NM_001256082, exon 16 of 49)	exon (NM_001256082, exon 16 of 49)	23799	NM_001256082	17921	Mm.1403	NM_008663	ENSMUSG00000030761	Myo7a	Hdb|Myo7|USH1B|nmf371|polka|sh-1|sh1	myosin VIIA	protein-coding
mm_156144.1	chrX	129757087	129757092	+	1	NA	intron (NM_172493, intron 1 of 26)	PB1|SINE|Alu	7347	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diaph2	Dia3|Diap2|Drf2|E430022I22Rik	diaphanous related formin 2	protein-coding
mm_128775.1	chr15	66702665	66702686	-	1	NA	intron (NM_009375, intron 20 of 47)	intron (NM_009375, intron 20 of 47)	31905	NM_009375	21819	Mm.441333	NM_009375	ENSMUSG00000053469	Tg	Tgn|cog	thyroglobulin	protein-coding
mm_154020.1	chr19	53318558	53318607	-	1	NA	intron (NM_001008542, intron 1 of 5)	intron (NM_001008542, intron 1 of 5)	8076	NM_001008542	17859	Mm.2154	NM_010847	ENSMUSG00000025025	Mxi1	ENSMUSG00000067085|Gm10197|Mad2|bHLHc11	MAX interactor 1, dimerization protein	protein-coding
mm_74138.1	chr8	123224834	123224875	+	1	NA	promoter-TSS (NM_194446)	promoter-TSS (NM_194446)	13	NM_194444	234854	Mm.190984	NM_194444	ENSMUSG00000033862	Cdk10	BC017131	cyclin-dependent kinase 10	protein-coding
mm_29567.1	chr3	116968564	116968568	-	1	NA	non-coding (NR_040596, exon 1 of 3)	non-coding (NR_040596, exon 1 of 3)	299	NR_040596	74654	Mm.410820	NR_040596	ENSMUSG00000080907	4930455H04Rik	-	RIKEN cDNA 4930455H04 gene	ncRNA
mm_16317.1	chr2	174304358	174304360	+	1	NA	intron (NM_001310085, intron 2 of 12)	RMER12C|LTR|ERVK	6500	NM_001310085	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_35734.1	chr4	45012288	45012325	-	1	NA	5' UTR (NM_001163284, exon 1 of 2)	5' UTR (NM_001163284, exon 1 of 2)	106	NM_001163284	230119	Mm.44222	NM_173399	ENSMUSG00000049657	Zbtb5	5930421I10|9430083K24Rik|AI646847|mKIAA0354	zinc finger and BTB domain containing 5	protein-coding
mm_79327.1	chr9	53321732	53321742	+	1	NA	intron (NM_176846, intron 1 of 5)	intron (NM_176846, intron 1 of 5)	20067	NM_176846	320051	Mm.277540	NM_176846	ENSMUSG00000034584	Exph5	AC079869.22gm5|B130009M24Rik|E030050P12|Kiaa0624|Slac2b|slac2-b	exophilin 5	protein-coding
mm_84877.1	chr9	79718742	79718752	-	1	NA	promoter-TSS (NM_001290308)	promoter-TSS (NM_001290308)	-25	NM_001290308	12816	Mm.3819	NM_007730	ENSMUSG00000032332	Col12a1	-	collagen, type XII, alpha 1	protein-coding
mm_65108.1	chr7	19309741	19309751	-	1	NA	5' UTR (NM_008036, exon 1 of 4)	5' UTR (NM_008036, exon 1 of 4)	299	NM_008036	14282	Mm.248335	NM_008036	ENSMUSG00000003545	Fosb	-	FBJ osteosarcoma oncogene B	protein-coding
mm_158754.1	chrX	166440672	166440715	-	1	NA	promoter-TSS (NM_001313722)	promoter-TSS (NM_001313722)	11	NM_177429	237222	Mm.247480	NM_177429	ENSMUSG00000040586	Ofd1	Cxorf5|DXGgc7e|ORF2	oral-facial-digital syndrome 1 gene homolog (human)	protein-coding
mm_119891.1	chr14	54937740	54937749	+	1	NA	intron (NM_029390, intron 1 of 3)	intron (NM_029390, intron 1 of 3)	1247	NM_029390	67272	Mm.41614	NM_026066	ENSMUSG00000040759	Cmtm5	1500005P16Rik|2900052H21Rik|Cklfsf5	CKLF-like MARVEL transmembrane domain containing 5	protein-coding
mm_165558.1	chr3	14886205	14886320	+	1	NA	promoter-TSS (NM_009801)	promoter-TSS (NM_009801)	-164	NM_009801	12349	Mm.1186	NM_009801	ENSMUSG00000027562	Car2	AI131712|CAII|Ca2|Car-2|Ltw-5|Lvtw-5	carbonic anhydrase 2	protein-coding
mm_71945.1	chr8	70376302	70376321	+	1	NA	exon (NM_016685, exon 7 of 19)	exon (NM_016685, exon 7 of 19)	2763	NM_016685	12845	Mm.45071	NM_016685	ENSMUSG00000031849	Comp	TSP5	cartilage oligomeric matrix protein	protein-coding
mm_148656.1	chr19	5510731	5510760	+	1	NA	promoter-TSS (NM_001024560)	promoter-TSS (NM_001024560)	-256	NM_001024560	225861	Mm.20071	NM_001024560	ENSMUSG00000056185	Snx32	B930037P14Rik|Snx6b	sorting nexin 32	protein-coding
mm_116767.1	chr13	52735593	52735612	-	1	NA	intron (NR_027893, intron 1 of 2)	intron (NR_027893, intron 1 of 2)	21603	NR_027893	105404	Mm.184173	NR_027893		BB123696	-	expressed sequence BB123696	ncRNA
mm_76185.1	chr8	82402487	82402491	-	1	NA	promoter-TSS (NM_001254747)	promoter-TSS (NM_001254747)	97	NM_001254747	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_57136.1	chr6	122608533	122608551	-	1	NA	intron (NM_008108, intron 1 of 1)	B1F|SINE|Alu	1545	NM_008108	14562	Mm.299742	NM_008108	ENSMUSG00000030117	Gdf3	C78318|Gdf-3|Vgr-2|Vgr2|ecat9	growth differentiation factor 3	protein-coding
mm_114741.1	chr13	83739185	83739189	+	1	NA	TTS (NR_029545)	TTS (NR_029545)	373	NR_029545	723967		NR_029545	ENSMUSG00000065424	Mir9-2	Mirn9-2|mir-9-2|mmu-mir-9-2	microRNA 9-2	ncRNA
mm_61604.1	chr7	80027607	80027610	+	1	NA	intron (NM_175433, intron 1 of 4)	intron (NM_175433, intron 1 of 4)	1380	NM_175433	209225	Mm.290925	NM_175433	ENSMUSG00000048897	Zfp710	5430400N05Rik|9830165K13|AI324798|Znf710	zinc finger protein 710	protein-coding
mm_59814.1	chr7	29171405	29171427	+	1	NA	exon (NM_182694, exon 2 of 3)	exon (NM_182694, exon 2 of 3)	1026	NM_182696	243897	Mm.389886	NM_182694	ENSMUSG00000031493	Ggn	AI593290	gametogenetin	protein-coding
mm_142529.1	chr17	46438446	46438470	-	1	NA	promoter-TSS (NM_144856)	promoter-TSS (NM_144856)	19	NM_144856	108114	Mm.387538	NM_144856	ENSMUSG00000067144	Slc22a7	NLT|OAT2	solute carrier family 22 (organic anion transporter), member 7	protein-coding
mm_139720.1	chr17	57467386	57467397	+	1	NA	intron (NM_010130, intron 18 of 21)	Lx|LINE|L1	77923	NM_001104591	224916	Mm.469889	NM_001104591	ENSMUSG00000090655	Vmn2r120	EG224916	vomeronasal 2, receptor 120	protein-coding
mm_2013.1	chr1	87127729	87127740	+	1	NA	exon (NM_007432, exon 11 of 11)	exon (NM_007432, exon 11 of 11)	2726	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_1760.1	chr1	75546058	75546095	+	1	NA	promoter-TSS (NM_009208)	promoter-TSS (NM_009208)	-190	NM_009208	20536	Mm.5053	NM_009208	ENSMUSG00000006576	Slc4a3	A930038D23Rik|Ae3	solute carrier family 4 (anion exchanger), member 3	protein-coding
mm_30015.1	chr3	135665192	135665198	-	1	NA	intron (NM_008689, intron 3 of 24)	intron (NM_008689, intron 3 of 24)	26352	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_146782.1	chr18	20101918	20101932	-	1	NA	exon (NM_001291804, exon 6 of 16)	exon (NM_001291804, exon 6 of 16)	12848	NM_001291804	13505	Mm.33740	NM_013504	ENSMUSG00000044322	Dsc1	1110020A10Rik|AI507491	desmocollin 1	protein-coding
mm_106313.1	chr11	118302616	118302633	-	1	NA	3' UTR (NM_011594, exon 5 of 5)	3' UTR (NM_011594, exon 5 of 5)	-12380	NM_001033528	72344	Mm.232293	NM_001033528	ENSMUSG00000033909	Usp36	2700002L06Rik|mKIAA1453	ubiquitin specific peptidase 36	protein-coding
mm_108112.1	chr12	75308628	75308634	+	1	NA	5' UTR (NM_023275, exon 1 of 5)	5' UTR (NM_023275, exon 1 of 5)	318	NM_023275	80837	Mm.27467	NM_023275	ENSMUSG00000046768	Rhoj	1110005O19Rik|AW210585|Arhj|TC10L|TCL	ras homolog family member J	protein-coding
mm_164990.1	chr19	11447556	11447579	+	1	NA	intron (NM_021718, intron 1 of 6)	intron (NM_021718, intron 1 of 6)	4009	NM_021718	60361	Mm.33957	NM_021718	ENSMUSG00000056290	Ms4a4b	AI463180|Chandra|Ly116	membrane-spanning 4-domains, subfamily A, member 4B	protein-coding
mm_126253.1	chr15	79030886	79030933	+	1	NA	promoter-TSS (NM_001161712)	promoter-TSS (NM_001161712)	35	NM_001161712	26912	Mm.237085	NM_013847	ENSMUSG00000006378	Gcat	AI526977|Kbl	glycine C-acetyltransferase (2-amino-3-ketobutyrate-coenzyme A ligase)	protein-coding
mm_27283.1	chr3	41494945	41494951	-	1	NA	Intergenic	Intergenic	-1749	NR_040385	78706	Mm.366094	NR_040385	ENSMUSG00000097639	Platr4	C430002E04Rik	pluripotency associated transcript 4	ncRNA
mm_148885.1	chr19	6857625	6857636	+	1	NA	intron (NM_001081291, intron 2 of 26)	intron (NM_001081291, intron 2 of 26)	581	NM_001081291	78317	Mm.329596	NM_198008	ENSMUSG00000047810	Ccdc88b	2610041P08Rik|Ccdc88	coiled-coil domain containing 88B	protein-coding
mm_142169.1	chr17	36168533	36168546	-	1	NA	promoter-TSS (NM_001081032)	promoter-TSS (NM_001081032)	-2	NM_001081032	667977	Mm.441651	NM_001081032	ENSMUSG00000073402	Gm8909	EG667977|H2-Tw5l|H2-gs17	predicted gene 8909	protein-coding
mm_112404.1	chr13	3538615	3538635	+	1	NA	intron (NM_008112, intron 1 of 10)	intron (NM_008112, intron 1 of 10)	550	NM_008112	14569	Mm.153226	NM_008112	ENSMUSG00000021218	Gdi2	GDI-B|GDIB|Gdi3	guanosine diphosphate (GDP) dissociation inhibitor 2	protein-coding
mm_33668.1	chr4	133185622	133185647	+	1	NA	exon (NM_153423, exon 4 of 9)	exon (NM_153423, exon 4 of 9)	-10021	NR_105984	102466215		NR_105984	ENSMUSG00000099202	Mir7017	Gm27945|mmu-mir-7017	microRNA 7017	ncRNA
mm_48831.1	chr5	149184207	149184241	-	1	NA	promoter-TSS (NM_001115151)	promoter-TSS (NM_001115151)	-336	NM_001115153	231915	Mm.29402	NM_001013378	ENSMUSG00000041264	Uspl1	E430026A01Rik	ubiquitin specific peptidase like 1	protein-coding
mm_137755.1	chr17	29465048	29465057	+	1	NA	Intergenic	RSINE1|SINE|B4	-25993	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_42210.1	chr5	112793257	112793265	+	1	NA	promoter-TSS (NR_040676)	promoter-TSS (NR_040676)	-31	NR_040675	67360	Mm.59218	NR_040675	ENSMUSG00000098230	1700095B10Rik	-	RIKEN cDNA 1700095B10 gene	ncRNA
mm_135256.1	chr16	37833913	37833945	-	1	NA	3' UTR (NM_008047, exon 11 of 11)	3' UTR (NM_008047, exon 11 of 11)	-34471	NM_177093	320184	Mm.390882	NM_177093	ENSMUSG00000034158	Lrrc58	1810012N18Rik|C330018J07Rik	leucine rich repeat containing 58	protein-coding
mm_112190.1	chr12	113422736	113422744	-	1	NA	Intergenic	Intergenic	-66825	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_115483.1	chr13	3601483	3601494	-	1	NA	intron (NM_134063, intron 1 of 19)	intron (NM_134063, intron 1 of 19)	9620	NM_134063	105203	Mm.221609	NM_134063	ENSMUSG00000033799	Fam208b	AI645998|Pap20|mKIAA2006	family with sequence similarity 208, member B	protein-coding
mm_122124.1	chr14	31128925	31128960	-	1	NA	promoter-TSS (NM_001308464)	promoter-TSS (NM_001308464)	-12	NM_001308464	66487	Mm.379116	NM_001308091	ENSMUSG00000058351	Smim4	2010107H07Rik|Gm41122	small integral membrane protein 4	protein-coding
mm_24584.1	chr3	93444870	93444879	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	2544	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_173026.1	chrX	104348454	104348458	-	1	NA	intron (NM_009592, intron 1 of 15)	CpG	65390	NM_009592	11306	Mm.426128	NM_009592	ENSMUSG00000031333	Abcb7	AA517758|AU019072|Abc7	ATP-binding cassette, sub-family B (MDR/TAP), member 7	protein-coding
mm_75923.1	chr8	71498159	71498170	-	1	NA	3' UTR (NM_032398, exon 6 of 6)	3' UTR (NM_032398, exon 6 of 6)	10061	NM_032544	70359	Mm.142112	NM_032544	ENSMUSG00000007610	Gtpbp3	2410009F13Rik|AI607903	GTP binding protein 3	protein-coding
mm_45819.1	chr5	87692652	87692679	-	1	NA	TTS (NM_001286023)	TTS (NM_001286023)	6760	NM_001286020	12991	Mm.268737	NM_009972	ENSMUSG00000063157	Csn2	Csnb	casein beta	protein-coding
mm_21757.1	chr2	164839774	164839782	-	1	NA	exon (NM_011125, exon 16 of 16)	exon (NM_011125, exon 16 of 16)	6005	NM_008906	19025	Mm.359633	NM_008906	ENSMUSG00000017760	Ctsa	AU019505|PPCA|Ppgb	cathepsin A	protein-coding
mm_117876.1	chr13	98926361	98926373	-	1	NA	promoter-TSS (NM_178716)	promoter-TSS (NM_178716)	17	NM_178716	238799	Mm.173286	NM_178716	ENSMUSG00000009470	Tnpo1	AU021749|D13Ertd688e|IPO2|Kpnb2|MIP|MIP1|TRN	transportin 1	protein-coding
mm_71129.1	chr8	36549352	36549371	+	1	NA	Intergenic	CpG	60170	NM_176952	319582	Mm.180924	NM_176952	ENSMUSG00000039620	6430573F11Rik	Kiaa1456|TRM9L	RIKEN cDNA 6430573F11 gene	protein-coding
mm_120211.1	chr14	62497562	62497572	+	1	NA	Intergenic	RMER19C|LTR|ERVK	-41278	NM_172810	239134	Mm.236557	NM_172810	ENSMUSG00000021933	Gucy1b2	B930025B03|GC-SB2	guanylate cyclase 1, soluble, beta 2	protein-coding
mm_105989.1	chr11	115627762	115627791	-	1	NA	5' UTR (NM_001252384, exon 2 of 8)	5' UTR (NM_001252384, exon 2 of 8)	519	NM_001252394	67283	Mm.383426	NM_026071	ENSMUSG00000020744	Slc25a19	2900089E13Rik|DNC|MUP1|TPC	solute carrier family 25 (mitochondrial thiamine pyrophosphate carrier), member 19	protein-coding
mm_163073.1	chr11	67294512	67294518	+	1	NA	exon (NM_177369, exon 22 of 40)	exon (NM_177369, exon 22 of 40)	17391	NM_177369	17885	Mm.340163	NM_177369	ENSMUSG00000055775	Myh8	4832426G23Rik|AI327267|MHCp|MyHC-pn|Myhs-p|Myhsp	myosin, heavy polypeptide 8, skeletal muscle, perinatal	protein-coding
mm_1895.1	chr1	85709334	85709361	+	1	NA	3' UTR (NM_013673, exon 20 of 20)	3' UTR (NM_013673, exon 20 of 20)	27259	NM_177055	319997	Mm.116691	NM_177055	ENSMUSG00000052760	A630001G21Rik	-	RIKEN cDNA A630001G21 gene	protein-coding
mm_150926.1	chr19	46227827	46227830	+	1	NA	intron (NM_178930, intron 3 of 39)	ID_B1|SINE|B4	75270	NM_178930	107338	Mm.271620	NM_178930	ENSMUSG00000025224	Gbf1	1700083E03Rik|AI035702|AW049900|mKIAA0248	golgi-specific brefeldin A-resistance factor 1	protein-coding
mm_13489.1	chr2	106693409	106693425	+	1	NA	promoter-TSS (NM_001143683)	promoter-TSS (NM_001143683)	-42	NM_001143683	77015	Mm.45628	NM_029837	ENSMUSG00000016386	Mpped2	239Fb|2700082O15Rik|AV354767|AW060960	metallophosphoesterase domain containing 2	protein-coding
mm_153212.1	chr19	34747134	34747186	-	1	NA	promoter-TSS (NM_172838)	promoter-TSS (NM_172838)	-49	NM_172838	240638	Mm.74636	NM_172838	ENSMUSG00000009378	Slc16a12	3230401A21|AW210596	solute carrier family 16 (monocarboxylic acid transporters), member 12	protein-coding
mm_24349.1	chr3	89911394	89911406	+	1	NA	intron (NM_001310676, intron 1 of 9)	intron (NM_001310676, intron 1 of 9)	1796	NM_001310676	16194	Mm.2856	NM_010559	ENSMUSG00000027947	Il6ra	CD126|IL-6R|IL-6R-alpha|IL-6RA|Il6r	interleukin 6 receptor, alpha	protein-coding
mm_57429.1	chr6	124914187	124914199	-	1	NA	exon (NM_026988, exon 5 of 5)	exon (NM_026988, exon 5 of 5)	-2488	NM_008479	16768	Mm.4528	NM_008479	ENSMUSG00000030124	Lag3	CD223|LAG-3|Ly66	lymphocyte-activation gene 3	protein-coding
mm_65586.1	chr7	27310644	27310693	-	1	NA	TTS (NM_001310678)	TTS (NM_001310678)	22980	NM_001113549	108075	Mm.272251	NM_175641	ENSMUSG00000040488	Ltbp4	2310046A13Rik	latent transforming growth factor beta binding protein 4	protein-coding
mm_24297.1	chr3	89339641	89339649	+	1	NA	TTS (NM_001037722)	TTS (NM_001037722)	-1617	NM_007910	13639	Mm.16332	NM_007910	ENSMUSG00000028040	Efna4	EFL-4|Epl4|LERK-4	ephrin A4	protein-coding
mm_13532.1	chr2	110600506	110600517	+	1	NA	intron (NM_001177624, intron 1 of 14)	Lx|LINE|L1	3212	NM_001177624	241612	Mm.277148	NM_001003915	ENSMUSG00000041644	Slc5a12	AI315119|D630015G19|SMCT2	solute carrier family 5 (sodium/glucose cotransporter), member 12	protein-coding
mm_131776.1	chr16	22894843	22894854	+	1	NA	promoter-TSS (NR_110508)	promoter-TSS (NR_110508)	-462	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_62263.1	chr7	99466022	99466032	+	1	NA	promoter-TSS (NM_028145)	promoter-TSS (NM_028145)	23	NM_028145	72184	Mm.153585	NM_028145	ENSMUSG00000035298	Klhl35	2810406K13Rik	kelch-like 35	protein-coding
mm_67370.1	chr7	79841125	79841159	-	1	NA	exon (NM_008486, exon 2 of 20)	exon (NM_008486, exon 2 of 20)	1210	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_20730.1	chr2	136891364	136891413	-	1	NA	promoter-TSS (NM_001286983)	promoter-TSS (NM_001286983)	18	NM_021527	59030	Mm.272570	NM_021527	ENSMUSG00000027274	Mkks	1300013E18Rik|AI463362|AI957237|Bbs6	McKusick-Kaufman syndrome	protein-coding
mm_171916.1	chr5	5782196	5782210	-	1	NA	Intergenic	Intergenic	-32886	NM_027399	70358	Mm.85429	NM_027399	ENSMUSG00000015652	Steap1	2410007B19Rik|Prss24|Steap	six transmembrane epithelial antigen of the prostate 1	protein-coding
mm_48311.1	chr5	138708542	138708546	-	1	NA	Intergenic	MLTR14|LTR|ERV1	-46537	NM_030565	80752	Mm.320355	NM_030565	ENSMUSG00000025854	Fam20c	C76981|DMP-4|DMP4|GEF-CK|mKIAA4081	family with sequence similarity 20, member C	protein-coding
mm_8168.1	chr1	136960536	136960553	-	1	NA	promoter-TSS (NM_030676)	promoter-TSS (NM_030676)	-96	NM_030676	26424	Mm.16794	NM_030676	ENSMUSG00000026398	Nr5a2	AU020803|D1Ertd308e|Ftf|LRH-1|UF2-H3B	nuclear receptor subfamily 5, group A, member 2	protein-coding
mm_70372.1	chr8	9977811	9977848	+	1	NA	5' UTR (NM_026868, exon 1 of 3)	5' UTR (NM_026868, exon 1 of 3)	112	NM_026868	68904	Mm.142570	NM_026868	ENSMUSG00000040396	Abhd13	1110065L07Rik|AI463703|AI788994	abhydrolase domain containing 13	protein-coding
mm_121525.1	chr14	122150826	122150857	+	1	NA	exon (NM_080556, exon 14 of 17)	exon (NM_080556, exon 14 of 17)	-30853	NM_029556	69634	Mm.34608	NM_029556	ENSMUSG00000025545	Clybl	0610033J05Rik|2310014M14Rik|AI256068|Clb	citrate lyase beta like	protein-coding
mm_132647.1	chr16	41290798	41290801	+	1	NA	Intergenic	L1_Mur3|LINE|L1	-242027	NM_001347236	268890	Mm.310524	NM_175548	ENSMUSG00000061080	Lsamp	5430428I19|AW046674|B130007O04Rik|D930023J12Rik|Lam|Lamp	limbic system-associated membrane protein	protein-coding
mm_62399.1	chr7	101108741	101108753	+	1	NA	promoter-TSS (NM_001146010)	promoter-TSS (NM_001146010)	-28	NM_001146010	207278	Mm.263041	NM_199012	ENSMUSG00000030691	Fchsd2	BC034086|R74866|Sh3md3|mKIAA0769	FCH and double SH3 domains 2	protein-coding
mm_58760.1	chr7	13623984	13624001	+	1	NA	promoter-TSS (NM_001184980)	promoter-TSS (NM_001184980)	25	NM_001184980	434264	Mm.359414	NM_001184980	ENSMUSG00000078799	Sult2a5	EG434264|Gm15438|OTTMUSG00000021844	sulfotransferase family 2A, dehydroepiandrosterone (DHEA)-preferring, member 5	protein-coding
mm_5215.1	chr1	13660640	13660650	-	1	NA	promoter-TSS (NM_145381)	promoter-TSS (NM_145381)	-136	NM_145381	212442	Mm.89572	NM_145381	ENSMUSG00000025937	Lactb2	Cgi-83|E430032H21Rik	lactamase, beta 2	protein-coding
mm_131318.1	chr16	11984108	11984153	+	1	NA	promoter-TSS (NM_028277)	promoter-TSS (NM_028277)	17	NM_001174086	72555	Mm.310139	NM_028277	ENSMUSG00000022494	Shisa9	2700045P11Rik|Ckamp44	shisa family member 9	protein-coding
mm_103822.1	chr11	83005149	83005173	-	1	NA	intron (NM_181545, intron 4 of 5)	ERVB5_2-LTR_MM|LTR|ERVK	-13331	NM_172796	237886	Mm.270253	NM_172796	ENSMUSG00000069793	Slfn9	9830137M10Rik	schlafen 9	protein-coding
mm_131284.1	chr16	11144096	11144118	+	1	NA	intron (NR_027502, intron 19 of 22)	LSU-rRNA_Hsa|rRNA|rRNA	-9575	NM_029582	106200	Mm.291015	NM_029582	ENSMUSG00000022498	Txndc11	2810408E11Rik|AI427833|EFP1|Txdc11	thioredoxin domain containing 11	protein-coding
mm_68268.1	chr7	105595608	105595619	-	1	NA	exon (NM_017371, exon 6 of 10)	exon (NM_017371, exon 6 of 10)	4503	NM_017371	15458	Mm.3485	NM_017371	ENSMUSG00000030895	Hpx	Hpxn|hx	hemopexin	protein-coding
mm_66064.1	chr7	30821093	30821099	-	1	NA	promoter-TSS (NM_001168512)	promoter-TSS (NM_001168512)	43	NM_001168511	233079	Mm.97338	NM_146187	ENSMUSG00000051314	Ffar2	GPCR43|Gpr43	free fatty acid receptor 2	protein-coding
mm_39885.1	chr5	31116583	31116587	+	1	NA	promoter-TSS (NM_021447)	promoter-TSS (NM_021447)	-27	NM_021447	58522	Mm.143796	NM_021447	ENSMUSG00000062077	Trim54	4930486E09Rik|4930566I02Rik|MURF|MURF-3|MuRF3|Rnf30	tripartite motif-containing 54	protein-coding
mm_53189.1	chr6	125482525	125482549	+	1	NA	intron (NM_007657, intron 1 of 7)	intron (NM_007657, intron 1 of 7)	12218	NM_007657	12527	Mm.210676	NM_007657	ENSMUSG00000030342	Cd9	Tspan29	CD9 antigen	protein-coding
mm_134601.1	chr16	20621355	20621421	-	1	NA	promoter-TSS (NM_028420)	promoter-TSS (NM_028420)	-110	NM_028420	73047	Mm.425977	NM_028420	ENSMUSG00000051146	Camk2n2	2900075A18Rik	calcium/calmodulin-dependent protein kinase II inhibitor 2	protein-coding
mm_78492.1	chr9	32705130	32705135	+	1	NA	intron (NM_011808, intron 1 of 7)	intron (NM_011808, intron 1 of 7)	9090	NM_001038642	23871	Mm.292415	NM_011808	ENSMUSG00000032035	Ets1	AI196000|AI448617|D230050P06|Ets-1|Tpl1|vs	E26 avian leukemia oncogene 1, 5' domain	protein-coding
mm_120220.1	chr14	62837680	62837726	+	1	NA	promoter-TSS (NR_106174)	promoter-TSS (NR_106174)	13	NM_175546	268752	Mm.1960	NM_175546	ENSMUSG00000014547	Wdfy2	5830485M08|B130024L21Rik|ProF|ZFYVE22	WD repeat and FYVE domain containing 2	protein-coding
mm_4098.1	chr1	167350166	167350170	+	1	NA	5' UTR (NM_019993, exon 1 of 11)	5' UTR (NM_019993, exon 1 of 11)	177	NM_019993	56752	Mm.292539	NM_019993	ENSMUSG00000026687	Aldh9a1	AA139417|Abaldh|ESTM40|TMABA-DH|Tmabadh	aldehyde dehydrogenase 9, subfamily A1	protein-coding
mm_41591.1	chr5	93268533	93268578	+	1	NA	intron (NM_007635, intron 1 of 7)	CpG	982	NM_007635	12452	Mm.3527	NM_007635	ENSMUSG00000029385	Ccng2	-	cyclin G2	protein-coding
mm_77975.1	chr9	7869763	7869765	+	1	NA	intron (NM_007464, intron 1 of 8)	L1MA4A|LINE|L1	3406	NM_007464	11796	Mm.2026	NM_007464	ENSMUSG00000032000	Birc3	AW107670|Api1|Api2|Birc2|C-IAP2|HIAP2|IAP1|IAP2|MIAP1|MIAP2|MIHB|MIHC|RNF49|cIAP-1|cIAP-2|cIAP1|cIAP2	baculoviral IAP repeat-containing 3	protein-coding
mm_149723.1	chr19	21778377	21778392	+	1	NA	promoter-TSS (NM_031997)	promoter-TSS (NM_031997)	44	NM_031997	83921	Mm.329776	NM_031997	ENSMUSG00000024754	Tmem2	-	transmembrane protein 2	protein-coding
mm_95690.1	chr11	54304249	54304259	+	1	NA	promoter-TSS (NM_144823)	promoter-TSS (NM_144823)	50	NM_001033597	216739	Mm.267478	NM_144823	ENSMUSG00000020333	Acsl6	A330035H04Rik|AW050338|Facl6|LACS|Lacsl|mKIAA0837	acyl-CoA synthetase long-chain family member 6	protein-coding
mm_14194.1	chr2	127133950	127133960	+	1	NA	promoter-TSS (NM_144818)	promoter-TSS (NM_144818)	-1	NM_144818	215387	Mm.29786	NM_144818	ENSMUSG00000034906	Ncaph	A730011O11Rik|Brrn1|HCAP-H|mKIAA0074	non-SMC condensin I complex, subunit H	protein-coding
mm_142632.1	chr17	47414668	47414670	-	1	NA	promoter-TSS (NM_001172091)	promoter-TSS (NM_001172091)	42	NM_001172091	75462	Mm.46129	NM_029296	ENSMUSG00000047150	1700001C19Rik	-	RIKEN cDNA 1700001C19 gene	protein-coding
mm_83105.1	chr9	40345241	40345255	-	1	NA	intron (NM_172768, intron 2 of 19)	intron (NM_172768, intron 2 of 19)	11776	NR_040728	73558	Mm.398307	NR_040728		1700110K17Rik	-	RIKEN cDNA 1700110K17 gene	ncRNA
mm_148870.1	chr19	6497675	6497687	+	1	NA	intron (NM_001205234, intron 17 of 22)	CpG	45389	NM_009203	20521	Mm.391146	NM_009203	ENSMUSG00000061742	Slc22a12	AI987855|OAT4L|Rst|Slc22al2|URAT1	solute carrier family 22 (organic anion/cation transporter), member 12	protein-coding
mm_82328.1	chr9	8752255	8752260	-	1	NA	Intergenic	Intergenic	-11269	NR_110513	102634431	Mm.387913	NR_110513	ENSMUSG00000111602	Gm32014	-	predicted gene, 32014	ncRNA
mm_130660.1	chr15	100644913	100644938	-	1	NA	exon (NM_001270537, exon 10 of 11)	exon (NM_001270537, exon 10 of 11)	4304	NR_105926	102465580		NR_105926	ENSMUSG00000098527	Mir6961	Gm27367|mmu-mir-6961	microRNA 6961	ncRNA
mm_102055.1	chr11	52231885	52231897	-	1	NA	promoter-TSS (NM_011543)	promoter-TSS (NM_011543)	-104	NM_011543	21402	Mm.42944	NM_011543	ENSMUSG00000036309	Skp1a	15kDa|2610043E24Rik|2610206H23Rik|EMC19|OCP-II|OCP2|SKP1|Tceb1l|p19A|p19Skp1	S-phase kinase-associated protein 1A	protein-coding
mm_92222.1	chr10	68278714	68278735	-	1	NA	promoter-TSS (NM_023598)	promoter-TSS (NM_023598)	2	NM_023598	71371	Mm.440357	NM_023598	ENSMUSG00000019947	Arid5b	4930580B11|5430435G07Rik|AI467247|Desrt|Mrf2|Mrf2alpha|Mrf2beta	AT rich interactive domain 5B (MRF1-like)	protein-coding
mm_9745.1	chr1	180403744	180403748	-	1	NA	intron (NM_001081175, intron 2 of 7)	intron (NM_001081175, intron 2 of 7)	-73197	NR_003623	277333	Mm.389223	NM_199472		Gm5069	EG277333	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_76014.1	chr8	73207711	73207714	-	1	NA	intron (NM_001317391, intron 3 of 15)	ID_B1|SINE|B4	145828	NM_001317391	16795	Mm.324371	NM_010687	ENSMUSG00000004383	Large1	BPFD#36|Gyltl1a|Large|Mbp-1|Mbp1|enr|fg|froggy|myd	LARGE xylosyl- and glucuronyltransferase 1	protein-coding
mm_10629.1	chr2	19743590	19743593	+	1	NA	Intergenic	Intergenic	85529	NM_027715	71198	Mm.83981	NM_027715	ENSMUSG00000043415	Otud1	4933428L19Rik	OTU domain containing 1	protein-coding
mm_115477.1	chr13	119488810	119488837	+	1	NA	promoter-TSS (NR_027974)	promoter-TSS (NR_027974)	-37	NM_001177666	633640	Mm.46679	NM_001039244	ENSMUSG00000074634	Tmem267	EG633640|Gm7120	transmembrane protein 267	protein-coding
mm_140487.1	chr17	3157875	3157889	-	1	NA	intron (NM_134123, intron 3 of 19)	intron (NM_134123, intron 3 of 19)	42910	NM_134123	106583	Mm.124373	NM_134123	ENSMUSG00000046201	Scaf8	A630086M08Rik|A930036P18Rik|AA408306|AI447644|AI448652|AU015035|Rbm16|mKIAA1116	SR-related CTD-associated factor 8	protein-coding
mm_100043.1	chr11	115134041	115134049	+	1	NA	promoter-TSS (NM_001169153)	promoter-TSS (NM_001169153)	-53	NM_145634	246746	Mm.277387	NM_145634	ENSMUSG00000047798	Cd300lf	CLIM1|CLM-1|CLM1|Digr2|F730004D16Rik|IREM1|IgSF13|LMIR3|Pigr3	CD300 molecule like family member F	protein-coding
mm_107880.1	chr12	69986828	69986836	+	1	NA	5' UTR (NM_022028, exon 1 of 5)	5' UTR (NM_022028, exon 1 of 5)	170	NM_022028	64010	Mm.390480	NM_022028	ENSMUSG00000021067	Sav1	1700040G09Rik|Salv|Sav|WW45|Wwp3|Wwp4	salvador family WW domain containing 1	protein-coding
mm_71605.1	chr8	56183298	56183304	+	1	NA	Intergenic	Intergenic	-111251	NM_008278	15446	Mm.18832	NM_008278	ENSMUSG00000031613	Hpgd	15-PGDH|AV026552	hydroxyprostaglandin dehydrogenase 15 (NAD)	protein-coding
mm_145916.1	chr18	66548892	66548897	+	1	NA	Intergenic	Intergenic	44716	NR_040528	100503565	Mm.98256	NR_040528		Gm9926	ENSMUSG00000053891	predicted gene 9926	ncRNA
mm_98289.1	chr11	89066316	89066355	+	1	NA	intron (NR_110336, intron 2 of 3)	intron (NR_110336, intron 2 of 3)	5584	NR_110336	414094	Mm.124287	NM_001001497		Dgkeos	A930013B10Rik	diacylglycerol kinase, epsilon, opposite strand	ncRNA
mm_159968.1	chr6	97060199	97060199	-	1	NA	5' UTR (NM_177233, exon 1 of 6)	5' UTR (NM_177233, exon 1 of 6)	212	NM_177233	320701	Mm.131700	NM_177233	ENSMUSG00000046500	Fam19a4	C130034I18Rik|Fam19a4 Tafa-4|Tafa-4	family with sequence similarity 19, member A4	protein-coding
mm_128142.1	chr15	31530839	31530849	-	1	NA	5' UTR (NM_172606, exon 1 of 26)	5' UTR (NM_172606, exon 1 of 26)	193	NM_172606	223455	Mm.272185	NM_172606	ENSMUSG00000039100	March6	3830408G03|F830029L24Rik|mKIAA0597	membrane-associated ring finger (C3HC4) 6	protein-coding
mm_80961.1	chr9	103085855	103085876	+	1	NA	exon (NM_033314, exon 14 of 14)	exon (NM_033314, exon 14 of 14)	-26209	NM_173781	270192	Mm.490252	NM_173781	ENSMUSG00000032549	Rab6b	9630015C03|AI844641|C330006L04Rik|D9Bwg0185e	RAB6B, member RAS oncogene family	protein-coding
mm_21120.1	chr2	153549918	153549933	-	1	NA	Intergenic	Intergenic	-19954	NM_001134300	329540	Mm.50600	NM_001001986	ENSMUSG00000061411	Nol4l	4931410H15|8430427H17Rik|AI429157|Gm1636	nucleolar protein 4-like	protein-coding
mm_402.1	chr1	34171113	34171149	+	1	NA	exon (NM_134448, exon 28 of 98)	exon (NM_134448, exon 28 of 98)	10801	NM_010081	13518	Mm.336625	NM_010081	ENSMUSG00000026131	Dst	2310001O04Rik|A830042E19Rik|AW554249|BP230|BPAG1-n|Bpag|Bpag1|Macf2|ah|athetoid|dt|mKIAA0728|nmf203|nmf339	dystonin	protein-coding
mm_127678.1	chr15	102921148	102921169	+	1	NA	promoter-TSS (NM_010464)	promoter-TSS (NM_010464)	27	NM_010464	15422	Mm.207062	NM_010464	ENSMUSG00000001655	Hoxc13	-	homeobox C13	protein-coding
mm_99428.1	chr11	102399830	102399842	+	1	NA	intron (NM_016759, intron 7 of 10)	CpG-2672	5151	NR_105895	102465561		NR_105895	ENSMUSG00000098774	Mir6930	Gm27436|mmu-mir-6930	microRNA 6930	ncRNA
mm_37429.1	chr4	122886081	122886096	-	1	NA	promoter-TSS (NM_007598)	promoter-TSS (NM_007598)	-31	NM_001301067	12331	Mm.8687	NM_007598	ENSMUSG00000028656	Cap1	-	CAP, adenylate cyclase-associated protein 1 (yeast)	protein-coding
mm_165112.1	chr19	58650365	58650370	+	1	NA	Intergenic	Intergenic	-19998	NM_026925	69060	Mm.20407	NM_026925	ENSMUSG00000046008	Pnlip	1810007A24Rik|PL|PTL	pancreatic lipase	protein-coding
mm_28921.1	chr3	98858101	98858120	-	1	NA	intron (NM_001304800, intron 1 of 3)	intron (NM_001304800, intron 1 of 3)	1684	NM_001304800	15492	Mm.140811	NM_008293	ENSMUSG00000027871	Hsd3b1	3-beta-HSD I|D3Ertd383e	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1	protein-coding
mm_35642.1	chr4	43519662	43519718	-	1	NA	exon (NM_009416, exon 3 of 9)	exon (NM_009416, exon 3 of 9)	3864	NM_009416	22004	Mm.646	NM_009416	ENSMUSG00000028464	Tpm2	Tpm-2|Trop-2	tropomyosin 2, beta	protein-coding
mm_85540.1	chr9	106673678	106673699	-	1	NA	exon (NM_001081654, exon 4 of 6)	exon (NM_001081654, exon 4 of 6)	12128	NM_011573	21767	Mm.22266	NM_011573	ENSMUSG00000040813	Tex264	TEG-264	testis expressed gene 264	protein-coding
mm_59832.1	chr7	29303959	29303983	+	1	NA	promoter-TSS (NM_013874)	promoter-TSS (NM_013874)	-34	NM_013874	29861	Mm.101885	NM_013874	ENSMUSG00000030584	Dpf1	Neud4	D4, zinc and double PHD fingers family 1	protein-coding
mm_36767.1	chr4	101390591	101390602	-	1	NA	intron (NR_040640, intron 3 of 3)	intron (NR_040640, intron 3 of 3)	-28693	NM_001177602	11639	Mm.42040	NM_009647	ENSMUSG00000028527	Ak4	AK 4|Ak-3|Ak-4|Ak3|Ak3l1|D4Ertd274e	adenylate kinase 4	protein-coding
mm_17178.1	chr2	25356320	25356366	-	1	NA	promoter-TSS (NM_031843)	promoter-TSS (NM_031843)	-11	NM_031843	83768	Mm.21440	NM_031843	ENSMUSG00000026958	Dpp7	DPPII|Dpp2|QPP	dipeptidylpeptidase 7	protein-coding
mm_104467.1	chr11	95225632	95225634	-	1	NA	Intergenic	Intergenic	-35896	NM_053093	93670	Mm.40085	NM_053093	ENSMUSG00000020872	Tac4	AW489379|PPT-C	tachykinin 4	protein-coding
mm_13616.1	chr2	113405217	113405225	+	1	NA	intron (NM_001285458, intron 2 of 16)	intron (NM_001285458, intron 2 of 16)	-35843	NM_001285459	14260	Mm.4938	NM_010230	ENSMUSG00000044042	Fmn1	Fmn|formin-1|ld	formin 1	protein-coding
mm_134656.1	chr16	22060143	22060155	-	1	NA	3' UTR (NM_183029, exon 16 of 16)	3' UTR (NM_183029, exon 16 of 16)	50665	NR_027488	75826	Mm.297431	NM_029457	ENSMUSG00000022855	Senp2	2310007L05Rik|4930538C18Rik|AI646780|AW554757|Smt3ip2|SuPr-1|mKIAA1331	SUMO/sentrin specific peptidase 2	protein-coding
mm_125964.1	chr15	76270962	76270978	+	1	NA	intron (NM_028852, intron 1 of 4)	B1F|SINE|Alu	-1131	NR_045747	100038659	Mm.448549	NR_045747		Mirt2	ENSMUSG00000075583|Gm10872|Gm24562	myocardial infraction associated transcript 2	ncRNA
mm_44121.1	chr5	149458789	149458798	+	1	NA	intron (NM_001310763, intron 4 of 6)	ORR1F|LTR|ERVL-MaLR	19133	NM_001310765	75860	Mm.159605	NM_029464	ENSMUSG00000029660	Tex26	4930588N13Rik	testis expressed 26	protein-coding
mm_164161.1	chr15	73021594	73021605	+	1	NA	intron (NM_029640, intron 6 of 21)	intron (NM_029640, intron 6 of 21)	34213	NM_029640	76510	Mm.158902	NM_029640	ENSMUSG00000047921	Trappc9	1810044A24Rik|2900005P22Rik|4632408O18Rik|Ibp|Nibp|TRS130|mKIAA1882	trafficking protein particle complex 9	protein-coding
mm_150767.1	chr19	44243679	44243709	+	1	NA	3' UTR (NM_024450, exon 6 of 6)	3' UTR (NM_024450, exon 6 of 6)	40406	NM_024450	30049	Mm.480594	NM_024450	ENSMUSG00000025202	Scd3	4930513N16Rik	stearoyl-coenzyme A desaturase 3	protein-coding
mm_117715.1	chr13	95327492	95327504	-	1	NA	intron (NM_001302539, intron 1 of 1)	RMER10A|LTR|ERVL	731	NM_001302539	72114	Mm.3774	NM_028106	ENSMUSG00000041995	Zbed3	0610037K01Rik|2610005H11Rik|AU018975|AU024588	zinc finger, BED type containing 3	protein-coding
mm_10569.1	chr2	18064341	18064348	+	1	NA	promoter-TSS (NM_001252561)	promoter-TSS (NM_001252561)	-241	NM_001252560	17354	Mm.209175	NM_010804	ENSMUSG00000026743	Mllt10	Af10|B130021D15Rik|D630001B22Rik|mKIAA4140	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 10	protein-coding
mm_49819.1	chr6	37442544	37442567	+	1	NA	promoter-TSS (NM_178661)	promoter-TSS (NM_178661)	-407	NM_178661	208647	Mm.169929	NM_178661	ENSMUSG00000038648	Creb3l2	BBF2H7|C530025K05Rik|SCIRR69	cAMP responsive element binding protein 3-like 2	protein-coding
mm_148803.1	chr19	6263606	6263632	+	1	NA	Intergenic	Intergenic	-1024	NR_029830	723957		NR_029830	ENSMUSG00000065582	Mir194-2	Mirn194-2|mir-194-2	microRNA 194-2	ncRNA
mm_74052.1	chr8	122282149	122282194	+	1	NA	promoter-TSS (NM_009569)	promoter-TSS (NM_009569)	30	NM_009569	22761	Mm.3105	NM_009569	ENSMUSG00000049577	Zfpm1	FOG|Fog1	zinc finger protein, multitype 1	protein-coding
mm_150644.1	chr19	41896292	41896312	+	1	NA	promoter-TSS (NM_199447)	promoter-TSS (NM_199447)	-149	NM_199447	107094	Mm.276044	NM_199447	ENSMUSG00000035049	Rrp12	AA408556|AA536972|mKIAA0690	ribosomal RNA processing 12 homolog (S. cerevisiae)	protein-coding
mm_146635.1	chr18	10610049	10610116	-	1	NA	5' UTR (NM_001081222, exon 1 of 11)	5' UTR (NM_001081222, exon 1 of 11)	270	NM_001081222	77805	Mm.210996	NM_144542	ENSMUSG00000024293	Esco1	A930014I12Rik	establishment of sister chromatid cohesion N-acetyltransferase 1	protein-coding
mm_99790.1	chr11	107428274	107428283	+	1	NA	intron (NM_145823, intron 1 of 9)	intron (NM_145823, intron 1 of 9)	42442	NM_145823	71795	Mm.397413	NM_145823	ENSMUSG00000040430	Pitpnc1	1110020B03Rik|5830436L09Rik|AI662802|AI851387|C330017I21Rik|Dnr411|RDGBB|RDGBB1|rdgB-beta	phosphatidylinositol transfer protein, cytoplasmic 1	protein-coding
mm_118680.1	chr14	22100647	22100659	+	1	NA	intron (NM_028275, intron 2 of 6)	MTEa|LTR|ERVL-MaLR	80941	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_14015.1	chr2	122149562	122149574	+	1	NA	intron (NM_009735, intron 1 of 3)	RSINE1|SINE|B4	1881	NM_009735	12010	Mm.163	NM_009735	ENSMUSG00000060802	B2m	Ly-m11|beta2-m|beta2m	beta-2 microglobulin	protein-coding
mm_93717.1	chr10	118924811	118924811	-	1	NA	intron (NR_110482, intron 3 of 3)	intron (NR_110482, intron 3 of 3)	2332	NR_110482	216377	Mm.208936	NR_110482		Gm38403	C230029M16	predicted gene, 38403	ncRNA
mm_68681.1	chr7	118995143	118995203	-	1	NA	promoter-TSS (NM_001195774)	promoter-TSS (NM_001195774)	38	NM_022420	64297	Mm.103439	NM_022420	ENSMUSG00000008734	Gprc5b	AW125761|Raig2	G protein-coupled receptor, family C, group 5, member B	protein-coding
mm_103992.1	chr11	84846301	84846331	-	1	NA	intron (NM_153144, intron 6 of 13)	MT2B|LTR|ERVL	17138	NR_046281	74995	Mm.84413	NR_046281	ENSMUSG00000086799	4930502E09Rik	-	RIKEN cDNA 4930502E09 gene	ncRNA
mm_30984.1	chr4	34893773	34893787	+	1	NA	promoter-TSS (NM_009889)	promoter-TSS (NM_009889)	1	NM_009889	12640	Mm.1361	NM_009889	ENSMUSG00000028298	Cga	CG-alpha|FSHA|GPHA1|GPHalpha|HCG|LHA|Tsha|aGSU|alpha-GSU|alphaGSU|alphaSU	glycoprotein hormones, alpha subunit	protein-coding
mm_88868.1	chr10	80940639	80940659	+	1	NA	Intergenic	Intergenic	10558	NM_008655	17873	Mm.1360	NM_008655	ENSMUSG00000015312	Gadd45b	AI323528|Myd118	growth arrest and DNA-damage-inducible 45 beta	protein-coding
mm_94863.1	chr11	24077966	24077974	+	1	NA	promoter-TSS (NM_001242934)	promoter-TSS (NM_001242934)	-86	NM_016707	14025	Mm.53687	NM_016707	ENSMUSG00000000861	Bcl11a	2810047E18Rik|BCL-11A|Ctip1|D930021L15Rik|Evi9|Evi9a|Evi9b|Evi9c|mKIAA1809	B cell CLL/lymphoma 11A (zinc finger protein)	protein-coding
mm_110791.1	chr12	72085309	72085320	-	1	NA	promoter-TSS (NM_024205)	promoter-TSS (NM_024205)	-1	NM_026038	67217	Mm.286120	NM_026038	ENSMUSG00000019718	L3hypdh	2810055F11Rik	L-3-hydroxyproline dehydratase (trans-)	protein-coding
mm_76726.1	chr8	94918013	94918084	-	1	NA	promoter-TSS (NM_001033533)	promoter-TSS (NM_001033533)	50	NM_001033533	234582	Mm.277871	NM_001033533	ENSMUSG00000063605	Ccdc102a	BC027663|Gm586	coiled-coil domain containing 102A	protein-coding
mm_96506.1	chr11	68447598	68447641	+	1	NA	intron (NM_177320, intron 1 of 18)	intron (NM_177320, intron 1 of 18)	15494	NM_177320	320207	Mm.244960	NM_177320	ENSMUSG00000020901	Pik3r5	AV230647|F730038I15Rik	phosphoinositide-3-kinase, regulatory subunit 5, p101	protein-coding
mm_83533.1	chr9	46230462	46230463	-	1	NA	TTS (NM_009692)	TTS (NM_009692)	1832	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2|apo-AI|apoA-I	apolipoprotein A-I	protein-coding
mm_69015.1	chr7	126704848	126704854	-	1	NA	promoter-TSS (NM_009898)	promoter-TSS (NM_009898)	-35	NM_009898	12721	Mm.290482	NM_009898	ENSMUSG00000030707	Coro1a	Clabp|Lmb3|TACO|p57	coronin, actin binding protein 1A	protein-coding
mm_170763.1	chr2	16032865	16032867	-	1	NA	intron (NM_001310455, intron 29 of 38)	RLTR9E|LTR|ERVK	-323438	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding
mm_39094.1	chr4	154899020	154899030	-	1	NA	promoter-TSS (NM_025582)	promoter-TSS (NM_025582)	18	NM_025582	66469	Mm.41868	NM_025582	ENSMUSG00000029059	Fam213b	2810405K02Rik|AI836168|PM/PGFS	family with sequence similarity 213, member B	protein-coding
mm_142334.1	chr17	43551264	43551294	-	1	NA	Intergenic	Intergenic	-7640	NM_001254953	100043332	Mm.17626	NM_001254953	ENSMUSG00000096140	Ankrd66	AU041848|D730048J04Rik|Gm4368	ankyrin repeat domain 66	protein-coding
mm_7103.1	chr1	89102857	89102875	-	1	NA	intron (NM_133816, intron 1 of 5)	intron (NM_133816, intron 1 of 5)	32404	NM_133816	98402	Mm.170983	NM_133816	ENSMUSG00000036206	Sh3bp4	AI594717|AW227605|BOG25	SH3-domain binding protein 4	protein-coding
mm_124976.1	chr15	20449097	20449109	+	1	NA	Intergenic	Intergenic	217647	NM_022816	64833	Mm.352763	NM_022816	ENSMUSG00000047565	Acot10	Acate3|MT-ACT48|p48	acyl-CoA thioesterase 10	protein-coding
mm_159856.1	chr5	138092837	138092837	+	1	NA	intron (NM_029869, intron 1 of 3)	B4|SINE|B4	7753	NM_029869	74570	Mm.213114	NM_029869	ENSMUSG00000029729	Zkscan1	5930429A01Rik|9130423L19Rik|9230118B16Rik|AI646829|AI788588|C87323|KOX18|PHZ-37|ZNF139	zinc finger with KRAB and SCAN domains 1	protein-coding
mm_34247.1	chr4	141245081	141245102	+	1	NA	intron (NM_172520, intron 2 of 16)	intron (NM_172520, intron 2 of 16)	2207	NM_172520	213649	Mm.134460	NM_172520	ENSMUSG00000028919	Arhgef19	6030432F23|6430573B13Rik|WGEF	Rho guanine nucleotide exchange factor (GEF) 19	protein-coding
mm_43587.1	chr5	137747644	137747684	+	1	NA	exon (NM_023910, exon 2 of 5)	exon (NM_023910, exon 2 of 5)	1695	NM_029805	78829	Mm.286399	NM_023910	ENSMUSG00000029723	Tsc22d4	0610009M14Rik|1700023B23Rik|AI415410|Thg-1pit|Tilz2	TSC22 domain family, member 4	protein-coding
mm_71182.1	chr8	40862262	40862272	+	1	NA	promoter-TSS (NM_001044740)	promoter-TSS (NM_001044740)	-100	NM_007514	11988	Mm.4676	NM_007514	ENSMUSG00000031596	Slc7a2	20.5|AI158848|Atrc2|CAT-2|Cat2|Tea	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	protein-coding
mm_134102.1	chr16	9995300	9995304	-	1	NA	Intergenic	CpG	-2769	NM_008170	14811	Mm.2953	NM_008170	ENSMUSG00000059003	Grin2a	GluN2A|NMDAR2A|NR2A	glutamate receptor, ionotropic, NMDA2A (epsilon 1)	protein-coding
mm_167321.1	chr8	67696043	67696060	-	1	NA	3' UTR (NM_027626, exon 8 of 8)	3' UTR (NM_027626, exon 8 of 8)	122244	NM_027626	234353	Mm.32525	NM_027626	ENSMUSG00000030465	Psd3	4931420C21Rik|AI661273|BC003498|D430018P08|EFA6D	pleckstrin and Sec7 domain containing 3	protein-coding
mm_78694.1	chr9	40809252	40809255	+	1	NA	Intergenic	Intergenic	7980	NM_031165	15481	Mm.290774	NM_031165	ENSMUSG00000015656	Hspa8	2410008N15Rik|Hsc70|Hsc71|Hsc73|Hsp73|Hspa10	heat shock protein 8	protein-coding
mm_145017.1	chr18	38714361	38714384	+	1	NA	Intergenic	Intergenic	-113104	NM_011898	24066	Mm.42038	NM_011898	ENSMUSG00000024427	Spry4	A030006O18Rik|sprouty4	sprouty homolog 4 (Drosophila)	protein-coding
mm_109255.1	chr12	109459771	109459784	+	1	NA	exon (NM_010052, exon 5 of 5)	exon (NM_010052, exon 5 of 5)	6322	NM_010052	13386	Mm.157069	NM_010052	ENSMUSG00000040856	Dlk1	AW742678|DLK-1|DlkI|FA1|Ly107|Peg9|SCP1|ZOG|pG2|pref-1	delta-like 1 homolog (Drosophila)	protein-coding
mm_87027.1	chr10	28498769	28498786	+	1	NA	intron (NM_008983, intron 13 of 31)	MIR|SINE|MIR	-169583	NM_001305663	210757	Mm.123021	NM_178666	ENSMUSG00000049109	Themis	E430004N04Rik|Gasp|Spot|Tsepa|thylex	thymocyte selection associated	protein-coding
mm_75899.1	chr8	71272314	71272321	-	1	NA	promoter-TSS (NM_001142322)	promoter-TSS (NM_001142322)	273	NM_001163042	76478	Mm.27355	NM_029621	ENSMUSG00000035439	Haus8	2410004L22Rik|Hice1	4HAUS augmin-like complex, subunit 8	protein-coding
mm_101505.1	chr11	32200274	32200286	-	1	NA	promoter-TSS (NM_008374)	promoter-TSS (NM_008374)	-1	NM_008374	16199	Mm.384	NM_008374	ENSMUSG00000020279	Il9r	-	interleukin 9 receptor	protein-coding
mm_39985.1	chr5	32459592	32459601	+	1	NA	intron (NM_172707, intron 1 of 7)	CpG	626	NM_172707	19046	Mm.241931	NM_172707	ENSMUSG00000014956	Ppp1cb	1200010B19	protein phosphatase 1, catalytic subunit, beta isoform	protein-coding
mm_69122.1	chr7	127026334	127026344	-	1	NA	exon (NM_010772, exon 1 of 5)	exon (NM_010772, exon 1 of 5)	140	NM_010772	17188	Mm.378964	NM_010772	ENSMUSG00000030678	Maz	MAZI|PUR1|Pur-1|SAF-1|SAF-2	MYC-associated zinc finger protein (purine-binding transcription factor)	protein-coding
mm_39457.1	chr5	17574727	17574780	+	1	NA	promoter-TSS (NM_013657)	promoter-TSS (NM_013657)	-63	NM_013657	20348	Mm.5071	NM_013657	ENSMUSG00000028780	Sema3c	1110036B02Rik|SemE|Semae	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	protein-coding
mm_114737.1	chr13	83732439	83732465	+	1	NA	intron (NR_015561, intron 2 of 3)	intron (NR_015561, intron 2 of 3)	4346	NR_015561	320203	Mm.245636	NM_177100	ENSMUSG00000050334	C130071C03Rik	2810449C10Rik	RIKEN cDNA C130071C03 gene	ncRNA
mm_95014.1	chr11	31965543	31965597	+	1	NA	promoter-TSS (NM_026262)	promoter-TSS (NM_026262)	-63	NM_026262	67592	Mm.78654	NM_026262	ENSMUSG00000020299	4930524B15Rik	-	RIKEN cDNA 4930524B15 gene	protein-coding
mm_151855.1	chr19	5796812	5796829	-	1	NA	promoter-TSS (NR_144621)	promoter-TSS (NR_144621)	-839	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_128271.1	chr15	36794145	36794154	-	1	NA	5' UTR (NM_011740, exon 1 of 7)	5' UTR (NM_011740, exon 1 of 7)	389	NM_011740	22631	Mm.3360	NM_011740	ENSMUSG00000022285	Ywhaz	1110013I11Rik|14-3-3zeta|AI596267|AL022924|AU020854	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide	protein-coding
mm_44856.1	chr5	34243405	34243418	-	1	NA	intron (NM_001015039, intron 1 of 12)	intron (NM_001015039, intron 1 of 12)	44913	NM_001015039	231125	Mm.113388	NM_001015039	ENSMUSG00000037224	Zfyve28	9630058O20Rik|Gm146|mKIAA1643	zinc finger, FYVE domain containing 28	protein-coding
mm_75622.1	chr8	64617653	64617663	-	1	NA	exon (NM_013494, exon 3 of 9)	exon (NM_013494, exon 3 of 9)	75451	NM_013494	12876	Mm.31395	NM_013494	ENSMUSG00000037852	Cpe	CPH|Cph-1|Cph1|R74677|fat	carboxypeptidase E	protein-coding
mm_118437.1	chr14	8063242	8063261	+	1	NA	Intergenic	Intergenic	-17062	NM_025938	67053	Mm.210048	NM_025938	ENSMUSG00000023156	Rpp14	2610511E03Rik|AA682089	ribonuclease P 14 subunit	protein-coding
mm_13315.1	chr2	102658934	102658950	+	1	NA	5' UTR (NM_001077514, exon 1 of 11)	5' UTR (NM_001077514, exon 1 of 11)	259	NM_001077514	20511	Mm.267547	NM_011393	ENSMUSG00000005089	Slc1a2	1700091C19Rik|2900019G14Rik|AI159670|Eaat2|GLT-1|GLT1|MGLT1	solute carrier family 1 (glial high affinity glutamate transporter), member 2	protein-coding
mm_45617.1	chr5	75835878	75835887	-	1	NA	Intergenic	Intergenic	142546	NM_010612	16542	Mm.285	NM_010612	ENSMUSG00000062960	Kdr	6130401C07|Flk-1|Flk1|Krd-1|Ly73|VEGFR-2|VEGFR2|sVEGFR-2	kinase insert domain protein receptor	protein-coding
mm_44753.1	chr5	31295674	31295697	-	1	NA	5' UTR (NM_022424, exon 1 of 7)	5' UTR (NM_022424, exon 1 of 7)	192	NM_022424	64339	Mm.292544	NM_022424	ENSMUSG00000038552	Fndc4	2810430J06Rik|6330410H20Rik|AB030187|AI838506|AW487863|FRCP1|Fnmp1	fibronectin type III domain containing 4	protein-coding
mm_57088.1	chr6	122586730	122586772	-	1	NA	intron (NM_001134391, intron 5 of 7)	B1_Mus1|SINE|Alu	15693	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_97148.1	chr11	75461599	75461609	+	1	NA	promoter-TSS (NR_030711)	promoter-TSS (NR_030711)	65	NR_030711	100042498	Mm.482242	NR_030711	ENSMUSG00000085148	Mir22hg	2210403K04Rik|mir-22	Mir22 host gene (non-protein coding)	ncRNA
mm_4171.1	chr1	171121647	171121669	+	1	NA	promoter-TSS (NM_001081275)	promoter-TSS (NM_001081275)	-3	NM_001081275	75472	Mm.32760	NM_029301	ENSMUSG00000026649	Cfap126	1700009P17Rik|AV282292|Flattop|Fltp	cilia and flagella associated protein 126	protein-coding
mm_8435.1	chr1	152625154	152625174	-	1	NA	promoter-TSS (NM_016846)	promoter-TSS (NM_016846)	53	NM_016846	19731	Mm.245270	NM_016846	ENSMUSG00000026482	Rgl1	Rgl|mKIAA0959	ral guanine nucleotide dissociation stimulator,-like 1	protein-coding
mm_125741.1	chr15	73558392	73558395	+	1	NA	intron (NM_001081066, intron 16 of 22)	intron (NM_001081066, intron 16 of 22)	38133	NM_001168255	106068	Mm.212813	NM_001033219	ENSMUSG00000079020	Slc45a4	9330175B01Rik|AW552276	solute carrier family 45, member 4	protein-coding
mm_54915.1	chr6	47798549	47798573	-	1	NA	exon (NM_009787, exon 9 of 10)	exon (NM_009787, exon 9 of 10)	5091	NR_030485	735289		NR_030485	ENSMUSG00000076060	Mir704	Mirn704|mir-704|mmu-mir-704	microRNA 704	ncRNA
mm_148749.1	chr19	6050631	6050653	+	1	NA	promoter-TSS (NR_105954)	promoter-TSS (NR_105954)	-692	NR_105954	102465597		NR_105954	ENSMUSG00000098928	Mir6988	Gm27593|mmu-mir-6988	microRNA 6988	ncRNA
mm_146705.1	chr18	13972086	13972091	-	1	NA	intron (NM_145492, intron 1 of 7)	intron (NM_145492, intron 1 of 7)	645	NM_145492	225207	Mm.40325	NM_145492	ENSMUSG00000024420	Zfp521	B930086A16Rik|Evi3|Znf521	zinc finger protein 521	protein-coding
mm_115675.1	chr13	12800078	12800081	-	1	NA	promoter-TSS (NM_011954)	promoter-TSS (NM_011954)	0	NM_011118	18812	Mm.457984	NM_011118	ENSMUSG00000056457	Prl2c3	Ghd1|MRP-2|MRP-3|Mrpplf3|PLF-2|PLF-3|Plf2|Prl2c4|mrp/plf3	prolactin family 2, subfamily c, member 3	protein-coding
mm_117053.1	chr13	58399146	58399186	-	1	NA	exon (NM_025279, exon 4 of 16)	exon (NM_025279, exon 4 of 16)	3003	NM_001301343	15387	Mm.142872	NM_025279	ENSMUSG00000021546	Hnrnpk	Hnrpk|KBBP|NOVA	heterogeneous nuclear ribonucleoprotein K	protein-coding
mm_18382.1	chr2	60098729	60098740	-	1	NA	intron (NM_001001182, intron 1 of 35)	intron (NM_001001182, intron 1 of 35)	27006	NM_001001182	407823	Mm.228071	NM_001001182	ENSMUSG00000026987	Baz2b	5830435C13Rik|BC053917|D2Ertd794e	bromodomain adjacent to zinc finger domain, 2B	protein-coding
mm_140089.1	chr17	75465556	75465568	+	1	NA	promoter-TSS (NM_207246)	promoter-TSS (NM_207246)	24	NM_207246	240168	Mm.329203	NM_207246	ENSMUSG00000071042	Rasgrp3	BC066069|Gm327	RAS, guanyl releasing protein 3	protein-coding
mm_76943.1	chr8	105943390	105943407	-	1	NA	promoter-TSS (NM_008490)	promoter-TSS (NM_008490)	4	NM_008490	16816	Mm.1593	NM_008490	ENSMUSG00000035237	Lcat	AI046659|D8Wsu61e	lecithin cholesterol acyltransferase	protein-coding
mm_17937.1	chr2	35979838	35979859	-	1	NA	promoter-TSS (NM_029774)	promoter-TSS (NM_029774)	-224	NM_029774	74410	Mm.21591	NM_028921	ENSMUSG00000026885	Ttll11	4932702F08Rik|4933424A20Rik|AU043211|D2Ertd624e	tubulin tyrosine ligase-like family, member 11	protein-coding
mm_67887.1	chr7	99350163	99350168	-	1	NA	intron (NM_001111044, intron 1 of 4)	intron (NM_001111044, intron 1 of 4)	3074	NM_009825	12406	Mm.22708	NM_009825	ENSMUSG00000070436	Serpinh1	BERF-1|Cbp1|Cbp2|Hsp47|J6|Serpinh2|gp46	serine (or cysteine) peptidase inhibitor, clade H, member 1	protein-coding
mm_10295.1	chr2	10372552	10372564	+	1	NA	5' UTR (NM_177386, exon 1 of 23)	5' UTR (NM_177386, exon 1 of 23)	122	NM_177386	353282	Mm.329991	NM_177386	ENSMUSG00000061186	Sfmbt2	D2Wsu23e|D330030P06Rik	Scm-like with four mbt domains 2	protein-coding
mm_151922.1	chr19	5799958	5799968	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	2709	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_24724.1	chr3	95282475	95282496	+	1	NA	promoter-TSS (NM_133858)	promoter-TSS (NM_133858)	-409	NM_173347	229589	Mm.14155	NM_173347	ENSMUSG00000015711	Prune1	9230112O05Rik|C130058A12|DRES-17|HTCD37|PRUNEM1|Prune|Prune-M1	prune exopolyphosphatase	protein-coding
mm_28706.1	chr3	95556395	95556403	-	1	NA	TTS (NM_021281)	TTS (NM_021281)	-3278	NM_026489	67981	Mm.179050	NM_026489	ENSMUSG00000028109	Hormad1	4921522K05Rik|Nohma	HORMA domain containing 1	protein-coding
mm_22468.1	chr3	4093866	4093874	+	1	NA	Intergenic	L1VL4|LINE|L1	585840	NM_013920	30942	Mm.330897	NM_013920	ENSMUSG00000017688	Hnf4g	NR2A2	hepatocyte nuclear factor 4, gamma	protein-coding
mm_89545.1	chr10	94575340	94575352	+	1	NA	promoter-TSS (NM_177026)	promoter-TSS (NM_177026)	89	NM_001168684	319880	Mm.23047	NM_172051	ENSMUSG00000020023	Tmcc3	AW488095|C630016B22Rik|C88213|Tmcc1	transmembrane and coiled coil domains 3	protein-coding
mm_133926.1	chr16	3718077	3718089	-	1	NA	promoter-TSS (NM_001161791)	promoter-TSS (NM_001161791)	41	NM_001161790	54483	Mm.143718	NM_019453	ENSMUSG00000022534	Mefv	FMF|TRIM20|pyrin	Mediterranean fever	protein-coding
mm_132186.1	chr16	32430896	32430978	+	1	NA	promoter-TSS (NM_009981)	promoter-TSS (NM_009981)	16	NM_009981	13026	Mm.98775	NM_009981	ENSMUSG00000005615	Pcyt1a	CTalpha|Cctalpha|Ctpct|Cttalpha	phosphate cytidylyltransferase 1, choline, alpha isoform	protein-coding
mm_65051.1	chr7	18656596	18656604	-	1	NA	5' UTR (NM_027403, exon 1 of 5)	5' UTR (NM_027403, exon 1 of 5)	125	NM_027403	72242	Mm.326858	NM_027403	ENSMUSG00000070796	Psg21	1600019C01Rik|1600025N01Rik|1600026N13Rik|cea8	pregnancy-specific glycoprotein 21	protein-coding
mm_103209.1	chr11	70653003	70653011	-	1	NA	intron (NM_011072, intron 1 of 2)	intron (NM_011072, intron 1 of 2)	1643	NM_011072	18643	Mm.2647	NM_011072	ENSMUSG00000018293	Pfn1	Pfn	profilin 1	protein-coding
mm_59754.1	chr7	28825274	28825285	+	1	NA	promoter-TSS (NM_016772)	promoter-TSS (NM_016772)	-59	NM_016772	51798	Mm.291776	NM_016772	ENSMUSG00000053898	Ech1	AA617331	enoyl coenzyme A hydratase 1, peroxisomal	protein-coding
mm_95479.1	chr11	51261720	51261731	+	1	NA	intron (NM_177567, intron 1 of 2)	intron (NM_177567, intron 1 of 2)	1226	NM_177567	193286	Mm.80975	NM_177567	ENSMUSG00000045942	BC049762	4930503F14	cDNA sequence BC049762	protein-coding
mm_149931.1	chr19	26753653	26753662	+	1	NA	intron (NM_001347439, intron 3 of 7)	intron (NM_001347439, intron 3 of 7)	5254	NM_026003	67155	Mm.342988	NM_011416	ENSMUSG00000024921	Smarca2	2610209L14Rik|SNF2alpha|Snf2l2|brahma|brm	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	protein-coding
mm_33733.1	chr4	134102582	134102610	+	1	NA	promoter-TSS (NM_026257)	promoter-TSS (NM_026257)	13	NM_026257	67586	Mm.282029	NM_026257	ENSMUSG00000012126	Ubxn11	4930506L07Rik|D4Bwg1540e|Soc|Soci|Ubxd5	UBX domain protein 11	protein-coding
mm_115482.1	chr13	3601459	3601471	-	1	NA	intron (NM_134063, intron 1 of 19)	intron (NM_134063, intron 1 of 19)	9643	NM_134063	105203	Mm.221609	NM_134063	ENSMUSG00000033799	Fam208b	AI645998|Pap20|mKIAA2006	family with sequence similarity 208, member B	protein-coding
mm_123533.1	chr14	66805209	66805219	-	1	NA	3' UTR (NM_009955, exon 14 of 14)	3' UTR (NM_009955, exon 14 of 14)	63386	NM_009955	12934	Mm.352648	NM_009955	ENSMUSG00000022048	Dpysl2	AI851130|Crmp2|DRP2|Musunc33|TOAD-64|Ulip2	dihydropyrimidinase-like 2	protein-coding
mm_168834.1	chr12	23010207	23010208	-	1	NA	promoter-TSS (NR_015504)	promoter-TSS (NR_015504)	36	NR_015504	69732	Mm.391403	NM_028362	ENSMUSG00000073164	2410018L13Rik	2810480C08Rik	RIKEN cDNA 2410018L13 gene	ncRNA
mm_11229.1	chr2	29802656	29802693	+	1	NA	promoter-TSS (NM_011989)	promoter-TSS (NM_011989)	-6	NM_011989	26569	Mm.330113	NM_011989	ENSMUSG00000059316	Slc27a4	BB144259|FATP4	solute carrier family 27 (fatty acid transporter), member 4	protein-coding
mm_75181.1	chr8	36952272	36952294	-	1	NA	5' UTR (NM_001194940, exon 1 of 18)	5' UTR (NM_001194940, exon 1 of 18)	159	NM_001194940	50768	Mm.125155	NM_015802	ENSMUSG00000031523	Dlc1	A730069N07Rik|Arhgap7|HP|STARD12|dlc-1	deleted in liver cancer 1	protein-coding
mm_103871.1	chr11	83525880	83525908	-	1	NA	3' UTR (NM_013653, exon 3 of 3)	3' UTR (NM_013653, exon 3 of 3)	-3795	NM_001045543	629303	Mm.390417	NM_001045543	ENSMUSG00000018925	Heatr9	Gm11435|OTTMUSG00000000990	HEAT repeat containing 9	protein-coding
mm_102480.1	chr11	60106524	60106545	-	1	NA	intron (NM_009021, intron 1 of 5)	intron (NM_009021, intron 1 of 5)	1521	NM_009021	19377	Mm.296366	NM_009021	ENSMUSG00000062115	Rai1	Gt1	retinoic acid induced 1	protein-coding
mm_9407.1	chr1	172274325	172274344	-	1	NA	3' UTR (NM_178405, exon 23 of 23)	3' UTR (NM_178405, exon 23 of 23)	-15910	NM_013734	27222	Mm.482392	NM_013734	ENSMUSG00000007107	Atp1a4	-	ATPase, Na+/K+ transporting, alpha 4 polypeptide	protein-coding
mm_4816.1	chr1	185418272	185418294	+	1	NA	exon (NM_029735, exon 28 of 32)	exon (NM_029735, exon 28 of 32)	23536	NR_038006	319562	Mm.184335	NM_176943	ENSMUSG00000051295	9630028B13Rik	-	RIKEN cDNA 9630028B13 gene	ncRNA
mm_50271.1	chr6	45158926	45158930	+	1	NA	intron (NM_001004357, intron 1 of 23)	intron (NM_001004357, intron 1 of 23)	98867	NM_001004357	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding
mm_69558.1	chr7	135700176	135700190	-	1	NA	exon (NM_001081117, exon 12 of 14)	exon (NM_001081117, exon 12 of 14)	16196	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_89236.1	chr10	87679858	87679866	+	1	NA	Intergenic	Intergenic	158067	NM_008777	18478	Mm.263539	NM_008777	ENSMUSG00000020051	Pah	AW106920	phenylalanine hydroxylase	protein-coding
mm_117653.1	chr13	93144558	93144577	-	1	NA	5' UTR (NM_023821, exon 1 of 13)	5' UTR (NM_023821, exon 1 of 13)	157	NM_023821	76469	Mm.33857	NM_023821	ENSMUSG00000047419	Cmya5	2310076E16Rik|2310076E21Rik|AA420382|AI504003|Srfsd|Tims|sr553	cardiomyopathy associated 5	protein-coding
mm_101195.1	chr11	18891120	18891131	-	1	NA	intron (NM_001193271, intron 9 of 12)	intron (NM_001193271, intron 9 of 12)	127844	NM_001193271	17268	Mm.356578	NM_010789	ENSMUSG00000020160	Meis1	C530044H18Rik|Evi8	Meis homeobox 1	protein-coding
mm_13214.1	chr2	96317821	96317831	+	1	NA	promoter-TSS (NM_001289742)	promoter-TSS (NM_001289742)	-343	NM_001289742	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_123212.1	chr14	59412156	59412174	-	1	NA	exon (NM_001320721, exon 10 of 13)	exon (NM_001320721, exon 10 of 13)	-18653	NM_001164289	628705	Mm.479244	NM_001164289	ENSMUSG00000091144	Phf11c	EG628705|Gm6907|Phf11	PHD finger protein 11C	protein-coding
mm_36699.1	chr4	96664079	96664098	-	1	NA	promoter-TSS (NM_010007)	promoter-TSS (NM_010007)	31	NM_010007	13109	Mm.12838	NM_010007	ENSMUSG00000052520	Cyp2j5	-	cytochrome P450, family 2, subfamily j, polypeptide 5	protein-coding
mm_173092.1	chrX	150814246	150814246	-	1	NA	promoter-TSS (NM_030700)	promoter-TSS (NM_030700)	93	NM_030700	80884	Mm.22575	NM_030700	ENSMUSG00000025268	Maged2	4833439A22Rik|Mage-d2|ORF1	melanoma antigen, family D, 2	protein-coding
mm_52460.1	chr6	113697169	113697185	+	1	NA	5' UTR (NM_001347356, exon 1 of 8)	5' UTR (NM_001347356, exon 1 of 8)	127	NM_001033463	381801	Mm.333322	NM_001033463	ENSMUSG00000056952	Tatdn2	AI646012|mKIAA0218	TatD DNase domain containing 2	protein-coding
mm_97000.1	chr11	70764429	70764483	+	1	NA	promoter-TSS (NM_177565)	promoter-TSS (NM_177565)	9	NM_177565	193043	Mm.40966	NM_177565	ENSMUSG00000043602	Zfp3	AI854635|B230309J24|Fnp-1|Zfp-3	zinc finger protein 3	protein-coding
mm_87714.1	chr10	60078871	60078884	+	1	NA	intron (NM_026937, intron 9 of 10)	intron (NM_026937, intron 9 of 10)	-27380	NM_052994	94214	Mm.153429	NM_052994	ENSMUSG00000058297	Spock2	AA407235|Gcap26|mKIAA0275	sparc/osteonectin, cwcv and kazal-like domains proteoglycan 2	protein-coding
mm_137194.1	chr17	23829213	23829241	+	1	NA	promoter-TSS (NM_026305)	promoter-TSS (NM_026305)	-118	NM_026305	67673	Mm.153758	NM_026305	ENSMUSG00000055839	Elob	0610040H15Rik|Tceb2	elongin B	protein-coding
mm_40620.1	chr5	64803589	64803607	+	1	NA	promoter-TSS (NM_008453)	promoter-TSS (NM_008453)	75	NM_008453	16599	Mm.392759	NM_008453	ENSMUSG00000029178	Klf3	9930027G08Rik|AL024007|Bklf|Tef-2	Kruppel-like factor 3 (basic)	protein-coding
mm_91647.1	chr10	42475071	42475085	-	1	NA	intron (NM_145743, intron 1 of 12)	intron (NM_145743, intron 1 of 12)	3487	NM_145743	215951	Mm.89646	NM_145743	ENSMUSG00000038302	Lace1	CG8520	lactation elevated 1	protein-coding
mm_131812.1	chr16	22919266	22919275	+	1	NA	promoter-TSS (NM_021564)	promoter-TSS (NM_021564)	888	NM_001083905	59083	Mm.28461	NM_021564	ENSMUSG00000022871	Fetub	2310011O17Rik|AI255764|D17980|Gugu	fetuin beta	protein-coding
mm_93353.1	chr10	102512397	102512417	-	1	NA	5' UTR (NM_146240, exon 1 of 2)	5' UTR (NM_146240, exon 1 of 2)	185	NM_146240	237504	Mm.282672	NM_146240	ENSMUSG00000044921	Rassf9	AW322107|Pamci	Ras association (RalGDS/AF-6) domain family (N-terminal) member 9	protein-coding
mm_9594.1	chr1	174921792	174921803	-	1	NA	promoter-TSS (NM_011825)	promoter-TSS (NM_011825)	22	NM_011825	23893	Mm.25760	NM_011825	ENSMUSG00000050069	Grem2	Gremlin2|Prdc	gremlin 2, DAN family BMP antagonist	protein-coding
mm_18340.1	chr2	58155791	58155807	-	1	NA	intron (NM_139200, intron 1 of 7)	intron (NM_139200, intron 1 of 7)	4323	NM_139200	227929	Mm.273905	NM_139200	ENSMUSG00000026832	Cytip	A130053M09Rik|AI462064|C80816|Cbp|Cybr|Pscdbp	cytohesin 1 interacting protein	protein-coding
mm_44759.1	chr5	31571350	31571358	-	1	NA	promoter-TSS (NR_102275)	promoter-TSS (NR_102275)	43	NR_102275	100740	Mm.23370	NR_102275		AI839979	-	expressed sequence AI839979	ncRNA
mm_163216.1	chr11	101176194	101176247	+	1	NA	promoter-TSS (NM_007721)	promoter-TSS (NM_007721)	103	NM_016782	53321	Mm.474527	NM_016782	ENSMUSG00000017167	Cntnap1	AI841080|Caspr|NCP1|Nrxn4|p190|shm	contactin associated protein-like 1	protein-coding
mm_123644.1	chr14	68655725	68655751	-	1	NA	non-coding (NR_102399, exon 1 of 22)	non-coding (NR_102399, exon 1 of 22)	104	NM_010082	13522	Mm.117450	NM_010082	ENSMUSG00000014725	Adam28	C130072N01Rik|D430033C21Rik|Dtgn1|MDC-L|MDCL|TECADAM|eMDCII	a disintegrin and metallopeptidase domain 28	protein-coding
mm_162368.1	chr1	65928212	65928220	+	1	NA	TTS (NM_027010)	TTS (NM_027010)	1694	NM_027010	12969	Mm.275362	NM_027010	ENSMUSG00000025945	Crygf	3110001K11Rik|Cryg-2|DGcry-2|Len-2	crystallin, gamma F	protein-coding
mm_163504.1	chr12	112914588	112914596	-	1	NA	intron (NM_010588, intron 12 of 25)	intron (NM_010588, intron 12 of 25)	5949	NR_105906	102465567		NR_105906	ENSMUSG00000098338	Mir6941	Gm27923|mmu-mir-6941	microRNA 6941	ncRNA
mm_78928.1	chr9	45079171	45079203	+	1	NA	promoter-TSS (NM_001005421)	promoter-TSS (NM_001005421)	4	NM_001005421	270152	Mm.190461	NM_001005421	ENSMUSG00000048534	Amica1	AMICA|Crea7|Gm638|Jaml	adhesion molecule, interacts with CXADR antigen 1	protein-coding
mm_6321.1	chr1	71606784	71606801	-	1	NA	exon (NM_001276413, exon 29 of 44)	exon (NM_001276413, exon 29 of 44)	46442	NM_010233	14268	Mm.193099	NM_010233	ENSMUSG00000026193	Fn1	E330027I09|Fn|Fn-1	fibronectin 1	protein-coding
mm_81593.1	chr9	110509951	110509970	+	1	NA	intron (NM_010628, intron 13 of 20)	intron (NM_010628, intron 13 of 20)	-22637	NM_001081340	235626	Mm.288949	NM_001081340	ENSMUSG00000044791	Setd2	4921524K10Rik|BC031601|KMT3A	SET domain containing 2	protein-coding
mm_22878.1	chr3	29314726	29314734	+	1	NA	intron (NM_001167748, intron 4 of 12)	intron (NM_001167748, intron 4 of 12)	-102093	NR_030422	791072		NR_030422	ENSMUSG00000076120	Mir551b	Mirn551b|mir-551b	microRNA 551b	ncRNA
mm_134482.1	chr16	18623348	18623350	-	1	NA	promoter-TSS (NM_010327)	promoter-TSS (NM_010327)	-946	NM_010327	14724	Mm.475622	NM_010327	ENSMUSG00000050761	Gp1bb	-	glycoprotein Ib, beta polypeptide	protein-coding
mm_98625.1	chr11	95973154	95973155	+	1	NA	exon (NM_009951, exon 7 of 15)	exon (NM_009951, exon 7 of 15)	-9771	NR_037223	100526468		NR_037223	ENSMUSG00000093358	Mir3063	mmu-mir-3063	microRNA 3063	ncRNA
mm_160085.1	chr7	13989658	13989658	-	1	NA	promoter-TSS (NM_001101534)	promoter-TSS (NM_001101534)	-70	NM_001101534	434121	Mm.482762	NM_001101534	ENSMUSG00000074377	Sult2a4	EG434121|Gm5584	sulfotransferase family 2A, dehydroepiandrosterone (DHEA)-preferring, member 4	protein-coding
mm_108432.1	chr12	82246658	82246669	+	1	NA	intron (NM_001167983, intron 2 of 23)	L1M4c|LINE|L1	-64686	NM_172579	217692	Mm.261333	NM_172579	ENSMUSG00000042700	Sipa1l1	4931426N11Rik|AW213287|Spar|mKIAA0440	signal-induced proliferation-associated 1 like 1	protein-coding
mm_17546.1	chr2	29870189	29870223	-	1	NA	intron (NM_207298, intron 1 of 11)	intron (NM_207298, intron 1 of 11)	712	NM_207298	99151	Mm.296336	NM_207298	ENSMUSG00000039787	Cercam	2600006K01Rik|AL024097|Ceecam1	cerebral endothelial cell adhesion molecule	protein-coding
mm_36229.1	chr4	62979574	62979582	-	1	NA	intron (NM_028326, intron 1 of 14)	intron (NM_028326, intron 1 of 14)	14004	NM_028326	72701	Mm.26479	NM_028326	ENSMUSG00000028358	Zfp618	2810031P15Rik|2810040O04Rik|AI415580|AI505139|D430033D05Rik|Nedd10|Znf618|bM257P7.1	zinc finger protein 618	protein-coding
mm_20594.1	chr2	131174789	131174815	-	1	NA	promoter-TSS (NM_027641)	promoter-TSS (NM_027641)	8	NM_027641	70997	Mm.252722	NM_027641	ENSMUSG00000027329	Spef1	4931426K16Rik|Clamp	sperm flagellar 1	protein-coding
mm_141357.1	chr17	28691220	28691234	-	1	NA	promoter-TSS (NM_011951)	promoter-TSS (NM_011951)	-115	NM_001168508	26416	Mm.311337	NM_011951	ENSMUSG00000053436	Mapk14	CSBP2|Crk1|Csbp1|Mxi2|PRKM14|PRKM15|p38|p38-alpha|p38MAPK|p38a|p38alpha	mitogen-activated protein kinase 14	protein-coding
mm_149031.1	chr19	8802487	8802521	+	1	NA	promoter-TSS (NM_001098237)	promoter-TSS (NM_001098237)	8	NM_133759	75291	Mm.23423	NM_133759	ENSMUSG00000071661	Zbtb3	4930563M09Rik	zinc finger and BTB domain containing 3	protein-coding
mm_13337.1	chr2	102787175	102787178	+	1	NA	3' UTR (NM_001077514, exon 11 of 11)	3' UTR (NM_001077514, exon 11 of 11)	80738	NM_001077515	20511	Mm.267547	NM_011393	ENSMUSG00000005089	Slc1a2	1700091C19Rik|2900019G14Rik|AI159670|Eaat2|GLT-1|GLT1|MGLT1	solute carrier family 1 (glial high affinity glutamate transporter), member 2	protein-coding
mm_172037.1	chr6	125191682	125191684	-	1	NA	promoter-TSS (NM_025595)	promoter-TSS (NM_025595)	-97	NM_146171	68298	Mm.257590	NM_146171	ENSMUSG00000038252	Ncapd2	2810406C15Rik|2810465G24Rik|CAP-D2|CNAP1|mKIAA0159	non-SMC condensin I complex, subunit D2	protein-coding
mm_117084.1	chr13	59694101	59694108	-	1	NA	promoter-TSS (NM_183290)	promoter-TSS (NM_183290)	-3	NM_183290	70900	Mm.73124	NM_183290	ENSMUSG00000049902	4921517D22Rik	-	RIKEN cDNA 4921517D22 gene	protein-coding
mm_105750.1	chr11	109472612	109472639	-	1	NA	promoter-TSS (NM_028710)	promoter-TSS (NM_028710)	604	NM_134038	104681	Mm.265874	NM_134038	ENSMUSG00000041920	Slc16a6	AW743111|ESTM12|MCT 6|MCT 7|MCT6	solute carrier family 16 (monocarboxylic acid transporters), member 6	protein-coding
mm_112527.1	chr13	9276717	9276727	+	1	NA	5' UTR (NM_001081426, exon 1 of 37)	5' UTR (NM_001081426, exon 1 of 37)	197	NM_001081426	208440	Mm.217326	NM_172459	ENSMUSG00000048264	Dip2c	2900024P20Rik|9630044M06|mKIAA0934	disco interacting protein 2 homolog C	protein-coding
mm_162982.1	chr11	21370772	21370778	-	1	NA	promoter-TSS (NM_139297)	promoter-TSS (NM_139297)	-146	NM_139297	216558	Mm.28877	NM_139297	ENSMUSG00000001891	Ugp2	UDPGP|UGPase	UDP-glucose pyrophosphorylase 2	protein-coding
mm_43199.1	chr5	129020505	129020523	+	1	NA	intron (NM_009391, intron 1 of 6)	CpG	358	NM_009391	19384	Mm.297440	NM_009391	ENSMUSG00000029430	Ran	-	RAN, member RAS oncogene family	protein-coding
mm_102952.1	chr11	69662570	69662596	-	1	NA	promoter-TSS (NR_035455)	promoter-TSS (NR_035455)	66	NR_125917	24070	Mm.89579	NM_011900	ENSMUSG00000018761	Mpdu1	LEC35|SL15|Supl15h	mannose-P-dolichol utilization defect 1	protein-coding
mm_29711.1	chr3	123688686	123688686	-	1	NA	intron (NR_121616, intron 1 of 13)	intron (NR_121616, intron 1 of 13)	2166	NR_121616	83398	Mm.443908	NM_031186	ENSMUSG00000027977	Ndst3	4921531K01Rik|4930511P15Rik|N-HSST 3|NDST-3	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 3	protein-coding
mm_138880.1	chr17	43360387	43360409	+	1	NA	Intergenic	Intergenic	-29068	NM_001081178	224792	Mm.23478	NM_001081178	ENSMUSG00000056492	Adgrf5	8430401C09Rik|9330185D23|AI528491|Gpr116|mKIAA0758	adhesion G protein-coupled receptor F5	protein-coding
mm_155904.1	chrX	101682937	101682948	+	1	NA	3' UTR (NM_001290535, exon 22 of 22)	3' UTR (NM_001290535, exon 22 of 22)	42724	NM_001290535	108155	Mm.487332	NM_139144	ENSMUSG00000034160	Ogt	1110038P24Rik|4831420N21Rik|AI115525|Ogtl	O-linked N-acetylglucosamine (GlcNAc) transferase (UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase)	protein-coding
mm_108602.1	chr12	85468974	85468988	+	1	NA	Intergenic	Intergenic	-4920	NM_010234	14281	Mm.246513	NM_010234	ENSMUSG00000021250	Fos	D12Rfj1|c-fos|cFos	FBJ osteosarcoma oncogene	protein-coding
mm_92059.1	chr10	62513477	62513499	-	1	NA	Intergenic	Intergenic	-5733	NM_011157	19073	Mm.338790	NM_011157	ENSMUSG00000020077	Srgn	Prg|Prg1|Sgc	serglycin	protein-coding
mm_87076.1	chr10	29211663	29211700	+	1	NA	promoter-TSS (NM_001162537)	promoter-TSS (NM_001162537)	38	NM_001162537	212448	Mm.132789	NM_001162537	ENSMUSG00000004360	9330159F19Rik	-	RIKEN cDNA 9330159F19 gene	protein-coding
mm_29967.1	chr3	133467768	133467780	-	1	NA	exon (NM_001346736, exon 12 of 12)	exon (NM_001346736, exon 12 of 12)	76616	NM_001346736	214133	Mm.347816	NM_145989	ENSMUSG00000040943	Tet2	Ayu17-449|E130014J05Rik|mKIAA1546	tet methylcytosine dioxygenase 2	protein-coding
mm_155080.1	chrX	47912433	47912442	+	1	NA	promoter-TSS (NM_177215)	promoter-TSS (NM_177215)	-19	NM_177215	320634	Mm.210343	NM_177215	ENSMUSG00000001173	Ocrl	9530014D17Rik|BB143339|OCRL1	oculocerebrorenal syndrome of Lowe	protein-coding
mm_118767.1	chr14	22468866	22468890	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	73920	NR_046307	74896	Mm.444661	NR_046307		4930405A10Rik	4930456G20Rik	RIKEN cDNA 4930405A10 gene	ncRNA
mm_16781.1	chr2	9887953	9888000	-	1	NA	intron (NR_040511, intron 1 of 3)	intron (NR_040511, intron 1 of 3)	1564	NR_040511	77682	Mm.488621	NR_040511	ENSMUSG00000079602	9230102O04Rik	-	RIKEN cDNA 9230102O04 gene	ncRNA
mm_46212.1	chr5	98185971	98185997	-	1	NA	exon (NM_029947, exon 4 of 4)	exon (NM_029947, exon 4 of 4)	5115	NM_029947	77630	Mm.332511	NM_029947	ENSMUSG00000035456	Prdm8	4930565F05Rik|PFM5	PR domain containing 8	protein-coding
mm_79875.1	chr9	65188864	65188864	+	1	NA	Intergenic	Intergenic	-25826	NM_177460	214424	Mm.31129	NM_177460	ENSMUSG00000032392	Parp16	ARTD15|BC055447|C79952|PARP-16	poly (ADP-ribose) polymerase family, member 16	protein-coding
mm_155937.1	chrX	103672564	103672565	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	41978	NM_029158	75064	Mm.159414	NM_029158	ENSMUSG00000031330	Zcchc13	4930513O09Rik|Cnbp2	zinc finger, CCHC domain containing 13	protein-coding
mm_63453.1	chr7	127519653	127519670	+	1	NA	exon (NM_001304266, exon 4 of 34)	exon (NM_001304266, exon 4 of 34)	-6792	NR_024331	629159	Mm.256720	NR_024331	ENSMUSG00000101225	1700008J07Rik	AW048743	RIKEN cDNA 1700008J07 gene	ncRNA
mm_111479.1	chr12	98733907	98733936	-	1	NA	intron (NM_001146199, intron 1 of 18)	intron (NM_001146199, intron 1 of 18)	724	NM_011877	24000	Mm.4420	NM_011877	ENSMUSG00000021009	Ptpn21	PTPD1|PTPRL10	protein tyrosine phosphatase, non-receptor type 21	protein-coding
mm_11238.1	chr2	29869485	29869535	+	1	NA	promoter-TSS (NM_207298)	promoter-TSS (NM_207298)	16	NM_207298	99151	Mm.296336	NM_207298	ENSMUSG00000039787	Cercam	2600006K01Rik|AL024097|Ceecam1	cerebral endothelial cell adhesion molecule	protein-coding
mm_56175.1	chr6	88044296	88044331	-	1	NA	intron (NM_001293652, intron 1 of 7)	intron (NM_001293652, intron 1 of 7)	704	NM_001293653	19349	Mm.333233	NM_009005	ENSMUSG00000079477	Rab7	Rab7a	RAB7, member RAS oncogene family	protein-coding
mm_15679.1	chr2	163551623	163551634	+	1	NA	exon (NM_001312906, exon 3 of 11)	exon (NM_001312906, exon 3 of 11)	4473	NM_008261	15378	Mm.202383	NM_008261	ENSMUSG00000017950	Hnf4a	HNF-4|Hnf4|Hnf4alpha|MODY1|Nr2a1|TCF-14|Tcf14	hepatic nuclear factor 4, alpha	protein-coding
mm_19131.1	chr2	80129536	80129549	-	1	NA	promoter-TSS (NM_016744)	promoter-TSS (NM_016744)	-130	NM_001159582	18573	Mm.40678	NM_016744	ENSMUSG00000059173	Pde1a	AI987702|AW125737	phosphodiesterase 1A, calmodulin-dependent	protein-coding
mm_96825.1	chr11	69995827	69995870	+	1	NA	promoter-TSS (NM_030064)	promoter-TSS (NM_030064)	82	NM_030064	78246	Mm.20805	NM_030064	ENSMUSG00000018572	Phf23	JUNE-1	PHD finger protein 23	protein-coding
mm_83367.1	chr9	44454716	44454726	-	1	NA	promoter-TSS (NM_009476)	promoter-TSS (NM_009476)	46	NM_009476	22269	Mm.4453	NM_009476	ENSMUSG00000041523	Upk2	AW491716|UPII	uroplakin 2	protein-coding
mm_7809.1	chr1	131527524	131527540	-	1	NA	promoter-TSS (NM_001081011)	promoter-TSS (NM_001081011)	-171	NM_001081011	14270	Mm.276259	NM_019520	ENSMUSG00000026425	Srgap2	9930124L22Rik|AI448945|FBP2|Fnbp2|srGAP3	SLIT-ROBO Rho GTPase activating protein 2	protein-coding
mm_12395.1	chr2	70070034	70070076	+	1	NA	intron (NM_177376, intron 2 of 34)	intron (NM_177376, intron 2 of 34)	30929	NM_177376	329421	Mm.99648	NM_177376	ENSMUSG00000042064	Myo3b	A430065P19Rik	myosin IIIB	protein-coding
mm_156452.1	chrX	142720428	142720443	+	1	NA	intron (NM_001199360, intron 2 of 6)	intron (NM_001199360, intron 2 of 6)	-18565	NR_030523	723976		NR_030523	ENSMUSG00000076011	Mir652	Mirn652|miRX|mmu-mir-652	microRNA 652	ncRNA
mm_152694.1	chr19	16781097	16781107	-	1	NA	promoter-TSS (NM_173028)	promoter-TSS (NM_173028)	-169	NM_173028	271564	Mm.211963	NM_173028	ENSMUSG00000046230	Vps13a	4930425F11|4930516E05Rik|4930543C13Rik|9930023P20|Chac|Chorein|D330038K10Rik|mKIAA0986	vacuolar protein sorting 13A	protein-coding
mm_80777.1	chr9	95581485	95581502	+	1	NA	Intergenic	Intergenic	21676	NM_198414	75552	Mm.151485	NM_198414	ENSMUSG00000064225	Paqr9	1700020G04Rik	progestin and adipoQ receptor family member IX	protein-coding
mm_10446.1	chr2	14271699	14271709	+	1	NA	intron (NM_008625, intron 9 of 29)	intron (NM_008625, intron 9 of 29)	10701	NR_030609	100124488		NR_030609	ENSMUSG00000077897	Mir511	Mirn511|mir-511|mmu-mir-511	microRNA 511	ncRNA
mm_70197.1	chr7	144553640	144553650	-	1	NA	promoter-TSS (NM_001195086)	promoter-TSS (NM_001195086)	84	NM_001033319	233977	Mm.490347	NM_001033319	ENSMUSG00000037519	Ppfia1	C030014K08Rik|C87158|LIP.1|LIP1	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1	protein-coding
mm_143625.1	chr17	78877266	78877293	-	1	NA	intron (NM_011163, intron 2 of 15)	RSINE1|SINE|B4	5293	NM_011163	19106	Mm.378990	NM_011163	ENSMUSG00000024079	Eif2ak2	2310047A08Rik|4732414G15Rik|AI467567|AI747578|Pkr|Prkr|Tik	eukaryotic translation initiation factor 2-alpha kinase 2	protein-coding
mm_93936.1	chr10	127188732	127188763	-	1	NA	intron (NM_001166413, intron 2 of 15)	CpG	1076	NM_001166413	52666	Mm.272230	NM_028027	ENSMUSG00000019467	Arhgef25	2410008H17Rik|D10Ertd610e|GEFT	Rho guanine nucleotide exchange factor (GEF) 25	protein-coding
mm_128140.1	chr15	31521346	31521349	-	1	NA	intron (NM_172606, intron 1 of 25)	intron (NM_172606, intron 1 of 25)	9690	NM_172606	223455	Mm.272185	NM_172606	ENSMUSG00000039100	March6	3830408G03|F830029L24Rik|mKIAA0597	membrane-associated ring finger (C3HC4) 6	protein-coding
mm_71188.1	chr8	40866608	40866625	+	1	NA	intron (NM_007514, intron 1 of 11)	intron (NM_007514, intron 1 of 11)	4249	NM_001044740	11988	Mm.4676	NM_007514	ENSMUSG00000031596	Slc7a2	20.5|AI158848|Atrc2|CAT-2|Cat2|Tea	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	protein-coding
mm_33404.1	chr4	129839163	129839166	+	1	NA	5' UTR (NM_001164745, exon 2 of 6)	5' UTR (NM_001164745, exon 2 of 6)	18456	NM_001164745	19244	Mm.193688	NM_008974	ENSMUSG00000028788	Ptp4a2	Prl-2	protein tyrosine phosphatase 4a2	protein-coding
mm_149599.1	chr19	16318411	16318429	+	1	NA	intron (NM_008139, intron 3 of 6)	intron (NM_008139, intron 3 of 6)	-3416	NR_105832	102465218		NR_105832	ENSMUSG00000098718	Mir496b	Gm28028|mmu-mir-496b	microRNA 496b	ncRNA
mm_147916.1	chr18	65584145	65584162	-	1	NA	intron (NM_207255, intron 2 of 5)	intron (NM_207255, intron 2 of 5)	3923	NM_207255	328977	Mm.286232	NM_207255	ENSMUSG00000042439	Zfp532	C530030I18Rik|Znf532|mKIAA1629	zinc finger protein 532	protein-coding
mm_50153.1	chr6	41544995	41545017	+	1	NA	Intergenic	Intergenic	23230	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_116488.1	chr13	44480307	44480309	-	1	NA	Intergenic	Intergenic	40581	NR_045489	69491	Mm.392410	NR_045489	ENSMUSG00000098144	1700029N11Rik	-	RIKEN cDNA 1700029N11 gene	ncRNA
mm_135825.1	chr16	58507605	58507633	-	1	NA	intron (NM_018784, intron 1 of 10)	intron (NM_018784, intron 1 of 10)	15693	NM_018784	54613	Mm.212742	NM_018784	ENSMUSG00000022747	St3gal6	1700023B24Rik|AI930218|AW552396|Siat10|St3galVI	ST3 beta-galactoside alpha-2,3-sialyltransferase 6	protein-coding
mm_48078.1	chr5	136869730	136869736	-	1	NA	intron (NM_001346699, intron 1 of 12)	intron (NM_001346699, intron 1 of 12)	13374	NM_024474	140709	Mm.295020	NM_024474	ENSMUSG00000004415	Col26a1	9430032K24Rik|BC002218|Col26a|Emid2|Emu2	collagen, type XXVI, alpha 1	protein-coding
mm_154401.1	chrM	13857	13867	+	1	NA	NA	Intergenic	NA	NA								
mm_40689.1	chr5	65763991	65764001	+	1	NA	intron (NM_001024917, intron 1 of 19)	CpG	475	NM_001024917	333789	Mm.332398	NM_001024917	ENSMUSG00000037795	N4bp2	B3bp|E430014I16|Gm1791|Gm868	NEDD4 binding protein 2	protein-coding
mm_153213.1	chr19	34747195	34747219	-	1	NA	promoter-TSS (NM_172838)	promoter-TSS (NM_172838)	-96	NM_172838	240638	Mm.74636	NM_172838	ENSMUSG00000009378	Slc16a12	3230401A21|AW210596	solute carrier family 16 (monocarboxylic acid transporters), member 12	protein-coding
mm_7493.1	chr1	121332663	121332671	-	1	NA	promoter-TSS (NM_178082)	promoter-TSS (NM_178082)	-78	NM_178082	72999	Mm.27136	NM_133748	ENSMUSG00000003721	Insig2	2900053I11Rik|C730043J18Rik|Insig-2	insulin induced gene 2	protein-coding
mm_76681.1	chr8	94012559	94012687	-	1	NA	promoter-TSS (NM_011787)	promoter-TSS (NM_011787)	17	NM_011787	23802	Mm.34641	NM_011787	ENSMUSG00000031751	Amfr	gp78	autocrine motility factor receptor	protein-coding
mm_70264.1	chr8	3567959	3568006	+	1	NA	promoter-TSS (NM_001024728)	promoter-TSS (NM_001024728)	-16	NM_001024728	546049	Mm.358733	NM_001024728	ENSMUSG00000065952	C330021F23Rik	2610027C06Rik|Rps23r1|Rps23rg1	RIKEN cDNA C330021F23 gene	protein-coding
mm_24918.1	chr3	96275028	96275032	+	1	NA	Intergenic	RSINE1|SINE|B4	5330	NM_175666	319189	Mm.297655	NM_175666	ENSMUSG00000105827	Hist2h2bb	H2b-616	histone cluster 2, H2bb	protein-coding
mm_53193.1	chr6	125494870	125494904	+	1	NA	promoter-TSS (NM_007657)	promoter-TSS (NM_007657)	-132	NM_007657	12527	Mm.210676	NM_007657	ENSMUSG00000030342	Cd9	Tspan29	CD9 antigen	protein-coding
mm_138342.1	chr17	34911244	34911257	+	1	NA	intron (NM_147151, intron 22 of 26)	intron (NM_147151, intron 22 of 26)	-3216	NM_023557	70129	Mm.183126	NM_023557	ENSMUSG00000007034	Slc44a4	2210409B01Rik|NG22	solute carrier family 44, member 4	protein-coding
mm_53543.1	chr6	136827746	136827760	+	1	NA	intron (NM_021714, intron 1 of 11)	CpG	463	NM_021714	60321	Mm.141197	NM_021714	ENSMUSG00000030216	Wbp11	2510026P17Rik|D6Wsu113e|Npwbp|SIPP1	WW domain binding protein 11	protein-coding
mm_44136.1	chr5	150080637	150080645	+	1	NA	intron (NM_001289566, intron 16 of 16)	intron (NM_001289566, intron 16 of 16)	61966	NM_001289566	140498	Mm.444643	NM_080468	ENSMUSG00000053368	Rxfp2	Gpr106|Great|Lgr8	relaxin/insulin-like family peptide receptor 2	protein-coding
mm_37497.1	chr4	123686708	123686729	-	1	NA	Intergenic	CpG	-2358	NM_001199136	11426	Mm.402299	NM_009600	ENSMUSG00000028649	Macf1	ABP620|Acf7|Aclp7|MACF|R74989|mKIAA0465	microtubule-actin crosslinking factor 1	protein-coding
mm_23810.1	chr3	79886113	79886121	+	1	NA	5' UTR (NM_133187, exon 1 of 4)	5' UTR (NM_133187, exon 1 of 4)	187	NM_133187	68659	Mm.427274	NM_133187	ENSMUSG00000027955	Fam198b	1110032E23Rik|2210419I08Rik|AV011458|Ened	family with sequence similarity 198, member B	protein-coding
mm_49824.1	chr6	37706045	37706048	+	1	NA	Intergenic	Intergenic	-164765	NM_001272064	21848	Mm.41063	NM_145076	ENSMUSG00000029833	Trim24	A130082H20Rik|AI447469|D430004I05Rik|TIF1|TIF1-alpha|TIF1alpha|Tif1a	tripartite motif-containing 24	protein-coding
mm_67223.1	chr7	74543275	74543302	-	1	NA	intron (NM_001038643, intron 1 of 10)	intron (NM_001038643, intron 1 of 10)	11492	NM_023908	108116	Mm.425467	NM_023908	ENSMUSG00000025790	Slco3a1	5830414C08Rik|Anr1|MJAM|OATP-D|R75096|Slc21a11	solute carrier organic anion transporter family, member 3a1	protein-coding
mm_34508.1	chr4	148804421	148804439	+	1	NA	promoter-TSS (NM_001159344)	promoter-TSS (NM_001159344)	38	NM_027195	69743	Mm.233879	NM_027195	ENSMUSG00000028977	Casz1	2410019P08Rik|AV096627|BC040081|Cst|D4Ertd432e	castor zinc finger 1	protein-coding
mm_108636.1	chr12	85746553	85746572	+	1	NA	promoter-TSS (NM_145447)	promoter-TSS (NM_145447)	23	NM_145447	217721	Mm.301076	NM_145447	ENSMUSG00000034258	Mfsd7c	CCT|Flvcr2	major facilitator superfamily domain containing 7C	protein-coding
mm_167126.1	chr7	126447639	126447640	-	1	NA	exon (NM_007504, exon 18 of 23)	exon (NM_007504, exon 18 of 23)	15434	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_21459.1	chr2	160872933	160872943	-	1	NA	promoter-TSS (NM_177263)	promoter-TSS (NM_177263)	52	NM_177263	320799	Mm.436734	NM_177263	ENSMUSG00000035877	Zhx3	1810059C13Rik|4932418O04Rik|9530010N21Rik|Tix1|mKIAA0395	zinc fingers and homeoboxes 3	protein-coding
mm_30599.1	chr4	6385019	6385105	+	1	NA	exon (NM_016807, exon 5 of 9)	exon (NM_016807, exon 5 of 9)	19382	NM_001098227	53378	Mm.247473	NM_016807	ENSMUSG00000028249	Sdcbp	MDA-9|Sycl|syntenin-1	syndecan binding protein	protein-coding
mm_160378.1	chr8	41084967	41084967	-	1	NA	intron (NM_001005863, intron 1 of 13)	intron (NM_001005863, intron 1 of 13)	29700	NM_001286413	102103	Mm.149438	NM_001005863	ENSMUSG00000045636	Mtus1	AI481402|ATBP135|Atip1|B430010I23Rik|B430305I03Rik|C85752|Cctsg1-440|MD44|MTSG1|mKIAA1288	mitochondrial tumor suppressor 1	protein-coding
mm_67179.1	chr7	73617662	73617708	-	1	NA	Intergenic	Intergenic	-59290	NR_037569	69170	Mm.34539	NR_037569	ENSMUSG00000101970	1810026B05Rik	-	RIKEN cDNA 1810026B05 gene	ncRNA
mm_20539.1	chr2	131056566	131056576	-	1	NA	intron (NR_136922, intron 4 of 21)	intron (NR_136922, intron 4 of 21)	7243	NR_136922	110751	Mm.108550	NM_033615	ENSMUSG00000027318	Adam33	Adaml	a disintegrin and metallopeptidase domain 33	protein-coding
mm_43243.1	chr5	130079453	130079461	+	1	NA	promoter-TSS (NM_001130476)	promoter-TSS (NM_001130476)	87	NM_001130476	22021	Mm.332720	NM_013837	ENSMUSG00000034118	Tpst1	R75054|Tango13a	protein-tyrosine sulfotransferase 1	protein-coding
mm_28603.1	chr3	94582688	94582708	-	1	NA	promoter-TSS (NM_029721)	promoter-TSS (NM_029721)	18	NM_001082484	76742	Mm.28160	NM_029721	ENSMUSG00000028136	Snx27	5730552M22Rik|ESTM45|ESTM47|R75405	sorting nexin family member 27	protein-coding
mm_66165.1	chr7	31291815	31291817	-	1	NA	promoter-TSS (NM_020563)	promoter-TSS (NM_020563)	0	NM_020563	57426	Mm.6205	NM_020563	ENSMUSG00000062556	Scgb1b2	Abpa2|Abph|Apbh|LGP|Mja1l|Scgb1b1	secretoglobin, family 1B, member 2	protein-coding
mm_131612.1	chr16	19760196	19760227	+	1	NA	promoter-TSS (NM_001159407)	promoter-TSS (NM_001159407)	-23	NM_001159408	108105	Mm.33935	NM_054052	ENSMUSG00000022686	B3gnt5	beta3GnT5	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5	protein-coding
mm_21941.1	chr2	167060448	167060456	-	1	NA	intron (NM_001033196, intron 1 of 13)	intron (NM_001033196, intron 1 of 13)	-2482	NR_138563	68949	Mm.391959	NM_001081005		Zfas1	1500012F01Rik|Zfos1	zinc finger, NFX1-type containing 1, antisense RNA 1	ncRNA
mm_5803.1	chr1	52190930	52190931	-	1	NA	intron (NM_001081081, intron 12 of 17)	intron (NM_001081081, intron 12 of 17)	42302	NM_001081081	14660	Mm.398608	NM_001081081	ENSMUSG00000026103	Gls	6330442B14|AI314027|B230365M23Rik	glutaminase	protein-coding
mm_82752.1	chr9	26829529	26829538	-	1	NA	intron (NM_001113323, intron 10 of 19)	intron (NM_001113323, intron 10 of 19)	-23065	NM_001310768	244757	Mm.293696	NM_153803	ENSMUSG00000036395	Glb1l2	-	galactosidase, beta 1-like 2	protein-coding
mm_79353.1	chr9	53771701	53771782	+	1	NA	5' UTR (NM_028060, exon 1 of 8)	5' UTR (NM_028060, exon 1 of 8)	206	NM_028060	72022	Mm.26159	NM_028060	ENSMUSG00000042195	Slc35f2	1500009K05Rik|AU019213	solute carrier family 35, member F2	protein-coding
mm_166374.1	chr5	128585354	128585355	+	1	NA	non-coding (NR_015517, exon 3 of 6)	non-coding (NR_015517, exon 3 of 6)	15333	NR_015517	319616	Mm.387738	NR_015517	ENSMUSG00000072591	5930412G12Rik	-	RIKEN cDNA 5930412G12 gene	ncRNA
mm_20257.1	chr2	126600570	126600595	-	1	NA	intron (NM_008230, intron 9 of 11)	MIR|SINE|MIR	18096	NM_008230	15186	Mm.18603	NM_008230	ENSMUSG00000027360	Hdc	AW108189|Hdc-a|Hdc-c|Hdc-e|Hdc-s	histidine decarboxylase	protein-coding
mm_429.1	chr1	34473214	34473245	+	1	NA	intron (NM_011206, intron 13 of 14)	intron (NM_011206, intron 13 of 14)	13483	NM_011206	19253	Mm.361	NM_011206	ENSMUSG00000026126	Ptpn18	FLP1|HSCF|PTP-HSCF|PTP-K1|Ptpk1	protein tyrosine phosphatase, non-receptor type 18	protein-coding
mm_42110.1	chr5	110594781	110594815	+	1	NA	intron (NM_198306, intron 4 of 10)	intron (NM_198306, intron 4 of 10)	-8707	NM_001122639	231605	Mm.275748	NM_198306	ENSMUSG00000033316	Galnt9	GalNAc-T9	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 9	protein-coding
mm_74742.1	chr8	18950933	18950965	-	1	NA	promoter-TSS (NM_001286469)	promoter-TSS (NM_001286469)	26	NM_176951	319581	Mm.111354	NM_176951	ENSMUSG00000039814	Xkr5	5430438H03Rik|XRG5	X-linked Kx blood group related 5	protein-coding
mm_54171.1	chr6	23650256	23650271	-	1	NA	promoter-TSS (NM_198251)	promoter-TSS (NM_198251)	42	NM_198251	386611	Mm.436547	NM_198251	ENSMUSG00000051956	Rnf133	Greul2	ring finger protein 133	protein-coding
mm_139558.1	chr17	56877128	56877140	+	1	NA	intron (NM_030141, intron 2 of 13)	BGLII|LTR|ERVK	1501	NM_030141	78625	Mm.160106	NM_030141	ENSMUSG00000024209	1700061G19Rik	1700026H02|AI507598	RIKEN cDNA 1700061G19 gene	protein-coding
mm_85103.1	chr9	94538262	94538307	-	1	NA	promoter-TSS (NM_001033145)	promoter-TSS (NM_001033145)	-203	NM_001033145	68861	Mm.258746	NM_001033145	ENSMUSG00000045414	1190002N15Rik	GoPro49|HASF	RIKEN cDNA 1190002N15 gene	protein-coding
mm_17668.1	chr2	32087421	32087423	-	1	NA	Intergenic	Intergenic	-3717	NM_175511	241303	Mm.250441	NM_175511	ENSMUSG00000050592	Fam78a	A130092J06Rik	family with sequence similarity 78, member A	protein-coding
mm_73019.1	chr8	93969167	93969184	+	1	NA	3' UTR (NM_010308, exon 9 of 9)	3' UTR (NM_010308, exon 9 of 9)	43465	NM_011787	23802	Mm.34641	NM_011787	ENSMUSG00000031751	Amfr	gp78	autocrine motility factor receptor	protein-coding
mm_137338.1	chr17	25133442	25133460	+	1	NA	promoter-TSS (NM_011930)	promoter-TSS (NM_011930)	60	NM_011930	26373	Mm.270587	NM_011930	ENSMUSG00000036636	Clcn7	ClC-7|D17Wsu51e	chloride channel, voltage-sensitive 7	protein-coding
mm_36103.1	chr4	58553748	58553770	-	1	NA	promoter-TSS (NM_010336)	promoter-TSS (NM_010336)	-268	NM_010336	14745	Mm.4772	NM_010336	ENSMUSG00000038668	Lpar1	AI326300|Edg2|Gpcr26|Kdt2|lpA1|vzg-1	lysophosphatidic acid receptor 1	protein-coding
mm_26369.1	chr3	142560573	142560602	+	1	NA	promoter-TSS (NM_001289493)	promoter-TSS (NM_001289493)	91	NM_001289493	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_93367.1	chr10	105195987	105195990	-	1	NA	intron (NM_177368, intron 11 of 11)	BC1_Mm|scRNA|scRNA	378491	NM_177368	278279	Mm.25225	NM_177368	ENSMUSG00000036019	Tmtc2	8430438D04Rik|D330034A10Rik	transmembrane and tetratricopeptide repeat containing 2	protein-coding
mm_27844.1	chr3	79156290	79156300	-	1	NA	Intergenic	Intergenic	-10420	NM_001099624	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_53141.1	chr6	125221890	125221903	+	1	NA	3' UTR (NM_001080557, exon 4 of 4)	3' UTR (NM_001080557, exon 4 of 4)	6315	NM_001080557	22317	Mm.32321	NM_009496	ENSMUSG00000030337	Vamp1	Syb-1|Syb1|VAMP-1|lew	vesicle-associated membrane protein 1	protein-coding
mm_127027.1	chr15	96287538	96287604	+	1	NA	promoter-TSS (NM_175251)	promoter-TSS (NM_175251)	49	NM_175251	77044	Mm.17166	NM_175251	ENSMUSG00000033237	Arid2	1700124K17Rik|4432409D24Rik|zipzap/p200	AT rich interactive domain 2 (ARID, RFX-like)	protein-coding
mm_7488.1	chr1	121327777	121327803	-	1	NA	promoter-TSS (NM_001271531)	promoter-TSS (NM_001271531)	-112	NM_001271531	72999	Mm.27136	NM_133748	ENSMUSG00000003721	Insig2	2900053I11Rik|C730043J18Rik|Insig-2	insulin induced gene 2	protein-coding
mm_100173.1	chr11	116532551	116532561	+	1	NA	promoter-TSS (NM_025367)	promoter-TSS (NM_025367)	112	NM_001172473	20698	Mm.20944	NM_011451	ENSMUSG00000061878	Sphk1	1110006G24Rik|Sk1|Spk1	sphingosine kinase 1	protein-coding
mm_149553.1	chr19	12627658	12627666	+	1	NA	TTS (NM_001167907)	TTS (NM_001167907)	-5646	NM_145935	107146	Mm.39974	NM_145935	ENSMUSG00000063683	Glyat	A330009E03Rik|ACGNAT|AI195249|AI315345|CAT|GAT	glycine-N-acyltransferase	protein-coding
mm_149911.1	chr19	26605107	26605117	+	1	NA	promoter-TSS (NM_011416)	promoter-TSS (NM_011416)	-48	NM_011416	67155	Mm.342988	NM_011416	ENSMUSG00000024921	Smarca2	2610209L14Rik|SNF2alpha|Snf2l2|brahma|brm	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	protein-coding
mm_14457.1	chr2	131189080	131189096	+	1	NA	exon (NM_001111075, exon 3 of 15)	exon (NM_001111075, exon 3 of 15)	2140	NM_001111075	12531	Mm.38444	NM_023117	ENSMUSG00000027330	Cdc25b	AI604853	cell division cycle 25B	protein-coding
mm_91341.1	chr10	26338138	26338159	-	1	NA	intron (NM_001347467, intron 6 of 20)	intron (NM_001347467, intron 6 of 20)	35886	NM_001347467	237339	Mm.338439	NM_172787	ENSMUSG00000039089	L3mbtl3	AI481284|MBT-1	l(3)mbt-like 3 (Drosophila)	protein-coding
mm_68662.1	chr7	118850774	118850784	-	1	NA	intron (NM_001168220, intron 2 of 4)	intron (NM_001168220, intron 2 of 4)	4834	NM_001168220	66356	Mm.482278	NM_023197	ENSMUSG00000030980	Knop1	2310008H09Rik|Tsg118	lysine rich nucleolar protein 1	protein-coding
mm_137054.1	chr17	17928279	17928304	+	1	NA	Intergenic	RMER12|LTR|ERVK	40467	NM_008039	14289	Mm.378918	NM_008039	ENSMUSG00000052270	Fpr2	E330010I07Rik|Fpr-rs2	formyl peptide receptor 2	protein-coding
mm_33480.1	chr4	130818891	130818901	+	1	NA	exon (NM_011520, exon 3 of 5)	exon (NM_011520, exon 3 of 5)	26359	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_1953.1	chr1	86357074	86357113	+	1	NA	promoter-TSS (NR_002851)	promoter-TSS (NR_002851)	-766	NR_002851	80828		NR_002851	ENSMUSG00000064823	Snord82	Rnu82|U82|Z25	small nucleolar RNA, C/D box 82	snoRNA
mm_26561.1	chr3	146500132	146500134	+	1	NA	promoter-TSS (NM_001316756)	promoter-TSS (NM_001316756)	297	NM_010318	14707	Mm.140804	NM_010318	ENSMUSG00000068523	Gng5	G(y)5	guanine nucleotide binding protein (G protein), gamma 5	protein-coding
mm_119425.1	chr14	45358762	45358765	+	1	NA	intron (NM_019637, intron 3 of 10)	intron (NM_019637, intron 3 of 10)	7577	NM_019637	56291	Mm.202561	NM_019637	ENSMUSG00000053205	Styx	0610039A20Rik|hStyxb	serine/threonine/tyrosine interaction protein	protein-coding
mm_73548.1	chr8	108937078	108937081	+	1	NA	TTS (NR_037295)	TTS (NR_037295)	219	NR_037295	100526511		NR_037295	ENSMUSG00000093241	Mir3108	mir-3108|mmu-mir-3108	microRNA 3108	ncRNA
mm_111678.1	chr12	103355968	103356017	-	1	NA	promoter-TSS (NM_023049)	promoter-TSS (NM_023049)	9	NM_023049	65256	Mm.27159	NM_023049	ENSMUSG00000021200	Asb2	1110008E15Rik	ankyrin repeat and SOCS box-containing 2	protein-coding
mm_50164.1	chr6	41553538	41553559	+	1	NA	Intergenic	L3b|LINE|CR1	31772	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_74363.1	chr8	128359325	128359344	+	1	NA	promoter-TSS (NR_035436)	promoter-TSS (NR_035436)	93	NR_035436	100316680		NR_035436	ENSMUSG00000084523	Mir1903	Mirn1903|mmu-mir-1903	microRNA 1903	ncRNA
mm_98161.1	chr11	87699896	87699914	+	1	NA	non-coding (NR_045139, exon 1 of 2)	non-coding (NR_045139, exon 1 of 2)	381	NR_045139	68690	Mm.342009	NR_045139		1110028F11Rik	-	RIKEN cDNA 1110028F11 gene	ncRNA
mm_90907.1	chr10	11281192	11281248	-	1	NA	promoter-TSS (NM_027968)	promoter-TSS (NM_027968)	-110	NM_027968	71865	Mm.276229	NM_027968	ENSMUSG00000047648	Fbxo30	1700026A16Rik|MUSA1	F-box protein 30	protein-coding
mm_106890.1	chr12	8012236	8012244	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	34563	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_91242.1	chr10	22306532	22306540	-	1	NA	promoter-TSS (NR_015465)	promoter-TSS (NR_015465)	-184	NR_015465	606736	Mm.387042	NR_015465	ENSMUSG00000097352	C920009B18Rik	-	RIKEN cDNA C920009B18 gene	ncRNA
mm_116154.1	chr13	30235191	30235204	-	1	NA	intron (NM_153546, intron 9 of 12)	intron (NM_153546, intron 9 of 12)	98707	NM_153546	218121	Mm.89682	NM_153546	ENSMUSG00000038732	Mboat1	9130215M02Rik|BC023845|LPEAT1|Moact1|Oact1	membrane bound O-acyltransferase domain containing 1	protein-coding
mm_14702.1	chr2	142576898	142576912	+	1	NA	Intergenic	Intergenic	324559	NM_001081133	16558	Mm.251934	NM_001081133	ENSMUSG00000038844	Kif16b	8430434E15Rik|AA623607|AI789011|C80253|C80902|mKIAA1590	kinesin family member 16B	protein-coding
mm_131275.1	chr16	11021644	11021682	+	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	12765	NR_040518	100043147	Mm.489001	NR_040518	ENSMUSG00000097056	Gm4262	-	predicted gene 4262	ncRNA
mm_14164.1	chr2	126607729	126607739	+	1	NA	intron (NM_008230, intron 2 of 11)	intron (NM_008230, intron 2 of 11)	10944	NM_008230	15186	Mm.18603	NM_008230	ENSMUSG00000027360	Hdc	AW108189|Hdc-a|Hdc-c|Hdc-e|Hdc-s	histidine decarboxylase	protein-coding
mm_159589.1	chr4	123294740	123294740	+	1	NA	exon (NM_130881, exon 8 of 15)	exon (NM_130881, exon 8 of 15)	11455	NM_148917	230721	Mm.277091	NM_130881	ENSMUSG00000011257	Pabpc4	-	poly(A) binding protein, cytoplasmic 4	protein-coding
mm_12335.1	chr2	69669899	69669913	+	1	NA	promoter-TSS (NM_001081087)	promoter-TSS (NM_001081087)	-214	NM_001081087	228003	Mm.178784	NM_001081087	ENSMUSG00000075307	Klhl41	Gm112|Kbtbd10|SARCOSIN	kelch-like 41	protein-coding
mm_12284.1	chr2	69008535	69008547	+	1	NA	intron (NM_172856, intron 4 of 9)	intron (NM_172856, intron 4 of 9)	-127259	NM_181547	329416	Mm.90047	NM_181547	ENSMUSG00000034738	Nostrin	Daip2|mDaIP2	nitric oxide synthase trafficker	protein-coding
mm_106470.1	chr11	120098674	120098702	-	1	NA	promoter-TSS (NM_183137)	promoter-TSS (NM_183137)	43	NM_183137	78777	Mm.23672	NM_183137	ENSMUSG00000025377	Tepsin	2410002I01Rik|Enthd2	TEPSIN, adaptor related protein complex 4 accessory protein	protein-coding
mm_8697.1	chr1	157412577	157412621	-	1	NA	promoter-TSS (NM_177644)	promoter-TSS (NM_177644)	-4	NM_177644	226525	Mm.235028	NM_177644	ENSMUSG00000070565	Rasal2	6530401P13|A330066M24Rik	RAS protein activator like 2	protein-coding
mm_109344.1	chr12	109600820	109600824	+	1	NA	Intergenic	Intergenic	-3123	NR_028261	75745	Mm.293263	NR_028261		Rian	5530401N18Rik|C130089L09Rik|Meg8	RNA imprinted and accumulated in nucleus	ncRNA
mm_52742.1	chr6	120465873	120465882	+	1	NA	intron (NM_008359, intron 1 of 12)	(CA)n|Simple_repeat|Simple_repeat	2680	NM_008359	16172	Mm.4481	NM_008359	ENSMUSG00000002897	Il17ra	AW538159|Cdw217|Il17r|VDw217	interleukin 17 receptor A	protein-coding
mm_25679.1	chr3	122082622	122082627	+	1	NA	intron (NM_007378, intron 7 of 49)	intron (NM_007378, intron 7 of 49)	38164	NM_007378	11304	Mm.3918	NM_007378	ENSMUSG00000028125	Abca4	AW050280|Abc10|Abcr|D430003I15Rik|RmP	ATP-binding cassette, sub-family A (ABC1), member 4	protein-coding
mm_13020.1	chr2	91028193	91028200	+	1	NA	Intergenic	RLTR48A|LTR|ERV1	-7431	NM_009023	19400	Mm.1272	NM_009023	ENSMUSG00000002104	Rapsn	43kDa|Nraps|Raps|rapsyn	receptor-associated protein of the synapse	protein-coding
mm_23554.1	chr3	62159232	62159242	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-179540	NM_001081295	622434	Mm.153974	NM_001081295	ENSMUSG00000036885	Arhgef26	4631416L12Rik|8430436L14Rik|AI303572|AW491953|SGEF	Rho guanine nucleotide exchange factor (GEF) 26	protein-coding
mm_54039.1	chr6	12786655	12786666	-	1	NA	Intergenic	Intergenic	-37407	NM_001164805	330267	Mm.11989	NM_001164805	ENSMUSG00000032625	Thsd7a	Gm837	thrombospondin, type I, domain containing 7A	protein-coding
mm_99270.1	chr11	101253574	101253594	+	1	NA	promoter-TSS (NM_026776)	promoter-TSS (NM_026776)	-123	NM_001284412	28084	Mm.301020	NM_026776	ENSMUSG00000078656	Vps25	1110020N13Rik|AW107467|D11Wsu68e	vacuolar protein sorting 25	protein-coding
mm_92637.1	chr10	80336362	80336372	-	1	NA	TTS (NM_139292)	TTS (NM_139292)	6222	NM_139292	70335	Mm.28147	NM_139292	ENSMUSG00000035504	Reep6	0610011M24Rik|Dp1l1	receptor accessory protein 6	protein-coding
mm_65143.1	chr7	19578029	19578043	-	1	NA	intron (NM_022409, intron 2 of 2)	intron (NM_022409, intron 2 of 2)	749	NM_022409	63872	Mm.23310	NM_022409	ENSMUSG00000011267	Zfp296	2210018A16Rik|Znf296	zinc finger protein 296	protein-coding
mm_105320.1	chr11	102888057	102888071	-	1	NA	3' UTR (NM_010277, exon 9 of 9)	3' UTR (NM_010277, exon 9 of 9)	2895	NM_025766	66784	Mm.483216	NM_025766	ENSMUSG00000075510	Fam187a	4933439F11Rik	family with sequence similarity 187, member A	protein-coding
mm_145356.1	chr18	56676282	56676286	+	1	NA	Intergenic	Intergenic	-31529	NM_010721	16906	Mm.4105	NM_010721	ENSMUSG00000024590	Lmnb1	-	lamin B1	protein-coding
mm_163820.1	chr14	19416717	19416738	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	185860	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_3851.1	chr1	160881545	160881561	+	1	NA	Intergenic	RMER17C|LTR|ERVK	-24858	NM_001024952	381305	Mm.329667	NM_001024952	ENSMUSG00000040423	Rc3h1	5730557L09Rik|Gm551|N28103|mKIAA2025	RING CCCH (C3H) domains 1	protein-coding
mm_144285.1	chr18	11947252	11947280	+	1	NA	Intergenic	Intergenic	-106828	NR_035447	100316686		NR_035447	ENSMUSG00000084565	Mir1901	Mirn1901|mmu-mir-1901	microRNA 1901	ncRNA
mm_73335.1	chr8	105304128	105304144	+	1	NA	intron (NM_148952, intron 7 of 9)	intron (NM_148952, intron 7 of 9)	-1465	NM_172760	234683	Mm.237966	NM_172760	ENSMUSG00000014791	Elmo3	9930107J06|BC058752|CED-12|Ced12	engulfment and cell motility 3	protein-coding
mm_96956.1	chr11	70615863	70615876	+	1	NA	promoter-TSS (NM_001145537)	promoter-TSS (NM_001145537)	-25	NM_001145537	668433	Mm.425687	NM_001145537	ENSMUSG00000087279	4930544D05Rik	-	RIKEN cDNA 4930544D05 gene	protein-coding
mm_22923.1	chr3	31098272	31098288	+	1	NA	exon (NM_001039090, exon 2 of 7)	exon (NM_001039090, exon 2 of 7)	3222	NM_001039090	20482	Mm.15406	NM_011386	ENSMUSG00000027660	Skil	Skir|SnoN|sno	SKI-like	protein-coding
mm_151284.1	chr19	55284247	55284261	+	1	NA	intron (NM_027976, intron 11 of 21)	intron (NM_027976, intron 11 of 21)	30885	NM_027976	433256	Mm.292056	NM_027976	ENSMUSG00000024981	Acsl5	1700030F05Rik|ACS2|ACS5|Facl5	acyl-CoA synthetase long-chain family member 5	protein-coding
mm_124727.1	chr15	6580346	6580354	+	1	NA	exon (NM_001278269, exon 1 of 17)	exon (NM_001278269, exon 1 of 17)	503	NM_011815	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_52156.1	chr6	98018488	98018500	+	1	NA	3' UTR (NM_001178049, exon 10 of 10)	3' UTR (NM_001178049, exon 10 of 10)	26711	NM_008601	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_65577.1	chr7	27196101	27196132	-	1	NA	promoter-TSS (NM_001046637)	promoter-TSS (NM_001046637)	155	NM_015782	53607	Mm.386890	NM_015782	ENSMUSG00000061479	Snrpa	C430021M15Rik|Rnu1a-1|Rnu1a1|U1-A|U1A	small nuclear ribonucleoprotein polypeptide A	protein-coding
mm_114213.1	chr13	56166524	56166526	+	1	NA	Intergenic	MT2C_Mm|LTR|ERVL	12360	NM_145976	212937	Mm.116697	NM_145976	ENSMUSG00000049625	Tifab	-	TRAF-interacting protein with forkhead-associated domain, family member B	protein-coding
mm_85301.1	chr9	100506845	100506856	-	1	NA	promoter-TSS (NM_001324530)	promoter-TSS (NM_001324530)	6	NM_001324530	17973	Mm.181485	NM_010878	ENSMUSG00000032475	Nck1	6330586M15Rik|D230010O13Rik|Nck|Nck-1	non-catalytic region of tyrosine kinase adaptor protein 1	protein-coding
mm_79633.1	chr9	59540926	59540955	+	1	NA	intron (NM_010421, intron 1 of 13)	ID_B1|SINE|B4	1400	NM_010421	15211	Mm.2284	NM_010421	ENSMUSG00000025232	Hexa	Hex-1	hexosaminidase A	protein-coding
mm_38813.1	chr4	148444745	148444783	-	1	NA	promoter-TSS (NM_027873)	promoter-TSS (NM_027873)	-13	NM_027873	71707	Mm.292503	NM_027873	ENSMUSG00000047719	Ubiad1	1200002M06Rik|AI426463|AW320947|Tere1	UbiA prenyltransferase domain containing 1	protein-coding
mm_160896.1	chr11	73234292	73234292	+	1	NA	5' UTR (NM_001001445, exon 1 of 16)	5' UTR (NM_001001445, exon 1 of 16)	143	NM_001001445	193034	Mm.447485	NM_001001445	ENSMUSG00000005952	Trpv1	OTRPC1|TRPV1alpha|TRPV1beta|VR-1|Vr1	transient receptor potential cation channel, subfamily V, member 1	protein-coding
mm_158789.1	chrX	167209160	167209164	-	1	NA	promoter-TSS (NM_021278)	promoter-TSS (NM_021278)	56	NM_021278	19241	Mm.142729	NM_021278	ENSMUSG00000049775	Tmsb4x	Ptmb4|Tb4	thymosin, beta 4, X chromosome	protein-coding
mm_68106.1	chr7	102018223	102018239	-	1	NA	promoter-TSS (NM_010531)	promoter-TSS (NM_010531)	-76	NM_010531	16068	Mm.422756	NM_010531	ENSMUSG00000070427	Il18bp	IL-18BP|Igifbp|MC54L	interleukin 18 binding protein	protein-coding
mm_66989.1	chr7	64052586	64052606	-	1	NA	Intergenic	MLT1H2|LTR|ERVL-MaLR	-101239	NM_001039104	17364	Mm.38875	NM_018752	ENSMUSG00000030523	Trpm1	4732499L03Rik|AI606771|Ltrpc1|Mlsn1	transient receptor potential cation channel, subfamily M, member 1	protein-coding
mm_88370.1	chr10	75993799	75993817	+	1	NA	intron (NM_198635, intron 8 of 13)	intron (NM_198635, intron 8 of 13)	-15118	NR_105836	102466646		NR_105836	ENSMUSG00000098817	Mir6409	Gm27787|mmu-mir-6409	microRNA 6409	ncRNA
mm_152315.1	chr19	9905862	9905876	-	1	NA	Intergenic	B1_Mus1|SINE|Alu	-6336	NM_016692	16319	Mm.29755	NM_016692	ENSMUSG00000024660	Incenp	2700067E22Rik|AU019509|C130081E20|C77457	inner centromere protein	protein-coding
mm_127625.1	chr15	102462299	102462311	+	1	NA	3' UTR (NM_025385, exon 5 of 5)	3' UTR (NM_025385, exon 5 of 5)	3135	NM_025385	66151	Mm.393955	NM_025385	ENSMUSG00000023048	Prr13	1110020C13Rik|2010324E22Rik	proline rich 13	protein-coding
mm_67153.1	chr7	73537688	73537766	-	1	NA	intron (NM_001081345, intron 2 of 38)	intron (NM_001081345, intron 2 of 38)	4019	NM_001081345	244059	Mm.34539	NM_001081345	ENSMUSG00000078671	Chd2	2810013C04Rik|2810040A01Rik|5630401D06Rik|AI851092|BC029703|CHD-2	chromodomain helicase DNA binding protein 2	protein-coding
mm_20513.1	chr2	130642771	130642811	-	1	NA	promoter-TSS (NM_001291028)	promoter-TSS (NM_001291028)	53	NM_197945	241638	Mm.440130	NM_197945	ENSMUSG00000037703	Lzts3	Prosapip1	leucine zipper, putative tumor suppressor family member 3	protein-coding
mm_35210.1	chr4	19611042	19611059	-	1	NA	non-coding (NR_074090, exon 25 of 25)	non-coding (NR_074090, exon 25 of 25)	35984	NM_025476	66302	Mm.440686	NM_025476	ENSMUSG00000028229	Rmdn1	Fam82b|RMD-1	regulator of microtubule dynamics 1	protein-coding
mm_111846.1	chr12	107938774	107938784	-	1	NA	intron (NM_001286343, intron 1 of 1)	intron (NM_001286343, intron 1 of 1)	64635	NM_001079883	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_147493.1	chr18	47368881	47368896	-	1	NA	promoter-TSS (NM_018744)	promoter-TSS (NM_018744)	-18	NM_001311097	20358	Mm.40909	NM_018744	ENSMUSG00000019647	Sema6a	A730020P05Rik|AI851735|Sema6A-1|Semaq|VIa	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A	protein-coding
mm_68853.1	chr7	126369462	126369472	-	1	NA	TTS (NM_023712)	TTS (NM_023712)	101	NM_010689	16797	Mm.10280	NM_010689	ENSMUSG00000030742	Lat	p36-38|pp36	linker for activation of T cells	protein-coding
mm_99228.1	chr11	101055496	101055533	+	1	NA	exon (NM_001243049, exon 20 of 21)	exon (NM_001243049, exon 20 of 21)	-14580	NM_013792	27419	Mm.95452	NM_013792	ENSMUSG00000001751	Naglu	-	alpha-N-acetylglucosaminidase (Sanfilippo disease IIIB)	protein-coding
mm_49227.1	chr6	15799474	15799490	+	1	NA	intron (NM_175088, intron 4 of 4)	intron (NM_175088, intron 4 of 4)	78821	NM_175088	16543	Mm.1314	NM_175088	ENSMUSG00000041390	Mdfic	Kdt1|Mdfid	MyoD family inhibitor domain containing	protein-coding
mm_83786.1	chr9	52168676	52168680	-	1	NA	promoter-TSS (NM_001162921)	promoter-TSS (NM_001162921)	-567	NM_001162921	244871	Mm.295686	NM_001162921	ENSMUSG00000035164	Zc3h12c	A230108E06|C230027N18Rik|mKIAA1726	zinc finger CCCH type containing 12C	protein-coding
mm_125896.1	chr15	75905466	75905474	+	1	NA	intron (NM_029663, intron 2 of 9)	intron (NM_029663, intron 2 of 9)	3874	NM_001285433	66656	Mm.258927	NM_023240	ENSMUSG00000055762	Eef1d	EF-1-delta	eukaryotic translation elongation factor 1 delta (guanine nucleotide exchange protein)	protein-coding
mm_100276.1	chr11	117782282	117782337	+	1	NA	promoter-TSS (NM_181856)	promoter-TSS (NM_181856)	12	NM_001195089	217356	Mm.116675	NM_181856	ENSMUSG00000050106	Tmc8	EVIN2|Ever2|mFLJ00400	transmembrane channel-like gene family 8	protein-coding
mm_5577.1	chr1	39551911	39551919	-	1	NA	3' UTR (NM_001033135, exon 7 of 7)	3' UTR (NM_001033135, exon 7 of 7)	-3075	NR_028555	100217461		NR_028555	ENSMUSG00000077704	Snord89	MBII-289	small nucleolar RNA, C/D box 89	snoRNA
mm_171787.1	chr5	113661741	113661742	-	1	NA	Intergenic	PB1D7|SINE|Alu	-11351	NM_008153	14747	Mm.5196	NM_008153	ENSMUSG00000042190	Cmklr1	ChemR23|DEZ|Gpcr27|mcmklr1	chemokine-like receptor 1	protein-coding
mm_52885.1	chr6	122521833	122521847	+	1	NA	intron (NM_001347434, intron 5 of 8)	intron (NM_001347434, intron 5 of 8)	8164	NM_015776	50530	Mm.41931	NM_015776	ENSMUSG00000030116	Mfap5	MAGP-2|MFAP-5	microfibrillar associated protein 5	protein-coding
mm_110466.1	chr12	51829282	51829357	-	1	NA	5' UTR (NM_144788, exon 1 of 43)	5' UTR (NM_144788, exon 1 of 43)	217	NM_144788	207304	Mm.249391	NM_144788	ENSMUSG00000035247	Hectd1	A630086P08Rik|AI844876|b2b327Clo|opm	HECT domain containing 1	protein-coding
mm_126148.1	chr15	78349301	78349311	+	1	NA	TTS (NR_106138)	TTS (NR_106138)	707	NR_106138	102466845		NR_106138	ENSMUSG00000099059	Mir7676-2	Gm27790|mmu-mir-7676-2	microRNA 7676-2	ncRNA
mm_38774.1	chr4	148002064	148002075	-	1	NA	TTS (NM_008725)	TTS (NM_008725)	1347	NM_008725	230899	Mm.482123	NM_008725	ENSMUSG00000041616	Nppa	ANP|Anf|Pnd	natriuretic peptide type A	protein-coding
mm_73696.1	chr8	111643426	111643450	+	1	NA	promoter-TSS (NM_011742)	promoter-TSS (NM_011742)	-5	NM_001037665	22640	Mm.4184	NM_011742	ENSMUSG00000055835	Zfp1	Fnp-1|Zfp-1|mkr-1	zinc finger protein 1	protein-coding
mm_78351.1	chr9	25481552	25481562	+	1	NA	promoter-TSS (NM_026189)	promoter-TSS (NM_026189)	-40	NM_026189	67484	Mm.112977	NM_026189	ENSMUSG00000036611	Eepd1	2310005P05Rik|AI481005	endonuclease/exonuclease/phosphatase family domain containing 1	protein-coding
mm_8366.1	chr1	150502688	150502714	-	1	NA	Intergenic	Intergenic	-36536	NM_001110146	96875	Mm.174256	NM_021400	ENSMUSG00000006014	Prg4	CACP|DOL54|JCAP|MSF|SZP|lubricin	proteoglycan 4 (megakaryocyte stimulating factor, articular superficial zone protein)	protein-coding
mm_34325.1	chr4	141873210	141873237	+	1	NA	intron (NM_025994, intron 1 of 3)	intron (NM_025994, intron 1 of 3)	1697	NM_025994	27984	Mm.395598	NM_025994	ENSMUSG00000040659	Efhd2	2600015J22Rik|AA408606|D4Wsu27e	EF hand domain containing 2	protein-coding
mm_116586.1	chr13	47106223	47106233	-	1	NA	promoter-TSS (NM_025900)	promoter-TSS (NM_025900)	-7	NM_025900	110052	Mm.131150	NM_025900	ENSMUSG00000021377	Dek	1810019E15Rik|D13H6S231E	DEK oncogene (DNA binding)	protein-coding
mm_145762.1	chr18	64908671	64908683	+	1	NA	intron (NM_001114386, intron 1 of 30)	MLT1D|LTR|ERVL-MaLR	20921	NM_001114386	83814	Mm.98668	NM_031881	ENSMUSG00000024589	Nedd4l	1300012C07Rik|Nedd4-2|Nedd4b	neural precursor cell expressed, developmentally down-regulated gene 4-like	protein-coding
mm_65424.1	chr7	25297583	25297633	-	1	NA	intron (NM_008776, intron 1 of 5)	CpG-12842	347	NM_008776	18476	Mm.597	NM_008776	ENSMUSG00000005447	Pafah1b3	Pafahg|mus[g]	platelet-activating factor acetylhydrolase, isoform 1b, subunit 3	protein-coding
mm_35370.1	chr4	32950814	32950866	-	1	NA	promoter-TSS (NM_001012451)	promoter-TSS (NM_001012451)	-14	NM_001012451	140577	Mm.214766	NM_080471	ENSMUSG00000040183	Ankrd6	-	ankyrin repeat domain 6	protein-coding
mm_66557.1	chr7	45238727	45238756	-	1	NA	promoter-TSS (NM_007645)	promoter-TSS (NM_007645)	98	NM_007645	12493	Mm.3689	NM_007645	ENSMUSG00000030798	Cd37	Tspan26	CD37 antigen	protein-coding
mm_126.1	chr1	9848376	9848398	+	1	NA	intron (NM_001037759, intron 1 of 16)	CpG	106	NM_001037759	170755	Mm.336410	NM_133220	ENSMUSG00000025915	Sgk3	2510015P22Rik|A330005P07Rik|Cisk|fy|fz	serum/glucocorticoid regulated kinase 3	protein-coding
mm_129848.1	chr15	83166870	83166883	-	1	NA	intron (NM_029787, intron 1 of 8)	intron (NM_029787, intron 1 of 8)	5332	NM_029787	109754	Mm.22560	NM_029787	ENSMUSG00000018042	Cyb5r3	0610016L08Rik|2500002N19Rik|C85115|Dia-1|Dia1|WU:AL591952.1-001|WU:AL591952.1-002|WU:AL591952.1-003|WU:Cyb5r3	cytochrome b5 reductase 3	protein-coding
mm_103570.1	chr11	77893844	77893854	-	1	NA	promoter-TSS (NM_008952)	promoter-TSS (NM_008952)	23	NM_008952	19193	Mm.8543	NM_008952	ENSMUSG00000017453	Pipox	LPIPOX|Pso	pipecolic acid oxidase	protein-coding
mm_51113.1	chr6	67609712	67609717	+	1	NA	Intergenic	Intergenic	-44015	NR_003100	75070	Mm.463364	NR_003100		4930515G16Rik	-	myc induced nuclear antigen pseudogene	pseudo
mm_67601.1	chr7	83735504	83735517	-	1	NA	promoter-TSS (NM_010551)	promoter-TSS (NM_010551)	-20	NM_010551	16170	Mm.10137	NM_010551	ENSMUSG00000001741	Il16	mKIAA4048	interleukin 16	protein-coding
mm_67284.1	chr7	78627458	78627461	-	1	NA	intron (NR_015542, intron 8 of 10)	B4|SINE|B4	-49621	NM_182809	18213	Mm.33496	NM_008746	ENSMUSG00000059146	Ntrk3	AW125844|Ntrk3_tv3|TrkC	neurotrophic tyrosine kinase, receptor, type 3	protein-coding
mm_20644.1	chr2	132029789	132029804	-	1	NA	5' UTR (NM_175445, exon 1 of 11)	5' UTR (NM_175445, exon 1 of 11)	192	NM_175445	215653	Mm.204737	NM_175445	ENSMUSG00000027339	Rassf2	3830431H01Rik|9030412M04Rik|AI852669|AW495050	Ras association (RalGDS/AF-6) domain family member 2	protein-coding
mm_28833.1	chr3	96557640	96557699	-	1	NA	promoter-TSS (NM_023719)	promoter-TSS (NM_023719)	-288	NM_001009935	56338	Mm.410189	NM_023719	ENSMUSG00000038393	Txnip	1200008J08Rik|AA682105|Hyplip1|THIF|Tbp-2|VDUP1	thioredoxin interacting protein	protein-coding
mm_23602.1	chr3	65109472	65109486	+	1	NA	5' UTR (NM_010597, exon 1 of 14)	5' UTR (NM_010597, exon 1 of 14)	111	NM_010597	16497	Mm.316402	NM_010597	ENSMUSG00000027827	Kcnab1	Akr8a8|Kvbeta1.1|mKv(beta)1	potassium voltage-gated channel, shaker-related subfamily, beta member 1	protein-coding
mm_70557.1	chr8	13068692	13068697	+	1	NA	intron (NM_025834, intron 6 of 7)	B1_Mus1|SINE|Alu	7786	NM_025834	66901	Mm.441140	NM_025834	ENSMUSG00000031445	Proz	1300015B06Rik	protein Z, vitamin K-dependent plasma glycoprotein	protein-coding
mm_17022.1	chr2	19048354	19048381	-	1	NA	Intergenic	Intergenic	50048	NR_024323	74629	Mm.117687	NR_024323	ENSMUSG00000026736	4930426L09Rik	-	RIKEN cDNA 4930426L09 gene	ncRNA
mm_128158.1	chr15	32767455	32767481	-	1	NA	Intergenic	Intergenic	-153255	NM_008304	15529	Mm.234266	NM_008304	ENSMUSG00000022261	Sdc2	4833414L08Rik|AA960457|Hspg1|Synd2|syndecan-2	syndecan 2	protein-coding
mm_147049.1	chr18	34931932	34931985	-	1	NA	promoter-TSS (NM_144866)	promoter-TSS (NM_144866)	45	NM_144866	225363	Mm.329353	NM_144866	ENSMUSG00000024360	Etf1	AI463371|D6Ertd109e|ERF|ERF1|SUP45L1|TB3-1	eukaryotic translation termination factor 1	protein-coding
mm_4514.1	chr1	174330519	174330521	+	1	NA	promoter-TSS (NM_025470)	promoter-TSS (NM_025470)	2	NM_025470	66289	Mm.7150	NM_025470	ENSMUSG00000026531	Mptx1	1810030J14Rik|AV054416|Mptx	mucosal pentraxin 1	protein-coding
mm_173289.1	chrY	2073308	2073308	-	1	NA	Intergenic	RLTR10C|LTR|ERVK	97101	NM_009571	22768	Mm.411381	NM_009571	ENSMUSG00000000103	Zfy2	Zfy-2	zinc finger protein 2, Y-linked	protein-coding
mm_65543.1	chr7	27121924	27121952	-	1	NA	exon (NM_007817, exon 3 of 10)	exon (NM_007817, exon 3 of 10)	1983	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_157706.1	chrX	64152102	64152111	-	1	NA	promoter-TSS (NM_001177377)	promoter-TSS (NM_001177377)	92	NM_001177377	627470	Mm.233605	NM_001177377	ENSMUSG00000079579	Gm6760	EG627470	predicted gene 6760	protein-coding
mm_48994.1	chr6	4756527	4756550	+	1	NA	exon (NM_130877, exon 2 of 2)	exon (NM_130877, exon 2 of 2)	9232	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_162393.1	chr1	79335030	79335034	+	1	NA	Intergenic	Intergenic	105058	NM_009129	20254	Mm.5038	NM_009129	ENSMUSG00000050711	Scg2	Chgc|SgII	secretogranin II	protein-coding
mm_138350.1	chr17	34956433	34956436	+	1	NA	TTS (NM_010478)	TTS (NM_010478)	2804	NM_010478	15511	Mm.372314	NM_010478	ENSMUSG00000090877	Hspa1b	Hsp70|Hsp70-1|Hsp70.1|hsp68	heat shock protein 1B	protein-coding
mm_55379.1	chr6	58907026	58907042	-	1	NA	promoter-TSS (NM_021432)	promoter-TSS (NM_021432)	92	NM_021432	58243	Mm.389747	NM_021432	ENSMUSG00000055430	Nap1l5	1110020M21Rik	nucleosome assembly protein 1-like 5	protein-coding
mm_151640.1	chr19	4036713	4036740	-	1	NA	exon (NM_013541, exon 5 of 7)	exon (NM_013541, exon 5 of 7)	1186	NM_013541	14870	Mm.299292	NM_013541	ENSMUSG00000060803	Gstp1	GstpiB	glutathione S-transferase, pi 1	protein-coding
mm_123203.1	chr14	59324152	59324172	-	1	NA	intron (NM_001164327, intron 6 of 8)	B3A|SINE|B2	17168	NM_001164327	236451	Mm.247736	NM_001164327	ENSMUSG00000091649	Phf11b	EG236451|Gm4902	PHD finger protein 11B	protein-coding
mm_109726.1	chr12	116281292	116281294	+	1	NA	promoter-TSS (NM_028731)	promoter-TSS (NM_028731)	71	NM_028731	52635	Mm.273755	NM_028731	ENSMUSG00000021171	Esyt2	2410017M09Rik|4921504I16Rik|CHR2SYT|D12Ertd551e|Fam62b	extended synaptotagmin-like protein 2	protein-coding
mm_82165.1	chr9	123806469	123806485	+	1	NA	promoter-TSS (NM_030712)	promoter-TSS (NM_030712)	0	NM_030712	80901	Mm.124289	NM_030712	ENSMUSG00000048521	Cxcr6	BB217514|BONZO|STRL33	chemokine (C-X-C motif) receptor 6	protein-coding
mm_122556.1	chr14	49066369	49066420	-	1	NA	promoter-TSS (NM_144535)	promoter-TSS (NM_144535)	-101	NM_144535	74385	Mm.379235	NM_144535	ENSMUSG00000036291	Ap5m1	4932432K03Rik|Mu5|Mudeng	adaptor-related protein complex 5, mu 1 subunit	protein-coding
mm_160080.1	chr7	13054625	13054625	-	1	NA	5' UTR (NM_145819, exon 1 of 6)	5' UTR (NM_145819, exon 1 of 6)	139	NM_001290452	109889	Mm.10103	NM_145819	ENSMUSG00000030380	Mzf1	Mzf-2|Mzf2|Zfp121|Zfp98|Znf42	myeloid zinc finger 1	protein-coding
mm_9002.1	chr1	165790064	165790081	-	1	NA	intron (NM_001113391, intron 1 of 7)	intron (NM_001113391, intron 1 of 7)	1391	NM_001113392	12503	Mm.217308	NM_031162	ENSMUSG00000005763	Cd247	4930549J05Rik|A430104F18Rik|AW552088|Cd3|Cd3-eta|Cd3-zeta|Cd3h|Cd3z|Cd3zeta|T3z|Tcrk|Tcrz	CD247 antigen	protein-coding
mm_105154.1	chr11	101466137	101466150	-	1	NA	promoter-TSS (NM_012037)	promoter-TSS (NM_012037)	56	NM_012037	26949	Mm.29210	NM_012037	ENSMUSG00000034993	Vat1	VAT-1	vesicle amine transport 1	protein-coding
mm_150464.1	chr19	38395768	38395796	+	1	NA	promoter-TSS (NM_175507)	promoter-TSS (NM_175507)	-198	NM_175507	240660	Mm.262085	NM_175507	ENSMUSG00000044026	Slc35g1	AA590464|D330039I19Rik|Tmem20	solute carrier family 35, member G1	protein-coding
mm_112810.1	chr13	20794213	20794223	+	1	NA	5' UTR (NM_001281854, exon 1 of 5)	5' UTR (NM_001281854, exon 1 of 5)	105	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_150450.1	chr19	38116751	38116762	+	1	NA	3' UTR (NM_011255, exon 6 of 6)	3' UTR (NM_011255, exon 6 of 6)	8055	NM_011255	19662	Mm.2605	NM_011255	ENSMUSG00000024990	Rbp4	Rbp-4	retinol binding protein 4, plasma	protein-coding
mm_47349.1	chr5	122560836	122560846	-	1	NA	intron (NM_009879, intron 14 of 18)	intron (NM_009879, intron 14 of 18)	53677	NM_009879	12589	Mm.10125	NM_009879	ENSMUSG00000029469	Ift81	AW060663|Cdv-1|Cdv-1r|Cdv1	intraflagellar transport 81	protein-coding
mm_90936.1	chr10	12915479	12915493	-	1	NA	Intergenic	Intergenic	7641	NR_038027	320273	Mm.417706	NR_038027	ENSMUSG00000097378	B230208H11Rik	-	RIKEN cDNA B230208H11 gene	ncRNA
mm_48039.1	chr5	136318428	136318432	-	1	NA	intron (NM_001291239, intron 12 of 22)	intron (NM_001291239, intron 12 of 22)	57373	NR_030500	723975		NR_030500	ENSMUSG00000106479	Mir721	Mirn721|miRY|mir-721|mmu-mir-721	microRNA 721	ncRNA
mm_36927.1	chr4	108296556	108296559	-	1	NA	intron (NM_001033634, intron 1 of 13)	B1_Mm|SINE|Alu	4533	NM_001033634	414872	Mm.426241	NM_001033634	ENSMUSG00000034636	Zyg11b	1110046I03Rik|2810482G21Rik|D4Mgi23|Gm431|mKIAA1730	zyg-ll family member B, cell cycle regulator	protein-coding
mm_139264.1	chr17	47768936	47768986	+	1	NA	intron (NM_001161723, intron 1 of 8)	intron (NM_001161723, intron 1 of 8)	-16783	NM_011549	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_36990.1	chr4	109977852	109977899	-	1	NA	promoter-TSS (NM_172296)	promoter-TSS (NM_172296)	-150	NM_172296	242620	Mm.32825	NM_172296	ENSMUSG00000047143	Dmrta2	Dmrt5	doublesex and mab-3 related transcription factor like family A2	protein-coding
mm_70133.1	chr7	143242453	143242474	-	1	NA	non-coding (NR_001461, exon 1 of 1)	non-coding (NR_001461, exon 1 of 1)	54084	NR_001461	63830	Mm.356096	NR_001461	ENSMUSG00000101609	Kcnq1ot1	Kvlqt1-as|Lit1|Tssc8	KCNQ1 overlapping transcript 1	ncRNA
mm_168530.1	chr1	161035470	161035470	+	1	NA	non-coding (NR_002840, exon 1 of 4)	non-coding (NR_002840, exon 1 of 4)	304	NR_002840	14455	Mm.270065	NR_002840	ENSMUSG00000053332	Gas5	Gas-5|Mir5117|Snhg2	growth arrest specific 5	ncRNA
mm_55543.1	chr6	70918903	70918908	-	1	NA	promoter-TSS (NM_028825)	promoter-TSS (NM_028825)	17	NM_028825	74221	Mm.273326	NM_028825	ENSMUSG00000051896	Tex37	1700011F03Rik	testis expressed 37	protein-coding
mm_17867.1	chr2	34870922	34870980	-	1	NA	promoter-TSS (NM_080554)	promoter-TSS (NM_080554)	11	NM_080554	66998	Mm.270632	NM_080554	ENSMUSG00000026869	Psmd5	1500032A03Rik|AW475925|S5b|W91691|mKIAA0072	proteasome (prosome, macropain) 26S subunit, non-ATPase, 5	protein-coding
mm_141169.1	chr17	26532711	26532723	-	1	NA	Intergenic	PB1D7|SINE|Alu	-24245	NM_013642	19252	Mm.239041	NM_013642	ENSMUSG00000024190	Dusp1	3CH134|MKP1|Ptpn16|U19515|erp|mkp-1	dual specificity phosphatase 1	protein-coding
mm_124397.1	chr14	112919102	112919105	-	1	NA	Intergenic	U2|snRNA|snRNA	897673	NR_030150	723922		NR_030150	ENSMUSG00000070099	Mir466	Mirn466|mmu-mir-466	microRNA 466	ncRNA
mm_83282.1	chr9	43105955	43106026	-	1	NA	promoter-TSS (NM_027144)	promoter-TSS (NM_027144)	-272	NM_027144	69632	Mm.275266	NM_027144	ENSMUSG00000059495	Arhgef12	2310014B11Rik|AU019857|Larg|mKIAA0382	Rho guanine nucleotide exchange factor (GEF) 12	protein-coding
mm_26908.1	chr3	19628670	19628685	-	1	NA	Intergenic	Intergenic	-15783	NM_001081281	381485	Mm.35419	NM_001081281	ENSMUSG00000060913	Trim55	D830041C10Rik|Murf2|Rnf29	tripartite motif-containing 55	protein-coding
mm_279.1	chr1	21256747	21256758	+	1	NA	intron (NM_001288617, intron 3 of 7)	intron (NM_001288617, intron 3 of 7)	16167	NM_010356	14859	Mm.394593	NM_010356	ENSMUSG00000025934	Gsta3	Gst2-3	glutathione S-transferase, alpha 3	protein-coding
mm_21697.1	chr2	164512172	164512182	-	1	NA	Intergenic	Intergenic	14652	NM_133779	78928	Mm.28228	NM_133779	ENSMUSG00000017721	Pigt	2510012P17Rik|4930534E15Rik|CGI-06|NDAP|Ndap7	phosphatidylinositol glycan anchor biosynthesis, class T	protein-coding
mm_141749.1	chr17	34239676	34239689	-	1	NA	intron (NM_010389, intron 1 of 5)	intron (NM_010389, intron 1 of 5)	777	NM_010389	15002	Mm.327358	NM_010389	ENSMUSG00000041538	H2-Ob	A-beta-2|A-beta2|H-2Ab|H-2I|H-2Ob|H2-Ab|H2-Ab2|H2-IAb2|Ob	histocompatibility 2, O region beta locus	protein-coding
mm_86938.1	chr10	24590943	24590943	+	1	NA	Intergenic	Intergenic	-4499	NM_010217	14219	Mm.390287	NM_010217	ENSMUSG00000019997	Ctgf	Ccn2|Fisp12|Hcs24|fisp-12	connective tissue growth factor	protein-coding
mm_24184.1	chr3	88593119	88593142	+	1	NA	Intergenic	Intergenic	13459	NM_025448	66256	Mm.7091	NM_025448	ENSMUSG00000041355	Ssr2	1500032E05Rik|AI315033|AU020133|TLAP|TRAPB|TRAPbeta	signal sequence receptor, beta	protein-coding
mm_10278.1	chr2	9884487	9884497	+	1	NA	non-coding (NR_024257, exon 5 of 5)	non-coding (NR_024257, exon 5 of 5)	3246	NR_024257	381347	Mm.441450	NR_024257		4930412O13Rik	ENSMUSG00000075535|Gm10853	RIKEN cDNA 4930412O13 gene	ncRNA
mm_162124.1	chrX	71962529	71962529	+	1	NA	promoter-TSS (NM_001303028)	promoter-TSS (NM_001303028)	-96	NM_001303028	208748	Mm.25626	NM_001081135	ENSMUSG00000033361	Prrg3	Gm368	proline rich Gla (G-carboxyglutamic acid) 3 (transmembrane)	protein-coding
mm_92758.1	chr10	81050996	81050999	-	1	NA	intron (NM_024499, intron 4 of 11)	intron (NM_024499, intron 4 of 11)	9157	NM_024499	52551	Mm.30068	NM_024499	ENSMUSG00000004937	Sgta	5330427H01Rik|AI194281|D10Ertd190e|Sgt|Stg	small glutamine-rich tetratricopeptide repeat (TPR)-containing, alpha	protein-coding
mm_85525.1	chr9	106464903	106464922	-	1	NA	TTS (NM_021567)	TTS (NM_021567)	1028	NM_001159652	436090	Mm.482905	NM_001159652	ENSMUSG00000091735	Gpr62	4933402E03Rik	G protein-coupled receptor 62	protein-coding
mm_65272.1	chr7	24208094	24208139	-	1	NA	promoter-TSS (NM_019940)	promoter-TSS (NM_019940)	33	NM_019940	56707	Mm.448367	NM_019940	ENSMUSG00000087598	Zfp111	-	zinc finger protein 111	protein-coding
mm_66056.1	chr7	30737983	30737991	-	1	NA	exon (NM_001290631, exon 2 of 11)	exon (NM_001290631, exon 2 of 11)	1420	NM_008085	14447	Mm.436562	NM_008085	ENSMUSG00000061099	Gapdhs	Gapd-s|Gapds	glyceraldehyde-3-phosphate dehydrogenase, spermatogenic	protein-coding
mm_51515.1	chr6	83137920	83137941	+	1	NA	5' UTR (NM_133641, exon 1 of 12)	5' UTR (NM_133641, exon 1 of 12)	846	NM_009106	20166	Mm.4139	NM_009106	ENSMUSG00000034930	Rtkn	-	rhotekin	protein-coding
mm_132796.1	chr16	45094007	45094021	+	1	NA	promoter-TSS (NM_026439)	promoter-TSS (NM_026439)	-39	NM_026439	67896	Mm.181074	NM_026439	ENSMUSG00000022665	Ccdc80	2610001E17Rik|DRO1|Ssg1|Urb	coiled-coil domain containing 80	protein-coding
mm_39388.1	chr5	13398829	13398871	+	1	NA	promoter-TSS (NM_009152)	promoter-TSS (NM_009152)	-147	NM_001243073	20346	Mm.372039	NM_009152	ENSMUSG00000028883	Sema3a	Hsema-I|SEMA1|SemD|Semad|coll-1	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	protein-coding
mm_145064.1	chr18	40530750	40530770	+	1	NA	exon (NM_026135, exon 2 of 2)	exon (NM_026135, exon 2 of 2)	272399	NM_026135	383348	Mm.76366	NM_026135	ENSMUSG00000051401	Kctd16	4930434H12Rik|Gm1267	potassium channel tetramerisation domain containing 16	protein-coding
mm_52796.1	chr6	121300281	121300297	+	1	NA	promoter-TSS (NM_144512)	promoter-TSS (NM_144512)	-7	NM_144512	14412	Mm.258596	NM_144512	ENSMUSG00000030108	Slc6a13	GAT3|Gabt3|Gat2	solute carrier family 6 (neurotransmitter transporter, GABA), member 13	protein-coding
mm_56764.1	chr6	116133849	116133893	-	1	NA	exon (NM_177412, exon 3 of 6)	exon (NM_177412, exon 3 of 6)	59503	NM_177412	330401	Mm.425352	NM_177412	ENSMUSG00000030126	Tmcc1	3632431M01Rik|mKIAA0779	transmembrane and coiled coil domains 1	protein-coding
mm_35015.1	chr4	3575126	3575142	-	1	NA	promoter-TSS (NM_028097)	promoter-TSS (NM_028097)	255	NM_054089	116940	Mm.171323	NM_054089	ENSMUSG00000028233	Tgs1	D4Ertd800e|Ncoa6ip|Pimt	trimethylguanosine synthase 1	protein-coding
mm_11114.1	chr2	28193250	28193278	+	1	NA	5' UTR (NM_001038613, exon 1 of 6)	5' UTR (NM_001038613, exon 1 of 6)	171	NM_001038614	56177	Mm.43278	NM_019498	ENSMUSG00000026833	Olfm1	AMY|AW742568|Noe1|OlfA|Pancortin|Pancortin3	olfactomedin 1	protein-coding
mm_123858.1	chr14	70994622	70994632	-	1	NA	Intergenic	Intergenic	104520	NM_001302094	14586	Mm.32619	NM_008115	ENSMUSG00000022103	Gfra2	-	glial cell line derived neurotrophic factor family receptor alpha 2	protein-coding
mm_173178.1	chrX	5329935	5329935	-	1	NA	Intergenic	L1_Mus3|LINE|L1	139330	NM_010850	17870	Mm.368515	NM_010850	ENSMUSG00000044597	Mycs	-	myc-like oncogene, s-myc protein	protein-coding
mm_90011.1	chr10	115269946	115269951	+	1	NA	Intergenic	Intergenic	-18455	NM_025706	66687	Mm.22252	NM_025706	ENSMUSG00000020130	Tbc1d15	4432405K22Rik|AU022358|AU023730|AW557774|Ly6dl|Rab7-GAP	TBC1 domain family, member 15	protein-coding
mm_64756.1	chr7	4844666	4844699	-	1	NA	promoter-TSS (NM_172737)	promoter-TSS (NM_172737)	14	NM_001290291	232813	Mm.44666	NM_172737	ENSMUSG00000053550	Shisa7	ckamp59	shisa family member 7	protein-coding
mm_4060.1	chr1	165856159	165856206	+	1	NA	intron (NM_001113391, intron 2 of 7)	intron (NM_001113391, intron 2 of 7)	67501	NM_001113392	12503	Mm.217308	NM_031162	ENSMUSG00000005763	Cd247	4930549J05Rik|A430104F18Rik|AW552088|Cd3|Cd3-eta|Cd3-zeta|Cd3h|Cd3z|Cd3zeta|T3z|Tcrk|Tcrz	CD247 antigen	protein-coding
mm_2114.1	chr1	87865102	87865106	+	1	NA	intron (NM_177646, intron 1 of 29)	intron (NM_177646, intron 1 of 29)	-10805	NR_136921	100503175	Mm.426422	NR_136921	ENSMUSG00000101942	Gm19582	-	predicted gene, 19582	ncRNA
mm_46315.1	chr5	100595223	100595270	-	1	NA	Intergenic	Intergenic	-23041	NM_139198	231507	Mm.34609	NM_139198	ENSMUSG00000029322	Plac8	C15|D5Wsu111e	placenta-specific 8	protein-coding
mm_15934.1	chr2	165596172	165596172	+	1	NA	intron (NM_001271963, intron 1 of 15)	intron (NM_001271963, intron 1 of 15)	1144	NM_001271963	14049	Mm.282719	NM_010165	ENSMUSG00000017897	Eya2	Eab1	EYA transcriptional coactivator and phosphatase 2	protein-coding
mm_89258.1	chr10	87859336	87859336	+	1	NA	5' UTR (NM_010512, exon 1 of 5)	5' UTR (NM_010512, exon 1 of 5)	284	NM_010512	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_139476.1	chr17	56005673	56005712	+	1	NA	promoter-TSS (NR_102313)	promoter-TSS (NR_102313)	-86	NR_102313	106766	Mm.204991	NM_145934	ENSMUSG00000038781	Stap2	AW049765|STAP-2	signal transducing adaptor family member 2	protein-coding
mm_115992.1	chr13	24376023	24376033	-	1	NA	intron (NM_001284519, intron 2 of 17)	intron (NM_001284519, intron 2 of 17)	-39094	NM_007717	12763	Mm.8396	NM_007717	ENSMUSG00000016756	Cmah	-	cytidine monophospho-N-acetylneuraminic acid hydroxylase	protein-coding
mm_163603.1	chr13	46968464	46968498	+	1	NA	Intergenic	Intergenic	-38763	NM_010617	16553	Mm.342703	NM_010617	ENSMUSG00000021375	Kif13a	4930505I07Rik|mKIAA4109	kinesin family member 13A	protein-coding
mm_63166.1	chr7	124018149	124018154	+	1	NA	intron (NM_001252072, intron 1 of 1)	intron (NM_001252072, intron 1 of 1)	34970	NM_001252072	628779	Mm.40210	NM_001252072	ENSMUSG00000078591	Hs3st4	EG628779|Gm6915	heparan sulfate (glucosamine) 3-O-sulfotransferase 4	protein-coding
mm_27073.1	chr3	28765367	28765389	-	1	NA	Intergenic	Intergenic	-15933	NM_177586	208691	Mm.193670	NM_177586	ENSMUSG00000050192	Eif5a2	9630038B20|eIF5AII	eukaryotic translation initiation factor 5A2	protein-coding
mm_50081.1	chr6	41521783	41521797	+	1	NA	promoter-TSS (NM_009430)	promoter-TSS (NM_009430)	14	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_13667.1	chr2	114294494	114294495	+	1	NA	Intergenic	Intergenic	-93062	NM_175466	228491	Mm.132523	NM_175466	ENSMUSG00000040321	Zfp770	6430601A21Rik|Znf770	zinc finger protein 770	protein-coding
mm_46279.1	chr5	100039825	100039888	-	1	NA	promoter-TSS (NM_016690)	promoter-TSS (NM_016690)	-138	NM_026421	67870	Mm.11311	NM_026421	ENSMUSG00000029326	Enoph1	2310057D15Rik|BB183658|C81437	enolase-phosphatase 1	protein-coding
mm_93153.1	chr10	93081598	93081644	-	1	NA	promoter-TSS (NM_001347060)	promoter-TSS (NM_001347060)	-25	NM_001347060	380654	Mm.34980	NM_001347060	ENSMUSG00000020014	Cfap54	4930485B16Rik|Gm872	cilia and flagella associated protein 54	protein-coding
mm_79076.1	chr9	46242104	46242120	+	1	NA	intron (NM_007468, intron 2 of 2)	intron (NM_007468, intron 2 of 2)	1268	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_9815.1	chr1	182020125	182020149	-	1	NA	promoter-TSS (NM_010135)	promoter-TSS (NM_010135)	-157	NM_010135	13800	Mm.87759	NM_008680	ENSMUSG00000022995	Enah	Mena|NDPP-1|Ndpp1|WBP8	enabled homolog (Drosophila)	protein-coding
mm_94650.1	chr11	17051627	17051651	+	1	NA	promoter-TSS (NM_029861)	promoter-TSS (NM_029861)	-295	NM_029861	380686	Mm.425666	NM_029861	ENSMUSG00000044629	Cnrip1	1500041B16Rik|3110054C06Rik|5330437A18Rik|AI854501|C2orf32	cannabinoid receptor interacting protein 1	protein-coding
mm_28152.1	chr3	87748534	87748555	-	1	NA	promoter-TSS (NM_028971)	promoter-TSS (NM_028971)	79	NM_028971	74485	Mm.474494	NM_028971	ENSMUSG00000023084	Lrrc71	4933430H15Rik	leucine rich repeat containing 71	protein-coding
mm_78925.1	chr9	45055167	45055195	+	1	NA	promoter-TSS (NM_001093749)	promoter-TSS (NM_001093749)	0	NM_001093749	319742	Mm.49611	NM_176993	ENSMUSG00000070305	Mpzl3	5430427F17Rik|A530065I17Rik|rc	myelin protein zero-like 3	protein-coding
mm_59620.1	chr7	28152917	28152930	+	1	NA	exon (NM_001164655, exon 11 of 20)	exon (NM_001164655, exon 11 of 20)	-16825	NM_007991	14113	Mm.4595	NM_007991	ENSMUSG00000046865	Fbl	AL022665|FIB|FLRN|RNU3IP1	fibrillarin	protein-coding
mm_171992.1	chr5	97526175	97526175	-	1	NA	intron (NR_045981, intron 3 of 7)	intron (NR_045981, intron 3 of 7)	-69167	NM_010294	14626	Mm.61206	NM_010294	ENSMUSG00000050553	Gk2	GKTA|Gk-rs2	glycerol kinase 2	protein-coding
mm_112356.1	chr12	118924577	118924582	-	1	NA	intron (NM_029961, intron 13 of 27)	MT2_Mm|LTR|ERVL	41842	NM_029961	77706	Mm.261496	NM_029961	ENSMUSG00000072791	Abcb5	9230106F14Rik	ATP-binding cassette, sub-family B (MDR/TAP), member 5	protein-coding
mm_165401.1	chr2	136552913	136552920	+	1	NA	intron (NM_175667, intron 8 of 10)	RMER17B2|LTR|ERVK	20595	NM_175667	319196	Mm.477841	NM_175667	ENSMUSG00000074771	Ankef1	AV276460|Ankrd5	ankyrin repeat and EF-hand domain containing 1	protein-coding
mm_40714.1	chr5	65934895	65934902	+	1	NA	Intergenic	Intergenic	-32226	NM_001081104	231252	Mm.140015	NM_001081104	ENSMUSG00000029205	Chrna9	2410015I05Rik|Acra9|EG666827|Gm8311	cholinergic receptor, nicotinic, alpha polypeptide 9	protein-coding
mm_22006.1	chr2	167773044	167773052	-	1	NA	Intergenic	Intergenic	81871	NR_015500	329562	Mm.123101	NM_177851	ENSMUSG00000006462	A530013C23Rik	-	RIKEN cDNA A530013C23 gene	ncRNA
mm_103390.1	chr11	75416378	75416392	-	1	NA	exon (NM_011340, exon 3 of 8)	exon (NM_011340, exon 3 of 8)	6238	NM_011340	20317	Mm.2044	NM_011340	ENSMUSG00000000753	Serpinf1	AI195227|EPC-1|Pedf|Pedfl|Sdf3	serine (or cysteine) peptidase inhibitor, clade F, member 1	protein-coding
mm_117596.1	chr13	89742552	89742569	-	1	NA	promoter-TSS (NM_001134474)	promoter-TSS (NM_001134474)	-48	NM_001134475	13003	Mm.158700	NM_019389	ENSMUSG00000021614	Vcan	5430420N07Rik|9430051N09|Cspg2|DPEAAE|NG2|PG-M|PG-M(V0)|PG-M(V1)|hdf	versican	protein-coding
mm_118528.1	chr14	15110447	15110451	+	1	NA	Intergenic	Lx9|LINE|L1	289634	NM_001195229	674895	Mm.317563	NM_001034865	ENSMUSG00000042567	Nek10	Gm282	NIMA (never in mitosis gene a)- related kinase 10	protein-coding
mm_24302.1	chr3	89389330	89389334	+	1	NA	intron (NM_009565, intron 1 of 2)	intron (NM_009565, intron 1 of 2)	-2532	NR_040403	545539	Mm.393389	NR_040403	ENSMUSG00000074466	Gm15417	ENSMUSG00000074466|OTTMUSG00000021274	predicted gene 15417	ncRNA
mm_67702.1	chr7	89527163	89527173	-	1	NA	Intergenic	Intergenic	-9582	NM_029614	76453	Mm.250438	NM_029614	ENSMUSG00000039405	Prss23	2310046G15Rik|4930479H08Rik|AI790574|Spuve	protease, serine 23	protein-coding
mm_34602.1	chr4	150237212	150237239	+	1	NA	promoter-TSS (NM_001025388).2	promoter-TSS (NM_001025388).2	28	NM_023119	13806	Mm.70666	NM_023119	ENSMUSG00000063524	Eno1	0610008I15|AL022784|Eno-1|MBP-1	enolase 1, alpha non-neuron	protein-coding
mm_104051.1	chr11	86358219	86358227	-	1	NA	promoter-TSS (NM_001080931)	promoter-TSS (NM_001080931)	-698	NM_001080931	327987	Mm.341886	NM_001080931	ENSMUSG00000034297	Med13	1110067M05Rik|D030023K18|Thrap1|Trap240	mediator complex subunit 13	protein-coding
mm_166775.1	chr6	136808358	136808366	+	1	NA	exon (NM_177688, exon 1 of 1)	exon (NM_177688, exon 1 of 1)	114	NM_177688	232440	Mm.154564	NM_177688	ENSMUSG00000060032	H2afj	E130307C13	H2A histone family, member J	protein-coding
mm_76605.1	chr8	90816991	90817017	-	1	NA	Intergenic	Intergenic	-11831	NM_177224	109151	Mm.100615	NM_177224	ENSMUSG00000056608	Chd9	1810014J18Rik|9030205D12Rik|A330063D19Rik|AD013|PRIC320|mKIAA0308	chromodomain helicase DNA binding protein 9	protein-coding
mm_70545.1	chr8	13055675	13055681	+	1	NA	exon (NM_007972, exon 9 of 9)	exon (NM_007972, exon 9 of 9)	-5230	NM_025834	66901	Mm.441140	NM_025834	ENSMUSG00000031445	Proz	1300015B06Rik	protein Z, vitamin K-dependent plasma glycoprotein	protein-coding
mm_60108.1	chr7	35449036	35449050	+	1	NA	promoter-TSS (NM_001199016)	promoter-TSS (NM_001199016)	-49	NM_001199015	30962	Mm.45874	NM_021291	ENSMUSG00000030492	Slc7a9	CSNU3	solute carrier family 7 (cationic amino acid transporter, y+ system), member 9	protein-coding
mm_12927.1	chr2	85037714	85037728	+	1	NA	intron (NM_001136081, intron 1 of 16)	intron (NM_001136081, intron 1 of 16)	270	NM_001136081	20833	Mm.219793	NM_182990	ENSMUSG00000027067	Ssrp1	C81323|Hmg1-rs1|Hmgi-rs3|Hmgox|T160	structure specific recognition protein 1	protein-coding
mm_90944.1	chr10	12964442	12964472	-	1	NA	promoter-TSS (NM_029075)	promoter-TSS (NM_029075)	-198	NM_001163591	74732	Mm.248648	NM_029075	ENSMUSG00000039232	Stx11	5830405C08Rik	syntaxin 11	protein-coding
mm_82319.1	chr9	7994816	7994819	-	1	NA	intron (NM_009534, intron 2 of 7)	B1_Mm|SINE|Alu	9779	NM_001171147	22601	Mm.221992	NM_009534	ENSMUSG00000053110	Yap1	AI325207|Yap|Yap65|Yki|Yorkie	yes-associated protein 1	protein-coding
mm_100648.1	chr11	3123906	3123920	-	1	NA	promoter-TSS (NR_003517)	promoter-TSS (NR_003517)	-108	NR_003517	236604	Mm.247625	NM_001004146		Pisd-ps1	-	phosphatidylserine decarboxylase, pseudogene 1	pseudo
mm_96789.1	chr11	69965727	69965741	+	1	NA	5' UTR (NM_016887, exon 1 of 4)	5' UTR (NM_016887, exon 1 of 4)	313	NM_016887	53624	Mm.281896	NM_016887	ENSMUSG00000018569	Cldn7	-	claudin 7	protein-coding
mm_37615.1	chr4	126968181	126968198	-	1	NA	promoter-TSS (NM_001114399)	promoter-TSS (NM_001114399)	-266	NM_001114399	67785	Mm.165401	NM_001114399	ENSMUSG00000042446	Zmym4	6330503C17Rik|AI480785|AW493829|CDIR|D630001M21|MYM|Zfp262|Znf262|mKIAA0425	zinc finger, MYM-type 4	protein-coding
mm_168687.1	chr11	96075643	96075648	-	1	NA	promoter-TSS (NM_001161419)	promoter-TSS (NM_001161419)	-14	NM_001161419	11951	Mm.258	NM_007506	ENSMUSG00000006057	Atp5g1	-	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit C1 (subunit 9)	protein-coding
mm_157401.1	chrX	38424342	38424360	-	1	NA	exon (NM_001017959, exon 8 of 9)	exon (NM_001017959, exon 8 of 9)	32109	NM_010685	16784	Mm.486	NM_010685	ENSMUSG00000016534	Lamp2	CD107b|LGP-B|Lamp II|Lamp-2|Lamp-2a|Lamp-2b|Lamp-2c|Mac3	lysosomal-associated membrane protein 2	protein-coding
mm_104196.1	chr11	87980435	87980445	-	1	NA	3' UTR (NM_001168471, exon 3 of 3)	3' UTR (NM_001168471, exon 3 of 3)	6145	NM_001168472	68097	Mm.246436	NM_026556	ENSMUSG00000020483	Dynll2	1700064A15Rik|6720463E02Rik|C87222|DLC8|DLC8b|Dlc2	dynein light chain LC8-type 2	protein-coding
mm_96266.1	chr11	62648831	62648839	+	1	NA	promoter-TSS (NM_198861)	promoter-TSS (NM_198861)	171	NM_175002	216829	Mm.295306	NM_175002	ENSMUSG00000048497	Mmgt2	AI852046	membrane magnesium transporter 2	protein-coding
mm_93209.1	chr10	94944171	94944235	-	1	NA	exon (NM_018797, exon 1 of 31)	exon (NM_018797, exon 1 of 31)	375	NM_018797	54712	Mm.256712	NM_018797	ENSMUSG00000074785	Plxnc1	2510048K12Rik|AW742158|CD232|Vespr	plexin C1	protein-coding
mm_59451.1	chr7	27133575	27133587	+	1	NA	TTS (NM_007817)	TTS (NM_007817)	13626	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_169929.1	chr16	57391592	57391593	-	1	NA	intron (NM_001040397, intron 1 of 4)	LSU-rRNA_Hsa|rRNA|rRNA	38315	NM_001040397	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding
mm_16116.1	chr2	169726051	169726054	+	1	NA	intron (NM_080455, intron 1 of 1)	intron (NM_080455, intron 1 of 1)	92406	NM_080455	228911	Mm.315789	NM_080455	ENSMUSG00000047907	Tshz2	2900073F20Rik|B830045G17|Mtsh2|Sdccag33l|Tsh2|Zfp218|mKIAA4248|teashirt2	teashirt zinc finger family member 2	protein-coding
mm_38516.1	chr4	141415971	141415997	-	1	NA	promoter-TSS (NM_019701)	promoter-TSS (NM_019701)	4	NM_019701	56365	Mm.24882	NM_019701	ENSMUSG00000006216	Clcnkb	CLCKB|Clc-Ka|Clck2|Clcnk1l	chloride channel, voltage-sensitive Kb	protein-coding
mm_137607.1	chr17	28232724	28232789	+	1	NA	promoter-TSS (NM_011145)	promoter-TSS (NM_011145)	2	NM_011145	19015	Mm.328914	NM_011145	ENSMUSG00000002250	Ppard	NUC-1|NUC1|Nr1c2|PPAR-beta|PPAR-delta|PPAR[b]|PPARdelta|Pparb|Pparb/d	peroxisome proliferator activator receptor delta	protein-coding
mm_131931.1	chr16	23610070	23610082	+	1	NA	exon (NM_023386, exon 1 of 2)	exon (NM_023386, exon 1 of 2)	157	NM_023386	67775	Mm.475107	NM_023386	ENSMUSG00000033355	Rtp4	5830458K16Rik|Ifrg28	receptor transporter protein 4	protein-coding
mm_74326.1	chr8	126869622	126869644	+	1	NA	Intergenic	Intergenic	76288	NM_024214	67952	Mm.6932	NM_024214	ENSMUSG00000093904	Tomm20	1810060K07Rik|BB284719|Gm19268|MAS20|MOM19|TOM20|mKIAA0016	translocase of outer mitochondrial membrane 20 homolog (yeast)	protein-coding
mm_85939.1	chr9	112099236	112099249	-	1	NA	intron (NM_001177618, intron 17 of 18)	B4|SINE|B4	19469	NR_029823	723815		NR_029823	ENSMUSG00000065441	Mir128-2	Mirn128-2|Mirn128b|mir-128-2|mir-128b	microRNA 128-2	ncRNA
mm_171943.1	chr5	7085995	7085995	+	1	NA	intron (NM_001163223, intron 1 of 3)	L1Md_T|LINE|L1	-218169	NM_027603	70920	Mm.158494	NM_027603	ENSMUSG00000040514	4921511H03Rik	-	RIKEN cDNA 4921511H03 gene	protein-coding
mm_143234.1	chr17	63499690	63499748	-	1	NA	exon (NM_015794, exon 1 of 9)	exon (NM_015794, exon 1 of 9)	861	NM_015794	50758	Mm.136366	NM_015794	ENSMUSG00000023965	Fbxl17	6330576B01Rik|AI452053|BB073797|C130023C01Rik|Fbx13|Fbxo13	F-box and leucine-rich repeat protein 17	protein-coding
mm_118013.1	chr13	100744090	100744129	-	1	NA	intron (NM_001190264, intron 1 of 3)	intron (NM_001190264, intron 1 of 3)	550	NM_001190264	66128	Mm.306173	NM_025369	ENSMUSG00000061474	Mrps36	1110018B13Rik|S36mt	mitochondrial ribosomal protein S36	protein-coding
mm_124788.1	chr15	8109297	8109307	+	1	NA	promoter-TSS (NM_133227)	promoter-TSS (NM_133227)	-11	NM_133227	170762	Mm.295168	NM_133227	ENSMUSG00000022142	Nup155	D930027M19Rik|mKIAA0791	nucleoporin 155	protein-coding
mm_101456.1	chr11	30253417	30253420	-	1	NA	Intergenic	L1VL2|LINE|L1	-33646	NM_175836	20742	Mm.123110	NM_009260	ENSMUSG00000020315	Sptbn1	9930031C03Rik|AL033301|SPTB2|Spnb-2|Spnb2|elf1|elf3|mKIAA4049	spectrin beta, non-erythrocytic 1	protein-coding
mm_14928.1	chr2	151540776	151540782	+	1	NA	Intergenic	RLTR24|LTR|ERV1	-1704	NR_126058	14225	Mm.278458	NM_008019	ENSMUSG00000032966	Fkbp1a	FKBP12|Fkbp|Fkbp1	FK506 binding protein 1a	protein-coding
mm_88407.1	chr10	76723489	76723512	+	1	NA	exon (NM_009933, exon 3 of 35)	exon (NM_009933, exon 3 of 35)	2544	NM_009933	12833	Mm.2509	NM_009933	ENSMUSG00000001119	Col6a1	AI747156|Col6a-1	collagen, type VI, alpha 1	protein-coding
mm_67033.1	chr7	66689590	66689603	-	1	NA	promoter-TSS (NR_003961)	promoter-TSS (NR_003961)	-35	NR_003961	117589	Mm.34785	NM_080443	ENSMUSG00000030509	Asb7	AI449039|Asb-7|D030055C23Rik	ankyrin repeat and SOCS box-containing 7	protein-coding
mm_170193.1	chr17	6601792	6601794	+	1	NA	promoter-TSS (NM_001166630)	promoter-TSS (NM_001166630)	14	NM_001166630	100040563	Mm.457381	NM_001166630	ENSMUSG00000000579	Dynlt1c	100040603|Dynlt1d	dynein light chain Tctex-type 1C	protein-coding
mm_98258.1	chr11	88851621	88851623	+	1	NA	promoter-TSS (NR_126433)	promoter-TSS (NR_126433)	18	NR_126433	75285	Mm.402023	NR_126433	ENSMUSG00000092399	4930556N13Rik	-	RIKEN cDNA 4930556N13 gene	ncRNA
mm_135727.1	chr16	55822526	55822556	-	1	NA	promoter-TSS (NM_001159394)	promoter-TSS (NM_001159394)	-403	NM_001159394	80859	Mm.247272	NM_030612	ENSMUSG00000035356	Nfkbiz	AA408868|INAP|Mail	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, zeta	protein-coding
mm_25525.1	chr3	114827649	114827651	+	1	NA	Intergenic	Intergenic	-35603	NR_030469	735255		NR_030469	ENSMUSG00000076126	Mir669b	Mirn669b	microRNA 669b	ncRNA
mm_112587.1	chr13	13784019	13784068	+	1	NA	promoter-TSS (NM_010317)	promoter-TSS (NM_010317)	-16	NM_001302997	14706	Mm.215394	NM_010317	ENSMUSG00000021303	Gng4	-	guanine nucleotide binding protein (G protein), gamma 4	protein-coding
mm_84153.1	chr9	59486597	59486601	-	1	NA	promoter-TSS (NM_019927)	promoter-TSS (NM_019927)	-225	NM_019927	23806	Mm.305925	NM_019927	ENSMUSG00000025234	Arih1	AU021774|Ari|Ari1|Hari|Hhari|Ubch7bp|Uip77	ariadne RBR E3 ubiquitin protein ligase 1	protein-coding
mm_18837.1	chr2	74753475	74753478	-	1	NA	non-coding (NR_110447, exon 2 of 2)	non-coding (NR_110447, exon 2 of 2)	792	NR_110447	102634401	Mm.235021	NR_110447	ENSMUSG00000085015	LOC102634401	-	uncharacterized LOC102634401	ncRNA
mm_151351.1	chr19	55897952	55897966	+	1	NA	intron (NM_001142924, intron 1 of 11)	intron (NM_001142924, intron 1 of 11)	2638	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_107219.1	chr12	26469374	26469397	+	1	NA	exon (NM_020557, exon 1 of 5)	exon (NM_020557, exon 1 of 5)	170	NM_020557	22169	Mm.271839	NM_020557	ENSMUSG00000020638	Cmpk2	1200004E04Rik|TDKI|Tyki	cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial	protein-coding
mm_67091.1	chr7	68749171	68749233	-	1	NA	promoter-TSS (NM_001042592)	promoter-TSS (NM_001042592)	36	NM_001042592	66412	Mm.251199	NM_025549	ENSMUSG00000042659	Arrdc4	2410003C09Rik|AV216361	arrestin domain containing 4	protein-coding
mm_149551.1	chr19	12600045	12600051	+	1	NA	promoter-TSS (NM_001167907)	promoter-TSS (NM_001167907)	32	NM_001013762	240549	Mm.302458	NM_001013762	ENSMUSG00000071633	Gm4952	EG240549	predicted gene 4952	protein-coding
mm_172378.1	chr7	13025030	13025047	+	1	NA	exon (NM_011588, exon 1 of 17)	exon (NM_011588, exon 1 of 17)	886	NM_011588	21849	Mm.15701	NM_011588	ENSMUSG00000005566	Trim28	AA408787|KAP-1|KRIP-1|MommeD9|Tif1b|Tif1beta	tripartite motif-containing 28	protein-coding
mm_16750.1	chr2	9857572	9857583	-	1	NA	3' UTR (NM_008091, exon 6 of 6)	3' UTR (NM_008091, exon 6 of 6)	21023	NM_008091	14462	Mm.313866	NM_008091	ENSMUSG00000015619	Gata3	Gata-3|jal	GATA binding protein 3	protein-coding
mm_165528.1	chr2	178414905	178414945	-	1	NA	promoter-TSS (NM_001085501)	promoter-TSS (NM_001085501)	391	NM_001081289	71532	Mm.40216	NM_001081289	ENSMUSG00000070476	Fam217b	9030418K01Rik|AI851938	family with sequence similarity 217, member B	protein-coding
mm_11286.1	chr2	30066710	30066723	+	1	NA	5' UTR (NM_001204875, exon 1 of 8)	5' UTR (NM_001204875, exon 1 of 8)	242	NM_001204875	56086	Mm.326055	NM_023871	ENSMUSG00000054766	Set	2610030F17Rik|5730420M11Rik|AA407739|I-2PP2A|StF-IT-1|TAF-I	SET nuclear oncogene	protein-coding
mm_170387.1	chr18	60382700	60382710	+	1	NA	5' UTR (NM_001146275, exon 2 of 3)	5' UTR (NM_001146275, exon 2 of 3)	6676	NM_001146275	60440	Mm.261140	NM_021792	ENSMUSG00000054072	Iigp1	2900074L10Rik|AI046432|AW111922|Ifgga1|Iigp|Irga6	interferon inducible GTPase 1	protein-coding
mm_73245.1	chr8	104250944	104250954	+	1	NA	promoter-TSS (NR_104433)	promoter-TSS (NR_104433)	88	NM_001286383	75458	Mm.269219	NM_029295	ENSMUSG00000054400	Cklf	1700001C14Rik|1810018M11Rik|A730028G07Rik|C32|CKLF1|CKLF3|CKLF4|CKLF5|Cklf2|Cklf6|HSPC224|UCK-1	chemokine-like factor	protein-coding
mm_34021.1	chr4	138019781	138019784	+	1	NA	intron (NM_172703, intron 2 of 34)	B1_Mur2|SINE|Alu	26326	NM_172703	230861	Mm.268903	NM_172703	ENSMUSG00000028760	Eif4g3	1500002J22Rik|4930523M17Rik|G1-419-52|eIF4GII|repro8	eukaryotic translation initiation factor 4 gamma, 3	protein-coding
mm_151619.1	chr19	3905178	3905196	-	1	NA	promoter-TSS (NM_016921)	promoter-TSS (NM_016921)	43	NM_016921	27060	Mm.271689	NM_016921	ENSMUSG00000001750	Tcirg1	ATP6N1C|ATP6a3|Atp6i|OC-116|OPTB1|Stv1|TIRC7|Vph1|oc	T cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 protein A3	protein-coding
mm_57488.1	chr6	125266463	125266471	-	1	NA	non-coding (NR_015527, exon 2 of 4)	non-coding (NR_015527, exon 2 of 4)	942	NR_015527	73870	Mm.440681	NR_015527	ENSMUSG00000108129	4930417O13Rik	-	RIKEN cDNA 4930417O13 gene	ncRNA
mm_115413.1	chr13	114839286	114839296	+	1	NA	intron (NM_008396, intron 28 of 29)	intron (NM_008396, intron 28 of 29)	21054	NM_001113374	17434	Mm.19027	NM_013826	ENSMUSG00000015536	Mocs2	AI415403	molybdenum cofactor synthesis 2	protein-coding
mm_131982.1	chr16	25026500	25026506	+	1	NA	Intergenic	RMER20B|LTR|ERVK	-33136	NR_040374	319487	Mm.137341	NR_040374	ENSMUSG00000096960	A230028O05Rik	-	RIKEN cDNA A230028O05 gene	ncRNA
mm_31983.1	chr4	89124250	89124260	+	1	NA	Intergenic	Intergenic	-13115	NM_024433	66902	Mm.28500	NM_024433	ENSMUSG00000062937	Mtap	1300019I21Rik|MSAP	methylthioadenosine phosphorylase	protein-coding
mm_132018.1	chr16	26251989	26251993	+	1	NA	Intergenic	Intergenic	119848	NM_016674	12737	Mm.289441	NM_016674	ENSMUSG00000022512	Cldn1	AI596271	claudin 1	protein-coding
mm_6775.1	chr1	84134189	84134241	-	1	NA	intron (NM_001003948, intron 2 of 2)	B4A|SINE|B4	84746	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_79860.1	chr9	65032414	65032466	+	1	NA	promoter-TSS (NM_028906)	promoter-TSS (NM_028906)	-18	NM_028906	74388	Mm.202749	NM_028906	ENSMUSG00000032393	Dpp8	2310004I03Rik|4932434F09Rik|AI666706|DPP VIII	dipeptidylpeptidase 8	protein-coding
mm_168601.1	chr1	174609750	174609751	+	1	NA	exon (NM_019445, exon 5 of 18)	exon (NM_019445, exon 5 of 18)	107925	NM_019445	54418	Mm.330620	NM_019445	ENSMUSG00000028354	Fmn2	AU024104	formin 2	protein-coding
mm_130934.1	chr15	103199623	103199637	-	1	NA	3' UTR (NM_001110216, exon 6 of 6)	3' UTR (NM_001110216, exon 6 of 6)	15722	NM_007626	12419	Mm.262059	NM_007626	ENSMUSG00000009575	Cbx5	2610029O15Rik|C75991|HP1|Hp1a|Hp1alpha	chromobox 5	protein-coding
mm_31340.1	chr4	46471395	46471400	+	1	NA	intron (NM_130889, intron 5 of 6)	intron (NM_130889, intron 5 of 6)	-17932	NM_053179	94181	Mm.249349	NM_053179	ENSMUSG00000028334	Nans	4632418E04Rik|BB056474|Sas	N-acetylneuraminic acid synthase (sialic acid synthase)	protein-coding
mm_75235.1	chr8	39629518	39629533	-	1	NA	intron (NM_001113326, intron 3 of 9)	intron (NM_001113326, intron 3 of 9)	13153	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_159329.1	chr3	37008415	37008415	+	1	NA	exon (NM_172679, exon 59 of 86)	exon (NM_172679, exon 59 of 86)	-55241	NM_009350	21744	Mm.8122	NM_009350	ENSMUSG00000027719	Adad1	Tenr	adenosine deaminase domain containing 1 (testis specific)	protein-coding
mm_45824.1	chr5	87694531	87694540	-	1	NA	exon (NM_001286023, exon 5 of 7)	exon (NM_001286023, exon 5 of 7)	4890	NM_001286020	12991	Mm.268737	NM_009972	ENSMUSG00000063157	Csn2	Csnb	casein beta	protein-coding
mm_89403.1	chr10	90576709	90576764	+	1	NA	promoter-TSS (NM_181398)	promoter-TSS (NM_181398)	45	NM_181398	77531	Mm.440605	NM_181398	ENSMUSG00000058589	Anks1b	AIDA-1b|C030032C09Rik|E530015N03Rik|ENSMUSG00000078431|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding
mm_3910.1	chr1	161896393	161896397	+	1	NA	Intergenic	Intergenic	-19734	NM_172645	226551	Mm.170002	NM_172645	ENSMUSG00000040297	Suco	4732491B11|AI848100|AU016931|Opt	SUN domain containing ossification factor	protein-coding
mm_14489.1	chr2	131909952	131909979	+	1	NA	promoter-TSS (NM_001278256)	promoter-TSS (NM_001278256)	37	NM_001278256	19122	Mm.648	NM_011170	ENSMUSG00000079037	Prnp	AA960666|AI325101|CD230|PrP|PrP<C>|PrPC|PrPSc|Prn-i|Prn-p|Sinc|prP27-30|prP33-35C	prion protein	protein-coding
mm_29191.1	chr3	106684892	106684902	-	1	NA	promoter-TSS (NM_001039478)	promoter-TSS (NM_001039478)	-90	NM_001039478	321000	Mm.259638	NM_028081	ENSMUSG00000056260	Lrif1	2010012G17Rik|4933421E11Rik|AI450568	ligand dependent nuclear receptor interacting factor 1	protein-coding
mm_9580.1	chr1	174028300	174028310	-	1	NA	exon (NM_172648, exon 2 of 7)	exon (NM_172648, exon 2 of 7)	3450	NM_172648	226695	Mm.425061	NM_172648	ENSMUSG00000054203	Ifi205	D3|D3cDNA|Ifi205a	interferon activated gene 205	protein-coding
mm_126554.1	chr15	82147239	82147275	+	1	NA	promoter-TSS (NM_033218)	promoter-TSS (NM_033218)	-12	NM_033218	20788	Mm.9002	NM_033218	ENSMUSG00000022463	Srebf2	AI608257|SREBP-2|SREBP2|SREBP2gc|bHLHd2|lop13|nuc	sterol regulatory element binding factor 2	protein-coding
mm_132136.1	chr16	31927025	31927043	+	1	NA	Intergenic	MERV1_LTR|LTR|ERV1	-6817	NM_172822	239827	Mm.440388	NM_172822	ENSMUSG00000045625	Pigz	F630022B06Rik	phosphatidylinositol glycan anchor biosynthesis, class Z	protein-coding
mm_88942.1	chr10	81319690	81319727	+	1	NA	3' UTR (NM_001146687, exon 17 of 17)	3' UTR (NM_001146687, exon 17 of 17)	-1395	NM_027381	70312	Mm.87628	NM_027381	ENSMUSG00000034889	Cactin	2510012J08Rik	cactin, spliceosome C complex subunit	protein-coding
mm_163833.1	chr14	19417725	19417753	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	184848	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_155795.1	chrX	98937749	98937796	+	1	NA	promoter-TSS (NM_207633)	promoter-TSS (NM_207633)	-9	NM_207633	77929	Mm.212290	NM_207633	ENSMUSG00000047694	Yipf6	A430107J06Rik	Yip1 domain family, member 6	protein-coding
mm_127001.1	chr15	95790904	95790914	+	1	NA	promoter-TSS (NM_001253813)	promoter-TSS (NM_001253813)	66	NM_001253813	105722	Mm.38087	NM_175344	ENSMUSG00000064210	Ano6	2900059G15Rik|AA407480|AW554778|F730003B03Rik|Tmem16f	anoctamin 6	protein-coding
mm_106201.1	chr11	116843164	116843232	-	1	NA	promoter-TSS (NM_028865)	promoter-TSS (NM_028865)	251	NM_033398	107817	Mm.481684	NM_033398	ENSMUSG00000056962	Jmjd6	5730436I23Rik|D11Ertd195e|PSR|PtdSerR|Ptdsr|mKIAA0585	jumonji domain containing 6	protein-coding
mm_12955.1	chr2	90189919	90189934	+	1	NA	Intergenic	Intergenic	34545	NM_001270423	100042690	Mm.271314	NM_001270423	ENSMUSG00000089859	Gm13769	Gm13766|OTTMUSG00000014164|OTTMUSG00000014278	predicted gene 13769	protein-coding
mm_79346.1	chr9	53537084	53537094	+	1	NA	promoter-TSS (NM_001081152)	promoter-TSS (NM_001081152)	42	NM_001081152	244879	Mm.116713	NM_001081152	ENSMUSG00000033054	Npat	6820401K01|AI427561|BB112559	nuclear protein in the AT region	protein-coding
mm_30519.1	chr3	158561359	158561422	-	1	NA	5' UTR (NM_001291453, exon 1 of 26)	5' UTR (NM_001291453, exon 1 of 26)	831	NM_001291453	242274	Mm.132162	NM_001081358	ENSMUSG00000028176	Lrrc7	AK122498|densin|mKIAA1365	leucine rich repeat containing 7	protein-coding
mm_150742.1	chr19	43782340	43782350	+	1	NA	promoter-TSS (NM_013806)	promoter-TSS (NM_013806)	37	NM_013806	12780	Mm.39054	NM_013806	ENSMUSG00000025194	Abcc2	AI173996|Abc30|Cmoat|Mrp2|cMRP	ATP-binding cassette, sub-family C (CFTR/MRP), member 2	protein-coding
mm_157446.1	chrX	41823518	41823545	-	1	NA	exon (NM_001033422, exon 28 of 39)	exon (NM_001033422, exon 28 of 39)	88370	NM_001033422	331401	Mm.259498	NM_001033422	ENSMUSG00000037475	Thoc2	6330441O12Rik|D130005M13Rik|Gm1139|Gm1793|Tho2	THO complex 2	protein-coding
mm_73155.1	chr8	94994794	94994803	+	1	NA	intron (NM_018882, intron 1 of 13)	intron (NM_018882, intron 1 of 13)	10399	NM_018882	14766	Mm.290834	NM_018882	ENSMUSG00000031785	Adgrg1	Cyt28|Gpr56|TM7LN4|TM7XN1	adhesion G protein-coupled receptor G1	protein-coding
mm_168627.1	chr1	180894593	180894594	+	1	NA	intron (NM_177099, intron 2 of 3)	CpG	1485	NM_177099	320202	Mm.87078	NM_177099	ENSMUSG00000066652	Lefty2	6030463A22Rik|Ebaf|Lefta|Leftb|lefty-2|lefty-B	left-right determination factor 2	protein-coding
mm_81181.1	chr9	107399859	107399872	+	1	NA	promoter-TSS (NM_001174049)	promoter-TSS (NM_001174049)	-15	NM_001174049	56808	Mm.273084	NM_020263	ENSMUSG00000010066	Cacna2d2	Cacna2d|a2d2|du|mKIAA0558|td|torpid	calcium channel, voltage-dependent, alpha 2/delta subunit 2	protein-coding
mm_120426.1	chr14	65666395	65666416	+	1	NA	promoter-TSS (NM_001168318)	promoter-TSS (NM_001168318)	2	NM_001168318	71145	Mm.83840	NM_028903	ENSMUSG00000022032	Scara5	4932433F15Rik|4933425F03Rik|AV278087|Tesr	scavenger receptor class A, member 5	protein-coding
mm_60280.1	chr7	43958780	43958788	+	1	NA	Intergenic	Intergenic	-7967	NM_010645	16623	Mm.447819	NM_010645	ENSMUSG00000063133	Klk1b1	Klk1|mGK-1|mK1	kallikrein 1-related peptidase b1	protein-coding
mm_83165.1	chr9	40489728	40489738	-	1	NA	Intergenic	Intergenic	-33969	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_141475.1	chr17	31074691	31074711	-	1	NA	intron (NM_009593, intron 2 of 14)	intron (NM_009593, intron 2 of 14)	17007	NM_009593	11307	Mm.15691	NM_009593	ENSMUSG00000024030	Abcg1	AW413978|Abc8|White	ATP-binding cassette, sub-family G (WHITE), member 1	protein-coding
mm_28346.1	chr3	89418288	89418316	-	1	NA	promoter-TSS (NM_011368)	promoter-TSS (NM_011368)	-11	NM_016904	54124	Mm.3049	NM_016904	ENSMUSG00000028044	Cks1b	2410005G18Rik|2610005D03Rik|AA407784|Cks1|sid1334	CDC28 protein kinase 1b	protein-coding
mm_56212.1	chr6	89348581	89348604	-	1	NA	intron (NM_008881, intron 3 of 31)	intron (NM_008881, intron 3 of 31)	14021	NM_008881	18844	Mm.3789	NM_008881	ENSMUSG00000030084	Plxna1	2600013D04Rik|NOV|PlexA1|Plxn1|mKIAA4053	plexin A1	protein-coding
mm_38328.1	chr4	137388136	137388167	-	1	NA	Intergenic	CpG	21640	NM_001126318	242711	Mm.475541	NM_001126318	ENSMUSG00000078520	Cela3a	Gm13011|OTTMUSG00000009877	chymotrypsin-like elastase family, member 3A	protein-coding
mm_87213.1	chr10	39801360	39801362	+	1	NA	intron (NM_011264, intron 5 of 31)	intron (NM_011264, intron 5 of 31)	69201	NM_011264	19714	Mm.439723	NM_011264	ENSMUSG00000019841	Rev3l	Rev|Rev3|Sez4	REV3 like, DNA directed polymerase zeta catalytic subunit	protein-coding
mm_165666.1	chr3	88553708	88553736	+	1	NA	promoter-TSS (NM_033526)	promoter-TSS (NM_033526)	6	NM_033526	94232	Mm.303059	NM_033526	ENSMUSG00000008604	Ubqln4	A1Up|A1u|AI663987|CIP75|UBIN	ubiquilin 4	protein-coding
mm_161342.1	chr14	52142714	52142714	+	1	NA	intron (NM_023879, intron 14 of 24)	PB1D9|SINE|Alu	31811	NM_023879	77945	Mm.21662	NM_023879	ENSMUSG00000057132	Rpgrip1	0610005A07Rik|4930401L23Rik|4930505G06Rik|A930002K18Rik|AA415034|nmf247	retinitis pigmentosa GTPase regulator interacting protein 1	protein-coding
mm_71966.1	chr8	70531519	70531546	+	1	NA	exon (NM_001199631, exon 5 of 9)	exon (NM_001199631, exon 5 of 9)	3686	NM_001199631	14232	Mm.141864	NM_010223	ENSMUSG00000019428	Fkbp8	38kDa|FKBP-38|FKBP-8|Fkbp38	FK506 binding protein 8	protein-coding
mm_83341.1	chr9	44288132	44288153	-	1	NA	5' UTR (NM_138955, exon 1 of 15)	5' UTR (NM_138955, exon 1 of 15)	102	NM_138955	192663	Mm.101876	NM_138955	ENSMUSG00000032131	Abcg4	6430517O04Rik	ATP-binding cassette, sub-family G (WHITE), member 4	protein-coding
mm_123967.1	chr14	75130587	75130605	-	1	NA	promoter-TSS (NM_001247984)	promoter-TSS (NM_001247984)	287	NM_027581	70859	Mm.320289	NM_027581	ENSMUSG00000021997	Lrrc63	4921509B22Rik	leucine rich repeat containing 63	protein-coding
mm_46511.1	chr5	105138615	105138642	-	1	NA	intron (NM_008620, intron 1 of 10)	L1M4|LINE|L1	924	NM_008620	17472	Mm.440525	NM_008620	ENSMUSG00000079363	Gbp4	AW228052|Mag-2|Mpa-2|Mpa2	guanylate binding protein 4	protein-coding
mm_119499.1	chr14	47380184	47380194	+	1	NA	exon (NM_010705, exon 3 of 6)	exon (NM_010705, exon 3 of 6)	6329	NM_001145953	16854	Mm.248615	NM_010705	ENSMUSG00000050335	Lgals3	GBP|L-34|Mac-2|gal3	lectin, galactose binding, soluble 3	protein-coding
mm_148063.1	chr18	72233605	72233649	-	1	NA	intron (NM_007831, intron 1 of 28)	L2|LINE|L2	117442	NM_007831	13176	Mm.167882	NM_007831	ENSMUSG00000060534	Dcc	C030036D22Rik|Igdcc1	deleted in colorectal carcinoma	protein-coding
mm_5063.1	chr1	194995511	194995520	+	1	NA	Intergenic	Intergenic	-18556	NR_033564	320400	Mm.417608	NR_033564	ENSMUSG00000097325	Gm16897	C030002c11rik	predicted gene, 16897	ncRNA
mm_110631.1	chr12	57543351	57543362	-	1	NA	exon (NM_008259, exon 2 of 2)	exon (NM_008259, exon 2 of 2)	2765	NM_008259	15375	Mm.4578	NM_008259	ENSMUSG00000035451	Foxa1	Hnf-3a|Hnf3a|Tcf-3a|Tcf3a	forkhead box A1	protein-coding
mm_4010.1	chr1	165236495	165236507	+	1	NA	intron (NM_145513, intron 1 of 6)	CpG	457	NM_145513	226591	Mm.21520	NM_145513	ENSMUSG00000040843	Tiprl	1810011K17Rik	TIP41, TOR signalling pathway regulator-like (S. cerevisiae)	protein-coding
mm_99064.1	chr11	99155314	99155322	+	1	NA	promoter-TSS (NM_007719)	promoter-TSS (NM_007719)	-241	NM_007719	12775	Mm.2932	NM_007719	ENSMUSG00000037944	Ccr7	CC-CKR-7|CCR-7|CD197|Cdw197|Cmkbr7|EBI1|Ebi1h	chemokine (C-C motif) receptor 7	protein-coding
mm_116063.1	chr13	27562542	27562552	-	1	NA	exon (NM_023332, exon 2 of 6)	exon (NM_023332, exon 2 of 6)	2059	NM_001316721	67310	Mm.46091	NM_023332	ENSMUSG00000006490	Prl8a9	1600019F10Rik|Ghd15|PLP-C2|PLP-Cbeta|Prlpc2	prolactin family8, subfamily a, member 9	protein-coding
mm_164840.1	chr18	42173318	42173323	+	1	NA	Intergenic	Intergenic	23389	NM_027072	69401	Mm.34841	NM_027072	ENSMUSG00000059455	Plac8l1	1700009N18Rik|1700015M15Rik	PLAC8-like 1	protein-coding
mm_33591.1	chr4	132563719	132563737	+	1	NA	promoter-TSS (NM_001081211)	promoter-TSS (NM_001081211)	-339	NM_001081211	19204	Mm.89389	NM_001081211	ENSMUSG00000056529	Ptafr	PAFR	platelet-activating factor receptor	protein-coding
mm_123017.1	chr14	55116166	55116190	-	1	NA	5' UTR (NM_177049, exon 1 of 6)	5' UTR (NM_177049, exon 1 of 6)	757	NM_177049	319984	Mm.19047	NM_177049	ENSMUSG00000022208	Jph4	9330157P13Rik|JP-4|JPHL1	junctophilin 4	protein-coding
mm_116729.1	chr13	51729083	51729099	-	1	NA	intron (NM_013660, intron 2 of 15)	intron (NM_013660, intron 2 of 15)	64656	NM_001281880	20354	Mm.33903	NM_013660	ENSMUSG00000021451	Sema4d	CD100|Semacl2|Semaj|Semcl2|coll-4	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D	protein-coding
mm_76433.1	chr8	84981055	84981076	-	1	NA	Intergenic	Intergenic	-2317	NM_008416	16477	Mm.1167	NM_008416	ENSMUSG00000052837	Junb	-	jun B proto-oncogene	protein-coding
mm_66685.1	chr7	45824716	45824740	-	1	NA	promoter-TSS (NM_145963)	promoter-TSS (NM_145963)	19	NM_145963	211480	Mm.68170	NM_145963	ENSMUSG00000058743	Kcnj14	A930026G01Rik|IRK4|Kir2.4	potassium inwardly-rectifying channel, subfamily J, member 14	protein-coding
mm_15165.1	chr2	154011413	154011418	+	1	NA	exon (NM_008953, exon 5 of 9)	exon (NM_008953, exon 5 of 9)	3139	NM_008953	19194	Mm.29197	NM_008953	ENSMUSG00000042459	Bpifa2	Bpifa2e|Psp	BPI fold containing family A, member 2	protein-coding
mm_80385.1	chr9	75468560	75468585	+	1	NA	Intergenic	Intergenic	27048	NM_001039522	235497	Mm.41508	NM_001006122	ENSMUSG00000042487	Leo1	Gm185	Leo1, Paf1/RNA polymerase II complex component	protein-coding
mm_99434.1	chr11	102432556	102432581	+	1	NA	intron (NM_008175, intron 1 of 12)	intron (NM_008175, intron 1 of 12)	2246	NM_008175	14824	Mm.1568	NM_008175	ENSMUSG00000034708	Grn	Pgrn|epithelin	granulin	protein-coding
mm_88269.1	chr10	74967085	74967098	+	1	NA	promoter-TSS (NM_010311)	promoter-TSS (NM_010311)	-140	NM_010311	14687	Mm.32595	NM_010311	ENSMUSG00000040009	Gnaz	AI847979|Gz	guanine nucleotide binding protein, alpha z subunit	protein-coding
mm_49635.1	chr6	30804984	30805006	+	1	NA	intron (NM_017478, intron 20 of 23)	intron (NM_017478, intron 20 of 23)	63696	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_136481.1	chr16	96017799	96017806	-	1	NA	intron (NM_001103179, intron 34 of 40)	(A)n|Simple_repeat|Simple_repeat	-26899	NM_019537	56088	Mm.396248	NM_019537	ENSMUSG00000022913	Psmg1	AW552102|Dscr2	proteasome (prosome, macropain) assembly chaperone 1	protein-coding
mm_102860.1	chr11	69399603	69399606	-	1	NA	3' UTR (NM_001017426, exon 23 of 23)	3' UTR (NM_001017426, exon 23 of 23)	-1370	NM_025915	67020	Mm.390406	NM_025915	ENSMUSG00000045377	Tmem88	2600017H02Rik	transmembrane protein 88	protein-coding
mm_47810.1	chr5	133790845	133790851	-	1	NA	Intergenic	Intergenic	-308900	NM_030719	80909	Mm.45218	NM_030719	ENSMUSG00000015944	Gatsl2	7530428J21Rik|AW742413|Gats|Gatsl1	GATS protein-like 2	protein-coding
mm_122141.1	chr14	31182769	31182778	-	1	NA	TTS (NM_001347583)	TTS (NM_001347583)	-14132	NM_138672	192187	Mm.220821	NM_138672	ENSMUSG00000042286	Stab1	FEEL-1|FELE-1|MFEEL-1|MS-1|STAB-1|mKIAA0246	stabilin 1	protein-coding
mm_125566.1	chr15	59275380	59275392	+	1	NA	Intergenic	Intergenic	-31562	NR_045613	100416830	Mm.490788	NR_045613	ENSMUSG00000098528	Zfp572	4930472F24Rik	zinc finger protein 572	pseudo
mm_11222.1	chr2	29761607	29761611	+	1	NA	promoter-TSS (NM_001177392)	promoter-TSS (NM_001177392)	81	NM_001177392	433416	Mm.330112	NM_001034887	ENSMUSG00000075425	Gm13547	OTTMUSG00000012686	predicted gene 13547	protein-coding
mm_104453.1	chr11	95041277	95041297	-	1	NA	promoter-TSS (NM_133667)	promoter-TSS (NM_133667)	84	NM_133667	18604	Mm.29768	NM_133667	ENSMUSG00000038967	Pdk2	-	pyruvate dehydrogenase kinase, isoenzyme 2	protein-coding
mm_4134.1	chr1	170644450	170644458	+	1	NA	promoter-TSS (NM_177068)	promoter-TSS (NM_177068)	-78	NM_177068	320078	Mm.287131	NM_177068	ENSMUSG00000038463	Olfml2b	1110018N05Rik|4832415H08Rik|AI467542	olfactomedin-like 2B	protein-coding
mm_67162.1	chr7	73543627	73543656	-	1	NA	non-coding (NR_037569, exon 5 of 5)	non-coding (NR_037569, exon 5 of 5)	-1895	NM_001081345	244059	Mm.34539	NM_001081345	ENSMUSG00000078671	Chd2	2810013C04Rik|2810040A01Rik|5630401D06Rik|AI851092|BC029703|CHD-2	chromodomain helicase DNA binding protein 2	protein-coding
mm_20522.1	chr2	130840051	130840054	-	1	NA	promoter-TSS (NM_001311147)	promoter-TSS (NM_001311147)	93	NM_029432	228602	Mm.271990	NM_028367	ENSMUSG00000027309	4930402H24Rik	2810487F15Rik|AI413763|C78926	RIKEN cDNA 4930402H24 gene	protein-coding
mm_47722.1	chr5	130013993	130014032	-	1	NA	exon (NM_133768, exon 10 of 17)	exon (NM_133768, exon 10 of 17)	10319	NM_133768	109900	Mm.23869	NM_133768	ENSMUSG00000025533	Asl	2510006M18Rik	argininosuccinate lyase	protein-coding
mm_147700.1	chr18	60808078	60808084	-	1	NA	intron (NM_001042605, intron 2 of 8)	intron (NM_001042605, intron 2 of 8)	-3995	NR_039567	100628611		NR_039567	ENSMUSG00000093327	Mir5107	mir-5107|mmu-mir-5107|mu-mir-5107	microRNA 5107	ncRNA
mm_134448.1	chr16	18343883	18343932	-	1	NA	promoter-TSS (NM_138583)	promoter-TSS (NM_138583)	25	NM_138583	27883	Mm.265990	NM_138583	ENSMUSG00000013539	Tango2	D16H22S680E|T10	transport and golgi organization 2	protein-coding
mm_77120.1	chr8	111281496	111281499	-	1	NA	intron (NM_146218, intron 8 of 12)	intron (NM_146218, intron 8 of 12)	18725	NM_146218	234736	Mm.334816	NM_146218	ENSMUSG00000033596	Rfwd3	BC027246	ring finger and WD repeat domain 3	protein-coding
mm_167377.1	chr8	92251254	92251259	-	1	NA	Intergenic	URR1B|DNA|hAT-Charlie	104864	NR_110452	71296	Mm.86664	NR_033641	ENSMUSG00000031736	Crnde	4933436C20Rik	colorectal neoplasia differentially expressed (non-protein coding)	ncRNA
mm_23105.1	chr3	37420258	37420272	+	1	NA	promoter-TSS (NM_001291044)	promoter-TSS (NM_001291044)	315	NM_021343	57815	Mm.172679	NM_021343	ENSMUSG00000027722	Spata5	2510048F20Rik|C78064|Spaf	spermatogenesis associated 5	protein-coding
mm_12683.1	chr2	75870715	75870718	+	1	NA	intron (NM_172666, intron 10 of 19)	B1_Mur2|SINE|Alu	38539	NM_172666	228061	Mm.31227	NM_172666	ENSMUSG00000042410	Agps	5832437L22|9930035G10Rik|AW123847|Adaps|Adas|Adhaps|Adps|Aldhpsy|bs2	alkylglycerone phosphate synthase	protein-coding
mm_46264.1	chr5	99729216	99729227	-	1	NA	promoter-TSS (NR_030692)	promoter-TSS (NR_030692)	-161	NR_030692	319818	Mm.295233	NR_030692	ENSMUSG00000089809	A930011G23Rik	-	RIKEN cDNA A930011G23 gene	ncRNA
mm_85611.1	chr9	107605296	107605331	-	1	NA	promoter-TSS (NM_009153)	promoter-TSS (NM_009153)	89	NM_009153	20347	Mm.4083	NM_009153	ENSMUSG00000057969	Sema3b	SemA|Semaa|sema5|semaV	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B	protein-coding
mm_29488.1	chr3	115714934	115714947	-	1	NA	5' UTR (NM_007901, exon 1 of 2)	5' UTR (NM_007901, exon 1 of 2)	115	NM_007901	13609	Mm.982	NM_007901	ENSMUSG00000045092	S1pr1	AI849002|Edg1|Lpb1|S1p|S1p1	sphingosine-1-phosphate receptor 1	protein-coding
mm_157793.1	chrX	73854583	73854603	-	1	NA	3' UTR (NM_008478, exon 29 of 29)	3' UTR (NM_008478, exon 29 of 29)	26241	NM_008478	16728	Mm.260568	NM_008478	ENSMUSG00000031391	L1cam	CD171|L1|N-CAM-L1|NCAM-L1	L1 cell adhesion molecule	protein-coding
mm_73145.1	chr8	94985441	94985451	+	1	NA	intron (NM_018882, intron 1 of 13)	intron (NM_018882, intron 1 of 13)	1047	NM_018882	14766	Mm.290834	NM_018882	ENSMUSG00000031785	Adgrg1	Cyt28|Gpr56|TM7LN4|TM7XN1	adhesion G protein-coupled receptor G1	protein-coding
mm_10988.1	chr2	26294707	26294723	+	1	NA	promoter-TSS (NM_177841)	promoter-TSS (NM_177841)	-158	NM_177841	329366	Mm.77712	NM_177841	ENSMUSG00000048038	Ccdc187	4932418E24Rik	coiled-coil domain containing 187	protein-coding
mm_92070.1	chr10	62578459	62578463	-	1	NA	promoter-TSS (NM_028197)	promoter-TSS (NM_028197)	-4	NM_028197	72320	Mm.258955	NM_028197	ENSMUSG00000036955	Kif1bp	0710007C18Rik|2510003E04Rik|KBP|mKIAA1279	KIF1 binding protein	protein-coding
mm_125493.1	chr15	55112332	55112346	+	1	NA	promoter-TSS (NM_145470)	promoter-TSS (NM_145470)	22	NM_145470	97998	Mm.295397	NM_145470	ENSMUSG00000022419	Deptor	Depdc6	DEP domain containing MTOR-interacting protein	protein-coding
mm_84389.1	chr9	65423093	65423105	-	1	NA	promoter-TSS (NM_178933)	promoter-TSS (NM_178933)	-326	NM_178933	330962	Mm.335247	NM_178933	ENSMUSG00000053862	Slc51b	Ostb	solute carrier family 51, beta subunit	protein-coding
mm_41749.1	chr5	102845139	102845146	+	1	NA	5' UTR (NM_001346585, exon 1 of 7)	5' UTR (NM_001346585, exon 1 of 7)	135	NM_001346585	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding
mm_39860.1	chr5	30968605	30968615	+	1	NA	promoter-TSS (NM_053085)	promoter-TSS (NM_053085)	-67	NM_053085	69852	Mm.57874	NM_053085	ENSMUSG00000006642	Tcf23	2010002O16Rik|Out|bHLHa24	transcription factor 23	protein-coding
mm_897.1	chr1	53313637	53313682	+	1	NA	promoter-TSS (NM_001285839)	promoter-TSS (NM_001285839)	35	NR_104360	72085	Mm.482256	NM_028091	ENSMUSG00000026096	Osgepl1	2610001M19Rik|AA416452	O-sialoglycoprotein endopeptidase-like 1	protein-coding
mm_5361.1	chr1	25829719	25829742	-	1	NA	promoter-TSS (NM_175642)	promoter-TSS (NM_175642)	-23	NM_175642	210933	Mm.336569	NM_175642	ENSMUSG00000033569	Adgrb3	A830096D10Rik|Bai3	adhesion G protein-coupled receptor B3	protein-coding
mm_82968.1	chr9	35777923	35777932	-	1	NA	5' UTR (NM_001167673, exon 1 of 3)	5' UTR (NM_001167673, exon 1 of 3)	182	NM_001167673	100312986	Mm.437659	NM_001167673	ENSMUSG00000090738	Gm17727	Pate-e|Pate7	predicted gene, 17727	protein-coding
mm_4423.1	chr1	172501945	172501989	+	1	NA	intron (NM_178598, intron 1 of 4)	intron (NM_178598, intron 1 of 4)	1721	NM_178598	21346	Mm.271711	NM_178598	ENSMUSG00000026547	Tagln2	2700094C18Rik|SM22beta|Sm22B|Sm22a	transgelin 2	protein-coding
mm_96296.1	chr11	63133137	63133145	+	1	NA	5' UTR (NM_008885, exon 2 of 5)	5' UTR (NM_008885, exon 2 of 5)	338	NM_001302260	18858	Mm.1237	NM_008885	ENSMUSG00000018217	Pmp22	22kDa|Gas-3|HNPP|Tr|trembler	peripheral myelin protein 22	protein-coding
mm_131494.1	chr16	17303277	17303280	+	1	NA	intron (NM_001001983, intron 33 of 54)	intron (NM_001001983, intron 33 of 54)	26978	NM_177473	224019	Mm.246388	NM_177473	ENSMUSG00000055692	Tmem191c	4933405M22Rik|D16Bwg1494e|MNCb-4137	transmembrane protein 191C	protein-coding
mm_124361.1	chr14	105177264	105177277	-	1	NA	promoter-TSS (NM_134077)	promoter-TSS (NM_134077)	57	NM_134077	74213	Mm.474531	NM_134077	ENSMUSG00000022119	Rbm26	1700009P03Rik|AI447318|C230097K14Rik|C86225|MLZ-393|Pro1777|Se70-2	RNA binding motif protein 26	protein-coding
mm_18600.1	chr2	67194696	67194736	-	1	NA	Intergenic	Intergenic	20882	NM_001033477	383709	Mm.244520	NM_001033477		Gm1322	-	predicted gene 1322	protein-coding
mm_171950.1	chr5	76959443	76959454	+	1	NA	exon (NM_025939, exon 3 of 9)	exon (NM_025939, exon 3 of 9)	-7870	NM_172146	231327	Mm.202337	NM_172146	ENSMUSG00000029246	Ppat	5730454C12Rik|AA408689|AA675351|AI507113|C79945	phosphoribosyl pyrophosphate amidotransferase	protein-coding
mm_139706.1	chr17	57455867	57455890	+	1	NA	intron (NM_010130, intron 17 of 21)	Lx3A|LINE|L1	89436	NM_001104591	224916	Mm.469889	NM_001104591	ENSMUSG00000090655	Vmn2r120	EG224916	vomeronasal 2, receptor 120	protein-coding
mm_75226.1	chr8	39618400	39618427	-	1	NA	intron (NM_001113326, intron 5 of 9)	intron (NM_001113326, intron 5 of 9)	24265	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_2874.1	chr1	131797427	131797431	+	1	NA	promoter-TSS (NM_178079)	promoter-TSS (NM_178079)	34	NM_178079	212933	Mm.23844	NM_178079	ENSMUSG00000042251	Pm20d1	4732466D17Rik|AI098026	peptidase M20 domain containing 1	protein-coding
mm_122716.1	chr14	52262871	52262898	-	1	NA	3' UTR (NM_172601, exon 8 of 8)	3' UTR (NM_172601, exon 8 of 8)	-16262	NM_023434	268741	Mm.246237	NM_023434	ENSMUSG00000016831	Tox4	5730589K01Rik|A630040M18|AA410149|LCP1	TOX high mobility group box family member 4	protein-coding
mm_119874.1	chr14	54686983	54687063	+	1	NA	promoter-TSS (NM_023190)	promoter-TSS (NM_023190)	-92	NM_023190	56215	Mm.297078	NM_019567	ENSMUSG00000022185	Acin1	2610036I19Rik|2610510L13Rik|Acinus|Acn|C79325|acinusL|acinusS|mKIAA0670	apoptotic chromatin condensation inducer 1	protein-coding
mm_120978.1	chr14	78699476	78699480	+	1	NA	intron (NM_001081336, intron 1 of 28)	intron (NM_001081336, intron 1 of 28)	25611	NM_001081336	380921	Mm.89591	NM_001081336	ENSMUSG00000034731	Dgkh	5930402B05Rik|D130015C16|DGK	diacylglycerol kinase, eta	protein-coding
mm_45744.1	chr5	86591434	86591472	-	1	NA	5' UTR (NM_178730, exon 2 of 11)	5' UTR (NM_178730, exon 2 of 11)	40971	NM_178730	243083	Mm.106867	NM_178730	ENSMUSG00000048764	Tmprss11f	4631408C20|4732406D01Rik	transmembrane protease, serine 11f	protein-coding
mm_56551.1	chr6	100287445	100287465	-	1	NA	promoter-TSS (NM_019743)	promoter-TSS (NM_019743)	-97	NM_019743	56353	Mm.321633	NM_019743	ENSMUSG00000072872	Rybp	2410018J24Rik|DEDAF|YEAF1	RING1 and YY1 binding protein	protein-coding
mm_47344.1	chr5	122520807	122520810	-	1	NA	Intergenic	Intergenic	-18583	NR_027838	11938	Mm.227583	NM_009722	ENSMUSG00000029467	Atp2a2	9530097L16Rik|D5Wsu150e|SERCA2|SERCA2B|Serca2a|mKIAA4195	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	protein-coding
mm_84643.1	chr9	71215373	71215389	-	1	NA	promoter-TSS (NM_009022)	promoter-TSS (NM_009022)	5	NR_110518	100041660	Mm.487231	NR_110518		Gm3458	-	predicted gene 3458	ncRNA
mm_137345.1	chr17	25145567	25145615	+	1	NA	exon (NM_011930, exon 3 of 25)	exon (NM_011930, exon 3 of 25)	8960	NM_001317404	26373	Mm.270587	NM_011930	ENSMUSG00000036636	Clcn7	ClC-7|D17Wsu51e	chloride channel, voltage-sensitive 7	protein-coding
mm_81718.1	chr9	111439099	111439133	+	1	NA	promoter-TSS (NM_172928)	promoter-TSS (NM_172928)	35	NM_172928	245038	Mm.26361	NM_172928	ENSMUSG00000032500	Dclk3	BC056929|C730036H08|Dcamkl3	doublecortin-like kinase 3	protein-coding
mm_110884.1	chr12	75221388	75221388	-	1	NA	Intergenic	RMER1B|Other|Other	-44056	NM_172805	238271	Mm.44465	NM_172805	ENSMUSG00000034402	Kcnh5	Eag2	potassium voltage-gated channel, subfamily H (eag-related), member 5	protein-coding
mm_79001.1	chr9	45409985	45410068	+	1	NA	non-coding (NR_028499, exon 6 of 6)	non-coding (NR_028499, exon 6 of 6)	3949	NM_007503	11936	Mm.22742	NM_007503	ENSMUSG00000059412	Fxyd2	Atp1g1	FXYD domain-containing ion transport regulator 2	protein-coding
mm_35003.1	chr4	156215921	156215944	+	1	NA	promoter-TSS (NM_172417)	promoter-TSS (NM_172417)	5	NM_172417	74183	Mm.431343	NM_172417	ENSMUSG00000078486	Perm1	2310042D19Rik	PPARGC1 and ESRR induced regulator, muscle 1	protein-coding
mm_140567.1	chr17	8565535	8565567	-	1	NA	intron (NM_001290707, intron 1 of 22)	(CAAAA)n|Simple_repeat|Simple_repeat	38750	NM_001290707	23984	Mm.87161	NM_011866	ENSMUSG00000023868	Pde10a	-	phosphodiesterase 10A	protein-coding
mm_139822.1	chr17	67722354	67722379	+	1	NA	intron (NM_008480, intron 3 of 62)	intron (NM_008480, intron 3 of 62)	25101	NM_008480	16772	Mm.303386	NM_008480	ENSMUSG00000032796	Lama1	AA408497|Lama	laminin, alpha 1	protein-coding
mm_88421.1	chr10	77202178	77202187	+	1	NA	Intergenic	Intergenic	-35652	NM_009929	12822	Mm.4352	NM_009929	ENSMUSG00000001435	Col18a1	-	collagen, type XVIII, alpha 1	protein-coding
mm_9971.1	chr1	191186458	191186492	-	1	NA	Intergenic	Intergenic	-3142	NM_007498	11910	Mm.2706	NM_007498	ENSMUSG00000026628	Atf3	LRG-21	activating transcription factor 3	protein-coding
mm_135560.1	chr16	50046284	50046294	-	1	NA	intron (NR_045935, intron 1 of 3)	intron (NR_045935, intron 1 of 3)	26563	NR_045935	224180	Mm.146439	NM_175010		Gm4827	B130050K08|EG224180	predicted gene 4827	ncRNA
mm_128206.1	chr15	36054844	36054869	-	1	NA	exon (NM_001195748, exon 15 of 28)	exon (NM_001195748, exon 15 of 28)	85544	NM_001195748	626596	Mm.321798	NM_001195748	ENSMUSG00000037627	Rgs22	-	regulator of G-protein signalling 22	protein-coding
mm_97818.1	chr11	82963307	82963315	+	1	NA	3' UTR (NM_183201, exon 6 of 6)	3' UTR (NM_183201, exon 6 of 6)	-2630	NR_045932	76392	Mm.295205	NR_045932	ENSMUSG00000086327	Slfn5os	1700003F17Rik	schlafen 5, opposite strand	ncRNA
mm_121120.1	chr14	101840502	101840554	+	1	NA	promoter-TSS (NM_001347628)	promoter-TSS (NM_001347628)	-95	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_79385.1	chr9	54772889	54772894	+	1	NA	3' UTR (NM_001284507, exon 3 of 3)	3' UTR (NM_001284507, exon 3 of 3)	8143	NM_013496	12903	Mm.34797	NM_013496	ENSMUSG00000032291	Crabp1	AI326249|CRABP-I|Crabp-1|CrabpI|Rbp-5	cellular retinoic acid binding protein I	protein-coding
mm_21005.1	chr2	152344044	152344068	-	1	NA	promoter-TSS (NM_175093)	promoter-TSS (NM_175093)	4	NM_175093	228775	Mm.276018	NM_144554	ENSMUSG00000032715	Trib3	Ifld2|Nipk|SINK|SKIP3|TRB-3|Trb3	tribbles pseudokinase 3	protein-coding
mm_154112.1	chr19	57134787	57134821	-	1	NA	intron (NM_001290813, intron 4 of 20)	intron (NM_001290813, intron 4 of 20)	-15780	NM_001103178	226251	Mm.217161	NM_178688	ENSMUSG00000025085	Ablim1	2210411C18Rik|2610209L21Rik|4833406P10Rik|9330196J19Rik|AV079770|AW060987|AW215784|Limab1|mKIAA0059	actin-binding LIM protein 1	protein-coding
mm_151857.1	chr19	5796925	5796964	-	1	NA	promoter-TSS (NR_144621)	promoter-TSS (NR_144621)	-963	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_157915.1	chrX	78552794	78552813	-	1	NA	intron (NM_027322, intron 1 of 3)	RLTR14-int|LTR|ERV1	31002	NM_001164275	546336	Mm.211712	NM_027322	ENSMUSG00000047996	Prrg1	2010007L08Rik	proline rich Gla (G-carboxyglutamic acid) 1	protein-coding
mm_84750.1	chr9	75422402	75422445	-	1	NA	Intergenic	ERV3-16A3_I-int|LTR|ERVL	12239	NR_040719	71274	Mm.399152	NR_040719	ENSMUSG00000097021	4933433G15Rik	4921522K19Rik	RIKEN cDNA 4933433G15 gene	ncRNA
mm_55350.1	chr6	56797762	56797786	-	1	NA	promoter-TSS (NM_145958)	promoter-TSS (NM_145958)	39	NM_145958	210973	Mm.57295	NM_145958	ENSMUSG00000059486	Kbtbd2	BC022962|Bklhd1|mKIAA1489	kelch repeat and BTB (POZ) domain containing 2	protein-coding
mm_93253.1	chr10	95501958	95501966	-	1	NA	promoter-TSS (NM_026065)	promoter-TSS (NM_026065)	-35	NM_026065	67270	Mm.30008	NM_026065	ENSMUSG00000062981	Mrpl42	2700009F22Rik|2900055D03Rik|D10Ertd322e|HSPC204|L31mt|MRP-L31|PTD007|Rpml31	mitochondrial ribosomal protein L42	protein-coding
mm_157880.1	chrX	75842975	75842993	-	1	NA	promoter-TSS (NM_001346520)	promoter-TSS (NM_001346520)	37	NM_001166454	102866	Mm.28777	NM_145629	ENSMUSG00000016382	Pls3	AI115446|AL024105	plastin 3 (T-isoform)	protein-coding
mm_26923.1	chr3	20249610	20249635	-	1	NA	3' UTR (NM_029706, exon 11 of 11)	3' UTR (NM_029706, exon 11 of 11)	-7441	NM_007753	12873	Mm.1135	NM_007753	ENSMUSG00000001865	Cpa3	MC-CPA	carboxypeptidase A3, mast cell	protein-coding
mm_143467.1	chr17	71002489	71002592	-	1	NA	promoter-TSS (NM_026064)	promoter-TSS (NM_026064)	-7	NM_026064	67268	Mm.489605	NM_026064	ENSMUSG00000024048	Myl12a	2900073G15Rik|AI838292|C80200	myosin, light chain 12A, regulatory, non-sarcomeric	protein-coding
mm_69974.1	chr7	142377098	142377114	-	1	NA	exon (NM_009983, exon 7 of 9)	exon (NM_009983, exon 7 of 9)	-3360	NM_001347541	320802	Mm.154486	NM_177265	ENSMUSG00000045777	Ifitm10	6330512M04Rik|AI848576|DSPA3	interferon induced transmembrane protein 10	protein-coding
mm_18760.1	chr2	73453870	73453884	-	1	NA	promoter-TSS (NM_001289722)	promoter-TSS (NM_001289722)	12	NM_001289722	215280	Mm.223504	NM_153138	ENSMUSG00000075284	Wipf1	AI115543|D2Ertd120e|WIP|Waspip	WAS/WASL interacting protein family, member 1	protein-coding
mm_52049.1	chr6	97210738	97210749	+	1	NA	promoter-TSS (NM_022992)	promoter-TSS (NM_022992)	-49	NM_022992	65106	Mm.291014	NM_022992	ENSMUSG00000035199	Arl6ip5	5930404D22Rik|AV001879|Aip-5|Gtrap3-18|addiscin	ADP-ribosylation factor-like 6 interacting protein 5	protein-coding
mm_102377.1	chr11	58801972	58801979	-	1	NA	promoter-TSS (NM_001162878)	promoter-TSS (NM_001162878)	-15	NM_029283	75429	Mm.296819	NM_029283	ENSMUSG00000049154	Fam183b	3100002J23Rik|Theg6	family with sequence similarity 183, member B	protein-coding
mm_34296.1	chr4	141623277	141623285	+	1	NA	exon (NM_001013780, exon 1 of 5)	exon (NM_001013780, exon 1 of 5)	553	NM_001013780	384071	Mm.295682	NM_001013780	ENSMUSG00000040740	Slc25a34	Gm1369	solute carrier family 25, member 34	protein-coding
mm_741.1	chr1	43494770	43494771	+	1	NA	intron (NM_010879, intron 1 of 4)	intron (NM_010879, intron 1 of 4)	49019	NM_010879	17974	Mm.389903	NM_010879	ENSMUSG00000066877	Nck2	4833426I10Rik|Grb4|NCKbeta|Nck-2	non-catalytic region of tyrosine kinase adaptor protein 2	protein-coding
mm_50726.1	chr6	52245996	52246012	+	1	NA	promoter-TSS (NM_010450)	promoter-TSS (NM_010450)	-194	NM_010450	15396	Mm.26954	NM_010450	ENSMUSG00000038210	Hoxa11	Hox-1.9|Hoxa-11	homeobox A11	protein-coding
mm_76651.1	chr8	93187802	93187804	-	1	NA	exon (NM_053200, exon 5 of 14)	exon (NM_053200, exon 5 of 14)	10001	NM_053200	104158	Mm.292803	NM_053200	ENSMUSG00000056973	Ces1d	Ces3|TGH	carboxylesterase 1D	protein-coding
mm_122427.1	chr14	44989674	44989679	-	1	NA	exon (NM_008964, exon 1 of 2)	exon (NM_008964, exon 1 of 2)	1565	NM_008964	19217	Mm.4630	NM_008964	ENSMUSG00000037759	Ptger2	EP2|Ptgerep2	prostaglandin E receptor 2 (subtype EP2)	protein-coding
mm_77845.1	chr9	5299477	5299501	+	1	NA	exon (NM_009807, exon 2 of 10)	exon (NM_009807, exon 2 of 10)	972	NM_009807	12362	Mm.1051	NM_009807	ENSMUSG00000025888	Casp1	ICE|Il1bc	caspase 1	protein-coding
mm_171770.1	chr5	108517106	108517114	+	1	NA	Intergenic	RLTR31A_Mm|LTR|ERVK	32917	NM_007756	12889	Mm.5195	NM_007756	ENSMUSG00000033615	Cplx1	921-S	complexin 1	protein-coding
mm_139819.1	chr17	67697228	67697246	+	1	NA	promoter-TSS (NM_008480)	promoter-TSS (NM_008480)	-28	NM_008480	16772	Mm.303386	NM_008480	ENSMUSG00000032796	Lama1	AA408497|Lama	laminin, alpha 1	protein-coding
mm_99710.1	chr11	106216997	106217008	+	1	NA	promoter-TSS (NM_026009)	promoter-TSS (NM_026009)	76	NM_028074	72047	Mm.41367	NM_028074	ENSMUSG00000020705	Ddx42	1810047H21Rik|AW319508|AW556242|B430002H05Rik|RHELP|RNAHP|SF3b125	DEAD (Asp-Glu-Ala-Asp) box polypeptide 42	protein-coding
mm_127090.1	chr15	97784366	97784457	+	1	NA	promoter-TSS (NM_026353)	promoter-TSS (NM_026353)	46	NM_026353	67739	Mm.28955	NM_026353	ENSMUSG00000081534	Slc48a1	4930570C03Rik	solute carrier family 48 (heme transporter), member 1	protein-coding
mm_131169.1	chr16	7039894	7039924	+	1	NA	intron (NM_021477, intron 5 of 16)	intron (NM_021477, intron 5 of 16)	-29926	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_96033.1	chr11	59556229	59556239	+	1	NA	intron (NM_145827, intron 6 of 9)	intron (NM_145827, intron 6 of 9)	13548	NM_145827	216799	Mm.54174	NM_145827	ENSMUSG00000032691	Nlrp3	AGTAVPRL|AII/AVP|Cias1|FCAS|FCU|MWS|Mmig1|NALP3|Pypaf1	NLR family, pyrin domain containing 3	protein-coding
mm_4093.1	chr1	167308719	167308807	+	1	NA	promoter-TSS (NM_001039483)	promoter-TSS (NM_001039483)	93	NM_001039483	68944	Mm.330045	NM_026881	ENSMUSG00000052428	Tmco1	1190006A08Rik|4930403O06Rik|AA109065|AU022572|ESTM39	transmembrane and coiled-coil domains 1	protein-coding
mm_5924.1	chr1	55226461	55226521	-	1	NA	5' UTR (NM_028713, exon 1 of 9)	5' UTR (NM_028713, exon 1 of 9)	291	NM_028713	74013	Mm.292050	NM_028713	ENSMUSG00000025978	Rftn2	2700010E02Rik|3222401M22Rik	raftlin family member 2	protein-coding
mm_100413.1	chr11	119426091	119426099	+	1	NA	Intergenic	Intergenic	35623	NR_035453	100316690		NR_035453	ENSMUSG00000088015	Mir1932	mir-1932|mmu-mir-1932	microRNA 1932	ncRNA
mm_74889.1	chr8	25102544	25102570	-	1	NA	promoter-TSS (NM_031257)	promoter-TSS (NM_031257)	-746	NM_031257	83436	Mm.261122	NM_031257	ENSMUSG00000031557	Plekha2	6430512N22Rik|AI851530|AU041791|TAPP2|W91773	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 2	protein-coding
mm_70127.1	chr7	143094006	143094041	-	1	NA	intron (NM_020277, intron 1 of 24)	intron (NM_020277, intron 1 of 24)	619	NM_020277	56843	Mm.286668	NM_020277	ENSMUSG00000009246	Trpm5	9430099A16Rik|LTrpC-5|Ltrpc5|Mtr1	transient receptor potential cation channel, subfamily M, member 5	protein-coding
mm_35279.1	chr4	20778528	20778593	-	1	NA	5' UTR (NM_172987, exon 1 of 5)	5' UTR (NM_172987, exon 1 of 5)	108	NM_001290410	269513	Mm.317473	NM_172987	ENSMUSG00000055761	Nkain3	C530048M05|E130310K16Rik	Na+/K+ transporting ATPase interacting 3	protein-coding
mm_30610.1	chr4	6688147	6688193	+	1	NA	3' UTR (NM_145711, exon 9 of 9)	3' UTR (NM_145711, exon 9 of 9)	-233899	NM_010945	18201	Mm.3059	NM_010945	ENSMUSG00000028245	Nsmaf	AA959567|C630007J05|Fan	neutral sphingomyelinase (N-SMase) activation associated factor	protein-coding
mm_164479.1	chr16	73678901	73678902	+	1	NA	Intergenic	Intergenic	663166	NR_030464	751561		NR_030464	ENSMUSG00000104758	Mir691	Mirn691|mir-691|mmu-mir-691	microRNA 691	ncRNA
mm_134353.1	chr16	16600534	16600576	-	1	NA	promoter-TSS (NM_001301817)	promoter-TSS (NM_001301817)	-577	NM_001301817	224014	Mm.256131	NM_139232	ENSMUSG00000022788	Fgd4	9030023J02Rik|9330209B17Rik|Frabp|ZFYVE6	FYVE, RhoGEF and PH domain containing 4	protein-coding
mm_63797.1	chr7	132931167	132931185	+	1	NA	Intergenic	CpG	-18446	NM_207302	360216	Mm.389984	NM_207302	ENSMUSG00000030967	Zranb1	9330160G10Rik|D7Wsu87e|Gm1956|Trabid	zinc finger, RAN-binding domain containing 1	protein-coding
mm_67757.1	chr7	92669889	92669912	-	1	NA	promoter-TSS (NM_029078)	promoter-TSS (NM_029078)	12	NM_029078	74737	Mm.288645	NM_029078	ENSMUSG00000041328	Pcf11	2500001H09Rik|5730417B17Rik|C77803	PCF11 cleavage and polyadenylation factor subunit	protein-coding
mm_81417.1	chr9	109055103	109055114	+	1	NA	intron (NM_026381, intron 1 of 3)	intron (NM_026381, intron 1 of 3)	242	NM_026381	66940	Mm.196533	NM_025858	ENSMUSG00000025647	Shisa5	2310008D10Rik|6430628I05Rik|Scotin|mShisa5	shisa family member 5	protein-coding
mm_125052.1	chr15	25843286	25843345	+	1	NA	promoter-TSS (NM_001034851)	promoter-TSS (NM_001034851)	17	NM_001034851	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_96646.1	chr11	69340449	69340457	+	1	NA	promoter-TSS (NR_027827)	promoter-TSS (NR_027827)	-316	NR_027827	80515	Mm.5324	NM_020591	ENSMUSG00000043419	Chd3os	2310043C11Rik|A030009H04Rik|AA589459|AB041807|MNCb-2875|RNF21	chromodomain helicase DNA binding protein 3, opposite strand	ncRNA
mm_102578.1	chr11	61720796	61720803	-	1	NA	promoter-TSS (NM_001033227)	promoter-TSS (NM_001033227)	0	NM_001033227	109342	Mm.441070	NM_001033227	ENSMUSG00000042371	Slc5a10	C330021F16Rik|SGLT5	solute carrier family 5 (sodium/glucose cotransporter), member 10	protein-coding
mm_97924.1	chr11	83588388	83588402	+	1	NA	3' UTR (NM_009139, exon 4 of 4)	3' UTR (NM_009139, exon 4 of 4)	4692	NM_009139	20305	Mm.137	NM_009139	ENSMUSG00000018927	Ccl6	MRP-1|Scya6|c10	chemokine (C-C motif) ligand 6	protein-coding
mm_103793.1	chr11	82871088	82871098	-	1	NA	promoter-TSS (NM_001164570)	promoter-TSS (NM_001164570)	117	NM_001007465	67338	Mm.341608	NM_026097	ENSMUSG00000020696	Rffl	1700051E09Rik|4930516L10Rik|BG080975|Carp2	ring finger and FYVE like domain containing protein	protein-coding
mm_71033.1	chr8	33652493	33652528	+	1	NA	promoter-TSS (NM_010344)	promoter-TSS (NM_010344)	-728	NM_010344	14782	Mm.283573	NM_010344	ENSMUSG00000031584	Gsr	AI325518|D8Ertd238e|Gr-1|Gr1	glutathione reductase	protein-coding
mm_141337.1	chr17	28512030	28512033	-	1	NA	Intergenic	Intergenic	-18830	NM_026290	67645	Mm.46170	NM_026290	ENSMUSG00000024223	Armc12	4930511I11Rik|AV041658	armadillo repeat containing 12	protein-coding
mm_92006.1	chr10	62327778	62327787	-	1	NA	intron (NM_010438, intron 4 of 21)	intron (NM_010438, intron 4 of 21)	12639	NM_001146100	15275	Mm.196605	NM_010438	ENSMUSG00000037012	Hk1	BB404130|Hk-1|Hk1-s|dea|mHk1-s	hexokinase 1	protein-coding
mm_31242.1	chr4	44807514	44807530	+	1	NA	intron (NM_138590, intron 2 of 8)	intron (NM_138590, intron 2 of 8)	50963	NM_138590	319885	Mm.331576	NM_138590	ENSMUSG00000035649	Zcchc7	4930572I07Rik|D4Wsu132e	zinc finger, CCHC domain containing 7	protein-coding
mm_74647.1	chr8	13388799	13388815	-	1	NA	exon (NM_009724, exon 5 of 7)	exon (NM_009724, exon 5 of 7)	7971	NM_009724	11945	Mm.154039	NM_009724	ENSMUSG00000031449	Atp4b	AV080843	ATPase, H+/K+ exchanging, beta polypeptide	protein-coding
mm_55564.1	chr6	71360820	71360845	-	1	NA	Intergenic	Intergenic	-12595	NM_009857	12525	Mm.1858	NM_009857	ENSMUSG00000053977	Cd8a	BB154331|Ly-2|Ly-35|Ly-B|Lyt-2	CD8 antigen, alpha chain	protein-coding
mm_169904.1	chr16	52084257	52084262	+	1	NA	intron (NM_001033238, intron 3 of 17)	(AGGTG)n|Simple_repeat|Simple_repeat	52710	NM_001033238	208650	Mm.328206	NM_001033238	ENSMUSG00000022637	Cblb	AI429560|AI851073|Cbl-b	Casitas B-lineage lymphoma b	protein-coding
mm_79326.1	chr9	53301572	53301599	+	1	NA	promoter-TSS (NM_176846)	promoter-TSS (NM_176846)	-85	NM_176846	320051	Mm.277540	NM_176846	ENSMUSG00000034584	Exph5	AC079869.22gm5|B130009M24Rik|E030050P12|Kiaa0624|Slac2b|slac2-b	exophilin 5	protein-coding
mm_28797.1	chr3	96094298	96094332	-	1	NA	intron (NR_035496, intron 1 of 1)	intron (NR_035496, intron 1 of 1)	-10212	NM_001025613	229603	Mm.272336	NM_001025613	ENSMUSG00000038495	Otud7b	2900060B22Rik|4930463P07Rik|AI462125|CEZANNE|Trabid2|Za20d1	OTU domain containing 7B	protein-coding
mm_39241.1	chr5	3341438	3341466	+	1	NA	Intergenic	CpG	-2441	NM_009873	12571	Mm.31672	NM_009873	ENSMUSG00000040274	Cdk6	AI504062|Crk2	cyclin-dependent kinase 6	protein-coding
mm_167770.1	chr9	111024468	111024486	+	1	NA	exon (NM_008522, exon 7 of 17)	exon (NM_008522, exon 7 of 17)	5185	NM_008522	17002	Mm.282359	NM_008522	ENSMUSG00000032496	Ltf	Csp82|Lf|MMS10R|Ms10r	lactotransferrin	protein-coding
mm_107746.1	chr12	58813907	58813912	+	1	NA	Intergenic	Intergenic	198108	NM_009147	20334	Mm.491137	NM_009147	ENSMUSG00000020986	Sec23a	Msec23|Sec23r	SEC23 homolog A, COPII coat complex component	protein-coding
mm_6324.1	chr1	71607979	71608001	-	1	NA	exon (NM_001276413, exon 28 of 44)	exon (NM_001276413, exon 28 of 44)	45244	NM_010233	14268	Mm.193099	NM_010233	ENSMUSG00000026193	Fn1	E330027I09|Fn|Fn-1	fibronectin 1	protein-coding
mm_116615.1	chr13	48871690	48871706	-	1	NA	promoter-TSS (NM_011078)	promoter-TSS (NM_011078)	-813	NM_011078	18676	Mm.486213	NM_011078	ENSMUSG00000038025	Phf2	GRC5	PHD finger protein 2	protein-coding
mm_54878.1	chr6	42693031	42693070	-	1	NA	promoter-TSS (NM_029930)	promoter-TSS (NM_029930)	9	NM_029930	77574	Mm.24652	NM_029930	ENSMUSG00000036667	Tcaf1	2810407D09Rik|3321401G04Rik|A230020K05Rik|AI848529|Fam115a	TRPM8 channel-associated factor 1	protein-coding
mm_166460.1	chr5	139547863	139547873	+	1	NA	3' UTR (NM_013702, exon 3 of 3)	3' UTR (NM_013702, exon 3 of 3)	3970	NM_013702	22255	Mm.42190	NM_013702	ENSMUSG00000029546	Uncx	Chx4|Uncx4.1	UNC homeobox	protein-coding
mm_167268.1	chr8	31111594	31111614	+	1	NA	promoter-TSS (NM_175136)	promoter-TSS (NM_175136)	-242	NM_175136	68867	Mm.29532	NM_175136	ENSMUSG00000039328	Rnf122	1110063C11Rik	ring finger protein 122	protein-coding
mm_121265.1	chr14	103074394	103074408	+	1	NA	intron (NM_001033242, intron 3 of 3)	B2_Mm2|SINE|B2	4185	NM_001033242	211286	Mm.295289	NM_001033242	ENSMUSG00000022125	Cln5	A730075N08Rik	ceroid-lipofuscinosis, neuronal 5	protein-coding
mm_150802.1	chr19	44333342	44333358	+	1	NA	promoter-TSS (NM_183216)	promoter-TSS (NM_183216)	24	NM_183216	329065	Mm.313583	NM_183216	ENSMUSG00000050195	Scd4	ACOD4	stearoyl-coenzyme A desaturase 4	protein-coding
mm_73536.1	chr8	108703671	108703710	+	1	NA	Intergenic	Intergenic	-10954	NM_007496	11906	Mm.416972	NM_007496	ENSMUSG00000038872	Zfhx3	A230102L03Rik|Atbf1|Sci|WBP9|mKIAA4228	zinc finger homeobox 3	protein-coding
mm_84224.1	chr9	61946731	61946744	-	1	NA	promoter-TSS (NM_024245)	promoter-TSS (NM_024245)	62	NM_024245	71819	Mm.259374	NM_024245	ENSMUSG00000032254	Kif23	3110001D19Rik|C87313|CHO1|Knsl5|MKLP-1|MKLP1	kinesin family member 23	protein-coding
mm_156576.1	chrX	152001875	152001908	+	1	NA	promoter-TSS (NM_016763)	promoter-TSS (NM_016763)	-5	NM_016763	15108	Mm.6994	NM_016763	ENSMUSG00000025260	Hsd17b10	17bHSD10|Ads9|ERAB|Hadh2	hydroxysteroid (17-beta) dehydrogenase 10	protein-coding
mm_118946.1	chr14	27342057	27342060	+	1	NA	intron (NM_001289687, intron 1 of 9)	intron (NM_001289687, intron 1 of 9)	6021	NM_001289687	71704	Mm.248606	NM_027871	ENSMUSG00000021895	Arhgef3	1200004I24Rik|9830169H03Rik|C76747|Xpln	Rho guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_51585.1	chr6	83795159	83795169	+	1	NA	promoter-TSS (NM_001164187)	promoter-TSS (NM_001164187)	6	NM_001164187	56174	Mm.190650	NM_019542	ENSMUSG00000034744	Nagk	Gnk	N-acetylglucosamine kinase	protein-coding
mm_74346.1	chr8	127485203	127485207	+	1	NA	intron (NM_001309391, intron 22 of 24)	intron (NM_001309391, intron 22 of 24)	185553	NM_001013580	93742	Mm.299254	NM_033620	ENSMUSG00000025812	Pard3	AA960621|AI256638|Asip|D8Ertd580e|Par-3|Par3|Pard-3|Pard3a|Phip	par-3 family cell polarity regulator	protein-coding
mm_59519.1	chr7	27597053	27597109	+	1	NA	5' UTR (NM_001331108, exon 1 of 14)	5' UTR (NM_001331108, exon 1 of 14)	251	NM_001331108	11652	Mm.177194	NM_007434	ENSMUSG00000004056	Akt2	2410016A19Rik|AW554154|PKB|PKBbeta	thymoma viral proto-oncogene 2	protein-coding
mm_3372.1	chr1	138963630	138963684	+	1	NA	promoter-TSS (NM_001166501)	promoter-TSS (NM_001166501)	-52	NM_001166501	329260	Mm.337604	NM_181347	ENSMUSG00000056268	Dennd1b	4632404N19Rik|4930467M19Rik|6820401H01Rik|F730008N07Rik	DENN/MADD domain containing 1B	protein-coding
mm_126860.1	chr15	89322930	89322960	+	1	NA	5' UTR (NM_182928, exon 1 of 3)	5' UTR (NM_182928, exon 1 of 3)	225	NM_182928	223780	Mm.210541	NM_182928	ENSMUSG00000054136	Adm2	Am2|IMD|Imdn	adrenomedullin 2	protein-coding
mm_141345.1	chr17	28558799	28558881	-	1	NA	promoter-TSS (NR_105935)	promoter-TSS (NR_105935)	-339	NR_105935	102465585		NR_105935	ENSMUSG00000099152	Mir6969	Gm27305|mmu-mir-6969	microRNA 6969	ncRNA
mm_45887.1	chr5	88526518	88526540	-	1	NA	intron (NM_152839, intron 1 of 3)	ID_B1|SINE|B4	1368	NM_152839	16069	Mm.1192	NM_152839	ENSMUSG00000067149	Jchain	9530090F24Rik|AI323815|Igj|Jch	immunoglobulin joining chain	protein-coding
mm_90880.1	chr10	9675826	9675847	-	1	NA	promoter-TSS (NM_177271)	promoter-TSS (NM_177271)	-628	NM_177271	320825	Mm.101115	NM_177271	ENSMUSG00000060487	Samd5	E130306M17Rik	sterile alpha motif domain containing 5	protein-coding
mm_126703.1	chr15	85177740	85177762	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-21619	NR_040360	100502602	Mm.390830	NR_040360		Gm19277	-	predicted gene, 19277	ncRNA
mm_28198.1	chr3	88254676	88254689	-	1	NA	promoter-TSS (NM_021375)	promoter-TSS (NM_021375)	2	NM_021375	58176	Mm.103777	NM_021375	ENSMUSG00000103766	Rhbg	-	Rhesus blood group-associated B glycoprotein	protein-coding
mm_21887.1	chr2	166155273	166155286	-	1	NA	promoter-TSS (NM_001252578)	promoter-TSS (NM_001252578)	6	NM_001252578	72043	Mm.1011	NM_028072	ENSMUSG00000006800	Sulf2	2010004N24Rik|AU020235|MSulf-2|mKIAA1247	sulfatase 2	protein-coding
mm_149075.1	chr19	8883849	8883861	+	1	NA	promoter-TSS (NM_001286103)	promoter-TSS (NM_001286103)	-23	NM_001286103	102308570	Mm.27503	NM_001286103	ENSMUSG00000096740	Lbhd1	Gm21743	LBH domain containing 1	protein-coding
mm_15511.1	chr2	158258238	158258246	+	1	NA	promoter-TSS (NM_177850)	promoter-TSS (NM_177850)	1	NM_177850	329547	Mm.260883	NM_177850	ENSMUSG00000052922	Bpi	9230105K17Rik|Bpifd1	bactericidal permeablility increasing protein	protein-coding
mm_166237.1	chr5	70176570	70176570	+	1	NA	Intergenic	L1_Mur3|LINE|L1	-584266	NM_001347363	67980	Mm.33830	NM_027681	ENSMUSG00000029209	Gnpda2	4921523I18Rik|4933412A11Rik|BB189630|GNPDA|Gnp2|Sb52|mKIAA4008	glucosamine-6-phosphate deaminase 2	protein-coding
mm_10700.1	chr2	22755985	22755993	+	1	NA	Intergenic	RMER1A|Other|Other	-18338	NM_019456	54519	Mm.14255	NM_019456	ENSMUSG00000026786	Apbb1ip	9930118P07Rik|Prp48	amyloid beta (A4) precursor protein-binding, family B, member 1 interacting protein	protein-coding
mm_131251.1	chr16	10545429	10545454	+	1	NA	5' UTR (NM_177562, exon 1 of 23)	5' UTR (NM_177562, exon 1 of 23)	102	NM_001204229	74374	Mm.159176	NM_177562	ENSMUSG00000068663	Clec16a	4932416N17Rik|curt|mKIAA0350	C-type lectin domain family 16, member A	protein-coding
mm_101285.1	chr11	21572194	21572211	-	1	NA	promoter-TSS (NM_001316675)	promoter-TSS (NM_001316675)	-79	NM_145425	216560	Mm.138090	NM_145425	ENSMUSG00000020319	Wdpcp	AV249152	WD repeat containing planar cell polarity effector	protein-coding
mm_106319.1	chr11	118303222	118303230	-	1	NA	3' UTR (NM_011594, exon 5 of 5)	3' UTR (NM_011594, exon 5 of 5)	-12982	NM_001033528	72344	Mm.232293	NM_001033528	ENSMUSG00000033909	Usp36	2700002L06Rik|mKIAA1453	ubiquitin specific peptidase 36	protein-coding
mm_21835.1	chr2	165717587	165717591	-	1	NA	intron (NM_001271962, intron 7 of 15)	intron (NM_001271962, intron 7 of 15)	62291	NM_010165	14049	Mm.282719	NM_010165	ENSMUSG00000017897	Eya2	Eab1	EYA transcriptional coactivator and phosphatase 2	protein-coding
mm_146580.1	chr18	7608332	7608335	-	1	NA	intron (NM_001081287, intron 1 of 16)	intron (NM_001081287, intron 1 of 16)	18530	NM_001081287	75739	Mm.133293	NM_001081287	ENSMUSG00000057440	Mpp7	1110068J02Rik|2810038M04Rik|5430426E14Rik|AI415104|Gm955	membrane protein, palmitoylated 7 (MAGUK p55 subfamily member 7)	protein-coding
mm_117243.1	chr13	64363689	64363699	-	1	NA	3' UTR (NM_009984, exon 8 of 8)	3' UTR (NM_009984, exon 8 of 8)	6826	NM_009984	13039	Mm.930	NM_009984	ENSMUSG00000021477	Ctsl	1190035F06Rik|CatL|Ctsl1|MEP|fs|nkt	cathepsin L	protein-coding
mm_77902.1	chr9	7348844	7348876	+	1	NA	intron (NM_001320077, intron 3 of 10)	intron (NM_001320077, intron 3 of 10)	1486	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_117771.1	chr13	96542480	96542523	-	1	NA	promoter-TSS (NM_001164222)	promoter-TSS (NM_001164222)	78	NM_012048	27015	Mm.89926	NM_012048	ENSMUSG00000021668	Polk	DINP|Dinb1	polymerase (DNA directed), kappa	protein-coding
mm_116852.1	chr13	54759508	54759518	-	1	NA	exon (NM_033610, exon 6 of 6)	exon (NM_033610, exon 6 of 6)	6927	NM_033610	104069	Mm.200843	NM_033610	ENSMUSG00000034891	Sncb	AI838531|betaSYN	synuclein, beta	protein-coding
mm_80156.1	chr9	70956031	70956039	+	1	NA	Intergenic	B4A|SINE|B4	-3814	NM_001324472	15450	Mm.390187	NM_008280	ENSMUSG00000032207	Lipc	AI256194|HL|Hpl	lipase, hepatic	protein-coding
mm_61461.1	chr7	75596662	75596665	+	1	NA	intron (NM_029332, intron 5 of 36)	intron (NM_029332, intron 5 of 36)	141129	NM_029332	75547	Mm.216107	NM_029332	ENSMUSG00000066406	Akap13	1700026G02Rik|5730522G15Rik|5830460E08Rik|AKAP-13|AKAP-Lbc|BRX|Ht31|LBC|PROTO-LB|PROTO-LBC	A kinase (PRKA) anchor protein 13	protein-coding
mm_101754.1	chr11	43385111	43385135	-	1	NA	Intergenic	Intergenic	-10662	NR_029558	387164		NR_029558	ENSMUSG00000065601	Mir146	Mirn146|miR-146a|mmu-mir-146	microRNA 146	ncRNA
mm_9698.1	chr1	178337775	178337794	-	1	NA	promoter-TSS (NM_016805)	promoter-TSS (NM_016805)	0	NM_016805	51810	Mm.86589	NM_016805	ENSMUSG00000039630	Hnrnpu	AA408410|AI256620|AL024194|AL024437|AW557595|C86794|Hnrpu|SAFA|Sp120|hnRNP U	heterogeneous nuclear ribonucleoprotein U	protein-coding
mm_163113.1	chr11	71597440	71597440	-	1	NA	Intergenic	Lx3C|LINE|L1	-153263	NM_177618	216881	Mm.48648	NM_177618	ENSMUSG00000020811	Wscd1	mKIAA0523	WSC domain containing 1	protein-coding
mm_172068.1	chr6	136533032	136533034	+	1	NA	intron (NM_019426, intron 1 of 14)	intron (NM_019426, intron 1 of 14)	14182	NM_019426	54343	Mm.173271	NM_019426	ENSMUSG00000030213	Atf7ip	2610204M12Rik|AM|Mcaf1	activating transcription factor 7 interacting protein	protein-coding
mm_28278.1	chr3	88950154	88950190	-	1	NA	5' UTR (NM_022994, exon 1 of 13)	5' UTR (NM_022994, exon 1 of 13)	110	NM_022994	65111	Mm.29028	NM_022994	ENSMUSG00000068921	Dap3	4921514D13Rik|DAP-3|MRP-S29|S29mt	death associated protein 3	protein-coding
mm_118247.1	chr13	111884361	111884376	-	1	NA	Intergenic	Intergenic	16432	NR_130345	102636620	Mm.402328	NR_130345	ENSMUSG00000086111	Gm15326	OTTMUSG00000020187	predicted gene 15326	ncRNA
mm_155098.1	chrX	48274898	48274924	+	1	NA	exon (NM_028276, exon 11 of 15)	exon (NM_028276, exon 11 of 15)	10515	NR_045916	100500713	Mm.396609	NR_045916	ENSMUSG00000097197	9530027J09Rik	-	RIKEN cDNA 9530027J09 gene	ncRNA
mm_125444.1	chr15	46324592	46324602	+	1	NA	promoter-TSS (NR_045509)	promoter-TSS (NR_045509)	12	NR_045509	71120	Mm.158571	NR_045509	ENSMUSG00000099751	1700022A22Rik	4933413D07Rik	RIKEN cDNA 1700022A22 gene	ncRNA
mm_37482.1	chr4	123572908	123572938	-	1	NA	intron (NM_001199136, intron 1 of 97)	intron (NM_001199136, intron 1 of 97)	-43497	NR_105824	102465214		NR_105824	ENSMUSG00000099005	Mir6398	Gm27657|mmu-mir-6398	microRNA 6398	ncRNA
mm_101416.1	chr11	29247209	29247329	-	1	NA	promoter-TSS (NM_025740)	promoter-TSS (NM_025740)	3	NM_025740	216618	Mm.128663	NM_025740	ENSMUSG00000020462	Cfap36	2300003H10|4931428D14Rik|Ccdc104	cilia and flagella associated protein 36	protein-coding
mm_49541.1	chr6	30186606	30186612	+	1	NA	Intergenic	Intergenic	9986	NR_038124	100463519	Mm.361139	NR_038124		BB283400	BF465573|Rncr4	expressed sequence BB283400	ncRNA
mm_150726.1	chr19	43675461	43675482	+	1	NA	promoter-TSS (NM_145156)	promoter-TSS (NM_145156)	293	NR_045645	100502982	Mm.313570	NR_045645		BC037704	-	cDNA sequence BC037704	ncRNA
mm_66646.1	chr7	45666293	45666325	-	1	NA	promoter-TSS (NM_001271993)	promoter-TSS (NM_001271993)	85	NM_018876	14344	Mm.290046	NM_018876	ENSMUSG00000055978	Fut2	-	fucosyltransferase 2	protein-coding
mm_65679.1	chr7	28331507	28331541	-	1	NA	exon (NM_013676, exon 3 of 30)	exon (NM_013676, exon 3 of 30)	7195	NM_013676	20924	Mm.285906	NM_013676	ENSMUSG00000003435	Supt5	AL033283|AL033321|AU019549|Spt5|Supt5h	suppressor of Ty 5	protein-coding
mm_165299.1	chr2	92024500	92024502	-	1	NA	promoter-TSS (NM_011957)	promoter-TSS (NM_011957)	-331	NM_011957	26427	Mm.10353	NM_011957	ENSMUSG00000027230	Creb3l1	Oasis	cAMP responsive element binding protein 3-like 1	protein-coding
mm_19921.1	chr2	116000185	116000193	-	1	NA	exon (NM_010825, exon 8 of 12)	exon (NM_010825, exon 8 of 12)	64430	NM_001346044	17536	Mm.247566	NM_010825	ENSMUSG00000027210	Meis2	A430109D20Rik|Mrg1|Stra10	Meis homeobox 2	protein-coding
mm_74571.1	chr8	11199341	11199353	-	1	NA	non-coding (NR_133670, exon 53 of 53)	non-coding (NR_133670, exon 53 of 53)	-113458	NM_009932	12827	Mm.181021	NM_009932	ENSMUSG00000031503	Col4a2	Col4a-2	collagen, type IV, alpha 2	protein-coding
mm_159526.1	chr4	61835327	61835327	-	1	NA	promoter-TSS (NM_008649)	promoter-TSS (NM_008649)	-147	NM_008649	17844	Mm.445286	NM_008649	ENSMUSG00000058523	Mup5	Mup18	major urinary protein 5	protein-coding
mm_132920.1	chr16	49772827	49772840	+	1	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	73539	NM_028680	73916	Mm.241276	NM_028680	ENSMUSG00000032965	Ift57	4833420A15Rik|Esrrbl1|Hippi|MHS4R2	intraflagellar transport 57	protein-coding
mm_149251.1	chr19	10389237	10389259	+	1	NA	5' UTR (NM_018801, exon 1 of 9)	5' UTR (NM_018801, exon 1 of 9)	158	NM_173068	54525	Mm.182654	NM_018801	ENSMUSG00000024743	Syt7	AI851541|B230112P13Rik	synaptotagmin VII	protein-coding
mm_125853.1	chr15	74989583	74989594	+	1	NA	Intergenic	Intergenic	-6158	NM_020498	57248	Mm.358339	NM_020498	ENSMUSG00000022586	Ly6i	AI789751|Ly-6I|Ly-6M	lymphocyte antigen 6 complex, locus I	protein-coding
mm_26698.1	chr3	157548819	157548821	+	1	NA	TTS (NM_017381)	TTS (NM_017381)	4541	NR_029572	387181		NR_029572	ENSMUSG00000065431	Mir186	Mirn186|mir-186|mmu-mir-186	microRNA 186	ncRNA
mm_105970.1	chr11	115491797	115491865	-	1	NA	promoter-TSS (NM_015807)	promoter-TSS (NM_015807)	-17	NM_015807	50773	Mm.390379	NM_015807	ENSMUSG00000020736	Nt5c	Dnt|Dnt1|Umph-2|Umph2	5',3'-nucleotidase, cytosolic	protein-coding
mm_122886.1	chr14	54946949	54946996	-	1	NA	exon (NM_010856, exon 33 of 39)	exon (NM_010856, exon 33 of 39)	2170	NR_029724	387204		NR_029724	ENSMUSG00000065432	Mir208a	Mirn208|Mirn208a|mir-208|mir-208a|mmu-mir-208	microRNA 208a	ncRNA
mm_6477.1	chr1	74070051	74070081	-	1	NA	intron (NM_027884, intron 2 of 34)	RMER1A|Other|Other	54381	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_91959.1	chr10	61147596	61147620	-	1	NA	promoter-TSS (NM_001316673)	promoter-TSS (NM_001316673)	76	NM_009163	20397	Mm.412319	NM_009163	ENSMUSG00000020097	Sgpl1	AI428538|D10Xrf456|S1PL|Spl	sphingosine phosphate lyase 1	protein-coding
mm_89724.1	chr10	98916110	98916127	+	1	NA	intron (NM_026482, intron 1 of 20)	intron (NM_026482, intron 1 of 20)	966	NM_026482	67972	Mm.166944	NM_026482	ENSMUSG00000019943	Atp2b1	2810442I22Rik|E130111D10Rik|Pmca1	ATPase, Ca++ transporting, plasma membrane 1	protein-coding
mm_161005.1	chr11	116775449	116775449	-	1	NA	promoter-TSS (NM_011371)	promoter-TSS (NM_011371)	58	NM_011371	20445	Mm.436887	NM_011371	ENSMUSG00000009588	St6galnac1	Siat7a	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 1	protein-coding
mm_111038.1	chr12	79192202	79192210	-	1	NA	promoter-TSS (NM_021557)	promoter-TSS (NM_021557)	-387	NM_021557	17252	Mm.291799	NM_021557	ENSMUSG00000066441	Rdh11	2610319N22Rik|AI428145|AU045252|Arsdr1|C85936|CGI-82|HCBP12|M42C60|Mdt1|Psdr1|SCALD|UBE-1c1|Ube-1c	retinol dehydrogenase 11	protein-coding
mm_22755.1	chr3	19980590	19980598	+	1	NA	exon (NM_007752, exon 12 of 19)	exon (NM_007752, exon 12 of 19)	23540	NM_007752	12870	Mm.13787	NM_007752	ENSMUSG00000003617	Cp	D3Ertd555e	ceruloplasmin	protein-coding
mm_247.1	chr1	19212272	19212273	+	1	NA	5' UTR (NM_001025305, exon 1 of 7)	5' UTR (NM_001025305, exon 1 of 7)	218	NM_001025305	21419	Mm.137021	NM_009334	ENSMUSG00000025927	Tfap2b	AI606113|AP-2(beta)|E130018K07Rik|Tcfap2b	transcription factor AP-2 beta	protein-coding
mm_91406.1	chr10	30978754	30978755	-	1	NA	Intergenic	RMER17C2|LTR|ERVK	-135971	NM_013904	15214	Mm.103573	NM_013904	ENSMUSG00000019789	Hey2	CHF1|Herp1|Hrt2|bHLHb32|hesr2	hairy/enhancer-of-split related with YRPW motif 2	protein-coding
mm_141825.1	chr17	34627083	34627092	-	1	NA	promoter-TSS (NM_019441)	promoter-TSS (NM_019441)	61	NM_019441	54397	Mm.373627	NM_019441	ENSMUSG00000015474	Ppt2	0610007M19Rik|AA672937	palmitoyl-protein thioesterase 2	protein-coding
mm_99644.1	chr11	105292700	105292714	+	1	NA	promoter-TSS (NM_008626)	promoter-TSS (NM_008626)	61	NM_008626	17534	Mm.235616	NM_008626	ENSMUSG00000020695	Mrc2	Endo180|mKIAA0709|uPARAP	mannose receptor, C type 2	protein-coding
mm_150214.1	chr19	32960131	32960171	+	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	202574	NM_008960	19211	Mm.245395	NM_008960	ENSMUSG00000013663	Pten	2310035O07Rik|A130070J02Rik|AI463227|B430203M17Rik|MMAC1|TEP1	phosphatase and tensin homolog	protein-coding
mm_20387.1	chr2	128968044	128968064	-	1	NA	intron (NM_178404, intron 1 of 11)	(CCG)n|Simple_repeat|Simple_repeat	652	NM_178404	78751	Mm.26377	NM_178404	ENSMUSG00000042851	Zc3h6	4631426G04Rik|4833425H18Rik|AU024389|AW060453|Zc3hdc6|mKIAA2035	zinc finger CCCH type containing 6	protein-coding
mm_149633.1	chr19	17222732	17222732	+	1	NA	3' UTR (NM_181348, exon 20 of 20)	3' UTR (NM_181348, exon 20 of 20)	116773	NM_001136484	14537	Mm.244825	NM_010265	ENSMUSG00000038843	Gcnt1	5630400D21Rik|B130048E03|C2 GlcNAcT|C2GNT|IGnT	glucosaminyl (N-acetyl) transferase 1, core 2	protein-coding
mm_93736.1	chr10	120112986	120113002	-	1	NA	promoter-TSS (NM_080446)	promoter-TSS (NM_080446)	-29	NM_080446	117599	Mm.214703	NM_080446	ENSMUSG00000020228	Helb	AI447783|D10Ertd664e	helicase (DNA) B	protein-coding
mm_162113.1	chrX	52164902	52164902	-	1	NA	promoter-TSS (NM_008150)	promoter-TSS (NM_008150)	21	NM_008150	14735	Mm.1528	NM_008150	ENSMUSG00000031119	Gpc4	9530073D23Rik|AF311610|AI385680|AI661372|K-glypican	glypican 4	protein-coding
mm_148381.1	chr19	3322293	3322315	+	1	NA	promoter-TSS (NM_013495)	promoter-TSS (NM_013495)	-997	NM_013495	12894	Mm.18522	NM_013495	ENSMUSG00000024900	Cpt1a	C730027G07|CPTI|Cpt1	carnitine palmitoyltransferase 1a, liver	protein-coding
mm_152564.1	chr19	11586977	11587041	-	1	NA	3' UTR (NM_026835, exon 7 of 7)	3' UTR (NM_026835, exon 7 of 7)	17795	NM_026835	68774	Mm.290390	NM_026835	ENSMUSG00000024679	Ms4a6d	1110058E16Rik|AI447446|Ms4a11	membrane-spanning 4-domains, subfamily A, member 6D	protein-coding
mm_122705.1	chr14	52180240	52180252	-	1	NA	exon (NM_033618, exon 7 of 26)	exon (NM_033618, exon 7 of 26)	16993	NM_033618	114741	Mm.21662	NM_033618	ENSMUSG00000035726	Supt16	Cdc68|Fact140|Spt16|Supt16h	suppressor of Ty 16	protein-coding
mm_2891.1	chr1	131867636	131867647	+	1	NA	5' UTR (NM_144875, exon 2 of 6)	5' UTR (NM_144875, exon 2 of 6)	364	NM_144875	226422	Mm.34027	NM_144875	ENSMUSG00000026433	Rab29	Rab7l1	RAB29, member RAS oncogene family	protein-coding
mm_55252.1	chr6	52909582	52909609	-	1	NA	promoter-TSS (NM_001168277)	promoter-TSS (NM_001168277)	25	NM_001168277	231986	Mm.386865	NM_173406	ENSMUSG00000063568	Jazf1	AI591476|C820002C15|Jaz1|Tip27	JAZF zinc finger 1	protein-coding
mm_42581.1	chr5	117292790	117292796	+	1	NA	Intergenic	Intergenic	-5229	NM_018858	23980	Mm.195898	NM_018858	ENSMUSG00000032959	Pebp1	HCNP|Pbp|Pbp1|Pbpr|Rkip	phosphatidylethanolamine binding protein 1	protein-coding
mm_105769.1	chr11	109676095	109676099	-	1	NA	intron (NM_153782, intron 7 of 10)	intron (NM_153782, intron 7 of 10)	25176	NM_001313976	19084	Mm.30039	NM_021880	ENSMUSG00000020612	Prkar1a	1300018C22Rik|RIalpha|Tse-1|Tse1	protein kinase, cAMP dependent regulatory, type I, alpha	protein-coding
mm_95024.1	chr11	32024696	32024708	+	1	NA	intron (NM_001290680, intron 3 of 4)	intron (NM_001290680, intron 3 of 4)	23425	NM_001290681	18197	Mm.3304	NM_008741	ENSMUSG00000020297	Nsg2	-	neuron specific gene family member 2	protein-coding
mm_116004.1	chr13	24603869	24603886	-	1	NA	intron (NR_024599, intron 1 of 1)	intron (NR_024599, intron 1 of 1)	890	NR_024599	76024	Mm.440710	NR_024599		Gm11346	5830431A10Rik|AI447617|Gm11347|OTTMUSG00000000601|OTTMUSG00000000602	X-linked lymphocyte-regulated 5 pseudogene	pseudo
mm_157658.1	chrX	57338738	57338781	-	1	NA	promoter-TSS (NM_152801)	promoter-TSS (NM_152801)	-30	NM_152801	73341	Mm.261443	NM_152801	ENSMUSG00000031133	Arhgef6	1600028C08Rik|1700038J06Rik|4930592P22Rik|alpha-PIX	Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_96433.1	chr11	67298466	67298480	+	1	NA	exon (NM_177369, exon 27 of 40)	exon (NM_177369, exon 27 of 40)	21349	NM_177369	17885	Mm.340163	NM_177369	ENSMUSG00000055775	Myh8	4832426G23Rik|AI327267|MHCp|MyHC-pn|Myhs-p|Myhsp	myosin, heavy polypeptide 8, skeletal muscle, perinatal	protein-coding
mm_109655.1	chr12	112976472	112976552	+	1	NA	promoter-TSS (NM_201646)	promoter-TSS (NM_201646)	30	NM_001145900	399566	Mm.440140	NM_201646	ENSMUSG00000002803	Btbd6	-	BTB (POZ) domain containing 6	protein-coding
mm_186.1	chr1	15287003	15287017	+	1	NA	Intergenic	CpG	-25442	NM_001098528	98741	Mm.156081	NM_001033195	ENSMUSG00000092083	Kcnb2	9630047L19Rik|BB130875|Kv2.2	potassium voltage gated channel, Shab-related subfamily, member 2	protein-coding
mm_166653.1	chr6	86616737	86616743	-	1	NA	Intergenic	Intergenic	-11434	NM_026414	67855	Mm.183043	NM_026414	ENSMUSG00000033508	Asprv1	2300003P22Rik|AA986851|SASP|SASPase|Taps	aspartic peptidase, retroviral-like 1	protein-coding
mm_92983.1	chr10	86694098	86694125	-	1	NA	exon (NM_011631, exon 13 of 18)	exon (NM_011631, exon 13 of 18)	8584	NR_015572	66263	Mm.392261	NR_015572		1810014B01Rik	-	RIKEN cDNA 1810014B01 gene	pseudo
mm_156032.1	chrX	107256157	107256167	+	1	NA	intron (NM_001177781, intron 1 of 4)	intron (NM_001177781, intron 1 of 4)	134	NM_001033251	213439	Mm.383562	NM_001033251	ENSMUSG00000073008	Gpr174	Gm376|Lypsr3	G protein-coupled receptor 174	protein-coding
mm_52645.1	chr6	117178984	117178990	+	1	NA	3' UTR (NM_001012477, exon 4 of 4)	3' UTR (NM_001012477, exon 4 of 4)	10452	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_151778.1	chr19	5364803	5364825	-	1	NA	non-coding (NR_104482, exon 2 of 2)	non-coding (NR_104482, exon 2 of 2)	1549	NM_001038231	23825	Mm.358649	NM_011793	ENSMUSG00000024844	Banf1	Baf|Bcrp1|L2bp1/Baf	barrier to autointegration factor 1	protein-coding
mm_89865.1	chr10	108162303	108162314	+	1	NA	promoter-TSS (NM_027892)	promoter-TSS (NM_027892)	-92	NM_027892	17931	Mm.422959	NM_027892	ENSMUSG00000019907	Ppp1r12a	1200015F06Rik|5730577I22Rik|AA792106|AV099298|D10Ertd625e|Mypt1	protein phosphatase 1, regulatory (inhibitor) subunit 12A	protein-coding
mm_167933.1	chrX	106186929	106186935	+	1	NA	promoter-TSS (NM_008828)	promoter-TSS (NM_008828)	-168	NM_008828	18655	Mm.316355	NM_008828	ENSMUSG00000062070	Pgk1	Pgk-1	phosphoglycerate kinase 1	protein-coding
mm_170132.1	chr17	39847291	39847293	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	4295	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_64.1	chr1	6599677	6599686	+	1	NA	intron (NM_001244693, intron 2 of 22)	intron (NM_001244693, intron 2 of 22)	112450	NM_001244692	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding
mm_68642.1	chr7	118447921	118447948	-	1	NA	Intergenic	CpG	-4382	NM_138649	110058	Mm.156558	NM_138649	ENSMUSG00000058420	Syt17	Bk	synaptotagmin XVII	protein-coding
mm_112670.1	chr13	16027472	16027485	+	1	NA	3' UTR (NM_008380, exon 5 of 5)	3' UTR (NM_008380, exon 5 of 5)	15627	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_4148.1	chr1	171018028	171018073	+	1	NA	promoter-TSS (NM_144559)	promoter-TSS (NM_144559)	-876	NM_144559	246256	Mm.251254	NM_144559	ENSMUSG00000059089	Fcgr4	4833442P21Rik|CD16-2|FcgRIV|FcgammaRIV|Fcgr3a|Fcrl3	Fc receptor, IgG, low affinity IV	protein-coding
mm_52652.1	chr6	117716341	117716343	+	1	NA	intron (NR_045731, intron 2 of 3)	intron (NR_045731, intron 2 of 3)	35427	NR_045731	72263	Mm.443289	NR_045731	ENSMUSG00000099869	1700030F04Rik	-	RIKEN cDNA 1700030F04 gene	ncRNA
mm_114426.1	chr13	64432764	64432779	+	1	NA	intron (NM_053180, intron 1 of 7)	CpG	218	NM_053180	105278	Mm.74982	NM_053180	ENSMUSG00000021483	Cdk20	4932702G04Rik|AU019450|AW558027|CDCH|Ccrk|PNQLARE|p42	cyclin-dependent kinase 20	protein-coding
mm_103420.1	chr11	75594737	75594741	-	1	NA	intron (NM_008850, intron 2 of 11)	intron (NM_008850, intron 2 of 11)	5492	NR_110477	654359	Mm.439961	NR_110477		Gm12338	OTTMUSG00000006216	cytochrome c oxidase, subunit VIIc pseudogene	pseudo
mm_121687.1	chr14	13914465	13914478	-	1	NA	Intergenic	Intergenic	46842	NM_001285780	66231	Mm.295875	NM_025435	ENSMUSG00000053453	Thoc7	Nif3l1bp1	THO complex 7	protein-coding
mm_10204.1	chr2	4976177	4976185	+	1	NA	promoter-TSS (NM_001165932)	promoter-TSS (NM_001165932)	59	NM_026754	68527	Mm.27791	NM_026754	ENSMUSG00000026668	Ucma	1110017I16Rik|AW121955|Grp	upper zone of growth plate and cartilage matrix associated	protein-coding
mm_158187.1	chrX	104382642	104382651	-	1	NA	intron (NM_009592, intron 1 of 15)	intron (NM_009592, intron 1 of 15)	31200	NM_009592	11306	Mm.426128	NM_009592	ENSMUSG00000031333	Abcb7	AA517758|AU019072|Abc7	ATP-binding cassette, sub-family B (MDR/TAP), member 7	protein-coding
mm_30340.1	chr3	151734858	151734868	-	1	NA	intron (NM_133871, intron 7 of 7)	Lx7|LINE|L1	15096	NM_133871	99899	Mm.30756	NM_133871	ENSMUSG00000028037	Ifi44	A430056A10Rik|AW261460|MTAP44|p44	interferon-induced protein 44	protein-coding
mm_1201.1	chr1	62718917	62718927	+	1	NA	intron (NM_001077405, intron 1 of 15)	intron (NM_001077405, intron 1 of 15)	15605	NM_001077405	18187	Mm.266341	NM_010939	ENSMUSG00000025969	Nrp2	1110048P06Rik|Np-2|Np2|Npn-2|Npn2	neuropilin 2	protein-coding
mm_32948.1	chr4	119540514	119540535	+	1	NA	intron (NM_172699, intron 1 of 12)	intron (NM_172699, intron 1 of 12)	863	NM_172699	230700	Mm.259227	NM_172699	ENSMUSG00000032998	Foxj3	C330039G02Rik|Fhd6	forkhead box J3	protein-coding
mm_80398.1	chr9	77046681	77046695	+	1	NA	promoter-TSS (NM_012033)	promoter-TSS (NM_012033)	-907	NM_012033	26944	Mm.23199	NM_012033	ENSMUSG00000032357	Tinag	AI452335|TIN-ag	tubulointerstitial nephritis antigen	protein-coding
mm_49783.1	chr6	35177719	35177758	+	1	NA	intron (NM_027513, intron 1 of 42)	CpG	122	NM_027513	70699	Mm.261208	NM_027513	ENSMUSG00000038759	Nup205	3830404O05Rik|AV248391|mKIAA0225	nucleoporin 205	protein-coding
mm_84945.1	chr9	83023988	83024007	-	1	NA	Intergenic	Intergenic	-48508	NM_001081216	83946	Mm.221688	NM_031879	ENSMUSG00000032253	Phip	2810004D21Rik|4632404O06Rik|Ndrp|Wdr11	pleckstrin homology domain interacting protein	protein-coding
mm_140846.1	chr17	23676588	23676629	-	1	NA	exon (NM_013749, exon 2 of 4)	exon (NM_013749, exon 2 of 4)	841	NM_001161746	27279	Mm.28518	NM_013749	ENSMUSG00000023905	Tnfrsf12a	AI255180|C87282|Fn14|HPIP|TWEAK-R|TweakR	tumor necrosis factor receptor superfamily, member 12a	protein-coding
mm_30188.1	chr3	144691942	144691966	-	1	NA	exon (NM_019464, exon 8 of 9)	exon (NM_019464, exon 8 of 9)	28381	NM_001282042	54673	Mm.271775	NM_019464	ENSMUSG00000037062	Sh3glb1	AA409932|AI314629|AU015566|Bif-1|mKIAA0491	SH3-domain GRB2-like B1 (endophilin)	protein-coding
mm_29182.1	chr3	106539452	106539472	-	1	NA	exon (NM_001293694, exon 2 of 9)	exon (NM_001293694, exon 2 of 9)	-8336	NM_001286986	67171	Mm.290488	NM_026013	ENSMUSG00000027900	Dram2	2010305N14Rik|2610318G18Rik|AI647667|Tmem77	DNA-damage regulated autophagy modulator 2	protein-coding
mm_98942.1	chr11	98386617	98386633	+	1	NA	promoter-TSS (NM_008890)	promoter-TSS (NM_008890)	-7	NM_008890	18948	Mm.57030	NM_008890	ENSMUSG00000038216	Pnmt	Pent	phenylethanolamine-N-methyltransferase	protein-coding
mm_147711.1	chr18	60812349	60812355	-	1	NA	TTS (NR_039567)	TTS (NR_039567)	276	NR_039567	100628611		NR_039567	ENSMUSG00000093327	Mir5107	mir-5107|mmu-mir-5107|mu-mir-5107	microRNA 5107	ncRNA
mm_146784.1	chr18	20114611	20114619	-	1	NA	5' UTR (NM_001291804, exon 1 of 16)	5' UTR (NM_001291804, exon 1 of 16)	158	NM_001291804	13505	Mm.33740	NM_013504	ENSMUSG00000044322	Dsc1	1110020A10Rik|AI507491	desmocollin 1	protein-coding
mm_72830.1	chr8	88272254	88272265	+	1	NA	promoter-TSS (NM_007406)	promoter-TSS (NM_007406)	-144	NM_007406	11513	Mm.288206	NM_007406	ENSMUSG00000031659	Adcy7	AA407758	adenylate cyclase 7	protein-coding
mm_55166.1	chr6	51888379	51888387	-	1	NA	intron (NM_018773, intron 9 of 12)	intron (NM_018773, intron 9 of 12)	124166	NM_018773	54353	Mm.221479	NM_018773	ENSMUSG00000059182	Skap2	2610021A10Rik|AA960083|BB137539|RA70|SKAP-HOM|Saps|Scap2|mSKAP55R	src family associated phosphoprotein 2	protein-coding
mm_27524.1	chr3	57301958	57301997	-	1	NA	promoter-TSS (NM_008536)	promoter-TSS (NM_008536)	-58	NM_008536	17112	Mm.856	NM_008536	ENSMUSG00000027800	Tm4sf1	L6|M3s1	transmembrane 4 superfamily member 1	protein-coding
mm_71518.1	chr8	46846636	46846649	+	1	NA	3' UTR (NM_008391, exon 9 of 9)	3' UTR (NM_008391, exon 9 of 9)	106897	NM_008391	16363	Mm.1149	NM_008391	ENSMUSG00000031627	Irf2	9830146E22Rik|AI646973|Irf-2	interferon regulatory factor 2	protein-coding
mm_33579.1	chr4	132530740	132530754	+	1	NA	exon (NM_007512, exon 4 of 4)	exon (NM_007512, exon 4 of 4)	4667	NM_007512	11983	Mm.2171	NM_007512	ENSMUSG00000054428	Atpif1	Atpi|IF(1)|If1	ATPase inhibitory factor 1	protein-coding
mm_109440.1	chr12	110737984	110738024	+	1	NA	promoter-TSS (NM_001347428)	promoter-TSS (NM_001347428)	72	NM_001347428	69641	Mm.475762	NM_027149	ENSMUSG00000037957	Wdr20	2310040A13Rik|AI549910|Wdr20a	WD repeat domain 20	protein-coding
mm_94458.1	chr11	6415831	6415867	+	1	NA	promoter-TSS (NM_008907)	promoter-TSS (NM_008907)	-21	NM_008907	268373	Mm.5246	NM_008907	ENSMUSG00000071866	Ppia	2700098C05|Cphn|CyP-18|CypA	peptidylprolyl isomerase A	protein-coding
mm_114346.1	chr13	60902527	60902542	+	1	NA	intron (NM_026429, intron 2 of 4)	intron (NM_026429, intron 2 of 4)	2313	NM_026429	116913	Mm.443229	NM_026429	ENSMUSG00000062705	Tpbpb	1600012N09Rik	trophoblast specific protein beta	protein-coding
mm_60435.1	chr7	44476895	44476903	+	1	NA	Intergenic	L1MEd|LINE|L1	6552	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_62244.1	chr7	98889911	98889913	+	1	NA	intron (NM_178635, intron 14 of 14)	intron (NM_178635, intron 14 of 14)	51067	NM_001285795	22411	Mm.22182	NM_009519	ENSMUSG00000015957	Wnt11	-	wingless-type MMTV integration site family, member 11	protein-coding
mm_25186.1	chr3	103373765	103373765	+	1	NA	Intergenic	Intergenic	94472	NM_001079830	94093	Mm.195036	NM_053170	ENSMUSG00000033014	Trim33	8030451N04Rik|AI413936|Ecto|Tif1g	tripartite motif-containing 33	protein-coding
mm_125523.1	chr15	57695663	57695685	+	1	NA	intron (NM_199449, intron 1 of 3)	CpG	1007	NM_199449	387609	Mm.36557	NM_199449	ENSMUSG00000071757	Zhx2	Afr-1|Afr1|Raf|mKIAA0854	zinc fingers and homeoboxes 2	protein-coding
mm_130618.1	chr15	100041398	100041412	-	1	NA	intron (NM_001159361, intron 1 of 37)	intron (NM_001159361, intron 1 of 37)	2741	NM_001159361	239667	Mm.243658	NM_172819	ENSMUSG00000023026	Dip2b	4932422C22|AI317237|AI854602|mKIAA1463	disco interacting protein 2 homolog B	protein-coding
mm_117970.1	chr13	100012499	100012501	-	1	NA	intron (NM_030026, intron 1 of 16)	intron (NM_030026, intron 1 of 16)	3139	NM_030026	78038	Mm.137327	NM_030026	ENSMUSG00000021646	Mccc2	4930552N12Rik|MCCB	methylcrotonoyl-Coenzyme A carboxylase 2 (beta)	protein-coding
mm_39127.1	chr4	155064014	155064045	-	1	NA	Intergenic	Intergenic	-3001	NM_001042407	668173	Mm.133114	NM_001042407	ENSMUSG00000029047	Pex10	AV128229|Gm142	peroxisomal biogenesis factor 10	protein-coding
mm_162840.1	chr10	85102589	85102607	+	1	NA	promoter-TSS (NM_001013028)	promoter-TSS (NM_001013028)	-29	NM_001013028	103266	Mm.335025	NM_001013028	ENSMUSG00000060935	Tmem263	AI597468	transmembrane protein 263	protein-coding
mm_5017.1	chr1	193145285	193145296	+	1	NA	Intergenic	Intergenic	-7822	NM_016851	54139	Mm.273695	NM_016851	ENSMUSG00000026638	Irf6	AI876454|E230028I05Rik|mirf6	interferon regulatory factor 6	protein-coding
mm_150759.1	chr19	44203266	44203284	+	1	NA	promoter-TSS (NM_024450)	promoter-TSS (NM_024450)	-13	NM_024450	30049	Mm.480594	NM_024450	ENSMUSG00000025202	Scd3	4930513N16Rik	stearoyl-coenzyme A desaturase 3	protein-coding
mm_27626.1	chr3	60320333	60320343	-	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-152492	NM_001253713	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_156344.1	chrX	139010146	139010233	+	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	75047	NM_177920	331535	Mm.211704	NM_177920	ENSMUSG00000031271	Serpina7	C730040N12Rik|Tbg	serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 7	protein-coding
mm_159196.1	chr2	119290211	119290211	+	1	NA	exon (NM_172269, exon 2 of 5)	exon (NM_172269, exon 2 of 5)	1469	NM_172269	228545	Mm.294761	NM_172269	ENSMUSG00000034216	Vps18	9930024E13Rik	VPS18 CORVET/HOPS core subunit	protein-coding
mm_158357.1	chrX	134600305	134600334	-	1	NA	promoter-TSS (NM_001313716)	promoter-TSS (NM_001313716)	686	NM_013463	11605	Mm.1114	NM_013463	ENSMUSG00000031266	Gla	Ags	galactosidase, alpha	protein-coding
mm_141866.1	chr17	34810089	34810109	-	1	NA	intron (NM_011413, intron 38 of 40)	intron (NM_011413, intron 38 of 40)	-5673	NM_009995	13079	Mm.440407	NM_009995	ENSMUSG00000024365	Cyp21a1	21-OH|21OH|21OHA|21OHB|CYP21OH-A|Cyp21|Cyp21-ps1|Cyp21B|Cyp21a2-ps|Cyp21a2ps|Oh21-1|Oh21-2	cytochrome P450, family 21, subfamily a, polypeptide 1	protein-coding
mm_160903.1	chr11	76495469	76495469	-	1	NA	promoter-TSS (NM_001346670)	promoter-TSS (NM_001346670)	-974	NM_001346670	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_14459.1	chr2	131207032	131207049	+	1	NA	intron (NR_037281, intron 2 of 2)	intron (NR_037281, intron 2 of 2)	-3320	NM_001291032	69596	Mm.2937	NM_027129	ENSMUSG00000068264	Ap5s1	0610038L13Rik|2310035K24Rik|AW060727|sigma5	adaptor-related protein 5 complex, sigma 1 subunit	protein-coding
mm_171853.1	chr5	16941529	16941529	+	1	NA	Intergenic	L1Md_T|LINE|L1	387628	NM_001289461	15234	Mm.267078	NM_010427	ENSMUSG00000028864	Hgf	C230052L06Rik|HGF/SF|NK1|NK2|SF|SF/HGF	hepatocyte growth factor	protein-coding
mm_135082.1	chr16	34514045	34514056	-	1	NA	promoter-TSS (NM_177357)	promoter-TSS (NM_177357)	-23	NM_177357	545156	Mm.82274	NM_177357	ENSMUSG00000061751	Kalrn	2210407G14Rik|AV235988|DUET|E530005C20Rik|Gm539|Hapip|TRAD	kalirin, RhoGEF kinase	protein-coding
mm_135599.1	chr16	51363890	51363901	-	1	NA	Intergenic	Intergenic	580486	NR_131005	78639	Mm.160109	NR_131005	ENSMUSG00000092276	1700116B05Rik	-	RIKEN cDNA 1700116B05 gene	ncRNA
mm_22617.1	chr3	14578892	14578925	+	1	NA	exon (NM_007892, exon 1 of 8)	exon (NM_007892, exon 1 of 8)	237	NM_007892	13559	Mm.153415	NM_007892	ENSMUSG00000027552	E2f5	AU024671|E2F-5	E2F transcription factor 5	protein-coding
mm_145522.1	chr18	60558193	60558197	+	1	NA	3' UTR (NM_026302, exon 13 of 13)	3' UTR (NM_026302, exon 13 of 13)	-2591	NM_025776	66810	Mm.275106	NM_025776	ENSMUSG00000024604	Rbm22	8430430L24Rik	RNA binding motif protein 22	protein-coding
mm_133305.1	chr16	77598109	77598130	+	1	NA	promoter-TSS (NR_029535)	promoter-TSS (NR_029535)	-817	NR_029535	387229		NR_029535	ENSMUSG00000065530	Mir99a	Mirn99a|mir-99a|mmu-mir-99a	microRNA 99a	ncRNA
mm_165793.1	chr3	138785505	138785507	+	1	NA	intron (NM_019571, intron 1 of 7)	intron (NM_019571, intron 1 of 7)	43298	NM_019571	56224	Mm.31927	NM_019571	ENSMUSG00000028152	Tspan5	2810455A09Rik|4930505M03Rik|NET-4|Tm4sf9	tetraspanin 5	protein-coding
mm_26522.1	chr3	145924439	145924449	+	1	NA	5' UTR (NM_009740, exon 1 of 3)	5' UTR (NM_009740, exon 1 of 3)	182	NM_009740	12042	Mm.239141	NM_009740	ENSMUSG00000028191	Bcl10	AI132454|BCL-10|C81403|CARMEN|CIPER|CLAP|ME10|cE10	B cell leukemia/lymphoma 10	protein-coding
mm_170427.1	chr18	74332442	74332445	-	1	NA	intron (NR_029424, intron 8 of 8)	RLTR1B|LTR|ERV1	49343	NM_028948	74453	Mm.182293	NM_028948	ENSMUSG00000035394	Cfap53	4933415I03Rik|Ccdc11	cilia and flagella associated protein 53	protein-coding
mm_149778.1	chr19	23134494	23134498	+	1	NA	Intergenic	(T)n|Simple_repeat|Simple_repeat	-6730	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_70373.1	chr8	9977852	9977872	+	1	NA	5' UTR (NM_026868, exon 1 of 3)	5' UTR (NM_026868, exon 1 of 3)	145	NM_026868	68904	Mm.142570	NM_026868	ENSMUSG00000040396	Abhd13	1110065L07Rik|AI463703|AI788994	abhydrolase domain containing 13	protein-coding
mm_76634.1	chr8	92354581	92354604	-	1	NA	intron (NR_110452, intron 1 of 3)	intron (NR_110452, intron 1 of 3)	1528	NR_110452	71296	Mm.86664	NR_033641	ENSMUSG00000031736	Crnde	4933436C20Rik	colorectal neoplasia differentially expressed (non-protein coding)	ncRNA
mm_145369.1	chr18	56733191	56733210	+	1	NA	intron (NM_010721, intron 4 of 10)	intron (NM_010721, intron 4 of 10)	25387	NM_010721	16906	Mm.4105	NM_010721	ENSMUSG00000024590	Lmnb1	-	lamin B1	protein-coding
mm_81113.1	chr9	106453913	106453933	+	1	NA	promoter-TSS (NM_021567)	promoter-TSS (NM_021567)	85	NM_021567	59092	Mm.286394	NM_021567	ENSMUSG00000023495	Pcbp4	1200003L19Rik|AlphaCP-4	poly(rC) binding protein 4	protein-coding
mm_54871.1	chr6	42598968	42598970	-	1	NA	Intergenic	Intergenic	-1597	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_131819.1	chr16	22920409	22920439	+	1	NA	5' UTR (NM_021564, exon 1 of 8)	5' UTR (NM_021564, exon 1 of 8)	202	NM_001083904	59083	Mm.28461	NM_021564	ENSMUSG00000022871	Fetub	2310011O17Rik|AI255764|D17980|Gugu	fetuin beta	protein-coding
mm_24223.1	chr3	88702115	88702119	+	1	NA	intron (NM_028814, intron 10 of 13)	B1_Mur3|SINE|Alu	-14737	NM_009069	19769	Mm.4009	NM_009069	ENSMUSG00000028057	Rit1	RIBB|ROC1|Rit	Ras-like without CAAX 1	protein-coding
mm_27101.1	chr3	30509463	30509509	-	1	NA	promoter-TSS (NM_021442)	promoter-TSS (NM_021442)	1	NM_021442	14013	Mm.56965	NM_007963	ENSMUSG00000027684	Mecom	D630039M04Rik|Evi-1|Evi1|Jbo|Mds|Mds1|Mds1-Evi1|Prdm3|Znfpr1b1	MDS1 and EVI1 complex locus	protein-coding
mm_131560.1	chr16	18127377	18127437	+	1	NA	promoter-TSS (NM_022982)	promoter-TSS (NM_022982)	-299	NM_022982	65079	Mm.40149	NM_022982	ENSMUSG00000043811	Rtn4r	NOGOR|NgR|NgR1	reticulon 4 receptor	protein-coding
mm_162975.1	chr11	17487201	17487207	+	1	NA	Intergenic	Intergenic	229516	NM_001330649	57316	Mm.287982	NM_020558	ENSMUSG00000000581	C1d	1110036E10Rik|AI875855|SUN-CoR	C1D nuclear receptor co-repressor	protein-coding
mm_129606.1	chr15	79931696	79931736	-	1	NA	intron (NM_144811, intron 1 of 6)	intron (NM_144811, intron 1 of 6)	930	NM_144811	52609	Mm.323442	NM_144811	ENSMUSG00000053411	Cbx7	1600014J01Rik|AI851678|D15Ertd417e	chromobox 7	protein-coding
mm_35826.1	chr4	47302551	47302563	-	1	NA	intron (NM_009928, intron 33 of 39)	intron (NM_009928, intron 33 of 39)	-50665	NM_001312868	21812	Mm.197552	NM_009370	ENSMUSG00000007613	Tgfbr1	ALK5|AU017191|Alk-5|ESK2|TGFR-1|TbetaR-I|TbetaRI	transforming growth factor, beta receptor I	protein-coding
mm_148268.1	chr18	81589259	81589262	-	1	NA	Intergenic	Intergenic	402820	NR_039589	100628596		NR_039589	ENSMUSG00000093036	Mir5127	mmu-mir-5127|mu-mir-5127	microRNA 5127	ncRNA
mm_70289.1	chr8	3659768	3659769	+	1	NA	TTS (NM_001204959)	TTS (NM_001204959)	3998	NM_022984	57264	Mm.1181	NM_022984	ENSMUSG00000012705	Retn	ADSF|Fizz3|Rstn|Xcp4	resistin	protein-coding
mm_154229.1	chr19	59943648	59943678	-	1	NA	promoter-TSS (NM_001164367)	promoter-TSS (NM_001164367)	-9	NM_001164367	74998	Mm.24167	NM_001033172	ENSMUSG00000040022	Rab11fip2	4930470G04Rik|A830046J09Rik|AW558126|Nrip11	RAB11 family interacting protein 2 (class I)	protein-coding
mm_153505.1	chr19	41359155	41359194	-	1	NA	intron (NM_031376, intron 2 of 16)	intron (NM_031376, intron 2 of 16)	25896	NM_031376	83490	Mm.222266	NM_031376	ENSMUSG00000025017	Pik3ap1	1810044J04Rik|BCAP	phosphoinositide-3-kinase adaptor protein 1	protein-coding
mm_171745.1	chr4	98665835	98665851	+	1	NA	intron (NM_001005787, intron 8 of 15)	intron (NM_001005787, intron 8 of 15)	-60911	NM_001081202	381591	Mm.34340	NM_001081202	ENSMUSG00000087166	L1td1	AA546746|AB211064|D76865|ECAT11	LINE-1 type transposase domain containing 1	protein-coding
mm_33051.1	chr4	123105130	123105138	+	1	NA	promoter-TSS (NM_007559)	promoter-TSS (NM_007559)	-27	NM_007559	12164	Mm.439764	NM_007559	ENSMUSG00000002384	Bmp8b	Op3	bone morphogenetic protein 8b	protein-coding
mm_94606.1	chr11	14599253	14599296	+	1	NA	promoter-TSS (NM_001164166)	promoter-TSS (NM_001164166)	34	NM_001164166	432536	Mm.33646	NM_001164166	ENSMUSG00000084135	Pom121l12	1700054H16Rik	POM121 membrane glycoprotein-like 12	protein-coding
mm_92681.1	chr10	80587298	80587316	-	1	NA	intron (NM_145421, intron 1 of 4)	intron (NM_145421, intron 1 of 4)	3034	NM_145421	216169	Mm.29802	NM_145421	ENSMUSG00000003346	Abhd17a	1700013O15Rik|BC005632|D10Bwg1364e|Fam108a	abhydrolase domain containing 17A	protein-coding
mm_168961.1	chr12	80260127	80260139	-	1	NA	5' UTR (NM_134156, exon 1 of 21)	5' UTR (NM_134156, exon 1 of 21)	238	NM_134156	109711	Mm.253564	NM_134156	ENSMUSG00000015143	Actn1	3110023F10Rik|Actn1a	actinin, alpha 1	protein-coding
mm_104304.1	chr11	90663804	90663807	-	1	NA	intron (NM_028011, intron 7 of 15)	intron (NM_028011, intron 7 of 15)	23796	NM_028011	71943	Mm.167868	NM_028011	ENSMUSG00000020541	Tom1l1	2310045L10Rik|C80573|Srcasm	target of myb1-like 1 (chicken)	protein-coding
mm_117401.1	chr13	73700689	73700702	-	1	NA	promoter-TSS (NM_028878)	promoter-TSS (NM_028878)	0	NM_028878	74338	Mm.271635	NM_028878	ENSMUSG00000021565	Slc6a19	4632401C08Rik|B<0>AT1	solute carrier family 6 (neurotransmitter transporter), member 19	protein-coding
mm_16650.1	chr2	6323075	6323096	-	1	NA	intron (NM_001080548, intron 1 of 14)	CpG	328	NM_001080548	98910	Mm.40673	NM_181399	ENSMUSG00000039046	Usp6nl	AI316785|RNTRE|TRE2NL|mKIAA0019	USP6 N-terminal like	protein-coding
mm_24681.1	chr3	94886967	94886998	+	1	NA	promoter-TSS (NM_008945)	promoter-TSS (NM_008945)	-24	NM_008945	19172	Mm.368	NM_008945	ENSMUSG00000005779	Psmb4	Pros-27	proteasome (prosome, macropain) subunit, beta type 4	protein-coding
mm_83589.1	chr9	48420600	48420638	-	1	NA	Intergenic	Intergenic	-33725	NR_026561	667933	Mm.491076	NR_026561		Gm8884	EG667933	predicted gene 8884	ncRNA
mm_23157.1	chr3	40531579	40531599	+	1	NA	Intergenic	CpG	-8677	NR_040445	100040882	Mm.272869	NR_040445	ENSMUSG00000037884	1700017G19Rik	-	RIKEN cDNA 1700017G19 gene	ncRNA
mm_76546.1	chr8	88118624	88118628	-	1	NA	promoter-TSS (NM_029074)	promoter-TSS (NM_029074)	-133	NM_029074	382030	Mm.216574	NM_029074	ENSMUSG00000036810	Cnep1r1	5033428A16Rik|NEP1-R1|Tmem188	CTD nuclear envelope phosphatase 1 regulatory subunit 1	protein-coding
mm_86336.1	chr9	123113207	123113213	-	1	NA	promoter-TSS (NM_026917)	promoter-TSS (NM_026917)	-5	NM_026917	69035	Mm.28300	NM_026917	ENSMUSG00000025786	Zdhhc3	1110020O22Rik|1810006O10Rik|2210017C02Rik|DHHC-3|GODZ|Gramp1|Zfp373	zinc finger, DHHC domain containing 3	protein-coding
mm_50448.1	chr6	48904961	48904973	+	1	NA	promoter-TSS (NM_001161622)	promoter-TSS (NM_001161622)	-19	NM_001161622	76507	Mm.213898	NM_029638	ENSMUSG00000029811	Aoc1	1600012D06Rik|Abp1|DAO	amine oxidase, copper-containing 1	protein-coding
mm_43173.1	chr5	127615701	127615718	+	1	NA	intron (NM_133895, intron 1 of 7)	intron (NM_133895, intron 1 of 7)	1683	NM_133895	100561	Mm.28506	NM_133895	ENSMUSG00000029416	Slc15a4	AA987064|AW742963|C130069N12Rik|PHT1|PTR4	solute carrier family 15, member 4	protein-coding
mm_168397.1	chr11	29172854	29172871	+	1	NA	promoter-TSS (NM_134034)	promoter-TSS (NM_134034)	-45	NM_134034	104570	Mm.276386	NM_134034	ENSMUSG00000020463	Smek2	AW011752|AW557776|Ppp4r3b|mKIAA1387	SMEK homolog 2, suppressor of mek1 (Dictyostelium)	protein-coding
mm_172168.1	chr6	44793148	44793148	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-266913	NM_001004357	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding
mm_150315.1	chr19	34573482	34573504	+	1	NA	exon (NM_008332, exon 3 of 3)	exon (NM_008332, exon 3 of 3)	-10036	NM_010501	15959	Mm.426079	NM_010501	ENSMUSG00000074896	Ifit3	Ifi49|P49	interferon-induced protein with tetratricopeptide repeats 3	protein-coding
mm_105200.1	chr11	102097531	102097537	-	1	NA	Intergenic	Intergenic	3766	NM_008918	19064	Mm.1269	NM_008918	ENSMUSG00000017316	Ppy	AV061413|IGSPP|PP	pancreatic polypeptide	protein-coding
mm_132884.1	chr16	48816962	48816976	+	1	NA	5' UTR (NM_023881, exon 1 of 4)	5' UTR (NM_023881, exon 1 of 4)	113	NM_023881	57263	Mm.21123	NM_023881	ENSMUSG00000022650	Retnlb	9030012B21Rik|Fizz2|RELMbeta|Relmb|Xcp3	resistin like beta	protein-coding
mm_20426.1	chr2	129304795	129304808	-	1	NA	exon (NM_010554, exon 5 of 7)	exon (NM_010554, exon 5 of 7)	5171	NM_010554	16175	Mm.15534	NM_010554	ENSMUSG00000027399	Il1a	Il-1a	interleukin 1 alpha	protein-coding
mm_145770.1	chr18	65023863	65023903	+	1	NA	5' UTR (NM_031881, exon 1 of 30)	5' UTR (NM_031881, exon 1 of 30)	356	NM_031881	83814	Mm.98668	NM_031881	ENSMUSG00000024589	Nedd4l	1300012C07Rik|Nedd4-2|Nedd4b	neural precursor cell expressed, developmentally down-regulated gene 4-like	protein-coding
mm_6076.1	chr1	61851485	61851497	-	1	NA	intron (NM_001081050, intron 2 of 22)	MLT1A|LTR|ERVL-MaLR	212667	NM_001081050	72823	Mm.35153	NM_001081050	ENSMUSG00000052062	Pard3b	1810008K04Rik|2010002N16Rik|2810455B10Rik|Als2cr19|PAR3B|PAR3L|PAR3beta	par-3 family cell polarity regulator beta	protein-coding
mm_168282.1	chr1	107823699	107823717	+	1	NA	Intergenic	L1Md_T|LINE|L1	-93551	NR_102306	319596	Mm.136054	NR_102306	ENSMUSG00000100457	D830032E09Rik	-	RIKEN cDNA D830032E09 gene	ncRNA
mm_67097.1	chr7	69908061	69908067	-	1	NA	Intergenic	Intergenic	411970	NR_045940	73796	Mm.410832	NR_045940	ENSMUSG00000108885	4930402F11Rik	-	RIKEN cDNA 4930402F11 gene	ncRNA
mm_77173.1	chr8	111690443	111690454	-	1	NA	promoter-TSS (NR_106044)	promoter-TSS (NR_106044)	562	NM_025583	66473	Mm.34374	NM_025583	ENSMUSG00000031957	Ctrb1	2200008D09Rik|AI504462|Ctrb|Prt-2	chymotrypsinogen B1	protein-coding
mm_153206.1	chr19	34649718	34649728	-	1	NA	3' UTR (NM_008331, exon 2 of 2)	3' UTR (NM_008331, exon 2 of 2)	8834	NM_008331	15957	Mm.439751	NM_008331	ENSMUSG00000034459	Ifit1	ISG56|Ifi56|P56	interferon-induced protein with tetratricopeptide repeats 1	protein-coding
mm_4374.1	chr1	172135378	172135408	+	1	NA	3' UTR (NM_001159525, exon 6 of 6)	3' UTR (NM_001159525, exon 6 of 6)	8638	NM_023041	19298	Mm.247764	NM_023041	ENSMUSG00000003464	Pex19	Pxf	peroxisomal biogenesis factor 19	protein-coding
mm_8638.1	chr1	156428530	156428532	-	1	NA	3' UTR (NM_009230, exon 16 of 16)	3' UTR (NM_009230, exon 16 of 16)	-7616	NM_001346967	77352	Mm.428709	NM_001033180	ENSMUSG00000026601	Axdnd1	9430070O13Rik|Gm979	axonemal dynein light chain domain containing 1	protein-coding
mm_4265.1	chr1	171466010	171466016	+	1	NA	Intergenic	Intergenic	28452	NM_172647	16456	Mm.294882	NM_172647	ENSMUSG00000038235	F11r	9130004G24|AA638916|ESTM33|JAM|JAM-1|JAM-A|Jcam|Jcam1|Ly106	F11 receptor	protein-coding
mm_95452.1	chr11	50357760	50357773	+	1	NA	TTS (NR_030529)	TTS (NR_030529)	113	NR_030529	100049547		NR_030529	ENSMUSG00000076450	Mir804	Mirn804|mmu-mir-804	microRNA 804	ncRNA
mm_75418.1	chr8	46739454	46739514	-	1	NA	promoter-TSS (NM_008391)	promoter-TSS (NM_008391)	31	NR_045750	100503498	Mm.187358	NR_045750	ENSMUSG00000097534	Gm16675	-	predicted gene, 16675	ncRNA
mm_111413.1	chr12	91384404	91384430	-	1	NA	promoter-TSS (NM_181815)	promoter-TSS (NM_181815)	-8	NM_181815	75216	Mm.312204	NM_181815	ENSMUSG00000061533	Cep128	4930534B04Rik|5430424K18Rik|AI449708|AI480494|E230024F20	centrosomal protein 128	protein-coding
mm_57271.1	chr6	123289234	123289236	-	1	NA	intron (NM_019948, intron 1 of 5)	intron (NM_019948, intron 1 of 5)	636	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_158545.1	chrX	145480643	145480657	-	1	NA	intron (NM_001290274, intron 1 of 8)	intron (NM_001290274, intron 1 of 8)	6989	NM_001290274	27494	Mm.100068	NM_153319	ENSMUSG00000041688	Amot	CAG-2|D0Kist1|Sii6	angiomotin	protein-coding
mm_11822.1	chr2	44335921	44335933	+	1	NA	intron (NM_001301831, intron 13 of 14)	intron (NM_001301831, intron 13 of 14)	-270603	NR_040622	320872	Mm.445023	NR_040622	ENSMUSG00000085089	Arhgap15os	A430092G05Rik	Rho GTPase activating protein 15, opposite strand	ncRNA
mm_128357.1	chr15	39944652	39944666	-	1	NA	promoter-TSS (NM_172814)	promoter-TSS (NM_172814)	-665	NM_001347036	239393	Mm.39874	NM_172814	ENSMUSG00000022305	Lrp12	AI848829|C820005L12Rik|LRP-12	low density lipoprotein-related protein 12	protein-coding
mm_38734.1	chr4	145245592	145245602	-	1	NA	intron (NM_011610, intron 1 of 9)	intron (NM_011610, intron 1 of 9)	1273	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_82050.1	chr9	122421303	122421307	+	1	NA	Intergenic	Intergenic	-22504	NR_045967	654800	Mm.393956	NR_045967		A730085K08Rik	-	RIKEN cDNA A730085K08 gene	ncRNA
mm_163645.1	chr13	63063890	63063891	+	1	NA	intron (NM_001289926, intron 4 of 15)	intron (NM_001289926, intron 4 of 15)	98997	NM_001289924	72061	Mm.188105	NM_028079	ENSMUSG00000021458	2010111I01Rik	2300006M17Rik|AP-O|AW742919|Aopep|ApO|mir-23b|mir-24-1|mir-27b	RIKEN cDNA 2010111I01 gene	protein-coding
mm_26031.1	chr3	135455929	135455932	+	1	NA	intron (NM_025356, intron 4 of 7)	intron (NM_025356, intron 4 of 7)	17171	NM_025356	66105	Mm.49884	NM_025356	ENSMUSG00000078578	Ube2d3	1100001F19Rik|9430029A22Rik|AA414951	ubiquitin-conjugating enzyme E2D 3	protein-coding
mm_69976.1	chr7	142377146	142377168	-	1	NA	exon (NM_009983, exon 7 of 9)	exon (NM_009983, exon 7 of 9)	-3411	NM_001347541	320802	Mm.154486	NM_177265	ENSMUSG00000045777	Ifitm10	6330512M04Rik|AI848576|DSPA3	interferon induced transmembrane protein 10	protein-coding
mm_100408.1	chr11	119422441	119422478	+	1	NA	Intergenic	B1_Mur3|SINE|Alu	31987	NR_035453	100316690		NR_035453	ENSMUSG00000088015	Mir1932	mir-1932|mmu-mir-1932	microRNA 1932	ncRNA
mm_148176.1	chr18	78142080	78142090	-	1	NA	promoter-TSS (NM_001171011)	promoter-TSS (NM_001171011)	34	NM_001171011	108052	Mm.33832	NM_028122	ENSMUSG00000059336	Slc14a1	2610507K20Rik|3021401A05Rik|UT-B|Utb1	solute carrier family 14 (urea transporter), member 1	protein-coding
mm_144763.1	chr18	35771677	35771710	+	1	NA	5' UTR (NM_019912, exon 1 of 7)	5' UTR (NM_019912, exon 1 of 7)	134	NM_019912	56550	Mm.180052	NM_019912	ENSMUSG00000091896	Ube2d2a	1500034D03Rik|Ubc2e|Ube2d2|ubc4	ubiquitin-conjugating enzyme E2D 2A	protein-coding
mm_159023.1	chr1	173203267	173203267	+	1	NA	promoter-TSS (NM_001001809)	promoter-TSS (NM_001001809)	-91	NM_001001809	258880	Mm.377732	NM_001001809	ENSMUSG00000046643	Olfr218	MOR267-3|Olfr1405-ps1|Olfr218-ps1	olfactory receptor 218	protein-coding
mm_81806.1	chr9	116370135	116370135	+	1	NA	Intergenic	Zaphod|DNA|hAT-Tip100	-194772	NM_009371	21813	Mm.172346	NM_009371	ENSMUSG00000032440	Tgfbr2	1110020H15Rik|AU042018|DNIIR|RIIDN|TBR-II|TbetaR-II|TbetaRII	transforming growth factor, beta receptor II	protein-coding
mm_34235.1	chr4	141107099	141107107	+	1	NA	intron (NM_177867, intron 10 of 14)	intron (NM_177867, intron 10 of 14)	18758	NM_177867	329972	Mm.247201	NM_177867	ENSMUSG00000045004	Spata21	4933414G08	spermatogenesis associated 21	protein-coding
mm_78388.1	chr9	28403539	28403552	+	1	NA	intron (NM_177906, intron 1 of 7)	CpG	612276	NM_177906	330908	Mm.379474	NM_177906	ENSMUSG00000062257	Opcml	2900075O15Rik|3732419F12|AI844366|B930023M13Rik|C230027C17|Gm181|Obcam	opioid binding protein/cell adhesion molecule-like	protein-coding
mm_68802.1	chr7	125491398	125491413	-	1	NA	intron (NM_026330, intron 1 of 7)	CpG	137	NM_026330	67711	Mm.4467	NM_026330	ENSMUSG00000030750	Nsmce1	2510027N19Rik	NSE1 homolog, SMC5-SMC6 complex component	protein-coding
mm_22519.1	chr3	7629204	7629241	+	1	NA	Intergenic	Intergenic	-15462	NM_001313888	16196	Mm.3825	NM_008371	ENSMUSG00000040329	Il7	A630026I06Rik|Il-7|hlb368	interleukin 7	protein-coding
mm_43825.1	chr5	142970515	142970526	+	1	NA	exon (NM_007984, exon 4 of 5)	exon (NM_007984, exon 4 of 5)	10165	NM_007984	14086	Mm.289707	NM_007984	ENSMUSG00000029581	Fscn1	AI663989|Fan1|fascin-1	fascin actin-bundling protein 1	protein-coding
mm_29063.1	chr3	103791388	103791410	-	1	NA	promoter-TSS (NM_010432)	promoter-TSS (NM_010432)	-124	NM_010432	15257	Mm.20827	NM_010432	ENSMUSG00000008730	Hipk1	1110062K04Rik|Myak	homeodomain interacting protein kinase 1	protein-coding
mm_101106.1	chr11	11932564	11932572	-	1	NA	3' UTR (NM_010345, exon 17 of 17)	3' UTR (NM_010345, exon 17 of 17)	-34424	NM_001190448	13195	Mm.12906	NM_016672	ENSMUSG00000020182	Ddc	Aadc	dopa decarboxylase	protein-coding
mm_160267.1	chr7	113280721	113280721	+	1	NA	exon (NM_007489, exon 5 of 20)	exon (NM_007489, exon 5 of 20)	73256	NM_007489	11865	Mm.33970	NM_007489	ENSMUSG00000055116	Arntl	Arnt3|BMAL1b|Bmal1|MOP3|bHLHe5|bmal1b'	aryl hydrocarbon receptor nuclear translocator-like	protein-coding
mm_154770.1	chrX	12615677	12615857	+	1	NA	exon (NM_027439, exon 9 of 9)	exon (NM_027439, exon 9 of 9)	28008	NM_027439	70495	Mm.25148	NM_027439	ENSMUSG00000031007	Atp6ap2	(P)RR|5730403E06Rik|APT6M8-9|ATP6M8-9|Atp6ip2|M8-9|PRR	ATPase, H+ transporting, lysosomal accessory protein 2	protein-coding
mm_147569.1	chr18	54992553	54992597	-	1	NA	Intergenic	Intergenic	-2395	NM_175751	269023	Mm.192984	NM_175751	ENSMUSG00000052713	Zfp608	4932417D18Rik|D430007A19Rik|Znf608	zinc finger protein 608	protein-coding
mm_29658.1	chr3	122551535	122551541	-	1	NA	intron (NM_153118, intron 9 of 13)	intron (NM_153118, intron 9 of 13)	-9857	NR_106117	102465764		NR_106117	ENSMUSG00000104773	Mir7657	mmu-mir-7657	microRNA 7657	ncRNA
mm_39833.1	chr5	30853797	30853801	+	1	NA	intron (NM_133350, intron 1 of 6)	intron (NM_133350, intron 1 of 6)	-8008	NM_001310516	100732	Mm.332295	NM_133350	ENSMUSG00000029166	Mapre3	AI790651|EB2|EB3|EBF3|RP3	microtubule-associated protein, RP/EB family, member 3	protein-coding
mm_133250.1	chr16	77261779	77261782	+	1	NA	Intergenic	Lx6|LINE|L1	-67548	NR_015543	77994	Mm.394688	NR_015543	ENSMUSG00000090386	Mir99ahg	2810055G20Rik|D730043B02Rik	Mir99a and Mirlet7c-1 host gene (non-protein coding)	ncRNA
mm_100935.1	chr11	6520865	6520866	-	1	NA	promoter-TSS (NM_178440)	promoter-TSS (NM_178440)	93	NM_178440	246177	Mm.239554	NM_178440	ENSMUSG00000020437	Myo1g	E430002D17Rik	myosin IG	protein-coding
mm_115938.1	chr13	23622018	23622106	-	1	NA	promoter-TSS (NM_178194)	promoter-TSS (NM_178194)	496	NM_015787	50709	Mm.170587	NM_015787	ENSMUSG00000051627	Hist1h1e	H1-4|H1.4|H1e|H1f4|H1s-4|H1var2	histone cluster 1, H1e	protein-coding
mm_170152.1	chr17	45571084	45571093	-	1	NA	exon (NM_008302, exon 4 of 11)	exon (NM_008302, exon 4 of 11)	2173	NM_008302	15516	Mm.2180	NM_008302	ENSMUSG00000023944	Hsp90ab1	90kDa|AL022974|C81438|Hsp84|Hsp84-1|Hsp90|Hspcb	heat shock protein 90 alpha (cytosolic), class B member 1	protein-coding
mm_165068.1	chr19	44407506	44407508	-	1	NA	5' UTR (NM_009127, exon 1 of 6)	5' UTR (NM_009127, exon 1 of 6)	202	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_30336.1	chr3	151732315	151732324	-	1	NA	3' UTR (NM_133871, exon 8 of 8)	3' UTR (NM_133871, exon 8 of 8)	17640	NM_133871	99899	Mm.30756	NM_133871	ENSMUSG00000028037	Ifi44	A430056A10Rik|AW261460|MTAP44|p44	interferon-induced protein 44	protein-coding
mm_79679.1	chr9	59750952	59750999	+	1	NA	promoter-TSS (NM_001172071)	promoter-TSS (NM_001172071)	-199	NM_173018	270163	Mm.249545	NM_173018	ENSMUSG00000039585	Myo9a	4732465J09Rik|C130068I12Rik|C230003M11	myosin IXa	protein-coding
mm_123849.1	chr14	70754556	70754556	-	1	NA	intron (NM_023045, intron 1 of 27)	intron (NM_023045, intron 1 of 27)	12072	NM_023045	65246	Mm.152987	NM_023045	ENSMUSG00000022100	Xpo7	4930506C02Rik|BB164534|Ranbp16|mKIAA0745	exportin 7	protein-coding
mm_77452.1	chr8	121829521	121829571	-	1	NA	promoter-TSS (NM_145605)	promoter-TSS (NM_145605)	23	NM_145605	234825	Mm.209329	NM_145605	ENSMUSG00000040263	Klhdc4	AA408426|AV352552|BC012312|G430025P05Rik	kelch domain containing 4	protein-coding
mm_9677.1	chr1	178331938	178331962	-	1	NA	exon (NM_016805, exon 8 of 14)	exon (NM_016805, exon 8 of 14)	5834	NM_016805	51810	Mm.86589	NM_016805	ENSMUSG00000039630	Hnrnpu	AA408410|AI256620|AL024194|AL024437|AW557595|C86794|Hnrpu|SAFA|Sp120|hnRNP U	heterogeneous nuclear ribonucleoprotein U	protein-coding
mm_26287.1	chr3	142506727	142506733	+	1	NA	exon (NM_153564, exon 8 of 11)	exon (NM_153564, exon 8 of 11)	9796	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_54581.1	chr6	38124503	38124538	-	1	NA	promoter-TSS (NM_080467)	promoter-TSS (NM_080467)	66	NM_080467	140494	Mm.462308	NM_080467	ENSMUSG00000038600	Atp6v0a4	Atp6n1b|a4	ATPase, H+ transporting, lysosomal V0 subunit A4	protein-coding
mm_95104.1	chr11	34048832	34048835	+	1	NA	intron (NM_010696, intron 1 of 20)	MIRb|SINE|MIR	1632	NM_010696	16822	Mm.265350	NM_010696	ENSMUSG00000002699	Lcp2	AI323664|BB161688|SLP-76|SLP76|m1Khoe|twm	lymphocyte cytosolic protein 2	protein-coding
mm_57345.1	chr6	124749504	124749522	-	1	NA	exon (NM_007881, exon 3 of 10)	exon (NM_007881, exon 3 of 10)	6974	NM_007881	13498	Mm.333380	NM_007881	ENSMUSG00000004263	Atn1	Atr1|Drpla|atrophin-1	atrophin 1	protein-coding
mm_32367.1	chr4	105258615	105258622	+	1	NA	Intergenic	Intergenic	101271	NM_080555	67916	Mm.348326	NM_080555	ENSMUSG00000028517	Plpp3	1110003O22Rik|2610002D05Rik|AV025606|D4Bwg0538e|D4Bwg1535e|Lpp3|Ppab2b|Ppap2b	phospholipid phosphatase 3	protein-coding
mm_22438.1	chr2	181693545	181693554	-	1	NA	5' UTR (NM_001291208, exon 1 of 5)	5' UTR (NM_001291208, exon 1 of 5)	261	NM_001291206	56470	Mm.274366	NM_026446	ENSMUSG00000002458	Rgs19	2610042F04Rik|AI324841|AW547781|GAIP	regulator of G-protein signaling 19	protein-coding
mm_95660.1	chr11	53771268	53771277	+	1	NA	intron (NM_001159396, intron 1 of 9)	intron (NM_001159396, intron 1 of 9)	799	NM_001159396	16362	Mm.105218	NM_008390	ENSMUSG00000018899	Irf1	AU020929|Irf-1	interferon regulatory factor 1	protein-coding
mm_61517.1	chr7	78913787	78913791	+	1	NA	promoter-TSS (NM_020583)	promoter-TSS (NM_020583)	24	NM_020583	57444	Mm.322843	NM_020583	ENSMUSG00000039236	Isg20	1600023I01Rik|2010107M23Rik|20kDa|DnaQL|HEM45	interferon-stimulated protein	protein-coding
mm_44653.1	chr5	28210171	28210179	-	1	NA	promoter-TSS (NM_001310511)	promoter-TSS (NM_001310511)	-7	NM_001310511	269637	Mm.68286	NM_175651	ENSMUSG00000044681	Cnpy1	1500012D20Rik|9630008K15Rik|AI853839	canopy FGF signaling regulator 1	protein-coding
mm_130191.1	chr15	94404289	94404327	-	1	NA	promoter-TSS (NM_001164785)	promoter-TSS (NM_001164785)	42	NM_001164785	223838	Mm.214132	NM_177431	ENSMUSG00000022449	Adamts20	Adamst20|bt	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 20	protein-coding
mm_103156.1	chr11	70408944	70408949	-	1	NA	intron (NM_029231, intron 1 of 16)	B1_Mur1|SINE|Alu	1085	NM_029231	75273	Mm.340601	NM_029231	ENSMUSG00000018921	Pelp1	4930563C04Rik|MNAR	proline, glutamic acid and leucine rich protein 1	protein-coding
mm_38683.1	chr4	145067221	145067229	-	1	NA	intron (NM_001276502, intron 56 of 68)	intron (NM_001276502, intron 56 of 68)	123441	NM_001276502	230895	Mm.240310	NM_001033190	ENSMUSG00000020220	Vps13d	-	vacuolar protein sorting 13D	protein-coding
mm_128579.1	chr15	57912903	57912917	-	1	NA	intron (NM_001167679, intron 1 of 17)	intron (NM_001167679, intron 1 of 17)	711	NM_001167679	210544	Mm.390835	NM_199300	ENSMUSG00000022364	Tbc1d31	4B3|D330013L20Rik|Gm85|Wdr67	TBC1 domain family, member 31	protein-coding
mm_162807.1	chr10	77880084	77880086	+	1	NA	intron (NM_001287074, intron 9 of 11)	intron (NM_001287074, intron 9 of 11)	-13335	NR_015547	75188	Mm.348012	NM_029200	ENSMUSG00000096573	1700009J07Rik	4930535B06Rik	RIKEN cDNA 1700009J07 gene	ncRNA
mm_138314.1	chr17	34661611	34661617	+	1	NA	Intergenic	Intergenic	-8921	NM_031176	81877	Mm.290527	NM_031176	ENSMUSG00000033327	Tnxb	Tn-mhc|Tnx	tenascin XB	protein-coding
mm_122267.1	chr14	34355384	34355401	-	1	NA	promoter-TSS (NM_183278)	promoter-TSS (NM_183278)	1	NM_183278	69134	Mm.27156	NM_183278	ENSMUSG00000043681	Fam25c	2200001I15Rik|Fam25	family with sequence similarity 25, member C	protein-coding
mm_155050.1	chrX	42152370	42152379	+	1	NA	intron (NM_021465, intron 1 of 32)	intron (NM_021465, intron 1 of 32)	1673	NM_021465	20843	Mm.290422	NM_021465	ENSMUSG00000025862	Stag2	9230105L23Rik|B230112I07Rik|SA-2|SAP2	stromal antigen 2	protein-coding
mm_61979.1	chr7	90887366	90887386	+	1	NA	Intergenic	Intergenic	-203410	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_154761.1	chrX	12005822	12005823	+	1	NA	Intergenic	Intergenic	74731	NM_175045	71458	Mm.196328	NM_029510	ENSMUSG00000040363	Bcor	2900008C10Rik|5830466J11Rik|8430401K06Rik|BcorR|D930024N20Rik|mKIAA1575	BCL6 interacting corepressor	protein-coding
mm_75591.1	chr8	61603006	61603044	-	1	NA	intron (NM_001293772, intron 10 of 21)	intron (NM_001293772, intron 10 of 21)	-11856	NM_001293774	72333	Mm.29933	NM_001081390	ENSMUSG00000058056	Palld	2410003B16Rik|6030492A02	palladin, cytoskeletal associated protein	protein-coding
mm_28174.1	chr3	88000198	88000223	-	1	NA	5' UTR (NM_001109758, exon 1 of 8)	5' UTR (NM_001109758, exon 1 of 8)	146	NM_007529	12032	Mm.4598	NM_007529	ENSMUSG00000004892	Bcan	Cspg7	brevican	protein-coding
mm_22199.1	chr2	173348902	173348907	-	1	NA	Intergenic	B4A|SINE|B4	-72371	NM_022995	65112	Mm.73682	NM_022995	ENSMUSG00000038400	Pmepa1	2210418I02Rik|AW455466|Erg1.2|N4wbp4|Stag1|Tmepai	prostate transmembrane protein, androgen induced 1	protein-coding
mm_131301.1	chr16	11420490	11420576	+	1	NA	intron (NM_001290148, intron 3 of 13)	Tigger17|DNA|TcMar-Tigger	14885	NM_001290148	74478	Mm.325831	NM_028964	ENSMUSG00000071669	Snx29	4933437K13Rik|ENSMUSG00000079738|Gm11170|Gm1737|Gm930|Rundc2a	sorting nexin 29	protein-coding
mm_24560.1	chr3	93443649	93443657	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	1323	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_21142.1	chr2	154220313	154220326	-	1	NA	TTS (NM_153418)	TTS (NM_153418)	-3423	NM_144890	228802	Mm.167411	NM_144890	ENSMUSG00000038572	Bpifb5	Lplunc5	BPI fold containing family B, member 5	protein-coding
mm_116614.1	chr13	48871107	48871159	-	1	NA	promoter-TSS (NM_011078)	promoter-TSS (NM_011078)	-248	NM_011078	18676	Mm.486213	NM_011078	ENSMUSG00000038025	Phf2	GRC5	PHD finger protein 2	protein-coding
mm_163731.1	chr13	119623827	119623869	+	1	NA	promoter-TSS (NM_020279)	promoter-TSS (NM_020279)	29	NM_020279	56838	Mm.143745	NM_020279	ENSMUSG00000074715	Ccl28	CCK1|MEC|Scya28	chemokine (C-C motif) ligand 28	protein-coding
mm_52702.1	chr6	119336370	119336417	+	1	NA	exon (NM_001033382, exon 27 of 38)	exon (NM_001033382, exon 27 of 38)	-5627	NM_172492	211187	Mm.121498	NM_172492	ENSMUSG00000055003	Lrtm2	A230084J22|AI841794	leucine-rich repeats and transmembrane domains 2	protein-coding
mm_12676.1	chr2	75832135	75832141	+	1	NA	promoter-TSS (NM_172666)	promoter-TSS (NM_172666)	-39	NM_172666	228061	Mm.31227	NM_172666	ENSMUSG00000042410	Agps	5832437L22|9930035G10Rik|AW123847|Adaps|Adas|Adhaps|Adps|Aldhpsy|bs2	alkylglycerone phosphate synthase	protein-coding
mm_16593.1	chr2	4652088	4652140	-	1	NA	promoter-TSS (NM_026045)	promoter-TSS (NM_026045)	-28	NM_026045	67229	Mm.38529	NM_026045	ENSMUSG00000039449	Prpf18	2810441A10Rik	pre-mRNA processing factor 18	protein-coding
mm_102223.1	chr11	54909979	54909987	-	1	NA	TTS (NM_021327)	TTS (NM_021327)	7129	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_45922.1	chr5	89441672	89441691	-	1	NA	exon (NM_008096, exon 5 of 13)	exon (NM_008096, exon 5 of 13)	16217	NM_008096	14473	Mm.196595	NM_008096	ENSMUSG00000035540	Gc	DBP|VDB	group specific component	protein-coding
mm_137360.1	chr17	25366316	25366328	+	1	NA	promoter-TSS (NM_010781)	promoter-TSS (NM_010781)	-11	NM_010781	17229	Mm.7409	NM_010781	ENSMUSG00000033825	Tpsb2	AV011504|MMCP-6|Mcp-6|Mcp6|Mcpt6	tryptase beta 2	protein-coding
mm_149048.1	chr19	8831696	8831700	+	1	NA	3' UTR (NM_001081196, exon 14 of 14)	3' UTR (NM_001081196, exon 14 of 14)	-5769	NM_001136064	14705	Mm.345134	NM_008144	ENSMUSG00000071657	Bscl2	2900097C17Rik|AI046355|Gng3lg	Berardinelli-Seip congenital lipodystrophy 2 (seipin)	protein-coding
mm_8939.1	chr1	164437849	164437859	-	1	NA	TTS (NM_001293313)	TTS (NM_001293313)	20501	NM_009721	11931	Mm.4550	NM_009721	ENSMUSG00000026576	Atp1b1	Atp4b|Atpb|Atpb-1|NKbeta1	ATPase, Na+/K+ transporting, beta 1 polypeptide	protein-coding
mm_157240.1	chrX	17572218	17572228	-	1	NA	promoter-TSS (NM_001313746)	promoter-TSS (NM_001313746)	102	NM_001313745	72018	Mm.41558	NM_028058	ENSMUSG00000025040	Fundc1	1500005J14Rik|1810033P05Rik	FUN14 domain containing 1	protein-coding
mm_113912.1	chr13	49493622	49493643	+	1	NA	intron (NM_025495, intron 5 of 7)	intron (NM_025495, intron 5 of 7)	-11178	NM_001012324	407800	Mm.386931	NM_001012324	ENSMUSG00000043631	Ecm2	9030618O22Rik|BC065151|tenonectin	extracellular matrix protein 2, female organ and adipocyte specific	protein-coding
mm_86397.1	chr9	123968640	123968644	-	1	NA	promoter-TSS (NM_009912)	promoter-TSS (NM_009912)	50	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_43757.1	chr5	140507735	140507743	+	1	NA	intron (NM_021528, intron 1 of 1)	intron (NM_021528, intron 1 of 1)	2130	NM_021528	59031	Mm.28934	NM_021528	ENSMUSG00000036599	Chst12	AI595374|C4S-2|C4ST2	carbohydrate sulfotransferase 12	protein-coding
mm_124872.1	chr15	10215980	10216020	+	1	NA	intron (NM_011169, intron 1 of 9)	intron (NM_011169, intron 1 of 9)	-7906	NM_001253781	19116	Mm.10516	NM_011169	ENSMUSG00000005268	Prlr	AI987712|Pr-1|Pr-3|Prlr-rs1	prolactin receptor	protein-coding
mm_140530.1	chr17	6746860	6746868	-	1	NA	intron (NM_009510, intron 7 of 12)	intron (NM_009510, intron 7 of 12)	35916	NM_009510	22350	Mm.277812	NM_009510	ENSMUSG00000052397	Ezr	AW146364|R75297|Vil2|p81	ezrin	protein-coding
mm_119765.1	chr14	54173539	54173554	+	1	NA	Intergenic	Intergenic	80383	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_112800.1	chr13	20472691	20472736	+	1	NA	promoter-TSS (NM_198093)	promoter-TSS (NM_198093)	-277	NM_198093	140580	Mm.342392	NM_080288	ENSMUSG00000041112	Elmo1	6330578D22Rik|C230095H21Rik|CED-12	engulfment and cell motility 1	protein-coding
mm_123693.1	chr14	69665073	69665088	-	1	NA	intron (NM_033325, intron 5 of 13)	intron (NM_033325, intron 5 of 13)	-27168	NR_105915	102465573		NR_105915	ENSMUSG00000098666	Mir6950	Gm27586|mmu-mir-6950	microRNA 6950	ncRNA
mm_60907.1	chr7	46752354	46752359	+	1	NA	exon (NM_011314, exon 2 of 4)	exon (NM_011314, exon 2 of 4)	523	NM_011314	20209	Mm.200941	NM_011314	ENSMUSG00000057465	Saa2	AW111173|Saa-2|Saa1	serum amyloid A 2	protein-coding
mm_89220.1	chr10	86874324	86874367	+	1	NA	intron (NM_138673, intron 46 of 68)	intron (NM_138673, intron 46 of 68)	95340	NM_175331	103466	Mm.200446	NM_175331	ENSMUSG00000054027	Nt5dc3	AU040402|AW540062|C630002B14Rik|TU12B1-TY	5'-nucleotidase domain containing 3	protein-coding
mm_12307.1	chr2	69113561	69113571	+	1	NA	3' UTR (NM_001347161, exon 11 of 11)	3' UTR (NM_001347161, exon 11 of 11)	-22234	NM_181547	329416	Mm.90047	NM_181547	ENSMUSG00000034738	Nostrin	Daip2|mDaIP2	nitric oxide synthase trafficker	protein-coding
mm_124349.1	chr14	104459484	104459486	-	1	NA	Intergenic	Intergenic	8514	NM_011143	18996	Mm.246550	NM_011143	ENSMUSG00000048349	Pou4f1	Brn-3|Brn-3.0|Brn3|Brn3.0|Brn3a|E130119J07Rik	POU domain, class 4, transcription factor 1	protein-coding
mm_154137.1	chr19	57360116	57360130	-	1	NA	promoter-TSS (NM_145505)	promoter-TSS (NM_145505)	776	NR_040316	320879	Mm.375089	NR_040316	ENSMUSG00000097785	B230217O12Rik	-	RIKEN cDNA B230217O12 gene	ncRNA
mm_46290.1	chr5	100379158	100379162	-	1	NA	intron (NM_026969, intron 19 of 27)	intron (NM_026969, intron 19 of 27)	37074	NM_026969	69162	Mm.18634	NM_026969	ENSMUSG00000035325	Sec31a	1810024J13Rik|ABP125|ABP130|AU042160|HSPC275|Sec31l1	Sec31 homolog A (S. cerevisiae)	protein-coding
mm_34494.1	chr4	148592093	148592105	+	1	NA	exon (NM_009272, exon 2 of 7)	exon (NM_009272, exon 2 of 7)	586	NM_009272	20810	Mm.10	NM_009272	ENSMUSG00000006442	Srm	AA407669|SpdST|SpdSy	spermidine synthase	protein-coding
mm_153200.1	chr19	34629810	34629813	-	1	NA	5' UTR (NM_053217, exon 2 of 3)	5' UTR (NM_053217, exon 2 of 3)	10932	NM_053217	112419	Mm.440727	NM_053217	ENSMUSG00000067297	Ifit1bl2	2010002M12Rik|AW412491|Ifit1b	interferon induced protein with tetratricopeptide repeats 1B like 2	protein-coding
mm_117756.1	chr13	95961654	95961672	-	1	NA	intron (NM_029210, intron 12 of 12)	intron (NM_029210, intron 12 of 12)	-69741	NM_027711	544963	Mm.38878	NM_027711	ENSMUSG00000021676	Iqgap2	4933417J23Rik|A630053O10|AI788777	IQ motif containing GTPase activating protein 2	protein-coding
mm_97107.1	chr11	74649463	74649520	+	1	NA	promoter-TSS (NM_001081158)	promoter-TSS (NM_001081158)	-4	NM_001081158	74148	Mm.214574	NM_001081158	ENSMUSG00000020741	Cluh	1300001I01Rik|Kiaa0664|mKIAA0664	clustered mitochondria (cluA/CLU1) homolog	protein-coding
mm_122981.1	chr14	54983412	54983417	-	1	NA	exon (NM_080728, exon 25 of 41)	exon (NM_080728, exon 25 of 41)	-7638	NR_030607	100124433		NR_030607	ENSMUSG00000077928	Mir208b	Mirn208b|mir-208b	microRNA 208b	ncRNA
mm_10996.1	chr2	26342283	26342295	+	1	NA	intron (NM_153410, intron 11 of 13)	intron (NM_153410, intron 11 of 13)	9821	NM_026828	52838	Mm.31239	NM_026828	ENSMUSG00000075467	Dnlz	1110034G11Rik|D2Bwg1335e|HEP1	DNL-type zinc finger	protein-coding
mm_27569.1	chr3	58637185	58637198	-	1	NA	promoter-TSS (NM_001081262)	promoter-TSS (NM_001081262)	16	NM_001081262	545527	Mm.357722	NM_001081262	ENSMUSG00000070471	Erich6	4932431H17Rik|Fam194a	glutamate rich 6	protein-coding
mm_133111.1	chr16	65523308	65523314	+	1	NA	intron (NM_008849, intron 1 of 5)	intron (NM_008849, intron 1 of 5)	2682	NM_008849	18736	Mm.355440	NM_008849	ENSMUSG00000004842	Pou1f1	GHF-1|Hmp1|Pit-1|Pit1|Pit1-rs1|dw|dwarf	POU domain, class 1, transcription factor 1	protein-coding
mm_78571.1	chr9	36481890	36481892	+	1	NA	Intergenic	Intergenic	6253	NM_001128510	671003	Mm.475847	NM_001128510	ENSMUSG00000090710	Gm9513	Pate-P|Pate11	predicted gene 9513	protein-coding
mm_45284.1	chr5	64959178	64959196	-	1	NA	intron (NM_011604, intron 1 of 1)	intron (NM_011604, intron 1 of 1)	847	NM_011604	21899	Mm.42146	NM_011604	ENSMUSG00000051498	Tlr6	-	toll-like receptor 6	protein-coding
mm_23430.1	chr3	59080977	59080979	+	1	NA	intron (NM_177855, intron 10 of 43)	intron (NM_177855, intron 10 of 43)	20843	NM_173398	229323	Mm.123648	NM_173398	ENSMUSG00000050075	Gpr171	A630006E05|F730001G15Rik|H963	G protein-coupled receptor 171	protein-coding
mm_94931.1	chr11	29693005	29693015	+	1	NA	promoter-TSS (NM_194051)	promoter-TSS (NM_194051)	112	NM_194052	68585	Mm.192580	NM_024226	ENSMUSG00000020458	Rtn4	1110020G17Rik|AA407876|AA409940|AA960376|ASY|C130026I10Rik|NOGO|NSP-CL|NgA|Nogo-A|Nogo-B|Nogo-C|mKIAA0886|mKIAA4153	reticulon 4	protein-coding
mm_63975.1	chr7	139953897	139953900	+	1	NA	Intergenic	B1_Mur3|SINE|Alu	3724	NR_106157	102465788		NR_106157	ENSMUSG00000105165	Mir7686	mmu-mir-7686	microRNA 7686	ncRNA
mm_46737.1	chr5	110810069	110810075	-	1	NA	promoter-TSS (NM_009469)	promoter-TSS (NM_009469)	9	NM_009469	22241	Mm.271898	NM_009469	ENSMUSG00000029512	Ulk1	AU041434|Unc51.1|mKIAA0722	unc-51 like kinase 1	protein-coding
mm_11720.1	chr2	36249696	36249717	+	1	NA	intron (NM_008969, intron 10 of 10)	ID4_|SINE|ID	19280	NM_008969	19224	Mm.275434	NM_008969	ENSMUSG00000047250	Ptgs1	COX1|Cox-1|Cox-3|PGHS-1|PHS 1|Pghs1	prostaglandin-endoperoxide synthase 1	protein-coding
mm_27279.1	chr3	41423464	41423468	-	1	NA	Intergenic	Intergenic	69733	NR_040385	78706	Mm.366094	NR_040385	ENSMUSG00000097639	Platr4	C430002E04Rik	pluripotency associated transcript 4	ncRNA
mm_146852.1	chr18	24112078	24112087	-	1	NA	intron (NM_172625, intron 3 of 4)	intron (NM_172625, intron 3 of 4)	9737	NM_172625	225280	Mm.258973	NM_172625	ENSMUSG00000047989	Ino80c	D030070L09Rik	INO80 complex subunit C	protein-coding
mm_76165.1	chr8	82380081	82380096	-	1	NA	intron (NM_001254747, intron 1 of 7)	intron (NM_001254747, intron 1 of 7)	22498	NM_001254747	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_106625.1	chr11	120852675	120852700	-	1	NA	intron (NM_027745, intron 18 of 18)	intron (NM_027745, intron 18 of 18)	-28140	NM_007988	14104	Mm.236443	NM_007988	ENSMUSG00000025153	Fasn	A630082H08Rik|FAS	fatty acid synthase	protein-coding
mm_102665.1	chr11	65003079	65003082	-	1	NA	3' UTR (NM_001099288, exon 20 of 20)	3' UTR (NM_001099288, exon 20 of 20)	24045	NM_023479	68626	Mm.157711	NM_023479	ENSMUSG00000020549	Elac2	1110017O07Rik|D11Wsu80e|Hpc2	elaC ribonuclease Z 2	protein-coding
mm_69354.1	chr7	130354326	130354354	-	1	NA	Intergenic	Intergenic	-87532	NM_201601	14183	Mm.16340	NM_010207	ENSMUSG00000030849	Fgfr2	AU043015|AW556123|Bek|Fgfr-2|Fgfr-7|Fgfr7|KGFR|KGFRTr|svs	fibroblast growth factor receptor 2	protein-coding
mm_43591.1	chr5	137758134	137758213	+	1	NA	intron (NM_029805, intron 3 of 5)	intron (NM_029805, intron 3 of 5)	12204	NM_029805	78829	Mm.286399	NM_023910	ENSMUSG00000029723	Tsc22d4	0610009M14Rik|1700023B23Rik|AI415410|Thg-1pit|Tilz2	TSC22 domain family, member 4	protein-coding
mm_55380.1	chr6	58907054	58907098	-	1	NA	promoter-TSS (NM_021432)	promoter-TSS (NM_021432)	50	NM_021432	58243	Mm.389747	NM_021432	ENSMUSG00000055430	Nap1l5	1110020M21Rik	nucleosome assembly protein 1-like 5	protein-coding
mm_21552.1	chr2	164075217	164075231	-	1	NA	intron (NM_021420, intron 1 of 10)	intron (NM_021420, intron 1 of 10)	1046	NM_021420	58231	Mm.234472	NM_021420	ENSMUSG00000018209	Stk4	AI447339|AU020804|Kas-2|Mst1|Ysk3	serine/threonine kinase 4	protein-coding
mm_33425.1	chr4	130047915	130047929	+	1	NA	promoter-TSS (NM_028266)	promoter-TSS (NM_028266)	82	NM_028266	107581	Mm.41860	NM_028266	ENSMUSG00000040690	Col16a1	2700007F12Rik|A530052M23Rik|AI838662|CA1F	collagen, type XVI, alpha 1	protein-coding
mm_33856.1	chr4	135895181	135895195	+	1	NA	promoter-TSS (NM_009924)	promoter-TSS (NM_009924)	-1	NM_009924	12802	Mm.297251	NM_009924	ENSMUSG00000062585	Cnr2	CB-2|CB2|CB2-R	cannabinoid receptor 2 (macrophage)	protein-coding
mm_22508.1	chr3	7576347	7576362	+	1	NA	intron (NM_008371, intron 3 of 4)	intron (NM_008371, intron 3 of 4)	36539	NM_001313890	16196	Mm.3825	NM_008371	ENSMUSG00000040329	Il7	A630026I06Rik|Il-7|hlb368	interleukin 7	protein-coding
mm_163157.1	chr11	83789533	83789565	+	1	NA	Intergenic	Intergenic	35912	NM_145432	217026	Mm.117874	NM_145432	ENSMUSG00000000976	Heatr6	2700008B19Rik|BB135312|BB249351	HEAT repeat containing 6	protein-coding
mm_120425.1	chr14	65501527	65501530	+	1	NA	Intergenic	Intergenic	-76056	NM_010932	18155	Mm.16347	NM_010932	ENSMUSG00000045731	Pnoc	N/OFQ|Npnc1|OFQ/N	prepronociceptin	protein-coding
mm_144475.1	chr18	23891468	23891479	+	1	NA	3' UTR (NM_001162942, exon 8 of 8)	3' UTR (NM_001162942, exon 8 of 8)	-63215	NM_027007	69256	Mm.218343	NM_027007	ENSMUSG00000024276	Zfp397	2810411K16Rik|6720480F11Rik|AI461664	zinc finger protein 397	protein-coding
mm_162076.1	chrX	24500726	24500726	-	1	NA	Intergenic	Intergenic	-1563	NM_001100444	546272		NM_001100444	ENSMUSG00000084063	Gm5934	EG546272	predicted gene 5934	protein-coding
mm_97427.1	chr11	78072643	78072658	+	1	NA	promoter-TSS (NR_029556)	promoter-TSS (NR_029556)	-355	NR_029556	387162		NR_029556	ENSMUSG00000065401	Mir144	Mirn144|mir-144|mmu-mir-144	microRNA 144	ncRNA
mm_103501.1	chr11	76577702	76577717	-	1	NA	promoter-TSS (NM_198894)	promoter-TSS (NM_198894)	30	NM_198894	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_93283.1	chr10	96176620	96176623	-	1	NA	Intergenic	ORR1A3|LTR|ERVL-MaLR	-49586	NR_110448	74881	Mm.410819	NR_110448		4930459C07Rik	-	RIKEN cDNA 4930459C07 gene	ncRNA
mm_2330.1	chr1	92831494	92831507	+	1	NA	promoter-TSS (NM_016696)	promoter-TSS (NM_016696)	-186	NM_016696	14733	Mm.297976	NM_016696	ENSMUSG00000034220	Gpc1	AI462976	glypican 1	protein-coding
mm_87601.1	chr10	57650963	57650971	+	1	NA	promoter-TSS (NM_001190402)	promoter-TSS (NM_001190402)	-14	NM_001039050	18768	Mm.262135	NM_008863	ENSMUSG00000019876	Pkib	Pkibeta|Prkacn2	protein kinase inhibitor beta, cAMP dependent, testis specific	protein-coding
mm_17754.1	chr2	32742403	32742410	-	1	NA	intron (NR_045535, intron 4 of 12)	intron (NR_045535, intron 4 of 12)	-1390	NM_027529	70730	Mm.401360	NM_027529	ENSMUSG00000009551	6330409D20Rik	AA517851	RIKEN cDNA 6330409D20 gene	protein-coding
mm_142464.1	chr17	45599605	45599623	-	1	NA	promoter-TSS (NM_001199115)	promoter-TSS (NM_001199115)	-11	NM_001199115	63959	Mm.29744	NM_022880	ENSMUSG00000023942	Slc29a1	1200014D21Rik|AA407560|ENT1	solute carrier family 29 (nucleoside transporters), member 1	protein-coding
mm_75178.1	chr8	36952181	36952193	-	1	NA	5' UTR (NM_001194940, exon 1 of 18)	5' UTR (NM_001194940, exon 1 of 18)	255	NM_001194940	50768	Mm.125155	NM_015802	ENSMUSG00000031523	Dlc1	A730069N07Rik|Arhgap7|HP|STARD12|dlc-1	deleted in liver cancer 1	protein-coding
mm_88952.1	chr10	81364398	81364414	+	1	NA	TTS (NM_028657)	TTS (NM_028657)	1414	NM_001014836	432479	Mm.440450	NM_001014836	ENSMUSG00000020234	4930404N11Rik	2210409H10Rik|5730551K18Rik|AI854616	RIKEN cDNA 4930404N11 gene	protein-coding
mm_13440.1	chr2	105126777	105126809	+	1	NA	promoter-TSS (NR_015462)	promoter-TSS (NR_015462)	264	NM_144783	22431	Mm.389339	NM_144783	ENSMUSG00000016458	Wt1	D630046I19Rik|Wt-1	Wilms tumor 1 homolog	protein-coding
mm_119261.1	chr14	33954041	33954059	+	1	NA	promoter-TSS (NM_015745)	promoter-TSS (NM_015745)	28	NM_015745	19661	Mm.436622	NM_015745	ENSMUSG00000041534	Rbp3	Irbp|Rbp-3	retinol binding protein 3, interstitial	protein-coding
mm_94864.1	chr11	24078023	24078076	+	1	NA	promoter-TSS (NM_001242934)	promoter-TSS (NM_001242934)	-7	NM_016707	14025	Mm.53687	NM_016707	ENSMUSG00000000861	Bcl11a	2810047E18Rik|BCL-11A|Ctip1|D930021L15Rik|Evi9|Evi9a|Evi9b|Evi9c|mKIAA1809	B cell CLL/lymphoma 11A (zinc finger protein)	protein-coding
mm_88256.1	chr10	73223748	73223751	+	1	NA	Intergenic	Intergenic	-137044	NR_040646	327768	Mm.417745	NR_040646		A330049N07Rik	-	RIKEN cDNA A330049N07 gene	ncRNA
mm_130786.1	chr15	101573884	101573913	-	1	NA	promoter-TSS (NM_133357)	promoter-TSS (NM_133357)	6	NM_133357	109052	Mm.106868	NM_133357	ENSMUSG00000022986	Krt75	4732468K03Rik|AA589387|K6hf|Krt2-6hf|Krtcap1	keratin 75	protein-coding
mm_77485.1	chr8	122551317	122551333	-	1	NA	promoter-TSS (NM_001037298)	promoter-TSS (NM_001037298)	4	NM_001037298	234839	Mm.37324	NM_001037298	ENSMUSG00000014444	Piezo1	9630020g22|Fam38a|mKIAA0233	piezo-type mechanosensitive ion channel component 1	protein-coding
mm_164985.1	chr19	10389087	10389100	+	1	NA	promoter-TSS (NM_018801)	promoter-TSS (NM_018801)	3	NM_173068	54525	Mm.182654	NM_018801	ENSMUSG00000024743	Syt7	AI851541|B230112P13Rik	synaptotagmin VII	protein-coding
mm_38923.1	chr4	150008978	150009086	-	1	NA	promoter-TSS (NM_173371)	promoter-TSS (NM_173371)	-9	NM_173371	100198	Mm.22183	NM_173371	ENSMUSG00000028980	H6pd	AI785303|G6pd1|Gpd-1|Gpd1	hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase)	protein-coding
mm_51929.1	chr6	91473696	91473787	+	1	NA	promoter-TSS (NM_133928)	promoter-TSS (NM_133928)	-10	NM_028766	74122	Mm.38801	NM_028766	ENSMUSG00000030095	Tmem43	1200015A22Rik|LUMA	transmembrane protein 43	protein-coding
mm_2829.1	chr1	131161267	131161288	+	1	NA	intron (NM_001136070, intron 6 of 14)	intron (NM_001136070, intron 6 of 14)	8070	NM_010709	16865	Mm.276294	NM_010709	ENSMUSG00000026427	Eif2d	D1Ertd5e|Lgtn	eukaryotic translation initiation factor 2D	protein-coding
mm_69830.1	chr7	141271757	141271768	-	1	NA	exon (NM_001114322, exon 13 of 15)	exon (NM_001114322, exon 13 of 15)	5024	NM_028069	72040	Mm.29080	NM_028069	ENSMUSG00000025497	Cdhr5	1810074H01Rik|AI481143|Mucdhl|Mupcdh	cadherin-related family member 5	protein-coding
mm_18825.1	chr2	74659853	74659865	-	1	NA	promoter-TSS (NM_007967)	promoter-TSS (NM_007967)	-302	NM_007967	14029	Mm.25365	NM_007967	ENSMUSG00000001815	Evx2	Evx-2	even-skipped homeobox 2	protein-coding
mm_20208.1	chr2	125505958	125505977	-	1	NA	intron (NM_007993, intron 1 of 65)	CpG	471	NM_007993	14118	Mm.271644	NM_007993	ENSMUSG00000027204	Fbn1	AI536462|B430209H23|Fib-1|Tsk	fibrillin 1	protein-coding
mm_136299.1	chr16	91547614	91547640	-	1	NA	intron (NM_008338, intron 1 of 6)	intron (NM_008338, intron 1 of 6)	533	NM_008338	15980	Mm.249364	NM_008338	ENSMUSG00000022965	Ifngr2	Ifgr2|Ifgt	interferon gamma receptor 2	protein-coding
mm_69056.1	chr7	126884679	126884728	-	1	NA	5' UTR (NM_001163775, exon 1 of 16)	5' UTR (NM_001163775, exon 1 of 16)	264	NM_001163775	381921	Mm.259634	NM_001163774	ENSMUSG00000059981	Taok2	1110033K02Rik|B230344N16|MAP3K17|PSK|PSK1|TAO1|TAO2|mKIAA0881	TAO kinase 2	protein-coding
mm_165284.1	chr2	84018733	84018751	+	1	NA	Intergenic	Intergenic	-77516	NM_027964	71861	Mm.116957	NM_027964	ENSMUSG00000034552	Zswim2	1700025P14Rik|4933437F18Rik|MEX	zinc finger SWIM-type containing 2	protein-coding
mm_56537.1	chr6	99666791	99666823	-	1	NA	promoter-TSS (NM_025829)	promoter-TSS (NM_025829)	-36	NM_025829	66892	Mm.32889	NM_025829	ENSMUSG00000093661	Eif4e3	1300018P11Rik|AI451927|eIF4E-3	eukaryotic translation initiation factor 4E member 3	protein-coding
mm_35122.1	chr4	11076161	11076211	-	1	NA	promoter-TSS (NM_001085493)	promoter-TSS (NM_001085493)	19	NM_001085493	76947	Mm.275265	NM_001085493	ENSMUSG00000050323	Ndufaf6	2310030N02Rik	NADH dehydrogenase (ubiquinone) complex I, assembly factor 6	protein-coding
mm_30375.1	chr3	152210033	152210123	-	1	NA	promoter-TSS (NM_027287)	promoter-TSS (NM_027287)	5	NM_027287	67035	Mm.46746	NM_025926	ENSMUSG00000028035	Dnajb4	1700029A20Rik|2010306G19Rik|5730460G06Rik	DnaJ heat shock protein family (Hsp40) member B4	protein-coding
mm_127636.1	chr15	102471296	102471301	+	1	NA	intron (NM_001174073, intron 1 of 12)	intron (NM_001174073, intron 1 of 12)	666	NM_001174073	18521	Mm.236513	NM_011042	ENSMUSG00000056851	Pcbp2	AW412548|Hnrpx|alphaCP-2	poly(rC) binding protein 2	protein-coding
mm_15652.1	chr2	163203141	163203149	+	1	NA	Intergenic	CpG	-22309	NM_001098799	269389	Mm.207709	NM_001098799	ENSMUSG00000074607	Tox2	AI851523|AV026525|BI987407|Gcx1|RxHMG1	TOX high mobility group box family member 2	protein-coding
mm_98263.1	chr11	88954261	88954273	+	1	NA	intron (NM_029023, intron 1 of 12)	RSINE1|SINE|B4	1175	NM_029023	74617	Mm.34126	NM_029023	ENSMUSG00000000278	Scpep1	2410018F01Rik|4833411K15Rik|AI957256|Risc	serine carboxypeptidase 1	protein-coding
mm_30743.1	chr4	14864024	14864043	+	1	NA	promoter-TSS (NM_028264)	promoter-TSS (NM_028264)	-186	NM_028264	72519	Mm.279158	NM_028264	ENSMUSG00000028221	Tmem55a	2610319K07Rik|AI315591|AV001360	transmembrane protein 55A	protein-coding
mm_54927.1	chr6	48048857	48048864	-	1	NA	promoter-TSS (NM_001081382)	promoter-TSS (NM_001081382)	-746	NM_001081382	72306	Mm.381553	NM_001081382	ENSMUSG00000071477	Zfp777	2500002G23Rik	zinc finger protein 777	protein-coding
mm_2245.1	chr1	91056623	91056636	+	1	NA	intron (NM_001310732, intron 1 of 24)	intron (NM_001310732, intron 1 of 24)	3185	NM_008515	16978	Mm.45039	NM_008515	ENSMUSG00000026305	Lrrfip1	AU024550|Fliiap1	leucine rich repeat (in FLII) interacting protein 1	protein-coding
mm_149334.1	chr19	10848628	10848638	+	1	NA	exon (NM_023044, exon 2 of 8)	exon (NM_023044, exon 2 of 8)	6089	NM_023044	65221	Mm.27387	NM_023044	ENSMUSG00000024737	Slc15a3	Ci1|cI-1	solute carrier family 15, member 3	protein-coding
mm_101205.1	chr11	19019695	19019710	-	1	NA	promoter-TSS (NM_010789)	promoter-TSS (NM_010789)	-733	NM_010789	17268	Mm.356578	NM_010789	ENSMUSG00000020160	Meis1	C530044H18Rik|Evi8	Meis homeobox 1	protein-coding
mm_74203.1	chr8	123892654	123892681	+	1	NA	exon (NM_009606, exon 5 of 7)	exon (NM_009606, exon 5 of 7)	2108	NM_001272041	11459	Mm.214950	NM_009606	ENSMUSG00000031972	Acta1	AA959943|Acta-2|Acts|Actsk-1	actin, alpha 1, skeletal muscle	protein-coding
mm_11713.1	chr2	36237682	36237703	+	1	NA	exon (NM_008969, exon 4 of 11)	exon (NM_008969, exon 4 of 11)	7266	NM_008969	19224	Mm.275434	NM_008969	ENSMUSG00000047250	Ptgs1	COX1|Cox-1|Cox-3|PGHS-1|PHS 1|Pghs1	prostaglandin-endoperoxide synthase 1	protein-coding
mm_40385.1	chr5	52581353	52581367	+	1	NA	Intergenic	Intergenic	-15054	NM_144945	246316	Mm.44721	NM_144945	ENSMUSG00000039252	Lgi2	mKIAA1916	leucine-rich repeat LGI family, member 2	protein-coding
mm_40005.1	chr5	32909344	32909346	+	1	NA	intron (NM_177786, intron 17 of 32)	intron (NM_177786, intron 17 of 32)	45624	NM_001170567	277854	Mm.101524	NM_177786	ENSMUSG00000037426	Depdc5	AV016528	DEP domain containing 5	protein-coding
mm_105260.1	chr11	102356829	102356839	-	1	NA	exon (NM_011403, exon 11 of 20)	exon (NM_011403, exon 11 of 20)	8447	NM_011403	20533	Mm.7248	NM_011403	ENSMUSG00000006574	Slc4a1	Ae1|CD233|Empb3|l11Jus51	solute carrier family 4 (anion exchanger), member 1	protein-coding
mm_77175.1	chr8	111690760	111690765	-	1	NA	intron (NM_025583, intron 1 of 6)	intron (NM_025583, intron 1 of 6)	248	NM_025583	66473	Mm.34374	NM_025583	ENSMUSG00000031957	Ctrb1	2200008D09Rik|AI504462|Ctrb|Prt-2	chymotrypsinogen B1	protein-coding
mm_137112.1	chr17	22424216	22424241	+	1	NA	promoter-TSS (NM_001331197)	promoter-TSS (NM_001331197)	26	NM_001331198	74149	Mm.30767	NM_198003	ENSMUSG00000071266	Zfp946	1300003B13Rik	zinc finger protein 946	protein-coding
mm_170129.1	chr17	39847174	39847175	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	4177	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_135421.1	chr16	45223726	45223735	-	1	NA	promoter-TSS (NM_001037719)	promoter-TSS (NM_001037719)	-607	NM_001037719	208154	Mm.38199	NM_177584	ENSMUSG00000052013	Btla	A630002H24	B and T lymphocyte associated	protein-coding
mm_62758.1	chr7	112077837	112077849	+	1	NA	exon (NM_177249, exon 12 of 29)	exon (NM_177249, exon 12 of 29)	54337	NM_177249	74996	Mm.16974	NM_133758	ENSMUSG00000059263	Usp47	4930502N04Rik|A630020C16Rik	ubiquitin specific peptidase 47	protein-coding
mm_75674.1	chr8	67920962	67920974	-	1	NA	intron (NM_177698, intron 3 of 14)	intron (NM_177698, intron 3 of 14)	-10022	NM_030263	234353	Mm.32525	NM_027626	ENSMUSG00000030465	Psd3	4931420C21Rik|AI661273|BC003498|D430018P08|EFA6D	pleckstrin and Sec7 domain containing 3	protein-coding
mm_137186.1	chr17	23819958	23819973	+	1	NA	exon (NM_175229, exon 10 of 14)	exon (NM_175229, exon 10 of 14)	9144	NM_026305	67673	Mm.153758	NM_026305	ENSMUSG00000055839	Elob	0610040H15Rik|Tceb2	elongin B	protein-coding
mm_11757.1	chr2	38511548	38511551	+	1	NA	promoter-TSS (NM_021606)	promoter-TSS (NM_021606)	-148	NM_021606	59126	Mm.143818	NM_021606	ENSMUSG00000026749	Nek6	1300007C09Rik	NIMA (never in mitosis gene a)-related expressed kinase 6	protein-coding
mm_17301.1	chr2	26300158	26300190	-	1	NA	Intergenic	Intergenic	-5617	NM_177841	329366	Mm.77712	NM_177841	ENSMUSG00000048038	Ccdc187	4932418E24Rik	coiled-coil domain containing 187	protein-coding
mm_51153.1	chr6	70718982	70719015	+	1	NA	Intergenic	Intergenic	73177	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_171991.1	chr5	97525713	97525716	-	1	NA	intron (NR_045981, intron 3 of 7)	L1Md_T|LINE|L1	-68706	NM_010294	14626	Mm.61206	NM_010294	ENSMUSG00000050553	Gk2	GKTA|Gk-rs2	glycerol kinase 2	protein-coding
mm_124986.1	chr15	21329400	21329406	+	1	NA	intron (NM_001008420, intron 2 of 11)	Lx6|LINE|L1	217951	NM_001008420	215654	Mm.300909	NM_001008420	ENSMUSG00000040452	Cdh12	Cdhb	cadherin 12	protein-coding
mm_43487.1	chr5	136919228	136919238	+	1	NA	promoter-TSS (NR_015555)	promoter-TSS (NR_015555)	87	NR_015555	66752	Mm.135764	NR_015555	ENSMUSG00000097908	4933404O12Rik	AW494809	RIKEN cDNA 4933404O12 gene	ncRNA
mm_147751.1	chr18	61197706	61197717	-	1	NA	3' UTR (NM_007885, exon 4 of 4)	3' UTR (NM_007885, exon 4 of 4)	13885	NM_007885	13521	Mm.24803	NM_007885	ENSMUSG00000034320	Slc26a2	Dtd|ST-OB	solute carrier family 26 (sulfate transporter), member 2	protein-coding
mm_150024.1	chr19	29373552	29373569	+	1	NA	exon (NM_021893, exon 3 of 7)	exon (NM_021893, exon 3 of 7)	6122	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_49878.1	chr6	38595633	38595641	+	1	NA	intron (NM_001331223, intron 11 of 12)	B2_Mm1t|SINE|B2	39914	NM_001331223	192196	Mm.276133	NM_138680	ENSMUSG00000029823	Luc7l2	4930471C18Rik|AA522013|AU015269|CGI59|Cgi74	LUC7-like 2 (S. cerevisiae)	protein-coding
mm_154077.1	chr19	56548014	56548046	-	1	NA	promoter-TSS (NM_025811)	promoter-TSS (NM_025811)	192	NM_018831	55947	Mm.2805	NM_018831	ENSMUSG00000025077	Dclre1a	2810043H12Rik|AU022226|Pso2|Smn1a|Snm1|mKIAA0086	DNA cross-link repair 1A	protein-coding
mm_94748.1	chr11	21105961	21105979	+	1	NA	intron (NM_023324, intron 1 of 6)	intron (NM_023324, intron 1 of 6)	14646	NM_023324	67245	Mm.28957	NM_023324	ENSMUSG00000020134	Peli1	2810468L03Rik|A930031K15Rik|AA409794|AI586297|D11Ertd676e	pellino 1	protein-coding
mm_38162.1	chr4	135216412	135216427	-	1	NA	3' UTR (NM_013885, exon 6 of 6)	3' UTR (NM_013885, exon 6 of 6)	56341	NM_013885	29876	Mm.257765	NM_013885	ENSMUSG00000037242	Clic4	D0Jmb3|TU-74|mc3s5|mtCLIC	chloride intracellular channel 4 (mitochondrial)	protein-coding
mm_79637.1	chr9	59543003	59543014	+	1	NA	intron (NM_010421, intron 1 of 13)	intron (NM_010421, intron 1 of 13)	3468	NM_010421	15211	Mm.2284	NM_010421	ENSMUSG00000025232	Hexa	Hex-1	hexosaminidase A	protein-coding
mm_166310.1	chr5	106705529	106705531	+	1	NA	Intergenic	Intergenic	-8700	NM_026856	52397	Mm.249474	NM_026856	ENSMUSG00000049606	Zfp644	1110068L01Rik|AA408882|BM-005|D5Ertd689e|Zep-2	zinc finger protein 644	protein-coding
mm_100146.1	chr11	116006524	116006542	+	1	NA	exon (NM_133663, exon 34 of 39)	exon (NM_133663, exon 34 of 39)	6186	NM_016905	14635	Mm.2820	NM_016905	ENSMUSG00000020766	Galk1	AA409894|GALK|Gk|Glk|Glk1	galactokinase 1	protein-coding
mm_971.1	chr1	58392593	58392598	+	1	NA	promoter-TSS (NM_025824)	promoter-TSS (NM_025824)	-541	NM_025824	66882	Mm.21848	NM_025824	ENSMUSG00000051223	Bzw1	1200015E15Rik|mKIAA0005	basic leucine zipper and W2 domains 1	protein-coding
mm_158775.1	chrX	167080096	167080099	-	1	NA	Intergenic	B1F1|SINE|Alu	-9727	NM_001101606	667794	Mm.302232	NM_001101606		Gm8817	EG667794	predicted gene 8817	protein-coding
mm_9814.1	chr1	182019998	182020004	-	1	NA	promoter-TSS (NM_010135)	promoter-TSS (NM_010135)	-21	NM_010135	13800	Mm.87759	NM_008680	ENSMUSG00000022995	Enah	Mena|NDPP-1|Ndpp1|WBP8	enabled homolog (Drosophila)	protein-coding
mm_141422.1	chr17	29436950	29436986	-	1	NA	Intergenic	Intergenic	-54077	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_6800.1	chr1	84150922	84150936	-	1	NA	intron (NM_001003948, intron 2 of 2)	L1MA5|LINE|L1	68032	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_124160.1	chr14	93631330	93631344	-	1	NA	intron (NM_001346722, intron 2 of 4)	intron (NM_001346722, intron 2 of 4)	257551	NM_001271800	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding
mm_123622.1	chr14	68121082	68121090	-	1	NA	exon (NM_008691, exon 3 of 3)	exon (NM_008691, exon 3 of 3)	-2666	NR_045897	100043072	Mm.242832	NR_045897		A230070E04Rik	Gm4210	RIKEN cDNA A230070E04 gene	ncRNA
mm_25769.1	chr3	126363909	126363954	+	1	NA	promoter-TSS (NM_173451)	promoter-TSS (NM_173451)	79	NM_173451	271970	Mm.317021	NM_173451	ENSMUSG00000046561	Arsj	9330196J05Rik|D830047F08	arylsulfatase J	protein-coding
mm_166804.1	chr7	4464732	4464747	+	1	NA	promoter-TSS (NM_001290416)	promoter-TSS (NM_001290416)	4	NM_026146	67425	Mm.360392	NM_026146	ENSMUSG00000006154	Eps8l1	2310051G19Rik|4632407K17Rik|AW060268|DRC3|EPS8R1	EPS8-like 1	protein-coding
mm_32163.1	chr4	100095804	100095867	+	1	NA	promoter-TSS (NM_013845)	promoter-TSS (NM_013845)	44	NM_001312690	26563	Mm.57252	NM_013845	ENSMUSG00000035305	Ror1	2810404D04Rik|Ntrkr1	receptor tyrosine kinase-like orphan receptor 1	protein-coding
mm_50237.1	chr6	42351324	42351334	+	1	NA	exon (NM_011777, exon 4 of 10)	exon (NM_011777, exon 4 of 10)	1501	NM_001289619	22793	Mm.282303	NM_011777	ENSMUSG00000029860	Zyx	9530098H06Rik|R75157	zyxin	protein-coding
mm_87155.1	chr10	36506951	36506997	+	1	NA	5' UTR (NM_001253356, exon 1 of 5)	5' UTR (NM_001253356, exon 1 of 5)	167	NM_001253356	319415	Mm.332442	NM_001081208	ENSMUSG00000044499	Hs3st5	D930005L05Rik|Gm1151|Hs3ost5	heparan sulfate (glucosamine) 3-O-sulfotransferase 5	protein-coding
mm_109904.1	chr12	7979297	7979320	-	1	NA	exon (NM_009693, exon 3 of 29)	exon (NM_009693, exon 3 of 29)	1631	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_32824.1	chr4	117550658	117550691	+	1	NA	exon (NM_080469, exon 1 of 9)	exon (NM_080469, exon 1 of 9)	309	NM_080469	140546	Mm.235891	NM_080469	ENSMUSG00000033423	Eri3	PINT1|Prnpip1	exoribonuclease 3	protein-coding
mm_42036.1	chr5	108388447	108388453	+	1	NA	promoter-TSS (NM_008806)	promoter-TSS (NM_008806)	77	NM_008806	18587	Mm.1372	NM_008806	ENSMUSG00000029491	Pde6b	Pdeb|r|rd|rd-1|rd1|rd10	phosphodiesterase 6B, cGMP, rod receptor, beta polypeptide	protein-coding
mm_126588.1	chr15	82343104	82343106	+	1	NA	5' UTR (NM_177391, exon 2 of 2)	5' UTR (NM_177391, exon 2 of 2)	1926	NM_177391	338368	Mm.444916	NM_177391	ENSMUSG00000049687	Fam109b	C920005C14Rik|IPIP27B|Ses2	family with sequence similarity 109, member B	protein-coding
mm_108973.1	chr12	102562594	102562628	+	1	NA	exon (NM_007693, exon 7 of 8)	exon (NM_007693, exon 7 of 8)	7670	NM_007693	12652	Mm.4137	NM_007693	ENSMUSG00000021194	Chga	ChrA|cgA	chromogranin A	protein-coding
mm_60783.1	chr7	45566652	45566662	+	1	NA	exon (NM_025330, exon 9 of 9)	exon (NM_025330, exon 9 of 9)	-3496	NM_009737	12036	Mm.24210	NM_009737	ENSMUSG00000030826	Bcat2	Bcat-2|Eca40	branched chain aminotransferase 2, mitochondrial	protein-coding
mm_120608.1	chr14	70159572	70159576	+	1	NA	promoter-TSS (NM_001112735)	promoter-TSS (NM_001112735)	-72	NM_001004155	268759	Mm.12148	NM_001004155	ENSMUSG00000044551	9930012K11Rik	-	RIKEN cDNA 9930012K11 gene	protein-coding
mm_120535.1	chr14	67233436	67233456	+	1	NA	5' UTR (NM_001276387, exon 1 of 17)	5' UTR (NM_001276387, exon 1 of 17)	154	NM_001276387	13592	Mm.319947	NM_010095	ENSMUSG00000022053	Ebf2	D14Ggc1e|EBF-2|Mmot1|O/E-3|OE-3	early B cell factor 2	protein-coding
mm_27346.1	chr3	50414883	50414893	-	1	NA	intron (NM_011990, intron 6 of 11)	intron (NM_011990, intron 6 of 11)	28725	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_60756.1	chr7	45514597	45514614	+	1	NA	promoter-TSS (NM_001290998)	promoter-TSS (NM_001290998)	3	NM_001290998	56734	Mm.439742	NM_008807	ENSMUSG00000023467	Tulp2	Pdet	tubby-like protein 2	protein-coding
mm_50223.1	chr6	42350100	42350110	+	1	NA	5' UTR (NM_001289618, exon 1 of 10)	5' UTR (NM_001289618, exon 1 of 10)	277	NM_001289619	22793	Mm.282303	NM_011777	ENSMUSG00000029860	Zyx	9530098H06Rik|R75157	zyxin	protein-coding
mm_119721.1	chr14	53946010	53946022	+	1	NA	Intergenic	Intergenic	307913	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_98871.1	chr11	97799609	97799619	+	1	NA	promoter-TSS (NM_010688)	promoter-TSS (NM_010688)	-58	NM_010688	16796	Mm.271967	NM_010688	ENSMUSG00000038366	Lasp1	AA408629|Def-4|SH3P6|Tg(Col1a1-lacZ)1Ngma	LIM and SH3 protein 1	protein-coding
mm_51795.1	chr6	88272401	88272407	+	1	NA	intron (NM_023060, intron 6 of 6)	intron (NM_023060, intron 6 of 6)	50136	NM_019964	56691	Mm.272871	NM_019964	ENSMUSG00000048206	Dnajb8	1700016F14Rik|1700031F10Rik|AI326313|mDj6	DnaJ heat shock protein family (Hsp40) member B8	protein-coding
mm_159983.1	chr6	113697516	113697516	+	1	NA	5' UTR (NM_001347356, exon 1 of 8)	5' UTR (NM_001347356, exon 1 of 8)	466	NM_001033463	381801	Mm.333322	NM_001033463	ENSMUSG00000056952	Tatdn2	AI646012|mKIAA0218	TatD DNase domain containing 2	protein-coding
mm_18781.1	chr2	73637836	73637837	-	1	NA	intron (NM_001166604, intron 1 of 5)	B1_Mm|SINE|Alu	-12096	NM_029716	108699	Mm.257073	NM_029716	ENSMUSG00000056486	Chn1	0610007I19Rik|0710001E19Rik|1700112L09Rik|2900046J01Rik|AI413815|ARHGAP2	chimerin 1	protein-coding
mm_153384.1	chr19	40376942	40377022	-	1	NA	exon (NM_178362, exon 7 of 29)	exon (NM_178362, exon 7 of 29)	25328	NM_001034964	20411	Mm.210815	NM_009166	ENSMUSG00000025006	Sorbs1	2310065E01Rik|9530001P15Rik|CAP|SH3P12|Sh3d5|mKIAA1296	sorbin and SH3 domain containing 1	protein-coding
mm_112486.1	chr13	5887086	5887121	+	1	NA	Intergenic	Intergenic	25614	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_81538.1	chr9	110244921	110244944	+	1	NA	5' UTR (NM_013884, exon 1 of 5)	5' UTR (NM_013884, exon 1 of 5)	1149	NM_001166273	29873	Mm.38496	NM_013884	ENSMUSG00000032482	Cspg5	Caleb|Ngc	chondroitin sulfate proteoglycan 5	protein-coding
mm_87014.1	chr10	26892888	26892900	+	1	NA	intron (NM_176837, intron 12 of 14)	B1_Mur1|SINE|Alu	120382	NM_176837	73910	Mm.356496	NM_176837	ENSMUSG00000039031	Arhgap18	4833419J07Rik|AI314906|AI843501	Rho GTPase activating protein 18	protein-coding
mm_17522.1	chr2	29252838	29252852	-	1	NA	non-coding (NR_029460, exon 1 of 2)	non-coding (NR_029460, exon 1 of 2)	148	NR_029460	76220	Mm.330108	NR_029460	ENSMUSG00000079499	6530402F18Rik	mKIAA1857	RIKEN cDNA 6530402F18 gene	ncRNA
mm_156777.1	chrX	161162995	161163054	+	1	NA	5' UTR (NM_001290652, exon 1 of 24)	5' UTR (NM_001290652, exon 1 of 24)	274	NM_001290651	107815	Mm.159173	NM_133194	ENSMUSG00000000037	Scml2	4932420G07Rik	sex comb on midleg-like 2 (Drosophila)	protein-coding
mm_137041.1	chr17	17899628	17899632	+	1	NA	Intergenic	RMER1B|Other|Other	11806	NM_008039	14289	Mm.378918	NM_008039	ENSMUSG00000052270	Fpr2	E330010I07Rik|Fpr-rs2	formyl peptide receptor 2	protein-coding
mm_68244.1	chr7	105481926	105481940	-	1	NA	exon (NM_028444, exon 1 of 2)	exon (NM_028444, exon 1 of 2)	264	NM_028444	109042	Mm.3124	NM_028444	ENSMUSG00000037060	Prkcdbp	3110015B12Rik|6330514M23Rik|SRBC	protein kinase C, delta binding protein	protein-coding
mm_75502.1	chr8	53591600	53591610	-	1	NA	intron (NM_146208, intron 8 of 9)	intron (NM_146208, intron 8 of 9)	47460	NM_146208	234258	Mm.281749	NM_146208	ENSMUSG00000039396	Neil3	AI449477|BC034753|C85903	nei like 3 (E. coli)	protein-coding
mm_45370.1	chr5	66022702	66022723	-	1	NA	exon (NM_139065, exon 6 of 7)	exon (NM_139065, exon 6 of 7)	-18427	NR_027961	231253	Mm.436542	NM_177679	ENSMUSG00000054598	9130230L23Rik	-	RIKEN cDNA 9130230L23 gene	ncRNA
mm_16013.1	chr2	167421693	167421703	+	1	NA	promoter-TSS (NM_001304542)	promoter-TSS (NM_001304542)	-12	NM_148929	77031	Mm.278924	NM_148929	ENSMUSG00000039463	Slc9a8	1200006P13Rik|6430709P13Rik|AI182282|NHE-8|NHE8	solute carrier family 9 (sodium/hydrogen exchanger), member 8	protein-coding
mm_55165.1	chr6	51881256	51881257	-	1	NA	intron (NM_018773, intron 9 of 12)	intron (NM_018773, intron 9 of 12)	131293	NM_018773	54353	Mm.221479	NM_018773	ENSMUSG00000059182	Skap2	2610021A10Rik|AA960083|BB137539|RA70|SKAP-HOM|Saps|Scap2|mSKAP55R	src family associated phosphoprotein 2	protein-coding
mm_143029.1	chr17	56609690	56609715	-	1	NA	promoter-TSS (NM_153152)	promoter-TSS (NM_153152)	69	NM_153152	224904	Mm.34002	NM_153152	ENSMUSG00000049760	2410015M20Rik	Mic13|QIL1|sr104	RIKEN cDNA 2410015M20 gene	protein-coding
mm_3029.1	chr1	133694751	133694764	+	1	NA	Intergenic	Intergenic	-4649	NM_001159649	240754	Mm.36534	NM_172842	ENSMUSG00000051998	Lax1	A530029E09|E430019B13Rik	lymphocyte transmembrane adaptor 1	protein-coding
mm_73274.1	chr8	104591511	104591520	+	1	NA	promoter-TSS (NM_001024606)	promoter-TSS (NM_001024606)	47	NM_001024606	382051	Mm.290750	NM_001024606	ENSMUSG00000048371	Pdp2	4833426J09Rik|Gm1705|mKIAA1348	pyruvate dehyrogenase phosphatase catalytic subunit 2	protein-coding
mm_118119.1	chr13	104109514	104109574	-	1	NA	promoter-TSS (NM_029447)	promoter-TSS (NM_029447)	70	NM_029447	75805	Mm.127692	NM_029447	ENSMUSG00000021710	Nln	4930472G13Rik|C79345	neurolysin (metallopeptidase M3 family)	protein-coding
mm_59310.1	chr7	25282224	25282254	+	1	NA	promoter-TSS (NM_027882)	promoter-TSS (NM_027882)	60	NM_027882	71722	Mm.28833	NM_027882	ENSMUSG00000005442	Cic	1200010B10Rik|mKIAA0306	capicua transcriptional repressor	protein-coding
mm_32713.1	chr4	116173365	116173380	+	1	NA	promoter-TSS (NM_001099295)	promoter-TSS (NM_001099295)	0	NM_001099295	67323	Mm.45442	NM_001099295	ENSMUSG00000078593	1700042G07Rik	-	RIKEN cDNA 1700042G07 gene	protein-coding
mm_133582.1	chr16	91407228	91407246	+	1	NA	intron (NM_008349, intron 1 of 6)	intron (NM_008349, intron 1 of 6)	1002	NM_008349	16155	Mm.4154	NM_008349	ENSMUSG00000022969	Il10rb	6620401D04Rik|AI528744|CRF2-4|Crfb4|D16H21S58|D21S58h|IL-10R2|Il10r2	interleukin 10 receptor, beta	protein-coding
mm_12830.1	chr2	80635227	80635237	+	1	NA	Intergenic	Intergenic	-3580	NM_027091	69482	Mm.29200	NM_027091	ENSMUSG00000026999	Nup35	2310006I24Rik|35kDa|5330402E05Rik|MP44|NO44	nucleoporin 35	protein-coding
mm_163355.1	chr12	25382015	25382023	+	1	NA	Intergenic	Intergenic	252845	NR_045844	432641	Mm.112955	NR_045844		Gm17746	-	predicted gene, 17746	ncRNA
mm_122541.1	chr14	47568408	47568425	-	1	NA	promoter-TSS (NM_172599)	promoter-TSS (NM_172599)	18	NM_172599	100504663	Mm.287279	NM_172599	ENSMUSG00000037526	Atg14	4832427M01|Atg14L|D14Ertd114e|D14Ertd436e	autophagy related 14	protein-coding
mm_105983.1	chr11	115612897	115612907	-	1	NA	promoter-TSS (NM_027162)	promoter-TSS (NM_027162)	67	NM_001243584	69674	Mm.390387	NM_027162	ENSMUSG00000020743	Mif4gd	1110014L05Rik|2310075G12Rik	MIF4G domain containing	protein-coding
mm_118679.1	chr14	22091200	22091206	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	71491	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_93202.1	chr10	94792046	94792049	-	1	NA	3' UTR (NM_018797, exon 31 of 31)	3' UTR (NM_018797, exon 31 of 31)	103257	NM_029852	77048	Mm.296971	NM_029852	ENSMUSG00000020024	Cep83	2600001G24Rik|4921537D05Rik|5730513H21Rik|Ccdc41	centrosomal protein 83	protein-coding
mm_12289.1	chr2	69022983	69023018	+	1	NA	intron (NM_172856, intron 4 of 9)	intron (NM_172856, intron 4 of 9)	-112800	NM_181547	329416	Mm.90047	NM_181547	ENSMUSG00000034738	Nostrin	Daip2|mDaIP2	nitric oxide synthase trafficker	protein-coding
mm_151126.1	chr19	47918707	47918741	+	1	NA	intron (NM_001001738, intron 1 of 1)	intron (NM_001001738, intron 1 of 1)	575	NM_001001738	414801	Mm.29457	NM_001001738	ENSMUSG00000044948	Itprip	4833424O12Rik|DANGER|mKIAA1754	inositol 1,4,5-triphosphate receptor interacting protein	protein-coding
mm_82927.1	chr9	35119136	35119144	-	1	NA	intron (NR_029475, intron 2 of 5)	intron (NR_029475, intron 2 of 5)	-2330	NM_009178	20443	Mm.275973	NM_009178	ENSMUSG00000032038	St3gal4	Siat4c	ST3 beta-galactoside alpha-2,3-sialyltransferase 4	protein-coding
mm_2406.1	chr1	93802152	93802167	+	1	NA	promoter-TSS (NM_001105667)	promoter-TSS (NM_001105667)	-225	NM_001105667	21915	Mm.250332	NM_023136	ENSMUSG00000026281	Dtymk	AU044245|CDC8|D10Ertd203e|TMPK|TYPK|Tmk|mtmk	deoxythymidylate kinase	protein-coding
mm_120127.1	chr14	60177378	60177385	+	1	NA	Intergenic	CpG	51534	NR_030458	751526		NR_030458	ENSMUSG00000076270	Mir719	Mirn719|mmu-mir-719	microRNA 719	ncRNA
mm_4020.1	chr1	165708196	165708240	+	1	NA	promoter-TSS (NM_001038846)	promoter-TSS (NM_001038846)	-124	NM_001038846	226594	Mm.265552	NM_178593	ENSMUSG00000040723	Rcsd1	A430105K13Rik|BC025872|CapZIP	RCSD domain containing 1	protein-coding
mm_173300.1	chrY	54758260	54758261	+	1	NA	Intergenic	Intergenic	-455460	NM_201530	382301	Mm.304354	NM_201530	ENSMUSG00000101155	Sly	-	Sycp3 like Y-linked	protein-coding
mm_46998.1	chr5	115341196	115341211	-	1	NA	promoter-TSS (NM_026933)	promoter-TSS (NM_026933)	-42	NM_029645	384281	Mm.229308	NM_029645	ENSMUSG00000029536	Gatc	2010003O18Rik	glutamyl-tRNA(Gln) amidotransferase, subunit C	protein-coding
mm_57245.1	chr6	123283259	123283283	-	1	NA	3' UTR (NM_019948, exon 6 of 6)	3' UTR (NM_019948, exon 6 of 6)	6600	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_4496.1	chr1	173641463	173641478	+	1	NA	intron (NM_175026, intron 4 of 6)	MTD|LTR|ERVL-MaLR	10611	NM_175026	236312	Mm.447	NM_175026	ENSMUSG00000043263	Ifi209	4930422C14|AI447904|Ifix|Pyhin-1|Pyhin1	interferon activated gene 209	protein-coding
mm_103983.1	chr11	84827299	84827311	-	1	NA	intron (NM_177564, intron 1 of 6)	intron (NM_177564, intron 1 of 6)	1698	NM_177564	192970	Mm.192213	NM_177564	ENSMUSG00000034449	Dhrs11	-	dehydrogenase/reductase (SDR family) member 11	protein-coding
mm_78564.1	chr9	35741031	35741034	+	1	NA	promoter-TSS (NM_001167588)	promoter-TSS (NM_001167588)	-17	NM_001167588	100312949	Mm.475848	NM_001167588	ENSMUSG00000091174	Gm17677	Pate-n|Pate10	predicted gene, 17677	protein-coding
mm_69797.1	chr7	141168672	141168811	-	1	NA	promoter-TSS (NM_001172101)	promoter-TSS (NM_001172101)	-55	NM_001172101	107702	Mm.197493	NM_145135	ENSMUSG00000038650	Rnh1	AW546468|C80305|RNH	ribonuclease/angiogenin inhibitor 1	protein-coding
mm_31563.1	chr4	57567846	57567869	+	1	NA	promoter-TSS (NM_172868)	promoter-TSS (NM_172868)	-391	NM_001304544	677884	Mm.331630	NM_001304544	ENSMUSG00000089945	Pakap	AF064781|Gm20459|Palm2-Akap2|Palm2Akap2|Palm2akap2	paralemmin A kinase anchor protein	protein-coding
mm_61617.1	chr7	80091675	80091684	+	1	NA	3' UTR (NM_175433, exon 5 of 5)	3' UTR (NM_175433, exon 5 of 5)	-16422	NR_045695	100859962	Mm.392575	NR_045695	ENSMUSG00000108714	Gm21057	-	predicted gene, 21057	ncRNA
mm_71541.1	chr8	47334458	47334471	+	1	NA	intron (NM_175162, intron 1 of 4)	intron (NM_175162, intron 1 of 4)	17884	NM_175162	71069	Mm.23973	NM_175162	ENSMUSG00000038143	Stox2	4933409N07Rik|AI449080|AI835114|mKIAA1392	storkhead box 2	protein-coding
mm_14328.1	chr2	129367352	129367363	+	1	NA	exon (NM_008361, exon 5 of 7)	exon (NM_008361, exon 5 of 7)	-2545	NR_015474	329514	Mm.207315	NM_177848	ENSMUSG00000074805	Il1bos	9430083I22|Gm14047|OTTMUSG00000015529	interleukin 1 beta, opposite strand	ncRNA
mm_82365.1	chr9	14543575	14543612	-	1	NA	3' UTR (NM_001081395, exon 13 of 13)	3' UTR (NM_001081395, exon 13 of 13)	42974	NM_023153	66070	Mm.245938	NM_023153	ENSMUSG00000004096	Cwc15	0610040D20Rik|2900052N06Rik|Ed1|c11orf5|mED1	CWC15 spliceosome-associated protein	protein-coding
mm_50224.1	chr6	42350248	42350356	+	1	NA	exon (NM_001289618, exon 2 of 10)	exon (NM_001289618, exon 2 of 10)	474	NM_001289619	22793	Mm.282303	NM_011777	ENSMUSG00000029860	Zyx	9530098H06Rik|R75157	zyxin	protein-coding
mm_33407.1	chr4	129848453	129848476	+	1	NA	3' UTR (NM_001164745, exon 6 of 6)	3' UTR (NM_001164745, exon 6 of 6)	27756	NM_001164745	19244	Mm.193688	NM_008974	ENSMUSG00000028788	Ptp4a2	Prl-2	protein tyrosine phosphatase 4a2	protein-coding
mm_144186.1	chr18	7868878	7868888	+	1	NA	promoter-TSS (NM_001146298)	promoter-TSS (NM_001146298)	51	NM_001282093	225131	Mm.204524	NM_153085	ENSMUSG00000024283	Wac	1110067P07Rik|A230035H12Rik|AI256735|AI256776|Wwp4	WW domain containing adaptor with coiled-coil	protein-coding
mm_102379.1	chr11	58802230	58802242	-	1	NA	promoter-TSS (NM_001162878)	promoter-TSS (NM_001162878)	-276	NM_029283	75429	Mm.296819	NM_029283	ENSMUSG00000049154	Fam183b	3100002J23Rik|Theg6	family with sequence similarity 183, member B	protein-coding
mm_151828.1	chr19	5661626	5661662	-	1	NA	intron (NM_001164480, intron 1 of 16)	intron (NM_001164480, intron 1 of 16)	2063	NM_001164482	20469	Mm.3072	NM_011379	ENSMUSG00000056917	Sipa1	Spa1	signal-induced proliferation associated gene 1	protein-coding
mm_14365.1	chr2	129616618	129616621	+	1	NA	intron (NM_001291019, intron 4 of 7)	intron (NM_001291019, intron 4 of 7)	23450	NM_001291022	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_44662.1	chr5	28467045	28467050	-	1	NA	promoter-TSS (NM_009170)	promoter-TSS (NM_009170)	54	NM_009170	20423	Mm.57202	NM_009170	ENSMUSG00000002633	Shh	9530036O11Rik|Dsh|Hhg1|Hx|Hxl3|M100081	sonic hedgehog	protein-coding
mm_115564.1	chr13	9764866	9764941	-	1	NA	promoter-TSS (NM_001347480)	promoter-TSS (NM_001347480)	53	NM_001347477	66505	Mm.397307	NM_144516	ENSMUSG00000021156	Zmynd11	2210402G22Rik|BS69	zinc finger, MYND domain containing 11	protein-coding
mm_129363.1	chr15	77969769	77969774	-	1	NA	intron (NM_018749, intron 1 of 14)	intron (NM_018749, intron 1 of 14)	1053	NM_018749	55944	Mm.3955	NM_018749	ENSMUSG00000016554	Eif3d	66/67kDa|AA407891|Eif3s7|eIF3p66	eukaryotic translation initiation factor 3, subunit D	protein-coding
mm_126139.1	chr15	78348152	78348163	+	1	NA	promoter-TSS (NR_106138)	promoter-TSS (NR_106138)	-442	NR_106137	102465776		NR_106137	ENSMUSG00000098996	Mir7676-1	Gm27600|mmu-mir-7676-1	microRNA 7676-1	ncRNA
mm_63262.1	chr7	126695943	126696009	+	1	NA	promoter-TSS (NM_029420)	promoter-TSS (NM_029420)	-24	NM_175103	66162	Mm.358692	NM_175103	ENSMUSG00000047721	Bola2	1110025L05Rik|BolA-2	bolA-like 2 (E. coli)	protein-coding
mm_15186.1	chr2	154200353	154200365	+	1	NA	promoter-TSS (NM_153418)	promoter-TSS (NM_153418)	-21	NM_153418	228801	Mm.3783	NM_153418	ENSMUSG00000027485	Bpifb1	Lplunc1	BPI fold containing family B, member 1	protein-coding
mm_161107.1	chr12	103738189	103738189	-	1	NA	promoter-TSS (NM_009244)	promoter-TSS (NM_009244)	0	NM_009244	20701	Mm.439692	NM_009244	ENSMUSG00000071178	Serpina1b	D12Ucla2|Dom2|PI2|Spi1-2	serine (or cysteine) preptidase inhibitor, clade A, member 1B	protein-coding
mm_5848.1	chr1	52972015	52972021	-	1	NA	Intergenic	Intergenic	-19178	NM_144953	67080	Mm.236287	NM_144953	ENSMUSG00000043629	1700019D03Rik	2410136C24Rik|AA410151|smAKAP	RIKEN cDNA 1700019D03 gene	protein-coding
mm_23229.1	chr3	50414460	50414472	+	1	NA	intron (NM_011990, intron 6 of 11)	intron (NM_011990, intron 6 of 11)	29147	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_123951.1	chr14	73525237	73525253	-	1	NA	5' UTR (NM_172527, exon 3 of 5)	5' UTR (NM_172527, exon 3 of 5)	15196	NM_026119	67381	Mm.282888	NM_026119	ENSMUSG00000022109	Med4	2410046H15Rik|DRIP36|HSPC126|TRAP36|Vdirp|Vdrip	mediator complex subunit 4	protein-coding
mm_50009.1	chr6	41059401	41059430	+	1	NA	Intergenic	Intergenic	-23906	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_117372.1	chr13	71963694	71963710	-	1	NA	promoter-TSS (NM_010573)	promoter-TSS (NM_010573)	21	NM_010573	16371	Mm.316056	NM_010573	ENSMUSG00000060969	Irx1	-	Iroquois related homeobox 1 (Drosophila)	protein-coding
mm_103090.1	chr11	69920582	69920591	-	1	NA	promoter-TSS (NM_001166590)	promoter-TSS (NM_001166590)	44	NM_001166590	276770	Mm.18026	NM_181582	ENSMUSG00000078812	Eif5a	AA410058|D19Wsu54e|Eif4d|Eif5a1|eIF-4D|eIF-5A|eIF-5A-1|eIF-5A1	eukaryotic translation initiation factor 5A	protein-coding
mm_152617.1	chr19	12436029	12436044	-	1	NA	Intergenic	B4A|SINE|B4	8131	NM_019540	56093	Mm.285849	NM_019540	ENSMUSG00000040065	Pfpl	Epcs5|Epcs50	pore forming protein-like	protein-coding
mm_52241.1	chr6	105531503	105531504	+	1	NA	Intergenic	Intergenic	-38835	NR_040297	100503536	Mm.366960	NR_040297	ENSMUSG00000108237	Gm19757	-	predicted gene, 19757	ncRNA
mm_110384.1	chr12	40223365	40223382	-	1	NA	promoter-TSS (NM_013562)	promoter-TSS (NM_013562)	9	NR_045157	629820	Mm.435540	NR_045157	ENSMUSG00000035983	Gm7008	EG629820	predicted gene 7008	ncRNA
mm_133708.1	chr16	93368254	93368267	+	1	NA	Intergenic	Intergenic	-1460	NR_030429	791074		NR_030429	ENSMUSG00000076457	Mir802	Mirn802|mir-802|mmu-mir-802	microRNA 802	ncRNA
mm_40918.1	chr5	75734819	75734835	+	1	NA	Intergenic	Intergenic	159836	NM_021099	16590	Mm.247073	NM_021099	ENSMUSG00000005672	Kit	Bs|CD117|Fdc|Gsfsco1|Gsfsco5|Gsfsow3|SCO1|SCO5|SOW3|Ssm|Tr-kit|W|c-KIT	KIT proto-oncogene receptor tyrosine kinase	protein-coding
mm_59628.1	chr7	28155235	28155244	+	1	NA	exon (NM_001164655, exon 14 of 20)	exon (NM_001164655, exon 14 of 20)	-14509	NM_007991	14113	Mm.4595	NM_007991	ENSMUSG00000046865	Fbl	AL022665|FIB|FLRN|RNU3IP1	fibrillarin	protein-coding
mm_35110.1	chr4	9652566	9652569	-	1	NA	intron (NM_001290367, intron 1 of 22)	intron (NM_001290367, intron 1 of 22)	-8850	NM_001177852	65973	Mm.222206	NM_023066	ENSMUSG00000028207	Asph	2310005F16Rik|3110001L23Rik|AI848629|AW261690|AW561901|BAH|C79816|cI-37	aspartate-beta-hydroxylase	protein-coding
mm_15276.1	chr2	155246984	155246988	+	1	NA	intron (NR_111890, intron 2 of 3)	intron (NR_111890, intron 2 of 3)	10378	NM_001291108	67068	Mm.23693	NM_025947	ENSMUSG00000047459	Dynlrb1	2010012N15Rik|2010320M17Rik|9430076K19Rik|AV124457|DNLC2A|Dncl2a|km23-1	dynein light chain roadblock-type 1	protein-coding
mm_14608.1	chr2	136532181	136532215	+	1	NA	promoter-TSS (NM_175667)	promoter-TSS (NM_175667)	-123	NM_175667	319196	Mm.477841	NM_175667	ENSMUSG00000074771	Ankef1	AV276460|Ankrd5	ankyrin repeat and EF-hand domain containing 1	protein-coding
mm_94586.1	chr11	11701643	11701644	+	1	NA	intron (NM_001025597, intron 2 of 7)	intron (NM_001025597, intron 2 of 7)	11466	NM_001301863	22778	Mm.103545	NM_009578	ENSMUSG00000018654	Ikzf1	5832432G11Rik|Ikaros|LyF-1|Zfpn1a1|Znfn1a1|hlk-1|mKIAA4227	IKAROS family zinc finger 1	protein-coding
mm_145102.1	chr18	44101827	44101832	+	1	NA	Intergenic	MERV1_LTR|LTR|ERV1	-2694	NM_030061	78242	Mm.99782	NM_030061	ENSMUSG00000061144	Spink12	9230117E20Rik	serine peptidase inhibitor, Kazal type 12	protein-coding
mm_152102.1	chr19	6921805	6921834	-	1	NA	promoter-TSS (NM_007953)	promoter-TSS (NM_007953)	-11	NM_007953	26379	Mm.386776	NM_007953	ENSMUSG00000024955	Esrra	ERRalpha|Err1|Estrra|Nr3b1	estrogen related receptor, alpha	protein-coding
mm_144802.1	chr18	36280552	36280567	+	1	NA	promoter-TSS (NM_008989)	promoter-TSS (NM_008989)	-603	NM_008989	19290	Mm.231802	NM_008989	ENSMUSG00000043991	Pura	CAGER-1|Pur-alpha|ssCRE-BP	purine rich element binding protein A	protein-coding
mm_171892.1	chr5	3893894	3893897	-	1	NA	promoter-TSS (NM_172135)	promoter-TSS (NM_172135)	38	NM_001013023	545725	Mm.99593	NM_172135	ENSMUSG00000040429	Mterf1a	4931431L11Rik|9230106K09Rik|Mterf|Mterf1|mTERF1b	mitochondrial transcription termination factor 1a	protein-coding
mm_105450.1	chr11	104464809	104464814	-	1	NA	Intergenic	ID_B1|SINE|B4	-22520	NM_001081045	76719	Mm.136418	NM_001081045	ENSMUSG00000018412	Kansl1	1700081L11Rik|9430041J06Rik|mKIAA1267	KAT8 regulatory NSL complex subunit 1	protein-coding
mm_19715.1	chr2	104192522	104192563	-	1	NA	exon (NM_001033347, exon 16 of 21)	exon (NM_001033347, exon 16 of 21)	69773	NM_026634	68243	Mm.158191	NM_026634	ENSMUSG00000032671	A930018P22Rik	-	RIKEN cDNA A930018P22 gene	protein-coding
mm_108757.1	chr12	89045921	89045925	+	1	NA	intron (NM_172544, intron 2 of 19)	intron (NM_172544, intron 2 of 19)	92533	NM_172544	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding
mm_63222.1	chr7	126323954	126323992	+	1	NA	Intergenic	Intergenic	44072	NR_106025	102466797		NR_106025	ENSMUSG00000099017	Mir7058	Gm27766|mmu-mir-7058	microRNA 7058	ncRNA
mm_35828.1	chr4	47474188	47474194	-	1	NA	promoter-TSS (NM_024171)	promoter-TSS (NM_024171)	176	NM_019998	56737	Mm.22218	NM_019998	ENSMUSG00000039740	Alg2	1110018A23Rik|1300013N08Rik|ALPG2|CDGIi|MNCb-5081	asparagine-linked glycosylation 2 (alpha-1,3-mannosyltransferase)	protein-coding
mm_122529.1	chr14	47381620	47381642	-	1	NA	exon (NM_010705, exon 4 of 6)	exon (NM_010705, exon 4 of 6)	7771	NM_001145953	16854	Mm.248615	NM_010705	ENSMUSG00000050335	Lgals3	GBP|L-34|Mac-2|gal3	lectin, galactose binding, soluble 3	protein-coding
mm_73647.1	chr8	110919875	110919902	+	1	NA	promoter-TSS (NM_009179)	promoter-TSS (NM_009179)	23	NM_009179	20444	Mm.200388	NM_009179	ENSMUSG00000031749	St3gal2	AI429591|AW822065|ST3GalII|Siat5	ST3 beta-galactoside alpha-2,3-sialyltransferase 2	protein-coding
mm_135368.1	chr16	44061482	44061484	-	1	NA	Intergenic	Intergenic	-33538	NM_001172107	207798	Mm.19316	NM_153528	ENSMUSG00000036292	Gramd1c	4921521N14Rik	GRAM domain containing 1C	protein-coding
mm_76887.1	chr8	105637364	105637392	-	1	NA	intron (NM_181322, intron 1 of 11)	CpG	840	NM_181322	13018	Mm.269474	NM_181322	ENSMUSG00000005698	Ctcf	AW108038	CCCTC-binding factor	protein-coding
mm_29762.1	chr3	127162543	127162580	-	1	NA	intron (NR_105029, intron 2 of 3)	intron (NR_105029, intron 2 of 3)	1256	NR_105029	100862268	Mm.444603	NR_105029	ENSMUSG00000097456	LOC100862268	-	uncharacterized LOC100862268	ncRNA
mm_9266.1	chr1	171632780	171632798	-	1	NA	3' UTR (NM_144539, exon 8 of 8)	3' UTR (NM_144539, exon 8 of 8)	9111	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_51584.1	chr6	83795023	83795034	+	1	NA	promoter-TSS (NM_001164187)	promoter-TSS (NM_001164187)	28	NM_001347315	56174	Mm.190650	NM_019542	ENSMUSG00000034744	Nagk	Gnk	N-acetylglucosamine kinase	protein-coding
mm_86527.1	chr10	7824964	7824979	+	1	NA	Intergenic	Intergenic	-7499	NM_172785	237256	Mm.140055	NM_172785	ENSMUSG00000039981	Zc3h12d	D730019B10Rik|TFL	zinc finger CCCH type containing 12D	protein-coding
mm_112109.1	chr12	112795687	112795754	-	1	NA	Intergenic	Intergenic	-13255	NM_145450	217887	Mm.186678	NM_145450	ENSMUSG00000037594	BC022687	AW050009|C130001I08Rik|Flj20080	cDNA sequence BC022687	protein-coding
mm_69290.1	chr7	128206347	128206359	-	1	NA	promoter-TSS (NM_009943)	promoter-TSS (NM_009943)	13	NM_009943	12862	Mm.43824	NM_009943	ENSMUSG00000030785	Cox6a2	CoxVIaH|VIaH	cytochrome c oxidase subunit VIa polypeptide 2	protein-coding
mm_62604.1	chr7	105740281	105740295	+	1	NA	exon (NM_001161724, exon 3 of 13)	exon (NM_001161724, exon 3 of 13)	-2903	NM_133951	101867	Mm.231400	NM_025897	ENSMUSG00000030888	Rrp8	1500003O22Rik|2900001K19Rik|AW538116	ribosomal RNA processing 8, methyltransferase, homolog (yeast)	protein-coding
mm_107351.1	chr12	32820531	32820541	+	1	NA	5' UTR (NM_021524, exon 1 of 11)	5' UTR (NM_021524, exon 1 of 11)	201	NM_021524	59027	Mm.202727	NM_021524	ENSMUSG00000020572	Nampt	1110035O14Rik|AI314458|AI480535|NAmPRTase|Pbef|Pbef1|Visfatin	nicotinamide phosphoribosyltransferase	protein-coding
mm_55287.1	chr6	54566279	54566281	-	1	NA	5' UTR (NM_027268, exon 1 of 8)	5' UTR (NM_027268, exon 1 of 8)	102	NM_027268	69938	Mm.41557	NM_027268	ENSMUSG00000019124	Scrn1	2810019K23Rik|6330535A03Rik|AI852905|SES1|mKIAA0193	secernin 1	protein-coding
mm_115560.1	chr13	9754165	9754167	-	1	NA	intron (NM_001347474, intron 1 of 14)	intron (NM_001347474, intron 1 of 14)	9644	NM_001347471	66505	Mm.397307	NM_144516	ENSMUSG00000021156	Zmynd11	2210402G22Rik|BS69	zinc finger, MYND domain containing 11	protein-coding
mm_93050.1	chr10	88504160	88504167	-	1	NA	promoter-TSS (NM_001146690)	promoter-TSS (NM_001146690)	-193	NM_001146690	212862	Mm.288897	NM_144807	ENSMUSG00000060002	Chpt1	-	choline phosphotransferase 1	protein-coding
mm_95236.1	chr11	44617311	44617336	+	1	NA	promoter-TSS (NM_001290711)	promoter-TSS (NM_001290711)	-777	NM_001290711	13591	Mm.439662	NM_007897	ENSMUSG00000057098	Ebf1	Ebf|O/E-1|OE-1|Olf-1|Olf1	early B cell factor 1	protein-coding
mm_47039.1	chr5	116021770	116021779	-	1	NA	intron (NM_031869, intron 1 of 6)	intron (NM_031869, intron 1 of 6)	2654	NM_031869	19079	Mm.458152	NM_031869	ENSMUSG00000029513	Prkab1	1300015D22Rik|AU021155|E430008F22	protein kinase, AMP-activated, beta 1 non-catalytic subunit	protein-coding
mm_95272.1	chr11	45829107	45829109	+	1	NA	intron (NR_045876, intron 1 of 3)	intron (NR_045876, intron 1 of 3)	21025	NR_045876	100009664	Mm.415439	NR_045876		F630206G17Rik	-	RIKEN cDNA F630206G17 gene	ncRNA
mm_166107.1	chr4	146932418	146932447	+	1	NA	Intergenic	CpG	-89418	NM_001177767	100043034	Mm.422606	NM_001177767	ENSMUSG00000067919	Rex2	Gm13138|OTTMUSG00000010655	reduced expression 2	protein-coding
mm_95131.1	chr11	34314758	34314786	+	1	NA	promoter-TSS (NM_001025382)	promoter-TSS (NM_001025382)	-50	NM_001025382	574403	Mm.444796	NM_001025382	ENSMUSG00000069911	Fam196b	EG574403|Gm6041	family with sequence similarity 196, member B	protein-coding
mm_167709.1	chr9	96650002	96650013	-	1	NA	Intergenic	Intergenic	-18504	NM_053268	114713	Mm.124502	NM_053268	ENSMUSG00000032413	Rasa2	5430433H21Rik|AA517451|AU023900|GAP1m	RAS p21 protein activator 2	protein-coding
mm_30781.1	chr4	19298258	19298258	+	1	NA	intron (NM_013927, intron 2 of 17)	intron (NM_013927, intron 2 of 17)	17408	NM_013927	30952	Mm.445778	NM_013927	ENSMUSG00000056494	Cngb3	CCNC2|CNG6|Cngbeta2	cyclic nucleotide gated channel beta 3	protein-coding
mm_143087.1	chr17	57078491	57078519	-	1	NA	promoter-TSS (NM_153551)	promoter-TSS (NM_153551)	5	NM_153551	70785	Mm.284447	NM_153551	ENSMUSG00000002668	Dennd1c	4432409M07Rik	DENN/MADD domain containing 1C	protein-coding
mm_52285.1	chr6	108661991	108661996	+	1	NA	intron (NM_011498, intron 3 of 4)	intron (NM_011498, intron 3 of 4)	-1059	NR_104577	75394	Mm.395061	NR_040757	ENSMUSG00000087341	0610040F04Rik	-	RIKEN cDNA 0610040F04 gene	ncRNA
mm_143463.1	chr17	70997982	70998000	-	1	NA	intron (NM_026064, intron 1 of 3)	intron (NM_026064, intron 1 of 3)	4542	NM_026064	67268	Mm.489605	NM_026064	ENSMUSG00000024048	Myl12a	2900073G15Rik|AI838292|C80200	myosin, light chain 12A, regulatory, non-sarcomeric	protein-coding
mm_66389.1	chr7	44116258	44116295	-	1	NA	exon (NM_010114, exon 4 of 5)	exon (NM_010114, exon 4 of 5)	3603	NM_010114	13646	Mm.5193	NM_010114	ENSMUSG00000060177	Klk1b22	EGF-BP A|Egfbp-1|Egfbp1|Klk22|mGk-22	kallikrein 1-related peptidase b22	protein-coding
mm_98644.1	chr11	96248595	96248602	+	1	NA	Intergenic	B1_Mus1|SINE|Alu	-3062	NR_037977	193022	Mm.169508	NR_037977		Gm53	-	predicted gene 53	ncRNA
mm_129686.1	chr15	81421474	81421496	-	1	NA	intron (NM_001347075, intron 2 of 9)	intron (NM_001347075, intron 2 of 9)	-13212	NM_021317	57755	Mm.440590	NM_021317	ENSMUSG00000047108	Dnajb7	4933424H20Rik|Dj5|mDj5	DnaJ heat shock protein family (Hsp40) member B7	protein-coding
mm_28798.1	chr3	96172385	96172462	-	1	NA	promoter-TSS (NM_153053)	promoter-TSS (NM_153053)	-83	NM_153053	107701	Mm.219671	NM_153053	ENSMUSG00000068856	Sf3b4	SF3b49|SF3b50|Sap49	splicing factor 3b, subunit 4	protein-coding
mm_79479.1	chr9	56994566	56994608	+	1	NA	promoter-TSS (NM_019651)	promoter-TSS (NM_019651)	-381	NM_019651	56294	Mm.325643	NM_019651	ENSMUSG00000032290	Ptpn9	MEG2	protein tyrosine phosphatase, non-receptor type 9	protein-coding
mm_172873.1	chr9	42689533	42689547	-	1	NA	intron (NM_175481, intron 3 of 20)	L1MB5|LINE|L1	-217314	NM_173038	272589	Mm.34483	NM_173038	ENSMUSG00000037287	Tbcel	D330014K23|E130107N23Rik|Lrrc35	tubulin folding cofactor E-like	protein-coding
mm_11021.1	chr2	26610689	26610692	+	1	NA	Intergenic	Intergenic	-6273	NM_026212	67512	Mm.24244	NM_026212	ENSMUSG00000026922	Agpat2	2510002J07Rik|AV000834|BSCL|BSCL1|LPAAB|LPAAT-beta	1-acylglycerol-3-phosphate O-acyltransferase 2 (lysophosphatidic acid acyltransferase, beta)	protein-coding
mm_160450.1	chr8	105413597	105413597	+	1	NA	promoter-TSS (NM_177791)	promoter-TSS (NM_177791)	-25	NM_001170788	270091	Mm.212709	NM_001033371	ENSMUSG00000054320	Lrrc36	BC036564	leucine rich repeat containing 36	protein-coding
mm_106427.1	chr11	119346828	119346845	-	1	NA	exon (NM_018822, exon 8 of 8)	exon (NM_018822, exon 8 of 8)	8674	NM_018822	27029	Mm.103788	NM_018822	ENSMUSG00000005043	Sgsh	4632406A19Rik	N-sulfoglucosamine sulfohydrolase (sulfamidase)	protein-coding
mm_160368.1	chr8	27229461	27229461	-	1	NA	5' UTR (NM_013462, exon 1 of 4)	5' UTR (NM_013462, exon 1 of 4)	127	NM_013462	11556	Mm.278475	NM_013462	ENSMUSG00000031489	Adrb3	Adrb-3	adrenergic receptor, beta 3	protein-coding
mm_107552.1	chr12	41151091	41151102	+	1	NA	intron (NM_053122, intron 4 of 6)	intron (NM_053122, intron 4 of 6)	127006	NM_053122	93757	Mm.363813	NM_053122	ENSMUSG00000056899	Immp2l	AI853880|IMP2	IMP2 inner mitochondrial membrane peptidase-like (S. cerevisiae)	protein-coding
mm_29977.1	chr3	133749531	133749541	-	1	NA	Intergenic	MLT1I|LTR|ERVL-MaLR	-205146	NM_001040400	214133	Mm.347816	NM_145989	ENSMUSG00000040943	Tet2	Ayu17-449|E130014J05Rik|mKIAA1546	tet methylcytosine dioxygenase 2	protein-coding
mm_89049.1	chr10	82866616	82866646	+	1	NA	promoter-TSS (NM_025499)	promoter-TSS (NM_025499)	5	NM_025499	66341	Mm.443284	NM_025499	ENSMUSG00000109864	Eid3	1700027M21Rik|NS4EB	EP300 interacting inhibitor of differentiation 3	protein-coding
mm_70898.1	chr8	25601592	25601607	+	1	NA	promoter-TSS (NM_001308482)	promoter-TSS (NM_001308482)	-2	NM_001308481	234135	Mm.217337	NM_001001735	ENSMUSG00000054823	Whsc1l1	6720429E03|A530023P05|AI528490|NSD3|WHISTLE	Wolf-Hirschhorn syndrome candidate 1-like 1 (human)	protein-coding
mm_141193.1	chr17	27020624	27020643	-	1	NA	3' UTR (NM_007523, exon 6 of 6)	3' UTR (NM_007523, exon 6 of 6)	2598	NM_001251881	70772	Mm.440437	NM_027544	ENSMUSG00000048731	Ggnbp1	0610031G08Rik|mdf	gametogenetin binding protein 1	protein-coding
mm_59655.1	chr7	28180051	28180055	+	1	NA	promoter-TSS (NM_001271370)	promoter-TSS (NM_001271370)	-263	NM_001271370	13549	Mm.57249	NM_010092	ENSMUSG00000002409	Dyrk1b	Mirk	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1b	protein-coding
mm_35214.1	chr4	19637202	19637211	-	1	NA	intron (NR_074089, intron 15 of 23)	Lx9|LINE|L1	62140	NM_025476	66302	Mm.440686	NM_025476	ENSMUSG00000028229	Rmdn1	Fam82b|RMD-1	regulator of microtubule dynamics 1	protein-coding
mm_170211.1	chr17	70963686	70963700	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	26823	NM_023402	67938	Mm.261329	NM_023402	ENSMUSG00000034868	Myl12b	1500001M02Rik|C77744|Mylc2b|RLC-B	myosin, light chain 12B, regulatory	protein-coding
mm_96140.1	chr11	60941659	60941669	+	1	NA	intron (NM_008928, intron 1 of 11)	intron (NM_008928, intron 1 of 11)	9607	NM_008928	26397	Mm.18494	NM_008928	ENSMUSG00000018932	Map2k3	AW212142|MEK3|MKK3|Prkmk3|mMKK3b	mitogen-activated protein kinase kinase 3	protein-coding
mm_151731.1	chr19	4876917	4876929	-	1	NA	intron (NM_013456, intron 1 of 20)	intron (NM_013456, intron 1 of 20)	986	NM_013456	11474	Mm.5316	NM_013456	ENSMUSG00000006457	Actn3	-	actinin alpha 3	protein-coding
mm_130082.1	chr15	89377104	89377114	-	1	NA	promoter-TSS (NM_138302)	promoter-TSS (NM_138302)	-72	NM_138302	72962	Mm.287977	NM_138302	ENSMUSG00000022615	Tymp	2900072D10Rik|Ecgf1|PD-ECGF|PDECGF|Pdgfec	thymidine phosphorylase	protein-coding
mm_27408.1	chr3	51340556	51340584	-	1	NA	promoter-TSS (NM_001291059)	promoter-TSS (NM_001291059)	74	NM_001291059	69257	Mm.131038	NM_023502	ENSMUSG00000037174	Elf2	2610036A20Rik|A230104O07Rik|AW111824|BB183398|EU32|NERF|NERF-1A|NERF-1B|NERF-2	E74-like factor 2	protein-coding
mm_119237.1	chr14	33351293	33351312	+	1	NA	intron (NM_153800, intron 5 of 10)	CpG	59722	NM_001310452	26419	Mm.21495	NM_016700	ENSMUSG00000021936	Mapk8	AI849689|JNK|JNK1|Prkm8|SAPK1	mitogen-activated protein kinase 8	protein-coding
mm_100592.1	chr11	120958218	120958236	+	1	NA	3' UTR (NM_001038654, exon 5 of 5)	3' UTR (NM_001038654, exon 5 of 5)	9160	NM_001038654	80879	Mm.28632	NM_030696	ENSMUSG00000025161	Slc16a3	Mct3|Mct4	solute carrier family 16 (monocarboxylic acid transporters), member 3	protein-coding
mm_16412.1	chr2	180042744	180042791	+	1	NA	promoter-TSS (NM_001289476)	promoter-TSS (NM_001289476)	284	NM_178750	269397	Mm.63068	NM_178750	ENSMUSG00000039086	Ss18l1	A230053O16Rik|CREST	SS18, nBAF chromatin remodeling complex subunit like 1	protein-coding
mm_102407.1	chr11	59164528	59164548	-	1	NA	promoter-TSS (NM_001270791)	promoter-TSS (NM_001270791)	-793	NM_173785	216792	Mm.266175	NM_173785	ENSMUSG00000049287	Iba57	4930543L23Rik|A230051G13Rik|C1orf69	IBA57 homolog, iron-sulfur cluster assembly	protein-coding
mm_168787.1	chr12	19093239	19093240	-	1	NA	Intergenic	B1_Mm|SINE|Alu	578729	NM_001201330	236366	Mm.352227	NM_001033157	ENSMUSG00000073197	5730507C01Rik	-	RIKEN cDNA 5730507C01 gene	protein-coding
mm_149574.1	chr19	12827958	12827971	+	1	NA	intron (NM_134152, intron 7 of 8)	L1Md_F2|LINE|L1	29355	NM_134152	107321	Mm.313136	NM_134152	ENSMUSG00000024696	Lpxn	4933402K05Rik|A530083L21Rik|AV278559|LDPL	leupaxin	protein-coding
mm_50146.1	chr6	41543582	41543620	+	1	NA	Intergenic	Intergenic	21825	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_61222.1	chr7	64501623	64501649	+	1	NA	promoter-TSS (NM_001291167)	promoter-TSS (NM_001291167)	-70	NM_007461	11784	Mm.4657	NM_007461	ENSMUSG00000030519	Apba2	X11-like|X11L|XllL|mXllL	amyloid beta (A4) precursor protein-binding, family A, member 2	protein-coding
mm_103233.1	chr11	70683323	70683397	-	1	NA	exon (NM_178116, exon 6 of 23)	exon (NM_178116, exon 6 of 23)	4745	NM_001190376	216874	Mm.473726	NM_178116	ENSMUSG00000040712	Camta2	Kiaa0909-hp|mKIAA0909	calmodulin binding transcription activator 2	protein-coding
mm_81473.1	chr9	109931775	109931798	+	1	NA	promoter-TSS (NM_008633)	promoter-TSS (NM_008633)	12	NM_008633	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_166672.1	chr6	94086590	94086591	+	1	NA	intron (NM_001029850, intron 1 of 23)	MER58A|DNA|hAT-Charlie	150852	NR_130996	78178	Mm.452749	NR_130996	ENSMUSG00000045095	4930511A08Rik	-	RIKEN cDNA 4930511A08 gene	ncRNA
mm_47548.1	chr5	124351226	124351255	-	1	NA	intron (NM_013812, intron 1 of 3)	intron (NM_013812, intron 1 of 3)	3388	NM_013812	13445	Mm.391838	NM_013812	ENSMUSG00000029394	Cdk2ap1	Apc10|Cdkap1|DORC1|Doc1|ST19|doc-1|p12	CDK2 (cyclin-dependent kinase 2)-associated protein 1	protein-coding
mm_154029.1	chr19	53424788	53424801	-	1	NA	Intergenic	Intergenic	-34221	NM_172429	76479	Mm.313687	NM_172429	ENSMUSG00000025024	Smndc1	2410004J23Rik|4933440I19Rik	survival motor neuron domain containing 1	protein-coding
mm_135079.1	chr16	34263077	34263099	-	1	NA	intron (NM_001164268, intron 10 of 33)	intron (NM_001164268, intron 10 of 33)	250939	NM_001164268	545156	Mm.82274	NM_177357	ENSMUSG00000061751	Kalrn	2210407G14Rik|AV235988|DUET|E530005C20Rik|Gm539|Hapip|TRAD	kalirin, RhoGEF kinase	protein-coding
mm_136627.1	chr17	5574952	5574964	+	1	NA	intron (NM_146073, intron 1 of 8)	MLT1H1|LTR|ERVL-MaLR	82358	NM_146073	224454	Mm.487663	NM_146073	ENSMUSG00000034265	Zdhhc14	B530001K09Rik|New1cp	zinc finger, DHHC domain containing 14	protein-coding
mm_51538.1	chr6	83195924	83195957	+	1	NA	intron (NM_001347310, intron 20 of 26)	intron (NM_001347310, intron 20 of 26)	9994	NM_001347310	13191	Mm.6919	NM_007835	ENSMUSG00000031865	Dctn1	AL022633|DAP-150|DP-150|Glued|p150|p150-glued|p150<glued>	dynactin 1	protein-coding
mm_105998.1	chr11	115696576	115696600	-	1	NA	intron (NM_001313937, intron 1 of 4)	intron (NM_001313937, intron 1 of 4)	2946	NM_001313937	14784	Mm.439649	NM_008163	ENSMUSG00000059923	Grb2	AA408164|Ash	growth factor receptor bound protein 2	protein-coding
mm_37761.1	chr4	129684736	129684745	-	1	NA	promoter-TSS (NR_105983)	promoter-TSS (NR_105983)	-169	NR_105983	102465615		NR_105983	ENSMUSG00000098422	Mir7016	Gm27994|mmu-mir-7016	microRNA 7016	ncRNA
mm_16443.1	chr2	180442267	180442277	+	1	NA	Intergenic	Intergenic	-18706	NM_148933	108115	Mm.133687	NM_148933	ENSMUSG00000038963	Slco4a1	OATP-E|Slc21a12	solute carrier organic anion transporter family, member 4a1	protein-coding
mm_127908.1	chr15	9528079	9528088	-	1	NA	intron (NM_008372, intron 1 of 7)	intron (NM_008372, intron 1 of 7)	1793	NM_008372	16197	Mm.389	NM_008372	ENSMUSG00000003882	Il7r	CD127|IL-7Ralpha	interleukin 7 receptor	protein-coding
mm_65432.1	chr7	25367693	25367703	-	1	NA	TTS (NM_028219)	TTS (NM_028219)	2026	NM_001081375	72383	Mm.34382	NM_028219	ENSMUSG00000063651	Cnfn	2210418J09Rik	cornifelin	protein-coding
mm_103671.1	chr11	79146391	79146395	-	1	NA	promoter-TSS (NM_013571)	promoter-TSS (NM_013571)	-39	NM_013571	16706	Mm.4745	NM_013571	ENSMUSG00000018334	Ksr1	AW492498|B-KSR1|D11Bhm183e|D11Bhm184e|Ksr|RSU2|hb	kinase suppressor of ras 1	protein-coding
mm_17009.1	chr2	18868290	18868293	-	1	NA	intron (NM_008845, intron 5 of 9)	B4|SINE|B4	-66473	NR_131254	66774	Mm.87075	NR_131254	ENSMUSG00000097638	Carlr	4933439G12Rik|Carl	cardiac and apoptosis-related long non-coding RNA	ncRNA
mm_153887.1	chr19	46961937	46961972	-	1	NA	intron (NM_001164363, intron 1 of 17)	CpG	397	NM_029810	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_163516.1	chr12	114048780	114048780	-	1	NA	Intergenic	Intergenic	420686	NR_106062	102465663		NR_106062	ENSMUSG00000105438	Mir7094-1	mmu-mir-7094-1	microRNA 7094-1	ncRNA
mm_80880.1	chr9	98991779	98991821	+	1	NA	intron (NM_001122851, intron 2 of 5)	intron (NM_001122851, intron 2 of 5)	5427	NM_011810	23873	Mm.74605	NM_011810	ENSMUSG00000032463	Faim	-	Fas apoptotic inhibitory molecule	protein-coding
mm_76678.1	chr8	93972104	93972107	-	1	NA	3' UTR (NM_011787, exon 14 of 14)	3' UTR (NM_011787, exon 14 of 14)	40535	NM_011787	23802	Mm.34641	NM_011787	ENSMUSG00000031751	Amfr	gp78	autocrine motility factor receptor	protein-coding
mm_147610.1	chr18	56974129	56974153	-	1	NA	intron (NM_029909, intron 1 of 4)	PB1D9|SINE|Alu	1238	NM_029909	77422	Mm.256874	NM_029909	ENSMUSG00000024592	C330018D20Rik	AU018666	RIKEN cDNA C330018D20 gene	protein-coding
mm_162681.1	chr10	13446063	13446104	-	1	NA	intron (NM_001195065, intron 1 of 12)	intron (NM_001195065, intron 1 of 12)	28313	NM_001195065	215789	Mm.283359	NM_001033257	ENSMUSG00000062866	Phactr2	AV158170|BC012871	phosphatase and actin regulator 2	protein-coding
mm_130064.1	chr15	89190516	89190563	-	1	NA	intron (NM_027081, intron 3 of 19)	intron (NM_027081, intron 3 of 19)	-5002	NR_105923	102465578		NR_105923	ENSMUSG00000098663	Mir6958	Gm27581|mmu-mir-6958	microRNA 6958	ncRNA
mm_102728.1	chr11	67243043	67243087	-	1	NA	exon (NM_010855, exon 9 of 40)	exon (NM_010855, exon 9 of 40)	5253	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_48586.1	chr5	143732465	143732475	-	1	NA	promoter-TSS (NM_029749)	promoter-TSS (NM_029749)	-190	NM_029749	76800	Mm.259620	NM_029749	ENSMUSG00000051306	Usp42	2410140K03Rik|3110031A07Rik|A630018G05Rik|D5Ertd591e	ubiquitin specific peptidase 42	protein-coding
mm_131631.1	chr16	20186545	20186549	+	1	NA	intron (NM_001033237, intron 10 of 29)	intron (NM_001033237, intron 10 of 29)	-10313	NR_030454	735274		NR_030454	ENSMUSG00000106252	Mir684-1	Mirn684-1	microRNA 684-1	ncRNA
mm_127448.1	chr15	101270660	101270666	+	1	NA	exon (NM_010444, exon 2 of 7)	exon (NM_010444, exon 2 of 7)	3817	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_78757.1	chr9	43265410	43265418	+	1	NA	exon (NM_001243261, exon 2 of 3)	exon (NM_001243261, exon 2 of 3)	5535	NM_001243261	235302	Mm.135745	NM_001243261	ENSMUSG00000095385	D630033O11Rik	Gm588	RIKEN cDNA D630033O11 gene	protein-coding
mm_72936.1	chr8	91318118	91318119	+	1	NA	intron (NM_011936, intron 1 of 8)	intron (NM_011936, intron 1 of 8)	4593	NM_011936	26383	Mm.4375	NM_011936	ENSMUSG00000055932	Fto	AW743446|mKIAA1752	fat mass and obesity associated	protein-coding
mm_168053.1	chrY	90812424	90812510	+	1	NA	intron (NM_133362, intron 2 of 3)	IMPB_01|Satellite|Satellite	26939	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_28450.1	chr3	90514371	90514379	-	1	NA	promoter-TSS (NM_009113)	promoter-TSS (NM_009113)	-45	NM_011309	20193	Mm.24662	NM_011309	ENSMUSG00000044080	S100a1	AI266795|S100|S100a	S100 calcium binding protein A1	protein-coding
mm_29383.1	chr3	108845052	108845075	-	1	NA	Intergenic	MTB_Mm|LTR|ERVL-MaLR	-4561	NM_011504	20912	Mm.316894	NM_011504	ENSMUSG00000027882	Stxbp3	Munc-18c|Stxbp3a|Sxtbp3|Unc18-3	syntaxin binding protein 3	protein-coding
mm_64290.1	chr7	141857648	141857659	+	1	NA	exon (NM_028801, exon 31 of 49)	exon (NM_028801, exon 31 of 49)	18581	NM_028801	74180	Mm.200752	NM_028801	ENSMUSG00000066108	Muc5b	2300002I04Rik|A130042M24|AV085033|MUC5|MUC9|mucin 5b	mucin 5, subtype B, tracheobronchial	protein-coding
mm_70153.1	chr7	143464221	143464230	-	1	NA	Intergenic	Intergenic	-3175	NM_001161624	12577	Mm.168789	NM_009876	ENSMUSG00000037664	Cdkn1c	AL024410|CDKI|Kip2|p57(kip2)|p57Kip2	cyclin-dependent kinase inhibitor 1C (P57)	protein-coding
mm_132202.1	chr16	32550338	32550355	+	1	NA	Intergenic	Intergenic	54065	NM_199309	245308	Mm.76859	NM_199309	ENSMUSG00000052363	Zdhhc19	Gm1744|Gm616	zinc finger, DHHC domain containing 19	protein-coding
mm_163003.1	chr11	34507078	34507083	+	1	NA	intron (NM_033374, intron 23 of 51)	intron (NM_033374, intron 23 of 51)	192258	NM_001025382	574403	Mm.444796	NM_001025382	ENSMUSG00000069911	Fam196b	EG574403|Gm6041	family with sequence similarity 196, member B	protein-coding
mm_87207.1	chr10	39732162	39732176	+	1	NA	promoter-TSS (NM_011264)	promoter-TSS (NM_011264)	9	NM_011264	19714	Mm.439723	NM_011264	ENSMUSG00000019841	Rev3l	Rev|Rev3|Sez4	REV3 like, DNA directed polymerase zeta catalytic subunit	protein-coding
mm_167469.1	chr8	126152791	126152793	-	1	NA	Intergenic	Intergenic	-145787	NM_175434	210027	Mm.405238	NM_175434	ENSMUSG00000057060	Slc35f3	B230375D17Rik	solute carrier family 35, member F3	protein-coding
mm_150683.1	chr19	42068697	42068729	+	1	NA	intron (NM_026152, intron 6 of 6)	intron (NM_026152, intron 6 of 6)	16485	NM_025752	66765	Mm.440412	NM_025752	ENSMUSG00000090369	4933411K16Rik	-	RIKEN cDNA 4933411K16 gene	protein-coding
mm_56292.1	chr6	91493185	91493213	-	1	NA	exon (NM_009531, exon 12 of 16)	exon (NM_009531, exon 12 of 16)	19448	NM_028766	74122	Mm.38801	NM_028766	ENSMUSG00000030095	Tmem43	1200015A22Rik|LUMA	transmembrane protein 43	protein-coding
mm_14466.1	chr2	131262470	131262563	+	1	NA	promoter-TSS (NM_153501)	promoter-TSS (NM_153501)	16	NM_153501	74450	Mm.101264	NM_153501	ENSMUSG00000037514	Pank2	4933409I19Rik|AI642621	pantothenate kinase 2	protein-coding
mm_99074.1	chr11	99385588	99385601	+	1	NA	3' UTR (NM_010660, exon 8 of 8)	3' UTR (NM_010660, exon 8 of 8)	3770	NM_010660	16661	Mm.22662	NM_010660	ENSMUSG00000019761	Krt10	D130054E02Rik|K10|K1C1|Krt-1.10|Krt1-10	keratin 10	protein-coding
mm_156053.1	chrX	109095540	109095554	+	1	NA	5' UTR (NM_019989, exon 1 of 4)	5' UTR (NM_019989, exon 1 of 4)	140	NM_019989	56726	Mm.260760	NM_019989	ENSMUSG00000031246	Sh3bgrl	1190008F14Rik	SH3-binding domain glutamic acid-rich protein like	protein-coding
mm_140916.1	chr17	24170760	24170778	-	1	NA	Intergenic	Intergenic	-1340	NM_009729	11984	Mm.30155	NM_009729	ENSMUSG00000024121	Atp6v0c	Atp6c|Atp6c2|Atp6l|Atpl|Atpl-rs1|PL16|VATL|Vma3	ATPase, H+ transporting, lysosomal V0 subunit C	protein-coding
mm_8995.1	chr1	165709748	165709769	-	1	NA	Intergenic	Intergenic	-1664	NM_001038846	226594	Mm.265552	NM_178593	ENSMUSG00000040723	Rcsd1	A430105K13Rik|BC025872|CapZIP	RCSD domain containing 1	protein-coding
mm_100639.1	chr11	121805487	121805490	+	1	NA	Intergenic	Intergenic	-24730	NM_029049	74675	Mm.61213	NM_029049	ENSMUSG00000039198	Ptchd3	4930451E13Rik|4933440L20Rik|RNDEu-3	patched domain containing 3	protein-coding
mm_95626.1	chr11	53584374	53584393	+	1	NA	exon (NM_008443, exon 8 of 18)	exon (NM_008443, exon 8 of 18)	17014	NM_001290806	16568	Mm.88694	NM_008443	ENSMUSG00000018395	Kif3a	Kif3|Kifl|Kns3	kinesin family member 3A	protein-coding
mm_65417.1	chr7	25248425	25248465	-	1	NA	intron (NM_010155, intron 1 of 3)	intron (NM_010155, intron 1 of 3)	2313	NM_010155	13875	Mm.8068	NM_010155	ENSMUSG00000040857	Erf	-	Ets2 repressor factor	protein-coding
mm_87453.1	chr10	51483630	51483648	+	1	NA	intron (NM_001291892, intron 5 of 8)	intron (NM_001291892, intron 5 of 8)	3027	NM_001291892	14727	Mm.439661	NM_008147	ENSMUSG00000062593	Lilr4b	Gp49a|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4B	protein-coding
mm_54838.1	chr6	42586366	42586368	-	1	NA	TTS (NM_203396)	TTS (NM_203396)	11005	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_1515.1	chr1	72711239	72711252	+	1	NA	promoter-TSS (NM_009084)	promoter-TSS (NM_009084)	-15	NM_009084	19981	Mm.21529	NM_009084	ENSMUSG00000046330	Rpl37a	-	ribosomal protein L37a	protein-coding
mm_85354.1	chr9	103211928	103211998	-	1	NA	exon (NM_133977, exon 15 of 17)	exon (NM_133977, exon 15 of 17)	-9898	NM_009275	20818	Mm.273053	NM_009275	ENSMUSG00000032553	Srprb	AA409543	signal recognition particle receptor, B subunit	protein-coding
mm_64398.1	chr7	142500231	142500244	+	1	NA	intron (NM_001347548, intron 1 of 14)	intron (NM_001347548, intron 1 of 14)	1401	NM_001347551	21957	Mm.389992	NM_011620	ENSMUSG00000061723	Tnnt3	fTnT	troponin T3, skeletal, fast	protein-coding
mm_133914.1	chr16	97557794	97557807	+	1	NA	intron (NM_013606, intron 12 of 13)	MTEb|LTR|ERVL-MaLR	21717	NM_013606	17858	Mm.14157	NM_013606	ENSMUSG00000023341	Mx2	AI528743|Mx-2	MX dynamin-like GTPase 2	protein-coding
mm_133486.1	chr16	90220621	90220632	+	1	NA	promoter-TSS (NM_011434)	promoter-TSS (NM_011434)	-116	NM_011434	20655	Mm.276325	NM_011434	ENSMUSG00000022982	Sod1	B430204E11Rik|Cu/Zn-SOD|CuZnSOD|Ipo-1|Ipo1|SODC|Sod-1	superoxide dismutase 1, soluble	protein-coding
mm_1686.1	chr1	74884731	74884739	+	1	NA	intron (NM_153111, intron 1 of 2)	CpG-298	673	NM_153111	260298	Mm.150496	NM_153111	ENSMUSG00000055197	Fev	Pet-1|Pet1|mPet-1	FEV (ETS oncogene family)	protein-coding
mm_33712.1	chr4	133816282	133816293	+	1	NA	Intergenic	Intergenic	58444	NM_001285506	20111	Mm.301827	NM_009097	ENSMUSG00000003644	Rps6ka1	Mapkapk-1a|Rsk|Rsk-1|Rsk1|S6K-alpha-1|p90-Rsk1|p90Rsk1|p90S6K|p90rsk	ribosomal protein S6 kinase polypeptide 1	protein-coding
mm_17996.1	chr2	38166160	38166166	-	1	NA	intron (NM_146122, intron 2 of 21)	intron (NM_146122, intron 2 of 21)	121221	NM_146122	227801	Mm.314245	NM_146122	ENSMUSG00000035392	Dennd1a	6030446I19Rik|connecdenn	DENN/MADD domain containing 1A	protein-coding
mm_47542.1	chr5	124263391	124263417	-	1	NA	intron (NR_102690, intron 17 of 22)	intron (NR_102690, intron 17 of 22)	-13644	NM_011256	19679	Mm.44261	NM_011256	ENSMUSG00000029406	Pitpnm2	NIR3|RDGBA2|Rdgb2|mKIAA1457	phosphatidylinositol transfer protein, membrane-associated 2	protein-coding
mm_160866.1	chr11	61720723	61720723	-	1	NA	promoter-TSS (NM_001033227)	promoter-TSS (NM_001033227)	76	NM_001033227	109342	Mm.441070	NM_001033227	ENSMUSG00000042371	Slc5a10	C330021F16Rik|SGLT5	solute carrier family 5 (sodium/glucose cotransporter), member 10	protein-coding
mm_162653.1	chr10	3859667	3859673	+	1	NA	intron (NM_001159942, intron 2 of 16)	intron (NM_001159942, intron 2 of 16)	-12997	NM_001033253	213783	Mm.150831	NM_001033253	ENSMUSG00000040624	Plekhg1	D10Ertd733e|Gm521|mKIAA1209	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	protein-coding
mm_113751.1	chr13	44731326	44731341	+	1	NA	promoter-TSS (NM_001205043)	promoter-TSS (NM_001205043)	62	NM_001205043	16468	Mm.25059	NM_021878	ENSMUSG00000038518	Jarid2	Jmj|jumonji	jumonji, AT rich interactive domain 2	protein-coding
mm_96723.1	chr11	69666503	69666515	+	1	NA	promoter-TSS (NR_110993)	promoter-TSS (NR_110993)	-339	NR_110993	12514	Mm.15819	NM_009853	ENSMUSG00000018774	Cd68	Lamp4|Scard1|gp110	CD68 antigen	protein-coding
mm_56520.1	chr6	99516867	99516870	-	1	NA	intron (NM_001347345, intron 1 of 19)	intron (NM_001347345, intron 1 of 19)	4125	NM_001347345	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_75664.1	chr8	66486541	66486551	-	1	NA	promoter-TSS (NM_025465)	promoter-TSS (NM_025465)	-39	NM_025465	66282	Mm.294985	NM_025465	ENSMUSG00000025591	Tma16	1810029B16Rik	translation machinery associated 16	protein-coding
mm_99859.1	chr11	109365099	109365154	+	1	NA	intron (NM_010303, intron 1 of 3)	intron (NM_010303, intron 1 of 3)	-1472	NR_038097	100036768	Mm.467767	NR_038097	ENSMUSG00000056687	Gm11696	OTTMUSG00000003456	predicted gene 11696	ncRNA
mm_162940.1	chr10	128439150	128439162	+	1	NA	non-coding (NR_104290, exon 8 of 8)	non-coding (NR_104290, exon 8 of 8)	-19524	NR_106183	102465894		NR_106183	ENSMUSG00000098957	Mir8105	Gm27346|mmu-mir-8105	microRNA 8105	ncRNA
mm_141251.1	chr17	27565679	27565757	-	1	NA	promoter-TSS (NM_001002895)	promoter-TSS (NM_001002895)	9	NM_001002895	106672	Mm.61488	NM_001002895	ENSMUSG00000062753	AI413582	AI854251	expressed sequence AI413582	protein-coding
mm_110479.1	chr12	51858329	51858348	-	1	NA	Intergenic	Intergenic	-28802	NM_144788	207304	Mm.249391	NM_144788	ENSMUSG00000035247	Hectd1	A630086P08Rik|AI844876|b2b327Clo|opm	HECT domain containing 1	protein-coding
mm_117056.1	chr13	58402120	58402149	-	1	NA	promoter-TSS (NR_031761)	promoter-TSS (NR_031761)	35	NM_001301343	15387	Mm.142872	NM_025279	ENSMUSG00000021546	Hnrnpk	Hnrpk|KBBP|NOVA	heterogeneous nuclear ribonucleoprotein K	protein-coding
mm_101385.1	chr11	23895176	23895189	-	1	NA	promoter-TSS (NM_172555)	promoter-TSS (NM_172555)	88	NM_172555	216578	Mm.470599	NM_172555	ENSMUSG00000020273	Papolg	9630006B20Rik	poly(A) polymerase gamma	protein-coding
mm_81708.1	chr9	111311568	111311586	+	1	NA	promoter-TSS (NM_001164659)	promoter-TSS (NM_001164659)	-162	NM_001164659	320429	Mm.270754	NM_001164659	ENSMUSG00000062296	Trank1	A230061D21Rik|C030048J01Rik|Gm187|Lba1	tetratricopeptide repeat and ankyrin repeat containing 1	protein-coding
mm_105593.1	chr11	106736476	106736486	-	1	NA	Intergenic	Intergenic	-14745	NM_001271375	380732	Mm.343952	NM_001033435	ENSMUSG00000040528	Milr1	Allergin-1|Gm885|Mca32	mast cell immunoglobulin like receptor 1	protein-coding
mm_5635.1	chr1	40437101	40437123	-	1	NA	intron (NM_001294171, intron 1 of 7)	intron (NM_001294171, intron 1 of 7)	-2517	NM_001025602	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_42315.1	chr5	114883352	114883360	+	1	NA	3' UTR (NM_026263, exon 12 of 12)	3' UTR (NM_026263, exon 12 of 12)	-13578	NM_011854	23962	Mm.228363	NM_011854	ENSMUSG00000029561	Oasl2	M1204|Mmu-OASL|Oasl	2'-5' oligoadenylate synthetase-like 2	protein-coding
mm_780.1	chr1	44652453	44652456	+	1	NA	intron (NM_028450, intron 1 of 10)	intron (NM_028450, intron 1 of 10)	92495	NR_040602	75066	Mm.416932	NR_040602	ENSMUSG00000101701	4930521E06Rik	-	RIKEN cDNA 4930521E06 gene	ncRNA
mm_86075.1	chr9	114778975	114778989	-	1	NA	intron (NM_001252479, intron 1 of 3)	intron (NM_001252479, intron 1 of 3)	3011	NM_133978	102545	Mm.35600	NM_133978	ENSMUSG00000032436	Cmtm7	AI481279|Cklfsf7|LNV	CKLF-like MARVEL transmembrane domain containing 7	protein-coding
mm_83795.1	chr9	52677864	52677874	-	1	NA	exon (NM_178906, exon 2 of 2)	exon (NM_178906, exon 2 of 2)	1568	NM_178906	330941	Mm.335160	NM_177907	ENSMUSG00000078307	AI593442	E130102D23	expressed sequence AI593442	protein-coding
mm_43435.1	chr5	136089669	136089679	+	1	NA	intron (NM_001039103, intron 2 of 19)	intron (NM_001039103, intron 2 of 19)	5758	NM_001039103	54153	Mm.290655	NM_133914	ENSMUSG00000004952	Rasa4	AA793972|AW112107|BB079060|CAPRI|GAPL	RAS p21 protein activator 4	protein-coding
mm_131340.1	chr16	13401074	13401089	+	1	NA	exon (NM_001122667, exon 12 of 17)	exon (NM_001122667, exon 12 of 17)	42660	NM_153588	239719	Mm.270643	NM_153588	ENSMUSG00000009569	Mkl2	ENSMUSG00000075401|Gt4-1|MRTF-B|Mrtfb|mKIAA1243	MKL/myocardin-like 2	protein-coding
mm_138290.1	chr17	34627793	34627838	+	1	NA	promoter-TSS (NM_019441)	promoter-TSS (NM_019441)	201	NM_001302394	54397	Mm.373627	NM_019441	ENSMUSG00000015474	Ppt2	0610007M19Rik|AA672937	palmitoyl-protein thioesterase 2	protein-coding
mm_78385.1	chr9	28403296	28403339	+	1	NA	intron (NM_177906, intron 1 of 7)	CpG	612048	NM_177906	330908	Mm.379474	NM_177906	ENSMUSG00000062257	Opcml	2900075O15Rik|3732419F12|AI844366|B930023M13Rik|C230027C17|Gm181|Obcam	opioid binding protein/cell adhesion molecule-like	protein-coding
mm_32770.1	chr4	116694081	116694095	+	1	NA	intron (NM_011034, intron 5 of 5)	intron (NM_011034, intron 5 of 5)	-8066	NR_040442	100502959	Mm.395400	NR_040442		AV051173	-	expressed sequence AV051173	ncRNA
mm_15040.1	chr2	152804831	152804837	+	1	NA	intron (NM_001289717, intron 2 of 2)	intron (NM_001289717, intron 2 of 2)	25883	NM_001289716	12048	Mm.238213	NM_009743	ENSMUSG00000007659	Bcl2l1	Bcl(X)L|Bcl-XL|Bcl2l|BclX|bcl-x|bcl2-L-1	BCL2-like 1	protein-coding
mm_146995.1	chr18	34371040	34371042	-	1	NA	intron (NM_007874, intron 2 of 4)	ID_B1|SINE|B4	2374	NM_007874	13476	Mm.280075	NM_007874	ENSMUSG00000005873	Reep5	AI324241|AU022809|AW495741|DP1/TB2|Dp1|R74856|TB2/DP1	receptor accessory protein 5	protein-coding
mm_127689.1	chr15	102981583	102981598	+	1	NA	5' UTR (NM_008272, exon 2 of 3)	5' UTR (NM_008272, exon 2 of 3)	4558	NM_008272	15427	Mm.4765	NM_008272	ENSMUSG00000036139	Hoxc9	Hox-3.2	homeobox C9	protein-coding
mm_79721.1	chr9	61509714	61509733	+	1	NA	Intergenic	Intergenic	137357	NM_001083927	21887	Mm.24255	NM_009389	ENSMUSG00000032280	Tle3	2610103N05Rik|ESG|Grg3a|Grg3b|mKIAA1547	transducin-like enhancer of split 3	protein-coding
mm_152406.1	chr19	10604305	10604315	-	1	NA	promoter-TSS (NM_145496)	promoter-TSS (NM_145496)	-52	NM_145496	225913	Mm.374868	NM_145496	ENSMUSG00000034371	Tkfc	BC021917|Dak	triokinase, FMN cyclase	protein-coding
mm_105074.1	chr11	100762932	100762936	-	1	NA	promoter-TSS (NM_010410)	promoter-TSS (NM_010410)	-3	NM_010410	15171	Mm.10096	NM_010410	ENSMUSG00000045471	Hcrt	PPOX	hypocretin	protein-coding
mm_150489.1	chr19	39007138	39007148	+	1	NA	exon (NM_028089, exon 1 of 9)	exon (NM_028089, exon 1 of 9)	124	NM_028089	72082	Mm.142581	NM_028089	ENSMUSG00000025002	Cyp2c55	2010318C06Rik	cytochrome P450, family 2, subfamily c, polypeptide 55	protein-coding
mm_137067.1	chr17	20661800	20661818	+	1	NA	Intergenic	Intergenic	-25699	NM_134191	171225	Mm.377184	NM_134191	ENSMUSG00000042848	Vmn1r226	V1re2	vomeronasal 1 receptor 226	protein-coding
mm_91377.1	chr10	30552154	30552154	-	1	NA	intron (NM_028604, intron 11 of 12)	intron (NM_028604, intron 11 of 12)	48595	NM_028604	73681	Mm.294503	NM_028604	ENSMUSG00000019792	Trmt11	2410075D05Rik|3110045I18Rik|AW213713	tRNA methyltransferase 11	protein-coding
mm_77425.1	chr8	121083917	121083934	-	1	NA	promoter-TSS (NM_010426)	promoter-TSS (NM_010426)	-461	NM_010426	15227	Mm.33897	NM_010426	ENSMUSG00000042812	Foxf1	AI450827|FREAC1|Foxf1a|Freac-1|HFH-8|Hfh8	forkhead box F1	protein-coding
mm_162922.1	chr10	121034155	121034159	+	1	NA	5' UTR (NM_011915, exon 1 of 10)	5' UTR (NM_011915, exon 1 of 10)	153	NM_011915	24117	Mm.32831	NM_011915	ENSMUSG00000020218	Wif1	AW107799|WIF-1	Wnt inhibitory factor 1	protein-coding
mm_83477.1	chr9	45828710	45828720	-	1	NA	promoter-TSS (NM_001081373)	promoter-TSS (NM_001081373)	-77	NM_001081373	214552	Mm.260103	NM_172531	ENSMUSG00000043987	Cep164	AI450905|BC027092|D030051D21|mKIAA1052	centrosomal protein 164	protein-coding
mm_73359.1	chr8	105566172	105566187	+	1	NA	promoter-TSS (NM_013477)	promoter-TSS (NM_013477)	-139	NM_013477	11972	Mm.17708	NM_013477	ENSMUSG00000013160	Atp6v0d1	AI267038|Ac39|Atp6d|P39|VATX|Vma6	ATPase, H+ transporting, lysosomal V0 subunit D1	protein-coding
mm_114151.1	chr13	55379170	55379179	+	1	NA	intron (NM_016758, intron 5 of 14)	intron (NM_016758, intron 5 of 14)	9442	NM_016758	51791	Mm.1426	NM_016758	ENSMUSG00000052087	Rgs14	RPIP1	regulator of G-protein signaling 14	protein-coding
mm_62220.1	chr7	98486895	98486901	+	1	NA	Intergenic	Intergenic	-7324	NM_001113379	434215	Mm.323057	NM_001113379	ENSMUSG00000090958	Lrrc32	AI426318|D11S833Eh|D7H11S833E|EG434215|Garp	leucine rich repeat containing 32	protein-coding
mm_37791.1	chr4	130519664	130519682	-	1	NA	Intergenic	B3A|SINE|B2	54363	NM_025998	67149	Mm.423029	NM_025998	ENSMUSG00000078532	Nkain1	2610200G18Rik|2810426C15Rik	Na+/K+ transporting ATPase interacting 1	protein-coding
mm_131688.1	chr16	20678638	20678648	+	1	NA	exon (NM_145941, exon 8 of 33)	exon (NM_145941, exon 8 of 33)	-5613	NR_028530	100217430		NR_028530		Snord66	MBII-142|snoRNA142	small nucleolar RNA, C/D box 66	snoRNA
mm_72799.1	chr8	87458428	87458447	+	1	NA	Intergenic	RMER19C|LTR|ERVK	14155	NM_019626	12404	Mm.4880	NM_019626	ENSMUSG00000031654	Cbln1	AI323299	cerebellin 1 precursor protein	protein-coding
mm_137053.1	chr17	17928230	17928239	+	1	NA	Intergenic	RMER12|LTR|ERVK	40410	NM_008039	14289	Mm.378918	NM_008039	ENSMUSG00000052270	Fpr2	E330010I07Rik|Fpr-rs2	formyl peptide receptor 2	protein-coding
mm_170501.1	chr19	24290202	24290206	-	1	NA	Intergenic	(CCA)n|Simple_repeat|Simple_repeat	-9618	NM_008044	14297	Mm.7319	NM_008044	ENSMUSG00000059363	Fxn	FA|FARR|Frda|X25	frataxin	protein-coding
mm_159978.1	chr6	113392623	113392623	+	1	NA	exon (NM_133923, exon 1 of 13)	exon (NM_133923, exon 1 of 13)	126	NM_133923	101100	Mm.388573	NM_133923	ENSMUSG00000030276	Ttll3	4833441J24Rik|AI450050	tubulin tyrosine ligase-like family, member 3	protein-coding
mm_148866.1	chr19	6418734	6418810	+	1	NA	promoter-TSS (NM_020253)	promoter-TSS (NM_020253)	34	NM_001205234	18190	Mm.329616	NM_020253	ENSMUSG00000033768	Nrxn2	6430591O13Rik|mKIAA0921	neurexin II	protein-coding
mm_328.1	chr1	24753617	24753621	+	1	NA	intron (NM_001310483, intron 14 of 15)	intron (NM_001310483, intron 14 of 15)	74701	NM_001310483	68421	Mm.336563	NM_026719	ENSMUSG00000073725	Lmbrd1	0910001K20Rik|AV347960	LMBR1 domain containing 1	protein-coding
mm_23411.1	chr3	58517489	58517501	+	1	NA	Intergenic	Intergenic	-8326	NM_001005509	229317	Mm.21617	NM_001005509	ENSMUSG00000027810	Eif2a	D030048D22|D3Ertd194e	eukaryotic translation initiation factor 2A	protein-coding
mm_42847.1	chr5	122182181	122182192	+	1	NA	Intergenic	Intergenic	23907	NM_013636	19047	Mm.280784	NM_013636	ENSMUSG00000004455	Ppp1cc	PP-1G|PP1|dis2m1	protein phosphatase 1, catalytic subunit, gamma isoform	protein-coding
mm_147874.1	chr18	64489043	64489082	-	1	NA	promoter-TSS (NM_007998)	promoter-TSS (NM_007998)	4	NM_007998	14151	Mm.1070	NM_007998	ENSMUSG00000024588	Fech	AI894116|Fcl|fch	ferrochelatase	protein-coding
mm_104447.1	chr11	95028743	95028770	-	1	NA	exon (NM_133667, exon 8 of 11)	exon (NM_133667, exon 8 of 11)	12615	NM_133667	18604	Mm.29768	NM_133667	ENSMUSG00000038967	Pdk2	-	pyruvate dehydrogenase kinase, isoenzyme 2	protein-coding
mm_160740.1	chr10	79973704	79973704	+	1	NA	exon (NM_130455, exon 3 of 9)	exon (NM_130455, exon 3 of 9)	2980	NM_130455	170483	Mm.391566	NM_130455	ENSMUSG00000035745	Grin3b	GluN3B|NR3B	glutamate receptor, ionotropic, NMDA3B	protein-coding
mm_68110.1	chr7	102062483	102062492	-	1	NA	intron (NM_029211, intron 1 of 8)	intron (NM_029211, intron 1 of 8)	2645	NM_029211	75212	Mm.101141	NM_029211	ENSMUSG00000070426	Rnf121	4930544L10Rik	ring finger protein 121	protein-coding
mm_20459.1	chr2	129365978	129366101	-	1	NA	exon (NM_008361, exon 6 of 7)	exon (NM_008361, exon 6 of 7)	-3863	NR_015474	329514	Mm.207315	NM_177848	ENSMUSG00000074805	Il1bos	9430083I22|Gm14047|OTTMUSG00000015529	interleukin 1 beta, opposite strand	ncRNA
mm_56513.1	chr6	99404056	99404060	-	1	NA	intron (NM_001347345, intron 2 of 19)	intron (NM_001347345, intron 2 of 19)	31287	NM_053202	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_9568.1	chr1	173979614	173979644	-	1	NA	intron (NM_008327, intron 1 of 6)	L1_Mur3|LINE|L1	3215	NM_008327	26388	Mm.218770	NM_008327	ENSMUSG00000026535	Ifi202b	Ifbip-1|Ifi202|Ifi202a|p202	interferon activated gene 202B	protein-coding
mm_162683.1	chr10	13966112	13966114	+	1	NA	promoter-TSS (NM_010437)	promoter-TSS (NM_010437)	-266	NM_010437	15273	Mm.42157	NM_010437	ENSMUSG00000015501	Hivep2	Gm20114|MIBP1|Schnurri-2|Shn-2	human immunodeficiency virus type I enhancer binding protein 2	protein-coding
mm_128566.1	chr15	56694526	56694554	-	1	NA	promoter-TSS (NM_008216)	promoter-TSS (NM_008216)	6	NM_008216	15117	Mm.5148	NM_008216	ENSMUSG00000022367	Has2	-	hyaluronan synthase 2	protein-coding
mm_135755.1	chr16	56017042	56017050	-	1	NA	3' UTR (NM_001024622, exon 5 of 5)	3' UTR (NM_001024622, exon 5 of 5)	12671	NM_001024622	76302	Mm.310642	NM_001024622	ENSMUSG00000071533	Pcnp	1110018D06Rik|AI647035	PEST proteolytic signal containing nuclear protein	protein-coding
mm_59586.1	chr7	28129805	28129810	+	1	NA	intron (NM_001164655, intron 1 of 19)	intron (NM_001164655, intron 1 of 19)	341	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_49057.1	chr6	5110653	5110664	+	1	NA	intron (NM_181595, intron 7 of 15)	intron (NM_181595, intron 7 of 15)	83288	NM_011134	18979	Mm.237657	NM_011134	ENSMUSG00000002588	Pon1	Pon	paraoxonase 1	protein-coding
mm_86078.1	chr9	114781386	114781408	-	1	NA	intron (NM_001252479, intron 1 of 3)	CpG	596	NM_133978	102545	Mm.35600	NM_133978	ENSMUSG00000032436	Cmtm7	AI481279|Cklfsf7|LNV	CKLF-like MARVEL transmembrane domain containing 7	protein-coding
mm_43438.1	chr5	136091228	136091264	+	1	NA	exon (NM_133914, exon 3 of 21)	exon (NM_133914, exon 3 of 21)	7330	NM_001039103	54153	Mm.290655	NM_133914	ENSMUSG00000004952	Rasa4	AA793972|AW112107|BB079060|CAPRI|GAPL	RAS p21 protein activator 4	protein-coding
mm_124512.1	chr14	121929376	121929388	-	1	NA	intron (NM_026861, intron 4 of 8)	intron (NM_026861, intron 4 of 8)	-13608	NM_182806	110168	Mm.37405	NM_182806	ENSMUSG00000050350	Gpr18	-	G protein-coupled receptor 18	protein-coding
mm_50978.1	chr6	62052084	62052087	+	1	NA	intron (NM_001164316, intron 10 of 10)	Lx2B2|LINE|L1	-871275	NR_040287	100504262	Mm.438066	NR_040287		A730020E08Rik	-	RIKEN cDNA A730020E08 gene	ncRNA
mm_154228.1	chr19	59943597	59943638	-	1	NA	promoter-TSS (NM_001164367)	promoter-TSS (NM_001164367)	37	NM_001164367	74998	Mm.24167	NM_001033172	ENSMUSG00000040022	Rab11fip2	4930470G04Rik|A830046J09Rik|AW558126|Nrip11	RAB11 family interacting protein 2 (class I)	protein-coding
mm_149185.1	chr19	9899724	9899738	+	1	NA	promoter-TSS (NM_016692)	promoter-TSS (NM_016692)	-198	NM_016692	16319	Mm.29755	NM_016692	ENSMUSG00000024660	Incenp	2700067E22Rik|AU019509|C130081E20|C77457	inner centromere protein	protein-coding
mm_49312.1	chr6	18170759	18170780	+	1	NA	promoter-TSS (NM_021050)	promoter-TSS (NM_021050)	82	NM_021050	12638	Mm.15621	NM_021050	ENSMUSG00000041301	Cftr	AW495489|Abcc7	cystic fibrosis transmembrane conductance regulator	protein-coding
mm_14757.1	chr2	144738411	144738430	+	1	NA	intron (NM_025314, intron 4 of 5)	intron (NM_025314, intron 4 of 5)	-85246	NM_025490	66328	Mm.45377	NM_025490	ENSMUSG00000027431	Scp2d1	1700010M22Rik	SCP2 sterol-binding domain containing 1	protein-coding
mm_82677.1	chr9	22132258	22132280	-	1	NA	promoter-TSS (NM_001102404)	promoter-TSS (NM_001102404)	-404	NM_001102404	11433	Mm.46354	NM_007388	ENSMUSG00000001348	Acp5	TRACP|TRAP	acid phosphatase 5, tartrate resistant	protein-coding
mm_60709.1	chr7	45241075	45241106	+	1	NA	5' UTR (NM_001324535, exon 1 of 13)	5' UTR (NM_001324535, exon 1 of 13)	337	NM_001324535	381884	Mm.490944	NM_001324535	ENSMUSG00000094152	Slc6a16	Gm1084	solute carrier family 6, member 16	protein-coding
mm_131090.1	chr16	4886209	4886219	+	1	NA	5' UTR (NM_029657, exon 1 of 17)	5' UTR (NM_029657, exon 1 of 17)	114	NM_001252437	17237	Mm.291326	NM_029657	ENSMUSG00000022517	Mgrn1	2610042J20Rik|mKIAA0544|md|nc	mahogunin, ring finger 1	protein-coding
mm_52686.1	chr6	118058186	118058196	+	1	NA	intron (NM_001316749, intron 1 of 12)	intron (NM_001316749, intron 1 of 12)	-8194	NM_027526	70727	Mm.87660	NM_027526	ENSMUSG00000030134	Rasgef1a	6330404M18Rik|AI835194	RasGEF domain family, member 1A	protein-coding
mm_55218.1	chr6	52226166	52226196	-	1	NA	exon (NM_001277238, exon 1 of 3)	exon (NM_001277238, exon 1 of 3)	1189	NM_010456	15405	Mm.4694	NM_010456	ENSMUSG00000038227	Hoxa9	D6a9|Hox-1.7	homeobox A9	protein-coding
mm_155104.1	chrX	48343759	48343776	+	1	NA	intron (NM_178782, intron 2 of 14)	CpG	2409	NM_178782	320376	Mm.210146	NM_178782	ENSMUSG00000036959	Bcorl1	6720425J07Rik|B930011H20Rik	BCL6 co-repressor-like 1	protein-coding
mm_18800.1	chr2	73892540	73892555	-	1	NA	promoter-TSS (NM_009715)	promoter-TSS (NM_009715)	92	NM_001284371	11909	Mm.209903	NM_009715	ENSMUSG00000027104	Atf2	Atf-2|CRE-BP|Creb2|D130078H02Rik|D18875|Tg(Gzma-Klra1)7Wum|mXBP	activating transcription factor 2	protein-coding
mm_82624.1	chr9	21809912	21809918	-	1	NA	promoter-TSS (NR_106051)	promoter-TSS (NR_106051)	85	NR_106051	102465657		NR_106051	ENSMUSG00000098473	Mir7083	Gm27888|mmu-mir-7083	microRNA 7083	ncRNA
mm_24781.1	chr3	95540189	95540190	+	1	NA	intron (NM_001267695, intron 3 of 7)	B2_Mm1t|SINE|B2	13403	NM_001267695	13040	Mm.3619	NM_021281	ENSMUSG00000038642	Ctss	Cats	cathepsin S	protein-coding
mm_56616.1	chr6	112659919	112659928	-	1	NA	intron (NM_021385, intron 9 of 11)	L2|LINE|L2	36747	NM_021385	58186	Mm.103812	NM_021385	ENSMUSG00000030254	Rad18	2810024C04Rik|Rad18sc	RAD18 E3 ubiquitin protein ligase	protein-coding
mm_55100.1	chr6	49829500	49829508	-	1	NA	TTS (NM_023456)	TTS (NM_023456)	6794	NM_023456	109648	Mm.154796	NM_023456	ENSMUSG00000029819	Npy	0710005A05Rik	neuropeptide Y	protein-coding
mm_75083.1	chr8	33916412	33916415	-	1	NA	intron (NM_001042674, intron 1 of 7)	intron (NM_001042674, intron 1 of 7)	13450	NM_019733	19663	Mm.323997	NM_019733	ENSMUSG00000031586	Rbpms	2010300K22Rik|2700019M19Rik|AU017537|RBP-MS|hermes	RNA binding protein gene with multiple splicing	protein-coding
mm_31091.1	chr4	41755211	41755267	+	1	NA	promoter-TSS (NM_016658)	promoter-TSS (NM_016658)	11	NM_016658	14430	Mm.439669	NM_016658	ENSMUSG00000036073	Galt	AW553376	galactose-1-phosphate uridyl transferase	protein-coding
mm_67638.1	chr7	84410028	84410048	-	1	NA	promoter-TSS (NM_007488)	promoter-TSS (NM_007488)	0	NM_007488	11864	Mm.38594	NM_007488	ENSMUSG00000015709	Arnt2	Hif-2b|bHLHe1|mKIAA0307	aryl hydrocarbon receptor nuclear translocator 2	protein-coding
mm_6644.1	chr1	79440104	79440108	-	1	NA	promoter-TSS (NM_009129)	promoter-TSS (NM_009129)	-16	NM_001310680	20254	Mm.5038	NM_009129	ENSMUSG00000050711	Scg2	Chgc|SgII	secretogranin II	protein-coding
mm_40181.1	chr5	36204017	36204027	+	1	NA	promoter-TSS (NM_175249)	promoter-TSS (NM_175249)	1	NM_175249	76943	Mm.44242	NM_175249	ENSMUSG00000043430	Psapl1	2310020A21Rik	prosaposin-like 1	protein-coding
mm_73928.1	chr8	119862240	119862294	+	1	NA	promoter-TSS (NM_146219)	promoter-TSS (NM_146219)	-38	NM_146219	234796	Mm.86446	NM_146219	ENSMUSG00000031828	Klhl36	-	kelch-like 36	protein-coding
mm_23321.1	chr3	53463695	53463709	+	1	NA	promoter-TSS (NM_172501)	promoter-TSS (NM_172501)	-115	NM_173382	212127	Mm.491292	NM_173382	ENSMUSG00000049504	Proser1	2810046L04Rik|9330161F11	proline and serine rich 1	protein-coding
mm_172858.1	chr9	40492090	40492098	+	1	NA	Intergenic	L1Md_T|LINE|L1	-36330	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_134284.1	chr16	14208287	14208305	-	1	NA	exon (NM_013607, exon 29 of 42)	exon (NM_013607, exon 29 of 42)	45021	NM_001114085	67203	Mm.24105	NM_023317	ENSMUSG00000022678	Nde1	2810027M15Rik|AU042936|AW822251|Nude|mNudE	nudE neurodevelopment protein 1	protein-coding
mm_23404.1	chr3	58414699	58414739	+	1	NA	promoter-TSS (NM_001347233)	promoter-TSS (NM_001347233)	-1	NM_001347233	72033	Mm.218409	NM_001081229	ENSMUSG00000027806	Tsc22d2	1810043J12Rik|5530402M19Rik	TSC22 domain family, member 2	protein-coding
mm_71322.1	chr8	44935993	44936007	+	1	NA	Intergenic	Intergenic	-14208	NM_001081286	14107	Mm.27365	NM_001081286	ENSMUSG00000070047	Fat1	2310038E12Rik|AU023433|Fath|mFat1	FAT atypical cadherin 1	protein-coding
mm_38694.1	chr4	145213814	145213845	-	1	NA	3' UTR (NM_011610, exon 10 of 10)	3' UTR (NM_011610, exon 10 of 10)	-18824	NM_001276465	230895	Mm.240310	NM_001033190	ENSMUSG00000020220	Vps13d	-	vacuolar protein sorting 13D	protein-coding
mm_1140.1	chr1	60704986	60705000	+	1	NA	Intergenic	Intergenic	-41395	NM_007642	12487	Mm.255003	NM_007642	ENSMUSG00000026012	Cd28	-	CD28 antigen	protein-coding
mm_110862.1	chr12	73508667	73508695	-	1	NA	Intergenic	Intergenic	37714	NM_178715	238257	Mm.251196	NM_178715	ENSMUSG00000034435	Tmem30b	9130011B11Rik	transmembrane protein 30B	protein-coding
mm_157157.1	chrX	9463804	9463814	-	1	NA	intron (NM_007807, intron 3 of 12)	intron (NM_007807, intron 3 of 12)	5515	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_21591.1	chr2	164237524	164237554	-	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	802	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_16294.1	chr2	174284611	174284625	+	1	NA	non-coding (NR_002846, exon 3 of 5)	non-coding (NR_002846, exon 3 of 5)	298	NM_022000	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_35170.1	chr4	14826391	14826447	-	1	NA	exon (NM_152812, exon 1 of 7)	exon (NM_152812, exon 1 of 7)	168	NM_152812	72201	Mm.387724	NM_152812	ENSMUSG00000040550	Otud6b	2600013N14Rik|AU015433	OTU domain containing 6B	protein-coding
mm_17821.1	chr2	33855167	33855171	-	1	NA	intron (NM_175184, intron 2 of 9)	PB1D10|SINE|Alu	32777	NM_175184	72543	Mm.254914	NM_175184	ENSMUSG00000038740	Mvb12b	2610200O14Rik|2610528K11Rik|AI414895|Fam125b	multivesicular body subunit 12B	protein-coding
mm_131194.1	chr16	7409782	7409794	+	1	NA	exon (NM_183188, exon 13 of 13)	exon (NM_183188, exon 13 of 13)	339953	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_71946.1	chr8	70376600	70376630	+	1	NA	intron (NM_016685, intron 8 of 18)	CpG-14088	3067	NM_016685	12845	Mm.45071	NM_016685	ENSMUSG00000031849	Comp	TSP5	cartilage oligomeric matrix protein	protein-coding
mm_118590.1	chr14	20641062	20641089	+	1	NA	Intergenic	CpG	15465	NM_021508	59011	Mm.439911	NM_021508	ENSMUSG00000068697	Myoz1	2310001N11Rik|AV090278|FATZ|Myoz	myozenin 1	protein-coding
mm_89850.1	chr10	107271698	107271720	+	1	NA	promoter-TSS (NM_001039354)	promoter-TSS (NM_001039354)	-122	NM_001039354	108030	Mm.268025	NM_001033223	ENSMUSG00000019906	Lin7a	AI848705|LIN-7A|MALS-1|TIP-33|Veli|Veli1	lin-7 homolog A (C. elegans)	protein-coding
mm_73578.1	chr8	109778864	109778921	+	1	NA	5' UTR (NM_009677, exon 1 of 24)	5' UTR (NM_009677, exon 1 of 24)	309	NM_001301211	11765	Mm.37210	NM_009677	ENSMUSG00000031731	Ap1g1	AA409002|AU041323|AW551707|Adtg|D8Ertd374e	adaptor protein complex AP-1, gamma 1 subunit	protein-coding
mm_126374.1	chr15	80165674	80165684	+	1	NA	Intergenic	Intergenic	-8042	NM_010795	17309	Mm.299693	NM_010795	ENSMUSG00000042428	Mgat3	1110038J12Rik|AI848272|GnT-III	mannoside acetylglucosaminyltransferase 3	protein-coding
mm_68945.1	chr7	126503639	126503643	-	1	NA	promoter-TSS (NM_183020)	promoter-TSS (NM_183020)	-339	NM_183020	233871	Mm.231450	NM_183020	ENSMUSG00000032637	Atxn2l	A2D|A2LG|A2RP|A2lp|Atxnl2	ataxin 2-like	protein-coding
mm_21165.1	chr2	154613381	154613416	-	1	NA	promoter-TSS (NM_199304)	promoter-TSS (NM_199304)	30	NM_199304	228807	Mm.103555	NM_199304	ENSMUSG00000059842	Zfp341	Znf341	zinc finger protein 341	protein-coding
mm_67588.1	chr7	83642255	83642258	-	1	NA	TTS (NM_010551)	TTS (NM_010551)	10239	NM_023377	170460	Mm.357953	NM_023377	ENSMUSG00000046027	Stard5	2310058G22Rik|AI607880|D7Ertd152e	StAR-related lipid transfer (START) domain containing 5	protein-coding
mm_20948.1	chr2	151645193	151645195	-	1	NA	TTS (NM_001276400)	TTS (NM_001276400)	-12601	NM_001291076	241727	Mm.39312	NM_198214	ENSMUSG00000027457	Snph	6430515A01|AW045671|AW556958|AW743098|mKIAA0374	syntaphilin	protein-coding
mm_83910.1	chr9	56324399	56324403	-	1	NA	intron (NM_172924, intron 2 of 6)	intron (NM_172924, intron 2 of 6)	93649	NM_172924	244895	Mm.490331	NM_172924	ENSMUSG00000074305	Peak1	1110049L02Rik|9530046P14|AA690169|BE132841|C230081A13Rik|SGK269|mKIAA2002	pseudopodium-enriched atypical kinase 1	protein-coding
mm_6067.1	chr1	60887095	60887109	-	1	NA	Intergenic	Intergenic	-21923	NM_009843	12477	Mm.390	NM_009843	ENSMUSG00000026011	Ctla4	Cd152|Ctla-4|Ly-56	cytotoxic T-lymphocyte-associated protein 4	protein-coding
mm_1130.1	chr1	60409545	60409600	+	1	NA	promoter-TSS (NM_001198570)	promoter-TSS (NM_001198570)	-47	NM_001198571	329165	Mm.212066	NM_198127	ENSMUSG00000026782	Abi2	8430425M24Rik|AI839867|C130078H13	abl-interactor 2	protein-coding
mm_75799.1	chr8	70139056	70139062	-	1	NA	promoter-TSS (NM_001145552)	promoter-TSS (NM_001145552)	138	NM_011266	19727	Mm.161167	NM_011266	ENSMUSG00000036120	Rfxank	Tvl1	regulatory factor X-associated ankyrin-containing protein	protein-coding
mm_144303.1	chr18	12490814	12490820	+	1	NA	intron (NM_010680, intron 32 of 74)	intron (NM_010680, intron 32 of 74)	-13382	NM_001347461	16774	Mm.42012	NM_010680	ENSMUSG00000024421	Lama3	Lama3B|[a]3B	laminin, alpha 3	protein-coding
mm_145673.1	chr18	61555309	61555345	+	1	NA	promoter-TSS (NM_146087)	promoter-TSS (NM_146087)	-255	NM_146087	93687	Mm.26908	NM_146087	ENSMUSG00000024576	Csnk1a1	2610208K14Rik|4632404G05Rik|5430427P18Rik|CK1a|Csnk1a	casein kinase 1, alpha 1	protein-coding
mm_95598.1	chr11	53350784	53350800	+	1	NA	promoter-TSS (NM_033565)	promoter-TSS (NM_033565)	25	NM_033565	93736	Mm.395281	NM_033565	ENSMUSG00000049470	Aff4	AF5Q31|Alf4|Laf4l|MCEF	AF4/FMR2 family, member 4	protein-coding
mm_123444.1	chr14	64949839	64949886	-	1	NA	promoter-TSS (NM_001253731)	promoter-TSS (NM_001253731)	-5	NM_001347626	219150	Mm.344074	NM_177338	ENSMUSG00000021972	Hmbox1	AI451877|AI604847|F830020C16Rik	homeobox containing 1	protein-coding
mm_25158.1	chr3	103030133	103030177	+	1	NA	intron (NM_001310693, intron 2 of 17)	intron (NM_001310693, intron 2 of 17)	9609	NM_144901	229663	Mm.277713	NM_144901	ENSMUSG00000068823	Csde1	AA960392|BC016898|D3Jfr1|mKIAA0885|unr	cold shock domain containing E1, RNA binding	protein-coding
mm_99592.1	chr11	104310388	104310417	+	1	NA	exon (NM_010838, exon 6 of 10)	exon (NM_010838, exon 6 of 10)	78966	NM_001285454	17762	Mm.1287	NM_010838	ENSMUSG00000018411	Mapt	AI413597|AW045860|Mtapt|Tau	microtubule-associated protein tau	protein-coding
mm_117229.1	chr13	64248496	64248538	-	1	NA	promoter-TSS (NR_045798)	promoter-TSS (NR_045798)	21	NM_001122989	218294	Mm.25335	NM_172587	ENSMUSG00000033102	Cdc14b	2810432N10Rik|A530086E13Rik|AA472821|CDC14B3|Cdc14B1	CDC14 cell division cycle 14B	protein-coding
mm_9103.1	chr1	170110316	170110332	-	1	NA	Intergenic	Intergenic	-21380	NM_022563	18214	Mm.229249	NM_022563	ENSMUSG00000026674	Ddr2	AW495251|Ntrkr3|tyro10	discoidin domain receptor family, member 2	protein-coding
mm_26183.1	chr3	138341969	138341981	+	1	NA	Intergenic	RMER15|LTR|ERVL	28689	NM_026945	69117	Mm.46265	NM_026945	ENSMUSG00000053054	Adh6a	1810009C16Rik|Adh5a	alcohol dehydrogenase 6A (class V)	protein-coding
mm_41780.1	chr5	103715950	103715958	+	1	NA	Intergenic	Intergenic	-38208	NM_133919	17355	Mm.6949	NM_133919	ENSMUSG00000029313	Aff1	9630032B01Rik|AW319193|Af4|Mllt2h|Rob	AF4/FMR2 family, member 1	protein-coding
mm_95963.1	chr11	58884090	58884098	+	1	NA	3' UTR (NM_172403, exon 5 of 5)	3' UTR (NM_172403, exon 5 of 5)	16854	NM_172403	69944	Mm.32118	NM_172403	ENSMUSG00000020491	2810021J22Rik	AI449137	RIKEN cDNA 2810021J22 gene	protein-coding
mm_125458.1	chr15	52241405	52241408	+	1	NA	Intergenic	Intergenic	-54147	NM_172816	239436	Mm.208831	NM_172816	ENSMUSG00000022315	Slc30a8	C820002P14Rik|ZnT-8|ZnT8	solute carrier family 30 (zinc transporter), member 8	protein-coding
mm_153612.1	chr19	43980853	43980863	-	1	NA	exon (NM_030703, exon 2 of 9)	exon (NM_030703, exon 2 of 9)	5662	NM_030703	93721	Mm.206774	NM_030703	ENSMUSG00000025196	Cpn1	0610011F20Rik|CPN	carboxypeptidase N, polypeptide 1	protein-coding
mm_19514.1	chr2	93984812	93984845	-	1	NA	intron (NM_026944, intron 8 of 9)	intron (NM_026944, intron 8 of 9)	4794	NR_045827	70852	Mm.437014	NR_045827	ENSMUSG00000027196	Alkbh3os1	4921507L20Rik	alkB homolog 3, opposite strand 1	ncRNA
mm_36875.1	chr4	107177757	107177772	-	1	NA	promoter-TSS (NM_029565)	promoter-TSS (NM_029565)	602	NM_025617	66526	Mm.246956	NM_025617	ENSMUSG00000028619	Tceanc2	2210010B22Rik|2210012G02Rik|6330404A07Rik|AU015593|Tdeanc2	transcription elongation factor A (SII) N-terminal and central domain containing 2	protein-coding
mm_93174.1	chr10	93380117	93380134	-	1	NA	Intergenic	Intergenic	43893	NR_038014	432488	Mm.32833	NR_038014		Gm17745	-	predicted gene, 17745	ncRNA
mm_51238.1	chr6	71543872	71543898	+	1	NA	promoter-TSS (NM_025783)	promoter-TSS (NM_025783)	31	NM_025783	66700	Mm.181278	NM_025783	ENSMUSG00000053119	Chmp3	25.1|4921505F14Rik|9130011K15Rik|CGI-49|D6Ertd286e|NEDF|Vps24	charged multivesicular body protein 3	protein-coding
mm_86253.1	chr9	121494850	121494865	-	1	NA	intron (NM_031161, intron 1 of 2)	intron (NM_031161, intron 1 of 2)	837	NM_001284508	12424	Mm.2619	NM_031161	ENSMUSG00000032532	Cck	-	cholecystokinin	protein-coding
mm_43613.1	chr5	137989949	137989957	+	1	NA	3' UTR (NM_013478, exon 4 of 4)	3' UTR (NM_013478, exon 4 of 4)	8432	NM_013478	12007	Mm.30061	NM_013478	ENSMUSG00000037053	Azgp1	Zag	alpha-2-glycoprotein 1, zinc	protein-coding
mm_11850.1	chr2	45246811	45246831	+	1	NA	Intergenic	Intergenic	-133542	NM_015753	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_32626.1	chr4	114909253	114909269	+	1	NA	promoter-TSS (NM_008593)	promoter-TSS (NM_008593)	-28	NR_030721	100040736	Mm.231287	NR_030721	ENSMUSG00000085399	Foxd2os	9130206I24Rik	forkhead box D2, opposite strand	ncRNA
mm_29639.1	chr3	121815161	121815209	-	1	NA	promoter-TSS (NM_008991)	promoter-TSS (NM_008991)	30	NM_008991	19299	Mm.399042	NM_008991	ENSMUSG00000028127	Abcd3	AI313901|AU018866|AW146054|PMP68|PMP70|Pxmp1	ATP-binding cassette, sub-family D (ALD), member 3	protein-coding
mm_91833.1	chr10	56982180	56982203	-	1	NA	Intergenic	Intergenic	504162	NR_045353	74928	Mm.416643	NR_045353	ENSMUSG00000097370	4930467K11Rik	-	RIKEN cDNA 4930467K11 gene	ncRNA
mm_49713.1	chr6	34423051	34423065	+	1	NA	TTS (NM_009731)	TTS (NM_009731)	10696	NM_009731	11997	Mm.482073	NM_009731	ENSMUSG00000052131	Akr1b7	AR|Avdp|MVDP	aldo-keto reductase family 1, member B7	protein-coding
mm_47955.1	chr5	135545109	135545128	-	1	NA	promoter-TSS (NM_146001)	promoter-TSS (NM_146001)	4	NM_146001	215114	Mm.280805	NM_146001	ENSMUSG00000039959	Hip1	2610109B09Rik|A930014B11Rik|E130315I21Rik|mKIAA4113	huntingtin interacting protein 1	protein-coding
mm_76287.1	chr8	84198404	84198423	-	1	NA	Intergenic	Intergenic	-10105	NR_029740	387216		NR_029740	ENSMUSG00000065611	Mir23a	Mirn23a|mir-23a|mmu-mir-23a	microRNA 23a	ncRNA
mm_128367.1	chr15	42472715	42472722	-	1	NA	intron (NM_009640, intron 5 of 8)	Lx7|LINE|L1	204259	NM_001286062	11600	Mm.309336	NM_009640	ENSMUSG00000022309	Angpt1	1110046O21Rik|Ang-1|Ang1	angiopoietin 1	protein-coding
mm_51674.1	chr6	86438361	86438405	+	1	NA	promoter-TSS (NM_001243742)	promoter-TSS (NM_001243742)	-15	NM_146170	232196	Mm.404040	NM_146170	ENSMUSG00000046679	C87436	-	expressed sequence C87436	protein-coding
mm_24762.1	chr3	95499224	95499229	+	1	NA	promoter-TSS (NM_007802)	promoter-TSS (NM_007802)	16	NM_007802	13038	Mm.272085	NM_007802	ENSMUSG00000028111	Ctsk	AI323530|MMS10-Q|Ms10q|catK	cathepsin K	protein-coding
mm_138466.1	chr17	35172126	35172161	+	1	NA	exon (NM_019467, exon 5 of 8)	exon (NM_019467, exon 5 of 8)	3858	NM_019467	11629	Mm.10747	NM_019467	ENSMUSG00000024397	Aif1	AI607846|AIF-1|D17H6S50E|G1|Iba1	allograft inflammatory factor 1	protein-coding
mm_98494.1	chr11	94951627	94951664	+	1	NA	3' UTR (NM_007742, exon 51 of 51)	3' UTR (NM_007742, exon 51 of 51)	15421	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_157463.1	chrX	44790180	44790210	-	1	NA	promoter-TSS (NM_178739)	promoter-TSS (NM_178739)	2	NM_178739	245404	Mm.55685	NM_178739	ENSMUSG00000045284	Dcaf12l1	9330180J20|A230038L21Rik|Decaf12l1|Wdr40b	DDB1 and CUL4 associated factor 12-like 1	protein-coding
mm_171615.1	chr4	150315486	150315495	-	1	NA	intron (NM_001085492, intron 1 of 22)	intron (NM_001085492, intron 1 of 22)	33574	NM_001085492	68703	Mm.291274	NM_001085492	ENSMUSG00000039852	Rere	1110033A15Rik|AI414665|ARG|ARP|ATN1L|AW742570|Atr2|DNB1|eye<m03Jus>|eyes3|mKIAA0458	arginine glutamic acid dipeptide (RE) repeats	protein-coding
mm_76138.1	chr8	81043409	81043423	-	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	-28510	NM_027554	74841	Mm.246018	NM_027554	ENSMUSG00000038250	Usp38	4631402N15Rik|4833420O05Rik|AA536967|AU044701|AW544820|mKIAA1891	ubiquitin specific peptidase 38	protein-coding
mm_34311.1	chr4	141817861	141817899	+	1	NA	exon (NM_007919, exon 7 of 8)	exon (NM_007919, exon 7 of 8)	8125	NM_007919	13706	Mm.45316	NM_007919	ENSMUSG00000058579	Cela2a	Ela-2|Ela2|Ela2a	chymotrypsin-like elastase family, member 2A	protein-coding
mm_135060.1	chr16	34040285	34040296	-	1	NA	intron (NM_177357, intron 37 of 59)	intron (NM_177357, intron 37 of 59)	-73287	NM_009471	22247	Mm.13145	NM_009471	ENSMUSG00000022814	Umps	1700095D23Rik|AA408257|AL033308|BB164745	uridine monophosphate synthetase	protein-coding
mm_79756.1	chr9	62373636	62373648	+	1	NA	exon (NM_009672, exon 4 of 7)	exon (NM_009672, exon 4 of 7)	32299	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	protein-coding
mm_98645.1	chr11	96251101	96251111	+	1	NA	promoter-TSS (NR_037977)	promoter-TSS (NR_037977)	-554	NR_037977	193022	Mm.169508	NR_037977		Gm53	-	predicted gene 53	ncRNA
mm_44952.1	chr5	36611741	36611746	-	1	NA	intron (NM_001081232, intron 6 of 8)	intron (NM_001081232, intron 6 of 8)	-25517	NM_001113362	100855	Mm.486203	NM_133910	ENSMUSG00000029192	Tbc1d14	2810413P16Rik|AU043625|C86258|D5Ertd110e|mKIAA1322	TBC1 domain family, member 14	protein-coding
mm_7058.1	chr1	87219634	87219656	-	1	NA	exon (NM_001039169, exon 2 of 7)	exon (NM_001039169, exon 2 of 7)	5706	NM_001039169	26987	Mm.227183	NM_023314	ENSMUSG00000026254	Eif4e2	2700069E09Rik|AI036339|AV129531|D0H0S6743E|Eif4el3	eukaryotic translation initiation factor 4E member 2	protein-coding
mm_31028.1	chr4	40875967	40875981	+	1	NA	Intergenic	Intergenic	-21437	NM_022305	14595	Mm.15622	NM_022305	ENSMUSG00000028413	B4galt1	B-1,4-GalT|B-1,4-GalT1|GalT|Ggtb|Ggtb2|b4Gal-T1|beta-1,4-GalT|beta-1,4-GalT1|beta4Gal-T1	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1	protein-coding
mm_61834.1	chr7	88280970	88280974	+	1	NA	intron (NM_001311790, intron 1 of 3)	Lx2|LINE|L1	2887	NM_001311790	13032	Mm.89295	NM_009982	ENSMUSG00000030560	Ctsc	AI047818|CatC|DPP1|DPPI	cathepsin C	protein-coding
mm_30639.1	chr4	8811422	8811440	+	1	NA	intron (NM_001277149, intron 6 of 37)	intron (NM_001277149, intron 6 of 37)	121025	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_90409.1	chr10	127420354	127420372	+	1	NA	promoter-TSS (NM_001168293)	promoter-TSS (NM_001168293)	-504	NM_027900	71750	Mm.29342	NM_027900	ENSMUSG00000025404	R3hdm2	1300003K24Rik|AU041262|mKIAA1002	R3H domain containing 2	protein-coding
mm_155040.1	chrX	42149317	42149327	+	1	NA	promoter-TSS (NM_001077712)	promoter-TSS (NM_001077712)	-90	NM_001077712	20843	Mm.290422	NM_021465	ENSMUSG00000025862	Stag2	9230105L23Rik|B230112I07Rik|SA-2|SAP2	stromal antigen 2	protein-coding
mm_139358.1	chr17	50528926	50528936	+	1	NA	intron (NM_013880, intron 1 of 5)	ID4|SINE|ID	19384	NM_013880	224860	Mm.217362	NM_013880	ENSMUSG00000038910	Plcl2	PLC-L2|PRIP-2|Plce2|mKIAA1092	phospholipase C-like 2	protein-coding
mm_8983.1	chr1	165678919	165678940	-	1	NA	intron (NM_178593, intron 1 of 6)	intron (NM_178593, intron 1 of 6)	29165	NM_178593	226594	Mm.265552	NM_178593	ENSMUSG00000040723	Rcsd1	A430105K13Rik|BC025872|CapZIP	RCSD domain containing 1	protein-coding
mm_65707.1	chr7	28378068	28378085	-	1	NA	exon (NM_011756, exon 2 of 2)	exon (NM_011756, exon 2 of 2)	1152	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_57001.1	chr6	121027436	121027442	-	1	NA	intron (NR_138097, intron 11 of 18)	intron (NR_138097, intron 11 of 18)	-37025	NR_138098	100043793	Mm.448053	NR_138098		Gm4651	-	predicted gene 4651	ncRNA
mm_8883.1	chr1	162866484	162866501	-	1	NA	5' UTR (NM_010231, exon 1 of 9)	5' UTR (NM_010231, exon 1 of 9)	118	NM_010231	14261	Mm.976	NM_010231	ENSMUSG00000040181	Fmo1	-	flavin containing monooxygenase 1	protein-coding
mm_131298.1	chr16	11405677	11405713	+	1	NA	promoter-TSS (NM_001290148)	promoter-TSS (NM_001290148)	47	NM_001290148	74478	Mm.325831	NM_028964	ENSMUSG00000071669	Snx29	4933437K13Rik|ENSMUSG00000079738|Gm11170|Gm1737|Gm930|Rundc2a	sorting nexin 29	protein-coding
mm_131902.1	chr16	23268417	23268432	+	1	NA	intron (NM_001252505, intron 2 of 7)	intron (NM_001252505, intron 2 of 7)	-22046	NM_001252506	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_72893.1	chr8	90828306	90828336	+	1	NA	promoter-TSS (NM_177224)	promoter-TSS (NM_177224)	-514	NM_177224	109151	Mm.100615	NM_177224	ENSMUSG00000056608	Chd9	1810014J18Rik|9030205D12Rik|A330063D19Rik|AD013|PRIC320|mKIAA0308	chromodomain helicase DNA binding protein 9	protein-coding
mm_12552.1	chr2	72406646	72406650	+	1	NA	3' UTR (NM_001164791, exon 12 of 12)	3' UTR (NM_001164791, exon 12 of 12)	-69571	NM_025866	66953	Mm.270676	NM_025866	ENSMUSG00000055612	Cdca7	2310021G01Rik|AU044109|JPO1	cell division cycle associated 7	protein-coding
mm_114201.1	chr13	55957716	55957725	+	1	NA	Intergenic	Intergenic	-126295	NM_011097	18740	Mm.135195	NM_011097	ENSMUSG00000021506	Pitx1	Bft|P-OTX|Potx|Ptx1	paired-like homeodomain transcription factor 1	protein-coding
mm_168784.1	chr12	18771230	18771231	-	1	NA	Intergenic	B1_Mm|SINE|Alu	256720	NM_001201330	236366	Mm.352227	NM_001033157	ENSMUSG00000073197	5730507C01Rik	-	RIKEN cDNA 5730507C01 gene	protein-coding
mm_85505.1	chr9	106223756	106223766	-	1	NA	exon (NM_031178, exon 2 of 2)	exon (NM_031178, exon 2 of 2)	1163	NM_031178	81897	Mm.44889	NM_031178	ENSMUSG00000045322	Tlr9	-	toll-like receptor 9	protein-coding
mm_1989.1	chr1	87125689	87125696	+	1	NA	exon (NM_007432, exon 4 of 11)	exon (NM_007432, exon 4 of 11)	684	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_91824.1	chr10	56132609	56132612	-	1	NA	intron (NM_001033385, intron 20 of 32)	Lx8|LINE|L1	25693	NM_001163833	73390	Mm.181475	NM_133751	ENSMUSG00000047669	Msl3l2	1700060H10Rik	male-specific lethal 3-like 2 (Drosophila)	protein-coding
mm_114561.1	chr13	74406388	74406396	+	1	NA	promoter-TSS (NR_035409)	promoter-TSS (NR_035409)	-673	NR_035409	100124641		NR_035409	ENSMUSG00000076033	Mir692-3	Mir692-2b|Mirn692-2b|mmu-mir-692-3	microRNA 692-3	ncRNA
mm_121677.1	chr14	12822888	12822907	-	1	NA	5' UTR (NM_001042617, exon 1 of 31)	5' UTR (NM_001042617, exon 1 of 31)	182	NM_001042617	27062	Mm.260881	NM_012061	ENSMUSG00000054423	Cadps	AU067781|CAPS|CAPS1|mKIAA1121	Ca2+-dependent secretion activator	protein-coding
mm_145887.1	chr18	65581705	65581761	+	1	NA	intron (NM_207255, intron 1 of 5)	intron (NM_207255, intron 1 of 5)	1503	NM_207255	328977	Mm.286232	NM_207255	ENSMUSG00000042439	Zfp532	C530030I18Rik|Znf532|mKIAA1629	zinc finger protein 532	protein-coding
mm_129510.1	chr15	79028890	79028915	-	1	NA	exon (NM_008197, exon 1 of 1)	exon (NM_008197, exon 1 of 1)	690	NM_008197	14958	Mm.24350	NM_008197	ENSMUSG00000096210	H1f0	D130017D06Rik|H1(0)|H1fv	H1 histone family, member 0	protein-coding
mm_141408.1	chr17	29393669	29393675	-	1	NA	Intergenic	Intergenic	32758	NM_001159538	26382	Mm.279187	NM_013710	ENSMUSG00000024013	Fgd2	Tcd-2|Tcd2|ZFYVE4|tcs-2|tcs2	FYVE, RhoGEF and PH domain containing 2	protein-coding
mm_124823.1	chr15	9072922	9072964	+	1	NA	intron (NM_001040395, intron 1 of 12)	intron (NM_001040395, intron 1 of 12)	1683	NM_001040395	68646	Mm.244226	NM_001040395	ENSMUSG00000022253	Nadk2	MNADK|Nadkd1	NAD kinase 2, mitochondrial	protein-coding
mm_143191.1	chr17	59640774	59640775	-	1	NA	Intergenic	L1_Mur2|LINE|L1	-627452	NM_026497	67993	Mm.36507	NM_026497	ENSMUSG00000024228	Nudt12	0610016O18Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 12	protein-coding
mm_9926.1	chr1	189755174	189755180	-	1	NA	intron (NM_008976, intron 1 of 18)	intron (NM_008976, intron 1 of 18)	26909	NM_008976	19250	Mm.4498	NM_008976	ENSMUSG00000026604	Ptpn14	C130080N23Rik|OTTMUSG00000022087|PTP36	protein tyrosine phosphatase, non-receptor type 14	protein-coding
mm_92578.1	chr10	79984228	79984319	-	1	NA	promoter-TSS (NM_001003949)	promoter-TSS (NM_001003949)	57	NM_001003949	216157	Mm.29442	NM_001003949	ENSMUSG00000013858	Tmem259	AC087114.7gm2|ORF61|R32184_3|mFLJ00277	transmembrane protein 259	protein-coding
mm_164749.1	chr17	74950350	74950356	+	1	NA	Intergenic	RMER1A|Other|Other	-55176	NM_019919	268977	Mm.269747	NM_019919	ENSMUSG00000001870	Ltbp1	9430031G15Rik|9830146M04|Ltbp-1|Ltbp1L|TGF-beta1-BP-1|Tgfb|b2b1000Clo	latent transforming growth factor beta binding protein 1	protein-coding
mm_91121.1	chr10	19577563	19577589	-	1	NA	Intergenic	RLTR40|LTR|ERVK	-14373	NM_010511	15979	Mm.549	NM_010511	ENSMUSG00000020009	Ifngr1	CD119|IFN-gammaR|Ifgr|Ifngr|Nktar	interferon gamma receptor 1	protein-coding
mm_23849.1	chr3	83008451	83008485	+	1	NA	exon (NM_133862, exon 3 of 10)	exon (NM_133862, exon 3 of 10)	744	NM_001317105	99571	Mm.16422	NM_133862	ENSMUSG00000033860	Fgg	3010002H13Rik|AI256424	fibrinogen gamma chain	protein-coding
mm_120111.1	chr14	59478836	59478852	+	1	NA	intron (NM_026908, intron 3 of 10)	intron (NM_026908, intron 3 of 10)	37863	NM_026908	69008	Mm.179091	NM_026908	ENSMUSG00000021981	Cab39l	1500031K13Rik|2810425O13Rik|4930520C08Rik|AA589432|MO2L	calcium binding protein 39-like	protein-coding
mm_54163.1	chr6	23098104	23098116	-	1	NA	intron (NM_013930, intron 11 of 23)	intron (NM_013930, intron 11 of 23)	34876	NM_013930	30956	Mm.18651	NM_013930	ENSMUSG00000029695	Aass	LKR|LKR/SDH|LOR|LOR/SDH|Lorsdh|SDH	aminoadipate-semialdehyde synthase	protein-coding
mm_158345.1	chrX	134276889	134276968	-	1	NA	promoter-TSS (NM_001167995)	promoter-TSS (NM_001167995)	56	NM_172540	215201	Mm.289368	NM_172540	ENSMUSG00000067369	Trmt2b	4732479N06Rik	TRM2 tRNA methyltransferase 2B	protein-coding
mm_113674.1	chr13	42745697	42745698	+	1	NA	intron (NM_001005740, intron 1 of 12)	intron (NM_001005740, intron 1 of 12)	36116	NM_001005740	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding
mm_26935.1	chr3	20263699	20263703	-	1	NA	exon (NM_029706, exon 7 of 11)	exon (NM_029706, exon 7 of 11)	12032	NM_029706	76703	Mm.34692	NM_029706	ENSMUSG00000011463	Cpb1	0910001A18Rik|1810063F02Rik|2210008M23Rik|AI504870	carboxypeptidase B1 (tissue)	protein-coding
mm_100257.1	chr11	117332195	117332210	+	1	NA	promoter-TSS (NM_001113488)	promoter-TSS (NM_001113488)	-111	NM_001113488	53860	Mm.38450	NM_017380	ENSMUSG00000059248	Sept9	MSF1|Msf|PNUTL4|Sint1	septin 9	protein-coding
mm_130437.1	chr15	98257410	98257432	-	1	NA	promoter-TSS (NM_027304)	promoter-TSS (NM_027304)	-114	NM_027304	70069	Mm.107718	NM_027304	ENSMUSG00000048077	H1fnt	1700026P10Rik|H1.7|H1t2|Hanp1|mH1t2	H1 histone family, member N, testis-specific	protein-coding
mm_35070.1	chr4	6776568	6776571	-	1	NA	intron (NM_145711, intron 3 of 8)	B1F|SINE|Alu	214154	NM_145711	252838	Mm.435828	NM_145711	ENSMUSG00000041272	Tox	1700007F02Rik	thymocyte selection-associated high mobility group box	protein-coding
mm_138967.1	chr17	44777128	44777198	+	1	NA	promoter-TSS (NM_178652)	promoter-TSS (NM_178652)	-8	NM_178652	109115	Mm.431327	NM_178652	ENSMUSG00000038954	Supt3	2310066G22Rik|AI315192|SPT3|SPT3L|Supt3h	suppressor of Ty 3	protein-coding
mm_88416.1	chr10	77035830	77035832	+	1	NA	intron (NM_031196, intron 1 of 5)	intron (NM_031196, intron 1 of 5)	2619	NM_031196	20509	Mm.265060	NM_031196	ENSMUSG00000001436	Slc19a1	AI323572|RFC|RFC-1|RFC1	solute carrier family 19 (folate transporter), member 1	protein-coding
mm_135259.1	chr16	37843530	37843550	-	1	NA	Intergenic	MLTR11B|LTR|ERVK	-24860	NM_177093	320184	Mm.390882	NM_177093	ENSMUSG00000034158	Lrrc58	1810012N18Rik|C330018J07Rik	leucine rich repeat containing 58	protein-coding
mm_38981.1	chr4	150944793	150944808	-	1	NA	exon (NM_001077508, exon 7 of 7)	exon (NM_001077508, exon 7 of 7)	16801	NM_001077509	21942	Mm.244187	NM_011612	ENSMUSG00000028965	Tnfrsf9	4-1BB|A930040I11Rik|AA408498|AI325004|CDw137|Cd137|ILA|Ly63	tumor necrosis factor receptor superfamily, member 9	protein-coding
mm_151241.1	chr19	53852915	53852923	+	1	NA	intron (NM_001170847, intron 11 of 13)	intron (NM_001170847, intron 11 of 13)	-39312	NM_011050	18569	Mm.1605	NM_011050	ENSMUSG00000024975	Pdcd4	D19Ucla1|Ma3|Tis	programmed cell death 4	protein-coding
mm_4427.1	chr1	172505794	172505806	+	1	NA	exon (NM_178598, exon 3 of 5)	exon (NM_178598, exon 3 of 5)	5554	NM_178598	21346	Mm.271711	NM_178598	ENSMUSG00000026547	Tagln2	2700094C18Rik|SM22beta|Sm22B|Sm22a	transgelin 2	protein-coding
mm_112253.1	chr12	113736642	113736659	-	1	NA	Intergenic	Intergenic	192742	NM_174885	238406	Mm.188683	NM_174885	ENSMUSG00000043945	Adam6a	Adam6|tMDCIV	a disintegrin and metallopeptidase domain 6A	protein-coding
mm_84658.1	chr9	71719350	71719359	-	1	NA	intron (NM_001304362, intron 4 of 18)	B4A|SINE|B4	52248	NM_026599	68178	Mm.99961	NM_026599	ENSMUSG00000032232	Cgnl1	4933421H10Rik|9930020M10Rik|AI503810|Jacop	cingulin-like 1	protein-coding
mm_133946.1	chr16	3959457	3959472	-	1	NA	exon (NM_001081280, exon 5 of 18)	exon (NM_001081280, exon 5 of 18)	17168	NM_175547	268857	Mm.215994	NM_175547	ENSMUSG00000049871	Nlrc3	CLR16.2|D230007K08Rik|mFLJ00348	NLR family, CARD domain containing 3	protein-coding
mm_117444.1	chr13	74768917	74768924	-	1	NA	intron (NM_001301153, intron 3 of 31)	intron (NM_001301153, intron 3 of 31)	1816	NM_001301156	12380	Mm.29163	NM_009817	ENSMUSG00000021585	Cast	-	calpastatin	protein-coding
mm_104762.1	chr11	98477384	98477395	-	1	NA	intron (NM_011771, intron 6 of 7)	intron (NM_011771, intron 6 of 7)	30555	NM_010346	14786	Mm.276702	NM_010346	ENSMUSG00000019312	Grb7	mKIAA4028	growth factor receptor bound protein 7	protein-coding
mm_172840.1	chr9	32136260	32136266	-	1	NA	intron (NM_001195632, intron 2 of 21)	BGLII|LTR|ERVK	20127	NM_001195632	330914	Mm.46683	NM_177379	ENSMUSG00000041444	Arhgap32	3426406O18Rik|Gc-gap|Grit|Px-rics|Rics|mKIAA0712|p200Rhogap|p250Gap	Rho GTPase activating protein 32	protein-coding
mm_59558.1	chr7	28084918	28084950	+	1	NA	exon (NM_001122603, exon 4 of 20)	exon (NM_001122603, exon 4 of 20)	13698	NM_001122603	215384	Mm.292276	NM_175444	ENSMUSG00000047730	Fcgbp	A430096B05Rik	Fc fragment of IgG binding protein	protein-coding
mm_47582.1	chr5	124579046	124579075	-	1	NA	promoter-TSS (NM_145371)	promoter-TSS (NM_145371)	71	NM_145371	209354	Mm.28839	NM_145371	ENSMUSG00000029388	Eif2b1	D5Ertd406e|EIF2BA	eukaryotic translation initiation factor 2B, subunit 1 (alpha)	protein-coding
mm_39751.1	chr5	29676529	29676532	+	1	NA	TTS (NM_133907)	TTS (NM_133907)	-59368	NM_001037940	23950	Mm.290110	NM_011847	ENSMUSG00000029131	Dnajb6	Mrj|mDj4	DnaJ heat shock protein family (Hsp40) member B6	protein-coding
mm_18302.1	chr2	53145900	53145924	-	1	NA	exon (NM_018785, exon 18 of 26)	exon (NM_018785, exon 18 of 26)	45275	NM_018785	56194	Mm.257474	NM_018785	ENSMUSG00000061136	Prpf40a	2810012K09Rik|FBP-11|FBP11|Fnbp11|Fnbp3	pre-mRNA processing factor 40A	protein-coding
mm_99199.1	chr11	101020955	101020969	+	1	NA	intron (NM_001243050, intron 4 of 20)	intron (NM_001243050, intron 4 of 20)	-9378	NR_105893	102466767		NR_105893	ENSMUSG00000098415	Mir6928	Gm27728|mmu-mir-6928	microRNA 6928	ncRNA
mm_100971.1	chr11	6719917	6719920	-	1	NA	non-coding (NR_046025, exon 1 of 5)	non-coding (NR_046025, exon 1 of 5)	119	NR_046025	626419	Mm.390334	NR_046025	ENSMUSG00000086808	Gm11981	OTTMUSG00000005129	predicted gene 11981	ncRNA
mm_25294.1	chr3	105904378	105904423	+	1	NA	promoter-TSS (NM_009631)	promoter-TSS (NM_009631)	-21	NM_009631	11542	Mm.235024	NM_009631	ENSMUSG00000000562	Adora3	A3AR|A3R|AA3R|ARA3|Gpcr2	adenosine A3 receptor	protein-coding
mm_142732.1	chr17	48351758	48351786	-	1	NA	exon (NM_031254, exon 4 of 5)	exon (NM_031254, exon 4 of 5)	5371	NM_001272078	83433	Mm.261623	NM_031254	ENSMUSG00000023992	Trem2	TREM-2|Trem2a|Trem2b|Trem2c	triggering receptor expressed on myeloid cells 2	protein-coding
mm_117718.1	chr13	95375330	95375369	-	1	NA	promoter-TSS (NM_025630)	promoter-TSS (NM_025630)	8	NM_025630	66549	Mm.36785	NM_025630	ENSMUSG00000021681	Aggf1	2010009L17Rik|2310029P06Rik|AW112072|Peg3|VG5Q	angiogenic factor with G patch and FHA domains 1	protein-coding
mm_40119.1	chr5	34975133	34975173	+	1	NA	intron (NM_173402, intron 2 of 16)	intron (NM_173402, intron 2 of 16)	-23925	NM_001163512	71729	Mm.196208	NM_173402	ENSMUSG00000029101	Rgs12	1200016K18Rik|4632412M04Rik|AI481290|E130309H11	regulator of G-protein signaling 12	protein-coding
mm_5260.1	chr1	16688938	16688963	-	1	NA	intron (NM_016923, intron 1 of 4)	intron (NM_016923, intron 1 of 4)	494	NM_016923	17087	Mm.116844	NM_016923	ENSMUSG00000025779	Ly96	ESOP-1|MD-2|MD2	lymphocyte antigen 96	protein-coding
mm_21094.1	chr2	153225378	153225394	-	1	NA	promoter-TSS (NM_198617)	promoter-TSS (NM_198617)	55	NM_198617	241732	Mm.277243	NM_198617	ENSMUSG00000074671	Tspyl3	AW212607|Gm36	TSPY-like 3	protein-coding
mm_131015.1	chr15	103563306	103563309	-	1	NA	exon (NM_008134, exon 3 of 4)	exon (NM_008134, exon 3 of 4)	1774	NM_001289587	14663	Mm.219621	NM_008134	ENSMUSG00000022491	Glycam1	MC26|Sgp50|glyCAM-1	glycosylation dependent cell adhesion molecule 1	protein-coding
mm_1049.1	chr1	58802538	58802542	+	1	NA	promoter-TSS (NM_001277926)	promoter-TSS (NM_001277926)	38	NM_001080126	12370	Mm.336851	NM_009812	ENSMUSG00000026029	Casp8	CASP-8|FLICE|MACH|Mch5	caspase 8	protein-coding
mm_145734.1	chr18	64265154	64265181	+	1	NA	5' UTR (NM_009182, exon 3 of 6)	5' UTR (NM_009182, exon 3 of 6)	10808	NM_009182	20451	Mm.252110	NM_009182	ENSMUSG00000056812	St8sia3	AI847333|ST8SiaIII|Siat8c	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3	protein-coding
mm_136796.1	chr17	12119275	12119348	+	1	NA	promoter-TSS (NM_026644)	promoter-TSS (NM_026644)	27	NM_026644	68262	Mm.258300	NM_026644	ENSMUSG00000023827	Agpat4	1500003P24Rik	1-acylglycerol-3-phosphate O-acyltransferase 4 (lysophosphatidic acid acyltransferase, delta)	protein-coding
mm_160045.1	chr6	140624759	140624759	+	1	NA	promoter-TSS (NM_001309437)	promoter-TSS (NM_001309437)	-150	NM_001309437	11569	Mm.86453	NM_009637	ENSMUSG00000030232	Aebp2	AU023766|B230313N05Rik	AE binding protein 2	protein-coding
mm_43837.1	chr5	142972775	142972781	+	1	NA	3' UTR (NM_007984, exon 5 of 5)	3' UTR (NM_007984, exon 5 of 5)	12423	NM_007984	14086	Mm.289707	NM_007984	ENSMUSG00000029581	Fscn1	AI663989|Fan1|fascin-1	fascin actin-bundling protein 1	protein-coding
mm_67621.1	chr7	84054323	84054326	-	1	NA	intron (NM_030728, intron 1 of 28)	intron (NM_030728, intron 1 of 28)	32181	NM_030728	80982	Mm.160389	NM_030728	ENSMUSG00000052353	Cemip	12H19.01.T7|6330404C01Rik|9930013L23Rik|AY007814|Kiaa1199	cell migration inducing protein, hyaluronan binding	protein-coding
mm_25496.1	chr3	109340794	109340820	+	1	NA	5' UTR (NM_020505, exon 1 of 27)	5' UTR (NM_020505, exon 1 of 27)	124	NM_020505	57257	Mm.282257	NM_020505	ENSMUSG00000033721	Vav3	A530094I06Rik|AA986410|Idd18.1	vav 3 oncogene	protein-coding
mm_46780.1	chr5	112475867	112475875	-	1	NA	intron (NM_001253917, intron 1 of 15)	intron (NM_001253917, intron 1 of 15)	26445	NM_001177504	625464	Mm.389676	NM_001177504	ENSMUSG00000072722	Gm6588	EG625464	predicted gene 6588	protein-coding
mm_68912.1	chr7	126458924	126458932	-	1	NA	intron (NM_007504, intron 5 of 22)	intron (NM_007504, intron 5 of 22)	4145	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_144759.1	chr18	35771489	35771558	+	1	NA	promoter-TSS (NM_019912)	promoter-TSS (NM_019912)	-36	NM_019912	56550	Mm.180052	NM_019912	ENSMUSG00000091896	Ube2d2a	1500034D03Rik|Ubc2e|Ube2d2|ubc4	ubiquitin-conjugating enzyme E2D 2A	protein-coding
mm_125754.1	chr15	73751310	73751325	+	1	NA	5' UTR (NM_008975, exon 2 of 6)	5' UTR (NM_008975, exon 2 of 6)	3291	NM_008975	19245	Mm.390807	NM_008975	ENSMUSG00000059895	Ptp4a3	AV088979|Prl-3|pPtp4a3	protein tyrosine phosphatase 4a3	protein-coding
mm_132510.1	chr16	37011295	37011297	+	1	NA	promoter-TSS (NM_001159369)	promoter-TSS (NM_001159369)	-490	NM_029977	77782	Mm.259114	NM_029977	ENSMUSG00000034206	Polq	A430110D14Rik	polymerase (DNA directed), theta	protein-coding
mm_3241.1	chr1	136018001	136018042	+	1	NA	promoter-TSS (NM_001160146)	promoter-TSS (NM_001160146)	20	NM_025439	66241	Mm.41773	NM_025439	ENSMUSG00000026411	Tmem9	1500015G18Rik|AW545782	transmembrane protein 9	protein-coding
mm_4248.1	chr1	171407903	171407911	+	1	NA	exon (NM_001005508, exon 12 of 12)	exon (NM_001005508, exon 12 of 12)	-3406	NM_001305678	22278	Mm.8	NM_009480	ENSMUSG00000026641	Usf1	bHLHb11	upstream transcription factor 1	protein-coding
mm_110045.1	chr12	17507202	17507212	-	1	NA	Intergenic	Intergenic	-37666	NM_013614	18263	Mm.34102	NM_013614	ENSMUSG00000011179	Odc1	ODC	ornithine decarboxylase, structural 1	protein-coding
mm_71631.1	chr8	57456021	57456036	+	1	NA	5' UTR (NM_009136, exon 1 of 3)	5' UTR (NM_009136, exon 1 of 3)	105	NM_009136	20284	Mm.12886	NM_009136	ENSMUSG00000031610	Scrg1	AW124307	scrapie responsive gene 1	protein-coding
mm_15695.1	chr2	163661496	163661498	+	1	NA	intron (NM_001039390, intron 2 of 4)	intron (NM_001039390, intron 2 of 4)	3039	NM_001164053	18769	Mm.10091	NM_011106	ENSMUSG00000035268	Pkig	PKIgamma	protein kinase inhibitor, gamma	protein-coding
mm_119070.1	chr14	30870629	30870633	+	1	NA	intron (NM_028839, intron 4 of 7)	intron (NM_028839, intron 4 of 7)	-8626	NM_181390	66175	Mm.220895	NM_181390	ENSMUSG00000042485	Mustn1	1110028G01Rik|Mustang	musculoskeletal, embryonic nuclear protein 1	protein-coding
mm_67400.1	chr7	79920600	79920658	-	1	NA	promoter-TSS (NM_009682)	promoter-TSS (NM_009682)	11	NM_009682	11778	Mm.220173	NM_009682	ENSMUSG00000063801	Ap3s2	[s]3B	adaptor-related protein complex 3, sigma 2 subunit	protein-coding
mm_32209.1	chr4	101508100	101508130	+	1	NA	exon (NM_001164584, exon 1 of 19)	exon (NM_001164584, exon 1 of 19)	139	NM_001164584	72685	Mm.76494	NM_198412	ENSMUSG00000028528	Dnajc6	2810027M23Rik|mKIAA0473	DnaJ heat shock protein family (Hsp40) member C6	protein-coding
mm_127852.1	chr15	7885200	7885242	-	1	NA	intron (NM_001081402, intron 16 of 17)	intron (NM_001081402, intron 16 of 17)	69671	NM_001301357	14573	Mm.4679	NM_010275	ENSMUSG00000022144	Gdnf	AI385739|ATF	glial cell line derived neurotrophic factor	protein-coding
mm_98243.1	chr11	88192750	88192769	+	1	NA	3' UTR (NM_001172099, exon 10 of 10)	3' UTR (NM_001172099, exon 10 of 10)	-1347	NM_001291270	64656	Mm.168680	NM_024174	ENSMUSG00000023723	Mrps23	D11Bwg1153e|MRP-S23|Rpms23|S23mt	mitochondrial ribosomal protein S23	protein-coding
mm_80139.1	chr9	70748193	70748206	+	1	NA	exon (NM_007399, exon 8 of 16)	exon (NM_007399, exon 8 of 16)	69217	NM_007399	11487	Mm.3037	NM_007399	ENSMUSG00000054693	Adam10	1700031C13Rik|MADM|kuz|kuzbanian	a disintegrin and metallopeptidase domain 10	protein-coding
mm_55452.1	chr6	67315264	67315270	-	1	NA	intron (NM_001311141, intron 3 of 9)	intron (NM_001311141, intron 3 of 9)	24427	NM_001311141	16162	Mm.188337	NM_008354	ENSMUSG00000018341	Il12rb2	A930027I18Rik|IL-12RB2|Ifnm	interleukin 12 receptor, beta 2	protein-coding
mm_25601.1	chr3	116904365	116904398	+	1	NA	TTS (NM_001113478)	TTS (NM_001113478)	42701	NM_009146	20321	Mm.66293	NM_009146	ENSMUSG00000033386	Frrs1	AI131732|Sdfr2	ferric-chelate reductase 1	protein-coding
mm_150311.1	chr19	34573219	34573229	+	1	NA	exon (NM_008332, exon 3 of 3)	exon (NM_008332, exon 3 of 3)	-10305	NM_010501	15959	Mm.426079	NM_010501	ENSMUSG00000074896	Ifit3	Ifi49|P49	interferon-induced protein with tetratricopeptide repeats 3	protein-coding
mm_172072.1	chr6	137648266	137648283	-	1	NA	intron (NM_007945, intron 1 of 21)	intron (NM_007945, intron 1 of 21)	1011	NM_001271588	13860	Mm.235346	NM_007945	ENSMUSG00000015766	Eps8	AW261790	epidermal growth factor receptor pathway substrate 8	protein-coding
mm_134412.1	chr16	17704389	17704399	-	1	NA	intron (NM_001285886, intron 2 of 16)	intron (NM_001285886, intron 2 of 16)	18506	NM_001285886	94112	Mm.208970	NM_033609	ENSMUSG00000012114	Med15	A230074L19Rik|AW536074|Pcqap|mPcqap	mediator complex subunit 15	protein-coding
mm_144502.1	chr18	24603557	24603576	+	1	NA	promoter-TSS (NM_021448)	promoter-TSS (NM_021448)	251	NM_139143	106957	Mm.21688	NM_139143	ENSMUSG00000024270	Slc39a6	Ermelin	solute carrier family 39 (metal ion transporter), member 6	protein-coding
mm_146379.1	chr18	82585149	82585154	+	1	NA	3' UTR (NM_010777, exon 7 of 7)	3' UTR (NM_010777, exon 7 of 7)	30643	NM_001025254	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_152846.1	chr19	24007335	24007354	-	1	NA	intron (NM_001114174, intron 2 of 10)	LTR78|LTR|ERV1	23675	NM_001114174	381217	Mm.426078	NM_001114174	ENSMUSG00000071604	Fam189a2	AI414343|AI666772|Gm967	family with sequence similarity 189, member A2	protein-coding
mm_15627.1	chr2	162943485	162943516	+	1	NA	promoter-TSS (NM_001081338)	promoter-TSS (NM_001081338)	35	NM_001081338	241764	Mm.187086	NM_001081338	ENSMUSG00000035576	L3mbtl1	C630004G01|L3mbtl|mKIAA0681	l(3)mbt-like (Drosophila)	protein-coding
mm_4704.1	chr1	180851132	180851172	+	1	NA	promoter-TSS (NM_145943)	promoter-TSS (NM_145943)	1	NM_145943	208768	Mm.272625	NM_145943	ENSMUSG00000038806	Sde2	-	SDE2 telomere maintenance homolog (S. pombe)	protein-coding
mm_169984.1	chr17	15021232	15021250	-	1	NA	intron (NM_001123372, intron 11 of 11)	BGLII|LTR|ERVK	-11057	NM_001123367	100041639	Mm.440445	NM_001123367	ENSMUSG00000079710	Gm3448	-	predicted gene 3448	protein-coding
mm_88236.1	chr10	71347830	71347843	+	1	NA	promoter-TSS (NM_001347191)	promoter-TSS (NM_001347191)	73	NM_027184	69718	Mm.245867	NM_027184	ENSMUSG00000060733	Ipmk	2410017C19Rik|AA408208|Impk	inositol polyphosphate multikinase	protein-coding
mm_123054.1	chr14	55643544	55643600	-	1	NA	5' UTR (NM_028780, exon 1 of 6)	5' UTR (NM_028780, exon 1 of 6)	234	NM_028780	74140	Mm.132857	NM_028780	ENSMUSG00000002320	Tm9sf1	1200014D02Rik|AI893436|MP70	transmembrane 9 superfamily member 1	protein-coding
mm_127165.1	chr15	98708188	98708216	+	1	NA	promoter-TSS (NM_153518)	promoter-TSS (NM_153518)	-25	NM_153518	105833	Mm.26205	NM_153518	ENSMUSG00000003354	Ccdc65	4933417K04Rik|AI428139|AU020178|NYD-SP28	coiled-coil domain containing 65	protein-coding
mm_118796.1	chr14	24490679	24490689	+	1	NA	promoter-TSS (NM_207634)	promoter-TSS (NM_207634)	3	NM_011297	20088	Mm.16775	NM_011297	ENSMUSG00000025290	Rps24	-	ribosomal protein S24	protein-coding
mm_129718.1	chr15	81926149	81926223	-	1	NA	promoter-TSS (NM_030229)	promoter-TSS (NM_030229)	27	NM_030229	78929	Mm.215115	NM_030229	ENSMUSG00000022476	Polr3h	5031409G22Rik|RPC8	polymerase (RNA) III (DNA directed) polypeptide H	protein-coding
mm_94377.1	chr11	5136239	5136254	+	1	NA	intron (NM_080595, intron 3 of 14)	intron (NM_080595, intron 3 of 14)	15976	NM_080595	140703	Mm.840	NM_080595	ENSMUSG00000034164	Emid1	AW122071|CO-5|Emu1	EMI domain containing 1	protein-coding
mm_56025.1	chr6	86607549	86607556	-	1	NA	Intergenic	Intergenic	-20622	NM_026414	67855	Mm.183043	NM_026414	ENSMUSG00000033508	Asprv1	2300003P22Rik|AA986851|SASP|SASPase|Taps	aspartic peptidase, retroviral-like 1	protein-coding
mm_46036.1	chr5	91962283	91962293	-	1	NA	promoter-TSS (NR_028429)	promoter-TSS (NR_028429)	268	NR_073442	68098	Mm.159453	NM_026557	ENSMUSG00000029397	Rchy1	ARNIP|CHIMP|Pirh2|Zfp363|Znf363	ring finger and CHY zinc finger domain containing 1	protein-coding
mm_109459.1	chr12	111166414	111166471	+	1	NA	promoter-TSS (NM_011632)	promoter-TSS (NM_011632)	72	NM_011632	22031	Mm.27431	NM_011632	ENSMUSG00000021277	Traf3	AI528849|CAP-1|CD40bp|CRAF1|LAP1|T-BAM|amn	TNF receptor-associated factor 3	protein-coding
mm_157811.1	chrX	73965995	73966044	-	1	NA	5' UTR (NM_008224, exon 1 of 26)	5' UTR (NM_008224, exon 1 of 26)	338	NM_008224	15161	Mm.491126	NM_008224	ENSMUSG00000031386	Hcfc1	AW060991|HCF|HCF1	host cell factor C1	protein-coding
mm_119002.1	chr14	29018108	29018119	+	1	NA	promoter-TSS (NM_176920)	promoter-TSS (NM_176920)	-95	NM_176920	319476	Mm.95780	NM_176920	ENSMUSG00000045776	Lrtm1	A930016D02Rik	leucine-rich repeats and transmembrane domains 1	protein-coding
mm_167181.1	chr7	141637473	141637486	-	1	NA	intron (NM_001330001, intron 31 of 33)	intron (NM_001330001, intron 31 of 33)	16778	NR_106030	102466798		NR_106030	ENSMUSG00000098759	Mir7063	Gm27654|mmu-mir-7063	microRNA 7063	ncRNA
mm_34299.1	chr4	141714045	141714049	+	1	NA	intron (NM_001017966, intron 1 of 9)	RLTR30D2_MM|LTR|ERV1	9372	NM_001017966	68817	Mm.393721	NM_001017966	ENSMUSG00000078515	Ddi2	1110056G13Rik|1700027M01Rik|9130022E05Rik|AI604911|AU040698	DNA-damage inducible protein 2	protein-coding
mm_147617.1	chr18	57533750	57533761	-	1	NA	promoter-TSS (NM_029290)	promoter-TSS (NM_029290)	-3	NR_015541	74916	Mm.444721	NR_015541	ENSMUSG00000085800	1700066O22Rik	4930500F21Rik|4930515O13Rik|4930542C11Rik	RIKEN cDNA 1700066O22 gene	ncRNA
mm_60861.1	chr7	45883338	45883360	+	1	NA	3' UTR (NM_133950, exon 5 of 5)	3' UTR (NM_133950, exon 5 of 5)	10509	NM_133950	68137	Mm.298433	NM_133950	ENSMUSG00000002778	Kdelr1	8030486F04Rik|AW215843|Erd2.1	KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 1	protein-coding
mm_95971.1	chr11	58948891	58948920	+	1	NA	promoter-TSS (NM_030082)	promoter-TSS (NM_030082)	-6	NM_030082	78303	Mm.28022	NM_030082	ENSMUSG00000056895	Hist3h2ba	1500011O09Rik|AI413321	histone cluster 3, H2ba	protein-coding
mm_4520.1	chr1	175631997	175632001	+	1	NA	promoter-TSS (NM_133809)	promoter-TSS (NM_133809)	-194	NM_133809	98256	Mm.27217	NM_133809	ENSMUSG00000039783	Kmo	AI046660	kynurenine 3-monooxygenase (kynurenine 3-hydroxylase)	protein-coding
mm_129169.1	chr15	76249310	76249350	-	1	NA	exon (NM_023168, exon 7 of 7)	exon (NM_023168, exon 7 of 7)	1139	NR_105918	102465575		NR_105918	ENSMUSG00000098625	Mir6953	Gm27738|mmu-mir-6953	microRNA 6953	ncRNA
mm_104179.1	chr11	87751615	87751633	-	1	NA	Intergenic	Intergenic	-5240	NR_029555	387160		NR_029555	ENSMUSG00000105196	Mir142	Mirn142|miR-142|mir-142a|mmu-mir-142|mmu-mir-142a	microRNA 142	ncRNA
mm_122942.1	chr14	54965413	54965434	-	1	NA	exon (NM_010856, exon 3 of 39)	exon (NM_010856, exon 3 of 39)	1184	NM_001164171	17888	Mm.290003	NM_010856	ENSMUSG00000040752	Myh6	A830009F23Rik|AA517445|Myhc-a|Myhca|alpha-MHC	myosin, heavy polypeptide 6, cardiac muscle, alpha	protein-coding
mm_71184.1	chr8	40862443	40862453	+	1	NA	promoter-TSS (NM_001044740)	promoter-TSS (NM_001044740)	81	NM_001044740	11988	Mm.4676	NM_007514	ENSMUSG00000031596	Slc7a2	20.5|AI158848|Atrc2|CAT-2|Cat2|Tea	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	protein-coding
mm_113214.1	chr13	25187439	25187456	+	1	NA	intron (NM_177577, intron 7 of 9)	intron (NM_177577, intron 7 of 9)	82549	NM_009513	22360	Mm.4766	NM_009513	ENSMUSG00000048978	Nrsn1	Neurensin-1|Neuro-p24|Vmp	neurensin 1	protein-coding
mm_81143.1	chr9	106822024	106822034	+	1	NA	promoter-TSS (NM_001015507)	promoter-TSS (NM_001015507)	53	NM_001015507	321006	Mm.440089	NM_001015507	ENSMUSG00000040325	Vprbp	AI447437|B930007L02Rik|mKIAA0800	Vpr (HIV-1) binding protein	protein-coding
mm_19477.1	chr2	92970684	92970711	-	1	NA	Intergenic	RLTR20C1_MM|LTR|ERVK	55596	NM_030725	80976	Mm.33490	NM_030725	ENSMUSG00000027220	Syt13	5730409J20Rik|AI549909|mKIAA1427	synaptotagmin XIII	protein-coding
mm_84879.1	chr9	79718766	79718777	-	1	NA	promoter-TSS (NM_001290308)	promoter-TSS (NM_001290308)	-49	NM_001290308	12816	Mm.3819	NM_007730	ENSMUSG00000032332	Col12a1	-	collagen, type XII, alpha 1	protein-coding
mm_110843.1	chr12	73041709	73041710	-	1	NA	TTS (NM_009189)	TTS (NM_009189)	5003	NM_009189	20471	Mm.4645	NM_009189	ENSMUSG00000051367	Six1	BB138287	sine oculis-related homeobox 1	protein-coding
mm_72710.1	chr8	84986448	84986461	+	1	NA	Intergenic	Intergenic	-4141	NM_133255	170833	Mm.247775	NM_133255	ENSMUSG00000052566	Hook2	A630054I03Rik	hook microtubule tethering protein 2	protein-coding
mm_49964.1	chr6	40735371	40735373	+	1	NA	intron (NM_001171003, intron 31 of 47)	intron (NM_001171003, intron 31 of 47)	106541	NM_001171003	232714	Mm.33401	NM_001171003	ENSMUSG00000068587	Mgam	6030407P20Rik|MGA	maltase-glucoamylase	protein-coding
mm_78411.1	chr9	30438869	30438899	+	1	NA	intron (NM_028874, intron 7 of 10)	intron (NM_028874, intron 7 of 10)	11555	NM_028874	102607	Mm.35084	NM_028874	ENSMUSG00000031993	Snx19	3526401K03Rik|AI195321|AI848208|mKIAA0254	sorting nexin 19	protein-coding
mm_68081.1	chr7	101870658	101870676	-	1	NA	5' UTR (NM_008034, exon 1 of 7)	5' UTR (NM_008034, exon 1 of 7)	121	NM_001252554	14275	Mm.2135	NM_008034	ENSMUSG00000001827	Folr1	FBP1|Folbp-1|Folbp1	folate receptor 1 (adult)	protein-coding
mm_130483.1	chr15	98742612	98742625	-	1	NA	exon (NM_007478, exon 2 of 5)	exon (NM_007478, exon 2 of 5)	-14420	NM_024169	66120	Mm.30729	NM_024169	ENSMUSG00000003355	Fkbp11	1110002O23Rik|FKBP-11	FK506 binding protein 11	protein-coding
mm_37480.1	chr4	123572818	123572845	-	1	NA	intron (NM_001199136, intron 1 of 97)	intron (NM_001199136, intron 1 of 97)	-43589	NR_105824	102465214		NR_105824	ENSMUSG00000099005	Mir6398	Gm27657|mmu-mir-6398	microRNA 6398	ncRNA
mm_40703.1	chr5	65861213	65861237	+	1	NA	Intergenic	Intergenic	-2344	NM_001081105	74734	Mm.20323	NM_001081105	ENSMUSG00000029204	Rhoh	5830400A04Rik|AU019774|Arhh	ras homolog family member H	protein-coding
mm_80475.1	chr9	78191973	78191999	+	1	NA	promoter-TSS (NM_010357)	promoter-TSS (NM_010357)	20	NM_010357	14860	Mm.2662	NM_010357	ENSMUSG00000032348	Gsta4	GST5.7|mGsta4	glutathione S-transferase, alpha 4	protein-coding
mm_88333.1	chr10	75573451	75573464	+	1	NA	promoter-TSS (NM_008116)	promoter-TSS (NM_008116)	-38	NM_008116	14598	Mm.4559	NM_008116	ENSMUSG00000006345	Ggt1	CD224|GGT|GGT 1|GGT-1|Ggtp|dwg	gamma-glutamyltransferase 1	protein-coding
mm_112141.1	chr12	113140127	113140143	-	1	NA	promoter-TSS (NM_024223)	promoter-TSS (NM_024223)	-101	NM_024223	68337	Mm.133825	NM_024223	ENSMUSG00000006356	Crip2	0610010I23Rik|AW743261|C77570|CRP2|CRP4|Crp|ESP1|Hlp	cysteine rich protein 2	protein-coding
mm_143130.1	chr17	57214841	57214850	-	1	NA	intron (NM_009778, intron 25 of 40)	intron (NM_009778, intron 25 of 40)	2383	NR_105944	102465591		NR_105944	ENSMUSG00000099066	Mir6978	Gm27858|mmu-mir-6978	microRNA 6978	ncRNA
mm_120451.1	chr14	65968634	65968651	+	1	NA	5' UTR (NM_013492, exon 1 of 9)	5' UTR (NM_013492, exon 1 of 9)	159	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_137310.1	chr17	24878725	24878781	+	1	NA	promoter-TSS (NM_008340)	promoter-TSS (NM_008340)	-17	NM_008340	16005	Mm.3135	NM_008340	ENSMUSG00000046070	Igfals	ALS|Albs|mKIAA4111	insulin-like growth factor binding protein, acid labile subunit	protein-coding
mm_59147.1	chr7	24369838	24369879	+	1	NA	promoter-TSS (NM_001163510)	promoter-TSS (NM_001163510)	-405	NM_001163510	16534	Mm.9911	NM_008433	ENSMUSG00000054342	Kcnn4	IK1|IKCA1|KCA4|KCa3.1|SK4|SKCas|mIKCa1	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4	protein-coding
mm_38787.1	chr4	148088059	148088069	-	1	NA	promoter-TSS (NM_001301281)	promoter-TSS (NM_001301281)	0	NM_009642	11610	Mm.46247	NM_009642	ENSMUSG00000029007	Agtrap	3300002E14Rik|AT1R|Atrap|D4Wsu124e	angiotensin II, type I receptor-associated protein	protein-coding
mm_77743.1	chr8	126971093	126971099	-	1	NA	promoter-TSS (NM_172762)	promoter-TSS (NM_172762)	-17	NM_172762	52202	Mm.28199	NM_172762	ENSMUSG00000033931	Rbm34	4930547K05Rik|6330444B11|D8Ertd233e	RNA binding motif protein 34	protein-coding
mm_117008.1	chr13	58001849	58001853	-	1	NA	Intergenic	Intergenic	21349	NR_030544	100124491		NR_030544	ENSMUSG00000077962	Mir874	Mirn874|mir-874|mmu-mir-874	microRNA 874	ncRNA
mm_78733.1	chr9	41582001	41582004	+	1	NA	promoter-TSS (NR_029822)	promoter-TSS (NR_029822)	76	NR_029822	387236		NR_029822	ENSMUSG00000093354	Mir125b-1	Mirn125b|Mirn125b-1|mir-125b-1	microRNA 125b-1	ncRNA
mm_172146.1	chr6	37686910	37686910	-	1	NA	Intergenic	Intergenic	156737	NM_145364	208665	Mm.262635	NM_145364	ENSMUSG00000038641	Akr1d1	-	aldo-keto reductase family 1, member D1	protein-coding
mm_40087.1	chr5	34536128	34536176	+	1	NA	intron (NM_011893, intron 1 of 12)	intron (NM_011893, intron 1 of 12)	-7213	NM_001145858	24055	Mm.5012	NM_011893	ENSMUSG00000054520	Sh3bp2	3BP2	SH3-domain binding protein 2	protein-coding
mm_45575.1	chr5	73630352	73630365	-	1	NA	intron (NM_153568, intron 1 of 4)	intron (NM_153568, intron 1 of 4)	2063	NM_153568	231296	Mm.168948	NM_153568	ENSMUSG00000067206	Lrrc66	-	leucine rich repeat containing 66	protein-coding
mm_98540.1	chr11	95010076	95010086	+	1	NA	5' UTR (NM_146025, exon 1 of 10)	5' UTR (NM_146025, exon 1 of 10)	202	NM_146025	217125	Mm.297199	NM_146025	ENSMUSG00000047181	Samd14	AI839049|AI854782|BC034054	sterile alpha motif domain containing 14	protein-coding
mm_7051.1	chr1	87127749	87127792	-	1	NA	exon (NM_007432, exon 11 of 11)	exon (NM_007432, exon 11 of 11)	2762	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_62743.1	chr7	111056778	111056781	+	1	NA	TTS (NM_009431)	TTS (NM_009431)	26251	NM_001040131	13690	Mm.185453	NM_013507	ENSMUSG00000005610	Eif4g2	DAP-5|E130105L11Rik|Nat1|Natm1|p97	eukaryotic translation initiation factor 4, gamma 2	protein-coding
mm_60385.1	chr7	44473945	44473969	+	1	NA	Intergenic	IMPB_01|Satellite|Satellite	3610	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_133682.1	chr16	92485706	92485736	+	1	NA	intron (NM_029740, intron 1 of 2)	intron (NM_029740, intron 1 of 2)	6979	NM_029740	76785	Mm.444318	NM_029740		2410124H12Rik	-	RIKEN cDNA 2410124H12 gene	protein-coding
mm_57019.1	chr6	121473589	121473628	-	1	NA	promoter-TSS (NM_001289685)	promoter-TSS (NM_001289685)	70	NM_001033354	243621	Mm.299442	NM_001033354	ENSMUSG00000040797	Iqsec3	AK122446|BRAG3|mKIAA1110|synarfGEF	IQ motif and Sec7 domain 3	protein-coding
mm_51512.1	chr6	83137805	83137837	+	1	NA	5' UTR (NM_133641, exon 1 of 12)	5' UTR (NM_133641, exon 1 of 12)	737	NM_009106	20166	Mm.4139	NM_009106	ENSMUSG00000034930	Rtkn	-	rhotekin	protein-coding
mm_12977.1	chr2	90777220	90777231	+	1	NA	intron (NM_018828, intron 14 of 16)	(T)n|Simple_repeat|Simple_repeat	-5519	NM_178755	271813	Mm.61146	NM_178755	ENSMUSG00000040812	Agbl2	4930524K04|A430081C19Rik|CCP2	ATP/GTP binding protein-like 2	protein-coding
mm_65000.1	chr7	17024914	17024945	-	1	NA	intron (NM_011155, intron 1 of 12)	intron (NM_011155, intron 1 of 12)	2985	NM_011155	19060	Mm.3294	NM_011155	ENSMUSG00000003099	Ppp5c	AU020526|PP5	protein phosphatase 5, catalytic subunit	protein-coding
mm_119275.1	chr14	34220029	34220058	+	1	NA	promoter-TSS (NM_176931)	promoter-TSS (NM_176931)	-3	NM_176931	319508	Mm.228006	NM_176931	ENSMUSG00000041479	Syt15	CHR10SYT|E230025K04Rik|sytXV	synaptotagmin XV	protein-coding
mm_162659.1	chr10	5032272	5032276	+	1	NA	intron (NM_001347732, intron 143 of 145)	intron (NM_001347732, intron 143 of 145)	36789	NM_022027	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_134895.1	chr16	29849608	29849621	-	1	NA	Intergenic	Lx8|LINE|L1	129510	NR_037689	328657	Mm.425982	NM_001033403		Gm1968	-	predicted gene 1968	ncRNA
mm_90171.1	chr10	119502725	119502736	+	1	NA	intron (NM_133442, intron 1 of 21)	intron (NM_133442, intron 1 of 21)	48696	NM_001277293	74053	Mm.196692	NM_028736	ENSMUSG00000034813	Grip1	4931400F03Rik|GRIP|eb	glutamate receptor interacting protein 1	protein-coding
mm_155854.1	chrX	101299144	101299201	+	1	NA	promoter-TSS (NM_172932)	promoter-TSS (NM_172932)	-7	NM_172932	245537	Mm.121508	NM_172932	ENSMUSG00000031302	Nlgn3	A230085M13Rik|HNL3|NL3	neuroligin 3	protein-coding
mm_51483.1	chr6	83048524	83048528	+	1	NA	intron (NM_013586, intron 5 of 13)	intron (NM_013586, intron 5 of 13)	-1185	NR_106007	102465630		NR_106007	ENSMUSG00000099035	Mir7040	Gm27489|mmu-mir-7040	microRNA 7040	ncRNA
mm_144664.1	chr18	34331133	34331197	+	1	NA	promoter-TSS (NM_025527)	promoter-TSS (NM_025527)	20	NM_025527	66384	Mm.29452	NM_025527	ENSMUSG00000014504	Srp19	2310020D23Rik	signal recognition particle 19	protein-coding
mm_59502.1	chr7	27553245	27553302	+	1	NA	promoter-TSS (NM_011116)	promoter-TSS (NM_011116)	-17	NM_175107	66367	Mm.29831	NM_175107	ENSMUSG00000049643	2310022A10Rik	-	RIKEN cDNA 2310022A10 gene	protein-coding
mm_77354.1	chr8	119605200	119605213	-	1	NA	promoter-TSS (NM_021441)	promoter-TSS (NM_021441)	34	NM_021441	21341	Mm.41977	NM_021441	ENSMUSG00000031832	Taf1c	Tafi95|mTAFI95	TATA-box binding protein associated factor, RNA polymerase I, C	protein-coding
mm_79752.1	chr9	62373458	62373488	+	1	NA	intron (NM_009672, intron 3 of 6)	intron (NM_009672, intron 3 of 6)	32130	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	protein-coding
mm_17917.1	chr2	35432782	35432797	-	1	NA	intron (NM_001308300, intron 1 of 6)	intron (NM_001308300, intron 1 of 6)	28660	NM_001308299	14594	Mm.281124	NM_010283	ENSMUSG00000035778	Ggta1	AW108479|GALT|Gal|Ggta|Ggta-1|alpha Gal|alpha3GalT	glycoprotein galactosyltransferase alpha 1, 3	protein-coding
mm_84776.1	chr9	75683910	75683914	-	1	NA	5' UTR (NM_001164790, exon 1 of 12)	5' UTR (NM_001164790, exon 1 of 12)	144	NM_001164790	20255	Mm.2386	NM_009130	ENSMUSG00000032181	Scg3	1B1075|AI385542|Chgd|SgIII	secretogranin III	protein-coding
mm_71593.1	chr8	54955027	54955037	+	1	NA	5' UTR (NM_153581, exon 1 of 7)	5' UTR (NM_153581, exon 1 of 7)	304	NM_001253756	234267	Mm.241700	NM_153581	ENSMUSG00000031517	Gpm6a	Gpm6|M6A	glycoprotein m6a	protein-coding
mm_97178.1	chr11	75532233	75532248	+	1	NA	5' UTR (NM_001199283, exon 1 of 14)	5' UTR (NM_001199283, exon 1 of 14)	128	NM_001199283	215113	Mm.11186	NM_173388	ENSMUSG00000038178	Slc43a2	7630402D21Rik|BC042513|Lat4	solute carrier family 43, member 2	protein-coding
mm_142024.1	chr17	35205306	35205317	-	1	NA	promoter-TSS (NM_010735)	promoter-TSS (NM_010735)	40	NM_010735	16992	Mm.87787	NM_010735	ENSMUSG00000024402	Lta	LT|LT-[a]|LT-alpha|LT[a]|LTalpha|Ltx|TNF-beta|TNFSF1|Tnfb|Tnfsf1b|Tnlg1e|hlb382	lymphotoxin A	protein-coding
mm_76889.1	chr8	105637908	105637932	-	1	NA	intron (NM_181322, intron 1 of 11)	intron (NM_181322, intron 1 of 11)	1382	NM_181322	13018	Mm.269474	NM_181322	ENSMUSG00000005698	Ctcf	AW108038	CCCTC-binding factor	protein-coding
mm_74538.1	chr8	9771487	9771525	-	1	NA	promoter-TSS (NM_173446)	promoter-TSS (NM_173446)	-349	NM_001347127	270028	Mm.268163	NM_173446	ENSMUSG00000079157	Fam155a	6430500D16|AW121567|Tmem28	family with sequence similarity 155, member A	protein-coding
mm_17976.1	chr2	37677897	37677901	-	1	NA	Intergenic	PB1D9|SINE|Alu	-30614	NM_009261	20744	Mm.237095	NM_009261	ENSMUSG00000026915	Strbp	6430510M02Rik|AI852513|C230082I21Rik|C86322|Spnr	spermatid perinuclear RNA binding protein	protein-coding
mm_13108.1	chr2	91526842	91526852	+	1	NA	Intergenic	CpG	-19475	NM_001165989	75786	Mm.168478	NM_029437	ENSMUSG00000040549	Ckap5	3110043H24Rik|4930432B04Rik|D730027C18Rik|T25636|mKIAA0097	cytoskeleton associated protein 5	protein-coding
mm_30955.1	chr4	33310391	33310403	+	1	NA	promoter-TSS (NM_001305273)	promoter-TSS (NM_001305273)	86	NM_001305273	24018	Mm.240024	NM_011884	ENSMUSG00000028274	Rngtt	AU020997|HCE|MCE1	RNA guanylyltransferase and 5'-phosphatase	protein-coding
mm_114222.1	chr13	56438382	56438393	+	1	NA	promoter-TSS (NM_177809)	promoter-TSS (NM_177809)	32	NM_177809	328258	Mm.482177	NM_177809	ENSMUSG00000021509	Slc25a48	AU042651|E230025K15	solute carrier family 25, member 48	protein-coding
mm_145097.1	chr18	43207725	43207737	+	1	NA	promoter-TSS (NM_178749)	promoter-TSS (NM_178749)	34	NM_178749	269019	Mm.150401	NM_178749	ENSMUSG00000039954	Stk32a	A930015B13Rik|YANK1	serine/threonine kinase 32A	protein-coding
mm_81504.1	chr9	110034622	110034648	+	1	NA	exon (NM_008633, exon 7 of 19)	exon (NM_008633, exon 7 of 19)	-17386	NM_001311163	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_32638.1	chr4	115056739	115056749	+	1	NA	intron (NM_011527, intron 1 of 4)	CpG	318	NM_011527	21349	Mm.239869	NM_011527	ENSMUSG00000028717	Tal1	Hpt|SCL/tal-1|Scl|bHLHa17|tal-1	T cell acute lymphocytic leukemia 1	protein-coding
mm_121048.1	chr14	84175256	84175256	+	1	NA	Intergenic	Intergenic	-268307	NM_001013753	219228	Mm.153643	NM_001013753	ENSMUSG00000035566	Pcdh17	C030033F14Rik|Gm78	protocadherin 17	protein-coding
mm_158272.1	chrX	111450663	111450673	-	1	NA	intron (NM_025949, intron 3 of 24)	MLT1E1A|LTR|ERVL-MaLR	87291	NM_025949	67071	Mm.37617	NM_025949	ENSMUSG00000025665	Rps6ka6	2610524K04Rik|RSK4|S6K-alpha-6	ribosomal protein S6 kinase polypeptide 6	protein-coding
mm_142896.1	chr17	51903921	51903930	-	1	NA	intron (NR_045095, intron 1 of 2)	intron (NR_045095, intron 1 of 2)	21198	NR_045095	100504169	Mm.417731	NR_045095		Gm20098	-	predicted gene, 20098	ncRNA
mm_65977.1	chr7	30444417	30444430	-	1	NA	exon (NM_007467, exon 2 of 17)	exon (NM_007467, exon 2 of 17)	1159	NM_007467	11803	Mm.2381	NM_007467	ENSMUSG00000006651	Aplp1	-	amyloid beta (A4) precursor-like protein 1	protein-coding
mm_13515.1	chr2	109917640	109917656	+	1	NA	promoter-TSS (NM_172671)	promoter-TSS (NM_172671)	1	NM_172671	107515	Mm.277351	NM_172671	ENSMUSG00000050199	Lgr4	9130225G07|A330106J01Rik|A930009A08Rik|Gpr48	leucine-rich repeat-containing G protein-coupled receptor 4	protein-coding
mm_59724.1	chr7	28787969	28788017	+	1	NA	promoter-TSS (NM_177158)	promoter-TSS (NM_177158)	-976	NM_177158	320435	Mm.74632	NM_177158	ENSMUSG00000051735	Rinl	5830482F20Rik|9930116N10Rik	Ras and Rab interactor-like	protein-coding
mm_159092.1	chr2	32395643	32395643	+	1	NA	promoter-TSS (NM_133783)	promoter-TSS (NM_133783)	-247	NM_133783	96979	Mm.28048	NM_133783	ENSMUSG00000026820	Ptges2	0610038H10Rik|C79137|Gbf1|Mpges2|Pges2	prostaglandin E synthase 2	protein-coding
mm_99200.1	chr11	101021438	101021451	+	1	NA	intron (NM_001243050, intron 5 of 20)	intron (NM_001243050, intron 5 of 20)	-8896	NR_105893	102466767		NR_105893	ENSMUSG00000098415	Mir6928	Gm27728|mmu-mir-6928	microRNA 6928	ncRNA
mm_106288.1	chr11	118206444	118206448	-	1	NA	intron (NM_001112699, intron 1 of 12)	intron (NM_001112699, intron 1 of 12)	6296	NM_001112700	19157	Mm.86413	NM_011180	ENSMUSG00000017132	Cyth1	CLM1|CTH-1|CYTIP|Pscd1	cytohesin 1	protein-coding
mm_49401.1	chr6	28426344	28426354	+	1	NA	3' UTR (NM_007480, exon 6 of 6)	3' UTR (NM_007480, exon 6 of 6)	-1552	NM_019569	56223	Mm.31708	NM_019569	ENSMUSG00000029707	Fscn3	-	fascin actin-bundling protein 3	protein-coding
mm_73601.1	chr8	109998927	109998941	+	1	NA	3' UTR (NM_146214, exon 12 of 12)	3' UTR (NM_146214, exon 12 of 12)	8498	NM_146214	234724	Mm.28110	NM_146214	ENSMUSG00000001670	Tat	-	tyrosine aminotransferase	protein-coding
mm_148282.1	chr18	82525929	82525960	-	1	NA	intron (NM_001025245, intron 3 of 3)	intron (NM_001025245, intron 3 of 3)	-28519	NM_001025256	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_65576.1	chr7	27195728	27195768	-	1	NA	promoter-TSS (NM_001046637)	promoter-TSS (NM_001046637)	12	NM_001046637	53607	Mm.386890	NM_015782	ENSMUSG00000061479	Snrpa	C430021M15Rik|Rnu1a-1|Rnu1a1|U1-A|U1A	small nuclear ribonucleoprotein polypeptide A	protein-coding
mm_41283.1	chr5	90461709	90461750	+	1	NA	exon (NM_009654, exon 2 of 15)	exon (NM_009654, exon 2 of 15)	859	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_26955.1	chr3	20506220	20506225	-	1	NA	Intergenic	Intergenic	-139045	NM_175086	11608	Mm.134863	NM_175086	ENSMUSG00000054988	Agtr1b	AT1B|AT2R1B|Agtr-1b|Angtr-1b	angiotensin II receptor, type 1b	protein-coding
mm_149568.1	chr19	12804710	12804720	+	1	NA	intron (NM_134152, intron 2 of 8)	intron (NM_134152, intron 2 of 8)	6106	NM_134152	107321	Mm.313136	NM_134152	ENSMUSG00000024696	Lpxn	4933402K05Rik|A530083L21Rik|AV278559|LDPL	leupaxin	protein-coding
mm_74434.1	chr8	3748942	3748953	-	1	NA	promoter-TSS (NM_133238)	promoter-TSS (NM_133238)	37	NM_133238	170786	Mm.32510	NM_133238	ENSMUSG00000031494	Cd209a	CD209|CDSIGN|CIRE|DC-SIGN|DC-SIGN1|Dcsign|SIGN-R1|SIGNR5	CD209a antigen	protein-coding
mm_80457.1	chr9	77983000	77983033	+	1	NA	3' UTR (NM_134255, exon 8 of 8)	3' UTR (NM_134255, exon 8 of 8)	65651	NM_134255	68801	Mm.430736	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	ELOVL family member 5, elongation of long chain fatty acids (yeast)	protein-coding
mm_159683.1	chr5	7344580	7344580	-	1	NA	promoter-TSS (NM_001163223)	promoter-TSS (NM_001163223)	-202	NM_001163223	207618	Mm.478808	NM_001163223	ENSMUSG00000092094	Zfp804b	Gm441	zinc finger protein 804B	protein-coding
mm_126318.1	chr15	79690870	79690905	+	1	NA	promoter-TSS (NM_013818)	promoter-TSS (NM_013818)	-9	NM_013818	14904	Mm.19080	NM_013818	ENSMUSG00000042535	Gtpbp1	AL022987|AW045683|C85212|GP-1|Gtpbp	GTP binding protein 1	protein-coding
mm_85578.1	chr9	107289835	107289845	-	1	NA	promoter-TSS (NM_178907)	promoter-TSS (NM_178907)	37	NM_178907	102626	Mm.222612	NM_178907	ENSMUSG00000032577	Mapkapk3	3PK|AI874665|MAPKAP-K3|MAPKAP3|MK-3|MK3|MapkKapk3	mitogen-activated protein kinase-activated protein kinase 3	protein-coding
mm_16349.1	chr2	174346453	174346515	+	1	NA	non-coding (NR_003258, exon 13 of 13)	non-coding (NR_003258, exon 13 of 13)	16395	NM_001077510	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_6818.1	chr1	84187073	84187082	-	1	NA	intron (NM_001003948, intron 1 of 2)	intron (NM_001003948, intron 1 of 2)	31884	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_73166.1	chr8	95020442	95020452	+	1	NA	intron (NM_173036, intron 1 of 11)	intron (NM_173036, intron 1 of 11)	2755	NM_173036	54672	Mm.27995	NM_173036	ENSMUSG00000060470	Adgrg3	A030001G24Rik|AW214383|Gpr97|Pb1|Pb99	adhesion G protein-coupled receptor G3	protein-coding
mm_133503.1	chr16	90738106	90738113	+	1	NA	promoter-TSS (NM_029844)	promoter-TSS (NM_029844)	-215	NM_029844	77037	Mm.22455	NM_029844	ENSMUSG00000039956	Mrap	1110025G12Rik|Falp|ORF61	melanocortin 2 receptor accessory protein	protein-coding
mm_104426.1	chr11	94942837	94942877	-	1	NA	exon (NM_007742, exon 21 of 51)	exon (NM_007742, exon 21 of 51)	6633	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_106122.1	chr11	116359481	116359510	-	1	NA	intron (NM_027258, intron 5 of 18)	intron (NM_027258, intron 5 of 18)	-24141	NM_008240	15223	Mm.378938	NM_008240	ENSMUSG00000034227	Foxj1	FKHL-13|HFH-4|Hfh4	forkhead box J1	protein-coding
mm_128561.1	chr15	56049849	56049851	-	1	NA	Intergenic	Intergenic	-142901	NM_016667	20649	Mm.309425	NM_016667	ENSMUSG00000060429	Sntb1	-	syntrophin, basic 1	protein-coding
mm_31948.1	chr4	86748527	86748558	+	1	NA	promoter-TSS (NM_184088)	promoter-TSS (NM_184088)	-13	NM_184088	329877	Mm.273718	NM_184088	ENSMUSG00000038024	Dennd4c	1700065A05Rik|AA420392	DENN/MADD domain containing 4C	protein-coding
mm_118756.1	chr14	22371846	22371893	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	170929	NR_046307	74896	Mm.444661	NR_046307		4930405A10Rik	4930456G20Rik	RIKEN cDNA 4930405A10 gene	ncRNA
mm_154862.1	chrX	20659011	20659031	+	1	NA	intron (NM_001276317, intron 1 of 25)	intron (NM_001276317, intron 1 of 25)	517	NM_001276317	22201	Mm.1104	NM_009457	ENSMUSG00000001924	Uba1	A1S9|Sbx|Ube-1|Ube1x	ubiquitin-like modifier activating enzyme 1	protein-coding
mm_64655.1	chr7	4150220	4150230	-	1	NA	promoter-TSS (NM_175529)	promoter-TSS (NM_175529)	-353	NM_175529	243813	Mm.347643	NM_175529	ENSMUSG00000043432	Leng9	9530024C23Rik|F630035L11Rik	leukocyte receptor cluster (LRC) member 9	protein-coding
mm_160771.1	chr10	114801321	114801321	-	1	NA	promoter-TSS (NM_146241)	promoter-TSS (NM_146241)	49	NM_146241	237553	Mm.445550	NM_146241	ENSMUSG00000050663	Trhde	9330155P21Rik	TRH-degrading enzyme	protein-coding
mm_114878.1	chr13	94174043	94174061	+	1	NA	5' UTR (NM_172589, exon 3 of 4)	5' UTR (NM_172589, exon 3 of 4)	111229	NM_029153	107767	Mm.201455	NM_029153	ENSMUSG00000021687	Scamp1	4930505M11Rik|AI415563|AW122395	secretory carrier membrane protein 1	protein-coding
mm_67955.1	chr7	100499509	100499536	-	1	NA	3' UTR (NM_011671, exon 8 of 8)	3' UTR (NM_011671, exon 8 of 8)	6164	NM_011671	22228	Mm.171378	NM_011671	ENSMUSG00000033685	Ucp2	Slc25a8	uncoupling protein 2 (mitochondrial, proton carrier)	protein-coding
mm_29193.1	chr3	106760517	106760530	-	1	NA	3' UTR (NM_007651, exon 8 of 8)	3' UTR (NM_007651, exon 8 of 8)	29626	NM_007651	12508	Mm.316861	NM_007651	ENSMUSG00000040747	Cd53	AI323659|Ox-44|Tspan25	CD53 antigen	protein-coding
mm_20076.1	chr2	120568110	120568118	-	1	NA	intron (NM_009222, intron 1 of 7)	intron (NM_009222, intron 1 of 7)	443	NM_009222	20619	Mm.245715	NM_009222	ENSMUSG00000027287	Snap23	23kDa|AA408749|SNAP-23|Sndt|Syndet	synaptosomal-associated protein 23	protein-coding
mm_125227.1	chr15	34131214	34131250	+	1	NA	exon (NM_026002, exon 8 of 12)	exon (NM_026002, exon 8 of 12)	48513	NM_026002	67154	Mm.130883	NM_026002	ENSMUSG00000022255	Mtdh	2610103J23Rik|3D3|3D3/Lyric|AEG-1|AV353288|D8Bwg1112e|Lyric	metadherin	protein-coding
mm_130079.1	chr15	89374040	89374074	-	1	NA	promoter-TSS (NM_001111288)	promoter-TSS (NM_001111288)	-239	NM_001111288	100126824	Mm.287977	NM_001111288	ENSMUSG00000091780	Sco2	-	SCO2 cytochrome c oxidase assembly protein	protein-coding
mm_126509.1	chr15	81802763	81802770	+	1	NA	promoter-TSS (NM_153484)	promoter-TSS (NM_153484)	93	NM_153484	21685	Mm.270278	NM_017376	ENSMUSG00000022389	Tef	2310028D20Rik	thyrotroph embryonic factor	protein-coding
mm_15992.1	chr2	167060517	167060547	+	1	NA	intron (NM_001033196, intron 1 of 13)	intron (NM_001033196, intron 1 of 13)	-2402	NR_138563	68949	Mm.391959	NM_001081005		Zfas1	1500012F01Rik|Zfos1	zinc finger, NFX1-type containing 1, antisense RNA 1	ncRNA
mm_97742.1	chr11	80467857	80467890	+	1	NA	intron (NM_178616, intron 9 of 13)	B1_Mus2|SINE|Alu	-9173	NM_009871	12569	Mm.142275	NM_009871	ENSMUSG00000048895	Cdk5r1	Cdk5r|D11Bwg0379e|p25|p35	cyclin-dependent kinase 5, regulatory subunit 1 (p35)	protein-coding
mm_91252.1	chr10	22731919	22731946	-	1	NA	promoter-TSS (NM_011603)	promoter-TSS (NM_011603)	-485	NM_011603	237336	Mm.86670	NM_011603	ENSMUSG00000071359	Tbpl1	4732475G08|AW011832|AW491032|D18347|STD|TLF|TRF2|TRP|Tlp	TATA box binding protein-like 1	protein-coding
mm_110850.1	chr12	73113408	73113435	-	1	NA	promoter-TSS (NM_011382)	promoter-TSS (NM_011382)	-176	NM_011382	20474	Mm.249575	NM_011382	ENSMUSG00000034460	Six4	AI047561|AREC3|TrexBF	sine oculis-related homeobox 4	protein-coding
mm_78640.1	chr9	40269355	40269366	+	1	NA	5' UTR (NM_001083917, exon 1 of 7)	5' UTR (NM_001083917, exon 1 of 7)	144	NM_178227	235281	Mm.290083	NM_153522	ENSMUSG00000049281	Scn3b	1110001K16Rik|4833414B02Rik|Scnb3	sodium channel, voltage-gated, type III, beta	protein-coding
mm_4264.1	chr1	171458334	171458359	+	1	NA	intron (NM_172647, intron 1 of 9)	B3A|SINE|B2	20785	NM_172647	16456	Mm.294882	NM_172647	ENSMUSG00000038235	F11r	9130004G24|AA638916|ESTM33|JAM|JAM-1|JAM-A|Jcam|Jcam1|Ly106	F11 receptor	protein-coding
mm_22000.1	chr2	167744118	167744127	-	1	NA	Intergenic	Intergenic	52945	NR_015500	329562	Mm.123101	NM_177851	ENSMUSG00000006462	A530013C23Rik	-	RIKEN cDNA A530013C23 gene	ncRNA
mm_148723.1	chr19	5846866	5846886	+	1	NA	Intergenic	Intergenic	-1396	NR_003513	66961	Mm.281895	NR_003513	ENSMUSG00000092274	Neat1	2310043N10Rik|VINC	nuclear paraspeckle assembly transcript 1 (non-protein coding)	ncRNA
mm_28335.1	chr3	89387133	89387148	-	1	NA	intron (NM_009565, intron 1 of 2)	intron (NM_009565, intron 1 of 2)	-4724	NR_040403	545539	Mm.393389	NR_040403	ENSMUSG00000074466	Gm15417	ENSMUSG00000074466|OTTMUSG00000021274	predicted gene 15417	ncRNA
mm_172324.1	chr7	106644627	106644627	-	1	NA	promoter-TSS (NM_001277183)	promoter-TSS (NM_001277183)	18	NM_001277179	434223	Mm.276443	NM_001277179		Gm1966	-	predicted gene 1966	protein-coding
mm_40541.1	chr5	58002725	58002736	+	1	NA	intron (NM_001310608, intron 3 of 3)	B3A|SINE|B2	284649	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_148955.1	chr19	7297725	7297733	+	1	NA	intron (NM_007928, intron 1 of 17)	intron (NM_007928, intron 1 of 17)	-2282	NM_001080390	13728	Mm.258986	NM_007928	ENSMUSG00000024969	Mark2	EMK-1|Emk|Par-1|Par-1b	MAP/microtubule affinity regulating kinase 2	protein-coding
mm_61774.1	chr7	83631975	83631981	+	1	NA	promoter-TSS (NM_023377)	promoter-TSS (NM_023377)	-39	NM_023377	170460	Mm.357953	NM_023377	ENSMUSG00000046027	Stard5	2310058G22Rik|AI607880|D7Ertd152e	StAR-related lipid transfer (START) domain containing 5	protein-coding
mm_128309.1	chr15	37792040	37792060	-	1	NA	promoter-TSS (NM_001170866)	promoter-TSS (NM_001170866)	-50	NM_001170866	52589	Mm.283370	NM_134094	ENSMUSG00000051359	Ncald	AI848120|D030020D09Rik|D15Ertd412e	neurocalcin delta	protein-coding
mm_122719.1	chr14	52279239	52279339	-	1	NA	5' UTR (NM_172601, exon 1 of 8)	5' UTR (NM_172601, exon 1 of 8)	106	NM_172601	76338	Mm.32870	NM_172601	ENSMUSG00000022159	Rab2b	1500012D09Rik|4930528G15Rik|A230002G14|D530043M21Rik	RAB2B, member RAS oncogene family	protein-coding
mm_147543.1	chr18	53861982	53861999	-	1	NA	promoter-TSS (NM_152809)	promoter-TSS (NM_152809)	-123	NM_152809	70425	Mm.368668	NM_152809	ENSMUSG00000073563	Csnk1g3	3300002K07Rik|C330049O21Rik	casein kinase 1, gamma 3	protein-coding
mm_162277.1	chr1	16661609	16661615	+	1	NA	intron (NR_037998, intron 3 of 3)	RLTR30D2_MM|LTR|ERV1	-3579	NM_027415	70397	Mm.194225	NM_026392	ENSMUSG00000025940	Tmem70	1110020A09Rik|2210416J16Rik	transmembrane protein 70	protein-coding
mm_86801.1	chr10	20312499	20312518	+	1	NA	promoter-TSS (NM_001025393)	promoter-TSS (NM_001025393)	39	NM_001025393	72567	Mm.294783	NM_153787	ENSMUSG00000037608	Bclaf1	2610102K23Rik|2700025J07Rik|2810454G14Rik|5730534O06Rik|AI450190|AW556225|Btf|mKIAA0164	BCL2-associated transcription factor 1	protein-coding
mm_58830.1	chr7	16781360	16781376	+	1	NA	promoter-TSS (NM_009201)	promoter-TSS (NM_009201)	22	NM_009201	20514	Mm.1056	NM_009201	ENSMUSG00000001918	Slc1a5	AAAT|ASCT2|ATBO|M7V1|M7VS1|R16|RDRC|Slc1a7	solute carrier family 1 (neutral amino acid transporter), member 5	protein-coding
mm_7501.1	chr1	121431017	121431027	-	1	NA	promoter-TSS (NM_029955)	promoter-TSS (NM_029955)	-45	NM_029955	70829	Mm.25788	NM_027567	ENSMUSG00000026339	Ccdc93	4633402D15Rik|9230102M16Rik	coiled-coil domain containing 93	protein-coding
mm_151204.1	chr19	53539704	53539718	+	1	NA	intron (NM_001085390, intron 3 of 3)	intron (NM_001085390, intron 3 of 3)	10393	NM_001085390	240672	Mm.482424	NM_001085390	ENSMUSG00000034765	Dusp5	Gm337	dual specificity phosphatase 5	protein-coding
mm_78103.1	chr9	19622298	19622331	+	1	NA	intron (NM_172918, intron 1 of 8)	intron (NM_172918, intron 1 of 8)	223	NM_172918	244713	Mm.67366	NM_172918	ENSMUSG00000057551	Zfp317	4932416G03|D230022C05Rik|KRAB9|Zfp67|Zfp75|mszf40	zinc finger protein 317	protein-coding
mm_35525.1	chr4	41275275	41275283	-	1	NA	promoter-TSS (NM_026872)	promoter-TSS (NM_026872)	-144	NM_026872	68926	Mm.41864	NM_026872	ENSMUSG00000028433	Ubap2	1190005K07Rik|AA408600|AU045235|UBAP-2|mKIAA1491	ubiquitin-associated protein 2	protein-coding
mm_122251.1	chr14	34015189	34015204	-	1	NA	Intergenic	Intergenic	-25882	NM_001034880	432838	Mm.318383	NM_001034880	ENSMUSG00000072624	Gm5460	EG432838	predicted gene 5460	protein-coding
mm_110740.1	chr12	69791312	69791323	-	1	NA	promoter-TSS (NM_183294)	promoter-TSS (NM_183294)	-610	NM_183294	71091	Mm.132325	NM_183294	ENSMUSG00000020990	Cdkl1	4933411O17Rik	cyclin-dependent kinase-like 1 (CDC2-related kinase)	protein-coding
mm_99157.1	chr11	100619218	100619283	+	1	NA	intron (NM_019795, intron 1 of 13)	CpG	918	NM_019795	56354	Mm.402409	NM_019795	ENSMUSG00000014195	Dnajc7	2010003F24Rik|2010004G07Rik|CCRP|Ttc2|mDj11|mTpr2	DnaJ heat shock protein family (Hsp40) member C7	protein-coding
mm_81548.1	chr9	110281343	110281352	+	1	NA	promoter-TSS (NR_105744)	promoter-TSS (NR_105744)	60	NR_105744	102465959		NR_105744	ENSMUSG00000098973	Mir6236	Gm27547|mmu-mir-6236	microRNA 6236	ncRNA
mm_40460.1	chr5	53609215	53609242	+	1	NA	intron (NM_001277116, intron 3 of 12)	B1F|SINE|Alu	18742	NM_001080927	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_60096.1	chr7	35119595	35119618	+	1	NA	exon (NM_001287514, exon 1 of 1)	exon (NM_001287514, exon 1 of 1)	313	NM_007678	12606	Mm.349667	NM_007678	ENSMUSG00000034957	Cebpa	C/ebpalpha|CBF-A|Cebp	CCAAT/enhancer binding protein (C/EBP), alpha	protein-coding
mm_108548.1	chr12	84409107	84409128	+	1	NA	promoter-TSS (NM_028377)	promoter-TSS (NM_028377)	49	NM_028377	72873	Mm.440428	NM_028377	ENSMUSG00000057265	Bbof1	2900006K08Rik|AI427784|Ccdc176	basal body orientation factor 1	protein-coding
mm_77755.1	chr8	128488576	128488592	-	1	NA	intron (NM_008737, intron 12 of 16)	intron (NM_008737, intron 12 of 16)	129343	NR_035436	100316680		NR_035436	ENSMUSG00000084523	Mir1903	Mirn1903|mmu-mir-1903	microRNA 1903	ncRNA
mm_162415.1	chr1	87620456	87620463	+	1	NA	non-coding (NR_122078, exon 1 of 28)	non-coding (NR_122078, exon 1 of 28)	147	NM_001110193	16331	Mm.15105	NM_010566	ENSMUSG00000026288	Inpp5d	SHIP|SHIP-1|SHIP1|SIP-145|p150Ship|s-SHIP	inositol polyphosphate-5-phosphatase D	protein-coding
mm_126832.1	chr15	88876934	88876935	+	1	NA	Intergenic	Intergenic	14740	NM_145478	223775	Mm.400129	NM_145478	ENSMUSG00000035828	Pim3	BC026639|Kid1	proviral integration site 3	protein-coding
mm_59426.1	chr7	27124933	27124971	+	1	NA	exon (NM_007817, exon 4 of 10)	exon (NM_007817, exon 4 of 10)	4997	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_14905.1	chr2	150311432	150311459	+	1	NA	intron (NM_027017, intron 3 of 3)	intron (NM_027017, intron 3 of 3)	51320	NM_027017	69277	Mm.272470	NM_027017	ENSMUSG00000063364	3300002I08Rik	2900016H11Rik	RIKEN cDNA 3300002I08 gene	protein-coding
mm_107489.1	chr12	38780818	38780854	+	1	NA	intron (NM_001347379, intron 1 of 11)	intron (NM_001347379, intron 1 of 11)	754	NM_007960	14009	Mm.4866	NM_007960	ENSMUSG00000004151	Etv1	ER81|Etsrp81	ets variant 1	protein-coding
mm_128131.1	chr15	31367528	31367580	-	1	NA	5' UTR (NM_001164441, exon 1 of 4)	5' UTR (NM_001164441, exon 1 of 4)	205	NM_001164441	67434	Mm.102470	NM_026153	ENSMUSG00000022237	Ankrd33b	0610012A05Rik|3021401C12Rik|5730557B15Rik	ankyrin repeat domain 33B	protein-coding
mm_26526.1	chr3	145988646	145988659	+	1	NA	exon (NM_001166064, exon 1 of 7)	exon (NM_001166064, exon 1 of 7)	782	NM_001166064	214804	Mm.268854	NM_001166064	ENSMUSG00000036863	Syde2	C430017H16Rik	synapse defective 1, Rho GTPase, homolog 2 (C. elegans)	protein-coding
mm_78582.1	chr9	37247714	37247760	+	1	NA	intron (NM_020258, intron 1 of 17)	intron (NM_020258, intron 1 of 17)	8001	NM_020258	56857	Mm.440037	NM_020258	ENSMUSG00000032122	Slc37a2	G3PP|Slc37a1|cI-2|ci2	solute carrier family 37 (glycerol-3-phosphate transporter), member 2	protein-coding
mm_31278.1	chr4	45804868	45804890	+	1	NA	TTS (NM_028270)	TTS (NM_028270)	5857	NM_028270	72535	Mm.331583	NM_028270	ENSMUSG00000035561	Aldh1b1	2700007F14Rik	aldehyde dehydrogenase 1 family, member B1	protein-coding
mm_156236.1	chrX	136139001	136139009	+	1	NA	promoter-TSS (NM_212457)	promoter-TSS (NM_212457)	-40	NM_212457	406217	Mm.336245	NM_212457	ENSMUSG00000047844	Bex4	-	brain expressed X-linked 4	protein-coding
mm_131936.1	chr16	23613288	23613319	+	1	NA	exon (NM_023386, exon 2 of 2)	exon (NM_023386, exon 2 of 2)	3384	NM_023386	67775	Mm.475107	NM_023386	ENSMUSG00000033355	Rtp4	5830458K16Rik|Ifrg28	receptor transporter protein 4	protein-coding
mm_163670.1	chr13	80884921	80884952	+	1	NA	intron (NM_001042591, intron 1 of 7)	intron (NM_001042591, intron 1 of 7)	1514	NM_001042591	105171	Mm.423137	NM_001042591	ENSMUSG00000074794	Arrdc3	AI450344|mKIAA1376	arrestin domain containing 3	protein-coding
mm_50954.1	chr6	58831552	58831566	+	1	NA	Intergenic	CpG	-2141	NM_028705	73998	Mm.191892	NM_028705	ENSMUSG00000029804	Herc3	5730409F18Rik|AI646603|mKIAA0032	hect domain and RLD 3	protein-coding
mm_149529.1	chr19	12461090	12461101	+	1	NA	5' UTR (NM_010821, exon 2 of 2)	5' UTR (NM_010821, exon 2 of 2)	316	NM_010821	17476	Mm.3999	NM_010821	ENSMUSG00000046805	Mpeg1	MPS1|Mpg-1	macrophage expressed gene 1	protein-coding
mm_140715.1	chr17	15329925	15329934	-	1	NA	Intergenic	Intergenic	24532	NR_033511	100038481	Mm.387544	NR_033511		Gm10510	ENSMUSG00000073453	predicted gene 10510	ncRNA
mm_9717.1	chr1	179803607	179803624	-	1	NA	5' UTR (NM_026375, exon 1 of 36)	5' UTR (NM_026375, exon 1 of 36)	400	NM_026375	226747	Mm.128165	NM_026375	ENSMUSG00000026491	Ahctf1	6230412P20Rik|AV011447|Elys	AT hook containing transcription factor 1	protein-coding
mm_132279.1	chr16	33056457	33056495	+	1	NA	promoter-TSS (NM_021338)	promoter-TSS (NM_021338)	-6	NM_001130484	57808	Mm.19355	NM_021338	ENSMUSG00000060636	Rpl35a	2810431L15Rik|Rpl35	ribosomal protein L35A	protein-coding
mm_104654.1	chr11	97575240	97575256	-	1	NA	promoter-TSS (NM_018873)	promoter-TSS (NM_018873)	-122	NM_018873	56013	Mm.342665	NM_018873	ENSMUSG00000038453	Srcin1	P140|SNIP|mKIAA1684|p140Cap	SRC kinase signaling inhibitor 1	protein-coding
mm_125931.1	chr15	76247527	76247541	+	1	NA	promoter-TSS (NR_105918)	promoter-TSS (NR_105918)	-657	NR_105918	102465575		NR_105918	ENSMUSG00000098625	Mir6953	Gm27738|mmu-mir-6953	microRNA 6953	ncRNA
mm_39214.1	chr4	156084304	156084329	-	1	NA	Intergenic	Intergenic	-24514	NR_132444	100415901	Mm.437006	NR_132444	ENSMUSG00000086549	Gm13648	OTTMUSG00000013217	predicted gene 13648	ncRNA
mm_109070.1	chr12	104345412	104345417	+	1	NA	exon (NM_011458, exon 5 of 5)	exon (NM_011458, exon 5 of 5)	6928	NM_011458	20714	Mm.291569	NM_011458	ENSMUSG00000058207	Serpina3k	1300001I07Rik|D12Rp54|MMCM2|MMSpi2|RP54|Spi-2|Spi2|contrapsin	serine (or cysteine) peptidase inhibitor, clade A, member 3K	protein-coding
mm_8994.1	chr1	165709719	165709742	-	1	NA	Intergenic	Intergenic	-1636	NM_001038846	226594	Mm.265552	NM_178593	ENSMUSG00000040723	Rcsd1	A430105K13Rik|BC025872|CapZIP	RCSD domain containing 1	protein-coding
mm_57003.1	chr6	121031641	121031643	-	1	NA	intron (NR_138097, intron 9 of 18)	ORR1D1-int|LTR|ERVL-MaLR	-32822	NR_138098	100043793	Mm.448053	NR_138098		Gm4651	-	predicted gene 4651	ncRNA
mm_15359.1	chr2	156401403	156401438	+	1	NA	Intergenic	Intergenic	-8441	NR_024329	347740	Mm.324242	NR_024329		2900097C17Rik	1810005K14Rik|4930563C06Rik	RIKEN cDNA 2900097C17 gene	ncRNA
mm_108157.1	chr12	76329058	76329070	+	1	NA	exon (NM_001101471, exon 2 of 2)	exon (NM_001101471, exon 2 of 2)	4173	NM_001101471	238276	Mm.311452	NM_001101471	ENSMUSG00000021057	Akap5	3526401B18Rik|AKAP 150|AKAP-5|AKAP150|BB098886|Gm258|P150	A kinase (PRKA) anchor protein 5	protein-coding
mm_50603.1	chr6	49263237	49263257	+	1	NA	intron (NM_001347209, intron 1 of 7)	CpG	805	NM_001347209	101214	Mm.196598	NM_198102	ENSMUSG00000029817	Tra2a	1500010G04Rik|AL022798|G430041M01Rik|mAWMS1	transformer 2 alpha homolog (Drosophila)	protein-coding
mm_105237.1	chr11	102318037	102318061	-	1	NA	promoter-TSS (NM_001044383)	promoter-TSS (NM_001044383)	-762	NM_001044383	21429	Mm.2845	NM_011551	ENSMUSG00000020923	Ubtf	A930005G04Rik|NOR-90|Tcfubf|UBF|UBF-1|UBF1	upstream binding transcription factor, RNA polymerase I	protein-coding
mm_37054.1	chr4	116018137	116018147	-	1	NA	promoter-TSS (NM_010173)	promoter-TSS (NM_010173)	-240	NM_010173	14073	Mm.256025	NM_010173	ENSMUSG00000034171	Faah	AW412498	fatty acid amide hydrolase	protein-coding
mm_10417.1	chr2	13580122	13580156	+	1	NA	exon (NM_011701, exon 6 of 9)	exon (NM_011701, exon 6 of 9)	5828	NM_011701	22352	Mm.268000	NM_011701	ENSMUSG00000026728	Vim	-	vimentin	protein-coding
mm_163264.1	chr11	113684519	113684525	+	1	NA	promoter-TSS (NM_138598)	promoter-TSS (NM_138598)	110	NM_177777	276852	Mm.239566	NM_177777	ENSMUSG00000041623	D11Wsu47e	-	DNA segment, Chr 11, Wayne State University 47, expressed	protein-coding
mm_47963.1	chr5	135735323	135735328	-	1	NA	TTS (NM_172541)	TTS (NM_172541)	564	NR_106001	102466791		NR_106001	ENSMUSG00000099197	Mir7034	Gm27372|mmu-mir-7034	microRNA 7034	ncRNA
mm_163673.1	chr13	83042440	83042455	+	1	NA	Intergenic	Intergenic	-344114	NR_039537	100628621		NR_039537	ENSMUSG00000106655	Mir3961	mmu-mir-3961	microRNA 3961	ncRNA
mm_136949.1	chr17	14595888	14595892	+	1	NA	Intergenic	Intergenic	98372	NM_011581	21826	Mm.26688	NM_011581	ENSMUSG00000023885	Thbs2	TSP2|Thbs-2	thrombospondin 2	protein-coding
mm_14474.1	chr2	131495671	131495675	+	1	NA	intron (NM_001177836, intron 1 of 7)	intron (NM_001177836, intron 1 of 7)	3811	NM_001177838	228608	Mm.136586	NM_145533	ENSMUSG00000027333	Smox	B130066H01Rik|PAO|PAOh1|SMO	spermine oxidase	protein-coding
mm_59048.1	chr7	19361208	19361262	+	1	NA	promoter-TSS (NM_001010836)	promoter-TSS (NM_001010836)	19	NM_001010836	333654	Mm.333640	NM_001010836	ENSMUSG00000040734	Ppp1r13l	AV260376|IASPP|Nkip1|wa3	protein phosphatase 1, regulatory (inhibitor) subunit 13 like	protein-coding
mm_165008.1	chr19	24556145	24556155	-	1	NA	promoter-TSS (NM_008846)	promoter-TSS (NM_008846)	-323	NM_008846	18719	Mm.217214	NM_008846	ENSMUSG00000024867	Pip5k1b	PI4P5K-I[b]|PIP5K1-beta|PIP5KIbeta|Pipk5b|STM7	phosphatidylinositol-4-phosphate 5-kinase, type 1 beta	protein-coding
mm_41476.1	chr5	91962441	91962445	+	1	NA	promoter-TSS (NR_028429)	promoter-TSS (NR_028429)	113	NR_073442	68098	Mm.159453	NM_026557	ENSMUSG00000029397	Rchy1	ARNIP|CHIMP|Pirh2|Zfp363|Znf363	ring finger and CHY zinc finger domain containing 1	protein-coding
mm_152420.1	chr19	10673734	10673745	-	1	NA	exon (NM_021453, exon 5 of 9)	exon (NM_021453, exon 5 of 9)	4332	NM_021453	58803	Mm.34037	NM_021453	ENSMUSG00000024738	Pga5	1110035E17Rik|Pepf	pepsinogen 5, group I	protein-coding
mm_152578.1	chr19	11602189	11602204	-	1	NA	intron (NM_026835, intron 2 of 6)	intron (NM_026835, intron 2 of 6)	2608	NM_026835	68774	Mm.290390	NM_026835	ENSMUSG00000024679	Ms4a6d	1110058E16Rik|AI447446|Ms4a11	membrane-spanning 4-domains, subfamily A, member 6D	protein-coding
mm_150980.1	chr19	46502881	46502912	+	1	NA	exon (NM_053100, exon 1 of 6)	exon (NM_053100, exon 1 of 6)	1248	NM_053100	93679	Mm.392177	NM_053100	ENSMUSG00000025034	Trim8	AA408830|BB006755|GERP|Rnf27	tripartite motif-containing 8	protein-coding
mm_160258.1	chr7	108422547	108422547	+	1	NA	promoter-TSS (NM_146738)	promoter-TSS (NM_146738)	-26	NM_146738	258733	Mm.377663	NM_146738	ENSMUSG00000095239	Olfr497	MOR204-9	olfactory receptor 497	protein-coding
mm_162364.1	chr1	65061844	65061844	+	1	NA	TTS (NM_007776)	TTS (NM_007776)	1596	NM_007776	12967	Mm.425031	NM_007776	ENSMUSG00000067299	Crygd	Aey4|Cryg-1|DGcry-1|Lop12	crystallin, gamma D	protein-coding
mm_40940.1	chr5	76677296	76677305	+	1	NA	Intergenic	Intergenic	85586	NM_199032	381644	Mm.332452	NM_199032	ENSMUSG00000036403	Cep135	BC062951|Cep4|Gm1044	centrosomal protein 135	protein-coding
mm_144387.1	chr18	20667711	20667721	+	1	NA	intron (NM_013697, intron 2 of 3)	B4A|SINE|B4	2466	NM_013697	22139	Mm.2108	NM_013697	ENSMUSG00000061808	Ttr	AA408768|AI787086|D17860|prealbumin	transthyretin	protein-coding
mm_74135.1	chr8	123212858	123212911	+	1	NA	promoter-TSS (NM_145606)	promoter-TSS (NM_145606)	26	NM_177279	320869	Mm.258354	NM_177279	ENSMUSG00000048478	Spata33	4732415M23Rik|AI847264	spermatogenesis associated 33	protein-coding
mm_71639.1	chr8	57511834	57511869	+	1	NA	promoter-TSS (NM_008252)	promoter-TSS (NM_008252)	8	NM_008252	97165	Mm.276881	NM_008252	ENSMUSG00000054717	Hmgb2	C80539|HMG-2|Hmg2	high mobility group box 2	protein-coding
mm_105991.1	chr11	115628126	115628164	-	1	NA	5' UTR (NM_001252384, exon 1 of 8)	5' UTR (NM_001252384, exon 1 of 8)	150	NM_001252394	67283	Mm.383426	NM_026071	ENSMUSG00000020744	Slc25a19	2900089E13Rik|DNC|MUP1|TPC	solute carrier family 25 (mitochondrial thiamine pyrophosphate carrier), member 19	protein-coding
mm_107760.1	chr12	59071807	59071830	+	1	NA	exon (NM_008891, exon 9 of 9)	exon (NM_008891, exon 9 of 9)	4899	NM_008891	18949	Mm.22347	NM_008891	ENSMUSG00000020994	Pnn	AU045199|D12Ertd512e	pinin	protein-coding
mm_113573.1	chr13	40321434	40321442	+	1	NA	Intergenic	Intergenic	-33427	NM_172143	218165	Mm.364096	NM_172143	ENSMUSG00000047094	Ofcc1	opo	orofacial cleft 1 candidate 1	protein-coding
mm_128744.1	chr15	64312794	64312814	-	1	NA	promoter-TSS (NM_001276463)	promoter-TSS (NM_001276463)	-131	NM_001276463	13196	Mm.277236	NM_010026	ENSMUSG00000022377	Asap1	AV239055|DEF-1|Ddef1|PAP|mKIAA1249|s19	ArfGAP with SH3 domain, ankyrin repeat and PH domain1	protein-coding
mm_92014.1	chr10	62342664	62342672	-	1	NA	intron (NR_038038, intron 1 of 1)	MIRc|SINE|MIR	2061	NR_038038	70162	Mm.441212	NR_038038		Hk1os	2210417K05Rik	hexokinase 1, opposite strand	ncRNA
mm_158802.1	chrX	167254623	167254625	-	1	NA	intron (NM_001313761, intron 1 of 2)	intron (NM_001313761, intron 1 of 2)	9705	NM_001313761	170744	Mm.196676	NM_133212	ENSMUSG00000040522	Tlr8	-	toll-like receptor 8	protein-coding
mm_117298.1	chr13	67061132	67061178	-	1	NA	promoter-TSS (NM_001166218)	promoter-TSS (NM_001166218)	15	NM_001166218	78251	Mm.297247	NM_001166218	ENSMUSG00000090641	Zfp712	4921504N20Rik|mszf31|mszf89	zinc finger protein 712	protein-coding
mm_88738.1	chr10	80265036	80265086	+	1	NA	promoter-TSS (NM_133188)	promoter-TSS (NM_133188)	70	NM_133188	70248	Mm.148693	NM_133188	ENSMUSG00000069565	Dazap1	2410042M16Rik|mPrrp	DAZ associated protein 1	protein-coding
mm_125118.1	chr15	28823514	28823516	+	1	NA	Intergenic	Intergenic	619749	NM_133365	110082	Mm.248464	NM_133365	ENSMUSG00000022262	Dnah5	AU022615|Dnahc5|Mdnah5|b2b1134Clo|b2b1154Clo|b2b1537Clo|b2b1565Clo|b2b601Clo|mKIAA1603	dynein, axonemal, heavy chain 5	protein-coding
mm_165570.1	chr3	19561780	19561784	+	1	NA	intron (NM_025489, intron 2 of 4)	intron (NM_025489, intron 2 of 4)	30535	NM_001163537	66326	Mm.45615	NM_025489	ENSMUSG00000027606	Dnajc5b	1700008A05Rik	DnaJ heat shock protein family (Hsp40) member C5 beta	protein-coding
mm_17041.1	chr2	20673360	20673369	-	1	NA	intron (NM_029895, intron 4 of 18)	intron (NM_029895, intron 4 of 18)	153851	NM_001177631	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding
mm_94546.1	chr11	10292214	10292215	+	1	NA	Intergenic	Intergenic	-821802	NM_177033	319922	Mm.337851	NM_177033	ENSMUSG00000050830	Vwc2	A930041G11Rik|G11|PSST739|UNQ739|cradin	von Willebrand factor C domain containing 2	protein-coding
mm_147383.1	chr18	43737504	43737511	-	1	NA	promoter-TSS (NM_009258)	promoter-TSS (NM_009258)	-270	NM_009258	20730	Mm.272	NM_009258	ENSMUSG00000024503	Spink1	Spink3|p12	serine peptidase inhibitor, Kazal type 1	protein-coding
mm_160843.1	chr11	50603398	50603398	+	1	NA	exon (NM_175643, exon 2 of 22)	exon (NM_175643, exon 2 of 22)	1313	NM_175643	216725	Mm.110597	NM_175643	ENSMUSG00000036545	Adamts2	ADAM-TS 2|ADAM-TS2|ADAMTS-2|PC I-NP|PCINP|pNPI	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 2	protein-coding
mm_49226.1	chr6	15794442	15794459	+	1	NA	intron (NM_175088, intron 4 of 4)	T-rich|Low_complexity|Low_complexity	73789	NM_175088	16543	Mm.1314	NM_175088	ENSMUSG00000041390	Mdfic	Kdt1|Mdfid	MyoD family inhibitor domain containing	protein-coding
mm_83885.1	chr9	55470301	55470303	-	1	NA	intron (NM_145615, intron 9 of 11)	intron (NM_145615, intron 9 of 11)	41941	NM_145615	110842	Mm.290853	NM_145615	ENSMUSG00000032314	Etfa	2010200I21Rik|D9Ertd394e	electron transferring flavoprotein, alpha polypeptide	protein-coding
mm_118495.1	chr14	13284802	13284827	+	1	NA	promoter-TSS (NM_028052)	promoter-TSS (NM_028052)	34	NM_028052	72003	Mm.317515	NM_028052	ENSMUSG00000056296	Synpr	1500003F20Rik|SPO	synaptoporin	protein-coding
mm_125887.1	chr15	75863229	75863238	+	1	NA	intron (NM_026960, intron 1 of 10)	intron (NM_026960, intron 1 of 10)	894	NM_026960	69146	Mm.27385	NM_026960	ENSMUSG00000022575	Gsdmd	1810036L03Rik|AW558049|DF5L|Dfna5l|Gsdmdc1|M2-4	gasdermin D	protein-coding
mm_27096.1	chr3	30211323	30211327	-	1	NA	Intergenic	Intergenic	-198121	NM_007963	14013	Mm.56965	NM_007963	ENSMUSG00000027684	Mecom	D630039M04Rik|Evi-1|Evi1|Jbo|Mds|Mds1|Mds1-Evi1|Prdm3|Znfpr1b1	MDS1 and EVI1 complex locus	protein-coding
mm_7234.1	chr1	93441863	93441863	-	1	NA	intron (NM_001301364, intron 2 of 27)	intron (NM_001301364, intron 2 of 27)	3838	NM_001301364	110611	Mm.30012	NM_133808	ENSMUSG00000034088	Hdlbp	1110005P14Rik|AA960365|AI118566|D1Ertd101e	high density lipoprotein (HDL) binding protein	protein-coding
mm_134038.1	chr16	5050782	5050795	-	1	NA	promoter-TSS (NM_028720)	promoter-TSS (NM_028720)	720	NM_026666	170644	Mm.66356	NM_026666	ENSMUSG00000039473	Ubn1	1110029L11Rik|2610108L02Rik|AA673476|AW124741	ubinuclein 1	protein-coding
mm_47856.1	chr5	134552454	134552476	-	1	NA	promoter-TSS (NM_001039162)	promoter-TSS (NM_001039162)	-31	NM_009990	269713	Mm.255138	NM_009990	ENSMUSG00000063146	Clip2	B230327O20|CLIP-115|Clip1|Cyln2|WSCR4|mKIAA0291|wbscr4	CAP-GLY domain containing linker protein 2	protein-coding
mm_150877.1	chr19	45076106	45076111	+	1	NA	promoter-TSS (NM_178929)	promoter-TSS (NM_178929)	-31	NM_178929	107250	Mm.24417	NM_178929	ENSMUSG00000025213	Kazald1	AI842353|Bono1|IGFBP-rP10	Kazal-type serine peptidase inhibitor domain 1	protein-coding
mm_164023.1	chr14	75184892	75184898	+	1	NA	intron (NM_008879, intron 2 of 16)	intron (NM_008879, intron 2 of 16)	48470	NM_008879	18826	Mm.153911	NM_008879	ENSMUSG00000021998	Lcp1	AW536232|D14Ertd310e|LCP-1|Pls2|pp65	lymphocyte cytosolic protein 1	protein-coding
mm_30778.1	chr4	19280863	19280907	+	1	NA	promoter-TSS (NM_013927)	promoter-TSS (NM_013927)	35	NM_013927	30952	Mm.445778	NM_013927	ENSMUSG00000056494	Cngb3	CCNC2|CNG6|Cngbeta2	cyclic nucleotide gated channel beta 3	protein-coding
mm_93657.1	chr10	117690222	117690232	-	1	NA	exon (NM_010786, exon 12 of 12)	exon (NM_010786, exon 12 of 12)	20531	NM_010786	17246	Mm.22670	NM_010786	ENSMUSG00000020184	Mdm2	1700007J15Rik|AA415488|Mdm-2	transformed mouse 3T3 cell double minute 2	protein-coding
mm_116576.1	chr13	47105522	47105524	-	1	NA	intron (NM_025900, intron 2 of 10)	intron (NM_025900, intron 2 of 10)	698	NM_025900	110052	Mm.131150	NM_025900	ENSMUSG00000021377	Dek	1810019E15Rik|D13H6S231E	DEK oncogene (DNA binding)	protein-coding
mm_64515.1	chr7	143823397	143823399	+	1	NA	promoter-TSS (NM_030221)	promoter-TSS (NM_030221)	231	NM_007856	13360	Mm.249342	NM_007856	ENSMUSG00000058454	Dhcr7	AA409147	7-dehydrocholesterol reductase	protein-coding
mm_136728.1	chr17	8245055	8245092	+	1	NA	promoter-TSS (NM_001190338)	promoter-TSS (NM_001190338)	15	NM_001190338	12458	Mm.8007	NM_009835	ENSMUSG00000040899	Ccr6	CC-CKR-6|CCR-6|Cmkbr6|KY411	chemokine (C-C motif) receptor 6	protein-coding
mm_106506.1	chr11	120453457	120453469	-	1	NA	promoter-TSS (NM_012065)	promoter-TSS (NM_012065)	37	NR_126089	18588	Mm.39200	NM_012065	ENSMUSG00000025386	Pde6g	Pdeg|p3AT	phosphodiesterase 6G, cGMP-specific, rod, gamma	protein-coding
mm_88232.1	chr10	71131541	71131561	+	1	NA	intron (NM_031397, intron 1 of 20)	intron (NM_031397, intron 1 of 20)	28139	NM_031397	83675	Mm.286834	NM_031397	ENSMUSG00000014329	Bicc1	Bic-C|bpk|jcpk	BicC family RNA binding protein 1	protein-coding
mm_11073.1	chr2	27677215	27677229	+	1	NA	promoter-TSS (NM_011305)	promoter-TSS (NM_011305)	21	NM_011305	20181	Mm.24624	NM_011305	ENSMUSG00000015846	Rxra	9530071D11Rik|Nr2b1|RXRalpha1	retinoid X receptor alpha	protein-coding
mm_133016.1	chr16	56204326	56204338	+	1	NA	promoter-TSS (NM_174876)	promoter-TSS (NM_174876)	19	NM_174876	224224	Mm.151998	NM_174876	ENSMUSG00000035270	Impg2	IPM200|PG10.2|Rsbp|Spacrcan	interphotoreceptor matrix proteoglycan 2	protein-coding
mm_95739.1	chr11	54691509	54691521	+	1	NA	exon (NM_001252494, exon 27 of 29)	exon (NM_001252494, exon 27 of 29)	95369	NM_001252497	192786	Mm.254404	NM_175258	ENSMUSG00000037533	Rapgef6	A530068K01|AI844632|BB085664|C030018K18Rik|PDZ-GEF2|Pdzgef2|RA-GEF-2|Ragef2|mKIAA4052	Rap guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_172387.1	chr7	133328825	133328831	-	1	NA	Intergenic	RMER19C|LTR|ERVK	200577	NR_046279	74970	Mm.491044	NR_046279	ENSMUSG00000109816	4930483O08Rik	-	RIKEN cDNA 4930483O08 gene	ncRNA
mm_51801.1	chr6	88724451	88724461	+	1	NA	promoter-TSS (NM_001166251)	promoter-TSS (NM_001166251)	44	NM_011844	23945	Mm.272197	NM_011844	ENSMUSG00000033174	Mgll	AA589436|Magl|Mgl	monoglyceride lipase	protein-coding
mm_48045.1	chr5	136458462	136458480	-	1	NA	intron (NM_001291239, intron 2 of 22)	intron (NM_001291239, intron 2 of 22)	-82668	NR_030500	723975		NR_030500	ENSMUSG00000106479	Mir721	Mirn721|miRY|mir-721|mmu-mir-721	microRNA 721	ncRNA
mm_44404.1	chr5	17847773	17847790	-	1	NA	intron (NM_001159558, intron 1 of 15)	intron (NM_001159558, intron 1 of 15)	2011	NM_001159557	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_129342.1	chr15	77842089	77842123	-	1	NA	promoter-TSS (NM_022410)	promoter-TSS (NM_022410)	69	NM_022410	17886	Mm.29677	NM_022410	ENSMUSG00000022443	Myh9	Fltn|Myhn-1|Myhn1|NMHCIIA|NMMHC-A|NMMHC-IIA|TU72.6	myosin, heavy polypeptide 9, non-muscle	protein-coding
mm_132582.1	chr16	38353099	38353139	+	1	NA	TTS (NM_001017429)	TTS (NM_001017429)	6120	NM_001017429	12856	Mm.27396	NM_001017429	ENSMUSG00000046516	Cox17	AI037035	cytochrome c oxidase assembly protein 17	protein-coding
mm_91724.1	chr10	44602168	44602193	-	1	NA	Intergenic	Intergenic	-143432	NM_007548	12142	Mm.4800	NM_007548	ENSMUSG00000038151	Prdm1	Blimp-1|Blimp1|PRDI-BF1|ZNFPR1A1|b2b1765Clo	PR domain containing 1, with ZNF domain	protein-coding
mm_158163.1	chrX	103483035	103483042	-	1	NA	non-coding (NR_002844, exon 4 of 4)	non-coding (NR_002844, exon 4 of 4)	195	NR_001570	213742	Mm.274770	NR_001463	ENSMUSG00000086503	Xist	A430022B11|AI314753	inactive X specific transcripts	ncRNA
mm_66007.1	chr7	30563188	30563229	-	1	NA	promoter-TSS (NM_025498)	promoter-TSS (NM_025498)	-24	NM_025498	66340	Mm.86557	NM_025498	ENSMUSG00000036835	Psenen	1700023M09Rik|Pen-2	presenilin enhancer gamma secretase subunit	protein-coding
mm_10183.1	chr2	4881488	4881571	+	1	NA	promoter-TSS (NM_175400)	promoter-TSS (NM_175400)	-35	NM_175400	109079	Mm.34329	NM_175400	ENSMUSG00000026662	Sephs1	1110046B24Rik|AA589574|AI505014|AW111620|SELD|SPS|SPS1	selenophosphate synthetase 1	protein-coding
mm_98684.1	chr11	96292154	96292159	+	1	NA	intron (NR_131758, intron 2 of 2)	intron (NR_131758, intron 2 of 2)	5510	NM_010460	15415	Mm.390366	NM_010460	ENSMUSG00000038721	Hoxb7	AI325018|Hox-2.3	homeobox B7	protein-coding
mm_6164.1	chr1	65061922	65061926	-	1	NA	TTS (NM_007776)	TTS (NM_007776)	1516	NM_007776	12967	Mm.425031	NM_007776	ENSMUSG00000067299	Crygd	Aey4|Cryg-1|DGcry-1|Lop12	crystallin, gamma D	protein-coding
mm_171489.1	chr4	146101701	146101702	+	1	NA	intron (NM_001037926, intron 1 of 3)	intron (NM_001037926, intron 1 of 3)	4389	NM_001037926	626316	Mm.270762	NM_001037926	ENSMUSG00000066009	Zfp987	Gm13051|OTTMUSG00000010104|OTTMUSG00000010173	zinc finger protein 987	protein-coding
mm_121200.1	chr14	103051859	103051876	+	1	NA	intron (NM_008392, intron 4 of 4)	intron (NM_008392, intron 4 of 4)	4855	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_65860.1	chr7	29344901	29344916	-	1	NA	intron (NM_001081028, intron 16 of 22)	intron (NM_001081028, intron 16 of 22)	40903	NM_013874	29861	Mm.101885	NM_013874	ENSMUSG00000030584	Dpf1	Neud4	D4, zinc and double PHD fingers family 1	protein-coding
mm_78496.1	chr9	32728561	32728595	+	1	NA	intron (NM_011808, intron 1 of 7)	intron (NM_011808, intron 1 of 7)	32536	NM_001038642	23871	Mm.292415	NM_011808	ENSMUSG00000032035	Ets1	AI196000|AI448617|D230050P06|Ets-1|Tpl1|vs	E26 avian leukemia oncogene 1, 5' domain	protein-coding
mm_104705.1	chr11	97999374	97999389	-	1	NA	Intergenic	Intergenic	-3208	NM_207231	217151	Mm.277896	NM_207231	ENSMUSG00000038352	Arl5c	Arl12|BC065791	ADP-ribosylation factor-like 5C	protein-coding
mm_126306.1	chr15	79527738	79527745	+	1	NA	TTS (NM_134090)	TTS (NM_134090)	5176	NM_152806	67040	Mm.29644	NM_152806	ENSMUSG00000055065	Ddx17	2610007K22Rik|A430025E01Rik|AI047725|C80929|Gm926|p72	DEAD (Asp-Glu-Ala-Asp) box polypeptide 17	protein-coding
mm_23007.1	chr3	34158727	34158728	+	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-77373	NM_026332	67713	Mm.274266	NM_026332	ENSMUSG00000027679	Dnajc19	1810055D05Rik|AA959924|Tim14	DnaJ heat shock protein family (Hsp40) member C19	protein-coding
mm_148933.1	chr19	7018753	7018769	+	1	NA	exon (NM_153795, exon 2 of 15)	exon (NM_153795, exon 2 of 15)	708	NM_153795	108101	Mm.157591	NM_153795	ENSMUSG00000024965	Fermt3	C79673|Kindlin3	fermitin family member 3	protein-coding
mm_131425.1	chr16	14708310	14708334	+	1	NA	3' UTR (NM_011415, exon 3 of 3)	3' UTR (NM_011415, exon 3 of 3)	2463	NM_011415	20583	Mm.4272	NM_011415	ENSMUSG00000022676	Snai2	Slug|Slugh|Snail2	snail family zinc finger 2	protein-coding
mm_161006.1	chr11	117782885	117782885	+	1	NA	intron (NM_001195088, intron 1 of 15)	intron (NM_001195088, intron 1 of 15)	227	NM_001195088	217356	Mm.116675	NM_181856	ENSMUSG00000050106	Tmc8	EVIN2|Ever2|mFLJ00400	transmembrane channel-like gene family 8	protein-coding
mm_98236.1	chr11	88099285	88099311	+	1	NA	non-coding (NR_045499, exon 4 of 4)	non-coding (NR_045499, exon 4 of 4)	152	NM_198013	103841	Mm.374846	NM_198013	ENSMUSG00000018378	Cuedc1	AI841487|C330016O16Rik	CUE domain containing 1	protein-coding
mm_113286.1	chr13	30166358	30166371	+	1	NA	intron (NM_153546, intron 1 of 12)	intron (NM_153546, intron 1 of 12)	29874	NM_153546	218121	Mm.89682	NM_153546	ENSMUSG00000038732	Mboat1	9130215M02Rik|BC023845|LPEAT1|Moact1|Oact1	membrane bound O-acyltransferase domain containing 1	protein-coding
mm_75344.1	chr8	43307043	43307047	-	1	NA	promoter-TSS (NM_009556)	promoter-TSS (NM_009556)	-36	NM_009556	22702	Mm.285848	NM_009556	ENSMUSG00000051176	Zfp42	Rex-1|Rex1|Zfp-42	zinc finger protein 42	protein-coding
mm_99545.1	chr11	103344766	103344812	+	1	NA	promoter-TSS (NM_133715)	promoter-TSS (NM_133715)	36	NR_045346	653030	Mm.440684	NR_045346	ENSMUSG00000085887	Arhgap27os3	F830206d12rik|Gm11648|OTTMUSG00000003073	Rho GTPase activating protein 27, opposite strand 3	ncRNA
mm_155162.1	chrX	52988156	52988199	+	1	NA	promoter-TSS (NM_013556)	promoter-TSS (NM_013556)	99	NM_013556	15452	Mm.299381	NM_013556	ENSMUSG00000025630	Hprt	C81579|HPGRT|Hprt1	hypoxanthine guanine phosphoribosyl transferase	protein-coding
mm_84108.1	chr9	58313176	58313186	-	1	NA	promoter-TSS (NM_010729)	promoter-TSS (NM_010729)	31	NM_010729	16949	Mm.250492	NM_010729	ENSMUSG00000032334	Loxl1	Loxl	lysyl oxidase-like 1	protein-coding
mm_40708.1	chr5	65863564	65863650	+	1	NA	promoter-TSS (NM_001081105)	promoter-TSS (NM_001081105)	38	NM_001081105	74734	Mm.20323	NM_001081105	ENSMUSG00000029204	Rhoh	5830400A04Rik|AU019774|Arhh	ras homolog family member H	protein-coding
mm_134016.1	chr16	4879850	4879864	-	1	NA	promoter-TSS (NM_145359)	promoter-TSS (NM_145359)	-6	NM_145359	207740	Mm.268895	NM_145359	ENSMUSG00000039568	Ubald1	1500031H01Rik|BC013706|Fam100a	UBA-like domain containing 1	protein-coding
mm_38742.1	chr4	145261406	145261419	-	1	NA	Intergenic	Intergenic	-14542	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_55797.1	chr6	82754034	82754054	-	1	NA	intron (NM_013820, intron 2 of 17)	intron (NM_013820, intron 2 of 17)	20410	NM_013820	15277	Mm.255848	NM_013820	ENSMUSG00000000628	Hk2	AI642394|HKII	hexokinase 2	protein-coding
mm_90831.1	chr10	8290225	8290229	-	1	NA	intron (NM_177387, intron 5 of 7)	intron (NM_177387, intron 5 of 7)	228598	NM_177387	338362	Mm.41163	NM_177387	ENSMUSG00000047712	Ust	D930010O20Rik|UA2OST	uronyl-2-sulfotransferase	protein-coding
mm_126235.1	chr15	78967498	78967500	+	1	NA	exon (NM_001039155, exon 8 of 8)	exon (NM_001039155, exon 8 of 8)	-15557	NM_001024716	110253	Mm.123714	NM_138579	ENSMUSG00000033088	Triobp	AI428493|EST478828|Tara|mKIAA1662	TRIO and F-actin binding protein	protein-coding
mm_93230.1	chr10	95323533	95323545	-	1	NA	5' UTR (NM_001330138, exon 1 of 3)	5' UTR (NM_001330138, exon 1 of 3)	170	NM_001330138	12905	Mm.473739	NM_009950	ENSMUSG00000045867	Cradd	RAIDD	CASP2 and RIPK1 domain containing adaptor with death domain	protein-coding
mm_12146.1	chr2	61804758	61804766	+	1	NA	exon (NM_009322, exon 1 of 6)	exon (NM_009322, exon 1 of 6)	309	NM_009322	21375	Mm.308525	NM_009322	ENSMUSG00000035033	Tbr1	-	T-box brain gene 1	protein-coding
mm_150094.1	chr19	29454483	29454504	+	1	NA	exon (NM_021396, exon 5 of 6)	exon (NM_021396, exon 5 of 6)	43574	NM_021396	58205	Mm.116737	NM_021396	ENSMUSG00000016498	Pdcd1lg2	B7-DC|Btdc|F730015O22Rik|PD-L2	programmed cell death 1 ligand 2	protein-coding
mm_106547.1	chr11	120579372	120579395	-	1	NA	exon (NM_133796, exon 6 of 6)	exon (NM_133796, exon 6 of 6)	2237	NM_133796	192662	Mm.30016	NM_133796	ENSMUSG00000025132	Arhgdia	5330430M07Rik|Gdi-1|Rho-GDI|RhoDGI|RhoGDI-1	Rho GDP dissociation inhibitor (GDI) alpha	protein-coding
mm_39864.1	chr5	31048628	31048673	+	1	NA	promoter-TSS (NM_177870)	promoter-TSS (NM_177870)	10	NM_027855	381629	Mm.28144	NM_027855	ENSMUSG00000013622	Atraid	0610007C21Rik|AI316792|Apr3|HSPC013|p18	all-trans retinoic acid induced differentiation factor	protein-coding
mm_121709.1	chr14	15934900	15934909	-	1	NA	Intergenic	Intergenic	-314410	NM_021504	59007	Mm.258381	NM_021504	ENSMUSG00000021785	Ngly1	1110002C09Rik|PNGase|Png1	N-glycanase 1	protein-coding
mm_170857.1	chr2	180604989	180604997	+	1	NA	intron (NM_009936, intron 10 of 31)	intron (NM_009936, intron 10 of 31)	6771	NM_009936	12841	Mm.141312	NM_009936	ENSMUSG00000027570	Col9a3	AV006866	collagen, type IX, alpha 3	protein-coding
mm_4368.1	chr1	172087479	172087481	+	1	NA	intron (NM_009938, intron 1 of 32)	intron (NM_009938, intron 1 of 32)	-4731	NM_021607	59287	Mm.218203	NM_021607	ENSMUSG00000003458	Ncstn	9430068N19Rik|AA727311|Aph2|D1Dau13e|Kiaa0253|Nct|mKIAA0253	nicastrin	protein-coding
mm_18506.1	chr2	62611825	62611866	-	1	NA	exon (NM_027835, exon 6 of 16)	exon (NM_027835, exon 6 of 16)	34410	NM_027835	71586	Mm.136224	NM_027835	ENSMUSG00000026896	Ifih1	9130009C22Rik|Helicard|Hlcd|MDA5|RLR-2	interferon induced with helicase C domain 1	protein-coding
mm_141946.1	chr17	35066172	35066189	-	1	NA	promoter-TSS (NM_001191012)	promoter-TSS (NM_001191012)	4	NM_001033221	106722	Mm.390956	NM_001033221	ENSMUSG00000073414	G6b	AU023871|C6orf25|Ng31	immunoreceptor tyrosine-based inhibitory motif (ITIM) containing platelet receptor	protein-coding
mm_117607.1	chr13	90886778	90886822	-	1	NA	intron (NM_001145879, intron 5 of 6)	intron (NM_001145879, intron 5 of 6)	18555	NM_001145879	435376	Mm.292579	NM_001145879	ENSMUSG00000078958	Atp6ap1l	EG435376	ATPase, H+ transporting, lysosomal accessory protein 1-like	protein-coding
mm_46757.1	chr5	112246537	112246554	-	1	NA	TTS (NM_021351)	TTS (NM_021351)	5973	NM_001312884	12959	Mm.40324	NM_021351	ENSMUSG00000066975	Cryba4	-	crystallin, beta A4	protein-coding
mm_99482.1	chr11	102605977	102606004	+	1	NA	exon (NM_020510, exon 1 of 1)	exon (NM_020510, exon 1 of 1)	1559	NM_020510	57265	Mm.36416	NM_020510	ENSMUSG00000050288	Fzd2	AL033370|AW456835|Fz10|Fzd10|Mfz10|Mfz10a	frizzled class receptor 2	protein-coding
mm_114184.1	chr13	55650445	55650486	+	1	NA	exon (NM_001282055, exon 6 of 23)	exon (NM_001282055, exon 6 of 23)	15466	NM_001282055	212880	Mm.202725	NM_145975	ENSMUSG00000021500	Ddx46	2200005K02Rik|8430438J23Rik|AI325430|AI957095|mKIAA0801	DEAD (Asp-Glu-Ala-Asp) box polypeptide 46	protein-coding
mm_86136.1	chr9	116618771	116618816	-	1	NA	intron (NM_001172122, intron 11 of 13)	B4|SINE|B4	-443430	NM_009371	21813	Mm.172346	NM_009371	ENSMUSG00000032440	Tgfbr2	1110020H15Rik|AU042018|DNIIR|RIIDN|TBR-II|TbetaR-II|TbetaRII	transforming growth factor, beta receptor II	protein-coding
mm_165992.1	chr4	109676767	109676771	+	1	NA	5' UTR (NM_007983, exon 1 of 19)	5' UTR (NM_007983, exon 1 of 19)	142	NM_007983	14084	Mm.318259	NM_007983	ENSMUSG00000010517	Faf1	AA408698|Dffrx|Fam	Fas-associated factor 1	protein-coding
mm_19320.1	chr2	90564506	90564526	-	1	NA	intron (NM_008982, intron 1 of 23)	(TCCC)n|Simple_repeat|Simple_repeat	16131	NM_008982	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_135818.1	chr16	58408319	58408327	-	1	NA	promoter-TSS (NM_028523)	promoter-TSS (NM_028523)	-212	NM_028523	73379	Mm.373589	NM_028523	ENSMUSG00000035107	Dcbld2	1700055P21Rik|AW146002|CLCP1|Esdn	discoidin, CUB and LCCL domain containing 2	protein-coding
mm_131778.1	chr16	22895200	22895291	+	1	NA	promoter-TSS (NR_110508)	promoter-TSS (NR_110508)	-859	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_113042.1	chr13	23571847	23571855	+	1	NA	promoter-TSS (NM_178187)	promoter-TSS (NM_178187)	451	NM_178196	319181	Mm.261673	NM_178196	ENSMUSG00000058385	Hist1h2bg	-	histone cluster 1, H2bg	protein-coding
mm_160728.1	chr10	75935298	75935298	+	1	NA	promoter-TSS (NM_175329)	promoter-TSS (NM_175329)	-275	NM_175329	103172	Mm.333849	NM_175329	ENSMUSG00000049422	Chchd10	1620401E04Rik|AI267078|Ndg2	coiled-coil-helix-coiled-coil-helix domain containing 10	protein-coding
mm_158597.1	chrX	151344811	151344830	-	1	NA	exon (NM_198105, exon 1 of 16)	exon (NM_198105, exon 1 of 16)	597	NM_198105	207375	Mm.391339	NM_198105	ENSMUSG00000025262	Fam120c	D930001I21Rik|ORF34	family with sequence similarity 120, member C	protein-coding
mm_99453.1	chr11	102434208	102434238	+	1	NA	exon (NM_008175, exon 6 of 13)	exon (NM_008175, exon 6 of 13)	3901	NM_008175	14824	Mm.1568	NM_008175	ENSMUSG00000034708	Grn	Pgrn|epithelin	granulin	protein-coding
mm_167309.1	chr8	61610046	61610046	+	1	NA	intron (NM_001293772, intron 10 of 21)	intron (NM_001293772, intron 10 of 21)	-18877	NM_001293774	72333	Mm.29933	NM_001081390	ENSMUSG00000058056	Palld	2410003B16Rik|6030492A02	palladin, cytoskeletal associated protein	protein-coding
mm_4203.1	chr1	171229858	171229895	+	1	NA	exon (NM_010185, exon 5 of 5)	exon (NM_010185, exon 5 of 5)	4473	NM_010185	14127	Mm.22673	NM_010185	ENSMUSG00000058715	Fcer1g	AI573376|CD23|FcR-gamma|FcR[g]|FcRgamma|Fce1g|FcepsilonRI|Ly-50	Fc receptor, IgE, high affinity I, gamma polypeptide	protein-coding
mm_12614.1	chr2	74691914	74691940	+	1	NA	promoter-TSS (NM_013554)	promoter-TSS (NM_013554)	36	NM_013554	15430	Mm.24420	NM_013554	ENSMUSG00000050368	Hoxd10	AI385591|AI874987|Hox-4.5|Hox-5.3	homeobox D10	protein-coding
mm_93631.1	chr10	117280781	117280815	-	1	NA	exon (NM_017372, exon 2 of 4)	exon (NM_017372, exon 2 of 4)	1474	NM_017372	17105	Mm.45436	NM_017372	ENSMUSG00000069516	Lyz2	AI326280|Lys|Lysm|Lyzf2|Lyzs|Lzm|Lzm-s1|Lzp	lysozyme 2	protein-coding
mm_102800.1	chr11	68854285	68854299	-	1	NA	Intergenic	Intergenic	-1161	NM_023668	83431	Mm.31979	NM_023668	ENSMUSG00000018736	Ndel1	2600006O07Rik|MITAP1|NUDEL|mNudel	nudE neurodevelopment protein 1 like 1	protein-coding
mm_128866.1	chr15	72820013	72820018	-	1	NA	intron (NM_001164641, intron 17 of 17)	intron (NM_001164641, intron 17 of 17)	-9691	NR_002864	353342	Mm.440245	NR_002864	ENSMUSG00000106847	Peg13	-	paternally expressed 13	ncRNA
mm_43195.1	chr5	129019728	129019761	+	1	NA	promoter-TSS (NM_009391)	promoter-TSS (NM_009391)	-412	NM_009391	19384	Mm.297440	NM_009391	ENSMUSG00000029430	Ran	-	RAN, member RAS oncogene family	protein-coding
mm_124150.1	chr14	93079716	93079725	-	1	NA	intron (NM_001346722, intron 4 of 4)	RMER1B|Other|Other	809168	NM_001271800	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding
mm_75193.1	chr8	38661524	38661545	-	1	NA	promoter-TSS (NM_145841)	promoter-TSS (NM_145841)	-26	NM_145841	244431	Mm.210388	NM_145841	ENSMUSG00000039539	Sgcz	C230085N17Rik	sarcoglycan zeta	protein-coding
mm_125221.1	chr15	34083347	34083353	+	1	NA	exon (NM_026002, exon 1 of 12)	exon (NM_026002, exon 1 of 12)	631	NM_026002	67154	Mm.130883	NM_026002	ENSMUSG00000022255	Mtdh	2610103J23Rik|3D3|3D3/Lyric|AEG-1|AV353288|D8Bwg1112e|Lyric	metadherin	protein-coding
mm_127070.1	chr15	97374047	97374059	+	1	NA	5' UTR (NM_172293, exon 5 of 6)	5' UTR (NM_172293, exon 5 of 6)	-126766	NM_001164602	105827	Mm.24005	NM_178114	ENSMUSG00000048218	Amigo2	AI415330|AMIGO-2|AW208913|Ali1	adhesion molecule with Ig like domain 2	protein-coding
mm_135411.1	chr16	45018952	45018993	-	1	NA	Intergenic	Intergenic	-75081	NM_026439	67896	Mm.181074	NM_026439	ENSMUSG00000022665	Ccdc80	2610001E17Rik|DRO1|Ssg1|Urb	coiled-coil domain containing 80	protein-coding
mm_112414.1	chr13	3924672	3924684	+	1	NA	promoter-TSS (NM_001033879)	promoter-TSS (NM_001033879)	-17	NM_001033879	238463	Mm.313659	NM_001033879	ENSMUSG00000021216	Tubal3	-	tubulin, alpha-like 3	protein-coding
mm_82670.1	chr9	22130568	22130581	-	1	NA	promoter-TSS (NM_007388)	promoter-TSS (NM_007388)	24	NM_007388	11433	Mm.46354	NM_007388	ENSMUSG00000001348	Acp5	TRACP|TRAP	acid phosphatase 5, tartrate resistant	protein-coding
mm_31167.1	chr4	43446006	43446028	+	1	NA	exon (NM_011571, exon 9 of 10)	exon (NM_011571, exon 9 of 10)	3740	NM_011571	21754	Mm.485441	NM_011571	ENSMUSG00000028458	Tesk1	AI326901	testis specific protein kinase 1	protein-coding
mm_110477.1	chr12	51851736	51851746	-	1	NA	Intergenic	Intergenic	-22205	NM_144788	207304	Mm.249391	NM_144788	ENSMUSG00000035247	Hectd1	A630086P08Rik|AI844876|b2b327Clo|opm	HECT domain containing 1	protein-coding
mm_69461.1	chr7	133123854	133123876	-	1	NA	promoter-TSS (NM_009980)	promoter-TSS (NM_009980)	-382	NM_009980	13017	Mm.246240	NM_009980	ENSMUSG00000030970	Ctbp2	AA407280|D7Ertd45e|Gtrgeo6|Ribeye	C-terminal binding protein 2	protein-coding
mm_119104.1	chr14	30951453	30951469	+	1	NA	promoter-TSS (NM_001308328)	promoter-TSS (NM_001308328)	84	NM_011849	23955	Mm.251494	NM_011849	ENSMUSG00000021918	Nek4	Stk2	NIMA (never in mitosis gene a)-related expressed kinase 4	protein-coding
mm_81787.1	chr9	114781087	114781125	+	1	NA	intron (NM_001252479, intron 1 of 3)	intron (NM_001252479, intron 1 of 3)	887	NM_133978	102545	Mm.35600	NM_133978	ENSMUSG00000032436	Cmtm7	AI481279|Cklfsf7|LNV	CKLF-like MARVEL transmembrane domain containing 7	protein-coding
mm_112941.1	chr13	20986396	20986410	+	1	NA	intron (NM_012054, intron 13 of 20)	MT2B|LTR|ERVL	86896	NM_146535	258528	Mm.377554	NM_146535	ENSMUSG00000042869	Olfr1370	MOR256-14	olfactory receptor 1370	protein-coding
mm_168948.1	chr12	75978445	75978451	-	1	NA	intron (NM_001005510, intron 51 of 115)	BGLII|LTR|ERVK	69345	NR_039560	100628610		NR_039560	ENSMUSG00000092922	Mir5101	mmu-mir-5101|mu-mir-5101	microRNA 5101	ncRNA
mm_111457.1	chr12	98386179	98386214	-	1	NA	Intergenic	Intergenic	117561	NM_008152	14744	Mm.378924	NM_008152	ENSMUSG00000021886	Gpr65	Dig1|Gpcr25|TDAG8	G-protein coupled receptor 65	protein-coding
mm_87214.1	chr10	39822567	39822581	+	1	NA	exon (NM_011264, exon 13 of 32)	exon (NM_011264, exon 13 of 32)	76664	NR_033628	213332	Mm.484359	NR_033628		Mfsd4b4	AA474331	major facilitator superfamily domain containing 4B4	pseudo
mm_75180.1	chr8	36952245	36952255	-	1	NA	5' UTR (NM_001194940, exon 1 of 18)	5' UTR (NM_001194940, exon 1 of 18)	192	NM_001194940	50768	Mm.125155	NM_015802	ENSMUSG00000031523	Dlc1	A730069N07Rik|Arhgap7|HP|STARD12|dlc-1	deleted in liver cancer 1	protein-coding
mm_62565.1	chr7	104218828	104218849	+	1	NA	promoter-TSS (NM_001013616)	promoter-TSS (NM_001013616)	43	NM_001013616	94088	Mm.274843	NM_001013616	ENSMUSG00000072244	Trim6	C430046K18Rik|D7Ertd684e	tripartite motif-containing 6	protein-coding
mm_25342.1	chr3	106721874	106721876	+	1	NA	5' UTR (NM_001039488, exon 1 of 4)	5' UTR (NM_001039488, exon 1 of 4)	193	NM_001286685	321000	Mm.259638	NM_028081	ENSMUSG00000056260	Lrif1	2010012G17Rik|4933421E11Rik|AI450568	ligand dependent nuclear receptor interacting factor 1	protein-coding
mm_141716.1	chr17	34028045	34028076	-	1	NA	promoter-TSS (NM_013543)	promoter-TSS (NM_013543)	-5	NM_013543	14979	Mm.275452	NM_013543	ENSMUSG00000073422	H2-Ke6	D17H6S112E|H-2Ke6|Hsd17b8|Ke-6|Ke6|Ring2	H2-K region expressed gene 6	protein-coding
mm_114613.1	chr13	75847169	75847191	+	1	NA	exon (NM_053108, exon 2 of 3)	exon (NM_053108, exon 2 of 3)	7294	NM_053108	93692	Mm.25844	NM_053108	ENSMUSG00000021591	Glrx	C86710|D13Wsu156e|Glrx1|Grx1|TTase	glutaredoxin	protein-coding
mm_71745.1	chr8	65209106	65209115	+	1	NA	Intergenic	RLTR9A3A|LTR|ERVK	-79573	NR_033217	407795	Mm.387876	NR_033217	ENSMUSG00000074300	BC030870	-	cDNA sequence BC030870	ncRNA
mm_142992.1	chr17	56300230	56300248	-	1	NA	promoter-TSS (NM_029799)	promoter-TSS (NM_029799)	47	NM_029799	76920	Mm.329132	NM_029799	ENSMUSG00000073380	Arrdc5	1700013E09Rik	arrestin domain containing 5	protein-coding
mm_149161.1	chr19	9018197	9018215	+	1	NA	TTS (NR_105786)	TTS (NR_105786)	302	NR_105786	102465190		NR_105786	ENSMUSG00000099308	Mir6367	Gm27467|mmu-mir-6367	microRNA 6367	ncRNA
mm_17141.1	chr2	25095096	25095110	-	1	NA	5' UTR (NM_001163626, exon 1 of 12)	5' UTR (NM_001163626, exon 1 of 12)	102	NM_001163626	241275	Mm.218774	NM_172204	ENSMUSG00000036805	Noxa1	NY-CO-31|SDCCAG31	NADPH oxidase activator 1	protein-coding
mm_6257.1	chr1	69103177	69103180	-	1	NA	intron (NM_010154, intron 1 of 26)	intron (NM_010154, intron 1 of 26)	4881	NM_010154	13869	Mm.442420	NM_010154	ENSMUSG00000062209	Erbb4	Her4|c-erbB-4	erb-b2 receptor tyrosine kinase 4	protein-coding
mm_117159.1	chr13	61999543	61999545	-	1	NA	Intergenic	Lx5|LINE|L1	-130346	NM_001039239	630579	Mm.440905	NM_001039239	ENSMUSG00000074867	Zfp808	EG630579|Gm7036	zinc finger protein 80	protein-coding
mm_141516.1	chr17	31681531	31681537	-	1	NA	3' UTR (NM_001278570, exon 3 of 3)	3' UTR (NM_001278570, exon 3 of 3)	3603	NM_001278570	12954	Mm.1228	NM_013501	ENSMUSG00000024041	Cryaa	Acry-1|Crya-1|Crya1|DAcry-1|lop18	crystallin, alpha A	protein-coding
mm_122934.1	chr14	54962743	54962783	-	1	NA	exon (NM_010856, exon 8 of 39)	exon (NM_010856, exon 8 of 39)	3844	NM_001164171	17888	Mm.290003	NM_010856	ENSMUSG00000040752	Myh6	A830009F23Rik|AA517445|Myhc-a|Myhca|alpha-MHC	myosin, heavy polypeptide 6, cardiac muscle, alpha	protein-coding
mm_47444.1	chr5	123394636	123394638	-	1	NA	promoter-TSS (NM_177582)	promoter-TSS (NM_177582)	-161	NM_133917	208104	Mm.83277	NM_133917	ENSMUSG00000038342	Mlxip	AW228700|Mir|bHLHe36	MLX interacting protein	protein-coding
mm_122335.1	chr14	37125309	37125334	-	1	NA	exon (NM_001199122, exon 8 of 9)	exon (NM_001199122, exon 8 of 9)	9818	NM_001199122	66092	Mm.182912	NM_078478	ENSMUSG00000041028	Ghitm	1010001P14Rik|C77840|MICS1|PTD010|Tmbim5	growth hormone inducible transmembrane protein	protein-coding
mm_144400.1	chr18	20762671	20762680	+	1	NA	Intergenic	MTC-int|LTR|ERVL-MaLR	-16271	NM_019737	56386	Mm.393827	NM_019737	ENSMUSG00000056124	B4galt6	AA536803|AU022389	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 6	protein-coding
mm_113729.1	chr13	43962205	43962226	+	1	NA	Intergenic	Intergenic	-158952	NR_045285	328235	Mm.188356	NR_045285	ENSMUSG00000089815	Gm5083	A730030A06	predicted gene 5083	ncRNA
mm_117213.1	chr13	64089258	64089267	-	1	NA	promoter-TSS (NM_008291)	promoter-TSS (NM_008291)	-61	NM_008291	15487	Mm.5109	NM_008291	ENSMUSG00000033122	Hsd17b3	-	hydroxysteroid (17-beta) dehydrogenase 3	protein-coding
mm_10985.1	chr2	26206676	26206686	+	1	NA	promoter-TSS (NM_001039653)	promoter-TSS (NM_001039653)	-106	NM_001039653	16871	Mm.386765	NM_010711	ENSMUSG00000026934	Lhx3	Lim3|P-LIM|mLIM3|mLim-3	LIM homeobox protein 3	protein-coding
mm_131184.1	chr16	7217662	7217671	+	1	NA	intron (NM_183188, intron 1 of 12)	intron (NM_183188, intron 1 of 12)	147831	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_2887.1	chr1	131867240	131867272	+	1	NA	promoter-TSS (NM_144875)	promoter-TSS (NM_144875)	-21	NM_144875	226422	Mm.34027	NM_144875	ENSMUSG00000026433	Rab29	Rab7l1	RAB29, member RAS oncogene family	protein-coding
mm_8295.1	chr1	143676040	143676043	-	1	NA	intron (NM_145991, intron 7 of 16)	AT_rich|Low_complexity|Low_complexity	26852	NM_145991	214498	Mm.156727	NM_145991	ENSMUSG00000026361	Cdc73	8430414L16Rik|C130030P16Rik|C81219|Hrpt2	cell division cycle 73, Paf1/RNA polymerase II complex component	protein-coding
mm_163609.1	chr13	49970007	49970024	+	1	NA	Intergenic	Intergenic	280293	NM_001033438	380882	Mm.425809	NM_001033438	ENSMUSG00000095300	Gm906	-	predicted gene 906	protein-coding
mm_37590.1	chr4	126468697	126468705	-	1	NA	promoter-TSS (NM_001317173)	promoter-TSS (NM_001317173)	-118	NM_153403	236511	Mm.30800	NM_153403	ENSMUSG00000041530	Ago1	Eif2c1	argonaute RISC catalytic subunit 1	protein-coding
mm_23381.1	chr3	55782531	55782549	+	1	NA	promoter-TSS (NM_010750)	promoter-TSS (NM_010750)	30	NM_010750	17116	Mm.440209	NM_010750	ENSMUSG00000056947	Mab21l1	AW047968	mab-21-like 1 (C. elegans)	protein-coding
mm_104608.1	chr11	97187931	97187948	-	1	NA	promoter-TSS (NM_008379)	promoter-TSS (NM_008379)	-47	NM_008379	16211	Mm.251013	NM_008379	ENSMUSG00000001440	Kpnb1	AA409963|IPOB|Impnb	karyopherin (importin) beta 1	protein-coding
mm_1542.1	chr1	72852155	72852162	+	1	NA	exon (NM_008342, exon 4 of 4)	exon (NM_008342, exon 4 of 4)	22707	NM_010518	16011	Mm.405761	NM_010518	ENSMUSG00000026185	Igfbp5	AI256729|AW208790|IGFBP-5|IGFBP-5P	insulin-like growth factor binding protein 5	protein-coding
mm_57606.1	chr6	128025741	128025787	-	1	NA	intron (NM_175414, intron 3 of 8)	intron (NM_175414, intron 3 of 8)	117814	NM_175414	109246	Mm.21814	NM_175414	ENSMUSG00000030352	Tspan9	6720474K14Rik|9430079M16Rik|AU018597	tetraspanin 9	protein-coding
mm_96092.1	chr11	60417153	60417181	+	1	NA	promoter-TSS (NM_145427)	promoter-TSS (NM_145427)	22	NM_025757	66771	Mm.29950	NM_025757	ENSMUSG00000018415	Gid4	4933439F18Rik	GID complex subunit 4, VID24 homolog	protein-coding
mm_166762.1	chr6	129385470	129385472	-	1	NA	promoter-TSS (NM_027709)	promoter-TSS (NM_027709)	32	NM_027709	71183	Mm.79402	NM_027709	ENSMUSG00000030158	Clec12b	4933425B16Rik	C-type lectin domain family 12, member B	protein-coding
mm_113614.1	chr13	41487096	41487140	+	1	NA	intron (NM_001111324, intron 1 of 7)	intron (NM_001111324, intron 1 of 7)	242	NM_001111324	18003	Mm.288980	NM_017464	ENSMUSG00000021365	Nedd9	Cas-L|CasL|HEF1|MEF1|Nedd-9|p105	neural precursor cell expressed, developmentally down-regulated gene 9	protein-coding
mm_89511.1	chr10	94147908	94147966	+	1	NA	promoter-TSS (NM_011629)	promoter-TSS (NM_011629)	6	NM_011629	22025	Mm.107483	NM_011629	ENSMUSG00000005897	Nr2c1	4831444H07Rik|80.3|Eenr|TR2|Tr2-11	nuclear receptor subfamily 2, group C, member 1	protein-coding
mm_77389.1	chr8	120177441	120177478	-	1	NA	promoter-TSS (NM_001033980)	promoter-TSS (NM_001033980)	10	NM_001033980	436062	Mm.334852	NM_001033980	ENSMUSG00000042269	Fam92b	1700120B06Rik	family with sequence similarity 92, member B	protein-coding
mm_149981.1	chr19	29121800	29121802	+	1	NA	exon (NM_021525, exon 5 of 9)	exon (NM_021525, exon 5 of 9)	-13478	NR_029778	724062		NR_029778	ENSMUSG00000065556	Mir101b	Mirn101b|mir-101b	microRNA 101b	ncRNA
mm_114914.1	chr13	95009983	95009990	+	1	NA	intron (NM_172590, intron 7 of 12)	intron (NM_172590, intron 7 of 12)	33642	NM_172590	218460	Mm.33856	NM_172590	ENSMUSG00000042015	Wdr41	B830029I03Rik|MSTP048	WD repeat domain 41	protein-coding
mm_22183.1	chr2	173218819	173218833	-	1	NA	promoter-TSS (NM_021394)	promoter-TSS (NM_021394)	96	NM_021394	58203	Mm.116687	NM_021394	ENSMUSG00000027514	Zbp1	2010010H03Rik|Dai|Dlm1|mZaDLM	Z-DNA binding protein 1	protein-coding
mm_119368.1	chr14	41122540	41122549	+	1	NA	exon (NM_133653, exon 10 of 10)	exon (NM_133653, exon 10 of 10)	-9244	NM_023134	20387	Mm.46062	NM_023134	ENSMUSG00000021789	Sftpa1	SP-A|Sftp-1|Sftp1	surfactant associated protein A1	protein-coding
mm_124026.1	chr14	76673845	76673865	-	1	NA	Intergenic	Intergenic	-3713	NR_015485	73272	Mm.116804	NR_015485	ENSMUSG00000101009	1700108F19Rik	1700020I02Rik|BB065030	RIKEN cDNA 1700108F19 gene	ncRNA
mm_134832.1	chr16	26105778	26105855	-	1	NA	promoter-TSS (NM_173379)	promoter-TSS (NM_173379)	-32	NM_173379	210530	Mm.326869	NM_173379	ENSMUSG00000038168	P3h2	4832416N06|AW553532|Leprel1|Mlat4	prolyl 3-hydroxylase 2	protein-coding
mm_103707.1	chr11	79516694	79516704	-	1	NA	exon (NM_001077496, exon 2 of 2)	exon (NM_001077496, exon 2 of 2)	7063	NM_001077496	216984	Mm.439665	NM_001077496	ENSMUSG00000093938	Evi2b	Evi-2|Evi2	ecotropic viral integration site 2b	protein-coding
mm_153972.1	chr19	47859494	47859539	-	1	NA	exon (NM_010362, exon 4 of 6)	exon (NM_010362, exon 4 of 6)	4543	NM_010362	14873	Mm.378931	NM_010362	ENSMUSG00000025068	Gsto1	AA407097|AI194287|AU018802|Gsto-1|Gstx|Spg-r|p28	glutathione S-transferase omega 1	protein-coding
mm_30851.1	chr4	25010381	25010385	+	1	NA	Intergenic	Intergenic	36964	NM_030733	81006	Mm.160412	NM_030733	ENSMUSG00000040372	Gpr63	PSP24beta|Psp24-2	G protein-coupled receptor 63	protein-coding
mm_121161.1	chr14	103008240	103008249	+	1	NA	intron (NR_045657, intron 2 of 2)	RMER13B|LTR|ERVK	25559	NR_045657	71264	Mm.399572	NR_045657		4933432I03Rik	-	RIKEN cDNA 4933432I03 gene	ncRNA
mm_165813.1	chr3	145758796	145758802	+	1	NA	5' UTR (NM_026993, exon 1 of 6)	5' UTR (NM_026993, exon 1 of 6)	107	NM_026993	69219	Mm.234247	NM_026993	ENSMUSG00000028194	Ddah1	2410006N07Rik|2510015N06Rik|AI987801|AW050362	dimethylarginine dimethylaminohydrolase 1	protein-coding
mm_25677.1	chr3	122076926	122076970	+	1	NA	intron (NM_007378, intron 6 of 49)	B4|SINE|B4	32488	NM_007378	11304	Mm.3918	NM_007378	ENSMUSG00000028125	Abca4	AW050280|Abc10|Abcr|D430003I15Rik|RmP	ATP-binding cassette, sub-family A (ABC1), member 4	protein-coding
mm_111815.1	chr12	105685131	105685142	-	1	NA	promoter-TSS (NM_178613)	promoter-TSS (NM_178613)	105	NM_029654	76559	Mm.114362	NM_029654	ENSMUSG00000041341	Atg2b	2410024A21Rik|AI047755|AI503411|AW558123|C030004M05Rik|C630028L02Rik|mKIAA4067	autophagy related 2B	protein-coding
mm_163631.1	chr13	58402031	58402059	-	1	NA	promoter-TSS (NR_031761)	promoter-TSS (NR_031761)	124	NM_001301343	15387	Mm.142872	NM_025279	ENSMUSG00000021546	Hnrnpk	Hnrpk|KBBP|NOVA	heterogeneous nuclear ribonucleoprotein K	protein-coding
mm_20398.1	chr2	129198569	129198588	-	1	NA	promoter-TSS (NM_015747)	promoter-TSS (NM_015747)	-195	NM_015747	20515	Mm.272675	NM_015747	ENSMUSG00000027397	Slc20a1	AI607883|Glvr-1|Glvr1	solute carrier family 20, member 1	protein-coding
mm_72618.1	chr8	84636399	84636417	+	1	NA	intron (NM_001252059, intron 43 of 45)	intron (NM_001252059, intron 43 of 45)	26444	NM_010499	15936	Mm.399	NM_010499	ENSMUSG00000053560	Ier2	AI317238|Ch1|Pip92	immediate early response 2	protein-coding
mm_142276.1	chr17	39848296	39848306	-	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	5304	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_118607.1	chr14	20843237	20843241	+	1	NA	3' UTR (NM_008873, exon 11 of 11)	3' UTR (NM_008873, exon 11 of 11)	6577	NM_008873	18792	Mm.4183	NM_008873	ENSMUSG00000021822	Plau	u-PA|uPA	plasminogen activator, urokinase	protein-coding
mm_144724.1	chr18	35154462	35154476	+	1	NA	exon (NM_009818, exon 3 of 18)	exon (NM_009818, exon 3 of 18)	35557	NM_009818	12385	Mm.18962	NM_009818	ENSMUSG00000037815	Ctnna1	2010010M04Rik|AA517462|AI988031|Catna1	catenin (cadherin associated protein), alpha 1	protein-coding
mm_137334.1	chr17	25089452	25089462	+	1	NA	exon (NM_134126, exon 23 of 30)	exon (NM_134126, exon 23 of 30)	-8343	NM_001001183	407831	Mm.34379	NM_001001183	ENSMUSG00000024168	Tmem204	-	transmembrane protein 204	protein-coding
mm_158046.1	chrX	98891009	98891047	-	1	NA	promoter-TSS (NM_052976)	promoter-TSS (NM_052976)	-3	NM_001313755	94190	Mm.33536	NM_052976	ENSMUSG00000031214	Ophn1	C130037N19Rik|Wtgr	oligophrenin 1	protein-coding
mm_92794.1	chr10	81350247	81350259	-	1	NA	5' UTR (NM_010440, exon 1 of 9)	5' UTR (NM_010440, exon 1 of 9)	173	NM_001163165	15353	Mm.38474	NM_010440	ENSMUSG00000020232	Hmg20b	AW610687|BRAF35|Hmgx2|Hmgxb2|Smarce1r	high mobility group 20B	protein-coding
mm_164179.1	chr15	76246578	76246589	-	1	NA	promoter-TSS (NM_023168)	promoter-TSS (NM_023168)	-224	NM_023168	66168	Mm.41665	NM_023168	ENSMUSG00000022564	Grina	1110025J15Rik|Lag|Tmbim3	glutamate receptor, ionotropic, N-methyl D-aspartate-associated protein 1 (glutamate binding)	protein-coding
mm_46912.1	chr5	114380460	114380487	-	1	NA	promoter-TSS (NM_001159941)	promoter-TSS (NM_001159941)	32	NM_001159941	330171	Mm.238285	NM_026145	ENSMUSG00000001098	Kctd10	AW536343|C87062|mBACURD3	potassium channel tetramerisation domain containing 10	protein-coding
mm_27264.1	chr3	38484803	38484822	-	1	NA	promoter-TSS (NM_001167883)	promoter-TSS (NM_001167883)	4	NM_001167883	99696	Mm.290937	NM_001033198	ENSMUSG00000044864	Ankrd50	AI662170|E430012K20Rik|mKIAA1223|mKIAA3019	ankyrin repeat domain 50	protein-coding
mm_13788.1	chr2	118814238	118814261	+	1	NA	exon (NM_026412, exon 1 of 9)	exon (NM_026412, exon 1 of 9)	246	NM_026412	51944	Mm.252695	NM_026412	ENSMUSG00000027331	Knstrn	1700025D04Rik|C15orf23|D2Ertd750e|SKAP|Traf4af1	kinetochore-localized astrin/SPAG5 binding	protein-coding
mm_99884.1	chr11	109440073	109440079	+	1	NA	promoter-TSS (NR_040680)	promoter-TSS (NR_040680)	-2	NR_040680	100503496	Mm.265874	NR_040680		LOC100503496	-	uncharacterized LOC100503496	ncRNA
mm_158324.1	chrX	133900174	133900198	-	1	NA	Intergenic	MIR|SINE|MIR	-1757	NM_019656	56496	Mm.46701	NM_019656	ENSMUSG00000067377	Tspan6	6720473L21Rik|AI316786|T245|TSPAN-6|Tm4sf|Tm4sf6	tetraspanin 6	protein-coding
mm_54027.1	chr6	11493060	11493062	-	1	NA	Intergenic	Intergenic	414385	NM_010886	17992	Mm.415865	NM_010886	ENSMUSG00000029632	Ndufa4	MLRQ	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 4	protein-coding
mm_65399.1	chr7	25179858	25179896	-	1	NA	Intergenic	CpG	24808	NR_045848	434147	Mm.59171	NM_001033781	ENSMUSG00000074274	D930028M14Rik	EG434147	RIKEN cDNA D930028M14 gene	ncRNA
mm_95075.1	chr11	32642519	32642537	+	1	NA	promoter-TSS (NM_134015)	promoter-TSS (NM_134015)	-27	NM_001271348	103583	Mm.28017	NM_134015	ENSMUSG00000020271	Fbxw11	2310065A07Rik|AA536858|BTRC2|BTRCP2|Fbxw1b|HOS	F-box and WD-40 domain protein 11	protein-coding
mm_9378.1	chr1	172210317	172210325	-	1	NA	3' UTR (NM_009813, exon 11 of 11)	3' UTR (NM_009813, exon 11 of 11)	-3517	NM_011063	18611	Mm.544	NM_011063	ENSMUSG00000013698	Pea15a	Mat1|PEA-15|Pea15|Pkcs15	phosphoprotein enriched in astrocytes 15A	protein-coding
mm_115836.1	chr13	21287100	21287119	-	1	NA	3' UTR (NM_010343, exon 5 of 5)	3' UTR (NM_010343, exon 5 of 5)	5577	NM_010343	14780	Mm.1332	NM_010343	ENSMUSG00000004344	Gpx5	AV379049|Arep	glutathione peroxidase 5	protein-coding
mm_170375.1	chr1	85526624	85526625	+	1	NA	Intergenic	Intergenic	72186	NM_030194	109032	Mm.335802	NM_030194	ENSMUSG00000070034	Sp110	5031415C07Rik|52kDa|5830484A20Rik|ENSMUSG00000075603|Ifi75|Ipr1	Sp110 nuclear body protein	protein-coding
mm_20124.1	chr2	121271356	121271397	-	1	NA	promoter-TSS (NM_013735)	promoter-TSS (NM_013735)	31	NM_001290830	27223	Mm.215389	NM_013735	ENSMUSG00000043909	Trp53bp1	53BP1|Tp53bp1|m53BP1|p53BP1	transformation related protein 53 binding protein 1	protein-coding
mm_15119.1	chr2	153741319	153741327	+	1	NA	promoter-TSS (NM_007896)	promoter-TSS (NM_007896)	36	NM_007896	13589	Mm.143877	NM_007896	ENSMUSG00000027479	Mapre1	5530600P05Rik|AI462499|AI504412|AW260097|BIM1p|D2Ertd459e|Eb1	microtubule-associated protein, RP/EB family, member 1	protein-coding
mm_91744.1	chr10	49272809	49272833	-	1	NA	exon (NM_010349, exon 12 of 18)	exon (NM_010349, exon 12 of 18)	-176978	NR_046212	100418235	Mm.185993	NR_046212		C130030K03Rik	-	proteasome (prosome, macropain) subunit, alpha type 6 pseudogene	pseudo
mm_119520.1	chr14	47473503	47473505	+	1	NA	intron (NM_030236, intron 1 of 1)	intron (NM_030236, intron 1 of 1)	943	NM_001146085	78938	Mm.11935	NM_030236	ENSMUSG00000037536	Fbxo34	2900057B08Rik|5830426G16Rik	F-box protein 34	protein-coding
mm_133021.1	chr16	57121456	57121486	+	1	NA	promoter-TSS (NM_138599)	promoter-TSS (NM_138599)	-243	NM_138599	28185	Mm.196933	NM_138599	ENSMUSG00000022752	Tomm70a	2610044B22Rik|D16Ium22|D16Ium22e|D16Wsu109e|Tom70|Tomm70|mKIAA0719	translocase of outer mitochondrial membrane 70 homolog A (yeast)	protein-coding
mm_88612.1	chr10	79824705	79824720	+	1	NA	intron (NM_030218, intron 1 of 4)	intron (NM_030218, intron 1 of 4)	3691	NM_030218	78906	Mm.33087	NM_030218	ENSMUSG00000035852	Misp	9130017N09Rik	mitotic spindle positioning	protein-coding
mm_87612.1	chr10	57785527	57785547	+	1	NA	exon (NM_021272, exon 2 of 4)	exon (NM_021272, exon 2 of 4)	614	NM_021272	12140	Mm.3644	NM_021272	ENSMUSG00000019874	Fabp7	B-FABP|BFABP|Blbp|MRG	fatty acid binding protein 7, brain	protein-coding
mm_53210.1	chr6	125711493	125711511	+	1	NA	intron (NM_153589, intron 2 of 25)	intron (NM_153589, intron 2 of 25)	21083	NM_153589	243634	Mm.333398	NM_153589	ENSMUSG00000038115	Ano2	BC033409|Tmem16b	anoctamin 2	protein-coding
mm_89300.1	chr10	87913748	87913761	+	1	NA	exon (NM_010512, exon 3 of 5)	exon (NM_010512, exon 3 of 5)	52643	NM_001111276	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_56464.1	chr6	98929394	98929398	-	1	NA	3' UTR (NM_053202, exon 19 of 19)	3' UTR (NM_053202, exon 19 of 19)	98902	NM_001197322	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_8952.1	chr1	164457995	164458012	-	1	NA	5' UTR (NM_009721, exon 1 of 6)	5' UTR (NM_009721, exon 1 of 6)	352	NM_009721	11931	Mm.4550	NM_009721	ENSMUSG00000026576	Atp1b1	Atp4b|Atpb|Atpb-1|NKbeta1	ATPase, Na+/K+ transporting, beta 1 polypeptide	protein-coding
mm_107142.1	chr12	21417873	21417887	+	1	NA	promoter-TSS (NM_011739)	promoter-TSS (NM_011739)	-444	NM_011739	22630	Mm.289630	NM_011739	ENSMUSG00000076432	Ywhaq	2700028P07Rik|AA409740|AU021156|R74690	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide	protein-coding
mm_22264.1	chr2	178407482	178407498	-	1	NA	intron (NM_177191, intron 1 of 43)	CpG	168	NM_177191	320558	Mm.70781	NM_177191	ENSMUSG00000060445	Sycp2	3830402K23Rik|4930518F03Rik	synaptonemal complex protein 2	protein-coding
mm_35430.1	chr4	36321166	36321170	-	1	NA	intron (NM_001165999, intron 3 of 7)	B3A|SINE|B2	324285	NR_030545	100124458		NR_030545	ENSMUSG00000077851	Mir876	Mirn876|mir-876|mmu-mir-876	microRNA 876	ncRNA
mm_105088.1	chr11	100850740	100850763	-	1	NA	promoter-TSS (NM_001113563)	promoter-TSS (NM_001113563)	-166	NM_001113563	20851	Mm.34064	NM_011489	ENSMUSG00000020919	Stat5b	-	signal transducer and activator of transcription 5B	protein-coding
mm_161869.1	chr18	36930163	36930163	+	1	NA	promoter-TSS (NM_054072)	promoter-TSS (NM_054072)	-122	NM_054072	116731	Mm.308500	NM_054072	ENSMUSG00000103442	Pcdha1	CNR	protocadherin alpha 1	protein-coding
mm_168984.1	chr12	93317496	93317498	+	1	NA	Intergenic	Intergenic	127326	NR_126436	75295	Mm.243878	NR_126436		4930559C10Rik	-	RIKEN cDNA 4930559C10 gene	ncRNA
mm_120188.1	chr14	61519350	61519383	+	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	26678	NR_045714	75349	Mm.233613	NR_045714		4930556J02Rik	-	RIKEN cDNA 4930556J02 gene	ncRNA
mm_80762.1	chr9	95559321	95559331	+	1	NA	promoter-TSS (NM_198414)	promoter-TSS (NM_198414)	-491	NM_198414	75552	Mm.151485	NM_198414	ENSMUSG00000064225	Paqr9	1700020G04Rik	progestin and adipoQ receptor family member IX	protein-coding
mm_56677.1	chr6	113719881	113719883	-	1	NA	promoter-TSS (NM_001286405)	promoter-TSS (NM_001286405)	29	NM_021488	58991	Mm.379095	NM_021488	ENSMUSG00000064177	Ghrl	2210006E23Rik|Ghr|MTLRP|MTLRPAP|m46	ghrelin	protein-coding
mm_53547.1	chr6	136828415	136828456	+	1	NA	promoter-TSS (NM_021714)	promoter-TSS (NM_021714)	-219	NM_021714	60321	Mm.141197	NM_021714	ENSMUSG00000030216	Wbp11	2510026P17Rik|D6Wsu113e|Npwbp|SIPP1	WW domain binding protein 11	protein-coding
mm_127287.1	chr15	100038675	100038721	+	1	NA	promoter-TSS (NM_001159361)	promoter-TSS (NM_001159361)	34	NM_001159361	239667	Mm.243658	NM_172819	ENSMUSG00000023026	Dip2b	4932422C22|AI317237|AI854602|mKIAA1463	disco interacting protein 2 homolog B	protein-coding
mm_70747.1	chr8	19198703	19198706	+	1	NA	promoter-TSS (NM_019728)	promoter-TSS (NM_019728)	0	NM_019728	56519	Mm.45276	NM_019728	ENSMUSG00000059230	Defb4	2310001F05Rik|BD-4	defensin beta 4	protein-coding
mm_12466.1	chr2	71389240	71389278	+	1	NA	promoter-TSS (NM_026115)	promoter-TSS (NM_026115)	-1	NM_026115	107435	Mm.272472	NM_026115	ENSMUSG00000027018	Hat1	2410071B14Rik|AA536933|Hat-1|KAT1	histone aminotransferase 1	protein-coding
mm_90069.1	chr10	116346881	116346889	+	1	NA	exon (NM_029928, exon 15 of 32)	exon (NM_029928, exon 15 of 32)	45511	NM_029928	19263	Mm.37213	NM_029928	ENSMUSG00000020154	Ptprb	3230402H02Rik|C130094E24|Ptpz|Rptpb|VE-PTP|Veptp	protein tyrosine phosphatase, receptor type, B	protein-coding
mm_117648.1	chr13	92794810	92794825	-	1	NA	promoter-TSS (NM_011582)	promoter-TSS (NM_011582)	1	NM_011582	21828	Mm.20865	NM_011582	ENSMUSG00000021702	Thbs4	TSP4	thrombospondin 4	protein-coding
mm_125038.1	chr15	25774073	25774092	+	1	NA	intron (NM_019472, intron 19 of 40)	intron (NM_019472, intron 19 of 40)	-69216	NM_001034851	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_27081.1	chr3	30013026	30013036	-	1	NA	5' UTR (NM_007963, exon 1 of 15)	5' UTR (NM_007963, exon 1 of 15)	173	NM_007963	14013	Mm.56965	NM_007963	ENSMUSG00000027684	Mecom	D630039M04Rik|Evi-1|Evi1|Jbo|Mds|Mds1|Mds1-Evi1|Prdm3|Znfpr1b1	MDS1 and EVI1 complex locus	protein-coding
mm_125337.1	chr15	39006021	39006048	+	1	NA	promoter-TSS (NM_008056)	promoter-TSS (NM_008056)	-246	NM_001162494	14368	Mm.4769	NM_008056	ENSMUSG00000022297	Fzd6	Fz6	frizzled class receptor 6	protein-coding
mm_7084.1	chr1	88509896	88509934	-	1	NA	5' UTR (NM_008132, exon 1 of 3)	5' UTR (NM_008132, exon 1 of 3)	151	NM_008132	14659	Mm.5187	NM_008132	ENSMUSG00000062310	Glrp1	GRP-1	glutamine repeat protein 1	protein-coding
mm_80026.1	chr9	68653627	68653639	+	1	NA	promoter-TSS (NM_001289917)	promoter-TSS (NM_001289917)	-153	NM_001289917	19883	Mm.378450	NM_013646	ENSMUSG00000032238	Rora	9530021D13Rik|Nr1f1|ROR1|ROR2|ROR3|nmf267|sg|staggerer|tmgc26	RAR-related orphan receptor alpha	protein-coding
mm_167512.1	chr9	13765916	13765920	+	1	NA	intron (NR_024025, intron 1 of 15)	intron (NR_024025, intron 1 of 15)	16737	NR_024025	77116	Mm.210405	NM_023858	ENSMUSG00000031918	Mtmr2	6030445P13Rik	myotubularin related protein 2	protein-coding
mm_92191.1	chr10	68116966	68116971	-	1	NA	intron (NM_023598, intron 8 of 9)	(TCCC)n|Simple_repeat|Simple_repeat	137370	NM_001081346	170799	Mm.209844	NM_133244	ENSMUSG00000037846	Rtkn2	B130039D23Rik|Mbf|Plekhk1	rhotekin 2	protein-coding
mm_110937.1	chr12	76547849	76547874	-	1	NA	promoter-TSS (NR_046044)	promoter-TSS (NR_046044)	64	NR_046044	100504549	Mm.440349	NR_046044		AI463170	-	expressed sequence AI463170	ncRNA
mm_121807.1	chr14	20348020	20348033	-	1	NA	promoter-TSS (NM_172379)	promoter-TSS (NM_172379)	95	NM_027475	70601	Mm.35105	NM_027475	ENSMUSG00000021810	Ecd	5730461K03Rik|Hsgt1	ecdysoneless homolog (Drosophila)	protein-coding
mm_109637.1	chr12	112785072	112785094	+	1	NA	Intergenic	Intergenic	-23892	NM_145450	217887	Mm.186678	NM_145450	ENSMUSG00000037594	BC022687	AW050009|C130001I08Rik|Flj20080	cDNA sequence BC022687	protein-coding
mm_76310.1	chr8	84656894	84656920	-	1	NA	Intergenic	CpG	5945	NM_010499	15936	Mm.399	NM_010499	ENSMUSG00000053560	Ier2	AI317238|Ch1|Pip92	immediate early response 2	protein-coding
mm_42164.1	chr5	112259323	112259337	+	1	NA	exon (NM_001312894, exon 3 of 6)	exon (NM_001312894, exon 3 of 6)	3510	NM_001312893	12960	Mm.29488	NM_023695	ENSMUSG00000029343	Crybb1	3110006K12Rik|BB1CRY	crystallin, beta B1	protein-coding
mm_133149.1	chr16	70314092	70314096	+	1	NA	5' UTR (NM_028803, exon 1 of 16)	5' UTR (NM_028803, exon 1 of 16)	145	NM_028803	74185	Mm.396102	NM_028803	ENSMUSG00000022707	Gbe1	2310045H19Rik|2810426P10Rik|D16Ertd536e	glucan (1,4-alpha-), branching enzyme 1	protein-coding
mm_172609.1	chr8	15652306	15652317	+	1	NA	Intergenic	L1Md_T|LINE|L1	516527	NR_037214	100526464		NR_037214	ENSMUSG00000093142	Mir3106	mir-3106|mmu-mir-3106	microRNA 3106	ncRNA
mm_45540.1	chr5	72813955	72813966	-	1	NA	intron (NM_001113461, intron 3 of 17)	intron (NM_001113461, intron 3 of 17)	54488	NM_001113461	21682	Mm.319581	NM_013689	ENSMUSG00000029217	Tec	-	tec protein tyrosine kinase	protein-coding
mm_149253.1	chr19	10389387	10389441	+	1	NA	5' UTR (NM_018801, exon 1 of 9)	5' UTR (NM_018801, exon 1 of 9)	324	NM_173068	54525	Mm.182654	NM_018801	ENSMUSG00000024743	Syt7	AI851541|B230112P13Rik	synaptotagmin VII	protein-coding
mm_146100.1	chr18	73948315	73948325	+	1	NA	intron (NM_172632, intron 2 of 5)	intron (NM_172632, intron 2 of 5)	-69587	NR_045390	77855	Mm.410760	NR_045390	ENSMUSG00000090263	D730045A05Rik	-	RIKEN cDNA D730045A05 gene	ncRNA
mm_148682.1	chr19	5688779	5688797	+	1	NA	promoter-TSS (NM_022012)	promoter-TSS (NM_022012)	120	NM_144868	104401	Mm.329650	NM_144868	ENSMUSG00000054874	Pcnx3	Pcnxl3|mKIAA4073	pecanex homolog 3	protein-coding
mm_120236.1	chr14	62894081	62894098	+	1	NA	intron (NM_175546, intron 2 of 11)	RMER17A|LTR|ERVK	28547	NR_105860	102465311		NR_105860	ENSMUSG00000098858	Mir6541	Gm27311|mmu-mir-6541	microRNA 6541	ncRNA
mm_173288.1	chrY	2073307	2073307	-	1	NA	Intergenic	RLTR10C|LTR|ERVK	97102	NM_009571	22768	Mm.411381	NM_009571	ENSMUSG00000000103	Zfy2	Zfy-2	zinc finger protein 2, Y-linked	protein-coding
mm_16057.1	chr2	167778093	167778106	+	1	NA	Intergenic	Intergenic	86922	NR_015500	329562	Mm.123101	NM_177851	ENSMUSG00000006462	A530013C23Rik	-	RIKEN cDNA A530013C23 gene	ncRNA
mm_35857.1	chr4	49451235	49451274	-	1	NA	promoter-TSS (NM_001164565)	promoter-TSS (NM_001164565)	-145	NM_001164565	230161	Mm.30101	NM_001164565	ENSMUSG00000070985	Acnat1	AI132189	acyl-coenzyme A amino acid N-acyltransferase 1	protein-coding
mm_367.1	chr1	33922469	33922476	+	1	NA	intron (NM_001276764, intron 2 of 102)	intron (NM_001276764, intron 2 of 102)	14247	NM_001276764	13518	Mm.336625	NM_010081	ENSMUSG00000026131	Dst	2310001O04Rik|A830042E19Rik|AW554249|BP230|BPAG1-n|Bpag|Bpag1|Macf2|ah|athetoid|dt|mKIAA0728|nmf203|nmf339	dystonin	protein-coding
mm_83935.1	chr9	56636020	56636026	-	1	NA	promoter-TSS (NM_001311076)	promoter-TSS (NM_001311076)	-375	NM_001311076	235402	Mm.246605	NM_181074	ENSMUSG00000049556	Lingo1	4930471K13Rik|AV148400|LERN1|LINGO-1|Lrrn6a|UNQ201	leucine rich repeat and Ig domain containing 1	protein-coding
mm_115451.1	chr13	118714679	118714701	+	1	NA	promoter-TSS (NM_008002)	promoter-TSS (NM_008002)	-9	NM_008002	14165	Mm.317323	NM_008002	ENSMUSG00000021732	Fgf10	AEY17|BB213776|Fgf-10|Gsfaey17	fibroblast growth factor 10	protein-coding
mm_124245.1	chr14	101608788	101608861	-	1	NA	5' UTR (NM_001081278, exon 1 of 19)	5' UTR (NM_001081278, exon 1 of 19)	367	NM_001081278	210789	Mm.320639	NM_173380	ENSMUSG00000033083	Tbc1d4	5930406J04Rik|A930035N22|AV295684|As160	TBC1 domain family, member 4	protein-coding
mm_17719.1	chr2	32387761	32387778	-	1	NA	promoter-TSS (NM_008491)	promoter-TSS (NM_008491)	-30	NM_008491	16819	Mm.9537	NM_008491	ENSMUSG00000026822	Lcn2	24p3|AW212229|NRL|Sip24	lipocalin 2	protein-coding
mm_158234.1	chrX	106485169	106485187	-	1	NA	promoter-TSS (NM_001007580)	promoter-TSS (NM_001007580)	51	NM_001007580	333564	Mm.298000	NM_001007580	ENSMUSG00000033737	Fndc3c1	Fndc3c|Gm784	fibronectin type III domain containing 3C1	protein-coding
mm_11422.1	chr2	31759933	31759989	+	1	NA	promoter-TSS (NM_009594)	promoter-TSS (NM_009594)	22	NM_009594	11350	Mm.1318	NM_009594	ENSMUSG00000026842	Abl1	AI325092|Abl|E430008G22Rik|c-Abl	c-abl oncogene 1, non-receptor tyrosine kinase	protein-coding
mm_77793.1	chr9	3027756	3027775	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	10978	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_88380.1	chr10	76442417	76442425	+	1	NA	intron (NM_008787, intron 1 of 41)	CpG	491	NM_008787	18541	Mm.251794	NM_008787	ENSMUSG00000001151	Pcnt	AW476095|C86676|KEN|Pcnt2|kendrin|m239Asp|m275Asp	pericentrin (kendrin)	protein-coding
mm_150452.1	chr19	38132768	38132793	+	1	NA	promoter-TSS (NM_001170959)	promoter-TSS (NM_001170959)	-1	NM_033614	110855	Mm.450141	NM_033614	ENSMUSG00000024992	Pde6c	cpfl1	phosphodiesterase 6C, cGMP specific, cone, alpha prime	protein-coding
mm_141624.1	chr17	32916997	32917003	-	1	NA	promoter-TSS (NM_022434)	promoter-TSS (NM_022434)	87	NM_022434	64385	Mm.486449	NM_022434	ENSMUSG00000024292	Cyp4f14	1300014O15Rik|cyp4f-14	cytochrome P450, family 4, subfamily f, polypeptide 14	protein-coding
mm_158847.1	chrX	169978937	169978952	-	1	NA	promoter-TSS (NR_029457)	promoter-TSS (NR_029457)	-27	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_172841.1	chr9	3258903	3258909	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-59093	NR_027988	114673	Mm.422774	NM_053265	ENSMUSG00000042360	4930433N12Rik	-	RIKEN cDNA 4930433N12 gene	ncRNA
mm_7328.1	chr1	102628265	102628293	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	1472511	NR_037989	100504525	Mm.87065	NR_037989	ENSMUSG00000100684	Gm20268	-	predicted gene, 20268	ncRNA
mm_39598.1	chr5	23502937	23502970	+	1	NA	TTS (NM_009274)	TTS (NM_009274)	68524	NM_026984	69188	Mm.205190	NM_026984	ENSMUSG00000029004	Kmt2e	1810033J14Rik|9530077A04Rik|D230038D11Rik|Mll5|NKp44L	lysine (K)-specific methyltransferase 2E	protein-coding
mm_76064.1	chr8	78147461	78147468	-	1	NA	Intergenic	Intergenic	-65878	NM_183096	73301	Mm.61243	NM_183096	ENSMUSG00000037101	Ttc29	1700031F13Rik	tetratricopeptide repeat domain 29	protein-coding
mm_169763.1	chr15	98631745	98631746	+	1	NA	promoter-TSS (NM_001044741)	promoter-TSS (NM_001044741)	-583	NM_001044741	12297	Mm.3544	NM_007581	ENSMUSG00000003352	Cacnb3	Beta3|CAB3|Ca(v)beta3|Cchb3	calcium channel, voltage-dependent, beta 3 subunit	protein-coding
mm_69394.1	chr7	132154645	132154651	-	1	NA	promoter-TSS (NM_018867)	promoter-TSS (NM_018867)	93	NM_018867	55987	Mm.471654	NM_018867	ENSMUSG00000030862	Cpxm2	4632435C11Rik|CPX-2|Cpx2	carboxypeptidase X 2 (M14 family)	protein-coding
mm_163691.1	chr13	99429593	99429635	+	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-16788	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_60724.1	chr7	45339978	45339988	+	1	NA	3' UTR (NM_029741, exon 30 of 30)	3' UTR (NM_029741, exon 30 of 30)	4714	NM_010473	15464	Mm.39968	NM_010473	ENSMUSG00000038239	Hrc	-	histidine rich calcium binding protein	protein-coding
mm_88310.1	chr10	75410020	75410054	+	1	NA	intron (NM_133995, intron 1 of 9)	intron (NM_133995, intron 1 of 9)	3126	NM_133995	103149	Mm.441195	NM_133995	ENSMUSG00000033427	Upb1	AI195023	ureidopropionase, beta	protein-coding
mm_44062.1	chr5	148398877	148398902	+	1	NA	intron (NM_007513, intron 1 of 12)	intron (NM_007513, intron 1 of 12)	1015	NM_007513	11987	Mm.275489	NM_007513	ENSMUSG00000041313	Slc7a1	4831426K01Rik|AI447493|Atrc-1|Atrc1|Cat1|Rec-1|Rev-1|mCAT-1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 1	protein-coding
mm_52911.1	chr6	122824636	122824647	+	1	NA	intron (NM_021899, intron 1 of 10)	intron (NM_021899, intron 1 of 10)	4457	NM_021899	60611	Mm.87142	NM_021899	ENSMUSG00000003154	Foxj2	Fhx	forkhead box J2	protein-coding
mm_170222.1	chr17	7952414	7952426	-	1	NA	intron (NM_025789, intron 1 of 7)	LSU-rRNA_Hsa|rRNA|rRNA	6806	NM_025789	66832	Mm.29830	NM_025789	ENSMUSG00000073471	Rsph3a	1700012G05Rik|4930524H12Rik|R74860|Rshl2|Rshl2a	radial spoke 3A homolog (Chlamydomonas)	protein-coding
mm_130552.1	chr15	98989865	98989876	-	1	NA	TTS (NR_045991)	TTS (NR_045991)	3905	NR_045991	75951	Mm.441657	NR_045991	ENSMUSG00000097587	4930578M01Rik	3010001K12Rik	RIKEN cDNA 4930578M01 gene	ncRNA
mm_94478.1	chr11	6561107	6561126	+	1	NA	intron (NM_001190344, intron 1 of 9)	intron (NM_001190344, intron 1 of 9)	933	NM_001190344	216527	Mm.221271	NM_146014	ENSMUSG00000000378	Ccm2	BC029157	cerebral cavernous malformation 2	protein-coding
mm_38959.1	chr4	150687130	150687134	-	1	NA	Intergenic	B1F2|SINE|Alu	-34958	NM_173774	242773	Mm.29280	NM_173774	ENSMUSG00000039838	Slc45a1	C230078B22|Dnb5	solute carrier family 45, member 1	protein-coding
mm_20152.1	chr2	121551384	121551419	-	1	NA	intron (NM_172673, intron 13 of 14)	intron (NM_172673, intron 13 of 14)	44678	NM_001290986	241627	Mm.293284	NM_030234	ENSMUSG00000027242	Wdr76	5830411K18Rik|6030457D09|AA517836	WD repeat domain 76	protein-coding
mm_49384.1	chr6	24748326	24748356	+	1	NA	promoter-TSS (NM_029848)	promoter-TSS (NM_029848)	-26	NM_029848	77042	Mm.66017	NM_029848	ENSMUSG00000029680	Hyal4	4632428M18Rik|CSHY	hyaluronoglucosaminidase 4	protein-coding
mm_35356.1	chr4	32335640	32335646	-	1	NA	Intergenic	Intergenic	-81792	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_58867.1	chr7	16945695	16945768	+	1	NA	exon (NM_001099636, exon 1 of 1)	exon (NM_001099636, exon 1 of 1)	1049	NM_001099636	434128	Mm.483018	NM_001099636	ENSMUSG00000070802	Pnmal2	EG434128	PNMA-like 2	protein-coding
mm_112683.1	chr13	16029188	16029200	+	1	NA	3' UTR (NM_008380, exon 5 of 5)	3' UTR (NM_008380, exon 5 of 5)	17343	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_154578.1	chrX	7571195	7571203	+	1	NA	intron (NM_138605, intron 1 of 3)	intron (NM_138605, intron 1 of 3)	-2401	NR_029473	78185	Mm.160055	NR_029473	ENSMUSG00000039545	Ppp1r3fos	4930524L23Rik	protein phosphatase 1, regulatory subunit 3F, opposite strand	ncRNA
mm_10674.1	chr2	21367533	21367540	+	1	NA	promoter-TSS (NM_001004761)	promoter-TSS (NM_001004761)	-31	NM_001004761	241263	Mm.166647	NM_175706	ENSMUSG00000045967	Gpr158	5330427M13Rik|mKIAA1136	G protein-coupled receptor 158	protein-coding
mm_101734.1	chr11	43311060	43311070	-	1	NA	Intergenic	Intergenic	63396	NR_029558	387164		NR_029558	ENSMUSG00000065601	Mir146	Mirn146|miR-146a|mmu-mir-146	microRNA 146	ncRNA
mm_98742.1	chr11	96464044	96464048	+	1	NA	promoter-TSS (NM_001177899)	promoter-TSS (NM_001177899)	501	NR_033524	100038600	Mm.483549	NR_033524		Gm11529	OTTMUSG00000001775	predicted gene 11529	ncRNA
mm_109177.1	chr12	108422879	108422889	+	1	NA	promoter-TSS (NM_001043335)	promoter-TSS (NM_001043335)	68	NM_001043335	68519	Mm.236645	NM_001043335	ENSMUSG00000058070	Eml1	1110008N23Rik|A930030P13Rik|AA171013|AI847476|AI853955|ELP79|EMAP|EMAPL|heco	echinoderm microtubule associated protein like 1	protein-coding
mm_146723.1	chr18	15064344	15064356	-	1	NA	promoter-TSS (NM_001142731)	promoter-TSS (NM_001142731)	-768	NM_001142731	106931	Mm.329299	NM_134112	ENSMUSG00000036225	Kctd1	4933402K10Rik|AI661543|AW553000	potassium channel tetramerisation domain containing 1	protein-coding
mm_120411.1	chr14	65227701	65227705	+	1	NA	intron (NM_021458, intron 4 of 6)	intron (NM_021458, intron 4 of 6)	34760	NM_021458	14365	Mm.214687	NM_021458	ENSMUSG00000007989	Fzd3	AU020229|D930050A07Rik|Fz3	frizzled class receptor 3	protein-coding
mm_72912.1	chr8	90955419	90955488	+	1	NA	intron (NM_001310530, intron 1 of 37)	intron (NM_001310530, intron 1 of 37)	23204	NM_001310530	109151	Mm.100615	NM_177224	ENSMUSG00000056608	Chd9	1810014J18Rik|9030205D12Rik|A330063D19Rik|AD013|PRIC320|mKIAA0308	chromodomain helicase DNA binding protein 9	protein-coding
mm_132550.1	chr16	37883600	37883628	+	1	NA	3' UTR (NM_177093, exon 4 of 4)	3' UTR (NM_177093, exon 4 of 4)	15214	NM_177093	320184	Mm.390882	NM_177093	ENSMUSG00000034158	Lrrc58	1810012N18Rik|C330018J07Rik	leucine rich repeat containing 58	protein-coding
mm_10760.1	chr2	24153174	24153197	+	1	NA	promoter-TSS (NM_027163)	promoter-TSS (NM_027163)	13	NM_027163	69677	Mm.45901	NM_027163	ENSMUSG00000026985	Il1f8	2310043N20Rik|Il36b	interleukin 1 family, member 8	protein-coding
mm_88177.1	chr10	69925485	69925502	+	1	NA	promoter-TSS (NM_009670)	promoter-TSS (NM_009670)	-39	NM_170687	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_59933.1	chr7	30423626	30423644	+	1	NA	5' UTR (NM_172142, exon 2 of 11)	5' UTR (NM_172142, exon 2 of 11)	331	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_154444.1	chrM	1500	1506	-	1	NA	NA	Intergenic	NA	NA								
mm_170991.1	chr2	75191584	75191586	-	1	NA	Intergenic	Intergenic	252594	NR_040635	77269	Mm.389278	NR_040635		9430019J16Rik	-	RIKEN cDNA 9430019J16 gene	ncRNA
mm_39954.1	chr5	32133806	32133817	+	1	NA	Intergenic	Intergenic	-2661	NM_008037	14284	Mm.24684	NM_008037	ENSMUSG00000029135	Fosl2	Fra-2	fos-like antigen 2	protein-coding
mm_65634.1	chr7	27572168	27572181	-	1	NA	intron (NM_175107, intron 7 of 9)	intron (NM_175107, intron 7 of 9)	11698	NM_001122767	66367	Mm.29831	NM_175107	ENSMUSG00000049643	2310022A10Rik	-	RIKEN cDNA 2310022A10 gene	protein-coding
mm_18901.1	chr2	76718063	76718073	-	1	NA	exon (NM_011652, exon 301 of 313)	exon (NM_011652, exon 301 of 313)	42753	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_160145.1	chr7	38528175	38528175	-	1	NA	promoter-TSS (NM_001013810)	promoter-TSS (NM_001013810)	18	NM_001013810	434171	Mm.60990	NM_001013810	ENSMUSG00000060565	Gm5591	EG434171	predicted gene 5591	protein-coding
mm_170855.1	chr2	180225894	180225894	-	1	NA	promoter-TSS (NM_001081171)	promoter-TSS (NM_001081171)	-35	NM_001081171	16776	Mm.4339	NM_001081171	ENSMUSG00000015647	Lama5	AA408760|AA408762|AI853660|[a]5|laminin-511|mKIAA0533	laminin, alpha 5	protein-coding
mm_1259.1	chr1	63115051	63115055	+	1	NA	promoter-TSS (NM_001114609)	promoter-TSS (NM_001114609)	313	NR_045914	100380944	Mm.392955	NR_045914	ENSMUSG00000084799	Ino80dos	Gm11602|OTTMUSG00000002611	INO80 complex subunit D, opposite strand	ncRNA
mm_45149.1	chr5	49285596	49285609	-	1	NA	promoter-TSS (NM_001199244)	promoter-TSS (NM_001199244)	57	NM_001199244	80334	Mm.160172	NM_030265	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding
mm_32544.1	chr4	109343030	109343081	+	1	NA	promoter-TSS (NM_001159964)	promoter-TSS (NM_001159964)	-1	NM_001159964	13858	Mm.318250	NM_007943	ENSMUSG00000028552	Eps15	2410112D09Rik	epidermal growth factor receptor pathway substrate 15	protein-coding
mm_115458.1	chr13	119428397	119428413	+	1	NA	promoter-TSS (NM_001079849)	promoter-TSS (NM_001079849)	-195	NM_001079849	218693	Mm.490243	NM_145457	ENSMUSG00000025451	Paip1	PAIP-1	polyadenylate binding protein-interacting protein 1	protein-coding
mm_88279.1	chr10	75060886	75060901	+	1	NA	promoter-TSS (NM_001081412)	promoter-TSS (NM_001081412)	-3	NM_001081412	110279	Mm.333722	NM_001081412	ENSMUSG00000009681	Bcr	5133400C09Rik|AI561783|AI853148|mKIAA3017	breakpoint cluster region	protein-coding
mm_43166.1	chr5	127241808	127241849	+	1	NA	promoter-TSS (NM_175432)	promoter-TSS (NM_175432)	2	NM_175432	208213	Mm.444235	NM_175432	ENSMUSG00000034324	Tmem132c	2810482M11Rik|3230401P16|4632425D07Rik	transmembrane protein 132C	protein-coding
mm_15970.1	chr2	166072548	166072548	+	1	NA	3' UTR (NM_008679, exon 23 of 23)	3' UTR (NM_008679, exon 23 of 23)	79911	NM_008679	17979	Mm.469663	NM_008679	ENSMUSG00000027678	Ncoa3	2010305B15Rik|AW321064|Actr|Aib1|KAT13B|Rac3|Src3|Tram-1|Tram1|bHLHe42|p/Cip|pCip	nuclear receptor coactivator 3	protein-coding
mm_136538.1	chr16	97763450	97763472	-	1	NA	intron (NM_023663, intron 1 of 7)	CpG	294	NM_023663	72388	Mm.35290	NM_023663	ENSMUSG00000005251	Ripk4	2310069J12Rik|AI552420|ANKK2|Ankrd3|DIk|PKK|RIP4	receptor-interacting serine-threonine kinase 4	protein-coding
mm_10646.1	chr2	20574716	20574719	+	1	NA	intron (NM_029895, intron 3 of 18)	T-rich|Low_complexity|Low_complexity	55204	NM_001177631	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding
mm_122770.1	chr14	54398025	54398066	-	1	NA	intron (NM_001253679, intron 3 of 10)	intron (NM_001253679, intron 3 of 10)	11427	NM_001253680	20540	Mm.142455	NM_011405	ENSMUSG00000000958	Slc7a7	AI790233|my+lat1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 7	protein-coding
mm_147015.1	chr18	34578772	34578776	-	1	NA	intron (NM_080637, intron 1 of 5)	intron (NM_080637, intron 1 of 5)	332	NM_080637	75533	Mm.275430	NM_080637	ENSMUSG00000035984	Nme5	1700019D05Rik|Nm23-M5	NME/NM23 family member 5	protein-coding
mm_85467.1	chr9	105521334	105521369	-	1	NA	promoter-TSS (NM_001253831)	promoter-TSS (NM_001253831)	-94	NM_001253831	235574	Mm.326247	NM_175025	ENSMUSG00000032570	Atp2c1	1700121J11Rik|ATP2C1A|AW061228|BCPM|D930003G21Rik|HHD|SPCA|pmr1	ATPase, Ca++-sequestering	protein-coding
mm_4865.1	chr1	187662488	187662508	+	1	NA	intron (NM_001243792, intron 1 of 7)	intron (NM_001243792, intron 1 of 7)	53492	NM_001243792	26381	Mm.89989	NM_011935	ENSMUSG00000026610	Esrrg	ERR3|Errg|NR3B3|mKIAA0832	estrogen-related receptor gamma	protein-coding
mm_112946.1	chr13	21002709	21002721	+	1	NA	intron (NM_012054, intron 17 of 20)	intron (NM_012054, intron 17 of 20)	70584	NM_146535	258528	Mm.377554	NM_146535	ENSMUSG00000042869	Olfr1370	MOR256-14	olfactory receptor 1370	protein-coding
mm_73087.1	chr8	94524873	94524882	+	1	NA	intron (NM_001033207, intron 46 of 48)	intron (NM_001033207, intron 46 of 48)	-8151	NM_153507	234577	Mm.291815	NM_153507	ENSMUSG00000034361	Cpne2	3322401K10Rik	copine II	protein-coding
mm_16415.1	chr2	180119302	180119407	+	1	NA	promoter-TSS (NM_144500)	promoter-TSS (NM_144500)	-12	NM_144500	228983	Mm.253578	NM_144500	ENSMUSG00000039050	Osbpl2	C130070J12Rik|ORP-2|Orp2|mKIAA0772	oxysterol binding protein-like 2	protein-coding
mm_143942.1	chr17	86403971	86403971	-	1	NA	intron (NM_011104, intron 2 of 14)	MLT1F1|LTR|ERVL-MaLR	-116793	NR_045435	72104	Mm.443401	NR_045435	ENSMUSG00000100738	2010106C02Rik	-	RIKEN cDNA 2010106C02 gene	ncRNA
mm_16996.1	chr2	18348967	18348970	-	1	NA	intron (NM_007869, intron 1 of 11)	intron (NM_007869, intron 1 of 11)	43862	NM_001190817	13418	Mm.246674	NM_007869	ENSMUSG00000026740	Dnajc1	4733401K02Rik|AA960110|D230036H06Rik|Dnajl1|ERdj1|ERj1p|MTJ1	DnaJ heat shock protein family (Hsp40) member C1	protein-coding
mm_70298.1	chr8	4087218	4087226	+	1	NA	Intergenic	Intergenic	18542	NM_026956	69142	Mm.171061	NM_026956	ENSMUSG00000051906	Cd209f	1810029C22Rik|AI647041|SIGNR8	CD209f antigen	protein-coding
mm_157156.1	chrX	9463499	9463510	-	1	NA	intron (NM_007807, intron 3 of 12)	intron (NM_007807, intron 3 of 12)	5820	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_60920.1	chr7	46841518	46841538	+	1	NA	Intergenic	Intergenic	-4276	NM_010699	16828	Mm.29324	NM_010699	ENSMUSG00000063229	Ldha	Ldh1|Ldhm|l7R2	lactate dehydrogenase A	protein-coding
mm_58066.1	chr6	136922153	136922167	-	1	NA	promoter-TSS (NM_026983)	promoter-TSS (NM_026983)	20	NM_026983	69187	Mm.33692	NM_026983	ENSMUSG00000030219	Erp27	1810033M07Rik|1810047B09Rik	endoplasmic reticulum protein 27	protein-coding
mm_44443.1	chr5	21645622	21645627	-	1	NA	promoter-TSS (NM_026034)	promoter-TSS (NM_026034)	-19	NM_177076	320118	Mm.442295	NM_177076	ENSMUSG00000048520	Fbxl13	4921539K22Rik	F-box and leucine-rich repeat protein 13	protein-coding
mm_92471.1	chr10	78038307	78038315	-	1	NA	intron (NM_001271558, intron 7 of 11)	RMER20A|LTR|ERVK	-3976	NM_001081695	54427	Mm.13433	NM_019448	ENSMUSG00000000730	Dnmt3l	D6Ertd14e|ecat7	DNA (cytosine-5-)-methyltransferase 3-like	protein-coding
mm_77121.1	chr8	111300190	111300206	-	1	NA	promoter-TSS (NM_146218)	promoter-TSS (NM_146218)	24	NM_146218	234736	Mm.334816	NM_146218	ENSMUSG00000033596	Rfwd3	BC027246	ring finger and WD repeat domain 3	protein-coding
mm_124230.1	chr14	101199065	101199073	-	1	NA	exon (NM_029680, exon 3 of 3)	exon (NM_029680, exon 3 of 3)	1000	NM_029680	76627	Mm.31415	NM_029680	ENSMUSG00000042888	Prr30	1700110M21Rik	proline rich 30	protein-coding
mm_142375.1	chr17	44724225	44724227	-	1	NA	intron (NR_073392, intron 3 of 7)	intron (NR_073392, intron 3 of 7)	11950	NR_073425	12393	Mm.391013	NM_009820	ENSMUSG00000039153	Runx2	AML3|Cbf|Cbfa-1|Cbfa1|LS3|Osf2|PEBP2aA|Pebp2a1|Pebpa2a	runt related transcription factor 2	protein-coding
mm_22368.1	chr2	181135221	181135304	-	1	NA	promoter-TSS (NM_010611)	promoter-TSS (NM_010611)	27	NM_001006668	16536	Mm.40615	NM_010611	ENSMUSG00000016346	Kcnq2	HNSPC|KQT2|Nmf134	potassium voltage-gated channel, subfamily Q, member 2	protein-coding
mm_90620.1	chr10	128413211	128413221	+	1	NA	intron (NR_104288, intron 1 of 6)	intron (NR_104288, intron 1 of 6)	1600	NM_026259	67588	Mm.294120	NM_026259	ENSMUSG00000025373	Rnf41	2210404G21Rik|4930511A05Rik|4933415P08Rik|D10Ertd722e|FLRF|Nrdp1	ring finger protein 41	protein-coding
mm_26488.1	chr3	145118565	145118622	+	1	NA	promoter-TSS (NM_025714)	promoter-TSS (NM_025714)	4	NM_001162538	52184	Mm.259105	NM_025714	ENSMUSG00000028256	Odf2l	4733401D09Rik|9630045K08Rik|D3Ertd250e	outer dense fiber of sperm tails 2-like	protein-coding
mm_2522.1	chr1	106518119	106518129	+	1	NA	Intergenic	Intergenic	28507	NR_106164	102466254		NR_106164	ENSMUSG00000098344	Mir3473f	Gm27846|mmu-mir-3473f	microRNA 3473f	ncRNA
mm_33886.1	chr4	136178213	136178235	+	1	NA	intron (NM_177733, intron 1 of 6)	intron (NM_177733, intron 1 of 6)	-2558	NM_001305399	242705	Mm.307932	NM_177733	ENSMUSG00000018983	E2f2	E2F-2	E2F transcription factor 2	protein-coding
mm_80570.1	chr9	83938464	83938467	+	1	NA	intron (NM_001305935, intron 1 of 10)	U6|snRNA|snRNA	-10316	NM_199195	12040	Mm.12819	NM_199195	ENSMUSG00000032263	Bckdhb	BCKDE1B|BCKDH E1-beta	branched chain ketoacid dehydrogenase E1, beta polypeptide	protein-coding
mm_46732.1	chr5	110780535	110780551	-	1	NA	promoter-TSS (NM_019700)	promoter-TSS (NM_019700)	53	NM_019700	56361	Mm.23528	NM_019700	ENSMUSG00000029507	Pus1	A730013B20Rik|MPUS1|mPus1p	pseudouridine synthase 1	protein-coding
mm_112539.1	chr13	9685116	9685120	+	1	NA	3' UTR (NM_001347480, exon 14 of 14)	3' UTR (NM_001347480, exon 14 of 14)	78692	NM_001347471	66505	Mm.397307	NM_144516	ENSMUSG00000021156	Zmynd11	2210402G22Rik|BS69	zinc finger, MYND domain containing 11	protein-coding
mm_131664.1	chr16	20629843	20629894	+	1	NA	promoter-TSS (NM_139293)	promoter-TSS (NM_139293)	17	NM_139293	107522	Mm.263319	NM_025462	ENSMUSG00000022842	Ece2	1810009K13Rik|6330509A19Rik|9630025D12Rik|BB127715|Ece-2	endothelin converting enzyme 2	protein-coding
mm_80747.1	chr9	95028599	95028611	+	1	NA	intron (NM_177909, intron 11 of 15)	L1M4c|LINE|L1	276776	NR_106116	102465763		NR_106116	ENSMUSG00000098251	Mir7656	Gm27614|mmu-mir-7656	microRNA 7656	ncRNA
mm_52039.1	chr6	96282418	96282420	+	1	NA	intron (NM_182808, intron 2 of 4)	intron (NM_182808, intron 2 of 4)	-116214	NR_003643	78482	Mm.391486	NM_030107	ENSMUSG00000072878	1700123L14Rik	-	nucleoporin 50 pseudogene	pseudo
mm_281.1	chr1	21262817	21262834	+	1	NA	exon (NM_010356, exon 6 of 7)	exon (NM_010356, exon 6 of 7)	22240	NM_010356	14859	Mm.394593	NM_010356	ENSMUSG00000025934	Gsta3	Gst2-3	glutathione S-transferase, alpha 3	protein-coding
mm_18396.1	chr2	60210520	60210534	-	1	NA	intron (NM_020575, intron 1 of 9)	intron (NM_020575, intron 1 of 9)	591	NM_020575	57438	Mm.260635	NM_020575	ENSMUSG00000026977	March7	Axo|Axot|Gtrgeo17	membrane-associated ring finger (C3HC4) 7	protein-coding
mm_50538.1	chr6	49046109	49046123	+	1	NA	intron (NM_053110, intron 4 of 10)	intron (NM_053110, intron 4 of 10)	9598	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_1999.1	chr1	87126975	87126982	+	1	NA	exon (NM_007432, exon 9 of 11)	exon (NM_007432, exon 9 of 11)	1970	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_21765.1	chr2	164844462	164844474	-	1	NA	exon (NM_011125, exon 12 of 16)	exon (NM_011125, exon 12 of 16)	10695	NM_008906	19025	Mm.359633	NM_008906	ENSMUSG00000017760	Ctsa	AU019505|PPCA|Ppgb	cathepsin A	protein-coding
mm_20400.1	chr2	129199206	129199267	-	1	NA	intron (NM_001159593, intron 1 of 5)	CpG	463	NM_001159593	20515	Mm.272675	NM_015747	ENSMUSG00000027397	Slc20a1	AI607883|Glvr-1|Glvr1	solute carrier family 20, member 1	protein-coding
mm_146920.1	chr18	31610509	31610513	-	1	NA	promoter-TSS (NM_026165)	promoter-TSS (NM_026165)	-609	NM_026165	67453	Mm.23896	NM_026165	ENSMUSG00000024259	Slc25a46	1200007B05Rik|AI325987	solute carrier family 25, member 46	protein-coding
mm_125273.1	chr15	36179300	36179327	+	1	NA	promoter-TSS (NM_012031)	promoter-TSS (NM_012031)	-217	NM_012031	26942	Mm.295539	NM_012031	ENSMUSG00000037617	Spag1	tpis	sperm associated antigen 1	protein-coding
mm_153038.1	chr19	32061331	32061346	-	1	NA	5' UTR (NM_018830, exon 3 of 24)	5' UTR (NM_018830, exon 3 of 24)	41802	NM_018830	54447	Mm.491229	NM_018830	ENSMUSG00000024887	Asah2	AI585898	N-acylsphingosine amidohydrolase 2	protein-coding
mm_42274.1	chr5	114146567	114146610	+	1	NA	Intergenic	Intergenic	15432	NM_011677	22256	Mm.1393	NM_011677	ENSMUSG00000029591	Ung	UNG1|UNG2	uracil DNA glycosylase	protein-coding
mm_107617.1	chr12	51348020	51348040	+	1	NA	promoter-TSS (NM_001015099)	promoter-TSS (NM_001015099)	-200	NM_001167964	217558	Mm.253264	NM_001015099	ENSMUSG00000035293	G2e3	6030408C04Rik|9030416F18|AW046379|D930034K21Rik|mKIAA1333	G2/M-phase specific E3 ubiquitin ligase	protein-coding
mm_120865.1	chr14	75229621	75229648	+	1	NA	3' UTR (NM_001247984, exon 16 of 16)	3' UTR (NM_001247984, exon 16 of 16)	-12653	NM_019775	56373	Mm.24242	NM_019775	ENSMUSG00000021999	Cpb2	1110032P04Rik|4930405E17Rik|AI255929|CPR|Cpu|TAFI	carboxypeptidase B2 (plasma)	protein-coding
mm_44751.1	chr5	31291014	31291024	-	1	NA	promoter-TSS (NM_026298)	promoter-TSS (NM_026298)	95	NM_026298	67661	Mm.293023	NM_026298	ENSMUSG00000038564	Ift172	4930553F24Rik|Slb|avc1|wim	intraflagellar transport 172	protein-coding
mm_111257.1	chr12	85097081	85097091	-	1	NA	intron (NM_175198, intron 1 of 4)	intron (NM_175198, intron 1 of 4)	9345	NM_175198	73422	Mm.311944	NM_175198	ENSMUSG00000042320	Prox2	1700058C01Rik	prospero homeobox 2	protein-coding
mm_166756.1	chr6	127474176	127474193	+	1	NA	intron (NM_181402, intron 4 of 8)	intron (NM_181402, intron 4 of 8)	20461	NM_181402	101187	Mm.110818	NM_181402	ENSMUSG00000037997	Parp11	5330431N24Rik|AI851877|ARTD11|HIN1L|PARP-11	poly (ADP-ribose) polymerase family, member 11	protein-coding
mm_10172.1	chr2	4559760	4559810	+	1	NA	promoter-TSS (NM_001177844)	promoter-TSS (NM_001177844)	31	NM_001177844	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding
mm_15177.1	chr2	154190750	154190759	+	1	NA	promoter-TSS (NM_001012392)	promoter-TSS (NM_001012392)	-64	NM_001012392	228801	Mm.3783	NM_153418	ENSMUSG00000027485	Bpifb1	Lplunc1	BPI fold containing family B, member 1	protein-coding
mm_19746.1	chr2	104816970	104817009	-	1	NA	promoter-TSS (NM_001123327)	promoter-TSS (NM_001123327)	-293	NM_001123327	99003	Mm.274314	NM_001123327	ENSMUSG00000074994	Qser1	4732486I23Rik|AI502974	glutamine and serine rich 1	protein-coding
mm_11932.1	chr2	52425005	52425021	+	1	NA	promoter-TSS (NM_182994)	promoter-TSS (NM_182994)	-139	NM_182994	75423	Mm.314378	NM_182994	ENSMUSG00000036093	Arl5a	2410015N24Rik|2810410P22Rik|AA408731|AW610751|Arl5|T25534	ADP-ribosylation factor-like 5A	protein-coding
mm_29609.1	chr3	121263159	121263174	-	1	NA	intron (NM_178936, intron 1 of 7)	CpG	150	NM_178936	99887	Mm.26088	NM_178936	ENSMUSG00000028132	Tmem56	4930577M16Rik|AU018104|AW109744|C730036B01Rik	transmembrane protein 56	protein-coding
mm_144230.1	chr18	10325149	10325222	+	1	NA	promoter-TSS (NM_001083628)	promoter-TSS (NM_001083628)	6	NM_001083628	381157	Mm.261535	NM_001083628	ENSMUSG00000042942	Greb1l	mKIAA4095	growth regulation by estrogen in breast cancer-like	protein-coding
mm_138593.1	chr17	35509435	35509452	+	1	NA	exon (NM_001252452, exon 3 of 5)	exon (NM_001252452, exon 3 of 5)	636	NM_001252452	18999	Mm.17031	NM_013633	ENSMUSG00000024406	Pou5f1	NF-A3|Oct-3|Oct-3/4|Oct-4|Oct3|Oct3/4|Oct4|Otf-3|Otf-4|Otf3|Otf3-rs7|Otf3g|Otf4	POU domain, class 5, transcription factor 1	protein-coding
mm_119606.1	chr14	51096389	51096408	+	1	NA	5' UTR (NM_201239, exon 1 of 2)	5' UTR (NM_201239, exon 1 of 2)	398	NM_201239	58809	Mm.202665	NM_021472	ENSMUSG00000021876	Rnase4	C730049F20Rik|Rab1	ribonuclease, RNase A family 4	protein-coding
mm_125719.1	chr15	72972078	72972094	+	1	NA	intron (NM_029640, intron 8 of 21)	ORR1D2|LTR|ERVL-MaLR	83726	NM_029640	76510	Mm.158902	NM_029640	ENSMUSG00000047921	Trappc9	1810044A24Rik|2900005P22Rik|4632408O18Rik|Ibp|Nibp|TRS130|mKIAA1882	trafficking protein particle complex 9	protein-coding
mm_83018.1	chr9	36797283	36797293	-	1	NA	promoter-TSS (NM_007915)	promoter-TSS (NM_007915)	105	NM_001199494	13663	Mm.4337	NM_007915	ENSMUSG00000062762	Ei24	AA536736|AI115355|PIG8	etoposide induced 2.4 mRNA	protein-coding
mm_116021.1	chr13	24831410	24831518	-	1	NA	promoter-TSS (NM_019551)	promoter-TSS (NM_019551)	25	NM_025790	66834	Mm.2125	NM_025790	ENSMUSG00000006717	Acot13	0610006O17Rik|Them2	acyl-CoA thioesterase 13	protein-coding
mm_108889.1	chr12	100003687	100003703	+	1	NA	intron (NM_146037, intron 2 of 2)	intron (NM_146037, intron 2 of 2)	39196	NM_001164427	217826	Mm.312335	NM_146037	ENSMUSG00000045404	Kcnk13	BB085247|F730021E22Rik|Gm1570|Gm1685	potassium channel, subfamily K, member 13	protein-coding
mm_51240.1	chr6	71543976	71543986	+	1	NA	5' UTR (NM_025783, exon 1 of 6)	5' UTR (NM_025783, exon 1 of 6)	127	NM_025783	66700	Mm.181278	NM_025783	ENSMUSG00000053119	Chmp3	25.1|4921505F14Rik|9130011K15Rik|CGI-49|D6Ertd286e|NEDF|Vps24	charged multivesicular body protein 3	protein-coding
mm_40292.1	chr5	43251699	43251713	+	1	NA	intron (NM_175937, intron 4 of 10)	intron (NM_175937, intron 4 of 10)	-16352	NR_028417	665934	Mm.381491	NR_028417	ENSMUSG00000085720	Gm7854	EG665934|ENSMUSG00000054483	predicted gene 7854	ncRNA
mm_118947.1	chr14	27344586	27344589	+	1	NA	intron (NM_001289687, intron 1 of 9)	intron (NM_001289687, intron 1 of 9)	8550	NM_001289687	71704	Mm.248606	NM_027871	ENSMUSG00000021895	Arhgef3	1200004I24Rik|9830169H03Rik|C76747|Xpln	Rho guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_104156.1	chr11	87212426	87212438	-	1	NA	intron (NM_197987, intron 22 of 23)	intron (NM_197987, intron 22 of 23)	85357	NM_197987	68729	Mm.17436	NM_197987	ENSMUSG00000018548	Trim37	1110032A10Rik|2810004E07Rik|AI848587|AU043018|MUL|TEF3|mKIAA0898	tripartite motif-containing 37	protein-coding
mm_83570.1	chr9	46328938	46328961	-	1	NA	Intergenic	Intergenic	-8963	NM_183104	74361	Mm.159169	NM_183104	ENSMUSG00000056617	4931429L15Rik	-	RIKEN cDNA 4931429L15 gene	protein-coding
mm_75857.1	chr8	70700071	70700088	-	1	NA	exon (NM_001286944, exon 1 of 1)	exon (NM_001286944, exon 1 of 1)	2340	NM_001286944	16478	Mm.419851	NM_010592	ENSMUSG00000071076	Jund	Jund1	jun D proto-oncogene	protein-coding
mm_151885.1	chr19	5798607	5798648	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	-2646	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_75867.1	chr8	70762960	70762976	-	1	NA	3' UTR (NM_023065, exon 8 of 8)	3' UTR (NM_023065, exon 8 of 8)	-2047	NM_183170	234384	Mm.213010	NM_183170	ENSMUSG00000035559	Mpv17l2	Fksg24	MPV17 mitochondrial membrane protein-like 2	protein-coding
mm_72961.1	chr8	92827435	92827439	+	1	NA	5' UTR (NM_008610, exon 1 of 13)	5' UTR (NM_008610, exon 1 of 13)	140	NM_008610	17390	Mm.29564	NM_008610	ENSMUSG00000031740	Mmp2	Clg4a|GelA|MMP-2	matrix metallopeptidase 2	protein-coding
mm_170754.1	chr2	156809283	156809292	+	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	-30720	NM_001291124	228839	Mm.315625	NM_173396	ENSMUSG00000062175	Tgif2	4921501K24|5730599O09Rik|C80753|C81206	TGFB-induced factor homeobox 2	protein-coding
mm_51416.1	chr6	78382008	78382016	+	1	NA	exon (NM_011259, exon 3 of 6)	exon (NM_011259, exon 3 of 6)	1303	NM_011259	19694	Mm.2552	NM_011259	ENSMUSG00000079516	Reg3a	AV063448	regenerating islet-derived 3 alpha	protein-coding
mm_154690.1	chrX	8046592	8046593	+	1	NA	Intergenic	Intergenic	27721	NM_001290716	20937	Mm.9244	NM_011514	ENSMUSG00000039231	Suv39h1	AI852103|AL022883|DXHXS7466e|H3-K9-HMTase 1|KMT1A|mIS6	suppressor of variegation 3-9 homolog 1 (Drosophila)	protein-coding
mm_131912.1	chr16	23307706	23307724	+	1	NA	intron (NM_001252506, intron 1 of 6)	intron (NM_001252506, intron 1 of 6)	17245	NM_001252506	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_165948.1	chr4	83465041	83465081	+	1	NA	exon (NM_001290527, exon 9 of 11)	exon (NM_001290527, exon 9 of 11)	21387	NM_001290527	101739	Mm.105331	NM_133948	ENSMUSG00000028484	Psip1	AA408851|AU015605|Dfs70|Ledgfa|Ledgfb|Psip2	PC4 and SFRS1 interacting protein 1	protein-coding
mm_167979.1	chrX	160792479	160792481	+	1	NA	intron (NM_011302, intron 5 of 5)	intron (NM_011302, intron 5 of 5)	24467	NM_011302	20147	Mm.41982	NM_011302	ENSMUSG00000031293	Rs1	Rs1h|Xlrs1|tmgc1	retinoschisis (X-linked, juvenile) 1 (human)	protein-coding
mm_60614.1	chr7	44591221	44591237	+	1	NA	exon (NM_001290682, exon 1 of 5)	exon (NM_001290682, exon 1 of 5)	343	NM_001290682	16504	Mm.40312	NM_008422	ENSMUSG00000062785	Kcnc3	KShIIID|Kcr2-3|Kv3.3	potassium voltage gated channel, Shaw-related subfamily, member 3	protein-coding
mm_144434.1	chr18	21072330	21072351	+	1	NA	promoter-TSS (NM_008586)	promoter-TSS (NM_008586)	-4	NM_008586	17288	Mm.2682	NM_008586	ENSMUSG00000024313	Mep1b	Mep-1b	meprin 1 beta	protein-coding
mm_35467.1	chr4	40805241	40805244	-	1	NA	3' UTR (NM_022305, exon 6 of 6)	3' UTR (NM_022305, exon 6 of 6)	44896	NR_039584	100628614		NR_039584	ENSMUSG00000096377	Mir5123	mmu-mir-5123|mu-mir-5123	microRNA 5123	ncRNA
mm_56789.1	chr6	116641732	116641747	-	1	NA	exon (NM_178045, exon 7 of 11)	exon (NM_178045, exon 7 of 11)	4308	NR_106010	102466793		NR_106010	ENSMUSG00000098334	Mir7043	Gm27776|mmu-mir-7043	microRNA 7043	ncRNA
mm_131547.1	chr16	17893581	17893609	+	1	NA	promoter-TSS (NM_009435)	promoter-TSS (NM_009435)	-608	NM_009435	22114	Mm.439725	NM_009435	ENSMUSG00000041566	Tssk1	Stk22a|TSK-1|Tsk1|Tssk|Tssk1b	testis-specific serine kinase 1	protein-coding
mm_2701.1	chr1	127868785	127868807	+	1	NA	promoter-TSS (NM_178690)	promoter-TSS (NM_178690)	23	NM_178690	226407	Mm.489713	NM_178690	ENSMUSG00000036104	Rab3gap1	1700003B17Rik|4732493F09Rik|AL117896|Rab3gap|p130	RAB3 GTPase activating protein subunit 1	protein-coding
mm_28910.1	chr3	98741855	98741866	-	1	NA	3' UTR (NM_001161745, exon 4 of 4)	3' UTR (NM_001161745, exon 4 of 4)	-17317	NM_153193	15493	Mm.482364	NM_153193	ENSMUSG00000063730	Hsd3b2	-	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 2	protein-coding
mm_20763.1	chr2	140956060	140956071	-	1	NA	intron (NM_001013802, intron 4 of 18)	intron (NM_001013802, intron 4 of 18)	-284589	NM_178382	71436	Mm.426781	NM_178382	ENSMUSG00000051379	Flrt3	5530600M07Rik|C430047I10Rik|mKIAA1469	fibronectin leucine rich transmembrane protein 3	protein-coding
mm_121494.1	chr14	121878565	121878575	+	1	NA	promoter-TSS (NM_026861)	promoter-TSS (NM_026861)	-36	NM_026861	68889	Mm.441151	NM_026861	ENSMUSG00000041765	Ubac2	1190008A14Rik|AW554959|Phgdhl1	ubiquitin associated domain containing 2	protein-coding
mm_95970.1	chr11	58926189	58926200	+	1	NA	intron (NM_138678, intron 4 of 4)	(CA)n|Simple_repeat|Simple_repeat	8137	NM_138678	192194	Mm.22540	NM_138678	ENSMUSG00000020490	Btnl10	BUTR-1|Butr1	butyrophilin-like 10	protein-coding
mm_88872.1	chr10	81070063	81070121	+	1	NA	promoter-TSS (NM_022653)	promoter-TSS (NM_022653)	9	NM_022653	50492	Mm.26995	NM_022653	ENSMUSG00000004929	Thop1	AI131655|AI327041|EP24.15	thimet oligopeptidase 1	protein-coding
mm_113326.1	chr13	30786568	30786574	+	1	NA	Intergenic	Intergenic	37338	NM_013674	16364	Mm.4677	NM_013674	ENSMUSG00000021356	Irf4	AI385587|IRF-4|LSIRF|NF-EM5|Spip	interferon regulatory factor 4	protein-coding
mm_138238.1	chr17	34434955	34434972	+	1	NA	intron (NM_001001177, intron 6 of 19)	intron (NM_001001177, intron 6 of 19)	36143	NM_001163855	407788	Mm.73205	NM_001001177	ENSMUSG00000057246	BC051142	NG8|TSBP|Tesb|Tesbp	cDNA sequence BC051142	protein-coding
mm_64004.1	chr7	140173346	140173378	+	1	NA	Intergenic	Intergenic	-2742	NM_146518	258511	Mm.334306	NM_146518	ENSMUSG00000051051	Olfr523	MOR104-4	olfactory receptor 523	protein-coding
mm_169094.1	chr13	40886834	40886836	+	1	NA	promoter-TSS (NM_008105)	promoter-TSS (NM_008105)	77	NM_008105	14538	Mm.314757	NM_008105	ENSMUSG00000021360	Gcnt2	5330430K10Rik|IGnT|IGnTA|IGnTB|IGnTC	glucosaminyl (N-acetyl) transferase 2, I-branching enzyme	protein-coding
mm_96696.1	chr11	69622045	69622101	+	1	NA	promoter-TSS (NM_026991)	promoter-TSS (NM_026991)	-36	NM_026991	69215	Mm.340410	NM_026991	ENSMUSG00000069835	Sat2	2610016A03Rik|SSAT-2|SSAT2	spermidine/spermine N1-acetyl transferase 2	protein-coding
mm_165805.1	chr3	144653930	144653930	+	1	NA	Intergenic	Intergenic	66405	NM_001282042	54673	Mm.271775	NM_019464	ENSMUSG00000037062	Sh3glb1	AA409932|AI314629|AU015566|Bif-1|mKIAA0491	SH3-domain GRB2-like B1 (endophilin)	protein-coding
mm_47981.1	chr5	135911449	135911466	-	1	NA	exon (NM_018871, exon 2 of 2)	exon (NM_018871, exon 2 of 2)	23184	NM_018871	22628	Mm.233813	NM_018871	ENSMUSG00000051391	Ywhag	14-3-3gamma|D7Bwg1348e	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, gamma polypeptide	protein-coding
mm_158331.1	chrX	133961761	133961761	-	1	NA	exon (NM_001290718, exon 3 of 14)	exon (NM_001290718, exon 3 of 14)	20051	NM_001290718	27359	Mm.38674	NM_013757	ENSMUSG00000031255	Sytl4	Gph|Slp4	synaptotagmin-like 4	protein-coding
mm_35810.1	chr4	46662636	46662652	-	1	NA	Intergenic	Intergenic	-12445	NM_198664	381605	Mm.331595	NM_198664	ENSMUSG00000039813	Tbc1d2	A630005A06Rik|BC022630|Gm1037|PARIS-1|PARIS1	TBC1 domain family, member 2	protein-coding
mm_167784.1	chr9	120004843	120004853	+	1	NA	Intergenic	MLTR14|LTR|ERV1	18750	NM_011724	22437	Mm.10117	NM_011724	ENSMUSG00000079243	Xirp1	AI415219|Cmya1	xin actin-binding repeat containing 1	protein-coding
mm_11414.1	chr2	31616596	31616599	+	1	NA	3' UTR (NM_001290548, exon 19 of 19)	3' UTR (NM_001290548, exon 19 of 19)	4176	NR_105964	102466214		NR_105964	ENSMUSG00000098904	Mir6998	Gm28024|mmu-mir-6998	microRNA 6998	ncRNA
mm_96798.1	chr11	69981128	69981214	+	1	NA	promoter-TSS (NM_026017)	promoter-TSS (NM_026017)	3	NM_026017	67181	Mm.41678	NM_026017	ENSMUSG00000018559	Ctdnep1	2610507E10Rik|Dullard	CTD nuclear envelope phosphatase 1	protein-coding
mm_69964.1	chr7	142376627	142376658	-	1	NA	exon (NM_009983, exon 9 of 9)	exon (NM_009983, exon 9 of 9)	-2896	NM_001347541	320802	Mm.154486	NM_177265	ENSMUSG00000045777	Ifitm10	6330512M04Rik|AI848576|DSPA3	interferon induced transmembrane protein 10	protein-coding
mm_159648.1	chr4	145121575	145121575	-	1	NA	intron (NM_001276502, intron 30 of 68)	intron (NM_001276502, intron 30 of 68)	69091	NM_001276502	230895	Mm.240310	NM_001033190	ENSMUSG00000020220	Vps13d	-	vacuolar protein sorting 13D	protein-coding
mm_159079.1	chr2	26319775	26319775	+	1	NA	promoter-TSS (NM_001199147)	promoter-TSS (NM_001199147)	5	NM_001199147	67839	Mm.266611	NM_153410	ENSMUSG00000026930	Gpsm1	1810037C22Rik|AW107933|Ags3	G-protein signalling modulator 1 (AGS3-like, C. elegans)	protein-coding
mm_172384.1	chr7	131482804	131482804	+	1	NA	Intergenic	B1_Mm|SINE|Alu	-60159	NM_008257	15373	Mm.323562	NM_008257	ENSMUSG00000040148	Hmx3	Nkx-5.1|Nkx5-1|Nkx5.1	H6 homeobox 3	protein-coding
mm_168607.1	chr11	75422583	75422583	-	1	NA	promoter-TSS (NM_011340)	promoter-TSS (NM_011340)	40	NM_011340	20317	Mm.2044	NM_011340	ENSMUSG00000000753	Serpinf1	AI195227|EPC-1|Pedf|Pedfl|Sdf3	serine (or cysteine) peptidase inhibitor, clade F, member 1	protein-coding
mm_67682.1	chr7	89338670	89338680	-	1	NA	5' UTR (NM_028343, exon 1 of 15)	5' UTR (NM_028343, exon 1 of 15)	112	NM_028343	72759	Mm.208477	NM_028343	ENSMUSG00000039428	Tmem135	2810439K08Rik|AW319712|PMP52	transmembrane protein 135	protein-coding
mm_135671.1	chr16	52411717	52411754	-	1	NA	intron (NM_009655, intron 1 of 15)	L1MA7|LINE|L1	41346	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_119914.1	chr14	54953284	54953336	+	1	NA	exon (NM_010856, exon 22 of 39)	exon (NM_010856, exon 22 of 39)	-4168	NR_029724	387204		NR_029724	ENSMUSG00000065432	Mir208a	Mirn208|Mirn208a|mir-208|mir-208a|mmu-mir-208	microRNA 208a	ncRNA
mm_71930.1	chr8	70278102	70278113	+	1	NA	Intergenic	Intergenic	-4892	NM_011984	26558	Mm.388127	NM_011984	ENSMUSG00000003573	Homer3	AW146114	homer scaffolding protein 3	protein-coding
mm_164860.1	chr18	53471135	53471137	+	1	NA	intron (NM_001033281, intron 1 of 6)	intron (NM_001033281, intron 1 of 6)	6590	NM_001033281	225518	Mm.297645	NM_001033281	ENSMUSG00000069378	Prdm6	Gm92|PRISM	PR domain containing 6	protein-coding
mm_153325.1	chr19	38124084	38124131	-	1	NA	exon (NM_011255, exon 4 of 6)	exon (NM_011255, exon 4 of 6)	704	NM_011255	19662	Mm.2605	NM_011255	ENSMUSG00000024990	Rbp4	Rbp-4	retinol binding protein 4, plasma	protein-coding
mm_167023.1	chr7	65861835	65861882	+	1	NA	promoter-TSS (NM_001291184)	promoter-TSS (NM_001291184)	-278	NM_001291184	18553	Mm.294007	NM_011048	ENSMUSG00000030513	Pcsk6	C86343|Pace4|SPC4	proprotein convertase subtilisin/kexin type 6	protein-coding
mm_149245.1	chr19	10204239	10204249	+	1	NA	promoter-TSS (NM_001271614)	promoter-TSS (NM_001271614)	42	NM_026919	69038	Mm.375100	NM_026919	ENSMUSG00000036372	Tmem258	1810006K21Rik	transmembrane protein 258	protein-coding
mm_166970.1	chr7	44572559	44572569	+	1	NA	5' UTR (NM_008437, exon 1 of 9)	5' UTR (NM_008437, exon 1 of 9)	119	NM_008437	16541	Mm.383181	NM_008437	ENSMUSG00000002204	Napsa	KAP|Kdap|NAP1|SNAPA|pronapsin	napsin A aspartic peptidase	protein-coding
mm_70037.1	chr7	142577415	142577426	-	1	NA	promoter-TSS (NR_030416)	promoter-TSS (NR_030416)	-273	NR_030416	735280		NR_030416	ENSMUSG00000076275	Mir675	Mirn675|mir-675|mmu-mir-675	microRNA 675	ncRNA
mm_65324.1	chr7	24972032	24972041	-	1	NA	intron (NM_010261, intron 2 of 4)	intron (NM_010261, intron 2 of 4)	692	NM_010261	14470	Mm.22473	NM_010261	ENSMUSG00000003380	Rabac1	2310040I06Rik|Gbpap1|PRA1|prenylin	Rab acceptor 1 (prenylated)	protein-coding
mm_162309.1	chr1	37153823	37153825	+	1	NA	Intergenic	Intergenic	-64454	NM_001282010	12790	Mm.214224	NM_009918	ENSMUSG00000026114	Cnga3	CNG3	cyclic nucleotide gated channel alpha 3	protein-coding
mm_161208.1	chr13	59809549	59809549	-	1	NA	intron (NM_153538, intron 8 of 27)	intron (NM_153538, intron 8 of 27)	13598	NM_153538	214290	Mm.233082	NM_153538	ENSMUSG00000035248	Zcchc6	6030448M23Rik|AA420405	zinc finger, CCHC domain containing 6	protein-coding
mm_126003.1	chr15	76526450	76526452	+	1	NA	Intergenic	Intergenic	-4322	NM_130893	170729	Mm.218747	NM_130893	ENSMUSG00000048385	Scrt1	-	scratch family zinc finger 1	protein-coding
mm_23721.1	chr3	69009483	69009496	+	1	NA	promoter-TSS (NR_029735)	promoter-TSS (NR_029735)	-283	NR_029529	387175		NR_029529	ENSMUSG00000065580	Mir15b	Mirn15b|mir-15b|mmu-mir-15b	microRNA 15b	ncRNA
mm_11470.1	chr2	32363193	32363262	+	1	NA	promoter-TSS (NM_001252534)	promoter-TSS (NM_001252534)	29	NM_028412	68379	Mm.170508	NM_028412	ENSMUSG00000039205	Ciz1	0610038H21Rik|2900056O04Rik|LSFR1|ZNF356	CDKN1A interacting zinc finger protein 1	protein-coding
mm_149816.1	chr19	23904590	23904632	+	1	NA	intron (NM_177034, intron 2 of 12)	intron (NM_177034, intron 2 of 12)	126408	NM_001114174	381217	Mm.426078	NM_001114174	ENSMUSG00000071604	Fam189a2	AI414343|AI666772|Gm967	family with sequence similarity 189, member A2	protein-coding
mm_167063.1	chr7	95384061	95384061	+	1	NA	Intergenic	B3A|SINE|B2	-787183	NM_001310762	23966	Mm.254610	NM_011858	ENSMUSG00000048078	Tenm4	Doc4|ELM2|Odz4|R75022|Ten-m4|l(7)-3Rn|l7Rn3|mKIAA1302	teneurin transmembrane protein 4	protein-coding
mm_128263.1	chr15	36771545	36771555	-	1	NA	3' UTR (NM_001253807, exon 5 of 5)	3' UTR (NM_001253807, exon 5 of 5)	19382	NM_001253807	22631	Mm.3360	NM_011740	ENSMUSG00000022285	Ywhaz	1110013I11Rik|14-3-3zeta|AI596267|AL022924|AU020854	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide	protein-coding
mm_139000.1	chr17	45561005	45561008	+	1	NA	intron (NM_001304956, intron 5 of 5)	intron (NM_001304956, intron 5 of 5)	-3146	NM_028662	73836	Mm.289716	NM_028662	ENSMUSG00000037089	Slc35b2	1110003M08Rik|AA407792|AI842275|PAPST1|Slc35b1	solute carrier family 35, member B2	protein-coding
mm_4800.1	chr1	185205929	185205937	+	1	NA	intron (NM_001163754, intron 1 of 34)	AT_rich|Low_complexity|Low_complexity	1765	NM_001163754	98732	Mm.275841	NM_172649	ENSMUSG00000039318	Rab3gap2	1110059F07Rik|2010002H18Rik|5830469C09|AI851069|AW743433|RAB3-GAP150|mKIAA0839	RAB3 GTPase activating protein subunit 2	protein-coding
mm_129346.1	chr15	77874942	77874967	-	1	NA	Intergenic	Intergenic	-32779	NM_022410	17886	Mm.29677	NM_022410	ENSMUSG00000022443	Myh9	Fltn|Myhn-1|Myhn1|NMHCIIA|NMMHC-A|NMMHC-IIA|TU72.6	myosin, heavy polypeptide 9, non-muscle	protein-coding
mm_165922.1	chr4	62088248	62088264	+	1	NA	promoter-TSS (NM_001039544)	promoter-TSS (NM_001039544)	-944	NM_001039544	17842	Mm.250267	NM_010845	ENSMUSG00000066154	Mup3	MUP15|MUPIII|Mup-3|Mup25	major urinary protein 3	protein-coding
mm_140274.1	chr17	84893797	84893832	+	1	NA	Intergenic	MLTR18_MM|LTR|ERVK	-62927	NM_001159497	19043	Mm.249695	NM_011151	ENSMUSG00000061130	Ppm1b	PP2CB	protein phosphatase 1B, magnesium dependent, beta isoform	protein-coding
mm_62078.1	chr7	92875290	92875315	+	1	NA	promoter-TSS (NM_028243)	promoter-TSS (NM_028243)	49	NM_028243	72461	Mm.389969	NM_028243	ENSMUSG00000061119	Prcp	2510048K03Rik|2610104A14Rik|AI451719|HUMPCP|PCP	prolylcarboxypeptidase (angiotensinase C)	protein-coding
mm_123641.1	chr14	68606471	68606476	-	1	NA	TTS (NM_010082)	TTS (NM_010082)	-24401	NM_021475	58860	Mm.36742	NM_021475	ENSMUSG00000022057	Adamdec1	2210414L24Rik|AI574231|Dcsn	ADAM-like, decysin 1	protein-coding
mm_23920.1	chr3	83055576	83055585	+	1	NA	promoter-TSS (NM_016784)	promoter-TSS (NM_016784)	42	NM_016784	53317	Mm.286349	NM_016784	ENSMUSG00000027998	Plrg1	AA958940|C80566|Tango4	pleiotropic regulator 1	protein-coding
mm_57264.1	chr6	123286226	123286301	-	1	NA	exon (NM_019948, exon 4 of 6)	exon (NM_019948, exon 4 of 6)	3608	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_39333.1	chr5	8728206	8728209	+	1	NA	intron (NM_011076, intron 21 of 27)	(TTTTC)n|Simple_repeat|Simple_repeat	68115	NM_011076	18671	Mm.207354	NM_011076	ENSMUSG00000040584	Abcb1a	Abcb4|Evi32|Mdr1a|Mdr3|P-gp|Pgp|Pgy-3|Pgy3|mdr-3	ATP-binding cassette, sub-family B (MDR/TAP), member 1A	protein-coding
mm_81990.1	chr9	121460231	121460239	+	1	NA	intron (NM_175114, intron 13 of 15)	intron (NM_175114, intron 13 of 15)	35459	NM_001284508	12424	Mm.2619	NM_031161	ENSMUSG00000032532	Cck	-	cholecystokinin	protein-coding
mm_22805.1	chr3	27014413	27014416	+	1	NA	Intergenic	(TTTC)n|Simple_repeat|Simple_repeat	139440	NM_007900	13605	Mm.261453	NM_007900	ENSMUSG00000027699	Ect2	AI528536|mKIAA4037	ect2 oncogene	protein-coding
mm_24254.1	chr3	89183400	89183410	+	1	NA	TTS (NM_011886)	TTS (NM_011886)	180	NM_001014995	68521	Mm.274708	NM_001014995	ENSMUSG00000032657	Fam189b	1110013L07Rik	family with sequence similarity 189, member B	protein-coding
mm_59343.1	chr7	25601286	25601294	+	1	NA	Intergenic	Intergenic	14602	NM_001039243	632778	Mm.423112	NM_001039243	ENSMUSG00000074261	Erich4	EG632778|Gm7092|Kseg1	glutamate rich 4	protein-coding
mm_103104.1	chr11	69948154	69948206	-	1	NA	promoter-TSS (NM_009204)	promoter-TSS (NM_009204)	10	NM_009204	20528	Mm.10661	NM_009204	ENSMUSG00000018566	Slc2a4	Glut-4|Glut4	solute carrier family 2 (facilitated glucose transporter), member 4	protein-coding
mm_39689.1	chr5	26904629	26904671	+	1	NA	promoter-TSS (NM_001198886)	promoter-TSS (NM_001198886)	-128	NM_001198886	13483	Mm.42078	NM_010075	ENSMUSG00000061576	Dpp6	B930011P16Rik|D5Buc3|D5Buc4|D5Buc5|DPP VI|Dpp-6|Gm1377|In(5)6H-p|Peplb|Rw	dipeptidylpeptidase 6	protein-coding
mm_154121.1	chr19	57197436	57197460	-	1	NA	5' UTR (NM_001103177, exon 1 of 22)	5' UTR (NM_001103177, exon 1 of 22)	183	NM_001103177	226251	Mm.217161	NM_178688	ENSMUSG00000025085	Ablim1	2210411C18Rik|2610209L21Rik|4833406P10Rik|9330196J19Rik|AV079770|AW060987|AW215784|Limab1|mKIAA0059	actin-binding LIM protein 1	protein-coding
mm_100628.1	chr11	121702592	121702616	+	1	NA	5' UTR (NM_144797, exon 1 of 4)	5' UTR (NM_144797, exon 1 of 4)	177	NM_144797	210029	Mm.153566	NM_144797	ENSMUSG00000039208	Metrnl	9430048M07Rik|BC019776	meteorin, glial cell differentiation regulator-like	protein-coding
mm_94772.1	chr11	21242628	21242677	+	1	NA	intron (NM_139061, intron 1 of 22)	B3|SINE|B2	3620	NM_001290628	245944	Mm.170103	NM_139061	ENSMUSG00000020128	Vps54	Hcc8|Vps54l|mSLP8|wr	VPS54 GARP complex subunit	protein-coding
mm_95567.1	chr11	52396391	52396395	+	1	NA	promoter-TSS (NM_153117)	promoter-TSS (NM_153117)	-35	NM_153117	213673	Mm.291979	NM_153117	ENSMUSG00000036275	9530068E07Rik	C85061|Kct2	RIKEN cDNA 9530068E07 gene	protein-coding
mm_164458.1	chr16	56839530	56839543	-	1	NA	intron (NM_019631, intron 1 of 5)	MER5A1|DNA|hAT-Charlie	-43678	NM_172825	239853	Mm.258979	NM_172825	ENSMUSG00000022755	Adgrg7	9130020O16Rik|Gpr128	adhesion G protein-coupled receptor G7	protein-coding
mm_161980.1	chr19	21680506	21680506	+	1	NA	intron (NM_146096, intron 2 of 3)	intron (NM_146096, intron 2 of 3)	27197	NM_146096	226016	Mm.28796	NM_146096	ENSMUSG00000047368	Abhd17b	5730446C15Rik|Cgi67|Fam108b|Fam108b1	abhydrolase domain containing 17B	protein-coding
mm_128660.1	chr15	60122411	60122412	-	1	NA	Intergenic	MER20|DNA|hAT-Charlie	-105793	NM_027668	71088	Mm.425950	NM_027668	ENSMUSG00000071749	4933412E24Rik	-	RIKEN cDNA 4933412E24 gene	protein-coding
mm_1668.1	chr1	74772013	74772019	+	1	NA	5' UTR (NM_009526, exon 1 of 4)	5' UTR (NM_009526, exon 1 of 4)	124	NM_009526	22420	Mm.268282	NM_009526	ENSMUSG00000033227	Wnt6	AA409270|Wnt-6	wingless-type MMTV integration site family, member 6	protein-coding
mm_160604.1	chr9	78289961	78289961	+	1	NA	promoter-TSS (NM_001122660)	promoter-TSS (NM_001122660)	33	NM_001122660	100042314	Mm.482247	NM_001122660	ENSMUSG00000074179	Gm10639	ENSMUSG00000074179	predicted gene 10639	protein-coding
mm_161876.1	chr18	37264844	37264844	+	1	NA	promoter-TSS (NM_053126)	promoter-TSS (NM_053126)	-154	NM_053126	93872	Mm.196703	NM_053126	ENSMUSG00000051663	Pcdhb1	PcdhbA	protocadherin beta 1	protein-coding
mm_16706.1	chr2	7081257	7081318	-	1	NA	promoter-TSS (NM_001160292)	promoter-TSS (NM_001160292)	15	NM_001110230	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_29051.1	chr3	103735742	103735754	-	1	NA	3' UTR (NM_133859, exon 3 of 3)	3' UTR (NM_133859, exon 3 of 3)	2253	NM_133859	99543	Mm.211535	NM_133859	ENSMUSG00000027848	Olfml3	2810002E22Rik|AI115209|AW550633|HNOEL-iso|ONT3|mONT3	olfactomedin-like 3	protein-coding
mm_27108.1	chr3	30699766	30699803	-	1	NA	promoter-TSS (NM_001309233)	promoter-TSS (NM_001309233)	59	NM_001309233	320352	Mm.229153	NM_001309233	ENSMUSG00000074653	Lrrc31	E230002P03Rik	leucine rich repeat containing 31	protein-coding
mm_106158.1	chr11	116624301	116624309	-	1	NA	promoter-TSS (NM_001167680)	promoter-TSS (NM_001167680)	-53	NM_001167680	217344	Mm.89695	NM_172572	ENSMUSG00000020806	Rhbdf2	4732465I17Rik|Rhbdl6|cub	rhomboid 5 homolog 2	protein-coding
mm_111878.1	chr12	108003762	108003772	-	1	NA	promoter-TSS (NM_021399)	promoter-TSS (NM_021399)	-353	NM_021399	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_114441.1	chr13	66203736	66203748	+	1	NA	Intergenic	Intergenic	90289	NM_001177832	628709	Mm.390595	NM_001177832	ENSMUSG00000095909	Gm10324	ENSMUSG00000071302	predicted gene 10324	protein-coding
mm_82306.1	chr9	7871826	7871843	-	1	NA	intron (NM_007464, intron 1 of 8)	intron (NM_007464, intron 1 of 8)	1336	NM_007464	11796	Mm.2026	NM_007464	ENSMUSG00000032000	Birc3	AW107670|Api1|Api2|Birc2|C-IAP2|HIAP2|IAP1|IAP2|MIAP1|MIAP2|MIHB|MIHC|RNF49|cIAP-1|cIAP-2|cIAP1|cIAP2	baculoviral IAP repeat-containing 3	protein-coding
mm_156590.1	chrX	152180486	152180507	+	1	NA	intron (NM_001005475, intron 1 of 13)	intron (NM_001005475, intron 1 of 13)	1487	NM_001005475	245666	Mm.33027	NM_001005475	ENSMUSG00000041115	Iqsec2	Brag1	IQ motif and Sec7 domain 2	protein-coding
mm_128531.1	chr15	54847403	54847420	-	1	NA	intron (NM_001136077, intron 22 of 25)	intron (NM_001136077, intron 22 of 25)	72735	NM_015744	18606	Mm.250256	NM_015744	ENSMUSG00000022425	Enpp2	ATX|E-NPP 2|Npps2|PD-Ialpha|Pdnp2|lysoPLD	ectonucleotide pyrophosphatase/phosphodiesterase 2	protein-coding
mm_126517.1	chr15	81858393	81858437	+	1	NA	promoter-TSS (NM_020507)	promoter-TSS (NM_020507)	-89	NM_020507	57259	Mm.323595	NM_020507	ENSMUSG00000048546	Tob2	2900090N22Rik|4930545K18Rik|AV071822|mKIAA1663	transducer of ERBB2, 2	protein-coding
mm_32772.1	chr4	116696020	116696047	+	1	NA	intron (NM_011034, intron 5 of 5)	B1_Mur4|SINE|Alu	-10011	NR_040442	100502959	Mm.395400	NR_040442		AV051173	-	expressed sequence AV051173	ncRNA
mm_94212.1	chr11	3131099	3131110	+	1	NA	TTS (NM_030207)	TTS (NM_030207)	7083	NR_003517	236604	Mm.247625	NM_001004146		Pisd-ps1	-	phosphatidylserine decarboxylase, pseudogene 1	pseudo
mm_115322.1	chr13	112427772	112427782	+	1	NA	Intergenic	Intergenic	-36293	NM_010560	16195	Mm.4364	NM_010560	ENSMUSG00000021756	Il6st	5133400A03Rik|AA389424|BB405851|CD130|D13Ertd699e|gp130	interleukin 6 signal transducer	protein-coding
mm_159119.1	chr2	66440931	66440931	-	1	NA	promoter-TSS (NR_033495)	promoter-TSS (NR_033495)	51	NR_033495	100038743	Mm.330264	NR_033495		Gm13629	OTTMUSG00000013098	predicted gene 13629	ncRNA
mm_75117.1	chr8	34622971	34622976	-	1	NA	intron (NR_040706, intron 1 of 4)	intron (NR_040706, intron 1 of 4)	17343	NR_040706	330734	Mm.149998	NR_040706	ENSMUSG00000109819	B930018H19Rik	B930018H19	RIKEN cDNA B930018H19 gene	ncRNA
mm_169827.1	chr16	24529316	24529316	+	1	NA	promoter-TSS (NR_038091)	promoter-TSS (NR_038091)	2	NR_038091	624582	Mm.439775	NR_038091		Morf4l1-ps1	A730098P11Rik	mortality factor 4 like 1, pseudogene 1	pseudo
mm_82137.1	chr9	123761440	123761447	+	1	NA	Intergenic	MLTR18C_MM|LTR|ERVK	-5768	NM_009913	12769	Mm.440604	NM_009913	ENSMUSG00000029530	Ccr9	A130091K22Rik|Cmkbr10|GPR-9-6	chemokine (C-C motif) receptor 9	protein-coding
mm_64155.1	chr7	141338940	141338950	+	1	NA	promoter-TSS (NM_001282073)	promoter-TSS (NM_001282073)	-57	NM_133191	98845	Mm.27451	NM_133191	ENSMUSG00000025504	Eps8l2	AI042819|AW545405|Eps8r2	EPS8-like 2	protein-coding
mm_104390.1	chr11	94486212	94486221	-	1	NA	promoter-TSS (NM_144827)	promoter-TSS (NM_144827)	-906	NM_144827	217116	Mm.156123	NM_144827	ENSMUSG00000020867	Spata20	Tisp78	spermatogenesis associated 20	protein-coding
mm_122837.1	chr14	54723803	54723821	-	1	NA	3' UTR (NM_016972, exon 11 of 11)	3' UTR (NM_016972, exon 11 of 11)	-11638	NM_207131	110794	Mm.236223	NM_207131	ENSMUSG00000052435	Cebpe	C/EBPe|CRP1|Gm294	CCAAT/enhancer binding protein (C/EBP), epsilon	protein-coding
mm_137712.1	chr17	29099689	29099699	+	1	NA	3' UTR (NM_007669, exon 3 of 3)	3' UTR (NM_007669, exon 3 of 3)	5925	NM_007669	12575	Mm.195663	NM_007669	ENSMUSG00000023067	Cdkn1a	CAP20|CDKI|CIP1|Cdkn1|P21|SDI1|Waf1|mda6|p21Cip1|p21WAF	cyclin-dependent kinase inhibitor 1A (P21)	protein-coding
mm_4784.1	chr1	184034427	184034437	+	1	NA	promoter-TSS (NM_028516)	promoter-TSS (NM_028516)	-29	NM_022019	63953	Mm.404024	NM_022019	ENSMUSG00000039384	Dusp10	2610306G15Rik|AI158871|MKP-5|MKP5	dual specificity phosphatase 10	protein-coding
mm_119248.1	chr14	33923429	33923466	+	1	NA	promoter-TSS (NM_145741)	promoter-TSS (NM_145741)	-140	NM_145741	14560	Mm.432071	NM_145741	ENSMUSG00000021943	Gdf10	Bmp3b	growth differentiation factor 10	protein-coding
mm_126648.1	chr15	84127301	84127320	+	1	NA	Intergenic	(CCTA)n|Simple_repeat|Simple_repeat	-4135	NM_029427	75772	Mm.159565	NM_029427	ENSMUSG00000018868	Pnpla5	4833426H19Rik|GS2L	patatin-like phospholipase domain containing 5	protein-coding
mm_162618.1	chr1	183369798	183369818	+	1	NA	promoter-TSS (NM_177389)	promoter-TSS (NM_177389)	-243	NM_177389	338366	Mm.41152	NM_177389		Mia3	9130229H14Rik|A930039G15Rik|AU022327|B230399H06Rik|C80126|Gm1525|TANGO1|Tango	melanoma inhibitory activity 3	protein-coding
mm_163292.1	chr11	118320097	118320145	+	1	NA	exon (NM_011594, exon 2 of 5)	exon (NM_011594, exon 2 of 5)	22413	NM_021440	58251	Mm.439815	NM_021440	ENSMUSG00000076433	BC100451	Cep295nl|Ddc8|FS39|Kiaa1731nl	cDNA sequence BC100451	protein-coding
mm_9658.1	chr1	177795505	177795510	-	1	NA	intron (NM_007422, intron 1 of 12)	(A)n|Simple_repeat|Simple_repeat	1002	NM_007422	11566	Mm.338021	NM_007422	ENSMUSG00000015961	Adss	AI314886|AS|Adss2	adenylosuccinate synthetase, non muscle	protein-coding
mm_59890.1	chr7	30307061	30307101	+	1	NA	3' UTR (NM_001081114, exon 14 of 14)	3' UTR (NM_001081114, exon 14 of 14)	-1672	NM_198027	233065	Mm.276277	NM_198027	ENSMUSG00000042831	Alkbh6	AI839550|Abh6|C130099A02	alkB homolog 6	protein-coding
mm_24192.1	chr3	88607508	88607520	+	1	NA	Intergenic	Intergenic	-8693	NM_001198911	16800	Mm.239329	NM_008487	ENSMUSG00000028059	Arhgef2	AA408978|GEF|GEF-H1|GEFH1|LFP40|Lbcl1|Lfc|P40|mKIAA0651	rho/rac guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_99475.1	chr11	102556496	102556513	+	1	NA	promoter-TSS (NM_001159492)	promoter-TSS (NM_001159492)	-346	NM_001159492	237943	Mm.260282	NM_001159492	ENSMUSG00000034621	Gpatch8	5430405G24Rik|AU018890|ENSMUSG00000075516|Fbm1|Gpatc8|mKIAA0553	G patch domain containing 8	protein-coding
mm_164623.1	chr17	31198907	31198912	-	1	NA	promoter-TSS (NM_001163776)	promoter-TSS (NM_001163776)	65	NM_001163776	140765	Mm.214638	NM_080727	ENSMUSG00000024034	Tmprss3	-	transmembrane protease, serine 3	protein-coding
mm_114702.1	chr13	83524502	83524520	+	1	NA	promoter-TSS (NM_001347567)	promoter-TSS (NM_001347567)	-232	NM_001347567	17260	Mm.24001	NM_025282	ENSMUSG00000005583	Mef2c	5430401D19Rik|9930028G15Rik|AV011172|Mef2	myocyte enhancer factor 2C	protein-coding
mm_91388.1	chr10	30655754	30655762	-	1	NA	5' UTR (NM_001111267, exon 1 of 6)	5' UTR (NM_001111267, exon 1 of 6)	109	NM_001111267	211329	Mm.297903	NM_172495	ENSMUSG00000039697	Ncoa7	9030406N13Rik	nuclear receptor coactivator 7	protein-coding
mm_49323.1	chr6	18866368	18866371	+	1	NA	promoter-TSS (NM_029202)	promoter-TSS (NM_029202)	51	NM_001167757	75196	Mm.67665	NM_029202	ENSMUSG00000029517	Ankrd7	4930532L20Rik|AV278427	ankyrin repeat domain 7	protein-coding
mm_121404.1	chr14	119268757	119268774	+	1	NA	intron (NM_015820, intron 1 of 1)	ORR1D2|LTR|ERVL-MaLR	130500	NM_015820	50787	Mm.445777	NM_015820	ENSMUSG00000053465	Hs6st3	6OST3|HS6ST-3	heparan sulfate 6-O-sulfotransferase 3	protein-coding
mm_44807.1	chr5	33274967	33275010	-	1	NA	promoter-TSS (NM_001198861)	promoter-TSS (NM_001198861)	16	NM_001310535	13016	Mm.7286	NM_013502	ENSMUSG00000037373	Ctbp1	BARS|CtBP3/BARS|D4S115h|D5H4S115|D5H4S115E	C-terminal binding protein 1	protein-coding
mm_115725.1	chr13	16027323	16027341	-	1	NA	3' UTR (NM_008380, exon 5 of 5)	3' UTR (NM_008380, exon 5 of 5)	15481	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_71263.1	chr8	40918513	40918523	+	1	NA	3' UTR (NM_001044740, exon 12 of 12)	3' UTR (NM_001044740, exon 12 of 12)	-7715	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_62928.1	chr7	118600237	118600264	+	1	NA	5' UTR (NM_001105252, exon 2 of 22)	5' UTR (NM_001105252, exon 2 of 22)	2953	NM_001105252	74424	Mm.11068	NM_028930	ENSMUSG00000030650	Tmc5	4932443L08Rik|AU016085	transmembrane channel-like gene family 5	protein-coding
mm_102894.1	chr11	69420329	69420353	-	1	NA	TTS (NM_001081330)	TTS (NM_001081330)	-6666	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_133868.1	chr16	96372577	96372583	+	1	NA	intron (NM_001177886, intron 2 of 8)	intron (NM_001177886, intron 2 of 8)	10816	NM_028078	72058	Mm.119714	NM_028078	ENSMUSG00000000159	Igsf5	2010003D20Rik|JCAM|Jam4	immunoglobulin superfamily, member 5	protein-coding
mm_147897.1	chr18	65322140	65322152	-	1	NA	intron (NM_001037294, intron 4 of 12)	intron (NM_001037294, intron 4 of 12)	71742	NM_001037294	225638	Mm.296528	NM_001037294	ENSMUSG00000032845	Alpk2	Gm549|Hak	alpha-kinase 2	protein-coding
mm_148701.1	chr19	5747744	5747753	+	1	NA	exon (NM_008520, exon 9 of 28)	exon (NM_008520, exon 9 of 28)	6844	NM_008520	16998	Mm.182396	NM_008520	ENSMUSG00000024940	Ltbp3	Ltbp2|mFLJ00070	latent transforming growth factor beta binding protein 3	protein-coding
mm_163363.1	chr12	32953718	32953725	-	1	NA	promoter-TSS (NM_198710)	promoter-TSS (NM_198710)	68	NR_044986	74076	Mm.50114	NR_044986	ENSMUSG00000097494	4933406C10Rik	-	RIKEN cDNA 4933406C10 gene	ncRNA
mm_1888.1	chr1	85682290	85682304	+	1	NA	3' UTR (NM_001313714, exon 12 of 12)	3' UTR (NM_001313714, exon 12 of 12)	32309	NM_001313714	20684	Mm.290906	NM_013673	ENSMUSG00000026222	Sp100	A430075G10Rik	nuclear antigen Sp100	protein-coding
mm_65354.1	chr7	24998996	24999007	-	1	NA	exon (NM_001290469, exon 5 of 23)	exon (NM_001290469, exon 5 of 23)	6936	NM_001290469	232975	Mm.44101	NM_144921	ENSMUSG00000040907	Atp1a3	Atpa-2	ATPase, Na+/K+ transporting, alpha 3 polypeptide	protein-coding
mm_86799.1	chr10	20312364	20312400	+	1	NA	promoter-TSS (NM_001025393)	promoter-TSS (NM_001025393)	-87	NM_001025392	72567	Mm.294783	NM_153787	ENSMUSG00000037608	Bclaf1	2610102K23Rik|2700025J07Rik|2810454G14Rik|5730534O06Rik|AI450190|AW556225|Btf|mKIAA0164	BCL2-associated transcription factor 1	protein-coding
mm_33721.1	chr4	134065678	134065691	+	1	NA	Intergenic	Intergenic	-2768	NM_001162970	230806	Mm.240080	NM_001162970	ENSMUSG00000012123	Aim1l	-	absent in melanoma 1-like	protein-coding
mm_122872.1	chr14	54925640	54925684	-	1	NA	5' UTR (NM_010112, exon 1 of 6)	5' UTR (NM_010112, exon 1 of 6)	1126	NM_010112	13644	Mm.236438	NM_010112	ENSMUSG00000022203	Efs	-	embryonal Fyn-associated substrate	protein-coding
mm_168507.1	chr11	55118712	55118719	-	1	NA	Intergenic	Intergenic	20730	NM_010299	14667	Mm.287807	NM_010299	ENSMUSG00000000594	Gm2a	AA408702|AW215435|GM2-AP|SAP-3	GM2 ganglioside activator protein	protein-coding
mm_151584.1	chr19	61224674	61224684	+	1	NA	3' UTR (NM_009970, exon 12 of 12)	3' UTR (NM_009970, exon 12 of 12)	3739	NM_009970	12982	Mm.287228	NM_009970	ENSMUSG00000059326	Csf2ra	CD116|Csfgmra|GM-CSF-Ra|GM-CSFR	colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)	protein-coding
mm_118552.1	chr14	17660957	17660963	+	1	NA	promoter-TSS (NM_001113417)	promoter-TSS (NM_001113417)	0	NM_001113417	21834	Mm.32563	NM_009380	ENSMUSG00000021779	Thrb	Nr1a2|T3R[b]|T3Rbeta|Thrb1|Thrb2|c-erbAbeta	thyroid hormone receptor beta	protein-coding
mm_8495.1	chr1	153851084	153851089	-	1	NA	exon (NM_178243, exon 1 of 1)	exon (NM_178243, exon 1 of 1)	109	NM_178243	240817	Mm.439405	NM_178243	ENSMUSG00000045968	Teddm2	5830403L16Rik|AJ554213|Me9|e92	transmembrane epididymal family member 2	protein-coding
mm_69191.1	chr7	127274048	127274066	-	1	NA	promoter-TSS (NM_009266)	promoter-TSS (NM_009266)	2	NM_009266	20768	Mm.20294	NM_009266	ENSMUSG00000049091	Sephs2	Sps2|Ysg3	selenophosphate synthetase 2	protein-coding
mm_27290.1	chr3	41742337	41742364	-	1	NA	promoter-TSS (NM_001099785)	promoter-TSS (NM_001099785)	164	NM_001081411	67161	Mm.331001	NM_026008	ENSMUSG00000059834	Sclt1	2610207F23Rik|4931421F20Rik	sodium channel and clathrin linker 1	protein-coding
mm_144586.1	chr18	31955108	31955129	+	1	NA	intron (NM_144862, intron 5 of 9)	intron (NM_144862, intron 5 of 9)	-5482	NM_001025381	574402	Mm.391108	NM_001025381	ENSMUSG00000052229	Gpr17	AI853548	G protein-coupled receptor 17	protein-coding
mm_40250.1	chr5	38219961	38219970	+	1	NA	promoter-TSS (NM_025281)	promoter-TSS (NM_025281)	463	NM_029162	75079	Mm.258741	NM_029162	ENSMUSG00000029127	Zbtb49	4930518A03Rik|Zfp509|Znf509	zinc finger and BTB domain containing 49	protein-coding
mm_94205.1	chr11	3104717	3104727	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	-19299	NR_003517	236604	Mm.247625	NM_001004146		Pisd-ps1	-	phosphatidylserine decarboxylase, pseudogene 1	pseudo
mm_76068.1	chr8	78508862	78508865	-	1	NA	promoter-TSS (NM_001282108)	promoter-TSS (NM_001282108)	65	NM_001252089	19656	Mm.24718	NM_009033	ENSMUSG00000037070	Rbmxl1	Hnrpg|Rbmx|Rbmxrt	RNA binding motif protein, X-linked like-1	protein-coding
mm_134749.1	chr16	23127703	23127746	-	1	NA	promoter-TSS (NM_145480)	promoter-TSS (NM_145480)	6	NM_145480	106344	Mm.386835	NM_145480	ENSMUSG00000022881	Rfc4	A1|AI894123|AU040575|RFC37	replication factor C (activator 1) 4	protein-coding
mm_106514.1	chr11	120531494	120531518	-	1	NA	intron (NM_008101, intron 1 of 13)	intron (NM_008101, intron 1 of 13)	779	NM_008101	14527	Mm.22329	NM_008101	ENSMUSG00000025127	Gcgr	GR	glucagon receptor	protein-coding
mm_95497.1	chr11	51763683	51763749	+	1	NA	promoter-TSS (NM_025535)	promoter-TSS (NM_025535)	53	NM_025535	66397	Mm.196592	NM_025535	ENSMUSG00000020386	Sar1b	2310075M17Rik|2900019I22Rik|CMRD|Sara1b|Sara2|Sarb	secretion associated Ras related GTPase 1B	protein-coding
mm_97940.1	chr11	83662557	83662559	+	1	NA	promoter-TSS (NM_013652)	promoter-TSS (NM_013652)	-26	NM_013652	20303	Mm.244263	NM_013652	ENSMUSG00000018930	Ccl4	AT744.1|Act-2|MIP-1B|Mip1b|Scya4	chemokine (C-C motif) ligand 4	protein-coding
mm_9193.1	chr1	171174088	171174098	-	1	NA	3' UTR (NM_025557, exon 3 of 3)	3' UTR (NM_025557, exon 3 of 3)	18575	NM_001315500	17528	Mm.9986	NM_008623	ENSMUSG00000056569	Mpz	Mpp|P-zero|P0	myelin protein zero	protein-coding
mm_142080.1	chr17	35702298	35702374	-	1	NA	promoter-TSS (NM_001198831)	promoter-TSS (NM_001198831)	-292	NM_001198831	12305	Mm.5021	NM_007584	ENSMUSG00000003534	Ddr1	6030432F18|AI323681|CD167a|Cak|Nep|PTK3A	discoidin domain receptor family, member 1	protein-coding
mm_67810.1	chr7	98119483	98119502	-	1	NA	promoter-TSS (NM_008663)	promoter-TSS (NM_008663)	1	NM_001256081	17921	Mm.1403	NM_008663	ENSMUSG00000030761	Myo7a	Hdb|Myo7|USH1B|nmf371|polka|sh-1|sh1	myosin VIIA	protein-coding
mm_130307.1	chr15	97020344	97020358	-	1	NA	intron (NM_027052, intron 1 of 15)	intron (NM_027052, intron 1 of 15)	35605	NM_027052	69354	Mm.250980	NM_027052	ENSMUSG00000022464	Slc38a4	1110012E16Rik|1700012A18Rik|Ata3|mATA3|mNAT3	solute carrier family 38, member 4	protein-coding
mm_172861.1	chr9	40803275	40803276	+	1	NA	exon (NM_031165, exon 5 of 9)	exon (NM_031165, exon 5 of 9)	2002	NM_031165	15481	Mm.290774	NM_031165	ENSMUSG00000015656	Hspa8	2410008N15Rik|Hsc70|Hsc71|Hsc73|Hsp73|Hspa10	heat shock protein 8	protein-coding
mm_133890.1	chr16	97356877	97356886	+	1	NA	exon (NM_019517, exon 1 of 9)	exon (NM_019517, exon 1 of 9)	153	NM_019517	56175	Mm.97885	NM_019517	ENSMUSG00000040605	Bace2	1110059C24Rik|AEPLC|AI850424|ALP56|ARP1|ASP1|ASP21|BAE2|CDA13|CEAP1|DRAP	beta-site APP-cleaving enzyme 2	protein-coding
mm_14519.1	chr2	132599443	132599462	+	1	NA	intron (NR_033469, intron 1 of 3)	intron (NR_033469, intron 1 of 3)	1256	NR_033469	767814	Mm.371752	NR_033468	ENSMUSG00000074783	AU019990	-	expressed sequence AU019990	ncRNA
mm_126248.1	chr15	79028443	79028456	+	1	NA	5' UTR (NM_008197, exon 1 of 1)	5' UTR (NM_008197, exon 1 of 1)	237	NM_008197	14958	Mm.24350	NM_008197	ENSMUSG00000096210	H1f0	D130017D06Rik|H1(0)|H1fv	H1 histone family, member 0	protein-coding
mm_51782.1	chr6	88198657	88198675	+	1	NA	promoter-TSS (NM_008090)	promoter-TSS (NM_008090)	2	NM_008090	14461	Mm.491156	NM_008090	ENSMUSG00000015053	Gata2	Gata-2	GATA binding protein 2	protein-coding
mm_23110.1	chr3	37481417	37481440	+	1	NA	intron (NM_001310473, intron 14 of 16)	LSU-rRNA_Hsa|rRNA|rRNA	61478	NM_021343	57815	Mm.172679	NM_021343	ENSMUSG00000027722	Spata5	2510048F20Rik|C78064|Spaf	spermatogenesis associated 5	protein-coding
mm_171753.1	chr5	104859988	104859999	-	1	NA	promoter-TSS (NM_001039231)	promoter-TSS (NM_001039231)	75	NM_001039231	626391	Mm.385405	NM_001039231	ENSMUSG00000072774	Zfp951	C230055K05Rik	zinc finger protein 951	protein-coding
mm_21822.1	chr2	165287854	165287863	-	1	NA	promoter-TSS (NM_001252574)	promoter-TSS (NM_001252574)	-20	NR_045544	228875	Mm.21184	NM_144893	ENSMUSG00000017664	Slc35c2	C85957|CGI-15|D2Wsu58e|Ovcov1	solute carrier family 35, member C2	protein-coding
mm_47559.1	chr5	124400073	124400108	-	1	NA	exon (NM_001081203, exon 14 of 32)	exon (NM_001081203, exon 14 of 32)	25824	NM_001081203	243272	Mm.23879	NM_001081203	ENSMUSG00000038095	Sbno1	9330180L10Rik|AI849128|AW557836|BC021875|Sbno|mSno1|sno	strawberry notch homolog 1 (Drosophila)	protein-coding
mm_2798.1	chr1	130851605	130851624	+	1	NA	3' UTR (NM_011082, exon 11 of 11)	3' UTR (NM_011082, exon 11 of 11)	-14163	NM_026976	69169	Mm.46042	NM_026976	ENSMUSG00000042474	Fcmr	1810037B05Rik|Faim3|FcmuR|Toso	Fc fragment of IgM receptor	protein-coding
mm_46412.1	chr5	104093334	104093350	-	1	NA	exon (NM_010097, exon 4 of 11)	exon (NM_010097, exon 4 of 11)	-15734	NM_001163772	100271704	Mm.366664	NM_001163772	ENSMUSG00000091034	Gm17660	Scpppq1	predicted gene, 17660	protein-coding
mm_161047.1	chr12	40789861	40789861	+	1	NA	intron (NM_172803, intron 31 of 52)	intron (NM_172803, intron 31 of 52)	-234229	NM_053122	93757	Mm.363813	NM_053122	ENSMUSG00000056899	Immp2l	AI853880|IMP2	IMP2 inner mitochondrial membrane peptidase-like (S. cerevisiae)	protein-coding
mm_112634.1	chr13	16011827	16011843	+	1	NA	promoter-TSS (NM_008380)	promoter-TSS (NM_008380)	-16	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_114734.1	chr13	83729476	83729494	+	1	NA	intron (NR_015561, intron 1 of 3)	intron (NR_015561, intron 1 of 3)	1379	NR_015561	320203	Mm.245636	NM_177100	ENSMUSG00000050334	C130071C03Rik	2810449C10Rik	RIKEN cDNA C130071C03 gene	ncRNA
mm_75937.1	chr8	71558971	71558983	-	1	NA	promoter-TSS (NM_001100462)	promoter-TSS (NM_001100462)	-106	NM_001100462	434325	Mm.33613	NM_001100462	ENSMUSG00000043664	Tmem221	-	transmembrane protein 221	protein-coding
mm_90525.1	chr10	128083302	128083309	+	1	NA	promoter-TSS (NM_016774)	promoter-TSS (NM_016774)	-2	NM_016774	11947	Mm.238973	NM_016774	ENSMUSG00000025393	Atp5b	-	ATP synthase, H+ transporting mitochondrial F1 complex, beta subunit	protein-coding
mm_59370.1	chr7	25697192	25697206	+	1	NA	exon (NM_011577, exon 5 of 7)	exon (NM_011577, exon 5 of 7)	10197	NM_011577	21803	Mm.248380	NM_011577	ENSMUSG00000002603	Tgfb1	TGF-beta1|TGFbeta1|Tgfb|Tgfb-1	transforming growth factor, beta 1	protein-coding
mm_127534.1	chr15	102103077	102103083	+	1	NA	promoter-TSS (NM_153533)	promoter-TSS (NM_153533)	92	NM_153533	209039	Mm.29389	NM_153533	ENSMUSG00000037003	Tns2	C1-ten|Tenc1|nep|nph	tensin 2	protein-coding
mm_58563.1	chr7	4771037	4771038	+	1	NA	exon (NM_172895, exon 1 of 11)	exon (NM_172895, exon 1 of 11)	233	NM_172895	243822	Mm.333542	NM_172895	ENSMUSG00000092518	Fam71e2	4930401F20Rik	family with sequence similarity 71, member E2	protein-coding
mm_8948.1	chr1	164438532	164438539	-	1	NA	exon (NM_009721, exon 6 of 6)	exon (NM_009721, exon 6 of 6)	19820	NM_009721	11931	Mm.4550	NM_009721	ENSMUSG00000026576	Atp1b1	Atp4b|Atpb|Atpb-1|NKbeta1	ATPase, Na+/K+ transporting, beta 1 polypeptide	protein-coding
mm_155079.1	chrX	47902776	47902792	+	1	NA	Intergenic	Intergenic	-9672	NM_177215	320634	Mm.210343	NM_177215	ENSMUSG00000001173	Ocrl	9530014D17Rik|BB143339|OCRL1	oculocerebrorenal syndrome of Lowe	protein-coding
mm_171756.1	chr5	105053567	105053580	-	1	NA	promoter-TSS (NM_029509)	promoter-TSS (NM_029509)	-12	NM_029509	76074	Mm.458519	NM_029509	ENSMUSG00000034438	Gbp8	5830443L24Rik|mGBP8	guanylate-binding protein 8	protein-coding
mm_32851.1	chr4	117982969	117982979	+	1	NA	intron (NM_009176, intron 5 of 11)	intron (NM_009176, intron 5 of 11)	-53211	NM_001284192	11876	Mm.56897	NM_009711	ENSMUSG00000028539	Artn	neublastin	artemin	protein-coding
mm_117989.1	chr13	100247333	100247343	-	1	NA	promoter-TSS (NM_010870)	promoter-TSS (NM_010870)	-2	NM_010870	17951	Mm.290476	NM_010870	ENSMUSG00000071203	Naip5	Birc1e|Lgn1|Naip-rs3	NLR family, apoptosis inhibitory protein 5	protein-coding
mm_58513.1	chr7	4129322	4129330	+	1	NA	exon (NM_001109765, exon 6 of 14)	exon (NM_001109765, exon 6 of 14)	7600	NR_033548	100037396	Mm.447887	NR_033548	ENSMUSG00000085886	D030047H15Rik	Gm15924|OTTMUSG00000027889	RIKEN cDNA D030047H15 gene	ncRNA
mm_45338.1	chr5	65698172	65698253	-	1	NA	promoter-TSS (NM_001081321)	promoter-TSS (NM_001081321)	-356	NM_001081321	71521	Mm.278974	NM_027818	ENSMUSG00000029202	Pds5a	9030416H16Rik|E230024D05Rik|mKIAA0648	PDS5 cohesin associated factor A	protein-coding
mm_49649.1	chr6	30806396	30806409	+	1	NA	intron (NM_017478, intron 20 of 23)	intron (NM_017478, intron 20 of 23)	65103	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_36225.1	chr4	62524783	62524805	-	1	NA	promoter-TSS (NM_177607)	promoter-TSS (NM_177607)	220	NM_021498	59001	Mm.27444	NM_021498	ENSMUSG00000028394	Pole3	1810034K18Rik|YBL1	polymerase (DNA directed), epsilon 3 (p17 subunit)	protein-coding
mm_58832.1	chr7	16792526	16792550	+	1	NA	intron (NM_009201, intron 5 of 8)	intron (NM_009201, intron 5 of 8)	11192	NM_009201	20514	Mm.1056	NM_009201	ENSMUSG00000001918	Slc1a5	AAAT|ASCT2|ATBO|M7V1|M7VS1|R16|RDRC|Slc1a7	solute carrier family 1 (neutral amino acid transporter), member 5	protein-coding
mm_36424.1	chr4	81572239	81572251	-	1	NA	Intergenic	Intergenic	-85232	NR_030570	100124446		NR_030570	ENSMUSG00000077941	Mir466h	Mirn466h	microRNA 466h	ncRNA
mm_64310.1	chr7	141864354	141864394	+	1	NA	exon (NM_028801, exon 31 of 49)	exon (NM_028801, exon 31 of 49)	25302	NM_028801	74180	Mm.200752	NM_028801	ENSMUSG00000066108	Muc5b	2300002I04Rik|A130042M24|AV085033|MUC5|MUC9|mucin 5b	mucin 5, subtype B, tracheobronchial	protein-coding
mm_61842.1	chr7	88290826	88290838	+	1	NA	3' UTR (NM_001311790, exon 4 of 4)	3' UTR (NM_001311790, exon 4 of 4)	12747	NM_001311790	13032	Mm.89295	NM_009982	ENSMUSG00000030560	Ctsc	AI047818|CatC|DPP1|DPPI	cathepsin C	protein-coding
mm_15533.1	chr2	158383036	158383036	+	1	NA	3' UTR (NM_175692, exon 5 of 5)	3' UTR (NM_175692, exon 5 of 5)	7398	NM_175692	319317	Mm.294494	NM_175692	ENSMUSG00000044349	Snhg11	A930034L06Rik|AI854265|AL022637|AW319638|E130013N09Rik	small nucleolar RNA host gene 11	protein-coding
mm_42059.1	chr5	108694358	108694366	+	1	NA	5' UTR (NM_001164259, exon 1 of 6)	5' UTR (NM_001164259, exon 1 of 6)	133	NM_054071	116701	Mm.35691	NM_054071	ENSMUSG00000008090	Fgfrl1	FGFR5|FGFR5beta|FGFR5gamma	fibroblast growth factor receptor-like 1	protein-coding
mm_30264.1	chr3	146770219	146770251	-	1	NA	promoter-TSS (NM_001164198)	promoter-TSS (NM_001164198)	3	NM_001164198	18749	Mm.16766	NM_011100	ENSMUSG00000005034	Prkacb	CbPKA|Pkacb	protein kinase, cAMP dependent, catalytic, beta	protein-coding
mm_106131.1	chr11	116459958	116459972	-	1	NA	Intergenic	MLT1D|LTR|ERVL-MaLR	-5618	NM_001033267	217341	Mm.387352	NM_001033267	ENSMUSG00000070331	Qrich2	Gm66	glutamine rich 2	protein-coding
mm_77566.1	chr8	123429073	123429081	-	1	NA	Intergenic	MuLV-int|LTR|ERV1	-13879	NM_001253784	23854	Mm.275127	NM_054046	ENSMUSG00000001482	Def8	AI449518|D8Ertd713e|DEF-8	differentially expressed in FDCP 8	protein-coding
mm_28109.1	chr3	86548528	86548543	-	1	NA	promoter-TSS (NM_011839)	promoter-TSS (NM_011839)	-252	NM_011839	23937	Mm.389466	NM_011839	ENSMUSG00000057777	Mab21l2	-	mab-21-like 2 (C. elegans)	protein-coding
mm_84460.1	chr9	66583183	66583184	-	1	NA	intron (NM_001302116, intron 1 of 13)	intron (NM_001302116, intron 1 of 13)	9932	NM_144937	235441	Mm.32465	NM_144937	ENSMUSG00000032376	Usp3	AA409661|BC017156	ubiquitin specific peptidase 3	protein-coding
mm_41820.1	chr5	103846593	103846596	+	1	NA	intron (NM_001080798, intron 16 of 19)	L1Md_F2|LINE|L1	64635	NM_178741	246293	Mm.179871	NM_178741	ENSMUSG00000029312	Klhl8	2310001P09Rik|D5Ertd431e	kelch-like 8	protein-coding
mm_94351.1	chr11	4902243	4902247	+	1	NA	intron (NM_172438, intron 4 of 19)	intron (NM_172438, intron 4 of 19)	6902	NM_172438	107829	Mm.28969	NM_172438	ENSMUSG00000034274	Thoc5	1700060C24Rik|A430085L24Rik|Fmip|PK1.3|Sgk2	THO complex 5	protein-coding
mm_26506.1	chr3	145758964	145758984	+	1	NA	exon (NM_026993, exon 1 of 6)	exon (NM_026993, exon 1 of 6)	282	NM_026993	69219	Mm.234247	NM_026993	ENSMUSG00000028194	Ddah1	2410006N07Rik|2510015N06Rik|AI987801|AW050362	dimethylarginine dimethylaminohydrolase 1	protein-coding
mm_7970.1	chr1	134060863	134060873	-	1	NA	Intergenic	Intergenic	18287	NM_007570	12227	Mm.392646	NM_007570	ENSMUSG00000020423	Btg2	AA959598|APRO1|Pc3|TIS21	B cell translocation gene 2, anti-proliferative	protein-coding
mm_77305.1	chr8	117461497	117461503	-	1	NA	TTS (NM_001163262)	TTS (NM_001163262)	2235	NR_106046	102465653		NR_106046	ENSMUSG00000098483	Mir7078	Gm27386|mmu-mir-7078	microRNA 7078	ncRNA
mm_167378.1	chr8	92355857	92355879	-	1	NA	non-coding (NR_033641, exon 1 of 7)	non-coding (NR_033641, exon 1 of 7)	252	NR_110452	71296	Mm.86664	NR_033641	ENSMUSG00000031736	Crnde	4933436C20Rik	colorectal neoplasia differentially expressed (non-protein coding)	ncRNA
mm_98125.1	chr11	87216952	87216958	+	1	NA	intron (NM_197987, intron 23 of 23)	T-rich|Low_complexity|Low_complexity	89880	NM_197987	68729	Mm.17436	NM_197987	ENSMUSG00000018548	Trim37	1110032A10Rik|2810004E07Rik|AI848587|AU043018|MUL|TEF3|mKIAA0898	tripartite motif-containing 37	protein-coding
mm_150437.1	chr19	37556719	37556719	+	1	NA	intron (NM_175353, intron 1 of 21)	(TCTCC)n|Simple_repeat|Simple_repeat	6301	NM_175353	107371	Mm.24865	NM_175353	ENSMUSG00000053799	Exoc6	4833405E05Rik|AW413330|C430002C19|Sec15|Sec15l1|hbd|msec15	exocyst complex component 6	protein-coding
mm_127445.1	chr15	101270543	101270577	+	1	NA	exon (NM_010444, exon 2 of 7)	exon (NM_010444, exon 2 of 7)	3714	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_140861.1	chr17	23740860	23740888	-	1	NA	promoter-TSS (NM_023824)	promoter-TSS (NM_023824)	-544	NM_023824	76498	Mm.491253	NM_023824	ENSMUSG00000023909	Paqr4	1500004C10Rik	progestin and adipoQ receptor family member IV	protein-coding
mm_133909.1	chr16	97551969	97551991	+	1	NA	non-coding (NR_003508, exon 10 of 14)	non-coding (NR_003508, exon 10 of 14)	15897	NM_013606	17858	Mm.14157	NM_013606	ENSMUSG00000023341	Mx2	AI528743|Mx-2	MX dynamin-like GTPase 2	protein-coding
mm_79445.1	chr9	56090374	56090399	+	1	NA	5' UTR (NM_011193, exon 1 of 15)	5' UTR (NM_011193, exon 1 of 15)	410	NM_011193	19200	Mm.2534	NM_011193	ENSMUSG00000032322	Pstpip1	CD2BP1|def-2	proline-serine-threonine phosphatase-interacting protein 1	protein-coding
mm_103038.1	chr11	69761890	69761899	-	1	NA	promoter-TSS (NM_019871)	promoter-TSS (NM_019871)	-50	NM_019871	56293	Mm.6211	NM_019871	ENSMUSG00000018776	Slc35g3	Amac1	solute carrier family 35, member G3	protein-coding
mm_154930.1	chrX	35888639	35888683	+	1	NA	promoter-TSS (NM_001009947)	promoter-TSS (NM_001009947)	-171	NM_001009947	75974	Mm.32873	NM_177745	ENSMUSG00000031093	Dock11	5033414A21Rik|8030476J24|Zizimin2|sph238	dedicator of cytokinesis 11	protein-coding
mm_41177.1	chr5	88008120	88008122	+	1	NA	exon (NM_011422, exon 3 of 3)	exon (NM_011422, exon 3 of 3)	5596	NM_011422	20599	Mm.261199	NM_011422	ENSMUSG00000029280	Smr3a	AA589601|MSG1|MSG3|Smr1|Smr3	submaxillary gland androgen regulated protein 3A	protein-coding
mm_49468.1	chr6	29467773	29467810	+	1	NA	promoter-TSS (NM_025381)	promoter-TSS (NM_025381)	8	NM_025381	66144	Mm.371614	NM_025381	ENSMUSG00000004285	Atp6v1f	1110004G16Rik	ATPase, H+ transporting, lysosomal V1 subunit F	protein-coding
mm_115693.1	chr13	14039596	14039639	-	1	NA	promoter-TSS (NM_178337)	promoter-TSS (NM_178337)	21	NR_130788	70430	Mm.260209	NM_178337	ENSMUSG00000039233	Tbce	2610206D02Rik|C530005D02Rik|pmn	tubulin-specific chaperone E	protein-coding
mm_55108.1	chr6	50381653	50381655	-	1	NA	intron (NM_001347213, intron 2 of 23)	intron (NM_001347213, intron 2 of 23)	1183	NM_027881	71720	Mm.44153	NM_027881	ENSMUSG00000029822	Osbpl3	1200014M06Rik|6720421I08Rik|A530055M08|ORP-3|ORP3|OSBP3	oxysterol binding protein-like 3	protein-coding
mm_168006.1	chrY	4453624	4453626	-	1	NA	Intergenic	MURVY-int|LTR|ERV1	681952	NM_011253	19657	Mm.4711	NM_011253	ENSMUSG00000094658	Rbmy	RBM|Rbm1|Rbm1-rs1|Rbmy1a1|Rbmy1a1-rs1|Rbmy1b	RNA binding motif protein, Y chromosome	protein-coding
mm_125050.1	chr15	25843252	25843262	+	1	NA	promoter-TSS (NM_001034851)	promoter-TSS (NM_001034851)	-41	NM_001034851	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_70820.1	chr8	23132135	23132148	+	1	NA	exon (NM_031158, exon 39 of 45)	exon (NM_031158, exon 39 of 45)	-6889	NM_001310436	11733	Mm.334444	NM_031158	ENSMUSG00000031543	Ank1	Ank-1|nb|pale	ankyrin 1, erythroid	protein-coding
mm_41439.1	chr5	90904367	90904410	+	1	NA	exon (NM_009140, exon 3 of 4)	exon (NM_009140, exon 3 of 4)	489	NM_009140	20310	Mm.4979	NM_009140	ENSMUSG00000058427	Cxcl2	CINC-2a|GROb|Gro2|MIP-2|MIP-2a|Mgsa-b|Mip2|Scyb|Scyb2	chemokine (C-X-C motif) ligand 2	protein-coding
mm_99851.1	chr11	109362874	109362878	+	1	NA	promoter-TSS (NM_010303)	promoter-TSS (NM_010303)	82	NM_010303	14674	Mm.193925	NM_010303	ENSMUSG00000020611	Gna13	AU024132|AU043124|Galpha13	guanine nucleotide binding protein, alpha 13	protein-coding
mm_161567.1	chr16	20152889	20152889	+	1	NA	intron (NM_001145930, intron 2 of 30)	intron (NM_001145930, intron 2 of 30)	11826	NM_001145930	208146	Mm.390895	NM_001033237	ENSMUSG00000041215	Yeats2	BC042768|mKIAA1197	YEATS domain containing 2	protein-coding
mm_95373.1	chr11	49088724	49088727	+	1	NA	intron (NM_010999, intron 2 of 5)	intron (NM_010999, intron 2 of 5)	1708	NM_008330	15953	Mm.24769	NM_008330	ENSMUSG00000078920	Ifi47	47kDa|IRG-47|Ifggc1|Igrd|Iigp4|Iipg4|Irgd	interferon gamma inducible protein 47	protein-coding
mm_40737.1	chr5	66260117	66260120	+	1	NA	promoter-TSS (NM_027602)	promoter-TSS (NM_027602)	220	NM_001302834	70918	Mm.23166	NM_027602	ENSMUSG00000029206	Nsun7	4921525L17Rik	NOL1/NOP2/Sun domain family, member 7	protein-coding
mm_1021.1	chr1	58749394	58749419	+	1	NA	intron (NM_001293805, intron 6 of 7)	intron (NM_001293805, intron 6 of 7)	18854	NM_001293805	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_3087.1	chr1	134406316	134406326	+	1	NA	exon (NM_028057, exon 2 of 9)	exon (NM_028057, exon 2 of 9)	331	NM_028057	72017	Mm.280230	NM_028057	ENSMUSG00000026456	Cyb5r1	1500005G05Rik|B5R.1|C80155|Nqo3a2	cytochrome b5 reductase 1	protein-coding
mm_22655.1	chr3	14871600	14871610	+	1	NA	exon (NM_007606, exon 7 of 7)	exon (NM_007606, exon 7 of 7)	8067	NM_007606	12350	Mm.300	NM_007606	ENSMUSG00000027559	Car3	BB219044|Ca3|Car-3	carbonic anhydrase 3	protein-coding
mm_70660.1	chr8	14849923	14849935	+	1	NA	Intergenic	Intergenic	-38607	NM_012000	26889	Mm.254027	NM_012000	ENSMUSG00000026317	Cln8	mnd	ceroid-lipofuscinosis, neuronal 8	protein-coding
mm_67896.1	chr7	99483646	99483654	-	1	NA	promoter-TSS (NM_012052)	promoter-TSS (NM_012052)	59	NM_012052	27050	Mm.236868	NM_012052	ENSMUSG00000030744	Rps3	D7Ertd795e|Rs_3	ribosomal protein S3	protein-coding
mm_17647.1	chr2	31481200	31481202	-	1	NA	intron (NR_002687, intron 5 of 15)	intron (NR_002687, intron 5 of 15)	10893	NR_002687	432466	Mm.333323	NR_002687	ENSMUSG00000046687	Gm5424	EG432466	argininosuccinate synthase pseudogene	pseudo
mm_71029.1	chr8	33599681	33599681	+	1	NA	promoter-TSS (NM_017374)	promoter-TSS (NM_017374)	60	NM_017374	19053	Mm.29301	NM_017374	ENSMUSG00000009630	Ppp2cb	AI115466|D8Ertd766e|PP2Ac	protein phosphatase 2 (formerly 2A), catalytic subunit, beta isoform	protein-coding
mm_66756.1	chr7	46714341	46714356	-	1	NA	intron (NM_011315, intron 2 of 3)	intron (NM_011315, intron 2 of 3)	1328	NM_011315	20210	Mm.14277	NM_011315	ENSMUSG00000040026	Saa3	AV098916|Saa-3|l7R3	serum amyloid A 3	protein-coding
mm_23484.1	chr3	60500682	60500705	+	1	NA	promoter-TSS (NM_001253711)	promoter-TSS (NM_001253711)	-486	NM_001253711	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_101933.1	chr11	50207181	50207197	-	1	NA	exon (NM_011018, exon 4 of 8)	exon (NM_011018, exon 4 of 8)	3631	NM_001290769	18412	Mm.40828	NM_011018	ENSMUSG00000015837	Sqstm1	A170|OSF-6|Osi|STAP|STONE14|p62	sequestosome 1	protein-coding
mm_147652.1	chr18	60501749	60501772	-	1	NA	5' UTR (NM_134133, exon 1 of 2)	5' UTR (NM_134133, exon 1 of 2)	223	NM_134133	106878	Mm.273197	NM_134133	ENSMUSG00000038059	Smim3	2010002N04Rik|AI195350|AW561905|Nid67|cI-41	small integral membrane protein 3	protein-coding
mm_57217.1	chr6	122934042	122934088	-	1	NA	3' UTR (NM_199311, exon 6 of 6)	3' UTR (NM_199311, exon 6 of 6)	12217	NM_199311	269799	Mm.297275	NM_199311	ENSMUSG00000049037	Clec4a1	BC049354|Dcir4	C-type lectin domain family 4, member a1	protein-coding
mm_16947.1	chr2	16571861	16571870	-	1	NA	intron (NM_026162, intron 4 of 13)	RMER17B|LTR|ERVK	215561	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding
mm_115648.1	chr13	12306657	12306658	-	1	NA	intron (NM_033268, intron 4 of 20)	intron (NM_033268, intron 4 of 20)	34075	NM_033268	11472	Mm.37638	NM_033268	ENSMUSG00000052374	Actn2	1110008F24Rik	actinin alpha 2	protein-coding
mm_140983.1	chr17	24719919	24719929	-	1	NA	promoter-TSS (NR_028515)	promoter-TSS (NR_028515)	41	NR_027900	73474	Mm.443320	NR_027900	ENSMUSG00000090101	Snhg9	1700072N11Rik	small nucleolar RNA host gene 9	ncRNA
mm_2912.1	chr1	132008286	132008316	+	1	NA	intron (NM_007923, intron 1 of 4)	CpG	696	NM_007923	13714	Mm.254233	NM_007923	ENSMUSG00000026436	Elk4	2310011G17Rik|A130026I01Rik|BB162516|SAP-1|Sap1	ELK4, member of ETS oncogene family	protein-coding
mm_89035.1	chr10	82795169	82795198	+	1	NA	Intergenic	ID_B1|SINE|B4	-16940	NR_038042	70003	Mm.48789	NR_038042	ENSMUSG00000056821	1700028I16Rik	-	RIKEN cDNA 1700028I16 gene	ncRNA
mm_130429.1	chr15	98157289	98157301	-	1	NA	intron (NM_001170711, intron 1 of 3)	MLTR18D_MM|LTR|ERVK	8283	NM_001170711	78541	Mm.200766	NM_030121	ENSMUSG00000048175	Asb8	4930539L19Rik|AI788835|C430011H06Rik	ankyrin repeat and SOCS box-containing 8	protein-coding
mm_157160.1	chrX	9465297	9465319	-	1	NA	intron (NM_007807, intron 3 of 12)	intron (NM_007807, intron 3 of 12)	4016	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_2630.1	chr1	121431052	121431124	+	1	NA	promoter-TSS (NM_029955)	promoter-TSS (NM_029955)	21	NM_001025156	70829	Mm.25788	NM_027567	ENSMUSG00000026339	Ccdc93	4633402D15Rik|9230102M16Rik	coiled-coil domain containing 93	protein-coding
mm_173003.1	chrM	1919	1919	+	1	NA	NA	Intergenic	NA	NA								
mm_81782.1	chr9	114689880	114689884	+	1	NA	intron (NM_146229, intron 2 of 12)	intron (NM_146229, intron 2 of 12)	1051	NM_146229	235661	Mm.128627	NM_146229	ENSMUSG00000032435	Dync1li1	1110053F02Rik|Dnclic1|LIC-1	dynein cytoplasmic 1 light intermediate chain 1	protein-coding
mm_45230.1	chr5	53590179	53590192	-	1	NA	promoter-TSS (NM_001277116)	promoter-TSS (NM_001277116)	-161	NM_009035	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_143633.1	chr17	78966333	78966352	-	1	NA	exon (NM_029239, exon 11 of 19)	exon (NM_029239, exon 11 of 19)	29207	NM_028611	73694	Mm.104959	NM_028611	ENSMUSG00000024082	Ndufaf7	2410091C18Rik|AL033374|PRO1853	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex assembly factor 7	protein-coding
mm_25242.1	chr3	103914561	103914605	+	1	NA	exon (NM_172684, exon 1 of 7)	exon (NM_172684, exon 1 of 7)	463	NM_172684	229675	Mm.29366	NM_172684	ENSMUSG00000044098	Rsbn1	C230004D03Rik|E330004N01|Rosbin|Rsbn|Rsbp|mKIAA3002	rosbin, round spermatid basic protein 1	protein-coding
mm_82157.1	chr9	123781203	123781249	+	1	NA	3' UTR (NM_001166625, exon 4 of 4)	3' UTR (NM_001166625, exon 4 of 4)	14015	NM_001166625	12769	Mm.440604	NM_009913	ENSMUSG00000029530	Ccr9	A130091K22Rik|Cmkbr10|GPR-9-6	chemokine (C-C motif) receptor 9	protein-coding
mm_180.1	chr1	13874370	13874377	+	1	NA	Intergenic	Intergenic	-87444	NR_004447	433273	Mm.304088	NR_004447	ENSMUSG00000097711	Gm5523	EG433273	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_50835.1	chr6	54816706	54816742	+	1	NA	promoter-TSS (NM_199143)	promoter-TSS (NM_199143)	-192	NM_199143	387524	Mm.286149	NM_199143	ENSMUSG00000058446	Znrf2	1190002C14Rik|AU044205|D6Ertd365e	zinc and ring finger 2	protein-coding
mm_90722.1	chr10	5068915	5068958	-	1	NA	5' UTR (NM_022027, exon 1 of 17)	5' UTR (NM_022027, exon 1 of 17)	127	NM_022027	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_42189.1	chr5	112269489	112269496	+	1	NA	TTS (NM_001312894)	TTS (NM_001312894)	-7199	NM_001326590	22022	Mm.250631	NM_009419	ENSMUSG00000029344	Tpst2	AI448750|D5Ucla3|Tango13b|grm|grt	protein-tyrosine sulfotransferase 2	protein-coding
mm_163133.1	chr11	78940573	78940581	+	1	NA	intron (NM_001313921, intron 10 of 25)	intron (NM_001313921, intron 10 of 25)	15286	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_30588.1	chr4	5724305	5724357	+	1	NA	intron (NM_173426, intron 1 of 2)	intron (NM_173426, intron 1 of 2)	80152	NM_173426	242297	Mm.331470	NM_173426	ENSMUSG00000049119	Fam110b	1700012H17Rik|5031405P22|AW049855	family with sequence similarity 110, member B	protein-coding
mm_15828.1	chr2	164653827	164653836	+	1	NA	intron (NM_001160414, intron 1 of 3)	intron (NM_001160414, intron 1 of 3)	1135	NM_001160414	629754	Mm.190489	NM_001160414	ENSMUSG00000074594	Wfdc9	OTTMUSG00000001088	WAP four-disulfide core domain 9	protein-coding
mm_60567.1	chr7	44481443	44481447	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-3072	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_52225.1	chr6	103511400	103511408	+	1	NA	intron (NM_007697, intron 1 of 26)	intron (NM_007697, intron 1 of 26)	528	NM_007697	12661	Mm.251288	NM_007697	ENSMUSG00000030077	Chl1	A530023M13Rik|AI465420|CALL|LICAM2	cell adhesion molecule L1-like	protein-coding
mm_49044.1	chr6	4760242	4760261	+	1	NA	3' UTR (NM_130877, exon 2 of 2)	3' UTR (NM_130877, exon 2 of 2)	12945	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_141319.1	chr17	28365147	28365180	-	1	NA	promoter-TSS (NM_021478)	promoter-TSS (NM_021478)	-20	NM_021478	22157	Mm.42102	NM_021478	ENSMUSG00000037446	Tulp1	Tulp1l	tubby like protein 1	protein-coding
mm_6356.1	chr1	71741326	71741330	-	1	NA	Intergenic	RMER20C_Mm|LTR|ERVK	87993	NR_040308	100042814	Mm.405775	NR_040308	ENSMUSG00000073652	Apol7d	ENSMUSG00000073652|Gm15456|OTTMUSG00000022136	apolipoprotein L 7d	ncRNA
mm_119539.1	chr14	48120741	48120782	+	1	NA	promoter-TSS (NM_033602)	promoter-TSS (NM_033602)	-108	NM_033602	93834	Mm.296457	NM_033602	ENSMUSG00000021846	Peli2	AW047589|BB129927	pellino 2	protein-coding
mm_104143.1	chr11	87026643	87026671	-	1	NA	intron (NR_106195, intron 4 of 8)	intron (NR_106195, intron 4 of 8)	-32895	NM_001005341	77864	Mm.191894	NM_001005341	ENSMUSG00000018427	Ypel2	6430570G24|E130113K08Rik	yippee-like 2 (Drosophila)	protein-coding
mm_8316.1	chr1	144307163	144307194	-	1	NA	Intergenic	L2|LINE|L2	-58074	NM_015811	50778	Mm.103701	NM_015811	ENSMUSG00000026358	Rgs1	BL34	regulator of G-protein signaling 1	protein-coding
mm_69506.1	chr7	134341976	134341996	-	1	NA	intron (NM_001199941, intron 3 of 8)	intron (NM_001199941, intron 3 of 8)	22898	NM_001199941	71007	Mm.334285	NM_001081331	ENSMUSG00000030994	D7Ertd443e	4933400E14Rik|FATS|Gm497	DNA segment, Chr 7, ERATO Doi 443, expressed	protein-coding
mm_94676.1	chr11	17905941	17905942	+	1	NA	Intergenic	Intergenic	47934	NM_026576	68145	Mm.178684	NM_026576	ENSMUSG00000016984	Etaa1	5730466H23Rik|AA672646	Ewing tumor-associated antigen 1	protein-coding
mm_170664.1	chr2	113920555	113920562	-	1	NA	Intergenic	Intergenic	-71897	NM_181416	228482	Mm.45753	NM_181416	ENSMUSG00000041219	Arhgap11a	6530401L14Rik|mKIAA0013	Rho GTPase activating protein 11A	protein-coding
mm_6980.1	chr1	86356304	86356328	-	1	NA	promoter-TSS (NR_002851)	promoter-TSS (NR_002851)	11	NR_002851	80828		NR_002851	ENSMUSG00000064823	Snord82	Rnu82|U82|Z25	small nucleolar RNA, C/D box 82	snoRNA
mm_172597.1	chr8	15519799	15519805	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	462149	NM_008664	17930	Mm.272115	NM_008664	ENSMUSG00000031461	Myom2	AW146149	myomesin 2	protein-coding
mm_74639.1	chr8	13254122	13254150	-	1	NA	promoter-TSS (NM_172750)	promoter-TSS (NM_172750)	26	NM_172750	234072	Mm.132785	NM_172750	ENSMUSG00000031448	Adprhl1	Arh2|D330008N11Rik	ADP-ribosylhydrolase like 1	protein-coding
mm_39579.1	chr5	23435380	23435396	+	1	NA	intron (NM_026984, intron 1 of 25)	intron (NM_026984, intron 1 of 25)	959	NM_026984	69188	Mm.205190	NM_026984	ENSMUSG00000029004	Kmt2e	1810033J14Rik|9530077A04Rik|D230038D11Rik|Mll5|NKp44L	lysine (K)-specific methyltransferase 2E	protein-coding
mm_135312.1	chr16	38713208	38713218	-	1	NA	promoter-TSS (NM_020260)	promoter-TSS (NM_020260)	-178	NM_020260	12549	Mm.370848	NM_020260	ENSMUSG00000022799	Arhgap31	5830477L08Rik|AU041750|Cdgap|D330026I07Rik	Rho GTPase activating protein 31	protein-coding
mm_143346.1	chr17	66694026	66694034	-	1	NA	intron (NM_008984, intron 22 of 30)	intron (NM_008984, intron 22 of 30)	-99408	NM_028998	74556	Mm.218634	NM_028998	ENSMUSG00000024105	Themis3	9130404H23Rik	thymocyte selection associated family member 3	protein-coding
mm_95443.1	chr11	50236851	50236870	+	1	NA	intron (NR_132732, intron 4 of 4)	CpG	1672	NM_001313968	17001	Mm.245151	NM_008521	ENSMUSG00000020377	Ltc4s	-	leukotriene C4 synthase	protein-coding
mm_37008.1	chr4	111902784	111902801	-	1	NA	promoter-TSS (NM_145551)	promoter-TSS (NM_145551)	4	NM_145551	230612	Mm.26630	NM_145551	ENSMUSG00000028544	Slc5a9	AI159731|SGLT4	solute carrier family 5 (sodium/glucose cotransporter), member 9	protein-coding
mm_131477.1	chr16	17070343	17070345	+	1	NA	exon (NM_001291053, exon 1 of 4)	exon (NM_001291053, exon 1 of 4)	205	NM_001291047	106369	Mm.237941	NM_023249	ENSMUSG00000022773	Ypel1	0610009L05Rik|1700016N17Rik|1700019O22Rik|4921520K19Rik|4930511F14Rik|AV118478|DGL-1|Dgl1|Ppil2|mdgl-1	yippee-like 1 (Drosophila)	protein-coding
mm_150411.1	chr19	36926670	36926674	+	1	NA	intron (NM_001080706, intron 1 of 37)	(T)n|Simple_repeat|Simple_repeat	593	NM_001080706	107182	Mm.295062	NM_001080706	ENSMUSG00000040565	Btaf1	AI414500|AI447930|E430027O22Rik|TAF170	B-TFIID TATA-box binding protein associated factor 1	protein-coding
mm_5903.1	chr1	54914242	54914249	-	1	NA	intron (NM_001081433, intron 1 of 27)	intron (NM_001081433, intron 1 of 27)	12142	NM_001081433	329154	Mm.397910	NM_001081433	ENSMUSG00000052331	Ankrd44	4930444A19Rik|A130096K20|E130014H08Rik|PP6-ARS-B	ankyrin repeat domain 44	protein-coding
mm_33832.1	chr4	135626763	135626806	+	1	NA	non-coding (NR_027909, exon 1 of 2)	non-coding (NR_027909, exon 1 of 2)	129	NR_027909	73937	Mm.292326	NM_028688	ENSMUSG00000086788	1700029M20Rik	4930406E24Rik	RIKEN cDNA 1700029M20 gene	ncRNA
mm_83641.1	chr9	49504312	49504325	-	1	NA	3' UTR (NM_001311065, exon 18 of 18)	3' UTR (NM_001311065, exon 18 of 18)	-13970	NR_029465	100036537	Mm.437541	NR_029465	ENSMUSG00000079564	Gm11149	ENSMUSG00000060603|ENSMUSG00000079564	predicted gene 11149	ncRNA
mm_95515.1	chr11	52098803	52098813	+	1	NA	promoter-TSS (NM_019411)	promoter-TSS (NM_019411)	-16	NM_019411	19052	Mm.260288	NM_019411	ENSMUSG00000020349	Ppp2ca	PP2A|R75353	protein phosphatase 2 (formerly 2A), catalytic subunit, alpha isoform	protein-coding
mm_150107.1	chr19	29522381	29522391	+	1	NA	promoter-TSS (NR_015567)	promoter-TSS (NR_015567)	104	NM_001081319	226089	Mm.353838	NM_177641	ENSMUSG00000038658	Ric1	C030046E11Rik|C130057E09Rik|Kiaa1432	RAB6A GEF complex partner 1	protein-coding
mm_112169.1	chr12	113415554	113415566	-	1	NA	Intergenic	Intergenic	-74005	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_135814.1	chr16	57606817	57606879	-	1	NA	promoter-TSS (NM_025599)	promoter-TSS (NM_025599)	19	NM_025599	66497	Mm.425976	NM_025599	ENSMUSG00000022748	Cmss1	1110001A06Rik|2610528E23Rik|4930572F24Rik|AV099812|AV122629	cms small ribosomal subunit 1	protein-coding
mm_84476.1	chr9	66804343	66804357	-	1	NA	Intergenic	RMER17C|LTR|ERVK	-8927	NM_177583	208117	Mm.41291	NM_177583	ENSMUSG00000032375	Aph1b	2310057K14Rik|Aph1c	aph1 homolog B, gamma secretase subunit	protein-coding
mm_41836.1	chr5	104309328	104309346	+	1	NA	exon (NM_008318, exon 6 of 7)	exon (NM_008318, exon 6 of 7)	10050	NM_008318	15891	Mm.4987	NM_008318	ENSMUSG00000029306	Ibsp	BSP|BSP II|BSPII|Bsp2	integrin binding sialoprotein	protein-coding
mm_142660.1	chr17	47688881	47688925	-	1	NA	promoter-TSS (NM_001164729)	promoter-TSS (NM_001164729)	-517	NM_001164729	66119	Mm.89912	NM_025365	ENSMUSG00000033475	Tomm6	1110002E23Rik|AI663970	translocase of outer mitochondrial membrane 6 homolog (yeast)	protein-coding
mm_89118.1	chr10	84756187	84756197	+	1	NA	5' UTR (NM_001024918, exon 1 of 18)	5' UTR (NM_001024918, exon 1 of 18)	144	NM_001024918	71137	Mm.79070	NM_027689	ENSMUSG00000020037	Rfx4	4933412G19Rik|NYD-sp10	regulatory factor X, 4 (influences HLA class II expression)	protein-coding
mm_50272.1	chr6	45267292	45267295	+	1	NA	intron (NM_001004357, intron 1 of 23)	intron (NM_001004357, intron 1 of 23)	207232	NM_001004357	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding
mm_163241.1	chr11	105456760	105456764	-	1	NA	promoter-TSS (NM_001039242)	promoter-TSS (NM_001039242)	-27	NM_001039242	632687	Mm.121570	NM_172568	ENSMUSG00000078627	March10	4933417C16Rik|AV039223|OTTMUSG00000002847|Rnf190	membrane-associated ring finger (C3HC4) 10	protein-coding
mm_157747.1	chrX	73435333	73435350	-	1	NA	promoter-TSS (NM_011907)	promoter-TSS (NM_011907)	2	NM_011907	24102	Mm.23312	NM_011907	ENSMUSG00000031372	Trex2	-	three prime repair exonuclease 2	protein-coding
mm_88963.1	chr10	81394808	81394824	+	1	NA	exon (NM_001099917, exon 4 of 4)	exon (NM_001099917, exon 4 of 4)	1752	NM_001099917	72273	Mm.253147	NM_001099917	ENSMUSG00000078439	Smim24	2210404O07Rik	small integral membrane protein 24	protein-coding
mm_95662.1	chr11	53771711	53771722	+	1	NA	intron (NM_001159393, intron 2 of 9)	intron (NM_001159393, intron 2 of 9)	1243	NM_001159396	16362	Mm.105218	NM_008390	ENSMUSG00000018899	Irf1	AU020929|Irf-1	interferon regulatory factor 1	protein-coding
mm_85158.1	chr9	96333279	96333310	-	1	NA	3' UTR (NM_007502, exon 7 of 7)	3' UTR (NM_007502, exon 7 of 7)	31005	NM_007502	11933	Mm.424	NM_007502	ENSMUSG00000032412	Atp1b3	AA409958|AI664000|AW212096	ATPase, Na+/K+ transporting, beta 3 polypeptide	protein-coding
mm_50191.1	chr6	41847544	41847557	+	1	NA	promoter-TSS (NM_008843)	promoter-TSS (NM_008843)	1	NM_008843	18716	Mm.214755	NM_008843	ENSMUSG00000058499	Pip	GCDFP-15|GP17|mSMGP	prolactin induced protein	protein-coding
mm_49119.1	chr6	8509858	8509875	+	1	NA	promoter-TSS (NR_040452)	promoter-TSS (NR_040452)	266	NM_133236	170772	Mm.210787	NM_133236	ENSMUSG00000029638	Glcci1	2310047L21Rik|A130036A18Rik|Fam117c|Gig18|Tssn1	glucocorticoid induced transcript 1	protein-coding
mm_23461.1	chr3	60472793	60472806	+	1	NA	promoter-TSS (NM_001253713)	promoter-TSS (NM_001253713)	-31	NM_001253713	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_84852.1	chr9	78480799	78480818	-	1	NA	intron (NM_010106, intron 1 of 7)	intron (NM_010106, intron 1 of 7)	916	NM_010106	13627	Mm.138471	NM_010106	ENSMUSG00000037742	Eef1a1	-	eukaryotic translation elongation factor 1 alpha 1	protein-coding
mm_162699.1	chr10	20952567	20952577	+	1	NA	promoter-TSS (NM_026203)	promoter-TSS (NM_026203)	25	NM_026203	52906	Mm.253280	NM_026203	ENSMUSG00000019986	Ahi1	1700015F03Rik|Ahi-1|D10Bwg0629e	Abelson helper integration site 1	protein-coding
mm_117760.1	chr13	96132522	96132530	-	1	NA	promoter-TSS (NM_029210)	promoter-TSS (NM_029210)	51	NM_029210	75209	Mm.40436	NM_029210	ENSMUSG00000051111	Sv2c	4930527L09Rik|AI841971	synaptic vesicle glycoprotein 2c	protein-coding
mm_138068.1	chr17	33940662	33940709	+	1	NA	promoter-TSS (NM_010385)	promoter-TSS (NM_010385)	-38	NM_020603	57315	Mm.2437	NM_020603	ENSMUSG00000024312	Wdr46	2310007I04Rik|Bing4|C78447|C78559	WD repeat domain 46	protein-coding
mm_156700.1	chrX	159532656	159532668	+	1	NA	promoter-TSS (NM_001033472)	promoter-TSS (NM_001033472)	-6	NM_001033472	382252	Mm.296254	NM_001033472	ENSMUSG00000044150	A830080D01Rik	2310067E24Rik|Gm1146	RIKEN cDNA A830080D01 gene	protein-coding
mm_79282.1	chr9	50856939	50856987	+	1	NA	promoter-TSS (NM_001286553)	promoter-TSS (NM_001286553)	39	NM_001286553	73699	Mm.7726	NM_028614	ENSMUSG00000032058	Ppp2r1b	2410091N08Rik|AI790395	protein phosphatase 2, regulatory subunit A, beta	protein-coding
mm_77483.1	chr8	122476097	122476115	-	1	NA	promoter-TSS (NM_153775)	promoter-TSS (NM_153775)	-37	NM_153775	66965	Mm.482288	NM_153775	ENSMUSG00000049482	Ctu2	2310061F22Rik|C16orf84|Ncs2	cytosolic thiouridylase subunit 2	protein-coding
mm_134928.1	chr16	30933411	30933416	-	1	NA	intron (NR_035427, intron 1 of 2)	MIR3|SINE|MIR	148019	NM_198626	268880	Mm.286693	NM_198626	ENSMUSG00000047434	Xxylt1	AI480653	xyloside xylosyltransferase 1	protein-coding
mm_153354.1	chr19	40157897	40157935	-	1	NA	intron (NM_145499, intron 7 of 8)	Lx7|LINE|L1	29370	NM_145499	226105	Mm.29119	NM_145499	ENSMUSG00000060613	Cyp2c70	-	cytochrome P450, family 2, subfamily c, polypeptide 70	protein-coding
mm_145587.1	chr18	60985777	60985785	+	1	NA	3' UTR (NM_001286809, exon 6 of 6)	3' UTR (NM_001286809, exon 6 of 6)	22227	NM_001286809	12322	Mm.131530	NM_009792	ENSMUSG00000024617	Camk2a	CaMKII|R74975|mKIAA0968	calcium/calmodulin-dependent protein kinase II alpha	protein-coding
mm_5176.1	chr1	11395463	11395499	-	1	NA	Intergenic	L1_Mus3|LINE|L1	-18624	NM_001310451	320492	Mm.52021	NM_177173	ENSMUSG00000057715	A830018L16Rik	-	RIKEN cDNA A830018L16 gene	protein-coding
mm_66709.1	chr7	45973283	45973303	-	1	NA	Intergenic	Intergenic	44895	NM_001033243	211535	Mm.227539	NM_001033243	ENSMUSG00000040189	Ccdc114	-	coiled-coil domain containing 114	protein-coding
mm_1554.1	chr1	72942745	72942754	+	1	NA	Intergenic	PB1D10|SINE|Alu	-67884	NM_010518	16011	Mm.405761	NM_010518	ENSMUSG00000026185	Igfbp5	AI256729|AW208790|IGFBP-5|IGFBP-5P	insulin-like growth factor binding protein 5	protein-coding
mm_128905.1	chr15	73423078	73423179	-	1	NA	promoter-TSS (NM_007982)	promoter-TSS (NM_007982)	63	NM_007982	14083	Mm.254494	NM_007982	ENSMUSG00000022607	Ptk2	FAK|FRNK|Fadk|mKIAA4203|p125FAK	PTK2 protein tyrosine kinase 2	protein-coding
mm_134846.1	chr16	26755499	26755503	-	1	NA	promoter-TSS (NR_105063)	promoter-TSS (NR_105063)	1	NR_105063	100504628	Mm.393275	NR_105063	ENSMUSG00000092545	Gm20319	-	predicted gene, 20319	ncRNA
mm_44103.1	chr5	149367552	149367583	+	1	NA	Intergenic	Intergenic	-44239	NM_027519	70717	Mm.252139	NM_027519	ENSMUSG00000029659	Medag	6330406I15Rik|Awms3|MEDA-4|Meda4|mAWMS3	mesenteric estrogen dependent adipogenesis	protein-coding
mm_19655.1	chr2	102901997	102902031	-	1	NA	promoter-TSS (NM_009851)	promoter-TSS (NM_009851)	-349	NM_001039150	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_100170.1	chr11	116531997	116532014	+	1	NA	promoter-TSS (NM_001172472)	promoter-TSS (NM_001172472)	94	NM_001172475	20698	Mm.20944	NM_011451	ENSMUSG00000061878	Sphk1	1110006G24Rik|Sk1|Spk1	sphingosine kinase 1	protein-coding
mm_109626.1	chr12	112766797	112766807	+	1	NA	exon (NM_178911, exon 7 of 11)	exon (NM_178911, exon 7 of 11)	6147	NM_178911	104759	Mm.203915	NM_178911	ENSMUSG00000052160	Pld4	AI132321|thss	phospholipase D family, member 4	protein-coding
mm_135091.1	chr16	34573922	34573936	-	1	NA	Intergenic	CpG	-59902	NM_177357	545156	Mm.82274	NM_177357	ENSMUSG00000061751	Kalrn	2210407G14Rik|AV235988|DUET|E530005C20Rik|Gm539|Hapip|TRAD	kalirin, RhoGEF kinase	protein-coding
mm_151428.1	chr19	56897847	56897858	+	1	NA	intron (NM_172840, intron 5 of 13)	intron (NM_172840, intron 5 of 13)	23436	NM_172840	240675	Mm.129534	NM_172840	ENSMUSG00000025082	Vwa2	Amaco	von Willebrand factor A domain containing 2	protein-coding
mm_105780.1	chr11	109722349	109722360	-	1	NA	promoter-TSS (NM_153782)	promoter-TSS (NM_153782)	-98	NM_153782	208659	Mm.208662	NM_153782	ENSMUSG00000020614	Fam20a	AI606893	family with sequence similarity 20, member A	protein-coding
mm_44237.1	chr5	5265791	5265806	-	1	NA	5' UTR (NM_001310448, exon 1 of 14)	5' UTR (NM_001310448, exon 1 of 14)	270	NM_001310448	18647	Mm.389061	NM_011074	ENSMUSG00000028926	Cdk14	Pftk1|mKIAA0834	cyclin-dependent kinase 14	protein-coding
mm_27759.1	chr3	69599186	69599202	-	1	NA	promoter-TSS (NM_020026)	promoter-TSS (NM_020026)	-234	NM_020026	26879	Mm.153710	NM_020026	ENSMUSG00000043300	B3galnt1	B3galt3|b3GT3	UDP-GalNAc:betaGlcNAc beta 1,3-galactosaminyltransferase, polypeptide 1	protein-coding
mm_96042.1	chr11	59557342	59557355	+	1	NA	intron (NM_145827, intron 6 of 9)	L1MB3|LINE|L1	14390	NM_001011789	257962	Mm.377316	NM_001011789	ENSMUSG00000059610	Olfr222	MOR256-45P	olfactory receptor 222	protein-coding
mm_105259.1	chr11	102356495	102356506	-	1	NA	exon (NM_011403, exon 12 of 20)	exon (NM_011403, exon 12 of 20)	8781	NM_011403	20533	Mm.7248	NM_011403	ENSMUSG00000006574	Slc4a1	Ae1|CD233|Empb3|l11Jus51	solute carrier family 4 (anion exchanger), member 1	protein-coding
mm_86350.1	chr9	123632494	123632525	-	1	NA	promoter-TSS (NM_011731)	promoter-TSS (NM_011731)	56	NM_011731	22599	Mm.41963	NM_011731	ENSMUSG00000025243	Slc6a20b	AA986306|Sit1|Slc6a20|XT3|Xtrp3	solute carrier family 6 (neurotransmitter transporter), member 20B	protein-coding
mm_43710.1	chr5	139377717	139377745	+	1	NA	promoter-TSS (NR_033147)	promoter-TSS (NR_033147)	34	NR_033147	320197	Mm.474295	NM_177097	ENSMUSG00000044197	D830046C22Rik	-	RIKEN cDNA D830046C22 gene	ncRNA
mm_61899.1	chr7	90129709	90129715	+	1	NA	promoter-TSS (NM_001252521)	promoter-TSS (NM_001252521)	224	NR_046007	78329	Mm.389940	NR_046006	ENSMUSG00000097162	2310010J17Rik	-	RIKEN cDNA 2310010J17 gene	ncRNA
mm_40404.1	chr5	53049122	53049136	+	1	NA	promoter-TSS (NM_011402)	promoter-TSS (NM_011402)	-224	NM_011402	20531	Mm.284891	NM_011402	ENSMUSG00000029188	Slc34a2	AA536683|D5Ertd227e|NaPi-2b|Npt2b	solute carrier family 34 (sodium phosphate), member 2	protein-coding
mm_56792.1	chr6	116647657	116647667	-	1	NA	exon (NM_178045, exon 4 of 11)	exon (NM_178045, exon 4 of 11)	-1615	NR_106010	102466793		NR_106010	ENSMUSG00000098334	Mir7043	Gm27776|mmu-mir-7043	microRNA 7043	ncRNA
mm_57209.1	chr6	122855561	122855578	-	1	NA	intron (NM_009779, intron 1 of 1)	B1_Mus1|SINE|Alu	588	NM_009779	12267	Mm.2408	NM_009779	ENSMUSG00000040552	C3ar1	AZ3B|C3AR|HNFAG09	complement component 3a receptor 1	protein-coding
mm_171264.1	chr3	85166613	85166616	-	1	NA	Intergenic	L1Md_T|LINE|L1	-150905	NR_040542	73283	Mm.489084	NR_040542	ENSMUSG00000099995	1700036G14Rik	-	RIKEN cDNA 1700036G14 gene	ncRNA
mm_80724.1	chr9	92457370	92457389	+	1	NA	promoter-TSS (NM_178711)	promoter-TSS (NM_178711)	1	NM_178711	235527	Mm.55289	NM_178711	ENSMUSG00000032377	Plscr4	AV245873	phospholipid scramblase 4	protein-coding
mm_22035.1	chr2	168204677	168204690	-	1	NA	5' UTR (NM_001310086, exon 2 of 5)	5' UTR (NM_001310086, exon 2 of 5)	2429	NM_009628	11538	Mm.201322	NM_009628	ENSMUSG00000051149	Adnp	AA589558|mKIAA0784	activity-dependent neuroprotective protein	protein-coding
mm_117528.1	chr13	81711302	81711347	-	1	NA	promoter-TSS (NM_028372)	promoter-TSS (NM_028372)	-93	NM_028372	72852	Mm.31095	NM_028372	ENSMUSG00000051098	Mblac2	2900024O10Rik	metallo-beta-lactamase domain containing 2	protein-coding
mm_39493.1	chr5	20951172	20951195	+	1	NA	non-coding (NR_030699, exon 1 of 1)	non-coding (NR_030699, exon 1 of 1)	194	NR_030699	320770	Mm.491217	NR_030699	ENSMUSG00000101013	A630072M18Rik	Aptr	RIKEN cDNA A630072M18 gene	ncRNA
mm_19434.1	chr2	91962492	91962494	-	1	NA	intron (NM_138306, intron 1 of 30)	A-rich|Low_complexity|Low_complexity	1070	NM_138306	104418	Mm.314923	NM_138306	ENSMUSG00000040479	Dgkz	E130307B02Rik|ENSMUSG00000075035|F730209L11Rik|mDGK[z]	diacylglycerol kinase zeta	protein-coding
mm_6158.1	chr1	65032739	65032754	-	1	NA	promoter-TSS (NM_027582)	promoter-TSS (NM_027582)	13	NM_027582	70861	Mm.18725	NM_027582	ENSMUSG00000025955	Akr1cl	4921521F21Rik|AI451536|AI503553	aldo-keto reductase family 1, member C-like	protein-coding
mm_97342.1	chr11	77462326	77462421	+	1	NA	Intergenic	CpG	-1540	NM_139129	216961	Mm.33477	NM_139128	ENSMUSG00000020836	Coro6	-	coronin 6	protein-coding
mm_68749.1	chr7	121064771	121064795	-	1	NA	3' UTR (NM_030691, exon 6 of 6)	3' UTR (NM_030691, exon 6 of 6)	9747	NM_030691	80719	Mm.160384	NM_030691	ENSMUSG00000035004	Igsf6	-	immunoglobulin superfamily, member 6	protein-coding
mm_145663.1	chr18	61130910	61130920	+	1	NA	TTS (NM_178277)	TTS (NM_178277)	13447	NR_105949	102466212		NR_105949	ENSMUSG00000098389	Mir6983	Gm27496|mmu-mir-6983	microRNA 6983	ncRNA
mm_108473.1	chr12	83651291	83651322	+	1	NA	exon (NM_027349, exon 6 of 19)	exon (NM_027349, exon 6 of 19)	19072	NM_027349	67039	Mm.46005	NM_027349	ENSMUSG00000010608	Rbm25	2600011C06Rik|2610015J01Rik|A130095G20Rik|AI159652|AL023075|AU043498|RNPC7	RNA binding motif protein 25	protein-coding
mm_48258.1	chr5	137836185	137836193	-	1	NA	promoter-TSS (NM_153510)	promoter-TSS (NM_153510)	89	NM_153510	231805	Mm.379385	NM_153510	ENSMUSG00000046245	Pilra	AV021745|FDF03	paired immunoglobin-like type 2 receptor alpha	protein-coding
mm_5905.1	chr1	54926312	54926402	-	1	NA	promoter-TSS (NM_001081433)	promoter-TSS (NM_001081433)	30	NM_001081433	329154	Mm.397910	NM_001081433	ENSMUSG00000052331	Ankrd44	4930444A19Rik|A130096K20|E130014H08Rik|PP6-ARS-B	ankyrin repeat domain 44	protein-coding
mm_119869.1	chr14	54625306	54625317	+	1	NA	promoter-TSS (NM_175204)	promoter-TSS (NM_175204)	1	NM_175204	73902	Mm.32009	NM_175204	ENSMUSG00000072423	Psmb11	5830406J20Rik|beta5t	proteasome (prosome, macropain) subunit, beta type, 11	protein-coding
mm_76570.1	chr8	88662374	88662384	-	1	NA	intron (NM_145857, intron 3 of 12)	intron (NM_145857, intron 3 of 12)	15032	NM_145857	257632	Mm.222633	NM_145857	ENSMUSG00000055994	Nod2	ACUG|BLAU|CD|Card15|F830032C23Rik|IBD1|Nlrc2	nucleotide-binding oligomerization domain containing 2	protein-coding
mm_128947.1	chr15	74746816	74746822	-	1	NA	promoter-TSS (NM_001081961)	promoter-TSS (NM_001081961)	-132	NM_001081961	69462	Mm.64338	NM_001081961	ENSMUSG00000075605	Slurp2	2300005B03Rik|SLURP-2	secreted Ly6/Plaur domain containing 2	protein-coding
mm_74754.1	chr8	19064948	19064950	-	1	NA	promoter-TSS (NM_183038)	promoter-TSS (NM_183038)	-139	NM_183038	360214	Mm.271559	NM_183038	ENSMUSG00000061847	Defb39	BD-39	defensin beta 39	protein-coding
mm_133929.1	chr16	3718154	3718164	-	1	NA	promoter-TSS (NM_001161791)	promoter-TSS (NM_001161791)	-35	NM_001161791	54483	Mm.143718	NM_019453	ENSMUSG00000022534	Mefv	FMF|TRIM20|pyrin	Mediterranean fever	protein-coding
mm_61133.1	chr7	55930159	55930174	+	1	NA	3' UTR (NM_001164662, exon 31 of 31)	3' UTR (NM_001164662, exon 31 of 31)	32327	NM_001256133	93790	Mm.37249	NM_023647	ENSMUSG00000030452	Nipa2	2600017P10Rik|3830408P04Rik|AB041581	non imprinted in Prader-Willi/Angelman syndrome 2 homolog (human)	protein-coding
mm_74209.1	chr8	123895854	123895862	+	1	NA	Intergenic	Intergenic	-1083	NM_009606	11459	Mm.214950	NM_009606	ENSMUSG00000031972	Acta1	AA959943|Acta-2|Acts|Actsk-1	actin, alpha 1, skeletal muscle	protein-coding
mm_42527.1	chr5	115631884	115631895	+	1	NA	promoter-TSS (NR_027810)	promoter-TSS (NR_027810)	-73	NR_027810	66123	Mm.133063	NM_021417	ENSMUSG00000107121	1110006O24Rik	-	RIKEN cDNA 1110006O24 gene	ncRNA
mm_17419.1	chr2	27426490	27426535	-	1	NA	non-coding (NR_133905, exon 1 of 30)	non-coding (NR_133905, exon 1 of 30)	1096	NR_133905	22325	Mm.179011	NM_009500	ENSMUSG00000009621	Vav2	2810040F13Rik|AI847175|Vav-2	vav 2 oncogene	protein-coding
mm_136326.1	chr16	92321455	92321461	-	1	NA	promoter-TSS (NM_029252)	promoter-TSS (NM_029252)	-17	NM_029252	75328	Mm.72970	NM_029252	ENSMUSG00000051728	4930563D23Rik	-	RIKEN cDNA 4930563D23 gene	protein-coding
mm_142738.1	chr17	48388597	48388609	-	1	NA	3' UTR (NM_010913, exon 9 of 9)	3' UTR (NM_010913, exon 9 of 9)	11977	NM_001347402	18044	Mm.4929	NM_010913	ENSMUSG00000023994	Nfya	AA407810|Cbf-b|SEZ-10|SEZ10	nuclear transcription factor-Y alpha	protein-coding
mm_75658.1	chr8	65132399	65132411	-	1	NA	Intergenic	RLTR35B_MM|LTR|ERVL	-2868	NR_033217	407795	Mm.387876	NR_033217	ENSMUSG00000074300	BC030870	-	cDNA sequence BC030870	ncRNA
mm_69937.1	chr7	142095244	142095253	-	1	NA	promoter-TSS (NM_008748)	promoter-TSS (NM_008748)	36	NM_008748	18218	Mm.39725	NM_008748	ENSMUSG00000037887	Dusp8	5530400B01Rik|AI593498|Nttp1	dual specificity phosphatase 8	protein-coding
mm_145368.1	chr18	56733182	56733186	+	1	NA	intron (NM_010721, intron 4 of 10)	intron (NM_010721, intron 4 of 10)	25371	NM_010721	16906	Mm.4105	NM_010721	ENSMUSG00000024590	Lmnb1	-	lamin B1	protein-coding
mm_167612.1	chr9	56090099	56090103	+	1	NA	5' UTR (NM_011193, exon 1 of 15)	5' UTR (NM_011193, exon 1 of 15)	125	NM_011193	19200	Mm.2534	NM_011193	ENSMUSG00000032322	Pstpip1	CD2BP1|def-2	proline-serine-threonine phosphatase-interacting protein 1	protein-coding
mm_69145.1	chr7	127091155	127091161	-	1	NA	promoter-TSS (NM_178901)	promoter-TSS (NM_178901)	-278	NM_178901	101602	Mm.490357	NM_178901	ENSMUSG00000045165	AI467606	-	expressed sequence AI467606	protein-coding
mm_46517.1	chr5	105293728	105293780	-	1	NA	promoter-TSS (NM_194336)	promoter-TSS (NM_194336)	-55	NM_194336	100702	Mm.491210	NM_194336	ENSMUSG00000079362	Gbp6	AI595338|Mpa2l	guanylate binding protein 6	protein-coding
mm_133675.1	chr16	92292363	92292375	+	1	NA	promoter-TSS (NM_134110)	promoter-TSS (NM_134110)	-20	NM_134110	246133	Mm.156736	NM_134110	ENSMUSG00000039672	Kcne2	2200002I16Rik|AW048273|MiRP1	potassium voltage-gated channel, Isk-related subfamily, gene 2	protein-coding
mm_134767.1	chr16	23520692	23520701	-	1	NA	promoter-TSS (NM_008555)	promoter-TSS (NM_008555)	-106	NM_008555	17174	Mm.1213	NM_008555	ENSMUSG00000022887	Masp1	AW048060|CCPII|Crarf|Masp1/3	mannan-binding lectin serine peptidase 1	protein-coding
mm_95207.1	chr11	43594545	43594569	+	1	NA	Intergenic	RLTR23|LTR|ERV1	7005	NM_008375	16204	Mm.142716	NM_008375	ENSMUSG00000020405	Fabp6	GT|I-15P|I-BABP|ILBP|ILBP3|Illbp	fatty acid binding protein 6, ileal (gastrotropin)	protein-coding
mm_137217.1	chr17	24169980	24169984	+	1	NA	promoter-TSS (NM_009729)	promoter-TSS (NM_009729)	-553	NM_009729	11984	Mm.30155	NM_009729	ENSMUSG00000024121	Atp6v0c	Atp6c|Atp6c2|Atp6l|Atpl|Atpl-rs1|PL16|VATL|Vma3	ATPase, H+ transporting, lysosomal V0 subunit C	protein-coding
mm_16260.1	chr2	173291228	173291258	+	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-14710	NM_022995	65112	Mm.73682	NM_022995	ENSMUSG00000038400	Pmepa1	2210418I02Rik|AW455466|Erg1.2|N4wbp4|Stag1|Tmepai	prostate transmembrane protein, androgen induced 1	protein-coding
mm_87005.1	chr10	26801525	26801532	+	1	NA	intron (NM_176837, intron 1 of 14)	Lx4A|LINE|L1	29016	NM_176837	73910	Mm.356496	NM_176837	ENSMUSG00000039031	Arhgap18	4833419J07Rik|AI314906|AI843501	Rho GTPase activating protein 18	protein-coding
mm_162617.1	chr1	183369527	183369563	-	1	NA	promoter-TSS (NM_177389)	promoter-TSS (NM_177389)	20	NM_177389	338366	Mm.41152	NM_177389		Mia3	9130229H14Rik|A930039G15Rik|AU022327|B230399H06Rik|C80126|Gm1525|TANGO1|Tango	melanoma inhibitory activity 3	protein-coding
mm_57075.1	chr6	122578664	122578674	-	1	NA	3' UTR (NM_031159, exon 8 of 8)	3' UTR (NM_031159, exon 8 of 8)	23775	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_79868.1	chr9	65082483	65082514	+	1	NA	3' UTR (NM_028906, exon 21 of 21)	3' UTR (NM_028906, exon 21 of 21)	-18988	NM_001290315	56741	Mm.209041	NM_020043	ENSMUSG00000032816	Igdcc4	DDM36|Nope	immunoglobulin superfamily, DCC subclass, member 4	protein-coding
mm_11277.1	chr2	30062046	30062078	+	1	NA	promoter-TSS (NM_023871)	promoter-TSS (NM_023871)	66	NM_023871	56086	Mm.326055	NM_023871	ENSMUSG00000054766	Set	2610030F17Rik|5730420M11Rik|AA407739|I-2PP2A|StF-IT-1|TAF-I	SET nuclear oncogene	protein-coding
mm_157282.1	chrX	20860978	20861000	-	1	NA	TTS (NM_009703)	TTS (NM_009703)	2193	NR_049190	100885829		NR_049190	ENSMUSG00000093408	Mir5617	Gm25192|mir-5617|mmu-mir-5617	microRNA 5617	ncRNA
mm_107301.1	chr12	30911776	30911786	+	1	NA	promoter-TSS (NM_021330)	promoter-TSS (NM_021330)	112	NM_013709	24057	Mm.218624	NM_013709	ENSMUSG00000020669	Sh3yl1	AI314953|Ray|YSC84	Sh3 domain YSC-like 1	protein-coding
mm_83509.1	chr9	45984563	45984586	-	1	NA	intron (NM_008775, intron 1 of 5)	CpG	297	NM_008775	18475	Mm.200859	NM_008775	ENSMUSG00000003131	Pafah1b2	AI747451|AU021353|Pafahb|mus[b]	platelet-activating factor acetylhydrolase, isoform 1b, subunit 2	protein-coding
mm_32964.1	chr4	119847786	119847814	+	1	NA	intron (NM_010657, intron 1 of 8)	intron (NM_010657, intron 1 of 8)	33122	NM_010657	16656	Mm.302758	NM_010657	ENSMUSG00000028634	Hivep3	2900056N03Rik|A130075N07|AI848000|E030045D18Rik|KBP-1|KBP1|Krc|Rc|Schnurri-3|Shn3|Zas3	human immunodeficiency virus type I enhancer binding protein 3	protein-coding
mm_88924.1	chr10	81195081	81195083	+	1	NA	intron (NR_015477, intron 1 of 2)	B1_Mur2|SINE|Alu	391	NR_015477	69678	Mm.81562	NR_015477		Atcayos	2310050B05Rik	ataxia, cerebellar, Cayman type, opposite strand	ncRNA
mm_86092.1	chr9	114986706	114986707	-	1	NA	Intergenic	Intergenic	-52719	NM_175380	333433	Mm.38198	NM_175380	ENSMUSG00000050627	Gpd1l	2210409H23Rik|D9Ertd660e	glycerol-3-phosphate dehydrogenase 1-like	protein-coding
mm_43452.1	chr5	136136272	136136274	+	1	NA	promoter-TSS (NM_027891)	promoter-TSS (NM_027891)	128	NM_001347492	72041	Mm.486605	NM_028070	ENSMUSG00000039754	Alkbh4	2010004B12Rik|Abj4	alkB homolog 4, lysine demethylase	protein-coding
mm_93518.1	chr10	115288023	115288033	-	1	NA	Intergenic	Intergenic	27563	NM_024454	216344	Mm.21936	NM_024454	ENSMUSG00000020132	Rab21	9630024B22	RAB21, member RAS oncogene family	protein-coding
mm_133566.1	chr16	91399975	91400016	+	1	NA	intron (NM_010509, intron 8 of 8)	intron (NM_010509, intron 8 of 8)	-6240	NM_008349	16155	Mm.4154	NM_008349	ENSMUSG00000022969	Il10rb	6620401D04Rik|AI528744|CRF2-4|Crfb4|D16H21S58|D21S58h|IL-10R2|Il10r2	interleukin 10 receptor, beta	protein-coding
mm_167297.1	chr8	47674825	47674833	-	1	NA	5' UTR (NM_023503, exon 1 of 2)	5' UTR (NM_023503, exon 1 of 2)	330	NM_023503	69260	Mm.430733	NM_023503	ENSMUSG00000063049	Ing2	2810011M06Rik|Ing1l|Ing2b|P33ING2	inhibitor of growth family, member 2	protein-coding
mm_125249.1	chr15	35024028	35024069	+	1	NA	intron (NM_019635, intron 6 of 10)	intron (NM_019635, intron 6 of 10)	131758	NM_019635	56274	Mm.262330	NM_019635	ENSMUSG00000022329	Stk3	0610042I06Rik|MST|Mst2|Mst3|Ste20|mess1	serine/threonine kinase 3	protein-coding
mm_160526.1	chr9	36582625	36582625	-	1	NA	promoter-TSS (NM_001167584)	promoter-TSS (NM_001167584)	10	NM_001167584	100312948	Mm.475849	NM_001167584	ENSMUSG00000091248	Gm17689	Pate-g|Pate8	predicted gene, 17689	protein-coding
mm_30111.1	chr3	139019612	139019613	-	1	NA	intron (NM_145544, intron 3 of 13)	intron (NM_145544, intron 3 of 13)	55589	NM_145544	229877	Mm.28893	NM_145544	ENSMUSG00000028149	Rap1gds1	BC011279|GDS1	RAP1, GTP-GDP dissociation stimulator 1	protein-coding
mm_56439.1	chr6	97457250	97457281	-	1	NA	intron (NM_145148, intron 2 of 23)	Lx8b|LINE|L1	2021	NM_001346639	232288	Mm.27789	NM_145148	ENSMUSG00000030064	Frmd4b	6030440G05Rik|C87375|GOBLIN|GRSP1|R74720	FERM domain containing 4B	protein-coding
mm_23261.1	chr3	51416602	51416613	+	1	NA	intron (NM_053089, intron 1 of 19)	CpG	591	NM_053089	74838	Mm.275281	NM_053089	ENSMUSG00000063273	Naa15	5730450D16Rik|6330400I15|ASTBDN|Narg1|Tbdn-1|mNAT1	N(alpha)-acetyltransferase 15, NatA auxiliary subunit	protein-coding
mm_140660.1	chr17	12868127	12868148	-	1	NA	promoter-TSS (NM_008552)	promoter-TSS (NM_008552)	6	NM_008552	17171	Mm.425994	NM_008552	ENSMUSG00000068037	Mas1	Mas-1|Mgra	MAS1 oncogene	protein-coding
mm_97753.1	chr11	80505255	80505276	+	1	NA	intron (NM_177390, intron 21 of 21)	intron (NM_177390, intron 21 of 21)	3841	NR_126552	77417	Mm.437510	NR_126552	ENSMUSG00000085078	C030013C21Rik	-	RIKEN cDNA C030013C21 gene	ncRNA
mm_148079.1	chr18	72351138	72351156	-	1	NA	promoter-TSS (NM_007831)	promoter-TSS (NM_007831)	-78	NM_007831	13176	Mm.167882	NM_007831	ENSMUSG00000060534	Dcc	C030036D22Rik|Igdcc1	deleted in colorectal carcinoma	protein-coding
mm_98533.1	chr11	95006433	95006457	+	1	NA	3' UTR (NM_172261, exon 10 of 10)	3' UTR (NM_172261, exon 10 of 10)	-3434	NM_146025	217125	Mm.297199	NM_146025	ENSMUSG00000047181	Samd14	AI839049|AI854782|BC034054	sterile alpha motif domain containing 14	protein-coding
mm_48766.1	chr5	148399852	148399862	-	1	NA	promoter-TSS (NM_007513)	promoter-TSS (NM_007513)	47	NM_007513	11987	Mm.275489	NM_007513	ENSMUSG00000041313	Slc7a1	4831426K01Rik|AI447493|Atrc-1|Atrc1|Cat1|Rec-1|Rev-1|mCAT-1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 1	protein-coding
mm_12431.1	chr2	70661456	70661460	+	1	NA	promoter-TSS (NM_027352)	promoter-TSS (NM_027352)	-51	NR_027343	70231	Mm.271950	NM_027352	ENSMUSG00000014959	Gorasp2	0610011A07Rik|2410043M02Rik|5730520M13Rik|9430094F20Rik|AW552058|ENSMUSG00000075299|GOLPH2|GRASP55|GRS2|p59	golgi reassembly stacking protein 2	protein-coding
mm_132237.1	chr16	32750652	32750662	+	1	NA	exon (NM_080457, exon 2 of 27)	exon (NM_080457, exon 2 of 27)	14771	NM_080457	140474	Mm.214599	NM_080457	ENSMUSG00000079620	Muc4	4933405I11Rik|Asgp	mucin 4	protein-coding
mm_160498.1	chr9	14500554	14500554	-	1	NA	promoter-TSS (NM_023153)	promoter-TSS (NM_023153)	-65	NM_023153	66070	Mm.245938	NM_023153	ENSMUSG00000004096	Cwc15	0610040D20Rik|2900052N06Rik|Ed1|c11orf5|mED1	CWC15 spliceosome-associated protein	protein-coding
mm_69570.1	chr7	135700842	135700857	-	1	NA	exon (NM_001081117, exon 12 of 14)	exon (NM_001081117, exon 12 of 14)	15530	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_23018.1	chr3	34561228	34561233	+	1	NA	intron (NR_015580, intron 2 of 4)	intron (NR_015580, intron 2 of 4)	849	NR_015580	320478	Mm.444063	NR_015580	ENSMUSG00000105265	Sox2ot	B230215L15Rik	SOX2 overlapping transcript (non-protein coding)	ncRNA
mm_103660.1	chr11	78984948	78984957	-	1	NA	promoter-TSS (NM_010708)	promoter-TSS (NM_010708)	-28	NM_010708	16859	Mm.341434	NM_010708	ENSMUSG00000001123	Lgals9	AA407335|AI194909|AI265545|LGALS35|Lgals5|gal-9|galectin-9	lectin, galactose binding, soluble 9	protein-coding
mm_8959.1	chr1	164899581	164899596	-	1	NA	Intergenic	Intergenic	35922	NM_008510	16963	Mm.190	NM_008510	ENSMUSG00000026573	Xcl1	AI661682|ATAC|LTN|Lptn|SCM-1|SCM-1a|Scyc1	chemokine (C motif) ligand 1	protein-coding
mm_16992.1	chr2	18292014	18292018	-	1	NA	intron (NM_007869, intron 7 of 11)	intron (NM_007869, intron 7 of 11)	100814	NM_001190817	13418	Mm.246674	NM_007869	ENSMUSG00000026740	Dnajc1	4733401K02Rik|AA960110|D230036H06Rik|Dnajl1|ERdj1|ERj1p|MTJ1	DnaJ heat shock protein family (Hsp40) member C1	protein-coding
mm_10415.1	chr2	13580031	13580095	+	1	NA	exon (NM_011701, exon 6 of 9)	exon (NM_011701, exon 6 of 9)	5752	NM_011701	22352	Mm.268000	NM_011701	ENSMUSG00000026728	Vim	-	vimentin	protein-coding
mm_59918.1	chr7	30419680	30419692	+	1	NA	intron (NM_011827, intron 1 of 3)	intron (NM_011827, intron 1 of 3)	168	NM_011827	23900	Mm.379050	NM_011827	ENSMUSG00000064109	Hcst	DAP10|KAP10	hematopoietic cell signal transducer	protein-coding
mm_984.1	chr1	58445511	58445528	+	1	NA	promoter-TSS (NM_027351)	promoter-TSS (NM_027351)	-33	NM_001285827	70225	Mm.340195	NM_027351	ENSMUSG00000026035	Ppil3	2310076N22Rik|2510026K04Rik|Cyp10l	peptidylprolyl isomerase (cyclophilin)-like 3	protein-coding
mm_121556.1	chr14	122480058	122480063	+	1	NA	3' UTR (NM_009574, exon 3 of 3)	3' UTR (NM_009574, exon 3 of 3)	4676	NM_009574	22772	Mm.308936	NM_009574	ENSMUSG00000061524	Zic2	HPE5|Ku	zinc finger protein of the cerebellum 2	protein-coding
mm_58219.1	chr6	144209405	144209435	-	1	NA	5' UTR (NM_011444, exon 1 of 15)	5' UTR (NM_011444, exon 1 of 15)	148	NM_001113559	20678	Mm.1752	NM_011444	ENSMUSG00000041540	Sox5	A730017D01Rik|AI528773	SRY (sex determining region Y)-box 5	protein-coding
mm_150648.1	chr19	41911897	41911908	+	1	NA	promoter-TSS (NM_023418)	promoter-TSS (NM_023418)	31	NM_023418	18648	Mm.16783	NM_023418	ENSMUSG00000011752	Pgam1	2310050F24Rik|Pgam-1	phosphoglycerate mutase 1	protein-coding
mm_40241.1	chr5	37737274	37737282	+	1	NA	intron (NM_001081106, intron 1 of 3)	intron (NM_001081106, intron 1 of 3)	1759	NM_001081106	231162	Mm.76407	NM_001081106	ENSMUSG00000062329	Cytl1	4930443F05Rik|4Cytl1|C17|Cyt1|Gm147	cytokine-like 1	protein-coding
mm_33936.1	chr4	136909852	136909858	+	1	NA	Intergenic	Intergenic	-11011	NM_007572	12259	Mm.439957	NM_007572	ENSMUSG00000036887	C1qa	AI255395|C1q	complement component 1, q subcomponent, alpha polypeptide	protein-coding
mm_142312.1	chr17	42876443	42876455	-	1	NA	promoter-TSS (NM_009847)	promoter-TSS (NM_009847)	-25	NM_009847	12488	Mm.218637	NM_009847	ENSMUSG00000061665	Cd2ap	AL024079|C78928|METS-1|Mets1	CD2-associated protein	protein-coding
mm_134723.1	chr16	22898819	22898852	-	1	NA	exon (NM_001276450, exon 7 of 7)	exon (NM_001276450, exon 7 of 7)	-4449	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_138425.1	chr17	35069724	35069749	+	1	NA	3' UTR (NM_023463, exon 3 of 3)	3' UTR (NM_023463, exon 3 of 3)	2411	NM_023463	68468	Mm.215096	NM_023463	ENSMUSG00000092586	Ly6g6c	1110003M04Rik|AU016360|G6c|NG24	lymphocyte antigen 6 complex, locus G6C	protein-coding
mm_17650.1	chr2	31845926	31845952	-	1	NA	promoter-TSS (NM_178887)	promoter-TSS (NM_178887)	66	NM_178887	98970	Mm.32080	NM_178887	ENSMUSG00000026841	Fibcd1	AI448887	fibrinogen C domain containing 1	protein-coding
mm_104699.1	chr11	97988691	97988702	-	1	NA	TTS (NM_207231)	TTS (NM_207231)	-2250	NM_001163608	72324	Mm.39617	NM_028199	ENSMUSG00000017417	Plxdc1	2410003I07Rik|AI848450|Tem7	plexin domain containing 1	protein-coding
mm_132701.1	chr16	43363856	43363888	+	1	NA	intron (NM_181058, intron 2 of 6)	intron (NM_181058, intron 2 of 6)	56324	NR_046026	626693	Mm.447083	NR_046026	ENSMUSG00000085499	Gm15713	OTTMUSG00000025617	predicted gene 15713	ncRNA
mm_12661.1	chr2	75634057	75634067	+	1	NA	Intergenic	RMER20B|LTR|ERVK	-25197	NM_146130	229279	Mm.316306	NM_053263	ENSMUSG00000059005	Hnrnpa3	2410013L13Rik|2610209F03Rik|2610510D13Rik|Hnrpa3	heterogeneous nuclear ribonucleoprotein A3	protein-coding
mm_165215.1	chr2	38166144	38166151	-	1	NA	intron (NM_146122, intron 2 of 21)	intron (NM_146122, intron 2 of 21)	121237	NM_146122	227801	Mm.314245	NM_146122	ENSMUSG00000035392	Dennd1a	6030446I19Rik|connecdenn	DENN/MADD domain containing 1A	protein-coding
mm_99451.1	chr11	102434161	102434171	+	1	NA	exon (NM_008175, exon 6 of 13)	exon (NM_008175, exon 6 of 13)	3844	NM_008175	14824	Mm.1568	NM_008175	ENSMUSG00000034708	Grn	Pgrn|epithelin	granulin	protein-coding
mm_93124.1	chr10	91171703	91171715	-	1	NA	promoter-TSS (NM_001080132)	promoter-TSS (NM_001080132)	-90	NM_001080130	21917	Mm.159684	NM_011605	ENSMUSG00000019961	Tmpo	5630400D24Rik|AI195756|AI606875|AW214352|AW547477|LAP2|TP	thymopoietin	protein-coding
mm_93102.1	chr10	90587155	90587186	-	1	NA	intron (NM_001177396, intron 1 of 11)	intron (NM_001177396, intron 1 of 11)	10479	NM_181398	77531	Mm.440605	NM_181398	ENSMUSG00000058589	Anks1b	AIDA-1b|C030032C09Rik|E530015N03Rik|ENSMUSG00000078431|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding
mm_18953.1	chr2	76786705	76786715	-	1	NA	exon (NM_011652, exon 221 of 313)	exon (NM_011652, exon 221 of 313)	111395	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_172956.1	chr9	88482146	88482146	-	1	NA	5' UTR (NM_001284328, exon 1 of 12)	5' UTR (NM_001284328, exon 1 of 12)	251	NM_019666	56403	Mm.260545	NM_019666	ENSMUSG00000032423	Syncrip	2610109K23Rik|4632417O19Rik|GRY-RBP|Nsap1|Nsap1l|hnRNP Q|pp68	synaptotagmin binding, cytoplasmic RNA interacting protein	protein-coding
mm_143053.1	chr17	56982121	56982161	-	1	NA	promoter-TSS (NM_175731)	promoter-TSS (NM_175731)	-15	NM_175731	171168	Mm.218784	NM_175731	ENSMUSG00000045019	Acer1	2310024P18Rik|AI662009|Alkcdase1|Asah3|Cer1	alkaline ceramidase 1	protein-coding
mm_83767.1	chr9	52048700	52048712	-	1	NA	promoter-TSS (NR_023357)	promoter-TSS (NR_023357)	-1	NR_023357	629557	Mm.422775	NR_023357		Gm6981	EG629557	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_64698.1	chr7	4532420	4532470	-	1	NA	promoter-TSS (NM_001033548)	promoter-TSS (NM_001033548)	-3	NM_001033548	436022	Mm.425359	NM_001033548	ENSMUSG00000055809	Dnaaf3	6030429G01Rik|b2b1739Clo	dynein, axonemal assembly factor 3	protein-coding
mm_169155.1	chr13	63437643	63437643	+	1	NA	Intergenic	L1_Mm|LINE|L1	-5898	NM_001282942	14088	Mm.126106	NM_007985	ENSMUSG00000021461	Fancc	Facc	Fanconi anemia, complementation group C	protein-coding
mm_28895.1	chr3	97931659	97931718	-	1	NA	intron (NM_001033779, intron 1 of 1)	intron (NM_001033779, intron 1 of 1)	1515	NM_001033779	433632	Mm.212421	NM_001033779		Gm5544	EG433632	predicted gene 5544	protein-coding
mm_152397.1	chr19	10554791	10554834	-	1	NA	intron (NM_001277860, intron 2 of 4)	intron (NM_001277860, intron 2 of 4)	951	NM_001277861	68642	Mm.31236	NM_026798	ENSMUSG00000024667	Tmem216	1110017C22Rik|2810441K11Rik|4921533J23Rik|A930021F15Rik|AI482550	transmembrane protein 216	protein-coding
mm_113793.1	chr13	46273701	46273712	+	1	NA	promoter-TSS (NM_001005422)	promoter-TSS (NM_001005422)	-15	NM_001005422	380842	Mm.188108	NM_001005422	ENSMUSG00000063529	Stmnd1	Gm1574	stathmin domain containing 1	protein-coding
mm_154474.1	chrM	4043	4055	-	1	NA	NA	Intergenic	NA	NA								
mm_39933.1	chr5	31697961	31698042	+	1	NA	promoter-TSS (NM_181282)	promoter-TSS (NM_181282)	-49	NM_181281	107976	Mm.482126	NM_144541	ENSMUSG00000052139	Bre	6030405P19Rik|AI429776|B830038C02Rik	brain and reproductive organ-expressed protein	protein-coding
mm_37754.1	chr4	129640992	129641051	-	1	NA	promoter-TSS (NM_001199695)	promoter-TSS (NM_001199695)	44	NM_001199695	109658	Mm.268863	NM_001005506	ENSMUSG00000053841	Txlna	2600010N21Rik|AI425952|AW209241|Il14|Txln	taxilin alpha	protein-coding
mm_14059.1	chr2	122636963	122636973	+	1	NA	promoter-TSS (NM_001004174)	promoter-TSS (NM_001004174)	-919	NM_001004174	433470	Mm.36783	NM_001004174	ENSMUSG00000033213	AA467197	Nmes1|mir-147	expressed sequence AA467197	protein-coding
mm_153314.1	chr19	38043560	38043600	-	1	NA	promoter-TSS (NM_001099634)	promoter-TSS (NM_001099634)	-3	NM_001302140	226101	Mm.34674	NM_177035	ENSMUSG00000048612	Myof	2310004N10Rik|2310051D19Rik|E030042N20Rik|Fer1l3	myoferlin	protein-coding
mm_1614.1	chr1	74391542	74391550	+	1	NA	promoter-TSS (NM_153088)	promoter-TSS (NM_153088)	-63	NM_153088	227292	Mm.165042	NM_153088	ENSMUSG00000026176	Ctdsp1	GIP|NLIIF|Nif3|SCP1	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 1	protein-coding
mm_40310.1	chr5	43842966	43842980	+	1	NA	3' UTR (NM_009763, exon 9 of 9)	3' UTR (NM_009763, exon 9 of 9)	24080	NM_009763	12182	Mm.246332	NM_009763	ENSMUSG00000029082	Bst1	114/A10|A530073F09|BP-3|Bp3|Bsta1|CD157|Ly65	bone marrow stromal cell antigen 1	protein-coding
mm_57924.1	chr6	134262038	134262047	-	1	NA	intron (NM_001303102, intron 7 of 8)	intron (NM_001303102, intron 7 of 8)	-134287	NM_025778	66813	Mm.474472	NM_025778	ENSMUSG00000030200	Bcl2l14	4930452K23Rik|4933405K19Rik|9030625M01Rik|AI429211|Bclg	BCL2-like 14 (apoptosis facilitator)	protein-coding
mm_49647.1	chr6	30806218	30806237	+	1	NA	intron (NM_017478, intron 20 of 23)	intron (NM_017478, intron 20 of 23)	64928	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_157812.1	chrX	73966330	73966376	-	1	NA	promoter-TSS (NM_008224)	promoter-TSS (NM_008224)	4	NM_008224	15161	Mm.491126	NM_008224	ENSMUSG00000031386	Hcfc1	AW060991|HCF|HCF1	host cell factor C1	protein-coding
mm_80043.1	chr9	69226857	69226860	+	1	NA	intron (NM_013646, intron 2 of 10)	intron (NM_013646, intron 2 of 10)	-62983	NM_001289916	19883	Mm.378450	NM_013646	ENSMUSG00000032238	Rora	9530021D13Rik|Nr1f1|ROR1|ROR2|ROR3|nmf267|sg|staggerer|tmgc26	RAR-related orphan receptor alpha	protein-coding
mm_63920.1	chr7	139264761	139264765	+	1	NA	intron (NM_001098636, intron 2 of 2)	(T)n|Simple_repeat|Simple_repeat	16281	NM_001098636	101631	Mm.334300	NM_001033206	ENSMUSG00000060260	Pwwp2b	AI594893|D7Ertd517e|D930023J19Rik|Pwwp2	PWWP domain containing 2B	protein-coding
mm_80905.1	chr9	100597954	100598002	+	1	NA	Intergenic	Intergenic	-26893	NM_001101483	245020	Mm.236289	NM_001101483	ENSMUSG00000070287	Slc35g2	Gm519|Tmem22	solute carrier family 35, member G2	protein-coding
mm_53181.1	chr6	125432663	125432674	+	1	NA	Intergenic	Intergenic	-52164	NM_198604	213522	Mm.333396	NM_198604	ENSMUSG00000038167	Plekhg6	BC026778|Gm155	pleckstrin homology domain containing, family G (with RhoGef domain) member 6	protein-coding
mm_48956.1	chr6	4540857	4540861	+	1	NA	3' UTR (NM_007743, exon 52 of 52)	3' UTR (NM_007743, exon 52 of 52)	35241	NM_007743	12843	Mm.277792	NM_007743	ENSMUSG00000029661	Col1a2	AA960264|AI325291|Col1a-2|Cola-2|Cola2|oim	collagen, type I, alpha 2	protein-coding
mm_106149.1	chr11	116581476	116581513	-	1	NA	promoter-TSS (NM_173755)	promoter-TSS (NM_173755)	-47	NM_173755	217342	Mm.243950	NM_173755	ENSMUSG00000020802	Ube2o	9630022H21|B230113M03Rik|E2-230K|mKIAA1734	ubiquitin-conjugating enzyme E2O	protein-coding
mm_156900.1	chrX	167245494	167245516	+	1	NA	exon (NM_001313760, exon 2 of 2)	exon (NM_001313760, exon 2 of 2)	18824	NM_001313761	170744	Mm.196676	NM_133212	ENSMUSG00000040522	Tlr8	-	toll-like receptor 8	protein-coding
mm_80578.1	chr9	84045888	84045894	+	1	NA	intron (NM_001305935, intron 8 of 10)	intron (NM_001305935, intron 8 of 10)	97110	NM_199195	12040	Mm.12819	NM_199195	ENSMUSG00000032263	Bckdhb	BCKDE1B|BCKDH E1-beta	branched chain ketoacid dehydrogenase E1, beta polypeptide	protein-coding
mm_135.1	chr1	10260329	10260334	+	1	NA	Intergenic	MTB|LTR|ERVL-MaLR	-27661	NM_001102430	211673	Mm.229141	NM_001102430	ENSMUSG00000067851	Arfgef1	ARFGEP1|BIG1|D130059B05Rik|D730028O18Rik|P200	ADP-ribosylation factor guanine nucleotide-exchange factor 1(brefeldin A-inhibited)	protein-coding
mm_46852.1	chr5	113650391	113650448	-	1	NA	promoter-TSS (NM_008153)	promoter-TSS (NM_008153)	-29	NM_008153	14747	Mm.5196	NM_008153	ENSMUSG00000042190	Cmklr1	ChemR23|DEZ|Gpcr27|mcmklr1	chemokine-like receptor 1	protein-coding
mm_145196.1	chr18	49910425	49910439	+	1	NA	intron (NM_001081371, intron 28 of 42)	B4|SINE|B4	-68995	NM_001177760	106869	Mm.27740	NM_134131	ENSMUSG00000062210	Tnfaip8	AA987150|E130304C20Rik|ENSMUSG00000073567|Gg2-1|Gm10539|Nded|Ssc-2|Tipe	tumor necrosis factor, alpha-induced protein 8	protein-coding
mm_2860.1	chr1	131696619	131696630	+	1	NA	intron (NM_001311096, intron 1 of 4)	intron (NM_001311096, intron 1 of 4)	7929	NM_001311096	226421	Mm.44508	NM_145509	ENSMUSG00000052688	Rab7b	5430435G22Rik	RAB7B, member RAS oncogene family	protein-coding
mm_130271.1	chr15	96698777	96698792	-	1	NA	5' UTR (NM_175121, exon 2 of 16)	5' UTR (NM_175121, exon 2 of 16)	914	NM_175121	67760	Mm.46754	NM_175121	ENSMUSG00000022462	Slc38a2	5033402L14Rik|AI316867|ATA2|SAT2|mKIAA1382	solute carrier family 38, member 2	protein-coding
mm_52812.1	chr6	121343386	121343414	+	1	NA	intron (NM_001347433, intron 1 of 14)	intron (NM_001347433, intron 1 of 14)	324	NM_001347433	14411	Mm.274506	NM_133661	ENSMUSG00000030109	Slc6a12	BGT1|GAT-2|GAT2|Gabt2	solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12	protein-coding
mm_138605.1	chr17	35590814	35590826	+	1	NA	Intergenic	Intergenic	23335	NM_175148	69542	Mm.265291	NM_175148	ENSMUSG00000039269	2300002M23Rik	Stg|emprin	RIKEN cDNA 2300002M23 gene	protein-coding
mm_91638.1	chr10	42273922	42273943	-	1	NA	intron (NM_019740, intron 2 of 3)	intron (NM_019740, intron 2 of 3)	2810	NM_019740	56484	Mm.338613	NM_019740	ENSMUSG00000048756	Foxo3	1110048B16Rik|2010203A17Rik|C76856|FKHRL1|Fkhr2|Foxo3a	forkhead box O3	protein-coding
mm_55560.1	chr6	71341294	71341303	-	1	NA	Intergenic	Intergenic	18486	NM_009858	12526	Mm.333148	NM_009858	ENSMUSG00000053044	Cd8b1	Cd8b|Ly-3|Ly-C|Lyt-3	CD8 antigen, beta chain 1	protein-coding
mm_30561.1	chr4	3789922	3789928	+	1	NA	exon (NM_001111096, exon 13 of 13)	exon (NM_001111096, exon 13 of 13)	45730	NM_026147	67427	Mm.21938	NM_026147	ENSMUSG00000028234	Rps20	4632426K06Rik|Dsk4	ribosomal protein S20	protein-coding
mm_91685.1	chr10	43971918	43971928	-	1	NA	intron (NM_172393, intron 11 of 19)	intron (NM_172393, intron 11 of 19)	32923	NM_172393	11630	Mm.292082	NM_172393	ENSMUSG00000019866	Aim1	AI462491|AI463325	absent in melanoma 1	protein-coding
mm_69102.1	chr7	127020309	127020320	-	1	NA	5' UTR (NM_001102563, exon 2 of 4)	5' UTR (NM_001102563, exon 2 of 4)	897	NM_001102563	69017	Mm.392047	NM_001102563	ENSMUSG00000045114	Prrt2	1500031I19Rik|AI195361|DSPB3	proline-rich transmembrane protein 2	protein-coding
mm_9239.1	chr1	171294938	171295011	-	1	NA	promoter-TSS (NM_025388)	promoter-TSS (NM_025388)	8	NM_025388	66155	Mm.2815	NM_025388	ENSMUSG00000062963	Ufc1	1110021H02Rik|AA062310|ESTM29	ubiquitin-fold modifier conjugating enzyme 1	protein-coding
mm_118067.1	chr13	102905951	102905961	-	1	NA	intron (NM_175171, intron 4 of 28)	intron (NM_175171, intron 4 of 28)	145701	NR_130171	76624	Mm.426384	NR_130171	ENSMUSG00000091906	1700099I09Rik	-	RIKEN cDNA 1700099I09 gene	ncRNA
mm_148394.1	chr19	3767398	3767425	+	1	NA	promoter-TSS (NM_001167886)	promoter-TSS (NM_001167886)	-10	NM_001167889	225888	Mm.278578	NM_144871	ENSMUSG00000045098	Kmt5b	AA117471|C630029K18Rik|Suv4-20h1|Suv420h1	lysine methyltransferase 5B	protein-coding
mm_145599.1	chr18	61045240	61045248	+	1	NA	promoter-TSS (NM_001146268)	promoter-TSS (NM_001146268)	94	NM_008809	18596	Mm.4146	NM_008809	ENSMUSG00000024620	Pdgfrb	AI528809|CD140b|PDGFR-1|Pdgfr	platelet derived growth factor receptor, beta polypeptide	protein-coding
mm_145447.1	chr18	60212090	60212122	+	1	NA	promoter-TSS (NM_001033767)	promoter-TSS (NM_001033767)	29	NM_001033767	240327	Mm.357104	NM_001033767	ENSMUSG00000073555	Gm4951	EG240327|Ifgga2	predicted gene 4951	protein-coding
mm_55412.1	chr6	65022370	65022374	-	1	NA	Intergenic	Intergenic	-20295	NM_007958	13990	Mm.99113	NM_007958	ENSMUSG00000029920	Smarcad1	AV081750|AW226546|D6Pas1|Etl1|mKIAA1122	SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1	protein-coding
mm_109970.1	chr12	12937271	12937281	-	1	NA	exon (NM_008709, exon 3 of 3)	exon (NM_008709, exon 3 of 3)	4560	NM_008709	18109	Mm.16469	NM_008709	ENSMUSG00000037169	Mycn	N-myc|Nmyc|Nmyc-1|Nmyc1|bHLHe37|c-nmyc	v-myc avian myelocytomatosis viral related oncogene, neuroblastoma derived	protein-coding
mm_10102.1	chr2	3468589	3468613	+	1	NA	intron (NR_027509, intron 1 of 4)	intron (NR_027509, intron 1 of 4)	6385	NM_022724	64707	Mm.23483	NM_022724	ENSMUSG00000026646	Suv39h2	4930507K23Rik|AA536750|D030054H19Rik|D2Ertd544e|KMT1B	suppressor of variegation 3-9 homolog 2 (Drosophila)	protein-coding
mm_82680.1	chr9	22135655	22135665	-	1	NA	promoter-TSS (NM_001102405)	promoter-TSS (NM_001102405)	86	NM_001102405	11433	Mm.46354	NM_007388	ENSMUSG00000001348	Acp5	TRACP|TRAP	acid phosphatase 5, tartrate resistant	protein-coding
mm_56601.1	chr6	108828382	108828384	-	1	NA	promoter-TSS (NM_138677)	promoter-TSS (NM_138677)	-258	NM_138677	192193	Mm.21596	NM_138677	ENSMUSG00000030104	Edem1	A130059K23Rik|EDEM|mKIAA0212	ER degradation enhancer, mannosidase alpha-like 1	protein-coding
mm_117591.1	chr13	89742310	89742330	-	1	NA	5' UTR (NM_001134474, exon 1 of 14)	5' UTR (NM_001134474, exon 1 of 14)	192	NM_001081249	13003	Mm.158700	NM_019389	ENSMUSG00000021614	Vcan	5430420N07Rik|9430051N09|Cspg2|DPEAAE|NG2|PG-M|PG-M(V0)|PG-M(V1)|hdf	versican	protein-coding
mm_44840.1	chr5	34171715	34171718	-	1	NA	Intergenic	Intergenic	-2190	NM_001289803	272158	Mm.319286	NM_181857	ENSMUSG00000045102	Poln	POL4P	DNA polymerase N	protein-coding
mm_158986.1	chr1	132391247	132391247	-	1	NA	promoter-TSS (NM_001311107)	promoter-TSS (NM_001311107)	139	NM_178874	68875	Mm.273785	NM_178874	ENSMUSG00000042066	Tmcc2	1110063G11Rik	transmembrane and coiled-coil domains 2	protein-coding
mm_45208.1	chr5	52992284	52992298	-	1	NA	promoter-TSS (NR_040413)	promoter-TSS (NR_040413)	1	NR_040413	75954	Mm.258937	NR_040413	ENSMUSG00000106352	5033403H07Rik	-	RIKEN cDNA 5033403H07 gene	ncRNA
mm_85572.1	chr9	107280828	107280871	-	1	NA	intron (NM_001316691, intron 1 of 7)	intron (NM_001316691, intron 1 of 7)	8547	NM_001316691	102626	Mm.222612	NM_178907	ENSMUSG00000032577	Mapkapk3	3PK|AI874665|MAPKAP-K3|MAPKAP3|MK-3|MK3|MapkKapk3	mitogen-activated protein kinase-activated protein kinase 3	protein-coding
mm_26347.1	chr3	142547522	142547566	+	1	NA	3' UTR (NM_001083312, exon 11 of 11)	3' UTR (NM_001083312, exon 11 of 11)	-12508	NM_018734	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_55395.1	chr6	60759725	60759747	-	1	NA	intron (NM_009221, intron 4 of 5)	intron (NM_009221, intron 4 of 5)	69268	NM_001042451	20617	Mm.17484	NM_009221	ENSMUSG00000025889	Snca	NACP|alphaSYN	synuclein, alpha	protein-coding
mm_150480.1	chr19	38930988	38931004	+	1	NA	promoter-TSS (NM_008234)	promoter-TSS (NM_008234)	6	NM_008234	15201	Mm.57223	NM_008234	ENSMUSG00000025001	Hells	AI323785|E130115I21Rik|LSH|Lysh|PASG|YFK8	helicase, lymphoid specific	protein-coding
mm_7572.1	chr1	124845961	124845971	-	1	NA	Intergenic	Intergenic	589761	NM_023735	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding
mm_29582.1	chr3	117358370	117358373	-	1	NA	intron (NM_177664, intron 1 of 6)	intron (NM_177664, intron 1 of 6)	2505	NM_177664	229791	Mm.140138	NM_177664	ENSMUSG00000044667	Plppr4	A330086D10|D3Bwg0562e|Lppr4|PRG-1|mKIAA0455	phospholipid phosphatase related 4	protein-coding
mm_135039.1	chr16	32877638	32877674	-	1	NA	promoter-TSS (NM_001159349)	promoter-TSS (NM_001159349)	-128	NM_027226	69823	Mm.12831	NM_027226	ENSMUSG00000022800	Fyttd1	2010005M05Rik|3830411L18Rik|3830421F13Rik|4933423A17Rik|AI098218|AW539567|C85190	forty-two-three domain containing 1	protein-coding
mm_15591.1	chr2	160367346	160367357	+	1	NA	promoter-TSS (NM_010658)	promoter-TSS (NM_010658)	-286	NM_010658	16658	Mm.330745	NM_010658	ENSMUSG00000074622	Mafb	Kreisler|Krml|Krml1|kr	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein B (avian)	protein-coding
mm_161843.1	chr18	6061999	6061999	-	1	NA	intron (NM_029277, intron 6 of 17)	intron (NM_029277, intron 6 of 17)	74099	NM_029277	75415	Mm.239675	NM_029277	ENSMUSG00000041225	Arhgap12	2810011M08Rik	Rho GTPase activating protein 12	protein-coding
mm_107138.1	chr12	21373691	21373779	+	1	NA	promoter-TSS (NM_009615)	promoter-TSS (NM_009615)	-103	NM_009615	11491	Mm.27681	NM_009615	ENSMUSG00000052593	Adam17	CD156b|Tace	a disintegrin and metallopeptidase domain 17	protein-coding
mm_29851.1	chr3	129970153	129970167	-	1	NA	promoter-TSS (NM_025779)	promoter-TSS (NM_025779)	46	NM_025779	66815	Mm.31056	NM_025779	ENSMUSG00000027994	Ccdc109b	9030408N13Rik|MCUb	coiled-coil domain containing 109B	protein-coding
mm_98973.1	chr11	98685917	98685926	+	1	NA	intron (NM_009439, intron 2 of 11)	intron (NM_009439, intron 2 of 11)	3367	NM_009439	22123	Mm.12194	NM_009439	ENSMUSG00000017221	Psmd3	AI255837|AntP91a|D11Bwg1349e|Psd3|Tstap91a	proteasome (prosome, macropain) 26S subunit, non-ATPase, 3	protein-coding
mm_51881.1	chr6	90571775	90571791	+	1	NA	intron (NM_027406, intron 11 of 22)	intron (NM_027406, intron 11 of 22)	20935	NM_027406	107747	Mm.30035	NM_027406	ENSMUSG00000030088	Aldh1l1	1810048F20Rik|FDH|Fthfd|Neut2	aldehyde dehydrogenase 1 family, member L1	protein-coding
mm_123439.1	chr14	64948901	64948917	-	1	NA	intron (NM_001347627, intron 1 of 10)	intron (NM_001347627, intron 1 of 10)	948	NM_177338	219150	Mm.344074	NM_177338	ENSMUSG00000021972	Hmbox1	AI451877|AI604847|F830020C16Rik	homeobox containing 1	protein-coding
mm_85046.1	chr9	89704908	89705013	-	1	NA	promoter-TSS (NM_025360)	promoter-TSS (NM_025360)	83	NM_025360	66111	Mm.27606	NM_025360	ENSMUSG00000032353	Tmed3	1200002G13Rik|AW546672|P24b	transmembrane p24 trafficking protein 3	protein-coding
mm_23574.1	chr3	63299751	63299765	+	1	NA	intron (NM_001289463, intron 1 of 22)	intron (NM_001289463, intron 1 of 22)	3663	NM_001289463	17380	Mm.296022	NM_008604	ENSMUSG00000027820	Mme	6030454K05Rik|C85356|CALLA|CD10|NEP|SFE	membrane metallo endopeptidase	protein-coding
mm_94944.1	chr11	29718782	29718782	+	1	NA	5' UTR (NM_024226, exon 1 of 7)	5' UTR (NM_024226, exon 1 of 7)	219	NM_024226	68585	Mm.192580	NM_024226	ENSMUSG00000020458	Rtn4	1110020G17Rik|AA407876|AA409940|AA960376|ASY|C130026I10Rik|NOGO|NSP-CL|NgA|Nogo-A|Nogo-B|Nogo-C|mKIAA0886|mKIAA4153	reticulon 4	protein-coding
mm_89590.1	chr10	95893482	95893508	+	1	NA	Intergenic	Intergenic	-47168	NM_001001932	216238	Mm.210035	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding
mm_63393.1	chr7	127288202	127288225	+	1	NA	Intergenic	Intergenic	-8047	NM_001253873	16408	Mm.1618	NM_008400	ENSMUSG00000030830	Itgal	(p180)|Cd11a|LFA-1|LFA-1A|Ly-15|Ly-21	integrin alpha L	protein-coding
mm_77295.1	chr8	116978909	116978997	-	1	NA	promoter-TSS (NM_027103)	promoter-TSS (NM_027103)	-10	NM_027103	69528	Mm.272846	NM_027103	ENSMUSG00000031847	1700030J22Rik	-	RIKEN cDNA 1700030J22 gene	protein-coding
mm_142517.1	chr17	46270789	46270809	-	1	NA	intron (NM_001252475, intron 1 of 8)	intron (NM_001252475, intron 1 of 8)	12227	NM_001252475	74094	Mm.284594	NM_028751	ENSMUSG00000012296	Tjap1	0610041D19Rik|AI415281|AW121008|Pilt|Tjp4	tight junction associated protein 1	protein-coding
mm_48742.1	chr5	147726003	147726023	-	1	NA	promoter-TSS (NM_010228)	promoter-TSS (NM_010228)	-25	NM_010228	14254	Mm.389712	NM_010228	ENSMUSG00000029648	Flt1	AI323757|Flt-1|VEGFR-1|VEGFR1|sFlt1	FMS-like tyrosine kinase 1	protein-coding
mm_25403.1	chr3	107278845	107278864	+	1	NA	promoter-TSS (NM_026774)	promoter-TSS (NM_026774)	-4	NM_026774	68576	Mm.290035	NM_026774	ENSMUSG00000087260	Lamtor5	1110003H18Rik|Hbxip|XIP	late endosomal/lysosomal adaptor, MAPK and MTOR activator 5	protein-coding
mm_153078.1	chr19	32347048	32347059	-	1	NA	intron (NM_144792, intron 2 of 9)	intron (NM_144792, intron 2 of 9)	2263	NM_001168525	208449	Mm.329810	NM_144792	ENSMUSG00000040451	Sgms1	9530058O11Rik|AI841905|C80702|Mob|Sms1|Sor1|Tmem23	sphingomyelin synthase 1	protein-coding
mm_119909.1	chr14	54950578	54950617	+	1	NA	exon (NM_010856, exon 26 of 39)	exon (NM_010856, exon 26 of 39)	-1455	NR_029724	387204		NR_029724	ENSMUSG00000065432	Mir208a	Mirn208|Mirn208a|mir-208|mir-208a|mmu-mir-208	microRNA 208a	ncRNA
mm_86637.1	chr10	14086028	14086045	+	1	NA	intron (NM_010437, intron 2 of 8)	intron (NM_010437, intron 2 of 8)	119657	NM_010437	15273	Mm.42157	NM_010437	ENSMUSG00000015501	Hivep2	Gm20114|MIBP1|Schnurri-2|Shn-2	human immunodeficiency virus type I enhancer binding protein 2	protein-coding
mm_169937.1	chr16	62204778	62204779	-	1	NA	Intergenic	Lx5|LINE|L1	581938	NM_178925	106338	Mm.26321	NM_178925	ENSMUSG00000050312	Nsun3	6720484A09Rik|AU022521	NOL1/NOP2/Sun domain family member 3	protein-coding
mm_154238.1	chr19	60580994	60581011	-	1	NA	promoter-TSS (NM_001172096)	promoter-TSS (NM_001172096)	21	NM_001172097	78832	Mm.259026	NM_030197	ENSMUSG00000033417	Cacul1	2700078E11Rik|2810417M16Rik|9830127L17Rik|AI450346|D130033C15Rik	CDK2 associated, cullin domain 1	protein-coding
mm_142557.1	chr17	46640035	46640045	-	1	NA	exon (NM_029091, exon 5 of 16)	exon (NM_029091, exon 5 of 16)	5104	NM_029091	74764	Mm.279599	NM_029091	ENSMUSG00000003546	Klc4	1200014P03Rik|AA408085|AW146303|Knsl8	kinesin light chain 4	protein-coding
mm_141500.1	chr17	31633080	31633101	-	1	NA	5' UTR (NM_144855, exon 2 of 17)	5' UTR (NM_144855, exon 2 of 17)	4115	NM_144855	12411	Mm.206417	NM_144855	ENSMUSG00000024039	Cbs	AI047524|AI303044|HIP4	cystathionine beta-synthase	protein-coding
mm_84771.1	chr9	75642245	75642259	-	1	NA	Intergenic	RMER6D|LTR|ERVK	16520	NM_027309	70082	Mm.19119	NM_027309	ENSMUSG00000032184	Lysmd2	2210402C18Rik|AV033872|AW538442	LysM, putative peptidoglycan-binding, domain containing 2	protein-coding
mm_94695.1	chr11	20112448	20112480	+	1	NA	intron (NM_146243, intron 1 of 8)	CpG	487	NM_146243	66713	Mm.259045	NM_146243	ENSMUSG00000020152	Actr2	4921510D23Rik|AA409782|Arp2|D6Ertd746e	ARP2 actin-related protein 2	protein-coding
mm_10766.1	chr2	24186506	24186512	+	1	NA	promoter-TSS (NM_153511)	promoter-TSS (NM_153511)	33	NM_153511	215257	Mm.249379	NM_153511	ENSMUSG00000044103	Il1f9	Il36g	interleukin 1 family, member 9	protein-coding
mm_34594.1	chr4	150198092	150198138	+	1	NA	exon (NM_009802, exon 2 of 8)	exon (NM_009802, exon 2 of 8)	3020	NM_009802	12353	Mm.232523	NM_009802	ENSMUSG00000028972	Car6	Ca6|DOC1	carbonic anhydrase 6	protein-coding
mm_44872.1	chr5	34526161	34526165	-	1	NA	intron (NM_011893, intron 1 of 12)	intron (NM_011893, intron 1 of 12)	379	NM_011893	24055	Mm.5012	NM_011893	ENSMUSG00000054520	Sh3bp2	3BP2	SH3-domain binding protein 2	protein-coding
mm_38211.1	chr4	135876414	135876423	-	1	NA	Intergenic	Intergenic	-2572	NM_026383	52830	Mm.29159	NM_026383	ENSMUSG00000028675	Pnrc2	0610011E17Rik|D4Bwg0593e	proline-rich nuclear receptor coactivator 2	protein-coding
mm_148571.1	chr19	4859374	4859386	+	1	NA	intron (NM_019861, intron 9 of 13)	intron (NM_019861, intron 9 of 13)	4251	NM_019861	56464	Mm.29561	NM_019861	ENSMUSG00000083282	Ctsf	AI481912	cathepsin F	protein-coding
mm_49619.1	chr6	30752467	30752486	+	1	NA	intron (NM_017478, intron 20 of 23)	intron (NM_017478, intron 20 of 23)	11177	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_34254.1	chr4	141301260	141301276	+	1	NA	promoter-TSS (NM_010139)	promoter-TSS (NM_010139)	47	NM_010139	13836	Mm.2581	NM_010139	ENSMUSG00000006445	Epha2	AW545284|Eck|Myk2|Sek-2|Sek2	Eph receptor A2	protein-coding
mm_100301.1	chr11	117849274	117849282	+	1	NA	promoter-TSS (NM_009689)	promoter-TSS (NM_009689)	41	NM_009689	11799	Mm.8552	NM_009689	ENSMUSG00000017716	Birc5	AAC-11|Api4|TIAP|survivin40	baculoviral IAP repeat-containing 5	protein-coding
mm_82153.1	chr9	123775057	123775069	+	1	NA	intron (NM_009913, intron 2 of 2)	intron (NM_009913, intron 2 of 2)	7852	NM_001166625	12769	Mm.440604	NM_009913	ENSMUSG00000029530	Ccr9	A130091K22Rik|Cmkbr10|GPR-9-6	chemokine (C-C motif) receptor 9	protein-coding
mm_78720.1	chr9	41579851	41579892	+	1	NA	intron (NR_131930, intron 3 of 3)	intron (NR_131930, intron 3 of 3)	-1382	NR_015483	73144	Mm.38166	NM_001033153	ENSMUSG00000074415	3110039I08Rik	2610203C20Rik|AI848448|D230004N17Rik|D3Mgi9|Mir100hg	RIKEN cDNA 3110039I08 gene	ncRNA
mm_173227.1	chrX	77456474	77456491	+	1	NA	intron (NR_035475, intron 1 of 3)	intron (NR_035475, intron 1 of 3)	19454	NR_035475	100316834		NR_035475	ENSMUSG00000088980	Mir669m-2	mmu-mir-669m-2	microRNA 669m-2	ncRNA
mm_49069.1	chr6	5725739	5725801	+	1	NA	5' UTR (NM_010063, exon 1 of 17)	5' UTR (NM_010063, exon 1 of 17)	131	NM_001191026	13426	Mm.20893	NM_010063	ENSMUSG00000029757	Dync1i1	DH IC-1|DHIC-1|DIC|Dncic1|IC74	dynein cytoplasmic 1 intermediate chain 1	protein-coding
mm_147046.1	chr18	34931665	34931671	-	1	NA	5' UTR (NM_144866, exon 2 of 11)	5' UTR (NM_144866, exon 2 of 11)	335	NM_144866	225363	Mm.329353	NM_144866	ENSMUSG00000024360	Etf1	AI463371|D6Ertd109e|ERF|ERF1|SUP45L1|TB3-1	eukaryotic translation termination factor 1	protein-coding
mm_8328.1	chr1	149960721	149960743	-	1	NA	intron (NM_008869, intron 1 of 17)	intron (NM_008869, intron 1 of 17)	558	NM_008869	18783	Mm.4186	NM_008869	ENSMUSG00000056220	Pla2g4a	Pla2g4|cPLA2|cPLA2-alpha|cPLA2alpha	phospholipase A2, group IVA (cytosolic, calcium-dependent)	protein-coding
mm_9589.1	chr1	174240190	174240192	-	1	NA	exon (NM_011465, exon 44 of 52)	exon (NM_011465, exon 44 of 52)	10785	NM_146715	258710	Mm.377647	NM_146715	ENSMUSG00000050788	Olfr419	MOR267-6	olfactory receptor 419	protein-coding
mm_100612.1	chr11	121451974	121452036	+	1	NA	promoter-TSS (NM_029878)	promoter-TSS (NM_029878)	56	NM_029878	108903	Mm.23686	NM_029878	ENSMUSG00000039230	Tbcd	2310057L06Rik|A030005L14Rik|mKIAA0988	tubulin-specific chaperone d	protein-coding
mm_54009.1	chr6	7983425	7983445	-	1	NA	Intergenic	Intergenic	138211	NM_052993	94192	Mm.102752	NM_052993	ENSMUSG00000042460	C1galt1	2210410E06Rik|AV284120|T-synthase	core 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase, 1	protein-coding
mm_159244.1	chr2	151039356	151039356	-	1	NA	promoter-TSS (NM_026086)	promoter-TSS (NM_026086)	23	NM_026086	67311	Mm.480682	NM_026086	ENSMUSG00000053916	Nanp	1600031M04Rik|Hdhd4	N-acetylneuraminic acid phosphatase	protein-coding
mm_14026.1	chr2	122152609	122152619	+	1	NA	intron (NM_009735, intron 3 of 3)	intron (NM_009735, intron 3 of 3)	4927	NM_009735	12010	Mm.163	NM_009735	ENSMUSG00000060802	B2m	Ly-m11|beta2-m|beta2m	beta-2 microglobulin	protein-coding
mm_78672.1	chr9	40776763	40776785	+	1	NA	intron (NM_133733, intron 5 of 6)	intron (NM_133733, intron 5 of 6)	-24499	NM_031165	15481	Mm.290774	NM_031165	ENSMUSG00000015656	Hspa8	2410008N15Rik|Hsc70|Hsc71|Hsc73|Hsp73|Hspa10	heat shock protein 8	protein-coding
mm_154834.1	chrX	18226860	18226863	+	1	NA	intron (NM_001310444, intron 6 of 28)	ID_B1|SINE|B4	64286	NM_001310444	22289	Mm.257498	NM_009483	ENSMUSG00000037369	Kdm6a	Utx	lysine (K)-specific demethylase 6A	protein-coding
mm_5621.1	chr1	40107407	40107414	-	1	NA	intron (NM_010555, intron 3 of 8)	intron (NM_010555, intron 3 of 8)	-21559	NR_037980	100047133	Mm.447052	NR_037980	ENSMUSG00000097899	Gm16894	-	predicted gene, 16894	ncRNA
mm_119524.1	chr14	47526094	47526097	+	1	NA	intron (NR_027414, intron 4 of 5)	intron (NR_027414, intron 4 of 5)	42339	NM_172599	100504663	Mm.287279	NM_172599	ENSMUSG00000037526	Atg14	4832427M01|Atg14L|D14Ertd114e|D14Ertd436e	autophagy related 14	protein-coding
mm_109283.1	chr12	109549281	109549301	+	1	NA	non-coding (NR_027652, exon 6 of 10)	non-coding (NR_027652, exon 6 of 10)	3893	NR_003633	17263	Mm.289645	NM_144513	ENSMUSG00000021268	Meg3	2900016C05Rik|3110050O07Rik|6330408G06Rik|AI425946|AW108224|D12Bwg1266e|Gtl2|R74756|R75394	maternally expressed 3	ncRNA
mm_61177.1	chr7	60037033	60037040	+	1	NA	intron (NM_001082962, intron 2 of 10)	ORR1B1-int|LTR|ERVL-MaLR	-31880	NM_033174	84704	Mm.274995	NM_033174	ENSMUSG00000000948	Snurf	2410045I01Rik|Snrpn	SNRPN upstream reading frame	protein-coding
mm_60995.1	chr7	49276693	49276707	+	1	NA	intron (NM_175272, intron 1 of 37)	intron (NM_175272, intron 1 of 37)	30511	NM_175272	78286	Mm.333881	NM_175272	ENSMUSG00000052512	Nav2	5330421F07Rik|AU067780|BQ960892|HELAD1|POMFIL2|RAINB1|RAINB2|Unc53H2|mKIAA3015	neuron navigator 2	protein-coding
mm_2930.1	chr1	132298551	132298561	+	1	NA	promoter-TSS (NM_144810)	promoter-TSS (NM_144810)	-70	NM_144810	213417	Mm.39723	NM_144810	ENSMUSG00000042115	Klhdc8a	A630065K24Rik	kelch domain containing 8A	protein-coding
mm_98499.1	chr11	94951909	94951939	+	1	NA	3' UTR (NM_007742, exon 51 of 51)	3' UTR (NM_007742, exon 51 of 51)	-15669	NM_018792	54388	Mm.30482	NM_018792	ENSMUSG00000038994	Hils1	H1.9|TISP64	histone H1-like protein in spermatids 1	protein-coding
mm_9736.1	chr1	180245901	180245911	-	1	NA	promoter-TSS (NM_011183)	promoter-TSS (NM_011183)	44	NM_011183	19165	Mm.330850	NM_011183	ENSMUSG00000010609	Psen2	ALG-3|Ad4h|Alg3|PS-2|PS2|Psnl2|STM2	presenilin 2	protein-coding
mm_106499.1	chr11	120349415	120349427	-	1	NA	promoter-TSS (NM_009609)	promoter-TSS (NM_009609)	743	NR_038126	66838	Mm.375010	NR_038126	ENSMUSG00000043644	0610009L18Rik	-	RIKEN cDNA 0610009L18 gene	ncRNA
mm_101907.1	chr11	49244154	49244169	-	1	NA	promoter-TSS (NM_010794)	promoter-TSS (NM_010794)	-30	NM_010794	17308	Mm.196933	NM_010794	ENSMUSG00000020346	Mgat1	Mgat-1	mannoside acetylglucosaminyltransferase 1	protein-coding
mm_31380.1	chr4	47480035	47480040	+	1	NA	intron (NM_024171, intron 2 of 3)	intron (NM_024171, intron 2 of 3)	5376	NM_024171	66212	Mm.20188	NM_024171	ENSMUSG00000053317	Sec61b	1190006C12Rik|AI326121|AW122942	Sec61 beta subunit	protein-coding
mm_1639.1	chr1	74541434	74541449	+	1	NA	intron (NM_176972, intron 1 of 25)	intron (NM_176972, intron 1 of 25)	-1448	NM_001081456	18802	Mm.290731	NM_148937	ENSMUSG00000026173	Plcd4	4921507K24Rik	phospholipase C, delta 4	protein-coding
mm_132792.1	chr16	45093640	45093661	+	1	NA	promoter-TSS (NM_026439)	promoter-TSS (NM_026439)	-403	NM_026439	67896	Mm.181074	NM_026439	ENSMUSG00000022665	Ccdc80	2610001E17Rik|DRO1|Ssg1|Urb	coiled-coil domain containing 80	protein-coding
mm_149024.1	chr19	8757415	8757447	+	1	NA	promoter-TSS (NR_132424)	promoter-TSS (NR_132424)	314	NM_001276704	53319	Mm.7271	NM_016813	ENSMUSG00000010097	Nxf1	Mex67|Mvb1|Tap	nuclear RNA export factor 1	protein-coding
mm_138301.1	chr17	34632304	34632314	+	1	NA	TTS (NM_030890)	TTS (NM_030890)	2623	NM_030890	260297	Mm.390965	NM_030890	ENSMUSG00000015476	Prrt1	Bat-4|Bat4|D17H6S54E|DSPD1|G5b|NG5|ORF31	proline-rich transmembrane protein 1	protein-coding
mm_58493.1	chr7	3703980	3704024	+	1	NA	promoter-TSS (NM_029767)	promoter-TSS (NM_029767)	-39	NM_029767	76846	Mm.13944	NM_029767	ENSMUSG00000006333	Rps9	3010033P07Rik|AL022771|AL022885	ribosomal protein S9	protein-coding
mm_116344.1	chr13	38528396	38528407	-	1	NA	promoter-TSS (NM_145367)	promoter-TSS (NM_145367)	83	NM_145367	105245	Mm.28622	NM_145367	ENSMUSG00000038991	Txndc5	AL022641|ERp46|PC-TRP	thioredoxin domain containing 5	protein-coding
mm_34074.1	chr4	138457678	138457689	+	1	NA	3' UTR (NM_025451, exon 2 of 2)	3' UTR (NM_025451, exon 2 of 2)	2535	NM_025451	66259	Mm.41603	NM_025451	ENSMUSG00000046447	Camk2n1	1810006K23Rik|AI848599|AI891706	calcium/calmodulin-dependent protein kinase II inhibitor 1	protein-coding
mm_122568.1	chr14	50807562	50807565	-	1	NA	promoter-TSS (NM_009632)	promoter-TSS (NM_009632)	208	NR_002142	85029		NR_002142	ENSMUSG00000092837	Rpph1	Gm24821|H1RNA|Rmrp5|Rpr	ribonuclease P RNA component H1	ncRNA
mm_40929.1	chr5	76331185	76331197	+	1	NA	promoter-TSS (NM_023508)	promoter-TSS (NM_023508)	-35	NM_023508	79455	Mm.143764	NM_023508	ENSMUSG00000029235	Pdcl2	1700010B22Rik|1700016K07Rik|Mgcphlp|Tphlp	phosducin-like 2	protein-coding
mm_140012.1	chr17	73203810	73203820	+	1	NA	intron (NM_001177967, intron 5 of 5)	intron (NM_001177967, intron 5 of 5)	95830	NM_001177967	225010	Mm.329194	NM_001081071	ENSMUSG00000054469	Lclat1	AI181996|Agpat8|Alcat1|Gm91|Lycat	lysocardiolipin acyltransferase 1	protein-coding
mm_106074.1	chr11	116173233	116173258	-	1	NA	3' UTR (NM_015729, exon 14 of 14)	3' UTR (NM_015729, exon 14 of 14)	-5067	NM_172571	217335	Mm.35241	NM_172571	ENSMUSG00000020776	Fbf1	1110033G01Rik|5930413D20|mKIAA1863	Fas (TNFRSF6) binding factor 1	protein-coding
mm_76963.1	chr8	106136793	106136876	-	1	NA	5' UTR (NM_176838, exon 1 of 15)	5' UTR (NM_176838, exon 1 of 15)	140	NM_176838	77411	Mm.183003	NM_176838	ENSMUSG00000084128	Esrp2	9530027K23Rik|Rbm35b	epithelial splicing regulatory protein 2	protein-coding
mm_163221.1	chr11	101986957	101986957	-	1	NA	promoter-TSS (NM_029287)	promoter-TSS (NM_029287)	-99	NM_029287	75437	Mm.108632	NM_029287	ENSMUSG00000010841	1700006E09Rik	-	RIKEN cDNA 1700006E09 gene	protein-coding
mm_111317.1	chr12	85973678	85973686	-	1	NA	intron (NM_001347395, intron 29 of 32)	intron (NM_001347395, intron 29 of 32)	105359	NM_009368	21809	Mm.3992	NM_009368	ENSMUSG00000021253	Tgfb3	TGF-beta-3|Tgfb-3	transforming growth factor, beta 3	protein-coding
mm_133168.1	chr16	71249791	71249829	+	1	NA	promoter-TSS (NR_040576)	promoter-TSS (NR_040576)	-94	NR_040576	78221	Mm.399298	NR_040576		4930567J20Rik	-	RIKEN cDNA 4930567J20 gene	ncRNA
mm_98796.1	chr11	96988073	96988082	+	1	NA	Intergenic	Intergenic	-10389	NM_001080964	78912	Mm.491183	NM_030220	ENSMUSG00000018678	Sp2	4930480I16Rik|mKIAA0048	Sp2 transcription factor	protein-coding
mm_125393.1	chr15	41446824	41446835	+	1	NA	promoter-TSS (NM_001130166)	promoter-TSS (NM_001130166)	-653	NM_001130166	170719	Mm.254267	NM_130885	ENSMUSG00000022307	Oxr1	2210416C20Rik|C7|C7B	oxidation resistance 1	protein-coding
mm_68887.1	chr7	126448022	126448030	-	1	NA	exon (NM_007504, exon 17 of 23)	exon (NM_007504, exon 17 of 23)	15047	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_59894.1	chr7	30307234	30307278	+	1	NA	3' UTR (NM_001081114, exon 14 of 14)	3' UTR (NM_001081114, exon 14 of 14)	-1497	NM_198027	233065	Mm.276277	NM_198027	ENSMUSG00000042831	Alkbh6	AI839550|Abh6|C130099A02	alkB homolog 6	protein-coding
mm_25890.1	chr3	131110337	131110345	+	1	NA	promoter-TSS (NM_001276402)	promoter-TSS (NM_001276402)	44	NM_001276402	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_37799.1	chr4	130525188	130525197	-	1	NA	Intergenic	MTB_Mm|LTR|ERVL-MaLR	48844	NM_025998	67149	Mm.423029	NM_025998	ENSMUSG00000078532	Nkain1	2610200G18Rik|2810426C15Rik	Na+/K+ transporting ATPase interacting 1	protein-coding
mm_29057.1	chr3	103778136	103778151	-	1	NA	non-coding (NR_125731, exon 2 of 16)	non-coding (NR_125731, exon 2 of 16)	13132	NM_001301306	15257	Mm.20827	NM_010432	ENSMUSG00000008730	Hipk1	1110062K04Rik|Myak	homeodomain interacting protein kinase 1	protein-coding
mm_146546.1	chr18	6135897	6135999	-	1	NA	5' UTR (NM_001039692, exon 1 of 19)	5' UTR (NM_001039692, exon 1 of 19)	150	NM_029277	75415	Mm.239675	NM_029277	ENSMUSG00000041225	Arhgap12	2810011M08Rik	Rho GTPase activating protein 12	protein-coding
mm_124710.1	chr15	6569500	6569515	+	1	NA	Intergenic	Intergenic	-10340	NM_001278269	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_62169.1	chr7	97299273	97299283	+	1	NA	exon (NM_010248, exon 4 of 10)	exon (NM_010248, exon 4 of 10)	26686	NM_001177412	244144	Mm.297541	NM_001177412	ENSMUSG00000035713	Usp35	Gm1088|Gm493	ubiquitin specific peptidase 35	protein-coding
mm_76586.1	chr8	89042424	89042435	-	1	NA	5' UTR (NM_021390, exon 2 of 4)	5' UTR (NM_021390, exon 2 of 4)	1733	NM_021390	58198	Mm.214361	NM_021390	ENSMUSG00000031665	Sall1	Msal-3	sal-like 1 (Drosophila)	protein-coding
mm_126773.1	chr15	86074792	86074810	+	1	NA	intron (NM_001205353, intron 1 of 18)	intron (NM_001205353, intron 1 of 18)	16074	NM_001205353	223752	Mm.24442	NM_172611	ENSMUSG00000035900	Gramd4	9930016O13	GRAM domain containing 4	protein-coding
mm_27018.1	chr3	26027400	26027410	-	1	NA	intron (NM_138666, intron 3 of 7)	Lx9|LINE|L1	125902	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_92628.1	chr10	80323037	80323046	-	1	NA	exon (NM_008793, exon 12 of 15)	exon (NM_008793, exon 12 of 15)	-2493	NM_025521	66374	Mm.383824	NM_025521	ENSMUSG00000020133	2310011J03Rik	AI452186|AW545358	RIKEN cDNA 2310011J03 gene	protein-coding
mm_126672.1	chr15	84446054	84446064	+	1	NA	intron (NM_001347543, intron 1 of 5)	CpG	551	NM_001347543	72301	Mm.275387	NM_001163145	ENSMUSG00000062760	1810041L15Rik	Kiaa1644	RIKEN cDNA 1810041L15 gene	protein-coding
mm_51293.1	chr6	72305968	72305977	+	1	NA	intron (NM_147779, intron 4 of 11)	intron (NM_147779, intron 4 of 11)	1362	NM_147779	20388	Mm.46033	NM_147779	ENSMUSG00000056370	Sftpb	AI562151|SF-B|SP-B|Sftp-3|Sftp3	surfactant associated protein B	protein-coding
mm_10835.1	chr2	24563103	24563148	+	1	NA	Intergenic	Intergenic	-87526	NM_011040	18510	Mm.2533	NM_011040	ENSMUSG00000026976	Pax8	Pax-8	paired box 8	protein-coding
mm_128881.1	chr15	73096923	73096937	-	1	NA	Intergenic	Intergenic	6518	NM_053068	93696	Mm.23095	NM_053068	ENSMUSG00000068391	Chrac1	2410152E03Rik|2810406L04Rik|YCL1	chromatin accessibility complex 1	protein-coding
mm_143256.1	chr17	65580640	65580652	-	1	NA	3' UTR (NM_013933, exon 6 of 6)	3' UTR (NM_013933, exon 6 of 6)	32909	NM_013933	30960	Mm.266767	NM_013933	ENSMUSG00000024091	Vapa	33kDa|VAP33	vesicle-associated membrane protein, associated protein A	protein-coding
mm_97416.1	chr11	77982826	77982842	+	1	NA	promoter-TSS (NM_174852)	promoter-TSS (NM_174852)	18	NM_174852	268448	Mm.274329	NM_174852	ENSMUSG00000037791	Phf12	2410142K10Rik|F630045O13|PF1|mKIAA1523	PHD finger protein 12	protein-coding
mm_28739.1	chr3	95737683	95737699	-	1	NA	exon (NM_007899, exon 5 of 11)	exon (NM_007899, exon 5 of 11)	1878	NM_007899	13601	Mm.3433	NM_007899	ENSMUSG00000028108	Ecm1	AI663821|p85	extracellular matrix protein 1	protein-coding
mm_15789.1	chr2	164425728	164425761	+	1	NA	3' UTR (NM_011521, exon 5 of 5)	3' UTR (NM_011521, exon 5 of 5)	17444	NM_011521	20971	Mm.3815	NM_011521	ENSMUSG00000017009	Sdc4	AA959608|AW108331|S4|Synd4|ryudocan|syndecan-4	syndecan 4	protein-coding
mm_117559.1	chr13	85216077	85216089	-	1	NA	3' UTR (NM_145452, exon 25 of 25)	3' UTR (NM_145452, exon 25 of 25)	26698	NM_023243	66671	Mm.18474	NM_023243	ENSMUSG00000021548	Ccnh	6330408H09Rik|AI661354|AV102684|AW538719	cyclin H	protein-coding
mm_167686.1	chr9	85327273	85327283	-	1	NA	promoter-TSS (NM_001160378)	promoter-TSS (NM_001160378)	-128	NM_001160379	212943	Mm.74610	NM_001160378	ENSMUSG00000032265	Fam46a	BAP014|D930050G01Rik	family with sequence similarity 46, member A	protein-coding
mm_101567.1	chr11	34207587	34207593	-	1	NA	exon (NM_023907, exon 1 of 2)	exon (NM_023907, exon 1 of 2)	499	NM_023907	14233	Mm.32926	NM_023907	ENSMUSG00000047861	Foxi1	5830401E05Rik|FREAC6|Fkh10|HFH-3|Hfh3	forkhead box I1	protein-coding
mm_101065.1	chr11	9873809	9873816	-	1	NA	Intergenic	L1VL4|LINE|L1	681870	NM_178259	268379	Mm.39270	NM_178259	ENSMUSG00000004668	Abca13	9830132L24|A930002G16Rik|AI956815	ATP-binding cassette, sub-family A (ABC1), member 13	protein-coding
mm_93151.1	chr10	93042018	93042048	-	1	NA	intron (NM_001347060, intron 9 of 67)	intron (NM_001347060, intron 9 of 67)	39563	NM_001347060	380654	Mm.34980	NM_001347060	ENSMUSG00000020014	Cfap54	4930485B16Rik|Gm872	cilia and flagella associated protein 54	protein-coding
mm_38992.1	chr4	151123807	151123810	-	1	NA	intron (NM_001081557, intron 11 of 23)	intron (NM_001081557, intron 11 of 23)	34238	NM_001308446	105704528	Mm.415128	NM_001308446	ENSMUSG00000078491	Gm13090	OTTMUSG00000010356	predicted gene 13090	protein-coding
mm_26207.1	chr3	138550655	138550677	+	1	NA	intron (NM_001313980, intron 5 of 7)	intron (NM_001313980, intron 5 of 7)	23398	NM_001313980	13684	Mm.3941	NM_007917	ENSMUSG00000028156	Eif4e	EG668879|Eif4e-ps|If4e|eIF-4E	eukaryotic translation initiation factor 4E	protein-coding
mm_140619.1	chr17	11385403	11385409	-	1	NA	intron (NM_001317726, intron 4 of 6)	intron (NM_001317726, intron 4 of 6)	497783	NR_045808	52027	Mm.442257	NR_045808		D17Ertd648e	-	DNA segment, Chr 17, ERATO Doi 648, expressed	ncRNA
mm_16083.1	chr2	168590442	168590476	+	1	NA	promoter-TSS (NM_001291176)	promoter-TSS (NM_001291176)	-94	NM_001136073	18019	Mm.116802	NM_010899	ENSMUSG00000027544	Nfatc2	AI607462|NF-ATc2|NF-ATp|NFAT1|NFAT1-D|Nfatp	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 2	protein-coding
mm_21567.1	chr2	164221606	164221677	-	1	NA	promoter-TSS (NM_001045554)	promoter-TSS (NM_001045554)	22	NM_138685	192201	Mm.330764	NM_138685	ENSMUSG00000018211	Wfdc15b	9230106L14Rik|SWAM1|Wfdc15	WAP four-disulfide core domain 15B	protein-coding
mm_144308.1	chr18	12523993	12524020	+	1	NA	intron (NM_010680, intron 44 of 74)	intron (NM_010680, intron 44 of 74)	19807	NM_001347461	16774	Mm.42012	NM_010680	ENSMUSG00000024421	Lama3	Lama3B|[a]3B	laminin, alpha 3	protein-coding
mm_153261.1	chr19	36919632	36919646	-	1	NA	promoter-TSS (NM_028263)	promoter-TSS (NM_028263)	-40	NM_028263	72514	Mm.41674	NM_028263	ENSMUSG00000047632	Fgfbp3	2610306H15Rik|Fgf-bp3	fibroblast growth factor binding protein 3	protein-coding
mm_41290.1	chr5	90463985	90463985	+	1	NA	exon (NM_009654, exon 4 of 15)	exon (NM_009654, exon 4 of 15)	3115	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_30557.1	chr4	3750699	3750700	+	1	NA	intron (NM_010747, intron 8 of 12)	intron (NM_010747, intron 8 of 12)	35735	NR_028126	70720	Mm.445696	NR_028126		6330407A03Rik	-	RIKEN cDNA 6330407A03 gene	ncRNA
mm_92310.1	chr10	75273203	75273211	-	1	NA	intron (NM_153406, intron 10 of 15)	intron (NM_153406, intron 10 of 15)	-43670	NM_009630	11540	Mm.333734	NM_009630	ENSMUSG00000020178	Adora2a	A2AAR|A2aR|AA2AR	adenosine A2a receptor	protein-coding
mm_124758.1	chr15	6644822	6644833	+	1	NA	exon (NM_011815, exon 11 of 18)	exon (NM_011815, exon 11 of 18)	-63554	NM_030168	78757	Mm.275811	NM_030168	ENSMUSG00000050310	Rictor	4921505C17Rik|6030405M08Rik|AVO3|AW492497|D530039E11Rik	RPTOR independent companion of MTOR, complex 2	protein-coding
mm_38979.1	chr4	150915184	150915191	-	1	NA	Intergenic	Intergenic	-4968	NM_011612	21942	Mm.244187	NM_011612	ENSMUSG00000028965	Tnfrsf9	4-1BB|A930040I11Rik|AA408498|AI325004|CDw137|Cd137|ILA|Ly63	tumor necrosis factor receptor superfamily, member 9	protein-coding
mm_70798.1	chr8	22859529	22859554	+	1	NA	promoter-TSS (NM_001081149)	promoter-TSS (NM_001081149)	2	NM_001081149	244349	Mm.182776	NM_001081149	ENSMUSG00000031540	Kat6a	1500036M03|9930021N24Rik|MOZ|Myst3|Zfp220	K(lysine) acetyltransferase 6A	protein-coding
mm_31543.1	chr4	55478187	55478199	+	1	NA	Intergenic	Intergenic	54282	NM_010637	16600	Mm.4325	NM_010637	ENSMUSG00000003032	Klf4	EZF|Gklf|Zie	Kruppel-like factor 4 (gut)	protein-coding
mm_25445.1	chr3	108284064	108284074	+	1	NA	promoter-TSS (NM_019972)	promoter-TSS (NM_019972)	5	NM_019972	20661	Mm.157119	NM_019972	ENSMUSG00000068747	Sort1	2900053A11Rik|AI852375|Ntr3|Ntsr3	sortilin 1	protein-coding
mm_60176.1	chr7	41622800	41622805	+	1	NA	Intergenic	Intergenic	-10729	NM_023363	67607	Mm.384626	NM_023363	ENSMUSG00000074165	Zfp788	2810426N06Rik|AI256342|AI605193	zinc finger protein 788	protein-coding
mm_86781.1	chr10	20170824	20170834	+	1	NA	intron (NM_001198635, intron 1 of 17)	intron (NM_001198635, intron 1 of 17)	21909	NM_001198635	17761	Mm.20928	NM_008635	ENSMUSG00000019996	Map7	E-MAP-115|MAP-7|Mtap7|R75000|mshi|mste|ste	microtubule-associated protein 7	protein-coding
mm_6651.1	chr1	79761784	79761794	-	1	NA	promoter-TSS (NM_001111279)	promoter-TSS (NM_001111279)	-20	NM_027057	69368	Mm.293273	NM_027057	ENSMUSG00000073643	Wdfy1	1700013B03Rik|1700120F24Rik|FENS-1|Jr1|WDF1|ZFYVE17|mKIAA1435	WD repeat and FYVE domain containing 1	protein-coding
mm_162591.1	chr1	181232368	181232390	-	1	NA	Intergenic	Intergenic	-20401	NM_145514	226757	Mm.289082	NM_145514	ENSMUSG00000038733	Wdr26	1600024A01Rik|AA693241|AI447817|AU044014|C77982|Gid7	WD repeat domain 26	protein-coding
mm_1079.1	chr1	59482872	59482894	+	1	NA	5' UTR (NM_008057, exon 1 of 1)	5' UTR (NM_008057, exon 1 of 1)	736	NM_008057	14369	Mm.297906	NM_008057	ENSMUSG00000041075	Fzd7	Fz7	frizzled class receptor 7	protein-coding
mm_105145.1	chr11	101460439	101460481	-	1	NA	exon (NM_012037, exon 5 of 6)	exon (NM_012037, exon 5 of 6)	5739	NM_012037	26949	Mm.29210	NM_012037	ENSMUSG00000034993	Vat1	VAT-1	vesicle amine transport 1	protein-coding
mm_1232.1	chr1	62770928	62770937	+	1	NA	intron (NM_001077405, intron 11 of 15)	intron (NM_001077405, intron 11 of 15)	23800	NR_040601	74992	Mm.401979	NR_040601		4930487H11Rik	-	RIKEN cDNA 4930487H11 gene	ncRNA
mm_74152.1	chr8	123373851	123373858	+	1	NA	5' UTR (NM_001037877, exon 1 of 18)	5' UTR (NM_001037877, exon 1 of 18)	143	NM_001286363	66855	Mm.178818	NM_025804	ENSMUSG00000001472	Tcf25	1100001J13Rik|1810041K11Rik|D8Ertd325e|Nulp1|mKIAA1049	transcription factor 25 (basic helix-loop-helix)	protein-coding
mm_94691.1	chr11	19954186	19954189	+	1	NA	intron (NM_033523, intron 1 of 5)	intron (NM_033523, intron 1 of 5)	29745	NM_033523	114716	Mm.266627	NM_033523	ENSMUSG00000045671	Spred2	C79158	sprouty-related, EVH1 domain containing 2	protein-coding
mm_46924.1	chr5	114670054	114670067	-	1	NA	3' UTR (NM_019821, exon 5 of 5)	3' UTR (NM_019821, exon 5 of 5)	-11639	NM_022017	63873	Mm.266450	NM_022017	ENSMUSG00000014158	Trpv4	0610033B08Rik|OTRPC4|Trp12|VR-OAC|VRL-2|VROAC	transient receptor potential cation channel, subfamily V, member 4	protein-coding
mm_141550.1	chr17	32166749	32166772	-	1	NA	promoter-TSS (NM_008716)	promoter-TSS (NM_008716)	92	NM_008716	18131	Mm.439741	NM_008716	ENSMUSG00000038146	Notch3	AW229011|N3|hpbk	notch 3	protein-coding
mm_173137.1	chrX	20920646	20920663	-	1	NA	exon (NM_013680, exon 1 of 13)	exon (NM_013680, exon 1 of 13)	264	NM_001110780	20964	Mm.439844	NM_013680	ENSMUSG00000037217	Syn1	Syn-1|Syn1-S	synapsin I	protein-coding
mm_166333.1	chr5	114273791	114273802	-	1	NA	promoter-TSS (NM_148935)	promoter-TSS (NM_148935)	-35	NM_148935	116810	Mm.17709	NM_148935	ENSMUSG00000042002	Foxn4	-	forkhead box N4	protein-coding
mm_69392.1	chr7	131410496	131410520	-	1	NA	promoter-TSS (NM_025826)	promoter-TSS (NM_025826)	-30	NM_175115	67143	Mm.334273	NM_175115	ENSMUSG00000040167	Ikzf5	2610034F18Rik|PEGASUS|Zfpn1a5	IKAROS family zinc finger 5	protein-coding
mm_5449.1	chr1	36244133	36244176	-	1	NA	5' UTR (NM_198899, exon 1 of 41)	5' UTR (NM_198899, exon 1 of 41)	148	NM_198899	320011	Mm.261022	NM_198899	ENSMUSG00000037470	Uggt1	0910001L17Rik|A930007H10Rik|AA589501|AI414429|AI448372|C820010P03Rik|GT|UGT1|Ugcgl1	UDP-glucose glycoprotein glucosyltransferase 1	protein-coding
mm_28923.1	chr3	98858184	98858231	-	1	NA	5' UTR (NM_008293, exon 2 of 5)	5' UTR (NM_008293, exon 2 of 5)	1587	NM_001304800	15492	Mm.140811	NM_008293	ENSMUSG00000027871	Hsd3b1	3-beta-HSD I|D3Ertd383e	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1	protein-coding
mm_30601.1	chr4	6387029	6387071	+	1	NA	intron (NM_001098227, intron 6 of 8)	AT_rich|Low_complexity|Low_complexity	21370	NM_001098227	53378	Mm.247473	NM_016807	ENSMUSG00000028249	Sdcbp	MDA-9|Sycl|syntenin-1	syndecan binding protein	protein-coding
mm_85718.1	chr9	108263888	108263965	-	1	NA	promoter-TSS (NM_001276486)	promoter-TSS (NM_001276486)	32	NM_001276485	13138	Mm.7524	NM_010017	ENSMUSG00000039952	Dag1	D9Wsu13e|DG|Dp427|Dp71	dystroglycan 1	protein-coding
mm_104484.1	chr11	95587692	95587707	-	1	NA	promoter-TSS (NM_033217)	promoter-TSS (NM_033217)	-1	NM_033217	18053	Mm.283893	NM_033217	ENSMUSG00000000120	Ngfr	LNGFR|Tnfrsf16|p75|p75NGFR|p75NTR	nerve growth factor receptor (TNFR superfamily, member 16)	protein-coding
mm_121722.1	chr14	16575344	16575361	-	1	NA	5' UTR (NM_001289762, exon 1 of 8)	5' UTR (NM_001289762, exon 1 of 8)	124	NM_011243	218772	Mm.259318	NM_011243	ENSMUSG00000017491	Rarb	A830025K23|Hap|Nr1b2	retinoic acid receptor, beta	protein-coding
mm_2941.1	chr1	132316113	132316144	+	1	NA	promoter-TSS (NM_028778)	promoter-TSS (NM_028778)	3	NM_001195025	74137	Mm.100666	NM_028778	ENSMUSG00000009772	Nuak2	1200013B22Rik|Omphk2|Snark|mKIAA0537	NUAK family, SNF1-like kinase, 2	protein-coding
mm_110363.1	chr12	40083429	40083471	-	1	NA	intron (NM_009132, intron 5 of 13)	intron (NM_009132, intron 5 of 13)	-45463	NM_001039515	11861	Mm.12723	NM_007487	ENSMUSG00000047446	Arl4a	AI467555|Arl4	ADP-ribosylation factor-like 4A	protein-coding
mm_123293.1	chr14	61556784	61556797	-	1	NA	promoter-TSS (NM_001310603)	promoter-TSS (NM_001310603)	96	NM_025697	66674	Mm.282706	NM_025697	ENSMUSG00000021930	Spryd7	6330409N04Rik|Clld6	SPRY domain containing 7	protein-coding
mm_13208.1	chr2	93642308	93642334	+	1	NA	promoter-TSS (NM_007442)	promoter-TSS (NM_007442)	-113	NM_007442	11695	Mm.389389	NM_007442	ENSMUSG00000040310	Alx4	lst	aristaless-like homeobox 4	protein-coding
mm_44225.1	chr5	4832693	4832728	-	1	NA	intron (NM_011074, intron 14 of 14)	intron (NM_011074, intron 14 of 14)	-74494	NM_021457	14362	Mm.246003	NM_021457	ENSMUSG00000044674	Fzd1	AW227548|FZ-1|Fz1	frizzled class receptor 1	protein-coding
mm_57315.1	chr6	124727275	124727287	-	1	NA	intron (NM_001077705, intron 9 of 15)	RSINE1|SINE|B4	5873	NM_013545	15170	Mm.271799	NM_013545	ENSMUSG00000004266	Ptpn6	70Z-SHP|Hcph|PTPTY-42|Ptp1C|SH-PTP1|SHP-1|hcp|me	protein tyrosine phosphatase, non-receptor type 6	protein-coding
mm_40097.1	chr5	34573695	34573737	+	1	NA	promoter-TSS (NR_106111)	promoter-TSS (NR_106111)	52	NM_001331086	11518	Mm.289106	NM_013457	ENSMUSG00000029106	Add1	AI256389	adducin 1 (alpha)	protein-coding
mm_140244.1	chr17	84181219	84181239	+	1	NA	Intergenic	Intergenic	6718	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_30922.1	chr4	32723043	32723051	+	1	NA	exon (NM_001081392, exon 48 of 102)	exon (NM_001081392, exon 48 of 102)	65928	NM_001081392	100019	Mm.24627	NM_133874	ENSMUSG00000058006	Mdn1	4833432B22Rik|A130070M06|AA958993|D4Abb1e|Gm135	midasin AAA ATPase 1	protein-coding
mm_155121.1	chrX	48871339	48871349	+	1	NA	intron (NM_001085499, intron 8 of 20)	CT-rich|Low_complexity|Low_complexity	6369	NM_001085499	209005	Mm.336054	NM_001085499	ENSMUSG00000079606	Gm595	-	predicted gene 595	protein-coding
mm_106632.1	chr11	120903357	120903366	-	1	NA	exon (NM_027745, exon 6 of 19)	exon (NM_027745, exon 6 of 19)	29511	NM_027745	71276	Mm.275751	NM_027745	ENSMUSG00000048445	Ccdc57	4933434G05Rik	coiled-coil domain containing 57	protein-coding
mm_8640.1	chr1	156428966	156428986	-	1	NA	3' UTR (NM_009230, exon 16 of 16)	3' UTR (NM_009230, exon 16 of 16)	-8061	NM_001346967	77352	Mm.428709	NM_001033180	ENSMUSG00000026601	Axdnd1	9430070O13Rik|Gm979	axonemal dynein light chain domain containing 1	protein-coding
mm_60244.1	chr7	43768914	43768944	+	1	NA	promoter-TSS (NM_027097)	promoter-TSS (NM_027097)	-171	NM_027097	69511	Mm.20163	NM_027097	ENSMUSG00000044430	Klk12	2310008B01Rik|AI324852|KLK-L5	kallikrein related-peptidase 12	protein-coding
mm_108214.1	chr12	77038539	77038547	+	1	NA	Intergenic	Intergenic	-76295	NM_001146176	17187	Mm.268548	NM_008558	ENSMUSG00000059436	Max	AA960152|AI875693|bHLHd4|bHLHd5|bHLHd6|bHLHd7|bHLHd8	Max protein	protein-coding
mm_172902.1	chr9	58555317	58555325	-	1	NA	Intergenic	Intergenic	-14381	NM_133983	102657	Mm.5356	NM_133983	ENSMUSG00000035914	Cd276	6030411F23Rik|AU016588|B7RP-2|B7h3	CD276 antigen	protein-coding
mm_133287.1	chr16	77466076	77466101	+	1	NA	intron (NR_015543, intron 3 of 4)	Plat_L3|LINE|CR1	-132848	NR_029535	387229		NR_029535	ENSMUSG00000065530	Mir99a	Mirn99a|mir-99a|mmu-mir-99a	microRNA 99a	ncRNA
mm_45214.1	chr5	52994207	52994221	-	1	NA	Intergenic	Intergenic	-1922	NR_040413	75954	Mm.258937	NR_040413	ENSMUSG00000106352	5033403H07Rik	-	RIKEN cDNA 5033403H07 gene	ncRNA
mm_123695.1	chr14	69705498	69705508	-	1	NA	exon (NM_001146012, exon 4 of 8)	exon (NM_001146012, exon 4 of 8)	1990	NM_001301652	71843	Mm.27738	NM_001146012	ENSMUSG00000034194	R3hcc1	1700020M16Rik|AA407796	R3H domain and coiled-coil containing 1	protein-coding
mm_66137.1	chr7	31111149	31111158	-	1	NA	promoter-TSS (NM_001276269)	promoter-TSS (NM_001276269)	-156	NM_001276269	15451	Mm.19182	NM_008281	ENSMUSG00000001249	Hpn	Hlb320	hepsin	protein-coding
mm_107479.1	chr12	37880807	37880878	+	1	NA	5' UTR (NM_178681, exon 1 of 25)	5' UTR (NM_178681, exon 1 of 25)	137	NM_178681	217480	Mm.126525	NM_178681	ENSMUSG00000036095	Dgkb	6430574F24|90kda|C630029D13Rik|DAGK2|DGK|DGK-beta|mKIAA0718	diacylglycerol kinase, beta	protein-coding
mm_87137.1	chr10	34299065	34299068	+	1	NA	3' UTR (NM_030203, exon 1 of 1)	3' UTR (NM_030203, exon 1 of 1)	1645	NM_030203	72480	Mm.21485	NM_030203	ENSMUSG00000039485	Tspyl4	2610102M01Rik|B230210I21Rik|D10Bwg0791e	TSPY-like 4	protein-coding
mm_63738.1	chr7	130900537	130900545	+	1	NA	exon (NM_133942, exon 5 of 10)	exon (NM_133942, exon 5 of 10)	-7727	NR_106028	102466219		NR_106028	ENSMUSG00000104914	Mir7061	mmu-mir-7061	microRNA 7061	ncRNA
mm_162587.1	chr1	180849183	180849192	+	1	NA	Intergenic	Intergenic	-1964	NM_145943	208768	Mm.272625	NM_145943	ENSMUSG00000038806	Sde2	-	SDE2 telomere maintenance homolog (S. pombe)	protein-coding
mm_132396.1	chr16	35000973	35001002	+	1	NA	3' UTR (NM_139300, exon 32 of 32)	3' UTR (NM_139300, exon 32 of 32)	-21434	NM_023587	70757	Mm.27286	NM_023587	ENSMUSG00000035376	Hacd2	6330408J20Rik|AI255777|AI481689|Hcad2|Ptplb	3-hydroxyacyl-CoA dehydratase 2	protein-coding
mm_19807.1	chr2	110314216	110314227	-	1	NA	Intergenic	Intergenic	-8496	NM_130452	170442	Mm.27335	NM_130452	ENSMUSG00000041660	Bbox1	AI874739	butyrobetaine (gamma), 2-oxoglutarate dioxygenase 1 (gamma-butyrobetaine hydroxylase)	protein-coding
mm_14981.1	chr2	152143553	152143558	+	1	NA	promoter-TSS (NM_009328)	promoter-TSS (NM_009328)	-54	NM_009328	21407	Mm.3881	NM_009328	ENSMUSG00000068079	Tcf15	Meso1|bHLH-EC2	transcription factor 15	protein-coding
mm_57700.1	chr6	128526688	128526692	-	1	NA	promoter-TSS (NM_007376)	promoter-TSS (NM_007376)	30	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_43695.1	chr5	139161880	139161888	+	1	NA	exon (NM_001081265, exon 5 of 13)	exon (NM_001081265, exon 5 of 13)	11661	NM_001081265	433956	Mm.5547	NM_001081265	ENSMUSG00000025857	Dnaaf5	BC053401|C76907|Heatr2	dynein, axonemal assembly factor 5	protein-coding
mm_46866.1	chr5	113824328	113824338	-	1	NA	intron (NM_009151, intron 1 of 1)	intron (NM_009151, intron 1 of 1)	6168	NM_009151	20345	Mm.332590	NM_009151	ENSMUSG00000048163	Selplg	CD162|Psgl-1|Psgl1|Selp1|Selpl	selectin, platelet (p-selectin) ligand	protein-coding
mm_132468.1	chr16	36693973	36694000	+	1	NA	promoter-TSS (NM_134109)	promoter-TSS (NM_134109)	8	NM_001285791	106347	Mm.17807	NM_134109	ENSMUSG00000022900	Ildr1	AU041483|AU044638	immunoglobulin-like domain containing receptor 1	protein-coding
mm_163431.1	chr12	84177421	84177445	-	1	NA	intron (NM_001163501, intron 1 of 12)	intron (NM_001163501, intron 1 of 12)	16582	NM_001163502	238317	Mm.31256	NM_001163501	ENSMUSG00000042507	Elmsan1	9430029N19Rik|C130039O16Rik|Gm260	ELM2 and Myb/SANT-like domain containing 1	protein-coding
mm_66062.1	chr7	30752158	30752190	-	1	NA	exon (NM_172205, exon 1 of 4)	exon (NM_172205, exon 1 of 4)	703	NM_001083903	282619	Mm.250717	NM_172205	ENSMUSG00000046056	Sbsn	1110005D19Rik|AI747508	suprabasin	protein-coding
mm_13969.1	chr2	121431649	121431661	+	1	NA	exon (NM_007952, exon 6 of 13)	exon (NM_007952, exon 6 of 13)	10946	NM_145973	269344	Mm.330522	NM_145973	ENSMUSG00000027246	Ell3	A930015D22Rik	elongation factor RNA polymerase II-like 3	protein-coding
mm_159956.1	chr6	87730852	87730852	+	1	NA	promoter-TSS (NM_001159697)	promoter-TSS (NM_001159697)	-17	NM_001159697	58229	Mm.333229	NM_021418	ENSMUSG00000068263	Efcc1	Ccdc48	EF hand and coiled-coil domain containing 1	protein-coding
mm_78423.1	chr9	31163558	31163590	+	1	NA	intron (NM_001102455, intron 8 of 16)	intron (NM_001102455, intron 8 of 16)	-31775	NM_011176	19143	Mm.243926	NM_011176	ENSMUSG00000031995	St14	Epithin|MT-SP1|Prss14|Tmprss14|mCAP3|matriptase	suppression of tumorigenicity 14 (colon carcinoma)	protein-coding
mm_30079.1	chr3	138090325	138090333	-	1	NA	3' UTR (NM_001163457, exon 20 of 20)	3' UTR (NM_001163457, exon 20 of 20)	-22941	NR_037975	329763	Mm.169710	NM_177860	ENSMUSG00000049349	Gm5105	D830013H12|EG329763	predicted gene 5105	ncRNA
mm_82597.1	chr9	21291125	21291162	-	1	NA	promoter-TSS (NM_009878)	promoter-TSS (NM_009878)	66	NM_009878	12581	Mm.29020	NM_009878	ENSMUSG00000096472	Cdkn2d	INK4d|p19|p19INK4d	cyclin-dependent kinase inhibitor 2D (p19, inhibits CDK4)	protein-coding
mm_138309.1	chr17	34647129	34647173	+	1	NA	promoter-TSS (NM_017406)	promoter-TSS (NM_017406)	5	NM_017406	12915	Mm.4068	NM_017406	ENSMUSG00000015461	Atf6b	AA617266|ATF6beta|Creb-rp|Crebl1	activating transcription factor 6 beta	protein-coding
mm_118805.1	chr14	25378237	25378261	+	1	NA	Intergenic	CpG	-80936	NM_001310666	328365	Mm.227484	NM_183208	ENSMUSG00000007817	Zmiz1	BC065120|E330020C23|ENSMUSG00000072684|Gm10397|I920194n01|Rai17|Zimp10	zinc finger, MIZ-type containing 1	protein-coding
mm_86525.1	chr10	7802975	7802978	+	1	NA	intron (NM_026141, intron 8 of 12)	B4|SINE|B4	10082	NM_026141	67418	Mm.38927	NM_026141	ENSMUSG00000015757	Ppil4	3732410E19Rik|3830425H19Rik|AI788954|AW146233|PPIase	peptidylprolyl isomerase (cyclophilin)-like 4	protein-coding
mm_39154.1	chr4	155414782	155414804	-	1	NA	non-coding (NR_102287, exon 2 of 4)	non-coding (NR_102287, exon 2 of 4)	5603	NM_001166029	544678	Mm.472798	NM_177674	ENSMUSG00000078490	Cfap74	2010015L04Rik|A530045M11	cilia and flagella associated protein 74	protein-coding
mm_111355.1	chr12	86990469	86990483	-	1	NA	Intergenic	CpG	-1800	NM_001080943	238331	Mm.185890	NM_001080943	ENSMUSG00000048483	Zdhhc22	Gm262	zinc finger, DHHC-type containing 22	protein-coding
mm_38394.1	chr4	138819309	138819314	-	1	NA	promoter-TSS (NM_011110)	promoter-TSS (NM_011110)	-54	NM_011110	18784	Mm.486532	NM_011110	ENSMUSG00000041193	Pla2g5	PLA2|sPLA2	phospholipase A2, group V	protein-coding
mm_69104.1	chr7	127021047	127021057	-	1	NA	5' UTR (NM_001102563, exon 1 of 4)	5' UTR (NM_001102563, exon 1 of 4)	159	NM_001102563	69017	Mm.392047	NM_001102563	ENSMUSG00000045114	Prrt2	1500031I19Rik|AI195361|DSPB3	proline-rich transmembrane protein 2	protein-coding
mm_32984.1	chr4	120136291	120136307	+	1	NA	TTS (NM_010657)	TTS (NM_010657)	-24907	NM_007902	13615	Mm.284855	NM_007902	ENSMUSG00000028635	Edn2	ET-2|PPET2|VIC	endothelin 2	protein-coding
mm_13246.1	chr2	98662942	98662961	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	1195294	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_101818.1	chr11	46447260	46447270	-	1	NA	intron (NR_105955, intron 2 of 4)	MTEa|LTR|ERVL-MaLR	-7666	NM_134250	171285	Mm.72168	NM_134250	ENSMUSG00000020399	Havcr2	TIM-3|Tim3|Timd3	hepatitis A virus cellular receptor 2	protein-coding
mm_124686.1	chr15	6435268	6435302	+	1	NA	exon (NM_001102400, exon 10 of 13)	exon (NM_001102400, exon 10 of 13)	-10048	NM_013485	12279	Mm.29095	NM_013485	ENSMUSG00000022149	C9	-	complement component 9	protein-coding
mm_173084.1	chrX	142622881	142622884	-	1	NA	Intergenic	Intergenic	-58518	NM_177592	209497	Mm.249648	NM_177592	ENSMUSG00000047045	Tmem164	AI316850|AI852450|AW547186|F730011B02	transmembrane protein 164	protein-coding
mm_22096.1	chr2	168955530	168955593	-	1	NA	promoter-TSS (NM_009564)	promoter-TSS (NM_009564)	26	NM_009564	22722	Mm.2095	NM_009564	ENSMUSG00000027551	Zfp64	-	zinc finger protein 64	protein-coding
mm_75371.1	chr8	45310245	45310255	-	1	NA	exon (NM_133969, exon 8 of 11)	exon (NM_133969, exon 8 of 11)	-15415	NM_008455	16621	Mm.482691	NM_008455	ENSMUSG00000109764	Klkb1	APS|Kal-3|Kal3|Klk3|PSA	kallikrein B, plasma 1	protein-coding
mm_128269.1	chr15	36793520	36793554	-	1	NA	5' UTR (NM_011740, exon 2 of 7)	5' UTR (NM_011740, exon 2 of 7)	1001	NM_011740	22631	Mm.3360	NM_011740	ENSMUSG00000022285	Ywhaz	1110013I11Rik|14-3-3zeta|AI596267|AL022924|AU020854	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide	protein-coding
mm_164287.1	chr15	103503220	103503241	+	1	NA	5' UTR (NM_008800, exon 1 of 16)	5' UTR (NM_008800, exon 1 of 16)	196	NM_008800	18574	Mm.390792	NM_008800	ENSMUSG00000022489	Pde1b	Pde1b1	phosphodiesterase 1B, Ca2+-calmodulin dependent	protein-coding
mm_66422.1	chr7	44534296	44534316	-	1	NA	intron (NM_011131, intron 22 of 26)	intron (NM_011131, intron 22 of 26)	-2235	NM_019866	272382	Mm.8012	NM_019866	ENSMUSG00000008193	Spib	Spi-B	Spi-B transcription factor (Spi-1/PU.1 related)	protein-coding
mm_31486.1	chr4	52596286	52596299	+	1	NA	promoter-TSS (NM_026652)	promoter-TSS (NM_026652)	18	NM_026652	68274	Mm.85045	NM_026652	ENSMUSG00000028314	Toporsl	4930547C10Rik	topoisomerase I binding, arginine/serine-rich like	protein-coding
mm_167166.1	chr7	136268343	136268356	+	1	NA	promoter-TSS (NR_102277)	promoter-TSS (NR_102277)	25	NR_102277	77383	Mm.227745	NR_102277	ENSMUSG00000110027	C030029H02Rik	-	RIKEN cDNA C030029H02 gene	ncRNA
mm_86370.1	chr9	123797960	123797974	-	1	NA	intron (NM_148925, intron 16 of 18)	intron (NM_148925, intron 16 of 18)	-8510	NM_030712	80901	Mm.124289	NM_030712	ENSMUSG00000048521	Cxcr6	BB217514|BONZO|STRL33	chemokine (C-X-C motif) receptor 6	protein-coding
mm_43730.1	chr5	139723291	139723304	+	1	NA	intron (NM_174850, intron 1 of 16)	intron (NM_174850, intron 1 of 16)	13036	NM_174850	231830	Mm.240510	NM_174850	ENSMUSG00000036718	Micall2	A930021H16Rik|JRAB|MICAL-L2|mFLJ00139	MICAL-like 2	protein-coding
mm_116413.1	chr13	41487282	41487298	-	1	NA	promoter-TSS (NM_001111324)	promoter-TSS (NM_001111324)	70	NM_001111324	18003	Mm.288980	NM_017464	ENSMUSG00000021365	Nedd9	Cas-L|CasL|HEF1|MEF1|Nedd-9|p105	neural precursor cell expressed, developmentally down-regulated gene 9	protein-coding
mm_171320.1	chr3	96260696	96260711	-	1	NA	Intergenic	RMER19A|LTR|ERVK	2614	NM_033596	97122	Mm.227295	NM_033596	ENSMUSG00000091405	Hist2h4	H4|X04652	histone cluster 2, H4	protein-coding
mm_147704.1	chr18	60810355	60810410	-	1	NA	exon (NM_010545, exon 6 of 8)	exon (NM_010545, exon 6 of 8)	-1694	NR_039567	100628611		NR_039567	ENSMUSG00000093327	Mir5107	mir-5107|mmu-mir-5107|mu-mir-5107	microRNA 5107	ncRNA
mm_31162.1	chr4	43442561	43442567	+	1	NA	5' UTR (NM_011571, exon 1 of 10)	5' UTR (NM_011571, exon 1 of 10)	287	NM_011571	21754	Mm.485441	NM_011571	ENSMUSG00000028458	Tesk1	AI326901	testis specific protein kinase 1	protein-coding
mm_121379.1	chr14	118854696	118854700	+	1	NA	promoter-TSS (NM_001160099)	promoter-TSS (NM_001160099)	-252	NM_021386	58187	Mm.390755	NM_021386	ENSMUSG00000022132	Cldn10	6720456I16Rik|Cldn10a|Cldn10b|D14Ertd728e	claudin 10	protein-coding
mm_77862.1	chr9	5323710	5323723	+	1	NA	exon (NM_007609, exon 4 of 9)	exon (NM_007609, exon 4 of 9)	14867	NM_007609	12363	Mm.1569	NM_007609	ENSMUSG00000033538	Casp4	CASP-11|CASP-4|Casp11|Caspl|ich-3	caspase 4, apoptosis-related cysteine peptidase	protein-coding
mm_49966.1	chr6	40765964	40765979	+	1	NA	exon (NM_001171003, exon 47 of 48)	exon (NM_001171003, exon 47 of 48)	121523	NM_139296	194357	Mm.207087	NM_139296	ENSMUSG00000029885	Moxd2	Dbhl1	monooxygenase, DBH-like 2	protein-coding
mm_47605.1	chr5	125058536	125058540	-	1	NA	intron (NM_011424, intron 17 of 46)	intron (NM_011424, intron 17 of 46)	55063	NM_028443	73121	Mm.296138	NM_028443	ENSMUSG00000037962	Rflna	3110032G18Rik|Fam101a|cfm|cfm2	refilin A	protein-coding
mm_75740.1	chr8	69716851	69716912	-	1	NA	promoter-TSS (NM_181274)	promoter-TSS (NM_181274)	21	NM_001039967	66869	Mm.334581	NM_181274	ENSMUSG00000054648	Zfp869	1200003I07Rik	zinc finger protein 869	protein-coding
mm_94641.1	chr11	16914598	16914620	+	1	NA	TTS (NM_207655)	TTS (NM_207655)	36673	NR_110421	72735	Mm.268598	NR_015469		Eldr	2810442I21Rik|4930500E12Rik|Fabl	Egfr long non-coding downstream RNA	ncRNA
mm_35251.1	chr4	19877772	19877795	-	1	NA	3' UTR (NM_175406, exon 8 of 8)	3' UTR (NM_175406, exon 8 of 8)	44783	NM_175406	242341	Mm.19298	NM_175406	ENSMUSG00000028238	Atp6v0d2	1620401A02Rik|AI324824|V-ATPase	ATPase, H+ transporting, lysosomal V0 subunit D2	protein-coding
mm_2511.1	chr1	106230725	106230737	+	1	NA	intron (NM_133821, intron 1 of 16)	RMER19A|LTR|ERVK	58862	NM_133821	98432	Mm.24115	NM_133821	ENSMUSG00000044340	Phlpp1	AI836256|Phlpp|Plekhe1|SCOP|mKIAA0606	PH domain and leucine rich repeat protein phosphatase 1	protein-coding
mm_101437.1	chr11	30114856	30114874	-	1	NA	exon (NM_009260, exon 26 of 31)	exon (NM_009260, exon 26 of 31)	83392	NM_009260	20742	Mm.123110	NM_009260	ENSMUSG00000020315	Sptbn1	9930031C03Rik|AL033301|SPTB2|Spnb-2|Spnb2|elf1|elf3|mKIAA4049	spectrin beta, non-erythrocytic 1	protein-coding
mm_2805.1	chr1	130852175	130852178	+	1	NA	TTS (NM_011082)	TTS (NM_011082)	-13601	NM_026976	69169	Mm.46042	NM_026976	ENSMUSG00000042474	Fcmr	1810037B05Rik|Faim3|FcmuR|Toso	Fc fragment of IgM receptor	protein-coding
mm_16625.1	chr2	5676984	5676993	-	1	NA	promoter-TSS (NM_001290376)	promoter-TSS (NM_001290376)	-942	NM_001290376	227541	Mm.191949	NM_177343	ENSMUSG00000039145	Camk1d	A630059D12Rik|CKLiK|CaMKIdelta|E030025C11Rik|mCKLiK	calcium/calmodulin-dependent protein kinase ID	protein-coding
mm_150842.1	chr19	44956997	44957000	+	1	NA	intron (NM_001081225, intron 9 of 19)	ORR1B2|LTR|ERVL-MaLR	25879	NM_001081225	226151	Mm.212609	NM_172638	ENSMUSG00000036097	Fam178a	3632432H19|6030443O07Rik|AU014917|Slf2	family with sequence similarity 178, member A	protein-coding
mm_166812.1	chr7	16204248	16204252	-	1	NA	intron (NM_001285931, intron 9 of 16)	intron (NM_001285931, intron 9 of 16)	17743	NM_001285931	71723	Mm.75259	NM_027883	ENSMUSG00000006019	Dhx34	1200013B07Rik|1810012L18Rik|Ddx34|mKIAA0134	DEAH (Asp-Glu-Ala-His) box polypeptide 34	protein-coding
mm_157209.1	chrX	12761997	12762040	-	1	NA	promoter-TSS (NM_001048208)	promoter-TSS (NM_001048208)	-45	NM_001048208	26896	Mm.17616	NM_012005	ENSMUSG00000064127	Med14	9930001L01Rik|AU041628|Crsp2|ENSMUSG00000073278|Gm641|ORF1|Trap170	mediator complex subunit 14	protein-coding
mm_143032.1	chr17	56609929	56609939	-	1	NA	promoter-TSS (NM_153152)	promoter-TSS (NM_153152)	-163	NM_153152	224904	Mm.34002	NM_153152	ENSMUSG00000049760	2410015M20Rik	Mic13|QIL1|sr104	RIKEN cDNA 2410015M20 gene	protein-coding
mm_140388.1	chr17	87282881	87282950	+	1	NA	promoter-TSS (NM_028639)	promoter-TSS (NM_028639)	29	NM_028639	225049	Mm.77396	NM_028639	ENSMUSG00000036918	Ttc7	1110035E02Rik|1700007L07Rik|Ttc7a|fsn|hea	tetratricopeptide repeat domain 7	protein-coding
mm_162720.1	chr10	37075096	37075097	+	1	NA	Intergenic	Intergenic	63830	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_50302.1	chr6	47636578	47636607	+	1	NA	Intergenic	Intergenic	18502	NR_002841	19799		NR_002841		Rn4.5s	-	4.5S RNA	rRNA
mm_116315.1	chr13	37255400	37255404	-	1	NA	Intergenic	Lx7|LINE|L1	-89943	NM_010745	17084	Mm.2639	NM_010745	ENSMUSG00000021423	Ly86	MD-1|MD1|ly86_tv2	lymphocyte antigen 86	protein-coding
mm_163328.1	chr12	8480308	8480312	-	1	NA	Intergenic	Intergenic	19675	NM_007483	11852	Mm.687	NM_007483	ENSMUSG00000054364	Rhob	AA017882|Arh6|Arhb	ras homolog family member B	protein-coding
mm_79144.1	chr9	47697414	47697428	+	1	NA	intron (NM_001025600, intron 1 of 8)	(T)n|Simple_repeat|Simple_repeat	120787	NR_046048	100038460	Mm.447649	NR_046048		Gm10677	ENSMUSG00000074363	predicted gene 10677	ncRNA
mm_49696.1	chr6	33973262	33973282	+	1	NA	TTS (NM_009148)	TTS (NM_009148)	-56176	NM_028886	74354	Mm.127952	NM_028886	ENSMUSG00000056215	Lrguk	4921528H16Rik	leucine-rich repeats and guanylate kinase domain containing	protein-coding
mm_46109.1	chr5	92348872	92348886	-	1	NA	promoter-TSS (NM_021274)	promoter-TSS (NM_021274)	10	NM_021274	15945	Mm.877	NM_021274	ENSMUSG00000034855	Cxcl10	C7|CRG-2|INP10|IP-10|IP10|Ifi10|Scyb10|gIP-10|mob-1	chemokine (C-X-C motif) ligand 10	protein-coding
mm_100940.1	chr11	6528395	6528403	-	1	NA	intron (NR_045893, intron 1 of 3)	intron (NR_045893, intron 1 of 3)	361	NR_045893	100041286	Mm.459507	NR_045893	ENSMUSG00000085156	Snhg15	Gm11974|OTTMUSG00000005115	small nucleolar RNA host gene 15	ncRNA
mm_122861.1	chr14	54907158	54907168	-	1	NA	exon (NM_021551, exon 9 of 9)	exon (NM_021551, exon 9 of 9)	5969	NM_021551	59049	Mm.27435	NM_021551	ENSMUSG00000022199	Slc22a17	1700094C23Rik|24p3R|AU041908|AW555662|BOIT|Boct	solute carrier family 22 (organic cation transporter), member 17	protein-coding
mm_35601.1	chr4	43040152	43040173	-	1	NA	5' UTR (NM_001253353, exon 1 of 9)	5' UTR (NM_001253353, exon 1 of 9)	139	NM_001253353	230088	Mm.260162	NM_172691	ENSMUSG00000036002	Fam214b	B230312A22Rik	family with sequence similarity 214, member B	protein-coding
mm_20192.1	chr2	122702616	122702717	-	1	NA	promoter-TSS (NM_011774)	promoter-TSS (NM_011774)	-3	NM_001290993	22785	Mm.27801	NM_011774	ENSMUSG00000005802	Slc30a4	Znt4|lm|znT-4	solute carrier family 30 (zinc transporter), member 4	protein-coding
mm_73236.1	chr8	104142748	104142760	+	1	NA	exon (NM_009868, exon 12 of 12)	exon (NM_009868, exon 12 of 12)	-27759	NM_001141924	65115	Mm.41849	NM_001141922	ENSMUSG00000031872	Bean1	Bean	brain expressed, associated with Nedd4, 1	protein-coding
mm_147404.1	chr18	44641415	44641417	-	1	NA	intron (NM_001085373, intron 3 of 18)	intron (NM_001085373, intron 3 of 18)	-20249	NR_026853	626275	Mm.427116	NR_026853	ENSMUSG00000097610	A930012L18Rik	-	RIKEN cDNA A930012L18 gene	ncRNA
mm_142015.1	chr17	35200522	35200528	-	1	NA	exon (NM_013693, exon 4 of 4)	exon (NM_013693, exon 4 of 4)	1482	NM_013693	21926	Mm.1293	NM_013693	ENSMUSG00000024401	Tnf	DIF|TNF-a|TNF-alpha|TNFSF2|TNFalpha|Tnfa|Tnfsf1a|Tnlg1f	tumor necrosis factor	protein-coding
mm_70934.1	chr8	25849619	25849633	+	1	NA	promoter-TSS (NM_008432)	promoter-TSS (NM_008432)	3	NM_008432	16532	Mm.289679	NM_008432	ENSMUSG00000031576	Kcnu1	Kcnma3|Slo3|mSlo3	potassium channel, subfamily U, member 1	protein-coding
mm_130990.1	chr15	103393660	103393671	-	1	NA	Intergenic	Intergenic	-26874	NM_001314041	16402	Mm.16234	NM_010577	ENSMUSG00000000555	Itga5	Cd49e|Fnra|VLA5	integrin alpha 5 (fibronectin receptor alpha)	protein-coding
mm_70417.1	chr8	11458523	11458544	+	1	NA	intron (NM_011227, intron 1 of 1)	intron (NM_011227, intron 1 of 1)	-19396	NR_126558	102132	Mm.37632	NR_126558	ENSMUSG00000096957	E230013L22Rik	AI645545	RIKEN cDNA E230013L22 gene	ncRNA
mm_94078.1	chr10	128455571	128455574	-	1	NA	Intergenic	Intergenic	-3108	NR_106183	102465894		NR_106183	ENSMUSG00000098957	Mir8105	Gm27346|mmu-mir-8105	microRNA 8105	ncRNA
mm_113315.1	chr13	30764518	30764524	+	1	NA	3' UTR (NM_013674, exon 9 of 9)	3' UTR (NM_013674, exon 9 of 9)	15288	NM_013674	16364	Mm.4677	NM_013674	ENSMUSG00000021356	Irf4	AI385587|IRF-4|LSIRF|NF-EM5|Spip	interferon regulatory factor 4	protein-coding
mm_169267.1	chr1	38509515	38509525	+	1	NA	intron (NM_001290814, intron 4 of 21)	B3|SINE|B2	117724	NM_001290814	16764	Mm.336679	NM_010678	ENSMUSG00000037138	Aff3	3222402O04Rik|A730046J16|LAF-4|Laf4	AF4/FMR2 family, member 3	protein-coding
mm_87651.1	chr10	58422613	58422625	+	1	NA	3' UTR (NM_201242, exon 10 of 10)	3' UTR (NM_201242, exon 10 of 10)	-24233	NM_011240	19386	Mm.431695	NM_011240	ENSMUSG00000003226	Ranbp2	A430087B05Rik|AI256741|NUP358	RAN binding protein 2	protein-coding
mm_86404.1	chr9	123986671	123986677	-	1	NA	Intergenic	Intergenic	-8266	NM_007718	12770	Mm.423532	NM_007718	ENSMUSG00000064039	Ccr1l1	Cmkbr1l1	chemokine (C-C motif) receptor 1-like 1	protein-coding
mm_81945.1	chr9	120492625	120492640	+	1	NA	promoter-TSS (NM_026892)	promoter-TSS (NM_026892)	26	NM_026892	68969	Mm.28753	NM_026892	ENSMUSG00000006941	Eif1b	1500010M16Rik|3110001N14Rik|Gc20	eukaryotic translation initiation factor 1B	protein-coding
mm_70543.1	chr8	13042778	13042790	+	1	NA	intron (NM_001242368, intron 3 of 8)	intron (NM_001242368, intron 3 of 8)	5476	NM_001242368	14058	Mm.262589	NM_007972	ENSMUSG00000031444	F10	Cf10|fX	coagulation factor X	protein-coding
mm_41861.1	chr5	104440591	104440609	+	1	NA	exon (NM_001204203, exon 7 of 7)	exon (NM_001204203, exon 7 of 7)	4408	NM_001204233	20750	Mm.288474	NM_009263	ENSMUSG00000029304	Spp1	2AR|Apl-1|BNSP|BSPI|Bsp|ETA-1|Eta|OP|Opn|Opnl|Ric|Spp-1	secreted phosphoprotein 1	protein-coding
mm_172919.1	chr9	67049270	67049270	-	1	NA	promoter-TSS (NM_001164251)	promoter-TSS (NM_001164251)	-57	NM_001164251	22003	Mm.121878	NM_024427	ENSMUSG00000032366	Tpm1	AA986836|AI854628|TM2|Tm3|Tmpa|Tpm-1|alpha-TM	tropomyosin 1, alpha	protein-coding
mm_101447.1	chr11	30197901	30197962	-	1	NA	5' UTR (NM_009260, exon 1 of 31)	5' UTR (NM_009260, exon 1 of 31)	326	NM_009260	20742	Mm.123110	NM_009260	ENSMUSG00000020315	Sptbn1	9930031C03Rik|AL033301|SPTB2|Spnb-2|Spnb2|elf1|elf3|mKIAA4049	spectrin beta, non-erythrocytic 1	protein-coding
mm_79888.1	chr9	65294371	65294375	+	1	NA	5' UTR (NM_011802, exon 1 of 14)	5' UTR (NM_011802, exon 1 of 14)	113	NM_011802	270166	Mm.30088	NM_011802	ENSMUSG00000015357	Clpx	AU014732|E330029I21	caseinolytic mitochondrial matrix peptidase chaperone subunit	protein-coding
mm_40527.1	chr5	57919876	57919888	+	1	NA	intron (NM_001122758, intron 2 of 2)	B4A|SINE|B4	201801	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_104066.1	chr11	86585125	86585145	-	1	NA	promoter-TSS (NR_029738)	promoter-TSS (NR_029738)	-977	NR_029738	387140		NR_029738	ENSMUSG00000065455	Mir21a	Mir21|Mirn21|mmu-mir-21|mmu-mir-21a	microRNA 21a	ncRNA
mm_114823.1	chr13	91807702	91807720	+	1	NA	promoter-TSS (NM_145453)	promoter-TSS (NM_145453)	-15	NM_145453	69085	Mm.52356	NM_145453	ENSMUSG00000021621	Zcchc9	1810019C21Rik	zinc finger, CCHC domain containing 9	protein-coding
mm_66913.1	chr7	60005080	60005086	-	1	NA	promoter-TSS (NM_013670)	promoter-TSS (NM_013670)	73	NM_013670	20646	Mm.274995	NM_013670	ENSMUSG00000102252	Snrpn	2410045I01Rik|HCERN3|Peg4|Pwcr1|SMN	small nuclear ribonucleoprotein N	protein-coding
mm_8837.1	chr1	162675210	162675213	-	1	NA	intron (NM_001081290, intron 34 of 34)	intron (NM_001081290, intron 34 of 34)	-16992	NM_001177581	100038657	Mm.416999	NM_001177581	ENSMUSG00000091060	7420461P10Rik	ENSMUSG00000073516	RIKEN cDNA 7420461P10 gene	protein-coding
mm_122899.1	chr14	54952320	54952328	-	1	NA	exon (NM_010856, exon 25 of 39)	exon (NM_010856, exon 25 of 39)	-3182	NR_029724	387204		NR_029724	ENSMUSG00000065432	Mir208a	Mirn208|Mirn208a|mir-208|mir-208a|mmu-mir-208	microRNA 208a	ncRNA
mm_109856.1	chr12	4769071	4769088	-	1	NA	promoter-TSS (NM_028376)	promoter-TSS (NM_028376)	188	NM_175431	207921	Mm.184898	NM_175431	ENSMUSG00000050545	Fam228b	A830093I24Rik	family with sequence similarity 228, member B	protein-coding
mm_116932.1	chr13	55831231	55831261	-	1	NA	5' UTR (NM_011097, exon 1 of 3)	5' UTR (NM_011097, exon 1 of 3)	179	NM_011097	18740	Mm.135195	NM_011097	ENSMUSG00000021506	Pitx1	Bft|P-OTX|Potx|Ptx1	paired-like homeodomain transcription factor 1	protein-coding
mm_22188.1	chr2	173265935	173265939	-	1	NA	intron (NM_022995, intron 1 of 3)	intron (NM_022995, intron 1 of 3)	10596	NM_022995	65112	Mm.73682	NM_022995	ENSMUSG00000038400	Pmepa1	2210418I02Rik|AW455466|Erg1.2|N4wbp4|Stag1|Tmepai	prostate transmembrane protein, androgen induced 1	protein-coding
mm_102225.1	chr11	54910030	54910077	-	1	NA	TTS (NM_021327)	TTS (NM_021327)	7199	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_48174.1	chr5	137288657	137288668	-	1	NA	intron (NM_009599, intron 1 of 4)	intron (NM_009599, intron 1 of 4)	408	NM_001290010	11423	Mm.255464	NM_009599	ENSMUSG00000023328	Ache	-	acetylcholinesterase	protein-coding
mm_86922.1	chr10	23851558	23851580	+	1	NA	5' UTR (NM_011979, exon 1 of 7)	5' UTR (NM_011979, exon 1 of 7)	107	NM_011979	26464	Mm.27334	NM_011979	ENSMUSG00000020010	Vnn3	-	vanin 3	protein-coding
mm_55175.1	chr6	51990214	51990225	-	1	NA	intron (NM_018773, intron 4 of 12)	intron (NM_018773, intron 4 of 12)	22330	NM_018773	54353	Mm.221479	NM_018773	ENSMUSG00000059182	Skap2	2610021A10Rik|AA960083|BB137539|RA70|SKAP-HOM|Saps|Scap2|mSKAP55R	src family associated phosphoprotein 2	protein-coding
mm_115025.1	chr13	99100699	99100719	+	1	NA	Intergenic	Intergenic	-12788	NR_045495	69603	Mm.390632	NR_045495	ENSMUSG00000100410	2310020H05Rik	-	RIKEN cDNA 2310020H05 gene	ncRNA
mm_99271.1	chr11	101253721	101253757	+	1	NA	promoter-TSS (NM_026776)	promoter-TSS (NM_026776)	32	NM_026776	28084	Mm.301020	NM_026776	ENSMUSG00000078656	Vps25	1110020N13Rik|AW107467|D11Wsu68e	vacuolar protein sorting 25	protein-coding
mm_109176.1	chr12	108410881	108410899	+	1	NA	intron (NM_001286347, intron 1 of 22)	intron (NM_001286347, intron 1 of 22)	257	NM_001286347	68519	Mm.236645	NM_001043335	ENSMUSG00000058070	Eml1	1110008N23Rik|A930030P13Rik|AA171013|AI847476|AI853955|ELP79|EMAP|EMAPL|heco	echinoderm microtubule associated protein like 1	protein-coding
mm_74387.1	chr8	128724285	128724307	+	1	NA	exon (NM_010578, exon 14 of 16)	exon (NM_010578, exon 14 of 16)	38642	NM_010578	16412	Mm.263396	NM_010578	ENSMUSG00000025809	Itgb1	4633401G24Rik|AA409975|AA960159|CD29|ENSMUSG00000051907|Fnrb|Gm9863|gpIIa	integrin beta 1 (fibronectin receptor beta)	protein-coding
mm_113316.1	chr13	30764562	30764573	+	1	NA	3' UTR (NM_013674, exon 9 of 9)	3' UTR (NM_013674, exon 9 of 9)	15334	NM_013674	16364	Mm.4677	NM_013674	ENSMUSG00000021356	Irf4	AI385587|IRF-4|LSIRF|NF-EM5|Spip	interferon regulatory factor 4	protein-coding
mm_155637.1	chrX	85202620	85202631	+	1	NA	3' UTR (NM_007868, exon 79 of 79)	3' UTR (NM_007868, exon 79 of 79)	-47052	NM_028046	71996	Mm.20201	NM_028046	ENSMUSG00000035491	Fthl17a	1600014K23Rik|AI324104	ferritin, heavy polypeptide-like 17, member A	protein-coding
mm_166492.1	chr5	150129784	150129784	+	1	NA	Intergenic	B3|SINE|B2	111109	NM_001289566	140498	Mm.444643	NM_080468	ENSMUSG00000053368	Rxfp2	Gpr106|Great|Lgr8	relaxin/insulin-like family peptide receptor 2	protein-coding
mm_91932.1	chr10	60687213	60687232	-	1	NA	intron (NR_045556, intron 1 of 68)	CpG-1084	9268	NM_001252635	22295	Mm.440327	NM_023370	ENSMUSG00000012819	Cdh23	4930542A03Rik|USH1D|ahl|ahl1|bob|bus|mdfw|nmf112|nmf181|nmf252|sals|v	cadherin 23 (otocadherin)	protein-coding
mm_126211.1	chr15	78899756	78899775	+	1	NA	promoter-TSS (NM_009164)	promoter-TSS (NM_009164)	-3	NR_133564	20401	Mm.4462	NM_009164	ENSMUSG00000022436	Sh3bp1	3BP-1	SH3-domain binding protein 1	protein-coding
mm_172326.1	chr7	10699396	10699396	-	1	NA	intron (NM_172481, intron 2 of 8)	Lx2|LINE|L1	11603	NM_172481	210045	Mm.95244	NM_172481	ENSMUSG00000034087	Nlrp4b	AU022726|E330024M09|Nalp-gamma|Nalp4b	NLR family, pyrin domain containing 4B	protein-coding
mm_32936.1	chr4	119255495	119255504	+	1	NA	promoter-TSS (NM_153105)	promoter-TSS (NM_153105)	30	NM_001038590	242653	Mm.130701	NM_153105	ENSMUSG00000066058	Cldn19	-	claudin 19	protein-coding
mm_172340.1	chr7	110518469	110518471	+	1	NA	intron (NM_177324, intron 2 of 40)	ERVB7_1-LTR_MM|LTR|ERVK	96450	NM_177324	319934	Mm.102970	NM_177324	ENSMUSG00000038371	Sbf2	4833411B01Rik|AA414977|AI317167|B430219L04Rik|Mtmr13|mMTMH1	SET binding factor 2	protein-coding
mm_25517.1	chr3	114030485	114030493	+	1	NA	promoter-TSS (NM_007729)	promoter-TSS (NM_007729)	-51	NM_007729	12814	Mm.209715	NM_007729	ENSMUSG00000027966	Col11a1	C530001D20Rik|cho	collagen, type XI, alpha 1	protein-coding
mm_81471.1	chr9	109931543	109931552	+	1	NA	promoter-TSS (NM_008633)	promoter-TSS (NM_008633)	-227	NM_001205331	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_69761.1	chr7	141009714	141009723	-	1	NA	3' UTR (NM_025378, exon 2 of 2)	3' UTR (NM_025378, exon 2 of 2)	1026	NM_025378	66141	Mm.141021	NM_025378	ENSMUSG00000025492	Ifitm3	1110004C05Rik|Cd225|Cdw217|DSPA2b|Fgls|IP15|mil-1	interferon induced transmembrane protein 3	protein-coding
mm_17724.1	chr2	32424008	32424029	-	1	NA	promoter-TSS (NM_001290558)	promoter-TSS (NM_001290558)	48	NM_001290558	227731	Mm.37395	NM_146118	ENSMUSG00000026819	Slc25a25	1110030N17Rik|MCSC|mKIAA1896	solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 25	protein-coding
mm_127883.1	chr15	8643224	8643231	-	1	NA	intron (NM_148938, intron 6 of 9)	(A)n|Simple_repeat|Simple_repeat	67580	NM_148938	20512	Mm.204834	NM_148938	ENSMUSG00000005360	Slc1a3	AI504299|B430115D02Rik|Eaat1|GLAST|GLAST-1|GLU-T|GluT-1|Gmt1|MGluT1	solute carrier family 1 (glial high affinity glutamate transporter), member 3	protein-coding
mm_6279.1	chr1	69683276	69683286	-	1	NA	exon (NM_011770, exon 3 of 8)	exon (NM_011770, exon 3 of 8)	2679	NM_011770	22779	Mm.106343	NM_011770	ENSMUSG00000025997	Ikzf2	A730095J18Rik|Helios|Zfpn1a2|Znfn1a2	IKAROS family zinc finger 2	protein-coding
mm_27064.1	chr3	27711234	27711248	-	1	NA	promoter-TSS (NM_173182)	promoter-TSS (NM_173182)	-802	NM_173182	72007	Mm.38832	NM_173182	ENSMUSG00000039286	Fndc3b	1600019O04Rik|AW550168|Fad104|mKIAA4164	fibronectin type III domain containing 3B	protein-coding
mm_139653.1	chr17	57401171	57401205	+	1	NA	intron (NM_010130, intron 2 of 21)	L1VL2|LINE|L1	42502	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_32744.1	chr4	116649808	116649849	+	1	NA	intron (NM_021473, intron 1 of 8)	intron (NM_021473, intron 1 of 8)	1846	NM_021473	58810	Mm.30085	NM_021473	ENSMUSG00000028692	Akr1a1	2610201A18Rik|Akr1a4	aldo-keto reductase family 1, member A1 (aldehyde reductase)	protein-coding
mm_123010.1	chr14	55064015	55064052	-	1	NA	exon (NM_001039198, exon 9 of 10)	exon (NM_001039198, exon 9 of 10)	-9058	NR_004444	432855	Mm.490799	NR_004444	ENSMUSG00000093452	Zfhx2os	Zfhx2as	zinc finger homeobox 2, opposite strand	ncRNA
mm_164387.1	chr16	32118032	32118033	-	1	NA	Intergenic	L1ME3|LINE|L1	18230	NM_025892	66994	Mm.22990	NM_025892	ENSMUSG00000035790	Cep19	1500031L02Rik|AI428934|AL022620	centrosomal protein 19	protein-coding
mm_167132.1	chr7	126847708	126847759	+	1	NA	5' UTR (NM_010069, exon 1 of 11)	5' UTR (NM_010069, exon 1 of 11)	180	NM_010069	13446	Mm.266301	NM_010069	ENSMUSG00000052301	Doc2a	-	double C2, alpha	protein-coding
mm_115974.1	chr13	24155204	24155216	-	1	NA	intron (NM_001311122, intron 6 of 37)	intron (NM_001311122, intron 6 of 37)	125580	NM_001311122	68732	Mm.211047	NM_026825	ENSMUSG00000021338	Carmil1	1110037D04Rik|AI425970|CARMIL|CARML1|D130057M20|Lrrc16|Lrrc16a	capping protein regulator and myosin 1 linker 1	protein-coding
mm_133590.1	chr16	91425339	91425350	+	1	NA	3' UTR (NM_008349, exon 7 of 7)	3' UTR (NM_008349, exon 7 of 7)	19109	NM_008349	16155	Mm.4154	NM_008349	ENSMUSG00000022969	Il10rb	6620401D04Rik|AI528744|CRF2-4|Crfb4|D16H21S58|D21S58h|IL-10R2|Il10r2	interleukin 10 receptor, beta	protein-coding
mm_161868.1	chr18	36197022	36197022	-	1	NA	exon (NM_001167891, exon 1 of 10)	exon (NM_001167891, exon 1 of 10)	138	NM_001167891	100042150	Mm.380390	NM_001167891	ENSMUSG00000060275	Nrg2	Don1|NTAK	neuregulin 2	protein-coding
mm_100181.1	chr11	116624441	116624451	+	1	NA	promoter-TSS (NM_001167680)	promoter-TSS (NM_001167680)	-194	NM_001167680	217344	Mm.89695	NM_172572	ENSMUSG00000020806	Rhbdf2	4732465I17Rik|Rhbdl6|cub	rhomboid 5 homolog 2	protein-coding
mm_67764.1	chr7	92874197	92874244	-	1	NA	promoter-TSS (NM_001080995)	promoter-TSS (NM_001080995)	12	NM_001080995	74041	Mm.26468	NM_028729	ENSMUSG00000030641	Ddias	4632434I11Rik|noxin	DNA damage-induced apoptosis suppressor	protein-coding
mm_7341.1	chr1	105967715	105967786	-	1	NA	Intergenic	Lx9|LINE|L1	-22656	NM_001122676	227449	Mm.210188	NM_001122675	ENSMUSG00000038866	Zcchc2	9930114B20Rik|AW212015	zinc finger, CCHC domain containing 2	protein-coding
mm_74741.1	chr8	18902269	18902277	-	1	NA	Intergenic	Intergenic	48598	NM_001286469	319581	Mm.111354	NM_176951	ENSMUSG00000039814	Xkr5	5430438H03Rik|XRG5	X-linked Kx blood group related 5	protein-coding
mm_14845.1	chr2	148395339	148395356	+	1	NA	promoter-TSS (NM_009219)	promoter-TSS (NM_009219)	-30	NM_009219	20608	Mm.35324	NM_009219	ENSMUSG00000037014	Sstr4	Smstr4|sst4	somatostatin receptor 4	protein-coding
mm_111399.1	chr12	90739029	90739045	-	1	NA	promoter-TSS (NM_010050)	promoter-TSS (NM_010050)	0	NM_010050	13371	Mm.21389	NM_010050	ENSMUSG00000007682	Dio2	5DII|AI324267|DIOII	deiodinase, iodothyronine, type II	protein-coding
mm_163599.1	chr13	44528870	44528871	+	1	NA	Intergenic	MER90|LTR|ERV1	89143	NR_045489	69491	Mm.392410	NR_045489	ENSMUSG00000098144	1700029N11Rik	-	RIKEN cDNA 1700029N11 gene	ncRNA
mm_102179.1	chr11	54028612	54028630	-	1	NA	promoter-TSS (NM_001330304)	promoter-TSS (NM_001330304)	-517	NM_001330304	30805	Mm.274590	NM_019687	ENSMUSG00000020334	Slc22a4	Octn1	solute carrier family 22 (organic cation transporter), member 4	protein-coding
mm_44453.1	chr5	21785094	21785098	-	1	NA	promoter-TSS (NM_009584)	promoter-TSS (NM_009584)	69	NM_009584	22791	Mm.266312	NM_009584	ENSMUSG00000029014	Dnajc2	AU020218|MIDA1|Zrf1|Zrf2	DnaJ heat shock protein family (Hsp40) member C2	protein-coding
mm_38025.1	chr4	133814107	133814134	-	1	NA	Intergenic	CpG	-60509	NM_001080819	93760	Mm.22478	NM_001080819	ENSMUSG00000007880	Arid1a	1110030E03Rik|BAF250a|Osa1|Smarcf1	AT rich interactive domain 1A (SWI-like)	protein-coding
mm_102343.1	chr11	58073037	58073047	-	1	NA	Intergenic	Intergenic	-31111	NM_026949	69125	Mm.28910	NM_026949	ENSMUSG00000020515	Cnot8	1500015I04Rik|1810022F04Rik|AA536816|AU015770|AU043059	CCR4-NOT transcription complex, subunit 8	protein-coding
mm_110339.1	chr12	36039551	36039566	-	1	NA	intron (NM_025359, intron 1 of 5)	intron (NM_025359, intron 1 of 5)	2920	NM_025359	66109	Mm.254663	NM_025359	ENSMUSG00000020577	Tspan13	1100001I23Rik|NET-6|Tm4sf13	tetraspanin 13	protein-coding
mm_28611.1	chr3	94786431	94786466	-	1	NA	promoter-TSS (NM_001293727)	promoter-TSS (NM_001293727)	67	NM_001293727	70737	Mm.87634	NM_001037711	ENSMUSG00000068876	Cgn	6330408J11Rik	cingulin	protein-coding
mm_152530.1	chr19	11324556	11324638	-	1	NA	exon (NM_001276398, exon 5 of 7)	exon (NM_001276398, exon 5 of 7)	10098	NM_001276398	109225	Mm.491251	NM_027836	ENSMUSG00000024672	Ms4a7	9130422I10Rik|A430103C15Rik|CD20l4|CFFMA	membrane-spanning 4-domains, subfamily A, member 7	protein-coding
mm_31772.1	chr4	63554604	63554609	+	1	NA	Intergenic	Intergenic	-5754	NM_144905	230279	Mm.41523	NM_144905	ENSMUSG00000045917	Tmem268	6330416G13Rik|AW492431|bM230C2.2	transmembrane protein 268	protein-coding
mm_117090.1	chr13	59769752	59769826	-	1	NA	promoter-TSS (NR_015349)	promoter-TSS (NR_015349)	0	NM_026921	69046	Mm.7884	NM_026921	ENSMUSG00000044792	Isca1	1810010A06Rik|Hbld2	iron-sulfur cluster assembly 1	protein-coding
mm_69723.1	chr7	140760745	140760780	-	1	NA	Intergenic	Intergenic	-3070	NM_021282	13106	Mm.21758	NM_021282	ENSMUSG00000025479	Cyp2e1	Cyp2e	cytochrome P450, family 2, subfamily e, polypeptide 1	protein-coding
mm_12565.1	chr2	72979092	72979134	+	1	NA	promoter-TSS (NR_045269)	promoter-TSS (NR_045269)	168	NM_001098425	20687	Mm.124328	NM_011450	ENSMUSG00000027109	Sp3	D130027J01Rik	trans-acting transcription factor 3	protein-coding
mm_16701.1	chr2	6938431	6938436	-	1	NA	intron (NM_001110229, intron 2 of 14)	intron (NM_001110229, intron 2 of 14)	-9711	NR_027890	68144	Mm.483289	NM_026575		5031426D15Rik	-	RIKEN cDNA 5031426D15 gene	ncRNA
mm_51075.1	chr6	66896481	66896492	+	1	NA	promoter-TSS (NM_001177559)	promoter-TSS (NM_001177559)	89	NM_001177556	14701	Mm.234342	NM_025278	ENSMUSG00000036402	Gng12	2010305F15Rik|AA536815|AI115529|AI314170|AI842738	guanine nucleotide binding protein (G protein), gamma 12	protein-coding
mm_164059.1	chr14	109045200	109045204	+	1	NA	Intergenic	Lx8|LINE|L1	-130963	NM_199065	76965	Mm.257268	NM_199065	ENSMUSG00000075478	Slitrk1	3200001I04Rik	SLIT and NTRK-like family, member 1	protein-coding
mm_33808.1	chr4	135152537	135152554	+	1	NA	intron (NM_019732, intron 1 of 5)	CpG	31900	NM_019732	12399	Mm.378894	NM_019732	ENSMUSG00000070691	Runx3	AML2|Cbfa3|Pebp2a3	runt related transcription factor 3	protein-coding
mm_94616.1	chr11	16753321	16753333	+	1	NA	intron (NM_207655, intron 1 of 27)	intron (NM_207655, intron 1 of 27)	1124	NM_007912	13649	Mm.8534	NM_007912	ENSMUSG00000020122	Egfr	9030024J15Rik|AI552599|Erbb|Errb1|Errp|Wa5|wa-2|wa2	epidermal growth factor receptor	protein-coding
mm_35647.1	chr4	43523747	43523766	-	1	NA	promoter-TSS (NM_009416)	promoter-TSS (NM_009416)	-202	NM_001277875	22004	Mm.646	NM_009416	ENSMUSG00000028464	Tpm2	Tpm-2|Trop-2	tropomyosin 2, beta	protein-coding
mm_83692.1	chr9	50561321	50561331	-	1	NA	promoter-TSS (NM_025687)	promoter-TSS (NM_025687)	-58	NM_025687	66654	Mm.442255	NM_025687	ENSMUSG00000032065	Tex12	5730518K06Rik	testis expressed gene 12	protein-coding
mm_24046.1	chr3	87857972	87857978	+	1	NA	TTS (NM_033573)	TTS (NM_033573)	11220	NM_021309	27371	Mm.86361	NM_021309	ENSMUSG00000028071	Sh2d2a	Lad|Ribp|Tsad	SH2 domain containing 2A	protein-coding
mm_143517.1	chr17	73107842	73107876	-	1	NA	promoter-TSS (NM_001081071)	promoter-TSS (NM_001081071)	-126	NM_001177968	225010	Mm.329194	NM_001081071	ENSMUSG00000054469	Lclat1	AI181996|Agpat8|Alcat1|Gm91|Lycat	lysocardiolipin acyltransferase 1	protein-coding
mm_118597.1	chr14	20694957	20694985	+	1	NA	promoter-TSS (NM_028428)	promoter-TSS (NM_028428)	3	NM_028428	73068	Mm.277552	NM_028428	ENSMUSG00000039357	Fut11	3110009G03Rik|AI317183	fucosyltransferase 11	protein-coding
mm_123492.1	chr14	66124483	66124505	-	1	NA	promoter-TSS (NM_007940)	promoter-TSS (NM_007940)	28	NM_001271402	13850	Mm.15295	NM_007940	ENSMUSG00000022040	Ephx2	CEH|Eph2|SEH|sEP	epoxide hydrolase 2, cytoplasmic	protein-coding
mm_132105.1	chr16	31428871	31428881	+	1	NA	5' UTR (NM_001122683, exon 1 of 7)	5' UTR (NM_001122683, exon 1 of 7)	123	NM_001122683	71911	Mm.293470	NM_175177	ENSMUSG00000046598	Bdh1	2310032J20Rik|AI327223|Bdh	3-hydroxybutyrate dehydrogenase, type 1	protein-coding
mm_47741.1	chr5	130254377	130254431	-	1	NA	intron (NM_023248, intron 1 of 4)	intron (NM_023248, intron 1 of 4)	1126	NM_023248	66711	Mm.280484	NM_023248	ENSMUSG00000025337	Sbds	4733401P19Rik|AI836084|CGI-97|SDS	Shwachman-Bodian-Diamond syndrome homolog (human)	protein-coding
mm_64753.1	chr7	4812352	4812362	-	1	NA	promoter-TSS (NM_133777)	promoter-TSS (NM_133777)	-17	NM_133777	77891	Mm.389787	NM_133777	ENSMUSG00000060860	Ube2s	0910001J09Rik|6720465F12Rik|AA409170|E2-EPF	ubiquitin-conjugating enzyme E2S	protein-coding
mm_44637.1	chr5	28055441	28055464	-	1	NA	Intergenic	Intergenic	-15960	NM_153526	231070	Mm.30221	NM_153526	ENSMUSG00000045294	Insig1	1810013C12Rik|Insig-1	insulin induced gene 1	protein-coding
mm_92832.1	chr10	81482649	81482653	-	1	NA	promoter-TSS (NM_176954)	promoter-TSS (NM_176954)	58	NM_176954	319586	Mm.152689	NM_176954	ENSMUSG00000034818	Celf5	4930565A21Rik|Brunol5	CUGBP, Elav-like family member 5	protein-coding
mm_11532.1	chr2	32629302	32629308	+	1	NA	promoter-TSS (NM_021515)	promoter-TSS (NM_021515)	-195	NM_021515	11636	Mm.29189	NM_021515	ENSMUSG00000026817	Ak1	Ak-1|B430205N08Rik	adenylate kinase 1	protein-coding
mm_25354.1	chr3	107036157	107036181	+	1	NA	promoter-TSS (NM_008418)	promoter-TSS (NM_008418)	7	NM_008418	16491	Mm.30640	NM_008418	ENSMUSG00000047959	Kcna3	Kca1-3|Kv1.3|Mk-3	potassium voltage-gated channel, shaker-related subfamily, member 3	protein-coding
mm_84758.1	chr9	75597644	75597656	-	1	NA	intron (NM_016711, intron 1 of 9)	intron (NM_016711, intron 1 of 9)	1483	NM_001038710	50876	Mm.291880	NM_016711	ENSMUSG00000032186	Tmod2	N-Tmod|NTMOD	tropomodulin 2	protein-coding
mm_61977.1	chr7	90887283	90887312	+	1	NA	Intergenic	Intergenic	-203489	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_59707.1	chr7	28716778	28716840	+	1	NA	promoter-TSS (NM_015796)	promoter-TSS (NM_015796)	19	NM_015796	50760	Mm.358659	NM_015796	ENSMUSG00000030598	Fbxo17	Fbg4|Fbx17|Fbxo26	F-box protein 17	protein-coding
mm_107551.1	chr12	41024380	41024390	+	1	NA	intron (NM_053122, intron 1 of 6)	CpG	295	NM_053122	93757	Mm.363813	NM_053122	ENSMUSG00000056899	Immp2l	AI853880|IMP2	IMP2 inner mitochondrial membrane peptidase-like (S. cerevisiae)	protein-coding
mm_57824.1	chr6	129462956	129463002	-	1	NA	non-coding (NR_132130, exon 6 of 6)	non-coding (NR_132130, exon 6 of 6)	9800	NM_001309637	56644	Mm.239516	NM_020008	ENSMUSG00000079293	Clec7a	BGR|Clecsf12|beta-GR	C-type lectin domain family 7, member a	protein-coding
mm_2457.1	chr1	104768597	104768608	+	1	NA	promoter-TSS (NM_011800)	promoter-TSS (NM_011800)	-217	NM_011800	23836	Mm.103640	NM_011800	ENSMUSG00000050840	Cdh20	Cdh7	cadherin 20	protein-coding
mm_10687.1	chr2	22622184	22622200	+	1	NA	promoter-TSS (NM_008078)	promoter-TSS (NM_008078)	-135	NM_008078	14417	Mm.4784	NM_008078	ENSMUSG00000026787	Gad2	6330404F12Rik|GAD(65)|GAD65|Gad-2	glutamic acid decarboxylase 2	protein-coding
mm_95102.1	chr11	34047322	34047326	+	1	NA	5' UTR (NM_010696, exon 1 of 21)	5' UTR (NM_010696, exon 1 of 21)	123	NM_010696	16822	Mm.265350	NM_010696	ENSMUSG00000002699	Lcp2	AI323664|BB161688|SLP-76|SLP76|m1Khoe|twm	lymphocyte cytosolic protein 2	protein-coding
mm_46196.1	chr5	98030631	98030647	-	1	NA	5' UTR (NM_133738, exon 1 of 17)	5' UTR (NM_133738, exon 1 of 17)	323	NM_133738	71914	Mm.24842	NM_133738	ENSMUSG00000029338	Antxr2	2310046B19Rik|AW561899|CMG-2|CMG2|cI-35	anthrax toxin receptor 2	protein-coding
mm_159090.1	chr2	32315849	32315849	-	1	NA	non-coding (NR_125959, exon 16 of 22)	non-coding (NR_125959, exon 16 of 22)	-2416	NR_128563	104795665		NR_128563	ENSMUSG00000092765	Gm23363	Mir3154|mir-3154|mmu-mir-3154	predicted gene, 23363	ncRNA
mm_128902.1	chr15	73360436	73360451	-	1	NA	intron (NM_007982, intron 2 of 31)	intron (NM_007982, intron 2 of 31)	62748	NM_007982	14083	Mm.254494	NM_007982	ENSMUSG00000022607	Ptk2	FAK|FRNK|Fadk|mKIAA4203|p125FAK	PTK2 protein tyrosine kinase 2	protein-coding
mm_73427.1	chr8	106135465	106135480	+	1	NA	promoter-TSS (NR_040346)	promoter-TSS (NR_040346)	72	NR_040346	69771	Mm.393274	NR_040344		1810019D21Rik	-	RIKEN cDNA 1810019D21 gene	ncRNA
mm_148802.1	chr19	6263262	6263283	+	1	NA	TTS (NM_194348)	TTS (NM_194348)	-1371	NR_029830	723957		NR_029830	ENSMUSG00000065582	Mir194-2	Mirn194-2|mir-194-2	microRNA 194-2	ncRNA
mm_109954.1	chr12	11436608	11436618	-	1	NA	promoter-TSS (NM_012038)	promoter-TSS (NM_012038)	36	NM_012038	26950	Mm.27005	NM_012038	ENSMUSG00000054459	Vsnl1	VILIP|Vnsl1	visinin-like 1	protein-coding
mm_168895.1	chr12	50789972	50789975	-	1	NA	Intergenic	L1Md_F2|LINE|L1	-140750	NM_008858	18760	Mm.133719	NM_008858	ENSMUSG00000002688	Prkd1	PKD|PKD1|Pkcm|Prkcm	protein kinase D1	protein-coding
mm_121531.1	chr14	122280678	122280699	+	1	NA	intron (NM_029556, intron 1 of 7)	intron (NM_029556, intron 1 of 7)	-47050	NR_015532	68245	Mm.443285	NR_015532	ENSMUSG00000100585	1700108J01Rik	-	RIKEN cDNA 1700108J01 gene	ncRNA
mm_118891.1	chr14	26626870	26626896	+	1	NA	exon (NM_001285466, exon 15 of 18)	exon (NM_001285466, exon 15 of 18)	-11314	NM_007479	11843	Mm.297768	NM_007479	ENSMUSG00000021877	Arf4	AA407803	ADP-ribosylation factor 4	protein-coding
mm_77021.1	chr8	108584541	108584556	-	1	NA	non-coding (NR_077224, exon 1 of 2)	non-coding (NR_077224, exon 1 of 2)	129	NR_077224	109215	Mm.65282	NR_077224	ENSMUSG00000110613	Lncbate1	3010033K07Rik|Lnc-BATE1	brown adipose tissue enriched long non-coding RNA 1	ncRNA
mm_49104.1	chr6	8217383	8217386	+	1	NA	intron (NM_145374, intron 4 of 11)	intron (NM_145374, intron 4 of 11)	8157	NM_145374	252875	Mm.257151	NM_145374	ENSMUSG00000042447	Mios	C81488	missing oocyte, meiosis regulator, homolog (Drosophila)	protein-coding
mm_144552.1	chr18	31568419	31568421	+	1	NA	Intergenic	MMERGLN_LTR|LTR|ERV1	41482	NM_026165	67453	Mm.23896	NM_026165	ENSMUSG00000024259	Slc25a46	1200007B05Rik|AI325987	solute carrier family 25, member 46	protein-coding
mm_166938.1	chr7	40541086	40541087	-	1	NA	Intergenic	PB1D7|SINE|Alu	-133651	NR_045504	71029	Mm.399496	NR_045504	ENSMUSG00000102004	4933402C06Rik	-	RIKEN cDNA 4933402C06 gene	ncRNA
mm_20040.1	chr2	120090072	120090087	-	1	NA	3' UTR (NM_133838, exon 6 of 6)	3' UTR (NM_133838, exon 6 of 6)	56646	NM_145378	211429	Mm.41467	NM_145378	ENSMUSG00000098488	Pla2g4b	A030011C02Rik|Gm1013|cPLA2-beta	phospholipase A2, group IVB (cytosolic)	protein-coding
mm_86178.1	chr9	119190314	119190318	-	1	NA	promoter-TSS (NM_001037749)	promoter-TSS (NM_001037749)	77	NM_001037749	382113	Mm.335525	NM_001037749	ENSMUSG00000070280	Slc22a14	Gm1128	solute carrier family 22 (organic cation transporter), member 14	protein-coding
mm_43538.1	chr5	137350163	137350177	+	1	NA	promoter-TSS (NM_010144)	promoter-TSS (NM_010144)	61	NM_010144	13846	Mm.34533	NM_010144	ENSMUSG00000029710	Ephb4	AI042935|Htk|MDK2|Myk1|Tyro11	Eph receptor B4	protein-coding
mm_140097.1	chr17	78264829	78264833	+	1	NA	intron (NM_015800, intron 2 of 16)	intron (NM_015800, intron 2 of 16)	64583	NM_015800	50766	Mm.311912	NM_015800	ENSMUSG00000024074	Crim1	AU015004	cysteine rich transmembrane BMP regulator 1 (chordin like)	protein-coding
mm_158566.1	chrX	150458804	150458808	-	1	NA	intron (NM_001164683, intron 1 of 2)	intron (NM_001164683, intron 1 of 2)	344	NM_001164683	382245	Mm.277309	NM_001164683	ENSMUSG00000041353	Tmem29	2700081K05Rik|6330540D07Rik|CXorf44-like	transmembrane protein 29	protein-coding
mm_87693.1	chr10	59582327	59582338	+	1	NA	intron (NM_001033259, intron 1 of 7)	ID4_|SINE|ID	34360	NM_001033259	215999	Mm.296470	NM_001033259	ENSMUSG00000009647	Mcu	2010012O16Rik|AV064928|C10orf42|Ccdc109a|D130073L02Rik|Gm64	mitochondrial calcium uniporter	protein-coding
mm_150114.1	chr19	29703793	29703806	+	1	NA	intron (NM_029993, intron 2 of 4)	intron (NM_029993, intron 2 of 4)	5858	NM_029993	77836	Mm.138437	NM_029993	ENSMUSG00000024806	Mlana	A930034P04Rik|Mart1	melan-A	protein-coding
mm_121896.1	chr14	21831124	21831129	-	1	NA	promoter-TSS (NM_011695)	promoter-TSS (NM_011695)	-435	NM_011695	22334	Mm.262327	NM_011695	ENSMUSG00000021771	Vdac2	Vdac6|mVDAC2|mVDAC6	voltage-dependent anion channel 2	protein-coding
mm_170663.1	chr2	113920538	113920538	-	1	NA	Intergenic	Intergenic	-71877	NM_181416	228482	Mm.45753	NM_181416	ENSMUSG00000041219	Arhgap11a	6530401L14Rik|mKIAA0013	Rho GTPase activating protein 11A	protein-coding
mm_118760.1	chr14	22405464	22405466	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	137333	NR_046307	74896	Mm.444661	NR_046307		4930405A10Rik	4930456G20Rik	RIKEN cDNA 4930405A10 gene	ncRNA
mm_150339.1	chr19	34576120	34576131	+	1	NA	3' UTR (NM_008332, exon 3 of 3)	3' UTR (NM_008332, exon 3 of 3)	-7404	NM_010501	15959	Mm.426079	NM_010501	ENSMUSG00000074896	Ifit3	Ifi49|P49	interferon-induced protein with tetratricopeptide repeats 3	protein-coding
mm_113017.1	chr13	21981453	21981504	+	1	NA	5' UTR (NM_001162929, exon 1 of 2)	5' UTR (NM_001162929, exon 1 of 2)	284	NM_001162929	195236	Mm.204664	NM_001162928	ENSMUSG00000016982	Pom121l2	Gm24	POM121 membrane glycoprotein-like 2 (rat)	protein-coding
mm_130233.1	chr15	96460872	96460926	-	1	NA	promoter-TSS (NM_028148)	promoter-TSS (NM_028148)	-56	NM_028148	72193	Mm.324474	NM_028148	ENSMUSG00000033228	Scaf11	1110061H03Rik|2610510E10Rik|AI462454|CASP11|SIP1|SRRP129|Sfrs2ip|Srsf2ip|mKIAA3013	SR-related CTD-associated factor 11	protein-coding
mm_146388.1	chr18	82692590	82692630	+	1	NA	intron (NM_177832, intron 1 of 29)	C-rich|Low_complexity|Low_complexity	124	NM_177832	329002	Mm.34438	NM_177832	ENSMUSG00000041258	Zfp236	AI447957|Gm335	zinc finger protein 236	protein-coding
mm_133201.1	chr16	73072364	73072366	+	1	NA	Intergenic	MTC-int|LTR|ERVL-MaLR	409216	NM_019413	19876	Mm.310772	NM_019413	ENSMUSG00000022883	Robo1	AW494633|AW742721|DUTT1|Gm310	roundabout guidance receptor 1	protein-coding
mm_155990.1	chrX	106143873	106143877	+	1	NA	intron (NM_205820, intron 1 of 2)	intron (NM_205820, intron 1 of 2)	600	NM_205820	279572	Mm.336203	NM_205820	ENSMUSG00000033777	Tlr13	AI666735|Gm713	toll-like receptor 13	protein-coding
mm_158903.1	chr1	34579568	34579568	+	1	NA	promoter-TSS (NM_213727)	promoter-TSS (NM_213727)	-125	NM_213727	211383	Mm.330696	NM_213727	ENSMUSG00000045174	Amer3	9430069J07Rik|Fam123c	APC membrane recruitment 3	protein-coding
mm_81760.1	chr9	114057429	114057449	+	1	NA	promoter-TSS (NM_001101510)	promoter-TSS (NM_001101510)	85	NM_001101510	382111	Mm.376140	NM_001101510	ENSMUSG00000086596	Susd5	Gm1126	sushi domain containing 5	protein-coding
mm_79458.1	chr9	56418388	56418399	+	1	NA	promoter-TSS (NM_025812)	promoter-TSS (NM_025812)	-343	NM_172924	244895	Mm.490331	NM_172924	ENSMUSG00000074305	Peak1	1110049L02Rik|9530046P14|AA690169|BE132841|C230081A13Rik|SGK269|mKIAA2002	pseudopodium-enriched atypical kinase 1	protein-coding
mm_103911.1	chr11	83588157	83588167	-	1	NA	3' UTR (NM_009139, exon 4 of 4)	3' UTR (NM_009139, exon 4 of 4)	4925	NM_009139	20305	Mm.137	NM_009139	ENSMUSG00000018927	Ccl6	MRP-1|Scya6|c10	chemokine (C-C motif) ligand 6	protein-coding
mm_139456.1	chr17	55952745	55952758	+	1	NA	5' UTR (NM_015766, exon 1 of 5)	5' UTR (NM_015766, exon 1 of 5)	128	NM_015766	50498	Mm.256798	NM_015766	ENSMUSG00000003206	Ebi3	EBI-3|IL-27	Epstein-Barr virus induced gene 3	protein-coding
mm_162858.1	chr10	90892627	90892634	-	1	NA	intron (NM_001347053, intron 1 of 8)	intron (NM_001347053, intron 1 of 8)	62787	NM_001347053	77531	Mm.440605	NM_181398	ENSMUSG00000058589	Anks1b	AIDA-1b|C030032C09Rik|E530015N03Rik|ENSMUSG00000078431|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding
mm_19910.1	chr2	114228677	114228681	-	1	NA	Intergenic	BC1_Mm|scRNA|scRNA	-27247	NM_175466	228491	Mm.132523	NM_175466	ENSMUSG00000040321	Zfp770	6430601A21Rik|Znf770	zinc finger protein 770	protein-coding
mm_91621.1	chr10	41716434	41716463	-	1	NA	Intergenic	Intergenic	93215	NM_001243075	103268	Mm.338605	NM_026643	ENSMUSG00000019813	Cep57l1	2410017P07Rik|4930484D11Rik|AI607327|cep57R	centrosomal protein 57-like 1	protein-coding
mm_134905.1	chr16	30258355	30258366	-	1	NA	3' UTR (NM_027904, exon 2 of 2)	3' UTR (NM_027904, exon 2 of 2)	9172	NM_027904	71756	Mm.290614	NM_027904	ENSMUSG00000023176	Cpn2	1300018K11Rik	carboxypeptidase N, polypeptide 2	protein-coding
mm_136760.1	chr17	8801461	8801497	+	1	NA	promoter-TSS (NM_011866)	promoter-TSS (NM_011866)	-266	NM_011866	23984	Mm.87161	NM_011866	ENSMUSG00000023868	Pde10a	-	phosphodiesterase 10A	protein-coding
mm_132563.1	chr16	38089482	38089536	+	1	NA	promoter-TSS (NR_033221)	promoter-TSS (NR_033221)	-249	NR_033221	414072	Mm.483602	NR_033221		BC031361	-	cDNA sequence BC031361	ncRNA
mm_54872.1	chr6	42601617	42601623	-	1	NA	Intergenic	Intergenic	-4248	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_170883.1	chr2	21062882	21062884	+	1	NA	Intergenic	B1_Mm|SINE|Alu	94009	NR_033225	433408	Mm.386941	NR_033225		Gm13375	OTTMUSG00000011664	predicted gene 13375	ncRNA
mm_1871.1	chr1	85600673	85600704	+	1	NA	promoter-TSS (NM_001013817)	promoter-TSS (NM_001013817)	-15	NM_001013817	434484	Mm.445821	NM_001013817	ENSMUSG00000070031	Sp140	-	Sp140 nuclear body protein	protein-coding
mm_16391.1	chr2	178850619	178850637	+	1	NA	Intergenic	Intergenic	420113	NM_198656	381409	Mm.330860	NM_198656	ENSMUSG00000039155	Cdh26	Gm1010	cadherin-like 26	protein-coding
mm_3347.1	chr1	138137415	138137424	+	1	NA	intron (NM_001111316, intron 1 of 31)	intron (NM_001111316, intron 1 of 31)	37707	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_53666.1	chr6	141629500	141629527	+	1	NA	promoter-TSS (NM_020495)	promoter-TSS (NM_020495)	-5	NM_020495	28253	Mm.272223	NM_020495	ENSMUSG00000030236	Slco1b2	7330442B20Rik|OATP-C|OATP2|Oatp1b2|Oatp4|Slc21a10|Slc21a6|lst-1|mlst-1	solute carrier organic anion transporter family, member 1b2	protein-coding
mm_125573.1	chr15	59323610	59323645	+	1	NA	exon (NM_009270, exon 5 of 11)	exon (NM_009270, exon 5 of 11)	8535	NM_009270	20775	Mm.296169	NM_009270	ENSMUSG00000022351	Sqle	AI323792	squalene epoxidase	protein-coding
mm_134272.1	chr16	13986875	13986906	-	1	NA	promoter-TSS (NM_001270718)	promoter-TSS (NM_001270718)	-23	NM_001270718	74482	Mm.484026	NM_028968	ENSMUSG00000065968	Ifitm7	4933438K12Rik|Mil4	interferon induced transmembrane protein 7	protein-coding
mm_82128.1	chr9	123510525	123510536	+	1	NA	exon (NM_013860, exon 3 of 8)	exon (NM_013860, exon 3 of 8)	-19352	NM_030692	83493	Mm.273671	NM_030692	ENSMUSG00000025240	Sacm1l	SAC1|Sac1p|mKIAA0851	SAC1 suppressor of actin mutations 1-like (yeast)	protein-coding
mm_153304.1	chr19	38022615	38022627	-	1	NA	exon (NM_001099634, exon 3 of 53)	exon (NM_001099634, exon 3 of 53)	20956	NM_001099634	226101	Mm.34674	NM_177035	ENSMUSG00000048612	Myof	2310004N10Rik|2310051D19Rik|E030042N20Rik|Fer1l3	myoferlin	protein-coding
mm_19644.1	chr2	102861641	102861691	-	1	NA	exon (NM_009851, exon 3 of 19)	exon (NM_009851, exon 3 of 19)	39999	NM_001177785	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_123018.1	chr14	55116205	55116226	-	1	NA	5' UTR (NM_177049, exon 1 of 6)	5' UTR (NM_177049, exon 1 of 6)	720	NM_177049	319984	Mm.19047	NM_177049	ENSMUSG00000022208	Jph4	9330157P13Rik|JP-4|JPHL1	junctophilin 4	protein-coding
mm_129489.1	chr15	78773453	78773486	-	1	NA	promoter-TSS (NM_008595)	promoter-TSS (NM_008595)	-24	NM_008595	17305	Mm.149235	NM_008595	ENSMUSG00000018169	Mfng	AW546563	MFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	protein-coding
mm_112021.1	chr12	111442301	111442309	-	1	NA	promoter-TSS (NM_009396)	promoter-TSS (NM_009396)	-356	NM_009396	21928	Mm.255332	NM_009396	ENSMUSG00000021281	Tnfaip2	B94|Exoc3l3|M-sec|Tnfip2|tnfb94	tumor necrosis factor, alpha-induced protein 2	protein-coding
mm_45132.1	chr5	48786925	48786925	-	1	NA	intron (NM_001199244, intron 1 of 7)	intron (NM_001199244, intron 1 of 7)	102632	NM_030265	80334	Mm.160172	NM_030265	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding
mm_25970.1	chr3	132843097	132843129	+	1	NA	intron (NR_102297, intron 3 of 3)	GA-rich|Low_complexity|Low_complexity	35483	NR_102297	101243624	Mm.306256	NR_102297	ENSMUSG00000106230	Gm29811	-	predicted gene, 29811	ncRNA
mm_142575.1	chr17	46680765	46680775	-	1	NA	promoter-TSS (NM_010787)	promoter-TSS (NM_010787)	-13	NM_001277311	17256	Mm.329083	NM_010787	ENSMUSG00000002768	Mea1	Mea-1	male enhanced antigen 1	protein-coding
mm_112553.1	chr13	12468858	12468877	+	1	NA	Intergenic	PB1D7|SINE|Alu	-7129	NM_001291057	56048	Mm.474138	NM_018886	ENSMUSG00000057554	Lgals8	1200015E08Rik|AI326142|D13Ertd524e|Lgals-8	lectin, galactose binding, soluble 8	protein-coding
mm_151908.1	chr19	5799530	5799536	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	3139	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_112793.1	chr13	20240807	20240814	+	1	NA	intron (NM_080288, intron 4 of 21)	intron (NM_080288, intron 4 of 21)	150303	NM_080288	140580	Mm.342392	NM_080288	ENSMUSG00000041112	Elmo1	6330578D22Rik|C230095H21Rik|CED-12	engulfment and cell motility 1	protein-coding
mm_15955.1	chr2	165992626	165992667	+	1	NA	promoter-TSS (NM_008679)	promoter-TSS (NM_008679)	9	NM_008679	17979	Mm.469663	NM_008679	ENSMUSG00000027678	Ncoa3	2010305B15Rik|AW321064|Actr|Aib1|KAT13B|Rac3|Src3|Tram-1|Tram1|bHLHe42|p/Cip|pCip	nuclear receptor coactivator 3	protein-coding
mm_114627.1	chr13	76115273	76115278	+	1	NA	intron (NM_001081352, intron 9 of 43)	intron (NM_001081352, intron 9 of 43)	16541	NM_001081352	218343	Mm.277964	NM_001081352	ENSMUSG00000033991	Ttc37	mKIAA0372	tetratricopeptide repeat domain 37	protein-coding
mm_80708.1	chr9	92250125	92250127	+	1	NA	promoter-TSS (NM_011636)	promoter-TSS (NM_011636)	-68	NM_011636	22038	Mm.421956	NM_011636	ENSMUSG00000032369	Plscr1	MmTRA1a|MmTRA1b|Nor1|Tra1|Tra1a|Tra1b|Tras1|Tras2	phospholipid scramblase 1	protein-coding
mm_38058.1	chr4	134012382	134012404	-	1	NA	intron (NM_145833, intron 2 of 3)	intron (NM_145833, intron 2 of 3)	6423	NM_145833	83557	Mm.302567	NM_145833	ENSMUSG00000050966	Lin28a	AL024421|ENSMUSG00000070700|Gm10299|Lin-28|Lin28|Tex17|lin-28A	lin-28 homolog A (C. elegans)	protein-coding
mm_30351.1	chr3	151749557	151749617	-	1	NA	5' UTR (NM_133871, exon 2 of 8)	5' UTR (NM_133871, exon 2 of 8)	372	NM_133871	99899	Mm.30756	NM_133871	ENSMUSG00000028037	Ifi44	A430056A10Rik|AW261460|MTAP44|p44	interferon-induced protein 44	protein-coding
mm_90557.1	chr10	128190484	128190500	+	1	NA	Intergenic	B2_Mm2|SINE|B2	-4143	NM_001285777	216456	Mm.30102	NM_001033264	ENSMUSG00000044005	Gls2	A330074B06Rik|AI195532|GA|GLS|Lga	glutaminase 2 (liver, mitochondrial)	protein-coding
mm_108443.1	chr12	82420456	82420469	+	1	NA	intron (NM_172579, intron 11 of 20)	intron (NM_172579, intron 11 of 20)	109113	NM_172579	217692	Mm.261333	NM_172579	ENSMUSG00000042700	Sipa1l1	4931426N11Rik|AW213287|Spar|mKIAA0440	signal-induced proliferation-associated 1 like 1	protein-coding
mm_131385.1	chr16	14205501	14205529	+	1	NA	exon (NM_013607, exon 33 of 42)	exon (NM_013607, exon 33 of 42)	42240	NM_001114085	67203	Mm.24105	NM_023317	ENSMUSG00000022678	Nde1	2810027M15Rik|AU042936|AW822251|Nude|mNudE	nudE neurodevelopment protein 1	protein-coding
mm_16436.1	chr2	180394467	180394496	+	1	NA	intron (NR_045331, intron 3 of 3)	intron (NR_045331, intron 3 of 3)	-3898	NR_029901	723954		NR_029901	ENSMUSG00000065460	Mir133a-2	Mirn133a-2|mir-133a-2	microRNA 133a-2	ncRNA
mm_78949.1	chr9	45138617	45138631	+	1	NA	promoter-TSS (NM_001013390)	promoter-TSS (NM_001013390)	-418	NM_001013390	399548	Mm.335112	NM_001013390	ENSMUSG00000046480	Scn4b	Gm1471	sodium channel, type IV, beta	protein-coding
mm_17626.1	chr2	31031859	31031862	-	1	NA	intron (NM_001038700, intron 14 of 14)	A-rich|Low_complexity|Low_complexity	49581	NM_028846	74270	Mm.346654	NM_028846	ENSMUSG00000026854	Usp20	1700055M05Rik|AI467231|Vdu2	ubiquitin specific peptidase 20	protein-coding
mm_96262.1	chr11	62648687	62648700	+	1	NA	promoter-TSS (NM_175002)	promoter-TSS (NM_175002)	29	NM_175002	216829	Mm.295306	NM_175002	ENSMUSG00000048497	Mmgt2	AI852046	membrane magnesium transporter 2	protein-coding
mm_5025.1	chr1	193173737	193173757	+	1	NA	5' UTR (NM_181048, exon 1 of 2)	5' UTR (NM_181048, exon 1 of 2)	170	NM_181048	319266	Mm.482460	NM_181048	ENSMUSG00000079144	A130010J15Rik	-	RIKEN cDNA A130010J15 gene	protein-coding
mm_79701.1	chr9	60840722	60840735	+	1	NA	intron (NM_028283, intron 1 of 18)	intron (NM_028283, intron 1 of 18)	46180	NM_028283	72565	Mm.68819	NM_028283	ENSMUSG00000034485	Uaca	2700059D02Rik|nucling	uveal autoantigen with coiled-coil domains and ankyrin repeats	protein-coding
mm_162341.1	chr1	47659353	47659356	+	1	NA	Intergenic	Intergenic	-192229	NR_105768	102466969		NR_105768	ENSMUSG00000098876	Mir6350	Gm27958|mmu-mir-6350	microRNA 6350	ncRNA
mm_146204.1	chr18	76343056	76343062	+	1	NA	Intergenic	Intergenic	80614	NM_001311070	17126	Mm.152699	NM_010754	ENSMUSG00000024563	Smad2	7120426M23Rik|Madh2|Madr2|Smad-2|mMad2	SMAD family member 2	protein-coding
mm_86173.1	chr9	119184127	119184153	-	1	NA	intron (NM_001037749, intron 1 of 11)	intron (NM_001037749, intron 1 of 11)	6253	NM_001037749	382113	Mm.335525	NM_001037749	ENSMUSG00000070280	Slc22a14	Gm1128	solute carrier family 22 (organic cation transporter), member 14	protein-coding
mm_43533.1	chr5	137294642	137294665	+	1	NA	promoter-TSS (NM_027356)	promoter-TSS (NM_027356)	-16	NM_027356	70240	Mm.124666	NM_027356	ENSMUSG00000051502	Ufsp1	2700038N03Rik|D5Ertd655e	UFM1-specific peptidase 1	protein-coding
mm_2859.1	chr1	131688772	131688784	+	1	NA	promoter-TSS (NM_145509)	promoter-TSS (NM_145509)	83	NM_001311096	226421	Mm.44508	NM_145509	ENSMUSG00000052688	Rab7b	5430435G22Rik	RAB7B, member RAS oncogene family	protein-coding
mm_134294.1	chr16	14270076	14270080	-	1	NA	intron (NM_001161775, intron 2 of 40)	B1_Mm|SINE|Alu	21330	NM_001161775	17880	Mm.250705	NM_013607	ENSMUSG00000018830	Myh11	AV071570|SM1|SM2|smMHC	myosin, heavy polypeptide 11, smooth muscle	protein-coding
mm_122642.1	chr14	51256124	51256138	-	1	NA	promoter-TSS (NM_053113)	promoter-TSS (NM_053113)	-19	NM_053113	93726	Mm.153688	NM_053113	ENSMUSG00000047222	Rnase2a	Ear11	ribonuclease, RNase A family, 2A (liver, eosinophil-derived neurotoxin)	protein-coding
mm_66352.1	chr7	43527453	43527456	-	1	NA	TTS (NM_001111058)	TTS (NM_001111058)	5717	NM_001111058	12489	Mm.140157	NM_021293	ENSMUSG00000004609	Cd33	Siglec-3|gp67	CD33 antigen	protein-coding
mm_14438.1	chr2	130667792	130667848	+	1	NA	promoter-TSS (NM_025922)	promoter-TSS (NM_025922)	-21	NM_025922	16434	Mm.21399	NM_025922	ENSMUSG00000074797	Itpa	2010016I08Rik|AU020102|Itp	inosine triphosphatase (nucleoside triphosphate pyrophosphatase)	protein-coding
mm_127935.1	chr15	10496278	10496290	-	1	NA	3' UTR (NM_001289448, exon 6 of 6)	3' UTR (NM_001289448, exon 6 of 6)	10246	NM_001289447	19355	Mm.38376	NM_011232	ENSMUSG00000022248	Rad1	mRAD1	RAD1 checkpoint DNA exonuclease	protein-coding
mm_164112.1	chr15	30033557	30033582	+	1	NA	Intergenic	Intergenic	-139024	NM_008729	18163	Mm.321648	NM_008729	ENSMUSG00000022240	Ctnnd2	Catnd2|Nprap|neurojugin	catenin (cadherin associated protein), delta 2	protein-coding
mm_128896.1	chr15	73268368	73268370	-	1	NA	intron (NM_001130409, intron 18 of 29)	intron (NM_001130409, intron 18 of 29)	-13487	NR_029561	387169		NR_029561	ENSMUSG00000065612	Mir151	Mirn151|mir-151|mmu-mir-151	microRNA 151	ncRNA
mm_80228.1	chr9	72663756	72663769	+	1	NA	intron (NM_010890, intron 1 of 28)	intron (NM_010890, intron 1 of 28)	1415	NM_010890	17999	Mm.279923	NM_010890	ENSMUSG00000032216	Nedd4	AA959633|AL023035|AU019897|E430025J12Rik|Nedd4-1|Nedd4a|mKIAA0093	neural precursor cell expressed, developmentally down-regulated 4	protein-coding
mm_30593.1	chr4	6365675	6365688	+	1	NA	promoter-TSS (NM_016807)	promoter-TSS (NM_016807)	1	NM_001098227	53378	Mm.247473	NM_016807	ENSMUSG00000028249	Sdcbp	MDA-9|Sycl|syntenin-1	syndecan binding protein	protein-coding
mm_62152.1	chr7	97133746	97133778	+	1	NA	intron (NM_001162477, intron 1 of 9)	L1_Mur1|LINE|L1	52011	NM_010248	14389	Mm.42033	NM_010248	ENSMUSG00000004508	Gab2	AI463667|D130058I17Rik|p97	growth factor receptor bound protein 2-associated protein 2	protein-coding
mm_137675.1	chr17	28801092	28801145	+	1	NA	promoter-TSS (NM_001081315)	promoter-TSS (NM_001081315)	-8	NM_001081315	268936	Mm.291877	NM_199061	ENSMUSG00000063952	Brpf3	AI413466|AW493400|mKIAA1286	bromodomain and PHD finger containing, 3	protein-coding
mm_125941.1	chr15	76248062	76248072	+	1	NA	promoter-TSS (NR_105918)	promoter-TSS (NR_105918)	-124	NR_105918	102465575		NR_105918	ENSMUSG00000098625	Mir6953	Gm27738|mmu-mir-6953	microRNA 6953	ncRNA
mm_59497.1	chr7	27537574	27537596	+	1	NA	exon (NM_011116, exon 10 of 14)	exon (NM_011116, exon 10 of 14)	14324	NM_001033315	233020	Mm.429716	NM_001033315	ENSMUSG00000040424	Hipk4	Gm162	homeodomain interacting protein kinase 4	protein-coding
mm_32076.1	chr4	98111476	98111480	+	1	NA	3' UTR (NM_001122953, exon 10 of 10)	3' UTR (NM_001122953, exon 10 of 10)	271787	NM_053157	94043	Mm.331719	NM_053157	ENSMUSG00000028563	Tm2d1	2310026L18Rik|AA990549|Bbp	TM2 domain containing 1	protein-coding
mm_141392.1	chr17	29189092	29189107	-	1	NA	intron (NM_153166, intron 8 of 20)	intron (NM_153166, intron 8 of 20)	48691	NM_153166	240058	Mm.39905	NM_153166	ENSMUSG00000024008	Cpne5	A830083G22Rik	copine V	protein-coding
mm_10856.1	chr2	25054397	25054440	+	1	NA	promoter-TSS (NM_020276)	promoter-TSS (NM_020276)	39	NM_001177655	56876	Mm.42956	NM_020276	ENSMUSG00000006476	Nsmf	Jacob|Nelf	NMDA receptor synaptonuclear signaling and neuronal migration factor	protein-coding
mm_133299.1	chr16	77530742	77530772	+	1	NA	intron (NR_015543, intron 4 of 4)	RMER6C|LTR|ERVK	-68179	NR_029535	387229		NR_029535	ENSMUSG00000065530	Mir99a	Mirn99a|mir-99a|mmu-mir-99a	microRNA 99a	ncRNA
mm_79897.1	chr9	65346092	65346129	+	1	NA	promoter-TSS (NM_016688)	promoter-TSS (NM_016688)	42	NM_016688	50996	Mm.29193	NM_016688	ENSMUSG00000041837	Pdcd7	C80112|ES18	programmed cell death 7	protein-coding
mm_83846.1	chr9	54489198	54489201	-	1	NA	intron (NM_172771, intron 1 of 43)	B1F|SINE|Alu	12427	NM_172771	235380	Mm.93636	NM_172771	ENSMUSG00000041268	Dmxl2	6330586A12|6430411K14Rik|E130119P06Rik|mKIAA0856	Dmx-like 2	protein-coding
mm_59457.1	chr7	27195842	27195885	+	1	NA	promoter-TSS (NM_001046637)	promoter-TSS (NM_001046637)	82	NM_001243888	414069	Mm.379069	NM_001243888	ENSMUSG00000078786	BC024978	-	cDNA sequence BC024978	protein-coding
mm_16104.1	chr2	169632997	169633016	+	1	NA	promoter-TSS (NM_080455)	promoter-TSS (NM_080455)	-640	NM_080455	228911	Mm.315789	NM_080455	ENSMUSG00000047907	Tshz2	2900073F20Rik|B830045G17|Mtsh2|Sdccag33l|Tsh2|Zfp218|mKIAA4248|teashirt2	teashirt zinc finger family member 2	protein-coding
mm_84672.1	chr9	72028506	72028509	-	1	NA	intron (NM_001253862, intron 3 of 19)	AT_rich|Low_complexity|Low_complexity	65066	NR_029879	723889		NR_029879	ENSMUSG00000105200	Mir378a	Mir378|Mirn378|mmu-mir-378|mmu-mir-378a	microRNA 378a	ncRNA
mm_136349.1	chr16	92694923	92694926	-	1	NA	intron (NM_001111023, intron 1 of 5)	intron (NM_001111023, intron 1 of 5)	2405	NM_001111023	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_49295.1	chr6	17694052	17694091	+	1	NA	promoter-TSS (NM_001289625)	promoter-TSS (NM_001289625)	77	NM_001289625	64213	Mm.12051	NM_022332	ENSMUSG00000029534	St7	9430001H04Rik|Fam4a2|HELG|RAY1|SEN4|TSG7	suppression of tumorigenicity 7	protein-coding
mm_148815.1	chr19	6297944	6297969	+	1	NA	intron (NM_010119, intron 4 of 4)	intron (NM_010119, intron 4 of 4)	-8501	NM_001033342	240505	Mm.329622	NM_001033342	ENSMUSG00000024769	Cdc42bpg	BC046418|MRCKgamma	CDC42 binding protein kinase gamma (DMPK-like)	protein-coding
mm_26276.1	chr3	142505496	142505504	+	1	NA	exon (NM_153564, exon 7 of 11)	exon (NM_153564, exon 7 of 11)	8566	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_151833.1	chr19	5688615	5688706	-	1	NA	promoter-TSS (NM_022012)	promoter-TSS (NM_022012)	248	NM_144868	104401	Mm.329650	NM_144868	ENSMUSG00000054874	Pcnx3	Pcnxl3|mKIAA4073	pecanex homolog 3	protein-coding
mm_81286.1	chr9	108306324	108306456	+	1	NA	promoter-TSS (NM_133986)	promoter-TSS (NM_133986)	230	NM_016802	11848	Mm.757	NM_016802	ENSMUSG00000007815	Rhoa	Arha|Arha1|Arha2	ras homolog family member A	protein-coding
mm_81248.1	chr9	107975623	107975631	+	1	NA	promoter-TSS (NM_023738)	promoter-TSS (NM_023738)	60	NM_023738	74153	Mm.277125	NM_023738	ENSMUSG00000032596	Uba7	1300004C08Rik|Ube1l	ubiquitin-like modifier activating enzyme 7	protein-coding
mm_153312.1	chr19	38043325	38043384	-	1	NA	5' UTR (NM_001099634, exon 1 of 53)	5' UTR (NM_001099634, exon 1 of 53)	223	NM_001099634	226101	Mm.34674	NM_177035	ENSMUSG00000048612	Myof	2310004N10Rik|2310051D19Rik|E030042N20Rik|Fer1l3	myoferlin	protein-coding
mm_7690.1	chr1	128712836	128712846	-	1	NA	Intergenic	Intergenic	-120542	NM_009911	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding
mm_138548.1	chr17	35263962	35263990	+	1	NA	exon (NM_001267808, exon 7 of 11)	exon (NM_001267808, exon 7 of 11)	853	NM_001267808	14980	Mm.439675	NM_001267808		H2-L	H-2L	histocompatibility 2, D region locus L	protein-coding
mm_110911.1	chr12	76216864	76216872	-	1	NA	intron (NM_001159532, intron 5 of 8)	intron (NM_001159532, intron 5 of 8)	29878	NM_019784	80384	Mm.78551	NM_019784	ENSMUSG00000021056	Tex21	4931406F04Rik|4931412D23Rik|4931421K24Rik|tsec-2	testis expressed gene 21	protein-coding
mm_169675.1	chr15	66424490	66424490	-	1	NA	intron (NM_019457, intron 10 of 11)	B1_Mm|SINE|Alu	76420	NM_019457	54562	Mm.244890	NM_019457	ENSMUSG00000022375	Lrrc6	LRTP	leucine rich repeat containing 6 (testis)	protein-coding
mm_166572.1	chr6	49068854	49068868	+	1	NA	Intergenic	Intergenic	-4934	NM_029353	75593	Mm.439947	NM_029353	ENSMUSG00000029815	Malsu1	2410003K15Rik|Matsu1	mitochondrial assembly of ribosomal large subunit 1	protein-coding
mm_104733.1	chr11	98328344	98328357	-	1	NA	intron (NM_010895, intron 1 of 1)	CpG	1295	NM_010895	18013	Mm.4814	NM_010895	ENSMUSG00000038255	Neurod2	Ndrf|bHLHa1	neurogenic differentiation 2	protein-coding
mm_16848.1	chr2	11596717	11596745	-	1	NA	exon (NM_152824, exon 4 of 12)	exon (NM_152824, exon 4 of 12)	6468	NM_152824	76938	Mm.182769	NM_152824	ENSMUSG00000037197	Rbm17	2700027J02Rik	RNA binding motif protein 17	protein-coding
mm_44633.1	chr5	27791427	27791437	-	1	NA	5' UTR (NM_018878, exon 1 of 21)	5' UTR (NM_018878, exon 1 of 21)	118	NM_018878	55982	Mm.277190	NM_018878	ENSMUSG00000002221	Paxip1	D5Ertd149e|PTIP	PAX interacting (with transcription-activation domain) protein 1	protein-coding
mm_118777.1	chr14	23432476	23432485	+	1	NA	intron (NM_001253361, intron 19 of 30)	intron (NM_001253361, intron 19 of 30)	-337909	NR_033550	791307	Mm.364384	NR_033550	ENSMUSG00000068680	Gm10248	ENSMUSG00000068680	predicted gene 10248	ncRNA
mm_56413.1	chr6	97248521	97248544	-	1	NA	exon (NM_001081157, exon 2 of 3)	exon (NM_001081157, exon 2 of 3)	4248	NM_001081157	320502	Mm.68163	NM_001081157	ENSMUSG00000044086	Lmod3	5430424A14Rik	leiomodin 3 (fetal)	protein-coding
mm_164579.1	chr17	25184559	25184563	+	1	NA	promoter-TSS (NM_183150)	promoter-TSS (NM_183150)	0	NM_183150	214489	Mm.274433	NM_183150	ENSMUSG00000067722	BC003965	Ccsmst1	cDNA sequence BC003965	protein-coding
mm_106705.1	chr12	3806004	3806031	+	1	NA	promoter-TSS (NM_007872)	promoter-TSS (NM_007872)	-963	NM_007872	13435	Mm.5001	NM_007872	ENSMUSG00000020661	Dnmt3a	MmuIIIA	DNA methyltransferase 3A	protein-coding
mm_77760.1	chr9	3000092	3000120	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	38637	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_119678.1	chr14	52795084	52795094	+	1	NA	Intergenic	Intergenic	-299394	NM_001170918	57269	Mm.88822	NM_020512	ENSMUSG00000059887	Olfr1507	MOR244-1|Mor28|Or28	olfactory receptor 1507	protein-coding
mm_31715.1	chr4	62634441	62634487	+	1	NA	exon (NM_001081650, exon 7 of 11)	exon (NM_001081650, exon 7 of 11)	14792	NM_134257	50780	Mm.286753	NM_019492	ENSMUSG00000059810	Rgs3	4930506N09Rik|C2PA-RGS3|C2pa|PDZ-RGS3|RGS3S	regulator of G-protein signaling 3	protein-coding
mm_132437.1	chr16	35928670	35928699	+	1	NA	3' UTR (NM_001013371, exon 5 of 5)	3' UTR (NM_001013371, exon 5 of 5)	-9786	NM_030253	80285	Mm.49074	NM_030253	ENSMUSG00000022906	Parp9	ARTD9|AW214463|BC003281|Bagl|Bal|PARP-9	poly (ADP-ribose) polymerase family, member 9	protein-coding
mm_35085.1	chr4	7687357	7687365	-	1	NA	Intergenic	Intergenic	126673	NR_040645	71510	Mm.410775	NR_040645	ENSMUSG00000086070	8430436N08Rik	-	RIKEN cDNA 8430436N08 gene	ncRNA
mm_27756.1	chr3	69598877	69598929	-	1	NA	promoter-TSS (NM_020026)	promoter-TSS (NM_020026)	57	NM_020026	26879	Mm.153710	NM_020026	ENSMUSG00000043300	B3galnt1	B3galt3|b3GT3	UDP-GalNAc:betaGlcNAc beta 1,3-galactosaminyltransferase, polypeptide 1	protein-coding
mm_110151.1	chr12	26450716	26450778	-	1	NA	exon (NM_021384, exon 3 of 6)	exon (NM_021384, exon 3 of 6)	5705	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_33686.1	chr4	133412017	133412031	+	1	NA	exon (NM_016981, exon 2 of 12)	exon (NM_016981, exon 2 of 12)	42248	NR_039582	100628620		NR_039582	ENSMUSG00000092745	Mir5122	mmu-mir-5122|mu-mir-5122	microRNA 5122	ncRNA
mm_46356.1	chr5	103100055	103100088	-	1	NA	intron (NM_001318102, intron 2 of 13)	intron (NM_001318102, intron 2 of 13)	-41679	NM_001318131	26414	Mm.39253	NM_009158	ENSMUSG00000046709	Mapk10	C230008H04Rik|JNK3|JNK3B1|JNK3B2|SAPK(beta)|Serk2|p493F12|p54bSAPK	mitogen-activated protein kinase 10	protein-coding
mm_81872.1	chr9	119063469	119063492	+	1	NA	intron (NM_001164567, intron 10 of 19)	intron (NM_001164567, intron 10 of 19)	10702	NM_001164567	22351	Mm.83817	NM_011700	ENSMUSG00000038775	Vill	Villp	villin-like	protein-coding
mm_48923.1	chr6	4505220	4505260	+	1	NA	promoter-TSS (NM_007743)	promoter-TSS (NM_007743)	-378	NM_007743	12843	Mm.277792	NM_007743	ENSMUSG00000029661	Col1a2	AA960264|AI325291|Col1a-2|Cola-2|Cola2|oim	collagen, type I, alpha 2	protein-coding
mm_143823.1	chr17	83847888	83847923	-	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	-1115	NM_025325	107766	Mm.30100	NM_025325	ENSMUSG00000000673	Haao	0610007K21Rik|0610012J07Rik|3-HAO|3-HAOxase|3HAO	3-hydroxyanthranilate 3,4-dioxygenase	protein-coding
mm_19893.1	chr2	114051930	114051982	-	1	NA	exon (NM_009608, exon 2 of 7)	exon (NM_009608, exon 2 of 7)	919	NM_009608	11464	Mm.686	NM_009608	ENSMUSG00000068614	Actc1	Actc-1	actin, alpha, cardiac muscle 1	protein-coding
mm_47994.1	chr5	136116519	136116564	-	1	NA	promoter-TSS (NM_011293)	promoter-TSS (NM_011293)	-150	NM_011293	20022	Mm.4896	NM_011293	ENSMUSG00000039771	Polr2j	14.5kDa|Polr2i|Rpb11a|Rpo2-4	polymerase (RNA) II (DNA directed) polypeptide J	protein-coding
mm_3646.1	chr1	152954967	152955059	+	1	NA	promoter-TSS (NM_175460)	promoter-TSS (NM_175460)	-88	NM_175460	226518	Mm.40548	NM_175460	ENSMUSG00000042751	Nmnat2	AI843915|D030041I09Rik|PNAT1|PNAT2	nicotinamide nucleotide adenylyltransferase 2	protein-coding
mm_34932.1	chr4	155839725	155839762	+	1	NA	promoter-TSS (NM_024263)	promoter-TSS (NM_024263)	63	NM_024263	74761	Mm.159028	NM_024263	ENSMUSG00000029070	Mxra8	1200013A08Rik|1700095D18Rik|AI131686|Asp3|Dicam	matrix-remodelling associated 8	protein-coding
mm_123322.1	chr14	62761128	62761145	-	1	NA	promoter-TSS (NM_008715)	promoter-TSS (NM_008715)	-24	NM_008715	18130	Mm.319684	NM_008715	ENSMUSG00000035161	Ints6	2900075H24Rik|AI480962|DICE1|Ddx26|HDB|Notch2l	integrator complex subunit 6	protein-coding
mm_128718.1	chr15	64012830	64012836	-	1	NA	intron (NM_144846, intron 1 of 11)	intron (NM_144846, intron 1 of 11)	47615	NM_144846	223601	Mm.246108	NM_144846	ENSMUSG00000022378	Fam49b	0910001A06Rik|AW122079	family with sequence similarity 49, member B	protein-coding
mm_117805.1	chr13	97482539	97482550	-	1	NA	promoter-TSS (NR_110431)	promoter-TSS (NR_110431)	-157	NR_110430	100039691	Mm.219358	NR_110430	ENSMUSG00000078952	Lncenc1	ENSMUSG00000078952|Gm11019|Gm2373|Lincenc1|Platr18|linc-Enc1	long non-coding RNA, embryonic stem cells expressed 1	ncRNA
mm_48865.1	chr5	149831584	149831594	-	1	NA	Intergenic	Intergenic	-16158	NR_045758	70969	Mm.78499	NR_045758	ENSMUSG00000107214	4930500F04Rik	4931407C17Rik	RIKEN cDNA 4930500F04 gene	ncRNA
mm_44823.1	chr5	33657890	33657940	-	1	NA	promoter-TSS (NM_026698)	promoter-TSS (NM_026698)	-83	NM_026698	68366	Mm.491151	NM_026698	ENSMUSG00000019295	Tmem129	0610039G24Rik|2410015J15Rik|AA409575	transmembrane protein 129	protein-coding
mm_114883.1	chr13	94224879	94224893	+	1	NA	intron (NM_001346609, intron 6 of 8)	intron (NM_001346609, intron 6 of 8)	60395	NM_029153	107767	Mm.201455	NM_029153	ENSMUSG00000021687	Scamp1	4930505M11Rik|AI415563|AW122395	secretory carrier membrane protein 1	protein-coding
mm_146118.1	chr18	74288380	74288394	+	1	NA	intron (NR_029424, intron 2 of 8)	intron (NR_029424, intron 2 of 8)	5287	NM_028948	74453	Mm.182293	NM_028948	ENSMUSG00000035394	Cfap53	4933415I03Rik|Ccdc11	cilia and flagella associated protein 53	protein-coding
mm_22823.1	chr3	27231503	27231522	+	1	NA	intron (NM_178772, intron 3 of 4)	intron (NM_178772, intron 3 of 4)	48508	NM_178772	320024	Mm.24576	NM_178772	ENSMUSG00000027698	Nceh1	Aadacl1|B230106I24Rik|CPO-BP|Nceh	neutral cholesterol ester hydrolase 1	protein-coding
mm_4855.1	chr1	187608979	187608991	+	1	NA	promoter-TSS (NM_001243792)	promoter-TSS (NM_001243792)	-21	NM_001243792	26381	Mm.89989	NM_011935	ENSMUSG00000026610	Esrrg	ERR3|Errg|NR3B3|mKIAA0832	estrogen-related receptor gamma	protein-coding
mm_46023.1	chr5	90932953	90932958	-	1	NA	intron (NM_026788, intron 1 of 7)	intron (NM_026788, intron 1 of 7)	1759	NM_026788	665563	Mm.153030	NM_026788	ENSMUSG00000029376	Mthfd2l	1110019K23Rik|C630010D07Rik	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2-like	protein-coding
mm_106558.1	chr11	120630098	120630123	-	1	NA	intron (NM_010756, intron 1 of 2)	intron (NM_010756, intron 1 of 2)	3437	NM_010756	17134	Mm.268010	NM_010756	ENSMUSG00000051510	Mafg	AA545192|C630022N07Rik	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein G (avian)	protein-coding
mm_131579.1	chr16	18426401	18426409	+	1	NA	promoter-TSS (NM_013711)	promoter-TSS (NM_013711)	-12	NM_013711	26462	Mm.390906	NM_013711	ENSMUSG00000075704	Txnrd2	AA118373|ESTM573010|TGR|Tr3|Trxr2|Trxrd2	thioredoxin reductase 2	protein-coding
mm_113108.1	chr13	24416172	24416180	+	1	NA	intron (NM_007717, intron 1 of 15)	intron (NM_007717, intron 1 of 15)	1054	NM_001284520	12763	Mm.8396	NM_007717	ENSMUSG00000016756	Cmah	-	cytidine monophospho-N-acetylneuraminic acid hydroxylase	protein-coding
mm_147078.1	chr18	35615398	35615407	-	1	NA	3' UTR (NM_011397, exon 15 of 15)	3' UTR (NM_011397, exon 15 of 15)	11825	NM_011397	20522	Mm.22702	NM_011397	ENSMUSG00000024354	Slc23a1	D18Ucla2|SVCT1|Slc23a2|YSPL3	solute carrier family 23 (nucleobase transporters), member 1	protein-coding
mm_154380.1	chrM	11292	11305	+	1	NA	NA	Intergenic	NA	NA								
mm_71065.1	chr8	34080774	34080802	+	1	NA	Intergenic	Intergenic	27026	NM_001293758	22428	Mm.150373	NM_011722	ENSMUSG00000031516	Dctn6	AU044699|WS-3|p27	dynactin 6	protein-coding
mm_41552.1	chr5	92940530	92940554	+	1	NA	exon (NM_001077596, exon 4 of 10)	exon (NM_001077596, exon 4 of 10)	42549	NM_001077596	27428	Mm.46014	NM_015756	ENSMUSG00000029381	Shroom3	AL022960|D5Ertd287e|Shrm|Shrm3	shroom family member 3	protein-coding
mm_4994.1	chr1	191817468	191817478	+	1	NA	Intergenic	Lx10|LINE|L1	-4000	NM_010892	18005	Mm.33773	NM_010892	ENSMUSG00000026622	Nek2	AA617254|C77054	NIMA (never in mitosis gene a)-related expressed kinase 2	protein-coding
mm_50238.1	chr6	42351476	42351501	+	1	NA	exon (NM_001289618, exon 4 of 10)	exon (NM_001289618, exon 4 of 10)	1660	NM_001289619	22793	Mm.282303	NM_011777	ENSMUSG00000029860	Zyx	9530098H06Rik|R75157	zyxin	protein-coding
mm_149913.1	chr19	26605165	26605185	+	1	NA	promoter-TSS (NM_011416)	promoter-TSS (NM_011416)	15	NM_011416	67155	Mm.342988	NM_011416	ENSMUSG00000024921	Smarca2	2610209L14Rik|SNF2alpha|Snf2l2|brahma|brm	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	protein-coding
mm_140718.1	chr17	15375219	15375264	-	1	NA	5' UTR (NM_007865, exon 1 of 11)	5' UTR (NM_007865, exon 1 of 11)	582	NM_007865	13388	Mm.4875	NM_007865	ENSMUSG00000014773	Dll1	Delta1	delta-like 1 (Drosophila)	protein-coding
mm_42697.1	chr5	119876579	119876589	+	1	NA	intron (NM_011537, intron 8 of 8)	intron (NM_011537, intron 8 of 8)	41921	NM_011537	21388	Mm.103636	NM_011537	ENSMUSG00000018263	Tbx5	-	T-box 5	protein-coding
mm_32380.1	chr4	106316302	106316328	+	1	NA	5' UTR (NM_183225, exon 1 of 68)	5' UTR (NM_183225, exon 1 of 68)	102	NM_183225	329908	Mm.234544	NM_183225	ENSMUSG00000028514	Usp24	2700066K03Rik|2810030C21Rik|AI414051|B130021E18|C79851	ubiquitin specific peptidase 24	protein-coding
mm_85908.1	chr9	111056841	111056893	-	1	NA	5' UTR (NM_017466, exon 1 of 2)	5' UTR (NM_017466, exon 1 of 2)	377	NM_001302377	54199	Mm.7336	NM_017466	ENSMUSG00000043953	Ccrl2	1810047I05Rik|Ackr5|CCR11|Cmkbr1l2|E01|L-CCR	chemokine (C-C motif) receptor-like 2	protein-coding
mm_19887.1	chr2	114050406	114050449	-	1	NA	exon (NM_009608, exon 3 of 7)	exon (NM_009608, exon 3 of 7)	2448	NM_009608	11464	Mm.686	NM_009608	ENSMUSG00000068614	Actc1	Actc-1	actin, alpha, cardiac muscle 1	protein-coding
mm_135121.1	chr16	35841518	35841552	-	1	NA	exon (NM_001039530, exon 13 of 17)	exon (NM_001039530, exon 13 of 17)	29847	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_56899.1	chr6	119188611	119188618	-	1	NA	intron (NM_001033379, intron 3 of 8)	intron (NM_001033379, intron 3 of 8)	7795	NM_001255997	12288	Mm.41628	NM_009781	ENSMUSG00000051331	Cacna1c	Cav1.2|Cchl1a1|D930026N18Rik|MBC|MELC-CC	calcium channel, voltage-dependent, L type, alpha 1C subunit	protein-coding
mm_95407.1	chr11	49846885	49846937	+	1	NA	5' UTR (NM_001163671, exon 1 of 12)	5' UTR (NM_001163671, exon 1 of 12)	160	NM_016961	26420	Mm.68933	NM_016961	ENSMUSG00000020366	Mapk9	AI851083|JNK2|Prkm9|p54aSAPK	mitogen-activated protein kinase 9	protein-coding
mm_82257.1	chr9	4796219	4796267	-	1	NA	promoter-TSS (NM_001113181)	promoter-TSS (NM_001113181)	-9	NM_019691	14802	Mm.209263	NM_019691	ENSMUSG00000025892	Gria4	GluA4|GluR-D|Glur-4|Glur4|Gluralpha4|spkw1	glutamate receptor, ionotropic, AMPA4 (alpha 4)	protein-coding
mm_54430.1	chr6	34041788	34041793	-	1	NA	intron (NM_028886, intron 3 of 19)	ORR1D2|LTR|ERVL-MaLR	12342	NM_028886	74354	Mm.127952	NM_028886	ENSMUSG00000056215	Lrguk	4921528H16Rik	leucine-rich repeats and guanylate kinase domain containing	protein-coding
mm_113293.1	chr13	30345529	30345558	+	1	NA	intron (NM_177322, intron 2 of 2)	intron (NM_177322, intron 2 of 2)	9187	NM_177322	11607	Mm.35062	NM_177322	ENSMUSG00000049115	Agtr1a	1810074K20Rik|AG2S|AI551199|AT1|AT1a|AT2R1|AT2R1A|Agtr-1a|Agtr1|Angtr-1a	angiotensin II receptor, type 1a	protein-coding
mm_24696.1	chr3	95122521	95122532	+	1	NA	exon (NM_009336, exon 6 of 6)	exon (NM_009336, exon 6 of 6)	-1988	NM_016712	50874	Mm.71935	NM_016712	ENSMUSG00000005628	Tmod4	MTMOD|Sk-Tmod	tropomodulin 4	protein-coding
mm_111470.1	chr12	98574749	98574775	-	1	NA	promoter-TSS (NM_001316665)	promoter-TSS (NM_001316665)	-50	NM_001316665	72258	Mm.196158	NM_029911	ENSMUSG00000033854	Kcnk10	1700024D23Rik|3010005K24Rik|Trek2	potassium channel, subfamily K, member 10	protein-coding
mm_214.1	chr1	16688406	16688458	+	1	NA	promoter-TSS (NM_001159711)	promoter-TSS (NM_001159711)	-24	NM_001159711	17087	Mm.116844	NM_016923	ENSMUSG00000025779	Ly96	ESOP-1|MD-2|MD2	lymphocyte antigen 96	protein-coding
mm_106684.1	chr12	3235803	3235839	+	1	NA	promoter-TSS (NR_015551)	promoter-TSS (NR_015551)	30	NR_015551	74173	Mm.309774	NM_028796	ENSMUSG00000079179	Rab10os	1700012B15Rik|1810036A22Rik	RAB10, member RAS oncogene family, opposite strand	ncRNA
mm_115099.1	chr13	102733256	102733266	+	1	NA	3' UTR (NM_175171, exon 29 of 29)	3' UTR (NM_175171, exon 29 of 29)	-26994	NR_130318	76624	Mm.426384	NR_130171	ENSMUSG00000091906	1700099I09Rik	-	RIKEN cDNA 1700099I09 gene	ncRNA
mm_28693.1	chr3	95524880	95524895	-	1	NA	Intergenic	Intergenic	-1899	NM_021281	13040	Mm.3619	NM_021281	ENSMUSG00000038642	Ctss	Cats	cathepsin S	protein-coding
mm_172834.1	chr9	25252600	25252619	+	1	NA	5' UTR (NM_001205367, exon 1 of 13)	5' UTR (NM_001205367, exon 1 of 13)	170	NM_001205367	235072	Mm.270259	NM_009859	ENSMUSG00000001833	Sept7	Cdc10|E430034N22	septin 7	protein-coding
mm_74575.1	chr8	11211574	11211577	-	1	NA	intron (NR_133670, intron 44 of 52)	PB1D11|SINE|Alu	-101230	NM_009932	12827	Mm.181021	NM_009932	ENSMUSG00000031503	Col4a2	Col4a-2	collagen, type IV, alpha 2	protein-coding
mm_3826.1	chr1	159313786	159313786	+	1	NA	intron (NM_011931, intron 14 of 19)	intron (NM_011931, intron 14 of 19)	20013	NR_144489	100846986		NR_144489		Pou5f1-rs1	Gm21053|Oct4P2|Otf-3rs|Otf3-rs1|Otf3a	POU domain, class 5, transcription factor 1, related sequence 1	pseudo
mm_78819.1	chr9	44086202	44086202	+	1	NA	intron (NM_198091, intron 1 of 11)	intron (NM_198091, intron 1 of 11)	1282	NM_198091	53376	Mm.272770	NM_016808	ENSMUSG00000032010	Usp2	B930035K21Rik|Ubp41	ubiquitin specific peptidase 2	protein-coding
mm_11969.1	chr2	53605160	53605163	+	1	NA	Intergenic	Intergenic	413077	NM_022989	65103	Mm.37623	NM_022989	ENSMUSG00000026960	Arl6ip6	2310057C01Rik|2610529A11Rik|Aip-6	ADP-ribosylation factor-like 6 interacting protein 6	protein-coding
mm_102707.1	chr11	66526711	66526734	-	1	NA	promoter-TSS (NM_001034874)	promoter-TSS (NM_001034874)	-596	NM_001034874	380702	Mm.351764	NM_001034874	ENSMUSG00000053930	Shisa6	Gm879|ckamp52	shisa family member 6	protein-coding
mm_91854.1	chr10	59221727	59221744	-	1	NA	promoter-TSS (NM_172939)	promoter-TSS (NM_172939)	112	NM_001024911	103080	Mm.346842	NM_001024910	ENSMUSG00000019917	Sept10	4921515A04Rik|9430099J10Rik|AA408298|AI874685	septin 10	protein-coding
mm_17364.1	chr2	26671319	26671323	-	1	NA	promoter-TSS (NM_010695)	promoter-TSS (NM_010695)	-39	NM_010695	16821	Mm.123925	NM_010695	ENSMUSG00000026919	Lcn4	A630045M08Rik|Vnsp2	lipocalin 4	protein-coding
mm_45252.1	chr5	62765578	62765587	-	1	NA	intron (NM_178407, intron 1 of 32)	intron (NM_178407, intron 1 of 32)	595	NM_178407	212285	Mm.244403	NM_178407	ENSMUSG00000037999	Arap2	Centd1|Gm148|mKIAA0580	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2	protein-coding
mm_144880.1	chr18	36793919	36793937	+	1	NA	promoter-TSS (NM_025594)	promoter-TSS (NM_025594)	5	NM_025594	66492	Mm.251155	NM_025594	ENSMUSG00000001383	Zmat2	2610510D14Rik|2900082I05Rik	zinc finger, matrin type 2	protein-coding
mm_135934.1	chr16	74053004	74053007	-	1	NA	intron (NM_175549, intron 2 of 27)	intron (NM_175549, intron 2 of 27)	289062	NR_030464	751561		NR_030464	ENSMUSG00000104758	Mir691	Mirn691|mir-691|mmu-mir-691	microRNA 691	ncRNA
mm_114279.1	chr13	58281159	58281171	+	1	NA	Intergenic	Intergenic	-6977	NM_019832	56278	Mm.296625	NM_019832	ENSMUSG00000021552	Gkap1	42kDa|4933400B15Rik|D13Ertd340e|Gkap42	G kinase anchoring protein 1	protein-coding
mm_109919.1	chr12	8498281	8498313	-	1	NA	3' UTR (NM_007483, exon 1 of 1)	3' UTR (NM_007483, exon 1 of 1)	1688	NM_007483	11852	Mm.687	NM_007483	ENSMUSG00000054364	Rhob	AA017882|Arh6|Arhb	ras homolog family member B	protein-coding
mm_22797.1	chr3	22331468	22331503	+	1	NA	Intergenic	Intergenic	80115	NR_004439	19784		NR_004439		Rprl2	RPRH3|Rmrp3	ribonuclease P RNA-like 2	ncRNA
mm_102822.1	chr11	69012464	69012500	-	1	NA	Intergenic	RLTR34C_MM|LTR|ERVK	-3429	NM_001281465	68964	Mm.285785	NM_001013256	ENSMUSG00000020898	Ctc1	1500010J02Rik|AAF-132|AAF132	CTS telomere maintenance complex component 1	protein-coding
mm_120332.1	chr14	63370610	63370622	+	1	NA	Intergenic	Intergenic	46571	NM_007549	12143	Mm.3962	NM_007549	ENSMUSG00000014453	Blk	-	B lymphoid kinase	protein-coding
mm_132333.1	chr16	33819535	33819568	+	1	NA	3' UTR (NM_010739, exon 13 of 13)	3' UTR (NM_010739, exon 13 of 13)	-10114	NM_010580	16419	Mm.6424	NM_010580	ENSMUSG00000022817	Itgb5	AA475909|AI874634|ESTM23|[b]-5|[b]5|[b]5A|[b]5B|beta-5|beta5	integrin beta 5	protein-coding
mm_17593.1	chr2	30658421	30658434	-	1	NA	non-coding (NR_136917, exon 4 of 4)	non-coding (NR_136917, exon 4 of 4)	19584	NR_136917	665635	Mm.450149	NR_136917		Gm14486	OTTMUSG00000016802	predicted gene 14486	ncRNA
mm_88513.1	chr10	78049837	78049847	+	1	NA	promoter-TSS (NM_019448)	promoter-TSS (NM_019448)	0	NM_019448	54427	Mm.13433	NM_019448	ENSMUSG00000000730	Dnmt3l	D6Ertd14e|ecat7	DNA (cytosine-5-)-methyltransferase 3-like	protein-coding
mm_167656.1	chr9	70389752	70389753	+	1	NA	intron (NM_181072, intron 26 of 27)	intron (NM_181072, intron 26 of 27)	16001	NR_049200	100885839		NR_049200	ENSMUSG00000093763	Mir5626	Gm25590|mir-5626|mmu-mir-5626	microRNA 5626	ncRNA
mm_51359.1	chr6	72627530	72627552	+	1	NA	exon (NM_009332, exon 12 of 12)	exon (NM_009332, exon 12 of 12)	-1747	NR_040422	100038714	Mm.321330	NR_040421		Gm15401	ENSMUSG00000072999|OTTMUSG00000021199	predicted gene 15401	ncRNA
mm_121162.1	chr14	103010207	103010215	+	1	NA	intron (NR_045657, intron 2 of 2)	intron (NR_045657, intron 2 of 2)	23592	NR_045657	71264	Mm.399572	NR_045657		4933432I03Rik	-	RIKEN cDNA 4933432I03 gene	ncRNA
mm_111309.1	chr12	85816402	85816418	-	1	NA	exon (NM_021446, exon 4 of 5)	exon (NM_021446, exon 4 of 5)	8135	NM_021446	58520	Mm.143795	NM_021446	ENSMUSG00000021252	0610007P14Rik	1190004E09Rik|AU019315|C77855|ORF11	RIKEN cDNA 0610007P14 gene	protein-coding
mm_102338.1	chr11	57832085	57832095	-	1	NA	promoter-TSS (NM_008213)	promoter-TSS (NM_008213)	57	NM_008213	15110	Mm.4746	NM_008213	ENSMUSG00000037335	Hand1	Ehand1|Hxt|Th1|Thing1|bHLHa27|eHAND	heart and neural crest derivatives expressed transcript 1	protein-coding
mm_86004.1	chr9	112233120	112233128	-	1	NA	promoter-TSS (NM_001177616)	promoter-TSS (NM_001177616)	-623	NM_001177616	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_82140.1	chr9	123769173	123769183	+	1	NA	intron (NM_009913, intron 1 of 2)	intron (NM_009913, intron 1 of 2)	1967	NM_001166625	12769	Mm.440604	NM_009913	ENSMUSG00000029530	Ccr9	A130091K22Rik|Cmkbr10|GPR-9-6	chemokine (C-C motif) receptor 9	protein-coding
mm_167832.1	chr9	124424175	124424198	-	1	NA	non-coding (NR_015516, exon 1 of 1)	non-coding (NR_015516, exon 1 of 1)	399	NR_015516	75135	Mm.476814	NR_015516		4930526I15Rik	1600027J15Rik	RIKEN cDNA 4930526I15 gene	ncRNA
mm_81284.1	chr9	108306289	108306300	+	1	NA	promoter-TSS (NM_133986)	promoter-TSS (NM_133986)	134	NM_016802	11848	Mm.757	NM_016802	ENSMUSG00000007815	Rhoa	Arha|Arha1|Arha2	ras homolog family member A	protein-coding
mm_107330.1	chr12	31949587	31949609	+	1	NA	intron (NM_177993, intron 1 of 8)	CpG	937	NM_177993	73389	Mm.390461	NM_153198	ENSMUSG00000002996	Hbp1	1700058O05Rik|BE629963|C330012F01Rik|C86454	high mobility group box transcription factor 1	protein-coding
mm_107832.1	chr12	69258160	69258168	+	1	NA	intron (NM_178253, intron 7 of 12)	intron (NM_178253, intron 7 of 12)	16332	NM_178253	271005	Mm.180969	NM_178253	ENSMUSG00000051890	Klhdc1	-	kelch domain containing 1	protein-coding
mm_114332.1	chr13	60647507	60647510	+	1	NA	intron (NM_029653, intron 2 of 25)	Lx8b|LINE|L1	45297	NM_134062	69635	Mm.24103	NM_029653	ENSMUSG00000021559	Dapk1	D13Ucla1|DAP-Kinase	death associated protein kinase 1	protein-coding
mm_126035.1	chr15	76879303	76879334	+	1	NA	promoter-TSS (NM_145916)	promoter-TSS (NM_145916)	42	NM_145916	223669	Mm.38948	NM_145916	ENSMUSG00000033669	Zfp7	KRAB20|KRAB7|Krox-2|Zfp-7|Zfp65|Zfp80|Zfp86-rs1|mszf73-2	zinc finger protein 7	protein-coding
mm_79977.1	chr9	66872560	66872594	+	1	NA	intron (NM_173413, intron 1 of 7)	intron (NM_173413, intron 1 of 7)	-37871	NM_026674	68318	Mm.284229	NM_026674	ENSMUSG00000053040	Aph1c	0610008A10Rik|APH-1b|Aph1b	aph1 homolog C, gamma secretase subunit	protein-coding
mm_22548.1	chr3	9250037	9250047	+	1	NA	promoter-TSS (NM_177660)	promoter-TSS (NM_177660)	-525	NM_177660	229055	Mm.103262	NM_177660	ENSMUSG00000069114	Zbtb10	4832414A18|AU021107|RINZF	zinc finger and BTB domain containing 10	protein-coding
mm_33274.1	chr4	128654687	128654729	+	1	NA	promoter-TSS (NM_001195130)	promoter-TSS (NM_001195130)	6	NM_001195130	54383	Mm.473738	NM_018774	ENSMUSG00000028796	Phc2	A3galt2|AA415044|D130050K19Rik|D4Ertd810e|Edr2|Mph2|p36	polyhomeotic-like 2 (Drosophila)	protein-coding
mm_169646.1	chr15	52089255	52089273	+	1	NA	Intergenic	RodERV21-int|LTR|ERV1	49157	NM_175503	239435	Mm.24204	NM_175503	ENSMUSG00000068522	Aard	A5D3|AV328152	alanine and arginine rich domain containing protein	protein-coding
mm_9783.1	chr1	181211972	181212000	-	1	NA	promoter-TSS (NM_145514)	promoter-TSS (NM_145514)	-8	NM_145514	226757	Mm.289082	NM_145514	ENSMUSG00000038733	Wdr26	1600024A01Rik|AA693241|AI447817|AU044014|C77982|Gid7	WD repeat domain 26	protein-coding
mm_151156.1	chr19	53185760	53185772	+	1	NA	intron (NM_013758, intron 1 of 15)	intron (NM_013758, intron 1 of 15)	41769	NM_013758	27360	Mm.426080	NM_013758	ENSMUSG00000025026	Add3	AI463285|R75380	adducin 3 (gamma)	protein-coding
mm_44001.1	chr5	146845131	146845150	+	1	NA	promoter-TSS (NM_026864)	promoter-TSS (NM_026864)	69	NM_026864	68895	Mm.266978	NM_026864	ENSMUSG00000029641	Rasl11a	1110065D03Rik|AI852031	RAS-like, family 11, member A	protein-coding
mm_88466.1	chr10	77581325	77581335	+	1	NA	promoter-TSS (NM_145925)	promoter-TSS (NM_145925)	-437	NM_145925	108705	Mm.28853	NM_145925	ENSMUSG00000009291	Pttg1ip	1810010L20Rik|AI314311|AU018448|C79540	pituitary tumor-transforming 1 interacting protein	protein-coding
mm_154291.1	chr19	61122610	61122613	-	1	NA	3' UTR (NM_001001737, exon 3 of 3)	3' UTR (NM_001001737, exon 3 of 3)	18229	NR_131956	414758	Mm.100056	NM_001001737	ENSMUSG00000074733	Zfp950	5830428H23Rik|AU016073|BC055757|Gm34518|Zfp826|mszf84	zinc finger protein 950	protein-coding
mm_168925.1	chr12	63048298	63048300	-	1	NA	Intergenic	Intergenic	360512	NR_131949	73309	Mm.276558	NR_131949		Spanxn4	1700047L15Rik	SPANX family, member N4	ncRNA
mm_37386.1	chr4	121008710	121008725	-	1	NA	intron (NM_133716, intron 1 of 9)	B1F2|SINE|Alu	8530	NM_133716	69780	Mm.271819	NM_133716	ENSMUSG00000032870	Smap2	1810031K02Rik|AA408614|Smap1l	small ArfGAP 2	protein-coding
mm_165282.1	chr2	83724525	83724528	+	1	NA	5' UTR (NM_008402, exon 1 of 30)	5' UTR (NM_008402, exon 1 of 30)	129	NM_008402	16410	Mm.227	NM_008402	ENSMUSG00000027087	Itgav	1110004F14Rik|2610028E01Rik|CD51|D430040G12Rik	integrin alpha V	protein-coding
mm_59167.1	chr7	24399814	24399818	+	1	NA	5' UTR (NM_028047, exon 1 of 14)	5' UTR (NM_028047, exon 1 of 14)	188	NM_028047	71997	Mm.150977	NM_028047	ENSMUSG00000002210	Smg9	1500002O20Rik|AI429693|N28092	smg-9 homolog, nonsense mediated mRNA decay factor (C. elegans)	protein-coding
mm_39921.1	chr5	31527106	31527112	+	1	NA	promoter-TSS (NM_028150)	promoter-TSS (NM_028150)	114	NM_001347328	20534	Mm.352407	NM_009206	ENSMUSG00000029141	Slc4a1ap	kanadaptin	solute carrier family 4 (anion exchanger), member 1, adaptor protein	protein-coding
mm_171416.1	chr4	13124947	13124952	-	1	NA	Intergenic	L1Md_T|LINE|L1	218112	NM_001171801	208820	Mm.12057	NM_173746	ENSMUSG00000055963	Triqk	C130086A10|Gm11818|OTTMUSG00000004461	triple QxxK/R motif containing	protein-coding
mm_14587.1	chr2	136007343	136007356	+	1	NA	exon (NM_013829, exon 35 of 37)	exon (NM_013829, exon 35 of 37)	-50578	NM_029530	76161	Mm.41638	NM_029530	ENSMUSG00000027270	Lamp5	3110035N03Rik|6330527O06Rik|BAD-LAMP|LAMP-5	lysosomal-associated membrane protein family, member 5	protein-coding
mm_25183.1	chr3	103325415	103325420	+	1	NA	intron (NM_001079830, intron 6 of 18)	B1_Mus1|SINE|Alu	46124	NM_001079830	94093	Mm.195036	NM_053170	ENSMUSG00000033014	Trim33	8030451N04Rik|AI413936|Ecto|Tif1g	tripartite motif-containing 33	protein-coding
mm_64709.1	chr7	4628378	4628387	-	1	NA	exon (NM_023440, exon 3 of 3)	exon (NM_023440, exon 3 of 3)	2100	NM_023440	68255	Mm.389784	NM_023440	ENSMUSG00000045282	Tmem86b	C330014O21Rik	transmembrane protein 86B	protein-coding
mm_57876.1	chr6	130337527	130337577	-	1	NA	promoter-TSS (NM_010648)	promoter-TSS (NM_010648)	74	NM_001289605	16634	Mm.425338	NM_010648	ENSMUSG00000067591	Klra3	5E6|Ly49c|NK-2.1|Nk-2|Nk2|Nk2.1	killer cell lectin-like receptor, subfamily A, member 3	protein-coding
mm_71562.1	chr8	51375803	51375804	+	1	NA	Intergenic	Charlie24|DNA|hAT-Charlie	1007691	NR_046067	100039954	Mm.400419	NR_046067	ENSMUSG00000110281	Gm2516	-	predicted gene 2516	ncRNA
mm_19171.1	chr2	84343894	84343906	-	1	NA	intron (NM_018782, intron 13 of 15)	intron (NM_018782, intron 13 of 15)	81366	NM_018782	54598	Mm.75467	NM_018782	ENSMUSG00000059588	Calcrl	AV071593|CRLR	calcitonin receptor-like	protein-coding
mm_72654.1	chr8	84842681	84842736	+	1	NA	exon (NM_007591, exon 9 of 9)	exon (NM_007591, exon 9 of 9)	-2043	NM_009010	19358	Mm.255539	NM_009010	ENSMUSG00000003813	Rad23a	2310040P19Rik|AL024030|HR23A|mHR23A	RAD23 homolog A, nucleotide excision repair protein	protein-coding
mm_39727.1	chr5	28324443	28324446	+	1	NA	intron (NM_028234, intron 1 of 18)	AT_rich|Low_complexity|Low_complexity	7255	NM_028234	381626	Mm.304075	NM_028234	ENSMUSG00000048271	Rbm33	3200001K10Rik|6430512A10Rik|AA386890|Prr8	RNA binding motif protein 33	protein-coding
mm_150115.1	chr19	29703824	29703843	+	1	NA	intron (NM_029993, intron 2 of 4)	intron (NM_029993, intron 2 of 4)	5892	NM_029993	77836	Mm.138437	NM_029993	ENSMUSG00000024806	Mlana	A930034P04Rik|Mart1	melan-A	protein-coding
mm_33568.1	chr4	132260505	132260517	+	1	NA	intron (NM_001122992, intron 1 of 10)	intron (NM_001122992, intron 1 of 10)	1038	NM_020273	56809	Mm.103489	NM_020273	ENSMUSG00000028901	Gmeb1	1110050A04Rik|AI256615|AI481278	glucocorticoid modulatory element binding protein 1	protein-coding
mm_79240.1	chr9	50504350	50504367	+	1	NA	exon (NM_029639, exon 4 of 4)	exon (NM_029639, exon 4 of 4)	447	NR_040714	69631	Mm.414996	NR_040714	ENSMUSG00000101304	Plet1os	2310014F07Rik	placenta expressed transcript 1, opposite strand	ncRNA
mm_70782.1	chr8	22411379	22411460	+	1	NA	promoter-TSS (NM_020560)	promoter-TSS (NM_020560)	79	NM_020560	57312	Mm.289402	NM_020560	ENSMUSG00000031533	Mrps31	1500002D03Rik|AA960481|Imogen38|Imogen44	mitochondrial ribosomal protein S31	protein-coding
mm_141635.1	chr17	32965722	32965733	-	1	NA	promoter-TSS (NM_153063)	promoter-TSS (NM_153063)	-11	NR_033585	77875	Mm.245027	NR_033585		Cyp4f41-ps	6030422M01Rik	cytochrome P450, family 4, subfamily f, polypeptide 41 pseudogene	pseudo
mm_28415.1	chr3	90389937	90389958	-	1	NA	promoter-TSS (NM_001316688)	promoter-TSS (NM_001316688)	-9	NM_011988	26568	Mm.45519	NM_011988	ENSMUSG00000027932	Slc27a3	Acsvl3|FATP-3|FATP3|Vlcs-3	solute carrier family 27 (fatty acid transporter), member 3	protein-coding
mm_119411.1	chr14	44997171	44997191	+	1	NA	intron (NM_008964, intron 1 of 1)	(T)n|Simple_repeat|Simple_repeat	9070	NM_008964	19217	Mm.4630	NM_008964	ENSMUSG00000037759	Ptger2	EP2|Ptgerep2	prostaglandin E receptor 2 (subtype EP2)	protein-coding
mm_105184.1	chr11	101967006	101967021	-	1	NA	promoter-TSS (NM_024449)	promoter-TSS (NM_024449)	2	NM_024449	74499	Mm.265602	NM_024449	ENSMUSG00000001494	Sost	5430411E23Rik	sclerostin	protein-coding
mm_31401.1	chr4	48047241	48047258	+	1	NA	intron (NM_015743, intron 1 of 7)	CpG	1944	NM_015743	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_58916.1	chr7	17713196	17713201	+	1	NA	promoter-TSS (NM_028480)	promoter-TSS (NM_028480)	-54	NM_028480	73250	Mm.244138	NM_028480	ENSMUSG00000008789	Ceacam5	1600029H12Rik|Psg30	carcinoembryonic antigen-related cell adhesion molecule 5	protein-coding
mm_139542.1	chr17	56717760	56717819	+	1	NA	promoter-TSS (NM_027244)	promoter-TSS (NM_027244)	27	NM_027244	69875	Mm.279823	NM_027244	ENSMUSG00000002379	Ndufa11	2010012C24Rik|AV006275|B14.7	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex 11	protein-coding
mm_1190.1	chr1	62703383	62703399	+	1	NA	promoter-TSS (NM_001077407)	promoter-TSS (NM_001077407)	74	NM_001077405	18187	Mm.266341	NM_010939	ENSMUSG00000025969	Nrp2	1110048P06Rik|Np-2|Np2|Npn-2|Npn2	neuropilin 2	protein-coding
mm_63450.1	chr7	127512082	127512090	+	1	NA	non-coding (NR_024331, exon 1 of 1)	non-coding (NR_024331, exon 1 of 1)	103	NM_001304266	100043597	Mm.428042	NM_175144	ENSMUSG00000053877	Srcap	B930091H02Rik|D030022P06Rik|F630004O05Rik	Snf2-related CREBBP activator protein	protein-coding
mm_29137.1	chr3	105801300	105801315	-	1	NA	promoter-TSS (NM_145541)	promoter-TSS (NM_145541)	74	NM_145541	109905	Mm.101922	NM_145541	ENSMUSG00000068798	Rap1a	AI848598|G-22K|Krev-1|Rap1	RAS-related protein-1a	protein-coding
mm_54135.1	chr6	21852435	21852443	-	1	NA	promoter-TSS (NM_173007)	promoter-TSS (NM_173007)	76	NM_173007	269831	Mm.21950	NM_173007	ENSMUSG00000029669	Tspan12	9030619E17|AI426782|AI663988|AW111457|Tm4sf12	tetraspanin 12	protein-coding
mm_119218.1	chr14	33216818	33216903	+	1	NA	promoter-TSS (NM_153800)	promoter-TSS (NM_153800)	37	NM_153800	239027	Mm.318350	NM_153800	ENSMUSG00000063506	Arhgap22	B230341L19Rik|RHOGAP2|p68RacGAP	Rho GTPase activating protein 22	protein-coding
mm_5469.1	chr1	36557518	36557561	-	1	NA	promoter-TSS (NM_001304329)	promoter-TSS (NM_001304329)	18	NM_001304330	20353	Mm.29558	NM_001126047	ENSMUSG00000026121	Sema4c	AI426163|M-Sema F|Semacl1|Semaf|Semai|sema I	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4C	protein-coding
mm_150079.1	chr19	29386985	29386993	+	1	NA	3' UTR (NM_021893, exon 7 of 7)	3' UTR (NM_021893, exon 7 of 7)	19551	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_117624.1	chr13	91861376	91861380	-	1	NA	intron (NM_198415, intron 4 of 9)	intron (NM_198415, intron 4 of 9)	15507	NM_198415	76722	Mm.316438	NM_198415	ENSMUSG00000021622	Ckmt2	2300008A19Rik|ScCKmit	creatine kinase, mitochondrial 2	protein-coding
mm_13081.1	chr2	91206510	91206526	+	1	NA	intron (NM_007387, intron 6 of 10)	intron (NM_007387, intron 6 of 10)	3606	NM_007387	11432	Mm.45570	NM_007387	ENSMUSG00000002103	Acp2	Acp-2|LAP	acid phosphatase 2, lysosomal	protein-coding
mm_11586.1	chr2	33207022	33207029	+	1	NA	intron (NM_001290572, intron 8 of 17)	intron (NM_001290572, intron 8 of 17)	-8936	NM_011923	26360	Mm.208919	NM_011923	ENSMUSG00000004105	Angptl2	AI593246|AW260363|Arp2	angiopoietin-like 2	protein-coding
mm_10981.1	chr2	25877848	25877883	+	1	NA	promoter-TSS (NM_001302351)	promoter-TSS (NM_001302351)	82	NM_001302351	227632	Mm.119462	NM_175462	ENSMUSG00000058740	Kcnt1	C030030G16Rik|Slack|Slo2.2|slo2	potassium channel, subfamily T, member 1	protein-coding
mm_91568.1	chr10	40072261	40072268	-	1	NA	intron (NM_001114332, intron 3 of 5)	intron (NM_001114332, intron 3 of 5)	-46996	NM_144821	215929	Mm.55513	NM_144821	ENSMUSG00000038522	Mfsd4b1	AI317395|AI482555|Naglt1a	major facilitator superfamily domain containing 4B1	protein-coding
mm_71096.1	chr8	35206540	35206542	+	1	NA	Intergenic	Intergenic	-169200	NM_177741	244416	Mm.247126	NM_177741	ENSMUSG00000046794	Ppp1r3b	6430576E21|AW821953|GL|PTG	protein phosphatase 1, regulatory (inhibitor) subunit 3B	protein-coding
mm_141870.1	chr17	34823454	34823465	-	1	NA	promoter-TSS (NM_011413)	promoter-TSS (NM_011413)	-5	NM_011413	625018	Mm.439678	NM_011413		C4a	Slp|SlpA	complement component 4A (Rodgers blood group)	protein-coding
mm_55418.1	chr6	65125784	65125796	-	1	NA	intron (NM_019455, intron 4 of 5)	intron (NM_019455, intron 4 of 5)	18940	NM_019455	54486	Mm.410688	NM_019455	ENSMUSG00000029919	Hpgds	H-PGDS|Ptgds2	hematopoietic prostaglandin D synthase	protein-coding
mm_35716.1	chr4	44526274	44526285	-	1	NA	Intergenic	Intergenic	-176521	NR_073462	70602	Mm.491142	NR_073462	ENSMUSG00000103995	5730488B01Rik	-	RIKEN cDNA 5730488B01 gene	ncRNA
mm_151277.1	chr19	55253642	55253678	+	1	NA	5' UTR (NM_027976, exon 1 of 22)	5' UTR (NM_027976, exon 1 of 22)	291	NM_027976	433256	Mm.292056	NM_027976	ENSMUSG00000024981	Acsl5	1700030F05Rik|ACS2|ACS5|Facl5	acyl-CoA synthetase long-chain family member 5	protein-coding
mm_103883.1	chr11	83573674	83573684	-	1	NA	3' UTR (NM_011338, exon 4 of 4)	3' UTR (NM_011338, exon 4 of 4)	4957	NM_011338	20308	Mm.416125	NM_011338	ENSMUSG00000019122	Ccl9	CCF18|MRP-2|Scya10|Scya9	chemokine (C-C motif) ligand 9	protein-coding
mm_138014.1	chr17	33909410	33909429	+	1	NA	promoter-TSS (NM_001199733)	promoter-TSS (NM_001199733)	-26	NM_007829	13163	Mm.271809	NM_007829	ENSMUSG00000002307	Daxx	-	Fas death domain-associated protein	protein-coding
mm_48508.1	chr5	142821286	142821290	-	1	NA	Intergenic	Intergenic	-3901	NM_001122730	231861	Mm.354649	NM_178242	ENSMUSG00000039477	Tnrc18	BC025631|EG381742|Zfp469	trinucleotide repeat containing 18	protein-coding
mm_90400.1	chr10	127325656	127325675	+	1	NA	intron (NM_146011, intron 3 of 14)	intron (NM_146011, intron 3 of 14)	1938	NM_146011	216445	Mm.227198	NM_146011	ENSMUSG00000040345	Arhgap9	AU043488	Rho GTPase activating protein 9	protein-coding
mm_68966.1	chr7	126584413	126584433	-	1	NA	promoter-TSS (NM_138310)	promoter-TSS (NM_138310)	-585	NM_138310	171504	Mm.170665	NM_138310	ENSMUSG00000042759	Apobr	Apob-48r|Apob48r	apolipoprotein B receptor	protein-coding
mm_62293.1	chr7	99979711	99979732	+	1	NA	intron (NM_175388, intron 1 of 5)	intron (NM_175388, intron 1 of 5)	737	NM_175388	108937	Mm.323087	NM_175388	ENSMUSG00000058761	Rnf169	2900057K09Rik	ring finger protein 169	protein-coding
mm_152981.1	chr19	29499193	29499224	-	1	NA	Intergenic	Intergenic	22779	NR_015567	77779	Mm.458738	NR_015567	ENSMUSG00000097855	A930007I19Rik	-	RIKEN cDNA A930007I19 gene	ncRNA
mm_113168.1	chr13	24813455	24813487	+	1	NA	TTS (NM_024473)	TTS (NM_024473)	11814	NM_024473	79555	Mm.266668	NM_024473	ENSMUSG00000019132	BC005537	8030460C05Rik|C78201	cDNA sequence BC005537	protein-coding
mm_92394.1	chr10	76599707	76599718	-	1	NA	exon (NM_001347207, exon 28 of 28)	exon (NM_001347207, exon 28 of 28)	23692	NM_146007	12834	Mm.1949	NM_146007	ENSMUSG00000020241	Col6a2	Col6a-2	collagen, type VI, alpha 2	protein-coding
mm_91031.1	chr10	18023230	18023265	-	1	NA	promoter-TSS (NM_028440)	promoter-TSS (NM_028440)	5	NM_028440	73112	Mm.276041	NM_028440	ENSMUSG00000078453	Abracl	1700028I04Rik|3110003A17Rik	ABRA C-terminal like	protein-coding
mm_160380.1	chr8	43182893	43182893	+	1	NA	promoter-TSS (NM_001160412)	promoter-TSS (NM_001160412)	-229	NM_001160412	622117	Mm.390031	NM_001160412	ENSMUSG00000091490	Triml2	EG622117|Tu4	tripartite motif family-like 2	protein-coding
mm_160623.1	chr9	98422747	98422747	+	1	NA	promoter-TSS (NM_011254)	promoter-TSS (NM_011254)	-214	NM_011254	19659	Mm.279741	NM_011254	ENSMUSG00000046402	Rbp1	CRBPI|Crbp|Rbp-1	retinol binding protein 1, cellular	protein-coding
mm_110031.1	chr12	16850719	16850757	-	1	NA	Intergenic	ERV3-16A3_LTR|LTR|ERVL	39773	NM_033270	50496	Mm.23296	NM_033270	ENSMUSG00000057469	E2f6	AI462434|E2F6a|E2F6b|EMA	E2F transcription factor 6	protein-coding
mm_149825.1	chr19	24476756	24476766	+	1	NA	exon (NM_026520, exon 1 of 1)	exon (NM_026520, exon 1 of 1)	713	NM_026520	68034	Mm.440181	NM_026520	ENSMUSG00000074922	Fam122a	2410124L17Rik|2900009I07Rik|ENSMUSG00000051082|Gm9849	family with sequence similarity 122, member A	protein-coding
mm_121957.1	chr14	24486995	24487064	-	1	NA	promoter-TSS (NM_001081247)	promoter-TSS (NM_001081247)	17	NM_001081247	218832	Mm.343610	NM_183157	ENSMUSG00000025280	Polr3a	9330175N20Rik|BC053071|RPC1|RPC155	polymerase (RNA) III (DNA directed) polypeptide A	protein-coding
mm_67636.1	chr7	84409883	84409924	-	1	NA	5' UTR (NM_007488, exon 1 of 19)	5' UTR (NM_007488, exon 1 of 19)	135	NM_007488	11864	Mm.38594	NM_007488	ENSMUSG00000015709	Arnt2	Hif-2b|bHLHe1|mKIAA0307	aryl hydrocarbon receptor nuclear translocator 2	protein-coding
mm_11719.1	chr2	36249656	36249664	+	1	NA	intron (NM_008969, intron 10 of 10)	ID4_|SINE|ID	19234	NM_008969	19224	Mm.275434	NM_008969	ENSMUSG00000047250	Ptgs1	COX1|Cox-1|Cox-3|PGHS-1|PHS 1|Pghs1	prostaglandin-endoperoxide synthase 1	protein-coding
mm_80599.1	chr9	86467225	86467261	+	1	NA	promoter-TSS (NM_177208)	promoter-TSS (NM_177208)	89	NM_177208	320615	Mm.245500	NM_177208	ENSMUSG00000034973	Dopey1	B130005I07Rik|BC035275|C130028L17|D9Ertd809e	dopey family member 1	protein-coding
mm_94215.1	chr11	3163912	3163929	+	1	NA	intron (NM_030207, intron 9 of 32)	RLTR51B_Mm|LTR|ERVK?	29543	NM_030207	78887	Mm.394071	NM_030207	ENSMUSG00000023764	Sfi1	-	Sfi1 homolog, spindle assembly associated (yeast)	protein-coding
mm_68348.1	chr7	106507147	106507172	-	1	NA	Intergenic	Intergenic	-66086	NR_003967	209380	Mm.461779	NM_001001318		Gm4759	EG209380	GTPase, very large interferon inducible 1 pseudogene	pseudo
mm_70492.1	chr8	12573018	12573060	+	1	NA	promoter-TSS (NM_024279)	promoter-TSS (NM_024279)	-10	NM_024279	78634	Mm.116871	NM_024279	ENSMUSG00000010435	Spaca7	1700094C09Rik	sperm acrosome associated 7	protein-coding
mm_153866.1	chr19	46672884	46672900	-	1	NA	5' UTR (NM_007809, exon 1 of 8)	5' UTR (NM_007809, exon 1 of 8)	108	NM_007809	13074	Mm.1262	NM_007809	ENSMUSG00000003555	Cyp17a1	Cyp17|p450c17	cytochrome P450, family 17, subfamily a, polypeptide 1	protein-coding
mm_31195.1	chr4	43631588	43631598	+	1	NA	promoter-TSS (NM_173788)	promoter-TSS (NM_173788)	-342	NM_173788	230103	Mm.103477	NM_173788	ENSMUSG00000028469	Npr2	GC-B|GC-B2|GC-B3|cn|mNPR-B|pwe	natriuretic peptide receptor 2	protein-coding
mm_121145.1	chr14	101898559	101898567	+	1	NA	exon (NM_201529, exon 13 of 31)	exon (NM_201529, exon 13 of 31)	57940	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_156280.1	chrX	136837125	136837147	+	1	NA	3' UTR (NM_011123, exon 7 of 7)	3' UTR (NM_011123, exon 7 of 7)	14390	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_133345.1	chr16	81238707	81238711	+	1	NA	intron (NM_001113208, intron 1 of 17)	intron (NM_001113208, intron 1 of 17)	38012	NM_010954	17968	Mm.433941	NM_010954	ENSMUSG00000022762	Ncam2	Ncam-2|Ocam|RNCAM	neural cell adhesion molecule 2	protein-coding
mm_49337.1	chr6	21312207	21312219	+	1	NA	intron (NM_019697, intron 1 of 5)	B3A|SINE|B2	96104	NM_019697	16508	Mm.425316	NM_019697	ENSMUSG00000060882	Kcnd2	AI839615|AW555701|Kv4.2|R75121|mKIAA1044	potassium voltage-gated channel, Shal-related family, member 2	protein-coding
mm_149044.1	chr19	8820694	8820704	+	1	NA	exon (NM_001081196, exon 1 of 14)	exon (NM_001081196, exon 1 of 14)	1298	NM_001081196	68693	Mm.476519	NM_001081196	ENSMUSG00000071659	Hnrnpul2	1110031M08Rik|AI465155|Hnrpul2	heterogeneous nuclear ribonucleoprotein U-like 2	protein-coding
mm_133883.1	chr16	96525406	96525455	+	1	NA	exon (NM_008791, exon 3 of 3)	exon (NM_008791, exon 3 of 3)	57824	NM_008791	18546	Mm.5023	NM_008791	ENSMUSG00000090223	Pcp4	P16Rimb19|Pcp-4|Pep19	Purkinje cell protein 4	protein-coding
mm_26301.1	chr3	142509883	142509891	+	1	NA	intron (NM_153564, intron 10 of 10)	intron (NM_153564, intron 10 of 10)	12953	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_87632.1	chr10	58324686	58324688	+	1	NA	intron (NM_026148, intron 1 of 9)	Charlie1|DNA|hAT-Charlie	1221	NM_026148	110829	Mm.57734	NM_026148	ENSMUSG00000019920	Lims1	2310016J22Rik|4921524A02Rik|AI507642|AU021743|AW551584|C430041B13Rik|Lims1l|PINCH|PINCH1	LIM and senescent cell antigen-like domains 1	protein-coding
mm_61912.1	chr7	90144739	90144764	+	1	NA	intron (NM_001252520, intron 1 of 20)	B1_Mus2|SINE|Alu	14519	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_120393.1	chr14	64652486	64652494	+	1	NA	promoter-TSS (NM_001081177)	promoter-TSS (NM_001081177)	-41	NM_001081177	16554	Mm.23611	NM_001081177	ENSMUSG00000060012	Kif13b	5330429L19Rik|6030414C01|AI429803|C130021D12Rik|GAKIN	kinesin family member 13B	protein-coding
mm_137730.1	chr17	29274221	29274229	+	1	NA	intron (NM_030561, intron 1 of 8)	intron (NM_030561, intron 1 of 8)	5437	NM_030561	80748	Mm.290116	NM_030561	ENSMUSG00000052712	BC004004	2400006G15Rik	cDNA sequence BC004004	protein-coding
mm_129125.1	chr15	76172068	76172077	-	1	NA	3' UTR (NM_201393, exon 32 of 32)	3' UTR (NM_201393, exon 32 of 32)	23638	NM_201394	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
mm_3948.1	chr1	163994925	163994935	+	1	NA	promoter-TSS (NM_201364)	promoter-TSS (NM_201364)	-15	NM_027279	69962	Mm.27284	NM_027279	ENSMUSG00000041396	Mettl18	2810422O20Rik|C78571	methyltransferase like 18	protein-coding
mm_132740.1	chr16	44123541	44123559	+	1	NA	intron (NM_007508, intron 1 of 14)	intron (NM_007508, intron 1 of 14)	15469	NM_007508	11964	Mm.217787	NM_007508	ENSMUSG00000052459	Atp6v1a	AI647066|Atp6a1|Atp6a2|Atp6v1a1|VA68|VPP2	ATPase, H+ transporting, lysosomal V1 subunit A	protein-coding
mm_114163.1	chr13	55413583	55413592	+	1	NA	exon (NM_011392, exon 13 of 13)	exon (NM_011392, exon 13 of 13)	1645	NM_029303	75477	Mm.432537	NM_029303	ENSMUSG00000044444	Pfn3	1700012P12Rik	profilin 3	protein-coding
mm_75029.1	chr8	31950083	31950091	-	1	NA	Intergenic	Intergenic	-31884	NM_178591	211323	Mm.153432	NM_178591	ENSMUSG00000062991	Nrg1	6030402G23Rik|ARIA|D230005F13Rik|GGF|GGFII|HRG|HRGalpha|Hgl|NDF|SMDF	neuregulin 1	protein-coding
mm_149454.1	chr19	11497576	11497580	+	1	NA	intron (NM_001164202, intron 1 of 4)	intron (NM_001164202, intron 1 of 4)	5540	NM_001164202	666926	Mm.486382	NM_001164202	ENSMUSG00000058470	Gm8369	EG666926	predicted gene 8369	protein-coding
mm_16799.1	chr2	10116724	10116735	-	1	NA	exon (NM_010582, exon 8 of 21)	exon (NM_010582, exon 8 of 21)	13954	NM_010582	16425	Mm.182043	NM_010582	ENSMUSG00000037254	Itih2	AI747202|Intin2|Itih-2	inter-alpha trypsin inhibitor, heavy chain 2	protein-coding
mm_54901.1	chr6	47550971	47550981	-	1	NA	intron (NM_007971, intron 8 of 19)	ID4_|SINE|ID	44054	NM_007971	14056	Mm.246688	NM_007971	ENSMUSG00000029687	Ezh2	Enx-1|Enx1h|KMT6|mKIAA4065	enhancer of zeste 2 polycomb repressive complex 2 subunit	protein-coding
mm_19474.1	chr2	92540950	92540953	-	1	NA	Intergenic	Intergenic	-51255	NR_106080	102466819		NR_106080	ENSMUSG00000099223	Mir7221	Gm27378|mmu-mir-7221	microRNA 7221	ncRNA
mm_12700.1	chr2	76537331	76537335	+	1	NA	intron (NM_001290733, intron 4 of 26)	intron (NM_001290733, intron 4 of 26)	38327	NM_001290735	99031	Mm.240435	NM_145525	ENSMUSG00000042359	Osbpl6	1110062M20Rik|AI596402|ORP-6|mKIAA4128	oxysterol binding protein-like 6	protein-coding
mm_160899.1	chr11	74045385	74045385	-	1	NA	promoter-TSS (NM_147003)	promoter-TSS (NM_147003)	-113	NM_147003	259005	Mm.377784	NM_147003	ENSMUSG00000047444	Olfr139	M5|MOR255-2	olfactory receptor 139	protein-coding
mm_141078.1	chr17	25861457	25861510	-	1	NA	promoter-TSS (NM_001163766)	promoter-TSS (NM_001163766)	32	NM_001163766	106618	Mm.35470	NM_134124	ENSMUSG00000073434	Wdr90	3230401M21Rik|AI551153|mKIAA1924	WD repeat domain 90	protein-coding
mm_103521.1	chr11	76844318	76844320	-	1	NA	intron (NM_007754, intron 1 of 20)	intron (NM_007754, intron 1 of 20)	2689	NM_007754	12874	Mm.276736	NM_007754	ENSMUSG00000020841	Cpd	AA960140|AW322530|D830034L15Rik	carboxypeptidase D	protein-coding
mm_59117.1	chr7	19832057	19832108	+	1	NA	Intergenic	Intergenic	-9327	NM_033601	12051	Mm.439658	NM_033601	ENSMUSG00000053175	Bcl3	AI528691|Bcl-3	B cell leukemia/lymphoma 3	protein-coding
mm_118798.1	chr14	24490750	24490756	+	1	NA	promoter-TSS (NM_207634)	promoter-TSS (NM_207634)	72	NM_011297	20088	Mm.16775	NM_011297	ENSMUSG00000025290	Rps24	-	ribosomal protein S24	protein-coding
mm_43492.1	chr5	136953690	136953693	+	1	NA	intron (NM_001347504, intron 1 of 3)	PB1D10|SINE|Alu	416	NM_001347504	66437	Mm.25849	NM_025562	ENSMUSG00000019054	Fis1	2010003O14Rik|Ttc11	fission, mitochondrial 1	protein-coding
mm_140774.1	chr17	17876669	17876680	-	1	NA	exon (NM_013521, exon 2 of 2)	exon (NM_013521, exon 2 of 2)	7265	NM_013521	14293	Mm.56951	NM_013521	ENSMUSG00000045551	Fpr1	FPR|LXA4R|fMLF-R	formyl peptide receptor 1	protein-coding
mm_89995.1	chr10	112227563	112227564	+	1	NA	Intergenic	RMER17C|LTR|ERVK	-43560	NM_001025581	268345	Mm.336242	NM_001025581	ENSMUSG00000035681	Kcnc2	AW047325|B230117I07|KShIIIA|Kv3.2	potassium voltage gated channel, Shaw-related subfamily, member 2	protein-coding
mm_5795.1	chr1	52091067	52091078	-	1	NA	intron (NM_001308266, intron 15 of 24)	L1_Mus1|LINE|L1	-28366	NM_009283	20846	Mm.277406	NM_009283	ENSMUSG00000026104	Stat1	2010005J02Rik|AA408197	signal transducer and activator of transcription 1	protein-coding
mm_115063.1	chr13	100770401	100770401	+	1	NA	intron (NM_021886, intron 4 of 8)	intron (NM_021886, intron 4 of 8)	5498	NM_021886	26886	Mm.273502	NM_021886	ENSMUSG00000045273	Cenph	1700021I11Rik|2410018A12Rik|2610042E16Rik|2810046K12Rik|AU044255|CENP-H|ENP	centromere protein H	protein-coding
mm_85582.1	chr9	107296472	107296507	-	1	NA	promoter-TSS (NM_009895)	promoter-TSS (NM_009895)	-170	NM_001317354	12700	Mm.4592	NM_009895	ENSMUSG00000032578	Cish	CIS-1|CIS1|Cis|F17|F23|SOCS	cytokine inducible SH2-containing protein	protein-coding
mm_61985.1	chr7	91090698	91090727	+	1	NA	promoter-TSS (NM_011807)	promoter-TSS (NM_011807)	-74	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_69131.1	chr7	127026983	127027025	-	1	NA	promoter-TSS (NM_010772)	promoter-TSS (NM_010772)	-525	NM_010772	17188	Mm.378964	NM_010772	ENSMUSG00000030678	Maz	MAZI|PUR1|Pur-1|SAF-1|SAF-2	MYC-associated zinc finger protein (purine-binding transcription factor)	protein-coding
mm_75325.1	chr8	43141487	43141506	-	1	NA	promoter-TSS (NM_177742)	promoter-TSS (NM_177742)	-10	NM_177742	244448	Mm.64542	NM_177742	ENSMUSG00000031651	Triml1	4933403D14|BC050188	tripartite motif family-like 1	protein-coding
mm_138237.1	chr17	34417348	34417361	+	1	NA	5' UTR (NM_001001177, exon 3 of 20)	5' UTR (NM_001001177, exon 3 of 20)	18534	NM_001163855	407788	Mm.73205	NM_001001177	ENSMUSG00000057246	BC051142	NG8|TSBP|Tesb|Tesbp	cDNA sequence BC051142	protein-coding
mm_165024.1	chr19	32389426	32389464	+	1	NA	promoter-TSS (NM_144792)	promoter-TSS (NM_144792)	229	NR_033198	67188	Mm.391160	NR_033198	ENSMUSG00000097787	2700046G09Rik	-	RIKEN cDNA 2700046G09 gene	ncRNA
mm_22689.1	chr3	17790052	17790068	+	1	NA	non-coding (NR_033490, exon 1 of 3)	non-coding (NR_033490, exon 1 of 3)	139	NR_033490	70441	Mm.458192	NR_033490	ENSMUSG00000100252	Mir124-2hg	100040120|2610100L16Rik|6430547I21Rik|A930005K07Rik|AW125202|Gm2612	Mir124-2 host gene (non-protein coding)	ncRNA
mm_90598.1	chr10	128322402	128322412	+	1	NA	promoter-TSS (NM_019953)	promoter-TSS (NM_019953)	-52	NM_019953	56530	Mm.44220	NM_019953	ENSMUSG00000025381	Cnpy2	5330432A10Rik|AW229003|D10Bwg1546e|Tmem4|Zsig9	canopy FGF signaling regulator 2	protein-coding
mm_114442.1	chr13	66441277	66441288	+	1	NA	promoter-TSS (NM_001290196)	promoter-TSS (NM_001290196)	-164	NM_001290196	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
mm_60243.1	chr7	43727098	43727102	+	1	NA	TTS (NM_001039042)	TTS (NM_001039042)	14533	NM_001039042	626834	Mm.389891	NM_001039042	ENSMUSG00000054046	Klk13	Egfbp-2|mGk-13	kallikrein related-peptidase 13	protein-coding
mm_54016.1	chr6	8364468	8364477	-	1	NA	intron (NM_001302353, intron 2 of 4)	intron (NM_001302353, intron 2 of 4)	105184	NM_001302353	100036521	Mm.446106	NM_001302353	ENSMUSG00000089862	Umad1	Gm16039|OTTMUSG00000029336	UMAP1-MVP12 associated (UMA) domain containing 1	protein-coding
mm_91573.1	chr10	40128314	40128345	-	1	NA	intron (NM_001114332, intron 1 of 5)	RLTR16|LTR|ERVK	13925	NM_028247	72472	Mm.186778	NM_028247	ENSMUSG00000019838	Slc16a10	2610103N14Rik|9830169E08|Mct10|PRO0813|TAT1	solute carrier family 16 (monocarboxylic acid transporters), member 10	protein-coding
mm_82923.1	chr9	35116761	35116793	-	1	NA	promoter-TSS (NR_029475)	promoter-TSS (NR_029475)	33	NM_009178	20443	Mm.275973	NM_009178	ENSMUSG00000032038	St3gal4	Siat4c	ST3 beta-galactoside alpha-2,3-sialyltransferase 4	protein-coding
mm_96813.1	chr11	69992368	69992385	+	1	NA	exon (NM_019749, exon 2 of 4)	exon (NM_019749, exon 2 of 4)	1006	NM_019749	56486	Mm.272460	NM_019749	ENSMUSG00000018567	Gabarap	-	gamma-aminobutyric acid receptor associated protein	protein-coding
mm_85648.1	chr9	107656676	107656692	-	1	NA	intron (NM_023805, intron 7 of 15)	intron (NM_023805, intron 7 of 15)	10715	NM_023805	76257	Mm.296560	NM_023805	ENSMUSG00000010064	Slc38a3	0610012J02Rik|D9Ucla2|Nat1|Slc38-3|Sn1|Snat3|mNAT	solute carrier family 38, member 3	protein-coding
mm_57171.1	chr6	122846513	122846535	-	1	NA	TTS (NM_009779)	TTS (NM_009779)	9633	NM_009779	12267	Mm.2408	NM_009779	ENSMUSG00000040552	C3ar1	AZ3B|C3AR|HNFAG09	complement component 3a receptor 1	protein-coding
mm_30766.1	chr4	15989017	15989042	+	1	NA	exon (NM_013752, exon 14 of 16)	exon (NM_013752, exon 14 of 16)	24848	NM_145950	209212	Mm.46455	NM_145950	ENSMUSG00000041153	Osgin2	BC010311|C230027H09Rik	oxidative stress induced growth inhibitor family member 2	protein-coding
mm_52076.1	chr6	97827446	97827461	+	1	NA	intron (NM_001113198, intron 1 of 9)	intron (NM_001113198, intron 1 of 9)	20395	NM_001113198	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_90399.1	chr10	127325636	127325651	+	1	NA	intron (NM_146011, intron 3 of 14)	intron (NM_146011, intron 3 of 14)	1916	NM_146011	216445	Mm.227198	NM_146011	ENSMUSG00000040345	Arhgap9	AU043488	Rho GTPase activating protein 9	protein-coding
mm_162533.1	chr1	165839887	165839898	-	1	NA	intron (NM_001113391, intron 1 of 7)	intron (NM_001113391, intron 1 of 7)	51211	NM_001113392	12503	Mm.217308	NM_031162	ENSMUSG00000005763	Cd247	4930549J05Rik|A430104F18Rik|AW552088|Cd3|Cd3-eta|Cd3-zeta|Cd3h|Cd3z|Cd3zeta|T3z|Tcrk|Tcrz	CD247 antigen	protein-coding
mm_159567.1	chr4	112081528	112081528	+	1	NA	promoter-TSS (NM_178786)	promoter-TSS (NM_178786)	58	NM_178786	320640	Mm.253775	NM_178786	ENSMUSG00000055960	Skint4	9530098N22Rik	selection and upkeep of intraepithelial T cells 4	protein-coding
mm_128219.1	chr15	36346174	36346181	-	1	NA	Intergenic	Intergenic	-63030	NM_013923	30945	Mm.5181	NM_013923	ENSMUSG00000022280	Rnf19a	AA032313|Dorfin|Rnf19|UIP117|Ubce7ip2|XYbp	ring finger protein 19A	protein-coding
mm_40645.1	chr5	64970093	64970132	+	1	NA	promoter-TSS (NR_030577)	promoter-TSS (NR_030577)	37	NM_026667	68303	Mm.258545	NM_026667	ENSMUSG00000029185	Fam114a1	1190001N04Rik|9130005N14Rik|Noxp20	family with sequence similarity 114, member A1	protein-coding
mm_165857.1	chr4	19709174	19709180	-	1	NA	promoter-TSS (NM_177327)	promoter-TSS (NM_177327)	-173	NR_074090	107568	Mm.78312	NM_177327	ENSMUSG00000041058	Wwp1	8030445B08Rik|AIP5|SDRP1|Tiul1	WW domain containing E3 ubiquitin protein ligase 1	protein-coding
mm_110709.1	chr12	69357110	69357116	-	1	NA	promoter-TSS (NM_025441)	promoter-TSS (NM_025441)	63	NM_025441	66244	Mm.46705	NM_025441	ENSMUSG00000020982	Nemf	1500011I12Rik|4933405E14Rik|Sdccag1	nuclear export mediator factor	protein-coding
mm_83515.1	chr9	46031228	46031228	-	1	NA	intron (NM_027498, intron 1 of 24)	intron (NM_027498, intron 1 of 24)	18408	NM_027498	70661	Mm.219459	NM_027498	ENSMUSG00000034135	Sik3	5730525O22Rik|9030204A07Rik|AI447252|AI846254|AI849445|Qsk|SIK-3|mKIAA0999	SIK family kinase 3	protein-coding
mm_28665.1	chr3	95281664	95281687	-	1	NA	5' UTR (NM_173347, exon 1 of 8)	5' UTR (NM_173347, exon 1 of 8)	401	NM_173347	229589	Mm.14155	NM_173347	ENSMUSG00000015711	Prune1	9230112O05Rik|C130058A12|DRES-17|HTCD37|PRUNEM1|Prune|Prune-M1	prune exopolyphosphatase	protein-coding
mm_135935.1	chr16	74279196	74279206	-	1	NA	intron (NM_175549, intron 2 of 27)	(TG)n|Simple_repeat|Simple_repeat	62866	NR_030464	751561		NR_030464	ENSMUSG00000104758	Mir691	Mirn691|mir-691|mmu-mir-691	microRNA 691	ncRNA
mm_118085.1	chr13	103753125	103753148	-	1	NA	exon (NM_172592, exon 6 of 10)	exon (NM_172592, exon 6 of 10)	11446	NM_172592	218543	Mm.458176	NM_172592	ENSMUSG00000032621	Srek1	8430401B01|AI450757|AI462342|SRrp508|SRrp86|Sfrs12|Srsf12	splicing regulatory glutamine/lysine-rich protein 1	protein-coding
mm_69824.1	chr7	141265961	141265993	-	1	NA	5' UTR (NM_001252601, exon 2 of 10)	5' UTR (NM_001252601, exon 2 of 10)	447	NM_001252601	54123	Mm.3233	NM_016850	ENSMUSG00000025498	Irf7	-	interferon regulatory factor 7	protein-coding
mm_50371.1	chr6	48676409	48676422	+	1	NA	intron (NM_174960, intron 1 of 1)	intron (NM_174960, intron 1 of 1)	280	NM_174960	317758	Mm.116971	NM_174960	ENSMUSG00000051124	Gimap9	A630002K24|BB145400	GTPase, IMAP family member 9	protein-coding
mm_86906.1	chr10	22645088	22645109	+	1	NA	promoter-TSS (NM_178934)	promoter-TSS (NM_178934)	87	NM_178934	353169	Mm.473705	NM_178934	ENSMUSG00000037490	Slc2a12	GLUT-12|Glut12	solute carrier family 2 (facilitated glucose transporter), member 12	protein-coding
mm_79070.1	chr9	46240783	46240793	+	1	NA	promoter-TSS (NM_007468)	promoter-TSS (NM_007468)	-56	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_30288.1	chr3	148989444	148989496	-	1	NA	Intergenic	CpG	-34835	NM_001081298	99633	Mm.9776	NM_001081298	ENSMUSG00000028184	Adgrl2	AI450192|CIRL-2|Gm619|Lec1|Lphh1|Lphn2|mKIAA0786	adhesion G protein-coupled receptor L2	protein-coding
mm_164645.1	chr17	35253533	35253593	+	1	NA	3' UTR (NM_001252457, exon 11 of 11)	3' UTR (NM_001252457, exon 11 of 11)	2274	NR_106169	102465886		NR_106169	ENSMUSG00000098269	Mir8094	Gm27513|mmu-mir-8094	microRNA 8094	ncRNA
mm_70040.1	chr7	142577831	142577843	-	1	NA	promoter-TSS (NR_030416)	promoter-TSS (NR_030416)	309	NR_130974	14955	Mm.14802	NR_001592	ENSMUSG00000000031	H19	AI747191	H19, imprinted maternally expressed transcript	ncRNA
mm_100405.1	chr11	119410195	119410206	+	1	NA	Intergenic	Intergenic	19728	NR_035453	100316690		NR_035453	ENSMUSG00000088015	Mir1932	mir-1932|mmu-mir-1932	microRNA 1932	ncRNA
mm_18517.1	chr2	62645943	62645964	-	1	NA	5' UTR (NM_027835, exon 1 of 16)	5' UTR (NM_027835, exon 1 of 16)	302	NM_027835	71586	Mm.136224	NM_027835	ENSMUSG00000026896	Ifih1	9130009C22Rik|Helicard|Hlcd|MDA5|RLR-2	interferon induced with helicase C domain 1	protein-coding
mm_80140.1	chr9	70754169	70754180	+	1	NA	exon (NM_007399, exon 9 of 16)	exon (NM_007399, exon 9 of 16)	75192	NM_007399	11487	Mm.3037	NM_007399	ENSMUSG00000054693	Adam10	1700031C13Rik|MADM|kuz|kuzbanian	a disintegrin and metallopeptidase domain 10	protein-coding
mm_67748.1	chr7	92258675	92258688	-	1	NA	intron (NM_001243047, intron 1 of 10)	intron (NM_001243047, intron 1 of 10)	23711	NM_001243047	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_41566.1	chr5	93154967	93155017	+	1	NA	exon (NM_001310669, exon 4 of 11)	exon (NM_001310669, exon 4 of 11)	51503	NM_017367	12453	Mm.250419	NM_017367	ENSMUSG00000063015	Ccni	-	cyclin I	protein-coding
mm_71551.1	chr8	48110004	48110023	+	1	NA	promoter-TSS (NR_027759)	promoter-TSS (NR_027759)	0	NM_001161515	320685	Mm.121549	NM_178788	ENSMUSG00000031562	Dctd	6030466N05Rik	dCMP deaminase	protein-coding
mm_97947.1	chr11	83664389	83664483	+	1	NA	3' UTR (NM_013652, exon 3 of 3)	3' UTR (NM_013652, exon 3 of 3)	1852	NM_013652	20303	Mm.244263	NM_013652	ENSMUSG00000018930	Ccl4	AT744.1|Act-2|MIP-1B|Mip1b|Scya4	chemokine (C-C motif) ligand 4	protein-coding
mm_1866.1	chr1	85272401	85272416	+	1	NA	Intergenic	Intergenic	-1842	NM_001037909	620078	Mm.386456	NM_175219	ENSMUSG00000052477	C130026I21Rik	4930565N07Rik|OTTMUSG00000029174	RIKEN cDNA C130026I21 gene	protein-coding
mm_72832.1	chr8	88272439	88272451	+	1	NA	promoter-TSS (NM_007406)	promoter-TSS (NM_007406)	42	NM_007406	11513	Mm.288206	NM_007406	ENSMUSG00000031659	Adcy7	AA407758	adenylate cyclase 7	protein-coding
mm_37180.1	chr4	117277641	117277652	-	1	NA	intron (NM_025739, intron 10 of 14)	intron (NM_025739, intron 10 of 14)	11809	NM_001310730	66743	Mm.318331	NM_025739	ENSMUSG00000028677	Rnf220	4732477A13|4931406I20Rik|5730503K05Rik|AV302541	ring finger protein 220	protein-coding
mm_74376.1	chr8	128685395	128685458	+	1	NA	promoter-TSS (NM_010578)	promoter-TSS (NM_010578)	-228	NM_010578	16412	Mm.263396	NM_010578	ENSMUSG00000025809	Itgb1	4633401G24Rik|AA409975|AA960159|CD29|ENSMUSG00000051907|Fnrb|Gm9863|gpIIa	integrin beta 1 (fibronectin receptor beta)	protein-coding
mm_14975.1	chr2	152105723	152105739	+	1	NA	exon (NM_029688, exon 1 of 2)	exon (NM_029688, exon 1 of 2)	207	NM_029688	76650	Mm.218639	NM_029688	ENSMUSG00000032802	Srxn1	1700127B04Rik|AI854065|AW488194|Npn3|Srx|Srx1|TX01	sulfiredoxin 1 homolog (S. cerevisiae)	protein-coding
mm_109723.1	chr12	116281181	116281229	+	1	NA	promoter-TSS (NM_028731)	promoter-TSS (NM_028731)	-17	NM_028731	52635	Mm.273755	NM_028731	ENSMUSG00000021171	Esyt2	2410017M09Rik|4921504I16Rik|CHR2SYT|D12Ertd551e|Fam62b	extended synaptotagmin-like protein 2	protein-coding
mm_66380.1	chr7	43953968	43954001	-	1	NA	exon (NM_008457, exon 3 of 5)	exon (NM_008457, exon 3 of 5)	3318	NM_008457	16624	Mm.435488	NM_008457	ENSMUSG00000063089	Klk1b8	Klk8|Nrpn|TADG14|kallikrein|mGK-8	kallikrein 1-related peptidase b8	protein-coding
mm_104756.1	chr11	98463842	98463850	-	1	NA	TTS (NM_011771)	TTS (NM_011771)	17012	NM_010346	14786	Mm.276702	NM_010346	ENSMUSG00000019312	Grb7	mKIAA4028	growth factor receptor bound protein 7	protein-coding
mm_157890.1	chrX	75987630	75987638	-	1	NA	Intergenic	Intergenic	-112452	NM_001346519	102866	Mm.28777	NM_145629	ENSMUSG00000016382	Pls3	AI115446|AL024105	plastin 3 (T-isoform)	protein-coding
mm_159547.1	chr4	96077410	96077410	-	1	NA	exon (NM_145548, exon 1 of 9)	exon (NM_145548, exon 1 of 9)	130	NM_145548	230459	Mm.268175	NM_145548	ENSMUSG00000028571	Cyp2j13	-	cytochrome P450, family 2, subfamily j, polypeptide 13	protein-coding
mm_76467.1	chr8	85380997	85381053	-	1	NA	promoter-TSS (NM_001297612)	promoter-TSS (NM_001297612)	16	NM_001297612	213435	Mm.32804	NM_175441	ENSMUSG00000031698	Mylk3	D830007F02Rik|MLCK	myosin light chain kinase 3	protein-coding
mm_18009.1	chr2	38287175	38287195	-	1	NA	5' UTR (NM_146122, exon 1 of 22)	5' UTR (NM_146122, exon 1 of 22)	199	NM_146122	227801	Mm.314245	NM_146122	ENSMUSG00000035392	Dennd1a	6030446I19Rik|connecdenn	DENN/MADD domain containing 1A	protein-coding
mm_39847.1	chr5	30913399	30913403	+	1	NA	promoter-TSS (NM_133918)	promoter-TSS (NM_133918)	-385	NM_133918	100952	Mm.286375	NM_133918	ENSMUSG00000029163	Emilin1	5830419M17Rik|AW229038|BB105748|EMILIN-1|gp115	elastin microfibril interfacer 1	protein-coding
mm_138457.1	chr17	35138592	35138601	+	1	NA	exon (NM_001252469, exon 4 of 24)	exon (NM_001252469, exon 4 of 24)	2882	NM_001252469	224727	Mm.203962	NM_057171	ENSMUSG00000024392	Bag6	2410045D21Rik|AA408914|BAG-6|Bat3|D17H6S52E|G3|Scythe	BCL2-associated athanogene 6	protein-coding
mm_62825.1	chr7	113513830	113513846	+	1	NA	promoter-TSS (NM_027379)	promoter-TSS (NM_027379)	4	NM_027379	67420	Mm.206919	NM_026143	ENSMUSG00000030759	Far1	2600011M19Rik|2900034E22Rik|3732409C05Rik|AI850429|Mlstd2	fatty acyl CoA reductase 1	protein-coding
mm_10325.1	chr2	11339326	11339341	+	1	NA	promoter-TSS (NR_040369)	promoter-TSS (NR_040369)	-156	NR_040369	100503147	Mm.91961	NR_040369	ENSMUSG00000086006	Gm13293	OTTMUSG00000011311	predicted gene 13293	ncRNA
mm_34972.1	chr4	156012558	156012566	+	1	NA	3' UTR (NM_011341, exon 7 of 7)	3' UTR (NM_011341, exon 7 of 7)	-1133	NM_011659	22163	Mm.13885	NM_011659	ENSMUSG00000029075	Tnfrsf4	ACT35|CD134|Ly-70|Ox40|TXGP1L|Txgp1	tumor necrosis factor receptor superfamily, member 4	protein-coding
mm_157653.1	chrX	57326687	57326712	-	1	NA	intron (NM_152801, intron 2 of 21)	intron (NM_152801, intron 2 of 21)	12030	NM_152801	73341	Mm.261443	NM_152801	ENSMUSG00000031133	Arhgef6	1600028C08Rik|1700038J06Rik|4930592P22Rik|alpha-PIX	Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_172253.1	chr6	70217442	70217449	-	1	NA	Intergenic	Intergenic	574730	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_87134.1	chr10	34284906	34284911	+	1	NA	TTS (NM_009433)	TTS (NM_009433)	2718	NM_009433	22110	Mm.20445	NM_009433	ENSMUSG00000047514	Tspyl1	Tspyl	testis-specific protein, Y-encoded-like 1	protein-coding
mm_80588.1	chr9	85748728	85748756	+	1	NA	intron (NM_001081282, intron 1 of 28)	intron (NM_001081282, intron 1 of 28)	592	NM_001081282	108837	Mm.22315	NM_175371	ENSMUSG00000035941	Ibtk	5430411K16Rik|AA409502|BTKI|mKIAA1417	inhibitor of Bruton agammaglobulinemia tyrosine kinase	protein-coding
mm_24808.1	chr3	95559672	95559691	+	1	NA	promoter-TSS (NM_001289534)	promoter-TSS (NM_001289534)	4	NM_001289532	67981	Mm.179050	NM_026489	ENSMUSG00000028109	Hormad1	4921522K05Rik|Nohma	HORMA domain containing 1	protein-coding
mm_139759.1	chr17	64600703	64600739	+	1	NA	promoter-TSS (NM_008549)	promoter-TSS (NM_008549)	-928	NM_008549	17158	Mm.2433	NM_008549	ENSMUSG00000024085	Man2a1	Mana-2|Mana2|Map-2	mannosidase 2, alpha 1	protein-coding
mm_70383.1	chr8	10435790	10435799	+	1	NA	exon (NM_001319151, exon 17 of 35)	exon (NM_001319151, exon 17 of 35)	281883	NM_001319151	244281	Mm.422761	NM_001081397	ENSMUSG00000039057	Myo16	BM140241|C230040D10Rik|Gm1105|NYAP3|mKIAA0865	myosin XVI	protein-coding
mm_87545.1	chr10	53597015	53597021	+	1	NA	promoter-TSS (NM_025541)	promoter-TSS (NM_025541)	57	NM_025541	66403	Mm.272989	NM_025541	ENSMUSG00000019857	Asf1a	2310079C17Rik|C79052	anti-silencing function 1A histone chaperone	protein-coding
mm_161055.1	chr12	57307171	57307171	+	1	NA	intron (NM_001164370, intron 3 of 9)	intron (NM_001164370, intron 3 of 9)	76746	NM_001164370	73490	Mm.268180	NM_001164370	ENSMUSG00000047022	Mipol1	1700081O04Rik|6030439O22Rik|AU021838|AW536152|D12Ertd19e	mirror-image polydactyly 1	protein-coding
mm_65299.1	chr7	24589769	24589775	-	1	NA	intron (NM_023154, intron 1 of 7)	intron (NM_023154, intron 1 of 7)	-2131	NM_001033205	101544	Mm.20117	NM_001033205	ENSMUSG00000066721	Zfp575	AI326876|Znf575	zinc finger protein 575	protein-coding
mm_141147.1	chr17	26506145	26506166	-	1	NA	3' UTR (NM_013642, exon 4 of 4)	3' UTR (NM_013642, exon 4 of 4)	2317	NM_013642	19252	Mm.239041	NM_013642	ENSMUSG00000024190	Dusp1	3CH134|MKP1|Ptpn16|U19515|erp|mkp-1	dual specificity phosphatase 1	protein-coding
mm_31454.1	chr4	48636896	48636908	+	1	NA	exon (NM_021436, exon 6 of 10)	exon (NM_021436, exon 6 of 10)	-26612	NM_026509	68016	Mm.133444	NM_026509	ENSMUSG00000028348	Murc	2310039E09Rik	muscle-related coiled-coil protein	protein-coding
mm_11298.1	chr2	30171503	30171520	+	1	NA	promoter-TSS (NM_007931)	promoter-TSS (NM_007931)	-13	NM_007931	13804	Mm.474473	NM_007931	ENSMUSG00000015337	Endog	-	endonuclease G	protein-coding
mm_117478.1	chr13	77047406	77047418	-	1	NA	intron (NM_134071, intron 18 of 20)	intron (NM_134071, intron 18 of 20)	88056	NM_134071	105377	Mm.209730	NM_134071	ENSMUSG00000021597	Slf1	2700017A04Rik|AW545819|Ankrd32|Brctd1|Brctx|C730024G01Rik	SMC5-SMC6 complex localization factor 1	protein-coding
mm_124884.1	chr15	10253358	10253363	+	1	NA	intron (NM_001253781, intron 1 of 9)	L1MA8|LINE|L1	29454	NM_001253781	19116	Mm.10516	NM_011169	ENSMUSG00000005268	Prlr	AI987712|Pr-1|Pr-3|Prlr-rs1	prolactin receptor	protein-coding
mm_33045.1	chr4	122995945	122995958	+	1	NA	promoter-TSS (NM_008506)	promoter-TSS (NM_008506)	20	NM_008506	16918	Mm.1055	NM_008506	ENSMUSG00000028654	Mycl	AW536278|L-myc|Lmyc-1|Lmyc1|Mycl1|bHLHe38	v-myc avian myelocytomatosis viral oncogene lung carcinoma derived	protein-coding
mm_159430.1	chr3	108940449	108940449	+	1	NA	promoter-TSS (NM_001078646)	promoter-TSS (NM_001078646)	-108	NM_001078646	66715	Mm.158124	NM_025723	ENSMUSG00000045662	Henmt1	4921515J06Rik|Hen1|mHEN1	HEN1 methyltransferase homolog 1 (Arabidopsis)	protein-coding
mm_38914.1	chr4	149996431	149996445	-	1	NA	intron (NM_173371, intron 1 of 4)	intron (NM_173371, intron 1 of 4)	6798	NM_001291004	100198	Mm.22183	NM_173371	ENSMUSG00000028980	H6pd	AI785303|G6pd1|Gpd-1|Gpd1	hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase)	protein-coding
mm_79338.1	chr9	53367643	53367654	+	1	NA	intron (NM_176846, intron 5 of 5)	intron (NM_176846, intron 5 of 5)	-16375	NM_212445	68304	Mm.427519	NM_212445	ENSMUSG00000034487	Kdelc2	2010004J24Rik|4833410J10Rik|AW549401	KDEL (Lys-Asp-Glu-Leu) containing 2	protein-coding
mm_115678.1	chr13	13232963	13232970	-	1	NA	Intergenic	Intergenic	50250	NM_001311129	107849	Mm.392548	NM_181852	ENSMUSG00000055360	Prl2c5	Ghd3|MRP-4|Mrpplf4|PLF-4	prolactin family 2, subfamily c, member 5	protein-coding
mm_33824.1	chr4	135495963	135495967	+	1	NA	promoter-TSS (NM_030189)	promoter-TSS (NM_030189)	-22	NM_030189	78806	Mm.374844	NM_030189	ENSMUSG00000028801	Stpg1	4930403G18Rik|4930555I21Rik|Mapo2	sperm tail PG rich repeat containing 1	protein-coding
mm_37632.1	chr4	127358110	127358120	-	1	NA	promoter-TSS (NM_010291)	promoter-TSS (NM_010291)	49	NM_010291	14622	Mm.26859	NM_010291	ENSMUSG00000042357	Gjb5	Cnx31.1|Cx31.1|Gjb-5	gap junction protein, beta 5	protein-coding
mm_42756.1	chr5	120847412	120847423	+	1	NA	promoter-TSS (NM_145153)	promoter-TSS (NM_145153)	50	NM_145153	243262	Mm.105369	NM_145153	ENSMUSG00000053765	Oas1f	-	2'-5' oligoadenylate synthetase 1F	protein-coding
mm_54831.1	chr6	42585971	42585981	-	1	NA	Intergenic	Intergenic	11396	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_92171.1	chr10	67571981	67571989	-	1	NA	Intergenic	MLT1L|LTR|ERVL-MaLR	-23030	NM_001005419	211488	Mm.297250	NM_001005419	ENSMUSG00000057134	Ado	Gm237	2-aminoethanethiol (cysteamine) dioxygenase	protein-coding
mm_20191.1	chr2	122611239	122611283	-	1	NA	promoter-TSS (NM_025961)	promoter-TSS (NM_025961)	16	NM_025961	67092	Mm.29975	NM_025961	ENSMUSG00000027199	Gatm	1810003P21Rik|AI314789|AT	glycine amidinotransferase (L-arginine:glycine amidinotransferase)	protein-coding
mm_146637.1	chr18	10610270	10610288	-	1	NA	promoter-TSS (NM_001081222)	promoter-TSS (NM_001081222)	73	NM_001081222	77805	Mm.210996	NM_144542	ENSMUSG00000024293	Esco1	A930014I12Rik	establishment of sister chromatid cohesion N-acetyltransferase 1	protein-coding
mm_109269.1	chr12	109545540	109545548	+	1	NA	TTS (NR_035440).2	TTS (NR_035440).2	146	NR_003633	17263	Mm.289645	NM_144513	ENSMUSG00000021268	Meg3	2900016C05Rik|3110050O07Rik|6330408G06Rik|AI425946|AW108224|D12Bwg1266e|Gtl2|R74756|R75394	maternally expressed 3	ncRNA
mm_62430.1	chr7	101361466	101361507	+	1	NA	intron (NM_001040111, intron 1 of 33)	intron (NM_001040111, intron 1 of 33)	13417	NM_001040111	69710	Mm.277687	NM_027180	ENSMUSG00000032812	Arap1	2410002L19Rik|Centd2|mKIAA0782	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	protein-coding
mm_121980.1	chr14	25856954	25856991	-	1	NA	intron (NM_013469, intron 1 of 14)	HAL1|LINE|L1	14817	NM_013469	11744	Mm.294083	NM_013469	ENSMUSG00000021866	Anxa11	A830099O17Rik|Anx11	annexin A11	protein-coding
mm_95321.1	chr11	46454922	46454946	+	1	NA	promoter-TSS (NM_134250)	promoter-TSS (NM_134250)	3	NM_134250	171285	Mm.72168	NM_134250	ENSMUSG00000020399	Havcr2	TIM-3|Tim3|Timd3	hepatitis A virus cellular receptor 2	protein-coding
mm_99862.1	chr11	109386559	109386588	+	1	NA	intron (NM_010303, intron 2 of 3)	B1_Mm|SINE|Alu	-22919	NR_038097	100036768	Mm.467767	NR_038097	ENSMUSG00000056687	Gm11696	OTTMUSG00000003456	predicted gene 11696	ncRNA
mm_7054.1	chr1	87128350	87128365	-	1	NA	TTS (NM_007432)	TTS (NM_007432)	3349	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_85726.1	chr9	108339922	108339984	-	1	NA	exon (NM_008160, exon 2 of 2)	exon (NM_008160, exon 2 of 2)	873	NM_001329528	14775	Mm.1090	NM_008160	ENSMUSG00000063856	Gpx1	AI195024|AL033363|CGPx|GPx-1|GSHPx-1|Gpx	glutathione peroxidase 1	protein-coding
mm_98975.1	chr11	98690525	98690538	+	1	NA	exon (NM_009439, exon 5 of 12)	exon (NM_009439, exon 5 of 12)	7977	NM_009439	22123	Mm.12194	NM_009439	ENSMUSG00000017221	Psmd3	AI255837|AntP91a|D11Bwg1349e|Psd3|Tstap91a	proteasome (prosome, macropain) 26S subunit, non-ATPase, 3	protein-coding
mm_111233.1	chr12	84765304	84765366	-	1	NA	exon (NM_023409, exon 2 of 4)	exon (NM_023409, exon 2 of 4)	7777	NM_023409	67963	Mm.282556	NM_023409	ENSMUSG00000021242	Npc2	2700012J19Rik|AA408070|AU045843|HE1	Niemann-Pick type C2	protein-coding
mm_55757.1	chr6	78378923	78378961	-	1	NA	promoter-TSS (NM_001161741)	promoter-TSS (NM_001161741)	-77	NM_013893	30053	Mm.33691	NM_013893	ENSMUSG00000068341	Reg3d	INGAP|Ingaprp	regenerating islet-derived 3 delta	protein-coding
mm_135255.1	chr16	37697369	37697369	-	1	NA	Intergenic	Intergenic	-43001	NM_026610	68194	Mm.379154	NM_026610	ENSMUSG00000022820	Ndufb4	0610006N12Rik|1300010H20Rik	NADH dehydrogenase (ubiquinone) 1 beta subcomplex 4	protein-coding
mm_74930.1	chr8	25661475	25661480	-	1	NA	intron (NM_001001735, intron 5 of 9)	B1_Mur2|SINE|Alu	20900	NM_001081269	234135	Mm.217337	NM_001001735	ENSMUSG00000054823	Whsc1l1	6720429E03|A530023P05|AI528490|NSD3|WHISTLE	Wolf-Hirschhorn syndrome candidate 1-like 1 (human)	protein-coding
mm_28191.1	chr3	88139930	88139945	-	1	NA	Intergenic	Intergenic	-2435	NM_001310587	17261	Mm.28184	NM_133665	ENSMUSG00000001419	Mef2d	C80750	myocyte enhancer factor 2D	protein-coding
mm_96267.1	chr11	62650488	62650502	+	1	NA	intron (NM_175002, intron 1 of 1)	MER31A|LTR|ERV1	1831	NM_175002	216829	Mm.295306	NM_175002	ENSMUSG00000048497	Mmgt2	AI852046	membrane magnesium transporter 2	protein-coding
mm_84835.1	chr9	78347163	78347190	-	1	NA	promoter-TSS (NM_008182)	promoter-TSS (NM_008182)	-31	NM_008182	14858	Mm.422778	NM_008182	ENSMUSG00000057933	Gsta2	Gst2-2|Gstc-2|Gstc2	glutathione S-transferase, alpha 2 (Yc2)	protein-coding
mm_150826.1	chr19	44565065	44565068	+	1	NA	intron (NM_176958, intron 2 of 7)	intron (NM_176958, intron 2 of 7)	2212	NM_176958	319594	Mm.145278	NM_176958	ENSMUSG00000036450	Hif1an	2310046M24Rik|A830014H24Rik|FIH|FIH1	hypoxia-inducible factor 1, alpha subunit inhibitor	protein-coding
mm_84842.1	chr9	78378526	78378536	-	1	NA	promoter-TSS (NM_026480)	promoter-TSS (NM_026480)	57	NM_026480	67968	Mm.26883	NM_026480	ENSMUSG00000032346	Ooep	2410146L05Rik|Floped|Moep19|Sddr	oocyte expressed protein	protein-coding
mm_24640.1	chr3	94377434	94377451	+	1	NA	promoter-TSS (NM_001293734)	promoter-TSS (NM_001293734)	10	NR_121656	19885	Mm.4372	NM_011281	ENSMUSG00000028150	Rorc	Nr1f3|RORgamma|TOR|Thor	RAR-related orphan receptor gamma	protein-coding
mm_133438.1	chr16	87700156	87700168	+	1	NA	intron (NM_007520, intron 1 of 4)	intron (NM_007520, intron 1 of 4)	1208	NM_007520	12013	Mm.26147	NM_007520	ENSMUSG00000025612	Bach1	6230421P05Rik|AI323795	BTB and CNC homology 1, basic leucine zipper transcription factor 1	protein-coding
mm_4358.1	chr1	171917725	171917731	+	1	NA	exon (NM_030710, exon 1 of 8)	exon (NM_030710, exon 1 of 8)	191	NM_030710	30925	Mm.486404	NM_030710	ENSMUSG00000015314	Slamf6	KAL1|KAL1b|Ly108|NTB-A|NTBA|SF2000	SLAM family member 6	protein-coding
mm_163442.1	chr12	85487842	85487853	-	1	NA	Intergenic	Intergenic	13946	NM_010234	14281	Mm.246513	NM_010234	ENSMUSG00000021250	Fos	D12Rfj1|c-fos|cFos	FBJ osteosarcoma oncogene	protein-coding
mm_18099.1	chr2	44987799	44987821	-	1	NA	3' UTR (NM_015753, exon 10 of 10)	3' UTR (NM_015753, exon 10 of 10)	35367	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_97895.1	chr11	83321648	83321650	+	1	NA	intron (NM_027915, intron 3 of 20)	intron (NM_027915, intron 3 of 20)	18952	NM_001035854	71770	Mm.39053	NM_027915	ENSMUSG00000035152	Ap2b1	1300012O03Rik|AI788979	adaptor-related protein complex 2, beta 1 subunit	protein-coding
mm_32208.1	chr4	101507948	101508032	+	1	NA	promoter-TSS (NM_001164585)	promoter-TSS (NM_001164585)	14	NM_001164584	72685	Mm.76494	NM_198412	ENSMUSG00000028528	Dnajc6	2810027M23Rik|mKIAA0473	DnaJ heat shock protein family (Hsp40) member C6	protein-coding
mm_52573.1	chr6	116338301	116338332	+	1	NA	5' UTR (NM_027920, exon 1 of 7)	5' UTR (NM_027920, exon 1 of 7)	294	NM_027920	71779	Mm.27064	NM_027920	ENSMUSG00000025702	March8	1300017E09Rik|MARCH-VIII|Mir	membrane-associated ring finger (C3HC4) 8	protein-coding
mm_23121.1	chr3	37644028	37644036	+	1	NA	3' UTR (NM_011896, exon 3 of 3)	3' UTR (NM_011896, exon 3 of 3)	4085	NM_001305442	24063	Mm.330986	NM_011896	ENSMUSG00000037211	Spry1	sprouty1|spry-1	sprouty homolog 1 (Drosophila)	protein-coding
mm_146219.1	chr18	77038562	77038597	+	1	NA	intron (NM_027721, intron 1 of 13)	MLTR25A|LTR|ERVK	8717	NM_027721	71206	Mm.35803	NM_027721	ENSMUSG00000025420	Katnal2	3110023G01Rik|4933439B08Rik	katanin p60 subunit A-like 2	protein-coding
mm_24597.1	chr3	93445324	93445330	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	2997	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_112727.1	chr13	19192681	19192687	+	1	NA	Intergenic	Intergenic	203129	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_77999.1	chr9	8900564	8900574	+	1	NA	exon (NM_008829, exon 1 of 8)	exon (NM_008829, exon 1 of 8)	736	NM_008829	18667	Mm.12798	NM_008829	ENSMUSG00000031870	Pgr	9930019P03Rik|BB114106|ENSMUSG00000074510|NR3C3|PR|PR-A|PR-B	progesterone receptor	protein-coding
mm_95862.1	chr11	58009132	58009144	+	1	NA	promoter-TSS (NM_028451)	promoter-TSS (NM_028451)	74	NM_028451	73158	Mm.248843	NM_028451	ENSMUSG00000037331	Larp1	1810024J12Rik|3110040D16Rik|Larp|mKIAA0731	La ribonucleoprotein domain family, member 1	protein-coding
mm_137608.1	chr17	28232795	28232829	+	1	NA	promoter-TSS (NM_011145)	promoter-TSS (NM_011145)	58	NM_011145	19015	Mm.328914	NM_011145	ENSMUSG00000002250	Ppard	NUC-1|NUC1|Nr1c2|PPAR-beta|PPAR-delta|PPAR[b]|PPARdelta|Pparb|Pparb/d	peroxisome proliferator activator receptor delta	protein-coding
mm_56642.1	chr6	113326727	113326750	-	1	NA	promoter-TSS (NM_010957)	promoter-TSS (NM_010957)	-238	NM_010957	18294	Mm.43612	NM_010957	ENSMUSG00000030271	Ogg1	Mmh	8-oxoguanine DNA-glycosylase 1	protein-coding
mm_66795.1	chr7	47132487	47132562	-	1	NA	promoter-TSS (NM_001163565)	promoter-TSS (NM_001163565)	74	NM_001163565	19259	Mm.4654	NM_013643	ENSMUSG00000030854	Ptpn5	Step	protein tyrosine phosphatase, non-receptor type 5	protein-coding
mm_105158.1	chr11	101468025	101468066	-	1	NA	promoter-TSS (NM_009708)	promoter-TSS (NM_009708)	-293	NM_009708	11858	Mm.378883	NM_009708	ENSMUSG00000001313	Rnd2	Arhn|Rohn	Rho family GTPase 2	protein-coding
mm_31445.1	chr4	48585249	48585268	+	1	NA	promoter-TSS (NM_021436)	promoter-TSS (NM_021436)	65	NM_021436	230157	Mm.422686	NM_021436	ENSMUSG00000028347	Tmeff1	A830033E11|M7365|Tr1	transmembrane protein with EGF-like and two follistatin-like domains 1	protein-coding
mm_874.1	chr1	52155138	52155162	+	1	NA	intron (NM_001205313, intron 23 of 24)	intron (NM_001205313, intron 23 of 24)	35528	NM_001205313	20846	Mm.277406	NM_009283	ENSMUSG00000026104	Stat1	2010005J02Rik|AA408197	signal transducer and activator of transcription 1	protein-coding
mm_100094.1	chr11	115604131	115604164	+	1	NA	promoter-TSS (NM_173048)	promoter-TSS (NM_173048)	-4	NM_025305	50529	Mm.193040	NM_025305	ENSMUSG00000046756	Mrps7	MRP-S7|Rpms7	mitchondrial ribosomal protein S7	protein-coding
mm_67029.1	chr7	66684295	66684299	-	1	NA	intron (NM_080443, intron 2 of 5)	intron (NM_080443, intron 2 of 5)	5264	NM_080443	117589	Mm.34785	NM_080443	ENSMUSG00000030509	Asb7	AI449039|Asb-7|D030055C23Rik	ankyrin repeat and SOCS box-containing 7	protein-coding
mm_62099.1	chr7	96211657	96211680	+	1	NA	promoter-TSS (NM_001310760)	promoter-TSS (NM_001310760)	-3	NM_001310760	23966	Mm.254610	NM_011858	ENSMUSG00000048078	Tenm4	Doc4|ELM2|Odz4|R75022|Ten-m4|l(7)-3Rn|l7Rn3|mKIAA1302	teneurin transmembrane protein 4	protein-coding
mm_4589.1	chr1	178331913	178331929	+	1	NA	exon (NM_016805, exon 8 of 14)	exon (NM_016805, exon 8 of 14)	5863	NM_016805	51810	Mm.86589	NM_016805	ENSMUSG00000039630	Hnrnpu	AA408410|AI256620|AL024194|AL024437|AW557595|C86794|Hnrpu|SAFA|Sp120|hnRNP U	heterogeneous nuclear ribonucleoprotein U	protein-coding
mm_155751.1	chrX	96167346	96167356	+	1	NA	3' UTR (NM_010833, exon 13 of 13)	3' UTR (NM_010833, exon 13 of 13)	71306	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_130874.1	chr15	102243263	102243280	-	1	NA	intron (NM_011244, intron 3 of 9)	intron (NM_011244, intron 3 of 9)	3229	NM_001042727	19411	Mm.1273	NM_011244	ENSMUSG00000001288	Rarg	Nr1b3|RAR-gamma|RARD|RARgamma2	retinoic acid receptor, gamma	protein-coding
mm_160995.1	chr11	113709511	113709511	-	1	NA	promoter-TSS (NM_001164532)	promoter-TSS (NM_001164532)	15	NM_026682	52670	Mm.229207	NM_026682	ENSMUSG00000018727	Cpsf4l	0610010C04Rik|1500000C01Rik|D11Ertd636e	cleavage and polyadenylation specific factor 4-like	protein-coding
mm_33448.1	chr4	130663418	130663420	+	1	NA	promoter-TSS (NM_001159603)	promoter-TSS (NM_001159603)	60	NM_001159605	80912	Mm.440206	NM_030722	ENSMUSG00000028580	Pum1	AA517475|Pumm|mKIAA0099	pumilio RNA-binding family member 1	protein-coding
mm_36451.1	chr4	82499293	82499325	-	1	NA	intron (NM_001113210, intron 1 of 11)	intron (NM_001113210, intron 1 of 11)	6470	NM_001286127	18028	Mm.317947	NM_008687	ENSMUSG00000008575	Nfib	6720429L07Rik|CTF|E030026I10Rik|NF-I/B|NF1-B|NFI-B	nuclear factor I/B	protein-coding
mm_58887.1	chr7	17088653	17088655	+	1	NA	intron (NM_001310628, intron 1 of 5)	intron (NM_001310628, intron 1 of 5)	14614	NM_007676	26436	Mm.143686	NM_007676	ENSMUSG00000066760	Psg16	Cea11|PSG|bCEA	pregnancy specific glycoprotein 16	protein-coding
mm_31303.1	chr4	46039203	46039213	+	1	NA	promoter-TSS (NM_021883)	promoter-TSS (NM_021883)	-14	NM_021883	21916	Mm.249594	NM_021883	ENSMUSG00000028328	Tmod1	E-Tmod|Tmod	tropomodulin 1	protein-coding
mm_153270.1	chr19	37174991	37175009	-	1	NA	intron (NM_001290827, intron 1 of 10)	intron (NM_001290827, intron 1 of 10)	1063	NM_001290826	208922	Mm.391176	NM_198300	ENSMUSG00000039652	Cpeb3	4831444O18Rik|CPE-BP3|mKIAA0940	cytoplasmic polyadenylation element binding protein 3	protein-coding
mm_53096.1	chr6	125009666	125009717	+	1	NA	promoter-TSS (NM_175557)	promoter-TSS (NM_175557)	22	NM_175557	269800	Mm.108677	NM_175557	ENSMUSG00000038346	Zfp384	BB163993|C130073D16Rik|Ciz|NP|Nmp4	zinc finger protein 384	protein-coding
mm_70600.1	chr8	13338761	13338817	+	1	NA	promoter-TSS (NM_001291765)	promoter-TSS (NM_001291765)	-15	NM_001291766	21781	Mm.925	NM_009361	ENSMUSG00000038482	Tfdp1	Dp1|Drtf1	transcription factor Dp 1	protein-coding
mm_61078.1	chr7	51621995	51622013	+	1	NA	5' UTR (NM_080853, exon 1 of 12)	5' UTR (NM_080853, exon 1 of 12)	174	NM_080853	140919	Mm.256618	NM_080853	ENSMUSG00000030500	Slc17a6	2900073D12Rik|DNPI|VGLUT2	solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 6	protein-coding
mm_10713.1	chr2	22779917	22779934	+	1	NA	intron (NM_019456, intron 1 of 13)	intron (NM_019456, intron 1 of 13)	5598	NM_019456	54519	Mm.14255	NM_019456	ENSMUSG00000026786	Apbb1ip	9930118P07Rik|Prp48	amyloid beta (A4) precursor protein-binding, family B, member 1 interacting protein	protein-coding
mm_110262.1	chr12	31713874	31713898	-	1	NA	promoter-TSS (NM_175191)	promoter-TSS (NM_175191)	40	NM_175191	73010	Mm.441517	NM_175191	ENSMUSG00000044067	Gpr22	2900068K05Rik|AW061316	G protein-coupled receptor 22	protein-coding
mm_162521.1	chr1	157256776	157256787	-	1	NA	intron (NM_177644, intron 3 of 17)	intron (NM_177644, intron 3 of 17)	-148101	NM_001305063	73435	Mm.116705	NM_028540	ENSMUSG00000026592	Tex35	1700057K13Rik	testis expressed 35	protein-coding
mm_129833.1	chr15	83149308	83149350	-	1	NA	promoter-TSS (NM_178627)	promoter-TSS (NM_178627)	7	NM_178627	73826	Mm.23758	NM_178627	ENSMUSG00000041815	Poldip3	1110008P04Rik|AA408269|AL022852|C77954|PDIP46|SKAR|mKIAA1649	polymerase (DNA-directed), delta interacting protein 3	protein-coding
mm_76829.1	chr8	104631313	104631319	-	1	NA	promoter-TSS (NM_019662)	promoter-TSS (NM_019662)	5	NM_019662	56437	Mm.29467	NM_019662	ENSMUSG00000031880	Rrad	REM3|Rad	Ras-related associated with diabetes	protein-coding
mm_103504.1	chr11	76584285	76584288	-	1	NA	Intergenic	PB1|SINE|Alu	-6547	NM_198894	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_119355.1	chr14	41114819	41114827	+	1	NA	exon (NM_133653, exon 6 of 10)	exon (NM_133653, exon 6 of 10)	9790	NM_133653	11720	Mm.14064	NM_133653	ENSMUSG00000037798	Mat1a	AI046368|AdoMet|Ams|MAT|MATA1|SAMS|SAMS1	methionine adenosyltransferase I, alpha	protein-coding
mm_52866.1	chr6	122308954	122308966	+	1	NA	promoter-TSS (NM_010749)	promoter-TSS (NM_010749)	-50	NM_010749	17113	Mm.249225	NM_010749	ENSMUSG00000007458	M6pr	CD-MPR|Mpr46	mannose-6-phosphate receptor, cation dependent	protein-coding
mm_34075.1	chr4	138457893	138457917	+	1	NA	3' UTR (NM_025451, exon 2 of 2)	3' UTR (NM_025451, exon 2 of 2)	2757	NM_025451	66259	Mm.41603	NM_025451	ENSMUSG00000046447	Camk2n1	1810006K23Rik|AI848599|AI891706	calcium/calmodulin-dependent protein kinase II inhibitor 1	protein-coding
mm_19688.1	chr2	103467198	103467234	-	1	NA	exon (NM_009804, exon 8 of 13)	exon (NM_009804, exon 8 of 13)	17937	NM_009804	12359	Mm.4215	NM_009804	ENSMUSG00000027187	Cat	2210418N07|Cas-1|Cas1|Cs-1	catalase	protein-coding
mm_110414.1	chr12	46698621	46698623	-	1	NA	3' UTR (NM_021361, exon 5 of 5)	3' UTR (NM_021361, exon 5 of 5)	120153	NM_021361	664883	Mm.247195	NM_021361	ENSMUSG00000021047	Nova1	9430099M15Rik|G630039L02|Nova-1	neuro-oncological ventral antigen 1	protein-coding
mm_104793.1	chr11	98768225	98768237	-	1	NA	exon (NM_145434, exon 8 of 8)	exon (NM_145434, exon 8 of 8)	7146	NM_145434	217166	Mm.390397	NM_145434	ENSMUSG00000020889	Nr1d1	A530070C09Rik|R75201	nuclear receptor subfamily 1, group D, member 1	protein-coding
mm_106181.1	chr11	116694803	116694882	-	1	NA	promoter-TSS (NM_009180)	promoter-TSS (NM_009180)	-182	NM_009180	20446	Mm.3947	NM_009180	ENSMUSG00000057286	St6galnac2	II|ST6GalNAc|Siat7|Siat7b	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2	protein-coding
mm_120105.1	chr14	59201228	59201267	+	1	NA	promoter-TSS (NM_027764)	promoter-TSS (NM_027764)	19	NM_027764	71330	Mm.234195	NM_027764	ENSMUSG00000035469	Rcbtb1	5430409I18Rik|AW111883|CLLD7|CLLL7	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 1	protein-coding
mm_104817.1	chr11	98968801	98968809	-	1	NA	intron (NM_001176528, intron 3 of 7)	intron (NM_001176528, intron 3 of 7)	8334	NM_001176528	19401	Mm.439744	NM_009024	ENSMUSG00000037992	Rara	Nr1b1|RAR|RARalpha1	retinoic acid receptor, alpha	protein-coding
mm_26845.1	chr3	14766611	14766616	-	1	NA	exon (NM_001083957, exon 7 of 7)	exon (NM_001083957, exon 7 of 7)	11847	NM_001083957	12346	Mm.273195	NM_009799	ENSMUSG00000027556	Car1	AW555628|Ca1|Car-1	carbonic anhydrase 1	protein-coding
mm_90261.1	chr10	122626851	122626855	+	1	NA	Intergenic	RMER17D|LTR|ERVK	-51909	NM_176919	319468	Mm.489703	NM_176919	ENSMUSG00000034613	Ppm1h	A430075L18Rik|ARHCL1|C030002B11Rik	protein phosphatase 1H (PP2C domain containing)	protein-coding
mm_113442.1	chr13	34924429	34924436	+	1	NA	promoter-TSS (NM_025750)	promoter-TSS (NM_025750)	23	NM_025750	66761	Mm.157047	NM_025750	ENSMUSG00000021415	4933417A18Rik	-	RIKEN cDNA 4933417A18 gene	protein-coding
mm_59975.1	chr7	30459692	30459700	+	1	NA	promoter-TSS (NM_019459)	promoter-TSS (NM_019459)	-362	NM_019459	54631	Mm.437830	NM_019459	ENSMUSG00000006649	Nphs1	NephrinB|nephrin	nephrosis 1, nephrin	protein-coding
mm_148214.1	chr18	80236346	80236354	-	1	NA	intron (NM_001136181, intron 2 of 4)	intron (NM_001136181, intron 2 of 4)	10752	NM_001136181	66255	Mm.272341	NM_001136181	ENSMUSG00000078963	Hsbp1l1	1810005K13Rik	heat shock factor binding protein 1-like 1	protein-coding
mm_80276.1	chr9	72995743	72995753	+	1	NA	intron (NM_028181, intron 1 of 8)	intron (NM_028181, intron 1 of 8)	10244	NM_028181	72278	Mm.268475	NM_028181	ENSMUSG00000034563	Ccpg1	1700030B06Rik|1810073J13Rik|9430028F23Rik|AI426686|AI875170|CPR8|D9Ertd392e	cell cycle progression 1	protein-coding
mm_93730.1	chr10	119850664	119850673	-	1	NA	intron (NR_131760, intron 3 of 4)	intron (NR_131760, intron 3 of 4)	1722	NR_131760	78105	Mm.399086	NR_131760	ENSMUSG00000085418	Grip1os1	4930404E01Rik|4930483C13Rik	glutamate receptor interacting protein 1, opposite strand 1	ncRNA
mm_49706.1	chr6	34412118	34412128	+	1	NA	promoter-TSS (NM_009731)	promoter-TSS (NM_009731)	-239	NM_009731	11997	Mm.482073	NM_009731	ENSMUSG00000052131	Akr1b7	AR|Avdp|MVDP	aldo-keto reductase family 1, member B7	protein-coding
mm_171682.1	chr4	5704877	5704895	-	1	NA	intron (NM_173426, intron 1 of 2)	(TCC)n|Simple_repeat|Simple_repeat	60707	NM_173426	242297	Mm.331470	NM_173426	ENSMUSG00000049119	Fam110b	1700012H17Rik|5031405P22|AW049855	family with sequence similarity 110, member B	protein-coding
mm_11996.1	chr2	55597521	55597543	+	1	NA	3' UTR (NM_001304810, exon 3 of 3)	3' UTR (NM_001304810, exon 3 of 3)	161562	NM_008426	16519	Mm.5127	NM_008426	ENSMUSG00000026824	Kcnj3	GIRK-1|GIRK1|Kcnf3|Kir3.1	potassium inwardly-rectifying channel, subfamily J, member 3	protein-coding
mm_67454.1	chr7	80401750	80401754	-	1	NA	intron (NM_001081454, intron 1 of 15)	Charlie15a|DNA|hAT-Charlie	1060	NM_011046	18550	Mm.5241	NM_011046	ENSMUSG00000030530	Furin	9130404I01Rik|Fur|PACE|Pcsk3|SPC1	furin (paired basic amino acid cleaving enzyme)	protein-coding
mm_20814.1	chr2	144527426	144527432	-	1	NA	promoter-TSS (NM_029763)	promoter-TSS (NM_029763)	-31	NM_172859	241688	Mm.442156	NM_172859	ENSMUSG00000037259	Dzank1	2810039F03Rik|6330439K17Rik|6430408C01|AI851115|Ankrd64	double zinc ribbon and ankyrin repeat domains 1	protein-coding
mm_75571.1	chr8	60951916	60951918	-	1	NA	intron (NM_007711, intron 1 of 11)	intron (NM_007711, intron 1 of 11)	2882	NM_173876	12725	Mm.25263	NM_007711	ENSMUSG00000004319	Clcn3	Clc3	chloride channel, voltage-sensitive 3	protein-coding
mm_112848.1	chr13	20836072	20836086	+	1	NA	intron (NM_012054, intron 2 of 20)	intron (NM_012054, intron 2 of 20)	41966	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_132310.1	chr16	33700711	33700713	+	1	NA	intron (NM_175256, intron 1 of 14)	intron (NM_175256, intron 1 of 14)	16246	NM_175256	77446	Mm.245741	NM_172934	ENSMUSG00000075254	Heg1	4632417D23Rik|5530401I02Rik|9530025L16Rik|BC038614|Gm629|OTTMUSG00000027315	heart development protein with EGF-like domains 1	protein-coding
mm_101162.1	chr11	16973212	16973244	-	1	NA	3' UTR (NM_019549, exon 10 of 10)	3' UTR (NM_019549, exon 10 of 10)	21818	NM_176982	319701	Mm.120672	NM_176982	ENSMUSG00000044966	Fbxo48	A630050E13Rik	F-box protein 48	protein-coding
mm_132924.1	chr16	49791172	49791185	+	1	NA	Intergenic	Intergenic	-64476	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_139552.1	chr17	56861533	56861542	+	1	NA	intron (NM_001039114, intron 6 of 14)	intron (NM_001039114, intron 6 of 14)	12910	NM_001039114	328845	Mm.179421	NM_001039114	ENSMUSG00000024207	Acsbg2	Bgr	acyl-CoA synthetase bubblegum family member 2	protein-coding
mm_74377.1	chr8	128685472	128685484	+	1	NA	promoter-TSS (NM_010578)	promoter-TSS (NM_010578)	-176	NM_010578	16412	Mm.263396	NM_010578	ENSMUSG00000025809	Itgb1	4633401G24Rik|AA409975|AA960159|CD29|ENSMUSG00000051907|Fnrb|Gm9863|gpIIa	integrin beta 1 (fibronectin receptor beta)	protein-coding
mm_86707.1	chr10	18845057	18845067	+	1	NA	promoter-TSS (NM_022032)	promoter-TSS (NM_022032)	-9	NM_022032	64058	Mm.28209	NM_022032	ENSMUSG00000019851	Perp	1110017A08Rik|KCP1|KRTCAP1|PIGPC1|THW	PERP, TP53 apoptosis effector	protein-coding
mm_110315.1	chr12	34212724	34212731	-	1	NA	intron (NM_001271386, intron 23 of 27)	ORR1D1|LTR|ERVL-MaLR	255056	NM_011658	22160	Mm.3280	NM_011658	ENSMUSG00000035799	Twist1	M-Twist|Pde|Ska10|Ska<m10Jus>|Twist|bHLHa38|pdt	twist basic helix-loop-helix transcription factor 1	protein-coding
mm_37127.1	chr4	116684336	116684358	-	1	NA	TTS (NR_040442)	TTS (NR_040442)	-1252	NM_011034	18477	Mm.30929	NM_011034	ENSMUSG00000028691	Prdx1	MSP23|NkefA|OSF-3|OSF3|PAG|Paga|PrdxI|PrxI|TDX2|TPxA|Tdpx2|prx1	peroxiredoxin 1	protein-coding
mm_126388.1	chr15	80173779	80173812	+	1	NA	promoter-TSS (NM_010795)	promoter-TSS (NM_010795)	74	NM_010795	17309	Mm.299693	NM_010795	ENSMUSG00000042428	Mgat3	1110038J12Rik|AI848272|GnT-III	mannoside acetylglucosaminyltransferase 3	protein-coding
mm_58715.1	chr7	13010129	13010135	+	1	NA	promoter-TSS (NM_001024699)	promoter-TSS (NM_001024699)	-332	NM_001024699	232879	Mm.279272	NM_001024699	ENSMUSG00000049600	Zbtb45	BB161562|Gm157|Zfp499	zinc finger and BTB domain containing 45	protein-coding
mm_49638.1	chr6	30805166	30805176	+	1	NA	intron (NM_017478, intron 20 of 23)	intron (NM_017478, intron 20 of 23)	63872	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_148843.1	chr19	6373642	6373660	+	1	NA	non-coding (NR_122118, exon 8 of 12)	non-coding (NR_122118, exon 8 of 12)	9961	NR_122118	22668	Mm.256422	NM_011750	ENSMUSG00000024949	Sf1	BBP|MZFM|WBP4|Zfp162	splicing factor 1	protein-coding
mm_88582.1	chr10	79704479	79704496	+	1	NA	5' UTR (NM_001077184, exon 1 of 7)	5' UTR (NM_001077184, exon 1 of 7)	129	NM_009768	12215	Mm.726	NM_009768	ENSMUSG00000023175	Bsg	AI115436|AI325119|CD147|EMMPRIN|HT-7	basigin	protein-coding
mm_120258.1	chr14	63046944	63046958	+	1	NA	promoter-TSS (NM_001034910)	promoter-TSS (NM_001034910)	-40	NM_001034910	619548	Mm.387101	NM_001034910	ENSMUSG00000054763	Defb42	BD-42|Defb44|mBD-42	defensin beta 42	protein-coding
mm_39996.1	chr5	32611196	32611245	+	1	NA	promoter-TSS (NM_009535)	promoter-TSS (NM_009535)	49	NM_009535	22612	Mm.4558	NM_009535	ENSMUSG00000014932	Yes1	Yes|p61-Yes	YES proto-oncogene 1, Src family tyrosine kinase	protein-coding
mm_170699.1	chr2	134803889	134803906	+	1	NA	intron (NM_019677, intron 1 of 32)	intron (NM_019677, intron 1 of 32)	17733	NM_001145830	18795	Mm.330607	NM_019677	ENSMUSG00000051177	Plcb1	3110043I21Rik|AI132408|Plcb|mKIAA0581	phospholipase C, beta 1	protein-coding
mm_68736.1	chr7	120982324	120982332	-	1	NA	promoter-TSS (NM_007672)	promoter-TSS (NM_007672)	-16	NM_007672	12585	Mm.1640	NM_007672	ENSMUSG00000030878	Cdr2	AA617262	cerebellar degeneration-related 2	protein-coding
mm_44735.1	chr5	31154206	31154253	-	1	NA	promoter-TSS (NM_001294322)	promoter-TSS (NM_001294322)	22	NM_001310528	17527	Mm.271923	NM_008622	ENSMUSG00000107283	Mpv17	Tg.Mpv17	MpV17 mitochondrial inner membrane protein	protein-coding
mm_95348.1	chr11	48801800	48801809	+	1	NA	promoter-TSS (NR_028563)	promoter-TSS (NR_028563)	-229	NR_028563	100216534		NR_028563	ENSMUSG00000064725	Snord96a	U96	small nucleolar RNA, C/D box 96A	snoRNA
mm_74449.1	chr8	4213567	4213579	-	1	NA	exon (NM_207203, exon 6 of 7)	exon (NM_207203, exon 6 of 7)	3739	NM_207203	73072	Mm.477379	NM_207203	ENSMUSG00000064125	Prr36	-	proline rich 36	protein-coding
mm_76148.1	chr8	82340774	82340787	-	1	NA	intron (NM_008357, intron 5 of 7)	L1MDb|LINE|L1	61806	NM_001254747	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_97218.1	chr11	75630975	75631076	+	1	NA	promoter-TSS (NM_008916)	promoter-TSS (NM_008916)	5	NM_008916	19062	Mm.1458	NM_008916	ENSMUSG00000006127	Inpp5k	C62|Pps|SKIP	inositol polyphosphate 5-phosphatase K	protein-coding
mm_56534.1	chr6	99595001	99595011	-	1	NA	Intergenic	B4A|SINE|B4	71765	NM_025829	66892	Mm.32889	NM_025829	ENSMUSG00000093661	Eif4e3	1300018P11Rik|AI451927|eIF4E-3	eukaryotic translation initiation factor 4E member 3	protein-coding
mm_72696.1	chr8	84976699	84976742	+	1	NA	TTS (NM_008416)	TTS (NM_008416)	2028	NM_008416	16477	Mm.1167	NM_008416	ENSMUSG00000052837	Junb	-	jun B proto-oncogene	protein-coding
mm_128010.1	chr15	13173608	13173644	-	1	NA	promoter-TSS (NM_007666)	promoter-TSS (NM_007666)	49	NM_007666	12563	Mm.57048	NM_007666	ENSMUSG00000039385	Cdh6	cad6	cadherin 6	protein-coding
mm_66867.1	chr7	57312767	57312793	-	1	NA	intron (NM_008074, intron 3 of 9)	Lx8|LINE|L1	74091	NM_008074	14407	Mm.434343	NM_008074	ENSMUSG00000055026	Gabrg3	B230362M20Rik|Gabrg-3	gamma-aminobutyric acid (GABA) A receptor, subunit gamma 3	protein-coding
mm_145108.1	chr18	44104685	44104698	+	1	NA	exon (NM_030061, exon 1 of 4)	exon (NM_030061, exon 1 of 4)	168	NM_030061	78242	Mm.99782	NM_030061	ENSMUSG00000061144	Spink12	9230117E20Rik	serine peptidase inhibitor, Kazal type 12	protein-coding
mm_7670.1	chr1	128588758	128588774	-	1	NA	3' UTR (NM_009911, exon 2 of 2)	3' UTR (NM_009911, exon 2 of 2)	3533	NM_009911	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding
mm_52316.1	chr6	108836262	108836272	+	1	NA	intron (NM_138677, intron 1 of 11)	intron (NM_138677, intron 1 of 11)	7626	NM_138677	192193	Mm.21596	NM_138677	ENSMUSG00000030104	Edem1	A130059K23Rik|EDEM|mKIAA0212	ER degradation enhancer, mannosidase alpha-like 1	protein-coding
mm_10371.1	chr2	11724368	11724373	+	1	NA	intron (NR_073191, intron 4 of 5)	intron (NR_073191, intron 4 of 5)	18658	NM_001271500	16169	Mm.200196	NM_008358	ENSMUSG00000023206	Il15ra	AA690181|IL-15RA	interleukin 15 receptor, alpha chain	protein-coding
mm_78913.1	chr9	44981848	44981864	+	1	NA	promoter-TSS (NM_013487)	promoter-TSS (NM_013487)	70	NM_013487	12500	Mm.4527	NM_013487	ENSMUSG00000032094	Cd3d	T3d	CD3 antigen, delta polypeptide	protein-coding
mm_167138.1	chr7	127478159	127478195	+	1	NA	Intergenic	G-rich|Low_complexity|Low_complexity	6563	NM_145589	233895	Mm.44183	NM_145589	ENSMUSG00000030822	Prr14	BC006909	proline rich 14	protein-coding
mm_44703.1	chr5	30588761	30588775	-	1	NA	promoter-TSS (NR_040427)	promoter-TSS (NR_040427)	-149	NR_040427	100502829	Mm.39944	NR_040427	ENSMUSG00000053214	Gm9899	ENSMUSG00000053214	predicted gene 9899	ncRNA
mm_78774.1	chr9	43743975	43744019	+	1	NA	promoter-TSS (NM_021424)	promoter-TSS (NM_021424)	-579	NM_021424	58235	Mm.335096	NM_021424	ENSMUSG00000032012	Nectin1	AI835281|AW549174|Cd111|HIgR|HveC|PRR|PRR1|Pvrl1|nectin-1	nectin cell adhesion molecule 1	protein-coding
mm_35234.1	chr4	19709138	19709163	-	1	NA	promoter-TSS (NM_177327)	promoter-TSS (NM_177327)	-146	NR_074090	107568	Mm.78312	NM_177327	ENSMUSG00000041058	Wwp1	8030445B08Rik|AIP5|SDRP1|Tiul1	WW domain containing E3 ubiquitin protein ligase 1	protein-coding
mm_130326.1	chr15	97680473	97680483	-	1	NA	exon (NM_028003, exon 14 of 17)	exon (NM_028003, exon 14 of 17)	25344	NM_028003	71919	Mm.12255	NM_028003	ENSMUSG00000022466	Rpap3	2310042P20Rik|D15Ertd682e	RNA polymerase II associated protein 3	protein-coding
mm_150639.1	chr19	41829995	41830026	+	1	NA	promoter-TSS (NM_008043)	promoter-TSS (NM_008043)	40	NM_008043	14296	Mm.4573	NM_008043	ENSMUSG00000067199	Frat1	AW060382	frequently rearranged in advanced T cell lymphomas	protein-coding
mm_145845.1	chr18	65448270	65448295	+	1	NA	exon (NM_172833, exon 5 of 16)	exon (NM_172833, exon 5 of 16)	17285	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_121314.1	chr14	108929809	108929816	+	1	NA	Intergenic	Intergenic	-15573	NM_199065	76965	Mm.257268	NM_199065	ENSMUSG00000075478	Slitrk1	3200001I04Rik	SLIT and NTRK-like family, member 1	protein-coding
mm_46991.1	chr5	115334099	115334169	-	1	NA	3' UTR (NM_029645, exon 3 of 3)	3' UTR (NM_029645, exon 3 of 3)	6957	NR_036616	108014	Mm.287826	NM_025573	ENSMUSG00000029538	Srsf9	25kDa|2610029M16Rik|SRp30c|Sfrs9	serine/arginine-rich splicing factor 9	protein-coding
mm_145165.1	chr18	46741853	46741900	+	1	NA	promoter-TSS (NM_026217)	promoter-TSS (NM_026217)	0	NM_009681	11777	Mm.312536	NM_009681	ENSMUSG00000024480	Ap3s1	-	adaptor-related protein complex 3, sigma 1 subunit	protein-coding
mm_154615.1	chrX	7657356	7657426	+	1	NA	promoter-TSS (NM_001290624)	promoter-TSS (NM_001290624)	12	NM_001290624	54630	Mm.232232	NM_175097	ENSMUSG00000031145	Prickle3	Lmo6|Sfc16	prickle planar cell polarity protein 3	protein-coding
mm_67690.1	chr7	89510552	89510564	-	1	NA	exon (NM_029614, exon 2 of 2)	exon (NM_029614, exon 2 of 2)	7028	NM_029614	76453	Mm.250438	NM_029614	ENSMUSG00000039405	Prss23	2310046G15Rik|4930479H08Rik|AI790574|Spuve	protease, serine 23	protein-coding
mm_162780.1	chr10	69706174	69706184	+	1	NA	intron (NM_170730, intron 1 of 17)	intron (NM_170730, intron 1 of 17)	172471	NM_146005	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_125162.1	chr15	31235784	31235805	+	1	NA	exon (NM_146057, exon 2 of 4)	exon (NM_146057, exon 2 of 4)	11409	NM_146057	223453	Mm.222867	NM_146057	ENSMUSG00000039168	Dap	4921531N22Rik|AI789753|AU040360	death-associated protein	protein-coding
mm_26622.1	chr3	152477919	152477941	+	1	NA	intron (NM_001081277, intron 12 of 13)	intron (NM_001081277, intron 12 of 13)	81246	NM_001287139	108946	Mm.379292	NM_198416	ENSMUSG00000039068	Zzz3	3110065C23Rik|6430567E01Rik|AA408566|AI481057|AW556059|R75514	zinc finger, ZZ domain containing 3	protein-coding
mm_97249.1	chr11	75752035	75752057	+	1	NA	exon (NM_009536, exon 2 of 6)	exon (NM_009536, exon 2 of 6)	19159	NM_009536	22627	Mm.234700	NM_009536	ENSMUSG00000020849	Ywhae	AU019196	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide	protein-coding
mm_84373.1	chr9	65008467	65008473	-	1	NA	intron (NM_021345, intron 2 of 10)	ID_B1|SINE|B4	13247	NM_021345	57874	Mm.308180	NM_021345	ENSMUSG00000033629	Hacd3	4930523M17Rik|AW742319|B-ind1|Hcad3|Hspc121|Ptplad1	3-hydroxyacyl-CoA dehydratase 3	protein-coding
mm_41733.1	chr5	102691128	102691134	+	1	NA	intron (NM_146161, intron 2 of 8)	intron (NM_146161, intron 2 of 8)	-77679	NM_001286468	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding
mm_133187.1	chr16	72663198	72663210	+	1	NA	promoter-TSS (NM_019413)	promoter-TSS (NM_019413)	55	NM_019413	19876	Mm.310772	NM_019413	ENSMUSG00000022883	Robo1	AW494633|AW742721|DUTT1|Gm310	roundabout guidance receptor 1	protein-coding
mm_13820.1	chr2	119237512	119237524	+	1	NA	intron (NM_016907, intron 1 of 10)	CpG	158	NM_016907	20732	Mm.104955	NM_016907	ENSMUSG00000027315	Spint1	HAI-1	serine protease inhibitor, Kunitz type 1	protein-coding
mm_126466.1	chr15	81190497	81190505	+	1	NA	promoter-TSS (NR_015603)	promoter-TSS (NR_015603)	256	NM_001082536	223701	Mm.439814	NM_153049	ENSMUSG00000042292	Mkl1	AMKL|Bsac|Mal|Mrtf-A	MKL (megakaryoblastic leukemia)/myocardin-like 1	protein-coding
mm_108561.1	chr12	84756491	84756493	+	1	NA	3' UTR (NM_023409, exon 4 of 4)	3' UTR (NM_023409, exon 4 of 4)	16620	NM_023409	67963	Mm.282556	NM_023409	ENSMUSG00000021242	Npc2	2700012J19Rik|AA408070|AU045843|HE1	Niemann-Pick type C2	protein-coding
mm_64342.1	chr7	142377327	142377343	+	1	NA	exon (NM_009983, exon 6 of 9)	exon (NM_009983, exon 6 of 9)	-3589	NM_001347541	320802	Mm.154486	NM_177265	ENSMUSG00000045777	Ifitm10	6330512M04Rik|AI848576|DSPA3	interferon induced transmembrane protein 10	protein-coding
mm_82170.1	chr9	123845455	123845463	+	1	NA	intron (NM_148925, intron 1 of 18)	intron (NM_148925, intron 1 of 18)	6202	NM_148925	17281	Mm.252941	NM_148925	ENSMUSG00000025241	Fyco1	2810409M01Rik|Mem2|RUFY3|ZFYVE7	FYVE and coiled-coil domain containing 1	protein-coding
mm_107607.1	chr12	49384511	49384523	+	1	NA	exon (NM_008241, exon 2 of 2)	exon (NM_008241, exon 2 of 2)	1510	NM_008241	15228	Mm.4704	NM_008241	ENSMUSG00000020950	Foxg1	2900064B05Rik|BF-1|Bf1|Hfh9|Hfhbf1	forkhead box G1	protein-coding
mm_71622.1	chr8	57340971	57340990	+	1	NA	intron (NR_131041, intron 1 of 2)	CpG	8545	NR_131041	75996	Mm.399754	NR_131041	ENSMUSG00000097910	5033428I22Rik	-	RIKEN cDNA 5033428I22 gene	ncRNA
mm_2628.1	chr1	121049830	121049836	+	1	NA	Intergenic	Intergenic	-37572	NR_038008	98452	Mm.131017	NR_038008	ENSMUSG00000097881	Celrr	AI848258|B230209K01Rik|Celr|Gm818	cerebellum expressed regulatory RNA	ncRNA
mm_123782.1	chr14	70331459	70331477	-	1	NA	intron (NM_001135151, intron 1 of 9)	intron (NM_001135151, intron 1 of 9)	16965	NM_001135152	213053	Mm.270647	NM_144808	ENSMUSG00000022094	Slc39a14	FAD-123|ZIP-14|Zip14|fad123	solute carrier family 39 (zinc transporter), member 14	protein-coding
mm_3968.1	chr1	164151889	164151897	+	1	NA	promoter-TSS (NM_007976)	promoter-TSS (NM_007976)	58	NM_007976	14067	Mm.12900	NM_007976	ENSMUSG00000026579	F5	AI173222|Cf-5|Cf5	coagulation factor V	protein-coding
mm_165963.1	chr4	94331655	94331655	-	1	NA	Intergenic	Intergenic	225141	NM_026368	67770	Mm.35170	NM_026368	ENSMUSG00000028578	Caap1	5830433M19Rik|AI536248|CAAP	caspase activity and apoptosis inhibitor 1	protein-coding
mm_25297.1	chr3	105914135	105914151	+	1	NA	intron (NM_027025, intron 1 of 6)	intron (NM_027025, intron 1 of 6)	9722	NM_009631	11542	Mm.235024	NM_009631	ENSMUSG00000000562	Adora3	A3AR|A3R|AA3R|ARA3|Gpcr2	adenosine A3 receptor	protein-coding
mm_125537.1	chr15	58040370	58040380	+	1	NA	Intergenic	L1MB4|LINE|L1	-6081	NM_029418	75758	Mm.455792	NM_029418	ENSMUSG00000101892	9130401M01Rik	AI849328	RIKEN cDNA 9130401M01 gene	protein-coding
mm_81699.1	chr9	111211413	111211416	+	1	NA	intron (NM_027742, intron 8 of 13)	intron (NM_027742, intron 8 of 13)	60194	NM_026810	17350	Mm.486383	NM_026810	ENSMUSG00000032498	Mlh1	1110035C23Rik|AI317206|AI325952|AI561766	mutL homolog 1	protein-coding
mm_65772.1	chr7	28761835	28761846	-	1	NA	exon (NM_010908, exon 3 of 7)	exon (NM_010908, exon 3 of 7)	4804	NM_001306222	18036	Mm.220333	NM_010908	ENSMUSG00000030595	Nfkbib	I(Kappa)B(beta)|I-kappa-B-beta|IKB-beta|IKappaBbeta|IkB|IkBb|NF-kappa-BIB|ikB-B	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, beta	protein-coding
mm_18109.1	chr2	44989793	44989817	-	1	NA	intron (NM_001289521, intron 8 of 8)	intron (NM_001289521, intron 8 of 8)	33372	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_172591.1	chr8	126945814	126945814	-	1	NA	5' UTR (NM_024214, exon 1 of 5)	5' UTR (NM_024214, exon 1 of 5)	107	NM_024214	67952	Mm.6932	NM_024214	ENSMUSG00000093904	Tomm20	1810060K07Rik|BB284719|Gm19268|MAS20|MOM19|TOM20|mKIAA0016	translocase of outer mitochondrial membrane 20 homolog (yeast)	protein-coding
mm_122460.1	chr14	45444967	45444968	-	1	NA	Intergenic	RMER17C2|LTR|ERVK	-56171	NM_019425	54342	Mm.312945	NM_019425	ENSMUSG00000037722	Gnpnat1	AU017428|AU040593|EMeg32|Gpnat1|Gsnpat	glucosamine-phosphate N-acetyltransferase 1	protein-coding
mm_26430.1	chr3	142618502	142618513	+	1	NA	3' UTR (NM_010259, exon 11 of 11)	3' UTR (NM_010259, exon 11 of 11)	-2156	NM_010260	14469	Mm.24038	NM_010260	ENSMUSG00000028270	Gbp2	-	guanylate binding protein 2	protein-coding
mm_83590.1	chr9	48480461	48480487	-	1	NA	exon (NM_024233, exon 1 of 7)	exon (NM_024233, exon 1 of 7)	137	NM_024233	104444	Mm.21911	NM_024233	ENSMUSG00000032026	Rexo2	1810038D15Rik|AW107347|Rex2|Sfn|Smfn	RNA exonuclease 2	protein-coding
mm_54104.1	chr6	16898348	16898391	-	1	NA	promoter-TSS (NM_031198)	promoter-TSS (NM_031198)	72	NM_031198	21426	Mm.36217	NM_031198	ENSMUSG00000029553	Tfec	BB107417|Tcfec|bHLHe34	transcription factor EC	protein-coding
mm_119871.1	chr14	54686202	54686230	+	1	NA	promoter-TSS (NM_021437)	promoter-TSS (NM_021437)	45	NM_021437	58248	Mm.197509	NM_021437	ENSMUSG00000040822	1700123O20Rik	MNCb-2990	RIKEN cDNA 1700123O20 gene	protein-coding
mm_88072.1	chr10	67909247	67909262	+	1	NA	exon (NM_178679, exon 2 of 5)	exon (NM_178679, exon 2 of 5)	3408	NM_178679	216049	Mm.268346	NM_178679	ENSMUSG00000037855	Zfp365	AI839779|AV340892|DBZ|Su48|Znf365|talanin	zinc finger protein 365	protein-coding
mm_81999.1	chr9	121642769	121642783	+	1	NA	promoter-TSS (NM_011703)	promoter-TSS (NM_011703)	60	NM_011703	22354	Mm.282007	NM_011703	ENSMUSG00000032528	Vipr1	AV071699|VIP-R1|VPAC1	vasoactive intestinal peptide receptor 1	protein-coding
mm_145964.1	chr18	67794450	67794462	+	1	NA	3' UTR (NM_001039088, exon 9 of 9)	3' UTR (NM_001039088, exon 9 of 9)	5487	NR_045376	75286	Mm.307315	NR_045376		4930549G23Rik	-	RIKEN cDNA 4930549G23 gene	ncRNA
mm_161575.1	chr16	23429191	23429191	+	1	NA	promoter-TSS (NM_001004151)	promoter-TSS (NM_001004151)	58	NM_001004151	239766	Mm.208751	NM_001004151	ENSMUSG00000033383	Rtp1	Gm1766|Gm604	receptor transporter protein 1	protein-coding
mm_6531.1	chr1	74749441	74749453	-	1	NA	promoter-TSS (NM_153744)	promoter-TSS (NM_153744)	-492	NM_153744	241113	Mm.166501	NM_153744	ENSMUSG00000006542	Prkag3	AMPKg3L|AMPKg3S|Amkg3|Ampkg3	protein kinase, AMP-activated, gamma 3 non-catatlytic subunit	protein-coding
mm_24812.1	chr3	95589036	95589044	+	1	NA	exon (NM_001177669, exon 1 of 4)	exon (NM_001177669, exon 1 of 4)	106	NM_001177670	229593	Mm.245830	NM_146133	ENSMUSG00000046519	Golph3l	2010204I15Rik|AU015439|AW549227|C77637|Gpp34r	golgi phosphoprotein 3-like	protein-coding
mm_12445.1	chr2	71118040	71118061	+	1	NA	promoter-TSS (NM_028593)	promoter-TSS (NM_028593)	-4	NM_028593	73649	Mm.45435	NM_028593	ENSMUSG00000027015	Cybrd1	2210407P13Rik|Dcytb	cytochrome b reductase 1	protein-coding
mm_26855.1	chr3	14863236	14863254	-	1	NA	promoter-TSS (NM_007606)	promoter-TSS (NM_007606)	-293	NM_007606	12350	Mm.300	NM_007606	ENSMUSG00000027559	Car3	BB219044|Ca3|Car-3	carbonic anhydrase 3	protein-coding
mm_78209.1	chr9	21490519	21490529	+	1	NA	intron (NM_007871, intron 13 of 19)	intron (NM_007871, intron 13 of 19)	6040	NR_029585	387194		NR_029585	ENSMUSG00000065547	Mir199a-1	Mirn199|Mirn199a-1|mir-199a-1	microRNA 199a-1	ncRNA
mm_159208.1	chr2	121765082	121765082	-	1	NA	intron (NM_172673, intron 1 of 14)	intron (NM_172673, intron 1 of 14)	41975	NM_172673	228564	Mm.121514	NM_172673	ENSMUSG00000027238	Frmd5	1500032A09Rik|5830442F04|A930004K21Rik|R75430	FERM domain containing 5	protein-coding
mm_34234.1	chr4	141099790	141099792	+	1	NA	intron (NM_177867, intron 7 of 14)	intron (NM_177867, intron 7 of 14)	11446	NM_177867	329972	Mm.247201	NM_177867	ENSMUSG00000045004	Spata21	4933414G08	spermatogenesis associated 21	protein-coding
mm_170405.1	chr18	65104044	65104047	-	1	NA	intron (NM_001114386, intron 5 of 30)	(CCCTAA)n|Simple_repeat|Simple_repeat	80518	NM_031881	83814	Mm.98668	NM_031881	ENSMUSG00000024589	Nedd4l	1300012C07Rik|Nedd4-2|Nedd4b	neural precursor cell expressed, developmentally down-regulated gene 4-like	protein-coding
mm_143323.1	chr17	66349669	66349672	-	1	NA	intron (NM_001114098, intron 10 of 14)	intron (NM_001114098, intron 10 of 14)	100080	NM_172963	68617	Mm.33421	NM_172963	ENSMUSG00000052105	Mtcl1	1110012J17Rik|Ccdc165|D130071O13|Kiaa0802|Soga2|mKIAA0802|t8219b25	microtubule crosslinking factor 1	protein-coding
mm_119498.1	chr14	47380157	47380182	+	1	NA	exon (NM_010705, exon 3 of 6)	exon (NM_010705, exon 3 of 6)	6309	NM_001145953	16854	Mm.248615	NM_010705	ENSMUSG00000050335	Lgals3	GBP|L-34|Mac-2|gal3	lectin, galactose binding, soluble 3	protein-coding
mm_1101.1	chr1	59763507	59763525	+	1	NA	promoter-TSS (NM_007561)	promoter-TSS (NM_007561)	-763	NM_007561	12168	Mm.7106	NM_007561	ENSMUSG00000067336	Bmpr2	2610024H22Rik|AL117858|AW546137|BB189135|BMP-2|BMPR-2|BMPR-II|BMPRII|BRK-3|Gm20272	bone morphogenetic protein receptor, type II (serine/threonine kinase)	protein-coding
mm_87546.1	chr10	53597061	53597075	+	1	NA	5' UTR (NM_025541, exon 1 of 4)	5' UTR (NM_025541, exon 1 of 4)	107	NM_025541	66403	Mm.272989	NM_025541	ENSMUSG00000019857	Asf1a	2310079C17Rik|C79052	anti-silencing function 1A histone chaperone	protein-coding
mm_130488.1	chr15	98763228	98763238	-	1	NA	promoter-TSS (NM_007478)	promoter-TSS (NM_007478)	-115	NM_007478	11842	Mm.221298	NM_007478	ENSMUSG00000051853	Arf3	5430400P17Rik|AI854770	ADP-ribosylation factor 3	protein-coding
mm_110003.1	chr12	15816763	15816881	-	1	NA	promoter-TSS (NM_144551)	promoter-TSS (NM_144551)	-37	NM_144551	217410	Mm.491136	NM_144551	ENSMUSG00000020601	Trib2	AW319517|TRB-2|TRB2	tribbles pseudokinase 2	protein-coding
mm_61268.1	chr7	66174739	66174739	+	1	NA	TTS (NM_001081163)	TTS (NM_001081163)	65224	NM_001081163	269941	Mm.333916	NM_001081163	ENSMUSG00000032640	Chsy1	mKIAA0990	chondroitin sulfate synthase 1	protein-coding
mm_115532.1	chr13	6404714	6404732	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	-143434	NM_145131	69617	Mm.41933	NM_145131	ENSMUSG00000021193	Pitrm1	2310012C15Rik|AA410010|MP-1|MP1|Ntup1|PreP|mKIAA1104	pitrilysin metallepetidase 1	protein-coding
mm_37940.1	chr4	133070878	133070882	-	1	NA	intron (NM_146155, intron 6 of 6)	MIRb|SINE|MIR	59374	NM_146155	230793	Mm.31816	NM_146155	ENSMUSG00000037692	Ahdc1	D030015G18Rik	AT hook, DNA binding motif, containing 1	protein-coding
mm_165588.1	chr3	32905714	32905717	+	1	NA	intron (NM_001013024, intron 13 of 20)	intron (NM_001013024, intron 13 of 20)	79364	NM_001163517	58869	Mm.151332	NM_021483	ENSMUSG00000027674	Pex5l	1700016J08Rik|PXR2|Pex2|TRIP8b|pex5Rp	peroxisomal biogenesis factor 5-like	protein-coding
mm_98134.1	chr11	87566657	87566661	+	1	NA	Intergenic	Intergenic	-11730	NM_001284398	18952	Mm.2214	NM_011129	ENSMUSG00000020486	Sept4	ARTS|Bh5|OTTMUSG00000001265|Pnutl2	septin 4	protein-coding
mm_39037.1	chr4	152317814	152317824	-	1	NA	intron (NM_001033489, intron 1 of 16)	intron (NM_001033489, intron 1 of 16)	806	NM_001033489	433809	Mm.156205	NM_001033489	ENSMUSG00000058498	Rnf207	D330010C22Rik|Gm143	ring finger protein 207	protein-coding
mm_139493.1	chr17	56162487	56162549	+	1	NA	promoter-TSS (NM_025566)	promoter-TSS (NM_025566)	27	NM_025566	66443	Mm.2312	NM_025566	ENSMUSG00000044469	Tnfaip8l1	2600017J23Rik|TIPE1	tumor necrosis factor, alpha-induced protein 8-like 1	protein-coding
mm_36508.1	chr4	83486242	83486276	-	1	NA	intron (NM_001347143, intron 1 of 10)	CpG-10005	189	NM_001290527	101739	Mm.105331	NM_133948	ENSMUSG00000028484	Psip1	AA408851|AU015605|Dfs70|Ledgfa|Ledgfb|Psip2	PC4 and SFRS1 interacting protein 1	protein-coding
mm_128133.1	chr15	31449040	31449065	-	1	NA	exon (NM_145852, exon 3 of 5)	exon (NM_145852, exon 3 of 5)	4637	NM_145852	252967	Mm.436668	NM_145852	ENSMUSG00000022236	Ropn1l	ASP|AV047578|Akapasp	ropporin 1-like	protein-coding
mm_83206.1	chr9	41934052	41934053	-	1	NA	Intergenic	Intergenic	190237	NM_011436	20660	Mm.121920	NM_011436	ENSMUSG00000049313	Sorl1	2900010L19Rik|AI596264|AW261561|LR11|SorLA|gp250|mSorLA	sortilin-related receptor, LDLR class A repeats-containing	protein-coding
mm_3783.1	chr1	156674978	156675006	+	1	NA	promoter-TSS (NM_023141)	promoter-TSS (NM_023141)	-653	NM_023141	30935	Mm.206737	NM_023141	ENSMUSG00000060519	Tor3a	Adir	torsin family 3, member A	protein-coding
mm_54416.1	chr6	32752287	32752293	-	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	-164098	NM_175750	243743	Mm.444029	NM_175750	ENSMUSG00000029765	Plxna4	9330117B14|Plxa4|mKIAA1550	plexin A4	protein-coding
mm_110337.1	chr12	36019676	36019693	-	1	NA	intron (NM_025359, intron 5 of 5)	RMER4B|LTR|ERVK	22794	NM_025359	66109	Mm.254663	NM_025359	ENSMUSG00000020577	Tspan13	1100001I23Rik|NET-6|Tm4sf13	tetraspanin 13	protein-coding
mm_156993.1	chrX	7422931	7422941	-	1	NA	promoter-TSS (NR_027924)	promoter-TSS (NR_027924)	52	NR_027924	68355	Mm.45111	NR_027924		2010204K13Rik	0610010M13Rik|Cip7	RIKEN cDNA 2010204K13 gene	ncRNA
mm_4811.1	chr1	185357036	185357045	+	1	NA	3' UTR (NM_011794, exon 9 of 9)	3' UTR (NM_011794, exon 9 of 9)	-6055	NM_029735	107508	Mm.154511	NM_029735	ENSMUSG00000026615	Eprs	2410081F06Rik|3010002K18Rik|C79379|Qprs	glutamyl-prolyl-tRNA synthetase	protein-coding
mm_138587.1	chr17	35506244	35506254	+	1	NA	exon (NM_013633, exon 1 of 5)	exon (NM_013633, exon 1 of 5)	217	NM_013633	18999	Mm.17031	NM_013633	ENSMUSG00000024406	Pou5f1	NF-A3|Oct-3|Oct-3/4|Oct-4|Oct3|Oct3/4|Oct4|Otf-3|Otf-4|Otf3|Otf3-rs7|Otf3g|Otf4	POU domain, class 5, transcription factor 1	protein-coding
mm_102314.1	chr11	56269953	56269963	-	1	NA	Intergenic	L2|LINE|L2	-228971	NM_153079	216749	Mm.213205	NM_153079	ENSMUSG00000037393	Nmur2	Nmu2r	neuromedin U receptor 2	protein-coding
mm_69317.1	chr7	128461314	128461326	-	1	NA	5' UTR (NM_009383, exon 1 of 12)	5' UTR (NM_009383, exon 1 of 12)	193	NM_009383	21843	Mm.242072	NM_009383	ENSMUSG00000030846	Tial1	5330433G13Rik|AL033329|TIAR|mTIAR	Tia1 cytotoxic granule-associated RNA binding protein-like 1	protein-coding
mm_66293.1	chr7	38019478	38019488	-	1	NA	promoter-TSS (NM_011274)	promoter-TSS (NM_011274)	69	NM_011274	19777	Mm.387220	NM_011274	ENSMUSG00000030421	Uri1	C80913|NNX3|Rmp	URI1, prefoldin-like chaperone	protein-coding
mm_65614.1	chr7	27532464	27532479	-	1	NA	exon (NM_011116, exon 14 of 14)	exon (NM_011116, exon 14 of 14)	9210	NM_001033315	233020	Mm.429716	NM_001033315	ENSMUSG00000040424	Hipk4	Gm162	homeodomain interacting protein kinase 4	protein-coding
mm_45026.1	chr5	38563245	38563252	-	1	NA	Intergenic	Intergenic	-1653	NM_011715	22388	Mm.2654	NM_011715	ENSMUSG00000005103	Wdr1	Aip1|D5Wsu185e|rede	WD repeat domain 1	protein-coding
mm_166027.1	chr4	125146255	125146270	+	1	NA	Intergenic	Intergenic	-18381	NM_153159	230738	Mm.402	NM_153159	ENSMUSG00000042677	Zc3h12a	BC036563|MCPIP|MCPIP-1|Mcpip1|Reg1	zinc finger CCCH type containing 12A	protein-coding
mm_167187.1	chr7	142471435	142471453	+	1	NA	promoter-TSS (NM_019391)	promoter-TSS (NM_019391)	-399	NM_001271508	16985	Mm.234003	NM_019391	ENSMUSG00000018819	Lsp1	Lsp-1|WP34|p50|pp52	lymphocyte specific 1	protein-coding
mm_60947.1	chr7	47008543	47008566	+	1	NA	promoter-TSS (NM_175318)	promoter-TSS (NM_175318)	-140	NM_175318	101685	Mm.155687	NM_175318	ENSMUSG00000049516	Spty2d1	5830435K17Rik|AI852426|P16H6	SPT2, Suppressor of Ty, domain containing 1 (S. cerevisiae)	protein-coding
mm_63696.1	chr7	130624626	130624640	+	1	NA	exon (NM_001004468, exon 3 of 22)	exon (NM_001004468, exon 3 of 22)	47149	NM_206856	57752	Mm.86322	NM_021314	ENSMUSG00000030852	Tacc2	mKIAA4180	transforming, acidic coiled-coil containing protein 2	protein-coding
mm_66115.1	chr7	31042306	31042333	-	1	NA	promoter-TSS (NM_001111073)	promoter-TSS (NM_001111073)	12	NM_008761	18301	Mm.1870	NM_008761	ENSMUSG00000009687	Fxyd5	EF-8|Oit2|RIC	FXYD domain-containing ion transport regulator 5	protein-coding
mm_40338.1	chr5	44224506	44224515	+	1	NA	intron (NM_173764, intron 1 of 13)	intron (NM_173764, intron 1 of 13)	2096	NM_173764	231225	Mm.30688	NM_173764	ENSMUSG00000046985	Tapt1	4932414K18Rik	transmembrane anterior posterior transformation 1	protein-coding
mm_125039.1	chr15	25774192	25774196	+	1	NA	intron (NM_019472, intron 19 of 40)	intron (NM_019472, intron 19 of 40)	-69104	NM_001034851	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_141875.1	chr17	34839433	34839446	-	1	NA	TTS (NM_001163770)	TTS (NM_001163770)	2420	NM_001163770	112403	Mm.275309	NM_033613	ENSMUSG00000040482	Dxo	Dom3z|NG6	decapping exoribonuclease	protein-coding
mm_141467.1	chr17	30597888	30597901	-	1	NA	intron (NM_025374, intron 3 of 5)	intron (NM_025374, intron 3 of 5)	14765	NM_025374	109801	Mm.261984	NM_025374	ENSMUSG00000024026	Glo1	0610009E22Rik|1110008E19Rik|2510049H23Rik|AW550643|GLY1|Glo-1|Glo-1r|Glo-1s|Glo1-r|Glo1-s|Qglo	glyoxalase 1	protein-coding
mm_70666.1	chr8	14888878	14888900	+	1	NA	5' UTR (NM_012000, exon 1 of 3)	5' UTR (NM_012000, exon 1 of 3)	353	NM_012000	26889	Mm.254027	NM_012000	ENSMUSG00000026317	Cln8	mnd	ceroid-lipofuscinosis, neuronal 8	protein-coding
mm_49726.1	chr6	34685095	34685105	+	1	NA	intron (NM_001347100, intron 2 of 13)	intron (NM_001347100, intron 2 of 13)	-24344	NM_145575	109624	Mm.308134	NM_145575	ENSMUSG00000029761	Cald1	4833423D12Rik|AI195384|AV071549|AW536160|C920027I18Rik	caldesmon 1	protein-coding
mm_15792.1	chr2	164425879	164425915	+	1	NA	3' UTR (NM_011521, exon 5 of 5)	3' UTR (NM_011521, exon 5 of 5)	17291	NM_011521	20971	Mm.3815	NM_011521	ENSMUSG00000017009	Sdc4	AA959608|AW108331|S4|Synd4|ryudocan|syndecan-4	syndecan 4	protein-coding
mm_1670.1	chr1	74791751	74791768	+	1	NA	promoter-TSS (NM_009518)	promoter-TSS (NM_009518)	-260	NM_009518	22409	Mm.5130	NM_009518	ENSMUSG00000026167	Wnt10a	-	wingless-type MMTV integration site family, member 10A	protein-coding
mm_13130.1	chr2	91774312	91774319	+	1	NA	intron (NM_172669, intron 7 of 17)	intron (NM_172669, intron 7 of 17)	44177	NM_001080754	228361	Mm.436667	NM_172669	ENSMUSG00000040506	Ambra1	2310079H06Rik|A130023A14|AA474864|AV021921|D030051N19Rik|mKIAA1736	autophagy/beclin 1 regulator 1	protein-coding
mm_137959.1	chr17	33139500	33139509	+	1	NA	5' UTR (NM_177719, exon 1 of 2)	5' UTR (NM_177719, exon 1 of 2)	179	NM_177719	240069	Mm.157765	NM_177719	ENSMUSG00000048602	Morc2b	4932411A10Rik|Tce6	microrchidia 2B	protein-coding
mm_63302.1	chr7	126823825	126823835	+	1	NA	promoter-TSS (NM_001146347)	promoter-TSS (NM_001146347)	527	NM_029978	68952	Mm.440393	NM_026884	ENSMUSG00000058966	Fam57b	1500016O10Rik|A330104J06Rik|AI413816|AW060769	family with sequence similarity 57, member B	protein-coding
mm_96855.1	chr11	70054386	70054466	+	1	NA	promoter-TSS (NM_009714)	promoter-TSS (NM_009714)	71	NM_001291132	11889	Mm.6559	NM_009714	ENSMUSG00000020884	Asgr1	ASGPR1|Asgr|Asgr-1|HL-1	asialoglycoprotein receptor 1	protein-coding
mm_102078.1	chr11	52275523	52275533	-	1	NA	intron (NM_001313981, intron 3 of 10)	intron (NM_001313981, intron 3 of 10)	7067	NM_009331	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_104913.1	chr11	99710272	99710275	-	1	NA	Intergenic	Intergenic	-44313	NM_026834	68768	Mm.416844	NM_026834	ENSMUSG00000075566	Krtap4-6	1110054P19Rik	keratin associated protein 4-6	protein-coding
mm_42309.1	chr5	114851965	114851980	+	1	NA	promoter-TSS (NR_105748)	promoter-TSS (NR_105748)	24	NR_105748	102466620		NR_105748	ENSMUSG00000098343	Mir6240	Gm27850|mmu-mir-6240	microRNA 6240	ncRNA
mm_147628.1	chr18	58210057	58210067	-	1	NA	promoter-TSS (NM_010181)	promoter-TSS (NM_010181)	-136	NM_010181	14119	Mm.20271	NM_010181	ENSMUSG00000024598	Fbn2	BC063774|Fib-2|mKIAA4226|sne|sy	fibrillin 2	protein-coding
mm_40754.1	chr5	66890265	66890282	+	1	NA	intron (NM_001001980, intron 3 of 25)	intron (NM_001001980, intron 3 of 25)	-78143	NM_001256122	77569	Mm.374778	NM_001001980	ENSMUSG00000037736	Limch1	3732412D22Rik|mKIAA1102	LIM and calponin homology domains 1	protein-coding
mm_38758.1	chr4	147868609	147868622	-	1	NA	promoter-TSS (NM_010244)	promoter-TSS (NM_010244)	104	NM_001025365	28010	Mm.250504	NM_133873	ENSMUSG00000029022	Miip	AA553001|AI853621|D4Wsu114e|IIP45	migration and invasion inhibitory protein	protein-coding
mm_78878.1	chr9	44487231	44487265	+	1	NA	Intergenic	Intergenic	-11888	NM_030256	80288	Mm.370270	NM_030256	ENSMUSG00000063382	Bcl9l	B9L|BC003321|BCL9-2|DLNB11	B cell CLL/lymphoma 9-like	protein-coding
mm_21449.1	chr2	160646565	160646570	-	1	NA	intron (NM_009408, intron 1 of 20)	CpG	670	NM_009408	21969	Mm.217233	NM_009408	ENSMUSG00000070544	Top1	AI467334|D130064I21Rik|Top-1	topoisomerase (DNA) I	protein-coding
mm_20278.1	chr2	126890703	126890725	-	1	NA	3' UTR (NM_023220, exon 15 of 15)	3' UTR (NM_023220, exon 15 of 15)	11671	NR_106202	102466258		NR_106202	ENSMUSG00000098896	Mir3473g	Gm27751|mmu-mir-3473g	microRNA 3473g	ncRNA
mm_33887.1	chr4	136178241	136178253	+	1	NA	intron (NM_177733, intron 1 of 6)	intron (NM_177733, intron 1 of 6)	-2535	NM_001305399	242705	Mm.307932	NM_177733	ENSMUSG00000018983	E2f2	E2F-2	E2F transcription factor 2	protein-coding
mm_114894.1	chr13	94388882	94388898	+	1	NA	intron (NM_009680, intron 1 of 26)	intron (NM_009680, intron 1 of 26)	29930	NM_009680	11774	Mm.21185	NM_009680	ENSMUSG00000021686	Ap3b1	AP-3|AU015684|C78395|Hps2|beta3A|pe|pearl|rim2	adaptor-related protein complex 3, beta 1 subunit	protein-coding
mm_165004.1	chr19	22767956	22767956	+	1	NA	3' UTR (NM_001035246, exon 8 of 8)	3' UTR (NM_001035246, exon 8 of 8)	17351	NR_029591	387200		NR_029591	ENSMUSG00000065507	Mir204	Mirn204|mir-204|mmu-mir-204	microRNA 204	ncRNA
mm_93041.1	chr10	88357467	88357469	-	1	NA	promoter-TSS (NM_027878)	promoter-TSS (NM_027878)	-393	NM_027878	71712	Mm.35450	NM_027878	ENSMUSG00000020057	Dram1	1200002N14Rik|Dram	DNA-damage regulated autophagy modulator 1	protein-coding
mm_71831.1	chr8	68896780	68896791	+	1	NA	exon (NM_008509, exon 6 of 10)	exon (NM_008509, exon 6 of 10)	16230	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_10030.1	chr1	192137895	192137933	-	1	NA	5' UTR (NM_144814, exon 1 of 10)	5' UTR (NM_144814, exon 1 of 10)	126	NM_001290278	214742	Mm.207457	NM_144814	ENSMUSG00000037395	Rcor3	4921514E24Rik|C730034D20Rik|E130101E15Rik	REST corepressor 3	protein-coding
mm_116187.1	chr13	31241073	31241088	-	1	NA	promoter-TSS (NR_045957)	promoter-TSS (NR_045957)	6	NR_045957	73924	Mm.417825	NR_045957	ENSMUSG00000087460	4930401O12Rik	-	RIKEN cDNA 4930401O12 gene	ncRNA
mm_9645.1	chr1	177258183	177258214	-	1	NA	Intergenic	CpG	-9431	NM_011785	23797	Mm.235194	NM_011785	ENSMUSG00000019699	Akt3	AI851531|D930002M15Rik|Nmf350	thymoma viral proto-oncogene 3	protein-coding
mm_127231.1	chr15	99405899	99405929	+	1	NA	exon (NM_026669, exon 6 of 10)	exon (NM_026669, exon 6 of 10)	12695	NM_001171035	110213	Mm.16769	NM_026669	ENSMUSG00000023010	Tmbim6	5031406P05Rik|Bi1|Tegt	transmembrane BAX inhibitor motif containing 6	protein-coding
mm_150976.1	chr19	46501739	46501773	+	1	NA	5' UTR (NM_053100, exon 1 of 6)	5' UTR (NM_053100, exon 1 of 6)	108	NM_053100	93679	Mm.392177	NM_053100	ENSMUSG00000025034	Trim8	AA408830|BB006755|GERP|Rnf27	tripartite motif-containing 8	protein-coding
mm_2427.1	chr1	95498773	95498800	+	1	NA	Intergenic	Intergenic	168808	NM_009183	20452	Mm.306228	NM_009183	ENSMUSG00000040710	St8sia4	PST|PST-1|SIAT8-D|ST8SiaIV|Siat8d	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4	protein-coding
mm_148042.1	chr18	70462842	70462849	-	1	NA	intron (NM_172967, intron 6 of 8)	intron (NM_172967, intron 6 of 8)	-9609	NM_029019	170461	Mm.83623	NM_029019	ENSMUSG00000079608	Stard6	1700011K09Rik|4833424I06Rik|4933429L05Rik|AI644424	StAR-related lipid transfer (START) domain containing 6	protein-coding
mm_110934.1	chr12	76370951	76370977	-	1	NA	intron (NM_178744, intron 1 of 1)	CpG-3289	698	NM_178744	268564	Mm.77065	NM_178744	ENSMUSG00000033454	Zbtb1	9430077A12|AI256369|Bsg2|C430003J21Rik	zinc finger and BTB domain containing 1	protein-coding
mm_155394.1	chrX	72918583	72918612	+	1	NA	promoter-TSS (NM_019405)	promoter-TSS (NM_019405)	76	NM_010941	18194	Mm.38792	NM_010941	ENSMUSG00000031349	Nsdhl	AI747449|Bpa|H105E3|Str|XAP104	NAD(P) dependent steroid dehydrogenase-like	protein-coding
mm_132829.1	chr16	45244977	45244979	+	1	NA	intron (NM_177584, intron 4 of 5)	intron (NM_177584, intron 4 of 5)	20641	NM_177584	208154	Mm.38199	NM_177584	ENSMUSG00000052013	Btla	A630002H24	B and T lymphocyte associated	protein-coding
mm_149861.1	chr19	25107808	25107809	+	1	NA	intron (NM_028785, intron 14 of 47)	intron (NM_028785, intron 14 of 47)	108279	NM_028785	76088	Mm.102485	NM_028785	ENSMUSG00000052085	Dock8	1200017A24Rik|5830472H07Rik|A130095G14Rik|AI461977	dedicator of cytokinesis 8	protein-coding
mm_131199.1	chr16	8618895	8618904	+	1	NA	3' UTR (NM_001170978, exon 15 of 15)	3' UTR (NM_001170978, exon 15 of 15)	18802	NM_025708	66690	Mm.10068	NM_025708	ENSMUSG00000043140	Tmem186	2810440M13Rik|4432406C05Rik|AI648175|AW210586	transmembrane protein 186	protein-coding
mm_50452.1	chr6	48906096	48906112	+	1	NA	exon (NM_001161622, exon 2 of 5)	exon (NM_001161622, exon 2 of 5)	1118	NM_001161621	76507	Mm.213898	NM_029638	ENSMUSG00000029811	Aoc1	1600012D06Rik|Abp1|DAO	amine oxidase, copper-containing 1	protein-coding
mm_42031.1	chr5	108367733	108367774	+	1	NA	Intergenic	CpG	-20620	NM_008806	18587	Mm.1372	NM_008806	ENSMUSG00000029491	Pde6b	Pdeb|r|rd|rd-1|rd1|rd10	phosphodiesterase 6B, cGMP, rod receptor, beta polypeptide	protein-coding
mm_69414.1	chr7	132576361	132576371	-	1	NA	promoter-TSS (NM_016978)	promoter-TSS (NM_016978)	32	NM_016978	18242	Mm.13694	NM_016978	ENSMUSG00000030934	Oat	AI194874|rhg	ornithine aminotransferase	protein-coding
mm_131359.1	chr16	13754555	13754628	+	1	NA	Intergenic	CpG	-24107	NM_011987	26565	Mm.4214	NM_011987	ENSMUSG00000022683	Pla2g10	GX sPLA2|PLA2GX|sPLA2-X	phospholipase A2, group X	protein-coding
mm_85787.1	chr9	109074050	109074140	-	1	NA	promoter-TSS (NM_172774)	promoter-TSS (NM_172774)	29	NM_172774	235610	Mm.100622	NM_172774	ENSMUSG00000025646	Atrip	6620401K05Rik	ATR interacting protein	protein-coding
mm_149336.1	chr19	10850257	10850274	+	1	NA	intron (NM_023044, intron 2 of 7)	MTD|LTR|ERVL-MaLR	7721	NM_023044	65221	Mm.27387	NM_023044	ENSMUSG00000024737	Slc15a3	Ci1|cI-1	solute carrier family 15, member 3	protein-coding
mm_169486.1	chr14	73797301	73797302	-	1	NA	Intergenic	Intergenic	244515	NM_011506	20916	Mm.38951	NM_011506	ENSMUSG00000022110	Sucla2	4930547K18Rik|A-SCS	succinate-Coenzyme A ligase, ADP-forming, beta subunit	protein-coding
mm_128988.1	chr15	74834686	74834704	-	1	NA	TTS (NM_001033229)	TTS (NM_001033229)	6948	NM_001033229	110115	Mm.322606	NM_001033229	ENSMUSG00000075604	Cyp11b1	AA389061|CPN1|Cyp11b|Cyp11b-1|FHI	cytochrome P450, family 11, subfamily b, polypeptide 1	protein-coding
mm_157966.1	chrX	90744970	90744985	-	1	NA	Intergenic	Intergenic	-147165	NM_001101450	212952	Mm.477436	NM_001101450	ENSMUSG00000091497	Gm44	-	predicted gene 44	protein-coding
mm_15316.1	chr2	155611239	155611247	+	1	NA	promoter-TSS (NM_001085378)	promoter-TSS (NM_001085378)	0	NM_001085378	668940	Mm.469980	NM_001085378	ENSMUSG00000074652	Myh7b	Myh14	myosin, heavy chain 7B, cardiac muscle, beta	protein-coding
mm_129741.1	chr15	82222989	82222992	-	1	NA	3' UTR (NM_028075, exon 3 of 3)	3' UTR (NM_028075, exon 3 of 3)	1346	NM_028075	72049	Mm.240047	NM_028075	ENSMUSG00000068105	Tnfrsf13c	2010006P15Rik|BAFF-R|Baffr|Bcmd|Bcmd-1|Bcmd1|Lvis22	tumor necrosis factor receptor superfamily, member 13c	protein-coding
mm_37572.1	chr4	126242259	126242286	-	1	NA	exon (NM_144941, exon 2 of 17)	exon (NM_144941, exon 2 of 17)	14047	NM_144941	245877	Mm.266716	NM_144941	ENSMUSG00000028849	Map7d1	AV028413|BC019977|Mtap7d1|Parcc1|Rprc1|mKIAA1187	MAP7 domain containing 1	protein-coding
mm_93792.1	chr10	120782048	120782065	-	1	NA	3' UTR (NM_177092, exon 7 of 7)	3' UTR (NM_177092, exon 7 of 7)	16324	NR_038003	70874	Mm.427286	NR_038000	ENSMUSG00000044544	4921513I03Rik	-	RIKEN cDNA 4921513I03 gene	ncRNA
mm_112279.1	chr12	114358281	114358292	-	1	NA	Intergenic	Intergenic	111180	NR_106062	102465663		NR_106062	ENSMUSG00000105438	Mir7094-1	mmu-mir-7094-1	microRNA 7094-1	ncRNA
mm_12459.1	chr2	71334218	71334234	+	1	NA	intron (NM_172436, intron 3 of 17)	RLTR17|LTR|ERVK	33328	NM_172436	78830	Mm.30928	NM_172436	ENSMUSG00000027010	Slc25a12	2610002D09Rik|AI839531|B230107K20Rik|BB129864	solute carrier family 25 (mitochondrial carrier, Aralar), member 12	protein-coding
mm_1911.1	chr1	85907009	85907021	+	1	NA	exon (NM_022417, exon 5 of 6)	exon (NM_022417, exon 5 of 6)	12505	NM_022417	64294	Mm.29870	NM_022417	ENSMUSG00000026223	Itm2c	3110038L02Rik|BRI3|Bricd2c|E25|E25C|ITM3	integral membrane protein 2C	protein-coding
mm_38363.1	chr4	138138491	138138495	-	1	NA	promoter-TSS (NR_126429)	promoter-TSS (NR_126429)	25	NR_126429	73563	Mm.444294	NR_126429	ENSMUSG00000084804	1700095J12Rik	-	RIKEN cDNA 1700095J12 gene	ncRNA
mm_134466.1	chr16	18426544	18426583	-	1	NA	5' UTR (NM_001111062, exon 1 of 6)	5' UTR (NM_001111062, exon 1 of 6)	146	NM_013711	26462	Mm.390906	NM_013711	ENSMUSG00000075704	Txnrd2	AA118373|ESTM573010|TGR|Tr3|Trxr2|Trxrd2	thioredoxin reductase 2	protein-coding
mm_337.1	chr1	29979024	29979028	+	1	NA	Intergenic	RLTR13B2|LTR|ERVK	557538	NR_105760	102465174		NR_105760	ENSMUSG00000099257	Mir6342	Gm27268|mmu-mir-6342	microRNA 6342	ncRNA
mm_143944.1	chr17	86710474	86710507	-	1	NA	Intergenic	Intergenic	-43374	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_24094.1	chr3	88030853	88030863	+	1	NA	Intergenic	Intergenic	-3347	NM_022031	73940	Mm.294467	NM_022031	ENSMUSG00000004894	Hapln2	4930401E20Rik|Bral1	hyaluronan and proteoglycan link protein 2	protein-coding
mm_162375.1	chr1	69871136	69871136	-	1	NA	intron (NM_001271533, intron 6 of 10)	ORR1E|LTR|ERVL-MaLR	44166	NM_001271533	66722	Mm.440554	NM_025728	ENSMUSG00000053153	Spag16	4921511D23Rik|4930524F24Rik|4930585K05Rik|AV261009|Pf20|Wdr29	sperm associated antigen 16	protein-coding
mm_11566.1	chr2	32878044	32878051	+	1	NA	intron (NM_146119, intron 1 of 13)	(T)n|Simple_repeat|Simple_repeat	1913	NM_146119	227737	Mm.301646	NM_146119	ENSMUSG00000026796	Fam129b	9130404D14Rik	family with sequence similarity 129, member B	protein-coding
mm_128423.1	chr15	46496153	46496161	-	1	NA	promoter-TSS (NR_040451)	promoter-TSS (NR_040451)	22	NR_040451	74726	Mm.78172	NR_040451		4930523O13Rik	4921524H24Rik	RIKEN cDNA 4930523O13 gene	ncRNA
mm_66327.1	chr7	42642576	42642609	-	1	NA	promoter-TSS (NM_001242388)	promoter-TSS (NM_001242388)	12	NM_001242388	208111	Mm.387841	NM_001034857	ENSMUSG00000074158	Zfp976	9830147E19Rik|C330019L16Rik	zinc finger protein 976	protein-coding
mm_33041.1	chr4	122935262	122935271	+	1	NA	Intergenic	Intergenic	25922	NM_029662	76574	Mm.331842	NM_029662	ENSMUSG00000028655	Mfsd2a	1700018O18Rik|Mfsd2|NLS1	major facilitator superfamily domain containing 2A	protein-coding
mm_33130.1	chr4	124881786	124881836	+	1	NA	promoter-TSS (NM_177671)	promoter-TSS (NM_177671)	26	NM_177671	230735	Mm.171490	NM_177671	ENSMUSG00000028876	Epha10	A330090H18	Eph receptor A10	protein-coding
mm_125244.1	chr15	34453286	34453303	+	1	NA	promoter-TSS (NM_173421)	promoter-TSS (NM_173421)	-18	NM_173421	239368	Mm.211977	NM_173421	ENSMUSG00000044726	Erich5	-	glutamate rich 5	protein-coding
mm_132991.1	chr16	52829130	52829138	+	1	NA	Intergenic	L1_Mur3|LINE|L1	-13390	NR_040495	73820	Mm.60493	NR_040495		4930404A05Rik	-	RIKEN cDNA 4930404A05 gene	ncRNA
mm_121454.1	chr14	120478531	120478535	+	1	NA	promoter-TSS (NM_029519)	promoter-TSS (NM_029519)	72	NM_029519	76108	Mm.261448	NM_029519	ENSMUSG00000051615	Rap2a	5830461H18Rik	RAS related protein 2a	protein-coding
mm_158690.1	chrX	160906999	160907014	-	1	NA	promoter-TSS (NM_001001496)	promoter-TSS (NM_001001496)	46	NM_001001496	414089	Mm.123113	NM_001001496	ENSMUSG00000055691	Gja6	A530015O12Rik|Cnx33|Cx33|Gja-6	gap junction protein, alpha 6	protein-coding
mm_123067.1	chr14	55681461	55681558	-	1	NA	exon (NM_145705, exon 1 of 9)	exon (NM_145705, exon 1 of 9)	308	NM_145705	28113	Mm.29346	NM_145705	ENSMUSG00000007589	Tinf2	AW552114|D14Wsu146e|Tin2	Terf1 (TRF1)-interacting nuclear factor 2	protein-coding
mm_80117.1	chr9	70543046	70543056	+	1	NA	exon (NM_025690, exon 1 of 21)	exon (NM_025690, exon 1 of 21)	181	NM_025690	66660	Mm.22379	NM_025690	ENSMUSG00000032212	Sltm	5730455C01Rik|5730555F13Rik|9130215G10Rik|Met	SAFB-like, transcription modulator	protein-coding
mm_171211.1	chr3	5860485	5860490	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-284239	NM_001163305	19302	Mm.132336	NM_008994	ENSMUSG00000040374	Pex2	D3Ertd138e|PAF-1|PMP35|Pxmp3	peroxisomal biogenesis factor 2	protein-coding
mm_20183.1	chr2	122599672	122599698	-	1	NA	intron (NM_025961, intron 6 of 8)	intron (NM_025961, intron 6 of 8)	11592	NM_025961	67092	Mm.29975	NM_025961	ENSMUSG00000027199	Gatm	1810003P21Rik|AI314789|AT	glycine amidinotransferase (L-arginine:glycine amidinotransferase)	protein-coding
mm_171135.1	chr3	149052691	149052698	+	1	NA	Intergenic	(TTAGGG)n|Simple_repeat|Simple_repeat	-98059	NM_001081298	99633	Mm.9776	NM_001081298	ENSMUSG00000028184	Adgrl2	AI450192|CIRL-2|Gm619|Lec1|Lphh1|Lphn2|mKIAA0786	adhesion G protein-coupled receptor L2	protein-coding
mm_25627.1	chr3	118980048	118980059	+	1	NA	intron (NM_170778, intron 12 of 22)	L1MEd|LINE|L1	417875	NM_170778	99586	Mm.27907	NM_170778	ENSMUSG00000033308	Dpyd	AI315208|DPD|E330028L06Rik	dihydropyrimidine dehydrogenase	protein-coding
mm_64554.1	chr7	144582120	144582174	+	1	NA	exon (NM_010175, exon 1 of 2)	exon (NM_010175, exon 1 of 2)	289	NM_010175	14082	Mm.5126	NM_010175	ENSMUSG00000031077	Fadd	Mort1/FADD	Fas (TNFRSF6)-associated via death domain	protein-coding
mm_94024.1	chr10	127667650	127667665	-	1	NA	promoter-TSS (NM_008668)	promoter-TSS (NM_008668)	534	NR_045171	72243	Mm.482902	NR_045171	ENSMUSG00000040195	1700012D01Rik	-	RIKEN cDNA 1700012D01 gene	ncRNA
mm_91468.1	chr10	34186486	34186496	-	1	NA	intron (NM_172508, intron 1 of 5)	BC1_Mm|scRNA|scRNA	21060	NM_172508	212898	Mm.34557	NM_172508	ENSMUSG00000039497	Dse	6030499O08|AI480506|B130024B19Rik|DS-epi1|Sart2	dermatan sulfate epimerase	protein-coding
mm_53995.1	chr6	6881987	6882007	-	1	NA	promoter-TSS (NM_010056)	promoter-TSS (NM_010056)	71	NM_198854	13395	Mm.4873	NM_010056	ENSMUSG00000029755	Dlx5	AI385752	distal-less homeobox 5	protein-coding
mm_152929.1	chr19	28283862	28283882	-	1	NA	intron (NM_001305671, intron 7 of 9)	intron (NM_001305671, intron 7 of 9)	-272706	NM_011265	19726	Mm.313321	NM_011265	ENSMUSG00000040929	Rfx3	C230093O12Rik|MRFX3	regulatory factor X, 3 (influences HLA class II expression)	protein-coding
mm_25007.1	chr3	97658556	97658615	+	1	NA	intron (NM_182997, intron 1 of 7)	CpG	373	NM_182997	108097	Mm.31175	NM_182997	ENSMUSG00000038205	Prkab2	5730553K21Rik|AW049591|BB124140	protein kinase, AMP-activated, beta 2 non-catalytic subunit	protein-coding
mm_122497.1	chr14	46673822	46673835	-	1	NA	promoter-TSS (NR_131909)	promoter-TSS (NR_131909)	-53	NR_131909	328385	Mm.271545	NR_131909		D330046F09Rik	Gm808	RIKEN cDNA D330046F09 gene	ncRNA
mm_21982.1	chr2	167485650	167485658	-	1	NA	intron (NM_170756, intron 1 of 2)	intron (NM_170756, intron 1 of 2)	-6991	NM_030743	81018	Mm.22225	NM_030743	ENSMUSG00000006418	Rnf114	1110008J21Rik|AI225886|AW549494|Zfp228|Zfp313|Znf228	ring finger protein 114	protein-coding
mm_24492.1	chr3	92365179	92365193	+	1	NA	promoter-TSS (NM_011472)	promoter-TSS (NM_011472)	-1	NM_011472	20760	Mm.10692	NM_011472	ENSMUSG00000050635	Sprr2f	-	small proline-rich protein 2F	protein-coding
mm_137210.1	chr17	24152090	24152100	+	1	NA	Intergenic	Intergenic	-1173	NM_001286662	18607	Mm.10504	NM_011062	ENSMUSG00000024122	Pdpk1	Pdk1	3-phosphoinositide dependent protein kinase 1	protein-coding
mm_125806.1	chr15	74926118	74926121	+	1	NA	Intergenic	Intergenic	-28932	NM_001164039	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_118276.1	chr13	112652242	112652255	-	1	NA	promoter-TSS (NM_010029)	promoter-TSS (NM_010029)	62	NM_010029	13206	Mm.12818	NM_010029	ENSMUSG00000021758	Ddx4	AV206478|Mvh|VASA	DEAD (Asp-Glu-Ala-Asp) box polypeptide 4	protein-coding
mm_42457.1	chr5	115435483	115435498	+	1	NA	exon (NM_008629, exon 6 of 15)	exon (NM_008629, exon 6 of 15)	5805	NM_008629	17690	Mm.5077	NM_008629	ENSMUSG00000054256	Msi1	Msi1h|Musahi1|m-Msi-1	musashi RNA-binding protein 1	protein-coding
mm_155672.1	chrX	90744771	90744783	+	1	NA	Intergenic	Intergenic	-147365	NM_001101450	212952	Mm.477436	NM_001101450	ENSMUSG00000091497	Gm44	-	predicted gene 44	protein-coding
mm_75754.1	chr8	69903159	69903222	-	1	NA	promoter-TSS (NM_023312)	promoter-TSS (NM_023312)	-632	NM_023312	67184	Mm.21162	NM_023312	ENSMUSG00000036199	Ndufa13	2700054G14Rik|AU022060|CDA016|CGI-39|GRIM-19|Grim19	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 13	protein-coding
mm_63073.1	chr7	122208625	122208648	+	1	NA	Intergenic	Intergenic	-10860	NM_027363	70261	Mm.96997	NM_027363	ENSMUSG00000030865	Chp2	2010110P09Rik|Cbhp2	calcineurin-like EF hand protein 2	protein-coding
mm_42472.1	chr5	115454556	115454583	+	1	NA	TTS (NM_008629)	TTS (NM_008629)	-11697	NM_011107	18778	Mm.20190	NM_011107	ENSMUSG00000029522	Pla2g1b	Pla2a|sPLA2IB	phospholipase A2, group IB, pancreas	protein-coding
mm_107611.1	chr12	49384987	49385028	+	1	NA	exon (NM_008241, exon 2 of 2)	exon (NM_008241, exon 2 of 2)	2000	NM_008241	15228	Mm.4704	NM_008241	ENSMUSG00000020950	Foxg1	2900064B05Rik|BF-1|Bf1|Hfh9|Hfhbf1	forkhead box G1	protein-coding
mm_78121.1	chr9	20644334	20644357	+	1	NA	promoter-TSS (NM_001310746)	promoter-TSS (NM_001310746)	422	NM_001286529	30843	Mm.24608	NM_013911	ENSMUSG00000066892	Fbxl12	3110048D16Rik|Fbl12	F-box and leucine-rich repeat protein 12	protein-coding
mm_32920.1	chr4	119136827	119136858	+	1	NA	3' UTR (NM_011400, exon 10 of 10)	3' UTR (NM_011400, exon 10 of 10)	28097	NM_011400	20525	Mm.21002	NM_011400	ENSMUSG00000028645	Slc2a1	Glut-1|Glut1	solute carrier family 2 (facilitated glucose transporter), member 1	protein-coding
mm_94508.1	chr11	7207366	7207380	+	1	NA	3' UTR (NM_008343, exon 5 of 5)	3' UTR (NM_008343, exon 5 of 5)	6550	NM_008343	16009	Mm.29254	NM_008343	ENSMUSG00000020427	Igfbp3	AI649005|IGFBP-3|IGgfbp3	insulin-like growth factor binding protein 3	protein-coding
mm_111893.1	chr12	108489092	108489095	-	1	NA	intron (NM_001043335, intron 4 of 21)	intron (NM_001043335, intron 4 of 21)	-65627	NM_001163394	14026	Mm.238841	NM_007965	ENSMUSG00000021262	Evl	AI528774	Ena-vasodilator stimulated phosphoprotein	protein-coding
mm_32386.1	chr4	106581790	106581801	+	1	NA	intron (NM_053272, intron 6 of 8)	L2|LINE|L2	20757	NM_053272	74754	Mm.133370	NM_053272	ENSMUSG00000034926	Dhcr24	2310076D10Rik|5830417J06Rik|mKIAA0018	24-dehydrocholesterol reductase	protein-coding
mm_26096.1	chr3	136903076	136903089	+	1	NA	intron (NM_008913, intron 8 of 13)	intron (NM_008913, intron 8 of 13)	233016	NM_001293622	19055	Mm.331389	NM_008913	ENSMUSG00000028161	Ppp3ca	2900074D19Rik|CN|Caln|Calna|CnA	protein phosphatase 3, catalytic subunit, alpha isoform	protein-coding
mm_77130.1	chr8	111338423	111338434	-	1	NA	promoter-TSS (NM_001310613)	promoter-TSS (NM_001310613)	-223	NM_029005	74568	Mm.207971	NM_029005	ENSMUSG00000012519	Mlkl	9130019I15Rik	mixed lineage kinase domain-like	protein-coding
mm_42816.1	chr5	121848988	121849002	+	1	NA	promoter-TSS (NM_175474)	promoter-TSS (NM_175474)	-33	NM_175474	231717	Mm.12654	NM_175474	ENSMUSG00000044134	Fam109a	A230106M15Rik|AU017694|IPIP27A|Ses1	family with sequence similarity 109, member A	protein-coding
mm_167285.1	chr8	40511217	40511229	-	1	NA	promoter-TSS (NM_033560)	promoter-TSS (NM_033560)	531	NM_001271543	18983	Mm.272551	NM_011135	ENSMUSG00000031601	Cnot7	AU022737|CAF-1|Caf1|Pop2	CCR4-NOT transcription complex, subunit 7	protein-coding
mm_54968.1	chr6	48737023	48737065	-	1	NA	Intergenic	Intergenic	-2003	NM_175860	16205	Mm.252599	NM_008376	ENSMUSG00000090019	Gimap1	IAP38|Imap38|imap	GTPase, IMAP family member 1	protein-coding
mm_19574.1	chr2	101643590	101643598	-	1	NA	exon (NM_009019, exon 2 of 2)	exon (NM_009019, exon 2 of 2)	5938	NM_009019	19373	Mm.828	NM_009019	ENSMUSG00000061311	Rag1	Rag-1	recombination activating gene 1	protein-coding
mm_2034.1	chr1	87213910	87213918	+	1	NA	promoter-TSS (NM_001039169)	promoter-TSS (NM_001039169)	0	NM_023314	26987	Mm.227183	NM_023314	ENSMUSG00000026254	Eif4e2	2700069E09Rik|AI036339|AV129531|D0H0S6743E|Eif4el3	eukaryotic translation initiation factor 4E member 2	protein-coding
mm_145018.1	chr18	38714515	38714533	+	1	NA	Intergenic	Intergenic	-113256	NM_011898	24066	Mm.42038	NM_011898	ENSMUSG00000024427	Spry4	A030006O18Rik|sprouty4	sprouty homolog 4 (Drosophila)	protein-coding
mm_106233.1	chr11	117421158	117421162	-	1	NA	intron (NR_136918, intron 1 of 1)	intron (NR_136918, intron 1 of 1)	557	NR_136918	667423	Mm.383716	NR_136918	ENSMUSG00000083705	Gm8624	EG667423	ribosomal protein S23 pseudogene	pseudo
mm_62179.1	chr7	97451301	97451309	+	1	NA	promoter-TSS (NM_001136235)	promoter-TSS (NM_001136235)	-29	NM_001136235	233529	Mm.334033	NM_001010826	ENSMUSG00000051727	Kctd14	AI449310|D7Ertd760e	potassium channel tetramerisation domain containing 14	protein-coding
mm_152353.1	chr19	10001586	10001622	-	1	NA	promoter-TSS (NM_011913)	promoter-TSS (NM_011913)	29	NM_011913	24115	Mm.31577	NM_011913	ENSMUSG00000037418	Best1	Bmd|Vmd2|mBest1	bestrophin 1	protein-coding
mm_93617.1	chr10	117277483	117277530	-	1	NA	TTS (NM_017372)	TTS (NM_017372)	4766	NM_017372	17105	Mm.45436	NM_017372	ENSMUSG00000069516	Lyz2	AI326280|Lys|Lysm|Lyzf2|Lyzs|Lzm|Lzm-s1|Lzp	lysozyme 2	protein-coding
mm_32645.1	chr4	115057650	115057671	+	1	NA	promoter-TSS (NM_001287388)	promoter-TSS (NM_001287388)	-151	NM_001287388	21349	Mm.239869	NM_011527	ENSMUSG00000028717	Tal1	Hpt|SCL/tal-1|Scl|bHLHa17|tal-1	T cell acute lymphocytic leukemia 1	protein-coding
mm_35841.1	chr4	48049049	48049063	-	1	NA	5' UTR (NM_015743, exon 2 of 8)	5' UTR (NM_015743, exon 2 of 8)	-2190	NM_001307989	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_95346.1	chr11	48800392	48800393	+	1	NA	promoter-TSS (NM_008143)	promoter-TSS (NM_008143)	32	NM_008143	14694	Mm.5305	NM_008143	ENSMUSG00000020372	Rack1	AL033335|GB-like|Gnb2-rs1|Gnb2l1|p205	receptor for activated C kinase 1	protein-coding
mm_16942.1	chr2	15049117	15049126	-	1	NA	5' UTR (NM_001165942, exon 1 of 4)	5' UTR (NM_001165942, exon 1 of 4)	191	NM_001165942	74455	Mm.478923	NM_028950	ENSMUSG00000026707	Nsun6	4933403D21Rik|4933414E04Rik|NOPD1	NOL1/NOP2/Sun domain family member 6	protein-coding
mm_126668.1	chr15	84324726	84324777	+	1	NA	promoter-TSS (NM_022321)	promoter-TSS (NM_022321)	31	NM_022321	64099	Mm.251356	NM_022321	ENSMUSG00000022439	Parvg	AI413459	parvin, gamma	protein-coding
mm_73173.1	chr8	95049998	95050001	+	1	NA	Intergenic	RLTR30D2_MM|LTR|ERV1	-5104	NM_001042715	330830	Mm.277112	NM_001042715	ENSMUSG00000031786	Drc7	Ccdc135|Gm770|SRG-L|SRG-S	dynein regulatory complex subunit 7	protein-coding
mm_70336.1	chr8	4524623	4524635	+	1	NA	3' UTR (NM_026058, exon 11 of 11)	3' UTR (NM_026058, exon 11 of 11)	31224	NM_026058	67260	Mm.35511	NM_026058	ENSMUSG00000008206	Cers4	2900019C14Rik|Lass4|Trh1	ceramide synthase 4	protein-coding
mm_162188.1	chrX	105764411	105764411	+	1	NA	promoter-TSS (NM_030614)	promoter-TSS (NM_030614)	-66	NM_030614	80903	Mm.154768	NM_030614	ENSMUSG00000031230	Fgf16	-	fibroblast growth factor 16	protein-coding
mm_39721.1	chr5	28165691	28165717	+	1	NA	promoter-TSS (NM_010134)	promoter-TSS (NM_010134)	8	NM_010134	13799	Mm.4298	NM_010134	ENSMUSG00000039095	En2	BB131122|En-2	engrailed 2	protein-coding
mm_130487.1	chr15	98763196	98763220	-	1	NA	promoter-TSS (NM_007478)	promoter-TSS (NM_007478)	-90	NM_007478	11842	Mm.221298	NM_007478	ENSMUSG00000051853	Arf3	5430400P17Rik|AI854770	ADP-ribosylation factor 3	protein-coding
mm_47966.1	chr5	135744207	135744271	-	1	NA	promoter-TSS (NM_172541)	promoter-TSS (NM_172541)	-67	NM_172541	215210	Mm.11688	NM_172541	ENSMUSG00000039886	Tmem120a	2010310D06Rik|Tmpit	transmembrane protein 120A	protein-coding
mm_31144.1	chr4	43383519	43383528	+	1	NA	intron (NM_001037709, intron 1 of 11)	intron (NM_001037709, intron 1 of 11)	1541	NM_001037709	100213	Mm.235730	NM_199057	ENSMUSG00000035969	Rusc2	AI840675|mKIAA0375	RUN and SH3 domain containing 2	protein-coding
mm_151601.1	chr19	3549424	3549427	-	1	NA	intron (NM_029456, intron 1 of 22)	intron (NM_029456, intron 1 of 22)	26324	NM_001164159	52036	Mm.284686	NM_028999	ENSMUSG00000024908	Ppp6r3	4930528G08Rik|9130026N02Rik|D19Bwg1430e|D19Ertd703e|Pp6r3|Ppcs3|Pptcs3|Sapl|Saps3|mKIAA1558	protein phosphatase 6, regulatory subunit 3	protein-coding
mm_146224.1	chr18	77065585	77065587	+	1	NA	promoter-TSS (NM_001164168)	promoter-TSS (NM_001164168)	-94	NM_001164170	17344	Mm.6370	NM_008602	ENSMUSG00000025423	Pias2	6330408K17Rik|AI462206|ARIP3|AU018068|Dib|Miz1|PIASxalpha|PIASxb|PIASxbeta|SIZ2	protein inhibitor of activated STAT 2	protein-coding
mm_67479.1	chr7	80688853	80688923	-	1	NA	promoter-TSS (NM_173863)	promoter-TSS (NM_173863)	-11	NM_173863	70461	Mm.392175	NM_173863	ENSMUSG00000030527	Crtc3	2610312F20Rik|6332415K15Rik|AI429792|BC011210|TORC3	CREB regulated transcription coactivator 3	protein-coding
mm_20839.1	chr2	147431404	147431411	-	1	NA	Intergenic	L2a|LINE|L2	66413	NM_008780	18503	Mm.315502	NM_008780	ENSMUSG00000037034	Pax1	Pax-1|hbs|hunchback|un|undulated|wt	paired box 1	protein-coding
mm_65486.1	chr7	25675101	25675187	-	1	NA	promoter-TSS (NM_177102)	promoter-TSS (NM_177102)	22	NM_001290497	320208	Mm.207484	NM_177102	ENSMUSG00000061702	Tmem91	A830041P22Rik|DSPC3	transmembrane protein 91	protein-coding
mm_59274.1	chr7	24904238	24904252	+	1	NA	promoter-TSS (NM_001130152)	promoter-TSS (NM_001130152)	-101	NM_001130152	16801	Mm.3181	NM_008488	ENSMUSG00000040940	Arhgef1	Lbcl2|Lsc	Rho guanine nucleotide exchange factor (GEF) 1	protein-coding
mm_27587.1	chr3	59130532	59130543	-	1	NA	5' UTR (NM_001287124, exon 1 of 2)	5' UTR (NM_001287124, exon 1 of 2)	225	NM_001008497	140795	Mm.439021	NM_133200	ENSMUSG00000036381	P2ry14	A330108O13Rik|Gpr105|P2Y14	purinergic receptor P2Y, G-protein coupled, 14	protein-coding
mm_134690.1	chr16	22504686	22504693	-	1	NA	intron (NM_001346673, intron 20 of 23)	intron (NM_001346673, intron 20 of 23)	-6791	NR_130988	78082	Mm.243927	NR_130988	ENSMUSG00000089874	9230117E06Rik	-	RIKEN cDNA 9230117E06 gene	ncRNA
mm_122845.1	chr14	54726817	54726827	-	1	NA	exon (NM_016972, exon 9 of 11)	exon (NM_016972, exon 9 of 11)	-14648	NM_207131	110794	Mm.236223	NM_207131	ENSMUSG00000052435	Cebpe	C/EBPe|CRP1|Gm294	CCAAT/enhancer binding protein (C/EBP), epsilon	protein-coding
mm_131480.1	chr16	17146940	17146985	+	1	NA	promoter-TSS (NM_026940)	promoter-TSS (NM_026940)	-5	NM_026940	69101	Mm.101656	NM_026940	ENSMUSG00000041774	Ydjc	1810015A11Rik|4930521M19Rik	YdjC homolog (bacterial)	protein-coding
mm_168733.1	chr12	114616322	114616323	-	1	NA	Intergenic	Intergenic	-102628	NR_106063	102465664		NR_106063	ENSMUSG00000098357	Mir7094-2	Gm27508|mmu-mir-7094-2	microRNA 7094-2	ncRNA
mm_112572.1	chr13	13590370	13590376	+	1	NA	promoter-TSS (NM_010748)	promoter-TSS (NM_010748)	-36	NM_010748	17101	Mm.342337	NM_010748	ENSMUSG00000019726	Lyst	D13Sfk13|beige|bg	lysosomal trafficking regulator	protein-coding
mm_159529.1	chr4	62559793	62559793	+	1	NA	promoter-TSS (NM_019492)	promoter-TSS (NM_019492)	-54	NM_019492	50780	Mm.286753	NM_019492	ENSMUSG00000059810	Rgs3	4930506N09Rik|C2PA-RGS3|C2pa|PDZ-RGS3|RGS3S	regulator of G-protein signaling 3	protein-coding
mm_30609.1	chr4	6509942	6509947	+	1	NA	Intergenic	MT2A|LTR|ERVL	-55673	NM_010945	18201	Mm.3059	NM_010945	ENSMUSG00000028245	Nsmaf	AA959567|C630007J05|Fan	neutral sphingomyelinase (N-SMase) activation associated factor	protein-coding
mm_26291.1	chr3	142506839	142506852	+	1	NA	exon (NM_153564, exon 8 of 11)	exon (NM_153564, exon 8 of 11)	9911	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_37886.1	chr4	132510494	132510509	-	1	NA	promoter-TSS (NM_144907)	promoter-TSS (NM_144907)	-45	NM_144907	230784	Mm.23608	NM_144907	ENSMUSG00000028893	Sesn2	HI95|SEST2|Ses2	sestrin 2	protein-coding
mm_123374.1	chr14	63245220	63245265	-	1	NA	promoter-TSS (NM_008092)	promoter-TSS (NM_008092)	29	NM_008092	14463	Mm.247669	NM_008092	ENSMUSG00000021944	Gata4	Gata-4	GATA binding protein 4	protein-coding
mm_9309.1	chr1	171641115	171641127	-	1	NA	TTS (NR_106151)	TTS (NR_106151)	779	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_72202.1	chr8	72572070	72572114	+	1	NA	promoter-TSS (NM_144534)	promoter-TSS (NM_144534)	-11	NM_144534	74166	Mm.212927	NM_144534	ENSMUSG00000031791	Tmem38a	1110001E17Rik|AI413399|TRIC-A|mg33a	transmembrane protein 38A	protein-coding
mm_165240.1	chr2	62412198	62412206	-	1	NA	promoter-TSS (NM_010074)	promoter-TSS (NM_010074)	29	NM_010074	13482	Mm.1151	NM_010074	ENSMUSG00000035000	Dpp4	Cd26|Dpp-4|THAM	dipeptidylpeptidase 4	protein-coding
mm_67529.1	chr7	81213652	81213671	-	1	NA	promoter-TSS (NM_008803)	promoter-TSS (NM_008803)	-143	NM_008803	18584	Mm.371577	NM_008803	ENSMUSG00000025584	Pde8a	AI551852|Pde8	phosphodiesterase 8A	protein-coding
mm_141937.1	chr17	35047740	35047743	-	1	NA	promoter-TSS (NM_001146215)	promoter-TSS (NM_001146215)	-996	NM_001146215	17687	Mm.24192	NM_013600	ENSMUSG00000007035	Msh5	Mut5	mutS homolog 5	protein-coding
mm_91872.1	chr10	59582919	59582933	-	1	NA	intron (NM_001033259, intron 1 of 7)	IMPB_01|Satellite|Satellite	33766	NM_001033259	215999	Mm.296470	NM_001033259	ENSMUSG00000009647	Mcu	2010012O16Rik|AV064928|C10orf42|Ccdc109a|D130073L02Rik|Gm64	mitochondrial calcium uniporter	protein-coding
mm_118901.1	chr14	26649247	26649249	+	1	NA	intron (NM_007479, intron 3 of 5)	intron (NM_007479, intron 3 of 5)	11051	NM_007479	11843	Mm.297768	NM_007479	ENSMUSG00000021877	Arf4	AA407803	ADP-ribosylation factor 4	protein-coding
mm_127374.1	chr15	100790848	100790853	+	1	NA	intron (NM_001347102, intron 8 of 23)	intron (NM_001347102, intron 8 of 23)	9596	NM_001347102	59033	Mm.209856	NM_021530	ENSMUSG00000023032	Slc4a8	AW493845|C230026C11|NDCBE|kNBC-3	solute carrier family 4 (anion exchanger), member 8	protein-coding
mm_152996.1	chr19	29865223	29865257	-	1	NA	Intergenic	ORR1A1|LTR|ERVL-MaLR	-52266	NM_177721	240614	Mm.125503	NM_177721	ENSMUSG00000074909	Ranbp6	C630001B19	RAN binding protein 6	protein-coding
mm_20169.1	chr2	122305672	122305680	-	1	NA	exon (NM_001305262, exon 7 of 10)	exon (NM_001305262, exon 7 of 10)	6776	NM_025777	66811	Mm.171333	NM_025777	ENSMUSG00000027225	Duoxa2	9030623N16Rik|Nip2	dual oxidase maturation factor 2	protein-coding
mm_147041.1	chr18	34886664	34886668	-	1	NA	Intergenic	ID4|SINE|ID	25459	NM_007913	13653	Mm.181959	NM_007913	ENSMUSG00000038418	Egr1	A530045N19Rik|ETR103|Egr-1|Krox-1|Krox-24|Krox24|NGF1-A|NGFI-A|NGFIA|TIS8|Zenk|Zfp-6|Zif268|egr	early growth response 1	protein-coding
mm_156235.1	chrX	135885987	135886019	+	1	NA	5' UTR (NM_198161, exon 1 of 5)	5' UTR (NM_198161, exon 1 of 5)	152	NM_198161	70237	Mm.440847	NM_198161	ENSMUSG00000072964	Bhlhb9	2700087I09Rik	basic helix-loop-helix domain containing, class B9	protein-coding
mm_61766.1	chr7	82867207	82867217	+	1	NA	promoter-TSS (NM_175366)	promoter-TSS (NM_175366)	-121	NM_175366	108797	Mm.306789	NM_175366	ENSMUSG00000057706	Mex3b	4931439A04Rik|M-04814|Rkhd3|mKIAA2009	mex3 RNA binding family member B	protein-coding
mm_68591.1	chr7	116034598	116034619	-	1	NA	intron (NM_001025559, intron 1 of 15)	intron (NM_001025559, intron 1 of 15)	-3561	NM_001025560	20679	Mm.323365	NM_011445	ENSMUSG00000051910	Sox6	AI987981|SOX-LZ	SRY (sex determining region Y)-box 6	protein-coding
mm_143778.1	chr17	81713027	81713037	-	1	NA	intron (NR_104580, intron 1 of 8)	intron (NR_104580, intron 1 of 8)	25355	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_42047.1	chr5	108517132	108517141	+	1	NA	Intergenic	Intergenic	32891	NM_007756	12889	Mm.5195	NM_007756	ENSMUSG00000033615	Cplx1	921-S	complexin 1	protein-coding
mm_31736.1	chr4	63152573	63152592	+	1	NA	intron (NM_007443, intron 2 of 9)	intron (NM_007443, intron 2 of 9)	1590	NM_007443	11699	Mm.2197	NM_007443	ENSMUSG00000028356	Ambp	AI194774|ASPI|HI-30|Intin4|Itil|UTI	alpha 1 microglobulin/bikunin	protein-coding
mm_155991.1	chrX	106146643	106146652	+	1	NA	intron (NM_205820, intron 1 of 2)	intron (NM_205820, intron 1 of 2)	3372	NM_205820	279572	Mm.336203	NM_205820	ENSMUSG00000033777	Tlr13	AI666735|Gm713	toll-like receptor 13	protein-coding
mm_50711.1	chr6	52172876	52172887	+	1	NA	intron (NM_010452, intron 3 of 4)	intron (NM_010452, intron 3 of 4)	7207	NR_131182	105242657	Mm.490651	NR_131182	ENSMUSG00000056445	Hoxaas2	2810043O09Rik|5730446D14Rik	Hoxa cluster antisense RNA 2	ncRNA
mm_126039.1	chr15	76904289	76904306	+	1	NA	intron (NM_012053, intron 1 of 5)	CpG	226	NM_012053	26961	Mm.30066	NM_012053	ENSMUSG00000003970	Rpl8	-	ribosomal protein L8	protein-coding
mm_69321.1	chr7	128461580	128461622	-	1	NA	promoter-TSS (NM_009383)	promoter-TSS (NM_009383)	72	NM_001347641	21843	Mm.242072	NM_009383	ENSMUSG00000030846	Tial1	5330433G13Rik|AL033329|TIAR|mTIAR	Tia1 cytotoxic granule-associated RNA binding protein-like 1	protein-coding
mm_145957.1	chr18	67774780	67774819	+	1	NA	promoter-TSS (NM_001039088)	promoter-TSS (NM_001039088)	-77	NM_028112	72124	Mm.307315	NM_028112	ENSMUSG00000079614	Seh1l	2610007A16Rik|AW540070|SEC13L|SEH1A|SEH1B|Seh1	SEH1-like (S. cerevisiae	protein-coding
mm_115371.1	chr13	113035228	113035231	+	1	NA	promoter-TSS (NM_001281487)	promoter-TSS (NM_001281487)	-150	NM_001281487	238896		NM_001281487	ENSMUSG00000078926	Cdc20b	EG238896|EG622422	cell division cycle 20B	protein-coding
mm_75003.1	chr8	27228582	27228587	-	1	NA	5' UTR (NM_013462, exon 2 of 4)	5' UTR (NM_013462, exon 2 of 4)	1004	NM_013462	11556	Mm.278475	NM_013462	ENSMUSG00000031489	Adrb3	Adrb-3	adrenergic receptor, beta 3	protein-coding
mm_82820.1	chr9	31030256	31030278	-	1	NA	promoter-TSS (NM_001115130)	promoter-TSS (NM_001115130)	-377	NM_001115130	235132	Mm.239355	NM_172765	ENSMUSG00000047412	Zbtb44	6030404E16Rik|Btbd15|E230011F09	zinc finger and BTB domain containing 44	protein-coding
mm_71672.1	chr8	60674572	60674583	+	1	NA	3' UTR (NM_001177882, exon 3 of 3)	3' UTR (NM_001177882, exon 3 of 3)	19020	NM_001177882	71306	Mm.23242	NM_027756	ENSMUSG00000031647	Mfap3l	4933428A15Rik|5430405D20Rik|AI461995|AW125052|NYD-sp9|mKIAA0626	microfibrillar-associated protein 3-like	protein-coding
mm_56388.1	chr6	94683877	94683880	-	1	NA	intron (NM_008377, intron 1 of 18)	intron (NM_008377, intron 1 of 18)	16267	NM_008377	16206	Mm.245210	NM_008377	ENSMUSG00000030029	Lrig1	D6Bwg0781e|Img|LIG-1	leucine-rich repeats and immunoglobulin-like domains 1	protein-coding
mm_142099.1	chr17	35835386	35835413	-	1	NA	exon (NM_011655, exon 4 of 4)	exon (NM_011655, exon 4 of 4)	2902	NM_011655	22154	Mm.273538	NM_011655	ENSMUSG00000001525	Tubb5	AA408537|AI596182|B130022C14Rik|M(beta)5	tubulin, beta 5 class I	protein-coding
mm_43049.1	chr5	124076915	124076922	+	1	NA	intron (NM_019875, intron 8 of 11)	intron (NM_019875, intron 8 of 11)	18880	NM_019875	56325	Mm.254839	NM_019875	ENSMUSG00000029408	Abcb9	TAPL|mKIAA1520	ATP-binding cassette, sub-family B (MDR/TAP), member 9	protein-coding
mm_159618.1	chr4	134227514	134227514	-	1	NA	promoter-TSS (NM_177866)	promoter-TSS (NM_177866)	-131	NM_177866	329954	Mm.79072	NM_177866	ENSMUSG00000048003	Catsper4	4933412L05	cation channel, sperm associated 4	protein-coding
mm_167435.1	chr8	119423989	119424003	+	1	NA	Intergenic	Intergenic	-13166	NM_027950	71839	Mm.272357	NM_027950	ENSMUSG00000074063	Osgin1	1700012B18Rik|Okl38	oxidative stress induced growth inhibitor 1	protein-coding
mm_164633.1	chr17	34039335	34039344	+	1	NA	TTS (NM_001205216)	TTS (NM_001205216)	201	NM_001317722	12815	Mm.20230	NM_009926	ENSMUSG00000024330	Col11a2	-	collagen, type XI, alpha 2	protein-coding
mm_89244.1	chr10	87858657	87858665	+	1	NA	promoter-TSS (NM_010512)	promoter-TSS (NM_010512)	-391	NM_001111275	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_33241.1	chr4	127023659	127023740	+	1	NA	exon (NM_023603, exon 4 of 10)	exon (NM_023603, exon 4 of 10)	2398	NM_023603	71514	Mm.257276	NM_023603	ENSMUSG00000028820	Sfpq	1110004P21Rik|2810416M14Rik|5730453G22Rik|9030402K04Rik|AU021830|D4Ertd314e|Gm12940|OTTMUSG00000009329|PSF|REP1	splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)	protein-coding
mm_4946.1	chr1	191192610	191192625	+	1	NA	Intergenic	Intergenic	-9284	NM_007498	11910	Mm.2706	NM_007498	ENSMUSG00000026628	Atf3	LRG-21	activating transcription factor 3	protein-coding
mm_160688.1	chr10	22273415	22273415	+	1	NA	promoter-TSS (NM_001177775)	promoter-TSS (NM_001177775)	-59	NM_001177775	667281	Mm.484254	NM_001177775	ENSMUSG00000075297	H60b	EG667281	histocompatibility 60b	protein-coding
mm_90348.1	chr10	127163390	127163417	+	1	NA	Intergenic	Intergenic	-1753	NR_045166	14421	Mm.386762	NM_008080	ENSMUSG00000006731	B4galnt1	4933429D13Rik|Gal-NAc-T|GalNAc-T|GalNAcT|Galgt1|Ggm-2|Ggm2	beta-1,4-N-acetyl-galactosaminyl transferase 1	protein-coding
mm_129098.1	chr15	75981945	75982000	-	1	NA	exon (NM_001163518, exon 1 of 1)	exon (NM_001163518, exon 1 of 1)	313	NM_001163518	223648	Mm.17610	NM_146059	ENSMUSG00000098176	Ccdc166	2410075B13Rik	coiled-coil domain containing 166	protein-coding
mm_158424.1	chrX	139714504	139714507	-	1	NA	intron (NM_001081499, intron 7 of 20)	intron (NM_001081499, intron 7 of 20)	29509	NM_001081499	245638	Mm.275869	NM_001081499	ENSMUSG00000042473	Tbc1d8b	4921505D17Rik|9030605E16Rik	TBC1 domain family, member 8B	protein-coding
mm_162789.1	chr10	75406934	75406936	+	1	NA	promoter-TSS (NM_133995)	promoter-TSS (NM_133995)	24	NM_133995	103149	Mm.441195	NM_133995	ENSMUSG00000033427	Upb1	AI195023	ureidopropionase, beta	protein-coding
mm_88457.1	chr10	77560231	77560242	+	1	NA	exon (NM_008404, exon 13 of 16)	exon (NM_008404, exon 13 of 16)	-21531	NM_145925	108705	Mm.28853	NM_145925	ENSMUSG00000009291	Pttg1ip	1810010L20Rik|AI314311|AU018448|C79540	pituitary tumor-transforming 1 interacting protein	protein-coding
mm_162895.1	chr10	112271591	112271601	+	1	NA	intron (NM_001025581, intron 1 of 4)	intron (NM_001025581, intron 1 of 4)	473	NM_001025581	268345	Mm.336242	NM_001025581	ENSMUSG00000035681	Kcnc2	AW047325|B230117I07|KShIIIA|Kv3.2	potassium voltage gated channel, Shaw-related subfamily, member 2	protein-coding
mm_110914.1	chr12	76222243	76222262	-	1	NA	intron (NM_001159532, intron 3 of 8)	B1_Mur2|SINE|Alu	24494	NM_019784	80384	Mm.78551	NM_019784	ENSMUSG00000021056	Tex21	4931406F04Rik|4931412D23Rik|4931421K24Rik|tsec-2	testis expressed gene 21	protein-coding
mm_77728.1	chr8	126852179	126852181	-	1	NA	Intergenic	Intergenic	93741	NM_024214	67952	Mm.6932	NM_024214	ENSMUSG00000093904	Tomm20	1810060K07Rik|BB284719|Gm19268|MAS20|MOM19|TOM20|mKIAA0016	translocase of outer mitochondrial membrane 20 homolog (yeast)	protein-coding
mm_4045.1	chr1	165774806	165774818	+	1	NA	3' UTR (NM_011804, exon 4 of 4)	3' UTR (NM_011804, exon 4 of 4)	11032	NM_011804	433375	Mm.294885	NM_011804	ENSMUSG00000040713	Creg1	AA755314|Creg	cellular repressor of E1A-stimulated genes 1	protein-coding
mm_71340.1	chr8	45627689	45627699	+	1	NA	promoter-TSS (NM_001310707)	promoter-TSS (NM_001310707)	-57	NM_001310707	234214	Mm.211096	NM_172752	ENSMUSG00000031626	Sorbs2	2010203O03Rik|9430041O17Rik|A530071H08|Argbp2|mKIAA0777|nArgBP2	sorbin and SH3 domain containing 2	protein-coding
mm_171422.1	chr4	133956636	133956643	+	1	NA	Intergenic	BGLII_A|LTR|ERVK	11352	NM_016957	15331	Mm.319660	NM_016957	ENSMUSG00000003038	Hmgn2	HMG-17|Hmg17	high mobility group nucleosomal binding domain 2	protein-coding
mm_142325.1	chr17	43477783	43477796	-	1	NA	intron (NM_008585, intron 12 of 13)	L1MA6|LINE|L1	24984	NM_008585	17287	Mm.5346	NM_008585	ENSMUSG00000023914	Mep1a	AI098089|AW107200|Mep-1|Mep-1a|Mep1	meprin 1 alpha	protein-coding
mm_23839.1	chr3	82358190	82358200	+	1	NA	5' UTR (NM_001081230, exon 1 of 14)	5' UTR (NM_001081230, exon 1 of 14)	123	NM_001081230	213582	Mm.271269	NM_001081230	ENSMUSG00000033900	Map9	5033421J10Rik|5330427D05Rik|ASAP|Mtap9	microtubule-associated protein 9	protein-coding
mm_113806.1	chr13	46502050	46502107	+	1	NA	5' UTR (NM_026056, exon 1 of 13)	5' UTR (NM_026056, exon 1 of 13)	175	NM_026056	67252	Mm.44529	NM_026056	ENSMUSG00000021373	Cap2	2810452G09Rik|AV045235	CAP, adenylate cyclase-associated protein, 2 (yeast)	protein-coding
mm_69838.1	chr7	141327558	141327607	-	1	NA	promoter-TSS (NM_001141950)	promoter-TSS (NM_001141950)	143	NM_016874	54006	Mm.28392	NM_016874	ENSMUSG00000058886	Deaf1	AU042387|C230009B13Rik|NUDR	deformed epidermal autoregulatory factor 1 (Drosophila)	protein-coding
mm_92587.1	chr10	80053360	80053414	-	1	NA	promoter-TSS (NM_008162)	promoter-TSS (NM_008162)	-101	NM_008162	625249	Mm.332810	NM_008162	ENSMUSG00000075706	Gpx4	GPx-4|GSHPx-4|PHGPx|mtPHGPx|snGPx	glutathione peroxidase 4	protein-coding
mm_168289.1	chr11	101624720	101624728	+	1	NA	Intergenic	RLTR27|LTR|ERVK	-3225	NM_025654	66599	Mm.41449	NM_025654	ENSMUSG00000010362	Rdm1	2410008M22Rik|AW212028|Rad52b	RAD52 motif 1	protein-coding
mm_136206.1	chr16	89833165	89833177	-	1	NA	exon (NM_001145886, exon 15 of 28)	exon (NM_001145886, exon 15 of 28)	-14819	NM_001145887	21844	Mm.310902	NM_009384	ENSMUSG00000002489	Tiam1	AI847750|D16Ium10|D16Ium10e	T cell lymphoma invasion and metastasis 1	protein-coding
mm_79914.1	chr9	65462796	65462840	+	1	NA	intron (NM_138584, intron 1 of 8)	intron (NM_138584, intron 1 of 8)	1881	NM_138584	27965	Mm.272475	NM_138584	ENSMUSG00000032388	Spg21	ACP33|BM-019|C78576|D9Wsu18e|GL010|MAST	spastic paraplegia 21 homolog (human)	protein-coding
mm_92075.1	chr10	62651195	62651234	-	1	NA	promoter-TSS (NM_053183)	promoter-TSS (NM_053183)	-16	NM_053183	94213	Mm.114116	NM_053183	ENSMUSG00000020076	Ddx50	4933429B04Rik|8430408E17Rik|GU2|RH-II	DEAD (Asp-Glu-Ala-Asp) box polypeptide 50	protein-coding
mm_137873.1	chr17	31442915	31442928	+	1	NA	intron (NM_008804, intron 4 of 18)	intron (NM_008804, intron 4 of 18)	56687	NM_001163748	18585	Mm.10812	NM_008804	ENSMUSG00000041119	Pde9a	PDE9A1	phosphodiesterase 9A	protein-coding
mm_164385.1	chr16	31744400	31744403	+	1	NA	intron (NR_045516, intron 5 of 24)	L1_Mur2|LINE|L1	-9949	NM_001252436	13383	Mm.382	NM_007862	ENSMUSG00000022770	Dlg1	B130052P05Rik|Dlgh1|E-dlg/SAP97|SAP-97|SAP97|mKIAA4187	discs, large homolog 1 (Drosophila)	protein-coding
mm_139938.1	chr17	71141373	71141385	+	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-42599	NM_022882	64898	Mm.227924	NM_022882	ENSMUSG00000024052	Lpin2	2610511G02Rik|AI481352|AW742896	lipin 2	protein-coding
mm_10685.1	chr2	22622014	22622024	+	1	NA	promoter-TSS (NM_008078)	promoter-TSS (NM_008078)	-308	NM_008078	14417	Mm.4784	NM_008078	ENSMUSG00000026787	Gad2	6330404F12Rik|GAD(65)|GAD65|Gad-2	glutamic acid decarboxylase 2	protein-coding
mm_151842.1	chr19	5729513	5729530	-	1	NA	TTS (NM_020491)	TTS (NM_020491)	145	NM_181452	17826	Mm.391142	NM_023166	ENSMUSG00000024939	Fam89b	1110021A21Rik|MMTV|Mtvr2	family with sequence similarity 89, member B	protein-coding
mm_138015.1	chr17	33909482	33909576	+	1	NA	promoter-TSS (NM_001199733)	promoter-TSS (NM_001199733)	-72	NM_001199733	13163	Mm.271809	NM_007829	ENSMUSG00000002307	Daxx	-	Fas death domain-associated protein	protein-coding
mm_124318.1	chr14	103346640	103346661	-	1	NA	5' UTR (NM_207215, exon 1 of 85)	5' UTR (NM_207215, exon 1 of 85)	150	NM_207215	105689	Mm.6478	NM_207215	ENSMUSG00000033004	Mycbp2	AU023734|AW107953|AW546647|C130061D10Rik|Pam|Phr1|R75243	MYC binding protein 2	protein-coding
mm_12359.1	chr2	69749814	69749824	+	1	NA	exon (NM_001081086, exon 14 of 14)	exon (NM_001081086, exon 14 of 14)	26731	NM_001081086	228005	Mm.11815	NM_001081086	ENSMUSG00000042133	Ppig	AU019516|AU022200|B230312B02Rik|CYP|SRCyp	peptidyl-prolyl isomerase G (cyclophilin G)	protein-coding
mm_97680.1	chr11	79993144	79993152	+	1	NA	promoter-TSS (NM_001163018)	promoter-TSS (NM_001163018)	42	NM_199196	52615	Mm.283410	NM_199196	ENSMUSG00000017548	Suz12	2610028O16Rik|AI195385|AU016842|AW536442|D11Ertd530e|mKIAA0160	suppressor of zeste 12 homolog (Drosophila)	protein-coding
mm_27479.1	chr3	53657125	53657190	-	1	NA	5' UTR (NM_172862, exon 1 of 24)	5' UTR (NM_172862, exon 1 of 24)	198	NM_172862	242022	Mm.38378	NM_172862	ENSMUSG00000037016	Frem2	6030440P17Rik|8430406N05Rik|Gm409|b2b1562Clo|my|ne|nv1	Fras1 related extracellular matrix protein 2	protein-coding
mm_118177.1	chr13	106962028	106962031	-	1	NA	3' UTR (NM_008442, exon 22 of 22)	3' UTR (NM_008442, exon 22 of 22)	14900	NM_025447	66254	Mm.9563	NM_025447	ENSMUSG00000021692	Dimt1	1500031M22Rik|AV111347|Dimt1l	DIM1 dimethyladenosine transferase 1-like (S. cerevisiae)	protein-coding
mm_119470.1	chr14	47296510	47296545	+	1	NA	Intergenic	RSINE1|SINE|B4	-1787	NM_178684	218975	Mm.212297	NM_178684	ENSMUSG00000021840	Mapk1ip1l	9130202B12|C130032J12Rik	mitogen-activated protein kinase 1 interacting protein 1-like	protein-coding
mm_101323.1	chr11	22860433	22860456	-	1	NA	promoter-TSS (NM_001169114)	promoter-TSS (NM_001169114)	-108	NM_001169114	53625	Mm.395495	NM_016888	ENSMUSG00000051650	B3gnt2	AA408337|AA409404|AW260308|B3Galt6|B3gnt1|BGnT-1|BGnT-2|BGnT1|BGnT2|Beta3gnt	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 2	protein-coding
mm_154308.1	chr19	61227194	61227218	-	1	NA	intron (NM_009970, intron 2 of 11)	CpG-7695	1212	NM_009970	12982	Mm.287228	NM_009970	ENSMUSG00000059326	Csf2ra	CD116|Csfgmra|GM-CSF-Ra|GM-CSFR	colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)	protein-coding
mm_106390.1	chr11	118570313	118570323	-	1	NA	intron (NM_001285436, intron 3 of 13)	CpG	93358	NM_172573	217364	Mm.473963	NM_172573	ENSMUSG00000033857	Engase	C130099A03|D230014K01Rik	endo-beta-N-acetylglucosaminidase	protein-coding
mm_96975.1	chr11	70652132	70652149	+	1	NA	TTS (NM_001316728)	TTS (NM_001316728)	2510	NM_011072	18643	Mm.2647	NM_011072	ENSMUSG00000018293	Pfn1	Pfn	profilin 1	protein-coding
mm_2416.1	chr1	94020460	94020485	+	1	NA	promoter-TSS (NM_173772)	promoter-TSS (NM_173772)	-21	NM_173772	241159	Mm.214565	NM_173772	ENSMUSG00000034000	Neu4	9330166I04	sialidase 4	protein-coding
mm_88102.1	chr10	68808161	68808186	+	1	NA	Intergenic	Intergenic	84427	NM_177794	327766	Mm.2479	NM_177794	ENSMUSG00000060044	Tmem26	3230401A06|AI195372	transmembrane protein 26	protein-coding
mm_109587.1	chr12	112619922	112619947	+	1	NA	promoter-TSS (NM_007421)	promoter-TSS (NM_007421)	-113	NM_007421	11565	Mm.3440	NM_007421	ENSMUSG00000011148	Adssl1	AI528595|Adss|Adss1	adenylosuccinate synthetase like 1	protein-coding
mm_103083.1	chr11	69901035	69901041	-	1	NA	promoter-TSS (NM_001291119)	promoter-TSS (NM_001291119)	-52	NM_027419	70419	Mm.272859	NM_027419	ENSMUSG00000018570	2810408A11Rik	1700019L01Rik|4930470J18Rik	RIKEN cDNA 2810408A11 gene	protein-coding
mm_135901.1	chr16	67016256	67016258	-	1	NA	intron (NM_178721, intron 1 of 9)	B1_Mus1|SINE|Alu	359139	NR_040512	75501	Mm.394300	NR_040512	ENSMUSG00000092599	1700010K23Rik	-	RIKEN cDNA 1700010K23 gene	ncRNA
mm_148443.1	chr19	3958804	3958832	+	1	NA	promoter-TSS (NM_028545)	promoter-TSS (NM_028545)	10	NM_028545	73458	Mm.482922	NM_028545	ENSMUSG00000037263	Aldh3b3	1700055N04Rik	aldehyde dehydrogenase 3 family, member B3	protein-coding
mm_91649.1	chr10	42478400	42478443	-	1	NA	5' UTR (NM_145743, exon 1 of 13)	5' UTR (NM_145743, exon 1 of 13)	144	NM_145743	215951	Mm.89646	NM_145743	ENSMUSG00000038302	Lace1	CG8520	lactation elevated 1	protein-coding
mm_168964.1	chr12	80441469	80441485	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-4876	NM_177267	320808	Mm.220310	NM_177267	ENSMUSG00000049106	Dcaf5	9430020B07Rik|AI325023|AI430035|AI848110|AW124614|BCRG2|BCRP2|Wdr22	DDB1 and CUL4 associated factor 5	protein-coding
mm_168089.1	chr10	128011739	128011749	+	1	NA	Intergenic	Intergenic	-3471	NM_008921	19075	Mm.2903	NM_008921	ENSMUSG00000025395	Prim1	AI324982	DNA primase, p49 subunit	protein-coding
mm_107749.1	chr12	59066874	59066882	+	1	NA	promoter-TSS (NM_008891)	promoter-TSS (NM_008891)	-41	NM_008891	18949	Mm.22347	NM_008891	ENSMUSG00000020994	Pnn	AU045199|D12Ertd512e	pinin	protein-coding
mm_14382.1	chr2	129630937	129630961	+	1	NA	3' UTR (NM_001291022, exon 5 of 5)	3' UTR (NM_001291022, exon 5 of 5)	37780	NM_001291022	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_78194.1	chr9	21351966	21351969	+	1	NA	intron (NM_152808, intron 20 of 21)	B1_Mur1|SINE|Alu	14139	NM_152808	68682	Mm.148425	NM_152808	ENSMUSG00000057193	Slc44a2	1110028E10Rik|CTL2	solute carrier family 44, member 2	protein-coding
mm_57227.1	chr6	123282580	123282582	-	1	NA	3' UTR (NM_019948, exon 6 of 6)	3' UTR (NM_019948, exon 6 of 6)	7290	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_27376.1	chr3	50443484	50443496	-	1	NA	5' UTR (NM_011990, exon 1 of 12)	5' UTR (NM_011990, exon 1 of 12)	123	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_136712.1	chr17	7928405	7928420	+	1	NA	intron (NM_145968, intron 4 of 9)	intron (NM_145968, intron 4 of 9)	2412	NM_145968	72536	Mm.119680	NM_145968	ENSMUSG00000033450	Tagap	2610315E15Rik	T cell activation Rho GTPase activating protein	protein-coding
mm_89230.1	chr10	87533367	87533391	+	1	NA	intron (NM_008777, intron 2 of 12)	intron (NM_008777, intron 2 of 12)	11584	NM_008777	18478	Mm.263539	NM_008777	ENSMUSG00000020051	Pah	AW106920	phenylalanine hydroxylase	protein-coding
mm_34911.1	chr4	155705089	155705183	+	1	NA	5' UTR (NM_026899, exon 1 of 5)	5' UTR (NM_026899, exon 1 of 5)	321	NM_026899	68991	Mm.294770	NM_026899	ENSMUSG00000029038	Ssu72	1190002E22Rik|1500011L16Rik|2610101M12Rik	Ssu72 RNA polymerase II CTD phosphatase homolog (yeast)	protein-coding
mm_31908.1	chr4	84884277	84884314	+	1	NA	promoter-TSS (NM_177385)	promoter-TSS (NM_177385)	-14	NM_175275	338349	Mm.440562	NM_175275	ENSMUSG00000038070	Cntln	AI448092|B430108F07Rik|D530005L17Rik	centlein, centrosomal protein	protein-coding
mm_107612.1	chr12	49385190	49385199	+	1	NA	exon (NM_008241, exon 2 of 2)	exon (NM_008241, exon 2 of 2)	2187	NM_008241	15228	Mm.4704	NM_008241	ENSMUSG00000020950	Foxg1	2900064B05Rik|BF-1|Bf1|Hfh9|Hfhbf1	forkhead box G1	protein-coding
mm_138536.1	chr17	35248967	35248991	+	1	NA	exon (NM_001252457, exon 6 of 11)	exon (NM_001252457, exon 6 of 11)	-2310	NR_106169	102465886		NR_106169	ENSMUSG00000098269	Mir8094	Gm27513|mmu-mir-8094	microRNA 8094	ncRNA
mm_128932.1	chr15	74636739	74636745	-	1	NA	promoter-TSS (NM_001177437)	promoter-TSS (NM_001177437)	-424	NM_001177437	69439	Mm.263708	NM_001177437	ENSMUSG00000022603	Mroh4	1700016M24Rik	maestro heat-like repeat family member 4	protein-coding
mm_47753.1	chr5	131245963	131245966	-	1	NA	intron (NM_145218, intron 1 of 10)	intron (NM_145218, intron 1 of 10)	61558	NM_145218	212996	Mm.299204	NM_145218	ENSMUSG00000034040	Wbscr17	AA388321|E330012B09Rik	Williams-Beuren syndrome chromosome region 17 homolog (human)	protein-coding
mm_37674.1	chr4	129121700	129121734	-	1	NA	promoter-TSS (NM_010471)	promoter-TSS (NM_010471)	30	NM_001130419	15444	Mm.384452	NM_010471	ENSMUSG00000028785	Hpca	-	hippocalcin	protein-coding
mm_27607.1	chr3	59195032	59195054	-	1	NA	promoter-TSS (NM_001302203)	promoter-TSS (NM_001302203)	61	NM_001302203	84111	Mm.60267	NM_032399	ENSMUSG00000051431	Gpr87	-	G protein-coupled receptor 87	protein-coding
mm_151746.1	chr19	5072075	5072090	-	1	NA	Intergenic	Intergenic	4004	NM_054042	70445	Mm.29597	NM_054042	ENSMUSG00000056481	Cd248	2610111G01Rik|AI842296|Cd164l1|Tem1	CD248 antigen, endosialin	protein-coding
mm_2188.1	chr1	89070365	89070371	+	1	NA	promoter-TSS (NM_133816)	promoter-TSS (NM_133816)	-94	NM_133816	98402	Mm.170983	NM_133816	ENSMUSG00000036206	Sh3bp4	AI594717|AW227605|BOG25	SH3-domain binding protein 4	protein-coding
mm_142274.1	chr17	39848032	39848059	-	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	5048	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_163485.1	chr12	109453529	109453541	+	1	NA	promoter-TSS (NM_010052)	promoter-TSS (NM_010052)	80	NM_010052	13386	Mm.157069	NM_010052	ENSMUSG00000040856	Dlk1	AW742678|DLK-1|DlkI|FA1|Ly107|Peg9|SCP1|ZOG|pG2|pref-1	delta-like 1 homolog (Drosophila)	protein-coding
mm_105790.1	chr11	109986895	109986906	-	1	NA	intron (NM_013851, intron 1 of 38)	B4|SINE|B4	8916	NM_013851	27404	Mm.341004	NM_013851	ENSMUSG00000020620	Abca8b	Abca8	ATP-binding cassette, sub-family A (ABC1), member 8b	protein-coding
mm_94368.1	chr11	5058022	5058045	+	1	NA	promoter-TSS (NM_145216)	promoter-TSS (NM_145216)	-95	NM_145216	75668	Mm.374836	NM_145216	ENSMUSG00000034209	Rasl10a	2210403B10Rik|AI852688	RAS-like, family 10, member A	protein-coding
mm_106559.1	chr11	120630127	120630160	-	1	NA	intron (NM_010756, intron 1 of 2)	intron (NM_010756, intron 1 of 2)	3404	NM_010756	17134	Mm.268010	NM_010756	ENSMUSG00000051510	Mafg	AA545192|C630022N07Rik	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein G (avian)	protein-coding
mm_156111.1	chrX	114474484	114474499	+	1	NA	exon (NM_001290478, exon 1 of 11)	exon (NM_001290478, exon 1 of 11)	158	NM_001290477	237010	Mm.132583	NM_172781	ENSMUSG00000025597	Klhl4	B130014A11|C130018J01Rik	kelch-like 4	protein-coding
mm_56775.1	chr6	116629008	116629014	-	1	NA	promoter-TSS (NM_026057)	promoter-TSS (NM_026057)	-12	NM_026057	67255	Mm.18810	NM_026057	ENSMUSG00000059878	Zfp422	2900028O21Rik|AU041373|KOX15|Krox-25-2|Krox-26|Krox25|Krox26|Znf22	zinc finger protein 422	protein-coding
mm_108749.1	chr12	88863047	88863054	+	1	NA	intron (NM_001198587, intron 3 of 19)	intron (NM_001198587, intron 3 of 19)	68546	NM_001198587	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding
mm_67914.1	chr7	99828288	99828308	-	1	NA	5' UTR (NM_016720, exon 1 of 3)	5' UTR (NM_016720, exon 1 of 3)	119	NM_016720	50877	Mm.103703	NM_016720	ENSMUSG00000035239	Neu3	-	neuraminidase 3	protein-coding
mm_87479.1	chr10	51493155	51493185	+	1	NA	exon (NM_013532, exon 5 of 9)	exon (NM_013532, exon 5 of 9)	2272	NM_013532	14728	Mm.34408	NM_013532	ENSMUSG00000062593	Lilrb4a	CD85K|Gp49b|HM18|ILT3|LIR-5|Lilrb4|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4A	protein-coding
mm_155100.1	chrX	48275872	48275881	+	1	NA	TTS (NR_045916)	TTS (NR_045916)	9550	NR_045916	100500713	Mm.396609	NR_045916	ENSMUSG00000097197	9530027J09Rik	-	RIKEN cDNA 9530027J09 gene	ncRNA
mm_170191.1	chr17	65661837	65661856	-	1	NA	intron (NM_133685, intron 6 of 6)	intron (NM_133685, intron 6 of 6)	-19642	NM_001146002	213272	Mm.255732	NM_153519	ENSMUSG00000050612	Txndc2	AU021712|Sptrx-1|Sptrx1|Trx4	thioredoxin domain containing 2 (spermatozoa)	protein-coding
mm_113859.1	chr13	47247622	47247627	+	1	NA	3' UTR (NM_146042, exon 8 of 8)	3' UTR (NM_146042, exon 8 of 8)	53621	NM_001170643	218215	Mm.287609	NM_146042	ENSMUSG00000038068	Rnf144b	BC025007|E130105P19Rik|Ibrdc2|Pir2	ring finger protein 144B	protein-coding
mm_15378.1	chr2	156475845	156475862	+	1	NA	5' UTR (NM_001006664, exon 1 of 22)	5' UTR (NM_001006664, exon 1 of 22)	319	NM_001006664	13821	Mm.20852	NM_013510	ENSMUSG00000027624	Epb41l1	4.1N|Epb4.1l1|NBL1|mKIAA0338	erythrocyte membrane protein band 4.1 like 1	protein-coding
mm_162677.1	chr10	9976644	9976665	+	1	NA	Intergenic	Intergenic	-75614	NM_001081344	78808	Mm.331751	NM_030191	ENSMUSG00000019790	Stxbp5	0710001E20Rik|4930565N16Rik|AW742610|LGL3|mKIAA1006	syntaxin binding protein 5 (tomosyn)	protein-coding
mm_94266.1	chr11	3530229	3530239	+	1	NA	exon (NM_001284429, exon 11 of 22)	exon (NM_001284429, exon 11 of 22)	9058	NM_013870	29856	Mm.188516	NM_013870	ENSMUSG00000020439	Smtn	smsmo	smoothelin	protein-coding
mm_156940.1	chrX	169927075	169927103	+	1	NA	exon (NM_001290504, exon 2 of 10)	exon (NM_001290504, exon 2 of 10)	47470	NM_001290505	17318	Mm.34441	NM_010797	ENSMUSG00000035299	Mid1	61B3-R|DXHXS1141|Fxy|Trim18	midline 1	protein-coding
mm_12895.1	chr2	84798842	84798861	+	1	NA	promoter-TSS (NM_019949)	promoter-TSS (NM_019949)	23	NM_019949	56791	Mm.38261	NM_019949	ENSMUSG00000027078	Ube2l6	2810489I21Rik|RIG-B|UBCH8|Ubce8|Ubcm8	ubiquitin-conjugating enzyme E2L 6	protein-coding
mm_141820.1	chr17	34615796	34615809	-	1	NA	TTS (NM_019441)	TTS (NM_019441)	169	NM_152922	81701	Mm.231343	NM_152922	ENSMUSG00000015467	Egfl8	Ng3	EGF-like domain 8	protein-coding
mm_8982.1	chr1	165678823	165678843	-	1	NA	intron (NM_178593, intron 1 of 6)	intron (NM_178593, intron 1 of 6)	29261	NM_178593	226594	Mm.265552	NM_178593	ENSMUSG00000040723	Rcsd1	A430105K13Rik|BC025872|CapZIP	RCSD domain containing 1	protein-coding
mm_58889.1	chr7	17090520	17090522	+	1	NA	5' UTR (NM_007676, exon 2 of 5)	5' UTR (NM_007676, exon 2 of 5)	16481	NM_007676	26436	Mm.143686	NM_007676	ENSMUSG00000066760	Psg16	Cea11|PSG|bCEA	pregnancy specific glycoprotein 16	protein-coding
mm_59196.1	chr7	24504493	24504500	+	1	NA	TTS (NM_153112)	TTS (NM_153112)	-2591	NM_001290461	232969	Mm.181332	NM_146183	ENSMUSG00000064264	Zfp428	2410005H09Rik|AV271806|AW047854|Znf428	zinc finger protein 428	protein-coding
mm_75219.1	chr8	39605919	39605925	-	1	NA	3' UTR (NM_031195, exon 9 of 9)	3' UTR (NM_031195, exon 9 of 9)	36756	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_8214.1	chr1	138142323	138142333	-	1	NA	intron (NM_001111316, intron 1 of 31)	intron (NM_001111316, intron 1 of 31)	32798	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_91319.1	chr10	24959584	24959590	-	1	NA	Intergenic	MLT1B|LTR|ERVL-MaLR	-32117	NM_007482	11846	Mm.154144	NM_007482	ENSMUSG00000019987	Arg1	AI|AI256583|Arg-1|PGIF	arginase, liver	protein-coding
mm_31755.1	chr4	63356153	63356168	+	1	NA	promoter-TSS (NM_013623)	promoter-TSS (NM_013623)	-2	NM_013623	18407	Mm.381399	NM_013623	ENSMUSG00000028359	Orm3	Agp-3|Orm-3	orosomucoid 3	protein-coding
mm_64900.1	chr7	15959819	15959832	-	1	NA	intron (NM_153068, intron 3 of 5)	B3A|SINE|B2	7710	NM_153068	259300	Mm.138215	NM_153068	ENSMUSG00000074364	Ehd2	BC027084|C130052H20Rik	EH-domain containing 2	protein-coding
mm_108351.1	chr12	80518558	80518575	+	1	NA	promoter-TSS (NM_001081421)	promoter-TSS (NM_001081421)	-424	NM_001081421	108760	Mm.308296	NM_001081421	ENSMUSG00000021130	Galnt16	5730405L21Rik|AI415388|Galntl1|mpp-GalNAc-T16	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 16	protein-coding
mm_151845.1	chr19	5731698	5731733	-	1	NA	promoter-TSS (NM_020491)	promoter-TSS (NM_020491)	17	NM_020491	56390	Mm.455818	NM_020491	ENSMUSG00000079478	Sssca1	1500016H19Rik|C184L	Sjogren's syndrome/scleroderma autoantigen 1 homolog (human)	protein-coding
mm_69845.1	chr7	141365175	141365190	-	1	NA	promoter-TSS (NR_033532)	promoter-TSS (NR_033532)	-72	NR_033532	320871	Mm.475463	NM_177280	ENSMUSG00000086844	B230206H07Rik	-	RIKEN cDNA B230206H07 gene	ncRNA
mm_150485.1	chr19	38953578	38953605	+	1	NA	exon (NM_008234, exon 13 of 22)	exon (NM_008234, exon 13 of 22)	22601	NM_008234	15201	Mm.57223	NM_008234	ENSMUSG00000025001	Hells	AI323785|E130115I21Rik|LSH|Lysh|PASG|YFK8	helicase, lymphoid specific	protein-coding
mm_123292.1	chr14	61556747	61556781	-	1	NA	5' UTR (NM_001310603, exon 1 of 4)	5' UTR (NM_001310603, exon 1 of 4)	122	NM_025697	66674	Mm.282706	NM_025697	ENSMUSG00000021930	Spryd7	6330409N04Rik|Clld6	SPRY domain containing 7	protein-coding
mm_123971.1	chr14	75131006	75131046	-	1	NA	promoter-TSS (NM_001247984)	promoter-TSS (NM_001247984)	-97	NM_001247984	18826	Mm.153911	NM_008879	ENSMUSG00000021998	Lcp1	AW536232|D14Ertd310e|LCP-1|Pls2|pp65	lymphocyte cytosolic protein 1	protein-coding
mm_152456.1	chr19	10869746	10869752	-	1	NA	promoter-TSS (NM_133804)	promoter-TSS (NM_133804)	30	NM_133804	98170	Mm.490254	NM_133804	ENSMUSG00000024736	Tmem132a	6720481D13Rik|Hspa5bp1|Orai1|R74613	transmembrane protein 132A	protein-coding
mm_161469.1	chr15	78901578	78901578	+	1	NA	intron (NR_133564, intron 3 of 18)	intron (NR_133564, intron 3 of 18)	1810	NM_009164	20401	Mm.4462	NM_009164	ENSMUSG00000022436	Sh3bp1	3BP-1	SH3-domain binding protein 1	protein-coding
mm_13574.1	chr2	112305983	112306009	+	1	NA	intron (NM_133648, intron 1 of 24)	intron (NM_133648, intron 1 of 24)	21308	NM_133648	107723	Mm.491155	NM_133648	ENSMUSG00000027130	Slc12a6	9530023I19Rik|KCC3|gaxp	solute carrier family 12, member 6	protein-coding
mm_89308.1	chr10	87916393	87916419	+	1	NA	intron (NM_001111274, intron 4 of 4)	MLT1B|LTR|ERVL-MaLR	-50265	NR_000040	22172	Mm.391420	NR_000040		Tyms-ps	-	thymidylate synthase, pseudogene	pseudo
mm_14505.1	chr2	132252786	132252819	+	1	NA	intron (NM_011045, intron 1 of 5)	CpG	378	NM_011045	18538	Mm.7141	NM_011045	ENSMUSG00000027342	Pcna	-	proliferating cell nuclear antigen	protein-coding
mm_139872.1	chr17	70662733	70662757	+	1	NA	exon (NM_177639, exon 5 of 12)	exon (NM_177639, exon 5 of 12)	100998	NM_001128181	224997	Mm.311840	NM_027712	ENSMUSG00000003279	Dlgap1	4933422O14Rik|9630002F18|AI845682|AI848168|BB075781|D17Bwg0511e|GKAP/SAPAP|GKPA/SAPAP|Gkap|Sapap1|mKIAA4162	discs, large (Drosophila) homolog-associated protein 1	protein-coding
mm_78703.1	chr9	41355214	41355218	+	1	NA	Intergenic	Intergenic	-21310	NR_040725	73144	Mm.38166	NM_001033153	ENSMUSG00000074415	3110039I08Rik	2610203C20Rik|AI848448|D230004N17Rik|D3Mgi9|Mir100hg	RIKEN cDNA 3110039I08 gene	ncRNA
mm_122494.1	chr14	46634459	46634469	-	1	NA	intron (NR_046460, intron 1 of 4)	intron (NR_046460, intron 1 of 4)	2959	NR_046460	74458	Mm.390708	NR_046460		4933425B07Rik	-	RIKEN cDNA 4933425B07 gene	ncRNA
mm_99697.1	chr11	106142436	106142452	+	1	NA	exon (NM_011947, exon 7 of 16)	exon (NM_011947, exon 7 of 16)	17698	NM_172397	67803	Mm.21687	NM_172397	ENSMUSG00000040699	Limd2	0610025L06Rik|AI413966	LIM domain containing 2	protein-coding
mm_111373.1	chr12	87254965	87254982	-	1	NA	intron (NM_001142580, intron 6 of 19)	B1_Mur4|SINE|Alu	9271	NM_134044	104799	Mm.208750	NM_134044	ENSMUSG00000021038	Vipas39	6720456H09Rik|9330175H22Rik|AI413782|SPE-39|Spe39|Vipar|hSPE-39	VPS33B interacting protein, apical-basolateral polarity regulator, spe-39 homolog	protein-coding
mm_88519.1	chr10	78054826	78054836	+	1	NA	promoter-TSS (NM_001284200)	promoter-TSS (NM_001284200)	-504	NM_001284198	54427	Mm.13433	NM_019448	ENSMUSG00000000730	Dnmt3l	D6Ertd14e|ecat7	DNA (cytosine-5-)-methyltransferase 3-like	protein-coding
mm_120470.1	chr14	65973337	65973368	+	1	NA	exon (NM_013492, exon 3 of 9)	exon (NM_013492, exon 3 of 9)	4869	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_45490.1	chr5	71657887	71657899	-	1	NA	5' UTR (NM_010251, exon 1 of 9)	5' UTR (NM_010251, exon 1 of 9)	415	NM_010251	14397	Mm.248731	NM_010251	ENSMUSG00000029211	Gabra4	Gabra-4	gamma-aminobutyric acid (GABA) A receptor, subunit alpha 4	protein-coding
mm_46862.1	chr5	113819302	113819325	-	1	NA	exon (NM_009151, exon 2 of 2)	exon (NM_009151, exon 2 of 2)	11188	NM_009151	20345	Mm.332590	NM_009151	ENSMUSG00000048163	Selplg	CD162|Psgl-1|Psgl1|Selp1|Selpl	selectin, platelet (p-selectin) ligand	protein-coding
mm_71172.1	chr8	40595550	40595579	+	1	NA	intron (NM_001040699, intron 4 of 13)	intron (NM_001040699, intron 4 of 13)	39228	NM_001040699	54384	Mm.294871	NM_019433	ENSMUSG00000039431	Mtmr7	-	myotubularin related protein 7	protein-coding
mm_148363.1	chr18	85698181	85698187	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-696768	NM_144946	246317	Mm.329578	NM_144946	ENSMUSG00000050321	Neto1	AI851453|Btcl1|C130005O10Rik	neuropilin (NRP) and tolloid (TLL)-like 1	protein-coding
mm_8391.1	chr1	151345225	151345278	-	1	NA	intron (NM_001039511, intron 1 of 7)	CpG	753	NM_001039511	117198	Mm.33764	NM_028582	ENSMUSG00000023150	Ivns1abp	1190004M08Rik|1700126I16Rik|AA960440|HSPC068|ND1|NS-1|NS1-BP|Nd1-L|Nd1-S|mKIAA0850	influenza virus NS1A binding protein	protein-coding
mm_12832.1	chr2	80635253	80635269	+	1	NA	Intergenic	Intergenic	-3551	NM_027091	69482	Mm.29200	NM_027091	ENSMUSG00000026999	Nup35	2310006I24Rik|35kDa|5330402E05Rik|MP44|NO44	nucleoporin 35	protein-coding
mm_68530.1	chr7	113263034	113263038	-	1	NA	intron (NM_001243048, intron 2 of 16)	LTRIS2|LTR|ERV1	55571	NM_007489	11865	Mm.33970	NM_007489	ENSMUSG00000055116	Arntl	Arnt3|BMAL1b|Bmal1|MOP3|bHLHe5|bmal1b'	aryl hydrocarbon receptor nuclear translocator-like	protein-coding
mm_158086.1	chrX	101268183	101268209	-	1	NA	promoter-TSS (NM_001308535)	promoter-TSS (NM_001308535)	59	NM_001308535	16186	Mm.2923	NM_013563	ENSMUSG00000031304	Il2rg	CD132|[g]c|gamma(c)|gc|p64	interleukin 2 receptor, gamma chain	protein-coding
mm_77536.1	chr8	123032751	123032751	-	1	NA	intron (NM_001081379, intron 1 of 12)	intron (NM_001081379, intron 1 of 12)	9533	NR_037865	77087	Mm.31567	NM_001081379	ENSMUSG00000035569	Ankrd11	2410104C19Rik|3010027A04Rik|6330578C09Rik|9530048I21Rik|AA930108|Gm176|Yod	ankyrin repeat domain 11	protein-coding
mm_124389.1	chr14	110754852	110754893	-	1	NA	5' UTR (NM_175499, exon 1 of 2)	5' UTR (NM_175499, exon 1 of 2)	277	NM_175499	239250	Mm.49728	NM_175499	ENSMUSG00000045871	Slitrk6	4832410J21Rik|Sltk6	SLIT and NTRK-like family, member 6	protein-coding
mm_156836.1	chrX	164373428	164373433	+	1	NA	promoter-TSS (NM_010216)	promoter-TSS (NM_010216)	-92	NM_001308489	14205	Mm.297978	NM_010216	ENSMUSG00000031380	Vegfd	AI325264|Figf|VEGF-D	vascular endothelial growth factor D	protein-coding
mm_124704.1	chr15	6540314	6540329	+	1	NA	Intergenic	Intergenic	-39526	NM_001278269	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_158544.1	chrX	145480617	145480625	-	1	NA	intron (NM_001290274, intron 1 of 8)	intron (NM_001290274, intron 1 of 8)	7018	NM_001290274	27494	Mm.100068	NM_153319	ENSMUSG00000041688	Amot	CAG-2|D0Kist1|Sii6	angiomotin	protein-coding
mm_67559.1	chr7	81789427	81789490	-	1	NA	promoter-TSS (NM_026077)	promoter-TSS (NM_026077)	-5	NM_026077	67290	Mm.248391	NM_026077	ENSMUSG00000025102	3110040N11Rik	AI851475	RIKEN cDNA 3110040N11 gene	protein-coding
mm_20919.1	chr2	150689015	150689020	-	1	NA	5' UTR (NM_054068, exon 1 of 5)	5' UTR (NM_054068, exon 1 of 5)	120	NM_054068	114889	Mm.207061	NM_054068	ENSMUSG00000033080	Vsx1	CHX10-like	visual system homeobox 1	protein-coding
mm_145496.1	chr18	60390540	60390566	+	1	NA	exon (NM_001146275, exon 3 of 3)	exon (NM_001146275, exon 3 of 3)	14524	NM_001146275	60440	Mm.261140	NM_021792	ENSMUSG00000054072	Iigp1	2900074L10Rik|AI046432|AW111922|Ifgga1|Iigp|Irga6	interferon inducible GTPase 1	protein-coding
mm_142735.1	chr17	48387997	48388017	-	1	NA	3' UTR (NM_010913, exon 9 of 9)	3' UTR (NM_010913, exon 9 of 9)	12573	NM_001347402	18044	Mm.4929	NM_010913	ENSMUSG00000023994	Nfya	AA407810|Cbf-b|SEZ-10|SEZ10	nuclear transcription factor-Y alpha	protein-coding
mm_40704.1	chr5	65861262	65861318	+	1	NA	Intergenic	Intergenic	-2279	NM_001081105	74734	Mm.20323	NM_001081105	ENSMUSG00000029204	Rhoh	5830400A04Rik|AU019774|Arhh	ras homolog family member H	protein-coding
mm_101406.1	chr11	26594655	26594717	-	1	NA	promoter-TSS (NM_027260)	promoter-TSS (NM_027260)	-766	NM_001252447	69922	Mm.285351	NM_027260	ENSMUSG00000064090	Vrk2	2810003O05Rik|AI447698	vaccinia related kinase 2	protein-coding
mm_166304.1	chr5	105696132	105696144	-	1	NA	Intergenic	Intergenic	-3831	NM_001122768	231549	Mm.23837	NM_178701	ENSMUSG00000046079	Lrrc8d	2810473G09Rik|4930525N13Rik|A930019F03|Lrrc5	leucine rich repeat containing 8D	protein-coding
mm_16988.1	chr2	18055982	18055990	-	1	NA	intron (NM_010804, intron 1 of 22)	intron (NM_010804, intron 1 of 22)	749	NM_010804	17354	Mm.209175	NM_010804	ENSMUSG00000026743	Mllt10	Af10|B130021D15Rik|D630001B22Rik|mKIAA4140	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 10	protein-coding
mm_160669.1	chr9	122263924	122263924	-	1	NA	intron (NM_001271873, intron 4 of 12)	intron (NM_001271873, intron 4 of 12)	10104	NR_106185	102465896		NR_106185	ENSMUSG00000098922	Mir8106	Gm27594|mmu-mir-8106	microRNA 8106	ncRNA
mm_113138.1	chr13	24636094	24636094	+	1	NA	intron (NM_178658, intron 1 of 13)	intron (NM_178658, intron 1 of 13)	-2554	NM_001080381	193385	Mm.217319	NM_029679	ENSMUSG00000036006	Fam65b	-	family with sequence similarity 65, member B	protein-coding
mm_135288.1	chr16	38458672	38458684	-	1	NA	promoter-TSS (NM_009855)	promoter-TSS (NM_009855)	-255	NM_009855	12519	Mm.89474	NM_009855	ENSMUSG00000075122	Cd80	B71|Cd28l|Ly-53|Ly53|MIC17|TSA1	CD80 antigen	protein-coding
mm_133234.1	chr16	77013811	77013817	+	1	NA	promoter-TSS (NM_013918)	promoter-TSS (NM_013918)	-255	NM_013918	30940	Mm.40986	NM_013918	ENSMUSG00000022867	Usp25	-	ubiquitin specific peptidase 25	protein-coding
mm_12446.1	chr2	71118076	71118096	+	1	NA	promoter-TSS (NM_028593)	promoter-TSS (NM_028593)	32	NM_028593	73649	Mm.45435	NM_028593	ENSMUSG00000027015	Cybrd1	2210407P13Rik|Dcytb	cytochrome b reductase 1	protein-coding
mm_30275.1	chr3	146812989	146813013	-	1	NA	promoter-TSS (NM_011100)	promoter-TSS (NM_011100)	-55	NM_011100	18749	Mm.16766	NM_011100	ENSMUSG00000005034	Prkacb	CbPKA|Pkacb	protein kinase, cAMP dependent, catalytic, beta	protein-coding
mm_64684.1	chr7	4514372	4514483	-	1	NA	intron (NM_011618, intron 1 of 13)	intron (NM_011618, intron 1 of 13)	1548	NM_001277903	21955	Mm.358643	NM_011618	ENSMUSG00000064179	Tnnt1	AW146156|Tnt|sTnT|ssTnT	troponin T1, skeletal, slow	protein-coding
mm_165650.1	chr3	83841287	83841332	-	1	NA	intron (NM_011905, intron 1 of 2)	intron (NM_011905, intron 1 of 2)	299	NM_011905	24088	Mm.87596	NM_011905	ENSMUSG00000027995	Tlr2	Ly105	toll-like receptor 2	protein-coding
mm_116211.1	chr13	32783918	32783929	-	1	NA	Intergenic	Intergenic	-2144	NM_001166030	238564	Mm.60041	NM_001166030	ENSMUSG00000044951	Mylk4	EG238564	myosin light chain kinase family, member 4	protein-coding
mm_71901.1	chr8	70043093	70043110	+	1	NA	promoter-TSS (NM_001167939)	promoter-TSS (NM_001167939)	288	NM_027481	70616	Mm.17665	NM_027481	ENSMUSG00000011306	Sugp1	5730496N02Rik|Sf4	SURP and G patch domain containing 1	protein-coding
mm_131514.1	chr16	17509159	17509173	+	1	NA	promoter-TSS (NM_001331226)	promoter-TSS (NM_001331226)	-46	NM_001331226	66863	Mm.161726	NM_025808	ENSMUSG00000022761	Lztr1	1200003E21Rik|AI591627|AW550890	leucine-zipper-like transcriptional regulator, 1	protein-coding
mm_45601.1	chr5	75043184	75043201	-	1	NA	intron (NM_028850, intron 1 of 5)	intron (NM_028850, intron 1 of 5)	1449	NM_028850	74277	Mm.239814	NM_028850	ENSMUSG00000029229	Chic2	1700081B18Rik|4930502K01Rik|BTL	cysteine-rich hydrophobic domain 2	protein-coding
mm_118186.1	chr13	107503440	107503453	-	1	NA	Intergenic	Intergenic	33624	NR_045084	105120	Mm.417700	NR_045083		AI197445	-	expressed sequence AI197445	ncRNA
mm_45222.1	chr5	53246901	53246911	-	1	NA	Intergenic	MTE2b|LTR|ERVL-MaLR	-20200	NM_001145433	66278	Mm.27900	NM_001145433	ENSMUSG00000061461	Smim20	1110067B18Rik|1810013D10Rik|N28078	small integral membrane protein 20	protein-coding
mm_11697.1	chr2	35978727	35978742	+	1	NA	intron (NM_029774, intron 1 of 9)	intron (NM_029774, intron 1 of 9)	890	NM_029774	74410	Mm.21591	NM_028921	ENSMUSG00000026885	Ttll11	4932702F08Rik|4933424A20Rik|AU043211|D2Ertd624e	tubulin tyrosine ligase-like family, member 11	protein-coding
mm_138847.1	chr17	40580441	40580446	+	1	NA	TTS (NM_001287195)	TTS (NM_001287195)	5732	NM_001287194	102577427		NM_001287194		Esp5	-	exocrine gland secreted peptide 5	protein-coding
mm_72972.1	chr8	92885866	92885879	+	1	NA	intron (NM_173014, intron 8 of 13)	B4A|SINE|B4	-15523	NM_027112	69543	Mm.440514	NM_027112	ENSMUSG00000078144	Capns2	2310005G05Rik|30K-2	calpain, small subunit 2	protein-coding
mm_109479.1	chr12	111428627	111428652	+	1	NA	intron (NM_001289487, intron 11 of 13)	intron (NM_001289487, intron 11 of 13)	11194	NM_001289488	74190	Mm.248640	NM_028807	ENSMUSG00000021280	Exoc3l4	1200009I06Rik|1600013K19Rik	exocyst complex component 3-like 4	protein-coding
mm_121582.1	chr14	123660292	123660311	+	1	NA	5' UTR (NM_145467, exon 1 of 11)	5' UTR (NM_145467, exon 1 of 11)	161	NM_145467	223272	Mm.383176	NM_145467	ENSMUSG00000032925	Itgbl1	B930011D01Rik	integrin, beta-like 1	protein-coding
mm_157640.1	chrX	57224121	57224153	-	1	NA	TTS (NM_011616)	TTS (NM_011616)	11994	NM_011616	21947	Mm.4861	NM_011616	ENSMUSG00000031132	Cd40lg	CD154|CD40-L|Cd40l|HIGM1|IGM|IMD3|Ly-62|Ly62|T-BAM|TRAP|Tnfsf5|Tnlg8b|gp39	CD40 ligand	protein-coding
mm_12324.1	chr2	69393057	69393090	+	1	NA	exon (NM_175512, exon 2 of 5)	exon (NM_175512, exon 2 of 5)	12611	NM_175512	241452	Mm.211655	NM_175512	ENSMUSG00000027068	Dhrs9	C730025I08Rik|Rdh15	dehydrogenase/reductase (SDR family) member 9	protein-coding
mm_17148.1	chr2	25196760	25196823	-	1	NA	promoter-TSS (NM_146115)	promoter-TSS (NM_146115)	22	NM_146115	227612	Mm.119747	NM_146115	ENSMUSG00000059555	Tor4a	A830007P12Rik	torsin family 4, member A	protein-coding
mm_150637.1	chr19	41495114	41495115	+	1	NA	Intergenic	Intergenic	-30138	NM_001326287	627352	Mm.395111	NM_001326287		Morf4l1b	EG627352|Gm6747	mortality factor 4 like 1B	protein-coding
mm_52430.1	chr6	113483514	113483524	+	1	NA	promoter-TSS (NM_133930)	promoter-TSS (NM_133930)	-50	NM_133930	171508	Mm.41593	NM_133930	ENSMUSG00000030284	Creld1	AI843811	cysteine-rich with EGF-like domains 1	protein-coding
mm_121135.1	chr14	101884128	101884136	+	1	NA	intron (NM_001347628, intron 4 of 26)	intron (NM_001347628, intron 4 of 26)	43509	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_62883.1	chr7	114768785	114768798	+	1	NA	intron (NM_173767, intron 1 of 12)	intron (NM_173767, intron 1 of 12)	23025	NM_173767	233752	Mm.83037	NM_173767	ENSMUSG00000048782	Insc	3830422K02Rik|C730020D23	inscuteable homolog (Drosophila)	protein-coding
mm_76278.1	chr8	84184063	84184086	-	1	NA	Intergenic	CpG	-5113	NR_029821	723819		NR_029821	ENSMUSG00000065483	Mir181c	Mirn181c|mir-181c	microRNA 181c	ncRNA
mm_33368.1	chr4	129513625	129513644	+	1	NA	promoter-TSS (NM_010807)	promoter-TSS (NM_010807)	53	NM_010807	17357	Mm.424974	NM_010807	ENSMUSG00000047945	Marcksl1	AL022768|AW215397|AW536807|D4Bc1|F52|MacMARCKS|Macs2|Macs3|Mlp|Mrp	MARCKS-like 1	protein-coding
mm_162933.1	chr10	126573070	126573073	-	1	NA	Intergenic	Intergenic	137320	NR_105841	102465224		NR_105841	ENSMUSG00000098756	Mir378d	Gm27650|mmu-mir-378d	microRNA 378d	ncRNA
mm_151310.1	chr19	55800906	55800909	+	1	NA	intron (NM_001331150, intron 4 of 14)	intron (NM_001331150, intron 4 of 14)	59097	NM_001142923	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_146640.1	chr18	10706689	10706694	-	1	NA	promoter-TSS (NM_134130)	promoter-TSS (NM_134130)	5	NM_134130	106861	Mm.273108	NM_134130	ENSMUSG00000002475	Abhd3	AA675331|LABH3	abhydrolase domain containing 3	protein-coding
mm_97710.1	chr11	80178756	80178761	+	1	NA	TTS (NM_172133)	TTS (NM_172133)	-5114	NM_028019	71956	Mm.22985	NM_028019	ENSMUSG00000020707	Rnf135	0610037N03Rik|2410006N06Rik	ring finger protein 135	protein-coding
mm_46542.1	chr5	105731154	105731168	-	1	NA	intron (NM_178701, intron 1 of 2)	RSINE1|SINE|B4	30351	NM_178701	231549	Mm.23837	NM_178701	ENSMUSG00000046079	Lrrc8d	2810473G09Rik|4930525N13Rik|A930019F03|Lrrc5	leucine rich repeat containing 8D	protein-coding
mm_171098.1	chr3	131951853	131951855	-	1	NA	Intergenic	Intergenic	-133438	NM_020265	56811	Mm.103593	NM_020265	ENSMUSG00000028031	Dkk2	-	dickkopf WNT signaling pathway inhibitor 2	protein-coding
mm_104042.1	chr11	86328518	86328526	-	1	NA	exon (NM_001080931, exon 7 of 30)	exon (NM_001080931, exon 7 of 30)	29003	NM_001080931	327987	Mm.341886	NM_001080931	ENSMUSG00000034297	Med13	1110067M05Rik|D030023K18|Thrap1|Trap240	mediator complex subunit 13	protein-coding
mm_27491.1	chr3	54807771	54807804	-	1	NA	promoter-TSS (NM_133231)	promoter-TSS (NM_133231)	4	NM_133231	170767	Mm.185735	NM_133231	ENSMUSG00000036615	Rfxap	5730495K23Rik	regulatory factor X-associated protein	protein-coding
mm_28245.1	chr3	88503062	88503067	-	1	NA	exon (NM_001111102, exon 1 of 10)	exon (NM_001111102, exon 1 of 10)	288	NM_001111102	16905	Mm.243014	NM_019390	ENSMUSG00000028063	Lmna	Dhe	lamin A	protein-coding
mm_150433.1	chr19	37536798	37536822	+	1	NA	Intergenic	Intergenic	-13608	NM_175353	107371	Mm.24865	NM_175353	ENSMUSG00000053799	Exoc6	4833405E05Rik|AW413330|C430002C19|Sec15|Sec15l1|hbd|msec15	exocyst complex component 6	protein-coding
mm_71891.1	chr8	69832746	69832754	+	1	NA	promoter-TSS (NM_001024954)	promoter-TSS (NM_001024954)	46	NM_001024954	80720	Mm.210823	NM_030555	ENSMUSG00000031860	Pbx4	2410015M21Rik|AI429113|AW045266	pre B cell leukemia homeobox 4	protein-coding
mm_1266.1	chr1	63200568	63200578	+	1	NA	5' UTR (NM_001285937, exon 1 of 6)	5' UTR (NM_001285937, exon 1 of 6)	215	NM_001285936	73884	Mm.86986	NM_028673	ENSMUSG00000027520	Zdbf2	4930431J08Rik|9330107J05Rik	zinc finger, DBF-type containing 2	protein-coding
mm_155722.1	chrX	96152544	96152628	+	1	NA	exon (NM_010833, exon 4 of 13)	exon (NM_010833, exon 4 of 13)	56541	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_50974.1	chr6	61180491	61180513	+	1	NA	5' UTR (NM_183310, exon 1 of 11)	5' UTR (NM_183310, exon 1 of 11)	177	NM_183310	232035	Mm.150324	NM_183310	ENSMUSG00000039578	Ccser1	6230405M12Rik|C130092O11Rik|Fam190a	coiled-coil serine rich 1	protein-coding
mm_57341.1	chr6	124747124	124747163	-	1	NA	exon (NM_007881, exon 5 of 10)	exon (NM_007881, exon 5 of 10)	-6064	NM_013535	14790	Mm.439877	NM_013535	ENSMUSG00000072772	Grcc10	2310033H05Rik|C10	gene rich cluster, C10 gene	protein-coding
mm_37416.1	chr4	122862672	122862721	-	1	NA	exon (NM_007598, exon 10 of 13)	exon (NM_007598, exon 10 of 13)	23361	NM_007598	12331	Mm.8687	NM_007598	ENSMUSG00000028656	Cap1	-	CAP, adenylate cyclase-associated protein 1 (yeast)	protein-coding
mm_2211.1	chr1	89737698	89737702	+	1	NA	intron (NM_001037136, intron 10 of 16)	Charlie1a|DNA|hAT-Charlie	-53808	NR_015540	74403	Mm.444291	NR_015540		4933400F21Rik	1700091C04Rik|4930565K10Rik	RIKEN cDNA 4933400F21 gene	ncRNA
mm_8926.1	chr1	163994768	163994808	-	1	NA	promoter-TSS (NM_201364)	promoter-TSS (NM_201364)	-7	NM_201364	381306	Mm.28152	NM_201364	ENSMUSG00000041406	BC055324	-	cDNA sequence BC055324	protein-coding
mm_123435.1	chr14	64441857	64441861	-	1	NA	promoter-TSS (NM_001253715)	promoter-TSS (NM_001253715)	-819	NM_001253712	110265	Mm.26713	NM_026322	ENSMUSG00000054733	Msra	2310045J23Rik|6530413P12Rik|MSR-A	methionine sulfoxide reductase A	protein-coding
mm_170752.1	chr2	156356693	156356706	-	1	NA	exon (NM_001316755, exon 10 of 10)	exon (NM_001316755, exon 10 of 10)	36280	NR_024329	347740	Mm.324242	NR_024329		2900097C17Rik	1810005K14Rik|4930563C06Rik	RIKEN cDNA 2900097C17 gene	ncRNA
mm_83247.1	chr9	42399941	42399960	-	1	NA	promoter-TSS (NM_001324548)	promoter-TSS (NM_001324548)	-21	NM_001324548	21683	Mm.42209	NM_009347	ENSMUSG00000037705	Tecta	Tctna	tectorin alpha	protein-coding
mm_89498.1	chr10	93897165	93897175	+	1	NA	Intergenic	Intergenic	-5968	NM_019648	56307	Mm.289329	NM_019648	ENSMUSG00000036112	Metap2	4930584B20Rik|A930035J23Rik|AI047573|AL024412|AU014659|Amp2|Mnpep|p67|p67eIF2	methionine aminopeptidase 2	protein-coding
mm_32553.1	chr4	109407122	109407165	+	1	NA	promoter-TSS (NM_153392)	promoter-TSS (NM_153392)	43	NM_153392	230603	Mm.33091	NM_153392	ENSMUSG00000028555	Ttc39a	4922503N01Rik	tetratricopeptide repeat domain 39A	protein-coding
mm_160486.1	chr8	125734397	125734397	+	1	NA	intron (NM_001310688, intron 1 of 3)	CpG	194	NM_001310688	66566	Mm.25296	NM_025636	ENSMUSG00000031851	Ntpcr	2310079N02Rik|AI449709	nucleoside-triphosphatase, cancer-related	protein-coding
mm_56460.1	chr6	98504853	98504858	-	1	NA	Intergenic	(A)n|Simple_repeat|Simple_repeat	-162101	NM_001128092	330390	Mm.484161	NM_001128092	ENSMUSG00000090667	Gm765	-	predicted gene 765	protein-coding
mm_39600.1	chr5	23676115	23676129	+	1	NA	Intergenic	CpG	36545	NR_038090	433855	Mm.205125	NR_015554	ENSMUSG00000105987	AI506816	-	expressed sequence AI506816	ncRNA
mm_60616.1	chr7	44595318	44595329	+	1	NA	exon (NM_001290682, exon 2 of 5)	exon (NM_001290682, exon 2 of 5)	4437	NM_001290682	16504	Mm.40312	NM_008422	ENSMUSG00000062785	Kcnc3	KShIIID|Kcr2-3|Kv3.3	potassium voltage gated channel, Shaw-related subfamily, member 3	protein-coding
mm_117317.1	chr13	67637741	67637749	-	1	NA	promoter-TSS (NM_183146)	promoter-TSS (NM_183146)	8	NM_183146	212281	Mm.342918	NM_183146	ENSMUSG00000021510	Zfp729a	A530054K11Rik|Rslcan3	zinc finger protein 729a	protein-coding
mm_117493.1	chr13	78198543	78198618	-	1	NA	5' UTR (NM_010151, exon 1 of 3)	5' UTR (NM_010151, exon 1 of 3)	293	NM_010151	13865	Mm.439653	NM_010151	ENSMUSG00000069171	Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR-3|EAR3|Erbal3|SVP44|Tcfcoup1	nuclear receptor subfamily 2, group F, member 1	protein-coding
mm_119722.1	chr14	53960913	53960925	+	1	NA	Intergenic	Intergenic	293010	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_70865.1	chr8	24725969	24725999	+	1	NA	promoter-TSS (NM_001324489)	promoter-TSS (NM_001324489)	-132	NM_001324489	11497	Mm.5168	NM_009619	ENSMUSG00000031553	Adam3	Cyrn1|Taz83|tMDC	a disintegrin and metallopeptidase domain 3 (cyritestin)	protein-coding
mm_137173.1	chr17	23815273	23815284	+	1	NA	exon (NM_175229, exon 10 of 14)	exon (NM_175229, exon 10 of 14)	12091	NM_175229	75956	Mm.5222	NM_175229	ENSMUSG00000039218	Srrm2	5033413A03Rik|AA410130|SRm300|mKIAA0324	serine/arginine repetitive matrix 2	protein-coding
mm_44014.1	chr5	147270111	147270139	+	1	NA	promoter-TSS (NM_008814)	promoter-TSS (NM_008814)	-6	NM_008814	18609	Mm.389714	NM_008814	ENSMUSG00000029644	Pdx1	IDX-1|IPF-1|Ipf1|Mody4|STF-1|pdx-1	pancreatic and duodenal homeobox 1	protein-coding
mm_43821.1	chr5	142960959	142960990	+	1	NA	exon (NM_007984, exon 1 of 5)	exon (NM_007984, exon 1 of 5)	619	NM_007984	14086	Mm.289707	NM_007984	ENSMUSG00000029581	Fscn1	AI663989|Fan1|fascin-1	fascin actin-bundling protein 1	protein-coding
mm_11754.1	chr2	38481372	38481386	+	1	NA	Intergenic	Intergenic	-30318	NM_021606	59126	Mm.143818	NM_021606	ENSMUSG00000026749	Nek6	1300007C09Rik	NIMA (never in mitosis gene a)-related expressed kinase 6	protein-coding
mm_103286.1	chr11	72266597	72266611	-	1	NA	promoter-TSS (NM_001004148)	promoter-TSS (NM_001004148)	0	NM_001004148	237831	Mm.340778	NM_001004148	ENSMUSG00000020805	Slc13a5	Indy|NaC2/NaCT|Nact|mINDY	solute carrier family 13 (sodium-dependent citrate transporter), member 5	protein-coding
mm_96289.1	chr11	63129028	63129036	+	1	NA	promoter-TSS (NM_001302258)	promoter-TSS (NM_001302258)	50	NM_001302261	18858	Mm.1237	NM_008885	ENSMUSG00000018217	Pmp22	22kDa|Gas-3|HNPP|Tr|trembler	peripheral myelin protein 22	protein-coding
mm_57909.1	chr6	132572183	132572184	-	1	NA	exon (NM_011174, exon 2 of 2)	exon (NM_011174, exon 2 of 2)	2341	NM_011174	19131	Mm.425348	NM_011174	ENSMUSG00000059934	Prh1	MP2|Prp	proline rich protein HaeIII subfamily 1	protein-coding
mm_109969.1	chr12	12936945	12936948	-	1	NA	3' UTR (NM_008709, exon 3 of 3)	3' UTR (NM_008709, exon 3 of 3)	4890	NM_008709	18109	Mm.16469	NM_008709	ENSMUSG00000037169	Mycn	N-myc|Nmyc|Nmyc-1|Nmyc1|bHLHe37|c-nmyc	v-myc avian myelocytomatosis viral related oncogene, neuroblastoma derived	protein-coding
mm_76184.1	chr8	82402452	82402469	-	1	NA	5' UTR (NM_001254747, exon 1 of 8)	5' UTR (NM_001254747, exon 1 of 8)	126	NM_001254747	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_156077.1	chrX	109196751	109196763	+	1	NA	promoter-TSS (NM_001037917)	promoter-TSS (NM_001037917)	1	NM_001037917	622976	Mm.482747	NM_001037917	ENSMUSG00000048621	Gm6377	EG622976	predicted gene 6377	protein-coding
mm_112668.1	chr13	16027400	16027414	+	1	NA	3' UTR (NM_008380, exon 5 of 5)	3' UTR (NM_008380, exon 5 of 5)	15556	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_67683.1	chr7	89338686	89338705	-	1	NA	promoter-TSS (NM_028343)	promoter-TSS (NM_028343)	92	NM_028343	72759	Mm.208477	NM_028343	ENSMUSG00000039428	Tmem135	2810439K08Rik|AW319712|PMP52	transmembrane protein 135	protein-coding
mm_96983.1	chr11	70656696	70656721	+	1	NA	promoter-TSS (NM_007933)	promoter-TSS (NM_007933)	-468	NM_001136062	13808	Mm.251322	NM_007933	ENSMUSG00000060600	Eno3	Eno-3|MSE	enolase 3, beta muscle	protein-coding
mm_167236.1	chr8	15031609	15031615	+	1	NA	3' UTR (NM_029116, exon 2 of 2)	3' UTR (NM_029116, exon 2 of 2)	14466	NR_037972	434285	Mm.334425	NM_001007591	ENSMUSG00000049008	BB014433	-	expressed sequence BB014433	ncRNA
mm_31210.1	chr4	43957462	43957496	+	1	NA	promoter-TSS (NM_027450)	promoter-TSS (NM_027450)	-223	NM_027450	384009	Mm.22213	NM_027450	ENSMUSG00000028480	Glipr2	5730414A08Rik|C77180|GAPR-1	GLI pathogenesis-related 2	protein-coding
mm_141184.1	chr17	26939245	26939258	-	1	NA	intron (NM_026948, intron 1 of 5)	intron (NM_026948, intron 1 of 5)	207	NR_104458	67675	Mm.439919	NM_026307	ENSMUSG00000024194	Cuta	0610039D01Rik|1810022E02Rik|1810060C03Rik|2700094G22Rik|AI326454	cutA divalent cation tolerance homolog	protein-coding
mm_78512.1	chr9	32910923	32910933	+	1	NA	intron (NR_131058, intron 3 of 3)	intron (NR_131058, intron 3 of 3)	18038	NR_131058	330917	Mm.488283	NR_131058		Gm27162	A430016B06	predicted gene 27162	ncRNA
mm_133386.1	chr16	84773891	84773904	+	1	NA	promoter-TSS (NM_023844)	promoter-TSS (NM_023844)	-226	NM_023844	67374	Mm.41758	NM_023844	ENSMUSG00000053062	Jam2	1110002N23Rik|2410030G21Rik|2410167M24Rik|JAM-2|JAM-B|Jcam2|VE-JAM	junction adhesion molecule 2	protein-coding
mm_17926.1	chr2	35461366	35461413	-	1	NA	promoter-TSS (NM_001145821)	promoter-TSS (NM_001145821)	60	NM_001308299	14594	Mm.281124	NM_010283	ENSMUSG00000035778	Ggta1	AW108479|GALT|Gal|Ggta|Ggta-1|alpha Gal|alpha3GalT	glycoprotein galactosyltransferase alpha 1, 3	protein-coding
mm_90760.1	chr10	5550637	5550706	-	1	NA	promoter-TSS (NM_153399)	promoter-TSS (NM_153399)	21	NM_153399	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_128955.1	chr15	74784930	74784937	-	1	NA	Intergenic	Intergenic	-6074	NR_027837	78725	Mm.171357	NM_172433	ENSMUSG00000101026	D730001G18Rik	Ly6g6g	RIKEN cDNA D730001G18 gene	ncRNA
mm_115619.1	chr13	12075774	12075788	-	1	NA	intron (NM_023868, intron 1 of 104)	B1_Mus1|SINE|Alu	31164	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding
mm_170697.1	chr2	134730963	134730973	-	1	NA	Intergenic	Intergenic	-55196	NM_019677	18795	Mm.330607	NM_019677	ENSMUSG00000051177	Plcb1	3110043I21Rik|AI132408|Plcb|mKIAA0581	phospholipase C, beta 1	protein-coding
mm_82582.1	chr9	21166856	21166895	-	1	NA	intron (NM_183408, intron 1 of 14)	intron (NM_183408, intron 1 of 14)	1161	NM_183408	18577	Mm.191749	NM_019798	ENSMUSG00000032177	Pde4a	D9Ertd60e|Dpde2	phosphodiesterase 4A, cAMP specific	protein-coding
mm_24617.1	chr3	93506583	93506601	+	1	NA	Intergenic	Intergenic	-13904	NM_016740	20195	Mm.280038	NM_016740	ENSMUSG00000027907	S100a11	EMAPI|Emap1|S100a14|S100c|cal	S100 calcium binding protein A11	protein-coding
mm_171715.1	chr4	81148933	81148933	-	1	NA	Intergenic	L1Md_T|LINE|L1	238247	NM_026821	52829	Mm.273986	NM_026821	ENSMUSG00000048706	Lurap1l	1110029A09Rik|AV077978|AV175137|D4Bwg0951e|WI-13707|bM350F23.1	leucine rich adaptor protein 1-like	protein-coding
mm_129007.1	chr15	74881695	74881710	-	1	NA	promoter-TSS (NM_025929)	promoter-TSS (NM_025929)	2	NM_025929	67038	Mm.154566	NM_025929	ENSMUSG00000063522	2010109I03Rik	Ly6m	RIKEN cDNA 2010109I03 gene	protein-coding
mm_100773.1	chr11	4789793	4789813	-	1	NA	exon (NM_001252253, exon 12 of 15)	exon (NM_001252253, exon 12 of 15)	-43025	NM_138948	192650	Mm.207056	NM_138948	ENSMUSG00000009075	Cabp7	-	calcium binding protein 7	protein-coding
mm_80737.1	chr9	94669975	94669985	+	1	NA	promoter-TSS (NM_177909)	promoter-TSS (NM_177909)	88	NM_177909	331004	Mm.326125	NM_177909	ENSMUSG00000031129	Slc9a9	5730527A11Rik|9930105B05|AI854429|Nhe9	solute carrier family 9 (sodium/hydrogen exchanger), member 9	protein-coding
mm_40152.1	chr5	35392839	35392842	+	1	NA	TTS (NM_010445)	TTS (NM_010445)	3723	NM_010445	15371	Mm.358606	NM_010445	ENSMUSG00000067438	Hmx1	Nkx5-3	H6 homeobox 1	protein-coding
mm_152105.1	chr19	6925368	6925381	-	1	NA	promoter-TSS (NM_001039494)	promoter-TSS (NM_001039494)	6	NM_001039494	67077	Mm.251306	NM_001039494	ENSMUSG00000050623	Tex40	1700019N12Rik|A430107B04Rik|MLZ-622	testis expressed 40	protein-coding
mm_117917.1	chr13	99433015	99433027	-	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-20195	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_168216.1	chr10	7617321	7617324	-	1	NA	intron (NM_172784, intron 6 of 6)	intron (NM_172784, intron 6 of 6)	27522	NM_172784	237253	Mm.206759	NM_172784	ENSMUSG00000019796	Lrp11	1700034J19Rik|6330533B21|9830160H19Rik	low density lipoprotein receptor-related protein 11	protein-coding
mm_133038.1	chr16	57353297	57353308	+	1	NA	promoter-TSS (NM_001040397)	promoter-TSS (NM_001040397)	25	NM_001040397	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding
mm_31155.1	chr4	43442237	43442315	+	1	NA	promoter-TSS (NM_011571)	promoter-TSS (NM_011571)	-1	NM_011571	21754	Mm.485441	NM_011571	ENSMUSG00000028458	Tesk1	AI326901	testis specific protein kinase 1	protein-coding
mm_86343.1	chr9	123307939	123307957	-	1	NA	Intergenic	Intergenic	-47159	NM_001002267	72309	Mm.8569	NM_001002267	ENSMUSG00000054871	Tmem158	2310037P21Rik|Ris1	transmembrane protein 158	protein-coding
mm_43703.1	chr5	139253490	139253519	+	1	NA	promoter-TSS (NM_001163316)	promoter-TSS (NM_001163316)	7	NM_001163316	67604	Mm.270137	NM_026269	ENSMUSG00000025858	Get4	1110007L15Rik|AW412535|Cee	golgi to ER traffic protein 4	protein-coding
mm_133318.1	chr16	77658429	77658444	+	1	NA	Intergenic	Intergenic	12163	NR_029540	723952		NR_029540	ENSMUSG00000065472	Mir125b-2	Mirn125b-2|mir-125b-2	microRNA 125b-2	ncRNA
mm_28017.1	chr3	83044913	83044966	-	1	NA	exon (NM_181849, exon 4 of 8)	exon (NM_181849, exon 4 of 8)	4924	NM_181849	110135	Mm.30063	NM_181849	ENSMUSG00000033831	Fgb	2510049G14Rik	fibrinogen beta chain	protein-coding
mm_128370.1	chr15	42586291	42586295	-	1	NA	intron (NM_009640, intron 1 of 8)	intron (NM_009640, intron 1 of 8)	90684	NM_001286062	11600	Mm.309336	NM_009640	ENSMUSG00000022309	Angpt1	1110046O21Rik|Ang-1|Ang1	angiopoietin 1	protein-coding
mm_144795.1	chr18	35999336	35999358	+	1	NA	intron (NR_110349, intron 7 of 14)	L1MB7|LINE|L1	34517	NR_110349	74002	Mm.196944	NM_028707	ENSMUSG00000024347	Psd2	6330404E20Rik|AW125584|EFA6C	pleckstrin and Sec7 domain containing 2	protein-coding
mm_92460.1	chr10	77924127	77924135	-	1	NA	exon (NM_138301, exon 23 of 34)	exon (NM_138301, exon 23 of 34)	-21595	NM_145152	237387	Mm.133301	NM_145152	ENSMUSG00000051652	Lrrc3	1300011L04Rik|C21orf102	leucine rich repeat containing 3	protein-coding
mm_49296.1	chr6	17694171	17694179	+	1	NA	5' UTR (NM_001289625, exon 1 of 16)	5' UTR (NM_001289625, exon 1 of 16)	181	NM_001289625	64213	Mm.12051	NM_022332	ENSMUSG00000029534	St7	9430001H04Rik|Fam4a2|HELG|RAY1|SEN4|TSG7	suppression of tumorigenicity 7	protein-coding
mm_58601.1	chr7	5051486	5051496	+	1	NA	promoter-TSS (NM_026900)	promoter-TSS (NM_026900)	-41	NM_026900	68992	Mm.41484	NM_026900	ENSMUSG00000055633	Zfp580	1500015O20Rik|AI838225|Znf580	zinc finger protein 580	protein-coding
mm_97380.1	chr11	77715195	77715198	+	1	NA	3' UTR (NM_001024205, exon 4 of 4)	3' UTR (NM_001024205, exon 4 of 4)	10097	NM_001313933	12957	Mm.22830	NM_009965	ENSMUSG00000000724	Cryba1	BA3/A1|Cryb	crystallin, beta A1	protein-coding
mm_73464.1	chr8	106660945	106661001	+	1	NA	exon (NM_009864, exon 10 of 16)	exon (NM_009864, exon 10 of 16)	-22095	NM_173037	272538	Mm.87151	NM_173037	ENSMUSG00000041949	Tango6	AW413431|E330010G16|Tmco7	transport and golgi organization 6	protein-coding
mm_151747.1	chr19	5072110	5072129	-	1	NA	Intergenic	Intergenic	4041	NM_054042	70445	Mm.29597	NM_054042	ENSMUSG00000056481	Cd248	2610111G01Rik|AI842296|Cd164l1|Tem1	CD248 antigen, endosialin	protein-coding
mm_82061.1	chr9	122739279	122739284	+	1	NA	Intergenic	RMER17B2|LTR|ERVK	-8065	NM_001199736	671232	Mm.296421	NM_001199736	ENSMUSG00000094985	Topaz1	Gm9524	testis and ovary specific PAZ domain containing 1	protein-coding
mm_113998.1	chr13	52583439	52583449	+	1	NA	promoter-TSS (NM_001198977)	promoter-TSS (NM_001198977)	7	NM_001198977	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_35305.1	chr4	24850873	24850916	-	1	NA	5' UTR (NM_001163020, exon 1 of 11)	5' UTR (NM_001163020, exon 1 of 11)	192	NM_001163020	212390	Mm.412074	NM_001033531	ENSMUSG00000040387	Klhl32	6430524H05Rik|D4Ertd389e|Gm1356|mKIAA1900	kelch-like 32	protein-coding
mm_36671.1	chr4	95967006	95967017	-	1	NA	promoter-TSS (NR_045777)	promoter-TSS (NR_045777)	24	NR_045777	319247	Mm.473527	NM_175680	ENSMUSG00000044125	9530080O11Rik	-	RIKEN cDNA 9530080O11 gene	ncRNA
mm_120528.1	chr14	67015944	67015948	+	1	NA	3' UTR (NM_028032, exon 10 of 10)	3' UTR (NM_028032, exon 10 of 10)	-7069	NM_009761	12177	Mm.29820	NM_009761	ENSMUSG00000022051	Bnip3l	C86132|D14Ertd719e|Nip3L|Nix	BCL2/adenovirus E1B interacting protein 3-like	protein-coding
mm_73613.1	chr8	110090146	110090155	+	1	NA	exon (NM_175480, exon 5 of 5)	exon (NM_175480, exon 5 of 5)	10416	NM_175480	234725	Mm.87487	NM_175480	ENSMUSG00000044676	Zfp612	B230354B21Rik	zinc finger protein 612	protein-coding
mm_50837.1	chr6	54816784	54816819	+	1	NA	promoter-TSS (NM_199143)	promoter-TSS (NM_199143)	-115	NM_199143	387524	Mm.286149	NM_199143	ENSMUSG00000058446	Znrf2	1190002C14Rik|AU044205|D6Ertd365e	zinc and ring finger 2	protein-coding
mm_81567.1	chr9	110419842	110419862	+	1	NA	promoter-TSS (NM_008694)	promoter-TSS (NM_008694)	44	NM_008694	18054	Mm.236225	NM_008694	ENSMUSG00000032484	Ngp	bectenecin	neutrophilic granule protein	protein-coding
mm_90234.1	chr10	121377187	121377215	+	1	NA	intron (NM_029364, intron 5 of 13)	intron (NM_029364, intron 5 of 13)	12111	NM_029364	75612	Mm.207683	NM_029364	ENSMUSG00000034707	Gns	2610016K11Rik|AU042285|C87209|G6S|N28088	glucosamine (N-acetyl)-6-sulfatase	protein-coding
mm_143967.1	chr17	87265867	87265921	-	1	NA	promoter-TSS (NM_176808)	promoter-TSS (NM_176808)	53	NM_176808	193813	Mm.30251	NM_139295	ENSMUSG00000024150	Mcfd2	1810021C21Rik|F5f8d|Lman1ip|Sdnsf	multiple coagulation factor deficiency 2	protein-coding
mm_125639.1	chr15	62086290	62086293	+	1	NA	intron (NR_132746, intron 1 of 6)	intron (NR_132746, intron 1 of 6)	47034	NR_132746	19296	Mm.4608	NM_011222	ENSMUSG00000097039	Pvt1	Ayu21-84Imeg|Gt(pU21)84Imeg|Mis-1|Mlvi-1|Pvt-1	plasmacytoma variant translocation 1	ncRNA
mm_58541.1	chr7	4520447	4520482	+	1	NA	exon (NM_009406, exon 6 of 8)	exon (NM_009406, exon 6 of 8)	1979	NM_009406	21954	Mm.27674	NM_009406	ENSMUSG00000035458	Tnni3	Tn1|cTnI	troponin I, cardiac 3	protein-coding
mm_96759.1	chr11	69914153	69914163	+	1	NA	promoter-TSS (NM_019726)	promoter-TSS (NM_019726)	-34	NM_019726	56310	Mm.477738	NM_019726	ENSMUSG00000023170	Gps2	AI505953	G protein pathway suppressor 2	protein-coding
mm_111037.1	chr12	79191876	79191889	-	1	NA	promoter-TSS (NM_021557)	promoter-TSS (NM_021557)	-63	NM_021557	17252	Mm.291799	NM_021557	ENSMUSG00000066441	Rdh11	2610319N22Rik|AI428145|AU045252|Arsdr1|C85936|CGI-82|HCBP12|M42C60|Mdt1|Psdr1|SCALD|UBE-1c1|Ube-1c	retinol dehydrogenase 11	protein-coding
mm_60607.1	chr7	44573308	44573311	+	1	NA	intron (NM_008437, intron 1 of 8)	RLTR28|LTR|ERVL	864	NM_008437	16541	Mm.383181	NM_008437	ENSMUSG00000002204	Napsa	KAP|Kdap|NAP1|SNAPA|pronapsin	napsin A aspartic peptidase	protein-coding
mm_165555.1	chr3	14767481	14767485	-	1	NA	exon (NM_001083957, exon 6 of 7)	exon (NM_001083957, exon 6 of 7)	10977	NM_001083957	12346	Mm.273195	NM_009799	ENSMUSG00000027556	Car1	AW555628|Ca1|Car-1	carbonic anhydrase 1	protein-coding
mm_16100.1	chr2	169599796	169599796	+	1	NA	Intergenic	Intergenic	-33850	NM_080455	228911	Mm.315789	NM_080455	ENSMUSG00000047907	Tshz2	2900073F20Rik|B830045G17|Mtsh2|Sdccag33l|Tsh2|Zfp218|mKIAA4248|teashirt2	teashirt zinc finger family member 2	protein-coding
mm_37475.1	chr4	123565462	123565474	-	1	NA	intron (NM_001199136, intron 1 of 97)	intron (NM_001199136, intron 1 of 97)	-50952	NR_105824	102465214		NR_105824	ENSMUSG00000099005	Mir6398	Gm27657|mmu-mir-6398	microRNA 6398	ncRNA
mm_108310.1	chr12	79532573	79532577	+	1	NA	intron (NM_009014, intron 7 of 10)	intron (NM_009014, intron 7 of 10)	235224	NM_001252562	19363	Mm.341756	NM_009014	ENSMUSG00000059060	Rad51b	AI553500|R51H2|Rad51l1|mREC2	RAD51 paralog B	protein-coding
mm_119135.1	chr14	31166539	31166553	+	1	NA	intron (NM_138672, intron 1 of 68)	intron (NM_138672, intron 1 of 68)	2095	NM_138672	192187	Mm.220821	NM_138672	ENSMUSG00000042286	Stab1	FEEL-1|FELE-1|MFEEL-1|MS-1|STAB-1|mKIAA0246	stabilin 1	protein-coding
mm_25295.1	chr3	105904692	105904699	+	1	NA	5' UTR (NM_009631, exon 1 of 2)	5' UTR (NM_009631, exon 1 of 2)	274	NM_009631	11542	Mm.235024	NM_009631	ENSMUSG00000000562	Adora3	A3AR|A3R|AA3R|ARA3|Gpcr2	adenosine A3 receptor	protein-coding
mm_23863.1	chr3	83012899	83012916	+	1	NA	exon (NM_133862, exon 8 of 10)	exon (NM_133862, exon 8 of 10)	5183	NM_001317105	99571	Mm.16422	NM_133862	ENSMUSG00000033860	Fgg	3010002H13Rik|AI256424	fibrinogen gamma chain	protein-coding
mm_148059.1	chr18	72159181	72159189	-	1	NA	intron (NM_007831, intron 1 of 28)	intron (NM_007831, intron 1 of 28)	191884	NM_007831	13176	Mm.167882	NM_007831	ENSMUSG00000060534	Dcc	C030036D22Rik|Igdcc1	deleted in colorectal carcinoma	protein-coding
mm_151399.1	chr19	56461630	56461646	+	1	NA	promoter-TSS (NM_001164263)	promoter-TSS (NM_001164263)	1	NM_172641	226245	Mm.156742	NM_172641	ENSMUSG00000035818	Plekhs1	9930023K05Rik	pleckstrin homology domain containing, family S member 1	protein-coding
mm_28522.1	chr3	92588983	92589017	-	1	NA	promoter-TSS (NM_008574)	promoter-TSS (NM_008574)	24	NM_008574	17235	Mm.331192	NM_008574		Smcp	Mcs|Mcsp	sperm mitochondria-associated cysteine-rich protein	protein-coding
mm_64487.1	chr7	143067536	143067541	+	1	NA	3' UTR (NM_133655, exon 8 of 8)	3' UTR (NM_133655, exon 8 of 8)	-1830	NM_020285	56844	Mm.139675	NM_020285	ENSMUSG00000045752	Tssc4	AA241958|ESTM671070	tumor-suppressing subchromosomal transferable fragment 4	protein-coding
mm_10914.1	chr2	25373256	25373266	+	1	NA	intron (NM_001290407, intron 1 of 5)	intron (NM_001290407, intron 1 of 5)	1226	NM_001081085	72080	Mm.250293	NM_001081085	ENSMUSG00000026955	Sapcd2	2010317E24Rik|6030458L21Rik|AL033337|ang	suppressor APC domain containing 2	protein-coding
mm_157686.1	chrX	60147886	60147894	-	1	NA	promoter-TSS (NM_133197)	promoter-TSS (NM_133197)	-190	NM_001289730	109904	Mm.93796	NM_133197	ENSMUSG00000031139	Mcf2	B230117G22Rik|Dbl|Mcf-2	mcf.2 transforming sequence	protein-coding
mm_166293.1	chr5	104092885	104092936	+	1	NA	exon (NM_010097, exon 4 of 11)	exon (NM_010097, exon 4 of 11)	-15302	NM_001163772	100271704	Mm.366664	NM_001163772	ENSMUSG00000091034	Gm17660	Scpppq1	predicted gene, 17660	protein-coding
mm_51568.1	chr6	83714537	83714552	+	1	NA	intron (NM_011912, intron 1 of 2)	intron (NM_011912, intron 1 of 2)	-2343	NR_002871	574519	Mm.487605	NR_002871	ENSMUSG00000085794	Vax2os	Vas2os|Vax2os1|Vax2os2	ventral anterior homeobox 2, opposite strand	ncRNA
mm_162477.1	chr1	133386081	133386124	-	1	NA	intron (NM_011439, intron 10 of 13)	intron (NM_011439, intron 10 of 13)	22530	NM_175443	214253	Mm.52111	NM_175443	ENSMUSG00000070644	Etnk2	4933417N20Rik|AI197444|EKI 2|Eki2|Tuc1	ethanolamine kinase 2	protein-coding
mm_144973.1	chr18	37890900	37890923	+	1	NA	exon (NM_001305981, exon 17 of 29)	exon (NM_001305981, exon 17 of 29)	-36251	NR_105945	102465592		NR_105945	ENSMUSG00000098706	Mir6979	Gm27524|mmu-mir-6979	microRNA 6979	ncRNA
mm_46453.1	chr5	105116894	105116894	-	1	NA	3' UTR (NM_001256005, exon 11 of 11)	3' UTR (NM_001256005, exon 11 of 11)	-6602	NM_172777	236573	Mm.425261	NM_172777	ENSMUSG00000029298	Gbp9	-	guanylate-binding protein 9	protein-coding
mm_119906.1	chr14	54950042	54950063	+	1	NA	promoter-TSS (NR_029724)	promoter-TSS (NR_029724)	-910	NR_029724	387204		NR_029724	ENSMUSG00000065432	Mir208a	Mirn208|Mirn208a|mir-208|mir-208a|mmu-mir-208	microRNA 208a	ncRNA
mm_105279.1	chr11	102408458	102408473	-	1	NA	promoter-TSS (NM_026542)	promoter-TSS (NM_026542)	-948	NM_026542	68066	Mm.44226	NM_026542	ENSMUSG00000018677	Slc25a39	3010027G13Rik|D11Ertd333e	solute carrier family 25, member 39	protein-coding
mm_122485.1	chr14	46387299	46387312	-	1	NA	intron (NM_007554, intron 1 of 3)	intron (NM_007554, intron 1 of 3)	3364	NM_001316360	12159	Mm.6813	NM_007554	ENSMUSG00000021835	Bmp4	Bmp-4|Bmp2b|Bmp2b-1|Bmp2b1	bone morphogenetic protein 4	protein-coding
mm_85462.1	chr9	105495038	105495117	-	1	NA	promoter-TSS (NM_175025)	promoter-TSS (NM_175025)	56	NM_175025	235574	Mm.326247	NM_175025	ENSMUSG00000032570	Atp2c1	1700121J11Rik|ATP2C1A|AW061228|BCPM|D930003G21Rik|HHD|SPCA|pmr1	ATPase, Ca++-sequestering	protein-coding
mm_83899.1	chr9	56145277	56145284	-	1	NA	intron (NM_019793, intron 6 of 6)	(A)n|Simple_repeat|Simple_repeat	15790	NM_019793	56434	Mm.28484	NM_019793	ENSMUSG00000032324	Tspan3	1700055K04Rik|TM4-A|Tm4sf8	tetraspanin 3	protein-coding
mm_79832.1	chr9	64794698	64794726	+	1	NA	Intergenic	Intergenic	-16299	NM_001162917	102442	Mm.222473	NM_176935	ENSMUSG00000053641	Dennd4a	AI115600|AI851943|F730015K02Rik	DENN/MADD domain containing 4A	protein-coding
mm_139405.1	chr17	52458681	52458691	+	1	NA	Intergenic	Intergenic	-144023	NM_001031811	211468	Mm.399068	NM_001031811	ENSMUSG00000035580	Kcnh8	C130090D05Rik|ELK|ELK1|ELK3|Kv12.1	potassium voltage-gated channel, subfamily H (eag-related), member 8	protein-coding
mm_118196.1	chr13	107858080	107858087	-	1	NA	intron (NM_145456, intron 2 of 14)	PB1D7|SINE|Alu	31981	NM_145456	67263	Mm.490418	NM_145456	ENSMUSG00000032846	Zswim6	2900036G02Rik|mKIAA1577	zinc finger SWIM-type containing 6	protein-coding
mm_123411.1	chr14	63987775	63987793	-	1	NA	promoter-TSS (NM_026359)	promoter-TSS (NM_026359)	-4	NM_026359	67750	Mm.33864	NM_026359	ENSMUSG00000021961	4930578I06Rik	AI429111	RIKEN cDNA 4930578I06 gene	protein-coding
mm_130445.1	chr15	98482778	98482784	-	1	NA	promoter-TSS (NM_010679)	promoter-TSS (NM_010679)	-98	NM_010679	16770	Mm.5074	NM_010679	ENSMUSG00000022991	Lalba	AW208827|Lyzg	lactalbumin, alpha	protein-coding
mm_11176.1	chr2	28700152	28700154	+	1	NA	promoter-TSS (NM_027283)	promoter-TSS (NM_027283)	-8	NM_001033874	68870	Mm.273318	NM_001033874	ENSMUSG00000026807	Ak8	1190002A17Rik|AK 8	adenylate kinase 8	protein-coding
mm_142284.1	chr17	40230876	40230877	-	1	NA	intron (NM_009639, intron 5 of 7)	MTB_Mm-int|LTR|ERVL-MaLR	11382	NM_009639	11572	Mm.14138	NM_009639	ENSMUSG00000025433	Crisp3	Aeg2|CRISP-3|CRS3|SGP28	cysteine-rich secretory protein 3	protein-coding
mm_81709.1	chr9	111311675	111311758	+	1	NA	promoter-TSS (NM_001164659)	promoter-TSS (NM_001164659)	-23	NM_001164659	320429	Mm.270754	NM_001164659	ENSMUSG00000062296	Trank1	A230061D21Rik|C030048J01Rik|Gm187|Lba1	tetratricopeptide repeat and ankyrin repeat containing 1	protein-coding
mm_85978.1	chr9	112164641	112164652	-	1	NA	intron (NM_001177623, intron 9 of 9)	intron (NM_001177623, intron 9 of 9)	21303	NM_001177618	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_162529.1	chr1	164039832	164039838	+	1	NA	Intergenic	Intergenic	-8399	NM_011345	20339	Mm.5245	NM_011345	ENSMUSG00000026582	Sele	CD62E|E-selectin|ELAM-1|Elam|LECAM2	selectin, endothelial cell	protein-coding
mm_35839.1	chr4	48046936	48046961	-	1	NA	intron (NM_015743, intron 1 of 7)	intron (NM_015743, intron 1 of 7)	1643	NM_015743	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_55152.1	chr6	51468452	51468469	-	1	NA	intron (NR_104468, intron 1 of 10)	intron (NR_104468, intron 1 of 10)	1434	NM_182650	53379	Mm.155896	NM_016806	ENSMUSG00000004980	Hnrnpa2b1	9130414A06Rik|Hnrpa2|Hnrpa2b1|hnrnp-A	heterogeneous nuclear ribonucleoprotein A2/B1	protein-coding
mm_120304.1	chr14	63140675	63140702	+	1	NA	intron (NM_007798, intron 8 of 9)	B1_Mur1|SINE|Alu	18226	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_76948.1	chr8	105988741	105988763	-	1	NA	exon (NM_176913, exon 7 of 12)	exon (NM_176913, exon 7 of 12)	3021	NM_001301204	319446	Mm.248357	NM_176913	ENSMUSG00000053687	Dpep2	F630103D06Rik|MBD-2	dipeptidase 2	protein-coding
mm_72283.1	chr8	75100509	75100525	+	1	NA	TTS (NM_010442)	TTS (NM_010442)	6899	NM_010442	15368	Mm.276389	NM_010442	ENSMUSG00000005413	Hmox1	D8Wsu38e|HO-1|HO1|Hemox|Hmox|Hsp32	heme oxygenase 1	protein-coding
mm_48388.1	chr5	139813238	139813250	-	1	NA	promoter-TSS (NM_144914)	promoter-TSS (NM_144914)	-1	NM_144914	231832	Mm.482655	NM_144914	ENSMUSG00000036687	Tmem184a	Sdmg1	transmembrane protein 184a	protein-coding
mm_3890.1	chr1	161175630	161175641	+	1	NA	Intergenic	Intergenic	-16321	NM_001195189	100502590	Mm.449990	NM_001195189		4930469G21Rik	-	RIKEN cDNA 4930469G21 gene	protein-coding
mm_13333.1	chr2	102785966	102785985	+	1	NA	3' UTR (NM_001077514, exon 11 of 11)	3' UTR (NM_001077514, exon 11 of 11)	79537	NM_001077515	20511	Mm.267547	NM_011393	ENSMUSG00000005089	Slc1a2	1700091C19Rik|2900019G14Rik|AI159670|Eaat2|GLT-1|GLT1|MGLT1	solute carrier family 1 (glial high affinity glutamate transporter), member 2	protein-coding
mm_169721.1	chr15	77902115	77902115	-	1	NA	Intergenic	IAPLTR1_Mm|LTR|ERVK	26879	NM_019913	56551	Mm.291917	NM_019913	ENSMUSG00000005354	Txn2	2510006J11Rik|AI788873|Trx2	thioredoxin 2	protein-coding
mm_139115.1	chr17	47410508	47410549	+	1	NA	Intergenic	CpG	4183	NM_001172091	75462	Mm.46129	NM_029296	ENSMUSG00000047150	1700001C19Rik	-	RIKEN cDNA 1700001C19 gene	protein-coding
mm_145537.1	chr18	60805979	60805987	+	1	NA	intron (NM_001042605, intron 1 of 8)	intron (NM_001042605, intron 1 of 8)	2134	NM_010545	16149	Mm.439737	NM_010545	ENSMUSG00000024610	Cd74	CLIP|DHLAG|HLADG|Ia-GAMMA|Ii	CD74 antigen (invariant polypeptide of major histocompatibility complex, class II antigen-associated)	protein-coding
mm_68836.1	chr7	126324919	126324932	-	1	NA	Intergenic	RMER15|LTR|ERVL	43120	NR_106025	102466797		NR_106025	ENSMUSG00000099017	Mir7058	Gm27766|mmu-mir-7058	microRNA 7058	ncRNA
mm_53525.1	chr6	136532904	136532919	+	1	NA	intron (NM_019426, intron 1 of 14)	intron (NM_019426, intron 1 of 14)	14060	NM_019426	54343	Mm.173271	NM_019426	ENSMUSG00000030213	Atf7ip	2610204M12Rik|AM|Mcaf1	activating transcription factor 7 interacting protein	protein-coding
mm_19829.1	chr2	111229559	111229612	-	1	NA	promoter-TSS (NM_026248)	promoter-TSS (NM_026248)	15	NM_026248	67575	Mm.84331	NM_026248	ENSMUSG00000027157	4930430A15Rik	-	RIKEN cDNA 4930430A15 gene	protein-coding
mm_87274.1	chr10	41810845	41810861	+	1	NA	promoter-TSS (NM_026643)	promoter-TSS (NM_026643)	279	NM_001162908	140742	Mm.139418	NM_001013370	ENSMUSG00000038332	Sesn1	1110002G11Rik|AU044290|Pa26|Sest1	sestrin 1	protein-coding
mm_39914.1	chr5	31452526	31452534	+	1	NA	promoter-TSS (NM_172993)	promoter-TSS (NM_172993)	94	NM_172993	269639	Mm.259127	NM_172993	ENSMUSG00000062761	Zfp512	2500002M11Rik|AI450173|D230008H22|Znf512	zinc finger protein 512	protein-coding
mm_33974.1	chr4	137626835	137626838	+	1	NA	intron (NM_001347227, intron 14 of 26)	intron (NM_001347227, intron 14 of 26)	32647	NM_130879	170707	Mm.218478	NM_130879	ENSMUSG00000043411	Usp48	2810449C13Rik|AI115503|BC021769|D330022K21Rik|Usp31	ubiquitin specific peptidase 48	protein-coding
mm_125212.1	chr15	34082665	34082734	+	1	NA	promoter-TSS (NM_026002)	promoter-TSS (NM_026002)	-20	NM_026002	67154	Mm.130883	NM_026002	ENSMUSG00000022255	Mtdh	2610103J23Rik|3D3|3D3/Lyric|AEG-1|AV353288|D8Bwg1112e|Lyric	metadherin	protein-coding
mm_134904.1	chr16	30187955	30187961	-	1	NA	Intergenic	Intergenic	79574	NM_027904	71756	Mm.290614	NM_027904	ENSMUSG00000023176	Cpn2	1300018K11Rik	carboxypeptidase N, polypeptide 2	protein-coding
mm_69844.1	chr7	141365081	141365111	-	1	NA	promoter-TSS (NR_033532)	promoter-TSS (NR_033532)	14	NR_033532	320871	Mm.475463	NM_177280	ENSMUSG00000086844	B230206H07Rik	-	RIKEN cDNA B230206H07 gene	ncRNA
mm_57663.1	chr6	128487524	128487547	-	1	NA	intron (NM_007376, intron 30 of 35)	intron (NM_007376, intron 30 of 35)	39185	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_31559.1	chr4	57434468	57434482	+	1	NA	Intergenic	CpG	-70183	NR_038178	73349	Mm.393774	NR_038178		1700042G15Rik	-	RIKEN cDNA 1700042G15 gene	ncRNA
mm_145397.1	chr18	57142824	57142828	+	1	NA	intron (NM_001001979, intron 1 of 24)	intron (NM_001001979, intron 1 of 24)	9736	NM_001001979	70417	Mm.297863	NM_001001979	ENSMUSG00000024593	Megf10	3000002B06Rik|Gm331	multiple EGF-like-domains 10	protein-coding
mm_121322.1	chr14	113314603	113314608	+	1	NA	Intergenic	Intergenic	1293175	NR_030150	723922		NR_030150	ENSMUSG00000070099	Mir466	Mirn466|mmu-mir-466	microRNA 466	ncRNA
mm_56260.1	chr6	90810119	90810160	-	1	NA	promoter-TSS (NM_001134384)	promoter-TSS (NM_001134384)	-16	NM_001134384	232227	Mm.196943	NM_182784	ENSMUSG00000034312	Iqsec1	AW561907|BC026481|BRAG2|D6Ertd349e|cI-43	IQ motif and Sec7 domain 1	protein-coding
mm_97826.1	chr11	83040608	83040612	+	1	NA	promoter-TSS (NR_073524)	promoter-TSS (NR_073524)	-77	NR_073524	237887	Mm.341645	NM_181542	ENSMUSG00000072621	Slfn10-ps	Slfn10|mFLJ00257	schlafen 10, pseudogene	pseudo
mm_26428.1	chr3	142618384	142618402	+	1	NA	3' UTR (NM_010259, exon 11 of 11)	3' UTR (NM_010259, exon 11 of 11)	-2270	NM_010260	14469	Mm.24038	NM_010260	ENSMUSG00000028270	Gbp2	-	guanylate binding protein 2	protein-coding
mm_37059.1	chr4	116053419	116053453	-	1	NA	intron (NM_028142, intron 1 of 5)	G-rich|Low_complexity|Low_complexity	440	NM_028142	72181	Mm.282560	NM_028142	ENSMUSG00000028706	Nsun4	2310010O12Rik|2810405F18Rik|AI507900|Shtap	NOL1/NOP2/Sun domain family, member 4	protein-coding
mm_4736.1	chr1	181804099	181804113	+	1	NA	Intergenic	Intergenic	38295	NM_133815	98386	Mm.4538	NM_133815	ENSMUSG00000004880	Lbr	AI505894|ic	lamin B receptor	protein-coding
mm_45475.1	chr5	69590767	69590774	-	1	NA	intron (NM_001347363, intron 1 of 6)	intron (NM_001347363, intron 1 of 6)	1515	NM_001038015	67980	Mm.33830	NM_027681	ENSMUSG00000029209	Gnpda2	4921523I18Rik|4933412A11Rik|BB189630|GNPDA|Gnp2|Sb52|mKIAA4008	glucosamine-6-phosphate deaminase 2	protein-coding
mm_24667.1	chr3	94492083	94492100	+	1	NA	non-coding (NR_110353, exon 12 of 12)	non-coding (NR_110353, exon 12 of 12)	9369	NR_110353	78784	Mm.44292	NM_172434	ENSMUSG00000028137	Celf3	4930415M08Rik|BRUNOL1|CAGH4|ERDA4|Tnrc4	CUGBP, Elav-like family member 3	protein-coding
mm_116790.1	chr13	53414822	53414832	-	1	NA	intron (NR_037991, intron 4 of 7)	intron (NR_037991, intron 4 of 7)	21138	NR_037991	100040421	Mm.83967	NR_037991	ENSMUSG00000107008	Gm2762	1700025I17Rik	predicted gene 2762	ncRNA
mm_96286.1	chr11	63115307	63115313	+	1	NA	intron (NR_105772, intron 5 of 6)	intron (NR_105772, intron 5 of 6)	-13672	NM_001302258	18858	Mm.1237	NM_008885	ENSMUSG00000018217	Pmp22	22kDa|Gas-3|HNPP|Tr|trembler	peripheral myelin protein 22	protein-coding
mm_142458.1	chr17	45595758	45595768	-	1	NA	promoter-TSS (NM_001199116)	promoter-TSS (NM_001199116)	139	NM_001199114	63959	Mm.29744	NM_022880	ENSMUSG00000023942	Slc29a1	1200014D21Rik|AA407560|ENT1	solute carrier family 29 (nucleoside transporters), member 1	protein-coding
mm_70360.1	chr8	8533655	8533663	+	1	NA	Intergenic	Intergenic	127114	NM_010111	13642	Mm.209813	NM_010111	ENSMUSG00000001300	Efnb2	ELF-2|Epl5|Eplg5|Htk-L|LERK-5|Lerk5|NLERK-1	ephrin B2	protein-coding
mm_63602.1	chr7	128147420	128147468	+	1	NA	intron (NM_021334, intron 23 of 29)	intron (NM_021334, intron 23 of 29)	17876	NM_021334	16411	Mm.22378	NM_021334	ENSMUSG00000030789	Itgax	AI449405|Cd11c|Cr4|N418	integrin alpha X	protein-coding
mm_103987.1	chr11	84828954	84828966	-	1	NA	promoter-TSS (NR_046281)	promoter-TSS (NR_046281)	43	NM_177564	192970	Mm.192213	NM_177564	ENSMUSG00000034449	Dhrs11	-	dehydrogenase/reductase (SDR family) member 11	protein-coding
mm_594.1	chr1	39551831	39551856	+	1	NA	3' UTR (NM_001033135, exon 7 of 7)	3' UTR (NM_001033135, exon 7 of 7)	-3003	NR_028555	100217461		NR_028555	ENSMUSG00000077704	Snord89	MBII-289	small nucleolar RNA, C/D box 89	snoRNA
mm_102360.1	chr11	58323359	58323372	-	1	NA	promoter-TSS (NM_001256517)	promoter-TSS (NM_001256517)	0	NM_001256517	319475	Mm.72124	NM_178761	ENSMUSG00000049755	Zfp672	4930488P06Rik|4930511N19Rik|Znf672	zinc finger protein 672	protein-coding
mm_128120.1	chr15	30458816	30458840	-	1	NA	intron (NM_008729, intron 2 of 22)	intron (NM_008729, intron 2 of 22)	286235	NM_008729	18163	Mm.321648	NM_008729	ENSMUSG00000022240	Ctnnd2	Catnd2|Nprap|neurojugin	catenin (cadherin associated protein), delta 2	protein-coding
mm_99950.1	chr11	112782183	112782248	+	1	NA	promoter-TSS (NM_011448)	promoter-TSS (NM_011448)	5	NM_011448	20682	Mm.286407	NM_011448	ENSMUSG00000000567	Sox9	2010306G03Rik|AV220920|mKIAA4243	SRY (sex determining region Y)-box 9	protein-coding
mm_164526.1	chr17	4994613	4994658	+	1	NA	promoter-TSS (NM_001085355)	promoter-TSS (NM_001085355)	-439	NM_001085355	239985	Mm.133401	NM_001085355	ENSMUSG00000069729	Arid1b	8030481M12|9330189K18Rik|AI836955|Ardi1b|B230217J03Rik|mKIAA1235	AT rich interactive domain 1B (SWI-like)	protein-coding
mm_93255.1	chr10	95514771	95514789	-	1	NA	promoter-TSS (NM_080560)	promoter-TSS (NM_080560)	-382	NM_080560	93765	Mm.371667	NM_080560	ENSMUSG00000074781	Ube2n	1500026J17Rik|AL022654|BB101821|UBC13	ubiquitin-conjugating enzyme E2N	protein-coding
mm_44471.1	chr5	23418515	23418557	-	1	NA	Intergenic	CpG	15817	NR_040469	269630	Mm.425231	NR_040469	ENSMUSG00000073147	5031425E22Rik	-	RIKEN cDNA 5031425E22 gene	ncRNA
mm_101031.1	chr11	8579960	8579965	-	1	NA	intron (NM_001083587, intron 3 of 30)	intron (NM_001083587, intron 3 of 30)	84573	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_51134.1	chr6	68541620	68541632	+	1	NA	Intergenic	Intergenic	785548	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_78243.1	chr9	21632991	21633021	+	1	NA	exon (NM_001174078, exon 2 of 34)	exon (NM_001174078, exon 2 of 34)	16837	NM_001174078	20586	Mm.286593	NM_011417	ENSMUSG00000032187	Smarca4	Brg1|HP1-BP72|SNF2beta|SW1/SNF|b2b508.1Clo|b2b692Clo	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	protein-coding
mm_151333.1	chr19	55894509	55894521	+	1	NA	promoter-TSS (NM_001142924)	promoter-TSS (NM_001142924)	-806	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_38553.1	chr4	141617997	141618056	-	1	NA	TTS (NM_001013780)	TTS (NM_001013780)	607	NM_145987	213989	Mm.34891	NM_145987	ENSMUSG00000043085	Tmem82	-	transmembrane protein 82	protein-coding
mm_33769.1	chr4	134402176	134402190	+	1	NA	promoter-TSS (NM_001285877)	promoter-TSS (NM_001285877)	-729	NM_001285874	100163	Mm.22116	NM_133880	ENSMUSG00000037366	Pafah2	2310074E22Rik|AI507170	platelet-activating factor acetylhydrolase 2	protein-coding
mm_107733.1	chr12	57513179	57513188	+	1	NA	Intergenic	Intergenic	32938	NM_008259	15375	Mm.4578	NM_008259	ENSMUSG00000035451	Foxa1	Hnf-3a|Hnf3a|Tcf-3a|Tcf3a	forkhead box A1	protein-coding
mm_49469.1	chr6	29468077	29468113	+	1	NA	intron (NM_025381, intron 1 of 1)	intron (NM_025381, intron 1 of 1)	312	NM_025381	66144	Mm.371614	NM_025381	ENSMUSG00000004285	Atp6v1f	1110004G16Rik	ATPase, H+ transporting, lysosomal V1 subunit F	protein-coding
mm_77004.1	chr8	107421552	107421558	-	1	NA	exon (NM_026277, exon 3 of 9)	exon (NM_026277, exon 3 of 9)	3483	NM_026277	67619	Mm.36817	NM_026277	ENSMUSG00000003848	Nob1	1700021I09Rik|ART-4|Nob1p|Psmd8bp1	NIN1/RPN12 binding protein 1 homolog	protein-coding
mm_58874.1	chr7	16986915	16986937	+	1	NA	Intergenic	Intergenic	-7662	NM_001101535	434130	Mm.459162	NM_001101535	ENSMUSG00000041117	Ccdc8	ENSMUSG00000041117	coiled-coil domain containing 8	protein-coding
mm_83770.1	chr9	52048765	52048779	-	1	NA	promoter-TSS (NR_023357)	promoter-TSS (NR_023357)	-67	NR_023357	629557	Mm.422775	NR_023357		Gm6981	EG629557	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_110369.1	chr12	40199261	40199266	-	1	NA	promoter-TSS (NM_001033437)	promoter-TSS (NM_001033437)	52	NM_001033437	380755	Mm.390463	NM_001033437	ENSMUSG00000071342	Lsmem1	Gm889	leucine-rich single-pass membrane protein 1	protein-coding
mm_111526.1	chr12	100206158	100206231	-	1	NA	exon (NM_009790, exon 5 of 6)	exon (NM_009790, exon 5 of 6)	6050	NM_001313934	12313	Mm.285993	NM_009790	ENSMUSG00000001175	Calm1	AI256814|AI327027|AI461935|AL024000|CaM|Calm	calmodulin 1	protein-coding
mm_20386.1	chr2	128967997	128968030	-	1	NA	intron (NM_178404, intron 1 of 11)	(CCG)n|Simple_repeat|Simple_repeat	611	NM_178404	78751	Mm.26377	NM_178404	ENSMUSG00000042851	Zc3h6	4631426G04Rik|4833425H18Rik|AU024389|AW060453|Zc3hdc6|mKIAA2035	zinc finger CCCH type containing 6	protein-coding
mm_36624.1	chr4	91372029	91372047	-	1	NA	promoter-TSS (NM_207686)	promoter-TSS (NM_207686)	17	NM_010486	15569	Mm.318042	NM_010486	ENSMUSG00000008489	Elavl2	Hub|mel-N1	ELAV (embryonic lethal, abnormal vision, Drosophila)-like 2 (Hu antigen B)	protein-coding
mm_141317.1	chr17	28364590	28364605	-	1	NA	intron (NM_021478, intron 2 of 14)	intron (NM_021478, intron 2 of 14)	546	NM_021478	22157	Mm.42102	NM_021478	ENSMUSG00000037446	Tulp1	Tulp1l	tubby like protein 1	protein-coding
mm_148336.1	chr18	84339534	84339552	-	1	NA	intron (NM_001033341, intron 7 of 8)	intron (NM_001033341, intron 7 of 8)	249961	NM_001033341	240476	Mm.329575	NM_001033341	ENSMUSG00000048410	Zfp407	6430585N13Rik|Gm333|Gm334|Gm948|ZNF407	zinc finger protein 407	protein-coding
mm_83543.1	chr9	46235290	46235306	-	1	NA	promoter-TSS (NM_001289755)	promoter-TSS (NM_001289755)	1	NM_001289833	11814	Mm.390161	NM_023114	ENSMUSG00000032081	Apoc3	apo-CIII|apoC-III	apolipoprotein C-III	protein-coding
mm_77174.1	chr8	111690699	111690709	-	1	NA	intron (NM_025583, intron 1 of 6)	intron (NM_025583, intron 1 of 6)	306	NM_025583	66473	Mm.34374	NM_025583	ENSMUSG00000031957	Ctrb1	2200008D09Rik|AI504462|Ctrb|Prt-2	chymotrypsinogen B1	protein-coding
mm_54694.1	chr6	39527394	39527433	-	1	NA	intron (NM_172477, intron 1 of 18)	intron (NM_172477, intron 1 of 18)	30421	NM_172477	209773	Mm.440021	NM_172477	ENSMUSG00000038456	Dennd2a	B930096L08Rik|C130031G22|mKIAA1277	DENN/MADD domain containing 2A	protein-coding
mm_3410.1	chr1	144077584	144077593	+	1	NA	Intergenic	Intergenic	-73439	NM_009061	19735	Mm.28262	NM_009061	ENSMUSG00000026360	Rgs2	GOS8	regulator of G-protein signaling 2	protein-coding
mm_9317.1	chr1	171648389	171648401	-	1	NA	intron (NM_001347184, intron 1 of 5)	intron (NM_001347184, intron 1 of 5)	604	NM_001347184	75345	Mm.164642	NM_144539	ENSMUSG00000038179	Slamf7	19A|19A24|4930560D03Rik|CRACC|CS1	SLAM family member 7	protein-coding
mm_113224.1	chr13	27061528	27061538	+	1	NA	exon (NM_011164, exon 3 of 5)	exon (NM_011164, exon 3 of 5)	3963	NM_011164	19109	Mm.1270	NM_011164	ENSMUSG00000021342	Prl	AV290867|Gha1|Prl1a1	prolactin	protein-coding
mm_21639.1	chr2	164333354	164333356	-	1	NA	exon (NM_009301, exon 2 of 3)	exon (NM_009301, exon 2 of 3)	590	NM_009301	20944	Mm.140154	NM_009301	ENSMUSG00000017004	Svs5	BB115186|Semg1|Svp-1|Svp1|Svp5	seminal vesicle secretory protein 5	protein-coding
mm_18934.1	chr2	76750492	76750505	-	1	NA	exon (NM_011652, exon 275 of 313)	exon (NM_011652, exon 275 of 313)	75183	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_10089.1	chr2	3119468	3119473	+	1	NA	intron (NM_001347067, intron 1 of 7)	intron (NM_001347067, intron 1 of 7)	785	NM_001347067	269233	Mm.23044	NM_001081161	ENSMUSG00000050530	Fam171a1	9630050M13Rik|AA409679	family with sequence similarity 171, member A1	protein-coding
mm_63890.1	chr7	138834902	138834902	+	1	NA	TTS (NM_027115)	TTS (NM_027115)	11365	NM_001045483	69546	Mm.31598	NM_027115	ENSMUSG00000041775	Mapk1ip1	2310009E07Rik|AU043776|MISS	mitogen-activated protein kinase 1 interacting protein 1	protein-coding
mm_167406.1	chr8	104322258	104322268	+	1	NA	promoter-TSS (NM_028524)	promoter-TSS (NM_028524)	36	NM_028524	75502	Mm.232593	NM_028524	ENSMUSG00000035785	Cmtm2b	1700013O04Rik|Cklfsf22|Cklfsf2b	CKLF-like MARVEL transmembrane domain containing 2B	protein-coding
mm_73133.1	chr8	94974687	94974700	+	1	NA	Intergenic	Intergenic	-2416	NM_001198894	14766	Mm.290834	NM_018882	ENSMUSG00000031785	Adgrg1	Cyt28|Gpr56|TM7LN4|TM7XN1	adhesion G protein-coupled receptor G1	protein-coding
mm_30380.1	chr3	152243877	152243898	-	1	NA	exon (NM_199465, exon 9 of 13)	exon (NM_199465, exon 9 of 13)	22433	NM_199465	68810	Mm.200188	NM_199465	ENSMUSG00000039103	Nexn	1110046H09Rik|AA553326|NELIN	nexilin	protein-coding
mm_165232.1	chr2	58770048	58770050	+	1	NA	intron (NM_029692, intron 2 of 6)	(CACAC)n|Simple_repeat|Simple_repeat	14865	NM_029692	76654	Mm.200370	NM_029692	ENSMUSG00000026839	Upp2	1700124F02Rik|AI266885|UDRPASE2|UP2|UPASE2	uridine phosphorylase 2	protein-coding
mm_168940.1	chr12	70825482	70825482	+	1	NA	promoter-TSS (NM_028127)	promoter-TSS (NM_028127)	-32	NM_028127	319710	Mm.2962	NM_028127	ENSMUSG00000048285	Frmd6	2610019M19Rik|4930488L10Rik|AW212977|Willin	FERM domain containing 6	protein-coding
mm_17592.1	chr2	30629892	30629895	-	1	NA	Intergenic	ID4_|SINE|ID	34849	NM_030137	78617	Mm.40413	NM_030137	ENSMUSG00000047363	Cstad	9530039B02Rik	CSA-conditional, T cell activation-dependent protein	protein-coding
mm_145744.1	chr18	64340053	64340067	+	1	NA	promoter-TSS (NM_194268)	promoter-TSS (NM_194268)	-304	NM_194268	225631	Mm.234723	NM_194268	ENSMUSG00000045991	Onecut2	C730009D12|OC-2|Oc2	one cut domain, family member 2	protein-coding
mm_171735.1	chr4	94739313	94739314	+	1	NA	promoter-TSS (NM_001290551)	promoter-TSS (NM_001290551)	24	NM_001290551	21687	Mm.14313	NM_013690	ENSMUSG00000006386	Tek	AA517024|Cd202b|Hyk|STK1|Tie-2|Tie2	endothelial-specific receptor tyrosine kinase	protein-coding
mm_165670.1	chr3	89238407	89238450	-	1	NA	intron (NM_001039466, intron 7 of 8)	intron (NM_001039466, intron 7 of 8)	6585	NR_121683	360213	Mm.331156	NM_183037	ENSMUSG00000042766	Trim46	TRIFIC	tripartite motif-containing 46	protein-coding
mm_139307.1	chr17	48348547	48348566	+	1	NA	exon (NM_031254, exon 2 of 5)	exon (NM_031254, exon 2 of 5)	2155	NM_001272078	83433	Mm.261623	NM_031254	ENSMUSG00000023992	Trem2	TREM-2|Trem2a|Trem2b|Trem2c	triggering receptor expressed on myeloid cells 2	protein-coding
mm_59960.1	chr7	30427590	30427593	+	1	NA	intron (NM_172142, intron 10 of 10)	intron (NM_172142, intron 10 of 10)	4287	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_117892.1	chr13	99422891	99422904	-	1	NA	3' UTR (NM_008634, exon 7 of 7)	3' UTR (NM_008634, exon 7 of 7)	-10071	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_30322.1	chr3	151731784	151731816	-	1	NA	3' UTR (NM_133871, exon 8 of 8)	3' UTR (NM_133871, exon 8 of 8)	18159	NM_133871	99899	Mm.30756	NM_133871	ENSMUSG00000028037	Ifi44	A430056A10Rik|AW261460|MTAP44|p44	interferon-induced protein 44	protein-coding
mm_10714.1	chr2	22785700	22785701	+	1	NA	intron (NM_019456, intron 1 of 13)	MER2|DNA|TcMar-Tigger	11373	NM_019456	54519	Mm.14255	NM_019456	ENSMUSG00000026786	Apbb1ip	9930118P07Rik|Prp48	amyloid beta (A4) precursor protein-binding, family B, member 1 interacting protein	protein-coding
mm_52004.1	chr6	92827780	92827790	+	1	NA	intron (NM_175314, intron 18 of 29)	intron (NM_175314, intron 18 of 29)	73656	NM_175314	101401	Mm.158235	NM_175314	ENSMUSG00000030022	Adamts9	1810011L16Rik|8430403M15Rik|AW743315|E030027K14Rik	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 9	protein-coding
mm_22693.1	chr3	17794016	17794042	+	1	NA	intron (NR_033490, intron 1 of 2)	intron (NR_033490, intron 1 of 2)	-1633	NR_029814	723950		NR_029814	ENSMUSG00000093073	Mir124a-2	Mirn124a-2|mir-124-2|mir-124a-2	microRNA 124a-2	ncRNA
mm_3409.1	chr1	144004452	144004460	+	1	NA	promoter-TSS (NM_009061)	promoter-TSS (NM_009061)	-307	NM_009061	19735	Mm.28262	NM_009061	ENSMUSG00000026360	Rgs2	GOS8	regulator of G-protein signaling 2	protein-coding
mm_162853.1	chr10	88605135	88605154	-	1	NA	promoter-TSS (NM_001252372)	promoter-TSS (NM_001252372)	8	NM_001252372	109272	Mm.147208	NM_175418	ENSMUSG00000020061	Mybpc1	8030451F13Rik	myosin binding protein C, slow-type	protein-coding
mm_83819.1	chr9	53667430	53667521	-	1	NA	promoter-TSS (NM_001161618)	promoter-TSS (NM_001161618)	32	NM_001161618	75717	Mm.218910	NM_027807	ENSMUSG00000032030	Cul5	4921514I20Rik|8430423K24Rik|AI852817|C030032G03Rik|C330021I08Rik|VACM-1|VACM1	cullin 5	protein-coding
mm_26049.1	chr3	135689152	135689168	+	1	NA	intron (NM_008689, intron 1 of 24)	intron (NM_008689, intron 1 of 24)	2387	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_151362.1	chr19	55917349	55917362	+	1	NA	exon (NM_001142918, exon 8 of 15)	exon (NM_001142918, exon 8 of 15)	22034	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_106401.1	chr11	118909469	118909479	-	1	NA	promoter-TSS (NM_001039167)	promoter-TSS (NM_001039167)	98	NM_001024931	52897	Mm.341103	NM_001024931	ENSMUSG00000025576	Rbfox3	Fox-3|Hrnbp3|NeuN|Neuna60	RNA binding protein, fox-1 homolog (C. elegans) 3	protein-coding
mm_126705.1	chr15	85206047	85206072	+	1	NA	promoter-TSS (NM_010180)	promoter-TSS (NM_010180)	51	NM_010180	14114	Mm.297992	NM_010180	ENSMUSG00000006369	Fbln1	-	fibulin 1	protein-coding
mm_133071.1	chr16	58670742	58670764	+	1	NA	exon (NM_007757, exon 1 of 7)	exon (NM_007757, exon 1 of 7)	545	NM_007757	12892	Mm.291519	NM_007757	ENSMUSG00000022742	Cpox	CPX|Cpo|HCP|cac|nct	coproporphyrinogen oxidase	protein-coding
mm_85144.1	chr9	95819411	95819413	-	1	NA	intron (NM_001033210, intron 1 of 15)	ID_B1|SINE|B4	25867	NM_001033210	102502	Mm.11869	NM_001033210	ENSMUSG00000049493	Pls1	AI427122	plastin 1 (I-isoform)	protein-coding
mm_137776.1	chr17	29491801	29491805	+	1	NA	exon (NM_008842, exon 4 of 6)	exon (NM_008842, exon 4 of 6)	758	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_24896.1	chr3	96172353	96172368	+	1	NA	promoter-TSS (NM_153053)	promoter-TSS (NM_153053)	-146	NM_153053	107701	Mm.219671	NM_153053	ENSMUSG00000068856	Sf3b4	SF3b49|SF3b50|Sap49	splicing factor 3b, subunit 4	protein-coding
mm_10438.1	chr2	14201549	14201551	+	1	NA	intron (NM_001081310, intron 3 of 3)	intron (NM_001081310, intron 3 of 3)	27026	NM_001081310	625286	Mm.158781	NM_001081310	ENSMUSG00000061531	Tmem236	2010003H20Rik|Fam23a|Gm613	transmembrane protein 236	protein-coding
mm_131069.1	chr16	4649167	4649180	+	1	NA	exon (NM_139307, exon 2 of 2)	exon (NM_139307, exon 2 of 2)	9228	NM_139307	246154	Mm.482140	NM_139307	ENSMUSG00000039646	Vasn	2610528G05Rik|Atia|Slitl2	vasorin	protein-coding
mm_114983.1	chr13	97434922	97434941	+	1	NA	promoter-TSS (NR_110432)	promoter-TSS (NR_110432)	-39	NR_110432	100039691	Mm.219358	NR_110430	ENSMUSG00000078952	Lncenc1	ENSMUSG00000078952|Gm11019|Gm2373|Lincenc1|Platr18|linc-Enc1	long non-coding RNA, embryonic stem cells expressed 1	ncRNA
mm_63465.1	chr7	127573679	127573683	+	1	NA	intron (NM_026888, intron 1 of 9)	C-rich|Low_complexity|Low_complexity	333	NM_026888	68961	Mm.274473	NM_026888	ENSMUSG00000030815	Phkg2	1500017I02Rik	phosphorylase kinase, gamma 2 (testis)	protein-coding
mm_24644.1	chr3	94377540	94377550	+	1	NA	non-coding (NR_121656, exon 1 of 10)	non-coding (NR_121656, exon 1 of 10)	113	NR_121656	19885	Mm.4372	NM_011281	ENSMUSG00000028150	Rorc	Nr1f3|RORgamma|TOR|Thor	RAR-related orphan receptor gamma	protein-coding
mm_15435.1	chr2	157279027	157279064	+	1	NA	promoter-TSS (NM_019642)	promoter-TSS (NM_019642)	-53	NM_019642	20014	Mm.22130	NM_019642	ENSMUSG00000027642	Rpn2	1300012C06Rik|AV261018|Rpn-2	ribophorin II	protein-coding
mm_168608.1	chr11	75732883	75732883	+	1	NA	promoter-TSS (NM_009536)	promoter-TSS (NM_009536)	-4	NM_009536	22627	Mm.234700	NM_009536	ENSMUSG00000020849	Ywhae	AU019196	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide	protein-coding
mm_136616.1	chr17	5404076	5404082	+	1	NA	Intergenic	MTE2a|LTR|ERVL-MaLR	14688	NM_175349	106557	Mm.432764	NM_175349	ENSMUSG00000101959	Ldhal6b	4933402O15Rik|AI326310|LDHL|Ldhal	lactate dehydrogenase A-like 6B	protein-coding
mm_9087.1	chr1	168432192	168432202	-	1	NA	promoter-TSS (NM_001291509)	promoter-TSS (NM_001291509)	-28	NM_008783	18514	Mm.43358	NM_008783	ENSMUSG00000052534	Pbx1	2310056B04Rik|D230003C07Rik|Pbx-1	pre B cell leukemia homeobox 1	protein-coding
mm_88280.1	chr10	75098455	75098455	+	1	NA	intron (NM_001081412, intron 1 of 22)	(T)n|Simple_repeat|Simple_repeat	37559	NM_001081412	110279	Mm.333722	NM_001081412	ENSMUSG00000009681	Bcr	5133400C09Rik|AI561783|AI853148|mKIAA3017	breakpoint cluster region	protein-coding
mm_162289.1	chr1	26617004	26617008	+	1	NA	Intergenic	RLTR16|LTR|ERVK	70454	NM_001033764	210940	Mm.297614	NM_001033764	ENSMUSG00000073722	4931408C20Rik	-	RIKEN cDNA 4931408C20 gene	protein-coding
mm_148365.1	chr18	88866266	88866268	-	1	NA	Intergenic	Intergenic	27940	NM_018821	54607	Mm.91920	NM_018821	ENSMUSG00000056153	Socs6	1500012M23Rik|5830401B18Rik|AI447482|Cis4|Cish4|HSPC060|SOCS-4|SOCS-6|SSI4|STAI4|STATI4|Socs4	suppressor of cytokine signaling 6	protein-coding
mm_155577.1	chrX	77848041	77848044	+	1	NA	exon (NM_017471, exon 2 of 7)	exon (NM_017471, exon 2 of 7)	5458	NM_017471	54192	Mm.8034	NM_017471	ENSMUSG00000000003	Pbsn	PB|Prbs	probasin	protein-coding
mm_143151.1	chr17	57222920	57222937	-	1	NA	exon (NM_009778, exon 13 of 41)	exon (NM_009778, exon 13 of 41)	5208	NM_009778	12266	Mm.19131	NM_009778	ENSMUSG00000024164	C3	AI255234|ASP|HSE-MSF|Plp	complement component 3	protein-coding
mm_55665.1	chr6	72520004	72520037	-	1	NA	Intergenic	Intergenic	-24371	NM_007599	12332	Mm.18626	NM_007599	ENSMUSG00000056737	Capg	gCap39|mbh1	capping protein (actin filament), gelsolin-like	protein-coding
mm_28658.1	chr3	95241045	95241103	-	1	NA	promoter-TSS (NM_001024841)	promoter-TSS (NM_001024841)	35	NM_001024841	229588	Mm.387177	NM_001024841	ENSMUSG00000068860	Gm128	Ment|pmis1	predicted gene 128	protein-coding
mm_16108.1	chr2	169633339	169633359	+	1	NA	promoter-TSS (NM_080455)	promoter-TSS (NM_080455)	-297	NM_080455	228911	Mm.315789	NM_080455	ENSMUSG00000047907	Tshz2	2900073F20Rik|B830045G17|Mtsh2|Sdccag33l|Tsh2|Zfp218|mKIAA4248|teashirt2	teashirt zinc finger family member 2	protein-coding
mm_107119.1	chr12	18610081	18610114	+	1	NA	Intergenic	CpG	95587	NM_001201330	236366	Mm.352227	NM_001033157	ENSMUSG00000073197	5730507C01Rik	-	RIKEN cDNA 5730507C01 gene	protein-coding
mm_44800.1	chr5	32854186	32854248	-	1	NA	promoter-TSS (NM_194340)	promoter-TSS (NM_194340)	13	NM_194340	215476	Mm.248721	NM_194340	ENSMUSG00000054280	Prr14l	6030436E02Rik|C330019G07Rik|Prl14l	proline rich 14-like	protein-coding
mm_144497.1	chr18	24238240	24238267	+	1	NA	5' UTR (NM_013814, exon 3 of 13)	5' UTR (NM_013814, exon 3 of 13)	32259	NM_001160404	14423	Mm.30249	NM_013814	ENSMUSG00000000420	Galnt1	-	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 1	protein-coding
mm_9226.1	chr1	171237608	171237624	-	1	NA	intron (NM_153064, intron 8 of 12)	intron (NM_153064, intron 8 of 12)	-3267	NM_010185	14127	Mm.22673	NM_010185	ENSMUSG00000058715	Fcer1g	AI573376|CD23|FcR-gamma|FcR[g]|FcRgamma|Fce1g|FcepsilonRI|Ly-50	Fc receptor, IgE, high affinity I, gamma polypeptide	protein-coding
mm_35612.1	chr4	43399770	43399799	-	1	NA	intron (NM_001037709, intron 1 of 11)	intron (NM_001037709, intron 1 of 11)	-6718	NM_199057	100213	Mm.235730	NM_199057	ENSMUSG00000035969	Rusc2	AI840675|mKIAA0375	RUN and SH3 domain containing 2	protein-coding
mm_128113.1	chr15	28025968	28025981	-	1	NA	promoter-TSS (NM_001081302)	promoter-TSS (NM_001081302)	-126	NM_001081302	223435	Mm.485422	NM_001081302	ENSMUSG00000022263	Trio	6720464I07Rik|AA408740|Solo	triple functional domain (PTPRF interacting)	protein-coding
mm_100024.1	chr11	114903620	114903631	+	1	NA	3' UTR (NM_170758, exon 7 of 7)	3' UTR (NM_170758, exon 7 of 7)	13584	NM_170758	217303	Mm.294439	NM_170758	ENSMUSG00000034652	Cd300a	B230315M08Rik|Clm8|LMIR1|MAIR-I|MAIR-Ia|MMAC8|Pigr4|mcpir1	CD300A molecule	protein-coding
mm_53048.1	chr6	124715231	124715233	+	1	NA	intron (NM_007531, intron 6 of 8)	intron (NM_007531, intron 6 of 8)	2753	NR_029554	387159		NR_029554	ENSMUSG00000065474	Mir141	Mirn141|mir-141|mmu-mir-141	microRNA 141	ncRNA
mm_44887.1	chr5	34660565	34660595	-	1	NA	promoter-TSS (NM_029278)	promoter-TSS (NM_029278)	201	NM_019497	14772	Mm.117076	NM_019497	ENSMUSG00000052783	Grk4	A830025H08Rik|GRK|Gprk2l|Gprk4	G protein-coupled receptor kinase 4	protein-coding
mm_15240.1	chr2	154656960	154657108	+	1	NA	promoter-TSS (NM_029362)	promoter-TSS (NM_029362)	8	NM_029362	75608	Mm.262480	NM_029362	ENSMUSG00000038467	Chmp4b	2010012F05Rik|C76846|Snf7-2	charged multivesicular body protein 4B	protein-coding
mm_42220.1	chr5	113335268	113335278	+	1	NA	Intergenic	Intergenic	2372	NR_106089	102466821		NR_106089	ENSMUSG00000104840	Mir7230	mmu-mir-7230	microRNA 7230	ncRNA
mm_71307.1	chr8	42246835	42246837	+	1	NA	Intergenic	Intergenic	419569	NR_045497	69966	Mm.416903	NR_045497	ENSMUSG00000102046	2810404M03Rik	-	RIKEN cDNA 2810404M03 gene	ncRNA
mm_16989.1	chr2	18179481	18179481	-	1	NA	intron (NR_045539, intron 15 of 24)	intron (NR_045539, intron 15 of 24)	114896	NM_001252561	17354	Mm.209175	NM_010804	ENSMUSG00000026743	Mllt10	Af10|B130021D15Rik|D630001B22Rik|mKIAA4140	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 10	protein-coding
mm_140258.1	chr17	84512229	84512240	+	1	NA	intron (NM_177606, intron 1 of 29)	CpG	339	NM_177606	213556	Mm.215159	NM_177606	ENSMUSG00000040852	Plekhh2	AI256725|E030001K05|mKIAA2028	pleckstrin homology domain containing, family H (with MyTH4 domain) member 2	protein-coding
mm_6880.1	chr1	84370502	84370504	-	1	NA	3' UTR (NM_152915, exon 13 of 13)	3' UTR (NM_152915, exon 13 of 13)	-85858	NM_001003948	98496	Mm.187470	NM_001003948	ENSMUSG00000045658	Pid1	5033414K04Rik|NYGGF4	phosphotyrosine interaction domain containing 1	protein-coding
mm_61212.1	chr7	64226580	64226584	+	1	NA	intron (NM_001039104, intron 15 of 26)	intron (NM_001039104, intron 15 of 26)	20776	NR_029805	387207		NR_029805	ENSMUSG00000065585	Mir211	Mirn211|mir-211|mmu-mir-211	microRNA 211	ncRNA
mm_93406.1	chr10	107912337	107912357	-	1	NA	promoter-TSS (NM_001177567)	promoter-TSS (NM_001177567)	-213	NM_001177567	628870	Mm.336090	NM_001177567	ENSMUSG00000091455	Otogl	EG628870|Gm6924	otogelin-like	protein-coding
mm_115589.1	chr13	11827054	11827067	-	1	NA	intron (NM_023868, intron 15 of 104)	intron (NM_023868, intron 15 of 104)	279885	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding
mm_60316.1	chr7	44200998	44201028	+	1	NA	intron (NM_008693, intron 2 of 4)	intron (NM_008693, intron 2 of 4)	2822	NM_008693	18050	Mm.439740	NM_008693	ENSMUSG00000066515	Klk1b3	Ngfg|gamma-NGF|mGk-3	kallikrein 1-related peptidase b3	protein-coding
mm_138265.1	chr17	34598153	34598164	+	1	NA	TTS (NM_017463)	TTS (NM_017463)	308	NR_073173	11596	Mm.3383	NM_007425	ENSMUSG00000015452	Ager	RAGE	advanced glycosylation end product-specific receptor	protein-coding
mm_15743.1	chr2	164237414	164237430	+	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	919	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_123763.1	chr14	70206083	70206101	-	1	NA	promoter-TSS (NM_001271407)	promoter-TSS (NM_001271407)	-70	NM_001271407	20410	Mm.5068	NM_011366	ENSMUSG00000022091	Sorbs3	SCAM-1|SH3P3|Sh3d4|vinexin-g	sorbin and SH3 domain containing 3	protein-coding
mm_126519.1	chr15	81910431	81910435	+	1	NA	exon (NM_080633, exon 12 of 18)	exon (NM_080633, exon 12 of 18)	15780	NM_030229	78929	Mm.215115	NM_030229	ENSMUSG00000022476	Polr3h	5031409G22Rik|RPC8	polymerase (RNA) III (DNA directed) polypeptide H	protein-coding
mm_145437.1	chr18	59062345	59062376	+	1	NA	promoter-TSS (NR_033765)	promoter-TSS (NR_033765)	-21	NR_033764	225583	Mm.209711	NM_173759	ENSMUSG00000050875	A730017C20Rik	-	RIKEN cDNA A730017C20 gene	protein-coding
mm_112329.1	chr12	115862315	115862353	-	1	NA	Intergenic	Intergenic	-166540	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
mm_60578.1	chr7	44482279	44482289	+	1	NA	Intergenic	B1_Mur4|SINE|Alu	-2233	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_140708.1	chr17	14909505	14909524	-	1	NA	intron (NM_175173, intron 16 of 24)	MT2A|LTR|ERVL	33610	NM_175173	71682	Mm.122698	NM_175173	ENSMUSG00000046991	Wdr27	0610012K18Rik	WD repeat domain 27	protein-coding
mm_8978.1	chr1	165627658	165627661	-	1	NA	intron (NM_001347128, intron 1 of 2)	L1M4|LINE|L1	6882	NM_001001880	68481	Mm.46438	NM_001001880	ENSMUSG00000026566	Mpzl1	1110007A10Rik|PZR	myelin protein zero-like 1	protein-coding
mm_41130.1	chr5	87788545	87788561	+	1	NA	3' UTR (NM_001304768, exon 13 of 13)	3' UTR (NM_001304768, exon 13 of 13)	14103	NM_007785	12993	Mm.4908	NM_007785	ENSMUSG00000061937	Csn1s2a	Csng|PP22	casein alpha s2-like A	protein-coding
mm_2440.1	chr1	98131445	98131458	+	1	NA	promoter-TSS (NR_040439)	promoter-TSS (NR_040439)	-16	NR_040439	69030	Mm.402692	NR_040439	ENSMUSG00000100182	1810006J02Rik	-	RIKEN cDNA 1810006J02 gene	ncRNA
mm_163744.1	chr13	119732773	119732774	-	1	NA	intron (NM_175538, intron 1 of 3)	B4A|SINE|B4	23109	NM_175538	245269	Mm.403943	NM_175538	ENSMUSG00000095930	Nim1k	E130304F04Rik|Nim1	NIM1 serine/threonine protein kinase	protein-coding
mm_150010.1	chr19	29312251	29312263	+	1	NA	3' UTR (NM_008413, exon 25 of 25)	3' UTR (NM_008413, exon 25 of 25)	13061	NM_013754	27356	Mm.306511	NM_013754	ENSMUSG00000050957	Insl6	RIF1	insulin-like 6	protein-coding
mm_27240.1	chr3	36565311	36565315	-	1	NA	3' UTR (NM_009828, exon 8 of 8)	3' UTR (NM_009828, exon 8 of 8)	6683	NM_009828	12428	Mm.4189	NM_009828	ENSMUSG00000027715	Ccna2	AA408589|Ccn-1|Ccn1|Ccna|CycA2|Cyca	cyclin A2	protein-coding
mm_25689.1	chr3	122245777	122245829	+	1	NA	5' UTR (NM_008129, exon 1 of 7)	5' UTR (NM_008129, exon 1 of 7)	246	NM_008129	14630	Mm.292676	NM_008129	ENSMUSG00000028124	Gclm	AI649393|Gcmc|Glclr	glutamate-cysteine ligase, modifier subunit	protein-coding
mm_141836.1	chr17	34637986	34638060	-	1	NA	Intergenic	Intergenic	-6860	NM_019873	56299	Mm.10025	NM_019873	ENSMUSG00000033739	Fkbpl	DIR1|NG7|Ppiase-X|Wisp39	FK506 binding protein-like	protein-coding
mm_118620.1	chr14	21076170	21076222	+	1	NA	promoter-TSS (NM_001243041)	promoter-TSS (NM_001243041)	44	NM_001243041	11534	Mm.188734	NM_134079	ENSMUSG00000039197	Adk	2310026J05Rik|5033405D03Rik|AI255373|AI987814|Ak	adenosine kinase	protein-coding
mm_30717.1	chr4	13096491	13096501	+	1	NA	Intergenic	Intergenic	189659	NM_001171801	208820	Mm.12057	NM_173746	ENSMUSG00000055963	Triqk	C130086A10|Gm11818|OTTMUSG00000004461	triple QxxK/R motif containing	protein-coding
mm_138632.1	chr17	35861242	35861246	+	1	NA	promoter-TSS (NM_134122)	promoter-TSS (NM_134122)	-74	NM_134122	106582	Mm.390992	NM_134122	ENSMUSG00000059791	Nrm	2610307M02Rik|AI429796	nurim (nuclear envelope membrane protein)	protein-coding
mm_61270.1	chr7	66196139	66196177	+	1	NA	Intergenic	Intergenic	86643	NM_001081163	269941	Mm.333916	NM_001081163	ENSMUSG00000032640	Chsy1	mKIAA0990	chondroitin sulfate synthase 1	protein-coding
mm_98400.1	chr11	94328081	94328089	+	1	NA	promoter-TSS (NM_027799)	promoter-TSS (NM_027799)	84	NM_146024	71452	Mm.141054	NM_027799	ENSMUSG00000020864	Ankrd40	1110011C06Rik|5530600A18Rik|Gcap15	ankyrin repeat domain 40	protein-coding
mm_110968.1	chr12	76937814	76937863	-	1	NA	3' UTR (NM_001146176, exon 4 of 4)	3' UTR (NM_001146176, exon 4 of 4)	24410	NM_008558	17187	Mm.268548	NM_008558	ENSMUSG00000059436	Max	AA960152|AI875693|bHLHd4|bHLHd5|bHLHd6|bHLHd7|bHLHd8	Max protein	protein-coding
mm_135930.1	chr16	73913097	73913098	-	1	NA	intron (NM_175549, intron 24 of 27)	intron (NM_175549, intron 24 of 27)	428970	NR_030464	751561		NR_030464	ENSMUSG00000104758	Mir691	Mirn691|mir-691|mmu-mir-691	microRNA 691	ncRNA
mm_100727.1	chr11	3931506	3931544	-	1	NA	5' UTR (NM_001130458, exon 2 of 10)	5' UTR (NM_001130458, exon 2 of 10)	436	NM_001130459	21452	Mm.20948	NM_015749	ENSMUSG00000020432	Tcn2	AW208754|Tcn-2	transcobalamin 2	protein-coding
mm_107633.1	chr12	52079101	52079117	+	1	NA	Intergenic	Intergenic	-18637	NM_029760	76826	Mm.244781	NM_029760	ENSMUSG00000035142	Nubpl	2410170E07Rik	nucleotide binding protein-like	protein-coding
mm_75264.1	chr8	40634751	40634775	-	1	NA	promoter-TSS (NM_001040699)	promoter-TSS (NM_001040699)	29	NM_001040699	54384	Mm.294871	NM_019433	ENSMUSG00000039431	Mtmr7	-	myotubularin related protein 7	protein-coding
mm_166168.1	chr5	23434579	23434587	+	1	NA	promoter-TSS (NR_040469)	promoter-TSS (NR_040469)	154	NM_026984	69188	Mm.205190	NM_026984	ENSMUSG00000029004	Kmt2e	1810033J14Rik|9530077A04Rik|D230038D11Rik|Mll5|NKp44L	lysine (K)-specific methyltransferase 2E	protein-coding
mm_112949.1	chr13	21023942	21023983	+	1	NA	3' UTR (NM_012054, exon 21 of 21)	3' UTR (NM_012054, exon 21 of 21)	49337	NM_146535	258528	Mm.377554	NM_146535	ENSMUSG00000042869	Olfr1370	MOR256-14	olfactory receptor 1370	protein-coding
mm_127220.1	chr15	99393256	99393279	+	1	NA	promoter-TSS (NM_001171035)	promoter-TSS (NM_001171035)	48	NM_001171035	110213	Mm.16769	NM_026669	ENSMUSG00000023010	Tmbim6	5031406P05Rik|Bi1|Tegt	transmembrane BAX inhibitor motif containing 6	protein-coding
mm_69548.1	chr7	135697599	135697600	-	1	NA	exon (NM_001081117, exon 12 of 14)	exon (NM_001081117, exon 12 of 14)	18780	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_49387.1	chr6	24857970	24858001	+	1	NA	promoter-TSS (NM_028957)	promoter-TSS (NM_028957)	-12	NM_028957	74468	Mm.251601	NM_028957	ENSMUSG00000029678	Hyal5	4933439A12Rik	hyaluronoglucosaminidase 5	protein-coding
mm_144339.1	chr18	14783195	14783221	+	1	NA	promoter-TSS (NM_001100449)	promoter-TSS (NM_001100449)	-37	NM_001100449	72504	Mm.312233	NM_001100449	ENSMUSG00000054321	Taf4b	105kDa|2610524B04Rik|4932409F03Rik|AW987595|TAFII-105|TAFII105|Taf2c2	TATA-box binding protein associated factor 4b	protein-coding
mm_89588.1	chr10	95801212	95801213	+	1	NA	Intergenic	Intergenic	-139451	NM_001001932	216238	Mm.210035	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding
mm_164025.1	chr14	75845157	75845175	-	1	NA	promoter-TSS (NM_009429)	promoter-TSS (NM_009429)	-90	NM_009429	22070	Mm.297482	NM_009429	ENSMUSG00000060126	Tpt1	TCTP|Trt|p21|p23	tumor protein, translationally-controlled 1	protein-coding
mm_38586.1	chr4	141821365	141821466	-	1	NA	exon (NM_007919, exon 5 of 8)	exon (NM_007919, exon 5 of 8)	4590	NM_007919	13706	Mm.45316	NM_007919	ENSMUSG00000058579	Cela2a	Ela-2|Ela2|Ela2a	chymotrypsin-like elastase family, member 2A	protein-coding
mm_38605.1	chr4	141860625	141860653	-	1	NA	exon (NM_025994, exon 3 of 4)	exon (NM_025994, exon 3 of 4)	-14280	NM_001033875	76701	Mm.489680	NM_001033875	ENSMUSG00000062478	Ctrc	1810044E12Rik	chymotrypsin C (caldecrin)	protein-coding
mm_123521.1	chr14	66558510	66558524	-	1	NA	Intergenic	L1M3|LINE|L1	-76734	NM_001271759	11549	Mm.57064	NM_013461	ENSMUSG00000045875	Adra1a	Adra1c	adrenergic receptor, alpha 1a	protein-coding
mm_68969.1	chr7	126584636	126584648	-	1	NA	promoter-TSS (NM_138310)	promoter-TSS (NM_138310)	-366	NM_138310	171504	Mm.170665	NM_138310	ENSMUSG00000042759	Apobr	Apob-48r|Apob48r	apolipoprotein B receptor	protein-coding
mm_57684.1	chr6	128512232	128512242	-	1	NA	exon (NM_007376, exon 12 of 36)	exon (NM_007376, exon 12 of 36)	14483	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_58660.1	chr7	6717832	6717860	+	1	NA	exon (NM_008817, exon 4 of 9)	exon (NM_008817, exon 4 of 9)	11086	NR_023846	100169889	Mm.491213	NR_023846		Peg3os	Apeg3|Peg3as	Peg3 opposite strand	ncRNA
mm_163283.1	chr11	116657152	116657152	+	1	NA	promoter-TSS (NM_001163318)	promoter-TSS (NM_001163318)	44	NM_001163318	100038570	Mm.390349	NM_001163318	ENSMUSG00000075410	Prcd	Gm11744|OTTMUSG00000003947	progressive rod cone degeneration protein	protein-coding
mm_52872.1	chr6	122342344	122342371	+	1	NA	Intergenic	Intergenic	-2130	NM_001271579	13619	Mm.6822	NM_007905	ENSMUSG00000040669	Phc1	AW557034|Edr|Edr1|Mph1|Rae-28|rae28	polyhomeotic-like 1 (Drosophila)	protein-coding
mm_147930.1	chr18	65970185	65970201	-	1	NA	promoter-TSS (NM_145493)	promoter-TSS (NM_145493)	-15	NM_145493	225644	Mm.192285	NM_145493	ENSMUSG00000024519	Cplx4	A930004D23Rik|CPXIV|Gm957	complexin 4	protein-coding
mm_38656.1	chr4	143390176	143390198	-	1	NA	Intergenic	GA-rich|Low_complexity|Low_complexity	-4254	NM_031377	83491	Mm.190607	NM_031377	ENSMUSG00000041805	Pramel1	-	preferentially expressed antigen in melanoma-like 1	protein-coding
mm_7247.1	chr1	93635751	93635761	-	1	NA	promoter-TSS (NM_021537)	promoter-TSS (NM_021537)	-29	NM_021537	59041	Mm.28761	NM_021537	ENSMUSG00000026277	Stk25	1500019J11Rik|AU018434|C86992|Ste20-like|Ysk1	serine/threonine kinase 25 (yeast)	protein-coding
mm_8944.1	chr1	164438176	164438195	-	1	NA	TTS (NM_001293313)	TTS (NM_001293313)	20170	NM_009721	11931	Mm.4550	NM_009721	ENSMUSG00000026576	Atp1b1	Atp4b|Atpb|Atpb-1|NKbeta1	ATPase, Na+/K+ transporting, beta 1 polypeptide	protein-coding
mm_58087.1	chr6	137169679	137169706	-	1	NA	promoter-TSS (NM_001164214)	promoter-TSS (NM_001164214)	26	NM_001164214	232441	Mm.46233	NM_181988	ENSMUSG00000030222	Rerg	-	RAS-like, estrogen-regulated, growth-inhibitor	protein-coding
mm_50776.1	chr6	53680979	53680989	+	1	NA	exon (NM_172728, exon 4 of 7)	exon (NM_172728, exon 4 of 7)	107610	NM_172728	231991	Mm.227444	NM_172728	ENSMUSG00000053007	Creb5	9430076C15Rik|CRE-BPa|Crebpa|D430026C09Rik	cAMP responsive element binding protein 5	protein-coding
mm_140921.1	chr17	24205515	24205542	-	1	NA	promoter-TSS (NM_001163849)	promoter-TSS (NM_001163849)	34	NM_001163851	224617	Mm.301585	NM_173186	ENSMUSG00000036473	Tbc1d24	9630033P11|C530046L02Rik|mKIAA1171	TBC1 domain family, member 24	protein-coding
mm_105918.1	chr11	115001643	115001645	-	1	NA	5' UTR (NM_134158, exon 1 of 4)	5' UTR (NM_134158, exon 1 of 4)	236	NM_134158	140497	Mm.2699	NM_134158	ENSMUSG00000044811	Cd300c2	CLM4|Cd300c|Cd300d|DIgR1|Igsf7|Lmir2|MAIR-II	CD300C molecule 2	protein-coding
mm_140288.1	chr17	85395796	85395818	+	1	NA	intron (NM_028576, intron 6 of 10)	intron (NM_028576, intron 6 of 10)	222589	NR_038084	100043902	Mm.150838	NR_015385	ENSMUSG00000093460	Six3os1	D17Mgi26|E130112H22Rik|Rncr1|Six3os	SIX homeobox 3, opposite strand 1	ncRNA
mm_24741.1	chr3	95286739	95286782	+	1	NA	intron (NM_199475, intron 1 of 9)	intron (NM_199475, intron 1 of 9)	3825	NM_199475	75007	Mm.279287	NM_133858	ENSMUSG00000038712	Fam63a	1810005H09Rik|4930504E06Rik|AA562754|AA960384|AW561904|cI-40|mKIAA1390|ni	family with sequence similarity 63, member A	protein-coding
mm_67441.1	chr7	80387872	80387901	-	1	NA	promoter-TSS (NM_010194)	promoter-TSS (NM_010194)	60	NM_010194	14159	Mm.48757	NM_010194	ENSMUSG00000053158	Fes	AI586313|BB137047|FPS|c-fes	feline sarcoma oncogene	protein-coding
mm_20801.1	chr2	144270441	144270486	-	1	NA	promoter-TSS (NM_028984)	promoter-TSS (NM_028984)	109	NM_024225	69178	Mm.273379	NM_024225	ENSMUSG00000027423	Snx5	0910001N05Rik|1810032P22Rik|AU019504|D2Ertd52e	sorting nexin 5	protein-coding
mm_78996.1	chr9	45405936	45406009	+	1	NA	promoter-TSS (NM_007503)	promoter-TSS (NM_007503)	-105	NM_007503	11936	Mm.22742	NM_007503	ENSMUSG00000059412	Fxyd2	Atp1g1	FXYD domain-containing ion transport regulator 2	protein-coding
mm_156308.1	chrX	136838074	136838086	+	1	NA	3' UTR (NM_011123, exon 7 of 7)	3' UTR (NM_011123, exon 7 of 7)	15334	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_28805.1	chr3	96240318	96240338	-	1	NA	promoter-TSS (NM_178212)	promoter-TSS (NM_178212)	6	NM_013549	15267	Mm.5220	NM_013549	ENSMUSG00000064220	Hist2h2aa1	AI448581|H2a-614|H2a-615|Hist2	histone cluster 2, H2aa1	protein-coding
mm_19671.1	chr2	103454229	103454242	-	1	NA	3' UTR (NM_009804, exon 13 of 13)	3' UTR (NM_009804, exon 13 of 13)	30167	NM_010125	13711	Mm.20888	NM_010125	ENSMUSG00000027186	Elf5	ESE-2|ESE-5|ESE-5.	E74-like factor 5	protein-coding
mm_35798.1	chr4	46549254	46549266	-	1	NA	intron (NM_178893, intron 4 of 12)	intron (NM_178893, intron 4 of 12)	-13119	NM_029077	74735	Mm.240252	NM_029077	ENSMUSG00000039853	Trim14	5830400N10Rik|pub	tripartite motif-containing 14	protein-coding
mm_51986.1	chr6	92091437	92091466	+	1	NA	promoter-TSS (NM_011630)	promoter-TSS (NM_011630)	33	NM_011630	22026	Mm.87062	NM_011630	ENSMUSG00000005893	Nr2c2	TAK1|Tr4|mKIAA4145	nuclear receptor subfamily 2, group C, member 2	protein-coding
mm_172508.1	chr7	70193244	70193244	+	1	NA	intron (NR_131145, intron 3 of 3)	intron (NR_131145, intron 3 of 3)	144578	NR_131145	624549	Mm.116344	NR_131144	ENSMUSG00000109097	Gm29683	-	predicted gene, 29683	ncRNA
mm_166661.1	chr6	88578312	88578312	+	1	NA	intron (NM_001278671, intron 5 of 5)	intron (NM_001278671, intron 5 of 5)	49136	NM_001278671	74589	Mm.196226	NM_029013	ENSMUSG00000033182	Kbtbd12	4833415F11Rik|4933428M03Rik|Klhdc6	kelch repeat and BTB (POZ) domain containing 12	protein-coding
mm_49700.1	chr6	34179255	34179285	+	1	NA	Intergenic	Intergenic	-2216	NM_021435	58246	Mm.245527	NM_021435	ENSMUSG00000018999	Slc35b4	4930474D06Rik|AB041549|AW494345	solute carrier family 35, member B4	protein-coding
mm_171987.1	chr5	93643842	93643846	+	1	NA	intron (NM_001164285, intron 1 of 3)	L1Md_T|LINE|L1	27619	NM_001164284	381654	Mm.326591	NM_001164284	ENSMUSG00000070686	C87414	-	expressed sequence C87414	protein-coding
mm_96598.1	chr11	69090990	69091009	+	1	NA	3' UTR (NM_009497, exon 5 of 5)	3' UTR (NM_009497, exon 5 of 5)	2471	NM_009497	22318	Mm.28643	NM_009497	ENSMUSG00000020894	Vamp2	Syb-2|Syb2|sybII	vesicle-associated membrane protein 2	protein-coding
mm_45131.1	chr5	48781200	48781210	-	1	NA	intron (NM_001199244, intron 1 of 7)	Lx9|LINE|L1	108352	NM_030265	80334	Mm.160172	NM_030265	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding
mm_89254.1	chr10	87859256	87859266	+	1	NA	5' UTR (NM_010512, exon 1 of 5)	5' UTR (NM_010512, exon 1 of 5)	209	NM_010512	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_107164.1	chr12	24679781	24679790	+	1	NA	intron (NM_001004455, intron 1 of 4)	intron (NM_001004455, intron 1 of 4)	2010	NM_138686	12879	Mm.52265	NM_138686	ENSMUSG00000062563	Cys1	2900006B19Rik|AV218859|Ccap|ck|cpk	cystin 1	protein-coding
mm_54762.1	chr6	41218551	41218578	-	1	NA	Intergenic	Intergenic	-83708	NM_011646	22074	Mm.383263	NM_011646	ENSMUSG00000054106	Try4	0910001B19Rik|Td	trypsin 4	protein-coding
mm_115981.1	chr13	24272857	24272860	-	1	NA	intron (NM_001311122, intron 2 of 37)	intron (NM_001311122, intron 2 of 37)	7932	NM_001311122	68732	Mm.211047	NM_026825	ENSMUSG00000021338	Carmil1	1110037D04Rik|AI425970|CARMIL|CARML1|D130057M20|Lrrc16|Lrrc16a	capping protein regulator and myosin 1 linker 1	protein-coding
mm_111826.1	chr12	107123709	107123720	-	1	NA	Intergenic	Intergenic	-407390	NR_015512	71033	Mm.159404	NR_015512	ENSMUSG00000085820	4933406K04Rik	4930426M03Rik|4930485I22Rik|4933427G14Rik	RIKEN cDNA 4933406K04 gene	ncRNA
mm_65956.1	chr7	30428569	30428584	-	1	NA	3' UTR (NM_172142, exon 11 of 11)	3' UTR (NM_172142, exon 11 of 11)	5272	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_20246.1	chr2	126499715	126499725	-	1	NA	Intergenic	Intergenic	-8167	NM_001080944	241633	Mm.222235	NM_001080944	ENSMUSG00000060131	Atp8b4	A530043E15|Im	ATPase, class I, type 8B, member 4	protein-coding
mm_130796.1	chr15	101690509	101690514	-	1	NA	exon (NM_008476, exon 9 of 9)	exon (NM_008476, exon 9 of 9)	3794	NM_008476	16687	Mm.302399	NM_008476	ENSMUSG00000058354	Krt6a	2310016L08Rik|Krt2-6a|Krt2-6c|MK6a|mK6[a]	keratin 6A	protein-coding
mm_11890.1	chr2	49744498	49744566	+	1	NA	intron (NM_008449, intron 20 of 25)	intron (NM_008449, intron 20 of 25)	-43154	NM_027990	71897	Mm.41381	NM_027990	ENSMUSG00000026765	Lypd6b	2310010M24Rik|AW049525	LY6/PLAUR domain containing 6B	protein-coding
mm_148200.1	chr18	79109865	79109881	-	1	NA	promoter-TSS (NM_053099)	promoter-TSS (NM_053099)	-482	NM_053099	240427	Mm.312871	NM_053099	ENSMUSG00000024548	Setbp1	C130092E12|Seb|mKIAA0437	SET binding protein 1	protein-coding
mm_44004.1	chr5	146948730	146948748	+	1	NA	promoter-TSS (NM_025652)	promoter-TSS (NM_025652)	82	NM_025652	66596	Mm.196528	NM_025652	ENSMUSG00000016503	Gtf3a	2010015D03Rik|2610111I01Rik|5330403M05Rik	general transcription factor III A	protein-coding
mm_36520.1	chr4	84546457	84546472	-	1	NA	intron (NM_172870, intron 2 of 5)	intron (NM_172870, intron 2 of 5)	128622	NM_172870	242509	Mm.190774	NM_172870	ENSMUSG00000028487	Bnc2	5031434M05Rik|8430420F16Rik	basonuclin 2	protein-coding
mm_146489.1	chr18	90523532	90523539	+	1	NA	exon (NM_198295, exon 7 of 16)	exon (NM_198295, exon 7 of 16)	13381	NM_198295	67988	Mm.268041	NM_198295	ENSMUSG00000024614	Tmx3	6430411B10Rik|A730024F05Rik|AV259382|Txndc10|mKIAA1830	thioredoxin-related transmembrane protein 3	protein-coding
mm_97913.1	chr11	83525778	83525788	+	1	NA	TTS (NM_013653)	TTS (NM_013653)	-3684	NM_001045543	629303	Mm.390417	NM_001045543	ENSMUSG00000018925	Heatr9	Gm11435|OTTMUSG00000000990	HEAT repeat containing 9	protein-coding
mm_74595.1	chr8	11635027	11635048	-	1	NA	promoter-TSS (NR_030781)	promoter-TSS (NR_030781)	-1	NR_030781	102334	Mm.12459	NM_133971	ENSMUSG00000031508	Ankrd10	4833425P12Rik|AW549277	ankyrin repeat domain 10	protein-coding
mm_24777.1	chr3	95538709	95538738	+	1	NA	exon (NM_021281, exon 3 of 8)	exon (NM_021281, exon 3 of 8)	11937	NM_001267695	13040	Mm.3619	NM_021281	ENSMUSG00000038642	Ctss	Cats	cathepsin S	protein-coding
mm_85183.1	chr9	96637255	96637270	-	1	NA	Intergenic	Intergenic	-5759	NM_053268	114713	Mm.124502	NM_053268	ENSMUSG00000032413	Rasa2	5430433H21Rik|AA517451|AU023900|GAP1m	RAS p21 protein activator 2	protein-coding
mm_71034.1	chr8	33653490	33653548	+	1	NA	5' UTR (NM_010344, exon 1 of 13)	5' UTR (NM_010344, exon 1 of 13)	281	NM_010344	14782	Mm.283573	NM_010344	ENSMUSG00000031584	Gsr	AI325518|D8Ertd238e|Gr-1|Gr1	glutathione reductase	protein-coding
mm_144842.1	chr18	36560661	36560674	+	1	NA	promoter-TSS (NM_175375)	promoter-TSS (NM_175375)	64	NM_175375	108857	Mm.482287	NM_175375	ENSMUSG00000024483	Ankhd1	1110004O12Rik|4933432B13Rik|9130019P20Rik|A530027J04Rik|A630021B20Rik|AA571404|Mask|mFLJ00246|mKIAA1085	ankyrin repeat and KH domain containing 1	protein-coding
mm_129287.1	chr15	77163096	77163114	-	1	NA	intron (NM_053104, intron 2 of 13)	intron (NM_053104, intron 2 of 13)	-9293	NM_001286418	93686	Mm.202774	NM_053104	ENSMUSG00000033565	Rbfox2	Fbm2|Fxh|Hrnbp2|Rbm9	RNA binding protein, fox-1 homolog (C. elegans) 2	protein-coding
mm_125478.1	chr15	54571359	54571439	+	1	NA	promoter-TSS (NM_178920)	promoter-TSS (NM_178920)	33	NM_178920	105853	Mm.410994	NM_178920	ENSMUSG00000024479	Mal2	AI461653	mal, T cell differentiation protein 2	protein-coding
mm_84367.1	chr9	64811091	64811107	-	1	NA	promoter-TSS (NM_001162917)	promoter-TSS (NM_001162917)	88	NM_001162917	102442	Mm.222473	NM_176935	ENSMUSG00000053641	Dennd4a	AI115600|AI851943|F730015K02Rik	DENN/MADD domain containing 4A	protein-coding
mm_41727.1	chr5	102481646	102481657	+	1	NA	5' UTR (NM_029270, exon 1 of 10)	5' UTR (NM_029270, exon 1 of 10)	260	NM_029270	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding
mm_99051.1	chr11	99048080	99048116	+	1	NA	intron (NM_010517, intron 1 of 3)	intron (NM_010517, intron 1 of 3)	6838	NM_010517	16010	Mm.233799	NM_010517	ENSMUSG00000017493	Igfbp4	AI875747|Deb2|IGFBP-4	insulin-like growth factor binding protein 4	protein-coding
mm_106444.1	chr11	119836912	119836953	-	1	NA	intron (NM_028898, intron 13 of 33)	intron (NM_028898, intron 13 of 33)	-2567	NR_045312	319454	Mm.442144	NR_045312	ENSMUSG00000085081	Rptoros	A430071A18Rik	regulatory associated protein of MTOR, complex 1, opposite strand	ncRNA
mm_125228.1	chr15	34133506	34133554	+	1	NA	intron (NM_026002, intron 8 of 11)	RMER1A|Other|Other	50811	NM_026002	67154	Mm.130883	NM_026002	ENSMUSG00000022255	Mtdh	2610103J23Rik|3D3|3D3/Lyric|AEG-1|AV353288|D8Bwg1112e|Lyric	metadherin	protein-coding
mm_12800.1	chr2	79707917	79707927	+	1	NA	non-coding (NR_110980, exon 1 of 3)	non-coding (NR_110980, exon 1 of 3)	142	NM_001290743	75276	Mm.257373	NM_172420	ENSMUSG00000034683	Ppp1r1c	4930565M23Rik|4930579P15Rik	protein phosphatase 1, regulatory (inhibitor) subunit 1C	protein-coding
mm_117307.1	chr13	67421403	67421454	-	1	NA	promoter-TSS (NM_177811)	promoter-TSS (NM_177811)	-10	NM_177811	328274	Mm.222470	NM_177811	ENSMUSG00000055560	Zfp459	9930025G17Rik|Rslcan-14	zinc finger protein 459	protein-coding
mm_79345.1	chr9	53537022	53537074	+	1	NA	promoter-TSS (NM_001081152)	promoter-TSS (NM_001081152)	1	NM_001081152	244879	Mm.116713	NM_001081152	ENSMUSG00000033054	Npat	6820401K01|AI427561|BB112559	nuclear protein in the AT region	protein-coding
mm_17101.1	chr2	23524069	23524079	-	1	NA	intron (NM_001165998, intron 7 of 10)	Lx9|LINE|L1	48030	NM_029773	76857	Mm.276415	NM_029773	ENSMUSG00000026771	Spopl	4921517N04Rik|AU014935|BB233739|E430033K04Rik	speckle-type POZ protein-like	protein-coding
mm_99557.1	chr11	103649570	103649574	+	1	NA	promoter-TSS (NM_001033212)	promoter-TSS (NM_001033212)	63	NM_001033212	104582	Mm.44618	NM_001033212	ENSMUSG00000046215	Rprml	AW049332	reprimo-like	protein-coding
mm_129844.1	chr15	83158903	83158930	-	1	NA	exon (NM_029787, exon 8 of 9)	exon (NM_029787, exon 8 of 9)	9271	NR_004432	104307	Mm.471434	NR_004432	ENSMUSG00000065176	Rnu12	-	RNA U12, small nuclear	snRNA
mm_78541.1	chr9	35305217	35305239	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	24123	NR_040715	71133	Mm.158577	NR_040715	ENSMUSG00000111746	4933422A05Rik	-	RIKEN cDNA 4933422A05 gene	ncRNA
mm_30821.1	chr4	21869695	21869699	+	1	NA	intron (NM_025669, intron 8 of 11)	intron (NM_025669, intron 8 of 11)	-9978	NM_172687	230027	Mm.5662	NM_172687	ENSMUSG00000028247	Coq3	4732433J24|C77934	coenzyme Q3 methyltransferase	protein-coding
mm_24852.1	chr3	95819320	95819322	+	1	NA	promoter-TSS (NM_001081293)	promoter-TSS (NM_001081293)	-368	NM_001081293	75137	Mm.196275	NM_028328	ENSMUSG00000028106	Rprd2	2810036A19Rik|4930535B03Rik|6720469I21Rik|AL022841|AL022940|AU021304|BB077382|mKIAA0460	regulation of nuclear pre-mRNA domain containing 2	protein-coding
mm_96189.1	chr11	61855131	61855141	+	1	NA	promoter-TSS (NM_013881)	promoter-TSS (NM_013881)	-44	NM_013881	29869	Mm.162025	NM_013881	ENSMUSG00000004798	Ulk2	A830085I22Rik|AU015340|Unc51.2|mKIAA0623	unc-51 like kinase 2	protein-coding
mm_32498.1	chr4	108458802	108458838	+	1	NA	promoter-TSS (NM_175472)	promoter-TSS (NM_175472)	-606	NM_175472	230594	Mm.25181	NM_175472	ENSMUSG00000034610	Zcchc11	6030404K05Rik|9230115F04Rik|PPAPD3|mKIAA0191	zinc finger, CCHC domain containing 11	protein-coding
mm_147080.1	chr18	35627139	35627200	-	1	NA	promoter-TSS (NM_011397)	promoter-TSS (NM_011397)	58	NM_011397	20522	Mm.22702	NM_011397	ENSMUSG00000024354	Slc23a1	D18Ucla2|SVCT1|Slc23a2|YSPL3	solute carrier family 23 (nucleobase transporters), member 1	protein-coding
mm_14412.1	chr2	130371347	130371349	+	1	NA	TTS (NM_001110513)	TTS (NM_001110513)	26281	NM_019696	56264	Mm.112701	NM_019696	ENSMUSG00000027408	Cpxm1	AA986902|Cpx-1|Cpx1|Cpxm	carboxypeptidase X 1 (M14 family)	protein-coding
mm_134772.1	chr16	23609788	23609826	-	1	NA	promoter-TSS (NM_023386)	promoter-TSS (NM_023386)	-112	NM_023386	67775	Mm.475107	NM_023386	ENSMUSG00000033355	Rtp4	5830458K16Rik|Ifrg28	receptor transporter protein 4	protein-coding
mm_169961.1	chr16	94359352	94359372	-	1	NA	intron (NM_001159620, intron 3 of 3)	intron (NM_001159620, intron 3 of 3)	10968	NM_001159619	56176	Mm.474449	NM_019543	ENSMUSG00000022940	Pigp	Dcrc|Dscr5	phosphatidylinositol glycan anchor biosynthesis, class P	protein-coding
mm_136787.1	chr17	10840362	10840405	+	1	NA	promoter-TSS (NM_016694)	promoter-TSS (NM_016694)	24	NM_016694	50873	Mm.311110	NM_016694	ENSMUSG00000023826	Park2	PRKN	Parkinson disease (autosomal recessive, juvenile) 2, parkin	protein-coding
mm_99594.1	chr11	104321344	104321359	+	1	NA	exon (NM_010838, exon 8 of 10)	exon (NM_010838, exon 8 of 10)	89915	NM_001285454	17762	Mm.1287	NM_010838	ENSMUSG00000018411	Mapt	AI413597|AW045860|Mtapt|Tau	microtubule-associated protein tau	protein-coding
mm_142345.1	chr17	43612028	43612056	-	1	NA	3' UTR (NM_013737, exon 12 of 12)	3' UTR (NM_013737, exon 12 of 12)	18257	NM_001161366	210510	Mm.329058	NM_198418	ENSMUSG00000040140	Tdrd6	AB097085|Tdr2	tudor domain containing 6	protein-coding
mm_97077.1	chr11	73009681	73009691	+	1	NA	intron (NM_008771, intron 6 of 11)	intron (NM_008771, intron 6 of 11)	-9322	NM_018883	55984	Mm.9998	NM_018883	ENSMUSG00000020785	Camkk1	AI846603|CaMKKalpha|Camkk	calcium/calmodulin-dependent protein kinase kinase 1, alpha	protein-coding
mm_78371.1	chr9	27317353	27317383	+	1	NA	exon (NM_001129787, exon 4 of 18)	exon (NM_001129787, exon 4 of 18)	18140	NM_001129787	235086	Mm.48719	NM_001033323	ENSMUSG00000034275	Igsf9b	AI414108|AI854107|Gm508|mKIAA1030	immunoglobulin superfamily, member 9B	protein-coding
mm_83562.1	chr9	46257693	46257705	-	1	NA	Intergenic	Intergenic	-10909	NM_080434	66113	Mm.29738	NM_080434	ENSMUSG00000032079	Apoa5	1300007O05Rik|Apoav|RAP3	apolipoprotein A-V	protein-coding
mm_40799.1	chr5	67613204	67613223	+	1	NA	3' UTR (NM_001033415, exon 2 of 2)	3' UTR (NM_001033415, exon 2 of 2)	5330	NM_001033415	330096	Mm.442747	NM_001033415	ENSMUSG00000050010	Shisa3	D830007B15Rik	shisa family member 3	protein-coding
mm_107780.1	chr12	61523861	61523880	+	1	NA	5' UTR (NM_001310586, exon 1 of 6)	5' UTR (NM_001310586, exon 1 of 6)	703	NM_001310586	238205	Mm.28802	NM_178714	ENSMUSG00000035653	Lrfn5	AI427653|AI604817|C130061B21|mKIAA4208	leucine rich repeat and fibronectin type III domain containing 5	protein-coding
mm_77352.1	chr8	119585822	119585851	-	1	NA	intron (NM_026648, intron 5 of 11)	RLTR1B-int|LTR|ERV1	10601	NM_026648	68270	Mm.41977	NM_026648	ENSMUSG00000031831	Dnaaf1	4930457P18Rik|Lrrc50	dynein, axonemal assembly factor 1	protein-coding
mm_130390.1	chr15	97884927	97884945	-	1	NA	exon (NM_009504, exon 3 of 10)	exon (NM_009504, exon 3 of 10)	23360	NM_009504	22337	Mm.245084	NM_009504	ENSMUSG00000022479	Vdr	Nr1i1	vitamin D receptor	protein-coding
mm_118112.1	chr13	103921532	103921687	-	1	NA	Intergenic	CpG	-1023	NM_001005868	59079	Mm.277354	NM_021563	ENSMUSG00000021709	Erbin	1700028E05Rik|Erbb2ip|mKIAA1225	Erbb2 interacting protein	protein-coding
mm_60068.1	chr7	31302667	31302703	+	1	NA	promoter-TSS (NM_207262)	promoter-TSS (NM_207262)	-84	NM_207262	381970	Mm.333771	NM_207262	ENSMUSG00000036521	Scgb2b2	Abpbg2|Abpe|lacrimal	secretoglobin, family 2B, member 2	protein-coding
mm_122781.1	chr14	54410191	54410218	-	1	NA	promoter-TSS (NM_001253680)	promoter-TSS (NM_001253680)	-732	NM_001253680	20540	Mm.142455	NM_011405	ENSMUSG00000000958	Slc7a7	AI790233|my+lat1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 7	protein-coding
mm_31900.1	chr4	83525618	83525629	+	1	NA	promoter-TSS (NM_001081012)	promoter-TSS (NM_001081012)	78	NM_001081012	320226	Mm.180032	NM_029117	ENSMUSG00000052407	Ccdc171	4930418J05Rik|4930473A06Rik|A330015D16Rik	coiled-coil domain containing 171	protein-coding
mm_17376.1	chr2	26964278	26964363	-	1	NA	promoter-TSS (NM_207234)	promoter-TSS (NM_207234)	66	NM_207234	227656	Mm.291874	NM_207234	ENSMUSG00000052406	Rexo4	Gm111|Rex4|Xpmc2h	REX4, 3'-5' exonuclease	protein-coding
mm_38009.1	chr4	133751619	133751629	-	1	NA	intron (NM_001080819, intron 1 of 19)	intron (NM_001080819, intron 1 of 19)	1987	NM_001080819	93760	Mm.22478	NM_001080819	ENSMUSG00000007880	Arid1a	1110030E03Rik|BAF250a|Osa1|Smarcf1	AT rich interactive domain 1A (SWI-like)	protein-coding
mm_29886.1	chr3	131233907	131233920	-	1	NA	3' UTR (NM_008212, exon 8 of 8)	3' UTR (NM_008212, exon 8 of 8)	38188	NM_008212	15107	Mm.260164	NM_008212	ENSMUSG00000027984	Hadh	AA409008|AU019341|AW742602|HCDH|Hadhsc|Schad	hydroxyacyl-Coenzyme A dehydrogenase	protein-coding
mm_89080.1	chr10	83360207	83360264	+	1	NA	promoter-TSS (NM_026579)	promoter-TSS (NM_026579)	14	NM_026579	28109	Mm.196210	NM_026579	ENSMUSG00000020255	D10Wsu102e	AI747614|C430041I18Rik	DNA segment, Chr 10, Wayne State University 102, expressed	protein-coding
mm_108309.1	chr12	79490144	79490154	+	1	NA	intron (NM_009014, intron 7 of 10)	intron (NM_009014, intron 7 of 10)	192798	NM_001252562	19363	Mm.341756	NM_009014	ENSMUSG00000059060	Rad51b	AI553500|R51H2|Rad51l1|mREC2	RAD51 paralog B	protein-coding
mm_161636.1	chr16	90260273	90260273	-	1	NA	exon (NM_001346799, exon 4 of 20)	exon (NM_001346799, exon 4 of 20)	24230	NM_178923	224432	Mm.439811	NM_178923	ENSMUSG00000022983	Scaf4	AA517739|Sfrs15|Sra4|Srsf15	SR-related CTD-associated factor 4	protein-coding
mm_162135.1	chrX	73265389	73265389	-	1	NA	promoter-TSS (NM_011727)	promoter-TSS (NM_011727)	1	NM_011727	22446	Mm.336117	NM_011727	ENSMUSG00000058147	Xlr3c	Xlr3b	X-linked lymphocyte-regulated 3C	protein-coding
mm_126677.1	chr15	84669646	84669647	+	1	NA	intron (NM_001346662, intron 1 of 8)	intron (NM_001346662, intron 1 of 8)	6440	NM_001346662	109270	Mm.291372	NM_146061	ENSMUSG00000036106	Prr5	AU043908|Arhgap8|C030017C09Rik|C78947|Protor-1|Protor1	proline rich 5 (renal)	protein-coding
mm_10830.1	chr2	24386534	24386542	+	1	NA	intron (NM_177611, intron 1 of 16)	intron (NM_177611, intron 1 of 16)	1141	NM_177611	215632	Mm.490434	NM_177611	ENSMUSG00000026979	Psd4	BC046518|EFA6B	pleckstrin and Sec7 domain containing 4	protein-coding
mm_84183.1	chr9	60134818	60134833	-	1	NA	intron (NM_001040426, intron 7 of 17)	L1M5|LINE|L1	6395	NM_172444	207596	Mm.28791	NM_172444	ENSMUSG00000032289	Thsd4	ADAMTSL-6|ADAMTSL6|AI585901|Adamtsl4|B230114P05Rik	thrombospondin, type I, domain containing 4	protein-coding
mm_124479.1	chr14	121505248	121505264	-	1	NA	promoter-TSS (NM_053079)	promoter-TSS (NM_053079)	-2	NM_053079	56643	Mm.155618	NM_053079	ENSMUSG00000025557	Slc15a1	D630032F02|PECT1|PEPT1	solute carrier family 15 (oligopeptide transporter), member 1	protein-coding
mm_111423.1	chr12	91589982	91589992	-	1	NA	promoter-TSS (NM_031391)	promoter-TSS (NM_031391)	-338	NM_031391	83602	Mm.275728	NM_031391	ENSMUSG00000020962	Gtf2a1	6330549H03Rik|AA536742|AA959775|AW060250|TfIIAa/b|Tfiia1	general transcription factor II A, 1	protein-coding
mm_167535.1	chr9	21291745	21291761	+	1	NA	promoter-TSS (NM_009878)	promoter-TSS (NM_009878)	-544	NM_009878	12581	Mm.29020	NM_009878	ENSMUSG00000096472	Cdkn2d	INK4d|p19|p19INK4d	cyclin-dependent kinase inhibitor 2D (p19, inhibits CDK4)	protein-coding
mm_158655.1	chrX	155624136	155624146	-	1	NA	promoter-TSS (NM_001093750)	promoter-TSS (NM_001093750)	-814	NM_001093750	211612	Mm.218811	NM_001093750	ENSMUSG00000041552	Ptchd1	9630036J22Rik|AI848149|Gm387	patched domain containing 1	protein-coding
mm_146832.1	chr18	22171393	22171423	-	1	NA	promoter-TSS (NM_027616)	promoter-TSS (NM_027616)	-12	NM_027616	70950	Mm.235716	NM_027616	ENSMUSG00000024306	Ccdc178	4921528I01Rik	coiled coil domain containing 178	protein-coding
mm_100.1	chr1	9545380	9545388	+	1	NA	promoter-TSS (NM_021511)	promoter-TSS (NM_021511)	-24	NM_021511	59014	Mm.29061	NM_021511	ENSMUSG00000061024	Rrs1	5730466A07Rik|AA415037|D1Ertd701e|Rrr	ribosome biogenesis regulator 1	protein-coding
mm_98115.1	chr11	87113079	87113080	+	1	NA	promoter-TSS (NR_029652)	promoter-TSS (NR_029652)	75	NR_029652	723834		NR_029652	ENSMUSG00000065589	Mir301	Mirn301|mir-301a|mmu-mir-301	microRNA 301	ncRNA
mm_63015.1	chr7	121032474	121032520	+	1	NA	Intergenic	Intergenic	-1948	NM_021554	59052	Mm.29122	NM_021554	ENSMUSG00000030876	Mettl9	0610012D09Rik|AA517660|Drev|MNCb-5680	methyltransferase like 9	protein-coding
mm_157561.1	chrX	52165313	52165335	-	1	NA	promoter-TSS (NM_008150)	promoter-TSS (NM_008150)	-401	NM_008150	14735	Mm.1528	NM_008150	ENSMUSG00000031119	Gpc4	9530073D23Rik|AF311610|AI385680|AI661372|K-glypican	glypican 4	protein-coding
mm_8787.1	chr1	161251503	161251528	-	1	NA	promoter-TSS (NM_007453)	promoter-TSS (NM_007453)	-305	NM_007453	11758	Mm.186185	NM_007453	ENSMUSG00000026701	Prdx6	1-Cys Prx|1-cysPrx|9430088D19Rik|AA690119|Aop2|Brp-12|CP-3|GPx|Ltw-4|Ltw4|Lvtw-4|NSGPx|ORF06|Prdx5|aiPLA2	peroxiredoxin 6	protein-coding
mm_5654.1	chr1	40790643	40790686	-	1	NA	promoter-TSS (NM_172499)	promoter-TSS (NM_172499)	-7	NM_172499	211798	Mm.235443	NM_172499	ENSMUSG00000041945	Mfsd9	4931419K03Rik	major facilitator superfamily domain containing 9	protein-coding
mm_145962.1	chr18	67774985	67775021	+	1	NA	5' UTR (NM_001039088, exon 1 of 9)	5' UTR (NM_001039088, exon 1 of 9)	127	NM_001039088	72124	Mm.307315	NM_028112	ENSMUSG00000079614	Seh1l	2610007A16Rik|AW540070|SEC13L|SEH1A|SEH1B|Seh1	SEH1-like (S. cerevisiae	protein-coding
mm_50018.1	chr6	41115999	41115999	+	1	NA	Intergenic	Intergenic	-80490	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_163962.1	chr14	54966412	54966415	-	1	NA	intron (NM_001164171, intron 1 of 38)	intron (NM_001164171, intron 1 of 38)	194	NM_001164171	17888	Mm.290003	NM_010856	ENSMUSG00000040752	Myh6	A830009F23Rik|AA517445|Myhc-a|Myhca|alpha-MHC	myosin, heavy polypeptide 6, cardiac muscle, alpha	protein-coding
mm_65867.1	chr7	29505448	29505473	-	1	NA	promoter-TSS (NM_001081028)	promoter-TSS (NM_001081028)	0	NM_001081028	74206	Mm.447042	NM_001081028	ENSMUSG00000030583	Sipa1l3	2610511M17Rik	signal-induced proliferation-associated 1 like 3	protein-coding
mm_141378.1	chr17	29078927	29078944	-	1	NA	non-coding (NR_036469, exon 1 of 2)	non-coding (NR_036469, exon 1 of 2)	191	NR_036469	100504267	Mm.438550	NR_036469	ENSMUSG00000085912	Trp53cor1	Gm16197|OTTMUSG00000031656|linc-p21|lincRNA-p21	tumor protein p53 pathway corepressor 1	ncRNA
mm_11545.1	chr2	32657499	32657509	+	1	NA	intron (NM_001146348, intron 1 of 14)	intron (NM_001146348, intron 1 of 14)	10909	NM_001146348	13805	Mm.225297	NM_007932	ENSMUSG00000026814	Eng	AI528660|AI662476|CD105|Endo|S-endoglin	endoglin	protein-coding
mm_152329.1	chr19	9954474	9954491	-	1	NA	Intergenic	Intergenic	-26118	NR_073181	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
mm_148681.1	chr19	5688724	5688770	+	1	NA	promoter-TSS (NM_022012)	promoter-TSS (NM_022012)	161	NM_144868	104401	Mm.329650	NM_144868	ENSMUSG00000054874	Pcnx3	Pcnxl3|mKIAA4073	pecanex homolog 3	protein-coding
mm_78538.1	chr9	35211422	35211454	+	1	NA	promoter-TSS (NM_172291)	promoter-TSS (NM_172291)	235	NM_026130	67398	Mm.284688	NM_026130	ENSMUSG00000032042	Srpr	1300011P19Rik|D11Mgi27|Srpra	signal recognition particle receptor ('docking protein')	protein-coding
mm_171278.1	chr3	88832487	88832487	-	1	NA	promoter-TSS (NR_015498)	promoter-TSS (NR_015498)	0	NR_015498	319830	Mm.400394	NR_015498		1500004A13Rik	5430404N14Rik|BB132176	RIKEN cDNA 1500004A13 gene	ncRNA
mm_112960.1	chr13	21180180	21180245	+	1	NA	5' UTR (NM_009054, exon 1 of 8)	5' UTR (NM_009054, exon 1 of 8)	281	NM_009054	19720	Mm.314056	NM_009054	ENSMUSG00000021326	Trim27	AW538890|Gm19403|Rfp	tripartite motif-containing 27	protein-coding
mm_86056.1	chr9	114564316	114564334	-	1	NA	promoter-TSS (NM_001042503)	promoter-TSS (NM_001042503)	44	NM_001042503	636931	Mm.17857	NM_001042503	ENSMUSG00000079259	Trim71	2610206G21Rik|AL022943|Gm1127|Lin41|lin-41|mLin41|mlin-41	tripartite motif-containing 71	protein-coding
mm_43416.1	chr5	135984159	135984161	+	1	NA	intron (NM_011776, intron 2 of 7)	intron (NM_011776, intron 2 of 7)	4055	NM_011776	22788	Mm.1381	NM_011776	ENSMUSG00000004948	Zp3	Zp-3	zona pellucida glycoprotein 3	protein-coding
mm_133454.1	chr16	88829111	88829135	+	1	NA	exon (NM_013713, exon 1 of 1)	exon (NM_013713, exon 1 of 1)	114	NM_013713	26560	Mm.86430	NM_013713	ENSMUSG00000022931	Krtap15	Krtap15-1|Pmg-2|Pmg2	keratin associated protein 15	protein-coding
mm_55083.1	chr6	49214819	49214827	-	1	NA	5' UTR (NM_023670, exon 1 of 15)	5' UTR (NM_023670, exon 1 of 15)	131	NM_023670	140488	Mm.281018	NM_023670	ENSMUSG00000029814	Igf2bp3	2610101N11Rik|AA522010|AL022933|AU045931|IMP-3|IMP3|Koc13|Neilsen|mimp3	insulin-like growth factor 2 mRNA binding protein 3	protein-coding
mm_125131.1	chr15	30333208	30333214	+	1	NA	intron (NM_008729, intron 2 of 22)	intron (NM_008729, intron 2 of 22)	160618	NM_008729	18163	Mm.321648	NM_008729	ENSMUSG00000022240	Ctnnd2	Catnd2|Nprap|neurojugin	catenin (cadherin associated protein), delta 2	protein-coding
mm_132133.1	chr16	31878869	31878883	+	1	NA	promoter-TSS (NM_013900)	promoter-TSS (NM_013900)	66	NM_013900	30060	Mm.30988	NM_013900	ENSMUSG00000022780	Mfi2	CD228|MTf|Meltf	antigen p97 (melanoma associated) identified by monoclonal antibodies 133.2 and 96.5	protein-coding
mm_83083.1	chr9	40191122	40191125	-	1	NA	Intergenic	Intergenic	-1193	NM_030713	80902	Mm.132196	NM_030713	ENSMUSG00000025602	Zfp202	C130037E22Rik|Znf202	zinc finger protein 202	protein-coding
mm_17444.1	chr2	28524512	28524526	-	1	NA	intron (NM_001145834, intron 1 of 17)	intron (NM_001145834, intron 1 of 17)	-8945	NM_001145835	19730	Mm.5236	NM_009058	ENSMUSG00000026821	Ralgds	Gnds|Rgds|mKIAA1308	ral guanine nucleotide dissociation stimulator	protein-coding
mm_96320.1	chr11	63989794	63989801	+	1	NA	intron (NM_178379, intron 5 of 6)	intron (NM_178379, intron 5 of 6)	25571	NR_131111	78883	Mm.410764	NR_131111	ENSMUSG00000086359	9630013K17Rik	-	RIKEN cDNA 9630013K17 gene	ncRNA
mm_149028.1	chr19	8771038	8771055	+	1	NA	promoter-TSS (NM_025791)	promoter-TSS (NM_025791)	50	NM_025791	66836	Mm.440071	NM_025791	ENSMUSG00000010097	Tmem223	0610006I08Rik	transmembrane protein 223	protein-coding
mm_131725.1	chr16	21794321	21794381	+	1	NA	promoter-TSS (NR_037958)	promoter-TSS (NR_037958)	4	NR_037957	100043489	Mm.326535	NR_037957	ENSMUSG00000097290	1300002E11Rik	1500026P21Rik	RIKEN cDNA 1300002E11 gene	ncRNA
mm_143705.1	chr17	80598448	80598453	-	1	NA	intron (NM_001290345, intron 28 of 33)	RLTR51B_Mm|LTR|ERVK?	-34616	NM_001033443	381113	Mm.329216	NM_001033443	ENSMUSG00000033966	Cdkl4	AU067824|Gm942	cyclin-dependent kinase-like 4	protein-coding
mm_42353.1	chr5	114911583	114911594	+	1	NA	3' UTR (NM_011854, exon 6 of 6)	3' UTR (NM_011854, exon 6 of 6)	-11652	NM_145209	231655	Mm.95479	NM_145209	ENSMUSG00000041827	Oasl1	7530414C13Rik|oasl9	2'-5' oligoadenylate synthetase-like 1	protein-coding
mm_24730.1	chr3	95282998	95283010	+	1	NA	promoter-TSS (NM_133858)	promoter-TSS (NM_133858)	69	NM_199475	75007	Mm.279287	NM_133858	ENSMUSG00000038712	Fam63a	1810005H09Rik|4930504E06Rik|AA562754|AA960384|AW561904|cI-40|mKIAA1390|ni	family with sequence similarity 63, member A	protein-coding
mm_118639.1	chr14	21477288	21477289	+	1	NA	Intergenic	Intergenic	-22482	NM_001205241	54169	Mm.248967	NM_017479	ENSMUSG00000021767	Kat6b	AI507552|B130044K16Rik|MYST-4|Morf|Myst4|mKIAA0383|qkf|querkopf	K(lysine) acetyltransferase 6B	protein-coding
mm_5698.1	chr1	43187276	43187296	-	1	NA	intron (NM_001289533, intron 1 of 5)	intron (NM_001289533, intron 1 of 5)	9475	NM_001289533	14200	Mm.6799	NM_010212	ENSMUSG00000008136	Fhl2	FHL-2|SLIM-3|SLIM3	four and a half LIM domains 2	protein-coding
mm_47037.1	chr5	116021704	116021714	-	1	NA	intron (NM_031869, intron 1 of 6)	intron (NM_031869, intron 1 of 6)	2719	NM_031869	19079	Mm.458152	NM_031869	ENSMUSG00000029513	Prkab1	1300015D22Rik|AU021155|E430008F22	protein kinase, AMP-activated, beta 1 non-catalytic subunit	protein-coding
mm_456.1	chr1	36265423	36265436	+	1	NA	3' UTR (NM_153408, exon 4 of 4)	3' UTR (NM_153408, exon 4 of 4)	7996	NM_153408	214854	Mm.389110	NM_153408	ENSMUSG00000047180	Neurl3	2010300P06Rik|Lincr	neuralized E3 ubiquitin protein ligase 3	protein-coding
mm_134571.1	chr16	20364158	20364169	-	1	NA	intron (NM_013790, intron 22 of 29)	intron (NM_013790, intron 22 of 29)	-38759	NM_183158	224044	Mm.276400	NM_183158	ENSMUSG00000022818	Cyp2ab1	EG224044|F730023N20	cytochrome P450, family 2, subfamily ab, polypeptide 1	protein-coding
mm_68711.1	chr7	119893043	119893043	-	1	NA	intron (NM_001163703, intron 1 of 2)	intron (NM_001163703, intron 1 of 2)	2415	NM_173408	233805	Mm.31539	NM_173408	ENSMUSG00000048787	Dcun1d3	1700020A13Rik|BC030335	DCN1, defective in cullin neddylation 1, domain containing 3 (S. cerevisiae)	protein-coding
mm_8998.1	chr1	165766608	165766638	-	1	NA	intron (NM_011804, intron 1 of 3)	intron (NM_011804, intron 1 of 3)	2843	NM_011804	433375	Mm.294885	NM_011804	ENSMUSG00000040713	Creg1	AA755314|Creg	cellular repressor of E1A-stimulated genes 1	protein-coding
mm_111882.1	chr12	108179211	108179225	-	1	NA	promoter-TSS (NM_009832)	promoter-TSS (NM_009832)	66	NM_028262	52690	Mm.159185	NM_028262	ENSMUSG00000056770	Setd3	2610102I01Rik|2610305M23Rik|6030490B17Rik|D12Ertd771e	SET domain containing 3	protein-coding
mm_3776.1	chr1	156558760	156558806	+	1	NA	promoter-TSS (NM_009595)	promoter-TSS (NM_009595)	-4	NM_009595	11352	Mm.329515	NM_009595	ENSMUSG00000026596	Abl2	AA536808|Abll|Arg	v-abl Abelson murine leukemia viral oncogene 2 (arg, Abelson-related gene)	protein-coding
mm_147221.1	chr18	38150800	38150810	-	1	NA	Intergenic	Intergenic	58957	NM_029357	75599	Mm.36560	NM_029357	ENSMUSG00000051375	Pcdh1	2010005A06Rik|AI585920	protocadherin 1	protein-coding
mm_62888.1	chr7	115110013	115110016	+	1	NA	Intergenic	Intergenic	158740	NR_040319	101786	Mm.395157	NR_040317	ENSMUSG00000108379	A730082K24Rik	AU044236	RIKEN cDNA A730082K24 gene	ncRNA
mm_53434.1	chr6	134079659	134079671	+	1	NA	intron (NM_001303102, intron 2 of 8)	intron (NM_001303102, intron 2 of 8)	43965	NM_007961	14011	Mm.269995	NM_007961	ENSMUSG00000030199	Etv6	AW123102|AW557856|Tel	ets variant 6	protein-coding
mm_106744.1	chr12	3908221	3908229	+	1	NA	3' UTR (NM_153743, exon 18 of 18)	3' UTR (NM_153743, exon 18 of 18)	16481	NM_153743	13435	Mm.5001	NM_007872	ENSMUSG00000020661	Dnmt3a	MmuIIIA	DNA methyltransferase 3A	protein-coding
mm_1818.1	chr1	82339088	82339115	+	1	NA	promoter-TSS (NM_001122685)	promoter-TSS (NM_001122685)	52	NM_001122685	76867	Mm.226994	NM_029777	ENSMUSG00000026142	Rhbdd1	4930418P06Rik|RRP4|mRHBDD1	rhomboid domain containing 1	protein-coding
mm_4777.1	chr1	182957642	182957650	+	1	NA	intron (NM_016928, intron 1 of 3)	intron (NM_016928, intron 1 of 3)	2858	NM_016928	53791	Mm.116894	NM_016928	ENSMUSG00000079164	Tlr5	-	toll-like receptor 5	protein-coding
mm_135302.1	chr16	38705821	38705824	-	1	NA	intron (NM_020260, intron 1 of 11)	intron (NM_020260, intron 1 of 11)	7213	NM_020260	12549	Mm.370848	NM_020260	ENSMUSG00000022799	Arhgap31	5830477L08Rik|AU041750|Cdgap|D330026I07Rik	Rho GTPase activating protein 31	protein-coding
mm_42422.1	chr5	115327202	115327267	+	1	NA	promoter-TSS (NM_025573)	promoter-TSS (NM_025573)	57	NR_036616	108014	Mm.287826	NM_025573	ENSMUSG00000029538	Srsf9	25kDa|2610029M16Rik|SRp30c|Sfrs9	serine/arginine-rich splicing factor 9	protein-coding
mm_99172.1	chr11	100846303	100846317	+	1	NA	intron (NM_001113563, intron 1 of 18)	intron (NM_001113563, intron 1 of 18)	4275	NM_001113563	20851	Mm.34064	NM_011489	ENSMUSG00000020919	Stat5b	-	signal transducer and activator of transcription 5B	protein-coding
mm_118965.1	chr14	27622387	27622412	+	1	NA	promoter-TSS (NM_001347497)	promoter-TSS (NM_001347497)	-8	NM_001347497	238988	Mm.318004	NM_177814	ENSMUSG00000040640	Erc2	6430531D06|CAST|CAST1/ERC2|D14Ertd171e|ELKS2alpha	ELKS/RAB6-interacting/CAST family member 2	protein-coding
mm_55401.1	chr6	60828100	60828111	-	1	NA	intron (NM_009221, intron 1 of 5)	intron (NM_009221, intron 1 of 5)	899	NM_001042451	20617	Mm.17484	NM_009221	ENSMUSG00000025889	Snca	NACP|alphaSYN	synuclein, alpha	protein-coding
mm_147236.1	chr18	38284323	38284328	-	1	NA	promoter-TSS (NM_017378)	promoter-TSS (NM_017378)	76	NM_017378	53601	Mm.12862	NM_017378	ENSMUSG00000024440	Pcdh12	Pcdh14|VE-cad-2	protocadherin 12	protein-coding
mm_126663.1	chr15	84321932	84321968	+	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	-2770	NM_022321	64099	Mm.251356	NM_022321	ENSMUSG00000022439	Parvg	AI413459	parvin, gamma	protein-coding
mm_35139.1	chr4	11386719	11386730	-	1	NA	promoter-TSS (NM_001290383)	promoter-TSS (NM_001290383)	54	NM_001347052	207920	Mm.387719	NM_194055	ENSMUSG00000040728	Esrp1	2210008M09Rik|A630065D16|BC031468|Rbm35a	epithelial splicing regulatory protein 1	protein-coding
mm_17814.1	chr2	33718783	33718783	-	1	NA	Intergenic	Intergenic	77590	NR_046275	100504399	Mm.72070	NM_177842		C130021I20Rik	-	Riken cDNA C130021I20 gene	ncRNA
mm_21513.1	chr2	163626306	163626342	-	1	NA	exon (NM_012032, exon 9 of 10)	exon (NM_012032, exon 9 of 10)	-18526	NR_028113	68386	Mm.410649	NR_028113	ENSMUSG00000058812	0610039K10Rik	-	RIKEN cDNA 0610039K10 gene	ncRNA
mm_8772.1	chr1	161034960	161035004	-	1	NA	promoter-TSS (NM_173424)	promoter-TSS (NM_173424)	-184	NR_002840	14455	Mm.270065	NR_002840	ENSMUSG00000053332	Gas5	Gas-5|Mir5117|Snhg2	growth arrest specific 5	ncRNA
mm_97097.1	chr11	73213392	73213399	+	1	NA	exon (NM_029031, exon 3 of 7)	exon (NM_029031, exon 3 of 7)	13913	NM_029031	74637	Mm.200905	NM_029031	ENSMUSG00000005951	Shpk	4930431K22Rik|AI194947|AW260459|Carkl	sedoheptulokinase	protein-coding
mm_61285.1	chr7	67421331	67421346	+	1	NA	Intergenic	Intergenic	-48480	NM_001291195	17258	Mm.132788	NM_001033713	ENSMUSG00000030557	Mef2a	A430079H05Rik	myocyte enhancer factor 2A	protein-coding
mm_68895.1	chr7	126448822	126448830	-	1	NA	exon (NM_007504, exon 15 of 23)	exon (NM_007504, exon 15 of 23)	14247	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_60011.1	chr7	30731175	30731177	+	1	NA	intron (NM_008085, intron 9 of 10)	B1_Mur2|SINE|Alu	-1642	NM_027215	69804	Mm.27499	NM_027215	ENSMUSG00000006315	Tmem147	2010004E11Rik|5033425B17Rik|Nifie14	transmembrane protein 147	protein-coding
mm_113633.1	chr13	42051749	42051773	+	1	NA	promoter-TSS (NM_007772)	promoter-TSS (NM_007772)	-260	NM_007772	110521	Mm.4808	NM_007772	ENSMUSG00000021366	Hivep1	Cryabp1	human immunodeficiency virus type I enhancer binding protein 1	protein-coding
mm_134820.1	chr16	25960248	25960258	-	1	NA	TTS (NM_173379)	TTS (NM_173379)	145531	NM_173379	210530	Mm.326869	NM_173379	ENSMUSG00000038168	P3h2	4832416N06|AW553532|Leprel1|Mlat4	prolyl 3-hydroxylase 2	protein-coding
mm_33982.1	chr4	137717331	137717355	+	1	NA	intron (NM_001256218, intron 10 of 24)	intron (NM_001256218, intron 10 of 24)	-7118	NR_138592	110351	Mm.180763	NM_029563	ENSMUSG00000041351	Rap1gap	1300019I11Rik|2310004O14Rik|AI427470|ARPP-90|Gap|Rap1GAP1|Rap1ga1	Rap1 GTPase-activating protein	protein-coding
mm_161986.1	chr19	29422193	29422193	+	1	NA	intron (NM_021396, intron 1 of 5)	intron (NM_021396, intron 1 of 5)	11274	NM_021396	58205	Mm.116737	NM_021396	ENSMUSG00000016498	Pdcd1lg2	B7-DC|Btdc|F730015O22Rik|PD-L2	programmed cell death 1 ligand 2	protein-coding
mm_91909.1	chr10	60277461	60277492	-	1	NA	promoter-TSS (NM_011179)	promoter-TSS (NM_011179)	-152	NM_001146123	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_95650.1	chr11	53724498	53724508	+	1	NA	3' UTR (NM_010558, exon 4 of 4)	3' UTR (NM_010558, exon 4 of 4)	3709	NM_010558	16191	Mm.4461	NM_010558	ENSMUSG00000036117	Il5	Il-5	interleukin 5	protein-coding
mm_63861.1	chr7	135683990	135684006	+	1	NA	3' UTR (NM_011212, exon 21 of 21)	3' UTR (NM_011212, exon 21 of 21)	-31684	NR_015548	67765	Mm.445272	NR_015548	ENSMUSG00000097471	5830432E09Rik	-	RIKEN cDNA 5830432E09 gene	ncRNA
mm_119303.1	chr14	34746837	34746841	+	1	NA	3' UTR (NM_001301330, exon 19 of 19)	3' UTR (NM_001301330, exon 19 of 19)	72911	NM_001301330	218914	Mm.27957	NM_001004436	ENSMUSG00000041408	Wapl	A530089A20Rik|BC037674|DIF-2|FOE|Wapal	WAPL cohesin release factor	protein-coding
mm_118811.1	chr14	25460465	25460491	+	1	NA	intron (NM_001310666, intron 1 of 23)	CpG	1293	NM_183208	328365	Mm.227484	NM_183208	ENSMUSG00000007817	Zmiz1	BC065120|E330020C23|ENSMUSG00000072684|Gm10397|I920194n01|Rai17|Zimp10	zinc finger, MIZ-type containing 1	protein-coding
mm_92369.1	chr10	76028065	76028091	-	1	NA	Intergenic	RMER10A|LTR|ERVL	-4534	NM_177475	64453	Mm.80609	NM_177475	ENSMUSG00000049764	Zfp280b	D10Jhu82e|Suhw2	zinc finger protein 280B	protein-coding
mm_86592.1	chr10	13129576	13129584	+	1	NA	3' UTR (NM_009538, exon 6 of 6)	3' UTR (NM_009538, exon 6 of 6)	38735	NR_131912	338438		NR_131912		Hymai	-	hydatidiform mole associated and imprinted transcript	ncRNA
mm_81323.1	chr9	108490687	108490692	+	1	NA	promoter-TSS (NM_001168373)	promoter-TSS (NM_001168373)	13	NM_027804	71472	Mm.289706	NM_027804	ENSMUSG00000006676	Usp19	8430421I07Rik|AI047774|Zmynd9	ubiquitin specific peptidase 19	protein-coding
mm_74219.1	chr8	124021453	124021515	+	1	NA	promoter-TSS (NM_133966)	promoter-TSS (NM_133966)	-175	NM_133966	102162	Mm.291777	NM_133966	ENSMUSG00000038697	Taf5l	1110005N04Rik|AI849020	TATA-box binding protein associated factor 5 like	protein-coding
mm_57748.1	chr6	129097702	129097714	-	1	NA	intron (NM_153506, intron 2 of 4)	B1_Mus1|SINE|Alu	3195	NM_153506	232409	Mm.30870	NM_153506	ENSMUSG00000030155	Clec2e	Clra|clr-a	C-type lectin domain family 2, member e	protein-coding
mm_109027.1	chr12	103950791	103950837	+	1	NA	exon (NM_009247, exon 2 of 5)	exon (NM_009247, exon 2 of 5)	6083	NM_009247	20704	Mm.312593	NM_009247	ENSMUSG00000072849	Serpina1e	Dom5|PI5|Spi1-5	serine (or cysteine) peptidase inhibitor, clade A, member 1E	protein-coding
mm_127314.1	chr15	100251709	100251724	+	1	NA	intron (NM_007497, intron 3 of 6)	intron (NM_007497, intron 3 of 6)	23857	NM_007497	11908	Mm.676	NM_007497	ENSMUSG00000023027	Atf1	-	activating transcription factor 1	protein-coding
mm_82772.1	chr9	26977854	26977861	-	1	NA	intron (NM_025862, intron 9 of 10)	intron (NM_025862, intron 9 of 10)	21692	NM_025862	66948	Mm.289244	NM_025862	ENSMUSG00000031969	Acad8	2310016C19Rik|AI786953	acyl-Coenzyme A dehydrogenase family, member 8	protein-coding
mm_162402.1	chr1	85330435	85330435	+	1	NA	Intergenic	Intergenic	-59869	NM_001037909	620078	Mm.386456	NM_175219	ENSMUSG00000052477	C130026I21Rik	4930565N07Rik|OTTMUSG00000029174	RIKEN cDNA C130026I21 gene	protein-coding
mm_3578.1	chr1	151132944	151132964	+	1	NA	Intergenic	RLTR20A1|LTR|ERVK	-5080	NR_038011	402734	Mm.337666	NR_038011		C730036E19Rik	lncLSTR	RIKEN cDNA C730036E19 gene	ncRNA
mm_104145.1	chr11	87045846	87045860	-	1	NA	exon (NM_025638, exon 5 of 10)	exon (NM_025638, exon 5 of 10)	28284	NM_025638	66569	Mm.281887	NM_025638	ENSMUSG00000061666	Gdpd1	2610020H15Rik	glycerophosphodiester phosphodiesterase domain containing 1	protein-coding
mm_54033.1	chr6	12726181	12726199	-	1	NA	intron (NM_001164805, intron 1 of 26)	intron (NM_001164805, intron 1 of 26)	23063	NM_001164805	330267	Mm.11989	NM_001164805	ENSMUSG00000032625	Thsd7a	Gm837	thrombospondin, type I, domain containing 7A	protein-coding
mm_19643.1	chr2	102861605	102861626	-	1	NA	exon (NM_009851, exon 3 of 19)	exon (NM_009851, exon 3 of 19)	40050	NM_001177785	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_52818.1	chr6	121346713	121346731	+	1	NA	promoter-TSS (NM_133661)	promoter-TSS (NM_133661)	25	NM_133661	14411	Mm.274506	NM_133661	ENSMUSG00000030109	Slc6a12	BGT1|GAT-2|GAT2|Gabt2	solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12	protein-coding
mm_38049.1	chr4	133980565	133980578	-	1	NA	intron (NM_026144, intron 7 of 8)	B1_Mur1|SINE|Alu	-12580	NM_016957	15331	Mm.319660	NM_016957	ENSMUSG00000003038	Hmgn2	HMG-17|Hmg17	high mobility group nucleosomal binding domain 2	protein-coding
mm_95138.1	chr11	34839417	34839420	+	1	NA	Intergenic	RLTR8|LTR|ERVK	-5777	NM_027411	70385	Mm.194368	NM_027411	ENSMUSG00000069910	Spdl1	1700018I02Rik|2600001J17Rik|2810049B11Rik|AA409762|Ccdc99	spindle apparatus coiled-coil protein 1	protein-coding
mm_100864.1	chr11	5897987	5897997	-	1	NA	intron (NM_022879, intron 3 of 6)	intron (NM_022879, intron 3 of 6)	790	NM_022879	17898	Mm.46514	NM_022879	ENSMUSG00000020469	Myl7	MLC-2alpha|MLC2a|MYL2A|Mylc2a|RLC-A	myosin, light polypeptide 7, regulatory	protein-coding
mm_92789.1	chr10	81303511	81303546	-	1	NA	intron (NM_008844, intron 1 of 17)	intron (NM_008844, intron 1 of 17)	10565	NM_001146687	18717	Mm.24222	NM_008844	ENSMUSG00000034902	Pip5k1c	AI115456|AI835305|Pip5kIgamma	phosphatidylinositol-4-phosphate 5-kinase, type 1 gamma	protein-coding
mm_12189.1	chr2	65553819	65553828	+	1	NA	intron (NM_018732, intron 1 of 26)	intron (NM_018732, intron 1 of 26)	13669	NM_018732	20269	Mm.330256	NM_018732	ENSMUSG00000057182	Scn3a	Gm1000|Nav1.3	sodium channel, voltage-gated, type III, alpha	protein-coding
mm_112462.1	chr13	5867614	5867642	+	1	NA	3' UTR (NM_011803, exon 4 of 4)	3' UTR (NM_011803, exon 4 of 4)	6139	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_148532.1	chr19	4594313	4594332	+	1	NA	promoter-TSS (NM_008797)	promoter-TSS (NM_008797)	3	NM_008797	18563	Mm.1845	NM_008797	ENSMUSG00000024892	Pcx	Pc|Pcb	pyruvate carboxylase	protein-coding
mm_143856.1	chr17	84185565	84185587	-	1	NA	3' UTR (NM_001001806, exon 2 of 2)	3' UTR (NM_001001806, exon 2 of 2)	2371	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_159408.1	chr3	101022376	101022376	-	1	NA	intron (NM_001167906, intron 1 of 8)	L1ME3B|LINE|L1	7119	NM_001167906	630146	Mm.190915	NM_001099332	ENSMUSG00000086564	Cd101	EWI-101|Gm1016|Gm734|Igsf2	CD101 antigen	protein-coding
mm_3425.1	chr1	146497672	146497707	+	1	NA	promoter-TSS (NM_001145807)	promoter-TSS (NM_001145807)	2	NM_001145807	215378	Mm.441817	NM_153539	ENSMUSG00000035131	Brinp3	B830045N13Rik|Fam5c	bone morphogenetic protein/retinoic acid inducible neural specific 3	protein-coding
mm_167655.1	chr9	67636108	67636126	+	1	NA	Intergenic	Intergenic	-76414	NM_001081242	70549	Mm.33645	NM_027458	ENSMUSG00000052698	Tln2	5730421P04Rik|AI507121|AI787438|AL118320|mKIAA0320	talin 2	protein-coding
mm_5210.1	chr1	13588976	13588977	-	1	NA	intron (NM_028173, intron 1 of 10)	intron (NM_028173, intron 1 of 10)	934	NM_028173	72265	Mm.28765	NM_028173	ENSMUSG00000025935	Tram1	1810049E02Rik|TRAMP	translocating chain-associating membrane protein 1	protein-coding
mm_3615.1	chr1	152399825	152399881	+	1	NA	promoter-TSS (NM_177756)	promoter-TSS (NM_177756)	-14	NM_177756	269132	Mm.23782	NM_177756	ENSMUSG00000032649	Colgalt2	AI427652|D730024P12|Glt25d2	collagen beta(1-O)galactosyltransferase 2	protein-coding
mm_53808.1	chr6	146888633	146888654	+	1	NA	5' UTR (NM_001170433, exon 1 of 28)	5' UTR (NM_001170433, exon 1 of 28)	149	NM_026221	67533	Mm.103382	NM_026221	ENSMUSG00000016487	Ppfibp1	4632409B19Rik|AW214454|AW261454	PTPRF interacting protein, binding protein 1 (liprin beta 1)	protein-coding
mm_111498.1	chr12	99376979	99376985	-	1	NA	intron (NM_183186, intron 2 of 5)	intron (NM_183186, intron 2 of 5)	73092	NM_183186	71375	Mm.341972	NM_183186	ENSMUSG00000033713	Foxn3	5430426H20Rik|AA589593|AW556347|Ches1|Ches1l|HTLFL1	forkhead box N3	protein-coding
mm_62379.1	chr7	100786342	100786374	+	1	NA	intron (NM_178764, intron 2 of 8)	intron (NM_178764, intron 2 of 8)	77055	NM_177073	320100	Mm.40336	NM_177073	ENSMUSG00000008318	Relt	E430021K24Rik|Tnfrsf19l	RELT tumor necrosis factor receptor	protein-coding
mm_80618.1	chr9	88532923	88532928	+	1	NA	Intergenic	Intergenic	-10028	NR_040721	72655	Mm.21798	NR_040721	ENSMUSG00000097195	Snhg5	2810026P18Rik|4933428I09Rik|mU50HG-b	small nucleolar RNA host gene 5	ncRNA
mm_133361.1	chr16	84703325	84703341	+	1	NA	Intergenic	CpG	-9690	NR_132106	100653389	Mm.261808	NR_132106	ENSMUSG00000097418	Mir155hg	Bic|Gm26667	Mir155 host gene (non-protein coding)	ncRNA
mm_93554.1	chr10	116176963	116176968	-	1	NA	promoter-TSS (NM_001161839)	promoter-TSS (NM_001161839)	-293	NM_001161839	19279	Mm.336316	NM_011217	ENSMUSG00000020151	Ptprr	Gmcp1|PTP-SL|PTPBR7|RPTPRR|mPTP213	protein tyrosine phosphatase, receptor type, R	protein-coding
mm_125801.1	chr15	74904619	74904626	+	1	NA	Intergenic	RMER17C|LTR|ERVK	-22918	NM_025929	67038	Mm.154566	NM_025929	ENSMUSG00000063522	2010109I03Rik	Ly6m	RIKEN cDNA 2010109I03 gene	protein-coding
mm_88814.1	chr10	80798614	80798616	+	1	NA	promoter-TSS (NM_013651)	promoter-TSS (NM_013651)	11	NM_023900	78670	Mm.41479	NM_023900	ENSMUSG00000035278	Plekhj1	9530063M10Rik	pleckstrin homology domain containing, family J member 1	protein-coding
mm_153666.1	chr19	44395940	44395949	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	11765	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_132038.1	chr16	27422926	27422967	+	1	NA	intron (NM_001025615, intron 5 of 9)	B3A|SINE|B2	33990	NM_001289436	67501	Mm.258985	NM_026202	ENSMUSG00000038127	Ccdc50	C3orf6	coiled-coil domain containing 50	protein-coding
mm_71148.1	chr8	39298445	39298475	+	1	NA	intron (NR_044988, intron 1 of 3)	intron (NR_044988, intron 1 of 3)	480	NR_044988	621335	Mm.208080	NR_044988	ENSMUSG00000109827	Gm6213	EG621335	predicted gene 6213	ncRNA
mm_67688.1	chr7	89404211	89404237	-	1	NA	promoter-TSS (NM_008055)	promoter-TSS (NM_008055)	-142	NM_008055	14366	Mm.86755	NM_008055	ENSMUSG00000049791	Fzd4	Fz4	frizzled class receptor 4	protein-coding
mm_35891.1	chr4	49546735	49546738	-	1	NA	intron (NM_144903, intron 1 of 8)	intron (NM_144903, intron 1 of 8)	2810	NM_144903	230163	Mm.482116	NM_144903	ENSMUSG00000028307	Aldob	Aldo-2|Aldo2|BC016435	aldolase B, fructose-bisphosphate	protein-coding
mm_60001.1	chr7	30650412	30650439	+	1	NA	promoter-TSS (NM_133693)	promoter-TSS (NM_133693)	-197	NM_133693	68035	Mm.401747	NM_133693	ENSMUSG00000036733	Rbm42	1700003D06Rik|3100004P22Rik	RNA binding motif protein 42	protein-coding
mm_56087.1	chr6	87335708	87335724	-	1	NA	promoter-TSS (NM_054041)	promoter-TSS (NM_054041)	59	NM_054041	69538	Mm.232525	NM_054041	ENSMUSG00000033420	Antxr1	2310008J16Rik|2810405N18Rik|Antrx1|Tem8	anthrax toxin receptor 1	protein-coding
mm_94426.1	chr11	6273751	6273782	+	1	NA	exon (NM_134020, exon 4 of 5)	exon (NM_134020, exon 4 of 5)	1071	NM_134020	103694	Mm.254495	NM_134020	ENSMUSG00000004394	Tmed4	1110014L17Rik|AI326346	transmembrane p24 trafficking protein 4	protein-coding
mm_40199.1	chr5	36923001	36923011	+	1	NA	exon (NM_172994, exon 2 of 9)	exon (NM_172994, exon 2 of 9)	-46127	NR_045505	71054	Mm.444807	NR_045505	ENSMUSG00000087487	Ppp2r2cos	4933401P06Rik	protein phosphatase 2, regulatory subunit B, gamma, opposite strand	ncRNA
mm_162039.1	chr19	56830788	56830788	+	1	NA	promoter-TSS (NM_001002241)	promoter-TSS (NM_001002241)	76	NM_001002241	83561	Mm.247541	NM_031387	ENSMUSG00000025081	Tdrd1	MTR-1	tudor domain containing 1	protein-coding
mm_4803.1	chr1	185252722	185252756	+	1	NA	intron (NM_001163754, intron 17 of 34)	intron (NM_001163754, intron 17 of 34)	9764	NR_035529	100316737		NR_035529	ENSMUSG00000105770	Mir664	mir-664|mmu-mir-664	microRNA 664	ncRNA
mm_38666.1	chr4	144565194	144565201	-	1	NA	promoter-TSS (NM_001085542)	promoter-TSS (NM_001085542)	-63	NM_001085542	627085	Mm.457899	NM_001085542	ENSMUSG00000078506	Gm13124	OTTMUSG00000010546	predicted gene 13124	protein-coding
mm_152437.1	chr19	10738845	10738866	-	1	NA	5' UTR (NM_007650, exon 1 of 11)	5' UTR (NM_007650, exon 1 of 11)	119	NM_007650	12507	Mm.779	NM_007650	ENSMUSG00000024669	Cd5	Ly-1|Ly-12|Ly-A|Lyt-1	CD5 antigen	protein-coding
mm_139602.1	chr17	57281717	57281732	+	1	NA	intron (NM_001163816, intron 1 of 25)	RMER10A|LTR|ERVL	2624	NM_001163815	22324	Mm.248172	NM_011691	ENSMUSG00000034116	Vav1	Vav|vav-T	vav 1 oncogene	protein-coding
mm_100377.1	chr11	119268005	119268099	+	1	NA	promoter-TSS (NM_008064)	promoter-TSS (NM_008064)	89	NM_008064	14387	Mm.4793	NM_008064	ENSMUSG00000025579	Gaa	E430018M07Rik	glucosidase, alpha, acid	protein-coding
mm_160694.1	chr10	29362649	29362649	-	1	NA	promoter-TSS (NM_001110198)	promoter-TSS (NM_001110198)	-207	NM_001110197	68031	Mm.28930	NM_026518	ENSMUSG00000038876	Rnf146	2610509H23Rik|Iduna	ring finger protein 146	protein-coding
mm_156270.1	chrX	136833373	136833386	+	1	NA	exon (NM_011123, exon 4 of 7)	exon (NM_011123, exon 4 of 7)	10633	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_100317.1	chr11	117987434	117987459	+	1	NA	intron (NM_133757, intron 1 of 9)	intron (NM_133757, intron 1 of 9)	589	NM_133757	74451	Mm.28864	NM_133757	ENSMUSG00000017715	Pgs1	2610019F11Rik|4933424M23Rik|SAF	phosphatidylglycerophosphate synthase 1	protein-coding
mm_155799.1	chrX	99003225	99003288	+	1	NA	Intergenic	Intergenic	-39325	NM_199018	236920	Mm.236928	NM_199018	ENSMUSG00000031216	Stard8	Dlc3|mKIAA0189	START domain containing 8	protein-coding
mm_28336.1	chr3	89387313	89387323	-	1	NA	intron (NM_009565, intron 1 of 2)	intron (NM_009565, intron 1 of 2)	-4546	NR_040403	545539	Mm.393389	NR_040403	ENSMUSG00000074466	Gm15417	ENSMUSG00000074466|OTTMUSG00000021274	predicted gene 15417	ncRNA
mm_123913.1	chr14	73358412	73358415	-	1	NA	Intergenic	Intergenic	26858	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_36179.1	chr4	62208427	62208487	-	1	NA	promoter-TSS (NM_009554)	promoter-TSS (NM_009554)	89	NM_001290351	22696	Mm.5011	NM_009554	ENSMUSG00000028389	Zfp37	Tzn|Zfp-37	zinc finger protein 37	protein-coding
mm_158959.1	chr1	91322083	91322083	+	1	NA	promoter-TSS (NM_001033292)	promoter-TSS (NM_001033292)	8	NM_001033292	227357	Mm.318167	NM_001033292	ENSMUSG00000049515	Espnl	Gm556	espin-like	protein-coding
mm_144504.1	chr18	24603976	24603993	+	1	NA	promoter-TSS (NM_021448)	promoter-TSS (NM_021448)	23	NM_021448	58523	Mm.25298	NM_021448	ENSMUSG00000024271	Elp2	AU023723|Epl2|StIP1|Statip1	elongator acetyltransferase complex subunit 2	protein-coding
mm_141914.1	chr17	34998679	34998718	-	1	NA	exon (NM_033075, exon 2 of 2)	exon (NM_033075, exon 2 of 2)	2048	NM_033075	110956	Mm.22506	NM_033075		D17H6S56E-5	G7e	DNA segment, Chr 17, human D6S56E 5	protein-coding
mm_26472.1	chr3	144570397	144570407	+	1	NA	promoter-TSS (NM_053102)	promoter-TSS (NM_053102)	-25	NM_053102	93684	Mm.29812	NM_053102	ENSMUSG00000037072	Selenof	9430015P09Rik|Sep15	selenoprotein F	protein-coding
mm_90664.1	chr10	128821727	128821737	+	1	NA	promoter-TSS (NM_024180)	promoter-TSS (NM_024180)	-39	NM_025364	66118	Mm.235562	NM_025364	ENSMUSG00000078427	Sarnp	1110005A23Rik|Cip29	SAP domain containing ribonucleoprotein	protein-coding
mm_133696.1	chr16	92823840	92823853	+	1	NA	intron (NM_001111022, intron 2 of 6)	intron (NM_001111022, intron 2 of 6)	2228	NM_001111021	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_166656.1	chr6	87379351	87379356	+	1	NA	3' UTR (NM_025467, exon 6 of 6)	3' UTR (NM_025467, exon 6 of 6)	5988	NM_025467	66284	Mm.46446	NM_025467	ENSMUSG00000030049	Gkn2	1810036H07Rik|Bricd1b	gastrokine 2	protein-coding
mm_171085.1	chr3	123385857	123385865	-	1	NA	5' UTR (NM_201638, exon 1 of 11)	5' UTR (NM_201638, exon 1 of 11)	129	NM_201638	210529	Mm.260039	NM_201638	ENSMUSG00000028114	Mettl14	G430022H21Rik|mKIAA1627	methyltransferase like 14	protein-coding
mm_21698.1	chr2	164512205	164512218	-	1	NA	Intergenic	MIR|SINE|MIR	14686	NM_133779	78928	Mm.28228	NM_133779	ENSMUSG00000017721	Pigt	2510012P17Rik|4930534E15Rik|CGI-06|NDAP|Ndap7	phosphatidylinositol glycan anchor biosynthesis, class T	protein-coding
mm_69533.1	chr7	135694365	135694396	-	1	NA	exon (NM_001081117, exon 12 of 14)	exon (NM_001081117, exon 12 of 14)	21999	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_97419.1	chr11	78032275	78032310	+	1	NA	promoter-TSS (NM_183286)	promoter-TSS (NM_183286)	-21	NM_183286	70451	Mm.390342	NM_183286	ENSMUSG00000020834	Dhrs13	2610209N15Rik	dehydrogenase/reductase (SDR family) member 13	protein-coding
mm_6533.1	chr1	74892814	74892826	-	1	NA	exon (NM_021541, exon 2 of 5)	exon (NM_021541, exon 2 of 5)	323	NM_021541	12958	Mm.86656	NM_021541	ENSMUSG00000006546	Cryba2	E130107M19Rik	crystallin, beta A2	protein-coding
mm_107952.1	chr12	72441853	72441864	+	1	NA	promoter-TSS (NM_001142728)	promoter-TSS (NM_001142728)	-8	NM_001142728	78257	Mm.266280	NM_030070	ENSMUSG00000021090	Lrrc9	4921529O18Rik|4930432K16Rik	leucine rich repeat containing 9	protein-coding
mm_111992.1	chr12	110695765	110695808	-	1	NA	intron (NM_010480, intron 1 of 10)	CpG	609	NM_010480	15519	Mm.1843	NM_010480	ENSMUSG00000021270	Hsp90aa1	86kDa|89kDa|AL024080|AL024147|Hsp86-1|Hsp89|Hsp90|Hspca|hsp4	heat shock protein 90, alpha (cytosolic), class A member 1	protein-coding
mm_60404.1	chr7	44475953	44475963	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	5611	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_115607.1	chr13	11991807	11991845	-	1	NA	intron (NM_023868, intron 1 of 104)	B4A|SINE|B4	115119	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding
mm_90492.1	chr10	128033348	128033352	+	1	NA	Intergenic	RMER10A|LTR|ERVL	-1996	NM_013608	17938	Mm.3746	NM_013608	ENSMUSG00000061315	Naca	AL022831|AL024382|Gm1878|mKIAA0363|skNAC	nascent polypeptide-associated complex alpha polypeptide	protein-coding
mm_128953.1	chr15	74778854	74778864	-	1	NA	promoter-TSS (NR_027837)	promoter-TSS (NR_027837)	0	NR_027836	78725	Mm.171357	NM_172433	ENSMUSG00000101026	D730001G18Rik	Ly6g6g	RIKEN cDNA D730001G18 gene	ncRNA
mm_31918.1	chr4	85205676	85205685	+	1	NA	intron (NM_019535, intron 1 of 8)	CpG	224	NM_019535	20404	Mm.143603	NM_019535	ENSMUSG00000028488	Sh3gl2	9530001L19Rik|AI120490|AW555077|B930049H17Rik|EEN-B1|SH3PA|Sh3d2a	SH3-domain GRB2-like 2	protein-coding
mm_23195.1	chr3	41090019	41090026	+	1	NA	Intergenic	Charlie2b|DNA|hAT-Charlie	-6976	NM_027558	70804	Mm.40321	NM_027558	ENSMUSG00000049940	Pgrmc2	4631434O19Rik|5730409G06Rik|DG6|PMBP	progesterone receptor membrane component 2	protein-coding
mm_45202.1	chr5	52566359	52566390	-	1	NA	promoter-TSS (NM_144945)	promoter-TSS (NM_144945)	-68	NM_144945	246316	Mm.44721	NM_144945	ENSMUSG00000039252	Lgi2	mKIAA1916	leucine-rich repeat LGI family, member 2	protein-coding
mm_138327.1	chr17	34850495	34850526	+	1	NA	promoter-TSS (NM_021337)	promoter-TSS (NM_021337)	119	NM_001045864	27632	Mm.653	NM_138580	ENSMUSG00000024369	Nelfe	D17H6S45|NELF-E|RD|Rdbp	negative elongation factor complex member E, Rdbp	protein-coding
mm_9355.1	chr1	172197752	172197764	-	1	NA	3' UTR (NM_001329871, exon 4 of 4)	3' UTR (NM_001329871, exon 4 of 4)	9046	NM_001329871	18611	Mm.544	NM_011063	ENSMUSG00000013698	Pea15a	Mat1|PEA-15|Pea15|Pkcs15	phosphoprotein enriched in astrocytes 15A	protein-coding
mm_98852.1	chr11	97662730	97662746	+	1	NA	promoter-TSS (NM_139311)	promoter-TSS (NM_139311)	-674	NM_139311	246198	Mm.23685	NM_139311	ENSMUSG00000038437	Mllt6	AI315037|Af17	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 6	protein-coding
mm_52109.1	chr6	97892356	97892371	+	1	NA	intron (NM_001113198, intron 1 of 9)	intron (NM_001113198, intron 1 of 9)	-37454	NM_001178049	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_141052.1	chr17	25727345	25727363	-	1	NA	promoter-TSS (NM_145409)	promoter-TSS (NM_145409)	61	NM_145409	214901	Mm.102540	NM_145409	ENSMUSG00000019214	Chtf18	6030457M03Rik|CTF18|Chl12	CTF18, chromosome transmission fidelity factor 18	protein-coding
mm_56574.1	chr6	106748044	106748053	-	1	NA	intron (NM_008370, intron 1 of 12)	intron (NM_008370, intron 1 of 12)	989	NM_008370	16192	Mm.3448	NM_008370	ENSMUSG00000005364	Il5ra	CD125|CDw125|Il5r	interleukin 5 receptor, alpha	protein-coding
mm_34268.1	chr4	141422509	141422523	+	1	NA	exon (NM_013868, exon 2 of 3)	exon (NM_013868, exon 2 of 3)	1737	NM_013868	29818	Mm.46181	NM_013868	ENSMUSG00000006221	Hspb7	27kDa|Hsp25-2|cvHsp	heat shock protein family, member 7 (cardiovascular)	protein-coding
mm_145216.1	chr18	50052998	50053004	+	1	NA	promoter-TSS (NM_134131)	promoter-TSS (NM_134131)	-281	NM_134131	106869	Mm.27740	NM_134131	ENSMUSG00000062210	Tnfaip8	AA987150|E130304C20Rik|ENSMUSG00000073567|Gg2-1|Gm10539|Nded|Ssc-2|Tipe	tumor necrosis factor, alpha-induced protein 8	protein-coding
mm_110956.1	chr12	76710121	76710153	-	1	NA	5' UTR (NM_013675, exon 1 of 36)	5' UTR (NM_013675, exon 1 of 36)	410	NM_013675	20741	Mm.32881	NM_013675	ENSMUSG00000021061	Sptb	AI842465|D330027P03Rik|Gm1301|Spnb-1|Spnb1|ja|jaundiced|mKIAA4219	spectrin beta, erythrocytic	protein-coding
mm_111945.1	chr12	109053724	109053761	-	1	NA	intron (NM_001163175, intron 1 of 6)	CpG-3504	14475	NM_001163175	380785	Mm.342085	NM_001163175	ENSMUSG00000040867	Begain	BM948371|Gm897	brain-enriched guanylate kinase-associated	protein-coding
mm_40168.1	chr5	35814376	35814400	+	1	NA	intron (NM_001177696, intron 6 of 21)	intron (NM_001177696, intron 6 of 21)	56508	NM_001177698	231148	Mm.254446	NM_177678	ENSMUSG00000029095	Ablim2	AI606905|C230091L11	actin-binding LIM protein 2	protein-coding
mm_113518.1	chr13	37802060	37802092	+	1	NA	Intergenic	Intergenic	-23962	NM_026830	68750	Mm.491109	NM_026830	ENSMUSG00000039087	Rreb1	1110037N09Rik|AA414966|B930013M22Rik	ras responsive element binding protein 1	protein-coding
mm_143934.1	chr17	86162012	86162020	-	1	NA	Intergenic	Intergenic	-5769	NM_011104	18754	Mm.24614	NM_011104	ENSMUSG00000045038	Prkce	5830406C15Rik|PKC[e]|PKCepsilon|Pkce|R75156	protein kinase C, epsilon	protein-coding
mm_140642.1	chr17	12675743	12675775	-	1	NA	promoter-TSS (NM_009202)	promoter-TSS (NM_009202)	79	NM_009202	20517	Mm.594	NM_009202	ENSMUSG00000023829	Slc22a1	Lx1|Oct1|Orct|Orct1	solute carrier family 22 (organic cation transporter), member 1	protein-coding
mm_81611.1	chr9	110763671	110763702	+	1	NA	promoter-TSS (NM_010859)	promoter-TSS (NM_010859)	5	NM_010859	17897	Mm.7353	NM_010859	ENSMUSG00000059741	Myl3	MLC1s|MLC1v|Mylc|VLC1	myosin, light polypeptide 3	protein-coding
mm_86151.1	chr9	117252666	117252724	-	1	NA	promoter-TSS (NM_001172126)	promoter-TSS (NM_001172126)	-212	NM_001172126	207181	Mm.326411	NM_178660	ENSMUSG00000039607	Rbms3	6720477E09Rik|8430436O14Rik	RNA binding motif, single stranded interacting protein	protein-coding
mm_43511.1	chr5	137030669	137030692	+	1	NA	intron (NM_001039385, intron 1 of 1)	CpG	385	NM_001039385	381677	Mm.389697	NM_001039385	ENSMUSG00000037428	Vgf	Gm1052	VGF nerve growth factor inducible	protein-coding
mm_145603.1	chr18	61061257	61061258	+	1	NA	exon (NM_001146268, exon 3 of 23)	exon (NM_001146268, exon 3 of 23)	16107	NM_008809	18596	Mm.4146	NM_008809	ENSMUSG00000024620	Pdgfrb	AI528809|CD140b|PDGFR-1|Pdgfr	platelet derived growth factor receptor, beta polypeptide	protein-coding
mm_111412.1	chr12	91384371	91384397	-	1	NA	promoter-TSS (NM_181815)	promoter-TSS (NM_181815)	25	NM_181815	75216	Mm.312204	NM_181815	ENSMUSG00000061533	Cep128	4930534B04Rik|5430424K18Rik|AI449708|AI480494|E230024F20	centrosomal protein 128	protein-coding
mm_114132.1	chr13	55212054	55212086	+	1	NA	intron (NM_008739, intron 1 of 22)	CpG	2288	NM_008739	18193	Mm.12964	NM_008739	ENSMUSG00000021488	Nsd1	AI528500|KMT3B	nuclear receptor-binding SET-domain protein 1	protein-coding
mm_22591.1	chr3	13525947	13525947	+	1	NA	intron (NM_178631, intron 2 of 9)	intron (NM_178631, intron 2 of 9)	54292	NM_001163328	76897	Mm.422625	NM_178631	ENSMUSG00000039717	Ralyl	0710005M24Rik	RALY RNA binding protein-like	protein-coding
mm_97815.1	chr11	82962992	82962992	+	1	NA	3' UTR (NM_183201, exon 6 of 6)	3' UTR (NM_183201, exon 6 of 6)	-2311	NR_045932	76392	Mm.295205	NR_045932	ENSMUSG00000086327	Slfn5os	1700003F17Rik	schlafen 5, opposite strand	ncRNA
mm_92629.1	chr10	80323065	80323088	-	1	NA	exon (NM_008793, exon 12 of 15)	exon (NM_008793, exon 12 of 15)	-2528	NM_025521	66374	Mm.383824	NM_025521	ENSMUSG00000020133	2310011J03Rik	AI452186|AW545358	RIKEN cDNA 2310011J03 gene	protein-coding
mm_13838.1	chr2	119353707	119353709	+	1	NA	3' UTR (NM_026929, exon 3 of 3)	3' UTR (NM_026929, exon 3 of 3)	2466	NM_026929	69065	Mm.35083	NM_026929	ENSMUSG00000027313	Chac1	1810008K03Rik	ChaC, cation transport regulator 1	protein-coding
mm_15118.1	chr2	153741279	153741294	+	1	NA	promoter-TSS (NM_007896)	promoter-TSS (NM_007896)	-1	NM_007896	13589	Mm.143877	NM_007896	ENSMUSG00000027479	Mapre1	5530600P05Rik|AI462499|AI504412|AW260097|BIM1p|D2Ertd459e|Eb1	microtubule-associated protein, RP/EB family, member 1	protein-coding
mm_167434.1	chr8	119419028	119419032	+	1	NA	Intergenic	Intergenic	-18132	NM_027950	71839	Mm.272357	NM_027950	ENSMUSG00000074063	Osgin1	1700012B18Rik|Okl38	oxidative stress induced growth inhibitor 1	protein-coding
mm_111630.1	chr12	102439745	102439758	-	1	NA	promoter-TSS (NM_011175)	promoter-TSS (NM_011175)	62	NM_011175	19141	Mm.17185	NM_011175	ENSMUSG00000021190	Lgmn	AEP|AI746452|AU022324|Prsc1	legumain	protein-coding
mm_115889.1	chr13	22006406	22006417	-	1	NA	intron (NM_019429, intron 7 of 11)	intron (NM_019429, intron 7 of 11)	3330	NM_019429	54373	Mm.32043	NM_019429	ENSMUSG00000006179	Prss16	AI448615|TSSP	protease, serine 16 (thymus)	protein-coding
mm_52401.1	chr6	113327020	113327031	+	1	NA	promoter-TSS (NM_010957)	promoter-TSS (NM_010957)	49	NM_010957	18294	Mm.43612	NM_010957	ENSMUSG00000030271	Ogg1	Mmh	8-oxoguanine DNA-glycosylase 1	protein-coding
mm_105519.1	chr11	106272928	106273006	-	1	NA	promoter-TSS (NM_001130187)	promoter-TSS (NM_001130187)	5	NM_001130187	83796	Mm.21772	NM_031878	ENSMUSG00000078619	Smarcd2	AW322457|Baf60b	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2	protein-coding
mm_15651.1	chr2	163203073	163203133	+	1	NA	Intergenic	CpG	-22351	NM_001098799	269389	Mm.207709	NM_001098799	ENSMUSG00000074607	Tox2	AI851523|AV026525|BI987407|Gcx1|RxHMG1	TOX high mobility group box family member 2	protein-coding
mm_55324.1	chr6	55679059	55679072	-	1	NA	exon (NM_009717, exon 2 of 2)	exon (NM_009717, exon 2 of 2)	2198	NM_009717	11922	Mm.5106	NM_009717	ENSMUSG00000037984	Neurod6	Atoh2|Math-2|Math2|Nex|Nex1m|bHLHa2	neurogenic differentiation 6	protein-coding
mm_84520.1	chr9	67043825	67043829	-	1	NA	promoter-TSS (NM_001164256)	promoter-TSS (NM_001164256)	44	NM_001164252	22003	Mm.121878	NM_024427	ENSMUSG00000032366	Tpm1	AA986836|AI854628|TM2|Tm3|Tmpa|Tpm-1|alpha-TM	tropomyosin 1, alpha	protein-coding
mm_60394.1	chr7	44475259	44475259	+	1	NA	Intergenic	Intergenic	4912	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_42573.1	chr5	117240474	117240492	+	1	NA	intron (NM_001081308, intron 12 of 19)	intron (NM_001081308, intron 12 of 19)	47081	NM_018858	23980	Mm.195898	NM_018858	ENSMUSG00000032959	Pebp1	HCNP|Pbp|Pbp1|Pbpr|Rkip	phosphatidylethanolamine binding protein 1	protein-coding
mm_9859.1	chr1	184811260	184811264	-	1	NA	promoter-TSS (NM_001290273)	promoter-TSS (NM_001290273)	38	NM_001290273	66112	Mm.272457	NM_001081361	ENSMUSG00000026621	Marc1	1300013F15Rik|Mosc1	mitochondrial amidoxime reducing component 1	protein-coding
mm_157151.1	chrX	9462715	9462732	-	1	NA	intron (NM_007807, intron 3 of 12)	intron (NM_007807, intron 3 of 12)	6601	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_152566.1	chr19	11588006	11588034	-	1	NA	exon (NM_026835, exon 6 of 7)	exon (NM_026835, exon 6 of 7)	16784	NM_026835	68774	Mm.290390	NM_026835	ENSMUSG00000024679	Ms4a6d	1110058E16Rik|AI447446|Ms4a11	membrane-spanning 4-domains, subfamily A, member 6D	protein-coding
mm_64296.1	chr7	141861362	141861365	+	1	NA	exon (NM_028801, exon 31 of 49)	exon (NM_028801, exon 31 of 49)	22291	NM_028801	74180	Mm.200752	NM_028801	ENSMUSG00000066108	Muc5b	2300002I04Rik|A130042M24|AV085033|MUC5|MUC9|mucin 5b	mucin 5, subtype B, tracheobronchial	protein-coding
mm_120732.1	chr14	73146510	73146522	+	1	NA	intron (NR_033185, intron 1 of 15)	RMER6A|LTR|ERVK	3731	NR_033185	105670	Mm.280068	NM_134083	ENSMUSG00000022106	Rcbtb2	2610028E02Rik|2810420M18Rik|AI448345|AW240694|Chc1l|RC/BTB2	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 2	protein-coding
mm_24577.1	chr3	93444694	93444705	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	2369	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_87428.1	chr10	50803782	50803793	+	1	NA	intron (NM_198007, intron 36 of 41)	intron (NM_198007, intron 36 of 41)	-91864	NM_011376	20464	Mm.4774	NM_011376	ENSMUSG00000019913	Sim1	bHLHe14|mSIM1	single-minded homolog 1 (Drosophila)	protein-coding
mm_56921.1	chr6	119401983	119401998	-	1	NA	intron (NM_197985, intron 1 of 7)	MTD|LTR|ERVL-MaLR	15493	NM_197985	68465	Mm.291826	NM_197985	ENSMUSG00000030168	Adipor2	1110001I14Rik|ADCR2|AI115388|AW554121|D6Ucla1e|Paqr2	adiponectin receptor 2	protein-coding
mm_83811.1	chr9	53592081	53592097	-	1	NA	exon (NM_144784, exon 6 of 12)	exon (NM_144784, exon 6 of 12)	18261	NM_144784	110446	Mm.293233	NM_144784	ENSMUSG00000032047	Acat1	6330585C21Rik|Acat	acetyl-Coenzyme A acetyltransferase 1	protein-coding
mm_152729.1	chr19	18936155	18936156	-	1	NA	3' UTR (NM_001289921, exon 11 of 11)	3' UTR (NM_001289921, exon 11 of 11)	64962	NM_146095	225998	Mm.234641	NM_146095	ENSMUSG00000036192	Rorb	Nr1f2|RZR-beta|RZRB|Rorbeta|hstp	RAR-related orphan receptor beta	protein-coding
mm_5329.1	chr1	23877771	23877783	-	1	NA	exon (NM_028534, exon 3 of 10)	exon (NM_028534, exon 3 of 10)	31959	NR_110972	98366	Mm.329963	NM_028534	ENSMUSG00000026155	Smap1	1700056O10Rik|4921514B13Rik|4921525H11Rik|AI462175	small ArfGAP 1	protein-coding
mm_132880.1	chr16	48790204	48790212	+	1	NA	Intergenic	Intergenic	-18252	NM_198297	77647	Mm.167298	NM_198297	ENSMUSG00000030775	Trat1	C030046M14Rik|Tcrim|Trim	T cell receptor associated transmembrane adaptor 1	protein-coding
mm_146769.1	chr18	20002094	20002104	-	1	NA	promoter-TSS (NM_001291809)	promoter-TSS (NM_001291809)	-2	NM_001291809	13507	Mm.89935	NM_007882	ENSMUSG00000059898	Dsc3	5430426I24Rik	desmocollin 3	protein-coding
mm_146573.1	chr18	6983604	6983607	-	1	NA	intron (NM_177595, intron 5 of 6)	intron (NM_177595, intron 5 of 6)	21174	NM_177595	210719	Mm.257186	NM_177595	ENSMUSG00000061013	Mkx	9430023B20Rik|Irxl1	mohawk homeobox	protein-coding
mm_29049.1	chr3	103646032	103646040	-	1	NA	promoter-TSS (NM_174875)	promoter-TSS (NM_174875)	32	NM_174875	666468	Mm.102230	NM_174875	ENSMUSG00000079418	Atg4a	AI627006|AV169859|Apg4a|Atg4al|Autl2	autophagy related 4A, cysteine peptidase	protein-coding
mm_140937.1	chr17	24442158	24442184	-	1	NA	intron (NM_025718, intron 4 of 7)	intron (NM_025718, intron 4 of 7)	930	NM_025718	66705	Mm.29017	NM_025718	ENSMUSG00000024136	Dnase1l2	4733401H14Rik	deoxyribonuclease 1-like 2	protein-coding
mm_104549.1	chr11	96777498	96777546	-	1	NA	promoter-TSS (NM_028965)	promoter-TSS (NM_028965)	33	NM_028965	74479	Mm.270781	NM_028965	ENSMUSG00000020876	Snx11	4933439F10Rik|A930041K09Rik|AI117694	sorting nexin 11	protein-coding
mm_134557.1	chr16	20241305	20241363	-	1	NA	promoter-TSS (NM_198599)	promoter-TSS (NM_198599)	24	NM_198599	208158	Mm.326383	NM_198599	ENSMUSG00000041205	Map6d1	A330066I15Rik	MAP6 domain containing 1	protein-coding
mm_72122.1	chr8	71689245	71689258	+	1	NA	promoter-TSS (NM_013564)	promoter-TSS (NM_013564)	-1	NM_013564	16336	Mm.476857	NM_013564	ENSMUSG00000079019	Insl3	Rlf|Rlnl	insulin-like 3	protein-coding
mm_93848.1	chr10	121807099	121807109	-	1	NA	intron (NM_001242411, intron 16 of 21)	intron (NM_001242411, intron 16 of 21)	67167	NM_173022	270802	Mm.209172	NM_173022	ENSMUSG00000053684	BC048403	E030027L10	cDNA sequence BC048403	protein-coding
mm_154820.1	chrX	16618564	16618576	+	1	NA	Intergenic	CpG	-1128	NM_173740	17161	Mm.21108	NM_173740	ENSMUSG00000025037	Maoa	1110061B18Rik|AA407771	monoamine oxidase A	protein-coding
mm_96447.1	chr11	67492318	67492338	+	1	NA	Intergenic	Intergenic	-40670	NM_008088	14457	Mm.40338	NM_008088	ENSMUSG00000033066	Gas7	AW124766|B230343A10Rik|Gas7-cb	growth arrest specific 7	protein-coding
mm_54469.1	chr6	34910448	34910462	-	1	NA	intron (NM_001013366, intron 1 of 14)	MIR3|SINE|MIR	376	NM_001013366	101240	Mm.152120	NM_001013366	ENSMUSG00000058486	Wdr91	9530020G05Rik|AI987683|AU018665	WD repeat domain 91	protein-coding
mm_53183.1	chr6	125432701	125432724	+	1	NA	Intergenic	Intergenic	-52208	NM_198604	213522	Mm.333396	NM_198604	ENSMUSG00000038167	Plekhg6	BC026778|Gm155	pleckstrin homology domain containing, family G (with RhoGef domain) member 6	protein-coding
mm_54229.1	chr6	28213253	28213270	-	1	NA	Intergenic	L2a|LINE|L2	48340	NM_001081678	627049	Mm.84441	NM_001081678	ENSMUSG00000039841	Zfp800	AA407452|Znf800	zinc finger protein 800	protein-coding
mm_166443.1	chr5	137264339	137264358	+	1	NA	Intergenic	Intergenic	-23906	NM_009599	11423	Mm.255464	NM_009599	ENSMUSG00000023328	Ache	-	acetylcholinesterase	protein-coding
mm_166490.1	chr5	149180233	149180235	+	1	NA	intron (NR_015478, intron 1 of 2)	intron (NR_015478, intron 1 of 2)	1802	NR_015478	433966	Mm.207047	NR_015478	ENSMUSG00000097191	5730422E09Rik	-	RIKEN cDNA 5730422E09 gene	ncRNA
mm_48079.1	chr5	136883078	136883093	-	1	NA	promoter-TSS (NM_024474)	promoter-TSS (NM_024474)	22	NM_024474	140709	Mm.295020	NM_024474	ENSMUSG00000004415	Col26a1	9430032K24Rik|BC002218|Col26a|Emid2|Emu2	collagen, type XXVI, alpha 1	protein-coding
mm_67533.1	chr7	81345162	81345179	-	1	NA	promoter-TSS (NM_009092)	promoter-TSS (NM_009092)	64	NM_009092	20068	Mm.42767	NM_009092	ENSMUSG00000061787	Rps17	-	ribosomal protein S17	protein-coding
mm_48853.1	chr5	149636199	149636213	-	1	NA	5' UTR (NM_013559, exon 1 of 18)	5' UTR (NM_013559, exon 1 of 18)	109	NM_013559	15505	Mm.270681	NM_013559	ENSMUSG00000029657	Hsph1	105kDa|AI790491|Hsp105|Hsp110|hsp-E7I|hsp110/105	heat shock 105kDa/110kDa protein 1	protein-coding
mm_81936.1	chr9	120180286	120180298	+	1	NA	Intergenic	Intergenic	30550	NM_001039364	17433	Mm.486167	NM_008614	ENSMUSG00000032517	Mobp	AI835053|AI839848|MOBP155|MOBP170|MOBP69|MOBP73|MOBP81|R74645	myelin-associated oligodendrocytic basic protein	protein-coding
mm_131114.1	chr16	5306828	5306865	+	1	NA	Intergenic	CpG	-50890	NM_027446	70511	Mm.45780	NM_027446	ENSMUSG00000022544	Eef2kmt	5730409G15Rik|Fam86|Fam86a|eEF2-KMT	eukaryotic elongation factor 2 lysine methyltransferase	protein-coding
mm_128176.1	chr15	34443509	34443574	-	1	NA	promoter-TSS (NR_028101)	promoter-TSS (NR_028101)	-265	NM_001163485	19946	Mm.358632	NM_009083	ENSMUSG00000058600	Rpl30	-	ribosomal protein L30	protein-coding
mm_13120.1	chr2	91664121	91664158	+	1	NA	intron (NR_027371, intron 5 of 13)	intron (NR_027371, intron 5 of 13)	10931	NM_146124	228359	Mm.22413	NM_146124	ENSMUSG00000027247	Arhgap1	B230365D05Rik|C76222|Cdc42GAP|p50rhoGAP	Rho GTPase activating protein 1	protein-coding
mm_87928.1	chr10	62598827	62598854	+	1	NA	exon (NM_019553, exon 2 of 15)	exon (NM_019553, exon 2 of 15)	3458	NM_019553	56200	Mm.413275	NM_019553	ENSMUSG00000020075	Ddx21	AI255159|AL022742|D10Ertd645e|D10Wsu42e	DEAD (Asp-Glu-Ala-Asp) box polypeptide 21	protein-coding
mm_62594.1	chr7	105642616	105642622	+	1	NA	TTS (NM_019502)	TTS (NM_019502)	2079	NM_019502	14356	Mm.220330	NM_019502	ENSMUSG00000089847	Timm10b	Fxc1|Tim10b|Tim9b	translocase of inner mitochondrial membrane 10B	protein-coding
mm_101132.1	chr11	12429016	12429028	-	1	NA	intron (NM_172496, intron 1 of 14)	intron (NM_172496, intron 1 of 14)	-16882	NM_001282994	12808	Mm.22847	NM_172496	ENSMUSG00000020173	Cobl	-	cordon-bleu WH2 repeat	protein-coding
mm_8590.1	chr1	156005833	156005857	-	1	NA	3' UTR (NM_144791, exon 7 of 7)	3' UTR (NM_144791, exon 7 of 7)	28972	NM_001160019	208263	Mm.211654	NM_144791	ENSMUSG00000026466	Tor1aip1	LAP1|Lap1B	torsin A interacting protein 1	protein-coding
mm_86860.1	chr10	21978644	21978689	+	1	NA	promoter-TSS (NM_001161847)	promoter-TSS (NM_001161847)	-6	NM_001161847	20393	Mm.28405	NM_011361	ENSMUSG00000019970	Sgk1	Sgk	serum/glucocorticoid regulated kinase 1	protein-coding
mm_25800.1	chr3	127789188	127789202	+	1	NA	promoter-TSS (NM_145133)	promoter-TSS (NM_145133)	-718	NM_145133	211550	Mm.31852	NM_145133	ENSMUSG00000046688	Tifa	T2bp	TRAF-interacting protein with forkhead-associated domain	protein-coding
mm_161348.1	chr14	54625487	54625487	+	1	NA	exon (NM_175204, exon 1 of 1)	exon (NM_175204, exon 1 of 1)	177	NM_175204	73902	Mm.32009	NM_175204	ENSMUSG00000072423	Psmb11	5830406J20Rik|beta5t	proteasome (prosome, macropain) subunit, beta type, 11	protein-coding
mm_67531.1	chr7	81222871	81222884	-	1	NA	intron (NM_008803, intron 1 of 21)	intron (NM_008803, intron 1 of 21)	9073	NM_008803	18584	Mm.371577	NM_008803	ENSMUSG00000025584	Pde8a	AI551852|Pde8	phosphodiesterase 8A	protein-coding
mm_161086.1	chr12	85350890	85350890	-	1	NA	intron (NM_026775, intron 2 of 4)	intron (NM_026775, intron 2 of 4)	-11528	NM_145138	217718	Mm.29071	NM_145138	ENSMUSG00000034290	Nek9	C130021H08Rik	NIMA (never in mitosis gene a)-related expressed kinase 9	protein-coding
mm_171536.1	chr4	146909532	146909532	-	1	NA	Intergenic	Intergenic	-112318	NM_001177767	100043034	Mm.422606	NM_001177767	ENSMUSG00000067919	Rex2	Gm13138|OTTMUSG00000010655	reduced expression 2	protein-coding
mm_134661.1	chr16	22162940	22163056	-	1	NA	5' UTR (NM_183029, exon 1 of 16)	5' UTR (NM_183029, exon 1 of 16)	301	NM_183029	319765	Mm.489442	NM_183029	ENSMUSG00000033581	Igf2bp2	C330012H03Rik|IMP-2|Imp2|Neilsen	insulin-like growth factor 2 mRNA binding protein 2	protein-coding
mm_114573.1	chr13	75089821	75089833	+	1	NA	promoter-TSS (NM_013628)	promoter-TSS (NM_013628)	-160	NM_013628	18548	Mm.1333	NM_013628	ENSMUSG00000021587	Pcsk1	Nec-1|Nec1|PC1|PC3|Phpp-1|SPC3	proprotein convertase subtilisin/kexin type 1	protein-coding
mm_20572.1	chr2	131085589	131085599	-	1	NA	exon (NM_011426, exon 2 of 21)	exon (NM_011426, exon 2 of 21)	1171	NM_011426	20612	Mm.1374	NM_011426	ENSMUSG00000027322	Siglec1	Cd169|Siglec-1|Sn	sialic acid binding Ig-like lectin 1, sialoadhesin	protein-coding
mm_146088.1	chr18	73572698	73572712	+	1	NA	promoter-TSS (NM_001039214)	promoter-TSS (NM_001039214)	0	NM_001039214	240396	Mm.24131	NM_001039214	ENSMUSG00000037253	Mex3c	A130001D14Rik|BC035207|BM-013|Rkhd2	mex3 RNA binding family member C	protein-coding
mm_160750.1	chr10	81473290	81473290	-	1	NA	promoter-TSS (NM_001311127)	promoter-TSS (NM_001311127)	-159	NM_001311127	319586	Mm.152689	NM_176954	ENSMUSG00000034818	Celf5	4930565A21Rik|Brunol5	CUGBP, Elav-like family member 5	protein-coding
mm_110389.1	chr12	41348094	41348104	-	1	NA	intron (NM_053122, intron 4 of 6)	intron (NM_053122, intron 4 of 6)	137958	NM_001271708	16981	Mm.404786	NM_010733	ENSMUSG00000036295	Lrrn3	NLRR-3	leucine rich repeat protein 3, neuronal	protein-coding
mm_74001.1	chr8	120832953	120832954	+	1	NA	Intergenic	Intergenic	94314	NM_001301811	15900	Mm.334861	NM_008320	ENSMUSG00000041515	Irf8	AI893568|ICSBP|IRF-8|Icsbp1|Myls	interferon regulatory factor 8	protein-coding
mm_35736.1	chr4	45108070	45108128	-	1	NA	promoter-TSS (NM_001134646)	promoter-TSS (NM_001134646)	14	NM_001134646	68512	Mm.282081	NM_001099675	ENSMUSG00000078713	Tomm5	1110019J04Rik|Tom5	translocase of outer mitochondrial membrane 5 homolog (yeast)	protein-coding
mm_66055.1	chr7	30737949	30737974	-	1	NA	exon (NM_001290631, exon 2 of 11)	exon (NM_001290631, exon 2 of 11)	1446	NM_008085	14447	Mm.436562	NM_008085	ENSMUSG00000061099	Gapdhs	Gapd-s|Gapds	glyceraldehyde-3-phosphate dehydrogenase, spermatogenic	protein-coding
mm_151714.1	chr19	4625324	4625361	-	1	NA	TTS (NM_001033447)	TTS (NM_001033447)	275	NM_023131	19671	Mm.391143	NM_023131	ENSMUSG00000024889	Rce1	D19Ertd283e|D19Ertd98e	Ras converting CAAX endopeptidase 1	protein-coding
mm_87111.1	chr10	33197825	33197840	+	1	NA	intron (NM_029726, intron 8 of 37)	intron (NM_029726, intron 8 of 37)	58525	NR_040657	442820	Mm.490725	NR_040657		D830005E20Rik	-	RIKEN cDNA D830005E20 gene	ncRNA
mm_110147.1	chr12	26448717	26448742	-	1	NA	exon (NM_021384, exon 4 of 6)	exon (NM_021384, exon 4 of 6)	7723	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_114064.1	chr13	54379819	54379829	+	1	NA	3' UTR (NM_009946, exon 4 of 4)	3' UTR (NM_009946, exon 4 of 4)	8475	NM_009946	12890	Mm.268902	NM_009946	ENSMUSG00000025867	Cplx2	921-L|AI413745|AW492120	complexin 2	protein-coding
mm_97054.1	chr11	72607222	72607307	+	1	NA	promoter-TSS (NM_025985)	promoter-TSS (NM_025985)	3	NM_025985	67128	Mm.458052	NM_025985	ENSMUSG00000020794	Ube2g1	2700059C12Rik|AI256795|AU014992|AW552068|D130023C12Rik	ubiquitin-conjugating enzyme E2G 1	protein-coding
mm_44141.1	chr5	150197124	150197128	+	1	NA	Intergenic	Intergenic	-62804	NM_172887	320365	Mm.216590	NM_172887	ENSMUSG00000056602	Fry	13CDNA73|9330186A19Rik|AF346502|AI462658|C87180|D930046M03|cg003|mKIAA4143	FRY microtubule binding protein	protein-coding
mm_119918.1	chr14	54953916	54953925	+	1	NA	exon (NM_010856, exon 21 of 39)	exon (NM_010856, exon 21 of 39)	-4778	NR_029724	387204		NR_029724	ENSMUSG00000065432	Mir208a	Mirn208|Mirn208a|mir-208|mir-208a|mmu-mir-208	microRNA 208a	ncRNA
mm_162094.1	chrX	37557533	37557533	+	1	NA	5' UTR (NM_201236, exon 1 of 4)	5' UTR (NM_201236, exon 1 of 4)	121	NM_201236	194856	Mm.379498	NM_201236	ENSMUSG00000071770	Rhox4e	Rhox4|Rhox4.5|Rhox4d	reproductive homeobox 4E	protein-coding
mm_141789.1	chr17	34309818	34309831	-	1	NA	exon (NM_010382, exon 2 of 6)	exon (NM_010382, exon 2 of 6)	3957	NM_010382	14969	Mm.22564	NM_010382	ENSMUSG00000060586	H2-Eb1	Eb|H-2Eb|H2Eb|Ia-4|Ia4	histocompatibility 2, class II antigen E beta	protein-coding
mm_48670.1	chr5	146009022	146009049	-	1	NA	intron (NR_030782, intron 1 of 11)	MTD|LTR|ERVL-MaLR	582	NM_019792	56388	Mm.301900	NM_019792	ENSMUSG00000029630	Cyp3a25	AI327008	cytochrome P450, family 3, subfamily a, polypeptide 25	protein-coding
mm_120226.1	chr14	62857506	62857525	+	1	NA	intron (NM_175546, intron 1 of 11)	intron (NM_175546, intron 1 of 11)	-8027	NR_105860	102465311		NR_105860	ENSMUSG00000098858	Mir6541	Gm27311|mmu-mir-6541	microRNA 6541	ncRNA
mm_32700.1	chr4	116075377	116075387	+	1	NA	promoter-TSS (NM_025641)	promoter-TSS (NM_025641)	113	NM_153521	230654	Mm.3655	NM_153521	ENSMUSG00000028703	Lrrc41	AA409966|AW555107|D630045E04Rik|D730026A16Rik|MUF1	leucine rich repeat containing 41	protein-coding
mm_138738.1	chr17	36973684	36973694	+	1	NA	Intergenic	B1_Mur2|SINE|Alu	7548	NM_029747	76797	Mm.159787	NM_029747	ENSMUSG00000064308	2410137M14Rik	-	RIKEN cDNA 2410137M14 gene	protein-coding
mm_29007.1	chr3	101595089	101595115	-	1	NA	exon (NM_144900, exon 2 of 23)	exon (NM_144900, exon 2 of 23)	9605	NM_144900	11928	Mm.193670	NM_144900	ENSMUSG00000033161	Atp1a1	Atpa-1|BC010319	ATPase, Na+/K+ transporting, alpha 1 polypeptide	protein-coding
mm_5258.1	chr1	16657034	16657049	-	1	NA	promoter-TSS (NM_026456)	promoter-TSS (NM_026456)	78	NM_001310470	67923	Mm.289248	NM_026456	ENSMUSG00000079658	Eloc	2610043E24Rik|2610301I15Rik|AA407206|AI987979|AW049146|Tceb1	elongin C	protein-coding
mm_71045.1	chr8	33673946	33673960	+	1	NA	intron (NM_010344, intron 4 of 12)	ID_B1|SINE|B4	20715	NM_010344	14782	Mm.283573	NM_010344	ENSMUSG00000031584	Gsr	AI325518|D8Ertd238e|Gr-1|Gr1	glutathione reductase	protein-coding
mm_40801.1	chr5	67642169	67642202	+	1	NA	intron (NM_001284345, intron 33 of 36)	intron (NM_001284345, intron 33 of 36)	34302	NM_001033415	330096	Mm.442747	NM_001033415	ENSMUSG00000050010	Shisa3	D830007B15Rik	shisa family member 3	protein-coding
mm_45296.1	chr5	65091620	65091637	-	1	NA	Intergenic	Intergenic	-15940	NM_001347355	71778	Mm.10281	NM_175174	ENSMUSG00000054920	Klhl5	1300013C10Rik	kelch-like 5	protein-coding
mm_8256.1	chr1	138847617	138847631	-	1	NA	promoter-TSS (NM_010714)	promoter-TSS (NM_010714)	-45	NM_010714	16876	Mm.250732	NM_010714	ENSMUSG00000019230	Lhx9	3110009O07Rik|BB104635|LH2B	LIM homeobox protein 9	protein-coding
mm_156350.1	chrX	139317691	139317717	+	1	NA	intron (NR_045455, intron 4 of 19)	RLTR9D|LTR|ERVK	-15979	NM_011635	22037	Mm.1297	NM_011635	ENSMUSG00000051257	Trap1a	Tra-P1A	tumor rejection antigen P1A	protein-coding
mm_107851.1	chr12	69374900	69374910	+	1	NA	3' UTR (NM_007481, exon 2 of 2)	3' UTR (NM_007481, exon 2 of 2)	2755	NM_007481	11845	Mm.27308	NM_007481	ENSMUSG00000044147	Arf6	AI788669|AW496366	ADP-ribosylation factor 6	protein-coding
mm_77037.1	chr8	109565845	109565854	-	1	NA	promoter-TSS (NM_178380)	promoter-TSS (NM_178380)	-43	NM_175646	234723	Mm.37667	NM_175646	ENSMUSG00000031723	Txnl4b	AI595343|D530025J19Rik|DLP|Dim2	thioredoxin-like 4B	protein-coding
mm_119555.1	chr14	48667652	48667653	+	1	NA	promoter-TSS (NM_001286482)	promoter-TSS (NM_001286482)	-8	NM_001286481	18424	Mm.134516	NM_144841	ENSMUSG00000021848	Otx2	E130306E05Rik	orthodenticle homeobox 2	protein-coding
mm_28555.1	chr3	93411974	93412004	-	1	NA	Intergenic	RLTR12BD_Mm|LTR|ERVK	-16502	NR_039585	100628630		NR_039585	ENSMUSG00000093269	Mir5124a	Mir5124|mmu-mir-5124|mmu-mir-5124a|mu-mir-5124	microRNA 5124a	ncRNA
mm_143929.1	chr17	85800417	85800427	-	1	NA	Intergenic	CpG	-112168	NM_011380	20472	Mm.5039	NM_011380	ENSMUSG00000024134	Six2	-	sine oculis-related homeobox 2	protein-coding
mm_37678.1	chr4	129189570	129189594	-	1	NA	promoter-TSS (NM_029036)	promoter-TSS (NM_029036)	-100	NM_029036	74648	Mm.172064	NM_029036	ENSMUSG00000040928	S100pbp	4930429A08Rik|AI851343|S100pbpr	S100P binding protein	protein-coding
mm_62339.1	chr7	100496872	100496895	+	1	NA	exon (NM_011671, exon 3 of 8)	exon (NM_011671, exon 3 of 8)	3525	NM_011671	22228	Mm.171378	NM_011671	ENSMUSG00000033685	Ucp2	Slc25a8	uncoupling protein 2 (mitochondrial, proton carrier)	protein-coding
mm_82468.1	chr9	16186501	16186503	-	1	NA	intron (NM_001080814, intron 2 of 24)	intron (NM_001080814, intron 2 of 24)	191729	NM_001080814	270120	Mm.195010	NM_001080814	ENSMUSG00000074505	Fat3	9430076A06Rik|D430038H04Rik|Gm1132|Gm510|MFAT3F	FAT atypical cadherin 3	protein-coding
mm_159193.1	chr2	118703853	118703853	-	1	NA	5' UTR (NM_001081971, exon 1 of 1)	5' UTR (NM_001081971, exon 1 of 1)	110	NM_001081971	383787	Mm.35758	NM_001081971	ENSMUSG00000078137	Ankrd63	Gm1337	ankyrin repeat domain 63	protein-coding
mm_88169.1	chr10	69764654	69764669	+	1	NA	intron (NM_170730, intron 1 of 17)	intron (NM_170730, intron 1 of 17)	-160871	NM_170687	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_83207.1	chr9	41985634	41985647	-	1	NA	exon (NM_011436, exon 39 of 48)	exon (NM_011436, exon 39 of 48)	138649	NM_011436	20660	Mm.121920	NM_011436	ENSMUSG00000049313	Sorl1	2900010L19Rik|AI596264|AW261561|LR11|SorLA|gp250|mSorLA	sortilin-related receptor, LDLR class A repeats-containing	protein-coding
mm_67774.1	chr7	97082944	97082982	-	1	NA	intron (NM_001162477, intron 1 of 9)	intron (NM_001162477, intron 1 of 9)	1212	NM_010248	14389	Mm.42033	NM_010248	ENSMUSG00000004508	Gab2	AI463667|D130058I17Rik|p97	growth factor receptor bound protein 2-associated protein 2	protein-coding
mm_34638.1	chr4	150615171	150615194	+	1	NA	exon (NM_001085492, exon 18 of 23)	exon (NM_001085492, exon 18 of 23)	36992	NM_173774	242773	Mm.29280	NM_173774	ENSMUSG00000039838	Slc45a1	C230078B22|Dnb5	solute carrier family 45, member 1	protein-coding
mm_1302.1	chr1	64690367	64690371	+	1	NA	promoter-TSS (NM_001097644)	promoter-TSS (NM_001097644)	290	NR_038009	69941	Mm.69044	NR_038009	ENSMUSG00000087213	2810408I11Rik	-	RIKEN cDNA 2810408I11 gene	ncRNA
mm_109433.1	chr12	110694178	110694185	+	1	NA	exon (NM_010480, exon 5 of 11)	exon (NM_010480, exon 5 of 11)	2214	NM_010480	15519	Mm.1843	NM_010480	ENSMUSG00000021270	Hsp90aa1	86kDa|89kDa|AL024080|AL024147|Hsp86-1|Hsp89|Hsp90|Hspca|hsp4	heat shock protein 90, alpha (cytosolic), class A member 1	protein-coding
mm_64353.1	chr7	142387001	142387011	+	1	NA	intron (NM_009983, intron 1 of 8)	intron (NM_009983, intron 1 of 8)	864	NM_009983	13033	Mm.231395	NM_009983	ENSMUSG00000007891	Ctsd	CD|CatD	cathepsin D	protein-coding
mm_167913.1	chrX	93969203	93969224	+	1	NA	non-coding (NR_028320, exon 1 of 3)	non-coding (NR_028320, exon 1 of 3)	557	NR_028320	385493	Mm.328014	NM_001033480	ENSMUSG00000081044	AU015836	-	expressed sequence AU015836	ncRNA
mm_7458.1	chr1	120435740	120435750	-	1	NA	Intergenic	Intergenic	69339	NM_010766	17167	Mm.1856	NM_010766	ENSMUSG00000026390	Marco	AI323439|Ly112|Scara2	macrophage receptor with collagenous structure	protein-coding
mm_118431.1	chr14	8006533	8006541	+	1	NA	intron (NM_001331064, intron 1 of 8)	ID4|SINE|ID	3571	NM_001331064	66082	Mm.181473	NM_025341	ENSMUSG00000025277	Abhd6	0610041D24Rik|AA673485|AV065425	abhydrolase domain containing 6	protein-coding
mm_61819.1	chr7	87584141	87584173	+	1	NA	promoter-TSS (NM_001081414)	promoter-TSS (NM_001081414)	-11	NM_001081414	108071	Mm.235018	NM_001033224	ENSMUSG00000049583	Grm5	6430542K11Rik|AI850523|Glu5R|Gprc1e|mGluR5|mGluR5b	glutamate receptor, metabotropic 5	protein-coding
mm_120977.1	chr14	78692347	78692395	+	1	NA	intron (NM_001081336, intron 1 of 28)	intron (NM_001081336, intron 1 of 28)	32718	NM_001081336	380921	Mm.89591	NM_001081336	ENSMUSG00000034731	Dgkh	5930402B05Rik|D130015C16|DGK	diacylglycerol kinase, eta	protein-coding
mm_134120.1	chr16	10313901	10313907	-	1	NA	promoter-TSS (NM_007929)	promoter-TSS (NM_007929)	64	NM_007929	13731	Mm.246009	NM_007929	ENSMUSG00000022505	Emp2	XMP	epithelial membrane protein 2	protein-coding
mm_25610.1	chr3	117869021	117869049	+	1	NA	promoter-TSS (NM_029655)	promoter-TSS (NM_029655)	-99	NM_029655	76561	Mm.33824	NM_029655	ENSMUSG00000028007	Snx7	2510028H01Rik	sorting nexin 7	protein-coding
mm_5596.1	chr1	39558932	39558943	-	1	NA	intron (NM_001033135, intron 4 of 6)	intron (NM_001033135, intron 4 of 6)	-10097	NR_028555	100217461		NR_028555	ENSMUSG00000077704	Snord89	MBII-289	small nucleolar RNA, C/D box 89	snoRNA
mm_61957.1	chr7	90209000	90209010	+	1	NA	3' UTR (NM_001252521, exon 20 of 20)	3' UTR (NM_001252521, exon 20 of 20)	56427	NM_029256	75338	Mm.487222	NM_029256	ENSMUSG00000030617	Ccdc83	4930549K11Rik|4930554C01Rik|4932423M01Rik	coiled-coil domain containing 83	protein-coding
mm_149273.1	chr19	10589110	10589119	+	1	NA	3' UTR (NM_201351, exon 8 of 8)	3' UTR (NM_201351, exon 8 of 8)	-11728	NR_126092	72982	Mm.391194	NM_028411	ENSMUSG00000024666	Tmem138	1700113I01Rik|2900055D14Rik	transmembrane protein 138	protein-coding
mm_46794.1	chr5	112790704	112790713	-	1	NA	intron (NM_028901, intron 30 of 43)	intron (NM_028901, intron 30 of 43)	-2584	NR_040675	67360	Mm.59218	NR_040675	ENSMUSG00000098230	1700095B10Rik	-	RIKEN cDNA 1700095B10 gene	ncRNA
mm_47199.1	chr5	120812507	120812539	-	1	NA	promoter-TSS (NR_003507)	promoter-TSS (NR_003507)	-9	NM_033541	114643	Mm.43230	NM_033541	ENSMUSG00000001166	Oas1c	Oasl2|Oasl5	2'-5' oligoadenylate synthetase 1C	protein-coding
mm_38129.1	chr4	134577317	134577338	-	1	NA	intron (NM_207237, intron 7 of 11)	intron (NM_207237, intron 7 of 11)	-9476	NR_105829	102465216		NR_105829	ENSMUSG00000099289	Mir6403	Gm27992|mmu-mir-6403	microRNA 6403	ncRNA
mm_60197.1	chr7	43409253	43409262	+	1	NA	exon (NM_172900, exon 4 of 12)	exon (NM_172900, exon 4 of 12)	977	NM_172900	243958	Mm.24444	NM_172900	ENSMUSG00000030468	Siglecg	9830164H23|A630096C01Rik|Siglec-G|Siglec10|mSiglec-G	sialic acid binding Ig-like lectin G	protein-coding
mm_101121.1	chr11	12026773	12026823	-	1	NA	intron (NM_010345, intron 1 of 16)	intron (NM_010345, intron 1 of 16)	1173	NM_001177629	14783	Mm.273117	NM_010345	ENSMUSG00000020176	Grb10	5730571D09Rik|AI325020|Meg1|mKIAA0207	growth factor receptor bound protein 10	protein-coding
mm_61037.1	chr7	49609767	49609777	+	1	NA	3' UTR (NM_001111016, exon 39 of 39)	3' UTR (NM_001111016, exon 39 of 39)	27063	NM_001005232	13172	Mm.307176	NM_001005232	ENSMUSG00000030507	Dbx1	AI426026|Dbx	developing brain homeobox 1	protein-coding
mm_52013.1	chr6	94221956	94221958	+	1	NA	intron (NR_130996, intron 1 of 1)	URR1B|DNA|hAT-Charlie	15485	NR_130996	78178	Mm.452749	NR_130996	ENSMUSG00000045095	4930511A08Rik	-	RIKEN cDNA 4930511A08 gene	ncRNA
mm_34318.1	chr4	141821354	141821366	+	1	NA	exon (NM_007919, exon 5 of 8)	exon (NM_007919, exon 5 of 8)	4645	NM_007919	13706	Mm.45316	NM_007919	ENSMUSG00000058579	Cela2a	Ela-2|Ela2|Ela2a	chymotrypsin-like elastase family, member 2A	protein-coding
mm_59884.1	chr7	30292259	30292303	+	1	NA	exon (NM_001081114, exon 2 of 14)	exon (NM_001081114, exon 2 of 14)	528	NM_001081114	76686	Mm.159258	NM_001081114	ENSMUSG00000013921	Clip3	1500005P14Rik|AI844915|Clipr-59	CAP-GLY domain containing linker protein 3	protein-coding
mm_1111.1	chr1	59860376	59860383	+	1	NA	intron (NM_007561, intron 10 of 12)	ID_B1|SINE|B4	-52627	NM_001037725	72750	Mm.258250	NM_001037725	ENSMUSG00000041040	Fam117b	2810425F24Rik|6330416D14Rik|Als2cr13	family with sequence similarity 117, member B	protein-coding
mm_81435.1	chr9	109095536	109095547	+	1	NA	5' UTR (NM_172775, exon 1 of 38)	5' UTR (NM_172775, exon 1 of 38)	105	NM_172775	235611	Mm.53862	NM_172775	ENSMUSG00000053646	Plxnb1	2900002G15Rik|AU042020|mKIAA0407	plexin B1	protein-coding
mm_108769.1	chr12	89765387	89765390	+	1	NA	intron (NM_172544, intron 14 of 19)	intron (NM_172544, intron 14 of 19)	-47095	NM_001252074	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding
mm_60881.1	chr7	46240957	46240970	+	1	NA	promoter-TSS (NM_013624)	promoter-TSS (NM_013624)	-24	NM_013624	18419	Mm.8020	NM_013624	ENSMUSG00000009487	Otog	4932420K09|Otgn|twt	otogelin	protein-coding
mm_128037.1	chr15	25364259	25364297	-	1	NA	exon (NM_027395, exon 2 of 2)	exon (NM_027395, exon 2 of 2)	49486	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	brain abundant, membrane attached signal protein 1	protein-coding
mm_154787.1	chrX	13071471	13071499	+	1	NA	promoter-TSS (NM_009481)	promoter-TSS (NM_009481)	-13	NM_009481	22284	Mm.242646	NM_009481	ENSMUSG00000031010	Usp9x	5730589N07Rik|AA407302|AA407699|AL022658|AL022749|Dffrx|FAF-X|Fafl	ubiquitin specific peptidase 9, X chromosome	protein-coding
mm_138211.1	chr17	34305911	34305934	+	1	NA	promoter-TSS (NM_010382)	promoter-TSS (NM_010382)	55	NM_010382	14969	Mm.22564	NM_010382	ENSMUSG00000060586	H2-Eb1	Eb|H-2Eb|H2Eb|Ia-4|Ia4	histocompatibility 2, class II antigen E beta	protein-coding
mm_97067.1	chr11	72960289	72960295	+	1	NA	promoter-TSS (NM_001163337)	promoter-TSS (NM_001163337)	-877	NM_016745	53313	Mm.6306	NM_016745	ENSMUSG00000020788	Atp2a3	SERCA3b|Serca3	ATPase, Ca++ transporting, ubiquitous	protein-coding
mm_172663.1	chr8	41965882	41965907	-	1	NA	intron (NR_045497, intron 3 of 5)	RLTRETN_Mm|LTR|ERVK	138627	NR_045497	69966	Mm.416903	NR_045497	ENSMUSG00000102046	2810404M03Rik	-	RIKEN cDNA 2810404M03 gene	ncRNA
mm_154939.1	chrX	36112098	36112113	+	1	NA	promoter-TSS (NM_133990)	promoter-TSS (NM_133990)	-3	NM_133990	16164	Mm.24208	NM_133990	ENSMUSG00000017057	Il13ra1	AI882074|CD213a1|IL-13R-alpha-1|IL-13r[a]|Il13ra|NR4	interleukin 13 receptor, alpha 1	protein-coding
mm_153080.1	chr19	32374242	32374246	-	1	NA	intron (NM_144792, intron 1 of 9)	intron (NM_144792, intron 1 of 9)	14210	NM_144792	208449	Mm.329810	NM_144792	ENSMUSG00000040451	Sgms1	9530058O11Rik|AI841905|C80702|Mob|Sms1|Sor1|Tmem23	sphingomyelin synthase 1	protein-coding
mm_13905.1	chr2	120484344	120484355	+	1	NA	intron (NM_001109761, intron 3 of 20)	intron (NM_001109761, intron 3 of 20)	7440	NM_001109761	12335	Mm.458021	NM_007601	ENSMUSG00000079110	Capn3	AI323605|Capa-3|Capa3|Lp82|p94	calpain 3	protein-coding
mm_148610.1	chr19	5335645	5335651	+	1	NA	promoter-TSS (NM_139301)	promoter-TSS (NM_139301)	-93	NM_139301	225865	Mm.87321	NM_139301	ENSMUSG00000038498	Catsper1	Catsper|KSper	cation channel, sperm associated 1	protein-coding
mm_44678.1	chr5	30014191	30014194	-	1	NA	intron (NM_001314054, intron 2 of 4)	B1_Mur2|SINE|Alu	1078	NM_031168	16193	Mm.1019	NM_031168	ENSMUSG00000025746	Il6	Il-6	interleukin 6	protein-coding
mm_3110.1	chr1	134560158	134560180	+	1	NA	promoter-TSS (NM_152895)	promoter-TSS (NM_152895)	-9	NM_152895	75605	Mm.28995	NM_152895	ENSMUSG00000042207	Kdm5b	2010009J12Rik|2210016I17Rik|AW556288|D1Ertd202e|Jarid1b|PLU-1|PUT1|Plu1|RBBP2H1A|Rb-Bp2|mKIAA4034	lysine (K)-specific demethylase 5B	protein-coding
mm_128914.1	chr15	73645666	73645750	-	1	NA	Intergenic	CpG	-20964	NM_001033219	106068	Mm.212813	NM_001033219	ENSMUSG00000079020	Slc45a4	9330175B01Rik|AW552276	solute carrier family 45, member 4	protein-coding
mm_165289.1	chr2	86867531	86867531	+	1	NA	Intergenic	U2|snRNA|snRNA	-15835	NM_146730	258725	Mm.377658	NM_146730	ENSMUSG00000075171	Olfr1095	MOR179-1	olfactory receptor 1095	protein-coding
mm_31554.1	chr4	56802338	56802359	+	1	NA	promoter-TSS (NM_026079)	promoter-TSS (NM_026079)	-17	NM_026079	230233	Mm.282743	NM_026079	ENSMUSG00000028431	Ikbkap	3110040G09Rik|6030413P05|C78473|Elp1|IKAP	inhibitor of kappa light polypeptide enhancer in B cells, kinase complex-associated protein	protein-coding
mm_127575.1	chr15	102280504	102280529	+	1	NA	exon (NM_134100, exon 2 of 2)	exon (NM_134100, exon 2 of 2)	1060	NM_134100	106073	Mm.287740	NM_134100	ENSMUSG00000045665	Mfsd5	AA409375|AW556797|D15Mgi27	major facilitator superfamily domain containing 5	protein-coding
mm_24546.1	chr3	93319741	93319754	+	1	NA	promoter-TSS (NM_133698)	promoter-TSS (NM_133698)	-2	NM_133698	68723	Mm.208047	NM_133698	ENSMUSG00000041991	Hrnr	1110033K19Rik|A530063N20Rik|S100a18	hornerin	protein-coding
mm_119160.1	chr14	31665813	31665823	+	1	NA	intron (NM_025295, intron 2 of 3)	intron (NM_025295, intron 2 of 3)	24761	NM_025295	26363	Mm.282679	NM_025295	ENSMUSG00000021900	Btd	-	biotinidase	protein-coding
mm_136229.1	chr16	90284301	90284348	-	1	NA	5' UTR (NM_001346799, exon 1 of 20)	5' UTR (NM_001346799, exon 1 of 20)	179	NM_178923	224432	Mm.439811	NM_178923	ENSMUSG00000022983	Scaf4	AA517739|Sfrs15|Sra4|Srsf15	SR-related CTD-associated factor 4	protein-coding
mm_81385.1	chr9	108953579	108953593	+	1	NA	promoter-TSS (NM_007738)	promoter-TSS (NM_007738)	-159	NM_007738	12836	Mm.6200	NM_007738	ENSMUSG00000025650	Col7a1	AW209154	collagen, type VII, alpha 1	protein-coding
mm_30122.1	chr3	141464576	141464578	-	1	NA	promoter-TSS (NM_009472)	promoter-TSS (NM_009472)	-987	NM_009472	22253	Mm.24430	NM_009472	ENSMUSG00000059921	Unc5c	B130051O18Rik|Unc5h3|rcm	unc-5 netrin receptor C	protein-coding
mm_137909.1	chr17	32109112	32109114	+	1	NA	Intergenic	RLTR48A|LTR|ERV1	-17690	NR_027316	435518	Mm.328944	NR_027316	ENSMUSG00000002791	Pdxk-ps	ENSMUSG00000002791|Gm9743	pyridoxal (pyridoxine, vitamin B6) kinase, pseudogene	pseudo
mm_53320.1	chr6	129187509	129187520	+	1	NA	TTS (NM_053109)	TTS (NM_053109)	6899	NM_053109	93694	Mm.197536	NM_053109	ENSMUSG00000030157	Clec2d	Clr-b|Clrb|Ocil	C-type lectin domain family 2, member d	protein-coding
mm_46615.1	chr5	108122110	108122142	-	1	NA	3' UTR (NM_028876, exon 4 of 4)	3' UTR (NM_028876, exon 4 of 4)	10465	NM_001347383	73130	Mm.363960	NM_028876	ENSMUSG00000063406	Tmed5	3110020O18Rik|4432412D15Rik	transmembrane p24 trafficking protein 5	protein-coding
mm_107019.1	chr12	12766010	12766020	+	1	NA	Intergenic	Intergenic	-96098	NR_136889	102637952	Mm.421393	NR_136889		Gm34637	-	predicted gene, 34637	ncRNA
mm_56414.1	chr6	97252326	97252337	-	1	NA	exon (NM_001081157, exon 1 of 3)	exon (NM_001081157, exon 1 of 3)	449	NM_001081157	320502	Mm.68163	NM_001081157	ENSMUSG00000044086	Lmod3	5430424A14Rik	leiomodin 3 (fetal)	protein-coding
mm_100194.1	chr11	116752325	116752350	+	1	NA	non-coding (NR_003364, exon 1 of 4)	non-coding (NR_003364, exon 1 of 4)	170	NR_003364	193217	Mm.100084	NR_003364		BC018473	-	cDNA sequence BC018473	ncRNA
mm_63540.1	chr7	128004550	128004582	+	1	NA	exon (NM_001079932, exon 1 of 6)	exon (NM_001079932, exon 1 of 6)	188	NM_001079932	434246	Mm.389924	NM_001079932	ENSMUSG00000042828	Trim72	BC067209|MG53	tripartite motif-containing 72	protein-coding
mm_51449.1	chr6	80401606	80401612	+	1	NA	intron (NM_001347261, intron 2 of 2)	GA-rich|Low_complexity|Low_complexity	381966	NM_178731	243499	Mm.483425	NM_178731	ENSMUSG00000052581	Lrrtm4	7530419J18Rik|A230052N11	leucine rich repeat transmembrane neuronal 4	protein-coding
mm_64549.1	chr7	144417811	144417826	+	1	NA	intron (NM_001113373, intron 15 of 15)	intron (NM_001113373, intron 15 of 15)	25615	NR_037302	100499519		NR_037302	ENSMUSG00000093912	Mir3470b	mmu-mir-3470b	microRNA 3470b	ncRNA
mm_64440.1	chr7	142653666	142653699	+	1	NA	3' UTR (NM_010514, exon 4 of 4)	3' UTR (NM_010514, exon 4 of 4)	1314	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_46582.1	chr5	107478773	107478776	-	1	NA	intron (NM_001255991, intron 5 of 8)	intron (NM_001255991, intron 5 of 8)	-18971	NM_001007574	231570	Mm.261891	NM_001007574	ENSMUSG00000044060	A830010M20Rik	AI849226|Kiaa1107|mKIAA1107	RIKEN cDNA A830010M20 gene	protein-coding
mm_85870.1	chr9	110887956	110887989	-	1	NA	intron (NM_146228, intron 8 of 26)	intron (NM_146228, intron 8 of 26)	7650	NM_001146060	235633	Mm.86338	NM_146228	ENSMUSG00000044037	Als2cl	79H19D|79H19E|BC022645|D930044G19Rik|mRn.49018	ALS2 C-terminal like	protein-coding
mm_127337.1	chr15	100469791	100469801	+	1	NA	exon (NM_134093, exon 2 of 9)	exon (NM_134093, exon 2 of 9)	762	NM_134093	68614	Mm.275272	NM_134093	ENSMUSG00000037353	Letmd1	1110019O13Rik|AI593524|BB130465|BB235638|HCCR-2|HCCR1|MCC-32|Mccr	LETM1 domain containing 1	protein-coding
mm_99111.1	chr11	100135467	100135482	+	1	NA	exon (NM_008469, exon 1 of 8)	exon (NM_008469, exon 1 of 8)	475	NM_008469	16665	Mm.440010	NM_008469	ENSMUSG00000054146	Krt15	AI528832|K15|Krt1-15	keratin 15	protein-coding
mm_156153.1	chrX	129953024	129953027	+	1	NA	intron (NM_172493, intron 10 of 26)	intron (NM_172493, intron 10 of 26)	203283	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diaph2	Dia3|Diap2|Drf2|E430022I22Rik	diaphanous related formin 2	protein-coding
mm_120950.1	chr14	76780801	76780829	+	1	NA	Intergenic	Intergenic	103247	NR_015485	73272	Mm.116804	NR_015485	ENSMUSG00000101009	1700108F19Rik	1700020I02Rik|BB065030	RIKEN cDNA 1700108F19 gene	ncRNA
mm_70770.1	chr8	21970571	21970575	+	1	NA	promoter-TSS (NM_026459)	promoter-TSS (NM_026459)	-23	NM_026459	67929	Mm.60688	NM_026459	ENSMUSG00000017049	Ccdc70	1700112P19Rik	coiled-coil domain containing 70	protein-coding
mm_31389.1	chr4	48043641	48043652	+	1	NA	Intergenic	Intergenic	-1659	NM_015743	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_126783.1	chr15	86195092	86195116	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-8963	NM_145475	223753	Mm.222685	NM_145475	ENSMUSG00000035891	Cerk	AI848610|D330016D08Rik|mKIAA1646	ceramide kinase	protein-coding
mm_25145.1	chr3	102734904	102734952	+	1	NA	promoter-TSS (NM_001243132)	promoter-TSS (NM_001243132)	158	NM_027533	70747	Mm.27469	NM_027533	ENSMUSG00000027858	Tspan2	6330415F13Rik|B230119D02Rik|tspan-2	tetraspanin 2	protein-coding
mm_33125.1	chr4	124802834	124802844	+	1	NA	intron (NM_008636, intron 1 of 10)	intron (NM_008636, intron 1 of 10)	290	NM_008636	17764	Mm.272397	NM_008636	ENSMUSG00000028890	Mtf1	MTF-1|Thyls	metal response element binding transcription factor 1	protein-coding
mm_35211.1	chr4	19630000	19630032	-	1	NA	intron (NR_074089, intron 17 of 23)	L2a|LINE|L2	54950	NM_025476	66302	Mm.440686	NM_025476	ENSMUSG00000028229	Rmdn1	Fam82b|RMD-1	regulator of microtubule dynamics 1	protein-coding
mm_123021.1	chr14	55116548	55116554	-	1	NA	5' UTR (NM_177049, exon 1 of 6)	5' UTR (NM_177049, exon 1 of 6)	384	NM_177049	319984	Mm.19047	NM_177049	ENSMUSG00000022208	Jph4	9330157P13Rik|JP-4|JPHL1	junctophilin 4	protein-coding
mm_95703.1	chr11	54438189	54438220	+	1	NA	promoter-TSS (NM_173753)	promoter-TSS (NM_173753)	25	NM_173753	216742	Mm.34087	NM_173753	ENSMUSG00000035992	Fnip1	A730024A03Rik|AI838773|AW557298	folliculin interacting protein 1	protein-coding
mm_82617.1	chr9	21770173	21770202	-	1	NA	intron (NM_145611, intron 9 of 11)	intron (NM_145611, intron 9 of 11)	-9901	NM_026282	67629	Mm.295642	NM_026282	ENSMUSG00000074476	Spc24	2410030K01Rik|AV109292|Spbc24	SPC24, NDC80 kinetochore complex component, homolog (S. cerevisiae)	protein-coding
mm_137946.1	chr17	32877518	32877518	+	1	NA	Intergenic	Intergenic	14085	NM_207245	240066	Mm.26636	NM_207245	ENSMUSG00000095325	Zfp870	AI173952	zinc finger protein 870	protein-coding
mm_4834.1	chr1	186587405	186587413	+	1	NA	Intergenic	MIR|SINE|MIR	-28728	NR_131158	320449	Mm.404477	NR_131124	ENSMUSG00000103690	A730004F24Rik	-	RIKEN cDNA A730004F24 gene	ncRNA
mm_56929.1	chr6	119481558	119481580	-	1	NA	3' UTR (NM_133940, exon 1 of 1)	3' UTR (NM_133940, exon 1 of 1)	1901	NM_133940	101358	Mm.125477	NM_133940	ENSMUSG00000030019	Fbxl14	AW322056|Fbx14l	F-box and leucine-rich repeat protein 14	protein-coding
mm_143886.1	chr17	84313677	84313696	-	1	NA	intron (NM_183021, intron 28 of 37)	intron (NM_183021, intron 28 of 37)	-125739	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_42050.1	chr5	108629792	108629876	+	1	NA	promoter-TSS (NM_153569)	promoter-TSS (NM_153569)	24	NM_028223	72392	Mm.258324	NM_028223	ENSMUSG00000013495	Tmem175	3010001K23Rik|AI504381|mTMEM175	transmembrane protein 175	protein-coding
mm_169169.1	chr13	65605184	65605200	+	1	NA	Intergenic	RLTR27|LTR|ERVK	326338	NM_178364	170936	Mm.151546	NM_178364	ENSMUSG00000021514	Zfp369	B930030B22Rik|D230020H11Rik|NRIF2	zinc finger protein 369	protein-coding
mm_81617.1	chr9	110769762	110769771	+	1	NA	TTS (NM_010859)	TTS (NM_010859)	6085	NM_010859	17897	Mm.7353	NM_010859	ENSMUSG00000059741	Myl3	MLC1s|MLC1v|Mylc|VLC1	myosin, light polypeptide 3	protein-coding
mm_86743.1	chr10	19352690	19352737	+	1	NA	Intergenic	Intergenic	-3826	NM_053008	94222	Mm.156946	NM_053008	ENSMUSG00000045591	Olig3	Bhlhb7|bHLHe20|oligo3	oligodendrocyte transcription factor 3	protein-coding
mm_98170.1	chr11	87751820	87751843	+	1	NA	Intergenic	Intergenic	-5033	NR_029555	387160		NR_029555	ENSMUSG00000105196	Mir142	Mirn142|miR-142|mir-142a|mmu-mir-142|mmu-mir-142a	microRNA 142	ncRNA
mm_54938.1	chr6	48445827	48445847	-	1	NA	promoter-TSS (NM_001085417)	promoter-TSS (NM_001085417)	-12	NM_001085417	68910	Mm.2464	NM_020589	ENSMUSG00000068551	Zfp467	1190001I08Rik|AB041616|AI426952|AV017623|EZI|MNCb-3350|Znf467	zinc finger protein 467	protein-coding
mm_153606.1	chr19	43940147	43940165	-	1	NA	promoter-TSS (NM_028029)	promoter-TSS (NM_028029)	42	NM_028029	71972	Mm.159024	NM_028029	ENSMUSG00000025195	Dnmbp	2410003L07Rik|2410003M15Rik|TUBA	dynamin binding protein	protein-coding
mm_141063.1	chr17	25785534	25785591	-	1	NA	promoter-TSS (NM_026897)	promoter-TSS (NM_026897)	24	NM_001271437	68977	Mm.29230	NM_026897	ENSMUSG00000061046	Haghl	1500017E18Rik|2810014I23Rik|C330022E15Rik	hydroxyacylglutathione hydrolase-like	protein-coding
mm_16550.1	chr2	181767041	181767073	+	1	NA	promoter-TSS (NM_008665)	promoter-TSS (NM_008665)	28	NM_001171616	17932	Mm.458718	NM_008665	ENSMUSG00000010505	Myt1	Nzf2|Nzf2a|Nzf2b|Nztf2	myelin transcription factor 1	protein-coding
mm_143539.1	chr17	74016838	74016845	-	1	NA	TTS (NM_053188)	TTS (NM_053188)	31075	NM_053188	94224	Mm.38933	NM_053188	ENSMUSG00000038541	Srd5a2	5ART2|S5AR 2	steroid 5 alpha-reductase 2	protein-coding
mm_16554.1	chr2	181837875	181837910	+	1	NA	promoter-TSS (NM_153594)	promoter-TSS (NM_153594)	38	NM_001291211	245867	Mm.491085	NM_153594	ENSMUSG00000027589	Pcmtd2	5330414D10Rik|AI314201	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 2	protein-coding
mm_75556.1	chr8	57778404	57778414	-	1	NA	intron (NM_175032, intron 11 of 11)	intron (NM_175032, intron 11 of 11)	-125354	NM_144731	108150	Mm.62886	NM_144731	ENSMUSG00000031608	Galnt7	AI225872	UDP-N-acetyl-alpha-D-galactosamine: polypeptide N-acetylgalactosaminyltransferase 7	protein-coding
mm_160944.1	chr11	95587647	95587647	-	1	NA	promoter-TSS (NM_033217)	promoter-TSS (NM_033217)	51	NM_033217	18053	Mm.283893	NM_033217	ENSMUSG00000000120	Ngfr	LNGFR|Tnfrsf16|p75|p75NGFR|p75NTR	nerve growth factor receptor (TNFR superfamily, member 16)	protein-coding
mm_113366.1	chr13	32965694	32965712	+	1	NA	intron (NM_011454, intron 1 of 6)	intron (NM_011454, intron 1 of 6)	190	NM_011454	20708	Mm.36526	NM_011454	ENSMUSG00000042842	Serpinb6b	NK13|Spi12|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 6b	protein-coding
mm_78577.1	chr9	36768013	36768031	+	1	NA	promoter-TSS (NM_008408)	promoter-TSS (NM_008408)	-444	NM_008408	16430	Mm.2863	NM_008408	ENSMUSG00000032116	Stt3a	AA408947|BB081708|Itm1	STT3, subunit of the oligosaccharyltransferase complex, homolog A (S. cerevisiae)	protein-coding
mm_150718.1	chr19	43523720	43523730	+	1	NA	intron (NM_010324, intron 1 of 8)	intron (NM_010324, intron 1 of 8)	880	NM_010324	14718	Mm.19039	NM_010324	ENSMUSG00000025190	Got1	AI789014|Got-1|cAspAT|cCAT	glutamic-oxaloacetic transaminase 1, soluble	protein-coding
mm_1714.1	chr1	75236754	75236761	+	1	NA	promoter-TSS (NM_001159885)	promoter-TSS (NM_001159885)	55	NM_001159885	56812	Mm.489660	NM_020266	ENSMUSG00000026203	Dnajb2	2700059H22Rik|Dnajb10|Hsj1|mDj8	DnaJ heat shock protein family (Hsp40) member B2	protein-coding
mm_61571.1	chr7	79743171	79743187	+	1	NA	promoter-TSS (NM_001037927)	promoter-TSS (NM_001037927)	16	NM_001037927	626359	Mm.387216	NM_001037927	ENSMUSG00000039099	Wdr93	EG626359	WD repeat domain 93	protein-coding
mm_75450.1	chr8	47675180	47675190	-	1	NA	promoter-TSS (NM_023503)	promoter-TSS (NM_023503)	-26	NM_023503	69260	Mm.430733	NM_023503	ENSMUSG00000063049	Ing2	2810011M06Rik|Ing1l|Ing2b|P33ING2	inhibitor of growth family, member 2	protein-coding
mm_152405.1	chr19	10593176	10593186	-	1	NA	exon (NM_145496, exon 16 of 17)	exon (NM_145496, exon 16 of 17)	11077	NM_145496	225913	Mm.374868	NM_145496	ENSMUSG00000034371	Tkfc	BC021917|Dak	triokinase, FMN cyclase	protein-coding
mm_123489.1	chr14	66077764	66077774	-	1	NA	promoter-TSS (NM_009618)	promoter-TSS (NM_009618)	0	NM_009618	11495	Mm.422850	NM_009618	ENSMUSG00000022039	Adam2	AI323749|Ftnb|Ph30-beta	a disintegrin and metallopeptidase domain 2	protein-coding
mm_53519.1	chr6	136488734	136488769	+	1	NA	Intergenic	Intergenic	-30100	NM_019426	54343	Mm.173271	NM_019426	ENSMUSG00000030213	Atf7ip	2610204M12Rik|AM|Mcaf1	activating transcription factor 7 interacting protein	protein-coding
mm_38744.1	chr4	145270157	145270167	-	1	NA	intron (NM_009401, intron 12 of 12)	intron (NM_009401, intron 12 of 12)	-23292	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_138257.1	chr17	34590835	34590847	+	1	NA	exon (NM_134116, exon 3 of 4)	exon (NM_134116, exon 3 of 4)	1035	NM_134116	106512	Mm.26584	NM_134116	ENSMUSG00000034786	Gpsm3	AA960287|AGS4	G-protein signalling modulator 3 (AGS3-like, C. elegans)	protein-coding
mm_89845.1	chr10	106879958	106879968	+	1	NA	intron (NM_001205341, intron 21 of 31)	(CA)n|Simple_repeat|Simple_repeat	243701	NM_001142804	380660	Mm.336072	NM_198636	ENSMUSG00000035948	Acss3	8430416H19Rik|Gm874	acyl-CoA synthetase short-chain family member 3	protein-coding
mm_69478.1	chr7	133760138	133760171	-	1	NA	5' UTR (NM_001286030, exon 1 of 12)	5' UTR (NM_001286030, exon 1 of 12)	115	NM_001286030	101437	Mm.199223	NM_133941	ENSMUSG00000030986	Dhx32	3110079L04Rik|4732469F02Rik|AA408140|Ddx32	DEAH (Asp-Glu-Ala-His) box polypeptide 32	protein-coding
mm_27242.1	chr3	36571919	36571931	-	1	NA	promoter-TSS (NM_009828)	promoter-TSS (NM_009828)	71	NM_009828	12428	Mm.4189	NM_009828	ENSMUSG00000027715	Ccna2	AA408589|Ccn-1|Ccn1|Ccna|CycA2|Cyca	cyclin A2	protein-coding
mm_104120.1	chr11	86750463	86750475	-	1	NA	intron (NM_001003908, intron 1 of 31)	intron (NM_001003908, intron 1 of 31)	7023	NM_001003908	67300	Mm.254588	NM_001003908	ENSMUSG00000047126	Cltc	3110065L21Rik|CHC|R74732	clathrin, heavy polypeptide (Hc)	protein-coding
mm_32178.1	chr4	100776795	100776806	+	1	NA	5' UTR (NM_198037, exon 1 of 27)	5' UTR (NM_198037, exon 1 of 27)	121	NM_198037	320508	Mm.151962	NM_198037	ENSMUSG00000028532	Cachd1	1190007F10Rik|AI852726|B430218L07Rik|Vwcd1|mKIAA1573	cache domain containing 1	protein-coding
mm_37364.1	chr4	120814111	120814116	-	1	NA	intron (NM_001048168, intron 1 of 9)	intron (NM_001048168, intron 1 of 9)	11628	NM_001277095	18046	Mm.435590	NM_008692	ENSMUSG00000032897	Nfyc	-	nuclear transcription factor-Y gamma	protein-coding
mm_101028.1	chr11	8579703	8579720	-	1	NA	intron (NM_001083587, intron 3 of 30)	intron (NM_001083587, intron 3 of 30)	84824	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_173275.1	chrX	99557263	99557265	+	1	NA	Intergenic	Intergenic	-86529	NM_008853	18744	Mm.8211	NM_008853	ENSMUSG00000034403	Pja1	praja-1	praja ring finger 1, E3 ubiquitin protein ligase	protein-coding
mm_49703.1	chr6	34354156	34354199	+	1	NA	promoter-TSS (NM_008012)	promoter-TSS (NM_008012)	13	NM_008012	14187	Mm.5378	NM_008012	ENSMUSG00000029762	Akr1b8	FR-1|Fgfrp|Fgrp	aldo-keto reductase family 1, member B8	protein-coding
mm_48574.1	chr5	143329184	143329245	-	1	NA	promoter-TSS (NM_028379)	promoter-TSS (NM_028379)	24	NM_028379	72881	Mm.261606	NM_028379	ENSMUSG00000001844	Zdhhc4	1810021D01Rik|2900029I10Rik	zinc finger, DHHC domain containing 4	protein-coding
mm_68168.1	chr7	103812686	103812696	-	1	NA	exon (NM_016956, exon 3 of 3)	exon (NM_016956, exon 3 of 3)	1232	NM_016956	15130	Mm.288567	NM_016956		Hbb-b2	AI036344|Hbb2|Hbbt2|beta2	hemoglobin, beta adult minor chain	protein-coding
mm_8831.1	chr1	162571396	162571408	-	1	NA	intron (NM_001347125, intron 1 of 7)	CpG	574	NM_001347125	53330	Mm.10699	NM_016796	ENSMUSG00000026696	Vamp4	D1Ertd147e	vesicle-associated membrane protein 4	protein-coding
mm_20137.1	chr2	121413052	121413055	-	1	NA	promoter-TSS (NM_007952)	promoter-TSS (NM_007952)	739	NM_153075	212670	Mm.384318	NM_153075	ENSMUSG00000033486	Catsper2	-	cation channel, sperm associated 2	protein-coding
mm_97875.1	chr11	83191297	83191316	+	1	NA	promoter-TSS (NM_011409)	promoter-TSS (NM_011409)	-24	NM_011409	20557	Mm.290922	NM_011409	ENSMUSG00000018986	Slfn3	-	schlafen 3	protein-coding
mm_89870.1	chr10	108259774	108259786	+	1	NA	exon (NM_027892, exon 15 of 26)	exon (NM_027892, exon 15 of 26)	-72409	NM_054056	114774	Mm.391419	NM_054056	ENSMUSG00000035873	Pawr	2310001G03Rik|PAR4|Par-4	PRKC, apoptosis, WT1, regulator	protein-coding
mm_812.1	chr1	45857737	45857757	+	1	NA	Intergenic	Intergenic	62246	NM_028599	73674	Mm.270376	NM_028599	ENSMUSG00000025995	Wdr75	1300003A18Rik|2410118I19Rik|C77608	WD repeat domain 75	protein-coding
mm_54107.1	chr6	16898444	16898459	-	1	NA	promoter-TSS (NM_031198)	promoter-TSS (NM_031198)	-10	NM_031198	21426	Mm.36217	NM_031198	ENSMUSG00000029553	Tfec	BB107417|Tcfec|bHLHe34	transcription factor EC	protein-coding
mm_171609.1	chr4	149856272	149856283	+	1	NA	Intergenic	Intergenic	-82010	NM_027460	70556	Mm.41877	NM_027460	ENSMUSG00000028982	Slc25a33	5730438N18Rik|Pnc1	solute carrier family 25, member 33	protein-coding
mm_137274.1	chr17	24720044	24720057	+	1	NA	promoter-TSS (NR_028515)	promoter-TSS (NR_028515)	-13	NM_008503	16898	Mm.157452	NM_008503	ENSMUSG00000044533	Rps2	Llrep3|S4	ribosomal protein S2	protein-coding
mm_101350.1	chr11	23739462	23739473	-	1	NA	Intergenic	Intergenic	31503	NM_009044	19696	Mm.4869	NM_009044	ENSMUSG00000020275	Rel	c-Rel	reticuloendotheliosis oncogene	protein-coding
mm_72496.1	chr8	83738438	83738449	+	1	NA	intron (NM_001163031, intron 1 of 17)	intron (NM_001163031, intron 1 of 17)	2868	NM_001163029	26364	Mm.334648	NM_011925	ENSMUSG00000002885	Adgre5	AA409984|Cd97|TM7LN1	adhesion G protein-coupled receptor E5	protein-coding
mm_16644.1	chr2	6130098	6130106	-	1	NA	promoter-TSS (NM_001159657)	promoter-TSS (NM_001159657)	83	NM_144883	227545	Mm.133542	NM_144883	ENSMUSG00000045319	Proser2	5430407P10Rik|AU067770	proline and serine rich 2	protein-coding
mm_107266.1	chr12	29528472	29528498	+	1	NA	5' UTR (NM_008666, exon 1 of 25)	5' UTR (NM_008666, exon 1 of 25)	101	NM_008666	17933	Mm.253067	NM_008666	ENSMUSG00000061911	Myt1l	2900046C06Rik|2900093J19Rik|C630034G21Rik|Nztf1|Pmng1|Png-1|mKIAA1106	myelin transcription factor 1-like	protein-coding
mm_120723.1	chr14	73138756	73138778	+	1	NA	Intergenic	Intergenic	-3743	NM_001170694	105670	Mm.280068	NM_134083	ENSMUSG00000022106	Rcbtb2	2610028E02Rik|2810420M18Rik|AI448345|AW240694|Chc1l|RC/BTB2	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 2	protein-coding
mm_84784.1	chr9	76567093	76567123	-	1	NA	Intergenic	Intergenic	-21304	NM_001045518	208994	Mm.256929	NM_001045518	ENSMUSG00000032358	Fam83b	C530008M07Rik|Gm516	family with sequence similarity 83, member B	protein-coding
mm_57382.1	chr6	124814298	124814310	-	1	NA	promoter-TSS (NM_009415)	promoter-TSS (NM_009415)	-8	NM_009415	21991	Mm.4222	NM_009415	ENSMUSG00000023456	Tpi1	AI255506|Tpi|Tpi-1	triosephosphate isomerase 1	protein-coding
mm_122492.1	chr14	46597158	46597166	-	1	NA	Intergenic	Intergenic	-21311	NR_046459	100873094	Mm.318596	NR_046459		Rubie	-	RNA upstream of Bmp4 expressed in inner ear	ncRNA
mm_39632.1	chr5	24451938	24451969	+	1	NA	promoter-TSS (NM_001256431)	promoter-TSS (NM_001256431)	-224	NM_001256431	213990	Mm.250703	NM_139153	ENSMUSG00000023353	Agap3	AGAP-3|AV028425|Centg3|Crag|Crag.|MRIP-1|cnt-g3	ArfGAP with GTPase domain, ankyrin repeat and PH domain 3	protein-coding
mm_170022.1	chr17	21474966	21474975	+	1	NA	Intergenic	MMVL30-int|LTR|ERV1	-14018	NM_013843	24132	Mm.42140	NM_013843	ENSMUSG00000057409	Zfp53	D030067O06Rik|KRAZ1|Zfp-53|Zfp118|zfas8	zinc finger protein 53	protein-coding
mm_81346.1	chr9	108560423	108560451	+	1	NA	promoter-TSS (NM_011830)	promoter-TSS (NM_011830)	-64	NM_011830	23918	Mm.6065	NM_011830	ENSMUSG00000062867	Impdh2	IMPD	inosine 5'-phosphate dehydrogenase 2	protein-coding
mm_65698.1	chr7	28377131	28377169	-	1	NA	3' UTR (NM_011756, exon 2 of 2)	3' UTR (NM_011756, exon 2 of 2)	2078	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_91237.1	chr10	22303855	22303866	-	1	NA	intron (NM_009018, intron 5 of 5)	intron (NM_009018, intron 5 of 5)	-2860	NR_015465	606736	Mm.387042	NR_015465	ENSMUSG00000097352	C920009B18Rik	-	RIKEN cDNA C920009B18 gene	ncRNA
mm_158396.1	chrX	136741280	136741307	-	1	NA	promoter-TSS (NM_001168229)	promoter-TSS (NM_001168229)	59	NM_001168229	56397	Mm.27218	NM_019768	ENSMUSG00000031422	Morf4l2	2410017O14Rik|Mrgx|Sid393p|mKIAA0026	mortality factor 4 like 2	protein-coding
mm_143788.1	chr17	81731516	81731527	-	1	NA	intron (NR_104580, intron 1 of 8)	intron (NR_104580, intron 1 of 8)	6866	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_107642.1	chr12	52504036	52504051	+	1	NA	Intergenic	CpG	-12034	NM_009706	11855	Mm.35059	NM_009706	ENSMUSG00000035133	Arhgap5	p190-B|p190B	Rho GTPase activating protein 5	protein-coding
mm_84012.1	chr9	57645533	57645541	-	1	NA	5' UTR (NM_007783, exon 1 of 13)	5' UTR (NM_007783, exon 1 of 13)	116	NM_007783	12988	Mm.21974	NM_007783	ENSMUSG00000032312	Csk	AW212630|p50CSK	c-src tyrosine kinase	protein-coding
mm_130287.1	chr15	97008683	97008688	-	1	NA	exon (NM_027052, exon 11 of 16)	exon (NM_027052, exon 11 of 16)	47271	NM_027052	69354	Mm.250980	NM_027052	ENSMUSG00000022464	Slc38a4	1110012E16Rik|1700012A18Rik|Ata3|mATA3|mNAT3	solute carrier family 38, member 4	protein-coding
mm_159564.1	chr4	109235400	109235400	+	1	NA	promoter-TSS (NM_001033226)	promoter-TSS (NM_001033226)	138	NM_001285897	108802	Mm.318248	NM_001033226	ENSMUSG00000028558	Calr4	4933403L16Rik|AU017583	calreticulin 4	protein-coding
mm_73507.1	chr8	107367108	107367118	+	1	NA	exon (NM_018823, exon 13 of 15)	exon (NM_018823, exon 13 of 15)	36092	NM_008706	18104	Mm.252	NM_008706	ENSMUSG00000003849	Nqo1	AV001255|Dia4|Dtd|Nmo-1|Nmo1|Nmor1|Ox-1|Ox1|Qr1	NAD(P)H dehydrogenase, quinone 1	protein-coding
mm_162804.1	chr10	77568671	77568678	-	1	NA	Intergenic	RMER17C2|LTR|ERVK	-13093	NM_145925	108705	Mm.28853	NM_145925	ENSMUSG00000009291	Pttg1ip	1810010L20Rik|AI314311|AU018448|C79540	pituitary tumor-transforming 1 interacting protein	protein-coding
mm_143741.1	chr17	81499061	81499065	-	1	NA	intron (NR_104580, intron 2 of 8)	intron (NR_104580, intron 2 of 8)	239324	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_162460.1	chr1	128592237	128592262	-	1	NA	promoter-TSS (NM_009911)	promoter-TSS (NM_009911)	50	NM_009911	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding
mm_83551.1	chr9	46242466	46242514	-	1	NA	exon (NM_007468, exon 3 of 3)	exon (NM_007468, exon 3 of 3)	1646	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_100992.1	chr11	8446134	8446154	-	1	NA	intron (NM_001083587, intron 24 of 30)	intron (NM_001083587, intron 24 of 30)	218391	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_59217.1	chr7	24593901	24593914	+	1	NA	5' UTR (NM_023154, exon 2 of 8)	5' UTR (NM_023154, exon 2 of 8)	-6266	NM_001033205	101544	Mm.20117	NM_001033205	ENSMUSG00000066721	Zfp575	AI326876|Znf575	zinc finger protein 575	protein-coding
mm_77190.1	chr8	111910172	111910190	-	1	NA	promoter-TSS (NM_019950)	promoter-TSS (NM_019950)	18	NM_019950	56773	Mm.432506	NM_019950	ENSMUSG00000031952	Chst5	AI173964|GST-4|Gn6st-3|I-GlcNAc-6-ST	carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 5	protein-coding
mm_58221.1	chr6	144209449	144209469	-	1	NA	5' UTR (NM_011444, exon 1 of 15)	5' UTR (NM_011444, exon 1 of 15)	109	NM_001113559	20678	Mm.1752	NM_011444	ENSMUSG00000041540	Sox5	A730017D01Rik|AI528773	SRY (sex determining region Y)-box 5	protein-coding
mm_35178.1	chr4	15149052	15149070	-	1	NA	promoter-TSS (NM_178617)	promoter-TSS (NM_178617)	70	NM_178617	69352	Mm.389031	NM_178617	ENSMUSG00000040536	Necab1	1700003H21Rik|Efcbp1|STIP-1	N-terminal EF-hand calcium binding protein 1	protein-coding
mm_135488.1	chr16	46039369	46039385	-	1	NA	intron (NM_032465, intron 13 of 14)	RMER17A2|LTR|ERVK	-28964	NM_001134480	433022	Mm.380993	NM_001134480	ENSMUSG00000087141	Plcxd2	AW494639|EG433022	phosphatidylinositol-specific phospholipase C, X domain containing 2	protein-coding
mm_157052.1	chrX	8074571	8074626	-	1	NA	promoter-TSS (NM_001290716)	promoter-TSS (NM_001290716)	162	NM_011514	20937	Mm.9244	NM_011514	ENSMUSG00000039231	Suv39h1	AI852103|AL022883|DXHXS7466e|H3-K9-HMTase 1|KMT1A|mIS6	suppressor of variegation 3-9 homolog 1 (Drosophila)	protein-coding
mm_57327.1	chr6	124738795	124738826	-	1	NA	promoter-TSS (NM_001077705)	promoter-TSS (NM_001077705)	-101	NM_001077705	15170	Mm.271799	NM_013545	ENSMUSG00000004266	Ptpn6	70Z-SHP|Hcph|PTPTY-42|Ptp1C|SH-PTP1|SHP-1|hcp|me	protein tyrosine phosphatase, non-receptor type 6	protein-coding
mm_148344.1	chr18	84659937	84659943	-	1	NA	Intergenic	Intergenic	-9845	NM_177450	338403	Mm.23278	NM_177450	ENSMUSG00000056162	Cndp1	AI746433|Cn1	carnosine dipeptidase 1 (metallopeptidase M20 family)	protein-coding
mm_92575.1	chr10	79916913	79916945	-	1	NA	promoter-TSS (NM_177994)	promoter-TSS (NM_177994)	1	NM_177994	109284	Mm.300416	NM_177994	ENSMUSG00000035781	R3hdm4	AI503502|C030046I01Rik	R3H domain containing 4	protein-coding
mm_155176.1	chrX	53607988	53608015	+	1	NA	promoter-TSS (NM_028375)	promoter-TSS (NM_028375)	79	NM_028375	72865	Mm.158897	NM_028375	ENSMUSG00000051851	Cxx1c	2900027G03Rik|Mar8.1|Mart8a	CAAX box 1C	protein-coding
mm_13314.1	chr2	102658898	102658908	+	1	NA	5' UTR (NM_001077514, exon 1 of 11)	5' UTR (NM_001077514, exon 1 of 11)	220	NM_001077514	20511	Mm.267547	NM_011393	ENSMUSG00000005089	Slc1a2	1700091C19Rik|2900019G14Rik|AI159670|Eaat2|GLT-1|GLT1|MGLT1	solute carrier family 1 (glial high affinity glutamate transporter), member 2	protein-coding
mm_116354.1	chr13	39899288	39899299	-	1	NA	Intergenic	Intergenic	388718	NM_172143	218165	Mm.364096	NM_172143	ENSMUSG00000047094	Ofcc1	opo	orofacial cleft 1 candidate 1	protein-coding
mm_76317.1	chr8	84687079	84687099	-	1	NA	intron (NM_025788, intron 1 of 5)	intron (NM_025788, intron 1 of 5)	773	NM_025788	66830	Mm.289698	NM_025788	ENSMUSG00000001910	Nacc1	2010001H03Rik|4930511N13Rik|Btbd14b|Nac1	nucleus accumbens associated 1, BEN and BTB (POZ) domain containing	protein-coding
mm_28459.1	chr3	90692836	90692865	-	1	NA	exon (NM_001281852, exon 3 of 3)	exon (NM_001281852, exon 3 of 3)	2871	NM_001281852	20202	Mm.2128	NM_009114	ENSMUSG00000056071	S100a9	60B8Ag|AW546964|BEE22|Cagb|GAGB|L1Ag|MRP14|p14	S100 calcium binding protein A9 (calgranulin B)	protein-coding
mm_15845.1	chr2	164769964	164769974	+	1	NA	promoter-TSS (NM_026785)	promoter-TSS (NM_026785)	40	NM_026785	68612	Mm.89830	NM_026785	ENSMUSG00000001403	Ube2c	1110015A16Rik|D2Ertd695e	ubiquitin-conjugating enzyme E2C	protein-coding
mm_40851.1	chr5	73481052	73481062	+	1	NA	promoter-TSS (NM_001190734)	promoter-TSS (NM_001190734)	2	NM_001190734	100737	Mm.220312	NM_178896	ENSMUSG00000051674	Dcun1d4	AI836376	DCN1, defective in cullin neddylation 1, domain containing 4 (S. cerevisiae)	protein-coding
mm_91355.1	chr10	27617020	27617047	-	1	NA	promoter-TSS (NM_008481)	promoter-TSS (NM_008481)	-91	NM_008481	16773	Mm.256087	NM_008481	ENSMUSG00000019899	Lama2	5830440B04|dy|mKIAA4087|mer|merosin	laminin, alpha 2	protein-coding
mm_105107.1	chr11	100970158	100970175	-	1	NA	exon (NM_008986, exon 1 of 2)	exon (NM_008986, exon 1 of 2)	451	NM_008986	19285	Mm.21864	NM_008986	ENSMUSG00000004044	Ptrf	2310075E07Rik|AW546441|Cav-p60|Cavin	polymerase I and transcript release factor	protein-coding
mm_38764.1	chr4	147904628	147904638	-	1	NA	promoter-TSS (NM_001285923)	promoter-TSS (NM_001285923)	65	NM_001285923	170731	Mm.154312	NM_133201	ENSMUSG00000029020	Mfn2	D630023P19Rik|Fzo	mitofusin 2	protein-coding
mm_12027.1	chr2	58161024	58161032	+	1	NA	promoter-TSS (NM_139200)	promoter-TSS (NM_139200)	-906	NM_139200	227929	Mm.273905	NM_139200	ENSMUSG00000026832	Cytip	A130053M09Rik|AI462064|C80816|Cbp|Cybr|Pscdbp	cytohesin 1 interacting protein	protein-coding
mm_130412.1	chr15	97977873	97977888	-	1	NA	exon (NM_001113515, exon 50 of 53)	exon (NM_001113515, exon 50 of 53)	13651	NM_001252153	380967	Mm.196630	NM_201359	ENSMUSG00000052369	Tmem106c	AI046681|BC046621|D15Ertd405e	transmembrane protein 106C	protein-coding
mm_41291.1	chr5	90463992	90464055	+	1	NA	exon (NM_009654, exon 4 of 15)	exon (NM_009654, exon 4 of 15)	3153	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_122950.1	chr14	54966926	54966937	-	1	NA	promoter-TSS (NM_010856)	promoter-TSS (NM_010856)	-324	NM_010856	17888	Mm.290003	NM_010856	ENSMUSG00000040752	Myh6	A830009F23Rik|AA517445|Myhc-a|Myhca|alpha-MHC	myosin, heavy polypeptide 6, cardiac muscle, alpha	protein-coding
mm_96107.1	chr11	60539725	60539729	+	1	NA	intron (NM_172943, intron 1 of 3)	intron (NM_172943, intron 1 of 3)	2044	NM_172943	268420	Mm.262056	NM_172943	ENSMUSG00000042650	Alkbh5	AW050020|AW215868|Abh5|E130207K11|Ofoxd	alkB homolog 5, RNA demethylase	protein-coding
mm_65.1	chr1	6634406	6634416	+	1	NA	intron (NM_001244693, intron 2 of 22)	intron (NM_001244693, intron 2 of 22)	-95640	NR_045189	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding
mm_22211.1	chr2	174276005	174276008	-	1	NA	Intergenic	Intergenic	-8314	NM_019690	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_149317.1	chr19	10839716	10839737	+	1	NA	Intergenic	PB1D11|SINE|Alu	-2818	NM_023044	65221	Mm.27387	NM_023044	ENSMUSG00000024737	Slc15a3	Ci1|cI-1	solute carrier family 15, member 3	protein-coding
mm_58779.1	chr7	16061869	16061886	+	1	NA	Intergenic	GC_rich|Low_complexity|Low_complexity	-9968	NM_001347559	666528	Mm.290718	NM_001099277	ENSMUSG00000078796	Zfp541	EG666528|Znf541	zinc finger protein 541	protein-coding
mm_110994.1	chr12	77625040	77625042	-	1	NA	Intergenic	MTC|LTR|ERVL-MaLR	214900	NM_001252616	53618	Mm.35628	NM_016893	ENSMUSG00000021065	Fut8	-	fucosyltransferase 8	protein-coding
mm_18076.1	chr2	42653063	42653077	-	1	NA	5' UTR (NM_053011, exon 1 of 91)	5' UTR (NM_053011, exon 1 of 91)	528	NM_053011	94217	Mm.441398	NM_053011	ENSMUSG00000049252	Lrp1b	9630004P12Rik|LRP-DIT	low density lipoprotein-related protein 1B (deleted in tumors)	protein-coding
mm_2766.1	chr1	130716131	130716171	+	1	NA	promoter-TSS (NM_008825)	promoter-TSS (NM_008825)	-330	NM_008825	18640	Mm.249861	NM_008825	ENSMUSG00000026409	Pfkfb2	4930568D07Rik	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2	protein-coding
mm_91206.1	chr10	21161434	21161448	-	1	NA	promoter-TSS (NM_001198914)	promoter-TSS (NM_001198914)	-457	NM_010848	17863	Mm.52109	NM_010848	ENSMUSG00000019982	Myb	AI550390|M16449|c-myb	myeloblastosis oncogene	protein-coding
mm_151069.1	chr19	47511005	47511025	+	1	NA	intron (NM_175360, intron 7 of 9)	intron (NM_175360, intron 7 of 9)	-1967	NR_045322	100503104	Mm.442735	NR_045322	ENSMUSG00000097990	Gm19557	-	predicted gene, 19557	ncRNA
mm_89854.1	chr10	107349907	107349918	+	1	NA	intron (NM_001039354, intron 2 of 5)	intron (NM_001039354, intron 2 of 5)	77518	NM_001284329	108030	Mm.268025	NM_001033223	ENSMUSG00000019906	Lin7a	AI848705|LIN-7A|MALS-1|TIP-33|Veli|Veli1	lin-7 homolog A (C. elegans)	protein-coding
mm_55216.1	chr6	52225946	52225956	-	1	NA	exon (NM_010456, exon 1 of 2)	exon (NM_010456, exon 1 of 2)	1419	NM_010456	15405	Mm.4694	NM_010456	ENSMUSG00000038227	Hoxa9	D6a9|Hox-1.7	homeobox A9	protein-coding
mm_73661.1	chr8	111033938	111033949	+	1	NA	5' UTR (NM_146217, exon 1 of 21)	5' UTR (NM_146217, exon 1 of 21)	101	NM_146217	234734	Mm.24174	NM_146217	ENSMUSG00000031960	Aars	AI316495|C76919|sti	alanyl-tRNA synthetase	protein-coding
mm_44666.1	chr5	29365148	29365151	-	1	NA	intron (NM_020295, intron 1 of 16)	L1MA9|LINE|L1	13241	NM_020295	56873	Mm.41572	NM_020295	ENSMUSG00000010721	Lmbr1	1110048D14Rik|AU017641	limb region 1	protein-coding
mm_17847.1	chr2	34372664	34372760	-	1	NA	promoter-TSS (NM_001290576)	promoter-TSS (NM_001290576)	-667	NM_016768	18516	Mm.239941	NM_016768	ENSMUSG00000038718	Pbx3	-	pre B cell leukemia homeobox 3	protein-coding
mm_107792.1	chr12	61716543	61716544	+	1	NA	intron (NM_178714, intron 2 of 3)	L1_Mur1|LINE|L1	193376	NM_001310586	238205	Mm.28802	NM_178714	ENSMUSG00000035653	Lrfn5	AI427653|AI604817|C130061B21|mKIAA4208	leucine rich repeat and fibronectin type III domain containing 5	protein-coding
mm_21486.1	chr2	163087790	163087801	-	1	NA	5' UTR (NM_026630, exon 2 of 2)	5' UTR (NM_026630, exon 2 of 2)	1806	NM_026630	68236	Mm.33648	NM_026630	ENSMUSG00000070708	Gtsf1l	2410116G06Rik	gametocyte specific factor 1-like	protein-coding
mm_4321.1	chr1	171851961	171851973	+	1	NA	exon (NM_013489, exon 3 of 9)	exon (NM_013489, exon 3 of 9)	12270	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_112325.1	chr12	115446878	115446905	-	1	NA	Intergenic	Intergenic	248903	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
mm_74431.1	chr8	3720641	3720682	-	1	NA	promoter-TSS (NM_029465)	promoter-TSS (NM_029465)	-10	NM_029465	75863	Mm.109183	NM_029465	ENSMUSG00000074491	Clec4g	4930572L20Rik	C-type lectin domain family 4, member g	protein-coding
mm_40874.1	chr5	74093113	74093129	+	1	NA	promoter-TSS (NR_145131)	promoter-TSS (NR_145131)	61	NR_145131	70036	Mm.46547	NR_015531	ENSMUSG00000053656	Dancr	2700023E23Rik	differentiation antagonizing non-protein coding RNA	ncRNA
mm_113896.1	chr13	49195711	49195738	+	1	NA	3' UTR (NM_013610, exon 4 of 4)	3' UTR (NM_013610, exon 4 of 4)	8177	NM_013610	18081	Mm.18503	NM_013610	ENSMUSG00000037966	Ninj1	AU024536	ninjurin 1	protein-coding
mm_18675.1	chr2	71055535	71055611	-	1	NA	promoter-TSS (NM_001165981)	promoter-TSS (NM_001165981)	33	NM_145524	228019	Mm.490343	NM_145524	ENSMUSG00000041975	Mettl8	BC004636|Tip	methyltransferase like 8	protein-coding
mm_168355.1	chr1	113964109	113964114	-	1	NA	Intergenic	RLTR9E|LTR|ERVK	-1721026	NM_001077425	636808	Mm.101576	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding
mm_124964.1	chr15	16728908	16728921	+	1	NA	Intergenic	Intergenic	-49187	NM_009869	12565	Mm.439758	NM_009869	ENSMUSG00000025370	Cdh9	-	cadherin 9	protein-coding
mm_100719.1	chr11	3895142	3895165	-	1	NA	promoter-TSS (NM_026150)	promoter-TSS (NM_026150)	-27	NM_026150	67430	Mm.347950	NM_026150	ENSMUSG00000020434	4921536K21Rik	AV043724	RIKEN cDNA 4921536K21 gene	protein-coding
mm_73003.1	chr8	93810820	93810828	+	1	NA	promoter-TSS (NM_010308)	promoter-TSS (NM_010308)	-14	NM_010308	14681	Mm.251445	NM_010308	ENSMUSG00000031748	Gnao1	AW050213|Galphao|Gnao|alphaO	guanine nucleotide binding protein, alpha O	protein-coding
mm_127003.1	chr15	95790952	95790965	+	1	NA	5' UTR (NM_001253813, exon 1 of 21)	5' UTR (NM_001253813, exon 1 of 21)	115	NM_001253813	105722	Mm.38087	NM_175344	ENSMUSG00000064210	Ano6	2900059G15Rik|AA407480|AW554778|F730003B03Rik|Tmem16f	anoctamin 6	protein-coding
mm_171203.1	chr3	54482210	54482224	+	1	NA	Intergenic	(TGG)n|Simple_repeat|Simple_repeat	121110	NM_015784	50706	Mm.236067	NM_015784	ENSMUSG00000027750	Postn	A630052E07Rik|AI747096|OSF-2|Osf2|PLF|PN	periostin, osteoblast specific factor	protein-coding
mm_172219.1	chr6	65061080	65061080	-	1	NA	intron (NM_001253392, intron 3 of 21)	RLTR9E|LTR|ERVK	17874	NM_001253392	13990	Mm.99113	NM_007958	ENSMUSG00000029920	Smarcad1	AV081750|AW226546|D6Pas1|Etl1|mKIAA1122	SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1	protein-coding
mm_12414.1	chr2	70561259	70561268	+	1	NA	promoter-TSS (NM_008077)	promoter-TSS (NM_008077)	-866	NM_001312900	14415	Mm.272120	NM_008077	ENSMUSG00000070880	Gad1	EP10|Gad-1	glutamate decarboxylase 1	protein-coding
mm_103171.1	chr11	70459718	70459730	-	1	NA	5' UTR (NM_001029929, exon 1 of 14)	5' UTR (NM_001029929, exon 1 of 14)	102	NM_001029929	574428	Mm.472771	NM_001029929	ENSMUSG00000040829	Zmynd15	-	zinc finger, MYND-type containing 15	protein-coding
mm_79652.1	chr9	59617285	59617301	+	1	NA	promoter-TSS (NM_029922)	promoter-TSS (NM_029922)	9	NR_038074	67287	Mm.439943	NM_029922	ENSMUSG00000025237	Parp6	1700119G14Rik|2310028P13Rik|3110038K10Rik|ARTD17|C030013N01Rik|PARP-6	poly (ADP-ribose) polymerase family, member 6	protein-coding
mm_15732.1	chr2	164236983	164236995	+	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	1352	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_149206.1	chr19	9980683	9980697	+	1	NA	promoter-TSS (NR_073181)	promoter-TSS (NR_073181)	90	NR_073181	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
mm_67196.1	chr7	74013677	74013699	-	1	NA	promoter-TSS (NM_009181)	promoter-TSS (NM_009181)	-6	NM_009181	20450	Mm.4954	NM_009181	ENSMUSG00000025789	St8sia2	AI323367|ST8SiaII|STX|Siat8b	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 2	protein-coding
mm_20556.1	chr2	131072637	131072651	-	1	NA	exon (NM_011426, exon 17 of 21)	exon (NM_011426, exon 17 of 21)	-8830	NM_001163529	110751	Mm.108550	NM_033615	ENSMUSG00000027318	Adam33	Adaml	a disintegrin and metallopeptidase domain 33	protein-coding
mm_101254.1	chr11	20831174	20831189	-	1	NA	promoter-TSS (NM_173752)	promoter-TSS (NM_173752)	-73	NM_173752	216551	Mm.76694	NM_173752	ENSMUSG00000042363	Lgalsl	1110067D22Rik|A530071M23|Grpa|Hspc159|Lgalsla	lectin, galactoside binding-like	protein-coding
mm_88317.1	chr10	75561270	75561279	+	1	NA	promoter-TSS (NM_198860)	promoter-TSS (NM_198860)	-944	NM_198860	192734	Mm.259320	NM_198860	ENSMUSG00000046807	Lrrc75b	AI646023|Fam211b	leucine rich repeat containing 75B	protein-coding
mm_93047.1	chr10	88503913	88503923	-	1	NA	promoter-TSS (NM_001146690)	promoter-TSS (NM_001146690)	52	NR_027477	212862	Mm.288897	NM_144807	ENSMUSG00000060002	Chpt1	-	choline phosphotransferase 1	protein-coding
mm_31536.1	chr4	55368040	55368053	+	1	NA	exon (NM_009011, exon 3 of 10)	exon (NM_009011, exon 3 of 10)	18004	NM_009011	19359	Mm.196846	NM_009011	ENSMUSG00000028426	Rad23b	0610007D13Rik|AV001138|HR23B|mHR23B|p58	RAD23 homolog B, nucleotide excision repair protein	protein-coding
mm_133726.1	chr16	93777242	93777265	+	1	NA	intron (NM_027293, intron 22 of 36)	intron (NM_027293, intron 22 of 36)	-54868	NM_001045529	338467	Mm.287329	NM_001045529	ENSMUSG00000039456	Morc3	1110051N18Rik|AI452146|BF318192|D16Jhu32e|NXP2|Zcwcc3	microrchidia 3	protein-coding
mm_101280.1	chr11	21569969	21569971	-	1	NA	intron (NM_008618, intron 1 of 8)	intron (NM_008618, intron 1 of 8)	1964	NM_008618	17449	Mm.212703	NM_008618	ENSMUSG00000020321	Mdh1	B230377B03Rik|D17921|MDH-s|MDHA|Mor-2|Mor2	malate dehydrogenase 1, NAD (soluble)	protein-coding
mm_134603.1	chr16	20621449	20621481	-	1	NA	promoter-TSS (NM_028420)	promoter-TSS (NM_028420)	-187	NM_028420	73047	Mm.425977	NM_028420	ENSMUSG00000051146	Camk2n2	2900075A18Rik	calcium/calmodulin-dependent protein kinase II inhibitor 2	protein-coding
mm_102117.1	chr11	53300333	53300341	-	1	NA	5' UTR (NM_008300, exon 1 of 19)	5' UTR (NM_008300, exon 1 of 19)	142	NM_008300	15525	Mm.239865	NM_008300	ENSMUSG00000020361	Hspa4	70kDa|AI317151|APG-2|Hsp110|Hsp70RY|mKIAA4025	heat shock protein 4	protein-coding
mm_161242.1	chr13	97067065	97067065	+	1	NA	promoter-TSS (NM_001146045)	promoter-TSS (NM_001146045)	-222	NM_001146045	320557	Mm.458280	NM_001100458	ENSMUSG00000041817	Fam169a	B230112C05Rik|SLAP75	family with sequence similarity 169, member A	protein-coding
mm_134672.1	chr16	22402575	22402601	-	1	NA	intron (NM_023794, intron 7 of 12)	intron (NM_023794, intron 7 of 12)	36982	NM_023794	104156	Mm.155708	NM_023794	ENSMUSG00000013089	Etv5	1110005E01Rik|8430401F14Rik|ERM	ets variant 5	protein-coding
mm_93979.1	chr10	127341966	127341976	-	1	NA	promoter-TSS (NM_010296)	promoter-TSS (NM_010296)	-392	NM_010296	14632	Mm.391450	NM_010296	ENSMUSG00000025407	Gli1	AV235269|Zfp-5|Zfp5	GLI-Kruppel family member GLI1	protein-coding
mm_6423.1	chr1	73929318	73929358	-	1	NA	intron (NM_001289895, intron 22 of 32)	intron (NM_001289895, intron 22 of 32)	-64872	NR_045311	109198	Mm.359721	NR_045311	ENSMUSG00000100301	6030407O03Rik	-	RIKEN cDNA 6030407O03 gene	ncRNA
mm_117807.1	chr13	97588078	97588122	-	1	NA	Intergenic	Intergenic	28100	NR_046157	328314	Mm.138047	NR_046157	ENSMUSG00000110235	Gm5086	B230311A21|EG328314	predicted gene 5086	ncRNA
mm_135517.1	chr16	48772146	48772157	-	1	NA	promoter-TSS (NM_198297)	promoter-TSS (NM_198297)	-195	NM_198297	77647	Mm.167298	NM_198297	ENSMUSG00000030775	Trat1	C030046M14Rik|Tcrim|Trim	T cell receptor associated transmembrane adaptor 1	protein-coding
mm_47951.1	chr5	135489249	135489277	-	1	NA	intron (NM_146001, intron 1 of 30)	CpG	55859	NM_146001	215114	Mm.280805	NM_146001	ENSMUSG00000039959	Hip1	2610109B09Rik|A930014B11Rik|E130315I21Rik|mKIAA4113	huntingtin interacting protein 1	protein-coding
mm_140189.1	chr17	83277933	83277952	+	1	NA	Intergenic	Intergenic	62659	NM_134117	106522	Mm.311974	NM_134117	ENSMUSG00000024247	Pkdcc	AI115348|AW548124|Adtk1|ESTM17|MAd1|Sgk493|Vlk|X83346	protein kinase domain containing, cytoplasmic	protein-coding
mm_165949.1	chr4	83465099	83465116	+	1	NA	exon (NM_001290527, exon 9 of 11)	exon (NM_001290527, exon 9 of 11)	21341	NM_001290527	101739	Mm.105331	NM_133948	ENSMUSG00000028484	Psip1	AA408851|AU015605|Dfs70|Ledgfa|Ledgfb|Psip2	PC4 and SFRS1 interacting protein 1	protein-coding
mm_148913.1	chr19	6975077	6975104	+	1	NA	promoter-TSS (NM_008889)	promoter-TSS (NM_008889)	42	NM_008889	18938	Mm.140	NM_008889	ENSMUSG00000056612	Ppp1r14b	AOM172|PHI-1|PLCB3N|Png	protein phosphatase 1, regulatory (inhibitor) subunit 14B	protein-coding
mm_146833.1	chr18	22811714	22811718	-	1	NA	intron (NM_001347510, intron 6 of 9)	intron (NM_001347510, intron 6 of 9)	226947	NM_001161483	319211	Mm.209896	NM_199024	ENSMUSG00000041923	Nol4	1700013J13Rik|4930568N03Rik|Gm1262	nucleolar protein 4	protein-coding
mm_66939.1	chr7	61888556	61888558	-	1	NA	intron (NR_015533, intron 6 of 8)	intron (NR_015533, intron 6 of 8)	-10693	NR_029772	723931		NR_029772	ENSMUSG00000065568	Mir344	Mirn344|mir-344-1|mmu-mir-344	microRNA 344	ncRNA
mm_110008.1	chr12	16537793	16537810	-	1	NA	3' UTR (NM_015763, exon 21 of 21)	3' UTR (NM_015763, exon 21 of 21)	51969	NM_015763	14245	Mm.153625	NM_015763	ENSMUSG00000020593	Lpin1	4631420P06|Kiaa0188|Lipin1|fld|mKIAA0188	lipin 1	protein-coding
mm_159920.1	chr6	53978636	53978636	-	1	NA	promoter-TSS (NM_027749)	promoter-TSS (NM_027749)	37	NM_001289714	71287	Mm.158654	NM_027749	ENSMUSG00000052955	Cpvl	4933436L16Rik|HVLP	carboxypeptidase, vitellogenic-like	protein-coding
mm_117793.1	chr13	97190635	97190639	-	1	NA	intron (NM_010422, intron 3 of 13)	intron (NM_010422, intron 3 of 13)	7720	NM_010422	15212	Mm.27816	NM_010422	ENSMUSG00000021665	Hexb	-	hexosaminidase B	protein-coding
mm_98510.1	chr11	94952331	94952347	+	1	NA	3' UTR (NM_007742, exon 51 of 51)	3' UTR (NM_007742, exon 51 of 51)	-15254	NM_018792	54388	Mm.30482	NM_018792	ENSMUSG00000038994	Hils1	H1.9|TISP64	histone H1-like protein in spermatids 1	protein-coding
mm_139203.1	chr17	47688960	47688970	+	1	NA	promoter-TSS (NM_001164729)	promoter-TSS (NM_001164729)	-579	NM_001164729	66119	Mm.89912	NM_025365	ENSMUSG00000033475	Tomm6	1110002E23Rik|AI663970	translocase of outer mitochondrial membrane 6 homolog (yeast)	protein-coding
mm_64483.1	chr7	143065934	143065949	+	1	NA	intron (NM_133655, intron 3 of 7)	intron (NM_133655, intron 3 of 7)	-3427	NM_020285	56844	Mm.139675	NM_020285	ENSMUSG00000045752	Tssc4	AA241958|ESTM671070	tumor-suppressing subchromosomal transferable fragment 4	protein-coding
mm_85885.1	chr9	111053620	111053639	-	1	NA	Intergenic	RSINE1|SINE|B4	3615	NM_001302377	54199	Mm.7336	NM_017466	ENSMUSG00000043953	Ccrl2	1810047I05Rik|Ackr5|CCR11|Cmkbr1l2|E01|L-CCR	chemokine (C-C motif) receptor-like 2	protein-coding
mm_137631.1	chr17	28329210	28329244	+	1	NA	intron (NM_011287, intron 3 of 5)	CpG-6176	756	NM_011287	19896	Mm.336955	NM_011287	ENSMUSG00000037805	Rpl10a	CsA-19|Nedd6	ribosomal protein L10A	protein-coding
mm_130370.1	chr15	97814831	97814878	-	1	NA	promoter-TSS (NM_001204281)	promoter-TSS (NM_001204281)	9	NM_001204281	56233	Mm.384027	NM_019572	ENSMUSG00000022475	Hdac7	5830434K02Rik|HD7|HD7a|Hdac7a|mFLJ00062	histone deacetylase 7	protein-coding
mm_58467.1	chr7	3390182	3390231	+	1	NA	Intergenic	Intergenic	-3836	NM_133190	81905	Mm.357990	NM_133190	ENSMUSG00000053395	Cacng8	-	calcium channel, voltage-dependent, gamma subunit 8	protein-coding
mm_98505.1	chr11	94952122	94952132	+	1	NA	3' UTR (NM_007742, exon 51 of 51)	3' UTR (NM_007742, exon 51 of 51)	-15466	NM_018792	54388	Mm.30482	NM_018792	ENSMUSG00000038994	Hils1	H1.9|TISP64	histone H1-like protein in spermatids 1	protein-coding
mm_141041.1	chr17	25274300	25274317	-	1	NA	promoter-TSS (NM_011665)	promoter-TSS (NM_011665)	2	NM_011665	22196	Mm.240044	NM_011665	ENSMUSG00000015120	Ube2i	5830467E05Rik|F830028O17Rik|UBC9|Ubce2i|Ubce9	ubiquitin-conjugating enzyme E2I	protein-coding
mm_61350.1	chr7	68288210	68288219	+	1	NA	intron (NM_001013811, intron 1 of 8)	L1_Mus4|LINE|L1	-11620	NR_040340	100504026	Mm.426764	NR_040340	ENSMUSG00000086628	Gm16157	OTTMUSG00000031023	predicted gene 16157	ncRNA
mm_99826.1	chr11	108920500	108920510	+	1	NA	5' UTR (NM_015732, exon 1 of 11)	5' UTR (NM_015732, exon 1 of 11)	156	NM_015732	12006	Mm.71710	NM_015732	ENSMUSG00000000142	Axin2	Axi1|Axil|Conductin	axin 2	protein-coding
mm_36565.1	chr4	87230492	87230501	-	1	NA	promoter-TSS (NM_172426)	promoter-TSS (NM_172426)	44	NM_172426	76376	Mm.490487	NM_172426	ENSMUSG00000037996	Slc24a2	2810021B17Rik|6330417K15Rik|AI847460|Nckx2	solute carrier family 24 (sodium/potassium/calcium exchanger), member 2	protein-coding
mm_164001.1	chr14	65980844	65980870	+	1	NA	exon (NM_013492, exon 8 of 9)	exon (NM_013492, exon 8 of 9)	12374	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_13611.1	chr2	113405104	113405112	+	1	NA	intron (NM_001285458, intron 2 of 16)	intron (NM_001285458, intron 2 of 16)	-35956	NM_001285459	14260	Mm.4938	NM_010230	ENSMUSG00000044042	Fmn1	Fmn|formin-1|ld	formin 1	protein-coding
mm_163250.1	chr11	108181833	108181865	+	1	NA	intron (NM_011101, intron 3 of 16)	intron (NM_011101, intron 3 of 16)	162039	NM_011101	18750	Mm.222178	NM_011101	ENSMUSG00000050965	Prkca	AI875142|Pkca	protein kinase C, alpha	protein-coding
mm_27821.1	chr3	79076305	79076331	-	1	NA	intron (NM_001310536, intron 19 of 23)	RSINE1|SINE|B4	68569	NM_001310536	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_11211.1	chr2	29621437	29621460	+	1	NA	intron (NM_001039087, intron 1 of 25)	B3|SINE|B2	1728	NM_001039086	107746	Mm.298274	NM_054050	ENSMUSG00000039844	Rapgef1	4932418O06Rik|C3G|Grf2	Rap guanine nucleotide exchange factor (GEF) 1	protein-coding
mm_124301.1	chr14	103056072	103056108	-	1	NA	3' UTR (NM_008392, exon 5 of 5)	3' UTR (NM_008392, exon 5 of 5)	9078	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_94069.1	chr10	128401219	128401234	-	1	NA	promoter-TSS (NM_028092)	promoter-TSS (NM_028092)	-2	NM_001136237	72002	Mm.22983	NM_028051	ENSMUSG00000039878	Slc39a5	1810013D05Rik|2010205A06Rik|Zip5	solute carrier family 39 (metal ion transporter), member 5	protein-coding
mm_35722.1	chr4	44683910	44683918	-	1	NA	intron (NM_008782, intron 3 of 9)	intron (NM_008782, intron 3 of 9)	-18886	NR_073462	70602	Mm.491142	NR_073462	ENSMUSG00000103995	5730488B01Rik	-	RIKEN cDNA 5730488B01 gene	ncRNA
mm_97817.1	chr11	82963271	82963294	+	1	NA	3' UTR (NM_183201, exon 6 of 6)	3' UTR (NM_183201, exon 6 of 6)	-2601	NR_045932	76392	Mm.295205	NR_045932	ENSMUSG00000086327	Slfn5os	1700003F17Rik	schlafen 5, opposite strand	ncRNA
mm_161056.1	chr12	57564066	57564066	+	1	NA	promoter-TSS (NM_001312644)	promoter-TSS (NM_001312644)	-49	NM_001312644	70846	Mm.84118	NM_001037743	ENSMUSG00000046782	Ttc6	4921506M07Rik|EG639426|ENSMUSG00000046782|Gm69|Gm9813	tetratricopeptide repeat domain 6	protein-coding
mm_3285.1	chr1	136638579	136638584	+	1	NA	Intergenic	Intergenic	13680	NM_001160251	226442	Mm.62521	NM_177643	ENSMUSG00000041483	Zfp281	Znf281	zinc finger protein 281	protein-coding
mm_34928.1	chr4	155831617	155831628	+	1	NA	5' UTR (NM_025338, exon 1 of 4)	5' UTR (NM_025338, exon 1 of 4)	353	NM_025338	66077	Mm.28999	NM_025338	ENSMUSG00000065990	Aurkaip1	0610033H09Rik|Aip|Akip|MRP-S38	aurora kinase A interacting protein 1	protein-coding
mm_12042.1	chr2	58780018	58780028	+	1	NA	exon (NM_001289659, exon 7 of 8)	exon (NM_001289659, exon 7 of 8)	24839	NM_029692	76654	Mm.200370	NM_029692	ENSMUSG00000026839	Upp2	1700124F02Rik|AI266885|UDRPASE2|UP2|UPASE2	uridine phosphorylase 2	protein-coding
mm_89380.1	chr10	89443437	89443445	+	1	NA	intron (NM_001079876, intron 1 of 10)	intron (NM_001079876, intron 1 of 10)	526	NM_001284344	237436	Mm.11982	NM_001033331	ENSMUSG00000074802	Gas2l3	8430435B07Rik|Gm240	growth arrest-specific 2 like 3	protein-coding
mm_87388.1	chr10	45067293	45067303	+	1	NA	promoter-TSS (NM_011156)	promoter-TSS (NM_011156)	84	NM_011156	19072	Mm.10281	NM_011156	ENSMUSG00000019849	Prep	AI047692|AI450383|D10Wsu136e|PEP|Pop	prolyl endopeptidase	protein-coding
mm_48007.1	chr5	136162023	136162033	-	1	NA	intron (NM_178751, intron 1 of 2)	B4A|SINE|B4	8628	NM_178751	269717	Mm.308396	NM_178751	ENSMUSG00000039747	Orai2	A730041O15Rik|Tmem142b	ORAI calcium release-activated calcium modulator 2	protein-coding
mm_144682.1	chr18	34762635	34762643	+	1	NA	5' UTR (NM_175104, exon 2 of 5)	5' UTR (NM_175104, exon 2 of 5)	3733	NM_175104	66306	Mm.29424	NM_175104	ENSMUSG00000034300	Fam53c	2810012G03Rik|Gm21179	family with sequence similarity 53, member C	protein-coding
mm_136418.1	chr16	93929513	93929528	-	1	NA	promoter-TSS (NM_001165925)	promoter-TSS (NM_001165925)	47	NM_001165925	56173	Mm.328716	NM_019500	ENSMUSG00000047109	Cldn14	AI851731	claudin 14	protein-coding
mm_167231.1	chr8	13435111	13435117	+	1	NA	promoter-TSS (NM_001143672)	promoter-TSS (NM_001143672)	-345	NM_001143671	272465	Mm.250502	NM_001143671	ENSMUSG00000038457	Tmem255b	Fam70b|Gm687	transmembrane protein 255B	protein-coding
mm_104828.1	chr11	99089277	99089289	-	1	NA	promoter-TSS (NM_172564)	promoter-TSS (NM_172564)	23	NM_172564	217169	Mm.262067	NM_172564	ENSMUSG00000017607	Tns4	9930017A07Rik|AA589547|AU016405|Cten	tensin 4	protein-coding
mm_94359.1	chr11	4986951	4986964	+	1	NA	5' UTR (NM_001243044, exon 1 of 22)	5' UTR (NM_001243044, exon 1 of 22)	133	NM_007454	11764	Mm.274816	NM_007454	ENSMUSG00000009090	Ap1b1	Adtb1|b2b1660Clo	adaptor protein complex AP-1, beta 1 subunit	protein-coding
mm_164425.1	chr16	45094241	45094249	+	1	NA	5' UTR (NM_026439, exon 1 of 8)	5' UTR (NM_026439, exon 1 of 8)	192	NM_026439	67896	Mm.181074	NM_026439	ENSMUSG00000022665	Ccdc80	2610001E17Rik|DRO1|Ssg1|Urb	coiled-coil domain containing 80	protein-coding
mm_146212.1	chr18	76944095	76944168	+	1	NA	promoter-TSS (NM_001039201)	promoter-TSS (NM_001039201)	16	NM_001039202	76987	Mm.236127	NM_029826	ENSMUSG00000025421	Hdhd2	0610039H12Rik|3110052N05Rik	haloacid dehalogenase-like hydrolase domain containing 2	protein-coding
mm_116636.1	chr13	48971203	48971205	-	1	NA	Intergenic	MTC|LTR|ERVL-MaLR	3092	NR_015601	68128	Mm.426304	NR_015601		Fam120aos	C030044B11Rik	family with sequence similarity 120A, opposite strand	ncRNA
mm_102596.1	chr11	62205166	62205176	-	1	NA	intron (NM_001029936, intron 10 of 12)	intron (NM_001029936, intron 10 of 12)	-43813	NM_007413	11541	Mm.40740	NM_007413	ENSMUSG00000018500	Adora2b	A2BAR|A2BR|A2b|AA2BR|AI480866|AI605384	adenosine A2b receptor	protein-coding
mm_161596.1	chr16	36210353	36210353	+	1	NA	promoter-TSS (NM_001082542)	promoter-TSS (NM_001082542)	-50	NM_001082542	408196	Mm.432544	NM_001082542	ENSMUSG00000094733	Gm5416	EG408196|Stfna1l1	predicted gene 5416	protein-coding
mm_67600.1	chr7	83735473	83735489	-	1	NA	promoter-TSS (NM_010551)	promoter-TSS (NM_010551)	9	NM_010551	16170	Mm.10137	NM_010551	ENSMUSG00000001741	Il16	mKIAA4048	interleukin 16	protein-coding
mm_119068.1	chr14	30825668	30825677	+	1	NA	promoter-TSS (NM_028839)	promoter-TSS (NM_028839)	78	NM_028839	69179	Mm.143025	NM_028839	ENSMUSG00000006526	Tmem110	1810038N08Rik|2310014H19Rik|AW554125|STIMATE	transmembrane protein 110	protein-coding
mm_6191.1	chr1	65123309	65123321	-	1	NA	promoter-TSS (NM_001285881)	promoter-TSS (NM_001285881)	-101	NM_001285882	98303	Mm.348057	NM_175293	ENSMUSG00000044816	D630023F18Rik	AI314969	RIKEN cDNA D630023F18 gene	protein-coding
mm_33197.1	chr4	126286766	126286770	+	1	NA	promoter-TSS (NM_199473)	promoter-TSS (NM_199473)	-26	NM_199473	329941	Mm.296327	NM_199473	ENSMUSG00000056174	Col8a2	AI429819	collagen, type VIII, alpha 2	protein-coding
mm_79634.1	chr9	59541835	59541860	+	1	NA	intron (NM_010421, intron 1 of 13)	intron (NM_010421, intron 1 of 13)	2307	NM_010421	15211	Mm.2284	NM_010421	ENSMUSG00000025232	Hexa	Hex-1	hexosaminidase A	protein-coding
mm_166781.1	chr6	140601689	140601693	+	1	NA	Intergenic	MLTR18_MM|LTR|ERVK	-20972	NM_178803	11569	Mm.86453	NM_009637	ENSMUSG00000030232	Aebp2	AU023766|B230313N05Rik	AE binding protein 2	protein-coding
mm_129296.1	chr15	77306574	77306607	-	1	NA	5' UTR (NM_175387, exon 1 of 13)	5' UTR (NM_175387, exon 1 of 13)	463	NM_001110827	93686	Mm.202774	NM_053104	ENSMUSG00000033565	Rbfox2	Fbm2|Fxh|Hrnbp2|Rbm9	RNA binding protein, fox-1 homolog (C. elegans) 2	protein-coding
mm_34129.1	chr4	139280457	139280489	+	1	NA	exon (NM_001271405, exon 6 of 9)	exon (NM_001271405, exon 6 of 9)	30227	NM_145384	212555	Mm.45131	NM_145384	ENSMUSG00000028744	Pqlc2	BC019216	PQ loop repeat containing 2	protein-coding
mm_69700.1	chr7	140049149	140049180	-	1	NA	promoter-TSS (NM_010836)	promoter-TSS (NM_010836)	-76	NM_001347609	17703	Mm.4816	NM_010836	ENSMUSG00000025469	Msx3	AI323377	msh homeobox 3	protein-coding
mm_77075.1	chr8	110161366	110161366	-	1	NA	intron (NM_007586, intron 1 of 10)	intron (NM_007586, intron 1 of 10)	6840	NM_007586	12308	Mm.2755	NM_007586	ENSMUSG00000003657	Calb2	CR	calbindin 2	protein-coding
mm_65142.1	chr7	19573794	19573845	-	1	NA	promoter-TSS (NM_027189)	promoter-TSS (NM_027189)	-476	NM_027189	69731	Mm.24540	NM_027189	ENSMUSG00000044709	Gemin7	2400008I04Rik|AI120175|AI461688	gem (nuclear organelle) associated protein 7	protein-coding
mm_40904.1	chr5	75180183	75180193	+	1	NA	exon (NM_001083316, exon 13 of 23)	exon (NM_001083316, exon 13 of 23)	3357	NR_105992	102465620		NR_105992	ENSMUSG00000099060	Mir7025	Gm27860|mmu-mir-7025	microRNA 7025	ncRNA
mm_114393.1	chr13	63273616	63273618	+	1	NA	intron (NR_110520, intron 2 of 5)	intron (NR_110520, intron 2 of 5)	23530	NR_045794	100504114	Mm.437070	NR_045794	ENSMUSG00000097242	Gm16907	-	predicted gene, 16907	ncRNA
mm_154934.1	chrX	35888809	35888859	+	1	NA	promoter-TSS (NM_001009947)	promoter-TSS (NM_001009947)	2	NM_001009947	75974	Mm.32873	NM_177745	ENSMUSG00000031093	Dock11	5033414A21Rik|8030476J24|Zizimin2|sph238	dedicator of cytokinesis 11	protein-coding
mm_30927.1	chr4	32768332	32768345	+	1	NA	intron (NM_001081392, intron 96 of 101)	intron (NM_001081392, intron 96 of 101)	-31921	NM_175364	108755	Mm.1182	NM_175364	ENSMUSG00000045854	Lyrm2	2610208E05Rik	LYR motif containing 2	protein-coding
mm_55920.1	chr6	83831737	83831750	-	1	NA	promoter-TSS (NM_146169)	promoter-TSS (NM_146169)	-2	NM_146169	232164	Mm.404420	NM_146169	ENSMUSG00000045896	Paip2b	-	poly(A) binding protein interacting protein 2B	protein-coding
mm_29394.1	chr3	108904444	108904463	-	1	NA	exon (NM_025845, exon 6 of 6)	exon (NM_025845, exon 6 of 6)	7251	NM_025845	66921	Mm.51049	NM_025845	ENSMUSG00000027881	Prpf38b	1110021E09Rik|AU018955	PRP38 pre-mRNA processing factor 38 (yeast) domain containing B	protein-coding
mm_153579.1	chr19	43388356	43388369	-	1	NA	promoter-TSS (NM_001081257)	promoter-TSS (NM_001081257)	-7	NM_001081257	545291	Mm.442200	NM_001081257	ENSMUSG00000074852	Hpse2	Gm968|Hpa2	heparanase 2	protein-coding
mm_113880.1	chr13	48968901	48968904	+	1	NA	intron (NR_015601, intron 1 of 1)	intron (NR_015601, intron 1 of 1)	790	NR_015601	68128	Mm.426304	NR_015601		Fam120aos	C030044B11Rik	family with sequence similarity 120A, opposite strand	ncRNA
mm_164987.1	chr19	10952349	10952391	+	1	NA	Intergenic	MIR|SINE|MIR	-3104	NM_023731	108673	Mm.294908	NM_023731	ENSMUSG00000024732	Ccdc86	4933411H20Rik|6720480F16Rik|D19Ertd678e	coiled-coil domain containing 86	protein-coding
mm_126123.1	chr15	78326045	78326059	+	1	NA	promoter-TSS (NM_007780)	promoter-TSS (NM_007780)	62	NM_007780	12983	Mm.235324	NM_007780	ENSMUSG00000071713	Csf2rb	AI848964|AIC2B|Bc|CDw131|Csf2rb1|Csfgmrb|Il3r|Il3rb|Il3rb1|Il5rb	colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage)	protein-coding
mm_140898.1	chr17	24078853	24078874	-	1	NA	3' UTR (NM_011062, exon 14 of 14)	3' UTR (NM_011062, exon 14 of 14)	-5378	NM_027008	69259	Mm.28171	NM_027008	ENSMUSG00000016946	Kctd5	2610030N08Rik|mKIAA0176	potassium channel tetramerisation domain containing 5	protein-coding
mm_3637.1	chr1	152811417	152811441	+	1	NA	intron (NM_010877, intron 3 of 15)	intron (NM_010877, intron 3 of 15)	11276	NM_010877	17970	Mm.270307	NM_010877	ENSMUSG00000026480	Ncf2	NOXA2|Ncf-2|p67phox	neutrophil cytosolic factor 2	protein-coding
mm_106964.1	chr12	8928233	8928237	+	1	NA	intron (NM_008640, intron 1 of 6)	MTD|LTR|ERVL-MaLR	6928	NM_008640	17775	Mm.30071	NM_008640	ENSMUSG00000020585	Laptm4a	AA286466|LAPTM4|MTP|Mtrp|mKIAA0108	lysosomal-associated protein transmembrane 4A	protein-coding
mm_168910.1	chr12	55230411	55230424	+	1	NA	promoter-TSS (NM_001100110)	promoter-TSS (NM_001100110)	-61	NM_001100110	100101806	Mm.471968	NM_001100110	ENSMUSG00000079108	Srp54c	E330029E12Rik	signal recognition particle 54C	protein-coding
mm_1162.1	chr1	60909149	60909159	+	1	NA	5' UTR (NM_009843, exon 1 of 4)	5' UTR (NM_009843, exon 1 of 4)	129	NM_001281976	12477	Mm.390	NM_009843	ENSMUSG00000026011	Ctla4	Cd152|Ctla-4|Ly-56	cytotoxic T-lymphocyte-associated protein 4	protein-coding
mm_53395.1	chr6	129588092	129588098	+	1	NA	Intergenic	Intergenic	-3716	NM_010654	16643	Mm.391515	NM_010654	ENSMUSG00000030165	Klrd1	CD94	killer cell lectin-like receptor, subfamily D, member 1	protein-coding
mm_108129.1	chr12	76049690	76049694	+	1	NA	intron (NM_001005510, intron 85 of 115)	L1MB8|LINE|L1	127567	NM_010157	13983	Mm.2561	NM_010157	ENSMUSG00000021055	Esr2	ER[b]|ERbeta|Estrb	estrogen receptor 2 (beta)	protein-coding
mm_65654.1	chr7	28137099	28137107	-	1	NA	exon (NM_001164655, exon 4 of 20)	exon (NM_001164655, exon 4 of 20)	7637	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_118944.1	chr14	27336024	27336067	+	1	NA	promoter-TSS (NM_001289687)	promoter-TSS (NM_001289687)	8	NM_001289687	71704	Mm.248606	NM_027871	ENSMUSG00000021895	Arhgef3	1200004I24Rik|9830169H03Rik|C76747|Xpln	Rho guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_69547.1	chr7	135695928	135695938	-	1	NA	exon (NM_001081117, exon 12 of 14)	exon (NM_001081117, exon 12 of 14)	20446	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_36057.1	chr4	57359514	57359516	-	1	NA	TTS (NR_038178)	TTS (NR_038178)	4777	NR_038179	73349	Mm.393774	NR_038178		1700042G15Rik	-	RIKEN cDNA 1700042G15 gene	ncRNA
mm_82133.1	chr9	123529844	123529859	+	1	NA	promoter-TSS (NM_030692)	promoter-TSS (NM_030692)	-31	NM_030692	83493	Mm.273671	NM_030692	ENSMUSG00000025240	Sacm1l	SAC1|Sac1p|mKIAA0851	SAC1 suppressor of actin mutations 1-like (yeast)	protein-coding
mm_89885.1	chr10	108436693	108436695	+	1	NA	Intergenic	Intergenic	104505	NM_054056	114774	Mm.391419	NM_054056	ENSMUSG00000035873	Pawr	2310001G03Rik|PAR4|Par-4	PRKC, apoptosis, WT1, regulator	protein-coding
mm_117461.1	chr13	75930236	75930242	-	1	NA	intron (NM_028493, intron 3 of 11)	intron (NM_028493, intron 3 of 11)	13585	NM_028493	73296	Mm.276200	NM_028493	ENSMUSG00000021589	Rhobtb3	1700040C17Rik|2610033K01Rik|4930503C18Rik|AI317148|AW208826|mKIAA0878	Rho-related BTB domain containing 3	protein-coding
mm_90609.1	chr10	128337762	128337818	+	1	NA	promoter-TSS (NM_026444)	promoter-TSS (NM_026444)	63	NM_026444	12974	Mm.58836	NM_026444	ENSMUSG00000005683	Cs	2610511A05Rik|9030605P22Rik|Ahl4|BB234005|Cis	citrate synthase	protein-coding
mm_62307.1	chr7	100227312	100227384	+	1	NA	promoter-TSS (NM_027629)	promoter-TSS (NM_027629)	-259	NM_027629	70974	Mm.440524	NM_027629	ENSMUSG00000030729	Pgm2l1	4931406N15Rik|AI553438|BM32A	phosphoglucomutase 2-like 1	protein-coding
mm_147075.1	chr18	35498845	35498853	-	1	NA	promoter-TSS (NM_030749)	promoter-TSS (NM_030749)	76	NM_030749	81500	Mm.291482	NM_030749	ENSMUSG00000024357	Sil1	1810057E01Rik|AI042831|wz	endoplasmic reticulum chaperone SIL1 homolog (S. cerevisiae)	protein-coding
mm_61458.1	chr7	75596330	75596343	+	1	NA	intron (NM_029332, intron 5 of 36)	intron (NM_029332, intron 5 of 36)	140802	NM_029332	75547	Mm.216107	NM_029332	ENSMUSG00000066406	Akap13	1700026G02Rik|5730522G15Rik|5830460E08Rik|AKAP-13|AKAP-Lbc|BRX|Ht31|LBC|PROTO-LB|PROTO-LBC	A kinase (PRKA) anchor protein 13	protein-coding
mm_145925.1	chr18	67133079	67133086	+	1	NA	promoter-TSS (NM_010307)	promoter-TSS (NM_010307)	-478	NM_010307	14680	Mm.440746	NM_010307	ENSMUSG00000024524	Gnal	2610011C15Rik|9630020G10Rik|Galphaolf|Gna10|Golf	guanine nucleotide binding protein, alpha stimulating, olfactory type	protein-coding
mm_88440.1	chr10	77546027	77546035	+	1	NA	exon (NM_008404, exon 4 of 16)	exon (NM_008404, exon 4 of 16)	15683	NM_008404	16414	Mm.1137	NM_008404	ENSMUSG00000000290	Itgb2	2E6|AI528527|Cd18|LAD|LCAMB|Lfa1|MF17	integrin beta 2	protein-coding
mm_28341.1	chr3	89393630	89393684	-	1	NA	promoter-TSS (NM_009565)	promoter-TSS (NM_009565)	-454	NM_009565	22724	Mm.262184	NM_009565	ENSMUSG00000028042	Zbtb7b	Thpok|Zfp67|c-Krox	zinc finger and BTB domain containing 7B	protein-coding
mm_142011.1	chr17	35200389	35200399	-	1	NA	exon (NM_013693, exon 4 of 4)	exon (NM_013693, exon 4 of 4)	1613	NM_013693	21926	Mm.1293	NM_013693	ENSMUSG00000024401	Tnf	DIF|TNF-a|TNF-alpha|TNFSF2|TNFalpha|Tnfa|Tnfsf1a|Tnlg1f	tumor necrosis factor	protein-coding
mm_96224.1	chr11	62511763	62511769	+	1	NA	intron (NM_001039536, intron 5 of 6)	intron (NM_001039536, intron 5 of 6)	27495	NM_028448	73139	Mm.390409	NM_028448	ENSMUSG00000018509	Cenpv	3110013H01Rik|AA671303|Prr6	centromere protein V	protein-coding
mm_125690.1	chr15	66812235	66812244	+	1	NA	intron (NM_001029841, intron 1 of 7)	MIRb|SINE|MIR	19590	NM_001029841	20491	Mm.7601	NM_009192	ENSMUSG00000022372	Sla	Slap|Slap-1	src-like adaptor	protein-coding
mm_131826.1	chr16	22951080	22951090	+	1	NA	promoter-TSS (NM_053176)	promoter-TSS (NM_053176)	13	NM_053176	94175	Mm.358794	NM_053176	ENSMUSG00000022877	Hrg	AI265597|AW413091|D16jh2|D18020|Hprg|Hrgp	histidine-rich glycoprotein	protein-coding
mm_172826.1	chr9	17030312	17030317	+	1	NA	Intergenic	Intergenic	-652083	NM_001080814	270120	Mm.195010	NM_001080814	ENSMUSG00000074505	Fat3	9430076A06Rik|D430038H04Rik|Gm1132|Gm510|MFAT3F	FAT atypical cadherin 3	protein-coding
mm_18929.1	chr2	76746407	76746419	-	1	NA	exon (NM_011652, exon 275 of 313)	exon (NM_011652, exon 275 of 313)	71098	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_3442.1	chr1	150102724	150102730	+	1	NA	exon (NM_011198, exon 5 of 10)	exon (NM_011198, exon 5 of 10)	2696	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_113914.1	chr13	49504853	49504880	+	1	NA	promoter-TSS (NM_001012324)	promoter-TSS (NM_001012324)	56	NM_001012324	407800	Mm.386931	NM_001012324	ENSMUSG00000043631	Ecm2	9030618O22Rik|BC065151|tenonectin	extracellular matrix protein 2, female organ and adipocyte specific	protein-coding
mm_47718.1	chr5	130002814	130002834	-	1	NA	promoter-TSS (NM_010368)	promoter-TSS (NM_010368)	4	NM_010368	110006	Mm.3317	NM_010368	ENSMUSG00000025534	Gusb	AI747421|Gur|Gus|Gus-r|Gus-s|Gus-t|Gus-u|Gut|asd|g	glucuronidase, beta	protein-coding
mm_154671.1	chrX	7882381	7882402	+	1	NA	exon (NM_138606, exon 6 of 6)	exon (NM_138606, exon 6 of 6)	-1853	NM_001083937	22232	Mm.214976	NM_078484	ENSMUSG00000031156	Slc35a2	AI327289|Had-1|Had1|Sfc8|UGT|Ugalt	solute carrier family 35 (UDP-galactose transporter), member A2	protein-coding
mm_116212.1	chr13	32783935	32783946	-	1	NA	Intergenic	Intergenic	-2161	NM_001166030	238564	Mm.60041	NM_001166030	ENSMUSG00000044951	Mylk4	EG238564	myosin light chain kinase family, member 4	protein-coding
mm_101165.1	chr11	16973927	16973988	-	1	NA	3' UTR (NM_019549, exon 10 of 10)	3' UTR (NM_019549, exon 10 of 10)	22547	NM_176982	319701	Mm.120672	NM_176982	ENSMUSG00000044966	Fbxo48	A630050E13Rik	F-box protein 48	protein-coding
mm_155743.1	chrX	96166768	96166792	+	1	NA	3' UTR (NM_010833, exon 13 of 13)	3' UTR (NM_010833, exon 13 of 13)	70735	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_109136.1	chr12	106030704	106030725	+	1	NA	intron (NM_001029843, intron 1 of 13)	intron (NM_001029843, intron 1 of 13)	20451	NM_001029843	22367	Mm.2981	NM_011705	ENSMUSG00000021115	Vrk1	51PK	vaccinia related kinase 1	protein-coding
mm_39781.1	chr5	30159857	30159864	+	1	NA	intron (NM_001289798, intron 1 of 15)	MLT1F|LTR|ERVL-MaLR	4607	NM_001289798	231086	Mm.291463	NM_145558	ENSMUSG00000059447	Hadhb	4930479F15Rik|Mtpb|TP-beta	hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), beta subunit	protein-coding
mm_136203.1	chr16	89818359	89818397	-	1	NA	promoter-TSS (NM_001145887)	promoter-TSS (NM_001145887)	-26	NM_001145887	21844	Mm.310902	NM_009384	ENSMUSG00000002489	Tiam1	AI847750|D16Ium10|D16Ium10e	T cell lymphoma invasion and metastasis 1	protein-coding
mm_91953.1	chr10	61099982	61099995	-	1	NA	3' UTR (NM_001316673, exon 15 of 15)	3' UTR (NM_001316673, exon 15 of 15)	10657	NM_025273	13180	Mm.39473	NM_025273	ENSMUSG00000020098	Pcbd1	Dcoh|Pcbd|Pcd|Phs	pterin 4 alpha carbinolamine dehydratase/dimerization cofactor of hepatocyte nuclear factor 1 alpha (TCF1) 1	protein-coding
mm_128871.1	chr15	72930190	72930216	-	1	NA	intron (NM_029640, intron 14 of 21)	intron (NM_029640, intron 14 of 21)	-119879	NR_002864	353342	Mm.440245	NR_002864	ENSMUSG00000106847	Peg13	-	paternally expressed 13	ncRNA
mm_63433.1	chr7	127478984	127478999	+	1	NA	Intergenic	CpG	-6230	NM_010183	14123	Mm.323505	NM_010183	ENSMUSG00000042423	Fbrs	Fbs|Fbs1	fibrosin	protein-coding
mm_99792.1	chr11	107428322	107428353	+	1	NA	intron (NM_145823, intron 1 of 9)	intron (NM_145823, intron 1 of 9)	42383	NM_145823	71795	Mm.397413	NM_145823	ENSMUSG00000040430	Pitpnc1	1110020B03Rik|5830436L09Rik|AI662802|AI851387|C330017I21Rik|Dnr411|RDGBB|RDGBB1|rdgB-beta	phosphatidylinositol transfer protein, cytoplasmic 1	protein-coding
mm_90023.1	chr10	115388930	115388937	+	1	NA	intron (NM_001033261, intron 1 of 34)	intron (NM_001033261, intron 1 of 34)	3974	NM_001033261	216345	Mm.207621	NM_001033261	ENSMUSG00000034163	Zfc3h1	BC033596|Ccdc131|Psrc2	zinc finger, C3H1-type containing	protein-coding
mm_34278.1	chr4	141424587	141424593	+	1	NA	3' UTR (NM_013868, exon 3 of 3)	3' UTR (NM_013868, exon 3 of 3)	3811	NM_013868	29818	Mm.46181	NM_013868	ENSMUSG00000006221	Hspb7	27kDa|Hsp25-2|cvHsp	heat shock protein family, member 7 (cardiovascular)	protein-coding
mm_31711.1	chr4	62634134	62634148	+	1	NA	intron (NM_134257, intron 6 of 15)	intron (NM_134257, intron 6 of 15)	14469	NM_134257	50780	Mm.286753	NM_019492	ENSMUSG00000059810	Rgs3	4930506N09Rik|C2PA-RGS3|C2pa|PDZ-RGS3|RGS3S	regulator of G-protein signaling 3	protein-coding
mm_164298.1	chr15	103896032	103896046	-	1	NA	exon (NM_009267, exon 4 of 4)	exon (NM_009267, exon 4 of 4)	3261	NM_009268	20771	Mm.30276	NM_009268		Mucl1	Spt-2|Spt2	mucin-like 1	protein-coding
mm_114623.1	chr13	76055688	76055737	+	1	NA	exon (NM_175495, exon 1 of 1)	exon (NM_175495, exon 1 of 1)	1284	NM_175495	238725	Mm.167172	NM_175495	ENSMUSG00000045509	Gpr150	C030001A19Rik|PGR11	G protein-coupled receptor 150	protein-coding
mm_123373.1	chr14	63199259	63199284	-	1	NA	3' UTR (NM_008092, exon 7 of 7)	3' UTR (NM_008092, exon 7 of 7)	-5746	NM_201610	382913	Mm.239490	NM_201610	ENSMUSG00000035121	Neil2	Gm1212|NEH2	nei like 2 (E. coli)	protein-coding
mm_90061.1	chr10	116275582	116275590	+	1	NA	TTS (NM_001161837)	TTS (NM_001161837)	-25788	NM_029928	19263	Mm.37213	NM_029928	ENSMUSG00000020154	Ptprb	3230402H02Rik|C130094E24|Ptpz|Rptpb|VE-PTP|Veptp	protein tyrosine phosphatase, receptor type, B	protein-coding
mm_16389.1	chr2	178502142	178502161	+	1	NA	Intergenic	Intergenic	71636	NM_198656	381409	Mm.330860	NM_198656	ENSMUSG00000039155	Cdh26	Gm1010	cadherin-like 26	protein-coding
mm_99988.1	chr11	114720233	114720235	+	1	NA	3' UTR (NM_053273, exon 14 of 14)	3' UTR (NM_053273, exon 14 of 14)	-7178	NM_001034878	432611	Mm.212764	NM_001034878	ENSMUSG00000034706	Dnaic2	C030015H18Rik|Dnai2|Gm728	dynein, axonemal, intermediate chain 2	protein-coding
mm_88304.1	chr10	75324942	75324963	+	1	NA	promoter-TSS (NM_001331096)	promoter-TSS (NM_001331096)	94	NM_001331096	11540	Mm.333734	NM_009630	ENSMUSG00000020178	Adora2a	A2AAR|A2aR|AA2AR	adenosine A2a receptor	protein-coding
mm_88120.1	chr10	69219358	69219382	+	1	NA	intron (NM_001252637, intron 2 of 10)	intron (NM_001252637, intron 2 of 10)	6176	NM_001252638	69288	Mm.26659	NM_001081347	ENSMUSG00000019944	Rhobtb1	1700008H16Rik|3110048G13Rik|AI173445|AI573858|AV350930	Rho-related BTB domain containing 1	protein-coding
mm_141434.1	chr17	29492841	29492859	-	1	NA	intron (NM_008842, intron 4 of 5)	intron (NM_008842, intron 4 of 5)	1805	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_75746.1	chr8	69888202	69888215	-	1	NA	promoter-TSS (NM_026818)	promoter-TSS (NM_026818)	-816	NM_026818	68709	Mm.334584	NM_026818	ENSMUSG00000044006	Cilp2	1110031K21Rik|AA407300|CLIP-2	cartilage intermediate layer protein 2	protein-coding
mm_9457.1	chr1	172894599	172894603	-	1	NA	exon (NM_011318, exon 2 of 2)	exon (NM_011318, exon 2 of 2)	453	NM_011318	20219	Mm.330510	NM_011318	ENSMUSG00000026542	Apcs	Sap	serum amyloid P-component	protein-coding
mm_88863.1	chr10	80930975	80930983	+	1	NA	intron (NM_008655, intron 2 of 3)	intron (NM_008655, intron 2 of 3)	888	NM_008655	17873	Mm.1360	NM_008655	ENSMUSG00000015312	Gadd45b	AI323528|Myd118	growth arrest and DNA-damage-inducible 45 beta	protein-coding
mm_83877.1	chr9	55204995	55204996	-	1	NA	intron (NM_001346657, intron 11 of 11)	B4A|SINE|B4	-3940	NM_028049	71999	Mm.276429	NM_028049	ENSMUSG00000032309	Fbxo22	0610033L19Rik|1600016C16Rik	F-box protein 22	protein-coding
mm_86244.1	chr9	121285959	121285971	-	1	NA	Intergenic	Intergenic	-8793	NM_177589	209012	Mm.371804	NM_177589	ENSMUSG00000040936	Ulk4	4932415A06Rik|A730098P15	unc-51-like kinase 4	protein-coding
mm_43604.1	chr5	137887921	137887930	+	1	NA	Intergenic	Intergenic	-16167	NM_001024932	545812	Mm.332769	NM_001024932	ENSMUSG00000066682	Pilrb2	EG545812	paired immunoglobin-like type 2 receptor beta 2	protein-coding
mm_150196.1	chr19	32727300	32727308	+	1	NA	Intergenic	Intergenic	-15006	NM_026487	67979	Mm.27123	NM_026487	ENSMUSG00000013662	Atad1	4921525H23Rik|AW107648|Thorase	ATPase family, AAA domain containing 1	protein-coding
mm_8485.1	chr1	153549839	153549855	-	1	NA	promoter-TSS (NM_028749)	promoter-TSS (NM_028749)	-133	NM_028749	74091	Mm.24887	NM_028749	ENSMUSG00000042684	Npl	0610033B02Rik	N-acetylneuraminate pyruvate lyase	protein-coding
mm_54490.1	chr6	35326124	35326155	-	1	NA	promoter-TSS (NM_173375)	promoter-TSS (NM_173375)	2	NM_173375	208164	Mm.257766	NM_173375	ENSMUSG00000047420	Fam180a	B230314O19	family with sequence similarity 180, member A	protein-coding
mm_162370.1	chr1	66935536	66935546	-	1	NA	promoter-TSS (NM_001113387)	promoter-TSS (NM_001113387)	-175	NM_001113387	17901	Mm.1000	NM_021285	ENSMUSG00000061816	Myl1	AI325107|MLC1f|MLC3f|Mylf	myosin, light polypeptide 1	protein-coding
mm_146415.1	chr18	84293220	84293236	+	1	NA	intron (NM_001033341, intron 8 of 8)	intron (NM_001033341, intron 8 of 8)	205070	NM_146090	225791	Mm.147052	NM_146090	ENSMUSG00000049090	Zadh2	C530046K17Rik|PTGR-3|Pthr3	zinc binding alcohol dehydrogenase, domain containing 2	protein-coding
mm_38804.1	chr4	148159821	148159837	-	1	NA	promoter-TSS (NM_176848)	promoter-TSS (NM_176848)	-240	NM_001161851	230903	Mm.220327	NM_173401	ENSMUSG00000029001	Fbxo44	5730411K09|AV001623|FBG3|FBX30|Fbx6a|Fbxo6a	F-box protein 44	protein-coding
mm_152026.1	chr19	6062112	6062156	-	1	NA	TTS (NM_028454)	TTS (NM_028454)	927	NM_013859	29805	Mm.2310	NM_013859	ENSMUSG00000075227	Znhit2	C11orf5|Fon|ORF6|Znhit2-ps	zinc finger, HIT domain containing 2	protein-coding
mm_169175.1	chr13	65703781	65703783	-	1	NA	Intergenic	Intergenic	-409671	NM_001177832	628709	Mm.390595	NM_001177832	ENSMUSG00000095909	Gm10324	ENSMUSG00000071302	predicted gene 10324	protein-coding
mm_133809.1	chr16	95702100	95702110	+	1	NA	promoter-TSS (NM_011809)	promoter-TSS (NM_011809)	-302	NM_011809	23872	Mm.290207	NM_011809	ENSMUSG00000022895	Ets2	AU022856|Ets-2	E26 avian leukemia oncogene 2, 3' domain	protein-coding
mm_23811.1	chr3	79886182	79886209	+	1	NA	5' UTR (NM_133187, exon 1 of 4)	5' UTR (NM_133187, exon 1 of 4)	265	NM_133187	68659	Mm.427274	NM_133187	ENSMUSG00000027955	Fam198b	1110032E23Rik|2210419I08Rik|AV011458|Ened	family with sequence similarity 198, member B	protein-coding
mm_94348.1	chr11	4891206	4891210	+	1	NA	promoter-TSS (NR_105883)	promoter-TSS (NR_105883)	-137	NR_105883	102466764		NR_105883	ENSMUSG00000098296	Mir6918	Gm27968|mmu-mir-6918	microRNA 6918	ncRNA
mm_87191.1	chr10	39451285	39451325	+	1	NA	intron (NM_001122892, intron 2 of 12)	intron (NM_001122892, intron 2 of 12)	81506	NM_001122893	14360	Mm.4848	NM_008054	ENSMUSG00000019843	Fyn	AI448320|AW552119	Fyn proto-oncogene	protein-coding
mm_161172.1	chr13	38345532	38345532	+	1	NA	promoter-TSS (NM_007556)	promoter-TSS (NM_007556)	-184	NM_007556	12161	Mm.385759	NM_007556	ENSMUSG00000039004	Bmp6	D13Wsu115e|Vgr1	bone morphogenetic protein 6	protein-coding
mm_64462.1	chr7	142665130	142665157	+	1	NA	intron (NR_002855, intron 1 of 3)	intron (NR_002855, intron 1 of 3)	1673	NM_001315488	16002	Mm.3862	NM_010514	ENSMUSG00000048583	Igf2	AL033362|Igf-2|Igf-II|M6pr|Mpr|Peg2	insulin-like growth factor 2	protein-coding
mm_86229.1	chr9	120136336	120136350	-	1	NA	Intergenic	Intergenic	5909	NR_002902	104433	Mm.453530	NR_002902	ENSMUSG00000064925	Snora62	E2|MBI-13|MBI-136|Rnu108	small nucleolar RNA, H/ACA box 62	snoRNA
mm_130273.1	chr15	96698810	96698855	-	1	NA	intron (NM_175121, intron 1 of 15)	CpG	866	NM_175121	67760	Mm.46754	NM_175121	ENSMUSG00000022462	Slc38a2	5033402L14Rik|AI316867|ATA2|SAT2|mKIAA1382	solute carrier family 38, member 2	protein-coding
mm_77092.1	chr8	110793632	110793641	-	1	NA	intron (NM_029646, intron 1 of 7)	intron (NM_029646, intron 1 of 7)	12288	NM_029646	76527	Mm.77697	NM_029646	ENSMUSG00000031750	Il34	2010004A03Rik|AI593503	interleukin 34	protein-coding
mm_109784.1	chr12	3235291	3235297	-	1	NA	promoter-TSS (NR_015551)	promoter-TSS (NR_015551)	-497	NR_015551	74173	Mm.309774	NM_028796	ENSMUSG00000079179	Rab10os	1700012B15Rik|1810036A22Rik	RAB10, member RAS oncogene family, opposite strand	ncRNA
mm_81998.1	chr9	121642727	121642757	+	1	NA	promoter-TSS (NM_011703)	promoter-TSS (NM_011703)	26	NM_011703	22354	Mm.282007	NM_011703	ENSMUSG00000032528	Vipr1	AV071699|VIP-R1|VPAC1	vasoactive intestinal peptide receptor 1	protein-coding
mm_76792.1	chr8	102785070	102785089	-	1	NA	promoter-TSS (NM_009866)	promoter-TSS (NM_009866)	32	NM_009866	12552	Mm.1571	NM_009866	ENSMUSG00000031673	Cdh11	Cad11|OSF-4	cadherin 11	protein-coding
mm_49274.1	chr6	17635739	17635791	+	1	NA	Intergenic	Intergenic	-1333	NM_007604	12343	Mm.392504	NM_007604	ENSMUSG00000015733	Capza2	1110053K06Rik|AW208808|Cappa2	capping protein (actin filament) muscle Z-line, alpha 2	protein-coding
mm_54500.1	chr6	35510378	35510387	-	1	NA	3' UTR (NM_008098, exon 4 of 4)	3' UTR (NM_008098, exon 4 of 4)	29506	NM_008098	14489	Mm.182746	NM_008098	ENSMUSG00000029840	Mtpn	5033418D15Rik|Gcdp|V1	myotrophin	protein-coding
mm_73206.1	chr8	95678320	95678330	+	1	NA	Intergenic	CpG	-24712	NM_001195006	234593	Mm.29846	NM_145602	ENSMUSG00000036564	Ndrg4	D8Bwg1337e|Ndr1-rs|Ndr4|R74996|SMAP-8	N-myc downstream regulated gene 4	protein-coding
mm_37109.1	chr4	116639959	116640005	-	1	NA	exon (NM_021473, exon 5 of 9)	exon (NM_021473, exon 5 of 9)	11692	NM_021473	58810	Mm.30085	NM_021473	ENSMUSG00000028692	Akr1a1	2610201A18Rik|Akr1a4	aldo-keto reductase family 1, member A1 (aldehyde reductase)	protein-coding
mm_52797.1	chr6	121300733	121300755	+	1	NA	intron (NM_144512, intron 1 of 14)	MIRb|SINE|MIR	448	NM_144512	14412	Mm.258596	NM_144512	ENSMUSG00000030108	Slc6a13	GAT3|Gabt3|Gat2	solute carrier family 6 (neurotransmitter transporter, GABA), member 13	protein-coding
mm_17296.1	chr2	26294512	26294515	-	1	NA	promoter-TSS (NM_177841)	promoter-TSS (NM_177841)	44	NM_177841	329366	Mm.77712	NM_177841	ENSMUSG00000048038	Ccdc187	4932418E24Rik	coiled-coil domain containing 187	protein-coding
mm_121931.1	chr14	23967113	23967115	-	1	NA	intron (NM_001253366, intron 1 of 29)	intron (NM_001253366, intron 1 of 29)	37091	NM_001253375	16531	Mm.343607	NM_010610	ENSMUSG00000063142	Kcnma1	5730414M22Rik|BKCa|MaxiK|Slo|Slo1|mSlo|mSlo1	potassium large conductance calcium-activated channel, subfamily M, alpha member 1	protein-coding
mm_27294.1	chr3	45378207	45378248	-	1	NA	promoter-TSS (NR_045172)	promoter-TSS (NR_045172)	33	NR_045172	72511	Mm.140700	NR_045172	ENSMUSG00000097040	2610316D01Rik	-	RIKEN cDNA 2610316D01 gene	ncRNA
mm_2884.1	chr1	131843992	131844006	+	1	NA	exon (NM_173865, exon 9 of 11)	exon (NM_173865, exon 9 of 11)	15987	NM_173865	98396	Mm.389181	NM_173865	ENSMUSG00000013275	Slc41a1	AI573938|B230315F01Rik	solute carrier family 41, member 1	protein-coding
mm_154731.1	chrX	9490381	9490383	+	1	NA	Intergenic	Intergenic	-21058	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_73701.1	chr8	111686553	111686634	+	1	NA	TTS (NM_025583)	TTS (NM_025583)	3081	NR_106044	102466993		NR_106044	ENSMUSG00000099129	Mir7076	Gm27318|mmu-mir-7076	microRNA 7076	ncRNA
mm_9981.1	chr1	191232742	191232748	-	1	NA	Intergenic	RMER15|LTR|ERVL	-49412	NM_007498	11910	Mm.2706	NM_007498	ENSMUSG00000026628	Atf3	LRG-21	activating transcription factor 3	protein-coding
mm_5180.1	chr1	12990474	12990482	-	1	NA	exon (NM_172841, exon 1 of 9)	exon (NM_172841, exon 1 of 9)	657	NM_172841	240726	Mm.24481	NM_172841	ENSMUSG00000025938	Slco5a1	4732454B15|A630033C23Rik|AA407151	solute carrier organic anion transporter family, member 5A1	protein-coding
mm_154942.1	chrX	36195939	36195945	+	1	NA	promoter-TSS (NM_028325)	promoter-TSS (NM_028325)	38	NM_028325	72693	Mm.297698	NM_028325	ENSMUSG00000036699	Zcchc12	2810028A01Rik|AV136720|Sizn1	zinc finger, CCHC domain containing 12	protein-coding
mm_10171.1	chr2	4559743	4559755	+	1	NA	promoter-TSS (NM_001177844)	promoter-TSS (NM_001177844)	-5	NM_001177844	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding
mm_144567.1	chr18	31777405	31777416	+	1	NA	intron (NM_153515, intron 6 of 7)	intron (NM_153515, intron 6 of 7)	-11749	NM_027002	69241	Mm.279898	NM_027002	ENSMUSG00000024258	Polr2d	2310002G05Rik|2610028L19Rik|HSRBP4|RBP4	polymerase (RNA) II (DNA directed) polypeptide D	protein-coding
mm_64465.1	chr7	142678687	142678711	+	1	NA	TTS (NM_001185083)	TTS (NM_001185083)	1027	NM_001185083	16334	Mm.4946	NM_008387	ENSMUSG00000000215	Ins2	AA986540|Ins-2|InsII|Mody|Mody4	insulin II	protein-coding
mm_114066.1	chr13	54380595	54380610	+	1	NA	3' UTR (NM_009946, exon 4 of 4)	3' UTR (NM_009946, exon 4 of 4)	9253	NM_009946	12890	Mm.268902	NM_009946	ENSMUSG00000025867	Cplx2	921-L|AI413745|AW492120	complexin 2	protein-coding
mm_123032.1	chr14	55524939	55524967	-	1	NA	promoter-TSS (NM_008736)	promoter-TSS (NM_008736)	28	NM_001271916	18185	Mm.20422	NM_008736	ENSMUSG00000040632	Nrl	D14H14S46E	neural retina leucine zipper gene	protein-coding
mm_12928.1	chr2	85039745	85039780	+	1	NA	intron (NM_182990, intron 3 of 16)	intron (NM_182990, intron 3 of 16)	2311	NM_001136081	20833	Mm.219793	NM_182990	ENSMUSG00000027067	Ssrp1	C81323|Hmg1-rs1|Hmgi-rs3|Hmgox|T160	structure specific recognition protein 1	protein-coding
mm_87817.1	chr10	60302185	60302189	+	1	NA	TTS (NM_001252635)	TTS (NM_001252635)	17726	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_112867.1	chr13	20849713	20849723	+	1	NA	intron (NM_012054, intron 3 of 20)	intron (NM_012054, intron 3 of 20)	55605	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_51715.1	chr6	86849267	86849335	+	1	NA	promoter-TSS (NM_177762)	promoter-TSS (NM_177762)	139	NR_028298	67170	Mm.119489	NR_028298	ENSMUSG00000100164	2610306M01Rik	-	RIKEN cDNA 2610306M01 gene	ncRNA
mm_40253.1	chr5	38220593	38220603	+	1	NA	promoter-TSS (NM_029162)	promoter-TSS (NM_029162)	116	NM_025281	17089	Mm.28560	NM_025281	ENSMUSG00000067367	Lyar	MLZ-264	Ly1 antibody reactive clone	protein-coding
mm_8112.1	chr1	135919200	135919212	-	1	NA	promoter-TSS (NM_019645)	promoter-TSS (NM_019645)	1	NM_001313701	18772	Mm.4494	NM_019645	ENSMUSG00000026413	Pkp1	-	plakophilin 1	protein-coding
mm_48917.1	chr6	4004090	4004100	+	1	NA	5' UTR (NM_025331, exon 1 of 2)	5' UTR (NM_025331, exon 1 of 2)	108	NM_025331	66066	Mm.25547	NM_025331	ENSMUSG00000032766	Gng11	0610037B21Rik	guanine nucleotide binding protein (G protein), gamma 11	protein-coding
mm_145620.1	chr18	61106042	61106052	+	1	NA	intron (NM_001037859, intron 2 of 21)	intron (NM_001037859, intron 2 of 21)	475	NM_001037859	12978	Mm.22574	NM_007779	ENSMUSG00000024621	Csf1r	AI323359|CD115|CSF-1R|Csfmr|Fim-2|Fim2|Fms|M-CSF-R|M-CSFR	colony stimulating factor 1 receptor	protein-coding
mm_2301.1	chr1	91538734	91538772	+	1	NA	Intergenic	Intergenic	-1812	NM_001039126	65247	Mm.234152	NM_023046	ENSMUSG00000026311	Asb1	1700029O08Rik|1700054C17Rik|AI426616|AI851378|mKIAA1146	ankyrin repeat and SOCS box-containing 1	protein-coding
mm_44329.1	chr5	14692960	14692960	-	1	NA	intron (NM_001110796, intron 6 of 19)	intron (NM_001110796, intron 6 of 19)	178042	NM_001110796	26875	Mm.146275	NM_011995	ENSMUSG00000061601	Pclo	Acz|Pico	piccolo (presynaptic cytomatrix protein)	protein-coding
mm_144310.1	chr18	12599895	12599925	+	1	NA	Intergenic	Intergenic	-43623	NM_028341	72747	Mm.52526	NM_028341	ENSMUSG00000024424	Ttc39c	1700008N02Rik|2810439F02Rik	tetratricopeptide repeat domain 39C	protein-coding
mm_62959.1	chr7	119739883	119739910	+	1	NA	Intergenic	Intergenic	-19098	NM_145585	233802	Mm.26392	NM_145585	ENSMUSG00000030942	Thumpd1	6330575P11Rik	THUMP domain containing 1	protein-coding
mm_55759.1	chr6	78466305	78466316	-	1	NA	TTS (NM_011260)	TTS (NM_011260)	2564	NM_011260	19695	Mm.252385	NM_011260	ENSMUSG00000030017	Reg3g	AI449515|REG-3-gamma|reg III-gamma	regenerating islet-derived 3 gamma	protein-coding
mm_165658.1	chr3	87512816	87512828	+	1	NA	Intergenic	Intergenic	-12756	NM_001083318	27049	Mm.219460	NM_012051	ENSMUSG00000003382	Etv3	AI414410|METS|Pe1	ets variant 3	protein-coding
mm_161334.1	chr14	50795685	50795685	-	1	NA	promoter-TSS (NM_001111119)	promoter-TSS (NM_001111119)	43	NM_001111119	239083	Mm.343880	NM_001111119	ENSMUSG00000071470	Ccnb1ip1	Gm288|Hei10|mei4	cyclin B1 interacting protein 1	protein-coding
mm_170753.1	chr2	156363241	156363254	-	1	NA	intron (NM_027585, intron 9 of 12)	RLTR4_Mm|LTR|ERV1	29732	NR_024329	347740	Mm.324242	NR_024329		2900097C17Rik	1810005K14Rik|4930563C06Rik	RIKEN cDNA 2900097C17 gene	ncRNA
mm_94191.1	chr10	128980940	128980952	-	1	NA	Intergenic	Intergenic	-8968	NM_146861	18373	Mm.377111	NM_146861	ENSMUSG00000069430	Olfr9	MOR269-3	olfactory receptor 9	protein-coding
mm_131632.1	chr16	20186573	20186577	+	1	NA	intron (NM_001033237, intron 10 of 29)	B1F|SINE|Alu	-10341	NR_030454	735274		NR_030454	ENSMUSG00000106252	Mir684-1	Mirn684-1	microRNA 684-1	ncRNA
mm_113180.1	chr13	24879866	24879870	+	1	NA	intron (NR_131787, intron 13 of 19)	intron (NR_131787, intron 13 of 19)	-25732	NR_045182	73326	Mm.458692	NR_045182		4932702P03Rik	1700047I16Rik	RIKEN cDNA 4932702P03 gene	ncRNA
mm_159642.1	chr4	143412338	143412338	+	1	NA	promoter-TSS (NM_172877)	promoter-TSS (NM_172877)	-88	NM_172877	242736	Mm.275953	NM_172877	ENSMUSG00000046862	Pramef8	4732496O08Rik|AU023234	PRAME family member 8	protein-coding
mm_5834.1	chr1	52817739	52817778	-	1	NA	promoter-TSS (NM_008384)	promoter-TSS (NM_008384)	-70	NM_008384	16329	Mm.917	NM_008384	ENSMUSG00000026102	Inpp1	2300002C06Rik|AV137389	inositol polyphosphate-1-phosphatase	protein-coding
mm_126756.1	chr15	85811300	85811318	+	1	NA	intron (NM_197998, intron 1 of 4)	CpG	388	NM_001164626	72355	Mm.33706	NM_197998	ENSMUSG00000064284	Cdpf1	2210021J22Rik	cysteine rich, DPF motif domain containing 1	protein-coding
mm_35395.1	chr4	34381083	34381083	-	1	NA	Intergenic	Lx9|LINE|L1	-169532	NM_001007589	433693	Mm.389532	NM_026019	ENSMUSG00000028291	Akirin2	2700059D21Rik|AA114675|AA522011|AU019887|Akirin-2	akirin 2	protein-coding
mm_95513.1	chr11	52004341	52004366	+	1	NA	5' UTR (NM_001166657, exon 1 of 8)	5' UTR (NM_001166657, exon 1 of 8)	132	NM_001166653	213084	Mm.280557	NM_153785	ENSMUSG00000020389	Cdkl3	AI852479|B230379H01Rik	cyclin-dependent kinase-like 3	protein-coding
mm_173031.1	chrX	105875727	105875732	-	1	NA	exon (NM_009530, exon 9 of 35)	exon (NM_009530, exon 9 of 35)	53643	NM_009530	22589	Mm.10141	NM_009530	ENSMUSG00000031229	Atrx	4833408C14Rik|AI447451|ATR2|DXHXS6677E|HP1-BP38|Hp1bp2|Hp1bp38|MRXS3|RAD54L|Rad54|XH2|Xnp|ZNF-HX	alpha thalassemia/mental retardation syndrome X-linked	protein-coding
mm_76772.1	chr8	95853502	95853530	-	1	NA	promoter-TSS (NM_172758)	promoter-TSS (NM_172758)	-25	NM_172758	234595	Mm.29267	NM_172758	ENSMUSG00000036534	Slc38a7	D430050E18	solute carrier family 38, member 7	protein-coding
mm_55133.1	chr6	51269824	51269828	-	1	NA	promoter-TSS (NR_029719)	promoter-TSS (NR_029719)	84	NR_029719	387166		NR_029719	ENSMUSG00000065505	Mir148a	Mirn148|Mirn148a|mir-148a	microRNA 148a	ncRNA
mm_25146.1	chr3	102734957	102734977	+	1	NA	promoter-TSS (NM_001243132)	promoter-TSS (NM_001243132)	197	NM_027533	70747	Mm.27469	NM_027533	ENSMUSG00000027858	Tspan2	6330415F13Rik|B230119D02Rik|tspan-2	tetraspanin 2	protein-coding
mm_1712.1	chr1	75236617	75236627	+	1	NA	promoter-TSS (NM_001159885)	promoter-TSS (NM_001159885)	-80	NM_001159885	56812	Mm.489660	NM_020266	ENSMUSG00000026203	Dnajb2	2700059H22Rik|Dnajb10|Hsj1|mDj8	DnaJ heat shock protein family (Hsp40) member B2	protein-coding
mm_155475.1	chrX	73640752	73640782	+	1	NA	exon (NM_029352, exon 2 of 4)	exon (NM_029352, exon 2 of 4)	1326	NM_029352	75590	Mm.16479	NM_029352	ENSMUSG00000031383	Dusp9	Dusp4|Mpk4|Pyst3	dual specificity phosphatase 9	protein-coding
mm_156835.1	chrX	164373387	164373412	+	1	NA	promoter-TSS (NM_010216)	promoter-TSS (NM_010216)	-123	NM_001308489	14205	Mm.297978	NM_010216	ENSMUSG00000031380	Vegfd	AI325264|Figf|VEGF-D	vascular endothelial growth factor D	protein-coding
mm_125576.1	chr15	59441039	59441043	+	1	NA	intron (NM_001164604, intron 3 of 4)	intron (NM_001164604, intron 3 of 4)	66843	NM_001164604	68501	Mm.27762	NM_026746	ENSMUSG00000059586	Nsmce2	1110014D18Rik|AI661537	NSE2/MMS21 homolog, SMC5-SMC6 complex SUMO ligase	protein-coding
mm_73360.1	chr8	105594070	105594088	+	1	NA	Intergenic	Intergenic	-11150	NM_001081241	75687	Mm.41261	NM_001081241	ENSMUSG00000038604	Fam65a	2310066E14Rik|AI837433	family with sequence similarity 65, member A	protein-coding
mm_160053.1	chr7	3720383	3720383	-	1	NA	promoter-TSS (NM_011095)	promoter-TSS (NM_011095)	-1	NM_011095	18733	Mm.326531	NM_011095	ENSMUSG00000058818	Pirb	Gp91|LIR-3|Lilrb3|PIR-B	paired Ig-like receptor B	protein-coding
mm_22405.1	chr2	181287959	181288007	-	1	NA	promoter-TSS (NM_198169)	promoter-TSS (NM_198169)	-17	NM_198169	229004	Mm.220423	NM_198169	ENSMUSG00000038705	Gmeb2	AI839884	glucocorticoid modulatory element binding protein 2	protein-coding
mm_47127.1	chr5	120139248	120139276	-	1	NA	promoter-TSS (NR_045793)	promoter-TSS (NR_045793)	1	NR_045793	100503427	Mm.446834	NR_045793	ENSMUSG00000097368	Gm10390	ENSMUSG00000072671	predicted gene 10390	ncRNA
mm_153259.1	chr19	36919078	36919134	-	1	NA	exon (NM_028263, exon 2 of 2)	exon (NM_028263, exon 2 of 2)	493	NM_028263	72514	Mm.41674	NM_028263	ENSMUSG00000047632	Fgfbp3	2610306H15Rik|Fgf-bp3	fibroblast growth factor binding protein 3	protein-coding
mm_13499.1	chr2	107290591	107290660	+	1	NA	promoter-TSS (NM_021275)	promoter-TSS (NM_021275)	36	NM_021275	16492	Mm.142718	NM_021275	ENSMUSG00000042604	Kcna4	Kv1.4	potassium voltage-gated channel, shaker-related subfamily, member 4	protein-coding
mm_19366.1	chr2	91173186	91173192	-	1	NA	exon (NM_145527, exon 7 of 34)	exon (NM_145527, exon 7 of 34)	6132	NM_001177720	228355	Mm.36410	NM_145527	ENSMUSG00000040687	Madd	9630059K23Rik|IG20	MAP-kinase activating death domain	protein-coding
mm_63764.1	chr7	131146432	131146448	+	1	NA	promoter-TSS (NM_173409)	promoter-TSS (NM_173409)	1	NR_040531	69495	Mm.271181	NR_040531	ENSMUSG00000100759	1700029B22Rik	-	RIKEN cDNA 1700029B22 gene	ncRNA
mm_90221.1	chr10	121034145	121034153	+	1	NA	5' UTR (NM_011915, exon 1 of 10)	5' UTR (NM_011915, exon 1 of 10)	145	NM_011915	24117	Mm.32831	NM_011915	ENSMUSG00000020218	Wif1	AW107799|WIF-1	Wnt inhibitory factor 1	protein-coding
mm_75683.1	chr8	68121053	68121074	-	1	NA	Intergenic	Intergenic	-146489	NM_177698	234353	Mm.32525	NM_027626	ENSMUSG00000030465	Psd3	4931420C21Rik|AI661273|BC003498|D430018P08|EFA6D	pleckstrin and Sec7 domain containing 3	protein-coding
mm_147837.1	chr18	62578938	62578942	-	1	NA	intron (NM_177829, intron 1 of 8)	intron (NM_177829, intron 1 of 8)	17324	NM_001001803	408198	Mm.478742	NM_001001803	ENSMUSG00000060201	Spink7	EG408198|Ecg2	serine peptidase inhibitor, Kazal type 7 (putative)	protein-coding
mm_2437.1	chr1	97770159	97770209	+	1	NA	promoter-TSS (NM_001310773)	promoter-TSS (NM_001310773)	12	NM_026250	252876	Mm.86090	NM_026250	ENSMUSG00000026333	Gin1	4930429M06Rik|8430411H10Rik|Gin-1|Zh2c2	gypsy retrotransposon integrase 1	protein-coding
mm_13997.1	chr2	121955965	121955982	+	1	NA	promoter-TSS (NM_001290992)	promoter-TSS (NM_001290992)	-28	NM_001290992	329506	Mm.249405	NM_212450	ENSMUSG00000033411	Ctdspl2	D2Ertd485e	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase like 2	protein-coding
mm_83495.1	chr9	45946558	45946565	-	1	NA	exon (NM_001289668, exon 13 of 27)	exon (NM_001289668, exon 13 of 27)	-6971	NR_106055	102465659		NR_106055	ENSMUSG00000098327	Mir7087	Gm27273|mmu-mir-7087	microRNA 7087	ncRNA
mm_93976.1	chr10	127336897	127336904	-	1	NA	intron (NM_010296, intron 6 of 12)	intron (NM_010296, intron 6 of 12)	4679	NM_010296	14632	Mm.391450	NM_010296	ENSMUSG00000025407	Gli1	AV235269|Zfp-5|Zfp5	GLI-Kruppel family member GLI1	protein-coding
mm_137685.1	chr17	28858467	28858499	+	1	NA	promoter-TSS (NM_001034885)	promoter-TSS (NM_001034885)	72	NM_001034885	433091	Mm.328925	NM_001034885	ENSMUSG00000043286	Pnpla1	-	patatin-like phospholipase domain containing 1	protein-coding
mm_122228.1	chr14	33125276	33125279	-	1	NA	intron (NM_001146022, intron 13 of 58)	intron (NM_001146022, intron 13 of 58)	59789	NM_001146022	545030	Mm.318345	NM_001146022	ENSMUSG00000051506	Wdfy4	Gm18810	WD repeat and FYVE domain containing 4	protein-coding
mm_102542.1	chr11	61267156	61267173	-	1	NA	promoter-TSS (NM_007437)	promoter-TSS (NM_007437)	22	NM_001331114	11671	Mm.398221	NM_007437	ENSMUSG00000010025	Aldh3a2	AI194803|Ahd-3|Ahd-3r|Ahd3|Ahd3-r|Aldh4|Aldh4-r|FALDH	aldehyde dehydrogenase family 3, subfamily A2	protein-coding
mm_92502.1	chr10	78352290	78352317	-	1	NA	promoter-TSS (NM_053014)	promoter-TSS (NM_053014)	-603	NM_053014	28169	Mm.141230	NM_053014	ENSMUSG00000001211	Agpat3	AW061257|AW493985|D10Jhu12e|lpaat3	1-acylglycerol-3-phosphate O-acyltransferase 3	protein-coding
mm_21106.1	chr2	153345792	153345794	-	1	NA	promoter-TSS (NM_001039939)	promoter-TSS (NM_001039939)	17	NR_040318	72326	Mm.400102	NR_040318	ENSMUSG00000073236	2500004C02Rik	-	RIKEN cDNA 2500004C02 gene	ncRNA
mm_155324.1	chrX	63315251	63315267	+	1	NA	Intergenic	Intergenic	-788248	NR_045442	75545	Mm.391270	NR_045442	ENSMUSG00000085757	1700019B21Rik	-	RIKEN cDNA 1700019B21 gene	ncRNA
mm_10563.1	chr2	18055173	18055202	+	1	NA	promoter-TSS (NM_010804)	promoter-TSS (NM_010804)	-50	NM_010804	17354	Mm.209175	NM_010804	ENSMUSG00000026743	Mllt10	Af10|B130021D15Rik|D630001B22Rik|mKIAA4140	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 10	protein-coding
mm_93328.1	chr10	99263047	99263085	-	1	NA	promoter-TSS (NM_026268)	promoter-TSS (NM_026268)	-165	NM_026268	67603	Mm.1791	NM_026268	ENSMUSG00000019960	Dusp6	1300019I03Rik|MKP-3|MKP3|PYST1	dual specificity phosphatase 6	protein-coding
mm_85964.1	chr9	112140552	112140554	-	1	NA	intron (NM_001177617, intron 10 of 14)	intron (NM_001177617, intron 10 of 14)	-21842	NR_029823	723815		NR_029823	ENSMUSG00000065441	Mir128-2	Mirn128-2|Mirn128b|mir-128-2|mir-128b	microRNA 128-2	ncRNA
mm_80497.1	chr9	78503512	78503529	+	1	NA	Intergenic	LTR72_RN|LTR|ERV1	-21796	NM_010106	13627	Mm.138471	NM_010106	ENSMUSG00000037742	Eef1a1	-	eukaryotic translation elongation factor 1 alpha 1	protein-coding
mm_58815.1	chr7	16401188	16401233	+	1	NA	promoter-TSS (NM_198631)	promoter-TSS (NM_198631)	14	NM_198631	330474	Mm.333594	NM_198631	ENSMUSG00000059273	Zc3h4	Bwq1|Gm768|Kiaa1064-hp|mKIAA1064	zinc finger CCCH-type containing 4	protein-coding
mm_42543.1	chr5	115989816	115989820	+	1	NA	intron (NM_007708, intron 38 of 46)	intron (NM_007708, intron 38 of 46)	34610	NM_031869	19079	Mm.458152	NM_031869	ENSMUSG00000029513	Prkab1	1300015D22Rik|AU021155|E430008F22	protein kinase, AMP-activated, beta 1 non-catalytic subunit	protein-coding
mm_62208.1	chr7	97843008	97843016	+	1	NA	promoter-TSS (NM_011035)	promoter-TSS (NM_011035)	73	NM_011035	18479	Mm.260227	NM_011035	ENSMUSG00000030774	Pak1	AW045634|PAK-1|Paka	p21 protein (Cdc42/Rac)-activated kinase 1	protein-coding
mm_6330.1	chr1	71624145	71624160	-	1	NA	exon (NM_001276413, exon 20 of 44)	exon (NM_001276413, exon 20 of 44)	29082	NM_010233	14268	Mm.193099	NM_010233	ENSMUSG00000026193	Fn1	E330027I09|Fn|Fn-1	fibronectin 1	protein-coding
mm_47702.1	chr5	129879026	129879034	-	1	NA	promoter-TSS (NM_011079)	promoter-TSS (NM_011079)	53	NM_011079	18682	Mm.3159	NM_011079	ENSMUSG00000025537	Phkg1	Phkg	phosphorylase kinase gamma 1	protein-coding
mm_34677.1	chr4	150944988	150945000	+	1	NA	3' UTR (NM_001077508, exon 7 of 7)	3' UTR (NM_001077508, exon 7 of 7)	16995	NM_001077509	21942	Mm.244187	NM_011612	ENSMUSG00000028965	Tnfrsf9	4-1BB|A930040I11Rik|AA408498|AI325004|CDw137|Cd137|ILA|Ly63	tumor necrosis factor receptor superfamily, member 9	protein-coding
mm_38293.1	chr4	136892851	136892854	-	1	NA	promoter-TSS (NM_007574)	promoter-TSS (NM_007574)	62	NM_007574	12262	Mm.439732	NM_007574	ENSMUSG00000036896	C1qc	AI385742|C1qg|Ciqc	complement component 1, q subcomponent, C chain	protein-coding
mm_68033.1	chr7	101301684	101301697	-	1	NA	intron (NM_001111111, intron 1 of 17)	intron (NM_001111111, intron 1 of 17)	398	NM_001111111	73683	Mm.275744	NM_001111111	ENSMUSG00000047767	Atg16l2	2410118P20Rik	autophagy related 16-like 2 (S. cerevisiae)	protein-coding
mm_116748.1	chr13	51793651	51793713	-	1	NA	promoter-TSS (NM_001281880)	promoter-TSS (NM_001281880)	65	NM_001281880	20354	Mm.33903	NM_013660	ENSMUSG00000021451	Sema4d	CD100|Semacl2|Semaj|Semcl2|coll-4	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D	protein-coding
mm_8171.1	chr1	137751593	137751619	-	1	NA	Intergenic	Intergenic	-214849	NR_029795	735252		NR_029795	ENSMUSG00000065565	Mir181a-1	Mirn181a-1|Mirn213|miR-213|mir-181a-1|mmu-mir-213	microRNA 181a-1	ncRNA
mm_139678.1	chr17	57415023	57415046	+	1	NA	intron (NM_010130, intron 10 of 21)	L1_Mur2|LINE|L1	56348	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_10380.1	chr2	12300795	12300834	+	1	NA	promoter-TSS (NR_040353)	promoter-TSS (NR_040353)	-432	NR_040353	338535	Mm.483275	NR_040353	ENSMUSG00000086843	E030013I19Rik	-	RIKEN cDNA E030013I19 gene	ncRNA
mm_56401.1	chr6	97148835	97148845	-	1	NA	promoter-TSS (NM_175313)	promoter-TSS (NM_175313)	43	NM_175313	101351	Mm.116802	NM_175313	ENSMUSG00000035245	Eogt	A130022J15Rik|AI447490|AW214473|AW259391|Aer61	EGF domain-specific O-linked N-acetylglucosamine (GlcNAc) transferase	protein-coding
mm_122756.1	chr14	54218655	54218666	-	1	NA	Intergenic	Intergenic	35269	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_33028.1	chr4	122673822	122673832	+	1	NA	Intergenic	Intergenic	-15432	NM_023865	77432	Mm.491436	NM_023865	ENSMUSG00000023263	9530002B09Rik	Aump|Vpp1|Vppl	RIKEN cDNA 9530002B09 gene	protein-coding
mm_129516.1	chr15	79062867	79062941	-	1	NA	promoter-TSS (NM_144849)	promoter-TSS (NM_144849)	-45	NM_144849	223690	Mm.24262	NM_144849	ENSMUSG00000033055	Ankrd54	C730048E16Rik|EST1068184|EST475269|Liar	ankyrin repeat domain 54	protein-coding
mm_61638.1	chr7	80294460	80294492	+	1	NA	promoter-TSS (NM_145150)	promoter-TSS (NM_145150)	25	NM_001285998	233406	Mm.227274	NM_145150	ENSMUSG00000038943	Prc1	D7Ertd348e	protein regulator of cytokinesis 1	protein-coding
mm_24742.1	chr3	95287641	95287654	+	1	NA	5' UTR (NM_133858, exon 2 of 10)	5' UTR (NM_133858, exon 2 of 10)	4712	NM_199475	75007	Mm.279287	NM_133858	ENSMUSG00000038712	Fam63a	1810005H09Rik|4930504E06Rik|AA562754|AA960384|AW561904|cI-40|mKIAA1390|ni	family with sequence similarity 63, member A	protein-coding
mm_28115.1	chr3	86799146	86799177	-	1	NA	intron (NM_001195497, intron 11 of 15)	intron (NM_001195497, intron 11 of 15)	121723	NM_001195496	70762	Mm.44490	NM_027539	ENSMUSG00000028078	Dclk2	6330415M09Rik|AU044875|CL2|CLICK2|Click-II|Dcamkl2	doublecortin-like kinase 2	protein-coding
mm_96390.1	chr11	67249826	67249833	+	1	NA	exon (NM_010855, exon 18 of 40)	exon (NM_010855, exon 18 of 40)	12017	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_158273.1	chrX	111463037	111463048	-	1	NA	exon (NM_025949, exon 3 of 25)	exon (NM_025949, exon 3 of 25)	74917	NM_025949	67071	Mm.37617	NM_025949	ENSMUSG00000025665	Rps6ka6	2610524K04Rik|RSK4|S6K-alpha-6	ribosomal protein S6 kinase polypeptide 6	protein-coding
mm_79836.1	chr9	64806092	64806100	+	1	NA	Intergenic	Intergenic	-4915	NM_001162917	102442	Mm.222473	NM_176935	ENSMUSG00000053641	Dennd4a	AI115600|AI851943|F730015K02Rik	DENN/MADD domain containing 4A	protein-coding
mm_65803.1	chr7	28962237	28962247	-	1	NA	promoter-TSS (NM_021895)	promoter-TSS (NM_021895)	38	NM_021895	60595	Mm.81144	NM_021895	ENSMUSG00000054808	Actn4	C77391	actinin alpha 4	protein-coding
mm_44910.1	chr5	35663682	35663690	-	1	NA	intron (NM_001042615, intron 6 of 6)	intron (NM_001042615, intron 6 of 6)	16094	NM_001042615	78558	Mm.274255	NM_030127	ENSMUSG00000029096	Htra3	2210021K23Rik|9530081K03Rik|Prsp|Tasp	HtrA serine peptidase 3	protein-coding
mm_38928.1	chr4	150189186	150189190	-	1	NA	exon (NM_009802, exon 7 of 8)	exon (NM_009802, exon 7 of 8)	11947	NM_009802	12353	Mm.232523	NM_009802	ENSMUSG00000028972	Car6	Ca6|DOC1	carbonic anhydrase 6	protein-coding
mm_133881.1	chr16	96499477	96499485	+	1	NA	intron (NM_008791, intron 2 of 2)	intron (NM_008791, intron 2 of 2)	31875	NM_008791	18546	Mm.5023	NM_008791	ENSMUSG00000090223	Pcp4	P16Rimb19|Pcp-4|Pep19	Purkinje cell protein 4	protein-coding
mm_26404.1	chr3	142606739	142606748	+	1	NA	exon (NM_010259, exon 7 of 11)	exon (NM_010259, exon 7 of 11)	11896	NM_010259	14468	Mm.457978	NM_010259	ENSMUSG00000040264	Gbp2b	Gbp-1|Gbp1|Mag-1|Mpa-1|Mpa1	guanylate binding protein 2b	protein-coding
mm_90481.1	chr10	127898516	127898532	+	1	NA	promoter-TSS (NM_027301)	promoter-TSS (NM_027301)	-11	NM_027301	70061	Mm.158320	NM_027301	ENSMUSG00000040127	Sdr9c7	1810054F20Rik|Rdh20|Rdhs|SDR-O|Sdro	4short chain dehydrogenase/reductase family 9C, member 7	protein-coding
mm_152688.1	chr19	16731454	16731456	-	1	NA	intron (NM_173028, intron 19 of 71)	RLTR31C_MM|LTR|ERVK	49478	NM_173028	271564	Mm.211963	NM_173028	ENSMUSG00000046230	Vps13a	4930425F11|4930516E05Rik|4930543C13Rik|9930023P20|Chac|Chorein|D330038K10Rik|mKIAA0986	vacuolar protein sorting 13A	protein-coding
mm_112643.1	chr13	16016925	16016942	+	1	NA	intron (NM_008380, intron 3 of 4)	C-rich|Low_complexity|Low_complexity	5082	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_116820.1	chr13	54589143	54589147	-	1	NA	intron (NM_178605, intron 2 of 4)	intron (NM_178605, intron 2 of 4)	929	NM_178605	28126	Mm.439993	NM_178605	ENSMUSG00000025869	Nop16	AA409471|D13Wsu177e	NOP16 nucleolar protein	protein-coding
mm_161794.1	chr17	48300059	48300059	+	1	NA	promoter-TSS (NM_001033405)	promoter-TSS (NM_001033405)	21	NM_001033405	328833	Mm.329104	NM_001033405	ENSMUSG00000071068	Treml2	AW049306|Gm750|Tlt2	triggering receptor expressed on myeloid cells-like 2	protein-coding
mm_37062.1	chr4	116053826	116053849	-	1	NA	promoter-TSS (NM_028142)	promoter-TSS (NM_028142)	39	NM_028142	72181	Mm.282560	NM_028142	ENSMUSG00000028706	Nsun4	2310010O12Rik|2810405F18Rik|AI507900|Shtap	NOL1/NOP2/Sun domain family, member 4	protein-coding
mm_169697.1	chr15	75086426	75086427	+	1	NA	Intergenic	Intergenic	25523	NM_001099217	100041546	Mm.482110	NM_001099217	ENSMUSG00000022584	Ly6c2	Ly-6C.2|Ly-6C2	lymphocyte antigen 6 complex, locus C2	protein-coding
mm_61236.1	chr7	64754110	64754120	+	1	NA	TTS (NM_001291167)	TTS (NM_001291167)	118925	NM_023239	66647	Mm.19944	NM_023239	ENSMUSG00000070520	Ndnl2	5730494G16Rik|AI642138|BB044375|HCA4|Mageg1|Nsmce3|mage-g1	necdin-like 2	protein-coding
mm_111784.1	chr12	104512658	104512659	-	1	NA	Intergenic	MIRc|SINE|MIR	-39422	NM_010351	14836	Mm.129	NM_010351	ENSMUSG00000021095	Gsc	-	goosecoid homeobox	protein-coding
mm_64598.1	chr7	3204137	3204143	-	1	NA	Intergenic	Intergenic	-14486	NR_029640	100049710		NR_029640	ENSMUSG00000077815	Mir290a	Mir290|Mirn290|mir-290a|mmu-miR-290|mmu-mir-290a	microRNA 290a	ncRNA
mm_166972.1	chr7	44668281	44668289	+	1	NA	intron (NM_001271540, intron 1 of 41)	intron (NM_001271540, intron 1 of 41)	2558	NM_001271540	71960	Mm.158289	NM_028021	ENSMUSG00000030739	Myh14	2400004E04Rik|II-C|NHMCII|NMHC II-C	myosin, heavy polypeptide 14	protein-coding
mm_88431.1	chr10	77515893	77515909	+	1	NA	promoter-TSS (NM_133998)	promoter-TSS (NM_133998)	-88	NM_133998	108707	Mm.259547	NM_133998	ENSMUSG00000032977	Fam207a	1810008A18Rik|AI303072	family with sequence similarity 207, member A	protein-coding
mm_96585.1	chr11	69089142	69089162	+	1	NA	exon (NM_009497, exon 2 of 5)	exon (NM_009497, exon 2 of 5)	624	NM_009497	22318	Mm.28643	NM_009497	ENSMUSG00000020894	Vamp2	Syb-2|Syb2|sybII	vesicle-associated membrane protein 2	protein-coding
mm_112188.1	chr12	113422653	113422661	-	1	NA	Intergenic	Intergenic	-66908	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_81559.1	chr9	110362434	110362470	+	1	NA	exon (NM_001001144, exon 3 of 23)	exon (NM_001001144, exon 3 of 23)	29096	NM_001001144	235623	Mm.288741	NM_001001144	ENSMUSG00000032485	Scap	9530044G19|mKIAA0199	SREBF chaperone	protein-coding
mm_85065.1	chr9	90828848	90828861	-	1	NA	Intergenic	Intergenic	536945	NM_009573	22771	Mm.335350	NM_009573	ENSMUSG00000032368	Zic1	ZIC|ZNF201	zinc finger protein of the cerebellum 1	protein-coding
mm_124326.1	chr14	103843139	103843155	-	1	NA	exon (NM_001136061, exon 2 of 8)	exon (NM_001136061, exon 2 of 8)	554	NM_007904	13618	Mm.229532	NM_007904	ENSMUSG00000022122	Ednrb	ET-B|ET-BR|ETR-b|ETb|Sox10m1	endothelin receptor type B	protein-coding
mm_68954.1	chr7	126564734	126564753	-	1	NA	exon (NM_146200, exon 3 of 21)	exon (NM_146200, exon 3 of 21)	1623	NM_146200	56347	Mm.22776	NM_146200	ENSMUSG00000030738	Eif3c	110kDa|3230401O13Rik|Eif3s8|NIPIL(A3)|NipilA3|Xs|Xsl	eukaryotic translation initiation factor 3, subunit C	protein-coding
mm_119872.1	chr14	54686243	54686261	+	1	NA	promoter-TSS (NM_021437)	promoter-TSS (NM_021437)	81	NM_021437	58248	Mm.197509	NM_021437	ENSMUSG00000040822	1700123O20Rik	MNCb-2990	RIKEN cDNA 1700123O20 gene	protein-coding
mm_88285.1	chr10	75173967	75173980	+	1	NA	intron (NM_001081412, intron 16 of 22)	intron (NM_001081412, intron 16 of 22)	-38100	NM_153406	74392	Mm.27716	NM_153406	ENSMUSG00000033444	Specc1l	4930470P14Rik|4932439K10Rik|9530057A13Rik|AI317249|Cytsa|mKIAA0376	sperm antigen with calponin homology and coiled-coil domains 1-like	protein-coding
mm_79983.1	chr9	66946429	66946452	+	1	NA	intron (NM_001311101, intron 1 of 4)	CpG	364	NM_026467	67941	Mm.30120	NM_026467	ENSMUSG00000036781	Rps27l	1810034D23Rik	ribosomal protein S27-like	protein-coding
mm_61932.1	chr7	90166111	90166123	+	1	NA	intron (NM_001252520, intron 4 of 20)	intron (NM_001252520, intron 4 of 20)	35885	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_168034.1	chrY	90741369	90741375	+	1	NA	Intergenic	CpG	13678	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_42638.1	chr5	118560359	118560453	+	1	NA	promoter-TSS (NM_172424)	promoter-TSS (NM_172424)	-313	NM_001347445	76199	Mm.206238	NM_172424	ENSMUSG00000018076	Med13l	2210413I17Rik|6330591G05Rik|9030618F05Rik|Thrap2|Trap240L|mKIAA1025	mediator complex subunit 13-like	protein-coding
mm_34516.1	chr4	148901302	148901311	+	1	NA	intron (NM_027195, intron 3 of 15)	CpG	96914	NM_027195	69743	Mm.233879	NM_027195	ENSMUSG00000028977	Casz1	2410019P08Rik|AV096627|BC040081|Cst|D4Ertd432e	castor zinc finger 1	protein-coding
mm_165026.1	chr19	32666359	32666371	+	1	NA	3' UTR (NM_011864, exon 13 of 13)	3' UTR (NM_011864, exon 13 of 13)	45933	NM_026487	67979	Mm.27123	NM_026487	ENSMUSG00000013662	Atad1	4921525H23Rik|AW107648|Thorase	ATPase family, AAA domain containing 1	protein-coding
mm_85361.1	chr9	103217444	103217459	-	1	NA	exon (NM_133977, exon 12 of 17)	exon (NM_133977, exon 12 of 17)	12835	NM_133977	22041	Mm.37214	NM_133977	ENSMUSG00000032554	Trf	AI266983|Cd176|HP|Tf|Tfn|hpx	transferrin	protein-coding
mm_90483.1	chr10	127898551	127898555	+	1	NA	promoter-TSS (NM_027301)	promoter-TSS (NM_027301)	18	NM_027301	70061	Mm.158320	NM_027301	ENSMUSG00000040127	Sdr9c7	1810054F20Rik|Rdh20|Rdhs|SDR-O|Sdro	4short chain dehydrogenase/reductase family 9C, member 7	protein-coding
mm_73443.1	chr8	106210961	106210974	+	1	NA	promoter-TSS (NM_001007567)	promoter-TSS (NM_001007567)	-34	NM_001007567	66432	Mm.269029	NM_001007567	ENSMUSG00000033106	Slc7a6os	2010007L18Rik|2400002F02Rik	solute carrier family 7, member 6 opposite strand	protein-coding
mm_14503.1	chr2	132212582	132212628	+	1	NA	Intergenic	Intergenic	35183	NM_027478	70612	Mm.30116	NM_027478	ENSMUSG00000027341	Tmem230	5730494N06Rik|AA407821	transmembrane protein 230	protein-coding
mm_146110.1	chr18	74240858	74240867	+	1	NA	Intergenic	MYSERV16_I-int|LTR|ERVK	24650	NM_028868	74322	Mm.17537	NM_028868	ENSMUSG00000024560	Cxxc1	2410002I16Rik|5830420C16Rik|AI426635|Cfp1|Cgbp|PHF18	CXXC finger 1 (PHD domain)	protein-coding
mm_143655.1	chr17	79707646	79707659	-	1	NA	3' UTR (NM_009994, exon 3 of 3)	3' UTR (NM_009994, exon 3 of 3)	7389	NM_009994	13078	Mm.214016	NM_009994	ENSMUSG00000024087	Cyp1b1	CP1B|P4501b1	cytochrome P450, family 1, subfamily b, polypeptide 1	protein-coding
mm_78867.1	chr9	44402487	44402494	+	1	NA	3' UTR (NM_008063, exon 8 of 8)	3' UTR (NM_008063, exon 8 of 8)	2067	NR_106053	102465658		NR_106053	ENSMUSG00000099309	Mir7085	Gm27423|mmu-mir-7085	microRNA 7085	ncRNA
mm_103693.1	chr11	79515768	79515779	-	1	NA	exon (NM_001077496, exon 2 of 2)	exon (NM_001077496, exon 2 of 2)	7989	NM_001077496	216984	Mm.439665	NM_001077496	ENSMUSG00000093938	Evi2b	Evi-2|Evi2	ecotropic viral integration site 2b	protein-coding
mm_158502.1	chrX	142390435	142390446	-	1	NA	promoter-TSS (NM_207625)	promoter-TSS (NM_207625)	95	NM_001033600	50790	Mm.391337	NM_019477	ENSMUSG00000031278	Acsl4	9430020A05Rik|ACS4|AU018108|Facl4|Lacs4	acyl-CoA synthetase long-chain family member 4	protein-coding
mm_121440.1	chr14	120430041	120430080	+	1	NA	3' UTR (NM_207515, exon 8 of 8)	3' UTR (NM_207515, exon 8 of 8)	-48401	NM_029519	76108	Mm.261448	NM_029519	ENSMUSG00000051615	Rap2a	5830461H18Rik	RAS related protein 2a	protein-coding
mm_140799.1	chr17	21650437	21650468	-	1	NA	promoter-TSS (NM_001166497)	promoter-TSS (NM_001166497)	-159	NM_001166497	73229	Mm.296733	NM_001166497	ENSMUSG00000035868	Zfp983	3110052M02Rik|mszf57|mszf71	zinc finger protein 983	protein-coding
mm_35242.1	chr4	19877354	19877395	-	1	NA	3' UTR (NM_175406, exon 8 of 8)	3' UTR (NM_175406, exon 8 of 8)	45192	NM_175406	242341	Mm.19298	NM_175406	ENSMUSG00000028238	Atp6v0d2	1620401A02Rik|AI324824|V-ATPase	ATPase, H+ transporting, lysosomal V0 subunit D2	protein-coding
mm_125843.1	chr15	74958843	74958854	+	1	NA	3' UTR (NM_001164036, exon 4 of 4)	3' UTR (NM_001164036, exon 4 of 4)	3742	NM_001164040	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_51236.1	chr6	71494075	71494085	+	1	NA	5' UTR (NM_009543, exon 1 of 4)	5' UTR (NM_009543, exon 1 of 4)	203	NM_001308303	22644	Mm.422969	NM_009543	ENSMUSG00000052656	Rnf103	AW146237|AW212918|Zfp103|kf-1	ring finger protein 103	protein-coding
mm_125765.1	chr15	74516517	74516527	+	1	NA	5' UTR (NM_174991, exon 1 of 31)	5' UTR (NM_174991, exon 1 of 31)	326	NM_174991	107831	Mm.43133	NM_174991	ENSMUSG00000034730	Adgrb1	B830018M07Rik|Bai1|R75078|mKIAA4089	adhesion G protein-coupled receptor B1	protein-coding
mm_145426.1	chr18	58659444	58659522	+	1	NA	promoter-TSS (NM_025478)	promoter-TSS (NM_025478)	1	NM_025478	66307	Mm.182574	NM_025478	ENSMUSG00000024601	Isoc1	2610034N03Rik	isochorismatase domain containing 1	protein-coding
mm_97528.1	chr11	78503499	78503503	+	1	NA	promoter-TSS (NM_008759)	promoter-TSS (NM_008759)	-12	NM_008759	18292	Mm.134360	NM_008759	ENSMUSG00000001103	Sebox	OG9|Og9x	SEBOX homeobox	protein-coding
mm_102205.1	chr11	54780072	54780076	-	1	NA	intron (NM_178626, intron 1 of 5)	intron (NM_178626, intron 1 of 5)	7629	NM_178626	72729	Mm.29476	NM_178626	ENSMUSG00000052298	Cdc42se2	2810404F18Rik|AA408783|AA536669|SPEC2	CDC42 small effector 2	protein-coding
mm_117527.1	chr13	81711285	81711299	-	1	NA	promoter-TSS (NM_028372)	promoter-TSS (NM_028372)	-125	NM_028372	72852	Mm.31095	NM_028372	ENSMUSG00000051098	Mblac2	2900024O10Rik	metallo-beta-lactamase domain containing 2	protein-coding
mm_49404.1	chr6	28427883	28427909	+	1	NA	promoter-TSS (NM_019569)	promoter-TSS (NM_019569)	-5	NM_019569	56223	Mm.31708	NM_019569	ENSMUSG00000029707	Fscn3	-	fascin actin-bundling protein 3	protein-coding
mm_120070.1	chr14	57057875	57057884	+	1	NA	promoter-TSS (NM_001271623)	promoter-TSS (NM_001271623)	151	NM_016975	14611	Mm.57207	NM_016975	ENSMUSG00000048582	Gja3	Cnx46|Cx43|Cx46|Gja-3	gap junction protein, alpha 3	protein-coding
mm_14078.1	chr2	124610279	124610285	+	1	NA	promoter-TSS (NM_199238)	promoter-TSS (NM_199238)	-14	NM_199238	214968	Mm.330536	NM_172537	ENSMUSG00000027200	Sema6d	1110067B02Rik|AA409156|D330011G23|mKIAA1479	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	protein-coding
mm_10698.1	chr2	22622643	22622653	+	1	NA	5' UTR (NM_008078, exon 1 of 16)	5' UTR (NM_008078, exon 1 of 16)	321	NM_008078	14417	Mm.4784	NM_008078	ENSMUSG00000026787	Gad2	6330404F12Rik|GAD(65)|GAD65|Gad-2	glutamic acid decarboxylase 2	protein-coding
mm_129901.1	chr15	83919393	83919399	-	1	NA	promoter-TSS (NM_001161629)	promoter-TSS (NM_001161629)	-23	NM_001161629	77627	Mm.196288	NM_029946	ENSMUSG00000022441	Efcab6	4931407K02Rik|4932408N08Rik|bM150J22.2|mKIAA1672	EF-hand calcium binding domain 6	protein-coding
mm_13313.1	chr2	102658855	102658872	+	1	NA	5' UTR (NM_001077514, exon 1 of 11)	5' UTR (NM_001077514, exon 1 of 11)	180	NM_001077514	20511	Mm.267547	NM_011393	ENSMUSG00000005089	Slc1a2	1700091C19Rik|2900019G14Rik|AI159670|Eaat2|GLT-1|GLT1|MGLT1	solute carrier family 1 (glial high affinity glutamate transporter), member 2	protein-coding
mm_122106.1	chr14	30921740	30921763	-	1	NA	exon (NM_008407, exon 4 of 21)	exon (NM_008407, exon 4 of 21)	1836	NM_008407	16426	Mm.4517	NM_008407	ENSMUSG00000006522	Itih3	AW108094|ITI-HC3|Intin3|Itih-3	inter-alpha trypsin inhibitor, heavy chain 3	protein-coding
mm_58475.1	chr7	3391099	3391115	+	1	NA	Intergenic	Intergenic	-2935	NM_133190	81905	Mm.357990	NM_133190	ENSMUSG00000053395	Cacng8	-	calcium channel, voltage-dependent, gamma subunit 8	protein-coding
mm_137542.1	chr17	27556802	27556814	+	1	NA	5' UTR (NM_016660, exon 1 of 5)	intron (NM_001025427, intron 1 of 4)	155	NM_001166477	111241	Mm.426212	NM_001166476	ENSMUSG00000078249	Hmga1-rs1	ENSMUSG00000041059|Hmgi-rs1	high mobility group AT-hook I, related sequence 1	protein-coding
mm_32710.1	chr4	116151416	116151424	+	1	NA	promoter-TSS (NM_001290658)	promoter-TSS (NM_001290658)	-11	NM_001290658	68273	Mm.196045	NM_026651	ENSMUSG00000028700	Pomgnt1	0610016I07Rik|4930467B06Rik	protein O-linked mannose beta 1,2-N-acetylglucosaminyltransferase	protein-coding
mm_86577.1	chr10	12963520	12963523	+	1	NA	intron (NM_029075, intron 1 of 2)	intron (NM_029075, intron 1 of 2)	738	NM_029075	74732	Mm.248648	NM_029075	ENSMUSG00000039232	Stx11	5830405C08Rik	syntaxin 11	protein-coding
mm_41213.1	chr5	88568471	88568474	+	1	NA	intron (NM_001289774, intron 1 of 17)	PB1D10|SINE|Alu	3432	NM_001289775	52822	Mm.270469	NM_027530	ENSMUSG00000029291	Rufy3	2810428M05Rik|6330416M07Rik|AW455998|AW538594|D5Bwg0860e|Ripx|Rpipx	RUN and FYVE domain containing 3	protein-coding
mm_103840.1	chr11	83040472	83040480	-	1	NA	promoter-TSS (NR_073524)	promoter-TSS (NR_073524)	57	NR_073524	237887	Mm.341645	NM_181542	ENSMUSG00000072621	Slfn10-ps	Slfn10|mFLJ00257	schlafen 10, pseudogene	pseudo
mm_1949.1	chr1	86350810	86350845	+	1	NA	TTS (NR_028478)	TTS (NR_028478)	458	NR_028478	100303740	Mm.154378	NR_028478	ENSMUSG00000064837	Snora75	MBI-55	small nucleolar RNA, H/ACA box 75	snoRNA
mm_48575.1	chr5	143375702	143375737	-	1	NA	exon (NM_001159321, exon 7 of 22)	exon (NM_001159321, exon 7 of 22)	5627	NM_001347529	170935	Mm.197460	NM_133355	ENSMUSG00000010825	Grid2ip	-	glutamate receptor, ionotropic, delta 2 (Grid2) interacting protein 1	protein-coding
mm_147122.1	chr18	35740500	35740542	-	1	NA	promoter-TSS (NM_001289592)	promoter-TSS (NM_001289592)	33	NM_001289592	72512	Mm.45995	NM_028261	ENSMUSG00000024349	Tmem173	2610307O08Rik|ERIS|MPYS|Mita|STING	transmembrane protein 173	protein-coding
mm_104151.1	chr11	87086753	87086781	-	1	NA	promoter-TSS (NM_024262)	promoter-TSS (NM_024262)	10	NM_024262	74133	Mm.23257	NM_024262	ENSMUSG00000020495	Smg8	1200011M11Rik	smg-8 homolog, nonsense mediated mRNA decay factor (C. elegans)	protein-coding
mm_163395.1	chr12	67059251	67059297	+	1	NA	intron (NM_001193266, intron 1 of 16)	GSAT_MM|Satellite|Satellite	163275	NM_001193266	320772	Mm.227680	NM_207010	ENSMUSG00000034912	Mdga2	6720489L24Rik|9330209L04Rik|Adp|Mamdc1	MAM domain containing glycosylphosphatidylinositol anchor 2	protein-coding
mm_7446.1	chr1	120121031	120121041	-	1	NA	promoter-TSS (NM_001172074)	promoter-TSS (NM_001172074)	60	NM_007830	13167	Mm.2785	NM_007830	ENSMUSG00000026385	Dbi	ACBD1|Acbp|EP|endozepine	diazepam binding inhibitor	protein-coding
mm_142823.1	chr17	51759548	51759549	-	1	NA	intron (NM_009122, intron 9 of 10)	intron (NM_009122, intron 9 of 10)	52506	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_142040.1	chr17	35267001	35267088	-	1	NA	TTS (NM_001267808)	TTS (NM_001267808)	3921	NM_001267808	14980	Mm.439675	NM_001267808		H2-L	H-2L	histocompatibility 2, D region locus L	protein-coding
mm_71433.1	chr8	46505639	46505719	+	1	NA	exon (NM_007981, exon 3 of 21)	exon (NM_007981, exon 3 of 21)	14713	NM_001302163	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_1918.1	chr1	86026204	86026213	+	1	NA	intron (NM_027300, intron 2 of 3)	intron (NM_027300, intron 2 of 3)	4266	NM_027029	70060	Mm.196313	NM_027029	ENSMUSG00000026226	Spata3	1700011N12Rik|1700029H01Rik|4930424D10Rik|Mtsarg1|Tsarg1	spermatogenesis associated 3	protein-coding
mm_30471.1	chr3	154594266	154594277	-	1	NA	intron (NM_001168358, intron 2 of 4)	intron (NM_001168358, intron 2 of 4)	-2440	NM_009968	12972	Mm.374855	NM_009968	ENSMUSG00000028199	Cryz	Sez9	crystallin, zeta	protein-coding
mm_153391.1	chr19	40382891	40382893	-	1	NA	intron (NM_001034963, intron 4 of 22)	intron (NM_001034963, intron 4 of 22)	19418	NM_001034964	20411	Mm.210815	NM_009166	ENSMUSG00000025006	Sorbs1	2310065E01Rik|9530001P15Rik|CAP|SH3P12|Sh3d5|mKIAA1296	sorbin and SH3 domain containing 1	protein-coding
mm_59326.1	chr7	25316918	25316968	+	1	NA	promoter-TSS (NM_001160400)	promoter-TSS (NM_001160400)	-221	NM_001160400	269878	Mm.38527	NM_001160400	ENSMUSG00000045039	Megf8	AW049492|Egfl4|b2b1702.2Clo|b2b1702Clo|b2b288Clo|m687Ddg|mKIAA0817	multiple EGF-like-domains 8	protein-coding
mm_33978.1	chr4	137681664	137681719	+	1	NA	promoter-TSS (NM_001081155)	promoter-TSS (NM_001081155)	64	NM_001256218	110351	Mm.180763	NM_029563	ENSMUSG00000041351	Rap1gap	1300019I11Rik|2310004O14Rik|AI427470|ARPP-90|Gap|Rap1GAP1|Rap1ga1	Rap1 GTPase-activating protein	protein-coding
mm_59553.1	chr7	28075205	28075215	+	1	NA	exon (NM_001122603, exon 3 of 20)	exon (NM_001122603, exon 3 of 20)	3974	NM_001122603	215384	Mm.292276	NM_175444	ENSMUSG00000047730	Fcgbp	A430096B05Rik	Fc fragment of IgG binding protein	protein-coding
mm_136695.1	chr17	7138464	7138483	+	1	NA	Intergenic	Intergenic	-31642	NM_011299	20112	Mm.268383	NM_011299	ENSMUSG00000023809	Rps6ka2	90kDa|D17Wsu134e|Rps6ka-rs1|Rsk3|p90rsk|pp90rsk	ribosomal protein S6 kinase, polypeptide 2	protein-coding
mm_150796.1	chr19	44303469	44303477	+	1	NA	TTS (NR_039574)	TTS (NR_039574)	302	NR_039574	100628619		NR_039574	ENSMUSG00000093315	Mir5114	mmu-mir-5114|mu-mir-5114	microRNA 5114	ncRNA
mm_107815.1	chr12	65225514	65225544	+	1	NA	promoter-TSS (NM_027614)	promoter-TSS (NM_027614)	12	NM_027614	70948	Mm.219475	NM_027614	ENSMUSG00000035560	Wdr20rt	4921538B03Rik|4930427E19Rik|Wdr20|Wdr20b	WD repeat domain 20, retrogene	protein-coding
mm_167906.1	chrX	78186775	78186780	+	1	NA	promoter-TSS (NM_001310328)	promoter-TSS (NM_001310328)	-31	NM_001310328	628991		NM_001310328	ENSMUSG00000067679	Obp1b	EG628991|OBP-1b|OBP7	odorant binding protein IB	protein-coding
mm_158625.1	chrX	152910147	152910156	-	1	NA	Intergenic	Lx3B|LINE|L1	-96318	NM_001137547	635253	Mm.426169	NM_001137547	ENSMUSG00000067215	Usp51	AV136873	ubiquitin specific protease 51	protein-coding
mm_167690.1	chr9	86798915	86798933	-	1	NA	intron (NR_102729, intron 15 of 30)	intron (NR_102729, intron 15 of 30)	55291	NM_178738	244954	Mm.257629	NM_178738	ENSMUSG00000033491	Prss35	6030424L22Rik|P3D9	protease, serine 35	protein-coding
mm_155220.1	chrX	57053550	57053597	+	1	NA	promoter-TSS (NM_029371)	promoter-TSS (NM_029371)	3	NM_028242	72459	Mm.2152	NM_028242	ENSMUSG00000067873	Htatsf1	1600023H17Rik|2600017A12Rik|2700077B20Rik|TAT-SF1	HIV TAT specific factor 1	protein-coding
mm_84942.1	chr9	82975408	82975466	-	1	NA	promoter-TSS (NM_001081216)	promoter-TSS (NM_001081216)	52	NM_001081216	83946	Mm.221688	NM_031879	ENSMUSG00000032253	Phip	2810004D21Rik|4632404O06Rik|Ndrp|Wdr11	pleckstrin homology domain interacting protein	protein-coding
mm_53252.1	chr6	127796418	127796436	+	1	NA	Intergenic	Intergenic	-8284	NR_106092	102466996		NR_106092	ENSMUSG00000104804	Mir7233	mmu-mir-7233	microRNA 7233	ncRNA
mm_34177.1	chr4	140699936	140699955	+	1	NA	Intergenic	Intergenic	-1528	NM_173867	108911	Mm.253	NM_173867	ENSMUSG00000040945	Rcc2	2610510H01Rik|2610529N02Rik|AA536646|AA675016|Td60|mKIAA1470	regulator of chromosome condensation 2	protein-coding
mm_74185.1	chr8	123631215	123631218	+	1	NA	Intergenic	Intergenic	-22713	NM_133955	69581	Mm.168257	NM_133955	ENSMUSG00000039960	Rhou	2310026M05Rik|AI182090|Arhu|CDC42L1|G28K|WRCH-1|WRCH1|mG28K	ras homolog family member U	protein-coding
mm_11686.1	chr2	35622011	35622063	+	1	NA	promoter-TSS (NM_001114124)	promoter-TSS (NM_001114124)	56	NM_001114124	69601	Mm.29629	NM_001001602	ENSMUSG00000026883	Dab2ip	2310011D08Rik|AI480459|Aip1|mKIAA1743	disabled 2 interacting protein	protein-coding
mm_5044.1	chr1	194619888	194619914	+	1	NA	promoter-TSS (NM_008882)	promoter-TSS (NM_008882)	72	NM_008882	18845	Mm.2251	NM_008882	ENSMUSG00000026640	Plxna2	2810428A13Rik|AA589422|AW457381|OCT|PlexA2|Plxn2|mKIAA0463	plexin A2	protein-coding
mm_129244.1	chr15	76659659	76659681	-	1	NA	promoter-TSS (NM_001276335)	promoter-TSS (NM_001276335)	66	NM_001276333	54151	Mm.247752	NM_019396	ENSMUSG00000053929	Cyhr1	1110031M01Rik|AU042374|Chrp	cysteine and histidine rich 1	protein-coding
mm_81797.1	chr9	115216505	115216531	+	1	NA	intron (NM_148958, intron 5 of 9)	intron (NM_148958, intron 5 of 9)	65552	NR_029430	111186	Mm.484753	NR_029430		Stmn1-rs1	Lag-rs1|Lap18-rs1	stathmin 1, related sequence 1	pseudo
mm_38093.1	chr4	134238373	134238398	-	1	NA	promoter-TSS (NM_001081047)	promoter-TSS (NM_001081047)	14	NM_001081047	194231	Mm.331958	NM_001081047	ENSMUSG00000028841	Cnksr1	BC037758	connector enhancer of kinase suppressor of Ras 1	protein-coding
mm_98232.1	chr11	88068541	88068571	+	1	NA	intron (NM_016686, intron 1 of 5)	CpG	277	NM_016686	22344	Mm.46628	NM_016686	ENSMUSG00000018377	Vezf1	AI848691|AW046909|db1	vascular endothelial zinc finger 1	protein-coding
mm_137990.1	chr17	33629556	33629607	+	1	NA	intron (NM_026712, intron 1 of 5)	intron (NM_026712, intron 1 of 5)	489	NM_026712	328801	Mm.181488	NM_026712	ENSMUSG00000073423	Zfp414	0610030H11Rik|Znf414	zinc finger protein 414	protein-coding
mm_12266.1	chr2	68963264	68963274	+	1	NA	intron (NM_172856, intron 3 of 9)	intron (NM_172856, intron 3 of 9)	101828	NM_001347161	241447	Mm.222222	NM_172856	ENSMUSG00000027035	Cers6	4732462C07Rik|AW544719|Lass6|T1L	ceramide synthase 6	protein-coding
mm_146467.1	chr18	87292934	87292935	+	1	NA	Intergenic	RLTR9A3B|LTR|ERVK	580869	NM_172633	12405	Mm.70775	NM_172633	ENSMUSG00000024647	Cbln2	6330593N19Rik|A730004O05	cerebellin 2 precursor protein	protein-coding
mm_44166.1	chr5	150756835	150756846	+	1	NA	intron (NM_001346503, intron 15 of 34)	intron (NM_001346503, intron 15 of 34)	83013	NM_001346503	100710	Mm.32959	NM_175310	ENSMUSG00000034021	Pds5b	AI646570|AS3|AW212954|Aprin|Tg(Wap-ERBB2)229Wzw|WAP-Her-2|mKIAA0979	PDS5 cohesin associated factor B	protein-coding
mm_115549.1	chr13	8871668	8871680	-	1	NA	promoter-TSS (NM_172445)	promoter-TSS (NM_172445)	62	NM_001039388	207615	Mm.284654	NM_172445	ENSMUSG00000021147	Wdr37	-	WD repeat domain 37	protein-coding
mm_51131.1	chr6	68437877	68437892	+	1	NA	Intergenic	Intergenic	-872185	NR_003100	75070	Mm.463364	NR_003100		4930515G16Rik	-	myc induced nuclear antigen pseudogene	pseudo
mm_40761.1	chr5	66968560	66968575	+	1	NA	5' UTR (NM_001256122, exon 1 of 21)	5' UTR (NM_001256122, exon 1 of 21)	151	NM_001256122	77569	Mm.374778	NM_001001980	ENSMUSG00000037736	Limch1	3732412D22Rik|mKIAA1102	LIM and calponin homology domains 1	protein-coding
mm_147792.1	chr18	61652358	61652373	-	1	NA	non-coding (NR_045402, exon 3 of 5)	non-coding (NR_045402, exon 3 of 5)	-3107	NR_029601	387161		NR_029601	ENSMUSG00000065445	Mir143	Mirn143|mir-143|mmu-mir-143	microRNA 143	ncRNA
mm_128303.1	chr15	37680494	37680502	-	1	NA	intron (NM_134094, intron 1 of 6)	intron (NM_134094, intron 1 of 6)	111502	NM_001170866	52589	Mm.283370	NM_134094	ENSMUSG00000051359	Ncald	AI848120|D030020D09Rik|D15Ertd412e	neurocalcin delta	protein-coding
mm_22244.1	chr2	174614044	174614060	-	1	NA	Intergenic	Intergenic	-29482	NM_001099328	100043757	Mm.48711	NM_001099328	ENSMUSG00000050600	Zfp831	ENSMUSG00000050600|OTTMUSG00000017459	zinc finger protein 831	protein-coding
mm_68240.1	chr7	105396232	105396242	-	1	NA	intron (NM_001242363, intron 1 of 12)	intron (NM_001242363, intron 1 of 12)	3817	NM_001242364	74349	Mm.30254	NM_199009	ENSMUSG00000044465	Fam160a2	4632419K20Rik|6530415H11Rik|FHIP	family with sequence similarity 160, member A2	protein-coding
mm_108106.1	chr12	75308340	75308358	+	1	NA	promoter-TSS (NM_023275)	promoter-TSS (NM_023275)	36	NM_023275	80837	Mm.27467	NM_023275	ENSMUSG00000046768	Rhoj	1110005O19Rik|AW210585|Arhj|TC10L|TCL	ras homolog family member J	protein-coding
mm_3026.1	chr1	133664421	133664442	+	1	NA	Intergenic	Intergenic	-3032	NM_144530	70579	Mm.245357	NM_144530	ENSMUSG00000102976	Zc3h11a	1110003F06Rik|5730454B08Rik|G630041M05Rik|Zc3hdc11a|Zc3hh11a|mKIAA0663	zinc finger CCCH type containing 11A	protein-coding
mm_160987.1	chr11	104468853	104468853	-	1	NA	Intergenic	CpG	-26562	NM_001081045	76719	Mm.136418	NM_001081045	ENSMUSG00000018412	Kansl1	1700081L11Rik|9430041J06Rik|mKIAA1267	KAT8 regulatory NSL complex subunit 1	protein-coding
mm_18478.1	chr2	62480491	62480499	-	1	NA	exon (NM_008100, exon 2 of 6)	exon (NM_008100, exon 2 of 6)	3158	NM_008100	14526	Mm.45494	NM_008100	ENSMUSG00000000394	Gcg	GLP-1|Glu|PPG	glucagon	protein-coding
mm_96471.1	chr11	67652549	67652563	+	1	NA	intron (NM_001109657, intron 4 of 13)	intron (NM_001109657, intron 4 of 13)	-42770	NM_009038	19674	Mm.439726	NM_009038	ENSMUSG00000020907	Rcvrn	CAR|S-modulin	recoverin	protein-coding
mm_54888.1	chr6	43678978	43678978	-	1	NA	Intergenic	Intergenic	-12700	NM_013861	29807	Mm.320979	NM_013861	ENSMUSG00000029735	Tpk1	-	thiamine pyrophosphokinase	protein-coding
mm_92974.1	chr10	86498837	86498858	-	1	NA	promoter-TSS (NM_013722)	promoter-TSS (NM_013722)	49	NM_001164495	27204	Mm.394931	NM_013722	ENSMUSG00000059602	Syn3	-	synapsin III	protein-coding
mm_23809.1	chr3	79886041	79886064	+	1	NA	5' UTR (NM_133187, exon 1 of 4)	5' UTR (NM_133187, exon 1 of 4)	122	NM_133187	68659	Mm.427274	NM_133187	ENSMUSG00000027955	Fam198b	1110032E23Rik|2210419I08Rik|AV011458|Ened	family with sequence similarity 198, member B	protein-coding
mm_101891.1	chr11	49017355	49017381	-	1	NA	Intergenic	L1_Mus1|LINE|L1	-25122	NM_011579	21822	Mm.15793	NM_011579	ENSMUSG00000078922	Tgtp1	Gtp2|Irgb6|Mg21|Tgtp	T cell specific GTPase 1	protein-coding
mm_122631.1	chr14	51145831	51145851	-	1	NA	exon (NM_011271, exon 2 of 2)	exon (NM_011271, exon 2 of 2)	926	NM_011271	19752	Mm.235538	NM_011271	ENSMUSG00000035896	Rnase1	AI574248|Rib-1|Rib1	ribonuclease, RNase A family, 1 (pancreatic)	protein-coding
mm_161917.1	chr18	67552732	67552732	-	1	NA	promoter-TSS (NM_194355)	promoter-TSS (NM_194355)	-11	NM_194355	68166	Mm.208723	NM_176832	ENSMUSG00000024533	Spire1	6030430B19Rik|AI415299|AU022898|AW550622|Spir-1	spire homolog 1 (Drosophila)	protein-coding
mm_145858.1	chr18	65455981	65455991	+	1	NA	intron (NM_172833, intron 8 of 15)	intron (NM_172833, intron 8 of 15)	24989	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_82332.1	chr9	9238990	9239001	-	1	NA	promoter-TSS (NM_027823)	promoter-TSS (NM_027823)	18	NM_027823	71544	Mm.334955	NM_027823	ENSMUSG00000050730	Arhgap42	9030420J04Rik|BE136619	Rho GTPase activating protein 42	protein-coding
mm_168908.1	chr12	55199533	55199537	+	1	NA	promoter-TSS (NM_028527).2	promoter-TSS (NM_028527).2	-57	NM_001100116	100101807	Mm.439875	NM_001100116	ENSMUSG00000094103	1700047I17Rik2	-	RIKEN cDNA 1700047I17 gene 2	protein-coding
mm_147654.1	chr18	60525977	60525986	-	1	NA	promoter-TSS (NM_026302)	promoter-TSS (NM_026302)	-240	NM_026302	67665	Mm.272801	NM_026302	ENSMUSG00000024603	Dctn4	1110001K06Rik|4930547K17Rik|C130039E17Rik|p62	dynactin 4	protein-coding
mm_121052.1	chr14	84536542	84536560	+	1	NA	3' UTR (NM_001013753, exon 4 of 4)	3' UTR (NM_001013753, exon 4 of 4)	-60127	NR_015539	319903	Mm.440481	NR_015539		9630013A20Rik	-	RIKEN cDNA 9630013A20 gene	ncRNA
mm_109869.1	chr12	4910490	4910495	-	1	NA	Intergenic	MERV1_LTR|LTR|ERV1	-2972	NM_145441	217379	Mm.259170	NM_145441	ENSMUSG00000020634	Ubxn2a	6330407P03Rik|Ubxd4	UBX domain protein 2A	protein-coding
mm_107187.1	chr12	25096453	25096487	+	1	NA	promoter-TSS (NM_010496)	promoter-TSS (NM_010496)	-378	NM_010496	15902	Mm.34871	NM_010496	ENSMUSG00000020644	Id2	AI255428|C78922|Idb2|bHLHb26	inhibitor of DNA binding 2	protein-coding
mm_51151.1	chr6	70698433	70698450	+	1	NA	Intergenic	Intergenic	93734	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_28322.1	chr3	89338006	89338066	-	1	NA	promoter-TSS (NM_007910)	promoter-TSS (NM_007910)	-8	NM_007910	13639	Mm.16332	NM_007910	ENSMUSG00000028040	Efna4	EFL-4|Epl4|LERK-4	ephrin A4	protein-coding
mm_144010.1	chr17	88388556	88388574	-	1	NA	Intergenic	Intergenic	-52147	NM_180974	14236	Mm.112824	NM_180974	ENSMUSG00000034998	Foxn2	3230402J05Rik|6030465J18Rik|Fkh19|Foxn1|HTLF	forkhead box N2	protein-coding
mm_105150.1	chr11	101462710	101462732	-	1	NA	intron (NM_012037, intron 2 of 5)	intron (NM_012037, intron 2 of 5)	3478	NM_012037	26949	Mm.29210	NM_012037	ENSMUSG00000034993	Vat1	VAT-1	vesicle amine transport 1	protein-coding
mm_78888.1	chr9	44604073	44604087	+	1	NA	promoter-TSS (NM_001110826)	promoter-TSS (NM_001110826)	-812	NM_001110826	13209	Mm.267061	NM_007841	ENSMUSG00000032097	Ddx6	1110001P04Rik|E230023J21Rik|HLR2|mRCK/P54|p54|rck	DEAD (Asp-Glu-Ala-Asp) box polypeptide 6	protein-coding
mm_104208.1	chr11	88118880	88118909	-	1	NA	intron (NM_198013, intron 1 of 10)	intron (NM_198013, intron 1 of 10)	19748	NM_198013	103841	Mm.374846	NM_198013	ENSMUSG00000018378	Cuedc1	AI841487|C330016O16Rik	CUE domain containing 1	protein-coding
mm_103588.1	chr11	78232065	78232079	-	1	NA	exon (NM_009297, exon 5 of 37)	exon (NM_009297, exon 5 of 37)	13631	NM_009297	20926	Mm.20755	NM_009297	ENSMUSG00000002052	Supt6	5131400N11Rik|AI132449|SPT6|Supt6h|mKIAA0162	suppressor of Ty 6	protein-coding
mm_142880.1	chr17	51826579	51826601	-	1	NA	promoter-TSS (NM_001163631)	promoter-TSS (NM_001163631)	-2	NM_001163631	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_65095.1	chr7	19271605	19271617	-	1	NA	non-coding (NR_104069, exon 1 of 11)	non-coding (NR_104069, exon 1 of 11)	243	NM_001282021	22323	Mm.9684	NM_009499	ENSMUSG00000030403	Vasp	-	vasodilator-stimulated phosphoprotein	protein-coding
mm_45376.1	chr5	66054500	66054561	-	1	NA	intron (NM_178446, intron 2 of 6)	intron (NM_178446, intron 2 of 6)	43649	NM_139065	245945	Mm.36863	NM_139065	ENSMUSG00000070780	Rbm47	9530077J19Rik	RNA binding motif protein 47	protein-coding
mm_171742.1	chr4	9669114	9669115	-	1	NA	promoter-TSS (NM_001177850)	promoter-TSS (NM_001177850)	48	NM_023066	65973	Mm.222206	NM_023066	ENSMUSG00000028207	Asph	2310005F16Rik|3110001L23Rik|AI848629|AW261690|AW561901|BAH|C79816|cI-37	aspartate-beta-hydroxylase	protein-coding
mm_94656.1	chr11	17052145	17052151	+	1	NA	5' UTR (NM_029861, exon 1 of 3)	5' UTR (NM_029861, exon 1 of 3)	214	NM_029861	380686	Mm.425666	NM_029861	ENSMUSG00000044629	Cnrip1	1500041B16Rik|3110054C06Rik|5330437A18Rik|AI854501|C2orf32	cannabinoid receptor interacting protein 1	protein-coding
mm_92988.1	chr10	86701827	86701862	-	1	NA	exon (NM_011631, exon 5 of 18)	exon (NM_011631, exon 5 of 18)	3600	NM_011631	22027	Mm.87773	NM_011631	ENSMUSG00000020048	Hsp90b1	ERp99|GRP94|TA-3|Targ2|Tra-1|Tra1|endoplasmin|gp96	heat shock protein 90, beta (Grp94), member 1	protein-coding
mm_105796.1	chr11	110079121	110079137	-	1	NA	exon (NM_153145, exon 7 of 39)	exon (NM_153145, exon 7 of 39)	16808	NM_153145	217258	Mm.344148	NM_153145	ENSMUSG00000041828	Abca8a	-	ATP-binding cassette, sub-family A (ABC1), member 8a	protein-coding
mm_123596.1	chr14	67715565	67715577	-	1	NA	promoter-TSS (NM_001111028)	promoter-TSS (NM_001111028)	39	NM_001110162	108912	Mm.33831	NM_175384	ENSMUSG00000048922	Cdca2	2610311M19Rik|AI586158	cell division cycle associated 2	protein-coding
mm_152579.1	chr19	11602212	11602222	-	1	NA	intron (NM_026835, intron 2 of 6)	intron (NM_026835, intron 2 of 6)	2587	NM_026835	68774	Mm.290390	NM_026835	ENSMUSG00000024679	Ms4a6d	1110058E16Rik|AI447446|Ms4a11	membrane-spanning 4-domains, subfamily A, member 6D	protein-coding
mm_90321.1	chr10	127066155	127066182	+	1	NA	exon (NM_009870, exon 7 of 8)	exon (NM_009870, exon 7 of 8)	2565	NM_009870	12567	Mm.6839	NM_009870	ENSMUSG00000006728	Cdk4	Crk3	cyclin-dependent kinase 4	protein-coding
mm_130352.1	chr15	97750766	97750774	-	1	NA	intron (NM_144850, intron 19 of 27)	intron (NM_144850, intron 19 of 27)	16896	NM_001177810	223864	Mm.24028	NM_144850	ENSMUSG00000022469	Rapgef3	2310016P22Rik|9330170P05Rik|Epac|Epac1	Rap guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_65383.1	chr7	25091195	25091232	-	1	NA	TTS (NM_001163556)	TTS (NM_001163556)	5962	NR_105855	102465968		NR_105855	ENSMUSG00000098441	Mir6537	Gm27808|mmu-mir-6537	microRNA 6537	ncRNA
mm_80499.1	chr9	78520677	78520705	+	1	NA	Intergenic	RLTR51A_Mm|LTR|ERVK?	-38967	NM_010106	13627	Mm.138471	NM_010106	ENSMUSG00000037742	Eef1a1	-	eukaryotic translation elongation factor 1 alpha 1	protein-coding
mm_142730.1	chr17	48324369	48324386	-	1	NA	3' UTR (NM_177083, exon 6 of 6)	3' UTR (NM_177083, exon 6 of 6)	8215	NM_177083	320148	Mm.123455	NM_177083	ENSMUSG00000043740	B430306N03Rik	Treml6	RIKEN cDNA B430306N03 gene	protein-coding
mm_108429.1	chr12	82245686	82245701	+	1	NA	intron (NM_001167983, intron 2 of 23)	L1M4c|LINE|L1	-65656	NM_172579	217692	Mm.261333	NM_172579	ENSMUSG00000042700	Sipa1l1	4931426N11Rik|AW213287|Spar|mKIAA0440	signal-induced proliferation-associated 1 like 1	protein-coding
mm_133690.1	chr16	92519054	92519077	+	1	NA	intron (NM_172469, intron 1 of 5)	intron (NM_172469, intron 1 of 5)	20918	NM_172469	209195	Mm.44747	NM_172469	ENSMUSG00000022949	Clic6	5730466J16Rik|AL022908|AW045520|CLIC1L	chloride intracellular channel 6	protein-coding
mm_101435.1	chr11	30100409	30100499	-	1	NA	3' UTR (NM_175836, exon 35 of 35)	3' UTR (NM_175836, exon 35 of 35)	-74421	NM_146016	237711	Mm.445271	NM_146016	ENSMUSG00000044072	Eml6	2900083P10Rik|C230094A16Rik|EMAP-6	echinoderm microtubule associated protein like 6	protein-coding
mm_113811.1	chr13	46609793	46609801	+	1	NA	intron (NM_026056, intron 5 of 12)	intron (NM_026056, intron 5 of 12)	-59725	NM_001033192	97863	Mm.275934	NM_001033192	ENSMUSG00000069237	Fam8a1	C78339	family with sequence similarity 8, member A1	protein-coding
mm_88538.1	chr10	78465165	78465190	+	1	NA	promoter-TSS (NM_172134)	promoter-TSS (NM_172134)	-229	NM_172134	216134	Mm.206159	NM_172134	ENSMUSG00000032788	Pdxk	2310036D04Rik|AA119688|C77999	pyridoxal (pyridoxine, vitamin B6) kinase	protein-coding
mm_119557.1	chr14	48670148	48670153	+	1	NA	intron (NR_029384, intron 1 of 4)	intron (NR_029384, intron 1 of 4)	862	NR_029384	606497	Mm.165199	NR_029384	ENSMUSG00000098682	Otx2os1	-	orthodenticle homeobox 2 opposite strand 1	ncRNA
mm_83995.1	chr9	57447707	57447738	-	1	NA	intron (NM_001301634, intron 3 of 6)	intron (NM_001301634, intron 3 of 6)	-7608	NM_176831	66812	Mm.250508	NM_176831	ENSMUSG00000063849	Ppcdc	1810057I13Rik|8430432M10Rik	phosphopantothenoylcysteine decarboxylase	protein-coding
mm_108452.1	chr12	82616578	82616581	+	1	NA	promoter-TSS (NM_001282061)	promoter-TSS (NM_001282061)	-346	NM_001310478	50779	Mm.126176	NM_015812	ENSMUSG00000021219	Rgs6	-	regulator of G-protein signaling 6	protein-coding
mm_115325.1	chr13	112463600	112463638	+	1	NA	promoter-TSS (NM_010560)	promoter-TSS (NM_010560)	-451	NM_010560	16195	Mm.4364	NM_010560	ENSMUSG00000021756	Il6st	5133400A03Rik|AA389424|BB405851|CD130|D13Ertd699e|gp130	interleukin 6 signal transducer	protein-coding
mm_92554.1	chr10	79766873	79766950	-	1	NA	promoter-TSS (NM_144528)	promoter-TSS (NM_144528)	41	NM_144528	70294	Mm.466670	NM_144528	ENSMUSG00000035890	Rnf126	2610010O19Rik	ring finger protein 126	protein-coding
mm_157381.1	chrX	37901384	37901410	-	1	NA	exon (NM_023894, exon 2 of 4)	exon (NM_023894, exon 2 of 4)	373	NM_023894	104384	Mm.156958	NM_023894	ENSMUSG00000068048	Rhox9	1600026O01Rik|Gpbox|Psx2	reproductive homeobox 9	protein-coding
mm_137030.1	chr17	17887841	17887865	+	1	NA	promoter-TSS (NM_008039)	promoter-TSS (NM_008039)	29	NM_008039	14289	Mm.378918	NM_008039	ENSMUSG00000052270	Fpr2	E330010I07Rik|Fpr-rs2	formyl peptide receptor 2	protein-coding
mm_7727.1	chr1	130716935	130716975	-	1	NA	promoter-TSS (NM_178691)	promoter-TSS (NM_178691)	-372	NM_178691	226418	Mm.106553	NM_178691	ENSMUSG00000046404	Yod1	6330564D18Rik|9930028C20Rik|Hshin7	YOD1 deubiquitinase	protein-coding
mm_4102.1	chr1	167562829	167562837	+	1	NA	Intergenic	Intergenic	-35529	NM_009107	20183	Mm.3475	NM_009107	ENSMUSG00000015843	Rxrg	Nr2b3	retinoid X receptor gamma	protein-coding
mm_155746.1	chrX	96166941	96166955	+	1	NA	3' UTR (NM_010833, exon 13 of 13)	3' UTR (NM_010833, exon 13 of 13)	70903	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_128780.1	chr15	66801578	66801599	-	1	NA	intron (NM_001029841, intron 1 of 7)	intron (NM_001029841, intron 1 of 7)	30241	NM_001029841	20491	Mm.7601	NM_009192	ENSMUSG00000022372	Sla	Slap|Slap-1	src-like adaptor	protein-coding
mm_114010.1	chr13	52607216	52607233	+	1	NA	intron (NM_011518, intron 1 of 13)	RLTR17D_Mm|LTR|ERVK	10342	NM_011518	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_37713.1	chr4	129491131	129491131	-	1	NA	promoter-TSS (NM_080442)	promoter-TSS (NM_080442)	-59	NM_001085491	68233	Mm.424983	NM_001085491	ENSMUSG00000078554	Fam229a	1700125D06Rik	family with sequence similarity 229, member A	protein-coding
mm_22984.1	chr3	33011956	33011959	+	1	NA	intron (NM_001310460, intron 5 of 15)	intron (NM_001310460, intron 5 of 15)	-12820	NR_040595	73874	Mm.444676	NR_040595	ENSMUSG00000087625	4930419G24Rik	-	RIKEN cDNA 4930419G24 gene	ncRNA
mm_121822.1	chr14	20471534	20471563	-	1	NA	exon (NM_001110794, exon 3 of 13)	exon (NM_001110794, exon 3 of 13)	8585	NM_001110794	11750	Mm.280231	NM_009674	ENSMUSG00000021814	Anxa7	AI265384|AI316497|Anx7|synexin	annexin A7	protein-coding
mm_104831.1	chr11	99141698	99141717	-	1	NA	Intergenic	Intergenic	13370	NM_001301713	12775	Mm.2932	NM_007719	ENSMUSG00000037944	Ccr7	CC-CKR-7|CCR-7|CD197|Cdw197|Cmkbr7|EBI1|Ebi1h	chemokine (C-C motif) receptor 7	protein-coding
mm_55902.1	chr6	83656083	83656125	-	1	NA	promoter-TSS (NM_016751)	promoter-TSS (NM_016751)	12	NM_016751	51811	Mm.3115	NM_016751	ENSMUSG00000014542	Clec4f	Clecsf13|D18063|KUCR_MOUSE|Kclr	C-type lectin domain family 4, member f	protein-coding
mm_156937.1	chrX	169916069	169916082	+	1	NA	intron (NM_001290506, intron 1 of 9)	intron (NM_001290506, intron 1 of 9)	36456	NM_001290505	17318	Mm.34441	NM_010797	ENSMUSG00000035299	Mid1	61B3-R|DXHXS1141|Fxy|Trim18	midline 1	protein-coding
mm_109910.1	chr12	8480069	8480071	-	1	NA	Intergenic	Intergenic	19915	NM_007483	11852	Mm.687	NM_007483	ENSMUSG00000054364	Rhob	AA017882|Arh6|Arhb	ras homolog family member B	protein-coding
mm_11795.1	chr2	43555322	43555338	+	1	NA	promoter-TSS (NM_001289593)	promoter-TSS (NM_001289593)	5	NM_027552	70789	Mm.105278	NM_027552	ENSMUSG00000026866	Kynu	4432411A05Rik	kynureninase (L-kynurenine hydrolase)	protein-coding
mm_92618.1	chr10	80159707	80159719	-	1	NA	intron (NR_038088, intron 1 of 4)	intron (NR_038088, intron 1 of 4)	-8128	NM_007705	12696	Mm.17898	NM_007705	ENSMUSG00000045193	Cirbp	Cirp|R74941	cold inducible RNA binding protein	protein-coding
mm_138725.1	chr17	36898320	36898339	+	1	NA	5' UTR (NM_146077, exon 1 of 8)	5' UTR (NM_146077, exon 1 of 8)	199	NM_146077	224762	Mm.213417	NM_146077	ENSMUSG00000058063	Trim31	BC026666|HCG1|HCGI|RNF	tripartite motif-containing 31	protein-coding
mm_88030.1	chr10	67254646	67254650	+	1	NA	intron (NM_207221, intron 25 of 25)	intron (NM_207221, intron 25 of 25)	30633	NM_001036293	641340	Mm.136223	NM_001036293	ENSMUSG00000075000	Nrbf2	NRBF-2	nuclear receptor binding factor 2	protein-coding
mm_128274.1	chr15	36794291	36794301	-	1	NA	5' UTR (NM_011740, exon 1 of 7)	5' UTR (NM_011740, exon 1 of 7)	242	NM_011740	22631	Mm.3360	NM_011740	ENSMUSG00000022285	Ywhaz	1110013I11Rik|14-3-3zeta|AI596267|AL022924|AU020854	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide	protein-coding
mm_162117.1	chrX	56787971	56787971	+	1	NA	intron (NM_001287800, intron 1 of 5)	intron (NM_001287800, intron 1 of 5)	1444	NM_001287800	14199	Mm.3126	NM_010211	ENSMUSG00000023092	Fhl1	FHL-1|KyoT|RAM14-1|SLIM|SLIM-1	four and a half LIM domains 1	protein-coding
mm_117250.1	chr13	64365254	64365331	-	1	NA	exon (NM_009984, exon 7 of 8)	exon (NM_009984, exon 7 of 8)	5228	NM_009984	13039	Mm.930	NM_009984	ENSMUSG00000021477	Ctsl	1190035F06Rik|CatL|Ctsl1|MEP|fs|nkt	cathepsin L	protein-coding
mm_149241.1	chr19	10193758	10193771	+	1	NA	exon (NM_146094, exon 8 of 12)	exon (NM_146094, exon 8 of 12)	2389	NR_105959	102465600		NR_105959	ENSMUSG00000098363	Mir6993	Gm27642|mmu-mir-6993	microRNA 6993	ncRNA
mm_104204.1	chr11	87998290	87998300	-	1	NA	promoter-TSS (NM_001168471)	promoter-TSS (NM_001168471)	3	NM_001168471	68097	Mm.246436	NM_026556	ENSMUSG00000020483	Dynll2	1700064A15Rik|6720463E02Rik|C87222|DLC8|DLC8b|Dlc2	dynein light chain LC8-type 2	protein-coding
mm_88836.1	chr10	80826670	80826693	+	1	NA	promoter-TSS (NR_027656)	promoter-TSS (NR_027656)	-15	NR_027656	100041965	Mm.328806	NR_027656		Oaz1-ps	ENSMUSG00000043801|Gm1823|Gm9786|Oaz-ps	ornithine decarboxylase antizyme 1, pseudogene	pseudo
mm_9656.1	chr1	177773409	177773413	-	1	NA	intron (NM_007422, intron 8 of 12)	intron (NM_007422, intron 8 of 12)	23098	NM_007422	11566	Mm.338021	NM_007422	ENSMUSG00000015961	Adss	AI314886|AS|Adss2	adenylosuccinate synthetase, non muscle	protein-coding
mm_33302.1	chr4	129010697	129010708	+	1	NA	non-coding (NR_138540, exon 7 of 7)	non-coding (NR_138540, exon 7 of 7)	17478	NM_001033966	11637	Mm.29460	NM_016895	ENSMUSG00000028792	Ak2	Ak-2|D4Ertd220e	adenylate kinase 2	protein-coding
mm_57552.1	chr6	126849110	126849141	-	1	NA	promoter-TSS (NM_025358)	promoter-TSS (NM_025358)	19	NM_025358	66108	Mm.29939	NM_025358	ENSMUSG00000000399	Ndufa9	1010001N11Rik	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 9	protein-coding
mm_133039.1	chr16	57391475	57391509	+	1	NA	intron (NM_001040397, intron 1 of 4)	LSU-rRNA_Hsa|rRNA|rRNA	38215	NM_001040397	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding
mm_32436.1	chr4	107200803	107200818	+	1	NA	3' UTR (NM_029565, exon 8 of 8)	3' UTR (NM_029565, exon 8 of 8)	-8370	NM_001081272	546840	Mm.331755	NM_001081272	ENSMUSG00000070877	Ldlrad1	OTTMUSG00000008594	low density lipoprotein receptor class A domain containing 1	protein-coding
mm_145740.1	chr18	64265419	64265430	+	1	NA	5' UTR (NM_009182, exon 3 of 6)	5' UTR (NM_009182, exon 3 of 6)	11065	NM_009182	20451	Mm.252110	NM_009182	ENSMUSG00000056812	St8sia3	AI847333|ST8SiaIII|Siat8c	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3	protein-coding
mm_34064.1	chr4	138454379	138454413	+	1	NA	promoter-TSS (NM_025451)	promoter-TSS (NM_025451)	-752	NM_025451	66259	Mm.41603	NM_025451	ENSMUSG00000046447	Camk2n1	1810006K23Rik|AI848599|AI891706	calcium/calmodulin-dependent protein kinase II inhibitor 1	protein-coding
mm_171700.1	chr4	71381950	71381950	+	1	NA	Intergenic	IAPEY_LTR|LTR|ERVK	818943	NM_011599	21885	Mm.278444	NM_011599	ENSMUSG00000008305	Tle1	C230057C06Rik|Estm14|Grg-1|Grg1|Tle4l	transducin-like enhancer of split 1	protein-coding
mm_149582.1	chr19	15923691	15923696	+	1	NA	intron (NM_177420, intron 1 of 8)	MTC|LTR|ERVL-MaLR	929	NM_001205339	107272	Mm.289936	NM_177420	ENSMUSG00000024640	Psat1	D8Ertd814e|EPIP|PSA|Psat	phosphoserine aminotransferase 1	protein-coding
mm_142601.1	chr17	46763773	46763779	-	1	NA	promoter-TSS (NM_011195)	promoter-TSS (NM_011195)	-64	NM_011195	19208	Mm.215173	NM_011195	ENSMUSG00000036858	Ptcra	gp33|pT-alpha|pT-alpha-TCR|pT[a]|pTa|pTalpha	pre T cell antigen receptor alpha	protein-coding
mm_110270.1	chr12	31996928	31996932	-	1	NA	intron (NM_011158, intron 2 of 10)	MamRep605|LTR?|LTR?	-46395	NM_153198	73389	Mm.390461	NM_153198	ENSMUSG00000002996	Hbp1	1700058O05Rik|BE629963|C330012F01Rik|C86454	high mobility group box transcription factor 1	protein-coding
mm_142641.1	chr17	47433409	47433430	-	1	NA	exon (NM_029296, exon 3 of 4)	exon (NM_029296, exon 3 of 4)	-3220	NM_145489	224833	Mm.218444	NM_145489	ENSMUSG00000034382	AI661453	-	expressed sequence AI661453	protein-coding
mm_133387.1	chr16	84774087	84774093	+	1	NA	promoter-TSS (NM_023844)	promoter-TSS (NM_023844)	-33	NM_023844	67374	Mm.41758	NM_023844	ENSMUSG00000053062	Jam2	1110002N23Rik|2410030G21Rik|2410167M24Rik|JAM-2|JAM-B|Jcam2|VE-JAM	junction adhesion molecule 2	protein-coding
mm_160534.1	chr9	39613718	39613718	+	1	NA	exon (NM_146505, exon 1 of 1)	exon (NM_146505, exon 1 of 1)	149	NM_146505	258498	Mm.377537	NM_146505	ENSMUSG00000048299	Olfr148	M30|MOR224-4	olfactory receptor 148	protein-coding
mm_107788.1	chr12	61603881	61603883	+	1	NA	intron (NM_178714, intron 1 of 3)	Lx8b|LINE|L1	80715	NM_001310586	238205	Mm.28802	NM_178714	ENSMUSG00000035653	Lrfn5	AI427653|AI604817|C130061B21|mKIAA4208	leucine rich repeat and fibronectin type III domain containing 5	protein-coding
mm_63507.1	chr7	127841867	127841880	+	1	NA	promoter-TSS (NM_009294)	promoter-TSS (NM_009294)	65	NM_009294	20909	Mm.24867	NM_009294	ENSMUSG00000030805	Stx4a	Stx4|Syn-4|Syn4	syntaxin 4A (placental)	protein-coding
mm_48396.1	chr5	140105825	140105852	-	1	NA	intron (NM_010752, intron 14 of 17)	intron (NM_010752, intron 14 of 17)	197895	NM_175522	243312	Mm.237102	NM_175522	ENSMUSG00000048988	Elfn1	A930017N06Rik|AI197272|Ppp1r28	leucine rich repeat and fibronectin type III, extracellular 1	protein-coding
mm_144058.1	chr17	90622377	90622407	-	1	NA	intron (NM_177284, intron 9 of 20)	intron (NM_177284, intron 9 of 20)	-166512	NM_001346959	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_46305.1	chr5	100562797	100562818	-	1	NA	intron (NM_139198, intron 1 of 4)	intron (NM_139198, intron 1 of 4)	9398	NM_139198	231507	Mm.34609	NM_139198	ENSMUSG00000029322	Plac8	C15|D5Wsu111e	placenta-specific 8	protein-coding
mm_97433.1	chr11	78115566	78115601	+	1	NA	intron (NM_001346762, intron 1 of 2)	intron (NM_001346762, intron 1 of 2)	20910	NM_145430	216971	Mm.119387	NM_145430	ENSMUSG00000037750	Fam222b	9630020I17Rik	family with sequence similarity 222, member B	protein-coding
mm_124451.1	chr14	118925325	118925345	-	1	NA	5' UTR (NM_025943, exon 1 of 22)	5' UTR (NM_025943, exon 1 of 22)	135	NM_025943	66573	Mm.87456	NM_025943	ENSMUSG00000042156	Dzip1	2510025K24Rik|2810422M04Rik	DAZ interacting protein 1	protein-coding
mm_119656.1	chr14	52136464	52136475	+	1	NA	intron (NM_023879, intron 10 of 24)	intron (NM_023879, intron 10 of 24)	25566	NM_023879	77945	Mm.21662	NM_023879	ENSMUSG00000057132	Rpgrip1	0610005A07Rik|4930401L23Rik|4930505G06Rik|A930002K18Rik|AA415034|nmf247	retinitis pigmentosa GTPase regulator interacting protein 1	protein-coding
mm_93510.1	chr10	115185016	115185029	-	1	NA	promoter-TSS (NM_173391)	promoter-TSS (NM_173391)	0	NM_173391	216343	Mm.31597	NM_173391	ENSMUSG00000006764	Tph2	AU043594|Ntph	tryptophan hydroxylase 2	protein-coding
mm_93416.1	chr10	108642380	108642391	-	1	NA	exon (NM_001252342, exon 5 of 11)	exon (NM_001252342, exon 5 of 11)	57775	NM_203660	368203	Mm.452758	NM_203660		Gm5136	C6.1AL|EG368203	predicted gene 5136	protein-coding
mm_66626.1	chr7	45488836	45488860	-	1	NA	promoter-TSS (NM_027903)	promoter-TSS (NM_027903)	-52	NM_027903	71755	Mm.34208	NM_027903	ENSMUSG00000011382	Dhdh	1300018L09Rik|AA591799|Xld-1|Xld1	dihydrodiol dehydrogenase (dimeric)	protein-coding
mm_46455.1	chr5	105117720	105117734	-	1	NA	3' UTR (NM_001256005, exon 11 of 11)	3' UTR (NM_001256005, exon 11 of 11)	-7435	NM_172777	236573	Mm.425261	NM_172777	ENSMUSG00000029298	Gbp9	-	guanylate-binding protein 9	protein-coding
mm_83981.1	chr9	57295752	57295762	-	1	NA	Intergenic	Intergenic	-33158	NM_028820	74211	Mm.428905	NM_028820	ENSMUSG00000032300	1700017B05Rik	AA682102|D9Ertd278e	RIKEN cDNA 1700017B05 gene	protein-coding
mm_69310.1	chr7	128418128	128418145	-	1	NA	promoter-TSS (NM_026418)	promoter-TSS (NM_026418)	36	NM_026418	67865	Mm.18635	NM_026418	ENSMUSG00000030844	Rgs10	2310010N19Rik	regulator of G-protein signalling 10	protein-coding
mm_23101.1	chr3	37348486	37348493	+	1	NA	promoter-TSS (NM_008006)	promoter-TSS (NM_008006)	-164	NM_008006	14173	Mm.473689	NM_008006	ENSMUSG00000037225	Fgf2	Fgf-2|Fgfb|bFGF	fibroblast growth factor 2	protein-coding
mm_61353.1	chr7	68329245	68329284	+	1	NA	exon (NM_001013811, exon 5 of 9)	exon (NM_001013811, exon 5 of 9)	-52670	NR_040340	100504026	Mm.426764	NR_040340	ENSMUSG00000086628	Gm16157	OTTMUSG00000031023	predicted gene 16157	ncRNA
mm_100515.1	chr11	120530672	120530687	+	1	NA	promoter-TSS (NM_008101)	promoter-TSS (NM_008101)	-48	NM_008101	14527	Mm.22329	NM_008101	ENSMUSG00000025127	Gcgr	GR	glucagon receptor	protein-coding
mm_13550.1	chr2	112239785	112239795	+	1	NA	promoter-TSS (NM_207206)	promoter-TSS (NM_207206)	-51	NM_207206	99010	Mm.33438	NM_207206	ENSMUSG00000027134	Lpcat4	AI505034|Agpat7|Aytl3|LPEAT2	lysophosphatidylcholine acyltransferase 4	protein-coding
mm_90843.1	chr10	8749133	8749164	-	1	NA	intron (NM_175155, intron 10 of 19)	intron (NM_175155, intron 10 of 19)	136922	NM_175155	70097	Mm.338275	NM_175155	ENSMUSG00000015305	Sash1	1100001C18Rik|2500002E12Rik|A330076K04Rik|mKIAA0790	SAM and SH3 domain containing 1	protein-coding
mm_141259.1	chr17	27622786	27622854	-	1	NA	5' UTR (NM_001291046, exon 1 of 5)	5' UTR (NM_001291046, exon 1 of 5)	144	NM_001291046	56409	Mm.144699	NM_019837	ENSMUSG00000024213	Nudt3	1110011B09Rik|AA960325|Dipp|Dipp1	nudix (nucleotide diphosphate linked moiety X)-type motif 3	protein-coding
mm_109807.1	chr12	3347797	3347799	-	1	NA	Intergenic	PB1D9|SINE|Alu	-17334	NM_008445	16570	Mm.7688	NM_008445	ENSMUSG00000020668	Kif3c	mKIAA4058	kinesin family member 3C	protein-coding
mm_55000.1	chr6	48834536	48834581	-	1	NA	exon (NM_001164209, exon 7 of 8)	exon (NM_001164209, exon 7 of 8)	6430	NM_023056	65963	Mm.28385	NM_023056	ENSMUSG00000029810	Tmem176b	1810009M01Rik|Clast1|Lr8	transmembrane protein 176B	protein-coding
mm_9216.1	chr1	171231246	171231264	-	1	NA	exon (NM_010185, exon 2 of 5)	exon (NM_010185, exon 2 of 5)	3094	NM_010185	14127	Mm.22673	NM_010185	ENSMUSG00000058715	Fcer1g	AI573376|CD23|FcR-gamma|FcR[g]|FcRgamma|Fce1g|FcepsilonRI|Ly-50	Fc receptor, IgE, high affinity I, gamma polypeptide	protein-coding
mm_171330.1	chr3	98522315	98522328	-	1	NA	Intergenic	Intergenic	-11754	NM_008294	15495	Mm.14309	NM_008294	ENSMUSG00000095143	Hsd3b4	-	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 4	protein-coding
mm_131266.1	chr16	10835087	10835093	+	1	NA	promoter-TSS (NM_001162932)	promoter-TSS (NM_001162932)	31	NM_001162932	223970	Mm.325777	NM_001033278	ENSMUSG00000037991	Rmi2	A630055G03Rik|Gm537|Gm929	RecQ mediated genome instability 2	protein-coding
mm_47332.1	chr5	122500825	122500833	-	1	NA	intron (NM_001110140, intron 2 of 19)	(A)n|Simple_repeat|Simple_repeat	1396	NM_001110140	11938	Mm.227583	NM_009722	ENSMUSG00000029467	Atp2a2	9530097L16Rik|D5Wsu150e|SERCA2|SERCA2B|Serca2a|mKIAA4195	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	protein-coding
mm_20680.1	chr2	132512490	132512509	-	1	NA	intron (NR_028286, intron 2 of 3)	L1M3|LINE|L1	21771	NR_028286	70371	Mm.394667	NR_028286	ENSMUSG00000086379	1700026D11Rik	-	RIKEN cDNA 1700026D11 gene	ncRNA
mm_166722.1	chr6	120466696	120466705	+	1	NA	intron (NM_008359, intron 1 of 12)	intron (NM_008359, intron 1 of 12)	3503	NM_008359	16172	Mm.4481	NM_008359	ENSMUSG00000002897	Il17ra	AW538159|Cdw217|Il17r|VDw217	interleukin 17 receptor A	protein-coding
mm_149481.1	chr19	11770358	11770406	+	1	NA	promoter-TSS (NM_025606)	promoter-TSS (NM_025606)	-33	NM_025606	94063	Mm.203928	NM_025606	ENSMUSG00000024683	Mrpl16	2310039D06Rik	mitochondrial ribosomal protein L16	protein-coding
mm_149970.1	chr19	29047602	29047607	+	1	NA	non-coding (NR_028360, exon 1 of 1)	non-coding (NR_028360, exon 1 of 1)	121	NR_028360	67329	Mm.394933	NR_028360		1700018L02Rik	-	RIKEN cDNA 1700018L02 gene	ncRNA
mm_103425.1	chr11	75600047	75600051	-	1	NA	non-coding (NR_110477, exon 1 of 1)	non-coding (NR_110477, exon 1 of 1)	182	NR_110477	654359	Mm.439961	NR_110477		Gm12338	OTTMUSG00000006216	cytochrome c oxidase, subunit VIIc pseudogene	pseudo
mm_124162.1	chr14	93638356	93638373	-	1	NA	intron (NM_001346722, intron 2 of 4)	intron (NM_001346722, intron 2 of 4)	250524	NM_001271800	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding
mm_145701.1	chr18	62657257	62657279	+	1	NA	intron (NM_177829, intron 5 of 8)	intron (NM_177829, intron 5 of 8)	-61004	NM_001001803	408198	Mm.478742	NM_001001803	ENSMUSG00000060201	Spink7	EG408198|Ecg2	serine peptidase inhibitor, Kazal type 7 (putative)	protein-coding
mm_136304.1	chr16	91597637	91597735	-	1	NA	promoter-TSS (NM_030018)	promoter-TSS (NM_030018)	-6	NM_030018	77975	Mm.290341	NM_030018	ENSMUSG00000022964	Tmem50b	AU015466|AU019872|B230114J08Rik	transmembrane protein 50B	protein-coding
mm_55924.1	chr6	84010092	84010094	-	1	NA	intron (NM_001077694, intron 1 of 54)	intron (NM_001077694, intron 1 of 54)	1495	NM_001077694	26903	Mm.220982	NM_021469	ENSMUSG00000033788	Dysf	2310004N10Rik|AI604795|D6Pas3	dysferlin	protein-coding
mm_96179.1	chr11	61653245	61653253	+	1	NA	promoter-TSS (NM_027817)	promoter-TSS (NM_027817)	-72	NM_027817	71520	Mm.202760	NM_027817	ENSMUSG00000004837	Grap	8430435N19Rik|BB233594	GRB2-related adaptor protein	protein-coding
mm_125403.1	chr15	41511622	41511622	+	1	NA	intron (NM_001130166, intron 1 of 16)	L1_Mur3|LINE|L1	64140	NM_001130166	170719	Mm.254267	NM_130885	ENSMUSG00000022307	Oxr1	2210416C20Rik|C7|C7B	oxidation resistance 1	protein-coding
mm_121390.1	chr14	119099450	119099465	+	1	NA	promoter-TSS (NM_001081252)	promoter-TSS (NM_001081252)	-23	NM_001081252	66435	Mm.213406	NM_025561	ENSMUSG00000042104	Uggt2	1810064L21Rik|3110001A05Rik|3110027P15Rik|A230065J02Rik|AW047562|Ugcgl2	UDP-glucose glycoprotein glucosyltransferase 2	protein-coding
mm_83817.1	chr9	53648718	53648721	-	1	NA	intron (NM_027807, intron 3 of 18)	intron (NM_027807, intron 3 of 18)	18788	NM_001161618	75717	Mm.218910	NM_027807	ENSMUSG00000032030	Cul5	4921514I20Rik|8430423K24Rik|AI852817|C030032G03Rik|C330021I08Rik|VACM-1|VACM1	cullin 5	protein-coding
mm_54401.1	chr6	31528669	31528687	-	1	NA	exon (NM_013723, exon 2 of 8)	exon (NM_013723, exon 2 of 8)	35259	NM_013723	27205	Mm.89918	NM_013723	ENSMUSG00000025608	Podxl	AW121214|Ly102|PC|PCLP-1|Pclp1	podocalyxin-like	protein-coding
mm_34065.1	chr4	138454717	138454737	+	1	NA	promoter-TSS (NM_025451)	promoter-TSS (NM_025451)	-421	NM_025451	66259	Mm.41603	NM_025451	ENSMUSG00000046447	Camk2n1	1810006K23Rik|AI848599|AI891706	calcium/calmodulin-dependent protein kinase II inhibitor 1	protein-coding
mm_82681.1	chr9	22135676	22135724	-	1	NA	promoter-TSS (NM_001102405)	promoter-TSS (NM_001102405)	46	NM_001102405	11433	Mm.46354	NM_007388	ENSMUSG00000001348	Acp5	TRACP|TRAP	acid phosphatase 5, tartrate resistant	protein-coding
mm_75568.1	chr8	60516057	60516082	-	1	NA	exon (NM_011834, exon 3 of 13)	exon (NM_011834, exon 3 of 13)	9945	NM_011834	23923	Mm.35020	NM_011834	ENSMUSG00000057228	Aadat	AI875679|Aadt|KATII|Kat2|Kyat2|mKat-2	aminoadipate aminotransferase	protein-coding
mm_31995.1	chr4	89688197	89688197	+	1	NA	promoter-TSS (NM_175647)	promoter-TSS (NM_175647)	-1	NM_175647	242523	Mm.130167	NM_175647	ENSMUSG00000043753	Dmrta1	Dmrt4	doublesex and mab-3 related transcription factor like family A1	protein-coding
mm_171182.1	chr3	37108480	37108480	+	1	NA	intron (NM_009350, intron 11 of 11)	intron (NM_009350, intron 11 of 11)	17474	NM_008366	16183	Mm.14190	NM_008366	ENSMUSG00000027720	Il2	Il-2	interleukin 2	protein-coding
mm_123859.1	chr14	72284519	72284528	-	1	NA	Intergenic	Intergenic	425480	NM_207636	319448	Mm.205421	NM_207636	ENSMUSG00000033487	Fndc3a	1700094E19Rik|D14Ertd453e|F730017H24Rik|Fndc3|sys	fibronectin type III domain containing 3A	protein-coding
mm_32606.1	chr4	112034711	112034714	+	1	NA	Intergenic	L1Md_F2|LINE|L1	28443	NM_001102662	639781	Mm.398873	NM_001102662	ENSMUSG00000089773	Skint1	OTTMUSG00000008542|Skint-1	selection and upkeep of intraepithelial T cells 1	protein-coding
mm_166901.1	chr7	28442871	28442908	-	1	NA	intron (NM_001039192, intron 3 of 6)	intron (NM_001039192, intron 3 of 6)	1952	NM_001039192	63986	Mm.194536	NM_022024	ENSMUSG00000060791	Gmfg	0610039G16Rik|2310057N07Rik|AI324845	glia maturation factor, gamma	protein-coding
mm_169574.1	chr15	22699821	22699821	-	1	NA	Intergenic	LTRIS2|LTR|ERV1	15163	NM_001165971	545091	Mm.475598	NM_001165971		Gm5803	EG545091	predicted gene 5803	protein-coding
mm_66818.1	chr7	48456241	48456251	-	1	NA	promoter-TSS (NM_205810)	promoter-TSS (NM_205810)	96	NM_205810	233231	Mm.297430	NM_205810	ENSMUSG00000070547	Mrgprb1	MrgB1	MAS-related GPR, member B1	protein-coding
mm_31041.1	chr4	41135500	41135527	+	1	NA	promoter-TSS (NM_026275)	promoter-TSS (NM_026275)	-508	NM_026275	67615	Mm.389540	NM_026275	ENSMUSG00000036241	Ube2r2	1200003M11Rik|Cdc34b|Ubc3b	ubiquitin-conjugating enzyme E2R 2	protein-coding
mm_16255.1	chr2	173216884	173216898	+	1	NA	exon (NM_021394, exon 2 of 8)	exon (NM_021394, exon 2 of 8)	2031	NM_021394	58203	Mm.116687	NM_021394	ENSMUSG00000027514	Zbp1	2010010H03Rik|Dai|Dlm1|mZaDLM	Z-DNA binding protein 1	protein-coding
mm_167872.1	chrX	36795721	36795728	+	1	NA	5' UTR (NM_007451, exon 1 of 4)	5' UTR (NM_007451, exon 1 of 4)	127	NM_007451	11740	Mm.371544	NM_007451	ENSMUSG00000016319	Slc25a5	Ant2	solute carrier family 25 (mitochondrial carrier, adenine nucleotide translocator), member 5	protein-coding
mm_124330.1	chr14	103843627	103843633	-	1	NA	promoter-TSS (NM_001276296)	promoter-TSS (NM_001276296)	71	NM_007904	13618	Mm.229532	NM_007904	ENSMUSG00000022122	Ednrb	ET-B|ET-BR|ETR-b|ETb|Sox10m1	endothelin receptor type B	protein-coding
mm_155088.1	chrX	48108996	48109006	+	1	NA	5' UTR (NM_001289729, exon 1 of 21)	5' UTR (NM_001289729, exon 1 of 21)	276	NM_133213	170745	Mm.129279	NM_133213	ENSMUSG00000037005	Xpnpep2	9030008G12Rik|mAPP	X-prolyl aminopeptidase (aminopeptidase P) 2, membrane-bound	protein-coding
mm_168558.1	chr1	166431878	166431895	-	1	NA	Intergenic	Lx2|LINE|L1	-22058	NM_001142948	71592	Mm.192094	NM_175170	ENSMUSG00000040596	Pogk	9130401E23Rik|BASS2|mKIAA1513	pogo transposable element with KRAB domain	protein-coding
mm_244.1	chr1	19209141	19209153	+	1	NA	5' UTR (NM_009334, exon 1 of 7)	5' UTR (NM_009334, exon 1 of 7)	233	NM_001286340	21419	Mm.137021	NM_009334	ENSMUSG00000025927	Tfap2b	AI606113|AP-2(beta)|E130018K07Rik|Tcfap2b	transcription factor AP-2 beta	protein-coding
mm_65982.1	chr7	30453789	30453811	-	1	NA	intron (NM_172898, intron 7 of 14)	intron (NM_172898, intron 7 of 14)	3715	NM_172898	243911	Mm.113908	NM_172898	ENSMUSG00000036915	Kirrel2	C330019F22Rik|NEPH3|NLG1	kin of IRRE like 2 (Drosophila)	protein-coding
mm_13946.1	chr2	121295438	121295486	+	1	NA	promoter-TSS (NM_001173506)	promoter-TSS (NM_001173506)	8	NM_001173506	17754	Mm.36501	NM_032393	ENSMUSG00000027254	Map1a	6330416M19Rik|AI853608|Mtap-1|Mtap1|Mtap1a|moth1	microtubule-associated protein 1 A	protein-coding
mm_88643.1	chr10	79946274	79946296	+	1	NA	intron (NM_007880, intron 3 of 8)	intron (NM_007880, intron 3 of 8)	-13867	NM_175450	216156	Mm.35828	NM_175450	ENSMUSG00000035754	Wdr18	2310012I10Rik|AU044733|AW122032	WD repeat domain 18	protein-coding
mm_93001.1	chr10	86885781	86885803	-	1	NA	intron (NM_138673, intron 42 of 68)	intron (NM_138673, intron 42 of 68)	106787	NM_175331	103466	Mm.200446	NM_175331	ENSMUSG00000054027	Nt5dc3	AU040402|AW540062|C630002B14Rik|TU12B1-TY	5'-nucleotidase domain containing 3	protein-coding
mm_149525.1	chr19	12460750	12460783	+	1	NA	promoter-TSS (NM_010821)	promoter-TSS (NM_010821)	-13	NM_010821	17476	Mm.3999	NM_010821	ENSMUSG00000046805	Mpeg1	MPS1|Mpg-1	macrophage expressed gene 1	protein-coding
mm_1637.1	chr1	74511408	74511416	+	1	NA	intron (NM_021383, intron 1 of 7)	intron (NM_021383, intron 1 of 7)	5352	NM_021383	58184	Mm.291708	NM_021383	ENSMUSG00000026174	Cnot9	2610007F23Rik|AI593551|Fl10|Rqcd1	CCR4-NOT transcription complex, subunit 9	protein-coding
mm_60453.1	chr7	44477525	44477535	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-6987	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_153548.1	chr19	42086320	42086334	-	1	NA	promoter-TSS (NM_198108)	promoter-TSS (NM_198108)	43	NM_198108	226123	Mm.259441	NM_198108	ENSMUSG00000049670	Morn4	-	MORN repeat containing 4	protein-coding
mm_16428.1	chr2	180388063	180388065	+	1	NA	promoter-TSS (NR_029528)	promoter-TSS (NR_029528)	-984	NR_029528	387136		NR_029528	ENSMUSG00000070144	Mir1a-1	Mir1-1|Mirn1-1|Mirn1b|Mirn1c|Mirn1d|mir-1a-1|mmu-mir-1-1|mmu-mir-1a-1	microRNA 1a-1	ncRNA
mm_150216.1	chr19	32987932	32987972	+	1	NA	Intergenic	Intergenic	230375	NM_008960	19211	Mm.245395	NM_008960	ENSMUSG00000013663	Pten	2310035O07Rik|A130070J02Rik|AI463227|B430203M17Rik|MMAC1|TEP1	phosphatase and tensin homolog	protein-coding
mm_157385.1	chrX	38110914	38110920	-	1	NA	promoter-TSS (NM_001025083)	promoter-TSS (NM_001025083)	-10	NM_001025083	382282	Mm.219322	NM_001025083	ENSMUSG00000071766	Rhox12	Gm1148	reproductive homeobox 12	protein-coding
mm_80735.1	chr9	94669877	94669928	+	1	NA	promoter-TSS (NM_177909)	promoter-TSS (NM_177909)	10	NM_177909	331004	Mm.326125	NM_177909	ENSMUSG00000031129	Slc9a9	5730527A11Rik|9930105B05|AI854429|Nhe9	solute carrier family 9 (sodium/hydrogen exchanger), member 9	protein-coding
mm_169290.1	chr13	9834460	9834478	-	1	NA	Intergenic	L1Md_T|LINE|L1	-69148	NM_144516	66505	Mm.397307	NM_144516	ENSMUSG00000021156	Zmynd11	2210402G22Rik|BS69	zinc finger, MYND domain containing 11	protein-coding
mm_135805.1	chr16	57292846	57292867	-	1	NA	promoter-TSS (NM_027651)	promoter-TSS (NM_027651)	-5	NM_027651	71027	Mm.158563	NM_027651	ENSMUSG00000022753	Tmem30c	4933401B01Rik|4933409A18Rik|Cdc50c	transmembrane protein 30C	protein-coding
mm_158853.1	chrX	169994127	169994141	-	1	NA	Intergenic	CpG	-15217	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_31899.1	chr4	83525541	83525616	+	1	NA	promoter-TSS (NM_001081012)	promoter-TSS (NM_001081012)	33	NM_001081012	320226	Mm.180032	NM_029117	ENSMUSG00000052407	Ccdc171	4930418J05Rik|4930473A06Rik|A330015D16Rik	coiled-coil domain containing 171	protein-coding
mm_86584.1	chr10	13008535	13008547	+	1	NA	promoter-TSS (NM_175102)	promoter-TSS (NM_175102)	91	NM_175102	66125	Mm.29743	NM_175102	ENSMUSG00000078348	Sf3b5	10kDa|1110005L13Rik|AU043053|Sf3b10	splicing factor 3b, subunit 5	protein-coding
mm_56121.1	chr6	87532395	87532414	-	1	NA	intron (NM_001037727, intron 1 of 10)	intron (NM_001037727, intron 1 of 10)	855	NM_001037727	232201	Mm.119564	NM_175476	ENSMUSG00000030047	Arhgap25	A130039I20Rik	Rho GTPase activating protein 25	protein-coding
mm_172349.1	chr7	113491694	113491699	-	1	NA	Intergenic	Intergenic	-22138	NM_001285831	67420	Mm.206919	NM_026143	ENSMUSG00000030759	Far1	2600011M19Rik|2900034E22Rik|3732409C05Rik|AI850429|Mlstd2	fatty acyl CoA reductase 1	protein-coding
mm_155240.1	chrX	57212186	57212186	+	1	NA	promoter-TSS (NM_011616)	promoter-TSS (NM_011616)	43	NM_011616	21947	Mm.4861	NM_011616	ENSMUSG00000031132	Cd40lg	CD154|CD40-L|Cd40l|HIGM1|IGM|IMD3|Ly-62|Ly62|T-BAM|TRAP|Tnfsf5|Tnlg8b|gp39	CD40 ligand	protein-coding
mm_103828.1	chr11	83012922	83012930	-	1	NA	intron (NM_181545, intron 4 of 5)	intron (NM_181545, intron 4 of 5)	7796	NM_001167743	276950	Mm.491599	NM_181545	ENSMUSG00000035208	Slfn8	-	schlafen 8	protein-coding
mm_127754.1	chr15	103503039	103503045	+	1	NA	promoter-TSS (NM_008800)	promoter-TSS (NM_008800)	8	NM_008800	18574	Mm.390792	NM_008800	ENSMUSG00000022489	Pde1b	Pde1b1	phosphodiesterase 1B, Ca2+-calmodulin dependent	protein-coding
mm_2965.1	chr1	133020350	133020381	+	1	NA	intron (NM_008575, intron 1 of 11)	RLTR23|LTR|ERV1	5051	NR_126506	17248	Mm.426531	NM_008575	ENSMUSG00000054387	Mdm4	4933417N07Rik|AA414968|AL023055|AU018793|AU021806|C85810|Mdmx	transformed mouse 3T3 cell double minute 4	protein-coding
mm_55711.1	chr6	72958466	72958496	-	1	NA	promoter-TSS (NM_025284)	promoter-TSS (NM_025284)	2	NM_025284	19240	Mm.3532	NM_025284	ENSMUSG00000079523	Tmsb10	Ptmb10|Tb10	thymosin, beta 10	protein-coding
mm_115320.1	chr13	112418143	112418184	+	1	NA	Intergenic	Intergenic	-45907	NM_010560	16195	Mm.4364	NM_010560	ENSMUSG00000021756	Il6st	5133400A03Rik|AA389424|BB405851|CD130|D13Ertd699e|gp130	interleukin 6 signal transducer	protein-coding
mm_10029.1	chr1	192137577	192137627	-	1	NA	intron (NM_001346740, intron 1 of 11)	CpG-848	438	NM_001290278	214742	Mm.207457	NM_144814	ENSMUSG00000037395	Rcor3	4921514E24Rik|C730034D20Rik|E130101E15Rik	REST corepressor 3	protein-coding
mm_94419.1	chr11	5870552	5870562	+	1	NA	exon (NM_009636, exon 19 of 21)	exon (NM_009636, exon 19 of 21)	7699	NM_008894	18972	Mm.35788	NM_008894	ENSMUSG00000020471	Pold2	50kDa|p50|po1D2	polymerase (DNA directed), delta 2, regulatory subunit	protein-coding
mm_153416.1	chr19	40588490	40588502	-	1	NA	promoter-TSS (NM_153554)	promoter-TSS (NM_153554)	-33	NM_153554	56454	Mm.233117	NM_019698	ENSMUSG00000025007	Aldh18a1	2810433K04Rik|AI429789|Pycs	aldehyde dehydrogenase 18 family, member A1	protein-coding
mm_99705.1	chr11	106160294	106160319	+	1	NA	promoter-TSS (NM_172397)	promoter-TSS (NM_172397)	-164	NM_172397	67803	Mm.21687	NM_172397	ENSMUSG00000040699	Limd2	0610025L06Rik|AI413966	LIM domain containing 2	protein-coding
mm_54452.1	chr6	34746291	34746307	-	1	NA	intron (NM_001347100, intron 5 of 13)	intron (NM_001347100, intron 5 of 13)	-34133	NM_001289657	76223	Mm.150047	NM_178630	ENSMUSG00000038836	Agbl3	2900053G10Rik|4930431N21Rik|6530406M24Rik|CCP3	ATP/GTP binding protein-like 3	protein-coding
mm_79705.1	chr9	61110966	61110997	+	1	NA	Intergenic	Intergenic	-5595	NR_105026	66785	Mm.158134	NR_105026	ENSMUSG00000111807	4933433G08Rik	-	RIKEN cDNA 4933433G08 gene	ncRNA
mm_128584.1	chr15	58034337	58034349	-	1	NA	promoter-TSS (NM_029418)	promoter-TSS (NM_029418)	-49	NM_029418	75758	Mm.455792	NM_029418	ENSMUSG00000101892	9130401M01Rik	AI849328	RIKEN cDNA 9130401M01 gene	protein-coding
mm_31201.1	chr4	43727182	43727205	+	1	NA	promoter-TSS (NM_027511)	promoter-TSS (NM_027511)	-5	NM_027511	100039781	Mm.18796	NM_027511	ENSMUSG00000071001	Hrct1	3830408D24Rik	histidine rich carboxyl terminus 1	protein-coding
mm_160661.1	chr9	119578808	119578808	-	1	NA	intron (NM_021544, intron 1 of 27)	CpG	208	NM_021544	20271	Mm.103584	NM_021544	ENSMUSG00000032511	Scn5a	Nav1.5|Nav1.5c|SkM1|SkM2|mH1	sodium channel, voltage-gated, type V, alpha	protein-coding
mm_34140.1	chr4	139291693	139291741	+	1	NA	3' UTR (NM_001271405, exon 9 of 9)	3' UTR (NM_001271405, exon 9 of 9)	18983	NM_145384	212555	Mm.45131	NM_145384	ENSMUSG00000028744	Pqlc2	BC019216	PQ loop repeat containing 2	protein-coding
mm_92165.1	chr10	67549037	67549047	-	1	NA	promoter-TSS (NM_001005419)	promoter-TSS (NM_001005419)	-87	NM_001005419	211488	Mm.297250	NM_001005419	ENSMUSG00000057134	Ado	Gm237	2-aminoethanethiol (cysteamine) dioxygenase	protein-coding
mm_133134.1	chr16	66272676	66272678	+	1	NA	Intergenic	Intergenic	-384441	NR_040512	75501	Mm.394300	NR_040512	ENSMUSG00000092599	1700010K23Rik	-	RIKEN cDNA 1700010K23 gene	ncRNA
mm_37195.1	chr4	117497076	117497076	-	1	NA	promoter-TSS (NM_025739)	promoter-TSS (NM_025739)	-24	NM_025739	66743	Mm.318331	NM_025739	ENSMUSG00000028677	Rnf220	4732477A13|4931406I20Rik|5730503K05Rik|AV302541	ring finger protein 220	protein-coding
mm_27372.1	chr3	50442272	50442290	-	1	NA	intron (NM_011990, intron 1 of 11)	A-rich|Low_complexity|Low_complexity	1332	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_66048.1	chr7	30728813	30728837	-	1	NA	TTS (NM_001290631)	TTS (NM_001290631)	709	NM_027215	69804	Mm.27499	NM_027215	ENSMUSG00000006315	Tmem147	2010004E11Rik|5033425B17Rik|Nifie14	transmembrane protein 147	protein-coding
mm_35727.1	chr4	44710762	44710774	-	1	NA	promoter-TSS (NM_008782)	promoter-TSS (NM_008782)	-328	NM_008782	18507	Mm.439659	NM_008782	ENSMUSG00000014030	Pax5	BSAP|EBB-1|KLP|Pax-5	paired box 5	protein-coding
mm_56549.1	chr6	100244144	100244147	-	1	NA	intron (NM_019743, intron 2 of 4)	intron (NM_019743, intron 2 of 4)	43213	NM_019743	56353	Mm.321633	NM_019743	ENSMUSG00000072872	Rybp	2410018J24Rik|DEDAF|YEAF1	RING1 and YY1 binding protein	protein-coding
mm_48978.1	chr6	4755120	4755137	+	1	NA	exon (NM_130877, exon 2 of 2)	exon (NM_130877, exon 2 of 2)	7822	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_92255.1	chr10	70606037	70606042	-	1	NA	intron (NR_045292, intron 3 of 3)	Lx5|LINE|L1	-6748	NM_178621	70911	Mm.19825	NM_178621	ENSMUSG00000037747	Phyhipl	4921522K17Rik|AI267048	phytanoyl-CoA hydroxylase interacting protein-like	protein-coding
mm_39298.1	chr5	5573995	5574013	+	1	NA	non-coding (NR_033499, exon 1 of 2)	non-coding (NR_033499, exon 1 of 2)	205	NR_033499	667705	Mm.376656	NR_033499	ENSMUSG00000073234	Gm8773	EG667705|Gm29287	predicted gene 8773	ncRNA
mm_95229.1	chr11	44519406	44519450	+	1	NA	promoter-TSS (NM_001166553)	promoter-TSS (NM_001166553)	51	NM_001166553	74315	Mm.156771	NM_028862	ENSMUSG00000019189	Rnf145	3732413I11Rik|TMRF1	ring finger protein 145	protein-coding
mm_94535.1	chr11	9119280	9119296	+	1	NA	intron (NM_001159402, intron 1 of 8)	intron (NM_001159402, intron 1 of 8)	781	NM_001159402	22271	Mm.4610	NM_009477	ENSMUSG00000020407	Upp1	AI325217|UPase|UdRPase|Up|Upp	uridine phosphorylase 1	protein-coding
mm_133608.1	chr16	91492637	91492658	+	1	NA	exon (NM_010508, exon 3 of 11)	exon (NM_010508, exon 3 of 11)	7432	NM_010508	15975	Mm.502	NM_010508	ENSMUSG00000022967	Ifnar1	CD118|Ifar|Ifnar|Ifrc|Infar	interferon (alpha and beta) receptor 1	protein-coding
mm_92200.1	chr10	68136651	68136677	-	1	NA	intron (NM_023598, intron 4 of 9)	intron (NM_023598, intron 4 of 9)	142062	NM_023598	71371	Mm.440357	NM_023598	ENSMUSG00000019947	Arid5b	4930580B11|5430435G07Rik|AI467247|Desrt|Mrf2|Mrf2alpha|Mrf2beta	AT rich interactive domain 5B (MRF1-like)	protein-coding
mm_124224.1	chr14	100284920	100284942	-	1	NA	Intergenic	Intergenic	-135135	NM_010636	16597	Mm.396499	NM_010636	ENSMUSG00000072294	Klf12	2700063E05Rik|AI225908|AI315654|AP-2rep|B130052C06Rik|D530033K05Rik	Kruppel-like factor 12	protein-coding
mm_77658.1	chr8	124639337	124639340	-	1	NA	exon (NM_175149, exon 3 of 4)	exon (NM_175149, exon 3 of 4)	24031	NM_175149	69551	Mm.261920	NM_175149	ENSMUSG00000031983	2310022B05Rik	-	RIKEN cDNA 2310022B05 gene	protein-coding
mm_156371.1	chrX	139621505	139621521	+	1	NA	intron (NM_023270, intron 1 of 6)	intron (NM_023270, intron 1 of 6)	10893	NM_023270	66889	Mm.27764	NM_023270	ENSMUSG00000031438	Rnf128	1300002C13Rik|AI987883|GRAIL|Greul1	ring finger protein 128	protein-coding
mm_156151.1	chrX	129910891	129910922	+	1	NA	intron (NM_172493, intron 5 of 26)	intron (NM_172493, intron 5 of 26)	161164	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diaph2	Dia3|Diap2|Drf2|E430022I22Rik	diaphanous related formin 2	protein-coding
mm_54408.1	chr6	31563927	31563935	-	1	NA	promoter-TSS (NM_013723)	promoter-TSS (NM_013723)	6	NM_013723	27205	Mm.89918	NM_013723	ENSMUSG00000025608	Podxl	AW121214|Ly102|PC|PCLP-1|Pclp1	podocalyxin-like	protein-coding
mm_42652.1	chr5	118765184	118765196	+	1	NA	3' UTR (NM_172424, exon 31 of 31)	3' UTR (NM_172424, exon 31 of 31)	-187149	NR_040694	74627	Mm.410828	NR_040694	ENSMUSG00000107144	4930413E15Rik	-	RIKEN cDNA 4930413E15 gene	ncRNA
mm_124069.1	chr14	78565584	78565596	-	1	NA	Intergenic	Intergenic	-28730	NM_001164503	219181	Mm.89413	NM_001164503	ENSMUSG00000022016	Akap11	6330501D17Rik|AKAP220|Gm80|PRKA11|mKIAA0629	A kinase (PRKA) anchor protein 11	protein-coding
mm_5888.1	chr1	54175843	54175849	-	1	NA	intron (NM_001001883, intron 1 of 28)	intron (NM_001001883, intron 1 of 28)	19188	NM_001001883	329152	Mm.132150	NM_172655	ENSMUSG00000042807	Hecw2	A730039N16Rik|D030049F17Rik|Gm971|Nedl2|mKIAA1301	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2	protein-coding
mm_59395.1	chr7	26764547	26764549	+	1	NA	intron (NM_007814, intron 6 of 8)	intron (NM_007814, intron 6 of 8)	7406	NM_007814	13090	Mm.14098	NM_007814	ENSMUSG00000066704	Cyp2b19	CYPIIB19	cytochrome P450, family 2, subfamily b, polypeptide 19	protein-coding
mm_98070.1	chr11	85889982	85890006	+	1	NA	promoter-TSS (NM_011536)	promoter-TSS (NM_011536)	-69	NM_011536	21387	Mm.275336	NM_011536	ENSMUSG00000000094	Tbx4	3930401C23	T-box 4	protein-coding
mm_101468.1	chr11	30649365	30649374	-	1	NA	promoter-TSS (NM_029344)	promoter-TSS (NM_029344)	27	NM_029344	75572	Mm.390319	NM_029344	ENSMUSG00000060923	Acyp2	2310004B09Rik	acylphosphatase 2, muscle type	protein-coding
mm_28123.1	chr3	86920544	86920565	-	1	NA	5' UTR (NM_001195500, exon 1 of 12)	5' UTR (NM_001195500, exon 1 of 12)	330	NM_001195496	70762	Mm.44490	NM_027539	ENSMUSG00000028078	Dclk2	6330415M09Rik|AU044875|CL2|CLICK2|Click-II|Dcamkl2	doublecortin-like kinase 2	protein-coding
mm_145362.1	chr18	56677826	56677837	+	1	NA	Intergenic	Intergenic	-29982	NM_010721	16906	Mm.4105	NM_010721	ENSMUSG00000024590	Lmnb1	-	lamin B1	protein-coding
mm_114747.1	chr13	84222287	84222356	+	1	NA	promoter-TSS (NR_138587)	promoter-TSS (NR_138587)	25	NM_175187	72745	Mm.295063	NM_175187	ENSMUSG00000035762	Tmem161b	2810446P07Rik|AI843389	transmembrane protein 161B	protein-coding
mm_31279.1	chr4	45824269	45824312	+	1	NA	intron (NM_018741, intron 1 of 4)	intron (NM_018741, intron 1 of 4)	2537	NM_018741	75426	Mm.3919	NM_018741	ENSMUSG00000035551	Igfbpl1	2810011G06Rik|2810453O06Rik|IGFBPL	insulin-like growth factor binding protein-like 1	protein-coding
mm_139709.1	chr17	57460002	57460016	+	1	NA	intron (NM_010130, intron 17 of 21)	Lx9|LINE|L1	85305	NM_001104591	224916	Mm.469889	NM_001104591	ENSMUSG00000090655	Vmn2r120	EG224916	vomeronasal 2, receptor 120	protein-coding
mm_24488.1	chr3	92339075	92339081	+	1	NA	promoter-TSS (NM_011470)	promoter-TSS (NM_011470)	-62	NM_011470	20758	Mm.87820	NM_011470	ENSMUSG00000042212	Sprr2d	-	small proline-rich protein 2D	protein-coding
mm_89238.1	chr10	87817235	87817236	+	1	NA	Intergenic	Intergenic	-41030	NM_001314010	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_10218.1	chr2	5951441	5951468	+	1	NA	promoter-TSS (NM_001081132)	promoter-TSS (NM_001081132)	-15	NM_001081132	326622	Mm.31102	NM_001081132	ENSMUSG00000043241	Upf2	-	UPF2 regulator of nonsense transcripts homolog (yeast)	protein-coding
mm_78314.1	chr9	23306710	23306717	+	1	NA	intron (NM_028472, intron 6 of 14)	intron (NM_028472, intron 6 of 14)	83637	NM_028472	73230	Mm.335020	NM_028472	ENSMUSG00000031963	Bmper	3110056H04Rik|CV-2|Crim3|Cv2	BMP-binding endothelial regulator	protein-coding
mm_48276.1	chr5	137963136	137963138	-	1	NA	promoter-TSS (NM_080450)	promoter-TSS (NM_080450)	-178	NM_080450	118446	Mm.332771	NM_080450	ENSMUSG00000056966	Gjc3	Cx29|Gje1	gap junction protein, gamma 3	protein-coding
mm_55120.1	chr6	50404908	50404920	-	1	NA	intron (NM_001347213, intron 2 of 23)	intron (NM_001347213, intron 2 of 23)	-22077	NM_027881	71720	Mm.44153	NM_027881	ENSMUSG00000029822	Osbpl3	1200014M06Rik|6720421I08Rik|A530055M08|ORP-3|ORP3|OSBP3	oxysterol binding protein-like 3	protein-coding
mm_47767.1	chr5	131538635	131538641	-	1	NA	intron (NM_177047, intron 5 of 18)	CpG	-231116	NM_145218	212996	Mm.299204	NM_145218	ENSMUSG00000034040	Wbscr17	AA388321|E330012B09Rik	Williams-Beuren syndrome chromosome region 17 homolog (human)	protein-coding
mm_113658.1	chr13	42680886	42680894	+	1	NA	promoter-TSS (NM_001302635)	promoter-TSS (NM_001302635)	91	NM_001302635	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding
mm_4466.1	chr1	173350152	173350177	+	1	NA	intron (NM_053199, intron 1 of 8)	intron (NM_053199, intron 1 of 8)	-16661	NM_010045	13349	Mm.6393	NM_010045	ENSMUSG00000037872	Ackr1	AA162249|CCBP1|CD234|Darc|Dfy|ESTM35|FY|GPD	atypical chemokine receptor 1 (Duffy blood group)	protein-coding
mm_100905.1	chr11	6213744	6213752	-	1	NA	intron (NM_207242, intron 18 of 18)	intron (NM_207242, intron 18 of 18)	-13297	NM_173748	209586	Mm.25321	NM_173748	ENSMUSG00000053838	Nudcd3	AI427847|BC024322|mKIAA1068	NudC domain containing 3	protein-coding
mm_132266.1	chr16	32877776	32877831	+	1	NA	promoter-TSS (NM_001159349)	promoter-TSS (NM_001159349)	19	NM_001159349	69823	Mm.12831	NM_027226	ENSMUSG00000022800	Fyttd1	2010005M05Rik|3830411L18Rik|3830421F13Rik|4933423A17Rik|AI098218|AW539567|C85190	forty-two-three domain containing 1	protein-coding
mm_601.1	chr1	39900884	39900963	+	1	NA	promoter-TSS (NM_001252202)	promoter-TSS (NM_001252202)	10	NM_008696	26921	Mm.491139	NM_008696	ENSMUSG00000026074	Map4k4	9430080K19Rik|AU043147|AU045934|AW046177|HGK|Nik	mitogen-activated protein kinase kinase kinase kinase 4	protein-coding
mm_143288.1	chr17	65867616	65867650	-	1	NA	exon (NM_001198949, exon 2 of 10)	exon (NM_001198949, exon 2 of 10)	17290	NM_001198949	19765	Mm.17009	NM_009067	ENSMUSG00000024096	Ralbp1	RLIP76|Rip1	ralA binding protein 1	protein-coding
mm_167752.1	chr9	110420886	110420889	+	1	NA	exon (NM_008694, exon 2 of 4)	exon (NM_008694, exon 2 of 4)	1079	NM_008694	18054	Mm.236225	NM_008694	ENSMUSG00000032484	Ngp	bectenecin	neutrophilic granule protein	protein-coding
mm_110683.1	chr12	67122900	67122902	-	1	NA	intron (NM_001193266, intron 1 of 16)	intron (NM_001193266, intron 1 of 16)	99648	NM_001193266	320772	Mm.227680	NM_207010	ENSMUSG00000034912	Mdga2	6720489L24Rik|9330209L04Rik|Adp|Mamdc1	MAM domain containing glycosylphosphatidylinositol anchor 2	protein-coding
mm_106278.1	chr11	118130689	118130704	-	1	NA	Intergenic	Intergenic	-1477	NM_001167746	69926	Mm.473893	NM_001167746	ENSMUSG00000033987	Dnah17	2810003K23Rik|Dnahc17|Dnahcl1|Gm1178|mKIAA3028	dynein, axonemal, heavy chain 17	protein-coding
mm_104118.1	chr11	86741142	86741165	-	1	NA	intron (NM_001003908, intron 1 of 31)	B1_Mus1|SINE|Alu	16339	NM_001003908	67300	Mm.254588	NM_001003908	ENSMUSG00000047126	Cltc	3110065L21Rik|CHC|R74732	clathrin, heavy polypeptide (Hc)	protein-coding
mm_39371.1	chr5	12374656	12374670	+	1	NA	Intergenic	RMER17C2|LTR|ERVK	-8503	NM_028882	108151	Mm.89313	NM_028882	ENSMUSG00000040254	Sema3d	4631426B19Rik	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D	protein-coding
mm_110530.1	chr12	54986364	54986381	-	1	NA	promoter-TSS (NM_013815)	promoter-TSS (NM_013815)	-36	NM_013815	217578	Mm.479583	NM_013815	ENSMUSG00000035021	Baz1a	Acf1|B930060C03|BC065123|Gtl5|Wcrf180|cbp146	bromodomain adjacent to zinc finger domain 1A	protein-coding
mm_154598.1	chrX	7593246	7593252	+	1	NA	TTS (NM_138603)	TTS (NM_138603)	12171	NM_138603	54638	Mm.288192	NM_138603	ENSMUSG00000031143	Ccdc22	AI481216|DXImx40e|Ppp1r3f|Sfc22	coiled-coil domain containing 22	protein-coding
mm_25783.1	chr3	126653530	126653532	+	1	NA	intron (NM_001346636, intron 2 of 20)	intron (NM_001346636, intron 2 of 20)	56580	NM_023813	108058	Mm.255822	NM_023813	ENSMUSG00000053819	Camk2d	2810011D23Rik|8030469K03Rik|CaMK II|[d]-CaMKII	calcium/calmodulin-dependent protein kinase II, delta	protein-coding
mm_171925.1	chr5	5998838	5998839	+	1	NA	Intergenic	RLTR9E|LTR|ERVK	-249521	NM_027399	70358	Mm.85429	NM_027399	ENSMUSG00000015652	Steap1	2410007B19Rik|Prss24|Steap	six transmembrane epithelial antigen of the prostate 1	protein-coding
mm_131064.1	chr16	4594684	4594735	+	1	NA	promoter-TSS (NM_031184)	promoter-TSS (NM_031184)	-4	NM_031184	83396	Mm.134072	NM_031184	ENSMUSG00000014303	Glis2	Gli5|Klf16|Nkl	GLIS family zinc finger 2	protein-coding
mm_16932.1	chr2	13794033	13794041	-	1	NA	promoter-TSS (NM_145838)	promoter-TSS (NM_145838)	-517	NM_145838	241230	Mm.330004	NM_145838	ENSMUSG00000003418	St8sia6	1700007J08Rik|AI314453|AI875066|ST8SiaVI|Siat8f	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 6	protein-coding
mm_101758.1	chr11	43425688	43425695	-	1	NA	5' UTR (NM_013917, exon 1 of 4)	5' UTR (NM_013917, exon 1 of 4)	290	NM_013917	30939	Mm.6856	NM_013917	ENSMUSG00000020415	Pttg1	AW555095|C87862|Pttg|Pttg3	pituitary tumor-transforming gene 1	protein-coding
mm_107451.1	chr12	36816249	36816249	+	1	NA	promoter-TSS (NR_039558)	promoter-TSS (NR_039558)	44	NR_039558	100628578		NR_039558	ENSMUSG00000092998	Mir5099	mmu-mir-5099|mu-mir-5099	microRNA 5099	ncRNA
mm_153927.1	chr19	47343577	47343591	-	1	NA	intron (NM_001164717, intron 5 of 13)	CpG	-69995	NR_105961	102466782		NR_105961	ENSMUSG00000098786	Mir6995	Gm27576|mmu-mir-6995	microRNA 6995	ncRNA
mm_124567.1	chr14	124192354	124192427	-	1	NA	exon (NM_010201, exon 1 of 5)	exon (NM_010201, exon 1 of 5)	156	NM_010201	14169	Mm.206362	NM_010201	ENSMUSG00000025551	Fgf14	FHF-4|Fhf4|mFHF-4(1B)	fibroblast growth factor 14	protein-coding
mm_153427.1	chr19	40821472	40821478	-	1	NA	Intergenic	Intergenic	-9804	NM_172839	240665	Mm.309	NM_172839	ENSMUSG00000025010	Ccnj	D430039C20Rik	cyclin J	protein-coding
mm_166117.1	chr4	150797956	150797957	-	1	NA	Intergenic	Intergenic	56993	NR_040649	73348	Mm.396218	NR_040649	ENSMUSG00000078492	1700045H11Rik	-	RIKEN cDNA 1700045H11 gene	ncRNA
mm_38690.1	chr4	145212774	145212785	-	1	NA	3' UTR (NM_011610, exon 10 of 10)	3' UTR (NM_011610, exon 10 of 10)	-17774	NM_001276465	230895	Mm.240310	NM_001033190	ENSMUSG00000020220	Vps13d	-	vacuolar protein sorting 13D	protein-coding
mm_9732.1	chr1	180229960	180230000	-	1	NA	intron (NM_001128605, intron 7 of 10)	intron (NM_001128605, intron 7 of 10)	15970	NM_011183	19165	Mm.330850	NM_011183	ENSMUSG00000010609	Psen2	ALG-3|Ad4h|Alg3|PS-2|PS2|Psnl2|STM2	presenilin 2	protein-coding
mm_99206.1	chr11	101022959	101022972	+	1	NA	intron (NM_001243050, intron 5 of 20)	intron (NM_001243050, intron 5 of 20)	-7375	NR_105893	102466767		NR_105893	ENSMUSG00000098415	Mir6928	Gm27728|mmu-mir-6928	microRNA 6928	ncRNA
mm_171722.1	chr4	86856356	86856359	-	1	NA	intron (NM_009096, intron 2 of 4)	intron (NM_009096, intron 2 of 4)	1010	NM_009096	20104	Mm.379007	NM_009096	ENSMUSG00000028495	Rps6	S6R	ribosomal protein S6	protein-coding
mm_4460.1	chr1	172699371	172699379	+	1	NA	3' UTR (NM_007768, exon 2 of 2)	3' UTR (NM_007768, exon 2 of 2)	1319	NM_007768	12944	Mm.28767	NM_007768	ENSMUSG00000037942	Crp	AI255847	C-reactive protein, pentraxin-related	protein-coding
mm_74907.1	chr8	25205849	25205859	-	1	NA	Intergenic	Intergenic	-4312	NM_177089	320165	Mm.308452	NM_177089	ENSMUSG00000065954	Tacc1	4833447E04Rik|AA960202|B230378H13Rik	transforming, acidic coiled-coil containing protein 1	protein-coding
mm_3891.1	chr1	161395432	161395439	+	1	NA	promoter-TSS (NM_009452)	promoter-TSS (NM_009452)	-3	NM_009452	22164	Mm.4994	NM_009452	ENSMUSG00000026700	Tnfsf4	Ath-1|Ath1|CD134L|OX-40L|Ox40l|TXGP1|Tnlg2b|Txgp1l|gp34	tumor necrosis factor (ligand) superfamily, member 4	protein-coding
mm_18357.1	chr2	58268034	58268037	-	1	NA	3' UTR (NM_001111030, exon 9 of 9)	3' UTR (NM_001111030, exon 9 of 9)	-8744	NR_040365	100502932	Mm.417207	NR_040365	ENSMUSG00000086995	Gm13544	OTTMUSG00000012672	predicted gene 13544	ncRNA
mm_67661.1	chr7	86775760	86775776	-	1	NA	promoter-TSS (NM_001159706)	promoter-TSS (NM_001159706)	96	NM_016770	53320	Mm.269137	NM_016770	ENSMUSG00000001773	Folh1	GCP2|mopsm	folate hydrolase 1	protein-coding
mm_86191.1	chr9	119564693	119564705	-	1	NA	intron (NM_021544, intron 1 of 27)	intron (NM_021544, intron 1 of 27)	-2021	NM_001253860	20271	Mm.103584	NM_021544	ENSMUSG00000032511	Scn5a	Nav1.5|Nav1.5c|SkM1|SkM2|mH1	sodium channel, voltage-gated, type V, alpha	protein-coding
mm_80345.1	chr9	75167226	75167238	+	1	NA	intron (NM_010864, intron 19 of 40)	intron (NM_010864, intron 19 of 40)	-64782	NM_001081322	208943	Mm.41339	NM_001081322	ENSMUSG00000033590	Myo5c	9130003O20Rik|BB085560|C330029I24	myosin VC	protein-coding
mm_43551.1	chr5	137571375	137571395	+	1	NA	exon (NM_001289507, exon 2 of 18)	exon (NM_001289507, exon 2 of 18)	580	NM_001289507	50765	Mm.21757	NM_015799	ENSMUSG00000029716	Tfr2	Trfr2	transferrin receptor 2	protein-coding
mm_35265.1	chr4	19895758	19895780	-	1	NA	intron (NM_175406, intron 2 of 7)	intron (NM_175406, intron 2 of 7)	26797	NM_175406	242341	Mm.19298	NM_175406	ENSMUSG00000028238	Atp6v0d2	1620401A02Rik|AI324824|V-ATPase	ATPase, H+ transporting, lysosomal V0 subunit D2	protein-coding
mm_29794.1	chr3	127691292	127691304	-	1	NA	intron (NM_027808, intron 4 of 13)	intron (NM_027808, intron 4 of 13)	58153	NM_009718	11924	Mm.42017	NM_009718	ENSMUSG00000027967	Neurog2	Atoh4|Math4A|bHLHa8|ngn-2|ngn2	neurogenin 2	protein-coding
mm_8967.1	chr1	165194311	165194366	-	1	NA	promoter-TSS (NM_145512)	promoter-TSS (NM_145512)	95	NM_145512	108735	Mm.288369	NM_145512	ENSMUSG00000040848	Sft2d2	2010005O13Rik|AI506168|AW561909|cI-45	SFT2 domain containing 2	protein-coding
mm_4951.1	chr1	191224463	191224521	+	1	NA	Intergenic	CpG	-41159	NM_007498	11910	Mm.2706	NM_007498	ENSMUSG00000026628	Atf3	LRG-21	activating transcription factor 3	protein-coding
mm_137613.1	chr17	28271688	28271737	+	1	NA	promoter-TSS (NR_045427)	promoter-TSS (NR_045427)	4	NR_045427	69050	Mm.486938	NR_045427	ENSMUSG00000002250	1810013A23Rik	-	RIKEN cDNA 1810013A23 gene	ncRNA
mm_58126.1	chr6	140101164	140101172	-	1	NA	Intergenic	Intergenic	59643	NM_007605	12344	Mm.12817	NM_007605	ENSMUSG00000041791	Capza3	510-4|Cappa3|Gsg3|Tex8|repro32	capping protein (actin filament) muscle Z-line, alpha 3	protein-coding
mm_114835.1	chr13	92530908	92530923	+	1	NA	promoter-TSS (NM_173392)	promoter-TSS (NM_173392)	-105	NM_173392	218441	Mm.259585	NM_173392	ENSMUSG00000021706	Zfyve16	AI035632|B130024H06Rik|B130031L15|mKIAA0305	zinc finger, FYVE domain containing 16	protein-coding
mm_119664.1	chr14	52279582	52279630	+	1	NA	promoter-TSS (NM_172601)	promoter-TSS (NM_172601)	-211	NM_172601	76338	Mm.32870	NM_172601	ENSMUSG00000022159	Rab2b	1500012D09Rik|4930528G15Rik|A230002G14|D530043M21Rik	RAB2B, member RAS oncogene family	protein-coding
mm_81481.1	chr9	109948278	109948281	+	1	NA	intron (NM_001205330, intron 1 of 18)	ID_B1|SINE|B4	16505	NM_008633	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_33860.1	chr4	135911809	135911826	+	1	NA	5' UTR (NM_001305278, exon 1 of 2)	5' UTR (NM_001305278, exon 1 of 2)	137	NM_001305278	12802	Mm.297251	NM_009924	ENSMUSG00000062585	Cnr2	CB-2|CB2|CB2-R	cannabinoid receptor 2 (macrophage)	protein-coding
mm_88962.1	chr10	81394091	81394110	+	1	NA	exon (NM_001099917, exon 3 of 4)	exon (NM_001099917, exon 3 of 4)	1036	NM_001099917	72273	Mm.253147	NM_001099917	ENSMUSG00000078439	Smim24	2210404O07Rik	small integral membrane protein 24	protein-coding
mm_755.1	chr1	43887987	43888008	+	1	NA	Intergenic	Intergenic	-45997	NM_001310540	22019	Mm.401675	NM_009418	ENSMUSG00000041763	Tpp2	TPP-2|TppII	tripeptidyl peptidase II	protein-coding
mm_98844.1	chr11	97629842	97629886	+	1	NA	promoter-TSS (NM_175332)	promoter-TSS (NM_175332)	-148	NM_175332	103551	Mm.24506	NM_175332	ENSMUSG00000043439	Epop	AA409164|AI413509|AW539173|E13|E130012A19Rik|esPRC2p48	elongin BC and polycomb repressive complex 2 associated protein	protein-coding
mm_171360.1	chr4	117156112	117156112	-	1	NA	promoter-TSS (NR_030704)	promoter-TSS (NR_030704)	20	NM_009098	20116	Mm.260904	NM_009098	ENSMUSG00000047675	Rps8	-	ribosomal protein S8	protein-coding
mm_11909.1	chr2	52037986	52038001	+	1	NA	promoter-TSS (NM_009398)	promoter-TSS (NM_009398)	-120	NM_009398	21930	Mm.3509	NM_009398	ENSMUSG00000053475	Tnfaip6	TSG-6|Tnfip6|Tsg6	tumor necrosis factor alpha induced protein 6	protein-coding
mm_62412.1	chr7	101241057	101241061	+	1	NA	intron (NM_199012, intron 9 of 20)	L1_Mus3|LINE|L1	61029	NM_001111111	73683	Mm.275744	NM_001111111	ENSMUSG00000047767	Atg16l2	2410118P20Rik	autophagy related 16-like 2 (S. cerevisiae)	protein-coding
mm_55915.1	chr6	83775670	83775676	-	1	NA	exon (NM_009357, exon 1 of 6)	exon (NM_009357, exon 1 of 6)	139	NM_009357	21766	Mm.28371	NM_009357	ENSMUSG00000014748	Tex261	3110001O07Rik|AA409339|AI480706|AL033351|TEG-261	testis expressed gene 261	protein-coding
mm_106173.1	chr11	116680057	116680068	-	1	NA	intron (NM_009180, intron 6 of 8)	intron (NM_009180, intron 6 of 8)	5465	NR_028570	100216538		NR_028570	ENSMUSG00000065094	Snord1a	snR38	small nucleolar RNA, C/D box 1A	snoRNA
mm_113046.1	chr13	23578334	23578337	+	1	NA	Intergenic	Intergenic	2572	NM_178204	319149	Mm.347699	NM_178204	ENSMUSG00000099583	Hist1h3d	H3-b	histone cluster 1, H3d	protein-coding
mm_126057.1	chr15	76950168	76950174	+	1	NA	intron (NM_001347540, intron 4 of 4)	intron (NM_001347540, intron 4 of 4)	1627	NM_054099	117171	Mm.322968	NM_054099	ENSMUSG00000063236	1110038F14Rik	-	RIKEN cDNA 1110038F14 gene	protein-coding
mm_108103.1	chr12	75277716	75277723	+	1	NA	Intergenic	LTR16E1|LTR|ERVL	-30594	NM_023275	80837	Mm.27467	NM_023275	ENSMUSG00000046768	Rhoj	1110005O19Rik|AW210585|Arhj|TC10L|TCL	ras homolog family member J	protein-coding
mm_28030.1	chr3	83046820	83046846	-	1	NA	exon (NM_181849, exon 2 of 8)	exon (NM_181849, exon 2 of 8)	3030	NM_181849	110135	Mm.30063	NM_181849	ENSMUSG00000033831	Fgb	2510049G14Rik	fibrinogen beta chain	protein-coding
mm_96257.1	chr11	62603116	62603166	+	1	NA	promoter-TSS (NR_028526)	promoter-TSS (NR_028526)	55	NR_028526	100217426		NR_028526	ENSMUSG00000064437	Snord49b	MBII-252|MBII-366	small nucleolar RNA, C/D box 49B	snoRNA
mm_73309.1	chr8	105170843	105170923	+	1	NA	5' UTR (NM_001161458, exon 1 of 6)	5' UTR (NM_001161458, exon 1 of 6)	209	NM_001161458	12400	Mm.2018	NM_022309	ENSMUSG00000031885	Cbfb	AI893578|PEA2|PEBP2b|Pebp2|Pebpb2	core binding factor beta	protein-coding
mm_63662.1	chr7	129591860	129591871	+	1	NA	promoter-TSS (NM_172255)	promoter-TSS (NM_172255)	2	NM_172255	207425	Mm.229323	NM_172255	ENSMUSG00000042055	Wdr11	2900055P10Rik|AW489876|Brwd2|mKIAA1351	WD repeat domain 11	protein-coding
mm_123805.1	chr14	70521021	70521027	-	1	NA	promoter-TSS (NM_009755)	promoter-TSS (NM_009755)	-764	NR_033241	12153	Mm.27757	NM_009755	ENSMUSG00000022098	Bmp1	Pcp|Tld	bone morphogenetic protein 1	protein-coding
mm_71380.1	chr8	45885530	45885540	+	1	NA	promoter-TSS (NM_016798)	promoter-TSS (NM_016798)	50	NM_016798	53318	Mm.282900	NM_016798	ENSMUSG00000031636	Pdlim3	AI463105|ALP|Actn2lp	PDZ and LIM domain 3	protein-coding
mm_113943.1	chr13	49766331	49766346	+	1	NA	Intergenic	Intergenic	84208	NM_172015	105148	Mm.21118	NM_172015	ENSMUSG00000037851	Iars	2510016L12Rik|AI327140|AU044614|E430001P04Rik|ILRS	isoleucine-tRNA synthetase	protein-coding
mm_154351.1	chrM	5836	5848	+	1	NA	NA	Intergenic	NA	NA								
mm_66291.1	chr7	38018022	38018025	-	1	NA	intron (NM_011274, intron 1 of 10)	Lx8|LINE|L1	1529	NM_011274	19777	Mm.387220	NM_011274	ENSMUSG00000030421	Uri1	C80913|NNX3|Rmp	URI1, prefoldin-like chaperone	protein-coding
mm_91492.1	chr10	37135808	37135822	-	1	NA	3' UTR (NM_008538, exon 2 of 2)	3' UTR (NM_008538, exon 2 of 2)	3111	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_40188.1	chr5	36464793	36464797	+	1	NA	promoter-TSS (NM_024478)	promoter-TSS (NM_024478)	59	NR_126490	76710	Mm.165495	NR_126488	ENSMUSG00000039563	2210406O10Rik	-	RIKEN cDNA 2210406O10 gene	ncRNA
mm_83732.1	chr9	51057012	51057029	-	1	NA	3' UTR (NM_001033534, exon 8 of 8)	3' UTR (NM_001033534, exon 8 of 8)	20074	NM_001033534	244864	Mm.335152	NM_001033534	ENSMUSG00000060594	Layn	E030012M19Rik|Gm511	layilin	protein-coding
mm_163192.1	chr11	94991186	94991219	+	1	NA	promoter-TSS (NM_172261)	promoter-TSS (NM_172261)	-10	NM_172261	217124	Mm.229087	NM_172261	ENSMUSG00000038976	Ppp1r9b	SPL|Spn	protein phosphatase 1, regulatory subunit 9B	protein-coding
mm_68386.1	chr7	109439077	109439083	-	1	NA	promoter-TSS (NM_054103)	promoter-TSS (NM_054103)	-27	NM_054103	117229	Mm.389950	NM_054103	ENSMUSG00000031027	Stk33	4921505G21Rik|AW061264	serine/threonine kinase 33	protein-coding
mm_62602.1	chr7	105736777	105736785	+	1	NA	promoter-TSS (NM_025897)	promoter-TSS (NM_025897)	56	NM_010562	16202	Mm.274846	NM_010562	ENSMUSG00000030890	Ilk	AA511515|ESTM24	integrin linked kinase	protein-coding
mm_97460.1	chr11	78245744	78245821	+	1	NA	promoter-TSS (NM_009143)	promoter-TSS (NM_009143)	36	NM_009143	20316	Mm.20755	NM_009143	ENSMUSG00000002064	Sdf2	AI853825	stromal cell derived factor 2	protein-coding
mm_10015.1	chr1	192061723	192061736	-	1	NA	intron (NM_011633, intron 4 of 9)	(TG)n|Simple_repeat|Simple_repeat	30870	NM_011633	22033	Mm.380491	NM_011633		Traf5	-	TNF receptor-associated factor 5	protein-coding
mm_104031.1	chr11	86257418	86257419	-	1	NA	5' UTR (NM_027421, exon 1 of 25)	5' UTR (NM_027421, exon 1 of 25)	150	NM_027421	70422	Mm.171304	NM_027421	ENSMUSG00000018068	Ints2	2810417D08Rik|AA408260|AI987735|mKIAA1287	integrator complex subunit 2	protein-coding
mm_99136.1	chr11	100320494	100320515	+	1	NA	intron (NM_011508, intron 1 of 3)	CpG	555	NM_011508	20918	Mm.13886	NM_011508	ENSMUSG00000035530	Eif1	Sui1-rs1	eukaryotic translation initiation factor 1	protein-coding
mm_156260.1	chrX	136822782	136822840	+	1	NA	promoter-TSS (NM_011123)	promoter-TSS (NM_011123)	65	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_60301.1	chr7	44052298	44052306	+	1	NA	promoter-TSS (NM_020268)	promoter-TSS (NM_020268)	12	NM_020268	16619	Mm.445911	NM_020268	ENSMUSG00000063177	Klk1b27	Gk27|Klk21l|Klk27|mGK-27	kallikrein 1-related peptidase b27	protein-coding
mm_30874.1	chr4	32238714	32238802	+	1	NA	Intergenic	CpG	-178677	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_101913.1	chr11	49712675	49712726	-	1	NA	promoter-TSS (NM_212484)	promoter-TSS (NM_212484)	22	NM_212484	104625	Mm.247113	NM_212484	ENSMUSG00000020362	Cnot6	CCR4	CCR4-NOT transcription complex, subunit 6	protein-coding
mm_125230.1	chr15	34134360	34134401	+	1	NA	exon (NM_026002, exon 9 of 12)	exon (NM_026002, exon 9 of 12)	51661	NM_026002	67154	Mm.130883	NM_026002	ENSMUSG00000022255	Mtdh	2610103J23Rik|3D3|3D3/Lyric|AEG-1|AV353288|D8Bwg1112e|Lyric	metadherin	protein-coding
mm_47054.1	chr5	116289001	116289009	-	1	NA	promoter-TSS (NM_177759)	promoter-TSS (NM_177759)	-20	NM_177759	269693	Mm.10946	NM_177759	ENSMUSG00000043913	Ccdc60	AU018954|C130098D09	coiled-coil domain containing 60	protein-coding
mm_84694.1	chr9	72400236	72400248	-	1	NA	Intergenic	Intergenic	-38287	NM_008613	17427	Mm.387671	NM_008613	ENSMUSG00000032221	Mns1	AW546487	meiosis-specific nuclear structural protein 1	protein-coding
mm_142771.1	chr17	49564263	49564322	-	1	NA	promoter-TSS (NM_001008231)	promoter-TSS (NM_001008231)	45	NM_001008231	76441	Mm.211275	NM_001008231	ENSMUSG00000040260	Daam2	2310016D11Rik|AI843643|AW557870	dishevelled associated activator of morphogenesis 2	protein-coding
mm_86213.1	chr9	120012837	120012846	-	1	NA	TTS (NM_011724)	TTS (NM_011724)	10757	NM_011724	22437	Mm.10117	NM_011724	ENSMUSG00000079243	Xirp1	AI415219|Cmya1	xin actin-binding repeat containing 1	protein-coding
mm_145953.1	chr18	67641590	67641630	+	1	NA	promoter-TSS (NM_001081073)	promoter-TSS (NM_001081073)	11	NM_134138	107047	Mm.150701	NM_134138	ENSMUSG00000024537	Psmg2	1700017I17Rik|AW545363|Clast3|Tnfsf5ip1	proteasome (prosome, macropain) assembly chaperone 2	protein-coding
mm_115905.1	chr13	23423837	23423884	-	1	NA	promoter-TSS (NM_013924)	promoter-TSS (NM_013924)	6	NM_013924	30946	Mm.292094	NM_013924	ENSMUSG00000036376	Abt1	-	activator of basal transcription 1	protein-coding
mm_18338.1	chr2	58137745	58137780	-	1	NA	intron (NM_139200, intron 7 of 7)	intron (NM_139200, intron 7 of 7)	22360	NM_139200	227929	Mm.273905	NM_139200	ENSMUSG00000026832	Cytip	A130053M09Rik|AI462064|C80816|Cbp|Cybr|Pscdbp	cytohesin 1 interacting protein	protein-coding
mm_142406.1	chr17	45461618	45461631	-	1	NA	intron (NM_027649, intron 2 of 7)	RSINE1|SINE|B4	13314	NM_027649	71020	Mm.44257	NM_027649	ENSMUSG00000023935	Spats1	1700011H05Rik|4933400B06Rik|Daip2|Ddip|Srsp1	spermatogenesis associated, serine-rich 1	protein-coding
mm_99423.1	chr11	102393420	102393496	+	1	NA	promoter-TSS (NM_001252347)	promoter-TSS (NM_001252347)	55	NM_001252347	51799	Mm.2560	NM_016759	ENSMUSG00000006575	Rundc3a	RPIP-8|Rap2ip|Rpip8	RUN domain containing 3A	protein-coding
mm_169370.1	chr14	3412630	3412647	+	1	NA	promoter-TSS (NR_033121)	promoter-TSS (NR_033121)	24	NR_033121	100041530	Mm.444311	NR_033121	ENSMUSG00000096488	Gm10409	EG666890|ENSMUSG00000072740|Gm8348	predicted pseudogene 8348	pseudo
mm_13917.1	chr2	120587770	120587772	+	1	NA	intron (NM_009222, intron 5 of 7)	B2_Mm2|SINE|B2	20100	NM_009222	20619	Mm.245715	NM_009222	ENSMUSG00000027287	Snap23	23kDa|AA408749|SNAP-23|Sndt|Syndet	synaptosomal-associated protein 23	protein-coding
mm_19388.1	chr2	91312665	91312675	-	1	NA	intron (NM_001311144, intron 3 of 8)	intron (NM_001311144, intron 3 of 8)	47555	NM_023854	77038	Mm.43636	NM_023854	ENSMUSG00000027255	Arfgap2	2310032E02Rik|Zfp289	ADP-ribosylation factor GTPase activating protein 2	protein-coding
mm_57916.1	chr6	133851978	133851989	-	1	NA	exon (NM_010594, exon 2 of 4)	exon (NM_010594, exon 2 of 4)	1684	NM_010594	16483	Mm.13052	NM_010594	ENSMUSG00000032758	Kap	AW146435|FKSG22	kidney androgen regulated protein	protein-coding
mm_107060.1	chr12	16653989	16654003	+	1	NA	exon (NM_008747, exon 1 of 4)	exon (NM_008747, exon 1 of 4)	526	NM_008747	18217	Mm.281715	NM_008747	ENSMUSG00000020591	Ntsr2	NT2R|NTRL	neurotensin receptor 2	protein-coding
mm_101429.1	chr11	29944790	29944798	-	1	NA	intron (NM_146016, intron 2 of 41)	intron (NM_146016, intron 2 of 41)	81239	NM_146016	237711	Mm.445271	NM_146016	ENSMUSG00000044072	Eml6	2900083P10Rik|C230094A16Rik|EMAP-6	echinoderm microtubule associated protein like 6	protein-coding
mm_139125.1	chr17	47505044	47505066	+	1	NA	promoter-TSS (NM_001081636)	promoter-TSS (NM_001081636)	4	NM_001081635	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_48699.1	chr5	146920375	146920383	-	1	NA	Intergenic	Intergenic	-28278	NM_025652	66596	Mm.196528	NM_025652	ENSMUSG00000016503	Gtf3a	2010015D03Rik|2610111I01Rik|5330403M05Rik	general transcription factor III A	protein-coding
mm_145329.1	chr18	55939476	55939485	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	-492652	NM_026240	107022	Mm.24356	NM_026240	ENSMUSG00000001700	Gramd3	9030613F08Rik|9130427A09Rik|AW061306|NS3TP2	GRAM domain containing 3	protein-coding
mm_46676.1	chr5	109553185	109553216	-	1	NA	Intergenic	Intergenic	5793	NM_016715	57914	Mm.35771	NM_016715	ENSMUSG00000033467	Crlf2	CRLM2|Ly114|Tpte2|Tslpr	cytokine receptor-like factor 2	protein-coding
mm_52492.1	chr6	114652403	114652418	+	1	NA	intron (NM_001253718, intron 2 of 19)	intron (NM_001253718, intron 2 of 19)	9313	NM_001253717	74244	Mm.275332	NM_028835	ENSMUSG00000030314	Atg7	1810013K23Rik|Agp7|Apg7l|Atg7l|Gm21553	autophagy related 7	protein-coding
mm_151461.1	chr19	58606325	58606333	+	1	NA	promoter-TSS (NR_038136)	promoter-TSS (NR_038136)	0	NR_038136	69055	Mm.396318	NR_038136	ENSMUSG00000100001	1810007D17Rik	-	RIKEN cDNA 1810007D17 gene	ncRNA
mm_95984.1	chr11	58978411	58978421	+	1	NA	exon (NM_053168, exon 1 of 6)	exon (NM_053168, exon 1 of 6)	323	NM_053168	94091	Mm.248049	NM_053168	ENSMUSG00000020455	Trim11	-	tripartite motif-containing 11	protein-coding
mm_71139.1	chr8	39046025	39046036	+	1	NA	intron (NM_030254, intron 1 of 7)	intron (NM_030254, intron 1 of 7)	40163	NM_030254	80286	Mm.272722	NM_030254	ENSMUSG00000039530	Tusc3	AU022242|BC003311|N33	tumor suppressor candidate 3	protein-coding
mm_108426.1	chr12	82206130	82206133	+	1	NA	intron (NM_001167983, intron 1 of 23)	intron (NM_001167983, intron 1 of 23)	36115	NM_001167983	217692	Mm.261333	NM_172579	ENSMUSG00000042700	Sipa1l1	4931426N11Rik|AW213287|Spar|mKIAA0440	signal-induced proliferation-associated 1 like 1	protein-coding
mm_118423.1	chr14	7890616	7890624	+	1	NA	intron (NM_134080, intron 10 of 45)	intron (NM_134080, intron 10 of 45)	72663	NM_134080	286940	Mm.489652	NM_134080	ENSMUSG00000025278	Flnb	AL024016|Fln-b	filamin, beta	protein-coding
mm_164401.1	chr16	34921064	34921075	+	1	NA	exon (NM_139300, exon 15 of 32)	exon (NM_139300, exon 15 of 32)	18260	NR_040536	76649	Mm.420532	NR_040536	ENSMUSG00000100593	1700119H24Rik	-	RIKEN cDNA 1700119H24 gene	ncRNA
mm_95649.1	chr11	53724100	53724111	+	1	NA	3' UTR (NM_010558, exon 4 of 4)	3' UTR (NM_010558, exon 4 of 4)	3311	NM_010558	16191	Mm.4461	NM_010558	ENSMUSG00000036117	Il5	Il-5	interleukin 5	protein-coding
mm_95219.1	chr11	44215587	44215602	+	1	NA	Intergenic	Tigger7|DNA|TcMar-Tigger	-184469	NM_001303244	16160	Mm.239707	NM_008352	ENSMUSG00000004296	Il12b	Il-12b|Il-12p40|Il12p40|p40	interleukin 12b	protein-coding
mm_5433.1	chr1	34818073	34818099	-	1	NA	exon (NM_001160236, exon 6 of 7)	exon (NM_001160236, exon 6 of 7)	16364	NM_183019	226970	Mm.41604	NM_183019	ENSMUSG00000037509	Arhgef4	9330140K16Rik|Asef|ENSMUSG00000070955	Rho guanine nucleotide exchange factor (GEF) 4	protein-coding
mm_19599.1	chr2	102400533	102400539	-	1	NA	exon (NM_020267, exon 1 of 5)	exon (NM_020267, exon 1 of 5)	364	NM_020267	80985	Mm.315002	NM_020267	ENSMUSG00000027189	Trim44	Dipb|Mc7	tripartite motif-containing 44	protein-coding
mm_105455.1	chr11	104503678	104503725	-	1	NA	3' UTR (NM_145436, exon 19 of 19)	3' UTR (NM_145436, exon 19 of 19)	46919	NM_001285990	217232	Mm.89845	NM_145436	ENSMUSG00000020687	Cdc27	AI452358|APC3|BC023187	cell division cycle 27	protein-coding
mm_85746.1	chr9	108578595	108578656	-	1	NA	promoter-TSS (NM_031392)	promoter-TSS (NM_031392)	45	NM_031392	83669	Mm.335454	NM_031392	ENSMUSG00000066357	Wdr6	mWDR6	WD repeat domain 6	protein-coding
mm_62285.1	chr7	99863495	99863504	+	1	NA	intron (NM_001164258, intron 2 of 18)	intron (NM_001164258, intron 2 of 18)	4281	NM_001164258	446101	Mm.440757	NM_001164258	ENSMUSG00000035211	Xrra1	AI449753	X-ray radiation resistance associated 1	protein-coding
mm_134623.1	chr16	21650078	21650088	-	1	NA	3' UTR (NM_001001881, exon 2 of 2)	3' UTR (NM_001001881, exon 2 of 2)	44582	NM_001001881	72190	Mm.131606	NM_001001881	ENSMUSG00000043391	2510009E07Rik	AI194952	RIKEN cDNA 2510009E07 gene	protein-coding
mm_171856.1	chr5	20127418	20127422	-	1	NA	intron (NM_001170746, intron 3 of 22)	L1Md_T|LINE|L1	219902	NM_015823	50791	Mm.332231	NM_015823	ENSMUSG00000040003	Magi2	AIP-1|Acvri1|Acvrinp1|Acvrip1|Magi-2|S-SCAM|mKIAA0705	membrane associated guanylate kinase, WW and PDZ domain containing 2	protein-coding
mm_102006.1	chr11	51602622	51602639	-	1	NA	exon (NM_010448, exon 6 of 7)	exon (NM_010448, exon 6 of 7)	4251	NM_001048061	15384	Mm.256875	NM_010448	ENSMUSG00000020358	Hnrnpab	3010025C11Rik|CBF-A|Cgbfa|Hnrpab	heterogeneous nuclear ribonucleoprotein A/B	protein-coding
mm_38730.1	chr4	145240762	145240773	-	1	NA	intron (NM_011610, intron 1 of 9)	intron (NM_011610, intron 1 of 9)	6103	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_6052.1	chr1	60098105	60098118	-	1	NA	promoter-TSS (NM_139150)	promoter-TSS (NM_139150)	23	NM_001199061	57750	Mm.281079	NM_021312	ENSMUSG00000026019	Wdr12	4933402C23Rik|Ytm1|Ytm1p	WD repeat domain 12	protein-coding
mm_139160.1	chr17	47546397	47546408	+	1	NA	intron (NM_001081635, intron 1 of 6)	(T)n|Simple_repeat|Simple_repeat	41351	NM_001081635	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_5994.1	chr1	58712223	58712245	-	1	NA	intron (NM_001289704, intron 1 of 9)	intron (NM_001289704, intron 1 of 9)	743	NM_001293804	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_27718.1	chr3	68786855	68786857	-	1	NA	Intergenic	Intergenic	-82730	NM_001167996	68725	Mm.45741	NM_001167996	ENSMUSG00000046999	1110032F04Rik	AI115547	RIKEN cDNA 1110032F04 gene	protein-coding
mm_122807.1	chr14	54575667	54575708	-	1	NA	intron (NM_010590, intron 1 of 7)	CpG	1974	NM_010590	16475	Mm.100253	NM_010590	ENSMUSG00000022178	Ajuba	Jub	ajuba LIM protein	protein-coding
mm_105332.1	chr11	102946549	102946568	-	1	NA	promoter-TSS (NM_011795)	promoter-TSS (NM_011795)	-97	NM_011795	23829	Mm.57154	NM_011795	ENSMUSG00000045532	C1ql1	C1qrf|CRF|CTRP14|gliacolin	complement component 1, q subcomponent-like 1	protein-coding
mm_48202.1	chr5	137533213	137533290	-	1	NA	promoter-TSS (NM_010312)	promoter-TSS (NM_010312)	-22	NM_010312	14693	Mm.30141	NM_010312	ENSMUSG00000029713	Gnb2	Gnb-2	guanine nucleotide binding protein (G protein), beta 2	protein-coding
mm_112532.1	chr13	9418895	9418906	+	1	NA	intron (NM_001081426, intron 1 of 36)	(T)n|Simple_repeat|Simple_repeat	142375	NM_001081426	208440	Mm.217326	NM_172459	ENSMUSG00000048264	Dip2c	2900024P20Rik|9630044M06|mKIAA0934	disco interacting protein 2 homolog C	protein-coding
mm_71441.1	chr8	46513291	46513303	+	1	NA	exon (NM_007981, exon 6 of 21)	exon (NM_007981, exon 6 of 21)	22331	NM_001302163	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_33980.1	chr4	137707459	137707527	+	1	NA	promoter-TSS (NM_001331215)	promoter-TSS (NM_001331215)	-12	NM_001331215	110351	Mm.180763	NM_029563	ENSMUSG00000041351	Rap1gap	1300019I11Rik|2310004O14Rik|AI427470|ARPP-90|Gap|Rap1GAP1|Rap1ga1	Rap1 GTPase-activating protein	protein-coding
mm_132864.1	chr16	48594628	48594680	+	1	NA	intron (NM_010816, intron 20 of 26)	intron (NM_010816, intron 20 of 26)	163417	NM_010816	17450	Mm.250060	NM_010816	ENSMUSG00000022652	Morc1	Morc	microrchidia 1	protein-coding
mm_80372.1	chr9	75347890	75347893	+	1	NA	5' UTR (NM_013479, exon 1 of 2)	5' UTR (NM_013479, exon 1 of 2)	133	NM_013479	12049	Mm.25988	NM_013479	ENSMUSG00000032191	Bcl2l10	AA420380|AU023065|Boo|C85687|Diva	Bcl2-like 10	protein-coding
mm_74194.1	chr8	123805849	123805865	+	1	NA	promoter-TSS (NM_009003)	promoter-TSS (NM_009003)	-139	NM_009003	19341	Mm.9221	NM_009003	ENSMUSG00000019478	Rab4a	AI848268|Rab4	RAB4A, member RAS oncogene family	protein-coding
mm_153707.1	chr19	44397853	44397884	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	9841	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_17103.1	chr2	23961346	23961346	-	1	NA	Intergenic	Intergenic	88033	NM_080462	140483	Mm.33120	NM_080462	ENSMUSG00000026986	Hnmt	1500031F01Rik|AI788969	histamine N-methyltransferase	protein-coding
mm_44324.1	chr5	9725405	9725468	-	1	NA	promoter-TSS (NM_181850)	promoter-TSS (NM_181850)	-84	NM_181850	108069	Mm.318966	NM_181850	ENSMUSG00000003974	Grm3	0710001G23Rik|Gprc1c|mGlu3|mGluR3	glutamate receptor, metabotropic 3	protein-coding
mm_50061.1	chr6	41187393	41187403	+	1	NA	Intergenic	Intergenic	-114874	NM_011646	22074	Mm.383263	NM_011646	ENSMUSG00000054106	Try4	0910001B19Rik|Td	trypsin 4	protein-coding
mm_160444.1	chr8	104293174	104293174	-	1	NA	promoter-TSS (NM_027022)	promoter-TSS (NM_027022)	7	NM_027022	73381	Mm.272746	NM_027022	ENSMUSG00000074127	Cmtm2a	1700001K04Rik|1700041N15Rik|1700063K20Rik|AI449770|ARR19|C32|CKLF3|CKLF4|CKLF5|Cklf|Cklf1|Cklfsf2-1b|Cklfsf2a|UCK-1	CKLF-like MARVEL transmembrane domain containing 2A	protein-coding
mm_51546.1	chr6	83237563	83237580	+	1	NA	5' UTR (NM_001166067, exon 1 of 25)	5' UTR (NM_001166067, exon 1 of 25)	196	NM_001166067	232156	Mm.333189	NM_001166067	ENSMUSG00000068323	Slc4a5	C330006M16|C330016K18Rik	solute carrier family 4, sodium bicarbonate cotransporter, member 5	protein-coding
mm_64069.1	chr7	140882431	140882441	+	1	NA	promoter-TSS (NM_001127351)	promoter-TSS (NM_001127351)	42	NM_011875	23997	Mm.29760	NM_011875	ENSMUSG00000025487	Psmd13	S11	proteasome (prosome, macropain) 26S subunit, non-ATPase, 13	protein-coding
mm_160434.1	chr8	93048129	93048129	-	1	NA	promoter-TSS (NM_001013764)	promoter-TSS (NM_001013764)	63	NM_001013764	244595	Mm.390089	NM_001013764	ENSMUSG00000071047	Ces1a	Ces1l|EG244595|Gm4976	carboxylesterase 1A	protein-coding
mm_124354.1	chr14	105114621	105114754	-	1	NA	promoter-TSS (NR_040628)	promoter-TSS (NR_040628)	-11	NR_040628	100502987	Mm.124957	NR_040628		Gm17066	-	predicted gene 17066	ncRNA
mm_130474.1	chr15	98727556	98727609	-	1	NA	intron (NM_024169, intron 2 of 5)	intron (NM_024169, intron 2 of 5)	616	NM_024169	66120	Mm.30729	NM_024169	ENSMUSG00000003355	Fkbp11	1110002O23Rik|FKBP-11	FK506 binding protein 11	protein-coding
mm_16667.1	chr2	6721891	6721903	-	1	NA	promoter-TSS (NM_001310447)	promoter-TSS (NM_001310447)	-235	NM_001310447	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_109051.1	chr12	104339255	104339269	+	1	NA	intron (NM_011458, intron 1 of 4)	CT-rich|Low_complexity|Low_complexity	776	NM_011458	20714	Mm.291569	NM_011458	ENSMUSG00000058207	Serpina3k	1300001I07Rik|D12Rp54|MMCM2|MMSpi2|RP54|Spi-2|Spi2|contrapsin	serine (or cysteine) peptidase inhibitor, clade A, member 3K	protein-coding
mm_84739.1	chr9	75375959	75375981	-	1	NA	Intergenic	Intergenic	28212	NM_013479	12049	Mm.25988	NM_013479	ENSMUSG00000032191	Bcl2l10	AA420380|AU023065|Boo|C85687|Diva	Bcl2-like 10	protein-coding
mm_39142.1	chr4	155345492	155345494	-	1	NA	5' UTR (NM_001039079, exon 1 of 15)	5' UTR (NM_001039079, exon 1 of 15)	296	NM_001039079	18762	Mm.28561	NM_008860	ENSMUSG00000029053	Prkcz	AI098070|C80388|Pkcz|R74924|aPKCzeta|nPKC-zeta|zetaPKC	protein kinase C, zeta	protein-coding
mm_159144.1	chr2	86413991	86413991	-	1	NA	promoter-TSS (NM_207134)	promoter-TSS (NM_207134)	59	NM_207134	259022	Mm.377793	NM_207134	ENSMUSG00000075185	Olfr1061	MOR188-1|MOR188-7|MOR188-9|Olfr1515	olfactory receptor 1061	protein-coding
mm_93887.1	chr10	125328500	125328510	-	1	NA	promoter-TSS (NM_011391)	promoter-TSS (NM_011391)	30	NM_011391	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|Mct2	solute carrier family 16 (monocarboxylic acid transporters), member 7	protein-coding
mm_89105.1	chr10	84584652	84584662	+	1	NA	intron (NM_146008, intron 1 of 9)	intron (NM_146008, intron 1 of 9)	7710	NM_146008	216198	Mm.296142	NM_146008	ENSMUSG00000020034	Tcp11l2	E430026E19Rik	t-complex 11 (mouse) like 2	protein-coding
mm_13827.1	chr2	119267135	119267173	+	1	NA	Intergenic	Intergenic	4072	NM_145530	228543	Mm.120274	NM_145530	ENSMUSG00000034226	Rhov	A030005A06Rik|Arhv	ras homolog family member V	protein-coding
mm_89543.1	chr10	94575273	94575295	+	1	NA	promoter-TSS (NM_177026)	promoter-TSS (NM_177026)	27	NM_001168684	319880	Mm.23047	NM_172051	ENSMUSG00000020023	Tmcc3	AW488095|C630016B22Rik|C88213|Tmcc1	transmembrane and coiled coil domains 3	protein-coding
mm_102742.1	chr11	67254045	67254054	-	1	NA	exon (NM_010855, exon 28 of 40)	exon (NM_010855, exon 28 of 40)	16237	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_115542.1	chr13	6648782	6648789	-	1	NA	promoter-TSS (NM_001291071)	promoter-TSS (NM_001291071)	-14	NM_001291071	56421	Mm.273874	NM_019703	ENSMUSG00000021196	Pfkp	1200015H23Rik|9330125N24Rik|ATP-PFK|PFK-C|PFK-P	phosphofructokinase, platelet	protein-coding
mm_20311.1	chr2	127247769	127247780	-	1	NA	promoter-TSS (NM_175145)	promoter-TSS (NM_175145)	42	NM_025296	26371	Mm.45179	NM_025296	ENSMUSG00000003662	Ciao1	AW210570|Wdr39	cytosolic iron-sulfur protein assembly 1	protein-coding
mm_5876.1	chr1	53823946	53823963	-	1	NA	intron (NM_001001883, intron 28 of 28)	intron (NM_001001883, intron 28 of 28)	-25470	NR_106149	102465783		NR_106149	ENSMUSG00000098443	Mir7681	Gm27806|mmu-mir-7681	microRNA 7681	ncRNA
mm_24042.1	chr3	87846882	87846893	+	1	NA	5' UTR (NM_021309, exon 1 of 7)	5' UTR (NM_021309, exon 1 of 7)	132	NM_021309	27371	Mm.86361	NM_021309	ENSMUSG00000028071	Sh2d2a	Lad|Ribp|Tsad	SH2 domain containing 2A	protein-coding
mm_142559.1	chr17	46640083	46640118	-	1	NA	exon (NM_029091, exon 5 of 16)	exon (NM_029091, exon 5 of 16)	5044	NM_029091	74764	Mm.279599	NM_029091	ENSMUSG00000003546	Klc4	1200014P03Rik|AA408085|AW146303|Knsl8	kinesin light chain 4	protein-coding
mm_12014.1	chr2	57368449	57368465	+	1	NA	3' UTR (NM_010274, exon 17 of 17)	3' UTR (NM_010274, exon 17 of 17)	130075	NM_010274	14571	Mm.3711	NM_010274	ENSMUSG00000026827	Gpd2	AA408484|AI448216|AU021455|AW494132|GPDH|Gdm1|Gpd-m|Gpdh-m|TISP38	glycerol phosphate dehydrogenase 2, mitochondrial	protein-coding
mm_146357.1	chr18	82579016	82579019	+	1	NA	exon (NM_001025251, exon 6 of 7)	exon (NM_001025251, exon 6 of 7)	24509	NM_001025254	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_96348.1	chr11	66956621	66956667	+	1	NA	promoter-TSS (NR_130315)	promoter-TSS (NR_130315)	6	NR_130315	71576	Mm.340077	NR_130315	ENSMUSG00000085683	9130409J20Rik	-	RIKEN cDNA 9130409J20 gene	ncRNA
mm_171460.1	chr4	145670636	145670637	+	1	NA	promoter-TSS (NM_001103158)	promoter-TSS (NM_001103158)	-61	NM_001103158	100041379	Mm.276881	NM_001103158	ENSMUSG00000058186	Zfp980	Gm13242|OTTMUSG00000011070	zinc finger protein 980	protein-coding
mm_141432.1	chr17	29490285	29490310	-	1	NA	promoter-TSS (NM_008842)	promoter-TSS (NM_008842)	-748	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_49257.1	chr6	17463556	17463581	+	1	NA	promoter-TSS (NM_008591)	promoter-TSS (NM_008591)	-389	NM_008591	17295	Mm.86844	NM_008591	ENSMUSG00000009376	Met	AI838057|HGF|HGFR|Par4|c-Met	met proto-oncogene	protein-coding
mm_170498.1	chr19	24289903	24289910	-	1	NA	Intergenic	Intergenic	-9320	NM_008044	14297	Mm.7319	NM_008044	ENSMUSG00000059363	Fxn	FA|FARR|Frda|X25	frataxin	protein-coding
mm_127931.1	chr15	10482787	10482791	-	1	NA	intron (NM_026396, intron 2 of 9)	PB1D9|SINE|Alu	3148	NM_026396	67832	Mm.28057	NM_026396	ENSMUSG00000022247	Brix1	1110064N10Rik|Bxdc2|C76935	BRX1, biogenesis of ribosomes	protein-coding
mm_64386.1	chr7	142477008	142477018	+	1	NA	promoter-TSS (NM_001271523)	promoter-TSS (NM_001271523)	0	NM_001271523	16985	Mm.234003	NM_019391	ENSMUSG00000018819	Lsp1	Lsp-1|WP34|p50|pp52	lymphocyte specific 1	protein-coding
mm_73784.1	chr8	117095860	117095875	+	1	NA	promoter-TSS (NM_021486)	promoter-TSS (NM_021486)	2	NM_001163028	63857	Mm.174133	NM_021486	ENSMUSG00000031845	Bco1	Bcdo|Bcdo1|Bcmo1|CMO1|Cmoi|beta-CD|betaCMOOX	beta-carotene oxygenase 1	protein-coding
mm_86138.1	chr9	116715437	116715462	-	1	NA	intron (NM_001172122, intron 7 of 13)	(TG)n|Simple_repeat|Simple_repeat	537034	NM_001172123	207181	Mm.326411	NM_178660	ENSMUSG00000039607	Rbms3	6720477E09Rik|8430436O14Rik	RNA binding motif, single stranded interacting protein	protein-coding
mm_76134.1	chr8	81004702	81004704	-	1	NA	intron (NM_027554, intron 3 of 9)	intron (NM_027554, intron 3 of 9)	10203	NM_027554	74841	Mm.246018	NM_027554	ENSMUSG00000038250	Usp38	4631402N15Rik|4833420O05Rik|AA536967|AU044701|AW544820|mKIAA1891	ubiquitin specific peptidase 38	protein-coding
mm_105944.1	chr11	115276893	115276906	-	1	NA	promoter-TSS (NM_007997)	promoter-TSS (NM_007997)	70	NM_007997	14149	Mm.4719	NM_007997	ENSMUSG00000018861	Fdxr	-	ferredoxin reductase	protein-coding
mm_21125.1	chr2	153986456	153986472	-	1	NA	exon (NM_001080811, exon 4 of 11)	exon (NM_001080811, exon 4 of 11)	11519	NM_001080811	545477	Mm.379973	NM_001080811	ENSMUSG00000078998	Bpifa6	EG545477|Gm5840|Splunc6	BPI fold containing family A, member 6	protein-coding
mm_369.1	chr1	33974731	33974737	+	1	NA	intron (NM_001276764, intron 3 of 102)	intron (NM_001276764, intron 3 of 102)	-37091	NM_133833	13518	Mm.336625	NM_010081	ENSMUSG00000026131	Dst	2310001O04Rik|A830042E19Rik|AW554249|BP230|BPAG1-n|Bpag|Bpag1|Macf2|ah|athetoid|dt|mKIAA0728|nmf203|nmf339	dystonin	protein-coding
mm_23685.1	chr3	68691330	68691363	+	1	NA	promoter-TSS (NM_008351)	promoter-TSS (NM_008351)	-78	NM_008351	16159	Mm.103783	NM_008351	ENSMUSG00000027776	Il12a	IL-12p35|Il-12a|Ll12a|p35	interleukin 12a	protein-coding
mm_27206.1	chr3	35754510	35754516	-	1	NA	intron (NM_029570, intron 1 of 29)	CpG	375	NM_029570	76295	Mm.239416	NM_029570	ENSMUSG00000037400	Atp11b	1110019I14Rik|ATPIF|ATPIR|mKIAA0956	ATPase, class VI, type 11B	protein-coding
mm_155702.1	chrX	95325137	95325139	+	1	NA	Intergenic	Intergenic	119702	NM_175179	72345	Mm.182867	NM_175179	ENSMUSG00000050332	Amer1	2810002O09Rik|AW492303|Fam123b|Wtx	APC membrane recruitment 1	protein-coding
mm_40691.1	chr5	65764037	65764060	+	1	NA	intron (NM_001024917, intron 1 of 19)	CpG	527	NM_001024917	333789	Mm.332398	NM_001024917	ENSMUSG00000037795	N4bp2	B3bp|E430014I16|Gm1791|Gm868	NEDD4 binding protein 2	protein-coding
mm_62120.1	chr7	96694805	96694816	+	1	NA	exon (NM_011858, exon 6 of 33)	exon (NM_011858, exon 6 of 33)	106739	NR_045874	791381	Mm.402112	NR_045874	ENSMUSG00000053049	Gm15413	ENSMUSG00000053049|OTTMUSG00000021246	predicted gene 15413	ncRNA
mm_45879.1	chr5	88328320	88328370	-	1	NA	exon (NM_008644, exon 3 of 3)	exon (NM_008644, exon 3 of 3)	11033	NM_008644	17830	Mm.200411	NM_008644	ENSMUSG00000064156	Prol1	Muc10	proline rich, lacrimal 1	protein-coding
mm_48068.1	chr5	136581671	136581680	-	1	NA	Intergenic	Intergenic	-14185	NM_001291238	13047	Mm.320317	NM_009986	ENSMUSG00000029705	Cux1	CDP|Cutl1|Cux|Cux-1	cut-like homeobox 1	protein-coding
mm_143983.1	chr17	87611632	87611635	-	1	NA	Intergenic	ID_B1|SINE|B4	-24346	NM_008532	17075	Mm.4259	NM_008532	ENSMUSG00000045394	Epcam	CD326|EGP|EGP-2|Egp314|Ep-CAM|EpCAM1|GA733-2|Ly74|TROP1|Tacsd1|Tacstd1|gp40	epithelial cell adhesion molecule	protein-coding
mm_103780.1	chr11	82764275	82764277	-	1	NA	promoter-TSS (NM_025884)	promoter-TSS (NM_025884)	45	NM_009839	12467	Mm.4126	NM_009839	ENSMUSG00000020698	Cct6b	CCT-zeta-2|CCTzeta-2|Cctz-2|TCP-1-zeta-2	chaperonin containing Tcp1, subunit 6b (zeta)	protein-coding
mm_131553.1	chr16	18028658	18028662	+	1	NA	Intergenic	Intergenic	-24200	NM_010047	13353	Mm.27155	NM_010047	ENSMUSG00000003531	Dgcr6	-	DiGeorge syndrome critical region gene 6	protein-coding
mm_128179.1	chr15	34495151	34495159	-	1	NA	promoter-TSS (NM_008287)	promoter-TSS (NM_008287)	91	NM_008287	15473	Mm.491154	NM_008287	ENSMUSG00000022323	Rida	HR12|HRP12|Hrsp12	reactive intermediate imine deaminase A homolog	protein-coding
mm_79147.1	chr9	47708898	47708902	+	1	NA	intron (NM_001025600, intron 1 of 8)	intron (NM_001025600, intron 1 of 8)	109308	NR_046048	100038460	Mm.447649	NR_046048		Gm10677	ENSMUSG00000074363	predicted gene 10677	ncRNA
mm_72343.1	chr8	79639352	79639398	+	1	NA	promoter-TSS (NM_001256033)	promoter-TSS (NM_001256033)	-301	NM_001256033	73945	Mm.34348	NM_001081164	ENSMUSG00000036990	Otud4	4930431L18Rik|AI449692|D8Ertd69e|mKIAA1046	OTU domain containing 4	protein-coding
mm_144466.1	chr18	23753709	23753719	+	1	NA	promoter-TSS (NM_001162941)	promoter-TSS (NM_001162941)	-11	NM_001162941	212307	Mm.132237	NM_153058	ENSMUSG00000024277	Mapre2	AI314113|C820009F03Rik|D18Abb1e|EB1|EB2|RP1	microtubule-associated protein, RP/EB family, member 2	protein-coding
mm_33182.1	chr4	126096711	126096728	+	1	NA	promoter-TSS (NM_001163266)	promoter-TSS (NM_001163266)	66	NM_138721	116748	Mm.41865	NM_138721	ENSMUSG00000050188	Lsm10	-	U7 snRNP-specific Sm-like protein LSM10	protein-coding
mm_140920.1	chr17	24203094	24203106	-	1	NA	TTS (NM_010947)	TTS (NM_010947)	2462	NM_001163851	224617	Mm.301585	NM_173186	ENSMUSG00000036473	Tbc1d24	9630033P11|C530046L02Rik|mKIAA1171	TBC1 domain family, member 24	protein-coding
mm_153928.1	chr19	47343594	47343652	-	1	NA	intron (NM_001164717, intron 5 of 13)	CpG	-70034	NR_105961	102466782		NR_105961	ENSMUSG00000098786	Mir6995	Gm27576|mmu-mir-6995	microRNA 6995	ncRNA
mm_111450.1	chr12	98271010	98271018	-	1	NA	intron (NM_008152, intron 1 of 1)	intron (NM_008152, intron 1 of 1)	2379	NM_008152	14744	Mm.378924	NM_008152	ENSMUSG00000021886	Gpr65	Dig1|Gpcr25|TDAG8	G-protein coupled receptor 65	protein-coding
mm_129868.1	chr15	83377338	83377356	-	1	NA	3' UTR (NM_001159510, exon 11 of 11)	3' UTR (NM_001159510, exon 11 of 11)	-10050	NR_027980	69291	Mm.66794	NM_001033147		1700001L05Rik	-	RIKEN cDNA 1700001L05 gene	ncRNA
mm_103832.1	chr11	83020252	83020280	-	1	NA	intron (NM_181545, intron 1 of 5)	intron (NM_181545, intron 1 of 5)	456	NM_001167743	276950	Mm.491599	NM_181545	ENSMUSG00000035208	Slfn8	-	schlafen 8	protein-coding
mm_113919.1	chr13	49548581	49548601	+	1	NA	intron (NM_001172481, intron 1 of 7)	B1F2|SINE|Alu	4148	NM_025711	66695	Mm.383216	NM_025711	ENSMUSG00000021388	Aspn	4631401G09Rik|AA986886|Plap1|Slrr1c	asporin	protein-coding
mm_102002.1	chr11	51578544	51578557	-	1	NA	intron (NM_153393, intron 27 of 28)	intron (NM_153393, intron 27 of 28)	-6207	NM_028398	72947	Mm.256875	NM_028398	ENSMUSG00000020359	Phykpl	2900006B13Rik|Agxt2l2	5-phosphohydroxy-L-lysine phospholyase	protein-coding
mm_139308.1	chr17	48348646	48348680	+	1	NA	exon (NM_031254, exon 2 of 5)	exon (NM_031254, exon 2 of 5)	2262	NM_001272078	83433	Mm.261623	NM_031254	ENSMUSG00000023992	Trem2	TREM-2|Trem2a|Trem2b|Trem2c	triggering receptor expressed on myeloid cells 2	protein-coding
mm_97139.1	chr11	75193992	75193998	+	1	NA	promoter-TSS (NM_177708)	promoter-TSS (NM_177708)	2	NM_177708	237847	Mm.82661	NM_177708	ENSMUSG00000045287	Rtn4rl1	Ngr3|Ngrh2|Ngrl2	reticulon 4 receptor-like 1	protein-coding
mm_40354.1	chr5	47869957	47869963	+	1	NA	Intergenic	Intergenic	-113195	NR_111900	20563	Mm.289739	NM_178804	ENSMUSG00000031558	Slit2	Drad-1|E030015M03Rik|E130320P19Rik|Slil3|mKIAA4141|slit-2	slit homolog 2 (Drosophila)	protein-coding
mm_151414.1	chr19	56722088	56722094	+	1	NA	promoter-TSS (NM_007419)	promoter-TSS (NM_007419)	-281	NM_007419	11554	Mm.46797	NM_007419	ENSMUSG00000035283	Adrb1	Adrb-1|beta-AR	adrenergic receptor, beta 1	protein-coding
mm_122201.1	chr14	31781618	31781632	-	1	NA	intron (NM_001024604, intron 1 of 27)	intron (NM_001024604, intron 1 of 27)	48790	NM_001024604	105522	Mm.37660	NM_001024604	ENSMUSG00000014496	Ankrd28	AI465466|AI604979|E430019N21Rik|mKIAA0379	ankyrin repeat domain 28	protein-coding
mm_30035.1	chr3	135691386	135691407	-	1	NA	5' UTR (NM_008689, exon 1 of 25)	5' UTR (NM_008689, exon 1 of 25)	151	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_117544.1	chr13	83729133	83729135	-	1	NA	intron (NR_015561, intron 1 of 3)	intron (NR_015561, intron 1 of 3)	1028	NR_015561	320203	Mm.245636	NM_177100	ENSMUSG00000050334	C130071C03Rik	2810449C10Rik	RIKEN cDNA C130071C03 gene	ncRNA
mm_57865.1	chr6	129622686	129622711	-	1	NA	promoter-TSS (NM_033078)	promoter-TSS (NM_033078)	-15	NM_033078	27007	Mm.8217	NM_033078	ENSMUSG00000030149	Klrk1	D6H12S2489E|NKG2-D|Nkg2d	killer cell lectin-like receptor subfamily K, member 1	protein-coding
mm_38339.1	chr4	137758676	137758698	-	1	NA	5' UTR (NM_007431, exon 2 of 12)	5' UTR (NM_007431, exon 2 of 12)	7788	NM_001287172	11647	Mm.288186	NM_007431	ENSMUSG00000028766	Alpl	ALP|APTNAP|Akp-2|Akp2|TNAP|TNSALP	alkaline phosphatase, liver/bone/kidney	protein-coding
mm_10915.1	chr2	25395867	25395902	+	1	NA	promoter-TSS (NM_009849)	promoter-TSS (NM_009849)	10	NM_009849	12496	Mm.482100	NM_009849	ENSMUSG00000015085	Entpd2	Cd39l1|NTPDase2	ectonucleoside triphosphate diphosphohydrolase 2	protein-coding
mm_123252.1	chr14	61046155	61046174	-	1	NA	5' UTR (NM_013869, exon 1 of 10)	5' UTR (NM_013869, exon 1 of 10)	691	NM_013869	29820	Mm.281356	NM_013869	ENSMUSG00000060548	Tnfrsf19	AL023044|AW123854|TAJ|TAJ-ALPHA|TRADE|Troy	tumor necrosis factor receptor superfamily, member 19	protein-coding
mm_115380.1	chr13	113096198	113096239	+	1	NA	exon (NM_010370, exon 3 of 5)	exon (NM_010370, exon 3 of 5)	4763	NM_010370	14938	Mm.15510	NM_010370	ENSMUSG00000023132	Gzma	AW494114|Ctla-3|Ctla3|Hf|Hf1|SE1|TSP-1|TSP1	granzyme A	protein-coding
mm_47609.1	chr5	125119571	125119607	-	1	NA	exon (NM_011424, exon 3 of 47)	exon (NM_011424, exon 3 of 47)	59625	NM_001253905	20602	Mm.278646	NM_011424	ENSMUSG00000029478	Ncor2	N-CoR|SMRT|SMRTe	nuclear receptor co-repressor 2	protein-coding
mm_22496.1	chr3	7133294	7133296	+	1	NA	Intergenic	B4A|SINE|B4	-233309	NM_008862	18767	Mm.3193	NM_008862	ENSMUSG00000027499	Pkia	AI415001|PKIalpha	protein kinase inhibitor, alpha	protein-coding
mm_131150.1	chr16	6698220	6698224	+	1	NA	intron (NM_021477, intron 4 of 16)	MTEa|LTR|ERVL-MaLR	-371613	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_31871.1	chr4	80834205	80834221	+	1	NA	promoter-TSS (NM_031202)	promoter-TSS (NM_031202)	0	NM_031202	22178	Mm.30438	NM_031202	ENSMUSG00000005994	Tyrp1	Oca3|TRP-1|TRP1|Tyrp|b|brown|isa	tyrosinase-related protein 1	protein-coding
mm_30762.1	chr4	15957924	15958016	+	1	NA	promoter-TSS (NM_013752)	promoter-TSS (NM_013752)	3	NM_013752	27354	Mm.20866	NM_013752	ENSMUSG00000028224	Nbn	Nbs1	nibrin	protein-coding
mm_11765.1	chr2	38536128	38536144	+	1	NA	intron (NM_001159631, intron 1 of 9)	intron (NM_001159631, intron 1 of 9)	24260	NM_001159631	59126	Mm.143818	NM_021606	ENSMUSG00000026749	Nek6	1300007C09Rik	NIMA (never in mitosis gene a)-related expressed kinase 6	protein-coding
mm_144786.1	chr18	35858694	35858705	+	1	NA	exon (NM_133687, exon 2 of 3)	exon (NM_133687, exon 2 of 3)	28881	NM_133687	67393	Mm.94560	NM_133687	ENSMUSG00000046668	Cxxc5	4930415K17Rik	CXXC finger 5	protein-coding
mm_123625.1	chr14	68121362	68121373	-	1	NA	exon (NM_008691, exon 3 of 3)	exon (NM_008691, exon 3 of 3)	-2385	NR_045897	100043072	Mm.242832	NR_045897		A230070E04Rik	Gm4210	RIKEN cDNA A230070E04 gene	ncRNA
mm_168820.1	chr1	22220109	22220110	+	1	NA	Intergenic	L1Md_F|LINE|L1	212734	NM_053270	116837	Mm.60061	NM_053270	ENSMUSG00000041670	Rims1	C030033M19Rik|RIM1|RIM1a|RIM1alpha|Rab3ip1|Rim|Serg1|mKIAA0340	regulating synaptic membrane exocytosis 1	protein-coding
mm_73187.1	chr8	95346878	95346915	+	1	NA	3' UTR (NM_133954, exon 7 of 7)	3' UTR (NM_133954, exon 7 of 7)	-5400	NM_008609	17388	Mm.217116	NM_008609	ENSMUSG00000031790	Mmp15	AI503551|MT-MMP 2|MT2-MMP	matrix metallopeptidase 15	protein-coding
mm_123610.1	chr14	68120289	68120311	-	1	NA	exon (NM_008691, exon 3 of 3)	exon (NM_008691, exon 3 of 3)	-3452	NR_045897	100043072	Mm.242832	NR_045897		A230070E04Rik	Gm4210	RIKEN cDNA A230070E04 gene	ncRNA
mm_156882.1	chrX	166344759	166344770	+	1	NA	5' UTR (NM_001177959, exon 1 of 7)	5' UTR (NM_001177959, exon 1 of 7)	211	NM_001177960	14758	Mm.222320	NM_023122	ENSMUSG00000031342	Gpm6b	AI593561|Gpm6|M6B	glycoprotein m6b	protein-coding
mm_88127.1	chr10	69280041	69280041	+	1	NA	intron (NM_001252637, intron 8 of 10)	intron (NM_001252637, intron 8 of 10)	66847	NM_001252638	69288	Mm.26659	NM_001081347	ENSMUSG00000019944	Rhobtb1	1700008H16Rik|3110048G13Rik|AI173445|AI573858|AV350930	Rho-related BTB domain containing 1	protein-coding
mm_168852.1	chr12	24097258	24097269	-	1	NA	promoter-TSS (NM_001256489)	promoter-TSS (NM_001256489)	6	NM_001256489	66808	Mm.379124	NM_001256489	ENSMUSG00000073158	9030624G23Rik	-	RIKEN cDNA 9030624G23 gene	protein-coding
mm_58817.1	chr7	16415672	16415675	+	1	NA	intron (NM_198631, intron 1 of 13)	intron (NM_198631, intron 1 of 13)	14477	NM_198631	330474	Mm.333594	NM_198631	ENSMUSG00000059273	Zc3h4	Bwq1|Gm768|Kiaa1064-hp|mKIAA1064	zinc finger CCCH-type containing 4	protein-coding
mm_13556.1	chr2	112262329	112262337	+	1	NA	exon (NM_025403, exon 2 of 2)	exon (NM_025403, exon 2 of 2)	407	NM_025403	66181	Mm.272346	NM_025403	ENSMUSG00000027133	Nop10	1110036B12Rik|NOP10P|Nola3	NOP10 ribonucleoprotein	protein-coding
mm_77329.1	chr8	119428990	119429023	-	1	NA	Intergenic	Intergenic	-8156	NM_027950	71839	Mm.272357	NM_027950	ENSMUSG00000074063	Osgin1	1700012B18Rik|Okl38	oxidative stress induced growth inhibitor 1	protein-coding
mm_21754.1	chr2	164837454	164837477	-	1	NA	exon (NM_008906, exon 11 of 15)	exon (NM_008906, exon 11 of 15)	3692	NM_008906	19025	Mm.359633	NM_008906	ENSMUSG00000017760	Ctsa	AU019505|PPCA|Ppgb	cathepsin A	protein-coding
mm_11747.1	chr2	38354750	38354764	+	1	NA	exon (NM_010710, exon 3 of 5)	exon (NM_010710, exon 3 of 5)	3449	NM_010710	16870	Mm.142856	NM_010710	ENSMUSG00000000247	Lhx2	LH2A|Lh-2|Lim2|ap|apterous	LIM homeobox protein 2	protein-coding
mm_2553.1	chr1	109122613	109122619	+	1	NA	Intergenic	L1_Mur2|LINE|L1	-860284	NM_001316743	241201	Mm.213407	NM_172853	ENSMUSG00000026312	Cdh7	9330156F07Rik|CDH7L1	cadherin 7, type 2	protein-coding
mm_155169.1	chrX	53273446	53273455	+	1	NA	promoter-TSS (NM_028671)	promoter-TSS (NM_028671)	17	NM_028671	73866	Mm.84527	NM_028671	ENSMUSG00000036013	Fam122c	4930432H15Rik|4930527G05Rik	family with sequence similarity 122, member C	protein-coding
mm_76765.1	chr8	95788737	95788767	-	1	NA	5' UTR (NM_178078, exon 2 of 49)	5' UTR (NM_178078, exon 2 of 49)	-18078	NR_015574	319960	Mm.386996	NR_015574	ENSMUSG00000074136	4930513N10Rik	-	RIKEN cDNA 4930513N10 gene	ncRNA
mm_21043.1	chr2	152540036	152540073	-	1	NA	promoter-TSS (NM_001001444)	promoter-TSS (NM_001001444)	-13	NM_001001444	75400	Mm.45560	NM_001001444	ENSMUSG00000044249	Defb29	0610030I09Rik|BD-29|mBD-29	defensin beta 29	protein-coding
mm_147596.1	chr18	56707430	56707446	-	1	NA	promoter-TSS (NM_010721)	promoter-TSS (NM_010721)	-375	NM_010721	16906	Mm.4105	NM_010721	ENSMUSG00000024590	Lmnb1	-	lamin B1	protein-coding
mm_137354.1	chr17	25240226	25240245	+	1	NA	promoter-TSS (NM_001163718)	promoter-TSS (NM_001163718)	65	NM_026676	68327	Mm.180687	NM_026676	ENSMUSG00000015126	Tsr3	0610007P22Rik|1110014B11Rik|AL022759	TSR3 20S rRNA accumulation	protein-coding
mm_149035.1	chr19	8819561	8819574	+	1	NA	promoter-TSS (NM_027412)	promoter-TSS (NM_027412)	166	NM_001081196	68693	Mm.476519	NM_001081196	ENSMUSG00000071659	Hnrnpul2	1110031M08Rik|AI465155|Hnrpul2	heterogeneous nuclear ribonucleoprotein U-like 2	protein-coding
mm_80783.1	chr9	95857629	95857686	+	1	NA	promoter-TSS (NM_019864)	promoter-TSS (NM_019864)	60	NM_019864	245000	Mm.212462	NM_019864	ENSMUSG00000032409	Atr	-	ataxia telangiectasia and Rad3 related	protein-coding
mm_131543.1	chr16	17797308	17797325	+	1	NA	promoter-TSS (NM_153790)	promoter-TSS (NM_153790)	34	NM_153790	224024	Mm.194950	NM_153790	ENSMUSG00000012017	Scarf2	NSR1|SREC-II|SRECRP-1|Scatf1|Srec2|SrecII	scavenger receptor class F, member 2	protein-coding
mm_67747.1	chr7	90541238	90541240	-	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	-65244	NM_026734	68472	Mm.289791	NM_026734	ENSMUSG00000030614	Tmem126b	1110001A23Rik	transmembrane protein 126B	protein-coding
mm_8793.1	chr1	161788450	161788456	-	1	NA	promoter-TSS (NM_001205243)	promoter-TSS (NM_001205243)	42	NM_001205243	14103	Mm.3355	NM_010177	ENSMUSG00000000817	Fasl	APT1LG1|CD178|CD95-L|CD95L|Fas-L|Faslg|Tnfsf6|Tnlg1a|gld	Fas ligand (TNF superfamily, member 6)	protein-coding
mm_137147.1	chr17	23673899	23673987	+	1	NA	promoter-TSS (NM_001008425)	promoter-TSS (NM_001008425)	-173	NM_001008425	386612	Mm.328831	NM_001008425	ENSMUSG00000041319	Thoc6	F830014G06Rik|Wdr58	THO complex 6	protein-coding
mm_130302.1	chr15	97019892	97019902	-	1	NA	intron (NM_027052, intron 1 of 15)	intron (NM_027052, intron 1 of 15)	36059	NM_027052	69354	Mm.250980	NM_027052	ENSMUSG00000022464	Slc38a4	1110012E16Rik|1700012A18Rik|Ata3|mATA3|mNAT3	solute carrier family 38, member 4	protein-coding
mm_152945.1	chr19	28967795	28967852	-	1	NA	Intergenic	Intergenic	-3669	NM_198651	381218	Mm.280653	NM_198651	ENSMUSG00000064202	4430402I18Rik	AW122618|Spata6l	RIKEN cDNA 4430402I18 gene	protein-coding
mm_98375.1	chr11	94044290	94044296	+	1	NA	promoter-TSS (NM_001199205)	promoter-TSS (NM_001199205)	88	NM_001025429	70834	Mm.260737	NM_027569	ENSMUSG00000020859	Spag9	3110018C07Rik|4733401I23Rik|4831406C20Rik|AW552012|JLP|JSAP2|JSAP2a|Jip4|Mapk8ip4|syd1	sperm associated antigen 9	protein-coding
mm_39940.1	chr5	31746605	31746608	+	1	NA	intron (NM_144541, intron 3 of 11)	intron (NM_144541, intron 3 of 11)	48556	NM_144541	107976	Mm.482126	NM_144541	ENSMUSG00000052139	Bre	6030405P19Rik|AI429776|B830038C02Rik	brain and reproductive organ-expressed protein	protein-coding
mm_153836.1	chr19	46326544	46326598	-	1	NA	5' UTR (NM_001347454, exon 1 of 18)	5' UTR (NM_001347454, exon 1 of 18)	295	NM_001347454	73728	Mm.268532	NM_028627	ENSMUSG00000037126	Psd	1110007H17Rik|A930015K15|Efa6|Efa6a|Psdl|mKIAA2011	pleckstrin and Sec7 domain containing	protein-coding
mm_169384.1	chr14	41363356	41363374	+	1	NA	Intergenic	BGLII|LTR|ERVK	-178167	NM_009160	20390	Mm.1321	NM_009160	ENSMUSG00000021795	Sftpd	AI573415|SP-D|Sfpd|Sftp4	surfactant associated protein D	protein-coding
mm_53579.1	chr6	137410987	137411024	+	1	NA	exon (NM_011216, exon 13 of 27)	exon (NM_011216, exon 13 of 27)	284	NM_001164403	19277	Mm.186361	NM_011216	ENSMUSG00000030223	Ptpro	D28|GLEPP1|PTPBK|PTPROt|PTPU2|PTPoc|PTPphi|Ptpn15|R-PTP-O	protein tyrosine phosphatase, receptor type, O	protein-coding
mm_104254.1	chr11	88924284	88924293	-	1	NA	3' UTR (NM_029023, exon 13 of 13)	3' UTR (NM_029023, exon 13 of 13)	18360	NR_045955	73921	Mm.439148	NR_045955	ENSMUSG00000087338	Scpep1os	4930405P13Rik	serine carboxypeptidase 1, opposite strand	ncRNA
mm_98314.1	chr11	90187659	90187690	+	1	NA	Intergenic	Intergenic	-61802	NM_026178	67468	Mm.277518	NM_026178	ENSMUSG00000003948	Mmd	1200017E07Rik|1810073C06Rik|AA690185	monocyte to macrophage differentiation-associated	protein-coding
mm_11542.1	chr2	32646605	32646609	+	1	NA	promoter-TSS (NM_001146350)	promoter-TSS (NM_001146350)	12	NM_001146348	13805	Mm.225297	NM_007932	ENSMUSG00000026814	Eng	AI528660|AI662476|CD105|Endo|S-endoglin	endoglin	protein-coding
mm_134613.1	chr16	20803351	20803361	-	1	NA	Intergenic	Intergenic	-68845	NM_009379	21832	Mm.3943	NM_009379	ENSMUSG00000022847	Thpo	Mgdf|Ml|Mpllg|Tpo	thrombopoietin	protein-coding
mm_88405.1	chr10	76721837	76721899	+	1	NA	exon (NM_009933, exon 4 of 35)	exon (NM_009933, exon 4 of 35)	4176	NM_009933	12833	Mm.2509	NM_009933	ENSMUSG00000001119	Col6a1	AI747156|Col6a-1	collagen, type VI, alpha 1	protein-coding
mm_69450.1	chr7	133039713	133039714	-	1	NA	intron (NM_009980, intron 2 of 10)	intron (NM_009980, intron 2 of 10)	-24466	NM_001170744	13017	Mm.246240	NM_009980	ENSMUSG00000030970	Ctbp2	AA407280|D7Ertd45e|Gtrgeo6|Ribeye	C-terminal binding protein 2	protein-coding
mm_68000.1	chr7	100932141	100932200	-	1	NA	promoter-TSS (NM_001081116)	promoter-TSS (NM_001081116)	-9	NM_001081116	207212	Mm.29954	NM_001081116	ENSMUSG00000032875	Arhgef17	8030463K16|AI428794|AW558066|BC035332|mKIAA0337	Rho guanine nucleotide exchange factor (GEF) 17	protein-coding
mm_130724.1	chr15	101078883	101078932	-	1	NA	Intergenic	CpG	-24508	NM_001214911	668225	Mm.385011	NM_001214911	ENSMUSG00000095440	Fignl2	EG668225	fidgetin-like 2	protein-coding
mm_125199.1	chr15	32921081	32921096	+	1	NA	5' UTR (NM_008304, exon 1 of 5)	5' UTR (NM_008304, exon 1 of 5)	365	NM_008304	15529	Mm.234266	NM_008304	ENSMUSG00000022261	Sdc2	4833414L08Rik|AA960457|Hspg1|Synd2|syndecan-2	syndecan 2	protein-coding
mm_40237.1	chr5	37417492	37417495	+	1	NA	intron (NM_145920, intron 17 of 19)	intron (NM_145920, intron 17 of 19)	79015	NM_145920	68525	Mm.25506	NM_145920	ENSMUSG00000050248	Evc2	1110017L09Rik|Lbn|limbin	Ellis van Creveld syndrome 2	protein-coding
mm_148021.1	chr18	68449255	68449268	-	1	NA	Intergenic	Intergenic	-19941	NM_001271716	17200	Mm.426053	NM_008560	ENSMUSG00000045569	Mc2r	ACTH-R|ACTHR|MC2-R	melanocortin 2 receptor	protein-coding
mm_39994.1	chr5	32610326	32610335	+	1	NA	promoter-TSS (NM_009535)	promoter-TSS (NM_009535)	-841	NM_001205133	22612	Mm.4558	NM_009535	ENSMUSG00000014932	Yes1	Yes|p61-Yes	YES proto-oncogene 1, Src family tyrosine kinase	protein-coding
mm_93703.1	chr10	118103242	118103282	-	1	NA	Intergenic	Intergenic	-38525	NM_001162904	17245	Mm.101191	NM_010785	ENSMUSG00000020212	Mdm1	Arrd2|Mdm-1	transformed mouse 3T3 cell double minute 1	protein-coding
mm_1627.1	chr1	74418436	74418440	+	1	NA	exon (NM_009509, exon 4 of 20)	exon (NM_009509, exon 4 of 20)	9054	NM_009509	22349	Mm.471601	NM_009509	ENSMUSG00000026175	Vil1	Vil	villin 1	protein-coding
mm_132296.1	chr16	33381149	33381159	+	1	NA	promoter-TSS (NR_045709)	promoter-TSS (NR_045709)	379	NM_011749	22661	Mm.392667	NM_011749	ENSMUSG00000022811	Zfp148	2210405J08Rik|AI480666|AW045217|BERF-1|BFCOL1|ZBP-89|Znf148	zinc finger protein 148	protein-coding
mm_28962.1	chr3	100685432	100685494	-	1	NA	promoter-TSS (NM_010763)	promoter-TSS (NM_010763)	10	NM_010763	17156	Mm.271617	NM_010763	ENSMUSG00000008763	Man1a2	AI428775|AI528764|AI854422|Man1b|PCR2	mannosidase, alpha, class 1A, member 2	protein-coding
mm_14498.1	chr2	132027661	132027684	+	1	NA	intron (NM_175445, intron 1 of 10)	intron (NM_175445, intron 1 of 10)	2316	NM_175445	215653	Mm.204737	NM_175445	ENSMUSG00000027339	Rassf2	3830431H01Rik|9030412M04Rik|AI852669|AW495050	Ras association (RalGDS/AF-6) domain family member 2	protein-coding
mm_101843.1	chr11	48809047	48809050	-	1	NA	intron (NM_145377, intron 3 of 5)	intron (NM_145377, intron 3 of 5)	5909	NR_028564	100216540		NR_028564	ENSMUSG00000064780	Snord95	-	small nucleolar RNA, C/D box 95	snoRNA
mm_33520.1	chr4	130930763	130930780	+	1	NA	exon (NM_010686, exon 6 of 8)	exon (NM_010686, exon 6 of 8)	-13614	NM_010769	17180	Mm.271796	NM_010769	ENSMUSG00000040533	Matn1	CMP|Crtm|Mat1|matrilin-1	matrilin 1, cartilage matrix protein	protein-coding
mm_969.1	chr1	58210444	58210457	+	1	NA	promoter-TSS (NM_023631)	promoter-TSS (NM_023631)	53	NM_023631	71872	Mm.244525	NM_023631	ENSMUSG00000038242	Aox4	2310003G12Rik|Aoh2	aldehyde oxidase 4	protein-coding
mm_34488.1	chr4	148558736	148558746	+	1	NA	intron (NR_131061, intron 1 of 24)	CpG	314	NR_131061	50912	Mm.266635	NM_016699	ENSMUSG00000017264	Exosc10	PM-Scl|PM/Scl-100|Pmscl2|RRP6|p2|p3|p4	exosome component 10	protein-coding
mm_86912.1	chr10	22820269	22820279	+	1	NA	promoter-TSS (NM_011545)	promoter-TSS (NM_011545)	-146	NM_011545	21412	Mm.16497	NM_011545	ENSMUSG00000045680	Tcf21	Pod-1|Pod1|bHLHa23|capsulin|epc|epicardin	transcription factor 21	protein-coding
mm_45092.1	chr5	44102047	44102061	-	1	NA	promoter-TSS (NM_008935)	promoter-TSS (NM_008935)	-318	NM_001163577	19126	Mm.6250	NM_008935	ENSMUSG00000029086	Prom1	4932416E19Rik|AC133|CD133|Prom|Prom-1|Proml1	prominin 1	protein-coding
mm_37076.1	chr4	116167564	116167579	-	1	NA	promoter-TSS (NM_133681)	promoter-TSS (NM_133681)	27	NM_133681	66805	Mm.45994	NM_133681	ENSMUSG00000028699	Tspan1	9030418M05Rik	tetraspanin 1	protein-coding
mm_22742.1	chr3	19957038	19957073	+	1	NA	promoter-TSS (NM_007752)	promoter-TSS (NM_007752)	1	NM_007752	12870	Mm.13787	NM_007752	ENSMUSG00000003617	Cp	D3Ertd555e	ceruloplasmin	protein-coding
mm_141596.1	chr17	32424180	32424190	-	1	NA	promoter-TSS (NM_001271478)	promoter-TSS (NM_001271478)	-18	NM_001271478	57757	Mm.86752	NM_021319	ENSMUSG00000079563	Pglyrp2	C730002N09Rik|PGRP-L|Pglyrpl|tagL	peptidoglycan recognition protein 2	protein-coding
mm_108396.1	chr12	81026801	81026818	+	1	NA	promoter-TSS (NM_001146217)	promoter-TSS (NM_001146217)	1	NM_022316	64075	Mm.273295	NM_022316	ENSMUSG00000021136	Smoc1	2600002F22Rik|AI848508|SRG	SPARC related modular calcium binding 1	protein-coding
mm_80952.1	chr9	102988758	102988788	+	1	NA	Intergenic	Intergenic	-19716	NM_033314	24059	Mm.207106	NM_033314	ENSMUSG00000032548	Slco2a1	2310021C19Rik|Pgt|Slc21a2|mPgt	solute carrier organic anion transporter family, member 2a1	protein-coding
mm_56084.1	chr6	87335498	87335512	-	1	NA	5' UTR (NM_054041, exon 1 of 18)	5' UTR (NM_054041, exon 1 of 18)	270	NM_054041	69538	Mm.232525	NM_054041	ENSMUSG00000033420	Antxr1	2310008J16Rik|2810405N18Rik|Antrx1|Tem8	anthrax toxin receptor 1	protein-coding
mm_140055.1	chr17	74570604	74570614	+	1	NA	intron (NM_007566, intron 7 of 72)	AT_rich|Low_complexity|Low_complexity	42314	NM_007566	12211	Mm.442564	NM_007566	ENSMUSG00000024073	Birc6	A430032G04Rik|A430040A19Rik|AA501170|Bruce|D630005A10Rik|mKIAA1289	baculoviral IAP repeat-containing 6	protein-coding
mm_72190.1	chr8	72492224	72492265	+	1	NA	exon (NM_177766, exon 1 of 6)	exon (NM_177766, exon 1 of 6)	370	NM_177766	270066	Mm.291461	NM_177766	ENSMUSG00000019731	Slc35e1	6030458H05|AA408278	solute carrier family 35, member E1	protein-coding
mm_58898.1	chr7	17150248	17150252	+	1	NA	promoter-TSS (NM_054059)	promoter-TSS (NM_054059)	-150	NM_054059	384557	Mm.486145	NM_054059	ENSMUSG00000053228	Ceacam3	EG384557|Psg24|cea12	carcinoembryonic antigen-related cell adhesion molecule 3	protein-coding
mm_87944.1	chr10	62920712	62920716	+	1	NA	promoter-TSS (NM_175194)	promoter-TSS (NM_175194)	81	NM_175194	73132	Mm.37457	NM_175194	ENSMUSG00000071253	Slc25a16	3110021G18Rik|GDA|GDC|HGT.1|ML7	solute carrier family 25 (mitochondrial carrier, Graves disease autoantigen), member 16	protein-coding
mm_54326.1	chr6	30509707	30509733	-	1	NA	promoter-TSS (NM_027073)	promoter-TSS (NM_027073)	53	NM_001347087	72649	Mm.45418	NM_178625	ENSMUSG00000029782	Tmem209	2700094F01Rik|AI428435	transmembrane protein 209	protein-coding
mm_144908.1	chr18	37411694	37411732	+	1	NA	promoter-TSS (NM_053135)	promoter-TSS (NM_053135)	39	NM_053135	93881	Mm.115996	NM_053135	ENSMUSG00000045657	Pcdhb10	Pcdhb5D|PcdhbJ	protocadherin beta 10	protein-coding
mm_130237.1	chr15	96474737	96474755	-	1	NA	Intergenic	Intergenic	-13903	NM_028148	72193	Mm.324474	NM_028148	ENSMUSG00000033228	Scaf11	1110061H03Rik|2610510E10Rik|AI462454|CASP11|SIP1|SRRP129|Sfrs2ip|Srsf2ip|mKIAA3013	SR-related CTD-associated factor 11	protein-coding
mm_103844.1	chr11	83064909	83064920	-	1	NA	promoter-TSS (NM_011408)	promoter-TSS (NM_011408)	-198	NM_011408	20556	Mm.278689	NM_011408	ENSMUSG00000072620	Slfn2	Shlf2	schlafen 2	protein-coding
mm_102139.1	chr11	53480223	53480241	-	1	NA	promoter-TSS (NM_183173)	promoter-TSS (NM_183173)	-37	NM_183173	237761	Mm.145208	NM_183173	ENSMUSG00000044352	Sowaha	A830006N08Rik|Ankrd43	sosondowah ankyrin repeat domain family member A	protein-coding
mm_73999.1	chr8	120744805	120744810	+	1	NA	intron (NM_001301811, intron 3 of 8)	intron (NM_001301811, intron 3 of 8)	6168	NM_001301811	15900	Mm.334861	NM_008320	ENSMUSG00000041515	Irf8	AI893568|ICSBP|IRF-8|Icsbp1|Myls	interferon regulatory factor 8	protein-coding
mm_152675.1	chr19	15194233	15194234	-	1	NA	Intergenic	L1_Mus2|LINE|L1	-596050	NM_001302947	21888	Mm.103638	NM_011600	ENSMUSG00000024642	Tle4	5730411M05Rik|AA792082|Bce-1|Bce1|ESTM13|ESTM14|Grg4|X83332|X83333|grg-4	transducin-like enhancer of split 4	protein-coding
mm_9405.1	chr1	172274150	172274166	-	1	NA	3' UTR (NM_178405, exon 23 of 23)	3' UTR (NM_178405, exon 23 of 23)	-15734	NM_013734	27222	Mm.482392	NM_013734	ENSMUSG00000007107	Atp1a4	-	ATPase, Na+/K+ transporting, alpha 4 polypeptide	protein-coding
mm_70889.1	chr8	25555060	25555070	+	1	NA	intron (NR_110510, intron 2 of 4)	intron (NR_110510, intron 2 of 4)	1018	NR_110510	102633315	Mm.437828	NR_110510	ENSMUSG00000086134	Gm16159	OTTMUSG00000031030	predicted gene 16159	ncRNA
mm_43791.1	chr5	142692483	142692502	+	1	NA	Intergenic	Intergenic	-9609	NM_146257	243328	Mm.125942	NM_146257	ENSMUSG00000050822	Slc29a4	ENT4|mPMAT	solute carrier family 29 (nucleoside transporters), member 4	protein-coding
mm_115071.1	chr13	101545169	101545174	+	1	NA	Intergenic	Intergenic	147459	NM_001024955	18708	Mm.259333	NM_001024955	ENSMUSG00000041417	Pik3r1	PI3K|p50alpha|p55alpha|p85alpha	phosphatidylinositol 3-kinase, regulatory subunit, polypeptide 1 (p85 alpha)	protein-coding
mm_36232.1	chr4	63152647	63152670	-	1	NA	exon (NM_007443, exon 2 of 10)	exon (NM_007443, exon 2 of 10)	1514	NM_007443	11699	Mm.2197	NM_007443	ENSMUSG00000028356	Ambp	AI194774|ASPI|HI-30|Intin4|Itil|UTI	alpha 1 microglobulin/bikunin	protein-coding
mm_119207.1	chr14	32856898	32856916	+	1	NA	5' UTR (NM_178791, exon 1 of 8)	5' UTR (NM_178791, exon 1 of 8)	151	NM_178791	320736	Mm.187910	NM_178791	ENSMUSG00000050666	Vstm4	E130203B14Rik	V-set and transmembrane domain containing 4	protein-coding
mm_134227.1	chr16	11288293	11288318	-	1	NA	Intergenic	Intergenic	-25504	NM_011608	21935	Mm.12935	NM_011608	ENSMUSG00000022496	Tnfrsf17	BCM|BCMA|Tnfrsf13|Tnfrsf13a	tumor necrosis factor receptor superfamily, member 17	protein-coding
mm_40913.1	chr5	75627430	75627432	+	1	NA	intron (NM_021099, intron 7 of 20)	intron (NM_021099, intron 7 of 20)	52440	NM_021099	16590	Mm.247073	NM_021099	ENSMUSG00000005672	Kit	Bs|CD117|Fdc|Gsfsco1|Gsfsco5|Gsfsow3|SCO1|SCO5|SOW3|Ssm|Tr-kit|W|c-KIT	KIT proto-oncogene receptor tyrosine kinase	protein-coding
mm_14462.1	chr2	131210502	131210552	+	1	NA	non-coding (NR_110992, exon 1 of 2)	non-coding (NR_110992, exon 1 of 2)	167	NR_110992	69596	Mm.2937	NM_027129	ENSMUSG00000068264	Ap5s1	0610038L13Rik|2310035K24Rik|AW060727|sigma5	adaptor-related protein 5 complex, sigma 1 subunit	protein-coding
mm_140739.1	chr17	15826489	15826512	-	1	NA	promoter-TSS (NM_178615)	promoter-TSS (NM_178615)	86	NM_178615	68799	Mm.293466	NM_178615	ENSMUSG00000048027	Rgmb	1110059F19Rik|DRAGON	repulsive guidance molecule family member B	protein-coding
mm_101177.1	chr11	16995232	16995266	-	1	NA	exon (NM_019549, exon 2 of 10)	exon (NM_019549, exon 2 of 10)	13469	NM_019549	56193	Mm.98232	NM_019549	ENSMUSG00000020120	Plek	2010300B13Rik	pleckstrin	protein-coding
mm_117216.1	chr13	64089470	64089500	-	1	NA	promoter-TSS (NM_008291)	promoter-TSS (NM_008291)	-284	NM_008291	15487	Mm.5109	NM_008291	ENSMUSG00000033122	Hsd17b3	-	hydroxysteroid (17-beta) dehydrogenase 3	protein-coding
mm_97957.1	chr11	83711237	83711246	+	1	NA	3' UTR (NM_007969, exon 3 of 3)	3' UTR (NM_007969, exon 3 of 3)	2237	NM_007969	14038	Mm.1650	NM_007969	ENSMUSG00000000983	Wfdc18	Expi|Kal1|WDNM1	WAP four-disulfide core domain 18	protein-coding
mm_83358.1	chr9	44407038	44407076	-	1	NA	promoter-TSS (NM_024266)	promoter-TSS (NM_024266)	491	NM_021789	60409	Mm.29814	NM_021789	ENSMUSG00000032112	Trappc4	1500017G03Rik|AI303617|HSPC172|PTD009|Sbd|Sbdn|Sdcbp2|TRS23	trafficking protein particle complex 4	protein-coding
mm_129666.1	chr15	81251850	81251873	-	1	NA	promoter-TSS (NR_077230)	promoter-TSS (NR_077230)	1	NR_077230	78102	Mm.296832	NR_077229		8430426J06Rik	-	RIKEN cDNA 8430426J06 gene	ncRNA
mm_110158.1	chr12	26469153	26469163	-	1	NA	promoter-TSS (NM_020557)	promoter-TSS (NM_020557)	-57	NM_020557	22169	Mm.271839	NM_020557	ENSMUSG00000020638	Cmpk2	1200004E04Rik|TDKI|Tyki	cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial	protein-coding
mm_167835.1	chr9	124424472	124424495	-	1	NA	non-coding (NR_015516, exon 1 of 1)	non-coding (NR_015516, exon 1 of 1)	696	NR_015516	75135	Mm.476814	NR_015516		4930526I15Rik	1600027J15Rik	RIKEN cDNA 4930526I15 gene	ncRNA
mm_77285.1	chr8	116733324	116733354	-	1	NA	promoter-TSS (NM_029441)	promoter-TSS (NM_029441)	-348	NM_029441	75796	Mm.159575	NM_029441	ENSMUSG00000031758	Cdyl2	1700029M19Rik|4930453I21Rik|Gm20194	chromodomain protein, Y chromosome-like 2	protein-coding
mm_37125.1	chr4	116679326	116679333	-	1	NA	Intergenic	B1F2|SINE|Alu	-6270	NM_011034	18477	Mm.30929	NM_011034	ENSMUSG00000028691	Prdx1	MSP23|NkefA|OSF-3|OSF3|PAG|Paga|PrdxI|PrxI|TDX2|TPxA|Tdpx2|prx1	peroxiredoxin 1	protein-coding
mm_35449.1	chr4	40268445	40268565	-	1	NA	intron (NM_134097, intron 1 of 2)	CpG-9801	-1074	NR_045265	100504309	Mm.392019	NR_045265		Toporsos	2010003O02Rik	topoisomerase I binding, arginine/serine-rich, opposite strand	ncRNA
mm_81026.1	chr9	104566734	104566745	+	1	NA	Intergenic	Intergenic	-3049	NM_028719	74020	Mm.326240	NM_028719	ENSMUSG00000032564	Cpne4	3632411M23Rik|4933406O10Rik	copine IV	protein-coding
mm_134678.1	chr16	22411794	22411820	-	1	NA	exon (NM_023794, exon 7 of 13)	exon (NM_023794, exon 7 of 13)	27763	NM_023794	104156	Mm.155708	NM_023794	ENSMUSG00000013089	Etv5	1110005E01Rik|8430401F14Rik|ERM	ets variant 5	protein-coding
mm_146309.1	chr18	80264443	80264469	+	1	NA	intron (NM_001164420, intron 3 of 4)	PB1D10|SINE|Alu	8150	NM_001164423	66943	Mm.29247	NM_025861	ENSMUSG00000034006	Pqlc1	2310009N05Rik|4933425L21Rik|5730564E11Rik|C78974	PQ loop repeat containing 1	protein-coding
mm_85067.1	chr9	91085826	91085865	-	1	NA	Intergenic	RMER1B|Other|Other	279954	NM_009573	22771	Mm.335350	NM_009573	ENSMUSG00000032368	Zic1	ZIC|ZNF201	zinc finger protein of the cerebellum 1	protein-coding
mm_27382.1	chr3	50607175	50607186	-	1	NA	Intergenic	Intergenic	-163567	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_31434.1	chr4	48539910	48539924	+	1	NA	promoter-TSS (NM_028137)	promoter-TSS (NM_028137)	-29	NM_001145925	66665	Mm.140749	NM_028137	ENSMUSG00000039693	Msantd3	2410046L14Rik|2810429P03Rik|5730528L13Rik|Mysantd3	Myb/SANT-like DNA-binding domain containing 3	protein-coding
mm_50920.1	chr6	57605704	57605714	+	1	NA	intron (NM_025992, intron 6 of 22)	Lx8b|LINE|L1	24717	NM_025992	67138	Mm.297393	NM_025992	ENSMUSG00000029798	Herc6	1700121D12Rik|2510038N07Rik|4930427L17Rik|AI451296|CEB1|Herc5	hect domain and RLD 6	protein-coding
mm_65362.1	chr7	25005899	25005923	-	1	NA	promoter-TSS (NM_001290469)	promoter-TSS (NM_001290469)	26	NM_001290469	232975	Mm.44101	NM_144921	ENSMUSG00000040907	Atp1a3	Atpa-2	ATPase, Na+/K+ transporting, alpha 3 polypeptide	protein-coding
mm_58277.1	chr6	145614278	145614291	-	1	NA	Intergenic	Intergenic	-1679	NM_009449	22147	Mm.270295	NM_009449	ENSMUSG00000067338	Tuba3b	M[a]7|Tuba7	tubulin, alpha 3B	protein-coding
mm_1479.1	chr1	71557156	71557166	+	1	NA	promoter-TSS (NM_026195)	promoter-TSS (NM_026195)	5	NM_026195	108147	Mm.38010	NM_026195	ENSMUSG00000026192	Atic	2610509C24Rik|AA536954|AW212393	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	protein-coding
mm_107144.1	chr12	21496514	21496519	+	1	NA	Intergenic	Intergenic	-79080	NM_011739	22630	Mm.289630	NM_011739	ENSMUSG00000076432	Ywhaq	2700028P07Rik|AA409740|AU021156|R74690	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide	protein-coding
mm_101582.1	chr11	34407122	34407135	-	1	NA	intron (NM_001025382, intron 3 of 3)	intron (NM_001025382, intron 3 of 3)	92306	NM_001025382	574403	Mm.444796	NM_001025382	ENSMUSG00000069911	Fam196b	EG574403|Gm6041	family with sequence similarity 196, member B	protein-coding
mm_161825.1	chr17	78906896	78906896	-	1	NA	promoter-TSS (NM_001163625)	promoter-TSS (NM_001163625)	96	NM_001163625	73671	Mm.45514	NM_001163625	ENSMUSG00000038045	Sult6b1	2410078J06Rik|AV101767|ST6B1	sulfotransferase family, cytosolic, 6B, member 1	protein-coding
mm_144807.1	chr18	36281466	36281504	+	1	NA	5' UTR (NM_008989, exon 1 of 2)	5' UTR (NM_008989, exon 1 of 2)	323	NM_008989	19290	Mm.231802	NM_008989	ENSMUSG00000043991	Pura	CAGER-1|Pur-alpha|ssCRE-BP	purine rich element binding protein A	protein-coding
mm_35780.1	chr4	46404331	46404339	-	1	NA	promoter-TSS (NM_053149)	promoter-TSS (NM_053149)	-152	NM_053149	93966	Mm.25793	NM_053149	ENSMUSG00000028332	Hemgn	4921524M03Rik|AI317176|EDAG|Hgn|mNDR	hemogen	protein-coding
mm_108589.1	chr12	85339431	85339448	+	1	NA	promoter-TSS (NM_145138)	promoter-TSS (NM_145138)	-77	NM_145138	217718	Mm.29071	NM_145138	ENSMUSG00000034290	Nek9	C130021H08Rik	NIMA (never in mitosis gene a)-related expressed kinase 9	protein-coding
mm_45594.1	chr5	74702892	74702914	-	1	NA	promoter-TSS (NM_001159577)	promoter-TSS (NM_001159577)	0	NM_001159577	16924	Mm.440403	NM_010727	ENSMUSG00000029228	Lnx1	Lnx	ligand of numb-protein X 1	protein-coding
mm_54311.1	chr6	30147095	30147108	-	1	NA	intron (NM_010938, intron 11 of 11)	intron (NM_010938, intron 11 of 11)	18891	NR_029569	387177		NR_029569	ENSMUSG00000076361	Mir182	Mirn182|mir-182|mmu-mir-182	microRNA 182	ncRNA
mm_52059.1	chr6	97252880	97252898	+	1	NA	promoter-TSS (NM_001081157)	promoter-TSS (NM_001081157)	-109	NM_001081157	320502	Mm.68163	NM_001081157	ENSMUSG00000044086	Lmod3	5430424A14Rik	leiomodin 3 (fetal)	protein-coding
mm_145823.1	chr18	65435288	65435300	+	1	NA	intron (NM_172833, intron 1 of 15)	L2|LINE|L2	4297	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_97678.1	chr11	79974203	79974250	+	1	NA	Intergenic	CpG	-11839	NM_144826	216987	Mm.274961	NM_144826	ENSMUSG00000035575	Utp6	4732497O03Rik|HCA66	UTP6 small subunit processome component	protein-coding
mm_123939.1	chr14	73368431	73368439	-	1	NA	intron (NM_008410, intron 1 of 5)	intron (NM_008410, intron 1 of 5)	16836	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_94970.1	chr11	30954390	30954439	+	1	NA	promoter-TSS (NM_023906)	promoter-TSS (NM_023906)	16	NM_023906	65257	Mm.440539	NM_023906	ENSMUSG00000020305	Asb3	2400011J03Rik|Asb-3	ankyrin repeat and SOCS box-containing 3	protein-coding
mm_14386.1	chr2	129800285	129800293	+	1	NA	promoter-TSS (NM_183262)	promoter-TSS (NM_183262)	-228	NM_183262	67333	Mm.389329	NM_183262	ENSMUSG00000037885	Stk35	1700054C12Rik|CLIK1|Stk35l1	serine/threonine kinase 35	protein-coding
mm_101196.1	chr11	18891182	18891201	-	1	NA	intron (NM_001193271, intron 9 of 12)	intron (NM_001193271, intron 9 of 12)	127778	NM_001193271	17268	Mm.356578	NM_010789	ENSMUSG00000020160	Meis1	C530044H18Rik|Evi8	Meis homeobox 1	protein-coding
mm_122083.1	chr14	30616852	30616861	-	1	NA	intron (NM_011103, intron 1 of 17)	intron (NM_011103, intron 1 of 17)	-6546	NM_001310682	18753	Mm.2314	NM_011103	ENSMUSG00000021948	Prkcd	AI385711|D14Ertd420e|PKC[d]|PKCdelta|Pkcd	protein kinase C, delta	protein-coding
mm_136202.1	chr16	89818339	89818356	-	1	NA	promoter-TSS (NM_001145887)	promoter-TSS (NM_001145887)	5	NM_001145887	21844	Mm.310902	NM_009384	ENSMUSG00000002489	Tiam1	AI847750|D16Ium10|D16Ium10e	T cell lymphoma invasion and metastasis 1	protein-coding
mm_52359.1	chr6	112489055	112489067	+	1	NA	exon (NM_001081147, exon 1 of 2)	exon (NM_001081147, exon 1 of 2)	747	NM_001081147	18430	Mm.333310	NM_001081147	ENSMUSG00000049112	Oxtr	OTR	oxytocin receptor	protein-coding
mm_19297.1	chr2	90460894	90460905	-	1	NA	intron (NM_001135657, intron 7 of 25)	PB1D10|SINE|Alu	18275	NM_001135657	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_74794.1	chr8	22398350	22398361	-	1	NA	promoter-TSS (NR_045473)	promoter-TSS (NR_045473)	266	NM_181325	18408	Mm.200907	NM_181325	ENSMUSG00000031482	Slc25a15	D630044L02Rik|Ornt1	solute carrier family 25 (mitochondrial carrier ornithine transporter), member 15	protein-coding
mm_101073.1	chr11	11565311	11565315	-	1	NA	Intergenic	Intergenic	62525	NM_001305143	102631730	Mm.159430	NM_001305143	ENSMUSG00000062511	4930512M02Rik	-	RIKEN cDNA 4930512M02 gene	protein-coding
mm_21128.1	chr2	154094832	154094838	-	1	NA	Intergenic	Intergenic	-35501	NM_001291079	73388	Mm.71904	NM_028528	ENSMUSG00000027482	Bpifa3	1700058C13Rik|Splunc3	BPI fold containing family A, member 3	protein-coding
mm_65418.1	chr7	25250721	25250738	-	1	NA	promoter-TSS (NM_010155)	promoter-TSS (NM_010155)	29	NM_010155	13875	Mm.8068	NM_010155	ENSMUSG00000040857	Erf	-	Ets2 repressor factor	protein-coding
mm_125295.1	chr15	37007546	37007592	+	1	NA	promoter-TSS (NM_026521)	promoter-TSS (NM_026521)	-167	NM_026521	68036	Mm.371631	NM_026521	ENSMUSG00000062397	Zfp706	3110006P09Rik|AA793007|AW536850|C77232|Znf706	zinc finger protein 706	protein-coding
mm_13505.1	chr2	109280782	109280798	+	1	NA	promoter-TSS (NM_139303)	promoter-TSS (NM_139303)	52	NM_139303	228421	Mm.274086	NM_139303	ENSMUSG00000027115	Kif18a	AU024633|B130001M12Rik|gcd2	kinesin family member 18A	protein-coding
mm_12772.1	chr2	79326768	79326780	+	1	NA	3' UTR (NM_010576, exon 28 of 28)	3' UTR (NM_010576, exon 28 of 28)	71348	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D|Itga4B	integrin alpha 4	protein-coding
mm_75257.1	chr8	40584682	40584722	-	1	NA	intron (NM_001040699, intron 6 of 13)	intron (NM_001040699, intron 6 of 13)	50090	NM_001040699	54384	Mm.294871	NM_019433	ENSMUSG00000039431	Mtmr7	-	myotubularin related protein 7	protein-coding
mm_79312.1	chr9	52060831	52060835	+	1	NA	5' UTR (NM_009041, exon 2 of 14)	5' UTR (NM_009041, exon 2 of 14)	-12128	NR_023357	629557	Mm.422775	NR_023357		Gm6981	EG629557	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_67541.1	chr7	81455490	81455501	-	1	NA	promoter-TSS (NM_001252526)	promoter-TSS (NM_001252526)	-737	NM_001252526	12877	Mm.273122	NM_007755	ENSMUSG00000025586	Cpeb1	AU024112|Cpeb|mCPEB	cytoplasmic polyadenylation element binding protein 1	protein-coding
mm_20901.1	chr2	149798717	149798729	-	1	NA	Intergenic	Intergenic	-32060	NM_001085521	433485	Mm.330649	NM_001085521	ENSMUSG00000074736	Syndig1	AW123113|DSPC2|Gm14134|H2C20orf39|OTTMUSG00000015750|Tmem90b	synapse differentiation inducing 1	protein-coding
mm_18783.1	chr2	73659879	73659892	-	1	NA	exon (NM_175752, exon 1 of 7)	exon (NM_175752, exon 1 of 7)	538	NM_175752	108699	Mm.257073	NM_029716	ENSMUSG00000056486	Chn1	0610007I19Rik|0710001E19Rik|1700112L09Rik|2900046J01Rik|AI413815|ARHGAP2	chimerin 1	protein-coding
mm_124398.1	chr14	114842534	114842540	-	1	NA	intron (NR_045661, intron 1 of 5)	intron (NR_045661, intron 1 of 5)	10572	NR_045661	75822	Mm.410813	NR_045661		4930524C18Rik	-	RIKEN cDNA 4930524C18 gene	ncRNA
mm_46857.1	chr5	113771644	113771659	-	1	NA	promoter-TSS (NM_016926)	promoter-TSS (NM_016926)	-2	NM_016926	53890	Mm.29594	NM_016926	ENSMUSG00000018974	Sart3	AU045857|mKIAA0156	squamous cell carcinoma antigen recognized by T cells 3	protein-coding
mm_123326.1	chr14	62966212	62966225	-	1	NA	Intergenic	Intergenic	18292	NM_001037751	432867	Mm.99387	NM_001037751	ENSMUSG00000075574	Defb48	Defb42|EG432867	defensin beta 48	protein-coding
mm_82852.1	chr9	31279893	31279905	-	1	NA	Intergenic	Intergenic	8498	NM_001101597	638580	Mm.373655	NM_001101597		Gm7244	EG638580	predicted gene 7244	protein-coding
mm_144608.1	chr18	32430905	32430928	+	1	NA	intron (NM_009668, intron 15 of 18)	intron (NM_009668, intron 15 of 18)	-52632	NR_045403	402767	Mm.385109	NR_045403	ENSMUSG00000097413	A830052D11Rik	-	RIKEN cDNA A830052D11 gene	ncRNA
mm_17176.1	chr2	25332525	25332602	-	1	NA	promoter-TSS (NR_027448)	promoter-TSS (NR_027448)	8	NR_027448	100272219	Mm.382103	NR_027448	ENSMUSG00000097345	AA543186	-	expressed sequence AA543186	ncRNA
mm_91178.1	chr10	20725127	20725140	-	1	NA	promoter-TSS (NM_013875)	promoter-TSS (NM_013875)	-55	NM_013875	29863	Mm.425617	NM_013875	ENSMUSG00000019990	Pde7b	-	phosphodiesterase 7B	protein-coding
mm_72976.1	chr8	92901370	92901380	+	1	NA	promoter-TSS (NM_027112)	promoter-TSS (NM_027112)	-20	NM_027112	69543	Mm.440514	NM_027112	ENSMUSG00000078144	Capns2	2310005G05Rik|30K-2	calpain, small subunit 2	protein-coding
mm_130532.1	chr15	98934439	98934444	-	1	NA	promoter-TSS (NM_011654)	promoter-TSS (NM_011654)	-51	NM_011654	22143	Mm.392113	NM_011654	ENSMUSG00000023004	Tuba1b	Tuba2	tubulin, alpha 1B	protein-coding
mm_102265.1	chr11	55336651	55336657	-	1	NA	Intergenic	G-rich|Low_complexity|Low_complexity	-24397	NM_001029988	245827	Mm.339363	NM_001029988	ENSMUSG00000055333	Fat2	EMI2|Fath2|Gm523|mKIAA0811	FAT atypical cadherin 2	protein-coding
mm_19492.1	chr2	93334518	93334522	-	1	NA	promoter-TSS (NM_183180)	promoter-TSS (NM_183180)	-33	NM_183180	241556	Mm.274159	NM_183180	ENSMUSG00000027217	Tspan18	2610042G18Rik|6720430O15|BB226562	tetraspanin 18	protein-coding
mm_131431.1	chr16	15705226	15705249	+	1	NA	exon (NM_011159, exon 30 of 86)	exon (NM_011159, exon 30 of 86)	67371	NM_011159	19090	Mm.71	NM_011159	ENSMUSG00000022672	Prkdc	AI326420|AU019811|DNA-PKcs|DNAPDcs|DNAPK|DNPK1|DOXNPH|HYRC1|XRCC7|dxnph|p460|scid|slip	protein kinase, DNA activated, catalytic polypeptide	protein-coding
mm_7313.1	chr1	98095507	98095533	-	1	NA	5' UTR (NM_013626, exon 1 of 26)	5' UTR (NM_013626, exon 1 of 26)	112	NM_013626	18484	Mm.5121	NM_013626	ENSMUSG00000026335	Pam	PHM	peptidylglycine alpha-amidating monooxygenase	protein-coding
mm_66833.1	chr7	48866924	48866943	-	1	NA	3' UTR (NM_001013368, exon 13 of 13)	3' UTR (NM_001013368, exon 13 of 13)	14108	NM_001013368	108961	Mm.240566	NM_001013368	ENSMUSG00000046179	E2f8	4432406C08Rik|AA410048	E2F transcription factor 8	protein-coding
mm_85459.1	chr9	105428289	105428293	-	1	NA	intron (NM_001253834, intron 20 of 27)	intron (NM_001253834, intron 20 of 27)	27503	NM_001164828	66595	Mm.84941	NM_025651	ENSMUSG00000032567	Aste1	1100001A21Rik|AV006403	asteroid homolog 1 (Drosophila)	protein-coding
mm_77842.1	chr9	5299291	5299307	+	1	NA	exon (NM_009807, exon 2 of 10)	exon (NM_009807, exon 2 of 10)	782	NM_009807	12362	Mm.1051	NM_009807	ENSMUSG00000025888	Casp1	ICE|Il1bc	caspase 1	protein-coding
mm_57127.1	chr6	122600509	122600554	-	1	NA	intron (NM_001134391, intron 1 of 7)	MRLTR33|LTR|ERVK	1913	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_23368.1	chr3	55371986	55372009	+	1	NA	intron (NM_019978, intron 3 of 16)	B4|SINE|B4	-89761	NM_001195539	13175	Mm.393242	NM_019978	ENSMUSG00000027797	Dclk1	1700113D08Rik|2810480F11Rik|AI836758|Click-I|Cpg16|Dcamkl1|Dcl|Dclk|mKIAA0369	doublecortin-like kinase 1	protein-coding
mm_13013.1	chr2	90940467	90940523	+	1	NA	promoter-TSS (NM_198683)	promoter-TSS (NM_198683)	98	NM_017368	13046	Mm.29495	NM_017368	ENSMUSG00000005506	Celf1	1600010O03Rik|AA407467|Brunol2|CUG-BP|CUG-BP1|CUGBP|Cugbp1|D2Wsu101e|HNAB50|NAB50	CUGBP, Elav-like family member 1	protein-coding
mm_152971.1	chr19	29386776	29386842	-	1	NA	3' UTR (NM_021893, exon 7 of 7)	3' UTR (NM_021893, exon 7 of 7)	19371	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_160296.1	chr7	132316748	132316748	-	1	NA	non-coding (NR_028578, exon 1 of 1)	non-coding (NR_028578, exon 1 of 1)	407	NM_029935	77590	Mm.213582	NM_029935	ENSMUSG00000030930	Chst15	4631426J05Rik|BRAG|GalNAcS-6ST|MAd5|mKIAA0598	carbohydrate (N-acetylgalactosamine 4-sulfate 6-O) sulfotransferase 15	protein-coding
mm_121366.1	chr14	117370911	117370938	+	1	NA	intron (NM_001079844, intron 2 of 9)	intron (NM_001079844, intron 2 of 9)	445627	NM_011821	23888	Mm.440025	NM_011821	ENSMUSG00000058571	Gpc6	-	glypican 6	protein-coding
mm_137189.1	chr17	23821080	23821092	+	1	NA	exon (NM_175229, exon 10 of 14)	exon (NM_175229, exon 10 of 14)	8023	NM_026305	67673	Mm.153758	NM_026305	ENSMUSG00000055839	Elob	0610040H15Rik|Tceb2	elongin B	protein-coding
mm_61440.1	chr7	75455638	75455646	+	1	NA	5' UTR (NM_029332, exon 1 of 37)	5' UTR (NM_029332, exon 1 of 37)	108	NM_029332	75547	Mm.216107	NM_029332	ENSMUSG00000066406	Akap13	1700026G02Rik|5730522G15Rik|5830460E08Rik|AKAP-13|AKAP-Lbc|BRX|Ht31|LBC|PROTO-LB|PROTO-LBC	A kinase (PRKA) anchor protein 13	protein-coding
mm_90583.1	chr10	128268851	128268869	+	1	NA	intron (NM_133997, intron 1 of 1)	intron (NM_133997, intron 1 of 1)	863	NM_133997	103161	Mm.26513	NM_133997	ENSMUSG00000047631	Apof	AI255964	apolipoprotein F	protein-coding
mm_144096.1	chr18	3382980	3383065	+	1	NA	promoter-TSS (NM_029402)	promoter-TSS (NM_029402)	-203	NM_029402	71745	Mm.291707	NM_029402	ENSMUSG00000024231	Cul2	1300003D18Rik|4932411N15Rik|AI327301|mKIAA4106	cullin 2	protein-coding
mm_731.1	chr1	43197122	43197128	+	1	NA	promoter-TSS (NM_001289533)	promoter-TSS (NM_001289533)	-364	NM_001289533	14200	Mm.6799	NM_010212	ENSMUSG00000008136	Fhl2	FHL-2|SLIM-3|SLIM3	four and a half LIM domains 2	protein-coding
mm_122064.1	chr14	30469873	30469883	-	1	NA	intron (NM_028981, intron 1 of 46)	intron (NM_028981, intron 1 of 46)	-9687	NM_133761	75901	Mm.28733	NM_133761	ENSMUSG00000021962	Dcp1a	1110066A22Rik|4930568L04Rik|AU019772|D14Ertd817e|Mitc1|SMIF	decapping mRNA 1A	protein-coding
mm_12764.1	chr2	79256166	79256176	+	1	NA	intron (NM_010576, intron 1 of 27)	intron (NM_010576, intron 1 of 27)	745	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D|Itga4B	integrin alpha 4	protein-coding
mm_99977.1	chr11	114091475	114091515	+	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-25544	NM_172800	237979	Mm.130504	NM_172800	ENSMUSG00000041592	Sdk2	4632412F08Rik|5330435L01Rik|Sdk-2|mKIAA1514	sidekick cell adhesion molecule 2	protein-coding
mm_6824.1	chr1	84200334	84200358	-	1	NA	intron (NM_001003948, intron 1 of 2)	intron (NM_001003948, intron 1 of 2)	18615	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_81040.1	chr9	105395310	105395345	+	1	NA	promoter-TSS (NM_025651)	promoter-TSS (NM_025651)	-40	NM_172461	208583	Mm.347509	NM_172461	ENSMUSG00000035032	Nek11	4932416N14Rik	NIMA (never in mitosis gene a)-related expressed kinase 11	protein-coding
mm_135501.1	chr16	46496870	46496883	-	1	NA	promoter-TSS (NM_021495)	promoter-TSS (NM_021495)	91	NM_021496	58998	Mm.40477	NM_021495	ENSMUSG00000022656	Nectin3	2610301B19Rik|3000002N23Rik|4921513D19Rik|AA407785|AU016832|AW538082|CD113|Pvrl3	nectin cell adhesion molecule 3	protein-coding
mm_165723.1	chr3	102935253	102935256	-	1	NA	intron (NM_011516, intron 2 of 32)	intron (NM_011516, intron 2 of 32)	846	NM_011516	20957	Mm.243849	NM_011516	ENSMUSG00000027855	Sycp1	SCP1	synaptonemal complex protein 1	protein-coding
mm_32878.1	chr4	118621214	118621239	+	1	NA	promoter-TSS (NM_026789)	promoter-TSS (NM_026789)	427	NM_026932	69072	Mm.29906	NM_026932	ENSMUSG00000028729	Ebna1bp2	1810014B19Rik|AA537058|B830003A16Rik|C81321|Ebp2|Nobp|p40	EBNA1 binding protein 2	protein-coding
mm_18074.1	chr2	42653003	42653028	-	1	NA	5' UTR (NM_053011, exon 1 of 91)	5' UTR (NM_053011, exon 1 of 91)	583	NM_053011	94217	Mm.441398	NM_053011	ENSMUSG00000049252	Lrp1b	9630004P12Rik|LRP-DIT	low density lipoprotein-related protein 1B (deleted in tumors)	protein-coding
mm_167279.1	chr8	35400510	35400525	-	1	NA	Intergenic	Intergenic	24776	NM_177741	244416	Mm.247126	NM_177741	ENSMUSG00000046794	Ppp1r3b	6430576E21|AW821953|GL|PTG	protein phosphatase 1, regulatory (inhibitor) subunit 3B	protein-coding
mm_28521.1	chr3	92588955	92588979	-	1	NA	promoter-TSS (NM_008574)	promoter-TSS (NM_008574)	57	NM_008574	17235	Mm.331192	NM_008574		Smcp	Mcs|Mcsp	sperm mitochondria-associated cysteine-rich protein	protein-coding
mm_78393.1	chr9	28781187	28781190	+	1	NA	intron (NM_177906, intron 3 of 7)	AT_rich|Low_complexity|Low_complexity	989919	NM_177906	330908	Mm.379474	NM_177906	ENSMUSG00000062257	Opcml	2900075O15Rik|3732419F12|AI844366|B930023M13Rik|C230027C17|Gm181|Obcam	opioid binding protein/cell adhesion molecule-like	protein-coding
mm_127205.1	chr15	99212523	99212525	+	1	NA	TTS (NM_139140)	TTS (NM_139140)	-12452	NM_010601	16512	Mm.374793	NM_010601	ENSMUSG00000037579	Kcnh3	AU019351|C030044P22Rik|Elk2|Kv12.2|Melk2	potassium voltage-gated channel, subfamily H (eag-related), member 3	protein-coding
mm_19988.1	chr2	118549669	118549683	-	1	NA	promoter-TSS (NM_138313)	promoter-TSS (NM_138313)	10	NM_138313	171543	Mm.210125	NM_138313	ENSMUSG00000040093	Bmf	AW260063|AW411872	BCL2 modifying factor	protein-coding
mm_94079.1	chr10	128492904	128492914	-	1	NA	promoter-TSS (NM_001317220)	promoter-TSS (NM_001317220)	100	NM_001317220	17904	Mm.337074	NM_010860	ENSMUSG00000090841	Myl6	ESMLC|LC17|LC17-GI|MLC-3|MLC1SM|Myln	myosin, light polypeptide 6, alkali, smooth muscle and non-muscle	protein-coding
mm_12258.1	chr2	68936260	68936268	+	1	NA	intron (NM_172856, intron 2 of 9)	MER45C|DNA|hAT-Tip100	74823	NM_001347161	241447	Mm.222222	NM_172856	ENSMUSG00000027035	Cers6	4732462C07Rik|AW544719|Lass6|T1L	ceramide synthase 6	protein-coding
mm_144518.1	chr18	24746621	24746631	+	1	NA	intron (NM_175276, intron 1 of 26)	B3|SINE|B2	38003	NM_001289655	225288	Mm.329322	NM_175276	ENSMUSG00000034295	Fhod3	A930009H06Rik|FHOS2|mKIAA1695	formin homology 2 domain containing 3	protein-coding
mm_161468.1	chr15	78718110	78718110	-	1	NA	promoter-TSS (NM_183141)	promoter-TSS (NM_183141)	3	NM_183141	207393	Mm.323188	NM_183141	ENSMUSG00000043460	Elfn2	6330514E13|AW048948|BC094219|Lrrc62|Ppp1r29	leucine rich repeat and fibronectin type III, extracellular 2	protein-coding
mm_34731.1	chr4	152185996	152186006	+	1	NA	promoter-TSS (NM_001146057)	promoter-TSS (NM_001146057)	-133	NM_001146057	70025	Mm.296191	NM_133348	ENSMUSG00000028937	Acot7	2410041A17Rik|Ach1|Act|Bach|CTE-IIa|Cte-II|Lach1	acyl-CoA thioesterase 7	protein-coding
mm_145214.1	chr18	50038833	50038836	+	1	NA	intron (NM_001177759, intron 1 of 1)	intron (NM_001177759, intron 1 of 1)	-14448	NM_134131	106869	Mm.27740	NM_134131	ENSMUSG00000062210	Tnfaip8	AA987150|E130304C20Rik|ENSMUSG00000073567|Gg2-1|Gm10539|Nded|Ssc-2|Tipe	tumor necrosis factor, alpha-induced protein 8	protein-coding
mm_121633.1	chr14	8367282	8367297	-	1	NA	intron (NM_146050, intron 1 of 9)	intron (NM_146050, intron 1 of 9)	11474	NM_146050	18300	Mm.25351	NM_146050	ENSMUSG00000021749	Oit1	2310076N21Rik|AV067083|EF-7|Fam3d	oncoprotein induced transcript 1	protein-coding
mm_34089.1	chr4	138832938	138832948	+	1	NA	non-coding (NR_002926, exon 3 of 5)	non-coding (NR_002926, exon 3 of 5)	1067	NM_001082531	18780	Mm.4675	NM_011108	ENSMUSG00000058908	Pla2g2a	EF|Mom1|Pla2|sPLA2|sPla2-IIA	phospholipase A2, group IIA (platelets, synovial fluid)	protein-coding
mm_68910.1	chr7	126457976	126457993	-	1	NA	exon (NM_007504, exon 6 of 23)	exon (NM_007504, exon 6 of 23)	5089	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_31967.1	chr4	87718446	87718451	+	1	NA	Intergenic	Intergenic	87875	NM_001286158	70122	Mm.288898	NM_027326	ENSMUSG00000028496	Mllt3	2210011H10Rik|2610012I03Rik|3830408D16Rik|Af9|D4Ertd321e	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 3	protein-coding
mm_80415.1	chr9	77784693	77784704	+	1	NA	intron (NM_010295, intron 6 of 15)	intron (NM_010295, intron 6 of 15)	30163	NM_010295	14629	Mm.89888	NM_010295	ENSMUSG00000032350	Gclc	D9Wsu168e|GLCL-H|Ggcs-hs|Glclc	glutamate-cysteine ligase, catalytic subunit	protein-coding
mm_159798.1	chr5	112356037	112356037	-	1	NA	promoter-TSS (NM_001039228)	promoter-TSS (NM_001039228)	-4	NM_001039228	625424	Mm.389677	NM_001039228	ENSMUSG00000051503	Gm6583	EG625424	predicted gene 6583	protein-coding
mm_25244.1	chr3	103919627	103919630	+	1	NA	intron (NM_172684, intron 1 of 6)	intron (NM_172684, intron 1 of 6)	5508	NM_172684	229675	Mm.29366	NM_172684	ENSMUSG00000044098	Rsbn1	C230004D03Rik|E330004N01|Rosbin|Rsbn|Rsbp|mKIAA3002	rosbin, round spermatid basic protein 1	protein-coding
mm_120755.1	chr14	73362888	73362921	+	1	NA	3' UTR (NM_008410, exon 6 of 6)	3' UTR (NM_008410, exon 6 of 6)	22367	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_126506.1	chr15	81802687	81802695	+	1	NA	promoter-TSS (NM_153484)	promoter-TSS (NM_153484)	18	NM_153484	21685	Mm.270278	NM_017376	ENSMUSG00000022389	Tef	2310028D20Rik	thyrotroph embryonic factor	protein-coding
mm_87447.1	chr10	51481746	51481752	+	1	NA	exon (NM_008147, exon 4 of 9)	exon (NM_008147, exon 4 of 9)	1137	NM_001291892	14727	Mm.439661	NM_008147	ENSMUSG00000062593	Lilr4b	Gp49a|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4B	protein-coding
mm_105022.1	chr11	100441830	100441833	-	1	NA	promoter-TSS (NM_001102650)	promoter-TSS (NM_001102650)	-93	NM_025727	66720	Mm.34168	NM_025727	ENSMUSG00000001558	Klhl10	4921517C11Rik	kelch-like 10	protein-coding
mm_65314.1	chr7	24851084	24851094	-	1	NA	Intergenic	RSINE1|SINE|B4	18602	NM_182785	232973	Mm.189648	NM_182785	ENSMUSG00000062732	Lypd4	4933400F01Rik	Ly6/Plaur domain containing 4	protein-coding
mm_111304.1	chr12	85705636	85705674	-	1	NA	intron (NM_016767, intron 2 of 2)	intron (NM_016767, intron 2 of 2)	18935	NM_016767	53314	Mm.6672	NM_016767	ENSMUSG00000034266	Batf	B-ATF|SFA-2	basic leucine zipper transcription factor, ATF-like	protein-coding
mm_69647.1	chr7	139188463	139188535	-	1	NA	promoter-TSS (NM_021302)	promoter-TSS (NM_021302)	-5	NM_021302	57740	Mm.65336	NM_021302	ENSMUSG00000015981	Stk32c	PKE|Pkek|YANK3	serine/threonine kinase 32C	protein-coding
mm_90653.1	chr10	128748752	128748783	+	1	NA	intron (NM_001170869, intron 1 of 2)	intron (NM_001170869, intron 1 of 2)	312	NM_001253704	78428	Mm.27358	NM_030100	ENSMUSG00000064030	Pym1	A030010B05Rik|Pym|Wibg	PYM homolog 1, exon junction complex associated factor	protein-coding
mm_106329.1	chr11	118318868	118318874	-	1	NA	intron (NM_011594, intron 2 of 4)	intron (NM_011594, intron 2 of 4)	23663	NM_021440	58251	Mm.439815	NM_021440	ENSMUSG00000076433	BC100451	Cep295nl|Ddc8|FS39|Kiaa1731nl	cDNA sequence BC100451	protein-coding
mm_5434.1	chr1	34819756	34819769	-	1	NA	exon (NM_001160236, exon 5 of 7)	exon (NM_001160236, exon 5 of 7)	18040	NM_183019	226970	Mm.41604	NM_183019	ENSMUSG00000037509	Arhgef4	9330140K16Rik|Asef|ENSMUSG00000070955	Rho guanine nucleotide exchange factor (GEF) 4	protein-coding
mm_115943.1	chr13	23704325	23704334	-	1	NA	3' UTR (NM_001347493, exon 5 of 5)	3' UTR (NM_001347493, exon 5 of 5)	-5871	NM_178208	319155	Mm.261662	NM_178208	ENSMUSG00000060678	Hist1h4c	-	histone cluster 1, H4c	protein-coding
mm_132052.1	chr16	29579300	29579310	+	1	NA	promoter-TSS (NM_133752)	promoter-TSS (NM_133752)	-29	NM_133752	74143	Mm.274285	NM_133752	ENSMUSG00000038084	Opa1	1200011N24Rik|AI225888|AI847218|lilr3|mKIAA0567	OPA1, mitochondrial dynamin like GTPase	protein-coding
mm_98576.1	chr11	95712869	95712911	+	1	NA	promoter-TSS (NR_045780)	promoter-TSS (NR_045780)	-136	NR_045780	432396	Mm.426849	NR_045780	ENSMUSG00000086191	Zfp652os	1110035M17Rik	zinc finger protein 652, opposite strand	ncRNA
mm_114777.1	chr13	88821751	88821761	+	1	NA	5' UTR (NM_001037987, exon 1 of 11)	5' UTR (NM_001037987, exon 1 of 11)	284	NM_001037987	13612	Mm.125580	NM_010103	ENSMUSG00000034488	Edil3	Del-1|Del1	EGF-like repeats and discoidin I-like domains 3	protein-coding
mm_135524.1	chr16	48993932	48993949	-	1	NA	promoter-TSS (NM_172616)	promoter-TSS (NM_172616)	172	NM_001110017	224170	Mm.275138	NM_027341	ENSMUSG00000064061	Dzip3	2310047C04Rik|2A-HUB|6430549P11Rik|A230104G20	DAZ interacting protein 3, zinc finger	protein-coding
mm_5776.1	chr1	51478124	51478131	-	1	NA	5' UTR (NM_028696, exon 1 of 6)	5' UTR (NM_028696, exon 1 of 6)	272	NM_028696	109019	Mm.196290	NM_028696	ENSMUSG00000026107	Nabp1	4930434H03Rik|4930442A21Rik|4930488J04Rik|4933440J18Rik|5830411E10Rik|AI852561|Nbp1|Obfc2a|Ssb2	nucleic acid binding protein 1	protein-coding
mm_117173.1	chr13	63113095	63113105	-	1	NA	intron (NM_001289926, intron 5 of 15)	intron (NM_001289926, intron 5 of 15)	-126929	NR_110520	72061	Mm.188105	NM_028079	ENSMUSG00000021458	2010111I01Rik	2300006M17Rik|AP-O|AW742919|Aopep|ApO|mir-23b|mir-24-1|mir-27b	RIKEN cDNA 2010111I01 gene	protein-coding
mm_160064.1	chr7	5014270	5014270	-	1	NA	promoter-TSS (NM_011813)	promoter-TSS (NM_011813)	-17	NM_011813	23877	Mm.38911	NM_011813	ENSMUSG00000061374	Fiz1	AI790204|mFLJ00416	Flt3 interacting zinc finger protein 1	protein-coding
mm_36260.1	chr4	63452690	63452690	-	1	NA	intron (NM_001008791, intron 3 of 12)	intron (NM_001008791, intron 3 of 12)	43301	NM_001008793	73750	Mm.300397	NM_028640	ENSMUSG00000039137	Whrn	1110035G07Rik|AW122018|AW742671|C430046P22Rik|Dfnb31|Ush2d|wi	whirlin	protein-coding
mm_60393.1	chr7	44475074	44475076	+	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	4728	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_55642.1	chr6	72345145	72345206	-	1	NA	promoter-TSS (NM_138592)	promoter-TSS (NM_138592)	0	NM_138592	28035	Mm.281900	NM_138592	ENSMUSG00000056305	Usp39	AA408960|AI894154|CGI-21|D6Wsu157e|SAD1	ubiquitin specific peptidase 39	protein-coding
mm_101178.1	chr11	16995312	16995327	-	1	NA	exon (NM_019549, exon 2 of 10)	exon (NM_019549, exon 2 of 10)	13399	NM_019549	56193	Mm.98232	NM_019549	ENSMUSG00000020120	Plek	2010300B13Rik	pleckstrin	protein-coding
mm_81004.1	chr9	103426673	103426675	+	1	NA	non-coding (NR_040466, exon 2 of 6)	non-coding (NR_040466, exon 2 of 6)	3096	NR_040466	100529079	Mm.437003	NR_040466	ENSMUSG00000086236	5830418P13Rik	-	RIKEN cDNA 5830418P13 gene	ncRNA
mm_52810.1	chr6	121343313	121343320	+	1	NA	intron (NM_001347433, intron 1 of 14)	intron (NM_001347433, intron 1 of 14)	240	NM_001347433	14411	Mm.274506	NM_133661	ENSMUSG00000030109	Slc6a12	BGT1|GAT-2|GAT2|Gabt2	solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12	protein-coding
mm_13671.1	chr2	115581796	115581822	+	1	NA	promoter-TSS (NM_207264)	promoter-TSS (NM_207264)	93	NM_001145898	399568	Mm.134929	NM_207264	ENSMUSG00000040282	BC052040	-	cDNA sequence BC052040	protein-coding
mm_107204.1	chr12	26443742	26443753	+	1	NA	3' UTR (NM_021384, exon 6 of 6)	3' UTR (NM_021384, exon 6 of 6)	12705	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_157946.1	chrX	86354949	86354991	-	1	NA	promoter-TSS (NR_036689)	promoter-TSS (NR_036689)	24	NR_036689	245502	Mm.490821	NR_036689		Gm41	-	melanoma antigen, family B, 4 pseudogene	pseudo
mm_66167.1	chr7	33739304	33739322	-	1	NA	promoter-TSS (NM_177446)	promoter-TSS (NM_177446)	-18	NM_177446	233090	Mm.261648	NM_177446	ENSMUSG00000046438	Scgb2b24	Abpbg24|Abpz|C2b|Scgb2b3	secretoglobin, family 2B, member 24	protein-coding
mm_102463.1	chr11	59948080	59948101	-	1	NA	promoter-TSS (NR_045273)	promoter-TSS (NR_045273)	57	NR_045273	100504121	Mm.383770	NR_045273	ENSMUSG00000085260	Med9os	1700013G23Rik	mediator complex subunit 9, opposite strand	ncRNA
mm_91622.1	chr10	41746383	41746403	-	1	NA	intron (NM_001243074, intron 2 of 10)	intron (NM_001243074, intron 2 of 10)	63270	NM_001243075	103268	Mm.338605	NM_026643	ENSMUSG00000019813	Cep57l1	2410017P07Rik|4930484D11Rik|AI607327|cep57R	centrosomal protein 57-like 1	protein-coding
mm_69138.1	chr7	127050257	127050266	-	1	NA	3' UTR (NM_026918, exon 3 of 3)	3' UTR (NM_026918, exon 3 of 3)	1716	NM_026918	69036	Mm.21835	NM_026918	ENSMUSG00000049350	Zg16	1810010M01Rik|AI593689|ZG16p	zymogen granule protein 16	protein-coding
mm_62540.1	chr7	102268125	102268189	+	1	NA	5' UTR (NM_009287, exon 1 of 12)	5' UTR (NM_009287, exon 1 of 12)	333	NM_009287	20866	Mm.645	NM_009287	ENSMUSG00000030987	Stim1	SIM	stromal interaction molecule 1	protein-coding
mm_67384.1	chr7	79842344	79842354	-	1	NA	promoter-TSS (NM_008486)	promoter-TSS (NM_008486)	3	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_20744.1	chr2	140042123	140042132	-	1	NA	exon (NM_175225, exon 4 of 14)	exon (NM_175225, exon 4 of 14)	24678	NM_001159640	75812	Mm.293449	NM_175225	ENSMUSG00000039033	Tasp1	4930485D02Rik|AW986064	taspase, threonine aspartase 1	protein-coding
mm_23858.1	chr3	83010491	83010509	+	1	NA	exon (NM_133862, exon 6 of 10)	exon (NM_133862, exon 6 of 10)	2776	NM_001317105	99571	Mm.16422	NM_133862	ENSMUSG00000033860	Fgg	3010002H13Rik|AI256424	fibrinogen gamma chain	protein-coding
mm_110392.1	chr12	41485945	41485960	-	1	NA	5' UTR (NM_001271709, exon 1 of 2)	5' UTR (NM_001271709, exon 1 of 2)	105	NM_001271708	16981	Mm.404786	NM_010733	ENSMUSG00000036295	Lrrn3	NLRR-3	leucine rich repeat protein 3, neuronal	protein-coding
mm_52583.1	chr6	116650675	116650690	+	1	NA	promoter-TSS (NM_001166580)	promoter-TSS (NM_001166580)	-2	NM_145980	213393	Mm.38231	NM_145980	ENSMUSG00000048489	8430408G22Rik	Depp|Fseg	RIKEN cDNA 8430408G22 gene	protein-coding
mm_80640.1	chr9	89248551	89248564	+	1	NA	Intergenic	ORR1B2|LTR|ERVL-MaLR	37367	NM_026829	107885	Mm.486274	NM_026829	ENSMUSG00000066442	Mthfs	1110034I12Rik|2310020H23Rik|AI119695	5, 10-methenyltetrahydrofolate synthetase	protein-coding
mm_57741.1	chr6	129047461	129047480	-	1	NA	intron (NR_024262, intron 1 of 5)	intron (NR_024262, intron 1 of 5)	1569	NR_024263	232408	Mm.259262	NM_153094	ENSMUSG00000030154	Klrb1f	A630024B12Rik|Nkr-p1f|Nkrp1-f|Nkrp1f	killer cell lectin-like receptor subfamily B member 1F	protein-coding
mm_153987.1	chr19	47919270	47919305	-	1	NA	promoter-TSS (NM_001001738)	promoter-TSS (NM_001001738)	12	NM_001001738	414801	Mm.29457	NM_001001738	ENSMUSG00000044948	Itprip	4833424O12Rik|DANGER|mKIAA1754	inositol 1,4,5-triphosphate receptor interacting protein	protein-coding
mm_56096.1	chr6	87388879	87388892	-	1	NA	promoter-TSS (NM_026860)	promoter-TSS (NM_026860)	50	NM_026860	68888	Mm.46387	NM_026860	ENSMUSG00000030048	Gkn3	1190003M12Rik	gastrokine 3	protein-coding
mm_158596.1	chrX	151096511	151096530	-	1	NA	promoter-TSS (NM_175146)	promoter-TSS (NM_175146)	23	NM_001164578	69499	Mm.8142	NM_175146	ENSMUSG00000025264	Tsr2	2310007F12Rik	TSR2 20S rRNA accumulation	protein-coding
mm_79669.1	chr9	59668905	59668921	+	1	NA	exon (NM_011099, exon 5 of 11)	exon (NM_011099, exon 5 of 11)	12545	NM_001253883	18746	Mm.326167	NM_011099	ENSMUSG00000032294	Pkm	AA414905|AL024370|AL024424|Pk-2|Pk-3|Pk3|Pkm2	pyruvate kinase, muscle	protein-coding
mm_157846.1	chrX	74393110	74393176	-	1	NA	promoter-TSS (NM_001161424)	promoter-TSS (NM_001161424)	131	NM_025473	66294	Mm.166485	NM_025473	ENSMUSG00000031399	Fam3a	1810037C20Rik	family with sequence similarity 3, member A	protein-coding
mm_157754.1	chrX	73494725	73494749	-	1	NA	exon (NM_007542, exon 8 of 8)	exon (NM_007542, exon 8 of 8)	-8349	NM_001310537	320707	Mm.210095	NM_177236	ENSMUSG00000031376	Atp2b3	6430519O13Rik|Pmca3	ATPase, Ca++ transporting, plasma membrane 3	protein-coding
mm_83799.1	chr9	52679731	52679787	-	1	NA	promoter-TSS (NM_178906)	promoter-TSS (NM_178906)	21	NM_001286641	330941	Mm.335160	NM_177907	ENSMUSG00000078307	AI593442	E130102D23	expressed sequence AI593442	protein-coding
mm_90188.1	chr10	120169408	120169418	+	1	NA	intron (NM_028679, intron 6 of 11)	intron (NM_028679, intron 6 of 11)	32124	NM_028679	73914	Mm.146194	NM_028679	ENSMUSG00000020227	Irak3	4833428C18Rik|AI563835|IRAK-M	interleukin-1 receptor-associated kinase 3	protein-coding
mm_1706.1	chr1	75236401	75236429	+	1	NA	promoter-TSS (NM_001159883)	promoter-TSS (NM_001159883)	-8	NM_020266	56812	Mm.489660	NM_020266	ENSMUSG00000026203	Dnajb2	2700059H22Rik|Dnajb10|Hsj1|mDj8	DnaJ heat shock protein family (Hsp40) member B2	protein-coding
mm_132324.1	chr16	33794136	33794161	+	1	NA	intron (NM_010739, intron 1 of 12)	intron (NM_010739, intron 1 of 12)	111	NM_010739	17063	Mm.3177	NM_010739	ENSMUSG00000022824	Muc13	114/A10|14/A10|AI159736|Lrrp|Ly64|NJ-1	mucin 13, epithelial transmembrane	protein-coding
mm_19691.1	chr2	103485069	103485137	-	1	NA	promoter-TSS (NM_009804)	promoter-TSS (NM_009804)	50	NM_009804	12359	Mm.4215	NM_009804	ENSMUSG00000027187	Cat	2210418N07|Cas-1|Cas1|Cs-1	catalase	protein-coding
mm_976.1	chr1	58393472	58393482	+	1	NA	intron (NM_025824, intron 1 of 11)	CpG	341	NM_025824	66882	Mm.21848	NM_025824	ENSMUSG00000051223	Bzw1	1200015E15Rik|mKIAA0005	basic leucine zipper and W2 domains 1	protein-coding
mm_61257.1	chr7	66060529	66060597	+	1	NA	5' UTR (NM_021336, exon 1 of 9)	5' UTR (NM_021336, exon 1 of 9)	227	NM_021336	68981	Mm.22362	NM_021336	ENSMUSG00000030512	Snrpa1	1500015N06Rik	small nuclear ribonucleoprotein polypeptide A'	protein-coding
mm_102759.1	chr11	67581935	67581942	-	1	NA	intron (NM_008088, intron 1 of 13)	intron (NM_008088, intron 1 of 13)	-4562	NM_001109657	14457	Mm.40338	NM_008088	ENSMUSG00000033066	Gas7	AW124766|B230343A10Rik|Gas7-cb	growth arrest specific 7	protein-coding
mm_40073.1	chr5	34336402	34336459	+	1	NA	promoter-TSS (NM_001304270)	promoter-TSS (NM_001304270)	50	NM_001304269	19822	Mm.21281	NM_011278	ENSMUSG00000029110	Rnf4	AU018689|Gtrgeo8|SNURF	ring finger protein 4	protein-coding
mm_168330.1	chr11	117086789	117086789	+	1	NA	Intergenic	Intergenic	9441	NR_105853	102465258		NR_105853	ENSMUSG00000104740	Mir6516	mmu-mir-6516	microRNA 6516	ncRNA
mm_8186.1	chr1	138090470	138090477	-	1	NA	intron (NM_001111316, intron 16 of 31)	intron (NM_001111316, intron 16 of 31)	84653	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_81177.1	chr9	107334761	107334769	+	1	NA	intron (NM_133984, intron 4 of 10)	intron (NM_133984, intron 4 of 10)	3585	NM_133984	69536	Mm.259467	NM_133984	ENSMUSG00000032579	Hemk1	2310008M14Rik|AW049265	HemK methyltransferase family member 1	protein-coding
mm_144404.1	chr18	20944608	20944625	+	1	NA	promoter-TSS (NM_026301)	promoter-TSS (NM_026301)	-9	NM_026301	67664	Mm.45980	NM_026301	ENSMUSG00000033107	Rnf125	4930553F04Rik	ring finger protein 125	protein-coding
mm_24420.1	chr3	90526862	90526881	+	1	NA	promoter-TSS (NM_001163526)	promoter-TSS (NM_001163526)	22	NM_001163526	66166	Mm.24006	NM_025393	ENSMUSG00000042306	S100a14	1110013O05Rik|S100a15|S114	S100 calcium binding protein A14	protein-coding
mm_59560.1	chr7	28085414	28085424	+	1	NA	exon (NM_001122603, exon 4 of 20)	exon (NM_001122603, exon 4 of 20)	14183	NM_001122603	215384	Mm.292276	NM_175444	ENSMUSG00000047730	Fcgbp	A430096B05Rik	Fc fragment of IgG binding protein	protein-coding
mm_22063.1	chr2	168670089	168670102	-	1	NA	intron (NM_001289446, intron 13 of 27)	intron (NM_001289446, intron 13 of 27)	-29336	NR_105971	102466784		NR_105971	ENSMUSG00000105496	Mir7004	mmu-mir-7004	microRNA 7004	ncRNA
mm_39252.1	chr5	3502805	3502835	+	1	NA	intron (NM_009873, intron 5 of 7)	intron (NM_009873, intron 5 of 7)	-41013	NM_001042501	68152	Mm.240265	NM_026583	ENSMUSG00000058503	Fam133b	2900022K02Rik|5830415L20Rik	family with sequence similarity 133, member B	protein-coding
mm_101520.1	chr11	32614684	32614694	-	1	NA	exon (NM_009288, exon 16 of 19)	exon (NM_009288, exon 16 of 19)	-27866	NM_001271348	103583	Mm.28017	NM_134015	ENSMUSG00000020271	Fbxw11	2310065A07Rik|AA536858|BTRC2|BTRCP2|Fbxw1b|HOS	F-box and WD-40 domain protein 11	protein-coding
mm_151502.1	chr19	58729892	58729902	+	1	NA	intron (NM_018874, intron 2 of 12)	Lx7|LINE|L1	1010	NM_018874	18946	Mm.10753	NM_018874	ENSMUSG00000042179	Pnliprp1	Plrp1	pancreatic lipase related protein 1	protein-coding
mm_46240.1	chr5	99223584	99223614	-	1	NA	intron (NM_145839, intron 10 of 13)	intron (NM_145839, intron 10 of 13)	29328	NM_181318	320292	Mm.259074	NM_145839	ENSMUSG00000089809	Rasgef1b	4732452O09Rik|GPIgamma4|Gpig4	RasGEF domain family, member 1B	protein-coding
mm_121787.1	chr14	19977133	19977150	-	1	NA	promoter-TSS (NM_001285911)	promoter-TSS (NM_001285911)	108	NM_001038637	14702	Mm.41737	NM_010315	ENSMUSG00000043004	Gng2	-	guanine nucleotide binding protein (G protein), gamma 2	protein-coding
mm_29304.1	chr3	107943333	107943348	-	1	NA	intron (NM_008184, intron 1 of 7)	intron (NM_008184, intron 1 of 7)	409	NM_008184	14867	Mm.458154	NM_008184	ENSMUSG00000068762	Gstm6	-	glutathione S-transferase, mu 6	protein-coding
mm_8928.1	chr1	164062998	164063008	-	1	NA	intron (NM_011346, intron 1 of 8)	intron (NM_011346, intron 1 of 8)	927	NM_001164059	20343	Mm.1461	NM_011346	ENSMUSG00000026581	Sell	AI528707|CD62L|L-selectin|LECAM-1|Lnhr|Ly-22|Ly-m22|Lyam-1|Lyam1	selectin, lymphocyte	protein-coding
mm_3382.1	chr1	139491492	139491527	+	1	NA	intron (NM_009791, intron 25 of 27)	intron (NM_009791, intron 25 of 27)	-10198	NM_031164	14060	Mm.30105	NM_031164	ENSMUSG00000026368	F13b	Cf-13b|Cf13b	coagulation factor XIII, beta subunit	protein-coding
mm_67745.1	chr7	90457168	90457213	-	1	NA	promoter-TSS (NM_025460)	promoter-TSS (NM_025460)	18	NM_025460	66271	Mm.28963	NM_025460	ENSMUSG00000030615	Tmem126a	1810020E01Rik	transmembrane protein 126A	protein-coding
mm_88277.1	chr10	75060552	75060628	+	1	NA	promoter-TSS (NM_001081412)	promoter-TSS (NM_001081412)	-306	NM_001081412	110279	Mm.333722	NM_001081412	ENSMUSG00000009681	Bcr	5133400C09Rik|AI561783|AI853148|mKIAA3017	breakpoint cluster region	protein-coding
mm_118269.1	chr13	112591241	112591287	-	1	NA	Intergenic	Intergenic	-10602	NM_139299	218624	Mm.380801	NM_139299	ENSMUSG00000050377	Il31ra	CRL3|GLM-R|GPL|Glmr|NR10	interleukin 31 receptor A	protein-coding
mm_9796.1	chr1	181842335	181842384	-	1	NA	promoter-TSS (NM_133815)	promoter-TSS (NM_133815)	42	NM_133815	98386	Mm.4538	NM_133815	ENSMUSG00000004880	Lbr	AI505894|ic	lamin B receptor	protein-coding
mm_80639.1	chr9	89248538	89248548	+	1	NA	Intergenic	ORR1B2|LTR|ERVL-MaLR	37353	NM_026829	107885	Mm.486274	NM_026829	ENSMUSG00000066442	Mthfs	1110034I12Rik|2310020H23Rik|AI119695	5, 10-methenyltetrahydrofolate synthetase	protein-coding
mm_130300.1	chr15	97019841	97019847	-	1	NA	5' UTR (NM_027052, exon 2 of 16)	5' UTR (NM_027052, exon 2 of 16)	36112	NM_027052	69354	Mm.250980	NM_027052	ENSMUSG00000022464	Slc38a4	1110012E16Rik|1700012A18Rik|Ata3|mATA3|mNAT3	solute carrier family 38, member 4	protein-coding
mm_129944.1	chr15	84949002	84949062	-	1	NA	3' UTR (NM_001033273, exon 10 of 10)	3' UTR (NM_001033273, exon 10 of 10)	2591	NR_037206	100526461		NR_037206	ENSMUSG00000080441	Mir1249	mir-1249|mmu-mir-1249	microRNA 1249	ncRNA
mm_75007.1	chr8	27250835	27250857	-	1	NA	Intergenic	RMER6A|LTR|ERVK	-9481	NM_007918	13685	Mm.6700	NM_007918	ENSMUSG00000031490	Eif4ebp1	4e-bp1|AA959816|PHAS-I	eukaryotic translation initiation factor 4E binding protein 1	protein-coding
mm_35218.1	chr4	19651998	19652001	-	1	NA	intron (NR_074090, intron 8 of 24)	intron (NR_074090, intron 8 of 24)	57005	NM_177327	107568	Mm.78312	NM_177327	ENSMUSG00000041058	Wwp1	8030445B08Rik|AIP5|SDRP1|Tiul1	WW domain containing E3 ubiquitin protein ligase 1	protein-coding
mm_14290.1	chr2	128820699	128820718	+	1	NA	intron (NM_028248, intron 1 of 18)	intron (NM_028248, intron 1 of 18)	2405	NM_028248	72477	Mm.259688	NM_028248	ENSMUSG00000014353	Tmem87b	2610301K12Rik|2810431I02Rik|AU014804	transmembrane protein 87B	protein-coding
mm_139223.1	chr17	47730599	47730605	+	1	NA	exon (NM_025973, exon 5 of 9)	exon (NM_025973, exon 5 of 9)	3760	NM_025973	109820	Mm.22957	NM_025973	ENSMUSG00000023987	Pgc	2210410L06Rik|Upg-1|Upg1	progastricsin (pepsinogen C)	protein-coding
mm_122857.1	chr14	54877133	54877177	-	1	NA	exon (NM_001167908, exon 1 of 2)	exon (NM_001167908, exon 1 of 2)	383	NM_001167908	105651	Mm.297365	NM_001167908	ENSMUSG00000072494	Ppp1r3e	A630071A11Rik|AW049239|Gm1211	protein phosphatase 1, regulatory (inhibitor) subunit 3E	protein-coding
mm_82982.1	chr9	36135627	36135634	-	1	NA	promoter-TSS (NR_030729)	promoter-TSS (NR_030729)	0	NR_030729	100041618	Mm.484847	NR_030729	ENSMUSG00000098390	Gm3434	-	predicted gene 3434	ncRNA
mm_59032.1	chr7	19307238	19307256	+	1	NA	exon (NM_008036, exon 2 of 4)	exon (NM_008036, exon 2 of 4)	2798	NM_008036	14282	Mm.248335	NM_008036	ENSMUSG00000003545	Fosb	-	FBJ osteosarcoma oncogene B	protein-coding
mm_155555.1	chrX	75095886	75095922	+	1	NA	promoter-TSS (NM_001030307)	promoter-TSS (NM_001030307)	50	NM_001030307	245474	Mm.291062	NM_001030307	ENSMUSG00000031403	Dkc1	BC068171	dyskeratosis congenita 1, dyskerin	protein-coding
mm_49435.1	chr6	29281180	29281184	+	1	NA	promoter-TSS (NM_001101486)	promoter-TSS (NM_001101486)	41	NM_001101486	245884	Mm.33683	NM_001101486	ENSMUSG00000079652	Fam71f2	AI507611|GARI	family with sequence similarity 71, member F2	protein-coding
mm_126252.1	chr15	79030850	79030859	+	1	NA	promoter-TSS (NM_001161712)	promoter-TSS (NM_001161712)	-20	NM_013847	26912	Mm.237085	NM_013847	ENSMUSG00000006378	Gcat	AI526977|Kbl	glycine C-acetyltransferase (2-amino-3-ketobutyrate-coenzyme A ligase)	protein-coding
mm_9152.1	chr1	170927520	170927531	-	1	NA	promoter-TSS (NM_001160215)	promoter-TSS (NM_001160215)	58	NM_001160215	98752	Mm.1850	NM_145141	ENSMUSG00000038421	Fcrla	BB219290|FCRL|FCRL1|FREB|Fcrlm1|Fcrx|Freb1|mFREB|mFcrX	Fc receptor-like A	protein-coding
mm_142337.1	chr17	43569949	43569956	-	1	NA	intron (NM_013737, intron 1 of 11)	intron (NM_013737, intron 1 of 11)	1501	NM_013737	27226	Mm.9277	NM_013737	ENSMUSG00000023913	Pla2g7	PAF-AH|R75400	phospholipase A2, group VII (platelet-activating factor acetylhydrolase, plasma)	protein-coding
mm_108037.1	chr12	73867685	73867688	+	1	NA	Intergenic	Intergenic	-33638	NM_001313920	15251	Mm.3879	NM_010431	ENSMUSG00000021109	Hif1a	AA959795|HIF-1-alpha|HIF1-alpha|HIF1alpha|MOP1|bHLHe78	hypoxia inducible factor 1, alpha subunit	protein-coding
mm_98391.1	chr11	94214558	94214591	+	1	NA	exon (NM_009427, exon 2 of 2)	exon (NM_009427, exon 2 of 2)	3120	NM_009427	22057	Mm.259673	NM_009427	ENSMUSG00000037573	Tob1	Tob|Trob	transducer of ErbB-2.1	protein-coding
mm_106346.1	chr11	118393406	118393419	-	1	NA	exon (NM_011150, exon 6 of 6)	exon (NM_011150, exon 6 of 6)	8519	NM_011150	19039	Mm.3152	NM_011150	ENSMUSG00000033880	Lgals3bp	90K|CyCAP|MAC-2BP|Ppicap|Tango10b	lectin, galactoside-binding, soluble, 3 binding protein	protein-coding
mm_96581.1	chr11	69070923	69070933	+	1	NA	5' UTR (NM_025838, exon 1 of 5)	5' UTR (NM_025838, exon 1 of 5)	119	NM_028336	66910	Mm.33964	NM_025838	ENSMUSG00000020895	Tmem107	1110004B13Rik|2810049P21Rik	transmembrane protein 107	protein-coding
mm_8911.1	chr1	163313067	163313076	-	1	NA	5' UTR (NM_175686, exon 1 of 5)	5' UTR (NM_175686, exon 1 of 5)	579	NM_011127	18933	Mm.288642	NM_011127	ENSMUSG00000026586	Prrx1	A230024N07Rik|AA755424|AI385634|AI843499|K-2|Pmx|Pmx1|Prx1|mHox	paired related homeobox 1	protein-coding
mm_119830.1	chr14	54361031	54361135	+	1	NA	intron (NM_026936, intron 1 of 9)	CpG	242	NM_026936	69089	Mm.182340	NM_026936	ENSMUSG00000000959	Oxa1l	1810020M02Rik|AI894287	oxidase assembly 1-like	protein-coding
mm_104379.1	chr11	94456461	94456469	-	1	NA	intron (NM_001177888, intron 9 of 34)	intron (NM_001177888, intron 9 of 34)	17733	NM_001177888	12291	Mm.29585	NM_009783	ENSMUSG00000020866	Cacna1g	Cav3.1d|[a]1G|a1G|alpha-1G|mKIAA1123	calcium channel, voltage-dependent, T type, alpha 1G subunit	protein-coding
mm_148971.1	chr19	7539132	7539133	+	1	NA	TTS (NM_001163505)	TTS (NM_001163505)	-18327	NM_139269	225845	Mm.274810	NM_139269	ENSMUSG00000060675	Pla2g16	C78643|HRSL3|Hrasls3|Hrev107|MLP-3	phospholipase A2, group XVI	protein-coding
mm_94268.1	chr11	3530933	3530959	+	1	NA	intron (NM_001159284, intron 9 of 21)	intron (NM_001159284, intron 9 of 21)	8346	NM_013870	29856	Mm.188516	NM_013870	ENSMUSG00000020439	Smtn	smsmo	smoothelin	protein-coding
mm_83739.1	chr9	51101897	51101934	-	1	NA	exon (NM_177702, exon 1 of 6)	exon (NM_177702, exon 1 of 6)	163	NM_177702	235345	Mm.72828	NM_177702	ENSMUSG00000032057	4833427G06Rik	-	RIKEN cDNA 4833427G06 gene	protein-coding
mm_113572.1	chr13	39824176	39824213	+	1	NA	Intergenic	Intergenic	463817	NM_172143	218165	Mm.364096	NM_172143	ENSMUSG00000047094	Ofcc1	opo	orofacial cleft 1 candidate 1	protein-coding
mm_48494.1	chr5	142746720	142746721	-	1	NA	intron (NM_001122730, intron 16 of 27)	intron (NM_001122730, intron 16 of 27)	44619	NM_146257	243328	Mm.125942	NM_146257	ENSMUSG00000050822	Slc29a4	ENT4|mPMAT	solute carrier family 29 (nucleoside transporters), member 4	protein-coding
mm_4614.1	chr1	178566478	178566481	+	1	NA	intron (NM_001161665, intron 2 of 14)	intron (NM_001161665, intron 2 of 14)	37354	NM_001161665	269152	Mm.129727	NM_177724	ENSMUSG00000026494	Kif26b	4832420M10|BC056349|D230039L06Rik	kinesin family member 26B	protein-coding
mm_90856.1	chr10	8829803	8829828	-	1	NA	intron (NM_175155, intron 2 of 19)	(CCTG)n|Simple_repeat|Simple_repeat	56255	NM_175155	70097	Mm.338275	NM_175155	ENSMUSG00000015305	Sash1	1100001C18Rik|2500002E12Rik|A330076K04Rik|mKIAA0790	SAM and SH3 domain containing 1	protein-coding
mm_49436.1	chr6	29313458	29313472	+	1	NA	Intergenic	L1M6|LINE|L1	-5675	NM_001289663	330277	Mm.87624	NM_207258	ENSMUSG00000039742	Fam71f1	GARI-L1|Gm764|NYD-SP18	family with sequence similarity 71, member F1	protein-coding
mm_167935.1	chrX	107149646	107149656	+	1	NA	promoter-TSS (NM_175442)	promoter-TSS (NM_175442)	36	NM_175442	213438	Mm.265244	NM_175442	ENSMUSG00000054293	A630033H20Rik	AI662791|P2ry10	RIKEN cDNA A630033H20 gene	protein-coding
mm_20156.1	chr2	122118318	122118349	-	1	NA	promoter-TSS (NM_145531)	promoter-TSS (NM_145531)	53	NM_145531	214585	Mm.222303	NM_145531	ENSMUSG00000033396	Spg11	6030465E24Rik|A330015I11|C530005A01Rik	spastic paraplegia 11	protein-coding
mm_150977.1	chr19	46501791	46501802	+	1	NA	5' UTR (NM_053100, exon 1 of 6)	5' UTR (NM_053100, exon 1 of 6)	148	NM_053100	93679	Mm.392177	NM_053100	ENSMUSG00000025034	Trim8	AA408830|BB006755|GERP|Rnf27	tripartite motif-containing 8	protein-coding
mm_134969.1	chr16	32003123	32003183	-	1	NA	5' UTR (NM_177103, exon 1 of 10)	5' UTR (NM_177103, exon 1 of 10)	134	NM_177103	320213	Mm.152890	NM_023801	ENSMUSG00000022772	Senp5	6230429P13Rik|A730063F07Rik|AI851888|BB189556|SMT3IP3	SUMO/sentrin specific peptidase 5	protein-coding
mm_158010.1	chrX	95478108	95478137	-	1	NA	promoter-TSS (NM_080858)	promoter-TSS (NM_080858)	7	NM_080858	70392	Mm.79122	NM_080858	ENSMUSG00000031204	Asb12	2310036C05Rik|Asb-12	ankyrin repeat and SOCS box-containing 12	protein-coding
mm_121557.1	chr14	122484271	122484277	+	1	NA	Intergenic	Intergenic	8890	NM_009574	22772	Mm.308936	NM_009574	ENSMUSG00000061524	Zic2	HPE5|Ku	zinc finger protein of the cerebellum 2	protein-coding
mm_91809.1	chr10	53993770	53993776	-	1	NA	intron (NM_008548, intron 5 of 12)	intron (NM_008548, intron 5 of 12)	82023	NM_008548	17155	Mm.117294	NM_008548	ENSMUSG00000003746	Man1a	Man1a1|PCR1	mannosidase 1, alpha	protein-coding
mm_97442.1	chr11	78178990	78179002	+	1	NA	TTS (NR_106113)	TTS (NR_106113)	169	NR_106113	102465761		NR_106113	ENSMUSG00000099101	Mir7653	Gm27900|mmu-mir-7653	microRNA 7653	ncRNA
mm_127676.1	chr15	102921122	102921132	+	1	NA	promoter-TSS (NM_010464)	promoter-TSS (NM_010464)	-4	NM_010464	15422	Mm.207062	NM_010464	ENSMUSG00000001655	Hoxc13	-	homeobox C13	protein-coding
mm_129555.1	chr15	79455529	79455560	-	1	NA	Intergenic	Intergenic	-13487	NM_013767	27373	Mm.30199	NM_013767	ENSMUSG00000022433	Csnk1e	AI426939|AI551861|AW457082|CK1epsilon|CKIe|KC1epsilon|tau	casein kinase 1, epsilon	protein-coding
mm_32598.1	chr4	111777576	111777617	+	1	NA	intron (NM_026470, intron 6 of 12)	intron (NM_026470, intron 6 of 12)	57586	NM_026470	67946	Mm.275526	NM_026470	ENSMUSG00000034401	Spata6	1700062C23Rik|AI790763|Hash|KRP|Mash	spermatogenesis associated 6	protein-coding
mm_148548.1	chr19	4711367	4711381	+	1	NA	5' UTR (NM_021287, exon 1 of 37)	5' UTR (NM_021287, exon 1 of 37)	151	NM_021287	20743	Mm.329668	NM_021287	ENSMUSG00000067889	Sptbn2	Spnb3|mKIAA0302	spectrin beta, non-erythrocytic 2	protein-coding
mm_6674.1	chr1	80340654	80340675	-	1	NA	promoter-TSS (NM_016716)	promoter-TSS (NM_016716)	26	NM_001313728	26554	Mm.12665	NM_016716	ENSMUSG00000004364	Cul3	KIAA0617	cullin 3	protein-coding
mm_59875.1	chr7	30280535	30280584	+	1	NA	promoter-TSS (NM_146186)	promoter-TSS (NM_146186)	-138	NM_146186	233064	Mm.271677	NM_146186	ENSMUSG00000037020	Wdr62	2310038K02Rik	WD repeat domain 62	protein-coding
mm_52991.1	chr6	123266088	123266095	+	1	NA	intron (NM_001163161, intron 2 of 5)	L1ME3A|LINE|L1	3984	NM_010819	17474	Mm.441101	NM_010819	ENSMUSG00000030144	Clec4d	Clecsf8|Mpcl|mcl	C-type lectin domain family 4, member d	protein-coding
mm_40948.1	chr5	76822558	76822571	+	1	NA	Intergenic	Intergenic	-18035	NM_001163793	320827	Mm.101504	NM_001163793	ENSMUSG00000036377	C530008M17Rik	2810489J07Rik|4930529A19Rik|4931405B09Rik|Kiaa1211|mKIAA1211	RIKEN cDNA C530008M17 gene	protein-coding
mm_151851.1	chr19	5796354	5796381	-	1	NA	promoter-TSS (NR_144621)	promoter-TSS (NR_144621)	-386	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_165229.1	chr2	54610643	54610643	+	1	NA	intron (NM_173030, intron 3 of 12)	intron (NM_173030, intron 3 of 12)	174256	NM_173030	271786	Mm.330227	NM_173030	ENSMUSG00000060988	Galnt13	A230002A12|A230020F20|BB182356	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13	protein-coding
mm_97225.1	chr11	75650613	75650624	+	1	NA	promoter-TSS (NM_008659)	promoter-TSS (NM_008659)	-891	NM_008659	17913	Mm.234502	NM_008659	ENSMUSG00000017774	Myo1c	C80397|MMIb|MYO1E|NMI|mm1beta|myr2	myosin IC	protein-coding
mm_92570.1	chr10	79888096	79888122	-	1	NA	exon (NM_015779, exon 5 of 5)	exon (NM_015779, exon 5 of 5)	1797	NM_015779	50701	Mm.262194	NM_015779	ENSMUSG00000020125	Elane	Ela2|F430011M15Rik|NE	elastase, neutrophil expressed	protein-coding
mm_96563.1	chr11	69026044	69026055	+	1	NA	intron (NM_001143790, intron 5 of 22)	intron (NM_001143790, intron 5 of 22)	10138	NM_001013256	68964	Mm.285785	NM_001013256	ENSMUSG00000020898	Ctc1	1500010J02Rik|AAF-132|AAF132	CTS telomere maintenance complex component 1	protein-coding
mm_86206.1	chr9	119983734	119983748	-	1	NA	intron (NM_153287, intron 1 of 4)	CpG	917	NM_153287	215418	Mm.491094	NM_153287	ENSMUSG00000032515	Csrnp1	4931429D10Rik|Axud1|CSRNP-1|URAX1|taip-3	cysteine-serine-rich nuclear protein 1	protein-coding
mm_55568.1	chr6	71371302	71371308	-	1	NA	Intergenic	B4A|SINE|B4	-2122	NM_009857	12525	Mm.1858	NM_009857	ENSMUSG00000053977	Cd8a	BB154331|Ly-2|Ly-35|Ly-B|Lyt-2	CD8 antigen, alpha chain	protein-coding
mm_16981.1	chr2	18030968	18030972	-	1	NA	TTS (NR_028378)	TTS (NR_028378)	3721	NR_028378	100034739	Mm.401643	NR_028378		Gm17762	-	predicted gene, 17762	ncRNA
mm_27188.1	chr3	34653990	34654008	-	1	NA	intron (NR_015580, intron 4 of 4)	intron (NR_015580, intron 4 of 4)	4004	NM_011443	20674	Mm.65396	NM_011443	ENSMUSG00000074637	Sox2	Sox-2|lcc|ysb	SRY (sex determining region Y)-box 2	protein-coding
mm_73966.1	chr8	120488492	120488510	+	1	NA	promoter-TSS (NM_198671)	promoter-TSS (NM_198671)	-365	NM_198671	382034	Mm.334856	NM_198671	ENSMUSG00000031822	Gse1	2210013I18Rik|mKIAA0182	genetic suppressor element 1, coiled-coil protein	protein-coding
mm_144846.1	chr18	36597781	36597791	+	1	NA	intron (NM_175375, intron 9 of 33)	intron (NM_175375, intron 9 of 33)	37183	NM_175375	108857	Mm.482287	NM_175375	ENSMUSG00000024483	Ankhd1	1110004O12Rik|4933432B13Rik|9130019P20Rik|A530027J04Rik|A630021B20Rik|AA571404|Mask|mFLJ00246|mKIAA1085	ankyrin repeat and KH domain containing 1	protein-coding
mm_2557.1	chr1	112457567	112457578	+	1	NA	Intergenic	Intergenic	-592654	NM_001081316	319901	Mm.103468	NM_001081316	ENSMUSG00000038702	Dsel	9330132E09Rik|DS-epi2	dermatan sulfate epimerase-like	protein-coding
mm_50682.1	chr6	51575812	51575818	+	1	NA	intron (NM_028035, intron 2 of 6)	intron (NM_028035, intron 2 of 6)	31292	NM_001127348	71982	Mm.294166	NM_028035	ENSMUSG00000038301	Snx10	2410004M09Rik	sorting nexin 10	protein-coding
mm_1842.1	chr1	82851202	82851209	+	1	NA	intron (NM_001347077, intron 1 of 12)	intron (NM_001347077, intron 1 of 12)	11745	NM_001347077	15463	Mm.392569	NM_010472	ENSMUSG00000026159	Agfg1	AU045498|C130049H11Rik|C85612|D730048C23Rik|Hrb|RAB|Rip	ArfGAP with FG repeats 1	protein-coding
mm_99169.1	chr11	100736255	100736280	+	1	NA	intron (NM_024456, intron 1 of 5)	intron (NM_024456, intron 1 of 5)	1948	NM_024456	19345	Mm.29829	NM_024456	ENSMUSG00000019173	Rab5c	AI326010|Rabl	RAB5C, member RAS oncogene family	protein-coding
mm_6130.1	chr1	64532863	64532903	-	1	NA	promoter-TSS (NM_009952)	promoter-TSS (NM_009952)	79	NM_001037726	12912	Mm.422634	NM_009952	ENSMUSG00000025958	Creb1	2310001E10Rik|3526402H21Rik|AV083133|Creb|Creb-1	cAMP responsive element binding protein 1	protein-coding
mm_89813.1	chr10	103369328	103369346	+	1	NA	intron (NM_001252330, intron 1 of 11)	intron (NM_001252330, intron 1 of 11)	1529	NM_175328	103098	Mm.458408	NM_175328	ENSMUSG00000019894	Slc6a15	AA536730|AI326450|AI326451|v7-3	solute carrier family 6 (neurotransmitter transporter), member 15	protein-coding
mm_109627.1	chr12	112766844	112766854	+	1	NA	exon (NM_178911, exon 7 of 11)	exon (NM_178911, exon 7 of 11)	6194	NM_178911	104759	Mm.203915	NM_178911	ENSMUSG00000052160	Pld4	AI132321|thss	phospholipase D family, member 4	protein-coding
mm_7196.1	chr1	92997039	92997045	-	1	NA	Intergenic	Intergenic	-9292	NM_177587	208760	Mm.235537	NM_177587	ENSMUSG00000045091	Aqp12	AB084104|mAQP12	aquaporin 12	protein-coding
mm_91451.1	chr10	33951191	33951263	-	1	NA	promoter-TSS (NM_028287)	promoter-TSS (NM_028287)	-15	NM_028287	72580	Mm.248081	NM_028287	ENSMUSG00000039531	Zufsp	2700019D07Rik	zinc finger with UFM1-specific peptidase domain	protein-coding
mm_5372.1	chr1	30804209	30804251	-	1	NA	exon (NM_001081080, exon 15 of 15)	exon (NM_001081080, exon 15 of 15)	59026	NM_001081080	213109	Mm.194486	NM_025871	ENSMUSG00000048874	Phf3	2310061N19Rik|mKIAA0244	PHD finger protein 3	protein-coding
mm_135016.1	chr16	32487226	32487290	-	1	NA	intron (NM_145932, intron 1 of 8)	intron (NM_145932, intron 1 of 8)	621	NM_145932	106407	Mm.476915	NM_145932	ENSMUSG00000035699	Slc51a	AV001382|AW261577|D630035O19Rik|OSTalpha|Osta	solute carrier family 51, alpha subunit	protein-coding
mm_12611.1	chr2	74686554	74686557	+	1	NA	non-coding (NR_073086, exon 2 of 2)	non-coding (NR_073086, exon 2 of 2)	4232	NM_008273	15431	Mm.207763	NM_008273	ENSMUSG00000042499	Hoxd11	E230017H14Rik|Hox-4.6|Hox-5.4|Hox-5.5	homeobox D11	protein-coding
mm_171994.1	chr5	99964041	99964046	-	1	NA	exon (NM_007516, exon 6 of 8)	exon (NM_007516, exon 6 of 8)	14895	NM_001077266	11991	Mm.150231	NM_007516	ENSMUSG00000000568	Hnrnpd	Auf1|Hnrpd	heterogeneous nuclear ribonucleoprotein D	protein-coding
mm_44299.1	chr5	8623005	8623051	-	1	NA	promoter-TSS (NM_198620)	promoter-TSS (NM_198620)	-76	NM_198620	242819	Mm.332192	NM_198620	ENSMUSG00000040570	Rundc3b	Gm440	RUN domain containing 3B	protein-coding
mm_21788.1	chr2	164856908	164856954	-	1	NA	exon (NM_011125, exon 2 of 16)	exon (NM_011125, exon 2 of 16)	777	NM_011125	18830	Mm.6105	NM_011125	ENSMUSG00000017754	Pltp	Bpife|OD107	phospholipid transfer protein	protein-coding
mm_109802.1	chr12	3309841	3309851	-	1	NA	5' UTR (NM_016676, exon 1 of 6)	5' UTR (NM_016676, exon 1 of 6)	123	NM_016676	19325	Mm.378993	NM_016676	ENSMUSG00000020671	Rab10	AW107754	RAB10, member RAS oncogene family	protein-coding
mm_2255.1	chr1	91093562	91093568	+	1	NA	exon (NM_008515, exon 10 of 23)	exon (NM_008515, exon 10 of 23)	40121	NM_008515	16978	Mm.45039	NM_008515	ENSMUSG00000026305	Lrrfip1	AU024550|Fliiap1	leucine rich repeat (in FLII) interacting protein 1	protein-coding
mm_107616.1	chr12	49949202	49949218	+	1	NA	Intergenic	Intergenic	-468348	NR_045472	69054	Mm.417838	NR_045472	ENSMUSG00000100844	1810007C17Rik	-	RIKEN cDNA 1810007C17 gene	ncRNA
mm_20995.1	chr2	152332302	152332312	-	1	NA	5' UTR (NM_001083921, exon 1 of 12)	5' UTR (NM_001083921, exon 1 of 12)	118	NM_001083921	24105	Mm.182145	NM_019705	ENSMUSG00000027466	Rbck1	AL033326|HOIL-1|HOIL-1L|UIP28|Ubce7ip3	RanBP-type and C3HC4-type zinc finger containing 1	protein-coding
mm_6731.1	chr1	82798451	82798462	-	1	NA	Intergenic	Intergenic	-30000	NM_025453	66261	Mm.46325	NM_025453	ENSMUSG00000026149	Tm4sf20	1810018L02Rik	transmembrane 4 L six family member 20	protein-coding
mm_31410.1	chr4	48048068	48048089	+	1	NA	intron (NM_015743, intron 1 of 7)	intron (NM_015743, intron 1 of 7)	2773	NM_015743	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_170826.1	chr2	176798621	176798627	+	1	NA	promoter-TSS (NM_001205057)	promoter-TSS (NM_001205057)	24	NM_001205057	100039123	Mm.389409	NM_001205057	ENSMUSG00000078877	Gm14295	OTTMUSG00000016219	predicted gene 14295	protein-coding
mm_3824.1	chr1	159310109	159310125	+	1	NA	intron (NM_011931, intron 14 of 19)	intron (NM_011931, intron 14 of 19)	16344	NR_144489	100846986		NR_144489		Pou5f1-rs1	Gm21053|Oct4P2|Otf-3rs|Otf3-rs1|Otf3a	POU domain, class 5, transcription factor 1, related sequence 1	pseudo
mm_21089.1	chr2	153161461	153161471	-	1	NA	5' UTR (NM_133847, exon 1 of 18)	5' UTR (NM_133847, exon 1 of 18)	165	NM_133847	99237	Mm.330674	NM_133847	ENSMUSG00000068040	Tm9sf4	AA986553|AU045326|B930079E06|mKIAA0255	transmembrane 9 superfamily protein member 4	protein-coding
mm_99997.1	chr11	114790705	114790706	+	1	NA	TTS (NM_001102615)	TTS (NM_001102615)	5187	NM_028055	72014	Mm.38347	NM_028055	ENSMUSG00000000202	Btbd17	1500005I02Rik|Tango10a	BTB (POZ) domain containing 17	protein-coding
mm_119421.1	chr14	45337514	45337531	+	1	NA	exon (NM_025959, exon 7 of 14)	exon (NM_025959, exon 7 of 14)	7698	NM_025959	67089	Mm.18472	NM_025959	ENSMUSG00000021832	Psmc6	2300001E01Rik|AI451058	proteasome (prosome, macropain) 26S subunit, ATPase, 6	protein-coding
mm_81951.1	chr9	120539877	120539886	+	1	NA	promoter-TSS (NM_178676)	promoter-TSS (NM_178676)	63	NM_178676	215446	Mm.76648	NM_178676	ENSMUSG00000041608	Entpd3	Cd39l3|HB6|NTPDase-3	ectonucleoside triphosphate diphosphohydrolase 3	protein-coding
mm_83446.1	chr9	45009809	45009826	-	1	NA	promoter-TSS (NM_007648)	promoter-TSS (NM_007648)	-227	NM_007648	12501	Mm.210361	NM_007648	ENSMUSG00000032093	Cd3e	AI504783|CD3|CD3epsilon|T3e	CD3 antigen, epsilon polypeptide	protein-coding
mm_38599.1	chr4	141846362	141846374	-	1	NA	promoter-TSS (NM_001033875)	promoter-TSS (NM_001033875)	-9	NM_001033875	76701	Mm.489680	NM_001033875	ENSMUSG00000062478	Ctrc	1810044E12Rik	chymotrypsin C (caldecrin)	protein-coding
mm_147968.1	chr18	67244390	67244405	-	1	NA	intron (NM_172630, intron 1 of 10)	MTD|LTR|ERVL-MaLR	1433	NM_172630	225651	Mm.235792	NM_172630	ENSMUSG00000062526	Mppe1	A530095G11	metallophosphoesterase 1	protein-coding
mm_99236.1	chr11	101070082	101070121	+	1	NA	promoter-TSS (NM_013792)	promoter-TSS (NM_013792)	7	NM_013792	27419	Mm.95452	NM_013792	ENSMUSG00000001751	Naglu	-	alpha-N-acetylglucosaminidase (Sanfilippo disease IIIB)	protein-coding
mm_132506.1	chr16	36955976	36955977	+	1	NA	exon (NM_008225, exon 8 of 14)	exon (NM_008225, exon 8 of 14)	20993	NM_008225	15163	Mm.4091	NM_008225	ENSMUSG00000022831	Hcls1	AW213261|HS1	hematopoietic cell specific Lyn substrate 1	protein-coding
mm_158905.1	chr1	37368989	37368989	+	1	NA	promoter-TSS (NM_001290799)	promoter-TSS (NM_001290799)	-228	NM_001290798	269180	Mm.5294	NM_030266	ENSMUSG00000026113	Inpp4a	107kDa|9630012D15|D130048C09Rik|R74740	inositol polyphosphate-4-phosphatase, type I	protein-coding
mm_109794.1	chr12	3256969	3257009	-	1	NA	exon (NM_016676, exon 3 of 6)	exon (NM_016676, exon 3 of 6)	21198	NR_015551	74173	Mm.309774	NM_028796	ENSMUSG00000079179	Rab10os	1700012B15Rik|1810036A22Rik	RAB10, member RAS oncogene family, opposite strand	ncRNA
mm_163982.1	chr14	56575637	56575639	+	1	NA	promoter-TSS (NM_001145978)	promoter-TSS (NM_001145978)	19	NM_001145978	328417	Mm.379357	NM_001145978	ENSMUSG00000054509	Parp4	Adprtl1|C030027K23Rik|E230037B21Rik|Gm743|PARPL|PH5P|VAULT3|VPARP|p193	poly (ADP-ribose) polymerase family, member 4	protein-coding
mm_125768.1	chr15	74563500	74563547	+	1	NA	intron (NM_174991, intron 17 of 30)	intron (NM_174991, intron 17 of 30)	47327	NM_174991	107831	Mm.43133	NM_174991	ENSMUSG00000034730	Adgrb1	B830018M07Rik|Bai1|R75078|mKIAA4089	adhesion G protein-coupled receptor B1	protein-coding
mm_50660.1	chr6	51477476	51477478	+	1	NA	intron (NM_007624, intron 3 of 5)	B2_Mm2|SINE|B2	6861	NM_007624	12417	Mm.280968	NM_007624	ENSMUSG00000029836	Cbx3	HP1g|M32	chromobox 3	protein-coding
mm_110291.1	chr12	32208202	32208230	-	1	NA	5' UTR (NM_001146201, exon 1 of 11)	5' UTR (NM_001146201, exon 1 of 11)	122	NM_001146201	30955	Mm.101369	NM_020272	ENSMUSG00000020573	Pik3cg	5830428L06Rik|PI3Kgamma|p110gamma	phosphoinositide-3-kinase, catalytic, gamma polypeptide	protein-coding
mm_102780.1	chr11	68386975	68387002	-	1	NA	promoter-TSS (NM_008744)	promoter-TSS (NM_008744)	-162	NM_008744	18208	Mm.39095	NM_008744	ENSMUSG00000020902	Ntn1	AI561871|BC019633|Netrin-1	netrin 1	protein-coding
mm_44838.1	chr5	34169410	34169466	-	1	NA	promoter-TSS (NM_001289804)	promoter-TSS (NM_001289804)	-14	NM_146159	231123	Mm.319286	NM_146159	ENSMUSG00000079555	Haus3	D4S43h|D5H4S43|D5H4S43E	HAUS augmin-like complex, subunit 3	protein-coding
mm_146898.1	chr18	30420106	30420111	-	1	NA	Intergenic	L1_Mus2|LINE|L1	147212	NM_181414	225326	Mm.194127	NM_181414	ENSMUSG00000033628	Pik3c3	5330434F23Rik|Vps34	phosphoinositide-3-kinase, class 3	protein-coding
mm_71358.1	chr8	45658873	45658898	+	1	NA	5' UTR (NM_001205219, exon 2 of 24)	5' UTR (NM_001205219, exon 2 of 24)	-3108	NM_001310708	234214	Mm.211096	NM_172752	ENSMUSG00000031626	Sorbs2	2010203O03Rik|9430041O17Rik|A530071H08|Argbp2|mKIAA0777|nArgBP2	sorbin and SH3 domain containing 2	protein-coding
mm_13008.1	chr2	90909187	90909198	+	1	NA	exon (NM_025991, exon 4 of 4)	exon (NM_025991, exon 4 of 4)	4406	NM_025991	67136	Mm.330394	NM_025991	ENSMUSG00000005505	Kbtbd4	2510026C23Rik	kelch repeat and BTB (POZ) domain containing 4	protein-coding
mm_99638.1	chr11	105240382	105240401	+	1	NA	exon (NM_001112705, exon 8 of 22)	exon (NM_001112705, exon 8 of 22)	-52255	NM_008626	17534	Mm.235616	NM_008626	ENSMUSG00000020695	Mrc2	Endo180|mKIAA0709|uPARAP	mannose receptor, C type 2	protein-coding
mm_15839.1	chr2	164715300	164715310	+	1	NA	promoter-TSS (NM_001040055)	promoter-TSS (NM_001040055)	0	NM_001040055	641368	Mm.422380	NM_001040055	ENSMUSG00000074593	Spint5	Gm14316|OTTMUSG00000016293	serine protease inhibitor, Kunitz type 5	protein-coding
mm_110814.1	chr12	72375088	72375097	-	1	NA	intron (NM_153457, intron 1 of 8)	intron (NM_153457, intron 1 of 8)	33962	NM_001286448	104001	Mm.221275	NM_153457	ENSMUSG00000021087	Rtn1	Nsp	reticulon 1	protein-coding
mm_32129.1	chr4	99037549	99037559	+	1	NA	exon (NM_013913, exon 6 of 7)	exon (NM_013913, exon 6 of 7)	6600	NM_013913	30924	Mm.28341	NM_013913	ENSMUSG00000028553	Angptl3	hypl	angiopoietin-like 3	protein-coding
mm_31850.1	chr4	74384107	74384114	+	1	NA	intron (NM_001172095, intron 19 of 21)	Lx8|LINE|L1	132231	NM_144787	76804	Mm.209059	NM_144787	ENSMUSG00000028397	Kdm4c	2410141F18Rik|AA517467|Gasc1|Jmjd2c	lysine (K)-specific demethylase 4C	protein-coding
mm_30239.1	chr3	146405795	146405828	-	1	NA	intron (NM_001253769, intron 1 of 13)	intron (NM_001253769, intron 1 of 13)	1169	NM_138744	99167	Mm.200783	NM_138744	ENSMUSG00000036825	Ssx2ip	AU014939|AU042321|Adip	synovial sarcoma, X 2 interacting protein	protein-coding
mm_104555.1	chr11	96822730	96822755	-	1	NA	intron (NM_001130450, intron 2 of 4)	intron (NM_001130450, intron 2 of 4)	1271	NM_001130453	18023	Mm.6743	NM_008686	ENSMUSG00000038615	Nfe2l1	AA408798|AW212678|LCR-F1|Lcrf1|NRF1|TCF-11|TCF11	nuclear factor, erythroid derived 2,-like 1	protein-coding
mm_92081.1	chr10	62764395	62764408	-	1	NA	exon (NM_026201, exon 14 of 25)	exon (NM_026201, exon 14 of 25)	1205	NR_028557	100217463		NR_028557		Snord98	MBII-419	small nucleolar RNA, C/D box 98	snoRNA
mm_44478.1	chr5	23433954	23433963	-	1	NA	promoter-TSS (NM_026984)	promoter-TSS (NM_026984)	395	NR_040469	269630	Mm.425231	NR_040469	ENSMUSG00000073147	5031425E22Rik	-	RIKEN cDNA 5031425E22 gene	ncRNA
mm_23013.1	chr3	34560195	34560203	+	1	NA	promoter-TSS (NR_015580)	promoter-TSS (NR_015580)	-182	NR_015580	320478	Mm.444063	NR_015580	ENSMUSG00000105265	Sox2ot	B230215L15Rik	SOX2 overlapping transcript (non-protein coding)	ncRNA
mm_147641.1	chr18	60269664	60269670	-	1	NA	3' UTR (NM_001034859, exon 2 of 2)	3' UTR (NM_001034859, exon 2 of 2)	3600	NM_001034859	225594	Mm.329460	NM_001034859	ENSMUSG00000068606	Gm4841	EG225594|Ifgga3	predicted gene 4841	protein-coding
mm_14008.1	chr2	122116925	122116935	+	1	NA	intron (NM_145531, intron 1 of 39)	intron (NM_145531, intron 1 of 39)	1456	NM_145531	214585	Mm.222303	NM_145531	ENSMUSG00000033396	Spg11	6030465E24Rik|A330015I11|C530005A01Rik	spastic paraplegia 11	protein-coding
mm_89561.1	chr10	95319292	95319301	+	1	NA	intron (NM_009950, intron 2 of 2)	intron (NM_009950, intron 2 of 2)	4413	NM_001330138	12905	Mm.473739	NM_009950	ENSMUSG00000045867	Cradd	RAIDD	CASP2 and RIPK1 domain containing adaptor with death domain	protein-coding
mm_105014.1	chr11	100414830	100414852	-	1	NA	promoter-TSS (NM_010221)	promoter-TSS (NM_010221)	-22	NM_176830	66180	Mm.4940	NM_176830	ENSMUSG00000006931	P3h4	1110036O03Rik|AI413214|Leprel4|Sc65	prolyl 3-hydroxylase family member 4 (non-enzymatic)	protein-coding
mm_50102.1	chr6	41533205	41533219	+	1	NA	Intergenic	Intergenic	11436	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_98926.1	chr11	98349054	98349069	+	1	NA	promoter-TSS (NM_001313970)	promoter-TSS (NM_001313970)	655	NM_144828	19049	Mm.45372	NM_144828	ENSMUSG00000061718	Ppp1r1b	AU040756|DARPP-32|Darpp32	protein phosphatase 1, regulatory (inhibitor) subunit 1B	protein-coding
mm_160822.1	chr11	30890944	30890944	+	1	NA	intron (NM_175490, intron 1 of 1)	intron (NM_175490, intron 1 of 1)	5586	NM_175490	237716	Mm.338361	NM_175490	ENSMUSG00000043999	Gpr75	-	G protein-coupled receptor 75	protein-coding
mm_106895.1	chr12	8012555	8012562	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	34881	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_117139.1	chr13	60940634	60940653	-	1	NA	exon (NM_009411, exon 2 of 5)	exon (NM_009411, exon 2 of 5)	1292	NM_009411	21984	Mm.2372	NM_009411	ENSMUSG00000033834	Tpbpa	AV033951|Tb-1|Tb1|Tpbp|b2b1247Clo	trophoblast specific protein alpha	protein-coding
mm_9904.1	chr1	187199476	187199494	-	1	NA	intron (NM_028848, intron 1 of 9)	(GTGTG)n|Simple_repeat|Simple_repeat	15961	NM_029067	74717	Mm.250430	NM_028848	ENSMUSG00000026611	Spata17	1700065F16Rik|4930504I07Rik|4930513F16Rik|MSRG-11	spermatogenesis associated 17	protein-coding
mm_108135.1	chr12	76086864	76086878	+	1	NA	intron (NM_001005510, intron 99 of 115)	intron (NM_001005510, intron 99 of 115)	90388	NM_010157	13983	Mm.2561	NM_010157	ENSMUSG00000021055	Esr2	ER[b]|ERbeta|Estrb	estrogen receptor 2 (beta)	protein-coding
mm_71587.1	chr8	54954857	54954872	+	1	NA	5' UTR (NM_153581, exon 1 of 7)	5' UTR (NM_153581, exon 1 of 7)	136	NM_001253756	234267	Mm.241700	NM_153581	ENSMUSG00000031517	Gpm6a	Gpm6|M6A	glycoprotein m6a	protein-coding
mm_92843.1	chr10	81508203	81508227	-	1	NA	intron (NM_010304, intron 5 of 6)	intron (NM_010304, intron 5 of 6)	-8078	NM_010102	13611	Mm.33065	NM_010102	ENSMUSG00000044199	S1pr4	Edg6|Lpc1|S1p4	sphingosine-1-phosphate receptor 4	protein-coding
mm_33593.1	chr4	132564083	132564093	+	1	NA	promoter-TSS (NM_001081211)	promoter-TSS (NM_001081211)	21	NM_001081211	19204	Mm.89389	NM_001081211	ENSMUSG00000056529	Ptafr	PAFR	platelet-activating factor receptor	protein-coding
mm_27930.1	chr3	79567686	79567694	-	1	NA	promoter-TSS (NM_001162999)	promoter-TSS (NM_001162999)	-11	NM_001162999	329679	Mm.244005	NM_001162999	ENSMUSG00000061175	Fnip2	D630023B12Rik|mKIAA1450	folliculin interacting protein 2	protein-coding
mm_49212.1	chr6	15727217	15727231	+	1	NA	intron (NM_175088, intron 2 of 4)	intron (NM_175088, intron 2 of 4)	6563	NM_175088	16543	Mm.1314	NM_175088	ENSMUSG00000041390	Mdfic	Kdt1|Mdfid	MyoD family inhibitor domain containing	protein-coding
mm_151739.1	chr19	4961726	4961734	-	1	NA	promoter-TSS (NM_025553)	promoter-TSS (NM_025553)	-576	NM_025553	66419	Mm.28494	NM_025553	ENSMUSG00000024902	Mrpl11	2410001P07Rik|L11mt	mitochondrial ribosomal protein L11	protein-coding
mm_73695.1	chr8	111629849	111629852	+	1	NA	intron (NM_027570, intron 2 of 10)	intron (NM_027570, intron 2 of 10)	472	NM_027570	52815	Mm.27589	NM_027570	ENSMUSG00000031958	Ldhd	4733401P21Rik|D8Bwg1320e	lactate dehydrogenase D	protein-coding
mm_26377.1	chr3	142566414	142566424	+	1	NA	exon (NM_018734, exon 6 of 11)	exon (NM_018734, exon 6 of 11)	5923	NM_001289493	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_167722.1	chr9	101074093	101074112	+	1	NA	promoter-TSS (NM_001100451)	promoter-TSS (NM_001100451)	-660	NM_001100451	77853	Mm.326206	NM_001100451	ENSMUSG00000066415	Msl2	E130103E02Rik|Msl2l1|Rnf184	male-specific lethal 2 homolog (Drosophila)	protein-coding
mm_58504.1	chr7	3981106	3981118	+	1	NA	Intergenic	Intergenic	-65611	NR_028115	18726	Mm.440989	NM_011090	ENSMUSG00000030427	Lilra6	7M1|Pira3	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	protein-coding
mm_45085.1	chr5	44089542	44089556	-	1	NA	intron (NM_001163582, intron 1 of 21)	intron (NM_001163582, intron 1 of 21)	5219	NM_001163581	19126	Mm.6250	NM_008935	ENSMUSG00000029086	Prom1	4932416E19Rik|AC133|CD133|Prom|Prom-1|Proml1	prominin 1	protein-coding
mm_143554.1	chr17	74173829	74173835	-	1	NA	Intergenic	Intergenic	121031	NM_133771	76890	Mm.311874	NM_133771	ENSMUSG00000058704	Memo1	0610016J10Rik|D930048L02Rik	mediator of cell motility 1	protein-coding
mm_146857.1	chr18	24205852	24205860	-	1	NA	promoter-TSS (NM_001160404)	promoter-TSS (NM_001160404)	-138	NM_001160404	14423	Mm.30249	NM_013814	ENSMUSG00000000420	Galnt1	-	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 1	protein-coding
mm_8696.1	chr1	157412528	157412565	-	1	NA	promoter-TSS (NM_177644)	promoter-TSS (NM_177644)	49	NM_177644	226525	Mm.235028	NM_177644	ENSMUSG00000070565	Rasal2	6530401P13|A330066M24Rik	RAS protein activator like 2	protein-coding
mm_103638.1	chr11	78963122	78963138	-	1	NA	3' UTR (NM_010708, exon 11 of 11)	3' UTR (NM_010708, exon 11 of 11)	21794	NM_001159301	16859	Mm.341434	NM_010708	ENSMUSG00000001123	Lgals9	AA407335|AI194909|AI265545|LGALS35|Lgals5|gal-9|galectin-9	lectin, galactose binding, soluble 9	protein-coding
mm_150583.1	chr19	40660143	40660170	+	1	NA	intron (NM_009848, intron 1 of 9)	intron (NM_009848, intron 1 of 9)	386	NM_009848	12495	Mm.2824	NM_009848	ENSMUSG00000048120	Entpd1	2610206B08Rik|AA408691|Cd39|NTPDase-1	ectonucleoside triphosphate diphosphohydrolase 1	protein-coding
mm_68357.1	chr7	106511286	106511299	-	1	NA	Intergenic	Intergenic	-70219	NR_003967	209380	Mm.461779	NM_001001318		Gm4759	EG209380	GTPase, very large interferon inducible 1 pseudogene	pseudo
mm_65431.1	chr7	25367676	25367684	-	1	NA	TTS (NM_028219)	TTS (NM_028219)	2044	NM_001081375	72383	Mm.34382	NM_028219	ENSMUSG00000063651	Cnfn	2210418J09Rik	cornifelin	protein-coding
mm_55624.1	chr6	72235464	72235496	-	1	NA	promoter-TSS (NM_153778)	promoter-TSS (NM_153778)	97	NM_153778	71093	Mm.87449	NM_153778	ENSMUSG00000037621	Atoh8	4933425C05Rik|Hath6|Math6|bHLHa21|okadin	atonal bHLH transcription factor 8	protein-coding
mm_90945.1	chr10	12964489	12964515	-	1	NA	promoter-TSS (NM_029075)	promoter-TSS (NM_029075)	-243	NM_001163591	74732	Mm.248648	NM_029075	ENSMUSG00000039232	Stx11	5830405C08Rik	syntaxin 11	protein-coding
mm_162822.1	chr10	80855266	80855280	+	1	NA	promoter-TSS (NM_025349)	promoter-TSS (NM_025349)	-2	NM_175195	73218	Mm.3285	NM_175195	ENSMUSG00000035206	Sppl2b	3110056O03Rik|AW550292|PSL1	signal peptide peptidase like 2B	protein-coding
mm_66365.1	chr7	43533133	43533140	-	1	NA	promoter-TSS (NM_001111058)	promoter-TSS (NM_001111058)	35	NM_001111058	12489	Mm.140157	NM_021293	ENSMUSG00000004609	Cd33	Siglec-3|gp67	CD33 antigen	protein-coding
mm_118991.1	chr14	28505543	28505569	+	1	NA	promoter-TSS (NM_009524)	promoter-TSS (NM_009524)	83	NM_009524	22418	Mm.287544	NM_009524	ENSMUSG00000021994	Wnt5a	8030457G12Rik|Wnt-5a	wingless-type MMTV integration site family, member 5A	protein-coding
mm_23899.1	chr3	83031765	83031775	+	1	NA	exon (NM_010196, exon 5 of 5)	exon (NM_010196, exon 5 of 5)	5617	NM_001111048	14161	Mm.88793	NM_010196	ENSMUSG00000028001	Fga	ENSMUSG00000059807|Fib	fibrinogen alpha chain	protein-coding
mm_161909.1	chr18	62530843	62530843	-	1	NA	intron (NM_134136, intron 5 of 21)	intron (NM_134136, intron 5 of 21)	17900	NM_134136	107035	Mm.21295	NM_134136	ENSMUSG00000042211	Fbxo38	6030410I24Rik|AU044865|AW214031|Moka|SP329	F-box protein 38	protein-coding
mm_70216.1	chr7	144937982	144937998	-	1	NA	exon (NM_007631, exon 2 of 5)	exon (NM_007631, exon 2 of 5)	1935	NM_007631	12443	Mm.273049	NM_007631	ENSMUSG00000070348	Ccnd1	AI327039|CycD1|Cyl-1|PRAD1|bcl-1|cD1	cyclin D1	protein-coding
mm_140078.1	chr17	75178776	75178794	+	1	NA	promoter-TSS (NM_001331237)	promoter-TSS (NM_001331237)	4	NM_001331235	268977	Mm.269747	NM_019919	ENSMUSG00000001870	Ltbp1	9430031G15Rik|9830146M04|Ltbp-1|Ltbp1L|TGF-beta1-BP-1|Tgfb|b2b1000Clo	latent transforming growth factor beta binding protein 1	protein-coding
mm_163096.1	chr11	69735114	69735151	-	1	NA	exon (NM_001291068, exon 29 of 29)	exon (NM_001291068, exon 29 of 29)	23501	NM_001291068	20020	Mm.16533	NM_009089	ENSMUSG00000005198	Polr2a	220kDa|Rpb1|Rpo2-1	polymerase (RNA) II (DNA directed) polypeptide A	protein-coding
mm_108679.1	chr12	86693436	86693439	+	1	NA	3' UTR (NM_177354, exon 7 of 7)	3' UTR (NM_177354, exon 7 of 7)	14737	NM_177354	238328	Mm.216101	NM_177354	ENSMUSG00000021256	Vash1	AI834978|D930046M13Rik|G630009D10Rik	vasohibin 1	protein-coding
mm_10964.1	chr2	25702030	25702036	+	1	NA	intron (NM_153558, intron 4 of 6)	intron (NM_153558, intron 4 of 6)	1959	NM_153558	227627	Mm.44630	NM_153558	ENSMUSG00000062061	Obp2a	BC027556|Lcn13	odorant binding protein 2A	protein-coding
mm_32585.1	chr4	111290163	111290182	+	1	NA	intron (NM_001048189, intron 5 of 12)	intron (NM_001048189, intron 5 of 12)	-124834	NR_033793	67621	Mm.45533	NM_026279	ENSMUSG00000028545	Bend5	2310026E23Rik	BEN domain containing 5	protein-coding
mm_138985.1	chr17	45487436	45487446	+	1	NA	Intergenic	Intergenic	-12503	NM_027649	71020	Mm.44257	NM_027649	ENSMUSG00000023935	Spats1	1700011H05Rik|4933400B06Rik|Daip2|Ddip|Srsp1	spermatogenesis associated, serine-rich 1	protein-coding
mm_17852.1	chr2	34754365	34754432	-	1	NA	5' UTR (NM_025709, exon 2 of 27)	5' UTR (NM_025709, exon 2 of 27)	834	NM_025709	66691	Mm.156452	NM_025709	ENSMUSG00000026867	Gapvd1	2010005B09Rik|4432404J10Rik|AW108497|Gapex-5|RAP6|RME-6|mKIAA1521	GTPase activating protein and VPS9 domains 1	protein-coding
mm_15979.1	chr2	166714102	166714116	+	1	NA	promoter-TSS (NM_177782)	promoter-TSS (NM_177782)	-277	NM_177782	277360	Mm.34420	NM_177782	ENSMUSG00000039621	Prex1	G630042G04|P-REX1|Setd6	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	protein-coding
mm_2371.1	chr1	93235837	93235842	+	1	NA	promoter-TSS (NM_172463)	promoter-TSS (NM_172463)	-58	NM_172463	208777	Mm.271897	NM_172463	ENSMUSG00000047793	Sned1	6720455I24Rik|AI197264|AI642697|D430044C15Rik|SST3|Snep	sushi, nidogen and EGF-like domains 1	protein-coding
mm_59878.1	chr7	30291785	30291787	+	1	NA	promoter-TSS (NM_001081114)	promoter-TSS (NM_001081114)	33	NM_001081114	76686	Mm.159258	NM_001081114	ENSMUSG00000013921	Clip3	1500005P14Rik|AI844915|Clipr-59	CAP-GLY domain containing linker protein 3	protein-coding
mm_53195.1	chr6	125532593	125532603	+	1	NA	Intergenic	MLT1A0|LTR|ERVL-MaLR	-20350	NM_011708	22371	Mm.22339	NM_011708	ENSMUSG00000001930	Vwf	6820430P06Rik|AI551257|B130011O06Rik|C630030D09|F8VWF|VWD	Von Willebrand factor	protein-coding
mm_45485.1	chr5	71095741	71095758	-	1	NA	promoter-TSS (NM_008066)	promoter-TSS (NM_008066)	100	NM_008066	14395	Mm.5304	NM_008066	ENSMUSG00000000560	Gabra2	C630048P16Rik|Gabra-2	gamma-aminobutyric acid (GABA) A receptor, subunit alpha 2	protein-coding
mm_113965.1	chr13	51645269	51645276	+	1	NA	promoter-TSS (NM_025415)	promoter-TSS (NM_025415)	40	NM_025415	66197	Mm.222228	NM_025415	ENSMUSG00000062248	Cks2	1110038L14Rik|CKSHS2	CDC28 protein kinase regulatory subunit 2	protein-coding
mm_51590.1	chr6	83867104	83867125	+	1	NA	Intergenic	CpG	-35373	NM_146169	232164	Mm.404420	NM_146169	ENSMUSG00000045896	Paip2b	-	poly(A) binding protein interacting protein 2B	protein-coding
mm_149191.1	chr19	9939254	9939271	+	1	NA	Intergenic	Intergenic	-39729	NM_016692	16319	Mm.29755	NM_016692	ENSMUSG00000024660	Incenp	2700067E22Rik|AU019509|C130081E20|C77457	inner centromere protein	protein-coding
mm_70981.1	chr8	27177369	27177390	+	1	NA	Intergenic	Intergenic	-2733	NM_001080813	75767	Mm.205335	NM_029423	ENSMUSG00000031488	Rab11fip1	2010200K21Rik|4833414G05Rik|Rcp	RAB11 family interacting protein 1 (class I)	protein-coding
mm_23431.1	chr3	59081161	59081176	+	1	NA	intron (NM_177855, intron 10 of 43)	intron (NM_177855, intron 10 of 43)	20653	NM_173398	229323	Mm.123648	NM_173398	ENSMUSG00000050075	Gpr171	A630006E05|F730001G15Rik|H963	G protein-coupled receptor 171	protein-coding
mm_62922.1	chr7	118593699	118593702	+	1	NA	intron (NM_001331203, intron 1 of 2)	intron (NM_001331203, intron 1 of 2)	1254	NM_001331203	381914	Mm.291232	NM_001331201	ENSMUSG00000109284	B230311B06Rik	Gm1695	RIKEN cDNA B230311B06 gene	protein-coding
mm_76126.1	chr8	80879891	80879926	-	1	NA	5' UTR (NM_001301298, exon 1 of 11)	5' UTR (NM_001301298, exon 1 of 11)	571	NM_021356	14388	Mm.277409	NM_021356	ENSMUSG00000031714	Gab1	AA408973|AW107238	growth factor receptor bound protein 2-associated protein 1	protein-coding
mm_95063.1	chr11	32532846	32532870	+	1	NA	promoter-TSS (NM_009288)	promoter-TSS (NM_009288)	-408	NM_009288	20868	Mm.8235	NM_009288	ENSMUSG00000020272	Stk10	Gek1|Lok|mKIAA4026	serine/threonine kinase 10	protein-coding
mm_117926.1	chr13	99434217	99434235	-	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-21400	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_11403.1	chr2	31510031	31510036	+	1	NA	intron (NR_002687, intron 12 of 15)	intron (NR_002687, intron 12 of 15)	39725	NR_002687	432466	Mm.333323	NR_002687	ENSMUSG00000046687	Gm5424	EG432466	argininosuccinate synthase pseudogene	pseudo
mm_104292.1	chr11	90389581	90389602	-	1	NA	intron (NM_172563, intron 1 of 3)	intron (NM_172563, intron 1 of 3)	1326	NM_172563	217082	Mm.158903	NM_172563	ENSMUSG00000003949	Hlf	E230015K02Rik	hepatic leukemia factor	protein-coding
mm_162549.1	chr1	171196172	171196182	-	1	NA	promoter-TSS (NM_025557)	promoter-TSS (NM_025557)	91	NM_025557	66425	Mm.482117	NM_025557	ENSMUSG00000038370	Pcp4l1	1500036F01Rik	Purkinje cell protein 4-like 1	protein-coding
mm_104901.1	chr11	99620918	99620922	-	1	NA	promoter-TSS (NM_001177537)	promoter-TSS (NM_001177537)	-516	NM_001177537	100502803	Mm.351892	NM_001177537	ENSMUSG00000062278	Gm11562	OTTMUSG00000002199	predicted gene 11562	protein-coding
mm_68758.1	chr7	121517185	121517188	-	1	NA	Intergenic	ORR1B2|LTR|ERVL-MaLR	72650	NR_102286	75793	Mm.23397	NR_102286		4933432K03Rik	1700001C18Rik|4930433G11Rik|AI428127	RIKEN cDNA 4933432K03 gene	ncRNA
mm_99.1	chr1	9450589	9450594	+	1	NA	Intergenic	Intergenic	-94817	NM_021511	59014	Mm.29061	NM_021511	ENSMUSG00000061024	Rrs1	5730466A07Rik|AA415037|D1Ertd701e|Rrr	ribosome biogenesis regulator 1	protein-coding
mm_9019.1	chr1	166127931	166127941	-	1	NA	promoter-TSS (NM_001160049)	promoter-TSS (NM_001160049)	-38	NM_001160049	240892	Mm.35315	NM_001033344	ENSMUSG00000026564	Dusp27	C130085G02Rik|Gm209	dual specificity phosphatase 27 (putative)	protein-coding
mm_14683.1	chr2	140056036	140056047	+	1	NA	intron (NR_110350, intron 2 of 12)	intron (NR_110350, intron 2 of 12)	10764	NM_001159640	75812	Mm.293449	NM_175225	ENSMUSG00000039033	Tasp1	4930485D02Rik|AW986064	taspase, threonine aspartase 1	protein-coding
mm_96314.1	chr11	63963891	63963895	+	1	NA	promoter-TSS (NR_131111)	promoter-TSS (NR_131111)	-333	NR_131111	78883	Mm.410764	NR_131111	ENSMUSG00000086359	9630013K17Rik	-	RIKEN cDNA 9630013K17 gene	ncRNA
mm_103928.1	chr11	83648220	83648239	-	1	NA	3' UTR (NM_011337, exon 3 of 3)	3' UTR (NM_011337, exon 3 of 3)	1149	NM_011337	20302	Mm.1282	NM_011337	ENSMUSG00000000982	Ccl3	AI323804|G0S19-1|LD78alpha|MIP-1alpha|MIP1-(a)|MIP1-alpha|Mip1a|Scya3	chemokine (C-C motif) ligand 3	protein-coding
mm_8006.1	chr1	134784702	134784748	-	1	NA	intron (NM_001081307, intron 18 of 23)	intron (NM_001081307, intron 18 of 23)	18996	NR_015606	329251	Mm.188709	NM_001081307	ENSMUSG00000073557	Ppp1r12b	1810037O03Rik|9530009M10Rik|AI132431|Mypt2	protein phosphatase 1, regulatory (inhibitor) subunit 12B	protein-coding
mm_115698.1	chr13	14063396	14063436	-	1	NA	promoter-TSS (NM_001331176)	promoter-TSS (NM_001331176)	72	NM_001331119	14593	Mm.148039	NM_010282	ENSMUSG00000021302	Ggps1	1810026C22Rik|9530089B04Rik|AI843169|C79210	geranylgeranyl diphosphate synthase 1	protein-coding
mm_69462.1	chr7	133186427	133186433	-	1	NA	Intergenic	Intergenic	58179	NR_046279	74970	Mm.491044	NR_046279	ENSMUSG00000109816	4930483O08Rik	-	RIKEN cDNA 4930483O08 gene	ncRNA
mm_97882.1	chr11	83240273	83240296	+	1	NA	Intergenic	RLTR31_Mur|LTR|ERVK	16708	NR_015519	100043636	Mm.295569	NR_015519	ENSMUSG00000087107	AI662270	AW496474	expressed sequence AI662270	ncRNA
mm_71367.1	chr8	45746671	45746685	+	1	NA	intron (NM_172752, intron 6 of 22)	intron (NM_172752, intron 6 of 22)	72619	NR_045739	319940	Mm.441720	NR_045739	ENSMUSG00000085440	Sorbs2os	D330022K07Rik	sorbin and SH3 domain containing 2, opposite strand	ncRNA
mm_23382.1	chr3	55783383	55783404	+	1	NA	exon (NM_010750, exon 1 of 1)	exon (NM_010750, exon 1 of 1)	883	NM_010750	17116	Mm.440209	NM_010750	ENSMUSG00000056947	Mab21l1	AW047968	mab-21-like 1 (C. elegans)	protein-coding
mm_1426.1	chr1	67174600	67174612	+	1	NA	intron (NM_001080809, intron 19 of 37)	intron (NM_001080809, intron 19 of 37)	51579	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_28155.1	chr3	87748600	87748615	-	1	NA	promoter-TSS (NM_028971)	promoter-TSS (NM_028971)	16	NM_028971	74485	Mm.474494	NM_028971	ENSMUSG00000023084	Lrrc71	4933430H15Rik	leucine rich repeat containing 71	protein-coding
mm_81642.1	chr9	110896949	110896979	+	1	NA	intron (NM_146228, intron 23 of 26)	intron (NM_146228, intron 23 of 26)	16642	NM_001146060	235633	Mm.86338	NM_146228	ENSMUSG00000044037	Als2cl	79H19D|79H19E|BC022645|D930044G19Rik|mRn.49018	ALS2 C-terminal like	protein-coding
mm_7147.1	chr1	91398727	91398765	-	1	NA	promoter-TSS (NM_023343)	promoter-TSS (NM_023343)	37	NM_023343	67444	Mm.337240	NM_023343	ENSMUSG00000026309	Ilkap	0710007A14Rik|1600009O09Rik|PP2C-DELTA	integrin-linked kinase-associated serine/threonine phosphatase 2C	protein-coding
mm_156186.1	chrX	133908442	133908462	+	1	NA	promoter-TSS (NM_026838)	promoter-TSS (NM_026838)	27	NM_001083895	68792	Mm.263553	NM_026838	ENSMUSG00000031253	Srpx2	1110039C07Rik|SRP|SRPUL	sushi-repeat-containing protein, X-linked 2	protein-coding
mm_83103.1	chr9	40341498	40341536	-	1	NA	intron (NM_172768, intron 2 of 19)	intron (NM_172768, intron 2 of 19)	8045	NR_040728	73558	Mm.398307	NR_040728		1700110K17Rik	-	RIKEN cDNA 1700110K17 gene	ncRNA
mm_97454.1	chr11	78194744	78194756	+	1	NA	intron (NM_001045516, intron 1 of 3)	intron (NM_001045516, intron 1 of 3)	1358	NM_001045516	216974	Mm.50974	NM_001045516	ENSMUSG00000044122	Proca1	4933404M19Rik	protein interacting with cyclin A1	protein-coding
mm_172851.1	chr9	37038793	37038794	+	1	NA	intron (NM_001029838, intron 2 of 12)	intron (NM_001029838, intron 2 of 12)	108529	NM_148950	208076	Mm.260335	NM_148950	ENSMUSG00000035934	Pknox2	D230005H23Rik|Prep2	Pbx/knotted 1 homeobox 2	protein-coding
mm_172456.1	chr7	36118233	36118250	+	1	NA	Intergenic	Intergenic	-315252	NM_177739	668501	Mm.286296	NM_177739	ENSMUSG00000044452	Zfp507	1810022O10Rik|A230056M16Rik|AL024009|AU021817|BB105092|Gm480|Znf507|mKIAA1084	zinc finger protein 507	protein-coding
mm_58203.1	chr6	143233354	143233367	-	1	NA	Intergenic	Intergenic	-12528	NR_027803	52285	Mm.354898	NM_001033129		D6Ertd474e	1700001I24Rik|AU023129	DNA segment, Chr 6, ERATO Doi 474, expressed	ncRNA
mm_26222.1	chr3	138902475	138902485	+	1	NA	non-coding (NR_121195, exon 8 of 8)	non-coding (NR_121195, exon 8 of 8)	160272	NM_019571	56224	Mm.31927	NM_019571	ENSMUSG00000028152	Tspan5	2810455A09Rik|4930505M03Rik|NET-4|Tm4sf9	tetraspanin 5	protein-coding
mm_14709.1	chr2	143078468	143078482	+	1	NA	promoter-TSS (NM_020595)	promoter-TSS (NM_020595)	-17	NM_020595	57329	Mm.157751	NM_020595	ENSMUSG00000027416	Otor	CDRAP|Fdp|MIA|MIAL	otoraplin	protein-coding
mm_87604.1	chr10	57727941	57727968	+	1	NA	intron (NM_008863, intron 4 of 5)	intron (NM_008863, intron 4 of 5)	-56969	NM_021272	12140	Mm.3644	NM_021272	ENSMUSG00000019874	Fabp7	B-FABP|BFABP|Blbp|MRG	fatty acid binding protein 7, brain	protein-coding
mm_77576.1	chr8	123515467	123515498	-	1	NA	promoter-TSS (NM_028146)	promoter-TSS (NM_028146)	-27	NM_001170976	72185	Mm.27925	NM_028146	ENSMUSG00000031970	Dbndd1	2810427I04Rik|D8Ertd590e	dysbindin (dystrobrevin binding protein 1) domain containing 1	protein-coding
mm_102667.1	chr11	65032403	65032413	-	1	NA	intron (NM_175003, intron 10 of 20)	intron (NM_175003, intron 10 of 20)	53373	NM_023479	68626	Mm.157711	NM_023479	ENSMUSG00000020549	Elac2	1110017O07Rik|D11Wsu80e|Hpc2	elaC ribonuclease Z 2	protein-coding
mm_133169.1	chr16	72027462	72027470	+	1	NA	Intergenic	Intergenic	206861	NR_131116	319533	Mm.373754	NR_131115		8030451O07Rik	-	RIKEN cDNA 8030451O07 gene	ncRNA
mm_151115.1	chr19	47864535	47864541	+	1	NA	3' UTR (NM_010362, exon 6 of 6)	3' UTR (NM_010362, exon 6 of 6)	-1007	NM_030051	68214	Mm.63791	NM_026619	ENSMUSG00000025069	Gsto2	1700020F09Rik|4930425C18Rik|GSTO 2-2	glutathione S-transferase omega 2	protein-coding
mm_132148.1	chr16	32102532	32102541	+	1	NA	intron (NM_025892, intron 1 of 3)	intron (NM_025892, intron 1 of 3)	2734	NM_025892	66994	Mm.22990	NM_025892	ENSMUSG00000035790	Cep19	1500031L02Rik|AI428934|AL022620	centrosomal protein 19	protein-coding
mm_158643.1	chrX	155338390	155338456	-	1	NA	promoter-TSS (NM_016764)	promoter-TSS (NM_016764)	37	NM_016764	53381	Mm.247542	NM_016764	ENSMUSG00000025289	Prdx4	AOE372|Prx-iv|Prx4|TRANK	peroxiredoxin 4	protein-coding
mm_52087.1	chr6	97829574	97829576	+	1	NA	intron (NM_001113198, intron 1 of 9)	intron (NM_001113198, intron 1 of 9)	22517	NM_001113198	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_120871.1	chr14	75230585	75230612	+	1	NA	3' UTR (NM_001247984, exon 16 of 16)	3' UTR (NM_001247984, exon 16 of 16)	-11689	NM_019775	56373	Mm.24242	NM_019775	ENSMUSG00000021999	Cpb2	1110032P04Rik|4930405E17Rik|AI255929|CPR|Cpu|TAFI	carboxypeptidase B2 (plasma)	protein-coding
mm_102826.1	chr11	69070697	69070721	-	1	NA	promoter-TSS (NM_025838)	promoter-TSS (NM_025838)	-100	NM_025838	66910	Mm.33964	NM_025838	ENSMUSG00000020895	Tmem107	1110004B13Rik|2810049P21Rik	transmembrane protein 107	protein-coding
mm_123942.1	chr14	73376000	73376010	-	1	NA	intron (NM_008410, intron 1 of 5)	intron (NM_008410, intron 1 of 5)	9266	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_172540.1	chr7	96209983	96209988	+	1	NA	promoter-TSS (NM_011858)	promoter-TSS (NM_011858)	-652	NM_011858	23966	Mm.254610	NM_011858	ENSMUSG00000048078	Tenm4	Doc4|ELM2|Odz4|R75022|Ten-m4|l(7)-3Rn|l7Rn3|mKIAA1302	teneurin transmembrane protein 4	protein-coding
mm_142916.1	chr17	53568337	53568356	-	1	NA	intron (NM_020005, intron 1 of 17)	intron (NM_020005, intron 1 of 17)	1375	NM_020005	18519	Mm.255025	NM_020005	ENSMUSG00000000708	Kat2b	A930006P13Rik|AI461839|AW536563|Pcaf|p/CAF	K(lysine) acetyltransferase 2B	protein-coding
mm_140408.1	chr17	87646250	87646260	+	1	NA	exon (NM_008532, exon 8 of 10)	exon (NM_008532, exon 8 of 10)	10276	NM_008532	17075	Mm.4259	NM_008532	ENSMUSG00000045394	Epcam	CD326|EGP|EGP-2|Egp314|Ep-CAM|EpCAM1|GA733-2|Ly74|TROP1|Tacsd1|Tacstd1|gp40	epithelial cell adhesion molecule	protein-coding
mm_140345.1	chr17	86829394	86829434	+	1	NA	exon (NM_010137, exon 15 of 16)	exon (NM_010137, exon 15 of 16)	75550	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_171647.1	chr4	37225150	37225154	-	1	NA	Intergenic	L1Md_T|LINE|L1	-273408	NM_001165999	242384	Mm.132507	NM_175516	ENSMUSG00000045083	Lingo2	B230217C06Rik|Lern3|Lrrn6c	leucine rich repeat and Ig domain containing 2	protein-coding
mm_124141.1	chr14	87141132	87141148	-	1	NA	promoter-TSS (NM_019670)	promoter-TSS (NM_019670)	-26	NM_019670	56419	Mm.440585	NM_019670	ENSMUSG00000022021	Diaph3	4930417P13Rik|Dia2|Diap3|Drf3|mDia2|mKIAA4117|p134MDia2	diaphanous related formin 3	protein-coding
mm_70397.1	chr8	11175222	11175225	+	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-137582	NM_009932	12827	Mm.181021	NM_009932	ENSMUSG00000031503	Col4a2	Col4a-2	collagen, type IV, alpha 2	protein-coding
mm_161265.1	chr14	6108428	6108428	-	1	NA	Intergenic	CpG	178822	NM_001270812	100861615	Mm.488431	NM_001270812	ENSMUSG00000079396	LOC100861615	-	alpha takusan-like	protein-coding
mm_106248.1	chr11	117813482	117813495	-	1	NA	3' UTR (NM_009304, exon 4 of 4)	3' UTR (NM_009304, exon 4 of 4)	3821	NM_009304	20973	Mm.468228	NM_009304	ENSMUSG00000048277	Syngr2	Clast2|cellugyrin	synaptogyrin 2	protein-coding
mm_134965.1	chr16	31948414	31948430	-	1	NA	promoter-TSS (NR_027897)	promoter-TSS (NR_027897)	99	NR_027897	106264	Mm.347369	NM_025320	ENSMUSG00000107002	0610012G03Rik	AI839730	RIKEN cDNA 0610012G03 gene	ncRNA
mm_77334.1	chr8	119558469	119558488	-	1	NA	intron (NM_019709, intron 1 of 23)	CpG	283	NM_001167910	56453	Mm.206934	NM_019709	ENSMUSG00000031835	Mbtps1	0610038M03Rik|AV003995|S1P|SKI-1|Ski1|mKIAA0091	membrane-bound transcription factor peptidase, site 1	protein-coding
mm_169713.1	chr15	76337665	76337679	+	1	NA	Intergenic	Intergenic	-5851	NM_025567	66445	Mm.29196	NM_025567	ENSMUSG00000022551	Cyc1	2610002H19Rik|AA408921|Cyct1	cytochrome c-1	protein-coding
mm_93171.1	chr10	93310992	93311016	-	1	NA	5' UTR (NM_001322268, exon 1 of 6)	5' UTR (NM_001322268, exon 1 of 6)	155	NM_001322268	13713	Mm.4454	NM_013508	ENSMUSG00000008398	Elk3	D430049E23Rik|Erp|Etrp|Net|Sap-2	ELK3, member of ETS oncogene family	protein-coding
mm_82981.1	chr9	35969519	35969522	-	1	NA	Intergenic	Intergenic	-119640	NR_030730	100041605	Mm.99350	NR_030730	ENSMUSG00000098705	Gm3428	-	predicted gene 3428	ncRNA
mm_138849.1	chr17	40811090	40811133	+	1	NA	promoter-TSS (NM_011269)	promoter-TSS (NM_011269)	-38	NM_011269	19743	Mm.12961	NM_011269	ENSMUSG00000023926	Rhag	CD241|Rh50|Rh50A	Rhesus blood group-associated A glycoprotein	protein-coding
mm_124833.1	chr15	9186289	9186301	+	1	NA	intron (NM_177178, intron 15 of 17)	intron (NM_177178, intron 15 of 17)	-30870	NM_001285980	27401	Mm.35584	NM_013787	ENSMUSG00000054115	Skp2	4930500A04Rik|FBXL1|FWD1|p45	S-phase kinase-associated protein 2 (p45)	protein-coding
mm_91431.1	chr10	33256232	33256244	-	1	NA	non-coding (NR_040657, exon 1 of 3)	non-coding (NR_040657, exon 1 of 3)	119	NR_040657	442820	Mm.490725	NR_040657		D830005E20Rik	-	RIKEN cDNA D830005E20 gene	ncRNA
mm_19605.1	chr2	102451827	102451843	-	1	NA	promoter-TSS (NM_010218)	promoter-TSS (NM_010218)	-43	NM_010218	14221	Mm.29730	NM_010218	ENSMUSG00000075012	Fjx1	-	four jointed box 1 (Drosophila)	protein-coding
mm_28304.1	chr3	89214379	89214387	-	1	NA	promoter-TSS (NM_013604)	promoter-TSS (NM_013604)	-48	NM_013604	17827	Mm.280943	NM_013604	ENSMUSG00000064068	Mtx1	Gcap6|Mtx	metaxin 1	protein-coding
mm_154332.1	chrM	3172	3182	+	1	NA	NA	Intergenic	NA	NA								
mm_22527.1	chr3	7647156	7647170	+	1	NA	Intergenic	Intergenic	-33403	NM_001313888	16196	Mm.3825	NM_008371	ENSMUSG00000040329	Il7	A630026I06Rik|Il-7|hlb368	interleukin 7	protein-coding
mm_28879.1	chr3	97767917	97768024	-	1	NA	promoter-TSS (NM_178080)	promoter-TSS (NM_178080)	44	NR_110360	83679	Mm.129840	NM_031401	ENSMUSG00000038170	Pde4dip	4732458A06Rik|9430063L05Rik|C87016|D130016K21Rik|D3Bwg1078e|Usmg4|mKIAA0454	phosphodiesterase 4D interacting protein (myomegalin)	protein-coding
mm_28262.1	chr3	88607329	88607341	-	1	NA	Intergenic	Intergenic	-8872	NM_001198911	16800	Mm.239329	NM_008487	ENSMUSG00000028059	Arhgef2	AA408978|GEF|GEF-H1|GEFH1|LFP40|Lbcl1|Lfc|P40|mKIAA0651	rho/rac guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_57236.1	chr6	123282933	123282974	-	1	NA	3' UTR (NM_019948, exon 6 of 6)	3' UTR (NM_019948, exon 6 of 6)	6918	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_119037.1	chr14	30559781	30559799	+	1	NA	exon (NM_009388, exon 3 of 14)	exon (NM_009388, exon 3 of 14)	10659	NM_009388	21881	Mm.290692	NM_009388	ENSMUSG00000021957	Tkt	p68	transketolase	protein-coding
mm_25650.1	chr3	121449709	121449735	+	1	NA	intron (NM_028044, intron 1 of 6)	intron (NM_028044, intron 1 of 6)	23181	NM_028044	71994	Mm.275555	NM_028044	ENSMUSG00000053931	Cnn3	1600014M03Rik|C85854|Calpo3	calponin 3, acidic	protein-coding
mm_165718.1	chr3	101130744	101130768	+	1	NA	Intergenic	Intergenic	-20590	NM_011197	19221	Mm.24807	NM_011197	ENSMUSG00000027864	Ptgfrn	4833445A08Rik|AU042434|CD9P-1|FPRP|Trim45	prostaglandin F2 receptor negative regulator	protein-coding
mm_125194.1	chr15	32695944	32695959	+	1	NA	3' UTR (NM_009154, exon 23 of 23)	3' UTR (NM_009154, exon 23 of 23)	-224772	NM_008304	15529	Mm.234266	NM_008304	ENSMUSG00000022261	Sdc2	4833414L08Rik|AA960457|Hspg1|Synd2|syndecan-2	syndecan 2	protein-coding
mm_5947.1	chr1	56796170	56796180	-	1	NA	3' UTR (NM_139146, exon 11 of 11)	3' UTR (NM_139146, exon 11 of 11)	-158724	NM_027661	71066	Mm.152656	NM_027661	ENSMUSG00000045336	Hsfy2	4933413G11Rik|Hspy2l	heat shock transcription factor, Y-linked 2	protein-coding
mm_47373.1	chr5	122984997	122984997	-	1	NA	intron (NM_001003953, intron 2 of 22)	intron (NM_001003953, intron 2 of 22)	4102	NM_001003953	30841	Mm.86406	NM_013910	ENSMUSG00000029475	Kdm2b	Cxxc2|Fbl10|Fbxl10|Jhdm1b|PCCX2	lysine (K)-specific demethylase 2B	protein-coding
mm_45075.1	chr5	43869129	43869139	-	1	NA	intron (NM_007646, intron 1 of 7)	intron (NM_007646, intron 1 of 7)	325	NM_007646	12494	Mm.249873	NM_007646	ENSMUSG00000029084	Cd38	ADPRC 1|Cd38-rs1|I-19	CD38 antigen	protein-coding
mm_98172.1	chr11	87754861	87754871	+	1	NA	Intergenic	Intergenic	-1998	NR_029555	387160		NR_029555	ENSMUSG00000105196	Mir142	Mirn142|miR-142|mir-142a|mmu-mir-142|mmu-mir-142a	microRNA 142	ncRNA
mm_64466.1	chr7	142790511	142790515	+	1	NA	Intergenic	Intergenic	109453	NM_009377	21823	Mm.1292	NM_009377	ENSMUSG00000000214	Th	-	tyrosine hydroxylase	protein-coding
mm_10815.1	chr2	24350368	24350374	+	1	NA	3' UTR (NM_031167, exon 5 of 5)	3' UTR (NM_031167, exon 5 of 5)	5000	NM_001039701	16181	Mm.882	NM_031167	ENSMUSG00000026981	Il1rn	F630041P17Rik|IL-1ra	interleukin 1 receptor antagonist	protein-coding
mm_127817.1	chr15	5108425	5108433	-	1	NA	intron (NM_001163138, intron 1 of 3)	intron (NM_001163138, intron 1 of 3)	104	NM_001163138	239319	Mm.31252	NM_001163138	ENSMUSG00000041849	Card6	D730008L15	caspase recruitment domain family, member 6	protein-coding
mm_58228.1	chr6	144685807	144685810	-	1	NA	intron (NR_040519, intron 1 of 2)	B4|SINE|B4	12940	NR_040519	66760	Mm.233631	NR_040519	ENSMUSG00000085785	Sox5os3	4933425H06Rik	SRY (sex determining region Y)-box 5, opposite strand 3	ncRNA
mm_91598.1	chr10	40936175	40936188	-	1	NA	exon (NM_031877, exon 8 of 9)	exon (NM_031877, exon 8 of 9)	52647	NM_031877	83767	Mm.41353	NM_031877	ENSMUSG00000019831	Wasf1	AI195380|AI838537|Scar|WAVE|WAVE-1	WAS protein family, member 1	protein-coding
mm_48918.1	chr6	4004186	4004196	+	1	NA	5' UTR (NM_025331, exon 1 of 2)	5' UTR (NM_025331, exon 1 of 2)	204	NM_025331	66066	Mm.25547	NM_025331	ENSMUSG00000032766	Gng11	0610037B21Rik	guanine nucleotide binding protein (G protein), gamma 11	protein-coding
mm_161002.1	chr11	116454196	116454196	-	1	NA	5' UTR (NM_001033267, exon 1 of 14)	5' UTR (NM_001033267, exon 1 of 14)	151	NM_001033267	217341	Mm.387352	NM_001033267	ENSMUSG00000070331	Qrich2	Gm66	glutamine rich 2	protein-coding
mm_63341.1	chr7	126965019	126965024	+	1	NA	intron (NM_144926, intron 12 of 17)	B1_Mus1|SINE|Alu	-10893	NM_026638	52858	Mm.28219	NM_026638	ENSMUSG00000030682	Cdipt	9530042F15Rik|D7Bwg0575e|Pis|Pis1	CDP-diacylglycerol--inositol 3-phosphatidyltransferase (phosphatidylinositol synthase)	protein-coding
mm_146504.1	chr18	3309753	3309789	-	1	NA	intron (NR_073193, intron 3 of 7)	intron (NR_073193, intron 3 of 7)	-10215	NM_001110853	12916	Mm.5244	NM_013498	ENSMUSG00000063889	Crem	ICER|ICERI	cAMP responsive element modulator	protein-coding
mm_32228.1	chr4	102087716	102087734	+	1	NA	Intergenic	CpG	100885	NM_001085520	381536	Mm.297685	NM_001085520	ENSMUSG00000078625	Gm12789	OTTMUSG00000008445	predicted gene 12789	protein-coding
mm_139626.1	chr17	57367091	57367102	+	1	NA	intron (NM_010130, intron 2 of 21)	MTEb|LTR|ERVL-MaLR	8410	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_118481.1	chr14	11986237	11986240	+	1	NA	intron (NM_008981, intron 4 of 29)	B1_Mur3|SINE|Alu	-203705	NM_001347593	19270	Mm.431266	NM_008981	ENSMUSG00000021745	Ptprg	5430405N12Rik|AW046354|AW549872|RPTPgamma	protein tyrosine phosphatase, receptor type, G	protein-coding
mm_69577.1	chr7	135701053	135701071	-	1	NA	exon (NM_001081117, exon 12 of 14)	exon (NM_001081117, exon 12 of 14)	15317	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_18471.1	chr2	62411871	62411910	-	1	NA	5' UTR (NM_010074, exon 1 of 26)	5' UTR (NM_010074, exon 1 of 26)	341	NM_010074	13482	Mm.1151	NM_010074	ENSMUSG00000035000	Dpp4	Cd26|Dpp-4|THAM	dipeptidylpeptidase 4	protein-coding
mm_159425.1	chr3	108415455	108415455	-	1	NA	promoter-TSS (NM_017392)	promoter-TSS (NM_017392)	39	NM_017392	53883	Mm.39728	NM_017392	ENSMUSG00000068740	Celsr2	Adgrc2|EGFL2|Flamingo1|flamingo|mKIAA0279|mfmi1	cadherin, EGF LAG seven-pass G-type receptor 2	protein-coding
mm_12336.1	chr2	69670101	69670134	+	1	NA	promoter-TSS (NM_001081087)	promoter-TSS (NM_001081087)	-3	NM_001081087	228003	Mm.178784	NM_001081087	ENSMUSG00000075307	Klhl41	Gm112|Kbtbd10|SARCOSIN	kelch-like 41	protein-coding
mm_99105.1	chr11	100119406	100119416	+	1	NA	exon (NM_010662, exon 4 of 8)	exon (NM_010662, exon 4 of 8)	1166	NM_001313949	16663	Mm.4646	NM_010662	ENSMUSG00000044041	Krt13	CK13|K13|Krt-1.13|Krt1-13	keratin 13	protein-coding
mm_17243.1	chr2	25617673	25617689	-	1	NA	promoter-TSS (NM_029859)	promoter-TSS (NM_029859)	-3	NM_029859	77058	Mm.478493	NM_029859	ENSMUSG00000026940	Ccdc183	4921530D09Rik|Cccd183|Kiaa1984	coiled-coil domain containing 183	protein-coding
mm_68566.1	chr7	115597892	115597928	-	1	NA	intron (NM_001277327, intron 6 of 14)	intron (NM_001277327, intron 6 of 14)	203699	NM_001277328	20679	Mm.323365	NM_011445	ENSMUSG00000051910	Sox6	AI987981|SOX-LZ	SRY (sex determining region Y)-box 6	protein-coding
mm_140332.1	chr17	86754166	86754176	+	1	NA	5' UTR (NM_010137, exon 1 of 16)	5' UTR (NM_010137, exon 1 of 16)	307	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_171928.1	chr5	61313962	61313962	-	1	NA	Intergenic	Intergenic	-494881	NM_019468	14380	Mm.347430	NM_019468	ENSMUSG00000089992	G6pd2	G6pdx-ps1|Gpd-2|Gpd2	glucose-6-phosphate dehydrogenase 2	protein-coding
mm_143973.1	chr17	87427733	87427741	-	1	NA	promoter-TSS (NM_029298)	promoter-TSS (NM_029298)	4	NM_029298	75467	Mm.50108	NM_029298	ENSMUSG00000036557	Stpg4	1700011E24Rik|GSE	sperm tail PG rich repeat containing 4	protein-coding
mm_24206.1	chr3	88621204	88621214	+	1	NA	promoter-TSS (NM_001198913)	promoter-TSS (NM_001198913)	103	NM_008487	16800	Mm.239329	NM_008487	ENSMUSG00000028059	Arhgef2	AA408978|GEF|GEF-H1|GEFH1|LFP40|Lbcl1|Lfc|P40|mKIAA0651	rho/rac guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_47711.1	chr5	129997855	129997866	-	1	NA	exon (NM_010368, exon 8 of 12)	exon (NM_010368, exon 8 of 12)	4968	NM_010368	110006	Mm.3317	NM_010368	ENSMUSG00000025534	Gusb	AI747421|Gur|Gus|Gus-r|Gus-s|Gus-t|Gus-u|Gut|asd|g	glucuronidase, beta	protein-coding
mm_81713.1	chr9	111351852	111351870	+	1	NA	intron (NM_001164659, intron 7 of 21)	intron (NM_001164659, intron 7 of 21)	40122	NM_001164659	320429	Mm.270754	NM_001164659	ENSMUSG00000062296	Trank1	A230061D21Rik|C030048J01Rik|Gm187|Lba1	tetratricopeptide repeat and ankyrin repeat containing 1	protein-coding
mm_60953.1	chr7	47050696	47050702	+	1	NA	promoter-TSS (NM_026436)	promoter-TSS (NM_026436)	59	NM_026436	67893	Mm.27338	NM_026436	ENSMUSG00000010307	Tmem86a	1810054O13Rik|AI414959|AW742698	transmembrane protein 86A	protein-coding
mm_137537.1	chr17	27556614	27556635	+	1	NA	promoter-TSS (NM_001166545)	promoter-TSS (NM_001166545)	20	NM_001166537	15361	Mm.4438	NM_016660	ENSMUSG00000046711	Hmga1	AL023995|Hmga1a|Hmga1b|Hmgi|Hmgiy|Hmgy	high mobility group AT-hook 1	protein-coding
mm_98963.1	chr11	98664342	98664356	+	1	NA	promoter-TSS (NM_021347)	promoter-TSS (NM_021347)	-2	NM_021347	57911	Mm.458085	NM_021347	ENSMUSG00000017204	Gsdma	BB149167|Gsdm|Gsdm1|Gsdma1|H312E	gasdermin A	protein-coding
mm_115066.1	chr13	101442429	101442439	+	1	NA	Intergenic	Intergenic	-44854	NR_046187	78136	Mm.399065	NR_046187		4922502H24Rik	-	RIKEN cDNA 4922502H24 gene	ncRNA
mm_132666.1	chr16	42180450	42180454	+	1	NA	3' UTR (NM_001347236, exon 7 of 7)	3' UTR (NM_001347236, exon 7 of 7)	123017	NR_105858	102466172		NR_105858	ENSMUSG00000098300	Mir6540	Gm27780|mir-6540|mmu-mir-6540	microRNA 6540	ncRNA
mm_156720.1	chrX	159708615	159708642	+	1	NA	promoter-TSS (NM_021389)	promoter-TSS (NM_021389)	27	NR_110970	58194	Mm.286495	NM_021389	ENSMUSG00000040990	Sh3kbp1	1200007H22Rik|1700125L08Rik|5830464D22Rik|AI447724|Cin85|IN85|Ruk|Seta	SH3-domain kinase binding protein 1	protein-coding
mm_134704.1	chr16	22857492	22857505	-	1	NA	promoter-TSS (NM_001190805)	promoter-TSS (NM_001190805)	171	NM_001081368	70573	Mm.68291	NM_001081368	ENSMUSG00000004462	Tbccd1	5730478M09Rik|AU015083|BB165076	TBCC domain containing 1	protein-coding
mm_52838.1	chr6	121638289	121638299	+	1	NA	exon (NM_175628, exon 2 of 36)	exon (NM_175628, exon 2 of 36)	2121	NM_175628	232345	Mm.30151	NM_175628	ENSMUSG00000030111	A2m	A2mp	alpha-2-macroglobulin	protein-coding
mm_126530.1	chr15	82016379	82016419	+	1	NA	promoter-TSS (NM_010247)	promoter-TSS (NM_010247)	30	NM_010247	14375	Mm.288809	NM_010247	ENSMUSG00000022471	Xrcc6	70kDa|G22p1|Ku70	X-ray repair complementing defective repair in Chinese hamster cells 6	protein-coding
mm_39454.1	chr5	17574639	17574666	+	1	NA	promoter-TSS (NM_013657)	promoter-TSS (NM_013657)	-164	NM_013657	20348	Mm.5071	NM_013657	ENSMUSG00000028780	Sema3c	1110036B02Rik|SemE|Semae	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	protein-coding
mm_152056.1	chr19	6298892	6298902	-	1	NA	3' UTR (NM_010119, exon 5 of 5)	3' UTR (NM_010119, exon 5 of 5)	-7560	NM_001033342	240505	Mm.329622	NM_001033342	ENSMUSG00000024769	Cdc42bpg	BC046418|MRCKgamma	CDC42 binding protein kinase gamma (DMPK-like)	protein-coding
mm_38943.1	chr4	150198470	150198497	-	1	NA	intron (NM_009802, intron 1 of 7)	intron (NM_009802, intron 1 of 7)	2652	NM_009802	12353	Mm.232523	NM_009802	ENSMUSG00000028972	Car6	Ca6|DOC1	carbonic anhydrase 6	protein-coding
mm_16425.1	chr2	180290738	180290750	+	1	NA	promoter-TSS (NM_173031)	promoter-TSS (NM_173031)	-865	NM_173031	271887	Mm.246640	NM_173031	ENSMUSG00000038980	Rbbp8nl	4732416F18	RBBP8 N-terminal like	protein-coding
mm_18726.1	chr2	72955776	72955781	-	1	NA	intron (NM_001018042, intron 4 of 6)	B1_Mus1|SINE|Alu	23503	NM_001098425	20687	Mm.124328	NM_011450	ENSMUSG00000027109	Sp3	D130027J01Rik	trans-acting transcription factor 3	protein-coding
mm_146430.1	chr18	84859424	84859434	+	1	NA	intron (NM_025797, intron 1 of 4)	intron (NM_025797, intron 1 of 4)	8015	NM_025797	109672	Mm.31018	NM_025797	ENSMUSG00000024646	Cyb5a	0610009N12Rik|Cyb5	cytochrome b5 type A (microsomal)	protein-coding
mm_12.1	chr1	4857688	4857701	+	1	NA	promoter-TSS (NM_011541)	promoter-TSS (NM_011541)	0	NM_001159750	21399	Mm.207263	NM_011541	ENSMUSG00000033813	Tcea1	S-II	transcription elongation factor A (SII) 1	protein-coding
mm_23994.1	chr3	86539820	86539832	+	1	NA	intron (NM_001077687, intron 38 of 50)	intron (NM_001077687, intron 38 of 50)	8457	NM_011839	23937	Mm.389466	NM_011839	ENSMUSG00000057777	Mab21l2	-	mab-21-like 2 (C. elegans)	protein-coding
mm_51217.1	chr6	71353976	71353978	+	1	NA	Intergenic	Intergenic	-19450	NM_009857	12525	Mm.1858	NM_009857	ENSMUSG00000053977	Cd8a	BB154331|Ly-2|Ly-35|Ly-B|Lyt-2	CD8 antigen, alpha chain	protein-coding
mm_158800.1	chrX	167245724	167245746	-	1	NA	exon (NM_001313760, exon 2 of 2)	exon (NM_001313760, exon 2 of 2)	18594	NM_001313761	170744	Mm.196676	NM_133212	ENSMUSG00000040522	Tlr8	-	toll-like receptor 8	protein-coding
mm_42681.1	chr5	119796644	119796657	+	1	NA	Intergenic	CpG	-38013	NM_011537	21388	Mm.103636	NM_011537	ENSMUSG00000018263	Tbx5	-	T-box 5	protein-coding
mm_31869.1	chr4	80004454	80004482	+	1	NA	Intergenic	Intergenic	-829745	NM_031202	22178	Mm.30438	NM_031202	ENSMUSG00000005994	Tyrp1	Oca3|TRP-1|TRP1|Tyrp|b|brown|isa	tyrosinase-related protein 1	protein-coding
mm_31795.1	chr4	63979892	63979904	+	1	NA	intron (NM_011607, intron 15 of 25)	intron (NM_011607, intron 15 of 25)	67117	NM_011607	21923	Mm.980	NM_011607	ENSMUSG00000028364	Tnc	AI528729|C130033P17Rik|Hxb|TN|TN-C|Ten|cytotactin|tenascin-C	tenascin C	protein-coding
mm_36612.1	chr4	89282153	89282161	-	1	NA	promoter-TSS (NM_001040654)	promoter-TSS (NM_001040654)	35	NM_001040654	12578	Mm.4733	NM_009877	ENSMUSG00000044303	Cdkn2a	ARF-INK4a|Arf|INK4a-ARF|Ink4a/Arf|MTS1|Pctr1|p16|p16(INK4a)|p16INK4a|p19<ARF>|p19ARF	cyclin-dependent kinase inhibitor 2A	protein-coding
mm_105652.1	chr11	107189326	107189340	-	1	NA	promoter-TSS (NM_001161329)	promoter-TSS (NM_001161329)	48	NM_133702	68979	Mm.294617	NM_133702	ENSMUSG00000018433	Nol11	1500002M01Rik|AU015220|AU019874	nucleolar protein 11	protein-coding
mm_88869.1	chr10	81000717	81000721	+	1	NA	intron (NM_010319, intron 1 of 3)	MTEb|LTR|ERVL-MaLR	646	NM_001038655	14708	Mm.222496	NM_010319	ENSMUSG00000048240	Gng7	AI840417	guanine nucleotide binding protein (G protein), gamma 7	protein-coding
mm_129392.1	chr15	78206392	78206407	-	1	NA	promoter-TSS (NM_013645)	promoter-TSS (NM_013645)	1	NM_013645	19293	Mm.2766	NM_013645	ENSMUSG00000005716	Pvalb	PV|Parv|Pva	parvalbumin	protein-coding
mm_13459.1	chr2	105674427	105674437	+	1	NA	intron (NM_001244201, intron 1 of 11)	intron (NM_001244201, intron 1 of 11)	-1312	NM_001244200	18508	Mm.3608	NM_013627	ENSMUSG00000027168	Pax6	1500038E17Rik|AEY11|Dey|Gsfaey11|Pax-6|Sey	paired box 6	protein-coding
mm_1196.1	chr1	62703988	62703998	+	1	NA	5' UTR (NM_001077407, exon 1 of 16)	5' UTR (NM_001077407, exon 1 of 16)	676	NM_001077405	18187	Mm.266341	NM_010939	ENSMUSG00000025969	Nrp2	1110048P06Rik|Np-2|Np2|Npn-2|Npn2	neuropilin 2	protein-coding
mm_45004.1	chr5	38480154	38480239	-	1	NA	5' UTR (NM_001102415, exon 1 of 10)	5' UTR (NM_001102415, exon 1 of 10)	110	NM_001102414	117591	Mm.260137	NM_145559	ENSMUSG00000005107	Slc2a9	Glut9|SLC2A9B|SLC2a9A	solute carrier family 2 (facilitated glucose transporter), member 9	protein-coding
mm_153989.1	chr19	49368311	49368316	-	1	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	1162288	NM_025696	66673	Mm.70980	NM_025696	ENSMUSG00000063434	Sorcs3	6330404A12Rik|AW045579	sortilin-related VPS10 domain containing receptor 3	protein-coding
mm_17314.1	chr2	26438636	26438640	-	1	NA	exon (NM_153125, exon 2 of 30)	exon (NM_153125, exon 2 of 30)	6578	NM_153125	227648	Mm.206371	NM_153125	ENSMUSG00000026924	Sec16a	AU024582|C230052J16Rik	SEC16 homolog A, endoplasmic reticulum export factor	protein-coding
mm_157108.1	chrX	9437972	9437983	-	1	NA	3' UTR (NM_007807, exon 13 of 13)	3' UTR (NM_007807, exon 13 of 13)	31347	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_72756.1	chr8	85492476	85492490	+	1	NA	promoter-TSS (NM_173866)	promoter-TSS (NM_173866)	-134	NM_173866	108682	Mm.200423	NM_173866	ENSMUSG00000031700	Gpt2	4631422C05Rik|ALT2|AU014768|AU041193|C87201	glutamic pyruvate transaminase (alanine aminotransferase) 2	protein-coding
mm_150681.1	chr19	42053041	42053049	+	1	NA	exon (NM_025752, exon 1 of 1)	exon (NM_025752, exon 1 of 1)	817	NM_025752	66765	Mm.440412	NM_025752	ENSMUSG00000090369	4933411K16Rik	-	RIKEN cDNA 4933411K16 gene	protein-coding
mm_91082.1	chr10	19012543	19012547	-	1	NA	promoter-TSS (NM_001166402)	promoter-TSS (NM_001166402)	-582	NM_001166402	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_3332.1	chr1	137943157	137943188	+	1	NA	Intergenic	Intergenic	-23283	NR_029795	735252		NR_029795	ENSMUSG00000065565	Mir181a-1	Mirn181a-1|Mirn213|miR-213|mir-181a-1|mmu-mir-213	microRNA 181a-1	ncRNA
mm_10432.1	chr2	14074148	14074191	+	1	NA	promoter-TSS (NM_011484)	promoter-TSS (NM_011484)	57	NM_011484	20844	Mm.273174	NM_011484	ENSMUSG00000026718	Stam	STAM1	signal transducing adaptor molecule (SH3 domain and ITAM motif) 1	protein-coding
mm_107178.1	chr12	24973892	24973902	+	1	NA	Intergenic	Intergenic	-1035	NM_001081378	77480	Mm.250641	NM_001081378	ENSMUSG00000036333	Kidins220	3110039L19Rik|AI194387|AI316525|C330002I19Rik|mKIAA1250	kinase D-interacting substrate 220	protein-coding
mm_64516.1	chr7	143829648	143829683	+	1	NA	intron (NM_007856, intron 1 of 8)	intron (NM_007856, intron 1 of 8)	6498	NM_007856	13360	Mm.249342	NM_007856	ENSMUSG00000058454	Dhcr7	AA409147	7-dehydrocholesterol reductase	protein-coding
mm_115424.1	chr13	117220710	117220721	+	1	NA	5' UTR (NM_010330, exon 1 of 9)	5' UTR (NM_010330, exon 1 of 9)	142	NM_010330	13723	Mm.274926	NM_010330	ENSMUSG00000021728	Emb	AL022799|Gp70	embigin	protein-coding
mm_75310.1	chr8	41209828	41209841	-	1	NA	exon (NM_145594, exon 3 of 8)	exon (NM_145594, exon 3 of 8)	5322	NM_145594	234199	Mm.277955	NM_145594	ENSMUSG00000031594	Fgl1	Mfire1	fibrinogen-like protein 1	protein-coding
mm_54895.1	chr6	47190434	47190442	-	1	NA	intron (NM_001004357, intron 20 of 23)	RLTR17|LTR|ERVK	-53958	NM_025771	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding
mm_99510.1	chr11	103101736	103101749	+	1	NA	promoter-TSS (NM_025988)	promoter-TSS (NM_025988)	54	NM_025988	67131	Mm.390367	NM_025988	ENSMUSG00000056938	Acbd4	2010009P05Rik|2010015A21Rik|AI849317	acyl-Coenzyme A binding domain containing 4	protein-coding
mm_82394.1	chr9	14718382	14718393	-	1	NA	intron (NM_177905, intron 9 of 18)	intron (NM_177905, intron 9 of 18)	22346	NM_177905	330890	Mm.334969	NM_177905	ENSMUSG00000036912	Piwil4	9230101H05Rik|Miwi2	piwi-like RNA-mediated gene silencing 4	protein-coding
mm_44057.1	chr5	148264930	148264944	+	1	NA	intron (NM_029920, intron 7 of 14)	intron (NM_029920, intron 7 of 14)	127878	NM_001301424	11987	Mm.275489	NM_007513	ENSMUSG00000041313	Slc7a1	4831426K01Rik|AI447493|Atrc-1|Atrc1|Cat1|Rec-1|Rev-1|mCAT-1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 1	protein-coding
mm_136852.1	chr17	12793342	12793344	+	1	NA	intron (NR_027784, intron 2 of 2)	ID_B1|SINE|B4	-23637	NM_010515	16004	Mm.26553	NM_010515	ENSMUSG00000023830	Igf2r	AI661837|CD222|CI-MPR|M6P/IGF2R|Mpr300	insulin-like growth factor 2 receptor	protein-coding
mm_144989.1	chr18	38262007	38262033	+	1	NA	3' UTR (NM_024179, exon 13 of 13)	3' UTR (NM_024179, exon 13 of 13)	-11455	NR_027904	73516	Mm.48776	NR_015475	ENSMUSG00000097080	1700086O06Rik	-	RIKEN cDNA 1700086O06 gene	ncRNA
mm_115152.1	chr13	105898942	105898957	+	1	NA	Intergenic	Intergenic	455256	NM_008308	15550	Mm.4716	NM_008308	ENSMUSG00000021721	Htr1a	Gpcr18	5-hydroxytryptamine (serotonin) receptor 1A	protein-coding
mm_109519.1	chr12	111454444	111454461	+	1	NA	3' UTR (NM_009396, exon 12 of 12)	3' UTR (NM_009396, exon 12 of 12)	11791	NM_009396	21928	Mm.255332	NM_009396	ENSMUSG00000021281	Tnfaip2	B94|Exoc3l3|M-sec|Tnfip2|tnfb94	tumor necrosis factor, alpha-induced protein 2	protein-coding
mm_91736.1	chr10	46505634	46505635	-	1	NA	Intergenic	Intergenic	260885	NR_028276	108637		NR_028276	ENSMUSG00000096263	Snord14c	Gm23107|Rnu14|U14	small nucleolar RNA, C/D box 14C	snoRNA
mm_83655.1	chr9	49509858	49509916	-	1	NA	exon (NM_001311065, exon 16 of 18)	exon (NM_001311065, exon 16 of 18)	-8401	NR_029465	100036537	Mm.437541	NR_029465	ENSMUSG00000079564	Gm11149	ENSMUSG00000060603|ENSMUSG00000079564	predicted gene 11149	ncRNA
mm_23883.1	chr3	83031048	83031054	+	1	NA	exon (NM_010196, exon 5 of 5)	exon (NM_010196, exon 5 of 5)	4898	NM_001111048	14161	Mm.88793	NM_010196	ENSMUSG00000028001	Fga	ENSMUSG00000059807|Fib	fibrinogen alpha chain	protein-coding
mm_105170.1	chr11	101784428	101784441	-	1	NA	intron (NM_008815, intron 2 of 12)	intron (NM_008815, intron 2 of 12)	876	NM_008815	18612	Mm.5025	NM_008815	ENSMUSG00000017724	Etv4	AW414408|Pea-3|Pea3	ets variant 4	protein-coding
mm_92853.1	chr10	81524336	81524346	-	1	NA	promoter-TSS (NM_010304)	promoter-TSS (NM_010304)	-116	NM_010304	14676	Mm.1546	NM_010304	ENSMUSG00000034792	Gna15	G[a]15|Galpha15	guanine nucleotide binding protein, alpha 15	protein-coding
mm_150091.1	chr19	29454288	29454297	+	1	NA	intron (NM_021396, intron 4 of 5)	intron (NM_021396, intron 4 of 5)	43373	NM_021396	58205	Mm.116737	NM_021396	ENSMUSG00000016498	Pdcd1lg2	B7-DC|Btdc|F730015O22Rik|PD-L2	programmed cell death 1 ligand 2	protein-coding
mm_137131.1	chr17	23600806	23600820	+	1	NA	promoter-TSS (NM_001033425)	promoter-TSS (NM_001033425)	-13	NM_001033425	332221	Mm.270315	NM_001033425	ENSMUSG00000023902	Zscan10	BC068284|Zfp206|Zkscan10|Znf206	zinc finger and SCAN domain containing 10	protein-coding
mm_70900.1	chr8	25601695	25601703	+	1	NA	promoter-TSS (NM_001308482)	promoter-TSS (NM_001308482)	98	NM_001308481	234135	Mm.217337	NM_001001735	ENSMUSG00000054823	Whsc1l1	6720429E03|A530023P05|AI528490|NSD3|WHISTLE	Wolf-Hirschhorn syndrome candidate 1-like 1 (human)	protein-coding
mm_127637.1	chr15	102473483	102473491	+	1	NA	intron (NM_001103165, intron 2 of 14)	intron (NM_001103165, intron 2 of 14)	2855	NM_001174073	18521	Mm.236513	NM_011042	ENSMUSG00000056851	Pcbp2	AW412548|Hnrpx|alphaCP-2	poly(rC) binding protein 2	protein-coding
mm_40138.1	chr5	35057060	35057096	+	1	NA	promoter-TSS (NM_172708)	promoter-TSS (NM_172708)	-6	NM_172708	231134	Mm.205483	NM_172708	ENSMUSG00000044716	Dok7	A930013K19Rik|AW049091|Dok-7|EF-12|Oit5	docking protein 7	protein-coding
mm_8258.1	chr1	138856820	138856848	-	1	NA	promoter-TSS (NM_001081226)	promoter-TSS (NM_001081226)	20	NM_001081226	69549	Mm.264673	NM_001081226	ENSMUSG00000079283	2310009B15Rik	-	RIKEN cDNA 2310009B15 gene	protein-coding
mm_120051.1	chr14	56647800	56647803	+	1	NA	exon (NM_001145978, exon 32 of 35)	exon (NM_001145978, exon 32 of 35)	-20447	NM_023773	75339	Mm.152466	NM_023773	ENSMUSG00000079184	Mphosph8	1500035L22Rik|4930548G07Rik|AU040635	M-phase phosphoprotein 8	protein-coding
mm_144623.1	chr18	32938794	32938804	+	1	NA	promoter-TSS (NM_009793)	promoter-TSS (NM_009793)	-242	NM_009793	12326	Mm.222329	NM_009793	ENSMUSG00000038128	Camk4	A430110E23Rik|AI666733|CaMKIV|CaMKIV/Gr|D18Bwg0362e	calcium/calmodulin-dependent protein kinase IV	protein-coding
mm_100710.1	chr11	3774695	3774702	-	1	NA	intron (NM_152818, intron 2 of 13)	CpG	-52471	NM_001302630	74309	Mm.61022	NM_152818	ENSMUSG00000020435	Osbp2	1700095P05Rik|C630001G20Rik|Gm244|ORP-4|OSBPL1	oxysterol binding protein 2	protein-coding
mm_63852.1	chr7	135662239	135662257	+	1	NA	intron (NM_001316681, intron 4 of 17)	intron (NM_001316681, intron 4 of 17)	-9934	NR_015548	67765	Mm.445272	NR_015548	ENSMUSG00000097471	5830432E09Rik	-	RIKEN cDNA 5830432E09 gene	ncRNA
mm_141425.1	chr17	29437254	29437255	-	1	NA	Intergenic	Intergenic	-53791	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_56118.1	chr6	87532240	87532254	-	1	NA	intron (NM_001037727, intron 1 of 10)	intron (NM_001037727, intron 1 of 10)	1012	NM_001037727	232201	Mm.119564	NM_175476	ENSMUSG00000030047	Arhgap25	A130039I20Rik	Rho GTPase activating protein 25	protein-coding
mm_109464.1	chr12	111271090	111271121	+	1	NA	promoter-TSS (NM_033603)	promoter-TSS (NM_033603)	9	NM_033603	93835	Mm.197639	NM_033603	ENSMUSG00000021278	Amn	-	amnionless	protein-coding
mm_69720.1	chr7	140300664	140300664	-	1	NA	TTS (NM_001128145)	TTS (NM_001128145)	-22037	NM_146956	258958	Mm.347648	NM_146956	ENSMUSG00000061489	Olfr525	MOR251-2	olfactory receptor 525	protein-coding
mm_152878.1	chr19	24518555	24518602	-	1	NA	intron (NM_008846, intron 1 of 14)	(GTGTG)n|Simple_repeat|Simple_repeat	37249	NM_008846	18719	Mm.217214	NM_008846	ENSMUSG00000024867	Pip5k1b	PI4P5K-I[b]|PIP5K1-beta|PIP5KIbeta|Pipk5b|STM7	phosphatidylinositol-4-phosphate 5-kinase, type 1 beta	protein-coding
mm_79369.1	chr9	54595085	54595099	+	1	NA	intron (NM_029573, intron 3 of 10)	intron (NM_029573, intron 3 of 10)	8581	NM_029573	67834	Mm.279195	NM_029573	ENSMUSG00000032279	Idh3a	1110003P10Rik|1500012E04Rik|AA407078|AI316514	isocitrate dehydrogenase 3 (NAD+) alpha	protein-coding
mm_112924.1	chr13	20936382	20936409	+	1	NA	intron (NM_012054, intron 11 of 20)	BGLII_Mus|LTR|ERVK	136904	NM_146535	258528	Mm.377554	NM_146535	ENSMUSG00000042869	Olfr1370	MOR256-14	olfactory receptor 1370	protein-coding
mm_18622.1	chr2	68472280	68472317	-	1	NA	promoter-TSS (NM_016866)	promoter-TSS (NM_016866)	-317	NM_016866	53416	Mm.198414	NM_016866	ENSMUSG00000027030	Stk39	AW227544|AW556857|DCHT|RF005|Rnl5|SPAK	serine/threonine kinase 39	protein-coding
mm_28092.1	chr3	85887388	85887412	-	1	NA	5' UTR (NM_177130, exon 1 of 2)	5' UTR (NM_177130, exon 1 of 2)	118	NM_177130	320302	Mm.482978	NM_177130	ENSMUSG00000031286	Glt28d2	4732486J07Rik|Glt28d1l	glycosyltransferase 28 domain containing 2	protein-coding
mm_139752.1	chr17	63864042	63864052	+	1	NA	promoter-TSS (NM_001037997)	promoter-TSS (NM_001037997)	66	NM_001037997	14158	Mm.23039	NM_008000	ENSMUSG00000000127	Fer	AV082135|C330004K01Rik|Fert|Fert2	fer (fms/fps related) protein kinase	protein-coding
mm_78632.1	chr9	40050361	40050382	+	1	NA	promoter-TSS (NR_033613)	promoter-TSS (NR_033613)	-187	NR_033613	72224	Mm.235535	NR_033613	ENSMUSG00000101963	1700001J11Rik	-	ring finger protein 19A pseudogene	pseudo
mm_69673.1	chr7	139984560	139984568	-	1	NA	intron (NM_007403, intron 19 of 23)	intron (NM_007403, intron 19 of 23)	2310	NR_106029	102465643		NR_106029	ENSMUSG00000099092	Mir7062	Gm27339|mmu-mir-7062	microRNA 7062	ncRNA
mm_74250.1	chr8	124831784	124831799	+	1	NA	3' UTR (NM_198632, exon 10 of 10)	3' UTR (NM_198632, exon 10 of 10)	31238	NM_025615	66523	Mm.436864	NM_025615	ENSMUSG00000031984	2810004N23Rik	3110004G14Rik|Ayu21-55|Gt(pU21)55Imeg|GtAyu21-55	RIKEN cDNA 2810004N23 gene	protein-coding
mm_133295.1	chr16	77500169	77500199	+	1	NA	intron (NR_015543, intron 3 of 4)	intron (NR_015543, intron 3 of 4)	-98752	NR_029535	387229		NR_029535	ENSMUSG00000065530	Mir99a	Mirn99a|mir-99a|mmu-mir-99a	microRNA 99a	ncRNA
mm_119124.1	chr14	31134731	31134765	+	1	NA	promoter-TSS (NM_027289)	promoter-TSS (NM_027289)	-105	NM_027289	70021	Mm.261681	NM_027289	ENSMUSG00000071547	Nt5dc2	2510015F01Rik	5'-nucleotidase domain containing 2	protein-coding
mm_68071.1	chr7	101869013	101869023	-	1	NA	intron (NM_001252552, intron 2 of 6)	intron (NM_001252552, intron 2 of 6)	1770	NM_001252554	14275	Mm.2135	NM_008034	ENSMUSG00000001827	Folr1	FBP1|Folbp-1|Folbp1	folate receptor 1 (adult)	protein-coding
mm_78176.1	chr9	21181572	21181624	+	1	NA	intron (NR_106127, intron 1 of 3)	CpG	-2503	NM_001310750	18577	Mm.191749	NM_019798	ENSMUSG00000032177	Pde4a	D9Ertd60e|Dpde2	phosphodiesterase 4A, cAMP specific	protein-coding
mm_37021.1	chr4	114643123	114643126	-	1	NA	Intergenic	L1MEg|LINE|L1	-178596	NR_033617	433746	Mm.388908	NR_033617	ENSMUSG00000055198	Gm12830	OTTMUSG00000008584	predicted gene 12830	ncRNA
mm_7192.1	chr1	92919274	92919299	-	1	NA	exon (NM_181405, exon 10 of 11)	exon (NM_181405, exon 10 of 11)	8461	NM_181405	108657	Mm.200971	NM_181405	ENSMUSG00000026269	Rnpepl1	1110014H17Rik|AI894167	arginyl aminopeptidase (aminopeptidase B)-like 1	protein-coding
mm_27514.1	chr3	56183242	56183272	-	1	NA	5' UTR (NM_030595, exon 1 of 58)	5' UTR (NM_030595, exon 1 of 58)	444	NM_030595	26422	Mm.384353	NM_030595	ENSMUSG00000027799	Nbea	Lyst2|mKIAA1544	neurobeachin	protein-coding
mm_39431.1	chr5	16553750	16553761	+	1	NA	promoter-TSS (NM_001289461)	promoter-TSS (NM_001289461)	-146	NM_001289461	15234	Mm.267078	NM_010427	ENSMUSG00000028864	Hgf	C230052L06Rik|HGF/SF|NK1|NK2|SF|SF/HGF	hepatocyte growth factor	protein-coding
mm_80781.1	chr9	95637732	95637746	+	1	NA	5' UTR (NM_029620, exon 1 of 9)	5' UTR (NM_029620, exon 1 of 9)	111	NM_029620	76477	Mm.46016	NM_029620	ENSMUSG00000015354	Pcolce2	2400001O18Rik|Pcpe2	procollagen C-endopeptidase enhancer 2	protein-coding
mm_2096.1	chr1	87716972	87716975	+	1	NA	intron (NM_010566, intron 25 of 26)	intron (NM_010566, intron 25 of 26)	-39038	NM_029846	77040	Mm.272972	NM_029846	ENSMUSG00000026289	Atg16l1	1500009K01Rik|Apg16l|Atg16l|WDR30	autophagy related 16-like 1 (S. cerevisiae)	protein-coding
mm_167180.1	chr7	141637267	141637274	-	1	NA	intron (NM_001330001, intron 31 of 33)	intron (NM_001330001, intron 31 of 33)	16569	NR_106030	102466798		NR_106030	ENSMUSG00000098759	Mir7063	Gm27654|mmu-mir-7063	microRNA 7063	ncRNA
mm_146721.1	chr18	15064199	15064226	-	1	NA	promoter-TSS (NM_001142731)	promoter-TSS (NM_001142731)	-630	NM_001142731	106931	Mm.329299	NM_134112	ENSMUSG00000036225	Kctd1	4933402K10Rik|AI661543|AW553000	potassium channel tetramerisation domain containing 1	protein-coding
mm_101784.1	chr11	45955165	45955182	-	1	NA	promoter-TSS (NM_001290737)	promoter-TSS (NM_001290737)	15	NM_001290737	66628	Mm.269083	NM_001080969	ENSMUSG00000011254	Thg1l	-	tRNA-histidine guanylyltransferase 1-like (S. cerevisiae)	protein-coding
mm_9817.1	chr1	182276493	182276509	-	1	NA	3' UTR (NM_007853, exon 3 of 3)	3' UTR (NM_007853, exon 3 of 3)	6258	NM_007853	13244	Mm.29648	NM_007853	ENSMUSG00000038633	Degs1	AA536663|Degs|Des1|Mdes	delta(4)-desaturase, sphingolipid 1	protein-coding
mm_354.1	chr1	33669817	33669856	+	1	NA	promoter-TSS (NR_033199)	promoter-TSS (NR_033199)	12	NR_033199	67503	Mm.87069	NM_026204	ENSMUSG00000103746	1700001G17Rik	-	RIKEN cDNA 1700001G17 gene	ncRNA
mm_123915.1	chr14	73362754	73362870	-	1	NA	3' UTR (NM_008410, exon 6 of 6)	3' UTR (NM_008410, exon 6 of 6)	22459	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_58194.1	chr6	143076115	143076118	-	1	NA	intron (NM_001109688, intron 7 of 24)	intron (NM_001109688, intron 7 of 24)	24036	NM_001286578	74741	Mm.130260	NM_029081	ENSMUSG00000030279	C2cd5	5730419I09Rik|C030008B15Rik|CDP138	C2 calcium-dependent domain containing 5	protein-coding
mm_24355.1	chr3	90052825	90052857	+	1	NA	promoter-TSS (NM_001165987)	promoter-TSS (NM_001165987)	39	NM_027500	99650	Mm.300083	NM_025762	ENSMUSG00000027942	4933434E20Rik	5730552F22Rik|AI462154|NICE-3|NS5ATP4	RIKEN cDNA 4933434E20 gene	protein-coding
mm_11317.1	chr2	30392262	30392305	+	1	NA	promoter-TSS (NM_020329)	promoter-TSS (NM_020329)	29	NM_001290508	57170	Mm.285167	NM_020329	ENSMUSG00000026856	Dolpp1	0610011H20Rik|AB030189|LSFR2	dolichyl pyrophosphate phosphatase 1	protein-coding
mm_165121.1	chr2	3781829	3781832	+	1	NA	3' UTR (NM_025626, exon 4 of 4)	3' UTR (NM_025626, exon 4 of 4)	68372	NM_025626	66540	Mm.277864	NM_025626	ENSMUSG00000026655	Fam107b	3110001A13Rik|AA589595|AA959793|AI132312	family with sequence similarity 107, member B	protein-coding
mm_4730.1	chr1	181352682	181352693	+	1	NA	promoter-TSS (NM_001160212)	promoter-TSS (NM_001160212)	59	NM_001160211	72978	Mm.338083	NM_028408	ENSMUSG00000026514	Cnih3	2900075G08Rik|CNIH-3	cornichon family AMPA receptor auxiliary protein 3	protein-coding
mm_119686.1	chr14	53443244	53443262	+	1	NA	Intergenic	Intergenic	810676	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_52934.1	chr6	122933902	122933920	+	1	NA	exon (NM_199311, exon 6 of 6)	exon (NM_199311, exon 6 of 6)	12063	NM_199311	269799	Mm.297275	NM_199311	ENSMUSG00000049037	Clec4a1	BC049354|Dcir4	C-type lectin domain family 4, member a1	protein-coding
mm_14759.1	chr2	144746622	144746626	+	1	NA	intron (NM_025314, intron 4 of 5)	intron (NM_025314, intron 4 of 5)	-77042	NM_025490	66328	Mm.45377	NM_025490	ENSMUSG00000027431	Scp2d1	1700010M22Rik	SCP2 sterol-binding domain containing 1	protein-coding
mm_41538.1	chr5	92856455	92856465	+	1	NA	intron (NM_001077595, intron 1 of 9)	intron (NM_001077595, intron 1 of 9)	-41533	NM_001077596	27428	Mm.46014	NM_015756	ENSMUSG00000029381	Shroom3	AL022960|D5Ertd287e|Shrm|Shrm3	shroom family member 3	protein-coding
mm_166977.1	chr7	45128788	45128790	-	1	NA	promoter-TSS (NM_009438)	promoter-TSS (NM_009438)	-44	NM_009438	22121	Mm.180458	NM_009438	ENSMUSG00000074129	Rpl13a	1810026N22Rik|Tstap198-7|tum-antigen	ribosomal protein L13A	protein-coding
mm_71586.1	chr8	54954838	54954854	+	1	NA	5' UTR (NM_153581, exon 1 of 7)	5' UTR (NM_153581, exon 1 of 7)	118	NM_001253756	234267	Mm.241700	NM_153581	ENSMUSG00000031517	Gpm6a	Gpm6|M6A	glycoprotein m6a	protein-coding
mm_75212.1	chr8	39605430	39605446	-	1	NA	3' UTR (NM_031195, exon 9 of 9)	3' UTR (NM_031195, exon 9 of 9)	37240	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_155945.1	chrX	104506683	104506699	+	1	NA	TTS (NM_001081189)	TTS (NM_001081189)	23909	NM_001081189	331487	Mm.438275	NM_001081189	ENSMUSG00000073016	Uprt	Gm774	uracil phosphoribosyltransferase	protein-coding
mm_65010.1	chr7	17062388	17062423	-	1	NA	promoter-TSS (NM_001162950)	promoter-TSS (NM_001162950)	22	NM_001162950	53417	Mm.135110	NM_016868	ENSMUSG00000004328	Hif3a	Ipas|MOP7|NEPAS|bHLHe17	hypoxia inducible factor 3, alpha subunit	protein-coding
mm_60287.1	chr7	43979143	43979147	+	1	NA	intron (NM_010116, intron 2 of 4)	intron (NM_010116, intron 2 of 4)	3084	NM_010116	13648	Mm.440884	NM_010116	ENSMUSG00000059042	Klk1b9	EGF-BP C|Egfbp-3|Egfbp3|KAL|Klk9|kallikrein|mGk-9	kallikrein 1-related peptidase b9	protein-coding
mm_83473.1	chr9	45787674	45787720	-	1	NA	intron (NM_001081373, intron 10 of 29)	intron (NM_001081373, intron 10 of 29)	40941	NM_001081373	214552	Mm.260103	NM_172531	ENSMUSG00000043987	Cep164	AI450905|BC027092|D030051D21|mKIAA1052	centrosomal protein 164	protein-coding
mm_152855.1	chr19	24174053	24174099	-	1	NA	promoter-TSS (NM_001198985)	promoter-TSS (NM_001198985)	64	NM_001198985	21873	Mm.104744	NM_011597	ENSMUSG00000024812	Tjp2	ZO-2	tight junction protein 2	protein-coding
mm_171739.1	chr4	95509960	95509962	+	1	NA	Intergenic	L1Md_A|LINE|L1	-47546	NM_001113412	75578	Mm.276098	NM_029347	ENSMUSG00000028573	Fggy	2310009E04Rik	FGGY carbohydrate kinase domain containing	protein-coding
mm_39782.1	chr5	30159906	30159912	+	1	NA	intron (NM_001289798, intron 1 of 15)	MLT1F|LTR|ERVL-MaLR	4656	NM_001289798	231086	Mm.291463	NM_145558	ENSMUSG00000059447	Hadhb	4930479F15Rik|Mtpb|TP-beta	hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), beta subunit	protein-coding
mm_126627.1	chr15	83394102	83394113	+	1	NA	intron (NM_011862, intron 2 of 10)	intron (NM_011862, intron 2 of 10)	-26810	NR_027980	69291	Mm.66794	NM_001033147		1700001L05Rik	-	RIKEN cDNA 1700001L05 gene	ncRNA
mm_147697.1	chr18	60793793	60793825	-	1	NA	Intergenic	Intergenic	-10040	NM_001042605	16149	Mm.439737	NM_010545	ENSMUSG00000024610	Cd74	CLIP|DHLAG|HLADG|Ia-GAMMA|Ii	CD74 antigen (invariant polypeptide of major histocompatibility complex, class II antigen-associated)	protein-coding
mm_88938.1	chr10	81297355	81297370	+	1	NA	intron (NM_008844, intron 1 of 17)	ID_B1|SINE|B4	4399	NM_001146687	18717	Mm.24222	NM_008844	ENSMUSG00000034902	Pip5k1c	AI115456|AI835305|Pip5kIgamma	phosphatidylinositol-4-phosphate 5-kinase, type 1 gamma	protein-coding
mm_53623.1	chr6	140479806	140479824	+	1	NA	intron (NM_144920, intron 3 of 30)	L1MA4|LINE|L1	55716	NM_144920	109135	Mm.247670	NM_144920	ENSMUSG00000030231	Plekha5	2810431N21Rik|AI428202|AK129423|AMH-Cre|Ayu21-9|Gt(pU21)9Imeg|Pepp2|Tg(AMH-cre)1Flor	pleckstrin homology domain containing, family A member 5	protein-coding
mm_151721.1	chr19	4811590	4811619	-	1	NA	promoter-TSS (NM_019869)	promoter-TSS (NM_019869)	30	NM_001290127	102902673	Mm.426069	NM_001290127	ENSMUSG00000096370	Gm21992	Rbm14-rbm4	predicted gene 21992	protein-coding
mm_114491.1	chr13	69809849	69809859	+	1	NA	promoter-TSS (NM_138596)	promoter-TSS (NM_138596)	-28	NM_138596	28077	Mm.52583	NM_138596	ENSMUSG00000021598	Med10	AA959813|AI385605|C78613|D13Wsu50e	mediator complex subunit 10	protein-coding
mm_157832.1	chrX	74246536	74246556	-	1	NA	promoter-TSS (NM_001290421)	promoter-TSS (NM_001290421)	-12	NM_001290421	192176	Mm.295533	NM_010227	ENSMUSG00000031328	Flna	ABP-280|Dilp2|F730004A14Rik|Fln1|GENA 379|filamin-1	filamin, alpha	protein-coding
mm_46785.1	chr5	112589991	112590002	-	1	NA	promoter-TSS (NR_045397)	promoter-TSS (NR_045397)	0	NR_045396	67325	Mm.490791	NR_045396	ENSMUSG00000097962	1700034G24Rik	-	RIKEN cDNA 1700034G24 gene	ncRNA
mm_140001.1	chr17	72996750	72996758	+	1	NA	Intergenic	Intergenic	78449	NM_029999	77889	Mm.154109	NM_029999	ENSMUSG00000024063	Lbh	1810009F10Rik|6720416L16Rik	limb-bud and heart	protein-coding
mm_30980.1	chr4	34886689	34886712	+	1	NA	Intergenic	CpG	-3752	NM_013889	30046	Mm.38193	NM_013889	ENSMUSG00000039967	Zfp292	5730450D02Rik|5830493J20Rik|9430062L07Rik|AI449016|Krox-10|Zfp-15|Zfp15|Zn-15|Zn-16|mKIAA0530	zinc finger protein 292	protein-coding
mm_47876.1	chr5	134688596	134688637	-	1	NA	promoter-TSS (NM_010717)	promoter-TSS (NM_010717)	-26	NM_010717	16885	Mm.15409	NM_010717	ENSMUSG00000029674	Limk1	KIZ-1|LIMK-1|Limk	LIM-domain containing, protein kinase	protein-coding
mm_90671.1	chr10	128896236	128896246	+	1	NA	Intergenic	Intergenic	-4523	NM_010272	14561	Mm.299218	NM_010272	ENSMUSG00000025352	Gdf11	BMP-11|Bmp11	growth differentiation factor 11	protein-coding
mm_15604.1	chr2	160699608	160699611	+	1	NA	intron (NM_009408, intron 9 of 20)	PB1D9|SINE|Alu	-31701	NM_021280	18803	Mm.44463	NM_021280	ENSMUSG00000016933	Plcg1	AI894140|Cded|Plc-1|Plc-gamma1|Plcg-1	phospholipase C, gamma 1	protein-coding
mm_109707.1	chr12	113422041	113422075	+	1	NA	Intergenic	Intergenic	-67507	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_165410.1	chr2	144331441	144331445	+	1	NA	promoter-TSS (NM_152947)	promoter-TSS (NM_152947)	-81	NM_152947	107586	Mm.252750	NM_026924	ENSMUSG00000037279	Ovol2	1700108N11Rik|1810007D21Rik|M-OVO|M-OVO-A|M-OVO-B|MOVO|Ovo2|Zfp339|movo2	ovo like zinc finger 2	protein-coding
mm_122635.1	chr14	51146543	51146547	-	1	NA	intron (NM_011271, intron 1 of 1)	intron (NM_011271, intron 1 of 1)	222	NM_011271	19752	Mm.235538	NM_011271	ENSMUSG00000035896	Rnase1	AI574248|Rib-1|Rib1	ribonuclease, RNase A family, 1 (pancreatic)	protein-coding
mm_122236.1	chr14	33247765	33247779	-	1	NA	intron (NM_153800, intron 2 of 10)	intron (NM_153800, intron 2 of 10)	30949	NM_153800	239027	Mm.318350	NM_153800	ENSMUSG00000063506	Arhgap22	B230341L19Rik|RHOGAP2|p68RacGAP	Rho GTPase activating protein 22	protein-coding
mm_40251.1	chr5	38220482	38220560	+	1	NA	promoter-TSS (NM_029162)	promoter-TSS (NM_029162)	39	NM_025281	17089	Mm.28560	NM_025281	ENSMUSG00000067367	Lyar	MLZ-264	Ly1 antibody reactive clone	protein-coding
mm_120268.1	chr14	63122684	63122706	+	1	NA	intron (NM_007798, intron 1 of 9)	CpG	233	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_43472.1	chr5	136694144	136694149	+	1	NA	promoter-TSS (NM_001085387)	promoter-TSS (NM_001085387)	-31	NM_001085387	59310	Mm.5178	NM_021611	ENSMUSG00000005474	Myl10	1700027I08Rik|Mylc2pl|PLRLC	myosin, light chain 10, regulatory	protein-coding
mm_41269.1	chr5	89102051	89102059	+	1	NA	intron (NM_001197147, intron 7 of 25)	intron (NM_001197147, intron 7 of 25)	214795	NM_018760	54403	Mm.41044	NM_018760	ENSMUSG00000060961	Slc4a4	AI835705|NBC|NBC1	solute carrier family 4 (anion exchanger), member 4	protein-coding
mm_22703.1	chr3	18176341	18176341	+	1	NA	intron (NM_007825, intron 1 of 5)	intron (NM_007825, intron 1 of 5)	66997	NM_007825	13123	Mm.316000	NM_007825	ENSMUSG00000039519	Cyp7b1	AW261589|D3Ertd552e|hct-1	cytochrome P450, family 7, subfamily b, polypeptide 1	protein-coding
mm_137356.1	chr17	25298390	25298403	+	1	NA	promoter-TSS (NM_178372)	promoter-TSS (NM_178372)	2	NM_178372	328780	Mm.127166	NM_178372	ENSMUSG00000056399	Prss34	C130091P12|Mcp11|mMcp-11	protease, serine 34	protein-coding
mm_148097.1	chr18	73928682	73928695	-	1	NA	3' UTR (NM_172632, exon 6 of 6)	3' UTR (NM_172632, exon 6 of 6)	69303	NM_001305882	71263	Mm.126220	NM_027741	ENSMUSG00000064036	Mro	4930507C04Rik|4933435E20Rik	maestro	protein-coding
mm_120681.1	chr14	70635208	70635214	+	1	NA	TTS (NM_008004)	TTS (NM_008004)	837	NM_001252664	13829	Mm.210863	NM_013514	ENSMUSG00000022099	Dmtn	AI325486|Epb4.9|Epb49|dematin	dematin actin binding protein	protein-coding
mm_80958.1	chr9	103011505	103011509	+	1	NA	intron (NM_033314, intron 1 of 13)	5S|rRNA|rRNA	3018	NM_033314	24059	Mm.207106	NM_033314	ENSMUSG00000032548	Slco2a1	2310021C19Rik|Pgt|Slc21a2|mPgt	solute carrier organic anion transporter family, member 2a1	protein-coding
mm_66469.1	chr7	44974712	44974730	-	1	NA	5' UTR (NM_153679, exon 1 of 19)	5' UTR (NM_153679, exon 1 of 19)	130	NM_153679	78070	Mm.231465	NM_153679	ENSMUSG00000007783	Cpt1c	6530437J22Rik|9630004I06Rik	carnitine palmitoyltransferase 1c	protein-coding
mm_140814.1	chr17	22867076	22867110	-	1	NA	promoter-TSS (NM_177358)	promoter-TSS (NM_177358)	41	NM_177358	240041	Mm.328828	NM_177358	ENSMUSG00000059142	Zfp945	A630033E08Rik|C730040L01Rik	zinc finger protein 945	protein-coding
mm_102778.1	chr11	68386932	68386942	-	1	NA	promoter-TSS (NM_008744)	promoter-TSS (NM_008744)	-111	NM_008744	18208	Mm.39095	NM_008744	ENSMUSG00000020902	Ntn1	AI561871|BC019633|Netrin-1	netrin 1	protein-coding
mm_45197.1	chr5	52471535	52471589	-	1	NA	promoter-TSS (NM_001256059)	promoter-TSS (NM_001256059)	-19	NM_001256059	100503884	Mm.332379	NM_001256059	ENSMUSG00000045790	Ccdc149	Gm447	coiled-coil domain containing 149	protein-coding
mm_10052.1	chr1	193201436	193201584	-	1	NA	promoter-TSS (NM_153137)	promoter-TSS (NM_153137)	36	NM_153137	215243	Mm.261259	NM_153137	ENSMUSG00000037318	Traf3ip3	6030423D04Rik|AI115021|T3jam	TRAF3 interacting protein 3	protein-coding
mm_158344.1	chrX	134162978	134162998	-	1	NA	Intergenic	Intergenic	-1060	NM_183319	331524	Mm.235055	NM_183319	ENSMUSG00000031258	Xkrx	A630026F04	X-linked Kx blood group related, X-linked	protein-coding
mm_113238.1	chr13	27280330	27280333	+	1	NA	Intergenic	L1_Mur3|LINE|L1	20842	NM_025896	67000	Mm.69279	NM_025896	ENSMUSG00000038883	Prl3a1	1600016E11Rik|Ghd9|PLP-H|PLP-I|Plpi|Prlpi	prolactin family 3, subfamily a, member 1	protein-coding
mm_49324.1	chr6	18866388	18866391	+	1	NA	promoter-TSS (NM_029202)	promoter-TSS (NM_029202)	71	NM_001167757	75196	Mm.67665	NM_029202	ENSMUSG00000029517	Ankrd7	4930532L20Rik|AV278427	ankyrin repeat domain 7	protein-coding
mm_1379.1	chr1	66705175	66705180	+	1	NA	intron (NM_001310642, intron 2 of 6)	(T)n|Simple_repeat|Simple_repeat	4346	NM_001310644	66646	Mm.240912	NM_025683	ENSMUSG00000026005	Rpe	2810429B02Rik|5730518J08Rik	ribulose-5-phosphate-3-epimerase	protein-coding
mm_43853.1	chr5	143370105	143370118	+	1	NA	promoter-TSS (NM_001347529)	promoter-TSS (NM_001347529)	19	NM_001347529	170935	Mm.197460	NM_133355	ENSMUSG00000010825	Grid2ip	-	glutamate receptor, ionotropic, delta 2 (Grid2) interacting protein 1	protein-coding
mm_144699.1	chr18	34862674	34862698	+	1	NA	exon (NM_007913, exon 2 of 2)	exon (NM_007913, exon 2 of 2)	1479	NM_007913	13653	Mm.181959	NM_007913	ENSMUSG00000038418	Egr1	A530045N19Rik|ETR103|Egr-1|Krox-1|Krox-24|Krox24|NGF1-A|NGFI-A|NGFIA|TIS8|Zenk|Zfp-6|Zif268|egr	early growth response 1	protein-coding
mm_87916.1	chr10	62494583	62494617	+	1	NA	3' UTR (NM_011157, exon 3 of 3)	3' UTR (NM_011157, exon 3 of 3)	-7795	NM_133672	30930	Mm.260703	NM_133672	ENSMUSG00000020078	Vps26a	AA407240|HB58|Vps26	VPS26 retromer complex component A	protein-coding
mm_52903.1	chr6	122761253	122761275	+	1	NA	Intergenic	Intergenic	-18519	NM_011401	20527	Mm.395108	NM_011401	ENSMUSG00000003153	Slc2a3	AA408729|AL023014|AL024341|AU040424|C78366|Glut-3|Glut3	solute carrier family 2 (facilitated glucose transporter), member 3	protein-coding
mm_49816.1	chr6	37143226	37143246	+	1	NA	intron (NM_001347104, intron 2 of 32)	intron (NM_001347104, intron 2 of 32)	156740	NM_001081206	320127	Mm.119469	NM_001081206	ENSMUSG00000038665	Dgki	C130010K08Rik	diacylglycerol kinase, iota	protein-coding
mm_58295.1	chr6	145865386	145865412	-	1	NA	promoter-TSS (NM_001271768)	promoter-TSS (NM_001271768)	21	NM_001271768	79362	Mm.154529	NM_024469	ENSMUSG00000030256	Bhlhe41	6430520M22Rik|Bhlhb2l|Bhlhb3|DEC2|Sharp1	basic helix-loop-helix family, member e41	protein-coding
mm_30195.1	chr3	144710632	144710649	-	1	NA	intron (NM_001282042, intron 2 of 9)	B1_Mur4|SINE|Alu	9695	NM_001282042	54673	Mm.271775	NM_019464	ENSMUSG00000037062	Sh3glb1	AA409932|AI314629|AU015566|Bif-1|mKIAA0491	SH3-domain GRB2-like B1 (endophilin)	protein-coding
mm_110279.1	chr12	32060945	32060951	-	1	NA	exon (NM_011158, exon 1 of 11)	exon (NM_011158, exon 1 of 11)	331	NM_011158	19088	Mm.25594	NM_011158	ENSMUSG00000002997	Prkar2b	AI451071|AW061005|PKARIIbeta|Pkarb2|RII(beta)	protein kinase, cAMP dependent regulatory, type II beta	protein-coding
mm_144978.1	chr18	37955636	37955645	+	1	NA	promoter-TSS (NM_010411)	promoter-TSS (NM_010411)	81	NM_153793	225392	Mm.233516	NM_153793	ENSMUSG00000044024	Rell2	4631403P03Rik|ependolin	RELT-like 2	protein-coding
mm_75017.1	chr8	30183964	30183967	-	1	NA	Intergenic	Intergenic	-384430	NR_045856	71314	Mm.158666	NR_045856	ENSMUSG00000097044	4933433F19Rik	-	RIKEN cDNA 4933433F19 gene	ncRNA
mm_40777.1	chr5	67260819	67260827	+	1	NA	5' UTR (NM_001285452, exon 1 of 7)	5' UTR (NM_001285452, exon 1 of 7)	258	NM_030108	67878	Mm.23217	NM_028975	ENSMUSG00000037720	Tmem33	1110006G02Rik|1600019D15Rik|2410089A21Rik|2700052H22Rik|5430406L04Rik|AA388285|AI314185|AI426615|db83	transmembrane protein 33	protein-coding
mm_169033.1	chr13	12702319	12702330	+	1	NA	Intergenic	CpG	-51929	NR_003568	664862	Mm.415635	NR_003568		Gpr137b-ps	2310041G17Rik|ENSMUSG00000075118	G protein-coupled receptor 137B, pseudogene	pseudo
mm_168957.1	chr12	78351129	78351140	+	1	NA	intron (NM_145965, intron 2 of 22)	LSU-rRNA_Hsa|rRNA|rRNA	124479	NM_145965	268566	Mm.341742	NM_145965	ENSMUSG00000047454	Gphn	5730552E08Rik|AI662856|BC027112|C230040D23|GPH|GPHRYN|geph	gephyrin	protein-coding
mm_106581.1	chr11	120729571	120729581	-	1	NA	TTS (NM_007621)	TTS (NM_007621)	-2292	NM_001347608	67880	Mm.231091	NM_026428	ENSMUSG00000039450	Dcxr	0610038K04Rik|1810027P18Rik|XR	dicarbonyl L-xylulose reductase	protein-coding
mm_21989.1	chr2	167643144	167643161	-	1	NA	TTS (NM_145538)	TTS (NM_145538)	-11147	NM_023230	66589	Mm.278783	NM_023230	ENSMUSG00000078923	Ube2v1	0610011J09Rik|AI256840|CROC-1|CROC1|D7Bwg1382e|UEV-1	ubiquitin-conjugating enzyme E2 variant 1	protein-coding
mm_74686.1	chr8	14961574	14961590	-	1	NA	intron (NM_172751, intron 16 of 28)	intron (NM_172751, intron 16 of 28)	-49443	NM_029116	74901	Mm.46675	NM_029116	ENSMUSG00000055675	Kbtbd11	2900016B01Rik|4930465M17Rik|mKIAA0711	kelch repeat and BTB (POZ) domain containing 11	protein-coding
mm_26409.1	chr3	142608223	142608241	+	1	NA	exon (NM_010259, exon 8 of 11)	exon (NM_010259, exon 8 of 11)	-12431	NM_010260	14469	Mm.24038	NM_010260	ENSMUSG00000028270	Gbp2	-	guanylate binding protein 2	protein-coding
mm_100645.1	chr11	3101281	3101289	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	-22736	NR_003517	236604	Mm.247625	NM_001004146		Pisd-ps1	-	phosphatidylserine decarboxylase, pseudogene 1	pseudo
mm_33011.1	chr4	120854780	120854784	+	1	NA	Intergenic	CpG	-23087	NM_182929	242662	Mm.192502	NM_182929	ENSMUSG00000032890	Rims3	A730060M23Rik|Nim3|Rim3|mKIAA0237	regulating synaptic membrane exocytosis 3	protein-coding
mm_133273.1	chr16	77387916	77387932	+	1	NA	intron (NR_015543, intron 2 of 4)	intron (NR_015543, intron 2 of 4)	58596	NR_015543	77994	Mm.394688	NR_015543	ENSMUSG00000090386	Mir99ahg	2810055G20Rik|D730043B02Rik	Mir99a and Mirlet7c-1 host gene (non-protein coding)	ncRNA
mm_154185.1	chr19	58794401	58794428	-	1	NA	promoter-TSS (NM_026208)	promoter-TSS (NM_026208)	0	NM_026208	67507	Mm.27027	NM_026208	ENSMUSG00000026931	1700019N19Rik	-	RIKEN cDNA 1700019N19 gene	protein-coding
mm_73043.1	chr8	94329202	94329217	+	1	NA	promoter-TSS (NM_001205311)	promoter-TSS (NM_001205311)	1	NM_001205311	20497	Mm.25804	NM_019415	ENSMUSG00000031766	Slc12a3	AI035291|NCC|NCCT|TSC	solute carrier family 12, member 3	protein-coding
mm_58871.1	chr7	16959822	16959832	+	1	NA	promoter-TSS (NM_001007569)	promoter-TSS (NM_001007569)	32	NM_001007569	71691	Mm.275673	NM_001007569	ENSMUSG00000041141	Pnmal1	0710005I19Rik	PNMA-like 1	protein-coding
mm_44580.1	chr5	24842580	24842624	-	1	NA	promoter-TSS (NM_053075)	promoter-TSS (NM_053075)	-241	NM_053075	19744	Mm.319175	NM_053075	ENSMUSG00000028945	Rheb	Rheb1	Ras homolog enriched in brain	protein-coding
mm_7836.1	chr1	132192019	132192031	-	1	NA	intron (NM_001311104, intron 1 of 4)	intron (NM_001311104, intron 1 of 4)	589	NM_001033250	213409	Mm.426321	NM_001033250	ENSMUSG00000079330	Lemd1	4930540I23Rik|6430514M23Rik|AI428128|LEMP-1	LEM domain containing 1	protein-coding
mm_155963.1	chrX	106027260	106027293	+	1	NA	promoter-TSS (NM_009726)	promoter-TSS (NM_009726)	52	NM_009726	11977	Mm.254297	NM_009726	ENSMUSG00000033792	Atp7a	MNK	ATPase, Cu++ transporting, alpha polypeptide	protein-coding
mm_19062.1	chr2	77466539	77466561	-	1	NA	intron (NR_040368, intron 1 of 2)	intron (NR_040368, intron 1 of 2)	3906	NR_040368	100503106	Mm.443215	NR_040368	ENSMUSG00000085845	Gm13944	OTTMUSG00000015155	predicted gene 13944	ncRNA
mm_65564.1	chr7	27174553	27174576	-	1	NA	exon (NM_029391, exon 5 of 8)	exon (NM_029391, exon 5 of 8)	1529	NR_037283	100526505		NR_037283	ENSMUSG00000093348	Mir3101	mir-3101|mmu-mir-3101	microRNA 3101	ncRNA
mm_24675.1	chr3	94837429	94837458	+	1	NA	promoter-TSS (NM_172683)	promoter-TSS (NM_172683)	-124	NM_001165948	229584	Mm.274787	NM_172683	ENSMUSG00000038902	Pogz	9530006B08Rik	pogo transposable element with ZNF domain	protein-coding
mm_52863.1	chr6	122308685	122308711	+	1	NA	promoter-TSS (NM_010749)	promoter-TSS (NM_010749)	-312	NM_010749	17113	Mm.249225	NM_010749	ENSMUSG00000007458	M6pr	CD-MPR|Mpr46	mannose-6-phosphate receptor, cation dependent	protein-coding
mm_165958.1	chr4	87806347	87806353	-	1	NA	promoter-TSS (NM_029931)	promoter-TSS (NM_029931)	-27	NM_029931	70122	Mm.288898	NM_027326	ENSMUSG00000028496	Mllt3	2210011H10Rik|2610012I03Rik|3830408D16Rik|Af9|D4Ertd321e	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 3	protein-coding
mm_48536.1	chr5	142904638	142904648	-	1	NA	exon (NM_007393, exon 4 of 6)	exon (NM_007393, exon 4 of 6)	2111	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_158226.1	chrX	106208088	106208109	-	1	NA	3' UTR (NM_001167988, exon 8 of 8)	3' UTR (NM_001167988, exon 8 of 8)	11744	NM_001001176	407786	Mm.19440	NM_001001176	ENSMUSG00000047242	Taf9b	BC066223|Taf9l	TATA-box binding protein associated factor 9B	protein-coding
mm_154876.1	chrX	20688559	20688570	+	1	NA	5' UTR (NM_011049, exon 1 of 16)	5' UTR (NM_011049, exon 1 of 16)	138	NM_011049	18555	Mm.102574	NM_011049	ENSMUSG00000031065	Cdk16	Crk5|Pctaire1|Pctk1	cyclin-dependent kinase 16	protein-coding
mm_40498.1	chr5	57718265	57718307	+	1	NA	promoter-TSS (NR_015588)	promoter-TSS (NR_015588)	205	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_14877.1	chr2	148806020	148806025	+	1	NA	TTS (NM_009978)	TTS (NM_009978)	7183	NM_009978	13012	Mm.20435	NM_009978	ENSMUSG00000027442	Cst8	Cres|Cst-rs1	cystatin 8 (cystatin-related epididymal spermatogenic)	protein-coding
mm_93458.1	chr10	110455922	110456008	-	1	NA	Intergenic	CpG	-144685	NR_028438	109335	Mm.367727	NR_028438		9230102K24Rik	-	RIKEN cDNA 9230102K24 gene	ncRNA
mm_45563.1	chr5	73209633	73209635	-	1	NA	intron (NM_028194, intron 2 of 62)	intron (NM_028194, intron 2 of 62)	46984	NM_028194	72313	Mm.260594	NM_028194	ENSMUSG00000070733	Fryl	2010313D22Rik|2310004H21Rik|2510002A14Rik|9030227G01Rik|mKIAA0826	FRY like transcription coactivator	protein-coding
mm_95354.1	chr11	48837435	48837443	+	1	NA	promoter-TSS (NM_001347436)	promoter-TSS (NM_001347436)	-32	NM_001347446	94089	Mm.390335	NM_053166	ENSMUSG00000040350	Trim7	AI790312	tripartite motif-containing 7	protein-coding
mm_98439.1	chr11	94939384	94939430	+	1	NA	exon (NM_007742, exon 6 of 51)	exon (NM_007742, exon 6 of 51)	3183	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_2449.1	chr1	100252619	100252634	+	1	NA	intron (NM_172851, intron 11 of 23)	intron (NM_172851, intron 11 of 23)	479861	NM_172851	241175	Mm.251301	NM_172851	ENSMUSG00000067028	Cntnap5b	C230078M14Rik|Caspr5-2	contactin associated protein-like 5B	protein-coding
mm_61922.1	chr7	90153603	90153626	+	1	NA	intron (NM_001252520, intron 1 of 20)	B1F1|SINE|Alu	23382	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_51560.1	chr6	83353291	83353305	+	1	NA	intron (NM_175277, intron 3 of 3)	intron (NM_175277, intron 3 of 3)	3814	NM_175277	78653	Mm.391470	NM_175277	ENSMUSG00000045160	Bola3	1810056O20Rik	bolA-like 3 (E. coli)	protein-coding
mm_23650.1	chr3	67557524	67557534	+	1	NA	Intergenic	Intergenic	-25239	NM_025813	66868	Mm.491153	NM_025813	ENSMUSG00000027775	Mfsd1	1200003O06Rik	major facilitator superfamily domain containing 1	protein-coding
mm_88767.1	chr10	80335499	80335509	+	1	NA	3' UTR (NM_139292, exon 6 of 6)	3' UTR (NM_139292, exon 6 of 6)	5359	NM_139292	70335	Mm.28147	NM_139292	ENSMUSG00000035504	Reep6	0610011M24Rik|Dp1l1	receptor accessory protein 6	protein-coding
mm_81922.1	chr9	120149734	120149748	+	1	NA	promoter-TSS (NM_001039365)	promoter-TSS (NM_001039365)	-1	NM_008614	17433	Mm.486167	NM_008614	ENSMUSG00000032517	Mobp	AI835053|AI839848|MOBP155|MOBP170|MOBP69|MOBP73|MOBP81|R74645	myelin-associated oligodendrocytic basic protein	protein-coding
mm_114489.1	chr13	69802363	69802388	+	1	NA	Intergenic	MLT1G1|LTR|ERVL-MaLR	-7507	NM_138596	28077	Mm.52583	NM_138596	ENSMUSG00000021598	Med10	AA959813|AI385605|C78613|D13Wsu50e	mediator complex subunit 10	protein-coding
mm_110977.1	chr12	77052835	77052847	-	1	NA	Intergenic	Intergenic	-90593	NM_001146176	17187	Mm.268548	NM_008558	ENSMUSG00000059436	Max	AA960152|AI875693|bHLHd4|bHLHd5|bHLHd6|bHLHd7|bHLHd8	Max protein	protein-coding
mm_143894.1	chr17	84543263	84543272	-	1	NA	intron (NM_177606, intron 2 of 29)	intron (NM_177606, intron 2 of 29)	31372	NM_177606	213556	Mm.215159	NM_177606	ENSMUSG00000040852	Plekhh2	AI256725|E030001K05|mKIAA2028	pleckstrin homology domain containing, family H (with MyTH4 domain) member 2	protein-coding
mm_32941.1	chr4	119422807	119422841	+	1	NA	promoter-TSS (NM_026494)	promoter-TSS (NM_026494)	140	NM_001014900	332934	Mm.388911	NM_001014900	ENSMUSG00000070806	Zmynd12	AI414736	zinc finger, MYND domain containing 12	protein-coding
mm_171190.1	chr3	44191623	44191624	-	1	NA	Intergenic	L1Md_T|LINE|L1	1186637	NR_045172	72511	Mm.140700	NR_045172	ENSMUSG00000097040	2610316D01Rik	-	RIKEN cDNA 2610316D01 gene	ncRNA
mm_122868.1	chr14	54913090	54913128	-	1	NA	promoter-TSS (NM_021551)	promoter-TSS (NM_021551)	23	NM_021551	59049	Mm.27435	NM_021551	ENSMUSG00000022199	Slc22a17	1700094C23Rik|24p3R|AU041908|AW555662|BOIT|Boct	solute carrier family 22 (organic cation transporter), member 17	protein-coding
mm_85088.1	chr9	91385194	91385197	-	1	NA	intron (NM_009576, intron 4 of 4)	intron (NM_009576, intron 4 of 4)	16223	NM_009576	22774	Mm.8062	NM_009576	ENSMUSG00000036972	Zic4	-	zinc finger protein of the cerebellum 4	protein-coding
mm_119862.1	chr14	54468115	54468127	+	1	NA	exon (NM_022993, exon 5 of 7)	exon (NM_022993, exon 5 of 7)	3974	NM_022993	65107	Mm.472719	NM_022993	ENSMUSG00000022175	Lrp10	Lrp9	low-density lipoprotein receptor-related protein 10	protein-coding
mm_34259.1	chr4	141420758	141420798	+	1	NA	promoter-TSS (NM_013868)	promoter-TSS (NM_013868)	-1	NM_013868	29818	Mm.46181	NM_013868	ENSMUSG00000006221	Hspb7	27kDa|Hsp25-2|cvHsp	heat shock protein family, member 7 (cardiovascular)	protein-coding
mm_7292.1	chr1	97821442	97821446	-	1	NA	3' UTR (NM_013626, exon 26 of 26)	3' UTR (NM_013626, exon 26 of 26)	51272	NM_026250	252876	Mm.86090	NM_026250	ENSMUSG00000026333	Gin1	4930429M06Rik|8430411H10Rik|Gin-1|Zh2c2	gypsy retrotransposon integrase 1	protein-coding
mm_40334.1	chr5	43911038	43911051	+	1	NA	3' UTR (NM_007646, exon 8 of 8)	3' UTR (NM_007646, exon 8 of 8)	42235	NM_007646	12494	Mm.249873	NM_007646	ENSMUSG00000029084	Cd38	ADPRC 1|Cd38-rs1|I-19	CD38 antigen	protein-coding
mm_3349.1	chr1	138149191	138149200	+	1	NA	intron (NM_001111316, intron 1 of 31)	intron (NM_001111316, intron 1 of 31)	25931	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_157904.1	chrX	77853518	77853528	-	1	NA	promoter-TSS (NM_017471)	promoter-TSS (NM_017471)	-23	NM_017471	54192	Mm.8034	NM_017471	ENSMUSG00000000003	Pbsn	PB|Prbs	probasin	protein-coding
mm_102818.1	chr11	68973841	68973864	-	1	NA	promoter-TSS (NM_021329)	promoter-TSS (NM_021329)	3	NM_021329	57785	Mm.143774	NM_021329	ENSMUSG00000032892	Rangrf	2400006H24Rik|Mog1|Rangnrf	RAN guanine nucleotide release factor	protein-coding
mm_168395.1	chr11	28353785	28353785	-	1	NA	Intergenic	L1Md_T|LINE|L1	230539	NM_001166661	216613	Mm.93759	NM_181577	ENSMUSG00000032878	Ccdc85a	-	coiled-coil domain containing 85A	protein-coding
mm_173015.1	chrM	694	694	+	1	NA	NA	Intergenic	NA	NA								
mm_161160.1	chr13	27196476	27196476	+	1	NA	promoter-TSS (NM_013766)	promoter-TSS (NM_013766)	-184	NM_013766	27372	Mm.291456	NM_013766	ENSMUSG00000017922	Prl3c1	Ghd7|PLP-J|Prlpi|Prlpj|decidualin	prolactin family 3, subfamily c, member 1	protein-coding
mm_126736.1	chr15	85671261	85671279	+	1	NA	Intergenic	CpG	-32503	NR_110483	102800312	Mm.33117	NR_110483		Lncppara	Lincppara|Mirlet7bhg|linc-Ppara	long noncoding RNA near Ppara	ncRNA
mm_35012.1	chr4	3574777	3574821	-	1	NA	promoter-TSS (NM_028097)	promoter-TSS (NM_028097)	-31	NM_028097	72098	Mm.441135	NM_028097	ENSMUSG00000028232	Tmem68	2010300G19Rik|AA408325|AW123402	transmembrane protein 68	protein-coding
mm_167407.1	chr8	104442929	104442935	-	1	NA	5' UTR (NM_001013380, exon 1 of 13)	5' UTR (NM_001013380, exon 1 of 13)	115	NM_001013380	234663	Mm.289583	NM_001013380	ENSMUSG00000035770	Dync1li2	AA409702|C920003I06|Dncli2|Dnclic2|LIC2	dynein, cytoplasmic 1 light intermediate chain 2	protein-coding
mm_54180.1	chr6	23839287	23839315	-	1	NA	5' UTR (NM_153163, exon 1 of 30)	5' UTR (NM_153163, exon 1 of 30)	120	NM_001252106	320405	Mm.259632	NM_153163	ENSMUSG00000017978	Cadps2	A230044C21Rik|Caps-2|Caps2|Cpd2	Ca2+-dependent activator protein for secretion 2	protein-coding
mm_44095.1	chr5	149265036	149265058	+	1	NA	promoter-TSS (NM_009663)	promoter-TSS (NM_009663)	43	NM_009663	11690	Mm.19844	NM_009663	ENSMUSG00000060063	Alox5ap	Flap	arachidonate 5-lipoxygenase activating protein	protein-coding
mm_6133.1	chr1	64690619	64690638	-	1	NA	promoter-TSS (NM_001097644)	promoter-TSS (NM_001097644)	31	NR_038009	69941	Mm.69044	NR_038009	ENSMUSG00000087213	2810408I11Rik	-	RIKEN cDNA 2810408I11 gene	ncRNA
mm_14986.1	chr2	152226541	152226574	+	1	NA	promoter-TSS (NM_007788)	promoter-TSS (NM_007788)	-283	NM_007788	12995	Mm.23692	NM_007788	ENSMUSG00000074698	Csnk2a1	Csnk2a1-rs4	casein kinase 2, alpha 1 polypeptide	protein-coding
mm_87432.1	chr10	50907399	50907399	+	1	NA	intron (NM_011376, intron 2 of 10)	intron (NM_011376, intron 2 of 10)	11748	NM_011376	20464	Mm.4774	NM_011376	ENSMUSG00000019913	Sim1	bHLHe14|mSIM1	single-minded homolog 1 (Drosophila)	protein-coding
mm_68568.1	chr7	115697189	115697220	-	1	NA	intron (NM_001025560, intron 5 of 15)	intron (NM_001025560, intron 5 of 15)	104405	NM_001277328	20679	Mm.323365	NM_011445	ENSMUSG00000051910	Sox6	AI987981|SOX-LZ	SRY (sex determining region Y)-box 6	protein-coding
mm_39487.1	chr5	20945598	20945640	+	1	NA	intron (NM_001080977, intron 1 of 7)	MLT1B|LTR|ERVL-MaLR	-5370	NR_030699	320770	Mm.491217	NR_030699	ENSMUSG00000101013	A630072M18Rik	Aptr	RIKEN cDNA A630072M18 gene	ncRNA
mm_81943.1	chr9	120492502	120492512	+	1	NA	promoter-TSS (NM_026892)	promoter-TSS (NM_026892)	-99	NM_026892	68969	Mm.28753	NM_026892	ENSMUSG00000006941	Eif1b	1500010M16Rik|3110001N14Rik|Gc20	eukaryotic translation initiation factor 1B	protein-coding
mm_118339.1	chr13	114399022	114399036	-	1	NA	Intergenic	ORR1B2|LTR|ERVL-MaLR	-10935	NM_010887	17993	Mm.253142	NM_010887	ENSMUSG00000021764	Ndufs4	6720411N02Rik|C1-18k	NADH dehydrogenase (ubiquinone) Fe-S protein 4	protein-coding
mm_20308.1	chr2	127208275	127208289	-	1	NA	promoter-TSS (NM_177214)	promoter-TSS (NM_177214)	-2	NM_198630	329509	Mm.120738	NM_198630	ENSMUSG00000044145	1810024B03Rik	-	RIKEN cDNA 1810024B03 gene	protein-coding
mm_164809.1	chr18	31903517	31903517	-	1	NA	intron (NM_028866, intron 20 of 21)	intron (NM_028866, intron 20 of 21)	8386	NM_026006	67158	Mm.31537	NM_026006	ENSMUSG00000044982	Sft2d3	2610206C24Rik|AI847965|AW046173	SFT2 domain containing 3	protein-coding
mm_109442.1	chr12	110841022	110841037	+	1	NA	promoter-TSS (NM_011973)	promoter-TSS (NM_011973)	-90	NM_011973	26448	Mm.140948	NM_011973	ENSMUSG00000056458	Mok	RAGE1|Rage|Stk30	MOK protein kinase	protein-coding
mm_153393.1	chr19	40405768	40405798	-	1	NA	intron (NM_001034963, intron 1 of 22)	intron (NM_001034963, intron 1 of 22)	-3473	NM_001034964	20411	Mm.210815	NM_009166	ENSMUSG00000025006	Sorbs1	2310065E01Rik|9530001P15Rik|CAP|SH3P12|Sh3d5|mKIAA1296	sorbin and SH3 domain containing 1	protein-coding
mm_163816.1	chr14	19416455	19416475	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	186122	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_114363.1	chr13	61995288	61995297	+	1	NA	Intergenic	Intergenic	-134598	NM_001039239	630579	Mm.440905	NM_001039239	ENSMUSG00000074867	Zfp808	EG630579|Gm7036	zinc finger protein 80	protein-coding
mm_98767.1	chr11	96639184	96639185	+	1	NA	intron (NM_001033186, intron 4 of 12)	intron (NM_001033186, intron 4 of 12)	138371	NM_028965	74479	Mm.270781	NM_028965	ENSMUSG00000020876	Snx11	4933439F10Rik|A930041K09Rik|AI117694	sorting nexin 11	protein-coding
mm_25309.1	chr3	106034779	106034818	+	1	NA	Intergenic	Intergenic	-1903	NM_001080816	229687	Mm.39224	NM_170594	ENSMUSG00000043873	Chil5	Bclp|Bclp1|Bclp2|Chi3l7	chitinase-like 5	protein-coding
mm_153743.1	chr19	44696943	44696949	-	1	NA	Intergenic	Intergenic	-60448	NM_011037	18504	Mm.192158	NM_011037	ENSMUSG00000004231	Pax2	Opdc|Pax-2	paired box 2	protein-coding
mm_81037.1	chr9	105018401	105018408	+	1	NA	intron (NM_028719, intron 11 of 15)	intron (NM_028719, intron 11 of 15)	-34864	NM_053159	94062	Mm.29746	NM_053159	ENSMUSG00000032563	Mrpl3	2010320L16Rik|5930422H18Rik|AA407889	mitochondrial ribosomal protein L3	protein-coding
mm_15586.1	chr2	160210777	160210804	+	1	NA	Intergenic	Intergenic	116704	NM_001033411	329554	Mm.291144	NM_001033411	ENSMUSG00000074623	Gm826	-	predicted gene 826	protein-coding
mm_39192.1	chr4	155985319	155985319	-	1	NA	Intergenic	Intergenic	7359	NM_080445	117592	Mm.440185	NM_080445	ENSMUSG00000050796	B3galt6	BB129894|GalTII	UDP-Gal:betaGal beta 1,3-galactosyltransferase, polypeptide 6	protein-coding
mm_107846.1	chr12	69372052	69372062	+	1	NA	promoter-TSS (NM_007481)	promoter-TSS (NM_007481)	-93	NM_007481	11845	Mm.27308	NM_007481	ENSMUSG00000044147	Arf6	AI788669|AW496366	ADP-ribosylation factor 6	protein-coding
mm_72499.1	chr8	83740482	83740519	+	1	NA	intron (NM_001163031, intron 1 of 17)	intron (NM_001163031, intron 1 of 17)	811	NM_001163029	26364	Mm.334648	NM_011925	ENSMUSG00000002885	Adgre5	AA409984|Cd97|TM7LN1	adhesion G protein-coupled receptor E5	protein-coding
mm_11883.1	chr2	49619278	49619343	+	1	NA	promoter-TSS (NM_008449)	promoter-TSS (NM_008449)	-4	NM_008449	16574	Mm.256342	NM_008449	ENSMUSG00000026764	Kif5c	KINN|Khc|NKHC|NKHC2	kinesin family member 5C	protein-coding
mm_81383.1	chr9	108937041	108937060	+	1	NA	exon (NM_025407, exon 2 of 13)	exon (NM_025407, exon 2 of 13)	402	NM_025407	22273	Mm.335460	NM_025407	ENSMUSG00000025651	Uqcrc1	1110032G10Rik	ubiquinol-cytochrome c reductase core protein 1	protein-coding
mm_160485.1	chr8	125492778	125492778	-	1	NA	promoter-TSS (NM_001081337)	promoter-TSS (NM_001081337)	-68	NM_001081337	244668	Mm.271668	NM_001081337	ENSMUSG00000001995	Sipa1l2	BC058408|mKIAA1389	signal-induced proliferation-associated 1 like 2	protein-coding
mm_142486.1	chr17	45746822	45746874	-	1	NA	Intergenic	Intergenic	-13004	NM_028164	72240	Mm.482897	NM_028164	ENSMUSG00000094690	1600014C23Rik	-	RIKEN cDNA 1600014C23 gene	protein-coding
mm_8698.1	chr1	158355241	158355243	-	1	NA	intron (NM_207583, intron 1 of 7)	intron (NM_207583, intron 1 of 7)	1018	NM_207583	240843	Mm.329579	NM_207583	ENSMUSG00000004031	Brinp2	6430517E21Rik|BB361039|Fam5b|mKIAA1747	bone morphogenic protein/retinoic acid inducible neural-specific 2	protein-coding
mm_84272.1	chr9	62795004	62795007	-	1	NA	3' UTR (NM_010193, exon 2 of 2)	3' UTR (NM_010193, exon 2 of 2)	16643	NM_010193	14155	Mm.24069	NM_010193	ENSMUSG00000032244	Fem1b	mKIAA0396	feminization 1 homolog b (C. elegans)	protein-coding
mm_41632.1	chr5	97048877	97048888	+	1	NA	intron (NM_080708, intron 7 of 15)	intron (NM_080708, intron 7 of 15)	51193	NM_080708	140780	Mm.281490	NM_080708	ENSMUSG00000034663	Bmp2k	4933417M22Rik|AA673486|AV128808|BIKE	BMP2 inducible kinase	protein-coding
mm_149459.1	chr19	11518589	11518611	+	1	NA	promoter-TSS (NM_027209)	promoter-TSS (NM_027209)	41	NM_027209	69774	Mm.436639	NM_027209	ENSMUSG00000024677	Ms4a6b	1810027D10Rik	membrane-spanning 4-domains, subfamily A, member 6B	protein-coding
mm_112308.1	chr12	114829744	114829749	-	1	NA	Intergenic	Intergenic	-316052	NR_106063	102465664		NR_106063	ENSMUSG00000098357	Mir7094-2	Gm27508|mmu-mir-7094-2	microRNA 7094-2	ncRNA
mm_31237.1	chr4	44705444	44705447	+	1	NA	TTS (NR_073462)	TTS (NR_073462)	2645	NR_073462	70602	Mm.491142	NR_073462	ENSMUSG00000103995	5730488B01Rik	-	RIKEN cDNA 5730488B01 gene	ncRNA
mm_8728.1	chr1	160060640	160060650	-	1	NA	intron (NM_001162896, intron 1 of 2)	intron (NM_001162896, intron 1 of 2)	16265	NM_001162896	67647	Mm.171518	NM_001024470	ENSMUSG00000090394	4930523C07Rik	-	RIKEN cDNA 4930523C07 gene	protein-coding
mm_71861.1	chr8	69017636	69017672	+	1	NA	Intergenic	Intergenic	-71082	NM_007509	11966	Mm.249096	NM_007509	ENSMUSG00000006273	Atp6v1b2	AI194269|AI790362|Atp6b2|HO57|R74844	ATPase, H+ transporting, lysosomal V1 subunit B2	protein-coding
mm_51750.1	chr6	87429077	87429087	+	1	NA	promoter-TSS (NM_009756)	promoter-TSS (NM_009756)	88	NM_009756	12154	Mm.483321	NM_009756	ENSMUSG00000030046	Bmp10	-	bone morphogenetic protein 10	protein-coding
mm_142554.1	chr17	46629732	46629742	-	1	NA	promoter-TSS (NM_175168)	promoter-TSS (NM_175168)	-233	NM_175168	71461	Mm.181833	NM_175168	ENSMUSG00000023972	Ptk7	8430404F20Rik|chz|mPTK7/CCK4	PTK7 protein tyrosine kinase 7	protein-coding
mm_19758.1	chr2	105126527	105126543	-	1	NA	promoter-TSS (NM_144783)	promoter-TSS (NM_144783)	6	NM_144783	22431	Mm.389339	NM_144783	ENSMUSG00000016458	Wt1	D630046I19Rik|Wt-1	Wilms tumor 1 homolog	protein-coding
mm_43316.1	chr5	134957788	134957832	+	1	NA	Intergenic	Intergenic	-10876	NM_009903	12740	Mm.7339	NM_009903	ENSMUSG00000047501	Cldn4	Cep-r|Cpetr|Cpetr1	claudin 4	protein-coding
mm_17709.1	chr2	32385517	32385521	-	1	NA	exon (NM_008491, exon 5 of 6)	exon (NM_008491, exon 5 of 6)	2220	NM_008491	16819	Mm.9537	NM_008491	ENSMUSG00000026822	Lcn2	24p3|AW212229|NRL|Sip24	lipocalin 2	protein-coding
mm_131839.1	chr16	22960967	22960970	+	1	NA	exon (NM_053176, exon 7 of 7)	exon (NM_053176, exon 7 of 7)	9896	NM_053176	94175	Mm.358794	NM_053176	ENSMUSG00000022877	Hrg	AI265597|AW413091|D16jh2|D18020|Hprg|Hrgp	histidine-rich glycoprotein	protein-coding
mm_164830.1	chr18	37807940	37807960	-	1	NA	exon (NM_033581, exon 1 of 4)	exon (NM_033581, exon 1 of 4)	1540	NM_033581	93706	Mm.247203	NM_033581	ENSMUSG00000102918	Pcdhgc3	PC43|Pcdh2	protocadherin gamma subfamily C, 3	protein-coding
mm_144325.1	chr18	12955808	12955819	+	1	NA	Intergenic	Intergenic	-13972	NM_207530	64291	Mm.259470	NM_020573	ENSMUSG00000044252	Osbpl1a	G430090F17Rik|Gm753|ORP-1|Osbpl1b	oxysterol binding protein-like 1A	protein-coding
mm_142327.1	chr17	43502718	43502739	-	1	NA	promoter-TSS (NM_008585)	promoter-TSS (NM_008585)	45	NM_008585	17287	Mm.5346	NM_008585	ENSMUSG00000023914	Mep1a	AI098089|AW107200|Mep-1|Mep-1a|Mep1	meprin 1 alpha	protein-coding
mm_75244.1	chr8	39642654	39642664	-	1	NA	promoter-TSS (NM_031195)	promoter-TSS (NM_031195)	19	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_101175.1	chr11	16992967	16992981	-	1	NA	exon (NM_019549, exon 4 of 10)	exon (NM_019549, exon 4 of 10)	15744	NM_019549	56193	Mm.98232	NM_019549	ENSMUSG00000020120	Plek	2010300B13Rik	pleckstrin	protein-coding
mm_159953.1	chr6	86365724	86365724	+	1	NA	promoter-TSS (NM_025591)	promoter-TSS (NM_025591)	41	NM_025591	66488	Mm.422972	NM_025591	ENSMUSG00000057497	Fam136a	2010309E21Rik|AW124904|Hyccin	family with sequence similarity 136, member A	protein-coding
mm_142313.1	chr17	42876545	42876549	-	1	NA	promoter-TSS (NM_009847)	promoter-TSS (NM_009847)	-123	NM_009847	12488	Mm.218637	NM_009847	ENSMUSG00000061665	Cd2ap	AL024079|C78928|METS-1|Mets1	CD2-associated protein	protein-coding
mm_5296.1	chr1	21256502	21256512	-	1	NA	intron (NM_001288617, intron 3 of 7)	RMER10B|LTR|ERVL	15922	NM_010356	14859	Mm.394593	NM_010356	ENSMUSG00000025934	Gsta3	Gst2-3	glutathione S-transferase, alpha 3	protein-coding
mm_106138.1	chr11	116490279	116490289	-	1	NA	promoter-TSS (NM_026364)	promoter-TSS (NM_026364)	62	NM_026364	67763	Mm.25125	NM_026364	ENSMUSG00000015869	Prpsap1	5730409F23Rik|PAP39	phosphoribosyl pyrophosphate synthetase-associated protein 1	protein-coding
mm_34628.1	chr4	150570201	150570221	+	1	NA	intron (NM_001085492, intron 11 of 22)	intron (NM_001085492, intron 11 of 22)	81963	NM_173774	242773	Mm.29280	NM_173774	ENSMUSG00000039838	Slc45a1	C230078B22|Dnb5	solute carrier family 45, member 1	protein-coding
mm_56930.1	chr6	119517955	119517959	-	1	NA	intron (NM_009525, intron 1 of 4)	intron (NM_009525, intron 1 of 4)	26390	NM_009525	22419	Mm.321818	NM_009525	ENSMUSG00000030170	Wnt5b	AW545702|Wnt-5b	wingless-type MMTV integration site family, member 5B	protein-coding
mm_113655.1	chr13	42680566	42680575	+	1	NA	promoter-TSS (NM_001302635)	promoter-TSS (NM_001302635)	-229	NM_001302635	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding
mm_148996.1	chr19	8664047	8664120	+	1	NA	promoter-TSS (NM_007698)	promoter-TSS (NM_007698)	78	NM_001112697	12669	Mm.240607	NM_007698	ENSMUSG00000032773	Chrm1	Chrm-1|M1|M1R	cholinergic receptor, muscarinic 1, CNS	protein-coding
mm_72310.1	chr8	77554459	77554461	+	1	NA	intron (NM_001081240, intron 1 of 11)	intron (NM_001081240, intron 1 of 11)	5063	NM_001081240	102182	Mm.197630	NM_178903	ENSMUSG00000037134	Prmt9	AI931714|Prmt10	protein arginine methyltransferase 9	protein-coding
mm_98861.1	chr11	97703395	97703455	+	1	NA	promoter-TSS (NM_011971)	promoter-TSS (NM_011971)	-9	NM_011971	26446	Mm.21874	NM_011971	ENSMUSG00000069744	Psmb3	AL033320|C10-II	proteasome (prosome, macropain) subunit, beta type 3	protein-coding
mm_21440.1	chr2	158625247	158625254	-	1	NA	exon (NM_175419, exon 1 of 9)	exon (NM_175419, exon 1 of 9)	337	NM_175419	109275	Mm.27747	NM_175419	ENSMUSG00000037761	Actr5	AA545173|B430109J19Rik	ARP5 actin-related protein 5	protein-coding
mm_112537.1	chr13	9684285	9684308	+	1	NA	TTS (NM_001347480)	TTS (NM_001347480)	79514	NM_001347471	66505	Mm.397307	NM_144516	ENSMUSG00000021156	Zmynd11	2210402G22Rik|BS69	zinc finger, MYND domain containing 11	protein-coding
mm_31971.1	chr4	88157694	88157698	+	1	NA	intron (NM_001081184, intron 5 of 43)	intron (NM_001081184, intron 5 of 43)	35656	NR_030478	735282		NR_030478	ENSMUSG00000070077	Mir491	Mirn491|mir-491|mmu-mir-491	microRNA 491	ncRNA
mm_1768.1	chr1	77065867	77065878	+	1	NA	Intergenic	Intergenic	430896	NR_105770	102465180		NR_105770	ENSMUSG00000099141	Mir6352	Gm27481|mmu-mir-6352	microRNA 6352	ncRNA
mm_74425.1	chr8	3670524	3670526	-	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	4763	NM_026985	69189	Mm.175176	NM_026985	ENSMUSG00000013974	Mcemp1	1810033B17Rik	mast cell expressed membrane protein 1	protein-coding
mm_109643.1	chr12	112809290	112809329	+	1	NA	5' UTR (NM_145450, exon 1 of 5)	5' UTR (NM_145450, exon 1 of 5)	334	NM_145450	217887	Mm.186678	NM_145450	ENSMUSG00000037594	BC022687	AW050009|C130001I08Rik|Flj20080	cDNA sequence BC022687	protein-coding
mm_138966.1	chr17	44736209	44736219	+	1	NA	promoter-TSS (NM_001271631)	promoter-TSS (NM_001271631)	-38	NM_001271631	12393	Mm.391013	NM_009820	ENSMUSG00000039153	Runx2	AML3|Cbf|Cbfa-1|Cbfa1|LS3|Osf2|PEBP2aA|Pebp2a1|Pebpa2a	runt related transcription factor 2	protein-coding
mm_84293.1	chr9	63281261	63281271	-	1	NA	intron (NM_011840, intron 12 of 21)	intron (NM_011840, intron 12 of 21)	96586	NM_011840	23938	Mm.325746	NM_011840	ENSMUSG00000058444	Map2k5	AI324775|AI428457|MEK5|Mapkk5|Prkmk5	mitogen-activated protein kinase kinase 5	protein-coding
mm_41653.1	chr5	98329299	98329350	+	1	NA	promoter-TSS (NM_001024614)	promoter-TSS (NM_001024614)	20	NM_001024614	75784	Mm.443240	NM_001024614	ENSMUSG00000057816	1700007G11Rik	4930428O21Rik	RIKEN cDNA 1700007G11 gene	protein-coding
mm_172282.1	chr6	90905579	90905587	+	1	NA	Intergenic	CpG	-95460	NM_001134384	232227	Mm.196943	NM_182784	ENSMUSG00000034312	Iqsec1	AW561907|BC026481|BRAG2|D6Ertd349e|cI-43	IQ motif and Sec7 domain 1	protein-coding
mm_139930.1	chr17	71022864	71022875	+	1	NA	5' UTR (NM_001083934, exon 2 of 37)	5' UTR (NM_001083934, exon 2 of 37)	3312	NM_001083934	17929	Mm.4103	NM_010867	ENSMUSG00000024049	Myom1	D430047A17Rik	myomesin 1	protein-coding
mm_49965.1	chr6	40740420	40740422	+	1	NA	intron (NM_001171003, intron 31 of 47)	intron (NM_001171003, intron 31 of 47)	111590	NM_001171003	232714	Mm.33401	NM_001171003	ENSMUSG00000068587	Mgam	6030407P20Rik|MGA	maltase-glucoamylase	protein-coding
mm_24804.1	chr3	95556116	95556188	+	1	NA	exon (NM_021281, exon 8 of 8)	exon (NM_021281, exon 8 of 8)	-3525	NM_026489	67981	Mm.179050	NM_026489	ENSMUSG00000028109	Hormad1	4921522K05Rik|Nohma	HORMA domain containing 1	protein-coding
mm_133782.1	chr16	95011064	95011066	+	1	NA	Intergenic	Intergenic	-13369	NM_010606	16522	Mm.328720	NM_010606	ENSMUSG00000043301	Kcnj6	BIR1|GIRK2|KATP2|KCNJ7|Kir3.2|weaver|wv	potassium inwardly-rectifying channel, subfamily J, member 6	protein-coding
mm_170078.1	chr17	33824486	33824497	-	1	NA	promoter-TSS (NM_023202)	promoter-TSS (NM_023202)	7	NM_016844	54127	Mm.352374	NM_016844	ENSMUSG00000067288	Rps28	-	ribosomal protein S28	protein-coding
mm_93294.1	chr10	96391697	96391719	-	1	NA	Intergenic	Intergenic	165501	NR_110448	74881	Mm.410819	NR_110448		4930459C07Rik	-	RIKEN cDNA 4930459C07 gene	ncRNA
mm_88879.1	chr10	81118125	81118159	+	1	NA	intron (NM_023138, intron 3 of 10)	intron (NM_023138, intron 3 of 10)	12227	NM_001347144	26396	Mm.275436	NM_023138	ENSMUSG00000035027	Map2k2	AA589381|MEK2|MK2|Prkmk2	mitogen-activated protein kinase kinase 2	protein-coding
mm_135047.1	chr16	33186258	33186268	-	1	NA	intron (NM_176840, intron 1 of 12)	intron (NM_176840, intron 1 of 12)	1192	NM_176840	106326	Mm.486405	NM_176840	ENSMUSG00000022807	Osbpl11	9430097N02Rik|AI132306|AU019795|ORP-11	oxysterol binding protein-like 11	protein-coding
mm_94414.1	chr11	5861887	5861966	+	1	NA	promoter-TSS (NM_009636)	promoter-TSS (NM_009636)	60	NM_001291857	11568	Mm.3317	NM_009636	ENSMUSG00000020473	Aebp1	ACLP	AE binding protein 1	protein-coding
mm_136406.1	chr16	93712425	93712427	-	1	NA	intron (NM_027293, intron 1 of 36)	intron (NM_027293, intron 1 of 36)	519	NM_027293	70028	Mm.23230	NM_026700	ENSMUSG00000022946	Dopey2	0610038M01Rik|2610510B01Rik|AI503246|C21orf5|mKIAA0933	dopey family member 2	protein-coding
mm_149890.1	chr19	25406766	25406778	+	1	NA	intron (NM_181404, intron 4 of 13)	intron (NM_181404, intron 4 of 13)	-98934	NM_015826	50796	Mm.391208	NM_015826	ENSMUSG00000024837	Dmrt1	-	doublesex and mab-3 related transcription factor 1	protein-coding
mm_28179.1	chr3	88000844	88000866	-	1	NA	promoter-TSS (NM_001109758)	promoter-TSS (NM_001109758)	-499	NM_001109758	12032	Mm.4598	NM_007529	ENSMUSG00000004892	Bcan	Cspg7	brevican	protein-coding
mm_146547.1	chr18	6136058	6136068	-	1	NA	promoter-TSS (NM_001039692)	promoter-TSS (NM_001039692)	35	NM_029277	75415	Mm.239675	NM_029277	ENSMUSG00000041225	Arhgap12	2810011M08Rik	Rho GTPase activating protein 12	protein-coding
mm_48787.1	chr5	148590751	148590771	-	1	NA	Intergenic	Intergenic	-37973	NM_011908	24109	Mm.21846	NM_011908	ENSMUSG00000001687	Ubl3	AW108023|HCG	ubiquitin-like 3	protein-coding
mm_160278.1	chr7	121052073	121052073	+	1	NA	intron (NM_021554, intron 2 of 4)	intron (NM_021554, intron 2 of 4)	17628	NM_021554	59052	Mm.29122	NM_021554	ENSMUSG00000030876	Mettl9	0610012D09Rik|AA517660|Drev|MNCb-5680	methyltransferase like 9	protein-coding
mm_11479.1	chr2	32385410	32385453	+	1	NA	exon (NM_008491, exon 5 of 6)	exon (NM_008491, exon 5 of 6)	2308	NM_008491	16819	Mm.9537	NM_008491	ENSMUSG00000026822	Lcn2	24p3|AW212229|NRL|Sip24	lipocalin 2	protein-coding
mm_128266.1	chr15	36791247	36791251	-	1	NA	promoter-TSS (NM_001253807)	promoter-TSS (NM_001253807)	-317	NM_001253807	22631	Mm.3360	NM_011740	ENSMUSG00000022285	Ywhaz	1110013I11Rik|14-3-3zeta|AI596267|AL022924|AU020854	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide	protein-coding
mm_12935.1	chr2	85060962	85060973	+	1	NA	intron (NM_001081260, intron 5 of 11)	intron (NM_001081260, intron 5 of 11)	10507	NM_001081260	228140	Mm.23606	NM_001081260	ENSMUSG00000033955	Tnks1bp1	Tab182|mKIAA1741	tankyrase 1 binding protein 1	protein-coding
mm_166351.1	chr5	119881273	119881276	+	1	NA	intron (NM_011537, intron 8 of 8)	intron (NM_011537, intron 8 of 8)	46611	NM_011537	21388	Mm.103636	NM_011537	ENSMUSG00000018263	Tbx5	-	T-box 5	protein-coding
mm_60521.1	chr7	44479952	44479954	+	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	-4564	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_150967.1	chr19	46500612	46500651	+	1	NA	Intergenic	CpG	-1017	NM_053100	93679	Mm.392177	NM_053100	ENSMUSG00000025034	Trim8	AA408830|BB006755|GERP|Rnf27	tripartite motif-containing 8	protein-coding
mm_125967.1	chr15	76274232	76274236	+	1	NA	intron (NM_028852, intron 1 of 4)	RSINE1|SINE|B4	-4395	NR_045747	100038659	Mm.448549	NR_045747		Mirt2	ENSMUSG00000075583|Gm10872|Gm24562	myocardial infraction associated transcript 2	ncRNA
mm_66706.1	chr7	45921419	45921447	-	1	NA	promoter-TSS (NM_010129)	promoter-TSS (NM_010129)	-7	NM_010129	13732	Mm.20829	NM_010129	ENSMUSG00000040212	Emp3	H-4|H4|HNMP-1|MI-35|Ymp	epithelial membrane protein 3	protein-coding
mm_90354.1	chr10	127165314	127165327	+	1	NA	promoter-TSS (NM_027739)	promoter-TSS (NM_027739)	164	NM_001244617	14421	Mm.386762	NM_008080	ENSMUSG00000006731	B4galnt1	4933429D13Rik|Gal-NAc-T|GalNAc-T|GalNAcT|Galgt1|Ggm-2|Ggm2	beta-1,4-N-acetyl-galactosaminyl transferase 1	protein-coding
mm_84424.1	chr9	65771448	65771450	-	1	NA	intron (NM_172536, intron 2 of 9)	ID_B1|SINE|B4	56115	NM_172536	214812	Mm.139231	NM_172536	ENSMUSG00000040524	Zfp609	9830165N24|BC016271|Znf609|mKIAA0295	zinc finger protein 609	protein-coding
mm_65825.1	chr7	29178969	29179002	-	1	NA	exon (NM_026545, exon 3 of 7)	exon (NM_026545, exon 3 of 7)	1688	NM_026545	57296	Mm.273152	NM_026545	ENSMUSG00000030591	Psmd8	6720456J22Rik|AA407360|AL033291|AL033322|AL033323|C76433	proteasome (prosome, macropain) 26S subunit, non-ATPase, 8	protein-coding
mm_141505.1	chr17	31636604	31636624	-	1	NA	intron (NM_178224, intron 1 of 15)	CpG	591	NM_144855	12411	Mm.206417	NM_144855	ENSMUSG00000024039	Cbs	AI047524|AI303044|HIP4	cystathionine beta-synthase	protein-coding
mm_63107.1	chr7	122633144	122633190	+	1	NA	3' UTR (NM_008855, exon 17 of 17)	3' UTR (NM_008855, exon 17 of 17)	-38577	NM_019430	54376	Mm.444212	NM_019430	ENSMUSG00000066189	Cacng3	-	calcium channel, voltage-dependent, gamma subunit 3	protein-coding
mm_172703.1	chr8	64293722	64293738	-	1	NA	Intergenic	L1Md_T|LINE|L1	-87737	NM_009390	21892	Mm.418367	NM_009390	ENSMUSG00000053626	Tll1	Tll|Tll-1	tolloid-like	protein-coding
mm_11790.1	chr2	43128734	43128745	+	1	NA	Intergenic	RMER1B|Other|Other	-426586	NM_001289593	70789	Mm.105278	NM_027552	ENSMUSG00000026866	Kynu	4432411A05Rik	kynureninase (L-kynurenine hydrolase)	protein-coding
mm_59783.1	chr7	28881711	28881718	+	1	NA	promoter-TSS (NM_001110807)	promoter-TSS (NM_001110807)	58	NM_001110807	60594	Mm.476990	NM_021894	ENSMUSG00000054083	Capn12	CANP 12	calpain 12	protein-coding
mm_84783.1	chr9	76362165	76362176	-	1	NA	Intergenic	Intergenic	-38592	NM_198962	387285	Mm.335300	NM_198962	ENSMUSG00000032360	Hcrtr2	OX2R|mOX2aR|mOX2bR|mOXR2	hypocretin (orexin) receptor 2	protein-coding
mm_76256.1	chr8	83740147	83740158	-	1	NA	intron (NM_001163031, intron 1 of 17)	intron (NM_001163031, intron 1 of 17)	1159	NM_001163029	26364	Mm.334648	NM_011925	ENSMUSG00000002885	Adgre5	AA409984|Cd97|TM7LN1	adhesion G protein-coupled receptor E5	protein-coding
mm_2224.1	chr1	90564154	90564195	+	1	NA	Intergenic	Intergenic	-39251	NM_133805	108679	Mm.119177	NM_133805	ENSMUSG00000034432	Cops8	9430009J09Rik|AA408242|Csn8|Sgn8	COP9 signalosome subunit 8	protein-coding
mm_151367.1	chr19	55930470	55930475	+	1	NA	intron (NM_001142924, intron 11 of 11)	intron (NM_001142924, intron 11 of 11)	35151	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_126209.1	chr15	78892450	78892484	+	1	NA	TTS (NR_105920)	TTS (NR_105920)	627	NR_105920	102466210		NR_105920	ENSMUSG00000099267	Mir6955	Gm27769|mmu-mir-6955	microRNA 6955	ncRNA
mm_19216.1	chr2	84648554	84648564	-	1	NA	intron (NM_007615, intron 1 of 19)	intron (NM_007615, intron 1 of 19)	1951	NM_001085453	12388	Mm.35738	NM_007615	ENSMUSG00000034101	Ctnnd1	AA409437|AU019353|Catns|Ctnnd|P120|mKIAA0384	catenin (cadherin associated protein), delta 1	protein-coding
mm_171804.1	chr5	126074804	126074820	+	1	NA	Intergenic	(A)n|Simple_repeat|Simple_repeat	542394	NM_001190352	208151	Mm.40397	NM_001190352	ENSMUSG00000070498	Tmem132b	AK220418|mKIAA1786	transmembrane protein 132B	protein-coding
mm_140348.1	chr17	86831117	86831128	+	1	NA	3' UTR (NM_010137, exon 16 of 16)	3' UTR (NM_010137, exon 16 of 16)	77258	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_95758.1	chr11	54906288	54906328	+	1	NA	intron (NM_001329860, intron 1 of 5)	intron (NM_001329860, intron 1 of 5)	3454	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_17080.1	chr2	22913877	22913883	-	1	NA	intron (NM_019501, intron 5 of 10)	intron (NM_019501, intron 5 of 10)	18358	NM_019501	56075	Mm.249752	NM_019501	ENSMUSG00000026784	Pdss1	2610203G20Rik|2700031G06Rik|TPT|TPT 1|Tprt|mDLP1|mSPS1	prenyl (solanesyl) diphosphate synthase, subunit 1	protein-coding
mm_4863.1	chr1	187662377	187662384	+	1	NA	intron (NM_001243792, intron 1 of 7)	intron (NM_001243792, intron 1 of 7)	53374	NM_001243792	26381	Mm.89989	NM_011935	ENSMUSG00000026610	Esrrg	ERR3|Errg|NR3B3|mKIAA0832	estrogen-related receptor gamma	protein-coding
mm_2957.1	chr1	132865813	132865823	+	1	NA	Intergenic	MIR|SINE|MIR	-14537	NM_010732	16980	Mm.39640	NM_010732	ENSMUSG00000026443	Lrrn2	5730406J09Rik|NLRR-2	leucine rich repeat protein 2, neuronal	protein-coding
mm_117459.1	chr13	75920800	75920801	-	1	NA	intron (NM_028493, intron 3 of 11)	intron (NM_028493, intron 3 of 11)	23024	NM_028493	73296	Mm.276200	NM_028493	ENSMUSG00000021589	Rhobtb3	1700040C17Rik|2610033K01Rik|4930503C18Rik|AI317148|AW208826|mKIAA0878	Rho-related BTB domain containing 3	protein-coding
mm_40892.1	chr5	75152275	75152297	+	1	NA	promoter-TSS (NM_011058)	promoter-TSS (NM_011058)	35	NM_001347718	18595	Mm.221403	NM_011058	ENSMUSG00000029231	Pdgfra	AI115593|CD140a|Pdgfr-2	platelet derived growth factor receptor, alpha polypeptide	protein-coding
mm_74603.1	chr8	11678729	11678754	-	1	NA	promoter-TSS (NM_024271)	promoter-TSS (NM_024271)	9	NM_024271	76413	Mm.440041	NM_024271	ENSMUSG00000031509	1700016D06Rik	-	RIKEN cDNA 1700016D06 gene	protein-coding
mm_27413.1	chr3	51396529	51396551	-	1	NA	promoter-TSS (NM_026358)	promoter-TSS (NM_026358)	7	NM_026358	67749	Mm.273339	NM_026358	ENSMUSG00000037161	Mgarp	4930583H14Rik|AI195347|CESP-1|HUMMR|Osap|Qsap	mitochondria localized glutamic acid rich protein	protein-coding
mm_109600.1	chr12	112679538	112679548	+	1	NA	exon (NM_001100460, exon 2 of 2)	exon (NM_001100460, exon 2 of 2)	703	NM_001100460	382639	Mm.11350	NM_001100460	ENSMUSG00000037638	Zbtb42	EG382639|Gm5188|simiRP58	zinc finger and BTB domain containing 42	protein-coding
mm_45495.1	chr5	72163062	72163076	-	1	NA	intron (NM_178599, intron 2 of 4)	intron (NM_178599, intron 2 of 4)	5114	NM_178599	27784	Mm.44223	NM_178599	ENSMUSG00000029213	Commd8	C77770|D5Buc26e	COMM domain containing 8	protein-coding
mm_150822.1	chr19	44511198	44511208	+	1	NA	intron (NM_011720, intron 4 of 5)	intron (NM_011720, intron 4 of 5)	17731	NM_011720	22423	Mm.88365	NM_011720	ENSMUSG00000036961	Wnt8b	-	wingless-type MMTV integration site family, member 8B	protein-coding
mm_134632.1	chr16	21668292	21668324	-	1	NA	intron (NM_001001881, intron 1 of 1)	intron (NM_001001881, intron 1 of 1)	26357	NM_001001881	72190	Mm.131606	NM_001001881	ENSMUSG00000043391	2510009E07Rik	AI194952	RIKEN cDNA 2510009E07 gene	protein-coding
mm_46383.1	chr5	103977405	103977415	-	1	NA	promoter-TSS (NM_001163486)	promoter-TSS (NM_001163486)	-22	NM_001163486	243168	Mm.284944	NM_198030	ENSMUSG00000034528	Hsd17b13	AI047820|PAN1B-like|Pan1b	hydroxysteroid (17-beta) dehydrogenase 13	protein-coding
mm_74884.1	chr8	25101703	25101713	-	1	NA	5' UTR (NM_031257, exon 1 of 12)	5' UTR (NM_031257, exon 1 of 12)	103	NM_031257	83436	Mm.261122	NM_031257	ENSMUSG00000031557	Plekha2	6430512N22Rik|AI851530|AU041791|TAPP2|W91773	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 2	protein-coding
mm_68360.1	chr7	106511614	106511631	-	1	NA	Intergenic	Intergenic	-70549	NR_003967	209380	Mm.461779	NM_001001318		Gm4759	EG209380	GTPase, very large interferon inducible 1 pseudogene	pseudo
mm_84079.1	chr9	58202067	58202075	-	1	NA	promoter-TSS (NM_001161540)	promoter-TSS (NM_001161540)	214	NM_177193	320563	Mm.186499	NM_177193	ENSMUSG00000051243	Islr2	B930052A04Rik|Linx|Mbu-3|mKIAA1465	immunoglobulin superfamily containing leucine-rich repeat 2	protein-coding
mm_8367.1	chr1	150503149	150503153	-	1	NA	Intergenic	Intergenic	-36986	NM_001110146	96875	Mm.174256	NM_021400	ENSMUSG00000006014	Prg4	CACP|DOL54|JCAP|MSF|SZP|lubricin	proteoglycan 4 (megakaryocyte stimulating factor, articular superficial zone protein)	protein-coding
mm_147914.1	chr18	65565776	65565789	-	1	NA	intron (NR_105742, intron 1 of 6)	intron (NR_105742, intron 1 of 6)	-14448	NM_207255	328977	Mm.286232	NM_207255	ENSMUSG00000042439	Zfp532	C530030I18Rik|Znf532|mKIAA1629	zinc finger protein 532	protein-coding
mm_120397.1	chr14	64675418	64675453	+	1	NA	intron (NM_001081177, intron 2 of 39)	intron (NM_001081177, intron 2 of 39)	22904	NM_001081177	16554	Mm.23611	NM_001081177	ENSMUSG00000060012	Kif13b	5330429L19Rik|6030414C01|AI429803|C130021D12Rik|GAKIN	kinesin family member 13B	protein-coding
mm_20794.1	chr2	144254758	144254789	-	1	NA	exon (NM_024225, exon 10 of 13)	exon (NM_024225, exon 10 of 13)	11429	NR_030762	100313519	Mm.453538	NR_030762	ENSMUSG00000077714	Snord17	MBI-43	small nucleolar RNA, C/D box 17	snoRNA
mm_131606.1	chr16	19218614	19218620	+	1	NA	Intergenic	L1_Rod|LINE|L1	68124	NM_146451	258443	Mm.377506	NM_146451	ENSMUSG00000050742	Olfr164	MOR279-2	olfactory receptor 164	protein-coding
mm_80434.1	chr9	77923666	77923688	+	1	NA	intron (NM_134255, intron 1 of 7)	intron (NM_134255, intron 1 of 7)	6312	NM_134255	68801	Mm.430736	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	ELOVL family member 5, elongation of long chain fatty acids (yeast)	protein-coding
mm_144566.1	chr18	31775852	31775852	+	1	NA	intron (NM_153515, intron 5 of 7)	intron (NM_153515, intron 5 of 7)	-13307	NM_027002	69241	Mm.279898	NM_027002	ENSMUSG00000024258	Polr2d	2310002G05Rik|2610028L19Rik|HSRBP4|RBP4	polymerase (RNA) II (DNA directed) polypeptide D	protein-coding
mm_69417.1	chr7	132599598	132599609	-	1	NA	promoter-TSS (NM_009123)	promoter-TSS (NM_009123)	34	NM_009123	20231	Mm.334281	NM_009123	ENSMUSG00000048528	Nkx1-2	Nkx-1.1|Nkx-1.2|Sax1	NK1 transcription factor related, locus 2 (Drosophila)	protein-coding
mm_11836.1	chr2	45111151	45111166	+	1	NA	promoter-TSS (NM_001289521)	promoter-TSS (NM_001289521)	20	NR_110572	433424	Mm.441408	NR_110571	ENSMUSG00000052248	Zeb2os	Gm13476|OTTMUSG00000012358|Zeb2nat	zinc finger E-box binding homeobox 2, opposite strand	ncRNA
mm_65270.1	chr7	23947291	23947300	-	1	NA	Intergenic	L1_Mus2|LINE|L1	-5092	NM_206869	232962	Mm.377249	NM_206869	ENSMUSG00000092473	Vmn1r180	Gm475|V1rd16	vomeronasal 1 receptor 180	protein-coding
mm_15669.1	chr2	163419768	163419830	+	1	NA	promoter-TSS (NM_025699)	promoter-TSS (NM_025699)	-329	NM_025699	66680	Mm.25119	NM_025699	ENSMUSG00000035399	Oser1	3230401D17Rik|AI256769|Perit1	oxidative stress responsive serine rich 1	protein-coding
mm_169662.1	chr15	59370148	59370149	-	1	NA	5' UTR (NM_153548, exon 2 of 29)	5' UTR (NM_153548, exon 2 of 29)	4004	NM_153548	223593	Mm.218665	NM_153548	ENSMUSG00000022350	Washc5	AL022848|C76463|E430025E21Rik|Kiaa0196|mKIAA0196|strumpellin	WASH complex subunit 5	protein-coding
mm_42953.1	chr5	123016230	123016240	+	1	NA	intron (NM_175423, intron 1 of 1)	intron (NM_175423, intron 1 of 1)	1161	NM_175423	109305	Mm.218582	NM_175423	ENSMUSG00000049686	Orai1	D730049H07Rik|Tmem142a|orai-1	ORAI calcium release-activated calcium modulator 1	protein-coding
mm_130240.1	chr15	96597561	96597569	-	1	NA	intron (NM_001166458, intron 4 of 15)	B4A|SINE|B4	44397	NM_134086	105727	Mm.103568	NM_134086	ENSMUSG00000023169	Slc38a1	AA408026|AA409865|AL022800|AU015942|NAT2	solute carrier family 38, member 1	protein-coding
mm_134134.1	chr16	10683285	10683295	-	1	NA	intron (NM_001204229, intron 18 of 22)	PB1D10|SINE|Alu	102246	NM_009896	12703	Mm.130	NM_009896	ENSMUSG00000038037	Socs1	Cish1|Cish7|JAB|SOCS-1|SSI-1	suppressor of cytokine signaling 1	protein-coding
mm_14185.1	chr2	127080238	127080248	+	1	NA	intron (NM_026678, intron 1 of 7)	intron (NM_026678, intron 1 of 7)	9586	NM_026678	109778	Mm.22028	NM_026678	ENSMUSG00000001999	Blvra	0610006A11Rik|2500001N03Rik|Blvr	biliverdin reductase A	protein-coding
mm_91282.1	chr10	24711988	24712004	-	1	NA	5' UTR (NM_008813, exon 1 of 25)	5' UTR (NM_008813, exon 1 of 25)	163	NM_001308327	18605	Mm.27254	NM_008813	ENSMUSG00000037370	Enpp1	4833416E15Rik|AI428932|C76301|CD203c|E-NPP 1|E-NPP1|Ly-41|M6S1|NPP1|Npps|PC-1|Pca|Pca-1|Pdnp1|ttw|twy	ectonucleotide pyrophosphatase/phosphodiesterase 1	protein-coding
mm_80509.1	chr9	78634218	78634261	+	1	NA	intron (NM_153098, intron 2 of 32)	intron (NM_153098, intron 2 of 32)	18693	NM_153098	235505	Mm.32955	NM_153098	ENSMUSG00000046186	Cd109	9930012E15Rik|AI480638|GARP	CD109 antigen	protein-coding
mm_59495.1	chr7	27533646	27533672	+	1	NA	exon (NM_011116, exon 12 of 14)	exon (NM_011116, exon 12 of 14)	10398	NM_001033315	233020	Mm.429716	NM_001033315	ENSMUSG00000040424	Hipk4	Gm162	homeodomain interacting protein kinase 4	protein-coding
mm_162332.1	chr1	43098693	43098711	+	1	NA	promoter-TSS (NM_001013025)	promoter-TSS (NM_001013025)	-8	NM_133818	98404	Mm.28817	NM_133818	ENSMUSG00000010290	AI597479	-	expressed sequence AI597479	protein-coding
mm_119112.1	chr14	31019126	31019157	+	1	NA	promoter-TSS (NM_001081251)	promoter-TSS (NM_001081251)	3	NM_001081251	66923	Mm.27913	NM_025847	ENSMUSG00000042323	Pbrm1	2610016F04Rik|AI507524|BAF180|Pb1	polybromo 1	protein-coding
mm_21806.1	chr2	165034529	165034578	-	1	NA	intron (NM_144892, intron 1 of 7)	CpG	226	NM_144892	228869	Mm.233080	NM_144892	ENSMUSG00000039804	Ncoa5	CIA	nuclear receptor coactivator 5	protein-coding
mm_13425.1	chr2	104590535	104590548	+	1	NA	promoter-TSS (NM_145529)	promoter-TSS (NM_145529)	57	NM_001037326	228410	Mm.259876	NM_145529	ENSMUSG00000027176	Cstf3	4732468G05Rik|C79532|CstF-77	cleavage stimulation factor, 3' pre-RNA, subunit 3	protein-coding
mm_100478.1	chr11	120217240	120217247	+	1	NA	Intergenic	L1M5|LINE|L1	-15704	NM_001347621	268515	Mm.309498	NM_198423	ENSMUSG00000039741	Bahcc1	B930044J06|BC060615	BAH domain and coiled-coil containing 1	protein-coding
mm_16739.1	chr2	9375934	9375937	-	1	NA	Intergenic	Intergenic	186420	NR_038180	73438	Mm.23558	NR_038180	ENSMUSG00000085580	1700061F12Rik	-	RIKEN cDNA 1700061F12 gene	ncRNA
mm_144498.1	chr18	24397422	24397424	+	1	NA	Intergenic	LTRIS4|LTR|ERV1	31747	NR_029573	387182		NR_029573	ENSMUSG00000065532	Mir187	Mirn187|mir-187|mmu-mir-187	microRNA 187	ncRNA
mm_29362.1	chr3	108562425	108562438	-	1	NA	promoter-TSS (NM_026198)	promoter-TSS (NM_026198)	35	NM_026198	67495	Mm.32615	NM_026198	ENSMUSG00000068732	Tmem167b	2010200O16Rik	transmembrane protein 167B	protein-coding
mm_146967.1	chr18	33463416	33463443	-	1	NA	promoter-TSS (NR_045415)	promoter-TSS (NR_045415)	205	NM_001267717	27528	Mm.407415	NM_053078	ENSMUSG00000042834	Nrep	AI325076|D0H4S114|Harp|P311|PTZ17|SEZ17	neuronal regeneration related protein	protein-coding
mm_21746.1	chr2	164804849	164804863	-	1	NA	promoter-TSS (NM_178375)	promoter-TSS (NM_178375)	25	NM_133240	170789	Mm.277878	NM_133240	ENSMUSG00000017307	Acot8	PTE-2|Pte1	acyl-CoA thioesterase 8	protein-coding
mm_161649.1	chr17	6449116	6449116	-	1	NA	intron (NR_033520, intron 1 of 9)	intron (NR_033520, intron 1 of 9)	1878	NR_033520	547127	Mm.297552	NM_001045538		Tmem181b-ps	Tmem181b	transmembrane protein 181B, pseudogene	pseudo
mm_75647.1	chr8	65101086	65101098	-	1	NA	intron (NR_033217, intron 2 of 2)	intron (NR_033217, intron 2 of 2)	28445	NR_033217	407795	Mm.387876	NR_033217	ENSMUSG00000074300	BC030870	-	cDNA sequence BC030870	ncRNA
mm_120230.1	chr14	62865308	62865342	+	1	NA	promoter-TSS (NR_105860)	promoter-TSS (NR_105860)	-217	NR_105860	102465311		NR_105860	ENSMUSG00000098858	Mir6541	Gm27311|mmu-mir-6541	microRNA 6541	ncRNA
mm_43273.1	chr5	130448837	130448856	+	1	NA	promoter-TSS (NM_021371)	promoter-TSS (NM_021371)	54	NM_021371	140904	Mm.40875	NM_021371	ENSMUSG00000060371	Caln1	9630012C17Rik|Cabp8|MNCb-0849	calneuron 1	protein-coding
mm_44348.1	chr5	17785845	17785899	-	1	NA	exon (NM_001159558, exon 15 of 16)	exon (NM_001159558, exon 15 of 16)	50024	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_90924.1	chr10	12813541	12813590	-	1	NA	intron (NM_011682, intron 1 of 73)	intron (NM_011682, intron 1 of 73)	48170	NM_011682	22288	Mm.331784	NM_011682	ENSMUSG00000019820	Utrn	AA589569|DRP|Dmdl	utrophin	protein-coding
mm_172909.1	chr9	61914377	61914380	-	1	NA	exon (NM_018853, exon 1 of 3)	exon (NM_018853, exon 1 of 3)	132	NM_018853	56040	Mm.3158	NM_018853	ENSMUSG00000007892	Rplp1	2410042H16Rik|Arpp1|C430017H15Rik	ribosomal protein, large, P1	protein-coding
mm_146566.1	chr18	6490878	6490898	-	1	NA	promoter-TSS (NM_001276350)	promoter-TSS (NM_001276350)	-31	NM_027497	13831	Mm.312133	NM_007935	ENSMUSG00000024240	Epc1	2400007E14Rik|5730566F07Rik|A930032N02Rik|mir-1893	enhancer of polycomb homolog 1 (Drosophila)	protein-coding
mm_51721.1	chr6	86870811	86870813	+	1	NA	intron (NM_001040106, intron 1 of 20)	intron (NM_001040106, intron 1 of 20)	21295	NM_001040106	269774	Mm.221038	NM_177762	ENSMUSG00000057230	Aak1	5530400K14Rik|9630042K20|AU067724|AU067726|BC028270|C79663|D6Ertd245e|R75501|mKIAA1048	AP2 associated kinase 1	protein-coding
mm_105076.1	chr11	100803850	100803861	-	1	NA	intron (NM_001113563, intron 3 of 18)	intron (NM_001113563, intron 3 of 18)	18715	NM_011489	20851	Mm.34064	NM_011489	ENSMUSG00000020919	Stat5b	-	signal transducer and activator of transcription 5B	protein-coding
mm_113673.1	chr13	42741686	42741689	+	1	NA	intron (NM_001005740, intron 1 of 12)	B4A|SINE|B4	32106	NM_001005740	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding
mm_171432.1	chr4	136456647	136456661	-	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	-13107	NM_024452	269593	Mm.485824	NM_024452	ENSMUSG00000001089	Luzp1	2700072H04Rik|AI266952|Luzp|mFLJ00226	leucine zipper protein 1	protein-coding
mm_57298.1	chr6	124464697	124464759	-	1	NA	promoter-TSS (NM_153508)	promoter-TSS (NM_153508)	56	NM_153508	232370	Mm.193701	NM_153508	ENSMUSG00000008153	Clstn3	CSTN3|Cs3|Cst-3|alc-beta	calsyntenin 3	protein-coding
mm_152727.1	chr19	18631835	18631847	-	1	NA	promoter-TSS (NM_017375)	promoter-TSS (NM_017375)	-28	NM_017375	20409	Mm.172222	NM_017375	ENSMUSG00000024725	Ostf1	C78236|SH3P2|Sh3d3	osteoclast stimulating factor 1	protein-coding
mm_162253.1	chrX	164980614	164980614	+	1	NA	promoter-TSS (NM_175027)	promoter-TSS (NM_175027)	22	NM_175027	237211	Mm.336317	NM_175027	ENSMUSG00000047757	Fancb	BC022692	Fanconi anemia, complementation group B	protein-coding
mm_862.1	chr1	52139275	52139294	+	1	NA	exon (NM_001205314, exon 10 of 25)	exon (NM_001205314, exon 10 of 25)	19662	NM_001205313	20846	Mm.277406	NM_009283	ENSMUSG00000026104	Stat1	2010005J02Rik|AA408197	signal transducer and activator of transcription 1	protein-coding
mm_127372.1	chr15	100783804	100783818	+	1	NA	exon (NM_021530, exon 4 of 25)	exon (NM_021530, exon 4 of 25)	2557	NM_001347102	59033	Mm.209856	NM_021530	ENSMUSG00000023032	Slc4a8	AW493845|C230026C11|NDCBE|kNBC-3	solute carrier family 4 (anion exchanger), member 8	protein-coding
mm_42890.1	chr5	122391960	122391960	+	1	NA	promoter-TSS (NM_019824)	promoter-TSS (NM_019824)	82	NM_019824	56378	Mm.275942	NM_019824	ENSMUSG00000029465	Arpc3	1110006A04Rik|p21-ARC|p21-Ar|p21Arc	actin related protein 2/3 complex, subunit 3	protein-coding
mm_170356.1	chr1	85199649	85199666	+	1	NA	promoter-TSS (NM_001081746)	promoter-TSS (NM_001081746)	46	NM_001081746	665378	Mm.440912	NM_001081746		Gm7609	EG665378	predicted pseudogene 7609	protein-coding
mm_135801.1	chr16	57231435	57231509	-	1	NA	promoter-TSS (NM_026254)	promoter-TSS (NM_026254)	-6	NM_026254	67581	Mm.257819	NM_026254	ENSMUSG00000022749	Tbc1d23	4930451A13Rik|AU015720|AU043671|AU043778|D030022P07Rik|W51689	TBC1 domain family, member 23	protein-coding
mm_165562.1	chr3	14886606	14886615	+	1	NA	5' UTR (NM_009801, exon 1 of 7)	5' UTR (NM_009801, exon 1 of 7)	184	NM_009801	12349	Mm.1186	NM_009801	ENSMUSG00000027562	Car2	AI131712|CAII|Ca2|Car-2|Ltw-5|Lvtw-5	carbonic anhydrase 2	protein-coding
mm_19232.1	chr2	84691995	84692017	-	1	NA	exon (NM_144887, exon 9 of 12)	exon (NM_144887, exon 9 of 12)	-13178	NM_025868	66958	Mm.371621	NM_025868	ENSMUSG00000050043	Tmx2	2310042M24Rik|AA589631|Txndc14	thioredoxin-related transmembrane protein 2	protein-coding
mm_72474.1	chr8	83576189	83576251	+	1	NA	intron (NM_134118, intron 1 of 12)	intron (NM_134118, intron 1 of 12)	9462	NM_025843	66916	Mm.29683	NM_025843	ENSMUSG00000033938	Ndufb7	1110002H15Rik	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 7	protein-coding
mm_7879.1	chr1	133019426	133019448	-	1	NA	intron (NM_008575, intron 1 of 11)	intron (NM_008575, intron 1 of 11)	5979	NR_126506	17248	Mm.426531	NM_008575	ENSMUSG00000054387	Mdm4	4933417N07Rik|AA414968|AL023055|AU018793|AU021806|C85810|Mdmx	transformed mouse 3T3 cell double minute 4	protein-coding
mm_172069.1	chr6	136685514	136685516	-	1	NA	Intergenic	RMER20B|LTR|ERVK	-23622	NM_025806	66857	Mm.3311	NM_025806	ENSMUSG00000030214	Plbd1	1100001H23Rik	phospholipase B domain containing 1	protein-coding
mm_44605.1	chr5	25101053	25101064	-	1	NA	promoter-TSS (NM_145401)	promoter-TSS (NM_145401)	83	NR_027851	67261	Mm.461781	NM_026059	ENSMUSG00000043833	2900005J15Rik	-	RIKEN cDNA 2900005J15 gene	ncRNA
mm_103385.1	chr11	75415686	75415701	-	1	NA	exon (NM_011340, exon 4 of 8)	exon (NM_011340, exon 4 of 8)	6930	NM_011340	20317	Mm.2044	NM_011340	ENSMUSG00000000753	Serpinf1	AI195227|EPC-1|Pedf|Pedfl|Sdf3	serine (or cysteine) peptidase inhibitor, clade F, member 1	protein-coding
mm_162815.1	chr10	79710114	79710119	+	1	NA	exon (NM_001077184, exon 3 of 7)	exon (NM_001077184, exon 3 of 7)	5758	NM_009768	12215	Mm.726	NM_009768	ENSMUSG00000023175	Bsg	AI115436|AI325119|CD147|EMMPRIN|HT-7	basigin	protein-coding
mm_6195.1	chr1	65175134	65175140	-	1	NA	intron (NM_001111320, intron 2 of 8)	AT_rich|Low_complexity|Low_complexity	4005	NM_010497	15926	Mm.9925	NM_010497	ENSMUSG00000025950	Idh1	AI314845|AI788952|E030024J03Rik|Id-1|Idh-1|Idpc	isocitrate dehydrogenase 1 (NADP+), soluble	protein-coding
mm_26071.1	chr3	136670219	136670229	+	1	NA	5' UTR (NM_001293622, exon 1 of 13)	5' UTR (NM_001293622, exon 1 of 13)	158	NM_001293622	19055	Mm.331389	NM_008913	ENSMUSG00000028161	Ppp3ca	2900074D19Rik|CN|Caln|Calna|CnA	protein phosphatase 3, catalytic subunit, alpha isoform	protein-coding
mm_114154.1	chr13	55401183	55401201	+	1	NA	exon (NM_011392, exon 5 of 13)	exon (NM_011392, exon 5 of 13)	1544	NM_011392	20505	Mm.276355	NM_011392	ENSMUSG00000021490	Slc34a1	NaPi-IIa|Npt2|Npt2a|Slc17a2	solute carrier family 34 (sodium phosphate), member 1	protein-coding
mm_151137.1	chr19	52264946	52264970	+	1	NA	TTS (NM_008386)	TTS (NM_008386)	661	NM_008386	16333	Mm.46269	NM_008386	ENSMUSG00000035804	Ins1	Ins-1|Ins2-rs1	insulin I	protein-coding
mm_145686.1	chr18	61687912	61687922	+	1	NA	promoter-TSS (NM_019508)	promoter-TSS (NM_019508)	-18	NM_019508	56069	Mm.59313	NM_019508	ENSMUSG00000024578	Il17b	1110006O16Rik|1700006N07Rik|Zcyto7	interleukin 17B	protein-coding
mm_148088.1	chr18	73734850	73734852	-	1	NA	TTS (NM_053255)	TTS (NM_053255)	19628	NM_053255	114615	Mm.50642	NM_053255	ENSMUSG00000036941	Elac1	2610018O07Rik|8430417G19Rik	elaC ribonuclease Z 1	protein-coding
mm_98163.1	chr11	87737577	87737593	+	1	NA	promoter-TSS (NM_009296)	promoter-TSS (NM_009296)	20	NM_009296	20922	Mm.622	NM_009296	ENSMUSG00000020485	Supt4a	AL022777|Supt4h|Supt4h1|Supt4h1a	suppressor of Ty 4A	protein-coding
mm_80114.1	chr9	70542743	70542827	+	1	NA	promoter-TSS (NM_025690)	promoter-TSS (NM_025690)	7	NM_026337	66660	Mm.22379	NM_025690	ENSMUSG00000032212	Sltm	5730455C01Rik|5730555F13Rik|9130215G10Rik|Met	SAFB-like, transcription modulator	protein-coding
mm_147905.1	chr18	65393699	65393709	-	1	NA	5' UTR (NM_001037294, exon 1 of 13)	5' UTR (NM_001037294, exon 1 of 13)	184	NM_001037294	225638	Mm.296528	NM_001037294	ENSMUSG00000032845	Alpk2	Gm549|Hak	alpha-kinase 2	protein-coding
mm_150528.1	chr19	39229263	39229266	+	1	NA	promoter-TSS (NR_033614)	promoter-TSS (NR_033614)	10	NR_033614	638988	Mm.483843	NR_033614	ENSMUSG00000093610	Cyp2c53-ps	Cyp2c53|EG638988	cytochrome P450, family 2, subfamily c, polypeptide 53-ps	pseudo
mm_132125.1	chr16	31754583	31754595	+	1	NA	5' UTR (NM_001252436, exon 1 of 23)	5' UTR (NM_001252436, exon 1 of 23)	239	NM_001252436	13383	Mm.382	NM_007862	ENSMUSG00000022770	Dlg1	B130052P05Rik|Dlgh1|E-dlg/SAP97|SAP-97|SAP97|mKIAA4187	discs, large homolog 1 (Drosophila)	protein-coding
mm_119431.1	chr14	46173198	46173201	+	1	NA	Intergenic	Intergenic	89172	NR_002875	218963	Mm.282093	NR_002875		Gm1821	-	ubiquitin pseudogene	pseudo
mm_62992.1	chr7	120553061	120553074	+	1	NA	Intergenic	Intergenic	-44558	NR_024324	78552	Mm.289190	NR_024324	ENSMUSG00000044141	E130201H02Rik	-	Y box protein 1 pseudogene	pseudo
mm_126054.1	chr15	76949545	76949555	+	1	NA	exon (NM_054099, exon 3 of 4)	exon (NM_054099, exon 3 of 4)	1006	NM_054099	117171	Mm.322968	NM_054099	ENSMUSG00000063236	1110038F14Rik	-	RIKEN cDNA 1110038F14 gene	protein-coding
mm_23791.1	chr3	79568303	79568312	+	1	NA	promoter-TSS (NM_001162999)	promoter-TSS (NM_001162999)	-628	NM_001162999	329679	Mm.244005	NM_001162999	ENSMUSG00000061175	Fnip2	D630023B12Rik|mKIAA1450	folliculin interacting protein 2	protein-coding
mm_121767.1	chr14	19873297	19873317	-	1	NA	3' UTR (NM_001285911, exon 4 of 4)	3' UTR (NM_001285911, exon 4 of 4)	34382	NR_105025	52512	Mm.483998	NR_105025		D14Ertd670e	-	DNA segment, Chr 14, ERATO Doi 670, expressed	ncRNA
mm_131780.1	chr16	22895315	22895320	+	1	NA	promoter-TSS (NR_110508)	promoter-TSS (NR_110508)	-931	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_116126.1	chr13	28952567	28952573	-	1	NA	exon (NM_009238, exon 1 of 1)	exon (NM_009238, exon 1 of 1)	1112	NM_009238	20677	Mm.240627	NM_009238	ENSMUSG00000076431	Sox4	AA682046|Sox-4	SRY (sex determining region Y)-box 4	protein-coding
mm_33393.1	chr4	129820199	129820269	+	1	NA	promoter-TSS (NM_001164745)	promoter-TSS (NM_001164745)	-245	NM_008974	19244	Mm.193688	NM_008974	ENSMUSG00000028788	Ptp4a2	Prl-2	protein tyrosine phosphatase 4a2	protein-coding
mm_99610.1	chr11	104581640	104581686	+	1	NA	intron (NM_010858, intron 4 of 8)	intron (NM_010858, intron 4 of 8)	-19465	NR_130177	100415912	Mm.446786	NR_130177		Gm11665	Gm11664|OTTMUSG00000003182|OTTMUSG00000003183	predicted gene 11665	ncRNA
mm_130826.1	chr15	101845955	101845997	-	1	NA	exon (NM_008473, exon 9 of 9)	exon (NM_008473, exon 9 of 9)	4810	NM_008473	16678	Mm.183137	NM_008473	ENSMUSG00000046834	Krt1	Krt-2.1|Krt2-1|Krt86	keratin 1	protein-coding
mm_145029.1	chr18	39251832	39251836	+	1	NA	intron (NM_175164, intron 17 of 22)	intron (NM_175164, intron 17 of 22)	235411	NM_008173	14815	Mm.129481	NM_008173	ENSMUSG00000024431	Nr3c1	GR|Grl-1|Grl1	nuclear receptor subfamily 3, group C, member 1	protein-coding
mm_108665.1	chr12	86470184	86470194	+	1	NA	exon (NM_011934, exon 2 of 7)	exon (NM_011934, exon 2 of 7)	48545	NM_011934	26380	Mm.235550	NM_011934	ENSMUSG00000021255	Esrrb	Err2|Errb|Estrrb|Nr3b2	estrogen related receptor, beta	protein-coding
mm_163285.1	chr11	117654722	117654741	+	1	NA	intron (NM_198022, intron 1 of 21)	CpG	442	NM_198022	217351	Mm.40272	NM_198022	ENSMUSG00000025571	Tnrc6c	9930033H14Rik|mKIAA1582	trinucleotide repeat containing 6C	protein-coding
mm_123333.1	chr14	63070644	63070646	-	1	NA	Intergenic	Intergenic	15572	NR_046019	72609	Mm.387101	NR_046019		2700070H01Rik	-	RIKEN cDNA 2700070H01 gene	ncRNA
mm_148570.1	chr19	4859223	4859262	+	1	NA	intron (NM_019861, intron 9 of 13)	intron (NM_019861, intron 9 of 13)	4113	NM_019861	56464	Mm.29561	NM_019861	ENSMUSG00000083282	Ctsf	AI481912	cathepsin F	protein-coding
mm_48969.1	chr6	4747361	4747372	+	1	NA	promoter-TSS (NM_001130188)	promoter-TSS (NM_001130188)	60	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_135076.1	chr16	34263003	34263013	-	1	NA	intron (NM_001164268, intron 10 of 33)	intron (NM_001164268, intron 10 of 33)	251019	NM_001164268	545156	Mm.82274	NM_177357	ENSMUSG00000061751	Kalrn	2210407G14Rik|AV235988|DUET|E530005C20Rik|Gm539|Hapip|TRAD	kalirin, RhoGEF kinase	protein-coding
mm_138476.1	chr17	35194892	35194909	+	1	NA	promoter-TSS (NR_105939)	promoter-TSS (NR_105939)	-72	NR_105939	102465588		NR_105939	ENSMUSG00000098291	Mir6973a	Gm27967|mmu-mir-6973a	microRNA 6973a	ncRNA
mm_71305.1	chr8	41330687	41330699	+	1	NA	exon (NM_023662, exon 36 of 38)	exon (NM_023662, exon 36 of 38)	44004	NM_019734	11886	Mm.22547	NM_019734	ENSMUSG00000031591	Asah1	2310081N20Rik|AC|Asah	N-acylsphingosine amidohydrolase 1	protein-coding
mm_140474.1	chr17	94750126	94750141	+	1	NA	promoter-TSS (NM_176917)	promoter-TSS (NM_176917)	33	NR_024720	77022	Mm.440259	NR_024720	ENSMUSG00000098090	2700099C18Rik	9430041D22Rik	NDC80 homolog, kinetochore complex component pseudogene	pseudo
mm_86937.1	chr10	24447469	24447472	+	1	NA	Intergenic	Intergenic	-147972	NM_010217	14219	Mm.390287	NM_010217	ENSMUSG00000019997	Ctgf	Ccn2|Fisp12|Hcs24|fisp-12	connective tissue growth factor	protein-coding
mm_97052.1	chr11	72451159	72451178	+	1	NA	TTS (NM_001276383)	TTS (NM_001276383)	9790	NM_016776	18432	Mm.147946	NM_016776	ENSMUSG00000040463	Mybbp1a	AL024407|AU019902|P160|p160MBP|p67MBP	MYB binding protein (P160) 1a	protein-coding
mm_132853.1	chr16	48219073	48219110	+	1	NA	Intergenic	Intergenic	-64644	NM_028610	73693	Mm.35597	NM_028610	ENSMUSG00000058550	Dppa4	2410091M23Rik|C76608|ECAT15-1	developmental pluripotency associated 4	protein-coding
mm_159859.1	chr5	139907866	139907866	+	1	NA	promoter-TSS (NM_175522)	promoter-TSS (NM_175522)	-77	NM_175522	243312	Mm.237102	NM_175522	ENSMUSG00000048988	Elfn1	A930017N06Rik|AI197272|Ppp1r28	leucine rich repeat and fibronectin type III, extracellular 1	protein-coding
mm_69687.1	chr7	139990499	139990502	-	1	NA	intron (NM_007403, intron 2 of 23)	intron (NM_007403, intron 2 of 23)	2062	NM_007403	11501	Mm.15969	NM_007403	ENSMUSG00000025473	Adam8	ADAM 8|CD156|CD156a|E430039A18Rik|MS2	a disintegrin and metallopeptidase domain 8	protein-coding
mm_120594.1	chr14	70076927	70076935	+	1	NA	promoter-TSS (NM_001289927)	promoter-TSS (NM_001289927)	-514	NM_018781	13655	Mm.103737	NM_018781	ENSMUSG00000033730	Egr3	Pilot	early growth response 3	protein-coding
mm_139232.1	chr17	47731459	47731471	+	1	NA	intron (NM_025973, intron 5 of 8)	intron (NM_025973, intron 5 of 8)	4623	NM_025973	109820	Mm.22957	NM_025973	ENSMUSG00000023987	Pgc	2210410L06Rik|Upg-1|Upg1	progastricsin (pepsinogen C)	protein-coding
mm_157942.1	chrX	85776556	85776580	-	1	NA	5' UTR (NM_212444, exon 1 of 20)	5' UTR (NM_212444, exon 1 of 20)	251	NM_001294140	14933	Mm.246682	NM_008194	ENSMUSG00000025059	Gk	D930012N15Rik|Gyk	glycerol kinase	protein-coding
mm_172361.1	chr7	11949818	11949818	+	1	NA	Intergenic	IAPLTR4|LTR|ERVK	-18533	NM_134205	171239	Mm.377195	NM_134205	ENSMUSG00000045713	Vmn1r76	V1rg4	vomeronasal 1 receptor 76	protein-coding
mm_37380.1	chr4	120975467	120975474	-	1	NA	intron (NM_133716, intron 5 of 9)	intron (NM_133716, intron 5 of 9)	-2148	NR_105982	102465614		NR_105982	ENSMUSG00000106436	Mir7015	mmu-mir-7015	microRNA 7015	ncRNA
mm_168889.1	chr1	24614808	24614814	-	1	NA	Intergenic	Intergenic	-27374	NM_007733	12823	Mm.329196	NM_007733	ENSMUSG00000026141	Col19a1	-	collagen, type XIX, alpha 1	protein-coding
mm_157023.1	chrX	7790401	7790406	-	1	NA	intron (NM_207670, intron 1 of 24)	intron (NM_207670, intron 1 of 24)	410	NM_207670	54645	Mm.194811	NM_207670	ENSMUSG00000031153	Gripap1	AI854681|DXImx47e|GRASP-1|Sfc10|mKIAA1167	GRIP1 associated protein 1	protein-coding
mm_102109.1	chr11	53266000	53266035	-	1	NA	exon (NM_008300, exon 15 of 19)	exon (NM_008300, exon 15 of 19)	34462	NM_008300	15525	Mm.239865	NM_008300	ENSMUSG00000020361	Hspa4	70kDa|AI317151|APG-2|Hsp110|Hsp70RY|mKIAA4025	heat shock protein 4	protein-coding
mm_156653.1	chrX	157702850	157702856	+	1	NA	intron (NR_045569, intron 1 of 6)	intron (NR_045569, intron 1 of 6)	3880	NR_103722	66106	Mm.140340	NM_025357	ENSMUSG00000041476	Smpx	1010001C09Rik|Csl	small muscle protein, X-linked	protein-coding
mm_92376.1	chr10	76388879	76388906	-	1	NA	promoter-TSS (NR_040580)	promoter-TSS (NR_040580)	-123	NR_040580	67523	Mm.437833	NR_040580	ENSMUSG00000101695	1700094J05Rik	-	RIKEN cDNA 1700094J05 gene	ncRNA
mm_141002.1	chr17	24936931	24936967	-	1	NA	promoter-TSS (NM_001163447)	promoter-TSS (NM_001163447)	28	NM_001163448	30957	Mm.43081	NM_013931	ENSMUSG00000024163	Mapk8ip3	BB120594|D17Wsu15e|JIP-3|JSAP1|JSAP1a|JSAP1b|JSAP1c|JSAP1d|Jip3|Syd2|mKIAA1066	mitogen-activated protein kinase 8 interacting protein 3	protein-coding
mm_149383.1	chr19	11381893	11381927	+	1	NA	intron (NM_001310331, intron 3 of 6)	RMER6A|LTR|ERVK	6422	NM_001310331	666907		NM_001310331	ENSMUSG00000101389	Ms4a4a	EG666907	membrane-spanning 4-domains, subfamily A, member 4A	protein-coding
mm_63898.1	chr7	138940718	138940744	+	1	NA	promoter-TSS (NM_028708)	promoter-TSS (NM_028708)	1	NM_028708	74004	Mm.334298	NM_028708		Jakmip3	6330417G02Rik|AI593226|mKIAA4091	janus kinase and microtubule interacting protein 3	protein-coding
mm_67238.1	chr7	75308410	75308419	-	1	NA	promoter-TSS (NM_001109753)	promoter-TSS (NM_001109753)	-28	NM_001109753	64176	Mm.273082	NM_153579	ENSMUSG00000053025	Sv2b	A830038F04Rik|AI850768|mKIAA0735	synaptic vesicle glycoprotein 2 b	protein-coding
mm_33897.1	chr4	136247933	136248011	+	1	NA	promoter-TSS (NM_011542)	promoter-TSS (NM_011542)	15	NM_011542	21401	Mm.112	NM_011542	ENSMUSG00000001604	Tcea3	S-II|SII-K1	transcription elongation factor A (SII), 3	protein-coding
mm_112973.1	chr13	21287239	21287267	+	1	NA	3' UTR (NM_010343, exon 5 of 5)	3' UTR (NM_010343, exon 5 of 5)	5433	NM_010343	14780	Mm.1332	NM_010343	ENSMUSG00000004344	Gpx5	AV379049|Arep	glutathione peroxidase 5	protein-coding
mm_43029.1	chr5	123930666	123930674	+	1	NA	promoter-TSS (NM_001134767)	promoter-TSS (NM_001134767)	-19	NM_001134767	208908	Mm.243679	NM_001134767	ENSMUSG00000061882	Ccdc62	AI661708|Gm150	coiled-coil domain containing 62	protein-coding
mm_140601.1	chr17	10319297	10319317	-	1	NA	promoter-TSS (NM_001159517)	promoter-TSS (NM_001159517)	54	NM_021881	19317	Mm.130694	NM_021881	ENSMUSG00000062078	Qk	1110003F05Rik|1500005P18|QkI|l(17)-1Wis|l17Wis1	quaking	protein-coding
mm_102743.1	chr11	67254057	67254075	-	1	NA	exon (NM_010855, exon 28 of 40)	exon (NM_010855, exon 28 of 40)	16254	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_161549.1	chr16	10192808	10192808	+	1	NA	promoter-TSS (NM_029253)	promoter-TSS (NM_029253)	-98	NM_153123	75329	Mm.108729	NM_029253	ENSMUSG00000039200	Atf7ip2	4930558K11Rik|BC018510|Get-1|PSM2	activating transcription factor 7 interacting protein 2	protein-coding
mm_132961.1	chr16	50478935	50478948	+	1	NA	Intergenic	B1F2|SINE|Alu	-46475	NM_001347240	70508	Mm.28940	NM_027444	ENSMUSG00000022641	Bbx	5530401J07Rik|5730403O13Rik	bobby sox HMG box containing	protein-coding
mm_31077.1	chr4	41465135	41465159	+	1	NA	promoter-TSS (NM_025539)	promoter-TSS (NM_025539)	-1	NM_025539	66401	Mm.28574	NM_025539	ENSMUSG00000028443	Nudt2	2310051L06Rik|AA939917|APAH1	nudix (nucleoside diphosphate linked moiety X)-type motif 2	protein-coding
mm_29010.1	chr3	101604650	101604654	-	1	NA	promoter-TSS (NM_144900)	promoter-TSS (NM_144900)	55	NM_144900	11928	Mm.193670	NM_144900	ENSMUSG00000033161	Atp1a1	Atpa-1|BC010319	ATPase, Na+/K+ transporting, alpha 1 polypeptide	protein-coding
mm_2210.1	chr1	89659335	89659363	+	1	NA	intron (NM_001037136, intron 6 of 16)	ORR1D2|LTR|ERVL-MaLR	24543	NR_015540	74403	Mm.444291	NR_015540		4933400F21Rik	1700091C04Rik|4930565K10Rik	RIKEN cDNA 4933400F21 gene	ncRNA
mm_130832.1	chr15	101846880	101846904	-	1	NA	exon (NM_008473, exon 7 of 9)	exon (NM_008473, exon 7 of 9)	3894	NM_008473	16678	Mm.183137	NM_008473	ENSMUSG00000046834	Krt1	Krt-2.1|Krt2-1|Krt86	keratin 1	protein-coding
mm_114422.1	chr13	64422432	64422440	+	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	-10117	NM_053180	105278	Mm.74982	NM_053180	ENSMUSG00000021483	Cdk20	4932702G04Rik|AU019450|AW558027|CDCH|Ccrk|PNQLARE|p42	cyclin-dependent kinase 20	protein-coding
mm_12730.1	chr2	78869121	78869142	+	1	NA	promoter-TSS (NM_009454)	promoter-TSS (NM_009454)	84	NM_009454	22193	Mm.1485	NM_009454	ENSMUSG00000027011	Ube2e3	Ubce4|ubcM2	ubiquitin-conjugating enzyme E2E 3	protein-coding
mm_114915.1	chr13	95010011	95010028	+	1	NA	intron (NM_172590, intron 7 of 12)	intron (NM_172590, intron 7 of 12)	33675	NM_172590	218460	Mm.33856	NM_172590	ENSMUSG00000042015	Wdr41	B830029I03Rik|MSTP048	WD repeat domain 41	protein-coding
mm_115408.1	chr13	114447453	114447461	+	1	NA	Intergenic	LTR88b|LTR|Gypsy?	11494	NM_001301373	14313	Mm.4913	NM_008046	ENSMUSG00000021765	Fst	AL033346|FS	follistatin	protein-coding
mm_167823.1	chr9	124423231	124423262	+	1	NA	promoter-TSS (NR_015516)	promoter-TSS (NR_015516)	-5	NR_027950	75135	Mm.476814	NR_015516		4930526I15Rik	1600027J15Rik	RIKEN cDNA 4930526I15 gene	ncRNA
mm_172632.1	chr8	20424805	20424806	-	1	NA	promoter-TSS (NR_028428)	promoter-TSS (NR_028428)	9	NR_028428	381598	Mm.359054	NM_001024708	ENSMUSG00000071793	2610005L07Rik	2810038F24Rik|6720476A01Rik	cadherin 11 pseudogene	pseudo
mm_117176.1	chr13	63288502	63288506	-	1	NA	TTS (NR_045794)	TTS (NR_045794)	8643	NR_045794	100504114	Mm.437070	NR_045794	ENSMUSG00000097242	Gm16907	-	predicted gene, 16907	ncRNA
mm_117697.1	chr13	94328105	94328108	-	1	NA	Intergenic	Intergenic	30817	NR_045619	328309	Mm.174191	NM_183205		Gm9776	A530089L17|ENSMUSG00000042857	predicted gene 9776	ncRNA
mm_4880.1	chr1	187956817	187956821	+	1	NA	intron (NM_001243792, intron 2 of 7)	intron (NM_001243792, intron 2 of 7)	-41008	NM_011935	26381	Mm.89989	NM_011935	ENSMUSG00000026610	Esrrg	ERR3|Errg|NR3B3|mKIAA0832	estrogen-related receptor gamma	protein-coding
mm_40946.1	chr5	76822494	76822504	+	1	NA	Intergenic	Intergenic	-18100	NM_001163793	320827	Mm.101504	NM_001163793	ENSMUSG00000036377	C530008M17Rik	2810489J07Rik|4930529A19Rik|4931405B09Rik|Kiaa1211|mKIAA1211	RIKEN cDNA C530008M17 gene	protein-coding
mm_34136.1	chr4	139291137	139291200	+	1	NA	3' UTR (NM_001271405, exon 9 of 9)	3' UTR (NM_001271405, exon 9 of 9)	19532	NM_145384	212555	Mm.45131	NM_145384	ENSMUSG00000028744	Pqlc2	BC019216	PQ loop repeat containing 2	protein-coding
mm_158188.1	chrX	104413826	104413856	-	1	NA	promoter-TSS (NM_009592)	promoter-TSS (NM_009592)	5	NM_009592	11306	Mm.426128	NM_009592	ENSMUSG00000031333	Abcb7	AA517758|AU019072|Abc7	ATP-binding cassette, sub-family B (MDR/TAP), member 7	protein-coding
mm_62901.1	chr7	116546898	116546900	+	1	NA	Intergenic	Intergenic	42530	NM_001130479	53322	Mm.9901	NM_016773	ENSMUSG00000030659	Nucb2	AI607786|Calnuc|Nefa|Nesfatin-1	nucleobindin 2	protein-coding
mm_40494.1	chr5	57717534	57717555	+	1	NA	promoter-TSS (NM_001310606)	promoter-TSS (NM_001310606)	375	NR_015588	319216	Mm.332387	NR_015588	ENSMUSG00000097216	4932441J04Rik	-	RIKEN cDNA 4932441J04 gene	ncRNA
mm_28943.1	chr3	99253501	99253511	-	1	NA	promoter-TSS (NM_009323)	promoter-TSS (NM_009323)	-254	NM_009323	21384	Mm.88761	NM_009323	ENSMUSG00000027868	Tbx15	Tbx14|Tbx8|de	T-box 15	protein-coding
mm_96994.1	chr11	70700474	70700552	+	1	NA	promoter-TSS (NM_213729)	promoter-TSS (NM_213729)	-35	NM_153103	16562	Mm.99996	NM_153103	ENSMUSG00000020821	Kif1c	B430105J22Rik|D11Bwg1349e|Ltxs1|Orch3	kinesin family member 1C	protein-coding
mm_103386.1	chr11	75415720	75415733	-	1	NA	exon (NM_011340, exon 4 of 8)	exon (NM_011340, exon 4 of 8)	6897	NM_011340	20317	Mm.2044	NM_011340	ENSMUSG00000000753	Serpinf1	AI195227|EPC-1|Pedf|Pedfl|Sdf3	serine (or cysteine) peptidase inhibitor, clade F, member 1	protein-coding
mm_86010.1	chr9	112233552	112233570	-	1	NA	promoter-TSS (NR_015468)	promoter-TSS (NR_015468)	-716	NR_033432	620760	Mm.259863	NR_015468	ENSMUSG00000087038	2900079G21Rik	C130083B14|Gm6179	RIKEN cDNA 2900079G21 gene	ncRNA
mm_95991.1	chr11	59116460	59116460	+	1	NA	intron (NM_199152, intron 10 of 89)	intron (NM_199152, intron 10 of 89)	19915	NM_001171512	380698	Mm.339542	NM_199152	ENSMUSG00000061462	Obscn	BC046431|Gm878|OTTMUSG00000005786|UNC89	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	protein-coding
mm_48086.1	chr5	136987682	136987696	-	1	NA	promoter-TSS (NM_001310748)	promoter-TSS (NM_001310748)	270	NM_027318	70103	Mm.273147	NM_027318	ENSMUSG00000059518	Znhit1	2700001K05Rik|ZNFN4A1	zinc finger, HIT domain containing 1	protein-coding
mm_150260.1	chr19	34192817	34192827	+	1	NA	intron (NM_029682, intron 1 of 10)	intron (NM_029682, intron 1 of 10)	552	NM_029682	76630	Mm.130952	NM_029682	ENSMUSG00000024776	Stambpl1	1700095N21Rik|8230401J17Rik|ALMalpha|AMSH-FP	STAM binding protein like 1	protein-coding
mm_139895.1	chr17	70852406	70852431	+	1	NA	promoter-TSS (NM_001164075)	promoter-TSS (NM_001164075)	-684	NM_001164075	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_45398.1	chr5	66151649	66151681	-	1	NA	promoter-TSS (NM_001291226)	promoter-TSS (NM_001291226)	289	NM_001127382	245945	Mm.36863	NM_139065	ENSMUSG00000070780	Rbm47	9530077J19Rik	RNA binding motif protein 47	protein-coding
mm_158626.1	chrX	153036571	153036573	-	1	NA	3' UTR (NM_023788, exon 1 of 1)	3' UTR (NM_023788, exon 1 of 1)	991	NM_023788	75625	Mm.6890	NM_023788	ENSMUSG00000047238	Mageh1	2010107K23Rik|APR-1|APR1	melanoma antigen, family H, 1	protein-coding
mm_169864.1	chr16	33844528	33844531	+	1	NA	intron (NM_010580, intron 1 of 14)	intron (NM_010580, intron 1 of 14)	14864	NM_001145884	16419	Mm.6424	NM_010580	ENSMUSG00000022817	Itgb5	AA475909|AI874634|ESTM23|[b]-5|[b]5|[b]5A|[b]5B|beta-5|beta5	integrin beta 5	protein-coding
mm_87760.1	chr10	60284438	60284494	+	1	NA	promoter-TSS (NM_001146124)	promoter-TSS (NM_001146124)	5	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_51819.1	chr6	89000610	89000626	+	1	NA	Intergenic	Intergenic	-95492	NR_134978	232217	Mm.281744	NM_175017	ENSMUSG00000055403	4933427D06Rik	-	RIKEN cDNA 4933427D06 gene	ncRNA
mm_163508.1	chr12	113140708	113140718	+	1	NA	5' UTR (NM_001347443, exon 1 of 7)	5' UTR (NM_001347443, exon 1 of 7)	108	NM_001347443	68337	Mm.133825	NM_024223	ENSMUSG00000006356	Crip2	0610010I23Rik|AW743261|C77570|CRP2|CRP4|Crp|ESP1|Hlp	cysteine rich protein 2	protein-coding
mm_151602.1	chr19	3554894	3554896	-	1	NA	intron (NM_029456, intron 1 of 22)	B1_Mus2|SINE|Alu	20854	NM_001164159	52036	Mm.284686	NM_028999	ENSMUSG00000024908	Ppp6r3	4930528G08Rik|9130026N02Rik|D19Bwg1430e|D19Ertd703e|Pp6r3|Ppcs3|Pptcs3|Sapl|Saps3|mKIAA1558	protein phosphatase 6, regulatory subunit 3	protein-coding
mm_167227.1	chr8	13055849	13055853	+	1	NA	exon (NM_007972, exon 9 of 9)	exon (NM_007972, exon 9 of 9)	-5057	NM_025834	66901	Mm.441140	NM_025834	ENSMUSG00000031445	Proz	1300015B06Rik	protein Z, vitamin K-dependent plasma glycoprotein	protein-coding
mm_92945.1	chr10	85102442	85102471	-	1	NA	promoter-TSS (NM_001013028)	promoter-TSS (NM_001013028)	39	NM_010214	14202	Mm.46163	NM_010214	ENSMUSG00000050035	Fhl4	-	four and a half LIM domains 4	protein-coding
mm_117092.1	chr13	59796816	59796821	-	1	NA	intron (NM_153538, intron 16 of 27)	intron (NM_153538, intron 16 of 27)	26329	NM_153538	214290	Mm.233082	NM_153538	ENSMUSG00000035248	Zcchc6	6030448M23Rik|AA420405	zinc finger, CCHC domain containing 6	protein-coding
mm_119778.1	chr14	54179648	54179660	+	1	NA	Intergenic	Intergenic	74275	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_54793.1	chr6	41636390	41636409	-	1	NA	promoter-TSS (NM_022413)	promoter-TSS (NM_022413)	6	NM_022413	64177	Mm.296889	NM_022413	ENSMUSG00000029868	Trpv6	CAT|CaT1|Cac|Ecac2|Otrpc3	transient receptor potential cation channel, subfamily V, member 6	protein-coding
mm_87696.1	chr10	59702559	59702628	+	1	NA	promoter-TSS (NM_001291442)	promoter-TSS (NM_001291442)	30	NM_001291443	216001	Mm.27199	NM_144822	ENSMUSG00000020111	Micu1	C730016L05Rik|Calc|Cbara1	mitochondrial calcium uptake 1	protein-coding
mm_83407.1	chr9	44801779	44801791	-	1	NA	intron (NM_138951, intron 1 of 2)	intron (NM_138951, intron 1 of 2)	1166	NM_138951	192653	Mm.325487	NM_138951	ENSMUSG00000039438	Ttc36	-	tetratricopeptide repeat domain 36	protein-coding
mm_112147.1	chr12	113259671	113259706	-	1	NA	Intergenic	GA-rich|Low_complexity|Low_complexity	73785	NM_153776	69195	Mm.313244	NM_153776	ENSMUSG00000049036	Tmem121	2410008J05Rik|Hole	transmembrane protein 121	protein-coding
mm_171404.1	chr4	126047060	126047060	+	1	NA	5' UTR (NM_025544, exon 1 of 8)	5' UTR (NM_025544, exon 1 of 8)	132	NM_025544	66407	Mm.195628	NM_025544	ENSMUSG00000028861	Mrps15	1500003E24Rik|2410002B11Rik|Mprs15	mitochondrial ribosomal protein S15	protein-coding
mm_74826.1	chr8	23165945	23165950	-	1	NA	Intergenic	MTC|LTR|ERVL-MaLR	12676	NM_029002	74561	Mm.290028	NM_029002	ENSMUSG00000063672	Nkx6-3	9130417I07Rik|Nkx6.3	NK6 homeobox 3	protein-coding
mm_60523.1	chr7	44480023	44480035	+	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	-4488	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_102047.1	chr11	52000433	52000475	-	1	NA	promoter-TSS (NM_009458)	promoter-TSS (NM_009458)	12	NM_009458	22210	Mm.384918	NM_009458	ENSMUSG00000020390	Ube2b	2610301N02Rik|E2-14k|HR6B|Rad6b|mHR6B	ubiquitin-conjugating enzyme E2B	protein-coding
mm_117910.1	chr13	99430510	99430525	-	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-17691	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_168368.1	chr1	11783771	11783771	-	1	NA	intron (NM_001160369, intron 8 of 13)	intron (NM_001160369, intron 8 of 13)	369666	NM_001160371	320492	Mm.52021	NM_177173	ENSMUSG00000057715	A830018L16Rik	-	RIKEN cDNA A830018L16 gene	protein-coding
mm_13363.1	chr2	103454260	103454280	+	1	NA	3' UTR (NM_009804, exon 13 of 13)	3' UTR (NM_009804, exon 13 of 13)	30202	NM_010125	13711	Mm.20888	NM_010125	ENSMUSG00000027186	Elf5	ESE-2|ESE-5|ESE-5.	E74-like factor 5	protein-coding
mm_7969.1	chr1	134060812	134060815	-	1	NA	Intergenic	Intergenic	18342	NM_007570	12227	Mm.392646	NM_007570	ENSMUSG00000020423	Btg2	AA959598|APRO1|Pc3|TIS21	B cell translocation gene 2, anti-proliferative	protein-coding
mm_144282.1	chr18	11839537	11839551	+	1	NA	promoter-TSS (NR_045421)	promoter-TSS (NR_045421)	-167	NR_045421	621998	Mm.353277	NR_045421		Gm6277	-	predicted gene 6277	ncRNA
mm_64824.1	chr7	10656969	10656977	-	1	NA	Intergenic	Intergenic	23386	NM_134228	171262	Mm.222634	NM_134228	ENSMUSG00000045340	Vmn1r70	V1rd2|V1rl1	vomeronasal 1 receptor 70	protein-coding
mm_30523.1	chr3	158562200	158562290	-	1	NA	promoter-TSS (NM_001291453)	promoter-TSS (NM_001291453)	-24	NM_001081358	242274	Mm.132162	NM_001081358	ENSMUSG00000028176	Lrrc7	AK122498|densin|mKIAA1365	leucine rich repeat containing 7	protein-coding
mm_64904.1	chr7	16044494	16044498	-	1	NA	Intergenic	Intergenic	-27349	NM_001347559	666528	Mm.290718	NM_001099277	ENSMUSG00000078796	Zfp541	EG666528|Znf541	zinc finger protein 541	protein-coding
mm_168977.1	chr12	91473353	91473354	-	1	NA	intron (NM_011648, intron 1 of 9)	L1Md_T|LINE|L1	72360	NM_011648	22095	Mm.173847	NM_011648	ENSMUSG00000020963	Tshr	AI481368|hypothroid|hyt|pet	thyroid stimulating hormone receptor	protein-coding
mm_137426.1	chr17	26252988	26252996	+	1	NA	promoter-TSS (NM_025881)	promoter-TSS (NM_025881)	82	NR_037905	66978	Mm.440216	NM_025881	ENSMUSG00000024188	Luc7l	1810045C04Rik|2410018D03Rik	Luc7-like	protein-coding
mm_36999.1	chr4	110292502	110292504	-	1	NA	intron (NM_001163397, intron 1 of 5)	intron (NM_001163397, intron 1 of 5)	-4976	NM_001347178	15572	Mm.3970	NM_010488	ENSMUSG00000028546	Elavl4	Elav|Hud|PNEM	ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4 (Hu antigen D)	protein-coding
mm_90106.1	chr10	117224247	117224268	+	1	NA	intron (NM_026570, intron 1 of 6)	CpG	250	NM_026570	64050	Mm.233529	NM_026570	ENSMUSG00000020171	Yeats4	4930573H17Rik|B230215M10Rik|GAS41|NuBI-1	YEATS domain containing 4	protein-coding
mm_61214.1	chr7	64287654	64287662	+	1	NA	promoter-TSS (NM_172742)	promoter-TSS (NM_172742)	-12	NM_172742	233315	Mm.214959	NM_172742	ENSMUSG00000030522	Mtmr10	BB128963|C79734	myotubularin related protein 10	protein-coding
mm_146521.1	chr18	4352945	4352962	-	1	NA	promoter-TSS (NM_007746)	promoter-TSS (NM_007746)	0	NM_007746	26410	Mm.3275	NM_007746	ENSMUSG00000024235	Map3k8	Cot|Cot/Tpl2|Est|Estf|Tpl-2|Tpl2|c-COT	mitogen-activated protein kinase kinase kinase 8	protein-coding
mm_100979.1	chr11	7208411	7208428	-	1	NA	exon (NM_008343, exon 4 of 5)	exon (NM_008343, exon 4 of 5)	5504	NM_008343	16009	Mm.29254	NM_008343	ENSMUSG00000020427	Igfbp3	AI649005|IGFBP-3|IGgfbp3	insulin-like growth factor binding protein 3	protein-coding
mm_5165.1	chr1	10040008	10040017	-	1	NA	intron (NM_026493, intron 1 of 29)	CpG	1794	NM_026493	211660	Mm.244046	NM_026493	ENSMUSG00000056763	Cspp1	2310020J12Rik|4930413O22Rik|AA387550|BC055915|Cspp2|Cspp3	centrosome and spindle pole associated protein 1	protein-coding
mm_152133.1	chr19	7021094	7021104	-	1	NA	exon (NM_016737, exon 14 of 14)	exon (NM_016737, exon 14 of 14)	-1630	NM_153795	108101	Mm.157591	NM_153795	ENSMUSG00000024965	Fermt3	C79673|Kindlin3	fermitin family member 3	protein-coding
mm_35749.1	chr4	45489269	45489279	-	1	NA	intron (NM_001033306, intron 1 of 5)	intron (NM_001033306, intron 1 of 5)	41554	NM_001033306	230126	Mm.251716	NM_001033306	ENSMUSG00000044813	Shb	BC028832	src homology 2 domain-containing transforming protein B	protein-coding
mm_55839.1	chr6	83156354	83156387	-	1	NA	promoter-TSS (NM_023790)	promoter-TSS (NM_023790)	9	NM_023790	75659	Mm.130665	NM_023790	ENSMUSG00000030032	Wdr54	1700030E05Rik	WD repeat domain 54	protein-coding
mm_159451.1	chr3	144696979	144696979	-	1	NA	intron (NM_001282042, intron 6 of 9)	intron (NM_001282042, intron 6 of 9)	23356	NM_001282042	54673	Mm.271775	NM_019464	ENSMUSG00000037062	Sh3glb1	AA409932|AI314629|AU015566|Bif-1|mKIAA0491	SH3-domain GRB2-like B1 (endophilin)	protein-coding
mm_113250.1	chr13	27559310	27559328	+	1	NA	exon (NM_023332, exon 5 of 6)	exon (NM_023332, exon 5 of 6)	5287	NM_001316721	67310	Mm.46091	NM_023332	ENSMUSG00000006490	Prl8a9	1600019F10Rik|Ghd15|PLP-C2|PLP-Cbeta|Prlpc2	prolactin family8, subfamily a, member 9	protein-coding
mm_83311.1	chr9	44047006	44047011	-	1	NA	intron (NM_009382, intron 3 of 3)	intron (NM_009382, intron 3 of 3)	3624	NM_009382	21838	Mm.3951	NM_009382	ENSMUSG00000032011	Thy1	CD90|T25|Thy-1|Thy-1.2|Thy1.1|Thy1.2	thymus cell antigen 1, theta	protein-coding
mm_42984.1	chr5	123253667	123253692	+	1	NA	Intergenic	Intergenic	25489	NM_026000	67151	Mm.278997	NM_026000	ENSMUSG00000029440	Psmd9	1500011J20Rik|2610202L11Rik|Bridge-1|P27	proteasome (prosome, macropain) 26S subunit, non-ATPase, 9	protein-coding
mm_82936.1	chr9	35210965	35210987	-	1	NA	promoter-TSS (NM_172291)	promoter-TSS (NM_172291)	79	NM_172291	235169	Mm.138512	NM_172291	ENSMUSG00000039048	Foxred1	BC024806|TEG-23|Tex23	FAD-dependent oxidoreductase domain containing 1	protein-coding
mm_113500.1	chr13	37483406	37483427	+	1	NA	Intergenic	Intergenic	138071	NM_010745	17084	Mm.2639	NM_010745	ENSMUSG00000021423	Ly86	MD-1|MD1|ly86_tv2	lymphocyte antigen 86	protein-coding
mm_145666.1	chr18	61220468	61220486	+	1	NA	promoter-TSS (NM_146086)	promoter-TSS (NM_146086)	-22	NM_146086	225600	Mm.391106	NM_146086	ENSMUSG00000024575	Pde6a	Pdea|nmf282	phosphodiesterase 6A, cGMP-specific, rod, alpha	protein-coding
mm_167513.1	chr9	13827373	13827388	-	1	NA	promoter-TSS (NM_001310721)	promoter-TSS (NM_001310721)	-273	NM_026665	74360	Mm.157212	NM_026665	ENSMUSG00000031922	Cep57	3110002L15Rik|4921510P06Rik|4931428M20Rik|AI467480|Tsp57|mKIAA0092	centrosomal protein 57	protein-coding
mm_29590.1	chr3	119709611	119709613	-	1	NA	Intergenic	Lx5|LINE|L1	73776	NM_001310711	56195	Mm.29966	NM_019550	ENSMUSG00000028134	Ptbp2	Ptb2|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding
mm_67142.1	chr7	73375723	73375744	-	1	NA	promoter-TSS (NR_040324)	promoter-TSS (NR_040324)	41	NR_040325	319783	Mm.349813	NR_040324	ENSMUSG00000097756	A730056A06Rik	C76391	RIKEN cDNA A730056A06 gene	ncRNA
mm_20502.1	chr2	130424297	130424306	-	1	NA	promoter-TSS (NM_178762)	promoter-TSS (NM_178762)	-13	NM_178762	319513	Mm.482539	NM_178762	ENSMUSG00000037773	Pced1a	A930025D01Rik|AI480484|Fam113a	PC-esterase domain containing 1A	protein-coding
mm_90780.1	chr10	6980347	6980355	-	1	NA	promoter-TSS (NM_001347225)	promoter-TSS (NM_001347225)	-70	NM_001347225	320495	Mm.331674	NM_001033391	ENSMUSG00000064065	Ipcef1	A130090K04Rik	interaction protein for cytohesin exchange factors 1	protein-coding
mm_103410.1	chr11	75454639	75454654	-	1	NA	promoter-TSS (NM_138950)	promoter-TSS (NM_138950)	71	NM_138950	192652	Mm.340378	NM_138950	ENSMUSG00000045374	Wdr81	BC054822|Gm883|mFLJ00182|nur5	WD repeat domain 81	protein-coding
mm_130858.1	chr15	102188935	102188951	-	1	NA	promoter-TSS (NM_144942)	promoter-TSS (NM_144942)	100	NM_144942	246277	Mm.296382	NM_144942	ENSMUSG00000023044	Csad	Csd	cysteine sulfinic acid decarboxylase	protein-coding
mm_140070.1	chr17	75005700	75005726	+	1	NA	5' UTR (NM_019919, exon 1 of 34)	5' UTR (NM_019919, exon 1 of 34)	184	NM_019919	268977	Mm.269747	NM_019919	ENSMUSG00000001870	Ltbp1	9430031G15Rik|9830146M04|Ltbp-1|Ltbp1L|TGF-beta1-BP-1|Tgfb|b2b1000Clo	latent transforming growth factor beta binding protein 1	protein-coding
mm_154864.1	chrX	20662917	20662943	+	1	NA	promoter-TSS (NM_001136085)	promoter-TSS (NM_001136085)	34	NM_001136085	22201	Mm.1104	NM_009457	ENSMUSG00000001924	Uba1	A1S9|Sbx|Ube-1|Ube1x	ubiquitin-like modifier activating enzyme 1	protein-coding
mm_1697.1	chr1	75142814	75142824	+	1	NA	promoter-TSS (NM_026977)	promoter-TSS (NM_026977)	33	NM_001305231	227298	Mm.273062	NM_170755	ENSMUSG00000049339	Fam134a	-	family with sequence similarity 134, member A	protein-coding
mm_165225.1	chr2	52319253	52319264	-	1	NA	intron (NM_010889, intron 10 of 156)	intron (NM_010889, intron 10 of 156)	19540	NM_010889	17996	Mm.389247	NM_010889	ENSMUSG00000026950	Neb	AI595938	nebulin	protein-coding
mm_145572.1	chr18	60911985	60912002	+	1	NA	promoter-TSS (NM_001038499)	promoter-TSS (NM_001038499)	-247	NM_001038499	545260	Mm.20147	NM_001038499	ENSMUSG00000036412	Arsi	BC020108	arylsulfatase i	protein-coding
mm_79816.1	chr9	64294004	64294022	+	1	NA	exon (NM_025372, exon 5 of 8)	exon (NM_025372, exon 5 of 8)	12428	NM_001324557	66131	Mm.196219	NM_025372	ENSMUSG00000032397	Tipin	1110005A05Rik|1110018P21Rik	timeless interacting protein	protein-coding
mm_27714.1	chr3	68633635	68633641	-	1	NA	Intergenic	Intergenic	-57006	NM_001159424	16159	Mm.103783	NM_008351	ENSMUSG00000027776	Il12a	IL-12p35|Il-12a|Ll12a|p35	interleukin 12a	protein-coding
mm_109332.1	chr12	109571676	109571702	+	1	NA	promoter-TSS (NR_030438)	promoter-TSS (NR_030438)	-301	NR_030438	751547		NR_030438	ENSMUSG00000076316	Mir673	Mirn673|mir-673|mmu-mir-673	microRNA 673	ncRNA
mm_130924.1	chr15	102722151	102722162	-	1	NA	promoter-TSS (NM_026192)	promoter-TSS (NM_026192)	22	NM_026192	67488	Mm.71682	NM_026192	ENSMUSG00000023055	Calcoco1	1810009B06Rik|Cocoa|Gcap11|mKIAA1536	calcium binding and coiled coil domain 1	protein-coding
mm_49684.1	chr6	33289662	33289665	+	1	NA	intron (NM_001347089, intron 3 of 9)	intron (NM_001347089, intron 3 of 9)	40513	NM_009148	20336	Mm.265512	NM_009148	ENSMUSG00000029763	Exoc4	C78892|Sec8|Sec8l1	exocyst complex component 4	protein-coding
mm_112463.1	chr13	5867696	5867730	+	1	NA	3' UTR (NM_011803, exon 4 of 4)	3' UTR (NM_011803, exon 4 of 4)	6224	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_64831.1	chr7	12818867	12818871	-	1	NA	promoter-TSS (NM_026046)	promoter-TSS (NM_026046)	-9	NM_026046	67230	Mm.333574	NM_026046	ENSMUSG00000057894	Zfp329	2810439M05Rik|4632409L22Rik|ZNF329	zinc finger protein 329	protein-coding
mm_25151.1	chr3	102995710	102995788	+	1	NA	promoter-TSS (NM_025679)	promoter-TSS (NM_025679)	9	NM_025679	66641	Mm.33937	NM_025679	ENSMUSG00000027854	Sike1	2810005O12Rik|5730470L24Rik|AI450236|AI839862|Sike|Sikeb	suppressor of IKBKE 1	protein-coding
mm_171023.1	chr2	84505385	84505393	+	1	NA	intron (NR_046046, intron 1 of 2)	IAPLTR1_Mm|LTR|ERVK	1484	NR_046046	672763	Mm.491046	NR_046046	ENSMUSG00000087362	Gm13710	OTTMUSG00000013441	predicted gene 13710	ncRNA
mm_83840.1	chr9	54419596	54419619	-	1	NA	intron (NM_172771, intron 17 of 43)	intron (NM_172771, intron 17 of 43)	82019	NM_172771	235380	Mm.93636	NM_172771	ENSMUSG00000041268	Dmxl2	6330586A12|6430411K14Rik|E130119P06Rik|mKIAA0856	Dmx-like 2	protein-coding
mm_19024.1	chr2	76961701	76961711	-	1	NA	intron (NM_028004, intron 12 of 191)	intron (NM_028004, intron 12 of 191)	20841	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_123168.1	chr14	57376089	57376093	-	1	NA	intron (NM_030004, intron 2 of 7)	intron (NM_030004, intron 2 of 7)	22392	NM_030004	68631	Mm.25539	NM_030004	ENSMUSG00000021947	Cryl1	1110025H08Rik|A230106J09Rik|C85932|gul3dh	crystallin, lambda 1	protein-coding
mm_40381.1	chr5	52368778	52368789	+	1	NA	3' UTR (NM_011435, exon 2 of 2)	3' UTR (NM_011435, exon 2 of 2)	4979	NM_011435	20657	Mm.2407	NM_011435	ENSMUSG00000072941	Sod3	AI314465|EC-SOD	superoxide dismutase 3, extracellular	protein-coding
mm_114219.1	chr13	56426613	56426624	+	1	NA	Intergenic	Intergenic	-11737	NM_177809	328258	Mm.482177	NM_177809	ENSMUSG00000021509	Slc25a48	AU042651|E230025K15	solute carrier family 25, member 48	protein-coding
mm_120202.1	chr14	61680964	61680995	+	1	NA	intron (NR_028264, intron 1 of 6)	intron (NR_028264, intron 1 of 6)	1394	NR_028264	668253	Mm.32886	NR_028264	ENSMUSG00000097589	Dleu2	1810047A16Rik|4932411A06Rik|7730401J12Rik|AI197277|AI788824|Alt1|Gm9069|Leu2	deleted in lymphocytic leukemia, 2	ncRNA
mm_146764.1	chr18	17018976	17018985	-	1	NA	Intergenic	RMER17B|LTR|ERVK	-16528	NR_130158	75433	Mm.60907	NR_130158	ENSMUSG00000087170	1700001G01Rik	-	RIKEN cDNA 1700001G01 gene	ncRNA
mm_7275.1	chr1	97128269	97128291	-	1	NA	promoter-TSS (NM_028942)	promoter-TSS (NM_028942)	23	NM_028942	74441	Mm.60362	NM_028942	ENSMUSG00000026331	Slco6c1	4933404A18Rik|C79179	solute carrier organic anion transporter family, member 6c1	protein-coding
mm_85503.1	chr9	106199191	106199246	-	1	NA	promoter-TSS (NM_026447)	promoter-TSS (NM_026447)	15	NM_026447	67905	Mm.23018	NM_026447	ENSMUSG00000020253	Ppm1m	2810423O19Rik|AW610647|C77250|PP2Ceta	protein phosphatase 1M	protein-coding
mm_51902.1	chr6	91110594	91110612	+	1	NA	intron (NM_018815, intron 1 of 39)	L1MB3|LINE|L1	6223	NM_018815	54563	Mm.28162	NM_018815	ENSMUSG00000030091	Nup210	9830001L10|AI836801|Pom210|gp190|gp210	nucleoporin 210	protein-coding
mm_74074.1	chr8	122443636	122443659	+	1	NA	promoter-TSS (NM_138656)	promoter-TSS (NM_138656)	-9	NR_045696	100689703	Mm.271989	NR_045696		9330133O14Rik	-	RIKEN cDNA 9330133O14 gene	ncRNA
mm_18609.1	chr2	68366518	68366538	-	1	NA	intron (NM_016866, intron 7 of 17)	intron (NM_016866, intron 7 of 17)	105453	NM_016866	53416	Mm.198414	NM_016866	ENSMUSG00000027030	Stk39	AW227544|AW556857|DCHT|RF005|Rnl5|SPAK	serine/threonine kinase 39	protein-coding
mm_4747.1	chr1	182163307	182163324	+	1	NA	Intergenic	Intergenic	-5217	NM_001166728	625823	Mm.479992	NM_001166728	ENSMUSG00000091013	Vmn1r1	EG625823|Gm6628	vomeronasal 1 receptor 1	protein-coding
mm_28094.1	chr3	85887473	85887499	-	1	NA	promoter-TSS (NM_177130)	promoter-TSS (NM_177130)	32	NM_177130	320302	Mm.482978	NM_177130	ENSMUSG00000031286	Glt28d2	4732486J07Rik|Glt28d1l	glycosyltransferase 28 domain containing 2	protein-coding
mm_154875.1	chrX	20688483	20688532	+	1	NA	promoter-TSS (NM_011049)	promoter-TSS (NM_011049)	81	NM_011049	18555	Mm.102574	NM_011049	ENSMUSG00000031065	Cdk16	Crk5|Pctaire1|Pctk1	cyclin-dependent kinase 16	protein-coding
mm_8843.1	chr1	162702209	162702231	-	1	NA	exon (NM_001081290, exon 17 of 35)	exon (NM_001081290, exon 17 of 35)	38336	NM_001081290	226562	Mm.245446	NM_001081290	ENSMUSG00000040225	Prrc2c	1810043M20Rik|9630039I18Rik|A630006J20|Bat2d|Bat2d1|Bat2l2|E130112L15Rik|Prrc3|mKIAA1096	proline-rich coiled-coil 2C	protein-coding
mm_76532.1	chr8	87943558	87943589	-	1	NA	intron (NM_033327, intron 1 of 7)	intron (NM_033327, intron 1 of 7)	16022	NM_033327	94187	Mm.23452	NM_033327	ENSMUSG00000045333	Zfp423	Ebfaz|Roaz|Zfp104|Znf423|ataxia1|mKIAA0760|nur12	zinc finger protein 423	protein-coding
mm_68783.1	chr7	123286895	123286911	-	1	NA	exon (NM_001122643, exon 18 of 20)	exon (NM_001122643, exon 18 of 20)	72037	NM_146198	233836	Mm.211838	NM_146198	ENSMUSG00000030769	Slc5a11	2010013B02Rik|Kst1|RKST2|SMIT2|Slc5a10	solute carrier family 5 (sodium/glucose cotransporter), member 11	protein-coding
mm_134859.1	chr16	28445850	28445867	-	1	NA	5' UTR (NM_183064, exon 1 of 5)	5' UTR (NM_183064, exon 1 of 5)	217	NM_183064	14167	Mm.7996	NM_010199	ENSMUSG00000022523	Fgf12	AV114868|B230343J05Rik|FGF-12|FHF-1|Fhf1	fibroblast growth factor 12	protein-coding
mm_170024.1	chr17	21650611	21650612	+	1	NA	promoter-TSS (NM_001166497)	promoter-TSS (NM_001166497)	0	NM_001166497	73229	Mm.296733	NM_001166497	ENSMUSG00000035868	Zfp983	3110052M02Rik|mszf57|mszf71	zinc finger protein 983	protein-coding
mm_130619.1	chr15	100227722	100227761	-	1	NA	promoter-TSS (NM_007497)	promoter-TSS (NM_007497)	-118	NM_007497	11908	Mm.676	NM_007497	ENSMUSG00000023027	Atf1	-	activating transcription factor 1	protein-coding
mm_40544.1	chr5	58030148	58030153	+	1	NA	intron (NM_001310608, intron 3 of 3)	intron (NM_001310608, intron 3 of 3)	312069	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_136530.1	chr16	97504893	97504915	-	1	NA	promoter-TSS (NM_020622)	promoter-TSS (NM_020622)	32	NM_020622	52793	Mm.327932	NM_020622	ENSMUSG00000022938	Fam3b	2-21|9030624C24Rik|D16Jhu19e|ORF9|Pander	family with sequence similarity 3, member B	protein-coding
mm_75156.1	chr8	36248097	36248107	-	1	NA	intron (NM_001081150, intron 1 of 11)	CpG	1414	NM_001081150	244421	Mm.324032	NM_001081150	ENSMUSG00000039633	Lonrf1	-	LON peptidase N-terminal domain and ring finger 1	protein-coding
mm_170044.1	chr17	24666005	24666024	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-3738	NM_183149	213753	Mm.219581	NM_183149	ENSMUSG00000041130	Zfp598	BC023040|Ntrap|Znf598	zinc finger protein 598	protein-coding
mm_30907.1	chr4	32424737	32424747	+	1	NA	intron (NM_001109661, intron 1 of 4)	intron (NM_001109661, intron 1 of 4)	7307	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_26362.1	chr3	142554916	142554922	+	1	NA	Intergenic	RMER17C|LTR|ERVK	-5133	NM_018734	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_114971.1	chr13	97241097	97241116	+	1	NA	promoter-TSS (NM_007930)	promoter-TSS (NM_007930)	1	NM_007930	13803	Mm.241073	NM_007930	ENSMUSG00000041773	Enc1	Nrpb|PIG10	ectodermal-neural cortex 1	protein-coding
mm_157898.1	chrX	77837967	77837976	-	1	NA	TTS (NM_017471)	TTS (NM_017471)	15529	NM_017471	54192	Mm.8034	NM_017471	ENSMUSG00000000003	Pbsn	PB|Prbs	probasin	protein-coding
mm_10991.1	chr2	26315484	26315502	+	1	NA	promoter-TSS (NM_001199146)	promoter-TSS (NM_001199146)	-40	NM_001199146	67839	Mm.266611	NM_153410	ENSMUSG00000026930	Gpsm1	1810037C22Rik|AW107933|Ags3	G-protein signalling modulator 1 (AGS3-like, C. elegans)	protein-coding
mm_37710.1	chr4	129491060	129491060	-	1	NA	promoter-TSS (NM_080442)	promoter-TSS (NM_080442)	-130	NM_001085491	68233	Mm.424983	NM_001085491	ENSMUSG00000078554	Fam229a	1700125D06Rik	family with sequence similarity 229, member A	protein-coding
mm_17293.1	chr2	26208282	26208293	-	1	NA	promoter-TSS (NM_010711)	promoter-TSS (NM_010711)	-38	NM_010711	16871	Mm.386765	NM_010711	ENSMUSG00000026934	Lhx3	Lim3|P-LIM|mLIM3|mLim-3	LIM homeobox protein 3	protein-coding
mm_58677.1	chr7	12478295	12478313	+	1	NA	promoter-TSS (NM_026112)	promoter-TSS (NM_026112)	-1	NM_001039951	67370	Mm.98929	NM_026112	ENSMUSG00000030386	Zfp606	2410022M24Rik|AW494727	zinc finger protein 606	protein-coding
mm_107891.1	chr12	70459867	70459873	+	1	NA	intron (NM_028339, intron 4 of 7)	intron (NM_028339, intron 4 of 7)	6716	NM_028339	72736	Mm.204670	NM_028339	ENSMUSG00000021072	Tmx1	2810425A04Rik|AI465319|Txndc1	thioredoxin-related transmembrane protein 1	protein-coding
mm_42344.1	chr5	114909898	114909909	+	1	NA	intron (NM_011854, intron 5 of 5)	B1_Mus2|SINE|Alu	12969	NM_011854	23962	Mm.228363	NM_011854	ENSMUSG00000029561	Oasl2	M1204|Mmu-OASL|Oasl	2'-5' oligoadenylate synthetase-like 2	protein-coding
mm_108735.1	chr12	88360536	88360603	+	1	NA	promoter-TSS (NM_001277297)	promoter-TSS (NM_001277297)	55	NM_001277297	72113	Mm.181387	NM_028105	ENSMUSG00000021044	Adck1	2610005A10Rik	aarF domain containing kinase 1	protein-coding
mm_54098.1	chr6	16837604	16837617	-	1	NA	intron (NM_031198, intron 5 of 6)	intron (NM_031198, intron 5 of 6)	60831	NM_031198	21426	Mm.36217	NM_031198	ENSMUSG00000029553	Tfec	BB107417|Tcfec|bHLHe34	transcription factor EC	protein-coding
mm_151215.1	chr19	53639328	53639369	+	1	NA	exon (NM_007790, exon 23 of 29)	exon (NM_007790, exon 23 of 29)	-37958	NM_001170847	73713	Mm.313695	NM_001170847	ENSMUSG00000043639	Rbm20	1110018J23Rik|2010003H22Rik|AI646761	RNA binding motif protein 20	protein-coding
mm_101500.1	chr11	32136108	32136145	-	1	NA	Intergenic	Intergenic	-34898	NR_130637	104692	Mm.414035	NR_130637	ENSMUSG00000086386	Gm12108	BB052462|OTTMUSG00000005365	predicted gene 12108	ncRNA
mm_9799.1	chr1	181853144	181853152	-	1	NA	Intergenic	Intergenic	-10747	NM_133815	98386	Mm.4538	NM_133815	ENSMUSG00000004880	Lbr	AI505894|ic	lamin B receptor	protein-coding
mm_68103.1	chr7	102017631	102017650	-	1	NA	5' UTR (NM_010531, exon 2 of 7)	5' UTR (NM_010531, exon 2 of 7)	515	NM_010531	16068	Mm.422756	NM_010531	ENSMUSG00000070427	Il18bp	IL-18BP|Igifbp|MC54L	interleukin 18 binding protein	protein-coding
mm_171938.1	chr5	66248652	66248672	-	1	NA	Intergenic	B4|SINE|B4	-11236	NM_001302833	70918	Mm.23166	NM_027602	ENSMUSG00000029206	Nsun7	4921525L17Rik	NOL1/NOP2/Sun domain family, member 7	protein-coding
mm_101575.1	chr11	34313857	34313868	-	1	NA	promoter-TSS (NM_001025382)	promoter-TSS (NM_001025382)	-960	NM_001025382	574403	Mm.444796	NM_001025382	ENSMUSG00000069911	Fam196b	EG574403|Gm6041	family with sequence similarity 196, member B	protein-coding
mm_128314.1	chr15	37960917	37960935	-	1	NA	5' UTR (NM_199476, exon 1 of 9)	5' UTR (NM_199476, exon 1 of 9)	129	NM_199476	382985	Mm.24738	NM_199476	ENSMUSG00000022292	Rrm2b	p53R2	ribonucleotide reductase M2 B (TP53 inducible)	protein-coding
mm_6272.1	chr1	69662790	69662793	-	1	NA	intron (NM_011770, intron 3 of 7)	intron (NM_011770, intron 3 of 7)	23169	NM_011770	22779	Mm.106343	NM_011770	ENSMUSG00000025997	Ikzf2	A730095J18Rik|Helios|Zfpn1a2|Znfn1a2	IKAROS family zinc finger 2	protein-coding
mm_114497.1	chr13	69959875	69959881	+	1	NA	promoter-TSS (NR_138559)	promoter-TSS (NR_138559)	45	NR_138559	67550	Mm.158159	NR_138559		4933416O17Rik	-	RIKEN cDNA 4933416O17 gene	ncRNA
mm_76273.1	chr8	84134059	84134098	-	1	NA	intron (NM_145970, intron 24 of 28)	intron (NM_145970, intron 24 of 28)	8089	NM_001013384	244550	Mm.334654	NM_001013384	ENSMUSG00000012889	Podnl1	5832418A03Rik|Gm506	podocan-like 1	protein-coding
mm_20232.1	chr2	125858986	125859027	-	1	NA	promoter-TSS (NM_001285513)	promoter-TSS (NM_001285513)	76	NM_009939	12848	Mm.3596	NM_009939	ENSMUSG00000027206	Cops2	AI315723|C85265|Csn2|Sgn2|TRIP-15|Trip15	COP9 signalosome subunit 2	protein-coding
mm_11608.1	chr2	34406883	34406896	+	1	NA	promoter-TSS (NM_177345)	promoter-TSS (NM_177345)	38	NM_001290626	227743	Mm.270866	NM_177345	ENSMUSG00000038696	Mapkap1	AI591529|D230039K05Rik|Sin1	mitogen-activated protein kinase associated protein 1	protein-coding
mm_10505.1	chr2	16356011	16356021	+	1	NA	promoter-TSS (NM_026162)	promoter-TSS (NM_026162)	-288	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding
mm_107509.1	chr12	40108369	40108374	+	1	NA	intron (NM_009132, intron 3 of 13)	intron (NM_009132, intron 3 of 13)	25857	NM_009132	20259	Mm.2416	NM_009132	ENSMUSG00000002565	Scin	AW545522|adseverin	scinderin	protein-coding
mm_16954.1	chr2	17390875	17390884	-	1	NA	intron (NM_028757, intron 4 of 6)	intron (NM_028757, intron 4 of 6)	-172635	NR_105847	102465964		NR_105847	ENSMUSG00000099161	Mir6419	Gm27713|mmu-mir-6419	microRNA 6419	ncRNA
mm_146785.1	chr18	20114633	20114637	-	1	NA	5' UTR (NM_001291804, exon 1 of 16)	5' UTR (NM_001291804, exon 1 of 16)	138	NM_001291804	13505	Mm.33740	NM_013504	ENSMUSG00000044322	Dsc1	1110020A10Rik|AI507491	desmocollin 1	protein-coding
mm_3543.1	chr1	150403962	150403974	+	1	NA	exon (NM_133780, exon 7 of 52)	exon (NM_133780, exon 7 of 52)	-10913	NM_145511	226499	Mm.222093	NM_145511	ENSMUSG00000006010	BC003331	1810053E15Rik|Odr4|odr-4	cDNA sequence BC003331	protein-coding
mm_125185.1	chr15	32251816	32251818	+	1	NA	intron (NM_009154, intron 1 of 22)	intron (NM_009154, intron 1 of 22)	7004	NM_009154	20356	Mm.260374	NM_009154	ENSMUSG00000022231	Sema5a	5930434A13|9130201M22Rik|AI464145|Semaf|semF	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A	protein-coding
mm_15896.1	chr2	164948232	164948245	+	1	NA	promoter-TSS (NM_013599)	promoter-TSS (NM_013599)	19	NM_013599	17395	Mm.4406	NM_013599	ENSMUSG00000017737	Mmp9	AW743869|B/MMP9|Clg4b|Gel B|MMP-9|pro-MMP-9	matrix metallopeptidase 9	protein-coding
mm_22464.1	chr3	3556494	3556503	+	1	NA	intron (NM_013920, intron 1 of 9)	intron (NM_013920, intron 1 of 9)	48468	NM_013920	30942	Mm.330897	NM_013920	ENSMUSG00000017688	Hnf4g	NR2A2	hepatocyte nuclear factor 4, gamma	protein-coding
mm_141074.1	chr17	25844445	25844472	-	1	NA	TTS (NM_001163766)	TTS (NM_001163766)	393	NM_145999	214952	Mm.40907	NM_145999	ENSMUSG00000025733	Rhot2	Arht2|Miro2	ras homolog family member T2	protein-coding
mm_127296.1	chr15	100182274	100182314	+	1	NA	intron (NM_001159361, intron 21 of 37)	L2a|LINE|L2	5742	NR_037311	100499528		NR_037311	ENSMUSG00000092752	Mir3473a	Mir3473|mir-3473a|mmu-mir-3473|mmu-mir-3473a	microRNA 3473a	ncRNA
mm_67717.1	chr7	90023060	90023080	-	1	NA	Intergenic	Intergenic	-6089	NR_110365	319711	Mm.31753	NR_015614	ENSMUSG00000097585	E230029C05Rik	AI452102|B230337J15	RIKEN cDNA E230029C05 gene	ncRNA
mm_25675.1	chr3	122044429	122044469	+	1	NA	promoter-TSS (NM_007378)	promoter-TSS (NM_007378)	-11	NM_007378	11304	Mm.3918	NM_007378	ENSMUSG00000028125	Abca4	AW050280|Abc10|Abcr|D430003I15Rik|RmP	ATP-binding cassette, sub-family A (ABC1), member 4	protein-coding
mm_161820.1	chr17	71183958	71183958	+	1	NA	promoter-TSS (NM_022882)	promoter-TSS (NM_022882)	-20	NM_022882	64898	Mm.227924	NM_022882	ENSMUSG00000024052	Lpin2	2610511G02Rik|AI481352|AW742896	lipin 2	protein-coding
mm_146588.1	chr18	9282755	9282766	-	1	NA	promoter-TSS (NM_153086)	promoter-TSS (NM_153086)	49	NM_153086	225152	Mm.119273	NM_153086	ENSMUSG00000036855	Gjd4	9430022F06Rik|Cx39	gap junction protein, delta 4	protein-coding
mm_167458.1	chr8	123332856	123332869	+	1	NA	exon (NM_172287, exon 1 of 15)	exon (NM_172287, exon 1 of 15)	149	NM_172287	234857	Mm.150200	NM_172287	ENSMUSG00000010154	Spire2	BC026502|Spir-2|Spir2	spire homolog 2 (Drosophila)	protein-coding
mm_69972.1	chr7	142377067	142377082	-	1	NA	exon (NM_009983, exon 7 of 9)	exon (NM_009983, exon 7 of 9)	-3328	NM_001347541	320802	Mm.154486	NM_177265	ENSMUSG00000045777	Ifitm10	6330512M04Rik|AI848576|DSPA3	interferon induced transmembrane protein 10	protein-coding
mm_95865.1	chr11	58009990	58009999	+	1	NA	intron (NM_028451, intron 1 of 18)	CpG	930	NM_028451	73158	Mm.248843	NM_028451	ENSMUSG00000037331	Larp1	1810024J12Rik|3110040D16Rik|Larp|mKIAA0731	La ribonucleoprotein domain family, member 1	protein-coding
mm_156958.1	chrX	169989286	169989313	+	1	NA	3' UTR (NM_001290504, exon 10 of 10)	3' UTR (NM_001290504, exon 10 of 10)	-10382	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_166503.1	chr6	4747299	4747354	+	1	NA	promoter-TSS (NM_001130188)	promoter-TSS (NM_001130188)	20	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_78762.1	chr9	43307570	43307581	+	1	NA	Intergenic	Intergenic	-3188	NM_023655	72169	Mm.273277	NM_023655	ENSMUSG00000032013	Trim29	1110047J21Rik|2810431N19Rik|4732461M22Rik|AI119726	tripartite motif-containing 29	protein-coding
mm_51915.1	chr6	91233753	91233768	+	1	NA	exon (NM_001081437, exon 2 of 17)	exon (NM_001081437, exon 2 of 17)	20996	NM_007992	14115	Mm.249146	NM_007992	ENSMUSG00000064080	Fbln2	5730577E14Rik|FIBL-2	fibulin 2	protein-coding
mm_58049.1	chr6	136835398	136835424	-	1	NA	promoter-TSS (NM_001039558)	promoter-TSS (NM_001039558)	39	NM_001039558	654818	Mm.386899	NM_001039558	ENSMUSG00000043298	Smco3	C030030A07Rik	single-pass membrane protein with coiled-coil domains 3	protein-coding
mm_64810.1	chr7	6708748	6708769	-	1	NA	exon (NM_008817, exon 9 of 9)	exon (NM_008817, exon 9 of 9)	1998	NR_023846	100169889	Mm.491213	NR_023846		Peg3os	Apeg3|Peg3as	Peg3 opposite strand	ncRNA
mm_1622.1	chr1	74391873	74391885	+	1	NA	5' UTR (NM_153088, exon 1 of 7)	5' UTR (NM_153088, exon 1 of 7)	270	NM_153088	227292	Mm.165042	NM_153088	ENSMUSG00000026176	Ctdsp1	GIP|NLIIF|Nif3|SCP1	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 1	protein-coding
mm_61830.1	chr7	88278781	88278788	+	1	NA	intron (NM_001311790, intron 1 of 3)	(T)n|Simple_repeat|Simple_repeat	699	NM_001311790	13032	Mm.89295	NM_009982	ENSMUSG00000030560	Ctsc	AI047818|CatC|DPP1|DPPI	cathepsin C	protein-coding
mm_122788.1	chr14	54416999	54417006	-	1	NA	intron (NM_001253679, intron 1 of 10)	B4A|SINE|B4	677	NM_001253679	20540	Mm.142455	NM_011405	ENSMUSG00000000958	Slc7a7	AI790233|my+lat1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 7	protein-coding
mm_103791.1	chr11	82866143	82866146	-	1	NA	intron (NM_001164569, intron 1 of 7)	intron (NM_001164569, intron 1 of 7)	4600	NM_001164570	67338	Mm.341608	NM_026097	ENSMUSG00000020696	Rffl	1700051E09Rik|4930516L10Rik|BG080975|Carp2	ring finger and FYVE like domain containing protein	protein-coding
mm_15656.1	chr2	163204451	163204468	+	1	NA	Intergenic	CpG	-20995	NM_001098799	269389	Mm.207709	NM_001098799	ENSMUSG00000074607	Tox2	AI851523|AV026525|BI987407|Gcx1|RxHMG1	TOX high mobility group box family member 2	protein-coding
mm_85982.1	chr9	112172478	112172487	-	1	NA	intron (NM_001177623, intron 9 of 9)	intron (NM_001177623, intron 9 of 9)	13467	NM_001177618	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_70119.1	chr7	142969239	142969251	-	1	NA	promoter-TSS (NM_008554)	promoter-TSS (NM_008554)	19	NM_008554	17173	Mm.196417	NM_008554	ENSMUSG00000009248	Ascl2	2410083I15Rik|Mash2|bHLHa45	achaete-scute family bHLH transcription factor 2	protein-coding
mm_142627.1	chr17	47395685	47395725	-	1	NA	intron (NM_008189, intron 1 of 3)	intron (NM_008189, intron 1 of 3)	4901	NM_008189	14913	Mm.16224	NM_008189	ENSMUSG00000023982	Guca1a	GC-A|Gcap1|Guca1|mGCAP1	guanylate cyclase activator 1a (retina)	protein-coding
mm_131190.1	chr16	7224325	7224335	+	1	NA	exon (NM_183188, exon 2 of 13)	exon (NM_183188, exon 2 of 13)	154495	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_44366.1	chr5	17808381	17808381	-	1	NA	intron (NM_007643, intron 8 of 14)	MTC|LTR|ERVL-MaLR	27515	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_5716.1	chr1	44079743	44079749	-	1	NA	Intergenic	Intergenic	22642	NM_029368	75623	Mm.348017	NM_029368	ENSMUSG00000026049	Tex30	1700029F09Rik|3110030D08Rik	testis expressed 30	protein-coding
mm_130794.1	chr15	101690379	101690392	-	1	NA	3' UTR (NM_008476, exon 9 of 9)	3' UTR (NM_008476, exon 9 of 9)	3920	NM_008476	16687	Mm.302399	NM_008476	ENSMUSG00000058354	Krt6a	2310016L08Rik|Krt2-6a|Krt2-6c|MK6a|mK6[a]	keratin 6A	protein-coding
mm_38184.1	chr4	135300229	135300261	-	1	NA	Intergenic	Intergenic	-27485	NM_013885	29876	Mm.257765	NM_013885	ENSMUSG00000037242	Clic4	D0Jmb3|TU-74|mc3s5|mtCLIC	chloride intracellular channel 4 (mitochondrial)	protein-coding
mm_37235.1	chr4	118054735	118054755	-	1	NA	intron (NM_009176, intron 2 of 11)	intron (NM_009176, intron 2 of 11)	80201	NM_001285520	20441	Mm.251002	NM_009176	ENSMUSG00000028538	St3gal3	ST3GalIII|ST3N|Siat3|Siat6	ST3 beta-galactoside alpha-2,3-sialyltransferase 3	protein-coding
mm_120016.1	chr14	55745922	55745932	+	1	NA	promoter-TSS (NM_026819)	promoter-TSS (NM_026819)	234	NM_026403	67842	Mm.180338	NM_026403	ENSMUSG00000019297	Nop9	2610027L16Rik	NOP9 nucleolar protein	protein-coding
mm_71422.1	chr8	46490969	46490995	+	1	NA	promoter-TSS (NM_001302163)	promoter-TSS (NM_001302163)	16	NM_001302163	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_172633.1	chr8	20550303	20550319	+	1	NA	Intergenic	CpG	-64616	NM_001270553	100861668	Mm.491087	NM_001270553	ENSMUSG00000095294	Gm21119	-	predicted gene, 21119	protein-coding
mm_122071.1	chr14	30595749	30595782	-	1	NA	3' UTR (NM_001310682, exon 17 of 17)	3' UTR (NM_001310682, exon 17 of 17)	14545	NM_001310682	18753	Mm.2314	NM_011103	ENSMUSG00000021948	Prkcd	AI385711|D14Ertd420e|PKC[d]|PKCdelta|Pkcd	protein kinase C, delta	protein-coding
mm_93201.1	chr10	94711145	94711145	-	1	NA	intron (NM_029852, intron 1 of 15)	intron (NM_029852, intron 1 of 15)	22355	NM_029852	77048	Mm.296971	NM_029852	ENSMUSG00000020024	Cep83	2600001G24Rik|4921537D05Rik|5730513H21Rik|Ccdc41	centrosomal protein 83	protein-coding
mm_102441.1	chr11	59526859	59526885	-	1	NA	Intergenic	Intergenic	-15814	NM_145827	216799	Mm.54174	NM_145827	ENSMUSG00000032691	Nlrp3	AGTAVPRL|AII/AVP|Cias1|FCAS|FCU|MWS|Mmig1|NALP3|Pypaf1	NLR family, pyrin domain containing 3	protein-coding
mm_38977.1	chr4	150909813	150909884	-	1	NA	promoter-TSS (NM_020569)	promoter-TSS (NM_020569)	73	NM_020569	57320	Mm.277349	NM_020569	ENSMUSG00000028964	Park7	DJ-1|Dj1	Parkinson disease (autosomal recessive, early onset) 7	protein-coding
mm_101321.1	chr11	22859663	22859680	-	1	NA	promoter-TSS (NM_016888)	promoter-TSS (NM_016888)	64	NM_016888	53625	Mm.395495	NM_016888	ENSMUSG00000051650	B3gnt2	AA408337|AA409404|AW260308|B3Galt6|B3gnt1|BGnT-1|BGnT-2|BGnT1|BGnT2|Beta3gnt	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 2	protein-coding
mm_12251.1	chr2	68905301	68905303	+	1	NA	intron (NM_172856, intron 1 of 9)	AT_rich|Low_complexity|Low_complexity	43861	NM_001347161	241447	Mm.222222	NM_172856	ENSMUSG00000027035	Cers6	4732462C07Rik|AW544719|Lass6|T1L	ceramide synthase 6	protein-coding
mm_140369.1	chr17	86963319	86963329	+	1	NA	5' UTR (NM_145491, exon 1 of 5)	5' UTR (NM_145491, exon 1 of 5)	213	NM_145491	104215	Mm.826	NM_145491	ENSMUSG00000024143	Rhoq	Arhq|TC10A|Tc10	ras homolog family member Q	protein-coding
mm_142728.1	chr17	48234754	48234766	-	1	NA	intron (NM_001347399, intron 1 of 2)	intron (NM_001347399, intron 1 of 2)	2021	NM_021406	58217	Mm.248352	NM_021406	ENSMUSG00000042265	Trem1	-	triggering receptor expressed on myeloid cells 1	protein-coding
mm_156136.1	chrX	127039969	127039998	+	1	NA	promoter-TSS (NM_001033241)	promoter-TSS (NM_001033241)	11	NM_001033241	211208	Mm.300684	NM_001033241	ENSMUSG00000062791	Gm382	-	predicted gene 382	protein-coding
mm_91166.1	chr10	20689386	20689414	-	1	NA	intron (NM_013875, intron 1 of 12)	L1MA6|LINE|L1	35678	NM_013875	29863	Mm.425617	NM_013875	ENSMUSG00000019990	Pde7b	-	phosphodiesterase 7B	protein-coding
mm_55445.1	chr6	67237889	67237899	-	1	NA	Intergenic	Intergenic	-29085	NM_001113564	66870	Mm.240490	NM_025814	ENSMUSG00000036371	Serbp1	1200009K13Rik|9330147J08Rik|AL022786|Pairbp1	serpine1 mRNA binding protein 1	protein-coding
mm_43955.1	chr5	145231758	145231783	+	1	NA	promoter-TSS (NM_028298)	promoter-TSS (NM_028298)	11	NM_028298	72611	Mm.206555	NM_028298	ENSMUSG00000007812	Zfp655	2700038I16Rik|9030409O18Rik|mKIAA4222	zinc finger protein 655	protein-coding
mm_82131.1	chr9	123529746	123529756	+	1	NA	promoter-TSS (NM_030692)	promoter-TSS (NM_030692)	-131	NM_030692	83493	Mm.273671	NM_030692	ENSMUSG00000025240	Sacm1l	SAC1|Sac1p|mKIAA0851	SAC1 suppressor of actin mutations 1-like (yeast)	protein-coding
mm_7962.1	chr1	133930075	133930092	-	1	NA	Intergenic	Intergenic	-8682	NM_054077	116847	Mm.214514	NM_054077	ENSMUSG00000041577	Prelp	7330409J17Rik|SLRR2A	proline arginine-rich end leucine-rich repeat	protein-coding
mm_172108.1	chr6	3200853	3200854	+	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	-87666	NR_036696	667335	Mm.380219	NR_036696	ENSMUSG00000106779	Gm8579	EG667335	spermatogenesis associated glutamate (E)-rich protein 4a pseudogene	pseudo
mm_95900.1	chr11	58201507	58201538	+	1	NA	5' UTR (NM_018738, exon 2 of 3)	5' UTR (NM_018738, exon 2 of 3)	1966	NM_018738	16145	Mm.33902	NM_018738	ENSMUSG00000078853	Igtp	AW558444|Irgm3	interferon gamma induced GTPase	protein-coding
mm_158364.1	chrX	134808985	134809002	-	1	NA	5' UTR (NM_001166397, exon 1 of 6)	5' UTR (NM_001166397, exon 1 of 6)	228	NM_001166397	67416	Mm.285969	NM_026139	ENSMUSG00000033436	Armcx2	3230401N03Rik|AI043003|ALEX2	armadillo repeat containing, X-linked 2	protein-coding
mm_129277.1	chr15	77153603	77153611	-	1	NA	5' UTR (NM_001110830, exon 1 of 13)	5' UTR (NM_001110830, exon 1 of 13)	205	NM_001110830	93686	Mm.202774	NM_053104	ENSMUSG00000033565	Rbfox2	Fbm2|Fxh|Hrnbp2|Rbm9	RNA binding protein, fox-1 homolog (C. elegans) 2	protein-coding
mm_63672.1	chr7	130519658	130519668	+	1	NA	promoter-TSS (NM_001136054)	promoter-TSS (NM_001136054)	-83	NM_013799	11907	Mm.216321	NM_013799	ENSMUSG00000030850	Ate1	AI225793|AW547406	arginyltransferase 1	protein-coding
mm_150778.1	chr19	44294903	44294919	+	1	NA	exon (NM_009128, exon 2 of 6)	exon (NM_009128, exon 2 of 6)	1235	NM_009128	20250	Mm.487021	NM_009128	ENSMUSG00000025203	Scd2	Mir5114|Scd-2|mir-5114|swty	stearoyl-Coenzyme A desaturase 2	protein-coding
mm_148141.1	chr18	77016582	77016592	-	1	NA	intron (NM_027721, intron 3 of 13)	intron (NM_027721, intron 3 of 13)	30709	NM_027721	71206	Mm.35803	NM_027721	ENSMUSG00000025420	Katnal2	3110023G01Rik|4933439B08Rik	katanin p60 subunit A-like 2	protein-coding
mm_132124.1	chr16	31754560	31754581	+	1	NA	5' UTR (NM_001252436, exon 1 of 23)	5' UTR (NM_001252436, exon 1 of 23)	220	NM_001252436	13383	Mm.382	NM_007862	ENSMUSG00000022770	Dlg1	B130052P05Rik|Dlgh1|E-dlg/SAP97|SAP-97|SAP97|mKIAA4187	discs, large homolog 1 (Drosophila)	protein-coding
mm_9012.1	chr1	166047842	166047850	-	1	NA	Intergenic	Intergenic	-45212	NM_011137	18986	Mm.245261	NM_011137	ENSMUSG00000026565	Pou2f1	2810482H01Rik|NF-A1|Oct-1|Oct1|Otf-1|Otf1	POU domain, class 2, transcription factor 1	protein-coding
mm_96623.1	chr11	69134136	69134164	+	1	NA	intron (NM_011786, intron 8 of 14)	intron (NM_011786, intron 8 of 14)	7773	NM_011786	23801	Mm.41989	NM_011786	ENSMUSG00000020892	Aloxe3	e-LOX-3|eLOX-3	arachidonate lipoxygenase 3	protein-coding
mm_57963.1	chr6	135254298	135254316	-	1	NA	promoter-TSS (NM_010352)	promoter-TSS (NM_010352)	29	NM_010352	14840	Mm.272306	NM_010352	ENSMUSG00000030206	Gsg1	-	germ cell associated 1	protein-coding
mm_46677.1	chr5	109555537	109555547	-	1	NA	exon (NM_001164735, exon 6 of 8)	exon (NM_001164735, exon 6 of 8)	3451	NM_016715	57914	Mm.35771	NM_016715	ENSMUSG00000033467	Crlf2	CRLM2|Ly114|Tpte2|Tslpr	cytokine receptor-like factor 2	protein-coding
mm_16346.1	chr2	174346255	174346314	+	1	NA	non-coding (NR_003258, exon 13 of 13)	non-coding (NR_003258, exon 13 of 13)	16195	NM_001077510	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_3319.1	chr1	137908913	137908949	+	1	NA	Intergenic	Intergenic	-57524	NR_029795	735252		NR_029795	ENSMUSG00000065565	Mir181a-1	Mirn181a-1|Mirn213|miR-213|mir-181a-1|mmu-mir-213	microRNA 181a-1	ncRNA
mm_152766.1	chr19	20390997	20391010	-	1	NA	promoter-TSS (NM_010730)	promoter-TSS (NM_010730)	-332	NM_010730	16952	Mm.248360	NM_010730	ENSMUSG00000024659	Anxa1	Anx-1|Anx-A1|C430014K04Rik|Lpc-1|Lpc1	annexin A1	protein-coding
mm_65865.1	chr7	29481615	29481621	-	1	NA	intron (NM_001081028, intron 2 of 22)	intron (NM_001081028, intron 2 of 22)	23842	NM_001081028	74206	Mm.447042	NM_001081028	ENSMUSG00000030583	Sipa1l3	2610511M17Rik	signal-induced proliferation-associated 1 like 3	protein-coding
mm_132820.1	chr16	45224129	45224139	+	1	NA	promoter-TSS (NM_001037719)	promoter-TSS (NM_001037719)	-203	NM_001037719	208154	Mm.38199	NM_177584	ENSMUSG00000052013	Btla	A630002H24	B and T lymphocyte associated	protein-coding
mm_137551.1	chr17	27561341	27561347	+	1	NA	intron (NM_001166546, intron 3 of 4)	intron (NM_001166546, intron 3 of 4)	4383	NM_001002895	106672	Mm.61488	NM_001002895	ENSMUSG00000062753	AI413582	AI854251	expressed sequence AI413582	protein-coding
mm_77297.1	chr8	116993460	116993538	-	1	NA	promoter-TSS (NM_026572)	promoter-TSS (NM_026572)	-50	NM_026572	68133	Mm.258462	NM_026572	ENSMUSG00000034424	Gcsh	1100001L02Rik|5730591C18Rik	glycine cleavage system protein H (aminomethyl carrier)	protein-coding
mm_132098.1	chr16	31325277	31325294	+	1	NA	Intergenic	Intergenic	-10477	NM_001301354	11815	Mm.2082	NM_007470	ENSMUSG00000022548	Apod	-	apolipoprotein D	protein-coding
mm_67859.1	chr7	98993550	98993551	-	1	NA	intron (NM_178635, intron 8 of 14)	L1M4|LINE|L1	147594	NM_178635	78610	Mm.323072	NM_178635	ENSMUSG00000035354	Uvrag	9530039D02Rik|AI648770|BB124205|Uvrag1|Uvragl	UV radiation resistance associated gene	protein-coding
mm_43486.1	chr5	136919138	136919188	+	1	NA	promoter-TSS (NR_015555)	promoter-TSS (NR_015555)	17	NR_015555	66752	Mm.135764	NR_015555	ENSMUSG00000097908	4933404O12Rik	AW494809	RIKEN cDNA 4933404O12 gene	ncRNA
mm_159729.1	chr5	44094698	44094698	-	1	NA	promoter-TSS (NM_001163583)	promoter-TSS (NM_001163583)	70	NM_001163581	19126	Mm.6250	NM_008935	ENSMUSG00000029086	Prom1	4932416E19Rik|AC133|CD133|Prom|Prom-1|Proml1	prominin 1	protein-coding
mm_23351.1	chr3	55055218	55055236	+	1	NA	promoter-TSS (NM_007628)	promoter-TSS (NM_007628)	-15	NR_040593	70970	Mm.251485	NR_040593	ENSMUSG00000106589	4931419H13Rik	-	RIKEN cDNA 4931419H13 gene	ncRNA
mm_104216.1	chr11	88344248	88344260	-	1	NA	3' UTR (NM_054043, exon 14 of 14)	3' UTR (NM_054043, exon 14 of 14)	-8519	NR_039545	100628571		NR_039545	ENSMUSG00000092985	Mir378b	mir-378b|mmu-mir-378b	microRNA 378b	ncRNA
mm_111615.1	chr12	102403475	102403512	-	1	NA	exon (NM_011175, exon 6 of 14)	exon (NM_011175, exon 6 of 14)	36320	NM_011175	19141	Mm.17185	NM_011175	ENSMUSG00000021190	Lgmn	AEP|AI746452|AU022324|Prsc1	legumain	protein-coding
mm_76158.1	chr8	82367602	82367614	-	1	NA	intron (NM_008357, intron 2 of 7)	intron (NM_008357, intron 2 of 7)	34978	NM_001254747	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_78111.1	chr9	20642685	20642698	+	1	NA	promoter-TSS (NM_025401)	promoter-TSS (NM_025401)	115	NM_013911	30843	Mm.24608	NM_013911	ENSMUSG00000066892	Fbxl12	3110048D16Rik|Fbl12	F-box and leucine-rich repeat protein 12	protein-coding
mm_25491.1	chr3	109340663	109340670	+	1	NA	promoter-TSS (NM_020505)	promoter-TSS (NM_020505)	-17	NM_020505	57257	Mm.282257	NM_020505	ENSMUSG00000033721	Vav3	A530094I06Rik|AA986410|Idd18.1	vav 3 oncogene	protein-coding
mm_107254.1	chr12	28653900	28653903	+	1	NA	intron (NM_011275, intron 3 of 7)	intron (NM_011275, intron 3 of 7)	4299	NM_001286865	19819	Mm.10152	NM_011275	ENSMUSG00000020630	Rnaseh1	-	ribonuclease H1	protein-coding
mm_131884.1	chr16	23224968	23224985	+	1	NA	5' UTR (NM_145933, exon 1 of 8)	5' UTR (NM_145933, exon 1 of 8)	236	NM_145933	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_139516.1	chr17	56584962	56584968	+	1	NA	promoter-TSS (NM_001163300)	promoter-TSS (NM_001163300)	-17	NM_001163300	224903	Mm.255066	NM_001163300	ENSMUSG00000071054	Safb	3110021E02Rik|5330423C17Rik|AU018122|D18386|E130307D12|HAP|HET|SAF-B1|SAFB1	scaffold attachment factor B	protein-coding
mm_33080.1	chr4	123905131	123905150	+	1	NA	intron (NM_019660, intron 1 of 4)	CpG	127	NM_019660	56309	Mm.446553	NM_019660	ENSMUSG00000028647	Mycbp	5730488M09Rik|AW552132|AW742590|Amy-1	MYC binding protein	protein-coding
mm_5965.1	chr1	56978495	56978511	-	1	NA	Intergenic	Intergenic	7034	NR_024325	329160	Mm.419039	NR_024325	ENSMUSG00000087022	9130024F11Rik	B530002L08|EG329160	RIKEN cDNA 9130024F11 gene	ncRNA
mm_134957.1	chr16	31311148	31311165	-	1	NA	5' UTR (NM_007470, exon 3 of 6)	5' UTR (NM_007470, exon 3 of 6)	3652	NM_001301353	11815	Mm.2082	NM_007470	ENSMUSG00000022548	Apod	-	apolipoprotein D	protein-coding
mm_163230.1	chr11	103104817	103104826	+	1	NA	exon (NM_025988, exon 7 of 10)	exon (NM_025988, exon 7 of 10)	3133	NM_025988	67131	Mm.390367	NM_025988	ENSMUSG00000056938	Acbd4	2010009P05Rik|2010015A21Rik|AI849317	acyl-Coenzyme A binding domain containing 4	protein-coding
mm_81432.1	chr9	109095251	109095271	+	1	NA	promoter-TSS (NM_172775)	promoter-TSS (NM_172775)	-175	NM_172775	235611	Mm.53862	NM_172775	ENSMUSG00000053646	Plxnb1	2900002G15Rik|AU042020|mKIAA0407	plexin B1	protein-coding
mm_144276.1	chr18	11657522	11657553	+	1	NA	non-coding (NR_045526, exon 1 of 18)	non-coding (NR_045526, exon 1 of 18)	188	NM_001081223	225182	Mm.154275	NM_175458	ENSMUSG00000041238	Rbbp8	9930104E21Rik|CtIP|RBBP-8|RIM|SAE2	retinoblastoma binding protein 8	protein-coding
mm_135697.1	chr16	52451876	52451887	-	1	NA	intron (NM_009655, intron 1 of 15)	AT_rich|Low_complexity|Low_complexity	1200	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_142227.1	chr17	37480752	37480768	-	1	NA	TTS (NM_008204)	TTS (NM_008204)	2769	NM_008204	14990	Mm.329041	NM_008204	ENSMUSG00000016283	H2-M2	H-2M2|Thy19.4	histocompatibility 2, M region locus 2	protein-coding
mm_156755.1	chrX	160434902	160434906	+	1	NA	intron (NM_001079847, intron 2 of 26)	intron (NM_001079847, intron 2 of 26)	44214	NM_001290445	237175	Mm.213016	NM_178712	ENSMUSG00000031298	Adgrg2	AW212196|B830041D06Rik|Gpr64|Me6	adhesion G protein-coupled receptor G2	protein-coding
mm_114696.1	chr13	83504033	83504050	+	1	NA	promoter-TSS (NM_025282)	promoter-TSS (NM_025282)	7	NM_001347564	17260	Mm.24001	NM_025282	ENSMUSG00000005583	Mef2c	5430401D19Rik|9930028G15Rik|AV011172|Mef2	myocyte enhancer factor 2C	protein-coding
mm_79429.1	chr9	55938266	55938296	+	1	NA	promoter-TSS (NM_001081341)	promoter-TSS (NM_001081341)	-166	NM_001081341	244891	Mm.86588	NM_175536	ENSMUSG00000034007	Scaper	C430017I08|D530014O03Rik|Zfp291	S phase cyclin A-associated protein in the ER	protein-coding
mm_14399.1	chr2	130040416	130040448	+	1	NA	intron (NM_009374, intron 9 of 12)	intron (NM_009374, intron 9 of 12)	-24024	NR_105757	102466628		NR_105757	ENSMUSG00000098347	Mir6339	Gm27848|mmu-mir-6339	microRNA 6339	ncRNA
mm_38976.1	chr4	150909781	150909791	-	1	NA	5' UTR (NM_020569, exon 1 of 7)	5' UTR (NM_020569, exon 1 of 7)	135	NM_020569	57320	Mm.277349	NM_020569	ENSMUSG00000028964	Park7	DJ-1|Dj1	Parkinson disease (autosomal recessive, early onset) 7	protein-coding
mm_156298.1	chrX	136837627	136837647	+	1	NA	3' UTR (NM_011123, exon 7 of 7)	3' UTR (NM_011123, exon 7 of 7)	14891	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_15263.1	chr2	155047605	155047622	+	1	NA	intron (NM_015770, intron 2 of 3)	intron (NM_015770, intron 2 of 3)	26884	NM_016661	269378	Mm.330692	NM_016661	ENSMUSG00000027597	Ahcy	AA987153|AL024110|CuBP|SAHH	S-adenosylhomocysteine hydrolase	protein-coding
mm_103114.1	chr11	69996871	69996875	-	1	NA	promoter-TSS (NM_001291127)	promoter-TSS (NM_001291127)	-68	NM_001291126	78246	Mm.20805	NM_030064	ENSMUSG00000018572	Phf23	JUNE-1	PHD finger protein 23	protein-coding
mm_92946.1	chr10	85102488	85102549	-	1	NA	promoter-TSS (NM_001013028)	promoter-TSS (NM_001013028)	-23	NM_010214	14202	Mm.46163	NM_010214	ENSMUSG00000050035	Fhl4	-	four and a half LIM domains 4	protein-coding
mm_85553.1	chr9	106685869	106685890	-	1	NA	promoter-TSS (NM_001081654)	promoter-TSS (NM_001081654)	-63	NM_011573	21767	Mm.22266	NM_011573	ENSMUSG00000040813	Tex264	TEG-264	testis expressed gene 264	protein-coding
mm_132013.1	chr16	25865816	25865822	+	1	NA	intron (NM_001127259, intron 7 of 13)	intron (NM_001127259, intron 7 of 13)	63903	NM_001127264	22061	Mm.20894	NM_011641	ENSMUSG00000022510	Trp63	AI462811|Ket|P51/P63|P63|P73l|Tp63|Trp53rp1	transformation related protein 63	protein-coding
mm_41879.1	chr5	105198418	105198431	+	1	NA	Intergenic	Intergenic	41109	NM_001039646	626578	Mm.275893	NM_001039646	ENSMUSG00000105096	Gbp10	-	guanylate-binding protein 10	protein-coding
mm_102227.1	chr11	54910106	54910113	-	1	NA	TTS (NM_021327)	TTS (NM_021327)	7255	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_148568.1	chr19	4839410	4839482	+	1	NA	promoter-TSS (NM_016892)	promoter-TSS (NM_016892)	80	NM_207268	399599	Mm.444704	NM_207268	ENSMUSG00000067872	Ccdc87	4931419P11Rik	coiled-coil domain containing 87	protein-coding
mm_108925.1	chr12	100898465	100898500	+	1	NA	intron (NM_001177673, intron 1 of 2)	intron (NM_001177673, intron 1 of 2)	1042	NM_001177674	238377	Mm.32160	NM_175493	ENSMUSG00000047415	Gpr68	BB131428|Ogr1	G protein-coupled receptor 68	protein-coding
mm_123643.1	chr14	68655707	68655719	-	1	NA	non-coding (NR_102399, exon 1 of 22)	non-coding (NR_102399, exon 1 of 22)	129	NM_010082	13522	Mm.117450	NM_010082	ENSMUSG00000014725	Adam28	C130072N01Rik|D430033C21Rik|Dtgn1|MDC-L|MDCL|TECADAM|eMDCII	a disintegrin and metallopeptidase domain 28	protein-coding
mm_130740.1	chr15	101256002	101256006	-	1	NA	Intergenic	Intergenic	-10842	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_163027.1	chr11	49846939	49846949	+	1	NA	5' UTR (NM_001163671, exon 1 of 12)	5' UTR (NM_001163671, exon 1 of 12)	193	NM_016961	26420	Mm.68933	NM_016961	ENSMUSG00000020366	Mapk9	AI851083|JNK2|Prkm9|p54aSAPK	mitogen-activated protein kinase 9	protein-coding
mm_8166.1	chr1	136960472	136960494	-	1	NA	promoter-TSS (NM_030676)	promoter-TSS (NM_030676)	-35	NM_030676	26424	Mm.16794	NM_030676	ENSMUSG00000026398	Nr5a2	AU020803|D1Ertd308e|Ftf|LRH-1|UF2-H3B	nuclear receptor subfamily 5, group A, member 2	protein-coding
mm_51017.1	chr6	65024964	65024974	+	1	NA	Intergenic	Intergenic	-17698	NM_007958	13990	Mm.99113	NM_007958	ENSMUSG00000029920	Smarcad1	AV081750|AW226546|D6Pas1|Etl1|mKIAA1122	SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1	protein-coding
mm_144626.1	chr18	32938902	32938910	+	1	NA	promoter-TSS (NM_009793)	promoter-TSS (NM_009793)	-135	NM_009793	12326	Mm.222329	NM_009793	ENSMUSG00000038128	Camk4	A430110E23Rik|AI666733|CaMKIV|CaMKIV/Gr|D18Bwg0362e	calcium/calmodulin-dependent protein kinase IV	protein-coding
mm_66408.1	chr7	44479794	44479808	-	1	NA	Intergenic	Intergenic	-4716	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_54275.1	chr6	29164655	29164707	-	1	NA	promoter-TSS (NM_133925)	promoter-TSS (NM_133925)	43	NM_133925	68272	Mm.40802	NM_026650	ENSMUSG00000029701	Rbm28	2810480G15Rik|AI503051	RNA binding motif protein 28	protein-coding
mm_75272.1	chr8	40862240	40862248	-	1	NA	promoter-TSS (NM_001044740)	promoter-TSS (NM_001044740)	-123	NM_007514	11988	Mm.4676	NM_007514	ENSMUSG00000031596	Slc7a2	20.5|AI158848|Atrc2|CAT-2|Cat2|Tea	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	protein-coding
mm_75016.1	chr8	29219628	29219640	-	1	NA	promoter-TSS (NM_001347499)	promoter-TSS (NM_001347499)	2	NM_001347499	210801	Mm.248433	NM_153135	ENSMUSG00000063626	Unc5d	D930029E11Rik|Unc5h4|mKIAA1777	unc-5 netrin receptor D	protein-coding
mm_88807.1	chr10	80755293	80755303	+	1	NA	promoter-TSS (NM_199322)	promoter-TSS (NM_199322)	92	NM_199322	208266	Mm.152371	NM_199322	ENSMUSG00000061589	Dot1l	A630076O07|AW907654|Dot1|KMT4|mDot1	DOT1-like, histone H3 methyltransferase (S. cerevisiae)	protein-coding
mm_40590.1	chr5	64230286	64230312	+	1	NA	promoter-TSS (NM_001289514)	promoter-TSS (NM_001289514)	-58	NM_001289514	57915	Mm.286353	NM_019636	ENSMUSG00000029174	Tbc1d1	1110062G02Rik|AI385682|AW555803|Nob1|Nobq1|Tbc1|mKIAA1108	TBC1 domain family, member 1	protein-coding
mm_29274.1	chr3	107518002	107518023	-	1	NA	promoter-TSS (NM_001293689)	promoter-TSS (NM_001293689)	6	NM_001293689	229706	Mm.212867	NM_172271	ENSMUSG00000027894	Slc6a17	D130012J15Rik|Ntt4	solute carrier family 6 (neurotransmitter transporter), member 17	protein-coding
mm_17850.1	chr2	34733098	34733108	-	1	NA	intron (NM_025709, intron 2 of 26)	PB1D7|SINE|Alu	22129	NM_025709	66691	Mm.156452	NM_025709	ENSMUSG00000026867	Gapvd1	2010005B09Rik|4432404J10Rik|AW108497|Gapex-5|RAP6|RME-6|mKIAA1521	GTPase activating protein and VPS9 domains 1	protein-coding
mm_78620.1	chr9	37555694	37555704	+	1	NA	Intergenic	Intergenic	-2954	NM_022029	64011	Mm.335065	NM_022029	ENSMUSG00000053310	Nrgn	0710001B06Rik|AI838505|NG|NG/RC3|Pss1|R75334|RC3	neurogranin	protein-coding
mm_1750.1	chr1	75507168	75507184	+	1	NA	promoter-TSS (NM_178884)	promoter-TSS (NM_178884)	99	NM_010564	16322	Mm.1100	NM_010564	ENSMUSG00000032968	Inha	AW555078	inhibin alpha	protein-coding
mm_111268.1	chr12	85280343	85280347	-	1	NA	promoter-TSS (NM_025421)	promoter-TSS (NM_025421)	90	NM_025421	66204	Mm.311985	NM_025421	ENSMUSG00000008822	Acyp1	1110039O14Rik|AI325944	acylphosphatase 1, erythrocyte (common) type	protein-coding
mm_79297.1	chr9	51765305	51765317	+	1	NA	promoter-TSS (NM_175535)	promoter-TSS (NM_175535)	-41	NM_175535	244867	Mm.400352	NM_175535	ENSMUSG00000053199	Arhgap20	6530403F17Rik|A530023E23Rik|RARhoGAP|mKIAA1391	Rho GTPase activating protein 20	protein-coding
mm_132826.1	chr16	45224946	45224958	+	1	NA	intron (NM_177584, intron 1 of 5)	intron (NM_177584, intron 1 of 5)	615	NM_177584	208154	Mm.38199	NM_177584	ENSMUSG00000052013	Btla	A630002H24	B and T lymphocyte associated	protein-coding
mm_97293.1	chr11	76261457	76261461	+	1	NA	intron (NM_008750, intron 7 of 7)	intron (NM_008750, intron 7 of 7)	17723	NM_183263	67390	Mm.24886	NM_183263	ENSMUSG00000038046	Rnmtl1	4833420N02Rik|AI255153|HC90|Mrm3	RNA methyltransferase like 1	protein-coding
mm_14749.1	chr2	144556236	144556298	+	1	NA	promoter-TSS (NM_001252545)	promoter-TSS (NM_001252545)	38	NM_001252545	27054	Mm.248492	NM_019787	ENSMUSG00000027429	Sec23b	-	SEC23 homolog B, COPII coat complex component	protein-coding
mm_165755.1	chr3	112202871	112202871	+	1	NA	Intergenic	L1_Mur2|LINE|L1	320968	NR_045362	625585	Mm.389497	NR_045362	ENSMUSG00000104543	Gm6602	-	predicted gene 6602	ncRNA
mm_156942.1	chrX	169936750	169936756	+	1	NA	intron (NM_001290505, intron 2 of 9)	intron (NM_001290505, intron 2 of 9)	42164	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_65510.1	chr7	25754682	25754692	-	1	NA	promoter-TSS (NM_178089)	promoter-TSS (NM_178089)	14	NM_178089	232989	Mm.254223	NM_144922	ENSMUSG00000040725	Hnrnpul1	E130317O14Rik|E1B-AP5|E1BAP5|Hnrnpul|Hnrpul1	heterogeneous nuclear ribonucleoprotein U-like 1	protein-coding
mm_44186.1	chr5	151400240	151400250	+	1	NA	intron (NR_045700, intron 2 of 3)	RLTR51B_Mm|LTR|ERVK?	-6259	NR_131166	100042166	Mm.443286	NR_131166	ENSMUSG00000097321	Gm3704	-	predicted gene 3704	ncRNA
mm_18140.1	chr2	45043605	45043637	-	1	NA	intron (NM_001289521, intron 1 of 8)	intron (NM_001289521, intron 1 of 8)	-20444	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_13781.1	chr2	118779704	118779777	+	1	NA	promoter-TSS (NM_170593)	promoter-TSS (NM_170593)	21	NM_170593	214240	Mm.221499	NM_170593	ENSMUSG00000040035	Disp2	AI840597|B230210L08Rik|DispB|mKIAA1742	dispatched RND tramsporter family member 2	protein-coding
mm_31149.1	chr4	43394954	43394958	+	1	NA	intron (NM_001037709, intron 1 of 11)	intron (NM_001037709, intron 1 of 11)	-11546	NM_199057	100213	Mm.235730	NM_199057	ENSMUSG00000035969	Rusc2	AI840675|mKIAA0375	RUN and SH3 domain containing 2	protein-coding
mm_68396.1	chr7	109545281	109545299	-	1	NA	intron (NM_001001326, intron 4 of 19)	intron (NM_001001326, intron 4 of 19)	25158	NR_028079	100302499	Mm.482651	NR_028079	ENSMUSG00000065016	Snora3	MBI-28	small nucleolar RNA, H/ACA box 3	snoRNA
mm_119750.1	chr14	54153207	54153231	+	1	NA	Intergenic	Intergenic	100710	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_164327.1	chr16	7039394	7039421	+	1	NA	intron (NM_021477, intron 5 of 16)	intron (NM_021477, intron 5 of 16)	-30428	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_151336.1	chr19	55894949	55894960	+	1	NA	promoter-TSS (NM_001142924)	promoter-TSS (NM_001142924)	-367	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_32619.1	chr4	114406207	114406256	+	1	NA	promoter-TSS (NM_001085549)	promoter-TSS (NM_001085549)	-493	NM_001085549	666048	Mm.331779	NM_001085549	ENSMUSG00000070867	Trabd2b	Gm12824|Hkat|OTTMUSG00000008561	TraB domain containing 2B	protein-coding
mm_171601.1	chr4	147807055	147807065	-	1	NA	intron (NM_001127189, intron 2 of 5)	intron (NM_001127189, intron 2 of 5)	2728	NM_001127189	100041677	Mm.327194	NM_001127189	ENSMUSG00000078495	Zfp984	Gm13157|OTTMUSG00000010679	zinc finger protein 984	protein-coding
mm_15108.1	chr2	153601143	153601183	+	1	NA	Intergenic	Intergenic	31618	NM_001195390	99311	Mm.294478	NM_133850	ENSMUSG00000056941	Commd7	2310010I22Rik|AW060956|mU3	COMM domain containing 7	protein-coding
mm_124156.1	chr14	93256912	93256916	-	1	NA	intron (NM_001346722, intron 4 of 4)	intron (NM_001346722, intron 4 of 4)	631974	NM_001271800	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding
mm_168055.1	chrY	90812665	90812797	-	1	NA	intron (NM_133362, intron 2 of 3)	IMPB_01|Satellite|Satellite	26675	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_171306.1	chr3	94054883	94054889	-	1	NA	promoter-TSS (NM_001163730).2	promoter-TSS (NM_001163730).2	-1	NM_001163730	668359	Mm.80593	NM_001163730	ENSMUSG00000094328	Gm9125	EG668359	predicted gene 9125	protein-coding
mm_14062.1	chr2	122640868	122640890	+	1	NA	promoter-TSS (NR_030547)	promoter-TSS (NR_030547)	76	NR_030547	387165		NR_030547	ENSMUSG00000076309	Mir147	Mirn147|mmu-mir-147	microRNA 147	ncRNA
mm_60264.1	chr7	43824520	43824557	+	1	NA	promoter-TSS (NM_011177)	promoter-TSS (NM_011177)	-6	NM_001164697	19144	Mm.3944	NM_011177	ENSMUSG00000050063	Klk6	AI849898|BSP|Bssp|Klk29|MSP|Prss18|Prss9|neurosin	kallikrein related-peptidase 6	protein-coding
mm_13476.1	chr2	105691589	105691596	+	1	NA	exon (NM_013627, exon 8 of 13)	exon (NM_013627, exon 8 of 13)	9129	NM_001310145	18508	Mm.3608	NM_013627	ENSMUSG00000027168	Pax6	1500038E17Rik|AEY11|Dey|Gsfaey11|Pax-6|Sey	paired box 6	protein-coding
mm_19001.1	chr2	76870487	76870511	-	1	NA	exon (NM_011652, exon 103 of 313)	exon (NM_011652, exon 103 of 313)	112048	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_148707.1	chr19	5801934	5801946	+	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	732	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_84792.1	chr9	77046262	77046266	-	1	NA	promoter-TSS (NM_012033)	promoter-TSS (NM_012033)	-483	NM_012033	26944	Mm.23199	NM_012033	ENSMUSG00000032357	Tinag	AI452335|TIN-ag	tubulointerstitial nephritis antigen	protein-coding
mm_70606.1	chr8	13404907	13404912	+	1	NA	promoter-TSS (NM_011881)	promoter-TSS (NM_011881)	-172	NM_011881	24013	Mm.257501	NM_011881	ENSMUSG00000031450	Grk1	Gprk1|Rhok|Rk	G protein-coupled receptor kinase 1	protein-coding
mm_80919.1	chr9	100899124	100899125	+	1	NA	intron (NM_009282, intron 21 of 33)	intron (NM_009282, intron 21 of 33)	135760	NM_001311149	66904	Mm.335385	NM_025835	ENSMUSG00000032527	Pccb	1300012P06Rik|AI314687|R74805	propionyl Coenzyme A carboxylase, beta polypeptide	protein-coding
mm_23142.1	chr3	38885889	38885905	+	1	NA	Intergenic	CpG	-1043	NM_183221	329628	Mm.316210	NM_183221	ENSMUSG00000046743	Fat4	6030410K14Rik|9430004M15	FAT atypical cadherin 4	protein-coding
mm_107056.1	chr12	16653710	16653763	+	1	NA	exon (NM_008747, exon 1 of 4)	exon (NM_008747, exon 1 of 4)	266	NM_008747	18217	Mm.281715	NM_008747	ENSMUSG00000020591	Ntsr2	NT2R|NTRL	neurotensin receptor 2	protein-coding
mm_152366.1	chr19	10101728	10101750	-	1	NA	promoter-TSS (NM_019699)	promoter-TSS (NM_019699)	-236	NM_019699	56473	Mm.38901	NM_019699	ENSMUSG00000024665	Fads2	2900042M13Rik|Fadsd2	fatty acid desaturase 2	protein-coding
mm_115819.1	chr13	19927915	19927921	-	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-103661	NM_181754	353346	Mm.239268	NM_181754	ENSMUSG00000053101	Gpr141	PGR13	G protein-coupled receptor 141	protein-coding
mm_24548.1	chr3	93397934	93397944	+	1	NA	exon (NM_009100, exon 3 of 3)	exon (NM_009100, exon 3 of 3)	4240	NM_009100	20129	Mm.1417	NM_009100	ENSMUSG00000041984	Rptn	-	repetin	protein-coding
mm_128607.1	chr15	58389264	58389280	-	1	NA	promoter-TSS (NM_027211)	promoter-TSS (NM_027211)	2	NM_027211	69787	Mm.237985	NM_027211		Anxa13	1810034H17Rik|AV055219	annexin A13	protein-coding
mm_39704.1	chr5	27262069	27262125	+	1	NA	5' UTR (NM_001136060, exon 1 of 26)	5' UTR (NM_001136060, exon 1 of 26)	162	NM_001136060	13483	Mm.42078	NM_010075	ENSMUSG00000061576	Dpp6	B930011P16Rik|D5Buc3|D5Buc4|D5Buc5|DPP VI|Dpp-6|Gm1377|In(5)6H-p|Peplb|Rw	dipeptidylpeptidase 6	protein-coding
mm_171061.1	chr3	108840517	108840533	-	1	NA	promoter-TSS (NM_011504)	promoter-TSS (NM_011504)	-23	NM_011504	20912	Mm.316894	NM_011504	ENSMUSG00000027882	Stxbp3	Munc-18c|Stxbp3a|Sxtbp3|Unc18-3	syntaxin binding protein 3	protein-coding
mm_139680.1	chr17	57415095	57415115	+	1	NA	intron (NM_010130, intron 10 of 21)	L1_Mur2|LINE|L1	56419	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_72034.1	chr8	70776779	70776829	+	1	NA	promoter-TSS (NR_029440)	promoter-TSS (NR_029440)	-58	NR_029440	72093	Mm.271208	NR_029440		2010320M18Rik	-	RIKEN cDNA 2010320M18 gene	ncRNA
mm_151220.1	chr19	53677364	53677379	+	1	NA	promoter-TSS (NM_001170847)	promoter-TSS (NM_001170847)	65	NM_001170847	73713	Mm.313695	NM_001170847	ENSMUSG00000043639	Rbm20	1110018J23Rik|2010003H22Rik|AI646761	RNA binding motif protein 20	protein-coding
mm_70761.1	chr8	21565369	21565373	+	1	NA	promoter-TSS (NM_001270613)	promoter-TSS (NM_001270613)	-15	NM_001270613	100862126	Mm.459166	NM_001270613	ENSMUSG00000094662	Defa36	Gm21498	defensin, alpha, 36	protein-coding
mm_164503.1	chr16	92621286	92621289	+	1	NA	intron (NM_001111022, intron 5 of 6)	intron (NM_001111022, intron 5 of 6)	76042	NM_001111023	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_114245.1	chr13	56627932	56627967	+	1	NA	exon (NM_009369, exon 7 of 17)	exon (NM_009369, exon 7 of 17)	18346	NM_009369	21810	Mm.14455	NM_009369	ENSMUSG00000035493	Tgfbi	68kDa|AI181842|AI747162|Beta-ig|big-h3	transforming growth factor, beta induced	protein-coding
mm_126036.1	chr15	76899909	76899960	+	1	NA	promoter-TSS (NM_025536)	promoter-TSS (NM_025536)	-7	NM_025536	66398	Mm.291716	NM_025536	ENSMUSG00000055041	Commd5	2310065H03Rik|AI854466|D15Ertd81e|Hcarg	COMM domain containing 5	protein-coding
mm_120586.1	chr14	69807795	69807819	+	1	NA	Intergenic	Intergenic	-2262	NM_153514	246710	Mm.102367	NM_153514	ENSMUSG00000022075	Rhobtb2	Dbc2|E130206H14Rik|mKIAA0717	Rho-related BTB domain containing 2	protein-coding
mm_120017.1	chr14	55757831	55757856	+	1	NA	exon (NM_009894, exon 2 of 5)	exon (NM_009894, exon 2 of 5)	581	NM_009894	12684	Mm.466766	NM_009894	ENSMUSG00000022219	Cideb	1110030C18Rik|AI790179|CIDE-B	cell death-inducing DNA fragmentation factor, alpha subunit-like effector B	protein-coding
mm_43354.1	chr5	135187252	135187269	+	1	NA	promoter-TSS (NM_011714)	promoter-TSS (NM_011714)	-63	NM_011714	22385	Mm.40331	NM_011714	ENSMUSG00000002748	Baz1b	C87820|WSTF|Wbscr9	bromodomain adjacent to zinc finger domain, 1B	protein-coding
mm_87492.1	chr10	51495396	51495403	+	1	NA	intron (NM_001291894, intron 7 of 8)	intron (NM_001291894, intron 7 of 8)	4501	NM_013532	14728	Mm.34408	NM_013532	ENSMUSG00000062593	Lilrb4a	CD85K|Gp49b|HM18|ILT3|LIR-5|Lilrb4|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4A	protein-coding
mm_153452.1	chr19	41032046	41032056	-	1	NA	intron (NM_009345, intron 1 of 11)	RSINE1|SINE|B4	2776	NM_009345	21673	Mm.25620	NM_009345	ENSMUSG00000025014	Dntt	Tdt	deoxynucleotidyltransferase, terminal	protein-coding
mm_129211.1	chr15	76522311	76522351	-	1	NA	promoter-TSS (NM_130893)	promoter-TSS (NM_130893)	-202	NM_130893	170729	Mm.218747	NM_130893	ENSMUSG00000048385	Scrt1	-	scratch family zinc finger 1	protein-coding
mm_170661.1	chr2	113728932	113728933	+	1	NA	Intergenic	Intergenic	-20382	NR_040614	75166	Mm.410811	NR_040614	ENSMUSG00000084798	4930533B01Rik	-	RIKEN cDNA 4930533B01 gene	ncRNA
mm_51283.1	chr6	72277393	72277403	+	1	NA	Intergenic	Intergenic	-27212	NM_001282071	20388	Mm.46033	NM_147779	ENSMUSG00000056370	Sftpb	AI562151|SF-B|SP-B|Sftp-3|Sftp3	surfactant associated protein B	protein-coding
mm_171488.1	chr4	146101651	146101665	+	1	NA	intron (NM_001037926, intron 1 of 3)	intron (NM_001037926, intron 1 of 3)	4346	NM_001037926	626316	Mm.270762	NM_001037926	ENSMUSG00000066009	Zfp987	Gm13051|OTTMUSG00000010104|OTTMUSG00000010173	zinc finger protein 987	protein-coding
mm_147678.1	chr18	60660136	60660172	-	1	NA	Intergenic	Intergenic	-3256	NR_045401	328963	Mm.417203	NR_045401		G630071F17Rik	G630071F17	RIKEN cDNA G630071F17 gene	ncRNA
mm_67645.1	chr7	84605747	84605760	-	1	NA	5' UTR (NM_010176, exon 1 of 14)	5' UTR (NM_010176, exon 1 of 14)	189	NM_010176	14085	Mm.3798	NM_010176	ENSMUSG00000030630	Fah	-	fumarylacetoacetate hydrolase	protein-coding
mm_17372.1	chr2	26916506	26916551	-	1	NA	promoter-TSS (NM_013677)	promoter-TSS (NM_013677)	2	NR_073420	20930	Mm.347512	NM_013677	ENSMUSG00000015790	Surf1	0610010F23Rik|Surf-1	surfeit gene 1	protein-coding
mm_117349.1	chr13	69738929	69738951	-	1	NA	exon (NM_001145162, exon 1 of 2)	exon (NM_001145162, exon 1 of 2)	957	NM_001145162	76980	Mm.23960	NM_001145162	ENSMUSG00000052981	Ube2ql1	3110006E14Rik	ubiquitin-conjugating enzyme E2Q family-like 1	protein-coding
mm_42536.1	chr5	115907536	115907550	+	1	NA	intron (NM_007708, intron 8 of 46)	intron (NM_007708, intron 8 of 46)	61887	NM_007708	12704	Mm.8321	NM_007708	ENSMUSG00000029516	Cit	C030025P15Rik|CRIK|CRIK-SK|Cit-k	citron	protein-coding
mm_17960.1	chr2	37422896	37422958	-	1	NA	promoter-TSS (NM_001100591)	promoter-TSS (NM_001100591)	-24	NM_001290642	319817	Mm.288785	NM_001100591	ENSMUSG00000075376	Rc3h2	2900024N03Rik|9430019J22Rik|D930043C02Rik|Mnab|Rnf164	ring finger and CCCH-type zinc finger domains 2	protein-coding
mm_138514.1	chr17	35237760	35237777	+	1	NA	exon (NM_023179, exon 3 of 3)	exon (NM_023179, exon 3 of 3)	1172	NM_023179	66237	Mm.396107	NM_023179	ENSMUSG00000024403	Atp6v1g2	1500002D01Rik|Atp6g2|NG38|VAG2	ATPase, H+ transporting, lysosomal V1 subunit G2	protein-coding
mm_106720.1	chr12	3856396	3856411	+	1	NA	intron (NM_007872, intron 3 of 22)	intron (NM_007872, intron 3 of 22)	5841	NR_045884	100038522	Mm.417270	NR_045884	ENSMUSG00000073242	Dnmt3aos	ENSMUSG00000073242|Gm10485	DNA methyltransferase 3A, opposite strand	ncRNA
mm_154872.1	chrX	20682141	20682156	+	1	NA	exon (NM_009457, exon 25 of 26)	exon (NM_009457, exon 25 of 26)	-5806	NM_001310456	18555	Mm.102574	NM_011049	ENSMUSG00000031065	Cdk16	Crk5|Pctaire1|Pctk1	cyclin-dependent kinase 16	protein-coding
mm_22360.1	chr2	181039161	181039192	-	1	NA	promoter-TSS (NM_015730)	promoter-TSS (NM_015730)	1	NM_015730	11438	Mm.252369	NM_015730	ENSMUSG00000027577	Chrna4	Acra-4|Acra4|EBN1|ENFL1	cholinergic receptor, nicotinic, alpha polypeptide 4	protein-coding
mm_63801.1	chr7	132933582	132933599	+	1	NA	Intergenic	B1_Mus1|SINE|Alu	-16032	NM_207302	360216	Mm.389984	NM_207302	ENSMUSG00000030967	Zranb1	9330160G10Rik|D7Wsu87e|Gm1956|Trabid	zinc finger, RAN-binding domain containing 1	protein-coding
mm_23188.1	chr3	40950639	40950657	+	1	NA	promoter-TSS (NM_001040399)	promoter-TSS (NM_001040399)	17	NM_001040399	214048	Mm.46782	NM_027663	ENSMUSG00000025762	Larp1b	1700108L22Rik|4933421B21Rik|AA690246|Larp2	La ribonucleoprotein domain family, member 1B	protein-coding
mm_112323.1	chr12	115312649	115312655	-	1	NA	Intergenic	Intergenic	383142	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
mm_145788.1	chr18	65172150	65172153	+	1	NA	intron (NM_001114386, intron 13 of 30)	T-rich|Low_complexity|Low_complexity	-76710	NR_029600	387231		NR_029600	ENSMUSG00000065402	Mir122	Mir122a|Mirn122a|mir-122|mmu-mir-122	microRNA 122	ncRNA
mm_85475.1	chr9	105828055	105828066	-	1	NA	promoter-TSS (NM_001102607)	promoter-TSS (NM_001102607)	25	NM_001102607	245026	Mm.482507	NM_172927	ENSMUSG00000043719	Col6a6	E330019B14|E330026B02Rik	collagen, type VI, alpha 6	protein-coding
mm_111011.1	chr12	78980713	78980719	-	1	NA	intron (NM_178745, intron 1 of 2)	intron (NM_178745, intron 1 of 2)	2762	NM_001170401	268567	Mm.341747	NM_178745	ENSMUSG00000046157	Tmem229b	6330442E10Rik|9830138K24|AU019070	transmembrane protein 229B	protein-coding
mm_59903.1	chr7	30321754	30321774	+	1	NA	3' UTR (NM_001033140, exon 1 of 1)	3' UTR (NM_001033140, exon 1 of 1)	611	NM_001033140	68332	Mm.6844	NM_001033140	ENSMUSG00000074211	Sdhaf1	0610010E21Rik|AI430885|AW490662|Lyrm8	succinate dehydrogenase complex assembly factor 1	protein-coding
mm_81400.1	chr9	109017373	109017398	+	1	NA	intron (NM_173019, intron 9 of 13)	intron (NM_173019, intron 9 of 13)	-21182	NM_025858	66940	Mm.196533	NM_025858	ENSMUSG00000025647	Shisa5	2310008D10Rik|6430628I05Rik|Scotin|mShisa5	shisa family member 5	protein-coding
mm_108188.1	chr12	76573105	76573115	+	1	NA	intron (NM_153804, intron 16 of 18)	intron (NM_153804, intron 16 of 18)	-25185	NR_046044	100504549	Mm.440349	NR_046044		AI463170	-	expressed sequence AI463170	ncRNA
mm_101669.1	chr11	37104352	37104353	-	1	NA	Intergenic	Intergenic	-160111	NM_011856	23964	Mm.439889	NM_011856	ENSMUSG00000049336	Tenm2	Odz2|Odz3|Ten-2|Ten-m2	teneurin transmembrane protein 2	protein-coding
mm_20381.1	chr2	128802676	128802680	-	1	NA	TTS (NM_008587)	TTS (NM_008587)	-15625	NM_028248	72477	Mm.259688	NM_028248	ENSMUSG00000014353	Tmem87b	2610301K12Rik|2810431I02Rik|AU014804	transmembrane protein 87B	protein-coding
mm_34564.1	chr4	149854568	149854578	+	1	NA	Intergenic	Intergenic	-80306	NM_027460	70556	Mm.41877	NM_027460	ENSMUSG00000028982	Slc25a33	5730438N18Rik|Pnc1	solute carrier family 25, member 33	protein-coding
mm_74402.1	chr8	3279607	3279622	-	1	NA	promoter-TSS (NM_001330056)	promoter-TSS (NM_001330056)	3	NM_010568	16337	Mm.268003	NM_010568	ENSMUSG00000005534	Insr	4932439J01Rik|CD220|D630014A15Rik|IR|IR-A|IR-B	insulin receptor	protein-coding
mm_17749.1	chr2	32716663	32716665	-	1	NA	Intergenic	RMER19B|LTR|ERVK	-3692	NR_039536	100628606		NR_039536	ENSMUSG00000105841	Mir3960	mmu-mir-3960	microRNA 3960	ncRNA
mm_65548.1	chr7	27131235	27131256	-	1	NA	exon (NM_007817, exon 8 of 10)	exon (NM_007817, exon 8 of 10)	11290	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_153734.1	chr19	44410476	44410491	-	1	NA	Intergenic	Intergenic	-2774	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_45186.1	chr5	52034200	52034245	-	1	NA	Intergenic	Intergenic	101795	NR_105845	102466648		NR_105845	ENSMUSG00000098726	Mir6417	Gm27334|mmu-mir-6417	microRNA 6417	ncRNA
mm_85465.1	chr9	105495476	105495489	-	1	NA	promoter-TSS (NM_175025)	promoter-TSS (NM_175025)	-349	NM_001253836	235574	Mm.326247	NM_175025	ENSMUSG00000032570	Atp2c1	1700121J11Rik|ATP2C1A|AW061228|BCPM|D930003G21Rik|HHD|SPCA|pmr1	ATPase, Ca++-sequestering	protein-coding
mm_149831.1	chr19	24556327	24556337	+	1	NA	promoter-TSS (NM_008846)	promoter-TSS (NM_008846)	-505	NM_008846	18719	Mm.217214	NM_008846	ENSMUSG00000024867	Pip5k1b	PI4P5K-I[b]|PIP5K1-beta|PIP5KIbeta|Pipk5b|STM7	phosphatidylinositol-4-phosphate 5-kinase, type 1 beta	protein-coding
mm_168703.1	chr11	98027867	98027885	+	1	NA	exon (NM_001159483, exon 2 of 6)	exon (NM_001159483, exon 2 of 6)	952	NM_009078	19921	Mm.10247	NM_009078	ENSMUSG00000017404	Rpl19	-	ribosomal protein L19	protein-coding
mm_17305.1	chr2	26352235	26352237	-	1	NA	promoter-TSS (NM_001139504)	promoter-TSS (NM_001139504)	-126	NM_001139504	52838	Mm.31239	NM_026828	ENSMUSG00000075467	Dnlz	1110034G11Rik|D2Bwg1335e|HEP1	DNL-type zinc finger	protein-coding
mm_122656.1	chr14	51911501	51911511	-	1	NA	exon (NM_001145959, exon 2 of 15)	exon (NM_001145959, exon 2 of 15)	1982	NM_001145959	29811	Mm.26722	NM_013864	ENSMUSG00000004558	Ndrg2	AI182517|AU040374|Ndr2|SYLD	N-myc downstream regulated gene 2	protein-coding
mm_140913.1	chr17	24168829	24168840	-	1	NA	intron (NR_037854, intron 1 of 2)	intron (NR_037854, intron 1 of 2)	561	NR_037854	100039636	Mm.30155	NR_037854		Atp6v0c-ps2	Atp6l-ps2|Gm15487	ATPase, H+ transporting, lysosomal V0 subunit C, pseudogene 2	pseudo
mm_156532.1	chrX	151047194	151047227	+	1	NA	promoter-TSS (NM_008001)	promoter-TSS (NM_008001)	40	NM_008001	14163	Mm.8142	NM_008001	ENSMUSG00000025265	Fgd1	ZFYVE3	FYVE, RhoGEF and PH domain containing 1	protein-coding
mm_108996.1	chr12	102949451	102949487	+	1	NA	5' UTR (NM_001081017, exon 1 of 49)	5' UTR (NM_001081017, exon 1 of 49)	610	NM_001081017	217843	Mm.387073	NM_177621	ENSMUSG00000021198	Unc79	9030205A07Rik|Mlca3	unc-79 homolog (C. elegans)	protein-coding
mm_67472.1	chr7	80495288	80495299	-	1	NA	intron (NM_001042527, intron 10 of 21)	L1MC4|LINE|L1	39705	NM_007550	12144	Mm.12932	NM_007550	ENSMUSG00000030528	Blm	-	Bloom syndrome, RecQ helicase-like	protein-coding
mm_20832.1	chr2	147085465	147085483	-	1	NA	promoter-TSS (NM_023504)	promoter-TSS (NM_023504)	-129	NM_023504	228731	Mm.315498	NM_023504	ENSMUSG00000054160	Nkx2-4	1700001P03Rik|Nkx-2.4|tinman	NK2 homeobox 4	protein-coding
mm_66555.1	chr7	45234284	45234315	-	1	NA	TTS (NM_001285498)	TTS (NM_001285498)	4540	NM_007645	12493	Mm.3689	NM_007645	ENSMUSG00000030798	Cd37	Tspan26	CD37 antigen	protein-coding
mm_42844.1	chr5	122158266	122158340	+	1	NA	promoter-TSS (NM_013636)	promoter-TSS (NM_013636)	24	NM_013636	19047	Mm.280784	NM_013636	ENSMUSG00000004455	Ppp1cc	PP-1G|PP1|dis2m1	protein phosphatase 1, catalytic subunit, gamma isoform	protein-coding
mm_110615.1	chr12	56613302	56613318	-	1	NA	promoter-TSS (NM_008701)	promoter-TSS (NM_008701)	-26	NM_008701	18094	Mm.129420	NM_008701	ENSMUSG00000058669	Nkx2-9	Nkx-2.9|Nkx2-8|Nkx2.9|tinman	NK2 homeobox 9	protein-coding
mm_21249.1	chr2	156179973	156179983	-	1	NA	promoter-TSS (NM_001291115)	promoter-TSS (NM_001291115)	260	NM_001291114	170791	Mm.392436	NM_133242	ENSMUSG00000027620	Rbm39	1500012C14Rik|2310040E03Rik|B330012G18Rik|C79248|R75070|Rnpc2|caper	RNA binding motif protein 39	protein-coding
mm_123557.1	chr14	66847619	66847631	-	1	NA	intron (NM_009955, intron 3 of 13)	intron (NM_009955, intron 3 of 13)	20975	NM_009955	12934	Mm.352648	NM_009955	ENSMUSG00000022048	Dpysl2	AI851130|Crmp2|DRP2|Musunc33|TOAD-64|Ulip2	dihydropyrimidinase-like 2	protein-coding
mm_39967.1	chr5	32150088	32150126	+	1	NA	intron (NM_008037, intron 2 of 3)	intron (NM_008037, intron 2 of 3)	13635	NM_008037	14284	Mm.24684	NM_008037	ENSMUSG00000029135	Fosl2	Fra-2	fos-like antigen 2	protein-coding
mm_77632.1	chr8	124080822	124080824	-	1	NA	Intergenic	Intergenic	57350	NM_001029876	382038	Mm.334891	NM_001029876	ENSMUSG00000031976	Urb2	C77575|mKIAA0133	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	protein-coding
mm_56915.1	chr6	119359488	119359517	-	1	NA	exon (NM_197985, exon 5 of 8)	exon (NM_197985, exon 5 of 8)	-28736	NM_172492	211187	Mm.121498	NM_172492	ENSMUSG00000055003	Lrtm2	A230084J22|AI841794	leucine-rich repeats and transmembrane domains 2	protein-coding
mm_133889.1	chr16	97356735	97356798	+	1	NA	promoter-TSS (NM_019517)	promoter-TSS (NM_019517)	38	NM_019517	56175	Mm.97885	NM_019517	ENSMUSG00000040605	Bace2	1110059C24Rik|AEPLC|AI850424|ALP56|ARP1|ASP1|ASP21|BAE2|CDA13|CEAP1|DRAP	beta-site APP-cleaving enzyme 2	protein-coding
mm_170984.1	chr2	73214335	73214336	-	1	NA	5' UTR (NM_025942, exon 1 of 11)	5' UTR (NM_025942, exon 1 of 11)	112	NM_030091	67059	Mm.22661	NM_025942	ENSMUSG00000027108	Ola1	2510025G09Rik|2810405J23Rik|2810409H07Rik|Gtpbp9|PTD004	Obg-like ATPase 1	protein-coding
mm_136779.1	chr17	10324615	10324623	+	1	NA	promoter-TSS (NR_045461)	promoter-TSS (NR_045461)	17	NR_045461	76634	Mm.491052	NR_045461	ENSMUSG00000099384	1700110C19Rik	-	RIKEN cDNA 1700110C19 gene	ncRNA
mm_133310.1	chr16	77625483	77625487	+	1	NA	Intergenic	Intergenic	-20788	NR_029540	723952		NR_029540	ENSMUSG00000065472	Mir125b-2	Mirn125b-2|mir-125b-2	microRNA 125b-2	ncRNA
mm_154683.1	chrX	7922238	7922259	+	1	NA	exon (NM_013892, exon 2 of 3)	exon (NM_013892, exon 2 of 3)	2426	NM_013892	30052	Mm.4881	NM_013892	ENSMUSG00000039278	Pcsk1n	AI848336|KEP|PEN|PEN19|PEN20|Pan3|SAAS|SAASCT|bLEN|lLEN|proSAAS	proprotein convertase subtilisin/kexin type 1 inhibitor	protein-coding
mm_77578.1	chr8	123518816	123518825	-	1	NA	promoter-TSS (NM_018855)	promoter-TSS (NM_018855)	-15	NM_018855	104346	Mm.117265	NM_018855	ENSMUSG00000040220	Gas8	Gas11	growth arrest specific 8	protein-coding
mm_2647.1	chr1	125444565	125444571	+	1	NA	Intergenic	MLT1J|LTR|ERVL-MaLR	-8841	NM_001205386	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding
mm_147634.1	chr18	59774500	59774502	-	1	NA	Intergenic	L1_Mus3|LINE|L1	194871	NR_105773	102465182		NR_105773	ENSMUSG00000098287	Mir6355	Gm27473|mmu-mir-6355	microRNA 6355	ncRNA
mm_18735.1	chr2	72995746	72995766	-	1	NA	Intergenic	LTR88c|LTR|Gypsy?	-15310	NM_001018042	20687	Mm.124328	NM_011450	ENSMUSG00000027109	Sp3	D130027J01Rik	trans-acting transcription factor 3	protein-coding
mm_168953.1	chr12	78350869	78350882	+	1	NA	intron (NM_145965, intron 2 of 22)	LSU-rRNA_Hsa|rRNA|rRNA	124220	NM_145965	268566	Mm.341742	NM_145965	ENSMUSG00000047454	Gphn	5730552E08Rik|AI662856|BC027112|C230040D23|GPH|GPHRYN|geph	gephyrin	protein-coding
mm_61998.1	chr7	91162534	91162544	+	1	NA	intron (NM_011807, intron 1 of 22)	B4A|SINE|B4	71753	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_73096.1	chr8	94564701	94564718	+	1	NA	intron (NM_153507, intron 14 of 15)	intron (NM_153507, intron 14 of 15)	31681	NM_153507	234577	Mm.291815	NM_153507	ENSMUSG00000034361	Cpne2	3322401K10Rik	copine II	protein-coding
mm_144034.1	chr17	90088280	90088320	-	1	NA	promoter-TSS (NM_001347419)	promoter-TSS (NM_001347419)	68	NM_001346962	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_13940.1	chr2	121171156	121171198	+	1	NA	promoter-TSS (NR_110985)	promoter-TSS (NR_110985)	9	NM_001290824	51885	Mm.383499	NM_153387	ENSMUSG00000027263	Tubgcp4	4932441P04Rik|76p|D2Ertd435e|GCP-4	tubulin, gamma complex associated protein 4	protein-coding
mm_57809.1	chr6	129451784	129451864	-	1	NA	5' UTR (NM_175526, exon 1 of 6)	5' UTR (NM_175526, exon 1 of 6)	176	NM_175526	243653	Mm.131289	NM_175526	ENSMUSG00000033082	Clec1a	5930406N14Rik	C-type lectin domain family 1, member a	protein-coding
mm_121306.1	chr14	105897921	105897938	+	1	NA	Intergenic	Intergenic	-1110	NM_011897	24064	Mm.89982	NM_011897	ENSMUSG00000022114	Spry2	sprouty2	sprouty homolog 2 (Drosophila)	protein-coding
mm_51460.1	chr6	82070678	82070688	+	1	NA	intron (NM_145570, intron 1 of 2)	intron (NM_145570, intron 1 of 2)	29055	NM_145570	232146	Mm.489683	NM_145570	ENSMUSG00000035104	Eva1a	BC014699|Fam176a|Tmem166	eva-1 homolog A (C. elegans)	protein-coding
mm_88898.1	chr10	81151461	81151474	+	1	NA	3' UTR (NM_010731, exon 3 of 3)	3' UTR (NM_010731, exon 3 of 3)	15196	NM_010731	16969	Mm.20920	NM_010731	ENSMUSG00000035011	Zbtb7a	9030619K07Rik|9130006G12Rik|AI452336|FBI-1|Lrf|Pokemon|Zbtb7	zinc finger and BTB domain containing 7a	protein-coding
mm_153986.1	chr19	47919238	47919260	-	1	NA	promoter-TSS (NM_001001738)	promoter-TSS (NM_001001738)	50	NM_001001738	414801	Mm.29457	NM_001001738	ENSMUSG00000044948	Itprip	4833424O12Rik|DANGER|mKIAA1754	inositol 1,4,5-triphosphate receptor interacting protein	protein-coding
mm_97160.1	chr11	75468196	75468204	+	1	NA	5' UTR (NM_001291156, exon 1 of 5)	5' UTR (NM_001291156, exon 1 of 5)	150	NM_027249	380712	Mm.41393	NM_027249	ENSMUSG00000038217	Tlcd2	-	TLC domain containing 2	protein-coding
mm_172899.1	chr9	57334098	57334116	+	1	NA	Intergenic	Intergenic	-56963	NR_040729	73772	Mm.444684	NR_040729		4930430J02Rik	-	RIKEN cDNA 4930430J02 gene	ncRNA
mm_84133.1	chr9	59036367	59036383	-	1	NA	promoter-TSS (NM_008684)	promoter-TSS (NM_008684)	66	NM_008684	18007	Mm.42249	NM_008684	ENSMUSG00000032340	Neo1	2610028H22Rik|AI327052|D930014N22Rik|Igdcc2	neogenin	protein-coding
mm_19788.1	chr2	107059647	107059658	-	1	NA	promoter-TSS (NM_008045)	promoter-TSS (NM_008045)	-1	NM_008045	14308	Mm.249525	NM_008045	ENSMUSG00000027120	Fshb	FSH|FSH-B|FSH-beta|Fshbeta	follicle stimulating hormone beta	protein-coding
mm_110448.1	chr12	51609718	51609743	-	1	NA	3' UTR (NM_001172098, exon 16 of 16)	3' UTR (NM_001172098, exon 16 of 16)	16389	NM_001198835	12810	Mm.21325	NM_007728	ENSMUSG00000020953	Coch	AW122937|Coch-5B2|D12H14S564E	cochlin	protein-coding
mm_157059.1	chrX	8132482	8132492	-	1	NA	5' UTR (NM_026137, exon 1 of 9)	5' UTR (NM_026137, exon 1 of 9)	371	NM_001290783	73447	Mm.284162	NM_026137	ENSMUSG00000031166	Wdr13	1700060B08Rik|5730411P10Rik|DXHXS7467e|W51679|mMg21	WD repeat domain 13	protein-coding
mm_99511.1	chr11	103103016	103103026	+	1	NA	5' UTR (NM_025988, exon 2 of 10)	5' UTR (NM_025988, exon 2 of 10)	1333	NM_025988	67131	Mm.390367	NM_025988	ENSMUSG00000056938	Acbd4	2010009P05Rik|2010015A21Rik|AI849317	acyl-Coenzyme A binding domain containing 4	protein-coding
mm_84248.1	chr9	62377357	62377372	-	1	NA	intron (NM_009672, intron 6 of 6)	intron (NM_009672, intron 6 of 6)	36021	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	protein-coding
mm_41608.1	chr5	96406933	96406944	+	1	NA	intron (NM_175473, intron 2 of 73)	intron (NM_175473, intron 2 of 73)	32983	NM_175473	231470	Mm.291120	NM_175473	ENSMUSG00000034687	Fras1	E130113P14Rik|bl|mKIAA1500	Fraser extracellular matrix complex subunit 1	protein-coding
mm_51675.1	chr6	86438416	86438431	+	1	NA	promoter-TSS (NM_001243742)	promoter-TSS (NM_001243742)	25	NM_146170	232196	Mm.404040	NM_146170	ENSMUSG00000046679	C87436	-	expressed sequence C87436	protein-coding
mm_10302.1	chr2	10803065	10803083	+	1	NA	Intergenic	(TATAA)n|Simple_repeat|Simple_repeat	285470	NR_035417	100316668		NR_035417	ENSMUSG00000080657	Mir669i	Mirn669i|mir-669i|mmu-mir-669i	microRNA 669i	ncRNA
mm_108872.1	chr12	99645058	99645063	+	1	NA	Intergenic	Intergenic	-17086	NR_045288	73457	Mm.383439	NR_045288	ENSMUSG00000100211	1700064M15Rik	-	RIKEN cDNA 1700064M15 gene	ncRNA
mm_133821.1	chr16	95769218	95769227	+	1	NA	Intergenic	Intergenic	66815	NM_011809	23872	Mm.290207	NM_011809	ENSMUSG00000022895	Ets2	AU022856|Ets-2	E26 avian leukemia oncogene 2, 3' domain	protein-coding
mm_154569.1	chrX	6577311	6577327	+	1	NA	promoter-TSS (NM_001313765)	promoter-TSS (NM_001313765)	33	NM_001313765	208431	Mm.23208	NM_001040459	ENSMUSG00000068270	Shroom4	D430043L16Rik|Gm724|Shrm4	shroom family member 4	protein-coding
mm_66721.1	chr7	46100728	46100770	-	1	NA	promoter-TSS (NM_001204411)	promoter-TSS (NM_001204411)	15	NM_001204411	16514	Mm.333863	NM_010602	ENSMUSG00000096146	Kcnj11	Kir6.2|mBIR	potassium inwardly rectifying channel, subfamily J, member 11	protein-coding
mm_137630.1	chr17	28328781	28328803	+	1	NA	intron (NM_011287, intron 1 of 5)	CpG	321	NM_011287	19896	Mm.336955	NM_011287	ENSMUSG00000037805	Rpl10a	CsA-19|Nedd6	ribosomal protein L10A	protein-coding
mm_46142.1	chr5	93165340	93165381	-	1	NA	exon (NM_001310669, exon 8 of 11)	exon (NM_001310669, exon 8 of 11)	41135	NM_017367	12453	Mm.250419	NM_017367	ENSMUSG00000063015	Ccni	-	cyclin I	protein-coding
mm_140011.1	chr17	73163065	73163109	+	1	NA	intron (NM_001177967, intron 2 of 5)	MT2B|LTR|ERVL	55102	NM_001177967	225010	Mm.329194	NM_001081071	ENSMUSG00000054469	Lclat1	AI181996|Agpat8|Alcat1|Gm91|Lycat	lysocardiolipin acyltransferase 1	protein-coding
mm_92697.1	chr10	80678107	80678129	-	1	NA	Intergenic	Intergenic	-1825	NM_021462	17347	Mm.42126	NM_021462	ENSMUSG00000020190	Mknk2	2010016G11Rik|Gprk7|Mnk2	MAP kinase-interacting serine/threonine kinase 2	protein-coding
mm_22345.1	chr2	180893402	180893404	-	1	NA	promoter-TSS (NR_029538)	promoter-TSS (NR_029538)	-637	NR_029538	723951		NR_029538	ENSMUSG00000065454	Mir124a-3	Mirn124a-3|mir-124-3|mir-124a-3	microRNA 124a-3	ncRNA
mm_51334.1	chr6	72385225	72385236	+	1	NA	TTS (NM_016794)	TTS (NM_016794)	-4762	NM_001080742	53620	Mm.440321	NM_016872	ENSMUSG00000073002	Vamp5	AF119384|Camp	vesicle-associated membrane protein 5	protein-coding
mm_111463.1	chr12	98528702	98528708	-	1	NA	intron (NM_029911, intron 1 of 6)	intron (NM_029911, intron 1 of 6)	4861	NR_136759	105245437	Mm.446375	NR_136759		Gm40893	-	predicted gene, 40893	ncRNA
mm_106659.1	chr11	121229227	121229292	-	1	NA	promoter-TSS (NM_001254735)	promoter-TSS (NM_001254735)	50	NM_144832	217370	Mm.27182	NM_144832	ENSMUSG00000039294	BC017643	-	cDNA sequence BC017643	protein-coding
mm_156657.1	chrX	157711173	157711196	+	1	NA	intron (NR_045569, intron 3 of 6)	intron (NR_045569, intron 3 of 6)	12211	NR_103722	66106	Mm.140340	NM_025357	ENSMUSG00000041476	Smpx	1010001C09Rik|Csl	small muscle protein, X-linked	protein-coding
mm_90566.1	chr10	128231425	128231435	+	1	NA	promoter-TSS (NM_001136082)	promoter-TSS (NM_001136082)	-633	NM_001164080	21853	Mm.6458	NM_011589	ENSMUSG00000039994	Timeless	C77407|Debt69|tim	timeless circadian clock 1	protein-coding
mm_132757.1	chr16	44394772	44394804	+	1	NA	promoter-TSS (NM_001033247)	promoter-TSS (NM_001033247)	-11	NM_001033247	212517	Mm.327888	NM_001033247	ENSMUSG00000071550	Cfap44	6330444M21Rik|D16Ertd642e|Gm1750|Wdr52	cilia and flagella associated protein 44	protein-coding
mm_76155.1	chr8	82357015	82357032	-	1	NA	intron (NM_008357, intron 2 of 7)	MLT1E2|LTR|ERVL-MaLR	45563	NM_001254747	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_53104.1	chr6	125067953	125067955	+	1	NA	promoter-TSS (NM_001163269)	promoter-TSS (NM_001163269)	34	NM_001163269	381810	Mm.333386	NM_001163268	ENSMUSG00000067714	Lpar5	GPR93|Gm1072|Gpr92|LPA5	lysophosphatidic acid receptor 5	protein-coding
mm_111336.1	chr12	86883913	86883927	-	1	NA	5' UTR (NM_145836, exon 1 of 1)	5' UTR (NM_145836, exon 1 of 1)	894	NM_145836	238330	Mm.248358	NM_145836	ENSMUSG00000034168	Irf2bpl	6430527G18Rik|Eap1	interferon regulatory factor 2 binding protein-like	protein-coding
mm_19967.1	chr2	117996291	117996315	-	1	NA	intron (NR_126479, intron 8 of 9)	intron (NR_126479, intron 8 of 9)	114899	NR_126479	329496	Mm.235844	NR_126479	ENSMUSG00000087203	Gm13986	C230060E24|OTTMUSG00000015236	predicted gene 13986	ncRNA
mm_29453.1	chr3	113195162	113195191	-	1	NA	Intergenic	MuRRS4-int|LTR|ERV1	-38449	NM_001190403	545562	Mm.462977	NM_001190403		Amy2b	Amy-X|Amy2-2|OTTMUSG00000022462|mAmy2-1	amylase 2b	protein-coding
mm_77093.1	chr8	110805823	110805848	-	1	NA	promoter-TSS (NM_001135100)	promoter-TSS (NM_001135100)	89	NM_029646	76527	Mm.77697	NM_029646	ENSMUSG00000031750	Il34	2010004A03Rik|AI593503	interleukin 34	protein-coding
mm_25621.1	chr3	118562163	118562188	+	1	NA	promoter-TSS (NM_170778)	promoter-TSS (NM_170778)	-3	NM_170778	99586	Mm.27907	NM_170778	ENSMUSG00000033308	Dpyd	AI315208|DPD|E330028L06Rik	dihydropyrimidine dehydrogenase	protein-coding
mm_19187.1	chr2	84414180	84414183	-	1	NA	intron (NM_018782, intron 1 of 15)	RMER6D|LTR|ERVK	11085	NM_018782	54598	Mm.75467	NM_018782	ENSMUSG00000059588	Calcrl	AV071593|CRLR	calcitonin receptor-like	protein-coding
mm_125571.1	chr15	59315149	59315173	+	1	NA	promoter-TSS (NM_009270)	promoter-TSS (NM_009270)	69	NM_009270	20775	Mm.296169	NM_009270	ENSMUSG00000022351	Sqle	AI323792	squalene epoxidase	protein-coding
mm_30534.1	chr4	3574873	3574913	+	1	NA	promoter-TSS (NM_028097)	promoter-TSS (NM_028097)	14	NM_054089	116940	Mm.171323	NM_054089	ENSMUSG00000028233	Tgs1	D4Ertd800e|Ncoa6ip|Pimt	trimethylguanosine synthase 1	protein-coding
mm_161935.1	chr18	89769259	89769259	-	1	NA	promoter-TSS (NM_001039173)	promoter-TSS (NM_001039173)	-123	NM_001039173	623279	Mm.447164	NM_001039173	ENSMUSG00000073514	Dok6	Dok-6	docking protein 6	protein-coding
mm_100616.1	chr11	121549846	121549856	+	1	NA	intron (NM_029878, intron 14 of 38)	intron (NM_029878, intron 14 of 38)	-30509	NM_178763	319530	Mm.11395	NM_178763	ENSMUSG00000039238	Zfp750	A030007D23Rik|Znf750	zinc finger protein 750	protein-coding
mm_65439.1	chr7	25388972	25388984	-	1	NA	intron (NM_010719, intron 1 of 9)	intron (NM_010719, intron 1 of 9)	1134	NM_001039507	16890	Mm.158548	NM_010719	ENSMUSG00000003123	Lipe	4933403G17Rik|HSL	lipase, hormone sensitive	protein-coding
mm_11044.1	chr2	27121166	27121201	+	1	NA	intron (NM_175427, intron 1 of 2)	SSU-rRNA_Hsa|rRNA|rRNA	21294	NM_175427	109349	Mm.314080	NM_175427	ENSMUSG00000009216	Fam163b	C630035N08Rik	family with sequence similarity 163, member B	protein-coding
mm_120364.1	chr14	64440727	64440747	+	1	NA	exon (NM_026322, exon 6 of 11)	exon (NM_026322, exon 6 of 11)	289	NM_001253715	110265	Mm.26713	NM_026322	ENSMUSG00000054733	Msra	2310045J23Rik|6530413P12Rik|MSR-A	methionine sulfoxide reductase A	protein-coding
mm_139689.1	chr17	57421666	57421678	+	1	NA	intron (NM_010130, intron 12 of 21)	Lx5|LINE|L1	62986	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_66114.1	chr7	31042107	31042174	-	1	NA	promoter-TSS (NM_001111073)	promoter-TSS (NM_001111073)	191	NM_008761	18301	Mm.1870	NM_008761	ENSMUSG00000009687	Fxyd5	EF-8|Oit2|RIC	FXYD domain-containing ion transport regulator 5	protein-coding
mm_105021.1	chr11	100441819	100441825	-	1	NA	promoter-TSS (NM_001102650)	promoter-TSS (NM_001102650)	-102	NM_025727	66720	Mm.34168	NM_025727	ENSMUSG00000001558	Klhl10	4921517C11Rik	kelch-like 10	protein-coding
mm_117879.1	chr13	98984559	98984571	-	1	NA	promoter-TSS (NM_027064)	promoter-TSS (NM_027064)	0	NM_027064	69382	Mm.45466	NM_027064	ENSMUSG00000045022	1700024P04Rik	H2bl1|Subh2bv	RIKEN cDNA 1700024P04 gene	protein-coding
mm_78897.1	chr9	44639149	44639158	+	1	NA	3' UTR (NM_001110826, exon 14 of 14)	3' UTR (NM_001110826, exon 14 of 14)	-34080	NM_001277851	58866	Mm.45380	NM_021481	ENSMUSG00000032098	Treh	2210412M19Rik	trehalase (brush-border membrane glycoprotein)	protein-coding
mm_171022.1	chr2	84086912	84086921	-	1	NA	Intergenic	L1Md_T|LINE|L1	-145690	NM_027964	71861	Mm.116957	NM_027964	ENSMUSG00000034552	Zswim2	1700025P14Rik|4933437F18Rik|MEX	zinc finger SWIM-type containing 2	protein-coding
mm_157210.1	chrX	12762070	12762080	-	1	NA	promoter-TSS (NM_001048208)	promoter-TSS (NM_001048208)	-102	NM_001048208	26896	Mm.17616	NM_012005	ENSMUSG00000064127	Med14	9930001L01Rik|AU041628|Crsp2|ENSMUSG00000073278|Gm641|ORF1|Trap170	mediator complex subunit 14	protein-coding
mm_5723.1	chr1	44102418	44102428	-	1	NA	promoter-TSS (NM_029368)	promoter-TSS (NM_029368)	-35	NM_029368	75623	Mm.348017	NM_029368	ENSMUSG00000026049	Tex30	1700029F09Rik|3110030D08Rik	testis expressed 30	protein-coding
mm_124862.1	chr15	10177229	10177243	+	1	NA	promoter-TSS (NM_011169)	promoter-TSS (NM_011169)	-2	NM_011169	19116	Mm.10516	NM_011169	ENSMUSG00000005268	Prlr	AI987712|Pr-1|Pr-3|Prlr-rs1	prolactin receptor	protein-coding
mm_21851.1	chr2	165875810	165875834	-	1	NA	intron (NM_027230, intron 1 of 23)	intron (NM_027230, intron 1 of 23)	2615	NM_001291158	228880	Mm.227598	NM_027230	ENSMUSG00000039671	Zmynd8	1110013E22Rik|2010005I16Rik|3632413B07Rik|AI316811|AL024039|Prkcbp1|RACK7	zinc finger, MYND-type containing 8	protein-coding
mm_154187.1	chr19	58807529	58807533	-	1	NA	intron (NM_001327998, intron 8 of 12)	intron (NM_001327998, intron 8 of 12)	-13117	NM_026208	67507	Mm.27027	NM_026208	ENSMUSG00000026931	1700019N19Rik	-	RIKEN cDNA 1700019N19 gene	protein-coding
mm_77051.1	chr8	109577214	109577238	-	1	NA	exon (NM_017370, exon 3 of 5)	exon (NM_017370, exon 3 of 5)	1946	NM_017370	15439	Mm.26730	NM_017370	ENSMUSG00000031722	Hp	HP-1|preHP2	haptoglobin	protein-coding
mm_10377.1	chr2	11777913	11777939	+	1	NA	promoter-TSS (NM_015792)	promoter-TSS (NM_015792)	173	NM_177268	320816	Mm.260201	NM_177268	ENSMUSG00000047909	Ankrd16	2810455F06Rik|AI646698|D430029B21Rik	ankyrin repeat domain 16	protein-coding
mm_89040.1	chr10	82833956	82833965	+	1	NA	promoter-TSS (NM_001042523)	promoter-TSS (NM_001042523)	9	NM_001042523	50493	Mm.210155	NM_015762	ENSMUSG00000020250	Txnrd1	TR|TR1|TrxR1	thioredoxin reductase 1	protein-coding
mm_33451.1	chr4	130680862	130680865	+	1	NA	intron (NM_001159606, intron 2 of 17)	intron (NM_001159606, intron 2 of 17)	17504	NM_001159605	80912	Mm.440206	NM_030722	ENSMUSG00000028580	Pum1	AA517475|Pumm|mKIAA0099	pumilio RNA-binding family member 1	protein-coding
mm_139515.1	chr17	56584949	56584959	+	1	NA	promoter-TSS (NM_001163300)	promoter-TSS (NM_001163300)	-28	NM_001163300	224903	Mm.255066	NM_001163300	ENSMUSG00000071054	Safb	3110021E02Rik|5330423C17Rik|AU018122|D18386|E130307D12|HAP|HET|SAF-B1|SAFB1	scaffold attachment factor B	protein-coding
mm_58924.1	chr7	17972001	17972002	+	1	NA	promoter-TSS (NM_023289)	promoter-TSS (NM_023289)	-166	NM_023289	66996	Mm.36666	NM_023289	ENSMUSG00000030368	Ceacam11	1600015D01Rik	carcinoembryonic antigen-related cell adhesion molecule 11	protein-coding
mm_15677.1	chr2	163547149	163547168	+	1	NA	promoter-TSS (NM_008261)	promoter-TSS (NM_008261)	3	NM_008261	15378	Mm.202383	NM_008261	ENSMUSG00000017950	Hnf4a	HNF-4|Hnf4|Hnf4alpha|MODY1|Nr2a1|TCF-14|Tcf14	hepatic nuclear factor 4, alpha	protein-coding
mm_160392.1	chr8	58911627	58911627	-	1	NA	promoter-TSS (NM_175032)	promoter-TSS (NM_175032)	0	NM_175032	270049	Mm.236368	NM_175032	ENSMUSG00000096914	Galntl6	1700021K10Rik|4930431L04Rik|A830023L05	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 6	protein-coding
mm_131892.1	chr16	23228290	23228294	+	1	NA	intron (NM_001252505, intron 1 of 7)	intron (NM_001252505, intron 1 of 7)	2271	NM_001252505	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_64117.1	chr7	141079747	141079755	+	1	NA	promoter-TSS (NM_019762)	promoter-TSS (NM_019762)	-18	NM_019762	56460	Mm.350037	NM_019762	ENSMUSG00000054065	Pkp3	2310056L12Rik	plakophilin 3	protein-coding
mm_21755.1	chr2	164839698	164839706	-	1	NA	3' UTR (NM_011125, exon 16 of 16)	3' UTR (NM_011125, exon 16 of 16)	5929	NM_008906	19025	Mm.359633	NM_008906	ENSMUSG00000017760	Ctsa	AU019505|PPCA|Ppgb	cathepsin A	protein-coding
mm_88425.1	chr10	77225923	77225971	+	1	NA	Intergenic	Intergenic	33276	NR_026944	100169878	Mm.420901	NR_026944	ENSMUSG00000078444	Gm10941	ENSMUSG00000078444	predicted gene 10941	ncRNA
mm_16940.1	chr2	14823908	14823927	-	1	NA	promoter-TSS (NM_001252533)	promoter-TSS (NM_001252533)	-175	NM_001252533	12296	Mm.313930	NM_023116	ENSMUSG00000057914	Cacnb2	AW060387|CAB2|Cavbeta2|Cchb2	calcium channel, voltage-dependent, beta 2 subunit	protein-coding
mm_2705.1	chr1	127985758	127985765	+	1	NA	intron (NM_027678, intron 12 of 20)	intron (NM_027678, intron 12 of 20)	116710	NM_027678	226409	Mm.425048	NM_027678	ENSMUSG00000036086	Zranb3	4933425L19Rik|AH2|AI316834|C730006D09	zinc finger, RAN-binding domain containing 3	protein-coding
mm_106371.1	chr11	118399854	118399856	-	1	NA	intron (NM_011150, intron 1 of 5)	intron (NM_011150, intron 1 of 5)	2076	NM_011150	19039	Mm.3152	NM_011150	ENSMUSG00000033880	Lgals3bp	90K|CyCAP|MAC-2BP|Ppicap|Tango10b	lectin, galactoside-binding, soluble, 3 binding protein	protein-coding
mm_59286.1	chr7	24918832	24918846	+	1	NA	intron (NM_001130150, intron 14 of 30)	intron (NM_001130150, intron 14 of 30)	14493	NM_001130152	16801	Mm.3181	NM_008488	ENSMUSG00000040940	Arhgef1	Lbcl2|Lsc	Rho guanine nucleotide exchange factor (GEF) 1	protein-coding
mm_123117.1	chr14	56085215	56085217	-	1	NA	promoter-TSS (NM_008572)	promoter-TSS (NM_008572)	-19	NM_008572	17231	Mm.41979	NM_008572	ENSMUSG00000022157	Mcpt8	BB139338|MMCP-8	mast cell protease 8	protein-coding
mm_98252.1	chr11	88357167	88357181	+	1	NA	intron (NM_054043, intron 11 of 13)	intron (NM_054043, intron 11 of 13)	4401	NR_039545	100628571		NR_039545	ENSMUSG00000092985	Mir378b	mir-378b|mmu-mir-378b	microRNA 378b	ncRNA
mm_8529.1	chr1	154884521	154884530	-	1	NA	Intergenic	Intergenic	-158605	NM_009782	12290	Mm.267517	NM_009782	ENSMUSG00000004110	Cacna1e	A430040I15|BII|Cach6|Cacnl1a6|Cav2.3|Cchra1|alpha1E	calcium channel, voltage-dependent, R type, alpha 1E subunit	protein-coding
mm_33419.1	chr4	129984834	129984876	+	1	NA	promoter-TSS (NM_173071)	promoter-TSS (NM_173071)	-15	NM_001290714	230775	Mm.262241	NM_173071	ENSMUSG00000028782	Adgrb2	Bai2	adhesion G protein-coupled receptor B2	protein-coding
mm_155423.1	chrX	73492044	73492061	+	1	NA	exon (NM_007542, exon 4 of 8)	exon (NM_007542, exon 4 of 8)	8451	NM_007542	12111	Mm.2608	NM_007542	ENSMUSG00000031375	Bgn	BG|DSPG1|PG-S1|PGI|SLRR1A	biglycan	protein-coding
mm_106825.1	chr12	7988667	7988681	+	1	NA	exon (NM_009693, exon 10 of 29)	exon (NM_009693, exon 10 of 29)	10997	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_90352.1	chr10	127165253	127165263	+	1	NA	promoter-TSS (NM_027739)	promoter-TSS (NM_027739)	102	NM_001244617	14421	Mm.386762	NM_008080	ENSMUSG00000006731	B4galnt1	4933429D13Rik|Gal-NAc-T|GalNAc-T|GalNAcT|Galgt1|Ggm-2|Ggm2	beta-1,4-N-acetyl-galactosaminyl transferase 1	protein-coding
mm_53776.1	chr6	146219807	146219818	+	1	NA	intron (NM_010586, intron 44 of 55)	intron (NM_010586, intron 44 of 55)	282411	NM_010586	16439	Mm.7800	NM_010586	ENSMUSG00000030287	Itpr2	AI649341|InsP3R-2|InsP3R-5|Ip3r2|Itpr5|insP3R2	inositol 1,4,5-triphosphate receptor 2	protein-coding
mm_119634.1	chr14	51884906	51884949	+	1	NA	promoter-TSS (NM_001029990)	promoter-TSS (NM_001029990)	85	NM_001029990	52535	Mm.5750	NM_001029990	ENSMUSG00000004561	Mettl17	2310032K15Rik|D14Ertd209e|Mett11d1	methyltransferase like 17	protein-coding
mm_26180.1	chr3	138313280	138313293	+	1	NA	promoter-TSS (NM_026945)	promoter-TSS (NM_026945)	0	NM_026945	69117	Mm.46265	NM_026945	ENSMUSG00000053054	Adh6a	1810009C16Rik|Adh5a	alcohol dehydrogenase 6A (class V)	protein-coding
mm_12621.1	chr2	74697740	74697751	+	1	NA	promoter-TSS (NM_013555)	promoter-TSS (NM_013555)	-18	NM_013555	15438	Mm.26544	NM_013555	ENSMUSG00000043342	Hoxd9	Hox-4.4|Hox-5.2	homeobox D9	protein-coding
mm_154789.1	chrX	13071625	13071663	+	1	NA	5' UTR (NM_009481, exon 1 of 45)	5' UTR (NM_009481, exon 1 of 45)	146	NM_009481	22284	Mm.242646	NM_009481	ENSMUSG00000031010	Usp9x	5730589N07Rik|AA407302|AA407699|AL022658|AL022749|Dffrx|FAF-X|Fafl	ubiquitin specific peptidase 9, X chromosome	protein-coding
mm_15837.1	chr2	164698525	164698539	+	1	NA	promoter-TSS (NM_030058)	promoter-TSS (NM_030058)	31	NM_030058	78239	Mm.160060	NM_030058	ENSMUSG00000017310	Spint4	9230105I15Rik	serine protease inhibitor, Kunitz type 4	protein-coding
mm_68599.1	chr7	116237616	116237630	-	1	NA	5' UTR (NM_001305186, exon 1 of 25)	5' UTR (NM_001305186, exon 1 of 25)	153	NM_001305186	233765	Mm.3741	NM_172743	ENSMUSG00000045659	Plekha7	A430081P20Rik|AI414265	pleckstrin homology domain containing, family A member 7	protein-coding
mm_146675.1	chr18	12819712	12819731	-	1	NA	non-coding (NR_045524, exon 1 of 12)	non-coding (NR_045524, exon 1 of 12)	186	NR_045524	64291	Mm.259470	NM_020573	ENSMUSG00000044252	Osbpl1a	G430090F17Rik|Gm753|ORP-1|Osbpl1b	oxysterol binding protein-like 1A	protein-coding
mm_98804.1	chr11	97044525	97044528	+	1	NA	intron (NM_026154, intron 1 of 4)	intron (NM_026154, intron 1 of 4)	2940	NM_026154	107732	Mm.208946	NM_026154	ENSMUSG00000001445	Mrpl10	0610040E02Rik|C78440|MRP-L8|Rpml8	mitochondrial ribosomal protein L10	protein-coding
mm_88964.1	chr10	81394911	81394924	+	1	NA	3' UTR (NM_001099917, exon 4 of 4)	3' UTR (NM_001099917, exon 4 of 4)	1853	NM_001099917	72273	Mm.253147	NM_001099917	ENSMUSG00000078439	Smim24	2210404O07Rik	small integral membrane protein 24	protein-coding
mm_131712.1	chr16	21204749	21204753	+	1	NA	promoter-TSS (NM_010143)	promoter-TSS (NM_010143)	-44	NM_010143	13845	Mm.6972	NM_010143	ENSMUSG00000005958	Ephb3	AW456895|Cek10|Etk2|HEK2|MDK5|Sek4|Tyro6	Eph receptor B3	protein-coding
mm_29881.1	chr3	131111934	131111948	-	1	NA	promoter-TSS (NM_001276403)	promoter-TSS (NM_001276403)	-850	NM_001276403	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_11457.1	chr2	32183024	32183049	+	1	NA	intron (NM_172661, intron 2 of 29)	intron (NM_172661, intron 2 of 29)	31888	NM_001159634	227723	Mm.25504	NM_172661	ENSMUSG00000039262	Prrc2b	5830434P21Rik|AI173903|Bat2l|Bat2l1|D430039P21|mKIAA0515	proline-rich coiled-coil 2B	protein-coding
mm_70380.1	chr8	10183314	10183334	+	1	NA	intron (NM_001319151, intron 1 of 34)	intron (NM_001319151, intron 1 of 34)	29413	NM_001319151	244281	Mm.422761	NM_001081397	ENSMUSG00000039057	Myo16	BM140241|C230040D10Rik|Gm1105|NYAP3|mKIAA0865	myosin XVI	protein-coding
mm_52850.1	chr6	121847964	121847978	+	1	NA	intron (NM_008645, intron 4 of 35)	CT-rich|Low_complexity|Low_complexity	9430	NM_008645	17836	Mm.1311	NM_008645	ENSMUSG00000059908	Mug1	-	murinoglobulin 1	protein-coding
mm_99016.1	chr11	98891184	98891201	+	1	NA	intron (NM_197940, intron 3 of 7)	intron (NM_197940, intron 3 of 7)	-16697	NM_001025779	23834	Mm.20912	NM_011799	ENSMUSG00000017499	Cdc6	CDC18L	cell division cycle 6	protein-coding
mm_12209.1	chr2	67173865	67173877	+	1	NA	promoter-TSS (NM_001033477)	promoter-TSS (NM_001033477)	37	NM_001033477	383709	Mm.244520	NM_001033477		Gm1322	-	predicted gene 1322	protein-coding
mm_164599.1	chr17	28864747	28864747	+	1	NA	intron (NM_001034885, intron 1 of 9)	intron (NM_001034885, intron 1 of 9)	6336	NM_001034885	433091	Mm.328925	NM_001034885	ENSMUSG00000043286	Pnpla1	-	patatin-like phospholipase domain containing 1	protein-coding
mm_90480.1	chr10	127893969	127893984	+	1	NA	Intergenic	MLTR11B|LTR|ERVK	-4559	NM_027301	70061	Mm.158320	NM_027301	ENSMUSG00000040127	Sdr9c7	1810054F20Rik|Rdh20|Rdhs|SDR-O|Sdro	4short chain dehydrogenase/reductase family 9C, member 7	protein-coding
mm_101246.1	chr11	20741581	20741622	-	1	NA	promoter-TSS (NM_001252503)	promoter-TSS (NM_001252503)	-45	NM_181411	216549	Mm.356580	NM_181411	ENSMUSG00000049659	Aftph	-	aftiphilin	protein-coding
mm_56902.1	chr6	119196527	119196539	-	1	NA	promoter-TSS (NM_009781)	promoter-TSS (NM_009781)	-124	NM_001255999	12288	Mm.41628	NM_009781	ENSMUSG00000051331	Cacna1c	Cav1.2|Cchl1a1|D930026N18Rik|MBC|MELC-CC	calcium channel, voltage-dependent, L type, alpha 1C subunit	protein-coding
mm_69431.1	chr7	132813716	132813733	-	1	NA	promoter-TSS (NM_212473)	promoter-TSS (NM_212473)	-528	NM_212473	77938	Mm.225649	NM_175268	ENSMUSG00000030956	Fam53b	A930008G19Rik|mKIAA0140	family with sequence similarity 53, member B	protein-coding
mm_48679.1	chr5	146221392	146221420	-	1	NA	promoter-TSS (NM_001256087)	promoter-TSS (NM_001256087)	51	NM_028774	74132	Mm.26696	NM_028774	ENSMUSG00000029634	Rnf6	1200013I08Rik|5730419H05Rik|AA537053	ring finger protein (C3H2C3 type) 6	protein-coding
mm_9651.1	chr1	177642867	177642926	-	1	NA	promoter-TSS (NR_037994)	promoter-TSS (NR_037994)	47	NR_037994	75589	Mm.86666	NR_037994	ENSMUSG00000101746	2310043L19Rik	-	RIKEN cDNA 2310043L19 gene	ncRNA
mm_47410.1	chr5	123134171	123134173	-	1	NA	Intergenic	Intergenic	-1543	NM_175092	23912	Mm.253876	NM_175092	ENSMUSG00000029449	Rhof	AI845056|AV026554|Arhf|Ifld1|Rif	ras homolog family member F (in filopodia)	protein-coding
mm_14242.1	chr2	127838815	127838836	+	1	NA	Intergenic	Intergenic	-6966	NM_009772	12235	Mm.2185	NM_009772	ENSMUSG00000027379	Bub1	AL022991|Bub1a|C80208|D2Xrf87	BUB1, mitotic checkpoint serine/threonine kinase	protein-coding
mm_152541.1	chr19	11334375	11334399	-	1	NA	exon (NM_001276398, exon 1 of 7)	exon (NM_001276398, exon 1 of 7)	308	NM_001276398	109225	Mm.491251	NM_027836	ENSMUSG00000024672	Ms4a7	9130422I10Rik|A430103C15Rik|CD20l4|CFFMA	membrane-spanning 4-domains, subfamily A, member 7	protein-coding
mm_96872.1	chr11	70213924	70213944	+	1	NA	promoter-TSS (NM_153081)	promoter-TSS (NM_153081)	24	NM_153081	216867	Mm.289238	NM_153081	ENSMUSG00000040938	Slc16a11	AB041591|MCT 11|MNCb-2717	solute carrier family 16 (monocarboxylic acid transporters), member 11	protein-coding
mm_66060.1	chr7	30744202	30744214	-	1	NA	promoter-TSS (NM_001290631)	promoter-TSS (NM_001290631)	-527	NM_001290631	14447	Mm.436562	NM_008085	ENSMUSG00000061099	Gapdhs	Gapd-s|Gapds	glyceraldehyde-3-phosphate dehydrogenase, spermatogenic	protein-coding
mm_129627.1	chr15	80219294	80219332	-	1	NA	Intergenic	Intergenic	-14767	NM_178719	239555	Mm.307163	NM_178719	ENSMUSG00000022412	Mief1	A230016E22|AI452372|Smcr7l	mitochondrial elongation factor 1	protein-coding
mm_22195.1	chr2	173276981	173276991	-	1	NA	promoter-TSS (NM_022995)	promoter-TSS (NM_022995)	-453	NM_022995	65112	Mm.73682	NM_022995	ENSMUSG00000038400	Pmepa1	2210418I02Rik|AW455466|Erg1.2|N4wbp4|Stag1|Tmepai	prostate transmembrane protein, androgen induced 1	protein-coding
mm_47874.1	chr5	134688557	134688563	-	1	NA	promoter-TSS (NM_010717)	promoter-TSS (NM_010717)	30	NM_010717	16885	Mm.15409	NM_010717	ENSMUSG00000029674	Limk1	KIZ-1|LIMK-1|Limk	LIM-domain containing, protein kinase	protein-coding
mm_141443.1	chr17	29842315	29842325	-	1	NA	exon (NM_001081160, exon 9 of 16)	exon (NM_001081160, exon 9 of 16)	45562	NM_001081160	74762	Mm.40901	NM_001081160	ENSMUSG00000043557	Mdga1	1200011I03Rik|GPIM|Mamdc3	MAM domain containing glycosylphosphatidylinositol anchor 1	protein-coding
mm_24122.1	chr3	88200271	88200279	+	1	NA	Intergenic	Intergenic	-14896	NR_037276	100526540		NR_037276	ENSMUSG00000092988	Mir3093	mir-3093|mmu-mir-3093	microRNA 3093	ncRNA
mm_41964.1	chr5	106977655	106977661	+	1	NA	intron (NM_001271568, intron 9 of 10)	(T)n|Simple_repeat|Simple_repeat	13097	NM_001271566	12545	Mm.20842	NM_009863	ENSMUSG00000029283	Cdc7	AI597260|Cdc7l1|muCdc7	cell division cycle 7 (S. cerevisiae)	protein-coding
mm_94645.1	chr11	16916066	16916109	+	1	NA	Intergenic	Intergenic	35195	NR_110421	72735	Mm.268598	NR_015469		Eldr	2810442I21Rik|4930500E12Rik|Fabl	Egfr long non-coding downstream RNA	ncRNA
mm_171761.1	chr5	105239571	105239574	-	1	NA	promoter-TSS (NM_001039646)	promoter-TSS (NM_001039646)	-39	NM_001039646	626578	Mm.275893	NM_001039646	ENSMUSG00000105096	Gbp10	-	guanylate-binding protein 10	protein-coding
mm_41172.1	chr5	88002531	88002552	+	1	NA	promoter-TSS (NM_011422)	promoter-TSS (NM_011422)	16	NM_011422	20599	Mm.261199	NM_011422	ENSMUSG00000029280	Smr3a	AA589601|MSG1|MSG3|Smr1|Smr3	submaxillary gland androgen regulated protein 3A	protein-coding
mm_56974.1	chr6	120257447	120257493	-	1	NA	intron (NM_198884, intron 1 of 19)	intron (NM_198884, intron 1 of 19)	37089	NM_198884	330406	Mm.321840	NM_198884	ENSMUSG00000041372	B4galnt3	AB114826|B4GalNAcT3|C330047A21	beta-1,4-N-acetyl-galactosaminyl transferase 3	protein-coding
mm_37932.1	chr4	132921144	132921147	-	1	NA	intron (NM_001163792, intron 1 of 7)	intron (NM_001163792, intron 1 of 7)	1406	NM_145553	230789	Mm.11473	NM_145553	ENSMUSG00000028878	Fam76a	-	family with sequence similarity 76, member A	protein-coding
mm_13373.1	chr2	103606416	103606425	+	1	NA	intron (NM_178890, intron 1 of 16)	intron (NM_178890, intron 1 of 16)	40110	NM_178890	99382	Mm.35850	NM_178890	ENSMUSG00000032724	Abtb2	AW539457|BPOZ-2	ankyrin repeat and BTB (POZ) domain containing 2	protein-coding
mm_72377.1	chr8	81342702	81342718	+	1	NA	5' UTR (NM_001297596, exon 1 of 25)	5' UTR (NM_001297596, exon 1 of 25)	148	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_142706.1	chr17	47878977	47878985	-	1	NA	intron (NM_001110824, intron 5 of 16)	(CACG)n|Simple_repeat|Simple_repeat	-44290	NM_001109973	17240	Mm.329100	NM_010783	ENSMUSG00000032717	Mdfi	I-mf|I-mfa	MyoD family inhibitor	protein-coding
mm_119029.1	chr14	30025664	30025676	+	1	NA	intron (NM_175343, intron 1 of 7)	L1MCc|LINE|L1	3037	NM_175343	218865	Mm.259916	NM_172264	ENSMUSG00000015970	Chdh	AU041472|D630034H06Rik	choline dehydrogenase	protein-coding
mm_128616.1	chr15	58929838	58929840	-	1	NA	intron (NM_175151, intron 1 of 11)	intron (NM_175151, intron 1 of 11)	3891	NM_175151	69694	Mm.383230	NM_175151	ENSMUSG00000050891	Tatdn1	2310079P03Rik|CDA11	TatD DNase domain containing 1	protein-coding
mm_170143.1	chr17	42007482	42007483	-	1	NA	Intergenic	L1Md_A|LINE|L1	-308465	NM_028474	627626	Mm.390999	NM_028474	ENSMUSG00000042256	Ptchd4	3110082D06Rik|Gm321	patched domain containing 4	protein-coding
mm_76989.1	chr8	107056698	107056707	-	1	NA	promoter-TSS (NM_139229)	promoter-TSS (NM_139229)	35	NM_139229	97484	Mm.288641	NM_139229	ENSMUSG00000031916	Cog8	BB235941|C87832	component of oligomeric golgi complex 8	protein-coding
mm_11434.1	chr2	31974451	31974498	+	1	NA	promoter-TSS (NM_172268)	promoter-TSS (NM_172268)	24	NM_172268	227720	Mm.289686	NM_172268	ENSMUSG00000001855	Nup214	BC039282|CAN|D2H9S46E	nucleoporin 214	protein-coding
mm_129935.1	chr15	84855131	84855145	-	1	NA	intron (NR_030731, intron 1 of 11)	CpG-5189	991	NM_001081166	271305	Mm.101022	NM_001081166	ENSMUSG00000016624	Phf21b	A730032D07Rik	PHD finger protein 21B	protein-coding
mm_73416.1	chr8	106058858	106058870	+	1	NA	promoter-TSS (NM_010901)	promoter-TSS (NM_010901)	-739	NM_010901	18021	Mm.383185	NM_010901	ENSMUSG00000031902	Nfatc3	C80703|D8Ertd281e|NFAT4|NFATx	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 3	protein-coding
mm_6902.1	chr1	84811655	84811658	-	1	NA	intron (NM_133975, intron 2 of 40)	intron (NM_133975, intron 2 of 40)	27648	NM_133975	14897	Mm.209265	NM_133975	ENSMUSG00000026219	Trip12	1110036I07Rik|6720416K24Rik|AA410158|Gtl6|TRIP-12	thyroid hormone receptor interactor 12	protein-coding
mm_142146.1	chr17	36006410	36006435	-	1	NA	3' UTR (NM_008207, exon 6 of 6)	3' UTR (NM_008207, exon 6 of 6)	11918	NR_015618	77810	Mm.483143	NR_015618		A930015D03Rik	-	RIKEN cDNA A930015D03 gene	ncRNA
mm_63577.1	chr7	128117910	128117916	+	1	NA	3' UTR (NM_008401, exon 30 of 30)	3' UTR (NM_008401, exon 30 of 30)	-11655	NM_021334	16411	Mm.22378	NM_021334	ENSMUSG00000030789	Itgax	AI449405|Cd11c|Cr4|N418	integrin alpha X	protein-coding
mm_74270.1	chr8	125012929	125012948	+	1	NA	promoter-TSS (NM_016909)	promoter-TSS (NM_016909)	-59	NM_016909	53424	Mm.5248	NM_016909	ENSMUSG00000056820	Tsnax	R74833|Trax	translin-associated factor X	protein-coding
mm_94684.1	chr11	19582829	19582834	+	1	NA	Intergenic	Intergenic	-341611	NM_033523	114716	Mm.266627	NM_033523	ENSMUSG00000045671	Spred2	C79158	sprouty-related, EVH1 domain containing 2	protein-coding
mm_164566.1	chr17	17882949	17882979	+	1	NA	intron (NM_013521, intron 1 of 1)	intron (NM_013521, intron 1 of 1)	975	NM_013521	14293	Mm.56951	NM_013521	ENSMUSG00000045551	Fpr1	FPR|LXA4R|fMLF-R	formyl peptide receptor 1	protein-coding
mm_139935.1	chr17	71090370	71090373	+	1	NA	intron (NM_010867, intron 21 of 37)	intron (NM_010867, intron 21 of 37)	70814	NM_001083934	17929	Mm.4103	NM_010867	ENSMUSG00000024049	Myom1	D430047A17Rik	myomesin 1	protein-coding
mm_132131.1	chr16	31865485	31865488	+	1	NA	intron (NR_045516, intron 23 of 24)	intron (NR_045516, intron 23 of 24)	-13324	NM_013900	30060	Mm.30988	NM_013900	ENSMUSG00000022780	Mfi2	CD228|MTf|Meltf	antigen p97 (melanoma associated) identified by monoclonal antibodies 133.2 and 96.5	protein-coding
mm_74792.1	chr8	22396233	22396248	-	1	NA	intron (NM_181325, intron 1 of 6)	intron (NM_181325, intron 1 of 6)	2381	NM_181325	18408	Mm.200907	NM_181325	ENSMUSG00000031482	Slc25a15	D630044L02Rik|Ornt1	solute carrier family 25 (mitochondrial carrier ornithine transporter), member 15	protein-coding
mm_16148.1	chr2	172288121	172288137	+	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	39637	NM_008561	17201	Mm.57183	NM_008561	ENSMUSG00000038537	Mc3r	MC3-R	melanocortin 3 receptor	protein-coding
mm_111752.1	chr12	103951257	103951267	-	1	NA	exon (NM_009247, exon 2 of 5)	exon (NM_009247, exon 2 of 5)	5635	NM_009247	20704	Mm.312593	NM_009247	ENSMUSG00000072849	Serpina1e	Dom5|PI5|Spi1-5	serine (or cysteine) peptidase inhibitor, clade A, member 1E	protein-coding
mm_155915.1	chrX	102017403	102017467	+	1	NA	intron (NM_001163610, intron 1 of 7)	intron (NM_001163610, intron 1 of 7)	53872	NM_001278534	331474	Mm.23297	NM_183318	ENSMUSG00000049191	Rgag4	6430402L03Rik|Mar5|Mart5|mKIAA2001	retrotransposon gag domain containing 4	protein-coding
mm_80452.1	chr9	77981507	77981524	+	1	NA	exon (NM_134255, exon 7 of 8)	exon (NM_134255, exon 7 of 8)	64150	NM_134255	68801	Mm.430736	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	ELOVL family member 5, elongation of long chain fatty acids (yeast)	protein-coding
mm_36083.1	chr4	58206640	58206648	-	1	NA	promoter-TSS (NM_022814)	promoter-TSS (NM_022814)	-48	NM_022814	64817	Mm.261024	NM_022814	ENSMUSG00000028369	Svep1	1110021D17Rik|4833413O10Rik|AA387071|D430029O09Rik|Polydom	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	protein-coding
mm_29173.1	chr3	106516102	106516116	-	1	NA	intron (NM_133869, intron 4 of 8)	B3|SINE|B2	30069	NM_028110	72121	Mm.14816	NM_028110	ENSMUSG00000027901	Dennd2d	2010308M01Rik|AI451421	DENN/MADD domain containing 2D	protein-coding
mm_172821.1	chr9	14845752	14845772	-	1	NA	Intergenic	Intergenic	-14448	NM_001310734	14608	Mm.4672	NM_010287	ENSMUSG00000031932	Gpr83	AW045253|Gir|Gpr72|RP105|RP39|RP82	G protein-coupled receptor 83	protein-coding
mm_65340.1	chr7	24980589	24980622	-	1	NA	exon (NM_001290469, exon 19 of 23)	exon (NM_001290469, exon 19 of 23)	7062	NR_106014	102465634		NR_106014	ENSMUSG00000099258	Mir7047	Gm27270|mmu-mir-7047	microRNA 7047	ncRNA
mm_75722.1	chr8	69077453	69077463	-	1	NA	intron (NM_153054, intron 1 of 16)	intron (NM_153054, intron 1 of 16)	-11278	NM_007509	11966	Mm.249096	NM_007509	ENSMUSG00000006273	Atp6v1b2	AI194269|AI790362|Atp6b2|HO57|R74844	ATPase, H+ transporting, lysosomal V1 subunit B2	protein-coding
mm_168437.1	chr1	136364891	136364906	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-18794	NM_001347110	67886	Mm.144143	NM_001081360	ENSMUSG00000041570	Camsap2	1600013L13Rik|4930541M15Rik|Camsap1l1|mKIAA1078	calmodulin regulated spectrin-associated protein family, member 2	protein-coding
mm_68917.1	chr7	126461666	126461676	-	1	NA	intron (NM_007504, intron 3 of 22)	intron (NM_007504, intron 3 of 22)	1402	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_43018.1	chr5	123907523	123907560	+	1	NA	intron (NM_026603, intron 1 of 7)	intron (NM_026603, intron 1 of 7)	266	NM_026603	68184	Mm.28549	NM_026603	ENSMUSG00000023106	Denr	1500003K04Rik	density-regulated protein	protein-coding
mm_84883.1	chr9	79758368	79758372	-	1	NA	intron (NM_009945, intron 2 of 3)	intron (NM_009945, intron 2 of 3)	1483	NM_009945	12866	Mm.152627	NM_009945	ENSMUSG00000032330	Cox7a2	COX7AL|Cox7a3|CoxVIIa-L	cytochrome c oxidase subunit VIIa 2	protein-coding
mm_115825.1	chr13	20976281	20976282	-	1	NA	intron (NM_012054, intron 12 of 20)	Lx9|LINE|L1	97018	NM_146535	258528	Mm.377554	NM_146535	ENSMUSG00000042869	Olfr1370	MOR256-14	olfactory receptor 1370	protein-coding
mm_26483.1	chr3	144697355	144697360	+	1	NA	intron (NM_001282042, intron 6 of 9)	intron (NM_001282042, intron 6 of 9)	22978	NM_001282042	54673	Mm.271775	NM_019464	ENSMUSG00000037062	Sh3glb1	AA409932|AI314629|AU015566|Bif-1|mKIAA0491	SH3-domain GRB2-like B1 (endophilin)	protein-coding
mm_165379.1	chr2	128429548	128429579	+	1	NA	promoter-TSS (NR_028591)	promoter-TSS (NR_028591)	-212	NR_028590	100043424	Mm.297222	NR_028589		Gm14005	OTTMUSG00000015351	predicted gene 14005	ncRNA
mm_153524.1	chr19	41774183	41774195	-	1	NA	intron (NM_027667, intron 9 of 11)	intron (NM_027667, intron 9 of 11)	27228	NR_040320	100502871	Mm.394485	NR_040320		Gm19424	-	predicted gene, 19424	ncRNA
mm_8999.1	chr1	165769232	165769256	-	1	NA	intron (NM_011804, intron 1 of 3)	intron (NM_011804, intron 1 of 3)	5464	NM_011804	433375	Mm.294885	NM_011804	ENSMUSG00000040713	Creg1	AA755314|Creg	cellular repressor of E1A-stimulated genes 1	protein-coding
mm_160330.1	chr8	8660805	8660805	-	1	NA	promoter-TSS (NM_010111)	promoter-TSS (NM_010111)	-32	NM_010111	13642	Mm.209813	NM_010111	ENSMUSG00000001300	Efnb2	ELF-2|Epl5|Eplg5|Htk-L|LERK-5|Lerk5|NLERK-1	ephrin B2	protein-coding
mm_13172.1	chr2	92915081	92915115	+	1	NA	promoter-TSS (NM_030725)	promoter-TSS (NM_030725)	-3	NM_030725	80976	Mm.33490	NM_030725	ENSMUSG00000027220	Syt13	5730409J20Rik|AI549909|mKIAA1427	synaptotagmin XIII	protein-coding
mm_97568.1	chr11	78937809	78937852	+	1	NA	exon (NM_010927, exon 9 of 27)	exon (NM_010927, exon 9 of 27)	12539	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_23066.1	chr3	36066047	36066063	+	1	NA	promoter-TSS (NM_172678)	promoter-TSS (NM_172678)	55	NM_172678	229211	Mm.260997	NM_172678	ENSMUSG00000027710	Acad9	2600017P15Rik|4732402K02|C630012L17Rik|NPD002	acyl-Coenzyme A dehydrogenase family, member 9	protein-coding
mm_97275.1	chr11	75999953	75999977	+	1	NA	promoter-TSS (NM_198637)	promoter-TSS (NM_198637)	53	NM_198637	74230	Mm.271247	NM_198637	ENSMUSG00000053783	1700016K19Rik	Liat1	RIKEN cDNA 1700016K19 gene	protein-coding
mm_8791.1	chr1	161775190	161775206	-	1	NA	Intergenic	Intergenic	13297	NM_001205243	14103	Mm.3355	NM_010177	ENSMUSG00000000817	Fasl	APT1LG1|CD178|CD95-L|CD95L|Fas-L|Faslg|Tnfsf6|Tnlg1a|gld	Fas ligand (TNF superfamily, member 6)	protein-coding
mm_74026.1	chr8	121730373	121730387	+	1	NA	promoter-TSS (NM_020605)	promoter-TSS (NM_020605)	-179	NM_020605	57340	Mm.306870	NM_020605	ENSMUSG00000025318	Jph3	JP-3|Jp3	junctophilin 3	protein-coding
mm_39618.1	chr5	24394389	24394430	+	1	NA	5' UTR (NM_029020, exon 1 of 16)	5' UTR (NM_029020, exon 1 of 16)	253	NM_029020	74610	Mm.283914	NM_029020	ENSMUSG00000028973	Abcb8	4833412N02Rik|AA409895	ATP-binding cassette, sub-family B (MDR/TAP), member 8	protein-coding
mm_136424.1	chr16	94222990	94222993	-	1	NA	intron (NM_139145, intron 5 of 9)	intron (NM_139145, intron 5 of 9)	64865	NM_139145	110948	Mm.30921	NM_139145	ENSMUSG00000040820	Hlcs	410I21.SP6|D16Jhu34	holocarboxylase synthetase (biotin- [propriony-Coenzyme A-carboxylase (ATP-hydrolysing)] ligase)	protein-coding
mm_74973.1	chr8	27128616	27128687	-	1	NA	promoter-TSS (NM_025686)	promoter-TSS (NM_025686)	-19	NM_025686	66653	Mm.334467	NM_025686	ENSMUSG00000031487	Brf2	2700059M06Rik|5730512K07Rik|AU018504|AU022602|BRFU|TFIIIB50	BRF2, RNA polymerase III transcription initiation factor 50kDa subunit	protein-coding
mm_22852.1	chr3	28263397	28263413	+	1	NA	5' UTR (NM_001163009, exon 1 of 31)	5' UTR (NM_001163009, exon 1 of 31)	191	NM_001163009	665113	Mm.126193	NM_026910	ENSMUSG00000027692	Tnik	1500031A17Rik|4831440I19Rik|AI451411|C530008O15Rik|C630040K21Rik	TRAF2 and NCK interacting kinase	protein-coding
mm_151951.1	chr19	5801242	5801272	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	1415	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_143624.1	chr17	78870478	78870491	-	1	NA	intron (NM_011163, intron 7 of 15)	intron (NM_011163, intron 7 of 15)	12088	NM_011163	19106	Mm.378990	NM_011163	ENSMUSG00000024079	Eif2ak2	2310047A08Rik|4732414G15Rik|AI467567|AI747578|Pkr|Prkr|Tik	eukaryotic translation initiation factor 2-alpha kinase 2	protein-coding
mm_112700.1	chr13	17711161	17711165	+	1	NA	Intergenic	Intergenic	15750	NM_025479	66308	Mm.291109	NM_025479	ENSMUSG00000012429	Mplkip	2810021B07Rik|C330007M08Rik|Ttdn1	M-phase specific PLK1 intereacting protein	protein-coding
mm_156291.1	chrX	136837495	136837498	+	1	NA	3' UTR (NM_011123, exon 7 of 7)	3' UTR (NM_011123, exon 7 of 7)	14750	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_45631.1	chr5	76331089	76331099	-	1	NA	promoter-TSS (NM_023508)	promoter-TSS (NM_023508)	62	NM_001310637	79455	Mm.143764	NM_023508	ENSMUSG00000029235	Pdcl2	1700010B22Rik|1700016K07Rik|Mgcphlp|Tphlp	phosducin-like 2	protein-coding
mm_115700.1	chr13	14317989	14318016	-	1	NA	intron (NM_001081348, intron 9 of 28)	intron (NM_001081348, intron 9 of 28)	205224	NM_001081348	94253	Mm.125298	NM_153130	ENSMUSG00000021301	Hecw1	9330116H24Rik|AV273951|E130207I19Rik|Nedl1	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	protein-coding
mm_80862.1	chr9	98490546	98490562	+	1	NA	promoter-TSS (NM_009034)	promoter-TSS (NM_009034)	17	NM_009034	19660	Mm.12825	NM_009034	ENSMUSG00000032454	Rbp2	Crbp-2|CrbpII|Rbp-2	retinol binding protein 2, cellular	protein-coding
mm_89925.1	chr10	111229441	111229465	+	1	NA	intron (NM_175489, intron 3 of 23)	ORR1A2-int|LTR|ERVL-MaLR	64651	NM_175489	237542	Mm.220204	NM_175489	ENSMUSG00000020189	Osbpl8	AA536976|AA536995|C730029P18Rik|D330025H14Rik|ORP-8	oxysterol binding protein-like 8	protein-coding
mm_144255.1	chr18	10921954	10921958	+	1	NA	Intergenic	Intergenic	-130554	NM_010258	14465	Mm.329287	NM_010258	ENSMUSG00000005836	Gata6	AA410133|GATA-6	GATA binding protein 6	protein-coding
mm_532.1	chr1	37890520	37890542	+	1	NA	promoter-TSS (NM_027098)	promoter-TSS (NM_027098)	-22	NM_027098	107734	Mm.26614	NM_027098	ENSMUSG00000026087	Mrpl30	2310001L22Rik|MRP-L28|Rpml28	mitochondrial ribosomal protein L30	protein-coding
mm_117094.1	chr13	59822605	59822642	-	1	NA	intron (NM_153538, intron 1 of 27)	CpG	524	NM_153538	214290	Mm.233082	NM_153538	ENSMUSG00000035248	Zcchc6	6030448M23Rik|AA420405	zinc finger, CCHC domain containing 6	protein-coding
mm_166439.1	chr5	137210835	137210876	-	1	NA	Intergenic	Intergenic	-77399	NM_009599	11423	Mm.255464	NM_009599	ENSMUSG00000023328	Ache	-	acetylcholinesterase	protein-coding
mm_156110.1	chrX	114474424	114474434	+	1	NA	promoter-TSS (NM_001290478)	promoter-TSS (NM_001290478)	96	NM_001290477	237010	Mm.132583	NM_172781	ENSMUSG00000025597	Klhl4	B130014A11|C130018J01Rik	kelch-like 4	protein-coding
mm_2709.1	chr1	128103313	128103360	+	1	NA	promoter-TSS (NM_001285945)	promoter-TSS (NM_001285945)	30	NM_181750	226412	Mm.221041	NM_181750	ENSMUSG00000056211	R3hdm1	R3hdm	R3H domain containing 1	protein-coding
mm_141920.1	chr17	35000778	35000801	-	1	NA	promoter-TSS (NM_011690)	promoter-TSS (NM_011690)	-43	NM_033075	110956	Mm.22506	NM_033075		D17H6S56E-5	G7e	DNA segment, Chr 17, human D6S56E 5	protein-coding
mm_81374.1	chr9	108854687	108854706	+	1	NA	5' UTR (NM_134420, exon 1 of 18)	5' UTR (NM_134420, exon 1 of 18)	653	NM_134420	171429	Mm.45201	NM_134420	ENSMUSG00000023259	Slc26a6	B930010B04Rik|CFEX|Pat-1|Pat1	solute carrier family 26, member 6	protein-coding
mm_2610.1	chr1	120340656	120340664	+	1	NA	promoter-TSS (NM_207233)	promoter-TSS (NM_207233)	78	NM_207233	226359	Mm.337409	NM_207233	ENSMUSG00000036907	C1ql2	BC040774|CTRP10	complement component 1, q subcomponent-like 2	protein-coding
mm_95410.1	chr11	49983102	49983121	+	1	NA	Intergenic	L1M4b|LINE|L1	-42220	NM_021540	59044	Mm.359004	NM_021540	ENSMUSG00000020376	Rnf130	2510042A13Rik|G1RZFP|G1rp|GOLIATH|GP	ring finger protein 130	protein-coding
mm_88211.1	chr10	70204646	70204652	+	1	NA	promoter-TSS (NM_001304739)	promoter-TSS (NM_001304739)	-15	NM_001304739	69563	Mm.64672	NM_001304739	ENSMUSG00000019933	Mrln	2310015B20Rik|Mln	myoregulin	protein-coding
mm_137974.1	chr17	33558848	33558862	+	1	NA	intron (NM_053214, intron 1 of 27)	ID_B1|SINE|B4	3148	NM_053214	17916	Mm.42019	NM_053214	ENSMUSG00000024300	Myo1f	C330006B10Rik	myosin IF	protein-coding
mm_107926.1	chr12	71111403	71111413	+	1	NA	promoter-TSS (NM_029227)	promoter-TSS (NM_029227)	-20	NM_029227	75266	Mm.402075	NM_029227	ENSMUSG00000021078	Tomm20l	4930553D19Rik	translocase of outer mitochondrial membrane 20 homolog (yeast)-like	protein-coding
mm_35961.1	chr4	53142740	53142755	-	1	NA	intron (NM_013454, intron 2 of 49)	Charlie29a|DNA|hAT-Charlie	17148	NM_013454	11303	Mm.277376	NM_013454	ENSMUSG00000015243	Abca1	ABC-1|Abc1	ATP-binding cassette, sub-family A (ABC1), member 1	protein-coding
mm_14133.1	chr2	126035667	126035690	+	1	NA	5' UTR (NM_008008, exon 2 of 4)	5' UTR (NM_008008, exon 2 of 4)	1020	NM_008008	14178	Mm.330557	NM_008008	ENSMUSG00000027208	Fgf7	Kgf	fibroblast growth factor 7	protein-coding
mm_172428.1	chr7	28350728	28350728	+	1	NA	promoter-TSS (NM_013647)	promoter-TSS (NM_013647)	39	NM_013647	20055	Mm.702	NM_013647	ENSMUSG00000037563	Rps16	AA420385|AI317031	ribosomal protein S16	protein-coding
mm_55935.1	chr6	84588964	84588983	-	1	NA	intron (NM_175475, intron 1 of 6)	intron (NM_175475, intron 1 of 6)	4837	NM_175475	232174	Mm.255246	NM_175475	ENSMUSG00000063415	Cyp26b1	CP26|P450RAI-2	cytochrome P450, family 26, subfamily b, polypeptide 1	protein-coding
mm_20205.1	chr2	125301724	125301736	-	1	NA	exon (NM_007993, exon 66 of 66)	exon (NM_007993, exon 66 of 66)	54215	NM_023595	110074	Mm.282499	NM_023595	ENSMUSG00000027203	Dut	5031412I06Rik|5133400F09Rik|D2Bwg0749e|Dutp|dUTPase	deoxyuridine triphosphatase	protein-coding
mm_10548.1	chr2	16657416	16657420	+	1	NA	intron (NM_026162, intron 6 of 13)	B1_Mm|SINE|Alu	301114	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding
mm_103405.1	chr11	75439574	75439581	-	1	NA	promoter-TSS (NM_008878)	promoter-TSS (NM_008878)	-76	NM_008878	18816	Mm.279733	NM_008878	ENSMUSG00000038224	Serpinf2	AI747498|Pli|Serpimf2	serine (or cysteine) peptidase inhibitor, clade F, member 2	protein-coding
mm_156511.1	chrX	150550941	150550954	+	1	NA	intron (NM_001102446, intron 1 of 10)	intron (NM_001102446, intron 1 of 10)	-3502	NR_106147	102465782		NR_106147	ENSMUSG00000099172	Mir3620	Gm27984|mmu-mir-3620	microRNA 3620	ncRNA
mm_126075.1	chr15	77729092	77729096	+	1	NA	promoter-TSS (NM_173743)	promoter-TSS (NM_173743)	22	NM_173743	71898	Mm.422856	NM_173743	ENSMUSG00000068246	Apol9b	2310016F22Rik	apolipoprotein L 9b	protein-coding
mm_131073.1	chr16	4701183	4701195	+	1	NA	exon (NM_023646, exon 9 of 12)	exon (NM_023646, exon 9 of 12)	17119	NM_001135112	83945	Mm.248337	NM_023646	ENSMUSG00000004069	Dnaja3	1200003J13Rik|1810053A11Rik|C81173|Tid-1|Tid1l	DnaJ heat shock protein family (Hsp40) member A3	protein-coding
mm_125849.1	chr15	74959122	74959166	+	1	NA	3' UTR (NM_001164036, exon 4 of 4)	3' UTR (NM_001164036, exon 4 of 4)	4038	NM_001164040	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_46300.1	chr5	100500003	100500032	-	1	NA	intron (NM_001346583, intron 1 of 12)	CpG	622	NM_172714	231506	Mm.212568	NM_172714	ENSMUSG00000035310	Lin54	AI461788	lin-54 homolog (C. elegans)	protein-coding
mm_45341.1	chr5	65764351	65764405	-	1	NA	intron (NM_001024917, intron 1 of 19)	CpG	857	NM_001024917	333789	Mm.332398	NM_001024917	ENSMUSG00000037795	N4bp2	B3bp|E430014I16|Gm1791|Gm868	NEDD4 binding protein 2	protein-coding
mm_111522.1	chr12	100180954	100180976	-	1	NA	Intergenic	Intergenic	-7003	NR_045282	100038378	Mm.387075	NR_045282	ENSMUSG00000072884	Gm10433	ENSMUSG00000072884	predicted gene 10433	ncRNA
mm_69403.1	chr7	132317199	132317220	-	1	NA	promoter-TSS (NM_029935)	promoter-TSS (NM_029935)	-54	NM_029935	77590	Mm.213582	NM_029935	ENSMUSG00000030930	Chst15	4631426J05Rik|BRAG|GalNAcS-6ST|MAd5|mKIAA0598	carbohydrate (N-acetylgalactosamine 4-sulfate 6-O) sulfotransferase 15	protein-coding
mm_167409.1	chr8	105664298	105664312	+	1	NA	exon (NM_181322, exon 3 of 12)	exon (NM_181322, exon 3 of 12)	-26601	NM_001033320	234695	Mm.471640	NM_001033320	ENSMUSG00000050357	Carmil2	CG1399-PB|D130029J02Rik|Gm585|Rltpr	capping protein regulator and myosin 1 linker 2	protein-coding
mm_125923.1	chr15	76199580	76199590	+	1	NA	promoter-TSS (NM_201392)	promoter-TSS (NM_201392)	-179	NM_201392	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
mm_134676.1	chr16	22406154	22406162	-	1	NA	intron (NM_023794, intron 7 of 12)	MIRb|SINE|MIR	33412	NM_023794	104156	Mm.155708	NM_023794	ENSMUSG00000013089	Etv5	1110005E01Rik|8430401F14Rik|ERM	ets variant 5	protein-coding
mm_44289.1	chr5	8368169	8368181	-	1	NA	promoter-TSS (NM_001007221)	promoter-TSS (NM_001007221)	-15	NM_001310439	11496	Mm.275895	NM_001007220	ENSMUSG00000040537	Adam22	2900022I03Rik|AI854032|MDC2	a disintegrin and metallopeptidase domain 22	protein-coding
mm_43301.1	chr5	134612009	134612051	+	1	NA	intron (NM_020044, intron 1 of 12)	intron (NM_020044, intron 1 of 12)	2995	NM_022964	56743	Mm.391375	NM_020044	ENSMUSG00000040751	Lat2	AW125574|LAB|NTAL|WSCR5|Wbscr15|Wbscr5	linker for activation of T cells family, member 2	protein-coding
mm_53155.1	chr6	125266264	125266283	+	1	NA	intron (NR_015527, intron 1 of 3)	intron (NR_015527, intron 1 of 3)	748	NR_015527	73870	Mm.440681	NR_015527	ENSMUSG00000108129	4930417O13Rik	-	RIKEN cDNA 4930417O13 gene	ncRNA
mm_57886.1	chr6	131353558	131353610	-	1	NA	Intergenic	Intergenic	34866	NM_139117	56449	Mm.458000	NM_011733	ENSMUSG00000030189	Ybx3	Csda|Dpba|MSY3|MSY4|Yb2|dbpA|oxyR	Y box protein 3	protein-coding
mm_162748.1	chr10	58371506	58371536	+	1	NA	promoter-TSS (NM_201242)	promoter-TSS (NM_201242)	67	NM_201242	110829	Mm.57734	NM_026148	ENSMUSG00000019920	Lims1	2310016J22Rik|4921524A02Rik|AI507642|AU021743|AW551584|C430041B13Rik|Lims1l|PINCH|PINCH1	LIM and senescent cell antigen-like domains 1	protein-coding
mm_68417.1	chr7	109703564	109703574	-	1	NA	promoter-TSS (NM_020616)	promoter-TSS (NM_020616)	-168	NM_020616	57373	Mm.334138	NM_020616	ENSMUSG00000031023	Akip1	BCA3|C11orf17|D7H11orf17|D930014E17Rik|ICRFP703B1614Q5.6|ORF27	A kinase (PRKA) interacting protein 1	protein-coding
mm_84899.1	chr9	79830999	79831017	-	1	NA	intron (NM_001081243, intron 4 of 5)	intron (NM_001081243, intron 4 of 5)	37367	NR_040734	74633	Mm.262175	NR_040734	ENSMUSG00000086918	4930429F24Rik	-	RIKEN cDNA 4930429F24 gene	ncRNA
mm_103081.1	chr11	69900931	69900941	-	1	NA	promoter-TSS (NM_001291119)	promoter-TSS (NM_001291119)	50	NM_001316696	70419	Mm.272859	NM_027419	ENSMUSG00000018570	2810408A11Rik	1700019L01Rik|4930470J18Rik	RIKEN cDNA 2810408A11 gene	protein-coding
mm_160062.1	chr7	4970984	4970984	-	1	NA	promoter-TSS (NM_001200041)	promoter-TSS (NM_001200041)	-23	NM_001200041	381835	Mm.297828	NM_001200041	ENSMUSG00000085272	Sbk3	Gm1078|Sgk110	SH3 domain binding kinase family, member 3	protein-coding
mm_25509.1	chr3	109598543	109598546	+	1	NA	intron (NM_146139, intron 2 of 9)	intron (NM_146139, intron 2 of 9)	24537	NM_146139	57257	Mm.282257	NM_020505	ENSMUSG00000033721	Vav3	A530094I06Rik|AA986410|Idd18.1	vav 3 oncogene	protein-coding
mm_138433.1	chr17	35108267	35108273	+	1	NA	promoter-TSS (NM_148947)	promoter-TSS (NM_148947)	-30	NM_148947	114652	Mm.222643	NM_148947	ENSMUSG00000034482	Ly6g5c	G5c|NG33	lymphocyte antigen 6 complex, locus G5C	protein-coding
mm_16526.1	chr2	181525765	181525808	+	1	NA	intron (NM_001271584, intron 2 of 5)	intron (NM_001271584, intron 2 of 5)	5301	NM_001271584	13002	Mm.140761	NM_016775	ENSMUSG00000000826	Dnajc5	2610314I24Rik|AU018536|Csp	DnaJ heat shock protein family (Hsp40) member C5	protein-coding
mm_9095.1	chr1	169046892	169046896	-	1	NA	Intergenic	Intergenic	484570	NM_023284	66977	Mm.151315	NM_023284	ENSMUSG00000026683	Nuf2	2410003C07Rik|AU044112|C85691|Cdca1|NUF2R	NUF2, NDC80 kinetochore complex component	protein-coding
mm_117433.1	chr13	74591364	74591397	-	1	NA	Intergenic	Intergenic	-48492	NM_030711	80898	Mm.83526	NM_030711	ENSMUSG00000021583	Erap1	Arts1|ERAAP|PILSA|PILSAP	endoplasmic reticulum aminopeptidase 1	protein-coding
mm_48305.1	chr5	138365609	138365610	-	1	NA	Intergenic	Intergenic	-75867	NM_028130	72154	Mm.20263	NM_028130	ENSMUSG00000036898	Zfp157	2610020C11Rik|A630094N24Rik|AI327407|mszf12|mszf23-1	zinc finger protein 157	protein-coding
mm_114606.1	chr13	75794528	75794560	+	1	NA	Intergenic	Intergenic	-45342	NM_053108	93692	Mm.25844	NM_053108	ENSMUSG00000021591	Glrx	C86710|D13Wsu156e|Glrx1|Grx1|TTase	glutaredoxin	protein-coding
mm_155678.1	chrX	91632201	91632230	+	1	NA	promoter-TSS (NM_001205268)	promoter-TSS (NM_001205268)	21	NM_001205268	629542	Mm.490235	NM_001205268	ENSMUSG00000064129	Gm14781	OTTMUSG00000017976|OTTMUSG000000179761	predicted gene 14781	protein-coding
mm_51821.1	chr6	89096155	89096163	+	1	NA	promoter-TSS (NR_134977)	promoter-TSS (NR_134977)	49	NR_134977	232217	Mm.281744	NM_175017	ENSMUSG00000055403	4933427D06Rik	-	RIKEN cDNA 4933427D06 gene	ncRNA
mm_133647.1	chr16	91793878	91793892	+	1	NA	intron (NM_001110275, intron 5 of 28)	intron (NM_001110275, intron 5 of 28)	64514	NM_010587	16443	Mm.40546	NM_010587	ENSMUSG00000022957	Itsn1	AA517634|AA545208|AI316805|AI839402|AI848451|Ehsh1|Ese1|Itsn|Sh3p17	intersectin 1 (SH3 domain protein 1A)	protein-coding
mm_48269.1	chr5	137962934	137962938	-	1	NA	promoter-TSS (NM_080450)	promoter-TSS (NM_080450)	23	NM_080450	118446	Mm.332771	NM_080450	ENSMUSG00000056966	Gjc3	Cx29|Gje1	gap junction protein, gamma 3	protein-coding
mm_27111.1	chr3	30793550	30793595	-	1	NA	intron (NM_027016, intron 1 of 7)	CpG	696	NM_027016	69276	Mm.26017	NM_027016	ENSMUSG00000027706	Sec62	3100002M17Rik|AI844545|AW545092|Dtrp1|HTP1|Tloc1	SEC62 homolog (S. cerevisiae)	protein-coding
mm_136255.1	chr16	90972049	90972066	-	1	NA	intron (NM_001164483, intron 12 of 31)	Tigger9b|DNA|TcMar-Tigger	-37208	NM_026502	68001	Mm.45374	NM_026502	ENSMUSG00000022972	1110004E09Rik	-	RIKEN cDNA 1110004E09 gene	protein-coding
mm_37848.1	chr4	132192279	132192281	-	1	NA	intron (NM_145393, intron 4 of 4)	B3A|SINE|B2	19976	NM_145393	213541	Mm.23998	NM_145393	ENSMUSG00000040025	Ythdf2	9430020E02Rik|HGRG8|NY-REN-2	YTH domain family 2	protein-coding
mm_13431.1	chr2	104886319	104886344	+	1	NA	promoter-TSS (NM_177600)	promoter-TSS (NM_177600)	7	NM_177600	211936	Mm.416538	NM_177600	ENSMUSG00000045106	Ccdc73	2210415I11Rik|4931417A20|AV080665|BC095976	coiled-coil domain containing 73	protein-coding
mm_36629.1	chr4	91376491	91376502	-	1	NA	promoter-TSS (NM_001177883)	promoter-TSS (NM_001177883)	0	NM_001177883	15569	Mm.318042	NM_010486	ENSMUSG00000008489	Elavl2	Hub|mel-N1	ELAV (embryonic lethal, abnormal vision, Drosophila)-like 2 (Hu antigen B)	protein-coding
mm_39644.1	chr5	24645448	24645463	+	1	NA	promoter-TSS (NR_003953)	promoter-TSS (NR_003953)	2	NR_003953	72252	Mm.87446	NR_003953	ENSMUSG00000038165	1700022A21Rik	-	glycerol-3-phosphate dehydrogenase 1-like pseudogene	pseudo
mm_152128.1	chr19	7014151	7014213	-	1	NA	exon (NM_153795, exon 5 of 15)	exon (NM_153795, exon 5 of 15)	5287	NM_153795	108101	Mm.157591	NM_153795	ENSMUSG00000024965	Fermt3	C79673|Kindlin3	fermitin family member 3	protein-coding
mm_138723.1	chr17	36898111	36898129	+	1	NA	promoter-TSS (NM_146077)	promoter-TSS (NM_146077)	-10	NM_146077	224762	Mm.213417	NM_146077	ENSMUSG00000058063	Trim31	BC026666|HCG1|HCGI|RNF	tripartite motif-containing 31	protein-coding
mm_114935.1	chr13	95960657	95960670	+	1	NA	3' UTR (NM_029210, exon 13 of 13)	3' UTR (NM_029210, exon 13 of 13)	-68741	NM_027711	544963	Mm.38878	NM_027711	ENSMUSG00000021676	Iqgap2	4933417J23Rik|A630053O10|AI788777	IQ motif containing GTPase activating protein 2	protein-coding
mm_150539.1	chr19	39309646	39309667	+	1	NA	exon (NM_007815, exon 5 of 9)	exon (NM_007815, exon 5 of 9)	22571	NM_007815	13095	Mm.20764	NM_007815	ENSMUSG00000003053	Cyp2c29	AHOH|AHOHase|AI159681|AI196010|Ah-2|Ahh-1|Cyp2c|P450-2C	cytochrome P450, family 2, subfamily c, polypeptide 29	protein-coding
mm_102917.1	chr11	69592085	69592091	-	1	NA	TTS (NM_011640)	TTS (NM_011640)	11729	NM_001127233	22059	Mm.222	NM_011640	ENSMUSG00000059552	Trp53	Tp53|bbl|bfy|bhy|p44|p53	transformation related protein 53	protein-coding
mm_140287.1	chr17	85393817	85393818	+	1	NA	intron (NM_028576, intron 5 of 10)	intron (NM_028576, intron 5 of 10)	224579	NR_038084	100043902	Mm.150838	NR_015385	ENSMUSG00000093460	Six3os1	D17Mgi26|E130112H22Rik|Rncr1|Six3os	SIX homeobox 3, opposite strand 1	ncRNA
mm_86956.1	chr10	24927592	24927611	+	1	NA	promoter-TSS (NM_007482)	promoter-TSS (NM_007482)	-131	NM_007482	11846	Mm.154144	NM_007482	ENSMUSG00000019987	Arg1	AI|AI256583|Arg-1|PGIF	arginase, liver	protein-coding
mm_151570.1	chr19	60766381	60766471	+	1	NA	exon (NM_010123, exon 19 of 22)	exon (NM_010123, exon 19 of 22)	7959	NR_034047	100217439		NR_034047		Snora19	MBI-51	small nucleolar RNA, H/ACA box 19	snoRNA
mm_85774.1	chr9	109052461	109052464	-	1	NA	intron (NM_025858, intron 3 of 5)	intron (NM_025858, intron 3 of 5)	-2404	NM_026381	66940	Mm.196533	NM_025858	ENSMUSG00000025647	Shisa5	2310008D10Rik|6430628I05Rik|Scotin|mShisa5	shisa family member 5	protein-coding
mm_78754.1	chr9	42571612	42571616	+	1	NA	intron (NM_175481, intron 13 of 20)	intron (NM_175481, intron 13 of 20)	-99388	NM_173038	272589	Mm.34483	NM_173038	ENSMUSG00000037287	Tbcel	D330014K23|E130107N23Rik|Lrrc35	tubulin folding cofactor E-like	protein-coding
mm_63399.1	chr7	127296370	127296389	+	1	NA	5' UTR (NM_001253873, exon 1 of 31)	5' UTR (NM_001253873, exon 1 of 31)	119	NM_001253874	16408	Mm.1618	NM_008400	ENSMUSG00000030830	Itgal	(p180)|Cd11a|LFA-1|LFA-1A|Ly-15|Ly-21	integrin alpha L	protein-coding
mm_33500.1	chr4	130826022	130826038	+	1	NA	3' UTR (NM_011520, exon 5 of 5)	3' UTR (NM_011520, exon 5 of 5)	33493	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_13348.1	chr2	102968708	102968716	+	1	NA	Intergenic	LTR16D2|LTR|ERVL	-67047	NM_001039150	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_128851.1	chr15	71954353	71954364	-	1	NA	intron (NM_027174, intron 12 of 63)	intron (NM_027174, intron 12 of 63)	79869	NM_027174	69700	Mm.322500	NM_027174	ENSMUSG00000079022	Col22a1	2310067L16Rik|C80743	collagen, type XXII, alpha 1	protein-coding
mm_45687.1	chr5	77355836	77355840	-	1	NA	intron (NM_008048, intron 1 of 4)	intron (NM_008048, intron 1 of 4)	45354	NM_153798	231329	Mm.273217	NM_153798	ENSMUSG00000029250	Polr2b	Pol2rb|Rpb140|Rpb2	polymerase (RNA) II (DNA directed) polypeptide B	protein-coding
mm_16261.1	chr2	173407057	173407067	+	1	NA	Intergenic	Intergenic	-115530	NM_028158	72221	Mm.46132	NM_028158	ENSMUSG00000027518	1700021F07Rik	-	RIKEN cDNA 1700021F07 gene	protein-coding
mm_70118.1	chr7	142968761	142968777	-	1	NA	intron (NM_008554, intron 1 of 2)	CpG-13755	495	NM_008554	17173	Mm.196417	NM_008554	ENSMUSG00000009248	Ascl2	2410083I15Rik|Mash2|bHLHa45	achaete-scute family bHLH transcription factor 2	protein-coding
mm_52937.1	chr6	122934025	122934039	+	1	NA	3' UTR (NM_199311, exon 6 of 6)	3' UTR (NM_199311, exon 6 of 6)	12184	NM_199311	269799	Mm.297275	NM_199311	ENSMUSG00000049037	Clec4a1	BC049354|Dcir4	C-type lectin domain family 4, member a1	protein-coding
mm_50174.1	chr6	41558546	41558569	+	1	NA	Intergenic	Intergenic	36781	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_44099.1	chr5	149289283	149289308	+	1	NA	Intergenic	Intergenic	24291	NM_009663	11690	Mm.19844	NM_009663	ENSMUSG00000060063	Alox5ap	Flap	arachidonate 5-lipoxygenase activating protein	protein-coding
mm_46992.1	chr5	115334225	115334240	-	1	NA	3' UTR (NM_029645, exon 3 of 3)	3' UTR (NM_029645, exon 3 of 3)	6929	NM_029645	384281	Mm.229308	NM_029645	ENSMUSG00000029536	Gatc	2010003O18Rik	glutamyl-tRNA(Gln) amidotransferase, subunit C	protein-coding
mm_34769.1	chr4	153806287	153806316	+	1	NA	Intergenic	Intergenic	144175	NR_040670	407793	Mm.260950	NR_040670		BC039966	-	cDNA sequence BC039966	ncRNA
mm_7414.1	chr1	119471050	119471053	-	1	NA	3' UTR (NM_022327, exon 5 of 5)	3' UTR (NM_022327, exon 5 of 5)	33731	NM_022327	64143	Mm.27832	NM_022327	ENSMUSG00000004451	Ralb	5730472O18Rik	v-ral simian leukemia viral oncogene B	protein-coding
mm_135416.1	chr16	45158516	45158520	-	1	NA	promoter-TSS (NM_026402)	promoter-TSS (NM_026402)	155	NM_028756	74102	Mm.264984	NM_028756	ENSMUSG00000022664	Slc35a5	1010001J06Rik|AU021179|BB097433|D16Ertd450e|D730043G07Rik	solute carrier family 35, member A5	protein-coding
mm_31050.1	chr4	41136075	41136085	+	1	NA	promoter-TSS (NM_026275)	promoter-TSS (NM_026275)	59	NM_026275	67615	Mm.389540	NM_026275	ENSMUSG00000036241	Ube2r2	1200003M11Rik|Cdc34b|Ubc3b	ubiquitin-conjugating enzyme E2R 2	protein-coding
mm_64284.1	chr7	141844744	141844788	+	1	NA	exon (NM_028801, exon 8 of 49)	exon (NM_028801, exon 8 of 49)	5694	NM_028801	74180	Mm.200752	NM_028801	ENSMUSG00000066108	Muc5b	2300002I04Rik|A130042M24|AV085033|MUC5|MUC9|mucin 5b	mucin 5, subtype B, tracheobronchial	protein-coding
mm_119977.1	chr14	55561048	55561056	+	1	NA	intron (NM_001199009, intron 1 of 14)	intron (NM_001199009, intron 1 of 14)	129	NM_001199009	28199	Mm.11535	NM_133734	ENSMUSG00000022214	Dcaf11	0710008A13Rik|C76035|D14Ucla1|Dacf11|GLO14|Wdr23	DDB1 and CUL4 associated factor 11	protein-coding
mm_14531.1	chr2	132781438	132781446	+	1	NA	5' UTR (NM_007694, exon 1 of 5)	5' UTR (NM_007694, exon 1 of 5)	164	NM_007694	12653	Mm.255241	NM_007694	ENSMUSG00000027350	Chgb	Scg-1	chromogranin B	protein-coding
mm_79245.1	chr9	50554864	50554948	+	1	NA	intron (NM_133217, intron 1 of 11)	intron (NM_133217, intron 1 of 11)	232	NM_133217	170752	Mm.390149	NM_133217	ENSMUSG00000032066	Bco2	B-diox-II|Bcdo2|Bcmo2|CMO2	beta-carotene oxygenase 2	protein-coding
mm_5587.1	chr1	39552370	39552374	-	1	NA	3' UTR (NM_001033135, exon 7 of 7)	3' UTR (NM_001033135, exon 7 of 7)	-3532	NR_028555	100217461		NR_028555	ENSMUSG00000077704	Snord89	MBII-289	small nucleolar RNA, C/D box 89	snoRNA
mm_110256.1	chr12	31634593	31634677	-	1	NA	promoter-TSS (NM_001164090)	promoter-TSS (NM_001164090)	23	NM_001164090	12033	Mm.242379	NM_007530	ENSMUSG00000020650	Bcap29	AW208404|Bap29	B cell receptor associated protein 29	protein-coding
mm_33441.1	chr4	130308732	130308752	+	1	NA	promoter-TSS (NM_010174)	promoter-TSS (NM_010174)	-36	NM_010174	14077	Mm.388886	NM_010174	ENSMUSG00000028773	Fabp3	Fabph-1|Fabph-4|Fabph1|Fabph4|H-FABP|Mdgi	fatty acid binding protein 3, muscle and heart	protein-coding
mm_10682.1	chr2	22588982	22589011	+	1	NA	Intergenic	Intergenic	-33331	NM_008078	14417	Mm.4784	NM_008078	ENSMUSG00000026787	Gad2	6330404F12Rik|GAD(65)|GAD65|Gad-2	glutamic acid decarboxylase 2	protein-coding
mm_91322.1	chr10	25098092	25098114	-	1	NA	Intergenic	L1M4c|LINE|L1	102067	NM_001347460	432442	Mm.485937	NM_018747	ENSMUSG00000039166	Akap7	6430401D08|AI662165|AKAP15|Akap18|BB170514	A kinase (PRKA) anchor protein 7	protein-coding
mm_141710.1	chr17	34000301	34000318	-	1	NA	promoter-TSS (NM_001001892)	promoter-TSS (NM_001001892)	24	NM_001001892	14972	Mm.422886	NM_001001892	ENSMUSG00000061232	H2-K1	H-2K|H-2K(d)|H2-K|K-f	histocompatibility 2, K1, K region	protein-coding
mm_5205.1	chr1	13426840	13426850	-	1	NA	Intergenic	ID_B1|SINE|B4	-52762	NM_008678	17978	Mm.2537	NM_008678	ENSMUSG00000005886	Ncoa2	D1Ertd433e|GRIP-1|Grip1|KAT13C|NCoA-2|SRC-2|TIF2|bHLHe75	nuclear receptor coactivator 2	protein-coding
mm_75442.1	chr8	47533406	47533412	-	1	NA	promoter-TSS (NM_203507)	promoter-TSS (NM_203507)	61	NM_177240	320714	Mm.39461	NM_177240	ENSMUSG00000038102	Trappc11	AW558465|D030016E14Rik|R75422	trafficking protein particle complex 11	protein-coding
mm_169845.1	chr16	3120666	3120666	-	1	NA	Intergenic	Intergenic	-471732	NM_146860	258859	Mm.377723	NM_146860	ENSMUSG00000051003	Olfr161	MOR131-1|OR912-47M6	olfactory receptor 161	protein-coding
mm_139753.1	chr17	63896052	63896063	+	1	NA	5' UTR (NM_001286415, exon 2 of 18)	5' UTR (NM_001286415, exon 2 of 18)	17991	NM_001286415	14158	Mm.23039	NM_008000	ENSMUSG00000000127	Fer	AV082135|C330004K01Rik|Fert|Fert2	fer (fms/fps related) protein kinase	protein-coding
mm_109850.1	chr12	4689952	4689955	-	1	NA	intron (NM_011365, intron 28 of 38)	intron (NM_011365, intron 28 of 38)	48430	NM_029107	74855	Mm.269534	NM_029107	ENSMUSG00000079177	Fam228a	4930417G10Rik	family with sequence similarity 228, member A	protein-coding
mm_167855.1	chrX	10697432	10697434	-	1	NA	Intergenic	Intergenic	-19932	NM_026524	68041	Mm.29429	NM_026524	ENSMUSG00000008035	Mid1ip1	3110038L01Rik|Mig12|S14R	Mid1 interacting protein 1 (gastrulation specific G12-like (zebrafish))	protein-coding
mm_62499.1	chr7	101970691	101970730	+	1	NA	intron (NM_133947, intron 1 of 24)	intron (NM_133947, intron 1 of 24)	867	NM_133947	101706	Mm.27259	NM_133947	ENSMUSG00000066306	Numa1	6720401E04Rik|AA764025|AL022610|AU014979|NuMA	nuclear mitotic apparatus protein 1	protein-coding
mm_78722.1	chr9	41579971	41579991	+	1	NA	intron (NR_131930, intron 3 of 3)	intron (NR_131930, intron 3 of 3)	-1272	NR_015483	73144	Mm.38166	NM_001033153	ENSMUSG00000074415	3110039I08Rik	2610203C20Rik|AI848448|D230004N17Rik|D3Mgi9|Mir100hg	RIKEN cDNA 3110039I08 gene	ncRNA
mm_36835.1	chr4	106492188	106492200	-	1	NA	promoter-TSS (NM_080458)	promoter-TSS (NM_080458)	49	NM_080458	140475	Mm.135448	NM_080458	ENSMUSG00000025418	Bsnd	-	Bartter syndrome, infantile, with sensorineural deafness (Barttin)	protein-coding
mm_121948.1	chr14	24176724	24176729	-	1	NA	intron (NM_001163513, intron 6 of 31)	intron (NM_001163513, intron 6 of 31)	69194	NM_001163513	71228	Mm.68971	NM_027726	ENSMUSG00000021782	Dlg5	4933429D20Rik|T25557|mKIAA0583	discs, large homolog 5 (Drosophila)	protein-coding
mm_24076.1	chr3	87930257	87930350	+	1	NA	promoter-TSS (NM_177663)	promoter-TSS (NM_177663)	-11	NM_177663	229504	Mm.45744	NM_177663	ENSMUSG00000048039	Isg20l2	4930429N24|C80587	interferon stimulated exonuclease gene 20-like 2	protein-coding
mm_42162.1	chr5	112257570	112257582	+	1	NA	intron (NM_023695, intron 2 of 5)	intron (NM_023695, intron 2 of 5)	1756	NM_001312893	12960	Mm.29488	NM_023695	ENSMUSG00000029343	Crybb1	3110006K12Rik|BB1CRY	crystallin, beta B1	protein-coding
mm_108813.1	chr12	95692249	95692258	+	1	NA	promoter-TSS (NM_201518)	promoter-TSS (NM_201518)	27	NM_201518	399558	Mm.341948	NM_201518	ENSMUSG00000047414	Flrt2	-	fibronectin leucine rich transmembrane protein 2	protein-coding
mm_155279.1	chrX	61127952	61127960	+	1	NA	intron (NR_030706, intron 5 of 7)	intron (NR_030706, intron 5 of 7)	11578	NR_030706	331424	Mm.127263	NM_177916	ENSMUSG00000071753	C230004F18Rik	-	RIKEN cDNA C230004F18 gene	ncRNA
mm_150473.1	chr19	38734944	38734947	+	1	NA	intron (NM_019588, intron 15 of 31)	L1_Mur3|LINE|L1	84292	NM_021315	57753	Mm.86482	NM_021315	ENSMUSG00000024999	Noc3l	AF233884|Fad24	NOC3 like DNA replication regulator	protein-coding
mm_1906.1	chr1	85894450	85894454	+	1	NA	promoter-TSS (NM_022417)	promoter-TSS (NM_022417)	-58	NM_022417	64294	Mm.29870	NM_022417	ENSMUSG00000026223	Itm2c	3110038L02Rik|BRI3|Bricd2c|E25|E25C|ITM3	integral membrane protein 2C	protein-coding
mm_91024.1	chr10	17920052	17920056	-	1	NA	intron (NM_001033432, intron 1 of 3)	intron (NM_001033432, intron 1 of 3)	28013	NM_001033432	380629	Mm.276430	NM_001033432	ENSMUSG00000039879	Heca	Gm869|HDC|HDCL	hdc homolog, cell cycle regulator	protein-coding
mm_20119.1	chr2	121211968	121211977	-	1	NA	intron (NM_001290830, intron 17 of 26)	intron (NM_001290830, intron 17 of 26)	40804	NM_001290824	51885	Mm.383499	NM_153387	ENSMUSG00000027263	Tubgcp4	4932441P04Rik|76p|D2Ertd435e|GCP-4	tubulin, gamma complex associated protein 4	protein-coding
mm_121307.1	chr14	105921742	105921743	+	1	NA	Intergenic	Intergenic	-24923	NM_011897	24064	Mm.89982	NM_011897	ENSMUSG00000022114	Spry2	sprouty2	sprouty homolog 2 (Drosophila)	protein-coding
mm_130706.1	chr15	100720196	100720206	-	1	NA	5' UTR (NM_172451, exon 2 of 12)	5' UTR (NM_172451, exon 2 of 12)	276	NM_001161768	207839	Mm.22969	NM_172451	ENSMUSG00000037280	Galnt6	4632410F13|AW047994|GalNAc-T6	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 6	protein-coding
mm_90680.1	chr10	128909630	128909636	+	1	NA	promoter-TSS (NM_007653)	promoter-TSS (NM_007653)	-233	NM_007653	12512	Mm.371552	NM_007653	ENSMUSG00000025351	Cd63	C75951|ME491|Tspan30	CD63 antigen	protein-coding
mm_106251.1	chr11	117825768	117825776	-	1	NA	promoter-TSS (NM_027827)	promoter-TSS (NM_027827)	-147	NM_027827	71562	Mm.273958	NM_027827	ENSMUSG00000017718	Afmid	9030621K19Rik|Ammd|FKF|KFA|Kf|formylase	arylformamidase	protein-coding
mm_34460.1	chr4	148140481	148140507	+	1	NA	promoter-TSS (NM_027985)	promoter-TSS (NM_027985)	4	NM_027985	71890	Mm.9648	NM_027985	ENSMUSG00000029003	Mad2l2	2310033C13Rik|G1-453-4|MAD2B|REV7|repro22	MAD2 mitotic arrest deficient-like 2	protein-coding
mm_164255.1	chr15	99671116	99671123	+	1	NA	intron (NM_009597, intron 1 of 11)	intron (NM_009597, intron 1 of 11)	401	NM_009597	11419	Mm.440107	NM_009597	ENSMUSG00000023017	Asic1	AI843610|ASIC|ASIC1a|Accn2|B530003N02Rik|BNaC2	acid-sensing (proton-gated) ion channel 1	protein-coding
mm_104169.1	chr11	87421983	87421993	-	1	NA	intron (NM_031386, intron 1 of 30)	RMER15|LTR|ERVL	-5603	NM_001199293	83560	Mm.440758	NM_031386	ENSMUSG00000010342	Tex14	C85585	testis expressed gene 14	protein-coding
mm_117408.1	chr13	73963729	73963737	-	1	NA	promoter-TSS (NM_027704)	promoter-TSS (NM_027704)	-129	NM_027704	71164	Mm.66995	NM_027704	ENSMUSG00000069189	Zdhhc11	4933421L13Rik|DHHC-11|Zdhhc20	zinc finger, DHHC domain containing 11	protein-coding
mm_163314.1	chr12	6022657	6022659	+	1	NA	Intergenic	Intergenic	646156	NR_015579	72669	Mm.10434	NM_028318		2810032G03Rik	AI461720	RIKEN cDNA 2810032G03 gene	ncRNA
mm_58671.1	chr7	7298830	7298849	+	1	NA	promoter-TSS (NM_001302387)	promoter-TSS (NM_001302387)	-3	NM_001302386	12727	Mm.297883	NM_011334	ENSMUSG00000000605	Clcn4	Clc4-2|Clcn4-2	chloride channel, voltage-sensitive 4	protein-coding
mm_81724.1	chr9	112234258	112234313	+	1	NA	promoter-TSS (NR_015468)	promoter-TSS (NR_015468)	8	NR_033431	620760	Mm.259863	NR_015468	ENSMUSG00000087038	2900079G21Rik	C130083B14|Gm6179	RIKEN cDNA 2900079G21 gene	ncRNA
mm_16917.1	chr2	13572016	13572019	-	1	NA	Intergenic	Intergenic	-2294	NM_011701	22352	Mm.268000	NM_011701	ENSMUSG00000026728	Vim	-	vimentin	protein-coding
mm_102761.1	chr11	67695210	67695224	-	1	NA	promoter-TSS (NM_009038)	promoter-TSS (NM_009038)	-109	NM_009038	19674	Mm.439726	NM_009038	ENSMUSG00000020907	Rcvrn	CAR|S-modulin	recoverin	protein-coding
mm_45156.1	chr5	49497202	49497203	-	1	NA	Intergenic	Intergenic	-211543	NM_001199244	80334	Mm.160172	NM_030265	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding
mm_17549.1	chr2	30048828	30048891	-	1	NA	promoter-TSS (NM_001008498)	promoter-TSS (NM_001008498)	20	NM_001008498	71820	Mm.88053	NM_001008498	ENSMUSG00000039715	Wdr34	3200002I06Rik	WD repeat domain 34	protein-coding
mm_95371.1	chr11	49087023	49087052	+	1	NA	promoter-TSS (NM_008330)	promoter-TSS (NM_008330)	20	NM_008330	15953	Mm.24769	NM_008330	ENSMUSG00000078920	Ifi47	47kDa|IRG-47|Ifggc1|Igrd|Iigp4|Iipg4|Irgd	interferon gamma inducible protein 47	protein-coding
mm_134072.1	chr16	8666522	8666558	-	1	NA	intron (NM_025821, intron 1 of 3)	intron (NM_025821, intron 1 of 3)	5613	NM_025821	52502	Mm.142095	NM_025821	ENSMUSG00000008393	Carhsp1	1200011K09Rik|Crhsp-24|D16Ertd465e	calcium regulated heat stable protein 1	protein-coding
mm_84516.1	chr9	67036043	67036086	-	1	NA	exon (NM_001164251, exon 3 of 10)	exon (NM_001164251, exon 3 of 10)	7807	NM_001164252	22003	Mm.121878	NM_024427	ENSMUSG00000032366	Tpm1	AA986836|AI854628|TM2|Tm3|Tmpa|Tpm-1|alpha-TM	tropomyosin 1, alpha	protein-coding
mm_69239.1	chr7	127769751	127769763	-	1	NA	promoter-TSS (NM_198424)	promoter-TSS (NM_198424)	-58	NM_198424	269999	Mm.36852	NM_198424	ENSMUSG00000043964	Orai3	9930124N15|BC061259|Tmem142c	ORAI calcium release-activated calcium modulator 3	protein-coding
mm_110825.1	chr12	72628834	72628840	-	1	NA	Intergenic	Intergenic	35991	NM_025522	66375	Mm.289653	NM_025522	ENSMUSG00000021094	Dhrs7	2310016E22Rik|5730564L20Rik|AW061210|Retdsr4|Retsdr4	dehydrogenase/reductase (SDR family) member 7	protein-coding
mm_44262.1	chr5	5514907	5514918	-	1	NA	promoter-TSS (NM_001193660)	promoter-TSS (NM_001193660)	-63	NM_001193659	64945	Mm.40132	NM_022890	ENSMUSG00000046798	Cldn12	-	claudin 12	protein-coding
mm_28220.1	chr3	88425095	88425139	-	1	NA	promoter-TSS (NM_001281795)	promoter-TSS (NM_001281795)	17	NM_001281795	229517	Mm.301740	NM_178696	ENSMUSG00000050144	Slc25a44	6720482A19|B430110G05Rik	solute carrier family 25, member 44	protein-coding
mm_66619.1	chr7	45474652	45474682	-	1	NA	3' UTR (NM_027903, exon 7 of 7)	3' UTR (NM_027903, exon 7 of 7)	-7769	NM_007527	12028	Mm.19904	NM_007527	ENSMUSG00000003873	Bax	-	BCL2-associated X protein	protein-coding
mm_79639.1	chr9	59554161	59554190	+	1	NA	exon (NM_010421, exon 2 of 14)	exon (NM_010421, exon 2 of 14)	14635	NM_010421	15211	Mm.2284	NM_010421	ENSMUSG00000025232	Hexa	Hex-1	hexosaminidase A	protein-coding
mm_131484.1	chr16	17208870	17208903	+	1	NA	exon (NM_001033338, exon 1 of 1)	exon (NM_001033338, exon 1 of 1)	751	NM_001033338	239731	Mm.86671	NM_001033338	ENSMUSG00000071636	Rimbp3	Gm1759|Gm603|RIM-BP3|mKIAA1666	RIMS binding protein 3	protein-coding
mm_73092.1	chr8	94533104	94533114	+	1	NA	promoter-TSS (NM_153507)	promoter-TSS (NM_153507)	81	NM_153507	234577	Mm.291815	NM_153507	ENSMUSG00000034361	Cpne2	3322401K10Rik	copine II	protein-coding
mm_141271.1	chr17	27777938	27777948	-	1	NA	intron (NM_001033279, intron 3 of 4)	ORR1D1|LTR|ERVL-MaLR	42599	NM_001033279	224647	Mm.196577	NM_001033279	ENSMUSG00000056692	D17Wsu92e	AU020189|C030010A15|C80239	DNA segment, Chr 17, Wayne State University 92, expressed	protein-coding
mm_75010.1	chr8	27413880	27413892	-	1	NA	promoter-TSS (NM_021369)	promoter-TSS (NM_021369)	58	NM_021369	11440	Mm.283137	NM_021369	ENSMUSG00000031491	Chrna6	Acra6|Nica6	cholinergic receptor, nicotinic, alpha polypeptide 6	protein-coding
mm_53555.1	chr6	136923922	136923934	+	1	NA	3' UTR (NM_007486, exon 6 of 6)	3' UTR (NM_007486, exon 6 of 6)	-1748	NM_026983	69187	Mm.33692	NM_026983	ENSMUSG00000030219	Erp27	1810033M07Rik|1810047B09Rik	endoplasmic reticulum protein 27	protein-coding
mm_49967.1	chr6	40768413	40768422	+	1	NA	3' UTR (NM_001171003, exon 48 of 48)	3' UTR (NM_001171003, exon 48 of 48)	119077	NM_139296	194357	Mm.207087	NM_139296	ENSMUSG00000029885	Moxd2	Dbhl1	monooxygenase, DBH-like 2	protein-coding
mm_86027.1	chr9	113653575	113653599	-	1	NA	3' UTR (NM_001164677, exon 18 of 18)	3' UTR (NM_001164677, exon 18 of 18)	54672	NM_001164678	18571	Mm.29816	NM_011052	ENSMUSG00000032504	Pdcd6ip	AI480591|AW544830|Aip1|Alix|C76364|Eig2|mKIAA1375	programmed cell death 6 interacting protein	protein-coding
mm_57157.1	chr6	122742483	122742502	-	1	NA	5' UTR (NM_011401, exon 1 of 10)	5' UTR (NM_011401, exon 1 of 10)	253	NM_011401	20527	Mm.395108	NM_011401	ENSMUSG00000003153	Slc2a3	AA408729|AL023014|AL024341|AU040424|C78366|Glut-3|Glut3	solute carrier family 2 (facilitated glucose transporter), member 3	protein-coding
mm_143262.1	chr17	65613865	65613911	-	1	NA	promoter-TSS (NM_013933)	promoter-TSS (NM_013933)	-333	NM_013933	30960	Mm.266767	NM_013933	ENSMUSG00000024091	Vapa	33kDa|VAP33	vesicle-associated membrane protein, associated protein A	protein-coding
mm_19413.1	chr2	91710408	91710434	-	1	NA	promoter-TSS (NM_178724)	promoter-TSS (NM_178724)	171	NM_145528	51897	Mm.28492	NM_145528	ENSMUSG00000027244	Atg13	1110053A20Rik|D2Ertd391e|Harbi1	autophagy related 13	protein-coding
mm_37450.1	chr4	123411807	123411825	-	1	NA	promoter-TSS (NM_001167918)	promoter-TSS (NM_001167918)	95	NM_001167918	442834	Mm.483803	NM_001167918		D830031N03Rik	Kiaa0754|mKIAA0754	RIKEN cDNA D830031N03 gene	protein-coding
mm_57257.1	chr6	123283675	123283685	-	1	NA	exon (NM_019948, exon 6 of 6)	exon (NM_019948, exon 6 of 6)	6191	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_95011.1	chr11	31933660	31933674	+	1	NA	3' UTR (NM_026252, exon 10 of 10)	3' UTR (NM_026252, exon 10 of 10)	-31966	NM_026262	67592	Mm.78654	NM_026262	ENSMUSG00000020299	4930524B15Rik	-	RIKEN cDNA 4930524B15 gene	protein-coding
mm_85245.1	chr9	99035680	99035718	-	1	NA	promoter-TSS (NM_001080776)	promoter-TSS (NM_001080776)	-9	NM_001080776	382097	Mm.293727	NM_001080776	ENSMUSG00000044860	Gm1123	AV052824|CLSP	predicted gene 1123	protein-coding
mm_56382.1	chr6	94283836	94283846	-	1	NA	promoter-TSS (NM_010367)	promoter-TSS (NM_010367)	76	NM_001286786	14924	Mm.217216	NM_010367	ENSMUSG00000045095	Magi1	AIP3|BAP1|Baiap1|Gukmi1|MAGI1c|Magi-1|TNRC19|WWP3|mKIAA4129	membrane associated guanylate kinase, WW and PDZ domain containing 1	protein-coding
mm_132937.1	chr16	49856073	49856112	+	1	NA	intron (NM_010581, intron 1 of 9)	intron (NM_010581, intron 1 of 9)	438	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_91811.1	chr10	53993810	53993820	-	1	NA	intron (NM_008548, intron 5 of 12)	intron (NM_008548, intron 5 of 12)	81981	NM_008548	17155	Mm.117294	NM_008548	ENSMUSG00000003746	Man1a	Man1a1|PCR1	mannosidase 1, alpha	protein-coding
mm_7840.1	chr1	132357542	132357555	-	1	NA	exon (NM_178874, exon 5 of 5)	exon (NM_178874, exon 5 of 5)	10400	NM_001311108	68875	Mm.273785	NM_178874	ENSMUSG00000042066	Tmcc2	1110063G11Rik	transmembrane and coiled-coil domains 2	protein-coding
mm_67881.1	chr7	99345996	99346009	-	1	NA	3' UTR (NM_009825, exon 5 of 5)	3' UTR (NM_009825, exon 5 of 5)	7237	NM_009825	12406	Mm.22708	NM_009825	ENSMUSG00000070436	Serpinh1	BERF-1|Cbp1|Cbp2|Hsp47|J6|Serpinh2|gp46	serine (or cysteine) peptidase inhibitor, clade H, member 1	protein-coding
mm_3770.1	chr1	156406985	156406996	+	1	NA	intron (NM_001346967, intron 4 of 25)	B4A|SINE|B4	-7000	NM_001198597	77352	Mm.428709	NM_001033180	ENSMUSG00000026601	Axdnd1	9430070O13Rik|Gm979	axonemal dynein light chain domain containing 1	protein-coding
mm_163293.1	chr11	118869444	118869458	-	1	NA	intron (NM_001285437, intron 1 of 13)	intron (NM_001285437, intron 1 of 13)	40121	NM_001024931	52897	Mm.341103	NM_001024931	ENSMUSG00000025576	Rbfox3	Fox-3|Hrnbp3|NeuN|Neuna60	RNA binding protein, fox-1 homolog (C. elegans) 3	protein-coding
mm_140087.1	chr17	75465279	75465289	+	1	NA	promoter-TSS (NM_207246)	promoter-TSS (NM_207246)	-254	NM_207246	240168	Mm.329203	NM_207246	ENSMUSG00000071042	Rasgrp3	BC066069|Gm327	RAS, guanyl releasing protein 3	protein-coding
mm_94381.1	chr11	5485871	5485914	+	1	NA	Intergenic	Intergenic	-34749	NM_013842	22433	Mm.469937	NM_013842	ENSMUSG00000020484	Xbp1	D11Ertd39e|TREB-5|TREB5|XBP-1	X-box binding protein 1	protein-coding
mm_8135.1	chr1	136247479	136247507	-	1	NA	Intergenic	Intergenic	-13213	NM_028872	67313	Mm.36763	NM_028872	ENSMUSG00000041605	5730559C18Rik	1700034M08Rik|4933426C09Rik|AI586180|D1Mgi54	RIKEN cDNA 5730559C18 gene	protein-coding
mm_88001.1	chr10	67005087	67005093	+	1	NA	promoter-TSS (NR_110511)	promoter-TSS (NR_110511)	15	NR_110511	102634101	Mm.445258	NR_110511		Gm31763	-	predicted gene, 31763	ncRNA
mm_28034.1	chr3	83773174	83773193	-	1	NA	exon (NM_009144, exon 3 of 3)	exon (NM_009144, exon 3 of 3)	6862	NM_009144	20319	Mm.19155	NM_009144	ENSMUSG00000027996	Sfrp2	AI851596|Sdf5	secreted frizzled-related protein 2	protein-coding
mm_25375.1	chr3	107211385	107211407	+	1	NA	exon (NM_001111143, exon 9 of 9)	exon (NM_001111143, exon 9 of 9)	10336	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_58026.1	chr6	136661914	136661922	-	1	NA	promoter-TSS (NM_025806)	promoter-TSS (NM_025806)	-25	NM_025806	66857	Mm.3311	NM_025806	ENSMUSG00000030214	Plbd1	1100001H23Rik	phospholipase B domain containing 1	protein-coding
mm_140525.1	chr17	6739804	6739830	-	1	NA	exon (NM_009510, exon 12 of 13)	exon (NM_009510, exon 12 of 13)	33987	NM_183368	83672	Mm.442201	NM_031395	ENSMUSG00000041831	Sytl3	A430092N21|Slp3|Slp3-a|Slp3-b|mFLJ00307	synaptotagmin-like 3	protein-coding
mm_4124.1	chr1	169928808	169928815	+	1	NA	promoter-TSS (NM_001033185)	promoter-TSS (NM_001033185)	-128	NM_001033185	78465	Mm.291078	NM_001033185	ENSMUSG00000070532	Ccdc190	1700084C01Rik	coiled-coil domain containing 190	protein-coding
mm_67442.1	chr7	80387905	80387922	-	1	NA	promoter-TSS (NM_010194)	promoter-TSS (NM_010194)	33	NM_010194	14159	Mm.48757	NM_010194	ENSMUSG00000053158	Fes	AI586313|BB137047|FPS|c-fes	feline sarcoma oncogene	protein-coding
mm_20802.1	chr2	144270505	144270533	-	1	NA	promoter-TSS (NM_024225)	promoter-TSS (NM_024225)	53	NM_024225	69178	Mm.273379	NM_024225	ENSMUSG00000027423	Snx5	0910001N05Rik|1810032P22Rik|AU019504|D2Ertd52e	sorting nexin 5	protein-coding
mm_49288.1	chr6	17666187	17666206	+	1	NA	3' UTR (NM_007604, exon 10 of 10)	3' UTR (NM_007604, exon 10 of 10)	-27798	NM_001289624	64213	Mm.12051	NM_022332	ENSMUSG00000029534	St7	9430001H04Rik|Fam4a2|HELG|RAY1|SEN4|TSG7	suppression of tumorigenicity 7	protein-coding
mm_148760.1	chr19	6061339	6061377	+	1	NA	exon (NM_013859, exon 1 of 1)	exon (NM_013859, exon 1 of 1)	151	NM_013859	29805	Mm.2310	NM_013859	ENSMUSG00000075227	Znhit2	C11orf5|Fon|ORF6|Znhit2-ps	zinc finger, HIT domain containing 2	protein-coding
mm_90642.1	chr10	128705175	128705209	+	1	NA	promoter-TSS (NM_016756)	promoter-TSS (NM_016756)	-141	NM_016756	12566	Mm.111326	NM_016756	ENSMUSG00000025358	Cdk2	A630093N05Rik	cyclin-dependent kinase 2	protein-coding
mm_171648.1	chr4	37343444	37343445	+	1	NA	Intergenic	L1Md_T|LINE|L1	-391700	NM_001165999	242384	Mm.132507	NM_175516	ENSMUSG00000045083	Lingo2	B230217C06Rik|Lern3|Lrrn6c	leucine rich repeat and Ig domain containing 2	protein-coding
mm_71717.1	chr8	61947632	61947646	+	1	NA	intron (NM_001293783, intron 6 of 37)	intron (NM_001293783, intron 6 of 37)	19552	NM_001293783	234311	Mm.275233	NM_144928	ENSMUSG00000037921	Ddx60	9830118M07	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	protein-coding
mm_159252.1	chr2	152511576	152511576	-	1	NA	intron (NM_001039120, intron 1 of 1)	intron (NM_001039120, intron 1 of 1)	160	NM_001039120	654457	Mm.389363	NM_001039120	ENSMUSG00000074680	Defb26	EG654457	defensin beta 26	protein-coding
mm_88097.1	chr10	68723892	68723902	+	1	NA	5' UTR (NM_177794, exon 1 of 6)	5' UTR (NM_177794, exon 1 of 6)	151	NM_177794	327766	Mm.2479	NM_177794	ENSMUSG00000060044	Tmem26	3230401A06|AI195372	transmembrane protein 26	protein-coding
mm_144856.1	chr18	36679194	36679253	+	1	NA	promoter-TSS (NM_026404)	promoter-TSS (NM_026404)	8	NM_026404	67843	Mm.273350	NM_026404	ENSMUSG00000033272	Slc35a4	2610030J16Rik	solute carrier family 35, member A4	protein-coding
mm_135221.1	chr16	36778762	36778765	-	1	NA	intron (NM_001145899, intron 3 of 6)	intron (NM_001145899, intron 3 of 6)	6199	NM_001145899	57738	Mm.281804	NM_021301	ENSMUSG00000022899	Slc15a2	8430408C16Rik|C78862|Pept2	solute carrier family 15 (H+/peptide transporter), member 2	protein-coding
mm_66477.1	chr7	45008728	45008751	-	1	NA	exon (NM_001008422, exon 7 of 11)	exon (NM_001008422, exon 7 of 11)	3748	NR_106021	102466218		NR_106021	ENSMUSG00000098839	Mir7054	Gm27557|mmu-mir-7054	microRNA 7054	ncRNA
mm_46257.1	chr5	99363466	99363470	-	1	NA	intron (NR_030692, intron 3 of 3)	(A)n|Simple_repeat|Simple_repeat	-110541	NM_145839	320292	Mm.259074	NM_145839	ENSMUSG00000089809	Rasgef1b	4732452O09Rik|GPIgamma4|Gpig4	RasGEF domain family, member 1B	protein-coding
mm_138060.1	chr17	33929515	33929586	+	1	NA	promoter-TSS (NM_009059)	promoter-TSS (NM_009059)	-344	NM_009059	19732	Mm.43777	NM_009059	ENSMUSG00000041354	Rgl2	KE1.5|Rab2l|Rgt2|Rlf	ral guanine nucleotide dissociation stimulator-like 2	protein-coding
mm_91065.1	chr10	19005010	19005021	-	1	NA	exon (NM_009397, exon 7 of 9)	exon (NM_009397, exon 7 of 9)	6948	NM_001166402	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_44528.1	chr5	24423542	24423589	-	1	NA	promoter-TSS (NM_007668)	promoter-TSS (NM_007668)	-35	NM_007668	12568	Mm.298798	NM_007668	ENSMUSG00000028969	Cdk5	AW048668|Crk6	cyclin-dependent kinase 5	protein-coding
mm_111942.1	chr12	109033325	109033328	-	1	NA	exon (NM_001163175, exon 7 of 7)	exon (NM_001163175, exon 7 of 7)	34891	NM_001163175	380785	Mm.342085	NM_001163175	ENSMUSG00000040867	Begain	BM948371|Gm897	brain-enriched guanylate kinase-associated	protein-coding
mm_78399.1	chr9	28920496	28920514	+	1	NA	3' UTR (NM_177906, exon 8 of 8)	3' UTR (NM_177906, exon 8 of 8)	1042624	NM_172290	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding
mm_82067.1	chr9	122805627	122805668	+	1	NA	promoter-TSS (NM_001013405)	promoter-TSS (NM_001013405)	100	NM_001013405	382117	Mm.215892	NM_001013405	ENSMUSG00000046603	Tcaim	D9Ertd402e|Gm1129|TOAG-1	T cell activation inhibitor, mitochondrial	protein-coding
mm_104543.1	chr11	96747420	96747432	-	1	NA	intron (NM_001177898, intron 10 of 10)	intron (NM_001177898, intron 10 of 10)	30129	NM_028965	74479	Mm.270781	NM_028965	ENSMUSG00000020876	Snx11	4933439F10Rik|A930041K09Rik|AI117694	sorting nexin 11	protein-coding
mm_156833.1	chrX	164373328	164373352	+	1	NA	promoter-TSS (NM_010216)	promoter-TSS (NM_010216)	-182	NM_001308489	14205	Mm.297978	NM_010216	ENSMUSG00000031380	Vegfd	AI325264|Figf|VEGF-D	vascular endothelial growth factor D	protein-coding
mm_84145.1	chr9	59404477	59404482	-	1	NA	intron (NM_019927, intron 10 of 13)	BC1_Mm|scRNA|scRNA	-50971	NM_175325	102774	Mm.200714	NM_175325	ENSMUSG00000025235	Bbs4	AW537059|AW742241|D9Ertd464e	Bardet-Biedl syndrome 4 (human)	protein-coding
mm_98317.1	chr11	90249470	90249482	+	1	NA	promoter-TSS (NM_026178)	promoter-TSS (NM_026178)	0	NM_026178	67468	Mm.277518	NM_026178	ENSMUSG00000003948	Mmd	1200017E07Rik|1810073C06Rik|AA690185	monocyte to macrophage differentiation-associated	protein-coding
mm_35206.1	chr4	19553638	19553642	-	1	NA	intron (NM_027769, intron 3 of 15)	B1F1|SINE|Alu	16464	NM_027769	70568	Mm.38390	NM_027769	ENSMUSG00000028228	Cpne3	5430428M23Rik|5730450C07Rik|C85108|CPN3	copine III	protein-coding
mm_22066.1	chr2	168722548	168722549	-	1	NA	intron (NM_001289446, intron 1 of 27)	ORR1A2|LTR|ERVL-MaLR	11791	NM_001289445	11981	Mm.330819	NM_015731	ENSMUSG00000027546	Atp9a	IIa	ATPase, class II, type 9A	protein-coding
mm_64210.1	chr7	141476375	141476388	+	1	NA	promoter-TSS (NM_001252588)	promoter-TSS (NM_001252588)	1	NM_001252588	64540	Mm.489619	NM_053082	ENSMUSG00000025511	Tspan4	AI325509|AI746565|D130042I01Rik|NAG-2|Tm4sf7|Tspan-4	tetraspanin 4	protein-coding
mm_113233.1	chr13	27245806	27245821	+	1	NA	exon (NM_008865, exon 3 of 5)	exon (NM_008865, exon 3 of 5)	3383	NM_008865	18776	Mm.37203	NM_008865	ENSMUSG00000038891	Prl3b1	Csh2|Ghd8|PL|Pl-2|Pl2|mPL-II|mplII	prolactin family 3, subfamily b, member 1	protein-coding
mm_46243.1	chr5	99240396	99240406	-	1	NA	intron (NM_145839, intron 4 of 13)	intron (NM_145839, intron 4 of 13)	12526	NM_181318	320292	Mm.259074	NM_145839	ENSMUSG00000089809	Rasgef1b	4732452O09Rik|GPIgamma4|Gpig4	RasGEF domain family, member 1B	protein-coding
mm_149475.1	chr19	11747584	11747604	+	1	NA	promoter-TSS (NM_008118)	promoter-TSS (NM_008118)	35	NM_008118	14603	Mm.456	NM_008118	ENSMUSG00000024682	Gif	AV073125	gastric intrinsic factor	protein-coding
mm_163021.1	chr11	47097683	47097691	+	1	NA	intron (NM_011891, intron 5 of 7)	intron (NM_011891, intron 5 of 7)	281615	NM_011891	24052	Mm.338890	NM_011891	ENSMUSG00000020354	Sgcd	35kDa|delta-SG	sarcoglycan, delta (dystrophin-associated glycoprotein)	protein-coding
mm_53591.1	chr6	137772006	137772009	+	1	NA	intron (NM_172733, intron 1 of 8)	ID_B1|SINE|B4	17430	NM_172733	232449	Mm.29181	NM_172733	ENSMUSG00000030225	Dera	2010002D22Rik|2500002K03Rik|DEOC	deoxyribose-phosphate aldolase (putative)	protein-coding
mm_13845.1	chr2	119547766	119547802	+	1	NA	promoter-TSS (NM_172857)	promoter-TSS (NM_172857)	77	NM_019769	56398	Mm.214765	NM_019769	ENSMUSG00000014077	Chp1	1500003O03Rik|AA960066|AI046351|Cahp|Chp|Sid470p|p24|vac	calcineurin-like EF hand protein 1	protein-coding
mm_80635.1	chr9	89211413	89211444	+	1	NA	intron (NM_026829, intron 1 of 2)	CpG	238	NM_026829	107885	Mm.486274	NM_026829	ENSMUSG00000066442	Mthfs	1110034I12Rik|2310020H23Rik|AI119695	5, 10-methenyltetrahydrofolate synthetase	protein-coding
mm_65394.1	chr7	25116089	25116121	-	1	NA	exon (NM_001163556, exon 5 of 14)	exon (NM_001163556, exon 5 of 14)	16355	NM_011138	18987	Mm.76683	NM_011138	ENSMUSG00000008496	Pou2f2	Oct-2|Oct2a|Oct2b|Oct2c|Oct2d|Otf-2|Otf2	POU domain, class 2, transcription factor 2	protein-coding
mm_95543.1	chr11	52300077	52300084	+	1	NA	Intergenic	Intergenic	-17066	NM_001313981	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_40739.1	chr5	66676201	66676221	+	1	NA	promoter-TSS (NM_011670)	promoter-TSS (NM_011670)	90	NM_011670	22223	Mm.29807	NM_011670	ENSMUSG00000029223	Uchl1	AW822034|C88048|PGP 9.5|PGP9.5|R75593|UCH-L1|UCHL-1|gad	ubiquitin carboxy-terminal hydrolase L1	protein-coding
mm_250.1	chr1	19235494	19235503	+	1	NA	3' UTR (NM_009334, exon 7 of 7)	3' UTR (NM_009334, exon 7 of 7)	23444	NM_001025305	21419	Mm.137021	NM_009334	ENSMUSG00000025927	Tfap2b	AI606113|AP-2(beta)|E130018K07Rik|Tcfap2b	transcription factor AP-2 beta	protein-coding
mm_128824.1	chr15	67129014	67129027	-	1	NA	intron (NM_009177, intron 2 of 8)	intron (NM_009177, intron 2 of 8)	47862	NM_009177	20442	Mm.248334	NM_009177	ENSMUSG00000013846	St3gal1	5330418N22Rik|AI467004|ST3GalI|Siat4|Siat4a|St3gal-1	ST3 beta-galactoside alpha-2,3-sialyltransferase 1	protein-coding
mm_168536.1	chr1	16104437	16104438	-	1	NA	promoter-TSS (NM_011291)	promoter-TSS (NM_011291)	-4	NM_011291	19989	Mm.319659	NM_011291	ENSMUSG00000043716	Rpl7	Rpl7a|Surf-3	ribosomal protein L7	protein-coding
mm_144289.1	chr18	12128853	12128868	+	1	NA	promoter-TSS (NM_024182)	promoter-TSS (NM_024182)	10	NM_024182	66878	Mm.28551	NM_024182	ENSMUSG00000024404	Riok3	1200013N13Rik|D18Ertd331e|E130306C24Rik|Sudd	RIO kinase 3	protein-coding
mm_52028.1	chr6	95250265	95250274	+	1	NA	Intergenic	Intergenic	83724	NR_033559	414067	Mm.355990	NR_033559	ENSMUSG00000068180	AY512915	-	cDNA sequence AY512915	ncRNA
mm_29472.1	chr3	115669394	115669424	-	1	NA	Intergenic	ORR1D1|LTR|ERVL-MaLR	45646	NM_007901	13609	Mm.982	NM_007901	ENSMUSG00000045092	S1pr1	AI849002|Edg1|Lpb1|S1p|S1p1	sphingosine-1-phosphate receptor 1	protein-coding
mm_163555.1	chr13	23867984	23868013	+	1	NA	Intergenic	ID_B1|SINE|B4	-1020	NR_121611	20504	Mm.2656	NM_009198	ENSMUSG00000021335	Slc17a1	NAPI-1|Napi1|Npt1	solute carrier family 17 (sodium phosphate), member 1	protein-coding
mm_156015.1	chrX	107089633	107089641	+	1	NA	5' UTR (NM_172435, exon 2 of 3)	5' UTR (NM_172435, exon 2 of 3)	302	NM_172435	78826	Mm.74639	NM_172435	ENSMUSG00000050921	P2ry10	5830408N17Rik|Lypsr2|P2Y10	purinergic receptor P2Y, G-protein coupled 10	protein-coding
mm_80841.1	chr9	98003454	98003456	+	1	NA	promoter-TSS (NR_110443)	promoter-TSS (NR_110443)	35	NR_110443	66737	Mm.445908	NR_110443	ENSMUSG00000090255	4921534H16Rik	-	RIKEN cDNA 4921534H16 gene	ncRNA
mm_148324.1	chr18	84037397	84037401	-	1	NA	intron (NM_001081300, intron 1 of 1)	(A)n|Simple_repeat|Simple_repeat	49163	NM_001081300	110796	Mm.102136	NM_001081300	ENSMUSG00000046982	Tshz1	5730407I04Rik|D18Bwg1409e|Mtsh1|NY-CO-33|Sdccag33|Tsh1|mKIAA4206|teashirt1	teashirt zinc finger family member 1	protein-coding
mm_70256.1	chr8	3515379	3515397	+	1	NA	promoter-TSS (NM_015801)	promoter-TSS (NM_015801)	4	NM_015801	50767	Mm.23085	NM_015801	ENSMUSG00000004565	Pnpla6	AI661849|MSws|Nte	patatin-like phospholipase domain containing 6	protein-coding
mm_133664.1	chr16	92052301	92052302	+	1	NA	Intergenic	Intergenic	-6021	NM_017391	53881	Mm.217354	NM_017391	ENSMUSG00000089774	Slc5a3	AA623876|BF642829|Smit1	solute carrier family 5 (inositol transporters), member 3	protein-coding
mm_1083.1	chr1	59544192	59544245	+	1	NA	intron (NM_001013771, intron 3 of 19)	intron (NM_001013771, intron 3 of 19)	27954	NM_001013771	381260	Mm.486706	NM_001013771	ENSMUSG00000047361	Gm973	AW554518	predicted gene 973	protein-coding
mm_117327.1	chr13	68582057	68582067	-	1	NA	promoter-TSS (NM_001308475)	promoter-TSS (NM_001308475)	42	NM_001308475	210009	Mm.205514	NM_172480	ENSMUSG00000034617	Mtrr	4732420G08|MSR	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	protein-coding
mm_111483.1	chr12	98737549	98737567	-	1	NA	promoter-TSS (NM_001146199)	promoter-TSS (NM_001146199)	-153	NM_001146199	24000	Mm.4420	NM_011877	ENSMUSG00000021009	Ptpn21	PTPD1|PTPRL10	protein tyrosine phosphatase, non-receptor type 21	protein-coding
mm_36925.1	chr4	108225329	108225336	-	1	NA	Intergenic	RLTR16|LTR|ERVK	-7410	NM_001167936	230590	Mm.301798	NM_001167936	ENSMUSG00000034645	Zyg11a	BC022150	zyg-11 family member A, cell cycle regulator	protein-coding
mm_94081.1	chr10	128492972	128493034	-	1	NA	promoter-TSS (NM_001317220)	promoter-TSS (NM_001317220)	6	NM_001317220	17904	Mm.337074	NM_010860	ENSMUSG00000090841	Myl6	ESMLC|LC17|LC17-GI|MLC-3|MLC1SM|Myln	myosin, light polypeptide 6, alkali, smooth muscle and non-muscle	protein-coding
mm_70290.1	chr8	3664747	3664783	+	1	NA	promoter-TSS (NM_026985)	promoter-TSS (NM_026985)	-997	NM_026985	69189	Mm.175176	NM_026985	ENSMUSG00000013974	Mcemp1	1810033B17Rik	mast cell expressed membrane protein 1	protein-coding
mm_171102.1	chr3	133518266	133518286	-	1	NA	intron (NM_001040400, intron 1 of 10)	intron (NM_001040400, intron 1 of 10)	26114	NM_001346736	214133	Mm.347816	NM_145989	ENSMUSG00000040943	Tet2	Ayu17-449|E130014J05Rik|mKIAA1546	tet methylcytosine dioxygenase 2	protein-coding
mm_127408.1	chr15	101254201	101254329	+	1	NA	Intergenic	CpG	-12581	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_115396.1	chr13	113794605	113794618	+	1	NA	5' UTR (NM_172595, exon 1 of 5)	5' UTR (NM_172595, exon 1 of 5)	103	NM_172595	218639	Mm.79837	NM_172595	ENSMUSG00000042348	Arl15	A430036I03|Arfrp2|C230032K13Rik	ADP-ribosylation factor-like 15	protein-coding
mm_12310.1	chr2	69114722	69114724	+	1	NA	TTS (NM_001347161)	TTS (NM_001347161)	-21077	NM_181547	329416	Mm.90047	NM_181547	ENSMUSG00000034738	Nostrin	Daip2|mDaIP2	nitric oxide synthase trafficker	protein-coding
mm_19421.1	chr2	91931662	91931670	-	1	NA	promoter-TSS (NM_001291481)	promoter-TSS (NM_001291481)	36	NM_001291481	17242	Mm.906	NM_010784	ENSMUSG00000027239	Mdk	MK|Mek	midkine	protein-coding
mm_56529.1	chr6	99522656	99522736	-	1	NA	Intergenic	CpG-12329	-1703	NM_001347345	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_151522.1	chr19	58740488	58740505	+	1	NA	exon (NM_018874, exon 11 of 13)	exon (NM_018874, exon 11 of 13)	11609	NM_018874	18946	Mm.10753	NM_018874	ENSMUSG00000042179	Pnliprp1	Plrp1	pancreatic lipase related protein 1	protein-coding
mm_101735.1	chr11	43311111	43311111	-	1	NA	Intergenic	MER5A|DNA|hAT-Charlie	63350	NR_029558	387164		NR_029558	ENSMUSG00000065601	Mir146	Mirn146|miR-146a|mmu-mir-146	microRNA 146	ncRNA
mm_64908.1	chr7	16048112	16048123	-	1	NA	Intergenic	Intergenic	-23728	NM_001347559	666528	Mm.290718	NM_001099277	ENSMUSG00000078796	Zfp541	EG666528|Znf541	zinc finger protein 541	protein-coding
mm_79530.1	chr9	57708632	57708661	+	1	NA	promoter-TSS (NM_153799)	promoter-TSS (NM_153799)	77	NM_153799	353190	Mm.268104	NM_153799	ENSMUSG00000038957	Edc3	AA517853|Lsm16|Yjdc	enhancer of mRNA decapping 3	protein-coding
mm_83228.1	chr9	42343875	42343875	-	1	NA	exon (NM_001324548, exon 16 of 24)	exon (NM_001324548, exon 16 of 24)	56054	NM_009347	21683	Mm.42209	NM_009347	ENSMUSG00000037705	Tecta	Tctna	tectorin alpha	protein-coding
mm_9747.1	chr1	180580611	180580629	-	1	NA	exon (NM_007415, exon 5 of 23)	exon (NM_007415, exon 5 of 23)	-6581	NR_105869	102466761		NR_105869	ENSMUSG00000098926	Mir6904	Gm27426|mmu-mir-6904	microRNA 6904	ncRNA
mm_144704.1	chr18	34863361	34863376	+	1	NA	exon (NM_007913, exon 2 of 2)	exon (NM_007913, exon 2 of 2)	2161	NM_007913	13653	Mm.181959	NM_007913	ENSMUSG00000038418	Egr1	A530045N19Rik|ETR103|Egr-1|Krox-1|Krox-24|Krox24|NGF1-A|NGFI-A|NGFIA|TIS8|Zenk|Zfp-6|Zif268|egr	early growth response 1	protein-coding
mm_103466.1	chr11	76468397	76468473	-	1	NA	promoter-TSS (NM_001291186)	promoter-TSS (NM_001291186)	30	NM_001291186	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_108284.1	chr12	79132365	79132367	+	1	NA	intron (NM_009705, intron 2 of 7)	intron (NM_009705, intron 2 of 7)	1578	NM_009705	11847	Mm.3506	NM_009705	ENSMUSG00000021125	Arg2	AII|AU022422	arginase type II	protein-coding
mm_49444.1	chr6	29319274	29319284	+	1	NA	exon (NM_001289664, exon 1 of 7)	exon (NM_001289664, exon 1 of 7)	139	NM_001289664	330277	Mm.87624	NM_207258	ENSMUSG00000039742	Fam71f1	GARI-L1|Gm764|NYD-SP18	family with sequence similarity 71, member F1	protein-coding
mm_128909.1	chr15	73487309	73487318	-	1	NA	Intergenic	Intergenic	-25247	NM_001081066	105841	Mm.322557	NM_001081066	ENSMUSG00000036661	Dennd3	AI447457|E030003N15Rik	DENN/MADD domain containing 3	protein-coding
mm_134180.1	chr16	10960708	10960714	-	1	NA	3' UTR (NM_019980, exon 4 of 4)	3' UTR (NM_019980, exon 4 of 4)	32410	NM_019980	56722	Mm.294753	NM_019980	ENSMUSG00000022500	Litaf	3222402J11Rik|C85531|N4WBP3|TBX1	LPS-induced TN factor	protein-coding
mm_70282.1	chr8	3621530	3621583	+	1	NA	promoter-TSS (NM_026156)	promoter-TSS (NM_026156)	5	NM_001195244	100503890	Mm.254898	NM_001195244	ENSMUSG00000087687	Pet100	2900053A13Rik	PET100 homolog	protein-coding
mm_166161.1	chr5	16553506	16553517	+	1	NA	promoter-TSS (NM_010427)	promoter-TSS (NM_010427)	16	NM_010427	15234	Mm.267078	NM_010427	ENSMUSG00000028864	Hgf	C230052L06Rik|HGF/SF|NK1|NK2|SF|SF/HGF	hepatocyte growth factor	protein-coding
mm_153795.1	chr19	46031571	46031574	-	1	NA	Intergenic	Intergenic	8049	NM_010697	16825	Mm.327442	NM_010697	ENSMUSG00000025223	Ldb1	CLIM2|NLI	LIM domain binding 1	protein-coding
mm_168766.1	chr12	12390576	12390591	+	1	NA	intron (NR_045829, intron 2 of 4)	ERVB7_1-LTR_MM|LTR|ERVK	1892	NR_045829	70858	Mm.410838	NR_045829		4921511I17Rik	-	RIKEN cDNA 4921511I17 gene	ncRNA
mm_50428.1	chr6	48842670	48842680	+	1	NA	exon (NM_025326, exon 3 of 7)	exon (NM_025326, exon 3 of 7)	1019	NM_001098271	66058	Mm.27061	NM_025326	ENSMUSG00000023367	Tmem176a	0610011I04Rik|AU040201|AU041743|Keg2	transmembrane protein 176A	protein-coding
mm_155559.1	chrX	75382408	75382430	+	1	NA	promoter-TSS (NM_026126)	promoter-TSS (NM_026126)	20	NM_026126	67391	Mm.126404	NM_026126	ENSMUSG00000031198	Fundc2	4833415N24Rik|DC44|HCBP6	FUN14 domain containing 2	protein-coding
mm_85416.1	chr9	103449893	103449920	-	1	NA	exon (NM_001002896, exon 3 of 7)	exon (NM_001002896, exon 3 of 7)	26328	NR_040466	100529079	Mm.437003	NR_040466	ENSMUSG00000086236	5830418P13Rik	-	RIKEN cDNA 5830418P13 gene	ncRNA
mm_96276.1	chr11	62862110	62862114	+	1	NA	intron (NM_001033669, intron 7 of 12)	intron (NM_001033669, intron 7 of 12)	14989	NM_001291441	213980	Mm.482259	NM_001033669	ENSMUSG00000090173	Fbxw10	Fbw10|HREP|SM25H2|SM2SH2	F-box and WD-40 domain protein 10	protein-coding
mm_128713.1	chr15	63985529	63985532	-	1	NA	intron (NM_144846, intron 1 of 11)	intron (NM_144846, intron 1 of 11)	71069	NR_029414	74460	Mm.390801	NR_029414	ENSMUSG00000100127	Gsdmcl-ps	4933426G20Rik	gasdermin C-like, pseudogene	pseudo
mm_36238.1	chr4	63154838	63154848	-	1	NA	promoter-TSS (NM_007443)	promoter-TSS (NM_007443)	-671	NM_007443	11699	Mm.2197	NM_007443	ENSMUSG00000028356	Ambp	AI194774|ASPI|HI-30|Intin4|Itil|UTI	alpha 1 microglobulin/bikunin	protein-coding
mm_118544.1	chr14	17659200	17659216	+	1	NA	Intergenic	Intergenic	-1752	NM_001113417	21834	Mm.32563	NM_009380	ENSMUSG00000021779	Thrb	Nr1a2|T3R[b]|T3Rbeta|Thrb1|Thrb2|c-erbAbeta	thyroid hormone receptor beta	protein-coding
mm_1502.1	chr1	72236602	72236611	+	1	NA	Intergenic	CpG	-24299	NM_001005423	381269	Mm.422636	NM_001005423	ENSMUSG00000039395	Mreg	Gm974|Wdt2|dsu	melanoregulin	protein-coding
mm_88601.1	chr10	79793678	79793721	+	1	NA	5' UTR (NM_001161747, exon 1 of 8)	5' UTR (NM_001161747, exon 1 of 8)	127	NM_001161747	18483	Mm.34650	NM_023128	ENSMUSG00000035863	Palm	-	paralemmin	protein-coding
mm_57404.1	chr6	124865249	124865256	-	1	NA	3' UTR (NM_013488, exon 10 of 10)	3' UTR (NM_013488, exon 10 of 10)	-1335	NM_013533	14788	Mm.2514	NM_013533	ENSMUSG00000038390	Gpr162	A-2|BC031437|Grca	G protein-coupled receptor 162	protein-coding
mm_54036.1	chr6	12749154	12749167	-	1	NA	promoter-TSS (NM_001164805)	promoter-TSS (NM_001164805)	93	NM_001164805	330267	Mm.11989	NM_001164805	ENSMUSG00000032625	Thsd7a	Gm837	thrombospondin, type I, domain containing 7A	protein-coding
mm_2524.1	chr1	106712547	106712557	+	1	NA	exon (NM_177410, exon 1 of 1)	exon (NM_177410, exon 1 of 1)	1738	NM_009741	12043	Mm.257460	NM_009741	ENSMUSG00000057329	Bcl2	AW986256|Bcl-2|C430015F12Rik|D630044D05Rik|D830018M01Rik	B cell leukemia/lymphoma 2	protein-coding
mm_34342.1	chr4	143719450	143719452	+	1	NA	promoter-TSS (NM_001085412)	promoter-TSS (NM_001085412)	0	NM_001085412	277666	Mm.332023	NM_001085412	ENSMUSG00000046435	Gm13078	OTTMUSG00000010322	predicted gene 13078	protein-coding
mm_22093.1	chr2	168955230	168955240	-	1	NA	5' UTR (NM_009564, exon 1 of 6)	5' UTR (NM_009564, exon 1 of 6)	352	NM_009564	22722	Mm.2095	NM_009564	ENSMUSG00000027551	Zfp64	-	zinc finger protein 64	protein-coding
mm_157118.1	chrX	9442608	9442681	-	1	NA	exon (NM_007807, exon 11 of 13)	exon (NM_007807, exon 11 of 13)	26680	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_78765.1	chr9	43309886	43309928	+	1	NA	promoter-TSS (NM_023655)	promoter-TSS (NM_023655)	-856	NM_023655	72169	Mm.273277	NM_023655	ENSMUSG00000032013	Trim29	1110047J21Rik|2810431N19Rik|4732461M22Rik|AI119726	tripartite motif-containing 29	protein-coding
mm_7763.1	chr1	131139297	131139339	-	1	NA	Intergenic	Intergenic	-1084	NM_145508	226419	Mm.39299	NM_145508	ENSMUSG00000016526	Dyrk3	BC006704	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 3	protein-coding
mm_11663.1	chr2	35256366	35256448	+	1	NA	promoter-TSS (NM_001206367)	promoter-TSS (NM_001206367)	48	NM_001206368	227753	Mm.443	NM_146120	ENSMUSG00000026879	Gsn	ADF	gelsolin	protein-coding
mm_93381.1	chr10	105574390	105574407	-	1	NA	promoter-TSS (NM_177368)	promoter-TSS (NM_177368)	81	NM_177368	278279	Mm.25225	NM_177368	ENSMUSG00000036019	Tmtc2	8430438D04Rik|D330034A10Rik	transmembrane and tetratricopeptide repeat containing 2	protein-coding
mm_69397.1	chr7	132270398	132270419	-	1	NA	exon (NM_029935, exon 2 of 8)	exon (NM_029935, exon 2 of 8)	-45256	NR_028578	100043682	Mm.482794	NR_028578	ENSMUSG00000109270	Gm10584	ENSMUSG00000073814	predicted gene 10584	ncRNA
mm_39537.1	chr5	21424866	21424891	+	1	NA	promoter-TSS (NM_177869)	promoter-TSS (NM_177869)	-25	NM_177869	330050	Mm.40655	NM_177869	ENSMUSG00000047221	Fam185a	4631428I10|AI847670	family with sequence similarity 185, member A	protein-coding
mm_53551.1	chr6	136872435	136872438	+	1	NA	TTS (NM_008597)	TTS (NM_008597)	3387	NM_008597	17313	Mm.243085	NM_008597	ENSMUSG00000030218	Mgp	Mglap	matrix Gla protein	protein-coding
mm_136387.1	chr16	93127922	93127934	-	1	NA	Intergenic	Intergenic	225261	NR_040486	69857	Mm.81192	NR_040486	ENSMUSG00000100277	1810053B23Rik	1810008L18Rik|1810056K14Rik	RIKEN cDNA 1810053B23 gene	ncRNA
mm_161955.1	chr19	6910165	6910165	+	1	NA	promoter-TSS (NM_012021)	promoter-TSS (NM_012021)	467	NM_026306	67674	Mm.318804	NM_026306	ENSMUSG00000038812	Trmt112	0610038D11Rik|Trm112p	tRNA methyltransferase 11-2	protein-coding
mm_153532.1	chr19	41896133	41896155	-	1	NA	promoter-TSS (NM_199447)	promoter-TSS (NM_199447)	9	NM_199447	107094	Mm.276044	NM_199447	ENSMUSG00000035049	Rrp12	AA408556|AA536972|mKIAA0690	ribosomal RNA processing 12 homolog (S. cerevisiae)	protein-coding
mm_7271.1	chr1	96872166	96872179	-	1	NA	promoter-TSS (NM_172658)	promoter-TSS (NM_172658)	-1	NM_172658	227394	Mm.11662	NM_172658	ENSMUSG00000040693	Slco4c1	9530051F04|C330017E21Rik|OATP-H|OATP-M1|OATP4C1|OATPX|PRO2176|SLC21A20|oatp-R	solute carrier organic anion transporter family, member 4C1	protein-coding
mm_74611.1	chr8	12573206	12573262	-	1	NA	intron (NM_024279, intron 1 of 6)	intron (NM_024279, intron 1 of 6)	185	NM_024279	78634	Mm.116871	NM_024279	ENSMUSG00000010435	Spaca7	1700094C09Rik	sperm acrosome associated 7	protein-coding
mm_127811.1	chr15	5063742	5063758	-	1	NA	promoter-TSS (NM_001243837)	promoter-TSS (NM_001243837)	23	NM_001243837	109828	Mm.208034	NM_001243837	ENSMUSG00000079105	C7	A530026G17|Gm1238	complement component 7	protein-coding
mm_164447.1	chr16	49913253	49913260	+	1	NA	Intergenic	Intergenic	57602	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_163469.1	chr12	102743599	102743613	-	1	NA	promoter-TSS (NM_177140)	promoter-TSS (NM_177140)	55	NM_001142937	64113	Mm.291222	NM_022323	ENSMUSG00000096458	Moap1	AA987038|Map-1|Pnma4	modulator of apoptosis 1	protein-coding
mm_163095.1	chr11	69734966	69734973	-	1	NA	exon (NM_001291068, exon 29 of 29)	exon (NM_001291068, exon 29 of 29)	23664	NM_001291068	20020	Mm.16533	NM_009089	ENSMUSG00000005198	Polr2a	220kDa|Rpb1|Rpo2-1	polymerase (RNA) II (DNA directed) polypeptide A	protein-coding
mm_169538.1	chr1	50812458	50812464	+	1	NA	Intergenic	IAP1-MM_LTR|LTR|ERVK	-115062	NM_019790	56363	Mm.245154	NM_019790	ENSMUSG00000026109	Tmeff2	4832418D20Rik|7630402F16Rik|TR-2	transmembrane protein with EGF-like and two follistatin-like domains 2	protein-coding
mm_37170.1	chr4	117178759	117178779	-	1	NA	promoter-TSS (NM_001290662)	promoter-TSS (NM_001290662)	3	NM_001290662	73804	Mm.247651	NM_134471	ENSMUSG00000028678	Kif2c	4930402F02Rik|ESTM5|Knsl6|MCAK|X83316	kinesin family member 2C	protein-coding
mm_137037.1	chr17	17890698	17890700	+	1	NA	intron (NM_008039, intron 1 of 1)	RMER15|LTR|ERVL	2875	NM_008039	14289	Mm.378918	NM_008039	ENSMUSG00000052270	Fpr2	E330010I07Rik|Fpr-rs2	formyl peptide receptor 2	protein-coding
mm_46138.1	chr5	93045027	93045064	-	1	NA	promoter-TSS (NM_175270)	promoter-TSS (NM_175270)	-23	NM_175270	78088	Mm.245085	NM_175270	ENSMUSG00000045314	Sowahb	5730467H21Rik|Ankrd56	sosondowah ankyrin repeat domain family member B	protein-coding
mm_14898.1	chr2	149830841	149830879	+	1	NA	promoter-TSS (NM_001085521)	promoter-TSS (NM_001085521)	77	NM_001085521	433485	Mm.330649	NM_001085521	ENSMUSG00000074736	Syndig1	AW123113|DSPC2|Gm14134|H2C20orf39|OTTMUSG00000015750|Tmem90b	synapse differentiation inducing 1	protein-coding
mm_109074.1	chr12	104345549	104345559	+	1	NA	3' UTR (NM_011458, exon 5 of 5)	3' UTR (NM_011458, exon 5 of 5)	7068	NM_011458	20714	Mm.291569	NM_011458	ENSMUSG00000058207	Serpina3k	1300001I07Rik|D12Rp54|MMCM2|MMSpi2|RP54|Spi-2|Spi2|contrapsin	serine (or cysteine) peptidase inhibitor, clade A, member 3K	protein-coding
mm_120654.1	chr14	70531653	70531673	+	1	NA	intron (NM_145219, intron 1 of 7)	intron (NM_145219, intron 1 of 7)	842	NM_145219	213469	Mm.41708	NM_145219	ENSMUSG00000033595	Lgi3	AI841179|AW049851	leucine-rich repeat LGI family, member 3	protein-coding
mm_154901.1	chrX	20928644	20928661	+	1	NA	exon (NM_008823, exon 4 of 9)	exon (NM_008823, exon 4 of 9)	2903	NM_008823	18636	Mm.3064	NM_008823	ENSMUSG00000001128	Cfp	BCFG|Pfc	complement factor properdin	protein-coding
mm_3095.1	chr1	134415711	134415785	+	1	NA	promoter-TSS (NM_001306069)	promoter-TSS (NM_001306069)	84	NM_001306069	72674	Mm.259976	NM_028320	ENSMUSG00000026457	Adipor1	2810031L11Rik|ACDCR1|CGI-45|Paqr1	adiponectin receptor 1	protein-coding
mm_45111.1	chr5	45450212	45450220	-	1	NA	promoter-TSS (NM_024236)	promoter-TSS (NM_024236)	13	NM_024236	110391	Mm.30204	NM_024236	ENSMUSG00000015806	Qdpr	2610008L04Rik|D5Ertd371e|Dhpr|PKU2	quinoid dihydropteridine reductase	protein-coding
mm_162310.1	chr1	37344355	37344366	-	1	NA	intron (NM_001290797, intron 1 of 25)	intron (NM_001290797, intron 1 of 25)	-24857	NM_001290798	269180	Mm.5294	NM_030266	ENSMUSG00000026113	Inpp4a	107kDa|9630012D15|D130048C09Rik|R74740	inositol polyphosphate-4-phosphatase, type I	protein-coding
mm_54063.1	chr6	13871688	13871707	-	1	NA	promoter-TSS (NR_024619)	promoter-TSS (NR_024619)	128	NR_045995	76311	Mm.367129	NR_045995	ENSMUSG00000097616	1110019D14Rik	-	RIKEN cDNA 1110019D14 gene	ncRNA
mm_66005.1	chr7	30562955	30562966	-	1	NA	promoter-TSS (NM_170760)	promoter-TSS (NM_170760)	224	NM_025498	66340	Mm.86557	NM_025498	ENSMUSG00000036835	Psenen	1700023M09Rik|Pen-2	presenilin enhancer gamma secretase subunit	protein-coding
mm_140676.1	chr17	12992173	12992186	-	1	NA	promoter-TSS (NM_001113533)	promoter-TSS (NM_001113533)	80	NM_001113533	60532	Mm.275521	NM_175394	ENSMUSG00000060475	Wtap	2810408K05Rik|9430038B09Rik	Wilms tumour 1-associating protein	protein-coding
mm_21426.1	chr2	158229216	158229240	-	1	NA	promoter-TSS (NM_177657)	promoter-TSS (NM_177657)	-4	NM_177657	228846	Mm.187574	NM_177657	ENSMUSG00000037813	D630003M21Rik	-	RIKEN cDNA D630003M21 gene	protein-coding
mm_23693.1	chr3	68692056	68692069	+	1	NA	exon (NM_008351, exon 2 of 7)	exon (NM_008351, exon 2 of 7)	638	NM_008351	16159	Mm.103783	NM_008351	ENSMUSG00000027776	Il12a	IL-12p35|Il-12a|Ll12a|p35	interleukin 12a	protein-coding
mm_150917.1	chr19	46075979	46075991	+	1	NA	5' UTR (NM_001039352, exon 1 of 13)	5' UTR (NM_001039352, exon 1 of 13)	138	NM_001039351	70769	Mm.402190	NM_053086	ENSMUSG00000015176	Nolc1	NOPP130|NOPP140|P130	nucleolar and coiled-body phosphoprotein 1	protein-coding
mm_67408.1	chr7	80074875	80074887	-	1	NA	intron (NR_045695, intron 1 of 2)	intron (NR_045695, intron 1 of 2)	376	NR_045695	100859962	Mm.392575	NR_045695	ENSMUSG00000108714	Gm21057	-	predicted gene, 21057	ncRNA
mm_55267.1	chr6	53820716	53820747	-	1	NA	promoter-TSS (NM_025817)	promoter-TSS (NM_025817)	94	NM_025817	66873	Mm.422727	NM_025817	ENSMUSG00000043496	Tril	1200009O22Rik|AI316813|mKIAA0644	TLR4 interactor with leucine-rich repeats	protein-coding
mm_105693.1	chr11	107794660	107794729	-	1	NA	promoter-TSS (NM_019431)	promoter-TSS (NM_019431)	-230	NM_019431	54377	Mm.103724	NM_019431	ENSMUSG00000020723	Cacng4	AI413107|AW491861	calcium channel, voltage-dependent, gamma subunit 4	protein-coding
mm_28466.1	chr3	90695685	90695697	-	1	NA	promoter-TSS (NM_001281852)	promoter-TSS (NM_001281852)	30	NM_001281852	20202	Mm.2128	NM_009114	ENSMUSG00000056071	S100a9	60B8Ag|AW546964|BEE22|Cagb|GAGB|L1Ag|MRP14|p14	S100 calcium binding protein A9 (calgranulin B)	protein-coding
mm_113759.1	chr13	44742074	44742097	+	1	NA	intron (NM_001205044, intron 2 of 18)	intron (NM_001205044, intron 2 of 18)	10814	NM_001205043	16468	Mm.25059	NM_021878	ENSMUSG00000038518	Jarid2	Jmj|jumonji	jumonji, AT rich interactive domain 2	protein-coding
mm_23600.1	chr3	65109330	65109340	+	1	NA	promoter-TSS (NM_010597)	promoter-TSS (NM_010597)	-33	NM_010597	16497	Mm.316402	NM_010597	ENSMUSG00000027827	Kcnab1	Akr8a8|Kvbeta1.1|mKv(beta)1	potassium voltage-gated channel, shaker-related subfamily, beta member 1	protein-coding
mm_82025.1	chr9	121857733	121857752	+	1	NA	5' UTR (NM_019814, exon 1 of 4)	5' UTR (NM_019814, exon 1 of 4)	258	NM_019814	56295	Mm.347915	NM_019814	ENSMUSG00000038412	Higd1a	2210020B17Rik|7420700H20Rik|AI303276|AW049839|HIMP1|Hig1	HIG1 domain family, member 1A	protein-coding
mm_97287.1	chr11	76202085	76202103	+	1	NA	promoter-TSS (NM_027773)	promoter-TSS (NM_027773)	38	NM_027773	116972	Mm.188413	NM_027773	ENSMUSG00000069808	Fam57a	2310047D13Rik|4932415L08Rik|5430402E13Rik|5430420K21Rik|Wdt3	family with sequence similarity 57, member A	protein-coding
mm_166284.1	chr5	96997439	96997485	+	1	NA	promoter-TSS (NM_080708)	promoter-TSS (NM_080708)	-227	NM_080708	140780	Mm.281490	NM_080708	ENSMUSG00000034663	Bmp2k	4933417M22Rik|AA673486|AV128808|BIKE	BMP2 inducible kinase	protein-coding
mm_143263.1	chr17	65613923	65613937	-	1	NA	promoter-TSS (NM_013933)	promoter-TSS (NM_013933)	-375	NM_013933	30960	Mm.266767	NM_013933	ENSMUSG00000024091	Vapa	33kDa|VAP33	vesicle-associated membrane protein, associated protein A	protein-coding
mm_112565.1	chr13	13526144	13526146	+	1	NA	Intergenic	Intergenic	-64264	NM_010748	17101	Mm.342337	NM_010748	ENSMUSG00000019726	Lyst	D13Sfk13|beige|bg	lysosomal trafficking regulator	protein-coding
mm_108827.1	chr12	95747125	95747128	+	1	NA	intron (NM_201518, intron 1 of 1)	intron (NM_201518, intron 1 of 1)	54900	NM_201518	399558	Mm.341948	NM_201518	ENSMUSG00000047414	Flrt2	-	fibronectin leucine rich transmembrane protein 2	protein-coding
mm_95404.1	chr11	49846733	49846758	+	1	NA	promoter-TSS (NM_001163671)	promoter-TSS (NM_001163671)	-6	NM_001163671	26420	Mm.68933	NM_016961	ENSMUSG00000020366	Mapk9	AI851083|JNK2|Prkm9|p54aSAPK	mitogen-activated protein kinase 9	protein-coding
mm_67295.1	chr7	79143302	79143327	-	1	NA	exon (NM_008594, exon 4 of 10)	exon (NM_008594, exon 4 of 10)	5746	NM_001045489	17304	Mm.1451	NM_008594	ENSMUSG00000030605	Mfge8	AA408458|AI325141|MFG-E8|MP47|Mfgm|P47|SED1|lactadherin	milk fat globule-EGF factor 8 protein	protein-coding
mm_20655.1	chr2	132103419	132103446	-	1	NA	intron (NM_018824, intron 1 of 15)	intron (NM_018824, intron 1 of 15)	41676	NM_018824	54338	Mm.103581	NM_018824	ENSMUSG00000027340	Slc23a2	AI844736|NBTL1|SVCT2|Slc23a1|YSPL2|YSPL3|mKIAA0238	solute carrier family 23 (nucleobase transporters), member 2	protein-coding
mm_98603.1	chr11	95831525	95831538	+	1	NA	3' UTR (NM_001163464, exon 8 of 8)	3' UTR (NM_001163464, exon 8 of 8)	7031	NM_153104	237928	Mm.133075	NM_153104	ENSMUSG00000050860	Phospho1	D11Moh36|Phospo1	phosphatase, orphan 1	protein-coding
mm_108254.1	chr12	78248588	78248591	+	1	NA	intron (NM_145965, intron 1 of 22)	intron (NM_145965, intron 1 of 22)	21934	NM_145965	268566	Mm.341742	NM_145965	ENSMUSG00000047454	Gphn	5730552E08Rik|AI662856|BC027112|C230040D23|GPH|GPHRYN|geph	gephyrin	protein-coding
mm_85834.1	chr9	110476605	110476627	-	1	NA	promoter-TSS (NM_001163569)	promoter-TSS (NM_001163569)	78	NM_177771	270201	Mm.41744	NM_177771	ENSMUSG00000054792	Klhl18	A930041K15|AW545966	kelch-like 18	protein-coding
mm_32439.1	chr4	107253888	107253902	+	1	NA	promoter-TSS (NM_029985)	promoter-TSS (NM_029985)	-39	NM_028394	72938	Mm.21787	NM_028394	ENSMUSG00000063172	Hspb11	2900042B11Rik|IFT25	heat shock protein family B (small), member 11	protein-coding
mm_65036.1	chr7	18560613	18560624	-	1	NA	exon (NM_001037168, exon 4 of 5)	exon (NM_001037168, exon 4 of 5)	6687	NM_001037168	545925	Mm.440302	NM_001037168	ENSMUSG00000070797	Psg27	EG545925|cea15	pregnancy-specific glycoprotein 27	protein-coding
mm_106831.1	chr12	8003285	8003307	+	1	NA	exon (NM_009693, exon 24 of 29)	exon (NM_009693, exon 24 of 29)	25619	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_91086.1	chr10	19015260	19015271	-	1	NA	5' UTR (NM_009397, exon 1 of 9)	5' UTR (NM_009397, exon 1 of 9)	145	NM_009397	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_92133.1	chr10	66124059	66124069	-	1	NA	promoter-TSS (NR_038039)	promoter-TSS (NR_038039)	0	NR_038039	69433	Mm.23366	NR_038039	ENSMUSG00000100000	1700023F02Rik	AV205046	RIKEN cDNA 1700023F02 gene	ncRNA
mm_16266.1	chr2	173659596	173659616	+	1	NA	promoter-TSS (NM_024436)	promoter-TSS (NM_024436)	-67	NR_027957	100043911	Mm.260590	NM_001033179	ENSMUSG00000055897	Ppp4r1l-ps	1700007P14Rik|5830403E09Rik|C030010B13Rik|Ppp4r1l	protein phosphatase 4, regulatory subunit 1-like, pseudogene	pseudo
mm_65347.1	chr7	24989953	24989970	-	1	NA	exon (NM_001290469, exon 13 of 23)	exon (NM_001290469, exon 13 of 23)	-2294	NR_106014	102465634		NR_106014	ENSMUSG00000099258	Mir7047	Gm27270|mmu-mir-7047	microRNA 7047	ncRNA
mm_169887.1	chr16	46155070	46155077	-	1	NA	promoter-TSS (NM_001304528)	promoter-TSS (NM_001304528)	4	NM_001304528	11615	Mm.330692	NM_001304528	ENSMUSG00000048087	Gm4737	AL024110|EG11615|ENSMUSG00000048087	predicted gene 4737	protein-coding
mm_84962.1	chr9	83805343	83805343	-	1	NA	intron (NM_148941, intron 1 of 5)	intron (NM_148941, intron 1 of 5)	962	NM_148941	83603	Mm.83949	NM_148941	ENSMUSG00000032262	Elovl4	-	elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 4	protein-coding
mm_69866.1	chr7	141455069	141455079	-	1	NA	promoter-TSS (NR_028142)	promoter-TSS (NR_028142)	-114	NM_025802	66853	Mm.29998	NM_025802	ENSMUSG00000025509	Pnpla2	0610039C21Rik|1110001C14Rik|Atgl|TTS-2.2	patatin-like phospholipase domain containing 2	protein-coding
mm_62978.1	chr7	120173828	120173832	+	1	NA	promoter-TSS (NM_028085)	promoter-TSS (NM_028085)	-28	NM_028085	72074	Mm.23165	NM_028085	ENSMUSG00000030909	Anks4b	2010013E14Rik|AI956809|Harp	ankyrin repeat and sterile alpha motif domain containing 4B	protein-coding
mm_88199.1	chr10	70110025	70110027	+	1	NA	intron (NM_001111121, intron 1 of 8)	intron (NM_001111121, intron 1 of 8)	12905	NM_001111121	76551	Mm.281741	NM_001111121	ENSMUSG00000048701	Ccdc6	2810012H18Rik|AA536681|AA960498|AW061011	coiled-coil domain containing 6	protein-coding
mm_171937.1	chr5	65863713	65863713	+	1	NA	5' UTR (NM_001081105, exon 1 of 3)	5' UTR (NM_001081105, exon 1 of 3)	144	NM_001081105	74734	Mm.20323	NM_001081105	ENSMUSG00000029204	Rhoh	5830400A04Rik|AU019774|Arhh	ras homolog family member H	protein-coding
mm_33830.1	chr4	135626703	135626711	+	1	NA	promoter-TSS (NR_027909)	promoter-TSS (NR_027909)	52	NR_027909	73937	Mm.292326	NM_028688	ENSMUSG00000086788	1700029M20Rik	4930406E24Rik	RIKEN cDNA 1700029M20 gene	ncRNA
mm_87222.1	chr10	40349475	40349518	+	1	NA	5' UTR (NM_001168304, exon 1 of 13)	5' UTR (NM_001168304, exon 1 of 13)	188	NM_001291816	78334	Mm.200924	NM_198164	ENSMUSG00000038481	Cdk19	2700084L06Rik|AI845279|AW228747|CDK11|Cdc2l6|mKIAA1028	cyclin-dependent kinase 19	protein-coding
mm_25705.1	chr3	122483772	122483794	+	1	NA	intron (NM_013867, intron 3 of 11)	intron (NM_013867, intron 3 of 11)	57898	NR_106117	102465764		NR_106117	ENSMUSG00000104773	Mir7657	mmu-mir-7657	microRNA 7657	ncRNA
mm_157744.1	chrX	73242986	73243025	-	1	NA	5' UTR (NM_183094, exon 1 of 9)	5' UTR (NM_183094, exon 1 of 9)	125	NM_183094	72891	Mm.104764	NM_183094	ENSMUSG00000031362	Xlr4c	2900036K24Rik	X-linked lymphocyte-regulated 4C	protein-coding
mm_94655.1	chr11	17051977	17051996	+	1	NA	promoter-TSS (NM_029861)	promoter-TSS (NM_029861)	52	NM_029861	380686	Mm.425666	NM_029861	ENSMUSG00000044629	Cnrip1	1500041B16Rik|3110054C06Rik|5330437A18Rik|AI854501|C2orf32	cannabinoid receptor interacting protein 1	protein-coding
mm_148170.1	chr18	78057397	78057407	-	1	NA	promoter-TSS (NM_001101038)	promoter-TSS (NM_001101038)	-134	NM_001101038	620235	Mm.35607	NM_001101038	ENSMUSG00000091055	Siglec15	Cd33l3|EG620235|SIGLEC-I	sialic acid binding Ig-like lectin 15	protein-coding
mm_83322.1	chr9	44185399	44185401	-	1	NA	intron (NM_007619, intron 2 of 15)	intron (NM_007619, intron 2 of 15)	48646	NM_007619	12402	Mm.266871	NM_007619	ENSMUSG00000034342	Cbl	4732447J05Rik|Cbl-2|c-Cbl|cbl	Casitas B-lineage lymphoma	protein-coding
mm_142810.1	chr17	51171632	51171647	-	1	NA	intron (NM_028162, intron 1 of 21)	Lx9|LINE|L1	7713	NM_028162	72238	Mm.120650	NM_028162	ENSMUSG00000023923	Tbc1d5	1600014N05Rik	TBC1 domain family, member 5	protein-coding
mm_116527.1	chr13	45812386	45812389	-	1	NA	intron (NM_001199304, intron 3 of 6)	intron (NM_001199304, intron 3 of 6)	152604	NM_001199304	20238	Mm.342683	NM_009124	ENSMUSG00000046876	Atxn1	2900016G23Rik|Atx1|C85907|ENSMUSG00000074917|Gm10786|Sca1	ataxin 1	protein-coding
mm_79214.1	chr9	49102721	49102752	+	1	NA	promoter-TSS (NM_030709)	promoter-TSS (NM_030709)	-43	NM_030709	80893	Mm.72799	NM_030709	ENSMUSG00000032268	Tmprss5	spinesin	transmembrane protease, serine 5 (spinesin)	protein-coding
mm_38593.1	chr4	141825550	141825576	-	1	NA	exon (NM_007919, exon 2 of 8)	exon (NM_007919, exon 2 of 8)	442	NM_007919	13706	Mm.45316	NM_007919	ENSMUSG00000058579	Cela2a	Ela-2|Ela2|Ela2a	chymotrypsin-like elastase family, member 2A	protein-coding
mm_146353.1	chr18	82564809	82564828	+	1	NA	intron (NM_001025254, intron 2 of 5)	intron (NM_001025254, intron 2 of 5)	10310	NM_001025254	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_31980.1	chr4	89050297	89050324	+	1	NA	promoter-TSS (NR_033533)	promoter-TSS (NR_033533)	3	NR_033533	100040617	Mm.171720	NR_033533	ENSMUSG00000085183	Gm12603	OTTMUSG00000007693	predicted gene 12603	ncRNA
mm_60099.1	chr7	35186359	35186369	+	1	NA	promoter-TSS (NM_017394)	promoter-TSS (NM_017394)	-21	NM_017394	53896	Mm.35567	NM_017394	ENSMUSG00000030495	Slc7a10	AL024237|Asc-1|D7Bwg0847e	solute carrier family 7 (cationic amino acid transporter, y+ system), member 10	protein-coding
mm_5864.1	chr1	53774123	53774131	-	1	NA	intron (NM_133810, intron 2 of 7)	intron (NM_133810, intron 2 of 7)	11088	NM_133810	98267	Mm.25559	NM_133810	ENSMUSG00000026094	Stk17b	3110009A03Rik|AI120141|Drak2	serine/threonine kinase 17b (apoptosis-inducing)	protein-coding
mm_8288.1	chr1	143093575	143093603	-	1	NA	Intergenic	Intergenic	-547108	NM_020025	26878	Mm.285580	NM_020025	ENSMUSG00000033849	B3galt2	-	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 2	protein-coding
mm_99117.1	chr11	100141322	100141362	+	1	NA	exon (NM_008471, exon 5 of 6)	exon (NM_008471, exon 5 of 6)	2357	NM_001313963	16669	Mm.439699	NM_008471	ENSMUSG00000020911	Krt19	AI663979|CK-19|EndoC|K19|Krt-1.19|Krt1-19	keratin 19	protein-coding
mm_21789.1	chr2	164856958	164857024	-	1	NA	5' UTR (NM_011125, exon 2 of 16)	5' UTR (NM_011125, exon 2 of 16)	717	NM_011125	18830	Mm.6105	NM_011125	ENSMUSG00000017754	Pltp	Bpife|OD107	phospholipid transfer protein	protein-coding
mm_129931.1	chr15	84557777	84557875	-	1	NA	promoter-TSS (NM_177630)	promoter-TSS (NM_177630)	-3	NM_177630	223732	Mm.6471	NM_177630	ENSMUSG00000055745	Ldoc1l	BC058638|Mar6|Mart6	leucine zipper, down-regulated in cancer 1-like	protein-coding
mm_23275.1	chr3	51660379	51660395	+	1	NA	promoter-TSS (NM_174995)	promoter-TSS (NM_174995)	-792	NM_174995	211666	Mm.24679	NM_174995	ENSMUSG00000074604	Mgst2	GST2|MGST-II	microsomal glutathione S-transferase 2	protein-coding
mm_165083.1	chr19	46868972	46868993	-	1	NA	intron (NM_001102471, intron 5 of 6)	intron (NM_001102471, intron 5 of 6)	93369	NM_029810	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_48056.1	chr5	136565515	136565530	-	1	NA	exon (NM_001291240, exon 1 of 23)	exon (NM_001291240, exon 1 of 23)	459	NM_001291239	13047	Mm.320317	NM_009986	ENSMUSG00000029705	Cux1	CDP|Cutl1|Cux|Cux-1	cut-like homeobox 1	protein-coding
mm_30069.1	chr3	137954775	137954775	-	1	NA	intron (NM_011932, intron 3 of 8)	intron (NM_011932, intron 3 of 8)	26774	NM_011932	26377	Mm.254835	NM_011932	ENSMUSG00000028159	Dapp1	Bam32	dual adaptor for phosphotyrosine and 3-phosphoinositides 1	protein-coding
mm_28273.1	chr3	88832547	88832571	-	1	NA	promoter-TSS (NR_015498)	promoter-TSS (NR_015498)	-72	NR_015498	319830	Mm.400394	NR_015498		1500004A13Rik	5430404N14Rik|BB132176	RIKEN cDNA 1500004A13 gene	ncRNA
mm_97438.1	chr11	78178106	78178147	+	1	NA	promoter-TSS (NM_001291236)	promoter-TSS (NM_001291236)	-23	NM_001291235	68385	Mm.390375	NM_026708	ENSMUSG00000019437	Tlcd1	-	TLC domain containing 1	protein-coding
mm_119676.1	chr14	52654659	52654674	+	1	NA	Intergenic	Intergenic	-158971	NM_001170918	57269	Mm.88822	NM_020512	ENSMUSG00000059887	Olfr1507	MOR244-1|Mor28|Or28	olfactory receptor 1507	protein-coding
mm_36647.1	chr4	94555081	94555086	-	1	NA	intron (NM_026368, intron 1 of 5)	intron (NM_026368, intron 1 of 5)	1713	NM_026368	67770	Mm.35170	NM_026368	ENSMUSG00000028578	Caap1	5830433M19Rik|AI536248|CAAP	caspase activity and apoptosis inhibitor 1	protein-coding
mm_98600.1	chr11	95830754	95830768	+	1	NA	exon (NM_153104, exon 3 of 3)	exon (NM_153104, exon 3 of 3)	6261	NM_153104	237928	Mm.133075	NM_153104	ENSMUSG00000050860	Phospho1	D11Moh36|Phospo1	phosphatase, orphan 1	protein-coding
mm_172532.1	chr7	87095919	87095929	-	1	NA	Intergenic	RLTR9D|LTR|ERVK	99459	NM_001105190	621430	Mm.469903	NM_001105190	ENSMUSG00000090362	Vmn2r79	EG621430	vomeronasal 2, receptor 79	protein-coding
mm_22492.1	chr3	6107492	6107503	+	1	NA	Intergenic	Intergenic	512946	NM_027048	69347	Mm.45822	NM_027048	ENSMUSG00000069118	1700008P02Rik	-	RIKEN cDNA 1700008P02 gene	protein-coding
mm_14265.1	chr2	128591234	128591244	+	1	NA	Intergenic	Intergenic	-1102	NM_001310641	241634	Mm.297682	NM_001310641	ENSMUSG00000074812	Spdye4c	Gm355|SpeedyB3|SpyB3	speedy/RINGO cell cycle regulator family, member E4C	protein-coding
mm_16177.1	chr2	172551523	172551535	+	1	NA	exon (NM_001159696, exon 2 of 7)	exon (NM_001159696, exon 2 of 7)	538	NM_001159696	21420	Mm.3629	NM_009335	ENSMUSG00000028640	Tfap2c	AA409384|AP2gamma|Ap-2.2|Stra2|Tcfap2c	transcription factor AP-2, gamma	protein-coding
mm_110472.1	chr12	51829860	51829870	-	1	NA	promoter-TSS (NM_144788)	promoter-TSS (NM_144788)	-329	NM_144788	207304	Mm.249391	NM_144788	ENSMUSG00000035247	Hectd1	A630086P08Rik|AI844876|b2b327Clo|opm	HECT domain containing 1	protein-coding
mm_83687.1	chr9	50555128	50555151	-	1	NA	promoter-TSS (NM_133217)	promoter-TSS (NM_133217)	-1	NM_133217	170752	Mm.390149	NM_133217	ENSMUSG00000032066	Bco2	B-diox-II|Bcdo2|Bcmo2|CMO2	beta-carotene oxygenase 2	protein-coding
mm_60736.1	chr7	45439611	45439619	+	1	NA	exon (NM_030678, exon 4 of 16)	exon (NM_030678, exon 4 of 16)	4776	NM_030678	14936	Mm.275654	NM_030678	ENSMUSG00000003865	Gys1	Gys3|MGS	glycogen synthase 1, muscle	protein-coding
mm_151534.1	chr19	58943385	58943410	+	1	NA	promoter-TSS (NM_178689)	promoter-TSS (NM_178689)	-28	NM_178689	226265	Mm.103154	NM_178689	ENSMUSG00000048029	Eno4	6430537H07Rik	enolase 4	protein-coding
mm_44515.1	chr5	24344573	24344586	-	1	NA	intron (NM_013569, intron 2 of 14)	intron (NM_013569, intron 2 of 14)	7025	NM_013569	16511	Mm.6539	NM_013569	ENSMUSG00000038319	Kcnh2	AI326795|ERG1|LQT|Lqt2|M-erg|Merg1|merg1a|merg1b	potassium voltage-gated channel, subfamily H (eag-related), member 2	protein-coding
mm_137497.1	chr17	26971799	26971823	+	1	NA	Intergenic	Intergenic	-1368	NM_001005916	474156	Mm.328890	NM_001005916	ENSMUSG00000079605	Zbtb9	3930402F13Rik	zinc finger and BTB domain containing 9	protein-coding
mm_152251.1	chr19	8723126	8723135	-	1	NA	promoter-TSS (NR_002896)	promoter-TSS (NR_002896)	239	NM_001161413	17254	Mm.4114	NM_008577	ENSMUSG00000010095	Slc3a2	4F2|4F2HC|AI314110|Cd98|Ly-10|Ly-m10|Ly10|Mdu1|Mgp-2hc|NACAE	solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2	protein-coding
mm_167152.1	chr7	131322372	131322394	-	1	NA	promoter-TSS (NM_008411)	promoter-TSS (NM_008411)	-91	NM_008411	16433	Mm.142717	NM_008411	ENSMUSG00000040205	Cuzd1	Erg-1|Itmap1|Uo-44|Usg|Utczp	CUB and zona pellucida-like domains 1	protein-coding
mm_25268.1	chr3	104794282	104794305	+	1	NA	TTS (NM_008619)	TTS (NM_008619)	5259	NM_007484	11853	Mm.262	NM_007484	ENSMUSG00000002233	Rhoc	AI324259|Arh9|Arhc	ras homolog family member C	protein-coding
mm_3019.1	chr1	133365123	133365135	+	1	NA	intron (NM_175443, intron 1 of 7)	intron (NM_175443, intron 1 of 7)	1557	NM_175443	214253	Mm.52111	NM_175443	ENSMUSG00000070644	Etnk2	4933417N20Rik|AI197444|EKI 2|Eki2|Tuc1	ethanolamine kinase 2	protein-coding
mm_48437.1	chr5	140623452	140623472	-	1	NA	exon (NM_175274, exon 14 of 14)	exon (NM_175274, exon 14 of 14)	16121	NM_008494	16848	Mm.12834	NM_008494	ENSMUSG00000029570	Lfng	AW061165	LFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	protein-coding
mm_2883.1	chr1	131838797	131838809	+	1	NA	intron (NM_173865, intron 2 of 10)	intron (NM_173865, intron 2 of 10)	10791	NM_173865	98396	Mm.389181	NM_173865	ENSMUSG00000013275	Slc41a1	AI573938|B230315F01Rik	solute carrier family 41, member 1	protein-coding
mm_30603.1	chr4	6393649	6393701	+	1	NA	exon (NM_016807, exon 8 of 9)	exon (NM_016807, exon 8 of 9)	27995	NM_001098227	53378	Mm.247473	NM_016807	ENSMUSG00000028249	Sdcbp	MDA-9|Sycl|syntenin-1	syndecan binding protein	protein-coding
mm_165547.1	chr3	9801764	9801797	-	1	NA	intron (NM_001195031, intron 1 of 8)	intron (NM_001195031, intron 1 of 8)	31899	NM_053182	94212	Mm.23897	NM_053182	ENSMUSG00000027508	Pag1	Cbp|F730007C19Rik|Pag	phosphoprotein associated with glycosphingolipid microdomains 1	protein-coding
mm_20144.1	chr2	121473994	121474037	-	1	NA	promoter-TSS (NM_001081975)	promoter-TSS (NM_001081975)	8	NM_001081975	100034361	Mm.270393	NM_001081975	ENSMUSG00000048222	Mfap1b	-	microfibrillar-associated protein 1B	protein-coding
mm_12345.1	chr2	69748951	69748970	+	1	NA	intron (NM_001081086, intron 12 of 13)	intron (NM_001081086, intron 12 of 13)	25872	NM_001081086	228005	Mm.11815	NM_001081086	ENSMUSG00000042133	Ppig	AU019516|AU022200|B230312B02Rik|CYP|SRCyp	peptidyl-prolyl isomerase G (cyclophilin G)	protein-coding
mm_30408.1	chr3	152253802	152253812	-	1	NA	intron (NM_199465, intron 2 of 12)	intron (NM_199465, intron 2 of 12)	12513	NM_199465	68810	Mm.200188	NM_199465	ENSMUSG00000039103	Nexn	1110046H09Rik|AA553326|NELIN	nexilin	protein-coding
mm_89603.1	chr10	95991372	95991383	+	1	NA	intron (NM_001001932, intron 5 of 28)	intron (NM_001001932, intron 5 of 28)	50714	NM_001001932	216238	Mm.210035	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding
mm_80963.1	chr9	103085904	103085984	+	1	NA	3' UTR (NM_033314, exon 14 of 14)	3' UTR (NM_033314, exon 14 of 14)	-26130	NM_173781	270192	Mm.490252	NM_173781	ENSMUSG00000032549	Rab6b	9630015C03|AI844641|C330006L04Rik|D9Bwg0185e	RAB6B, member RAS oncogene family	protein-coding
mm_30302.1	chr3	149077342	149077363	-	1	NA	Intergenic	Intergenic	-122717	NM_001081298	99633	Mm.9776	NM_001081298	ENSMUSG00000028184	Adgrl2	AI450192|CIRL-2|Gm619|Lec1|Lphh1|Lphn2|mKIAA0786	adhesion G protein-coupled receptor L2	protein-coding
mm_109500.1	chr12	111451980	111451988	+	1	NA	intron (NM_009396, intron 11 of 11)	intron (NM_009396, intron 11 of 11)	9323	NM_009396	21928	Mm.255332	NM_009396	ENSMUSG00000021281	Tnfaip2	B94|Exoc3l3|M-sec|Tnfip2|tnfb94	tumor necrosis factor, alpha-induced protein 2	protein-coding
mm_73209.1	chr8	95713522	95713536	+	1	NA	3' UTR (NM_145602, exon 14 of 14)	3' UTR (NM_145602, exon 14 of 14)	-2384	NM_001035123	66083	Mm.261321	NM_001035123	ENSMUSG00000031671	Setd6	0610039J04Rik|3110004G14Rik|AI413388|C76402	SET domain containing 6	protein-coding
mm_93111.1	chr10	91118198	91118211	-	1	NA	exon (NM_133668, exon 6 of 8)	exon (NM_133668, exon 6 of 8)	5759	NM_133668	18674	Mm.298	NM_133668	ENSMUSG00000061904	Slc25a3	5730556H19Rik|PTP|Phc	solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 3	protein-coding
mm_63050.1	chr7	121865052	121865065	+	1	NA	promoter-TSS (NM_011325)	promoter-TSS (NM_011325)	20	NR_073548	20277	Mm.7709	NM_011325	ENSMUSG00000030873	Scnn1b	-	sodium channel, nonvoltage-gated 1 beta	protein-coding
mm_124085.1	chr14	78717191	78717206	-	1	NA	intron (NM_001081336, intron 1 of 28)	PB1D11|SINE|Alu	7891	NM_001081336	380921	Mm.89591	NM_001081336	ENSMUSG00000034731	Dgkh	5930402B05Rik|D130015C16|DGK	diacylglycerol kinase, eta	protein-coding
mm_33143.1	chr4	125125110	125125143	+	1	NA	intron (NM_153159, intron 2 of 5)	intron (NM_153159, intron 2 of 5)	2755	NM_153159	230738	Mm.402	NM_153159	ENSMUSG00000042677	Zc3h12a	BC036563|MCPIP|MCPIP-1|Mcpip1|Reg1	zinc finger CCCH type containing 12A	protein-coding
mm_76541.1	chr8	87960713	87960723	-	1	NA	Intergenic	CpG-14330	-1123	NM_033327	94187	Mm.23452	NM_033327	ENSMUSG00000045333	Zfp423	Ebfaz|Roaz|Zfp104|Znf423|ataxia1|mKIAA0760|nur12	zinc finger protein 423	protein-coding
mm_154041.1	chr19	53791840	53791847	-	1	NA	intron (NM_001170847, intron 1 of 13)	intron (NM_001170847, intron 1 of 13)	-100388	NM_011050	18569	Mm.1605	NM_011050	ENSMUSG00000024975	Pdcd4	D19Ucla1|Ma3|Tis	programmed cell death 4	protein-coding
mm_30710.1	chr4	12113459	12113464	+	1	NA	Intergenic	Intergenic	24091	NM_198957	77604	Mm.474129	NM_198957	ENSMUSG00000052137	Rbm12b2	AV299215|C430048L16Rik|Rbm12bb	RNA binding motif protein 12 B2	protein-coding
mm_131391.1	chr16	14215861	14215880	+	1	NA	exon (NM_013607, exon 25 of 42)	exon (NM_013607, exon 25 of 42)	52595	NM_001114085	67203	Mm.24105	NM_023317	ENSMUSG00000022678	Nde1	2810027M15Rik|AU042936|AW822251|Nude|mNudE	nudE neurodevelopment protein 1	protein-coding
mm_164744.1	chr17	73948375	73948393	+	1	NA	intron (NM_011723, intron 1 of 35)	intron (NM_011723, intron 1 of 35)	1812	NM_011723	22436	Mm.11223	NM_011723	ENSMUSG00000024066	Xdh	XO|Xor|Xox-1|Xox1	xanthine dehydrogenase	protein-coding
mm_98021.1	chr11	84957803	84957813	+	1	NA	promoter-TSS (NM_007607)	promoter-TSS (NM_007607)	54	NM_007607	12351	Mm.1641	NM_007607	ENSMUSG00000000805	Car4	AW456718|Ca4	carbonic anhydrase 4	protein-coding
mm_39345.1	chr5	8893901	8893911	+	1	NA	5' UTR (NM_008830, exon 1 of 28)	5' UTR (NM_008830, exon 1 of 28)	185	NM_008830	18670	Mm.297825	NM_008830	ENSMUSG00000042476	Abcb4	Mdr2|Pgy-2|Pgy2|mdr-2	ATP-binding cassette, sub-family B (MDR/TAP), member 4	protein-coding
mm_84473.1	chr9	66795332	66795411	-	1	NA	promoter-TSS (NM_177583)	promoter-TSS (NM_177583)	52	NM_177583	208117	Mm.41291	NM_177583	ENSMUSG00000032375	Aph1b	2310057K14Rik|Aph1c	aph1 homolog B, gamma secretase subunit	protein-coding
mm_41833.1	chr5	104299282	104299296	+	1	NA	promoter-TSS (NM_008318)	promoter-TSS (NM_008318)	2	NM_008318	15891	Mm.4987	NM_008318	ENSMUSG00000029306	Ibsp	BSP|BSP II|BSPII|Bsp2	integrin binding sialoprotein	protein-coding
mm_103092.1	chr11	69920893	69920966	-	1	NA	promoter-TSS (NM_001166592)	promoter-TSS (NM_001166592)	18	NM_001166594	276770	Mm.18026	NM_181582	ENSMUSG00000078812	Eif5a	AA410058|D19Wsu54e|Eif4d|Eif5a1|eIF-4D|eIF-5A|eIF-5A-1|eIF-5A1	eukaryotic translation initiation factor 5A	protein-coding
mm_171921.1	chr5	5783226	5783229	-	1	NA	Intergenic	Intergenic	-33910	NM_027399	70358	Mm.85429	NM_027399	ENSMUSG00000015652	Steap1	2410007B19Rik|Prss24|Steap	six transmembrane epithelial antigen of the prostate 1	protein-coding
mm_100186.1	chr11	116671659	116671694	+	1	NA	promoter-TSS (NR_027821)	promoter-TSS (NR_027821)	16	NR_027820	66293	Mm.432051	NM_025472	ENSMUSG00000020812	1810032O08Rik	-	RIKEN cDNA 1810032O08 gene	ncRNA
mm_152424.1	chr19	10675120	10675158	-	1	NA	exon (NM_021453, exon 3 of 9)	exon (NM_021453, exon 3 of 9)	2932	NM_021453	58803	Mm.34037	NM_021453	ENSMUSG00000024738	Pga5	1110035E17Rik|Pepf	pepsinogen 5, group I	protein-coding
mm_124116.1	chr14	79481451	79481514	-	1	NA	promoter-TSS (NM_018765)	promoter-TSS (NM_018765)	-214	NM_018765	22380	Mm.476813	NM_018765	ENSMUSG00000022023	Wbp4	AW545037|BB101031|FBP21	WW domain binding protein 4	protein-coding
mm_163460.1	chr12	99874745	99874749	-	1	NA	intron (NM_030172, intron 3 of 5)	intron (NM_030172, intron 3 of 5)	8695	NM_030172	78767	Mm.235920	NM_030172	ENSMUSG00000021176	Efcab11	2610021K21Rik|2610110A13Rik	EF-hand calcium binding domain 11	protein-coding
mm_138442.1	chr17	35126428	35126442	+	1	NA	promoter-TSS (NM_033477)	promoter-TSS (NM_033477)	33	NM_033477	114585	Mm.42070	NM_033477	ENSMUSG00000043311	D17H6S53E	G4|NG34	DNA segment, Chr 17, human D6S53E	protein-coding
mm_158680.1	chrX	160138325	160138336	-	1	NA	promoter-TSS (NM_008810)	promoter-TSS (NM_008810)	100	NM_008810	18597	Mm.34775	NM_008810	ENSMUSG00000031299	Pdha1	Pdha-1	pyruvate dehydrogenase E1 alpha 1	protein-coding
mm_146057.1	chr18	69677933	69677972	+	1	NA	intron (NM_013685, intron 16 of 19)	intron (NM_013685, intron 16 of 19)	-247607	NM_201362	381175	Mm.266831	NM_201362	ENSMUSG00000038903	Ccdc68	BC046343	coiled-coil domain containing 68	protein-coding
mm_132459.1	chr16	36160047	36160052	+	1	NA	intron (NM_173869, intron 2 of 2)	intron (NM_173869, intron 2 of 2)	3238	NM_173869	268885	Mm.187847	NM_173869	ENSMUSG00000059657	Stfa2l1	-	stefin A2 like 1	protein-coding
mm_59649.1	chr7	28168863	28168908	+	1	NA	promoter-TSS (NM_007991)	promoter-TSS (NM_007991)	-863	NM_007991	14113	Mm.4595	NM_007991	ENSMUSG00000046865	Fbl	AL022665|FIB|FLRN|RNU3IP1	fibrillarin	protein-coding
mm_91855.1	chr10	59221758	59221803	-	1	NA	promoter-TSS (NM_001024910)	promoter-TSS (NM_001024910)	67	NM_001024911	103080	Mm.346842	NM_001024910	ENSMUSG00000019917	Sept10	4921515A04Rik|9430099J10Rik|AA408298|AI874685	septin 10	protein-coding
mm_29400.1	chr3	108904685	108904695	-	1	NA	exon (NM_025845, exon 6 of 6)	exon (NM_025845, exon 6 of 6)	7014	NM_025845	66921	Mm.51049	NM_025845	ENSMUSG00000027881	Prpf38b	1110021E09Rik|AU018955	PRP38 pre-mRNA processing factor 38 (yeast) domain containing B	protein-coding
mm_100879.1	chr11	5976193	5976216	-	1	NA	intron (NM_007595, intron 17 of 20)	intron (NM_007595, intron 17 of 20)	20446	NM_019661	56418	Mm.294821	NM_019661	ENSMUSG00000002741	Ykt6	0610042I15Rik|1810013M05Rik|AW105923	YKT6 v-SNARE homolog (S. cerevisiae)	protein-coding
mm_56772.1	chr6	116461152	116461172	-	1	NA	promoter-TSS (NM_009662)	promoter-TSS (NM_009662)	16	NM_009662	11689	Mm.41072	NM_009662	ENSMUSG00000025701	Alox5	5-LO|5-LOX|5LO|5LX|AI850497|F730011J02	arachidonate 5-lipoxygenase	protein-coding
mm_25001.1	chr3	97651786	97651797	+	1	NA	exon (NM_001161763, exon 9 of 9)	exon (NM_001161763, exon 9 of 9)	-6421	NM_182997	108097	Mm.31175	NM_182997	ENSMUSG00000038205	Prkab2	5730553K21Rik|AW049591|BB124140	protein kinase, AMP-activated, beta 2 non-catalytic subunit	protein-coding
mm_158823.1	chrX	167446550	167446567	-	1	NA	Intergenic	Intergenic	-63809	NM_001313758	110639	Mm.272955	NM_026662	ENSMUSG00000025742	Prps2	2610101M19Rik|AA589463|AI464149|Prps-2	phosphoribosyl pyrophosphate synthetase 2	protein-coding
mm_149419.1	chr19	11435220	11435245	+	1	NA	Intergenic	L1VL4|LINE|L1	-8326	NM_021718	60361	Mm.33957	NM_021718	ENSMUSG00000056290	Ms4a4b	AI463180|Chandra|Ly116	membrane-spanning 4-domains, subfamily A, member 4B	protein-coding
mm_119114.1	chr14	31019184	31019214	+	1	NA	promoter-TSS (NM_001081251)	promoter-TSS (NM_001081251)	61	NM_001081251	66923	Mm.27913	NM_025847	ENSMUSG00000042323	Pbrm1	2610016F04Rik|AI507524|BAF180|Pb1	polybromo 1	protein-coding
mm_61317.1	chr7	68133806	68133812	+	1	NA	intron (NM_010513, intron 2 of 20)	intron (NM_010513, intron 2 of 20)	130424	NM_030101	78444	Mm.425468	NM_030101	ENSMUSG00000030553	Pgpep1l	C330024D12Rik	pyroglutamyl-peptidase I-like	protein-coding
mm_41262.1	chr5	89028024	89028034	+	1	NA	intron (NM_001197147, intron 3 of 25)	intron (NM_001197147, intron 3 of 25)	140769	NM_018760	54403	Mm.41044	NM_018760	ENSMUSG00000060961	Slc4a4	AI835705|NBC|NBC1	solute carrier family 4 (anion exchanger), member 4	protein-coding
mm_57669.1	chr6	128488081	128488101	-	1	NA	exon (NM_007376, exon 30 of 36)	exon (NM_007376, exon 30 of 36)	38629	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_653.1	chr1	40430183	40430191	+	1	NA	intron (NM_001294171, intron 1 of 7)	intron (NM_001294171, intron 1 of 7)	617	NM_001294171	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_112888.1	chr13	20860631	20860641	+	1	NA	intron (NM_012054, intron 4 of 20)	MIR3|SINE|MIR	66523	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_2446.1	chr1	99772430	99772438	+	1	NA	promoter-TSS (NM_172851)	promoter-TSS (NM_172851)	-331	NM_172851	241175	Mm.251301	NM_172851	ENSMUSG00000067028	Cntnap5b	C230078M14Rik|Caspr5-2	contactin associated protein-like 5B	protein-coding
mm_90942.1	chr10	12964212	12964245	-	1	NA	promoter-TSS (NM_029075)	promoter-TSS (NM_029075)	31	NM_029075	74732	Mm.248648	NM_029075	ENSMUSG00000039232	Stx11	5830405C08Rik	syntaxin 11	protein-coding
mm_109161.1	chr12	108187172	108187185	+	1	NA	intron (NM_009832, intron 3 of 11)	intron (NM_009832, intron 3 of 11)	7440	NM_009832	12454	Mm.474441	NM_009832	ENSMUSG00000021258	Ccnk	AW123198|AW413594|CPR4|CycK	cyclin K	protein-coding
mm_66946.1	chr7	61985902	61985911	-	1	NA	Intergenic	RMER4B|LTR|ERVK	-3547	NR_037287	100526507		NR_037287	ENSMUSG00000092850	Mir344g	mir-344g|mmu-mir-344g	microRNA 344g	ncRNA
mm_152163.1	chr19	7288513	7288516	-	1	NA	intron (NM_007928, intron 3 of 17)	intron (NM_007928, intron 3 of 17)	6933	NM_001080390	13728	Mm.258986	NM_007928	ENSMUSG00000024969	Mark2	EMK-1|Emk|Par-1|Par-1b	MAP/microtubule affinity regulating kinase 2	protein-coding
mm_13446.1	chr2	105162982	105162998	+	1	NA	intron (NM_144783, intron 5 of 9)	intron (NM_144783, intron 5 of 9)	36461	NM_144783	22431	Mm.389339	NM_144783	ENSMUSG00000016458	Wt1	D630046I19Rik|Wt-1	Wilms tumor 1 homolog	protein-coding
mm_67865.1	chr7	99141267	99141294	-	1	NA	promoter-TSS (NM_178635)	promoter-TSS (NM_178635)	-136	NM_178635	78610	Mm.323072	NM_178635	ENSMUSG00000035354	Uvrag	9530039D02Rik|AI648770|BB124205|Uvrag1|Uvragl	UV radiation resistance associated gene	protein-coding
mm_157687.1	chrX	60147896	60147902	-	1	NA	promoter-TSS (NM_133197)	promoter-TSS (NM_133197)	-199	NM_001289730	109904	Mm.93796	NM_133197	ENSMUSG00000031139	Mcf2	B230117G22Rik|Dbl|Mcf-2	mcf.2 transforming sequence	protein-coding
mm_54168.1	chr6	23248372	23248390	-	1	NA	promoter-TSS (NM_028462)	promoter-TSS (NM_028462)	-117	NM_028462	73191	Mm.55115	NM_028462	ENSMUSG00000029697	Fezf1	3110069A13Rik|Fez|Zfp312-like|fez-like	Fez family zinc finger 1	protein-coding
mm_26036.1	chr3	135522913	135522938	+	1	NA	intron (NM_027288, intron 5 of 16)	intron (NM_027288, intron 5 of 16)	37314	NM_027288	110173	Mm.280536	NM_027288	ENSMUSG00000028164	Manba	2410030O07Rik|B930014J03Rik|Bmn	mannosidase, beta A, lysosomal	protein-coding
mm_132115.1	chr16	31664111	31664118	+	1	NA	non-coding (NR_045516, exon 1 of 25)	non-coding (NR_045516, exon 1 of 25)	179	NM_001252434	13383	Mm.382	NM_007862	ENSMUSG00000022770	Dlg1	B130052P05Rik|Dlgh1|E-dlg/SAP97|SAP-97|SAP97|mKIAA4187	discs, large homolog 1 (Drosophila)	protein-coding
mm_54780.1	chr6	41541803	41541816	-	1	NA	Intergenic	Intergenic	20033	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_17599.1	chr2	30807536	30807574	-	1	NA	promoter-TSS (NM_170592)	promoter-TSS (NM_170592)	-422	NM_170592	66617	Mm.33167	NM_170592	ENSMUSG00000026857	Ntmt1	2610205E22Rik|AL033331|AL033332|Mettl11a|NTM1A	N-terminal Xaa-Pro-Lys N-methyltransferase 1	protein-coding
mm_18584.1	chr2	66271220	66271222	-	1	NA	3' UTR (NM_001313997, exon 27 of 27)	3' UTR (NM_001313997, exon 27 of 27)	-14604	NM_001290669	73668	Mm.250868	NM_001047604	ENSMUSG00000034848	Ttc21b	2410066K11Rik|Thm1|aln|mKIAA1992	tetratricopeptide repeat domain 21B	protein-coding
mm_5377.1	chr1	30949091	30949101	-	1	NA	intron (NM_011200, intron 1 of 5)	CpG	614	NR_002688	433406	Mm.389003	NR_002688		Gm13363	OTTMUSG00000011595	predicted gene 13363	pseudo
mm_60153.1	chr7	39487346	39487366	+	1	NA	Intergenic	Intergenic	-30410	NM_001004139	70227	Mm.333800	NM_001004139	ENSMUSG00000068959	Zfp619	3000002G13Rik	zinc finger protein 619	protein-coding
mm_1095.1	chr1	59705660	59705693	+	1	NA	TTS (NR_028521)	TTS (NR_028521)	868	NR_028521	100217421		NR_028521		Snord11	MBII-95	small nucleolar RNA, C/D box 11	snoRNA
mm_82227.1	chr9	3027392	3027412	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	11341	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_66590.1	chr7	45406999	45407014	-	1	NA	exon (NM_010596, exon 1 of 2)	exon (NM_010596, exon 1 of 2)	1046	NM_010596	16495	Mm.12955	NM_010596	ENSMUSG00000038201	Kcna7	Kv1.7	potassium voltage-gated channel, shaker-related subfamily, member 7	protein-coding
mm_101903.1	chr11	49187169	49187195	-	1	NA	promoter-TSS (NM_172793)	promoter-TSS (NM_172793)	-93	NM_172793	237754	Mm.130787	NM_172793	ENSMUSG00000040283	Btnl9	B430208I01|Btn3|D330012D11Rik	butyrophilin-like 9	protein-coding
mm_169306.1	chr14	104715844	104715846	-	1	NA	intron (NR_015593, intron 1 of 5)	LSU-rRNA_Hsa|rRNA|rRNA	76698	NR_015593	320249	Mm.320725	NR_015593		D130009I18Rik	-	RIKEN cDNA D130009I18 gene	ncRNA
mm_17012.1	chr2	18888297	18888302	-	1	NA	intron (NM_008845, intron 4 of 9)	intron (NM_008845, intron 4 of 9)	-86481	NR_131254	66774	Mm.87075	NR_131254	ENSMUSG00000097638	Carlr	4933439G12Rik|Carl	cardiac and apoptosis-related long non-coding RNA	ncRNA
mm_14718.1	chr2	143919207	143919211	+	1	NA	intron (NM_019771, intron 1 of 3)	intron (NM_019771, intron 1 of 3)	3878	NM_019771	56431	Mm.28919	NM_019771	ENSMUSG00000015932	Dstn	2610043P17Rik|ADF|AU042046|Dsn|corn1|sid23p	destrin	protein-coding
mm_95985.1	chr11	58982121	58982141	+	1	NA	exon (NM_053168, exon 3 of 6)	exon (NM_053168, exon 3 of 6)	4038	NM_053168	94091	Mm.248049	NM_053168	ENSMUSG00000020455	Trim11	-	tripartite motif-containing 11	protein-coding
mm_54511.1	chr6	35511514	35511534	-	1	NA	3' UTR (NM_008098, exon 4 of 4)	3' UTR (NM_008098, exon 4 of 4)	28364	NM_008098	14489	Mm.182746	NM_008098	ENSMUSG00000029840	Mtpn	5033418D15Rik|Gcdp|V1	myotrophin	protein-coding
mm_137351.1	chr17	25212846	25212849	+	1	NA	intron (NM_001290736, intron 8 of 14)	PB1D7|SINE|Alu	-9735	NM_028789	74154	Mm.267353	NM_028789	ENSMUSG00000015127	Unkl	1300004G08Rik	unkempt family like zinc finger	protein-coding
mm_12737.1	chr2	78884301	78884304	+	1	NA	intron (NM_009454, intron 3 of 5)	(T)n|Simple_repeat|Simple_repeat	15255	NM_009454	22193	Mm.1485	NM_009454	ENSMUSG00000027011	Ube2e3	Ubce4|ubcM2	ubiquitin-conjugating enzyme E2E 3	protein-coding
mm_143863.1	chr17	84186578	84186612	-	1	NA	exon (NM_001001806, exon 2 of 2)	exon (NM_001001806, exon 2 of 2)	1352	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_73024.1	chr8	94152736	94152751	+	1	NA	5' UTR (NM_013603, exon 1 of 3)	5' UTR (NM_013603, exon 1 of 3)	136	NM_013603	17751	Mm.2064	NM_013603	ENSMUSG00000031760	Mt3	Mt-3	metallothionein 3	protein-coding
mm_70657.1	chr8	14604576	14604593	+	1	NA	intron (NM_172910, intron 4 of 15)	intron (NM_172910, intron 4 of 15)	-283952	NM_012000	26889	Mm.254027	NM_012000	ENSMUSG00000026317	Cln8	mnd	ceroid-lipofuscinosis, neuronal 8	protein-coding
mm_147834.1	chr18	62548854	62548878	-	1	NA	promoter-TSS (NM_177829)	promoter-TSS (NM_177829)	-45	NM_177829	328971	Mm.312675	NM_177829	ENSMUSG00000044176	Spink10	A230091H23Rik	serine peptidase inhibitor, Kazal type 10	protein-coding
mm_100245.1	chr11	117277190	117277200	+	1	NA	intron (NM_001113487, intron 1 of 10)	intron (NM_001113487, intron 1 of 10)	10949	NM_001113487	53860	Mm.38450	NM_017380	ENSMUSG00000059248	Sept9	MSF1|Msf|PNUTL4|Sint1	septin 9	protein-coding
mm_113364.1	chr13	32965324	32965330	+	1	NA	promoter-TSS (NM_011454)	promoter-TSS (NM_011454)	-186	NM_011454	20708	Mm.36526	NM_011454	ENSMUSG00000042842	Serpinb6b	NK13|Spi12|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 6b	protein-coding
mm_40989.1	chr5	77266366	77266389	+	1	NA	intron (NM_011263, intron 1 of 3)	CpG	883	NM_011263	19712	Mm.28840	NM_011263	ENSMUSG00000029249	Rest	2610008J04Rik|AA407358|NRSF|REST4	RE1-silencing transcription factor	protein-coding
mm_35132.1	chr4	11322077	11322089	-	1	NA	promoter-TSS (NM_001081201)	promoter-TSS (NM_001081201)	48	NM_001081201	381510	Mm.331486	NM_001081201	ENSMUSG00000045205	Dpy19l4	Gm1023|Narg3	dpy-19-like 4 (C. elegans)	protein-coding
mm_31508.1	chr4	53631461	53631505	+	1	NA	promoter-TSS (NM_176966)	promoter-TSS (NM_176966)	12	NM_001195284	319636	Mm.103464	NM_176966	ENSMUSG00000054752	Fsd1l	A230072O16Rik|Ccdc10|Csdufd1|Fsd1nl|OTTMUSG00000007002	fibronectin type III and SPRY domain containing 1-like	protein-coding
mm_27301.1	chr3	48609123	48609133	-	1	NA	promoter-TSS (NR_003617)	promoter-TSS (NR_003617)	-28	NR_003617	66332	Mm.46124	NM_025493		1700018B24Rik	-	enhancer of rudimentary homolog pseudogene	pseudo
mm_89503.1	chr10	94057362	94057366	+	1	NA	intron (NM_053072, intron 2 of 20)	B1_Mur1|SINE|Alu	21363	NM_053072	13998	Mm.269596	NM_053072	ENSMUSG00000020021	Fgd6	AA123052|Etohd4|ZFYVE24	FYVE, RhoGEF and PH domain containing 6	protein-coding
mm_162183.1	chrX	102906458	102906458	-	1	NA	promoter-TSS (NM_029378)	promoter-TSS (NM_029378)	11	NM_029378	70887	Mm.29672	NM_027591	ENSMUSG00000031323	Dmrtc1a	1700030H14Rik|4921520P21Rik|DMRTC1|Dmrt8.1	DMRT-like family C1a	protein-coding
mm_79285.1	chr9	51116000	51116006	+	1	NA	promoter-TSS (NM_019493)	promoter-TSS (NM_019493)	2	NM_019493	56057	Mm.431317	NM_019493	ENSMUSG00000032056	Btg4	C86116|PC3B	B cell translocation gene 4	protein-coding
mm_1022.1	chr1	58753695	58753699	+	1	NA	intron (NM_001293805, intron 7 of 7)	intron (NM_001293805, intron 7 of 7)	23145	NM_001293805	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_23697.1	chr3	68694031	68694047	+	1	NA	intron (NM_001159424, intron 3 of 7)	intron (NM_001159424, intron 3 of 7)	2615	NM_008351	16159	Mm.103783	NM_008351	ENSMUSG00000027776	Il12a	IL-12p35|Il-12a|Ll12a|p35	interleukin 12a	protein-coding
mm_145799.1	chr18	65302928	65302966	+	1	NA	intron (NM_001037294, intron 5 of 12)	intron (NM_001037294, intron 5 of 12)	54086	NR_029600	387231		NR_029600	ENSMUSG00000065402	Mir122	Mir122a|Mirn122a|mir-122|mmu-mir-122	microRNA 122	ncRNA
mm_89185.1	chr10	86346118	86346138	+	1	NA	3' UTR (NM_011595, exon 5 of 5)	3' UTR (NM_011595, exon 5 of 5)	45716	NM_011595	21859	Mm.4871	NM_011595	ENSMUSG00000020044	Timp3	Timp-3	tissue inhibitor of metalloproteinase 3	protein-coding
mm_32078.1	chr4	98113350	98113369	+	1	NA	3' UTR (NM_001122953, exon 10 of 10)	3' UTR (NM_001122953, exon 10 of 10)	269906	NM_053157	94043	Mm.331719	NM_053157	ENSMUSG00000028563	Tm2d1	2310026L18Rik|AA990549|Bbp	TM2 domain containing 1	protein-coding
mm_27095.1	chr3	30190363	30190376	-	1	NA	Intergenic	B4A|SINE|B4	-177165	NM_007963	14013	Mm.56965	NM_007963	ENSMUSG00000027684	Mecom	D630039M04Rik|Evi-1|Evi1|Jbo|Mds|Mds1|Mds1-Evi1|Prdm3|Znfpr1b1	MDS1 and EVI1 complex locus	protein-coding
mm_134751.1	chr16	23157231	23157232	-	1	NA	exon (NM_009605, exon 3 of 3)	exon (NM_009605, exon 3 of 3)	10695	NM_009605	11450	Mm.3969	NM_009605	ENSMUSG00000022878	Adipoq	30kDa|APN|Acdc|Acrp30|Ad|GBP28|adipo|apM1	adiponectin, C1Q and collagen domain containing	protein-coding
mm_71296.1	chr8	41218377	41218389	+	1	NA	Intergenic	Intergenic	-3227	NM_145594	234199	Mm.277955	NM_145594	ENSMUSG00000031594	Fgl1	Mfire1	fibrinogen-like protein 1	protein-coding
mm_31357.1	chr4	47208238	47208252	+	1	NA	5' UTR (NM_009928, exon 1 of 40)	5' UTR (NM_009928, exon 1 of 40)	233	NM_009928	12819	Mm.233547	NM_009928	ENSMUSG00000028339	Col15a1	-	collagen, type XV, alpha 1	protein-coding
mm_109585.1	chr12	112604130	112604142	+	1	NA	exon (NM_198411, exon 8 of 23)	exon (NM_198411, exon 8 of 23)	15352	NM_198411	70435	Mm.250193	NM_198411	ENSMUSG00000037679	Inf2	2610204M08Rik|AA589465|AW125550|EG629699	inverted formin, FH2 and WH2 domain containing	protein-coding
mm_64694.1	chr7	4524338	4524355	-	1	NA	intron (NM_001033548, intron 9 of 11)	B3A|SINE|B2	-1903	NM_009406	21954	Mm.27674	NM_009406	ENSMUSG00000035458	Tnni3	Tn1|cTnI	troponin I, cardiac 3	protein-coding
mm_94925.1	chr11	29526408	29526420	+	1	NA	promoter-TSS (NM_001282119)	promoter-TSS (NM_001282119)	17	NM_133767	76784	Mm.285429	NM_133767	ENSMUSG00000020459	Mtif2	2310038D14Rik|2410112O06Rik|IF-2(Mt)|IF-2mt|IF2(mt)	mitochondrial translational initiation factor 2	protein-coding
mm_155434.1	chrX	73494599	73494609	+	1	NA	exon (NM_007542, exon 8 of 8)	exon (NM_007542, exon 8 of 8)	-8482	NM_001310537	320707	Mm.210095	NM_177236	ENSMUSG00000031376	Atp2b3	6430519O13Rik|Pmca3	ATPase, Ca++ transporting, plasma membrane 3	protein-coding
mm_105392.1	chr11	103374105	103374120	-	1	NA	intron (NM_183034, intron 7 of 11)	intron (NM_183034, intron 7 of 11)	-10420	NM_001205236	544817	Mm.259113	NM_133715	ENSMUSG00000034255	Arhgap27	2310069I04Rik|5730442P18Rik|Gm21552|Sh3d20	Rho GTPase activating protein 27	protein-coding
mm_24634.1	chr3	94342093	94342112	+	1	NA	promoter-TSS (NM_025416)	promoter-TSS (NM_025416)	3	NM_025416	66198	Mm.180200	NM_025416	ENSMUSG00000028148	Them5	1110007B02Rik|1110038F21Rik	thioesterase superfamily member 5	protein-coding
mm_75195.1	chr8	39006186	39006192	-	1	NA	exon (NM_030254, exon 1 of 8)	exon (NM_030254, exon 1 of 8)	322	NM_030254	80286	Mm.272722	NM_030254	ENSMUSG00000039530	Tusc3	AU022242|BC003311|N33	tumor suppressor candidate 3	protein-coding
mm_98797.1	chr11	97018759	97018765	+	1	NA	intron (NM_031183, intron 1 of 1)	CpG	5193	NM_031183	83395	Mm.156282	NM_031183	ENSMUSG00000038560	Sp6	1110025J03Rik|AA591031|AI592962|Epfn|Klf14	trans-acting transcription factor 6	protein-coding
mm_63814.1	chr7	133747619	133747628	+	1	NA	intron (NM_133941, intron 3 of 11)	intron (NM_133941, intron 3 of 11)	12646	NM_001286030	101437	Mm.199223	NM_133941	ENSMUSG00000030986	Dhx32	3110079L04Rik|4732469F02Rik|AA408140|Ddx32	DEAH (Asp-Glu-Ala-His) box polypeptide 32	protein-coding
mm_106291.1	chr11	118212703	118212711	-	1	NA	promoter-TSS (NM_001112700)	promoter-TSS (NM_001112700)	35	NM_001112700	19157	Mm.86413	NM_011180	ENSMUSG00000017132	Cyth1	CLM1|CTH-1|CYTIP|Pscd1	cytohesin 1	protein-coding
mm_105510.1	chr11	106216311	106216317	-	1	NA	promoter-TSS (NM_026009)	promoter-TSS (NM_026009)	53	NM_026009	67163	Mm.22109	NM_026009	ENSMUSG00000078622	Ccdc47	2610204L23Rik|C88307|asp4|calumin	coiled-coil domain containing 47	protein-coding
mm_47604.1	chr5	125058368	125058411	-	1	NA	intron (NM_011424, intron 17 of 46)	intron (NM_011424, intron 17 of 46)	54914	NM_028443	73121	Mm.296138	NM_028443	ENSMUSG00000037962	Rflna	3110032G18Rik|Fam101a|cfm|cfm2	refilin A	protein-coding
mm_136224.1	chr16	90143809	90143823	-	1	NA	non-coding (NR_033476, exon 1 of 1)	non-coding (NR_033476, exon 1 of 1)	1579	NR_033476	100038709	Mm.484070	NR_033476		Gm10789	ENSMUSG00000074924	predicted gene 10789	ncRNA
mm_46098.1	chr5	92347328	92347334	-	1	NA	3' UTR (NM_021274, exon 4 of 4)	3' UTR (NM_021274, exon 4 of 4)	1558	NM_021274	15945	Mm.877	NM_021274	ENSMUSG00000034855	Cxcl10	C7|CRG-2|INP10|IP-10|IP10|Ifi10|Scyb10|gIP-10|mob-1	chemokine (C-X-C motif) ligand 10	protein-coding
mm_159923.1	chr6	55117860	55117860	-	1	NA	promoter-TSS (NM_001288619)	promoter-TSS (NM_001288619)	53	NM_001288619	12922	Mm.236081	NM_009953	ENSMUSG00000003476	Crhr2	CRF-R2|CRFR2alpha|CRFR2beta|Crfr2	corticotropin releasing hormone receptor 2	protein-coding
mm_166376.1	chr5	128736161	128736161	+	1	NA	promoter-TSS (NM_021311)	promoter-TSS (NM_021311)	-85	NM_021311	57749	Mm.272720	NM_021311	ENSMUSG00000029423	Piwil1	MIWI	piwi-like RNA-mediated gene silencing 1	protein-coding
mm_123209.1	chr14	59377623	59377626	-	1	NA	Intergenic	L1VL2|LINE|L1	-12134	NM_199015	219132	Mm.479285	NM_199015	ENSMUSG00000068245	Phf11d	D14Ertd668e|Phf11|Phf11l	PHD finger protein 11D	protein-coding
mm_24295.1	chr3	89302863	89302879	+	1	NA	Intergenic	Intergenic	20008	NM_010108	13638	Mm.331159	NM_010108	ENSMUSG00000028039	Efna3	AW494418|EFL-2|Ehk1-L|Epl3|LERK-3	ephrin A3	protein-coding
mm_98647.1	chr11	96251228	96251234	+	1	NA	promoter-TSS (NR_037977)	promoter-TSS (NR_037977)	-429	NR_037977	193022	Mm.169508	NR_037977		Gm53	-	predicted gene 53	ncRNA
mm_94159.1	chr10	128745088	128745122	-	1	NA	Intergenic	Intergenic	-1049	NM_016811	13139	Mm.291235	NM_016811	ENSMUSG00000025357	Dgka	80kDa|AW146112|Dagk1	diacylglycerol kinase, alpha	protein-coding
mm_97607.1	chr11	78950059	78950067	+	1	NA	exon (NM_010927, exon 20 of 27)	exon (NM_010927, exon 20 of 27)	24772	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_60236.1	chr7	43695084	43695111	+	1	NA	3' UTR (NM_174866, exon 5 of 5)	3' UTR (NM_174866, exon 5 of 5)	4679	NM_174866	317653	Mm.247377	NM_174866	ENSMUSG00000044737	Klk14	GK14	kallikrein related-peptidase 14	protein-coding
mm_78099.1	chr9	19093619	19093649	+	1	NA	Intergenic	RLTR9D|LTR|ERVK	-27323	NM_146564	258557	Mm.377566	NM_146564	ENSMUSG00000059303	Olfr836	MOR152-3	olfactory receptor 836	protein-coding
mm_103947.1	chr11	84067777	84067786	-	1	NA	intron (NM_019819, intron 1 of 2)	intron (NM_019819, intron 1 of 2)	576	NM_019819	56405	Mm.240885	NM_019819	ENSMUSG00000018648	Dusp14	1110014C10Rik|2310042C07Rik|D11Ertd395e|MKP-L|Mkp6	dual specificity phosphatase 14	protein-coding
mm_5870.1	chr1	53784321	53784336	-	1	NA	intron (NM_133810, intron 1 of 7)	intron (NM_133810, intron 1 of 7)	887	NM_133810	98267	Mm.25559	NM_133810	ENSMUSG00000026094	Stk17b	3110009A03Rik|AI120141|Drak2	serine/threonine kinase 17b (apoptosis-inducing)	protein-coding
mm_34013.1	chr4	137993682	137993733	+	1	NA	intron (NM_172703, intron 1 of 34)	CpG	251	NM_172703	230861	Mm.268903	NM_172703	ENSMUSG00000028760	Eif4g3	1500002J22Rik|4930523M17Rik|G1-419-52|eIF4GII|repro8	eukaryotic translation initiation factor 4 gamma, 3	protein-coding
mm_14744.1	chr2	144464395	144464433	+	1	NA	promoter-TSS (NR_038065)	promoter-TSS (NR_038065)	-762	NR_038065	171588	Mm.450554	NR_038065	ENSMUSG00000083674	Gm38402	-	zinc finger protein pseudogene	pseudo
mm_83054.1	chr9	37545103	37545121	-	1	NA	TTS (NM_020518)	TTS (NM_020518)	5857	NM_020518	57276	Mm.27478	NM_020518	ENSMUSG00000001943	Vsig2	1190004B15Rik|2210413P10Rik|AU040484|CTX|Ctm	V-set and immunoglobulin domain containing 2	protein-coding
mm_71300.1	chr8	41246488	41246490	+	1	NA	intron (NM_023662, intron 1 of 37)	RMER15-int|LTR|ERVL	6730	NM_023662	18536	Mm.117896	NM_023662	ENSMUSG00000031592	Pcm1	2600002H09Rik|9430077F19Rik|C030044G17Rik	pericentriolar material 1	protein-coding
mm_124379.1	chr14	108800533	108800535	-	1	NA	Intergenic	L1_Mus3|LINE|L1	113705	NM_199065	76965	Mm.257268	NM_199065	ENSMUSG00000075478	Slitrk1	3200001I04Rik	SLIT and NTRK-like family, member 1	protein-coding
mm_20196.1	chr2	122930188	122930195	-	1	NA	Intergenic	Intergenic	148192	NM_021507	59010	Mm.28986	NM_021507	ENSMUSG00000005803	Sqrdl	0610039J17Rik|4930557M22Rik|SQOR	sulfide quinone reductase-like (yeast)	protein-coding
mm_13807.1	chr2	119047163	119047214	+	1	NA	promoter-TSS (NM_029617)	promoter-TSS (NM_029617)	69	NM_029617	76464	Mm.202518	NM_029617	ENSMUSG00000027326	Knl1	2310043D08Rik|5730505K17Rik|Casc5	kinetochore scaffold 1	protein-coding
mm_157908.1	chrX	78452654	78452661	-	1	NA	3' UTR (NM_001289683, exon 5 of 5)	3' UTR (NM_001289683, exon 5 of 5)	83014	NM_001177966	74910	Mm.159364	NM_001177966	ENSMUSG00000035651	4930480E11Rik	-	RIKEN cDNA 4930480E11 gene	protein-coding
mm_59997.1	chr7	30565403	30565407	+	1	NA	promoter-TSS (NM_145580)	promoter-TSS (NM_145580)	-22	NM_145580	101883	Mm.333757	NM_145580	ENSMUSG00000036826	Igflr1	F630003I17Rik|Tmem149	IGF-like family receptor 1	protein-coding
mm_107583.1	chr12	44528909	44528933	+	1	NA	intron (NM_001146031, intron 3 of 27)	intron (NM_001146031, intron 3 of 27)	200036	NM_001146031	319504	Mm.208439	NM_176930	ENSMUSG00000020598	Nrcam	Bravo|C030017F07Rik|C130076O07Rik|mKIAA0343	neuronal cell adhesion molecule	protein-coding
mm_123987.1	chr14	75671054	75671064	-	1	NA	Intergenic	Intergenic	28800	NM_029230	75272	Mm.159483	NM_029230	ENSMUSG00000022002	Erich6b	4930564B18Rik	glutamate rich 6B	protein-coding
mm_80632.1	chr9	89211207	89211226	+	1	NA	promoter-TSS (NM_026829)	promoter-TSS (NM_026829)	26	NM_026829	107885	Mm.486274	NM_026829	ENSMUSG00000066442	Mthfs	1110034I12Rik|2310020H23Rik|AI119695	5, 10-methenyltetrahydrofolate synthetase	protein-coding
mm_3302.1	chr1	136949698	136949701	+	1	NA	intron (NM_030676, intron 2 of 8)	intron (NM_030676, intron 2 of 8)	3931	NM_001159769	26424	Mm.16794	NM_030676	ENSMUSG00000026398	Nr5a2	AU020803|D1Ertd308e|Ftf|LRH-1|UF2-H3B	nuclear receptor subfamily 5, group A, member 2	protein-coding
mm_172948.1	chr9	81678178	81678178	+	1	NA	Intergenic	Intergenic	-45626	NM_010482	15551	Mm.445308	NM_010482	ENSMUSG00000049511	Htr1b	-	5-hydroxytryptamine (serotonin) receptor 1B	protein-coding
mm_68187.1	chr7	104150519	104150525	-	1	NA	promoter-TSS (NM_198624)	promoter-TSS (NM_198624)	34	NM_198624	244179	Mm.189668	NM_198624	ENSMUSG00000051437	Ubqlnl	4922504M18Rik|Gm490	ubiquilin-like	protein-coding
mm_68330.1	chr7	106504105	106504146	-	1	NA	Intergenic	Intergenic	-63052	NR_003967	209380	Mm.461779	NM_001001318		Gm4759	EG209380	GTPase, very large interferon inducible 1 pseudogene	pseudo
mm_41148.1	chr5	87928262	87928274	+	1	NA	intron (NM_007786, intron 2 of 4)	intron (NM_007786, intron 2 of 4)	2635	NM_007786	12994	Mm.296303	NM_007786	ENSMUSG00000001622	Csn3	AW208918|CSN10|Csnk	casein kappa	protein-coding
mm_25703.1	chr3	122419867	122419872	+	1	NA	promoter-TSS (NM_013867)	promoter-TSS (NM_013867)	89	NM_013867	29815	Mm.45815	NM_013867	ENSMUSG00000028121	Bcar3	AI131758|AND-34	breast cancer anti-estrogen resistance 3	protein-coding
mm_83237.1	chr9	42399615	42399622	-	1	NA	intron (NM_009347, intron 1 of 23)	intron (NM_009347, intron 1 of 23)	311	NM_009347	21683	Mm.42209	NM_009347	ENSMUSG00000037705	Tecta	Tctna	tectorin alpha	protein-coding
mm_19583.1	chr2	101796452	101796471	-	1	NA	intron (NM_001110849, intron 2 of 9)	CpG	1246	NM_175181	72446	Mm.24138	NM_175181	ENSMUSG00000032841	Prr5l	2600010E01Rik|4833411O04Rik|Protor-2|Protor2	proline rich 5 like	protein-coding
mm_115070.1	chr13	101533433	101533452	+	1	NA	Intergenic	Intergenic	-135862	NR_046187	78136	Mm.399065	NR_046187		4922502H24Rik	-	RIKEN cDNA 4922502H24 gene	ncRNA
mm_150087.1	chr19	29410979	29410981	+	1	NA	promoter-TSS (NM_021396)	promoter-TSS (NM_021396)	61	NM_021396	58205	Mm.116737	NM_021396	ENSMUSG00000016498	Pdcd1lg2	B7-DC|Btdc|F730015O22Rik|PD-L2	programmed cell death 1 ligand 2	protein-coding
mm_154363.1	chrM	7025	7052	+	1	NA	NA	Intergenic	NA	NA								
mm_109706.1	chr12	113421642	113421661	+	1	NA	Intergenic	Intergenic	-67914	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_41126.1	chr5	87786608	87786637	+	1	NA	exon (NM_001304768, exon 11 of 13)	exon (NM_001304768, exon 11 of 13)	12172	NM_007785	12993	Mm.4908	NM_007785	ENSMUSG00000061937	Csn1s2a	Csng|PP22	casein alpha s2-like A	protein-coding
mm_147536.1	chr18	53418056	53418066	-	1	NA	promoter-TSS (NM_008908)	promoter-TSS (NM_008908)	-54	NM_008908	19038	Mm.4587	NM_008908	ENSMUSG00000024538	Ppic	CyP-20c	peptidylprolyl isomerase C	protein-coding
mm_91441.1	chr10	33933132	33933148	-	1	NA	intron (NM_028287, intron 6 of 9)	B3A|SINE|B2	18072	NM_028287	72580	Mm.248081	NM_028287	ENSMUSG00000039531	Zufsp	2700019D07Rik	zinc finger with UFM1-specific peptidase domain	protein-coding
mm_108734.1	chr12	87985393	87985396	+	1	NA	Intergenic	MTA_Mm|LTR|ERVL-MaLR	30914	NM_001270792	100039087	Mm.458830	NM_001270792	ENSMUSG00000096276	Gm2042	-	predicted gene 2042	protein-coding
mm_166690.1	chr6	112305063	112305073	+	1	NA	exon (NM_144799, exon 2 of 6)	exon (NM_144799, exon 2 of 6)	-14749	NR_045986	100503613	Mm.136719	NM_177012		5031434C07Rik	-	RIKEN cDNA 5031434C07 gene	ncRNA
mm_27865.1	chr3	79159413	79159430	-	1	NA	Intergenic	Intergenic	-13546	NM_001099624	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_154822.1	chrX	16619810	16619818	+	1	NA	5' UTR (NM_173740, exon 1 of 15)	5' UTR (NM_173740, exon 1 of 15)	116	NM_173740	17161	Mm.21108	NM_173740	ENSMUSG00000025037	Maoa	1110061B18Rik|AA407771	monoamine oxidase A	protein-coding
mm_137560.1	chr17	27685219	27685233	+	1	NA	promoter-TSS (NM_178365)	promoter-TSS (NM_178365)	-13	NM_178365	23969	Mm.4926	NM_011861	ENSMUSG00000040276	Pacsin1	A830061D09Rik|H74|mKIAA1379|syndapin	protein kinase C and casein kinase substrate in neurons 1	protein-coding
mm_149548.1	chr19	12595764	12595784	+	1	NA	intron (NR_015503, intron 1 of 1)	intron (NR_015503, intron 1 of 1)	792	NR_015503	74333	Mm.329744	NR_015503	ENSMUSG00000086213	A330040F15Rik	-	RIKEN cDNA A330040F15 gene	ncRNA
mm_162726.1	chr10	40645321	40645322	+	1	NA	intron (NR_133568, intron 3 of 4)	RLTR17B_Mm|LTR|ERVK	15310	NR_133568	70503	Mm.252862	NM_027442	ENSMUSG00000063428	Ddo	5330420D20Rik|5730402C02Rik|AI467244	D-aspartate oxidase	protein-coding
mm_82234.1	chr9	3036387	3036397	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	2351	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_38582.1	chr4	141819367	141819383	-	1	NA	intron (NM_007919, intron 5 of 7)	intron (NM_007919, intron 5 of 7)	6630	NM_007919	13706	Mm.45316	NM_007919	ENSMUSG00000058579	Cela2a	Ela-2|Ela2|Ela2a	chymotrypsin-like elastase family, member 2A	protein-coding
mm_148030.1	chr18	70053298	70053331	-	1	NA	5' UTR (NM_030554, exon 1 of 6)	5' UTR (NM_030554, exon 1 of 6)	274	NM_001302798	80718	Mm.246753	NM_030554	ENSMUSG00000024511	Rab27b	2310021G14Rik|B130064M09Rik	RAB27B, member RAS oncogene family	protein-coding
mm_38797.1	chr4	148151715	148151747	-	1	NA	5' UTR (NM_001163704, exon 1 of 6)	5' UTR (NM_001163704, exon 1 of 6)	194	NM_001163705	50762	Mm.27445	NM_015797	ENSMUSG00000055401	Fbxo6	AA408845|FBG2|Fbs2|Fbx6b|Fbxo6b	F-box protein 6	protein-coding
mm_67512.1	chr7	80803222	80803232	-	1	NA	5' UTR (NM_016721, exon 1 of 38)	5' UTR (NM_016721, exon 1 of 38)	104	NM_016721	29875	Mm.207619	NM_016721	ENSMUSG00000030536	Iqgap1	AA682088|D7Ertd237e|D7Ertd257e|mKIAA0051	IQ motif containing GTPase activating protein 1	protein-coding
mm_41154.1	chr5	87929830	87929849	+	1	NA	exon (NM_007786, exon 4 of 5)	exon (NM_007786, exon 4 of 5)	4206	NM_007786	12994	Mm.296303	NM_007786	ENSMUSG00000001622	Csn3	AW208918|CSN10|Csnk	casein kappa	protein-coding
mm_35254.1	chr4	19877895	19877903	-	1	NA	3' UTR (NM_175406, exon 8 of 8)	3' UTR (NM_175406, exon 8 of 8)	44667	NM_175406	242341	Mm.19298	NM_175406	ENSMUSG00000028238	Atp6v0d2	1620401A02Rik|AI324824|V-ATPase	ATPase, H+ transporting, lysosomal V0 subunit D2	protein-coding
mm_146324.1	chr18	80707228	80707239	+	1	NA	intron (NM_198429, intron 1 of 9)	intron (NM_198429, intron 1 of 9)	940	NM_001164111	18018	Mm.329560	NM_016791	ENSMUSG00000033016	Nfatc1	2210017P03Rik|AI449492|AV076380|NF-ATc|NFAT2|NFATc|Nfatcb	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 1	protein-coding
mm_93306.1	chr10	97644064	97644070	-	1	NA	promoter-TSS (NM_007884)	promoter-TSS (NM_007884)	-1	NM_007884	13516	Mm.148886	NM_007884	ENSMUSG00000019936	Epyc	Dspg3|PG-Lb|SLRR3B	epiphycan	protein-coding
mm_132489.1	chr16	36931143	36931178	+	1	NA	intron (NM_030035, intron 20 of 21)	PB1D10|SINE|Alu	-3823	NM_008225	15163	Mm.4091	NM_008225	ENSMUSG00000022831	Hcls1	AW213261|HS1	hematopoietic cell specific Lyn substrate 1	protein-coding
mm_148902.1	chr19	6927107	6927119	+	1	NA	exon (NM_008431, exon 6 of 7)	exon (NM_008431, exon 6 of 7)	-1733	NM_001039494	67077	Mm.251306	NM_001039494	ENSMUSG00000050623	Tex40	1700019N12Rik|A430107B04Rik|MLZ-622	testis expressed 40	protein-coding
mm_161950.1	chr19	5568134	5568134	+	1	NA	promoter-TSS (NM_001033448)	promoter-TSS (NM_001033448)	60	NM_001033448	381201	Mm.441906	NM_001033448	ENSMUSG00000049562	Ap5b1	Gm962	adaptor-related protein complex 5, beta 1 subunit	protein-coding
mm_101457.1	chr11	30256043	30256051	-	1	NA	Intergenic	Intergenic	-36275	NM_175836	20742	Mm.123110	NM_009260	ENSMUSG00000020315	Sptbn1	9930031C03Rik|AL033301|SPTB2|Spnb-2|Spnb2|elf1|elf3|mKIAA4049	spectrin beta, non-erythrocytic 1	protein-coding
mm_2143.1	chr1	88095096	88095121	+	1	NA	5' UTR (NM_201642, exon 1 of 5)	5' UTR (NM_201642, exon 1 of 5)	107	NM_201642	394432	Mm.300095	NM_201642	ENSMUSG00000090124	Ugt1a7c	A10'|A13|Ugt1a10	UDP glucuronosyltransferase 1 family, polypeptide A7C	protein-coding
mm_164488.1	chr16	85139363	85139369	-	1	NA	intron (NM_007471, intron 1 of 15)	intron (NM_007471, intron 1 of 15)	34341	NM_001198825	11820	Mm.277585	NM_007471	ENSMUSG00000022892	App	Abeta|Abpp|Adap|Ag|Cvap|E030013M08Rik|betaApp	amyloid beta (A4) precursor protein	protein-coding
mm_101998.1	chr11	51262941	51262968	-	1	NA	promoter-TSS (NM_177567)	promoter-TSS (NM_177567)	-3	NM_177567	193286	Mm.80975	NM_177567	ENSMUSG00000045942	BC049762	4930503F14	cDNA sequence BC049762	protein-coding
mm_15290.1	chr2	155276964	155276981	+	1	NA	exon (NM_025735, exon 2 of 4)	exon (NM_025735, exon 2 of 4)	608	NR_046364	66734	Mm.196239	NM_025735	ENSMUSG00000027602	Map1lc3a	1010001H21Rik|4922501H04Rik|LC3|LC3a	microtubule-associated protein 1 light chain 3 alpha	protein-coding
mm_120974.1	chr14	78461080	78461105	+	1	NA	Intergenic	Intergenic	61610	NM_001346784	219181	Mm.89413	NM_001164503	ENSMUSG00000022016	Akap11	6330501D17Rik|AKAP220|Gm80|PRKA11|mKIAA0629	A kinase (PRKA) anchor protein 11	protein-coding
mm_136359.1	chr16	92776499	92776515	-	1	NA	intron (NM_001111022, intron 2 of 6)	intron (NM_001111022, intron 2 of 6)	49567	NM_001111021	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_172011.1	chr6	109505344	109505344	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	676703	NM_138677	192193	Mm.21596	NM_138677	ENSMUSG00000030104	Edem1	A130059K23Rik|EDEM|mKIAA0212	ER degradation enhancer, mannosidase alpha-like 1	protein-coding
mm_12933.1	chr2	85060899	85060918	+	1	NA	intron (NM_001081260, intron 5 of 11)	intron (NM_001081260, intron 5 of 11)	10448	NM_001081260	228140	Mm.23606	NM_001081260	ENSMUSG00000033955	Tnks1bp1	Tab182|mKIAA1741	tankyrase 1 binding protein 1	protein-coding
mm_19254.1	chr2	84773638	84773649	-	1	NA	exon (NM_009776, exon 3 of 8)	exon (NM_009776, exon 3 of 8)	1786	NM_009776	12258	Mm.38888	NM_009776	ENSMUSG00000023224	Serping1	C1INH|C1nh	serine (or cysteine) peptidase inhibitor, clade G, member 1	protein-coding
mm_132005.1	chr16	25752143	25752151	+	1	NA	intron (NM_001127259, intron 1 of 13)	intron (NM_001127259, intron 1 of 13)	-49769	NM_001127263	22061	Mm.20894	NM_011641	ENSMUSG00000022510	Trp63	AI462811|Ket|P51/P63|P63|P73l|Tp63|Trp53rp1	transformation related protein 63	protein-coding
mm_115491.1	chr13	3611135	3611147	-	1	NA	promoter-TSS (NM_134063)	promoter-TSS (NM_134063)	-33	NM_134063	105203	Mm.221609	NM_134063	ENSMUSG00000033799	Fam208b	AI645998|Pap20|mKIAA2006	family with sequence similarity 208, member B	protein-coding
mm_53974.1	chr6	6357140	6357146	-	1	NA	intron (NR_136905, intron 3 of 3)	intron (NR_136905, intron 3 of 3)	108484	NR_136905	101056138	Mm.389085	NR_136904	ENSMUSG00000093482	Gm20619	-	predicted gene 20619	ncRNA
mm_41385.1	chr5	90768477	90768496	+	1	NA	promoter-TSS (NM_023785)	promoter-TSS (NM_023785)	-32	NM_023785	57349	Mm.293614	NM_023785	ENSMUSG00000029372	Ppbp	2400003M24Rik|AI854500|CTAP3|CTAPIII|Cxcl7|LA-PF4|LDGF|MDGF|NAP-2|NAP-2-L1|Scyb7|TGB|TGB1|THBGB1|b-TG1|beta-TG	pro-platelet basic protein	protein-coding
mm_46226.1	chr5	99022026	99022063	-	1	NA	intron (NM_008926, intron 2 of 18)	intron (NM_008926, intron 2 of 18)	15035	NM_008926	19092	Mm.263002	NM_008926	ENSMUSG00000029334	Prkg2	AW212535|CGKII|Prkgr2|cGK-II	protein kinase, cGMP-dependent, type II	protein-coding
mm_130070.1	chr15	89336887	89336896	-	1	NA	3' UTR (NM_019977, exon 10 of 10)	3' UTR (NM_019977, exon 10 of 10)	2418	NM_019977	56727	Mm.158200	NM_019977	ENSMUSG00000022613	Miox	0610009I10Rik|AI314022|Aldrl6|C85427|RSOR	myo-inositol oxygenase	protein-coding
mm_166858.1	chr7	23357682	23357716	-	1	NA	intron (NM_001004194, intron 8 of 8)	intron (NM_001004194, intron 8 of 8)	-28190	NM_001039143	23968	Mm.333653	NM_011860	ENSMUSG00000015721	Nlrp5	Mater|Nalp5|Op1|PAN11	NLR family, pyrin domain containing 5	protein-coding
mm_153669.1	chr19	44396073	44396081	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	11632	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_25995.1	chr3	134236586	134236594	+	1	NA	promoter-TSS (NM_001004367)	promoter-TSS (NM_001004367)	95	NM_001004367	319478	Mm.224814	NM_001004367	ENSMUSG00000044365	Cxxc4	9330210J02Rik|C030003J12Rik|Idax	CXXC finger 4	protein-coding
mm_87046.1	chr10	28791685	28791707	+	1	NA	intron (NM_001305663, intron 5 of 5)	L1_Mur1|LINE|L1	123336	NM_178666	210757	Mm.123021	NM_178666	ENSMUSG00000049109	Themis	E430004N04Rik|Gasp|Spot|Tsepa|thylex	thymocyte selection associated	protein-coding
mm_108670.1	chr12	86519297	86519335	+	1	NA	3' UTR (NM_011934, exon 7 of 7)	3' UTR (NM_011934, exon 7 of 7)	97672	NM_011934	26380	Mm.235550	NM_011934	ENSMUSG00000021255	Esrrb	Err2|Errb|Estrrb|Nr3b2	estrogen related receptor, beta	protein-coding
mm_96906.1	chr11	70458783	70458797	+	1	NA	promoter-TSS (NM_001029929)	promoter-TSS (NM_001029929)	-832	NM_001029929	574428	Mm.472771	NM_001029929	ENSMUSG00000040829	Zmynd15	-	zinc finger, MYND-type containing 15	protein-coding
mm_63201.1	chr7	125707946	125707958	+	1	NA	promoter-TSS (NM_207239)	promoter-TSS (NM_207239)	76	NM_001081022	233865	Mm.274389	NM_001081022	ENSMUSG00000032743	D430042O09Rik	Kiaa0556	RIKEN cDNA D430042O09 gene	protein-coding
mm_1689.1	chr1	75128551	75128552	+	1	NA	exon (NM_194333, exon 10 of 12)	exon (NM_194333, exon 10 of 12)	5339	NM_194333	22626	Mm.68157	NM_194333	ENSMUSG00000026205	Slc23a3	SVCT3|Yspl1	solute carrier family 23 (nucleobase transporters), member 3	protein-coding
mm_105657.1	chr11	107337526	107337553	-	1	NA	exon (NM_145823, exon 2 of 10)	exon (NM_145823, exon 2 of 10)	133181	NM_145823	71795	Mm.397413	NM_145823	ENSMUSG00000040430	Pitpnc1	1110020B03Rik|5830436L09Rik|AI662802|AI851387|C330017I21Rik|Dnr411|RDGBB|RDGBB1|rdgB-beta	phosphatidylinositol transfer protein, cytoplasmic 1	protein-coding
mm_99534.1	chr11	103192706	103192712	+	1	NA	exon (NM_001077698, exon 13 of 26)	exon (NM_001077698, exon 13 of 26)	15839	NM_001254724	69441	Mm.380648	NM_027082	ENSMUSG00000020940	1700023F06Rik	-	RIKEN cDNA 1700023F06 gene	protein-coding
mm_168541.1	chr11	62457163	62457185	-	1	NA	5' UTR (NM_177229, exon 1 of 9)	5' UTR (NM_177229, exon 1 of 9)	158	NM_177229	20185	Mm.271814	NM_011308	ENSMUSG00000018501	Ncor1	5730405M06Rik|A230020K14Rik|N-CoR|RIP13|Rxrip13|mKIAA1047	nuclear receptor co-repressor 1	protein-coding
mm_101670.1	chr11	37235966	37235994	-	1	NA	Intergenic	Intergenic	-291739	NM_011856	23964	Mm.439889	NM_011856	ENSMUSG00000049336	Tenm2	Odz2|Odz3|Ten-2|Ten-m2	teneurin transmembrane protein 2	protein-coding
mm_122269.1	chr14	34359047	34359068	-	1	NA	Intergenic	LTR33|LTR|ERVL	-3664	NM_183278	69134	Mm.27156	NM_183278	ENSMUSG00000043681	Fam25c	2200001I15Rik|Fam25	family with sequence similarity 25, member C	protein-coding
mm_123615.1	chr14	68120764	68120809	-	1	NA	exon (NM_008691, exon 3 of 3)	exon (NM_008691, exon 3 of 3)	-2966	NR_045897	100043072	Mm.242832	NR_045897		A230070E04Rik	Gm4210	RIKEN cDNA A230070E04 gene	ncRNA
mm_9485.1	chr1	173535986	173536030	-	1	NA	promoter-TSS (NM_001024721)	promoter-TSS (NM_001024721)	-51	NM_001024721	545384	Mm.371698	NM_001024721	ENSMUSG00000070501	Ifi214	Pyhin-B|p214	interferon activated gene 214	protein-coding
mm_64743.1	chr7	4771263	4771275	-	1	NA	promoter-TSS (NM_172895)	promoter-TSS (NM_172895)	1	NM_172895	243822	Mm.333542	NM_172895	ENSMUSG00000092518	Fam71e2	4930401F20Rik	family with sequence similarity 71, member E2	protein-coding
mm_34337.1	chr4	143390141	143390155	+	1	NA	Intergenic	Intergenic	-4293	NM_031377	83491	Mm.190607	NM_031377	ENSMUSG00000041805	Pramel1	-	preferentially expressed antigen in melanoma-like 1	protein-coding
mm_44447.1	chr5	21665265	21665279	-	1	NA	exon (NM_178728, exon 5 of 5)	exon (NM_178728, exon 5 of 5)	19288	NM_026034	67211	Mm.260782	NM_026034	ENSMUSG00000038525	Armc10	2810037C14Rik|Svh	armadillo repeat containing 10	protein-coding
mm_155776.1	chrX	96455398	96455411	+	1	NA	promoter-TSS (NM_010417)	promoter-TSS (NM_010417)	-32	NM_001159628	15203	Mm.277092	NM_010417	ENSMUSG00000031209	Heph	C130006F04Rik|Cpl|mKIAA0698|sla	hephaestin	protein-coding
mm_7847.1	chr1	132367070	132367084	-	1	NA	intron (NM_001311107, intron 2 of 4)	intron (NM_001311107, intron 2 of 4)	871	NM_001311108	68875	Mm.273785	NM_178874	ENSMUSG00000042066	Tmcc2	1110063G11Rik	transmembrane and coiled-coil domains 2	protein-coding
mm_139085.1	chr17	46752435	46752461	+	1	NA	promoter-TSS (NM_001305990)	promoter-TSS (NM_001305990)	-234	NM_001305988	72029	Mm.240325	NM_028065	ENSMUSG00000023973	Cnpy3	1600025D17Rik|2410050O22Rik|AI413153|CAG4A|ERDA5|PRAT4A|Tnrc5	canopy FGF signaling regulator 3	protein-coding
mm_91552.1	chr10	39899188	39899270	-	1	NA	promoter-TSS (NR_033628)	promoter-TSS (NR_033628)	9	NR_033628	213332	Mm.484359	NR_033628		Mfsd4b4	AA474331	major facilitator superfamily domain containing 4B4	pseudo
mm_111836.1	chr12	107912651	107912665	-	1	NA	3' UTR (NM_021399, exon 3 of 3)	3' UTR (NM_021399, exon 3 of 3)	90756	NM_001079883	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_85477.1	chr9	105828122	105828173	-	1	NA	promoter-TSS (NM_001102607)	promoter-TSS (NM_001102607)	-62	NM_001102607	245026	Mm.482507	NM_172927	ENSMUSG00000043719	Col6a6	E330019B14|E330026B02Rik	collagen, type VI, alpha 6	protein-coding
mm_170916.1	chr2	3713546	3713556	+	1	NA	promoter-TSS (NM_025626)	promoter-TSS (NM_025626)	93	NM_025626	66540	Mm.277864	NM_025626	ENSMUSG00000026655	Fam107b	3110001A13Rik|AA589595|AA959793|AI132312	family with sequence similarity 107, member B	protein-coding
mm_49410.1	chr6	28587425	28587435	+	1	NA	intron (NM_019776, intron 10 of 23)	intron (NM_019776, intron 10 of 23)	107082	NM_019776	56463	Mm.439987	NM_019776	ENSMUSG00000001424	Snd1	AL033314|Tudor-SN	staphylococcal nuclease and tudor domain containing 1	protein-coding
mm_61910.1	chr7	90140014	90140046	+	1	NA	intron (NM_001252520, intron 1 of 20)	intron (NM_001252520, intron 1 of 20)	9798	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_75467.1	chr8	47974308	47974309	-	1	NA	intron (NM_133791, intron 1 of 22)	intron (NM_133791, intron 1 of 22)	16243	NM_133791	52357	Mm.235074	NM_133791	ENSMUSG00000031563	Wwc2	5330431C14Rik|AU022508|C85457|D8Ertd594e	WW, C2 and coiled-coil domain containing 2	protein-coding
mm_130611.1	chr15	99915935	99915938	-	1	NA	Intergenic	Intergenic	15722	NM_028180	72277	Mm.272766	NM_028180	ENSMUSG00000045350	1700030F18Rik	FAM186A	RIKEN cDNA 1700030F18 gene	protein-coding
mm_56620.1	chr6	112696635	112696675	-	1	NA	promoter-TSS (NM_021385)	promoter-TSS (NM_021385)	15	NM_021385	58186	Mm.103812	NM_021385	ENSMUSG00000030254	Rad18	2810024C04Rik|Rad18sc	RAD18 E3 ubiquitin protein ligase	protein-coding
mm_155136.1	chrX	50537332	50537372	+	1	NA	promoter-TSS (NR_131207)	promoter-TSS (NR_131207)	-37	NR_131207	102639259	Mm.350898	NR_131207		Gm35612	-	predicted gene, 35612	ncRNA
mm_8415.1	chr1	152090242	152090254	-	1	NA	promoter-TSS (NM_197990)	promoter-TSS (NM_197990)	72	NM_197990	69399	Mm.278031	NM_197990	ENSMUSG00000032666	1700025G04Rik	2610510E02Rik|2900042O04Rik|ENSMUSG00000073540	RIKEN cDNA 1700025G04 gene	protein-coding
mm_42619.1	chr5	118036009	118036036	+	1	NA	intron (NM_021344, intron 1 of 7)	MTC|LTR|ERVL-MaLR	8198	NM_021344	57816	Mm.273285	NM_021344	ENSMUSG00000029359	Tesc	1010001A17Rik|2410011K10Rik|TE-1	tescalcin	protein-coding
mm_97600.1	chr11	78949177	78949185	+	1	NA	exon (NM_010927, exon 18 of 27)	exon (NM_010927, exon 18 of 27)	23890	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_58576.1	chr7	4877113	4877127	+	1	NA	promoter-TSS (NM_001101598)	promoter-TSS (NM_001101598)	67	NM_001101598	664994	Mm.302624	NM_001101598	ENSMUSG00000086784	Isoc2a	Isoc2	isochorismatase domain containing 2a	protein-coding
mm_9927.1	chr1	189867179	189867187	-	1	NA	intron (NM_008976, intron 18 of 18)	intron (NM_008976, intron 18 of 18)	55105	NM_026796	226830	Mm.156895	NM_026796	ENSMUSG00000026603	Smyd2	1110020E07Rik|4930402C15|KMT3C|Zmynd14	SET and MYND domain containing 2	protein-coding
mm_13468.1	chr2	105682195	105682205	+	1	NA	promoter-TSS (NM_001310145)	promoter-TSS (NM_001310145)	-263	NM_001310146	18508	Mm.3608	NM_013627	ENSMUSG00000027168	Pax6	1500038E17Rik|AEY11|Dey|Gsfaey11|Pax-6|Sey	paired box 6	protein-coding
mm_41509.1	chr5	92371710	92371710	+	1	NA	intron (NM_001310664, intron 2 of 10)	intron (NM_001310664, intron 2 of 10)	-8414	NR_038116	56066	Mm.131723	NM_019494	ENSMUSG00000060183	Cxcl11	Cxc11|H174|I-tac|Ip9|Itac|Scyb11|Scyb9b|b-R1|betaR1	chemokine (C-X-C motif) ligand 11	protein-coding
mm_73421.1	chr8	106081411	106081412	+	1	NA	intron (NM_010901, intron 2 of 9)	B1_Mur4|SINE|Alu	21808	NM_010901	18021	Mm.383185	NM_010901	ENSMUSG00000031902	Nfatc3	C80703|D8Ertd281e|NFAT4|NFATx	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 3	protein-coding
mm_104231.1	chr11	88631556	88631557	-	1	NA	intron (NM_054043, intron 5 of 13)	MTE2b|LTR|ERVL-MaLR	12305	NR_131025	68397	Mm.426889	NR_131025		0610039H22Rik	-	RIKEN cDNA 0610039H22 gene	ncRNA
mm_91519.1	chr10	37138667	37138677	-	1	NA	5' UTR (NM_008538, exon 1 of 2)	5' UTR (NM_008538, exon 1 of 2)	254	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_39876.1	chr5	31077105	31077108	+	1	NA	exon (NM_001289522, exon 39 of 43)	exon (NM_001289522, exon 39 of 43)	16421	NM_011773	22784	Mm.1396	NM_011773	ENSMUSG00000029151	Slc30a3	Znt3	solute carrier family 30 (zinc transporter), member 3	protein-coding
mm_148121.1	chr18	75297316	75297328	-	1	NA	promoter-TSS (NR_045394)	promoter-TSS (NR_045394)	-5	NR_045394	100503117	Mm.250517	NR_045393	ENSMUSG00000102047	2010010A06Rik	5033420E22Rik	RIKEN cDNA 2010010A06 gene	ncRNA
mm_123746.1	chr14	70192141	70192274	-	1	NA	promoter-TSS (NM_001271409)	promoter-TSS (NM_001271409)	39	NM_001271409	20410	Mm.5068	NM_011366	ENSMUSG00000022091	Sorbs3	SCAM-1|SH3P3|Sh3d4|vinexin-g	sorbin and SH3 domain containing 3	protein-coding
mm_106083.1	chr11	116175189	116175195	-	1	NA	intron (NM_001271898, intron 10 of 13)	intron (NM_001271898, intron 10 of 13)	-7014	NM_172571	217335	Mm.35241	NM_172571	ENSMUSG00000020776	Fbf1	1110033G01Rik|5930413D20|mKIAA1863	Fas (TNFRSF6) binding factor 1	protein-coding
mm_106920.1	chr12	8313426	8313454	+	1	NA	promoter-TSS (NM_021429)	promoter-TSS (NM_021429)	7	NM_021429	58240	Mm.309954	NM_021429	ENSMUSG00000020605	Hs1bp3	-	HCLS1 binding protein 3	protein-coding
mm_58071.1	chr6	136924113	136924128	-	1	NA	3' UTR (NM_007486, exon 6 of 6)	3' UTR (NM_007486, exon 6 of 6)	-1940	NM_026983	69187	Mm.33692	NM_026983	ENSMUSG00000030219	Erp27	1810033M07Rik|1810047B09Rik	endoplasmic reticulum protein 27	protein-coding
mm_94434.1	chr11	6292280	6292331	+	1	NA	promoter-TSS (NM_001252288)	promoter-TSS (NM_001252288)	-253	NM_001252288	18293	Mm.276348	NM_010956	ENSMUSG00000020456	Ogdh	2210403E04Rik|2210412K19Rik|AA409584|d1401|mKIAA4192	oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)	protein-coding
mm_7435.1	chr1	119936301	119936338	-	1	NA	intron (NM_001115074, intron 15 of 22)	intron (NM_001115074, intron 15 of 22)	-23151	NM_175106	66343	Mm.49942	NM_175106	ENSMUSG00000036975	Tmem177	2300008B03Rik	transmembrane protein 177	protein-coding
mm_35562.1	chr4	41569662	41569670	-	1	NA	promoter-TSS (NM_027993)	promoter-TSS (NM_027993)	-128	NM_175138	68922	Mm.79127	NM_175138	ENSMUSG00000061322	Dnaic1	1110066F04Rik|BB124644|Dnai1|b2b1526Clo	dynein, axonemal, intermediate chain 1	protein-coding
mm_1813.1	chr1	81323407	81323407	+	1	NA	Intergenic	Intergenic	246090	NM_172849	241134	Mm.313904	NM_172849	ENSMUSG00000054976	Nyap2	9430031J16Rik|Jr6|Kiaa1486	neuronal tyrosine-phophorylated phosphoinositide 3-kinase adaptor 2	protein-coding
mm_84801.1	chr9	77251843	77251859	-	1	NA	intron (NM_027150, intron 1 of 7)	intron (NM_027150, intron 1 of 7)	96019	NM_027150	69642	Mm.35008	NM_027150	ENSMUSG00000032355	Mlip	2310046A06Rik|AI931782|CIP	muscular LMNA-interacting protein	protein-coding
mm_160844.1	chr11	50841512	50841512	-	1	NA	promoter-TSS (NM_173387)	promoter-TSS (NM_173387)	40	NM_001290779	214779	Mm.191846	NM_173387	ENSMUSG00000044296	Zfp879	Znf879	zinc finger protein 879	protein-coding
mm_7162.1	chr1	91978487	91978489	-	1	NA	intron (NM_207225, intron 12 of 26)	intron (NM_207225, intron 12 of 26)	177027	NM_007855	13345	Mm.9474	NM_007855	ENSMUSG00000007805	Twist2	Dermo1|bHLHa39	twist basic helix-loop-helix transcription factor 2	protein-coding
mm_74448.1	chr8	4213481	4213540	-	1	NA	exon (NM_207203, exon 6 of 7)	exon (NM_207203, exon 6 of 7)	3802	NM_207203	73072	Mm.477379	NM_207203	ENSMUSG00000064125	Prr36	-	proline rich 36	protein-coding
mm_69072.1	chr7	126975788	126975843	-	1	NA	promoter-TSS (NM_026638)	promoter-TSS (NM_026638)	-99	NM_026638	52858	Mm.28219	NM_026638	ENSMUSG00000030682	Cdipt	9530042F15Rik|D7Bwg0575e|Pis|Pis1	CDP-diacylglycerol--inositol 3-phosphatidyltransferase (phosphatidylinositol synthase)	protein-coding
mm_73283.1	chr8	104831635	104831666	+	1	NA	promoter-TSS (NM_198171)	promoter-TSS (NM_198171)	6	NM_198171	234669	Mm.443387	NM_198171	ENSMUSG00000050097	Ces2b	-	carboxyesterase 2B	protein-coding
mm_105577.1	chr11	106613054	106613064	-	1	NA	promoter-TSS (NM_198292)	promoter-TSS (NM_198292)	-129	NM_198292	21763	Mm.102407	NM_198292	ENSMUSG00000040548	Tex2	4930568E07Rik|AI553404|Def-5|Taz4	testis expressed gene 2	protein-coding
mm_120764.1	chr14	73370287	73370292	+	1	NA	intron (NM_008410, intron 1 of 5)	intron (NM_008410, intron 1 of 5)	14982	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_8726.1	chr1	160053071	160053081	-	1	NA	intron (NM_001162896, intron 1 of 2)	intron (NM_001162896, intron 1 of 2)	8696	NM_001162896	67647	Mm.171518	NM_001024470	ENSMUSG00000090394	4930523C07Rik	-	RIKEN cDNA 4930523C07 gene	protein-coding
mm_141151.1	chr17	26506439	26506458	-	1	NA	exon (NM_013642, exon 4 of 4)	exon (NM_013642, exon 4 of 4)	2024	NM_013642	19252	Mm.239041	NM_013642	ENSMUSG00000024190	Dusp1	3CH134|MKP1|Ptpn16|U19515|erp|mkp-1	dual specificity phosphatase 1	protein-coding
mm_141192.1	chr17	26973028	26973052	-	1	NA	promoter-TSS (NM_001005916)	promoter-TSS (NM_001005916)	-139	NM_001005916	474156	Mm.328890	NM_001005916	ENSMUSG00000079605	Zbtb9	3930402F13Rik	zinc finger and BTB domain containing 9	protein-coding
mm_128500.1	chr15	52000081	52000129	-	1	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	-8345	NM_009009	19357	Mm.182628	NM_009009	ENSMUSG00000022314	Rad21	SCC1|mKIAA0078	RAD21 cohesin complex component	protein-coding
mm_67105.1	chr7	70352918	70352922	-	1	NA	3' UTR (NM_183261, exon 3 of 3)	3' UTR (NM_183261, exon 3 of 3)	7673	NM_009697	11819	Mm.158143	NM_009697	ENSMUSG00000030551	Nr2f2	2700033K02Rik|9430015G03Rik|ARP-1|Aporp1|COUP-TF2|COUP-TFII|COUPTFB|EAR3|SVP40|Tcfcoup2	nuclear receptor subfamily 2, group F, member 2	protein-coding
mm_126060.1	chr15	77015814	77015838	+	1	NA	3' UTR (NM_013593, exon 4 of 4)	3' UTR (NM_013593, exon 4 of 4)	6901	NM_001164048	17189	Mm.404074	NM_013593	ENSMUSG00000018893	Mb	AI325109	myoglobin	protein-coding
mm_34802.1	chr4	154864393	154864400	+	1	NA	intron (NM_172878, intron 6 of 6)	intron (NM_172878, intron 6 of 6)	-5189	NM_013783	27390	Mm.116944	NM_013783	ENSMUSG00000058183	Mmel1	Mell1|NEP2|NEPII|Nl1|SEP	membrane metallo-endopeptidase-like 1	protein-coding
mm_93155.1	chr10	93124390	93124411	-	1	NA	Intergenic	Intergenic	-36476	NM_146239	237459	Mm.217404	NM_146239	ENSMUSG00000020015	Cdk17	6430598J10Rik|Pctk2	cyclin-dependent kinase 17	protein-coding
mm_88096.1	chr10	68723879	68723889	+	1	NA	5' UTR (NM_177794, exon 1 of 6)	5' UTR (NM_177794, exon 1 of 6)	138	NM_177794	327766	Mm.2479	NM_177794	ENSMUSG00000060044	Tmem26	3230401A06|AI195372	transmembrane protein 26	protein-coding
mm_42429.1	chr5	115341289	115341297	+	1	NA	promoter-TSS (NM_026933)	promoter-TSS (NM_026933)	46	NM_026933	69076	Mm.27951	NM_026933	ENSMUSG00000029535	Triap1	1810015M01Rik|AU020874|AU043831|P53csv|Wf-1	TP53 regulated inhibitor of apoptosis 1	protein-coding
mm_41454.1	chr5	90905623	90905640	+	1	NA	3' UTR (NM_009140, exon 4 of 4)	3' UTR (NM_009140, exon 4 of 4)	1732	NM_009140	20310	Mm.4979	NM_009140	ENSMUSG00000058427	Cxcl2	CINC-2a|GROb|Gro2|MIP-2|MIP-2a|Mgsa-b|Mip2|Scyb|Scyb2	chemokine (C-X-C motif) ligand 2	protein-coding
mm_105219.1	chr11	102216666	102216669	-	1	NA	intron (NM_001284249, intron 3 of 27)	intron (NM_001284249, intron 3 of 27)	13483	NR_106179	102465892		NR_106179	ENSMUSG00000098863	Mir8101	Gm27705|mmu-mir-8101	microRNA 8101	ncRNA
mm_22924.1	chr3	31120031	31120051	+	1	NA	3' UTR (NM_001039090, exon 7 of 7)	3' UTR (NM_001039090, exon 7 of 7)	24983	NM_001039090	20482	Mm.15406	NM_011386	ENSMUSG00000027660	Skil	Skir|SnoN|sno	SKI-like	protein-coding
mm_45048.1	chr5	41708119	41708129	-	1	NA	promoter-TSS (NM_001310589)	promoter-TSS (NM_001310589)	55	NR_132325	100972	Mm.41555	NM_027295	ENSMUSG00000029128	Rab28	2700023P08Rik|AW496496	RAB28, member RAS oncogene family	protein-coding
mm_5543.1	chr1	38491807	38491810	-	1	NA	intron (NM_001290814, intron 4 of 21)	intron (NM_001290814, intron 4 of 21)	135436	NM_001290814	16764	Mm.336679	NM_010678	ENSMUSG00000037138	Aff3	3222402O04Rik|A730046J16|LAF-4|Laf4	AF4/FMR2 family, member 3	protein-coding
mm_130894.1	chr15	102366975	102367023	-	1	NA	promoter-TSS (NM_130458)	promoter-TSS (NM_130458)	-728	NM_130458	170574	Mm.263284	NM_130458	ENSMUSG00000060284	Sp7	6430578P22Rik|C22|Osx	Sp7 transcription factor 7	protein-coding
mm_87782.1	chr10	60296716	60296724	+	1	NA	intron (NM_011179, intron 8 of 14)	intron (NM_011179, intron 8 of 14)	12259	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_164605.1	chr17	29886910	29886956	+	1	NA	intron (NM_001081160, intron 1 of 15)	CpG	949	NM_001081160	74762	Mm.40901	NM_001081160	ENSMUSG00000043557	Mdga1	1200011I03Rik|GPIM|Mamdc3	MAM domain containing glycosylphosphatidylinositol anchor 1	protein-coding
mm_19912.1	chr2	114654923	114654939	-	1	NA	promoter-TSS (NM_025675)	promoter-TSS (NM_025675)	-3	NM_025675	66632	Mm.117809	NM_025675	ENSMUSG00000057147	Dph6	5730421E18Rik|Atpbd4	diphthamine biosynthesis 6	protein-coding
mm_62905.1	chr7	117380938	117380992	+	1	NA	promoter-TSS (NM_175645)	promoter-TSS (NM_175645)	-14	NM_175645	233781	Mm.461427	NM_175645	ENSMUSG00000030657	Xylt1	8030490L12	xylosyltransferase 1	protein-coding
mm_148457.1	chr19	4003369	4003385	+	1	NA	promoter-TSS (NM_021791)	promoter-TSS (NM_021791)	-8	NM_021791	60425	Mm.266972	NM_021791	ENSMUSG00000024871	Doc2g	D830013O18Rik	double C2, gamma	protein-coding
mm_142298.1	chr17	40934498	40934609	-	1	NA	promoter-TSS (NM_031863)	promoter-TSS (NM_031863)	-2	NM_031863	83815	Mm.9870	NM_031863	ENSMUSG00000023919	Cenpq	2610528M18Rik	centromere protein Q	protein-coding
mm_115050.1	chr13	100127930	100127942	+	1	NA	exon (NM_011420, exon 4 of 9)	exon (NM_011420, exon 4 of 9)	3081	NM_011420	20595	Mm.2025	NM_011420	ENSMUSG00000021645	Smn1	AI849087|Gemin1|Smn	survival motor neuron 1	protein-coding
mm_16863.1	chr2	11676924	11676944	-	1	NA	exon (NM_008367, exon 3 of 8)	exon (NM_008367, exon 3 of 8)	-28359	NM_001271498	16169	Mm.200196	NM_008358	ENSMUSG00000023206	Il15ra	AA690181|IL-15RA	interleukin 15 receptor, alpha chain	protein-coding
mm_39425.1	chr5	16293334	16293337	+	1	NA	intron (NM_001110846, intron 10 of 37)	intron (NM_001110846, intron 10 of 37)	-260160	NM_001289460	15234	Mm.267078	NM_010427	ENSMUSG00000028864	Hgf	C230052L06Rik|HGF/SF|NK1|NK2|SF|SF/HGF	hepatocyte growth factor	protein-coding
mm_88765.1	chr10	80335157	80335179	+	1	NA	3' UTR (NM_139292, exon 6 of 6)	3' UTR (NM_139292, exon 6 of 6)	5023	NM_139292	70335	Mm.28147	NM_139292	ENSMUSG00000035504	Reep6	0610011M24Rik|Dp1l1	receptor accessory protein 6	protein-coding
mm_17868.1	chr2	34914021	34914043	-	1	NA	promoter-TSS (NM_028716)	promoter-TSS (NM_028716)	-56	NM_028716	74016	Mm.65691	NM_028716	ENSMUSG00000026873	Phf19	3110009G19Rik|3321402G02Rik	PHD finger protein 19	protein-coding
mm_17031.1	chr2	20339429	20339444	-	1	NA	intron (NM_001081006, intron 1 of 21)	intron (NM_001081006, intron 1 of 21)	49523	NM_001081006	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding
mm_42289.1	chr5	114380816	114380851	+	1	NA	promoter-TSS (NM_001159941)	promoter-TSS (NM_001159941)	213	NR_138602	117146	Mm.28792	NM_054093	ENSMUSG00000029577	Ube3b	AI449831|AU020130	ubiquitin protein ligase E3B	protein-coding
mm_77624.1	chr8	123955770	123955773	-	1	NA	intron (NM_019552, intron 11 of 12)	intron (NM_019552, intron 11 of 12)	-6506	NM_172288	234865	Mm.267812	NM_172288	ENSMUSG00000039509	Nup133	mermaid	nucleoporin 133	protein-coding
mm_167487.1	chr9	3021290	3021309	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	17444	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_80072.1	chr9	69761050	69761067	+	1	NA	promoter-TSS (NR_040765)	promoter-TSS (NR_040765)	-88	NR_040765	319970	Mm.186434	NR_040765	ENSMUSG00000097623	B230323A14Rik	-	RIKEN cDNA B230323A14 gene	ncRNA
mm_19627.1	chr2	102813650	102813673	-	1	NA	3' UTR (NM_009851, exon 19 of 19)	3' UTR (NM_009851, exon 19 of 19)	88004	NM_001177785	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_155987.1	chrX	106143200	106143214	+	1	NA	promoter-TSS (NM_205820)	promoter-TSS (NM_205820)	-68	NM_205820	279572	Mm.336203	NM_205820	ENSMUSG00000033777	Tlr13	AI666735|Gm713	toll-like receptor 13	protein-coding
mm_42356.1	chr5	114911683	114911693	+	1	NA	3' UTR (NM_011854, exon 6 of 6)	3' UTR (NM_011854, exon 6 of 6)	-11552	NM_145209	231655	Mm.95479	NM_145209	ENSMUSG00000041827	Oasl1	7530414C13Rik|oasl9	2'-5' oligoadenylate synthetase-like 1	protein-coding
mm_14095.1	chr2	125188981	125188987	+	1	NA	intron (NM_183354, intron 15 of 27)	intron (NM_183354, intron 15 of 27)	36384	NM_001079690	20495	Mm.3914	NM_011389	ENSMUSG00000027202	Slc12a1	AI788571|D630042G03Rik|Nkcc2|mBSC1|urehr3	solute carrier family 12, member 1	protein-coding
mm_114488.1	chr13	69802345	69802360	+	1	NA	Intergenic	MLT1G1|LTR|ERVL-MaLR	-7530	NM_138596	28077	Mm.52583	NM_138596	ENSMUSG00000021598	Med10	AA959813|AI385605|C78613|D13Wsu50e	mediator complex subunit 10	protein-coding
mm_114684.1	chr13	80963105	80963122	+	1	NA	promoter-TSS (NR_015587)	promoter-TSS (NR_015587)	-961	NR_015587	319983	Mm.343027	NR_015587	ENSMUSG00000097098	9330111N05Rik	-	RIKEN cDNA 9330111N05 gene	ncRNA
mm_72988.1	chr8	92961366	92961380	+	1	NA	exon (NM_009209, exon 1 of 14)	exon (NM_009209, exon 1 of 14)	326	NM_009209	20538	Mm.57040	NM_009209	ENSMUSG00000055368	Slc6a2	NE-T|NET|Slc6a5	solute carrier family 6 (neurotransmitter transporter, noradrenalin), member 2	protein-coding
mm_39301.1	chr5	6951727	6951734	+	1	NA	intron (NM_001163223, intron 1 of 3)	intron (NM_001163223, intron 1 of 3)	-352434	NM_027603	70920	Mm.158494	NM_027603	ENSMUSG00000040514	4921511H03Rik	-	RIKEN cDNA 4921511H03 gene	protein-coding
mm_139016.1	chr17	45734586	45734630	+	1	NA	promoter-TSS (NM_028164)	promoter-TSS (NM_028164)	-764	NM_028164	72240	Mm.482897	NM_028164	ENSMUSG00000094690	1600014C23Rik	-	RIKEN cDNA 1600014C23 gene	protein-coding
mm_79241.1	chr9	50504553	50504566	+	1	NA	3' UTR (NM_029639, exon 4 of 4)	3' UTR (NM_029639, exon 4 of 4)	246	NR_040714	69631	Mm.414996	NR_040714	ENSMUSG00000101304	Plet1os	2310014F07Rik	placenta expressed transcript 1, opposite strand	ncRNA
mm_64413.1	chr7	142533145	142533174	+	1	NA	promoter-TSS (NM_011288)	promoter-TSS (NM_011288)	42	NM_011288	19935	Mm.12144	NM_011288	ENSMUSG00000037772	Mrpl23	L23mrp|Rpl23|Rpl23l	mitochondrial ribosomal protein L23	protein-coding
mm_55875.1	chr6	83506896	83506927	-	1	NA	promoter-TSS (NM_001162521)	promoter-TSS (NM_001162521)	58	NM_013764	27369	Mm.42234	NM_013764	ENSMUSG00000014554	Dguok	dGK|dGK1|dGK2|dGK3	deoxyguanosine kinase	protein-coding
mm_1077.1	chr1	59482134	59482166	+	1	NA	promoter-TSS (NM_008057)	promoter-TSS (NM_008057)	3	NM_008057	14369	Mm.297906	NM_008057	ENSMUSG00000041075	Fzd7	Fz7	frizzled class receptor 7	protein-coding
mm_23380.1	chr3	55782501	55782521	+	1	NA	promoter-TSS (NM_010750)	promoter-TSS (NM_010750)	1	NM_010750	17116	Mm.440209	NM_010750	ENSMUSG00000056947	Mab21l1	AW047968	mab-21-like 1 (C. elegans)	protein-coding
mm_89158.1	chr10	86039959	86040005	+	1	NA	intron (NM_001347151, intron 5 of 8)	L1_Mur2|LINE|L1	17828	NM_001347151	69754	Mm.44236	NM_153195	ENSMUSG00000001786	Fbxo7	2410015K21Rik|A230052G17Rik|AI117679|AW260462|C85118	F-box protein 7	protein-coding
mm_86693.1	chr10	18447326	18447329	+	1	NA	intron (NM_173390, intron 1 of 6)	intron (NM_173390, intron 1 of 6)	-22654	NM_001163592	215819	Mm.297971	NM_173390	ENSMUSG00000039835	Nhsl1	5730409E15Rik|A630035H13Rik|A730096F01|BC013565|D10Bwg0940e|mKIAA1357	NHS-like 1	protein-coding
mm_64574.1	chr7	144915125	144915193	+	1	NA	promoter-TSS (NM_028184)	promoter-TSS (NM_028184)	-35	NM_028184	72284	Mm.273049	NM_028184	ENSMUSG00000031072	Oraov1	2210010N10Rik|TAOS1	oral cancer overexpressed 1	protein-coding
mm_55195.1	chr6	52191696	52191716	-	1	NA	promoter-TSS (NM_008265)	promoter-TSS (NM_008265)	-3	NM_008265	15401	Mm.439647	NM_008265	ENSMUSG00000000942	Hoxa4	AV206827|Hox-1.4	homeobox A4	protein-coding
mm_69166.1	chr7	127214188	127214217	-	1	NA	TTS (NM_017461)	TTS (NM_017461)	2594	NM_016754	17907	Mm.14526	NM_016754	ENSMUSG00000030672	Mylpf	2410014J02Rik|MLC-2|Mlc2	myosin light chain, phosphorylatable, fast skeletal muscle	protein-coding
mm_83615.1	chr9	48738976	48738995	-	1	NA	intron (NM_001033324, intron 3 of 6)	intron (NM_001033324, intron 3 of 6)	96960	NM_001033324	235320	Mm.457803	NM_001033324	ENSMUSG00000066687	Zbtb16	AI467657|PLZF|Zfp145|lu	zinc finger and BTB domain containing 16	protein-coding
mm_135965.1	chr16	74826802	74826813	-	1	NA	Intergenic	B4|SINE|B4	-415895	NM_175549	268902	Mm.171736	NM_175549	ENSMUSG00000052516	Robo2	2600013A04Rik|9430089E08Rik|BB097918|D230004I22Rik|mKIAA1568	roundabout guidance receptor 2	protein-coding
mm_117585.1	chr13	89662027	89662034	-	1	NA	exon (NM_001134474, exon 12 of 14)	exon (NM_001134474, exon 12 of 14)	80482	NM_001081249	13003	Mm.158700	NM_019389	ENSMUSG00000021614	Vcan	5430420N07Rik|9430051N09|Cspg2|DPEAAE|NG2|PG-M|PG-M(V0)|PG-M(V1)|hdf	versican	protein-coding
mm_32027.1	chr4	95215364	95215368	+	1	NA	Intergenic	RMER19C|LTR|ERVK	-163144	NM_010591	16476	Mm.275071	NM_010591	ENSMUSG00000052684	Jun	AP-1|Junc|c-jun	jun proto-oncogene	protein-coding
mm_15672.1	chr2	163491606	163491617	+	1	NA	promoter-TSS (NM_001099331)	promoter-TSS (NM_001099331)	-707	NM_001099331	100043899	Mm.442535	NM_001099331	ENSMUSG00000078949	R3hdml	OTTMUSG00000001070	R3H domain containing-like	protein-coding
mm_27230.1	chr3	36453498	36453537	-	1	NA	exon (NM_009673, exon 9 of 13)	exon (NM_009673, exon 9 of 13)	22007	NR_105976	102466786		NR_105976	ENSMUSG00000098808	Mir7009	Gm27472|mmu-mir-7009	microRNA 7009	ncRNA
mm_171889.1	chr5	36781229	36781230	+	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	15525	NM_026242	67568	Mm.332336	NM_026242	ENSMUSG00000055302	Mrfap1	9130413I22Rik|AL022827|Pam14	Morf4 family associated protein 1	protein-coding
mm_99162.1	chr11	100622972	100622987	+	1	NA	promoter-TSS (NM_028024)	promoter-TSS (NM_028024)	24	NM_028024	71966	Mm.274734	NM_028024	ENSMUSG00000017837	Nkiras2	2410003M04Rik|4930527H08Rik|D630018G21Rik|KBRAS2	NFKB inhibitor interacting Ras-like protein 2	protein-coding
mm_102041.1	chr11	51931856	51931870	-	1	NA	Intergenic	Lx8|LINE|L1	-35768	NM_029976	52626	Mm.289456	NM_029976	ENSMUSG00000020392	Cdkn2aipnl	A430101B06Rik|AA409260|D11Ertd497e|MNCb-1520	CDKN2A interacting protein N-terminal like	protein-coding
mm_106914.1	chr12	8216613	8216619	+	1	NA	intron (NM_001167767, intron 1 of 5)	intron (NM_001167767, intron 1 of 5)	8489	NM_001167767	68832	Mm.25608	NM_172401	ENSMUSG00000037669	Ldah	1110057K04Rik|mLDAH	lipid droplet associated hydrolase	protein-coding
mm_97129.1	chr11	74927713	74927722	+	1	NA	intron (NM_001002764, intron 1 of 18)	intron (NM_001002764, intron 1 of 18)	1845	NM_001002764	103677	Mm.288460	NM_001002764	ENSMUSG00000038290	Smg6	AI317223|AU041178	Smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans)	protein-coding
mm_88182.1	chr10	69925979	69925985	+	1	NA	5' UTR (NM_009670, exon 1 of 20)	5' UTR (NM_009670, exon 1 of 20)	450	NM_009670	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_97001.1	chr11	70844746	70844816	+	1	NA	promoter-TSS (NM_019400)	promoter-TSS (NM_019400)	20	NM_001291142	54189	Mm.7087	NM_019400	ENSMUSG00000020817	Rabep1	Rab5ep|rabaptin-5|rabaptin-5alpha	rabaptin, RAB GTPase binding effector protein 1	protein-coding
mm_14708.1	chr2	143071499	143071515	+	1	NA	exon (NM_021335, exon 7 of 7)	exon (NM_021335, exon 7 of 7)	-6985	NM_020595	57329	Mm.157751	NM_020595	ENSMUSG00000027416	Otor	CDRAP|Fdp|MIA|MIAL	otoraplin	protein-coding
mm_29005.1	chr3	101592507	101592547	-	1	NA	exon (NM_144900, exon 4 of 23)	exon (NM_144900, exon 4 of 23)	12180	NM_144900	11928	Mm.193670	NM_144900	ENSMUSG00000033161	Atp1a1	Atpa-1|BC010319	ATPase, Na+/K+ transporting, alpha 1 polypeptide	protein-coding
mm_130505.1	chr15	98832476	98832480	-	1	NA	promoter-TSS (NM_016781)	promoter-TSS (NM_016781)	-970	NM_016781	19082	Mm.6670	NM_016781	ENSMUSG00000067713	Prkag1	AA571379|BB036179|Prkaac	protein kinase, AMP-activated, gamma 1 non-catalytic subunit	protein-coding
mm_85334.1	chr9	102615512	102615549	-	1	NA	intron (NM_001301689, intron 5 of 14)	intron (NM_001301689, intron 5 of 14)	10594	NM_001301689	28135	Mm.38910	NM_001081122	ENSMUSG00000032534	Cep63	4921501M07|AL450317.13gm1|AW107703|CD20R|D9Mgc41|D9Mgc48e|ET2	centrosomal protein 63	protein-coding
mm_48773.1	chr5	148509352	148509362	-	1	NA	intron (NM_011908, intron 2 of 4)	intron (NM_011908, intron 2 of 4)	43431	NM_011908	24109	Mm.21846	NM_011908	ENSMUSG00000001687	Ubl3	AW108023|HCG	ubiquitin-like 3	protein-coding
mm_2369.1	chr1	93217466	93217467	+	1	NA	intron (NM_001310428, intron 27 of 31)	intron (NM_001310428, intron 27 of 31)	-18431	NM_172463	208777	Mm.271897	NM_172463	ENSMUSG00000047793	Sned1	6720455I24Rik|AI197264|AI642697|D430044C15Rik|SST3|Snep	sushi, nidogen and EGF-like domains 1	protein-coding
mm_156801.1	chrX	163909107	163909128	+	1	NA	promoter-TSS (NM_026887)	promoter-TSS (NM_026887)	100	NM_001290379	108012	Mm.426783	NM_026887	ENSMUSG00000031367	Ap1s2	1500012A13Rik|AI853648|EST1	adaptor-related protein complex 1, sigma 2 subunit	protein-coding
mm_79205.1	chr9	48985468	48985478	+	1	NA	promoter-TSS (NM_175482)	promoter-TSS (NM_175482)	88	NM_175482	235323	Mm.21630	NM_175482	ENSMUSG00000032267	Usp28	9830148O20Rik|AU022237|mKIAA1515	ubiquitin specific peptidase 28	protein-coding
mm_148092.1	chr18	73815471	73815486	-	1	NA	promoter-TSS (NM_145494)	promoter-TSS (NM_145494)	-86	NM_145494	107029	Mm.36817	NM_145494	ENSMUSG00000024556	Me2	AW120568|D030040L20Rik|NAD-ME	malic enzyme 2, NAD(+)-dependent, mitochondrial	protein-coding
mm_154855.1	chrX	20557560	20557568	+	1	NA	exon (NM_009060, exon 4 of 7)	exon (NM_009060, exon 4 of 7)	7746	NM_009060	19733	Mm.2118	NM_009060	ENSMUSG00000023070	Rgn	AI265316|GNL|SMP30	regucalcin	protein-coding
mm_61649.1	chr7	80404439	80404445	+	1	NA	intron (NM_001081454, intron 1 of 15)	intron (NM_001081454, intron 1 of 15)	994	NM_001081454	18550	Mm.5241	NM_011046	ENSMUSG00000030530	Furin	9130404I01Rik|Fur|PACE|Pcsk3|SPC1	furin (paired basic amino acid cleaving enzyme)	protein-coding
mm_157850.1	chrX	74410989	74410996	-	1	NA	exon (NM_008062, exon 10 of 13)	exon (NM_008062, exon 10 of 13)	-13620	NM_001161421	16151	Mm.12967	NM_010547	ENSMUSG00000004221	Ikbkg	1110037D23Rik|AI848108|AI851264|AW124339|IKK[g]|NEMO	inhibitor of kappaB kinase gamma	protein-coding
mm_94572.1	chr11	11690079	11690079	+	1	NA	promoter-TSS (NM_001301865)	promoter-TSS (NM_001301865)	-98	NM_001301865	22778	Mm.103545	NM_009578	ENSMUSG00000018654	Ikzf1	5832432G11Rik|Ikaros|LyF-1|Zfpn1a1|Znfn1a1|hlk-1|mKIAA4227	IKAROS family zinc finger 1	protein-coding
mm_101596.1	chr11	34711926	34711937	-	1	NA	intron (NM_033374, intron 9 of 51)	intron (NM_033374, intron 9 of 51)	71974	NM_033374	94176	Mm.380679	NM_033374	ENSMUSG00000020143	Dock2	AI662014|AW122239|CED-5|Hch|MBC	dedicator of cyto-kinesis 2	protein-coding
mm_22903.1	chr3	30856005	30856007	+	1	NA	promoter-TSS (NM_027965)	promoter-TSS (NM_027965)	56	NM_001286994	71862	Mm.272019	NM_027965	ENSMUSG00000037661	Gpr160	1700025D19Rik|GPCR150	G protein-coupled receptor 160	protein-coding
mm_143222.1	chr17	63294972	63294984	-	1	NA	intron (NM_015794, intron 6 of 8)	intron (NM_015794, intron 6 of 8)	17995	NR_130176	414079	Mm.444282	NR_130176	ENSMUSG00000090565	4930405O22Rik	-	RIKEN cDNA 4930405O22 gene	ncRNA
mm_55931.1	chr6	84588601	84588609	-	1	NA	intron (NM_175475, intron 1 of 6)	G-rich|Low_complexity|Low_complexity	5205	NM_175475	232174	Mm.255246	NM_175475	ENSMUSG00000063415	Cyp26b1	CP26|P450RAI-2	cytochrome P450, family 26, subfamily b, polypeptide 1	protein-coding
mm_18701.1	chr2	71745741	71745772	-	1	NA	intron (NR_039557, intron 2 of 3).2	intron (NR_039557, intron 2 of 3).2	26339	NR_037979	381371	Mm.330284	NM_201366	ENSMUSG00000064263	Platr26	Gm1631	pluripotency associated transcript 26	ncRNA
mm_93640.1	chr10	117288493	117288526	-	1	NA	3' UTR (NM_013590, exon 4 of 4)	3' UTR (NM_013590, exon 4 of 4)	4359	NM_013590	17110	Mm.177539	NM_013590	ENSMUSG00000069515	Lyz1	Lyz|Lyzf3|Lzp-s	lysozyme 1	protein-coding
mm_98827.1	chr11	97376479	97376483	+	1	NA	exon (NM_138657, exon 3 of 10)	exon (NM_138657, exon 3 of 10)	13930	NM_138657	192157	Mm.34339	NM_138657	ENSMUSG00000038485	Socs7	2310063P06Rik|C85125|Nap4	suppressor of cytokine signaling 7	protein-coding
mm_10503.1	chr2	15526700	15526712	+	1	NA	exon (NM_001310455, exon 1 of 39)	exon (NM_001310455, exon 1 of 39)	227	NM_001310455	102635496		NM_001310455	ENSMUSG00000075520	Malrd1	-	MAM and LDL receptor class A domain containing 1	protein-coding
mm_144353.1	chr18	15324950	15324957	+	1	NA	Intergenic	Intergenic	78046	NM_001308647	11829	Mm.250786	NM_009700	ENSMUSG00000024411	Aqp4	WCH4	aquaporin 4	protein-coding
mm_72795.1	chr8	87047690	87047714	+	1	NA	Intergenic	Intergenic	152148	NR_040697	100038706	Mm.334690	NR_040697	ENSMUSG00000099207	Gm10637	ENSMUSG00000074176	predicted gene 10637	ncRNA
mm_82881.1	chr9	32492161	32492164	-	1	NA	intron (NM_008026, intron 1 of 8)	intron (NM_008026, intron 1 of 8)	49290	NM_008026	14247	Mm.258908	NM_008026	ENSMUSG00000016087	Fli1	EWSR2|Fli-1|SIC-1|Sic1	Friend leukemia integration 1	protein-coding
mm_31801.1	chr4	64020179	64020194	+	1	NA	exon (NM_011607, exon 2 of 26)	exon (NM_011607, exon 2 of 26)	26829	NM_011607	21923	Mm.980	NM_011607	ENSMUSG00000028364	Tnc	AI528729|C130033P17Rik|Hxb|TN|TN-C|Ten|cytotactin|tenascin-C	tenascin C	protein-coding
mm_89583.1	chr10	95773831	95773835	+	1	NA	Intergenic	Intergenic	-166830	NM_001001932	216238	Mm.210035	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding
mm_236.1	chr1	19208941	19208967	+	1	NA	promoter-TSS (NM_009334)	promoter-TSS (NM_009334)	40	NM_001286340	21419	Mm.137021	NM_009334	ENSMUSG00000025927	Tfap2b	AI606113|AP-2(beta)|E130018K07Rik|Tcfap2b	transcription factor AP-2 beta	protein-coding
mm_118856.1	chr14	25840150	25840166	+	1	NA	Intergenic	Intergenic	-1997	NM_013469	11744	Mm.294083	NM_013469	ENSMUSG00000021866	Anxa11	A830099O17Rik|Anx11	annexin A11	protein-coding
mm_65254.1	chr7	19871410	19871424	-	1	NA	Intergenic	Intergenic	-10118	NM_001033419	330483	Mm.260192	NM_001033419	ENSMUSG00000014686	Ceacam16	Gm769	carcinoembryonic antigen-related cell adhesion molecule 16	protein-coding
mm_140367.1	chr17	86963247	86963268	+	1	NA	5' UTR (NM_145491, exon 1 of 5)	5' UTR (NM_145491, exon 1 of 5)	146	NM_145491	104215	Mm.826	NM_145491	ENSMUSG00000024143	Rhoq	Arhq|TC10A|Tc10	ras homolog family member Q	protein-coding
mm_143922.1	chr17	85618496	85618504	-	1	NA	promoter-TSS (NR_015387)	promoter-TSS (NR_015387)	-104	NR_038082	100043902	Mm.150838	NR_015385	ENSMUSG00000093460	Six3os1	D17Mgi26|E130112H22Rik|Rncr1|Six3os	SIX homeobox 3, opposite strand 1	ncRNA
mm_80011.1	chr9	67840448	67840454	+	1	NA	promoter-TSS (NM_177184)	promoter-TSS (NM_177184)	55	NM_177184	320528	Mm.241454	NM_177184	ENSMUSG00000035284	Vps13c	AI552542|AV026040|C230055H22Rik|W51662|chorein	vacuolar protein sorting 13C	protein-coding
mm_54280.1	chr6	29212241	29212291	-	1	NA	promoter-TSS (NM_011829)	promoter-TSS (NM_011829)	31	NM_011829	23917	Mm.260707	NM_011829	ENSMUSG00000003500	Impdh1	B930086D20Rik|IMPDH-I	inosine 5'-phosphate dehydrogenase 1	protein-coding
mm_137706.1	chr17	29098730	29098740	+	1	NA	exon (NM_007669, exon 2 of 3)	exon (NM_007669, exon 2 of 3)	4966	NM_007669	12575	Mm.195663	NM_007669	ENSMUSG00000023067	Cdkn1a	CAP20|CDKI|CIP1|Cdkn1|P21|SDI1|Waf1|mda6|p21Cip1|p21WAF	cyclin-dependent kinase inhibitor 1A (P21)	protein-coding
mm_63447.1	chr7	127490345	127490358	+	1	NA	TTS (NR_106027)	TTS (NR_106027)	1100	NR_106027	102465642		NR_106027	ENSMUSG00000098267	Mir7060	Gm27515|mmu-mir-7060	microRNA 7060	ncRNA
mm_146334.1	chr18	81939931	81939940	+	1	NA	Intergenic	Intergenic	52145	NR_039589	100628596		NR_039589	ENSMUSG00000093036	Mir5127	mmu-mir-5127|mu-mir-5127	microRNA 5127	ncRNA
mm_141617.1	chr17	32871615	32871624	-	1	NA	Intergenic	RLTR23|LTR|ERV1	19984	NM_207245	240066	Mm.26636	NM_207245	ENSMUSG00000095325	Zfp870	AI173952	zinc finger protein 870	protein-coding
mm_86156.1	chr9	118108950	118108951	-	1	NA	intron (NM_026442, intron 2 of 3)	intron (NM_026442, intron 2 of 3)	41246	NM_026442	67899	Mm.9953	NM_026442	ENSMUSG00000039163	Cmc1	2010110K16Rik|2010312P05Rik|AI596001	COX assembly mitochondrial protein 1	protein-coding
mm_43516.1	chr5	137150139	137150143	+	1	NA	Intergenic	Intergenic	-33934	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_1063.1	chr1	59014191	59014209	+	1	NA	Intergenic	Intergenic	40629	NM_172656	227154	Mm.286006	NM_172656	ENSMUSG00000026027	Stradb	AA792893|Als2cr2|B830008M19|D1Ucla2|ILPIP|ILPIPA|PRO1038|Papk|Syradb	STE20-related kinase adaptor beta	protein-coding
mm_52418.1	chr6	113442572	113442627	+	1	NA	promoter-TSS (NM_001243739)	promoter-TSS (NM_001243739)	30	NM_001243739	67767	Mm.2053	NM_026365	ENSMUSG00000051256	Jagn1	5830427H10Rik	jagunal homolog 1	protein-coding
mm_100711.1	chr11	3774707	3774738	-	1	NA	intron (NM_152818, intron 2 of 13)	CpG	-52495	NM_001302630	74309	Mm.61022	NM_152818	ENSMUSG00000020435	Osbp2	1700095P05Rik|C630001G20Rik|Gm244|ORP-4|OSBPL1	oxysterol binding protein 2	protein-coding
mm_35661.1	chr4	43562175	43562185	-	1	NA	promoter-TSS (NM_013497)	promoter-TSS (NM_013497)	403	NM_011602	21894	Mm.208601	NM_011602	ENSMUSG00000028465	Tln1	Tln	talin 1	protein-coding
mm_106699.1	chr12	3572179	3572209	+	1	NA	promoter-TSS (NM_007886)	promoter-TSS (NM_007886)	-197	NM_001162465	13528	Mm.286202	NM_007886	ENSMUSG00000071454	Dtnb	-	dystrobrevin, beta	protein-coding
mm_61165.1	chr7	59228997	59229021	+	1	NA	5' UTR (NM_001033962, exon 1 of 11)	5' UTR (NM_001033962, exon 1 of 11)	257	NM_011668	22215	Mm.9002	NM_011668	ENSMUSG00000025326	Ube3a	4732496B02|5830462N02Rik|A130086L21Rik|Hpve6a|mKIAA4216	ubiquitin protein ligase E3A	protein-coding
mm_22930.1	chr3	31149935	31149958	+	1	NA	promoter-TSS (NM_008770)	promoter-TSS (NM_008770)	26	NM_008770	18417	Mm.4425	NM_008770	ENSMUSG00000037625	Cldn11	Claudin-11|Claudin11|Osp|Otm	claudin 11	protein-coding
mm_164553.1	chr17	13659359	13659382	+	1	NA	Intergenic	MER21C|LTR|ERVL	-101171	NM_010806	17356	Mm.59167	NM_010806	ENSMUSG00000068036	Afdn	5033403D15Rik|AF6|Af-6|Afadin|Gm314|I-afadin|Mllt4|S-afadin	afadin, adherens junction formation factor	protein-coding
mm_92155.1	chr10	67536780	67536803	-	1	NA	Intergenic	CpG	-1078	NM_010118	13654	Mm.290421	NM_010118	ENSMUSG00000037868	Egr2	Egr-2|Krox-20|Krox20|NGF1-B|Zfp-25|Zfp-6	early growth response 2	protein-coding
mm_167685.1	chr9	84673620	84673623	+	1	NA	Intergenic	Intergenic	-100777	NR_040739	75253	Mm.401984	NR_040739	ENSMUSG00000099724	4930554C24Rik	-	RIKEN cDNA 4930554C24 gene	ncRNA
mm_78110.1	chr9	20581508	20581588	+	1	NA	5' UTR (NM_172919, exon 1 of 6)	5' UTR (NM_172919, exon 1 of 6)	220	NM_172919	244721	Mm.86627	NM_172919	ENSMUSG00000058192	Zfp846	2210010B09Rik|9130221F13|Znf846	zinc finger protein 846	protein-coding
mm_144046.1	chr17	90429251	90429256	-	1	NA	intron (NM_001346957, intron 14 of 18)	intron (NM_001346957, intron 14 of 18)	26627	NM_001346958	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_154343.1	chrM	5016	5020	+	1	NA	NA	Intergenic	NA	NA								
mm_123414.1	chr14	64146884	64146885	-	1	NA	intron (NM_001347639, intron 5 of 5)	intron (NM_001347639, intron 5 of 5)	42561	NM_028525	73382	Mm.481055	NM_028525	ENSMUSG00000021966	Prss52	1700049K14Rik|Tesp3	protease, serine 52	protein-coding
mm_7633.1	chr1	127732578	127732629	-	1	NA	intron (NM_001033041, intron 1 of 9)	RCHARR1|DNA|hAT-Charlie	3190	NM_001033041	266645	Mm.25735	NM_001033041	ENSMUSG00000026348	Acmsd	-	amino carboxymuconate semialdehyde decarboxylase	protein-coding
mm_50248.1	chr6	42358282	42358299	+	1	NA	TTS (NM_023580)	TTS (NM_023580)	8462	NM_001289619	22793	Mm.282303	NM_011777	ENSMUSG00000029860	Zyx	9530098H06Rik|R75157	zyxin	protein-coding
mm_17454.1	chr2	28556175	28556195	-	1	NA	exon (NM_009885, exon 11 of 11)	exon (NM_009885, exon 11 of 11)	7218	NM_009885	12613	Mm.236017	NM_009885	ENSMUSG00000026818	Cel	1810036E18Rik|BAL	carboxyl ester lipase	protein-coding
mm_154101.1	chr19	57008599	57008607	-	1	NA	promoter-TSS (NM_001177797)	promoter-TSS (NM_001177797)	-28	NM_001177797	226250	Mm.226284	NM_146102	ENSMUSG00000025083	Afap1l2	AU041783|C86904|mKIAA1914	actin filament associated protein 1-like 2	protein-coding
mm_150804.1	chr19	44333403	44333411	+	1	NA	promoter-TSS (NM_183216)	promoter-TSS (NM_183216)	81	NM_183216	329065	Mm.313583	NM_183216	ENSMUSG00000050195	Scd4	ACOD4	stearoyl-coenzyme A desaturase 4	protein-coding
mm_105119.1	chr11	101119857	101119879	-	1	NA	promoter-TSS (NM_134024)	promoter-TSS (NM_134024)	-25	NM_028933	67998	Mm.33881	NM_026501	ENSMUSG00000017802	Fam134c	1300010M03Rik|4933404C01Rik|AI551748	family with sequence similarity 134, member C	protein-coding
mm_107424.1	chr12	35097694	35097720	+	1	NA	intron (NM_001014973, intron 8 of 25)	intron (NM_001014973, intron 8 of 25)	50518	NM_001014973	217463	Mm.213991	NM_001014973	ENSMUSG00000020590	Snx13	Rgs-px1|mKIAA0713	sorting nexin 13	protein-coding
mm_106789.1	chr12	4769376	4769386	+	1	NA	promoter-TSS (NM_175431)	promoter-TSS (NM_175431)	86	NM_028376	382562	Mm.251575	NM_028376	ENSMUSG00000020639	Pfn4	2900024P18Rik	profilin family, member 4	protein-coding
mm_129656.1	chr15	81045468	81045540	-	1	NA	intron (NM_001082536, intron 2 of 13)	intron (NM_001082536, intron 2 of 13)	59543	NM_153049	223701	Mm.439814	NM_153049	ENSMUSG00000042292	Mkl1	AMKL|Bsac|Mal|Mrtf-A	MKL (megakaryoblastic leukemia)/myocardin-like 1	protein-coding
mm_57132.1	chr6	122603084	122603112	-	1	NA	promoter-TSS (NM_031159)	promoter-TSS (NM_031159)	-654	NM_001134391	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_157833.1	chrX	74249820	74249840	-	1	NA	Intergenic	Intergenic	-3296	NM_001290421	192176	Mm.295533	NM_010227	ENSMUSG00000031328	Flna	ABP-280|Dilp2|F730004A14Rik|Fln1|GENA 379|filamin-1	filamin, alpha	protein-coding
mm_10421.1	chr2	13580709	13580748	+	1	NA	intron (NM_011701, intron 7 of 8)	intron (NM_011701, intron 7 of 8)	6417	NM_011701	22352	Mm.268000	NM_011701	ENSMUSG00000026728	Vim	-	vimentin	protein-coding
mm_167671.1	chr9	74739399	74739399	+	1	NA	Intergenic	Intergenic	-109038	NR_045284	100503019	Mm.482658	NR_045284	ENSMUSG00000066477	Gm16551	-	predicted gene 16551	ncRNA
mm_97094.1	chr11	73177201	73177235	+	1	NA	promoter-TSS (NM_025318)	promoter-TSS (NM_025318)	135	NM_029564	76281	Mm.371656	NM_029564	ENSMUSG00000040158	Tax1bp3	1300011C24Rik|TIP-1	Tax1 (human T cell leukemia virus type I) binding protein 3	protein-coding
mm_88035.1	chr10	67534513	67534525	+	1	NA	Intergenic	Intergenic	-3350	NM_010118	13654	Mm.290421	NM_010118	ENSMUSG00000037868	Egr2	Egr-2|Krox-20|Krox20|NGF1-B|Zfp-25|Zfp-6	early growth response 2	protein-coding
mm_57534.1	chr6	126638623	126638669	-	1	NA	3' UTR (NM_010595, exon 2 of 2)	3' UTR (NM_010595, exon 2 of 2)	7155	NM_010595	16485	Mm.40424	NM_010595	ENSMUSG00000047976	Kcna1	AI840627|Kca1-1|Kv1.1|MBK1|Mk-1|Shak|mceph	potassium voltage-gated channel, shaker-related subfamily, member 1	protein-coding
mm_124648.1	chr15	5143862	5143896	+	1	NA	promoter-TSS (NM_001013367)	promoter-TSS (NM_001013367)	18	NM_001013367	105787	Mm.207004	NM_001013367	ENSMUSG00000050697	Prkaa1	AI194361|AI450832|AL024255|AMPKalpha1|C130083N04Rik	protein kinase, AMP-activated, alpha 1 catalytic subunit	protein-coding
mm_27098.1	chr3	30358345	30358345	-	1	NA	intron (NM_021442, intron 1 of 2)	Lx8|LINE|L1	151142	NM_021442	14013	Mm.56965	NM_007963	ENSMUSG00000027684	Mecom	D630039M04Rik|Evi-1|Evi1|Jbo|Mds|Mds1|Mds1-Evi1|Prdm3|Znfpr1b1	MDS1 and EVI1 complex locus	protein-coding
mm_165367.1	chr2	126606154	126606166	-	1	NA	intron (NM_008230, intron 4 of 11)	intron (NM_008230, intron 4 of 11)	12518	NM_008230	15186	Mm.18603	NM_008230	ENSMUSG00000027360	Hdc	AW108189|Hdc-a|Hdc-c|Hdc-e|Hdc-s	histidine decarboxylase	protein-coding
mm_94025.1	chr10	127668522	127668589	-	1	NA	non-coding (NR_045171, exon 2 of 2)	non-coding (NR_045171, exon 2 of 2)	1432	NR_045171	72243	Mm.482902	NR_045171	ENSMUSG00000040195	1700012D01Rik	-	RIKEN cDNA 1700012D01 gene	ncRNA
mm_31258.1	chr4	45121574	45121590	+	1	NA	Intergenic	MIR3|SINE|MIR	-13469	NM_001099675	68512	Mm.282081	NM_001099675	ENSMUSG00000078713	Tomm5	1110019J04Rik|Tom5	translocase of outer mitochondrial membrane 5 homolog (yeast)	protein-coding
mm_24157.1	chr3	88454952	88454968	+	1	NA	intron (NM_001163489, intron 1 of 14)	intron (NM_001163489, intron 1 of 14)	801	NM_013658	20351	Mm.439752	NM_013658	ENSMUSG00000028064	Sema4a	AI132332|SemB|Semab	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A	protein-coding
mm_150141.1	chr19	31085546	31085549	+	1	NA	3' UTR (NM_031249, exon 1 of 1)	3' UTR (NM_031249, exon 1 of 1)	2706	NM_031249	83410	Mm.22031	NM_031249	ENSMUSG00000053536	Cstf2t	64kDa|C77975|tCstF-64|tauCstF-64	cleavage stimulation factor, 3' pre-RNA subunit 2, tau	protein-coding
mm_2264.1	chr1	91177720	91177723	+	1	NA	Intergenic	RLTR48A|LTR|ERV1	-2101	NM_016894	51801	Mm.3272	NM_016894	ENSMUSG00000034353	Ramp1	9130218E19Rik	receptor (calcitonin) activity modifying protein 1	protein-coding
mm_30808.1	chr4	20042047	20042107	+	1	NA	promoter-TSS (NM_010281)	promoter-TSS (NM_010281)	25	NM_010281	14590	Mm.20461	NM_010281	ENSMUSG00000073987	Ggh	gamma-GH	gamma-glutamyl hydrolase	protein-coding
mm_125596.1	chr15	59648645	59648687	+	1	NA	promoter-TSS (NM_144549)	promoter-TSS (NM_144549)	12	NM_144549	211770	Mm.40298	NM_144549	ENSMUSG00000032501	Trib1	A530090O15Rik|TRB-1|Trb1	tribbles pseudokinase 1	protein-coding
mm_48153.1	chr5	137151235	137151248	-	1	NA	Intergenic	Intergenic	-35034	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_105484.1	chr11	105944129	105944223	-	1	NA	promoter-TSS (NM_007805)	promoter-TSS (NM_007805)	-29	NM_007805	13056	Mm.149403	NM_007805	ENSMUSG00000019590	Cyb561	-	cytochrome b-561	protein-coding
mm_126497.1	chr15	81745043	81745051	+	1	NA	5' UTR (NM_001081016, exon 1 of 23)	5' UTR (NM_001081016, exon 1 of 23)	199	NM_001081016	20286	Mm.432075	NM_001081016	ENSMUSG00000022390	Zc3h7b	Gm627|Scrg3|Zc2h7b|mKIAA1031	zinc finger CCCH type containing 7B	protein-coding
mm_28446.1	chr3	90511134	90511174	-	1	NA	3' UTR (NM_011309, exon 3 of 3)	3' UTR (NM_011309, exon 3 of 3)	-1656	NM_001293782	66511	Mm.154136	NM_023215	ENSMUSG00000001017	Chtop	2500003M10Rik|Fop|Srag	chromatin target of PRMT1	protein-coding
mm_77857.1	chr9	5312857	5312867	+	1	NA	intron (NM_007609, intron 1 of 8)	L1M2|LINE|L1	4013	NM_007609	12363	Mm.1569	NM_007609	ENSMUSG00000033538	Casp4	CASP-11|CASP-4|Casp11|Caspl|ich-3	caspase 4, apoptosis-related cysteine peptidase	protein-coding
mm_19206.1	chr2	84513688	84513695	-	1	NA	Intergenic	ORR1A4-int|LTR|ERVL-MaLR	-6818	NR_046046	672763	Mm.491046	NR_046046	ENSMUSG00000087362	Gm13710	OTTMUSG00000013441	predicted gene 13710	ncRNA
mm_6204.1	chr1	66765710	66765728	-	1	NA	intron (NM_177645, intron 5 of 13)	RMER1A|Other|Other	51876	NM_177645	68691	Mm.240912	NM_177645	ENSMUSG00000026004	Kansl1l	1110028C15Rik|1190030G24|AI427598|C430010P07Rik|mKIAA4189	KAT8 regulatory NSL complex subunit 1-like	protein-coding
mm_74550.1	chr8	10865104	10865119	-	1	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	17343	NR_040705	320014	Mm.403203	NR_040705	ENSMUSG00000109473	B930025P03Rik	-	RIKEN cDNA B930025P03 gene	ncRNA
mm_143792.1	chr17	81789363	81789367	-	1	NA	Intergenic	Intergenic	-50978	NM_011406	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_10060.1	chr1	193275084	193275090	-	1	NA	Intergenic	Intergenic	-1899	NM_008059	14373	Mm.439721	NM_008059	ENSMUSG00000009633	G0s2	AI255151|AV006465	G0/G1 switch gene 2	protein-coding
mm_80574.1	chr9	84007493	84007495	+	1	NA	intron (NM_001305935, intron 6 of 10)	intron (NM_001305935, intron 6 of 10)	58713	NM_199195	12040	Mm.12819	NM_199195	ENSMUSG00000032263	Bckdhb	BCKDE1B|BCKDH E1-beta	branched chain ketoacid dehydrogenase E1, beta polypeptide	protein-coding
mm_138571.1	chr17	35384196	35384226	+	1	NA	3' UTR (NM_001143689, exon 6 of 6)	3' UTR (NM_001143689, exon 6 of 6)	4594	NM_001143689	15015	Mm.464284	NM_001143689	ENSMUSG00000035929	H2-Q4	H-2Q4|H2-Gs10|Qa-4|Qa4|Qat-4|Qb-1|Qb1	histocompatibility 2, Q region locus 4	protein-coding
mm_106637.1	chr11	120991040	120991074	-	1	NA	5' UTR (NM_139059, exon 1 of 9)	5' UTR (NM_139059, exon 1 of 9)	276	NM_139059	104318	Mm.216227	NM_027874	ENSMUSG00000025162	Csnk1d	1200006A05Rik|AA409348|D930010H05Rik	casein kinase 1, delta	protein-coding
mm_141862.1	chr17	34804332	34804343	-	1	NA	promoter-TSS (NM_009995)	promoter-TSS (NM_009995)	89	NM_009995	13079	Mm.440407	NM_009995	ENSMUSG00000024365	Cyp21a1	21-OH|21OH|21OHA|21OHB|CYP21OH-A|Cyp21|Cyp21-ps1|Cyp21B|Cyp21a2-ps|Cyp21a2ps|Oh21-1|Oh21-2	cytochrome P450, family 21, subfamily a, polypeptide 1	protein-coding
mm_103730.1	chr11	79704471	79704517	-	1	NA	Intergenic	CpG	-7475	NR_029579	387188		NR_029579	ENSMUSG00000065395	Mir193a	Mir193|Mirn193|mir-193a|mmu-mir-193|mmu-mir-193a	microRNA 193a	ncRNA
mm_136296.1	chr16	91484919	91484936	-	1	NA	promoter-TSS (NM_010508)	promoter-TSS (NM_010508)	-288	NM_010508	15975	Mm.502	NM_010508	ENSMUSG00000022967	Ifnar1	CD118|Ifar|Ifnar|Ifrc|Infar	interferon (alpha and beta) receptor 1	protein-coding
mm_43484.1	chr5	136908205	136908226	+	1	NA	promoter-TSS (NM_026073)	promoter-TSS (NM_026073)	65	NM_026073	67286	Mm.41779	NM_026073	ENSMUSG00000007987	Ift22	3110017O03Rik|AI835745|AI847427|Rabl5	intraflagellar transport 22	protein-coding
mm_33271.1	chr4	127987995	127988047	+	1	NA	promoter-TSS (NM_001281955)	promoter-TSS (NM_001281955)	-23	NM_001281955	329942	Mm.421342	NM_001281955	ENSMUSG00000028804	Csmd2	Gm139	CUB and Sushi multiple domains 2	protein-coding
mm_66763.1	chr7	46728797	46728805	-	1	NA	3' UTR (NM_011316, exon 4 of 4)	3' UTR (NM_011316, exon 4 of 4)	3802	NM_011316	20211	Mm.3489	NM_011316	ENSMUSG00000040017	Saa4	Saa-4|Saa-5	serum amyloid A 4	protein-coding
mm_39123.1	chr4	155019398	155019398	-	1	NA	Intergenic	(CTAG)n|Simple_repeat|Simple_repeat	-8414	NM_001113360	269615	Mm.379458	NM_175556	ENSMUSG00000029055	Plch2	A930027K05Rik|PLCeta2|Plc-eta2|Plcl4	phospholipase C, eta 2	protein-coding
mm_140572.1	chr17	9669650	9669663	-	1	NA	promoter-TSS (NM_001163836)	promoter-TSS (NM_001163836)	48	NM_001163836	67543	Mm.26987	NM_026226	ENSMUSG00000046173	Pabpc6	4932702K14Rik|AI428050|Pabpc3	poly(A) binding protein, cytoplasmic 6	protein-coding
mm_10033.1	chr1	192718211	192718213	-	1	NA	intron (NM_144881, intron 6 of 11)	intron (NM_144881, intron 6 of 11)	53007	NM_144881	226861	Mm.145857	NM_144881	ENSMUSG00000037375	Hhat	2810432O22Rik|AI462858|AP-2CRE|Skn|Tg(TFAP2A-cre)1Will	hedgehog acyltransferase	protein-coding
mm_70161.1	chr7	143549245	143549255	-	1	NA	promoter-TSS (NM_008672)	promoter-TSS (NM_008672)	-130	NM_008672	17955	Mm.294625	NM_008672	ENSMUSG00000059119	Nap1l4	2810410H14Rik|AI316776|D7Wsu30e|Nap2	nucleosome assembly protein 1-like 4	protein-coding
mm_9756.1	chr1	180813866	180813882	-	1	NA	promoter-TSS (NM_008210)	promoter-TSS (NM_008210)	-269	NM_008210	15078	Mm.138832	NM_008210	ENSMUSG00000060743	H3f3a	H3.3A	H3 histone, family 3A	protein-coding
mm_19749.1	chr2	104849663	104849714	-	1	NA	5' UTR (NM_178695, exon 1 of 6)	5' UTR (NM_178695, exon 1 of 6)	162	NM_178695	228413	Mm.259609	NM_178695	ENSMUSG00000027171	Prrg4	9930111I18Rik|TMG4	proline rich Gla (G-carboxyglutamic acid) 4 (transmembrane)	protein-coding
mm_108080.1	chr12	73946312	73946328	+	1	NA	3' UTR (NM_010431, exon 15 of 15)	3' UTR (NM_010431, exon 15 of 15)	-18210	NM_178392	75627	Mm.25937	NM_178392	ENSMUSG00000021113	Snapc1	2700033G17Rik|AU015787	small nuclear RNA activating complex, polypeptide 1	protein-coding
mm_80676.1	chr9	90245466	90245475	+	1	NA	intron (NM_194334, intron 2 of 12)	intron (NM_194334, intron 2 of 12)	25299	NM_194334	67016	Mm.335347	NM_194334	ENSMUSG00000037410	Tbc1d2b	1810061M12Rik|AI480956|AV021536|AV023399|AW491493|mKIAA1055	TBC1 domain family, member 2B	protein-coding
mm_127622.1	chr15	102462165	102462193	+	1	NA	exon (NM_025385, exon 5 of 5)	exon (NM_025385, exon 5 of 5)	3009	NM_025385	66151	Mm.393955	NM_025385	ENSMUSG00000023048	Prr13	1110020C13Rik|2010324E22Rik	proline rich 13	protein-coding
mm_33929.1	chr4	136880562	136880613	+	1	NA	exon (NM_009777, exon 3 of 3)	exon (NM_009777, exon 3 of 3)	5590	NM_009777	12260	Mm.2570	NM_009777	ENSMUSG00000036905	C1qb	-	complement component 1, q subcomponent, beta polypeptide	protein-coding
mm_136835.1	chr17	12746489	12746500	+	1	NA	intron (NR_027773, intron 1 of 2)	intron (NR_027773, intron 1 of 2)	5183	NR_027784	104103	Mm.26553	NR_002853	ENSMUSG00000078247	Airn	2810051F02Rik|2810434M15Rik|AI256653|AI597500|AW049873|Air|B930018I07Rik|D17Ertd663e|IGF2RAS	antisense Igf2r RNA	ncRNA
mm_125810.1	chr15	74931213	74931232	+	1	NA	Intergenic	RMER17C|LTR|ERVK	-23829	NM_001164039	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_158533.1	chrX	143923222	143923234	-	1	NA	exon (NM_010025, exon 3 of 7)	exon (NM_010025, exon 3 of 7)	9896	NM_001110222	13193	Mm.12871	NM_010025	ENSMUSG00000031285	Dcx	Dbct	doublecortin	protein-coding
mm_90819.1	chr10	7919988	7920017	-	1	NA	exon (NM_138667, exon 3 of 7)	exon (NM_138667, exon 3 of 7)	36121	NM_138667	68652	Mm.193041	NM_138667	ENSMUSG00000015755	Tab2	1110030N06Rik|A530078N03Rik|Map3k7ip2|mKIAA0733	TGF-beta activated kinase 1/MAP3K7 binding protein 2	protein-coding
mm_9503.1	chr1	173732372	173732395	-	1	NA	exon (NM_001204910, exon 4 of 8)	exon (NM_001204910, exon 4 of 8)	9426	NM_001204910	226691	Mm.440876	NM_001204910	ENSMUSG00000073490	Ifi207	AI607873|Pyhin-A	interferon activated gene 207	protein-coding
mm_62287.1	chr7	99906408	99906415	+	1	NA	intron (NM_001164258, intron 11 of 18)	AT_rich|Low_complexity|Low_complexity	47193	NM_001164258	446101	Mm.440757	NM_001164258	ENSMUSG00000035211	Xrra1	AI449753	X-ray radiation resistance associated 1	protein-coding
mm_55244.1	chr6	52640248	52640259	-	1	NA	promoter-TSS (NM_145567)	promoter-TSS (NM_145567)	47	NM_145567	58875	Mm.286458	NM_145567	ENSMUSG00000029776	Hibadh	6430402H10Rik|AI265272	3-hydroxyisobutyrate dehydrogenase	protein-coding
mm_160597.1	chr9	73933632	73933632	-	1	NA	promoter-TSS (NM_001081153)	promoter-TSS (NM_001081153)	-65	NM_001081153	208898	Mm.41035	NM_001081153	ENSMUSG00000062151	Unc13c	1500037O19Rik|AU019458|D9Ertd414e|Munc13-3|Unc13h3	unc-13 homolog C (C. elegans)	protein-coding
mm_81886.1	chr9	119392022	119392034	+	1	NA	3' UTR (NM_001199568, exon 20 of 20)	3' UTR (NM_001199568, exon 20 of 20)	-10150	NM_001313757	11481	Mm.8940	NM_007397	ENSMUSG00000061393	Acvr2b	4930516B21Rik|ActRIIB	activin receptor IIB	protein-coding
mm_140324.1	chr17	86753689	86753709	+	1	NA	promoter-TSS (NM_010137)	promoter-TSS (NM_010137)	-165	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_71802.1	chr8	68276804	68276815	+	1	NA	5' UTR (NM_028182, exon 1 of 9)	5' UTR (NM_028182, exon 1 of 9)	281	NM_028182	72281	Mm.40974	NM_028182	ENSMUSG00000053886	Sh2d4a	2210402M20Rik|SH2A	SH2 domain containing 4A	protein-coding
mm_155442.1	chrX	73494924	73494963	+	1	NA	3' UTR (NM_007542, exon 8 of 8)	3' UTR (NM_007542, exon 8 of 8)	-8143	NM_001310537	320707	Mm.210095	NM_177236	ENSMUSG00000031376	Atp2b3	6430519O13Rik|Pmca3	ATPase, Ca++ transporting, plasma membrane 3	protein-coding
mm_123455.1	chr14	65405187	65405192	-	1	NA	intron (NM_001205075, intron 2 of 3)	intron (NM_001205075, intron 2 of 3)	20283	NM_001205075	18155	Mm.16347	NM_010932	ENSMUSG00000045731	Pnoc	N/OFQ|Npnc1|OFQ/N	prepronociceptin	protein-coding
mm_47191.1	chr5	120754621	120754633	-	1	NA	exon (NM_145226, exon 15 of 16)	exon (NM_145226, exon 15 of 16)	-4779	NM_001347448	246728	Mm.260926	NM_145227	ENSMUSG00000032690	Oas2	Oasl11	2'-5' oligoadenylate synthetase 2	protein-coding
mm_56703.1	chr6	114969946	114969981	-	1	NA	Intergenic	CpG	-48211	NM_177683	232334	Mm.268357	NM_177683	ENSMUSG00000030315	Vgll4	BC048841|VGL-4	vestigial like family member 4	protein-coding
mm_96489.1	chr11	67695335	67695376	+	1	NA	promoter-TSS (NM_009038)	promoter-TSS (NM_009038)	29	NM_009038	19674	Mm.439726	NM_009038	ENSMUSG00000020907	Rcvrn	CAR|S-modulin	recoverin	protein-coding
mm_121248.1	chr14	103057309	103057319	+	1	NA	TTS (NM_008392)	TTS (NM_008392)	10302	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_106086.1	chr11	116178276	116178306	-	1	NA	exon (NM_015729, exon 9 of 14)	exon (NM_015729, exon 9 of 14)	-10113	NM_172571	217335	Mm.35241	NM_172571	ENSMUSG00000020776	Fbf1	1110033G01Rik|5930413D20|mKIAA1863	Fas (TNFRSF6) binding factor 1	protein-coding
mm_25691.1	chr3	122256687	122256691	+	1	NA	intron (NM_008129, intron 2 of 6)	intron (NM_008129, intron 2 of 6)	11132	NM_008129	14630	Mm.292676	NM_008129	ENSMUSG00000028124	Gclm	AI649393|Gcmc|Glclr	glutamate-cysteine ligase, modifier subunit	protein-coding
mm_91124.1	chr10	19591471	19591476	-	1	NA	promoter-TSS (NM_010511)	promoter-TSS (NM_010511)	-476	NM_010511	15979	Mm.549	NM_010511	ENSMUSG00000020009	Ifngr1	CD119|IFN-gammaR|Ifgr|Ifngr|Nktar	interferon gamma receptor 1	protein-coding
mm_47737.1	chr5	130245945	130245949	-	1	NA	3' UTR (NM_023248, exon 5 of 5)	3' UTR (NM_023248, exon 5 of 5)	9583	NM_023248	66711	Mm.280484	NM_023248	ENSMUSG00000025337	Sbds	4733401P19Rik|AI836084|CGI-97|SDS	Shwachman-Bodian-Diamond syndrome homolog (human)	protein-coding
mm_1293.1	chr1	64532053	64532070	+	1	NA	promoter-TSS (NM_009952)	promoter-TSS (NM_009952)	-743	NM_133828	12912	Mm.422634	NM_009952	ENSMUSG00000025958	Creb1	2310001E10Rik|3526402H21Rik|AV083133|Creb|Creb-1	cAMP responsive element binding protein 1	protein-coding
mm_145961.1	chr18	67774971	67774981	+	1	NA	promoter-TSS (NM_001039088)	promoter-TSS (NM_001039088)	100	NM_001039088	72124	Mm.307315	NM_028112	ENSMUSG00000079614	Seh1l	2610007A16Rik|AW540070|SEC13L|SEH1A|SEH1B|Seh1	SEH1-like (S. cerevisiae	protein-coding
mm_45069.1	chr5	43784769	43784770	-	1	NA	Intergenic	Intergenic	-2620	NM_178729	242960	Mm.25794	NM_178729	ENSMUSG00000039753	Fbxl5	Fbl4|Fir4	F-box and leucine-rich repeat protein 5	protein-coding
mm_32206.1	chr4	101507856	101507868	+	1	NA	promoter-TSS (NM_001164585)	promoter-TSS (NM_001164585)	-114	NM_001164585	72685	Mm.76494	NM_198412	ENSMUSG00000028528	Dnajc6	2810027M23Rik|mKIAA0473	DnaJ heat shock protein family (Hsp40) member C6	protein-coding
mm_134076.1	chr16	8672164	8672186	-	1	NA	promoter-TSS (NM_025821)	promoter-TSS (NM_025821)	-22	NM_025821	52502	Mm.142095	NM_025821	ENSMUSG00000008393	Carhsp1	1200011K09Rik|Crhsp-24|D16Ertd465e	calcium regulated heat stable protein 1	protein-coding
mm_7294.1	chr1	97885653	97885662	-	1	NA	exon (NM_013626, exon 13 of 26)	exon (NM_013626, exon 13 of 26)	115485	NM_026250	252876	Mm.86090	NM_026250	ENSMUSG00000026333	Gin1	4930429M06Rik|8430411H10Rik|Gin-1|Zh2c2	gypsy retrotransposon integrase 1	protein-coding
mm_87561.1	chr10	56114951	56114961	+	1	NA	5' UTR (NM_001163833, exon 2 of 2)	5' UTR (NM_001163833, exon 2 of 2)	8039	NM_001163833	73390	Mm.181475	NM_133751	ENSMUSG00000047669	Msl3l2	1700060H10Rik	male-specific lethal 3-like 2 (Drosophila)	protein-coding
mm_145413.1	chr18	57878597	57878607	+	1	NA	promoter-TSS (NM_009194)	promoter-TSS (NM_009194)	-76	NM_009194	20496	Mm.399997	NM_009194	ENSMUSG00000024597	Slc12a2	9330166H04Rik|Nkcc1|mBSC2|sy-ns	solute carrier family 12, member 2	protein-coding
mm_59369.1	chr7	25694239	25694253	+	1	NA	exon (NM_011577, exon 3 of 7)	exon (NM_011577, exon 3 of 7)	7244	NM_011577	21803	Mm.248380	NM_011577	ENSMUSG00000002603	Tgfb1	TGF-beta1|TGFbeta1|Tgfb|Tgfb-1	transforming growth factor, beta 1	protein-coding
mm_112713.1	chr13	19184987	19184998	+	1	NA	Intergenic	Intergenic	210821	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_131495.1	chr16	17331375	17331427	+	1	NA	promoter-TSS (NM_001331047)	promoter-TSS (NM_001331047)	30	NM_001331047	15160	Mm.6609	NM_008223	ENSMUSG00000022766	Serpind1	AA985900|AI303446|HC-II|HCII|Hcf2	serine (or cysteine) peptidase inhibitor, clade D, member 1	protein-coding
mm_103936.1	chr11	83649350	83649365	-	1	NA	promoter-TSS (NM_011337)	promoter-TSS (NM_011337)	21	NM_011337	20302	Mm.1282	NM_011337	ENSMUSG00000000982	Ccl3	AI323804|G0S19-1|LD78alpha|MIP-1alpha|MIP1-(a)|MIP1-alpha|Mip1a|Scya3	chemokine (C-C motif) ligand 3	protein-coding
mm_2430.1	chr1	95667782	95667813	+	1	NA	promoter-TSS (NM_001159745)	promoter-TSS (NM_001159745)	-203	NM_001159745	20452	Mm.306228	NM_009183	ENSMUSG00000040710	St8sia4	PST|PST-1|SIAT8-D|ST8SiaIV|Siat8d	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4	protein-coding
mm_153019.1	chr19	31079697	31079697	-	1	NA	intron (NM_011160, intron 3 of 17)	intron (NM_011160, intron 3 of 17)	-3144	NM_031249	83410	Mm.22031	NM_031249	ENSMUSG00000053536	Cstf2t	64kDa|C77975|tCstF-64|tauCstF-64	cleavage stimulation factor, 3' pre-RNA subunit 2, tau	protein-coding
mm_56962.1	chr6	120038306	120038363	-	1	NA	5' UTR (NM_001185020, exon 1 of 26)	5' UTR (NM_001185020, exon 1 of 26)	321	NM_001199083	232341	Mm.333349	NM_198703	ENSMUSG00000045962	Wnk1	6430573H23Rik|EG406236|Hsn2|Prkwnk1|mKIAA0344	WNK lysine deficient protein kinase 1	protein-coding
mm_142392.1	chr17	44880842	44880858	-	1	NA	promoter-TSS (NM_029257)	promoter-TSS (NM_029257)	35	NM_029257	75341	Mm.386821	NM_029257		4930564C03Rik	-	RIKEN cDNA 4930564C03 gene	protein-coding
mm_88554.1	chr10	78602545	78602548	+	1	NA	Intergenic	RMER15|LTR|ERVL	-10582	NM_027875	71709	Mm.86439	NM_027875	ENSMUSG00000032714	Syde1	1200008N06Rik|BB043000|mSYD1A	synapse defective 1, Rho GTPase, homolog 1 (C. elegans)	protein-coding
mm_134356.1	chr16	16718127	16718135	-	1	NA	promoter-TSS (NR_045920)	promoter-TSS (NR_045920)	-10	NR_045920	74066	Mm.61161	NM_028739		4933404G15Rik	4933401J20Rik	RIKEN cDNA 4933404G15 gene	ncRNA
mm_42832.1	chr5	122102651	122102659	+	1	NA	intron (NM_010861, intron 2 of 6)	intron (NM_010861, intron 2 of 6)	1675	NM_010861	17906	Mm.1529	NM_010861	ENSMUSG00000013936	Myl2	MLC-2|MLC-2s/v|MLC-2v|Mlc2v|Mylpc	myosin, light polypeptide 2, regulatory, cardiac, slow	protein-coding
mm_172317.1	chr7	106215347	106215349	-	1	NA	promoter-TSS (NM_001243039).2	promoter-TSS (NM_001243039).2	-8	NM_029000	74558	Mm.458429	NM_029000	ENSMUSG00000045868	Gvin1	9130002C22Rik|9830104F22Rik|Iigs1|VLIG|VLIG-1	GTPase, very large interferon inducible 1	protein-coding
mm_138158.1	chr17	34240016	34240057	+	1	NA	intron (NM_010389, intron 1 of 5)	intron (NM_010389, intron 1 of 5)	1131	NM_010389	15002	Mm.327358	NM_010389	ENSMUSG00000041538	H2-Ob	A-beta-2|A-beta2|H-2Ab|H-2I|H-2Ob|H2-Ab|H2-Ab2|H2-IAb2|Ob	histocompatibility 2, O region beta locus	protein-coding
mm_82248.1	chr9	4795915	4795928	-	1	NA	5' UTR (NM_001113181, exon 1 of 11)	5' UTR (NM_001113181, exon 1 of 11)	313	NM_001113180	14802	Mm.209263	NM_019691	ENSMUSG00000025892	Gria4	GluA4|GluR-D|Glur-4|Glur4|Gluralpha4|spkw1	glutamate receptor, ionotropic, AMPA4 (alpha 4)	protein-coding
mm_28142.1	chr3	87263597	87263607	-	1	NA	promoter-TSS (NM_030707)	promoter-TSS (NM_030707)	-78	NM_030707	80891	Mm.45173	NM_030707	ENSMUSG00000015852	Fcrls	2810439C17Rik|9330158F12|FcRH2sc|Fcrh2|IFGP2|IgSR|MMAN-g|Msr2|moFcRH2sc	Fc receptor-like S, scavenger receptor	protein-coding
mm_39924.1	chr5	31582229	31582238	+	1	NA	Intergenic	Intergenic	-10836	NR_102275	100740	Mm.23370	NR_102275		AI839979	-	expressed sequence AI839979	ncRNA
mm_153994.1	chr19	50620217	50620222	-	1	NA	intron (NM_001290356, intron 1 of 24)	intron (NM_001290356, intron 1 of 24)	58427	NM_001252501	58178	Mm.313672	NM_021377	ENSMUSG00000043531	Sorcs1	Sorcs|mSorCS	sortilin-related VPS10 domain containing receptor 1	protein-coding
mm_67978.1	chr7	100658346	100658356	-	1	NA	5' UTR (NM_001291336, exon 1 of 6)	5' UTR (NM_001291336, exon 1 of 6)	105	NM_001163185	27276	Mm.491216	NM_013746	ENSMUSG00000030701	Plekhb1	AI315628|PHR1|Phret1|evt-1	pleckstrin homology domain containing, family B (evectins) member 1	protein-coding
mm_37669.1	chr4	129118727	129118732	-	1	NA	exon (NM_010471, exon 2 of 4)	exon (NM_010471, exon 2 of 4)	1443	NM_001286083	15444	Mm.384452	NM_010471	ENSMUSG00000028785	Hpca	-	hippocalcin	protein-coding
mm_138368.1	chr17	35001024	35001097	+	1	NA	promoter-TSS (NM_033075)	promoter-TSS (NM_033075)	153	NM_011690	22321	Mm.28420	NM_011690	ENSMUSG00000007029	Vars	Bat6|D17H6S56E|G7a|Vars2	valyl-tRNA synthetase	protein-coding
mm_42079.1	chr5	110176580	110176600	+	1	NA	promoter-TSS (NM_008146)	promoter-TSS (NM_008146)	-86	NR_040430	100504007	Mm.441495	NR_040430	ENSMUSG00000086247	Gm15787	OTTMUSG00000026209	predicted gene 15787	ncRNA
mm_17006.1	chr2	18800048	18800063	-	1	NA	non-coding (NR_131254, exon 1 of 1)	non-coding (NR_131254, exon 1 of 1)	1763	NR_131254	66774	Mm.87075	NR_131254	ENSMUSG00000097638	Carlr	4933439G12Rik|Carl	cardiac and apoptosis-related long non-coding RNA	ncRNA
mm_57658.1	chr6	128486919	128486953	-	1	NA	exon (NM_007376, exon 32 of 36)	exon (NM_007376, exon 32 of 36)	39784	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_143828.1	chr17	84006865	84006873	-	1	NA	intron (NR_130994, intron 1 of 1)	intron (NR_130994, intron 1 of 1)	8317	NR_130994	78148	Mm.243918	NR_130994		8430430B14Rik	-	RIKEN cDNA 8430430B14 gene	ncRNA
mm_62786.1	chr7	112519613	112519650	+	1	NA	intron (NM_020606, intron 1 of 12)	intron (NM_020606, intron 1 of 12)	91925	NM_020606	57342	Mm.143763	NM_020606	ENSMUSG00000030770	Parva	2010012A22Rik|5430400F08Rik|AI225929|AU042898|Actp|CH-ILKBP|Parvin	parvin, alpha	protein-coding
mm_154196.1	chr19	58943577	58943593	-	1	NA	promoter-TSS (NM_001327998)	promoter-TSS (NM_001327998)	87	NM_001327998	73442	Mm.39739	NM_175199	ENSMUSG00000025092	Hspa12a	1700063D12Rik|AI118035|AI840429|AW048913|AW556406|D5Mgi40|Gm19925|mKIAA0417	heat shock protein 12A	protein-coding
mm_170735.1	chr2	152865987	152865987	-	1	NA	TTS (NR_049195)	TTS (NR_049195)	920	NR_049195	100885834		NR_049195	ENSMUSG00000093746	Mir5622	Gm24421|mmu-mir-5622	microRNA 5622	ncRNA
mm_104695.1	chr11	97949638	97949658	-	1	NA	intron (NM_001163608, intron 7 of 13)	B4A|SINE|B4	36798	NM_028199	72324	Mm.39617	NM_028199	ENSMUSG00000017417	Plxdc1	2410003I07Rik|AI848450|Tem7	plexin domain containing 1	protein-coding
mm_134135.1	chr16	10683319	10683356	-	1	NA	intron (NM_001204229, intron 18 of 22)	intron (NM_001204229, intron 18 of 22)	102199	NM_009896	12703	Mm.130	NM_009896	ENSMUSG00000038037	Socs1	Cish1|Cish7|JAB|SOCS-1|SSI-1	suppressor of cytokine signaling 1	protein-coding
mm_131324.1	chr16	12704400	12704416	+	1	NA	Intergenic	Intergenic	-106982	NR_040507	75493	Mm.396146	NR_040507	ENSMUSG00000101565	1700003L19Rik	-	RIKEN cDNA 1700003L19 gene	ncRNA
mm_172657.1	chr8	40362849	40362849	-	1	NA	intron (NM_030110, intron 8 of 14)	intron (NM_030110, intron 8 of 14)	54798	NM_030110	78506	Mm.169893	NM_030110	ENSMUSG00000039478	Micu3	2900075B16Rik|Efha2	mitochondrial calcium uptake family, member 3	protein-coding
mm_44898.1	chr5	35400016	35400023	-	1	NA	Intergenic	CpG	10902	NM_010445	15371	Mm.358606	NM_010445	ENSMUSG00000067438	Hmx1	Nkx5-3	H6 homeobox 1	protein-coding
mm_123274.1	chr14	61370515	61370531	-	1	NA	exon (NM_008466, exon 15 of 17)	exon (NM_008466, exon 15 of 17)	-10078	NM_026598	68177	Mm.22758	NM_026598	ENSMUSG00000021928	Ebpl	5730442K12Rik|EBRP	emopamil binding protein-like	protein-coding
mm_97137.1	chr11	75193798	75193864	+	1	NA	promoter-TSS (NM_177708)	promoter-TSS (NM_177708)	-162	NM_177708	237847	Mm.82661	NM_177708	ENSMUSG00000045287	Rtn4rl1	Ngr3|Ngrh2|Ngrl2	reticulon 4 receptor-like 1	protein-coding
mm_121371.1	chr14	118089675	118089702	+	1	NA	Intergenic	Intergenic	-37442	NM_010024	13190	Mm.19987	NM_010024	ENSMUSG00000022129	Dct	DT|TRP-2|TRP2|Tyrp-2|Tyrp2|slaty|slt	dopachrome tautomerase	protein-coding
mm_58005.1	chr6	136449347	136449357	-	1	NA	Intergenic	Intergenic	-33783	NM_001201390	100502936	Mm.21182	NM_001201390	ENSMUSG00000045291	E330021D16Rik	C85549	RIKEN cDNA E330021D16 gene	protein-coding
mm_83992.1	chr9	57443117	57443126	-	1	NA	3' UTR (NM_020270, exon 7 of 7)	3' UTR (NM_020270, exon 7 of 7)	-3007	NM_176831	66812	Mm.250508	NM_176831	ENSMUSG00000063849	Ppcdc	1810057I13Rik|8430432M10Rik	phosphopantothenoylcysteine decarboxylase	protein-coding
mm_92597.1	chr10	80101155	80101172	-	1	NA	intron (NM_183426, intron 1 of 31)	intron (NM_183426, intron 1 of 31)	1539	NM_183426	216161	Mm.262102	NM_183426	ENSMUSG00000035673	Sbno2	BC019206|F730040C21|Sno|Stno	strawberry notch homolog 2 (Drosophila)	protein-coding
mm_75603.1	chr8	61768836	61768840	-	1	NA	intron (NM_001081390, intron 2 of 19)	intron (NM_001081390, intron 2 of 19)	-8740	NM_001293773	72333	Mm.29933	NM_001081390	ENSMUSG00000058056	Palld	2410003B16Rik|6030492A02	palladin, cytoskeletal associated protein	protein-coding
mm_60860.1	chr7	45873168	45873187	+	1	NA	intron (NM_133950, intron 1 of 4)	intron (NM_133950, intron 1 of 4)	337	NM_133950	68137	Mm.298433	NM_133950	ENSMUSG00000002778	Kdelr1	8030486F04Rik|AW215843|Erd2.1	KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 1	protein-coding
mm_126409.1	chr15	80256018	80256078	+	1	NA	intron (NM_001287180, intron 2 of 3)	CpG	864	NM_009716	11911	Mm.641	NM_009716	ENSMUSG00000042406	Atf4	Atf-4|C/ATF|CREB2|TAXREB67	activating transcription factor 4	protein-coding
mm_55247.1	chr6	52713618	52713626	-	1	NA	promoter-TSS (NM_025816)	promoter-TSS (NM_025816)	-107	NM_025816	52440	Mm.389757	NM_025816	ENSMUSG00000004535	Tax1bp1	1200003J11Rik|1700069J21Rik|AA930106|D6Ertd404e|D6Ertd772e|T6bp|TXBP151	Tax1 (human T cell leukemia virus type I) binding protein 1	protein-coding
mm_123989.1	chr14	75754476	75754563	-	1	NA	promoter-TSS (NM_177381)	promoter-TSS (NM_177381)	-26	NM_177381	338337	Mm.86507	NM_177381	ENSMUSG00000034893	Cog3	E430004N23	component of oligomeric golgi complex 3	protein-coding
mm_60678.1	chr7	45083221	45083260	+	1	NA	3' UTR (NM_026555, exon 7 of 7)	3' UTR (NM_026555, exon 7 of 7)	8973	NM_026555	52377	Mm.29997	NM_026555	ENSMUSG00000019539	Rcn3	6030455P07Rik|D530026G20Rik|D7Ertd671e|RLP49	reticulocalbin 3, EF-hand calcium binding domain	protein-coding
mm_109649.1	chr12	112860139	112860187	+	1	NA	intron (NM_019925, intron 1 of 2)	intron (NM_019925, intron 1 of 2)	753	NM_019925	56696	Mm.20455	NM_019925	ENSMUSG00000021298	Gpr132	G2a	G protein-coupled receptor 132	protein-coding
mm_99671.1	chr11	105969686	105969704	+	1	NA	intron (NM_207624, intron 2 of 24)	intron (NM_207624, intron 2 of 24)	1750	NM_207624	11421	Mm.754	NM_009598	ENSMUSG00000020681	Ace	AW208573|CD143	angiotensin I converting enzyme (peptidyl-dipeptidase A) 1	protein-coding
mm_127781.1	chr15	3542372	3542380	-	1	NA	intron (NM_001048178, intron 1 of 8)	Tigger7|DNA|TcMar-Tigger	39466	NM_001286370	14600	Mm.3986	NM_010284	ENSMUSG00000055737	Ghr	GHBP|GHR/BP	growth hormone receptor	protein-coding
mm_52250.1	chr6	106771752	106771758	+	1	NA	intron (NM_001242360, intron 2 of 5)	intron (NM_001242360, intron 2 of 5)	2617	NM_001242358	70047	Mm.196332	NM_027296	ENSMUSG00000013736	Trnt1	2410043H24Rik|2610044E04Rik|9830143O18Rik|AA408384|C76540|CGI-47|mt-Trat	tRNA nucleotidyl transferase, CCA-adding, 1	protein-coding
mm_48684.1	chr5	146655601	146655614	-	1	NA	Intergenic	Intergenic	-70368	NM_001010941	14738	Mm.153539	NM_008151	ENSMUSG00000041468	Gpr12	Gpcr01|Gpcr12|Gpcr20|Gpcr21	G-protein coupled receptor 12	protein-coding
mm_13833.1	chr2	119351208	119351216	+	1	NA	promoter-TSS (NM_026929)	promoter-TSS (NM_026929)	-30	NM_026929	69065	Mm.35083	NM_026929	ENSMUSG00000027313	Chac1	1810008K03Rik	ChaC, cation transport regulator 1	protein-coding
mm_55134.1	chr6	51270871	51270889	-	1	NA	promoter-TSS (NR_029719)	promoter-TSS (NR_029719)	-970	NR_029719	387166		NR_029719	ENSMUSG00000065505	Mir148a	Mirn148|Mirn148a|mir-148a	microRNA 148a	ncRNA
mm_11173.1	chr2	28641347	28641358	+	1	NA	intron (NM_001289575, intron 1 of 22)	CpG	119	NM_022887	64930	Mm.224354	NM_022887	ENSMUSG00000026812	Tsc1	-	tuberous sclerosis 1	protein-coding
mm_162824.1	chr10	81160718	81160720	+	1	NA	intron (NM_021501, intron 2 of 10)	intron (NM_021501, intron 2 of 10)	7001	NM_021501	59004	Mm.34428	NM_021501	ENSMUSG00000004934	Pias4	PIASY|Pias-gamma|Piasg	protein inhibitor of activated STAT 4	protein-coding
mm_58128.1	chr6	140513699	140513702	-	1	NA	intron (NM_144920, intron 3 of 30)	intron (NM_144920, intron 3 of 30)	89601	NM_144920	109135	Mm.247670	NM_144920	ENSMUSG00000030231	Plekha5	2810431N21Rik|AI428202|AK129423|AMH-Cre|Ayu21-9|Gt(pU21)9Imeg|Pepp2|Tg(AMH-cre)1Flor	pleckstrin homology domain containing, family A member 5	protein-coding
mm_110408.1	chr12	45075110	45075153	-	1	NA	promoter-TSS (NM_144552)	promoter-TSS (NM_144552)	-648	NM_144552	217517	Mm.285400	NM_144552	ENSMUSG00000046314	Stxbp6	BC024598|C85317	syntaxin binding protein 6 (amisyn)	protein-coding
mm_58311.1	chr6	146257643	146257647	-	1	NA	intron (NM_010586, intron 36 of 55)	intron (NM_010586, intron 36 of 55)	244578	NM_010586	16439	Mm.7800	NM_010586	ENSMUSG00000030287	Itpr2	AI649341|InsP3R-2|InsP3R-5|Ip3r2|Itpr5|insP3R2	inositol 1,4,5-triphosphate receptor 2	protein-coding
mm_39685.1	chr5	25848356	25848364	+	1	NA	intron (NM_001310504, intron 8 of 10)	intron (NM_001310504, intron 8 of 10)	88387	NM_001004365	242894	Mm.150319	NM_001004365	ENSMUSG00000056367	Actr3b	9630005C02|ARP11|AW047569|Arp3b|Arp3beta	ARP3 actin-related protein 3B	protein-coding
mm_151618.1	chr19	3904710	3904723	-	1	NA	intron (NM_001136091, intron 1 of 19)	intron (NM_001136091, intron 1 of 19)	514	NM_016921	27060	Mm.271689	NM_016921	ENSMUSG00000001750	Tcirg1	ATP6N1C|ATP6a3|Atp6i|OC-116|OPTB1|Stv1|TIRC7|Vph1|oc	T cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 protein A3	protein-coding
mm_9299.1	chr1	171638748	171638761	-	1	NA	exon (NM_144539, exon 5 of 8)	exon (NM_144539, exon 5 of 8)	3146	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_77364.1	chr8	119810034	119810079	-	1	NA	3' UTR (NM_028071, exon 4 of 4)	3' UTR (NM_028071, exon 4 of 4)	30523	NM_028071	72042	Mm.393405	NM_028071	ENSMUSG00000031827	Cotl1	1810074P22Rik|2010004C08Rik|Clp	coactosin-like 1 (Dictyostelium)	protein-coding
mm_43278.1	chr5	130845096	130845107	+	1	NA	Intergenic	Intergenic	396309	NM_021371	140904	Mm.40875	NM_021371	ENSMUSG00000060371	Caln1	9630012C17Rik|Cabp8|MNCb-0849	calneuron 1	protein-coding
mm_134311.1	chr16	15863355	15863359	-	1	NA	promoter-TSS (NM_029354)	promoter-TSS (NM_029354)	-35	NM_029354	72083	Mm.22351	NM_029354	ENSMUSG00000022671	Mzt2	2410018G20Rik|2610001E06Rik|Fam128|Fam128b	mitotic spindle organizing protein 2	protein-coding
mm_129302.1	chr15	77307068	77307103	-	1	NA	promoter-TSS (NM_175387)	promoter-TSS (NM_175387)	-32	NM_053104	93686	Mm.202774	NM_053104	ENSMUSG00000033565	Rbfox2	Fbm2|Fxh|Hrnbp2|Rbm9	RNA binding protein, fox-1 homolog (C. elegans) 2	protein-coding
mm_141332.1	chr17	28507399	28507449	-	1	NA	Intergenic	Intergenic	-21275	NM_010220	14229	Mm.276405	NM_010220	ENSMUSG00000024222	Fkbp5	D17Ertd592e|Dit1|FKBP-5|FKBP51	FK506 binding protein 5	protein-coding
mm_107126.1	chr12	20196657	20196675	+	1	NA	Intergenic	CpG	619113	NR_015521	69513	Mm.273972	NR_015521	ENSMUSG00000099759	1700030C10Rik	-	RIKEN cDNA 1700030C10 gene	ncRNA
mm_119999.1	chr14	55618024	55618037	+	1	NA	promoter-TSS (NM_020002)	promoter-TSS (NM_020002)	-136	NM_020002	56739	Mm.23149	NM_020002	ENSMUSG00000002324	Rec8	Rec8L1|mrec	REC8 meiotic recombination protein	protein-coding
mm_37806.1	chr4	130818713	130818752	-	1	NA	exon (NM_011520, exon 3 of 5)	exon (NM_011520, exon 3 of 5)	26195	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_41349.1	chr5	90503564	90503640	+	1	NA	exon (NM_007423, exon 9 of 15)	exon (NM_007423, exon 9 of 15)	12888	NM_007423	11576	Mm.358570	NM_007423	ENSMUSG00000054932	Afp	-	alpha fetoprotein	protein-coding
mm_2058.1	chr1	87470294	87470304	+	1	NA	promoter-TSS (NM_028473)	promoter-TSS (NM_028473)	35	NM_028473	73234	Mm.7310	NM_028473	ENSMUSG00000026258	3110079O15Rik	Snorc	RIKEN cDNA 3110079O15 gene	protein-coding
mm_72484.1	chr8	83657557	83657564	+	1	NA	intron (NM_018771, intron 1 of 6)	intron (NM_018771, intron 1 of 6)	4882	NM_018771	67903	Mm.20945	NM_018771	ENSMUSG00000019433	Gipc1	GIPC|Glut1CIP|Rgs19ip1|Semcap1|TIP-2|TaxIP2	GIPC PDZ domain containing family, member 1	protein-coding
mm_41036.1	chr5	86081172	86081212	+	1	NA	exon (NM_019992, exon 3 of 9)	exon (NM_019992, exon 3 of 9)	9446	NM_001310639	56792	Mm.131237	NM_019992	ENSMUSG00000029254	Stap1	AI586015|Brdg1|STAP-1	signal transducing adaptor family member 1	protein-coding
mm_151643.1	chr19	4037945	4037959	-	1	NA	promoter-TSS (NM_013541)	promoter-TSS (NM_013541)	-40	NM_013541	14870	Mm.299292	NM_013541	ENSMUSG00000060803	Gstp1	GstpiB	glutathione S-transferase, pi 1	protein-coding
mm_124399.1	chr14	114945923	114945938	-	1	NA	promoter-TSS (NR_126551)	promoter-TSS (NR_126551)	18	NR_126551	74982		NR_126548		1700100I10Rik	1700085D13Rik|4930481K08Rik	RIKEN cDNA 1700100I10 gene	ncRNA
mm_124941.1	chr15	12321473	12321491	+	1	NA	promoter-TSS (NM_025673)	promoter-TSS (NM_025673)	-14	NM_025673	66629	Mm.157655	NM_025673	ENSMUSG00000022200	Golph3	4733401N08Rik|5730410D03Rik|AW413496	golgi phosphoprotein 3	protein-coding
mm_158820.1	chrX	167351777	167351783	-	1	NA	intron (NM_026662, intron 5 of 6)	L1Md_F3|LINE|L1	-21209	NM_001290756	170743	Mm.23979	NM_133211	ENSMUSG00000044583	Tlr7	-	toll-like receptor 7	protein-coding
mm_131880.1	chr16	23224818	23224828	+	1	NA	promoter-TSS (NM_145933)	promoter-TSS (NM_145933)	83	NM_145933	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_158773.1	chrX	167007991	167008018	-	1	NA	Intergenic	Intergenic	62366	NM_001101606	667794	Mm.302232	NM_001101606		Gm8817	EG667794	predicted gene 8817	protein-coding
mm_151259.1	chr19	53950036	53950052	+	1	NA	intron (NM_019658, intron 1 of 8)	U2|snRNA|snRNA	5168	NM_019658	56392	Mm.228669	NM_019658	ENSMUSG00000024976	Shoc2	AU017287|Sur8|mKIAA0862	soc-2 (suppressor of clear) homolog (C. elegans)	protein-coding
mm_126776.1	chr15	86182121	86182139	+	1	NA	intron (NM_145475, intron 1 of 12)	intron (NM_145475, intron 1 of 12)	4011	NM_145475	223753	Mm.222685	NM_145475	ENSMUSG00000035891	Cerk	AI848610|D330016D08Rik|mKIAA1646	ceramide kinase	protein-coding
mm_110281.1	chr12	32061222	32061301	-	1	NA	promoter-TSS (NM_011158)	promoter-TSS (NM_011158)	18	NM_011158	19088	Mm.25594	NM_011158	ENSMUSG00000002997	Prkar2b	AI451071|AW061005|PKARIIbeta|Pkarb2|RII(beta)	protein kinase, cAMP dependent regulatory, type II beta	protein-coding
mm_30213.1	chr3	144975041	144975046	-	1	NA	promoter-TSS (NM_207208)	promoter-TSS (NM_207208)	2	NM_207208	99663	Mm.442050	NM_207208	ENSMUSG00000068547	Clca4a	9130020L07Rik|AI504701|Clca4|Clca6	chloride channel accessory 4A	protein-coding
mm_144654.1	chr18	34246124	34246128	+	1	NA	intron (NM_007462, intron 1 of 15)	intron (NM_007462, intron 1 of 15)	-24354	NR_040534	633395	Mm.414290	NR_040534	ENSMUSG00000073607	Gm10548	ENSMUSG00000073607	ribosomal protein L29 pseudogene	pseudo
mm_65247.1	chr7	19844549	19844552	-	1	NA	Intergenic	Intergenic	-7453	NM_001270489	100502736	Mm.445354	NM_001270489	ENSMUSG00000092216	Gm19345	-	predicted gene, 19345	protein-coding
mm_86761.1	chr10	19933558	19933566	+	1	NA	promoter-TSS (NM_008580)	promoter-TSS (NM_008580)	-964	NM_008580	26408	Mm.6595	NM_008580	ENSMUSG00000071369	Map3k5	7420452D20Rik|ASK|ASK1|MAPKKK5|Mekk5	mitogen-activated protein kinase kinase kinase 5	protein-coding
mm_43234.1	chr5	129942043	129942088	+	1	NA	promoter-TSS (NM_001286382)	promoter-TSS (NM_001286382)	-44	NM_001001327	69568	Mm.288718	NM_027121	ENSMUSG00000066735	Vkorc1l1	2310024K08Rik	vitamin K epoxide reductase complex, subunit 1-like 1	protein-coding
mm_9869.1	chr1	184999879	184999974	-	1	NA	promoter-TSS (NM_145515)	promoter-TSS (NM_145515)	-377	NM_145515	226778	Mm.7445	NM_145515	ENSMUSG00000026620	Mark1	AW491150|B930025N23Rik|Emk3|Par-1c|mKIAA1477|mPar-1c	MAP/microtubule affinity regulating kinase 1	protein-coding
mm_8246.1	chr1	138606581	138606609	-	1	NA	intron (NM_001311148, intron 1 of 7)	intron (NM_001311148, intron 1 of 7)	13162	NM_021605	59125	Mm.143817	NM_021605	ENSMUSG00000026393	Nek7	2810460C19Rik|AU020186	NIMA (never in mitosis gene a)-related expressed kinase 7	protein-coding
mm_3013.1	chr1	133363625	133363633	+	1	NA	promoter-TSS (NM_175443)	promoter-TSS (NM_175443)	57	NM_175443	214253	Mm.52111	NM_175443	ENSMUSG00000070644	Etnk2	4933417N20Rik|AI197444|EKI 2|Eki2|Tuc1	ethanolamine kinase 2	protein-coding
mm_126872.1	chr15	89376343	89376364	+	1	NA	exon (NM_138302, exon 3 of 11)	exon (NM_138302, exon 3 of 11)	684	NM_138302	72962	Mm.287977	NM_138302	ENSMUSG00000022615	Tymp	2900072D10Rik|Ecgf1|PD-ECGF|PDECGF|Pdgfec	thymidine phosphorylase	protein-coding
mm_142862.1	chr17	51813873	51813883	-	1	NA	intron (NM_001163632, intron 1 of 10)	intron (NM_001163632, intron 1 of 10)	-1824	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_44581.1	chr5	24889915	24889927	-	1	NA	intron (NM_001310480, intron 3 of 13)	intron (NM_001310480, intron 3 of 13)	-12648	NR_040684	71161	Mm.443533	NR_040684	ENSMUSG00000086446	Prkag2os1	4933426D04Rik	protein kinase, AMP-activated, gamma 2 non-catalytic subunit, opposite strand 1	ncRNA
mm_34481.1	chr4	148448606	148448637	+	1	NA	promoter-TSS (NM_020009)	promoter-TSS (NM_020009)	39	NM_020009	56717	Mm.21158	NM_020009	ENSMUSG00000028991	Mtor	2610315D21Rik|AI327068|FRAP|FRAP2|Frap1|RAFT1|RAPT1|flat	mechanistic target of rapamycin (serine/threonine kinase)	protein-coding
mm_151892.1	chr19	5798776	5798831	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	-2822	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_138149.1	chr17	34208387	34208394	+	1	NA	intron (NM_011530, intron 3 of 11)	B1_Mus2|SINE|Alu	3911	NM_011530	21355	Mm.14814	NM_011530	ENSMUSG00000024339	Tap2	ABC18|AI462429|APT2|Abcb3|Ham-2|Ham2|MTP2|PSF2|RING11|Tap-2|Y1|jas	transporter 2, ATP-binding cassette, sub-family B (MDR/TAP)	protein-coding
mm_86383.1	chr9	123862024	123862035	-	1	NA	promoter-TSS (NM_011798)	promoter-TSS (NM_011798)	0	NM_011798	23832	Mm.390241	NM_011798	ENSMUSG00000060509	Xcr1	Ccxcr1|Gpr5|mXcr1	chemokine (C motif) receptor 1	protein-coding
mm_43743.1	chr5	140208832	140208850	+	1	NA	intron (NM_010752, intron 10 of 17)	intron (NM_010752, intron 10 of 17)	112711	NM_010752	17120	Mm.27250	NM_010752	ENSMUSG00000029554	Mad1l1	AI173502|AW550425|Mad1	MAD1 mitotic arrest deficient 1-like 1	protein-coding
mm_14500.1	chr2	132029981	132029986	+	1	NA	promoter-TSS (NM_175445)	promoter-TSS (NM_175445)	5	NM_175445	215653	Mm.204737	NM_175445	ENSMUSG00000027339	Rassf2	3830431H01Rik|9030412M04Rik|AI852669|AW495050	Ras association (RalGDS/AF-6) domain family member 2	protein-coding
mm_149769.1	chr19	23061471	23061481	+	1	NA	Intergenic	Intergenic	-79750	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_115801.1	chr13	19357301	19357311	-	1	NA	TTS (NM_024270)	TTS (NM_024270)	38507	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_42771.1	chr5	121283678	121283694	+	1	NA	intron (NM_181421, intron 11 of 75)	(CCA)n|Simple_repeat|Simple_repeat	63467	NM_181421	269700	Mm.184589	NM_181421	ENSMUSG00000042744	Gm15800	A130010L24|AU042671|BC019639|EG545802|OTTMUSG00000026283|mKIAA0614	predicted gene 15800	protein-coding
mm_88680.1	chr10	80053624	80053665	+	1	NA	promoter-TSS (NM_001037741)	promoter-TSS (NM_001037741)	156	NM_008162	625249	Mm.332810	NM_008162	ENSMUSG00000075706	Gpx4	GPx-4|GSHPx-4|PHGPx|mtPHGPx|snGPx	glutathione peroxidase 4	protein-coding
mm_129349.1	chr15	77915437	77915454	-	1	NA	3' UTR (NM_019913, exon 4 of 4)	3' UTR (NM_019913, exon 4 of 4)	13549	NM_019913	56551	Mm.291917	NM_019913	ENSMUSG00000005354	Txn2	2510006J11Rik|AI788873|Trx2	thioredoxin 2	protein-coding
mm_76537.1	chr8	87960586	87960619	-	1	NA	Intergenic	CpG-14330	-1007	NM_033327	94187	Mm.23452	NM_033327	ENSMUSG00000045333	Zfp423	Ebfaz|Roaz|Zfp104|Znf423|ataxia1|mKIAA0760|nur12	zinc finger protein 423	protein-coding
mm_167076.1	chr7	100681303	100681310	+	1	NA	Intergenic	Intergenic	-18912	NM_001163182	27276	Mm.491216	NM_013746	ENSMUSG00000030701	Plekhb1	AI315628|PHR1|Phret1|evt-1	pleckstrin homology domain containing, family B (evectins) member 1	protein-coding
mm_61729.1	chr7	81859408	81859433	+	1	NA	non-coding (NR_111910, exon 1 of 8)	non-coding (NR_111910, exon 1 of 8)	419	NM_145375	107769	Mm.221412	NM_145375	ENSMUSG00000038623	Tm6sf1	AI428514|BC023123|C630016D09Rik	transmembrane 6 superfamily member 1	protein-coding
mm_80669.1	chr9	90163103	90163120	+	1	NA	5' UTR (NM_001326351, exon 1 of 24)	5' UTR (NM_001326351, exon 1 of 24)	133	NM_001311115	108153	Mm.102141	NM_001003911	ENSMUSG00000032363	Adamts7	ADAM-TS7|ADAMTS7B	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 7	protein-coding
mm_83588.1	chr9	48420568	48420578	-	1	NA	Intergenic	Intergenic	-33771	NR_026561	667933	Mm.491076	NR_026561		Gm8884	EG667933	predicted gene 8884	ncRNA
mm_45444.1	chr5	67427675	67427691	-	1	NA	5' UTR (NM_001164806, exon 1 of 5)	5' UTR (NM_001164806, exon 1 of 5)	116	NM_001164806	666938	Mm.101339	NM_001164806	ENSMUSG00000092060	Bend4	D330027G24Rik|EG666938	BEN domain containing 4	protein-coding
mm_14578.1	chr2	135659594	135659604	+	1	NA	Intergenic	CpG	-76379	NR_015544	320684	Mm.421433	NR_015544	ENSMUSG00000085631	9630028H03Rik	-	RIKEN cDNA 9630028H03 gene	ncRNA
mm_12304.1	chr2	69109939	69109955	+	1	NA	3' UTR (NM_001347161, exon 11 of 11)	3' UTR (NM_001347161, exon 11 of 11)	-25853	NM_181547	329416	Mm.90047	NM_181547	ENSMUSG00000034738	Nostrin	Daip2|mDaIP2	nitric oxide synthase trafficker	protein-coding
mm_121882.1	chr14	21500377	21500398	-	1	NA	intron (NM_017479, intron 1 of 16)	CpG	602	NM_017479	54169	Mm.248967	NM_017479	ENSMUSG00000021767	Kat6b	AI507552|B130044K16Rik|MYST-4|Morf|Myst4|mKIAA0383|qkf|querkopf	K(lysine) acetyltransferase 6B	protein-coding
mm_83635.1	chr9	49486192	49486202	-	1	NA	promoter-TSS (NM_172770)	promoter-TSS (NM_172770)	28	NM_172770	235330	Mm.177413	NM_172770	ENSMUSG00000040219	Ttc12	E330017O07Rik	tetratricopeptide repeat domain 12	protein-coding
mm_15898.1	chr2	164951211	164951221	+	1	NA	exon (NM_013599, exon 8 of 13)	exon (NM_013599, exon 8 of 13)	2997	NM_013599	17395	Mm.4406	NM_013599	ENSMUSG00000017737	Mmp9	AW743869|B/MMP9|Clg4b|Gel B|MMP-9|pro-MMP-9	matrix metallopeptidase 9	protein-coding
mm_154262.1	chr19	60769961	60770000	-	1	NA	exon (NM_010123, exon 16 of 22)	exon (NM_010123, exon 16 of 22)	4405	NR_034047	100217439		NR_034047		Snora19	MBI-51	small nucleolar RNA, H/ACA box 19	snoRNA
mm_153188.1	chr19	34507118	34507155	-	1	NA	exon (NM_021460, exon 6 of 10)	exon (NM_021460, exon 6 of 10)	20338	NM_001111100	16889	Mm.157545	NM_021460	ENSMUSG00000024781	Lipa	AA960673|Lal|Lip-1|Lip1	lysosomal acid lipase A	protein-coding
mm_161619.1	chr16	57071102	57071102	-	1	NA	5' UTR (NM_183281, exon 2 of 7)	5' UTR (NM_183281, exon 2 of 7)	244	NM_183281	69457	Mm.58105	NM_183281	ENSMUSG00000046748	Tmem45a2	2310005G13Rik	transmembrane protein 45A2	protein-coding
mm_5907.1	chr1	55000119	55000144	-	1	NA	exon (NM_031179, exon 16 of 25)	exon (NM_031179, exon 16 of 25)	27347	NM_031179	81898	Mm.279736	NM_031179	ENSMUSG00000025982	Sf3b1	155kDa|2810001M05Rik|AA409119|Prp10|SAP155|SF3b155|TA-8|Targ4	splicing factor 3b, subunit 1	protein-coding
mm_42051.1	chr5	108629991	108630018	+	1	NA	promoter-TSS (NM_153569)	promoter-TSS (NM_153569)	194	NM_028223	72392	Mm.258324	NM_028223	ENSMUSG00000013495	Tmem175	3010001K23Rik|AI504381|mTMEM175	transmembrane protein 175	protein-coding
mm_19327.1	chr2	90573552	90573569	-	1	NA	intron (NM_008982, intron 1 of 23)	ID2|SINE|ID	7087	NM_008982	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_108138.1	chr12	76215372	76215382	+	1	NA	intron (NM_001159532, intron 5 of 8)	RMER10B|LTR|ERVL	31369	NM_019784	80384	Mm.78551	NM_019784	ENSMUSG00000021056	Tex21	4931406F04Rik|4931412D23Rik|4931421K24Rik|tsec-2	testis expressed gene 21	protein-coding
mm_13256.1	chr2	98665003	98665012	+	1	NA	Intergenic	SYNREP_MM|Satellite|Satellite	1197350	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_168391.1	chr11	27233914	27233914	+	1	NA	Intergenic	Intergenic	448806	NR_002890	654472	Mm.347777	NR_002890		Gm12070	OTTMUSG00000005300	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_93402.1	chr10	107876536	107876536	-	1	NA	intron (NM_001177567, intron 16 of 57)	intron (NM_001177567, intron 16 of 57)	35598	NM_001177567	628870	Mm.336090	NM_001177567	ENSMUSG00000091455	Otogl	EG628870|Gm6924	otogelin-like	protein-coding
mm_83875.1	chr9	55048749	55048792	-	1	NA	promoter-TSS (NM_148944)	promoter-TSS (NM_148944)	-226	NM_148944	108015	Mm.32694	NM_148944	ENSMUSG00000035200	Chrnb4	Acrb-4|Acrb4	cholinergic receptor, nicotinic, beta polypeptide 4	protein-coding
mm_36830.1	chr4	106316140	106316201	-	1	NA	promoter-TSS (NM_183225)	promoter-TSS (NM_183225)	-43	NM_183225	329908	Mm.234544	NM_183225	ENSMUSG00000028514	Usp24	2700066K03Rik|2810030C21Rik|AI414051|B130021E18|C79851	ubiquitin specific peptidase 24	protein-coding
mm_138907.1	chr17	43588650	43588669	+	1	NA	exon (NM_013737, exon 2 of 12)	exon (NM_013737, exon 2 of 12)	2850	NR_045445	73504	Mm.9277	NR_045444	ENSMUSG00000090307	1700071M16Rik	-	RIKEN cDNA 1700071M16 gene	ncRNA
mm_33394.1	chr4	129820286	129820292	+	1	NA	promoter-TSS (NM_001164745)	promoter-TSS (NM_001164745)	-190	NM_008974	19244	Mm.193688	NM_008974	ENSMUSG00000028788	Ptp4a2	Prl-2	protein tyrosine phosphatase 4a2	protein-coding
mm_36002.1	chr4	56741424	56741435	-	1	NA	promoter-TSS (NM_025271)	promoter-TSS (NM_025271)	-4	NM_025271	11471	Mm.251434	NM_025271	ENSMUSG00000070980	Actl7b	Tact1	actin-like 7b	protein-coding
mm_145304.1	chr18	53463411	53463423	+	1	NA	Intergenic	Intergenic	-1129	NM_001033281	225518	Mm.297645	NM_001033281	ENSMUSG00000069378	Prdm6	Gm92|PRISM	PR domain containing 6	protein-coding
mm_32309.1	chr4	103214844	103214865	+	1	NA	promoter-TSS (NM_177732)	promoter-TSS (NM_177732)	30	NM_177732	242585	Mm.281800	NM_177732	ENSMUSG00000028521	Slc35d1	AI834976|C330011J09|UGTREL7|mKIAA0260	solute carrier family 35 (UDP-glucuronic acid/UDP-N-acetylgalactosamine dual transporter), member D1	protein-coding
mm_145375.1	chr18	56734090	56734097	+	1	NA	intron (NM_010721, intron 5 of 10)	(CCTG)n|Simple_repeat|Simple_repeat	26280	NM_010721	16906	Mm.4105	NM_010721	ENSMUSG00000024590	Lmnb1	-	lamin B1	protein-coding
mm_35720.1	chr4	44640516	44640527	-	1	NA	intron (NM_008782, intron 6 of 9)	intron (NM_008782, intron 6 of 9)	-62279	NR_073462	70602	Mm.491142	NR_073462	ENSMUSG00000103995	5730488B01Rik	-	RIKEN cDNA 5730488B01 gene	ncRNA
mm_167514.1	chr9	14275947	14275959	-	1	NA	promoter-TSS (NM_030261)	promoter-TSS (NM_030261)	-348	NM_030261	75747	Mm.325126	NM_030261	ENSMUSG00000032009	Sesn3	5630400E15Rik|BC003348|SEST3	sestrin 3	protein-coding
mm_165058.1	chr19	41981114	41981118	-	1	NA	promoter-TSS (NM_028152)	promoter-TSS (NM_028152)	20	NM_028152	72199	Mm.218940	NM_028152	ENSMUSG00000025159	Mms19	2410001K24Rik|2610042O15Rik|AI316855|C79368|C86341|Mms19l	MMS19 (MET18 S. cerevisiae)	protein-coding
mm_141894.1	chr17	34862247	34862352	-	1	NA	TTS (NM_013484)	TTS (NM_013484)	215	NM_001142706	14962	Mm.653	NM_008198	ENSMUSG00000090231	Cfb	AI195813|AI255840|B|Bf|C2|Fb|H2-Bf	complement factor B	protein-coding
mm_22355.1	chr2	180954677	180954708	-	1	NA	promoter-TSS (NM_001141933)	promoter-TSS (NM_001141933)	7	NM_001141933	58237	Mm.40361	NM_021426	ENSMUSG00000027574	Nkain4	AB030182|C030019F02Rik	Na+/K+ transporting ATPase interacting 4	protein-coding
mm_140264.1	chr17	84683024	84683024	+	1	NA	promoter-TSS (NM_031884)	promoter-TSS (NM_031884)	-13	NM_031884	27409	Mm.289590	NM_031884	ENSMUSG00000040505	Abcg5	cmp|sterolin-1|trac	ATP-binding cassette, sub-family G (WHITE), member 5	protein-coding
mm_117853.1	chr13	98754332	98754361	-	1	NA	intron (NM_172591, intron 13 of 25)	B3|SINE|B2	-59515	NM_001025606	380863	Mm.28264	NM_001025606	ENSMUSG00000052485	Tmem171	Gm905	transmembrane protein 171	protein-coding
mm_125486.1	chr15	54601616	54601653	+	1	NA	3' UTR (NM_178920, exon 4 of 4)	3' UTR (NM_178920, exon 4 of 4)	30268	NM_178920	105853	Mm.410994	NM_178920	ENSMUSG00000024479	Mal2	AI461653	mal, T cell differentiation protein 2	protein-coding
mm_31325.1	chr4	46450872	46450887	+	1	NA	promoter-TSS (NM_130889)	promoter-TSS (NM_130889)	-47	NM_130889	67628	Mm.263913	NM_130889	ENSMUSG00000028333	Anp32b	2410015B15Rik|PAL31|PHAPI2a|Ssp29	acidic (leucine-rich) nuclear phosphoprotein 32 family, member B	protein-coding
mm_11392.1	chr2	31454452	31454468	+	1	NA	Intergenic	Intergenic	-15810	NM_007494	11898	Mm.3217	NM_007494	ENSMUSG00000076441	Ass1	AA408052|ASS|Ass-1|fold	argininosuccinate synthetase 1	protein-coding
mm_50071.1	chr6	41271422	41271424	+	1	NA	Intergenic	Intergenic	-30849	NM_011646	22074	Mm.383263	NM_011646	ENSMUSG00000054106	Try4	0910001B19Rik|Td	trypsin 4	protein-coding
mm_135766.1	chr16	56717542	56717576	-	1	NA	promoter-TSS (NM_001252443)	promoter-TSS (NM_001252443)	-109	NM_019678	21787	Mm.425970	NM_019678	ENSMUSG00000022757	Tfg	AI173908	Trk-fused gene	protein-coding
mm_80440.1	chr9	77941275	77941303	+	1	NA	intron (NM_134255, intron 1 of 7)	intron (NM_134255, intron 1 of 7)	23924	NM_134255	68801	Mm.430736	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	ELOVL family member 5, elongation of long chain fatty acids (yeast)	protein-coding
mm_148858.1	chr19	6399836	6399855	+	1	NA	promoter-TSS (NM_011242)	promoter-TSS (NM_011242)	-738	NM_011242	19395	Mm.77017	NM_011242	ENSMUSG00000032946	Rasgrp2	CDC25L|Caldaggef1	RAS, guanyl releasing protein 2	protein-coding
mm_62925.1	chr7	118600179	118600183	+	1	NA	intron (NM_001105252, intron 1 of 21)	intron (NM_001105252, intron 1 of 21)	2884	NM_001105252	74424	Mm.11068	NM_028930	ENSMUSG00000030650	Tmc5	4932443L08Rik|AU016085	transmembrane channel-like gene family 5	protein-coding
mm_122948.1	chr14	54966571	54966585	-	1	NA	promoter-TSS (NM_010856)	promoter-TSS (NM_010856)	29	NM_001164171	17888	Mm.290003	NM_010856	ENSMUSG00000040752	Myh6	A830009F23Rik|AA517445|Myhc-a|Myhca|alpha-MHC	myosin, heavy polypeptide 6, cardiac muscle, alpha	protein-coding
mm_155521.1	chrX	74255175	74255185	+	1	NA	intron (NM_007927, intron 1 of 5)	CpG	493	NM_007927	13726	Mm.18892	NM_007927	ENSMUSG00000001964	Emd	AW550900|Sta	emerin	protein-coding
mm_111157.1	chr12	83455940	83455942	-	1	NA	intron (NM_058212, intron 1 of 8)	ID_B1|SINE|B4	31795	NM_001267626	70127	Mm.151308	NM_058212	ENSMUSG00000021221	Dpf3	2810403B03Rik|6530402L11Rik|BAF45C|C78788|CERD4|cer-d4	D4, zinc and double PHD fingers, family 3	protein-coding
mm_49838.1	chr6	38109321	38109402	+	1	NA	promoter-TSS (NM_029921)	promoter-TSS (NM_029921)	8	NM_029921	77522	Mm.387207	NM_029921	ENSMUSG00000029829	Tmem213	D630002J15Rik	transmembrane protein 213	protein-coding
mm_24296.1	chr3	89302888	89302898	+	1	NA	Intergenic	Intergenic	19986	NM_010108	13638	Mm.331159	NM_010108	ENSMUSG00000028039	Efna3	AW494418|EFL-2|Ehk1-L|Epl3|LERK-3	ephrin A3	protein-coding
mm_150392.1	chr19	36409720	36409757	+	1	NA	intron (NM_029508, intron 1 of 8)	CpG	30671	NM_029508	76073	Mm.259180	NM_029508	ENSMUSG00000024805	Pcgf5	0610009F02Rik|1110054A01Rik|5830406C17Rik|5830443C21Rik|9530023M17Rik|AI324127	polycomb group ring finger 5	protein-coding
mm_106751.1	chr12	4082642	4082652	+	1	NA	promoter-TSS (NM_153082)	promoter-TSS (NM_153082)	73	NM_153082	217378	Mm.271656	NM_153082	ENSMUSG00000020657	Dnajc27	AI639580|C330021A05Rik|Rabj|Rbj	DnaJ heat shock protein family (Hsp40) member C27	protein-coding
mm_149613.1	chr19	16385925	16385944	+	1	NA	3' UTR (NM_008139, exon 7 of 7)	3' UTR (NM_008139, exon 7 of 7)	-49733	NM_008137	14675	Mm.313181	NM_008137	ENSMUSG00000024697	Gna14	AU023208	guanine nucleotide binding protein, alpha 14	protein-coding
mm_7926.1	chr1	133899189	133899214	-	1	NA	intron (NM_054076, intron 5 of 6)	MIRb|SINE|MIR	7972	NM_054076	269120	Mm.59985	NM_054076	ENSMUSG00000010311	Optc	-	opticin	protein-coding
mm_109469.1	chr12	111417602	111417679	+	1	NA	5' UTR (NM_028807, exon 1 of 13)	5' UTR (NM_028807, exon 1 of 13)	195	NM_001289488	74190	Mm.248640	NM_028807	ENSMUSG00000021280	Exoc3l4	1200009I06Rik|1600013K19Rik	exocyst complex component 3-like 4	protein-coding
mm_105177.1	chr11	101785167	101785182	-	1	NA	5' UTR (NM_001316366, exon 1 of 13)	5' UTR (NM_001316366, exon 1 of 13)	136	NM_008815	18612	Mm.5025	NM_008815	ENSMUSG00000017724	Etv4	AW414408|Pea-3|Pea3	ets variant 4	protein-coding
mm_131037.1	chr16	3872412	3872420	+	1	NA	promoter-TSS (NM_001033159)	promoter-TSS (NM_001033159)	-42	NM_001033159	71063	Mm.379190	NM_001033159	ENSMUSG00000039789	Zfp597	4933407K12Rik|AI462383|AI666357	zinc finger protein 597	protein-coding
mm_75985.1	chr8	72322525	72322534	-	1	NA	TTS (NM_008452)	TTS (NM_008452)	3467	NM_008452	16598	Mm.26938	NM_008452	ENSMUSG00000055148	Klf2	Lklf	Kruppel-like factor 2 (lung)	protein-coding
mm_115539.1	chr13	6640790	6640809	-	1	NA	intron (NM_019703, intron 1 of 21)	intron (NM_019703, intron 1 of 21)	7972	NM_019703	56421	Mm.273874	NM_019703	ENSMUSG00000021196	Pfkp	1200015H23Rik|9330125N24Rik|ATP-PFK|PFK-C|PFK-P	phosphofructokinase, platelet	protein-coding
mm_146938.1	chr18	32138163	32138169	-	1	NA	promoter-TSS (NM_001042768)	promoter-TSS (NM_001042768)	39	NM_008934	19123	Mm.2786	NM_008934	ENSMUSG00000024386	Proc	PC	protein C	protein-coding
mm_133962.1	chr16	4091905	4091931	-	1	NA	exon (NM_001025432, exon 28 of 31)	exon (NM_001025432, exon 28 of 31)	-14108	NM_026508	68015	Mm.123366	NM_026508	ENSMUSG00000005981	Trap1	2410002K23Rik|HSP75	TNF receptor-associated protein 1	protein-coding
mm_85988.1	chr9	112187822	112187862	-	1	NA	promoter-TSS (NM_001177620)	promoter-TSS (NM_001177620)	-76	NM_033264	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_33309.1	chr4	129058134	129058152	+	1	NA	promoter-TSS (NM_029219)	promoter-TSS (NM_029219)	-128	NM_029219	75234	Mm.259672	NM_029219	ENSMUSG00000028793	Rnf19b	4930534K13Rik|4930555L03Rik|Ibrdc3	ring finger protein 19B	protein-coding
mm_6127.1	chr1	64528322	64528326	-	1	NA	Intergenic	Intergenic	-4480	NM_133828	12912	Mm.422634	NM_009952	ENSMUSG00000025958	Creb1	2310001E10Rik|3526402H21Rik|AV083133|Creb|Creb-1	cAMP responsive element binding protein 1	protein-coding
mm_162583.1	chr1	178871443	178871443	+	1	NA	intron (NM_001161665, intron 8 of 14)	intron (NM_001161665, intron 8 of 14)	342318	NM_001161665	269152	Mm.129727	NM_177724	ENSMUSG00000026494	Kif26b	4832420M10|BC056349|D230039L06Rik	kinesin family member 26B	protein-coding
mm_69041.1	chr7	126800329	126800337	-	1	NA	5' UTR (NM_001177308, exon 1 of 9)	5' UTR (NM_001177308, exon 1 of 9)	114	NM_001177308	11674	Mm.275831	NM_007438	ENSMUSG00000030695	Aldoa	Aldo-1|Aldo1	aldolase A, fructose-bisphosphate	protein-coding
mm_154854.1	chrX	20552324	20552341	+	1	NA	exon (NM_009060, exon 3 of 7)	exon (NM_009060, exon 3 of 7)	2514	NM_009060	19733	Mm.2118	NM_009060	ENSMUSG00000023070	Rgn	AI265316|GNL|SMP30	regucalcin	protein-coding
mm_65689.1	chr7	28372535	28372547	-	1	NA	5' UTR (NM_001083912, exon 1 of 19)	5' UTR (NM_001083912, exon 1 of 19)	121	NM_138752	101497	Mm.235700	NM_138752	ENSMUSG00000037552	Plekhg2	AI194308|Clg|Cslg	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	protein-coding
mm_51071.1	chr6	66711646	66711650	+	1	NA	Intergenic	RMER12C|LTR|ERVK	5241	NM_134166	171184	Mm.377165	NM_134166	ENSMUSG00000093764	Vmn1r36	V1rc11	vomeronasal 1 receptor 36	protein-coding
mm_139647.1	chr17	57386643	57386653	+	1	NA	intron (NM_010130, intron 2 of 21)	L1_Mur1|LINE|L1	27962	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_38880.1	chr4	149698641	149698654	-	1	NA	promoter-TSS (NM_001164049)	promoter-TSS (NM_001164049)	61	NM_001164050	18707	Mm.229108	NM_008840	ENSMUSG00000039936	Pik3cd	2410099E07Rik|2610208K16Rik|AW545373|p110delta	phosphatidylinositol 3-kinase catalytic delta polypeptide	protein-coding
mm_154189.1	chr19	58822452	58822469	-	1	NA	intron (NM_001327998, intron 5 of 12)	intron (NM_001327998, intron 5 of 12)	-28046	NM_026208	67507	Mm.27027	NM_026208	ENSMUSG00000026931	1700019N19Rik	-	RIKEN cDNA 1700019N19 gene	protein-coding
mm_109411.1	chr12	110463902	110463914	+	1	NA	intron (NM_001135001, intron 2 of 13)	intron (NM_001135001, intron 2 of 13)	16729	NM_001135001	26931	Mm.240396	NM_012023	ENSMUSG00000017843	Ppp2r5c	2610043M05Rik|2700063L20Rik|AI060890|AW545884|C85228|D12Bwg0916e|mKIAA0044	protein phosphatase 2, regulatory subunit B', gamma	protein-coding
mm_14420.1	chr2	130450380	130450384	+	1	NA	5' UTR (NM_008980, exon 1 of 22)	5' UTR (NM_008980, exon 1 of 22)	104	NM_001163688	19262	Mm.224246	NM_008980	ENSMUSG00000027303	Ptpra	Ptpa|Ptpalpha|Rptpalpha|Rptra|Rptralpha	protein tyrosine phosphatase, receptor type, A	protein-coding
mm_133854.1	chr16	96273182	96273194	+	1	NA	intron (NM_001122993, intron 2 of 3)	intron (NM_001122993, intron 2 of 3)	-7844	NM_033149	93961	Mm.154783	NM_033149	ENSMUSG00000074892	B3galt5	1190002B21Rik|AU045265|b3Galt-V	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 5	protein-coding
mm_31253.1	chr4	45011759	45011771	+	1	NA	5' UTR (NM_001163284, exon 1 of 2)	5' UTR (NM_001163284, exon 1 of 2)	647	NM_001163284	230119	Mm.44222	NM_173399	ENSMUSG00000049657	Zbtb5	5930421I10|9430083K24Rik|AI646847|mKIAA0354	zinc finger and BTB domain containing 5	protein-coding
mm_35651.1	chr4	43533295	43533305	-	1	NA	intron (NM_011602, intron 53 of 56)	intron (NM_011602, intron 53 of 56)	-9746	NM_001277875	22004	Mm.646	NM_009416	ENSMUSG00000028464	Tpm2	Tpm-2|Trop-2	tropomyosin 2, beta	protein-coding
mm_129788.1	chr15	82813924	82813927	-	1	NA	intron (NM_013836, intron 4 of 4)	intron (NM_013836, intron 4 of 4)	-19680	NM_029562	76279	Mm.439931	NM_029562	ENSMUSG00000022445	Cyp2d26	1300006E06Rik	cytochrome P450, family 2, subfamily d, polypeptide 26	protein-coding
mm_23728.1	chr3	69024282	69024285	+	1	NA	exon (NM_133786, exon 12 of 24)	exon (NM_133786, exon 12 of 24)	14381	NR_029735	723949		NR_029735	ENSMUSG00000065606	Mir16-2	Mirn16-2|mir-16-2	microRNA 16-2	ncRNA
mm_16669.1	chr2	6722171	6722181	-	1	NA	promoter-TSS (NM_001310447)	promoter-TSS (NM_001310447)	-514	NM_001310447	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_90041.1	chr10	115817442	115817454	+	1	NA	5' UTR (NM_146010, exon 1 of 8)	5' UTR (NM_146010, exon 1 of 8)	164	NM_001168679	216350	Mm.22270	NM_146010	ENSMUSG00000034127	Tspan8	C76990|E330007O21Rik|Tm4sf3	tetraspanin 8	protein-coding
mm_59935.1	chr7	30424239	30424247	+	1	NA	5' UTR (NM_172142, exon 3 of 11)	5' UTR (NM_172142, exon 3 of 11)	939	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_72836.1	chr8	88289029	88289076	+	1	NA	promoter-TSS (NM_001037723)	promoter-TSS (NM_001037723)	-14	NM_001037723	11513	Mm.288206	NM_007406	ENSMUSG00000031659	Adcy7	AA407758	adenylate cyclase 7	protein-coding
mm_38929.1	chr4	150189236	150189245	-	1	NA	exon (NM_009802, exon 7 of 8)	exon (NM_009802, exon 7 of 8)	11895	NM_009802	12353	Mm.232523	NM_009802	ENSMUSG00000028972	Car6	Ca6|DOC1	carbonic anhydrase 6	protein-coding
mm_129022.1	chr15	74955516	74955541	-	1	NA	5' UTR (NM_001164036, exon 1 of 4)	5' UTR (NM_001164036, exon 1 of 4)	422	NM_001164040	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_80286.1	chr9	73064143	73064157	+	1	NA	promoter-TSS (NM_001301232)	promoter-TSS (NM_001301232)	2	NM_001301232	11891	Mm.34867	NM_023635	ENSMUSG00000032202	Rab27a	2210402C08Rik|2410003M20Rik|4933437C11Rik|ash	RAB27A, member RAS oncogene family	protein-coding
mm_38568.1	chr4	141723459	141723466	-	1	NA	promoter-TSS (NM_001017966)	promoter-TSS (NM_001017966)	-43	NM_001017966	68817	Mm.393721	NM_001017966	ENSMUSG00000078515	Ddi2	1110056G13Rik|1700027M01Rik|9130022E05Rik|AI604911|AU040698	DNA-damage inducible protein 2	protein-coding
mm_149395.1	chr19	11387822	11387834	+	1	NA	intron (NM_001310331, intron 4 of 6)	RMER19B2|LTR|ERVK	12340	NM_001310331	666907		NM_001310331	ENSMUSG00000101389	Ms4a4a	EG666907	membrane-spanning 4-domains, subfamily A, member 4A	protein-coding
mm_154521.1	chrM	13282	13334	-	1	NA	NA	Intergenic	NA	NA								
mm_173259.1	chrX	94831362	94831363	+	1	NA	Intergenic	IAP1-MM_LTR|LTR|ERVK	-33073	NR_003292	668171	Mm.426134	NR_003292		Zxda	4933406P09Rik|AW413531	zinc finger, X-linked, duplicated A	pseudo
mm_3177.1	chr1	135750599	135750615	+	1	NA	exon (NM_007791, exon 5 of 6)	exon (NM_007791, exon 5 of 6)	-15478	NM_013750	27280	Mm.34346	NM_013750	ENSMUSG00000041801	Phlda3	Tih1	pleckstrin homology like domain, family A, member 3	protein-coding
mm_73921.1	chr8	119809215	119809227	+	1	NA	TTS (NM_028071)	TTS (NM_028071)	-30805	NM_028883	74347	Mm.358759	NM_028883	ENSMUSG00000034105	Tldc1	4632415K11Rik|Kiaa1609	TBC/LysM associated domain containing 1	protein-coding
mm_111404.1	chr12	91063376	91063389	-	1	NA	intron (NM_181815, intron 21 of 25)	intron (NM_181815, intron 21 of 25)	17534	NR_045858	71349	Mm.442093	NR_045858		5430427M07Rik	-	RIKEN cDNA 5430427M07 gene	ncRNA
mm_92825.1	chr10	81461974	81461994	-	1	NA	3' UTR (NM_176954, exon 12 of 12)	3' UTR (NM_176954, exon 12 of 12)	11147	NM_001311127	319586	Mm.152689	NM_176954	ENSMUSG00000034818	Celf5	4930565A21Rik|Brunol5	CUGBP, Elav-like family member 5	protein-coding
mm_116279.1	chr13	34963792	34963816	-	1	NA	promoter-TSS (NM_026947)	promoter-TSS (NM_026947)	5	NM_026947	69123	Mm.482475	NM_026947	ENSMUSG00000021416	Eci3	1810022C23Rik|Kseg2	enoyl-Coenzyme A delta isomerase 3	protein-coding
mm_47443.1	chr5	123345856	123345860	-	1	NA	intron (NM_029850, intron 1 of 5)	intron (NM_029850, intron 1 of 5)	1410	NM_029850	77045	Mm.151960	NM_029850	ENSMUSG00000029438	Bcl7a	4432415N06Rik|AI448316	B cell CLL/lymphoma 7A	protein-coding
mm_9166.1	chr1	170972860	170972867	-	1	NA	intron (NM_010187, intron 1 of 6)	MIR|SINE|MIR	3208	NM_001077189	14130	Mm.425062	NM_010187	ENSMUSG00000026656	Fcgr2b	AI528646|CD32|F630109E10Rik|Fc[g]RII|FcgRII|Fcgr2|Fcgr2a|Fcr-2|Fcr-3|Ly-17|Ly-m20|LyM-1|Lym-1|fcRII	Fc receptor, IgG, low affinity IIb	protein-coding
mm_129870.1	chr15	83393958	83393974	-	1	NA	intron (NM_011862, intron 2 of 10)	intron (NM_011862, intron 2 of 10)	-26669	NR_027980	69291	Mm.66794	NM_001033147		1700001L05Rik	-	RIKEN cDNA 1700001L05 gene	ncRNA
mm_141073.1	chr17	25844420	25844428	-	1	NA	TTS (NM_001163766)	TTS (NM_001163766)	427	NM_145999	214952	Mm.40907	NM_145999	ENSMUSG00000025733	Rhot2	Arht2|Miro2	ras homolog family member T2	protein-coding
mm_67315.1	chr7	79594992	79595009	-	1	NA	intron (NM_019799, intron 9 of 10)	intron (NM_019799, intron 9 of 10)	22657	NM_019799	56315	Mm.10909	NM_019799	ENSMUSG00000030549	Rhcg	BB065800	Rhesus blood group-associated C glycoprotein	protein-coding
mm_10159.1	chr2	4400959	4400969	+	1	NA	promoter-TSS (NM_001177843)	promoter-TSS (NM_001177843)	-12	NM_001177843	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding
mm_101123.1	chr11	12028909	12028911	-	1	NA	promoter-TSS (NM_001177629)	promoter-TSS (NM_001177629)	-939	NM_001177629	14783	Mm.273117	NM_010345	ENSMUSG00000020176	Grb10	5730571D09Rik|AI325020|Meg1|mKIAA0207	growth factor receptor bound protein 10	protein-coding
mm_118293.1	chr13	113046738	113046758	-	1	NA	promoter-TSS (NM_027127)	promoter-TSS (NM_027127)	-360	NM_027127	69590	Mm.12715	NM_027127	ENSMUSG00000021760	Gpx8	2310016C16Rik|AU017063	glutathione peroxidase 8 (putative)	protein-coding
mm_60415.1	chr7	44476205	44476209	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	5860	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_148778.1	chr19	6108615	6108624	+	1	NA	exon (NM_001009546, exon 5 of 18)	exon (NM_001009546, exon 5 of 18)	2821	NM_001009546	381204	Mm.359041	NM_001009546	ENSMUSG00000054999	Naaladl1	Gm964|Naaladasel	N-acetylated alpha-linked acidic dipeptidase-like 1	protein-coding
mm_102389.1	chr11	58954442	58954459	-	1	NA	promoter-TSS (NM_178218)	promoter-TSS (NM_178218)	62	NR_134309	382522	Mm.377898	NR_134309	ENSMUSG00000080712	Hist3h2bb-ps	4930534G10Rik|4933432H21|B2Hist3h2bb|Hist3h2bb|R75370	histone cluster 3, H2bb, pseudogene	pseudo
mm_40759.1	chr5	66968422	66968447	+	1	NA	promoter-TSS (NM_001256122)	promoter-TSS (NM_001256122)	18	NM_001256122	77569	Mm.374778	NM_001001980	ENSMUSG00000037736	Limch1	3732412D22Rik|mKIAA1102	LIM and calponin homology domains 1	protein-coding
mm_96407.1	chr11	67253476	67253518	+	1	NA	exon (NM_010855, exon 27 of 40)	exon (NM_010855, exon 27 of 40)	15685	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_52884.1	chr6	122513678	122513688	+	1	NA	promoter-TSS (NM_015776)	promoter-TSS (NM_015776)	7	NM_015776	50530	Mm.41931	NM_015776	ENSMUSG00000030116	Mfap5	MAGP-2|MFAP-5	microfibrillar associated protein 5	protein-coding
mm_28420.1	chr3	90433554	90433565	-	1	NA	promoter-TSS (NM_178876)	promoter-TSS (NM_178876)	77	NM_145540	229543	Mm.268564	NM_145540	ENSMUSG00000027933	Ints3	C77668	integrator complex subunit 3	protein-coding
mm_89186.1	chr10	86346146	86346163	+	1	NA	3' UTR (NM_011595, exon 5 of 5)	3' UTR (NM_011595, exon 5 of 5)	45742	NM_011595	21859	Mm.4871	NM_011595	ENSMUSG00000020044	Timp3	Timp-3	tissue inhibitor of metalloproteinase 3	protein-coding
mm_25572.1	chr3	116829527	116829544	+	1	NA	Intergenic	Intergenic	-21369	NM_001081326	77559	Mm.237099	NM_001081326	ENSMUSG00000033400	Agl	1110061O17Rik|9430004C13Rik|9630046L06Rik|AI850929|C77197	amylo-1,6-glucosidase, 4-alpha-glucanotransferase	protein-coding
mm_152524.1	chr19	11314444	11314461	-	1	NA	Intergenic	Intergenic	20243	NM_001276398	109225	Mm.491251	NM_027836	ENSMUSG00000024672	Ms4a7	9130422I10Rik|A430103C15Rik|CD20l4|CFFMA	membrane-spanning 4-domains, subfamily A, member 7	protein-coding
mm_21781.1	chr2	164848084	164848111	-	1	NA	intron (NM_011125, intron 8 of 15)	intron (NM_011125, intron 8 of 15)	9611	NM_011125	18830	Mm.6105	NM_011125	ENSMUSG00000017754	Pltp	Bpife|OD107	phospholipid transfer protein	protein-coding
mm_152633.1	chr19	12501634	12501672	-	1	NA	5' UTR (NM_172442, exon 1 of 9)	5' UTR (NM_172442, exon 1 of 9)	343	NM_172442	207521	Mm.247695	NM_172442	ENSMUSG00000039982	Dtx4	AI449438|BC044798|D930042H13|RNF155	deltex 4, E3 ubiquitin ligase	protein-coding
mm_46528.1	chr5	105642683	105642697	-	1	NA	Intergenic	Intergenic	-57279	NM_001122768	231549	Mm.23837	NM_178701	ENSMUSG00000046079	Lrrc8d	2810473G09Rik|4930525N13Rik|A930019F03|Lrrc5	leucine rich repeat containing 8D	protein-coding
mm_31611.1	chr4	58994310	58994321	+	1	NA	Intergenic	RMER19B|LTR|ERVK	-7237	NM_025968	67103	Mm.34497	NM_025968	ENSMUSG00000028378	Ptgr1	2510002C21Rik|Ltb4dh|Zadh3	prostaglandin reductase 1	protein-coding
mm_54131.1	chr6	20970336	20970352	-	1	NA	Intergenic	Intergenic	-245765	NM_019697	16508	Mm.425316	NM_019697	ENSMUSG00000060882	Kcnd2	AI839615|AW555701|Kv4.2|R75121|mKIAA1044	potassium voltage-gated channel, Shal-related family, member 2	protein-coding
mm_139960.1	chr17	71616220	71616259	+	1	NA	promoter-TSS (NM_175639)	promoter-TSS (NM_175639)	24	NM_175639	72515	Mm.257762	NM_175639	ENSMUSG00000041057	Wdr43	2610318G08Rik|AU020887|AV024208|Wrd43|mKIAA0007	WD repeat domain 43	protein-coding
mm_73266.1	chr8	104347460	104347472	+	1	NA	TTS (NM_153582)	TTS (NM_153582)	6872	NM_024217	68119	Mm.390108	NM_024217	ENSMUSG00000031875	Cmtm3	9430096L06Rik|AI413895|BNAS2|Cklfsf3	CKLF-like MARVEL transmembrane domain containing 3	protein-coding
mm_27828.1	chr3	79097299	79097336	-	1	NA	intron (NM_001310536, intron 5 of 23)	intron (NM_001310536, intron 5 of 23)	47570	NM_001310536	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_137331.1	chr17	25086944	25086985	+	1	NA	exon (NM_134126, exon 19 of 30)	exon (NM_134126, exon 19 of 30)	-5850	NM_001001183	407831	Mm.34379	NM_001001183	ENSMUSG00000024168	Tmem204	-	transmembrane protein 204	protein-coding
mm_39910.1	chr5	31297604	31297616	+	1	NA	promoter-TSS (NM_144909)	promoter-TSS (NM_144909)	29	NM_144909	231103	Mm.100043	NM_144909	ENSMUSG00000059434	Gckr	GKRP	glucokinase regulatory protein	protein-coding
mm_148970.1	chr19	7537761	7537776	+	1	NA	3' UTR (NM_001163505, exon 13 of 13)	3' UTR (NM_001163505, exon 13 of 13)	-19691	NM_139269	225845	Mm.274810	NM_139269	ENSMUSG00000060675	Pla2g16	C78643|HRSL3|Hrasls3|Hrev107|MLP-3	phospholipase A2, group XVI	protein-coding
mm_98833.1	chr11	97435337	97435347	+	1	NA	Intergenic	Intergenic	-14818	NM_021493	58996	Mm.394118	NM_021493	ENSMUSG00000049807	Arhgap23	A330041B18Rik	Rho GTPase activating protein 23	protein-coding
mm_25505.1	chr3	109560712	109560715	+	1	NA	intron (NM_020505, intron 15 of 26)	intron (NM_020505, intron 15 of 26)	-13294	NM_146139	57257	Mm.282257	NM_020505	ENSMUSG00000033721	Vav3	A530094I06Rik|AA986410|Idd18.1	vav 3 oncogene	protein-coding
mm_72118.1	chr8	71678315	71678321	+	1	NA	intron (NM_010589, intron 1 of 24)	intron (NM_010589, intron 1 of 24)	1935	NM_010589	16453	Mm.249645	NM_010589	ENSMUSG00000031805	Jak3	fae|wil	Janus kinase 3	protein-coding
mm_101941.1	chr11	50207865	50207889	-	1	NA	exon (NM_011018, exon 2 of 8)	exon (NM_011018, exon 2 of 8)	2943	NM_001290769	18412	Mm.40828	NM_011018	ENSMUSG00000015837	Sqstm1	A170|OSF-6|Osi|STAP|STONE14|p62	sequestosome 1	protein-coding
mm_128839.1	chr15	68363201	68363228	-	1	NA	Intergenic	(CG)n|Simple_repeat|Simple_repeat	-21925	NR_029718	387228		NR_029718	ENSMUSG00000065437	Mir30d	Mirn30d|mir-30d|mmu-mir-30d	microRNA 30d	ncRNA
mm_152336.1	chr19	9978462	9978502	-	1	NA	Intergenic	Intergenic	-2118	NR_073181	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
mm_66212.1	chr7	34357806	34357822	-	1	NA	exon (NM_025948, exon 5 of 11)	exon (NM_025948, exon 5 of 11)	31726	NM_025948	67070	Mm.276503	NM_025948	ENSMUSG00000066568	Lsm14a	2700023B17Rik|AA407828|AU017544|Tral	LSM14A mRNA processing body assembly factor	protein-coding
mm_27237.1	chr3	36475689	36475705	-	1	NA	promoter-TSS (NR_105976)	promoter-TSS (NR_105976)	-173	NR_105976	102466786		NR_105976	ENSMUSG00000098808	Mir7009	Gm27472|mmu-mir-7009	microRNA 7009	ncRNA
mm_105601.1	chr11	106775943	106775954	-	1	NA	intron (NM_015810, intron 3 of 7)	ID4_|SINE|ID	3567	NR_027785	50776	Mm.859	NM_015810	ENSMUSG00000020718	Polg2	-	polymerase (DNA directed), gamma 2, accessory subunit	protein-coding
mm_45621.1	chr5	75967669	75967707	-	1	NA	exon (NM_010612, exon 6 of 30)	exon (NM_010612, exon 6 of 30)	10740	NM_010612	16542	Mm.285	NM_010612	ENSMUSG00000062960	Kdr	6130401C07|Flk-1|Flk1|Krd-1|Ly73|VEGFR-2|VEGFR2|sVEGFR-2	kinase insert domain protein receptor	protein-coding
mm_137510.1	chr17	27038622	27038632	+	1	NA	Intergenic	Intergenic	9368	NM_027544	70772	Mm.440437	NM_027544	ENSMUSG00000048731	Ggnbp1	0610031G08Rik|mdf	gametogenetin binding protein 1	protein-coding
mm_81107.1	chr9	106452148	106452165	+	1	NA	exon (NM_029631, exon 4 of 4)	exon (NM_029631, exon 4 of 4)	-1682	NM_021567	59092	Mm.286394	NM_021567	ENSMUSG00000023495	Pcbp4	1200003L19Rik|AlphaCP-4	poly(rC) binding protein 4	protein-coding
mm_121045.1	chr14	80022325	80022339	+	1	NA	TTS (NM_001030294)	TTS (NM_001030294)	22030	NM_001030294	380924	Mm.26456	NM_001030294	ENSMUSG00000022026	Olfm4	GC1|GW112|Gm296|Gm913|OlfD|pPD4	olfactomedin 4	protein-coding
mm_50506.1	chr6	49036606	49036625	+	1	NA	promoter-TSS (NM_053110)	promoter-TSS (NM_053110)	97	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_98101.1	chr11	86683887	86683897	+	1	NA	promoter-TSS (NM_001098810)	promoter-TSS (NM_001098810)	-70	NM_029478	75909	Mm.390398	NM_029478	ENSMUSG00000018171	Vmp1	3110098I04Rik|4930579A11Rik|AI787464|Tango5|Tmem49|mir-21a|ni-2	vacuole membrane protein 1	protein-coding
mm_3204.1	chr1	135818859	135818859	+	1	NA	5' UTR (NM_133664, exon 1 of 10)	5' UTR (NM_133664, exon 1 of 10)	261	NM_133664	16763	Mm.36726	NM_133664	ENSMUSG00000041782	Lad1	-	ladinin	protein-coding
mm_112893.1	chr13	20885212	20885262	+	1	NA	intron (NM_012054, intron 4 of 20)	MLT1D|LTR|ERVL-MaLR	91124	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_58877.1	chr7	16987198	16987217	+	1	NA	Intergenic	(CACAC)n|Simple_repeat|Simple_repeat	-7381	NM_001101535	434130	Mm.459162	NM_001101535	ENSMUSG00000041117	Ccdc8	ENSMUSG00000041117	coiled-coil domain containing 8	protein-coding
mm_105838.1	chr11	113683248	113683275	-	1	NA	intron (NM_138598, intron 1 of 2)	intron (NM_138598, intron 1 of 2)	890	NM_138598	28081	Mm.351688	NM_138598	ENSMUSG00000041629	Fam104a	D11Wsu99e	family with sequence similarity 104, member A	protein-coding
mm_81316.1	chr9	108436475	108436504	+	1	NA	promoter-TSS (NM_001004192)	promoter-TSS (NM_001004192)	7	NM_001004192	434439	Mm.78372	NM_001004192	ENSMUSG00000050641	BC048562	-	cDNA sequence BC048562	protein-coding
mm_167200.1	chr7	143069505	143069531	+	1	NA	intron (NM_138631, intron 1 of 3)	CpG	150	NM_001115085	56844	Mm.139675	NM_020285	ENSMUSG00000045752	Tssc4	AA241958|ESTM671070	tumor-suppressing subchromosomal transferable fragment 4	protein-coding
mm_117155.1	chr13	61541893	61541900	-	1	NA	promoter-TSS (NM_022326)	promoter-TSS (NM_022326)	-57	NM_022326	64139	Mm.279933	NM_022326	ENSMUSG00000074871	Ctsm	1600027J17Rik|AI324100|Catm	cathepsin M	protein-coding
mm_113155.1	chr13	24801333	24801339	+	1	NA	promoter-TSS (NM_024473)	promoter-TSS (NM_024473)	-321	NM_024473	79555	Mm.266668	NM_024473	ENSMUSG00000019132	BC005537	8030460C05Rik|C78201	cDNA sequence BC005537	protein-coding
mm_158252.1	chrX	108664927	108664951	-	1	NA	Intergenic	Intergenic	169416	NM_001081477	382236	Mm.100112	NM_001081477	ENSMUSG00000063663	Brwd3	Brodl|D030064D06Rik|Gm596	bromodomain and WD repeat domain containing 3	protein-coding
mm_60530.1	chr7	44480231	44480259	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-4272	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_116112.1	chr13	28950152	28950162	-	1	NA	TTS (NM_009238)	TTS (NM_009238)	3525	NM_009238	20677	Mm.240627	NM_009238	ENSMUSG00000076431	Sox4	AA682046|Sox-4	SRY (sex determining region Y)-box 4	protein-coding
mm_169095.1	chr13	40886853	40886853	+	1	NA	promoter-TSS (NM_008105)	promoter-TSS (NM_008105)	95	NM_008105	14538	Mm.314757	NM_008105	ENSMUSG00000021360	Gcnt2	5330430K10Rik|IGnT|IGnTA|IGnTB|IGnTC	glucosaminyl (N-acetyl) transferase 2, I-branching enzyme	protein-coding
mm_33469.1	chr4	130816840	130816853	+	1	NA	exon (NM_011520, exon 2 of 5)	exon (NM_011520, exon 2 of 5)	24309	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_166818.1	chr7	18009903	18009918	+	1	NA	promoter-TSS (NM_027210)	promoter-TSS (NM_027210)	21	NM_028171	69785	Mm.46086	NM_027210	ENSMUSG00000057195	Ceacam13	1600012K03Rik|1600025J19Rik	carcinoembryonic antigen-related cell adhesion molecule 13	protein-coding
mm_14281.1	chr2	128798045	128798048	+	1	NA	intron (NM_008587, intron 18 of 18)	B3|SINE|B2	-20257	NM_028248	72477	Mm.259688	NM_028248	ENSMUSG00000014353	Tmem87b	2610301K12Rik|2810431I02Rik|AU014804	transmembrane protein 87B	protein-coding
mm_142872.1	chr17	51816913	51816923	-	1	NA	intron (NM_001163632, intron 1 of 10)	intron (NM_001163632, intron 1 of 10)	-4864	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_138294.1	chr17	34630471	34630510	+	1	NA	intron (NM_030890, intron 1 of 3)	intron (NM_030890, intron 1 of 3)	804	NM_030890	260297	Mm.390965	NM_030890	ENSMUSG00000015476	Prrt1	Bat-4|Bat4|D17H6S54E|DSPD1|G5b|NG5|ORF31	proline-rich transmembrane protein 1	protein-coding
mm_96146.1	chr11	61022581	61022609	+	1	NA	promoter-TSS (NM_001267593)	promoter-TSS (NM_001267593)	31	NM_001267593	16515	Mm.4970	NM_010603	ENSMUSG00000042529	Kcnj12	IRK-2|IRK2|Kir2.2|MB-IRK2	potassium inwardly-rectifying channel, subfamily J, member 12	protein-coding
mm_56106.1	chr6	87496236	87496268	-	1	NA	promoter-TSS (NM_175476)	promoter-TSS (NM_175476)	75	NR_104483	232201	Mm.119564	NM_175476	ENSMUSG00000030047	Arhgap25	A130039I20Rik	Rho GTPase activating protein 25	protein-coding
mm_148713.1	chr19	5803742	5803795	+	1	NA	Intergenic	CpG	-1096	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_7111.1	chr1	89934495	89934520	-	1	NA	Intergenic	Intergenic	-3331	NM_010262	14472	Mm.204730	NM_010262	ENSMUSG00000034486	Gbx2	D130058E05Rik|Gbx-2|MMoxA|Stra7	gastrulation brain homeobox 2	protein-coding
mm_40671.1	chr5	65493437	65493468	+	1	NA	promoter-TSS (NM_133697)	promoter-TSS (NM_133697)	-617	NM_133697	68552	Mm.10709	NM_133697	ENSMUSG00000037822	Smim14	1110003E01Rik|1700127H04Rik|5430439C17Rik|MAd4	small integral membrane protein 14	protein-coding
mm_89350.1	chr10	88147055	88147059	+	1	NA	promoter-TSS (NM_027191)	promoter-TSS (NM_027191)	-14	NM_028334	69736	Mm.222184	NM_027191	ENSMUSG00000035351	Nup37	2410003L22Rik|2810039M17Rik	nucleoporin 37	protein-coding
mm_123950.1	chr14	73445095	73445127	-	1	NA	Intergenic	Intergenic	-59840	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_69813.1	chr7	141263898	141263917	-	1	NA	exon (NM_001252601, exon 8 of 10)	exon (NM_001252601, exon 8 of 10)	2517	NM_001252601	54123	Mm.3233	NM_016850	ENSMUSG00000025498	Irf7	-	interferon regulatory factor 7	protein-coding
mm_165368.1	chr2	127277933	127277941	+	1	NA	intron (NM_139308, intron 1 of 7)	intron (NM_139308, intron 1 of 7)	7708	NM_139308	99138	Mm.41271	NM_139308	ENSMUSG00000027367	Stard7	AI852671|AL022671|AW544915	START domain containing 7	protein-coding
mm_19344.1	chr2	90895342	90895344	-	1	NA	intron (NM_026688, intron 6 of 6)	B1_Mur2|SINE|Alu	9378	NM_026688	68349	Mm.30113	NM_026688	ENSMUSG00000005510	Ndufs3	0610010M09Rik|CI-30kD	NADH dehydrogenase (ubiquinone) Fe-S protein 3	protein-coding
mm_162100.1	chrX	37827144	37827144	+	1	NA	promoter-TSS (NM_008955)	promoter-TSS (NM_008955)	89	NM_008955	19202	Mm.10105	NM_008955	ENSMUSG00000006200	Rhox6	AV213605|AW548842|Psx1	reproductive homeobox 6	protein-coding
mm_79534.1	chr9	57767436	57767445	+	1	NA	Intergenic	U2|snRNA|snRNA	-1580	NM_007713	102414	Mm.25720	NM_007713	ENSMUSG00000032316	Clk3	AI256811	CDC-like kinase 3	protein-coding
mm_60417.1	chr7	44476264	44476282	+	1	NA	Intergenic	L1MEd|LINE|L1	5926	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_102660.1	chr11	64060207	64060225	-	1	NA	intron (NM_178379, intron 3 of 6)	intron (NM_178379, intron 3 of 6)	19256	NM_178379	70383	Mm.340211	NM_178379	ENSMUSG00000042148	Cox10	2410004F01Rik|AU042636	cytochrome c oxidase assembly protein 10	protein-coding
mm_115098.1	chr13	102733129	102733147	+	1	NA	3' UTR (NM_175171, exon 29 of 29)	3' UTR (NM_175171, exon 29 of 29)	-27117	NR_130318	76624	Mm.426384	NR_130171	ENSMUSG00000091906	1700099I09Rik	-	RIKEN cDNA 1700099I09 gene	ncRNA
mm_120762.1	chr14	73368361	73368375	+	1	NA	exon (NM_008410, exon 2 of 6)	exon (NM_008410, exon 2 of 6)	16903	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_42312.1	chr5	114865466	114865480	+	1	NA	intron (NM_026263, intron 5 of 11)	intron (NM_026263, intron 5 of 11)	11759	NM_026263	67593	Mm.251409	NM_026263	ENSMUSG00000029564	4930519G04Rik	1700014B12Rik	RIKEN cDNA 4930519G04 gene	protein-coding
mm_68632.1	chr7	118188061	118188073	-	1	NA	intron (NM_001031814, intron 18 of 62)	ID_B1|SINE|B4	55570	NM_001031814	233789	Mm.309053	NM_177180	ENSMUSG00000030655	Smg1	2610207I05Rik|5430435M13Rik|C130002K18Rik|mKIAA0421	SMG1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)	protein-coding
mm_66825.1	chr7	48691786	48691807	-	1	NA	Intergenic	Intergenic	-47995	NM_207537	404238	Mm.377926	NM_207537	ENSMUSG00000070546	Mrgprb3	MrgB3	MAS-related GPR, member B3	protein-coding
mm_152642.1	chr19	12527096	12527104	-	1	NA	Intergenic	L1MC3|LINE|L1	-25104	NM_172442	207521	Mm.247695	NM_172442	ENSMUSG00000039982	Dtx4	AI449438|BC044798|D930042H13|RNF155	deltex 4, E3 ubiquitin ligase	protein-coding
mm_53354.1	chr6	129350378	129350391	+	1	NA	5' UTR (NM_177686, exon 1 of 6)	5' UTR (NM_177686, exon 1 of 6)	140	NM_177686	232413	Mm.90241	NM_177686	ENSMUSG00000053063	Clec12a	CLL-1|D230024O04|KLRL1|Micl	C-type lectin domain family 12, member a	protein-coding
mm_33901.1	chr4	136284659	136284686	+	1	NA	Intergenic	Intergenic	-1397	NM_009557	22704	Mm.1504	NM_009557	ENSMUSG00000051351	Zfp46	AI426962|Mlz-4|Zfp-46|Znf436	zinc finger protein 46	protein-coding
mm_150001.1	chr19	29284935	29284948	+	1	NA	exon (NM_008413, exon 9 of 25)	exon (NM_008413, exon 9 of 25)	33138	NM_008413	16452	Mm.275839	NM_008413	ENSMUSG00000024789	Jak2	Fd17	Janus kinase 2	protein-coding
mm_9533.1	chr1	173871413	173871447	-	1	NA	exon (NM_001170853, exon 6 of 10)	exon (NM_001170853, exon 6 of 10)	8757	NM_001170853	100040462	Mm.463437	NM_001170853	ENSMUSG00000090272	Mndal	Gm2785|Ifi212	myeloid nuclear differentiation antigen like	protein-coding
mm_75756.1	chr8	69908916	69908926	-	1	NA	3' UTR (NM_001113346, exon 13 of 13)	3' UTR (NM_001113346, exon 13 of 13)	-6363	NM_023312	67184	Mm.21162	NM_023312	ENSMUSG00000036199	Ndufa13	2700054G14Rik|AU022060|CDA016|CGI-39|GRIM-19|Grim19	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 13	protein-coding
mm_85273.1	chr9	99436648	99436681	-	1	NA	promoter-TSS (NM_008624)	promoter-TSS (NM_008624)	48	NM_008624	17532	Mm.2045	NM_008624	ENSMUSG00000032470	Mras	2900078C09Rik|AI326250	muscle and microspikes RAS	protein-coding
mm_51206.1	chr6	71326000	71326017	+	1	NA	exon (NM_009858, exon 2 of 6)	exon (NM_009858, exon 2 of 6)	3196	NM_009858	12526	Mm.333148	NM_009858	ENSMUSG00000053044	Cd8b1	Cd8b|Ly-3|Ly-C|Lyt-3	CD8 antigen, beta chain 1	protein-coding
mm_144049.1	chr17	90448707	90448713	-	1	NA	intron (NM_001346957, intron 14 of 18)	MTE2a|LTR|ERVL-MaLR	7170	NM_001346958	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_87015.1	chr10	26895253	26895263	+	1	NA	intron (NM_176837, intron 12 of 14)	BC1_Mm|scRNA|scRNA	122746	NM_176837	73910	Mm.356496	NM_176837	ENSMUSG00000039031	Arhgap18	4833419J07Rik|AI314906|AI843501	Rho GTPase activating protein 18	protein-coding
mm_10196.1	chr2	4927375	4927389	+	1	NA	exon (NM_010726, exon 4 of 9)	exon (NM_010726, exon 4 of 9)	8386	NM_010726	16922	Mm.391704	NM_010726	ENSMUSG00000026664	Phyh	AI256161|AI265699|Lnap1|PAHX	phytanoyl-CoA hydroxylase	protein-coding
mm_134529.1	chr16	19241105	19241108	-	1	NA	Intergenic	Intergenic	45635	NM_146451	258443	Mm.377506	NM_146451	ENSMUSG00000050742	Olfr164	MOR279-2	olfactory receptor 164	protein-coding
mm_32277.1	chr4	102760295	102760375	+	1	NA	5' UTR (NM_144906, exon 1 of 24)	5' UTR (NM_144906, exon 1 of 24)	200	NM_001285859	73094	Mm.54201	NM_144906	ENSMUSG00000028524	Sgip1	3110007P09Rik|SGIP1alpha|gag	SH3-domain GRB2-like (endophilin) interacting protein 1	protein-coding
mm_5499.1	chr1	36985823	36985836	-	1	NA	Intergenic	Intergenic	-46302	NM_018872	56030	Mm.186943	NM_018872	ENSMUSG00000026116	Tmem131	2610524E03Rik|CC28|D1Bwg0491e|Neg|RW1|YR-23|mKIAA0257	transmembrane protein 131	protein-coding
mm_81539.1	chr9	110244950	110244964	+	1	NA	5' UTR (NM_013884, exon 1 of 5)	5' UTR (NM_013884, exon 1 of 5)	1174	NM_001166273	29873	Mm.38496	NM_013884	ENSMUSG00000032482	Cspg5	Caleb|Ngc	chondroitin sulfate proteoglycan 5	protein-coding
mm_31034.1	chr4	40948522	40948530	+	1	NA	promoter-TSS (NM_001171739)	promoter-TSS (NM_001171739)	-27	NM_029814	76959	Mm.212763	NM_029814	ENSMUSG00000028419	Chmp5	2210412K09Rik|AW545668	charged multivesicular body protein 5	protein-coding
mm_149749.1	chr19	22692348	22692372	+	1	NA	promoter-TSS (NM_001035246)	promoter-TSS (NM_001035246)	-259	NM_001035245	226025	Mm.131943	NM_177341	ENSMUSG00000052387	Trpm3	6330504P12Rik|9330180E14|AU018608|B930001P07Rik|LTRPC3|MLSN2	transient receptor potential cation channel, subfamily M, member 3	protein-coding
mm_70856.1	chr8	24044519	24044536	+	1	NA	intron (NM_001277239, intron 7 of 7)	intron (NM_001277239, intron 7 of 7)	374866	NM_177086	320158	Mm.121274	NM_177086	ENSMUSG00000037492	Zmat4	9630048M01Rik	zinc finger, matrin type 4	protein-coding
mm_101569.1	chr11	34227269	34227279	-	1	NA	3' UTR (NM_033374, exon 52 of 52)	3' UTR (NM_033374, exon 52 of 52)	-19185	NM_023907	14233	Mm.32926	NM_023907	ENSMUSG00000047861	Foxi1	5830401E05Rik|FREAC6|Fkh10|HFH-3|Hfh3	forkhead box I1	protein-coding
mm_85859.1	chr9	110747076	110747121	-	1	NA	promoter-TSS (NM_011199)	promoter-TSS (NM_011199)	47	NM_011199	19228	Mm.3542	NM_011199	ENSMUSG00000032492	Pth1r	PPR|Pthr|Pthr1	parathyroid hormone 1 receptor	protein-coding
mm_36231.1	chr4	63152618	63152628	-	1	NA	exon (NM_007443, exon 2 of 10)	exon (NM_007443, exon 2 of 10)	1549	NM_007443	11699	Mm.2197	NM_007443	ENSMUSG00000028356	Ambp	AI194774|ASPI|HI-30|Intin4|Itil|UTI	alpha 1 microglobulin/bikunin	protein-coding
mm_4797.1	chr1	185204110	185204163	+	1	NA	promoter-TSS (NM_001163754)	promoter-TSS (NM_001163754)	-32	NM_001163754	98732	Mm.275841	NM_172649	ENSMUSG00000039318	Rab3gap2	1110059F07Rik|2010002H18Rik|5830469C09|AI851069|AW743433|RAB3-GAP150|mKIAA0839	RAB3 GTPase activating protein subunit 2	protein-coding
mm_38411.1	chr4	139093047	139093056	-	1	NA	promoter-TSS (NM_008675)	promoter-TSS (NM_008675)	-81	NM_008675	17965	Mm.9404	NM_008675	ENSMUSG00000041120	Nbl1	D4H1S1733E|DAN|Dana|NO3	neuroblastoma, suppression of tumorigenicity 1	protein-coding
mm_115229.1	chr13	109902834	109902855	+	1	NA	promoter-TSS (NR_035442)	promoter-TSS (NR_035442)	-965	NR_035442	100316683		NR_035442	ENSMUSG00000084651	Mir1904	Mirn1904|mmu-mir-1904	microRNA 1904	ncRNA
mm_73940.1	chr8	120101399	120101431	+	1	NA	promoter-TSS (NM_133967)	promoter-TSS (NM_133967)	57	NM_133967	102193	Mm.240076	NM_133967	ENSMUSG00000031823	Zdhhc7	AL024087|Gramp2	zinc finger, DHHC domain containing 7	protein-coding
mm_51794.1	chr6	88272386	88272391	+	1	NA	intron (NM_023060, intron 6 of 6)	intron (NM_023060, intron 6 of 6)	50120	NM_019964	56691	Mm.272871	NM_019964	ENSMUSG00000048206	Dnajb8	1700016F14Rik|1700031F10Rik|AI326313|mDj6	DnaJ heat shock protein family (Hsp40) member B8	protein-coding
mm_114646.1	chr13	76891466	76891513	+	1	NA	intron (NM_030174, intron 15 of 20)	intron (NM_030174, intron 15 of 20)	243979	NM_134071	105377	Mm.209730	NM_134071	ENSMUSG00000021597	Slf1	2700017A04Rik|AW545819|Ankrd32|Brctd1|Brctx|C730024G01Rik	SMC5-SMC6 complex localization factor 1	protein-coding
mm_96377.1	chr11	67240912	67240946	+	1	NA	exon (NM_010855, exon 4 of 40)	exon (NM_010855, exon 4 of 40)	3117	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_57845.1	chr6	129467612	129467644	-	1	NA	exon (NM_020008, exon 4 of 6)	exon (NM_020008, exon 4 of 6)	5151	NM_001309637	56644	Mm.239516	NM_020008	ENSMUSG00000079293	Clec7a	BGR|Clecsf12|beta-GR	C-type lectin domain family 7, member a	protein-coding
mm_148677.1	chr19	5638281	5638306	+	1	NA	intron (NM_009045, intron 1 of 10)	intron (NM_009045, intron 1 of 10)	803	NM_009045	19697	Mm.249966	NM_009045	ENSMUSG00000024927	Rela	p65	v-rel reticuloendotheliosis viral oncogene homolog A (avian)	protein-coding
mm_166054.1	chr4	132345738	132345742	-	1	NA	promoter-TSS (NM_133878)	promoter-TSS (NM_133878)	10	NM_001197082	100088	Mm.255045	NM_133878	ENSMUSG00000028896	Rcc1	4931417M11Rik|AI326872|Chc1	regulator of chromosome condensation 1	protein-coding
mm_141362.1	chr17	28899705	28899716	-	1	NA	exon (NM_172450, exon 11 of 12)	exon (NM_172450, exon 11 of 12)	-5555	NR_045457	74179	Mm.248931	NR_045457	ENSMUSG00000085333	1700030A11Rik	-	RIKEN cDNA 1700030A11 gene	ncRNA
mm_61703.1	chr7	81213346	81213359	+	1	NA	promoter-TSS (NM_008803)	promoter-TSS (NM_008803)	-452	NM_008803	18584	Mm.371577	NM_008803	ENSMUSG00000025584	Pde8a	AI551852|Pde8	phosphodiesterase 8A	protein-coding
mm_42272.1	chr5	114146502	114146514	+	1	NA	Intergenic	Intergenic	15352	NM_011677	22256	Mm.1393	NM_011677	ENSMUSG00000029591	Ung	UNG1|UNG2	uracil DNA glycosylase	protein-coding
mm_37344.1	chr4	119658907	119658922	-	1	NA	promoter-TSS (NM_008191)	promoter-TSS (NM_008191)	31	NM_008191	14916	Mm.278	NM_008191	ENSMUSG00000032978	Guca2b	AV066530|Gcap2|Ugn	guanylate cyclase activator 2b (retina)	protein-coding
mm_109178.1	chr12	108423070	108423136	+	1	NA	5' UTR (NM_001043335, exon 1 of 22)	5' UTR (NM_001043335, exon 1 of 22)	287	NM_001043335	68519	Mm.236645	NM_001043335	ENSMUSG00000058070	Eml1	1110008N23Rik|A930030P13Rik|AA171013|AI847476|AI853955|ELP79|EMAP|EMAPL|heco	echinoderm microtubule associated protein like 1	protein-coding
mm_68512.1	chr7	111593937	111593949	-	1	NA	intron (NM_173739, intron 3 of 10)	L2a|LINE|L2	186034	NM_173739	233733	Mm.323322	NM_173739	ENSMUSG00000038296	Galnt18	2900011G21Rik|BC024988|Galntl4	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 18	protein-coding
mm_35228.1	chr4	19696698	19696747	-	1	NA	intron (NR_074089, intron 1 of 23)	intron (NR_074089, intron 1 of 23)	12282	NM_177327	107568	Mm.78312	NM_177327	ENSMUSG00000041058	Wwp1	8030445B08Rik|AIP5|SDRP1|Tiul1	WW domain containing E3 ubiquitin protein ligase 1	protein-coding
mm_128643.1	chr15	59374150	59374199	-	1	NA	promoter-TSS (NM_026746)	promoter-TSS (NM_026746)	-22	NM_153548	223593	Mm.218665	NM_153548	ENSMUSG00000022350	Washc5	AL022848|C76463|E430025E21Rik|Kiaa0196|mKIAA0196|strumpellin	WASH complex subunit 5	protein-coding
mm_86866.1	chr10	21993966	21993990	+	1	NA	promoter-TSS (NM_011361)	promoter-TSS (NM_011361)	88	NM_001161850	20393	Mm.28405	NM_011361	ENSMUSG00000019970	Sgk1	Sgk	serum/glucocorticoid regulated kinase 1	protein-coding
mm_110669.1	chr12	65066668	65066716	-	1	NA	exon (NM_013902, exon 4 of 7)	exon (NM_013902, exon 4 of 7)	7246	NM_013902	30795	Mm.28480	NM_013902	ENSMUSG00000020949	Fkbp3	25kDa|FKBP-3|FKBP25	FK506 binding protein 3	protein-coding
mm_172240.1	chr6	68704994	68705018	-	1	NA	Intergenic	Intergenic	622168	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_127952.1	chr15	10771374	10771386	-	1	NA	intron (NR_045063, intron 5 of 6)	intron (NR_045063, intron 5 of 6)	56480	NR_045065	75259	Mm.33928	NR_045063	ENSMUSG00000097058	4930556M19Rik	1700009D01Rik|C130022M03Rik	RIKEN cDNA 4930556M19 gene	ncRNA
mm_94200.1	chr11	3101725	3101736	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	-22291	NR_003517	236604	Mm.247625	NM_001004146		Pisd-ps1	-	phosphatidylserine decarboxylase, pseudogene 1	pseudo
mm_70476.1	chr8	12395501	12395511	+	1	NA	promoter-TSS (NM_009233)	promoter-TSS (NM_009233)	-13	NM_009233	20664	Mm.39088	NM_009233	ENSMUSG00000096014	Sox1	BB176347|Sox-1	SRY (sex determining region Y)-box 1	protein-coding
mm_57419.1	chr6	124911746	124911758	-	1	NA	promoter-TSS (NM_008479)	promoter-TSS (NM_008479)	-47	NM_008479	16768	Mm.4528	NM_008479	ENSMUSG00000030124	Lag3	CD223|LAG-3|Ly66	lymphocyte-activation gene 3	protein-coding
mm_94678.1	chr11	17953493	17953514	+	1	NA	promoter-TSS (NR_131916)	promoter-TSS (NR_131916)	372	NM_026576	68145	Mm.178684	NM_026576	ENSMUSG00000016984	Etaa1	5730466H23Rik|AA672646	Ewing tumor-associated antigen 1	protein-coding
mm_89997.1	chr10	112269936	112269955	+	1	NA	Intergenic	Intergenic	-1178	NM_001025581	268345	Mm.336242	NM_001025581	ENSMUSG00000035681	Kcnc2	AW047325|B230117I07|KShIIIA|Kv3.2	potassium voltage gated channel, Shaw-related subfamily, member 2	protein-coding
mm_109607.1	chr12	112721830	112721849	+	1	NA	promoter-TSS (NM_001024602)	promoter-TSS (NM_001024602)	-335	NM_001024602	217882	Mm.23689	NM_001024602	ENSMUSG00000072825	Cep170b	AI466840|AW555464|Kiaa0284|mKIAA0284	centrosomal protein 170B	protein-coding
mm_159381.1	chr3	90243467	90243467	-	1	NA	promoter-TSS (NM_001307935)	promoter-TSS (NM_001307935)	45	NM_030080	78284	Mm.299952	NM_030080	ENSMUSG00000027938	Creb3l4	1700012K17Rik|5330432F22Rik|AIBZIP|AV040530|AV258827|CREB4|JAL|TISP40|acre1	cAMP responsive element binding protein 3-like 4	protein-coding
mm_132944.1	chr16	49894208	49894220	+	1	NA	exon (NM_010581, exon 5 of 10)	exon (NM_010581, exon 5 of 10)	38560	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_104492.1	chr11	95834169	95834180	-	1	NA	intron (NM_025659, intron 4 of 7)	intron (NM_025659, intron 4 of 7)	-8121	NM_023121	14710	Mm.46299	NM_023121	ENSMUSG00000038811	Gngt2	AV096488	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 2	protein-coding
mm_42895.1	chr5	122403357	122403404	+	1	NA	exon (NM_019824, exon 4 of 7)	exon (NM_019824, exon 4 of 7)	11502	NM_019824	56378	Mm.275942	NM_019824	ENSMUSG00000029465	Arpc3	1110006A04Rik|p21-ARC|p21-Ar|p21Arc	actin related protein 2/3 complex, subunit 3	protein-coding
mm_8148.1	chr1	136580530	136580547	-	1	NA	Intergenic	Intergenic	-44363	NM_177643	226442	Mm.62521	NM_177643	ENSMUSG00000041483	Zfp281	Znf281	zinc finger protein 281	protein-coding
mm_80855.1	chr9	98424960	98424970	+	1	NA	5' UTR (NM_011254, exon 1 of 4)	5' UTR (NM_011254, exon 1 of 4)	2004	NM_011254	19659	Mm.279741	NM_011254	ENSMUSG00000046402	Rbp1	CRBPI|Crbp|Rbp-1	retinol binding protein 1, cellular	protein-coding
mm_2827.1	chr1	131153176	131153186	+	1	NA	promoter-TSS (NM_010709)	promoter-TSS (NM_010709)	-26	NM_001136070	16865	Mm.276294	NM_010709	ENSMUSG00000026427	Eif2d	D1Ertd5e|Lgtn	eukaryotic translation initiation factor 2D	protein-coding
mm_48659.1	chr5	145879312	145879344	-	1	NA	intron (NM_007818, intron 1 of 12)	RLTR12H|LTR|ERVK	526	NM_007818	13112	Mm.332844	NM_007818	ENSMUSG00000056035	Cyp3a11	AI256190|Cyp3a|IIIAm1|Pcn	cytochrome P450, family 3, subfamily a, polypeptide 11	protein-coding
mm_39451.1	chr5	17574572	17574578	+	1	NA	promoter-TSS (NM_013657)	promoter-TSS (NM_013657)	-241	NM_013657	20348	Mm.5071	NM_013657	ENSMUSG00000028780	Sema3c	1110036B02Rik|SemE|Semae	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	protein-coding
mm_58678.1	chr7	12478320	12478372	+	1	NA	promoter-TSS (NM_026112)	promoter-TSS (NM_026112)	41	NM_026112	67370	Mm.98929	NM_026112	ENSMUSG00000030386	Zfp606	2410022M24Rik|AW494727	zinc finger protein 606	protein-coding
mm_92167.1	chr10	67549102	67549149	-	1	NA	promoter-TSS (NM_001005419)	promoter-TSS (NM_001005419)	-170	NM_001005419	211488	Mm.297250	NM_001005419	ENSMUSG00000057134	Ado	Gm237	2-aminoethanethiol (cysteamine) dioxygenase	protein-coding
mm_47543.1	chr5	124327813	124327879	-	1	NA	promoter-TSS (NM_001134717)	promoter-TSS (NM_001134717)	126	NM_001081323	269702	Mm.60224	NM_001081323	ENSMUSG00000038126	Mphosph9	4930548D04Rik|9630025B04Rik|AW413446|AW547060|B930097C17Rik|C87456|MPP-9|MPP9	M-phase phosphoprotein 9	protein-coding
mm_22450.1	chr2	181764705	181764715	-	1	NA	intron (NM_001171615, intron 1 of 22)	intron (NM_001171615, intron 1 of 22)	1378	NM_001171615	17932	Mm.458718	NM_008665	ENSMUSG00000010505	Myt1	Nzf2|Nzf2a|Nzf2b|Nztf2	myelin transcription factor 1	protein-coding
mm_132135.1	chr16	31897848	31897892	+	1	NA	3' UTR (NM_013900, exon 16 of 16)	3' UTR (NM_013900, exon 16 of 16)	19060	NM_013900	30060	Mm.30988	NM_013900	ENSMUSG00000022780	Mfi2	CD228|MTf|Meltf	antigen p97 (melanoma associated) identified by monoclonal antibodies 133.2 and 96.5	protein-coding
mm_114942.1	chr13	96542542	96542562	+	1	NA	promoter-TSS (NM_001164222)	promoter-TSS (NM_001164222)	27	NM_012048	27015	Mm.89926	NM_012048	ENSMUSG00000021668	Polk	DINP|Dinb1	polymerase (DNA directed), kappa	protein-coding
mm_134281.1	chr16	14203196	14203209	-	1	NA	exon (NM_013607, exon 37 of 42)	exon (NM_013607, exon 37 of 42)	39927	NM_001114085	67203	Mm.24105	NM_023317	ENSMUSG00000022678	Nde1	2810027M15Rik|AU042936|AW822251|Nude|mNudE	nudE neurodevelopment protein 1	protein-coding
mm_95980.1	chr11	58974602	58974628	+	1	NA	Intergenic	RLTR23|LTR|ERV1	-3478	NM_001290988	94091	Mm.248049	NM_053168	ENSMUSG00000020455	Trim11	-	tripartite motif-containing 11	protein-coding
mm_32718.1	chr4	116221634	116221650	+	1	NA	promoter-TSS (NM_181585)	promoter-TSS (NM_181585)	-272	NM_181585	18710	Mm.253819	NM_181585	ENSMUSG00000028698	Pik3r3	AA414954|p55pik	phosphatidylinositol 3 kinase, regulatory subunit, polypeptide 3 (p55)	protein-coding
mm_166166.1	chr5	21186260	21186276	+	1	NA	promoter-TSS (NM_175437)	promoter-TSS (NM_175437)	1	NM_175437	212167	Mm.121705	NM_175437	ENSMUSG00000039934	Gsap	A530088I07Rik|Pion	gamma-secretase activating protein	protein-coding
mm_133477.1	chr16	89585955	89585962	+	1	NA	Intergenic	RMER17B|LTR|ERVK	-14775	NM_001113406	16693	Mm.310906	NM_001113406	ENSMUSG00000091212	Krtap11-1	AA162070|AA589467|AV018433|Hacl1|KAP11.1|PRED29	keratin associated protein 11-1	protein-coding
mm_163544.1	chr13	17857243	17857262	+	1	NA	Intergenic	Intergenic	-52155	NM_027118	69562	Mm.193924	NM_027118	ENSMUSG00000041297	Cdk13	2310015O17Rik|Cdc2l5	cyclin-dependent kinase 13	protein-coding
mm_80222.1	chr9	72581387	72581389	+	1	NA	intron (NM_001033536, intron 2 of 8)	intron (NM_001033536, intron 2 of 8)	49148	NM_001033536	319758	Mm.32081	NM_001033536	ENSMUSG00000037674	Rfx7	2510005N23Rik|9930116O05Rik|D130086K05Rik|Rfxdc2	regulatory factor X, 7	protein-coding
mm_163370.1	chr12	38783418	38783420	+	1	NA	promoter-TSS (NM_001163154)	promoter-TSS (NM_001163154)	-292	NM_001163154	14009	Mm.4866	NM_007960	ENSMUSG00000004151	Etv1	ER81|Etsrp81	ets variant 1	protein-coding
mm_25050.1	chr3	98309156	98309169	+	1	NA	3' UTR (NM_008256, exon 10 of 10)	3' UTR (NM_008256, exon 10 of 10)	28731	NM_008256	15360	Mm.289131	NM_008256	ENSMUSG00000027875	Hmgcs2	1300002P16|mHS	3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2	protein-coding
mm_3873.1	chr1	160989696	160989702	+	1	NA	exon (NM_080844, exon 3 of 8)	exon (NM_080844, exon 3 of 8)	11093	NM_080844	11905	Mm.260770	NM_080844	ENSMUSG00000026715	Serpinc1	AI114908|ATIII|At-3|At3	serine (or cysteine) peptidase inhibitor, clade C (antithrombin), member 1	protein-coding
mm_8955.1	chr1	164460840	164460849	-	1	NA	Intergenic	MIRb|SINE|MIR	-2489	NM_009721	11931	Mm.4550	NM_009721	ENSMUSG00000026576	Atp1b1	Atp4b|Atpb|Atpb-1|NKbeta1	ATPase, Na+/K+ transporting, beta 1 polypeptide	protein-coding
mm_44820.1	chr5	33655167	33655181	-	1	NA	intron (NM_026698, intron 2 of 3)	(A)n|Simple_repeat|Simple_repeat	-2600	NM_009193	20492	Mm.4172	NM_009193	ENSMUSG00000004642	Slbp	-	stem-loop binding protein	protein-coding
mm_74040.1	chr8	121950558	121950656	+	1	NA	5' UTR (NM_001110100, exon 1 of 14)	5' UTR (NM_001110100, exon 1 of 14)	115	NM_001285983	53325	Mm.287163	NM_016812	ENSMUSG00000025316	Banp	AA408158|SMAR1	BTG3 associated nuclear protein	protein-coding
mm_127138.1	chr15	98168302	98168316	+	1	NA	5' UTR (NM_177716, exon 1 of 1)	5' UTR (NM_177716, exon 1 of 1)	503	NM_177716	239650	Mm.54140	NM_177716	ENSMUSG00000029875	Ccdc184	5630400A08|AI836003	coiled-coil domain containing 184	protein-coding
mm_87192.1	chr10	39451488	39451495	+	1	NA	intron (NM_001122892, intron 2 of 12)	intron (NM_001122892, intron 2 of 12)	81692	NM_001122893	14360	Mm.4848	NM_008054	ENSMUSG00000019843	Fyn	AI448320|AW552119	Fyn proto-oncogene	protein-coding
mm_169422.1	chr14	53173706	53173713	-	1	NA	Intergenic	Intergenic	-678014	NM_001170918	57269	Mm.88822	NM_020512	ENSMUSG00000059887	Olfr1507	MOR244-1|Mor28|Or28	olfactory receptor 1507	protein-coding
mm_135553.1	chr16	49848780	49848794	-	1	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	-6867	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_56453.1	chr6	97821894	97821898	-	1	NA	intron (NM_001113198, intron 1 of 9)	intron (NM_001113198, intron 1 of 9)	14838	NM_001113198	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_58951.1	chr7	18718200	18718212	+	1	NA	5' UTR (NM_001004152, exon 1 of 5)	5' UTR (NM_001004152, exon 1 of 5)	116	NM_001004152	243862	Mm.389833	NM_001004152	ENSMUSG00000044903	Psg22	AA408604|cea9	pregnancy-specific glycoprotein 22	protein-coding
mm_133494.1	chr16	90385948	90385969	+	1	NA	promoter-TSS (NM_015755)	promoter-TSS (NM_015755)	-439	NM_015755	26559	Mm.125874	NM_015755	ENSMUSG00000053414	Hunk	Bstk1|Mak-v	hormonally upregulated Neu-associated kinase	protein-coding
mm_72787.1	chr8	86884374	86884382	+	1	NA	intron (NM_030563, intron 1 of 6)	intron (NM_030563, intron 1 of 6)	880	NM_030563	80750	Mm.25117	NM_030563	ENSMUSG00000031652	N4bp1	AI481586|C81621	NEDD4 binding protein 1	protein-coding
mm_137090.1	chr17	21503816	21503818	+	1	NA	intron (NM_013843, intron 3 of 4)	intron (NM_013843, intron 3 of 4)	14829	NM_013843	24132	Mm.42140	NM_013843	ENSMUSG00000057409	Zfp53	D030067O06Rik|KRAZ1|Zfp-53|Zfp118|zfas8	zinc finger protein 53	protein-coding
mm_161663.1	chr17	8340863	8340863	+	1	NA	5' UTR (NM_178774, exon 1 of 2)	5' UTR (NM_178774, exon 1 of 2)	124	NM_178774	320111	Mm.442510	NM_178774	ENSMUSG00000055945	Prr18	9630019K15Rik	proline rich 18	protein-coding
mm_103082.1	chr11	69900950	69901001	-	1	NA	promoter-TSS (NM_001291119)	promoter-TSS (NM_001291119)	11	NM_001316696	70419	Mm.272859	NM_027419	ENSMUSG00000018570	2810408A11Rik	1700019L01Rik|4930470J18Rik	RIKEN cDNA 2810408A11 gene	protein-coding
mm_155959.1	chrX	105764263	105764267	+	1	NA	promoter-TSS (NM_030614)	promoter-TSS (NM_030614)	-212	NM_030614	80903	Mm.154768	NM_030614	ENSMUSG00000031230	Fgf16	-	fibroblast growth factor 16	protein-coding
mm_1603.1	chr1	74381644	74381652	+	1	NA	intron (NM_013612, intron 8 of 14)	intron (NM_013612, intron 8 of 14)	6445	NM_013612	18173	Mm.2913	NM_013612	ENSMUSG00000026177	Slc11a1	Bcg|Ity|Ity1|Lsh|Nramp|Nramp1|ity	solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1	protein-coding
mm_89194.1	chr10	86347552	86347566	+	1	NA	3' UTR (NM_011595, exon 5 of 5)	3' UTR (NM_011595, exon 5 of 5)	47147	NM_011595	21859	Mm.4871	NM_011595	ENSMUSG00000020044	Timp3	Timp-3	tissue inhibitor of metalloproteinase 3	protein-coding
mm_58349.1	chr6	147263983	147264028	-	1	NA	promoter-TSS (NM_008970)	promoter-TSS (NM_008970)	8	NM_008970	19227	Mm.28440	NM_008970	ENSMUSG00000048776	Pthlh	PLP|PTH-like|Pthrp	parathyroid hormone-like peptide	protein-coding
mm_27441.1	chr3	51789126	51789129	-	1	NA	intron (NM_001004176, intron 2 of 4)	intron (NM_001004176, intron 2 of 4)	127948	NM_001310482	211666	Mm.24679	NM_174995	ENSMUSG00000074604	Mgst2	GST2|MGST-II	microsomal glutathione S-transferase 2	protein-coding
mm_96413.1	chr11	67255422	67255440	+	1	NA	exon (NM_010855, exon 31 of 40)	exon (NM_010855, exon 31 of 40)	17619	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_70424.1	chr8	11477019	11477030	+	1	NA	promoter-TSS (NR_126558)	promoter-TSS (NR_126558)	-905	NR_126558	102132	Mm.37632	NR_126558	ENSMUSG00000096957	E230013L22Rik	AI645545	RIKEN cDNA E230013L22 gene	ncRNA
mm_25701.1	chr3	122419773	122419787	+	1	NA	promoter-TSS (NM_013867)	promoter-TSS (NM_013867)	0	NM_013867	29815	Mm.45815	NM_013867	ENSMUSG00000028121	Bcar3	AI131758|AND-34	breast cancer anti-estrogen resistance 3	protein-coding
mm_33850.1	chr4	135859201	135859205	+	1	NA	intron (NM_010178, intron 2 of 5)	intron (NM_010178, intron 2 of 5)	3132	NM_010178	14105	Mm.10229	NM_010178	ENSMUSG00000028676	Srsf10	FUSIP2|Fusip1|NSSR1|NSSR2|Nssr|SRrp40|Sfrs13a|Srsf13a|TASR|TASR1|TASR2	serine/arginine-rich splicing factor 10	protein-coding
mm_16089.1	chr2	168778633	168778633	+	1	NA	Intergenic	Intergenic	-11432	NM_175303	99377	Mm.434054	NM_175303	ENSMUSG00000027547	Sall4	5730441M18Rik|AA407717|AL022809|AW536104|C330011P20Rik|C78083|C78563|Tex20	sal-like 4 (Drosophila)	protein-coding
mm_56319.1	chr6	92246381	92246416	-	1	NA	Intergenic	Intergenic	-1748	NM_009426	22044	Mm.1363	NM_009426	ENSMUSG00000005892	Trh	Pro-TRH|Trf	thyrotropin releasing hormone	protein-coding
mm_93675.1	chr10	117710746	117710773	-	1	NA	promoter-TSS (NM_010786)	promoter-TSS (NM_010786)	-1	NM_001288586	17246	Mm.22670	NM_010786	ENSMUSG00000020184	Mdm2	1700007J15Rik|AA415488|Mdm-2	transformed mouse 3T3 cell double minute 2	protein-coding
mm_13076.1	chr2	91202904	91202934	+	1	NA	promoter-TSS (NM_007387)	promoter-TSS (NM_007387)	7	NM_007387	11432	Mm.45570	NM_007387	ENSMUSG00000002103	Acp2	Acp-2|LAP	acid phosphatase 2, lysosomal	protein-coding
mm_122410.1	chr14	41008364	41008364	-	1	NA	promoter-TSS (NM_001316740)	promoter-TSS (NM_001316740)	-98	NM_001316740	70564	Mm.27227	NM_027464	ENSMUSG00000021792	Fam213a	5730469M10Rik|AU040822|Adrx|Pamm	family with sequence similarity 213, member A	protein-coding
mm_121763.1	chr14	19755545	19755582	-	1	NA	intron (NM_008695, intron 2 of 20)	intron (NM_008695, intron 2 of 20)	4306	NM_008695	18074	Mm.20348	NM_008695	ENSMUSG00000021806	Nid2	AW547149|Ly111|NID-2|entactin-2|nidogen-2	nidogen 2	protein-coding
mm_8834.1	chr1	162571495	162571505	-	1	NA	intron (NM_001347125, intron 1 of 7)	CpG	672	NM_001347125	53330	Mm.10699	NM_016796	ENSMUSG00000026696	Vamp4	D1Ertd147e	vesicle-associated membrane protein 4	protein-coding
mm_91849.1	chr10	58675632	58675654	-	1	NA	promoter-TSS (NM_010100)	promoter-TSS (NM_010100)	53	NM_010100	13608	Mm.174523	NM_010100	ENSMUSG00000003227	Edar	ED1R|ED3|ED5|EDA-A1R|EDA3|dl	ectodysplasin-A receptor	protein-coding
mm_132134.1	chr16	31897597	31897619	+	1	NA	3' UTR (NM_013900, exon 16 of 16)	3' UTR (NM_013900, exon 16 of 16)	18798	NM_013900	30060	Mm.30988	NM_013900	ENSMUSG00000022780	Mfi2	CD228|MTf|Meltf	antigen p97 (melanoma associated) identified by monoclonal antibodies 133.2 and 96.5	protein-coding
mm_55509.1	chr6	69901123	69901132	-	1	NA	Intergenic	Intergenic	-573953	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_135426.1	chr16	45382600	45382609	-	1	NA	3' UTR (NM_010818, exon 6 of 6)	3' UTR (NM_010818, exon 6 of 6)	26449	NM_010818	17470	Mm.245851	NM_010818	ENSMUSG00000022661	Cd200	Mox2|OX2	CD200 antigen	protein-coding
mm_165961.1	chr4	89447352	89447352	+	1	NA	intron (NR_132431, intron 5 of 9)	intron (NR_132431, intron 5 of 9)	-136320	NM_007670	12579	Mm.423094	NM_007670	ENSMUSG00000073802	Cdkn2b	AV083695|INK4b|MTS2|p15|p15(INK4b)|p15INK4b	cyclin-dependent kinase inhibitor 2B (p15, inhibits CDK4)	protein-coding
mm_78777.1	chr9	43794144	43794157	+	1	NA	exon (NM_021424, exon 5 of 6)	exon (NM_021424, exon 5 of 6)	49574	NM_021424	58235	Mm.335096	NM_021424	ENSMUSG00000032012	Nectin1	AI835281|AW549174|Cd111|HIgR|HveC|PRR|PRR1|Pvrl1|nectin-1	nectin cell adhesion molecule 1	protein-coding
mm_35160.1	chr4	12865471	12865472	-	1	NA	Intergenic	Intergenic	-41366	NM_173746	208820	Mm.12057	NM_173746	ENSMUSG00000055963	Triqk	C130086A10|Gm11818|OTTMUSG00000004461	triple QxxK/R motif containing	protein-coding
mm_84808.1	chr9	77347769	77347782	-	1	NA	promoter-TSS (NM_027150)	promoter-TSS (NM_027150)	95	NM_027150	69642	Mm.35008	NM_027150	ENSMUSG00000032355	Mlip	2310046A06Rik|AI931782|CIP	muscular LMNA-interacting protein	protein-coding
mm_22136.1	chr2	170470712	170470720	-	1	NA	Intergenic	RLTR51B_Mm|LTR|ERVK?	-25712	NM_001013369	109054	Mm.28808	NM_001013369	ENSMUSG00000052033	Pfdn4	0610025M10Rik|1810063B06Rik|C-1|C1|Pfd4	prefoldin 4	protein-coding
mm_49181.1	chr6	15184632	15184662	+	1	NA	promoter-TSS (NM_001286607)	promoter-TSS (NM_001286607)	-859	NM_212435	114142	Mm.332919	NM_053242	ENSMUSG00000029563	Foxp2	2810043D05Rik|AI449000|CAG-16|D0Kist7	forkhead box P2	protein-coding
mm_30959.1	chr4	33924015	33924040	+	1	NA	promoter-TSS (NM_007726)	promoter-TSS (NM_007726)	-605	NM_007726	12801	Mm.7992	NM_007726	ENSMUSG00000044288	Cnr1	CB-R|CB1|CB1R	cannabinoid receptor 1 (brain)	protein-coding
mm_88977.1	chr10	81525396	81525419	+	1	NA	Intergenic	Intergenic	-1182	NM_010304	14676	Mm.1546	NM_010304	ENSMUSG00000034792	Gna15	G[a]15|Galpha15	guanine nucleotide binding protein, alpha 15	protein-coding
mm_14999.1	chr2	152427640	152427699	+	1	NA	non-coding (NR_110368, exon 2 of 11)	non-coding (NR_110368, exon 2 of 11)	12082	NR_110368	228778	Mm.70959	NM_177656	ENSMUSG00000032680	6820408C15Rik	-	RIKEN cDNA 6820408C15 gene	protein-coding
mm_59578.1	chr7	28129103	28129106	+	1	NA	promoter-TSS (NM_001164655)	promoter-TSS (NM_001164655)	-362	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_9628.1	chr1	176813921	176813931	-	1	NA	promoter-TSS (NM_029756)	promoter-TSS (NM_029756)	-734	NM_029756	76816	Mm.171399	NM_029756	ENSMUSG00000026504	Sdccag8	2700048G21Rik|5730470G24Rik|Cccap	serologically defined colon cancer antigen 8	protein-coding
mm_55735.1	chr6	77394428	77394433	-	1	NA	intron (NM_001109764, intron 8 of 19)	Lx9|LINE|L1	-11955	NR_045141	70753	Mm.490700	NR_045141	ENSMUSG00000108077	6330415B21Rik	-	RIKEN cDNA 6330415B21 gene	ncRNA
mm_27809.1	chr3	78594340	78594365	-	1	NA	Intergenic	Intergenic	550535	NM_001310536	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_34113.1	chr4	139197738	139197739	+	1	NA	intron (NM_001271405, intron 1 of 8)	intron (NM_001271405, intron 1 of 8)	3627	NM_001271405	12345	Mm.2945	NM_009798	ENSMUSG00000028745	Capzb	1700120C01Rik|AI325129|CPB1|CPB2|CPbeat2|CPbeta1|CPbeta2|Cappb1	capping protein (actin filament) muscle Z-line, beta	protein-coding
mm_87421.1	chr10	50727186	50727199	+	1	NA	intron (NM_198007, intron 24 of 41)	Lx3A|LINE|L1	134523	NM_198007	77987	Mm.222497	NM_198007	ENSMUSG00000038774	Ascc3	ASC1p200|B630009I04Rik|BC023451|D430001L07Rik|D630041L21|Helic1|RNAH	activating signal cointegrator 1 complex subunit 3	protein-coding
mm_29984.1	chr3	135423476	135423486	-	1	NA	promoter-TSS (NM_025902)	promoter-TSS (NM_025902)	-48	NM_025902	67006	Mm.269993	NM_025902	ENSMUSG00000028165	Cisd2	1500009M05Rik|1500026J14Rik|1500031D15Rik|AI848398|B630006A20Rik|Miner1|Naf-1|Noxp70|Zcd2	CDGSH iron sulfur domain 2	protein-coding
mm_148275.1	chr18	81927645	81927662	-	1	NA	Intergenic	Intergenic	64427	NR_039589	100628596		NR_039589	ENSMUSG00000093036	Mir5127	mmu-mir-5127|mu-mir-5127	microRNA 5127	ncRNA
mm_114581.1	chr13	75707485	75707510	+	1	NA	promoter-TSS (NM_138953)	promoter-TSS (NM_138953)	13	NM_138953	192657	Mm.21288	NM_138953	ENSMUSG00000001542	Ell2	-	elongation factor RNA polymerase II 2	protein-coding
mm_23114.1	chr3	37639665	37639693	+	1	NA	promoter-TSS (NM_011896)	promoter-TSS (NM_011896)	-268	NM_001305441	24063	Mm.330986	NM_011896	ENSMUSG00000037211	Spry1	sprouty1|spry-1	sprouty homolog 1 (Drosophila)	protein-coding
mm_67900.1	chr7	99626905	99626933	-	1	NA	5' UTR (NM_001195529, exon 1 of 1)	5' UTR (NM_001195529, exon 1 of 1)	184	NM_001195529	100503386	Mm.180719	NM_001195529	ENSMUSG00000096606	Tpbgl	EG245190|Gm4980	trophoblast glycoprotein-like	protein-coding
mm_139368.1	chr17	51479692	51479693	+	1	NA	intron (NR_037250, intron 3 of 4)	intron (NR_037250, intron 3 of 4)	-31423	NR_046166	328837	Mm.236143	NR_046166		C330011F03Rik	C330011F03	RIKEN cDNA C330011F03 gene	ncRNA
mm_84024.1	chr9	57683645	57683663	-	1	NA	promoter-TSS (NM_009993)	promoter-TSS (NM_009993)	1	NM_009993	13077	Mm.15537	NM_009993	ENSMUSG00000032310	Cyp1a2	CP12|Cyp1a1|P450-3	cytochrome P450, family 1, subfamily a, polypeptide 2	protein-coding
mm_15703.1	chr2	163995151	163995229	+	1	NA	promoter-TSS (NM_018753)	promoter-TSS (NM_018753)	-7	NM_018753	54401	Mm.34319	NM_018753	ENSMUSG00000018326	Ywhab	1300003C17Rik|14-3-3b	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta polypeptide	protein-coding
mm_16911.1	chr2	13493652	13493657	-	1	NA	Intergenic	Intergenic	-1778	NM_001081084	65969	Mm.313915	NM_001081084	ENSMUSG00000026726	Cubn	AA408369|AL022750|D2Wsu88e	cubilin (intrinsic factor-cobalamin receptor)	protein-coding
mm_144433.1	chr18	21002027	21002035	+	1	NA	promoter-TSS (NM_207623)	promoter-TSS (NM_207623)	74	NM_207623	56515	Mm.253542	NM_019706	ENSMUSG00000024317	Rnf138	2410015A17Rik|2810480D20Rik|STRIN|Trif|Trif-d	ring finger protein 138	protein-coding
mm_128247.1	chr15	36609512	36609528	-	1	NA	promoter-TSS (NM_008774)	promoter-TSS (NM_008774)	-547	NM_008774	18458	Mm.371570	NM_008774	ENSMUSG00000022283	Pabpc1	PABP|Pabp1|PabpI|Pabpl1|ePAB	poly(A) binding protein, cytoplasmic 1	protein-coding
mm_59747.1	chr7	28818780	28818807	+	1	NA	exon (NM_177301, exon 8 of 13)	exon (NM_177301, exon 8 of 13)	-6545	NM_016772	51798	Mm.291776	NM_016772	ENSMUSG00000053898	Ech1	AA617331	enoyl coenzyme A hydratase 1, peroxisomal	protein-coding
mm_155421.1	chrX	73491966	73492004	+	1	NA	exon (NM_007542, exon 4 of 8)	exon (NM_007542, exon 4 of 8)	8384	NM_007542	12111	Mm.2608	NM_007542	ENSMUSG00000031375	Bgn	BG|DSPG1|PG-S1|PGI|SLRR1A	biglycan	protein-coding
mm_166758.1	chr6	128526854	128526854	+	1	NA	promoter-TSS (NM_007376)	promoter-TSS (NM_007376)	-134	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_160322.1	chr7	144861316	144861316	+	1	NA	promoter-TSS (NM_010202)	promoter-TSS (NM_010202)	-70	NM_010202	14175	Mm.4956	NM_010202	ENSMUSG00000050917	Fgf4	Fgf-4|Fgfk|HBGF-4|Hst1|Hstf-1|KS3|hst|hst-1|kFGF	fibroblast growth factor 4	protein-coding
mm_108007.1	chr12	73584663	73584687	+	1	NA	promoter-TSS (NM_008856)	promoter-TSS (NM_008856)	-121	NM_001313977	18755	Mm.341677	NM_008856	ENSMUSG00000021108	Prkch	Pkch	protein kinase C, eta	protein-coding
mm_156689.1	chrX	159414638	159414655	+	1	NA	promoter-TSS (NM_001081124)	promoter-TSS (NM_001081124)	74	NM_001313751	78283	Mm.160079	NM_001081124	ENSMUSG00000041020	Map7d2	1600028E09Rik|2900002G04Rik|5330432J06Rik|C030036K04Rik|Mtap7d2	MAP7 domain containing 2	protein-coding
mm_3687.1	chr1	153749497	153749523	+	1	NA	promoter-TSS (NM_011882)	promoter-TSS (NM_011882)	84	NM_011882	24014	Mm.259254	NM_011882	ENSMUSG00000066800	Rnasel	E230029I04Rik	ribonuclease L (2', 5'-oligoisoadenylate synthetase-dependent)	protein-coding
mm_150095.1	chr19	29457864	29457887	+	1	NA	intron (NM_021396, intron 5 of 5)	RCHARR1|DNA|hAT-Charlie	46956	NM_021396	58205	Mm.116737	NM_021396	ENSMUSG00000016498	Pdcd1lg2	B7-DC|Btdc|F730015O22Rik|PD-L2	programmed cell death 1 ligand 2	protein-coding
mm_68385.1	chr7	109439026	109439066	-	1	NA	promoter-TSS (NM_054103)	promoter-TSS (NM_054103)	7	NM_054103	117229	Mm.389950	NM_054103	ENSMUSG00000031027	Stk33	4921505G21Rik|AW061264	serine/threonine kinase 33	protein-coding
mm_70405.1	chr8	11336214	11336224	+	1	NA	intron (NM_009932, intron 3 of 47)	intron (NM_009932, intron 3 of 47)	-23393	NM_009931	12826	Mm.738	NM_009931	ENSMUSG00000031502	Col4a1	Bru|Col4a-1|Raw|Svc	collagen, type IV, alpha 1	protein-coding
mm_30853.1	chr4	28353708	28353708	+	1	NA	Intergenic	Intergenic	-459423	NM_001290434	13841	Mm.257266	NM_010141	ENSMUSG00000028289	Epha7	Cek11|Ebk|Ehk3|Hek11|Mdk1	Eph receptor A7	protein-coding
mm_99832.1	chr11	108941568	108941571	+	1	NA	intron (NM_015732, intron 4 of 10)	intron (NM_015732, intron 4 of 10)	21220	NM_015732	12006	Mm.71710	NM_015732	ENSMUSG00000000142	Axin2	Axi1|Axil|Conductin	axin 2	protein-coding
mm_13161.1	chr2	92600071	92600096	+	1	NA	5' UTR (NM_023850, exon 1 of 3)	5' UTR (NM_023850, exon 1 of 3)	376	NM_023850	76969	Mm.38021	NM_023850	ENSMUSG00000027221	Chst1	2610008E20Rik|AW125896|C6ST|GST-1|Gst1|KSGAL6ST	carbohydrate (keratan sulfate Gal-6) sulfotransferase 1	protein-coding
mm_168359.1	chr1	114809402	114809403	-	1	NA	Intergenic	MYSERV16_I-int|LTR|ERVK	-875735	NM_001077425	636808	Mm.101576	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding
mm_128455.1	chr15	50774642	50774651	-	1	NA	intron (NM_001310485, intron 5 of 7)	intron (NM_001310485, intron 5 of 7)	114403	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_26016.1	chr3	135438145	135438153	+	1	NA	promoter-TSS (NM_025356)	promoter-TSS (NM_025356)	516	NR_030689	319587	Mm.358971	NR_030689	ENSMUSG00000097032	4930539J05Rik	8030475D13Rik	RIKEN cDNA 4930539J05 gene	ncRNA
mm_147734.1	chr18	61036212	61036226	-	1	NA	promoter-TSS (NM_009880)	promoter-TSS (NM_009880)	-20	NM_009880	12590	Mm.144448	NM_009880	ENSMUSG00000024619	Cdx1	Cdx|Cdx-1	caudal type homeobox 1	protein-coding
mm_107587.1	chr12	47812878	47812889	+	1	NA	Intergenic	Intergenic	488579	NR_039586	100628593		NR_039586	ENSMUSG00000092981	Mir5125	mmu-mir-5125|mu-mir-5125	microRNA 5125	ncRNA
mm_3355.1	chr1	138166771	138166782	+	1	NA	intron (NM_001111316, intron 1 of 31)	intron (NM_001111316, intron 1 of 31)	8350	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_112259.1	chr12	113897005	113897010	-	1	NA	Intergenic	Intergenic	353099	NM_174885	238406	Mm.188683	NM_174885	ENSMUSG00000043945	Adam6a	Adam6|tMDCIV	a disintegrin and metallopeptidase domain 6A	protein-coding
mm_118525.1	chr14	14748313	14748318	+	1	NA	intron (NM_001033270, intron 7 of 24)	intron (NM_001033270, intron 7 of 24)	45290	NM_001033270	218756	Mm.258893	NM_001033270	ENSMUSG00000021733	Slc4a7	E430014N10Rik|NBC3|NBCn1|NBCn1-G	solute carrier family 4, sodium bicarbonate cotransporter, member 7	protein-coding
mm_60977.1	chr7	48959052	48959085	+	1	NA	promoter-TSS (NM_001111016)	promoter-TSS (NM_001111016)	-5	NM_001111016	78286	Mm.333881	NM_175272	ENSMUSG00000052512	Nav2	5330421F07Rik|AU067780|BQ960892|HELAD1|POMFIL2|RAINB1|RAINB2|Unc53H2|mKIAA3015	neuron navigator 2	protein-coding
mm_160106.1	chr7	23658550	23658550	+	1	NA	intron (NM_030735, intron 1 of 1)	intron (NM_030735, intron 1 of 1)	234	NM_030735	81010	Mm.379267	NM_030735	ENSMUSG00000035523	Vmn1r172	V1rd9|V3R9	vomeronasal 1 receptor 172	protein-coding
mm_55168.1	chr6	51915870	51915891	-	1	NA	intron (NM_018773, intron 6 of 12)	intron (NM_018773, intron 6 of 12)	96669	NM_018773	54353	Mm.221479	NM_018773	ENSMUSG00000059182	Skap2	2610021A10Rik|AA960083|BB137539|RA70|SKAP-HOM|Saps|Scap2|mSKAP55R	src family associated phosphoprotein 2	protein-coding
mm_58593.1	chr7	5020416	5020426	+	1	NA	promoter-TSS (NM_001290426)	promoter-TSS (NM_001290426)	45	NM_001033383	319748	Mm.86607	NM_001033383	ENSMUSG00000074405	Zfp865	6430526N21Rik|Znf865	zinc finger protein 865	protein-coding
mm_15666.1	chr2	163323404	163323424	+	1	NA	TTS (NM_001098799)	TTS (NM_001098799)	74559	NM_021566	59091	Mm.34459	NM_021566	ENSMUSG00000017817	Jph2	1110002E14Rik|JP-2|Jp2	junctophilin 2	protein-coding
mm_71306.1	chr8	41374840	41374881	+	1	NA	promoter-TSS (NM_019734)	promoter-TSS (NM_019734)	-163	NM_019734	11886	Mm.22547	NM_019734	ENSMUSG00000031591	Asah1	2310081N20Rik|AC|Asah	N-acylsphingosine amidohydrolase 1	protein-coding
mm_146455.1	chr18	86395276	86395285	+	1	NA	5' UTR (NM_144946, exon 1 of 11)	5' UTR (NM_144946, exon 1 of 11)	328	NM_144946	246317	Mm.329578	NM_144946	ENSMUSG00000050321	Neto1	AI851453|Btcl1|C130005O10Rik	neuropilin (NRP) and tolloid (TLL)-like 1	protein-coding
mm_68091.1	chr7	101921176	101921181	-	1	NA	promoter-TSS (NM_001162974)	promoter-TSS (NM_001162974)	-404	NM_001162974	69358	Mm.214841	NM_027053	ENSMUSG00000064307	Lrrc51	1700008D07Rik|Lrtomt	leucine rich repeat containing 51	protein-coding
mm_38609.1	chr4	141871083	141871118	-	1	NA	intron (NM_025994, intron 1 of 3)	intron (NM_025994, intron 1 of 3)	3820	NM_025994	27984	Mm.395598	NM_025994	ENSMUSG00000040659	Efhd2	2600015J22Rik|AA408606|D4Wsu27e	EF hand domain containing 2	protein-coding
mm_147633.1	chr18	58210764	58210771	-	1	NA	promoter-TSS (NM_010181)	promoter-TSS (NM_010181)	-841	NM_010181	14119	Mm.20271	NM_010181	ENSMUSG00000024598	Fbn2	BC063774|Fib-2|mKIAA4226|sne|sy	fibrillin 2	protein-coding
mm_8421.1	chr1	152386627	152386666	-	1	NA	promoter-TSS (NM_025677)	promoter-TSS (NM_025677)	36	NM_025677	66637	Mm.379120	NM_025677	ENSMUSG00000014980	Tsen15	5730449L18Rik|AL023077|Sen15	tRNA splicing endonuclease subunit 15	protein-coding
mm_168520.1	chr11	58214986	58214987	+	1	NA	promoter-TSS (NM_019440)	promoter-TSS (NM_019440)	9	NM_019440	54396	Mm.458517	NM_019440	ENSMUSG00000069874	Irgm2	AI481100|GTPI|Ifggd2|Iigp2	immunity-related GTPase family M member 2	protein-coding
mm_26867.1	chr3	16183643	16183687	-	1	NA	intron (NR_027375, intron 1 of 5)	CpG	482	NM_001145919	229096	Mm.23834	NM_172677	ENSMUSG00000047213	Ythdf3	9130022A11Rik	YTH domain family 3	protein-coding
mm_75626.1	chr8	64692450	64692454	-	1	NA	intron (NM_013494, intron 1 of 8)	intron (NM_013494, intron 1 of 8)	657	NM_013494	12876	Mm.31395	NM_013494	ENSMUSG00000037852	Cpe	CPH|Cph-1|Cph1|R74677|fat	carboxypeptidase E	protein-coding
mm_87822.1	chr10	60347282	60347292	+	1	NA	intron (NM_028732, intron 1 of 6)	intron (NM_028732, intron 1 of 6)	436	NM_028732	74048	Mm.273584	NM_028732	ENSMUSG00000020101	Vsir	4632428N05Rik|Dies1|PD-1H|VISTA	V-set immunoregulatory receptor	protein-coding
mm_124142.1	chr14	87141159	87141203	-	1	NA	promoter-TSS (NM_019670)	promoter-TSS (NM_019670)	-67	NM_019670	56419	Mm.440585	NM_019670	ENSMUSG00000022021	Diaph3	4930417P13Rik|Dia2|Diap3|Drf3|mDia2|mKIAA4117|p134MDia2	diaphanous related formin 3	protein-coding
mm_99721.1	chr11	106300306	106300336	+	1	NA	TTS (NM_008117)	TTS (NM_008117)	1575	NM_008117	14599	Mm.343934	NM_008117	ENSMUSG00000020713	Gh	Gh1|Ghb1	growth hormone	protein-coding
mm_163038.1	chr11	53350925	53350931	+	1	NA	5' UTR (NM_033565, exon 1 of 21)	5' UTR (NM_033565, exon 1 of 21)	161	NM_033565	93736	Mm.395281	NM_033565	ENSMUSG00000049470	Aff4	AF5Q31|Alf4|Laf4l|MCEF	AF4/FMR2 family, member 4	protein-coding
mm_48602.1	chr5	144243991	144244009	-	1	NA	promoter-TSS (NM_001163709)	promoter-TSS (NM_001163709)	-437	NM_001163709	55950	Mm.38011	NM_018772	ENSMUSG00000047843	Bri3	I3	brain protein I3	protein-coding
mm_171824.1	chr5	142903865	142903868	-	1	NA	exon (NM_007393, exon 6 of 6)	exon (NM_007393, exon 6 of 6)	2888	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_139792.1	chr17	65886469	65886479	+	1	NA	promoter-TSS (NM_009067)	promoter-TSS (NM_009067)	-719	NM_009067	19765	Mm.17009	NM_009067	ENSMUSG00000024096	Ralbp1	RLIP76|Rip1	ralA binding protein 1	protein-coding
mm_146893.1	chr18	27129960	27129962	-	1	NA	Intergenic	Lx9|LINE|L1	-1375978	NM_001174074	108013	Mm.266435	NM_133195	ENSMUSG00000024268	Celf4	A230070D14Rik|BRUNOL-4|Brul4|Brunol4|C130060B05Rik	CUGBP, Elav-like family member 4	protein-coding
mm_124733.1	chr15	6580879	6580900	+	1	NA	exon (NM_001278269, exon 1 of 17)	exon (NM_001278269, exon 1 of 17)	1042	NM_011815	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_115525.1	chr13	5864306	5864314	-	1	NA	intron (NM_011803, intron 1 of 3)	intron (NM_011803, intron 1 of 3)	2821	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_32099.1	chr4	98546898	98546909	+	1	NA	5' UTR (NM_007704, exon 1 of 18)	5' UTR (NM_007704, exon 1 of 18)	269	NM_001005787	12695	Mm.90218	NM_007704	ENSMUSG00000061859	Patj	Cipp|Inadl	PATJ, crumbs cell polarity complex component	protein-coding
mm_41136.1	chr5	87811351	87811353	+	1	NA	intron (NM_001301334, intron 2 of 11)	Lx6|LINE|L1	3231	NM_009973	12992	Mm.153308	NM_009973	ENSMUSG00000061388	Csn1s2b	AW987150|Csnd|Csne	casein alpha s2-like B	protein-coding
mm_66554.1	chr7	45233725	45233745	-	1	NA	TTS (NM_001285498)	TTS (NM_001285498)	5104	NM_007645	12493	Mm.3689	NM_007645	ENSMUSG00000030798	Cd37	Tspan26	CD37 antigen	protein-coding
mm_106526.1	chr11	120572823	120572842	-	1	NA	5' UTR (NM_011032, exon 1 of 11)	5' UTR (NM_011032, exon 1 of 11)	104	NM_011032	18453	Mm.16660	NM_011032	ENSMUSG00000025130	P4hb	ERp59|PDI|Pdia1|Thbp	prolyl 4-hydroxylase, beta polypeptide	protein-coding
mm_91890.1	chr10	59951518	59951528	-	1	NA	5' UTR (NM_029083, exon 2 of 3)	5' UTR (NM_029083, exon 2 of 3)	247	NM_029083	74747	Mm.21697	NM_029083	ENSMUSG00000020108	Ddit4	5830413E08Rik|AA415483|REDD1|Rtp801|dig2	DNA-damage-inducible transcript 4	protein-coding
mm_49315.1	chr6	18369271	18369271	+	1	NA	intron (NM_080285, intron 22 of 22)	intron (NM_080285, intron 22 of 22)	145554	NM_080285	30785	Mm.224189	NM_080285	ENSMUSG00000000416	Cttnbp2	3010022N24Rik|4732477G22Rik|6430526E05|9130022E09Rik|AU040881|Cortbp2|ORF4|mKIAA1758	cortactin binding protein 2	protein-coding
mm_144472.1	chr18	23880454	23880454	+	1	NA	intron (NM_153058, intron 5 of 6)	PB1D10|SINE|Alu	-74234	NM_027007	69256	Mm.218343	NM_027007	ENSMUSG00000024276	Zfp397	2810411K16Rik|6720480F11Rik|AI461664	zinc finger protein 397	protein-coding
mm_171161.1	chr3	24333043	24333062	+	1	NA	intron (NM_001326288, intron 5 of 13)	intron (NM_001326288, intron 5 of 13)	450954	NM_001326288	635702	Mm.448351	NM_001326288	ENSMUSG00000102758	Naaladl2	2810043G22Rik|EG635702|Gm1021	N-acetylated alpha-linked acidic dipeptidase-like 2	protein-coding
mm_92178.1	chr10	67901264	67901270	-	1	NA	intron (NM_178679, intron 2 of 4)	MTE2b|LTR|ERVL-MaLR	11395	NM_178679	216049	Mm.268346	NM_178679	ENSMUSG00000037855	Zfp365	AI839779|AV340892|DBZ|Su48|Znf365|talanin	zinc finger protein 365	protein-coding
mm_136785.1	chr17	10703203	10703207	+	1	NA	intron (NM_027032, intron 2 of 4)	intron (NM_027032, intron 2 of 4)	136986	NM_027032	69310	Mm.18889	NM_027032	ENSMUSG00000037196	Pacrg	1700008H23Rik	PARK2 co-regulated	protein-coding
mm_117509.1	chr13	78200557	78200565	-	1	NA	intron (NR_045195, intron 1 of 2)	intron (NR_045195, intron 1 of 2)	-1688	NM_010151	13865	Mm.439653	NM_010151	ENSMUSG00000069171	Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR-3|EAR3|Erbal3|SVP44|Tcfcoup1	nuclear receptor subfamily 2, group F, member 1	protein-coding
mm_54174.1	chr6	23655130	23655140	-	1	NA	promoter-TSS (NM_027754)	promoter-TSS (NM_027754)	1	NM_027754	71300	Mm.443309	NM_027754	ENSMUSG00000078179	Rnf148	4933432M07Rik|Greul3	ring finger protein 148	protein-coding
mm_11241.1	chr2	29889218	29889243	+	1	NA	promoter-TSS (NM_001113213)	promoter-TSS (NM_001113213)	-490	NM_001177661	18286	Mm.330116	NM_013615	ENSMUSG00000026790	Odf2	AI848335|MMTEST29	outer dense fiber of sperm tails 2	protein-coding
mm_65903.1	chr7	30192945	30192951	-	1	NA	intron (NM_009795, intron 2 of 10)	intron (NM_009795, intron 2 of 10)	2100	NM_009795	12336	Mm.439782	NM_009795	ENSMUSG00000001794	Capns1	Capa-4|Capa4|Capn4|D7Ertd146e	calpain, small subunit 1	protein-coding
mm_15758.1	chr2	164277147	164277205	+	1	NA	exon (NM_009300, exon 2 of 3)	exon (NM_009300, exon 2 of 3)	1131	NM_009300	20941	Mm.1286	NM_009300	ENSMUSG00000016998	Svs4	SVS-IV|Svp-2|Svp-4|Svp2|Svp4	seminal vesicle secretory protein 4	protein-coding
mm_172864.1	chr9	40803737	40803750	+	1	NA	exon (NM_031165, exon 6 of 9)	exon (NM_031165, exon 6 of 9)	2470	NM_031165	15481	Mm.290774	NM_031165	ENSMUSG00000015656	Hspa8	2410008N15Rik|Hsc70|Hsc71|Hsc73|Hsp73|Hspa10	heat shock protein 8	protein-coding
mm_8060.1	chr1	135375251	135375264	-	1	NA	promoter-TSS (NM_175259)	promoter-TSS (NM_175259)	-194	NM_175259	77552	Mm.41407	NM_175259	ENSMUSG00000041889	Shisa4	9330132O05Rik|Tmem58|mShisa4	shisa family member 4	protein-coding
mm_95091.1	chr11	33940209	33940251	+	1	NA	intron (NM_001190886, intron 1 of 7)	RLTR14_RN|LTR|ERV1	-22783	NM_031169	16533	Mm.6206	NM_031169	ENSMUSG00000020155	Kcnmb1	BKbeta1	potassium large conductance calcium-activated channel, subfamily M, beta member 1	protein-coding
mm_9824.1	chr1	182517369	182517399	-	1	NA	promoter-TSS (NM_009794)	promoter-TSS (NM_009794)	99	NM_009794	12334	Mm.19306	NM_009794	ENSMUSG00000026509	Capn2	AI326419|Capa-2|Capa2|m-calpain|m-calpin	calpain 2	protein-coding
mm_133508.1	chr16	90738301	90738311	+	1	NA	promoter-TSS (NM_029844)	promoter-TSS (NM_029844)	-18	NM_029844	77037	Mm.22455	NM_029844	ENSMUSG00000039956	Mrap	1110025G12Rik|Falp|ORF61	melanocortin 2 receptor accessory protein	protein-coding
mm_50592.1	chr6	49068484	49068504	+	1	NA	Intergenic	Intergenic	-5301	NM_029353	75593	Mm.439947	NM_029353	ENSMUSG00000029815	Malsu1	2410003K15Rik|Matsu1	mitochondrial assembly of ribosomal large subunit 1	protein-coding
mm_165772.1	chr3	126997994	126998021	-	1	NA	intron (NM_001327938, intron 21 of 47)	intron (NM_001327938, intron 21 of 47)	445	NM_178655	109676	Mm.220242	NM_178655	ENSMUSG00000032826	Ank2	100043364|AI835472|AW491075|Ank-2|Gm4392	ankyrin 2, brain	protein-coding
mm_5368.1	chr1	28895558	28895568	-	1	NA	Intergenic	Intergenic	-115311	NM_001013750	210962	Mm.214178	NM_001013750	ENSMUSG00000048411	Gm597	-	predicted gene 597	protein-coding
mm_16978.1	chr2	18028645	18028655	-	1	NA	non-coding (NR_028378, exon 1 of 1)	non-coding (NR_028378, exon 1 of 1)	1401	NR_028378	100034739	Mm.401643	NR_028378		Gm17762	-	predicted gene, 17762	ncRNA
mm_102823.1	chr11	69059425	69059443	-	1	NA	promoter-TSS (NM_028005)	promoter-TSS (NM_028005)	-341	NM_028005	71923	Mm.340257	NM_028005	ENSMUSG00000045176	Borcs6	2310047M10Rik	BLOC-1 related complex subunit 6	protein-coding
mm_37955.1	chr4	133339165	133339183	-	1	NA	5' UTR (NM_199306, exon 1 of 16)	5' UTR (NM_199306, exon 1 of 16)	141	NM_199306	230796	Mm.226576	NM_199306	ENSMUSG00000037622	Wdtc1	Gm695|adipose|adp	WD and tetratricopeptide repeats 1	protein-coding
mm_169478.1	chr14	69609166	69609173	+	1	NA	promoter-TSS (NM_033325)	promoter-TSS (NM_033325)	-307	NM_033325	94352	Mm.116714	NM_033325	ENSMUSG00000034205	Loxl2	1110004B06Rik|4930526G11Rik|9430067E15Rik	lysyl oxidase-like 2	protein-coding
mm_96996.1	chr11	70702286	70702296	+	1	NA	intron (NM_153103, intron 1 of 22)	intron (NM_153103, intron 1 of 22)	1743	NM_153103	16562	Mm.99996	NM_153103	ENSMUSG00000020821	Kif1c	B430105J22Rik|D11Bwg1349e|Ltxs1|Orch3	kinesin family member 1C	protein-coding
mm_154880.1	chrX	20696546	20696558	+	1	NA	exon (NM_011049, exon 11 of 16)	exon (NM_011049, exon 11 of 16)	-7357	NM_145628	236733	Mm.34489	NM_145628	ENSMUSG00000031066	Usp11	6230415D12Rik|mKIAA4085	ubiquitin specific peptidase 11	protein-coding
mm_31957.1	chr4	86857447	86857478	+	1	NA	promoter-TSS (NM_009096)	promoter-TSS (NM_009096)	-95	NM_009096	20104	Mm.379007	NM_009096	ENSMUSG00000028495	Rps6	S6R	ribosomal protein S6	protein-coding
mm_146472.1	chr18	88972003	88972040	+	1	NA	promoter-TSS (NR_105777)	promoter-TSS (NR_105777)	-9	NR_105777	102466633		NR_105777	ENSMUSG00000098676	Mir6359	Gm27328|mmu-mir-6359	microRNA 6359	ncRNA
mm_153209.1	chr19	34716850	34716856	-	1	NA	intron (NM_172838, intron 1 of 6)	MTD|LTR|ERVL-MaLR	30258	NM_172838	240638	Mm.74636	NM_172838	ENSMUSG00000009378	Slc16a12	3230401A21|AW210596	solute carrier family 16 (monocarboxylic acid transporters), member 12	protein-coding
mm_105516.1	chr11	106272030	106272035	-	1	NA	intron (NM_001130187, intron 1 of 12)	(A)n|Simple_repeat|Simple_repeat	940	NM_001130187	83796	Mm.21772	NM_031878	ENSMUSG00000078619	Smarcd2	AW322457|Baf60b	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2	protein-coding
mm_156127.1	chrX	117709394	117709431	+	1	NA	Intergenic	Intergenic	694655	NM_001102665	100039319	Mm.469831	NM_001102665	ENSMUSG00000067441	Gm14920	ENSMUSG00000067441|Gm1539|H2A.Bbd1|H2A.Lap1|OTTMUSG00000018481	predicted pseudogene 14920	protein-coding
mm_109273.1	chr12	109545943	109545956	+	1	NA	non-coding (NR_003633, exon 1 of 5)	non-coding (NR_003633, exon 1 of 5)	551	NR_003633	17263	Mm.289645	NM_144513	ENSMUSG00000021268	Meg3	2900016C05Rik|3110050O07Rik|6330408G06Rik|AI425946|AW108224|D12Bwg1266e|Gtl2|R74756|R75394	maternally expressed 3	ncRNA
mm_110165.1	chr12	27160499	27160522	-	1	NA	promoter-TSS (NR_045869)	promoter-TSS (NR_045869)	6	NR_045868	636791	Mm.423496	NM_001039248	ENSMUSG00000094002	Gm9866	EG636791|ENSMUSG00000052076	predicted gene 9866	ncRNA
mm_143606.1	chr17	78418084	78418128	-	1	NA	promoter-TSS (NM_199448)	promoter-TSS (NM_199448)	46	NM_001285949	225020	Mm.236835	NM_199448	ENSMUSG00000056121	Fez2	9030616F16|D17Ertd315e	fasciculation and elongation protein zeta 2 (zygin II)	protein-coding
mm_158374.1	chrX	135210622	135210630	-	1	NA	promoter-TSS (NM_025355)	promoter-TSS (NM_025355)	61	NM_025355	66104	Mm.336239	NM_025355	ENSMUSG00000031409	Tceal6	1500026B10Rik	transcription elongation factor A (SII)-like 6	protein-coding
mm_69278.1	chr7	127993171	127993185	-	1	NA	intron (NM_023258, intron 1 of 2)	intron (NM_023258, intron 1 of 2)	689	NM_023258	66824	Mm.24163	NM_023258	ENSMUSG00000030793	Pycard	9130417A21Rik|Asc|CARD5|TMS-1|TNS1|masc	PYD and CARD domain containing	protein-coding
mm_169477.1	chr14	69390891	69390898	+	1	NA	Intergenic	CpG	53743	NM_026174	67464	Mm.489765	NM_026174	ENSMUSG00000095463	Entpd4	1200014F22Rik|4930513O14Rik|A430102M06Rik|AI414893|Lysal1|mKIAA0392	ectonucleoside triphosphate diphosphohydrolase 4	protein-coding
mm_114890.1	chr13	94359057	94359097	+	1	NA	promoter-TSS (NR_045619)	promoter-TSS (NR_045619)	117	NM_009680	11774	Mm.21185	NM_009680	ENSMUSG00000021686	Ap3b1	AP-3|AU015684|C78395|Hps2|beta3A|pe|pearl|rim2	adaptor-related protein complex 3, beta 1 subunit	protein-coding
mm_37466.1	chr4	123512119	123512138	-	1	NA	exon (NM_001199137, exon 9 of 93)	exon (NM_001199137, exon 9 of 93)	-100217	NM_001167918	442834	Mm.483803	NM_001167918		D830031N03Rik	Kiaa0754|mKIAA0754	RIKEN cDNA D830031N03 gene	protein-coding
mm_132769.1	chr16	44765833	44765837	+	1	NA	promoter-TSS (NM_021325)	promoter-TSS (NM_021325)	99	NM_021325	57781	Mm.416152	NM_021325	ENSMUSG00000022667	Cd200r1	CD200R|Mox2r|OX2R	CD200 receptor 1	protein-coding
mm_17815.1	chr2	33718790	33718799	-	1	NA	Intergenic	Intergenic	77601	NR_046275	100504399	Mm.72070	NM_177842		C130021I20Rik	-	Riken cDNA C130021I20 gene	ncRNA
mm_146149.1	chr18	74792416	74792428	+	1	NA	exon (NM_177470, exon 3 of 10)	exon (NM_177470, exon 3 of 10)	13210	NM_177470	52538	Mm.245724	NM_177470	ENSMUSG00000036880	Acaa2	0610011L04Rik|AI255831|AI265397|D18Ertd240e	acetyl-Coenzyme A acyltransferase 2 (mitochondrial 3-oxoacyl-Coenzyme A thiolase)	protein-coding
mm_69967.1	chr7	142376720	142376732	-	1	NA	exon (NM_009983, exon 9 of 9)	exon (NM_009983, exon 9 of 9)	-2980	NM_001347541	320802	Mm.154486	NM_177265	ENSMUSG00000045777	Ifitm10	6330512M04Rik|AI848576|DSPA3	interferon induced transmembrane protein 10	protein-coding
mm_17653.1	chr2	32058661	32058664	-	1	NA	Intergenic	Intergenic	7716	NR_106135	102466844		NR_106135	ENSMUSG00000099075	Mir7674	Gm27563|mmu-mir-7674	microRNA 7674	ncRNA
mm_143519.1	chr17	73399270	73399281	-	1	NA	promoter-TSS (NM_001033444)	promoter-TSS (NM_001033444)	21	NM_001033444	381122	Mm.81496	NM_001033444	ENSMUSG00000043705	Capn13	CANP 13|Gm943	calpain 13	protein-coding
mm_164712.1	chr17	54298452	54298460	-	1	NA	intron (NM_022025, intron 1 of 8)	intron (NM_022025, intron 1 of 8)	578	NM_022025	63993	Mm.155241	NM_022025	ENSMUSG00000023945	Slc5a7	CHT1	solute carrier family 5 (choline transporter), member 7	protein-coding
mm_62707.1	chr7	110628535	110628545	+	1	NA	exon (NM_009627, exon 3 of 4)	exon (NM_009627, exon 3 of 4)	871	NM_009627	11535	Mm.1408	NM_009627	ENSMUSG00000030790	Adm	AM	adrenomedullin	protein-coding
mm_104049.1	chr11	86358168	86358172	-	1	NA	promoter-TSS (NM_001080931)	promoter-TSS (NM_001080931)	-645	NM_001080931	327987	Mm.341886	NM_001080931	ENSMUSG00000034297	Med13	1110067M05Rik|D030023K18|Thrap1|Trap240	mediator complex subunit 13	protein-coding
mm_36199.1	chr4	62359130	62359133	-	1	NA	intron (NM_001045528, intron 1 of 27)	intron (NM_001045528, intron 1 of 27)	1417	NM_001045528	338355	Mm.357792	NM_001045528	ENSMUSG00000066151	Fkbp15	BB131447|C430014M02Rik|FKBO133|FKBP-133|FKBP-15|FKBP133|mKIAA0674	FK506 binding protein 15	protein-coding
mm_26193.1	chr3	138488892	138488902	+	1	NA	intron (NM_175224, intron 1 of 10)	intron (NM_175224, intron 1 of 10)	485	NM_175224	75624	Mm.26833	NM_175224	ENSMUSG00000005813	Metap1	1700029C17Rik|AW047992|mKIAA0094	methionyl aminopeptidase 1	protein-coding
mm_30956.1	chr4	33342536	33342540	+	1	NA	intron (NM_011884, intron 8 of 15)	AT_rich|Low_complexity|Low_complexity	32227	NM_001305273	24018	Mm.240024	NM_011884	ENSMUSG00000028274	Rngtt	AU020997|HCE|MCE1	RNA guanylyltransferase and 5'-phosphatase	protein-coding
mm_136794.1	chr17	12119155	12119180	+	1	NA	promoter-TSS (NM_026644)	promoter-TSS (NM_026644)	-117	NM_026644	68262	Mm.258300	NM_026644	ENSMUSG00000023827	Agpat4	1500003P24Rik	1-acylglycerol-3-phosphate O-acyltransferase 4 (lysophosphatidic acid acyltransferase, delta)	protein-coding
mm_72259.1	chr8	75097067	75097077	+	1	NA	exon (NM_010442, exon 3 of 5)	exon (NM_010442, exon 3 of 5)	3454	NM_010442	15368	Mm.276389	NM_010442	ENSMUSG00000005413	Hmox1	D8Wsu38e|HO-1|HO1|Hemox|Hmox|Hsp32	heme oxygenase 1	protein-coding
mm_10750.1	chr2	23187792	23187804	+	1	NA	exon (NM_013771, exon 12 of 19)	exon (NM_013771, exon 12 of 19)	-19678	NM_027635	70981	Mm.314026	NM_027635	ENSMUSG00000026774	4931423N10Rik	-	RIKEN cDNA 4931423N10 gene	protein-coding
mm_104704.1	chr11	97998196	97998207	-	1	NA	Intergenic	Intergenic	-2028	NM_207231	217151	Mm.277896	NM_207231	ENSMUSG00000038352	Arl5c	Arl12|BC065791	ADP-ribosylation factor-like 5C	protein-coding
mm_83963.1	chr9	57148296	57148325	-	1	NA	Intergenic	Intergenic	-1276	NM_028347	72774	Mm.35749	NM_028347	ENSMUSG00000032298	Neil1	2810450N13Rik|Nei1	nei endonuclease VIII-like 1 (E. coli)	protein-coding
mm_139815.1	chr17	66714469	66714491	+	1	NA	intron (NM_008984, intron 21 of 30)	RLTR10B|LTR|ERVK	-119858	NM_028998	74556	Mm.218634	NM_028998	ENSMUSG00000024105	Themis3	9130404H23Rik	thymocyte selection associated family member 3	protein-coding
mm_51976.1	chr6	91758940	91758959	+	1	NA	3' UTR (NM_009320, exon 15 of 15)	3' UTR (NM_009320, exon 15 of 15)	48444	NM_001159507	243547	Mm.333264	NM_001033353	ENSMUSG00000030098	Grip2	-	glutamate receptor interacting protein 2	protein-coding
mm_95782.1	chr11	54909907	54909924	+	1	NA	TTS (NM_021327)	TTS (NM_021327)	7061	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_71520.1	chr8	46846776	46846798	+	1	NA	3' UTR (NM_008391, exon 9 of 9)	3' UTR (NM_008391, exon 9 of 9)	107042	NM_008391	16363	Mm.1149	NM_008391	ENSMUSG00000031627	Irf2	9830146E22Rik|AI646973|Irf-2	interferon regulatory factor 2	protein-coding
mm_144432.1	chr18	21001878	21002012	+	1	NA	promoter-TSS (NM_207623)	promoter-TSS (NM_207623)	-12	NM_001303011	56515	Mm.253542	NM_019706	ENSMUSG00000024317	Rnf138	2410015A17Rik|2810480D20Rik|STRIN|Trif|Trif-d	ring finger protein 138	protein-coding
mm_128852.1	chr15	71954369	71954381	-	1	NA	intron (NM_027174, intron 12 of 63)	intron (NM_027174, intron 12 of 63)	79852	NM_027174	69700	Mm.322500	NM_027174	ENSMUSG00000079022	Col22a1	2310067L16Rik|C80743	collagen, type XXII, alpha 1	protein-coding
mm_171465.1	chr4	145730303	145730314	-	1	NA	Intergenic	CpG	-51235	NM_001083918	666532	Mm.392861	NM_001083918	ENSMUSG00000067916	Zfp991	Gm13139|OTTMUSG00000010657	zinc finger protein 991	protein-coding
mm_125015.1	chr15	25626222	25626233	+	1	NA	intron (NM_019472, intron 1 of 40)	intron (NM_019472, intron 1 of 40)	3677	NM_019472	17909	Mm.60590	NM_019472	ENSMUSG00000022272	Myo10	AW048724|D15Ertd600e|mKIAA0799|myosin-X	myosin X	protein-coding
mm_88123.1	chr10	69219448	69219455	+	1	NA	intron (NM_001252637, intron 2 of 10)	intron (NM_001252637, intron 2 of 10)	6257	NM_001252638	69288	Mm.26659	NM_001081347	ENSMUSG00000019944	Rhobtb1	1700008H16Rik|3110048G13Rik|AI173445|AI573858|AV350930	Rho-related BTB domain containing 1	protein-coding
mm_20008.1	chr2	119175143	119175172	-	1	NA	exon (NM_001039223, exon 1 of 1)	exon (NM_001039223, exon 1 of 1)	648	NM_001039223	623781	Mm.389344	NM_001039223	ENSMUSG00000055926	Gm14137	OTTMUSG00000015762	predicted gene 14137	protein-coding
mm_83989.1	chr9	57434960	57434985	-	1	NA	exon (NM_176831, exon 3 of 7)	exon (NM_176831, exon 3 of 7)	5142	NM_176831	66812	Mm.250508	NM_176831	ENSMUSG00000063849	Ppcdc	1810057I13Rik|8430432M10Rik	phosphopantothenoylcysteine decarboxylase	protein-coding
mm_42168.1	chr5	112261617	112261636	+	1	NA	intron (NM_023695, intron 3 of 5)	MIRb|SINE|MIR	5806	NM_001312893	12960	Mm.29488	NM_023695	ENSMUSG00000029343	Crybb1	3110006K12Rik|BB1CRY	crystallin, beta B1	protein-coding
mm_162016.1	chr19	45009225	45009225	+	1	NA	intron (NM_153796, intron 1 of 4)	B1_Mus1|SINE|Alu	2667	NM_153796	226153	Mm.105585	NM_153796	ENSMUSG00000025209	Twnk	D19Ertd626e|PEO|Peo1|Twinl	twinkle mtDNA helicase	protein-coding
mm_129077.1	chr15	75812913	75812922	-	1	NA	intron (NM_172121, intron 3 of 11)	intron (NM_172121, intron 3 of 11)	28991	NM_172121	223642	Mm.209800	NM_172121	ENSMUSG00000075600	Zc3h3	BC049953|Kiaa0150|Smicl|Zc3hdc3	zinc finger CCCH type containing 3	protein-coding
mm_13594.1	chr2	112507115	112507136	+	1	NA	intron (NM_028844, intron 1 of 5)	intron (NM_028844, intron 1 of 5)	14161	NM_028844	74268	Mm.315125	NM_028844	ENSMUSG00000003604	Aven	1700013A01Rik|1700056A21Rik|mAven-L|mAven-S	apoptosis, caspase activation inhibitor	protein-coding
mm_65490.1	chr7	25687538	25687573	-	1	NA	TTS (NM_172148)	TTS (NM_172148)	553	NM_011577	21803	Mm.248380	NM_011577	ENSMUSG00000002603	Tgfb1	TGF-beta1|TGFbeta1|Tgfb|Tgfb-1	transforming growth factor, beta 1	protein-coding
mm_153502.1	chr19	41333944	41333964	-	1	NA	intron (NM_031376, intron 2 of 16)	MTD|LTR|ERVL-MaLR	51116	NM_031376	83490	Mm.222266	NM_031376	ENSMUSG00000025017	Pik3ap1	1810044J04Rik|BCAP	phosphoinositide-3-kinase adaptor protein 1	protein-coding
mm_13135.1	chr2	91929673	91929676	+	1	NA	TTS (NM_010784)	TTS (NM_010784)	2028	NM_001291481	17242	Mm.906	NM_010784	ENSMUSG00000027239	Mdk	MK|Mek	midkine	protein-coding
mm_157901.1	chrX	77848049	77848051	-	1	NA	exon (NM_017471, exon 2 of 7)	exon (NM_017471, exon 2 of 7)	5450	NM_017471	54192	Mm.8034	NM_017471	ENSMUSG00000000003	Pbsn	PB|Prbs	probasin	protein-coding
mm_25350.1	chr3	106788800	106788808	+	1	NA	intron (NM_007651, intron 1 of 7)	intron (NM_007651, intron 1 of 7)	1345	NM_007651	12508	Mm.316861	NM_007651	ENSMUSG00000040747	Cd53	AI323659|Ox-44|Tspan25	CD53 antigen	protein-coding
mm_141646.1	chr17	33639912	33639915	-	1	NA	intron (NR_028279, intron 1 of 9)	intron (NR_028279, intron 1 of 9)	1818	NR_028279	378460	Mm.272606	NM_001002842	ENSMUSG00000032739	Pram1	AY665714	PML-RAR alpha-regulated adaptor molecule 1	protein-coding
mm_150900.1	chr19	45560570	45560644	+	1	NA	promoter-TSS (NM_172639)	promoter-TSS (NM_172639)	-8	NM_172639	226162	Mm.21978	NM_172639	ENSMUSG00000041035	Dpcd	5330431N19Rik|Ndac	deleted in primary ciliary dyskinesia	protein-coding
mm_113809.1	chr13	46502890	46502914	+	1	NA	intron (NM_026056, intron 1 of 12)	intron (NM_026056, intron 1 of 12)	999	NM_026056	67252	Mm.44529	NM_026056	ENSMUSG00000021373	Cap2	2810452G09Rik|AV045235	CAP, adenylate cyclase-associated protein, 2 (yeast)	protein-coding
mm_69004.1	chr7	126701144	126701170	-	1	NA	intron (NM_001301374, intron 6 of 10)	intron (NM_001301374, intron 6 of 10)	3063	NM_001301374	12721	Mm.290482	NM_009898	ENSMUSG00000030707	Coro1a	Clabp|Lmb3|TACO|p57	coronin, actin binding protein 1A	protein-coding
mm_15451.1	chr2	157403105	157403148	+	1	NA	Intergenic	MLT1D|LTR|ERVL-MaLR	-21167	NM_009271	20779	Mm.22845	NM_009271	ENSMUSG00000027646	Src	AW259666|pp60c-src	Rous sarcoma oncogene	protein-coding
mm_27749.1	chr3	69316442	69316467	-	1	NA	promoter-TSS (NM_178726)	promoter-TSS (NM_178726)	-464	NM_178726	242083	Mm.40577	NM_178726	ENSMUSG00000027784	Ppm1l	3222401G13|5930404J21Rik|AI481720|AW045850|PP2C|PP2Cepsilon|Pp2ce|Ppp2ce|mKIAA4175	protein phosphatase 1 (formerly 2C)-like	protein-coding
mm_151535.1	chr19	58943414	58943431	+	1	NA	promoter-TSS (NM_178689)	promoter-TSS (NM_178689)	-3	NM_178689	226265	Mm.103154	NM_178689	ENSMUSG00000048029	Eno4	6430537H07Rik	enolase 4	protein-coding
mm_118939.1	chr14	27238019	27238046	+	1	NA	promoter-TSS (NM_027871)	promoter-TSS (NM_027871)	22	NM_027871	71704	Mm.248606	NM_027871	ENSMUSG00000021895	Arhgef3	1200004I24Rik|9830169H03Rik|C76747|Xpln	Rho guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_58536.1	chr7	4465330	4465375	+	1	NA	intron (NM_001290416, intron 1 of 19)	intron (NM_001290416, intron 1 of 19)	503	NM_001290416	67425	Mm.360392	NM_026146	ENSMUSG00000006154	Eps8l1	2310051G19Rik|4632407K17Rik|AW060268|DRC3|EPS8R1	EPS8-like 1	protein-coding
mm_57089.1	chr6	122587060	122587081	-	1	NA	intron (NM_001134391, intron 5 of 7)	(GA)n|Simple_repeat|Simple_repeat	15374	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_85171.1	chr9	96478632	96478647	-	1	NA	promoter-TSS (NM_011279)	promoter-TSS (NM_011279)	36	NM_011279	19823	Mm.28235	NM_011279	ENSMUSG00000051234	Rnf7	Rbx2|SAG	ring finger protein 7	protein-coding
mm_152011.1	chr19	5955606	5955609	-	1	NA	intron (NM_001164057, intron 5 of 17)	intron (NM_001164057, intron 5 of 17)	8599	NM_001164057	18969	Mm.209931	NM_008893	ENSMUSG00000024833	Pola2	AI573378	polymerase (DNA directed), alpha 2	protein-coding
mm_117707.1	chr13	95059099	95059116	-	1	NA	intron (NM_001170669, intron 7 of 18)	intron (NM_001170669, intron 7 of 18)	82763	NM_172590	218460	Mm.33856	NM_172590	ENSMUSG00000042015	Wdr41	B830029I03Rik|MSTP048	WD repeat domain 41	protein-coding
mm_65969.1	chr7	30437066	30437083	-	1	NA	intron (NM_007467, intron 11 of 16)	intron (NM_007467, intron 11 of 16)	8508	NM_007467	11803	Mm.2381	NM_007467	ENSMUSG00000006651	Aplp1	-	amyloid beta (A4) precursor-like protein 1	protein-coding
mm_49108.1	chr6	8259380	8259460	+	1	NA	promoter-TSS (NM_026632)	promoter-TSS (NM_026632)	132	NM_001302353	100036521	Mm.446106	NM_001302353	ENSMUSG00000089862	Umad1	Gm16039|OTTMUSG00000029336	UMAP1-MVP12 associated (UMA) domain containing 1	protein-coding
mm_17583.1	chr2	30415573	30415612	-	1	NA	promoter-TSS (NM_138748)	promoter-TSS (NM_138748)	156	NM_007760	12908	Mm.20396	NM_007760	ENSMUSG00000026853	Crat	AW107812|CARAT	carnitine acetyltransferase	protein-coding
mm_113.1	chr1	9759105	9759112	+	1	NA	intron (NR_040462, intron 2 of 3)	intron (NR_040462, intron 2 of 3)	-10726	NM_173443	70675	Mm.274493	NM_173443	ENSMUSG00000045210	Vcpip1	4932442A08|5730421J18Rik|5730538E15Rik|VCIP135|mKIAA1850	valosin containing protein (p97)/p47 complex interacting protein 1	protein-coding
mm_138031.1	chr17	33919564	33919579	+	1	NA	promoter-TSS (NM_009318)	promoter-TSS (NM_009318)	93	NM_009318	21356	Mm.154457	NM_009318	ENSMUSG00000024308	Tapbp	D17Wsu91e|TPN	TAP binding protein	protein-coding
mm_61529.1	chr7	78920147	78920157	+	1	NA	exon (NM_020583, exon 4 of 4)	exon (NM_020583, exon 4 of 4)	5917	NM_001113527	57444	Mm.322843	NM_020583	ENSMUSG00000039236	Isg20	1600023I01Rik|2010107M23Rik|20kDa|DnaQL|HEM45	interferon-stimulated protein	protein-coding
mm_26759.1	chr3	8666998	8667012	-	1	NA	promoter-TSS (NM_010423)	promoter-TSS (NM_010423)	33	NM_010423	15213	Mm.29581	NM_010423	ENSMUSG00000040289	Hey1	AI316788|AI414254|CHF2|HRT1|Herp2|Hesr1|bHLHb31|hesr-1	hairy/enhancer-of-split related with YRPW motif 1	protein-coding
mm_166644.1	chr6	84019395	84019406	+	1	NA	promoter-TSS (NM_021469)	promoter-TSS (NM_021469)	14	NM_021469	26903	Mm.220982	NM_021469	ENSMUSG00000033788	Dysf	2310004N10Rik|AI604795|D6Pas3	dysferlin	protein-coding
mm_144212.1	chr18	9728074	9728077	+	1	NA	intron (NM_130449, intron 2 of 9)	intron (NM_130449, intron 2 of 9)	20427	NM_130449	140792	Mm.218571	NM_130449	ENSMUSG00000036103	Colec12	CL-P1|SRCL|Scara4	collectin sub-family member 12	protein-coding
mm_78046.1	chr9	14501981	14501998	+	1	NA	exon (NM_023153, exon 2 of 7)	exon (NM_023153, exon 2 of 7)	1370	NM_023153	66070	Mm.245938	NM_023153	ENSMUSG00000004096	Cwc15	0610040D20Rik|2900052N06Rik|Ed1|c11orf5|mED1	CWC15 spliceosome-associated protein	protein-coding
mm_26209.1	chr3	138742229	138742322	+	1	NA	promoter-TSS (NR_121195)	promoter-TSS (NR_121195)	67	NM_019571	56224	Mm.31927	NM_019571	ENSMUSG00000028152	Tspan5	2810455A09Rik|4930505M03Rik|NET-4|Tm4sf9	tetraspanin 5	protein-coding
mm_105144.1	chr11	101460085	101460102	-	1	NA	3' UTR (NM_012037, exon 6 of 6)	3' UTR (NM_012037, exon 6 of 6)	6106	NM_012037	26949	Mm.29210	NM_012037	ENSMUSG00000034993	Vat1	VAT-1	vesicle amine transport 1	protein-coding
mm_146416.1	chr18	84386125	84386125	+	1	NA	intron (NM_001033341, intron 4 of 8)	Lx2B2|LINE|L1	203379	NM_001033341	240476	Mm.329575	NM_001033341	ENSMUSG00000048410	Zfp407	6430585N13Rik|Gm333|Gm334|Gm948|ZNF407	zinc finger protein 407	protein-coding
mm_42974.1	chr5	123142231	123142286	+	1	NA	promoter-TSS (NM_001040398)	promoter-TSS (NM_001040398)	65	NM_001040398	208043	Mm.250391	NM_177581	ENSMUSG00000038384	Setd1b	AA516740|BC035291|KMT2G|mKIAA1076	SET domain containing 1B	protein-coding
mm_15498.1	chr2	157832304	157832315	+	1	NA	intron (NM_025680, intron 10 of 15)	ORR1G|LTR|ERVL-MaLR	-82344	NM_198627	277432	Mm.441156	NM_198627	ENSMUSG00000037843	Vstm2l	Gm691	V-set and transmembrane domain containing 2-like	protein-coding
mm_102876.1	chr11	69409548	69409569	-	1	NA	intron (NM_001017426, intron 1 of 22)	intron (NM_001017426, intron 1 of 22)	4117	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_168353.1	chr1	113904213	113904219	-	1	NA	Intergenic	L1Md_F3|LINE|L1	-1780921	NM_001077425	636808	Mm.101576	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding
mm_46916.1	chr5	114443994	114444033	-	1	NA	promoter-TSS (NM_029956)	promoter-TSS (NM_029956)	14	NM_029956	77697	Mm.105182	NM_029956	ENSMUSG00000029575	Mmab	9130222L19Rik|ATR	methylmalonic aciduria (cobalamin deficiency) cblB type homolog (human)	protein-coding
mm_95064.1	chr11	32533291	32533301	+	1	NA	promoter-TSS (NM_009288)	promoter-TSS (NM_009288)	30	NM_009288	20868	Mm.8235	NM_009288	ENSMUSG00000020272	Stk10	Gek1|Lok|mKIAA4026	serine/threonine kinase 10	protein-coding
mm_112983.1	chr13	21356897	21356905	+	1	NA	Intergenic	MERVK26-int|LTR|ERVK	-5919	NM_016684	22758	Mm.24124	NM_016684	ENSMUSG00000036721	Zscan12	2510038J07Rik|FPM315|Zfp96|mKIAA0426|zfp-96	zinc finger and SCAN domain containing 12	protein-coding
mm_129693.1	chr15	81528655	81528665	-	1	NA	Intergenic	RMER17B|LTR|ERVK	-57554	NM_177821	328572	Mm.258397	NM_177821	ENSMUSG00000055024	Ep300	A430090G16|A730011L11|KAT3B|p300|p300 HAT	E1A binding protein p300	protein-coding
mm_8378.1	chr1	151250742	151250754	-	1	NA	Intergenic	MLT1H|LTR|ERVL-MaLR	-93750	NM_001039512	117198	Mm.33764	NM_028582	ENSMUSG00000023150	Ivns1abp	1190004M08Rik|1700126I16Rik|AA960440|HSPC068|ND1|NS-1|NS1-BP|Nd1-L|Nd1-S|mKIAA0850	influenza virus NS1A binding protein	protein-coding
mm_87147.1	chr10	34787755	34787757	+	1	NA	Intergenic	Intergenic	304356	NM_010237	14302	Mm.332432	NM_010237	ENSMUSG00000019779	Frk	BSK|BSK/IYK|C85044|GTK|RAK	fyn-related kinase	protein-coding
mm_84341.1	chr9	64184287	64184297	-	1	NA	Intergenic	Intergenic	4995	NM_183316	330959	Mm.24082	NM_183316	ENSMUSG00000032398	Snapc5	2010103A03Rik	small nuclear RNA activating complex, polypeptide 5	protein-coding
mm_41701.1	chr5	100862018	100862021	+	1	NA	intron (NM_172715, intron 3 of 12)	intron (NM_172715, intron 3 of 12)	15790	NM_172715	231510	Mm.271911	NM_172715	ENSMUSG00000029314	Agpat9	1-AGPAT|1-AGPAT 9|4933407I02Rik|4933408F15|A230097K15Rik|GPAT-3|Gpat3|mGPAT3	1-acylglycerol-3-phosphate O-acyltransferase 9	protein-coding
mm_101375.1	chr11	23770921	23770925	-	1	NA	promoter-TSS (NM_009044)	promoter-TSS (NM_009044)	47	NM_009044	19696	Mm.4869	NM_009044	ENSMUSG00000020275	Rel	c-Rel	reticuloendotheliosis oncogene	protein-coding
mm_158440.1	chrX	140384705	140384706	-	1	NA	intron (NM_001320946, intron 5 of 14)	intron (NM_001320946, intron 5 of 14)	17211	NM_177750	245643	Mm.208683	NM_177750	ENSMUSG00000042425	Frmpd3	B930041G04|EG245643|Gm29750	FERM and PDZ domain containing 3	protein-coding
mm_120098.1	chr14	58036679	58036693	+	1	NA	Intergenic	Intergenic	-36000	NM_013518	14180	Mm.8846	NM_013518	ENSMUSG00000021974	Fgf9	Eks	fibroblast growth factor 9	protein-coding
mm_52733.1	chr6	120394632	120394635	+	1	NA	intron (NM_145997, intron 12 of 27)	B1_Mur2|SINE|Alu	-30264	NR_045558	67200	Mm.45767	NM_026028	ENSMUSG00000030177	Ccdc77	2400002C23Rik|2700091N06Rik|AV168274	coiled-coil domain containing 77	protein-coding
mm_152113.1	chr19	6969747	6969808	-	1	NA	promoter-TSS (NM_001290349)	promoter-TSS (NM_001290349)	37	NM_008874	18797	Mm.273204	NM_008874	ENSMUSG00000024960	Plcb3	mKIAA4098	phospholipase C, beta 3	protein-coding
mm_17856.1	chr2	34790332	34790356	-	1	NA	intron (NM_145522, intron 4 of 7)	ORR1A2|LTR|ERVL-MaLR	9568	NM_145522	227746	Mm.158705	NM_145522	ENSMUSG00000070953	Rabepk	8430412M01Rik|9530020D24Rik|AV073337|C87311|Rab9p40	Rab9 effector protein with kelch motifs	protein-coding
mm_58215.1	chr6	144204182	144204194	-	1	NA	intron (NM_001113559, intron 1 of 13)	intron (NM_001113559, intron 1 of 13)	5380	NM_001113559	20678	Mm.1752	NM_011444	ENSMUSG00000041540	Sox5	A730017D01Rik|AI528773	SRY (sex determining region Y)-box 5	protein-coding
mm_155064.1	chrX	42502508	42502522	+	1	NA	promoter-TSS (NM_011364)	promoter-TSS (NM_011364)	-50	NM_011364	20400	Mm.441197	NM_011364	ENSMUSG00000005696	Sh2d1a	Gm686|SAP	SH2 domain containing 1A	protein-coding
mm_116502.1	chr13	44982975	44982979	-	1	NA	intron (NM_025772, intron 4 of 9)	intron (NM_025772, intron 4 of 9)	19119	NM_025772	94245	Mm.352311	NM_025772	ENSMUSG00000057531	Dtnbp1	5430437B18Rik|AW048963|Bloc1s8|dysbindin|sdy	dystrobrevin binding protein 1	protein-coding
mm_99781.1	chr11	107336004	107336011	+	1	NA	intron (NM_145823, intron 2 of 9)	intron (NM_145823, intron 2 of 9)	134713	NM_145823	71795	Mm.397413	NM_145823	ENSMUSG00000040430	Pitpnc1	1110020B03Rik|5830436L09Rik|AI662802|AI851387|C330017I21Rik|Dnr411|RDGBB|RDGBB1|rdgB-beta	phosphatidylinositol transfer protein, cytoplasmic 1	protein-coding
mm_8054.1	chr1	135374920	135374933	-	1	NA	exon (NM_175259, exon 1 of 5)	exon (NM_175259, exon 1 of 5)	137	NM_175259	77552	Mm.41407	NM_175259	ENSMUSG00000041889	Shisa4	9330132O05Rik|Tmem58|mShisa4	shisa family member 4	protein-coding
mm_125623.1	chr15	61988227	61988237	+	1	NA	exon (NM_001177354, exon 2 of 3)	exon (NM_001177354, exon 2 of 3)	2891	NM_001177352	17869	Mm.2444	NM_010849	ENSMUSG00000022346	Myc	AU016757|Myc2|Niard|Nird|bHLHe39	myelocytomatosis oncogene	protein-coding
mm_125374.1	chr15	40014922	40014934	+	1	NA	Intergenic	Intergenic	52279	NR_045719	105976	Mm.394885	NR_045719		AU022793	-	expressed sequence AU022793	ncRNA
mm_147637.1	chr18	60269559	60269565	-	1	NA	3' UTR (NM_001034859, exon 2 of 2)	3' UTR (NM_001034859, exon 2 of 2)	3705	NM_001034859	225594	Mm.329460	NM_001034859	ENSMUSG00000068606	Gm4841	EG225594|Ifgga3	predicted gene 4841	protein-coding
mm_166608.1	chr6	69587839	69587867	-	1	NA	Intergenic	Intergenic	-260679	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_82997.1	chr9	36693131	36693141	-	1	NA	promoter-TSS (NM_007391)	promoter-TSS (NM_007391)	53	NR_040741	75567	Mm.426883	NR_040741	ENSMUSG00000098304	1700027I24Rik	-	RIKEN cDNA 1700027I24 gene	ncRNA
mm_147057.1	chr18	34946542	34946556	-	1	NA	exon (NM_010481, exon 8 of 17)	exon (NM_010481, exon 8 of 17)	7802	NM_010481	15526	Mm.209419	NM_010481	ENSMUSG00000024359	Hspa9	74kDa|Csa|Grp75|Hsc74|Hsp74|Hsp74a|Hspa9a|Mortalin|Mot-2|Mot2|Mthsp70|Pbp74	heat shock protein 9	protein-coding
mm_10715.1	chr2	22799612	22799645	+	1	NA	intron (NM_019456, intron 1 of 13)	intron (NM_019456, intron 1 of 13)	25301	NM_019456	54519	Mm.14255	NM_019456	ENSMUSG00000026786	Apbb1ip	9930118P07Rik|Prp48	amyloid beta (A4) precursor protein-binding, family B, member 1 interacting protein	protein-coding
mm_13486.1	chr2	106693123	106693139	+	1	NA	promoter-TSS (NM_001143683)	promoter-TSS (NM_001143683)	-328	NM_001143683	77015	Mm.45628	NM_029837	ENSMUSG00000016386	Mpped2	239Fb|2700082O15Rik|AV354767|AW060960	metallophosphoesterase domain containing 2	protein-coding
mm_135777.1	chr16	56867662	56867670	-	1	NA	intron (NM_019631, intron 1 of 5)	intron (NM_019631, intron 1 of 5)	18497	NM_019631	56277	Mm.262328	NM_019631	ENSMUSG00000022754	Tmem45a	C630002M10Rik|M32486|p19.5	transmembrane protein 45a	protein-coding
mm_35008.1	chr4	3090216	3090234	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	-81858	NM_001167534	100312470	Mm.480297	NM_001167534	ENSMUSG00000094798	Vmn1r2	Gm11776|OTTMUSG00000004179	vomeronasal 1 receptor 2	protein-coding
mm_137721.1	chr17	29114501	29114504	+	1	NA	Intergenic	ID_B1|SINE|B4	-20554	NM_001002786	442827	Mm.440341	NM_001002786	ENSMUSG00000064147	Rab44	9830134C10Rik	RAB44, member RAS oncogene family	protein-coding
mm_82849.1	chr9	31170608	31170622	-	1	NA	exon (NM_009691, exon 5 of 16)	exon (NM_009691, exon 5 of 16)	-38816	NM_011176	19143	Mm.243926	NM_011176	ENSMUSG00000031995	St14	Epithin|MT-SP1|Prss14|Tmprss14|mCAP3|matriptase	suppression of tumorigenicity 14 (colon carcinoma)	protein-coding
mm_136815.1	chr17	12396602	12396612	+	1	NA	exon (NM_008877, exon 9 of 19)	exon (NM_008877, exon 9 of 19)	17998	NM_008877	18815	Mm.971	NM_008877	ENSMUSG00000059481	Plg	AI649309|Pg	plasminogen	protein-coding
mm_162872.1	chr10	95766830	95766854	+	1	NA	Intergenic	Intergenic	-173821	NM_001001932	216238	Mm.210035	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding
mm_88666.1	chr10	80016902	80016905	+	1	NA	promoter-TSS (NM_001347074)	promoter-TSS (NM_001347074)	-12	NM_001347074	70719	Mm.243954	NM_027521	ENSMUSG00000035697	Hmha1	6330406L22Rik|AW539505|Ha-1	histocompatibility (minor) HA-1	protein-coding
mm_122203.1	chr14	31781663	31781731	-	1	NA	intron (NM_001024604, intron 1 of 27)	intron (NM_001024604, intron 1 of 27)	48718	NM_001024604	105522	Mm.37660	NM_001024604	ENSMUSG00000014496	Ankrd28	AI465466|AI604979|E430019N21Rik|mKIAA0379	ankyrin repeat domain 28	protein-coding
mm_168019.1	chrY	90737786	90737948	-	1	NA	Intergenic	RLTR31D_MM|LTR|ERVK	17183	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_63396.1	chr7	127296252	127296275	+	1	NA	promoter-TSS (NM_001253873)	promoter-TSS (NM_001253873)	3	NM_001253874	16408	Mm.1618	NM_008400	ENSMUSG00000030830	Itgal	(p180)|Cd11a|LFA-1|LFA-1A|Ly-15|Ly-21	integrin alpha L	protein-coding
mm_46758.1	chr5	112249325	112249340	-	1	NA	intron (NM_001312884, intron 2 of 4)	intron (NM_001312884, intron 2 of 4)	3186	NM_001312884	12959	Mm.40324	NM_021351	ENSMUSG00000066975	Cryba4	-	crystallin, beta A4	protein-coding
mm_144793.1	chr18	35965037	35965087	+	1	NA	non-coding (NR_110349, exon 1 of 15)	non-coding (NR_110349, exon 1 of 15)	232	NR_110349	74002	Mm.196944	NM_028707	ENSMUSG00000024347	Psd2	6330404E20Rik|AW125584|EFA6C	pleckstrin and Sec7 domain containing 2	protein-coding
mm_17349.1	chr2	26607986	26608001	-	1	NA	Intergenic	GA-rich|Low_complexity|Low_complexity	-3576	NM_026212	67512	Mm.24244	NM_026212	ENSMUSG00000026922	Agpat2	2510002J07Rik|AV000834|BSCL|BSCL1|LPAAB|LPAAT-beta	1-acylglycerol-3-phosphate O-acyltransferase 2 (lysophosphatidic acid acyltransferase, beta)	protein-coding
mm_4847.1	chr1	187125108	187125122	+	1	NA	promoter-TSS (NR_040554)	promoter-TSS (NR_040554)	-23	NR_040554	69308	Mm.490882	NR_040554	ENSMUSG00000089730	1700007P06Rik	-	RIKEN cDNA 1700007P06 gene	ncRNA
mm_161013.1	chr11	119228508	119228508	+	1	NA	promoter-TSS (NM_172443)	promoter-TSS (NM_172443)	-9	NM_172443	207592	Mm.205263	NM_172443	ENSMUSG00000039976	Tbc1d16	B930087K01|BC026530|Tcd1d16	TBC1 domain family, member 16	protein-coding
mm_143267.1	chr17	65639823	65639839	-	1	NA	promoter-TSS (NM_153519)	promoter-TSS (NM_153519)	-75	NM_153519	213272	Mm.255732	NM_153519	ENSMUSG00000050612	Txndc2	AU021712|Sptrx-1|Sptrx1|Trx4	thioredoxin domain containing 2 (spermatozoa)	protein-coding
mm_171125.1	chr3	144727791	144727791	+	1	NA	Intergenic	Intergenic	-7456	NM_001282037	54673	Mm.271775	NM_019464	ENSMUSG00000037062	Sh3glb1	AA409932|AI314629|AU015566|Bif-1|mKIAA0491	SH3-domain GRB2-like B1 (endophilin)	protein-coding
mm_146002.1	chr18	68442325	68442334	+	1	NA	Intergenic	B3|SINE|B2	-13009	NM_001271716	17200	Mm.426053	NM_008560	ENSMUSG00000045569	Mc2r	ACTH-R|ACTHR|MC2-R	melanocortin 2 receptor	protein-coding
mm_83950.1	chr9	56926855	56926858	-	1	NA	5' UTR (NM_175483, exon 1 of 2)	5' UTR (NM_175483, exon 1 of 2)	1515	NM_175483	235406	Mm.191459	NM_175483	ENSMUSG00000032733	Snx33	E130307J07Rik|Sh3px3	sorting nexin 33	protein-coding
mm_35925.1	chr4	53032206	53032217	-	1	NA	3' UTR (NM_013454, exon 50 of 50)	3' UTR (NM_013454, exon 50 of 50)	20331	NM_025623	66536	Mm.38244	NM_025623	ENSMUSG00000015247	Nipsnap3b	2700063N13Rik|Nipsnap3a	nipsnap homolog 3B (C. elegans)	protein-coding
mm_30716.1	chr4	13037964	13037965	+	1	NA	Intergenic	L1_Mus1|LINE|L1	131127	NM_001171801	208820	Mm.12057	NM_173746	ENSMUSG00000055963	Triqk	C130086A10|Gm11818|OTTMUSG00000004461	triple QxxK/R motif containing	protein-coding
mm_9460.1	chr1	172894984	172895003	-	1	NA	promoter-TSS (NM_011318)	promoter-TSS (NM_011318)	61	NM_011318	20219	Mm.330510	NM_011318	ENSMUSG00000026542	Apcs	Sap	serum amyloid P-component	protein-coding
mm_144536.1	chr18	25568136	25568142	+	1	NA	intron (NM_001146292, intron 2 of 12)	intron (NM_001146292, intron 2 of 12)	185844	NM_133195	108013	Mm.266435	NM_133195	ENSMUSG00000024268	Celf4	A230070D14Rik|BRUNOL-4|Brul4|Brunol4|C130060B05Rik	CUGBP, Elav-like family member 4	protein-coding
mm_138356.1	chr17	34981948	34981948	+	1	NA	promoter-TSS (NM_001110101)	promoter-TSS (NM_001110101)	94	NM_001204274	27756	Mm.165735	NM_030597	ENSMUSG00000007050	Lsm2	D17H6S56E-2|D17H6S56E2|Dmapl|Dmpkap|G7b|Sm-X5|SmX5|snRNP	LSM2 homolog, U6 small nuclear RNA and mRNA degradation associated	protein-coding
mm_172774.1	chr8	94857504	94857520	+	1	NA	promoter-TSS (NM_009090)	promoter-TSS (NM_009090)	62	NM_009090	20021	Mm.292492	NM_009090	ENSMUSG00000031783	Polr2c	33kDa|RPB3|Rpo2-3|mRBP31	polymerase (RNA) II (DNA directed) polypeptide C	protein-coding
mm_51787.1	chr6	88200288	88200297	+	1	NA	exon (NM_008090, exon 3 of 6)	exon (NM_008090, exon 3 of 6)	1628	NM_008090	14461	Mm.491156	NM_008090	ENSMUSG00000015053	Gata2	Gata-2	GATA binding protein 2	protein-coding
mm_79933.1	chr9	65676567	65676621	+	1	NA	promoter-TSS (NM_010952)	promoter-TSS (NM_010952)	46	NM_001301307	18247	Mm.116749	NM_010952	ENSMUSG00000040652	Oaz2	AZ-2|AZ2|Oaz2-ps|Sez15	ornithine decarboxylase antizyme 2	protein-coding
mm_12610.1	chr2	74683894	74683901	+	1	NA	intron (NM_008273, intron 1 of 1)	intron (NM_008273, intron 1 of 1)	1574	NM_008273	15431	Mm.207763	NM_008273	ENSMUSG00000042499	Hoxd11	E230017H14Rik|Hox-4.6|Hox-5.4|Hox-5.5	homeobox D11	protein-coding
mm_88171.1	chr10	69785508	69785523	+	1	NA	intron (NM_170730, intron 1 of 17)	intron (NM_170730, intron 1 of 17)	-140017	NM_170687	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_100039.1	chr11	114996722	114996728	+	1	NA	TTS (NM_134158)	TTS (NM_134158)	5155	NM_134158	140497	Mm.2699	NM_134158	ENSMUSG00000044811	Cd300c2	CLM4|Cd300c|Cd300d|DIgR1|Igsf7|Lmir2|MAIR-II	CD300C molecule 2	protein-coding
mm_136648.1	chr17	5841425	5841463	+	1	NA	promoter-TSS (NM_025664)	promoter-TSS (NM_025664)	64	NM_025664	66616	Mm.89515	NM_025664	ENSMUSG00000002365	Snx9	2700073N08Rik|SDP1|SH3PX1	sorting nexin 9	protein-coding
mm_101678.1	chr11	40429746	40429748	-	1	NA	Intergenic	Intergenic	262935	NM_134017	108645	Mm.293771	NM_134017	ENSMUSG00000042032	Mat2b	1110064C04Rik|2410018D16Rik|AI182287|AU022853|MAT-II|MATIIbeta|TGR	methionine adenosyltransferase II, beta	protein-coding
mm_168825.1	chr12	22558895	22558897	+	1	NA	Intergenic	Intergenic	-402250	NR_136920	100043416		NM_001004167	ENSMUSG00000093846	Gm4425	EG432637|Gm5433	KRAB-domain protein pseudogene	pseudo
mm_18153.1	chr2	45088244	45088259	-	1	NA	intron (NM_001289521, intron 1 of 8)	intron (NM_001289521, intron 1 of 8)	22026	NM_001289521	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_93893.1	chr10	125380445	125380453	-	1	NA	Intergenic	MTC|LTR|ERVL-MaLR	-51914	NM_011391	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|Mct2	solute carrier family 16 (monocarboxylic acid transporters), member 7	protein-coding
mm_85938.1	chr9	112099202	112099225	-	1	NA	intron (NM_001177618, intron 17 of 18)	B4|SINE|B4	19498	NR_029823	723815		NR_029823	ENSMUSG00000065441	Mir128-2	Mirn128-2|Mirn128b|mir-128-2|mir-128b	microRNA 128-2	ncRNA
mm_134975.1	chr16	32052324	32052350	-	1	NA	exon (NM_177326, exon 2 of 15)	exon (NM_177326, exon 2 of 15)	27005	NM_177326	224105	Mm.234204	NM_177326	ENSMUSG00000022781	Pak2	5330420P17Rik|A130002K10Rik|AI836325|D16Ertd269e|PAK-2|mKIAA4182	p21 protein (Cdc42/Rac)-activated kinase 2	protein-coding
mm_12140.1	chr2	61752362	61752365	+	1	NA	intron (NM_021526, intron 3 of 11)	intron (NM_021526, intron 3 of 11)	40669	NM_021526	59029	Mm.218198	NM_021526	ENSMUSG00000026914	Psmd14	2610312C03Rik|3200001M20Rik|AA986732|Pad1|Poh1|rpm11	proteasome (prosome, macropain) 26S subunit, non-ATPase, 14	protein-coding
mm_30226.1	chr3	145649267	145649280	-	1	NA	exon (NM_010516, exon 2 of 5)	exon (NM_010516, exon 2 of 5)	712	NM_010516	16007	Mm.1231	NM_010516	ENSMUSG00000028195	Cyr61	AI325051|CCN1|Igfbp10	cysteine rich protein 61	protein-coding
mm_163202.1	chr11	96934965	96934969	-	1	NA	3' UTR (NM_146026, exon 3 of 3)	3' UTR (NM_146026, exon 3 of 3)	5643	NM_146026	217138	Mm.342551	NM_146026	ENSMUSG00000047040	Prr15l	Atad4|BC022765|E230006A12Rik	proline rich 15-like	protein-coding
mm_27984.1	chr3	81974544	81974550	-	1	NA	intron (NM_019911, intron 2 of 11)	intron (NM_019911, intron 2 of 11)	1181	NM_019911	56720	Mm.258622	NM_019911	ENSMUSG00000028011	Tdo2	AA407491|TDO|TO|chky	tryptophan 2,3-dioxygenase	protein-coding
mm_47864.1	chr5	134627708	134627750	-	1	NA	exon (NM_033561, exon 2 of 7)	exon (NM_033561, exon 2 of 7)	11680	NM_001312867	22384	Mm.27955	NM_033561	ENSMUSG00000040731	Eif4h	AU018978|D5Ertd355e|E430026L18Rik|Ef4h|Wbscr1|Wscr1|eIF-4H	eukaryotic translation initiation factor 4H	protein-coding
mm_72673.1	chr8	84909255	84909273	+	1	NA	exon (NM_010062, exon 3 of 6)	exon (NM_010062, exon 3 of 6)	640	NM_010062	13423	Mm.350831	NM_010062	ENSMUSG00000003812	Dnase2a	Dnase2	deoxyribonuclease II alpha	protein-coding
mm_57195.1	chr6	122850268	122850279	-	1	NA	exon (NM_009779, exon 2 of 2)	exon (NM_009779, exon 2 of 2)	5884	NM_009779	12267	Mm.2408	NM_009779	ENSMUSG00000040552	C3ar1	AZ3B|C3AR|HNFAG09	complement component 3a receptor 1	protein-coding
mm_52739.1	chr6	120463201	120463253	+	1	NA	promoter-TSS (NM_008359)	promoter-TSS (NM_008359)	30	NM_008359	16172	Mm.4481	NM_008359	ENSMUSG00000002897	Il17ra	AW538159|Cdw217|Il17r|VDw217	interleukin 17 receptor A	protein-coding
mm_117156.1	chr13	61567915	61567920	-	1	NA	intron (NM_026906, intron 4 of 7)	intron (NM_026906, intron 4 of 7)	2210	NM_026906	117066	Mm.485905	NM_026906	ENSMUSG00000074870	Cts3	1600000I23Rik	cathepsin 3	protein-coding
mm_12208.1	chr2	67169249	67169250	+	1	NA	Intergenic	Intergenic	-4585	NM_001033477	383709	Mm.244520	NM_001033477		Gm1322	-	predicted gene 1322	protein-coding
mm_34105.1	chr4	139188207	139188231	+	1	NA	Intergenic	Intergenic	-4680	NM_009798	12345	Mm.2945	NM_009798	ENSMUSG00000028745	Capzb	1700120C01Rik|AI325129|CPB1|CPB2|CPbeat2|CPbeta1|CPbeta2|Cappb1	capping protein (actin filament) muscle Z-line, beta	protein-coding
mm_101085.1	chr11	11821570	11821571	-	1	NA	intron (NM_001190448, intron 12 of 14)	intron (NM_001190448, intron 12 of 14)	-12608	NM_001163360	60530	Mm.236114	NM_021891	ENSMUSG00000035455	Fignl1	-	fidgetin-like 1	protein-coding
mm_102722.1	chr11	67140971	67140994	-	1	NA	Intergenic	Intergenic	-20902	NR_038055	74184	Mm.162554	NR_038055	ENSMUSG00000087410	2310065F04Rik	linc-Myh	RIKEN cDNA 2310065F04 gene	ncRNA
mm_57747.1	chr6	129097496	129097506	-	1	NA	intron (NM_153506, intron 2 of 4)	intron (NM_153506, intron 2 of 4)	3402	NM_153506	232409	Mm.30870	NM_153506	ENSMUSG00000030155	Clec2e	Clra|clr-a	C-type lectin domain family 2, member e	protein-coding
mm_40345.1	chr5	45520283	45520327	+	1	NA	promoter-TSS (NM_025895)	promoter-TSS (NM_025895)	76	NM_025895	66999	Mm.283045	NM_025895	ENSMUSG00000015804	Med28	1500003D12Rik|AI451633|AU045690|Eg1|FKSG20|magicin	mediator complex subunit 28	protein-coding
mm_17972.1	chr2	37632924	37632926	-	1	NA	intron (NM_009261, intron 4 of 16)	intron (NM_009261, intron 4 of 16)	14360	NM_009261	20744	Mm.237095	NM_009261	ENSMUSG00000026915	Strbp	6430510M02Rik|AI852513|C230082I21Rik|C86322|Spnr	spermatid perinuclear RNA binding protein	protein-coding
mm_28529.1	chr3	92647381	92647385	-	1	NA	intron (NM_025984, intron 1 of 1)	intron (NM_025984, intron 1 of 1)	924	NM_025984	67127	Mm.41969	NM_025984	ENSMUSG00000057609	Lce1a1	2200008B06Rik|Sprrl3	late cornified envelope 1A1	protein-coding
mm_90430.1	chr10	127515719	127515755	+	1	NA	intron (NM_001098789, intron 2 of 3)	intron (NM_001098789, intron 2 of 3)	798	NM_001098789	407790	Mm.336856	NM_001098789	ENSMUSG00000040280	Ndufa4l2	BC064011	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 4-like 2	protein-coding
mm_109484.1	chr12	111429284	111429300	+	1	NA	intron (NM_001289487, intron 12 of 13)	intron (NM_001289487, intron 12 of 13)	11847	NM_001289488	74190	Mm.248640	NM_028807	ENSMUSG00000021280	Exoc3l4	1200009I06Rik|1600013K19Rik	exocyst complex component 3-like 4	protein-coding
mm_27058.1	chr3	27656867	27656878	-	1	NA	intron (NM_173182, intron 1 of 25)	intron (NM_173182, intron 1 of 25)	53567	NM_173182	72007	Mm.38832	NM_173182	ENSMUSG00000039286	Fndc3b	1600019O04Rik|AW550168|Fad104|mKIAA4164	fibronectin type III domain containing 3B	protein-coding
mm_38562.1	chr4	141664064	141664170	-	1	NA	promoter-TSS (NM_001033150)	promoter-TSS (NM_001033150)	-2	NM_001033150	69582	Mm.33220	NM_001033150	ENSMUSG00000028917	Plekhm2	2310034J19Rik|AI854247|mKIAA0842	pleckstrin homology domain containing, family M (with RUN domain) member 2	protein-coding
mm_142607.1	chr17	46812202	46812215	-	1	NA	intron (NM_001100452, intron 5 of 10)	B1_Mur1|SINE|Alu	19205	NM_001100452	210982	Mm.37642	NM_001100452	ENSMUSG00000036568	Gltscr1l	mKIAA0240	GLTSCR1-like	protein-coding
mm_136913.1	chr17	13017087	13017092	+	1	NA	3' UTR (NM_013671, exon 5 of 5)	3' UTR (NM_013671, exon 5 of 5)	9250	NM_013671	20656	Mm.290876	NM_013671	ENSMUSG00000006818	Sod2	MnSOD|Sod-2	superoxide dismutase 2, mitochondrial	protein-coding
mm_160550.1	chr9	45906469	45906469	+	1	NA	promoter-TSS (NM_008794)	promoter-TSS (NM_008794)	-100	NM_008794	18554	Mm.3255	NM_008794	ENSMUSG00000035382	Pcsk7	AA959856|PC7|SPC7	proprotein convertase subtilisin/kexin type 7	protein-coding
mm_57810.1	chr6	129451874	129451884	-	1	NA	5' UTR (NM_175526, exon 1 of 6)	5' UTR (NM_175526, exon 1 of 6)	121	NM_175526	243653	Mm.131289	NM_175526	ENSMUSG00000033082	Clec1a	5930406N14Rik	C-type lectin domain family 1, member a	protein-coding
mm_37031.1	chr4	115074910	115074920	-	1	NA	Intergenic	MIRb|SINE|MIR	-13793	NM_001164558	67182	Mm.30181	NM_026018	ENSMUSG00000028716	Pdzk1ip1	0610007F13Rik|2700030M23Rik|AU046042|Map17	PDZK1 interacting protein 1	protein-coding
mm_22011.1	chr2	167775468	167775479	-	1	NA	Intergenic	Intergenic	84296	NR_015500	329562	Mm.123101	NM_177851	ENSMUSG00000006462	A530013C23Rik	-	RIKEN cDNA A530013C23 gene	ncRNA
mm_118752.1	chr14	22365210	22365267	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	177560	NR_046307	74896	Mm.444661	NR_046307		4930405A10Rik	4930456G20Rik	RIKEN cDNA 4930405A10 gene	ncRNA
mm_61544.1	chr7	79323536	79323548	+	1	NA	exon (NM_018811, exon 4 of 11)	exon (NM_018811, exon 4 of 11)	50276	NM_018811	54608	Mm.365490	NM_018811	ENSMUSG00000039202	Abhd2	2210009N18Rik|LABH2|Labh-2	abhydrolase domain containing 2	protein-coding
mm_96188.1	chr11	61684457	61684471	+	1	NA	promoter-TSS (NM_178618)	promoter-TSS (NM_178618)	54	NM_178618	69640	Mm.458559	NM_178618	ENSMUSG00000042377	Fam83g	2310040C09Rik|AI506990|wly	family with sequence similarity 83, member G	protein-coding
mm_114901.1	chr13	94548433	94548439	+	1	NA	intron (NM_009680, intron 26 of 26)	intron (NM_009680, intron 26 of 26)	189476	NM_009680	11774	Mm.21185	NM_009680	ENSMUSG00000021686	Ap3b1	AP-3|AU015684|C78395|Hps2|beta3A|pe|pearl|rim2	adaptor-related protein complex 3, beta 1 subunit	protein-coding
mm_111378.1	chr12	87354146	87354151	-	1	NA	intron (NM_011479, intron 4 of 11)	B1_Mur2|SINE|Alu	34207	NM_011479	20773	Mm.565	NM_011479	ENSMUSG00000021036	Sptlc2	LCB2|LCB2a|Spt2	serine palmitoyltransferase, long chain base subunit 2	protein-coding
mm_148694.1	chr19	5741708	5741729	+	1	NA	5' UTR (NM_008520, exon 2 of 28)	5' UTR (NM_008520, exon 2 of 28)	814	NM_008520	16998	Mm.182396	NM_008520	ENSMUSG00000024940	Ltbp3	Ltbp2|mFLJ00070	latent transforming growth factor beta binding protein 3	protein-coding
mm_29120.1	chr3	105052688	105052717	-	1	NA	intron (NM_030249, intron 1 of 5)	CpG	251	NM_001163333	80281	Mm.200327	NM_030249	ENSMUSG00000062127	Cttnbp2nl	AA552995|AA589392|AU018624|BC003236|mKIAA1433	CTTNBP2 N-terminal like	protein-coding
mm_49597.1	chr6	30670233	30670242	+	1	NA	intron (NR_130781, intron 3 of 11)	intron (NR_130781, intron 3 of 11)	23512	NM_031998	83922	Mm.65389	NM_031998	ENSMUSG00000029790	Cep41	1700017E11Rik|2810431D15Rik|Tsga14	centrosomal protein 41	protein-coding
mm_36440.1	chr4	82296677	82296680	-	1	NA	3' UTR (NM_001113209, exon 12 of 12)	3' UTR (NM_001113209, exon 12 of 12)	209101	NM_001286127	18028	Mm.317947	NM_008687	ENSMUSG00000008575	Nfib	6720429L07Rik|CTF|E030026I10Rik|NF-I/B|NF1-B|NFI-B	nuclear factor I/B	protein-coding
mm_15251.1	chr2	154791345	154791362	+	1	NA	5' UTR (NM_001139513, exon 1 of 9)	5' UTR (NM_001139513, exon 1 of 9)	243	NM_001139511	19383	Mm.221440	NM_023130	ENSMUSG00000027593	Raly	AI663842|Merc	hnRNP-associated with lethal yellow	protein-coding
mm_27908.1	chr3	79521327	79521344	-	1	NA	intron (NM_001162999, intron 1 of 16)	B1F|SINE|Alu	46344	NM_001162999	329679	Mm.244005	NM_001162999	ENSMUSG00000061175	Fnip2	D630023B12Rik|mKIAA1450	folliculin interacting protein 2	protein-coding
mm_106735.1	chr12	3895469	3895487	+	1	NA	intron (NM_153743, intron 1 of 17)	intron (NM_153743, intron 1 of 17)	3734	NM_153743	13435	Mm.5001	NM_007872	ENSMUSG00000020661	Dnmt3a	MmuIIIA	DNA methyltransferase 3A	protein-coding
mm_68693.1	chr7	119523478	119523491	-	1	NA	promoter-TSS (NM_027943)	promoter-TSS (NM_027943)	-2	NM_027943	71830	Mm.84631	NM_027943	ENSMUSG00000030968	Pdilt	1700007B13Rik	protein disulfide isomerase-like, testis expressed	protein-coding
mm_57281.1	chr6	124357033	124357054	-	1	NA	promoter-TSS (NM_001177502)	promoter-TSS (NM_001177502)	43	NM_001177502	76921	Mm.425335	NM_001177502	ENSMUSG00000079346	1700013D24Rik	-	RIKEN cDNA 1700013D24 gene	protein-coding
mm_119277.1	chr14	34310767	34310778	+	1	NA	promoter-TSS (NM_008133)	promoter-TSS (NM_008133)	45	NM_008133	14661	Mm.10600	NM_008133	ENSMUSG00000021794	Glud1	AI118167|Gdh-X|Glud|Gludl	glutamate dehydrogenase 1	protein-coding
mm_54887.1	chr6	43666159	43666224	-	1	NA	promoter-TSS (NM_013861)	promoter-TSS (NM_013861)	87	NM_001311111	29807	Mm.320979	NM_013861	ENSMUSG00000029735	Tpk1	-	thiamine pyrophosphokinase	protein-coding
mm_130657.1	chr15	100637271	100637281	-	1	NA	promoter-TSS (NM_174992)	promoter-TSS (NM_174992)	-336	NM_001033872	207818	Mm.26282	NM_174992	ENSMUSG00000053559	Smagp	-	small cell adhesion glycoprotein	protein-coding
mm_103198.1	chr11	70650334	70650337	-	1	NA	intron (NM_027445, intron 7 of 8)	intron (NM_027445, intron 7 of 8)	3048	NM_027445	70510	Mm.261818	NM_027445	ENSMUSG00000040746	Rnf167	0610010G05Rik|5730408C10Rik|AU019305|AV328608	ring finger protein 167	protein-coding
mm_160168.1	chr7	44943376	44943376	+	1	NA	exon (NM_001077591, exon 1 of 11)	exon (NM_001077591, exon 1 of 11)	136	NM_011651	22116	Mm.84502	NM_011651	ENSMUSG00000059891	Tsks	Stk22s1|Tssks1	testis-specific serine kinase substrate	protein-coding
mm_168850.1	chr12	24083721	24083731	-	1	NA	intron (NM_001256489, intron 1 of 3)	MMVL30-int|LTR|ERV1	13543	NM_001256489	66808	Mm.379124	NM_001256489	ENSMUSG00000073158	9030624G23Rik	-	RIKEN cDNA 9030624G23 gene	protein-coding
mm_52549.1	chr6	115935589	115935596	+	1	NA	exon (NM_145383, exon 4 of 5)	exon (NM_145383, exon 4 of 5)	3665	NM_145383	212541	Mm.2965	NM_145383	ENSMUSG00000030324	Rho	Noerg1|Opn2|Ops|RP4	rhodopsin	protein-coding
mm_110086.1	chr12	24831124	24831136	-	1	NA	promoter-TSS (NM_026037)	promoter-TSS (NM_026037)	-469	NM_026037	67216	Mm.167671	NM_026037	ENSMUSG00000020646	Mboat2	2810049G06Rik|AU022889|AW547221|LPCAT4|Moact2|Oact2	membrane bound O-acyltransferase domain containing 2	protein-coding
mm_60406.1	chr7	44475986	44475996	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	5644	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_12853.1	chr2	83721110	83721123	+	1	NA	Intergenic	Intergenic	-3281	NM_008402	16410	Mm.227	NM_008402	ENSMUSG00000027087	Itgav	1110004F14Rik|2610028E01Rik|CD51|D430040G12Rik	integrin alpha V	protein-coding
mm_18965.1	chr2	76807419	76807430	-	1	NA	intron (NM_028004, intron 67 of 191)	intron (NM_028004, intron 67 of 191)	132109	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_50129.1	chr6	41541945	41541954	+	1	NA	Intergenic	Intergenic	20173	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_42359.1	chr5	114911873	114911883	+	1	NA	3' UTR (NM_011854, exon 6 of 6)	3' UTR (NM_011854, exon 6 of 6)	-11362	NM_145209	231655	Mm.95479	NM_145209	ENSMUSG00000041827	Oasl1	7530414C13Rik|oasl9	2'-5' oligoadenylate synthetase-like 1	protein-coding
mm_143992.1	chr17	87798030	87798049	-	1	NA	promoter-TSS (NM_199251)	promoter-TSS (NM_199251)	-45	NM_199251	210741	Mm.312046	NM_199251	ENSMUSG00000050138	Kcnk12	mntk1	potassium channel, subfamily K, member 12	protein-coding
mm_88257.1	chr10	73779606	73779611	+	1	NA	Intergenic	Lx9|LINE|L1	-42259	NM_001142760	11994	Mm.338933	NM_023115	ENSMUSG00000052613	Pcdh15	BB078305|ENSMUSG00000046980|Gm9815|Ush1f|av|nmf19|roda	protocadherin 15	protein-coding
mm_141105.1	chr17	26021815	26021821	-	1	NA	promoter-TSS (NM_153140)	promoter-TSS (NM_153140)	42	NM_153140	215445	Mm.41191	NM_153140	ENSMUSG00000037098	Rab11fip3	Cart1|D030060O14Rik|Rab11-FIP3|mKIAA0665	RAB11 family interacting protein 3 (class II)	protein-coding
mm_86477.1	chr10	4710120	4710166	+	1	NA	promoter-TSS (NM_001302533)	promoter-TSS (NM_001302533)	-15	NM_001302531	13982	Mm.9213	NM_007956	ENSMUSG00000019768	Esr1	ER|ER-alpha|ERa|ERalpha|ESR|Estr|Estra|Nr3a1	estrogen receptor 1 (alpha)	protein-coding
mm_89351.1	chr10	88147062	88147076	+	1	NA	promoter-TSS (NM_027191)	promoter-TSS (NM_027191)	-2	NM_028334	69736	Mm.222184	NM_027191	ENSMUSG00000035351	Nup37	2410003L22Rik|2810039M17Rik	nucleoporin 37	protein-coding
mm_150503.1	chr19	39022735	39022742	+	1	NA	intron (NM_028089, intron 4 of 8)	intron (NM_028089, intron 4 of 8)	15719	NM_028089	72082	Mm.142581	NM_028089	ENSMUSG00000025002	Cyp2c55	2010318C06Rik	cytochrome P450, family 2, subfamily c, polypeptide 55	protein-coding
mm_37673.1	chr4	129121648	129121662	-	1	NA	promoter-TSS (NM_010471)	promoter-TSS (NM_010471)	92	NM_001130419	15444	Mm.384452	NM_010471	ENSMUSG00000028785	Hpca	-	hippocalcin	protein-coding
mm_163654.1	chr13	70535501	70535503	+	1	NA	Intergenic	Intergenic	-37739	NR_045934	73584	Mm.442491	NR_045934	ENSMUSG00000101051	1700100L14Rik	-	RIKEN cDNA 1700100L14 gene	ncRNA
mm_141056.1	chr17	25752353	25752385	-	1	NA	exon (NM_018857, exon 5 of 16)	exon (NM_018857, exon 5 of 16)	1958	NM_018857	56047	Mm.17510	NM_018857	ENSMUSG00000063011	Msln	MPF	mesothelin	protein-coding
mm_1934.1	chr1	86111022	86111024	+	1	NA	5' UTR (NM_008311, exon 2 of 4)	5' UTR (NM_008311, exon 2 of 4)	947	NM_008311	15559	Mm.439747	NM_008311	ENSMUSG00000026228	Htr2b	5-HT2B|AJ012488|AV377389	5-hydroxytryptamine (serotonin) receptor 2B	protein-coding
mm_125642.1	chr15	62178263	62178286	+	1	NA	intron (NR_132746, intron 3 of 6)	intron (NR_132746, intron 3 of 6)	41177	NR_003523	67552	Mm.484027	NM_026230		H2afy3	4933432H23Rik	H2A histone family, member Y3	pseudo
mm_45906.1	chr5	89223858	89223887	-	1	NA	intron (NM_001197147, intron 21 of 25)	intron (NM_001197147, intron 21 of 25)	234026	NM_008096	14473	Mm.196595	NM_008096	ENSMUSG00000035540	Gc	DBP|VDB	group specific component	protein-coding
mm_62173.1	chr7	97371605	97371640	+	1	NA	promoter-TSS (NM_199035)	promoter-TSS (NM_199035)	5	NM_199035	381903	Mm.279683	NM_199035	ENSMUSG00000035704	Alg8	AI447372|Gm1089	asparagine-linked glycosylation 8 (alpha-1,3-glucosyltransferase)	protein-coding
mm_66780.1	chr7	46958445	46958474	-	1	NA	promoter-TSS (NM_001040695)	promoter-TSS (NM_001040695)	59	NM_001040695	54122	Mm.1999	NM_016855	ENSMUSG00000043262	Uevld	8430408E05Rik|Attp	UEV and lactate/malate dehyrogenase domains	protein-coding
mm_158936.1	chr1	74278383	74278383	+	1	NA	promoter-TSS (NM_174985)	promoter-TSS (NM_174985)	-217	NM_174985	227289	Mm.246587	NM_174985	ENSMUSG00000064272	Gpbar1	BG37|GPCR|GPR131|M-BAR|TGR5	G protein-coupled bile acid receptor 1	protein-coding
mm_69.1	chr1	6638090	6638124	+	1	NA	intron (NM_001244693, intron 2 of 22)	intron (NM_001244693, intron 2 of 22)	-91944	NR_045189	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding
mm_15996.1	chr2	167063214	167063227	+	1	NA	promoter-TSS (NM_001033196)	promoter-TSS (NM_001033196)	-205	NM_001033196	98999	Mm.297074	NM_001033196	ENSMUSG00000039501	Znfx1	AI481105|Astx3	zinc finger, NFX1-type containing 1	protein-coding
mm_86333.1	chr9	123100554	123100571	-	1	NA	exon (NM_026917, exon 2 of 7)	exon (NM_026917, exon 2 of 7)	12643	NM_026917	69035	Mm.28300	NM_026917	ENSMUSG00000025786	Zdhhc3	1110020O22Rik|1810006O10Rik|2210017C02Rik|DHHC-3|GODZ|Gramp1|Zfp373	zinc finger, DHHC domain containing 3	protein-coding
mm_31080.1	chr4	41517439	41517447	+	1	NA	promoter-TSS (NM_001048005)	promoter-TSS (NM_001048005)	6	NR_045726	76992	Mm.440546	NR_045726	ENSMUSG00000036162	Fam219aos	1700066J24Rik	family with sequence similarity 219, member A, opposite strand	ncRNA
mm_56113.1	chr6	87511139	87511151	-	1	NA	intron (NM_001037727, intron 1 of 10)	intron (NM_001037727, intron 1 of 10)	-14818	NM_175476	232201	Mm.119564	NM_175476	ENSMUSG00000030047	Arhgap25	A130039I20Rik	Rho GTPase activating protein 25	protein-coding
mm_50476.1	chr6	48988029	48988039	+	1	NA	exon (NM_172888, exon 1 of 5)	exon (NM_172888, exon 1 of 5)	1173	NM_172888	243377	Mm.446302	NM_172888	ENSMUSG00000039215	Svs1	9530003A11	seminal vesicle secretory protein 1	protein-coding
mm_8547.1	chr1	155146756	155146789	-	1	NA	promoter-TSS (NM_008209)	promoter-TSS (NM_008209)	8	NM_008209	15064	Mm.7580	NM_008209	ENSMUSG00000026471	Mr1	H2ls	major histocompatibility complex, class I-related	protein-coding
mm_136292.1	chr16	91441542	91441542	-	1	NA	Intergenic	Intergenic	-23562	NR_077219	100503120	Mm.387130	NR_077219	ENSMUSG00000084866	A930006K02Rik	-	RIKEN cDNA A930006K02 gene	ncRNA
mm_51963.1	chr6	91758080	91758086	+	1	NA	3' UTR (NM_009320, exon 15 of 15)	3' UTR (NM_009320, exon 15 of 15)	49310	NM_001159507	243547	Mm.333264	NM_001033353	ENSMUSG00000030098	Grip2	-	glutamate receptor interacting protein 2	protein-coding
mm_164760.1	chr17	84956941	84956945	-	1	NA	intron (NM_001159497, intron 1 of 5)	intron (NM_001159497, intron 1 of 5)	202	NM_001159497	19043	Mm.249695	NM_011151	ENSMUSG00000061130	Ppm1b	PP2CB	protein phosphatase 1B, magnesium dependent, beta isoform	protein-coding
mm_127657.1	chr15	102498730	102498740	+	1	NA	3' UTR (NM_001163643, exon 16 of 16)	3' UTR (NM_001163643, exon 16 of 16)	18269	NM_001163643	26404	Mm.172897	NM_009582	ENSMUSG00000023050	Map3k12	DLK|MUK|Zpk	mitogen-activated protein kinase kinase kinase 12	protein-coding
mm_47337.1	chr5	122502137	122502145	-	1	NA	promoter-TSS (NM_009722)	promoter-TSS (NM_009722)	84	NM_001110140	11938	Mm.227583	NM_009722	ENSMUSG00000029467	Atp2a2	9530097L16Rik|D5Wsu150e|SERCA2|SERCA2B|Serca2a|mKIAA4195	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	protein-coding
mm_100944.1	chr11	6528708	6528780	-	1	NA	promoter-TSS (NR_045893)	promoter-TSS (NR_045893)	16	NR_045893	100041286	Mm.459507	NR_045893	ENSMUSG00000085156	Snhg15	Gm11974|OTTMUSG00000005115	small nucleolar RNA host gene 15	ncRNA
mm_35936.1	chr4	53033048	53033070	-	1	NA	3' UTR (NM_013454, exon 50 of 50)	3' UTR (NM_013454, exon 50 of 50)	21179	NM_025623	66536	Mm.38244	NM_025623	ENSMUSG00000015247	Nipsnap3b	2700063N13Rik|Nipsnap3a	nipsnap homolog 3B (C. elegans)	protein-coding
mm_156838.1	chrX	164373489	164373505	+	1	NA	promoter-TSS (NM_010216)	promoter-TSS (NM_010216)	-25	NM_001308489	14205	Mm.297978	NM_010216	ENSMUSG00000031380	Vegfd	AI325264|Figf|VEGF-D	vascular endothelial growth factor D	protein-coding
mm_15202.1	chr2	154207138	154207146	+	1	NA	exon (NM_153418, exon 6 of 16)	exon (NM_153418, exon 6 of 16)	6762	NM_153418	228801	Mm.3783	NM_153418	ENSMUSG00000027485	Bpifb1	Lplunc1	BPI fold containing family B, member 1	protein-coding
mm_168697.1	chr11	97768040	97768054	+	1	NA	Intergenic	Intergenic	-1434	NM_026186	67480	Mm.33206	NM_026186	ENSMUSG00000018541	Cwc25	1300013D05Rik|AA473636|Ccdc49|R75228	CWC25 spliceosome-associated protein	protein-coding
mm_98690.1	chr11	96299090	96299102	+	1	NA	promoter-TSS (NM_008269)	promoter-TSS (NM_008269)	-75	NM_008269	15414	Mm.215	NM_008269	ENSMUSG00000000690	Hoxb6	Hox-2.2	homeobox B6	protein-coding
mm_11797.1	chr2	43555363	43555367	+	1	NA	promoter-TSS (NM_001289593)	promoter-TSS (NM_001289593)	40	NM_027552	70789	Mm.105278	NM_027552	ENSMUSG00000026866	Kynu	4432411A05Rik	kynureninase (L-kynurenine hydrolase)	protein-coding
mm_622.1	chr1	40101376	40101378	+	1	NA	intron (NM_010555, intron 1 of 8)	intron (NM_010555, intron 1 of 8)	-15526	NR_037980	100047133	Mm.447052	NR_037980	ENSMUSG00000097899	Gm16894	-	predicted gene, 16894	ncRNA
mm_133447.1	chr16	87823757	87823761	+	1	NA	Intergenic	Intergenic	124805	NM_007520	12013	Mm.26147	NM_007520	ENSMUSG00000025612	Bach1	6230421P05Rik|AI323795	BTB and CNC homology 1, basic leucine zipper transcription factor 1	protein-coding
mm_38696.1	chr4	145214199	145214217	-	1	NA	3' UTR (NM_011610, exon 10 of 10)	3' UTR (NM_011610, exon 10 of 10)	-19203	NM_001276465	230895	Mm.240310	NM_001033190	ENSMUSG00000020220	Vps13d	-	vacuolar protein sorting 13D	protein-coding
mm_160747.1	chr10	81252868	81252868	+	1	NA	promoter-TSS (NM_001285855)	promoter-TSS (NM_001285855)	-67	NM_001285855	17179	Mm.2918	NM_010768	ENSMUSG00000004933	Matk	CHK|HYL|Ntk|p56ntk	megakaryocyte-associated tyrosine kinase	protein-coding
mm_110438.1	chr12	49776820	49776820	-	1	NA	Intergenic	L1_Mur3|LINE|L1	-295958	NR_045472	69054	Mm.417838	NR_045472	ENSMUSG00000100844	1810007C17Rik	-	RIKEN cDNA 1810007C17 gene	ncRNA
mm_134118.1	chr16	10313837	10313851	-	1	NA	5' UTR (NM_007929, exon 1 of 5)	5' UTR (NM_007929, exon 1 of 5)	124	NM_007929	13731	Mm.246009	NM_007929	ENSMUSG00000022505	Emp2	XMP	epithelial membrane protein 2	protein-coding
mm_157646.1	chrX	57305035	57305045	-	1	NA	intron (NM_152801, intron 2 of 21)	intron (NM_152801, intron 2 of 21)	33689	NM_152801	73341	Mm.261443	NM_152801	ENSMUSG00000031133	Arhgef6	1600028C08Rik|1700038J06Rik|4930592P22Rik|alpha-PIX	Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_56365.1	chr6	93912955	93912977	-	1	NA	promoter-TSS (NR_104594)	promoter-TSS (NR_104594)	-3	NR_104594	14924	Mm.217216	NM_010367	ENSMUSG00000045095	Magi1	AIP3|BAP1|Baiap1|Gukmi1|MAGI1c|Magi-1|TNRC19|WWP3|mKIAA4129	membrane associated guanylate kinase, WW and PDZ domain containing 1	protein-coding
mm_159807.1	chr5	115731584	115731584	-	1	NA	promoter-TSS (NM_001080808)	promoter-TSS (NM_001080808)	-25	NM_001080808	75665	Mm.233914	NM_001080808	ENSMUSG00000041609	Ccdc64	2210403N09Rik|BICDR-1|Bicdl1	coiled-coil domain containing 64	protein-coding
mm_62937.1	chr7	118855736	118855798	+	1	NA	promoter-TSS (NM_001168220)	promoter-TSS (NM_001168220)	-8	NM_001081446	434232	Mm.458509	NM_001081446	ENSMUSG00000073856	Iqck	A230094G09Rik	IQ motif containing K	protein-coding
mm_63095.1	chr7	122366573	122366587	+	1	NA	intron (NM_001316672, intron 2 of 16)	(CACAC)n|Simple_repeat|Simple_repeat	77455	NM_008855	18751	Mm.207496	NM_008855	ENSMUSG00000052889	Prkcb	PKC-B|PKC-Beta|Pkcb|Prkcb1|Prkcb2	protein kinase C, beta	protein-coding
mm_95506.1	chr11	51961346	51961352	+	1	NA	Intergenic	Intergenic	-6282	NM_029976	52626	Mm.289456	NM_029976	ENSMUSG00000020392	Cdkn2aipnl	A430101B06Rik|AA409260|D11Ertd497e|MNCb-1520	CDKN2A interacting protein N-terminal like	protein-coding
mm_143857.1	chr17	84185603	84185641	-	1	NA	3' UTR (NM_001001806, exon 2 of 2)	3' UTR (NM_001001806, exon 2 of 2)	2325	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_102787.1	chr11	68431980	68432005	-	1	NA	promoter-TSS (NM_177320)	promoter-TSS (NM_177320)	-133	NM_177320	320207	Mm.244960	NM_177320	ENSMUSG00000020901	Pik3r5	AV230647|F730038I15Rik	phosphoinositide-3-kinase, regulatory subunit 5, p101	protein-coding
mm_134238.1	chr16	11909406	11909429	-	1	NA	promoter-TSS (NM_146067)	promoter-TSS (NM_146067)	6	NM_146067	223978	Mm.86360	NM_146067	ENSMUSG00000065979	Cpped1	C530044N13Rik	calcineurin-like phosphoesterase domain containing 1	protein-coding
mm_14248.1	chr2	128126031	128126056	+	1	NA	promoter-TSS (NM_009754)	promoter-TSS (NM_009754)	5	NM_009754	12125	Mm.141083	NM_009754	ENSMUSG00000027381	Bcl2l11	1500006F24Rik|Bim|Bod|bcl2-L-11	BCL2-like 11 (apoptosis facilitator)	protein-coding
mm_96384.1	chr11	67244638	67244649	+	1	NA	exon (NM_010855, exon 12 of 40)	exon (NM_010855, exon 12 of 40)	6831	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_47837.1	chr5	134314407	134314424	-	1	NA	5' UTR (NM_010365, exon 1 of 34)	5' UTR (NM_010365, exon 1 of 34)	345	NM_001080746	14886	Mm.261570	NM_010365	ENSMUSG00000060261	Gtf2i	6030441I21Rik|BAP-135|Diws1t|GtfII-I|Spin|TFII-I|WBSCR6	general transcription factor II I	protein-coding
mm_6053.1	chr1	60098141	60098151	-	1	NA	promoter-TSS (NM_139150)	promoter-TSS (NM_139150)	-12	NM_001199061	57750	Mm.281079	NM_021312	ENSMUSG00000026019	Wdr12	4933402C23Rik|Ytm1|Ytm1p	WD repeat domain 12	protein-coding
mm_43141.1	chr5	125441547	125441614	+	1	NA	promoter-TSS (NM_029752)	promoter-TSS (NM_029752)	12	NM_029752	76809	Mm.290720	NM_029752	ENSMUSG00000037905	Bri3bp	2410150I18Rik|AI841257|AW742481	Bri3 binding protein	protein-coding
mm_72514.1	chr8	83929915	83929934	+	1	NA	exon (NM_181039, exon 5 of 23)	exon (NM_181039, exon 5 of 23)	-25770	NM_024184	66929	Mm.29680	NM_024184	ENSMUSG00000005470	Asf1b	1700003K02Rik|AA409591	anti-silencing function 1B histone chaperone	protein-coding
mm_114258.1	chr13	56728906	56728909	+	1	NA	intron (NM_001164041, intron 4 of 6)	RMER1B|Other|Other	25239	NM_001164042	17129	Mm.272920	NM_008541	ENSMUSG00000021540	Smad5	1110051M15Rik|AI451355|Dwf-C|Madh5|MusMLP	SMAD family member 5	protein-coding
mm_72635.1	chr8	84686301	84686348	+	1	NA	intron (NM_025788, intron 1 of 5)	intron (NM_025788, intron 1 of 5)	1538	NM_025788	66830	Mm.289698	NM_025788	ENSMUSG00000001910	Nacc1	2010001H03Rik|4930511N13Rik|Btbd14b|Nac1	nucleus accumbens associated 1, BEN and BTB (POZ) domain containing	protein-coding
mm_109313.1	chr12	109560993	109561003	+	1	NA	non-coding (NR_003633, exon 5 of 5)	non-coding (NR_003633, exon 5 of 5)	-2694	NR_030427	791079		NR_030427	ENSMUSG00000076451	Mir770	Mirn770|mir-770|mmu-mir-770	microRNA 770	ncRNA
mm_161970.1	chr19	10993163	10993163	-	1	NA	promoter-TSS (NM_001034898)	promoter-TSS (NM_001034898)	87	NM_001034898	545279	Mm.329729	NM_001034898	ENSMUSG00000067571	Ms4a15	E530011F12Rik|Gm1286	membrane-spanning 4-domains, subfamily A, member 15	protein-coding
mm_86597.1	chr10	13304115	13304127	+	1	NA	intron (NM_001195065, intron 1 of 12)	intron (NM_001195065, intron 1 of 12)	20039	NM_001195096	215789	Mm.283359	NM_001033257	ENSMUSG00000062866	Phactr2	AV158170|BC012871	phosphatase and actin regulator 2	protein-coding
mm_75360.1	chr8	45277037	45277040	-	1	NA	exon (NM_008455, exon 8 of 15)	exon (NM_008455, exon 8 of 15)	-15007	NM_028066	109821	Mm.33326	NM_028066	ENSMUSG00000031645	F11	1600027G01Rik|AI503996|Cf11|FXI|PTA	coagulation factor XI	protein-coding
mm_102044.1	chr11	51998898	51998903	-	1	NA	intron (NM_009458, intron 1 of 5)	intron (NM_009458, intron 1 of 5)	1566	NM_009458	22210	Mm.384918	NM_009458	ENSMUSG00000020390	Ube2b	2610301N02Rik|E2-14k|HR6B|Rad6b|mHR6B	ubiquitin-conjugating enzyme E2B	protein-coding
mm_614.1	chr1	40025365	40025388	+	1	NA	3' UTR (NM_001252202, exon 30 of 30)	3' UTR (NM_001252202, exon 30 of 30)	-59392	NM_010555	16178	Mm.1349	NM_010555	ENSMUSG00000026073	Il1r2	CD121b|Il1r-2	interleukin 1 receptor, type II	protein-coding
mm_144367.1	chr18	20499210	20499216	+	1	NA	Intergenic	Intergenic	-11061	NM_030596	13512	Mm.106811	NM_030596	ENSMUSG00000056632	Dsg3	bal	desmoglein 3	protein-coding
mm_133720.1	chr16	93683230	93683249	+	1	NA	promoter-TSS (NM_173047)	promoter-TSS (NM_173047)	20	NM_173047	109857	Mm.4512	NM_173047	ENSMUSG00000022947	Cbr3	1110001J05Rik|C81353	carbonyl reductase 3	protein-coding
mm_23299.1	chr3	52276154	52276159	+	1	NA	intron (NM_019739, intron 1 of 2)	Lx8b|LINE|L1	7819	NM_019739	56458	Mm.29891	NM_019739	ENSMUSG00000044167	Foxo1	AI876417|Afxh|FKHR|Fkhr1|Foxo1a	forkhead box O1	protein-coding
mm_120423.1	chr14	65394775	65394793	+	1	NA	exon (NM_199029, exon 8 of 10)	exon (NM_199029, exon 8 of 10)	30688	NM_001205075	18155	Mm.16347	NM_010932	ENSMUSG00000045731	Pnoc	N/OFQ|Npnc1|OFQ/N	prepronociceptin	protein-coding
mm_101515.1	chr11	32409922	32409937	-	1	NA	intron (NM_177364, intron 8 of 12)	intron (NM_177364, intron 8 of 12)	-45443	NM_173784	327900	Mm.260956	NM_173784	ENSMUSG00000044949	Ubtd2	4930571L24|9630054F20Rik|AI645720	ubiquitin domain containing 2	protein-coding
mm_169586.1	chr15	25681729	25681730	+	1	NA	intron (NM_019472, intron 2 of 40)	intron (NM_019472, intron 2 of 40)	59179	NM_019472	17909	Mm.60590	NM_019472	ENSMUSG00000022272	Myo10	AW048724|D15Ertd600e|mKIAA0799|myosin-X	myosin X	protein-coding
mm_115922.1	chr13	23555552	23555585	-	1	NA	exon (NM_145713, exon 1 of 1)	exon (NM_145713, exon 1 of 1)	536	NM_145713	14957	Mm.247046	NM_145713	ENSMUSG00000052565	Hist1h1d	H1.3|H1D|H1f3|H1s-4	histone cluster 1, H1d	protein-coding
mm_90627.1	chr10	128459291	128459328	+	1	NA	promoter-TSS (NM_001114096)	promoter-TSS (NM_001114096)	73	NM_001114097	68094	Mm.417338	NM_198160	ENSMUSG00000025369	Smarcc2	5930405J04Rik	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2	protein-coding
mm_147845.1	chr18	63387125	63387189	-	1	NA	promoter-TSS (NM_001039485)	promoter-TSS (NM_001039485)	26	NM_001039485	667742	Mm.158720	NM_172629	ENSMUSG00000041482	Piezo2	5930434P17|9030411M15Rik|9430028L06Rik|Fam38b|Fam38b2	piezo-type mechanosensitive ion channel component 2	protein-coding
mm_5177.1	chr1	11401272	11401277	-	1	NA	Intergenic	RLTR9A2|LTR|ERVK	-12831	NM_001310451	320492	Mm.52021	NM_177173	ENSMUSG00000057715	A830018L16Rik	-	RIKEN cDNA A830018L16 gene	protein-coding
mm_30344.1	chr3	151742296	151742312	-	1	NA	intron (NM_133871, intron 5 of 7)	RMER20B|LTR|ERVK	7655	NM_133871	99899	Mm.30756	NM_133871	ENSMUSG00000028037	Ifi44	A430056A10Rik|AW261460|MTAP44|p44	interferon-induced protein 44	protein-coding
mm_122840.1	chr14	54724099	54724109	-	1	NA	exon (NM_016972, exon 11 of 11)	exon (NM_016972, exon 11 of 11)	-11930	NM_207131	110794	Mm.236223	NM_207131	ENSMUSG00000052435	Cebpe	C/EBPe|CRP1|Gm294	CCAAT/enhancer binding protein (C/EBP), epsilon	protein-coding
mm_81382.1	chr9	108936686	108936715	+	1	NA	promoter-TSS (NM_025407)	promoter-TSS (NM_025407)	52	NM_025407	22273	Mm.335460	NM_025407	ENSMUSG00000025651	Uqcrc1	1110032G10Rik	ubiquinol-cytochrome c reductase core protein 1	protein-coding
mm_98550.1	chr11	95057085	95057094	+	1	NA	exon (NM_001306162, exon 15 of 26)	exon (NM_001306162, exon 15 of 26)	12109	NM_001306071	16400	Mm.57035	NM_013565	ENSMUSG00000001507	Itga3	AA407068|CD49C|GAPB3	integrin alpha 3	protein-coding
mm_112293.1	chr12	114538971	114538982	-	1	NA	Intergenic	Intergenic	-25282	NR_106063	102465664		NR_106063	ENSMUSG00000098357	Mir7094-2	Gm27508|mmu-mir-7094-2	microRNA 7094-2	ncRNA
mm_60098.1	chr7	35120007	35120022	+	1	NA	exon (NM_001287514, exon 1 of 1)	exon (NM_001287514, exon 1 of 1)	721	NM_007678	12606	Mm.349667	NM_007678	ENSMUSG00000034957	Cebpa	C/ebpalpha|CBF-A|Cebp	CCAAT/enhancer binding protein (C/EBP), alpha	protein-coding
mm_31623.1	chr4	59189667	59189677	+	1	NA	exon (NM_011673, exon 1 of 9)	exon (NM_011673, exon 1 of 9)	122	NM_011673	22234	Mm.198803	NM_011673	ENSMUSG00000028381	Ugcg	AU043821|C80537|Epcs21|GlcT-1|Ugcgl	UDP-glucose ceramide glucosyltransferase	protein-coding
mm_37684.1	chr4	129223246	129223256	-	1	NA	exon (NM_001285867, exon 6 of 7)	exon (NM_001285867, exon 6 of 7)	4660	NM_001285866	97130	Mm.331907	NM_001033189	ENSMUSG00000050390	C77080	Kiaa1522|mKIAA1522	expressed sequence C77080	protein-coding
mm_147356.1	chr18	43373218	43373245	-	1	NA	promoter-TSS (NM_001136086)	promoter-TSS (NM_001136086)	41	NM_001136086	22240	Mm.8180	NM_009468	ENSMUSG00000024501	Dpysl3	CRMP-4|DRP-3|TUC4|ULIP-1|Ulip|Ulip1	dihydropyrimidinase-like 3	protein-coding
mm_138621.1	chr17	35835518	35835539	+	1	NA	exon (NM_011655, exon 4 of 4)	exon (NM_011655, exon 4 of 4)	2773	NM_011655	22154	Mm.273538	NM_011655	ENSMUSG00000001525	Tubb5	AA408537|AI596182|B130022C14Rik|M(beta)5	tubulin, beta 5 class I	protein-coding
mm_124642.1	chr15	4727203	4727230	+	1	NA	promoter-TSS (NM_016704)	promoter-TSS (NM_016704)	6	NM_016704	12274	Mm.20247	NM_016704	ENSMUSG00000022181	C6	AW111623	complement component 6	protein-coding
mm_159490.1	chr4	42650665	42650665	+	1	NA	promoter-TSS (NM_001199961).2	promoter-TSS (NM_001199961).2	61	NM_001199962	100039863	Mm.6660	NM_001164046	ENSMUSG00000073877	Gm13306	OTTMUSG00000011352	predicted gene 13306	protein-coding
mm_86087.1	chr9	114902335	114902340	-	1	NA	3' UTR (NM_175380, exon 8 of 8)	3' UTR (NM_175380, exon 8 of 8)	31650	NM_175380	333433	Mm.38198	NM_175380	ENSMUSG00000050627	Gpd1l	2210409H23Rik|D9Ertd660e	glycerol-3-phosphate dehydrogenase 1-like	protein-coding
mm_43447.1	chr5	136110607	136110629	+	1	NA	intron (NM_001039103, intron 18 of 19)	PB1D9|SINE|Alu	5096	NR_106002	102465626		NR_106002	ENSMUSG00000099003	Mir7035	Gm27661|mmu-mir-7035	microRNA 7035	ncRNA
mm_61537.1	chr7	79273249	79273270	+	1	NA	promoter-TSS (NM_018811)	promoter-TSS (NM_018811)	-7	NM_018811	54608	Mm.365490	NM_018811	ENSMUSG00000039202	Abhd2	2210009N18Rik|LABH2|Labh-2	abhydrolase domain containing 2	protein-coding
mm_166746.1	chr6	124996768	124996781	+	1	NA	promoter-TSS (NM_175696)	promoter-TSS (NM_175696)	54	NM_175696	319352	Mm.295327	NM_175696	ENSMUSG00000030329	Pianp	AI255183|AU067746|C530028O21Rik|Panp	PILR alpha associated neural protein	protein-coding
mm_155905.1	chrX	101683141	101683159	+	1	NA	3' UTR (NM_001290535, exon 22 of 22)	3' UTR (NM_001290535, exon 22 of 22)	42932	NM_001290535	108155	Mm.487332	NM_139144	ENSMUSG00000034160	Ogt	1110038P24Rik|4831420N21Rik|AI115525|Ogtl	O-linked N-acetylglucosamine (GlcNAc) transferase (UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase)	protein-coding
mm_92574.1	chr10	79916879	79916906	-	1	NA	promoter-TSS (NM_177994)	promoter-TSS (NM_177994)	38	NM_177994	109284	Mm.300416	NM_177994	ENSMUSG00000035781	R3hdm4	AI503502|C030046I01Rik	R3H domain containing 4	protein-coding
mm_92221.1	chr10	68277518	68277529	-	1	NA	intron (NM_023598, intron 2 of 9)	intron (NM_023598, intron 2 of 9)	1203	NM_023598	71371	Mm.440357	NM_023598	ENSMUSG00000019947	Arid5b	4930580B11|5430435G07Rik|AI467247|Desrt|Mrf2|Mrf2alpha|Mrf2beta	AT rich interactive domain 5B (MRF1-like)	protein-coding
mm_62714.1	chr7	110768831	110768847	+	1	NA	intron (NM_001276301, intron 1 of 14)	CpG	633	NM_001276301	11717	Mm.3238	NM_009667	ENSMUSG00000005686	Ampd3	-	adenosine monophosphate deaminase 3	protein-coding
mm_74490.1	chr8	4779514	4779591	-	1	NA	promoter-TSS (NM_011369)	promoter-TSS (NM_011369)	-18	NM_011369	20419	Mm.37801	NM_011369	ENSMUSG00000022322	Shcbp1	mPAL	Shc SH2-domain binding protein 1	protein-coding
mm_42089.1	chr5	110256003	110256014	+	1	NA	3' UTR (NM_001253814, exon 13 of 13)	3' UTR (NM_001253814, exon 13 of 13)	13891	NM_028273	72542	Mm.61682	NM_028273	ENSMUSG00000029500	Pgam5	2610528A17Rik	phosphoglycerate mutase family member 5	protein-coding
mm_109418.1	chr12	110486313	110486333	+	1	NA	intron (NM_012023, intron 1 of 13)	intron (NM_012023, intron 1 of 13)	584	NM_012023	26931	Mm.240396	NM_012023	ENSMUSG00000017843	Ppp2r5c	2610043M05Rik|2700063L20Rik|AI060890|AW545884|C85228|D12Bwg0916e|mKIAA0044	protein phosphatase 2, regulatory subunit B', gamma	protein-coding
mm_77983.1	chr9	7872952	7872976	+	1	NA	5' UTR (NM_007464, exon 1 of 9)	5' UTR (NM_007464, exon 1 of 9)	206	NM_007464	11796	Mm.2026	NM_007464	ENSMUSG00000032000	Birc3	AW107670|Api1|Api2|Birc2|C-IAP2|HIAP2|IAP1|IAP2|MIAP1|MIAP2|MIHB|MIHC|RNF49|cIAP-1|cIAP-2|cIAP1|cIAP2	baculoviral IAP repeat-containing 3	protein-coding
mm_80643.1	chr9	89428466	89428469	+	1	NA	Intergenic	ID_B1|SINE|B4	194519	NM_153509	209743	Mm.242899	NM_153509	ENSMUSG00000039313	AF529169	DD1|Kiaa1024	cDNA sequence AF529169	protein-coding
mm_160576.1	chr9	58489673	58489673	+	1	NA	5' UTR (NM_176921, exon 2 of 3)	5' UTR (NM_176921, exon 2 of 3)	1070	NM_176921	319477	Mm.153674	NM_176921	ENSMUSG00000066607	6030419C18Rik	-	RIKEN cDNA 6030419C18 gene	protein-coding
mm_100752.1	chr11	4236520	4236553	-	1	NA	promoter-TSS (NM_001013365)	promoter-TSS (NM_001013365)	-249	NM_001013365	18413	Mm.131422	NM_001013365	ENSMUSG00000058755	Osm	OncoM	oncostatin M	protein-coding
mm_123463.1	chr14	65833941	65833952	-	1	NA	promoter-TSS (NM_028039)	promoter-TSS (NM_028039)	23	NM_028039	71988	Mm.249280	NM_028039	ENSMUSG00000022034	Esco2	2410004I17Rik|D030072L07Rik	establishment of sister chromatid cohesion N-acetyltransferase 2	protein-coding
mm_127395.1	chr15	101128575	101128587	+	1	NA	promoter-TSS (NM_001277259)	promoter-TSS (NM_001277259)	59	NM_001277257	11482	Mm.279542	NM_009612	ENSMUSG00000000530	Acvrl1	AI115505|AI427544|Acvrlk1|Alk1	activin A receptor, type II-like 1	protein-coding
mm_118153.1	chr13	105249710	105249750	-	1	NA	exon (NM_027934, exon 4 of 8)	exon (NM_027934, exon 4 of 8)	43284	NM_027934	71816	Mm.317015	NM_027934	ENSMUSG00000021720	Rnf180	3110001E11Rik|Rines	ring finger protein 180	protein-coding
mm_169065.1	chr13	26521873	26521887	+	1	NA	Intergenic	L1Md_T|LINE|L1	-209474	NR_045933	73576	Mm.45473	NR_045933		1700092E19Rik	-	RIKEN cDNA 1700092E19 gene	ncRNA
mm_118809.1	chr14	25459268	25459297	+	1	NA	promoter-TSS (NM_183208)	promoter-TSS (NM_183208)	97	NM_183208	328365	Mm.227484	NM_183208	ENSMUSG00000007817	Zmiz1	BC065120|E330020C23|ENSMUSG00000072684|Gm10397|I920194n01|Rai17|Zimp10	zinc finger, MIZ-type containing 1	protein-coding
mm_17527.1	chr2	29253427	29253491	-	1	NA	promoter-TSS (NR_029460)	promoter-TSS (NR_029460)	-466	NR_029460	76220	Mm.330108	NR_029460	ENSMUSG00000079499	6530402F18Rik	mKIAA1857	RIKEN cDNA 6530402F18 gene	ncRNA
mm_101649.1	chr11	36598556	36598559	-	1	NA	intron (NM_011856, intron 2 of 28)	intron (NM_011856, intron 2 of 28)	345684	NM_001290702	23964	Mm.439889	NM_011856	ENSMUSG00000049336	Tenm2	Odz2|Odz3|Ten-2|Ten-m2	teneurin transmembrane protein 2	protein-coding
mm_164958.1	chr19	5797311	5797315	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	-1332	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_61076.1	chr7	51621852	51621866	+	1	NA	promoter-TSS (NM_080853)	promoter-TSS (NM_080853)	29	NM_080853	140919	Mm.256618	NM_080853	ENSMUSG00000030500	Slc17a6	2900073D12Rik|DNPI|VGLUT2	solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 6	protein-coding
mm_3678.1	chr1	153695334	153695339	+	1	NA	3' UTR (NM_026380, exon 7 of 7)	3' UTR (NM_026380, exon 7 of 7)	29663	NM_001347115	67792	Mm.379143	NM_026380	ENSMUSG00000042671	Rgs8	6530413N01Rik	regulator of G-protein signaling 8	protein-coding
mm_63112.1	chr7	122671203	122671207	+	1	NA	promoter-TSS (NM_019430)	promoter-TSS (NM_019430)	-539	NM_019430	54376	Mm.444212	NM_019430	ENSMUSG00000066189	Cacng3	-	calcium channel, voltage-dependent, gamma subunit 3	protein-coding
mm_130510.1	chr15	98846129	98846146	-	1	NA	exon (NM_001033276, exon 40 of 55)	exon (NM_001033276, exon 40 of 55)	-14629	NM_016781	19082	Mm.6670	NM_016781	ENSMUSG00000067713	Prkag1	AA571379|BB036179|Prkaac	protein kinase, AMP-activated, gamma 1 non-catalytic subunit	protein-coding
mm_48919.1	chr6	4004213	4004223	+	1	NA	5' UTR (NM_025331, exon 1 of 2)	5' UTR (NM_025331, exon 1 of 2)	231	NM_025331	66066	Mm.25547	NM_025331	ENSMUSG00000032766	Gng11	0610037B21Rik	guanine nucleotide binding protein (G protein), gamma 11	protein-coding
mm_162976.1	chr11	18829745	18829753	+	1	NA	Intergenic	Intergenic	189220	NM_001193271	17268	Mm.356578	NM_010789	ENSMUSG00000020160	Meis1	C530044H18Rik|Evi8	Meis homeobox 1	protein-coding
mm_2934.1	chr1	132298653	132298659	+	1	NA	promoter-TSS (NM_144810)	promoter-TSS (NM_144810)	30	NM_144810	213417	Mm.39723	NM_144810	ENSMUSG00000042115	Klhdc8a	A630065K24Rik	kelch domain containing 8A	protein-coding
mm_79722.1	chr9	61520596	61520598	+	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	148231	NM_001083927	21887	Mm.24255	NM_009389	ENSMUSG00000032280	Tle3	2610103N05Rik|ESG|Grg3a|Grg3b|mKIAA1547	transducin-like enhancer of split 3	protein-coding
mm_120167.1	chr14	60768082	60768094	+	1	NA	promoter-TSS (NM_183175)	promoter-TSS (NM_183175)	-46	NM_183175	239126	Mm.319636	NM_183175	ENSMUSG00000071347	C1qtnf9	9130217G22Rik|CTRP9|Ciqtnf9	C1q and tumor necrosis factor related protein 9	protein-coding
mm_146280.1	chr18	77882581	77882587	+	1	NA	3' UTR (NM_013831, exon 15 of 15)	3' UTR (NM_013831, exon 15 of 15)	-55883	NM_001195633	100502841	Mm.297782	NM_001195633	ENSMUSG00000039840	Epg5	4732475F16|5430411K18Rik|AI661957|AW456499|mKIAA1632	ectopic P-granules autophagy protein 5 homolog (C. elegans)	protein-coding
mm_154123.1	chr19	57197557	57197567	-	1	NA	promoter-TSS (NM_001103177)	promoter-TSS (NM_001103177)	69	NM_001103177	226251	Mm.217161	NM_178688	ENSMUSG00000025085	Ablim1	2210411C18Rik|2610209L21Rik|4833406P10Rik|9330196J19Rik|AV079770|AW060987|AW215784|Limab1|mKIAA0059	actin-binding LIM protein 1	protein-coding
mm_139868.1	chr17	70529155	70529162	+	1	NA	intron (NM_001347414, intron 1 of 10)	intron (NM_001347414, intron 1 of 10)	7048	NM_001128180	224997	Mm.311840	NM_027712	ENSMUSG00000003279	Dlgap1	4933422O14Rik|9630002F18|AI845682|AI848168|BB075781|D17Bwg0511e|GKAP/SAPAP|GKPA/SAPAP|Gkap|Sapap1|mKIAA4162	discs, large (Drosophila) homolog-associated protein 1	protein-coding
mm_10887.1	chr2	25262590	25262670	+	1	NA	promoter-TSS (NM_175286)	promoter-TSS (NM_175286)	32	NM_175286	97031	Mm.308539	NM_175286	ENSMUSG00000048707	Tprn	C430004E15Rik|C87750	taperin	protein-coding
mm_147020.1	chr18	34624563	34624591	-	1	NA	promoter-TSS (NM_009004)	promoter-TSS (NM_009004)	-47	NM_001166407	19348	Mm.258846	NM_009004	ENSMUSG00000003779	Kif20a	AA415432|Rab6kifl	kinesin family member 20A	protein-coding
mm_164654.1	chr17	36032669	36032679	-	1	NA	promoter-TSS (NM_010398)	promoter-TSS (NM_010398)	27	NM_010398	15040	Mm.439648	NM_010398	ENSMUSG00000067212	H2-T23	37b|37c|H-2T23|H2-Qa1|Qa-1|Qa-1(b)|Qa1|Qed-1|T18c|T18c(37)|T23b|T23d	histocompatibility 2, T region locus 23	protein-coding
mm_95455.1	chr11	50377014	50377024	+	1	NA	promoter-TSS (NM_021510)	promoter-TSS (NM_021510)	-700	NM_021510	59013	Mm.21740	NM_021510	ENSMUSG00000007850	Hnrnph1	AI642080|E430005G16Rik|Hnrnph|Hnrph1	heterogeneous nuclear ribonucleoprotein H1	protein-coding
mm_71680.1	chr8	60895568	60895585	+	1	NA	exon (NM_028299, exon 3 of 8)	exon (NM_028299, exon 3 of 8)	5125	NM_028299	72612	Mm.25263	NM_028299	ENSMUSG00000038005	Hpf1	2700029M09Rik|C230006B22Rik|C4orf27	histone PARylation factor 1	protein-coding
mm_99351.1	chr11	101583612	101583630	+	1	NA	exon (NM_144830, exon 3 of 9)	exon (NM_144830, exon 3 of 9)	1379	NM_144830	217203	Mm.280559	NM_144830	ENSMUSG00000034947	Tmem106a	0610008L10Rik|AI043106|BC022145	transmembrane protein 106A	protein-coding
mm_101617.1	chr11	35840451	35840479	-	1	NA	intron (NM_170779, intron 21 of 22)	intron (NM_170779, intron 21 of 22)	-5937	NM_025936	104458	Mm.284906	NM_025936	ENSMUSG00000018848	Rars	2610011N19Rik|2610037E21Rik|AL033339|AW985894	arginyl-tRNA synthetase	protein-coding
mm_169919.1	chr16	57391248	57391250	-	1	NA	intron (NM_001040397, intron 1 of 4)	LSU-rRNA_Hsa|rRNA|rRNA	37972	NM_001040397	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding
mm_15694.1	chr2	163659170	163659181	+	1	NA	5' UTR (NM_001039390, exon 2 of 5)	5' UTR (NM_001039390, exon 2 of 5)	717	NM_001164053	18769	Mm.10091	NM_011106	ENSMUSG00000035268	Pkig	PKIgamma	protein kinase inhibitor, gamma	protein-coding
mm_140456.1	chr17	88668663	88668701	+	1	NA	promoter-TSS (NM_023630)	promoter-TSS (NM_023630)	22	NM_023630	71828	Mm.61330	NM_023630	ENSMUSG00000024154	Gtf2a1l	1700011N16Rik|Alf|Gtf2a1lf	general transcription factor IIA, 1-like	protein-coding
mm_52079.1	chr6	97828291	97828295	+	1	NA	intron (NM_001113198, intron 1 of 9)	intron (NM_001113198, intron 1 of 9)	21235	NM_001113198	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_32276.1	chr4	102760272	102760278	+	1	NA	5' UTR (NM_144906, exon 1 of 24)	5' UTR (NM_144906, exon 1 of 24)	140	NM_001285859	73094	Mm.54201	NM_144906	ENSMUSG00000028524	Sgip1	3110007P09Rik|SGIP1alpha|gag	SH3-domain GRB2-like (endophilin) interacting protein 1	protein-coding
mm_86756.1	chr10	19609227	19609285	+	1	NA	exon (NM_010511, exon 7 of 7)	exon (NM_010511, exon 7 of 7)	-12772	NM_178258	237310	Mm.331979	NM_178258	ENSMUSG00000039760	Il22ra2	CRF2-10|CRF2-s1|CRF2X|Il-22bp	interleukin 22 receptor, alpha 2	protein-coding
mm_68132.1	chr7	102210383	102210408	-	1	NA	promoter-TSS (NM_001291358)	promoter-TSS (NM_001291358)	60	NM_001291358	233575	Mm.302013	NM_145583	ENSMUSG00000030990	Pgap2	1810006G21Rik|C76649|Frag1	post-GPI attachment to proteins 2	protein-coding
mm_54233.1	chr6	28236767	28236770	-	1	NA	Intergenic	Intergenic	24833	NM_001081678	627049	Mm.84441	NM_001081678	ENSMUSG00000039841	Zfp800	AA407452|Znf800	zinc finger protein 800	protein-coding
mm_68696.1	chr7	119620256	119620337	-	1	NA	intron (NM_054094, intron 1 of 13)	intron (NM_054094, intron 1 of 13)	2468	NM_054094	117147	Mm.427560	NM_054094	ENSMUSG00000033533	Acsm1	Acas3|Bucs1|Macs	acyl-CoA synthetase medium-chain family member 1	protein-coding
mm_112041.1	chr12	111671269	111671287	-	1	NA	exon (NM_021273, exon 4 of 8)	exon (NM_021273, exon 4 of 8)	1060	NM_021273	12709	Mm.16831	NM_021273	ENSMUSG00000001270	Ckb	B-CK|Bck|Ck-3|Ck3|Ckbb	creatine kinase, brain	protein-coding
mm_66385.1	chr7	43999189	43999229	-	1	NA	exon (NM_010640, exon 4 of 5)	exon (NM_010640, exon 4 of 5)	3332	NM_010640	16613	Mm.443378	NM_010640	ENSMUSG00000044485	Klk1b11	Klk11|mGK-11	kallikrein 1-related peptidase b11	protein-coding
mm_12909.1	chr2	84840395	84840437	+	1	NA	promoter-TSS (NM_001083809)	promoter-TSS (NM_001083809)	93	NM_024497	72401	Mm.22716	NM_024497	ENSMUSG00000027075	Slc43a1	2610016F07Rik|AA986141|Lat3|PB39|Pov1|R00504	solute carrier family 43, member 1	protein-coding
mm_11895.1	chr2	49811688	49811701	+	1	NA	intron (NM_027990, intron 1 of 9)	intron (NM_027990, intron 1 of 9)	24008	NM_027990	71897	Mm.41381	NM_027990	ENSMUSG00000026765	Lypd6b	2310010M24Rik|AW049525	LY6/PLAUR domain containing 6B	protein-coding
mm_52849.1	chr6	121847819	121847822	+	1	NA	intron (NM_008645, intron 4 of 35)	Lx8|LINE|L1	9279	NM_008645	17836	Mm.1311	NM_008645	ENSMUSG00000059908	Mug1	-	murinoglobulin 1	protein-coding
mm_96542.1	chr11	68692132	68692138	+	1	NA	5' UTR (NM_175260, exon 1 of 41)	5' UTR (NM_175260, exon 1 of 41)	220	NM_175260	77579	Mm.218233	NM_175260	ENSMUSG00000020900	Myh10	5730504C04Rik|9330167F11Rik|Fltn|Myhn-2|Myhn2|NMHC II-B|NMHC-B|NMHCII-B|NMMHC II-b|NMMHC-B|NMMHC-IIB|SMemb|mKIAA3005	myosin, heavy polypeptide 10, non-muscle	protein-coding
mm_6235.1	chr1	66945020	66945038	-	1	NA	promoter-TSS (NM_021285)	promoter-TSS (NM_021285)	27	NM_021285	17901	Mm.1000	NM_021285	ENSMUSG00000061816	Myl1	AI325107|MLC1f|MLC3f|Mylf	myosin, light polypeptide 1	protein-coding
mm_163532.1	chr13	9684316	9684322	+	1	NA	TTS (NM_001347480)	TTS (NM_001347480)	79491	NM_001347471	66505	Mm.397307	NM_144516	ENSMUSG00000021156	Zmynd11	2210402G22Rik|BS69	zinc finger, MYND domain containing 11	protein-coding
mm_172266.1	chr6	76684346	76684346	-	1	NA	Intergenic	Intergenic	-558371	NM_028880	74342	Mm.292568	NM_028880	ENSMUSG00000060780	Lrrtm1	4632401D06Rik|AW125451	leucine rich repeat transmembrane neuronal 1	protein-coding
mm_29248.1	chr3	107218213	107218242	-	1	NA	exon (NM_001111143, exon 4 of 9)	exon (NM_001111143, exon 4 of 9)	3505	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_17204.1	chr2	25469743	25469758	-	1	NA	promoter-TSS (NM_008963)	promoter-TSS (NM_008963)	-1	NM_008963	19215	Mm.1008	NM_008963	ENSMUSG00000015090	Ptgds	21kDa|L-PGDS|PGD2|PGDS|PGDS2|Ptgs3	prostaglandin D2 synthase (brain)	protein-coding
mm_153599.1	chr19	43752925	43753001	-	1	NA	promoter-TSS (NM_001113562)	promoter-TSS (NM_001113562)	37	NM_144874	226139	Mm.248237	NM_144874	ENSMUSG00000040018	Cox15	2900026G05Rik	cytochrome c oxidase assembly protein 15	protein-coding
mm_170696.1	chr2	133971867	133971878	-	1	NA	Intergenic	L1Md_A|LINE|L1	407164	NR_037273	100526500		NR_037273	ENSMUSG00000093338	Mir3090	mmu-mir-3090	microRNA 3090	ncRNA
mm_49777.1	chr6	34920915	34920916	+	1	NA	promoter-TSS (NM_009292)	promoter-TSS (NM_009292)	-45	NM_009292	20899	Mm.5171	NM_009292	ENSMUSG00000029848	Stra8	-	stimulated by retinoic acid gene 8	protein-coding
mm_108212.1	chr12	76966118	76966125	+	1	NA	Intergenic	RMER17C|LTR|ERVK	-3873	NM_001146176	17187	Mm.268548	NM_008558	ENSMUSG00000059436	Max	AA960152|AI875693|bHLHd4|bHLHd5|bHLHd6|bHLHd7|bHLHd8	Max protein	protein-coding
mm_129956.1	chr15	85127829	85127869	-	1	NA	exon (NM_080470, exon 3 of 25)	exon (NM_080470, exon 3 of 25)	4108	NM_080470	140557	Mm.182737	NM_080470	ENSMUSG00000022432	Smc1b	SMC-1B|SMC1beta|Smc1l2	structural maintenance of chromosomes 1B	protein-coding
mm_93764.1	chr10	120201091	120201109	-	1	NA	intron (NM_028679, intron 1 of 11)	intron (NM_028679, intron 1 of 11)	437	NM_028679	73914	Mm.146194	NM_028679	ENSMUSG00000020227	Irak3	4833428C18Rik|AI563835|IRAK-M	interleukin-1 receptor-associated kinase 3	protein-coding
mm_87175.1	chr10	38965590	38965598	+	1	NA	promoter-TSS (NM_010681)	promoter-TSS (NM_010681)	79	NM_010681	16775	Mm.258065	NM_010681	ENSMUSG00000019846	Lama4	-	laminin, alpha 4	protein-coding
mm_33117.1	chr4	124742933	124742943	+	1	NA	promoter-TSS (NR_030480)	promoter-TSS (NR_030480)	-843	NR_030480	735263		NR_030480	ENSMUSG00000076119	Mir698	Mirn698|mir-698|mmu-mir-698	microRNA 698	ncRNA
mm_95454.1	chr11	50376983	50377004	+	1	NA	promoter-TSS (NM_021510)	promoter-TSS (NM_021510)	-726	NM_021510	59013	Mm.21740	NM_021510	ENSMUSG00000007850	Hnrnph1	AI642080|E430005G16Rik|Hnrnph|Hnrph1	heterogeneous nuclear ribonucleoprotein H1	protein-coding
mm_169563.1	chr15	15879154	15879156	-	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	-898946	NM_009869	12565	Mm.439758	NM_009869	ENSMUSG00000025370	Cdh9	-	cadherin 9	protein-coding
mm_111480.1	chr12	98734628	98734693	-	1	NA	promoter-TSS (NM_011877)	promoter-TSS (NM_011877)	-15	NM_011877	24000	Mm.4420	NM_011877	ENSMUSG00000021009	Ptpn21	PTPD1|PTPRL10	protein tyrosine phosphatase, non-receptor type 21	protein-coding
mm_103551.1	chr11	77718769	77718778	-	1	NA	TTS (NM_001024205)	TTS (NM_001024205)	6520	NM_001313933	12957	Mm.22830	NM_009965	ENSMUSG00000000724	Cryba1	BA3/A1|Cryb	crystallin, beta A1	protein-coding
mm_39180.1	chr4	155785009	155785018	-	1	NA	intron (NM_001033394, intron 1 of 1)	intron (NM_001033394, intron 1 of 1)	861	NM_001033394	320587	Mm.384382	NM_001033394	ENSMUSG00000073680	Tmem88b	A230069A22Rik	transmembrane protein 88B	protein-coding
mm_120040.1	chr14	56402706	56402712	+	1	NA	promoter-TSS (NM_001033043)	promoter-TSS (NM_001033043)	12	NM_001033043	30054	Mm.287783	NM_001033043	ENSMUSG00000000365	Rnf17	MMIP-2|Mmip2|TDRD4	ring finger protein 17	protein-coding
mm_151002.1	chr19	46654372	46654418	+	1	NA	exon (NM_001177813, exon 4 of 4)	exon (NM_001177813, exon 4 of 4)	18605	NM_007809	13074	Mm.1262	NM_007809	ENSMUSG00000003555	Cyp17a1	Cyp17|p450c17	cytochrome P450, family 17, subfamily a, polypeptide 1	protein-coding
mm_56197.1	chr6	88841937	88841943	-	1	NA	promoter-TSS (NM_030251)	promoter-TSS (NM_030251)	-5	NM_030251	80283	Mm.166858	NM_030251	ENSMUSG00000030083	Abtb1	AI847549|BC003234|BPOZ|EF1ABP	ankyrin repeat and BTB (POZ) domain containing 1	protein-coding
mm_59170.1	chr7	24400014	24400030	+	1	NA	intron (NM_028047, intron 1 of 13)	CpG	394	NM_028047	71997	Mm.150977	NM_028047	ENSMUSG00000002210	Smg9	1500002O20Rik|AI429693|N28092	smg-9 homolog, nonsense mediated mRNA decay factor (C. elegans)	protein-coding
mm_93037.1	chr10	88343937	88343977	-	1	NA	intron (NM_027878, intron 2 of 6)	B1_Mur4|SINE|Alu	13118	NM_027878	71712	Mm.35450	NM_027878	ENSMUSG00000020057	Dram1	1200002N14Rik|Dram	DNA-damage regulated autophagy modulator 1	protein-coding
mm_89705.1	chr10	97647407	97647436	+	1	NA	5' UTR (NM_007884, exon 2 of 8)	5' UTR (NM_007884, exon 2 of 8)	3353	NM_007884	13516	Mm.148886	NM_007884	ENSMUSG00000019936	Epyc	Dspg3|PG-Lb|SLRR3B	epiphycan	protein-coding
mm_47358.1	chr5	122779617	122779676	-	1	NA	promoter-TSS (NM_001199676)	promoter-TSS (NM_001199676)	-236	NM_145358	207565	Mm.289237	NM_145358	ENSMUSG00000029471	Camkk2	6330570N16Rik|AW061083|mKIAA0787	calcium/calmodulin-dependent protein kinase kinase 2, beta	protein-coding
mm_31595.1	chr4	57892921	57892941	+	1	NA	exon (NM_001035533, exon 4 of 4)	exon (NM_001035533, exon 4 of 4)	23333	NM_178727	242484	Mm.23214	NM_178727	ENSMUSG00000052117	D630039A03Rik	-	RIKEN cDNA D630039A03 gene	protein-coding
mm_100646.1	chr11	3104757	3104767	-	1	NA	Intergenic	IAPLTR4|LTR|ERVK	-19259	NR_003517	236604	Mm.247625	NM_001004146		Pisd-ps1	-	phosphatidylserine decarboxylase, pseudogene 1	pseudo
mm_29378.1	chr3	108818368	108818384	-	1	NA	intron (NM_011504, intron 6 of 18)	B1_Mur4|SINE|Alu	22126	NM_011504	20912	Mm.316894	NM_011504	ENSMUSG00000027882	Stxbp3	Munc-18c|Stxbp3a|Sxtbp3|Unc18-3	syntaxin binding protein 3	protein-coding
mm_8626.1	chr1	156270776	156270791	-	1	NA	intron (NM_001134741, intron 12 of 17)	intron (NM_001134741, intron 12 of 17)	32565	NM_001134741	214575	Mm.252800	NM_001134741	ENSMUSG00000060985	Tdrd5	Gm103	tudor domain containing 5	protein-coding
mm_4362.1	chr1	171927994	171927996	+	1	NA	intron (NM_001347187, intron 1 of 7)	intron (NM_001347187, intron 1 of 7)	10458	NM_030710	30925	Mm.486404	NM_030710	ENSMUSG00000015314	Slamf6	KAL1|KAL1b|Ly108|NTB-A|NTBA|SF2000	SLAM family member 6	protein-coding
mm_139991.1	chr17	72911528	72911537	+	1	NA	Intergenic	Intergenic	-6773	NM_029999	77889	Mm.154109	NM_029999	ENSMUSG00000024063	Lbh	1810009F10Rik|6720416L16Rik	limb-bud and heart	protein-coding
mm_2733.1	chr1	128244343	128244353	+	1	NA	5' UTR (NM_026390, exon 1 of 13)	5' UTR (NM_026390, exon 1 of 13)	167	NM_026390	67812	Mm.293321	NM_026390	ENSMUSG00000026353	Ubxn4	1300013G12Rik|Ubxd2|mKIAA0242	UBX domain protein 4	protein-coding
mm_59962.1	chr7	30428155	30428166	+	1	NA	exon (NM_172142, exon 11 of 11)	exon (NM_172142, exon 11 of 11)	4856	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_119597.1	chr14	51007912	51007920	+	1	NA	promoter-TSS (NM_029145)	promoter-TSS (NM_029145)	-13	NM_029145	75019	Mm.318775	NM_029145	ENSMUSG00000021872	Rnase10	4930474F22Rik|Rah1	ribonuclease, RNase A family, 10 (non-active)	protein-coding
mm_168647.1	chr1	185401393	185401410	+	1	NA	exon (NM_029735, exon 18 of 32)	exon (NM_029735, exon 18 of 32)	38306	NM_029735	107508	Mm.154511	NM_029735	ENSMUSG00000026615	Eprs	2410081F06Rik|3010002K18Rik|C79379|Qprs	glutamyl-prolyl-tRNA synthetase	protein-coding
mm_143435.1	chr17	70851757	70851774	-	1	NA	promoter-TSS (NM_001164075)	promoter-TSS (NM_001164075)	-31	NM_001164075	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_296.1	chr1	23272336	23272339	+	1	NA	promoter-TSS (NR_029533)	promoter-TSS (NR_029533)	68	NR_029533	387225		NR_029533	ENSMUSG00000065405	Mir30a	Mirn30a|mir-30a|mmu-mir-30a	microRNA 30a	ncRNA
mm_135762.1	chr16	56717228	56717285	-	1	NA	5' UTR (NM_001252443, exon 1 of 7)	5' UTR (NM_001252443, exon 1 of 7)	194	NM_001252443	21787	Mm.425970	NM_019678	ENSMUSG00000022757	Tfg	AI173908	Trk-fused gene	protein-coding
mm_12807.1	chr2	80302256	80302258	+	1	NA	Intergenic	Intergenic	9787	NM_177256	320769	Mm.60992	NM_177256	ENSMUSG00000050114	Prdx6b	1-cysPrx-P1|4930414C22Rik|Aop2-rs1|Prdx5-rs1|Prdx6-ps1|Prdx6-rs1|Prdx6-rs1-ps	peroxiredoxin 6B	protein-coding
mm_138101.1	chr17	34092377	34092421	+	1	NA	promoter-TSS (NM_008206)	promoter-TSS (NM_008206)	20	NM_008206	15001	Mm.116	NM_008206	ENSMUSG00000024334	H2-Oa	H-2Oa	histocompatibility 2, O region alpha locus	protein-coding
mm_100994.1	chr11	8446287	8446291	-	1	NA	intron (NM_001083587, intron 24 of 30)	intron (NM_001083587, intron 24 of 30)	218246	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_43334.1	chr5	135009933	135010014	+	1	NA	non-coding (NR_033794, exon 1 of 5)	non-coding (NR_033794, exon 1 of 5)	517	NR_033794	68758	Mm.389700	NM_145215	ENSMUSG00000040532	Abhd11	1110054D16Rik|A630008N09Rik|Wbscr21	abhydrolase domain containing 11	protein-coding
mm_143307.1	chr17	65986893	65986902	-	1	NA	exon (NM_001025572, exon 9 of 13)	exon (NM_001025572, exon 9 of 13)	-35710	NM_023053	65960	Mm.10153	NM_023053	ENSMUSG00000024098	Twsg1	1810013J15Rik|9030422N06Rik|AW552143|D17Ertd403e|Tsg|Twg	twisted gastrulation BMP signaling modulator 1	protein-coding
mm_6772.1	chr1	84131330	84131340	-	1	NA	intron (NM_001003948, intron 2 of 2)	intron (NM_001003948, intron 2 of 2)	87626	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_153478.1	chr19	41274319	41274344	-	1	NA	exon (NM_031376, exon 17 of 17)	exon (NM_031376, exon 17 of 17)	-10327	NM_133352	107358	Mm.246440	NM_133352	ENSMUSG00000025016	Tm9sf3	1810073M23Rik|2810031D16Rik|AI115521|AI413748|AW146116|AW549777|Smbp|mKIAA4036	transmembrane 9 superfamily member 3	protein-coding
mm_105230.1	chr11	102316608	102316646	-	1	NA	intron (NM_001302955, intron 1 of 19)	intron (NM_001302955, intron 1 of 19)	660	NM_001044383	21429	Mm.2845	NM_011551	ENSMUSG00000020923	Ubtf	A930005G04Rik|NOR-90|Tcfubf|UBF|UBF-1|UBF1	upstream binding transcription factor, RNA polymerase I	protein-coding
mm_24713.1	chr3	95228748	95228752	+	1	NA	promoter-TSS (NM_019914)	promoter-TSS (NM_019914)	-73	NM_019914	56772	Mm.331208	NM_019914	ENSMUSG00000053192	Mllt11	AI839562|Af1q|Zfp692	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 11	protein-coding
mm_123800.1	chr14	70520210	70520226	-	1	NA	promoter-TSS (NM_009755)	promoter-TSS (NM_009755)	42	NM_009755	12153	Mm.27757	NM_009755	ENSMUSG00000022098	Bmp1	Pcp|Tld	bone morphogenetic protein 1	protein-coding
mm_93857.1	chr10	122097079	122097196	-	1	NA	promoter-TSS (NM_153059)	promoter-TSS (NM_153059)	-35	NM_153059	216395	Mm.236764	NM_153059	ENSMUSG00000034620	Tmem5	6330415D21Rik	transmembrane protein 5	protein-coding
mm_165434.1	chr2	153611445	153611446	-	1	NA	Intergenic	Intergenic	21336	NM_001195390	99311	Mm.294478	NM_133850	ENSMUSG00000056941	Commd7	2310010I22Rik|AW060956|mU3	COMM domain containing 7	protein-coding
mm_104174.1	chr11	87734629	87734639	-	1	NA	3' UTR (NM_172448, exon 10 of 10)	3' UTR (NM_172448, exon 10 of 10)	-2931	NM_009296	20922	Mm.622	NM_009296	ENSMUSG00000020485	Supt4a	AL022777|Supt4h|Supt4h1|Supt4h1a	suppressor of Ty 4A	protein-coding
mm_171729.1	chr4	91372066	91372067	-	1	NA	promoter-TSS (NM_207686)	promoter-TSS (NM_207686)	-11	NM_207686	15569	Mm.318042	NM_010486	ENSMUSG00000008489	Elavl2	Hub|mel-N1	ELAV (embryonic lethal, abnormal vision, Drosophila)-like 2 (Hu antigen B)	protein-coding
mm_150927.1	chr19	46267842	46267852	+	1	NA	intron (NM_178930, intron 18 of 39)	intron (NM_178930, intron 18 of 39)	-36890	NM_001177369	18034	Mm.102365	NM_019408	ENSMUSG00000025225	Nfkb2	NF-kappaB2|lyt|p49|p49/p100|p50B|p52	nuclear factor of kappa light polypeptide gene enhancer in B cells 2, p49/p100	protein-coding
mm_30144.1	chr3	142395662	142395683	-	1	NA	promoter-TSS (NM_001190853)	promoter-TSS (NM_001190853)	24	NM_001190853	56376	Mm.117709	NM_019808	ENSMUSG00000028273	Pdlim5	1110001A05Rik|AI987914|C87059|Enh|Enh1|Enh2|Enh3|LIM	PDZ and LIM domain 5	protein-coding
mm_52321.1	chr6	108836393	108836407	+	1	NA	intron (NM_138677, intron 1 of 11)	intron (NM_138677, intron 1 of 11)	7759	NM_138677	192193	Mm.21596	NM_138677	ENSMUSG00000030104	Edem1	A130059K23Rik|EDEM|mKIAA0212	ER degradation enhancer, mannosidase alpha-like 1	protein-coding
mm_148383.1	chr19	3323341	3323353	+	1	NA	promoter-TSS (NM_013495)	promoter-TSS (NM_013495)	46	NM_013495	12894	Mm.18522	NM_013495	ENSMUSG00000024900	Cpt1a	C730027G07|CPTI|Cpt1	carnitine palmitoyltransferase 1a, liver	protein-coding
mm_55487.1	chr6	69243718	69243741	-	1	NA	Intergenic	Intergenic	83445	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_141874.1	chr17	34839360	34839372	-	1	NA	TTS (NM_001163770)	TTS (NM_001163770)	2347	NM_001163770	112403	Mm.275309	NM_033613	ENSMUSG00000040482	Dxo	Dom3z|NG6	decapping exoribonuclease	protein-coding
mm_147028.1	chr18	34688816	34688819	-	1	NA	Intergenic	B1_Mus2|SINE|Alu	31570	NM_010280	14587	Mm.16520	NM_010280	ENSMUSG00000024366	Gfra3	GFRalpha3|Y15110	glial cell line derived neurotrophic factor family receptor alpha 3	protein-coding
mm_26154.1	chr3	138143889	138143919	+	1	NA	promoter-TSS (NM_001163457)	promoter-TSS (NM_001163457)	366	NM_175389	108943	Mm.471692	NM_175389	ENSMUSG00000004127	Trmt10a	3110023L08Rik|AA794508|Rg9mtd2|Rnmtd2	tRNA methyltransferase 10A	protein-coding
mm_110246.1	chr12	31351369	31351421	-	1	NA	promoter-TSS (NM_007861)	promoter-TSS (NM_007861)	76	NM_007861	13382	Mm.3131	NM_007861	ENSMUSG00000020664	Dld	-	dihydrolipoamide dehydrogenase	protein-coding
mm_172077.1	chr6	142537069	142537069	+	1	NA	Intergenic	(CAG)n|Simple_repeat|Simple_repeat	-29112	NM_001302765	16832	Mm.9745	NM_008492	ENSMUSG00000030246	Ldhb	AI790582|H-Ldh|LDH-B|LDH-H|Ldh-2|Ldh2	lactate dehydrogenase B	protein-coding
mm_4474.1	chr1	173419420	173419426	+	1	NA	Intergenic	Intergenic	-1181	NM_001013779	383619	Mm.131453	NM_001013779	ENSMUSG00000037860	Aim2	Gm1313|Ifi210	absent in melanoma 2	protein-coding
mm_141229.1	chr17	27426331	27426337	-	1	NA	3' UTR (NM_001291045, exon 10 of 10)	3' UTR (NM_001291045, exon 10 of 10)	68237	NR_106077	102466228		NR_106077	ENSMUSG00000106215	Mir7218	mmu-mir-7218	microRNA 7218	ncRNA
mm_16065.1	chr2	167940799	167940802	+	1	NA	intron (NM_011201, intron 1 of 8)	intron (NM_011201, intron 1 of 8)	8473	NM_011201	19246	Mm.277916	NM_011201	ENSMUSG00000027540	Ptpn1	PTP-1B|PTP-HA2|PTP1B	protein tyrosine phosphatase, non-receptor type 1	protein-coding
mm_139288.1	chr17	48300379	48300396	+	1	NA	5' UTR (NM_001033405, exon 1 of 5)	5' UTR (NM_001033405, exon 1 of 5)	349	NM_001033405	328833	Mm.329104	NM_001033405	ENSMUSG00000071068	Treml2	AW049306|Gm750|Tlt2	triggering receptor expressed on myeloid cells-like 2	protein-coding
mm_133910.1	chr16	97554029	97554032	+	1	NA	intron (NR_003508, intron 10 of 13)	L1M3|LINE|L1	17947	NM_013606	17858	Mm.14157	NM_013606	ENSMUSG00000023341	Mx2	AI528743|Mx-2	MX dynamin-like GTPase 2	protein-coding
mm_57187.1	chr6	122848869	122848880	-	1	NA	3' UTR (NM_009779, exon 2 of 2)	3' UTR (NM_009779, exon 2 of 2)	7283	NM_009779	12267	Mm.2408	NM_009779	ENSMUSG00000040552	C3ar1	AZ3B|C3AR|HNFAG09	complement component 3a receptor 1	protein-coding
mm_161793.1	chr17	47737828	47737828	+	1	NA	promoter-TSS (NM_001161723)	promoter-TSS (NM_001161723)	-103	NM_001161723	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_150666.1	chr19	42036026	42036032	+	1	NA	promoter-TSS (NM_020033)	promoter-TSS (NM_020033)	-9	NM_020033	56642	Mm.143737	NM_020033	ENSMUSG00000025172	Ankrd2	Arpp|mArpp	ankyrin repeat domain 2 (stretch responsive muscle)	protein-coding
mm_25098.1	chr3	101237542	101237549	+	1	NA	Intergenic	Intergenic	50394	NM_013486	12481	Mm.22842	NM_013486	ENSMUSG00000027863	Cd2	LFA-2|Ly-37|Ly37	CD2 antigen	protein-coding
mm_150773.1	chr19	44294194	44294206	+	1	NA	5' UTR (NM_009128, exon 1 of 6)	5' UTR (NM_009128, exon 1 of 6)	524	NM_009128	20250	Mm.487021	NM_009128	ENSMUSG00000025203	Scd2	Mir5114|Scd-2|mir-5114|swty	stearoyl-Coenzyme A desaturase 2	protein-coding
mm_160003.1	chr6	122337025	122337025	-	1	NA	intron (NM_001271579, intron 1 of 14)	intron (NM_001271579, intron 1 of 14)	2632	NM_001042623	13619	Mm.6822	NM_007905	ENSMUSG00000040669	Phc1	AW557034|Edr|Edr1|Mph1|Rae-28|rae28	polyhomeotic-like 1 (Drosophila)	protein-coding
mm_123227.1	chr14	59643539	59643541	-	1	NA	Intergenic	Intergenic	18259	NM_145463	219134	Mm.275409	NM_145463	ENSMUSG00000044461	Shisa2	9430059P22Rik|MAd2|Tmem46|mShisa|shisa	shisa family member 2	protein-coding
mm_110722.1	chr12	69681796	69681869	-	1	NA	promoter-TSS (NM_001135559)	promoter-TSS (NM_001135559)	20	NM_001135559	20663	Mm.3770	NM_001135559	ENSMUSG00000034801	Sos2	SOS-2|mSOS-2	son of sevenless homolog 2 (Drosophila)	protein-coding
mm_7599.1	chr1	125913131	125913149	-	1	NA	promoter-TSS (NM_145100)	promoter-TSS (NM_145100)	-212	NM_001311089	72585	Mm.490405	NM_145100	ENSMUSG00000026344	Lypd1	2700050C12Rik|AI853408|C530008O16Rik|Lynx2|Lypdc1	Ly6/Plaur domain containing 1	protein-coding
mm_53389.1	chr6	129542160	129542207	+	1	NA	3' UTR (NM_020590, exon 4 of 4)	3' UTR (NM_020590, exon 4 of 4)	-8899	NR_045270	100504641	Mm.398286	NR_045270	ENSMUSG00000097675	1700101I11Rik	-	RIKEN cDNA 1700101I11 gene	ncRNA
mm_166049.1	chr4	131389981	131389995	+	1	NA	Intergenic	T-rich|Low_complexity|Low_complexity	-379514	NR_130167	77835	Mm.348412	NR_130167	ENSMUSG00000086262	A930031H19Rik	A930004I12Rik	RIKEN cDNA A930031H19 gene	ncRNA
mm_11103.1	chr2	28192911	28192921	+	1	NA	promoter-TSS (NM_001038613)	promoter-TSS (NM_001038613)	-177	NM_001038613	56177	Mm.43278	NM_019498	ENSMUSG00000026833	Olfm1	AMY|AW742568|Noe1|OlfA|Pancortin|Pancortin3	olfactomedin 1	protein-coding
mm_129364.1	chr15	77970513	77970561	-	1	NA	intron (NM_018749, intron 1 of 14)	CpG	287	NM_018749	55944	Mm.3955	NM_018749	ENSMUSG00000016554	Eif3d	66/67kDa|AA407891|Eif3s7|eIF3p66	eukaryotic translation initiation factor 3, subunit D	protein-coding
mm_85608.1	chr9	107605131	107605173	-	1	NA	non-coding (NR_111986, exon 2 of 18)	non-coding (NR_111986, exon 2 of 18)	250	NM_009153	20347	Mm.4083	NM_009153	ENSMUSG00000057969	Sema3b	SemA|Semaa|sema5|semaV	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B	protein-coding
mm_94035.1	chr10	127998327	127998329	-	1	NA	intron (NM_013786, intron 2 of 5)	intron (NM_013786, intron 2 of 5)	9180	NM_013786	27400	Mm.26719	NM_013786	ENSMUSG00000025396	Hsd17b6	17betaHSD9|Hsd17b9|Rdh8	hydroxysteroid (17-beta) dehydrogenase 6	protein-coding
mm_94119.1	chr10	128626752	128626767	-	1	NA	promoter-TSS (NM_013765)	promoter-TSS (NM_013765)	-253	NM_013765	27370	Mm.32118	NM_013765	ENSMUSG00000025362	Rps26	-	ribosomal protein S26	protein-coding
mm_170230.1	chr17	82410025	82410037	-	1	NA	Intergenic	Intergenic	668194	NR_045094	100503434	Mm.187281	NR_045094		Gm19689	-	predicted gene, 19689	ncRNA
mm_111492.1	chr12	99162645	99162658	-	1	NA	non-coding (NR_038130, exon 1 of 2)	non-coding (NR_038130, exon 1 of 2)	157	NR_038130	67639	Mm.87374	NR_038130		4930474N09Rik	-	RIKEN cDNA 4930474N09 gene	ncRNA
mm_17942.1	chr2	36104068	36104073	-	1	NA	promoter-TSS (NM_001083127)	promoter-TSS (NM_001083127)	-10	NM_001083127	16874	Mm.12881	NM_008500	ENSMUSG00000026890	Lhx6	Lhx6.1	LIM homeobox protein 6	protein-coding
mm_72778.1	chr8	86745448	86745472	+	1	NA	promoter-TSS (NR_027829)	promoter-TSS (NR_027829)	-239	NR_027829	666945	Mm.391806	NR_027829		Gm10638	ENSMUSG00000074178	predicted gene 10638	ncRNA
mm_63614.1	chr7	128237331	128237387	+	1	NA	promoter-TSS (NM_146205)	promoter-TSS (NM_146205)	2	NM_146205	233912	Mm.475117	NM_146205	ENSMUSG00000042178	Armc5	AW049683|BC032200	armadillo repeat containing 5	protein-coding
mm_100316.1	chr11	117987417	117987429	+	1	NA	intron (NM_133757, intron 1 of 9)	intron (NM_133757, intron 1 of 9)	566	NM_133757	74451	Mm.28864	NM_133757	ENSMUSG00000017715	Pgs1	2610019F11Rik|4933424M23Rik|SAF	phosphatidylglycerophosphate synthase 1	protein-coding
mm_100026.1	chr11	114908270	114908312	+	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	18250	NM_170758	217303	Mm.294439	NM_170758	ENSMUSG00000034652	Cd300a	B230315M08Rik|Clm8|LMIR1|MAIR-I|MAIR-Ia|MMAC8|Pigr4|mcpir1	CD300A molecule	protein-coding
mm_33231.1	chr4	126850394	126850404	+	1	NA	intron (NM_001035525, intron 20 of 23)	intron (NM_001035525, intron 20 of 23)	96629	NM_001035526	100317	Mm.206206	NM_133886	ENSMUSG00000028830	AU040320	A730047D20Rik|AAVR|Kiaa0319l	expressed sequence AU040320	protein-coding
mm_105189.1	chr11	101986964	101986974	-	1	NA	promoter-TSS (NM_029287)	promoter-TSS (NM_029287)	-87	NM_029287	75437	Mm.108632	NM_029287	ENSMUSG00000010841	1700006E09Rik	-	RIKEN cDNA 1700006E09 gene	protein-coding
mm_70781.1	chr8	22407450	22407486	+	1	NA	Intergenic	Intergenic	-3872	NM_020560	57312	Mm.289402	NM_020560	ENSMUSG00000031533	Mrps31	1500002D03Rik|AA960481|Imogen38|Imogen44	mitochondrial ribosomal protein S31	protein-coding
mm_15769.1	chr2	164332741	164332745	+	1	NA	promoter-TSS (NM_009301)	promoter-TSS (NM_009301)	-22	NM_009301	20944	Mm.140154	NM_009301	ENSMUSG00000017004	Svs5	BB115186|Semg1|Svp-1|Svp1|Svp5	seminal vesicle secretory protein 5	protein-coding
mm_11199.1	chr2	29125217	29125238	+	1	NA	5' UTR (NM_198033, exon 1 of 26)	5' UTR (NM_198033, exon 1 of 26)	235	NM_198033	269254	Mm.41867	NM_198033	ENSMUSG00000043535	Setx	A130090N03|A930037J23Rik|AOA2|AW060766|Als4|SCAR1|Sen1|mKIAA0625	senataxin	protein-coding
mm_63441.1	chr7	127481338	127481358	+	1	NA	Intergenic	(T)n|Simple_repeat|Simple_repeat	-3873	NM_010183	14123	Mm.323505	NM_010183	ENSMUSG00000042423	Fbrs	Fbs|Fbs1	fibrosin	protein-coding
mm_168512.1	chr1	156524034	156524034	+	1	NA	Intergenic	Intergenic	-34753	NM_009595	11352	Mm.329515	NM_009595	ENSMUSG00000026596	Abl2	AA536808|Abll|Arg	v-abl Abelson murine leukemia viral oncogene 2 (arg, Abelson-related gene)	protein-coding
mm_162703.1	chr10	22148814	22148853	-	1	NA	exon (NM_001254744, exon 1 of 2)	exon (NM_001254744, exon 1 of 2)	437	NM_001254744	319887	Mm.177746	NM_001254744	ENSMUSG00000097327	E030030I06Rik	-	RIKEN cDNA E030030I06 gene	protein-coding
mm_3258.1	chr1	136247680	136247701	+	1	NA	Intergenic	Intergenic	13183	NM_001101516	383563	Mm.40367	NM_001101516	ENSMUSG00000052759	Gpr25	Gm1300	G protein-coupled receptor 25	protein-coding
mm_112398.1	chr12	119238868	119238892	-	1	NA	promoter-TSS (NM_177290)	promoter-TSS (NM_177290)	-604	NM_177290	320910	Mm.217000	NM_177290	ENSMUSG00000025321	Itgb8	4832412O06Rik	integrin beta 8	protein-coding
mm_49206.1	chr6	15720756	15720767	+	1	NA	promoter-TSS (NM_175088)	promoter-TSS (NM_175088)	100	NM_175088	16543	Mm.1314	NM_175088	ENSMUSG00000041390	Mdfic	Kdt1|Mdfid	MyoD family inhibitor domain containing	protein-coding
mm_9254.1	chr1	171535285	171535300	-	1	NA	promoter-TSS (NM_010584)	promoter-TSS (NM_010584)	2	NM_010584	16429	Mm.247426	NM_010584	ENSMUSG00000038209	Itln1	IntL|Itln|Itln2|Itln3|Itln5|Itlna|Lfr	intelectin 1 (galactofuranose binding)	protein-coding
mm_77758.1	chr8	128896628	128896661	-	1	NA	Intergenic	Intergenic	168848	NM_029061	74703	Mm.196017	NM_029061	ENSMUSG00000025808	Ccdc7a	4930517G15Rik|4930540C21Rik|Biot2|Ccdc7	coiled-coil domain containing 7A	protein-coding
mm_64312.1	chr7	141864660	141864669	+	1	NA	exon (NM_028801, exon 31 of 49)	exon (NM_028801, exon 31 of 49)	25592	NM_028801	74180	Mm.200752	NM_028801	ENSMUSG00000066108	Muc5b	2300002I04Rik|A130042M24|AV085033|MUC5|MUC9|mucin 5b	mucin 5, subtype B, tracheobronchial	protein-coding
mm_67251.1	chr7	75498641	75498649	-	1	NA	intron (NM_029332, intron 1 of 36)	intron (NM_029332, intron 1 of 36)	43111	NM_029332	75547	Mm.216107	NM_029332	ENSMUSG00000066406	Akap13	1700026G02Rik|5730522G15Rik|5830460E08Rik|AKAP-13|AKAP-Lbc|BRX|Ht31|LBC|PROTO-LB|PROTO-LBC	A kinase (PRKA) anchor protein 13	protein-coding
mm_20611.1	chr2	131853704	131853753	-	1	NA	TTS (NM_001166206)	TTS (NM_001166206)	6019	NM_001166206	71995	Mm.22	NM_028045	ENSMUSG00000037482	Erv3	1600014E20Rik|AA389086|AI426069|AI448024|D19349	endogenous retroviral sequence 3	protein-coding
mm_66682.1	chr7	45814278	45814300	-	1	NA	promoter-TSS (NM_001112701)	promoter-TSS (NM_001112701)	27	NM_011181	19158	Mm.272130	NM_011181	ENSMUSG00000003269	Cyth2	ARNO|CLM2|Pscd2	cytohesin 2	protein-coding
mm_81838.1	chr9	118480579	118480591	+	1	NA	exon (NM_010136, exon 2 of 6)	exon (NM_010136, exon 2 of 6)	2396	NM_010136	13813	Mm.200692	NM_010136	ENSMUSG00000032446	Eomes	C77258|TBR-2|Tbr2	eomesodermin	protein-coding
mm_117011.1	chr13	58113282	58113297	-	1	NA	Intergenic	Intergenic	-10861	NM_001195075	100503085	Mm.379256	NM_001195075	ENSMUSG00000014164	Klhl3	7530408C15Rik|AI430941|EG627648	kelch-like 3	protein-coding
mm_15606.1	chr2	160731685	160731760	+	1	NA	5' UTR (NM_021280, exon 2 of 34)	5' UTR (NM_021280, exon 2 of 34)	412	NM_021280	18803	Mm.44463	NM_021280	ENSMUSG00000016933	Plcg1	AI894140|Cded|Plc-1|Plc-gamma1|Plcg-1	phospholipase C, gamma 1	protein-coding
mm_31390.1	chr4	48043659	48043677	+	1	NA	Intergenic	Intergenic	-1637	NM_015743	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_20126.1	chr2	121290299	121290309	-	1	NA	intron (NM_032393, intron 1 of 6)	intron (NM_032393, intron 1 of 6)	702	NM_032393	17754	Mm.36501	NM_032393	ENSMUSG00000027254	Map1a	6330416M19Rik|AI853608|Mtap-1|Mtap1|Mtap1a|moth1	microtubule-associated protein 1 A	protein-coding
mm_85094.1	chr9	92250511	92250528	-	1	NA	intron (NM_011636, intron 1 of 8)	CpG	325	NM_011636	22038	Mm.421956	NM_011636	ENSMUSG00000032369	Plscr1	MmTRA1a|MmTRA1b|Nor1|Tra1|Tra1a|Tra1b|Tras1|Tras2	phospholipid scramblase 1	protein-coding
mm_87698.1	chr10	59702646	59702663	+	1	NA	promoter-TSS (NM_001291442)	promoter-TSS (NM_001291442)	91	NM_001291443	216001	Mm.27199	NM_144822	ENSMUSG00000020111	Micu1	C730016L05Rik|Calc|Cbara1	mitochondrial calcium uptake 1	protein-coding
mm_79545.1	chr9	57911103	57911115	+	1	NA	intron (NM_001122873, intron 1 of 10)	intron (NM_001122873, intron 1 of 10)	123	NM_001122873	69459	Mm.41735	NM_027086	ENSMUSG00000055720	Ubl7	2300004C15Rik	ubiquitin-like 7 (bone marrow stromal cell-derived)	protein-coding
mm_50931.1	chr6	57667322	57667340	+	1	NA	Intergenic	Intergenic	24747	NM_025574	66459	Mm.44201	NM_025574	ENSMUSG00000043162	Pyurf	2610022G08Rik|AI847956|Prey	Pigy upstream reading frame	protein-coding
mm_96022.1	chr11	59543573	59543607	+	1	NA	intron (NM_145827, intron 2 of 9)	L1MB2|LINE|L1	904	NM_145827	216799	Mm.54174	NM_145827	ENSMUSG00000032691	Nlrp3	AGTAVPRL|AII/AVP|Cias1|FCAS|FCU|MWS|Mmig1|NALP3|Pypaf1	NLR family, pyrin domain containing 3	protein-coding
mm_22559.1	chr3	9886943	9886952	+	1	NA	Intergenic	MER20|DNA|hAT-Charlie	-53268	NM_001195031	94212	Mm.23897	NM_053182	ENSMUSG00000027508	Pag1	Cbp|F730007C19Rik|Pag	phosphoprotein associated with glycosphingolipid microdomains 1	protein-coding
mm_58691.1	chr7	12922316	12922320	+	1	NA	promoter-TSS (NM_009095)	promoter-TSS (NM_009095)	7	NM_009095	20103	Mm.5291	NM_009095	ENSMUSG00000012848	Rps5	AA617411	ribosomal protein S5	protein-coding
mm_163502.1	chr12	112829457	112829479	-	1	NA	promoter-TSS (NM_028023)	promoter-TSS (NM_028023)	-79	NM_028023	71963	Mm.313185	NM_028023	ENSMUSG00000047832	Cdca4	2410018C03Rik|HEPP|SEI-3	cell division cycle associated 4	protein-coding
mm_102875.1	chr11	69409429	69409445	-	1	NA	intron (NM_001017426, intron 1 of 22)	intron (NM_001017426, intron 1 of 22)	4238	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_138207.1	chr17	34305010	34305014	+	1	NA	promoter-TSS (NM_010382)	promoter-TSS (NM_010382)	-855	NM_010382	14969	Mm.22564	NM_010382	ENSMUSG00000060586	H2-Eb1	Eb|H-2Eb|H2Eb|Ia-4|Ia4	histocompatibility 2, class II antigen E beta	protein-coding
mm_110370.1	chr12	40199269	40199312	-	1	NA	promoter-TSS (NM_001033437)	promoter-TSS (NM_001033437)	25	NM_001033437	380755	Mm.390463	NM_001033437	ENSMUSG00000071342	Lsmem1	Gm889	leucine-rich single-pass membrane protein 1	protein-coding
mm_131923.1	chr16	23320838	23320843	+	1	NA	intron (NM_001252505, intron 3 of 7)	intron (NM_001252505, intron 3 of 7)	30370	NM_001252506	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_169014.1	chr13	107890163	107890166	-	1	NA	promoter-TSS (NM_145456)	promoter-TSS (NM_145456)	-100	NM_145456	67263	Mm.490418	NM_145456	ENSMUSG00000032846	Zswim6	2900036G02Rik|mKIAA1577	zinc finger SWIM-type containing 6	protein-coding
mm_30436.1	chr3	153624737	153624756	-	1	NA	intron (NM_011372, intron 1 of 4)	intron (NM_011372, intron 1 of 4)	100387	NM_011372	20447	Mm.296453	NM_011372	ENSMUSG00000052544	St6galnac3	Siat7c	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 3	protein-coding
mm_44352.1	chr5	17795431	17795475	-	1	NA	intron (NM_007643, intron 11 of 14)	intron (NM_007643, intron 11 of 14)	40443	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_23619.1	chr3	65678398	65678403	+	1	NA	intron (NM_001166659, intron 2 of 12)	intron (NM_001166659, intron 2 of 12)	12172	NM_001166659	624866	Mm.296317	NM_001037923	ENSMUSG00000074579	Lekr1	EG546798|EG624866|Gm6534	leucine, glutamate and lysine rich 1	protein-coding
mm_99866.1	chr11	109397429	109397482	+	1	NA	3' UTR (NM_010303, exon 4 of 4)	3' UTR (NM_010303, exon 4 of 4)	-28491	NM_025275	13929	Mm.211850	NM_025275	ENSMUSG00000020610	Amz2	AA408420|ESTM12|X83328	archaelysin family metallopeptidase 2	protein-coding
mm_171418.1	chr4	133089180	133089180	-	1	NA	Intergenic	ID4|SINE|ID	-41453	NM_153423	242687	Mm.23566	NM_153423	ENSMUSG00000028868	Wasf2	AW742646|D4Ertd13e|WAVE2	WAS protein family, member 2	protein-coding
mm_42343.1	chr5	114906681	114906694	+	1	NA	exon (NM_011854, exon 5 of 6)	exon (NM_011854, exon 5 of 6)	9753	NM_011854	23962	Mm.228363	NM_011854	ENSMUSG00000029561	Oasl2	M1204|Mmu-OASL|Oasl	2'-5' oligoadenylate synthetase-like 2	protein-coding
mm_14675.1	chr2	139494193	139494197	+	1	NA	5' UTR (NM_175467, exon 2 of 13)	5' UTR (NM_175467, exon 2 of 13)	275	NM_175467	228677	Mm.100450	NM_175467	ENSMUSG00000039092	Sptlc3	C130053K05Rik	serine palmitoyltransferase, long chain base subunit 3	protein-coding
mm_38839.1	chr4	149166085	149166098	-	1	NA	intron (NM_001081274, intron 1 of 12)	intron (NM_001081274, intron 1 of 12)	616	NM_001081274	110208	Mm.252080	NM_025801	ENSMUSG00000028961	Pgd	0610042A05Rik|AU019875|C78335	phosphogluconate dehydrogenase	protein-coding
mm_104976.1	chr11	100246117	100246159	-	1	NA	TTS (NM_008470)	TTS (NM_008470)	2764	NM_001313958	16666	Mm.422799	NM_008470	ENSMUSG00000053797	Krt16	AI324768|CK-16|K16|Krt1-16	keratin 16	protein-coding
mm_57517.1	chr6	125494639	125494669	-	1	NA	5' UTR (NM_007657, exon 1 of 8)	5' UTR (NM_007657, exon 1 of 8)	101	NM_007657	12527	Mm.210676	NM_007657	ENSMUSG00000030342	Cd9	Tspan29	CD9 antigen	protein-coding
mm_148676.1	chr19	5638238	5638263	+	1	NA	intron (NM_009045, intron 1 of 10)	intron (NM_009045, intron 1 of 10)	760	NM_009045	19697	Mm.249966	NM_009045	ENSMUSG00000024927	Rela	p65	v-rel reticuloendotheliosis viral oncogene homolog A (avian)	protein-coding
mm_44248.1	chr5	5374767	5374780	-	1	NA	intron (NM_011074, intron 1 of 14)	PB1D7|SINE|Alu	5478	NM_011074	18647	Mm.389061	NM_011074	ENSMUSG00000028926	Cdk14	Pftk1|mKIAA0834	cyclin-dependent kinase 14	protein-coding
mm_62306.1	chr7	100178733	100178739	+	1	NA	promoter-TSS (NM_001190950)	promoter-TSS (NM_001190950)	53	NM_001190871	57442	Mm.282386	NM_020574	ENSMUSG00000035165	Kcne3	2210017H05Rik|MiRP2	potassium voltage-gated channel, Isk-related subfamily, gene 3	protein-coding
mm_70169.1	chr7	143627909	143627963	-	1	NA	promoter-TSS (NM_175649)	promoter-TSS (NM_175649)	-91	NM_175649	244237	Mm.247498	NM_175649	ENSMUSG00000045362	Tnfrsf26	Tnfrh3|Tnfrsf24	tumor necrosis factor receptor superfamily, member 26	protein-coding
mm_110707.1	chr12	69322289	69322303	-	1	NA	exon (NM_025441, exon 23 of 33)	exon (NM_025441, exon 23 of 33)	25615	NM_027117	69554	Mm.234368	NM_027117	ENSMUSG00000020978	Klhdc2	2310022K15Rik|D12Ertd522e|HCLP-1|LCP	kelch domain containing 2	protein-coding
mm_58178.1	chr6	142804494	142804511	-	1	NA	promoter-TSS (NM_001145390)	promoter-TSS (NM_001145390)	-36	NM_001145390	330440	Mm.484618	NM_001033417	ENSMUSG00000048473	Sult6b2	Gm766	sulfotransferase family 6B, member 2	protein-coding
mm_44303.1	chr5	8996656	8996667	-	1	NA	intron (NM_023733, intron 1 of 17)	intron (NM_023733, intron 1 of 17)	485	NM_023733	74114	Mm.28197	NM_023733	ENSMUSG00000003623	Crot	1200003H03Rik	carnitine O-octanoyltransferase	protein-coding
mm_69230.1	chr7	127708051	127708084	-	1	NA	promoter-TSS (NR_030428)	promoter-TSS (NR_030428)	-420	NR_030428	791073		NR_030428	ENSMUSG00000076454	Mir762	Mirn762|mir-762|mmu-mir-762	microRNA 762	ncRNA
mm_120368.1	chr14	64583716	64583742	+	1	NA	Intergenic	Intergenic	-4386	NR_040709	268755	Mm.194050	NR_040709	ENSMUSG00000097545	Mir124a-1hg	A930011O12Rik|Rncr3|mir-124-1|mir-3078	Mir124-1 host gene (non-protein coding)	ncRNA
mm_17679.1	chr2	32288002	32288017	-	1	NA	promoter-TSS (NM_133852)	promoter-TSS (NM_133852)	60	NR_110965	72931	Mm.27344	NM_175190	ENSMUSG00000044627	Swi5	1500019F05Rik|2900010J23Rik|AI046671	SWI5 recombination repair homolog (yeast)	protein-coding
mm_86884.1	chr10	22158470	22158481	+	1	NA	promoter-TSS (NM_009016)	promoter-TSS (NM_009016)	-134	NM_009016	19368	Mm.458004	NM_009016		Raet1a	RAE-1alpha|Rae1alpha|Raet1	retinoic acid early transcript 1, alpha	protein-coding
mm_65428.1	chr7	25297867	25297958	-	1	NA	promoter-TSS (NM_008776)	promoter-TSS (NM_008776)	43	NM_008776	18476	Mm.597	NM_008776	ENSMUSG00000005447	Pafah1b3	Pafahg|mus[g]	platelet-activating factor acetylhydrolase, isoform 1b, subunit 3	protein-coding
mm_104934.1	chr11	100088266	100088270	-	1	NA	promoter-TSS (NM_001159374)	promoter-TSS (NM_001159374)	-42	NM_001159374	16670	Mm.4161	NM_010665	ENSMUSG00000046095	Krt32	Ha3|Hka2|K32|Krt1-2|Krtha2	keratin 32	protein-coding
mm_87165.1	chr10	36997044	36997061	+	1	NA	exon (NM_008229, exon 9 of 14)	exon (NM_008229, exon 9 of 14)	22508	NM_008229	15182	Mm.19806	NM_008229	ENSMUSG00000019777	Hdac2	D10Wsu179e|YAF1|Yy1bp|mRPD3	histone deacetylase 2	protein-coding
mm_121276.1	chr14	103650209	103650243	+	1	NA	promoter-TSS (NM_198014)	promoter-TSS (NM_198014)	-17	NM_198014	105439	Mm.27548	NM_198014	ENSMUSG00000055717	Slain1	9630044O09Rik|AA675320|AW742596	SLAIN motif family, member 1	protein-coding
mm_55392.1	chr6	60403693	60403712	-	1	NA	promoter-TSS (NR_015565)	promoter-TSS (NR_015565)	5	NR_015565	208079	Mm.131226	NM_177329	ENSMUSG00000046764	A530053G22Rik	-	RIKEN cDNA A530053G22 gene	ncRNA
mm_115241.1	chr13	110392922	110392960	+	1	NA	Intergenic	Intergenic	-2103	NM_152804	20620	Mm.380	NM_152804	ENSMUSG00000021701	Plk2	Snk	polo-like kinase 2	protein-coding
mm_61687.1	chr7	81005364	81005367	+	1	NA	intron (NM_178707, intron 1 of 9)	PB1D11|SINE|Alu	11681	NM_178707	233410	Mm.29525	NM_178707	ENSMUSG00000005621	Zfp592	8430405N24|A730014M16Rik|Znf592|mKIAA0211	zinc finger protein 592	protein-coding
mm_2273.1	chr1	91250312	91250380	+	1	NA	promoter-TSS (NM_026454)	promoter-TSS (NM_026454)	27	NM_026454	67921	Mm.337238	NM_026454	ENSMUSG00000034343	Ube2f	2510010F15Rik|AI851109	ubiquitin-conjugating enzyme E2F (putative)	protein-coding
mm_72908.1	chr8	90935240	90935245	+	1	NA	intron (NM_001310530, intron 1 of 37)	MIR|SINE|MIR	2993	NM_001310530	109151	Mm.100615	NM_177224	ENSMUSG00000056608	Chd9	1810014J18Rik|9030205D12Rik|A330063D19Rik|AD013|PRIC320|mKIAA0308	chromodomain helicase DNA binding protein 9	protein-coding
mm_121072.1	chr14	98167404	98167430	+	1	NA	intron (NM_007826, intron 1 of 11)	intron (NM_007826, intron 1 of 11)	2348	NM_001038610	13134	Mm.320593	NM_007826	ENSMUSG00000055639	Dach1	Dac|Dach	dachshund 1 (Drosophila)	protein-coding
mm_64926.1	chr7	16273913	16273926	-	1	NA	promoter-TSS (NM_001136270)	promoter-TSS (NM_001136270)	-227	NM_001136270	66300	Mm.218698	NM_001136270	ENSMUSG00000091811	Inafm1	2610014I16Rik|Prr24	InaF motif containing 1	protein-coding
mm_122376.1	chr14	39474024	39474046	-	1	NA	promoter-TSS (NM_008734)	promoter-TSS (NM_008734)	-947	NM_008734	18183	Mm.258705	NM_008734	ENSMUSG00000041014	Nrg3	ska	neuregulin 3	protein-coding
mm_68401.1	chr7	109602743	109602747	-	1	NA	intron (NM_001001326, intron 1 of 19)	intron (NM_001001326, intron 1 of 19)	13823	NR_037617	76954	Mm.252009	NM_029811	ENSMUSG00000031024	St5	2010004M01Rik|2610305K15Rik	suppression of tumorigenicity 5	protein-coding
mm_76106.1	chr8	80395178	80395192	-	1	NA	Intergenic	Intergenic	-98860	NM_010369	14934	Mm.13123	NM_010369	ENSMUSG00000051839	Gypa	AI853584|CD235a|GPA	glycophorin A	protein-coding
mm_89547.1	chr10	94576255	94576270	+	1	NA	promoter-TSS (NM_177026)	promoter-TSS (NM_177026)	-1	NM_177026	319880	Mm.23047	NM_172051	ENSMUSG00000020023	Tmcc3	AW488095|C630016B22Rik|C88213|Tmcc1	transmembrane and coiled coil domains 3	protein-coding
mm_143373.1	chr17	67632672	67632689	-	1	NA	promoter-TSS (NM_001033340)	promoter-TSS (NM_001033340)	43	NM_001033340	240131	Mm.295736	NM_001033340	ENSMUSG00000073375	Lrrc30	Gm326	leucine rich repeat containing 30	protein-coding
mm_106481.1	chr11	120189864	120189939	-	1	NA	promoter-TSS (NR_030682)	promoter-TSS (NR_030682)	-45	NR_030682	100042332	Mm.269766	NR_030682		2810410L24Rik	-	RIKEN cDNA 2810410L24 gene	ncRNA
mm_119166.1	chr14	32085678	32085695	+	1	NA	promoter-TSS (NM_001284346)	promoter-TSS (NM_001284346)	6	NR_104303	105638	Mm.2519	NM_172254	ENSMUSG00000021905	Dph3	DELGIP1|DelgipP1|Desr1|KTI11|Zcsl2	diphthamine biosynthesis 3	protein-coding
mm_107496.1	chr12	38783704	38783722	+	1	NA	promoter-TSS (NM_001163154)	promoter-TSS (NM_001163154)	2	NM_001163154	14009	Mm.4866	NM_007960	ENSMUSG00000004151	Etv1	ER81|Etsrp81	ets variant 1	protein-coding
mm_108417.1	chr12	81971169	81971199	+	1	NA	intron (NM_018814, intron 19 of 35)	intron (NM_018814, intron 19 of 35)	111154	NM_018814	54604	Mm.86584	NM_018814	ENSMUSG00000021140	Pcnx	2900024E21Rik|3526401J03Rik|AF096286|AI327143|AI413187|Pcnx1|Pcnxl1	pecanex homolog (Drosophila)	protein-coding
mm_18242.1	chr2	52175134	52175147	-	1	NA	exon (NM_010889, exon 133 of 157)	exon (NM_010889, exon 133 of 157)	102303	NM_175238	51869	Mm.254530	NM_175238	ENSMUSG00000036202	Rif1	5730435J01Rik|6530403D07Rik|AU016181|AW549474|D2Ertd145e	replication timing regulatory factor 1	protein-coding
mm_112231.1	chr12	113482288	113482311	-	1	NA	Intergenic	Intergenic	-7266	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_42086.1	chr5	110204775	110204808	+	1	NA	exon (NM_008146, exon 13 of 24)	exon (NM_008146, exon 13 of 24)	-26213	NM_001253814	71782	Mm.288442	NM_027922	ENSMUSG00000029501	Ankle2	1110001J12Rik|AI661024|D5Ertd585e	ankyrin repeat and LEM domain containing 2	protein-coding
mm_122347.1	chr14	38657976	38657990	-	1	NA	intron (NM_001190188, intron 3 of 8)	Lx4B|LINE|L1	-240319	NR_045713	75170	Mm.372967	NR_045713	ENSMUSG00000093528	Nrg3os	4930529F24Rik	neuregulin 3, opposite strand	ncRNA
mm_67534.1	chr7	81345190	81345237	-	1	NA	promoter-TSS (NM_009092)	promoter-TSS (NM_009092)	21	NM_009092	20068	Mm.42767	NM_009092	ENSMUSG00000061787	Rps17	-	ribosomal protein S17	protein-coding
mm_23898.1	chr3	83031734	83031748	+	1	NA	exon (NM_010196, exon 5 of 5)	exon (NM_010196, exon 5 of 5)	5588	NM_001111048	14161	Mm.88793	NM_010196	ENSMUSG00000028001	Fga	ENSMUSG00000059807|Fib	fibrinogen alpha chain	protein-coding
mm_80021.1	chr9	67984676	67984678	+	1	NA	intron (NM_177184, intron 81 of 84)	intron (NM_177184, intron 81 of 84)	41037	NR_045745	434412	Mm.490707	NR_045745	ENSMUSG00000111841	Gm20745	-	predicted gene, 20745	ncRNA
mm_109250.1	chr12	109454986	109454991	+	1	NA	exon (NM_010052, exon 2 of 5)	exon (NM_010052, exon 2 of 5)	1533	NM_010052	13386	Mm.157069	NM_010052	ENSMUSG00000040856	Dlk1	AW742678|DLK-1|DlkI|FA1|Ly107|Peg9|SCP1|ZOG|pG2|pref-1	delta-like 1 homolog (Drosophila)	protein-coding
mm_154210.1	chr19	59076285	59076320	-	1	NA	promoter-TSS (NM_001114312)	promoter-TSS (NM_001114312)	-233	NM_001114312	71653	Mm.37338	NM_175172	ENSMUSG00000041362	Shtn1	4930506M07Rik|Kiaa1598|Shootin1|mKIAA1598	shootin 1	protein-coding
mm_68961.1	chr7	126581764	126581776	-	1	NA	intron (NM_001146311, intron 5 of 17)	intron (NM_001146311, intron 5 of 17)	1466	NM_001329789	12752	Mm.268930	NM_009907	ENSMUSG00000030720	Cln3	AI323623	ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease)	protein-coding
mm_49643.1	chr6	30805536	30805546	+	1	NA	intron (NM_017478, intron 20 of 23)	intron (NM_017478, intron 20 of 23)	64242	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_114531.1	chr13	73604008	73604120	+	1	NA	promoter-TSS (NM_146047)	promoter-TSS (NM_146047)	62	NM_146047	218335	Mm.30099	NM_146047	ENSMUSG00000021610	Clptm1l	C130052I12Rik|Crr9	CLPTM1-like	protein-coding
mm_165617.1	chr3	57413902	57413909	+	1	NA	Intergenic	Intergenic	-11505	NM_145539	229302	Mm.26618	NM_145539	ENSMUSG00000027801	Tm4sf4	Iltmp	transmembrane 4 superfamily member 4	protein-coding
mm_144133.1	chr18	4928784	4928800	+	1	NA	Intergenic	Intergenic	116306	NR_045881	100038439	Mm.387569	NR_045881	ENSMUSG00000097043	Gm10556	ENSMUSG00000073646	predicted gene 10556	ncRNA
mm_16734.1	chr2	9176861	9176869	-	1	NA	Intergenic	Intergenic	-12650	NR_038180	73438	Mm.23558	NR_038180	ENSMUSG00000085580	1700061F12Rik	-	RIKEN cDNA 1700061F12 gene	ncRNA
mm_156173.1	chrX	130213223	130213233	+	1	NA	intron (NM_172493, intron 23 of 26)	intron (NM_172493, intron 23 of 26)	463486	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diaph2	Dia3|Diap2|Drf2|E430022I22Rik	diaphanous related formin 2	protein-coding
mm_155446.1	chrX	73495077	73495109	+	1	NA	3' UTR (NM_007542, exon 8 of 8)	3' UTR (NM_007542, exon 8 of 8)	-7993	NM_001310537	320707	Mm.210095	NM_177236	ENSMUSG00000031376	Atp2b3	6430519O13Rik|Pmca3	ATPase, Ca++ transporting, plasma membrane 3	protein-coding
mm_86205.1	chr9	119983006	119983040	-	1	NA	intron (NM_153287, intron 1 of 4)	CpG	1635	NM_153287	215418	Mm.491094	NM_153287	ENSMUSG00000032515	Csrnp1	4931429D10Rik|Axud1|CSRNP-1|URAX1|taip-3	cysteine-serine-rich nuclear protein 1	protein-coding
mm_159563.1	chr4	109117944	109117944	-	1	NA	promoter-TSS (NM_173350)	promoter-TSS (NM_173350)	92	NM_173350	100273	Mm.366315	NM_133885	ENSMUSG00000028559	Osbpl9	2600011I06Rik|AU015843|Orp-9	oxysterol binding protein-like 9	protein-coding
mm_134655.1	chr16	22060037	22060076	-	1	NA	3' UTR (NM_183029, exon 16 of 16)	3' UTR (NM_183029, exon 16 of 16)	50572	NR_027488	75826	Mm.297431	NM_029457	ENSMUSG00000022855	Senp2	2310007L05Rik|4930538C18Rik|AI646780|AW554757|Smt3ip2|SuPr-1|mKIAA1331	SUMO/sentrin specific peptidase 2	protein-coding
mm_77697.1	chr8	126589709	126589726	-	1	NA	3' UTR (NM_001164598, exon 2 of 2)	3' UTR (NM_001164598, exon 2 of 2)	3719	NM_001164598	270110	Mm.334918	NM_001164598	ENSMUSG00000051495	Irf2bp2	E130305N23Rik|IRF-2BP2	interferon regulatory factor 2 binding protein 2	protein-coding
mm_111920.1	chr12	108875588	108875616	-	1	NA	intron (NM_011710, intron 5 of 10)	intron (NM_011710, intron 5 of 10)	17596	NM_001164488	22375	Mm.38433	NM_011710	ENSMUSG00000021266	Wars	TrpRS|WRS	tryptophanyl-tRNA synthetase	protein-coding
mm_167123.1	chr7	121914149	121914157	+	1	NA	intron (NR_073548, intron 7 of 12)	intron (NR_073548, intron 7 of 12)	49115	NR_073548	20277	Mm.7709	NM_011325	ENSMUSG00000030873	Scnn1b	-	sodium channel, nonvoltage-gated 1 beta	protein-coding
mm_14618.1	chr2	136764037	136764055	+	1	NA	intron (NM_011428, intron 4 of 7)	intron (NM_011428, intron 4 of 7)	50596	NM_001291056	20614	Mm.45953	NM_011428	ENSMUSG00000027273	Snap25	Bdr|GENA70|SNAP-25|SUP|sp	synaptosomal-associated protein 25	protein-coding
mm_120744.1	chr14	73231943	73231951	+	1	NA	intron (NM_009029, intron 17 of 26)	intron (NM_009029, intron 17 of 26)	-5944	NM_175116	67168	Mm.390681	NM_175116	ENSMUSG00000033446	Lpar6	2610302I02Rik|P2ry5|P2y5	lysophosphatidic acid receptor 6	protein-coding
mm_20444.1	chr2	129309965	129309978	-	1	NA	promoter-TSS (NM_010554)	promoter-TSS (NM_010554)	1	NM_010554	16175	Mm.15534	NM_010554	ENSMUSG00000027399	Il1a	Il-1a	interleukin 1 alpha	protein-coding
mm_82378.1	chr9	14634236	14634240	-	1	NA	Intergenic	Intergenic	-19238	NM_001081395	75723	Mm.159552	NM_001081395	ENSMUSG00000013076	Amotl1	2310010G08Rik|2310067L22Rik|4932416D09Rik|JEAP|mFLJ00155	angiomotin-like 1	protein-coding
mm_149869.1	chr19	25148467	25148482	+	1	NA	intron (NM_028785, intron 25 of 47)	B3A|SINE|B2	-88728	NM_181404	107351	Mm.260722	NM_181404	ENSMUSG00000032702	Kank1	A930031B09Rik|AU015049|AW121052|Ankrd15|D330024H06Rik|mKIAA0172	KN motif and ankyrin repeat domains 1	protein-coding
mm_119098.1	chr14	30896599	30896636	+	1	NA	exon (NM_001289633, exon 16 of 22)	exon (NM_001289633, exon 16 of 22)	10141	NM_001289632	16427	Mm.34819	NM_018746	ENSMUSG00000021922	Itih4	ITI-HC4|Itih-4|PK-120	inter alpha-trypsin inhibitor, heavy chain 4	protein-coding
mm_134810.1	chr16	25040112	25040122	-	1	NA	Intergenic	Intergenic	-19522	NR_040374	319487	Mm.137341	NR_040374	ENSMUSG00000096960	A230028O05Rik	-	RIKEN cDNA A230028O05 gene	ncRNA
mm_74811.1	chr8	22653407	22653458	-	1	NA	promoter-TSS (NM_011130)	promoter-TSS (NM_011130)	5	NM_011130	18970	Mm.123211	NM_011130	ENSMUSG00000031536	Polb	A430088C08Rik	polymerase (DNA directed), beta	protein-coding
mm_79859.1	chr9	65021786	65021814	+	1	NA	promoter-TSS (NM_021345)	promoter-TSS (NM_021345)	-83	NM_021345	57874	Mm.308180	NM_021345	ENSMUSG00000033629	Hacd3	4930523M17Rik|AW742319|B-ind1|Hcad3|Hspc121|Ptplad1	3-hydroxyacyl-CoA dehydratase 3	protein-coding
mm_125979.1	chr15	76328252	76328255	+	1	NA	intron (NM_175399, intron 1 of 2)	intron (NM_175399, intron 1 of 2)	856	NM_175399	109075	Mm.322752	NM_175399	ENSMUSG00000034259	Exosc4	1110039I09Rik|1500001N04Rik|Rrp41	exosome component 4	protein-coding
mm_86468.1	chr10	4605831	4605875	+	1	NA	Intergenic	Intergenic	-6136	NM_001302532	13982	Mm.9213	NM_007956	ENSMUSG00000019768	Esr1	ER|ER-alpha|ERa|ERalpha|ESR|Estr|Estra|Nr3a1	estrogen receptor 1 (alpha)	protein-coding
mm_97563.1	chr11	78935465	78935476	+	1	NA	exon (NM_010927, exon 6 of 27)	exon (NM_010927, exon 6 of 27)	10179	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_62313.1	chr7	100235120	100235122	+	1	NA	intron (NM_027629, intron 1 of 13)	intron (NM_027629, intron 1 of 13)	7514	NM_027629	70974	Mm.440524	NM_027629	ENSMUSG00000030729	Pgm2l1	4931406N15Rik|AI553438|BM32A	phosphoglucomutase 2-like 1	protein-coding
mm_132122.1	chr16	31716097	31716099	+	1	NA	intron (NR_045516, intron 4 of 24)	intron (NR_045516, intron 4 of 24)	-38252	NM_001252436	13383	Mm.382	NM_007862	ENSMUSG00000022770	Dlg1	B130052P05Rik|Dlgh1|E-dlg/SAP97|SAP-97|SAP97|mKIAA4187	discs, large homolog 1 (Drosophila)	protein-coding
mm_49690.1	chr6	33476964	33476981	+	1	NA	3' UTR (NM_001347089, exon 10 of 10)	3' UTR (NM_001347089, exon 10 of 10)	227822	NM_009148	20336	Mm.265512	NM_009148	ENSMUSG00000029763	Exoc4	C78892|Sec8|Sec8l1	exocyst complex component 4	protein-coding
mm_87352.1	chr10	43593418	43593446	+	1	NA	promoter-TSS (NR_033558)	promoter-TSS (NR_033558)	5	NR_033558	414125	Mm.244305	NR_033558	ENSMUSG00000075184	F830002L21Rik	F930017D23Rik	RIKEN cDNA F830002L21 gene	ncRNA
mm_45050.1	chr5	41764039	41764042	-	1	NA	5' UTR (NM_007524, exon 1 of 2)	5' UTR (NM_007524, exon 1 of 2)	180	NM_007524	12020	Mm.2530	NM_007524	ENSMUSG00000049691	Nkx3-2	Bapx1|NKX3.2|Nkx-3.2	NK3 homeobox 2	protein-coding
mm_138977.1	chr17	45433824	45433868	+	1	NA	promoter-TSS (NM_152810)	promoter-TSS (NM_152810)	15	NR_130961	105246278	Mm.206588	NR_130960	ENSMUSG00000097119	B230354K17Rik	-	RIKEN cDNA B230354K17 gene	ncRNA
mm_135062.1	chr16	34081894	34081938	-	1	NA	intron (NM_177357, intron 34 of 59)	intron (NM_177357, intron 34 of 59)	-114913	NM_009471	22247	Mm.13145	NM_009471	ENSMUSG00000022814	Umps	1700095D23Rik|AA408257|AL033308|BB164745	uridine monophosphate synthetase	protein-coding
mm_136051.1	chr16	78576650	78576666	-	1	NA	promoter-TSS (NM_001252440)	promoter-TSS (NM_001252440)	30	NM_001252438	67102	Mm.37332	NM_025967	ENSMUSG00000022864	D16Ertd472e	1700010I10Rik|2310009O17Rik|E330003K22Rik|Eurl	DNA segment, Chr 16, ERATO Doi 472, expressed	protein-coding
mm_35431.1	chr4	36654163	36654165	-	1	NA	intron (NM_001165999, intron 2 of 7)	Lx2B2|LINE|L1	-8711	NR_030545	100124458		NR_030545	ENSMUSG00000077851	Mir876	Mirn876|mir-876|mmu-mir-876	microRNA 876	ncRNA
mm_95387.1	chr11	49245459	49245506	+	1	NA	5' UTR (NM_010794, exon 2 of 3)	5' UTR (NM_010794, exon 2 of 3)	1291	NM_001110148	17308	Mm.196933	NM_010794	ENSMUSG00000020346	Mgat1	Mgat-1	mannoside acetylglucosaminyltransferase 1	protein-coding
mm_4666.1	chr1	180382206	180382228	+	1	NA	intron (NM_001081175, intron 2 of 7)	intron (NM_001081175, intron 2 of 7)	-51668	NR_003623	277333	Mm.389223	NM_199472		Gm5069	EG277333	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_131124.1	chr16	5855729	5855743	+	1	NA	Intergenic	Intergenic	-29057	NM_021477	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_92228.1	chr10	68673630	68673650	-	1	NA	Intergenic	MLT1E2|LTR|ERVL-MaLR	-50106	NM_177794	327766	Mm.2479	NM_177794	ENSMUSG00000060044	Tmem26	3230401A06|AI195372	transmembrane protein 26	protein-coding
mm_98342.1	chr11	93099221	93099230	+	1	NA	promoter-TSS (NM_028296)	promoter-TSS (NM_028296)	-65	NM_028296	72605	Mm.342160	NM_028296	ENSMUSG00000056158	Car10	2700029L05Rik|BB085816|Ca10	carbonic anhydrase 10	protein-coding
mm_10024.1	chr1	192092428	192092455	-	1	NA	5' UTR (NM_011633, exon 1 of 10)	5' UTR (NM_011633, exon 1 of 10)	158	NM_011633	22033	Mm.380491	NM_011633		Traf5	-	TNF receptor-associated factor 5	protein-coding
mm_20777.1	chr2	143952266	143952281	-	1	NA	exon (NM_024281, exon 19 of 24)	exon (NM_024281, exon 19 of 24)	36942	NM_019771	56431	Mm.28919	NM_019771	ENSMUSG00000015932	Dstn	2610043P17Rik|ADF|AU042046|Dsn|corn1|sid23p	destrin	protein-coding
mm_141974.1	chr17	35158440	35158455	-	1	NA	exon (NM_020027, exon 13 of 31)	exon (NM_020027, exon 13 of 31)	6430	NM_001199044	53761	Mm.272462	NM_020027	ENSMUSG00000024393	Prrc2a	3110039B05Rik|Bat-2|Bat2|D17H6S51E|G2|Wbp12|mKIAA4178	proline-rich coiled-coil 2A	protein-coding
mm_129044.1	chr15	75135126	75135129	-	1	NA	Intergenic	Intergenic	-20134	NM_001310438	546644		NM_008531	ENSMUSG00000022582	Ly6g	Gr-1|Gr1|Ly-6G	lymphocyte antigen 6 complex, locus G	protein-coding
mm_164244.1	chr15	95654349	95654371	-	1	NA	exon (NM_207533, exon 1 of 4)	exon (NM_207533, exon 1 of 4)	411	NM_207533	223843	Mm.152937	NM_207533	ENSMUSG00000045608	Dbx2	9430056A22Rik|9630005K15|AI846217|Gm1229	developing brain homeobox 2	protein-coding
mm_384.1	chr1	34068570	34068601	+	1	NA	intron (NM_133833, intron 1 of 92)	ORR1E|LTR|ERVL-MaLR	-48774	NR_105861	102466987		NR_105861	ENSMUSG00000105982	Mir6896	mmu-mir-6896	microRNA 6896	ncRNA
mm_14414.1	chr2	130405772	130405782	+	1	NA	promoter-TSS (NM_025753)	promoter-TSS (NM_025753)	481	NM_001163483	75656	Mm.174788	NM_029375	ENSMUSG00000027409	1700020A23Rik	-	RIKEN cDNA 1700020A23 gene	protein-coding
mm_154326.1	chrM	2420	2428	+	1	NA	NA	Intergenic	NA	NA								
mm_55476.1	chr6	68880694	68880713	-	1	NA	Intergenic	Intergenic	446471	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_67257.1	chr7	75669583	75669593	-	1	NA	intron (NM_029332, intron 10 of 36)	intron (NM_029332, intron 10 of 36)	-178750	NM_001122780	207952	Mm.206223	NM_029652	ENSMUSG00000055652	Klhl25	2810402K13Rik|BC027373|Enc-1	kelch-like 25	protein-coding
mm_20617.1	chr2	131855453	131855490	-	1	NA	3' UTR (NM_001166206, exon 2 of 2)	3' UTR (NM_001166206, exon 2 of 2)	4276	NM_001166206	71995	Mm.22	NM_028045	ENSMUSG00000037482	Erv3	1600014E20Rik|AA389086|AI426069|AI448024|D19349	endogenous retroviral sequence 3	protein-coding
mm_158199.1	chrX	105279047	105279057	-	1	NA	Intergenic	Intergenic	65317	NR_029910	723861		NR_029910	ENSMUSG00000065499	Mir384	Mirn384|mir-384|mmu-mir-384	microRNA 384	ncRNA
mm_46398.1	chr5	104092872	104092882	-	1	NA	exon (NM_010097, exon 4 of 11)	exon (NM_010097, exon 4 of 11)	-15269	NM_001163772	100271704	Mm.366664	NM_001163772	ENSMUSG00000091034	Gm17660	Scpppq1	predicted gene, 17660	protein-coding
mm_41322.1	chr5	90472496	90472506	+	1	NA	exon (NM_009654, exon 12 of 15)	exon (NM_009654, exon 12 of 15)	11631	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_147398.1	chr18	44429519	44429522	-	1	NA	3' UTR (NM_001085373, exon 19 of 19)	3' UTR (NM_001085373, exon 19 of 19)	49020	NM_027490	70640	Mm.87629	NM_027490	ENSMUSG00000024472	Dcp2	2410015D23Rik|5730537H01Rik|AL118268	decapping mRNA 2	protein-coding
mm_98395.1	chr11	94297010	94297048	+	1	NA	exon (NM_026313, exon 8 of 11)	exon (NM_026313, exon 8 of 11)	24882	NM_026313	67684	Mm.30927	NM_026313	ENSMUSG00000020863	Luc7l3	3300001P08Rik|Luc7a	LUC7-like 3 (S. cerevisiae)	protein-coding
mm_142166.1	chr17	36167648	36167682	-	1	NA	exon (NM_001081032, exon 3 of 8)	exon (NM_001081032, exon 3 of 8)	872	NM_001081032	667977	Mm.441651	NM_001081032	ENSMUSG00000073402	Gm8909	EG667977|H2-Tw5l|H2-gs17	predicted gene 8909	protein-coding
mm_62518.1	chr7	102229970	102230023	+	1	NA	intron (NR_111937, intron 2 of 5)	intron (NR_111937, intron 2 of 5)	6968	NR_111937	233575	Mm.302013	NM_145583	ENSMUSG00000030990	Pgap2	1810006G21Rik|C76649|Frag1	post-GPI attachment to proteins 2	protein-coding
mm_27486.1	chr3	54686754	54686780	-	1	NA	Intergenic	Intergenic	-6338	NM_019995	56790	Mm.486375	NM_019995	ENSMUSG00000027751	Supt20	AA667204|AI450544|D3Ertd300e|Fam48a|Supt20h|p38IP	suppressor of Ty 20	protein-coding
mm_90113.1	chr10	117277465	117277495	+	1	NA	TTS (NM_017372)	TTS (NM_017372)	4792	NM_017372	17105	Mm.45436	NM_017372	ENSMUSG00000069516	Lyz2	AI326280|Lys|Lysm|Lyzf2|Lyzs|Lzm|Lzm-s1|Lzp	lysozyme 2	protein-coding
mm_29509.1	chr3	116253468	116253483	-	1	NA	promoter-TSS (NM_022427)	promoter-TSS (NM_022427)	9	NM_022427	64378	Mm.40025	NM_022427	ENSMUSG00000068696	Gpr88	AW061286|Strg	G-protein coupled receptor 88	protein-coding
mm_107241.1	chr12	26479109	26479121	+	1	NA	3' UTR (NM_020557, exon 5 of 5)	3' UTR (NM_020557, exon 5 of 5)	9900	NM_020557	22169	Mm.271839	NM_020557	ENSMUSG00000020638	Cmpk2	1200004E04Rik|TDKI|Tyki	cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial	protein-coding
mm_148814.1	chr19	6297903	6297924	+	1	NA	intron (NM_010119, intron 4 of 4)	intron (NM_010119, intron 4 of 4)	-8544	NM_001033342	240505	Mm.329622	NM_001033342	ENSMUSG00000024769	Cdc42bpg	BC046418|MRCKgamma	CDC42 binding protein kinase gamma (DMPK-like)	protein-coding
mm_98484.1	chr11	94951158	94951171	+	1	NA	exon (NM_007742, exon 50 of 51)	exon (NM_007742, exon 50 of 51)	14940	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_144885.1	chr18	36799302	36799306	+	1	NA	3' UTR (NM_025594, exon 6 of 6)	3' UTR (NM_025594, exon 6 of 6)	-2459	NR_027885	378472	Mm.482379	NR_027885		Vaultrc5	Gm22653|Mvg1	vault RNA component 5	ncRNA
mm_88820.1	chr10	80803282	80803292	+	1	NA	intron (NM_013651, intron 5 of 8)	intron (NM_013651, intron 5 of 8)	-1961	NM_007445	11705	Mm.376094	NM_007445	ENSMUSG00000035262	Amh	MIS	anti-Mullerian hormone	protein-coding
mm_142741.1	chr17	48409478	48409525	-	1	NA	promoter-TSS (NM_001289491)	promoter-TSS (NM_001289491)	319	NM_001110832	18044	Mm.4929	NM_010913	ENSMUSG00000023994	Nfya	AA407810|Cbf-b|SEZ-10|SEZ10	nuclear transcription factor-Y alpha	protein-coding
mm_169832.1	chr1	62540996	62541015	-	1	NA	intron (NM_001081050, intron 21 of 22)	IAPLTR1_Mm|LTR|ERVK	-162312	NM_001077406	18187	Mm.266341	NM_010939	ENSMUSG00000025969	Nrp2	1110048P06Rik|Np-2|Np2|Npn-2|Npn2	neuropilin 2	protein-coding
mm_35858.1	chr4	49473871	49473887	-	1	NA	Intergenic	Intergenic	-22770	NM_001164565	230161	Mm.30101	NM_001164565	ENSMUSG00000070985	Acnat1	AI132189	acyl-coenzyme A amino acid N-acyltransferase 1	protein-coding
mm_154498.1	chrM	11668	11677	-	1	NA	NA	Intergenic	NA	NA								
mm_46454.1	chr5	105117636	105117647	-	1	NA	3' UTR (NM_001256005, exon 11 of 11)	3' UTR (NM_001256005, exon 11 of 11)	-7349	NM_172777	236573	Mm.425261	NM_172777	ENSMUSG00000029298	Gbp9	-	guanylate-binding protein 9	protein-coding
mm_156802.1	chrX	163909133	163909169	+	1	NA	5' UTR (NM_026887, exon 1 of 5)	5' UTR (NM_026887, exon 1 of 5)	134	NM_001290379	108012	Mm.426783	NM_026887	ENSMUSG00000031367	Ap1s2	1500012A13Rik|AI853648|EST1	adaptor-related protein complex 1, sigma 2 subunit	protein-coding
mm_40847.1	chr5	73380531	73380546	+	1	NA	Intergenic	Intergenic	-25540	NM_181323	231293	Mm.280211	NM_181323	ENSMUSG00000029154	Cwh43	C130090K23Rik|imds-60	cell wall biogenesis 43 C-terminal homolog	protein-coding
mm_96800.1	chr11	69981333	69981369	+	1	NA	promoter-TSS (NM_018740)	promoter-TSS (NM_018740)	-116	NM_018740	54351	Mm.13430	NM_018740	ENSMUSG00000018565	Elp5	Derp6|Rai12	elongator acetyltransferase complex subunit 5	protein-coding
mm_170761.1	chr2	159656247	159656247	+	1	NA	Intergenic	Intergenic	-291094	NR_040498	71081	Mm.383491	NR_040498	ENSMUSG00000085198	4933416E03Rik	-	RIKEN cDNA 4933416E03 gene	ncRNA
mm_157943.1	chrX	85776607	85776643	-	1	NA	5' UTR (NM_212444, exon 1 of 20)	5' UTR (NM_212444, exon 1 of 20)	194	NM_001294140	14933	Mm.246682	NM_008194	ENSMUSG00000025059	Gk	D930012N15Rik|Gyk	glycerol kinase	protein-coding
mm_88619.1	chr10	79859368	79859383	+	1	NA	exon (NM_008956, exon 5 of 13)	exon (NM_008956, exon 5 of 13)	-3212	NR_105875	102465549		NR_105875	ENSMUSG00000098562	Mir6910	Gm27763|mmu-mir-6910	microRNA 6910	ncRNA
mm_94459.1	chr11	6416228	6416232	+	1	NA	intron (NM_008907, intron 1 of 4)	CpG	360	NM_008907	268373	Mm.5246	NM_008907	ENSMUSG00000071866	Ppia	2700098C05|Cphn|CyP-18|CypA	peptidylprolyl isomerase A	protein-coding
mm_95977.1	chr11	58963775	58963785	+	1	NA	promoter-TSS (NM_031172)	promoter-TSS (NM_031172)	-1	NM_031172	56631	Mm.179733	NM_031172	ENSMUSG00000036964	Trim17	Rnf16|terf	tripartite motif-containing 17	protein-coding
mm_93607.1	chr10	117234303	117234310	-	1	NA	3' UTR (NM_029906, exon 4 of 4)	3' UTR (NM_029906, exon 4 of 4)	4375	NM_029906	77397	Mm.118350	NM_029906	ENSMUSG00000020177	9530003J23Rik	Lyzf1	RIKEN cDNA 9530003J23 gene	protein-coding
mm_725.1	chr1	42952985	42953028	+	1	NA	5' UTR (NM_053107, exon 1 of 2)	5' UTR (NM_053107, exon 1 of 2)	134	NM_053107	93690	Mm.444976	NM_053107	ENSMUSG00000041907	Gpr45	9230112G11Rik|AW046772	G protein-coupled receptor 45	protein-coding
mm_19965.1	chr2	117968802	117968812	-	1	NA	intron (NR_126479, intron 8 of 9)	intron (NR_126479, intron 8 of 9)	142395	NR_126479	329496	Mm.235844	NR_126479	ENSMUSG00000087203	Gm13986	C230060E24|OTTMUSG00000015236	predicted gene 13986	ncRNA
mm_103733.1	chr11	79962415	79962425	-	1	NA	promoter-TSS (NM_144826)	promoter-TSS (NM_144826)	-33	NM_144826	216987	Mm.274961	NM_144826	ENSMUSG00000035575	Utp6	4732497O03Rik|HCA66	UTP6 small subunit processome component	protein-coding
mm_68918.1	chr7	126461688	126461709	-	1	NA	intron (NM_007504, intron 3 of 22)	intron (NM_007504, intron 3 of 22)	1375	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_145407.1	chr18	57468548	57468560	+	1	NA	promoter-TSS (NM_001134697)	promoter-TSS (NM_001134697)	68	NM_001134697	629147	Mm.57415	NM_001134697	ENSMUSG00000069372	Ctxn3	ENSMUSG00000069372	cortexin 3	protein-coding
mm_119192.1	chr14	32513487	32513548	+	1	NA	promoter-TSS (NM_001081221)	promoter-TSS (NM_001081221)	-4	NM_001081221	319955	Mm.318310	NM_177043	ENSMUSG00000054051	Ercc6	4732403I04|C130058G22Rik|CSB	excision repair cross-complementing rodent repair deficiency, complementation group 6	protein-coding
mm_26418.1	chr3	142611344	142611463	+	1	NA	exon (NM_010259, exon 10 of 11)	exon (NM_010259, exon 10 of 11)	-9260	NM_010260	14469	Mm.24038	NM_010260	ENSMUSG00000028270	Gbp2	-	guanylate binding protein 2	protein-coding
mm_24130.1	chr3	88207309	88207328	+	1	NA	Intergenic	Intergenic	-7853	NR_037276	100526540		NR_037276	ENSMUSG00000092988	Mir3093	mir-3093|mmu-mir-3093	microRNA 3093	ncRNA
mm_59263.1	chr7	24884783	24884802	+	1	NA	promoter-TSS (NM_023133)	promoter-TSS (NM_023133)	78	NM_023133	20085	Mm.300281	NM_023133	ENSMUSG00000040952	Rps19	Dsk3	ribosomal protein S19	protein-coding
mm_30971.1	chr4	34485783	34485797	+	1	NA	Intergenic	Intergenic	-64825	NM_001007589	433693	Mm.389532	NM_026019	ENSMUSG00000028291	Akirin2	2700059D21Rik|AA114675|AA522011|AU019887|Akirin-2	akirin 2	protein-coding
mm_11868.1	chr2	48950114	48950128	+	1	NA	promoter-TSS (NM_001177313)	promoter-TSS (NM_001177313)	613	NM_029924	109241	Mm.440436	NM_029924	ENSMUSG00000036792	Mbd5	9430004D19Rik|AA536666|AI426407|C030040A15Rik|Gm1630|OTTMUSG00000012483	methyl-CpG binding domain protein 5	protein-coding
mm_34159.1	chr4	139431131	139431141	+	1	NA	intron (NM_001160319, intron 48 of 105)	intron (NM_001160319, intron 48 of 105)	50477	NM_001160319	69116	Mm.271956	NM_001160319	ENSMUSG00000066036	Ubr4	1810009A16Rik|A930005E13Rik|D930005K06Rik|Gm1032|Gm1666|N28143|RBAF600|Zubr1|mKIAA0462|p600	ubiquitin protein ligase E3 component n-recognin 4	protein-coding
mm_139121.1	chr17	47436732	47436743	+	1	NA	promoter-TSS (NM_145489)	promoter-TSS (NM_145489)	98	NM_145489	224833	Mm.218444	NM_145489	ENSMUSG00000034382	AI661453	-	expressed sequence AI661453	protein-coding
mm_98905.1	chr11	98026919	98026931	+	1	NA	promoter-TSS (NM_009078)	promoter-TSS (NM_009078)	1	NM_009078	19921	Mm.10247	NM_009078	ENSMUSG00000017404	Rpl19	-	ribosomal protein L19	protein-coding
mm_118417.1	chr14	7801142	7801145	+	1	NA	Intergenic	Intergenic	-16814	NM_001081427	286940	Mm.489652	NM_134080	ENSMUSG00000025278	Flnb	AL024016|Fln-b	filamin, beta	protein-coding
mm_20464.1	chr2	129367986	129368006	-	1	NA	exon (NM_008361, exon 4 of 7)	exon (NM_008361, exon 4 of 7)	-1906	NR_015474	329514	Mm.207315	NM_177848	ENSMUSG00000074805	Il1bos	9430083I22|Gm14047|OTTMUSG00000015529	interleukin 1 beta, opposite strand	ncRNA
mm_66509.1	chr7	45101133	45101136	-	1	NA	intron (NM_010189, intron 4 of 6)	B2_Mm2|SINE|B2	2688	NM_010189	14132	Mm.3303	NM_010189	ENSMUSG00000003420	Fcgrt	FcRn	Fc receptor, IgG, alpha chain transporter	protein-coding
mm_98930.1	chr11	98355336	98355346	+	1	NA	exon (NM_001313970, exon 5 of 7)	exon (NM_001313970, exon 5 of 7)	2942	NR_045477	69338	Mm.398308	NR_045477	ENSMUSG00000085944	1700003D09Rik	-	RIKEN cDNA 1700003D09 gene	ncRNA
mm_64213.1	chr7	141476414	141476455	+	1	NA	promoter-TSS (NM_001252588)	promoter-TSS (NM_001252588)	54	NM_001252588	64540	Mm.489619	NM_053082	ENSMUSG00000025511	Tspan4	AI325509|AI746565|D130042I01Rik|NAG-2|Tm4sf7|Tspan-4	tetraspanin 4	protein-coding
mm_89596.1	chr10	95970855	95970863	+	1	NA	intron (NM_001001932, intron 1 of 28)	intron (NM_001001932, intron 1 of 28)	30196	NM_001001932	216238	Mm.210035	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding
mm_119513.1	chr14	47385600	47385665	+	1	NA	exon (NM_010705, exon 6 of 6)	exon (NM_010705, exon 6 of 6)	11772	NM_001145953	16854	Mm.248615	NM_010705	ENSMUSG00000050335	Lgals3	GBP|L-34|Mac-2|gal3	lectin, galactose binding, soluble 3	protein-coding
mm_60954.1	chr7	47052665	47052673	+	1	NA	intron (NM_026436, intron 1 of 2)	intron (NM_026436, intron 1 of 2)	2029	NM_026436	67893	Mm.27338	NM_026436	ENSMUSG00000010307	Tmem86a	1810054O13Rik|AI414959|AW742698	transmembrane protein 86A	protein-coding
mm_167739.1	chr9	107249787	107249789	-	1	NA	Intergenic	Intergenic	-17879	NM_153413	208869	Mm.150259	NM_153413	ENSMUSG00000039716	Dock3	MOCA|PBP|mKIAA0299	dedicator of cyto-kinesis 3	protein-coding
mm_43074.1	chr5	124446788	124446814	+	1	NA	promoter-TSS (NM_001310727)	promoter-TSS (NM_001310727)	97	NM_001310727	67956	Mm.137966	NM_030241	ENSMUSG00000049327	Kmt5a	2410195B05Rik|AA617402|AW536475|PR-SET7|PR/SET07|Setd8	lysine methyltransferase 5A	protein-coding
mm_171154.1	chr3	19934004	19934018	+	1	NA	Intergenic	Intergenic	-23043	NM_001276250	12870	Mm.13787	NM_007752	ENSMUSG00000003617	Cp	D3Ertd555e	ceruloplasmin	protein-coding
mm_52966.1	chr6	123129810	123129818	+	1	NA	intron (NM_011999, intron 3 of 5)	intron (NM_011999, intron 3 of 5)	6498	NM_001170333	26888	Mm.47384	NM_011999	ENSMUSG00000030148	Clec4a2	Clec4a|Clecsf6|DCIR|Dcir1	C-type lectin domain family 4, member a2	protein-coding
mm_128901.1	chr15	73311065	73311066	-	1	NA	intron (NM_001130409, intron 8 of 29)	intron (NM_001130409, intron 8 of 29)	-56183	NR_029561	387169		NR_029561	ENSMUSG00000065612	Mir151	Mirn151|mir-151|mmu-mir-151	microRNA 151	ncRNA
mm_143074.1	chr17	57031469	57031538	-	1	NA	promoter-TSS (NM_010613)	promoter-TSS (NM_010613)	4	NM_010613	16549	Mm.34296	NM_010613	ENSMUSG00000007670	Khsrp	6330409F21Rik|Fbp2|Fubp2|Ksrp	KH-type splicing regulatory protein	protein-coding
mm_80503.1	chr9	78615502	78615509	+	1	NA	promoter-TSS (NM_153098)	promoter-TSS (NM_153098)	-41	NM_153098	235505	Mm.32955	NM_153098	ENSMUSG00000046186	Cd109	9930012E15Rik|AI480638|GARP	CD109 antigen	protein-coding
mm_36051.1	chr4	57301476	57301510	-	1	NA	intron (NM_011207, intron 1 of 25)	intron (NM_011207, intron 1 of 25)	344	NM_011207	545622	Mm.246552	NM_011207	ENSMUSG00000038764	Ptpn3	9530011I20Rik|PTP-H1|PTPCL	protein tyrosine phosphatase, non-receptor type 3	protein-coding
mm_86286.1	chr9	121857953	121858012	-	1	NA	promoter-TSS (NM_019814)	promoter-TSS (NM_019814)	18	NM_019814	56295	Mm.347915	NM_019814	ENSMUSG00000038412	Higd1a	2210020B17Rik|7420700H20Rik|AI303276|AW049839|HIMP1|Hig1	HIG1 domain family, member 1A	protein-coding
mm_167530.1	chr9	21291034	21291055	-	1	NA	5' UTR (NM_009878, exon 1 of 2)	5' UTR (NM_009878, exon 1 of 2)	165	NM_009878	12581	Mm.29020	NM_009878	ENSMUSG00000096472	Cdkn2d	INK4d|p19|p19INK4d	cyclin-dependent kinase inhibitor 2D (p19, inhibits CDK4)	protein-coding
mm_43646.1	chr5	138262398	138262418	+	1	NA	intron (NM_153161, intron 5 of 10)	intron (NM_153161, intron 5 of 10)	-1637	NR_045821	69004	Mm.439868	NR_045821	ENSMUSG00000085227	6330418K02Rik	-	RIKEN cDNA 6330418K02 gene	ncRNA
mm_162475.1	chr1	133163935	133163945	+	1	NA	Intergenic	CpG	32774	NM_133819	108954	Mm.293628	NM_133819	ENSMUSG00000046062	Ppp1r15b	1810033K10Rik|AI606441|C530022L24Rik|CReP	protein phosphatase 1, regulatory (inhibitor) subunit 15b	protein-coding
mm_102408.1	chr11	59182795	59182801	-	1	NA	promoter-TSS (NM_175452)	promoter-TSS (NM_175452)	28	NM_175452	118454	Mm.40016	NM_080454	ENSMUSG00000043448	Gjc2	B230382L12Rik|Cx47|Gja12	gap junction protein, gamma 2	protein-coding
mm_94013.1	chr10	127643647	127643658	-	1	NA	intron (NM_009284, intron 1 of 21)	intron (NM_009284, intron 1 of 21)	666	NM_009284	20852	Mm.121721	NM_009284	ENSMUSG00000002147	Stat6	-	signal transducer and activator of transcription 6	protein-coding
mm_145792.1	chr18	65244310	65244322	+	1	NA	intron (NR_105742, intron 4 of 6)	intron (NR_105742, intron 4 of 6)	-4545	NR_029600	387231		NR_029600	ENSMUSG00000065402	Mir122	Mir122a|Mirn122a|mir-122|mmu-mir-122	microRNA 122	ncRNA
mm_29339.1	chr3	108213650	108213657	-	1	NA	3' UTR (NM_008596, exon 6 of 6)	3' UTR (NM_008596, exon 6 of 6)	-3126	NM_175183	72522	Mm.187326	NM_175183	ENSMUSG00000048997	Atxn7l2	2610528J18Rik	ataxin 7-like 2	protein-coding
mm_162280.1	chr1	17505271	17505272	+	1	NA	Intergenic	Intergenic	-96630	NM_053191	94227	Mm.442452	NM_053191	ENSMUSG00000067780	Pi15	P24TI|P25TI|PI-15|SugarCrisp	peptidase inhibitor 15	protein-coding
mm_54212.1	chr6	25689783	25689800	-	1	NA	5' UTR (NM_010338, exon 1 of 2)	5' UTR (NM_010338, exon 1 of 2)	189	NM_010338	14763	Mm.409670	NM_010338	ENSMUSG00000039904	Gpr37	AI848630|Pael-R	G protein-coupled receptor 37	protein-coding
mm_151182.1	chr19	53357244	53357252	+	1	NA	intron (NM_001008542, intron 3 of 5)	intron (NM_001008542, intron 3 of 5)	26802	NM_001008543	17859	Mm.2154	NM_010847	ENSMUSG00000025025	Mxi1	ENSMUSG00000067085|Gm10197|Mad2|bHLHc11	MAX interactor 1, dimerization protein	protein-coding
mm_1629.1	chr1	74427356	74427360	+	1	NA	exon (NM_009509, exon 15 of 20)	exon (NM_009509, exon 15 of 20)	17974	NM_009509	22349	Mm.471601	NM_009509	ENSMUSG00000026175	Vil1	Vil	villin 1	protein-coding
mm_79734.1	chr9	62344756	62344771	+	1	NA	intron (NM_009672, intron 1 of 6)	intron (NM_009672, intron 1 of 6)	3420	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	protein-coding
mm_39789.1	chr5	30466045	30466092	+	1	NA	promoter-TSS (NM_029285)	promoter-TSS (NM_029285)	-9	NM_029285	75434	Mm.332291	NM_029285	ENSMUSG00000029182	1700001C02Rik	1700047H18Rik	RIKEN cDNA 1700001C02 gene	protein-coding
mm_117905.1	chr13	99430304	99430326	-	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-17489	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_158969.1	chr1	106004222	106004222	+	1	NA	intron (NM_001122676, intron 3 of 13)	intron (NM_001122676, intron 3 of 13)	13816	NM_001122675	227449	Mm.210188	NM_001122675	ENSMUSG00000038866	Zcchc2	9930114B20Rik|AW212015	zinc finger, CCHC domain containing 2	protein-coding
mm_626.1	chr1	40225262	40225280	+	1	NA	5' UTR (NM_008362, exon 1 of 11)	5' UTR (NM_008362, exon 1 of 11)	191	NM_008362	16177	Mm.896	NM_008362	ENSMUSG00000026072	Il1r1	CD121a|CD121b|IL-1R1|IL-iR|Il1r-1	interleukin 1 receptor, type I	protein-coding
mm_79361.1	chr9	54328944	54328947	+	1	NA	intron (NM_177350, intron 4 of 9)	intron (NM_177350, intron 4 of 9)	-27375	NR_045805	73567	Mm.211290	NM_001033169	ENSMUSG00000074343	Gldnos	1700104A03Rik	gliomedin, opposite strand	ncRNA
mm_105092.1	chr11	100903460	100903470	-	1	NA	exon (NM_011486, exon 10 of 24)	exon (NM_011486, exon 10 of 24)	36075	NM_213660	20848	Mm.249934	NM_011486	ENSMUSG00000004040	Stat3	1110034C02Rik|AW109958|Aprf	signal transducer and activator of transcription 3	protein-coding
mm_96727.1	chr11	69684397	69684411	+	1	NA	intron (NM_001034097, intron 10 of 12)	intron (NM_001034097, intron 10 of 12)	1150	NM_001159505	69583	Mm.8983	NM_023517	ENSMUSG00000089669	Tnfsf13	2310026N09Rik|April|Tall2|Tnlg7b|Trdl1	tumor necrosis factor (ligand) superfamily, member 13	protein-coding
mm_14321.1	chr2	129365192	129365210	+	1	NA	exon (NM_008361, exon 7 of 7)	exon (NM_008361, exon 7 of 7)	-4701	NR_015474	329514	Mm.207315	NM_177848	ENSMUSG00000074805	Il1bos	9430083I22|Gm14047|OTTMUSG00000015529	interleukin 1 beta, opposite strand	ncRNA
mm_83934.1	chr9	56636003	56636007	-	1	NA	promoter-TSS (NM_001311076)	promoter-TSS (NM_001311076)	-357	NM_001311076	235402	Mm.246605	NM_181074	ENSMUSG00000049556	Lingo1	4930471K13Rik|AV148400|LERN1|LINGO-1|Lrrn6a|UNQ201	leucine rich repeat and Ig domain containing 1	protein-coding
mm_46937.1	chr5	114773489	114773517	-	1	NA	promoter-TSS (NM_019834)	promoter-TSS (NM_019834)	-11	NM_001347400	26431	Mm.195632	NM_019834	ENSMUSG00000041890	Git2	1500036H07Rik|5830420E16Rik|6430510B20Rik|9630056M03Rik|B230104M05Rik|CAT2|mKIAA0148	G protein-coupled receptor kinase-interactor 2	protein-coding
mm_52477.1	chr6	114306303	114306306	+	1	NA	intron (NM_178703, intron 7 of 15)	intron (NM_178703, intron 7 of 15)	23669	NM_178703	232333	Mm.5260	NM_178703	ENSMUSG00000030310	Slc6a1	A730043E01|GABATHG|GABATR|GAT-1|Gabt|Gabt1|Gat1|XT-1|Xtrp1	solute carrier family 6 (neurotransmitter transporter, GABA), member 1	protein-coding
mm_79769.1	chr9	62829096	62829121	+	1	NA	Intergenic	Intergenic	-9679	NM_001033175	76524	Mm.283636	NM_001033175	ENSMUSG00000032245	Cln6	1810065L06Rik|AW743417|D9Bwg1455e|nclf	ceroid-lipofuscinosis, neuronal 6	protein-coding
mm_71893.1	chr8	69832799	69832809	+	1	NA	promoter-TSS (NM_001024954)	promoter-TSS (NM_001024954)	100	NM_001024954	80720	Mm.210823	NM_030555	ENSMUSG00000031860	Pbx4	2410015M21Rik|AI429113|AW045266	pre B cell leukemia homeobox 4	protein-coding
mm_166395.1	chr5	135013160	135013170	-	1	NA	promoter-TSS (NR_026688)	promoter-TSS (NR_026688)	-8	NR_026688	69812	Mm.18422	NR_026688	ENSMUSG00000085042	Abhd11os	2010001M06Rik|AI462243|Wbscr26|Wnscr26	abhydrolase domain containing 11, opposite strand	ncRNA
mm_109244.1	chr12	109452800	109452820	+	1	NA	promoter-TSS (NM_010052)	promoter-TSS (NM_010052)	-13	NR_033813	13386	Mm.157069	NM_010052	ENSMUSG00000040856	Dlk1	AW742678|DLK-1|DlkI|FA1|Ly107|Peg9|SCP1|ZOG|pG2|pref-1	delta-like 1 homolog (Drosophila)	protein-coding
mm_8752.1	chr1	160307440	160307452	-	1	NA	intron (NM_001038621, intron 2 of 8)	intron (NM_001038621, intron 2 of 8)	-11474	NR_035448	100316784		NR_035448	ENSMUSG00000089204	Mir1927	mmu-mir-1927	microRNA 1927	ncRNA
mm_97752.1	chr11	80495045	80495051	+	1	NA	intron (NM_177390, intron 21 of 21)	intron (NM_177390, intron 21 of 21)	14058	NR_126552	77417	Mm.437510	NR_126552	ENSMUSG00000085078	C030013C21Rik	-	RIKEN cDNA C030013C21 gene	ncRNA
mm_50305.1	chr6	47796825	47796870	+	1	NA	exon (NM_009787, exon 10 of 10)	exon (NM_009787, exon 10 of 10)	6805	NR_030485	735289		NR_030485	ENSMUSG00000076060	Mir704	Mirn704|mir-704|mmu-mir-704	microRNA 704	ncRNA
mm_85423.1	chr9	103489322	103489344	-	1	NA	exon (NM_178638, exon 5 of 6)	exon (NM_178638, exon 5 of 6)	-9005	NM_001002896	107993	Mm.335403	NM_001002896	ENSMUSG00000032556	Bfsp2	AI448593|CP49	beaded filament structural protein 2, phakinin	protein-coding
mm_35141.1	chr4	11386758	11386775	-	1	NA	promoter-TSS (NM_001290383)	promoter-TSS (NM_001290383)	12	NM_001347052	207920	Mm.387719	NM_194055	ENSMUSG00000040728	Esrp1	2210008M09Rik|A630065D16|BC031468|Rbm35a	epithelial splicing regulatory protein 1	protein-coding
mm_156683.1	chrX	159371980	159372018	+	1	NA	promoter-TSS (NM_025437)	promoter-TSS (NM_025437)	-196	NM_025437	66235	Mm.294623	NM_025437	ENSMUSG00000067194	Eif1ax	1500010B24Rik|AI426898|Eif1ay	eukaryotic translation initiation factor 1A, X-linked	protein-coding
mm_20281.1	chr2	126890977	126890987	-	1	NA	3' UTR (NM_023220, exon 15 of 15)	3' UTR (NM_023220, exon 15 of 15)	11403	NR_106202	102466258		NR_106202	ENSMUSG00000098896	Mir3473g	Gm27751|mmu-mir-3473g	microRNA 3473g	ncRNA
mm_13734.1	chr2	118111880	118111899	+	1	NA	promoter-TSS (NM_011580)	promoter-TSS (NM_011580)	13	NM_001313914	21825	Mm.4159	NM_011580	ENSMUSG00000040152	Thbs1	TSP-1|TSP1|Thbs-1|tbsp1	thrombospondin 1	protein-coding
mm_63821.1	chr7	134669693	134669706	+	1	NA	promoter-TSS (NM_001033420)	promoter-TSS (NM_001033420)	-988	NM_001033420	330662	Mm.436572	NM_001033420	ENSMUSG00000058325	Dock1	9130006G06Rik|AI854900|D630004B07Rik	dedicator of cytokinesis 1	protein-coding
mm_160929.1	chr11	89418912	89418912	-	1	NA	promoter-TSS (NM_172534)	promoter-TSS (NM_172534)	36	NM_172534	382543	Mm.60997	NM_172534	ENSMUSG00000047773	Ankfn1	4932411E22Rik|Gm1175|nmf9	ankyrin-repeat and fibronectin type III domain containing 1	protein-coding
mm_79091.1	chr9	46242723	46242733	+	1	NA	exon (NM_007468, exon 3 of 3)	exon (NM_007468, exon 3 of 3)	1884	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_116672.1	chr13	49212362	49212373	-	1	NA	intron (NM_026738, intron 1 of 5)	B3|SINE|B2	3659	NM_026738	68480	Mm.3336	NM_026738	ENSMUSG00000037960	Card19	1110007C09Rik|AI851695|Bincard	caspase recruitment domain family, member 19	protein-coding
mm_105151.1	chr11	101462735	101462750	-	1	NA	intron (NM_012037, intron 2 of 5)	intron (NM_012037, intron 2 of 5)	3457	NM_012037	26949	Mm.29210	NM_012037	ENSMUSG00000034993	Vat1	VAT-1	vesicle amine transport 1	protein-coding
mm_99054.1	chr11	99051630	99051693	+	1	NA	3' UTR (NM_010517, exon 4 of 4)	3' UTR (NM_010517, exon 4 of 4)	10401	NM_010517	16010	Mm.233799	NM_010517	ENSMUSG00000017493	Igfbp4	AI875747|Deb2|IGFBP-4	insulin-like growth factor binding protein 4	protein-coding
mm_96621.1	chr11	69126187	69126210	+	1	NA	promoter-TSS (NM_011786)	promoter-TSS (NM_011786)	-179	NM_011786	23801	Mm.41989	NM_011786	ENSMUSG00000020892	Aloxe3	e-LOX-3|eLOX-3	arachidonate lipoxygenase 3	protein-coding
mm_111807.1	chr12	105032262	105032307	-	1	NA	promoter-TSS (NR_003145)	promoter-TSS (NR_003145)	-5	NR_003145	69434	Mm.380736	NR_003145		Snhg10	1700026B20Rik|AI642517	small nucleolar RNA host gene 10	ncRNA
mm_19148.1	chr2	80524722	80524738	-	1	NA	intron (NM_016965, intron 18 of 30)	intron (NM_016965, intron 18 of 30)	56452	NM_001290745	50884	Mm.25203	NM_016965	ENSMUSG00000027002	Nckap1	C79304|H19|Hem-2|Hem2|Nap1|mKIAA0587|mh19|p125Nap1	NCK-associated protein 1	protein-coding
mm_1696.1	chr1	75142776	75142797	+	1	NA	promoter-TSS (NM_026977)	promoter-TSS (NM_026977)	0	NM_170755	227298	Mm.273062	NM_170755	ENSMUSG00000049339	Fam134a	-	family with sequence similarity 134, member A	protein-coding
mm_91044.1	chr10	18546050	18546084	-	1	NA	promoter-TSS (NM_019487)	promoter-TSS (NM_019487)	9	NM_019487	56016	Mm.35551	NM_019487	ENSMUSG00000019853	Hebp2	SOUL	heme binding protein 2	protein-coding
mm_58701.1	chr7	12927411	12927439	+	1	NA	promoter-TSS (NM_029809)	promoter-TSS (NM_029809)	9	NM_029809	381845	Mm.439896	NM_029809	ENSMUSG00000033967	Rnf225	2310014L17Rik|AV237412|C77118	ring finger protein 225	protein-coding
mm_151112.1	chr19	47864422	47864430	+	1	NA	exon (NM_010362, exon 6 of 6)	exon (NM_010362, exon 6 of 6)	-1119	NM_030051	68214	Mm.63791	NM_026619	ENSMUSG00000025069	Gsto2	1700020F09Rik|4930425C18Rik|GSTO 2-2	glutathione S-transferase omega 2	protein-coding
mm_146180.1	chr18	75394550	75394553	+	1	NA	3' UTR (NM_001042660, exon 4 of 4)	3' UTR (NM_001042660, exon 4 of 4)	27186	NM_001042660	17131	Mm.34407	NM_008543	ENSMUSG00000025880	Smad7	Madh7	SMAD family member 7	protein-coding
mm_170921.1	chr2	37261909	37261909	-	1	NA	Intergenic	RLTR9D|LTR|ERVK	-5042	NM_001081010	545417	Mm.379955	NM_001081010		Olfr367-ps	EG545417|MOR128-1|ORL1283|OTTMUSG00000012147|Olfr367	olfactory receptor 367, pseudogene	protein-coding
mm_139284.1	chr17	48299922	48299941	+	1	NA	promoter-TSS (NM_001033405)	promoter-TSS (NM_001033405)	-107	NM_001033405	328833	Mm.329104	NM_001033405	ENSMUSG00000071068	Treml2	AW049306|Gm750|Tlt2	triggering receptor expressed on myeloid cells-like 2	protein-coding
mm_68254.1	chr7	105581273	105581283	-	1	NA	5' UTR (NM_001253886, exon 1 of 14)	5' UTR (NM_001253886, exon 1 of 14)	213	NM_001253885	11785	Mm.38469	NM_009685	ENSMUSG00000037032	Apbb1	Fe65|Rir	amyloid beta (A4) precursor protein-binding, family B, member 1	protein-coding
mm_66220.1	chr7	34654343	34654393	-	1	NA	Intergenic	CpG	-1527	NM_146188	233107	Mm.486198	NM_146188	ENSMUSG00000030499	Kctd15	BC031749	potassium channel tetramerisation domain containing 15	protein-coding
mm_172013.1	chr6	110010239	110010244	-	1	NA	Intergenic	L1Md_T|LINE|L1	-635271	NM_001346640	108073	Mm.240881	NM_177328	ENSMUSG00000056755	Grm7	6330570A01Rik|BB176677|C030018L03|E130018M02Rik|Gpr1g|Gprc1g|SMN2|Tg(SMN2)89Ahmb|mGluR7	glutamate receptor, metabotropic 7	protein-coding
mm_41181.1	chr5	88317078	88317086	+	1	NA	promoter-TSS (NM_008644)	promoter-TSS (NM_008644)	-230	NM_008644	17830	Mm.200411	NM_008644	ENSMUSG00000064156	Prol1	Muc10	proline rich, lacrimal 1	protein-coding
mm_109602.1	chr12	112679564	112679581	+	1	NA	exon (NM_001100460, exon 2 of 2)	exon (NM_001100460, exon 2 of 2)	732	NM_001100460	382639	Mm.11350	NM_001100460	ENSMUSG00000037638	Zbtb42	EG382639|Gm5188|simiRP58	zinc finger and BTB domain containing 42	protein-coding
mm_143851.1	chr17	84156399	84156410	-	1	NA	Intergenic	Intergenic	31543	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_60780.1	chr7	45565130	45565141	+	1	NA	intron (NM_025330, intron 6 of 8)	RLTR9A|LTR|ERVK	-5018	NM_009737	12036	Mm.24210	NM_009737	ENSMUSG00000030826	Bcat2	Bcat-2|Eca40	branched chain aminotransferase 2, mitochondrial	protein-coding
mm_28878.1	chr3	97767690	97767784	-	1	NA	non-coding (NR_110360, exon 1 of 17)	non-coding (NR_110360, exon 1 of 17)	277	NR_110360	83679	Mm.129840	NM_031401	ENSMUSG00000038170	Pde4dip	4732458A06Rik|9430063L05Rik|C87016|D130016K21Rik|D3Bwg1078e|Usmg4|mKIAA0454	phosphodiesterase 4D interacting protein (myomegalin)	protein-coding
mm_100151.1	chr11	116092197	116092200	+	1	NA	Intergenic	RMER1B|Other|Other	-5203	NM_001347642	22378	Mm.284792	NM_016852	ENSMUSG00000034341	Wbp2	-	WW domain binding protein 2	protein-coding
mm_114820.1	chr13	91741485	91741489	+	1	NA	promoter-TSS (NM_028790)	promoter-TSS (NM_028790)	-34	NM_028790	74156	Mm.275963	NM_028790	ENSMUSG00000021620	Acot12	1300004O04Rik|4930449F15Rik|AV027244|Cach|mCACH-1	acyl-CoA thioesterase 12	protein-coding
mm_73654.1	chr8	110956336	110956360	+	1	NA	intron (NM_009179, intron 1 of 6)	intron (NM_009179, intron 1 of 6)	36483	NM_009179	20444	Mm.200388	NM_009179	ENSMUSG00000031749	St3gal2	AI429591|AW822065|ST3GalII|Siat5	ST3 beta-galactoside alpha-2,3-sialyltransferase 2	protein-coding
mm_43352.1	chr5	135168923	135168955	+	1	NA	intron (NM_009745, intron 1 of 5)	CpG	567	NM_009745	12054	Mm.405834	NM_009745	ENSMUSG00000029681	Bcl7b	-	B cell CLL/lymphoma 7B	protein-coding
mm_145660.1	chr18	61130756	61130766	+	1	NA	TTS (NM_178277)	TTS (NM_178277)	13293	NR_105949	102466212		NR_105949	ENSMUSG00000098389	Mir6983	Gm27496|mmu-mir-6983	microRNA 6983	ncRNA
mm_129625.1	chr15	80098928	80098934	-	1	NA	intron (NM_207708, intron 1 of 3)	intron (NM_207708, intron 1 of 3)	7597	NM_207708	20972	Mm.230301	NM_009303	ENSMUSG00000022415	Syngr1	R75468|Syngr1b|p29	synaptogyrin 1	protein-coding
mm_135470.1	chr16	45844998	45845015	-	1	NA	promoter-TSS (NM_153412)	promoter-TSS (NM_153412)	-628	NM_001252442	208177	Mm.211477	NM_153412	ENSMUSG00000033149	Phldb2	AV253284|C820004H04Rik|LL5b|LL5beta	pleckstrin homology like domain, family B, member 2	protein-coding
mm_153002.1	chr19	30115264	30115272	-	1	NA	exon (NM_138595, exon 19 of 25)	exon (NM_138595, exon 19 of 25)	60173	NM_138595	104174	Mm.274852	NM_138595	ENSMUSG00000024827	Gldc	D030049L12Rik|D19Wsu57e	glycine decarboxylase	protein-coding
mm_75839.1	chr8	70599415	70599442	-	1	NA	exon (NM_133772, exon 9 of 17)	exon (NM_133772, exon 9 of 17)	4947	NM_023627	71780	Mm.29357	NM_023627	ENSMUSG00000019139	Isyna1	1300017C10Rik|AU018670	myo-inositol 1-phosphate synthase A1	protein-coding
mm_108643.1	chr12	85904236	85904249	+	1	NA	intron (NM_001347395, intron 17 of 32)	intron (NM_001347395, intron 17 of 32)	79292	NM_001081423	320244	Mm.132172	NM_177114	ENSMUSG00000012609	Ttll5	1700048H13Rik|2310009M18Rik|4930556H18Rik|AI428864|D630041K24Rik|R75373|Stamp|mKIAA0998	tubulin tyrosine ligase-like family, member 5	protein-coding
mm_110099.1	chr12	25272833	25272852	-	1	NA	Intergenic	Intergenic	143668	NR_045844	432641	Mm.112955	NR_045844		Gm17746	-	predicted gene, 17746	ncRNA
mm_25667.1	chr3	121851177	121851189	+	1	NA	Intergenic	Intergenic	-35968	NM_008991	19299	Mm.399042	NM_008991	ENSMUSG00000028127	Abcd3	AI313901|AU018866|AW146054|PMP68|PMP70|Pxmp1	ATP-binding cassette, sub-family D (ALD), member 3	protein-coding
mm_161831.1	chr17	81649399	81649399	-	1	NA	exon (NM_001112798, exon 2 of 9)	exon (NM_001112798, exon 2 of 9)	88988	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_76953.1	chr8	106007099	106007110	-	1	NA	Intergenic	RLTR19|LTR|ERVK	-4374	NM_025518	66369	Mm.287500	NM_025518	ENSMUSG00000031901	Dus2	2310016K04Rik|Dus2l	dihydrouridine synthase 2	protein-coding
mm_48852.1	chr5	149636165	149636190	-	1	NA	5' UTR (NM_013559, exon 1 of 18)	5' UTR (NM_013559, exon 1 of 18)	138	NM_013559	15505	Mm.270681	NM_013559	ENSMUSG00000029657	Hsph1	105kDa|AI790491|Hsp105|Hsp110|hsp-E7I|hsp110/105	heat shock 105kDa/110kDa protein 1	protein-coding
mm_61479.1	chr7	75655942	75655967	+	1	NA	intron (NM_029332, intron 8 of 36)	L1M4|LINE|L1	-192384	NM_001122780	207952	Mm.206223	NM_029652	ENSMUSG00000055652	Klhl25	2810402K13Rik|BC027373|Enc-1	kelch-like 25	protein-coding
mm_95239.1	chr11	44617488	44617513	+	1	NA	promoter-TSS (NM_001290711)	promoter-TSS (NM_001290711)	-600	NM_001290711	13591	Mm.439662	NM_007897	ENSMUSG00000057098	Ebf1	Ebf|O/E-1|OE-1|Olf-1|Olf1	early B cell factor 1	protein-coding
mm_162366.1	chr1	65100649	65100652	+	1	NA	exon (NM_007774, exon 3 of 3)	exon (NM_007774, exon 3 of 3)	2713	NM_007774	12964	Mm.26904	NM_007774	ENSMUSG00000044429	Cryga	Cryg-4|DGcry-4	crystallin, gamma A	protein-coding
mm_173166.1	chrX	41959487	41959490	+	1	NA	Intergenic	B2_Mm2|SINE|B2	-47587	NM_001033422	331401	Mm.259498	NM_001033422	ENSMUSG00000037475	Thoc2	6330441O12Rik|D130005M13Rik|Gm1139|Gm1793|Tho2	THO complex 2	protein-coding
mm_66693.1	chr7	45916734	45916758	-	1	NA	3' UTR (NM_144801, exon 8 of 8)	3' UTR (NM_144801, exon 8 of 8)	4103	NM_001146346	13732	Mm.20829	NM_010129	ENSMUSG00000040212	Emp3	H-4|H4|HNMP-1|MI-35|Ymp	epithelial membrane protein 3	protein-coding
mm_166276.1	chr5	90696315	90696337	+	1	NA	Intergenic	Intergenic	-55799	NM_001310656	73246	Mm.30172	NM_028478	ENSMUSG00000029370	Rassf6	1600016B17Rik	Ras association (RalGDS/AF-6) domain family member 6	protein-coding
mm_171949.1	chr5	76905426	76905429	-	1	NA	promoter-TSS (NM_173765)	promoter-TSS (NM_173765)	87	NM_173765	231326	Mm.39271	NM_173765	ENSMUSG00000055923	Aasdh	A230062G08Rik|A830035E16|Acsf4|U26	aminoadipate-semialdehyde dehydrogenase	protein-coding
mm_165828.1	chr3	151439233	151439239	+	1	NA	intron (NM_133222, intron 1 of 15)	intron (NM_133222, intron 1 of 15)	1354	NM_133222	170757	Mm.317261	NM_133222	ENSMUSG00000039167	Adgrl4	1110033N21Rik|ETL1|Eltd1|Etl	adhesion G protein-coupled receptor L4	protein-coding
mm_159305.1	chr2	180026586	180026586	+	1	NA	intron (NM_177727, intron 1 of 8)	intron (NM_177727, intron 1 of 8)	1599	NM_177727	241846	Mm.21577	NM_177727	ENSMUSG00000039108	Lsm14b	9430078B04|BC040823	LSM family member 14B	protein-coding
mm_63418.1	chr7	127471044	127471054	+	1	NA	promoter-TSS (NM_145589)	promoter-TSS (NM_145589)	-565	NM_145589	233895	Mm.44183	NM_145589	ENSMUSG00000030822	Prr14	BC006909	proline rich 14	protein-coding
mm_24260.1	chr3	89187391	89187409	+	1	NA	exon (NM_001014995, exon 9 of 12)	exon (NM_001014995, exon 9 of 12)	4175	NM_001014995	68521	Mm.274708	NM_001014995	ENSMUSG00000032657	Fam189b	1110013L07Rik	family with sequence similarity 189, member B	protein-coding
mm_41388.1	chr5	90768681	90768687	+	1	NA	exon (NM_023785, exon 1 of 3)	exon (NM_023785, exon 1 of 3)	166	NM_023785	57349	Mm.293614	NM_023785	ENSMUSG00000029372	Ppbp	2400003M24Rik|AI854500|CTAP3|CTAPIII|Cxcl7|LA-PF4|LDGF|MDGF|NAP-2|NAP-2-L1|Scyb7|TGB|TGB1|THBGB1|b-TG1|beta-TG	pro-platelet basic protein	protein-coding
mm_158131.1	chrX	103185969	103185979	-	1	NA	exon (NM_008671, exon 1 of 1)	exon (NM_008671, exon 1 of 1)	690	NM_008671	17954	Mm.388694	NM_008671	ENSMUSG00000082229	Nap1l2	Bpx	nucleosome assembly protein 1-like 2	protein-coding
mm_64403.1	chr7	142509924	142509925	+	1	NA	intron (NM_001347548, intron 7 of 14)	intron (NM_001347548, intron 7 of 14)	-3153	NR_033261	677289	Mm.350054	NR_033261	ENSMUSG00000043795	Prr33	ENSMUSG00000043795|Gm14492|OTTMUSG00000016823	proline rich 33	ncRNA
mm_129753.1	chr15	82354226	82354261	-	1	NA	promoter-TSS (NM_025987)	promoter-TSS (NM_025987)	48	NM_025987	67130	Mm.27570	NM_025987	ENSMUSG00000022450	Ndufa6	14kDa|2700038D15Rik|B230217P19Rik	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 6 (B14)	protein-coding
mm_19247.1	chr2	84743768	84743783	-	1	NA	Intergenic	Intergenic	-2597	NR_029544	387149		NR_029544	ENSMUSG00000065484	Mir130a	Mirn130|Mirn130a|mir-130a	microRNA 130a	ncRNA
mm_161139.1	chr13	21363172	21363172	+	1	NA	intron (NM_016684, intron 1 of 3)	intron (NM_016684, intron 1 of 3)	352	NM_016684	22758	Mm.24124	NM_016684	ENSMUSG00000036721	Zscan12	2510038J07Rik|FPM315|Zfp96|mKIAA0426|zfp-96	zinc finger and SCAN domain containing 12	protein-coding
mm_171479.1	chr4	145868773	145868773	+	1	NA	Intergenic	Intergenic	31554	NR_033612	236069	Mm.276881	NR_033612	ENSMUSG00000096233	Gm13238	OTTMUSG00000011065	carnitine deficiency-associated gene expressed in ventricle 3 pseudogene	pseudo
mm_16147.1	chr2	172287978	172288014	+	1	NA	Intergenic	Intergenic	39504	NM_008561	17201	Mm.57183	NM_008561	ENSMUSG00000038537	Mc3r	MC3-R	melanocortin 3 receptor	protein-coding
mm_147427.1	chr18	46280821	46280841	-	1	NA	promoter-TSS (NM_172627)	promoter-TSS (NM_172627)	19	NM_172627	225467	Mm.262096	NM_172627	ENSMUSG00000024477	Pggt1b	2010207C17Rik|2610100E13|AI451237|AI551093|BGG1|GGT1	protein geranylgeranyltransferase type I, beta subunit	protein-coding
mm_9287.1	chr1	171634794	171634823	-	1	NA	3' UTR (NM_144539, exon 8 of 8)	3' UTR (NM_144539, exon 8 of 8)	7092	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_153623.1	chr19	44005229	44005229	-	1	NA	3' UTR (NM_001001446, exon 9 of 9)	3' UTR (NM_001001446, exon 9 of 9)	-18709	NM_030703	93721	Mm.206774	NM_030703	ENSMUSG00000025196	Cpn1	0610011F20Rik|CPN	carboxypeptidase N, polypeptide 1	protein-coding
mm_168128.1	chr10	23475984	23475987	-	1	NA	Intergenic	Intergenic	-126042	NM_010167	14051	Mm.332128	NM_010167	ENSMUSG00000010461	Eya4	B130023L16Rik	EYA transcriptional coactivator and phosphatase 4	protein-coding
mm_24954.1	chr3	96635841	96635868	+	1	NA	promoter-TSS (NM_001162388)	promoter-TSS (NM_001162388)	7	NM_001162388	18632	Mm.20901	NM_011069	ENSMUSG00000028102	Pex11b	PEX11beta|Pex11pbeta	peroxisomal biogenesis factor 11 beta	protein-coding
mm_101045.1	chr11	8624621	8624657	-	1	NA	intron (NM_001083587, intron 1 of 30)	CpG	39896	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_86916.1	chr10	23797053	23797070	+	1	NA	promoter-TSS (NM_183116)	promoter-TSS (NM_183116)	75	NM_183116	76306	Mm.294271	NM_183116	ENSMUSG00000037455	Slc18b1	1110021L09Rik	solute carrier family 18, subfamily B, member 1	protein-coding
mm_140862.1	chr17	23745347	23745363	-	1	NA	intron (NM_028416, intron 1 of 9)	intron (NM_028416, intron 1 of 9)	474	NM_028416	73016	Mm.221319	NM_028416	ENSMUSG00000040680	Kremen2	2900054E04Rik|Krm2	kringle containing transmembrane protein 2	protein-coding
mm_149961.1	chr19	28990376	28990392	+	1	NA	promoter-TSS (NM_025950)	promoter-TSS (NM_025950)	32	NM_025950	67072	Mm.78875	NM_025950	ENSMUSG00000024780	Cdc37l1	2700033A15Rik|BB159850|Cdc37l|Harc	cell division cycle 37-like 1	protein-coding
mm_84553.1	chr9	67633982	67634078	-	1	NA	Intergenic	CpG	-74327	NM_001081242	70549	Mm.33645	NM_027458	ENSMUSG00000052698	Tln2	5730421P04Rik|AI507121|AI787438|AL118320|mKIAA0320	talin 2	protein-coding
mm_41913.1	chr5	105591442	105591508	+	1	NA	intron (NM_133897, intron 3 of 3)	intron (NM_133897, intron 3 of 3)	72004	NM_133897	100604	Mm.319847	NM_133897	ENSMUSG00000054720	Lrrc8c	AD158|AI326115|E430036I04Rik|fad158	leucine rich repeat containing 8 family, member C	protein-coding
mm_32480.1	chr4	107879830	107879840	+	1	NA	promoter-TSS (NM_001282737)	promoter-TSS (NM_001282737)	80	NM_001282737	17149	Mm.808	NM_001282737	ENSMUSG00000028609	Magoh	Mago-m|Mos2	mago homolog, exon junction complex core component	protein-coding
mm_163910.1	chr14	32029221	32029237	+	1	NA	5' UTR (NM_030166, exon 1 of 10)	5' UTR (NM_030166, exon 1 of 10)	126	NM_030166	78754	Mm.40681	NM_030166	ENSMUSG00000021903	Galnt15	4631401E18Rik|Galntl2|mpp-GalNAc-T15	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 15	protein-coding
mm_114909.1	chr13	94876649	94876657	+	1	NA	intron (NM_011021, intron 1 of 2)	intron (NM_011021, intron 1 of 2)	1026	NM_011021	18420	Mm.42051	NM_011021	ENSMUSG00000021685	Otp	-	orthopedia homeobox	protein-coding
mm_82861.1	chr9	31913259	31913303	-	1	NA	promoter-TSS (NM_013800)	promoter-TSS (NM_013800)	4	NM_013800	12023	Mm.261044	NM_013800	ENSMUSG00000032033	Barx2	2310006E12Rik|Barx2b	BarH-like homeobox 2	protein-coding
mm_75788.1	chr8	70095240	70095258	-	1	NA	3' UTR (NM_007789, exon 15 of 15)	3' UTR (NM_007789, exon 15 of 15)	7337	NR_106033	102465646		NR_106033	ENSMUSG00000099042	Mir7066	Gm27290|mmu-mir-7066	microRNA 7066	ncRNA
mm_55721.1	chr6	73469511	73469521	-	1	NA	exon (NM_025737, exon 1 of 1)	exon (NM_025737, exon 1 of 1)	151	NM_025737	66740	Mm.440760	NM_025737	ENSMUSG00000056197	4931417E11Rik	-	RIKEN cDNA 4931417E11 gene	protein-coding
mm_164361.1	chr16	22895332	22895341	+	1	NA	promoter-TSS (NR_110508)	promoter-TSS (NR_110508)	-950	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_155705.1	chrX	95711642	95711685	+	1	NA	promoter-TSS (NM_001034907)	promoter-TSS (NM_001034907)	-15	NM_001034907	547176	Mm.302708	NM_001034907	ENSMUSG00000035045	Zc3h12b	A130028J20Rik|CXorf32|Gm373	zinc finger CCCH-type containing 12B	protein-coding
mm_135396.1	chr16	44558641	44558686	-	1	NA	promoter-TSS (NR_037242)	promoter-TSS (NR_037242)	207	NM_172506	117606	Mm.41561	NM_172506	ENSMUSG00000022687	Boc	4732455C11|mFLJ00376	biregional cell adhesion molecule-related/down-regulated by oncogenes (Cdon) binding protein	protein-coding
mm_98180.1	chr11	87761063	87761067	+	1	NA	5' UTR (NM_172449, exon 1 of 32)	5' UTR (NM_172449, exon 1 of 32)	524	NM_172449	207777	Mm.342019	NM_172449	ENSMUSG00000034156	Bzrap1	D230016K05|PRAX-1|Tspoap1|mKIAA0612	benzodiazepine receptor associated protein 1	protein-coding
mm_149715.1	chr19	21653483	21653507	+	1	NA	promoter-TSS (NM_025423)	promoter-TSS (NM_025423)	186	NM_146096	226016	Mm.28796	NM_146096	ENSMUSG00000047368	Abhd17b	5730446C15Rik|Cgi67|Fam108b|Fam108b1	abhydrolase domain containing 17B	protein-coding
mm_138315.1	chr17	34661653	34661661	+	1	NA	Intergenic	Intergenic	-8878	NM_031176	81877	Mm.290527	NM_031176	ENSMUSG00000033327	Tnxb	Tn-mhc|Tnx	tenascin XB	protein-coding
mm_134431.1	chr16	17928019	17928022	-	1	NA	exon (NM_153150, exon 1 of 9)	exon (NM_153150, exon 1 of 9)	199	NM_153150	13358	Mm.229291	NM_153150	ENSMUSG00000003528	Slc25a1	1300019P08Rik|2610100G11Rik|AI194714|Ctp|Dgsj|Slc20a3	solute carrier family 25 (mitochondrial carrier, citrate transporter), member 1	protein-coding
mm_133313.1	chr16	77642907	77642915	+	1	NA	Intergenic	(T)n|Simple_repeat|Simple_repeat	-3362	NR_029540	723952		NR_029540	ENSMUSG00000065472	Mir125b-2	Mirn125b-2|mir-125b-2	microRNA 125b-2	ncRNA
mm_135503.1	chr16	46496956	46496986	-	1	NA	promoter-TSS (NM_021495)	promoter-TSS (NM_021495)	-4	NM_021497	58998	Mm.40477	NM_021495	ENSMUSG00000022656	Nectin3	2610301B19Rik|3000002N23Rik|4921513D19Rik|AA407785|AU016832|AW538082|CD113|Pvrl3	nectin cell adhesion molecule 3	protein-coding
mm_97062.1	chr11	72742314	72742318	+	1	NA	intron (NM_009671, intron 10 of 24)	Charlie1a|DNA|hAT-Charlie	52314	NM_009671	11736	Mm.10313	NM_009671	ENSMUSG00000020790	Ankfy1	Ankhzn|ZFYVE14|mKIAA1255	ankyrin repeat and FYVE domain containing 1	protein-coding
mm_16768.1	chr2	9878581	9878607	-	1	NA	promoter-TSS (NM_008091)	promoter-TSS (NM_008091)	6	NM_008091	14462	Mm.313866	NM_008091	ENSMUSG00000015619	Gata3	Gata-3|jal	GATA binding protein 3	protein-coding
mm_85963.1	chr9	112139428	112139438	-	1	NA	intron (NM_001177617, intron 10 of 14)	L1MB7|LINE|L1	-20722	NR_029823	723815		NR_029823	ENSMUSG00000065441	Mir128-2	Mirn128-2|Mirn128b|mir-128-2|mir-128b	microRNA 128-2	ncRNA
mm_94274.1	chr11	3895224	3895310	+	1	NA	promoter-TSS (NM_026150)	promoter-TSS (NM_026150)	27	NM_173745	75219	Mm.32588	NM_173745	ENSMUSG00000047205	Dusp18	4930527G07Rik|AI430870|BB028064|DSP18|DUSP20|LMWDSP20	dual specificity phosphatase 18	protein-coding
mm_146524.1	chr18	4353283	4353330	-	1	NA	promoter-TSS (NM_007746)	promoter-TSS (NM_007746)	-241	NR_040328	73915	Mm.482777	NR_040328		4833419F23Rik	-	RIKEN cDNA 4833419F23 gene	ncRNA
mm_151493.1	chr19	58680823	58680837	+	1	NA	exon (NM_026925, exon 12 of 13)	exon (NM_026925, exon 12 of 13)	10465	NM_026925	69060	Mm.20407	NM_026925	ENSMUSG00000046008	Pnlip	1810007A24Rik|PL|PTL	pancreatic lipase	protein-coding
mm_86498.1	chr10	6788700	6788716	+	1	NA	5' UTR (NM_001304950, exon 1 of 5)	5' UTR (NM_001304950, exon 1 of 5)	132	NM_001039652	18390	Mm.438000	NM_011013	ENSMUSG00000000766	Oprm1	M-OR-1|MOP-R|MOR-1|MOR-1O|Oprm|mor|muOR	opioid receptor, mu 1	protein-coding
mm_121181.1	chr14	103049266	103049276	+	1	NA	intron (NM_008392, intron 1 of 4)	intron (NM_008392, intron 1 of 4)	2259	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_9921.1	chr1	189402763	189402770	-	1	NA	promoter-TSS (NM_001281848)	promoter-TSS (NM_001281848)	-493	NM_001281848	16526	Mm.33304	NM_010607	ENSMUSG00000037624	Kcnk2	A430027H14Rik|AI848635|TREK-1	potassium channel, subfamily K, member 2	protein-coding
mm_45791.1	chr5	87535114	87535143	-	1	NA	intron (NM_019878, intron 1 of 7)	intron (NM_019878, intron 1 of 7)	3067	NM_019878	56362	Mm.23502	NM_019878	ENSMUSG00000029269	Sult1b1	ST1B1|St2b2	sulfotransferase family 1B, member 1	protein-coding
mm_14779.1	chr2	145830887	145830900	+	1	NA	intron (NM_028724, intron 4 of 12)	(GGGAGA)n|Simple_repeat|Simple_repeat	44777	NM_028724	74030	Mm.228799	NM_028724	ENSMUSG00000001768	Rin2	2010003K16Rik|4632403N06Rik|AW821980|RASSF4	Ras and Rab interactor 2	protein-coding
mm_159220.1	chr2	127587151	127587151	-	1	NA	promoter-TSS (NM_029963)	promoter-TSS (NM_029963)	-275	NM_029963	77721	Mm.274601	NM_029963	ENSMUSG00000027374	Mrps5	1620401I16Rik|AI850294	mitochondrial ribosomal protein S5	protein-coding
mm_25550.1	chr3	115974621	115974635	+	1	NA	intron (NM_023214, intron 8 of 10)	intron (NM_023214, intron 8 of 10)	-5274	NR_130332	100316705		NR_130332	ENSMUSG00000089261	Mir669n	mmu-mir-669n	microRNA 669n	ncRNA
mm_14853.1	chr2	148672635	148672722	+	1	NA	promoter-TSS (NM_001110159)	promoter-TSS (NM_001110159)	37	NM_001110159	56488	Mm.34663	NM_019761	ENSMUSG00000036992	Nxt1	1110001N02Rik	NTF2-related export protein 1	protein-coding
mm_28510.1	chr3	92577121	92577128	-	1	NA	Intergenic	Intergenic	-3389	NM_008412	16447	Mm.207365	NM_008412	ENSMUSG00000049128	Ivl	1110019C06Rik	involucrin	protein-coding
mm_7358.1	chr1	106705520	106705523	-	1	NA	intron (NM_009741, intron 1 of 1)	AT_rich|Low_complexity|Low_complexity	8769	NM_009741	12043	Mm.257460	NM_009741	ENSMUSG00000057329	Bcl2	AW986256|Bcl-2|C430015F12Rik|D630044D05Rik|D830018M01Rik	B cell leukemia/lymphoma 2	protein-coding
mm_146683.1	chr18	12860198	12860235	-	1	NA	intron (NM_207530, intron 15 of 27)	intron (NM_207530, intron 15 of 27)	2497	NM_001252493	64291	Mm.259470	NM_020573	ENSMUSG00000044252	Osbpl1a	G430090F17Rik|Gm753|ORP-1|Osbpl1b	oxysterol binding protein-like 1A	protein-coding
mm_125399.1	chr15	41447439	41447479	+	1	NA	promoter-TSS (NM_001130166)	promoter-TSS (NM_001130166)	-23	NM_001130166	170719	Mm.254267	NM_130885	ENSMUSG00000022307	Oxr1	2210416C20Rik|C7|C7B	oxidation resistance 1	protein-coding
mm_94127.1	chr10	128673870	128673888	-	1	NA	promoter-TSS (NM_173733)	promoter-TSS (NM_173733)	39	NM_173733	211389	Mm.23352	NM_173733	ENSMUSG00000049858	Suox	SO	sulfite oxidase	protein-coding
mm_92494.1	chr10	78311985	78312005	-	1	NA	intron (NM_053014, intron 2 of 9)	intron (NM_053014, intron 2 of 9)	28212	NR_106119	102465765		NR_106119	ENSMUSG00000098885	Mir7659	Gm27433|mmu-mir-7659	microRNA 7659	ncRNA
mm_12226.1	chr2	68013635	68013637	+	1	NA	Intergenic	Intergenic	-91036	NM_020283	26877	Mm.226435	NM_020283	ENSMUSG00000034780	B3galt1	beta3Gal-T1	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 1	protein-coding
mm_72506.1	chr8	83899959	83899969	+	1	NA	promoter-TSS (NM_181039)	promoter-TSS (NM_181039)	-134	NM_181039	330814	Mm.260733	NM_181039	ENSMUSG00000013033	Adgrl1	2900070I05Rik|AI182398|CLIBA|Lec2|Lphn1|mKIAA0821	adhesion G protein-coupled receptor L1	protein-coding
mm_1017.1	chr1	58738653	58738673	+	1	NA	intron (NM_001293805, intron 4 of 7)	B1_Mus1|SINE|Alu	8111	NM_001293805	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_136282.1	chr16	91199948	91199992	-	1	NA	Intergenic	RLTR31D_MM|LTR|ERVK	-25580	NM_016967	50913	Mm.37289	NM_016967	ENSMUSG00000039830	Olig2	AI604895|Bhlhb1|Olg-2|Oligo2|RK17|bHLHe19	oligodendrocyte transcription factor 2	protein-coding
mm_33984.1	chr4	137719215	137719223	+	1	NA	intron (NM_001256218, intron 14 of 24)	intron (NM_001256218, intron 14 of 24)	-5242	NR_138592	110351	Mm.180763	NM_029563	ENSMUSG00000041351	Rap1gap	1300019I11Rik|2310004O14Rik|AI427470|ARPP-90|Gap|Rap1GAP1|Rap1ga1	Rap1 GTPase-activating protein	protein-coding
mm_71826.1	chr8	68896608	68896651	+	1	NA	exon (NM_008509, exon 6 of 10)	exon (NM_008509, exon 6 of 10)	16074	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_147459.1	chr18	46597300	46597347	-	1	NA	promoter-TSS (NM_010120)	promoter-TSS (NM_010120)	212	NM_025698	66676	Mm.296043	NM_025698	ENSMUSG00000033184	Tmed7	3930401E15Rik|5830493P14Rik|AU044611|AW545765|TRAM	transmembrane p24 trafficking protein 7	protein-coding
mm_143541.1	chr17	74016928	74016934	-	1	NA	TTS (NM_053188)	TTS (NM_053188)	30985	NM_053188	94224	Mm.38933	NM_053188	ENSMUSG00000038541	Srd5a2	5ART2|S5AR 2	steroid 5 alpha-reductase 2	protein-coding
mm_58085.1	chr6	136947044	136947048	-	1	NA	Intergenic	RMER17C|LTR|ERVK	-5147	NM_001301309	11857	Mm.2241	NM_007486	ENSMUSG00000030220	Arhgdib	D4|Gdid4|Ly-GDI	Rho, GDP dissociation inhibitor (GDI) beta	protein-coding
mm_169222.1	chr13	66802570	66802577	-	1	NA	Intergenic	Intergenic	102777	NM_026219	67530	Mm.379136	NM_026219	ENSMUSG00000021520	Uqcrb	2210415M14Rik|QP-C|QPC|UQBC|UQBP|UQPC	ubiquinol-cytochrome c reductase binding protein	protein-coding
mm_68107.1	chr7	102019492	102019516	-	1	NA	TTS (NM_029211)	TTS (NM_029211)	-1349	NM_010531	16068	Mm.422756	NM_010531	ENSMUSG00000070427	Il18bp	IL-18BP|Igifbp|MC54L	interleukin 18 binding protein	protein-coding
mm_145422.1	chr18	58556201	58556216	+	1	NA	promoter-TSS (NM_001081072)	promoter-TSS (NM_001081072)	-32	NM_001081072	225579	Mm.258517	NM_001081072	ENSMUSG00000024600	Slc27a6	4732438L20Rik|FACVL2|FATP6|VLCS-H1	solute carrier family 27 (fatty acid transporter), member 6	protein-coding
mm_63313.1	chr7	126863333	126863355	+	1	NA	exon (NM_172746, exon 4 of 7)	exon (NM_172746, exon 4 of 7)	1372	NM_172746	233876	Mm.363427	NM_172746	ENSMUSG00000042606	Hirip3	B130036O03|C86302	HIRA interacting protein 3	protein-coding
mm_35674.1	chr4	43584387	43584393	-	1	NA	5' UTR (NM_001099314, exon 1 of 3)	5' UTR (NM_001099314, exon 1 of 3)	104	NM_001099314	100039672	Mm.415110	NM_001099314	ENSMUSG00000078719	Msmp	OTTMUSG00000007017|Psmp	microseminoprotein, prostate associated	protein-coding
mm_153566.1	chr19	42563066	42563098	-	1	NA	exon (NM_177464, exon 2 of 7)	exon (NM_177464, exon 2 of 7)	44277	NM_177464	52013	Mm.254169	NM_177464	ENSMUSG00000025184	R3hcc1l	1700036B12Rik|AI450607|C10orf28|D19Ertd386e|GIDRP86|Gidrp88	R3H domain and coiled-coil containing 1 like	protein-coding
mm_170597.1	chr19	5802363	5802367	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	307	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_51712.1	chr6	86785063	86785082	+	1	NA	intron (NM_013471, intron 1 of 12)	intron (NM_013471, intron 1 of 12)	8512	NM_013471	11746	Mm.259702	NM_013471	ENSMUSG00000029994	Anxa4	AI265406|AIV|AW106930|Anx4|Xanx-4	annexin A4	protein-coding
mm_117127.1	chr13	60905121	60905133	-	1	NA	promoter-TSS (NM_026429)	promoter-TSS (NM_026429)	-280	NM_026429	116913	Mm.443229	NM_026429	ENSMUSG00000062705	Tpbpb	1600012N09Rik	trophoblast specific protein beta	protein-coding
mm_115602.1	chr13	11898936	11898947	-	1	NA	intron (NM_023868, intron 4 of 104)	intron (NM_023868, intron 4 of 104)	208004	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding
mm_60374.1	chr7	44467988	44468014	+	1	NA	promoter-TSS (NM_001205073)	promoter-TSS (NM_001205073)	21	NM_001205070	66124	Mm.358691	NM_025368	ENSMUSG00000038695	Josd2	1110007C05Rik	Josephin domain containing 2	protein-coding
mm_29713.1	chr3	123690742	123690800	-	1	NA	promoter-TSS (NR_121616)	promoter-TSS (NR_121616)	81	NR_121616	83398	Mm.443908	NM_031186	ENSMUSG00000027977	Ndst3	4921531K01Rik|4930511P15Rik|N-HSST 3|NDST-3	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 3	protein-coding
mm_108401.1	chr12	81183880	81183889	+	1	NA	intron (NM_022316, intron 11 of 12)	intron (NM_022316, intron 11 of 12)	17733	NR_037227	100526532		NR_037227	ENSMUSG00000092673	Mir3067	mir-3067|mmu-mir-3067	microRNA 3067	ncRNA
mm_141663.1	chr17	33781188	33781280	-	1	NA	exon (NM_020581, exon 1 of 7)	exon (NM_020581, exon 1 of 7)	341	NM_020581	57875	Mm.196189	NM_020581	ENSMUSG00000002289	Angptl4	Arp4|Bk89|Fiaf|Hfarp|Ng27|Pgar|Pgarg|Pp1158	angiopoietin-like 4	protein-coding
mm_106224.1	chr11	117114954	117114964	-	1	NA	promoter-TSS (NM_001166506)	promoter-TSS (NM_001166506)	-213	NR_029459	74136	Mm.272312	NM_028777	ENSMUSG00000020823	Sec14l1	1200017E04Rik|2810012L19Rik|Naa-35	SEC14-like lipid binding 1	protein-coding
mm_144538.1	chr18	25754382	25754387	+	1	NA	promoter-TSS (NM_001146295)	promoter-TSS (NM_001146295)	-401	NM_001174074	108013	Mm.266435	NM_133195	ENSMUSG00000024268	Celf4	A230070D14Rik|BRUNOL-4|Brul4|Brunol4|C130060B05Rik	CUGBP, Elav-like family member 4	protein-coding
mm_95393.1	chr11	49259041	49259051	+	1	NA	intron (NM_001110148, intron 3 of 3)	B1_Mur4|SINE|Alu	8494	NM_001110150	17308	Mm.196933	NM_010794	ENSMUSG00000020346	Mgat1	Mgat-1	mannoside acetylglucosaminyltransferase 1	protein-coding
mm_123034.1	chr14	55524990	55524996	-	1	NA	promoter-TSS (NM_008736)	promoter-TSS (NM_008736)	-12	NM_001271917	18185	Mm.20422	NM_008736	ENSMUSG00000040632	Nrl	D14H14S46E	neural retina leucine zipper gene	protein-coding
mm_52070.1	chr6	97807647	97807668	+	1	NA	intron (NM_001113198, intron 1 of 9)	intron (NM_001113198, intron 1 of 9)	599	NM_001113198	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_158069.1	chrX	101263987	101264002	-	1	NA	promoter-TSS (NM_001317221)	promoter-TSS (NM_001317221)	-2	NM_001317221	245536	Mm.212463	NM_001033362	ENSMUSG00000090141	Gm614	-	predicted gene 614	protein-coding
mm_17923.1	chr2	35457846	35457866	-	1	NA	intron (NM_001308300, intron 1 of 6)	B3|SINE|B2	3593	NM_001308299	14594	Mm.281124	NM_010283	ENSMUSG00000035778	Ggta1	AW108479|GALT|Gal|Ggta|Ggta-1|alpha Gal|alpha3GalT	glycoprotein galactosyltransferase alpha 1, 3	protein-coding
mm_74428.1	chr8	3694168	3694183	-	1	NA	promoter-TSS (NM_013517)	promoter-TSS (NM_013517)	-1	NM_001253743	14128	Mm.1233	NM_013517	ENSMUSG00000005540	Fcer2a	CD23|Fce2|Fcer2|Ly-42	Fc receptor, IgE, low affinity II, alpha polypeptide	protein-coding
mm_84393.1	chr9	65529782	65529828	-	1	NA	Intergenic	MIRc|SINE|MIR	50282	NM_153119	102595	Mm.247303	NM_153119	ENSMUSG00000050721	Plekho2	AI840980|Plekhq1	pleckstrin homology domain containing, family O member 2	protein-coding
mm_41753.1	chr5	102845301	102845328	+	1	NA	5' UTR (NM_001346585, exon 1 of 7)	5' UTR (NM_001346585, exon 1 of 7)	307	NM_001346585	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding
mm_139092.1	chr17	46858218	46858252	+	1	NA	Intergenic	Intergenic	-26822	NM_001100452	210982	Mm.37642	NM_001100452	ENSMUSG00000036568	Gltscr1l	mKIAA0240	GLTSCR1-like	protein-coding
mm_165498.1	chr2	166825129	166825137	-	1	NA	intron (NM_001085495, intron 1 of 38)	intron (NM_001085495, intron 1 of 38)	19552	NM_001085495	99371	Mm.297192	NM_001085495	ENSMUSG00000074582	Arfgef2	AI463430|AW493672|BIG2|E230011G24Rik	ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited)	protein-coding
mm_99212.1	chr11	101023295	101023308	+	1	NA	intron (NM_001243050, intron 5 of 20)	intron (NM_001243050, intron 5 of 20)	-7039	NR_105893	102466767		NR_105893	ENSMUSG00000098415	Mir6928	Gm27728|mmu-mir-6928	microRNA 6928	ncRNA
mm_7914.1	chr1	133719113	133719116	-	1	NA	intron (NM_213616, intron 15 of 19)	MIRb|SINE|MIR	7531	NR_105868	102466206		NR_105868	ENSMUSG00000098606	Mir6903	Gm27797|mmu-mir-6903	microRNA 6903	ncRNA
mm_95740.1	chr11	54691526	54691540	+	1	NA	exon (NM_001252494, exon 27 of 29)	exon (NM_001252494, exon 27 of 29)	95387	NM_001252497	192786	Mm.254404	NM_175258	ENSMUSG00000037533	Rapgef6	A530068K01|AI844632|BB085664|C030018K18Rik|PDZ-GEF2|Pdzgef2|RA-GEF-2|Ragef2|mKIAA4052	Rap guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_165541.1	chr2	181385904	181385907	+	1	NA	non-coding (NR_045164, exon 2 of 3)	non-coding (NR_045164, exon 2 of 3)	1655	NR_045164	329584	Mm.386906	NR_045164	ENSMUSG00000085028	Slc2a4rg-ps	C430010C01|Gm14462|OTTMUSG00000016710	Slc2a4 regulator, pseudogene	pseudo
mm_6085.1	chr1	63108029	63108032	-	1	NA	intron (NM_001081436, intron 1 of 11)	intron (NM_001081436, intron 1 of 11)	6237	NM_001081436	227195	Mm.74718	NM_001081436	ENSMUSG00000040865	Ino80d	7330405I11|A430093A21Rik|BC010584|OTTMUSG00000002594	INO80 complex subunit D	protein-coding
mm_21242.1	chr2	156172992	156173024	-	1	NA	exon (NM_001291114, exon 4 of 17)	exon (NM_001291114, exon 4 of 17)	6572	NM_001291115	170791	Mm.392436	NM_133242	ENSMUSG00000027620	Rbm39	1500012C14Rik|2310040E03Rik|B330012G18Rik|C79248|R75070|Rnpc2|caper	RNA binding motif protein 39	protein-coding
mm_103537.1	chr11	77489980	77489990	-	1	NA	promoter-TSS (NM_172945)	promoter-TSS (NM_172945)	-307	NM_172945	268445	Mm.39296	NM_172945	ENSMUSG00000037907	Ankrd13b	AW124583|B930093C12Rik	ankyrin repeat domain 13b	protein-coding
mm_123066.1	chr14	55672194	55672208	-	1	NA	promoter-TSS (NM_177992)	promoter-TSS (NM_177992)	-34	NM_177992	105446	Mm.390685	NM_177992	ENSMUSG00000002326	Gmpr2	1810008P16Rik|5730544D12Rik|AA959850|GMPR 2	guanosine monophosphate reductase 2	protein-coding
mm_32057.1	chr4	97777430	97777450	+	1	NA	promoter-TSS (NM_001122953)	promoter-TSS (NM_001122953)	-186	NM_001122953	18027	Mm.31274	NM_010905	ENSMUSG00000028565	Nfia	1110047K16Rik|9430022M17Rik|CTF|NF1-A|NF1A	nuclear factor I/A	protein-coding
mm_116785.1	chr13	53369776	53369779	-	1	NA	intron (NM_009269, intron 3 of 14)	intron (NM_009269, intron 3 of 14)	7584	NM_009269	268656	Mm.240336	NM_009269	ENSMUSG00000021468	Sptlc1	AW552086|C77762|E030036H05|Lcb1	serine palmitoyltransferase, long chain base subunit 1	protein-coding
mm_1969.1	chr1	86503630	86503638	+	1	NA	Intergenic	Intergenic	-23102	NM_008972	19231	Mm.19187	NM_008972	ENSMUSG00000026238	Ptma	Thym	prothymosin alpha	protein-coding
mm_77667.1	chr8	124751809	124751875	-	1	NA	promoter-TSS (NM_001081120)	promoter-TSS (NM_001081120)	-33	NM_001081120	69627	Mm.271600	NM_001081120	ENSMUSG00000043068	Fam89a	2310031A18Rik	family with sequence similarity 89, member A	protein-coding
mm_95653.1	chr11	53724655	53724655	+	1	NA	3' UTR (NM_010558, exon 4 of 4)	3' UTR (NM_010558, exon 4 of 4)	3861	NM_010558	16191	Mm.4461	NM_010558	ENSMUSG00000036117	Il5	Il-5	interleukin 5	protein-coding
mm_74975.1	chr8	27141450	27141462	-	1	NA	3' UTR (NM_001080813, exon 6 of 6)	3' UTR (NM_001080813, exon 6 of 6)	-1454	NR_045840	71082	Mm.395259	NR_045840		4933416M07Rik	-	RIKEN cDNA 4933416M07 gene	ncRNA
mm_185.1	chr1	15286901	15286963	+	1	NA	Intergenic	CpG	-25520	NM_001098528	98741	Mm.156081	NM_001033195	ENSMUSG00000092083	Kcnb2	9630047L19Rik|BB130875|Kv2.2	potassium voltage gated channel, Shab-related subfamily, member 2	protein-coding
mm_153421.1	chr19	40665920	40665931	-	1	NA	intron (NM_009848, intron 1 of 9)	intron (NM_009848, intron 1 of 9)	6155	NM_009848	12495	Mm.2824	NM_009848	ENSMUSG00000048120	Entpd1	2610206B08Rik|AA408691|Cd39|NTPDase-1	ectonucleoside triphosphate diphosphohydrolase 1	protein-coding
mm_114900.1	chr13	94520761	94520774	+	1	NA	intron (NM_009680, intron 22 of 26)	L1M3|LINE|L1	161807	NM_009680	11774	Mm.21185	NM_009680	ENSMUSG00000021686	Ap3b1	AP-3|AU015684|C78395|Hps2|beta3A|pe|pearl|rim2	adaptor-related protein complex 3, beta 1 subunit	protein-coding
mm_95106.1	chr11	34054290	34054311	+	1	NA	intron (NM_010696, intron 2 of 20)	intron (NM_010696, intron 2 of 20)	7099	NM_010696	16822	Mm.265350	NM_010696	ENSMUSG00000002699	Lcp2	AI323664|BB161688|SLP-76|SLP76|m1Khoe|twm	lymphocyte cytosolic protein 2	protein-coding
mm_88673.1	chr10	80018100	80018111	+	1	NA	intron (NM_001347074, intron 2 of 22)	intron (NM_001347074, intron 2 of 22)	1190	NM_001347074	70719	Mm.243954	NM_027521	ENSMUSG00000035697	Hmha1	6330406L22Rik|AW539505|Ha-1	histocompatibility (minor) HA-1	protein-coding
mm_81367.1	chr9	108795972	108795994	+	1	NA	promoter-TSS (NM_029634)	promoter-TSS (NM_029634)	-11	NM_029634	76500	Mm.276336	NM_029634	ENSMUSG00000032599	Ip6k2	1500005N04Rik|AW050208|Ihpk2	inositol hexaphosphate kinase 2	protein-coding
mm_78348.1	chr9	25306180	25306198	+	1	NA	exon (NM_001205367, exon 12 of 13)	exon (NM_001205367, exon 12 of 13)	53750	NM_001205367	235072	Mm.270259	NM_009859	ENSMUSG00000001833	Sept7	Cdc10|E430034N22	septin 7	protein-coding
mm_4178.1	chr1	171126092	171126113	+	1	NA	exon (NM_001081275, exon 5 of 6)	exon (NM_001081275, exon 5 of 6)	4441	NM_001081275	75472	Mm.32760	NM_029301	ENSMUSG00000026649	Cfap126	1700009P17Rik|AV282292|Flattop|Fltp	cilia and flagella associated protein 126	protein-coding
mm_165046.1	chr19	40187202	40187213	-	1	NA	promoter-TSS (NM_145499)	promoter-TSS (NM_145499)	79	NM_145499	226105	Mm.29119	NM_145499	ENSMUSG00000060613	Cyp2c70	-	cytochrome P450, family 2, subfamily c, polypeptide 70	protein-coding
mm_67520.1	chr7	80923268	80923274	-	1	NA	intron (NM_019951, intron 3 of 5)	intron (NM_019951, intron 3 of 5)	-18209	NM_001291280	68039	Mm.22246	NM_026523	ENSMUSG00000025723	Nmb	3110023K12Rik	neuromedin B	protein-coding
mm_129066.1	chr15	75633828	75633846	-	1	NA	Intergenic	RLTR14-int|LTR|ERV1	17153	NM_011759	22701	Mm.87210	NM_011759	ENSMUSG00000047003	Zfp41	CTfin92|Zfp-41	zinc finger protein 41	protein-coding
mm_22055.1	chr2	168571198	168571218	-	1	NA	exon (NM_010899, exon 2 of 10)	exon (NM_010899, exon 2 of 10)	19157	NM_001291178	18019	Mm.116802	NM_010899	ENSMUSG00000027544	Nfatc2	AI607462|NF-ATc2|NF-ATp|NFAT1|NFAT1-D|Nfatp	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 2	protein-coding
mm_40937.1	chr5	76657754	76657764	+	1	NA	Intergenic	CpG	66045	NM_199032	381644	Mm.332452	NM_199032	ENSMUSG00000036403	Cep135	BC062951|Cep4|Gm1044	centrosomal protein 135	protein-coding
mm_28078.1	chr3	84480420	84480456	-	1	NA	promoter-TSS (NM_001205355)	promoter-TSS (NM_001205355)	1	NM_001033301	229474	Mm.331107	NM_001033301	ENSMUSG00000041842	Fhdc1	6330505N24Rik|Gm126	FH2 domain containing 1	protein-coding
mm_142742.1	chr17	48409589	48409599	-	1	NA	promoter-TSS (NM_001289491)	promoter-TSS (NM_001289491)	226	NM_001110832	18044	Mm.4929	NM_010913	ENSMUSG00000023994	Nfya	AA407810|Cbf-b|SEZ-10|SEZ10	nuclear transcription factor-Y alpha	protein-coding
mm_129268.1	chr15	76925392	76925405	-	1	NA	promoter-TSS (NM_172817)	promoter-TSS (NM_172817)	50	NM_172817	239546	Mm.183650	NM_172817	ENSMUSG00000054967	Zfp647	6030449J21|Es492|Znf250	zinc finger protein 647	protein-coding
mm_163040.1	chr11	53351078	53351085	+	1	NA	5' UTR (NM_033565, exon 1 of 21)	5' UTR (NM_033565, exon 1 of 21)	314	NM_033565	93736	Mm.395281	NM_033565	ENSMUSG00000049470	Aff4	AF5Q31|Alf4|Laf4l|MCEF	AF4/FMR2 family, member 4	protein-coding
mm_168643.1	chr1	185076733	185076735	-	1	NA	Intergenic	RLTR1B|LTR|ERV1	-77185	NM_145515	226778	Mm.7445	NM_145515	ENSMUSG00000026620	Mark1	AW491150|B930025N23Rik|Emk3|Par-1c|mKIAA1477|mPar-1c	MAP/microtubule affinity regulating kinase 1	protein-coding
mm_116152.1	chr13	29985979	29986037	-	1	NA	promoter-TSS (NM_010093)	promoter-TSS (NM_010093)	55	NM_010093	13557	Mm.268356	NM_010093	ENSMUSG00000016477	E2f3	E2F3b|E2f3a	E2F transcription factor 3	protein-coding
mm_163922.1	chr14	44988769	44988812	-	1	NA	5' UTR (NM_008964, exon 1 of 2)	5' UTR (NM_008964, exon 1 of 2)	679	NM_008964	19217	Mm.4630	NM_008964	ENSMUSG00000037759	Ptger2	EP2|Ptgerep2	prostaglandin E receptor 2 (subtype EP2)	protein-coding
mm_63199.1	chr7	125634397	125634410	+	1	NA	TTS (NM_021887)	TTS (NM_021887)	30974	NM_021887	60504	Mm.155643	NM_021887	ENSMUSG00000030745	Il21r	NILR	interleukin 21 receptor	protein-coding
mm_139423.1	chr17	53479503	53479511	+	1	NA	5' UTR (NM_025887, exon 1 of 6)	5' UTR (NM_025887, exon 1 of 6)	273	NM_025887	271457	Mm.329123	NM_025887	ENSMUSG00000017831	Rab5a	2410015H04Rik|AI663973|AU021172|nnyRab5a	RAB5A, member RAS oncogene family	protein-coding
mm_139469.1	chr17	55970452	55970485	+	1	NA	promoter-TSS (NM_009168)	promoter-TSS (NM_009168)	-14	NM_001159523	20420	Mm.20908	NM_009168	ENSMUSG00000039154	Shd	AI413439	src homology 2 domain-containing transforming protein D	protein-coding
mm_108179.1	chr12	76417552	76417585	+	1	NA	promoter-TSS (NM_001163103)	promoter-TSS (NM_001163103)	-31	NM_001163103	210762	Mm.292354	NM_001163103	ENSMUSG00000052221	Ppp1r36	Gm70	protein phosphatase 1, regulatory subunit 36	protein-coding
mm_81453.1	chr9	109832757	109832802	+	1	NA	promoter-TSS (NM_018757)	promoter-TSS (NM_018757)	-15	NM_018757	54369	Mm.12951	NM_018757	ENSMUSG00000032478	Nme6	nm23-M6	NME/NM23 nucleoside diphosphate kinase 6	protein-coding
mm_27407.1	chr3	51340544	51340554	-	1	NA	promoter-TSS (NM_001291059)	promoter-TSS (NM_001291059)	95	NM_001291059	69257	Mm.131038	NM_023502	ENSMUSG00000037174	Elf2	2610036A20Rik|A230104O07Rik|AW111824|BB183398|EU32|NERF|NERF-1A|NERF-1B|NERF-2	E74-like factor 2	protein-coding
mm_147722.1	chr18	60848863	60848900	-	1	NA	promoter-TSS (NM_011552)	promoter-TSS (NM_011552)	83	NM_011552	21453	Mm.486251	NM_011552	ENSMUSG00000024613	Tcof1	AA408847|AW209012|treacle	treacle ribosome biogenesis factor 1	protein-coding
mm_170715.1	chr2	144368996	144369001	+	1	NA	promoter-TSS (NM_001166640)	promoter-TSS (NM_001166640)	15	NM_001164813	100048644	Mm.227925	NM_001164813	ENSMUSG00000098387	Pet117	Gm20571	PET117 homolog	protein-coding
mm_13525.1	chr2	110021911	110021942	+	1	NA	exon (NM_026613, exon 2 of 6)	exon (NM_026613, exon 2 of 6)	4109	NM_026613	68201	Mm.181767	NM_026613	ENSMUSG00000027160	Ccdc34	2810027O19Rik|4930522P10Rik|AI596202	coiled-coil domain containing 34	protein-coding
mm_102305.1	chr11	55608211	55608217	-	1	NA	promoter-TSS (NM_020492)	promoter-TSS (NM_020492)	-16	NM_020492	14654	Mm.89320	NM_020492	ENSMUSG00000000263	Glra1	nmf11|oscillator|ot|spasmodic|spd	glycine receptor, alpha 1 subunit	protein-coding
mm_14057.1	chr2	122630600	122630676	+	1	NA	promoter-TSS (NM_001033256)	promoter-TSS (NM_001033256)	13	NM_001033256	214616	Mm.271306	NM_001033256		Spata5l1	AV141009|C130039A10Rik	spermatogenesis associated 5-like 1	protein-coding
mm_106593.1	chr11	120730503	120730515	-	1	NA	exon (NM_007621, exon 5 of 8)	exon (NM_007621, exon 5 of 8)	1512	NM_007621	12409	Mm.21454	NM_007621	ENSMUSG00000025150	Cbr2	MLCR	carbonyl reductase 2	protein-coding
mm_86668.1	chr10	18022965	18022969	+	1	NA	intron (NM_028440, intron 1 of 2)	CpG	285	NM_028440	73112	Mm.276041	NM_028440	ENSMUSG00000078453	Abracl	1700028I04Rik|3110003A17Rik	ABRA C-terminal like	protein-coding
mm_130299.1	chr15	97019528	97019538	-	1	NA	intron (NM_027052, intron 2 of 15)	intron (NM_027052, intron 2 of 15)	36423	NM_027052	69354	Mm.250980	NM_027052	ENSMUSG00000022464	Slc38a4	1110012E16Rik|1700012A18Rik|Ata3|mATA3|mNAT3	solute carrier family 38, member 4	protein-coding
mm_54143.1	chr6	22306869	22306872	-	1	NA	3' UTR (NM_138587, exon 10 of 10)	3' UTR (NM_138587, exon 10 of 10)	18643	NM_053116	93735	Mm.137403	NM_053116	ENSMUSG00000029671	Wnt16	E130309I19Rik	wingless-type MMTV integration site family, member 16	protein-coding
mm_26147.1	chr3	138066686	138066704	+	1	NA	intron (NR_037975, intron 1 of 3)	intron (NR_037975, intron 1 of 3)	693	NR_037975	329763	Mm.169710	NM_177860	ENSMUSG00000049349	Gm5105	D830013H12|EG329763	predicted gene 5105	ncRNA
mm_14646.1	chr2	136910152	136910171	+	1	NA	intron (NM_001038641, intron 2 of 7)	intron (NM_001038641, intron 2 of 7)	10810	NM_001038641	74243	Mm.330612	NM_028201	ENSMUSG00000027281	Slx4ip	2210009G21Rik|2410004I22Rik|C85661|Slxip	SLX4 interacting protein	protein-coding
mm_31305.1	chr4	46040978	46040981	+	1	NA	intron (NM_021883, intron 1 of 9)	MIR3|SINE|MIR	1757	NM_021883	21916	Mm.249594	NM_021883	ENSMUSG00000028328	Tmod1	E-Tmod|Tmod	tropomodulin 1	protein-coding
mm_24023.1	chr3	87527319	87527327	+	1	NA	intron (NM_001286844, intron 2 of 4)	intron (NM_001286844, intron 2 of 4)	1745	NM_012051	27049	Mm.219460	NM_012051	ENSMUSG00000003382	Etv3	AI414410|METS|Pe1	ets variant 3	protein-coding
mm_161888.1	chr18	37815018	37815018	+	1	NA	promoter-TSS (NM_033582)	promoter-TSS (NM_033582)	-61	NM_033582	93707	Mm.247203	NM_033582	ENSMUSG00000023036	Pcdhgc4	-	protocadherin gamma subfamily C, 4	protein-coding
mm_54414.1	chr6	32588248	32588258	-	1	NA	promoter-TSS (NM_175750)	promoter-TSS (NM_175750)	-61	NM_175750	243743	Mm.444029	NM_175750	ENSMUSG00000029765	Plxna4	9330117B14|Plxa4|mKIAA1550	plexin A4	protein-coding
mm_121337.1	chr14	115044498	115044500	+	1	NA	promoter-TSS (NR_029816)	promoter-TSS (NR_029816)	72	NR_029816	751549		NR_029816	ENSMUSG00000076062	Mir92-1	Mirn92-1|mir-92a-1	microRNA 92-1	ncRNA
mm_99237.1	chr11	101071971	101072011	+	1	NA	exon (NM_013792, exon 3 of 6)	exon (NM_013792, exon 3 of 6)	1897	NM_013792	27419	Mm.95452	NM_013792	ENSMUSG00000001751	Naglu	-	alpha-N-acetylglucosaminidase (Sanfilippo disease IIIB)	protein-coding
mm_91315.1	chr10	24927445	24927460	-	1	NA	promoter-TSS (NM_007482)	promoter-TSS (NM_007482)	18	NM_007482	11846	Mm.154144	NM_007482	ENSMUSG00000019987	Arg1	AI|AI256583|Arg-1|PGIF	arginase, liver	protein-coding
mm_88871.1	chr10	81070038	81070046	+	1	NA	promoter-TSS (NM_022653)	promoter-TSS (NM_022653)	-41	NM_022653	50492	Mm.26995	NM_022653	ENSMUSG00000004929	Thop1	AI131655|AI327041|EP24.15	thimet oligopeptidase 1	protein-coding
mm_74415.1	chr8	3625026	3625042	-	1	NA	promoter-TSS (NM_001129804)	promoter-TSS (NM_001129804)	15	NM_001129804	18545	Mm.440882	NM_008790	ENSMUSG00000004630	Pcp2	L7|Pcp-2	Purkinje cell protein 2 (L7)	protein-coding
mm_70972.1	chr8	27085836	27085888	+	1	NA	promoter-TSS (NM_054044)	promoter-TSS (NM_054044)	21	NM_054044	78560	Mm.87046	NM_054044	ENSMUSG00000031486	Adgra2	8430414O08Rik|9530074E10Rik|Gpr124|Tem5|mKIAA1531	adhesion G protein-coupled receptor A2	protein-coding
mm_102758.1	chr11	67500969	67501006	-	1	NA	Intergenic	Intergenic	-32011	NM_008088	14457	Mm.40338	NM_008088	ENSMUSG00000033066	Gas7	AW124766|B230343A10Rik|Gas7-cb	growth arrest specific 7	protein-coding
mm_27463.1	chr3	52180004	52180014	-	1	NA	Intergenic	Intergenic	-75003	NM_001004176	433586	Mm.234972	NM_001004176	ENSMUSG00000061143	Maml3	AV234550|BC049812|Mam-2|mKIAA1816	mastermind like 3 (Drosophila)	protein-coding
mm_74141.1	chr8	123235106	123235117	+	1	NA	promoter-TSS (NR_045849)	promoter-TSS (NR_045849)	20	NR_045849	71186	Mm.449984	NR_045849	ENSMUSG00000097637	4933417D19Rik	-	RIKEN cDNA 4933417D19 gene	ncRNA
mm_158326.1	chrX	133960727	133960755	-	1	NA	exon (NM_001290718, exon 5 of 14)	exon (NM_001290718, exon 5 of 14)	21071	NM_001290718	27359	Mm.38674	NM_013757	ENSMUSG00000031255	Sytl4	Gph|Slp4	synaptotagmin-like 4	protein-coding
mm_61073.1	chr7	51621686	51621703	+	1	NA	promoter-TSS (NM_080853)	promoter-TSS (NM_080853)	-136	NM_080853	140919	Mm.256618	NM_080853	ENSMUSG00000030500	Slc17a6	2900073D12Rik|DNPI|VGLUT2	solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 6	protein-coding
mm_149000.1	chr19	8664384	8664394	+	1	NA	5' UTR (NM_007698, exon 1 of 2)	5' UTR (NM_007698, exon 1 of 2)	384	NM_001112697	12669	Mm.240607	NM_007698	ENSMUSG00000032773	Chrm1	Chrm-1|M1|M1R	cholinergic receptor, muscarinic 1, CNS	protein-coding
mm_146391.1	chr18	82767287	82767319	+	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-8264	NR_045389	76961	Mm.396392	NR_045389	ENSMUSG00000101773	2210420H20Rik	-	RIKEN cDNA 2210420H20 gene	ncRNA
mm_39995.1	chr5	32610355	32610374	+	1	NA	promoter-TSS (NM_009535)	promoter-TSS (NM_009535)	-807	NM_001205133	22612	Mm.4558	NM_009535	ENSMUSG00000014932	Yes1	Yes|p61-Yes	YES proto-oncogene 1, Src family tyrosine kinase	protein-coding
mm_109892.1	chr12	7380325	7380361	-	1	NA	promoter-TSS (NR_045045)	promoter-TSS (NR_045045)	-13	NR_045045	73575	Mm.179463	NR_045045	ENSMUSG00000102096	1700101O22Rik	-	RIKEN cDNA 1700101O22 gene	ncRNA
mm_64402.1	chr7	142507721	142507755	+	1	NA	promoter-TSS (NR_033261)	promoter-TSS (NR_033261)	-967	NR_033261	677289	Mm.350054	NR_033261	ENSMUSG00000043795	Prr33	ENSMUSG00000043795|Gm14492|OTTMUSG00000016823	proline rich 33	ncRNA
mm_29752.1	chr3	127063713	127063750	-	1	NA	intron (NM_001327938, intron 4 of 47)	MLTR11B|LTR|ERVK	-65279	NM_178655	109676	Mm.220242	NM_178655	ENSMUSG00000032826	Ank2	100043364|AI835472|AW491075|Ank-2|Gm4392	ankyrin 2, brain	protein-coding
mm_24051.1	chr3	87906531	87906607	+	1	NA	promoter-TSS (NM_001331051)	promoter-TSS (NM_001331051)	248	NM_008231	15191	Mm.292208	NM_008231	ENSMUSG00000004897	Hdgf	AI118077|D3Ertd299e	hepatoma-derived growth factor	protein-coding
mm_56271.1	chr6	91024037	91024040	-	1	NA	intron (NM_018815, intron 33 of 39)	intron (NM_018815, intron 33 of 39)	92788	NM_018815	54563	Mm.28162	NM_018815	ENSMUSG00000030091	Nup210	9830001L10|AI836801|Pom210|gp190|gp210	nucleoporin 210	protein-coding
mm_104055.1	chr11	86485253	86485260	-	1	NA	intron (NM_029788, intron 1 of 8)	intron (NM_029788, intron 1 of 8)	599	NM_029788	76892	Mm.262707	NM_029788	ENSMUSG00000020521	Rnft1	0610013E23Rik|AV007605	ring finger protein, transmembrane 1	protein-coding
mm_14103.1	chr2	125256471	125256476	+	1	NA	intron (NM_023595, intron 3 of 5)	intron (NM_023595, intron 3 of 5)	8958	NM_023595	110074	Mm.282499	NM_023595	ENSMUSG00000027203	Dut	5031412I06Rik|5133400F09Rik|D2Bwg0749e|Dutp|dUTPase	deoxyuridine triphosphatase	protein-coding
mm_16385.1	chr2	178455401	178455417	+	1	NA	intron (NM_001291189, intron 3 of 13)	intron (NM_001291189, intron 3 of 13)	24894	NM_198656	381409	Mm.330860	NM_198656	ENSMUSG00000039155	Cdh26	Gm1010	cadherin-like 26	protein-coding
mm_62870.1	chr7	114743716	114743733	+	1	NA	Intergenic	Intergenic	-2042	NM_173767	233752	Mm.83037	NM_173767	ENSMUSG00000048782	Insc	3830422K02Rik|C730020D23	inscuteable homolog (Drosophila)	protein-coding
mm_130223.1	chr15	96204706	96204714	-	1	NA	Intergenic	Intergenic	-6736	NR_040423	70040	Mm.437832	NR_040423		2610037D02Rik	AU024679	RIKEN cDNA 2610037D02 gene	ncRNA
mm_65413.1	chr7	25245441	25245453	-	1	NA	exon (NM_010155, exon 4 of 4)	exon (NM_010155, exon 4 of 4)	5311	NM_010155	13875	Mm.8068	NM_010155	ENSMUSG00000040857	Erf	-	Ets2 repressor factor	protein-coding
mm_91560.1	chr10	39986626	39986648	-	1	NA	promoter-TSS (NM_001113385)	promoter-TSS (NM_001113385)	9	NM_001113385	215928	Mm.31744	NM_001001489	ENSMUSG00000038528	Mfsd4b5	Naglt1c	major facilitator superfamily domain containing 4B5	protein-coding
mm_68199.1	chr7	104380137	104380178	-	1	NA	Intergenic	Lx2B2|LINE|L1	-21511	NM_175648	244183	Mm.347647	NM_175648	ENSMUSG00000052749	Trim30b	A530023O14Rik|Trim30-1	tripartite motif-containing 30B	protein-coding
mm_85758.1	chr9	108649565	108649569	-	1	NA	promoter-TSS (NM_011790)	promoter-TSS (NM_011790)	-187	NM_011790	23807	Mm.290447	NM_011790	ENSMUSG00000064145	Arih2	AI843547|ARI2|TRIAD1|UIP48	ariadne RBR E3 ubiquitin protein ligase 2	protein-coding
mm_160842.1	chr11	50158521	50158521	+	1	NA	exon (NM_001290759, exon 13 of 22)	exon (NM_001290759, exon 13 of 22)	-16330	NM_026543	68067	Mm.40828	NM_026543	ENSMUSG00000020381	Mrnip	2900016G09Rik|3010026O09Rik|AI851514|AW475975	MRN complex interacting protein	protein-coding
mm_27510.1	chr3	55792417	55792437	-	1	NA	intron (NM_030595, intron 40 of 57)	intron (NM_030595, intron 40 of 57)	9917	NM_010750	17116	Mm.440209	NM_010750	ENSMUSG00000056947	Mab21l1	AW047968	mab-21-like 1 (C. elegans)	protein-coding
mm_84500.1	chr9	66918341	66918377	-	1	NA	intron (NM_173413, intron 1 of 7)	intron (NM_173413, intron 1 of 7)	1346	NM_173413	235442	Mm.260376	NM_173413	ENSMUSG00000036943	Rab8b	5930437D16|D330025I23Rik	RAB8B, member RAS oncogene family	protein-coding
mm_91491.1	chr10	37135681	37135690	-	1	NA	3' UTR (NM_008538, exon 2 of 2)	3' UTR (NM_008538, exon 2 of 2)	3241	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_140714.1	chr17	15240748	15240755	-	1	NA	promoter-TSS (NR_046164)	promoter-TSS (NR_046164)	32	NR_046164	328747	Mm.256835	NR_046164	ENSMUSG00000097624	Gm5091	C330048F19	predicted gene 5091	ncRNA
mm_141513.1	chr17	31678182	31678194	-	1	NA	exon (NM_001278570, exon 1 of 3)	exon (NM_001278570, exon 1 of 3)	257	NM_001278570	12954	Mm.1228	NM_013501	ENSMUSG00000024041	Cryaa	Acry-1|Crya-1|Crya1|DAcry-1|lop18	crystallin, alpha A	protein-coding
mm_165815.1	chr3	145988687	145988695	+	1	NA	exon (NM_001166064, exon 1 of 7)	exon (NM_001166064, exon 1 of 7)	821	NM_001166064	214804	Mm.268854	NM_001166064	ENSMUSG00000036863	Syde2	C430017H16Rik	synapse defective 1, Rho GTPase, homolog 2 (C. elegans)	protein-coding
mm_137094.1	chr17	21535573	21535589	+	1	NA	promoter-TSS (NM_144515)	promoter-TSS (NM_144515)	42	NM_144515	22710	Mm.296100	NM_144515	ENSMUSG00000051341	Zfp52	KRAB11|Zfp-52|Zfp76|mszf23-2|mszf24|mszf34|mszf75|zfec29	zinc finger protein 52	protein-coding
mm_66533.1	chr7	45136392	45136451	-	1	NA	promoter-TSS (NM_013520)	promoter-TSS (NM_013520)	11	NM_013520	14256	Mm.1658	NM_013520	ENSMUSG00000110206	Flt3l	Flt3lg|Ly72L	FMS-like tyrosine kinase 3 ligand	protein-coding
mm_144265.1	chr18	11053309	11053319	+	1	NA	promoter-TSS (NR_105023)	promoter-TSS (NR_105023)	-747	NR_105023	68434	Mm.57626	NR_105022	ENSMUSG00000097222	1010001N08Rik	Gata6as	RIKEN cDNA 1010001N08 gene	ncRNA
mm_1295.1	chr1	64532611	64532620	+	1	NA	promoter-TSS (NM_009952)	promoter-TSS (NM_009952)	-189	NM_133828	12912	Mm.422634	NM_009952	ENSMUSG00000025958	Creb1	2310001E10Rik|3526402H21Rik|AV083133|Creb|Creb-1	cAMP responsive element binding protein 1	protein-coding
mm_153290.1	chr19	37337846	37337853	-	1	NA	Intergenic	Intergenic	-7236	NM_031156	15925	Mm.28366	NM_031156	ENSMUSG00000056999	Ide	1300012G03Rik|4833415K22Rik|AA675336|AI507533	insulin degrading enzyme	protein-coding
mm_167480.1	chr8	129233993	129234030	-	1	NA	promoter-TSS (NM_153780)	promoter-TSS (NM_153780)	35	NM_153780	72139	Mm.426514	NM_153780	ENSMUSG00000071302	2610044O15Rik8	2610044O15Rik	RIKEN cDNA 2610044O15 gene	protein-coding
mm_31679.1	chr4	62294991	62295009	+	1	NA	intron (NM_001290518, intron 2 of 3)	ID4|SINE|ID	3453	NM_001290518	20530	Mm.292539	NM_025286	ENSMUSG00000066152	Slc31a2	AI604396|CTR2	solute carrier family 31, member 2	protein-coding
mm_108111.1	chr12	75308596	75308606	+	1	NA	5' UTR (NM_023275, exon 1 of 5)	5' UTR (NM_023275, exon 1 of 5)	288	NM_023275	80837	Mm.27467	NM_023275	ENSMUSG00000046768	Rhoj	1110005O19Rik|AW210585|Arhj|TC10L|TCL	ras homolog family member J	protein-coding
mm_59253.1	chr7	24862194	24862209	+	1	NA	Intergenic	Intergenic	7490	NM_182785	232973	Mm.189648	NM_182785	ENSMUSG00000062732	Lypd4	4933400F01Rik	Ly6/Plaur domain containing 4	protein-coding
mm_69432.1	chr7	132813775	132813795	-	1	NA	promoter-TSS (NM_212473)	promoter-TSS (NM_212473)	-589	NM_212473	77938	Mm.225649	NM_175268	ENSMUSG00000030956	Fam53b	A930008G19Rik|mKIAA0140	family with sequence similarity 53, member B	protein-coding
mm_157728.1	chrX	70365053	70365112	-	1	NA	promoter-TSS (NM_010498)	promoter-TSS (NM_010498)	3	NM_010498	15931	Mm.233083	NM_010498	ENSMUSG00000035847	Ids	AW214631	iduronate 2-sulfatase	protein-coding
mm_145327.1	chr18	55057558	55057580	+	1	NA	Intergenic	Intergenic	-67389	NM_175751	269023	Mm.192984	NM_175751	ENSMUSG00000052713	Zfp608	4932417D18Rik|D430007A19Rik|Znf608	zinc finger protein 608	protein-coding
mm_161927.1	chr18	77307717	77307717	+	1	NA	intron (NM_172834, intron 4 of 38)	intron (NM_172834, intron 4 of 38)	25759	NM_172834	240411	Mm.380247	NM_172834	ENSMUSG00000032818	Loxhd1	1700096C21Rik|4932417K07|sba	lipoxygenase homology domains 1	protein-coding
mm_168413.1	chr11	31982605	31982612	-	1	NA	Intergenic	RLTR9E|LTR|ERVK	16975	NM_026262	67592	Mm.78654	NM_026262	ENSMUSG00000020299	4930524B15Rik	-	RIKEN cDNA 4930524B15 gene	protein-coding
mm_53574.1	chr6	137410732	137410740	+	1	NA	promoter-TSS (NM_001164403)	promoter-TSS (NM_001164403)	15	NM_001164403	19277	Mm.186361	NM_011216	ENSMUSG00000030223	Ptpro	D28|GLEPP1|PTPBK|PTPROt|PTPU2|PTPoc|PTPphi|Ptpn15|R-PTP-O	protein tyrosine phosphatase, receptor type, O	protein-coding
mm_41271.1	chr5	89108734	89108744	+	1	NA	intron (NM_001197147, intron 7 of 25)	intron (NM_001197147, intron 7 of 25)	221479	NM_018760	54403	Mm.41044	NM_018760	ENSMUSG00000060961	Slc4a4	AI835705|NBC|NBC1	solute carrier family 4 (anion exchanger), member 4	protein-coding
mm_70090.1	chr7	142656075	142656098	-	1	NA	intron (NM_001315488, intron 1 of 3)	intron (NM_001315488, intron 1 of 3)	-1090	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_25459.1	chr3	108534141	108534147	+	1	NA	intron (NM_001346518, intron 1 of 21)	intron (NM_001346518, intron 1 of 21)	2378	NM_001033304	229722	Mm.316890	NM_001033304	ENSMUSG00000040412	5330417C22Rik	BB183350	RIKEN cDNA 5330417C22 gene	protein-coding
mm_76741.1	chr8	95202793	95202832	-	1	NA	Intergenic	Intergenic	-60272	NM_001145831	16582	Mm.378951	NM_010631	ENSMUSG00000031788	Kifc3	AI325457|BB123200	kinesin family member C3	protein-coding
mm_5095.1	chr1	4807719	4807747	-	1	NA	promoter-TSS (NM_008866)	promoter-TSS (NM_008866)	-160	NM_008866	18777	Mm.299955	NM_008866	ENSMUSG00000025903	Lypla1	Pla1a	lysophospholipase 1	protein-coding
mm_122945.1	chr14	54965814	54965824	-	1	NA	5' UTR (NM_010856, exon 2 of 39)	5' UTR (NM_010856, exon 2 of 39)	788	NM_001164171	17888	Mm.290003	NM_010856	ENSMUSG00000040752	Myh6	A830009F23Rik|AA517445|Myhc-a|Myhca|alpha-MHC	myosin, heavy polypeptide 6, cardiac muscle, alpha	protein-coding
mm_54114.1	chr6	17655212	17655249	-	1	NA	intron (NM_007604, intron 4 of 9)	intron (NM_007604, intron 4 of 9)	18132	NM_007604	12343	Mm.392504	NM_007604	ENSMUSG00000015733	Capza2	1110053K06Rik|AW208808|Cappa2	capping protein (actin filament) muscle Z-line, alpha 2	protein-coding
mm_89571.1	chr10	95514963	95514970	+	1	NA	promoter-TSS (NM_080560)	promoter-TSS (NM_080560)	-196	NM_080560	93765	Mm.371667	NM_080560	ENSMUSG00000074781	Ube2n	1500026J17Rik|AL022654|BB101821|UBC13	ubiquitin-conjugating enzyme E2N	protein-coding
mm_76320.1	chr8	84687840	84687884	-	1	NA	promoter-TSS (NM_025788)	promoter-TSS (NM_025788)	0	NM_025788	66830	Mm.289698	NM_025788	ENSMUSG00000001910	Nacc1	2010001H03Rik|4930511N13Rik|Btbd14b|Nac1	nucleus accumbens associated 1, BEN and BTB (POZ) domain containing	protein-coding
mm_1374.1	chr1	66472060	66472080	+	1	NA	exon (NM_175510, exon 3 of 65)	exon (NM_175510, exon 3 of 65)	3623	NM_175510	329178	Mm.44798	NM_175510	ENSMUSG00000055567	Unc80	C030018G13Rik|C230061B10Rik|UNC-80	unc-80, NALCN activator	protein-coding
mm_53175.1	chr6	125349777	125349787	+	1	NA	promoter-TSS (NM_011609)	promoter-TSS (NM_011609)	59	NM_011609	21937	Mm.1258	NM_011609	ENSMUSG00000030341	Tnfrsf1a	CD120a|FPF|TNF-R|TNF-R-I|TNF-R1|TNF-R55|TNF-alphaR1|TNFAR|TNFR60|TNFRI|TNFRp55|TNFalpha-R1|Tnfr-2|Tnfr1|p55|p55-R	tumor necrosis factor receptor superfamily, member 1a	protein-coding
mm_160251.1	chr7	106975456	106975456	-	1	NA	promoter-TSS (NM_147035)	promoter-TSS (NM_147035)	-5	NM_147035	259037	Mm.223420	NM_147035	ENSMUSG00000045013	Olfr711	MOR103-4	olfactory receptor 711	protein-coding
mm_48476.1	chr5	140995828	140995841	-	1	NA	intron (NM_175362, intron 1 of 24)	B4|SINE|B4	4762	NM_175362	108723	Mm.46187	NM_175362	ENSMUSG00000036526	Card11	0610008L17Rik|2410011D02Rik|BIMP3|CARMA1	caspase recruitment domain family, member 11	protein-coding
mm_10880.1	chr2	25242398	25242408	+	1	NA	promoter-TSS (NM_176834)	promoter-TSS (NM_176834)	-526	NM_176834	68846	Mm.24777	NM_176834	ENSMUSG00000044628	Rnf208	1110061N23Rik	ring finger protein 208	protein-coding
mm_45855.1	chr5	87785307	87785322	-	1	NA	intron (NM_007785, intron 11 of 13)	intron (NM_007785, intron 11 of 13)	10864	NM_007785	12993	Mm.4908	NM_007785	ENSMUSG00000061937	Csn1s2a	Csng|PP22	casein alpha s2-like A	protein-coding
mm_126539.1	chr15	82022858	82022872	+	1	NA	exon (NM_010247, exon 5 of 13)	exon (NM_010247, exon 5 of 13)	6496	NM_010247	14375	Mm.288809	NM_010247	ENSMUSG00000022471	Xrcc6	70kDa|G22p1|Ku70	X-ray repair complementing defective repair in Chinese hamster cells 6	protein-coding
mm_160110.1	chr7	25395987	25395987	-	1	NA	promoter-TSS (NM_010719)	promoter-TSS (NM_010719)	0	NM_010719	16890	Mm.158548	NM_010719	ENSMUSG00000003123	Lipe	4933403G17Rik|HSL	lipase, hormone sensitive	protein-coding
mm_140993.1	chr17	24874436	24874449	-	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	-4328	NM_008340	16005	Mm.3135	NM_008340	ENSMUSG00000046070	Igfals	ALS|Albs|mKIAA4111	insulin-like growth factor binding protein, acid labile subunit	protein-coding
mm_65941.1	chr7	30394565	30394575	-	1	NA	Intergenic	LTR33A|LTR|ERVL	-19218	NM_011662	22177	Mm.46301	NM_011662	ENSMUSG00000030579	Tyrobp	DAP12|KARAP|Ly83	TYRO protein tyrosine kinase binding protein	protein-coding
mm_148773.1	chr19	6105775	6105789	+	1	NA	promoter-TSS (NM_001009546)	promoter-TSS (NM_001009546)	-16	NM_001009546	381204	Mm.359041	NM_001009546	ENSMUSG00000054999	Naaladl1	Gm964|Naaladasel	N-acetylated alpha-linked acidic dipeptidase-like 1	protein-coding
mm_146397.1	chr18	82910840	82910862	+	1	NA	promoter-TSS (NM_183033)	promoter-TSS (NM_183033)	-28	NM_183033	329003	Mm.326526	NM_183033	ENSMUSG00000058881	Zfp516	C330029B10Rik|D230016L03|Zfp26l|Znf516|mKIAA0222	zinc finger protein 516	protein-coding
mm_117020.1	chr13	58128543	58128567	-	1	NA	promoter-TSS (NM_029872)	promoter-TSS (NM_029872)	1	NM_029872	77134	Mm.490274	NM_029872	ENSMUSG00000007836	Hnrnpa0	1110055B05Rik|3010025E17Rik|Hnrpa0|hnRNP A0	heterogeneous nuclear ribonucleoprotein A0	protein-coding
mm_156662.1	chrX	157711566	157711576	+	1	NA	intron (NR_045569, intron 3 of 6)	Lx9|LINE|L1	12598	NR_103722	66106	Mm.140340	NM_025357	ENSMUSG00000041476	Smpx	1010001C09Rik|Csl	small muscle protein, X-linked	protein-coding
mm_70182.1	chr7	143766957	143766962	-	1	NA	promoter-TSS (NM_203492)	promoter-TSS (NM_203492)	34	NM_203492	381974	Mm.297839	NM_203492	ENSMUSG00000050276	Mrgprg	Gm1098|Mrgg	MAS-related GPR, member G	protein-coding
mm_171057.1	chr3	105955949	105955967	-	1	NA	exon (NM_009725, exon 5 of 9)	exon (NM_009725, exon 5 of 9)	-3540	NM_027432	70465	Mm.5110	NM_027432	ENSMUSG00000000561	Wdr77	2610003I18Rik|2610312E17Rik|C79984|p44/MEP50	WD repeat domain 77	protein-coding
mm_150865.1	chr19	45018115	45018153	+	1	NA	promoter-TSS (NM_001130526)	promoter-TSS (NM_001130526)	-1	NM_001130526	226154	Mm.28204	NM_145503	ENSMUSG00000035342	Lzts2	BC014695|LAPSER1|mKIAA1813	leucine zipper, putative tumor suppressor 2	protein-coding
mm_60121.1	chr7	36234217	36234225	+	1	NA	Intergenic	Intergenic	-431232	NM_177739	668501	Mm.286296	NM_177739	ENSMUSG00000044452	Zfp507	1810022O10Rik|A230056M16Rik|AL024009|AU021817|BB105092|Gm480|Znf507|mKIAA1084	zinc finger protein 507	protein-coding
mm_93791.1	chr10	120782016	120782043	-	1	NA	3' UTR (NM_177092, exon 7 of 7)	3' UTR (NM_177092, exon 7 of 7)	16297	NR_038003	70874	Mm.427286	NR_038000	ENSMUSG00000044544	4921513I03Rik	-	RIKEN cDNA 4921513I03 gene	ncRNA
mm_52002.1	chr6	92827673	92827685	+	1	NA	intron (NM_175314, intron 18 of 29)	intron (NM_175314, intron 18 of 29)	73762	NM_175314	101401	Mm.158235	NM_175314	ENSMUSG00000030022	Adamts9	1810011L16Rik|8430403M15Rik|AW743315|E030027K14Rik	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 9	protein-coding
mm_95447.1	chr11	50291118	50291136	+	1	NA	intron (NM_175334, intron 1 of 4)	intron (NM_175334, intron 1 of 4)	1209	NM_175334	103806	Mm.51116	NM_175334	ENSMUSG00000050567	Maml1	AI644666|AW743257|D930008C07Rik|Mam-1|Mam1|mKIAA0200	mastermind like 1 (Drosophila)	protein-coding
mm_50804.1	chr6	54272807	54272854	+	1	NA	promoter-TSS (NM_023543)	promoter-TSS (NM_023543)	8	NM_023543	69993	Mm.321147	NM_023543	ENSMUSG00000004633	Chn2	1700026N20Rik|4930557O16Rik|ARHGAP3|Bch	chimerin 2	protein-coding
mm_159316.1	chr3	10351313	10351313	-	1	NA	promoter-TSS (NM_001331013)	promoter-TSS (NM_001331013)	4	NM_001331015	66361	Mm.371617	NM_025512	ENSMUSG00000039795	Zfand1	2310008M20Rik|AW048890	zinc finger, AN1-type domain 1	protein-coding
mm_60286.1	chr7	43979127	43979129	+	1	NA	intron (NM_010116, intron 2 of 4)	intron (NM_010116, intron 2 of 4)	3067	NM_010116	13648	Mm.440884	NM_010116	ENSMUSG00000059042	Klk1b9	EGF-BP C|Egfbp-3|Egfbp3|KAL|Klk9|kallikrein|mGk-9	kallikrein 1-related peptidase b9	protein-coding
mm_161403.1	chr14	121592468	121592468	-	1	NA	intron (NM_001347596, intron 37 of 52)	intron (NM_001347596, intron 37 of 52)	-87214	NM_053079	56643	Mm.155618	NM_053079	ENSMUSG00000025557	Slc15a1	D630032F02|PECT1|PEPT1	solute carrier family 15 (oligopeptide transporter), member 1	protein-coding
mm_7734.1	chr1	130780013	130780020	-	1	NA	Intergenic	RMER19B|LTR|ERVK	-20886	NM_001170632	64435	Mm.31821	NM_144960	ENSMUSG00000026415	Fcamr	-	Fc receptor, IgA, IgM, high affinity	protein-coding
mm_165976.1	chr4	102507099	102507102	+	1	NA	intron (NM_019840, intron 5 of 14)	intron (NM_019840, intron 5 of 14)	-62960	NM_001177980	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_79899.1	chr9	65361050	65361056	+	1	NA	promoter-TSS (NM_001111145)	promoter-TSS (NM_001111145)	-7	NM_001111145	208080	Mm.291862	NM_001111145	ENSMUSG00000086228	Ubap1l	Gm514	ubiquitin-associated protein 1-like	protein-coding
mm_55828.1	chr6	83122025	83122069	-	1	NA	promoter-TSS (NM_001083922)	promoter-TSS (NM_001083922)	-586	NM_001083922	22377	Mm.1109	NM_016757	ENSMUSG00000030035	Wbp1	AI255152	WW domain binding protein 1	protein-coding
mm_143865.1	chr17	84186670	84186691	-	1	NA	exon (NM_001001806, exon 2 of 2)	exon (NM_001001806, exon 2 of 2)	1267	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_137833.1	chr17	30845710	30845710	+	1	NA	intron (NM_013811, intron 88 of 92)	intron (NM_013811, intron 88 of 92)	-56157	NM_021332	14652	Mm.390969	NM_021332	ENSMUSG00000024027	Glp1r	GLP-1R|GLP1Rc	glucagon-like peptide 1 receptor	protein-coding
mm_5005.1	chr1	191977402	191977445	+	1	NA	promoter-TSS (NM_001303132)	promoter-TSS (NM_001303132)	53	NM_023727	74023	Mm.274393	NM_023727	ENSMUSG00000049353	Rd3	3322402L07Rik|rd-3|rd3	retinal degeneration 3	protein-coding
mm_162943.1	chr10	128805331	128805351	-	1	NA	promoter-TSS (NM_178066)	promoter-TSS (NM_178066)	-335	NM_028873	74330	Mm.296915	NM_028873	ENSMUSG00000025354	Dnajc14	5730551F12Rik|DNAJ|DRIP78|HDJ3|LIP6	DnaJ heat shock protein family (Hsp40) member C14	protein-coding
mm_97566.1	chr11	78936492	78936499	+	1	NA	intron (NM_001313921, intron 6 of 25)	intron (NM_001313921, intron 6 of 25)	11204	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_145028.1	chr18	39174871	39174916	+	1	NA	intron (NM_175164, intron 11 of 22)	B4A|SINE|B4	181748	NM_175164	71302	Mm.329396	NM_175164	ENSMUSG00000036452	Arhgap26	1810044B20Rik|2610010G17Rik|4933432P15Rik|AI853435|mKIAA0621	Rho GTPase activating protein 26	protein-coding
mm_170100.1	chr17	39843240	39843243	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	244	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_17611.1	chr2	30924914	30924954	-	1	NA	Intergenic	Intergenic	-21637	NM_022415	64292	Mm.28768	NM_022415	ENSMUSG00000050737	Ptges	2410099E23Rik|D2Ertd369e|Pges|mPGES|mPGES-1	prostaglandin E synthase	protein-coding
mm_4359.1	chr1	171917877	171917883	+	1	NA	intron (NM_001347187, intron 1 of 7)	intron (NM_001347187, intron 1 of 7)	343	NM_030710	30925	Mm.486404	NM_030710	ENSMUSG00000015314	Slamf6	KAL1|KAL1b|Ly108|NTB-A|NTBA|SF2000	SLAM family member 6	protein-coding
mm_90778.1	chr10	6980066	6980068	-	1	NA	intron (NM_001039652, intron 4 of 5)	intron (NM_001039652, intron 4 of 5)	214	NM_001347225	320495	Mm.331674	NM_001033391	ENSMUSG00000064065	Ipcef1	A130090K04Rik	interaction protein for cytohesin exchange factors 1	protein-coding
mm_8297.1	chr1	143702783	143702797	-	1	NA	5' UTR (NM_145991, exon 1 of 17)	5' UTR (NM_145991, exon 1 of 17)	103	NM_145991	214498	Mm.156727	NM_145991	ENSMUSG00000026361	Cdc73	8430414L16Rik|C130030P16Rik|C81219|Hrpt2	cell division cycle 73, Paf1/RNA polymerase II complex component	protein-coding
mm_154916.1	chrX	21715078	21715092	+	1	NA	5' UTR (NM_020049, exon 1 of 14)	5' UTR (NM_020049, exon 1 of 14)	185	NM_020049	56774	Mm.253984	NM_020049	ENSMUSG00000031089	Slc6a14	1110007A17Rik|9030613J17Rik|ATB0plus|CATB0plus	solute carrier family 6 (neurotransmitter transporter), member 14	protein-coding
mm_123821.1	chr14	70599833	70599887	-	1	NA	promoter-TSS (NM_194345)	promoter-TSS (NM_194345)	-25	NM_194345	239170	Mm.247582	NM_194345	ENSMUSG00000022095	Fam160b2	G430067P06Rik|Rai16	family with sequence similarity 160, member B2	protein-coding
mm_21855.1	chr2	165879732	165879748	-	1	NA	intron (NM_027230, intron 1 of 23)	intron (NM_027230, intron 1 of 23)	-1303	NM_001291158	228880	Mm.227598	NM_027230	ENSMUSG00000039671	Zmynd8	1110013E22Rik|2010005I16Rik|3632413B07Rik|AI316811|AL024039|Prkcbp1|RACK7	zinc finger, MYND-type containing 8	protein-coding
mm_93105.1	chr10	91045933	91045936	-	1	NA	intron (NM_009684, intron 14 of 26)	L1_Mur3|LINE|L1	36809	NM_001042558	11783	Mm.220289	NM_009684	ENSMUSG00000019979	Apaf1	6230400I06Rik|Apaf-1|Apaf1l|fog|mKIAA0413	apoptotic peptidase activating factor 1	protein-coding
mm_140892.1	chr17	23998095	23998109	-	1	NA	promoter-TSS (NM_133731)	promoter-TSS (NM_133731)	-2	NM_133731	70835	Mm.157351	NM_133731	ENSMUSG00000045027	Prss22	4733401N09Rik|BSSP-4|SP001LA	protease, serine 22	protein-coding
mm_145817.1	chr18	65431013	65431037	+	1	NA	promoter-TSS (NM_172833)	promoter-TSS (NM_172833)	28	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_109547.1	chr12	111698634	111698640	+	1	NA	Intergenic	Intergenic	14316	NM_001324481	70369	Mm.44239	NM_027404	ENSMUSG00000049792	Bag5	1600025G07Rik|4930405J06Rik|Bag-5	BCL2-associated athanogene 5	protein-coding
mm_116904.1	chr13	55432259	55432265	-	1	NA	Intergenic	L1MA4|LINE|L1	-5458	NM_021489	58992	Mm.42224	NM_021489	ENSMUSG00000021492	F12	FXII|HAF	coagulation factor XII (Hageman factor)	protein-coding
mm_13993.1	chr2	121867084	121867159	+	1	NA	promoter-TSS (NM_001205371)	promoter-TSS (NM_001205371)	151	NM_001205369	319996	Mm.292109	NM_177054	ENSMUSG00000060227	Casc4	D130060C09Rik|VGFG2573	cancer susceptibility candidate 4	protein-coding
mm_45381.1	chr5	66131969	66131999	-	1	NA	intron (NM_001127382, intron 2 of 7)	intron (NM_001127382, intron 2 of 7)	18994	NM_001291226	245945	Mm.36863	NM_139065	ENSMUSG00000070780	Rbm47	9530077J19Rik	RNA binding motif protein 47	protein-coding
mm_87991.1	chr10	64686470	64686471	+	1	NA	intron (NM_177612, intron 13 of 17)	ORR1D2|LTR|ERVL-MaLR	-596215	NM_178678	216028	Mm.431318	NM_178678	ENSMUSG00000042846	Lrrtm3	9630044H04Rik	leucine rich repeat transmembrane neuronal 3	protein-coding
mm_19682.1	chr2	103454699	103454707	-	1	NA	3' UTR (NM_009804, exon 13 of 13)	3' UTR (NM_009804, exon 13 of 13)	30450	NM_009804	12359	Mm.4215	NM_009804	ENSMUSG00000027187	Cat	2210418N07|Cas-1|Cas1|Cs-1	catalase	protein-coding
mm_74143.1	chr8	123254293	123254317	+	1	NA	promoter-TSS (NM_028200)	promoter-TSS (NM_028200)	-83	NM_028200	72325	Mm.276193	NM_028200	ENSMUSG00000001062	Vps9d1	1300018I17Rik|2410004N05Rik|5DOS1|Vsp9d1	VPS9 domain containing 1	protein-coding
mm_49472.1	chr6	29526091	29526158	+	1	NA	promoter-TSS (NM_012057)	promoter-TSS (NM_012057)	-501	NM_001311083	27056	Mm.6479	NM_012057	ENSMUSG00000029771	Irf5	AW491843|mirf5	interferon regulatory factor 5	protein-coding
mm_167955.1	chrX	140998787	140998805	+	1	NA	Intergenic	Intergenic	-42085	NM_001164177	53380	Mm.17640	NM_016883	ENSMUSG00000031429	Psmd10	AW554874	proteasome (prosome, macropain) 26S subunit, non-ATPase, 10	protein-coding
mm_23045.1	chr3	34826606	34826646	+	1	NA	Intergenic	Intergenic	54551	NR_110488	102638436	Mm.261793	NR_110488	ENSMUSG00000106519	Gm38509	Peril	predicted gene, 38509	ncRNA
mm_17179.1	chr2	25363489	25363521	-	1	NA	intron (NM_001033293, intron 5 of 8)	intron (NM_001033293, intron 5 of 8)	2121	NM_001033293	227620	Mm.33797	NM_001033293	ENSMUSG00000026956	Uap1l1	5730445F03Rik	UDP-N-acteylglucosamine pyrophosphorylase 1-like 1	protein-coding
mm_78458.1	chr9	32372484	32372500	+	1	NA	promoter-TSS (NM_019659)	promoter-TSS (NM_019659)	74	NM_019659	56379	Mm.390168	NM_019659	ENSMUSG00000041248	Kcnj1	Kir1.1|ROMK|Romk2	potassium inwardly-rectifying channel, subfamily J, member 1	protein-coding
mm_72250.1	chr8	75093613	75093629	+	1	NA	promoter-TSS (NM_010442)	promoter-TSS (NM_010442)	3	NM_010442	15368	Mm.276389	NM_010442	ENSMUSG00000005413	Hmox1	D8Wsu38e|HO-1|HO1|Hemox|Hmox|Hsp32	heme oxygenase 1	protein-coding
mm_95403.1	chr11	49826716	49826725	+	1	NA	intron (NM_013529, intron 13 of 18)	intron (NM_013529, intron 13 of 18)	-20031	NM_001163671	26420	Mm.68933	NM_016961	ENSMUSG00000020366	Mapk9	AI851083|JNK2|Prkm9|p54aSAPK	mitogen-activated protein kinase 9	protein-coding
mm_69572.1	chr7	135700896	135700902	-	1	NA	exon (NM_001081117, exon 12 of 14)	exon (NM_001081117, exon 12 of 14)	15480	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_60363.1	chr7	44441968	44441972	+	1	NA	promoter-TSS (NM_198250)	promoter-TSS (NM_198250)	-517	NM_198250	272381	Mm.44173	NM_198250	ENSMUSG00000047085	Lrrc4b	A830007M12|Lrig4	leucine rich repeat containing 4B	protein-coding
mm_121383.1	chr14	118953153	118953166	+	1	NA	exon (NM_008929, exon 2 of 12)	exon (NM_008929, exon 2 of 12)	15227	NM_008929	100037258	Mm.12616	NM_008929	ENSMUSG00000022136	Dnajc3	AA408985|AU067833|Dnajc3a|Dnajc3b|Prkri|mp58|p58|p58IPK	DnaJ heat shock protein family (Hsp40) member C3	protein-coding
mm_111929.1	chr12	108885884	108885891	-	1	NA	intron (NM_011710, intron 2 of 10)	intron (NM_011710, intron 2 of 10)	7311	NM_001164488	22375	Mm.38433	NM_011710	ENSMUSG00000021266	Wars	TrpRS|WRS	tryptophanyl-tRNA synthetase	protein-coding
mm_8144.1	chr1	136345968	136345983	-	1	NA	5' UTR (NM_001081360, exon 1 of 19)	5' UTR (NM_001081360, exon 1 of 19)	129	NM_001081360	67886	Mm.144143	NM_001081360	ENSMUSG00000041570	Camsap2	1600013L13Rik|4930541M15Rik|Camsap1l1|mKIAA1078	calmodulin regulated spectrin-associated protein family, member 2	protein-coding
mm_56165.1	chr6	87993455	87993457	-	1	NA	Intergenic	B1_Mm|SINE|Alu	11773	NR_026990	434064	Mm.371796	NR_026990	ENSMUSG00000084950	Gm5577	EG434064	predicted gene 5577	ncRNA
mm_159847.1	chr5	136373288	136373288	-	1	NA	intron (NM_001291239, intron 5 of 22)	intron (NM_001291239, intron 5 of 22)	2515	NR_030500	723975		NR_030500	ENSMUSG00000106479	Mir721	Mirn721|miRY|mir-721|mmu-mir-721	microRNA 721	ncRNA
mm_126784.1	chr15	86202819	86202834	+	1	NA	Intergenic	Intergenic	-11633	NM_145476	223754	Mm.28904	NM_145476	ENSMUSG00000051864	Tbc1d22a	BC023106|D15Ertd781e	TBC1 domain family, member 22a	protein-coding
mm_50730.1	chr6	52492479	52492499	+	1	NA	promoter-TSS (NR_046049)	promoter-TSS (NR_046049)	38	NR_046049	74304	Mm.490579	NR_046049	ENSMUSG00000107895	1700094M24Rik	-	RIKEN cDNA 1700094M24 gene	ncRNA
mm_60240.1	chr7	43713219	43713232	+	1	NA	intron (NM_001039042, intron 1 of 5)	intron (NM_001039042, intron 1 of 5)	658	NM_001039042	626834	Mm.389891	NM_001039042	ENSMUSG00000054046	Klk13	Egfbp-2|mGk-13	kallikrein related-peptidase 13	protein-coding
mm_138213.1	chr17	34306649	34306655	+	1	NA	intron (NM_010382, intron 1 of 5)	intron (NM_010382, intron 1 of 5)	785	NM_010382	14969	Mm.22564	NM_010382	ENSMUSG00000060586	H2-Eb1	Eb|H-2Eb|H2Eb|Ia-4|Ia4	histocompatibility 2, class II antigen E beta	protein-coding
mm_133504.1	chr16	90738191	90738212	+	1	NA	promoter-TSS (NM_029844)	promoter-TSS (NM_029844)	-123	NM_029844	77037	Mm.22455	NM_029844	ENSMUSG00000039956	Mrap	1110025G12Rik|Falp|ORF61	melanocortin 2 receptor accessory protein	protein-coding
mm_9939.1	chr1	190170179	190170212	-	1	NA	intron (NM_008937, intron 1 of 4)	intron (NM_008937, intron 1 of 4)	485	NM_008937	19130	Mm.132579	NM_008937	ENSMUSG00000010175	Prox1	A230003G05Rik	prospero homeobox 1	protein-coding
mm_24575.1	chr3	93444667	93444669	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	2338	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_130186.1	chr15	93575170	93575201	-	1	NA	intron (NM_001033217, intron 1 of 7)	B4|SINE|B4	20706	NM_001033217	106042	Mm.150314	NM_001033217	ENSMUSG00000036158	Prickle1	1110058P22Rik|AW215793|Prickle|b2b019Clo|mpk1	prickle planar cell polarity protein 1	protein-coding
mm_21967.1	chr2	167300904	167300917	-	1	NA	3' UTR (NM_019835, exon 9 of 9)	3' UTR (NM_019835, exon 9 of 9)	48268	NM_019835	56336	Mm.200886	NM_019835	ENSMUSG00000017929	B4galt5	9430078I07Rik|AW049941|AW539721	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 5	protein-coding
mm_168023.1	chrY	90738154	90738195	+	1	NA	Intergenic	IMPB_01|Satellite|Satellite	16876	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_76567.1	chr8	88650124	88650139	-	1	NA	intron (NM_145857, intron 1 of 12)	intron (NM_145857, intron 1 of 12)	2784	NM_145857	257632	Mm.222633	NM_145857	ENSMUSG00000055994	Nod2	ACUG|BLAU|CD|Card15|F830032C23Rik|IBD1|Nlrc2	nucleotide-binding oligomerization domain containing 2	protein-coding
mm_123618.1	chr14	68120890	68120900	-	1	NA	exon (NM_008691, exon 3 of 3)	exon (NM_008691, exon 3 of 3)	-2857	NR_045897	100043072	Mm.242832	NR_045897		A230070E04Rik	Gm4210	RIKEN cDNA A230070E04 gene	ncRNA
mm_122381.1	chr14	40893309	40893319	-	1	NA	promoter-TSS (NM_177816)	promoter-TSS (NM_177816)	-349	NM_177816	328381	Mm.235694	NM_177816	ENSMUSG00000037833	Sh2d4b	A430109M18Rik|D030001E08	SH2 domain containing 4B	protein-coding
mm_81851.1	chr9	118629184	118629185	+	1	NA	intron (NM_133721, intron 3 of 27)	intron (NM_133721, intron 3 of 27)	22475	NM_133721	104099	Mm.335520	NM_133721	ENSMUSG00000039115	Itga9	(alpha)9|2610002H11Rik|6720458D17Rik|AI461869|D130073C02|D9Ertd428e	integrin alpha 9	protein-coding
mm_28339.1	chr3	89393136	89393192	-	1	NA	promoter-TSS (NM_009565)	promoter-TSS (NM_009565)	39	NM_009565	22724	Mm.262184	NM_009565	ENSMUSG00000028042	Zbtb7b	Thpok|Zfp67|c-Krox	zinc finger and BTB domain containing 7B	protein-coding
mm_15782.1	chr2	164334293	164334304	+	1	NA	TTS (NM_009301)	TTS (NM_009301)	1533	NM_009301	20944	Mm.140154	NM_009301	ENSMUSG00000017004	Svs5	BB115186|Semg1|Svp-1|Svp1|Svp5	seminal vesicle secretory protein 5	protein-coding
mm_147773.1	chr18	61484601	61484613	-	1	NA	promoter-TSS (NR_045419)	promoter-TSS (NR_045419)	0	NR_045419	442846	Mm.417648	NR_045419		A530050N04Rik	-	RIKEN cDNA A530050N04 gene	ncRNA
mm_106386.1	chr11	118513342	118513350	-	1	NA	exon (NM_001039167, exon 5 of 15)	exon (NM_001039167, exon 5 of 15)	36386	NM_172573	217364	Mm.473963	NM_172573	ENSMUSG00000033857	Engase	C130099A03|D230014K01Rik	endo-beta-N-acetylglucosaminidase	protein-coding
mm_128294.1	chr15	37234399	37234415	-	1	NA	intron (NM_026496, intron 1 of 15)	CpG	1371	NM_026496	252973	Mm.244612	NM_026496	ENSMUSG00000022286	Grhl2	0610015A08Rik|BOM|Tcfcp2l3|clft3	grainyhead-like 2 (Drosophila)	protein-coding
mm_14241.1	chr2	127838785	127838799	+	1	NA	Intergenic	Intergenic	-6933	NM_009772	12235	Mm.2185	NM_009772	ENSMUSG00000027379	Bub1	AL022991|Bub1a|C80208|D2Xrf87	BUB1, mitotic checkpoint serine/threonine kinase	protein-coding
mm_135481.1	chr16	46008900	46008903	-	1	NA	intron (NM_001134480, intron 1 of 3)	intron (NM_001134480, intron 1 of 3)	1512	NM_001134480	433022	Mm.380993	NM_001134480	ENSMUSG00000087141	Plcxd2	AW494639|EG433022	phosphatidylinositol-specific phospholipase C, X domain containing 2	protein-coding
mm_83102.1	chr9	40339581	40339612	-	1	NA	intron (NM_172768, intron 2 of 19)	intron (NM_172768, intron 2 of 19)	6124	NR_040728	73558	Mm.398307	NR_040728		1700110K17Rik	-	RIKEN cDNA 1700110K17 gene	ncRNA
mm_1417.1	chr1	67159434	67159471	+	1	NA	intron (NM_001080809, intron 11 of 37)	intron (NM_001080809, intron 11 of 37)	36425	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_157778.1	chrX	73786853	73786871	-	1	NA	promoter-TSS (NM_008323)	promoter-TSS (NM_008323)	35	NM_008323	15929	Mm.14825	NM_008323	ENSMUSG00000002010	Idh3g	-	isocitrate dehydrogenase 3 (NAD+), gamma	protein-coding
mm_54763.1	chr6	41218597	41218608	-	1	NA	Intergenic	Intergenic	-83670	NM_011646	22074	Mm.383263	NM_011646	ENSMUSG00000054106	Try4	0910001B19Rik|Td	trypsin 4	protein-coding
mm_34297.1	chr4	141664188	141664231	+	1	NA	promoter-TSS (NM_001033150)	promoter-TSS (NM_001033150)	-94	NM_001033150	69582	Mm.33220	NM_001033150	ENSMUSG00000028917	Plekhm2	2310034J19Rik|AI854247|mKIAA0842	pleckstrin homology domain containing, family M (with RUN domain) member 2	protein-coding
mm_65875.1	chr7	29518543	29518565	-	1	NA	Intergenic	CpG	-13094	NM_001081028	74206	Mm.447042	NM_001081028	ENSMUSG00000030583	Sipa1l3	2610511M17Rik	signal-induced proliferation-associated 1 like 3	protein-coding
mm_51256.1	chr6	71926080	71926110	+	1	NA	intron (NM_009088, intron 7 of 33)	intron (NM_009088, intron 7 of 33)	17042	NM_009088	20019	Mm.135581	NM_009088	ENSMUSG00000049553	Polr1a	194kDa|3010014K16Rik|RPA194|Rpo1-4|mRPA1	polymerase (RNA) I polypeptide A	protein-coding
mm_35725.1	chr4	44710649	44710672	-	1	NA	promoter-TSS (NM_008782)	promoter-TSS (NM_008782)	-220	NM_008782	18507	Mm.439659	NM_008782	ENSMUSG00000014030	Pax5	BSAP|EBB-1|KLP|Pax-5	paired box 5	protein-coding
mm_72719.1	chr8	85036887	85036902	+	1	NA	promoter-TSS (NM_145390)	promoter-TSS (NM_145390)	-21	NM_145390	212999	Mm.220357	NM_145390	ENSMUSG00000031691	Tnpo2	1110034O24Rik|AA414969|AI464345|AI852433|IPO3|Knpb2b|Kpnb2b|TRN2	transportin 2 (importin 3, karyopherin beta 2b)	protein-coding
mm_112751.1	chr13	19341966	19341987	+	1	NA	Intergenic	Intergenic	53837	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_42745.1	chr5	120753835	120753860	+	1	NA	3' UTR (NM_145226, exon 16 of 16)	3' UTR (NM_145226, exon 16 of 16)	-3999	NM_001347448	246728	Mm.260926	NM_145227	ENSMUSG00000032690	Oas2	Oasl11	2'-5' oligoadenylate synthetase 2	protein-coding
mm_39521.1	chr5	21258029	21258062	+	1	NA	intron (NM_175437, intron 19 of 30)	intron (NM_175437, intron 19 of 30)	71778	NM_175437	212167	Mm.121705	NM_175437	ENSMUSG00000039934	Gsap	A530088I07Rik|Pion	gamma-secretase activating protein	protein-coding
mm_138182.1	chr17	34267548	34267568	+	1	NA	exon (NM_207105, exon 3 of 6)	exon (NM_207105, exon 3 of 6)	4331	NM_207105	14961	Mm.254067	NM_207105	ENSMUSG00000073421	H2-Ab1	AI845868|Abeta|H-2Ab|H2-Ab|I-Abeta|IAb|Ia-2|Ia2|Rmcs1	histocompatibility 2, class II antigen A, beta 1	protein-coding
mm_7724.1	chr1	130715773	130715825	-	1	NA	promoter-TSS (NM_008825)	promoter-TSS (NM_008825)	22	NR_027859	18640	Mm.249861	NM_008825	ENSMUSG00000026409	Pfkfb2	4930568D07Rik	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2	protein-coding
mm_23187.1	chr3	40950403	40950418	+	1	NA	promoter-TSS (NM_001040399)	promoter-TSS (NM_001040399)	-221	NM_001040399	214048	Mm.46782	NM_027663	ENSMUSG00000025762	Larp1b	1700108L22Rik|4933421B21Rik|AA690246|Larp2	La ribonucleoprotein domain family, member 1B	protein-coding
mm_77529.1	chr8	123013242	123013272	-	1	NA	intron (NM_001081379, intron 1 of 12)	intron (NM_001081379, intron 1 of 12)	29027	NR_037865	77087	Mm.31567	NM_001081379	ENSMUSG00000035569	Ankrd11	2410104C19Rik|3010027A04Rik|6330578C09Rik|9530048I21Rik|AA930108|Gm176|Yod	ankyrin repeat domain 11	protein-coding
mm_90386.1	chr10	127290787	127290803	+	1	NA	promoter-TSS (NM_001290183)	promoter-TSS (NM_001290183)	2	NM_001290183	13198	Mm.110220	NM_007837	ENSMUSG00000025408	Ddit3	CHOP-10|CHOP10|chop|gadd153	DNA-damage inducible transcript 3	protein-coding
mm_105525.1	chr11	106300501	106300518	-	1	NA	exon (NM_008117, exon 5 of 5)	exon (NM_008117, exon 5 of 5)	1387	NM_008117	14599	Mm.343934	NM_008117	ENSMUSG00000020713	Gh	Gh1|Ghb1	growth hormone	protein-coding
mm_49677.1	chr6	32050267	32050278	+	1	NA	promoter-TSS (NM_029587)	promoter-TSS (NM_029587)	-16	NM_029587	76382	Mm.23510	NM_029587	ENSMUSG00000029766	1700012A03Rik	AI429084	RIKEN cDNA 1700012A03 gene	protein-coding
mm_89115.1	chr10	84756034	84756047	+	1	NA	promoter-TSS (NM_001024918)	promoter-TSS (NM_001024918)	-8	NM_001024918	71137	Mm.79070	NM_027689	ENSMUSG00000020037	Rfx4	4933412G19Rik|NYD-sp10	regulatory factor X, 4 (influences HLA class II expression)	protein-coding
mm_138197.1	chr17	34291819	34291828	+	1	NA	Intergenic	Intergenic	-4052	NM_010378	14960	Mm.235338	NM_010378	ENSMUSG00000036594	H2-Aa	Aalpha|H-2Aa|H2Aa|I-Aalpha|IAalpha|Ia-1|Ia1	histocompatibility 2, class II antigen A, alpha	protein-coding
mm_60989.1	chr7	49160728	49160768	+	1	NA	intron (NM_001111016, intron 2 of 38)	intron (NM_001111016, intron 2 of 38)	-85441	NM_175272	78286	Mm.333881	NM_175272	ENSMUSG00000052512	Nav2	5330421F07Rik|AU067780|BQ960892|HELAD1|POMFIL2|RAINB1|RAINB2|Unc53H2|mKIAA3015	neuron navigator 2	protein-coding
mm_17638.1	chr2	31142020	31142028	-	1	NA	promoter-TSS (NM_019406)	promoter-TSS (NM_019406)	-16	NM_001038700	14269	Mm.52297	NM_019406	ENSMUSG00000075415	Fnbp1	1110057E06Rik|2210010H06Rik|FBP1|Fbp17	formin binding protein 1	protein-coding
mm_107492.1	chr12	38783489	38783495	+	1	NA	promoter-TSS (NM_001163154)	promoter-TSS (NM_001163154)	-219	NM_001163154	14009	Mm.4866	NM_007960	ENSMUSG00000004151	Etv1	ER81|Etsrp81	ets variant 1	protein-coding
mm_114632.1	chr13	76384079	76384089	+	1	NA	promoter-TSS (NM_030174)	promoter-TSS (NM_030174)	-877	NM_030174	78771	Mm.316249	NM_030174	ENSMUSG00000021596	Mctp1	2810465F10Rik	multiple C2 domains, transmembrane 1	protein-coding
mm_82364.1	chr9	14500508	14500526	-	1	NA	promoter-TSS (NM_023153)	promoter-TSS (NM_023153)	-35	NM_173433	244694	Mm.240457	NM_173433	ENSMUSG00000053914	Kdm4d	4932416A15|Jmjd2d	lysine (K)-specific demethylase 4D	protein-coding
mm_55535.1	chr6	70744007	70744017	-	1	NA	Intergenic	Intergenic	48163	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_144346.1	chr18	15194469	15194483	+	1	NA	Intergenic	MLT1H|LTR|ERVL-MaLR	-43030	NM_134112	106931	Mm.329299	NM_134112	ENSMUSG00000036225	Kctd1	4933402K10Rik|AI661543|AW553000	potassium channel tetramerisation domain containing 1	protein-coding
mm_44238.1	chr5	5265968	5266031	-	1	NA	promoter-TSS (NM_001310448)	promoter-TSS (NM_001310448)	69	NM_001310448	18647	Mm.389061	NM_011074	ENSMUSG00000028926	Cdk14	Pftk1|mKIAA0834	cyclin-dependent kinase 14	protein-coding
mm_154246.1	chr19	60766522	60766533	-	1	NA	exon (NM_010123, exon 19 of 22)	exon (NM_010123, exon 19 of 22)	7858	NR_034047	100217439		NR_034047		Snora19	MBI-51	small nucleolar RNA, H/ACA box 19	snoRNA
mm_39753.1	chr5	29735740	29735751	+	1	NA	promoter-TSS (NM_001037941)	promoter-TSS (NM_001037941)	-153	NM_001037940	23950	Mm.290110	NM_011847	ENSMUSG00000029131	Dnajb6	Mrj|mDj4	DnaJ heat shock protein family (Hsp40) member B6	protein-coding
mm_92973.1	chr10	86491892	86491905	-	1	NA	intron (NM_001164495, intron 1 of 6)	intron (NM_001164495, intron 1 of 6)	6998	NM_001164495	27204	Mm.394931	NM_013722	ENSMUSG00000059602	Syn3	-	synapsin III	protein-coding
mm_39408.1	chr5	14521604	14521615	+	1	NA	exon (NM_011995, exon 2 of 25)	exon (NM_011995, exon 2 of 25)	6691	NM_001110796	26875	Mm.146275	NM_011995	ENSMUSG00000061601	Pclo	Acz|Pico	piccolo (presynaptic cytomatrix protein)	protein-coding
mm_129374.1	chr15	78120012	78120033	-	1	NA	promoter-TSS (NM_007583)	promoter-TSS (NM_007583)	-742	NM_007583	12300	Mm.277338	NM_007583	ENSMUSG00000019146	Cacng2	AW060990|B230105C07Rik|B930041E13Rik|stargazer|stargazin|stg|wag|waggler	calcium channel, voltage-dependent, gamma subunit 2	protein-coding
mm_8920.1	chr1	163314114	163314123	-	1	NA	promoter-TSS (NM_175686)	promoter-TSS (NM_175686)	-468	NM_175686	18933	Mm.288642	NM_011127	ENSMUSG00000026586	Prrx1	A230024N07Rik|AA755424|AI385634|AI843499|K-2|Pmx|Pmx1|Prx1|mHox	paired related homeobox 1	protein-coding
mm_108854.1	chr12	98628127	98628202	+	1	NA	promoter-TSS (NM_178914)	promoter-TSS (NM_178914)	22	NM_001289574	104871	Mm.210053	NM_178914	ENSMUSG00000021007	Spata7	AI661438|B230306G18Rik|HSD3	spermatogenesis associated 7	protein-coding
mm_68998.1	chr7	126676367	126676383	-	1	NA	promoter-TSS (NM_133670)	promoter-TSS (NM_133670)	-18	NM_133670	20887	Mm.368982	NM_133670	ENSMUSG00000030711	Sult1a1	AI266890|PST|ST1A1|Stp|Stp1	sulfotransferase family 1A, phenol-preferring, member 1	protein-coding
mm_122782.1	chr14	54410252	54410262	-	1	NA	promoter-TSS (NM_001253680)	promoter-TSS (NM_001253680)	-785	NM_001253680	20540	Mm.142455	NM_011405	ENSMUSG00000000958	Slc7a7	AI790233|my+lat1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 7	protein-coding
mm_110971.1	chr12	76962046	76962056	-	1	NA	5' UTR (NM_001146176, exon 1 of 4)	5' UTR (NM_001146176, exon 1 of 4)	197	NM_008558	17187	Mm.268548	NM_008558	ENSMUSG00000059436	Max	AA960152|AI875693|bHLHd4|bHLHd5|bHLHd6|bHLHd7|bHLHd8	Max protein	protein-coding
mm_29676.1	chr3	122871623	122871649	-	1	NA	Intergenic	MLTR14|LTR|ERV1	-23436	NM_007980	14079	Mm.28398	NM_007980	ENSMUSG00000023057	Fabp2	Fabpi|I-FABP	fatty acid binding protein 2, intestinal	protein-coding
mm_169654.1	chr15	55945007	55945007	-	1	NA	Intergenic	RLTR10A|LTR|ERVK	-38058	NM_016667	20649	Mm.309425	NM_016667	ENSMUSG00000060429	Sntb1	-	syntrophin, basic 1	protein-coding
mm_127690.1	chr15	102981605	102981641	+	1	NA	5' UTR (NM_008272, exon 2 of 3)	5' UTR (NM_008272, exon 2 of 3)	4591	NM_008272	15427	Mm.4765	NM_008272	ENSMUSG00000036139	Hoxc9	Hox-3.2	homeobox C9	protein-coding
mm_82674.1	chr9	22131768	22131779	-	1	NA	promoter-TSS (NM_001102404)	promoter-TSS (NM_001102404)	92	NM_001102404	11433	Mm.46354	NM_007388	ENSMUSG00000001348	Acp5	TRACP|TRAP	acid phosphatase 5, tartrate resistant	protein-coding
mm_114242.1	chr13	56625225	56625260	+	1	NA	exon (NM_009369, exon 4 of 17)	exon (NM_009369, exon 4 of 17)	15639	NM_009369	21810	Mm.14455	NM_009369	ENSMUSG00000035493	Tgfbi	68kDa|AI181842|AI747162|Beta-ig|big-h3	transforming growth factor, beta induced	protein-coding
mm_79020.1	chr9	45858625	45858630	+	1	NA	intron (NM_011792, intron 6 of 8)	PB1D10|SINE|Alu	20082	NM_011792	23821	Mm.24044	NM_011792	ENSMUSG00000032086	Bace1	ASP2|Bace|C76936	beta-site APP cleaving enzyme 1	protein-coding
mm_87736.1	chr10	60161626	60161637	+	1	NA	Intergenic	RMER17A2|LTR|ERVK	34855	NR_105871	102465546		NR_105871	ENSMUSG00000105468	Mir6906	mmu-mir-6906	microRNA 6906	ncRNA
mm_131643.1	chr16	20517001	20517072	+	1	NA	promoter-TSS (NM_007889)	promoter-TSS (NM_007889)	-28	NM_007889	13544	Mm.247259	NM_007889	ENSMUSG00000003233	Dvl3	-	dishevelled segment polarity protein 3	protein-coding
mm_74333.1	chr8	127064023	127064086	+	1	NA	promoter-TSS (NM_033620)	promoter-TSS (NM_033620)	-2	NM_033620	93742	Mm.299254	NM_033620	ENSMUSG00000025812	Pard3	AA960621|AI256638|Asip|D8Ertd580e|Par-3|Par3|Pard-3|Pard3a|Phip	par-3 family cell polarity regulator	protein-coding
mm_45199.1	chr5	52566191	52566218	-	1	NA	5' UTR (NM_144945, exon 1 of 7)	5' UTR (NM_144945, exon 1 of 7)	102	NM_001310604	246316	Mm.44721	NM_144945	ENSMUSG00000039252	Lgi2	mKIAA1916	leucine-rich repeat LGI family, member 2	protein-coding
mm_67192.1	chr7	73942449	73942477	-	1	NA	3' UTR (NM_009181, exon 6 of 6)	3' UTR (NM_009181, exon 6 of 6)	71219	NM_009181	20450	Mm.4954	NM_009181	ENSMUSG00000025789	St8sia2	AI323367|ST8SiaII|STX|Siat8b	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 2	protein-coding
mm_45710.1	chr5	84067117	84067139	-	1	NA	intron (NM_007937, intron 15 of 15)	intron (NM_007937, intron 15 of 15)	350254	NM_007937	13839	Mm.137991	NM_007937	ENSMUSG00000029245	Epha5	AI854630|AW125296|Cek7|Ehk1|Els1|Hek7|Rek7|bsk	Eph receptor A5	protein-coding
mm_20552.1	chr2	131071230	131071249	-	1	NA	exon (NM_011426, exon 18 of 21)	exon (NM_011426, exon 18 of 21)	-7425	NM_001163529	110751	Mm.108550	NM_033615	ENSMUSG00000027318	Adam33	Adaml	a disintegrin and metallopeptidase domain 33	protein-coding
mm_96278.1	chr11	62879561	62879580	+	1	NA	promoter-TSS (NM_026210)	promoter-TSS (NM_026210)	80	NM_026210	67510	Mm.9806	NM_026210	ENSMUSG00000014177	Tvp23b	1810036I24Rik|Fam18b|Fam18b1	trans-golgi network vesicle protein 23B	protein-coding
mm_8683.1	chr1	156939534	156939549	-	1	NA	promoter-TSS (NM_001159968)	promoter-TSS (NM_001159968)	85	NM_001159968	78255	Mm.28376	NM_023884	ENSMUSG00000026594	Ralgps2	1810020P17Rik|2210408F11Rik|4921528G01Rik|9130014M22Rik|AU043409|AW046161	Ral GEF with PH domain and SH3 binding motif 2	protein-coding
mm_10321.1	chr2	11250443	11250449	+	1	NA	intron (NM_008859, intron 8 of 17)	C-rich|Low_complexity|Low_complexity	78064	NM_008859	18761	Mm.329993	NM_008859	ENSMUSG00000026778	Prkcq	A130035A12Rik|AW494342|PKC-0|PKC-theta|PKCtheta|Pkcq	protein kinase C, theta	protein-coding
mm_150418.1	chr19	37263959	37263981	+	1	NA	non-coding (NR_040299, exon 1 of 3)	non-coding (NR_040299, exon 1 of 3)	125	NR_040299	77059	Mm.251476	NR_040298		4931408D14Rik	-	RIKEN cDNA 4931408D14 gene	ncRNA
mm_106260.1	chr11	117967278	117967290	-	1	NA	3' UTR (NM_007707, exon 2 of 2)	3' UTR (NM_007707, exon 2 of 2)	2082	NM_007707	12702	Mm.3468	NM_007707	ENSMUSG00000053113	Socs3	Cis3|Cish3|EF-10|Ef10|SSI-3|Ssi3	suppressor of cytokine signaling 3	protein-coding
mm_110507.1	chr12	54695787	54695797	-	1	NA	5' UTR (NM_001331162, exon 1 of 5)	5' UTR (NM_001331162, exon 1 of 5)	102	NM_001331162	66266	Mm.156440	NM_025456	ENSMUSG00000054302	Eapp	1810011O16Rik	E2F-associated phosphoprotein	protein-coding
mm_70111.1	chr7	142666820	142666842	-	1	NA	promoter-TSS (NM_001315488)	promoter-TSS (NM_001315488)	-15	NM_001315488	16002	Mm.3862	NM_010514	ENSMUSG00000048583	Igf2	AL033362|Igf-2|Igf-II|M6pr|Mpr|Peg2	insulin-like growth factor 2	protein-coding
mm_112519.1	chr13	9145379	9145391	+	1	NA	exon (NM_172585, exon 7 of 18)	exon (NM_172585, exon 7 of 18)	51504	NM_172585	217980	Mm.234944	NM_172585	ENSMUSG00000033499	Larp4b	A630096F19|AI256361|D13Wsu64e|Larp5	La ribonucleoprotein domain family, member 4B	protein-coding
mm_49652.1	chr6	30903557	30903565	+	1	NA	intron (NM_054073, intron 5 of 7)	intron (NM_054073, intron 5 of 7)	-6767	NM_017478	54160	Mm.39896	NM_017478	ENSMUSG00000025607	Copg2	AW227625|gamma-2-COP	coatomer protein complex, subunit gamma 2	protein-coding
mm_110244.1	chr12	31265133	31265147	-	1	NA	promoter-TSS (NM_008482)	promoter-TSS (NM_008482)	-154	NM_008482	16777	Mm.172674	NM_008482	ENSMUSG00000002900	Lamb1	C77966|C80098|C81607|D130003D08Rik|Lamb-1|Lamb1-1	laminin B1	protein-coding
mm_38712.1	chr4	145224851	145224866	-	1	NA	exon (NM_011610, exon 5 of 10)	exon (NM_011610, exon 5 of 10)	22012	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_149189.1	chr19	9938915	9938927	+	1	NA	Intergenic	Intergenic	-39388	NM_016692	16319	Mm.29755	NM_016692	ENSMUSG00000024660	Incenp	2700067E22Rik|AU019509|C130081E20|C77457	inner centromere protein	protein-coding
mm_929.1	chr1	55405997	55406007	+	1	NA	promoter-TSS (NM_001114663)	promoter-TSS (NM_001114663)	56	NM_001114663	227120	Mm.194183	NM_001114663	ENSMUSG00000038349	Plcl1	C230017K02Rik|PLC-L|PLC-L1|PLCE|PLCL|PLDL1|PRIP|PRIP-1	phospholipase C-like 1	protein-coding
mm_90542.1	chr10	128091577	128091595	+	1	NA	Intergenic	Intergenic	-1197	NM_054078	116848	Mm.252213	NM_054078	ENSMUSG00000040054	Baz2a	AA415431|C030005G16Rik|C78388|Tip5|Walp3|mKIAA0314	bromodomain adjacent to zinc finger domain, 2A	protein-coding
mm_122615.1	chr14	51105377	51105407	-	1	NA	3' UTR (NM_201239, exon 2 of 2)	3' UTR (NM_201239, exon 2 of 2)	9392	NM_201239	58809	Mm.202665	NM_021472	ENSMUSG00000021876	Rnase4	C730049F20Rik|Rab1	ribonuclease, RNase A family 4	protein-coding
mm_50612.1	chr6	49822712	49822727	+	1	NA	promoter-TSS (NM_023456)	promoter-TSS (NM_023456)	9	NM_023456	109648	Mm.154796	NM_023456	ENSMUSG00000029819	Npy	0710005A05Rik	neuropeptide Y	protein-coding
mm_59413.1	chr7	27121573	27121621	+	1	NA	exon (NM_007817, exon 2 of 10)	exon (NM_007817, exon 2 of 10)	1642	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_34948.1	chr4	155943825	155943883	+	1	NA	promoter-TSS (NM_001039158)	promoter-TSS (NM_001039158)	41	NM_021402	140499	Mm.371673	NM_021402	ENSMUSG00000023286	Ube2j2	1200007B18Rik|2400008G19Rik|5730472G04Rik|AL022923|NCUBE-2|Ubc6|Ubc6p	ubiquitin-conjugating enzyme E2J 2	protein-coding
mm_68668.1	chr7	118856034	118856040	-	1	NA	promoter-TSS (NM_001168218)	promoter-TSS (NM_001168218)	-39	NM_023197	66356	Mm.482278	NM_023197	ENSMUSG00000030980	Knop1	2310008H09Rik|Tsg118	lysine rich nucleolar protein 1	protein-coding
mm_121718.1	chr14	16466710	16466712	-	1	NA	intron (NM_011243, intron 3 of 7)	PB1D10|SINE|Alu	101505	NM_009409	21974	Mm.130362	NM_009409	ENSMUSG00000017485	Top2b	D230016L12Rik|Top-2	topoisomerase (DNA) II beta	protein-coding
mm_76896.1	chr8	105771255	105771268	-	1	NA	3' UTR (NM_145824, exon 14 of 14)	3' UTR (NM_145824, exon 14 of 14)	-12654	NM_027469	70575	Mm.40954	NM_027469	ENSMUSG00000013150	Gfod2	5730466C23Rik	glucose-fructose oxidoreductase domain containing 2	protein-coding
mm_154415.1	chrM	15569	15589	+	1	NA	NA	Intergenic	NA	NA								
mm_60696.1	chr7	45175299	45175308	+	1	NA	3' UTR (NM_182993, exon 12 of 12)	3' UTR (NM_182993, exon 12 of 12)	2000	NR_106022	102465638		NR_106022	ENSMUSG00000106470	Mir7055	mmu-mir-7055	microRNA 7055	ncRNA
mm_58726.1	chr7	13025735	13025743	+	1	NA	exon (NM_011588, exon 3 of 17)	exon (NM_011588, exon 3 of 17)	1587	NM_011588	21849	Mm.15701	NM_011588	ENSMUSG00000005566	Trim28	AA408787|KAP-1|KRIP-1|MommeD9|Tif1b|Tif1beta	tripartite motif-containing 28	protein-coding
mm_89430.1	chr10	91083037	91083075	+	1	NA	promoter-TSS (NM_026166)	promoter-TSS (NM_026166)	17	NM_026166	67454	Mm.252843	NM_026166	ENSMUSG00000019975	Ikbip	1200009F10Rik|1700023M03Rik|D18354|Ikip	IKBKB interacting protein	protein-coding
mm_98129.1	chr11	87405050	87405113	+	1	NA	promoter-TSS (NM_001291440)	promoter-TSS (NM_001291440)	16	NM_031386	83560	Mm.440758	NM_031386	ENSMUSG00000010342	Tex14	C85585	testis expressed gene 14	protein-coding
mm_87657.1	chr10	58480024	58480050	+	1	NA	exon (NM_011240, exon 20 of 29)	exon (NM_011240, exon 20 of 29)	-17900	NM_001162956	76138	Mm.211744	NM_001162956	ENSMUSG00000038010	Ccdc138	6230424H07Rik|BC042726	coiled-coil domain containing 138	protein-coding
mm_51024.1	chr6	65143062	65143072	+	1	NA	intron (NM_019455, intron 1 of 5)	intron (NM_019455, intron 1 of 5)	1663	NM_019455	54486	Mm.410688	NM_019455	ENSMUSG00000029919	Hpgds	H-PGDS|Ptgds2	hematopoietic prostaglandin D synthase	protein-coding
mm_142214.1	chr17	37023350	37023371	-	1	NA	promoter-TSS (NM_010814)	promoter-TSS (NM_010814)	38	NM_010814	17441	Mm.210857	NM_010814	ENSMUSG00000076439	Mog	B230317G11Rik	myelin oligodendrocyte glycoprotein	protein-coding
mm_146754.1	chr18	16767962	16768010	-	1	NA	intron (NM_007664, intron 2 of 15)	intron (NM_007664, intron 2 of 15)	41260	NM_007664	12558	Mm.257437	NM_007664	ENSMUSG00000024304	Cdh2	CDHN|N-CAD|Ncad	cadherin 2	protein-coding
mm_68041.1	chr7	101361914	101361930	-	1	NA	intron (NM_001040111, intron 1 of 33)	intron (NM_001040111, intron 1 of 33)	13853	NM_001040111	69710	Mm.277687	NM_027180	ENSMUSG00000032812	Arap1	2410002L19Rik|Centd2|mKIAA0782	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	protein-coding
mm_120838.1	chr14	75179804	75179808	+	1	NA	intron (NM_008879, intron 2 of 16)	intron (NM_008879, intron 2 of 16)	43381	NM_008879	18826	Mm.153911	NM_008879	ENSMUSG00000021998	Lcp1	AW536232|D14Ertd310e|LCP-1|Pls2|pp65	lymphocyte cytosolic protein 1	protein-coding
mm_157134.1	chrX	9453674	9453769	-	1	NA	exon (NM_007807, exon 6 of 13)	exon (NM_007807, exon 6 of 13)	15603	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_115223.1	chr13	109685995	109686018	+	1	NA	intron (NM_011056, intron 3 of 16)	intron (NM_011056, intron 3 of 16)	-217803	NR_035442	100316683		NR_035442	ENSMUSG00000084651	Mir1904	Mirn1904|mmu-mir-1904	microRNA 1904	ncRNA
mm_64771.1	chr7	4996024	4996032	-	1	NA	promoter-TSS (NM_026741)	promoter-TSS (NM_026741)	73	NM_026741	68490	Mm.76400	NM_026741	ENSMUSG00000051550	Zfp579	1110003A17Rik|Znf579	zinc finger protein 579	protein-coding
mm_123008.1	chr14	54994282	54994315	-	1	NA	intron (NM_080728, intron 1 of 40)	intron (NM_080728, intron 1 of 40)	251	NM_080728	140781	Mm.457983	NM_080728	ENSMUSG00000053093	Myh7	B-MHC|MyHC-I|Myhc-b|Myhcb|beta-MHC	myosin, heavy polypeptide 7, cardiac muscle, beta	protein-coding
mm_93918.1	chr10	127067827	127067842	-	1	NA	TTS (NM_009870)	TTS (NM_009870)	2427	NM_025982	67125	Mm.35650	NM_025982	ENSMUSG00000006736	Tspan31	2700085A14Rik|AW742554|Sas	tetraspanin 31	protein-coding
mm_115020.1	chr13	98613428	98613459	+	1	NA	Intergenic	CpG	23967	NM_026685	68344	Mm.28766	NM_026685	ENSMUSG00000046082	Tmem174	0610009B10Rik|AA986094	transmembrane protein 174	protein-coding
mm_28337.1	chr3	89387344	89387354	-	1	NA	intron (NM_009565, intron 1 of 2)	intron (NM_009565, intron 1 of 2)	-4515	NR_040403	545539	Mm.393389	NR_040403	ENSMUSG00000074466	Gm15417	ENSMUSG00000074466|OTTMUSG00000021274	predicted gene 15417	ncRNA
mm_57614.1	chr6	128138112	128138124	-	1	NA	intron (NM_175414, intron 1 of 8)	intron (NM_175414, intron 1 of 8)	5460	NM_175414	109246	Mm.21814	NM_175414	ENSMUSG00000030352	Tspan9	6720474K14Rik|9430079M16Rik|AU018597	tetraspanin 9	protein-coding
mm_46164.1	chr5	96163009	96163019	-	1	NA	Intergenic	Intergenic	-1024	NM_144910	231464	Mm.28374	NM_144910	ENSMUSG00000034724	Cnot6l	4932442K20Rik	CCR4-NOT transcription complex, subunit 6-like	protein-coding
mm_34525.1	chr4	149149993	149149996	+	1	NA	TTS (NM_001081274)	TTS (NM_001081274)	-12394	NM_027263	69928	Mm.260893	NM_027263	ENSMUSG00000073705	Apitd1	2610040C18Rik|2810407L01Rik|CENP-S	apoptosis-inducing, TAF9-like domain 1	protein-coding
mm_74022.1	chr8	121597780	121597794	+	1	NA	TTS (NM_080855)	TTS (NM_080855)	7319	NM_026160	67443	Mm.28357	NM_026160	ENSMUSG00000031812	Map1lc3b	1010001C15Rik|Atg8|LC3b|Map1lc3	microtubule-associated protein 1 light chain 3 beta	protein-coding
mm_32421.1	chr4	107097598	107097603	+	1	NA	5' UTR (NM_172873, exon 1 of 4)	5' UTR (NM_172873, exon 1 of 4)	709	NM_172873	242603	Mm.257231	NM_172873	ENSMUSG00000047636	Cdcp2	D030010E02Rik	CUB domain containing protein 2	protein-coding
mm_168151.1	chr10	39198853	39198856	+	1	NA	Intergenic	Intergenic	-35060	NM_001127376	327743	Mm.208111	NM_001127376	ENSMUSG00000062074	Wisp3	CCN6|ENSMUSG00000062074|Gm735|WISP-3	WNT1 inducible signaling pathway protein 3	protein-coding
mm_43283.1	chr5	133239569	133239572	+	1	NA	Intergenic	MTE2b|LTR|ERVL-MaLR	-697227	NM_177047	319974	Mm.409595	NM_177047	ENSMUSG00000029673	Auts2	2700063G02Rik|A730011F23Rik|D830032G16Rik	autism susceptibility candidate 2	protein-coding
mm_11863.1	chr2	48833306	48833312	+	1	NA	intron (NM_007396, intron 1 of 10)	intron (NM_007396, intron 1 of 10)	19200	NM_007396	11480	Mm.314338	NM_007396	ENSMUSG00000052155	Acvr2a	ActrIIa|Acvr2|TactrII	activin receptor IIA	protein-coding
mm_60925.1	chr7	46847129	46847150	+	1	NA	promoter-TSS (NM_001136069)	promoter-TSS (NM_001136069)	57	NM_001136069	16828	Mm.29324	NM_010699	ENSMUSG00000063229	Ldha	Ldh1|Ldhm|l7R2	lactate dehydrogenase A	protein-coding
mm_82746.1	chr9	26803662	26803668	-	1	NA	intron (NM_153803, intron 1 of 19)	intron (NM_153803, intron 1 of 19)	2752	NM_153803	244757	Mm.293696	NM_153803	ENSMUSG00000036395	Glb1l2	-	galactosidase, beta 1-like 2	protein-coding
mm_15492.1	chr2	157737426	157737490	+	1	NA	promoter-TSS (NM_025680)	promoter-TSS (NM_025680)	57	NM_025680	66642	Mm.45193	NM_025680	ENSMUSG00000027649	Ctnnbl1	5730471K09Rik|NAP|NYD-SP19|P14L	catenin, beta like 1	protein-coding
mm_123769.1	chr14	70212020	70212049	-	1	NA	Intergenic	Intergenic	-4363	NM_011366	20410	Mm.5068	NM_011366	ENSMUSG00000022091	Sorbs3	SCAM-1|SH3P3|Sh3d4|vinexin-g	sorbin and SH3 domain containing 3	protein-coding
mm_120550.1	chr14	67716346	67716359	+	1	NA	promoter-TSS (NM_175384)	promoter-TSS (NM_175384)	254	NM_001285933	105440	Mm.6720	NM_134073	ENSMUSG00000034327	Kctd9	-	potassium channel tetramerisation domain containing 9	protein-coding
mm_5024.1	chr1	193173575	193173595	+	1	NA	promoter-TSS (NM_181048)	promoter-TSS (NM_181048)	8	NM_181048	319266	Mm.482460	NM_181048	ENSMUSG00000079144	A130010J15Rik	-	RIKEN cDNA A130010J15 gene	protein-coding
mm_103982.1	chr11	84827275	84827294	-	1	NA	intron (NM_177564, intron 1 of 6)	intron (NM_177564, intron 1 of 6)	1719	NM_177564	192970	Mm.192213	NM_177564	ENSMUSG00000034449	Dhrs11	-	dehydrogenase/reductase (SDR family) member 11	protein-coding
mm_32164.1	chr4	100095878	100095889	+	1	NA	promoter-TSS (NM_013845)	promoter-TSS (NM_013845)	92	NM_001312690	26563	Mm.57252	NM_013845	ENSMUSG00000035305	Ror1	2810404D04Rik|Ntrkr1	receptor tyrosine kinase-like orphan receptor 1	protein-coding
mm_87158.1	chr10	36628236	36628248	+	1	NA	intron (NM_001253355, intron 2 of 5)	intron (NM_001253355, intron 2 of 5)	121435	NM_001253356	319415	Mm.332442	NM_001081208	ENSMUSG00000044499	Hs3st5	D930005L05Rik|Gm1151|Hs3ost5	heparan sulfate (glucosamine) 3-O-sulfotransferase 5	protein-coding
mm_115109.1	chr13	103774647	103774663	+	1	NA	Intergenic	CpG	-10073	NM_172592	218543	Mm.458176	NM_172592	ENSMUSG00000032621	Srek1	8430401B01|AI450757|AI462342|SRrp508|SRrp86|Sfrs12|Srsf12	splicing regulatory glutamine/lysine-rich protein 1	protein-coding
mm_112971.1	chr13	21286983	21286993	+	1	NA	3' UTR (NM_010343, exon 5 of 5)	3' UTR (NM_010343, exon 5 of 5)	5698	NM_010343	14780	Mm.1332	NM_010343	ENSMUSG00000004344	Gpx5	AV379049|Arep	glutathione peroxidase 5	protein-coding
mm_41351.1	chr5	90504340	90504352	+	1	NA	exon (NM_007423, exon 10 of 15)	exon (NM_007423, exon 10 of 15)	13632	NM_007423	11576	Mm.358570	NM_007423	ENSMUSG00000054932	Afp	-	alpha fetoprotein	protein-coding
mm_125184.1	chr15	32245115	32245128	+	1	NA	promoter-TSS (NR_038186)	promoter-TSS (NR_038186)	308	NM_009154	20356	Mm.260374	NM_009154	ENSMUSG00000022231	Sema5a	5930434A13|9130201M22Rik|AI464145|Semaf|semF	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A	protein-coding
mm_51108.1	chr6	67283934	67283981	+	1	NA	exon (NM_025814, exon 8 of 8)	exon (NM_025814, exon 8 of 8)	16978	NM_025814	66870	Mm.240490	NM_025814	ENSMUSG00000036371	Serbp1	1200009K13Rik|9330147J08Rik|AL022786|Pairbp1	serpine1 mRNA binding protein 1	protein-coding
mm_145357.1	chr18	56676608	56676619	+	1	NA	Intergenic	RMER17C2|LTR|ERVK	-31200	NM_010721	16906	Mm.4105	NM_010721	ENSMUSG00000024590	Lmnb1	-	lamin B1	protein-coding
mm_9993.1	chr1	191393688	191393691	-	1	NA	intron (NM_144880, intron 1 of 12)	intron (NM_144880, intron 1 of 12)	3352	NM_144880	226849	Mm.205569	NM_144880	ENSMUSG00000026626	Ppp2r5a	PR61alpha	protein phosphatase 2, regulatory subunit B', alpha	protein-coding
mm_50950.1	chr6	58644011	58644056	+	1	NA	intron (NM_011920, intron 1 of 15)	intron (NM_011920, intron 1 of 15)	47361	NM_011920	26357	Mm.333096	NM_011920	ENSMUSG00000029802	Abcg2	ABC15|ABCP|AI428558|BCRP|Bcrp1|MXR|MXR1	ATP-binding cassette, sub-family G (WHITE), member 2	protein-coding
mm_116682.1	chr13	49248183	49248184	-	1	NA	promoter-TSS (NM_025491)	promoter-TSS (NM_025491)	-20	NM_025491	66329	Mm.34308	NM_025491	ENSMUSG00000021384	Susd3	1700017I11Rik|2810440J20Rik	sushi domain containing 3	protein-coding
mm_118599.1	chr14	20695332	20695372	+	1	NA	TTS (NM_172596)	TTS (NM_172596)	384	NM_028428	73068	Mm.277552	NM_028428	ENSMUSG00000039357	Fut11	3110009G03Rik|AI317183	fucosyltransferase 11	protein-coding
mm_86420.1	chr10	3740254	3740271	+	1	NA	promoter-TSS (NM_001159942)	promoter-TSS (NM_001159942)	-115	NM_001159942	213783	Mm.150831	NM_001033253	ENSMUSG00000040624	Plekhg1	D10Ertd733e|Gm521|mKIAA1209	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	protein-coding
mm_41170.1	chr5	87979471	87979477	+	1	NA	promoter-TSS (NM_027631)	promoter-TSS (NM_027631)	23	NM_027631	70977	Mm.272787	NM_027631	ENSMUSG00000007907	Cabs1	4931407G18Rik|AI428159|Clph	calcium binding protein, spermatid specific 1	protein-coding
mm_14464.1	chr2	131234044	131234136	+	1	NA	promoter-TSS (NM_144888)	promoter-TSS (NM_144888)	27	NM_144888	228607	Mm.287226	NM_144888	ENSMUSG00000037523	Mavs	D430028G21Rik|IPS-1|Visa|cardif	mitochondrial antiviral signaling protein	protein-coding
mm_142408.1	chr17	45488376	45488391	-	1	NA	Intergenic	Intergenic	-13445	NM_027649	71020	Mm.44257	NM_027649	ENSMUSG00000023935	Spats1	1700011H05Rik|4933400B06Rik|Daip2|Ddip|Srsp1	spermatogenesis associated, serine-rich 1	protein-coding
mm_45280.1	chr5	64932892	64932904	-	1	NA	promoter-TSS (NM_030682)	promoter-TSS (NM_030682)	-199	NM_030682	21897	Mm.273024	NM_030682	ENSMUSG00000044827	Tlr1	-	toll-like receptor 1	protein-coding
mm_160575.1	chr9	58488474	58488474	+	1	NA	promoter-TSS (NM_176921)	promoter-TSS (NM_176921)	-129	NM_176921	319477	Mm.153674	NM_176921	ENSMUSG00000066607	6030419C18Rik	-	RIKEN cDNA 6030419C18 gene	protein-coding
mm_79108.1	chr9	46268750	46268755	+	1	NA	intron (NM_080434, intron 1 of 3)	intron (NM_080434, intron 1 of 3)	144	NM_080434	66113	Mm.29738	NM_080434	ENSMUSG00000032079	Apoa5	1300007O05Rik|Apoav|RAP3	apolipoprotein A-V	protein-coding
mm_82418.1	chr9	14903053	14903067	-	1	NA	intron (NM_022888, intron 1 of 4)	intron (NM_022888, intron 1 of 4)	891	NM_176807	64931	Mm.86738	NM_022888	ENSMUSG00000031933	Izumo1r	0910001L11Rik|C86255|Folbp3|Folr4|Juno	IZUMO1 receptor, JUNO	protein-coding
mm_88463.1	chr10	77564722	77564737	+	1	NA	exon (NM_008404, exon 15 of 16)	exon (NM_008404, exon 15 of 16)	-17038	NM_145925	108705	Mm.28853	NM_145925	ENSMUSG00000009291	Pttg1ip	1810010L20Rik|AI314311|AU018448|C79540	pituitary tumor-transforming 1 interacting protein	protein-coding
mm_118241.1	chr13	111796514	111796526	-	1	NA	intron (NM_011945, intron 1 of 19)	intron (NM_011945, intron 1 of 19)	12463	NM_011945	26401	Mm.15918	NM_011945	ENSMUSG00000021754	Map3k1	MAPKKK1|MEKK1|Mekk	mitogen-activated protein kinase kinase kinase 1	protein-coding
mm_16167.1	chr2	172545674	172545685	+	1	NA	Intergenic	Intergenic	-3914	NM_009335	21420	Mm.3629	NM_009335	ENSMUSG00000028640	Tfap2c	AA409384|AP2gamma|Ap-2.2|Stra2|Tcfap2c	transcription factor AP-2, gamma	protein-coding
mm_122308.1	chr14	36774497	36774501	-	1	NA	Intergenic	RLTR26B_MM|LTR|ERVK	145036	NM_001347503	72972	Mm.27621	NM_027045	ENSMUSG00000058690	Ccser2	1700012P13Rik|2900054P12Rik|AI035535|AW108503|Fam190b|Gcap14	coiled-coil serine rich 2	protein-coding
mm_16157.1	chr2	172393803	172393829	+	1	NA	promoter-TSS (NM_001276423)	promoter-TSS (NM_001276423)	22	NM_001276423	320664	Mm.210195	NM_001033538	ENSMUSG00000074570	Cass4	F730031O20Rik	Cas scaffolding protein family member 4	protein-coding
mm_142257.1	chr17	39843321	39843329	-	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	328	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_75480.1	chr8	48556008	48556088	-	1	NA	intron (NM_011857, intron 2 of 28)	CpG	118642	NM_001145937	23965	Mm.42191	NM_011857	ENSMUSG00000031561	Tenm3	2610100B16Rik|Odz1|Odz3|Ten-m3|mKIAA1455	teneurin transmembrane protein 3	protein-coding
mm_7140.1	chr1	91091627	91091635	-	1	NA	exon (NM_008515, exon 9 of 23)	exon (NM_008515, exon 9 of 23)	38187	NM_008515	16978	Mm.45039	NM_008515	ENSMUSG00000026305	Lrrfip1	AU024550|Fliiap1	leucine rich repeat (in FLII) interacting protein 1	protein-coding
mm_46506.1	chr5	105136147	105136152	-	1	NA	intron (NM_008620, intron 2 of 10)	intron (NM_008620, intron 2 of 10)	3403	NM_008620	17472	Mm.440525	NM_008620	ENSMUSG00000079363	Gbp4	AW228052|Mag-2|Mpa-2|Mpa2	guanylate binding protein 4	protein-coding
mm_17689.1	chr2	32331893	32331902	-	1	NA	intron (NM_010065, intron 10 of 20)	B1F|SINE|Alu	13437	NR_029811	387239		NR_029811	ENSMUSG00000092807	Mir199b	Mirn199b|mir-199b	microRNA 199b	ncRNA
mm_99901.1	chr11	109651460	109651470	+	1	NA	intron (NM_001313976, intron 1 of 10)	AT_rich|Low_complexity|Low_complexity	544	NM_001313976	19084	Mm.30039	NM_021880	ENSMUSG00000020612	Prkar1a	1300018C22Rik|RIalpha|Tse-1|Tse1	protein kinase, cAMP dependent regulatory, type I, alpha	protein-coding
mm_9871.1	chr1	185074176	185074177	-	1	NA	Intergenic	MER57C2|LTR|ERV1	-74627	NM_145515	226778	Mm.7445	NM_145515	ENSMUSG00000026620	Mark1	AW491150|B930025N23Rik|Emk3|Par-1c|mKIAA1477|mPar-1c	MAP/microtubule affinity regulating kinase 1	protein-coding
mm_14817.1	chr2	146834611	146834650	+	1	NA	Intergenic	CpG	-21259	NM_001033298	228730	Mm.292352	NM_001033298	ENSMUSG00000074749	Kiz	Gm114|Ncrna00153|Plk1s1	kizuna centrosomal protein	protein-coding
mm_126818.1	chr15	88751650	88751661	+	1	NA	promoter-TSS (NM_181412)	promoter-TSS (NM_181412)	-56	NM_181412	223773	Mm.396622	NM_181412	ENSMUSG00000034333	Zbed4	1700009F06Rik	zinc finger, BED type containing 4	protein-coding
mm_30165.1	chr3	144189012	144189030	-	1	NA	3' UTR (NM_010723, exon 5 of 5)	3' UTR (NM_010723, exon 5 of 5)	13311	NM_001161770	16911	Mm.29187	NM_010723	ENSMUSG00000028266	Lmo4	A730077C12Rik|Crp3|Etohi4	LIM domain only 4	protein-coding
mm_50529.1	chr6	49045410	49045425	+	1	NA	exon (NM_053110, exon 4 of 11)	exon (NM_053110, exon 4 of 11)	8899	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_92858.1	chr10	81545057	81545169	-	1	NA	promoter-TSS (NM_010301)	promoter-TSS (NM_010301)	-67	NM_010301	14672	Mm.260925	NM_010301	ENSMUSG00000034781	Gna11	Dsk7|E430025L19	guanine nucleotide binding protein, alpha 11	protein-coding
mm_135607.1	chr16	52249701	52249756	-	1	NA	3' UTR (NM_001331110, exon 15 of 15)	3' UTR (NM_001331110, exon 15 of 15)	203353	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_28544.1	chr3	92868996	92869007	-	1	NA	exon (NM_025621, exon 2 of 2)	exon (NM_025621, exon 2 of 2)	1204	NM_025621	66533	Mm.144259	NM_025621	ENSMUSG00000090314	2310050C09Rik	-	RIKEN cDNA 2310050C09 gene	protein-coding
mm_18946.1	chr2	76770489	76770502	-	1	NA	exon (NM_011652, exon 248 of 313)	exon (NM_011652, exon 248 of 313)	95180	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_143409.1	chr17	70829960	70829969	-	1	NA	Intergenic	MER45B|DNA|hAT-Tip100	16813	NM_001164077	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_29232.1	chr3	107213480	107213511	-	1	NA	exon (NM_001111143, exon 7 of 9)	exon (NM_001111143, exon 7 of 9)	8237	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_114436.1	chr13	65278840	65278866	+	1	NA	promoter-TSS (NM_178364)	promoter-TSS (NM_178364)	-1	NM_178364	170936	Mm.151546	NM_178364	ENSMUSG00000021514	Zfp369	B930030B22Rik|D230020H11Rik|NRIF2	zinc finger protein 369	protein-coding
mm_140333.1	chr17	86754180	86754193	+	1	NA	5' UTR (NM_010137, exon 1 of 16)	5' UTR (NM_010137, exon 1 of 16)	322	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_95210.1	chr11	43598669	43598689	+	1	NA	exon (NM_008375, exon 2 of 4)	exon (NM_008375, exon 2 of 4)	2883	NM_008375	16204	Mm.142716	NM_008375	ENSMUSG00000020405	Fabp6	GT|I-15P|I-BABP|ILBP|ILBP3|Illbp	fatty acid binding protein 6, ileal (gastrotropin)	protein-coding
mm_4896.1	chr1	189728331	189728337	+	1	NA	promoter-TSS (NM_008976)	promoter-TSS (NM_008976)	66	NM_008976	19250	Mm.4498	NM_008976	ENSMUSG00000026604	Ptpn14	C130080N23Rik|OTTMUSG00000022087|PTP36	protein tyrosine phosphatase, non-receptor type 14	protein-coding
mm_21234.1	chr2	156108029	156108032	-	1	NA	intron (NM_029397, intron 1 of 2)	B1_Mur3|SINE|Alu	3935	NM_170598	75710	Mm.27660	NM_029397	ENSMUSG00000089824	Rbm12	5730420G12Rik|9430070C08Rik|AI852903|SWAN|mKIAA0765	RNA binding motif protein 12	protein-coding
mm_100784.1	chr11	4833078	4833084	-	1	NA	promoter-TSS (NM_001252253)	promoter-TSS (NM_001252253)	54	NM_001252253	18016	Mm.297109	NM_010898	ENSMUSG00000009073	Nf2	merlin	neurofibromin 2	protein-coding
mm_63502.1	chr7	127840998	127841018	+	1	NA	promoter-TSS (NM_009294)	promoter-TSS (NM_009294)	-800	NM_009294	20909	Mm.24867	NM_009294	ENSMUSG00000030805	Stx4a	Stx4|Syn-4|Syn4	syntaxin 4A (placental)	protein-coding
mm_170452.1	chr18	85378070	85378076	-	1	NA	Intergenic	IAPLTR1_Mm|LTR|ERVK	-426549	NM_025969	67105	Mm.250617	NM_025969	ENSMUSG00000024645	Timm21	1700034H14Rik|2700002I20Rik	tranlocase of inner mitochondrial membrane 21	protein-coding
mm_31039.1	chr4	41045513	41045544	+	1	NA	intron (NM_007473, intron 2 of 7)	intron (NM_007473, intron 2 of 7)	2608	NM_007473	11832	Mm.8728	NM_007473	ENSMUSG00000028427	Aqp7	AQP7L|AQPap	aquaporin 7	protein-coding
mm_169928.1	chr16	57391589	57391591	-	1	NA	intron (NM_001040397, intron 1 of 4)	LSU-rRNA_Hsa|rRNA|rRNA	38313	NM_001040397	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding
mm_50253.1	chr6	42585351	42585375	+	1	NA	Intergenic	Intergenic	12009	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_25239.1	chr3	103914100	103914118	+	1	NA	promoter-TSS (NM_172684)	promoter-TSS (NM_172684)	-11	NM_172684	229675	Mm.29366	NM_172684	ENSMUSG00000044098	Rsbn1	C230004D03Rik|E330004N01|Rosbin|Rsbn|Rsbp|mKIAA3002	rosbin, round spermatid basic protein 1	protein-coding
mm_26283.1	chr3	142505757	142505765	+	1	NA	intron (NM_153564, intron 7 of 10)	intron (NM_153564, intron 7 of 10)	8827	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_148540.1	chr19	4609921	4609940	+	1	NA	exon (NM_001162946, exon 11 of 21)	exon (NM_001162946, exon 11 of 21)	5737	NM_153388	225875	Mm.329675	NM_153388	ENSMUSG00000045045	Lrfn4	BC023156|Salm3	leucine rich repeat and fibronectin type III domain containing 4	protein-coding
mm_138043.1	chr17	33922805	33922852	+	1	NA	intron (NM_001025313, intron 3 of 7)	intron (NM_001025313, intron 3 of 7)	3350	NM_009318	21356	Mm.154457	NM_009318	ENSMUSG00000024308	Tapbp	D17Wsu91e|TPN	TAP binding protein	protein-coding
mm_77269.1	chr8	116435764	116435774	-	1	NA	Intergenic	Intergenic	-69246	NM_029297	75465	Mm.23114	NM_029297	ENSMUSG00000034467	Dynlrb2	1700009A04Rik|DNLC2B|Dncl2b	dynein light chain roadblock-type 2	protein-coding
mm_156793.1	chrX	162846005	162846016	+	1	NA	intron (NR_038088, intron 3 of 5)	intron (NR_038088, intron 3 of 5)	-16556	NM_001290778	353170	Mm.270186	NM_178935	ENSMUSG00000038344	Txlng	4932441K18Rik|Fiat|Lrp	taxilin gamma	protein-coding
mm_22153.1	chr2	172463252	172463297	-	1	NA	exon (NM_025542, exon 6 of 9)	exon (NM_025542, exon 6 of 9)	-4678	NM_001039560	654821	Mm.389337	NM_001039560	ENSMUSG00000074569	Gcnt7	A330041C17Rik|gnt	glucosaminyl (N-acetyl) transferase family member 7	protein-coding
mm_18864.1	chr2	75705033	75705065	-	1	NA	promoter-TSS (NM_010902)	promoter-TSS (NM_010902)	-386	NM_010902	18024	Mm.1025	NM_010902	ENSMUSG00000015839	Nfe2l2	Nrf2	nuclear factor, erythroid derived 2, like 2	protein-coding
mm_150576.1	chr19	40612357	40612373	+	1	NA	promoter-TSS (NM_026260)	promoter-TSS (NM_026260)	-1	NM_001304721	12495	Mm.2824	NM_009848	ENSMUSG00000048120	Entpd1	2610206B08Rik|AA408691|Cd39|NTPDase-1	ectonucleoside triphosphate diphosphohydrolase 1	protein-coding
mm_156384.1	chrX	139684955	139684968	+	1	NA	promoter-TSS (NM_001081499)	promoter-TSS (NM_001081499)	-35	NM_001081499	245638	Mm.275869	NM_001081499	ENSMUSG00000042473	Tbc1d8b	4921505D17Rik|9030605E16Rik	TBC1 domain family, member 8B	protein-coding
mm_126529.1	chr15	81988284	81988286	+	1	NA	Intergenic	B3|SINE|B2	7745	NM_025503	66346	Mm.54292	NM_025503	ENSMUSG00000061633	1700029P11Rik	-	RIKEN cDNA 1700029P11 gene	protein-coding
mm_82883.1	chr9	32515051	32515053	-	1	NA	intron (NM_008026, intron 1 of 8)	intron (NM_008026, intron 1 of 8)	26400	NM_008026	14247	Mm.258908	NM_008026	ENSMUSG00000016087	Fli1	EWSR2|Fli-1|SIC-1|Sic1	Friend leukemia integration 1	protein-coding
mm_120720.1	chr14	73108234	73108267	+	1	NA	Intergenic	Intergenic	-34260	NM_001170694	105670	Mm.280068	NM_134083	ENSMUSG00000022106	Rcbtb2	2610028E02Rik|2810420M18Rik|AI448345|AW240694|Chc1l|RC/BTB2	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 2	protein-coding
mm_101605.1	chr11	34833604	34833626	-	1	NA	promoter-TSS (NM_027411)	promoter-TSS (NM_027411)	26	NM_027411	70385	Mm.194368	NM_027411	ENSMUSG00000069910	Spdl1	1700018I02Rik|2600001J17Rik|2810049B11Rik|AA409762|Ccdc99	spindle apparatus coiled-coil protein 1	protein-coding
mm_70148.1	chr7	143459335	143459344	-	1	NA	intron (NM_009876, intron 2 of 3)	CpG-13764	1711	NM_009876	12577	Mm.168789	NM_009876	ENSMUSG00000037664	Cdkn1c	AL024410|CDKI|Kip2|p57(kip2)|p57Kip2	cyclin-dependent kinase inhibitor 1C (P57)	protein-coding
mm_109865.1	chr12	4907539	4907558	-	1	NA	promoter-TSS (NM_145441)	promoter-TSS (NM_145441)	-28	NM_145441	217379	Mm.259170	NM_145441	ENSMUSG00000020634	Ubxn2a	6330407P03Rik|Ubxd4	UBX domain protein 2A	protein-coding
mm_156575.1	chrX	151934412	151934445	+	1	NA	3' UTR (NM_021523, exon 83 of 83)	3' UTR (NM_021523, exon 83 of 83)	21214	NR_029753	723947		NR_029753	ENSMUSG00000065536	Mir98	Mirn98|mir-98|mmu-mir-98	microRNA 98	ncRNA
mm_82521.1	chr9	20642587	20642606	-	1	NA	promoter-TSS (NM_025401)	promoter-TSS (NM_025401)	210	NM_013911	30843	Mm.24608	NM_013911	ENSMUSG00000066892	Fbxl12	3110048D16Rik|Fbl12	F-box and leucine-rich repeat protein 12	protein-coding
mm_159211.1	chr2	122186158	122186158	-	1	NA	promoter-TSS (NM_028914)	promoter-TSS (NM_028914)	31	NM_026251	67578	Mm.150462	NM_026251	ENSMUSG00000027233	Patl2	4930424G05Rik|Pat1a	protein associated with topoisomerase II homolog 2 (yeast)	protein-coding
mm_114670.1	chr13	78590552	78590554	+	1	NA	Intergenic	Intergenic	-391680	NM_010151	13865	Mm.439653	NM_010151	ENSMUSG00000069171	Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR-3|EAR3|Erbal3|SVP44|Tcfcoup1	nuclear receptor subfamily 2, group F, member 1	protein-coding
mm_145736.1	chr18	64265208	64265222	+	1	NA	5' UTR (NM_009182, exon 3 of 6)	5' UTR (NM_009182, exon 3 of 6)	10856	NM_009182	20451	Mm.252110	NM_009182	ENSMUSG00000056812	St8sia3	AI847333|ST8SiaIII|Siat8c	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3	protein-coding
mm_100799.1	chr11	4947992	4948009	-	1	NA	promoter-TSS (NM_010904)	promoter-TSS (NM_010904)	64	NM_010904	380684	Mm.298283	NM_010904	ENSMUSG00000020396	Nefh	NF-H|NF200|Nfh|mKIAA0845	neurofilament, heavy polypeptide	protein-coding
mm_158258.1	chrX	109005713	109005723	-	1	NA	exon (NM_016710, exon 6 of 6)	exon (NM_016710, exon 6 of 6)	4233	NR_033596	70550	Mm.482937	NR_033596	ENSMUSG00000081793	5730416F02Rik	-	capping protein (actin filament), gelsolin-like pseudogene	pseudo
mm_101018.1	chr11	8575316	8575363	-	1	NA	intron (NM_001083587, intron 4 of 30)	intron (NM_001083587, intron 4 of 30)	89196	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_113127.1	chr13	24605079	24605081	+	1	NA	promoter-TSS (NR_024599)	promoter-TSS (NR_024599)	-313	NR_024599	76024	Mm.440710	NR_024599		Gm11346	5830431A10Rik|AI447617|Gm11347|OTTMUSG00000000601|OTTMUSG00000000602	X-linked lymphocyte-regulated 5 pseudogene	pseudo
mm_74014.1	chr8	121542081	121542087	+	1	NA	promoter-TSS (NM_029597)	promoter-TSS (NM_029597)	-130	NM_029597	76405	Mm.165697	NM_029597	ENSMUSG00000031809	1700018B08Rik	1700084O22Rik	RIKEN cDNA 1700018B08 gene	protein-coding
mm_15041.1	chr2	152810469	152810472	+	1	NA	intron (NM_001289717, intron 2 of 2)	intron (NM_001289717, intron 2 of 2)	20247	NM_001289716	12048	Mm.238213	NM_009743	ENSMUSG00000007659	Bcl2l1	Bcl(X)L|Bcl-XL|Bcl2l|BclX|bcl-x|bcl2-L-1	BCL2-like 1	protein-coding
mm_48063.1	chr5	136567308	136567320	-	1	NA	5' UTR (NM_009986, exon 1 of 24)	5' UTR (NM_009986, exon 1 of 24)	176	NM_001291234	13047	Mm.320317	NM_009986	ENSMUSG00000029705	Cux1	CDP|Cutl1|Cux|Cux-1	cut-like homeobox 1	protein-coding
mm_172289.1	chr6	95543773	95543773	+	1	NA	intron (NM_001326558, intron 9 of 10)	RLTR27|LTR|ERVK	149109	NM_001326558	20917	Mm.371585	NM_011507	ENSMUSG00000061838	Suclg2	AF171077|AW556404|D6Wsu120e|G-SCS|GTPSCS|SCS-betaG	succinate-Coenzyme A ligase, GDP-forming, beta subunit	protein-coding
mm_122468.1	chr14	45530131	45530182	-	1	NA	promoter-TSS (NM_146054)	promoter-TSS (NM_146054)	-91	NM_146054	218952	Mm.210018	NM_146054	ENSMUSG00000037712	Fermt2	AA960555|Kindlin-2|Mig2|Plekhc1	fermitin family member 2	protein-coding
mm_4288.1	chr1	171712915	171712924	+	1	NA	Intergenic	L1_Mur3|LINE|L1	30864	NM_007649	12506	Mm.1738	NM_007649	ENSMUSG00000015355	Cd48	AI449234|AW610730|BCM1|BLAST|BLAST-1|BLAST1|Bcm-1|MEM-102|SLAMF2|Sgp-60	CD48 antigen	protein-coding
mm_130913.1	chr15	102583461	102583466	-	1	NA	intron (NM_001310066, intron 2 of 11)	intron (NM_001310066, intron 2 of 11)	42001	NM_001310070	223922	Mm.208714	NM_146065	ENSMUSG00000052414	Atf7	1110012F10Rik|9430065F09Rik|AI549878|C130020M04Rik	activating transcription factor 7	protein-coding
mm_6585.1	chr1	75236864	75236882	-	1	NA	5' UTR (NM_001159883, exon 2 of 9)	5' UTR (NM_001159883, exon 2 of 9)	171	NM_001159885	56812	Mm.489660	NM_020266	ENSMUSG00000026203	Dnajb2	2700059H22Rik|Dnajb10|Hsj1|mDj8	DnaJ heat shock protein family (Hsp40) member B2	protein-coding
mm_169071.1	chr13	29070828	29070845	-	1	NA	Intergenic	L1Md_T|LINE|L1	54581	NR_045075	77920	Mm.197051	NR_045073	ENSMUSG00000086363	A330102I10Rik	-	RIKEN cDNA A330102I10 gene	ncRNA
mm_42114.1	chr5	110653445	110653482	+	1	NA	promoter-TSS (NM_027156)	promoter-TSS (NM_027156)	12	NM_027156	69663	Mm.5267	NM_027156	ENSMUSG00000029504	Ddx51	2310061O04Rik|AA537002|C81583|R75505	DEAD (Asp-Glu-Ala-Asp) box polypeptide 51	protein-coding
mm_16717.1	chr2	7144770	7144780	-	1	NA	intron (NM_001110231, intron 3 of 15)	B4|SINE|B4	-63473	NM_001160292	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_54568.1	chr6	37871478	37871490	-	1	NA	intron (NM_001272064, intron 1 of 18)	CpG	673	NM_145076	21848	Mm.41063	NM_145076	ENSMUSG00000029833	Trim24	A130082H20Rik|AI447469|D430004I05Rik|TIF1|TIF1-alpha|TIF1alpha|Tif1a	tripartite motif-containing 24	protein-coding
mm_67574.1	chr7	81992583	81992593	-	1	NA	promoter-TSS (NM_007562)	promoter-TSS (NM_007562)	-289	NM_007562	12173	Mm.243802	NM_007562	ENSMUSG00000025105	Bnc1	AI047752|AW546376|Bnc	basonuclin 1	protein-coding
mm_20934.1	chr2	150858828	150858857	-	1	NA	intron (NM_024465, intron 1 of 12)	intron (NM_024465, intron 1 of 12)	45889	NM_024465	76192	Mm.112632	NM_024465	ENSMUSG00000032046	Abhd12	1500011G07Rik|6330583M11Rik|AI431047|AW547313	abhydrolase domain containing 12	protein-coding
mm_94557.1	chr11	11557933	11557943	+	1	NA	Intergenic	Intergenic	68672	NM_028669	73862	Mm.159077	NM_028669	ENSMUSG00000020191	4930415F15Rik	-	RIKEN cDNA 4930415F15 gene	protein-coding
mm_41860.1	chr5	104440579	104440588	+	1	NA	exon (NM_001204203, exon 7 of 7)	exon (NM_001204203, exon 7 of 7)	4391	NM_001204233	20750	Mm.288474	NM_009263	ENSMUSG00000029304	Spp1	2AR|Apl-1|BNSP|BSPI|Bsp|ETA-1|Eta|OP|Opn|Opnl|Ric|Spp-1	secreted phosphoprotein 1	protein-coding
mm_102103.1	chr11	52480917	52480923	-	1	NA	Intergenic	Intergenic	84492	NM_153117	213673	Mm.291979	NM_153117	ENSMUSG00000036275	9530068E07Rik	C85061|Kct2	RIKEN cDNA 9530068E07 gene	protein-coding
mm_6949.1	chr1	85752473	85752493	-	1	NA	TTS (NR_106172)	TTS (NR_106172)	535	NR_106172	102466882		NR_106172	ENSMUSG00000098634	Mir8096	Gm27479|mmu-mir-8096	microRNA 8096	ncRNA
mm_165652.1	chr3	83841730	83841760	-	1	NA	promoter-TSS (NM_011905)	promoter-TSS (NM_011905)	-137	NM_011905	24088	Mm.87596	NM_011905	ENSMUSG00000027995	Tlr2	Ly105	toll-like receptor 2	protein-coding
mm_166779.1	chr6	138563003	138563007	+	1	NA	intron (NM_207222, intron 1 of 4)	intron (NM_207222, intron 1 of 4)	-17619	NR_131103	77982	Mm.146702	NR_131103	ENSMUSG00000100166	B230110G15Rik	-	RIKEN cDNA B230110G15 gene	ncRNA
mm_61207.1	chr7	64158954	64158961	+	1	NA	intron (NM_001039104, intron 1 of 26)	intron (NM_001039104, intron 1 of 26)	5122	NM_001039104	17364	Mm.38875	NM_018752	ENSMUSG00000030523	Trpm1	4732499L03Rik|AI606771|Ltrpc1|Mlsn1	transient receptor potential cation channel, subfamily M, member 1	protein-coding
mm_172845.1	chr9	35305475	35305475	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	24370	NR_040715	71133	Mm.158577	NR_040715	ENSMUSG00000111746	4933422A05Rik	-	RIKEN cDNA 4933422A05 gene	ncRNA
mm_788.1	chr1	45332961	45332996	+	1	NA	exon (NM_009930, exon 21 of 51)	exon (NM_009930, exon 21 of 51)	21440	NM_009930	12825	Mm.249555	NM_009930	ENSMUSG00000026043	Col3a1	AW550625|Col3a-1|Tsk-2|Tsk2	collagen, type III, alpha 1	protein-coding
mm_76641.1	chr8	92854830	92854833	-	1	NA	promoter-TSS (NM_173014)	promoter-TSS (NM_173014)	-519	NM_173014	270084	Mm.21463	NM_173014	ENSMUSG00000033192	Lpcat2	A330042H22|Aytl1|Aytl1a|lpafat1	lysophosphatidylcholine acyltransferase 2	protein-coding
mm_56247.1	chr6	90736779	90736817	-	1	NA	intron (NM_001134384, intron 1 of 13)	CpG	-20269	NM_001134383	232227	Mm.196943	NM_182784	ENSMUSG00000034312	Iqsec1	AW561907|BC026481|BRAG2|D6Ertd349e|cI-43	IQ motif and Sec7 domain 1	protein-coding
mm_110650.1	chr12	59012097	59012103	-	1	NA	promoter-TSS (NM_009147)	promoter-TSS (NM_009147)	-83	NM_009147	20334	Mm.491137	NM_009147	ENSMUSG00000020986	Sec23a	Msec23|Sec23r	SEC23 homolog A, COPII coat complex component	protein-coding
mm_168007.1	chrY	4927923	4927923	-	1	NA	Intergenic	L1Md_A|LINE|L1	1156250	NM_011253	19657	Mm.4711	NM_011253	ENSMUSG00000094658	Rbmy	RBM|Rbm1|Rbm1-rs1|Rbmy1a1|Rbmy1a1-rs1|Rbmy1b	RNA binding motif protein, Y chromosome	protein-coding
mm_30297.1	chr3	149077090	149077100	-	1	NA	Intergenic	Intergenic	-122460	NM_001081298	99633	Mm.9776	NM_001081298	ENSMUSG00000028184	Adgrl2	AI450192|CIRL-2|Gm619|Lec1|Lphh1|Lphn2|mKIAA0786	adhesion G protein-coupled receptor L2	protein-coding
mm_107932.1	chr12	71309859	71309874	+	1	NA	promoter-TSS (NM_021532)	promoter-TSS (NM_021532)	-18	NM_021532	59036	Mm.46662	NM_021532	ENSMUSG00000044548	Dact1	4921528D17Rik|AI115603|DAPPER|DAPPER1|FRODO|Frd1|Frodo1|MDpr1|MTNG3|THYEX3	dishevelled-binding antagonist of beta-catenin 1	protein-coding
mm_158422.1	chrX	139356735	139356744	-	1	NA	promoter-TSS (NR_045455)	promoter-TSS (NR_045455)	31	NR_045455	78526	Mm.439073	NR_045455	ENSMUSG00000086807	Platr21	C330013F16Rik	pluripotency associated transcript 21	ncRNA
mm_32521.1	chr4	108834710	108834751	+	1	NA	promoter-TSS (NM_025334)	promoter-TSS (NM_025334)	52	NM_025334	66073	Mm.159965	NM_025334	ENSMUSG00000028567	Txndc12	0610040B21Rik|ERp16|ERp19	thioredoxin domain containing 12 (endoplasmic reticulum)	protein-coding
mm_39445.1	chr5	17574269	17574293	+	1	NA	promoter-TSS (NM_013657)	promoter-TSS (NM_013657)	-535	NM_013657	20348	Mm.5071	NM_013657	ENSMUSG00000028780	Sema3c	1110036B02Rik|SemE|Semae	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	protein-coding
mm_93012.1	chr10	87491864	87491874	-	1	NA	3' UTR (NM_008553, exon 2 of 2)	3' UTR (NM_008553, exon 2 of 2)	1791	NM_008553	17172	Mm.136217	NM_008553	ENSMUSG00000020052	Ascl1	AI225900|ASH1|Mash1|bHLHa46	achaete-scute family bHLH transcription factor 1	protein-coding
mm_85390.1	chr9	103230297	103230309	-	1	NA	promoter-TSS (NM_133977)	promoter-TSS (NM_133977)	-17	NM_133977	22041	Mm.37214	NM_133977	ENSMUSG00000032554	Trf	AI266983|Cd176|HP|Tf|Tfn|hpx	transferrin	protein-coding
mm_141286.1	chr17	27970109	27970117	-	1	NA	intron (NM_001286040, intron 1 of 24)	intron (NM_001286040, intron 1 of 24)	60807	NM_181413	224650	Mm.32556	NM_181413	ENSMUSG00000024219	Anks1	Anks1a|mKIAA0229	ankyrin repeat and SAM domain containing 1	protein-coding
mm_73678.1	chr8	111536794	111536826	+	1	NA	5' UTR (NM_133206, exon 1 of 4)	5' UTR (NM_133206, exon 1 of 4)	170	NM_001168621	170737	Mm.271578	NM_133206	ENSMUSG00000033545	Znrf1	B830022L21Rik|Rnf42|Zrfp1|nin283	zinc and ring finger 1	protein-coding
mm_141674.1	chr17	33909290	33909326	-	1	NA	promoter-TSS (NM_001199733)	promoter-TSS (NM_001199733)	-130	NR_045146	407803	Mm.250393	NR_045146	ENSMUSG00000092564	BC051226	-	cDNA sequence BC051226	ncRNA
mm_109840.1	chr12	4357010	4357018	-	1	NA	intron (NM_010881, intron 2 of 22)	RodERV21-int|LTR|ERV1	120168	NM_010881	17977	Mm.301039	NM_010881	ENSMUSG00000020647	Ncoa1	KAT13A|NCoA-1|NRC-1|SRC-1|SRC-a|SRC1|bHLHe74|mNRC-1	nuclear receptor coactivator 1	protein-coding
mm_157437.1	chrX	38635045	38635063	-	1	NA	promoter-TSS (NM_021550)	promoter-TSS (NM_021550)	89	NM_021550	59048	Mm.441410	NM_021550	ENSMUSG00000048970	C1galt1c1	1500002I11Rik|AB030184|C1GalT2|C81205|Cosmc	C1GALT1-specific chaperone 1	protein-coding
mm_98884.1	chr11	97815726	97815736	+	1	NA	exon (NM_010688, exon 3 of 7)	exon (NM_010688, exon 3 of 7)	16059	NM_010688	16796	Mm.271967	NM_010688	ENSMUSG00000038366	Lasp1	AA408629|Def-4|SH3P6|Tg(Col1a1-lacZ)1Ngma	LIM and SH3 protein 1	protein-coding
mm_15328.1	chr2	155754985	155754994	+	1	NA	3' UTR (NM_011171, exon 4 of 4)	3' UTR (NM_011171, exon 4 of 4)	3772	NM_011171	19124	Mm.3243	NM_011171	ENSMUSG00000027611	Procr	AI325044|Ccca|Ccd41|Epcr	protein C receptor, endothelial	protein-coding
mm_142829.1	chr17	51775453	51775462	-	1	NA	intron (NM_009122, intron 7 of 10)	intron (NM_009122, intron 7 of 10)	36597	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_126188.1	chr15	78615975	78615983	+	1	NA	intron (NM_028195, intron 9 of 12)	intron (NM_028195, intron 9 of 12)	18932	NM_028195	72318	Mm.32911	NM_028195	ENSMUSG00000018008	Cyth4	2510004M07Rik|5830469K17Rik|AI467541|Pscd4|mFLJ00017	cytohesin 4	protein-coding
mm_156544.1	chrX	151343863	151343906	+	1	NA	promoter-TSS (NM_198105)	promoter-TSS (NM_198105)	-339	NM_198105	207375	Mm.391339	NM_198105	ENSMUSG00000025262	Fam120c	D930001I21Rik|ORF34	family with sequence similarity 120, member C	protein-coding
mm_22004.1	chr2	167765288	167765301	-	1	NA	Intergenic	Intergenic	74117	NR_015500	329562	Mm.123101	NM_177851	ENSMUSG00000006462	A530013C23Rik	-	RIKEN cDNA A530013C23 gene	ncRNA
mm_127076.1	chr15	97384597	97384633	+	1	NA	exon (NM_172293, exon 6 of 6)	exon (NM_172293, exon 6 of 6)	-137328	NM_001164602	105827	Mm.24005	NM_178114	ENSMUSG00000048218	Amigo2	AI415330|AMIGO-2|AW208913|Ali1	adhesion molecule with Ig like domain 2	protein-coding
mm_138839.1	chr17	39848752	39848764	+	1	NA	TTS (NR_046233)	TTS (NR_046233)	5761	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_161425.1	chr15	43278541	43278541	-	1	NA	intron (NM_008388, intron 1 of 12)	RSINE1|SINE|B4	4195	NM_008388	16341	Mm.289992	NM_008388	ENSMUSG00000022336	Eif3e	48kDa|Eif3s6|Int6|eIF3-p46|eIF3-p48	eukaryotic translation initiation factor 3, subunit E	protein-coding
mm_50259.1	chr6	43265617	43265681	+	1	NA	promoter-TSS (NM_133674)	promoter-TSS (NM_133674)	5	NM_133674	54324	Mm.320978	NM_133674	ENSMUSG00000033542	Arhgef5	2210412D05Rik|AA717842|AW495314|Tim1	Rho guanine nucleotide exchange factor (GEF) 5	protein-coding
mm_114434.1	chr13	65278796	65278808	+	1	NA	promoter-TSS (NM_178364)	promoter-TSS (NM_178364)	-52	NM_178364	170936	Mm.151546	NM_178364	ENSMUSG00000021514	Zfp369	B930030B22Rik|D230020H11Rik|NRIF2	zinc finger protein 369	protein-coding
mm_154443.1	chrM	1449	1455	-	1	NA	NA	Intergenic	NA	NA								
mm_56908.1	chr6	119314125	119314155	-	1	NA	TTS (NM_172492)	TTS (NM_172492)	15064	NM_001172207	211187	Mm.121498	NM_172492	ENSMUSG00000055003	Lrtm2	A230084J22|AI841794	leucine-rich repeats and transmembrane domains 2	protein-coding
mm_152816.1	chr19	23132805	23132822	-	1	NA	Intergenic	MTB|LTR|ERVL-MaLR	-8413	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_140300.1	chr17	85621171	85621249	+	1	NA	5' UTR (NM_011381, exon 1 of 2)	5' UTR (NM_011381, exon 1 of 2)	376	NM_011381	20473	Mm.370208	NM_011381	ENSMUSG00000038805	Six3	E130112M24Rik|Six3a|Six3alpha|Six3b|Six3beta	sine oculis-related homeobox 3	protein-coding
mm_54911.1	chr6	47788109	47788140	-	1	NA	Intergenic	HY1|scRNA|scRNA	15528	NR_030485	735289		NR_030485	ENSMUSG00000076060	Mir704	Mirn704|mir-704|mmu-mir-704	microRNA 704	ncRNA
mm_77505.1	chr8	122699123	122699137	-	1	NA	promoter-TSS (NM_009824)	promoter-TSS (NM_009824)	-21	NM_009824	12398	Mm.194339	NM_009824	ENSMUSG00000006362	Cbfa2t3	A630044F12Rik|AI465270|AW229127|Cbfa2t3h|ETO-2|Eto2|MTGR2	core-binding factor, runt domain, alpha subunit 2, translocated to, 3 (human)	protein-coding
mm_123758.1	chr14	70203468	70203480	-	1	NA	intron (NM_011366, intron 1 of 20)	intron (NM_011366, intron 1 of 20)	1149	NM_001271408	20410	Mm.5068	NM_011366	ENSMUSG00000022091	Sorbs3	SCAM-1|SH3P3|Sh3d4|vinexin-g	sorbin and SH3 domain containing 3	protein-coding
mm_157174.1	chrX	9516299	9516300	-	1	NA	Intergenic	U2|snRNA|snRNA	-46975	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_31160.1	chr4	43442485	43442501	+	1	NA	5' UTR (NM_011571, exon 1 of 10)	5' UTR (NM_011571, exon 1 of 10)	216	NM_011571	21754	Mm.485441	NM_011571	ENSMUSG00000028458	Tesk1	AI326901	testis specific protein kinase 1	protein-coding
mm_133475.1	chr16	89404696	89404699	+	1	NA	promoter-TSS (NM_028621)	promoter-TSS (NM_028621)	-923	NM_028621	170656	Mm.46109	NM_028621	ENSMUSG00000058368	Krtap21-1	1110017B05Rik|AI506979|KAP21.1|Krtap16-7	keratin associated protein 21-1	protein-coding
mm_61846.1	chr7	88291000	88291012	+	1	NA	3' UTR (NM_001311790, exon 4 of 4)	3' UTR (NM_001311790, exon 4 of 4)	12921	NM_001311790	13032	Mm.89295	NM_009982	ENSMUSG00000030560	Ctsc	AI047818|CatC|DPP1|DPPI	cathepsin C	protein-coding
mm_24892.1	chr3	96161982	96162023	+	1	NA	promoter-TSS (NM_181409)	promoter-TSS (NM_181409)	32	NM_181409	194126	Mm.268536	NM_181409	ENSMUSG00000045934	Mtmr11	AI035306|BC051083|Cra	myotubularin related protein 11	protein-coding
mm_93561.1	chr10	116515395	116515397	-	1	NA	intron (NM_001037848, intron 4 of 4)	intron (NM_001037848, intron 4 of 4)	-41873	NM_021452	58802	Mm.440652	NM_021452	ENSMUSG00000054934	Kcnmb4	1700058G18Rik|2900045G12Rik	potassium large conductance calcium-activated channel, subfamily M, beta member 4	protein-coding
mm_77856.1	chr9	5312160	5312172	+	1	NA	intron (NM_007609, intron 1 of 8)	L1M2|LINE|L1	3317	NM_007609	12363	Mm.1569	NM_007609	ENSMUSG00000033538	Casp4	CASP-11|CASP-4|Casp11|Caspl|ich-3	caspase 4, apoptosis-related cysteine peptidase	protein-coding
mm_46269.1	chr5	99976558	99976593	-	1	NA	exon (NM_007516, exon 2 of 8)	exon (NM_007516, exon 2 of 8)	2363	NM_001077266	11991	Mm.150231	NM_007516	ENSMUSG00000000568	Hnrnpd	Auf1|Hnrpd	heterogeneous nuclear ribonucleoprotein D	protein-coding
mm_102626.1	chr11	62538884	62538898	-	1	NA	exon (NM_028448, exon 1 of 5)	exon (NM_028448, exon 1 of 5)	370	NM_028448	73139	Mm.390409	NM_028448	ENSMUSG00000018509	Cenpv	3110013H01Rik|AA671303|Prr6	centromere protein V	protein-coding
mm_150158.1	chr19	32255229	32255265	+	1	NA	intron (NM_144792, intron 3 of 9)	intron (NM_144792, intron 3 of 9)	-44234	NM_001168526	208449	Mm.329810	NM_144792	ENSMUSG00000040451	Sgms1	9530058O11Rik|AI841905|C80702|Mob|Sms1|Sor1|Tmem23	sphingomyelin synthase 1	protein-coding
mm_129264.1	chr15	76871066	76871105	-	1	NA	5' UTR (NM_001007568, exon 1 of 4)	5' UTR (NM_001007568, exon 1 of 4)	350	NM_001007568	71591	Mm.38195	NM_001007568	ENSMUSG00000022526	Zfp251	9130001M19Rik|AV339307	zinc finger protein 251	protein-coding
mm_57617.1	chr6	128200575	128200575	-	1	NA	Intergenic	CpG	-16772	NR_077223	330427	Mm.426356	NR_077223	ENSMUSG00000107879	9330102E08Rik	-	RIKEN cDNA 9330102E08 gene	ncRNA
mm_96695.1	chr11	69601239	69601249	+	1	NA	3' UTR (NM_013415, exon 7 of 7)	3' UTR (NM_013415, exon 7 of 7)	4716	NM_013415	11932	Mm.235204	NM_013415	ENSMUSG00000041329	Atp1b2	Amog|Atpb-2	ATPase, Na+/K+ transporting, beta 2 polypeptide	protein-coding
mm_42477.1	chr5	115466235	115466294	+	1	NA	promoter-TSS (NM_011107)	promoter-TSS (NM_011107)	-2	NM_011107	18778	Mm.20190	NM_011107	ENSMUSG00000029522	Pla2g1b	Pla2a|sPLA2IB	phospholipase A2, group IB, pancreas	protein-coding
mm_149407.1	chr19	11392810	11392821	+	1	NA	TTS (NM_001310331)	TTS (NM_001310331)	-14846	NM_029499	64380	Mm.440715	NM_029499	ENSMUSG00000024675	Ms4a4c	5830413L19Rik|AI449185|Ms4a9	membrane-spanning 4-domains, subfamily A, member 4C	protein-coding
mm_144427.1	chr18	21001473	21001491	+	1	NA	promoter-TSS (NM_207623)	promoter-TSS (NM_207623)	182	NM_001303005	56515	Mm.253542	NM_019706	ENSMUSG00000024317	Rnf138	2410015A17Rik|2810480D20Rik|STRIN|Trif|Trif-d	ring finger protein 138	protein-coding
mm_29804.1	chr3	127789743	127789758	-	1	NA	promoter-TSS (NM_145133)	promoter-TSS (NM_145133)	-163	NM_145133	211550	Mm.31852	NM_145133	ENSMUSG00000046688	Tifa	T2bp	TRAF-interacting protein with forkhead-associated domain	protein-coding
mm_12028.1	chr2	58161096	58161102	+	1	NA	promoter-TSS (NM_139200)	promoter-TSS (NM_139200)	-977	NM_139200	227929	Mm.273905	NM_139200	ENSMUSG00000026832	Cytip	A130053M09Rik|AI462064|C80816|Cbp|Cybr|Pscdbp	cytohesin 1 interacting protein	protein-coding
mm_80733.1	chr9	94668896	94668912	+	1	NA	promoter-TSS (NM_177909)	promoter-TSS (NM_177909)	-988	NM_177909	331004	Mm.326125	NM_177909	ENSMUSG00000031129	Slc9a9	5730527A11Rik|9930105B05|AI854429|Nhe9	solute carrier family 9 (sodium/hydrogen exchanger), member 9	protein-coding
mm_116824.1	chr13	54598831	54598841	-	1	NA	intron (NM_001347512, intron 3 of 5)	intron (NM_001347512, intron 3 of 5)	8605	NM_025933	67044	Mm.29353	NM_025933	ENSMUSG00000025868	Higd2a	2010110M21Rik|AA690237	HIG1 domain family, member 2A	protein-coding
mm_52822.1	chr6	121356873	121356877	+	1	NA	intron (NM_001347433, intron 6 of 14)	intron (NM_001347433, intron 6 of 14)	10178	NM_133661	14411	Mm.274506	NM_133661	ENSMUSG00000030109	Slc6a12	BGT1|GAT-2|GAT2|Gabt2	solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12	protein-coding
mm_23396.1	chr3	57796198	57796217	+	1	NA	exon (NM_011883, exon 5 of 9)	exon (NM_011883, exon 5 of 9)	51550	NM_019410	18645	Mm.271744	NM_019410	ENSMUSG00000027805	Pfn2	Pfn	profilin 2	protein-coding
mm_170259.1	chr18	14647931	14647940	-	1	NA	intron (NM_001161370, intron 4 of 9)	intron (NM_001161370, intron 4 of 9)	34979	NM_001161369	268996	Mm.31761	NM_009280	ENSMUSG00000037013	Ss18	D130059H17|Ssxt|Syt	SS18, nBAF chromatin remodeling complex subunit	protein-coding
mm_109195.1	chr12	108635705	108635726	+	1	NA	promoter-TSS (NM_001163396)	promoter-TSS (NM_001163396)	-38	NM_001163396	14026	Mm.238841	NM_007965	ENSMUSG00000021262	Evl	AI528774	Ena-vasodilator stimulated phosphoprotein	protein-coding
mm_136934.1	chr17	14169708	14169733	+	1	NA	Intergenic	Intergenic	34111	NM_172826	240025	Mm.79993	NM_172826	ENSMUSG00000048826	Dact2	2900084M21Rik|A630024E20|Dpr2|Frd2|dapper2	dishevelled-binding antagonist of beta-catenin 2	protein-coding
mm_30432.1	chr3	153263740	153263742	-	1	NA	intron (NM_011372, intron 3 of 4)	intron (NM_011372, intron 3 of 4)	34908	NR_126464	75489	Mm.443252	NR_126464	ENSMUSG00000105023	1700012D16Rik	-	RIKEN cDNA 1700012D16 gene	ncRNA
mm_11810.1	chr2	43950543	43950552	+	1	NA	intron (NM_001301832, intron 7 of 14)	(GGGA)n|Simple_repeat|Simple_repeat	114777	NR_040622	320872	Mm.445023	NR_040622	ENSMUSG00000085089	Arhgap15os	A430092G05Rik	Rho GTPase activating protein 15, opposite strand	ncRNA
mm_53798.1	chr6	146782446	146782446	+	1	NA	Intergenic	Intergenic	-23084	NM_172309	272322	Mm.333500	NM_172309	ENSMUSG00000040187	Arntl2	4632430A05Rik|BMAL2|CLIF|MOP9|bHLHe6	aryl hydrocarbon receptor nuclear translocator-like 2	protein-coding
mm_68387.1	chr7	109456628	109456658	-	1	NA	intron (NM_001170913, intron 16 of 19)	ORR1F|LTR|ERVL-MaLR	-17590	NM_054103	117229	Mm.389950	NM_054103	ENSMUSG00000031027	Stk33	4921505G21Rik|AW061264	serine/threonine kinase 33	protein-coding
mm_57283.1	chr6	124364471	124364477	-	1	NA	promoter-TSS (NR_131162)	promoter-TSS (NR_131162)	12	NR_131162	72268	Mm.420740	NR_131162		1700027F06Rik	-	RIKEN cDNA 1700027F06 gene	ncRNA
mm_73626.1	chr8	110703237	110703243	+	1	NA	intron (NM_146216, intron 14 of 18)	intron (NM_146216, intron 14 of 18)	-18236	NM_198625	244654	Mm.490385	NM_198625	ENSMUSG00000033763	Mtss1l	ABBA	metastasis suppressor 1-like	protein-coding
mm_40758.1	chr5	66958600	66958604	+	1	NA	intron (NM_001001980, intron 4 of 25)	intron (NM_001001980, intron 4 of 25)	-9814	NM_001256122	77569	Mm.374778	NM_001001980	ENSMUSG00000037736	Limch1	3732412D22Rik|mKIAA1102	LIM and calponin homology domains 1	protein-coding
mm_62184.1	chr7	97480921	97480927	+	1	NA	promoter-TSS (NM_027256)	promoter-TSS (NM_027256)	-32	NM_027256	101861	Mm.27383	NM_027256	ENSMUSG00000025133	Ints4	2610034N24Rik|AA692684|AW493223	integrator complex subunit 4	protein-coding
mm_104172.1	chr11	87591713	87591723	-	1	NA	promoter-TSS (NM_133215)	promoter-TSS (NM_133215)	-499	NM_133215	170749	Mm.399376	NM_133215	ENSMUSG00000018401	Mtmr4	AA596759|ESTM44|FYVE-DSP2|ZFYVE11|mKIAA0647	myotubularin related protein 4	protein-coding
mm_89368.1	chr10	88731094	88731106	+	1	NA	promoter-TSS (NM_025859)	promoter-TSS (NM_025859)	1	NM_001037166	237433	Mm.478763	NM_001037166		Gm4925	EG237433	predicted gene 4925	protein-coding
mm_92452.1	chr10	77777010	77777016	-	1	NA	intron (NM_001287074, intron 1 of 11)	intron (NM_001287074, intron 1 of 11)	-5688	NM_001101630	100041261	Mm.477434	NM_001101630	ENSMUSG00000095817	Gm3238	-	predicted gene 3238	protein-coding
mm_127731.1	chr15	103273806	103273808	+	1	NA	intron (NM_019817, intron 1 of 8)	intron (NM_019817, intron 1 of 8)	889	NM_019817	56447	Mm.29473	NM_019817	ENSMUSG00000060992	Copz1	5930435A22Rik|AA407760|D4Ertd360e	coatomer protein complex, subunit zeta 1	protein-coding
mm_156986.1	chrX	7319292	7319331	-	1	NA	promoter-TSS (NM_001243762)	promoter-TSS (NM_001243762)	47	NM_001243762	12728	Mm.486257	NM_016691	ENSMUSG00000004317	Clcn5	5430408K11Rik|ClC-5|Clc4-1|Clc5|Clcn4-1|D930009B12Rik|DXImx42e|Sfc13|T25545	chloride channel, voltage-sensitive 5	protein-coding
mm_16839.1	chr2	11501718	11501728	-	1	NA	5' UTR (NM_001177754, exon 1 of 16)	5' UTR (NM_001177754, exon 1 of 16)	367	NM_001177754	170768	Mm.19669	NM_133232	ENSMUSG00000026773	Pfkfb3	E330010H22Rik|iPFK-2|uPFK-2	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	protein-coding
mm_45502.1	chr5	72378731	72378732	-	1	NA	intron (NM_016869, intron 5 of 21)	intron (NM_016869, intron 5 of 21)	125477	NM_016869	53419	Mm.332425	NM_016869	ENSMUSG00000005220	Corin	AV273130|Lrp4	corin	protein-coding
mm_94136.1	chr10	128704286	128704311	-	1	NA	intron (NM_183417, intron 1 of 7)	intron (NM_183417, intron 1 of 7)	753	NM_183417	12566	Mm.111326	NM_016756	ENSMUSG00000025358	Cdk2	A630093N05Rik	cyclin-dependent kinase 2	protein-coding
mm_92251.1	chr10	70592861	70592865	-	1	NA	promoter-TSS (NM_001162846)	promoter-TSS (NM_001162846)	-51	NM_001162846	70911	Mm.19825	NM_178621	ENSMUSG00000037747	Phyhipl	4921522K17Rik|AI267048	phytanoyl-CoA hydroxylase interacting protein-like	protein-coding
mm_71769.1	chr8	66442549	66442559	+	1	NA	intron (NM_175188, intron 6 of 7)	intron (NM_175188, intron 6 of 7)	43953	NM_025465	66282	Mm.294985	NM_025465	ENSMUSG00000025591	Tma16	1810029B16Rik	translation machinery associated 16	protein-coding
mm_14032.1	chr2	122152903	122152926	+	1	NA	3' UTR (NM_009735, exon 4 of 4)	3' UTR (NM_009735, exon 4 of 4)	5227	NM_009735	12010	Mm.163	NM_009735	ENSMUSG00000060802	B2m	Ly-m11|beta2-m|beta2m	beta-2 microglobulin	protein-coding
mm_136888.1	chr17	13010359	13010404	+	1	NA	intron (NM_013671, intron 2 of 4)	intron (NM_013671, intron 2 of 4)	2542	NM_013671	20656	Mm.290876	NM_013671	ENSMUSG00000006818	Sod2	MnSOD|Sod-2	superoxide dismutase 2, mitochondrial	protein-coding
mm_152942.1	chr19	28929127	28929131	-	1	NA	intron (NM_198651, intron 10 of 12)	intron (NM_198651, intron 10 of 12)	-34791	NM_028922	74411	Mm.441887	NM_028922	ENSMUSG00000040105	Plpp6	4932443D16Rik|Ppapdc2	phospholipid phosphatase 6	protein-coding
mm_22399.1	chr2	181237567	181237579	-	1	NA	exon (NM_183162, exon 6 of 19)	exon (NM_183162, exon 6 of 19)	4454	NM_183162	229003	Mm.315872	NM_183162	ENSMUSG00000027580	Helz2	PDIP1|Pric285|mKIAA1769|mPDIP1	helicase with zinc finger 2, transcriptional coactivator	protein-coding
mm_2315.1	chr1	91801519	91801536	+	1	NA	promoter-TSS (NM_007855)	promoter-TSS (NM_007855)	66	NM_007855	13345	Mm.9474	NM_007855	ENSMUSG00000007805	Twist2	Dermo1|bHLHa39	twist basic helix-loop-helix transcription factor 2	protein-coding
mm_38418.1	chr4	139177063	139177096	-	1	NA	intron (NR_033543, intron 2 of 2)	intron (NR_033543, intron 2 of 2)	3576	NR_033543	100038595	Mm.385206	NR_033543	ENSMUSG00000073739	Gm16287	ENSMUSG00000073739|OTTMUSG00000009902|OTTMUSG00000033208	predicted gene 16287	ncRNA
mm_99156.1	chr11	100581284	100581298	+	1	NA	3' UTR (NM_009923, exon 4 of 4)	3' UTR (NM_009923, exon 4 of 4)	5400	NM_001146318	12799	Mm.15711	NM_009923	ENSMUSG00000006782	Cnp	CNPase|Cnp-1|Cnp1	2',3'-cyclic nucleotide 3' phosphodiesterase	protein-coding
mm_84727.1	chr9	74910441	74910446	-	1	NA	Intergenic	Intergenic	-42610	NM_001113283	235493	Mm.208955	NM_153584	ENSMUSG00000034858	Fam214a	6330415I01Rik|AI553555|C130047D21Rik|Kiaa1370|mKIAA1370	family with sequence similarity 214, member A	protein-coding
mm_11468.1	chr2	32363005	32363142	+	1	NA	promoter-TSS (NM_001252538)	promoter-TSS (NM_001252538)	63	NM_001252536	68379	Mm.170508	NM_028412	ENSMUSG00000039205	Ciz1	0610038H21Rik|2900056O04Rik|LSFR1|ZNF356	CDKN1A interacting zinc finger protein 1	protein-coding
mm_17886.1	chr2	34962982	34962991	-	1	NA	Intergenic	Intergenic	-1214	NM_001326601	22029	Mm.239514	NM_009421	ENSMUSG00000026875	Traf1	4732496E14Rik	TNF receptor-associated factor 1	protein-coding
mm_4188.1	chr1	171174444	171174466	+	1	NA	exon (NM_025557, exon 3 of 3)	exon (NM_025557, exon 3 of 3)	18937	NM_001315500	17528	Mm.9986	NM_008623	ENSMUSG00000056569	Mpz	Mpp|P-zero|P0	myelin protein zero	protein-coding
mm_115613.1	chr13	12040798	12040800	-	1	NA	intron (NM_023868, intron 1 of 104)	intron (NM_023868, intron 1 of 104)	66146	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding
mm_37865.1	chr4	132332549	132332561	-	1	NA	3' UTR (NM_133878, exon 10 of 10)	3' UTR (NM_133878, exon 10 of 10)	-3017	NM_027925	71787	Mm.239183	NM_027925	ENSMUSG00000028898	Trnau1ap	1110007F05Rik|AA387999|Secp43|Trspap1|WI1-2643G14.2	tRNA selenocysteine 1 associated protein 1	protein-coding
mm_105207.1	chr11	102107824	102107838	-	1	NA	promoter-TSS (NM_145435)	promoter-TSS (NM_145435)	1	NM_001346771	217212	Mm.46248	NM_145435	ENSMUSG00000017311	Pyy	-	peptide YY	protein-coding
mm_76604.1	chr8	90348344	90348386	-	1	NA	promoter-TSS (NM_172913)	promoter-TSS (NM_172913)	-113	NM_172913	244579	Mm.302755	NM_172913	ENSMUSG00000043668	Tox3	500-9|BC052044|C230068E13|CAGF9|Tnrc9	TOX high mobility group box family member 3	protein-coding
mm_63985.1	chr7	140090931	140090931	+	1	NA	Intergenic	RLTR21|LTR|ERVK	-2465	NM_009475	22264	Mm.439707	NM_009475	ENSMUSG00000025467	Prap1	Upa	proline-rich acidic protein 1	protein-coding
mm_136999.1	chr17	17448861	17448884	+	1	NA	intron (NM_025681, intron 4 of 5)	intron (NM_025681, intron 4 of 5)	46186	NM_025681	66643	Mm.268018	NM_025681	ENSMUSG00000047786	Lix1	5730466L18Rik	limb and CNS expressed 1	protein-coding
mm_113181.1	chr13	24905593	24905609	+	1	NA	promoter-TSS (NR_045182)	promoter-TSS (NR_045182)	1	NR_045182	73326	Mm.458692	NR_045182		4932702P03Rik	1700047I16Rik	RIKEN cDNA 4932702P03 gene	ncRNA
mm_127741.1	chr15	103305444	103305449	+	1	NA	Intergenic	Intergenic	4992	NM_030720	80910	Mm.160369	NM_030720	ENSMUSG00000063234	Gpr84	EX33	G protein-coupled receptor 84	protein-coding
mm_163803.1	chr14	19415797	19415821	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	186778	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_80168.1	chr9	71584588	71584591	+	1	NA	intron (NM_001033208, intron 1 of 12)	intron (NM_001033208, intron 1 of 12)	7771	NM_001033208	102371	Mm.27585	NM_001033208	ENSMUSG00000041361	Myzap	AA407270|AV006038|Gcom1|Gm640|Grinl1a7|Myozap	myocardial zonula adherens protein	protein-coding
mm_23572.1	chr3	63296202	63296223	+	1	NA	5' UTR (NM_001289463, exon 1 of 23)	5' UTR (NM_001289463, exon 1 of 23)	117	NM_001289463	17380	Mm.296022	NM_008604	ENSMUSG00000027820	Mme	6030454K05Rik|C85356|CALLA|CD10|NEP|SFE	membrane metallo endopeptidase	protein-coding
mm_172401.1	chr7	144255078	144255081	-	1	NA	intron (NM_001113373, intron 4 of 15)	RLTR12BD_Mm|LTR|ERVK	-29306	NM_001081370	210274	Mm.483624	NM_001081370	ENSMUSG00000037541	Shank2	ProSAP1|mKIAA1022	SH3/ankyrin domain gene 2	protein-coding
mm_171226.1	chr3	61889702	61889703	-	1	NA	Intergenic	RLTR44C|LTR|ERVK	-449075	NM_001081295	622434	Mm.153974	NM_001081295	ENSMUSG00000036885	Arhgef26	4631416L12Rik|8430436L14Rik|AI303572|AW491953|SGEF	Rho guanine nucleotide exchange factor (GEF) 26	protein-coding
mm_155974.1	chrX	106125994	106126009	+	1	NA	3' UTR (NM_009726, exon 23 of 23)	3' UTR (NM_009726, exon 23 of 23)	-17274	NM_205820	279572	Mm.336203	NM_205820	ENSMUSG00000033777	Tlr13	AI666735|Gm713	toll-like receptor 13	protein-coding
mm_72680.1	chr8	84948843	84948866	+	1	NA	intron (NM_144929, intron 1 of 5)	B3A|SINE|B2	1863	NM_144929	234542	Mm.461701	NM_144929	ENSMUSG00000048617	Rtbdn	A330096I21Rik|BC022744|Rtbnd	retbindin	protein-coding
mm_6355.1	chr1	71731047	71731049	-	1	NA	Intergenic	Intergenic	77713	NR_040308	100042814	Mm.405775	NR_040308	ENSMUSG00000073652	Apol7d	ENSMUSG00000073652|Gm15456|OTTMUSG00000022136	apolipoprotein L 7d	ncRNA
mm_71156.1	chr8	40308002	40308050	+	1	NA	promoter-TSS (NR_106126)	promoter-TSS (NR_106126)	-25	NM_030110	78506	Mm.169893	NM_030110	ENSMUSG00000039478	Micu3	2900075B16Rik|Efha2	mitochondrial calcium uptake family, member 3	protein-coding
mm_170163.1	chr17	52149357	52149363	+	1	NA	Intergenic	Intergenic	266633	NR_045095	100504169	Mm.417731	NR_045095		Gm20098	-	predicted gene, 20098	ncRNA
mm_118173.1	chr13	106836390	106836402	-	1	NA	intron (NM_029665, intron 27 of 29)	intron (NM_029665, intron 27 of 29)	100519	NM_029665	76582	Mm.132208	NM_029665	ENSMUSG00000042590	Ipo11	1700081H05Rik|2510001A17Rik|AI314624|AW555235|E330021B14Rik|Ranbp11	importin 11	protein-coding
mm_62134.1	chr7	97081780	97081794	+	1	NA	promoter-TSS (NM_010248)	promoter-TSS (NM_010248)	36	NM_010248	14389	Mm.42033	NM_010248	ENSMUSG00000004508	Gab2	AI463667|D130058I17Rik|p97	growth factor receptor bound protein 2-associated protein 2	protein-coding
mm_154874.1	chrX	20688380	20688481	+	1	NA	promoter-TSS (NM_011049)	promoter-TSS (NM_011049)	4	NM_011049	18555	Mm.102574	NM_011049	ENSMUSG00000031065	Cdk16	Crk5|Pctaire1|Pctk1	cyclin-dependent kinase 16	protein-coding
mm_72928.1	chr8	91112072	91112090	+	1	NA	3' UTR (NM_001302337, exon 10 of 10)	3' UTR (NM_001302337, exon 10 of 10)	21946	NM_001302337	14339	Mm.324588	NM_010241	ENSMUSG00000031667	Aktip	AL023020|Fif|Ft|Ft1|Fts	thymoma viral proto-oncogene 1 interacting protein	protein-coding
mm_64239.1	chr7	141701360	141701371	+	1	NA	exon (NM_023566, exon 24 of 46)	exon (NM_023566, exon 24 of 46)	11025	NM_023566	17831	Mm.2041	NM_023566		Muc2	2010015E03Rik|MCM|wnn	mucin 2	protein-coding
mm_170688.1	chr2	130880836	130880856	+	1	NA	intron (NR_015523, intron 1 of 2)	intron (NR_015523, intron 1 of 2)	25550	NR_015523	613258	Mm.271990	NR_015523		A730017L22Rik	-	RIKEN cDNA A730017L22 gene	ncRNA
mm_69063.1	chr7	126898226	126898247	-	1	NA	promoter-TSS (NM_028389)	promoter-TSS (NM_028389)	42	NM_026827	68742	Mm.248646	NM_026827	ENSMUSG00000060538	Tmem219	1110032O16Rik|2900045G02Rik|IGFBP-3R	transmembrane protein 219	protein-coding
mm_93722.1	chr10	119239736	119239750	-	1	NA	5' UTR (NM_027994, exon 1 of 15)	5' UTR (NM_027994, exon 1 of 15)	312	NM_027994	71902	Mm.203965	NM_027994	ENSMUSG00000020114	Cand1	2310038O07Rik|6330512O03Rik|AI195005|AI846556|D10Ertd516e|Tp120a|mKIAA0829	cullin associated and neddylation disassociated 1	protein-coding
mm_3084.1	chr1	134405803	134405813	+	1	NA	promoter-TSS (NM_028057)	promoter-TSS (NM_028057)	-182	NM_028057	72017	Mm.280230	NM_028057	ENSMUSG00000026456	Cyb5r1	1500005G05Rik|B5R.1|C80155|Nqo3a2	cytochrome b5 reductase 1	protein-coding
mm_56327.1	chr6	92534836	92534850	-	1	NA	promoter-TSS (NM_001134459)	promoter-TSS (NM_001134459)	18	NM_001134459	243548	Mm.248820	NM_001081146	ENSMUSG00000030020	Prickle2	6230400G14Rik|6720451F06Rik|mpk2	prickle planar cell polarity protein 2	protein-coding
mm_28700.1	chr3	95545365	95545386	-	1	NA	exon (NM_021281, exon 5 of 8)	exon (NM_021281, exon 5 of 8)	-14302	NM_026489	67981	Mm.179050	NM_026489	ENSMUSG00000028109	Hormad1	4921522K05Rik|Nohma	HORMA domain containing 1	protein-coding
mm_153368.1	chr19	40271845	40271865	-	1	NA	promoter-TSS (NM_016861)	promoter-TSS (NM_016861)	-239	NM_016861	54132	Mm.5567	NM_016861	ENSMUSG00000055044	Pdlim1	CLP36|Clim1|mClim1	PDZ and LIM domain 1 (elfin)	protein-coding
mm_91574.1	chr10	40128451	40128461	-	1	NA	intron (NM_001114332, intron 1 of 5)	intron (NM_001114332, intron 1 of 5)	13798	NM_028247	72472	Mm.186778	NM_028247	ENSMUSG00000019838	Slc16a10	2610103N14Rik|9830169E08|Mct10|PRO0813|TAT1	solute carrier family 16 (monocarboxylic acid transporters), member 10	protein-coding
mm_27754.1	chr3	69596292	69596294	-	1	NA	intron (NM_020026, intron 1 of 2)	ORR1A4|LTR|ERVL-MaLR	2667	NM_020026	26879	Mm.153710	NM_020026	ENSMUSG00000043300	B3galnt1	B3galt3|b3GT3	UDP-GalNAc:betaGlcNAc beta 1,3-galactosaminyltransferase, polypeptide 1	protein-coding
mm_77432.1	chr8	121544285	121544314	-	1	NA	promoter-TSS (NR_045903)	promoter-TSS (NR_045903)	-89	NR_045903	72259	Mm.396206	NR_045903	ENSMUSG00000097424	1700030M09Rik	-	RIKEN cDNA 1700030M09 gene	ncRNA
mm_136035.1	chr16	77421670	77421684	-	1	NA	intron (NR_015543, intron 2 of 4)	intron (NR_015543, intron 2 of 4)	92349	NR_015543	77994	Mm.394688	NR_015543	ENSMUSG00000090386	Mir99ahg	2810055G20Rik|D730043B02Rik	Mir99a and Mirlet7c-1 host gene (non-protein coding)	ncRNA
mm_90746.1	chr10	5424332	5424356	-	1	NA	exon (NM_153399, exon 8 of 32)	exon (NM_153399, exon 8 of 32)	63970	NM_001347711	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_108243.1	chr12	78226350	78226360	+	1	NA	promoter-TSS (NM_172952)	promoter-TSS (NM_172952)	-300	NM_172952	268566	Mm.341742	NM_145965	ENSMUSG00000047454	Gphn	5730552E08Rik|AI662856|BC027112|C230040D23|GPH|GPHRYN|geph	gephyrin	protein-coding
mm_81703.1	chr9	111271921	111271943	+	1	NA	promoter-TSS (NM_026810)	promoter-TSS (NM_026810)	87	NM_175266	77781	Mm.209005	NM_175266	ENSMUSG00000046785	Epm2aip1	A930003G21Rik|mKIAA0766	EPM2A (laforin) interacting protein 1	protein-coding
mm_13638.1	chr2	114047556	114047574	+	1	NA	exon (NM_009608, exon 7 of 7)	exon (NM_009608, exon 7 of 7)	5310	NM_009608	11464	Mm.686	NM_009608	ENSMUSG00000068614	Actc1	Actc-1	actin, alpha, cardiac muscle 1	protein-coding
mm_75929.1	chr8	71511736	71511761	-	1	NA	promoter-TSS (NM_032398)	promoter-TSS (NM_032398)	21	NM_032398	84094	Mm.260768	NM_032398	ENSMUSG00000034845	Plvap	MECA32|Pv1	plasmalemma vesicle associated protein	protein-coding
mm_109671.1	chr12	113052563	113052586	+	1	NA	intron (NM_001291444, intron 8 of 23)	L1MC1|LINE|L1	-21928	NM_029381	75671	Mm.23377	NM_029381	ENSMUSG00000012211	Tex22	1700028O09Rik|AV210422|Tep22	testis expressed gene 22	protein-coding
mm_134324.1	chr16	16313425	16313444	-	1	NA	non-coding (NR_075074, exon 20 of 20)	non-coding (NR_075074, exon 20 of 20)	10469	NM_198246	70120	Mm.37486	NM_198246	ENSMUSG00000022792	Yars2	2210023C10Rik|tyrRS	tyrosyl-tRNA synthetase 2 (mitochondrial)	protein-coding
mm_144352.1	chr18	15313459	15313465	+	1	NA	Intergenic	Intergenic	89537	NM_001308647	11829	Mm.250786	NM_009700	ENSMUSG00000024411	Aqp4	WCH4	aquaporin 4	protein-coding
mm_145183.1	chr18	48046646	48046646	+	1	NA	intron (NM_001025388, intron 1 of 1)	intron (NM_001025388, intron 1 of 1)	1311	NM_001025388	433182	Mm.70666	NM_001025388	ENSMUSG00000059040	Eno1b	EG433182|Eno1|Gm5506	enolase 1B, retrotransposed	protein-coding
mm_8824.1	chr1	162460223	162460227	-	1	NA	intron (NM_001038619, intron 1 of 20)	intron (NM_001038619, intron 1 of 20)	17805	NM_001038619	103967	Mm.441620	NM_172646	ENSMUSG00000040265	Dnm3	9630020E24Rik|AW061159|B230343F03Rik|C530045C17|mKIAA0820	dynamin 3	protein-coding
mm_89591.1	chr10	95940682	95940703	+	1	NA	promoter-TSS (NM_001001932)	promoter-TSS (NM_001001932)	29	NM_001001932	216238	Mm.210035	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding
mm_122960.1	chr14	54968421	54968430	-	1	NA	promoter-TSS (NR_033497)	promoter-TSS (NR_033497)	-362	NR_033497	791403	Mm.319176	NR_033497	ENSMUSG00000097652	Mhrt	D830015G02Rik|ENSMUSG00000053118|Myheart	myosin heavy chain associated RNA transcript	ncRNA
mm_136523.1	chr16	97459598	97459621	-	1	NA	intron (NR_003520, intron 2 of 8)	L1MEc|LINE|L1	3296	NM_010846	17857	Mm.33996	NM_010846	ENSMUSG00000000386	Mx1	AI893580|Mx|Mx-1	MX dynamin-like GTPase 1	protein-coding
mm_52384.1	chr6	113237846	113237874	+	1	NA	promoter-TSS (NM_026849)	promoter-TSS (NM_026849)	17	NM_026849	97287	Mm.197816	NM_026849	ENSMUSG00000030269	Mtmr14	1110061O04Rik|AW553738|C76151	myotubularin related protein 14	protein-coding
mm_90675.1	chr10	128908908	128908925	+	1	NA	promoter-TSS (NM_007653)	promoter-TSS (NM_007653)	-3	NM_001042580	12512	Mm.371552	NM_007653	ENSMUSG00000025351	Cd63	C75951|ME491|Tspan30	CD63 antigen	protein-coding
mm_14285.1	chr2	128802314	128802326	+	1	NA	TTS (NM_008587)	TTS (NM_008587)	-15983	NM_028248	72477	Mm.259688	NM_028248	ENSMUSG00000014353	Tmem87b	2610301K12Rik|2810431I02Rik|AU014804	transmembrane protein 87B	protein-coding
mm_158622.1	chrX	152769601	152769649	-	1	NA	promoter-TSS (NM_172441)	promoter-TSS (NM_172441)	-139	NM_172441	110380	Mm.40796	NM_172441	ENSMUSG00000045180	Shroom2	4832440C16|Apxl|C630003H05Rik|Shrm2	shroom family member 2	protein-coding
mm_139060.1	chr17	46428931	46428949	+	1	NA	promoter-TSS (NM_181664)	promoter-TSS (NM_181664)	-2	NM_053250	114570	Mm.25168	NM_053250	ENSMUSG00000023968	Crip3	TLP|TLP-A|TLP-B|Tlmp	cysteine-rich protein 3	protein-coding
mm_94397.1	chr11	5574157	5574167	+	1	NA	intron (NM_023816, intron 3 of 26)	intron (NM_023816, intron 3 of 26)	4478	NM_023816	76389	Mm.67300	NM_023816	ENSMUSG00000020481	Ankrd36	1700008J08Rik|1700012M14Rik|Ankrd48	ankyrin repeat domain 36	protein-coding
mm_87709.1	chr10	60003221	60003277	+	1	NA	promoter-TSS (NM_001199187)	promoter-TSS (NM_001199187)	-78	NM_001199187	69090	Mm.155839	NM_026937	ENSMUSG00000044475	Ascc1	1810015P09Rik|AI550520|ASC1p50|CGI-18	activating signal cointegrator 1 complex subunit 1	protein-coding
mm_79165.1	chr9	47848215	47848253	+	1	NA	exon (NM_018770, exon 9 of 10)	exon (NM_018770, exon 9 of 10)	-30026	NR_046048	100038460	Mm.447649	NR_046048		Gm10677	ENSMUSG00000074363	predicted gene 10677	ncRNA
mm_30393.1	chr3	152248258	152248274	-	1	NA	exon (NM_199465, exon 6 of 13)	exon (NM_199465, exon 6 of 13)	18054	NM_199465	68810	Mm.200188	NM_199465	ENSMUSG00000039103	Nexn	1110046H09Rik|AA553326|NELIN	nexilin	protein-coding
mm_28552.1	chr3	93279760	93279764	-	1	NA	Intergenic	Intergenic	-39987	NM_133698	68723	Mm.208047	NM_133698	ENSMUSG00000041991	Hrnr	1110033K19Rik|A530063N20Rik|S100a18	hornerin	protein-coding
mm_148785.1	chr19	6114459	6114471	+	1	NA	exon (NM_001009546, exon 14 of 18)	exon (NM_001009546, exon 14 of 18)	4121	NM_133678	66406	Mm.303924	NM_133678	ENSMUSG00000024790	Sac3d1	2410004C24Rik|AU015683|shd1	SAC3 domain containing 1	protein-coding
mm_14903.1	chr2	150257515	150257559	+	1	NA	promoter-TSS (NM_001142410)	promoter-TSS (NM_001142410)	20	NM_001142410	100216455	Mm.484816	NM_001142410	ENSMUSG00000079008	Gm14124	EG640962|ENSMUSG00000074735|Gm10749|OTTMUSG00000015734	predicted gene 14124	protein-coding
mm_79726.1	chr9	62341339	62341390	+	1	NA	promoter-TSS (NM_009672)	promoter-TSS (NM_009672)	21	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	protein-coding
mm_172363.1	chr7	120370267	120370284	-	1	NA	intron (NM_177213, intron 17 of 30)	BGLII|LTR|ERVK	-39372	NM_001278943	233810		NM_001278943	ENSMUSG00000051900	Abca16	AY243472	ATP-binding cassette, sub-family A (ABC1), member 16	protein-coding
mm_155926.1	chrX	103414462	103414481	+	1	NA	promoter-TSS (NM_009440)	promoter-TSS (NM_009440)	4	NM_009440	22127	Mm.358644	NM_009440	ENSMUSG00000031329	Tsx	AV207184	testis specific X-linked gene	protein-coding
mm_146487.1	chr18	90510299	90510316	+	1	NA	5' UTR (NM_198295, exon 1 of 16)	5' UTR (NM_198295, exon 1 of 16)	153	NM_198295	67988	Mm.268041	NM_198295	ENSMUSG00000024614	Tmx3	6430411B10Rik|A730024F05Rik|AV259382|Txndc10|mKIAA1830	thioredoxin-related transmembrane protein 3	protein-coding
mm_143768.1	chr17	81648847	81648857	-	1	NA	exon (NM_001112798, exon 2 of 9)	exon (NM_001112798, exon 2 of 9)	89535	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_108245.1	chr12	78226419	78226419	+	1	NA	promoter-TSS (NM_172952)	promoter-TSS (NM_172952)	-236	NM_172952	268566	Mm.341742	NM_145965	ENSMUSG00000047454	Gphn	5730552E08Rik|AI662856|BC027112|C230040D23|GPH|GPHRYN|geph	gephyrin	protein-coding
mm_31735.1	chr4	63151453	63151483	+	1	NA	exon (NM_007443, exon 3 of 10)	exon (NM_007443, exon 3 of 10)	2704	NM_007443	11699	Mm.2197	NM_007443	ENSMUSG00000028356	Ambp	AI194774|ASPI|HI-30|Intin4|Itil|UTI	alpha 1 microglobulin/bikunin	protein-coding
mm_94438.1	chr11	6292669	6292692	+	1	NA	5' UTR (NM_001252288, exon 1 of 23)	5' UTR (NM_001252288, exon 1 of 23)	122	NM_001252288	18293	Mm.276348	NM_010956	ENSMUSG00000020456	Ogdh	2210403E04Rik|2210412K19Rik|AA409584|d1401|mKIAA4192	oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)	protein-coding
mm_44047.1	chr5	147860616	147860670	+	1	NA	promoter-TSS (NM_025624)	promoter-TSS (NM_025624)	15	NM_025624	66537	Mm.332855	NM_025624	ENSMUSG00000029649	Pomp	2510048O06Rik|Ump1	proteasome maturation protein	protein-coding
mm_72544.1	chr8	83997614	83997654	+	1	NA	promoter-TSS (NM_001081415)	promoter-TSS (NM_001081415)	-38	NM_001081415	666704	Mm.298091	NM_001081415	ENSMUSG00000079003	Samd1	AA589507	sterile alpha motif domain containing 1	protein-coding
mm_29649.1	chr3	122245220	122245229	-	1	NA	promoter-TSS (NM_008129)	promoter-TSS (NM_008129)	-333	NM_008129	14630	Mm.292676	NM_008129	ENSMUSG00000028124	Gclm	AI649393|Gcmc|Glclr	glutamate-cysteine ligase, modifier subunit	protein-coding
mm_46712.1	chr5	110387091	110387154	-	1	NA	promoter-TSS (NM_028596)	promoter-TSS (NM_028596)	5	NM_028596	381668	Mm.348782	NM_028596	ENSMUSG00000043323	Fbrsl1	2410025L10Rik|AI467568|Gm1049|Gm29766|mKIAA1545	fibrosin-like 1	protein-coding
mm_37218.1	chr4	117914969	117915018	-	1	NA	promoter-TSS (NM_146152)	promoter-TSS (NM_146152)	6	NM_146152	230673	Mm.287810	NM_146152	ENSMUSG00000033365	Ipo13	Imp13|Kap13|Ranbp13	importin 13	protein-coding
mm_31332.1	chr4	46452161	46452224	+	1	NA	intron (NM_130889, intron 1 of 6)	CpG	1266	NM_130889	67628	Mm.263913	NM_130889	ENSMUSG00000028333	Anp32b	2410015B15Rik|PAL31|PHAPI2a|Ssp29	acidic (leucine-rich) nuclear phosphoprotein 32 family, member B	protein-coding
mm_38189.1	chr4	135337910	135337922	-	1	NA	exon (NM_001130477, exon 9 of 18)	exon (NM_001130477, exon 9 of 18)	15298	NM_016799	51796	Mm.1963	NM_016799	ENSMUSG00000028809	Srrm1	AA407769|POP101|Srm160	serine/arginine repetitive matrix 1	protein-coding
mm_132573.1	chr16	38177705	38177708	+	1	NA	intron (NM_001347232, intron 3 of 11)	intron (NM_001347232, intron 3 of 11)	-88446	NR_033221	414072	Mm.483602	NR_033221		BC031361	-	cDNA sequence BC031361	ncRNA
mm_60895.1	chr7	46397762	46397783	+	1	NA	exon (NM_001112739, exon 1 of 4)	exon (NM_001112739, exon 1 of 4)	1304	NM_001112739	16502	Mm.249386	NM_008421	ENSMUSG00000058975	Kcnc1	C230009H10Rik|KShIIIB|KV4|Kcr2-1|Kv3.1|NGK2|Shaw	potassium voltage gated channel, Shaw-related subfamily, member 1	protein-coding
mm_47279.1	chr5	122050219	122050231	-	1	NA	promoter-TSS (NM_001312908)	promoter-TSS (NM_001312908)	-374	NM_001312908	13048	Mm.156172	NM_007804	ENSMUSG00000042589	Cux2	1700051K22Rik|Cutl2|Cux-2|ENSMUSG00000072641	cut-like homeobox 2	protein-coding
mm_133613.1	chr16	91547049	91547114	+	1	NA	promoter-TSS (NM_008338)	promoter-TSS (NM_008338)	-13	NM_008338	15980	Mm.249364	NM_008338	ENSMUSG00000022965	Ifngr2	Ifgr2|Ifgt	interferon gamma receptor 2	protein-coding
mm_33424.1	chr4	130047857	130047901	+	1	NA	promoter-TSS (NM_028266)	promoter-TSS (NM_028266)	39	NM_028266	107581	Mm.41860	NM_028266	ENSMUSG00000040690	Col16a1	2700007F12Rik|A530052M23Rik|AI838662|CA1F	collagen, type XVI, alpha 1	protein-coding
mm_6182.1	chr1	65103364	65103378	-	1	NA	promoter-TSS (NM_007774)	promoter-TSS (NM_007774)	-8	NM_007774	12964	Mm.26904	NM_007774	ENSMUSG00000044429	Cryga	Cryg-4|DGcry-4	crystallin, gamma A	protein-coding
mm_173096.1	chrX	151958218	151958218	-	1	NA	Intergenic	L1Md_T|LINE|L1	-43678	NM_016763	15108	Mm.6994	NM_016763	ENSMUSG00000025260	Hsd17b10	17bHSD10|Ads9|ERAB|Hadh2	hydroxysteroid (17-beta) dehydrogenase 10	protein-coding
mm_159424.1	chr3	108398808	108398808	-	1	NA	intron (NM_001004177, intron 16 of 33)	intron (NM_001004177, intron 16 of 33)	14970	NM_019976	56742	Mm.389499	NM_019976	ENSMUSG00000068744	Psrc1	5430413I02Rik|AL033312|Dda3	proline/serine-rich coiled-coil 1	protein-coding
mm_145321.1	chr18	54771392	54771400	+	1	NA	Intergenic	Intergenic	159652	NR_045400	328957	Mm.402781	NR_045400		9330117O12Rik	9330117O12	RIKEN cDNA 9330117O12 gene	ncRNA
mm_57248.1	chr6	123283391	123283394	-	1	NA	3' UTR (NM_019948, exon 6 of 6)	3' UTR (NM_019948, exon 6 of 6)	6479	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_28613.1	chr3	94838345	94838350	-	1	NA	intron (NM_001165948, intron 1 of 18)	intron (NM_001165948, intron 1 of 18)	780	NM_172683	229584	Mm.274787	NM_172683	ENSMUSG00000038902	Pogz	9530006B08Rik	pogo transposable element with ZNF domain	protein-coding
mm_22759.1	chr3	19989152	19989164	+	1	NA	exon (NM_007752, exon 18 of 19)	exon (NM_007752, exon 18 of 19)	32104	NM_007752	12870	Mm.13787	NM_007752	ENSMUSG00000003617	Cp	D3Ertd555e	ceruloplasmin	protein-coding
mm_173059.1	chrX	126307321	126307322	+	1	NA	Intergenic	L1Md_F2|LINE|L1	526683	NM_177705	237029	Mm.60998	NM_177705	ENSMUSG00000058670	4932411N23Rik	-	RIKEN cDNA 4932411N23 gene	protein-coding
mm_52216.1	chr6	103510774	103510784	+	1	NA	promoter-TSS (NM_007697)	promoter-TSS (NM_007697)	-97	NM_007697	12661	Mm.251288	NM_007697	ENSMUSG00000030077	Chl1	A530023M13Rik|AI465420|CALL|LICAM2	cell adhesion molecule L1-like	protein-coding
mm_110340.1	chr12	36042452	36042462	-	1	NA	promoter-TSS (NM_025359)	promoter-TSS (NM_025359)	21	NM_025359	66109	Mm.254663	NM_025359	ENSMUSG00000020577	Tspan13	1100001I23Rik|NET-6|Tm4sf13	tetraspanin 13	protein-coding
mm_126563.1	chr15	82169991	82170001	+	1	NA	exon (NM_033218, exon 2 of 19)	exon (NM_033218, exon 2 of 19)	22727	NM_033218	20788	Mm.9002	NM_033218	ENSMUSG00000022463	Srebf2	AI608257|SREBP-2|SREBP2|SREBP2gc|bHLHd2|lop13|nuc	sterol regulatory element binding factor 2	protein-coding
mm_135033.1	chr16	32867511	32867517	-	1	NA	intron (NM_172615, intron 1 of 18)	intron (NM_172615, intron 1 of 18)	852	NM_001200038	100502698	Mm.327319	NM_172615	ENSMUSG00000035629	Rubcn	1700021K19Rik|5330403K09|Kiaa0226|Rubicon|mKIAA0226	RUN domain and cysteine-rich domain containing, Beclin 1-interacting protein	protein-coding
mm_6428.1	chr1	73948059	73948080	-	1	NA	intron (NM_027884, intron 19 of 34)	L2|LINE|L2	-83603	NR_045311	109198	Mm.359721	NR_045311	ENSMUSG00000100301	6030407O03Rik	-	RIKEN cDNA 6030407O03 gene	ncRNA
mm_141781.1	chr17	34296107	34296120	-	1	NA	Intergenic	Intergenic	-8342	NM_010378	14960	Mm.235338	NM_010378	ENSMUSG00000036594	H2-Aa	Aalpha|H-2Aa|H2Aa|I-Aalpha|IAalpha|Ia-1|Ia1	histocompatibility 2, class II antigen A, alpha	protein-coding
mm_35847.1	chr4	48442129	48442131	-	1	NA	intron (NM_172304, intron 12 of 15)	intron (NM_172304, intron 12 of 15)	31292	NM_172304	269536	Mm.272025	NM_172304	ENSMUSG00000028345	Tex10	2610206N19Rik|2810462N03Rik|BC006867	testis expressed gene 10	protein-coding
mm_110091.1	chr12	25096081	25096096	-	1	NA	promoter-TSS (NM_010496)	promoter-TSS (NM_010496)	4	NM_010496	15902	Mm.34871	NM_010496	ENSMUSG00000020644	Id2	AI255428|C78922|Idb2|bHLHb26	inhibitor of DNA binding 2	protein-coding
mm_29541.1	chr3	116712199	116712240	-	1	NA	promoter-TSS (NM_144902)	promoter-TSS (NM_144902)	61	NM_144902	229782	Mm.190758	NM_144902	ENSMUSG00000027957	Slc35a3	2310050P13Rik	solute carrier family 35 (UDP-N-acetylglucosamine (UDP-GlcNAc) transporter), member 3	protein-coding
mm_111153.1	chr12	83424890	83424903	-	1	NA	intron (NM_058212, intron 1 of 8)	intron (NM_058212, intron 1 of 8)	62840	NM_001267626	70127	Mm.151308	NM_058212	ENSMUSG00000021221	Dpf3	2810403B03Rik|6530402L11Rik|BAF45C|C78788|CERD4|cer-d4	D4, zinc and double PHD fingers, family 3	protein-coding
mm_85791.1	chr9	109543074	109543076	-	1	NA	Intergenic	RLTR45|LTR|ERVK	25187	NM_199036	382105	Mm.335468	NM_199036	ENSMUSG00000074060	Fbxw15	Fbxo12J	F-box and WD-40 domain protein 15	protein-coding
mm_28612.1	chr3	94786470	94786490	-	1	NA	promoter-TSS (NM_001293727)	promoter-TSS (NM_001293727)	35	NM_001293727	70737	Mm.87634	NM_001037711	ENSMUSG00000068876	Cgn	6330408J11Rik	cingulin	protein-coding
mm_52299.1	chr6	108794880	108794924	+	1	NA	intron (NM_026011, intron 1 of 6)	intron (NM_026011, intron 1 of 6)	11843	NM_026011	67166	Mm.271178	NM_026011	ENSMUSG00000030105	Arl8b	2610313E07Rik|3100002J04Rik|Arl10c|gie1	ADP-ribosylation factor-like 8B	protein-coding
mm_28416.1	chr3	90389964	90389976	-	1	NA	promoter-TSS (NM_001316688)	promoter-TSS (NM_001316688)	-32	NM_011988	26568	Mm.45519	NM_011988	ENSMUSG00000027932	Slc27a3	Acsvl3|FATP-3|FATP3|Vlcs-3	solute carrier family 27 (fatty acid transporter), member 3	protein-coding
mm_73036.1	chr8	94214568	94214608	+	1	NA	promoter-TSS (NM_172410)	promoter-TSS (NM_172410)	-13	NM_172410	71805	Mm.458170	NM_172410	ENSMUSG00000032939	Nup93	2410008G02Rik	nucleoporin 93	protein-coding
mm_123027.1	chr14	55490606	55490608	-	1	NA	promoter-TSS (NM_001024645)	promoter-TSS (NM_001024645)	-486	NM_001024645	268747	Mm.151577	NM_001024645	ENSMUSG00000022211	Carmil3	Lrrc16b|mFLJ00240	capping protein regulator and myosin 1 linker 3	protein-coding
mm_72792.1	chr8	86914782	86914788	+	1	NA	Intergenic	RMER3D-int|LTR|ERVK	-29527	NM_030563	80750	Mm.25117	NM_030563	ENSMUSG00000031652	N4bp1	AI481586|C81621	NEDD4 binding protein 1	protein-coding
mm_68688.1	chr7	119476799	119476808	-	1	NA	exon (NM_001278605, exon 3 of 11)	exon (NM_001278605, exon 3 of 11)	2459	NM_009470	22242	Mm.10826	NM_009470	ENSMUSG00000030963	Umod	THP|Urehd1|urehr4	uromodulin	protein-coding
mm_137401.1	chr17	25865571	25865572	+	1	NA	intron (NM_026633, intron 2 of 4)	intron (NM_026633, intron 2 of 4)	3167	NM_026633	68241	Mm.328870	NM_026633	ENSMUSG00000025732	Fam195a	9530058B02Rik|Mcrip2	family with sequence similarity 195, member A	protein-coding
mm_89331.1	chr10	87933198	87933209	+	1	NA	3' UTR (NM_010512, exon 5 of 5)	3' UTR (NM_010512, exon 5 of 5)	-33468	NR_000040	22172	Mm.391420	NR_000040		Tyms-ps	-	thymidylate synthase, pseudogene	pseudo
mm_11322.1	chr2	30416032	30416077	+	1	NA	promoter-TSS (NM_007760)	promoter-TSS (NM_007760)	4	NM_138748	110854	Mm.275393	NM_138748	ENSMUSG00000039515	Ptpa	2610042B21Rik|C77440|N28142|PR53|Ppp2r4	protein phosphatase 2 protein activator	protein-coding
mm_78364.1	chr9	26924461	26924500	+	1	NA	Intergenic	B1F|SINE|Alu	-1399	NM_001281475	382064	Mm.335028	NM_001177509	ENSMUSG00000079644	Gm1110	-	predicted gene 1110	protein-coding
mm_63915.1	chr7	139235862	139235878	+	1	NA	intron (NM_027164, intron 8 of 10)	intron (NM_027164, intron 8 of 10)	-12612	NM_001033206	101631	Mm.334300	NM_001033206	ENSMUSG00000060260	Pwwp2b	AI594893|D7Ertd517e|D930023J19Rik|Pwwp2	PWWP domain containing 2B	protein-coding
mm_119450.1	chr14	46889331	46889335	+	1	NA	intron (NM_001037221, intron 2 of 12)	intron (NM_001037221, intron 2 of 12)	6368	NM_001037221	74480	Mm.214454	NM_028966	ENSMUSG00000021838	Samd4	1700024G08Rik|1700111L17Rik|4933436G17Rik|Samd4a|Smaug|Smaug1|sunk	sterile alpha motif domain containing 4	protein-coding
mm_152976.1	chr19	29463675	29463712	-	1	NA	intron (NM_021396, intron 5 of 5)	intron (NM_021396, intron 5 of 5)	52774	NM_021396	58205	Mm.116737	NM_021396	ENSMUSG00000016498	Pdcd1lg2	B7-DC|Btdc|F730015O22Rik|PD-L2	programmed cell death 1 ligand 2	protein-coding
mm_74084.1	chr8	122549339	122549357	+	1	NA	intron (NM_001037298, intron 1 of 50)	intron (NM_001037298, intron 1 of 50)	1981	NM_001037298	234839	Mm.37324	NM_001037298	ENSMUSG00000014444	Piezo1	9630020g22|Fam38a|mKIAA0233	piezo-type mechanosensitive ion channel component 1	protein-coding
mm_45882.1	chr5	88328511	88328533	-	1	NA	exon (NM_008644, exon 3 of 3)	exon (NM_008644, exon 3 of 3)	11210	NM_008644	17830	Mm.200411	NM_008644	ENSMUSG00000064156	Prol1	Muc10	proline rich, lacrimal 1	protein-coding
mm_56848.1	chr6	117907754	117907761	-	1	NA	promoter-TSS (NM_001166429)	intron (NM_133834, intron 1 of 3)	-47	NM_001166428	98758	Mm.422979	NM_133834	ENSMUSG00000042079	Hnrnpf	4833420I20Rik|AA407306|Hnrpf	heterogeneous nuclear ribonucleoprotein F	protein-coding
mm_117409.1	chr13	74009304	74009327	-	1	NA	promoter-TSS (NM_182839)	promoter-TSS (NM_182839)	-104	NM_182839	72948	Mm.39752	NM_182839	ENSMUSG00000021573	Tppp	2900041A09Rik|AI849835	tubulin polymerization promoting protein	protein-coding
mm_131250.1	chr16	10545391	10545427	+	1	NA	promoter-TSS (NM_177562)	promoter-TSS (NM_177562)	70	NM_001204229	74374	Mm.159176	NM_177562	ENSMUSG00000068663	Clec16a	4932416N17Rik|curt|mKIAA0350	C-type lectin domain family 16, member A	protein-coding
mm_136379.1	chr16	92825923	92825931	-	1	NA	intron (NM_001111022, intron 1 of 6)	intron (NM_001111022, intron 1 of 6)	147	NM_001111021	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_97170.1	chr11	75513549	75513582	+	1	NA	promoter-TSS (NM_001004157)	promoter-TSS (NM_001004157)	24	NM_001004157	380713	Mm.10486	NM_001004157	ENSMUSG00000038188	Scarf1	AA986099|SREC|SREC-I|mKIAA0149	scavenger receptor class F, member 1	protein-coding
mm_137314.1	chr17	24886003	24886017	+	1	NA	promoter-TSS (NM_001163750)	promoter-TSS (NM_001163750)	340	NM_011956	26426	Mm.36718	NM_011956	ENSMUSG00000039183	Nubp2	D17Wsu11e	nucleotide binding protein 2	protein-coding
mm_57820.1	chr6	129462786	129462795	-	1	NA	non-coding (NR_132130, exon 6 of 6)	non-coding (NR_132130, exon 6 of 6)	9989	NM_001309637	56644	Mm.239516	NM_020008	ENSMUSG00000079293	Clec7a	BGR|Clecsf12|beta-GR	C-type lectin domain family 7, member a	protein-coding
mm_95077.1	chr11	32642827	32642841	+	1	NA	5' UTR (NM_134015, exon 1 of 14)	5' UTR (NM_134015, exon 1 of 14)	279	NM_001271347	103583	Mm.28017	NM_134015	ENSMUSG00000020271	Fbxw11	2310065A07Rik|AA536858|BTRC2|BTRCP2|Fbxw1b|HOS	F-box and WD-40 domain protein 11	protein-coding
mm_62376.1	chr7	100706706	100706731	+	1	NA	promoter-TSS (NM_178764)	promoter-TSS (NM_178764)	16	NM_178764	319604	Mm.260362	NM_178764	ENSMUSG00000029461	Fam168a	2610030B18Rik|B930006L02Rik|mKIAA0280	family with sequence similarity 168, member A	protein-coding
mm_75190.1	chr8	38473727	38473730	-	1	NA	intron (NM_145841, intron 1 of 7)	intron (NM_145841, intron 1 of 7)	187780	NM_145841	244431	Mm.210388	NM_145841	ENSMUSG00000039539	Sgcz	C230085N17Rik	sarcoglycan zeta	protein-coding
mm_159835.1	chr5	130073273	130073273	+	1	NA	promoter-TSS (NM_013837)	promoter-TSS (NM_013837)	-53	NM_013837	22021	Mm.332720	NM_013837	ENSMUSG00000034118	Tpst1	R75054|Tango13a	protein-tyrosine sulfotransferase 1	protein-coding
mm_142812.1	chr17	51179250	51179343	-	1	NA	promoter-TSS (NM_001285991)	promoter-TSS (NM_001285991)	56	NM_028162	72238	Mm.120650	NM_028162	ENSMUSG00000023923	Tbc1d5	1600014N05Rik	TBC1 domain family, member 5	protein-coding
mm_154438.1	chrM	1222	1243	-	1	NA	NA	Intergenic	NA	NA								
mm_65025.1	chr7	18431994	18432005	-	1	NA	promoter-TSS (NM_054063)	promoter-TSS (NM_054063)	56	NM_054063	114871	Mm.362025	NM_054063	ENSMUSG00000030373	Psg28	cea16	pregnancy-specific glycoprotein 28	protein-coding
mm_12423.1	chr2	70563319	70563330	+	1	NA	promoter-TSS (NR_040496)	promoter-TSS (NR_040496)	33	NR_040496	68986	Mm.437697	NR_040496	ENSMUSG00000087264	Gad1os	1500002O10Rik	glutamate decarboxylase 1, opposite strand	ncRNA
mm_65929.1	chr7	30322294	30322370	-	1	NA	promoter-TSS (NM_001033140)	promoter-TSS (NM_001033140)	43	NM_001033140	68332	Mm.6844	NM_001033140	ENSMUSG00000074211	Sdhaf1	0610010E21Rik|AI430885|AW490662|Lyrm8	succinate dehydrogenase complex assembly factor 1	protein-coding
mm_24837.1	chr3	95659303	95659320	+	1	NA	exon (NM_008562, exon 1 of 3)	exon (NM_008562, exon 1 of 3)	590	NM_008562	17210	Mm.1639	NM_008562	ENSMUSG00000038612	Mcl1	AW556805|Mcl-1	myeloid cell leukemia sequence 1	protein-coding
mm_137653.1	chr17	28558812	28558825	+	1	NA	promoter-TSS (NR_105935)	promoter-TSS (NR_105935)	-317	NR_105935	102465585		NR_105935	ENSMUSG00000099152	Mir6969	Gm27305|mmu-mir-6969	microRNA 6969	ncRNA
mm_160877.1	chr11	69100173	69100173	+	1	NA	promoter-TSS (NM_001159367)	promoter-TSS (NM_001159367)	15	NM_001159367	18626	Mm.7373	NM_011065	ENSMUSG00000020893	Per1	Hftm|Per|m-rigui|mPer1	period circadian clock 1	protein-coding
mm_125033.1	chr15	25754872	25754898	+	1	NA	intron (NM_019472, intron 19 of 40)	intron (NM_019472, intron 19 of 40)	-88413	NM_001034851	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_90759.1	chr10	5550616	5550631	-	1	NA	promoter-TSS (NM_153399)	promoter-TSS (NM_153399)	69	NM_153399	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_160749.1	chr10	81420713	81420713	-	1	NA	exon (NM_008688, exon 2 of 10)	exon (NM_008688, exon 2 of 10)	-4416	NR_106141	102465778		NR_106141	ENSMUSG00000105379	Mir1191b	mmu-mir-1191b	microRNA 1191b	ncRNA
mm_27727.1	chr3	69004566	69004585	-	1	NA	promoter-TSS (NM_133786)	promoter-TSS (NM_133786)	-5	NM_026641	68259	Mm.389451	NM_026641	ENSMUSG00000027778	Ift80	4921524P20Rik|Wdr56|mKIAA1374	intraflagellar transport 80	protein-coding
mm_106804.1	chr12	5643048	5643071	+	1	NA	Intergenic	Intergenic	266557	NR_015579	72669	Mm.10434	NM_028318		2810032G03Rik	AI461720	RIKEN cDNA 2810032G03 gene	ncRNA
mm_24829.1	chr3	95653931	95653933	+	1	NA	Intergenic	Intergenic	-4789	NM_008562	17210	Mm.1639	NM_008562	ENSMUSG00000038612	Mcl1	AW556805|Mcl-1	myeloid cell leukemia sequence 1	protein-coding
mm_168896.1	chr12	51377590	51377590	+	1	NA	promoter-TSS (NM_001306178)	promoter-TSS (NM_001306178)	77	NM_029825	76983	Mm.216511	NM_029825	ENSMUSG00000020952	Scfd1	3110021P21Rik|RA410|STXBP1L2	Sec1 family domain containing 1	protein-coding
mm_60889.1	chr7	46396882	46396894	+	1	NA	5' UTR (NM_001112739, exon 1 of 4)	5' UTR (NM_001112739, exon 1 of 4)	420	NM_001112739	16502	Mm.249386	NM_008421	ENSMUSG00000058975	Kcnc1	C230009H10Rik|KShIIIB|KV4|Kcr2-1|Kv3.1|NGK2|Shaw	potassium voltage gated channel, Shaw-related subfamily, member 1	protein-coding
mm_151689.1	chr19	4321554	4321563	-	1	NA	intron (NM_001001984, intron 18 of 20)	intron (NM_001001984, intron 18 of 20)	-15336	NM_001290818	110355	Mm.254144	NM_130863	ENSMUSG00000024858	Grk2	Adrbk-1|Adrbk1|Bark-1|beta ARK|betaARK1	G protein-coupled receptor kinase 2	protein-coding
mm_148470.1	chr19	4097393	4097415	+	1	NA	promoter-TSS (NM_026373)	promoter-TSS (NM_026373)	53	NM_026373	52004	Mm.29609	NM_026373	ENSMUSG00000024856	Cdk2ap2	5830466O21Rik|D19Ertd144e|Doc-1r	CDK2-associated protein 2	protein-coding
mm_143957.1	chr17	86958002	86958018	-	1	NA	Intergenic	Intergenic	-5101	NM_145491	104215	Mm.826	NM_145491	ENSMUSG00000024143	Rhoq	Arhq|TC10A|Tc10	ras homolog family member Q	protein-coding
mm_137200.1	chr17	23880877	23880881	+	1	NA	promoter-TSS (NM_019910)	promoter-TSS (NM_019910)	3	NM_019910	13184	Mm.371556	NM_019910	ENSMUSG00000096445	Dcpp1	BC005655|C86550|Dcpp|Dcpp-1|p20	demilune cell and parotid protein 1	protein-coding
mm_92465.1	chr10	77970555	77970586	-	1	NA	promoter-TSS (NM_138301)	promoter-TSS (NM_138301)	-698	NM_138301	28240	Mm.276762	NM_138301	ENSMUSG00000009292	Trpm2	9830168K16Rik|C79133|LTRPC2|TRPC7|Trp7|Trrp7	transient receptor potential cation channel, subfamily M, member 2	protein-coding
mm_117503.1	chr13	78200216	78200254	-	1	NA	intron (NR_045195, intron 1 of 2)	(GGAGA)n|Simple_repeat|Simple_repeat	-1362	NM_010151	13865	Mm.439653	NM_010151	ENSMUSG00000069171	Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR-3|EAR3|Erbal3|SVP44|Tcfcoup1	nuclear receptor subfamily 2, group F, member 1	protein-coding
mm_129078.1	chr15	75831789	75831789	-	1	NA	intron (NM_172121, intron 3 of 11)	intron (NM_172121, intron 3 of 11)	10119	NM_172121	223642	Mm.209800	NM_172121	ENSMUSG00000075600	Zc3h3	BC049953|Kiaa0150|Smicl|Zc3hdc3	zinc finger CCCH type containing 3	protein-coding
mm_104897.1	chr11	99610418	99610422	-	1	NA	promoter-TSS (NM_001099346)	promoter-TSS (NM_001099346)	-231	NM_001099346	100041488	Mm.465212	NM_001099346	ENSMUSG00000058725	Gm11937	-	predicted gene 11937	protein-coding
mm_129025.1	chr15	74958737	74958756	-	1	NA	3' UTR (NM_001164036, exon 4 of 4)	3' UTR (NM_001164036, exon 4 of 4)	3640	NM_001164040	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_100447.1	chr11	119491663	119491679	+	1	NA	promoter-TSS (NM_177394)	promoter-TSS (NM_177394)	51	NM_177394	338371	Mm.271946	NM_177394	ENSMUSG00000039850	Endov	A730011L01Rik	endonuclease V	protein-coding
mm_117187.1	chr13	63553322	63553325	-	1	NA	intron (NM_001328514, intron 2 of 23)	B1_Mur1|SINE|Alu	12412	NM_008957	19206	Mm.228798	NM_008957	ENSMUSG00000021466	Ptch1	A230106A15Rik|Ptc|Ptc1|Ptch|mes	patched 1	protein-coding
mm_212.1	chr1	16665190	16665264	+	1	NA	promoter-TSS (NM_027415)	promoter-TSS (NM_027415)	36	NM_026392	70397	Mm.194225	NM_026392	ENSMUSG00000025940	Tmem70	1110020A09Rik|2210416J16Rik	transmembrane protein 70	protein-coding
mm_135547.1	chr16	49801099	49801122	-	1	NA	Intergenic	RSINE1|SINE|B4	-54544	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_166986.1	chr7	45715399	45715420	+	1	NA	promoter-TSS (NM_020011)	promoter-TSS (NM_020011)	-202	NM_020011	56632	Mm.24222	NM_020011	ENSMUSG00000057342	Sphk2	C76851	sphingosine kinase 2	protein-coding
mm_88547.1	chr10	78577095	78577110	+	1	NA	intron (NM_173751, intron 4 of 15)	intron (NM_173751, intron 4 of 15)	2602	NM_173751	216136	Mm.2644	NM_173751	ENSMUSG00000032763	Ilvbl	5830463I21|AI415009	ilvB (bacterial acetolactate synthase)-like	protein-coding
mm_26002.1	chr3	135238046	135238058	+	1	NA	exon (NM_173762, exon 23 of 46)	exon (NM_173762, exon 23 of 46)	25489	NM_173762	229841	Mm.161470	NM_173762	ENSMUSG00000045328	Cenpe	312kDa|AU019344|BC049989|C530022J18|CENP-E|Kif10	centromere protein E	protein-coding
mm_9265.1	chr1	171632236	171632246	-	1	NA	TTS (NM_144539)	TTS (NM_144539)	9659	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_92539.1	chr10	79637910	79637922	-	1	NA	promoter-TSS (NM_001024539)	promoter-TSS (NM_001024539)	2	NM_001024539	216148	Mm.39424	NM_001024539	ENSMUSG00000020312	Shc2	6720466E06|SCK|ShcB|Sli	SHC (Src homology 2 domain containing) transforming protein 2	protein-coding
mm_150622.1	chr19	41263773	41263781	+	1	NA	exon (NM_133352, exon 1 of 15)	exon (NM_133352, exon 1 of 15)	227	NM_133352	107358	Mm.246440	NM_133352	ENSMUSG00000025016	Tm9sf3	1810073M23Rik|2810031D16Rik|AI115521|AI413748|AW146116|AW549777|Smbp|mKIAA4036	transmembrane 9 superfamily member 3	protein-coding
mm_121071.1	chr14	98110220	98110244	+	1	NA	intron (NM_007826, intron 1 of 11)	intron (NM_007826, intron 1 of 11)	59533	NM_001038610	13134	Mm.320593	NM_007826	ENSMUSG00000055639	Dach1	Dac|Dach	dachshund 1 (Drosophila)	protein-coding
mm_32996.1	chr4	120483299	120483303	+	1	NA	intron (NM_001159630, intron 8 of 17)	AT_rich|Low_complexity|Low_complexity	-48930	NM_177570	194219	Mm.29788	NM_177570	ENSMUSG00000047518	Slfnl1	4933406A14Rik	schlafen like 1	protein-coding
mm_100656.1	chr11	3193128	3193173	-	1	NA	intron (NM_030207, intron 1 of 32)	CpG	313	NM_030207	78887	Mm.394071	NM_030207	ENSMUSG00000023764	Sfi1	-	Sfi1 homolog, spindle assembly associated (yeast)	protein-coding
mm_133023.1	chr16	57121706	57121761	+	1	NA	promoter-TSS (NM_138599)	promoter-TSS (NM_138599)	19	NM_138599	28185	Mm.196933	NM_138599	ENSMUSG00000022752	Tomm70a	2610044B22Rik|D16Ium22|D16Ium22e|D16Wsu109e|Tom70|Tomm70|mKIAA0719	translocase of outer mitochondrial membrane 70 homolog A (yeast)	protein-coding
mm_166067.1	chr4	134548347	134548382	+	1	NA	intron (NM_029100, intron 2 of 11)	MIRc|SINE|MIR	3802	NM_029100	74777	Mm.29773	NM_029100	ENSMUSG00000050989	Selenon	1110019I12Rik|AI414492|SelN|Sepn1	selenoprotein N	protein-coding
mm_95931.1	chr11	58379637	58379676	+	1	NA	promoter-TSS (NM_001330197)	promoter-TSS (NM_001330197)	624	NM_001083884	70163	Mm.24119	NM_027339	ENSMUSG00000013643	Lypd8	2210415F13Rik	LY6/PLAUR domain containing 8	protein-coding
mm_54557.1	chr6	37299914	37299932	-	1	NA	promoter-TSS (NM_001081206)	promoter-TSS (NM_001081206)	53	NM_001081206	320127	Mm.119469	NM_001081206	ENSMUSG00000038665	Dgki	C130010K08Rik	diacylglycerol kinase, iota	protein-coding
mm_271.1	chr1	21218663	21218673	+	1	NA	promoter-TSS (NM_001290679)	promoter-TSS (NM_001290679)	93	NM_029398	75712	Mm.304763	NM_029398	ENSMUSG00000025933	Tmem14a	5730496E24Rik|C85783|PTD011	transmembrane protein 14A	protein-coding
mm_63429.1	chr7	127478554	127478563	+	1	NA	Intergenic	Intergenic	-6663	NM_010183	14123	Mm.323505	NM_010183	ENSMUSG00000042423	Fbrs	Fbs|Fbs1	fibrosin	protein-coding
mm_146727.1	chr18	15151186	15151213	-	1	NA	intron (NM_134112, intron 1 of 4)	CpG	247	NM_134112	106931	Mm.329299	NM_134112	ENSMUSG00000036225	Kctd1	4933402K10Rik|AI661543|AW553000	potassium channel tetramerisation domain containing 1	protein-coding
mm_143613.1	chr17	78736637	78736643	-	1	NA	promoter-TSS (NM_011500)	promoter-TSS (NM_011500)	-80	NM_011500	268980	Mm.311915	NM_011500	ENSMUSG00000024077	Strn	AU022939|D130055P19	striatin, calmodulin binding protein	protein-coding
mm_58909.1	chr7	17203536	17203541	+	1	NA	promoter-TSS (NM_054064)	promoter-TSS (NM_054064)	61	NM_054064	114872	Mm.322280	NM_054064	ENSMUSG00000023159	Psg29	AA102956|AA409969|cea17	pregnancy-specific glycoprotein 29	protein-coding
mm_54271.1	chr6	28867701	28867732	-	1	NA	intron (NM_019776, intron 16 of 23)	intron (NM_019776, intron 16 of 23)	-35969	NM_138682	192198	Mm.443660	NM_138682	ENSMUSG00000049939	Lrrc4	MBAG1|NGL-2|NGL2|NLG-2|Nag14	leucine rich repeat containing 4	protein-coding
mm_74120.1	chr8	123117355	123117379	+	1	NA	promoter-TSS (NM_170684)	promoter-TSS (NM_170684)	-7	NM_170684	102278	Mm.36434	NM_170684	ENSMUSG00000034796	Cpne7	AW047065	copine VII	protein-coding
mm_22378.1	chr2	181156770	181156786	-	1	NA	5' UTR (NM_007906, exon 1 of 8)	5' UTR (NM_007906, exon 1 of 8)	237	NM_007906	13628	Mm.2645	NM_007906	ENSMUSG00000016349	Eef1a2	Eef1a|S1|wasted|wst	eukaryotic translation elongation factor 1 alpha 2	protein-coding
mm_24161.1	chr3	88531530	88531545	+	1	NA	promoter-TSS (NM_001029890)	promoter-TSS (NM_001029890)	-858	NM_001029890	72640	Mm.275154	NM_001029890	ENSMUSG00000074480	Mex3a	2700083E18Rik|Gm411|Rkhd4	mex3 RNA binding family member A	protein-coding
mm_100232.1	chr11	117200340	117200343	+	1	NA	intron (NM_001113486, intron 1 of 11)	intron (NM_001113486, intron 1 of 11)	680	NM_001113486	53860	Mm.38450	NM_017380	ENSMUSG00000059248	Sept9	MSF1|Msf|PNUTL4|Sint1	septin 9	protein-coding
mm_159545.1	chr4	88850019	88850019	+	1	NA	promoter-TSS (NM_010502)	promoter-TSS (NM_010502)	-68	NM_010502	15962	Mm.57127	NM_010502	ENSMUSG00000095498	Ifna1	Ifa1	interferon alpha 1	protein-coding
mm_9105.1	chr1	170110442	170110480	-	1	NA	Intergenic	Intergenic	-21517	NM_022563	18214	Mm.229249	NM_022563	ENSMUSG00000026674	Ddr2	AW495251|Ntrkr3|tyro10	discoidin domain receptor family, member 2	protein-coding
mm_96367.1	chr11	67200138	67200148	+	1	NA	promoter-TSS (NM_030679)	promoter-TSS (NM_030679)	29	NM_030679	17879	Mm.477065	NM_030679	ENSMUSG00000056328	Myh1	A530084A17Rik|IId|IId/x|MHC-2X/D|MHC2X/D|MYHC-IIX|MdMs|MyHC-IId/x|MyHC-IIx/d|Myhs-f|Myhs-f2|Myhsf2	myosin, heavy polypeptide 1, skeletal muscle, adult	protein-coding
mm_146042.1	chr18	69592985	69593011	+	1	NA	intron (NM_013685, intron 8 of 19)	intron (NM_013685, intron 8 of 19)	247277	NM_001083967	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding
mm_91120.1	chr10	19506086	19506102	-	1	NA	Intergenic	Intergenic	-85855	NM_010511	15979	Mm.549	NM_010511	ENSMUSG00000020009	Ifngr1	CD119|IFN-gammaR|Ifgr|Ifngr|Nktar	interferon gamma receptor 1	protein-coding
mm_27456.1	chr3	52092733	52092736	-	1	NA	intron (NM_001004176, intron 1 of 4)	B4|SINE|B4	12272	NM_001004176	433586	Mm.234972	NM_001004176	ENSMUSG00000061143	Maml3	AV234550|BC049812|Mam-2|mKIAA1816	mastermind like 3 (Drosophila)	protein-coding
mm_165690.1	chr3	93277608	93277627	+	1	NA	Intergenic	Intergenic	-42132	NM_133698	68723	Mm.208047	NM_133698	ENSMUSG00000041991	Hrnr	1110033K19Rik|A530063N20Rik|S100a18	hornerin	protein-coding
mm_26528.1	chr3	146012080	146012084	+	1	NA	intron (NM_001166064, intron 4 of 6)	intron (NM_001166064, intron 4 of 6)	24212	NM_001166064	214804	Mm.268854	NM_001166064	ENSMUSG00000036863	Syde2	C430017H16Rik	synapse defective 1, Rho GTPase, homolog 2 (C. elegans)	protein-coding
mm_5836.1	chr1	52947988	52948009	-	1	NA	intron (NM_144953, intron 1 of 1)	B4A|SINE|B4	4842	NM_144953	67080	Mm.236287	NM_144953	ENSMUSG00000043629	1700019D03Rik	2410136C24Rik|AA410151|smAKAP	RIKEN cDNA 1700019D03 gene	protein-coding
mm_2279.1	chr1	91308619	91308627	+	1	NA	intron (NM_016717, intron 5 of 11)	intron (NM_016717, intron 5 of 11)	10285	NM_016717	50880	Mm.25724	NM_016717	ENSMUSG00000026307	Scly	9830169H08|A930015N15Rik|SCL|Scly1|Scly2	selenocysteine lyase	protein-coding
mm_47035.1	chr5	115922157	115922181	-	1	NA	intron (NM_007708, intron 9 of 46)	intron (NM_007708, intron 9 of 46)	76513	NM_007708	12704	Mm.8321	NM_007708	ENSMUSG00000029516	Cit	C030025P15Rik|CRIK|CRIK-SK|Cit-k	citron	protein-coding
mm_44773.1	chr5	31998870	31998893	-	1	NA	intron (NM_144541, intron 7 of 11)	intron (NM_144541, intron 7 of 11)	-137591	NM_008037	14284	Mm.24684	NM_008037	ENSMUSG00000029135	Fosl2	Fra-2	fos-like antigen 2	protein-coding
mm_66096.1	chr7	31002798	31002807	-	1	NA	Intergenic	Intergenic	20881	NM_001242647	76415	Mm.259739	NM_175240	ENSMUSG00000046826	Fam187b	1700020B09Rik|Tmem162	family with sequence similarity 187, member B	protein-coding
mm_53852.1	chr6	149146109	149146114	+	1	NA	intron (NM_001252095, intron 3 of 4)	intron (NM_001252095, intron 3 of 4)	4598	NM_177101	320204	Mm.274099	NM_177101	ENSMUSG00000039958	Etfbkmt	4833442J19Rik|AI256744|ETFB-KMT|Mettl20	electron transfer flavoprotein beta subunit lysine methyltransferase	protein-coding
mm_89600.1	chr10	95980341	95980355	+	1	NA	intron (NM_001001932, intron 2 of 28)	intron (NM_001001932, intron 2 of 28)	39685	NM_001001932	216238	Mm.210035	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding
mm_145210.1	chr18	50030687	50030745	+	1	NA	intron (NM_001177759, intron 1 of 1)	intron (NM_001177759, intron 1 of 1)	-22566	NM_134131	106869	Mm.27740	NM_134131	ENSMUSG00000062210	Tnfaip8	AA987150|E130304C20Rik|ENSMUSG00000073567|Gg2-1|Gm10539|Nded|Ssc-2|Tipe	tumor necrosis factor, alpha-induced protein 8	protein-coding
mm_9388.1	chr1	172215041	172215045	-	1	NA	exon (NM_009813, exon 6 of 11)	exon (NM_009813, exon 6 of 11)	4852	NM_009813	12372	Mm.12829	NM_009813	ENSMUSG00000007122	Casq1	CSQ|CSQ-1|CSQ1|sCSQ	calsequestrin 1	protein-coding
mm_48926.1	chr6	4510755	4510771	+	1	NA	exon (NM_007743, exon 5 of 52)	exon (NM_007743, exon 5 of 52)	5145	NM_007743	12843	Mm.277792	NM_007743	ENSMUSG00000029661	Col1a2	AA960264|AI325291|Col1a-2|Cola-2|Cola2|oim	collagen, type I, alpha 2	protein-coding
mm_55304.1	chr6	54964703	54964708	-	1	NA	intron (NM_172729, intron 1 of 11)	intron (NM_172729, intron 1 of 11)	6956	NM_001171007	107607	Mm.28498	NM_172729	ENSMUSG00000038058	Nod1	C230079P11|Card4|F830007N14Rik|Nlrc1	nucleotide-binding oligomerization domain containing 1	protein-coding
mm_167559.1	chr9	37489063	37489079	+	1	NA	promoter-TSS (NM_146222)	promoter-TSS (NM_146222)	-250	NM_146222	235184	Mm.127892	NM_146222	ENSMUSG00000042138	Msantd2	2810450G17Rik|9530092B10Rik	Myb/SANT-like DNA-binding domain containing 2	protein-coding
mm_53499.1	chr6	135362640	135362653	+	1	NA	promoter-TSS (NM_001288628)	promoter-TSS (NM_001288628)	-285	NM_010128	13730	Mm.182785	NM_010128	ENSMUSG00000030208	Emp1	I-8-09|TMP	epithelial membrane protein 1	protein-coding
mm_117851.1	chr13	98695685	98695692	-	1	NA	promoter-TSS (NM_001025606)	promoter-TSS (NM_001025606)	-857	NM_001025606	380863	Mm.28264	NM_001025606	ENSMUSG00000052485	Tmem171	Gm905	transmembrane protein 171	protein-coding
mm_82887.1	chr9	32541346	32541350	-	1	NA	5' UTR (NM_008026, exon 1 of 9)	5' UTR (NM_008026, exon 1 of 9)	104	NM_008026	14247	Mm.258908	NM_008026	ENSMUSG00000016087	Fli1	EWSR2|Fli-1|SIC-1|Sic1	Friend leukemia integration 1	protein-coding
mm_82253.1	chr9	4796071	4796081	-	1	NA	5' UTR (NM_001113181, exon 1 of 11)	5' UTR (NM_001113181, exon 1 of 11)	158	NM_001113180	14802	Mm.209263	NM_019691	ENSMUSG00000025892	Gria4	GluA4|GluR-D|Glur-4|Glur4|Gluralpha4|spkw1	glutamate receptor, ionotropic, AMPA4 (alpha 4)	protein-coding
mm_108165.1	chr12	76370538	76370620	+	1	NA	5' UTR (NM_178744, exon 1 of 2)	5' UTR (NM_178744, exon 1 of 2)	313	NM_178744	268564	Mm.77065	NM_178744	ENSMUSG00000033454	Zbtb1	9430077A12|AI256369|Bsg2|C430003J21Rik	zinc finger and BTB domain containing 1	protein-coding
mm_83768.1	chr9	52048715	52048732	-	1	NA	promoter-TSS (NR_023357)	promoter-TSS (NR_023357)	-18	NR_023357	629557	Mm.422775	NR_023357		Gm6981	EG629557	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_170563.1	chr19	46739274	46739277	+	1	NA	intron (NM_020577, intron 10 of 10)	intron (NM_020577, intron 10 of 10)	-22334	NM_033569	94219	Mm.306903	NM_033569	ENSMUSG00000064105	Cnnm2	AU015877|AW048635|Acdp2|Clp2	cyclin M2	protein-coding
mm_106709.1	chr12	3807002	3807016	+	1	NA	promoter-TSS (NM_001271753)	promoter-TSS (NM_001271753)	29	NM_007872	13435	Mm.5001	NM_007872	ENSMUSG00000020661	Dnmt3a	MmuIIIA	DNA methyltransferase 3A	protein-coding
mm_29188.1	chr3	106547583	106547593	-	1	NA	promoter-TSS (NM_026013)	promoter-TSS (NM_026013)	-210	NM_001286986	67171	Mm.290488	NM_026013	ENSMUSG00000027900	Dram2	2010305N14Rik|2610318G18Rik|AI647667|Tmem77	DNA-damage regulated autophagy modulator 2	protein-coding
mm_69406.1	chr7	132317368	132317378	-	1	NA	promoter-TSS (NM_029935)	promoter-TSS (NM_029935)	-218	NM_029935	77590	Mm.213582	NM_029935	ENSMUSG00000030930	Chst15	4631426J05Rik|BRAG|GalNAcS-6ST|MAd5|mKIAA0598	carbohydrate (N-acetylgalactosamine 4-sulfate 6-O) sulfotransferase 15	protein-coding
mm_45099.1	chr5	44644950	44644950	-	1	NA	intron (NM_001347349, intron 2 of 7)	intron (NM_001347349, intron 2 of 7)	154796	NM_001347349	16826	Mm.25785	NM_010698	ENSMUSG00000039706	Ldb2	AI035351|AW146358|CLIM1|CLP-36|Ldb3	LIM domain binding 2	protein-coding
mm_22661.1	chr3	14871725	14871735	+	1	NA	3' UTR (NM_007606, exon 7 of 7)	3' UTR (NM_007606, exon 7 of 7)	8192	NM_007606	12350	Mm.300	NM_007606	ENSMUSG00000027559	Car3	BB219044|Ca3|Car-3	carbonic anhydrase 3	protein-coding
mm_11651.1	chr2	34961885	34961896	+	1	NA	promoter-TSS (NM_001326601)	promoter-TSS (NM_001326601)	-118	NM_001326601	22029	Mm.239514	NM_009421	ENSMUSG00000026875	Traf1	4732496E14Rik	TNF receptor-associated factor 1	protein-coding
mm_150336.1	chr19	34575669	34575686	+	1	NA	3' UTR (NM_008332, exon 3 of 3)	3' UTR (NM_008332, exon 3 of 3)	-7852	NM_010501	15959	Mm.426079	NM_010501	ENSMUSG00000074896	Ifit3	Ifi49|P49	interferon-induced protein with tetratricopeptide repeats 3	protein-coding
mm_153941.1	chr19	47507851	47507857	-	1	NA	exon (NM_175360, exon 9 of 10)	exon (NM_175360, exon 9 of 10)	-5128	NR_045322	100503104	Mm.442735	NR_045322	ENSMUSG00000097990	Gm19557	-	predicted gene, 19557	ncRNA
mm_154418.1	chrM	16071	16093	+	1	NA	NA	Intergenic	NA	NA								
mm_92293.1	chr10	72589347	72589349	-	1	NA	Intergenic	Intergenic	-65498	NM_025635	52696	Mm.62876	NM_025635	ENSMUSG00000019923	Zwint	2010007E07Rik|2600001N01Rik|D10Ertd749e|Zwint-1	ZW10 interactor	protein-coding
mm_56220.1	chr6	89535056	89535070	-	1	NA	intron (NM_025351, intron 4 of 7)	Lx2B2|LINE|L1	60589	NM_025351	66098	Mm.20313	NM_025351	ENSMUSG00000030086	Chchd6	0710001P09Rik|1700021B03Rik	coiled-coil-helix-coiled-coil-helix domain containing 6	protein-coding
mm_73369.1	chr8	105613247	105613266	+	1	NA	intron (NM_001081241, intron 1 of 21)	intron (NM_001081241, intron 1 of 21)	-2210	NR_035492	100316712		NR_035492	ENSMUSG00000089432	Mir1966	mir-1966|mmu-mir-1966	microRNA 1966	ncRNA
mm_122570.1	chr14	50807601	50807658	-	1	NA	promoter-TSS (NM_009632)	promoter-TSS (NM_009632)	142	NR_002142	85029		NR_002142	ENSMUSG00000092837	Rpph1	Gm24821|H1RNA|Rmrp5|Rpr	ribonuclease P RNA component H1	ncRNA
mm_157766.1	chrX	73695245	73695247	-	1	NA	intron (NM_001313698, intron 4 of 7)	intron (NM_001313698, intron 4 of 7)	20958	NM_012060	27061	Mm.17	NM_012060	ENSMUSG00000002015	Bcap31	Bap31	B cell receptor associated protein 31	protein-coding
mm_132856.1	chr16	48303864	48303896	+	1	NA	Intergenic	Intergenic	-6394	NM_028615	73703	Mm.27857	NM_028615	ENSMUSG00000072419	Dppa2	2410088E07Rik|C80932|D19Mgi18|ECAT15-2	developmental pluripotency associated 2	protein-coding
mm_57334.1	chr6	124741379	124741402	-	1	NA	promoter-TSS (NM_013535)	promoter-TSS (NM_013535)	-311	NM_013535	14790	Mm.439877	NM_013535	ENSMUSG00000072772	Grcc10	2310033H05Rik|C10	gene rich cluster, C10 gene	protein-coding
mm_165056.1	chr19	41389018	41389021	-	1	NA	Intergenic	Intergenic	-3949	NM_031376	83490	Mm.222266	NM_031376	ENSMUSG00000025017	Pik3ap1	1810044J04Rik|BCAP	phosphoinositide-3-kinase adaptor protein 1	protein-coding
mm_131485.1	chr16	17222286	17222296	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-11296	NM_178922	58180	Mm.261602	NM_178922	ENSMUSG00000050240	Hic2	AA409108|HRG22|mKIAA1020	hypermethylated in cancer 2	protein-coding
mm_140052.1	chr17	74528468	74528547	+	1	NA	exon (NM_007566, exon 1 of 73)	exon (NM_007566, exon 1 of 73)	212	NM_007566	12211	Mm.442564	NM_007566	ENSMUSG00000024073	Birc6	A430032G04Rik|A430040A19Rik|AA501170|Bruce|D630005A10Rik|mKIAA1289	baculoviral IAP repeat-containing 6	protein-coding
mm_129086.1	chr15	75905350	75905388	-	1	NA	intron (NM_029663, intron 2 of 9)	intron (NM_029663, intron 2 of 9)	3975	NM_001285433	66656	Mm.258927	NM_023240	ENSMUSG00000055762	Eef1d	EF-1-delta	eukaryotic translation elongation factor 1 delta (guanine nucleotide exchange protein)	protein-coding
mm_61781.1	chr7	83660680	83660694	+	1	NA	intron (NM_010551, intron 12 of 18)	intron (NM_010551, intron 12 of 18)	28670	NM_023377	170460	Mm.357953	NM_023377	ENSMUSG00000046027	Stard5	2310058G22Rik|AI607880|D7Ertd152e	StAR-related lipid transfer (START) domain containing 5	protein-coding
mm_68507.1	chr7	111082530	111082540	-	1	NA	intron (NM_001040131, intron 1 of 20)	CpG	495	NM_001040131	13690	Mm.185453	NM_013507	ENSMUSG00000005610	Eif4g2	DAP-5|E130105L11Rik|Nat1|Natm1|p97	eukaryotic translation initiation factor 4, gamma 2	protein-coding
mm_49954.1	chr6	40628589	40628595	+	1	NA	promoter-TSS (NM_001171003)	promoter-TSS (NM_001171003)	-239	NM_001171003	232714	Mm.33401	NM_001171003	ENSMUSG00000068587	Mgam	6030407P20Rik|MGA	maltase-glucoamylase	protein-coding
mm_25907.1	chr3	131112538	131112549	+	1	NA	promoter-TSS (NM_001276403)	promoter-TSS (NM_001276403)	-248	NM_001276403	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_151798.1	chr19	5424090	5424106	-	1	NA	intron (NM_001291080, intron 3 of 6)	intron (NM_001291080, intron 3 of 6)	881	NM_024176	66556	Mm.275446	NM_024176	ENSMUSG00000024914	Drap1	2310074H19Rik|NC2-alpha	Dr1 associated protein 1 (negative cofactor 2 alpha)	protein-coding
mm_162992.1	chr11	26593755	26593761	-	1	NA	5' UTR (NM_027260, exon 1 of 13)	5' UTR (NM_027260, exon 1 of 13)	162	NM_027260	69922	Mm.285351	NM_027260	ENSMUSG00000064090	Vrk2	2810003O05Rik|AI447698	vaccinia related kinase 2	protein-coding
mm_46377.1	chr5	103886046	103886093	-	1	NA	exon (NM_178741, exon 2 of 10)	exon (NM_178741, exon 2 of 10)	25160	NM_178741	246293	Mm.179871	NM_178741	ENSMUSG00000029312	Klhl8	2310001P09Rik|D5Ertd431e	kelch-like 8	protein-coding
mm_60229.1	chr7	43634651	43634663	+	1	NA	promoter-TSS (NM_028236)	promoter-TSS (NM_028236)	-82	NM_028236	72431	Mm.158821	NM_028236	ENSMUSG00000030472	Ceacam18	2010110O04Rik	carcinoembryonic antigen-related cell adhesion molecule 18	protein-coding
mm_54800.1	chr6	41693301	41693304	-	1	NA	intron (NM_032540, intron 10 of 18)	intron (NM_032540, intron 10 of 18)	8871	NM_029671	76606	Mm.272520	NM_029671	ENSMUSG00000029867	1700034O15Rik	-	RIKEN cDNA 1700034O15 gene	protein-coding
mm_20781.1	chr2	143989003	143989017	-	1	NA	exon (NM_133626, exon 2 of 3)	exon (NM_133626, exon 2 of 3)	22253	NM_133626	81910	Mm.13705	NM_024281	ENSMUSG00000027422	Rrbp1	1700087N07Rik|5730465C04Rik|ES/130|mKIAA1398|mRRp0|mRRp1.8|mRRp10|mRRp15a|mRRp15b|mRRp16.8|mRRp2|mRRp41|mRRp47|mRRp5.4|p180	ribosome binding protein 1	protein-coding
mm_147457.1	chr18	46574492	46574503	-	1	NA	promoter-TSS (NM_173394)	promoter-TSS (NM_173394)	36	NM_173394	225471	Mm.149280	NM_173394	ENSMUSG00000056130	Ticam2	B430113A10|TICAM-2|TRAM|Tirp|Trif	toll-like receptor adaptor molecule 2	protein-coding
mm_91457.1	chr10	34044295	34044299	-	1	NA	promoter-TSS (NM_001081165)	promoter-TSS (NM_001081165)	16	NM_001081165	270711	Mm.303077	NM_001081165	ENSMUSG00000039508	Fam26d	4732454E20Rik|AI586164|Gm643	family with sequence similarity 26, member D	protein-coding
mm_3270.1	chr1	136466337	136466378	+	1	NA	Intergenic	CpG	-1491	NM_001287179	381293	Mm.458468	NM_001081258	ENSMUSG00000041498	Kif14	D1Ertd367e|E130203M01	kinesin family member 14	protein-coding
mm_66858.1	chr7	52995207	52995208	-	1	NA	Intergenic	Intergenic	896682	NR_105746	102466619		NR_105746	ENSMUSG00000099176	Mir6238	Gm27982|mmu-mir-6238	microRNA 6238	ncRNA
mm_139780.1	chr17	65783107	65783177	+	1	NA	promoter-TSS (NM_001114131)	promoter-TSS (NM_001114131)	-213	NM_001114131	70351	Mm.48686	NM_146081	ENSMUSG00000061950	Ppp4r1	3110001J10Rik|Pp4r1	protein phosphatase 4, regulatory subunit 1	protein-coding
mm_24259.1	chr3	89187364	89187375	+	1	NA	exon (NM_001014995, exon 9 of 12)	exon (NM_001014995, exon 9 of 12)	4144	NM_001014995	68521	Mm.274708	NM_001014995	ENSMUSG00000032657	Fam189b	1110013L07Rik	family with sequence similarity 189, member B	protein-coding
mm_75521.1	chr8	56229156	56229162	-	1	NA	Intergenic	Intergenic	-65393	NM_008278	15446	Mm.18832	NM_008278	ENSMUSG00000031613	Hpgd	15-PGDH|AV026552	hydroxyprostaglandin dehydrogenase 15 (NAD)	protein-coding
mm_66809.1	chr7	47252917	47252923	-	1	NA	promoter-TSS (NM_001288801)	promoter-TSS (NM_001288801)	-72	NM_001288801	668725	Mm.436563	NM_001177566	ENSMUSG00000074111	Mrgpra9	EG668725|MrgA9	MAS-related GPR, member A9	protein-coding
mm_14401.1	chr2	130044617	130044621	+	1	NA	exon (NM_009374, exon 11 of 13)	exon (NM_009374, exon 11 of 13)	-28211	NR_105757	102466628		NR_105757	ENSMUSG00000098347	Mir6339	Gm27848|mmu-mir-6339	microRNA 6339	ncRNA
mm_72520.1	chr8	83972952	83973028	+	1	NA	promoter-TSS (NM_008854)	promoter-TSS (NM_008854)	12	NM_008854	18747	Mm.19111	NM_008854	ENSMUSG00000005469	Prkaca	PKCD|Pkaca	protein kinase, cAMP dependent, catalytic, alpha	protein-coding
mm_102670.1	chr11	65174385	65174391	-	1	NA	Intergenic	Intergenic	-11427	NM_175003	216831	Mm.134338	NM_175003	ENSMUSG00000033389	Arhgap44	6330543G20|AI840762|AU040829|AW493732|Rich2	Rho GTPase activating protein 44	protein-coding
mm_167522.1	chr9	20898577	20898586	-	1	NA	promoter-TSS (NM_016876)	promoter-TSS (NM_016876)	9	NM_016876	53356	Mm.427309	NM_016876	ENSMUSG00000070319	Eif3g	44kDa|D0Jmb4|Eif3s4|TU-189B2|eIF3-p44|p44	eukaryotic translation initiation factor 3, subunit G	protein-coding
mm_75224.1	chr8	39614080	39614087	-	1	NA	intron (NM_001113326, intron 6 of 9)	intron (NM_001113326, intron 6 of 9)	28595	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_60129.1	chr7	36773144	36773151	+	1	NA	3' UTR (NM_172298, exon 2 of 2)	3' UTR (NM_172298, exon 2 of 2)	75029	NM_172298	243931	Mm.44141	NM_172298	ENSMUSG00000021217	Tshz3	A630038G13Rik|Tsh3|Zfp537|mKIAA1474|teashirt3	teashirt zinc finger family member 3	protein-coding
mm_34555.1	chr4	149627285	149627296	+	1	NA	exon (NM_023051, exon 4 of 19)	exon (NM_023051, exon 4 of 19)	28277	NR_105990	102465983		NR_105990	ENSMUSG00000098580	Mir7023	Gm27912|mmu-mir-7023	microRNA 7023	ncRNA
mm_152958.1	chr19	29334647	29334652	-	1	NA	promoter-TSS (NM_011272)	promoter-TSS (NM_011272)	21	NM_011272	19773	Mm.5033	NM_011272	ENSMUSG00000039097	Rln1	Rln|rlx	relaxin 1	protein-coding
mm_116907.1	chr13	55474515	55474527	-	1	NA	exon (NM_019813, exon 13 of 14)	exon (NM_019813, exon 13 of 14)	3255	NR_105909	102465569		NR_105909	ENSMUSG00000098341	Mir6944	Gm27710|mmu-mir-6944	microRNA 6944	ncRNA
mm_97552.1	chr11	78929777	78929788	+	1	NA	exon (NM_010927, exon 4 of 27)	exon (NM_010927, exon 4 of 27)	4491	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_57228.1	chr6	123282615	123282621	-	1	NA	3' UTR (NM_019948, exon 6 of 6)	3' UTR (NM_019948, exon 6 of 6)	7253	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_88621.1	chr10	79859432	79859460	+	1	NA	exon (NM_008956, exon 5 of 13)	exon (NM_008956, exon 5 of 13)	-3141	NR_105875	102465549		NR_105875	ENSMUSG00000098562	Mir6910	Gm27763|mmu-mir-6910	microRNA 6910	ncRNA
mm_100059.1	chr11	115307145	115307153	+	1	NA	promoter-TSS (NM_172801)	promoter-TSS (NM_172801)	-14	NM_172801	237987	Mm.44542	NM_172801	ENSMUSG00000050201	Otop2	4732464P15	otopetrin 2	protein-coding
mm_40242.1	chr5	37983686	37983694	+	1	NA	Intergenic	Intergenic	-55540	NM_001289536	71116	Mm.18959	NM_026959	ENSMUSG00000029125	Stx18	1810035L21Rik|4933425D03Rik|AU041562	syntaxin 18	protein-coding
mm_112246.1	chr12	113579057	113579073	-	1	NA	Intergenic	Intergenic	35157	NM_174885	238406	Mm.188683	NM_174885	ENSMUSG00000043945	Adam6a	Adam6|tMDCIV	a disintegrin and metallopeptidase domain 6A	protein-coding
mm_106351.1	chr11	118393542	118393556	-	1	NA	exon (NM_011150, exon 6 of 6)	exon (NM_011150, exon 6 of 6)	8382	NM_011150	19039	Mm.3152	NM_011150	ENSMUSG00000033880	Lgals3bp	90K|CyCAP|MAC-2BP|Ppicap|Tango10b	lectin, galactoside-binding, soluble, 3 binding protein	protein-coding
mm_94514.1	chr11	8594836	8594852	+	1	NA	intron (NM_001083587, intron 3 of 30)	URR1A|DNA|hAT-Charlie	69691	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_63026.1	chr7	121035620	121035660	+	1	NA	intron (NM_021554, intron 1 of 4)	intron (NM_021554, intron 1 of 4)	1195	NM_021554	59052	Mm.29122	NM_021554	ENSMUSG00000030876	Mettl9	0610012D09Rik|AA517660|Drev|MNCb-5680	methyltransferase like 9	protein-coding
mm_142740.1	chr17	48409011	48409027	-	1	NA	promoter-TSS (NM_001289491)	promoter-TSS (NM_001289491)	801	NM_001110832	18044	Mm.4929	NM_010913	ENSMUSG00000023994	Nfya	AA407810|Cbf-b|SEZ-10|SEZ10	nuclear transcription factor-Y alpha	protein-coding
mm_132451.1	chr16	36035365	36035373	+	1	NA	3' UTR (NM_008465, exon 14 of 14)	3' UTR (NM_008465, exon 14 of 14)	-5821	NM_027113	69544	Mm.37802	NM_027113	ENSMUSG00000034379	Wdr5b	2310009C03Rik|AI606931	WD repeat domain 5B	protein-coding
mm_19416.1	chr2	91717426	91717429	-	1	NA	intron (NM_178724, intron 2 of 2)	RSINE1|SINE|B4	6477	NM_178724	241547	Mm.130331	NM_178724	ENSMUSG00000027243	Harbi1	D230010M03Rik	harbinger transposase derived 1	protein-coding
mm_71540.1	chr8	47288404	47288419	+	1	NA	5' UTR (NM_001286376, exon 1 of 5)	5' UTR (NM_001286376, exon 1 of 5)	991	NM_001286376	71069	Mm.23973	NM_175162	ENSMUSG00000038143	Stox2	4933409N07Rik|AI449080|AI835114|mKIAA1392	storkhead box 2	protein-coding
mm_8741.1	chr1	160247648	160247661	-	1	NA	intron (NM_001038621, intron 3 of 8)	intron (NM_001038621, intron 3 of 8)	-34762	NM_009786	12301	Mm.10702	NM_009786	ENSMUSG00000014226	Cacybp	SIP	calcyclin binding protein	protein-coding
mm_5507.1	chr1	37430072	37430080	-	1	NA	promoter-TSS (NM_026123)	promoter-TSS (NM_026123)	27	NM_198006	76178	Mm.28085	NM_198006	ENSMUSG00000026112	Coa5	1700001A24Rik|6330578E17Rik|Pet191	cytochrome C oxidase assembly factor 5	protein-coding
mm_149575.1	chr19	12846775	12846781	+	1	NA	Intergenic	Intergenic	-14999	NM_146702	258697	Mm.223132	NM_146702	ENSMUSG00000046272	Olfr1444	MOR202-4	olfactory receptor 1444	protein-coding
mm_99420.1	chr11	102316875	102316969	+	1	NA	intron (NM_001302955, intron 1 of 19)	CpG	365	NM_001044383	21429	Mm.2845	NM_011551	ENSMUSG00000020923	Ubtf	A930005G04Rik|NOR-90|Tcfubf|UBF|UBF-1|UBF1	upstream binding transcription factor, RNA polymerase I	protein-coding
mm_100748.1	chr11	4160233	4160282	-	1	NA	promoter-TSS (NM_177616)	promoter-TSS (NM_177616)	36	NM_177616	216516	Mm.386854	NM_177616	ENSMUSG00000051427	Ccdc157	4930562D19Rik|mKIAA1656	coiled-coil domain containing 157	protein-coding
mm_12063.1	chr2	59471203	59471209	+	1	NA	Intergenic	Intergenic	-13447	NM_029723	76747	Mm.275769	NM_029723	ENSMUSG00000026989	Dapl1	2310032F03Rik|EEDA	death associated protein-like 1	protein-coding
mm_113549.1	chr13	38149448	38149452	+	1	NA	Intergenic	Intergenic	-1844	NM_023842	109620	Mm.355327	NM_023842	ENSMUSG00000054889	Dsp	2300002E22Rik|5730453H04Rik|AA407887|AA407888|AW109828|DP|rul	desmoplakin	protein-coding
mm_100270.1	chr11	117654799	117654824	+	1	NA	intron (NM_198022, intron 1 of 21)	CpG	522	NM_198022	217351	Mm.40272	NM_198022	ENSMUSG00000025571	Tnrc6c	9930033H14Rik|mKIAA1582	trinucleotide repeat containing 6C	protein-coding
mm_12936.1	chr2	85099145	85099185	+	1	NA	Intergenic	Intergenic	-12704	NR_040504	74687	Mm.66996	NR_040504	ENSMUSG00000086969	4930443O20Rik	-	RIKEN cDNA 4930443O20 gene	ncRNA
mm_18967.1	chr2	76809008	76809018	-	1	NA	exon (NM_011652, exon 186 of 313)	exon (NM_011652, exon 186 of 313)	133698	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_9849.1	chr1	184732445	184732491	-	1	NA	promoter-TSS (NM_008250)	promoter-TSS (NM_008250)	25	NM_008250	15284	Mm.1347	NM_008250	ENSMUSG00000039377	Hlx	Hlx1	H2.0-like homeobox	protein-coding
mm_861.1	chr1	52139248	52139268	+	1	NA	exon (NM_001205314, exon 10 of 25)	exon (NM_001205314, exon 10 of 25)	19636	NM_001205313	20846	Mm.277406	NM_009283	ENSMUSG00000026104	Stat1	2010005J02Rik|AA408197	signal transducer and activator of transcription 1	protein-coding
mm_97603.1	chr11	78949954	78949963	+	1	NA	exon (NM_010927, exon 20 of 27)	exon (NM_010927, exon 20 of 27)	24667	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_39599.1	chr5	23598280	23598284	+	1	NA	intron (NM_009274, intron 1 of 14)	intron (NM_009274, intron 1 of 14)	18289	NM_009274	20817	Mm.288728	NM_009274	ENSMUSG00000062604	Srpk2	AW226533|AW492537|AW547358|Wbp6|mSRPK2	serine/arginine-rich protein specific kinase 2	protein-coding
mm_44924.1	chr5	35790622	35790641	-	1	NA	intron (NM_001177696, intron 1 of 21)	intron (NM_001177696, intron 1 of 21)	32751	NM_001177698	231148	Mm.254446	NM_177678	ENSMUSG00000029095	Ablim2	AI606905|C230091L11	actin-binding LIM protein 2	protein-coding
mm_29958.1	chr3	133234918	133234932	-	1	NA	promoter-TSS (NM_029953)	promoter-TSS (NM_029953)	-36	NM_029953	77669	Mm.98630	NM_029953	ENSMUSG00000040969	Arhgef38	9130221D24Rik|D630013G24Rik	Rho guanine nucleotide exchange factor (GEF) 38	protein-coding
mm_2903.1	chr1	131969909	131969912	+	1	NA	promoter-TSS (NM_145977)	promoter-TSS (NM_145977)	-699	NM_145977	212980	Mm.200307	NM_145977	ENSMUSG00000026435	Slc45a3	2210413P12Rik|AU023994|AU043764|IPCA-6|PRST|Pcanap6	solute carrier family 45, member 3	protein-coding
mm_120262.1	chr14	63055212	63055236	+	1	NA	intron (NR_046019, intron 1 of 2)	IMPB_01|Satellite|Satellite	151	NR_046019	72609	Mm.387101	NR_046019		2700070H01Rik	-	RIKEN cDNA 2700070H01 gene	ncRNA
mm_47615.1	chr5	125141215	125141235	-	1	NA	intron (NM_011424, intron 1 of 46)	intron (NM_011424, intron 1 of 46)	37989	NM_001253905	20602	Mm.278646	NM_011424	ENSMUSG00000029478	Ncor2	N-CoR|SMRT|SMRTe	nuclear receptor co-repressor 2	protein-coding
mm_164661.1	chr17	40235872	40235876	-	1	NA	exon (NM_009639, exon 3 of 8)	exon (NM_009639, exon 3 of 8)	6384	NM_009639	11572	Mm.14138	NM_009639	ENSMUSG00000025433	Crisp3	Aeg2|CRISP-3|CRS3|SGP28	cysteine-rich secretory protein 3	protein-coding
mm_79150.1	chr9	47738693	47738700	+	1	NA	intron (NM_001025600, intron 1 of 8)	intron (NM_001025600, intron 1 of 8)	79512	NR_046048	100038460	Mm.447649	NR_046048		Gm10677	ENSMUSG00000074363	predicted gene 10677	ncRNA
mm_159176.1	chr2	110597072	110597072	+	1	NA	promoter-TSS (NM_001003915)	promoter-TSS (NM_001003915)	-227	NM_001003915	241612	Mm.277148	NM_001003915	ENSMUSG00000041644	Slc5a12	AI315119|D630015G19|SMCT2	solute carrier family 5 (sodium/glucose cotransporter), member 12	protein-coding
mm_8712.1	chr1	158969689	158969696	-	1	NA	Intergenic	Intergenic	-12254	NM_001085376	23850	Mm.458621	NM_001085376	ENSMUSG00000073530	Pappa2	PAPP-A2|PLAC3|Pappe	pappalysin 2	protein-coding
mm_116012.1	chr13	24640300	24640310	-	1	NA	intron (NM_029679, intron 1 of 22)	intron (NM_029679, intron 1 of 22)	1657	NM_029679	193385	Mm.217319	NM_029679	ENSMUSG00000036006	Fam65b	-	family with sequence similarity 65, member B	protein-coding
mm_92345.1	chr10	75837413	75837427	-	1	NA	Intergenic	CpG	-2539	NM_010361	14872	Mm.24118	NM_010361	ENSMUSG00000033318	Gstt2	AI266894|Yrs|mGSTT2	glutathione S-transferase, theta 2	protein-coding
mm_170518.1	chr19	30660700	30660703	-	1	NA	intron (NM_011160, intron 9 of 17)	L1Md_T|LINE|L1	-111205	NM_010051	13380	Mm.214717	NM_010051	ENSMUSG00000024868	Dkk1	mdkk-1	dickkopf WNT signaling pathway inhibitor 1	protein-coding
mm_3399.1	chr1	143739017	143739050	+	1	NA	promoter-TSS (NM_023505)	promoter-TSS (NM_023505)	-316	NM_001038593	69367	Mm.272727	NM_023505	ENSMUSG00000018196	Glrx2	1700010P22Rik|AI645710|Grx2	glutaredoxin 2 (thioltransferase)	protein-coding
mm_73692.1	chr8	111564032	111564043	+	1	NA	intron (NM_001168623, intron 1 of 4)	MLT1H1|LTR|ERVL-MaLR	25694	NM_001168623	170737	Mm.271578	NM_133206	ENSMUSG00000033545	Znrf1	B830022L21Rik|Rnf42|Zrfp1|nin283	zinc and ring finger 1	protein-coding
mm_153409.1	chr19	40564996	40565013	-	1	NA	exon (NM_153554, exon 13 of 19)	exon (NM_153554, exon 13 of 19)	23459	NM_019698	56454	Mm.233117	NM_019698	ENSMUSG00000025007	Aldh18a1	2810433K04Rik|AI429789|Pycs	aldehyde dehydrogenase 18 family, member A1	protein-coding
mm_62761.1	chr7	112093078	112093127	+	1	NA	exon (NM_177249, exon 21 of 29)	exon (NM_177249, exon 21 of 29)	65955	NM_015814	50781	Mm.55143	NM_015814	ENSMUSG00000030772	Dkk3	AW061014|C87148	dickkopf WNT signaling pathway inhibitor 3	protein-coding
mm_56609.1	chr6	112488962	112488970	-	1	NA	exon (NM_001081147, exon 1 of 2)	exon (NM_001081147, exon 1 of 2)	842	NM_001081147	18430	Mm.333310	NM_001081147	ENSMUSG00000049112	Oxtr	OTR	oxytocin receptor	protein-coding
mm_160086.1	chr7	14122960	14122960	-	1	NA	promoter-TSS (NM_001101586)	promoter-TSS (NM_001101586)	33	NM_001101586	629203	Mm.482066	NM_001101586	ENSMUSG00000074375	Sult2a3	EG629203|Gm6955	sulfotransferase family 2A, dehydroepiandrosterone (DHEA)-preferring, member 3	protein-coding
mm_11648.1	chr2	34961684	34961698	+	1	NA	promoter-TSS (NM_001326601)	promoter-TSS (NM_001326601)	81	NM_009421	22029	Mm.239514	NM_009421	ENSMUSG00000026875	Traf1	4732496E14Rik	TNF receptor-associated factor 1	protein-coding
mm_49268.1	chr6	17491269	17491273	+	1	NA	exon (NM_008591, exon 3 of 22)	exon (NM_008591, exon 3 of 22)	27314	NM_008591	17295	Mm.86844	NM_008591	ENSMUSG00000009376	Met	AI838057|HGF|HGFR|Par4|c-Met	met proto-oncogene	protein-coding
mm_152413.1	chr19	10605869	10605915	-	1	NA	intron (NM_015735, intron 1 of 26)	CpG	267	NM_015735	13194	Mm.289915	NM_015735	ENSMUSG00000024740	Ddb1	127kDa|AA408517|p127-Ddb1	damage specific DNA binding protein 1	protein-coding
mm_17884.1	chr2	34961954	34961969	-	1	NA	promoter-TSS (NM_001326601)	promoter-TSS (NM_001326601)	-189	NM_001326601	22029	Mm.239514	NM_009421	ENSMUSG00000026875	Traf1	4732496E14Rik	TNF receptor-associated factor 1	protein-coding
mm_67951.1	chr7	100498401	100498456	-	1	NA	exon (NM_011671, exon 6 of 8)	exon (NM_011671, exon 6 of 8)	5070	NM_011671	22228	Mm.171378	NM_011671	ENSMUSG00000033685	Ucp2	Slc25a8	uncoupling protein 2 (mitochondrial, proton carrier)	protein-coding
mm_74859.1	chr8	24818528	24818536	-	1	NA	intron (NM_001272059, intron 2 of 18)	intron (NM_001272059, intron 2 of 18)	5837	NM_001272058	11499	Mm.143889	NM_007401	ENSMUSG00000031554	Adam5	tMDC II|tMDCII	a disintegrin and metallopeptidase domain 5	protein-coding
mm_168372.1	chr1	120121048	120121049	-	1	NA	promoter-TSS (NM_001172074)	promoter-TSS (NM_001172074)	48	NM_007830	13167	Mm.2785	NM_007830	ENSMUSG00000026385	Dbi	ACBD1|Acbp|EP|endozepine	diazepam binding inhibitor	protein-coding
mm_134844.1	chr16	26526809	26526819	-	1	NA	promoter-TSS (NM_001101640)	promoter-TSS (NM_001101640)	-43	NM_001101640	100043057	Mm.295917	NM_001101640	ENSMUSG00000091972	Tmem207	Gm540	transmembrane protein 207	protein-coding
mm_115830.1	chr13	21286906	21286913	-	1	NA	3' UTR (NM_010343, exon 5 of 5)	3' UTR (NM_010343, exon 5 of 5)	5777	NM_010343	14780	Mm.1332	NM_010343	ENSMUSG00000004344	Gpx5	AV379049|Arep	glutathione peroxidase 5	protein-coding
mm_113012.1	chr13	21935422	21935424	+	1	NA	Intergenic	Intergenic	-9671	NM_183014	193452	Mm.187446	NM_183014	ENSMUSG00000006720	Zfp184	4930500C15Rik	zinc finger protein 184 (Kruppel-like)	protein-coding
mm_36631.1	chr4	91939948	91939957	-	1	NA	Intergenic	Intergenic	207269	NM_027034	69314	Mm.55891	NM_027034	ENSMUSG00000028533	Izumo3	1700011H22Rik	IZUMO family member 3	protein-coding
mm_46234.1	chr5	99217833	99217843	-	1	NA	3' UTR (NM_181318, exon 14 of 14)	3' UTR (NM_181318, exon 14 of 14)	35089	NM_181318	320292	Mm.259074	NM_145839	ENSMUSG00000089809	Rasgef1b	4732452O09Rik|GPIgamma4|Gpig4	RasGEF domain family, member 1B	protein-coding
mm_129757.1	chr15	82380141	82380150	-	1	NA	5' UTR (NM_019823, exon 1 of 10)	5' UTR (NM_019823, exon 1 of 10)	115	NM_019823	56448	Mm.474216	NM_019823	ENSMUSG00000061740	Cyp2d22	2D22	cytochrome P450, family 2, subfamily d, polypeptide 22	protein-coding
mm_1399.1	chr1	67144800	67144808	+	1	NA	intron (NM_001080809, intron 4 of 37)	intron (NM_001080809, intron 4 of 37)	21777	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_89000.1	chr10	81610149	81610159	+	1	NA	TTS (NR_030677)	TTS (NR_030677)	3846	NR_030677	268319	Mm.131825	NM_001033363	ENSMUSG00000074862	BC025920	-	zinc finger protein pseudogene	pseudo
mm_71873.1	chr8	69271091	69271143	+	1	NA	promoter-TSS (NM_172491)	promoter-TSS (NM_172491)	37	NM_172491	211135	Mm.294970	NM_172491	ENSMUSG00000079038	D130040H23Rik	-	RIKEN cDNA D130040H23 gene	protein-coding
mm_3368.1	chr1	138913658	138913662	+	1	NA	Intergenic	Intergenic	-36710	NR_138576	75546	Mm.71176	NR_138576	ENSMUSG00000099808	1700019P21Rik	-	RIKEN cDNA 1700019P21 gene	ncRNA
mm_98658.1	chr11	96271324	96271338	+	1	NA	promoter-TSS (NM_008270)	promoter-TSS (NM_008270)	1	NM_008270	15417	Mm.258271	NM_008270	ENSMUSG00000020875	Hoxb9	Hox-2.5	homeobox B9	protein-coding
mm_103805.1	chr11	82960694	82960698	-	1	NA	promoter-TSS (NR_045932)	promoter-TSS (NR_045932)	-15	NR_045932	76392	Mm.295205	NR_045932	ENSMUSG00000086327	Slfn5os	1700003F17Rik	schlafen 5, opposite strand	ncRNA
mm_125771.1	chr15	74586931	74586941	+	1	NA	exon (NM_174991, exon 28 of 31)	exon (NM_174991, exon 28 of 31)	49382	NM_001177437	69439	Mm.263708	NM_001177437	ENSMUSG00000022603	Mroh4	1700016M24Rik	maestro heat-like repeat family member 4	protein-coding
mm_83433.1	chr9	44998986	44999016	-	1	NA	3' UTR (NM_007648, exon 8 of 8)	3' UTR (NM_007648, exon 8 of 8)	10589	NM_007648	12501	Mm.210361	NM_007648	ENSMUSG00000032093	Cd3e	AI504783|CD3|CD3epsilon|T3e	CD3 antigen, epsilon polypeptide	protein-coding
mm_68926.1	chr7	126474935	126474979	-	1	NA	5' UTR (NM_001289538, exon 1 of 9)	5' UTR (NM_001289538, exon 1 of 9)	173	NM_001289538	20399	Mm.8538	NM_011363	ENSMUSG00000030733	Sh2b1	AI425885|C530001K22Rik|Irip|Psm|SH2-B|SH2-Bb|Sh2bpsm1|mKIAA1299	SH2B adaptor protein 1	protein-coding
mm_105539.1	chr11	106301548	106301561	-	1	NA	exon (NM_008117, exon 2 of 5)	exon (NM_008117, exon 2 of 5)	342	NM_008117	14599	Mm.343934	NM_008117	ENSMUSG00000020713	Gh	Gh1|Ghb1	growth hormone	protein-coding
mm_112416.1	chr13	3995362	3995365	+	1	NA	Intergenic	Intergenic	-50014	NM_031250	83428	Mm.313662	NM_031250	ENSMUSG00000044988	Ucn3	ucn III	urocortin 3	protein-coding
mm_127994.1	chr15	12674171	12674186	-	1	NA	Intergenic	Intergenic	-81622	NM_001081064	68070	Mm.423205	NM_001081064	ENSMUSG00000022197	Pdzd2	4930537L06Rik|A930022H17Rik|Gm21706|Gm82|Pdzk3|mKIAA0300	PDZ domain containing 2	protein-coding
mm_104258.1	chr11	88924605	88924615	-	1	NA	3' UTR (NM_029023, exon 13 of 13)	3' UTR (NM_029023, exon 13 of 13)	18682	NR_045955	73921	Mm.439148	NR_045955	ENSMUSG00000087338	Scpep1os	4930405P13Rik	serine carboxypeptidase 1, opposite strand	ncRNA
mm_125283.1	chr15	36608607	36608642	+	1	NA	5' UTR (NM_008774, exon 1 of 15)	5' UTR (NM_008774, exon 1 of 15)	349	NM_008774	18458	Mm.371570	NM_008774	ENSMUSG00000022283	Pabpc1	PABP|Pabp1|PabpI|Pabpl1|ePAB	poly(A) binding protein, cytoplasmic 1	protein-coding
mm_3051.1	chr1	134046679	134046698	+	1	NA	3' UTR (NM_021355, exon 3 of 3)	3' UTR (NM_021355, exon 3 of 3)	9173	NM_021355	14264	Mm.287146	NM_021355	ENSMUSG00000041559	Fmod	AI131919|AU041740|SLRR2E	fibromodulin	protein-coding
mm_163927.1	chr14	47200246	47200252	+	1	NA	Intergenic	Intergenic	-10847	NM_008102	14528	Mm.10651	NM_008102	ENSMUSG00000037580	Gch1	GTP-CH|GTPCH|Gch	GTP cyclohydrolase 1	protein-coding
mm_22720.1	chr3	19508590	19508600	+	1	NA	promoter-TSS (NM_001163536)	promoter-TSS (NM_001163536)	0	NM_001163536	66326	Mm.45615	NM_025489	ENSMUSG00000027606	Dnajc5b	1700008A05Rik	DnaJ heat shock protein family (Hsp40) member C5 beta	protein-coding
mm_56648.1	chr6	113377713	113377776	-	1	NA	promoter-TSS (NM_026552)	promoter-TSS (NM_026552)	-224	NM_133932	101206	Mm.266811	NM_133932	ENSMUSG00000048930	Tada3	1110004B19Rik|ADA3|AI987856|Tada3l	transcriptional adaptor 3	protein-coding
mm_61284.1	chr7	67421271	67421300	+	1	NA	Intergenic	Intergenic	-48427	NM_001291195	17258	Mm.132788	NM_001033713	ENSMUSG00000030557	Mef2a	A430079H05Rik	myocyte enhancer factor 2A	protein-coding
mm_59481.1	chr7	27462558	27462575	+	1	NA	intron (NM_001290525, intron 3 of 4)	intron (NM_001290525, intron 3 of 4)	10148	NM_001290525	233016	Mm.24021	NM_144923	ENSMUSG00000040466	Blvrb	-	biliverdin reductase B (flavin reductase (NADPH))	protein-coding
mm_28571.1	chr3	93445081	93445099	-	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	2760	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_1793.1	chr1	79197748	79197757	+	1	NA	Intergenic	RMER19C|LTR|ERVK	242338	NM_009129	20254	Mm.5038	NM_009129	ENSMUSG00000050711	Scg2	Chgc|SgII	secretogranin II	protein-coding
mm_52753.1	chr6	120773550	120773579	+	1	NA	promoter-TSS (NM_001081048)	promoter-TSS (NM_001081048)	-204	NM_001081048	71803	Mm.425340	NM_001081048	ENSMUSG00000004902	Slc25a18	1500015I14Rik|AW125787	solute carrier family 25 (mitochondrial carrier), member 18	protein-coding
mm_80787.1	chr9	95954787	95954800	+	1	NA	promoter-TSS (NM_001311130)	promoter-TSS (NM_001311130)	33	NM_001311130	24127	Mm.291179	NM_011916	ENSMUSG00000032410	Xrn1	Dhm2|exo|mXrn1	5'-3' exoribonuclease 1	protein-coding
mm_90067.1	chr10	116315056	116315076	+	1	NA	exon (NM_029928, exon 4 of 32)	exon (NM_029928, exon 4 of 32)	13692	NM_029928	19263	Mm.37213	NM_029928	ENSMUSG00000020154	Ptprb	3230402H02Rik|C130094E24|Ptpz|Rptpb|VE-PTP|Veptp	protein tyrosine phosphatase, receptor type, B	protein-coding
mm_147928.1	chr18	65939798	65939807	-	1	NA	promoter-TSS (NM_013833)	promoter-TSS (NM_013833)	-713	NM_013833	19434	Mm.431047	NM_013833	ENSMUSG00000024518	Rax	7530406A22Rik|E130303K03Rik|Rx|ey-1|ey1	retina and anterior neural fold homeobox	protein-coding
mm_68678.1	chr7	118984078	118984101	-	1	NA	exon (NM_001195774, exon 2 of 4)	exon (NM_001195774, exon 2 of 4)	11122	NM_022420	64297	Mm.103439	NM_022420	ENSMUSG00000008734	Gprc5b	AW125761|Raig2	G protein-coupled receptor, family C, group 5, member B	protein-coding
mm_171665.1	chr4	46511309	46511311	+	1	NA	intron (NM_029077, intron 4 of 5)	IAPLTR1_Mm|LTR|ERVK	21981	NM_053179	94181	Mm.249349	NM_053179	ENSMUSG00000028334	Nans	4632418E04Rik|BB056474|Sas	N-acetylneuraminic acid synthase (sialic acid synthase)	protein-coding
mm_169334.1	chr14	120275725	120275725	+	1	NA	promoter-TSS (NM_207515)	promoter-TSS (NM_207515)	56	NM_175341	105559	Mm.238266	NM_175341	ENSMUSG00000022139	Mbnl2	1110002M11Rik|AI047808|AI837313|AI849185|AL118326|MBLL|R75232|mKIAA4072	muscleblind-like 2	protein-coding
mm_24813.1	chr3	95622237	95622247	+	1	NA	Intergenic	Intergenic	-2738	NM_019561	56205	Mm.241365	NM_019561	ENSMUSG00000038619	Ensa	1700020C18Rik|2610007F17Rik|AI451924	endosulfine alpha	protein-coding
mm_13690.1	chr2	117120900	117120905	+	1	NA	promoter-TSS (NM_001277256)	promoter-TSS (NM_001277256)	-169	NM_001277256	114715	Mm.245890	NM_033524	ENSMUSG00000027351	Spred1	5730461F13Rik|AL024345|AW047647	sprouty protein with EVH-1 domain 1, related sequence	protein-coding
mm_154011.1	chr19	53076133	53076168	-	1	NA	promoter-TSS (NR_045320)	promoter-TSS (NR_045320)	-102	NR_045320	78457	Mm.76932	NR_045320	ENSMUSG00000099988	1700054A03Rik	-	RIKEN cDNA 1700054A03 gene	ncRNA
mm_149312.1	chr19	10781847	10781880	+	1	NA	non-coding (NR_027805, exon 2 of 4)	non-coding (NR_027805, exon 2 of 4)	40916	NR_027805	403202	Mm.34482	NM_207529	ENSMUSG00000067577	A430093F15Rik	Gm674	RIKEN cDNA A430093F15 gene	ncRNA
mm_76279.1	chr8	84184090	84184114	-	1	NA	Intergenic	CpG	-5141	NR_029821	723819		NR_029821	ENSMUSG00000065483	Mir181c	Mirn181c|mir-181c	microRNA 181c	ncRNA
mm_65520.1	chr7	25756179	25756198	-	1	NA	TTS (NM_001190974)	TTS (NM_001190974)	-1468	NM_144922	232989	Mm.254223	NM_144922	ENSMUSG00000040725	Hnrnpul1	E130317O14Rik|E1B-AP5|E1BAP5|Hnrnpul|Hnrpul1	heterogeneous nuclear ribonucleoprotein U-like 1	protein-coding
mm_99245.1	chr11	101079680	101079689	+	1	NA	exon (NM_010475, exon 5 of 6)	exon (NM_010475, exon 5 of 6)	1273	NM_010475	15485	Mm.188939	NM_010475	ENSMUSG00000019301	Hsd17b1	17HSDB1|17beta-HSD|E2DH|Hsd17ba	hydroxysteroid (17-beta) dehydrogenase 1	protein-coding
mm_18393.1	chr2	60209828	60209871	-	1	NA	promoter-TSS (NM_020575)	promoter-TSS (NM_020575)	-87	NM_020575	57438	Mm.260635	NM_020575	ENSMUSG00000026977	March7	Axo|Axot|Gtrgeo17	membrane-associated ring finger (C3HC4) 7	protein-coding
mm_10786.1	chr2	24345306	24345347	+	1	NA	promoter-TSS (NM_001039701)	promoter-TSS (NM_001039701)	35	NM_001159562	16181	Mm.882	NM_031167	ENSMUSG00000026981	Il1rn	F630041P17Rik|IL-1ra	interleukin 1 receptor antagonist	protein-coding
mm_37065.1	chr4	116075023	116075049	-	1	NA	promoter-TSS (NM_153521)	promoter-TSS (NM_153521)	34	NM_025641	66576	Mm.181721	NM_025641	ENSMUSG00000063882	Uqcrh	2210416J04Rik|2310021J10Rik|2610041P16Rik	ubiquinol-cytochrome c reductase hinge protein	protein-coding
mm_132166.1	chr16	32277450	32277462	+	1	NA	promoter-TSS (NM_027355)	promoter-TSS (NM_027355)	-5	NM_027355	70238	Mm.228263	NM_027355	ENSMUSG00000014074	Rnf168	3110001H15Rik	ring finger protein 168	protein-coding
mm_11632.1	chr2	34775759	34775781	+	1	NA	exon (NM_001163434, exon 9 of 9)	exon (NM_001163434, exon 9 of 9)	3680	NM_022310	14828	Mm.330160	NM_022310	ENSMUSG00000026864	Hspa5	AL022860|AU019543|Bip|D2Wsu141e|D2Wsu17e|Grp78|Hsce70|SEZ-7|Sez7|baffled|mBiP	heat shock protein 5	protein-coding
mm_32181.1	chr4	100911492	100911501	+	1	NA	intron (NM_198037, intron 3 of 26)	intron (NM_198037, intron 3 of 26)	134817	NM_198037	320508	Mm.151962	NM_198037	ENSMUSG00000028532	Cachd1	1190007F10Rik|AI852726|B430218L07Rik|Vwcd1|mKIAA1573	cache domain containing 1	protein-coding
mm_113942.1	chr13	49762473	49762487	+	1	NA	Intergenic	Intergenic	80350	NM_172015	105148	Mm.21118	NM_172015	ENSMUSG00000037851	Iars	2510016L12Rik|AI327140|AU044614|E430001P04Rik|ILRS	isoleucine-tRNA synthetase	protein-coding
mm_119735.1	chr14	54121471	54121491	+	1	NA	Intergenic	Intergenic	132448	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_168254.1	chr10	85957763	85957764	-	1	NA	promoter-TSS (NM_145422)	promoter-TSS (NM_145422)	30	NM_145422	28088	Mm.9257	NM_145422	ENSMUSG00000001783	Rtcb	AI255213|AI463255|D10Wsu52e|FAAP|HSPC117	RNA 2',3'-cyclic phosphate and 5'-OH ligase	protein-coding
mm_124486.1	chr14	121738496	121738506	-	1	NA	5' UTR (NM_001128307, exon 1 of 56)	5' UTR (NM_001128307, exon 1 of 56)	428	NM_001128308	105445	Mm.378591	NM_134074	ENSMUSG00000025558	Dock9	AA959601|AW538057|B230309H04Rik|D14Wsu89e|Zizimin1|mKIAA1058	dedicator of cytokinesis 9	protein-coding
mm_83152.1	chr9	40456313	40456337	-	1	NA	promoter-TSS (NM_172768)	promoter-TSS (NM_172768)	-561	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_102342.1	chr11	58073019	58073031	-	1	NA	Intergenic	Intergenic	-31128	NM_026949	69125	Mm.28910	NM_026949	ENSMUSG00000020515	Cnot8	1500015I04Rik|1810022F04Rik|AA536816|AU015770|AU043059	CCR4-NOT transcription complex, subunit 8	protein-coding
mm_102081.1	chr11	52279072	52279111	-	1	NA	intron (NM_001313981, intron 3 of 10)	intron (NM_001313981, intron 3 of 10)	3504	NM_009331	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_61205.1	chr7	64153917	64153923	+	1	NA	promoter-TSS (NM_001039104)	promoter-TSS (NM_001039104)	85	NM_001039104	17364	Mm.38875	NM_018752	ENSMUSG00000030523	Trpm1	4732499L03Rik|AI606771|Ltrpc1|Mlsn1	transient receptor potential cation channel, subfamily M, member 1	protein-coding
mm_85986.1	chr9	112185940	112185955	-	1	NA	promoter-TSS (NM_001177618)	promoter-TSS (NM_001177618)	2	NM_001177618	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_172286.1	chr6	93630183	93630189	+	1	NA	Intergenic	RLTR9D|LTR|ERVK	282777	NR_104594	14924	Mm.217216	NM_010367	ENSMUSG00000045095	Magi1	AIP3|BAP1|Baiap1|Gukmi1|MAGI1c|Magi-1|TNRC19|WWP3|mKIAA4129	membrane associated guanylate kinase, WW and PDZ domain containing 1	protein-coding
mm_73600.1	chr8	109998912	109998919	+	1	NA	3' UTR (NM_146214, exon 12 of 12)	3' UTR (NM_146214, exon 12 of 12)	8479	NM_146214	234724	Mm.28110	NM_146214	ENSMUSG00000001670	Tat	-	tyrosine aminotransferase	protein-coding
mm_93330.1	chr10	99430824	99430831	-	1	NA	Intergenic	L2a|LINE|L2	167596	NM_026268	67603	Mm.1791	NM_026268	ENSMUSG00000019960	Dusp6	1300019I03Rik|MKP-3|MKP3|PYST1	dual specificity phosphatase 6	protein-coding
mm_112972.1	chr13	21287154	21287164	+	1	NA	3' UTR (NM_010343, exon 5 of 5)	3' UTR (NM_010343, exon 5 of 5)	5527	NM_010343	14780	Mm.1332	NM_010343	ENSMUSG00000004344	Gpx5	AV379049|Arep	glutathione peroxidase 5	protein-coding
mm_149882.1	chr19	25300587	25300592	+	1	NA	intron (NM_181404, intron 2 of 13)	intron (NM_181404, intron 2 of 13)	63387	NM_181404	107351	Mm.260722	NM_181404	ENSMUSG00000032702	Kank1	A930031B09Rik|AU015049|AW121052|Ankrd15|D330024H06Rik|mKIAA0172	KN motif and ankyrin repeat domains 1	protein-coding
mm_83079.1	chr9	39603636	39603646	-	1	NA	promoter-TSS (NM_001199556)	promoter-TSS (NM_001199556)	11	NM_001199556	244810	Mm.208855	NM_178737	ENSMUSG00000038112	AW551984	3222402N16	expressed sequence AW551984	protein-coding
mm_94284.1	chr11	3983741	3983758	+	1	NA	5' UTR (NM_001177703, exon 1 of 3)	5' UTR (NM_001177703, exon 1 of 3)	113	NM_016922	53897	Mm.103414	NM_016922	ENSMUSG00000049721	Gal3st1	Cst|Gcst	galactose-3-O-sulfotransferase 1	protein-coding
mm_132212.1	chr16	32621473	32621479	+	1	NA	intron (NM_011638, intron 11 of 18)	PB1D9|SINE|Alu	12580	NM_011638	22042	Mm.28683	NM_011638	ENSMUSG00000022797	Tfrc	2610028K12Rik|CD71|E430033M20Rik|Mtvr1|TFR|TFR1|TR|Trfr|p90	transferrin receptor	protein-coding
mm_125739.1	chr15	73512694	73512705	+	1	NA	5' UTR (NM_001081066, exon 1 of 23)	5' UTR (NM_001081066, exon 1 of 23)	139	NM_001081066	105841	Mm.322557	NM_001081066	ENSMUSG00000036661	Dennd3	AI447457|E030003N15Rik	DENN/MADD domain containing 3	protein-coding
mm_170846.1	chr2	177578210	177578224	-	1	NA	Intergenic	Intergenic	79991	NR_036450	433520	Mm.425117	NM_001024825		Gm14403	OTTMUSG00000016571	predicted gene 14403	ncRNA
mm_169851.1	chr1	63200499	63200502	+	1	NA	5' UTR (NM_001285937, exon 1 of 6)	5' UTR (NM_001285937, exon 1 of 6)	142	NM_001285936	73884	Mm.86986	NM_028673	ENSMUSG00000027520	Zdbf2	4930431J08Rik|9330107J05Rik	zinc finger, DBF-type containing 2	protein-coding
mm_12322.1	chr2	69382102	69382108	+	1	NA	intron (NM_175512, intron 1 of 4)	intron (NM_175512, intron 1 of 4)	1643	NM_175512	241452	Mm.211655	NM_175512	ENSMUSG00000027068	Dhrs9	C730025I08Rik|Rdh15	dehydrogenase/reductase (SDR family) member 9	protein-coding
mm_129453.1	chr15	78564986	78565030	-	1	NA	exon (NM_009008, exon 5 of 7)	exon (NM_009008, exon 5 of 7)	7775	NM_009008	19354	Mm.1972	NM_009008	ENSMUSG00000033220	Rac2	AI323801|AI452260	RAS-related C3 botulinum substrate 2	protein-coding
mm_66140.1	chr7	31116893	31116904	-	1	NA	3' UTR (NM_011322, exon 6 of 6)	3' UTR (NM_011322, exon 6 of 6)	-1572	NM_001110252	15451	Mm.19182	NM_008281	ENSMUSG00000001249	Hpn	Hlb320	hepsin	protein-coding
mm_119357.1	chr14	41114928	41114938	+	1	NA	intron (NM_133653, intron 6 of 9)	intron (NM_133653, intron 6 of 9)	9900	NM_133653	11720	Mm.14064	NM_133653	ENSMUSG00000037798	Mat1a	AI046368|AdoMet|Ams|MAT|MATA1|SAMS|SAMS1	methionine adenosyltransferase I, alpha	protein-coding
mm_149501.1	chr19	11921388	11921414	+	1	NA	exon (NM_172635, exon 5 of 19)	exon (NM_172635, exon 5 of 19)	-2327	NR_105960	102465601		NR_105960	ENSMUSG00000104979	Mir6994	mmu-mir-6994	microRNA 6994	ncRNA
mm_30482.1	chr3	155025199	155025200	-	1	NA	intron (NM_177066, intron 5 of 24)	intron (NM_177066, intron 5 of 24)	30208	NM_177066	435766	Mm.210428	NM_177066	ENSMUSG00000040086	Tnni3k	Cark|D830019J24Rik	TNNI3 interacting kinase	protein-coding
mm_115919.1	chr13	23535166	23535219	-	1	NA	promoter-TSS (NM_145073)	promoter-TSS (NM_145073)	-226	NM_145073	97908	Mm.261657	NM_145073	ENSMUSG00000099517	Hist1h3g	H3.1-221|M32460	histone cluster 1, H3g	protein-coding
mm_103449.1	chr11	76179597	76179649	-	1	NA	promoter-TSS (NM_026664)	promoter-TSS (NM_026664)	7	NM_026664	68299	Mm.46397	NM_026664	ENSMUSG00000017288	Vps53	2010002A08Rik|2310040I21Rik|3100002B05Rik|Hccs1	VPS53 GARP complex subunit	protein-coding
mm_69947.1	chr7	142251551	142251553	-	1	NA	Intergenic	Intergenic	-21581	NM_001037822	114666	Mm.444495	NM_001037822	ENSMUSG00000073785	Krtap5-5	A030001H12Rik|AI586182|BB149782	keratin associated protein 5-5	protein-coding
mm_49742.1	chr6	34745874	34745892	+	1	NA	exon (NM_145575, exon 3 of 12)	exon (NM_145575, exon 3 of 12)	-34549	NM_001289657	76223	Mm.150047	NM_178630	ENSMUSG00000038836	Agbl3	2900053G10Rik|4930431N21Rik|6530406M24Rik|CCP3	ATP/GTP binding protein-like 3	protein-coding
mm_79998.1	chr9	67041729	67041731	+	1	NA	intron (NM_001164249, intron 2 of 8)	intron (NM_001164249, intron 2 of 8)	2141	NM_001164252	22003	Mm.121878	NM_024427	ENSMUSG00000032366	Tpm1	AA986836|AI854628|TM2|Tm3|Tmpa|Tpm-1|alpha-TM	tropomyosin 1, alpha	protein-coding
mm_83699.1	chr9	50659482	50659488	-	1	NA	5' UTR (NM_145614, exon 1 of 14)	5' UTR (NM_145614, exon 1 of 14)	295	NM_145614	235339	Mm.285076	NM_145614	ENSMUSG00000000168	Dlat	6332404G05Rik|DLTA|PDC-E2	dihydrolipoamide S-acetyltransferase (E2 component of pyruvate dehydrogenase complex)	protein-coding
mm_115983.1	chr13	24280949	24280995	-	1	NA	promoter-TSS (NM_026825)	promoter-TSS (NM_026825)	-182	NM_026825	68732	Mm.211047	NM_026825	ENSMUSG00000021338	Carmil1	1110037D04Rik|AI425970|CARMIL|CARML1|D130057M20|Lrrc16|Lrrc16a	capping protein regulator and myosin 1 linker 1	protein-coding
mm_17915.1	chr2	35402377	35402391	-	1	NA	exon (NM_001145821, exon 8 of 8)	exon (NM_001145821, exon 8 of 8)	-5210	NM_001272040	74854	Mm.159338	NM_001080709	ENSMUSG00000079421	4930402F06Rik	-	RIKEN cDNA 4930402F06 gene	protein-coding
mm_61891.1	chr7	89981248	89981266	+	1	NA	promoter-TSS (NM_021876)	promoter-TSS (NM_021876)	-281	NM_021876	13626	Mm.380914	NM_021876	ENSMUSG00000030619	Eed	ENSMUSG00000039373|l(7)5Rn|l7Rn5|lusk	embryonic ectoderm development	protein-coding
mm_51331.1	chr6	72356233	72356256	+	1	NA	5' UTR (NM_144916, exon 2 of 8)	5' UTR (NM_144916, exon 2 of 8)	761	NM_144916	232086	Mm.491165	NM_144916	ENSMUSG00000055912	Tmem150a	BC014685|Tmem150	transmembrane protein 150A	protein-coding
mm_170031.1	chr17	21962454	21962459	-	1	NA	promoter-TSS (NM_001025373)	promoter-TSS (NM_001025373)	8	NM_001199048	73233	Mm.311219	NM_001199048	ENSMUSG00000071267	Zfp942	3110048L19Rik	zinc finger protein 942	protein-coding
mm_116679.1	chr13	49242926	49242940	-	1	NA	intron (NM_028340, intron 1 of 4)	intron (NM_028340, intron 1 of 4)	5230	NM_025491	66329	Mm.34308	NM_025491	ENSMUSG00000021384	Susd3	1700017I11Rik|2810440J20Rik	sushi domain containing 3	protein-coding
mm_37638.1	chr4	127971667	127971709	-	1	NA	promoter-TSS (NM_001134733)	promoter-TSS (NM_001134733)	-847	NM_001134733	635169	Mm.346755	NM_001134733	ENSMUSG00000028813	CK137956	-	cDNA sequence CK137956	protein-coding
mm_23263.1	chr3	51458615	51458630	+	1	NA	exon (NM_053089, exon 13 of 20)	exon (NM_053089, exon 13 of 20)	-25344	NM_016858	19338	Mm.1664	NM_016858	ENSMUSG00000027739	Rab33b	-	RAB33B, member RAS oncogene family	protein-coding
mm_159628.1	chr4	137409779	137409779	-	1	NA	promoter-TSS (NM_001126318)	promoter-TSS (NM_001126318)	12	NM_001126318	242711	Mm.475541	NM_001126318	ENSMUSG00000078520	Cela3a	Gm13011|OTTMUSG00000009877	chymotrypsin-like elastase family, member 3A	protein-coding
mm_143383.1	chr17	67955998	67956008	-	1	NA	intron (NM_172964, intron 1 of 17)	L1MA4|LINE|L1	-5063	NM_001347410	268970	Mm.9935	NM_172964	ENSMUSG00000024043	Arhgap28	AU044757|AW550892|E130310N06	Rho GTPase activating protein 28	protein-coding
mm_119182.1	chr14	32175653	32175654	+	1	NA	intron (NM_001033988, intron 7 of 9)	ORR1D1|LTR|ERVL-MaLR	9864	NM_019744	27057	Mm.371598	NM_019744	ENSMUSG00000056234	Ncoa4	ARA70|Rfg	nuclear receptor coactivator 4	protein-coding
mm_75443.1	chr8	47533423	47533436	-	1	NA	promoter-TSS (NM_203507)	promoter-TSS (NM_203507)	41	NM_177240	320714	Mm.39461	NM_177240	ENSMUSG00000038102	Trappc11	AW558465|D030016E14Rik|R75422	trafficking protein particle complex 11	protein-coding
mm_172546.1	chr7	99979759	99979771	-	1	NA	intron (NM_175388, intron 1 of 5)	CpG	693	NM_175388	108937	Mm.323087	NM_175388	ENSMUSG00000058761	Rnf169	2900057K09Rik	ring finger protein 169	protein-coding
mm_124737.1	chr15	6581014	6581024	+	1	NA	exon (NM_001278269, exon 1 of 17)	exon (NM_001278269, exon 1 of 17)	1172	NM_011815	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_32597.1	chr4	111777554	111777562	+	1	NA	intron (NM_026470, intron 6 of 12)	intron (NM_026470, intron 6 of 12)	57548	NM_026470	67946	Mm.275526	NM_026470	ENSMUSG00000034401	Spata6	1700062C23Rik|AI790763|Hash|KRP|Mash	spermatogenesis associated 6	protein-coding
mm_140757.1	chr17	17526668	17526679	-	1	NA	Intergenic	Intergenic	97816	NM_172827	240028	Mm.328807	NM_172827	ENSMUSG00000023845	Lnpep	2010309L07Rik|4732490P18Rik|CAP|IRAP|PLAP|gp160|vp165	leucyl/cystinyl aminopeptidase	protein-coding
mm_29424.1	chr3	109009119	109009121	-	1	NA	intron (NM_001163567, intron 1 of 10)	intron (NM_001163567, intron 1 of 10)	18487	NM_001163567	329739	Mm.69013	NM_001163567	ENSMUSG00000040339	Fam102b	1600010D10Rik|B430201A12Rik	family with sequence similarity 102, member B	protein-coding
mm_16808.1	chr2	11159774	11159779	-	1	NA	Intergenic	Intergenic	-12606	NM_008859	18761	Mm.329993	NM_008859	ENSMUSG00000026778	Prkcq	A130035A12Rik|AW494342|PKC-0|PKC-theta|PKCtheta|Pkcq	protein kinase C, theta	protein-coding
mm_69514.1	chr7	134911873	134911900	-	1	NA	intron (NM_001143802, intron 2 of 3)	intron (NM_001143802, intron 2 of 3)	26544	NM_001143802	627214	Mm.323610	NM_001143802	ENSMUSG00000073805	Fam196a	B830028B13Rik	family with sequence similarity 196, member A	protein-coding
mm_140541.1	chr17	6784445	6784458	-	1	NA	Intergenic	Intergenic	-1671	NM_009510	22350	Mm.277812	NM_009510	ENSMUSG00000052397	Ezr	AW146364|R75297|Vil2|p81	ezrin	protein-coding
mm_126308.1	chr15	79546855	79546912	+	1	NA	promoter-TSS (NM_001040187)	promoter-TSS (NM_001040187)	-142	NM_199080	67040	Mm.29644	NM_152806	ENSMUSG00000055065	Ddx17	2610007K22Rik|A430025E01Rik|AI047725|C80929|Gm926|p72	DEAD (Asp-Glu-Ala-Asp) box polypeptide 17	protein-coding
mm_61227.1	chr7	64502062	64502072	+	1	NA	promoter-TSS (NM_001291167)	promoter-TSS (NM_001291167)	-71	NM_001291166	11784	Mm.4657	NM_007461	ENSMUSG00000030519	Apba2	X11-like|X11L|XllL|mXllL	amyloid beta (A4) precursor protein-binding, family A, member 2	protein-coding
mm_67537.1	chr7	81372469	81372506	-	1	NA	intron (NM_001252525, intron 2 of 11)	intron (NM_001252525, intron 2 of 11)	-27253	NM_009092	20068	Mm.42767	NM_009092	ENSMUSG00000061787	Rps17	-	ribosomal protein S17	protein-coding
mm_159173.1	chr2	109676106	109676106	+	1	NA	promoter-TSS (NM_001285419)	promoter-TSS (NM_001285419)	209	NM_001285416	12064	Mm.1442	NM_007540	ENSMUSG00000048482	Bdnf	-	brain derived neurotrophic factor	protein-coding
mm_22206.1	chr2	173659523	173659552	-	1	NA	promoter-TSS (NM_024436)	promoter-TSS (NM_024436)	2	NR_027957	100043911	Mm.260590	NM_001033179	ENSMUSG00000055897	Ppp4r1l-ps	1700007P14Rik|5830403E09Rik|C030010B13Rik|Ppp4r1l	protein phosphatase 4, regulatory subunit 1-like, pseudogene	pseudo
mm_3636.1	chr1	152810108	152810120	+	1	NA	intron (NM_010877, intron 2 of 15)	intron (NM_010877, intron 2 of 15)	9961	NM_010877	17970	Mm.270307	NM_010877	ENSMUSG00000026480	Ncf2	NOXA2|Ncf-2|p67phox	neutrophil cytosolic factor 2	protein-coding
mm_29998.1	chr3	135590578	135590605	-	1	NA	intron (NM_008689, intron 22 of 24)	intron (NM_008689, intron 22 of 24)	100956	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_3988.1	chr1	164373233	164373241	+	1	NA	intron (NM_138314, intron 9 of 13)	intron (NM_138314, intron 9 of 13)	65565	NM_178071	171567	Mm.219428	NM_138314	ENSMUSG00000026575	Nme7	D530024H21Rik|Nm23-M7|Nm23-r7	NME/NM23 family member 7	protein-coding
mm_54358.1	chr6	31088465	31088481	-	1	NA	Intergenic	Intergenic	-25380	NR_029532	387223		NR_029532	ENSMUSG00000065604	Mir29b-1	Mirn29b|Mirn29b-1|mir-29b-1	microRNA 29b-1	ncRNA
mm_28255.1	chr3	88552862	88552958	-	1	NA	promoter-TSS (NM_033526)	promoter-TSS (NM_033526)	17	NM_031248	83409	Mm.41680	NM_031248	ENSMUSG00000028062	Lamtor2	2010111E04Rik|AL022628|Mapbpip|P14|Rab25|Robld3	late endosomal/lysosomal adaptor, MAPK and MTOR activator 2	protein-coding
mm_13370.1	chr2	103572122	103572125	+	1	NA	intron (NM_178890, intron 1 of 16)	L1MEg|LINE|L1	5813	NM_178890	99382	Mm.35850	NM_178890	ENSMUSG00000032724	Abtb2	AW539457|BPOZ-2	ankyrin repeat and BTB (POZ) domain containing 2	protein-coding
mm_42483.1	chr5	115470854	115470865	+	1	NA	exon (NM_011107, exon 2 of 4)	exon (NM_011107, exon 2 of 4)	4593	NM_011107	18778	Mm.20190	NM_011107	ENSMUSG00000029522	Pla2g1b	Pla2a|sPLA2IB	phospholipase A2, group IB, pancreas	protein-coding
mm_6810.1	chr1	84157307	84157325	-	1	NA	intron (NM_001003948, intron 2 of 2)	intron (NM_001003948, intron 2 of 2)	61645	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_110500.1	chr12	54203862	54203887	-	1	NA	promoter-TSS (NM_028133)	promoter-TSS (NM_028133)	0	NM_028133	112407	Mm.133037	NM_028133	ENSMUSG00000035105	Egln3	2610021G09Rik|AI505553|AI648162|Hif-p4h-3|Phd3|SM-20	egl-9 family hypoxia-inducible factor 3	protein-coding
mm_73112.1	chr8	94746939	94746950	+	1	NA	exon (NM_009137, exon 2 of 3)	exon (NM_009137, exon 2 of 3)	1260	NM_009137	20299	Mm.12895	NM_009137	ENSMUSG00000031779	Ccl22	ABCD-1|DCBCK|MDC|Scya22	chemokine (C-C motif) ligand 22	protein-coding
mm_120516.1	chr14	66682726	66682730	+	1	NA	intron (NM_001271761, intron 2 of 2)	L1MDa|LINE|L1	47477	NM_001271760	11549	Mm.57064	NM_013461	ENSMUSG00000045875	Adra1a	Adra1c	adrenergic receptor, alpha 1a	protein-coding
mm_130995.1	chr15	103430385	103430385	-	1	NA	promoter-TSS (NM_028797)	promoter-TSS (NM_028797)	42	NM_028797	74174	Mm.325325	NM_028797	ENSMUSG00000022487	Gtsf1	1700006H03Rik|Cue110	gametocyte specific factor 1	protein-coding
mm_63342.1	chr7	126966604	126966637	+	1	NA	intron (NM_144926, intron 12 of 17)	intron (NM_144926, intron 12 of 17)	-9294	NM_026638	52858	Mm.28219	NM_026638	ENSMUSG00000030682	Cdipt	9530042F15Rik|D7Bwg0575e|Pis|Pis1	CDP-diacylglycerol--inositol 3-phosphatidyltransferase (phosphatidylinositol synthase)	protein-coding
mm_164429.1	chr16	45724621	45724627	-	1	NA	promoter-TSS (NM_019754)	promoter-TSS (NM_019754)	-93	NM_019754	56370	Mm.24183	NM_019754	ENSMUSG00000022658	Tagln3	2700038H05Rik|2900005O10Rik|AI426007|Np25	transgelin 3	protein-coding
mm_95448.1	chr11	50292471	50292516	+	1	NA	promoter-TSS (NM_175334)	promoter-TSS (NM_175334)	-157	NM_175334	103806	Mm.51116	NM_175334	ENSMUSG00000050567	Maml1	AI644666|AW743257|D930008C07Rik|Mam-1|Mam1|mKIAA0200	mastermind like 1 (Drosophila)	protein-coding
mm_114086.1	chr13	54590205	54590218	+	1	NA	promoter-TSS (NM_025933)	promoter-TSS (NM_025933)	-20	NM_025933	67044	Mm.29353	NM_025933	ENSMUSG00000025868	Higd2a	2010110M21Rik|AA690237	HIG1 domain family, member 2A	protein-coding
mm_172173.1	chr6	46530853	46530854	-	1	NA	intron (NM_001004357, intron 13 of 23)	B1F1|SINE|Alu	-713543	NM_025771	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding
mm_120433.1	chr14	65805952	65805967	+	1	NA	promoter-TSS (NM_023209)	promoter-TSS (NM_023209)	48	NM_023209	52033	Mm.24337	NM_023209	ENSMUSG00000022033	Pbk	2810434B10Rik|AW538537|D14Ertd732e|TOPK	PDZ binding kinase	protein-coding
mm_114866.1	chr13	93808463	93808471	+	1	NA	intron (NM_009712, intron 4 of 7)	intron (NM_009712, intron 4 of 7)	17690	NR_049198	100885837		NR_049198	ENSMUSG00000093480	Mir5624	Gm25075|mir-5624|mmu-mir-5624	microRNA 5624	ncRNA
mm_109282.1	chr12	109548830	109548848	+	1	NA	intron (NR_027651, intron 5 of 8)	intron (NR_027651, intron 5 of 8)	3441	NR_003633	17263	Mm.289645	NM_144513	ENSMUSG00000021268	Meg3	2900016C05Rik|3110050O07Rik|6330408G06Rik|AI425946|AW108224|D12Bwg1266e|Gtl2|R74756|R75394	maternally expressed 3	ncRNA
mm_63028.1	chr7	121046006	121046018	+	1	NA	intron (NM_021554, intron 1 of 4)	intron (NM_021554, intron 1 of 4)	11567	NM_021554	59052	Mm.29122	NM_021554	ENSMUSG00000030876	Mettl9	0610012D09Rik|AA517660|Drev|MNCb-5680	methyltransferase like 9	protein-coding
mm_8649.1	chr1	156441383	156441393	-	1	NA	exon (NM_009230, exon 7 of 16)	exon (NM_009230, exon 7 of 16)	-20473	NM_001346967	77352	Mm.428709	NM_001033180	ENSMUSG00000026601	Axdnd1	9430070O13Rik|Gm979	axonemal dynein light chain domain containing 1	protein-coding
mm_3620.1	chr1	152683010	152683026	+	1	NA	intron (NM_001346117, intron 1 of 18)	intron (NM_001346117, intron 1 of 18)	-57801	NM_016846	19731	Mm.245270	NM_016846	ENSMUSG00000026482	Rgl1	Rgl|mKIAA0959	ral guanine nucleotide dissociation stimulator,-like 1	protein-coding
mm_81492.1	chr9	110010465	110010495	+	1	NA	intron (NM_001205330, intron 3 of 18)	L1MB2|LINE|L1	-41541	NM_001311163	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_47777.1	chr5	131930585	131930587	-	1	NA	intron (NM_177047, intron 4 of 18)	intron (NM_177047, intron 4 of 18)	50317	NR_040704	75369	Mm.389696	NR_040704	ENSMUSG00000105773	4930563F08Rik	-	RIKEN cDNA 4930563F08 gene	ncRNA
mm_20865.1	chr2	148439881	148439900	-	1	NA	3' UTR (NM_010740, exon 2 of 2)	3' UTR (NM_010740, exon 2 of 2)	3645	NM_010740	17064	Mm.681	NM_010740	ENSMUSG00000027435	Cd93	6030404G09Rik|AA145088|AA4.1|AW555904|C1qr1|C1qrp|Ly68	CD93 antigen	protein-coding
mm_107949.1	chr12	72408378	72408387	+	1	NA	exon (NM_001286448, exon 1 of 7)	exon (NM_001286448, exon 1 of 7)	672	NM_001286448	104001	Mm.221275	NM_153457	ENSMUSG00000021087	Rtn1	Nsp	reticulon 1	protein-coding
mm_71059.1	chr8	33764859	33764886	+	1	NA	intron (NM_026584, intron 6 of 7)	RLTR10D2|LTR|ERVK	-17102	NM_001206849	72632	Mm.443483	NM_001206849	ENSMUSG00000094500	Smim18	2700090O03Rik|AI835723	small integral membrane protein 18	protein-coding
mm_8187.1	chr1	138097455	138097488	-	1	NA	intron (NM_001111316, intron 13 of 31)	MTE2b|LTR|ERVL-MaLR	77655	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_2535.1	chr1	107362307	107362319	+	1	NA	promoter-TSS (NM_025867)	promoter-TSS (NM_025867)	-1	NM_025867	66957	Mm.12638	NM_025867	ENSMUSG00000026327	Serpinb11	2310046M08Rik|AU015399	serine (or cysteine) peptidase inhibitor, clade B (ovalbumin), member 11	protein-coding
mm_91935.1	chr10	60716289	60716310	-	1	NA	exon (NM_023596, exon 6 of 6)	exon (NM_023596, exon 6 of 6)	-19809	NM_023370	22295	Mm.440327	NM_023370	ENSMUSG00000012819	Cdh23	4930542A03Rik|USH1D|ahl|ahl1|bob|bus|mdfw|nmf112|nmf181|nmf252|sals|v	cadherin 23 (otocadherin)	protein-coding
mm_41486.1	chr5	92113028	92113036	+	1	NA	Intergenic	Intergenic	-24906	NM_019490	56041	Mm.15868	NM_019490	ENSMUSG00000029407	Uso1	115kDa|TAP|Vdp	USO1 vesicle docking factor	protein-coding
mm_81843.1	chr9	118519577	118519580	+	1	NA	intron (NM_018748, intron 2 of 23)	intron (NM_018748, intron 2 of 23)	13260	NM_018748	54214	Mm.10409	NM_018748	ENSMUSG00000038708	Golga4	AI225887|AU019508|Olp-1	golgi autoantigen, golgin subfamily a, 4	protein-coding
mm_81523.1	chr9	110058810	110058815	+	1	NA	intron (NM_001311163, intron 1 of 10)	intron (NM_001311163, intron 1 of 10)	6791	NM_001311164	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_117275.1	chr13	65097140	65097157	-	1	NA	intron (NM_133680, intron 1 of 11)	ORR1D2-int|LTR|ERVL-MaLR	15834	NM_001083901	66631	Mm.239196	NM_133680	ENSMUSG00000038212	Mfsd14b	5730414C17Rik|AU045608|AW539692|Hiatl1	major facilitator superfamily domain containing 14B	protein-coding
mm_4292.1	chr1	171767124	171767138	+	1	NA	promoter-TSS (NM_013730)	promoter-TSS (NM_013730)	-1	NM_013730	27218	Mm.103648	NM_013730	ENSMUSG00000015316	Slamf1	4933415F16|AA177906|CD150|CDw150|ESTM51|IPO-3|Slam	signaling lymphocytic activation molecule family member 1	protein-coding
mm_93506.1	chr10	114516792	114516793	-	1	NA	intron (NM_146241, intron 7 of 18)	(A)n|Simple_repeat|Simple_repeat	284578	NM_146241	237553	Mm.445550	NM_146241	ENSMUSG00000050663	Trhde	9330155P21Rik	TRH-degrading enzyme	protein-coding
mm_104368.1	chr11	94352103	94352129	-	1	NA	exon (NM_029600, exon 27 of 31)	exon (NM_029600, exon 27 of 31)	24115	NM_146024	71452	Mm.141054	NM_027799	ENSMUSG00000020864	Ankrd40	1110011C06Rik|5530600A18Rik|Gcap15	ankyrin repeat domain 40	protein-coding
mm_46620.1	chr5	108367896	108367922	-	1	NA	Intergenic	CpG	-20464	NM_008806	18587	Mm.1372	NM_008806	ENSMUSG00000029491	Pde6b	Pdeb|r|rd|rd-1|rd1|rd10	phosphodiesterase 6B, cGMP, rod receptor, beta polypeptide	protein-coding
mm_147452.1	chr18	46572959	46573000	-	1	NA	intron (NM_173394, intron 1 of 2)	L2|LINE|L2	1554	NM_173394	225471	Mm.149280	NM_173394	ENSMUSG00000056130	Ticam2	B430113A10|TICAM-2|TRAM|Tirp|Trif	toll-like receptor adaptor molecule 2	protein-coding
mm_94669.1	chr11	17221424	17221453	+	1	NA	intron (NM_178909, intron 2 of 7)	LSU-rRNA_Hsa|rRNA|rRNA	9545	NM_178909	103784	Mm.298132	NM_178909	ENSMUSG00000078970	Wdr92	AI553587|HZGJ	WD repeat domain 92	protein-coding
mm_19356.1	chr2	91082240	91082259	-	1	NA	Intergenic	Intergenic	-11934	NM_001290765	68427	Mm.192375	NM_026721	ENSMUSG00000002105	Slc39a13	1100001L14Rik|AA387663|ZIP-13|ZIP13	solute carrier family 39 (metal ion transporter), member 13	protein-coding
mm_171015.1	chr2	83954891	83954908	+	1	NA	Intergenic	CpG	-13673	NM_027964	71861	Mm.116957	NM_027964	ENSMUSG00000034552	Zswim2	1700025P14Rik|4933437F18Rik|MEX	zinc finger SWIM-type containing 2	protein-coding
mm_16594.1	chr2	4936035	4936051	-	1	NA	exon (NM_010726, exon 7 of 9)	exon (NM_010726, exon 7 of 9)	17047	NM_010726	16922	Mm.391704	NM_010726	ENSMUSG00000026664	Phyh	AI256161|AI265699|Lnap1|PAHX	phytanoyl-CoA hydroxylase	protein-coding
mm_124534.1	chr14	122451110	122451121	-	1	NA	promoter-TSS (NR_033325)	promoter-TSS (NR_033325)	0	NR_033325	328479	Mm.86095	NR_033325	ENSMUSG00000064052	Gm5089	6530402A20|C030005G22Rik|EG328479	predicted gene 5089	ncRNA
mm_171043.1	chr2	98196138	98196139	-	1	NA	Intergenic	L1Md_T|LINE|L1	728481	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_105793.1	chr11	109995659	109995681	-	1	NA	5' UTR (NM_013851, exon 1 of 39)	5' UTR (NM_013851, exon 1 of 39)	146	NM_013851	27404	Mm.341004	NM_013851	ENSMUSG00000020620	Abca8b	Abca8	ATP-binding cassette, sub-family A (ABC1), member 8b	protein-coding
mm_78849.1	chr9	44335193	44335220	+	1	NA	3' UTR (NM_010436, exon 1 of 1)	3' UTR (NM_010436, exon 1 of 1)	491	NM_010436	15270	Mm.245931	NM_010436	ENSMUSG00000049932	H2afx	AW228881|H2A.X|H2ax|Hist5-2ax|gammaH2ax	H2A histone family, member X	protein-coding
mm_34166.1	chr4	139629400	139629407	+	1	NA	intron (NM_175438, intron 1 of 14)	intron (NM_175438, intron 1 of 14)	6509	NM_175438	212647	Mm.273571	NM_175438	ENSMUSG00000028737	Aldh4a1	A930035F14Rik|Ahd-1|Ahd1|Aldh4|Aldh5a1|E330022C09|P5cd|P5cdh|P5cdhl|P5cdhs|Ssdh1	aldehyde dehydrogenase 4 family, member A1	protein-coding
mm_145955.1	chr18	67668290	67668314	+	1	NA	3' UTR (NM_001127177, exon 9 of 9)	3' UTR (NM_001127177, exon 9 of 9)	26703	NM_134138	107047	Mm.150701	NM_134138	ENSMUSG00000024537	Psmg2	1700017I17Rik|AW545363|Clast3|Tnfsf5ip1	proteasome (prosome, macropain) assembly chaperone 2	protein-coding
mm_162304.1	chr1	36557696	36557731	+	1	NA	promoter-TSS (NM_001304329)	promoter-TSS (NM_001304329)	-156	NM_001304329	20353	Mm.29558	NM_001126047	ENSMUSG00000026121	Sema4c	AI426163|M-Sema F|Semacl1|Semaf|Semai|sema I	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4C	protein-coding
mm_159458.1	chr3	153912047	153912047	-	1	NA	TTS (NR_028525)	TTS (NR_028525)	142	NR_028525	100217425		NR_028525		Snord45c	MBII-401	small nucleolar RNA, C/D box 45C	snoRNA
mm_147014.1	chr18	34523059	34523071	-	1	NA	Intergenic	Intergenic	-16242	NM_146084	225358	Mm.226899	NM_146084	ENSMUSG00000036501	Fam13b	2610024E20Rik|AW060714|AW546153	family with sequence similarity 13, member B	protein-coding
mm_105100.1	chr11	100939588	100939607	-	1	NA	promoter-TSS (NM_011486)	promoter-TSS (NM_011486)	-57	NM_011486	20848	Mm.249934	NM_011486	ENSMUSG00000004040	Stat3	1110034C02Rik|AW109958|Aprf	signal transducer and activator of transcription 3	protein-coding
mm_17177.1	chr2	25356312	25356318	-	1	NA	promoter-TSS (NM_031843)	promoter-TSS (NM_031843)	17	NM_031843	83768	Mm.21440	NM_031843	ENSMUSG00000026958	Dpp7	DPPII|Dpp2|QPP	dipeptidylpeptidase 7	protein-coding
mm_136527.1	chr16	97461481	97461502	-	1	NA	intron (NM_010846, intron 1 of 10)	intron (NM_010846, intron 1 of 10)	1414	NM_010846	17857	Mm.33996	NM_010846	ENSMUSG00000000386	Mx1	AI893580|Mx|Mx-1	MX dynamin-like GTPase 1	protein-coding
mm_95983.1	chr11	58978094	58978149	+	1	NA	promoter-TSS (NM_053168)	promoter-TSS (NM_053168)	28	NM_053168	94091	Mm.248049	NM_053168	ENSMUSG00000020455	Trim11	-	tripartite motif-containing 11	protein-coding
mm_66029.1	chr7	30624535	30624570	-	1	NA	exon (NM_025628, exon 2 of 4)	exon (NM_025628, exon 2 of 4)	1599	NM_025628	110323	Mm.400	NM_025628	ENSMUSG00000036751	Cox6b1	2010000G05Rik|Cox6b	cytochrome c oxidase, subunit VIb polypeptide 1	protein-coding
mm_35188.1	chr4	16013784	16013802	-	1	NA	promoter-TSS (NM_145950)	promoter-TSS (NM_145950)	84	NM_145950	209212	Mm.46455	NM_145950	ENSMUSG00000041153	Osgin2	BC010311|C230027H09Rik	oxidative stress induced growth inhibitor family member 2	protein-coding
mm_28050.1	chr3	84040293	84040321	-	1	NA	promoter-TSS (NM_172681)	promoter-TSS (NM_172681)	-146	NM_172681	229473	Mm.28838	NM_172681	ENSMUSG00000033767	D930015E06Rik	Kiaa0922|mKIAA0922	RIKEN cDNA D930015E06 gene	protein-coding
mm_3115.1	chr1	134576421	134576424	+	1	NA	intron (NM_152895, intron 1 of 26)	intron (NM_152895, intron 1 of 26)	16244	NM_152895	75605	Mm.28995	NM_152895	ENSMUSG00000042207	Kdm5b	2010009J12Rik|2210016I17Rik|AW556288|D1Ertd202e|Jarid1b|PLU-1|PUT1|Plu1|RBBP2H1A|Rb-Bp2|mKIAA4034	lysine (K)-specific demethylase 5B	protein-coding
mm_97353.1	chr11	77493369	77493394	+	1	NA	promoter-TSS (NM_001004144)	promoter-TSS (NM_001004144)	-31	NM_001004144	216963	Mm.290182	NM_001004144	ENSMUSG00000011877	Git1	Cat-1|p95Cat	G protein-coupled receptor kinase-interactor 1	protein-coding
mm_109099.1	chr12	105003444	105003461	+	1	NA	intron (NM_172500, intron 1 of 16)	intron (NM_172500, intron 1 of 16)	-4775	NM_001042699	212073	Mm.212688	NM_172500	ENSMUSG00000054150	Syne3	nesprin-3	spectrin repeat containing, nuclear envelope family member 3	protein-coding
mm_99154.1	chr11	100580829	100580851	+	1	NA	3' UTR (NM_009923, exon 4 of 4)	3' UTR (NM_009923, exon 4 of 4)	4949	NM_001146318	12799	Mm.15711	NM_009923	ENSMUSG00000006782	Cnp	CNPase|Cnp-1|Cnp1	2',3'-cyclic nucleotide 3' phosphodiesterase	protein-coding
mm_90601.1	chr10	128322497	128322540	+	1	NA	promoter-TSS (NM_019953)	promoter-TSS (NM_019953)	59	NM_019953	56530	Mm.44220	NM_019953	ENSMUSG00000025381	Cnpy2	5330432A10Rik|AW229003|D10Bwg1546e|Tmem4|Zsig9	canopy FGF signaling regulator 2	protein-coding
mm_127736.1	chr15	103298664	103298669	+	1	NA	intron (NM_019817, intron 8 of 8)	intron (NM_019817, intron 8 of 8)	11772	NM_030720	80910	Mm.160369	NM_030720	ENSMUSG00000063234	Gpr84	EX33	G protein-coupled receptor 84	protein-coding
mm_45409.1	chr5	66323702	66323713	-	1	NA	intron (NM_001310626, intron 10 of 15)	intron (NM_001310626, intron 10 of 15)	13958	NM_001201416	11787	Mm.5159	NM_009686	ENSMUSG00000029207	Apbb2	2310007D03Rik|FE65L1|Rirl1|TR2L|Zfra	amyloid beta (A4) precursor protein-binding, family B, member 2	protein-coding
mm_57092.1	chr6	122587613	122587635	-	1	NA	intron (NM_001134391, intron 5 of 7)	intron (NM_001134391, intron 5 of 7)	14820	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_67964.1	chr7	100583073	100583124	-	1	NA	promoter-TSS (NM_198831)	promoter-TSS (NM_198831)	32	NM_198831	52443	Mm.473730	NM_198831	ENSMUSG00000030706	Mrpl48	1810030E20Rik|2610028L11Rik|CGI-118|D4Ertd786e	mitochondrial ribosomal protein L48	protein-coding
mm_109374.1	chr12	109650662	109650675	+	1	NA	promoter-TSS (NR_046305)	promoter-TSS (NR_046305)	-41	NR_028434	100303647		NR_028434		AF357359	MBII-426	snoRNA AF357359	snoRNA
mm_10923.1	chr2	25428592	25428605	+	1	NA	promoter-TSS (NM_007379)	promoter-TSS (NM_007379)	-76	NM_007379	11305	Mm.2210	NM_007379	ENSMUSG00000026944	Abca2	AI413825|Abc2|D2H0S1474E|mKIAA1062	ATP-binding cassette, sub-family A (ABC1), member 2	protein-coding
mm_160167.1	chr7	44885520	44885520	-	1	NA	intron (NM_029365, intron 5 of 17)	intron (NM_029365, intron 5 of 17)	6904	NM_001331208	75613	Mm.157778	NM_029365	ENSMUSG00000002968	Med25	2610034E13Rik|2610529E18Rik|ESTM2	mediator complex subunit 25	protein-coding
mm_38155.1	chr4	135120467	135120504	-	1	NA	promoter-TSS (NM_019732)	promoter-TSS (NM_019732)	-160	NM_019732	12399	Mm.378894	NM_019732	ENSMUSG00000070691	Runx3	AML2|Cbfa3|Pebp2a3	runt related transcription factor 3	protein-coding
mm_1599.1	chr1	74375567	74375577	+	1	NA	intron (NM_013612, intron 1 of 14)	intron (NM_013612, intron 1 of 14)	369	NM_013612	18173	Mm.2913	NM_013612	ENSMUSG00000026177	Slc11a1	Bcg|Ity|Ity1|Lsh|Nramp|Nramp1|ity	solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1	protein-coding
mm_48201.1	chr5	137533171	137533198	-	1	NA	promoter-TSS (NM_010312)	promoter-TSS (NM_010312)	45	NM_010312	14693	Mm.30141	NM_010312	ENSMUSG00000029713	Gnb2	Gnb-2	guanine nucleotide binding protein (G protein), beta 2	protein-coding
mm_34940.1	chr4	155843052	155843100	+	1	NA	exon (NM_024263, exon 9 of 10)	exon (NM_024263, exon 9 of 10)	3396	NM_024263	74761	Mm.159028	NM_024263	ENSMUSG00000029070	Mxra8	1200013A08Rik|1700095D18Rik|AI131686|Asp3|Dicam	matrix-remodelling associated 8	protein-coding
mm_145872.1	chr18	65470477	65470492	+	1	NA	exon (NM_172833, exon 13 of 16)	exon (NM_172833, exon 13 of 16)	39487	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_144969.1	chr18	37826701	37826707	+	1	NA	intron (NM_001301259, intron 2 of 3)	intron (NM_001301259, intron 2 of 3)	7158	NM_033583	93708	Mm.247203	NM_033583	ENSMUSG00000102543	Pcdhgc5	-	protocadherin gamma subfamily C, 5	protein-coding
mm_142087.1	chr17	35779604	35779627	-	1	NA	intron (NR_045459, intron 2 of 2)	intron (NR_045459, intron 2 of 2)	7165	NR_045459	74601	Mm.410840	NR_045459	ENSMUSG00000092171	4833427F10Rik	-	RIKEN cDNA 4833427F10 gene	ncRNA
mm_56561.1	chr6	101337910	101337913	-	1	NA	intron (NM_018884, intron 3 of 9)	intron (NM_018884, intron 3 of 9)	39986	NM_018884	55983	Mm.321654	NM_018884	ENSMUSG00000035357	Pdzrn3	1110020C07Rik|AI429718|AL023082|LNX3|SEMACAP3|Semcap3	PDZ domain containing RING finger 3	protein-coding
mm_170157.1	chr17	47141512	47141513	+	1	NA	intron (NM_001097623, intron 2 of 19)	intron (NM_001097623, intron 2 of 19)	570	NM_001097623	224829	Mm.260989	NM_172622		Trerf1	9430096I18Rik|AI429294|B830015H24|RAPA|Trep-132|Trep132	transcriptional regulating factor 1	protein-coding
mm_111211.1	chr12	84400852	84400900	-	1	NA	promoter-TSS (NM_001286049)	promoter-TSS (NM_001286049)	58	NM_001286058	12499	Mm.10211	NM_007647	ENSMUSG00000021236	Entpd5	AI196558|AI987697|Cd39l4|ER-UDPase|NTPDase-5|NTPDase5|Pcph|mNTPase	ectonucleoside triphosphate diphosphohydrolase 5	protein-coding
mm_118638.1	chr14	21460943	21460945	+	1	NA	Intergenic	RLTR51B_Mm|LTR|ERVK?	-38826	NM_001205241	54169	Mm.248967	NM_017479	ENSMUSG00000021767	Kat6b	AI507552|B130044K16Rik|MYST-4|Morf|Myst4|mKIAA0383|qkf|querkopf	K(lysine) acetyltransferase 6B	protein-coding
mm_60623.1	chr7	44708725	44708759	+	1	NA	promoter-TSS (NM_029317)	promoter-TSS (NM_029317)	-1	NM_029317	75510	Mm.273301	NM_029317	ENSMUSG00000066500	Izumo2	1700023D19Rik	IZUMO family member 2	protein-coding
mm_154236.1	chr19	60580358	60580405	-	1	NA	exon (NM_001172096, exon 1 of 8)	exon (NM_001172096, exon 1 of 8)	642	NM_001172097	78832	Mm.259026	NM_030197	ENSMUSG00000033417	Cacul1	2700078E11Rik|2810417M16Rik|9830127L17Rik|AI450346|D130033C15Rik	CDK2 associated, cullin domain 1	protein-coding
mm_51488.1	chr6	83055494	83055525	+	1	NA	promoter-TSS (NM_019752)	promoter-TSS (NM_019752)	-938	NM_019752	64704	Mm.21880	NM_019752	ENSMUSG00000068329	Htra2	AI481710|Omi|Prss25|mnd2	HtrA serine peptidase 2	protein-coding
mm_42413.1	chr5	115235497	115235511	+	1	NA	promoter-TSS (NM_026398)	promoter-TSS (NM_026398)	-347	NM_026398	117109	Mm.24636	NM_026398	ENSMUSG00000060152	Pop5	1500019J17Rik|2700077E03Rik|AW049989|Rnasep3	processing of precursor 5, ribonuclease P/MRP family (S. cerevisiae)	protein-coding
mm_39573.1	chr5	23433935	23433950	+	1	NA	promoter-TSS (NM_026984)	promoter-TSS (NM_026984)	411	NR_040469	269630	Mm.425231	NR_040469	ENSMUSG00000073147	5031425E22Rik	-	RIKEN cDNA 5031425E22 gene	ncRNA
mm_108969.1	chr12	102469228	102469318	+	1	NA	promoter-TSS (NM_013747)	promoter-TSS (NM_013747)	139	NM_001199004	27277	Mm.273370	NM_013747	ENSMUSG00000021192	Golga5	Ret-II	golgi autoantigen, golgin subfamily a, 5	protein-coding
mm_55708.1	chr6	72958424	72958429	-	1	NA	promoter-TSS (NM_025284)	promoter-TSS (NM_025284)	57	NM_025284	19240	Mm.3532	NM_025284	ENSMUSG00000079523	Tmsb10	Ptmb10|Tb10	thymosin, beta 10	protein-coding
mm_50319.1	chr6	47953391	47953451	+	1	NA	promoter-TSS (NM_178898)	promoter-TSS (NM_178898)	31	NM_178898	101197	Mm.241063	NM_178898	ENSMUSG00000045466	Zfp956	AI894139	zinc finger protein 956	protein-coding
mm_37030.1	chr4	115057508	115057522	-	1	NA	promoter-TSS (NM_001287388)	promoter-TSS (NM_001287388)	-296	NM_001287388	21349	Mm.239869	NM_011527	ENSMUSG00000028717	Tal1	Hpt|SCL/tal-1|Scl|bHLHa17|tal-1	T cell acute lymphocytic leukemia 1	protein-coding
mm_170036.1	chr17	22817737	22817740	-	1	NA	promoter-TSS (NR_030709)	promoter-TSS (NR_030709)	9	NR_030709	100042679	Mm.484007	NR_030709		Gm16386	EG545191|ENSMUSG00000073442|Gm21017	zinc finger protein 946 pseudogene	pseudo
mm_95147.1	chr11	35558756	35558756	+	1	NA	intron (NM_011412, intron 6 of 35)	intron (NM_011412, intron 6 of 35)	-58060	NR_029799	723924		NR_029799	ENSMUSG00000065583	Mir218-2	Mirn218-2|mir-218-2	microRNA 218-2	ncRNA
mm_137411.1	chr17	26113711	26113719	+	1	NA	intron (NM_021793, intron 1 of 12)	CpG	399	NM_021793	60455	Mm.304656	NM_021793	ENSMUSG00000024180	Tmem8	AW490096|M83|Tmem8a	transmembrane protein 8 (five membrane-spanning domains)	protein-coding
mm_70219.1	chr7	144941481	144941493	-	1	NA	Intergenic	CpG	-1562	NM_007631	12443	Mm.273049	NM_007631	ENSMUSG00000070348	Ccnd1	AI327039|CycD1|Cyl-1|PRAD1|bcl-1|cD1	cyclin D1	protein-coding
mm_128030.1	chr15	25363546	25363559	-	1	NA	3' UTR (NM_027395, exon 2 of 2)	3' UTR (NM_027395, exon 2 of 2)	50212	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	brain abundant, membrane attached signal protein 1	protein-coding
mm_142753.1	chr17	48647663	48647679	-	1	NA	Intergenic	MT2A|LTR|ERVL	192770	NM_152823	76589	Mm.311629	NM_152823	ENSMUSG00000043592	Unc5cl	2510009H09Rik|BB155270|Zud	unc-5 family C-terminal like	protein-coding
mm_163475.1	chr12	104862090	104862096	+	1	NA	intron (NM_001040682, intron 1 of 12)	intron (NM_001040682, intron 1 of 12)	2983	NR_104436	94040	Mm.244078	NM_053155	ENSMUSG00000021097	Clmn	9330188N17Rik|AI428889|AI788815|mKIAA1188	calmin	protein-coding
mm_130775.1	chr15	101488096	101488112	-	1	NA	intron (NM_001201323, intron 4 of 8)	intron (NM_001201323, intron 4 of 8)	3199	NM_016879	53622	Mm.347934	NM_016879		Krt85	AA589597|BB007925|Hb5|Krt2-18	keratin 85	protein-coding
mm_151010.1	chr19	46707659	46707708	+	1	NA	intron (NM_020577, intron 1 of 10)	intron (NM_020577, intron 1 of 10)	240	NM_020577	57344	Mm.28566	NM_020577	ENSMUSG00000003559	As3mt	2310045H08Rik|Cyt19	arsenic (+3 oxidation state) methyltransferase	protein-coding
mm_31356.1	chr4	47208006	47208088	+	1	NA	promoter-TSS (NM_009928)	promoter-TSS (NM_009928)	35	NM_009928	12819	Mm.233547	NM_009928	ENSMUSG00000028339	Col15a1	-	collagen, type XV, alpha 1	protein-coding
mm_165866.1	chr4	34434459	34434459	-	1	NA	Intergenic	Intergenic	-116156	NM_001007589	433693	Mm.389532	NM_026019	ENSMUSG00000028291	Akirin2	2700059D21Rik|AA114675|AA522011|AU019887|Akirin-2	akirin 2	protein-coding
mm_42497.1	chr5	115484484	115484520	+	1	NA	promoter-TSS (NM_001167691)	promoter-TSS (NM_001167691)	-18	NM_133760	75387	Mm.332616	NM_133760	ENSMUSG00000029524	Sirt4	4930596O17Rik	sirtuin 4	protein-coding
mm_53683.1	chr6	142345702	142345712	+	1	NA	promoter-TSS (NM_183165)	promoter-TSS (NM_183165)	10	NM_183165	232491	Mm.490474	NM_183165	ENSMUSG00000041671	Pyroxd1	-	pyridine nucleotide-disulphide oxidoreductase domain 1	protein-coding
mm_77430.1	chr8	121541940	121541946	-	1	NA	promoter-TSS (NM_029597)	promoter-TSS (NM_029597)	11	NM_029597	76405	Mm.165697	NM_029597	ENSMUSG00000031809	1700018B08Rik	1700084O22Rik	RIKEN cDNA 1700018B08 gene	protein-coding
mm_100689.1	chr11	3509225	3509227	-	1	NA	Intergenic	MIRb|SINE|MIR	-4405	NM_172439	170835	Mm.24313	NM_172439	ENSMUSG00000034570	Inpp5j	Pib5pa|Pipp	inositol polyphosphate 5-phosphatase J	protein-coding
mm_33194.1	chr4	126262383	126262402	+	1	NA	promoter-TSS (NM_013718)	promoter-TSS (NM_013718)	-13	NM_013718	27096	Mm.8392	NM_013718	ENSMUSG00000028847	Trappc3	1110058K12Rik|AI835942|AU019197|Bet3	trafficking protein particle complex 3	protein-coding
mm_96770.1	chr11	69935798	69935817	+	1	NA	promoter-TSS (NM_016875)	promoter-TSS (NM_016875)	-92	NM_016875	53422	Mm.29286	NM_016875	ENSMUSG00000018554	Ybx2	Msy2	Y box protein 2	protein-coding
mm_8476.1	chr1	153487640	153487662	-	1	NA	promoter-TSS (NM_007842)	promoter-TSS (NM_007842)	9	NM_007842	13211	Mm.20000	NM_007842	ENSMUSG00000042699	Dhx9	AI326842|Ddx9|HEL-5|NDHII|RHA|mHEL-5	DEAH (Asp-Glu-Ala-His) box polypeptide 9	protein-coding
mm_70184.1	chr7	143767007	143767012	-	1	NA	promoter-TSS (NM_203492)	promoter-TSS (NM_203492)	-16	NM_203492	381974	Mm.297839	NM_203492	ENSMUSG00000050276	Mrgprg	Gm1098|Mrgg	MAS-related GPR, member G	protein-coding
mm_98096.1	chr11	86614656	86614662	+	1	NA	intron (NM_029478, intron 7 of 11)	L1Md_F3|LINE|L1	-30501	NR_029738	387140		NR_029738	ENSMUSG00000065455	Mir21a	Mir21|Mirn21|mmu-mir-21|mmu-mir-21a	microRNA 21a	ncRNA
mm_79374.1	chr9	54698922	54698927	+	1	NA	promoter-TSS (NM_021422)	promoter-TSS (NM_021422)	-635	NM_021422	58233	Mm.489676	NM_021422	ENSMUSG00000032285	Dnaja4	1110021L12Rik|AV358213|Dj4|Hsj4|mmDjA4	DnaJ heat shock protein family (Hsp40) member A4	protein-coding
mm_12620.1	chr2	74697664	74697674	+	1	NA	promoter-TSS (NM_013555)	promoter-TSS (NM_013555)	-94	NM_013555	15438	Mm.26544	NM_013555	ENSMUSG00000043342	Hoxd9	Hox-4.4|Hox-5.2	homeobox D9	protein-coding
mm_142116.1	chr17	35841334	35841361	-	1	NA	promoter-TSS (NM_001010833)	promoter-TSS (NM_001010833)	-151	NM_001010833	240087	Mm.218511	NM_001010833	ENSMUSG00000061607	Mdc1	6820401C03|AA413496|Nfbd1|mKIAA0170	mediator of DNA damage checkpoint 1	protein-coding
mm_79107.1	chr9	46268708	46268727	+	1	NA	intron (NM_080434, intron 1 of 3)	intron (NM_080434, intron 1 of 3)	109	NM_080434	66113	Mm.29738	NM_080434	ENSMUSG00000032079	Apoa5	1300007O05Rik|Apoav|RAP3	apolipoprotein A-V	protein-coding
mm_166899.1	chr7	28441142	28441156	+	1	NA	intron (NM_001039192, intron 1 of 6)	intron (NM_001039192, intron 1 of 6)	212	NM_001039192	63986	Mm.194536	NM_022024	ENSMUSG00000060791	Gmfg	0610039G16Rik|2310057N07Rik|AI324845	glia maturation factor, gamma	protein-coding
mm_127069.1	chr15	97374013	97374036	+	1	NA	5' UTR (NM_172293, exon 5 of 6)	5' UTR (NM_172293, exon 5 of 6)	-126737	NM_001164602	105827	Mm.24005	NM_178114	ENSMUSG00000048218	Amigo2	AI415330|AMIGO-2|AW208913|Ali1	adhesion molecule with Ig like domain 2	protein-coding
mm_32686.1	chr4	115839193	115839238	+	1	NA	promoter-TSS (NM_001285488)	promoter-TSS (NM_001285488)	17	NM_001285487	17346	Mm.209327	NM_021461	ENSMUSG00000028708	Mknk1	2410048M24Rik|Mnk1	MAP kinase-interacting serine/threonine kinase 1	protein-coding
mm_80469.1	chr9	78113391	78113402	+	1	NA	5' UTR (NM_019987, exon 1 of 14)	5' UTR (NM_019987, exon 1 of 14)	158	NM_019987	56542	Mm.288719	NM_019987	ENSMUSG00000009828	Ick	2210420N10Rik|AI848300|Mrk	intestinal cell kinase	protein-coding
mm_110619.1	chr12	57104504	57104510	-	1	NA	intron (NM_172577, intron 1 of 9)	intron (NM_172577, intron 1 of 9)	56136	NM_001167976	217593	Mm.32835	NM_172577	ENSMUSG00000035472	Slc25a21	9930033G19Rik|A630030I10|BB158148	solute carrier family 25 (mitochondrial oxodicarboxylate carrier), member 21	protein-coding
mm_17697.1	chr2	32353252	32353282	-	1	NA	promoter-TSS (NR_125959)	promoter-TSS (NR_125959)	62	NM_001301737	13429	Mm.44736	NM_010065	ENSMUSG00000026825	Dnm1	AI838169|Dnm|Ftfl|mKIAA4093	dynamin 1	protein-coding
mm_127912.1	chr15	9529851	9529865	-	1	NA	promoter-TSS (NM_008372)	promoter-TSS (NM_008372)	18	NM_008372	16197	Mm.389	NM_008372	ENSMUSG00000003882	Il7r	CD127|IL-7Ralpha	interleukin 7 receptor	protein-coding
mm_107002.1	chr12	11282357	11282376	+	1	NA	exon (NM_025695, exon 7 of 27)	exon (NM_025695, exon 7 of 27)	16480	NM_025695	67241	Mm.173953	NM_025695	ENSMUSG00000020608	Smc6	2810489L22Rik|3830418C19Rik|AA990493|AU018782|AW742439|SMC-6|Smc6l1|mKIAA4103	structural maintenance of chromosomes 6	protein-coding
mm_27779.1	chr3	73708203	73708277	-	1	NA	5' UTR (NM_009738, exon 1 of 4)	5' UTR (NM_009738, exon 1 of 4)	175	NM_009738	12038	Mm.250719	NM_009738	ENSMUSG00000027792	Bche	C730038G20Rik	butyrylcholinesterase	protein-coding
mm_158907.1	chr1	38535172	38535172	-	1	NA	exon (NM_001290814, exon 4 of 22)	exon (NM_001290814, exon 4 of 22)	92072	NM_001290814	16764	Mm.336679	NM_010678	ENSMUSG00000037138	Aff3	3222402O04Rik|A730046J16|LAF-4|Laf4	AF4/FMR2 family, member 3	protein-coding
mm_142104.1	chr17	35835627	35835704	-	1	NA	exon (NM_011655, exon 4 of 4)	exon (NM_011655, exon 4 of 4)	2636	NM_011655	22154	Mm.273538	NM_011655	ENSMUSG00000001525	Tubb5	AA408537|AI596182|B130022C14Rik|M(beta)5	tubulin, beta 5 class I	protein-coding
mm_129060.1	chr15	75567165	75567175	-	1	NA	promoter-TSS (NM_011837)	promoter-TSS (NM_011837)	12	NM_011837	23934	Mm.22154	NM_011837	ENSMUSG00000022577	Ly6h	-	lymphocyte antigen 6 complex, locus H	protein-coding
mm_64299.1	chr7	141861677	141861687	+	1	NA	exon (NM_028801, exon 31 of 49)	exon (NM_028801, exon 31 of 49)	22610	NM_028801	74180	Mm.200752	NM_028801	ENSMUSG00000066108	Muc5b	2300002I04Rik|A130042M24|AV085033|MUC5|MUC9|mucin 5b	mucin 5, subtype B, tracheobronchial	protein-coding
mm_55268.1	chr6	53820750	53820758	-	1	NA	promoter-TSS (NM_025817)	promoter-TSS (NM_025817)	71	NM_025817	66873	Mm.422727	NM_025817	ENSMUSG00000043496	Tril	1200009O22Rik|AI316813|mKIAA0644	TLR4 interactor with leucine-rich repeats	protein-coding
mm_145038.1	chr18	39371971	39371976	+	1	NA	3' UTR (NM_175164, exon 23 of 23)	3' UTR (NM_175164, exon 23 of 23)	115272	NM_008173	14815	Mm.129481	NM_008173	ENSMUSG00000024431	Nr3c1	GR|Grl-1|Grl1	nuclear receptor subfamily 3, group C, member 1	protein-coding
mm_119897.1	chr14	54938580	54938585	+	1	NA	exon (NM_026066, exon 3 of 5)	exon (NM_026066, exon 3 of 5)	2085	NM_029390	67272	Mm.41614	NM_026066	ENSMUSG00000040759	Cmtm5	1500005P16Rik|2900052H21Rik|Cklfsf5	CKLF-like MARVEL transmembrane domain containing 5	protein-coding
mm_9942.1	chr1	190465687	190465699	-	1	NA	Intergenic	Intergenic	-295013	NM_008937	19130	Mm.132579	NM_008937	ENSMUSG00000010175	Prox1	A230003G05Rik	prospero homeobox 1	protein-coding
mm_93445.1	chr10	109903876	109903900	-	1	NA	intron (NM_001081035, intron 1 of 38)	intron (NM_001081035, intron 1 of 38)	96331	NM_001081035	260315	Mm.225050	NM_177797	ENSMUSG00000020181	Nav3	4732483H20Rik|9630020C08Rik|POMFIL1|Pomfil1p|mKIAA0938|unc53H3	neuron navigator 3	protein-coding
mm_107798.1	chr12	64917902	64917944	+	1	NA	promoter-TSS (NM_001025605)	promoter-TSS (NM_001025605)	12	NM_001025605	217648	Mm.341586	NM_001025605	ENSMUSG00000047227	Gm527	-	predicted gene 527	protein-coding
mm_72007.1	chr8	70700208	70700214	+	1	NA	3' UTR (NM_001286944, exon 1 of 1)	3' UTR (NM_001286944, exon 1 of 1)	2472	NM_001286944	16478	Mm.419851	NM_010592	ENSMUSG00000071076	Jund	Jund1	jun D proto-oncogene	protein-coding
mm_72017.1	chr8	70718535	70718549	+	1	NA	promoter-TSS (NM_001195253)	promoter-TSS (NM_001195253)	-1	NM_001195253	100502950	Mm.52981	NM_001195253	ENSMUSG00000095026	Gm3336	100041434|2410018E23Rik	predicted gene 3336	protein-coding
mm_157230.1	chrX	16817317	16817335	-	1	NA	promoter-TSS (NM_172778)	promoter-TSS (NM_172778)	40	NM_172778	109731	Mm.241656	NM_172778	ENSMUSG00000040147	Maob	6330414K01Rik|MAO-B	monoamine oxidase B	protein-coding
mm_65238.1	chr7	19770486	19770504	-	1	NA	promoter-TSS (NM_020486)	promoter-TSS (NM_020486)	37	NM_020486	57278	Mm.29236	NM_020486	ENSMUSG00000002980	Bcam	1200005K12Rik|B-CAM|Gplu|Lu	basal cell adhesion molecule	protein-coding
mm_91465.1	chr10	34127998	34128014	-	1	NA	promoter-TSS (NM_175449)	promoter-TSS (NM_175449)	-34	NM_175449	215900	Mm.34479	NM_175449	ENSMUSG00000046031	Fam26f	A630077B13Rik	family with sequence similarity 26, member F	protein-coding
mm_168199.1	chr10	65939616	65939616	+	1	NA	Intergenic	Intergenic	184448	NR_038039	69433	Mm.23366	NR_038039	ENSMUSG00000100000	1700023F02Rik	AV205046	RIKEN cDNA 1700023F02 gene	ncRNA
mm_22910.1	chr3	31076089	31076091	+	1	NA	Intergenic	Intergenic	-18968	NM_011386	20482	Mm.15406	NM_011386	ENSMUSG00000027660	Skil	Skir|SnoN|sno	SKI-like	protein-coding
mm_23444.1	chr3	59729783	59729790	+	1	NA	promoter-TSS (NM_001101531)	promoter-TSS (NM_001101531)	0	NM_001101531	433597	Mm.297801	NM_001101531	ENSMUSG00000090527	Gm5538	-	predicted gene 5538	protein-coding
mm_64238.1	chr7	141701333	141701345	+	1	NA	exon (NM_023566, exon 24 of 46)	exon (NM_023566, exon 24 of 46)	10999	NM_023566	17831	Mm.2041	NM_023566		Muc2	2010015E03Rik|MCM|wnn	mucin 2	protein-coding
mm_94257.1	chr11	3332495	3332511	+	1	NA	intron (NM_178149, intron 3 of 5)	intron (NM_178149, intron 3 of 5)	1772	NM_178149	216505	Mm.390323	NM_178149	ENSMUSG00000034614	Pik3ip1	1500004A08Rik|5830455E04Rik|Crkd|Hgfl	phosphoinositide-3-kinase interacting protein 1	protein-coding
mm_84323.1	chr9	64002566	64002569	-	1	NA	intron (NM_008542, intron 3 of 3)	AT_rich|Low_complexity|Low_complexity	19492	NM_008542	17130	Mm.325757	NM_008542	ENSMUSG00000036867	Smad6	Madh6|b2b390Clo	SMAD family member 6	protein-coding
mm_171376.1	chr4	119282816	119282818	-	1	NA	exon (NM_011732, exon 4 of 8)	exon (NM_011732, exon 4 of 8)	11696	NM_011732	22608	Mm.258204	NM_011732	ENSMUSG00000028639	Ybx1	1700102N10Rik|C79409|EF1A|MSY1|Nsep1|YB-1|dbpB|mYB-1a	Y box protein 1	protein-coding
mm_122510.1	chr14	47167794	47167811	-	1	NA	intron (NM_008102, intron 2 of 5)	intron (NM_008102, intron 2 of 5)	21600	NM_008102	14528	Mm.10651	NM_008102	ENSMUSG00000037580	Gch1	GTP-CH|GTPCH|Gch	GTP cyclohydrolase 1	protein-coding
mm_158139.1	chrX	103256598	103256608	-	1	NA	promoter-TSS (NM_029170)	promoter-TSS (NM_029170)	3	NM_029170	75106	Mm.1441	NM_029170		4930519F16Rik	Ppnx	RIKEN cDNA 4930519F16 gene	protein-coding
mm_72504.1	chr8	83748929	83748953	+	1	NA	Intergenic	Intergenic	-7630	NM_001163031	26364	Mm.334648	NM_011925	ENSMUSG00000002885	Adgre5	AA409984|Cd97|TM7LN1	adhesion G protein-coupled receptor E5	protein-coding
mm_67556.1	chr7	81706891	81706901	-	1	NA	promoter-TSS (NM_001164086)	promoter-TSS (NM_001164086)	29	NM_011983	26557	Mm.228	NM_011983	ENSMUSG00000025813	Homer2	9330120H11Rik|AW539445|CPD|Vesl-2	homer scaffolding protein 2	protein-coding
mm_20916.1	chr2	150619348	150619372	-	1	NA	3' UTR (NM_080575, exon 14 of 14)	3' UTR (NM_080575, exon 14 of 14)	-10837	NM_027977	71881	Mm.26599	NM_027977	ENSMUSG00000033096	Apmap	2310001A20Rik|AI314817	adipocyte plasma membrane associated protein	protein-coding
mm_81784.1	chr9	114723506	114723520	+	1	NA	3' UTR (NM_146229, exon 13 of 13)	3' UTR (NM_146229, exon 13 of 13)	-7690	NM_026036	67213	Mm.28858	NM_026036	ENSMUSG00000032434	Cmtm6	2810051A14Rik|AA536733|Cklfsf6	CKLF-like MARVEL transmembrane domain containing 6	protein-coding
mm_8605.1	chr1	156035787	156035801	-	1	NA	promoter-TSS (NM_001160182)	promoter-TSS (NM_001160182)	67	NM_001160180	240832	Mm.253335	NM_022329	ENSMUSG00000050565	Tor1aip2	1110020D10Rik|15kDa|A130072J07|AA103493|AW060462|AW610675|C77739|Ifrg15|Lull1	torsin A interacting protein 2	protein-coding
mm_4341.1	chr1	171856651	171856671	+	1	NA	intron (NM_001289470, intron 3 of 8)	L1_Mur3|LINE|L1	16964	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_108122.1	chr12	75853849	75853892	+	1	NA	intron (NM_001005510, intron 1 of 115)	intron (NM_001005510, intron 1 of 115)	35552	NM_001005510	319565	Mm.26652	NM_001005510	ENSMUSG00000063450	Syne2	6820443O06Rik|AW546258|Cpfl8|D12Ertd777e|NUA|Nesp2g|dice|mKIAA1011	spectrin repeat containing, nuclear envelope 2	protein-coding
mm_71942.1	chr8	70374928	70374934	+	1	NA	exon (NM_016685, exon 4 of 19)	exon (NM_016685, exon 4 of 19)	1383	NM_016685	12845	Mm.45071	NM_016685	ENSMUSG00000031849	Comp	TSP5	cartilage oligomeric matrix protein	protein-coding
mm_5585.1	chr1	39552318	39552346	-	1	NA	3' UTR (NM_001033135, exon 7 of 7)	3' UTR (NM_001033135, exon 7 of 7)	-3492	NR_028555	100217461		NR_028555	ENSMUSG00000077704	Snord89	MBII-289	small nucleolar RNA, C/D box 89	snoRNA
mm_116449.1	chr13	43171376	43171424	-	1	NA	5' UTR (NM_025935, exon 1 of 8)	5' UTR (NM_025935, exon 1 of 8)	101	NM_001252639	67046	Mm.269213	NM_025935	ENSMUSG00000021368	Tbc1d7	2610009C09Rik	TBC1 domain family, member 7	protein-coding
mm_94447.1	chr11	6389062	6389080	+	1	NA	Intergenic	(CCCCAG)n|Simple_repeat|Simple_repeat	-6054	NM_001005867	52915	Mm.1144	NM_028601	ENSMUSG00000041164	Zmiz2	Zimp7	zinc finger, MIZ-type containing 2	protein-coding
mm_156894.1	chrX	167089160	167089167	+	1	NA	Intergenic	Intergenic	-18793	NM_001101606	667794	Mm.302232	NM_001101606		Gm8817	EG667794	predicted gene 8817	protein-coding
mm_85501.1	chr9	106160121	106160143	-	1	NA	Intergenic	Intergenic	-1994	NM_174846	235582	Mm.335420	NM_174846	ENSMUSG00000020258	Glyctk	6230410P16Rik|C430006L12	glycerate kinase	protein-coding
mm_119989.1	chr14	55580915	55580948	+	1	NA	TTS (NM_033146)	TTS (NM_033146)	2437	NM_011189	19186	Mm.830	NM_011189	ENSMUSG00000022216	Psme1	AW413925|PA28a	proteasome (prosome, macropain) activator subunit 1 (PA28 alpha)	protein-coding
mm_135692.1	chr16	52436270	52436285	-	1	NA	intron (NM_009655, intron 1 of 15)	intron (NM_009655, intron 1 of 15)	16804	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_39321.1	chr5	8068657	8068678	+	1	NA	3' UTR (NM_025618, exon 8 of 8)	3' UTR (NM_025618, exon 8 of 8)	12125	NM_001080974	109552	Mm.96211	NM_025618	ENSMUSG00000003161	Sri	2210417O06Rik|2900070H08Rik|Sor	sorcin	protein-coding
mm_130184.1	chr15	93519553	93519564	-	1	NA	intron (NM_001033217, intron 1 of 7)	CpG	76333	NM_001033217	106042	Mm.150314	NM_001033217	ENSMUSG00000036158	Prickle1	1110058P22Rik|AW215793|Prickle|b2b019Clo|mpk1	prickle planar cell polarity protein 1	protein-coding
mm_156324.1	chrX	137671391	137671393	+	1	NA	intron (NM_030688, intron 2 of 10)	intron (NM_030688, intron 2 of 10)	100638	NM_030688	60367	Mm.328321	NM_030688	ENSMUSG00000059203	Il1rapl2	-	interleukin 1 receptor accessory protein-like 2	protein-coding
mm_162760.1	chr10	61784581	61784601	-	1	NA	promoter-TSS (NM_207000)	promoter-TSS (NM_207000)	-727	NM_207000	404634	Mm.272870	NM_207000	ENSMUSG00000020086	H2afy2	macroH2A2	H2A histone family, member Y2	protein-coding
mm_135200.1	chr16	36532219	36532235	-	1	NA	intron (NM_013803, intron 1 of 6)	intron (NM_013803, intron 1 of 6)	29907	NM_013803	12374	Mm.103619	NM_013803	ENSMUSG00000051980	Casr	CaR|Gprc2a	calcium-sensing receptor	protein-coding
mm_49807.1	chr6	36388187	36388207	+	1	NA	promoter-TSS (NR_015589)	promoter-TSS (NR_015589)	37	NR_015589	319472	Mm.226434	NR_015589	ENSMUSG00000073154	9330158H04Rik	-	RIKEN cDNA 9330158H04 gene	ncRNA
mm_2394.1	chr1	93685469	93685484	+	1	NA	promoter-TSS (NM_016778)	promoter-TSS (NM_016778)	-99	NM_016778	51800	Mm.3295	NM_016778	ENSMUSG00000026278	Bok	matador|mtd	BCL2-related ovarian killer	protein-coding
mm_111702.1	chr12	103676766	103676773	-	1	NA	promoter-TSS (NM_001310472)	promoter-TSS (NM_001310472)	-7	NM_001310472	194604		NM_001310472	ENSMUSG00000071179	Serpina16	Gm46	serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 16	protein-coding
mm_20487.1	chr2	130048344	130048348	-	1	NA	exon (NM_009374, exon 13 of 13)	exon (NM_009374, exon 13 of 13)	-31938	NR_105757	102466628		NR_105757	ENSMUSG00000098347	Mir6339	Gm27848|mmu-mir-6339	microRNA 6339	ncRNA
mm_145924.1	chr18	67088349	67088359	+	1	NA	promoter-TSS (NM_177137)	promoter-TSS (NM_177137)	56	NM_177137	14680	Mm.440746	NM_010307	ENSMUSG00000024524	Gnal	2610011C15Rik|9630020G10Rik|Galphaolf|Gna10|Golf	guanine nucleotide binding protein, alpha stimulating, olfactory type	protein-coding
mm_54091.1	chr6	16469893	16469908	-	1	NA	Intergenic	L2|LINE|L2	428541	NM_031198	21426	Mm.36217	NM_031198	ENSMUSG00000029553	Tfec	BB107417|Tcfec|bHLHe34	transcription factor EC	protein-coding
mm_168810.1	chr12	20990531	20990535	+	1	NA	Intergenic	CpG	-121223	NM_001004364	211914	Mm.358946	NM_001004364	ENSMUSG00000052632	Asap2	6530401G17Rik|Ddef2|Gm1523|Gm592|PAG3|PAP	ArfGAP with SH3 domain, ankyrin repeat and PH domain 2	protein-coding
mm_53641.1	chr6	140622696	140622708	+	1	NA	promoter-TSS (NM_178803)	promoter-TSS (NM_178803)	39	NM_178803	11569	Mm.86453	NM_009637	ENSMUSG00000030232	Aebp2	AU023766|B230313N05Rik	AE binding protein 2	protein-coding
mm_16647.1	chr2	6212981	6213002	-	1	NA	promoter-TSS (NM_024208)	promoter-TSS (NM_024208)	3	NM_024208	67856	Mm.38342	NM_024208	ENSMUSG00000039063	Echdc3	2310005D12Rik|AI662097	enoyl Coenzyme A hydratase domain containing 3	protein-coding
mm_116640.1	chr13	49043919	49043927	-	1	NA	intron (NM_029361, intron 25 of 27)	intron (NM_029361, intron 25 of 27)	75811	NR_015601	68128	Mm.426304	NR_015601		Fam120aos	C030044B11Rik	family with sequence similarity 120A, opposite strand	ncRNA
mm_103430.1	chr11	75756864	75756893	-	1	NA	exon (NM_009536, exon 4 of 6)	exon (NM_009536, exon 4 of 6)	23991	NM_009536	22627	Mm.234700	NM_009536	ENSMUSG00000020849	Ywhae	AU019196	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide	protein-coding
mm_61612.1	chr7	80081940	80081953	+	1	NA	exon (NM_175433, exon 2 of 5)	exon (NM_175433, exon 2 of 5)	-6689	NR_045695	100859962	Mm.392575	NR_045695	ENSMUSG00000108714	Gm21057	-	predicted gene, 21057	ncRNA
mm_35888.1	chr4	49542827	49542858	-	1	NA	exon (NM_144903, exon 4 of 9)	exon (NM_144903, exon 4 of 9)	6704	NM_144903	230163	Mm.482116	NM_144903	ENSMUSG00000028307	Aldob	Aldo-2|Aldo2|BC016435	aldolase B, fructose-bisphosphate	protein-coding
mm_166216.1	chr5	58315878	58315879	+	1	NA	Intergenic	Intergenic	137120	NR_046190	78163	Mm.243828	NR_046190	ENSMUSG00000105234	4930459L07Rik	-	RIKEN cDNA 4930459L07 gene	ncRNA
mm_130599.1	chr15	99772872	99772902	-	1	NA	promoter-TSS (NM_028015)	promoter-TSS (NM_028015)	-372	NM_028015	71949	Mm.390821	NM_028015	ENSMUSG00000023021	Cers5	2310081H14Rik|AU045339|AW544927|Lass5|Trh4	ceramide synthase 5	protein-coding
mm_8305.1	chr1	144003972	144004014	-	1	NA	intron (NM_009061, intron 1 of 4)	intron (NM_009061, intron 1 of 4)	156	NM_009061	19735	Mm.28262	NM_009061	ENSMUSG00000026360	Rgs2	GOS8	regulator of G-protein signaling 2	protein-coding
mm_126669.1	chr15	84324781	84324811	+	1	NA	promoter-TSS (NM_022321)	promoter-TSS (NM_022321)	76	NM_022321	64099	Mm.251356	NM_022321	ENSMUSG00000022439	Parvg	AI413459	parvin, gamma	protein-coding
mm_123847.1	chr14	70708018	70708030	-	1	NA	intron (NM_023045, intron 1 of 27)	intron (NM_023045, intron 1 of 27)	-54940	NM_181345	328440	Mm.347749	NM_181345	ENSMUSG00000047911	Npm2	-	nucleophosmin/nucleoplasmin 2	protein-coding
mm_172722.1	chr8	72305264	72305288	-	1	NA	Intergenic	Intergenic	-13786	NM_008452	16598	Mm.26938	NM_008452	ENSMUSG00000055148	Klf2	Lklf	Kruppel-like factor 2 (lung)	protein-coding
mm_39543.1	chr5	21543526	21543590	+	1	NA	promoter-TSS (NM_028977)	promoter-TSS (NM_028977)	31	NM_028977	74511	Mm.439963	NM_028977	ENSMUSG00000039883	Lrrc17	37kDa|4833425M04Rik|6130400C22Rik|P37nb	leucine rich repeat containing 17	protein-coding
mm_136077.1	chr16	84834965	84834976	-	1	NA	promoter-TSS (NM_001302216)	promoter-TSS (NM_001302216)	28	NM_001302216	11957	Mm.353	NM_016755	ENSMUSG00000022890	Atp5j	CF6	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit F	protein-coding
mm_101632.1	chr11	36307424	36307426	-	1	NA	intron (NM_011856, intron 3 of 28)	intron (NM_011856, intron 3 of 28)	-327336	NM_170779	211652	Mm.31267	NM_170779	ENSMUSG00000018849	Wwc1	AA408228|AU017197|BC037006|Kibra|mKIAA0869	WW, C2 and coiled-coil domain containing 1	protein-coding
mm_81273.1	chr9	108095238	108095251	+	1	NA	promoter-TSS (NM_146226)	promoter-TSS (NM_146226)	-764	NM_146226	235606	Mm.219639	NM_146226	ENSMUSG00000032590	Apeh	-	acylpeptide hydrolase	protein-coding
mm_119699.1	chr14	53683594	53683600	+	1	NA	Intergenic	Intergenic	570332	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_62038.1	chr7	92180875	92180896	+	1	NA	intron (NM_011807, intron 13 of 22)	intron (NM_011807, intron 13 of 22)	-54085	NM_001243047	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_42372.1	chr5	114928068	114928103	+	1	NA	exon (NM_145209, exon 3 of 7)	exon (NM_145209, exon 3 of 7)	4845	NM_145209	231655	Mm.95479	NM_145209	ENSMUSG00000041827	Oasl1	7530414C13Rik|oasl9	2'-5' oligoadenylate synthetase-like 1	protein-coding
mm_22821.1	chr3	27221138	27221141	+	1	NA	intron (NM_178772, intron 1 of 4)	intron (NM_178772, intron 1 of 4)	38135	NM_178772	320024	Mm.24576	NM_178772	ENSMUSG00000027698	Nceh1	Aadacl1|B230106I24Rik|CPO-BP|Nceh	neutral cholesterol ester hydrolase 1	protein-coding
mm_172600.1	chr8	15519851	15519851	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	462198	NM_008664	17930	Mm.272115	NM_008664	ENSMUSG00000031461	Myom2	AW146149	myomesin 2	protein-coding
mm_126473.1	chr15	81466340	81466365	+	1	NA	promoter-TSS (NM_019712)	promoter-TSS (NM_019712)	36	NM_019712	56438	Mm.29405	NM_019712	ENSMUSG00000022400	Rbx1	1500002P15Rik|AA517855|ROC1	ring-box 1	protein-coding
mm_65351.1	chr7	24997562	24997569	-	1	NA	exon (NM_001290469, exon 7 of 23)	exon (NM_001290469, exon 7 of 23)	8372	NM_001290469	232975	Mm.44101	NM_144921	ENSMUSG00000040907	Atp1a3	Atpa-2	ATPase, Na+/K+ transporting, alpha 3 polypeptide	protein-coding
mm_158205.1	chrX	105849075	105849075	-	1	NA	intron (NM_009530, intron 15 of 34)	MLT1E|LTR|ERVL-MaLR	80297	NM_009530	22589	Mm.10141	NM_009530	ENSMUSG00000031229	Atrx	4833408C14Rik|AI447451|ATR2|DXHXS6677E|HP1-BP38|Hp1bp2|Hp1bp38|MRXS3|RAD54L|Rad54|XH2|Xnp|ZNF-HX	alpha thalassemia/mental retardation syndrome X-linked	protein-coding
mm_30320.1	chr3	151731711	151731728	-	1	NA	3' UTR (NM_133871, exon 8 of 8)	3' UTR (NM_133871, exon 8 of 8)	18240	NM_133871	99899	Mm.30756	NM_133871	ENSMUSG00000028037	Ifi44	A430056A10Rik|AW261460|MTAP44|p44	interferon-induced protein 44	protein-coding
mm_107214.1	chr12	26445187	26445203	+	1	NA	3' UTR (NM_021384, exon 6 of 6)	3' UTR (NM_021384, exon 6 of 6)	11257	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_169285.1	chr13	97190613	97190613	-	1	NA	intron (NM_010422, intron 3 of 13)	LSU-rRNA_Hsa|rRNA|rRNA	7744	NM_010422	15212	Mm.27816	NM_010422	ENSMUSG00000021665	Hexb	-	hexosaminidase B	protein-coding
mm_71335.1	chr8	45507738	45507740	+	1	NA	promoter-TSS (NM_001205219)	promoter-TSS (NM_001205219)	-49	NM_172752	234214	Mm.211096	NM_172752	ENSMUSG00000031626	Sorbs2	2010203O03Rik|9430041O17Rik|A530071H08|Argbp2|mKIAA0777|nArgBP2	sorbin and SH3 domain containing 2	protein-coding
mm_95395.1	chr11	49651775	49651778	+	1	NA	3' UTR (NM_008029, exon 30 of 30)	3' UTR (NM_008029, exon 30 of 30)	-11819	NM_054037	68662	Mm.22802	NM_054037	ENSMUSG00000064057	Scgb3a1	HIN-1|LuLeu2|Pnsp2|UGRP2|Utgrp2	secretoglobin, family 3A, member 1	protein-coding
mm_148975.1	chr19	7557643	7557689	+	1	NA	intron (NM_139269, intron 1 of 4)	intron (NM_139269, intron 1 of 4)	207	NM_139269	225845	Mm.274810	NM_139269	ENSMUSG00000060675	Pla2g16	C78643|HRSL3|Hrasls3|Hrev107|MLP-3	phospholipase A2, group XVI	protein-coding
mm_44084.1	chr5	149175198	149175202	+	1	NA	intron (NR_015478, intron 1 of 2)	PB1D9|SINE|Alu	6836	NR_015478	433966	Mm.207047	NR_015478	ENSMUSG00000097191	5730422E09Rik	-	RIKEN cDNA 5730422E09 gene	ncRNA
mm_6238.1	chr1	66945426	66945451	-	1	NA	promoter-TSS (NM_021285)	promoter-TSS (NM_021285)	-382	NM_021285	17901	Mm.1000	NM_021285	ENSMUSG00000061816	Myl1	AI325107|MLC1f|MLC3f|Mylf	myosin, light polypeptide 1	protein-coding
mm_37727.1	chr4	129558809	129558821	-	1	NA	promoter-TSS (NM_010693)	promoter-TSS (NM_010693)	-443	NM_010693	16818	Mm.293753	NM_010693	ENSMUSG00000000409	Lck	Hck-3|Lsk|Lskt|p56<lck>|p56Lck	lymphocyte protein tyrosine kinase	protein-coding
mm_165695.1	chr3	93445161	93445162	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	2831	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_161371.1	chr14	66170477	66170477	-	1	NA	intron (NM_001162366, intron 18 of 29)	intron (NM_001162366, intron 18 of 29)	29517	NM_144803	110902	Mm.57350	NM_144803	ENSMUSG00000022041	Chrna2	Acra-2|Acra2|BC011490	cholinergic receptor, nicotinic, alpha polypeptide 2 (neuronal)	protein-coding
mm_98657.1	chr11	96271231	96271239	+	1	NA	promoter-TSS (NM_008270)	promoter-TSS (NM_008270)	-95	NM_008270	15417	Mm.258271	NM_008270	ENSMUSG00000020875	Hoxb9	Hox-2.5	homeobox B9	protein-coding
mm_7671.1	chr1	128588776	128588787	-	1	NA	3' UTR (NM_009911, exon 2 of 2)	3' UTR (NM_009911, exon 2 of 2)	3518	NM_009911	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding
mm_110300.1	chr12	32770912	32770921	-	1	NA	Intergenic	Intergenic	-49419	NM_021524	59027	Mm.202727	NM_021524	ENSMUSG00000020572	Nampt	1110035O14Rik|AI314458|AI480535|NAmPRTase|Pbef|Pbef1|Visfatin	nicotinamide phosphoribosyltransferase	protein-coding
mm_167637.1	chr9	63333639	63333646	+	1	NA	intron (NM_011840, intron 6 of 21)	intron (NM_011840, intron 6 of 21)	44210	NM_011840	23938	Mm.325746	NM_011840	ENSMUSG00000058444	Map2k5	AI324775|AI428457|MEK5|Mapkk5|Prkmk5	mitogen-activated protein kinase kinase 5	protein-coding
mm_57215.1	chr6	122921481	122921516	-	1	NA	promoter-TSS (NM_199311)	promoter-TSS (NM_199311)	-350	NM_199311	269799	Mm.297275	NM_199311	ENSMUSG00000049037	Clec4a1	BC049354|Dcir4	C-type lectin domain family 4, member a1	protein-coding
mm_71486.1	chr8	46739877	46739885	+	1	NA	promoter-TSS (NR_045750)	promoter-TSS (NR_045750)	136	NM_008391	16363	Mm.1149	NM_008391	ENSMUSG00000031627	Irf2	9830146E22Rik|AI646973|Irf-2	interferon regulatory factor 2	protein-coding
mm_149352.1	chr19	10895392	10895402	+	1	NA	5' UTR (NM_134129, exon 1 of 16)	5' UTR (NM_134129, exon 1 of 16)	166	NM_001253843	28000	Mm.491104	NM_134129	ENSMUSG00000024735	Prpf19	AA617263|AL024362|D19Wsu55e|NMP200|PSO4|Prp19|Snev	pre-mRNA processing factor 19	protein-coding
mm_60030.1	chr7	30977049	30977071	+	1	NA	promoter-TSS (NM_175240)	promoter-TSS (NM_175240)	17	NM_175240	76415	Mm.259739	NM_175240	ENSMUSG00000046826	Fam187b	1700020B09Rik|Tmem162	family with sequence similarity 187, member B	protein-coding
mm_58427.1	chr7	3296995	3297011	+	1	NA	exon (NM_016969, exon 3 of 3)	exon (NM_016969, exon 3 of 3)	3975	NM_001093766	50918	Mm.29874	NM_016969	ENSMUSG00000068566	Myadm	D7Wsu62e	myeloid-associated differentiation marker	protein-coding
mm_149497.1	chr19	11912309	11912325	+	1	NA	promoter-TSS (NM_172635)	promoter-TSS (NM_172635)	-82	NM_172635	225929	Mm.42711	NM_172635	ENSMUSG00000046139	Patl1	AV312086|Pat1b	protein associated with topoisomerase II homolog 1 (yeast)	protein-coding
mm_45781.1	chr5	87336498	87336526	-	1	NA	exon (NM_028094, exon 1 of 6)	exon (NM_028094, exon 1 of 6)	683	NM_028094	72094	Mm.482739	NM_028094	ENSMUSG00000035780	Ugt2a3	2010321J07Rik	UDP glucuronosyltransferase 2 family, polypeptide A3	protein-coding
mm_38068.1	chr4	134095033	134095059	-	1	NA	promoter-TSS (NM_013706)	promoter-TSS (NM_013706)	27	NM_013706	23833	Mm.24130	NM_013706	ENSMUSG00000000682	Cd52	AI463198|B7|B7-Ag|CAMPATH-1|CLS1|MB7	CD52 antigen	protein-coding
mm_129393.1	chr15	78242719	78242738	-	1	NA	Intergenic	Intergenic	-2083	NM_008677	17972	Mm.2068	NM_008677	ENSMUSG00000071715	Ncf4	AI451400|p40phox	neutrophil cytosolic factor 4	protein-coding
mm_37779.1	chr4	130174780	130174808	-	1	NA	promoter-TSS (NM_001168333)	promoter-TSS (NM_001168333)	8	NM_001168333	94242	Mm.15801	NM_023476	ENSMUSG00000028776	Tinagl1	1110021J17Rik|AZ-1|AZ1|Arg1|Lcn7|TARP|Tinagl	tubulointerstitial nephritis antigen-like 1	protein-coding
mm_32673.1	chr4	115738414	115738447	+	1	NA	5' UTR (NM_172698, exon 1 of 12)	5' UTR (NM_172698, exon 1 of 12)	357	NM_172698	230648	Mm.283565	NM_172698	ENSMUSG00000034210	Efcab14	4732418C07Rik	EF-hand calcium binding domain 14	protein-coding
mm_111064.1	chr12	80114520	80114536	-	1	NA	Intergenic	CpG	-1515	NM_007564	12192	Mm.235132	NM_007564	ENSMUSG00000021127	Zfp36l1	AW742437|AW743212|Berg36|Brf1|D530020L18Rik|ERF1|TIS11b|cMG1	zinc finger protein 36, C3H type-like 1	protein-coding
mm_108557.1	chr12	84571503	84571545	+	1	NA	intron (NM_001301427, intron 1 of 4)	CpG	1696	NM_001301427	12677	Mm.4405	NM_007701	ENSMUSG00000021239	Vsx2	Chx10|Hox-10|Hox10|or	visual system homeobox 2	protein-coding
mm_58054.1	chr6	136857523	136857534	-	1	NA	promoter-TSS (NM_026639)	promoter-TSS (NM_026639)	72	NM_026639	109978	Mm.31840	NM_026639	ENSMUSG00000030217	Art4	4432404K01Rik|ARTC4|DO|DOK1	ADP-ribosyltransferase 4	protein-coding
mm_88759.1	chr10	80329989	80330009	+	1	NA	promoter-TSS (NM_139292)	promoter-TSS (NM_139292)	-146	NM_001204931	70335	Mm.28147	NM_139292	ENSMUSG00000035504	Reep6	0610011M24Rik|Dp1l1	receptor accessory protein 6	protein-coding
mm_71241.1	chr8	40909663	40909676	+	1	NA	intron (NM_007514, intron 7 of 11)	intron (NM_007514, intron 7 of 11)	-16564	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_113552.1	chr13	38149500	38149513	+	1	NA	Intergenic	Intergenic	-1788	NM_023842	109620	Mm.355327	NM_023842	ENSMUSG00000054889	Dsp	2300002E22Rik|5730453H04Rik|AA407887|AA407888|AW109828|DP|rul	desmoplakin	protein-coding
mm_22735.1	chr3	19692495	19692520	+	1	NA	TTS (NM_001081281)	TTS (NM_001081281)	2889	NM_205769	12918	Mm.290689	NM_205769	ENSMUSG00000049796	Crh	CRF|Gm1347	corticotropin releasing hormone	protein-coding
mm_147583.1	chr18	56504394	56504419	-	1	NA	TTS (NM_026240)	TTS (NM_026240)	-33733	NR_106160	102465790		NR_106160	ENSMUSG00000099196	Mir1258	Gm27371|mmu-mir-1258	microRNA 1258	ncRNA
mm_50446.1	chr6	48895215	48895233	+	1	NA	promoter-TSS (NM_029638)	promoter-TSS (NM_029638)	-31	NM_029638	76507	Mm.213898	NM_029638	ENSMUSG00000029811	Aoc1	1600012D06Rik|Abp1|DAO	amine oxidase, copper-containing 1	protein-coding
mm_42150.1	chr5	111420250	111420260	+	1	NA	exon (NM_001081235, exon 1 of 2)	exon (NM_001081235, exon 1 of 2)	2089	NM_001081235	433938	Mm.332576	NM_001081235	ENSMUSG00000070576	Mn1	AA003644|AA009236	meningioma 1	protein-coding
mm_147234.1	chr18	38250480	38250514	-	1	NA	promoter-TSS (NR_015475)	promoter-TSS (NR_015475)	68	NR_027904	73516	Mm.48776	NR_015475	ENSMUSG00000097080	1700086O06Rik	-	RIKEN cDNA 1700086O06 gene	ncRNA
mm_167454.1	chr8	123042091	123042095	-	1	NA	promoter-TSS (NR_045268)	promoter-TSS (NR_045268)	191	NR_037865	77087	Mm.31567	NM_001081379	ENSMUSG00000035569	Ankrd11	2410104C19Rik|3010027A04Rik|6330578C09Rik|9530048I21Rik|AA930108|Gm176|Yod	ankyrin repeat domain 11	protein-coding
mm_62528.1	chr7	102233115	102233124	+	1	NA	intron (NR_111937, intron 2 of 5)	intron (NR_111937, intron 2 of 5)	10091	NR_111937	233575	Mm.302013	NM_145583	ENSMUSG00000030990	Pgap2	1810006G21Rik|C76649|Frag1	post-GPI attachment to proteins 2	protein-coding
mm_67491.1	chr7	80728899	80728913	-	1	NA	exon (NM_016721, exon 29 of 38)	exon (NM_016721, exon 29 of 38)	-40029	NM_173863	70461	Mm.392175	NM_173863	ENSMUSG00000030527	Crtc3	2610312F20Rik|6332415K15Rik|AI429792|BC011210|TORC3	CREB regulated transcription coactivator 3	protein-coding
mm_20851.1	chr2	148349383	148349393	-	1	NA	Intergenic	Intergenic	-45989	NM_009219	20608	Mm.35324	NM_009219	ENSMUSG00000037014	Sstr4	Smstr4|sst4	somatostatin receptor 4	protein-coding
mm_74323.1	chr8	126855247	126855272	+	1	NA	Intergenic	Intergenic	90662	NM_024214	67952	Mm.6932	NM_024214	ENSMUSG00000093904	Tomm20	1810060K07Rik|BB284719|Gm19268|MAS20|MOM19|TOM20|mKIAA0016	translocase of outer mitochondrial membrane 20 homolog (yeast)	protein-coding
mm_76006.1	chr8	72548225	72548287	-	1	NA	promoter-TSS (NM_027485)	promoter-TSS (NM_027485)	54	NM_027485	70625	Mm.235885	NM_027485	ENSMUSG00000045248	Med26	5730493L18Rik|AI414941|AW495270|Crsp7	mediator complex subunit 26	protein-coding
mm_139577.1	chr17	57078567	57078609	+	1	NA	promoter-TSS (NM_153551)	promoter-TSS (NM_153551)	-78	NM_153551	70785	Mm.284447	NM_153551	ENSMUSG00000002668	Dennd1c	4432409M07Rik	DENN/MADD domain containing 1C	protein-coding
mm_57589.1	chr6	127768969	127768993	-	1	NA	5' UTR (NM_201371, exon 1 of 10)	5' UTR (NM_201371, exon 1 of 10)	178	NM_201371	381813	Mm.39750	NM_201371	ENSMUSG00000030350	Prmt8	Hrmt1l3|Hrmt1l4	protein arginine N-methyltransferase 8	protein-coding
mm_166549.1	chr6	41032957	41032967	+	1	NA	exon (NM_023333, exon 3 of 5)	exon (NM_023333, exon 3 of 5)	2547	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_54001.1	chr6	7692868	7692903	-	1	NA	intron (NM_012055, intron 1 of 11)	intron (NM_012055, intron 1 of 11)	297	NM_012055	27053	Mm.2942	NM_012055	ENSMUSG00000029752	Asns	-	asparagine synthetase	protein-coding
mm_75706.1	chr8	68894667	68894693	-	1	NA	exon (NM_008509, exon 4 of 10)	exon (NM_008509, exon 4 of 10)	14125	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_4878.1	chr1	187943321	187943331	+	1	NA	intron (NM_001243792, intron 2 of 7)	intron (NM_001243792, intron 2 of 7)	-54501	NM_011935	26381	Mm.89989	NM_011935	ENSMUSG00000026610	Esrrg	ERR3|Errg|NR3B3|mKIAA0832	estrogen-related receptor gamma	protein-coding
mm_91749.1	chr10	49783491	49783582	-	1	NA	5' UTR (NM_010349, exon 2 of 18)	5' UTR (NM_010349, exon 2 of 18)	5218	NM_010349	14806	Mm.332838	NM_010349	ENSMUSG00000056073	Grik2	AW124492|GluK2|Glur-6|Glur6|Glurbeta2	glutamate receptor, ionotropic, kainate 2 (beta 2)	protein-coding
mm_118720.1	chr14	22212483	22212530	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	192794	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_760.1	chr1	43958820	43958825	+	1	NA	intron (NM_001310540, intron 8 of 28)	intron (NM_001310540, intron 8 of 28)	24828	NM_009418	22019	Mm.401675	NM_009418	ENSMUSG00000041763	Tpp2	TPP-2|TppII	tripeptidyl peptidase II	protein-coding
mm_117773.1	chr13	96649830	96649837	-	1	NA	3' UTR (NM_008255, exon 20 of 20)	3' UTR (NM_008255, exon 20 of 20)	21103	NM_008255	15357	Mm.316652	NM_008255	ENSMUSG00000021670	Hmgcr	HMG-CoAR|Red	3-hydroxy-3-methylglutaryl-Coenzyme A reductase	protein-coding
mm_99761.1	chr11	106787689	106787713	+	1	NA	intron (NM_007840, intron 1 of 12)	CpG	793	NM_007840	13207	Mm.491096	NM_007840	ENSMUSG00000020719	Ddx5	2600009A06Rik|G17P1|HUMP68|Hlr1|p68	DEAD (Asp-Glu-Ala-Asp) box polypeptide 5	protein-coding
mm_7466.1	chr1	120483188	120483212	-	1	NA	intron (NM_010766, intron 12 of 16)	B4|SINE|B4	21884	NM_010766	17167	Mm.1856	NM_010766	ENSMUSG00000026390	Marco	AI323439|Ly112|Scara2	macrophage receptor with collagenous structure	protein-coding
mm_101939.1	chr11	50207578	50207597	-	1	NA	exon (NM_011018, exon 3 of 8)	exon (NM_011018, exon 3 of 8)	3233	NM_001290769	18412	Mm.40828	NM_011018	ENSMUSG00000015837	Sqstm1	A170|OSF-6|Osi|STAP|STONE14|p62	sequestosome 1	protein-coding
mm_45421.1	chr5	66593438	66593458	-	1	NA	intron (NM_001310626, intron 1 of 15)	intron (NM_001310626, intron 1 of 15)	25369	NM_009686	11787	Mm.5159	NM_009686	ENSMUSG00000029207	Apbb2	2310007D03Rik|FE65L1|Rirl1|TR2L|Zfra	amyloid beta (A4) precursor protein-binding, family B, member 2	protein-coding
mm_28161.1	chr3	87783290	87783311	-	1	NA	exon (NM_001033124, exon 9 of 17)	exon (NM_001033124, exon 9 of 17)	11862	NM_001033124	18211	Mm.80682	NM_001033124	ENSMUSG00000028072	Ntrk1	C80751|Tkr|TrkA|trk	neurotrophic tyrosine kinase, receptor, type 1	protein-coding
mm_6328.1	chr1	71618626	71618638	-	1	NA	exon (NM_001276413, exon 23 of 44)	exon (NM_001276413, exon 23 of 44)	34602	NM_010233	14268	Mm.193099	NM_010233	ENSMUSG00000026193	Fn1	E330027I09|Fn|Fn-1	fibronectin 1	protein-coding
mm_172042.1	chr6	127411015	127411021	+	1	NA	Intergenic	Intergenic	-35822	NM_001346513	101187	Mm.110818	NM_181402	ENSMUSG00000037997	Parp11	5330431N24Rik|AI851877|ARTD11|HIN1L|PARP-11	poly (ADP-ribose) polymerase family, member 11	protein-coding
mm_41895.1	chr5	105519052	105519068	+	1	NA	promoter-TSS (NM_133897)	promoter-TSS (NM_133897)	-411	NM_133897	100604	Mm.319847	NM_133897	ENSMUSG00000054720	Lrrc8c	AD158|AI326115|E430036I04Rik|fad158	leucine rich repeat containing 8 family, member C	protein-coding
mm_152520.1	chr19	11304326	11304336	-	1	NA	Intergenic	Intergenic	-20518	NM_183190	269063	Mm.268940	NM_183190	ENSMUSG00000054523	Ms4a5	-	membrane-spanning 4-domains, subfamily A, member 5	protein-coding
mm_80169.1	chr9	71591366	71591370	+	1	NA	intron (NM_001033208, intron 1 of 12)	intron (NM_001033208, intron 1 of 12)	992	NM_001033208	102371	Mm.27585	NM_001033208	ENSMUSG00000041361	Myzap	AA407270|AV006038|Gcom1|Gm640|Grinl1a7|Myozap	myocardial zonula adherens protein	protein-coding
mm_138331.1	chr17	34894580	34894594	+	1	NA	promoter-TSS (NM_198886)	promoter-TSS (NM_198886)	28	NM_198886	193736	Mm.161119	NM_198886	ENSMUSG00000049823	Zbtb12	BC020447|Bat-9|Bat9|G10|NG35	zinc finger and BTB domain containing 12	protein-coding
mm_26240.1	chr3	141465487	141465491	+	1	NA	promoter-TSS (NM_009472)	promoter-TSS (NM_009472)	-75	NM_009472	22253	Mm.24430	NM_009472	ENSMUSG00000059921	Unc5c	B130051O18Rik|Unc5h3|rcm	unc-5 netrin receptor C	protein-coding
mm_170133.1	chr17	39847488	39847489	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	4491	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_83267.1	chr9	42770559	42770559	-	1	NA	intron (NM_175481, intron 3 of 20)	L1MB5|LINE|L1	173812	NM_175481	110637	Mm.370291	NM_175481	ENSMUSG00000032017	Grik4	6330551K01Rik|GluK4|GluRgamma1|KA-1|KA1	glutamate receptor, ionotropic, kainate 4	protein-coding
mm_141602.1	chr17	32769338	32769351	-	1	NA	3' UTR (NM_172458, exon 4 of 4)	3' UTR (NM_172458, exon 4 of 4)	18203	NM_001346705	208292	Mm.38813	NM_172458	ENSMUSG00000024298	Zfp871	4732483N19|9030612M13Rik|AI118577|AI265322|mKIAA3006	zinc finger protein 871	protein-coding
mm_106398.1	chr11	118868538	118868555	-	1	NA	intron (NM_001285437, intron 1 of 13)	intron (NM_001285437, intron 1 of 13)	41026	NM_001024931	52897	Mm.341103	NM_001024931	ENSMUSG00000025576	Rbfox3	Fox-3|Hrnbp3|NeuN|Neuna60	RNA binding protein, fox-1 homolog (C. elegans) 3	protein-coding
mm_109995.1	chr12	15815597	15815613	-	1	NA	5' UTR (NM_144551, exon 1 of 3)	5' UTR (NM_144551, exon 1 of 3)	1180	NM_144551	217410	Mm.491136	NM_144551	ENSMUSG00000020601	Trib2	AW319517|TRB-2|TRB2	tribbles pseudokinase 2	protein-coding
mm_155206.1	chrX	56734812	56734817	+	1	NA	intron (NM_001077361, intron 1 of 7)	intron (NM_001077361, intron 1 of 7)	2857	NM_001077361	14199	Mm.3126	NM_010211	ENSMUSG00000023092	Fhl1	FHL-1|KyoT|RAM14-1|SLIM|SLIM-1	four and a half LIM domains 1	protein-coding
mm_1539.1	chr1	72852070	72852076	+	1	NA	exon (NM_008342, exon 4 of 4)	exon (NM_008342, exon 4 of 4)	22792	NM_010518	16011	Mm.405761	NM_010518	ENSMUSG00000026185	Igfbp5	AI256729|AW208790|IGFBP-5|IGFBP-5P	insulin-like growth factor binding protein 5	protein-coding
mm_5116.1	chr1	6454280	6454305	-	1	NA	Intergenic	Intergenic	-32939	NM_001244693	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding
mm_141117.1	chr17	26090160	26090171	-	1	NA	promoter-TSS (NM_011933)	promoter-TSS (NM_011933)	-1	NM_011933	26378	Mm.292869	NM_011933	ENSMUSG00000036775	Decr2	-	2-4-dienoyl-Coenzyme A reductase 2, peroxisomal	protein-coding
mm_78228.1	chr9	21589204	21589221	+	1	NA	non-coding (NR_038062, exon 9 of 9)	non-coding (NR_038062, exon 9 of 9)	-3510	NM_178619	69773	Mm.39704	NM_178619	ENSMUSG00000048429	Timm29	1810026J23Rik	translocase of inner mitochondrial membrane 29	protein-coding
mm_20250.1	chr2	126499915	126499932	-	1	NA	Intergenic	Intergenic	-8370	NM_001080944	241633	Mm.222235	NM_001080944	ENSMUSG00000060131	Atp8b4	A530043E15|Im	ATPase, class I, type 8B, member 4	protein-coding
mm_94235.1	chr11	3291830	3291848	+	1	NA	exon (NM_001253691, exon 1 of 5)	exon (NM_001253691, exon 1 of 5)	1382	NM_019574	56218	Mm.275563	NM_019574	ENSMUSG00000020453	Patz1	8430401L15Rik|AI447519|Mazr|Patz|Zfp278	POZ (BTB) and AT hook containing zinc finger 1	protein-coding
mm_119515.1	chr14	47395058	47395088	+	1	NA	intron (NM_144553, intron 14 of 18)	intron (NM_144553, intron 14 of 18)	21213	NM_001145953	16854	Mm.248615	NM_010705	ENSMUSG00000050335	Lgals3	GBP|L-34|Mac-2|gal3	lectin, galactose binding, soluble 3	protein-coding
mm_71038.1	chr8	33657968	33657974	+	1	NA	intron (NM_010344, intron 1 of 12)	intron (NM_010344, intron 1 of 12)	4733	NM_010344	14782	Mm.283573	NM_010344	ENSMUSG00000031584	Gsr	AI325518|D8Ertd238e|Gr-1|Gr1	glutathione reductase	protein-coding
mm_140863.1	chr17	23755816	23755869	-	1	NA	exon (NM_153791, exon 7 of 7)	exon (NM_153791, exon 7 of 7)	6606	NR_015472	638247	Mm.382600	NR_015472	ENSMUSG00000097006	9530082P21Rik	E030034P13Rik	RIKEN cDNA 9530082P21 gene	ncRNA
mm_2963.1	chr1	132958051	132958055	+	1	NA	Intergenic	Intergenic	67363	NR_126506	17248	Mm.426531	NM_008575	ENSMUSG00000054387	Mdm4	4933417N07Rik|AA414968|AL023055|AU018793|AU021806|C85810|Mdmx	transformed mouse 3T3 cell double minute 4	protein-coding
mm_4713.1	chr1	180942501	180942529	+	1	NA	promoter-TSS (NM_144794)	promoter-TSS (NM_144794)	-3	NM_144794	208795	Mm.185518	NM_144794	ENSMUSG00000026519	Tmem63a	BC014795|Tmem64a	transmembrane protein 63a	protein-coding
mm_5932.1	chr1	55362786	55362786	-	1	NA	promoter-TSS (NM_001113367)	promoter-TSS (NM_001113367)	-79	NM_001113367	75388	Mm.483408	NM_029267	ENSMUSG00000025977	Boll	4930554P13Rik|4930597B14Rik	bol, boule-like (Drosophila)	protein-coding
mm_103007.1	chr11	69695949	69695959	-	1	NA	5' UTR (NM_001159503, exon 1 of 13)	5' UTR (NM_001159503, exon 1 of 13)	144	NM_011614	21944	Mm.8983	NM_011614	ENSMUSG00000097328	Tnfsf12	Apo3l|Dr3l|Dr3lg|Tweak	tumor necrosis factor (ligand) superfamily, member 12	protein-coding
mm_143286.1	chr17	65864679	65864697	-	1	NA	exon (NM_001198949, exon 3 of 10)	exon (NM_001198949, exon 3 of 10)	20235	NM_001198949	19765	Mm.17009	NM_009067	ENSMUSG00000024096	Ralbp1	RLIP76|Rip1	ralA binding protein 1	protein-coding
mm_17777.1	chr2	32847273	32847288	-	1	NA	promoter-TSS (NM_001113569)	promoter-TSS (NM_001113569)	-43	NM_001113569	20910	Mm.278865	NM_009295	ENSMUSG00000026797	Stxbp1	AI317162|AI326233|MMS10-G|Ms10g|Munc-18a|Munc18-1|N-sec1|Rb-sec1|Sxtbp1|Unc18-1|Unc18h|nsec1	syntaxin binding protein 1	protein-coding
mm_15977.1	chr2	166541718	166541719	+	1	NA	Intergenic	Intergenic	94267	NR_015558	319684	Mm.399746	NR_015558		5031425F14Rik	-	RIKEN cDNA 5031425F14 gene	ncRNA
mm_73350.1	chr8	105427635	105427646	+	1	NA	promoter-TSS (NM_001170789)	promoter-TSS (NM_001170789)	0	NM_001033371	270091	Mm.212709	NM_001033371	ENSMUSG00000054320	Lrrc36	BC036564	leucine rich repeat containing 36	protein-coding
mm_143801.1	chr17	83276611	83276634	-	1	NA	Intergenic	Intergenic	61339	NM_134117	106522	Mm.311974	NM_134117	ENSMUSG00000024247	Pkdcc	AI115348|AW548124|Adtk1|ESTM17|MAd1|Sgk493|Vlk|X83346	protein kinase domain containing, cytoplasmic	protein-coding
mm_141120.1	chr17	26095438	26095449	-	1	NA	promoter-TSS (NM_019731)	promoter-TSS (NM_019731)	27	NM_019731	56520	Mm.41787	NM_019731	ENSMUSG00000024177	Nme4	2610027N22Rik|2810024O08Rik|5730493H09Rik|NM23-M4|Nm23M4	NME/NM23 nucleoside diphosphate kinase 4	protein-coding
mm_162957.1	chr11	4260879	4260915	+	1	NA	intron (NM_008501, intron 1 of 3)	RLTR17B_Mm|LTR|ERVK	3329	NM_008501	16878	Mm.4964	NM_008501	ENSMUSG00000034394	Lif	-	leukemia inhibitory factor	protein-coding
mm_8950.1	chr1	164441608	164441618	-	1	NA	exon (NM_009721, exon 4 of 6)	exon (NM_009721, exon 4 of 6)	16742	NM_009721	11931	Mm.4550	NM_009721	ENSMUSG00000026576	Atp1b1	Atp4b|Atpb|Atpb-1|NKbeta1	ATPase, Na+/K+ transporting, beta 1 polypeptide	protein-coding
mm_73635.1	chr8	110728833	110728854	+	1	NA	exon (NM_198625, exon 7 of 14)	exon (NM_198625, exon 7 of 14)	3117	NM_001310591	244654	Mm.490385	NM_198625	ENSMUSG00000033763	Mtss1l	ABBA	metastasis suppressor 1-like	protein-coding
mm_38076.1	chr4	134127952	134127973	-	1	NA	exon (NM_080559, exon 2 of 3)	exon (NM_080559, exon 2 of 3)	791	NM_080559	73723	Mm.22240	NM_080559	ENSMUSG00000028843	Sh3bgrl3	1110004L05Rik|AU022188	SH3 domain binding glutamic acid-rich protein-like 3	protein-coding
mm_126568.1	chr15	82244777	82244791	+	1	NA	promoter-TSS (NM_001080158)	promoter-TSS (NM_001080158)	-37	NM_025639	66570	Mm.23596	NM_025639	ENSMUSG00000068101	Cenpm	2610019I03Rik|AI853711|Pane1	centromere protein M	protein-coding
mm_57807.1	chr6	129428550	129428555	-	1	NA	3' UTR (NM_175526, exon 6 of 6)	3' UTR (NM_175526, exon 6 of 6)	19690	NM_172732	232414	Mm.391518	NM_172732	ENSMUSG00000046080	Clec9a	9830005G06Rik|DNGR-1	C-type lectin domain family 9, member a	protein-coding
mm_44710.1	chr5	30907693	30907753	-	1	NA	promoter-TSS (NM_001134692)	promoter-TSS (NM_001134692)	65	NM_001134692	67695	Mm.21450	NM_024460	ENSMUSG00000038803	Ost4	2310016E02Rik	oligosaccharyltransferase complex subunit 4 (non-catalytic)	protein-coding
mm_143329.1	chr17	66449600	66449614	-	1	NA	5' UTR (NM_172963, exon 1 of 14)	5' UTR (NM_172963, exon 1 of 14)	143	NM_172963	68617	Mm.33421	NM_172963	ENSMUSG00000052105	Mtcl1	1110012J17Rik|Ccdc165|D130071O13|Kiaa0802|Soga2|mKIAA0802|t8219b25	microtubule crosslinking factor 1	protein-coding
mm_117050.1	chr13	58385191	58385242	-	1	NA	promoter-TSS (NM_027335)	promoter-TSS (NM_027335)	9	NM_027335	70153	Mm.296610	NM_027335	ENSMUSG00000021550	2210016F16Rik	-	RIKEN cDNA 2210016F16 gene	protein-coding
mm_62542.1	chr7	102310505	102310508	+	1	NA	intron (NM_009287, intron 1 of 11)	intron (NM_009287, intron 1 of 11)	42682	NM_009287	20866	Mm.645	NM_009287	ENSMUSG00000030987	Stim1	SIM	stromal interaction molecule 1	protein-coding
mm_35742.1	chr4	45397647	45397659	-	1	NA	3' UTR (NM_001009949, exon 3 of 3)	3' UTR (NM_001009949, exon 3 of 3)	11113	NM_001009949	230125	Mm.260210	NM_001009949	ENSMUSG00000045973	Slc25a51	9130208E07Rik|D130005A03Rik|Gm138|Mcart1	solute carrier family 25, member 51	protein-coding
mm_100458.1	chr11	119837266	119837307	+	1	NA	intron (NM_028898, intron 13 of 33)	B1_Mm|SINE|Alu	-2921	NR_045312	319454	Mm.442144	NR_045312	ENSMUSG00000085081	Rptoros	A430071A18Rik	regulatory associated protein of MTOR, complex 1, opposite strand	ncRNA
mm_83569.1	chr9	46328881	46328912	-	1	NA	Intergenic	Intergenic	-8910	NM_183104	74361	Mm.159169	NM_183104	ENSMUSG00000056617	4931429L15Rik	-	RIKEN cDNA 4931429L15 gene	protein-coding
mm_38496.1	chr4	141053661	141053697	-	1	NA	promoter-TSS (NM_172122)	promoter-TSS (NM_172122)	-18	NM_172122	230872	Mm.80685	NM_172122	ENSMUSG00000040860	Crocc	-	ciliary rootlet coiled-coil, rootletin	protein-coding
mm_29088.1	chr3	104523771	104523789	-	1	NA	Intergenic	Intergenic	-11862	NM_001025067	269473	Mm.34855	NM_001025067	ENSMUSG00000032913	Lrig2	4632419I10Rik|BB096938|LIG-2	leucine-rich repeats and immunoglobulin-like domains 2	protein-coding
mm_155341.1	chrX	68495426	68495441	+	1	NA	Intergenic	Intergenic	182966	NR_033481	100038638	Mm.368431	NR_033481	ENSMUSG00000096946	Fmr1os	Asfmr1|ENSMUSG00000073146|Gm10474	fragile X mental retardation syndrome 1, opposite strand	ncRNA
mm_62217.1	chr7	98334157	98334179	+	1	NA	Intergenic	Intergenic	-24641	NM_025408	66190	Mm.334041	NM_025408	ENSMUSG00000030760	Acer3	1110057L18Rik|5430429L08Rik|AV015045|Phca	alkaline ceramidase 3	protein-coding
mm_111120.1	chr12	80968076	80968086	-	1	NA	promoter-TSS (NM_001177561)	promoter-TSS (NM_001177561)	-2	NM_001177561	20493	Mm.486361	NM_011387	ENSMUSG00000021135	Slc10a1	Ntcp	solute carrier family 10 (sodium/bile acid cotransporter family), member 1	protein-coding
mm_71985.1	chr8	70616103	70616113	+	1	NA	promoter-TSS (NM_153074)	promoter-TSS (NM_153074)	-736	NM_153074	211228	Mm.132939	NM_153074	ENSMUSG00000049988	Lrrc25	Mapa	leucine rich repeat containing 25	protein-coding
mm_94888.1	chr11	27927041	27927043	+	1	NA	Intergenic	RMER17A|LTR|ERVK	657282	NM_001166661	216613	Mm.93759	NM_181577	ENSMUSG00000032878	Ccdc85a	-	coiled-coil domain containing 85A	protein-coding
mm_122170.1	chr14	31472573	31472575	-	1	NA	Intergenic	B1_Mus2|SINE|Alu	22403	NM_025907	67011	Mm.291731	NM_025907	ENSMUSG00000021891	Mettl6	1600013P15Rik|AI467521|AU020711	methyltransferase like 6	protein-coding
mm_128552.1	chr15	55856016	55856019	-	1	NA	intron (NM_016667, intron 1 of 6)	intron (NM_016667, intron 1 of 6)	50932	NM_016667	20649	Mm.309425	NM_016667	ENSMUSG00000060429	Sntb1	-	syntrophin, basic 1	protein-coding
mm_45695.1	chr5	82124648	82124655	-	1	NA	promoter-TSS (NR_138557)	promoter-TSS (NR_138557)	62	NR_138557	67327	Mm.87058	NR_138557		1700031L13Rik	-	RIKEN cDNA 1700031L13 gene	ncRNA
mm_140885.1	chr17	23844180	23844196	-	1	NA	promoter-TSS (NM_027644)	promoter-TSS (NM_027644)	-32	NM_027644	71003	Mm.328839	NM_027644	ENSMUSG00000024114	Prss41	4931440B09Rik|Tessp-1|Tessp1	protease, serine 41	protein-coding
mm_108800.1	chr12	91667003	91667017	+	1	NA	intron (NM_175367, intron 4 of 6)	intron (NM_175367, intron 4 of 6)	-76523	NM_175335	83602	Mm.275728	NM_031391	ENSMUSG00000020962	Gtf2a1	6330549H03Rik|AA536742|AA959775|AW060250|TfIIAa/b|Tfiia1	general transcription factor II A, 1	protein-coding
mm_156082.1	chrX	109199641	109199651	+	1	NA	3' UTR (NM_001037917, exon 2 of 2)	3' UTR (NM_001037917, exon 2 of 2)	2890	NM_001037917	622976	Mm.482747	NM_001037917	ENSMUSG00000048621	Gm6377	EG622976	predicted gene 6377	protein-coding
mm_54996.1	chr6	48833925	48833933	-	1	NA	non-coding (NR_104575, exon 7 of 7)	non-coding (NR_104575, exon 7 of 7)	7059	NM_023056	65963	Mm.28385	NM_023056	ENSMUSG00000029810	Tmem176b	1810009M01Rik|Clast1|Lr8	transmembrane protein 176B	protein-coding
mm_96347.1	chr11	66956566	66956575	+	1	NA	promoter-TSS (NR_130315)	promoter-TSS (NR_130315)	-68	NR_130645	71576	Mm.340077	NR_130315	ENSMUSG00000085683	9130409J20Rik	-	RIKEN cDNA 9130409J20 gene	ncRNA
mm_115803.1	chr13	19357940	19357955	-	1	NA	3' UTR (NM_024270, exon 9 of 9)	3' UTR (NM_024270, exon 9 of 9)	37866	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_56707.1	chr6	115251808	115251818	-	1	NA	promoter-TSS (NM_080639)	promoter-TSS (NM_080639)	36	NM_080639	110595	Mm.255607	NM_080639	ENSMUSG00000030317	Timp4	TIMP-4	tissue inhibitor of metalloproteinase 4	protein-coding
mm_80391.1	chr9	75626137	75626179	+	1	NA	intron (NM_027309, intron 1 of 2)	CpG	426	NM_027309	70082	Mm.19119	NM_027309	ENSMUSG00000032184	Lysmd2	2210402C18Rik|AV033872|AW538442	LysM, putative peptidoglycan-binding, domain containing 2	protein-coding
mm_129390.1	chr15	78204229	78204239	-	1	NA	promoter-TSS (NM_001330686)	promoter-TSS (NM_001330686)	3	NM_001330686	19293	Mm.2766	NM_013645	ENSMUSG00000005716	Pvalb	PV|Parv|Pva	parvalbumin	protein-coding
mm_107609.1	chr12	49384936	49384946	+	1	NA	exon (NM_008241, exon 2 of 2)	exon (NM_008241, exon 2 of 2)	1934	NM_008241	15228	Mm.4704	NM_008241	ENSMUSG00000020950	Foxg1	2900064B05Rik|BF-1|Bf1|Hfh9|Hfhbf1	forkhead box G1	protein-coding
mm_61632.1	chr7	80246507	80246520	+	1	NA	5' UTR (NM_177765, exon 1 of 15)	5' UTR (NM_177765, exon 1 of 15)	137	NM_177765	269954	Mm.276780	NM_177765	ENSMUSG00000045467	Ttll13	1700111A04Rik|4921538O11|BC024578	tubulin tyrosine ligase-like family, member 13	protein-coding
mm_30437.1	chr3	153631122	153631125	-	1	NA	intron (NM_011372, intron 1 of 4)	Charlie1|DNA|hAT-Charlie	94010	NM_011372	20447	Mm.296453	NM_011372	ENSMUSG00000052544	St6galnac3	Siat7c	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 3	protein-coding
mm_153240.1	chr19	36118139	36118152	-	1	NA	intron (NM_013468, intron 3 of 8)	intron (NM_013468, intron 3 of 8)	1699	NM_013468	107765	Mm.10279	NM_013468	ENSMUSG00000024803	Ankrd1	Alrp|CARP|Crap|MARP1	ankyrin repeat domain 1 (cardiac muscle)	protein-coding
mm_146512.1	chr18	3337540	3337600	-	1	NA	promoter-TSS (NM_001110852)	promoter-TSS (NM_001110852)	19	NM_001110851	12916	Mm.5244	NM_013498	ENSMUSG00000063889	Crem	ICER|ICERI	cAMP responsive element modulator	protein-coding
mm_60175.1	chr7	41599270	41599318	+	1	NA	Intergenic	CpG	-34237	NM_023363	67607	Mm.384626	NM_023363	ENSMUSG00000074165	Zfp788	2810426N06Rik|AI256342|AI605193	zinc finger protein 788	protein-coding
mm_146483.1	chr18	90510123	90510174	+	1	NA	promoter-TSS (NM_198295)	promoter-TSS (NM_198295)	-6	NM_198295	67988	Mm.268041	NM_198295	ENSMUSG00000024614	Tmx3	6430411B10Rik|A730024F05Rik|AV259382|Txndc10|mKIAA1830	thioredoxin-related transmembrane protein 3	protein-coding
mm_4072.1	chr1	166165417	166165428	+	1	NA	3' UTR (NM_021610, exon 7 of 7)	3' UTR (NM_021610, exon 7 of 7)	34962	NM_021610	59290	Mm.46357	NM_021610	ENSMUSG00000000544	Gpa33	2010310L10Rik|2210401D16Rik|BB116197	glycoprotein A33 (transmembrane)	protein-coding
mm_28530.1	chr3	92648304	92648308	-	1	NA	promoter-TSS (NM_025984)	promoter-TSS (NM_025984)	1	NM_025984	67127	Mm.41969	NM_025984	ENSMUSG00000057609	Lce1a1	2200008B06Rik|Sprrl3	late cornified envelope 1A1	protein-coding
mm_168590.1	chr1	173802444	173802448	-	1	NA	Intergenic	Intergenic	-35527	NM_008329	15951	Mm.261270	NM_008329	ENSMUSG00000073489	Ifi204	Ifi16|p204	interferon activated gene 204	protein-coding
mm_85389.1	chr9	103230263	103230280	-	1	NA	promoter-TSS (NM_133977)	promoter-TSS (NM_133977)	15	NM_133977	22041	Mm.37214	NM_133977	ENSMUSG00000032554	Trf	AI266983|Cd176|HP|Tf|Tfn|hpx	transferrin	protein-coding
mm_115096.1	chr13	102720785	102720788	+	1	NA	Intergenic	Lx2|LINE|L1	27228	NM_008533	17079	Mm.373974	NM_008533	ENSMUSG00000021624	Cd180	F630107B15|Ly78|RP105	CD180 antigen	protein-coding
mm_137028.1	chr17	17887808	17887818	+	1	NA	promoter-TSS (NM_008039)	promoter-TSS (NM_008039)	-11	NM_008039	14289	Mm.378918	NM_008039	ENSMUSG00000052270	Fpr2	E330010I07Rik|Fpr-rs2	formyl peptide receptor 2	protein-coding
mm_159639.1	chr4	141436076	141436076	-	1	NA	promoter-TSS (NM_001033374)	promoter-TSS (NM_001033374)	29	NM_001033374	277744	Mm.33952	NM_001033374	ENSMUSG00000070637	Gm694	-	predicted gene 694	protein-coding
mm_11705.1	chr2	36136621	36136672	+	1	NA	promoter-TSS (NM_026434)	promoter-TSS (NM_026434)	58	NM_026434	67889	Mm.205937	NM_026434	ENSMUSG00000026889	Rbm18	2010004P11Rik|AU015530	RNA binding motif protein 18	protein-coding
mm_48612.1	chr5	144479679	144479691	-	1	NA	Intergenic	B4A|SINE|B4	-66202	NM_016789	53324	Mm.10099	NM_016789	ENSMUSG00000059991	Nptx2	Narp|np2	neuronal pentraxin 2	protein-coding
mm_32031.1	chr4	95579418	95579428	+	1	NA	promoter-TSS (NM_029347)	promoter-TSS (NM_029347)	2	NM_029347	75578	Mm.276098	NM_029347	ENSMUSG00000028573	Fggy	2310009E04Rik	FGGY carbohydrate kinase domain containing	protein-coding
mm_26536.1	chr3	146121696	146121715	+	1	NA	promoter-TSS (NM_134160)	promoter-TSS (NM_134160)	-86	NM_134160	171166	Mm.114683	NM_134160	ENSMUSG00000036853	Mcoln3	6720490O21Rik|TRPML3|Va	mucolipin 3	protein-coding
mm_120924.1	chr14	76442710	76442714	+	1	NA	intron (NM_001310646, intron 3 of 4)	intron (NM_001310646, intron 3 of 4)	26891	NM_207652	21807	Mm.153272	NM_009366	ENSMUSG00000022010	Tsc22d1	AA589566|AW105905|Egr5|TSC-22|Tgfb1i4|Tsc|Tsc22	TSC22 domain family, member 1	protein-coding
mm_123201.1	chr14	59297511	59297529	-	1	NA	promoter-TSS (NM_172603)	promoter-TSS (NM_172603)	2	NM_172603	219131	Mm.254918	NM_172603	ENSMUSG00000044703	Phf11a	4933417L10Rik|Phf11|Phf11l	PHD finger protein 11A	protein-coding
mm_97063.1	chr11	72796165	72796246	+	1	NA	promoter-TSS (NM_001045536)	promoter-TSS (NM_001045536)	-21	NM_001045536	195018	Mm.272030	NM_001045536	ENSMUSG00000055670	Zzef1	8430405D05Rik|BC051585|C130099L13Rik|C85424|NSPA|mKIAA0399	zinc finger, ZZ-type with EF hand domain 1	protein-coding
mm_88705.1	chr10	80149659	80149685	+	1	NA	promoter-TSS (NM_001305799)	promoter-TSS (NM_001305799)	-10	NM_001305799	59090	Mm.143813	NM_021565	ENSMUSG00000035621	Midn	3000003C15Rik	midnolin	protein-coding
mm_158057.1	chrX	101059644	101059654	-	1	NA	promoter-TSS (NM_001167997)	promoter-TSS (NM_001167997)	-10	NM_001167997	83558	Mm.134024	NM_031384	ENSMUSG00000009670	Tex11	4930565P14Rik|BB024231|ZIP4H	testis expressed gene 11	protein-coding
mm_7846.1	chr1	132361100	132361147	-	1	NA	exon (NM_178874, exon 3 of 5)	exon (NM_178874, exon 3 of 5)	6825	NM_001311108	68875	Mm.273785	NM_178874	ENSMUSG00000042066	Tmcc2	1110063G11Rik	transmembrane and coiled-coil domains 2	protein-coding
mm_111013.1	chr12	78980759	78980817	-	1	NA	intron (NM_178745, intron 1 of 2)	intron (NM_178745, intron 1 of 2)	2690	NM_001170401	268567	Mm.341747	NM_178745	ENSMUSG00000046157	Tmem229b	6330442E10Rik|9830138K24|AU019070	transmembrane protein 229B	protein-coding
mm_139874.1	chr17	70747068	70747074	+	1	NA	intron (NM_001347411, intron 9 of 14)	intron (NM_001347411, intron 9 of 14)	99706	NM_001164077	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_106235.1	chr11	117654550	117654552	-	1	NA	5' UTR (NM_198022, exon 1 of 22)	5' UTR (NM_198022, exon 1 of 22)	262	NM_198022	217351	Mm.40272	NM_198022	ENSMUSG00000025571	Tnrc6c	9930033H14Rik|mKIAA1582	trinucleotide repeat containing 6C	protein-coding
mm_169023.1	chr13	113022018	113022023	-	1	NA	Intergenic	ERVB7_1-LTR_MM|LTR|ERVK	-13359	NM_001281487	238896		NM_001281487	ENSMUSG00000078926	Cdc20b	EG238896|EG622422	cell division cycle 20B	protein-coding
mm_98662.1	chr11	96271936	96271961	+	1	NA	exon (NM_008270, exon 1 of 2)	exon (NM_008270, exon 1 of 2)	618	NM_008270	15417	Mm.258271	NM_008270	ENSMUSG00000020875	Hoxb9	Hox-2.5	homeobox B9	protein-coding
mm_118861.1	chr14	25842202	25842222	+	1	NA	promoter-TSS (NM_013469)	promoter-TSS (NM_013469)	57	NM_013469	11744	Mm.294083	NM_013469	ENSMUSG00000021866	Anxa11	A830099O17Rik|Anx11	annexin A11	protein-coding
mm_26534.1	chr3	146120756	146120761	+	1	NA	Intergenic	Intergenic	-1033	NM_134160	171166	Mm.114683	NM_134160	ENSMUSG00000036853	Mcoln3	6720490O21Rik|TRPML3|Va	mucolipin 3	protein-coding
mm_76561.1	chr8	88454402	88454409	-	1	NA	Intergenic	CpG	-66939	NM_027280	93960	Mm.30219	NM_027280	ENSMUSG00000031661	Nkd1	2810434J10Rik|9030215G15Rik|Nkd	naked cuticle 1 homolog (Drosophila)	protein-coding
mm_172922.1	chr9	68152140	68152142	-	1	NA	Intergenic	Intergenic	-126427	NR_045745	434412	Mm.490707	NR_045745	ENSMUSG00000111841	Gm20745	-	predicted gene, 20745	ncRNA
mm_21313.1	chr2	157098737	157098747	-	1	NA	3' UTR (NM_001139520, exon 17 of 17)	3' UTR (NM_001139520, exon 17 of 17)	11687	NM_001177439	383766	Mm.480305	NM_001177439	ENSMUSG00000074628	Tldc2	Gm1332	TBC/LysM associated domain containing 2	protein-coding
mm_13541.1	chr2	110721633	110721646	+	1	NA	5' UTR (NM_001290786, exon 1 of 4)	5' UTR (NM_001290786, exon 1 of 4)	145	NM_172979	269328	Mm.32566	NM_172979	ENSMUSG00000050808	Muc15	4732460E09|D730046L02Rik|MUC-15	mucin 15	protein-coding
mm_49465.1	chr6	29433175	29433181	+	1	NA	promoter-TSS (NM_001081185)	promoter-TSS (NM_001081185)	25	NM_001081185	68794	Mm.39046	NM_026839	ENSMUSG00000068699	Flnc	1110055E19Rik|ABP-280|ABPL|Fln2	filamin C, gamma	protein-coding
mm_160856.1	chr11	58552336	58552336	-	1	NA	promoter-TSS (NM_146502)	promoter-TSS (NM_146502)	-99	NM_146502	258495	Mm.339498	NM_146502	ENSMUSG00000057654	Olfr328	MOR275-2	olfactory receptor 328	protein-coding
mm_116631.1	chr13	48968116	48968124	-	1	NA	promoter-TSS (NR_015601)	promoter-TSS (NR_015601)	8	NR_015601	68128	Mm.426304	NR_015601		Fam120aos	C030044B11Rik	family with sequence similarity 120A, opposite strand	ncRNA
mm_139215.1	chr17	47728848	47728873	+	1	NA	exon (NM_025973, exon 2 of 9)	exon (NM_025973, exon 2 of 9)	2018	NM_025973	109820	Mm.22957	NM_025973	ENSMUSG00000023987	Pgc	2210410L06Rik|Upg-1|Upg1	progastricsin (pepsinogen C)	protein-coding
mm_173279.1	chrY	1480656	1480665	+	1	NA	Intergenic	L1Md_T|LINE|L1	-20878	NM_148943	107868	Mm.347376	NM_148943	ENSMUSG00000069044	Usp9y	Dffry|Fafl2	ubiquitin specific peptidase 9, Y chromosome	protein-coding
mm_65397.1	chr7	25132474	25132493	-	1	NA	promoter-TSS (NM_001163556)	promoter-TSS (NM_001163556)	-23	NM_001163554	18987	Mm.76683	NM_011138	ENSMUSG00000008496	Pou2f2	Oct-2|Oct2a|Oct2b|Oct2c|Oct2d|Otf-2|Otf2	POU domain, class 2, transcription factor 2	protein-coding
mm_115049.1	chr13	100124851	100124886	+	1	NA	promoter-TSS (NM_011420)	promoter-TSS (NM_011420)	13	NM_011420	20595	Mm.2025	NM_011420	ENSMUSG00000021645	Smn1	AI849087|Gemin1|Smn	survival motor neuron 1	protein-coding
mm_168025.1	chrY	90738282	90738290	+	1	NA	Intergenic	IMPB_01|Satellite|Satellite	16764	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_36852.1	chr4	106800292	106800303	-	1	NA	promoter-TSS (NM_025590)	promoter-TSS (NM_025590)	-466	NM_025590	329910	Mm.222956	NM_025590	ENSMUSG00000034853	Acot11	1110020M10Rik|2010309H15Rik|AW060409|BFIT|BFIT1|Thea|Them1|mKIAA0707	acyl-CoA thioesterase 11	protein-coding
mm_162769.1	chr10	67185774	67185776	+	1	NA	promoter-TSS (NM_001242396)	promoter-TSS (NM_001242396)	25	NM_001242396	108829	Mm.23846	NM_207221	ENSMUSG00000037876	Jmjd1c	5430433L24Rik|D630035I23Rik|Jmjdic|TRIP8	jumonji domain containing 1C	protein-coding
mm_59392.1	chr7	26764450	26764474	+	1	NA	intron (NM_007814, intron 6 of 8)	intron (NM_007814, intron 6 of 8)	7320	NM_007814	13090	Mm.14098	NM_007814	ENSMUSG00000066704	Cyp2b19	CYPIIB19	cytochrome P450, family 2, subfamily b, polypeptide 19	protein-coding
mm_6722.1	chr1	82586748	82586758	-	1	NA	promoter-TSS (NM_007735)	promoter-TSS (NM_007735)	96	NM_007735	12829	Mm.40253	NM_007735	ENSMUSG00000067158	Col4a4	E130010M05Rik|[a]4(IV)	collagen, type IV, alpha 4	protein-coding
mm_26956.1	chr3	21489576	21489605	-	1	NA	Intergenic	Intergenic	-587062	NM_030732	81004	Mm.202966	NM_030732	ENSMUSG00000027630	Tbl1xr1	8030499H02Rik|A630076E03Rik|AW539987|C21|C230089I12Rik|DC42|Ira1|TBLR1	transducin (beta)-like 1X-linked receptor 1	protein-coding
mm_39070.1	chr4	154139872	154139879	-	1	NA	5' UTR (NM_011642, exon 1 of 14)	5' UTR (NM_011642, exon 1 of 14)	333	NM_011642	22062	Mm.78015	NM_011642	ENSMUSG00000029026	Trp73	TAp73|Tp73|deltaNp73|p73	transformation related protein 73	protein-coding
mm_2443.1	chr1	98457716	98457748	+	1	NA	intron (NM_001164233, intron 6 of 12)	intron (NM_001164233, intron 6 of 12)	36608	NM_027584	70866	Mm.389164	NM_027584	ENSMUSG00000026336	Slco6d1	4921511I05Rik	solute carrier organic anion transporter family, member 6d1	protein-coding
mm_97828.1	chr11	83063937	83063978	+	1	NA	Intergenic	Intergenic	-1155	NM_011408	20556	Mm.278689	NM_011408	ENSMUSG00000072620	Slfn2	Shlf2	schlafen 2	protein-coding
mm_159105.1	chr2	38339239	38339239	+	1	NA	promoter-TSS (NM_001290646)	promoter-TSS (NM_001290646)	-42	NM_001290646	16870	Mm.142856	NM_010710	ENSMUSG00000000247	Lhx2	LH2A|Lh-2|Lim2|ap|apterous	LIM homeobox protein 2	protein-coding
mm_9096.1	chr1	169087600	169087601	-	1	NA	Intergenic	Intergenic	443864	NM_023284	66977	Mm.151315	NM_023284	ENSMUSG00000026683	Nuf2	2410003C07Rik|AU044112|C85691|Cdca1|NUF2R	NUF2, NDC80 kinetochore complex component	protein-coding
mm_165564.1	chr3	14886716	14886721	+	1	NA	5' UTR (NM_009801, exon 1 of 7)	5' UTR (NM_009801, exon 1 of 7)	292	NM_009801	12349	Mm.1186	NM_009801	ENSMUSG00000027562	Car2	AI131712|CAII|Ca2|Car-2|Ltw-5|Lvtw-5	carbonic anhydrase 2	protein-coding
mm_145724.1	chr18	63981719	63981722	+	1	NA	intron (NM_001014981, intron 27 of 27)	intron (NM_001014981, intron 27 of 27)	-272639	NM_009182	20451	Mm.252110	NM_009182	ENSMUSG00000056812	St8sia3	AI847333|ST8SiaIII|Siat8c	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3	protein-coding
mm_99069.1	chr11	99168364	99168376	+	1	NA	Intergenic	Intergenic	-13293	NM_007719	12775	Mm.2932	NM_007719	ENSMUSG00000037944	Ccr7	CC-CKR-7|CCR-7|CD197|Cdw197|Cmkbr7|EBI1|Ebi1h	chemokine (C-C motif) receptor 7	protein-coding
mm_38000.1	chr4	133673217	133673242	-	1	NA	promoter-TSS (NM_178698)	promoter-TSS (NM_178698)	-582	NM_001145956	230801	Mm.217004	NM_178698	ENSMUSG00000043257	Pigv	B330013B03|D430024F16Rik	phosphatidylinositol glycan anchor biosynthesis, class V	protein-coding
mm_67760.1	chr7	92741404	92741410	-	1	NA	promoter-TSS (NM_029494)	promoter-TSS (NM_029494)	52	NR_015510	666737	Mm.473620	NR_015510	ENSMUSG00000074024	4632427E13Rik	AU015482	RIKEN cDNA 4632427E13 gene	ncRNA
mm_48806.1	chr5	148967972	148967976	-	1	NA	Intergenic	RMER17C2|LTR|ERVK	17724	NR_040686	71473	Mm.90306	NR_040686	ENSMUSG00000079069	8430423G03Rik	-	RIKEN cDNA 8430423G03 gene	ncRNA
mm_42580.1	chr5	117274652	117274657	+	1	NA	3' UTR (NM_001199685, exon 21 of 21)	3' UTR (NM_001199685, exon 21 of 21)	12910	NM_018858	23980	Mm.195898	NM_018858	ENSMUSG00000032959	Pebp1	HCNP|Pbp|Pbp1|Pbpr|Rkip	phosphatidylethanolamine binding protein 1	protein-coding
mm_42152.1	chr5	111454915	111454918	+	1	NA	3' UTR (NM_001081235, exon 2 of 2)	3' UTR (NM_001081235, exon 2 of 2)	36750	NM_001081235	433938	Mm.332576	NM_001081235	ENSMUSG00000070576	Mn1	AA003644|AA009236	meningioma 1	protein-coding
mm_110285.1	chr12	32123618	32123622	-	1	NA	Intergenic	Intergenic	-62341	NM_011158	19088	Mm.25594	NM_011158	ENSMUSG00000002997	Prkar2b	AI451071|AW061005|PKARIIbeta|Pkarb2|RII(beta)	protein kinase, cAMP dependent regulatory, type II beta	protein-coding
mm_109664.1	chr12	113022530	113022540	+	1	NA	intron (NM_001291444, intron 1 of 23)	ID_B1|SINE|B4	8027	NM_001291444	217893	Mm.35754	NM_198165	ENSMUSG00000021143	Pacs2	6720425G15Rik|AW208651|AW489976|E230011J22|Pacs1l|mKIAA0602	phosphofurin acidic cluster sorting protein 2	protein-coding
mm_144245.1	chr18	10747876	10747879	+	1	NA	intron (NM_144860, intron 4 of 20)	B2_Mm1a|SINE|B2	22252	NM_144860	225164	Mm.21500	NM_144860	ENSMUSG00000024294	Mib1	DIP-1|E430019M12Rik|Mib|mKIAA1323	mindbomb E3 ubiquitin protein ligase 1	protein-coding
mm_44796.1	chr5	32746318	32746341	-	1	NA	promoter-TSS (NM_001347332)	promoter-TSS (NM_001347332)	13	NM_001347332	320951	Mm.273765	NM_177298	ENSMUSG00000023452	Pisd	9030221M09Rik	phosphatidylserine decarboxylase	protein-coding
mm_115615.1	chr13	12053921	12053932	-	1	NA	intron (NM_023868, intron 1 of 104)	MTEa|LTR|ERVL-MaLR	53019	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding
mm_47684.1	chr5	129002709	129002737	-	1	NA	intron (NM_001286033, intron 1 of 9)	intron (NM_001286033, intron 1 of 9)	5849	NM_001286034	13852	Mm.260716	NM_007941	ENSMUSG00000029428	Stx2	AW538950|Epim|G1-536-1|Syn-2|repro34	syntaxin 2	protein-coding
mm_27080.1	chr3	30013005	30013020	-	1	NA	5' UTR (NM_007963, exon 1 of 15)	5' UTR (NM_007963, exon 1 of 15)	192	NM_007963	14013	Mm.56965	NM_007963	ENSMUSG00000027684	Mecom	D630039M04Rik|Evi-1|Evi1|Jbo|Mds|Mds1|Mds1-Evi1|Prdm3|Znfpr1b1	MDS1 and EVI1 complex locus	protein-coding
mm_146762.1	chr18	16809097	16809118	-	1	NA	5' UTR (NM_007664, exon 1 of 16)	5' UTR (NM_007664, exon 1 of 16)	139	NM_007664	12558	Mm.257437	NM_007664	ENSMUSG00000024304	Cdh2	CDHN|N-CAD|Ncad	cadherin 2	protein-coding
mm_111315.1	chr12	85824561	85824569	-	1	NA	promoter-TSS (NM_001081423)	promoter-TSS (NM_001081423)	-20	NM_021446	58520	Mm.143795	NM_021446	ENSMUSG00000021252	0610007P14Rik	1190004E09Rik|AU019315|C77855|ORF11	RIKEN cDNA 0610007P14 gene	protein-coding
mm_87190.1	chr10	39420049	39420074	+	1	NA	intron (NM_001122892, intron 2 of 12)	intron (NM_001122892, intron 2 of 12)	50262	NM_001122893	14360	Mm.4848	NM_008054	ENSMUSG00000019843	Fyn	AI448320|AW552119	Fyn proto-oncogene	protein-coding
mm_1375.1	chr1	66696695	66696715	+	1	NA	3' UTR (NM_175510, exon 65 of 65)	3' UTR (NM_175510, exon 65 of 65)	-4126	NM_025683	66646	Mm.240912	NM_025683	ENSMUSG00000026005	Rpe	2810429B02Rik|5730518J08Rik	ribulose-5-phosphate-3-epimerase	protein-coding
mm_109117.1	chr12	105590080	105590083	+	1	NA	intron (NM_009747, intron 2 of 2)	intron (NM_009747, intron 2 of 2)	-14010	NM_007539	12061	Mm.377078	NM_007539	ENSMUSG00000041347	Bdkrb1	B1BKR|B1R|BKR1|BRADYB1|Bdkrb	bradykinin receptor, beta 1	protein-coding
mm_144327.1	chr18	12972226	12972314	+	1	NA	promoter-TSS (NM_008378)	promoter-TSS (NM_008378)	18	NM_008378	16210	Mm.8154	NM_008378	ENSMUSG00000024423	Impact	E430016J11Rik	impact, RWD domain protein	protein-coding
mm_90853.1	chr10	8814399	8814419	-	1	NA	exon (NM_175155, exon 3 of 20)	exon (NM_175155, exon 3 of 20)	71661	NM_175155	70097	Mm.338275	NM_175155	ENSMUSG00000015305	Sash1	1100001C18Rik|2500002E12Rik|A330076K04Rik|mKIAA0790	SAM and SH3 domain containing 1	protein-coding
mm_150547.1	chr19	39315689	39315697	+	1	NA	intron (NM_007815, intron 5 of 8)	L1MEg|LINE|L1	28608	NM_007815	13095	Mm.20764	NM_007815	ENSMUSG00000003053	Cyp2c29	AHOH|AHOHase|AI159681|AI196010|Ah-2|Ahh-1|Cyp2c|P450-2C	cytochrome P450, family 2, subfamily c, polypeptide 29	protein-coding
mm_134082.1	chr16	8737734	8737741	-	1	NA	intron (NM_001003918, intron 1 of 30)	CpG	605	NM_001003918	252870	Mm.295330	NM_001003918	ENSMUSG00000022710	Usp7	2210010O09Rik|AA409944|AA617399|AU019296|AW548146|C80752|Hausp	ubiquitin specific peptidase 7	protein-coding
mm_22978.1	chr3	32817583	32817605	+	1	NA	promoter-TSS (NM_001013024)	promoter-TSS (NM_001013024)	-32	NM_001013024	72607	Mm.316153	NM_001013024	ENSMUSG00000056900	Usp13	2700071E21Rik|AI848077|ISOT3|IsoT-3	ubiquitin specific peptidase 13 (isopeptidase T-3)	protein-coding
mm_97780.1	chr11	82387442	82387502	+	1	NA	Intergenic	CpG	-1428	NM_001304439	270893	Mm.341593	NM_023438	ENSMUSG00000020701	Tmem132e	Gm644	transmembrane protein 132E	protein-coding
mm_127146.1	chr15	98532596	98532612	+	1	NA	intron (NM_133714, intron 2 of 9)	PB1D10|SINE|Alu	1665	NM_001289438	69612	Mm.229107	NM_133714	ENSMUSG00000022992	Kansl2	2310037I24Rik|B930009D17	KAT8 regulatory NSL complex subunit 2	protein-coding
mm_151154.1	chr19	53184433	53184435	+	1	NA	intron (NM_013758, intron 1 of 15)	intron (NM_013758, intron 1 of 15)	40437	NM_013758	27360	Mm.426080	NM_013758	ENSMUSG00000025026	Add3	AI463285|R75380	adducin 3 (gamma)	protein-coding
mm_86079.1	chr9	114781791	114781799	-	1	NA	exon (NM_133978, exon 1 of 5)	exon (NM_133978, exon 1 of 5)	198	NM_133978	102545	Mm.35600	NM_133978	ENSMUSG00000032436	Cmtm7	AI481279|Cklfsf7|LNV	CKLF-like MARVEL transmembrane domain containing 7	protein-coding
mm_43439.1	chr5	136093295	136093301	+	1	NA	intron (NM_001039103, intron 5 of 19)	intron (NM_001039103, intron 5 of 19)	9382	NM_001039103	54153	Mm.290655	NM_133914	ENSMUSG00000004952	Rasa4	AA793972|AW112107|BB079060|CAPRI|GAPL	RAS p21 protein activator 4	protein-coding
mm_161545.1	chr16	4213328	4213328	-	1	NA	promoter-TSS (NM_001025432)	promoter-TSS (NM_001025432)	76	NM_001025432	12914	Mm.132238	NM_001025432	ENSMUSG00000022521	Crebbp	AW558298|CBP|CBP/p300|KAT3A|p300/CBP	CREB binding protein	protein-coding
mm_67839.1	chr7	98491801	98491815	-	1	NA	Intergenic	Intergenic	-2414	NM_001113379	434215	Mm.323057	NM_001113379	ENSMUSG00000090958	Lrrc32	AI426318|D11S833Eh|D7H11S833E|EG434215|Garp	leucine rich repeat containing 32	protein-coding
mm_171347.1	chr4	10848390	10848409	+	1	NA	Intergenic	Intergenic	-26099	NM_026005	67157	Mm.440552	NM_026005	ENSMUSG00000059482	2610301B20Rik	AI428449	RIKEN cDNA 2610301B20 gene	protein-coding
mm_34141.1	chr4	139310733	139310793	+	1	NA	promoter-TSS (NM_025337)	promoter-TSS (NM_025337)	19	NM_025337	110198	Mm.482154	NM_025337	ENSMUSG00000028743	Akr7a5	0610025K21Rik|Afar|Afar1|Akr7a2	aldo-keto reductase family 7, member A5 (aflatoxin aldehyde reductase)	protein-coding
mm_126646.1	chr15	83792143	83792153	+	1	NA	exon (NM_172610, exon 2 of 7)	exon (NM_172610, exon 2 of 7)	12125	NM_172610	223726	Mm.36395	NM_172610	ENSMUSG00000041708	Mpped1	6230403M19|AW456965|D15Bwg0669e	metallophosphoesterase domain containing 1	protein-coding
mm_71310.1	chr8	43180471	43180479	+	1	NA	Intergenic	Intergenic	-2647	NM_001160412	622117	Mm.390031	NM_001160412	ENSMUSG00000091490	Triml2	EG622117|Tu4	tripartite motif family-like 2	protein-coding
mm_23375.1	chr3	55533779	55533795	+	1	NA	3' UTR (NM_001111052, exon 14 of 14)	3' UTR (NM_001111052, exon 14 of 14)	72029	NM_001195540	13175	Mm.393242	NM_019978	ENSMUSG00000027797	Dclk1	1700113D08Rik|2810480F11Rik|AI836758|Click-I|Cpg16|Dcamkl1|Dcl|Dclk|mKIAA0369	doublecortin-like kinase 1	protein-coding
mm_97848.1	chr11	83068399	83068420	+	1	NA	intron (NM_011408, intron 1 of 1)	B3|SINE|B2	3297	NM_011408	20556	Mm.278689	NM_011408	ENSMUSG00000072620	Slfn2	Shlf2	schlafen 2	protein-coding
mm_117214.1	chr13	64089375	64089394	-	1	NA	promoter-TSS (NM_008291)	promoter-TSS (NM_008291)	-183	NM_008291	15487	Mm.5109	NM_008291	ENSMUSG00000033122	Hsd17b3	-	hydroxysteroid (17-beta) dehydrogenase 3	protein-coding
mm_16813.1	chr2	11332552	11332567	-	1	NA	Intergenic	Intergenic	-6930	NR_040369	100503147	Mm.91961	NR_040369	ENSMUSG00000086006	Gm13293	OTTMUSG00000011311	predicted gene 13293	ncRNA
mm_103076.1	chr11	69895466	69895474	-	1	NA	promoter-TSS (NM_153788)	promoter-TSS (NM_153788)	69	NM_153788	216859	Mm.288671	NM_153788	ENSMUSG00000001588	Acap1	Centb1	ArfGAP with coiled-coil, ankyrin repeat and PH domains 1	protein-coding
mm_1319.1	chr1	65100509	65100516	+	1	NA	exon (NM_007774, exon 3 of 3)	exon (NM_007774, exon 3 of 3)	2851	NM_007774	12964	Mm.26904	NM_007774	ENSMUSG00000044429	Cryga	Cryg-4|DGcry-4	crystallin, gamma A	protein-coding
mm_60890.1	chr7	46397104	46397112	+	1	NA	5' UTR (NM_001112739, exon 1 of 4)	5' UTR (NM_001112739, exon 1 of 4)	640	NM_001112739	16502	Mm.249386	NM_008421	ENSMUSG00000058975	Kcnc1	C230009H10Rik|KShIIIB|KV4|Kcr2-1|Kv3.1|NGK2|Shaw	potassium voltage gated channel, Shaw-related subfamily, member 1	protein-coding
mm_11911.1	chr2	52038093	52038111	+	1	NA	promoter-TSS (NM_009398)	promoter-TSS (NM_009398)	-11	NM_009398	21930	Mm.3509	NM_009398	ENSMUSG00000053475	Tnfaip6	TSG-6|Tnfip6|Tsg6	tumor necrosis factor alpha induced protein 6	protein-coding
mm_162396.1	chr1	82452613	82452616	-	1	NA	3' UTR (NM_007735, exon 48 of 48)	3' UTR (NM_007735, exon 48 of 48)	113565	NM_001122685	76867	Mm.226994	NM_029777	ENSMUSG00000026142	Rhbdd1	4930418P06Rik|RRP4|mRHBDD1	rhomboid domain containing 1	protein-coding
mm_130090.1	chr15	89379589	89379618	-	1	NA	promoter-TSS (NM_001013022)	promoter-TSS (NM_001013022)	-349	NM_001013022	70113	Mm.247273	NM_001013022	ENSMUSG00000047394	Odf3b	2010001J22Rik	outer dense fiber of sperm tails 3B	protein-coding
mm_3138.1	chr1	135133259	135133269	+	1	NA	promoter-TSS (NM_007955)	promoter-TSS (NM_007955)	539	NM_177081	320139	Mm.258388	NM_177081	ENSMUSG00000031506	Ptpn7	BPTP-4|C920001D21Rik|HEPTP|LC-PTP|LPTP	protein tyrosine phosphatase, non-receptor type 7	protein-coding
mm_115993.1	chr13	24384020	24384061	-	1	NA	intron (NM_001284519, intron 2 of 17)	L1M2|LINE|L1	-31082	NM_007717	12763	Mm.8396	NM_007717	ENSMUSG00000016756	Cmah	-	cytidine monophospho-N-acetylneuraminic acid hydroxylase	protein-coding
mm_42034.1	chr5	108388413	108388434	+	1	NA	promoter-TSS (NM_008806)	promoter-TSS (NM_008806)	50	NM_008806	18587	Mm.1372	NM_008806	ENSMUSG00000029491	Pde6b	Pdeb|r|rd|rd-1|rd1|rd10	phosphodiesterase 6B, cGMP, rod receptor, beta polypeptide	protein-coding
mm_21115.1	chr2	153492512	153492541	-	1	NA	intron (NM_001134300, intron 1 of 10)	CpG	37445	NM_001134300	329540	Mm.50600	NM_001001986	ENSMUSG00000061411	Nol4l	4931410H15|8430427H17Rik|AI429157|Gm1636	nucleolar protein 4-like	protein-coding
mm_18509.1	chr2	62617281	62617291	-	1	NA	exon (NM_027835, exon 5 of 16)	exon (NM_027835, exon 5 of 16)	28969	NM_027835	71586	Mm.136224	NM_027835	ENSMUSG00000026896	Ifih1	9130009C22Rik|Helicard|Hlcd|MDA5|RLR-2	interferon induced with helicase C domain 1	protein-coding
mm_158484.1	chrX	142306171	142306187	-	1	NA	promoter-TSS (NM_021487)	promoter-TSS (NM_021487)	19	NM_021487	66240	Mm.58507	NM_021487	ENSMUSG00000090122	Kcne1l	1500015C14Rik|Kcne5|Mink	potassium voltage-gated channel, Isk-related family, member 1-like, pseudogene	protein-coding
mm_56949.1	chr6	119971014	119971036	-	1	NA	exon (NM_001185020, exon 6 of 26)	exon (NM_001185020, exon 6 of 26)	63286	NR_030487	735290		NR_030487	ENSMUSG00000076217	Mir706	Mirn706|mir-706|mmu-mir-706	microRNA 706	ncRNA
mm_34751.1	chr4	152297490	152297500	+	1	NA	exon (NM_133788, exon 1 of 5)	exon (NM_133788, exon 1 of 5)	281	NM_133788	57295	Mm.277464	NM_133788	ENSMUSG00000039662	Icmt	1700008E11Rik|C80758|Gm13095|HSTE14|OTTMUSG00000010406|PPMT|STE14|pcCMT	isoprenylcysteine carboxyl methyltransferase	protein-coding
mm_26608.1	chr3	152231968	152231984	+	1	NA	exon (NM_057172, exon 19 of 20)	exon (NM_057172, exon 19 of 20)	21518	NM_057172	51886	Mm.278922	NM_057172	ENSMUSG00000028034	Fubp1	9530027K12Rik|D3Ertd330e|FBP|Fubp|Fubp4	far upstream element (FUSE) binding protein 1	protein-coding
mm_82539.1	chr9	20815015	20815029	-	1	NA	promoter-TSS (NM_001317388)	promoter-TSS (NM_001317388)	45	NM_001317388	53867	Mm.334994	NM_016919	ENSMUSG00000004098	Col5a3	-	collagen, type V, alpha 3	protein-coding
mm_17394.1	chr2	27112205	27112215	-	1	NA	3' UTR (NM_175427, exon 3 of 3)	3' UTR (NM_175427, exon 3 of 3)	30267	NM_175427	109349	Mm.314080	NM_175427	ENSMUSG00000009216	Fam163b	C630035N08Rik	family with sequence similarity 163, member B	protein-coding
mm_89164.1	chr10	86186803	86186842	+	1	NA	intron (NM_013722, intron 6 of 13)	MER45B|DNA|hAT-Tip100	90968	NR_038024	78170	Mm.444790	NR_038024		4930486F22Rik	-	RIKEN cDNA 4930486F22 gene	ncRNA
mm_3966.1	chr1	164151816	164151862	+	1	NA	promoter-TSS (NM_007976)	promoter-TSS (NM_007976)	4	NM_007976	14067	Mm.12900	NM_007976	ENSMUSG00000026579	F5	AI173222|Cf-5|Cf5	coagulation factor V	protein-coding
mm_120947.1	chr14	76694228	76694241	+	1	NA	Intergenic	Intergenic	16666	NR_015485	73272	Mm.116804	NR_015485	ENSMUSG00000101009	1700108F19Rik	1700020I02Rik|BB065030	RIKEN cDNA 1700108F19 gene	ncRNA
mm_26138.1	chr3	137918537	137918547	+	1	NA	promoter-TSS (NM_019920)	promoter-TSS (NM_019920)	-13	NM_019920	56692	Mm.331392	NM_019920	ENSMUSG00000091512	Lamtor3	AW556229|Map2k1ip1|Mapbp|Mapksp1|Mp1	late endosomal/lysosomal adaptor, MAPK and MTOR activator 3	protein-coding
mm_171234.1	chr3	68902836	68902836	-	1	NA	intron (NM_026641, intron 18 of 19)	intron (NM_026641, intron 18 of 19)	33250	NM_001167996	68725	Mm.45741	NM_001167996	ENSMUSG00000046999	1110032F04Rik	AI115547	RIKEN cDNA 1110032F04 gene	protein-coding
mm_172593.1	chr8	128753602	128753617	-	1	NA	Intergenic	B3|SINE|B2	67955	NM_010578	16412	Mm.263396	NM_010578	ENSMUSG00000025809	Itgb1	4633401G24Rik|AA409975|AA960159|CD29|ENSMUSG00000051907|Fnrb|Gm9863|gpIIa	integrin beta 1 (fibronectin receptor beta)	protein-coding
mm_56488.1	chr6	99173593	99173597	-	1	NA	intron (NM_001347345, intron 4 of 19)	intron (NM_001347345, intron 4 of 19)	92920	NM_001197321	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_58113.1	chr6	138423095	138423144	-	1	NA	promoter-TSS (NR_126073)	promoter-TSS (NR_126073)	14	NR_126072	319702	Mm.403785	NR_126072	ENSMUSG00000089957	A830011K09Rik	-	RIKEN cDNA A830011K09 gene	ncRNA
mm_171442.1	chr4	142069534	142069550	-	1	NA	intron (NM_145402, intron 1 of 2)	MLTR73|LTR|ERV1	-14756	NR_027137	100038693	Mm.402714	NR_027137	ENSMUSG00000073728	Tmem51os1	ENSMUSG00000073728|Gm10565|Tmem51as1	Tmem51 opposite strand 1	ncRNA
mm_11471.1	chr2	32363681	32363693	+	1	NA	intron (NM_001252537, intron 1 of 17)	intron (NM_001252537, intron 1 of 17)	489	NM_028412	68379	Mm.170508	NM_028412	ENSMUSG00000039205	Ciz1	0610038H21Rik|2900056O04Rik|LSFR1|ZNF356	CDKN1A interacting zinc finger protein 1	protein-coding
mm_63369.1	chr7	127091427	127091450	+	1	NA	promoter-TSS (NM_178901)	promoter-TSS (NM_178901)	2	NM_178901	101602	Mm.490357	NM_178901	ENSMUSG00000045165	AI467606	-	expressed sequence AI467606	protein-coding
mm_141059.1	chr17	25754328	25754338	-	1	NA	promoter-TSS (NM_018857)	promoter-TSS (NM_018857)	-6	NM_018857	56047	Mm.17510	NM_018857	ENSMUSG00000063011	Msln	MPF	mesothelin	protein-coding
mm_114130.1	chr13	55211786	55211861	+	1	NA	intron (NM_008739, intron 1 of 22)	CpG	2041	NM_008739	18193	Mm.12964	NM_008739	ENSMUSG00000021488	Nsd1	AI528500|KMT3B	nuclear receptor-binding SET-domain protein 1	protein-coding
mm_136598.1	chr17	5090082	5090122	+	1	NA	intron (NM_001085355, intron 2 of 19)	intron (NM_001085355, intron 2 of 19)	95028	NM_001085355	239985	Mm.133401	NM_001085355	ENSMUSG00000069729	Arid1b	8030481M12|9330189K18Rik|AI836955|Ardi1b|B230217J03Rik|mKIAA1235	AT rich interactive domain 1B (SWI-like)	protein-coding
mm_58967.1	chr7	18991290	18991314	+	1	NA	promoter-TSS (NM_145579)	promoter-TSS (NM_145579)	57	NM_145579	232934	Mm.440069	NM_145579	ENSMUSG00000048481	Mypop	Myodysa|P42pop	Myb-related transcription factor, partner of profilin	protein-coding
mm_165899.1	chr4	46601926	46601944	-	1	NA	promoter-TSS (NM_001164804)	promoter-TSS (NM_001164804)	-6	NM_001164804	107684	Mm.416311	NM_178893	ENSMUSG00000028337	Coro2a	9030208C03Rik|AI563590|IR10	coronin, actin binding protein 2A	protein-coding
mm_4280.1	chr1	171630635	171630639	+	1	NA	Intergenic	Intergenic	11263	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_114591.1	chr13	75761874	75761889	+	1	NA	exon (NM_138953, exon 6 of 12)	exon (NM_138953, exon 6 of 12)	54397	NM_138953	192657	Mm.21288	NM_138953	ENSMUSG00000001542	Ell2	-	elongation factor RNA polymerase II 2	protein-coding
mm_51499.1	chr6	83108948	83108980	+	1	NA	promoter-TSS (NM_026744)	promoter-TSS (NM_026744)	-144	NM_026744	68499	Mm.333183	NM_026744	ENSMUSG00000030037	Mrpl53	1110007K17Rik	mitochondrial ribosomal protein L53	protein-coding
mm_73338.1	chr8	105305573	105305619	+	1	NA	promoter-TSS (NM_172760)	promoter-TSS (NM_172760)	-5	NM_172760	234683	Mm.237966	NM_172760	ENSMUSG00000014791	Elmo3	9930107J06|BC058752|CED-12|Ced12	engulfment and cell motility 3	protein-coding
mm_105265.1	chr11	102360566	102360570	-	1	NA	intron (NM_011403, intron 3 of 19)	intron (NM_011403, intron 3 of 19)	4713	NM_011403	20533	Mm.7248	NM_011403	ENSMUSG00000006574	Slc4a1	Ae1|CD233|Empb3|l11Jus51	solute carrier family 4 (anion exchanger), member 1	protein-coding
mm_18955.1	chr2	76789499	76789512	-	1	NA	exon (NM_011652, exon 215 of 313)	exon (NM_011652, exon 215 of 313)	114190	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_150442.1	chr19	37784210	37784259	+	1	NA	Intergenic	Intergenic	86426	NM_007811	13082	Mm.42230	NM_007811	ENSMUSG00000024987	Cyp26a1	Cyp26|P450RA|P450RAI|RAH	cytochrome P450, family 26, subfamily a, polypeptide 1	protein-coding
mm_64171.1	chr7	141455200	141455214	+	1	NA	promoter-TSS (NR_028142)	promoter-TSS (NR_028142)	19	NM_001163689	66853	Mm.29998	NM_025802	ENSMUSG00000025509	Pnpla2	0610039C21Rik|1110001C14Rik|Atgl|TTS-2.2	patatin-like phospholipase domain containing 2	protein-coding
mm_97231.1	chr11	75652202	75652242	+	1	NA	promoter-TSS (NM_001080774)	promoter-TSS (NM_001080774)	72	NM_001080774	17913	Mm.234502	NM_008659	ENSMUSG00000017774	Myo1c	C80397|MMIb|MYO1E|NMI|mm1beta|myr2	myosin IC	protein-coding
mm_109596.1	chr12	112644893	112644962	+	1	NA	promoter-TSS (NM_001161737)	promoter-TSS (NM_001161737)	99	NM_013929	30954	Mm.289812	NM_013929	ENSMUSG00000064326	Siva1	CD27bp|Siva	SIVA1, apoptosis-inducing factor	protein-coding
mm_91803.1	chr10	53751179	53751191	-	1	NA	promoter-TSS (NM_001081428)	promoter-TSS (NM_001081428)	-276	NM_001081428	75906	Mm.436785	NM_001081428	ENSMUSG00000019856	Fam184a	3110012E06Rik|4930438C08Rik|4930589M24Rik	family with sequence similarity 184, member A	protein-coding
mm_132329.1	chr16	33806025	33806041	+	1	NA	exon (NM_010739, exon 6 of 13)	exon (NM_010739, exon 6 of 13)	11996	NM_010739	17063	Mm.3177	NM_010739	ENSMUSG00000022824	Muc13	114/A10|14/A10|AI159736|Lrrp|Ly64|NJ-1	mucin 13, epithelial transmembrane	protein-coding
mm_61087.1	chr7	51622520	51622541	+	1	NA	5' UTR (NM_080853, exon 1 of 12)	5' UTR (NM_080853, exon 1 of 12)	700	NM_080853	140919	Mm.256618	NM_080853	ENSMUSG00000030500	Slc17a6	2900073D12Rik|DNPI|VGLUT2	solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 6	protein-coding
mm_66727.1	chr7	46238498	46238513	-	1	NA	promoter-TSS (NM_153677)	promoter-TSS (NM_153677)	-15	NM_153677	72088	Mm.119709	NM_023649	ENSMUSG00000030838	Ush1c	2010016F01Rik|harmonin	Usher syndrome 1C	protein-coding
mm_57044.1	chr6	122340589	122340599	-	1	NA	promoter-TSS (NM_001271579)	promoter-TSS (NM_001271579)	-367	NM_001271579	13619	Mm.6822	NM_007905	ENSMUSG00000040669	Phc1	AW557034|Edr|Edr1|Mph1|Rae-28|rae28	polyhomeotic-like 1 (Drosophila)	protein-coding
mm_15681.1	chr2	163602295	163602309	+	1	NA	promoter-TSS (NM_029512)	promoter-TSS (NM_029512)	-12	NM_181734	76080	Mm.89828	NM_029512	ENSMUSG00000017679	Ttpal	3110080A02Rik|5830472M02Rik	tocopherol (alpha) transfer protein-like	protein-coding
mm_94203.1	chr11	3103533	3103550	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	-20480	NR_003517	236604	Mm.247625	NM_001004146		Pisd-ps1	-	phosphatidylserine decarboxylase, pseudogene 1	pseudo
mm_8428.1	chr1	152550603	152550616	-	1	NA	intron (NM_001346119, intron 7 of 17)	intron (NM_001346119, intron 7 of 17)	74608	NM_016846	19731	Mm.245270	NM_016846	ENSMUSG00000026482	Rgl1	Rgl|mKIAA0959	ral guanine nucleotide dissociation stimulator,-like 1	protein-coding
mm_4164.1	chr1	171029432	171029438	+	1	NA	3' UTR (NM_144559, exon 5 of 5)	3' UTR (NM_144559, exon 5 of 5)	10509	NM_144559	246256	Mm.251254	NM_144559	ENSMUSG00000059089	Fcgr4	4833442P21Rik|CD16-2|FcgRIV|FcgammaRIV|Fcgr3a|Fcrl3	Fc receptor, IgG, low affinity IV	protein-coding
mm_58240.1	chr6	145047665	145047697	-	1	NA	intron (NM_007532, intron 1 of 10)	intron (NM_007532, intron 1 of 10)	1131	NM_001024468	12035	Mm.4606	NM_007532	ENSMUSG00000030268	Bcat1	BCATc|Eca39	branched chain aminotransferase 1, cytosolic	protein-coding
mm_81446.1	chr9	109812290	109812300	+	1	NA	Intergenic	Intergenic	-4332	NM_183136	78709	Mm.99613	NM_183136	ENSMUSG00000050074	Spink8	C630041L24Rik	serine peptidase inhibitor, Kazal type 8	protein-coding
mm_13041.1	chr2	91082398	91082418	+	1	NA	Intergenic	Intergenic	-12093	NM_001290765	68427	Mm.192375	NM_026721	ENSMUSG00000002105	Slc39a13	1100001L14Rik|AA387663|ZIP-13|ZIP13	solute carrier family 39 (metal ion transporter), member 13	protein-coding
mm_165689.1	chr3	92813517	92813521	-	1	NA	Intergenic	Intergenic	-5628	NM_001254760	631101	Mm.250525	NM_001254760	ENSMUSG00000095870	Lce1k	Gm7055|Sprrl6	late cornified envelope 1K	protein-coding
mm_89896.1	chr10	110931992	110932005	+	1	NA	exon (NM_007792, exon 2 of 6)	exon (NM_007792, exon 2 of 6)	11822	NM_007792	13008	Mm.2020	NM_007792	ENSMUSG00000020186	Csrp2	AW551867|Crp2|SmLim	cysteine and glycine-rich protein 2	protein-coding
mm_99214.1	chr11	101024972	101024974	+	1	NA	intron (NM_001243050, intron 5 of 20)	intron (NM_001243050, intron 5 of 20)	-5367	NR_105893	102466767		NR_105893	ENSMUSG00000098415	Mir6928	Gm27728|mmu-mir-6928	microRNA 6928	ncRNA
mm_150714.1	chr19	43281224	43281245	+	1	NA	intron (NM_001081257, intron 3 of 11)	intron (NM_001081257, intron 3 of 11)	107121	NM_001081257	545291	Mm.442200	NM_001081257	ENSMUSG00000074852	Hpse2	Gm968|Hpa2	heparanase 2	protein-coding
mm_138317.1	chr17	34836988	34837049	+	1	NA	promoter-TSS (NM_019442)	promoter-TSS (NM_019442)	-1	NM_033613	112403	Mm.275309	NM_033613	ENSMUSG00000040482	Dxo	Dom3z|NG6	decapping exoribonuclease	protein-coding
mm_60700.1	chr7	45176142	45176155	+	1	NA	TTS (NM_001195255)	TTS (NM_001195255)	2845	NR_106022	102465638		NR_106022	ENSMUSG00000106470	Mir7055	mmu-mir-7055	microRNA 7055	ncRNA
mm_58363.1	chr6	148444317	148444329	-	1	NA	promoter-TSS (NM_198967)	promoter-TSS (NM_198967)	29	NM_001347518	387314	Mm.137858	NM_198967	ENSMUSG00000030306	Tmtc1	Arg99|BC023818	transmembrane and tetratricopeptide repeat containing 1	protein-coding
mm_83564.1	chr9	46315901	46315901	-	1	NA	5' UTR (NM_183104, exon 3 of 13)	5' UTR (NM_183104, exon 3 of 13)	4085	NM_183104	74361	Mm.159169	NM_183104	ENSMUSG00000056617	4931429L15Rik	-	RIKEN cDNA 4931429L15 gene	protein-coding
mm_150054.1	chr19	29382499	29382507	+	1	NA	exon (NM_021893, exon 5 of 7)	exon (NM_021893, exon 5 of 7)	15065	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_98046.1	chr11	85688324	85688326	+	1	NA	intron (NM_138681, intron 24 of 25)	intron (NM_138681, intron 24 of 25)	31419	NR_045875	71489	Mm.442482	NR_045875	ENSMUSG00000086199	Bcas3os1	8430403D17Rik	breast carcinoma amplified sequence 3, opposite strand 1	ncRNA
mm_111982.1	chr12	110471376	110471393	-	1	NA	intron (NM_001135001, intron 3 of 13)	ORR1C1|LTR|ERVL-MaLR	-14355	NM_001081457	26931	Mm.240396	NM_012023	ENSMUSG00000017843	Ppp2r5c	2610043M05Rik|2700063L20Rik|AI060890|AW545884|C85228|D12Bwg0916e|mKIAA0044	protein phosphatase 2, regulatory subunit B', gamma	protein-coding
mm_55313.1	chr6	54992911	54992921	-	1	NA	promoter-TSS (NM_026637)	promoter-TSS (NM_026637)	-49	NM_026637	110175	Mm.294708	NM_026637	ENSMUSG00000002797	Ggct	A030007L17Rik|AA673177|Gctg|Ggc	gamma-glutamyl cyclotransferase	protein-coding
mm_114445.1	chr13	66589174	66589180	+	1	NA	Intergenic	Intergenic	-148059	NM_001290196	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
mm_35787.1	chr4	46469994	46470015	-	1	NA	exon (NM_130889, exon 5 of 7)	exon (NM_130889, exon 5 of 7)	19078	NM_130889	67628	Mm.263913	NM_130889	ENSMUSG00000028333	Anp32b	2410015B15Rik|PAL31|PHAPI2a|Ssp29	acidic (leucine-rich) nuclear phosphoprotein 32 family, member B	protein-coding
mm_83513.1	chr9	46009781	46009782	-	1	NA	Intergenic	MIR|SINE|MIR	-3039	NM_027498	70661	Mm.219459	NM_027498	ENSMUSG00000034135	Sik3	5730525O22Rik|9030204A07Rik|AI447252|AI846254|AI849445|Qsk|SIK-3|mKIAA0999	SIK family kinase 3	protein-coding
mm_164115.1	chr15	31595810	31595852	-	1	NA	exon (NM_007637, exon 4 of 11)	exon (NM_007637, exon 4 of 11)	5973	NM_007637	12465	Mm.282158	NM_007637	ENSMUSG00000022234	Cct5	CCT-epsilon|Ccte|TCP-1-epsilon|TCPE|mKIAA0098	chaperonin containing Tcp1, subunit 5 (epsilon)	protein-coding
mm_54816.1	chr6	42350448	42350476	-	1	NA	exon (NM_001289618, exon 2 of 10)	exon (NM_001289618, exon 2 of 10)	634	NM_001289619	22793	Mm.282303	NM_011777	ENSMUSG00000029860	Zyx	9530098H06Rik|R75157	zyxin	protein-coding
mm_32166.1	chr4	100160126	100160129	+	1	NA	intron (NM_001312690, intron 1 of 3)	intron (NM_001312690, intron 1 of 3)	64336	NM_001312690	26563	Mm.57252	NM_013845	ENSMUSG00000035305	Ror1	2810404D04Rik|Ntrkr1	receptor tyrosine kinase-like orphan receptor 1	protein-coding
mm_58481.1	chr7	3570943	3570986	+	1	NA	Intergenic	LTRIS2|LTR|ERV1	45193	NM_175632	232790	Mm.358882	NM_175632	ENSMUSG00000054594	Oscar	mOSCAR|mOSCAR-M1|mOSCAR-M2|mOSCAR-M3	osteoclast associated receptor	protein-coding
mm_112999.1	chr13	21754089	21754093	+	1	NA	promoter-TSS (NM_178201)	promoter-TSS (NM_178201)	-32	NM_178201	319187		NM_178201	ENSMUSG00000095217	Hist1h2bn	-	histone cluster 1, H2bn	protein-coding
mm_131171.1	chr16	7069739	7069749	+	1	NA	promoter-TSS (NM_183188)	promoter-TSS (NM_183188)	-91	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_153447.1	chr19	41020669	41020674	-	1	NA	Intergenic	L2a|LINE|L2	-8604	NM_001043228	21673	Mm.25620	NM_009345	ENSMUSG00000025014	Dntt	Tdt	deoxynucleotidyltransferase, terminal	protein-coding
mm_90347.1	chr10	127150741	127150746	+	1	NA	Intergenic	Intergenic	-14413	NR_045166	14421	Mm.386762	NM_008080	ENSMUSG00000006731	B4galnt1	4933429D13Rik|Gal-NAc-T|GalNAc-T|GalNAcT|Galgt1|Ggm-2|Ggm2	beta-1,4-N-acetyl-galactosaminyl transferase 1	protein-coding
mm_70629.1	chr8	13757664	13757714	+	1	NA	promoter-TSS (NM_027276)	promoter-TSS (NM_027276)	-1	NM_027276	69957	Mm.182412	NM_027276	ENSMUSG00000038416	Cdc16	2700071J12Rik|2810431D22Rik|APC6	CDC16 cell division cycle 16	protein-coding
mm_163568.1	chr13	28950332	28950334	-	1	NA	TTS (NM_009238)	TTS (NM_009238)	3349	NM_009238	20677	Mm.240627	NM_009238	ENSMUSG00000076431	Sox4	AA682046|Sox-4	SRY (sex determining region Y)-box 4	protein-coding
mm_152850.1	chr19	24042548	24042567	-	1	NA	Intergenic	Intergenic	-11538	NM_001114174	381217	Mm.426078	NM_001114174	ENSMUSG00000071604	Fam189a2	AI414343|AI666772|Gm967	family with sequence similarity 189, member A2	protein-coding
mm_94141.1	chr10	128721220	128721223	-	1	NA	TTS (NM_021882)	TTS (NM_021882)	14963	NM_021882	20431	Mm.16756	NM_021882	ENSMUSG00000025359	Pmel	D10H12S53E|D12S53Eh|Pmel17|Si|Silv|gp100|gp87	premelanosome protein	protein-coding
mm_166909.1	chr7	29281581	29281595	-	1	NA	exon (NM_001082548, exon 1 of 6)	exon (NM_001082548, exon 1 of 6)	389	NM_001082548	20733	Mm.295230	NM_011464	ENSMUSG00000074227	Spint2	AL024025|C76321|HAI-2	serine protease inhibitor, Kunitz type 2	protein-coding
mm_27365.1	chr3	50436498	50436519	-	1	NA	intron (NM_011990, intron 2 of 11)	intron (NM_011990, intron 2 of 11)	7105	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_18812.1	chr2	74521975	74521985	-	1	NA	3' UTR (NM_027133, exon 13 of 13)	3' UTR (NM_027133, exon 13 of 13)	56968	NM_001110209	69605	Mm.156113	NM_027133	ENSMUSG00000009207	Lnpk	2310011O18Rik|4921514L11Rik|9530051D01Rik|AI666268|Lnp|Lnpk1|Ul|ulnaless	lunapark, ER junction formation factor	protein-coding
mm_150134.1	chr19	30060381	30060384	+	1	NA	intron (NM_144873, intron 3 of 15)	intron (NM_144873, intron 3 of 15)	29869	NM_144873	109113	Mm.313364	NM_144873	ENSMUSG00000024817	Uhrf2	2310065A22Rik|AI426270|AW214556|D130071B19Rik|Nirf	ubiquitin-like, containing PHD and RING finger domains 2	protein-coding
mm_92518.1	chr10	78574865	78574880	-	1	NA	intron (NM_173751, intron 1 of 15)	CpG	372	NM_173751	216136	Mm.2644	NM_173751	ENSMUSG00000032763	Ilvbl	5830463I21|AI415009	ilvB (bacterial acetolactate synthase)-like	protein-coding
mm_163877.1	chr14	19419598	19419646	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	182965	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_163486.1	chr12	109453557	109453563	+	1	NA	5' UTR (NM_010052, exon 1 of 5)	5' UTR (NM_010052, exon 1 of 5)	105	NM_010052	13386	Mm.157069	NM_010052	ENSMUSG00000040856	Dlk1	AW742678|DLK-1|DlkI|FA1|Ly107|Peg9|SCP1|ZOG|pG2|pref-1	delta-like 1 homolog (Drosophila)	protein-coding
mm_14106.1	chr2	125673150	125673184	+	1	NA	promoter-TSS (NM_025613)	promoter-TSS (NM_025613)	67	NM_025613	58521	Mm.425101	NM_025613	ENSMUSG00000091337	Eid1	2610002K20Rik|Cri1|EID-1|ORF12|PNAS-22|PTD014	EP300 interacting inhibitor of differentiation 1	protein-coding
mm_18519.1	chr2	62773411	62773413	-	1	NA	intron (NM_133207, intron 8 of 15)	intron (NM_133207, intron 8 of 15)	109085	NM_145523	227960	Mm.219877	NM_145523	ENSMUSG00000026893	Gca	5133401E04Rik|AI573844	grancalcin	protein-coding
mm_34180.1	chr4	140700336	140700346	+	1	NA	Intergenic	Intergenic	-1132	NM_173867	108911	Mm.253	NM_173867	ENSMUSG00000040945	Rcc2	2610510H01Rik|2610529N02Rik|AA536646|AA675016|Td60|mKIAA1470	regulator of chromosome condensation 2	protein-coding
mm_38424.1	chr4	139193997	139194000	-	1	NA	promoter-TSS (NM_001271405)	promoter-TSS (NM_001271405)	-113	NM_001271405	12345	Mm.2945	NM_009798	ENSMUSG00000028745	Capzb	1700120C01Rik|AI325129|CPB1|CPB2|CPbeat2|CPbeta1|CPbeta2|Cappb1	capping protein (actin filament) muscle Z-line, beta	protein-coding
mm_167954.1	chrX	140956940	140956954	+	1	NA	promoter-TSS (NM_001164177)	promoter-TSS (NM_001164177)	-236	NM_001164177	53380	Mm.17640	NM_016883	ENSMUSG00000031429	Psmd10	AW554874	proteasome (prosome, macropain) 26S subunit, non-ATPase, 10	protein-coding
mm_82570.1	chr9	21079465	21079503	-	1	NA	exon (NM_027911, exon 9 of 13)	exon (NM_027911, exon 9 of 13)	-3896	NR_106050	102465656		NR_106050	ENSMUSG00000098907	Mir7082	Gm27933|mmu-mir-7082	microRNA 7082	ncRNA
mm_16759.1	chr2	9875391	9875404	-	1	NA	intron (NM_008091, intron 2 of 5)	intron (NM_008091, intron 2 of 5)	3203	NM_008091	14462	Mm.313866	NM_008091	ENSMUSG00000015619	Gata3	Gata-3|jal	GATA binding protein 3	protein-coding
mm_121245.1	chr14	103057223	103057239	+	1	NA	TTS (NM_008392)	TTS (NM_008392)	10219	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_128088.1	chr15	27772248	27772264	-	1	NA	intron (NM_001081302, intron 36 of 56)	intron (NM_001081302, intron 36 of 56)	-90714	NM_001242423	223433	Mm.266485	NM_198301	ENSMUSG00000056069	Fam105a	9830126M18	family with sequence similarity 105, member A	protein-coding
mm_133512.1	chr16	90738489	90738498	+	1	NA	5' UTR (NM_029844, exon 1 of 3)	5' UTR (NM_029844, exon 1 of 3)	169	NM_029844	77037	Mm.22455	NM_029844	ENSMUSG00000039956	Mrap	1110025G12Rik|Falp|ORF61	melanocortin 2 receptor accessory protein	protein-coding
mm_26646.1	chr3	153958398	153958405	+	1	NA	Intergenic	RLTR48A|LTR|ERV1	-13758	NM_007382	11364	Mm.10530	NM_007382	ENSMUSG00000062908	Acadm	AU018656|MCAD	acyl-Coenzyme A dehydrogenase, medium chain	protein-coding
mm_159421.1	chr3	108092830	108092830	+	1	NA	promoter-TSS (NM_008141)	promoter-TSS (NM_008141)	-236	NM_008141	14686	Mm.439652	NM_008141	ENSMUSG00000009108	Gnat2	AW490837|Gnat-2|Gt-2|Tcalpha	guanine nucleotide binding protein, alpha transducing 2	protein-coding
mm_87768.1	chr10	60293400	60293410	+	1	NA	exon (NM_011179, exon 4 of 15)	exon (NM_011179, exon 4 of 15)	8944	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_160454.1	chr8	106603465	106603465	+	1	NA	5' UTR (NM_009864, exon 1 of 16)	5' UTR (NM_009864, exon 1 of 16)	115	NM_009864	12550	Mm.35605	NM_009864	ENSMUSG00000000303	Cdh1	AA960649|ARC-1|E-cad|Ecad|L-CAM|UVO|Um	cadherin 1	protein-coding
mm_137148.1	chr17	23673991	23674001	+	1	NA	promoter-TSS (NM_001008425)	promoter-TSS (NM_001008425)	-226	NM_001008425	386612	Mm.328831	NM_001008425	ENSMUSG00000041319	Thoc6	F830014G06Rik|Wdr58	THO complex 6	protein-coding
mm_29081.1	chr3	104174615	104174619	-	1	NA	intron (NM_001159354, intron 1 of 20)	intron (NM_001159354, intron 1 of 20)	45789	NM_133853	99470	Mm.264849	NM_133853	ENSMUSG00000052539	Magi3	4732496O19Rik|6530407C02Rik|AA407180|AI120132|mKIAA1634	membrane associated guanylate kinase, WW and PDZ domain containing 3	protein-coding
mm_70356.1	chr8	5639515	5639535	+	1	NA	Intergenic	Intergenic	-534238	NM_011388	20494	Mm.3500	NM_011388	ENSMUSG00000023073	Slc10a2	9130221J18Rik|AI605518|ASBT|IBAT|ISBT	solute carrier family 10, member 2	protein-coding
mm_147953.1	chr18	67034504	67034507	-	1	NA	Intergenic	Intergenic	-53793	NM_177137	14680	Mm.440746	NM_010307	ENSMUSG00000024524	Gnal	2610011C15Rik|9630020G10Rik|Galphaolf|Gna10|Golf	guanine nucleotide binding protein, alpha stimulating, olfactory type	protein-coding
mm_77866.1	chr9	5332820	5332833	+	1	NA	intron (NM_007609, intron 7 of 8)	intron (NM_007609, intron 7 of 8)	-12650	NM_009808	12364	Mm.42163	NM_009808	ENSMUSG00000025887	Casp12	-	caspase 12	protein-coding
mm_159759.1	chr5	90304097	90304097	-	1	NA	intron (NM_198010, intron 1 of 32)	A-rich|Low_complexity|Low_complexity	62088	NM_030886	81702	Mm.245522	NM_030886	ENSMUSG00000055204	Ankrd17	4933425K22Rik|A130069E23Rik|A930008M01|AA407558|AA516750|AU040470|Foe|Gtar|Mask|mKIAA0697	ankyrin repeat domain 17	protein-coding
mm_61216.1	chr7	64287678	64287715	+	1	NA	promoter-TSS (NM_172742)	promoter-TSS (NM_172742)	26	NM_172742	233315	Mm.214959	NM_172742	ENSMUSG00000030522	Mtmr10	BB128963|C79734	myotubularin related protein 10	protein-coding
mm_126569.1	chr15	82244823	82244843	+	1	NA	promoter-TSS (NM_001080158)	promoter-TSS (NM_001080158)	-86	NM_025639	66570	Mm.23596	NM_025639	ENSMUSG00000068101	Cenpm	2610019I03Rik|AI853711|Pane1	centromere protein M	protein-coding
mm_95732.1	chr11	54626534	54626544	+	1	NA	intron (NM_175258, intron 10 of 27)	intron (NM_175258, intron 10 of 27)	30393	NM_001252497	192786	Mm.254404	NM_175258	ENSMUSG00000037533	Rapgef6	A530068K01|AI844632|BB085664|C030018K18Rik|PDZ-GEF2|Pdzgef2|RA-GEF-2|Ragef2|mKIAA4052	Rap guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_89746.1	chr10	99189487	99189495	+	1	NA	intron (NM_027740, intron 10 of 11)	intron (NM_027740, intron 10 of 11)	-73740	NM_026268	67603	Mm.1791	NM_026268	ENSMUSG00000019960	Dusp6	1300019I03Rik|MKP-3|MKP3|PYST1	dual specificity phosphatase 6	protein-coding
mm_27410.1	chr3	51340819	51340821	-	1	NA	promoter-TSS (NM_001291059)	promoter-TSS (NM_001291059)	-176	NM_023502	69257	Mm.131038	NM_023502	ENSMUSG00000037174	Elf2	2610036A20Rik|A230104O07Rik|AW111824|BB183398|EU32|NERF|NERF-1A|NERF-1B|NERF-2	E74-like factor 2	protein-coding
mm_162429.1	chr1	93489933	93489934	+	1	NA	intron (NM_001159719, intron 2 of 12)	LTR78B|LTR|ERV1	10872	NM_001159719	18000	Mm.428652	NM_010891	ENSMUSG00000026276	Sept2	AW208991|Nedd-5|Nedd5|mKIAA0158	septin 2	protein-coding
mm_109688.1	chr12	113142837	113142861	+	1	NA	intron (NM_001347443, intron 1 of 6)	intron (NM_001347443, intron 1 of 6)	2244	NM_001347443	68337	Mm.133825	NM_024223	ENSMUSG00000006356	Crip2	0610010I23Rik|AW743261|C77570|CRP2|CRP4|Crp|ESP1|Hlp	cysteine rich protein 2	protein-coding
mm_48429.1	chr5	140609683	140609691	-	1	NA	intron (NM_008494, intron 1 of 7)	intron (NM_008494, intron 1 of 7)	2346	NM_008494	16848	Mm.12834	NM_008494	ENSMUSG00000029570	Lfng	AW061165	LFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	protein-coding
mm_150858.1	chr19	45015169	45015187	+	1	NA	promoter-TSS (NM_001130525)	promoter-TSS (NM_001130525)	2	NM_145503	226154	Mm.28204	NM_145503	ENSMUSG00000035342	Lzts2	BC014695|LAPSER1|mKIAA1813	leucine zipper, putative tumor suppressor 2	protein-coding
mm_75907.1	chr8	71381694	71381714	-	1	NA	5' UTR (NM_010150, exon 1 of 4)	5' UTR (NM_010150, exon 1 of 4)	248	NM_010150	13864	Mm.28989	NM_010150	ENSMUSG00000002393	Nr2f6	AV090102|COUP-TF3|EAR2|Erbal2	nuclear receptor subfamily 2, group F, member 6	protein-coding
mm_125988.1	chr15	76351289	76351299	+	1	NA	promoter-TSS (NM_026859)	promoter-TSS (NM_026859)	0	NM_001164607	68877	Mm.289680	NM_026859	ENSMUSG00000022553	Maf1	1110068E11Rik|AU042856	MAF1 homolog, negative regulator of RNA polymerase III	protein-coding
mm_138881.1	chr17	43360424	43360456	+	1	NA	Intergenic	Intergenic	-29026	NM_001081178	224792	Mm.23478	NM_001081178	ENSMUSG00000056492	Adgrf5	8430401C09Rik|9330185D23|AI528491|Gpr116|mKIAA0758	adhesion G protein-coupled receptor F5	protein-coding
mm_34251.1	chr4	141284799	141284824	+	1	NA	Intergenic	MLTR14|LTR|ERV1	-16410	NM_010139	13836	Mm.2581	NM_010139	ENSMUSG00000006445	Epha2	AW545284|Eck|Myk2|Sek-2|Sek2	Eph receptor A2	protein-coding
mm_83384.1	chr9	44581518	44581531	-	1	NA	Intergenic	Intergenic	-23368	NM_001110826	13209	Mm.267061	NM_007841	ENSMUSG00000032097	Ddx6	1110001P04Rik|E230023J21Rik|HLR2|mRCK/P54|p54|rck	DEAD (Asp-Glu-Ala-Asp) box polypeptide 6	protein-coding
mm_63360.1	chr7	127021383	127021414	+	1	NA	promoter-TSS (NM_001102563)	promoter-TSS (NM_001102563)	-187	NM_001102563	69017	Mm.392047	NM_001102563	ENSMUSG00000045114	Prrt2	1500031I19Rik|AI195361|DSPB3	proline-rich transmembrane protein 2	protein-coding
mm_166313.1	chr5	108694429	108694459	+	1	NA	5' UTR (NM_001164259, exon 1 of 6)	5' UTR (NM_001164259, exon 1 of 6)	215	NM_054071	116701	Mm.35691	NM_054071	ENSMUSG00000008090	Fgfrl1	FGFR5|FGFR5beta|FGFR5gamma	fibroblast growth factor receptor-like 1	protein-coding
mm_61445.1	chr7	75573031	75573047	+	1	NA	intron (NM_029332, intron 3 of 36)	intron (NM_029332, intron 3 of 36)	117505	NM_029332	75547	Mm.216107	NM_029332	ENSMUSG00000066406	Akap13	1700026G02Rik|5730522G15Rik|5830460E08Rik|AKAP-13|AKAP-Lbc|BRX|Ht31|LBC|PROTO-LB|PROTO-LBC	A kinase (PRKA) anchor protein 13	protein-coding
mm_109468.1	chr12	111417487	111417493	+	1	NA	promoter-TSS (NM_001289489)	promoter-TSS (NM_001289489)	45	NM_001289488	74190	Mm.248640	NM_028807	ENSMUSG00000021280	Exoc3l4	1200009I06Rik|1600013K19Rik	exocyst complex component 3-like 4	protein-coding
mm_109518.1	chr12	111454431	111454441	+	1	NA	3' UTR (NM_009396, exon 12 of 12)	3' UTR (NM_009396, exon 12 of 12)	11775	NM_009396	21928	Mm.255332	NM_009396	ENSMUSG00000021281	Tnfaip2	B94|Exoc3l3|M-sec|Tnfip2|tnfb94	tumor necrosis factor, alpha-induced protein 2	protein-coding
mm_154416.1	chrM	15617	15625	+	1	NA	NA	Intergenic	NA	NA								
mm_34963.1	chr4	156008617	156008632	+	1	NA	intron (NM_001302468, intron 4 of 6)	intron (NM_001302468, intron 4 of 6)	-5071	NM_011659	22163	Mm.13885	NM_011659	ENSMUSG00000029075	Tnfrsf4	ACT35|CD134|Ly-70|Ox40|TXGP1L|Txgp1	tumor necrosis factor receptor superfamily, member 4	protein-coding
mm_46319.1	chr5	100674231	100674281	-	1	NA	promoter-TSS (NM_027978)	promoter-TSS (NM_027978)	0	NM_027978	71883	Mm.260661	NM_027978	ENSMUSG00000029319	Coq2	2310002F18Rik|PHB:PPT	coenzyme Q2 4-hydroxybenzoate polyprenyltransferase	protein-coding
mm_120445.1	chr14	65968534	65968539	+	1	NA	promoter-TSS (NM_013492)	promoter-TSS (NM_013492)	53	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_105536.1	chr11	106301436	106301460	-	1	NA	exon (NM_008117, exon 2 of 5)	exon (NM_008117, exon 2 of 5)	448	NM_008117	14599	Mm.343934	NM_008117	ENSMUSG00000020713	Gh	Gh1|Ghb1	growth hormone	protein-coding
mm_25045.1	chr3	98299172	98299178	+	1	NA	exon (NM_008256, exon 6 of 10)	exon (NM_008256, exon 6 of 10)	18744	NM_008256	15360	Mm.289131	NM_008256	ENSMUSG00000027875	Hmgcs2	1300002P16|mHS	3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2	protein-coding
mm_13582.1	chr2	112377235	112377245	+	1	NA	Intergenic	RLTR12D|LTR|ERVK	-1971	NM_024254	72425	Mm.425091	NM_024254	ENSMUSG00000027132	Katnbl1	2410042D21Rik|AA166487|AA473307|AI467442	katanin p80 subunit B like 1	protein-coding
mm_55834.1	chr6	83125157	83125167	-	1	NA	promoter-TSS (NM_023547)	promoter-TSS (NM_023547)	-133	NM_023547	70020	Mm.27814	NM_023547	ENSMUSG00000030034	Ino80b	2510009I23Rik|HMG1YL4|Hmga1l4|Papa1|Znhit4	INO80 complex subunit B	protein-coding
mm_24006.1	chr3	87357964	87357981	+	1	NA	promoter-TSS (NM_009690)	promoter-TSS (NM_009690)	91	NM_009690	11801	Mm.6676	NM_009690	ENSMUSG00000015854	Cd5l	1/6|AAC-11|AI047839|Api6|CT2|Pdp|Sp-alpha|mAIM	CD5 antigen-like	protein-coding
mm_91949.1	chr10	60958073	60958082	-	1	NA	Intergenic	Intergenic	-2646	NR_130327	100316671		NR_130327	ENSMUSG00000080526	Mir466j	Mirn466j|mmu-mir-466j	microRNA 466j	ncRNA
mm_167794.1	chr9	123924763	123924779	-	1	NA	Intergenic	CpG	43921	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_122298.1	chr14	34590285	34590297	-	1	NA	TTS (NM_001128599)	TTS (NM_001128599)	-1610	NM_001039073	24131	Mm.29733	NM_011918	ENSMUSG00000021798	Ldb3	AW742271|PDLIM6|ZASP	LIM domain binding 3	protein-coding
mm_164618.1	chr17	31162685	31162693	-	1	NA	exon (NM_009362, exon 2 of 3)	exon (NM_009362, exon 2 of 3)	2364	NM_009362	21784	Mm.2854	NM_009362	ENSMUSG00000024032	Tff1	Bcei|PS2	trefoil factor 1	protein-coding
mm_35034.1	chr4	4133806	4133822	-	1	NA	3' UTR (NM_001002927, exon 2 of 2)	3' UTR (NM_001002927, exon 2 of 2)	4631	NM_001002927	18619	Mm.475097	NM_001002927	ENSMUSG00000045573	Penk	AI326464|ENK|PPA|Penk1	preproenkephalin	protein-coding
mm_112476.1	chr13	5868750	5868761	+	1	NA	3' UTR (NM_011803, exon 4 of 4)	3' UTR (NM_011803, exon 4 of 4)	7266	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_102391.1	chr11	58991741	58991765	-	1	NA	TTS (NM_053168)	TTS (NM_053168)	13660	NM_053168	94091	Mm.248049	NM_053168	ENSMUSG00000020455	Trim11	-	tripartite motif-containing 11	protein-coding
mm_1557.1	chr1	73024604	73024621	+	1	NA	promoter-TSS (NR_038002)	promoter-TSS (NR_038002)	26	NR_038002	69449	Mm.250447	NR_038001	ENSMUSG00000101968	1700027A15Rik	-	RIKEN cDNA 1700027A15 gene	ncRNA
mm_20346.1	chr2	127705770	127705780	-	1	NA	3' UTR (NM_145532, exon 4 of 4)	3' UTR (NM_145532, exon 4 of 4)	24122	NM_145532	228576	Mm.133036	NM_145532	ENSMUSG00000027377	Mall	BC012256|BENE	mal, T cell differentiation protein-like	protein-coding
mm_125653.1	chr15	62981154	62981179	+	1	NA	Intergenic	Intergenic	498442	NR_045279	432958	Mm.255105	NR_045279		Gm20740	-	predicted gene, 20740	ncRNA
mm_80537.1	chr9	80306958	80306972	+	1	NA	exon (NM_001039546, exon 32 of 33)	exon (NM_001039546, exon 32 of 33)	141931	NM_001039546	17920	Mm.4040	NM_008662	ENSMUSG00000033577	Myo6	BC029719|Tlc|sv	myosin VI	protein-coding
mm_167481.1	chr8	129234034	129234055	-	1	NA	promoter-TSS (NM_153780)	promoter-TSS (NM_153780)	2	NM_153780	72139	Mm.426514	NM_153780	ENSMUSG00000071302	2610044O15Rik8	2610044O15Rik	RIKEN cDNA 2610044O15 gene	protein-coding
mm_112353.1	chr12	118301953	118301971	-	1	NA	promoter-TSS (NM_009239)	promoter-TSS (NM_009239)	-522	NM_001166385	20688	Mm.34699	NM_009239	ENSMUSG00000025323	Sp4	5730497N03Rik|HF-1b|HF1-b	trans-acting transcription factor 4	protein-coding
mm_135443.1	chr16	45454933	45454974	-	1	NA	intron (NM_001005854, intron 1 of 4)	intron (NM_001005854, intron 1 of 4)	38016	NM_001005854	208166	Mm.451852	NM_001005854	ENSMUSG00000053182	Gm609	Gm1749|isec1	predicted gene 609	protein-coding
mm_33238.1	chr4	127023407	127023434	+	1	NA	exon (NM_023603, exon 3 of 10)	exon (NM_023603, exon 3 of 10)	2119	NM_023603	71514	Mm.257276	NM_023603	ENSMUSG00000028820	Sfpq	1110004P21Rik|2810416M14Rik|5730453G22Rik|9030402K04Rik|AU021830|D4Ertd314e|Gm12940|OTTMUSG00000009329|PSF|REP1	splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)	protein-coding
mm_86467.1	chr10	4482503	4482520	+	1	NA	Intergenic	Intergenic	-27361	NM_001195672	100504234	Mm.291807	NM_001195672	ENSMUSG00000019767	Ccdc170	Gm221	coiled-coil domain containing 170	protein-coding
mm_148659.1	chr19	5560203	5560216	+	1	NA	exon (NM_019935, exon 1 of 4)	exon (NM_019935, exon 1 of 4)	366	NM_019935	18426	Mm.280225	NM_019935	ENSMUSG00000024922	Ovol1	BB147136|Ovo1|movo1	ovo like zinc finger 1	protein-coding
mm_13548.1	chr2	112239475	112239508	+	1	NA	promoter-TSS (NM_207206)	promoter-TSS (NM_207206)	-350	NM_207206	99010	Mm.33438	NM_207206	ENSMUSG00000027134	Lpcat4	AI505034|Agpat7|Aytl3|LPEAT2	lysophosphatidylcholine acyltransferase 4	protein-coding
mm_132318.1	chr16	33755572	33755589	+	1	NA	intron (NM_175256, intron 12 of 14)	intron (NM_175256, intron 12 of 14)	-38457	NM_010739	17063	Mm.3177	NM_010739	ENSMUSG00000022824	Muc13	114/A10|14/A10|AI159736|Lrrp|Ly64|NJ-1	mucin 13, epithelial transmembrane	protein-coding
mm_167307.1	chr8	60524236	60524241	+	1	NA	intron (NM_011834, intron 4 of 12)	L1VL4|LINE|L1	18114	NM_011834	23923	Mm.35020	NM_011834	ENSMUSG00000057228	Aadat	AI875679|Aadt|KATII|Kat2|Kyat2|mKat-2	aminoadipate aminotransferase	protein-coding
mm_11148.1	chr2	28513361	28513366	+	1	NA	5' UTR (NM_009058, exon 1 of 18)	5' UTR (NM_009058, exon 1 of 18)	196	NM_001145834	19730	Mm.5236	NM_009058	ENSMUSG00000026821	Ralgds	Gnds|Rgds|mKIAA1308	ral guanine nucleotide dissociation stimulator	protein-coding
mm_167890.1	chrX	61123543	61123546	+	1	NA	intron (NR_030706, intron 5 of 7)	MIR|SINE|MIR	7166	NR_030706	331424	Mm.127263	NM_177916	ENSMUSG00000071753	C230004F18Rik	-	RIKEN cDNA C230004F18 gene	ncRNA
mm_147277.1	chr18	39389421	39389431	-	1	NA	Intergenic	Intergenic	97819	NM_008173	14815	Mm.129481	NM_008173	ENSMUSG00000024431	Nr3c1	GR|Grl-1|Grl1	nuclear receptor subfamily 3, group C, member 1	protein-coding
mm_142545.1	chr17	46556159	46556188	-	1	NA	promoter-TSS (NM_020493)	promoter-TSS (NM_020493)	-11	NM_020493	20807	Mm.45044	NM_020493	ENSMUSG00000015605	Srf	AW049942|AW240594	serum response factor	protein-coding
mm_108017.1	chr12	73598460	73598468	+	1	NA	intron (NM_001313977, intron 2 of 14)	intron (NM_001313977, intron 2 of 14)	13668	NM_008856	18755	Mm.341677	NM_008856	ENSMUSG00000021108	Prkch	Pkch	protein kinase C, eta	protein-coding
mm_154016.1	chr19	53255186	53255196	-	1	NA	promoter-TSS (NR_036590)	promoter-TSS (NR_036590)	14	NR_036590	69319	Mm.57452	NR_036590		1700001K23Rik	-	RIKEN cDNA 1700001K23 gene	ncRNA
mm_169651.1	chr1	55445054	55445066	-	1	NA	intron (NM_001114663, intron 1 of 5)	intron (NM_001114663, intron 1 of 5)	39114	NM_001114663	227120	Mm.194183	NM_001114663	ENSMUSG00000038349	Plcl1	C230017K02Rik|PLC-L|PLC-L1|PLCE|PLCL|PLDL1|PRIP|PRIP-1	phospholipase C-like 1	protein-coding
mm_11657.1	chr2	34976698	34976708	+	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	-14931	NM_001326601	22029	Mm.239514	NM_009421	ENSMUSG00000026875	Traf1	4732496E14Rik	TNF receptor-associated factor 1	protein-coding
mm_74739.1	chr8	18768195	18768209	-	1	NA	intron (NM_173189, intron 12 of 13)	intron (NM_173189, intron 12 of 13)	-26640	NM_007426	11601	Mm.439874	NM_007426	ENSMUSG00000031465	Angpt2	Agpt2|Ang-2|Ang2	angiopoietin 2	protein-coding
mm_132418.1	chr16	35154871	35154929	+	1	NA	promoter-TSS (NM_001012765)	promoter-TSS (NM_001012765)	-736	NM_001012765	224129	Mm.41137	NM_001012765	ENSMUSG00000022840	Adcy5	AW121902|Ac5	adenylate cyclase 5	protein-coding
mm_145023.1	chr18	38993257	38993263	+	1	NA	5' UTR (NM_175164, exon 1 of 23)	5' UTR (NM_175164, exon 1 of 23)	115	NM_175164	71302	Mm.329396	NM_175164	ENSMUSG00000036452	Arhgap26	1810044B20Rik|2610010G17Rik|4933432P15Rik|AI853435|mKIAA0621	Rho GTPase activating protein 26	protein-coding
mm_105755.1	chr11	109473134	109473153	-	1	NA	promoter-TSS (NM_028710)	promoter-TSS (NM_028710)	86	NM_134038	104681	Mm.265874	NM_134038	ENSMUSG00000041920	Slc16a6	AW743111|ESTM12|MCT 6|MCT 7|MCT6	solute carrier family 16 (monocarboxylic acid transporters), member 6	protein-coding
mm_143427.1	chr17	70850354	70850358	-	1	NA	promoter-TSS (NM_001164076)	promoter-TSS (NM_001164076)	-566	NM_001164076	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_7917.1	chr1	133753487	133753535	-	1	NA	5' UTR (NM_001167949, exon 1 of 21)	5' UTR (NM_001167949, exon 1 of 21)	236	NM_001167949	381290	Mm.188617	NM_213616	ENSMUSG00000026463	Atp2b4	Pmca4	ATPase, Ca++ transporting, plasma membrane 4	protein-coding
mm_9973.1	chr1	191199290	191199296	-	1	NA	Intergenic	Intergenic	-15960	NM_007498	11910	Mm.2706	NM_007498	ENSMUSG00000026628	Atf3	LRG-21	activating transcription factor 3	protein-coding
mm_115017.1	chr13	98355103	98355114	+	1	NA	exon (NM_008242, exon 1 of 1)	exon (NM_008242, exon 1 of 1)	863	NM_008242	15229	Mm.347441	NM_008242	ENSMUSG00000078302	Foxd1	AI385632|BF-2|FREAC4|Hfh10|Hfhbf2	forkhead box D1	protein-coding
mm_21517.1	chr2	163629176	163629222	-	1	NA	exon (NM_012032, exon 7 of 10)	exon (NM_012032, exon 7 of 10)	-15651	NR_028113	68386	Mm.410649	NR_028113	ENSMUSG00000058812	0610039K10Rik	-	RIKEN cDNA 0610039K10 gene	ncRNA
mm_135239.1	chr16	36990208	36990264	-	1	NA	Intergenic	Intergenic	-11100	NM_001037321	207215	Mm.211899	NM_001037321	ENSMUSG00000047746	Fbxo40	9830003A13Rik|mKIAA1195	F-box protein 40	protein-coding
mm_167122.1	chr7	121589804	121589812	-	1	NA	promoter-TSS (NR_131051)	promoter-TSS (NR_131051)	28	NR_102286	75793	Mm.23397	NR_102286		4933432K03Rik	1700001C18Rik|4930433G11Rik|AI428127	RIKEN cDNA 4933432K03 gene	ncRNA
mm_163633.1	chr13	58744004	58744010	+	1	NA	non-coding (NR_045469, exon 2 of 3)	non-coding (NR_045469, exon 2 of 3)	18304	NR_045469	67585	Mm.84751	NR_045469		4930455J16Rik	-	RIKEN cDNA 4930455J16 gene	ncRNA
mm_147808.1	chr18	61697094	61697097	-	1	NA	3' UTR (NM_172832, exon 6 of 6)	3' UTR (NM_172832, exon 6 of 6)	9160	NM_019508	56069	Mm.59313	NM_019508	ENSMUSG00000024578	Il17b	1110006O16Rik|1700006N07Rik|Zcyto7	interleukin 17B	protein-coding
mm_7383.1	chr1	108440463	108440465	-	1	NA	Intergenic	Intergenic	523205	NR_102307	319596	Mm.136054	NR_102306	ENSMUSG00000100457	D830032E09Rik	-	RIKEN cDNA D830032E09 gene	ncRNA
mm_39303.1	chr5	7304114	7304124	+	1	NA	promoter-TSS (NM_027603)	promoter-TSS (NM_027603)	-45	NM_027603	70920	Mm.158494	NM_027603	ENSMUSG00000040514	4921511H03Rik	-	RIKEN cDNA 4921511H03 gene	protein-coding
mm_86583.1	chr10	13008443	13008519	+	1	NA	promoter-TSS (NM_175102)	promoter-TSS (NM_175102)	31	NM_175102	66125	Mm.29743	NM_175102	ENSMUSG00000078348	Sf3b5	10kDa|1110005L13Rik|AU043053|Sf3b10	splicing factor 3b, subunit 5	protein-coding
mm_123714.1	chr14	69824919	69824938	-	1	NA	Intergenic	tRNA-Ala-GCG|tRNA|tRNA	-15479	NM_028560	73523	Mm.23509	NM_028526	ENSMUSG00000022085	Pebp4	PEBP-4	phosphatidylethanolamine binding protein 4	protein-coding
mm_166820.1	chr7	18065925	18065933	+	1	NA	promoter-TSS (NM_001162524)	promoter-TSS (NM_001162524)	0	NM_001162524	67315	Mm.46089	NM_026087	ENSMUSG00000030366	Ceacam12	1600031J20Rik|Ceacam12-C1|Ceacam12-C3|Ceacam12C1|Ceacam12C3	carcinoembryonic antigen-related cell adhesion molecule 12	protein-coding
mm_80940.1	chr9	102717718	102717730	+	1	NA	promoter-TSS (NM_019764)	promoter-TSS (NM_019764)	-80	NM_019764	56332	Mm.21145	NM_019764	ENSMUSG00000032531	Amotl2	AW549739|C79691|Lccp|MASCOT|mKIAA0989	angiomotin-like 2	protein-coding
mm_6378.1	chr1	72700532	72700542	-	1	NA	promoter-TSS (NM_176980)	promoter-TSS (NM_176980)	27	NM_176980	319695	Mm.249056	NM_176980	ENSMUSG00000039342	Ankar	4932422E22Rik	ankyrin and armadillo repeat containing	protein-coding
mm_85528.1	chr9	106476135	106476157	-	1	NA	intron (NM_001311150, intron 1 of 10)	intron (NM_001311150, intron 1 of 10)	803	NM_001311150	235587	Mm.273659	NM_145619	ENSMUSG00000023249	Parp3	A930002C11Rik|AW990611|Adprt3|Adprtl3|PARP-3|pADPRT-3	poly (ADP-ribose) polymerase family, member 3	protein-coding
mm_54759.1	chr6	41121834	41121849	-	1	NA	Intergenic	Intergenic	-86332	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_41555.1	chr5	92962162	92962173	+	1	NA	exon (NM_001077596, exon 9 of 10)	exon (NM_001077596, exon 9 of 10)	64174	NM_001077596	27428	Mm.46014	NM_015756	ENSMUSG00000029381	Shroom3	AL022960|D5Ertd287e|Shrm|Shrm3	shroom family member 3	protein-coding
mm_9827.1	chr1	182517553	182517563	-	1	NA	promoter-TSS (NM_009794)	promoter-TSS (NM_009794)	-75	NM_009794	12334	Mm.19306	NM_009794	ENSMUSG00000026509	Capn2	AI326419|Capa-2|Capa2|m-calpain|m-calpin	calpain 2	protein-coding
mm_86389.1	chr9	123940203	123940220	-	1	NA	Intergenic	Intergenic	28481	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_43749.1	chr5	140419249	140419377	+	1	NA	promoter-TSS (NM_133916)	promoter-TSS (NM_133916)	8	NM_133916	27979	Mm.21671	NM_133916	ENSMUSG00000056076	Eif3b	AL033316|AL033334|AL033369|AW208965|D5Wsu45e|EIF3-ETA|EIF3-P110|EIF3-P116|Eif3s9|PRT1	eukaryotic translation initiation factor 3, subunit B	protein-coding
mm_142035.1	chr17	35258090	35258103	-	1	NA	Intergenic	Intergenic	-4998	NM_010380	14964	Mm.439675	NM_010380	ENSMUSG00000073411	H2-D1	H-2D|H2-D	histocompatibility 2, D region locus 1	protein-coding
mm_29822.1	chr3	129531997	129531999	-	1	NA	promoter-TSS (NM_130450)	promoter-TSS (NM_130450)	-388	NM_130450	170439	Mm.314113	NM_130450	ENSMUSG00000041220	Elovl6	C77826|FAE|LCE	ELOVL family member 6, elongation of long chain fatty acids (yeast)	protein-coding
mm_55575.1	chr6	71396201	71396221	-	1	NA	intron (NM_024288, intron 7 of 8)	intron (NM_024288, intron 7 of 8)	22784	NM_001081110	12525	Mm.1858	NM_009857	ENSMUSG00000053977	Cd8a	BB154331|Ly-2|Ly-35|Ly-B|Lyt-2	CD8 antigen, alpha chain	protein-coding
mm_105502.1	chr11	106160633	106160647	-	1	NA	promoter-TSS (NM_172397)	promoter-TSS (NM_172397)	-498	NM_172397	67803	Mm.21687	NM_172397	ENSMUSG00000040699	Limd2	0610025L06Rik|AI413966	LIM domain containing 2	protein-coding
mm_35584.1	chr4	41745101	41745113	-	1	NA	Intergenic	Intergenic	-3748	NM_001286551	18391	Mm.425181	NM_011014	ENSMUSG00000036078	Sigmar1	Oprs1|Sig1R|sigma1R	sigma non-opioid intracellular receptor 1	protein-coding
mm_140672.1	chr17	12960307	12960386	-	1	NA	intron (NM_009338, intron 1 of 8)	CpG	379	NM_009338	110460	Mm.439711	NM_009338	ENSMUSG00000023832	Acat2	AW742799|Tcp-1x|Tcp1-rs1	acetyl-Coenzyme A acetyltransferase 2	protein-coding
mm_157235.1	chrX	17251296	17251323	-	1	NA	intron (NM_028916, intron 2 of 14)	intron (NM_028916, intron 2 of 14)	68059	NM_028916	74405	Mm.248531	NM_028916	ENSMUSG00000025038	Efhc2	4933407D04Rik|mRib72-2	EF-hand domain (C-terminal) containing 2	protein-coding
mm_73676.1	chr8	111536493	111536553	+	1	NA	promoter-TSS (NM_133206)	promoter-TSS (NM_133206)	-117	NM_001168622	170737	Mm.271578	NM_133206	ENSMUSG00000033545	Znrf1	B830022L21Rik|Rnf42|Zrfp1|nin283	zinc and ring finger 1	protein-coding
mm_4839.1	chr1	186709470	186709471	+	1	NA	Intergenic	B4A|SINE|B4	-3481	NM_001329107	21808	Mm.18213	NM_009367	ENSMUSG00000039239	Tgfb2	BB105277|Tgf-beta2|Tgfb-2	transforming growth factor, beta 2	protein-coding
mm_79208.1	chr9	49002586	49002588	+	1	NA	intron (NM_175482, intron 3 of 23)	B4A|SINE|B4	17202	NM_175482	235323	Mm.21630	NM_175482	ENSMUSG00000032267	Usp28	9830148O20Rik|AU022237|mKIAA1515	ubiquitin specific peptidase 28	protein-coding
mm_2198.1	chr1	89455305	89455308	+	1	NA	5' UTR (NM_178119, exon 1 of 18)	5' UTR (NM_178119, exon 1 of 18)	495	NM_001037136	347722	Mm.291135	NM_178119	ENSMUSG00000055013	Agap1	Centg2|Ggap1|R75364|mKIAA1099	ArfGAP with GTPase domain, ankyrin repeat and PH domain 1	protein-coding
mm_79073.1	chr9	46241471	46241489	+	1	NA	exon (NM_007468, exon 2 of 3)	exon (NM_007468, exon 2 of 3)	636	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_7718.1	chr1	130661525	130661539	-	1	NA	promoter-TSS (NM_007576)	promoter-TSS (NM_007576)	86	NM_007576	12269	Mm.306720	NM_007576	ENSMUSG00000026405	C4bp	AI195242|C4bpa	complement component 4 binding protein	protein-coding
mm_40455.1	chr5	53604118	53604137	+	1	NA	intron (NM_001277116, intron 3 of 12)	intron (NM_001277116, intron 3 of 12)	13641	NM_001080927	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_29270.1	chr3	107460238	107460313	-	1	NA	Intergenic	CpG	-1377	NM_145922	99738	Mm.101976	NM_145922	ENSMUSG00000027895	Kcnc4	AI850292|KSHIIIC|Kcr2-4|Kv3.4	potassium voltage gated channel, Shaw-related subfamily, member 4	protein-coding
mm_7214.1	chr1	93160193	93160203	-	1	NA	5' UTR (NM_001159940, exon 2 of 6)	5' UTR (NM_001159940, exon 2 of 6)	672	NM_001159940	71874	Mm.158766	NM_172411	ENSMUSG00000034159	2310007B03Rik	-	RIKEN cDNA 2310007B03 gene	protein-coding
mm_84291.1	chr9	63223148	63223163	-	1	NA	intron (NM_011840, intron 17 of 21)	intron (NM_011840, intron 17 of 21)	-74194	NM_001163758	207667	Mm.36349	NM_172446	ENSMUSG00000022245	Skor1	AV273001|C230094B15Rik|Corl1|Lbxcor1	SKI family transcriptional corepressor 1	protein-coding
mm_41651.1	chr5	98254242	98254255	+	1	NA	promoter-TSS (NM_001277268)	promoter-TSS (NM_001277268)	64	NM_001277268	14176	Mm.5055	NM_010203	ENSMUSG00000029337	Fgf5	Fgf-5|HBGF-5|angora|go	fibroblast growth factor 5	protein-coding
mm_47577.1	chr5	124531309	124531393	-	1	NA	promoter-TSS (NM_021430)	promoter-TSS (NM_021430)	40	NM_021430	75695	Mm.41180	NM_021430	ENSMUSG00000029392	Rilpl1	2900002H16Rik|6330559I19Rik|GOSPEL	Rab interacting lysosomal protein-like 1	protein-coding
mm_97597.1	chr11	78949059	78949074	+	1	NA	intron (NM_001313921, intron 16 of 25)	intron (NM_001313921, intron 16 of 25)	23775	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_168523.1	chr11	58267677	58267692	+	1	NA	Intergenic	MLTR25A|LTR|ERVK	-39385	NM_182996	103836	Mm.41440	NM_182996	ENSMUSG00000037243	Zfp692	AI746306|AI839920|Zfp692-ps|Znf692	zinc finger protein 692	protein-coding
mm_131380.1	chr16	14100036	14100046	+	1	NA	3' UTR (NM_144518, exon 6 of 6)	3' UTR (NM_144518, exon 6 of 6)	59233	NM_001081154	223989	Mm.85442	NM_001081154	ENSMUSG00000060657	Marf1	4921513D23Rik|BC031575|C87306|E030019O05|Lkap|mKIAA0430	meiosis arrest female 1	protein-coding
mm_164240.1	chr15	93611780	93611785	+	1	NA	Intergenic	Intergenic	-15891	NM_001033217	106042	Mm.150314	NM_001033217	ENSMUSG00000036158	Prickle1	1110058P22Rik|AW215793|Prickle|b2b019Clo|mpk1	prickle planar cell polarity protein 1	protein-coding
mm_75780.1	chr8	69996369	69996388	-	1	NA	promoter-TSS (NM_001286450)	promoter-TSS (NM_001286450)	6	NM_001286450	234366	Mm.270044	NM_145596	ENSMUSG00000036180	Gatad2a	1110066C11Rik|BC031407|C80248	GATA zinc finger domain containing 2A	protein-coding
mm_135400.1	chr16	44558880	44558905	-	1	NA	promoter-TSS (NR_037242)	promoter-TSS (NR_037242)	-22	NM_172506	117606	Mm.41561	NM_172506	ENSMUSG00000022687	Boc	4732455C11|mFLJ00376	biregional cell adhesion molecule-related/down-regulated by oncogenes (Cdon) binding protein	protein-coding
mm_132169.1	chr16	32277649	32277651	+	1	NA	5' UTR (NM_027355, exon 1 of 6)	5' UTR (NM_027355, exon 1 of 6)	189	NM_027355	70238	Mm.228263	NM_027355	ENSMUSG00000014074	Rnf168	3110001H15Rik	ring finger protein 168	protein-coding
mm_74764.1	chr8	20902467	20902477	-	1	NA	promoter-TSS (NM_001177471)	promoter-TSS (NM_001177471)	-499	NM_001177471	100504014	Mm.490239	NM_001177471	ENSMUSG00000082976	Gm15056	Defb52|OTTMUSG00000018888	predicted gene 15056	protein-coding
mm_106218.1	chr11	117040183	117040200	-	1	NA	Intergenic	Intergenic	-36592	NR_027059	76972	Mm.309167	NR_027059	ENSMUSG00000086859	Snhg20	2810008D09Rik	small nucleolar RNA host gene 20	ncRNA
mm_73651.1	chr8	110940932	110940948	+	1	NA	intron (NM_009179, intron 1 of 6)	intron (NM_009179, intron 1 of 6)	21075	NM_009179	20444	Mm.200388	NM_009179	ENSMUSG00000031749	St3gal2	AI429591|AW822065|ST3GalII|Siat5	ST3 beta-galactoside alpha-2,3-sialyltransferase 2	protein-coding
mm_87215.1	chr10	39823934	39823950	+	1	NA	exon (NM_011264, exon 13 of 32)	exon (NM_011264, exon 13 of 32)	75296	NR_033628	213332	Mm.484359	NR_033628		Mfsd4b4	AA474331	major facilitator superfamily domain containing 4B4	pseudo
mm_72899.1	chr8	90876455	90876467	+	1	NA	intron (NM_177224, intron 2 of 39)	intron (NM_177224, intron 2 of 39)	47626	NM_177224	109151	Mm.100615	NM_177224	ENSMUSG00000056608	Chd9	1810014J18Rik|9030205D12Rik|A330063D19Rik|AD013|PRIC320|mKIAA0308	chromodomain helicase DNA binding protein 9	protein-coding
mm_140377.1	chr17	86997843	86997856	+	1	NA	3' UTR (NM_145491, exon 5 of 5)	3' UTR (NM_145491, exon 5 of 5)	27552	NM_008838	18701	Mm.219685	NM_008838	ENSMUSG00000024145	Pigf	-	phosphatidylinositol glycan anchor biosynthesis, class F	protein-coding
mm_28528.1	chr3	92621239	92621248	-	1	NA	5' UTR (NM_001166172, exon 2 of 3)	5' UTR (NM_001166172, exon 2 of 3)	417	NM_001166172	78382	Mm.235474	NM_001166172	ENSMUSG00000086848	Lce6a	2210420J11Rik	late cornified envelope 6A	protein-coding
mm_13784.1	chr2	118786091	118786097	+	1	NA	exon (NM_170593, exon 2 of 8)	exon (NM_170593, exon 2 of 8)	6375	NM_170593	214240	Mm.221499	NM_170593	ENSMUSG00000040035	Disp2	AI840597|B230210L08Rik|DispB|mKIAA1742	dispatched RND tramsporter family member 2	protein-coding
mm_168068.1	chr10	105238365	105238367	+	1	NA	intron (NM_177368, intron 11 of 11)	LSU-rRNA_Hsa|rRNA|rRNA	336113	NM_177368	278279	Mm.25225	NM_177368	ENSMUSG00000036019	Tmtc2	8430438D04Rik|D330034A10Rik	transmembrane and tetratricopeptide repeat containing 2	protein-coding
mm_163625.1	chr13	56133345	56133349	+	1	NA	intron (NM_001159514, intron 1 of 8)	intron (NM_001159514, intron 1 of 8)	2203	NM_012015	26914	Mm.283802	NM_012015	ENSMUSG00000015937	H2afy	H2AF12M|mH2a1|macroH2A1	H2A histone family, member Y	protein-coding
mm_58853.1	chr7	16876985	16876986	+	1	NA	intron (NM_001081655, intron 1 of 3)	intron (NM_001081655, intron 1 of 3)	1668	NM_001081655	629378	Mm.491123	NM_001081655	ENSMUSG00000078794	Dact3	EG666671|naa-3	dishevelled-binding antagonist of beta-catenin 3	protein-coding
mm_156678.1	chrX	159337961	159337978	+	1	NA	exon (NM_148945, exon 14 of 22)	exon (NM_148945, exon 14 of 22)	-34226	NM_025437	66235	Mm.294623	NM_025437	ENSMUSG00000067194	Eif1ax	1500010B24Rik|AI426898|Eif1ay	eukaryotic translation initiation factor 1A, X-linked	protein-coding
mm_57679.1	chr6	128502201	128502207	-	1	NA	exon (NM_007376, exon 16 of 36)	exon (NM_007376, exon 16 of 36)	24516	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_159387.1	chr3	92250675	92250675	+	1	NA	promoter-TSS (NM_011468).2	promoter-TSS (NM_011468).2	28	NM_011468	20755	Mm.6853	NM_011468	ENSMUSG00000078664	Sprr2a1	Sprr2a|Sprr2a3	small proline-rich protein 2A1	protein-coding
mm_103310.1	chr11	73094325	73094342	-	1	NA	intron (NM_172944, intron 1 of 25)	intron (NM_172944, intron 1 of 25)	3738	NM_008399	16407	Mm.96	NM_008399	ENSMUSG00000005947	Itgae	A530055J10|CD103|aM290|alpha-E1|alpha-M290	integrin alpha E, epithelial-associated	protein-coding
mm_88595.1	chr10	79777290	79777298	+	1	NA	promoter-TSS (NM_031380)	promoter-TSS (NM_031380)	20	NM_031380	83554	Mm.251710	NM_031380	ENSMUSG00000020325	Fstl3	E030038F23Rik|Flrg	follistatin-like 3	protein-coding
mm_82956.1	chr9	35570404	35570420	-	1	NA	promoter-TSS (NM_029762)	promoter-TSS (NM_029762)	-343	NM_029762	76832	Mm.482285	NM_029762	ENSMUSG00000050555	Hyls1	3010015K02Rik	hydrolethalus syndrome 1	protein-coding
mm_41980.1	chr5	107497875	107497885	+	1	NA	intron (NM_001168557, intron 1 of 5)	intron (NM_001168557, intron 1 of 5)	101	NM_001168557	231570	Mm.261891	NM_001007574	ENSMUSG00000044060	A830010M20Rik	AI849226|Kiaa1107|mKIAA1107	RIKEN cDNA A830010M20 gene	protein-coding
mm_39044.1	chr4	152448733	152448750	-	1	NA	5' UTR (NM_001252656, exon 1 of 16)	5' UTR (NM_001252656, exon 1 of 16)	114	NM_001252655	16498	Mm.388924	NM_010598	ENSMUSG00000028931	Kcnab2	F5|I2rf5|Kcnb3|kv-beta-2	potassium voltage-gated channel, shaker-related subfamily, beta member 2	protein-coding
mm_83783.1	chr9	52164566	52164576	-	1	NA	intron (NM_001162921, intron 1 of 5)	RSINE1|SINE|B4	3540	NM_001162921	244871	Mm.295686	NM_001162921	ENSMUSG00000035164	Zc3h12c	A230108E06|C230027N18Rik|mKIAA1726	zinc finger CCCH type containing 12C	protein-coding
mm_17776.1	chr2	32847248	32847258	-	1	NA	promoter-TSS (NM_001113569)	promoter-TSS (NM_001113569)	-16	NM_001113569	20910	Mm.278865	NM_009295	ENSMUSG00000026797	Stxbp1	AI317162|AI326233|MMS10-G|Ms10g|Munc-18a|Munc18-1|N-sec1|Rb-sec1|Sxtbp1|Unc18-1|Unc18h|nsec1	syntaxin binding protein 1	protein-coding
mm_112307.1	chr12	114812799	114812805	-	1	NA	Intergenic	Intergenic	-299108	NR_106063	102465664		NR_106063	ENSMUSG00000098357	Mir7094-2	Gm27508|mmu-mir-7094-2	microRNA 7094-2	ncRNA
mm_45735.1	chr5	86373538	86373567	-	1	NA	promoter-TSS (NM_145561)	promoter-TSS (NM_145561)	-165	NM_145561	231382	Mm.240139	NM_145561	ENSMUSG00000061259	Tmprss11d	AST|AsP|BC020151	transmembrane protease, serine 11d	protein-coding
mm_89531.1	chr10	94499070	94499077	+	1	NA	Intergenic	Intergenic	-15784	NM_172051	319880	Mm.23047	NM_172051	ENSMUSG00000020023	Tmcc3	AW488095|C630016B22Rik|C88213|Tmcc1	transmembrane and coiled coil domains 3	protein-coding
mm_8059.1	chr1	135375234	135375245	-	1	NA	promoter-TSS (NM_175259)	promoter-TSS (NM_175259)	-176	NM_175259	77552	Mm.41407	NM_175259	ENSMUSG00000041889	Shisa4	9330132O05Rik|Tmem58|mShisa4	shisa family member 4	protein-coding
mm_40900.1	chr5	75163795	75163805	+	1	NA	exon (NM_001083316, exon 3 of 23)	exon (NM_001083316, exon 3 of 23)	7634	NM_001083316	18595	Mm.221403	NM_011058	ENSMUSG00000029231	Pdgfra	AI115593|CD140a|Pdgfr-2	platelet derived growth factor receptor, alpha polypeptide	protein-coding
mm_25195.1	chr3	103771911	103771918	+	1	NA	intron (NM_001301304, intron 2 of 15)	intron (NM_001301304, intron 2 of 15)	19361	NM_001301306	15257	Mm.20827	NM_010432	ENSMUSG00000008730	Hipk1	1110062K04Rik|Myak	homeodomain interacting protein kinase 1	protein-coding
mm_140554.1	chr17	7765340	7765356	-	1	NA	exon (NM_001081416, exon 11 of 20)	exon (NM_001081416, exon 11 of 20)	39626	NM_001081416	68655	Mm.379161	NM_001081416	ENSMUSG00000071984	Fndc1	1110027O12Rik|1110051A18Rik|mKIAA1866	fibronectin type III domain containing 1	protein-coding
mm_37212.1	chr4	117887280	117887290	-	1	NA	promoter-TSS (NM_033617)	promoter-TSS (NM_033617)	44	NM_033617	114143	Mm.207052	NM_033617	ENSMUSG00000033379	Atp6v0b	2310024H13Rik|Atp6f|VMA16	ATPase, H+ transporting, lysosomal V0 subunit B	protein-coding
mm_27811.1	chr3	78594423	78594434	-	1	NA	Intergenic	Intergenic	550459	NM_001310536	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_80605.1	chr9	86743249	86743281	+	1	NA	promoter-TSS (NM_178738)	promoter-TSS (NM_178738)	-368	NM_178738	244954	Mm.257629	NM_178738	ENSMUSG00000033491	Prss35	6030424L22Rik|P3D9	protease, serine 35	protein-coding
mm_114056.1	chr13	54371357	54371387	+	1	NA	promoter-TSS (NM_009946)	promoter-TSS (NM_009946)	23	NM_009946	12890	Mm.268902	NM_009946	ENSMUSG00000025867	Cplx2	921-L|AI413745|AW492120	complexin 2	protein-coding
mm_60294.1	chr7	44014833	44014847	+	1	NA	exon (NM_010644, exon 2 of 5)	exon (NM_010644, exon 2 of 5)	2143	NM_010115	13647	Mm.439663	NM_010115		Egfbp2	Egfbp-2|Klk1b26|mGk-13	epidermal growth factor binding protein type B	protein-coding
mm_90505.1	chr10	128039409	128039421	+	1	NA	exon (NM_001113199, exon 3 of 9)	exon (NM_001113199, exon 3 of 9)	4069	NM_001113199	17938	Mm.3746	NM_013608	ENSMUSG00000061315	Naca	AL022831|AL024382|Gm1878|mKIAA0363|skNAC	nascent polypeptide-associated complex alpha polypeptide	protein-coding
mm_27239.1	chr3	36521810	36521820	-	1	NA	promoter-TSS (NR_040411)	promoter-TSS (NR_040411)	-370	NR_040411	100503068	Mm.389423	NR_040411	ENSMUSG00000085007	Gm11549	OTTMUSG00000002111	predicted gene 11549	ncRNA
mm_19507.1	chr2	93849779	93849836	-	1	NA	promoter-TSS (NM_183220)	promoter-TSS (NM_183220)	-8	NM_183220	329470	Mm.486910	NM_183220	ENSMUSG00000040272	Accs	2610203E10Rik|Phacs	1-aminocyclopropane-1-carboxylate synthase (non-functional)	protein-coding
mm_60597.1	chr7	44497243	44497253	+	1	NA	promoter-TSS (NM_197991)	promoter-TSS (NM_197991)	660	NM_028169	75538	Mm.258841	NM_028169	ENSMUSG00000051113	Fam71e1	0610007G24Rik|1700021N13Rik|1700021P22Rik|GARI-L5	family with sequence similarity 71, member E1	protein-coding
mm_59510.1	chr7	27575730	27575748	+	1	NA	intron (NM_175107, intron 8 of 9)	intron (NM_175107, intron 8 of 9)	15263	NM_001122767	66367	Mm.29831	NM_175107	ENSMUSG00000049643	2310022A10Rik	-	RIKEN cDNA 2310022A10 gene	protein-coding
mm_76397.1	chr8	84844596	84844633	-	1	NA	exon (NM_007591, exon 5 of 9)	exon (NM_007591, exon 5 of 9)	2317	NM_007591	12317	Mm.1971	NM_007591	ENSMUSG00000003814	Calr	CRT|Calregulin	calreticulin	protein-coding
mm_151023.1	chr19	46863904	46863922	+	1	NA	intron (NM_033569, intron 4 of 7)	PB1D10|SINE|Alu	98438	NM_029810	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_30645.1	chr4	8837729	8837754	+	1	NA	intron (NM_001277149, intron 15 of 37)	intron (NM_001277149, intron 15 of 37)	147335	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_17975.1	chr2	37661161	37661164	-	1	NA	Intergenic	PB1D9|SINE|Alu	-13877	NM_009261	20744	Mm.237095	NM_009261	ENSMUSG00000026915	Strbp	6430510M02Rik|AI852513|C230082I21Rik|C86322|Spnr	spermatid perinuclear RNA binding protein	protein-coding
mm_114342.1	chr13	60762513	60762527	+	1	NA	3' UTR (NM_134062, exon 27 of 27)	3' UTR (NM_134062, exon 27 of 27)	23844	NM_199148	218275	Mm.222427	NM_199148	ENSMUSG00000042243	BC051665	-	cDNA sequence BC051665	protein-coding
mm_73455.1	chr8	106504076	106504078	+	1	NA	Intergenic	B1_Mur2|SINE|Alu	-6775	NM_007665	12560	Mm.4658	NM_007665	ENSMUSG00000061048	Cdh3	AI385538|Cadp|Cdhp|P-cadherin|Pcad	cadherin 3	protein-coding
mm_52188.1	chr6	99665869	99665877	+	1	NA	intron (NM_025829, intron 1 of 6)	intron (NM_025829, intron 1 of 6)	898	NM_025829	66892	Mm.32889	NM_025829	ENSMUSG00000093661	Eif4e3	1300018P11Rik|AI451927|eIF4E-3	eukaryotic translation initiation factor 4E member 3	protein-coding
mm_45988.1	chr5	90498296	90498312	-	1	NA	exon (NM_007423, exon 6 of 15)	exon (NM_007423, exon 6 of 15)	7590	NM_007423	11576	Mm.358570	NM_007423	ENSMUSG00000054932	Afp	-	alpha fetoprotein	protein-coding
mm_54600.1	chr6	38306686	38306692	-	1	NA	3' UTR (NM_001347122, exon 13 of 13)	3' UTR (NM_001347122, exon 13 of 13)	-7430	NM_172467	209032	Mm.101389	NM_172467	ENSMUSG00000047749	Zc3hav1l	B130055L09Rik|E430016P22Rik	zinc finger CCCH-type, antiviral 1-like	protein-coding
mm_40124.1	chr5	34989698	34989719	+	1	NA	intron (NM_173402, intron 3 of 16)	intron (NM_173402, intron 3 of 16)	-9370	NM_001163512	71729	Mm.196208	NM_173402	ENSMUSG00000029101	Rgs12	1200016K18Rik|4632412M04Rik|AI481290|E130309H11	regulator of G-protein signaling 12	protein-coding
mm_67769.1	chr7	95193800	95193800	-	1	NA	Intergenic	Intergenic	-977444	NM_001310762	23966	Mm.254610	NM_011858	ENSMUSG00000048078	Tenm4	Doc4|ELM2|Odz4|R75022|Ten-m4|l(7)-3Rn|l7Rn3|mKIAA1302	teneurin transmembrane protein 4	protein-coding
mm_132397.1	chr16	35001109	35001130	+	1	NA	3' UTR (NM_139300, exon 32 of 32)	3' UTR (NM_139300, exon 32 of 32)	-21302	NM_023587	70757	Mm.27286	NM_023587	ENSMUSG00000035376	Hacd2	6330408J20Rik|AI255777|AI481689|Hcad2|Ptplb	3-hydroxyacyl-CoA dehydratase 2	protein-coding
mm_69788.1	chr7	141096712	141096768	-	1	NA	intron (NM_023059, intron 1 of 9)	intron (NM_023059, intron 1 of 9)	3806	NM_023059	24058	Mm.38017	NM_023059	ENSMUSG00000025494	Sigirr	AI256711|TIR8	single immunoglobulin and toll-interleukin 1 receptor (TIR) domain	protein-coding
mm_92533.1	chr10	79587086	79587093	-	1	NA	promoter-TSS (NM_199226)	promoter-TSS (NM_199226)	47	NM_199226	21830	Mm.89197	NM_011583	ENSMUSG00000020317	Theg	-	testicular haploid expressed gene	protein-coding
mm_95287.1	chr11	45979316	45979322	+	1	NA	promoter-TSS (NM_173384)	promoter-TSS (NM_173384)	-991	NM_173384	214105	Mm.66708	NM_173384	ENSMUSG00000040489	Sox30	-	SRY (sex determining region Y)-box 30	protein-coding
mm_166984.1	chr7	45699912	45699927	+	1	NA	promoter-TSS (NM_009800)	promoter-TSS (NM_009800)	-48	NM_009800	12348	Mm.27736	NM_009800	ENSMUSG00000003273	Car11	Ca11	carbonic anhydrase 11	protein-coding
mm_154169.1	chr19	58730001	58730017	-	1	NA	exon (NM_018874, exon 3 of 13)	exon (NM_018874, exon 3 of 13)	1122	NM_018874	18946	Mm.10753	NM_018874	ENSMUSG00000042179	Pnliprp1	Plrp1	pancreatic lipase related protein 1	protein-coding
mm_5295.1	chr1	21256187	21256216	-	1	NA	intron (NM_001288617, intron 3 of 7)	intron (NM_001288617, intron 3 of 7)	15616	NM_010356	14859	Mm.394593	NM_010356	ENSMUSG00000025934	Gsta3	Gst2-3	glutathione S-transferase, alpha 3	protein-coding
mm_9257.1	chr1	171602014	171602036	-	1	NA	exon (NM_001277968, exon 2 of 9)	exon (NM_001277968, exon 2 of 9)	5309	NR_102726	17085	Mm.560	NM_008534	ENSMUSG00000004707	Ly9	AI893573|CD229|Lgp100|Ly-9|SLAMF3|T100	lymphocyte antigen 9	protein-coding
mm_124079.1	chr14	78644424	78644436	-	1	NA	promoter-TSS (NR_104044)	promoter-TSS (NR_104044)	21	NR_104044	380921	Mm.89591	NM_001081336	ENSMUSG00000034731	Dgkh	5930402B05Rik|D130015C16|DGK	diacylglycerol kinase, eta	protein-coding
mm_28919.1	chr3	98857968	98857985	-	1	NA	5' UTR (NM_001304800, exon 2 of 4)	5' UTR (NM_001304800, exon 2 of 4)	1818	NM_001304800	15492	Mm.140811	NM_008293	ENSMUSG00000027871	Hsd3b1	3-beta-HSD I|D3Ertd383e	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1	protein-coding
mm_115669.1	chr13	12520055	12520097	-	1	NA	5' UTR (NM_133643, exon 1 of 6)	5' UTR (NM_133643, exon 1 of 6)	374	NM_133643	171211	Mm.159671	NM_133643	ENSMUSG00000095105	Edaradd	1810032E07Rik|5830469M23Rik|A630043P06|cr	EDAR (ectodysplasin-A receptor)-associated death domain	protein-coding
mm_84437.1	chr9	66094107	66094116	-	1	NA	intron (NM_019727, intron 10 of 14)	intron (NM_019727, intron 10 of 14)	-24380	NM_001025612	382083	Mm.477103	NM_001025612	ENSMUSG00000039452	Snx22	Gm1120	sorting nexin 22	protein-coding
mm_78266.1	chr9	21955772	21955799	+	1	NA	promoter-TSS (NM_025870)	promoter-TSS (NM_025870)	32	NM_025870	66962	Mm.46647	NM_025870	ENSMUSG00000051238	Swsap1	2310047B19Rik	SWIM type zinc finger 7 associated protein 1	protein-coding
mm_62953.1	chr7	119607015	119607029	+	1	NA	Intergenic	Intergenic	-10806	NM_054094	117147	Mm.427560	NM_054094	ENSMUSG00000033533	Acsm1	Acas3|Bucs1|Macs	acyl-CoA synthetase medium-chain family member 1	protein-coding
mm_19179.1	chr2	84389756	84389765	-	1	NA	intron (NM_018782, intron 2 of 15)	intron (NM_018782, intron 2 of 15)	35506	NM_018782	54598	Mm.75467	NM_018782	ENSMUSG00000059588	Calcrl	AV071593|CRLR	calcitonin receptor-like	protein-coding
mm_138820.1	chr17	39847595	39847614	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	4607	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_92292.1	chr10	71980683	71980718	-	1	NA	promoter-TSS (NR_003644)	promoter-TSS (NR_003644)	-10	NR_003644	108950	Mm.212793	NM_175390	ENSMUSG00000043859	1700049L16Rik	-	hematological and neurological expressed 1-like pseudogene	pseudo
mm_42967.1	chr5	123136640	123136672	+	1	NA	Intergenic	Intergenic	-4027	NM_175092	23912	Mm.253876	NM_175092	ENSMUSG00000029449	Rhof	AI845056|AV026554|Arhf|Ifld1|Rif	ras homolog family member F (in filopodia)	protein-coding
mm_66544.1	chr7	45189795	45189809	-	1	NA	intron (NM_201374, intron 10 of 19)	intron (NM_201374, intron 10 of 19)	8807	NM_053256	114640	Mm.207078	NM_053256	ENSMUSG00000038300	Pth2	Tifp39|Tip39	parathyroid hormone 2	protein-coding
mm_149183.1	chr19	9899670	9899692	+	1	NA	promoter-TSS (NM_016692)	promoter-TSS (NM_016692)	-148	NM_016692	16319	Mm.29755	NM_016692	ENSMUSG00000024660	Incenp	2700067E22Rik|AU019509|C130081E20|C77457	inner centromere protein	protein-coding
mm_134583.1	chr16	20412797	20412799	-	1	NA	intron (NM_176839, intron 2 of 6)	URR1B|DNA|hAT-Charlie	13596	NM_013790	27416	Mm.20845	NM_013790	ENSMUSG00000022822	Abcc5	2900011L11Rik|AI132311|Abcc5a|Abcc5b|Mrp5	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	protein-coding
mm_69328.1	chr7	128739633	128739637	-	1	NA	intron (NM_145955, intron 1 of 15)	intron (NM_145955, intron 1 of 15)	794	NM_145955	210711	Mm.58882	NM_145955	ENSMUSG00000048170	Mcmbp	1110007A13Rik|AU017382|BC025641|MCM-BP	minichromosome maintenance complex binding protein	protein-coding
mm_60669.1	chr7	45017944	45017946	+	1	NA	promoter-TSS (NM_009101)	promoter-TSS (NM_009101)	-62	NM_009101	20130	Mm.389894	NM_009101	ENSMUSG00000038387	Rras	AI573426	related RAS viral (r-ras) oncogene	protein-coding
mm_76960.1	chr8	106107217	106107241	-	1	NA	intron (NM_010901, intron 8 of 9)	PB1D10|SINE|Alu	-28171	NR_040345	69771	Mm.393274	NR_040344		1810019D21Rik	-	RIKEN cDNA 1810019D21 gene	ncRNA
mm_11015.1	chr2	26586608	26586664	+	1	NA	promoter-TSS (NM_001164564)	promoter-TSS (NM_001164564)	6	NM_001164564	353156	Mm.268933	NM_178444	ENSMUSG00000026921	Egfl7	VE-statin|Zneu1	EGF-like domain 7	protein-coding
mm_19527.1	chr2	94253509	94253513	-	1	NA	Intergenic	Intergenic	7888	NR_030431	735259		NR_030431	ENSMUSG00000076335	Mir670	Mirn670|mir-670|mmu-mir-670	microRNA 670	ncRNA
mm_139401.1	chr17	52309900	52309904	+	1	NA	Intergenic	Lx9|LINE|L1	-292807	NM_001031811	211468	Mm.399068	NM_001031811	ENSMUSG00000035580	Kcnh8	C130090D05Rik|ELK|ELK1|ELK3|Kv12.1	potassium voltage-gated channel, subfamily H (eag-related), member 8	protein-coding
mm_143358.1	chr17	67298980	67298983	-	1	NA	intron (NM_008984, intron 1 of 30)	intron (NM_008984, intron 1 of 30)	55478	NM_008984	19274	Mm.311809	NM_008984	ENSMUSG00000033278	Ptprm	RPTPmu|mKIAA4044	protein tyrosine phosphatase, receptor type, M	protein-coding
mm_14580.1	chr2	135659686	135659713	+	1	NA	Intergenic	CpG	-76479	NR_015544	320684	Mm.421433	NR_015544	ENSMUSG00000085631	9630028H03Rik	-	RIKEN cDNA 9630028H03 gene	ncRNA
mm_136416.1	chr16	93929465	93929475	-	1	NA	promoter-TSS (NM_001165925)	promoter-TSS (NM_001165925)	97	NM_001165925	56173	Mm.328716	NM_019500	ENSMUSG00000047109	Cldn14	AI851731	claudin 14	protein-coding
mm_85709.1	chr9	108161485	108161485	-	1	NA	intron (NM_007567, intron 1 of 11)	intron (NM_007567, intron 1 of 11)	24630	NR_126077	76873	Mm.436935	NR_126077	ENSMUSG00000102224	4930447F24Rik	-	RIKEN cDNA 4930447F24 gene	ncRNA
mm_147594.1	chr18	56677817	56677822	-	1	NA	Intergenic	Intergenic	-29994	NM_010721	16906	Mm.4105	NM_010721	ENSMUSG00000024590	Lmnb1	-	lamin B1	protein-coding
mm_47932.1	chr5	135078277	135078311	-	1	NA	promoter-TSS (NM_177574)	promoter-TSS (NM_177574)	-28	NM_001199677	194309	Mm.44356	NM_177574	ENSMUSG00000043614	Vps37d	Wbscr24	vacuolar protein sorting 37D	protein-coding
mm_167869.1	chrX	33416515	33416541	-	1	NA	Intergenic	L1Md_F2|LINE|L1	103190	NM_001099333	100040606	Mm.460713	NM_001099333	ENSMUSG00000101500	Btbd35f12	Gm2863	BTB domain containing 35, family member 12	protein-coding
mm_6296.1	chr1	71048117	71048120	-	1	NA	intron (NM_007525, intron 7 of 10)	intron (NM_007525, intron 7 of 10)	54854	NM_007525	12021	Mm.10764	NM_007525	ENSMUSG00000026196	Bard1	ENSMUSG00000060893|ENSMUSG00000073653	BRCA1 associated RING domain 1	protein-coding
mm_146081.1	chr18	70622594	70622623	+	1	NA	exon (NM_010773, exon 6 of 7)	exon (NM_010773, exon 6 of 7)	54316	NM_010773	17191	Mm.322	NM_010773	ENSMUSG00000024513	Mbd2	MBD2a	methyl-CpG binding domain protein 2	protein-coding
mm_1189.1	chr1	62703333	62703351	+	1	NA	promoter-TSS (NM_001077407)	promoter-TSS (NM_001077407)	25	NM_001077405	18187	Mm.266341	NM_010939	ENSMUSG00000025969	Nrp2	1110048P06Rik|Np-2|Np2|Npn-2|Npn2	neuropilin 2	protein-coding
mm_122648.1	chr14	51908367	51908391	-	1	NA	exon (NM_001145959, exon 8 of 15)	exon (NM_001145959, exon 8 of 15)	5109	NM_001145959	29811	Mm.26722	NM_013864	ENSMUSG00000004558	Ndrg2	AI182517|AU040374|Ndr2|SYLD	N-myc downstream regulated gene 2	protein-coding
mm_52896.1	chr6	122635572	122635610	+	1	NA	Intergenic	Intergenic	9167	NM_139218	73708	Mm.27982	NM_139218	ENSMUSG00000046323	Dppa3	2410075G02Rik|PCG7|PGC7|Stella	developmental pluripotency-associated 3	protein-coding
mm_162137.1	chrX	73673436	73673436	+	1	NA	5' UTR (NM_001142809, exon 1 of 13)	5' UTR (NM_001142809, exon 1 of 13)	303	NM_001142809	102857	Mm.274553	NM_133987	ENSMUSG00000019558	Slc6a8	AA589632|CRT|CRTR|CT1|CTR5|Creat	solute carrier family 6 (neurotransmitter transporter, creatine), member 8	protein-coding
mm_113036.1	chr13	23544459	23544476	+	1	NA	5' UTR (NM_013548, exon 1 of 1)	5' UTR (NM_013548, exon 1 of 1)	415	NM_013548	260423	Mm.221389	NM_013548	ENSMUSG00000100210	Hist1h3f	H3.2-221|Hist1	histone cluster 1, H3f	protein-coding
mm_94171.1	chr10	128804456	128804470	-	1	NA	promoter-TSS (NM_178066)	promoter-TSS (NM_178066)	-93	NM_178066	73827	Mm.24630	NM_178066	ENSMUSG00000047090	Tmem198b	1110012D08Rik	transmembrane protein 198b	protein-coding
mm_135751.1	chr16	55940733	55940735	-	1	NA	Intergenic	Intergenic	-5886	NM_001159365	74201	Mm.178427	NM_028815	ENSMUSG00000022604	Cep97	2810403B08Rik|4932439K18Rik|AA437768|E130116N02Rik|Lrriq2	centrosomal protein 97	protein-coding
mm_54960.1	chr6	48708175	48708203	-	1	NA	promoter-TSS (NM_153175)	promoter-TSS (NM_153175)	55	NM_153175	231931	Mm.321047	NM_153175	ENSMUSG00000047867	Gimap6	4833419H03Rik|Ian6|mFLJ00102	GTPase, IMAP family member 6	protein-coding
mm_23850.1	chr3	83008494	83008504	+	1	NA	exon (NM_133862, exon 3 of 10)	exon (NM_133862, exon 3 of 10)	775	NM_001317105	99571	Mm.16422	NM_133862	ENSMUSG00000033860	Fgg	3010002H13Rik|AI256424	fibrinogen gamma chain	protein-coding
mm_138038.1	chr17	33919863	33919877	+	1	NA	TTS (NM_020625)	TTS (NM_020625)	392	NM_009318	21356	Mm.154457	NM_009318	ENSMUSG00000024308	Tapbp	D17Wsu91e|TPN	TAP binding protein	protein-coding
mm_89291.1	chr10	87903967	87903991	+	1	NA	intron (NM_001314010, intron 3 of 4)	intron (NM_001314010, intron 3 of 4)	42868	NM_001111276	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_122967.1	chr14	54974038	54974050	-	1	NA	exon (NM_080728, exon 35 of 41)	exon (NM_080728, exon 35 of 41)	1732	NR_030607	100124433		NR_030607	ENSMUSG00000077928	Mir208b	Mirn208b|mir-208b	microRNA 208b	ncRNA
mm_101353.1	chr11	23739870	23739877	-	1	NA	Intergenic	Intergenic	31097	NM_009044	19696	Mm.4869	NM_009044	ENSMUSG00000020275	Rel	c-Rel	reticuloendotheliosis oncogene	protein-coding
mm_6476.1	chr1	74069880	74069888	-	1	NA	intron (NM_027884, intron 2 of 34)	intron (NM_027884, intron 2 of 34)	54563	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_87109.1	chr10	33197718	33197729	+	1	NA	intron (NM_029726, intron 8 of 37)	intron (NM_029726, intron 8 of 37)	58634	NR_040657	442820	Mm.490725	NR_040657		D830005E20Rik	-	RIKEN cDNA D830005E20 gene	ncRNA
mm_31003.1	chr4	40181980	40181994	+	1	NA	intron (NM_007386, intron 11 of 20)	intron (NM_007386, intron 11 of 20)	38722	NM_007386	11428	Mm.331547	NM_007386	ENSMUSG00000028405	Aco1	Aco-1|Irebp|Irp1	aconitase 1	protein-coding
mm_2772.1	chr1	130732042	130732052	+	1	NA	promoter-TSS (NM_177604)	promoter-TSS (NM_177604)	71	NM_177604	212439	Mm.268547	NM_177604	ENSMUSG00000042510	AA986860	E030025M07|Sarg	expressed sequence AA986860	protein-coding
mm_65194.1	chr7	19696756	19696767	-	1	NA	exon (NM_009696, exon 4 of 4)	exon (NM_009696, exon 4 of 4)	1637	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_99255.1	chr11	101155885	101155921	+	1	NA	promoter-TSS (NM_134028)	promoter-TSS (NM_134028)	19	NM_134028	103768	Mm.142348	NM_134028	ENSMUSG00000045007	Tubg2	AI504772|Tubgl	tubulin, gamma 2	protein-coding
mm_160729.1	chr10	76469305	76469305	-	1	NA	promoter-TSS (NM_172550)	promoter-TSS (NM_172550)	-191	NM_172550	216119	Mm.344778	NM_172550	ENSMUSG00000033126	Ybey	1110068N23Rik|A130042E20Rik|C21orf57|ORF57|ORF66	ybeY metallopeptidase	protein-coding
mm_122715.1	chr14	52257800	52257810	-	1	NA	Intergenic	CpG	-20233	NM_201637	67772	Mm.289934	NM_201637	ENSMUSG00000053754	Chd8	5830451P18Rik|AU015341|Duplin|HELSNF1|mKIAA1564	chromodomain helicase DNA binding protein 8	protein-coding
mm_163798.1	chr14	17847411	17847430	+	1	NA	intron (NM_001113417, intron 2 of 9)	intron (NM_001113417, intron 2 of 9)	-134224	NM_009380	21834	Mm.32563	NM_009380	ENSMUSG00000021779	Thrb	Nr1a2|T3R[b]|T3Rbeta|Thrb1|Thrb2|c-erbAbeta	thyroid hormone receptor beta	protein-coding
mm_14258.1	chr2	128190430	128190461	+	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	62870	NM_001284410	12125	Mm.141083	NM_009754	ENSMUSG00000027381	Bcl2l11	1500006F24Rik|Bim|Bod|bcl2-L-11	BCL2-like 11 (apoptosis facilitator)	protein-coding
mm_73123.1	chr8	94780479	94780491	+	1	NA	exon (NM_009142, exon 3 of 3)	exon (NM_009142, exon 3 of 3)	8305	NM_009142	20312	Mm.103711	NM_009142	ENSMUSG00000031778	Cx3cl1	AB030188|ABCD-3|AI848747|CX3C|Cxc3|D8Bwg0439e|Scyd1	chemokine (C-X3-C motif) ligand 1	protein-coding
mm_93974.1	chr10	127323605	127323621	-	1	NA	promoter-TSS (NM_146011)	promoter-TSS (NM_146011)	-114	NM_146011	216445	Mm.227198	NM_146011	ENSMUSG00000040345	Arhgap9	AU043488	Rho GTPase activating protein 9	protein-coding
mm_23160.1	chr3	40531683	40531705	+	1	NA	Intergenic	CpG	-8782	NR_040445	100040882	Mm.272869	NR_040445	ENSMUSG00000037884	1700017G19Rik	-	RIKEN cDNA 1700017G19 gene	ncRNA
mm_152969.1	chr19	29385419	29385425	-	1	NA	3' UTR (NM_021893, exon 7 of 7)	3' UTR (NM_021893, exon 7 of 7)	17984	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_69481.1	chr7	133776741	133776771	-	1	NA	promoter-TSS (NM_025850)	promoter-TSS (NM_025850)	47	NM_001286032	101437	Mm.199223	NM_133941	ENSMUSG00000030986	Dhx32	3110079L04Rik|4732469F02Rik|AA408140|Ddx32	DEAH (Asp-Glu-Ala-His) box polypeptide 32	protein-coding
mm_120756.1	chr14	73363020	73363056	+	1	NA	3' UTR (NM_008410, exon 6 of 6)	3' UTR (NM_008410, exon 6 of 6)	22233	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_71756.1	chr8	65966678	65966695	+	1	NA	intron (NM_001166372, intron 2 of 7)	intron (NM_001166372, intron 2 of 7)	348161	NM_175188	72925	Mm.380457	NM_175188	ENSMUSG00000036469	March1	2900024D24Rik|BB085186	membrane-associated ring finger (C3HC4) 1	protein-coding
mm_95081.1	chr11	32744920	32744935	+	1	NA	3' UTR (NM_134015, exon 14 of 14)	3' UTR (NM_134015, exon 14 of 14)	79667	NM_027050	69351	Mm.65488	NM_027050	ENSMUSG00000020270	Smim23	1700008A04Rik	small integral membrane protein 23	protein-coding
mm_9918.1	chr1	189343343	189343358	-	1	NA	promoter-TSS (NM_001159850)	promoter-TSS (NM_001159850)	3	NM_001159850	16526	Mm.33304	NM_010607	ENSMUSG00000037624	Kcnk2	A430027H14Rik|AI848635|TREK-1	potassium channel, subfamily K, member 2	protein-coding
mm_115813.1	chr13	19697734	19697771	-	1	NA	promoter-TSS (NM_001167909)	promoter-TSS (NM_001167909)	8	NM_001167909	73412	Mm.279939	NM_181591	ENSMUSG00000041138	Nme8	1700056P15Rik|Sptrx-2|Txndc3	NME/NM23 family member 8	protein-coding
mm_10009.1	chr1	191791403	191791403	-	1	NA	Intergenic	Intergenic	-30070	NM_010892	18005	Mm.33773	NM_010892	ENSMUSG00000026622	Nek2	AA617254|C77054	NIMA (never in mitosis gene a)-related expressed kinase 2	protein-coding
mm_35278.1	chr4	19923517	19923532	-	1	NA	promoter-TSS (NM_175406)	promoter-TSS (NM_175406)	-958	NM_175406	242341	Mm.19298	NM_175406	ENSMUSG00000028238	Atp6v0d2	1620401A02Rik|AI324824|V-ATPase	ATPase, H+ transporting, lysosomal V0 subunit D2	protein-coding
mm_28766.1	chr3	95892867	95892877	-	1	NA	promoter-TSS (NM_153513)	promoter-TSS (NM_153513)	-867	NM_153513	229600	Mm.89556	NM_153513	ENSMUSG00000038543	BC028528	L259	cDNA sequence BC028528	protein-coding
mm_102476.1	chr11	60036918	60036992	-	1	NA	promoter-TSS (NM_008819)	promoter-TSS (NM_008819)	50	NM_008819	18618	Mm.2731	NM_008819	ENSMUSG00000000301	Pemt	PEAMT|PEMT2|PLMT|Pempt|Pempt2	phosphatidylethanolamine N-methyltransferase	protein-coding
mm_70258.1	chr8	3515636	3515641	+	1	NA	TTS (NM_053177)	TTS (NM_053177)	254	NM_015801	50767	Mm.23085	NM_015801	ENSMUSG00000004565	Pnpla6	AI661849|MSws|Nte	patatin-like phospholipase domain containing 6	protein-coding
mm_92821.1	chr10	81461350	81461365	-	1	NA	3' UTR (NM_176954, exon 12 of 12)	3' UTR (NM_176954, exon 12 of 12)	11774	NM_001311127	319586	Mm.152689	NM_176954	ENSMUSG00000034818	Celf5	4930565A21Rik|Brunol5	CUGBP, Elav-like family member 5	protein-coding
mm_74913.1	chr8	25306204	25306217	-	1	NA	promoter-TSS (NR_040352)	promoter-TSS (NR_040352)	60	NR_040352	74489	Mm.256468	NR_040352	ENSMUSG00000110140	5430421F17Rik	-	RIKEN cDNA 5430421F17 gene	ncRNA
mm_59576.1	chr7	28117433	28117439	+	1	NA	exon (NM_001122603, exon 18 of 20)	exon (NM_001122603, exon 18 of 20)	-12030	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_139595.1	chr17	57233203	57233231	+	1	NA	Intergenic	Intergenic	-5081	NM_009778	12266	Mm.19131	NM_009778	ENSMUSG00000024164	C3	AI255234|ASP|HSE-MSF|Plp	complement component 3	protein-coding
mm_77615.1	chr8	123895748	123895766	-	1	NA	promoter-TSS (NM_009606)	promoter-TSS (NM_009606)	-982	NM_009606	11459	Mm.214950	NM_009606	ENSMUSG00000031972	Acta1	AA959943|Acta-2|Acts|Actsk-1	actin, alpha 1, skeletal muscle	protein-coding
mm_19150.1	chr2	80580996	80581020	-	1	NA	5' UTR (NM_001290745, exon 1 of 32)	5' UTR (NM_001290745, exon 1 of 32)	174	NM_001290745	50884	Mm.25203	NM_016965	ENSMUSG00000027002	Nckap1	C79304|H19|Hem-2|Hem2|Nap1|mKIAA0587|mh19|p125Nap1	NCK-associated protein 1	protein-coding
mm_79190.1	chr9	48450286	48450294	+	1	NA	Intergenic	Intergenic	-4054	NR_026561	667933	Mm.491076	NR_026561		Gm8884	EG667933	predicted gene 8884	ncRNA
mm_43077.1	chr5	124446940	124446963	+	1	NA	intron (NM_001310727, intron 1 of 6)	intron (NM_001310727, intron 1 of 6)	247	NM_001310727	67956	Mm.137966	NM_030241	ENSMUSG00000049327	Kmt5a	2410195B05Rik|AA617402|AW536475|PR-SET7|PR/SET07|Setd8	lysine methyltransferase 5A	protein-coding
mm_15137.1	chr2	153974704	153974709	+	1	NA	promoter-TSS (NM_001080811)	promoter-TSS (NM_001080811)	-239	NM_001080811	545477	Mm.379973	NM_001080811	ENSMUSG00000078998	Bpifa6	EG545477|Gm5840|Splunc6	BPI fold containing family A, member 6	protein-coding
mm_160825.1	chr11	35798690	35798690	-	1	NA	5' UTR (NM_001004147, exon 1 of 1)	5' UTR (NM_001004147, exon 1 of 1)	194	NM_001004147	237730	Mm.189222	NM_001004147	ENSMUSG00000051062	Fbll1	AI595406	fibrillarin-like 1	protein-coding
mm_100995.1	chr11	8455270	8455291	-	1	NA	intron (NM_001083587, intron 20 of 30)	intron (NM_001083587, intron 20 of 30)	209255	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_77656.1	chr8	124569846	124569867	-	1	NA	promoter-TSS (NM_007428)	promoter-TSS (NM_007428)	-149	NM_007428	11606	Mm.301626	NM_007428	ENSMUSG00000031980	Agt	AI265500|AngI|AngII|Aogen|Serpina8	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	protein-coding
mm_1588.1	chr1	74304289	74304293	+	1	NA	promoter-TSS (NM_027154)	promoter-TSS (NM_027154)	45	NM_027154	69660	Mm.261182	NM_027154	ENSMUSG00000006301	Tmbim1	2310061B02Rik|AA960455|AU024746|C78899|RECS1|Tmbib1|mKIAA4161	transmembrane BAX inhibitor motif containing 1	protein-coding
mm_129094.1	chr15	75929699	75929719	-	1	NA	promoter-TSS (NM_031201)	promoter-TSS (NM_031201)	21	NM_031201	22122	Mm.22596	NM_031201	ENSMUSG00000022570	Tsta3	AI256181|FX|Tstap35b	tissue specific transplantation antigen P35B	protein-coding
mm_110100.1	chr12	25319985	25319992	-	1	NA	Intergenic	MTE2b|LTR|ERVL-MaLR	190814	NR_045844	432641	Mm.112955	NR_045844		Gm17746	-	predicted gene, 17746	ncRNA
mm_41428.1	chr5	90892726	90892735	+	1	NA	3' UTR (NM_008176, exon 4 of 4)	3' UTR (NM_008176, exon 4 of 4)	1485	NM_008176	14825	Mm.21013	NM_008176	ENSMUSG00000029380	Cxcl1	Fsp|Gro1|KC|Mgsa|N51|Scyb1|gro	chemokine (C-X-C motif) ligand 1	protein-coding
mm_24173.1	chr3	88575760	88575770	+	1	NA	Intergenic	RLTR11A2|LTR|ERVK	-3906	NM_025448	66256	Mm.7091	NM_025448	ENSMUSG00000041355	Ssr2	1500032E05Rik|AI315033|AU020133|TLAP|TRAPB|TRAPbeta	signal sequence receptor, beta	protein-coding
mm_113466.1	chr13	36120855	36120863	+	1	NA	intron (NM_001039189, intron 1 of 5)	intron (NM_001039189, intron 1 of 5)	3216	NM_001039189	69955	Mm.70690	NM_024274	ENSMUSG00000021420	Fars2	Fars1|pheRS	phenylalanine-tRNA synthetase 2 (mitochondrial)	protein-coding
mm_128663.1	chr15	60141719	60141731	-	1	NA	Intergenic	Intergenic	-125107	NM_027668	71088	Mm.425950	NM_027668	ENSMUSG00000071749	4933412E24Rik	-	RIKEN cDNA 4933412E24 gene	protein-coding
mm_127351.1	chr15	100619729	100619762	+	1	NA	3' UTR (NM_011873, exon 4 of 4)	3' UTR (NM_011873, exon 4 of 4)	4083	NM_011873	23994	Mm.486175	NM_011873	ENSMUSG00000000346	Dazap2	AI314727|Brbp|Gcap28|Prtb|gt6-12|mKIAA0058	DAZ associated protein 2	protein-coding
mm_73946.1	chr8	120114145	120114176	+	1	NA	promoter-TSS (NM_001163762)	promoter-TSS (NM_001163762)	8	NM_001163761	234797	Mm.101958	NM_172286	ENSMUSG00000031824	6430548M08Rik	AW049007|Kiaa0513|mKIAA0513	RIKEN cDNA 6430548M08 gene	protein-coding
mm_4840.1	chr1	186749369	186749415	+	1	NA	promoter-TSS (NM_026041)	promoter-TSS (NM_026041)	-34	NM_026041	67223	Mm.289841	NM_026041	ENSMUSG00000001305	Rrp15	2810430M08Rik|5430437H21Rik	ribosomal RNA processing 15 homolog (S. cerevisiae)	protein-coding
mm_147854.1	chr18	63692387	63692391	-	1	NA	promoter-TSS (NM_016792)	promoter-TSS (NM_016792)	-30	NM_016792	53382	Mm.19169	NM_016792	ENSMUSG00000024583	Txnl1	32kDa|TRP32|Txnl	thioredoxin-like 1	protein-coding
mm_74313.1	chr8	126594896	126594917	+	1	NA	Intergenic	CpG-14677	-1470	NM_001164598	270110	Mm.334918	NM_001164598	ENSMUSG00000051495	Irf2bp2	E130305N23Rik|IRF-2BP2	interferon regulatory factor 2 binding protein 2	protein-coding
mm_117089.1	chr13	59769530	59769539	-	1	NA	promoter-TSS (NR_015349)	promoter-TSS (NR_015349)	255	NM_026921	69046	Mm.7884	NM_026921	ENSMUSG00000044792	Isca1	1810010A06Rik|Hbld2	iron-sulfur cluster assembly 1	protein-coding
mm_63655.1	chr7	128919473	128919476	+	1	NA	Intergenic	Intergenic	174604	NM_001029982	207352	Mm.297105	NM_001029982	ENSMUSG00000055319	Sec23ip	D7Ertd373e|p125	Sec23 interacting protein	protein-coding
mm_127800.1	chr15	3986833	3986836	-	1	NA	intron (NM_145930, intron 5 of 5)	intron (NM_145930, intron 5 of 5)	-7261	NM_134099	106052	Mm.234191	NM_134099	ENSMUSG00000022184	Fbxo4	1700096C12Rik|AI851261|AW494535|Fbx4	F-box protein 4	protein-coding
mm_92513.1	chr10	78439697	78439711	-	1	NA	3' UTR (NM_172134, exon 11 of 11)	3' UTR (NM_172134, exon 11 of 11)	4905	NR_105837	102465221		NR_105837	ENSMUSG00000098932	Mir6410	Gm27916|mmu-mir-6410	microRNA 6410	ncRNA
mm_66405.1	chr7	44477476	44477483	-	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-7038	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_110863.1	chr12	73546345	73546358	-	1	NA	promoter-TSS (NM_178715)	promoter-TSS (NM_178715)	44	NM_178715	238257	Mm.251196	NM_178715	ENSMUSG00000034435	Tmem30b	9130011B11Rik	transmembrane protein 30B	protein-coding
mm_97408.1	chr11	77953432	77953442	+	1	NA	exon (NM_021286, exon 2 of 17)	exon (NM_021286, exon 2 of 17)	22598	NM_021286	20370	Mm.229330	NM_021286	ENSMUSG00000000632	Sez6	BSRP-C|D11Bhm177e|sez-6	seizure related gene 6	protein-coding
mm_66844.1	chr7	49134275	49134281	-	1	NA	intron (NM_001111016, intron 2 of 38)	intron (NM_001111016, intron 2 of 38)	-111911	NM_175272	78286	Mm.333881	NM_175272	ENSMUSG00000052512	Nav2	5330421F07Rik|AU067780|BQ960892|HELAD1|POMFIL2|RAINB1|RAINB2|Unc53H2|mKIAA3015	neuron navigator 2	protein-coding
mm_34725.1	chr4	152178036	152178044	+	1	NA	promoter-TSS (NM_133348)	promoter-TSS (NM_133348)	-60	NM_133348	70025	Mm.296191	NM_133348	ENSMUSG00000028937	Acot7	2410041A17Rik|Ach1|Act|Bach|CTE-IIa|Cte-II|Lach1	acyl-CoA thioesterase 7	protein-coding
mm_151230.1	chr19	53739240	53739244	+	1	NA	intron (NM_001170847, intron 1 of 13)	intron (NM_001170847, intron 1 of 13)	61936	NM_001170847	73713	Mm.313695	NM_001170847	ENSMUSG00000043639	Rbm20	1110018J23Rik|2010003H22Rik|AI646761	RNA binding motif protein 20	protein-coding
mm_57872.1	chr6	129740469	129740500	-	1	NA	promoter-TSS (NM_177155)	promoter-TSS (NM_177155)	0	NM_177155	320407	Mm.123265	NM_177155	ENSMUSG00000043932	Klri2	A530090P03Rik	killer cell lectin-like receptor family I member 2	protein-coding
mm_166862.1	chr7	24457682	24457685	-	1	NA	Intergenic	Intergenic	-4800	NM_011113	18793	Mm.1359	NM_011113	ENSMUSG00000046223	Plaur	Cd87|u-PAR|uPAR	plasminogen activator, urokinase receptor	protein-coding
mm_130180.1	chr15	93398346	93398352	-	1	NA	promoter-TSS (NM_026025)	promoter-TSS (NM_026025)	-1	NM_001083114	223828	Mm.74208	NM_146062	ENSMUSG00000036167	Pphln1	CR|HSPC206|HSPC232	periphilin 1	protein-coding
mm_60898.1	chr7	46426756	46426757	+	1	NA	intron (NM_008421, intron 1 of 1)	intron (NM_008421, intron 1 of 1)	30288	NM_001112739	16502	Mm.249386	NM_008421	ENSMUSG00000058975	Kcnc1	C230009H10Rik|KShIIIB|KV4|Kcr2-1|Kv3.1|NGK2|Shaw	potassium voltage gated channel, Shaw-related subfamily, member 1	protein-coding
mm_33908.1	chr4	136310992	136311054	+	1	NA	promoter-TSS (NM_001277123)	promoter-TSS (NM_001277123)	81	NM_001277123	74326	Mm.31051	NM_028871	ENSMUSG00000066037	Hnrnpr	2610003J05Rik|2610528B01Rik|Hnrpr	heterogeneous nuclear ribonucleoprotein R	protein-coding
mm_75949.1	chr8	71592471	71592504	-	1	NA	exon (NM_025396, exon 1 of 5)	exon (NM_025396, exon 1 of 5)	303	NM_001294269	66171	Mm.282284	NM_025396	ENSMUSG00000031807	Pgls	1110030K05Rik|AI447866|Plgs	6-phosphogluconolactonase	protein-coding
mm_43368.1	chr5	135416587	135416589	+	1	NA	intron (NM_146001, intron 28 of 30)	B2_Mm2|SINE|B2	-22042	NM_148932	107939	Mm.28399	NM_148932	ENSMUSG00000053293	Pom121	2610027A18Rik|C80273|mKIAA0618	nuclear pore membrane protein 121	protein-coding
mm_152852.1	chr19	24142876	24142886	-	1	NA	intron (NM_011597, intron 1 of 22)	intron (NM_011597, intron 1 of 22)	31259	NM_001198985	21873	Mm.104744	NM_011597	ENSMUSG00000024812	Tjp2	ZO-2	tight junction protein 2	protein-coding
mm_167038.1	chr7	78896009	78896016	+	1	NA	promoter-TSS (NM_001162939)	promoter-TSS (NM_001162939)	85	NM_001162939	68048	Mm.34109	NM_026531	ENSMUSG00000030609	Aen	2700083B06Rik|Isg20l1	apoptosis enhancing nuclease	protein-coding
mm_132086.1	chr16	30599718	30599734	+	1	NA	promoter-TSS (NM_177632)	promoter-TSS (NM_177632)	3	NM_177632	224093	Mm.28244	NM_177632	ENSMUSG00000046546	Fam43a	Tuf1	family with sequence similarity 43, member A	protein-coding
mm_68363.1	chr7	106529159	106529202	-	1	NA	Intergenic	Intergenic	-88107	NR_003967	209380	Mm.461779	NM_001001318		Gm4759	EG209380	GTPase, very large interferon inducible 1 pseudogene	pseudo
mm_39714.1	chr5	27994469	27994474	+	1	NA	Intergenic	Intergenic	-76941	NM_153526	231070	Mm.30221	NM_153526	ENSMUSG00000045294	Insig1	1810013C12Rik|Insig-1	insulin induced gene 1	protein-coding
mm_154644.1	chrX	7789987	7790004	+	1	NA	promoter-TSS (NM_001290455)	promoter-TSS (NM_001290455)	2	NM_207670	54645	Mm.194811	NM_207670	ENSMUSG00000031153	Gripap1	AI854681|DXImx47e|GRASP-1|Sfc10|mKIAA1167	GRIP1 associated protein 1	protein-coding
mm_130559.1	chr15	99251914	99251924	-	1	NA	promoter-TSS (NM_016766)	promoter-TSS (NM_016766)	42	NM_001164156	51812	Mm.383472	NM_016766	ENSMUSG00000037570	Mcrs1	C78274|ICP22BP|MSP58|P78	microspherule protein 1	protein-coding
mm_41074.1	chr5	87669511	87669530	+	1	NA	exon (NM_007784, exon 5 of 34)	exon (NM_007784, exon 5 of 34)	3312	NM_001286016	12990	Mm.427467	NM_007784	ENSMUSG00000070702	Csn1s1	AA959832|AW212882|Csna	casein alpha s1	protein-coding
mm_102789.1	chr11	68446005	68446010	-	1	NA	intron (NM_177320, intron 1 of 18)	intron (NM_177320, intron 1 of 18)	13882	NM_177320	320207	Mm.244960	NM_177320	ENSMUSG00000020901	Pik3r5	AV230647|F730038I15Rik	phosphoinositide-3-kinase, regulatory subunit 5, p101	protein-coding
mm_28301.1	chr3	89213893	89213923	-	1	NA	exon (NM_013604, exon 1 of 8)	exon (NM_013604, exon 1 of 8)	427	NM_001161824	17827	Mm.280943	NM_013604	ENSMUSG00000064068	Mtx1	Gcap6|Mtx	metaxin 1	protein-coding
mm_8686.1	chr1	156940027	156940040	-	1	NA	promoter-TSS (NM_001159968)	promoter-TSS (NM_001159968)	-407	NM_023884	78255	Mm.28376	NM_023884	ENSMUSG00000026594	Ralgps2	1810020P17Rik|2210408F11Rik|4921528G01Rik|9130014M22Rik|AU043409|AW046161	Ral GEF with PH domain and SH3 binding motif 2	protein-coding
mm_69677.1	chr7	139985401	139985416	-	1	NA	exon (NM_001291066, exon 18 of 24)	exon (NM_001291066, exon 18 of 24)	1466	NR_106029	102465643		NR_106029	ENSMUSG00000099092	Mir7062	Gm27339|mmu-mir-7062	microRNA 7062	ncRNA
mm_119590.1	chr14	50944524	50944534	+	1	NA	5' UTR (NM_013632, exon 1 of 6)	5' UTR (NM_013632, exon 1 of 6)	226	NM_013632	18950	Mm.17932	NM_013632	ENSMUSG00000021871	Pnp	AL024301|AU015798|Np|Np-1|Np-2|Pnp1	purine-nucleoside phosphorylase	protein-coding
mm_121530.1	chr14	122280016	122280025	+	1	NA	intron (NM_029556, intron 1 of 7)	intron (NM_029556, intron 1 of 7)	-46382	NR_015532	68245	Mm.443285	NR_015532	ENSMUSG00000100585	1700108J01Rik	-	RIKEN cDNA 1700108J01 gene	ncRNA
mm_151424.1	chr19	56826505	56826513	+	1	NA	intron (NM_031387, intron 1 of 25)	CpG	223	NM_031387	83561	Mm.247541	NM_031387	ENSMUSG00000025081	Tdrd1	MTR-1	tudor domain containing 1	protein-coding
mm_1665.1	chr1	74771763	74771791	+	1	NA	promoter-TSS (NM_009526)	promoter-TSS (NM_009526)	-115	NM_009526	22420	Mm.268282	NM_009526	ENSMUSG00000033227	Wnt6	AA409270|Wnt-6	wingless-type MMTV integration site family, member 6	protein-coding
mm_147826.1	chr18	61930252	61930274	-	1	NA	Intergenic	Intergenic	-18411	NM_001164491	319713	Mm.329478	NM_198649	ENSMUSG00000032735	Ablim3	AW990719|D930036B08Rik	actin binding LIM protein family, member 3	protein-coding
mm_87385.1	chr10	45067036	45067042	+	1	NA	promoter-TSS (NM_011156)	promoter-TSS (NM_011156)	-175	NM_011156	19072	Mm.10281	NM_011156	ENSMUSG00000019849	Prep	AI047692|AI450383|D10Wsu136e|PEP|Pop	prolyl endopeptidase	protein-coding
mm_121797.1	chr14	20112570	20112570	-	1	NA	Intergenic	Intergenic	-29398	NM_026209	67509	Mm.292423	NM_026209	ENSMUSG00000045107	Saysd1	1810063B07Rik|4930488P03Rik	SAYSVFN motif domain containing 1	protein-coding
mm_60400.1	chr7	44475693	44475703	+	1	NA	Intergenic	Intergenic	5351	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_64788.1	chr7	6156167	6156200	-	1	NA	promoter-TSS (NM_001013012)	promoter-TSS (NM_001013012)	-212	NM_001013012	67109	Mm.3254	NM_001013012	ENSMUSG00000046792	Zfp787	2210018M03Rik|Znf787	zinc finger protein 787	protein-coding
mm_90887.1	chr10	10234829	10234837	-	1	NA	Intergenic	Intergenic	237481	NM_001127353	215772	Mm.246573	NM_172547	ENSMUSG00000050994	Adgb	9130014G24Rik	androglobin	protein-coding
mm_77362.1	chr8	119778381	119778431	-	1	NA	promoter-TSS (NM_028883)	promoter-TSS (NM_028883)	10	NM_028883	74347	Mm.358759	NM_028883	ENSMUSG00000034105	Tldc1	4632415K11Rik|Kiaa1609	TBC/LysM associated domain containing 1	protein-coding
mm_721.1	chr1	42699663	42699681	+	1	NA	promoter-TSS (NR_027891)	promoter-TSS (NR_027891)	-664	NR_027891	73100	Mm.467885	NR_027891		2900092D14Rik	-	RIKEN cDNA 2900092D14 gene	ncRNA
mm_27807.1	chr3	75956889	75956959	-	1	NA	promoter-TSS (NM_175193)	promoter-TSS (NM_175193)	25	NM_175193	73124	Mm.249232	NM_175193	ENSMUSG00000034109	Golim4	3110027H23Rik|GIMPC|GPP130|Golph4|P138	golgi integral membrane protein 4	protein-coding
mm_115378.1	chr13	113093964	113094012	+	1	NA	exon (NM_010370, exon 5 of 5)	exon (NM_010370, exon 5 of 5)	6993	NM_010370	14938	Mm.15510	NM_010370	ENSMUSG00000023132	Gzma	AW494114|Ctla-3|Ctla3|Hf|Hf1|SE1|TSP-1|TSP1	granzyme A	protein-coding
mm_63770.1	chr7	131334530	131334565	+	1	NA	promoter-TSS (NM_183272)	promoter-TSS (NM_183272)	-75	NM_183272	68223	Mm.233827	NM_183272	ENSMUSG00000030859	Fam24a	1700063I17Rik	family with sequence similarity 24, member A	protein-coding
mm_8682.1	chr1	156938812	156938853	-	1	NA	intron (NR_027640, intron 1 of 19)	intron (NR_027640, intron 1 of 19)	555	NM_001159966	78255	Mm.28376	NM_023884	ENSMUSG00000026594	Ralgps2	1810020P17Rik|2210408F11Rik|4921528G01Rik|9130014M22Rik|AU043409|AW046161	Ral GEF with PH domain and SH3 binding motif 2	protein-coding
mm_3236.1	chr1	135850713	135850736	+	1	NA	exon (NM_001130176, exon 10 of 13)	exon (NM_001130176, exon 10 of 13)	9863	NM_001130176	21956	Mm.247470	NM_011619	ENSMUSG00000026414	Tnnt2	Tnt|cTnT	troponin T2, cardiac	protein-coding
mm_127759.1	chr15	103514332	103514352	+	1	NA	promoter-TSS (NM_001285890)	promoter-TSS (NM_001285890)	-635	NM_001285890	18574	Mm.390792	NM_008800	ENSMUSG00000022489	Pde1b	Pde1b1	phosphodiesterase 1B, Ca2+-calmodulin dependent	protein-coding
mm_14098.1	chr2	125229553	125229561	+	1	NA	3' UTR (NM_001079690, exon 28 of 28)	3' UTR (NM_001079690, exon 28 of 28)	-17691	NM_001159646	110074	Mm.282499	NM_023595	ENSMUSG00000027203	Dut	5031412I06Rik|5133400F09Rik|D2Bwg0749e|Dutp|dUTPase	deoxyuridine triphosphatase	protein-coding
mm_141988.1	chr17	35165379	35165402	-	1	NA	promoter-TSS (NM_020027)	promoter-TSS (NM_020027)	-513	NM_020027	53761	Mm.272462	NM_020027	ENSMUSG00000024393	Prrc2a	3110039B05Rik|Bat-2|Bat2|D17H6S51E|G2|Wbp12|mKIAA4178	proline-rich coiled-coil 2A	protein-coding
mm_2970.1	chr1	133053301	133053327	+	1	NA	intron (NM_001099276, intron 1 of 32)	intron (NM_001099276, intron 1 of 32)	7302	NM_001099276	240752	Mm.387308	NM_001099276	ENSMUSG00000026447	Pik3c2b	C330011J12Rik|Gm199|PI3K-C2beta|PI3KC2beta	phosphoinositide-3-kinase, class 2, beta polypeptide	protein-coding
mm_130394.1	chr15	97964035	97964077	-	1	NA	promoter-TSS (NM_201359)	promoter-TSS (NM_201359)	-173	NM_201359	380967	Mm.196630	NM_201359	ENSMUSG00000052369	Tmem106c	AI046681|BC046621|D15Ertd405e	transmembrane protein 106C	protein-coding
mm_78737.1	chr9	41586486	41586512	+	1	NA	intron (NR_015483, intron 1 of 1)	intron (NR_015483, intron 1 of 1)	4573	NR_029822	387236		NR_029822	ENSMUSG00000093354	Mir125b-1	Mirn125b|Mirn125b-1|mir-125b-1	microRNA 125b-1	ncRNA
mm_109598.1	chr12	112678783	112678798	+	1	NA	promoter-TSS (NM_001100460)	promoter-TSS (NM_001100460)	-50	NM_001100460	382639	Mm.11350	NM_001100460	ENSMUSG00000037638	Zbtb42	EG382639|Gm5188|simiRP58	zinc finger and BTB domain containing 42	protein-coding
mm_39655.1	chr5	24750898	24750918	+	1	NA	TTS (NM_153076)	TTS (NM_153076)	6935	NM_153076	214301	Mm.63484	NM_153076	ENSMUSG00000038135	Crygn	-	crystallin, gamma N	protein-coding
mm_169783.1	chr16	11144266	11144273	+	1	NA	intron (NR_027502, intron 19 of 22)	LSU-rRNA_Hsa|rRNA|rRNA	-9737	NM_029582	106200	Mm.291015	NM_029582	ENSMUSG00000022498	Txndc11	2810408E11Rik|AI427833|EFP1|Txdc11	thioredoxin domain containing 11	protein-coding
mm_95814.1	chr11	55131657	55131704	+	1	NA	intron (NM_172258, intron 7 of 10)	intron (NM_172258, intron 7 of 10)	20026	NM_172258	215332	Mm.87054	NM_172258	ENSMUSG00000049491	Slc36a3	PAT3|TRAMD2|tramdorin2	solute carrier family 36 (proton/amino acid symporter), member 3	protein-coding
mm_63353.1	chr7	126976548	126976577	+	1	NA	5' UTR (NM_026638, exon 1 of 6)	5' UTR (NM_026638, exon 1 of 6)	648	NM_001347656	52858	Mm.28219	NM_026638	ENSMUSG00000030682	Cdipt	9530042F15Rik|D7Bwg0575e|Pis|Pis1	CDP-diacylglycerol--inositol 3-phosphatidyltransferase (phosphatidylinositol synthase)	protein-coding
mm_148587.1	chr19	5068088	5068098	+	1	NA	promoter-TSS (NM_054042)	promoter-TSS (NM_054042)	15	NM_054042	70445	Mm.29597	NM_054042	ENSMUSG00000056481	Cd248	2610111G01Rik|AI842296|Cd164l1|Tem1	CD248 antigen, endosialin	protein-coding
mm_82427.1	chr9	14903991	14904000	-	1	NA	promoter-TSS (NM_176807)	promoter-TSS (NM_176807)	-44	NM_022888	64931	Mm.86738	NM_022888	ENSMUSG00000031933	Izumo1r	0910001L11Rik|C86255|Folbp3|Folr4|Juno	IZUMO1 receptor, JUNO	protein-coding
mm_81060.1	chr9	106165998	106166009	+	1	NA	Intergenic	RLTR51B_Mm|LTR|ERVK?	-4926	NM_029896	77305	Mm.265125	NM_029896	ENSMUSG00000020257	Wdr82	9430077D24Rik|CDW5/WDR82	WD repeat domain containing 82	protein-coding
mm_48749.1	chr5	147894832	147894838	-	1	NA	promoter-TSS (NM_027872)	promoter-TSS (NM_027872)	-33	NM_027872	71706	Mm.153218	NM_027872	ENSMUSG00000029650	Slc46a3	1200006F02Rik	solute carrier family 46, member 3	protein-coding
mm_76490.1	chr8	85840735	85840780	-	1	NA	promoter-TSS (NM_199446)	promoter-TSS (NM_199446)	192	NM_028007	71927	Mm.61018	NM_028007	ENSMUSG00000031703	Itfg1	2310047C21Rik|AI314457|Cda08|D8Wsu49e	integrin alpha FG-GAP repeat containing 1	protein-coding
mm_102286.1	chr11	55401975	55402003	-	1	NA	exon (NM_009242, exon 6 of 10)	exon (NM_009242, exon 6 of 10)	18091	NM_009242	20692	Mm.291442	NM_009242	ENSMUSG00000018593	Sparc	BM-40|ON	secreted acidic cysteine rich glycoprotein	protein-coding
mm_87323.1	chr10	42860742	42860746	+	1	NA	5' UTR (NM_172938, exon 1 of 9)	5' UTR (NM_172938, exon 1 of 9)	232	NM_172938	268297	Mm.98731	NM_172938	ENSMUSG00000044770	Scml4	9330161D17|mFLJ00197	sex comb on midleg-like 4 (Drosophila)	protein-coding
mm_152788.1	chr19	21461301	21461309	-	1	NA	intron (NM_010266, intron 1 of 13)	L1MB5|LINE|L1	11356	NM_010266	14544	Mm.45054	NM_010266	ENSMUSG00000058624	Gda	AU015411|AW047581|GAH	guanine deaminase	protein-coding
mm_134869.1	chr16	28683595	28683596	-	1	NA	intron (NM_010199, intron 2 of 5)	intron (NM_010199, intron 2 of 5)	69648	NM_010199	14167	Mm.7996	NM_010199	ENSMUSG00000022523	Fgf12	AV114868|B230343J05Rik|FGF-12|FHF-1|Fhf1	fibroblast growth factor 12	protein-coding
mm_69546.1	chr7	135695893	135695914	-	1	NA	exon (NM_001081117, exon 12 of 14)	exon (NM_001081117, exon 12 of 14)	20476	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_118969.1	chr14	27876066	27876104	+	1	NA	intron (NM_177814, intron 3 of 15)	intron (NM_177814, intron 3 of 15)	253678	NM_177814	238988	Mm.318004	NM_177814	ENSMUSG00000040640	Erc2	6430531D06|CAST|CAST1/ERC2|D14Ertd171e|ELKS2alpha	ELKS/RAB6-interacting/CAST family member 2	protein-coding
mm_130448.1	chr15	98533933	98533950	-	1	NA	5' UTR (NM_001289439, exon 1 of 9)	5' UTR (NM_001289439, exon 1 of 9)	328	NM_001289438	69612	Mm.229107	NM_133714	ENSMUSG00000022992	Kansl2	2310037I24Rik|B930009D17	KAT8 regulatory NSL complex subunit 2	protein-coding
mm_82523.1	chr9	20643164	20643196	-	1	NA	promoter-TSS (NM_013911)	promoter-TSS (NM_013911)	-138	NM_025401	66177	Mm.390165	NM_025401	ENSMUSG00000084786	Ubl5	1110030M22Rik|beacon	ubiquitin-like 5	protein-coding
mm_93682.1	chr10	117814911	117814924	-	1	NA	3' UTR (NM_024457, exon 8 of 8)	3' UTR (NM_024457, exon 8 of 8)	-22212	NM_134010	103468	Mm.12568	NM_134010	ENSMUSG00000052798	Nup107	AW541137|C76801	nucleoporin 107	protein-coding
mm_94884.1	chr11	26412097	26412098	+	1	NA	intron (NM_001277273, intron 5 of 13)	intron (NM_001277273, intron 5 of 13)	25013	NR_102382	67030	Mm.18875	NM_025923	ENSMUSG00000004018	Fancl	2010322C19Rik|AW554273|B230118H11Rik|Phf9|Pog|gcd	Fanconi anemia, complementation group L	protein-coding
mm_152474.1	chr19	11017920	11017926	-	1	NA	promoter-TSS (NM_001251849)	promoter-TSS (NM_001251849)	40	NM_001251849	76002	Mm.139320	NM_001251849	ENSMUSG00000094584	Ms4a18	5033428B15Rik	membrane-spanning 4-domains, subfamily A, member 18	protein-coding
mm_135773.1	chr16	56831839	56831861	-	1	NA	intron (NM_019631, intron 1 of 5)	intron (NM_019631, intron 1 of 5)	-35992	NM_172825	239853	Mm.258979	NM_172825	ENSMUSG00000022755	Adgrg7	9130020O16Rik|Gpr128	adhesion G protein-coupled receptor G7	protein-coding
mm_83534.1	chr9	46233100	46233123	-	1	NA	TTS (NM_001289755)	TTS (NM_001289755)	2188	NM_001289833	11814	Mm.390161	NM_023114	ENSMUSG00000032081	Apoc3	apo-CIII|apoC-III	apolipoprotein C-III	protein-coding
mm_168835.1	chr12	23010259	23010268	-	1	NA	promoter-TSS (NR_015504)	promoter-TSS (NR_015504)	-20	NR_015504	69732	Mm.391403	NM_028362	ENSMUSG00000073164	2410018L13Rik	2810480C08Rik	RIKEN cDNA 2410018L13 gene	ncRNA
mm_51897.1	chr6	90619242	90619255	+	1	NA	promoter-TSS (NM_001037493)	promoter-TSS (NM_001037493)	2	NM_001037493	71699	Mm.272633	NM_027868	ENSMUSG00000030089	Slc41a3	1010001P06Rik|AI480742|SLC41A1-L2	solute carrier family 41, member 3	protein-coding
mm_140629.1	chr17	12420452	12420456	-	1	NA	3' UTR (NM_011395, exon 11 of 11)	3' UTR (NM_011395, exon 11 of 11)	41845	NM_008877	18815	Mm.971	NM_008877	ENSMUSG00000059481	Plg	AI649309|Pg	plasminogen	protein-coding
mm_790.1	chr1	45337295	45337314	+	1	NA	exon (NM_009930, exon 30 of 51)	exon (NM_009930, exon 30 of 51)	25766	NM_009930	12825	Mm.249555	NM_009930	ENSMUSG00000026043	Col3a1	AW550625|Col3a-1|Tsk-2|Tsk2	collagen, type III, alpha 1	protein-coding
mm_32029.1	chr4	95215469	95215475	+	1	NA	Intergenic	Intergenic	-163250	NM_010591	16476	Mm.275071	NM_010591	ENSMUSG00000052684	Jun	AP-1|Junc|c-jun	jun proto-oncogene	protein-coding
mm_65658.1	chr7	28139767	28139783	-	1	NA	exon (NM_001164655, exon 5 of 20)	exon (NM_001164655, exon 5 of 20)	10309	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_72472.1	chr8	83566725	83566815	+	1	NA	promoter-TSS (NM_025843)	promoter-TSS (NM_025843)	12	NM_025843	66916	Mm.29683	NM_025843	ENSMUSG00000033938	Ndufb7	1110002H15Rik	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 7	protein-coding
mm_49988.1	chr6	41046881	41046891	+	1	NA	Intergenic	Intergenic	-11377	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_24197.1	chr3	88611961	88611966	+	1	NA	Intergenic	B3A|SINE|B2	-4244	NM_001198911	16800	Mm.239329	NM_008487	ENSMUSG00000028059	Arhgef2	AA408978|GEF|GEF-H1|GEFH1|LFP40|Lbcl1|Lfc|P40|mKIAA0651	rho/rac guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_162984.1	chr11	21370993	21371026	+	1	NA	promoter-TSS (NM_139297)	promoter-TSS (NM_139297)	258	NM_001290634	216558	Mm.28877	NM_139297	ENSMUSG00000001891	Ugp2	UDPGP|UGPase	UDP-glucose pyrophosphorylase 2	protein-coding
mm_144653.1	chr18	34221109	34221120	+	1	NA	5' UTR (NM_007462, exon 1 of 16)	5' UTR (NM_007462, exon 1 of 16)	130	NM_007462	11789	Mm.384171	NM_007462	ENSMUSG00000005871	Apc	AI047805|AU020952|AW124434|CC1|Min|mAPC	adenomatosis polyposis coli	protein-coding
mm_71333.1	chr8	45186723	45186731	+	1	NA	Intergenic	RLTR17|LTR|ERVK	-21582	NR_040690	622523	Mm.390032	NR_040690	ENSMUSG00000110231	Gm6329	EG622523	predicted gene 6329	ncRNA
mm_36737.1	chr4	99655988	99655988	-	1	NA	promoter-TSS (NM_010425)	promoter-TSS (NM_010425)	-311	NM_010425	15221	Mm.4758	NM_010425	ENSMUSG00000067261	Foxd3	CWH3|Genesis|Hfh2	forkhead box D3	protein-coding
mm_28297.1	chr3	89101908	89101969	-	1	NA	promoter-TSS (NM_001253751)	promoter-TSS (NM_001253751)	29	NM_134469	110196	Mm.39472	NM_134469	ENSMUSG00000059743	Fdps	6030492I17Rik|AI256750|Fdpsl1|mKIAA1293	farnesyl diphosphate synthetase	protein-coding
mm_161046.1	chr12	38084127	38084127	+	1	NA	intron (NM_178681, intron 2 of 24)	intron (NM_178681, intron 2 of 24)	203422	NM_178681	217480	Mm.126525	NM_178681	ENSMUSG00000036095	Dgkb	6430574F24|90kda|C630029D13Rik|DAGK2|DGK|DGK-beta|mKIAA0718	diacylglycerol kinase, beta	protein-coding
mm_60589.1	chr7	44482910	44482922	+	1	NA	Intergenic	Intergenic	-1601	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_29221.1	chr3	107211402	107211404	-	1	NA	exon (NM_001111143, exon 9 of 9)	exon (NM_001111143, exon 9 of 9)	10329	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_14378.1	chr2	129630656	129630668	+	1	NA	3' UTR (NM_001291022, exon 5 of 5)	3' UTR (NM_001291022, exon 5 of 5)	37493	NM_001291022	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_73027.1	chr8	94153896	94153911	+	1	NA	exon (NM_013603, exon 3 of 3)	exon (NM_013603, exon 3 of 3)	1296	NM_013603	17751	Mm.2064	NM_013603	ENSMUSG00000031760	Mt3	Mt-3	metallothionein 3	protein-coding
mm_45844.1	chr5	87698055	87698056	-	1	NA	exon (NM_001286023, exon 2 of 7)	exon (NM_001286023, exon 2 of 7)	1370	NM_001286020	12991	Mm.268737	NM_009972	ENSMUSG00000063157	Csn2	Csnb	casein beta	protein-coding
mm_144833.1	chr18	36390923	36390926	+	1	NA	intron (NM_001081365, intron 2 of 2)	intron (NM_001081365, intron 2 of 2)	42300	NM_001081365	66060	Mm.272527	NM_001081365	ENSMUSG00000046727	Cystm1	0610010O12Rik	cysteine-rich transmembrane module containing 1	protein-coding
mm_101463.1	chr11	30471793	30471820	-	1	NA	promoter-TSS (NM_001100394)	promoter-TSS (NM_001100394)	23	NM_001100394	75087	Mm.159422	NM_001100394	ENSMUSG00000040919	4930505A04Rik	-	RIKEN cDNA 4930505A04 gene	protein-coding
mm_111203.1	chr12	84236475	84236485	-	1	NA	Intergenic	Intergenic	-17599	NM_001163501	238317	Mm.31256	NM_001163501	ENSMUSG00000042507	Elmsan1	9430029N19Rik|C130039O16Rik|Gm260	ELM2 and Myb/SANT-like domain containing 1	protein-coding
mm_6825.1	chr1	84200408	84200421	-	1	NA	intron (NM_001003948, intron 1 of 2)	intron (NM_001003948, intron 1 of 2)	18547	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_57020.1	chr6	121473631	121473680	-	1	NA	promoter-TSS (NM_001289685)	promoter-TSS (NM_001289685)	23	NM_001033354	243621	Mm.299442	NM_001033354	ENSMUSG00000040797	Iqsec3	AK122446|BRAG3|mKIAA1110|synarfGEF	IQ motif and Sec7 domain 3	protein-coding
mm_44585.1	chr5	24908561	24908583	-	1	NA	promoter-TSS (NM_001170556)	promoter-TSS (NM_001170556)	-63	NM_001170555	108099	Mm.33649	NM_145401	ENSMUSG00000028944	Prkag2	2410051C13Rik|AAKG|AAKG2|AI854673|H91620p|WPWS	protein kinase, AMP-activated, gamma 2 non-catalytic subunit	protein-coding
mm_82038.1	chr9	122128907	122128914	+	1	NA	intron (NM_001164572, intron 1 of 5)	intron (NM_001164572, intron 1 of 5)	11644	NM_133741	20623	Mm.257989	NM_133741	ENSMUSG00000038145	Snrk	2010012F07Rik|AI448042|AW547029|E030034B15|R74830|mKIAA0096	SNF related kinase	protein-coding
mm_92895.1	chr10	82961468	82961468	-	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-24029	NM_021439	58250	Mm.360747	NM_021439	ENSMUSG00000034612	Chst11	1110020P09Rik|C4ST|C4ST-1|C4ST1|C4s	carbohydrate sulfotransferase 11	protein-coding
mm_53586.1	chr6	137735103	137735151	+	1	NA	promoter-TSS (NM_011499)	promoter-TSS (NM_011499)	45	NM_011499	20901	Mm.22584	NM_011499	ENSMUSG00000030224	Strap	AW557906|C78091|C79202|Unrip	serine/threonine kinase receptor associated protein	protein-coding
mm_117195.1	chr13	63573401	63573430	-	1	NA	promoter-TSS (NM_001328514)	promoter-TSS (NM_001328514)	45	NM_001328514	19206	Mm.228798	NM_008957	ENSMUSG00000021466	Ptch1	A230106A15Rik|Ptc|Ptc1|Ptch|mes	patched 1	protein-coding
mm_107447.1	chr12	36676719	36676727	+	1	NA	intron (NM_178629, intron 9 of 9)	intron (NM_178629, intron 9 of 9)	-139482	NR_039558	100628578		NR_039558	ENSMUSG00000092998	Mir5099	mmu-mir-5099|mu-mir-5099	microRNA 5099	ncRNA
mm_161834.1	chr17	84435599	84435599	-	1	NA	exon (NM_183021, exon 16 of 38)	exon (NM_183021, exon 16 of 38)	30609	NM_183021	240174	Mm.246767	NM_177826	ENSMUSG00000024251	Thada	6530405K19|A930021O22|AU019899|BC052885|GITA	thyroid adenoma associated	protein-coding
mm_51938.1	chr6	91699139	91699155	+	1	NA	intron (NM_009320, intron 2 of 14)	intron (NM_009320, intron 2 of 14)	15080	NM_009320	21366	Mm.395650	NM_009320	ENSMUSG00000030096	Slc6a6	AA589629|C80501|Taut	solute carrier family 6 (neurotransmitter transporter, taurine), member 6	protein-coding
mm_148202.1	chr18	79109957	79109977	-	1	NA	promoter-TSS (NM_053099)	promoter-TSS (NM_053099)	-576	NM_053099	240427	Mm.312871	NM_053099	ENSMUSG00000024548	Setbp1	C130092E12|Seb|mKIAA0437	SET binding protein 1	protein-coding
mm_60369.1	chr7	44463024	44463047	+	1	NA	3' UTR (NM_198250, exon 3 of 3)	3' UTR (NM_198250, exon 3 of 3)	-2400	NM_026690	68352	Mm.88478	NM_026690	ENSMUSG00000038704	Aspdh	0610012D14Rik	aspartate dehydrogenase domain containing	protein-coding
mm_95831.1	chr11	55470166	55470181	+	1	NA	intron (NM_013716, intron 1 of 11)	intron (NM_013716, intron 1 of 11)	421	NM_013716	27041	Mm.39631	NM_013716	ENSMUSG00000018583	G3bp1	AI849976|B430204O07|C87777|G3bp|mKIAA4115	GTPase activating protein (SH3 domain) binding protein 1	protein-coding
mm_9749.1	chr1	180697023	180697028	-	1	NA	promoter-TSS (NM_013729)	promoter-TSS (NM_013729)	9	NM_013729	27217	Mm.103647	NM_013729	ENSMUSG00000026497	Mixl1	Mm1|Mml	Mix1 homeobox-like 1 (Xenopus laevis)	protein-coding
mm_99795.1	chr11	107479550	107479565	+	1	NA	promoter-TSS (NM_025894)	promoter-TSS (NM_025894)	29	NM_025894	66997	Mm.491171	NM_025894	ENSMUSG00000020720	Psmd12	1500002F15Rik|AI480719|P55	proteasome (prosome, macropain) 26S subunit, non-ATPase, 12	protein-coding
mm_96575.1	chr11	69059709	69059745	+	1	NA	promoter-TSS (NM_028005)	promoter-TSS (NM_028005)	-48	NM_028005	71923	Mm.340257	NM_028005	ENSMUSG00000045176	Borcs6	2310047M10Rik	BLOC-1 related complex subunit 6	protein-coding
mm_118770.1	chr14	22695041	22695051	+	1	NA	intron (NM_028275, intron 5 of 6)	B4A|SINE|B4	-152248	NR_046307	74896	Mm.444661	NR_046307		4930405A10Rik	4930456G20Rik	RIKEN cDNA 4930405A10 gene	ncRNA
mm_169926.1	chr16	57391432	57391432	-	1	NA	intron (NM_001040397, intron 1 of 4)	LSU-rRNA_Hsa|rRNA|rRNA	38155	NM_001040397	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding
mm_90738.1	chr10	5367689	5367700	-	1	NA	intron (NM_001347732, intron 14 of 145)	intron (NM_001347732, intron 14 of 145)	120620	NM_001347711	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_91660.1	chr10	42863998	42864000	-	1	NA	intron (NM_172938, intron 1 of 8)	intron (NM_172938, intron 1 of 8)	3487	NM_172938	268297	Mm.98731	NM_172938	ENSMUSG00000044770	Scml4	9330161D17|mFLJ00197	sex comb on midleg-like 4 (Drosophila)	protein-coding
mm_111738.1	chr12	103865727	103865740	-	1	NA	Intergenic	Intergenic	-2114	NM_009243	20700	Mm.439692	NM_009243	ENSMUSG00000066366	Serpina1a	Aat-2|Aat2|Dom1|PI1|Spi1-1|Spi1-3	serine (or cysteine) peptidase inhibitor, clade A, member 1A	protein-coding
mm_129395.1	chr15	78246242	78246270	-	1	NA	intron (NM_008677, intron 1 of 9)	intron (NM_008677, intron 1 of 9)	1445	NM_008677	17972	Mm.2068	NM_008677	ENSMUSG00000071715	Ncf4	AI451400|p40phox	neutrophil cytosolic factor 4	protein-coding
mm_10925.1	chr2	25428700	25428715	+	1	NA	promoter-TSS (NM_007379)	promoter-TSS (NM_007379)	33	NM_007379	11305	Mm.2210	NM_007379	ENSMUSG00000026944	Abca2	AI413825|Abc2|D2H0S1474E|mKIAA1062	ATP-binding cassette, sub-family A (ABC1), member 2	protein-coding
mm_90661.1	chr10	128805653	128805694	+	1	NA	promoter-TSS (NM_028873)	promoter-TSS (NM_028873)	-3	NM_028873	74330	Mm.296915	NM_028873	ENSMUSG00000025354	Dnajc14	5730551F12Rik|DNAJ|DRIP78|HDJ3|LIP6	DnaJ heat shock protein family (Hsp40) member C14	protein-coding
mm_136428.1	chr16	94291010	94291015	-	1	NA	Intergenic	Intergenic	-3156	NM_139145	110948	Mm.30921	NM_139145	ENSMUSG00000040820	Hlcs	410I21.SP6|D16Jhu34	holocarboxylase synthetase (biotin- [propriony-Coenzyme A-carboxylase (ATP-hydrolysing)] ligase)	protein-coding
mm_152662.1	chr19	12796575	12796605	-	1	NA	promoter-TSS (NM_053009)	promoter-TSS (NM_053009)	-467	NM_053009	109910	Mm.290924	NM_053009	ENSMUSG00000024695	Zfp91	9130014I08Rik|A530054C17Rik|AL024263|AW545902|Pzf|Zfp-91	zinc finger protein 91	protein-coding
mm_142624.1	chr17	47395366	47395378	-	1	NA	intron (NM_008189, intron 2 of 3)	intron (NM_008189, intron 2 of 3)	5234	NM_008189	14913	Mm.16224	NM_008189	ENSMUSG00000023982	Guca1a	GC-A|Gcap1|Guca1|mGCAP1	guanylate cyclase activator 1a (retina)	protein-coding
mm_79775.1	chr9	62844592	62844612	+	1	NA	exon (NM_001033175, exon 2 of 7)	exon (NM_001033175, exon 2 of 7)	5815	NM_001033175	76524	Mm.283636	NM_001033175	ENSMUSG00000032245	Cln6	1810065L06Rik|AW743417|D9Bwg1455e|nclf	ceroid-lipofuscinosis, neuronal 6	protein-coding
mm_63303.1	chr7	126823881	126823899	+	1	NA	promoter-TSS (NM_001146347)	promoter-TSS (NM_001146347)	587	NM_029978	68952	Mm.440393	NM_026884	ENSMUSG00000058966	Fam57b	1500016O10Rik|A330104J06Rik|AI413816|AW060769	family with sequence similarity 57, member B	protein-coding
mm_39459.1	chr5	17577821	17577831	+	1	NA	intron (NM_013657, intron 2 of 17)	intron (NM_013657, intron 2 of 17)	3010	NM_013657	20348	Mm.5071	NM_013657	ENSMUSG00000028780	Sema3c	1110036B02Rik|SemE|Semae	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	protein-coding
mm_124690.1	chr15	6435440	6435449	+	1	NA	exon (NM_001102400, exon 10 of 13)	exon (NM_001102400, exon 10 of 13)	-9889	NM_013485	12279	Mm.29095	NM_013485	ENSMUSG00000022149	C9	-	complement component 9	protein-coding
mm_13150.1	chr2	92375705	92375743	+	1	NA	intron (NM_145122, intron 1 of 10)	intron (NM_145122, intron 1 of 10)	485	NM_145122	18633	Mm.202782	NM_145122	ENSMUSG00000027222	Pex16	-	peroxisomal biogenesis factor 16	protein-coding
mm_117967.1	chr13	99853255	99853258	-	1	NA	Intergenic	Intergenic	47427	NM_013732	27220	Mm.75498	NM_013732	ENSMUSG00000021647	Cartpt	Cart	CART prepropeptide	protein-coding
mm_156605.1	chrX	153140075	153140091	+	1	NA	5' UTR (NM_001004154, exon 1 of 11)	5' UTR (NM_001004154, exon 1 of 11)	125	NM_001004154	245670	Mm.190922	NM_001004154	ENSMUSG00000041658	Rragb	-	Ras-related GTP binding B	protein-coding
mm_7137.1	chr1	91057711	91057734	-	1	NA	intron (NM_001310732, intron 1 of 24)	intron (NM_001310732, intron 1 of 24)	4278	NM_008515	16978	Mm.45039	NM_008515	ENSMUSG00000026305	Lrrfip1	AU024550|Fliiap1	leucine rich repeat (in FLII) interacting protein 1	protein-coding
mm_82834.1	chr9	31150249	31150267	-	1	NA	3' UTR (NM_009691, exon 16 of 16)	3' UTR (NM_009691, exon 16 of 16)	-18459	NM_011176	19143	Mm.243926	NM_011176	ENSMUSG00000031995	St14	Epithin|MT-SP1|Prss14|Tmprss14|mCAP3|matriptase	suppression of tumorigenicity 14 (colon carcinoma)	protein-coding
mm_46717.1	chr5	110448522	110448532	-	1	NA	promoter-TSS (NM_001142642)	promoter-TSS (NM_001142642)	-24	NM_001142642	381668	Mm.348782	NM_028596	ENSMUSG00000043323	Fbrsl1	2410025L10Rik|AI467568|Gm1049|Gm29766|mKIAA1545	fibrosin-like 1	protein-coding
mm_105274.1	chr11	102407438	102407448	-	1	NA	promoter-TSS (NM_026542)	promoter-TSS (NM_026542)	74	NM_026542	68066	Mm.44226	NM_026542	ENSMUSG00000018677	Slc25a39	3010027G13Rik|D11Ertd333e	solute carrier family 25, member 39	protein-coding
mm_84065.1	chr9	58201326	58201352	-	1	NA	exon (NM_001161535, exon 1 of 2)	exon (NM_001161535, exon 1 of 2)	376	NM_001161535	320563	Mm.186499	NM_177193	ENSMUSG00000051243	Islr2	B930052A04Rik|Linx|Mbu-3|mKIAA1465	immunoglobulin superfamily containing leucine-rich repeat 2	protein-coding
mm_61142.1	chr7	57468585	57468587	+	1	NA	intron (NM_176942, intron 5 of 9)	(T)n|Simple_repeat|Simple_repeat	41423	NM_176942	110886	Mm.273114	NM_176942	ENSMUSG00000055078	Gabra5	A230018I05Rik	gamma-aminobutyric acid (GABA) A receptor, subunit alpha 5	protein-coding
mm_31886.1	chr4	82505924	82505954	+	1	NA	promoter-TSS (NM_001113209)	promoter-TSS (NM_001113209)	-160	NM_008687	18028	Mm.317947	NM_008687	ENSMUSG00000008575	Nfib	6720429L07Rik|CTF|E030026I10Rik|NF-I/B|NF1-B|NFI-B	nuclear factor I/B	protein-coding
mm_135621.1	chr16	52272192	52272210	-	1	NA	intron (NM_009655, intron 11 of 15)	intron (NM_009655, intron 11 of 15)	180880	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_148947.1	chr19	7268195	7268212	+	1	NA	promoter-TSS (NM_001320554)	promoter-TSS (NM_001320554)	-76	NM_001320554	104383	Mm.283859	NM_054048	ENSMUSG00000024968	Rcor2	1A13|AW122124|CoREST|Rcor|Rcor1	REST corepressor 2	protein-coding
mm_116139.1	chr13	29431247	29431250	-	1	NA	intron (NR_131896, intron 13 of 16)	intron (NR_131896, intron 13 of 16)	414993	NR_045075	77920	Mm.197051	NR_045073	ENSMUSG00000086363	A330102I10Rik	-	RIKEN cDNA A330102I10 gene	ncRNA
mm_24793.1	chr3	95545473	95545489	+	1	NA	exon (NM_021281, exon 5 of 8)	exon (NM_021281, exon 5 of 8)	-14196	NM_026489	67981	Mm.179050	NM_026489	ENSMUSG00000028109	Hormad1	4921522K05Rik|Nohma	HORMA domain containing 1	protein-coding
mm_88819.1	chr10	80802808	80802822	+	1	NA	exon (NM_013651, exon 5 of 9)	exon (NM_013651, exon 5 of 9)	-2433	NM_007445	11705	Mm.376094	NM_007445	ENSMUSG00000035262	Amh	MIS	anti-Mullerian hormone	protein-coding
mm_86735.1	chr10	19087340	19087344	+	1	NA	Intergenic	Intergenic	-54407	NR_038021	100504265	Mm.383417	NR_038021		Gm20139	-	predicted gene, 20139	ncRNA
mm_135632.1	chr16	52332448	52332463	-	1	NA	intron (NM_009655, intron 1 of 15)	Lx7|LINE|L1	120626	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_47671.1	chr5	127632916	127632946	-	1	NA	intron (NM_177005, intron 1 of 11)	intron (NM_177005, intron 1 of 11)	669	NM_177005	319804	Mm.237888	NM_177005	ENSMUSG00000049971	Glt1d1	5730455A04Rik	glycosyltransferase 1 domain containing 1	protein-coding
mm_52629.1	chr6	117174246	117174265	+	1	NA	3' UTR (NM_021704, exon 3 of 3)	3' UTR (NM_021704, exon 3 of 3)	5720	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_82700.1	chr9	22445627	22445638	-	1	NA	TTS (NM_026739)	TTS (NM_026739)	22724	NM_018739	55934	Mm.38235	NM_018739	ENSMUSG00000032239	Rp9	PAP-1|Rp9h	retinitis pigmentosa 9 (human)	protein-coding
mm_12864.1	chr2	83806583	83806601	+	1	NA	3' UTR (NM_008402, exon 30 of 30)	3' UTR (NM_008402, exon 30 of 30)	-6136	NM_175514	241520	Mm.330351	NM_175514	ENSMUSG00000048388	Fam171b	D430039N05Rik	family with sequence similarity 171, member B	protein-coding
mm_88923.1	chr10	81194685	81194700	+	1	NA	promoter-TSS (NR_015477)	promoter-TSS (NR_015477)	1	NR_015477	69678	Mm.81562	NR_015477		Atcayos	2310050B05Rik	ataxia, cerebellar, Cayman type, opposite strand	ncRNA
mm_79920.1	chr9	65587150	65587185	+	1	NA	promoter-TSS (NM_172453)	promoter-TSS (NM_172453)	-38	NM_172453	208084	Mm.211032	NM_172453	ENSMUSG00000041064	Pif1	4631410M14|AI449441	PIF1 5'-to-3' DNA helicase	protein-coding
mm_146193.1	chr18	76165137	76165149	+	1	NA	Intergenic	Intergenic	-5409	NR_105776	102465184		NR_105776	ENSMUSG00000098276	Mir6358	Gm27830|mmu-mir-6358	microRNA 6358	ncRNA
mm_149368.1	chr19	11372532	11372540	+	1	NA	Intergenic	Intergenic	-2952	NM_001310331	666907		NM_001310331	ENSMUSG00000101389	Ms4a4a	EG666907	membrane-spanning 4-domains, subfamily A, member 4A	protein-coding
mm_172997.1	chrM	1534	1539	+	1	NA	NA	Intergenic	NA	NA								
mm_91382.1	chr10	30618484	30618494	-	1	NA	promoter-TSS (NM_025798)	promoter-TSS (NM_025798)	-123	NM_025798	66847	Mm.46218	NM_025798	ENSMUSG00000019791	Hint3	0610010I17Rik|AV009015|HINT-3|HINT-4|HINT4	histidine triad nucleotide binding protein 3	protein-coding
mm_152414.1	chr19	10667611	10667617	-	1	NA	Intergenic	B3A|SINE|B2	10457	NM_021453	58803	Mm.34037	NM_021453	ENSMUSG00000024738	Pga5	1110035E17Rik|Pepf	pepsinogen 5, group I	protein-coding
mm_2617.1	chr1	120490906	120490930	+	1	NA	exon (NM_010766, exon 6 of 17)	exon (NM_010766, exon 6 of 17)	14166	NM_010766	17167	Mm.1856	NM_010766	ENSMUSG00000026390	Marco	AI323439|Ly112|Scara2	macrophage receptor with collagenous structure	protein-coding
mm_115765.1	chr13	19304379	19304389	-	1	NA	Intergenic	Intergenic	91429	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_171673.1	chr4	4890454	4890460	-	1	NA	Intergenic	IAPLTR1_Mm|LTR|ERVK	-97151	NM_177730	242291	Mm.218889	NM_177730	ENSMUSG00000066324	Impad1	1110001C20Rik|AA408880|AI451589|AL022796|B230207P20|Jaws|gPAPP	inositol monophosphatase domain containing 1	protein-coding
mm_23607.1	chr3	65449544	65449553	+	1	NA	Intergenic	Intergenic	-56995	NM_026155	67437	Mm.232728	NM_026155	ENSMUSG00000027828	Ssr3	0610038P07Rik|AL022999|AU022074|AW553833|TRAPG	signal sequence receptor, gamma	protein-coding
mm_129465.1	chr15	78597941	78597974	-	1	NA	intron (NM_028195, intron 1 of 12)	intron (NM_028195, intron 1 of 12)	910	NM_028195	72318	Mm.32911	NM_028195	ENSMUSG00000018008	Cyth4	2510004M07Rik|5830469K17Rik|AI467541|Pscd4|mFLJ00017	cytohesin 4	protein-coding
mm_67329.1	chr7	79732904	79732919	-	1	NA	promoter-TSS (NM_175640)	promoter-TSS (NM_175640)	-135	NM_001113471	103968	Mm.254917	NM_175640	ENSMUSG00000030546	Plin1	6030432J05Rik|Peri|Plin	perilipin 1	protein-coding
mm_60685.1	chr7	45154434	45154442	+	1	NA	promoter-TSS (NM_145954)	promoter-TSS (NM_145954)	100	NM_145954	69748	Mm.82139	NM_145954	ENSMUSG00000007833	Aldh16a1	2410004H02Rik|AI452234|mFLJ00209	aldehyde dehydrogenase 16 family, member A1	protein-coding
mm_25013.1	chr3	97930395	97930422	+	1	NA	intron (NM_001033779, intron 1 of 1)	intron (NM_001033779, intron 1 of 1)	235	NM_001033779	433632	Mm.212421	NM_001033779		Gm5544	EG433632	predicted gene 5544	protein-coding
mm_21498.1	chr2	163419509	163419548	-	1	NA	promoter-TSS (NM_025699)	promoter-TSS (NM_025699)	-58	NM_025699	66680	Mm.25119	NM_025699	ENSMUSG00000035399	Oser1	3230401D17Rik|AI256769|Perit1	oxidative stress responsive serine rich 1	protein-coding
mm_106520.1	chr11	120551217	120551225	-	1	NA	promoter-TSS (NM_026814)	promoter-TSS (NM_026814)	-89	NM_026814	68701	Mm.46477	NM_026814	ENSMUSG00000025129	Ppp1r27	1110033I14Rik|Dysfip1|toonin	protein phosphatase 1, regulatory subunit 27	protein-coding
mm_155156.1	chrX	52926976	52927002	+	1	NA	intron (NM_027642, intron 3 of 10)	intron (NM_027642, intron 3 of 10)	14775	NM_001290546	70998	Mm.26870	NM_027642	ENSMUSG00000025626	Phf6	2700007B13Rik|4931428F02Rik|mKIAA1823	PHD finger protein 6	protein-coding
mm_151642.1	chr19	4037911	4037933	-	1	NA	promoter-TSS (NM_013541)	promoter-TSS (NM_013541)	-10	NM_013541	14870	Mm.299292	NM_013541	ENSMUSG00000060803	Gstp1	GstpiB	glutathione S-transferase, pi 1	protein-coding
mm_99301.1	chr11	101367710	101367724	+	1	NA	promoter-TSS (NM_008061)	promoter-TSS (NM_008061)	1	NM_008061	14377	Mm.18064	NM_008061	ENSMUSG00000078650	G6pc	AW107337|G6Pase|G6pt|Glc-6-Pase	glucose-6-phosphatase, catalytic	protein-coding
mm_126899.1	chr15	89523753	89523793	+	1	NA	intron (NM_021423, intron 10 of 21)	GC_rich|Low_complexity|Low_complexity	23916	NM_021423	58234	Mm.146855	NM_021423	ENSMUSG00000022623	Shank3	AI841104|SHANK3c-3|SHANK3c-4|Shank3b	SH3/ankyrin domain gene 3	protein-coding
mm_28988.1	chr3	101287883	101287893	-	1	NA	promoter-TSS (NM_013486)	promoter-TSS (NM_013486)	51	NM_013486	12481	Mm.22842	NM_013486	ENSMUSG00000027863	Cd2	LFA-2|Ly-37|Ly37	CD2 antigen	protein-coding
mm_110377.1	chr12	40204354	40204365	-	1	NA	exon (NM_013562, exon 10 of 12)	exon (NM_013562, exon 10 of 12)	-5044	NM_001033437	380755	Mm.390463	NM_001033437	ENSMUSG00000071342	Lsmem1	Gm889	leucine-rich single-pass membrane protein 1	protein-coding
mm_54441.1	chr6	34419432	34419445	-	1	NA	exon (NM_009731, exon 6 of 10)	exon (NM_009731, exon 6 of 10)	7076	NM_009731	11997	Mm.482073	NM_009731	ENSMUSG00000052131	Akr1b7	AR|Avdp|MVDP	aldo-keto reductase family 1, member B7	protein-coding
mm_13566.1	chr2	112266517	112266550	+	1	NA	5' UTR (NM_133649, exon 1 of 25)	5' UTR (NM_133649, exon 1 of 25)	219	NM_133649	107723	Mm.491155	NM_133648	ENSMUSG00000027130	Slc12a6	9530023I19Rik|KCC3|gaxp	solute carrier family 12, member 6	protein-coding
mm_109415.1	chr12	110484096	110484104	+	1	NA	intron (NM_001135001, intron 3 of 13)	intron (NM_001135001, intron 3 of 13)	-1639	NM_001081457	26931	Mm.240396	NM_012023	ENSMUSG00000017843	Ppp2r5c	2610043M05Rik|2700063L20Rik|AI060890|AW545884|C85228|D12Bwg0916e|mKIAA0044	protein phosphatase 2, regulatory subunit B', gamma	protein-coding
mm_64103.1	chr7	141022380	141022411	+	1	NA	Intergenic	MT2A|LTR|ERVL	-5503	NM_001033632	213002	Mm.276440	NM_001033632	ENSMUSG00000059108	Ifitm6	A330075D07|Dspa2f|Fgls5|fragilis5	interferon induced transmembrane protein 6	protein-coding
mm_111727.1	chr12	103767885	103767907	-	1	NA	exon (NM_009246, exon 2 of 5)	exon (NM_009246, exon 2 of 5)	5737	NM_009246	20703	Mm.439695	NM_009246	ENSMUSG00000071177	Serpina1d	AI118301|Dom4|PI4|Spi1-4	serine (or cysteine) peptidase inhibitor, clade A, member 1D	protein-coding
mm_3021.1	chr1	133365161	133365190	+	1	NA	intron (NM_175443, intron 1 of 7)	intron (NM_175443, intron 1 of 7)	1603	NM_175443	214253	Mm.52111	NM_175443	ENSMUSG00000070644	Etnk2	4933417N20Rik|AI197444|EKI 2|Eki2|Tuc1	ethanolamine kinase 2	protein-coding
mm_68443.1	chr7	109986251	109986306	-	1	NA	promoter-TSS (NM_153525)	promoter-TSS (NM_153525)	-48	NM_153525	233724	Mm.43212	NM_153525	ENSMUSG00000047554	Tmem41b	1500015G02Rik|1500031M19Rik|AU018901|D7Ertd70e|D7Ertd743e	transmembrane protein 41B	protein-coding
mm_58761.1	chr7	13733503	13733504	+	1	NA	promoter-TSS (NM_009286)	promoter-TSS (NM_009286)	-3	NM_009286	100043194	Mm.457986	NM_009286	ENSMUSG00000070811	Sult2a2	C730007P19Rik|ST|ST2A2|Sth2|mSTa2	sulfotransferase family 2A, dehydroepiandrosterone (DHEA)-preferring, member 2	protein-coding
mm_103471.1	chr11	76479700	76479719	-	1	NA	intron (NM_001346670, intron 2 of 21)	PB1D7|SINE|Alu	-11244	NM_001291186	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_129632.1	chr15	80229951	80229953	-	1	NA	Intergenic	Intergenic	-4128	NM_178719	239555	Mm.307163	NM_178719	ENSMUSG00000022412	Mief1	A230016E22|AI452372|Smcr7l	mitochondrial elongation factor 1	protein-coding
mm_8655.1	chr1	156471508	156471528	-	1	NA	intron (NM_009230, intron 1 of 15)	B1_Mus1|SINE|Alu	2810	NM_009230	20652	Mm.28099	NM_009230	ENSMUSG00000026600	Soat1	8430426K15Rik|ACAT-1|AW550831|Acact|ald|hid	sterol O-acyltransferase 1	protein-coding
mm_22128.1	chr2	170387941	170387969	-	1	NA	intron (NM_029815, intron 4 of 12)	intron (NM_029815, intron 4 of 12)	31594	NR_040610	73303	Mm.443297	NR_040610	ENSMUSG00000086999	Bcas1os2	1700040N02Rik	breast carcinoma amplified sequence 1, opposite strand 2	ncRNA
mm_121501.1	chr14	121928655	121928656	+	1	NA	intron (NM_026861, intron 4 of 8)	intron (NM_026861, intron 4 of 8)	-12881	NM_182806	110168	Mm.37405	NM_182806	ENSMUSG00000050350	Gpr18	-	G protein-coupled receptor 18	protein-coding
mm_129104.1	chr15	76048488	76048498	-	1	NA	exon (NM_134089, exon 33 of 38)	exon (NM_134089, exon 33 of 38)	16395	NR_105917	102466772		NR_105917	ENSMUSG00000098451	Mir6952	Gm27948|mmu-mir-6952	microRNA 6952	ncRNA
mm_90709.1	chr10	3267769	3267773	-	1	NA	promoter-TSS (NM_001204916)	promoter-TSS (NM_001204916)	0	NM_001204916	670558	Mm.398582	NM_001204916	ENSMUSG00000091618	H60c	4632413I24Rik|Gm9491	histocompatibility 60c	protein-coding
mm_162453.1	chr1	125677096	125677102	+	1	NA	5' UTR (NM_027677, exon 1 of 2)	5' UTR (NM_027677, exon 1 of 2)	103	NM_027677	71111	Mm.32727	NM_027677	ENSMUSG00000026343	Gpr39	4933415E13Rik	G protein-coupled receptor 39	protein-coding
mm_123997.1	chr14	75787032	75787042	-	1	NA	promoter-TSS (NM_026232)	promoter-TSS (NM_026232)	0	NM_026232	67554	Mm.46067	NM_026232	ENSMUSG00000022003	Slc25a30	4933433D23Rik|AV025504|AV221431|AW319655|KMCP1	solute carrier family 25, member 30	protein-coding
mm_109256.1	chr12	109459864	109459876	+	1	NA	exon (NM_010052, exon 5 of 5)	exon (NM_010052, exon 5 of 5)	6415	NM_010052	13386	Mm.157069	NM_010052	ENSMUSG00000040856	Dlk1	AW742678|DLK-1|DlkI|FA1|Ly107|Peg9|SCP1|ZOG|pG2|pref-1	delta-like 1 homolog (Drosophila)	protein-coding
mm_69511.1	chr7	134498932	134498939	-	1	NA	Intergenic	Intergenic	-122107	NM_001081331	71007	Mm.334285	NM_001081331	ENSMUSG00000030994	D7Ertd443e	4933400E14Rik|FATS|Gm497	DNA segment, Chr 7, ERATO Doi 443, expressed	protein-coding
mm_48186.1	chr5	137502359	137502390	-	1	NA	promoter-TSS (NM_028753)	promoter-TSS (NM_028753)	55	NM_028753	74097	Mm.290242	NM_028753	ENSMUSG00000029715	Pop7	0610037N12Rik|AI852017|Rpp20	processing of precursor 7, ribonuclease P family, (S. cerevisiae)	protein-coding
mm_30266.1	chr3	146770548	146770566	-	1	NA	promoter-TSS (NM_001164198)	promoter-TSS (NM_001164198)	136	NM_001164199	18749	Mm.16766	NM_011100	ENSMUSG00000005034	Prkacb	CbPKA|Pkacb	protein kinase, cAMP dependent, catalytic, beta	protein-coding
mm_100785.1	chr11	4833115	4833123	-	1	NA	promoter-TSS (NM_001252253)	promoter-TSS (NM_001252253)	16	NM_001252253	18016	Mm.297109	NM_010898	ENSMUSG00000009073	Nf2	merlin	neurofibromin 2	protein-coding
mm_28592.1	chr3	94436080	94436090	-	1	NA	exon (NM_016901, exon 2 of 5)	exon (NM_016901, exon 2 of 5)	566	NM_016901	53814	Mm.440422	NM_016901	ENSMUSG00000028141	Oaz3	AZ3|Az-3|Oaz-t	ornithine decarboxylase antizyme 3	protein-coding
mm_120114.1	chr14	59479015	59479032	+	1	NA	intron (NM_026908, intron 3 of 10)	intron (NM_026908, intron 3 of 10)	38042	NM_026908	69008	Mm.179091	NM_026908	ENSMUSG00000021981	Cab39l	1500031K13Rik|2810425O13Rik|4930520C08Rik|AA589432|MO2L	calcium binding protein 39-like	protein-coding
mm_45453.1	chr5	67744706	67744709	-	1	NA	intron (NM_001284345, intron 19 of 36)	B1_Mm|SINE|Alu	102724	NM_009727	11980	Mm.153230	NM_009727	ENSMUSG00000037685	Atp8a1	AI481521|AI853962|APLT|AW743152|AW822227|Atp3a2|B230107D19Rik|ClassI	ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1	protein-coding
mm_81811.1	chr9	117872224	117872236	+	1	NA	Intergenic	CpG	-168292	NM_001286508	27215	Mm.92705	NM_013727	ENSMUSG00000039285	Azi2	AA410145|AZ2	5-azacytidine induced gene 2	protein-coding
mm_98513.1	chr11	94952387	94952401	+	1	NA	3' UTR (NM_007742, exon 51 of 51)	3' UTR (NM_007742, exon 51 of 51)	-15199	NM_018792	54388	Mm.30482	NM_018792	ENSMUSG00000038994	Hils1	H1.9|TISP64	histone H1-like protein in spermatids 1	protein-coding
mm_157534.1	chrX	51115944	51115965	-	1	NA	3' UTR (NM_134163, exon 8 of 8)	3' UTR (NM_134163, exon 8 of 8)	90036	NM_001310515	171170	Mm.295324	NM_134163	ENSMUSG00000036109	Mbnl3	A530038J18Rik|AI661274|CHCR|E430034C16Rik|MBLX|MBLX39|MBXL	muscleblind-like 3 (Drosophila)	protein-coding
mm_167339.1	chr8	72772906	72772908	+	1	NA	Intergenic	Intergenic	11248	NM_007975	14065	Mm.12948	NM_007975	ENSMUSG00000050147	F2rl3	PAR4	coagulation factor II (thrombin) receptor-like 3	protein-coding
mm_147550.1	chr18	54908079	54908095	-	1	NA	intron (NM_175751, intron 3 of 9)	ID_B1|SINE|B4	82093	NM_175751	269023	Mm.192984	NM_175751	ENSMUSG00000052713	Zfp608	4932417D18Rik|D430007A19Rik|Znf608	zinc finger protein 608	protein-coding
mm_21965.1	chr2	167299718	167299734	-	1	NA	3' UTR (NM_019835, exon 9 of 9)	3' UTR (NM_019835, exon 9 of 9)	49452	NM_019835	56336	Mm.200886	NM_019835	ENSMUSG00000017929	B4galt5	9430078I07Rik|AW049941|AW539721	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 5	protein-coding
mm_71633.1	chr8	57488035	57488052	+	1	NA	promoter-TSS (NM_021788)	promoter-TSS (NM_021788)	80	NR_126555	78353	Mm.426240	NR_126553	ENSMUSG00000096917	2500002B13Rik	-	RIKEN cDNA 2500002B13 gene	ncRNA
mm_40945.1	chr5	76822474	76822481	+	1	NA	Intergenic	Intergenic	-18122	NM_001163793	320827	Mm.101504	NM_001163793	ENSMUSG00000036377	C530008M17Rik	2810489J07Rik|4930529A19Rik|4931405B09Rik|Kiaa1211|mKIAA1211	RIKEN cDNA C530008M17 gene	protein-coding
mm_48061.1	chr5	136566588	136566628	-	1	NA	promoter-TSS (NM_001291240)	promoter-TSS (NM_001291240)	-627	NM_001291233	13047	Mm.320317	NM_009986	ENSMUSG00000029705	Cux1	CDP|Cutl1|Cux|Cux-1	cut-like homeobox 1	protein-coding
mm_16364.1	chr2	174760367	174760379	+	1	NA	promoter-TSS (NM_007903)	promoter-TSS (NM_007903)	-246	NM_007903	13616	Mm.9478	NM_007903	ENSMUSG00000027524	Edn3	ET-3|PPET3|ls|tmgc48	endothelin 3	protein-coding
mm_32506.1	chr4	108473602	108473605	+	1	NA	intron (NM_175472, intron 2 of 30)	AT_rich|Low_complexity|Low_complexity	14177	NM_175472	230594	Mm.25181	NM_175472	ENSMUSG00000034610	Zcchc11	6030404K05Rik|9230115F04Rik|PPAPD3|mKIAA0191	zinc finger, CCHC domain containing 11	protein-coding
mm_55096.1	chr6	49366812	49366823	-	1	NA	promoter-TSS (NM_172727)	promoter-TSS (NM_172727)	-922	NM_001172216	231946	Mm.35199	NM_172727	ENSMUSG00000047115	Fam221a	D330028D13Rik	family with sequence similarity 221, member A	protein-coding
mm_96258.1	chr11	62603182	62603192	+	1	NA	promoter-TSS (NR_028550)	promoter-TSS (NR_028550)	101	NR_028526	100217426		NR_028526	ENSMUSG00000064437	Snord49b	MBII-252|MBII-366	small nucleolar RNA, C/D box 49B	snoRNA
mm_135741.1	chr16	55847807	55847817	-	1	NA	intron (NM_001134457, intron 5 of 5)	intron (NM_001134457, intron 5 of 5)	-9171	NM_001159395	80859	Mm.247272	NM_030612	ENSMUSG00000035356	Nfkbiz	AA408868|INAP|Mail	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, zeta	protein-coding
mm_68784.1	chr7	123286968	123287018	-	1	NA	exon (NM_001122643, exon 18 of 20)	exon (NM_001122643, exon 18 of 20)	72127	NM_146198	233836	Mm.211838	NM_146198	ENSMUSG00000030769	Slc5a11	2010013B02Rik|Kst1|RKST2|SMIT2|Slc5a10	solute carrier family 5 (sodium/glucose cotransporter), member 11	protein-coding
mm_135871.1	chr16	62786743	62786797	-	1	NA	promoter-TSS (NM_178925)	promoter-TSS (NM_178925)	-54	NM_178925	106338	Mm.26321	NM_178925	ENSMUSG00000050312	Nsun3	6720484A09Rik|AU022521	NOL1/NOP2/Sun domain family member 3	protein-coding
mm_125982.1	chr15	76331511	76331540	+	1	NA	TTS (NM_175399)	TTS (NM_175399)	231	NM_010331	14731	Mm.5903	NM_010331	ENSMUSG00000022561	Gpaa1	C80044|mGAA1	GPI anchor attachment protein 1	protein-coding
mm_129232.1	chr15	76616459	76616479	-	1	NA	intron (NM_028064, intron 1 of 11)	intron (NM_028064, intron 1 of 11)	383	NM_028064	72027	Mm.276829	NM_028064	ENSMUSG00000063354	Slc39a4	1600025H15Rik|AU041686|AWMS2|ZIP4	solute carrier family 39 (zinc transporter), member 4	protein-coding
mm_70949.1	chr8	26975938	26975964	+	1	NA	Intergenic	Intergenic	-1385	NM_001101502	353310	Mm.212469	NM_001101502	ENSMUSG00000085795	Zfp703	1110032O19Rik|AI430822|AL022941|Csmn1|End2|Zeppo1|Znf703|Zpo1	zinc finger protein 703	protein-coding
mm_100398.1	chr11	119392279	119392293	+	1	NA	Intergenic	Intergenic	1814	NR_035453	100316690		NR_035453	ENSMUSG00000088015	Mir1932	mir-1932|mmu-mir-1932	microRNA 1932	ncRNA
mm_127682.1	chr15	102936843	102936854	+	1	NA	promoter-TSS (NM_010463)	promoter-TSS (NM_010463)	-5	NM_010463	15421	Mm.221179	NM_010463	ENSMUSG00000050328	Hoxc12	Hox-3.8	homeobox C12	protein-coding
mm_111047.1	chr12	79692160	79692170	-	1	NA	intron (NM_009014, intron 8 of 10)	intron (NM_009014, intron 8 of 10)	232568	NR_131075	77290	Mm.395042	NR_131073		9430078K24Rik	-	RIKEN cDNA 9430078K24 gene	ncRNA
mm_168755.1	chr12	115964301	115964308	-	1	NA	Intergenic	Intergenic	-83420	NM_001004066	56220	Mm.254997	NM_019565	ENSMUSG00000042063	Zfp386	Kzf1|mKIAA4205	zinc finger protein 386 (Kruppel-like)	protein-coding
mm_98389.1	chr11	94213818	94213834	+	1	NA	exon (NM_009427, exon 2 of 2)	exon (NM_009427, exon 2 of 2)	2372	NM_009427	22057	Mm.259673	NM_009427	ENSMUSG00000037573	Tob1	Tob|Trob	transducer of ErbB-2.1	protein-coding
mm_136099.1	chr16	85082866	85082887	-	1	NA	exon (NM_001198823, exon 4 of 18)	exon (NM_001198823, exon 4 of 18)	90831	NM_001198825	11820	Mm.277585	NM_007471	ENSMUSG00000022892	App	Abeta|Abpp|Adap|Ag|Cvap|E030013M08Rik|betaApp	amyloid beta (A4) precursor protein	protein-coding
mm_31473.1	chr4	50177583	50177587	+	1	NA	Intergenic	MER67D|LTR|ERV1	-331816	NM_001276355	242443	Mm.440095	NM_001033351	ENSMUSG00000039579	Grin3a	6430537F04|A830097C19Rik|NMDAR-L|NR3A|mKIAA1973	glutamate receptor ionotropic, NMDA3A	protein-coding
mm_5108.1	chr1	5618201	5618211	-	1	NA	Intergenic	Intergenic	29713	NM_001204371	18387	Mm.7977	NM_011011	ENSMUSG00000025905	Oprk1	K-OR-1|KOR|KOR-1|MSL-1|Oprk2|R21	opioid receptor, kappa 1	protein-coding
mm_589.1	chr1	39535748	39535839	+	1	NA	promoter-TSS (NM_028043)	promoter-TSS (NM_028043)	-9	NM_028043	52846	Mm.259421	NM_028043	ENSMUSG00000003135	Cnot11	2410015L18Rik|C40|D1Bwg0212e	CCR4-NOT transcription complex, subunit 11	protein-coding
mm_18136.1	chr2	45022958	45022984	-	1	NA	TTS (NR_039591)	TTS (NR_039591)	206	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_46651.1	chr5	108629713	108629761	-	1	NA	promoter-TSS (NM_153569)	promoter-TSS (NM_153569)	40	NM_153569	231580	Mm.276647	NM_153569	ENSMUSG00000062234	Gak	D130045N16Rik	cyclin G associated kinase	protein-coding
mm_115621.1	chr13	12082545	12082558	-	1	NA	intron (NM_023868, intron 1 of 104)	MTEb|LTR|ERVL-MaLR	24394	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding
mm_71154.1	chr8	40124632	40124640	+	1	NA	intron (NR_035426, intron 1 of 5)	intron (NR_035426, intron 1 of 5)	103151	NR_035426	100316806		NR_035426	ENSMUSG00000080653	Mir669e	Mirn669e|mmu-mir-669e	microRNA 669e	ncRNA
mm_85316.1	chr9	101199082	101199088	-	1	NA	promoter-TSS (NM_172144)	promoter-TSS (NM_172144)	-12	NM_172144	235542	Mm.335386	NM_172144	ENSMUSG00000043154	Ppp2r3a	3222402P14Rik|A730042E07	protein phosphatase 2, regulatory subunit B'', alpha	protein-coding
mm_13513.1	chr2	109917572	109917592	+	1	NA	promoter-TSS (NM_172671)	promoter-TSS (NM_172671)	-65	NM_172671	107515	Mm.277351	NM_172671	ENSMUSG00000050199	Lgr4	9130225G07|A330106J01Rik|A930009A08Rik|Gpr48	leucine-rich repeat-containing G protein-coupled receptor 4	protein-coding
mm_72187.1	chr8	72475339	72475395	+	1	NA	promoter-TSS (NM_138585)	promoter-TSS (NM_138585)	-134	NM_138585	27967	Mm.30136	NM_138585	ENSMUSG00000052488	Cherp	5730408I11Rik|D8Wsu96e|DAN16|Scaf6	calcium homeostasis endoplasmic reticulum protein	protein-coding
mm_155592.1	chrX	81094535	81094547	+	1	NA	exon (NM_138751, exon 3 of 3)	exon (NM_138751, exon 3 of 3)	23897	NM_138751	192216	Mm.490421	NM_138751	ENSMUSG00000025666	Tmem47	3010015F07Rik|AI115536|BCMP1|Tm4sf10	transmembrane protein 47	protein-coding
mm_152162.1	chr19	7275937	7275964	-	1	NA	TTS (NM_054048)	TTS (NM_054048)	7671	NM_001320554	104383	Mm.283859	NM_054048	ENSMUSG00000024968	Rcor2	1A13|AW122124|CoREST|Rcor|Rcor1	REST corepressor 2	protein-coding
mm_138172.1	chr17	34264821	34264838	+	1	NA	exon (NM_207105, exon 2 of 6)	exon (NM_207105, exon 2 of 6)	1602	NM_207105	14961	Mm.254067	NM_207105	ENSMUSG00000073421	H2-Ab1	AI845868|Abeta|H-2Ab|H2-Ab|I-Abeta|IAb|Ia-2|Ia2|Rmcs1	histocompatibility 2, class II antigen A, beta 1	protein-coding
mm_24070.1	chr3	87919529	87919558	+	1	NA	promoter-TSS (NM_026591)	promoter-TSS (NM_026591)	-1	NM_026591	67707	Mm.393802	NM_026591	ENSMUSG00000019710	Mrpl24	2010005E08Rik|2810470K06Rik|6720473G22Rik|AA407670	mitochondrial ribosomal protein L24	protein-coding
mm_120688.1	chr14	70774376	70774401	+	1	NA	promoter-TSS (NM_010071)	promoter-TSS (NM_010071)	7	NM_010071	13449	Mm.243323	NM_010071	ENSMUSG00000022102	Dok2	DokR|Frip	docking protein 2	protein-coding
mm_73522.1	chr8	107506258	107506264	+	1	NA	intron (NM_025830, intron 6 of 23)	intron (NM_025830, intron 6 of 23)	-44983	NR_029553	387158		NR_029553	ENSMUSG00000065439	Mir140	Mirn140|mir-140|mmu-mir-140	microRNA 140	ncRNA
mm_153097.1	chr19	32712288	32712336	-	1	NA	promoter-TSS (NM_026487)	promoter-TSS (NM_026487)	-14	NM_026487	67979	Mm.27123	NM_026487	ENSMUSG00000013662	Atad1	4921525H23Rik|AW107648|Thorase	ATPase family, AAA domain containing 1	protein-coding
mm_17968.1	chr2	37583053	37583056	-	1	NA	3' UTR (NM_009261, exon 17 of 17)	3' UTR (NM_009261, exon 17 of 17)	64231	NM_009261	20744	Mm.237095	NM_009261	ENSMUSG00000026915	Strbp	6430510M02Rik|AI852513|C230082I21Rik|C86322|Spnr	spermatid perinuclear RNA binding protein	protein-coding
mm_11296.1	chr2	30146807	30146825	+	1	NA	exon (NM_146252, exon 8 of 12)	exon (NM_146252, exon 8 of 12)	13070	NM_146252	70296	Mm.19172	NM_146252	ENSMUSG00000039678	Tbc1d13	2600014A06Rik|BC025586	TBC1 domain family, member 13	protein-coding
mm_144487.1	chr18	24154561	24154567	+	1	NA	Intergenic	MTE2b|LTR|ERVL-MaLR	-32745	NM_172625	225280	Mm.258973	NM_172625	ENSMUSG00000047989	Ino80c	D030070L09Rik	INO80 complex subunit C	protein-coding
mm_164621.1	chr17	31186222	31186258	-	1	NA	intron (NM_001163776, intron 10 of 12)	intron (NM_001163776, intron 10 of 12)	11509	NM_080727	140765	Mm.214638	NM_080727	ENSMUSG00000024034	Tmprss3	-	transmembrane protease, serine 3	protein-coding
mm_4305.1	chr1	171840608	171840641	+	1	NA	5' UTR (NM_013489, exon 2 of 9)	5' UTR (NM_013489, exon 2 of 9)	927	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_62157.1	chr7	97148879	97148898	+	1	NA	intron (NM_001162477, intron 1 of 9)	L1MB3|LINE|L1	67137	NM_010248	14389	Mm.42033	NM_010248	ENSMUSG00000004508	Gab2	AI463667|D130058I17Rik|p97	growth factor receptor bound protein 2-associated protein 2	protein-coding
mm_1521.1	chr1	72824547	72824557	+	1	NA	promoter-TSS (NM_008342)	promoter-TSS (NM_008342)	72	NM_008342	16008	Mm.141936	NM_008342	ENSMUSG00000039323	Igfbp2	AI255832|IBP-2|Igfbp-2|mIGFBP-2	insulin-like growth factor binding protein 2	protein-coding
mm_147461.1	chr18	46597481	46597543	-	1	NA	promoter-TSS (NM_025698)	promoter-TSS (NM_025698)	23	NM_025698	66676	Mm.296043	NM_025698	ENSMUSG00000033184	Tmed7	3930401E15Rik|5830493P14Rik|AU044611|AW545765|TRAM	transmembrane p24 trafficking protein 7	protein-coding
mm_106697.1	chr12	3463401	3463409	+	1	NA	intron (NM_001270988, intron 4 of 11)	intron (NM_001270988, intron 4 of 11)	36548	NM_172421	75302	Mm.120475	NM_172421	ENSMUSG00000037486	Asxl2	4930556B16Rik|mKIAA1685	additional sex combs like 2 (Drosophila)	protein-coding
mm_63894.1	chr7	138846635	138846660	+	1	NA	promoter-TSS (NM_027115)	promoter-TSS (NM_027115)	261	NM_026391	52432	Mm.258739	NM_026391	ENSMUSG00000041769	Ppp2r2d	1300017E19Rik|D7Ertd753e|MDS026	protein phosphatase 2, regulatory subunit B, delta	protein-coding
mm_75596.1	chr8	61700441	61700456	-	1	NA	intron (NM_001081390, intron 8 of 19)	B3|SINE|B2	59650	NM_001293773	72333	Mm.29933	NM_001081390	ENSMUSG00000058056	Palld	2410003B16Rik|6030492A02	palladin, cytoskeletal associated protein	protein-coding
mm_152866.1	chr19	24225016	24225033	-	1	NA	promoter-TSS (NM_011597)	promoter-TSS (NM_011597)	2	NM_011597	21873	Mm.104744	NM_011597	ENSMUSG00000024812	Tjp2	ZO-2	tight junction protein 2	protein-coding
mm_50451.1	chr6	48906083	48906093	+	1	NA	exon (NM_001161622, exon 2 of 5)	exon (NM_001161622, exon 2 of 5)	1102	NM_001161621	76507	Mm.213898	NM_029638	ENSMUSG00000029811	Aoc1	1600012D06Rik|Abp1|DAO	amine oxidase, copper-containing 1	protein-coding
mm_39365.1	chr5	9161834	9161873	+	1	NA	promoter-TSS (NM_001110327)	promoter-TSS (NM_001110327)	-77	NM_011806	23857	Mm.22480	NM_011806	ENSMUSG00000042508	Dmtf1	Dimp|Dmp1	cyclin D binding myb-like transcription factor 1	protein-coding
mm_167721.1	chr9	101074043	101074077	+	1	NA	promoter-TSS (NM_001100451)	promoter-TSS (NM_001100451)	-702	NM_001100451	77853	Mm.326206	NM_001100451	ENSMUSG00000066415	Msl2	E130103E02Rik|Msl2l1|Rnf184	male-specific lethal 2 homolog (Drosophila)	protein-coding
mm_23820.1	chr3	80687991	80687994	+	1	NA	3' UTR (NM_013540, exon 16 of 16)	3' UTR (NM_013540, exon 16 of 16)	114799	NM_013540	14800	Mm.220224	NM_013540	ENSMUSG00000033981	Gria2	GluA2|GluR-B|Glur-2|Glur2	glutamate receptor, ionotropic, AMPA2 (alpha 2)	protein-coding
mm_135227.1	chr16	36784975	36785001	-	1	NA	promoter-TSS (NM_021301)	promoter-TSS (NM_021301)	-26	NM_021301	57738	Mm.281804	NM_021301	ENSMUSG00000022899	Slc15a2	8430408C16Rik|C78862|Pept2	solute carrier family 15 (H+/peptide transporter), member 2	protein-coding
mm_32354.1	chr4	105157358	105157374	+	1	NA	promoter-TSS (NM_080555)	promoter-TSS (NM_080555)	19	NM_080555	67916	Mm.348326	NM_080555	ENSMUSG00000028517	Plpp3	1110003O22Rik|2610002D05Rik|AV025606|D4Bwg0538e|D4Bwg1535e|Lpp3|Ppab2b|Ppap2b	phospholipid phosphatase 3	protein-coding
mm_130534.1	chr15	98934523	98934586	-	1	NA	promoter-TSS (NM_011654)	promoter-TSS (NM_011654)	-164	NM_011654	22143	Mm.392113	NM_011654	ENSMUSG00000023004	Tuba1b	Tuba2	tubulin, alpha 1B	protein-coding
mm_100149.1	chr11	116030666	116030698	+	1	NA	intron (NM_172569, intron 1 of 15)	CpG	366	NM_172569	217331	Mm.297706	NM_172569	ENSMUSG00000020770	Unk	B230379M23Rik|Zc3h5|Zc3hdc5|mKIAA1753	unkempt family zinc finger	protein-coding
mm_97366.1	chr11	77515105	77515128	+	1	NA	promoter-TSS (NM_026185)	promoter-TSS (NM_026185)	-1	NM_026185	67477	Mm.432526	NM_026185	ENSMUSG00000000686	Abhd15	1300007F04Rik	abhydrolase domain containing 15	protein-coding
mm_149835.1	chr19	24875680	24875689	+	1	NA	Intergenic	Intergenic	-13842	NM_175013	226041	Mm.105222	NM_175013	ENSMUSG00000041731	Pgm5	4833423B07|9530034F03Rik|D830025G17|aciculin	phosphoglucomutase 5	protein-coding
mm_14965.1	chr2	152081633	152081643	+	1	NA	5' UTR (NM_001160410, exon 1 of 2)	5' UTR (NM_001160410, exon 1 of 2)	109	NM_001160410	545474	Mm.214317	NM_001160410	ENSMUSG00000060257	Scrt2	AW060659	scratch family zinc finger 2	protein-coding
mm_26316.1	chr3	142520638	142520652	+	1	NA	intron (NM_153564, intron 10 of 10)	intron (NM_153564, intron 10 of 10)	-9691	NM_001083312	229900	Mm.45740	NM_145545	ENSMUSG00000040253	Gbp7	9830147J24Rik	guanylate binding protein 7	protein-coding
mm_31653.1	chr4	59805830	59805914	+	1	NA	5' UTR (NM_172468, exon 1 of 9)	5' UTR (NM_172468, exon 1 of 9)	222	NM_172468	209131	Mm.259705	NM_172468	ENSMUSG00000028385	Snx30	4732481H14Rik|C030041J06Rik	sorting nexin family member 30	protein-coding
mm_26753.1	chr3	7954860	7954874	-	1	NA	promoter-TSS (NR_040587)	promoter-TSS (NR_040587)	20	NR_040587	75476	Mm.491752	NR_040587	ENSMUSG00000100010	1700010I02Rik	-	RIKEN cDNA 1700010I02 gene	ncRNA
mm_93478.1	chr10	111993528	111993539	-	1	NA	exon (NM_028608, exon 2 of 6)	exon (NM_028608, exon 2 of 6)	3731	NM_028608	73690	Mm.173790	NM_028608	ENSMUSG00000056888	Glipr1	2410114O14Rik|RTVP-1|RTVP1|mRTVP-1	GLI pathogenesis-related 1 (glioma)	protein-coding
mm_115831.1	chr13	21286938	21286945	-	1	NA	3' UTR (NM_010343, exon 5 of 5)	3' UTR (NM_010343, exon 5 of 5)	5745	NM_010343	14780	Mm.1332	NM_010343	ENSMUSG00000004344	Gpx5	AV379049|Arep	glutathione peroxidase 5	protein-coding
mm_23997.1	chr3	86548879	86548883	+	1	NA	promoter-TSS (NM_011839)	promoter-TSS (NM_011839)	-598	NM_011839	23937	Mm.389466	NM_011839	ENSMUSG00000057777	Mab21l2	-	mab-21-like 2 (C. elegans)	protein-coding
mm_156130.1	chrX	120290320	120290333	+	1	NA	promoter-TSS (NM_001271810)	promoter-TSS (NM_001271810)	-1	NM_001271809	245578	Mm.39691	NM_001081385	ENSMUSG00000034755	Pcdh11x	PCDHX|PCDHX11|Pcdh11	protocadherin 11 X-linked	protein-coding
mm_54707.1	chr6	39654113	39654117	-	1	NA	intron (NM_139294, intron 8 of 21)	intron (NM_139294, intron 8 of 21)	61532	NM_026612	68198	Mm.29415	NM_026612	ENSMUSG00000002416	Ndufb2	1810011O01Rik|8kDa|AGGG|AI325567|CI-AGGG	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 2	protein-coding
mm_55995.1	chr6	86371379	86371412	-	1	NA	promoter-TSS (NM_026506)	promoter-TSS (NM_026506)	-145	NM_026506	68011	Mm.276802	NM_026506	ENSMUSG00000057278	Snrpg	2810024K17Rik|AL022803|SMG|sm-G|snRNP-G	small nuclear ribonucleoprotein polypeptide G	protein-coding
mm_36323.1	chr4	70378208	70378214	-	1	NA	intron (NM_145990, intron 4 of 36)	GSAT_MM|Satellite|Satellite	32224	NM_001313762	214444	Mm.370777	NM_145990	ENSMUSG00000039298	Cdk5rap2	2900018K03Rik|an|mKIAA1633	CDK5 regulatory subunit associated protein 2	protein-coding
mm_86723.1	chr10	19062637	19062646	+	1	NA	Intergenic	Intergenic	-47231	NM_009397	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_160943.1	chr11	95261583	95261583	+	1	NA	promoter-TSS (NM_053093)	promoter-TSS (NM_053093)	54	NM_053093	93670	Mm.40085	NM_053093	ENSMUSG00000020872	Tac4	AW489379|PPT-C	tachykinin 4	protein-coding
mm_7623.1	chr1	127242162	127242190	-	1	NA	intron (NM_145128, intron 1 of 17)	intron (NM_145128, intron 1 of 17)	37190	NM_145128	107895	Mm.214682	NM_145128	ENSMUSG00000036155	Mgat5	4930471A21Rik|5330407H02Rik|AI480971|GlcNAc-TV	mannoside acetylglucosaminyltransferase 5	protein-coding
mm_20176.1	chr2	122469132	122469138	-	1	NA	Intergenic	RMER19B|LTR|ERVK	-1338	NR_027919	81913	Mm.122640	NR_027919		Bambi-ps1	-	BMP and activin membrane-bound inhibitor, pseudogene (Xenopus laevis)	pseudo
mm_86014.1	chr9	112234831	112234858	-	1	NA	promoter-TSS (NM_001177619)	promoter-TSS (NM_001177619)	-3	NM_001177619	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_37375.1	chr4	120972113	120972125	-	1	NA	exon (NM_133716, exon 9 of 10)	exon (NM_133716, exon 9 of 10)	1203	NR_105982	102465614		NR_105982	ENSMUSG00000106436	Mir7015	mmu-mir-7015	microRNA 7015	ncRNA
mm_152177.1	chr19	7382986	7383000	-	1	NA	promoter-TSS (NM_001033139)	promoter-TSS (NM_001033139)	-10	NR_045703	654802	Mm.414924	NR_045703		1700105P06Rik	-	RIKEN cDNA 1700105P06 gene	ncRNA
mm_160915.1	chr11	83409481	83409481	+	1	NA	promoter-TSS (NM_001013386)	promoter-TSS (NM_001013386)	-591	NM_001013386	276952	Mm.66275	NM_001013386	ENSMUSG00000020684	Rasl10b	B230331P10Rik|Gm729|VTS58635	RAS-like, family 10, member B	protein-coding
mm_114269.1	chr13	58148514	58148524	+	1	NA	intron (NR_126543, intron 1 of 1)	intron (NR_126543, intron 1 of 1)	1570	NR_126543	67339	Mm.121929	NR_126543		1700066J03Rik	-	RIKEN cDNA 1700066J03 gene	ncRNA
mm_55419.1	chr6	65127296	65127307	-	1	NA	intron (NM_019455, intron 4 of 5)	intron (NM_019455, intron 4 of 5)	17429	NM_019455	54486	Mm.410688	NM_019455	ENSMUSG00000029919	Hpgds	H-PGDS|Ptgds2	hematopoietic prostaglandin D synthase	protein-coding
mm_124265.1	chr14	102979775	102979797	-	1	NA	3' UTR (NM_177715, exon 1 of 1)	3' UTR (NM_177715, exon 1 of 1)	2846	NR_039592	100628599		NR_039592	ENSMUSG00000092901	Mir5130	mir-5130|mmu-mir-5130|mu-mir-5130	microRNA 5130	ncRNA
mm_90903.1	chr10	11080988	11081023	-	1	NA	intron (NM_016976, intron 1 of 8)	intron (NM_016976, intron 1 of 8)	1326	NM_001114333	14816	Mm.391904	NM_016976	ENSMUSG00000019828	Grm1	4930455H15Rik|ENSMUSG00000075319|Gm10828|Gprc1a|mGluR1|nmf373|rcw|wobl	glutamate receptor, metabotropic 1	protein-coding
mm_160120.1	chr7	27607501	27607501	+	1	NA	intron (NM_001331109, intron 1 of 13)	intron (NM_001331109, intron 1 of 13)	165	NM_001331109	11652	Mm.177194	NM_007434	ENSMUSG00000004056	Akt2	2410016A19Rik|AW554154|PKB|PKBbeta	thymoma viral proto-oncogene 2	protein-coding
mm_13306.1	chr2	102658577	102658580	+	1	NA	promoter-TSS (NM_001077514)	promoter-TSS (NM_001077514)	-105	NM_001077514	20511	Mm.267547	NM_011393	ENSMUSG00000005089	Slc1a2	1700091C19Rik|2900019G14Rik|AI159670|Eaat2|GLT-1|GLT1|MGLT1	solute carrier family 1 (glial high affinity glutamate transporter), member 2	protein-coding
mm_137145.1	chr17	23665011	23665016	+	1	NA	intron (NM_153784, intron 2 of 9)	intron (NM_153784, intron 2 of 9)	4507	NM_153784	212733	Mm.59997	NM_153784	ENSMUSG00000043782	Ccdc64b	BICDR-2|Bicdl2	coiled-coil domain containing 64B	protein-coding
mm_54591.1	chr6	38147450	38147457	-	1	NA	intron (NM_194061, intron 14 of 19)	intron (NM_194061, intron 14 of 19)	-22867	NM_080467	140494	Mm.462308	NM_080467	ENSMUSG00000038600	Atp6v0a4	Atp6n1b|a4	ATPase, H+ transporting, lysosomal V0 subunit A4	protein-coding
mm_141609.1	chr17	32809841	32809856	-	1	NA	promoter-TSS (NM_001267583)	promoter-TSS (NM_001267583)	83	NM_001267583	240063	Mm.30675	NM_183177	ENSMUSG00000055202	Zfp811	BC052046	zinc finger protein 811	protein-coding
mm_127709.1	chr15	103009518	103009544	+	1	NA	promoter-TSS (NM_010465)	promoter-TSS (NM_010465)	-31	NM_010465	15425	Mm.4444	NM_010465	ENSMUSG00000001661	Hoxc6	Hox-3.3|Hox-6.1	homeobox C6	protein-coding
mm_155151.1	chrX	52912209	52912220	+	1	NA	promoter-TSS (NM_027642)	promoter-TSS (NM_027642)	0	NM_027642	70998	Mm.26870	NM_027642	ENSMUSG00000025626	Phf6	2700007B13Rik|4931428F02Rik|mKIAA1823	PHD finger protein 6	protein-coding
mm_91462.1	chr10	34096508	34096554	-	1	NA	promoter-TSS (NM_178908)	promoter-TSS (NM_178908)	-12	NM_178908	103511	Mm.66334	NM_178908	ENSMUSG00000049872	Fam26e	BB146404	family with sequence similarity 26, member E	protein-coding
mm_10053.1	chr1	193201598	193201608	-	1	NA	promoter-TSS (NM_153137)	promoter-TSS (NM_153137)	-57	NM_153137	215243	Mm.261259	NM_153137	ENSMUSG00000037318	Traf3ip3	6030423D04Rik|AI115021|T3jam	TRAF3 interacting protein 3	protein-coding
mm_76972.1	chr8	106283214	106283216	-	1	NA	intron (NR_126091, intron 1 of 2)	intron (NR_126091, intron 1 of 2)	986	NR_126090	75044	Mm.445896	NR_126090		4930506A18Rik	-	RIKEN cDNA 4930506A18 gene	ncRNA
mm_165137.1	chr2	11332789	11332802	+	1	NA	Intergenic	Intergenic	-6694	NR_040369	100503147	Mm.91961	NR_040369	ENSMUSG00000086006	Gm13293	OTTMUSG00000011311	predicted gene 13293	ncRNA
mm_32145.1	chr4	99656356	99656382	+	1	NA	promoter-TSS (NM_010425)	promoter-TSS (NM_010425)	70	NM_010425	15221	Mm.4758	NM_010425	ENSMUSG00000067261	Foxd3	CWH3|Genesis|Hfh2	forkhead box D3	protein-coding
mm_103105.1	chr11	69965234	69965243	-	1	NA	promoter-TSS (NM_016887)	promoter-TSS (NM_016887)	-183	NM_016887	53624	Mm.281896	NM_016887	ENSMUSG00000018569	Cldn7	-	claudin 7	protein-coding
mm_128059.1	chr15	26639528	26639528	-	1	NA	intron (NM_176959, intron 2 of 3)	intron (NM_176959, intron 2 of 3)	256036	NM_176959	448987	Mm.253378	NM_176959	ENSMUSG00000043556	Fbxl7	AL023057|D230018M15Rik|FBL7|Fbl6	F-box and leucine-rich repeat protein 7	protein-coding
mm_18527.1	chr2	63184254	63184292	-	1	NA	promoter-TSS (NM_133207)	promoter-TSS (NM_133207)	14	NM_133207	170738	Mm.242532	NM_133207	ENSMUSG00000059742	Kcnh7	9330137I11Rik|Kv11.3|erg3	potassium voltage-gated channel, subfamily H (eag-related), member 7	protein-coding
mm_95316.1	chr11	46436931	46436941	+	1	NA	promoter-TSS (NM_025426)	promoter-TSS (NM_025426)	-11	NM_001104557	66213	Mm.24159	NM_025426	ENSMUSG00000020397	Med7	1110063B05Rik|Crsp33|Crsp9	mediator complex subunit 7	protein-coding
mm_1946.1	chr1	86308556	86308578	+	1	NA	Intergenic	Intergenic	5346	NM_145222	227327	Mm.86467	NM_145222	ENSMUSG00000079445	B3gnt7	C330001H22Rik|beta-3GnT7	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 7	protein-coding
mm_77555.1	chr8	123284164	123284196	-	1	NA	exon (NM_016925, exon 28 of 43)	exon (NM_016925, exon 28 of 43)	-29958	NM_028200	72325	Mm.276193	NM_028200	ENSMUSG00000001062	Vps9d1	1300018I17Rik|2410004N05Rik|5DOS1|Vsp9d1	VPS9 domain containing 1	protein-coding
mm_164558.1	chr17	14961230	14961304	-	1	NA	promoter-TSS (NM_024250)	promoter-TSS (NM_024250)	-7	NM_024250	72057	Mm.440085	NM_024250	ENSMUSG00000023883	Phf10	1810055P05Rik|AV024533	PHD finger protein 10	protein-coding
mm_103901.1	chr11	83575914	83575958	-	1	NA	exon (NM_011338, exon 3 of 4)	exon (NM_011338, exon 3 of 4)	2700	NM_011338	20308	Mm.416125	NM_011338	ENSMUSG00000019122	Ccl9	CCF18|MRP-2|Scya10|Scya9	chemokine (C-C motif) ligand 9	protein-coding
mm_1767.1	chr1	77050294	77050294	+	1	NA	Intergenic	A-rich|Low_complexity|Low_complexity	446474	NR_105770	102465180		NR_105770	ENSMUSG00000099141	Mir6352	Gm27481|mmu-mir-6352	microRNA 6352	ncRNA
mm_93676.1	chr10	117715239	117715258	-	1	NA	Intergenic	RLTR30D_MM|LTR|ERV1	-4490	NM_001288586	17246	Mm.22670	NM_010786	ENSMUSG00000020184	Mdm2	1700007J15Rik|AA415488|Mdm-2	transformed mouse 3T3 cell double minute 2	protein-coding
mm_125279.1	chr15	36282500	36282511	+	1	NA	intron (NM_013923, intron 1 of 9)	CpG	642	NM_013923	30945	Mm.5181	NM_013923	ENSMUSG00000022280	Rnf19a	AA032313|Dorfin|Rnf19|UIP117|Ubce7ip2|XYbp	ring finger protein 19A	protein-coding
mm_137945.1	chr17	32810118	32810147	+	1	NA	promoter-TSS (NM_001267583)	promoter-TSS (NM_001267583)	-201	NM_183177	240063	Mm.30675	NM_183177	ENSMUSG00000055202	Zfp811	BC052046	zinc finger protein 811	protein-coding
mm_158774.1	chrX	167029649	167029652	-	1	NA	Intergenic	Intergenic	40720	NM_001101606	667794	Mm.302232	NM_001101606		Gm8817	EG667794	predicted gene 8817	protein-coding
mm_72080.1	chr8	71570618	71570631	+	1	NA	intron (NM_011977, intron 2 of 13)	CpG	1697	NM_011977	26457	Mm.38165	NM_011977	ENSMUSG00000031808	Slc27a1	FATP1|Fatp	solute carrier family 27 (fatty acid transporter), member 1	protein-coding
mm_49594.1	chr6	30670093	30670097	+	1	NA	intron (NR_130781, intron 3 of 11)	intron (NR_130781, intron 3 of 11)	23654	NM_031998	83922	Mm.65389	NM_031998	ENSMUSG00000029790	Cep41	1700017E11Rik|2810431D15Rik|Tsga14	centrosomal protein 41	protein-coding
mm_109391.1	chr12	109748034	109748051	+	1	NA	TTS (NR_037233)	TTS (NR_037233)	164	NR_037233	100499517		NR_037233	ENSMUSG00000093351	Mir3072	mir-3072|mmu-mir-3072	microRNA 3072	ncRNA
mm_65967.1	chr7	30436989	30437014	-	1	NA	intron (NM_007467, intron 11 of 16)	intron (NM_007467, intron 11 of 16)	8581	NM_007467	11803	Mm.2381	NM_007467	ENSMUSG00000006651	Aplp1	-	amyloid beta (A4) precursor-like protein 1	protein-coding
mm_78809.1	chr9	44067140	44067153	+	1	NA	5' UTR (NM_198092, exon 1 of 13)	5' UTR (NM_198092, exon 1 of 13)	125	NM_198092	53376	Mm.272770	NM_016808	ENSMUSG00000032010	Usp2	B930035K21Rik|Ubp41	ubiquitin specific peptidase 2	protein-coding
mm_1401.1	chr1	67144874	67144888	+	1	NA	intron (NM_001080809, intron 4 of 37)	intron (NM_001080809, intron 4 of 37)	21854	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_128493.1	chr15	51865499	51865517	-	1	NA	promoter-TSS (NM_080635)	promoter-TSS (NM_080635)	-47	NM_080635	68135	Mm.289800	NM_080635	ENSMUSG00000022312	Eif3h	1110008A16Rik|40kD|9430017H16Rik|EIF3-P40|EIF3-gamma|Eif3s3	eukaryotic translation initiation factor 3, subunit H	protein-coding
mm_83903.1	chr9	56161052	56161075	-	1	NA	promoter-TSS (NM_019793)	promoter-TSS (NM_019793)	7	NM_019793	56434	Mm.28484	NM_019793	ENSMUSG00000032324	Tspan3	1700055K04Rik|TM4-A|Tm4sf8	tetraspanin 3	protein-coding
mm_17145.1	chr2	25196608	25196640	-	1	NA	5' UTR (NM_146115, exon 1 of 2)	5' UTR (NM_146115, exon 1 of 2)	189	NM_146115	227612	Mm.119747	NM_146115	ENSMUSG00000059555	Tor4a	A830007P12Rik	torsin family 4, member A	protein-coding
mm_88622.1	chr10	79861681	79861693	+	1	NA	promoter-TSS (NR_105875)	promoter-TSS (NR_105875)	-900	NR_105875	102465549		NR_105875	ENSMUSG00000098562	Mir6910	Gm27763|mmu-mir-6910	microRNA 6910	ncRNA
mm_51244.1	chr6	71707827	71707837	+	1	NA	5' UTR (NM_178608, exon 1 of 7)	5' UTR (NM_178608, exon 1 of 7)	151	NM_178608	52250	Mm.146332	NM_178608	ENSMUSG00000052852	Reep1	D6Ertd253e	receptor accessory protein 1	protein-coding
mm_48463.1	chr5	140826846	140826868	-	1	NA	intron (NM_010302, intron 1 of 3)	intron (NM_010302, intron 1 of 3)	3574	NM_010302	14673	Mm.370185	NM_010302	ENSMUSG00000000149	Gna12	AI414047|AI504261|Galpha12	guanine nucleotide binding protein, alpha 12	protein-coding
mm_44767.1	chr5	31698332	31698341	-	1	NA	promoter-TSS (NM_153196)	promoter-TSS (NM_153196)	286	NM_144541	107976	Mm.482126	NM_144541	ENSMUSG00000052139	Bre	6030405P19Rik|AI429776|B830038C02Rik	brain and reproductive organ-expressed protein	protein-coding
mm_25872.1	chr3	130068391	130068391	+	1	NA	Intergenic	Intergenic	-7484	NM_207209	99683	Mm.192303	NM_207209	ENSMUSG00000001052	Sec24b	AI605202|SEC24	Sec24 related gene family, member B (S. cerevisiae)	protein-coding
mm_72850.1	chr8	88320749	88320760	+	1	NA	intron (NM_001037723, intron 17 of 27)	RSINE1|SINE|B4	26550	NM_001037724	11513	Mm.288206	NM_007406	ENSMUSG00000031659	Adcy7	AA407758	adenylate cyclase 7	protein-coding
mm_146285.1	chr18	78030067	78030078	+	1	NA	exon (NM_001195633, exon 42 of 44)	exon (NM_001195633, exon 42 of 44)	27196	NM_001101038	620235	Mm.35607	NM_001101038	ENSMUSG00000091055	Siglec15	Cd33l3|EG620235|SIGLEC-I	sialic acid binding Ig-like lectin 15	protein-coding
mm_44140.1	chr5	150196397	150196454	+	1	NA	Intergenic	Intergenic	-63505	NM_172887	320365	Mm.216590	NM_172887	ENSMUSG00000056602	Fry	13CDNA73|9330186A19Rik|AF346502|AI462658|C87180|D930046M03|cg003|mKIAA4143	FRY microtubule binding protein	protein-coding
mm_127517.1	chr15	101939163	101939178	+	1	NA	intron (NM_146063, intron 1 of 8)	intron (NM_146063, intron 1 of 8)	1154	NM_146063	223917	Mm.162744	NM_146063	ENSMUSG00000061397	Krt79	BC031593	keratin 79	protein-coding
mm_158164.1	chrX	103483206	103483225	-	1	NA	promoter-TSS (NR_001570)	promoter-TSS (NR_001570)	18	NR_001570	213742	Mm.274770	NR_001463	ENSMUSG00000086503	Xist	A430022B11|AI314753	inactive X specific transcripts	ncRNA
mm_360.1	chr1	33813408	33813422	+	1	NA	intron (NM_001290699, intron 2 of 12)	intron (NM_001290699, intron 2 of 12)	1180	NM_133817	98403	Mm.289103	NM_133817	ENSMUSG00000042197	Zfp451	4930515K21Rik|4933435G09Rik|AI596398|COASTER|Kiaa0576-hp|Znf451|mKIAA1702	zinc finger protein 451	protein-coding
mm_46083.1	chr5	92346815	92346817	-	1	NA	3' UTR (NM_021274, exon 4 of 4)	3' UTR (NM_021274, exon 4 of 4)	2073	NM_021274	15945	Mm.877	NM_021274	ENSMUSG00000034855	Cxcl10	C7|CRG-2|INP10|IP-10|IP10|Ifi10|Scyb10|gIP-10|mob-1	chemokine (C-X-C motif) ligand 10	protein-coding
mm_22275.1	chr2	178627808	178627825	-	1	NA	Intergenic	Intergenic	197301	NM_198656	381409	Mm.330860	NM_198656	ENSMUSG00000039155	Cdh26	Gm1010	cadherin-like 26	protein-coding
mm_54237.1	chr6	28242374	28242388	-	1	NA	intron (NM_001081678, intron 5 of 5)	intron (NM_001081678, intron 5 of 5)	19220	NM_001081678	627049	Mm.84441	NM_001081678	ENSMUSG00000039841	Zfp800	AA407452|Znf800	zinc finger protein 800	protein-coding
mm_146751.1	chr18	16745343	16745359	-	1	NA	intron (NM_007664, intron 2 of 15)	intron (NM_007664, intron 2 of 15)	63895	NM_007664	12558	Mm.257437	NM_007664	ENSMUSG00000024304	Cdh2	CDHN|N-CAD|Ncad	cadherin 2	protein-coding
mm_112355.1	chr12	118908924	118908926	-	1	NA	intron (NM_029961, intron 16 of 27)	intron (NM_029961, intron 16 of 27)	57496	NM_029961	77706	Mm.261496	NM_029961	ENSMUSG00000072791	Abcb5	9230106F14Rik	ATP-binding cassette, sub-family B (MDR/TAP), member 5	protein-coding
mm_93346.1	chr10	100487272	100487288	-	1	NA	promoter-TSS (NM_001110013)	promoter-TSS (NM_001110013)	67	NM_001033332	237500	Mm.296805	NM_001033332	ENSMUSG00000036676	Tmtc3	9130014E20Rik|B130008E12Rik|mSmile	transmembrane and tetratricopeptide repeat containing 3	protein-coding
mm_24702.1	chr3	95126241	95126249	+	1	NA	intron (NM_016712, intron 3 of 9)	intron (NM_016712, intron 3 of 9)	1731	NM_016712	50874	Mm.71935	NM_016712	ENSMUSG00000005628	Tmod4	MTMOD|Sk-Tmod	tropomodulin 4	protein-coding
mm_134445.1	chr16	18284952	18284955	-	1	NA	promoter-TSS (NR_035467)	promoter-TSS (NR_035467)	-316	NR_128565	104795666		NR_128565	ENSMUSG00000093246	Gm24572	Mir3618|mmu-mir-3618	predicted gene, 24572	ncRNA
mm_26227.1	chr3	138903261	138903265	+	1	NA	non-coding (NR_121195, exon 8 of 8)	non-coding (NR_121195, exon 8 of 8)	161055	NM_019571	56224	Mm.31927	NM_019571	ENSMUSG00000028152	Tspan5	2810455A09Rik|4930505M03Rik|NET-4|Tm4sf9	tetraspanin 5	protein-coding
mm_6661.1	chr1	80218452	80218457	-	1	NA	Intergenic	Intergenic	-4510	NM_173425	241128	Mm.145511	NM_173425	ENSMUSG00000043230	Fam124b	A830043J08Rik	family with sequence similarity 124, member B	protein-coding
mm_81175.1	chr9	107307709	107307743	+	1	NA	Intergenic	Intergenic	11067	NM_009895	12700	Mm.4592	NM_009895	ENSMUSG00000032578	Cish	CIS-1|CIS1|Cis|F17|F23|SOCS	cytokine inducible SH2-containing protein	protein-coding
mm_27207.1	chr3	35754640	35754641	-	1	NA	intron (NM_029570, intron 1 of 29)	CpG	502	NM_029570	76295	Mm.239416	NM_029570	ENSMUSG00000037400	Atp11b	1110019I14Rik|ATPIF|ATPIR|mKIAA0956	ATPase, class VI, type 11B	protein-coding
mm_144758.1	chr18	35771372	35771487	+	1	NA	promoter-TSS (NM_019912)	promoter-TSS (NM_019912)	-130	NM_019912	56550	Mm.180052	NM_019912	ENSMUSG00000091896	Ube2d2a	1500034D03Rik|Ubc2e|Ube2d2|ubc4	ubiquitin-conjugating enzyme E2D 2A	protein-coding
mm_36850.1	chr4	106799738	106799750	-	1	NA	promoter-TSS (NM_025590)	promoter-TSS (NM_025590)	87	NM_025590	329910	Mm.222956	NM_025590	ENSMUSG00000034853	Acot11	1110020M10Rik|2010309H15Rik|AW060409|BFIT|BFIT1|Thea|Them1|mKIAA0707	acyl-CoA thioesterase 11	protein-coding
mm_68816.1	chr7	125707772	125707785	-	1	NA	promoter-TSS (NM_207239)	promoter-TSS (NM_207239)	-90	NM_207239	233863	Mm.294173	NM_207239	ENSMUSG00000032777	Gtf3c1	-	general transcription factor III C 1	protein-coding
mm_529.1	chr1	37872209	37872233	+	1	NA	promoter-TSS (NM_001037918)	promoter-TSS (NM_001037918)	15	NM_001037918	623661	Mm.138000	NM_001037918	ENSMUSG00000037216	Lipt1	EG623661	lipoyltransferase 1	protein-coding
mm_139914.1	chr17	70963702	70963738	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	26796	NM_023402	67938	Mm.261329	NM_023402	ENSMUSG00000034868	Myl12b	1500001M02Rik|C77744|Mylc2b|RLC-B	myosin, light chain 12B, regulatory	protein-coding
mm_45125.1	chr5	46007592	46007602	-	1	NA	Intergenic	Intergenic	-75188	NR_110478	78106	Mm.243807	NR_110478	ENSMUSG00000106602	4930405L22Rik	-	RIKEN cDNA 4930405L22 gene	ncRNA
mm_16070.1	chr2	168081140	168081155	+	1	NA	5' UTR (NM_021409, exon 1 of 3)	5' UTR (NM_021409, exon 1 of 3)	143	NM_021409	58220	Mm.292834	NM_021409	ENSMUSG00000044641	Pard6b	AV025615|Par6b	par-6 family cell polarity regulator beta	protein-coding
mm_53823.1	chr6	147257156	147257161	+	1	NA	exon (NM_008970, exon 3 of 4)	exon (NM_008970, exon 3 of 4)	6855	NM_008970	19227	Mm.28440	NM_008970	ENSMUSG00000048776	Pthlh	PLP|PTH-like|Pthrp	parathyroid hormone-like peptide	protein-coding
mm_41777.1	chr5	103715224	103715275	+	1	NA	Intergenic	Lx8|LINE|L1	-38913	NM_133919	17355	Mm.6949	NM_133919	ENSMUSG00000029313	Aff1	9630032B01Rik|AW319193|Af4|Mllt2h|Rob	AF4/FMR2 family, member 1	protein-coding
mm_50847.1	chr6	54849200	54849210	+	1	NA	intron (NM_199143, intron 1 of 4)	intron (NM_199143, intron 1 of 4)	32289	NM_199143	387524	Mm.286149	NM_199143	ENSMUSG00000058446	Znrf2	1190002C14Rik|AU044205|D6Ertd365e	zinc and ring finger 2	protein-coding
mm_16533.1	chr2	181579357	181579367	+	1	NA	promoter-TSS (NR_027290)	promoter-TSS (NR_027290)	-170	NR_027290	100271841	Mm.438007	NR_027289	ENSMUSG00000010492	Uckl1os	Gm16119|OTTMUSG00000030649	uridine-cytidine kinase 1-like 1, opposite strand	ncRNA
mm_167894.1	chrX	69945299	69945308	+	1	NA	promoter-TSS (NM_029316)	promoter-TSS (NM_029316)	22	NM_029316	75509	Mm.233475	NM_029316	ENSMUSG00000059690	1700020N15Rik	-	RIKEN cDNA 1700020N15 gene	protein-coding
mm_89335.1	chr10	87933710	87933725	+	1	NA	3' UTR (NM_010512, exon 5 of 5)	3' UTR (NM_010512, exon 5 of 5)	-32954	NR_000040	22172	Mm.391420	NR_000040		Tyms-ps	-	thymidylate synthase, pseudogene	pseudo
mm_59064.1	chr7	19458931	19458935	+	1	NA	promoter-TSS (NM_172279)	promoter-TSS (NM_172279)	-439	NM_172279	232944	Mm.260504	NM_172279	ENSMUSG00000030397	Mark4	2410090P21Rik|C79806|Markl1	MAP/microtubule affinity regulating kinase 4	protein-coding
mm_57453.1	chr6	125165350	125165352	-	1	NA	intron (NM_001289726, intron 1 of 6)	CpG-12474	422	NM_008084	14433	Mm.304088	NM_008084	ENSMUSG00000057666	Gapdh	Gapd	glyceraldehyde-3-phosphate dehydrogenase	protein-coding
mm_117014.1	chr13	58123412	58123428	-	1	NA	Intergenic	Intergenic	5136	NM_029872	77134	Mm.490274	NM_029872	ENSMUSG00000007836	Hnrnpa0	1110055B05Rik|3010025E17Rik|Hnrpa0|hnRNP A0	heterogeneous nuclear ribonucleoprotein A0	protein-coding
mm_60668.1	chr7	45017934	45017938	+	1	NA	promoter-TSS (NM_009101)	promoter-TSS (NM_009101)	-71	NM_009101	20130	Mm.389894	NM_009101	ENSMUSG00000038387	Rras	AI573426	related RAS viral (r-ras) oncogene	protein-coding
mm_83595.1	chr9	48489334	48489357	-	1	NA	non-coding (NR_037589, exon 6 of 6)	non-coding (NR_037589, exon 6 of 6)	5985	NM_001326355	67010	Mm.76911	NM_144948	ENSMUSG00000042396	Rbm7	1200007M24Rik|1500011D06Rik|AU041934|AW554393	RNA binding motif protein 7	protein-coding
mm_15778.1	chr2	164333406	164333410	+	1	NA	exon (NM_009301, exon 2 of 3)	exon (NM_009301, exon 2 of 3)	643	NM_009301	20944	Mm.140154	NM_009301	ENSMUSG00000017004	Svs5	BB115186|Semg1|Svp-1|Svp1|Svp5	seminal vesicle secretory protein 5	protein-coding
mm_115796.1	chr13	19344325	19344348	-	1	NA	Intergenic	Intergenic	51477	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_26816.1	chr3	10301210	10301218	-	1	NA	promoter-TSS (NM_029310)	promoter-TSS (NM_029310)	-31	NM_029310	75497	Mm.47052	NM_029310	ENSMUSG00000027530	Fabp12	1700008G05Rik	fatty acid binding protein 12	protein-coding
mm_102067.1	chr11	52257725	52257781	-	1	NA	exon (NM_009331, exon 6 of 10)	exon (NM_009331, exon 6 of 10)	24842	NM_009331	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_2133.1	chr1	88070728	88070746	+	1	NA	promoter-TSS (NM_201644)	promoter-TSS (NM_201644)	-42	NM_201644	394434	Mm.300095	NM_201644	ENSMUSG00000090175	Ugt1a9	UDPGT|UDPGT 1-9|UGT1-09|UGT1.9|UGTP4|Ugt1a12|mUGTBr/P	UDP glucuronosyltransferase 1 family, polypeptide A9	protein-coding
mm_72089.1	chr8	71580430	71580446	+	1	NA	intron (NM_011977, intron 6 of 13)	intron (NM_011977, intron 6 of 13)	11511	NM_011977	26457	Mm.38165	NM_011977	ENSMUSG00000031808	Slc27a1	FATP1|Fatp	solute carrier family 27 (fatty acid transporter), member 1	protein-coding
mm_92702.1	chr10	80714015	80714033	-	1	NA	exon (NM_007460, exon 19 of 31)	exon (NM_007460, exon 19 of 31)	11331	NM_027829	71564	Mm.35802	NM_027829	ENSMUSG00000055862	Izumo4	9030607L17Rik|AI550407	IZUMO family member 4	protein-coding
mm_173232.1	chrX	8038958	8038961	-	1	NA	Intergenic	Intergenic	-20467	NM_027227	69824	Mm.279756	NM_027227	ENSMUSG00000031163	Glod5	2010001H14Rik|AV061890	glyoxalase domain containing 5	protein-coding
mm_134998.1	chr16	32165687	32165697	-	1	NA	promoter-TSS (NM_001347181)	promoter-TSS (NM_001347181)	-98	NM_001347181	224109	Mm.33498	NM_146069	ENSMUSG00000052384	Nrros	E430025L02Rik|Lrcc33|Lrrc33	negative regulator of reactive oxygen species	protein-coding
mm_39764.1	chr5	30013281	30013323	+	1	NA	intron (NM_001314054, intron 1 of 4)	intron (NM_001314054, intron 1 of 4)	188	NM_031168	16193	Mm.1019	NM_031168	ENSMUSG00000025746	Il6	Il-6	interleukin 6	protein-coding
mm_74480.1	chr8	4295535	4295554	-	1	NA	exon (NM_010485, exon 5 of 6)	exon (NM_010485, exon 5 of 6)	-19639	NM_011592	21856	Mm.195249	NM_011592	ENSMUSG00000002949	Timm44	0710005E20Rik|D8Ertd118e|Mimt44|Tim44	translocase of inner mitochondrial membrane 44	protein-coding
mm_36487.1	chr4	83052187	83052197	-	1	NA	promoter-TSS (NM_001198811)	promoter-TSS (NM_001198811)	-25	NM_001198811	329872	Mm.242337	NM_177863	ENSMUSG00000059049	Frem1	BC037594|D430009N09|D630008K06|crf11|eye<m02Jus>|eyes2|heb|qbrick	Fras1 related extracellular matrix protein 1	protein-coding
mm_13719.1	chr2	117249726	117249754	+	1	NA	promoter-TSS (NM_026620)	promoter-TSS (NM_026620)	1	NM_026620	68215	Mm.219389	NM_026620	ENSMUSG00000027349	Fam98b	2610510H03Rik	family with sequence similarity 98, member B	protein-coding
mm_156394.1	chrX	139806070	139806079	+	1	NA	intron (NM_016675, intron 1 of 1)	intron (NM_016675, intron 1 of 1)	5266	NM_016675	12738	Mm.117068	NM_016675	ENSMUSG00000047230	Cldn2	AL022813	claudin 2	protein-coding
mm_37274.1	chr4	118620764	118620792	-	1	NA	promoter-TSS (NM_026789)	promoter-TSS (NM_026789)	-21	NM_026932	69072	Mm.29906	NM_026932	ENSMUSG00000028729	Ebna1bp2	1810014B19Rik|AA537058|B830003A16Rik|C81321|Ebp2|Nobp|p40	EBNA1 binding protein 2	protein-coding
mm_115366.1	chr13	112993823	112993838	+	1	NA	promoter-TSS (NM_001037914)	promoter-TSS (NM_001037914)	-38	NM_001037914	622408	Mm.360976	NM_001037914	ENSMUSG00000074651	Mcidas	EG622408|Gm6320|Idas|Mci|Mcin	multiciliate differentiation and DNA synthesis associated cell cycle protein	protein-coding
mm_27997.1	chr3	82876384	82876423	-	1	NA	promoter-TSS (NM_001146328)	promoter-TSS (NM_001146328)	80	NM_001277170	633285	Mm.265114	NM_001146328	ENSMUSG00000033882	Rbm46	EG633285|ENSMUSG00000033882|Gm761	RNA binding motif protein 46	protein-coding
mm_55288.1	chr6	54566284	54566296	-	1	NA	promoter-TSS (NM_027268)	promoter-TSS (NM_027268)	92	NM_027268	69938	Mm.41557	NM_027268	ENSMUSG00000019124	Scrn1	2810019K23Rik|6330535A03Rik|AI852905|SES1|mKIAA0193	secernin 1	protein-coding
mm_468.1	chr1	36372199	36372208	+	1	NA	promoter-TSS (NM_001277076)	promoter-TSS (NM_001277076)	-88	NM_001277076	100534273	Mm.389112	NM_001277076	ENSMUSG00000037432	Fer1l5	4930533C12Rik	fer-1-like 5 (C. elegans)	protein-coding
mm_30526.1	chr4	3090304	3090310	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	-81776	NM_001167534	100312470	Mm.480297	NM_001167534	ENSMUSG00000094798	Vmn1r2	Gm11776|OTTMUSG00000004179	vomeronasal 1 receptor 2	protein-coding
mm_98199.1	chr11	87795784	87795792	+	1	NA	intron (NM_010824, intron 4 of 13)	intron (NM_010824, intron 4 of 13)	2004	NM_010824	17523	Mm.4668	NM_010824	ENSMUSG00000009350	Mpo	mKIAA4033	myeloperoxidase	protein-coding
mm_93235.1	chr10	95324147	95324157	-	1	NA	promoter-TSS (NM_001330175)	promoter-TSS (NM_001330175)	-15	NM_009950	12905	Mm.473739	NM_009950	ENSMUSG00000045867	Cradd	RAIDD	CASP2 and RIPK1 domain containing adaptor with death domain	protein-coding
mm_74142.1	chr8	123254232	123254278	+	1	NA	promoter-TSS (NM_020497)	promoter-TSS (NM_020497)	-33	NM_028200	72325	Mm.276193	NM_028200	ENSMUSG00000001062	Vps9d1	1300018I17Rik|2410004N05Rik|5DOS1|Vsp9d1	VPS9 domain containing 1	protein-coding
mm_128846.1	chr15	71727734	71727744	-	1	NA	promoter-TSS (NM_177819)	promoter-TSS (NM_177819)	99	NM_177819	70363	Mm.126450	NM_177819	ENSMUSG00000036800	Fam135b	1700010C24Rik|A830008O07Rik	family with sequence similarity 135, member B	protein-coding
mm_85216.1	chr9	96966576	96966585	-	1	NA	intron (NM_145134, intron 2 of 2)	intron (NM_145134, intron 2 of 2)	51775	NM_145134	211949	Mm.491271	NM_145134	ENSMUSG00000046997	Spsb4	D030068E18Rik|SSB-4|Ssb4	splA/ryanodine receptor domain and SOCS box containing 4	protein-coding
mm_38290.1	chr4	136890440	136890448	-	1	NA	exon (NM_007574, exon 3 of 3)	exon (NM_007574, exon 3 of 3)	2470	NM_007574	12262	Mm.439732	NM_007574	ENSMUSG00000036896	C1qc	AI385742|C1qg|Ciqc	complement component 1, q subcomponent, C chain	protein-coding
mm_128339.1	chr15	38519256	38519271	-	1	NA	promoter-TSS (NM_001301688)	promoter-TSS (NM_001301688)	3	NM_001301688	54375	Mm.250214	NM_018745	ENSMUSG00000037458	Azin1	1700085L02Rik|AZI|Oazi|Oazin	antizyme inhibitor 1	protein-coding
mm_153910.1	chr19	47138251	47138276	-	1	NA	promoter-TSS (NM_133746)	promoter-TSS (NM_133746)	31	NM_133746	72691	Mm.31663	NM_133746	ENSMUSG00000033033	Calhm2	2810048G17Rik|Fam26b	calcium homeostasis modulator 2	protein-coding
mm_150343.1	chr19	34607928	34607936	+	1	NA	promoter-TSS (NM_001005858)	promoter-TSS (NM_001005858)	-25	NM_001005858	667370	Mm.271850	NM_001005858	ENSMUSG00000062488	Ifit3b	I830012O16Rik	interferon-induced protein with tetratricopeptide repeats 3B	protein-coding
mm_12007.1	chr2	57295814	57295817	+	1	NA	intron (NM_001145820, intron 3 of 16)	intron (NM_001145820, intron 3 of 16)	57433	NM_010274	14571	Mm.3711	NM_010274	ENSMUSG00000026827	Gpd2	AA408484|AI448216|AU021455|AW494132|GPDH|Gdm1|Gpd-m|Gpdh-m|TISP38	glycerol phosphate dehydrogenase 2, mitochondrial	protein-coding
mm_148867.1	chr19	6497413	6497449	+	1	NA	intron (NM_001205234, intron 17 of 22)	CpG	45639	NM_009203	20521	Mm.391146	NM_009203	ENSMUSG00000061742	Slc22a12	AI987855|OAT4L|Rst|Slc22al2|URAT1	solute carrier family 22 (organic anion/cation transporter), member 12	protein-coding
mm_136945.1	chr17	14399236	14399246	+	1	NA	promoter-TSS (NR_027986)	promoter-TSS (NR_027986)	-299	NR_027986	74917	Mm.32228	NM_183107		4930474M22Rik	-	RIKEN cDNA 4930474M22 gene	ncRNA
mm_33919.1	chr4	136538260	136538296	+	1	NA	intron (NM_024452, intron 2 of 4)	LSU-rRNA_Hsa|rRNA|rRNA	64445	NM_133872	99982	Mm.28540	NM_133872	ENSMUSG00000036940	Kdm1a	1810043O07Rik|AA408884|Aof2|D4Ertd478e|Kdm1|Lsd1|mKIAA0601	lysine (K)-specific demethylase 1A	protein-coding
mm_136098.1	chr16	85079946	85079965	-	1	NA	exon (NM_001198823, exon 5 of 18)	exon (NM_001198823, exon 5 of 18)	93752	NM_001198825	11820	Mm.277585	NM_007471	ENSMUSG00000022892	App	Abeta|Abpp|Adap|Ag|Cvap|E030013M08Rik|betaApp	amyloid beta (A4) precursor protein	protein-coding
mm_57300.1	chr6	124496103	124496107	-	1	NA	intron (NM_181344, intron 2 of 5)	ID4_|SINE|ID	2992	NM_181344	232371	Mm.132974	NM_181344	ENSMUSG00000038527	C1rl	C1r-LP|C1rl1|C1rlp	complement component 1, r subcomponent-like	protein-coding
mm_101776.1	chr11	44618066	44618069	-	1	NA	promoter-TSS (NM_001290711)	promoter-TSS (NM_001290711)	-33	NM_001290711	13591	Mm.439662	NM_007897	ENSMUSG00000057098	Ebf1	Ebf|O/E-1|OE-1|Olf-1|Olf1	early B cell factor 1	protein-coding
mm_142526.1	chr17	46407553	46407587	-	1	NA	intron (NM_207671, intron 6 of 9)	intron (NM_207671, intron 6 of 9)	-21372	NM_053250	114570	Mm.25168	NM_053250	ENSMUSG00000023968	Crip3	TLP|TLP-A|TLP-B|Tlmp	cysteine-rich protein 3	protein-coding
mm_99577.1	chr11	104186346	104186358	+	1	NA	promoter-TSS (NM_001082535)	promoter-TSS (NM_001082535)	25	NM_199019	237958	Mm.117063	NM_199019	ENSMUSG00000049506	Sppl2c	4933407P14Rik|IMP5	signal peptide peptidase 2C	protein-coding
mm_42586.1	chr5	117319342	117319352	+	1	NA	promoter-TSS (NM_001033311)	promoter-TSS (NM_001033311)	81	NM_001033311	231668	Mm.298603	NM_001033311	ENSMUSG00000066894	Vsig10	-	V-set and immunoglobulin domain containing 10	protein-coding
mm_145109.1	chr18	44116190	44116196	+	1	NA	Intergenic	Intergenic	11670	NM_030061	78242	Mm.99782	NM_030061	ENSMUSG00000061144	Spink12	9230117E20Rik	serine peptidase inhibitor, Kazal type 12	protein-coding
mm_51043.1	chr6	65612222	65612225	+	1	NA	intron (NM_001001495, intron 6 of 7)	intron (NM_001001495, intron 6 of 7)	21825	NM_001001495	414084	Mm.117558	NM_001001495	ENSMUSG00000044162	Tnip3	9030611K07Rik|ABIN-3|LIND	TNFAIP3 interacting protein 3	protein-coding
mm_4426.1	chr1	172505752	172505771	+	1	NA	exon (NM_178598, exon 3 of 5)	exon (NM_178598, exon 3 of 5)	5515	NM_178598	21346	Mm.271711	NM_178598	ENSMUSG00000026547	Tagln2	2700094C18Rik|SM22beta|Sm22B|Sm22a	transgelin 2	protein-coding
mm_32429.1	chr4	107178661	107178671	+	1	NA	promoter-TSS (NM_029565)	promoter-TSS (NM_029565)	36	NM_029565	56374	Mm.291192	NM_029565	ENSMUSG00000028618	Tmem59	1110001M20Rik|3110046P06Rik|AI256529|D4Ertd20e|MTDCF1|ORF18	transmembrane protein 59	protein-coding
mm_165400.1	chr2	136502037	136502039	+	1	NA	Intergenic	Intergenic	-30283	NM_175667	319196	Mm.477841	NM_175667	ENSMUSG00000074771	Ankef1	AV276460|Ankrd5	ankyrin repeat and EF-hand domain containing 1	protein-coding
mm_46211.1	chr5	98185924	98185963	-	1	NA	exon (NM_029947, exon 4 of 4)	exon (NM_029947, exon 4 of 4)	5074	NM_029947	77630	Mm.332511	NM_029947	ENSMUSG00000035456	Prdm8	4930565F05Rik|PFM5	PR domain containing 8	protein-coding
mm_103231.1	chr11	70681650	70681673	-	1	NA	exon (NM_001190378, exon 9 of 22)	exon (NM_001190378, exon 9 of 22)	6444	NM_001190376	216874	Mm.473726	NM_178116	ENSMUSG00000040712	Camta2	Kiaa0909-hp|mKIAA0909	calmodulin binding transcription activator 2	protein-coding
mm_161182.1	chr13	47063154	47063154	+	1	NA	intron (NM_172262, intron 9 of 20)	intron (NM_172262, intron 9 of 20)	19655	NM_172262	218214	Mm.31259	NM_172262	ENSMUSG00000038080	Kdm1b	4632428N09Rik|AI482520|Aof1	lysine (K)-specific demethylase 1B	protein-coding
mm_161299.1	chr14	30610383	30610383	-	1	NA	promoter-TSS (NM_001310682)	promoter-TSS (NM_001310682)	-73	NM_001310682	18753	Mm.2314	NM_011103	ENSMUSG00000021948	Prkcd	AI385711|D14Ertd420e|PKC[d]|PKCdelta|Pkcd	protein kinase C, delta	protein-coding
mm_568.1	chr1	38035782	38035822	+	1	NA	intron (NM_198303, intron 9 of 23)	intron (NM_198303, intron 9 of 23)	37792	NM_198303	226982	Mm.260943	NM_198303	ENSMUSG00000026083	Eif5b	A030003E17Rik|BC018347|IF2	eukaryotic translation initiation factor 5B	protein-coding
mm_64179.1	chr7	141459217	141459230	+	1	NA	non-coding (NR_028142, exon 9 of 10)	non-coding (NR_028142, exon 9 of 10)	-1871	NM_001025103	213573	Mm.386851	NM_001025103	ENSMUSG00000048200	Cracr2b	6330520A15Rik|BC026645|Cracr2a|Efcab4|Efcab4a	calcium release activated channel regulator 2B	protein-coding
mm_145735.1	chr18	64265191	64265203	+	1	NA	5' UTR (NM_009182, exon 3 of 6)	5' UTR (NM_009182, exon 3 of 6)	10838	NM_009182	20451	Mm.252110	NM_009182	ENSMUSG00000056812	St8sia3	AI847333|ST8SiaIII|Siat8c	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3	protein-coding
mm_157798.1	chrX	73921840	73921916	-	1	NA	promoter-TSS (NM_019870)	promoter-TSS (NM_019870)	66	NM_001310538	56292	Mm.246654	NM_019870	ENSMUSG00000031388	Naa10	2310039H09Rik|Ard1|Ard1a|Te2	N(alpha)-acetyltransferase 10, NatA catalytic subunit	protein-coding
mm_27401.1	chr3	51277278	51277306	-	1	NA	non-coding (NR_073429, exon 1 of 1)	non-coding (NR_073429, exon 1 of 1)	222	NM_001291062	69257	Mm.131038	NM_023502	ENSMUSG00000037174	Elf2	2610036A20Rik|A230104O07Rik|AW111824|BB183398|EU32|NERF|NERF-1A|NERF-1B|NERF-2	E74-like factor 2	protein-coding
mm_39156.1	chr4	155482888	155482897	-	1	NA	Intergenic	Intergenic	-8469	NM_001160017	14688	Mm.2344	NM_008142	ENSMUSG00000029064	Gnb1	AA409223|C77571|Gnb-1	guanine nucleotide binding protein (G protein), beta 1	protein-coding
mm_76207.1	chr8	83442425	83442436	-	1	NA	5' UTR (NM_019708, exon 1 of 4)	5' UTR (NM_019708, exon 1 of 4)	232	NM_001285992	56367	Mm.246911	NM_019708	ENSMUSG00000063253	Scoc	0610011C06Rik|2810002J11Rik|AA415030|SCOCO	short coiled-coil protein	protein-coding
mm_9950.1	chr1	190979184	190979190	-	1	NA	promoter-TSS (NM_144879)	promoter-TSS (NM_144879)	109	NR_027352	226841	Mm.22856	NM_144879	ENSMUSG00000037568	Vash2	B130052G07Rik	vasohibin 2	protein-coding
mm_85674.1	chr9	107709897	107709994	-	1	NA	intron (NM_011349, intron 1 of 17)	CpG	530	NM_011349	20350	Mm.12903	NM_011349	ENSMUSG00000034684	Sema3f	Sema4|Semak	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F	protein-coding
mm_64767.1	chr7	4971805	4971814	-	1	NA	promoter-TSS (NM_001200041)	promoter-TSS (NM_001200041)	-848	NM_001200041	381835	Mm.297828	NM_001200041	ENSMUSG00000085272	Sbk3	Gm1078|Sgk110	SH3 domain binding kinase family, member 3	protein-coding
mm_84211.1	chr9	61370480	61370528	-	1	NA	Intergenic	Intergenic	-1862	NM_001083928	21887	Mm.24255	NM_009389	ENSMUSG00000032280	Tle3	2610103N05Rik|ESG|Grg3a|Grg3b|mKIAA1547	transducin-like enhancer of split 3	protein-coding
mm_14635.1	chr2	136781762	136781770	+	1	NA	3' UTR (NM_001291056, exon 8 of 8)	3' UTR (NM_001291056, exon 8 of 8)	68316	NM_001291056	20614	Mm.45953	NM_011428	ENSMUSG00000027273	Snap25	Bdr|GENA70|SNAP-25|SUP|sp	synaptosomal-associated protein 25	protein-coding
mm_100120.1	chr11	115899845	115899879	+	1	NA	promoter-TSS (NM_183259)	promoter-TSS (NM_183259)	-277	NM_183259	66528	Mm.275740	NM_183259	ENSMUSG00000048442	Smim5	2210020M01Rik	small integral membrane protein 5	protein-coding
mm_90773.1	chr10	5828098	5828108	-	1	NA	3' UTR (NM_019958, exon 5 of 5)	3' UTR (NM_019958, exon 5 of 5)	-4160	NM_175374	108853	Mm.55082	NM_175374	ENSMUSG00000019774	Mtrf1l	9130004K12Rik	mitochondrial translational release factor 1-like	protein-coding
mm_150978.1	chr19	46501813	46501832	+	1	NA	5' UTR (NM_053100, exon 1 of 6)	5' UTR (NM_053100, exon 1 of 6)	174	NM_053100	93679	Mm.392177	NM_053100	ENSMUSG00000025034	Trim8	AA408830|BB006755|GERP|Rnf27	tripartite motif-containing 8	protein-coding
mm_98640.1	chr11	96194320	96194326	+	1	NA	promoter-TSS (NM_008267)	promoter-TSS (NM_008267)	-38	NM_008267	15408	Mm.57221	NM_008267	ENSMUSG00000049604	Hoxb13	-	homeobox B13	protein-coding
mm_32263.1	chr4	102593715	102593718	+	1	NA	intron (NM_001177982, intron 2 of 9)	intron (NM_001177982, intron 2 of 9)	3873	NM_001177981	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_150894.1	chr19	45472733	45472741	+	1	NA	intron (NM_001286466, intron 4 of 13)	intron (NM_001286466, intron 4 of 13)	87827	NM_001330506	56626	Mm.46509	NM_020032	ENSMUSG00000025218	Poll	1110003P06Rik|AV007317	polymerase (DNA directed), lambda	protein-coding
mm_138201.1	chr17	34293869	34293880	+	1	NA	Intergenic	Intergenic	-6103	NM_010378	14960	Mm.235338	NM_010378	ENSMUSG00000036594	H2-Aa	Aalpha|H-2Aa|H2Aa|I-Aalpha|IAalpha|Ia-1|Ia1	histocompatibility 2, class II antigen A, alpha	protein-coding
mm_26210.1	chr3	138742324	138742332	+	1	NA	non-coding (NR_121195, exon 1 of 8)	non-coding (NR_121195, exon 1 of 8)	120	NM_019571	56224	Mm.31927	NM_019571	ENSMUSG00000028152	Tspan5	2810455A09Rik|4930505M03Rik|NET-4|Tm4sf9	tetraspanin 5	protein-coding
mm_26516.1	chr3	145892773	145892777	+	1	NA	3' UTR (NM_026993, exon 6 of 6)	3' UTR (NM_026993, exon 6 of 6)	-31487	NM_009740	12042	Mm.239141	NM_009740	ENSMUSG00000028191	Bcl10	AI132454|BCL-10|C81403|CARMEN|CIPER|CLAP|ME10|cE10	B cell leukemia/lymphoma 10	protein-coding
mm_117060.1	chr13	58555072	58555091	-	1	NA	3' UTR (NM_022317, exon 18 of 18)	3' UTR (NM_022317, exon 18 of 18)	55796	NM_022317	114304	Mm.18188	NM_022317	ENSMUSG00000021553	Slc28a3	Cnt3	solute carrier family 28 (sodium-coupled nucleoside transporter), member 3	protein-coding
mm_145172.1	chr18	46921843	46921852	+	1	NA	promoter-TSS (NM_001033446)	promoter-TSS (NM_001033446)	32	NM_001033446	381142	Mm.329423	NM_001033446	ENSMUSG00000073568	Arl14epl	Gm949	ADP-ribosylation factor-like 14 effector protein-like	protein-coding
mm_34445.1	chr4	148000634	148000641	+	1	NA	promoter-TSS (NM_008725)	promoter-TSS (NM_008725)	-85	NM_008725	230899	Mm.482123	NM_008725	ENSMUSG00000041616	Nppa	ANP|Anf|Pnd	natriuretic peptide type A	protein-coding
mm_72568.1	chr8	84127515	84127525	+	1	NA	intron (NM_001013384, intron 3 of 9)	intron (NM_001013384, intron 3 of 9)	1531	NM_001013384	244550	Mm.334654	NM_001013384	ENSMUSG00000012889	Podnl1	5832418A03Rik|Gm506	podocan-like 1	protein-coding
mm_91094.1	chr10	19062139	19062158	-	1	NA	Intergenic	Intergenic	-46738	NM_009397	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_67308.1	chr7	79388034	79388059	-	1	NA	Intergenic	RLTR41A2|LTR|ERV1	-1019	NM_001173483	19771	Mm.41653	NM_020599	ENSMUSG00000039194	Rlbp1	3110056M11Rik|CRALBP	retinaldehyde binding protein 1	protein-coding
mm_145235.1	chr18	50155518	50155521	+	1	NA	intron (NM_008292, intron 9 of 23)	intron (NM_008292, intron 9 of 23)	27318	NM_008292	15488	Mm.277857	NM_008292	ENSMUSG00000024507	Hsd17b4	17-beta-HSD|17[b]-HSD|DBP|MFE-2|MFP2|MPF-2|Mfp-2|perMFE-2	hydroxysteroid (17-beta) dehydrogenase 4	protein-coding
mm_69501.1	chr7	134232081	134232094	-	1	NA	Intergenic	Intergenic	-6990	NM_007400	11489	Mm.439714	NM_007400	ENSMUSG00000054555	Adam12	Mltna	a disintegrin and metallopeptidase domain 12 (meltrin alpha)	protein-coding
mm_40519.1	chr5	57859223	57859225	+	1	NA	intron (NM_001310608, intron 1 of 3)	intron (NM_001310608, intron 1 of 3)	141143	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_12245.1	chr2	68870377	68870400	+	1	NA	intron (NM_172856, intron 1 of 9)	intron (NM_172856, intron 1 of 9)	8947	NM_001347161	241447	Mm.222222	NM_172856	ENSMUSG00000027035	Cers6	4732462C07Rik|AW544719|Lass6|T1L	ceramide synthase 6	protein-coding
mm_142158.1	chr17	36084233	36084255	-	1	NA	promoter-TSS (NM_008199)	promoter-TSS (NM_008199)	5	NM_008199	14963	Mm.477808	NM_008199	ENSMUSG00000073406	H2-Bl	H2-B1|H2-Bl-like	histocompatibility 2, blastocyst	protein-coding
mm_157022.1	chrX	7765798	7765811	-	1	NA	intron (NM_001271489, intron 2 of 9)	intron (NM_001271489, intron 2 of 9)	1763	NM_001271491	209446	Mm.249142	NM_172472	ENSMUSG00000000134	Tfe3	F830016E06Rik|Tcfe3|Tfe-3|bHLHe33	transcription factor E3	protein-coding
mm_83020.1	chr9	36798697	36798701	-	1	NA	Intergenic	MT2B1|LTR|ERVL	-1306	NM_001199494	13663	Mm.4337	NM_007915	ENSMUSG00000062762	Ei24	AA536736|AI115355|PIG8	etoposide induced 2.4 mRNA	protein-coding
mm_19039.1	chr2	76977190	76977206	-	1	NA	exon (NM_011652, exon 3 of 313)	exon (NM_011652, exon 3 of 313)	5349	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_85643.1	chr9	107655665	107655679	-	1	NA	exon (NM_001199218, exon 12 of 16)	exon (NM_001199218, exon 12 of 16)	11727	NM_023805	76257	Mm.296560	NM_023805	ENSMUSG00000010064	Slc38a3	0610012J02Rik|D9Ucla2|Nat1|Slc38-3|Sn1|Snat3|mNAT	solute carrier family 38, member 3	protein-coding
mm_154710.1	chrX	8892355	8892372	+	1	NA	promoter-TSS (NR_045448)	promoter-TSS (NR_045448)	10	NR_045448	102941	Mm.41588	NM_175327	ENSMUSG00000052364	B630019K06Rik	AI843180	novel protein similar to F-box and leucine-rich repeat protein 17 (Fbxl17)	pseudo
mm_78078.1	chr9	15709751	15709771	+	1	NA	promoter-TSS (NM_172289)	promoter-TSS (NM_172289)	-8	NM_172289	234967	Mm.138815	NM_172289	ENSMUSG00000043885	Slc36a4	6330573I15Rik|PAT4	solute carrier family 36 (proton/amino acid symporter), member 4	protein-coding
mm_146903.1	chr18	31316903	31316911	-	1	NA	exon (NM_009065, exon 1 of 5)	exon (NM_009065, exon 1 of 5)	221	NM_009065	19762	Mm.5163	NM_009065	ENSMUSG00000057455	Rit2	RIBA|Rin|Roc2	Ras-like without CAAX 2	protein-coding
mm_81781.1	chr9	114688867	114688877	+	1	NA	promoter-TSS (NM_146229)	promoter-TSS (NM_146229)	41	NM_146229	235661	Mm.128627	NM_146229	ENSMUSG00000032435	Dync1li1	1110053F02Rik|Dnclic1|LIC-1	dynein cytoplasmic 1 light intermediate chain 1	protein-coding
mm_82941.1	chr9	35305367	35305371	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	24264	NR_040715	71133	Mm.158577	NR_040715	ENSMUSG00000111746	4933422A05Rik	-	RIKEN cDNA 4933422A05 gene	ncRNA
mm_33895.1	chr4	136206380	136206405	+	1	NA	promoter-TSS (NM_001008232)	promoter-TSS (NM_001008232)	27	NM_001008232	230837	Mm.77788	NM_001008232	ENSMUSG00000036995	Asap3	9430088F20Rik|Ddefl1|Gm140|UPLC1	ArfGAP with SH3 domain, ankyrin repeat and PH domain 3	protein-coding
mm_150897.1	chr19	45527366	45527394	+	1	NA	exon (NM_001286466, exon 13 of 14)	exon (NM_001286466, exon 13 of 14)	33184	NM_001330506	56626	Mm.46509	NM_020032	ENSMUSG00000025218	Poll	1110003P06Rik|AV007317	polymerase (DNA directed), lambda	protein-coding
mm_71232.1	chr8	40906268	40906281	+	1	NA	intron (NM_007514, intron 6 of 11)	intron (NM_007514, intron 6 of 11)	-19959	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_1802.1	chr1	80445924	80445936	+	1	NA	promoter-TSS (NR_040460)	promoter-TSS (NR_040460)	-2	NR_040460	72208	Mm.396181	NR_040460	ENSMUSG00000101483	1700016L21Rik	Jr3	RIKEN cDNA 1700016L21 gene	ncRNA
mm_141459.1	chr17	30571132	30571154	-	1	NA	intron (NM_172618, intron 1 of 11)	intron (NM_172618, intron 1 of 11)	5144	NM_172618	224671	Mm.41220	NM_027060	ENSMUSG00000062202	Btbd9	1700023F20Rik|4930402L05|AI464421	BTB (POZ) domain containing 9	protein-coding
mm_150345.1	chr19	34640874	34640897	+	1	NA	promoter-TSS (NM_053217)	promoter-TSS (NM_053217)	-4	NM_008331	15957	Mm.439751	NM_008331	ENSMUSG00000034459	Ifit1	ISG56|Ifi56|P56	interferon-induced protein with tetratricopeptide repeats 1	protein-coding
mm_107.1	chr1	9601164	9601256	+	1	NA	promoter-TSS (NM_178399)	promoter-TSS (NM_178399)	-57	NM_178399	76982	Mm.491098	NM_178399	ENSMUSG00000067879	3110035E14Rik	AI415019|AV164974|R75066	RIKEN cDNA 3110035E14 gene	protein-coding
mm_50993.1	chr6	63256622	63256627	+	1	NA	promoter-TSS (NM_008167)	promoter-TSS (NM_008167)	-233	NM_008167	14804	Mm.439651	NM_008167	ENSMUSG00000071424	Grid2	B230104L07Rik|GluD2|GluRdelta2|Lc|Lc<J>|MMS10-AC|Ms10ac|cpr|ho|nmf408|tpr	glutamate receptor, ionotropic, delta 2	protein-coding
mm_129952.1	chr15	85042263	85042269	-	1	NA	intron (NM_133750, intron 1 of 8)	intron (NM_133750, intron 1 of 8)	5204	NM_133750	73225	Mm.247535	NM_133750	ENSMUSG00000022434	Fam118a	-	family with sequence similarity 118, member A	protein-coding
mm_61051.1	chr7	49910113	49910127	+	1	NA	promoter-TSS (NM_001146013)	promoter-TSS (NM_001146013)	-179	NM_001146013	104245	Mm.207053	NM_148931	ENSMUSG00000039728	Slc6a5	Glyt2|prestin	solute carrier family 6 (neurotransmitter transporter, glycine), member 5	protein-coding
mm_54699.1	chr6	39557831	39557851	-	1	NA	promoter-TSS (NM_172477)	promoter-TSS (NM_172477)	-7	NM_172477	209773	Mm.440021	NM_172477	ENSMUSG00000038456	Dennd2a	B930096L08Rik|C130031G22|mKIAA1277	DENN/MADD domain containing 2A	protein-coding
mm_138253.1	chr17	34590410	34590448	+	1	NA	intron (NM_134116, intron 1 of 3)	intron (NM_134116, intron 1 of 3)	623	NM_134116	106512	Mm.26584	NM_134116	ENSMUSG00000034786	Gpsm3	AA960287|AGS4	G-protein signalling modulator 3 (AGS3-like, C. elegans)	protein-coding
mm_51876.1	chr6	90559357	90559363	+	1	NA	exon (NM_027406, exon 3 of 23)	exon (NM_027406, exon 3 of 23)	8512	NM_027406	107747	Mm.30035	NM_027406	ENSMUSG00000030088	Aldh1l1	1810048F20Rik|FDH|Fthfd|Neut2	aldehyde dehydrogenase 1 family, member L1	protein-coding
mm_44264.1	chr5	5559522	5559545	-	1	NA	promoter-TSS (NM_153116)	promoter-TSS (NM_153116)	-32	NM_153116	207704	Mm.323984	NM_153116	ENSMUSG00000040464	Gtpbp10	4930545J22Rik|BC034507	GTP-binding protein 10 (putative)	protein-coding
mm_32325.1	chr4	103851433	103851448	+	1	NA	Intergenic	Intergenic	468940	NR_040673	622167	Mm.244115	NR_040673	ENSMUSG00000086136	Gm12718	OTTMUSG00000008109	predicted gene 12718	ncRNA
mm_78709.1	chr9	41378433	41378464	+	1	NA	intron (NR_131928, intron 1 of 4)	intron (NR_131928, intron 1 of 4)	1922	NR_131928	73144	Mm.38166	NM_001033153	ENSMUSG00000074415	3110039I08Rik	2610203C20Rik|AI848448|D230004N17Rik|D3Mgi9|Mir100hg	RIKEN cDNA 3110039I08 gene	ncRNA
mm_122339.1	chr14	37135187	37135197	-	1	NA	promoter-TSS (NM_001199122)	promoter-TSS (NM_001199122)	-53	NM_001199122	66092	Mm.182912	NM_078478	ENSMUSG00000041028	Ghitm	1010001P14Rik|C77840|MICS1|PTD010|Tmbim5	growth hormone inducible transmembrane protein	protein-coding
mm_83854.1	chr9	54642658	54642669	-	1	NA	exon (NM_053178, exon 2 of 14)	exon (NM_053178, exon 2 of 14)	19222	NM_053178	94180	Mm.20592	NM_053178	ENSMUSG00000032281	Acsbg1	BG1|Bgm|E230019G03Rik|GR-LACS|Lpd|R75185	acyl-CoA synthetase bubblegum family member 1	protein-coding
mm_44742.1	chr5	31193077	31193090	-	1	NA	promoter-TSS (NM_001127356)	promoter-TSS (NM_001127356)	56	NM_001127355	13667	Mm.29394	NM_010122	ENSMUSG00000029145	Eif2b4	Eif2b	eukaryotic translation initiation factor 2B, subunit 4 delta	protein-coding
mm_152453.1	chr19	10841707	10841720	-	1	NA	promoter-TSS (NM_023044)	promoter-TSS (NM_023044)	-831	NM_023044	65221	Mm.27387	NM_023044	ENSMUSG00000024737	Slc15a3	Ci1|cI-1	solute carrier family 15, member 3	protein-coding
mm_151589.1	chr19	3282959	3283048	-	1	NA	promoter-TSS (NM_009212)	promoter-TSS (NM_009212)	7	NM_009212	20589	Mm.3179	NM_009212	ENSMUSG00000024831	Ighmbp2	AEP|Catf1|RIPE3b1|Smbp-2|Smbp2|Smubp2|nmd|sma	immunoglobulin mu binding protein 2	protein-coding
mm_115908.1	chr13	23445903	23445949	-	1	NA	Intergenic	CpG	-14909	NR_015492	320842	Mm.487476	NR_015492	ENSMUSG00000085024	C230035I16Rik	-	RIKEN cDNA C230035I16 gene	ncRNA
mm_112593.1	chr13	13954695	13954705	+	1	NA	promoter-TSS (NM_178640)	promoter-TSS (NM_178640)	26	NM_178640	97884	Mm.21686	NM_178640	ENSMUSG00000039242	B3galnt2	A930105D20Rik|C80633|D230016N13Rik	UDP-GalNAc:betaGlcNAc beta 1,3-galactosaminyltransferase, polypeptide 2	protein-coding
mm_119836.1	chr14	54426903	54426930	+	1	NA	promoter-TSS (NM_026851)	promoter-TSS (NM_026851)	7	NM_026851	68836	Mm.248163	NM_026851	ENSMUSG00000010406	Mrpl52	1110047B07Rik	mitochondrial ribosomal protein L52	protein-coding
mm_20109.1	chr2	121140344	121140362	-	1	NA	promoter-TSS (NM_001290812)	promoter-TSS (NM_001290812)	-75	NM_001290811	75894	Mm.384805	NM_029475	ENSMUSG00000027259	Adal	4930578F03Rik	adenosine deaminase-like	protein-coding
mm_40603.1	chr5	64360366	64360408	+	1	NA	Intergenic	MLTR14|LTR|ERV1	107555	NR_040681	69999	Mm.261413	NR_040681	ENSMUSG00000100911	1700027F09Rik	-	RIKEN cDNA 1700027F09 gene	ncRNA
mm_96250.1	chr11	62575936	62575964	+	1	NA	intron (NM_011706, intron 1 of 15)	intron (NM_011706, intron 1 of 15)	1464	NM_011706	22368	Mm.288064	NM_011706	ENSMUSG00000018507	Trpv2	GRC|OTRPC2|VRL-1|Vrl1	transient receptor potential cation channel, subfamily V, member 2	protein-coding
mm_3311.1	chr1	137901181	137901190	+	1	NA	Intergenic	Intergenic	-65270	NR_029795	735252		NR_029795	ENSMUSG00000065565	Mir181a-1	Mirn181a-1|Mirn213|miR-213|mir-181a-1|mmu-mir-213	microRNA 181a-1	ncRNA
mm_30334.1	chr3	151732240	151732284	-	1	NA	3' UTR (NM_133871, exon 8 of 8)	3' UTR (NM_133871, exon 8 of 8)	17697	NM_133871	99899	Mm.30756	NM_133871	ENSMUSG00000028037	Ifi44	A430056A10Rik|AW261460|MTAP44|p44	interferon-induced protein 44	protein-coding
mm_109399.1	chr12	109948838	109948849	+	1	NA	Intergenic	Intergenic	200965	NR_037233	100499517		NR_037233	ENSMUSG00000093351	Mir3072	mir-3072|mmu-mir-3072	microRNA 3072	ncRNA
mm_79786.1	chr9	63281326	63281360	+	1	NA	intron (NM_011840, intron 12 of 21)	intron (NM_011840, intron 12 of 21)	96509	NM_011840	23938	Mm.325746	NM_011840	ENSMUSG00000058444	Map2k5	AI324775|AI428457|MEK5|Mapkk5|Prkmk5	mitogen-activated protein kinase kinase 5	protein-coding
mm_168287.1	chr11	100859575	100859575	+	1	NA	promoter-TSS (NM_001164062)	promoter-TSS (NM_001164062)	224	NM_011488	20850	Mm.277403	NM_011488	ENSMUSG00000004043	Stat5a	AA959963|STAT5	signal transducer and activator of transcription 5A	protein-coding
mm_85695.1	chr9	108080275	108080306	-	1	NA	promoter-TSS (NM_008243)	promoter-TSS (NM_008243)	-146	NM_008243	15235	Mm.8369	NM_008243	ENSMUSG00000032591	Mst1	D3F15S2h|D9H3F15S2|DNF15S2h|Hgfl	macrophage stimulating 1 (hepatocyte growth factor-like)	protein-coding
mm_24718.1	chr3	95232292	95232315	+	1	NA	intron (NM_001038708, intron 2 of 4)	intron (NM_001038708, intron 2 of 4)	3360	NM_001038708	57912	Mm.28189	NM_172395	ENSMUSG00000046722	Cdc42se1	1300002M12Rik|AW558204|Cdcse1|SCIP1|Spec1	CDC42 small effector 1	protein-coding
mm_96421.1	chr11	67256199	67256215	+	1	NA	exon (NM_010855, exon 34 of 40)	exon (NM_010855, exon 34 of 40)	18395	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_51630.1	chr6	85587506	85587516	+	1	NA	promoter-TSS (NM_145223)	promoter-TSS (NM_145223)	-20	NM_145223	236266	Mm.246967	NM_145223	ENSMUSG00000063810	Alms1	bbb	Alstrom syndrome 1	protein-coding
mm_161414.1	chr15	20666813	20666813	-	1	NA	promoter-TSS (NM_022816)	promoter-TSS (NM_022816)	-63	NM_022816	64833	Mm.352763	NM_022816	ENSMUSG00000047565	Acot10	Acate3|MT-ACT48|p48	acyl-CoA thioesterase 10	protein-coding
mm_172213.1	chr6	59200131	59200139	+	1	NA	Intergenic	L1Md_Gf|LINE|L1	-8735	NM_001081145	68140	Mm.25843	NM_001081145	ENSMUSG00000049232	Tigd2	3632410O17Rik	tigger transposable element derived 2	protein-coding
mm_166436.1	chr5	137207669	137207675	-	1	NA	Intergenic	Intergenic	-80582	NM_009599	11423	Mm.255464	NM_009599	ENSMUSG00000023328	Ache	-	acetylcholinesterase	protein-coding
mm_146891.1	chr18	25754327	25754334	-	1	NA	promoter-TSS (NM_001146295)	promoter-TSS (NM_001146295)	-347	NM_001174074	108013	Mm.266435	NM_133195	ENSMUSG00000024268	Celf4	A230070D14Rik|BRUNOL-4|Brul4|Brunol4|C130060B05Rik	CUGBP, Elav-like family member 4	protein-coding
mm_25811.1	chr3	127790603	127790639	+	1	NA	intron (NM_145133, intron 1 of 2)	intron (NM_145133, intron 1 of 2)	708	NM_145133	211550	Mm.31852	NM_145133	ENSMUSG00000046688	Tifa	T2bp	TRAF-interacting protein with forkhead-associated domain	protein-coding
mm_44654.1	chr5	28210393	28210396	-	1	NA	promoter-TSS (NM_001310511)	promoter-TSS (NM_001310511)	-226	NM_001310511	269637	Mm.68286	NM_175651	ENSMUSG00000044681	Cnpy1	1500012D20Rik|9630008K15Rik|AI853839	canopy FGF signaling regulator 1	protein-coding
mm_102292.1	chr11	55410010	55410022	-	1	NA	intron (NM_001290817, intron 1 of 9)	intron (NM_001290817, intron 1 of 9)	10064	NM_009242	20692	Mm.291442	NM_009242	ENSMUSG00000018593	Sparc	BM-40|ON	secreted acidic cysteine rich glycoprotein	protein-coding
mm_8539.1	chr1	155059559	155059575	-	1	NA	Intergenic	Intergenic	40069	NM_010500	15939	Mm.12246	NM_010500	ENSMUSG00000056708	Ier5	-	immediate early response 5	protein-coding
mm_112629.1	chr13	15922192	15922199	+	1	NA	Intergenic	Intergenic	-89656	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_35441.1	chr4	40210134	40210138	-	1	NA	intron (NM_172689, intron 14 of 17)	intron (NM_172689, intron 14 of 17)	29689	NM_172689	230073	Mm.86382	NM_172689	ENSMUSG00000040296	Ddx58	6430573D20Rik|C330021E21|RIG-I|RLR-1	DEAD (Asp-Glu-Ala-Asp) box polypeptide 58	protein-coding
mm_157914.1	chrX	78552776	78552786	-	1	NA	intron (NM_027322, intron 1 of 3)	RLTR14-int|LTR|ERV1	31024	NM_001164275	546336	Mm.211712	NM_027322	ENSMUSG00000047996	Prrg1	2010007L08Rik	proline rich Gla (G-carboxyglutamic acid) 1	protein-coding
mm_78486.1	chr9	32699411	32699423	+	1	NA	intron (NM_011808, intron 1 of 7)	intron (NM_011808, intron 1 of 7)	3375	NM_001038642	23871	Mm.292415	NM_011808	ENSMUSG00000032035	Ets1	AI196000|AI448617|D230050P06|Ets-1|Tpl1|vs	E26 avian leukemia oncogene 1, 5' domain	protein-coding
mm_104238.1	chr11	88718079	88718104	-	1	NA	promoter-TSS (NR_038058)	promoter-TSS (NR_038058)	138	NM_054043	76626	Mm.400451	NM_054043	ENSMUSG00000069769	Msi2	1700105C15Rik|AI451722|AI563628|AW489193|Msi2h	musashi RNA-binding protein 2	protein-coding
mm_115095.1	chr13	102720435	102720471	+	1	NA	Intergenic	Lx2|LINE|L1	26895	NM_008533	17079	Mm.373974	NM_008533	ENSMUSG00000021624	Cd180	F630107B15|Ly78|RP105	CD180 antigen	protein-coding
mm_82084.1	chr9	123034723	123034728	+	1	NA	promoter-TSS (NM_177911)	promoter-TSS (NM_177911)	-16	NM_177911	331046	Mm.195309	NM_177911	ENSMUSG00000025787	Tgm4	9530008N10Rik|Eapa1|TGP	transglutaminase 4 (prostate)	protein-coding
mm_66788.1	chr7	47091379	47091389	-	1	NA	exon (NM_001163565, exon 3 of 14)	exon (NM_001163565, exon 3 of 14)	-8160	NR_106023	102465639		NR_106023	ENSMUSG00000098960	Mir7056	Gm27696|mmu-mir-7056	microRNA 7056	ncRNA
mm_150278.1	chr19	34251727	34251741	+	1	NA	exon (NM_007392, exon 3 of 9)	exon (NM_007392, exon 3 of 9)	3639	NM_007392	11475	Mm.213025	NM_007392	ENSMUSG00000035783	Acta2	0610041G09Rik|Actvs|SMalphaA|a-SMA|alphaSMA	actin, alpha 2, smooth muscle, aorta	protein-coding
mm_101263.1	chr11	21174603	21174626	-	1	NA	Intergenic	Intergenic	-64418	NM_139061	245944	Mm.170103	NM_139061	ENSMUSG00000020128	Vps54	Hcc8|Vps54l|mSLP8|wr	VPS54 GARP complex subunit	protein-coding
mm_85323.1	chr9	101862395	101862401	-	1	NA	Intergenic	Intergenic	442577	NR_106163	102466241		NR_106163	ENSMUSG00000098521	Mir7243	Gm27363|mmu-mir-7243	microRNA 7243	ncRNA
mm_93455.1	chr10	110149586	110149615	-	1	NA	Intergenic	L1_Mus1|LINE|L1	-149381	NM_001081035	260315	Mm.225050	NM_177797	ENSMUSG00000020181	Nav3	4732483H20Rik|9630020C08Rik|POMFIL1|Pomfil1p|mKIAA0938|unc53H3	neuron navigator 3	protein-coding
mm_41011.1	chr5	81021211	81021241	+	1	NA	promoter-TSS (NM_198702)	promoter-TSS (NM_198702)	-367	NM_198702	319387	Mm.273631	NM_198702	ENSMUSG00000037605	Adgrl3	5430402I23Rik|CIRL-3|D130075K09Rik|Gm1379|LEC3|Lphn3|mKIAA0768	adhesion G protein-coupled receptor L3	protein-coding
mm_31688.1	chr4	62314064	62314073	+	1	NA	intron (NM_001045528, intron 20 of 27)	intron (NM_001045528, intron 20 of 27)	22521	NM_001290518	20530	Mm.292539	NM_025286	ENSMUSG00000066152	Slc31a2	AI604396|CTR2	solute carrier family 31, member 2	protein-coding
mm_109471.1	chr12	111420597	111420607	+	1	NA	intron (NM_001289487, intron 2 of 13)	intron (NM_001289487, intron 2 of 13)	3157	NM_001289488	74190	Mm.248640	NM_028807	ENSMUSG00000021280	Exoc3l4	1200009I06Rik|1600013K19Rik	exocyst complex component 3-like 4	protein-coding
mm_1438.1	chr1	67211320	67211332	+	1	NA	intron (NM_001080809, intron 29 of 37)	intron (NM_001080809, intron 29 of 37)	88299	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_11681.1	chr2	35562747	35562750	+	1	NA	intron (NM_001114125, intron 1 of 16)	intron (NM_001114125, intron 1 of 16)	-4046	NR_045894	100042194	Mm.330165	NR_045894	ENSMUSG00000086555	Gm13446	OTTMUSG00000012261	predicted gene 13446	ncRNA
mm_156592.1	chrX	152201968	152201975	+	1	NA	intron (NM_001005475, intron 2 of 13)	intron (NM_001005475, intron 2 of 13)	22962	NM_001005475	245666	Mm.33027	NM_001005475	ENSMUSG00000041115	Iqsec2	Brag1	IQ motif and Sec7 domain 2	protein-coding
mm_148291.1	chr18	82584514	82584541	-	1	NA	3' UTR (NM_010777, exon 7 of 7)	3' UTR (NM_010777, exon 7 of 7)	30019	NM_001025254	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_67741.1	chr7	90265447	90265457	-	1	NA	promoter-TSS (NM_183293)	promoter-TSS (NM_183293)	-20	NR_111924	75338	Mm.487222	NM_029256	ENSMUSG00000030617	Ccdc83	4930549K11Rik|4930554C01Rik|4932423M01Rik	coiled-coil domain containing 83	protein-coding
mm_12542.1	chr2	72297921	72297946	+	1	NA	intron (NM_023057, intron 1 of 19)	intron (NM_023057, intron 1 of 19)	12232	NM_178084	65964	Mm.304143	NM_023057	ENSMUSG00000004085	Map3k20	AV006891|B230120H23Rik|MLTK|MLTKalpha|MLTKbeta|Zak	mitogen-activated protein kinase kinase kinase 20	protein-coding
mm_106787.1	chr12	4769279	4769338	+	1	NA	promoter-TSS (NM_175431)	promoter-TSS (NM_175431)	13	NM_028376	382562	Mm.251575	NM_028376	ENSMUSG00000020639	Pfn4	2900024P18Rik	profilin family, member 4	protein-coding
mm_139979.1	chr17	71782635	71782721	+	1	NA	intron (NM_030179, intron 1 of 15)	CpG	731	NM_030179	78785	Mm.196382	NM_030179	ENSMUSG00000024059	Clip4	1700024K14Rik|1700074B05Rik|4833417L20Rik|5830409B12Rik|Rsnl2	CAP-GLY domain containing linker protein family, member 4	protein-coding
mm_141218.1	chr17	27203088	27203088	-	1	NA	intron (NM_146075, intron 1 of 8)	intron (NM_146075, intron 1 of 8)	1350	NM_146075	224640	Mm.29689	NM_146075	ENSMUSG00000044857	Lemd2	BC026588|Lem2|NET25	LEM domain containing 2	protein-coding
mm_53176.1	chr6	125349792	125349805	+	1	NA	promoter-TSS (NM_011609)	promoter-TSS (NM_011609)	75	NM_011609	21937	Mm.1258	NM_011609	ENSMUSG00000030341	Tnfrsf1a	CD120a|FPF|TNF-R|TNF-R-I|TNF-R1|TNF-R55|TNF-alphaR1|TNFAR|TNFR60|TNFRI|TNFRp55|TNFalpha-R1|Tnfr-2|Tnfr1|p55|p55-R	tumor necrosis factor receptor superfamily, member 1a	protein-coding
mm_131699.1	chr16	20716816	20716835	+	1	NA	promoter-TSS (NM_009900)	promoter-TSS (NM_009900)	-189	NM_009900	12724	Mm.177761	NM_009900	ENSMUSG00000022843	Clcn2	AL118368|ClC-2|Clc2|nmf240	chloride channel, voltage-sensitive 2	protein-coding
mm_60416.1	chr7	44476226	44476242	+	1	NA	Intergenic	L1MEd|LINE|L1	5887	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_34957.1	chr4	155993306	155993316	+	1	NA	promoter-TSS (NM_080445)	promoter-TSS (NM_080445)	-26	NM_001302468	20318	Mm.293517	NM_011341	ENSMUSG00000029076	Sdf4	Cab45	stromal cell derived factor 4	protein-coding
mm_125140.1	chr15	30500580	30500584	+	1	NA	intron (NM_008729, intron 3 of 22)	intron (NM_008729, intron 3 of 22)	327989	NM_008729	18163	Mm.321648	NM_008729	ENSMUSG00000022240	Ctnnd2	Catnd2|Nprap|neurojugin	catenin (cadherin associated protein), delta 2	protein-coding
mm_72375.1	chr8	81342562	81342575	+	1	NA	promoter-TSS (NM_001297596)	promoter-TSS (NM_001297596)	6	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_143314.1	chr17	66102008	66102018	-	1	NA	promoter-TSS (NM_028388)	promoter-TSS (NM_028388)	-454	NM_028388	72900	Mm.2206	NM_028388	ENSMUSG00000024099	Ndufv2	2900010C23Rik	NADH dehydrogenase (ubiquinone) flavoprotein 2	protein-coding
mm_84544.1	chr9	67321963	67321973	-	1	NA	intron (NM_001081242, intron 28 of 57)	intron (NM_001081242, intron 28 of 57)	-85242	NR_029576	387185		NR_029576	ENSMUSG00000076379	Mir190a	Mir190|Mirn190|mir-190|mir-190a|mmu-mir-190|mmu-mir-190a	microRNA 190a	ncRNA
mm_41904.1	chr5	105579485	105579503	+	1	NA	exon (NM_133897, exon 3 of 4)	exon (NM_133897, exon 3 of 4)	60023	NM_133897	100604	Mm.319847	NM_133897	ENSMUSG00000054720	Lrrc8c	AD158|AI326115|E430036I04Rik|fad158	leucine rich repeat containing 8 family, member C	protein-coding
mm_43778.1	chr5	142341335	142341346	+	1	NA	Intergenic	RMER17C|LTR|ERVK	-60157	NM_199068	17425	Mm.24214	NM_010812	ENSMUSG00000056493	Foxk1	A630048H08Rik|AI463295|ENSMUSG00000075577|Gm10868|Mnf	forkhead box K1	protein-coding
mm_25799.1	chr3	127780645	127780653	+	1	NA	promoter-TSS (NM_027808)	promoter-TSS (NM_027808)	-122	NM_027808	71481	Mm.158704	NM_027808	ENSMUSG00000028028	Alpk1	8430410J10Rik|LAK	alpha-kinase 1	protein-coding
mm_130021.1	chr15	88819280	88819335	-	1	NA	promoter-TSS (NM_001142357)	promoter-TSS (NM_001142357)	11	NM_001142357	223774	Mm.41512	NM_145477	ENSMUSG00000035845	Alg12	ECM39	asparagine-linked glycosylation 12 (alpha-1,6-mannosyltransferase)	protein-coding
mm_69455.1	chr7	133123161	133123185	-	1	NA	5' UTR (NM_009980, exon 1 of 11)	5' UTR (NM_009980, exon 1 of 11)	310	NM_009980	13017	Mm.246240	NM_009980	ENSMUSG00000030970	Ctbp2	AA407280|D7Ertd45e|Gtrgeo6|Ribeye	C-terminal binding protein 2	protein-coding
mm_2817.1	chr1	130878421	130878442	+	1	NA	intron (NM_026976, intron 6 of 7)	CpG	8980	NM_053095	93672	Mm.196691	NM_053095	ENSMUSG00000026420	Il24	FISP|Mda-7|Mda7|St16	interleukin 24	protein-coding
mm_49823.1	chr6	37539715	37539726	+	1	NA	intron (NM_145364, intron 3 of 8)	MLTR18C_MM|LTR|ERVK	9547	NM_145364	208665	Mm.262635	NM_145364	ENSMUSG00000038641	Akr1d1	-	aldo-keto reductase family 1, member D1	protein-coding
mm_148882.1	chr19	6532486	6532498	+	1	NA	3' UTR (NM_020253, exon 23 of 23)	3' UTR (NM_020253, exon 23 of 23)	10578	NM_009203	20521	Mm.391146	NM_009203	ENSMUSG00000061742	Slc22a12	AI987855|OAT4L|Rst|Slc22al2|URAT1	solute carrier family 22 (organic anion/cation transporter), member 12	protein-coding
mm_46048.1	chr5	92075652	92075655	-	1	NA	intron (NM_001080795, intron 1 of 10)	AT_rich|Low_complexity|Low_complexity	7264	NM_001080797	23881	Mm.290530	NM_011816	ENSMUSG00000029405	G3bp2	AA409541|E430034L04Rik|G3BP|mKIAA0660	GTPase activating protein (SH3 domain) binding protein 2	protein-coding
mm_144314.1	chr18	12643476	12643500	+	1	NA	promoter-TSS (NM_028341)	promoter-TSS (NM_028341)	-45	NM_028341	72747	Mm.52526	NM_028341	ENSMUSG00000024424	Ttc39c	1700008N02Rik|2810439F02Rik	tetratricopeptide repeat domain 39C	protein-coding
mm_12388.1	chr2	69870672	69870712	+	1	NA	TTS (NR_110977)	TTS (NR_110977)	9130	NM_009278	20823	Mm.10508	NM_009278	ENSMUSG00000068882	Ssb	SS-B	Sjogren syndrome antigen B	protein-coding
mm_1892.1	chr1	85688241	85688245	+	1	NA	intron (NM_001313712, intron 11 of 16)	intron (NM_001313712, intron 11 of 16)	38255	NM_001313714	20684	Mm.290906	NM_013673	ENSMUSG00000026222	Sp100	A430075G10Rik	nuclear antigen Sp100	protein-coding
mm_4054.1	chr1	165809731	165809734	+	1	NA	intron (NM_001113391, intron 1 of 7)	U6|snRNA|snRNA	21051	NM_001113392	12503	Mm.217308	NM_031162	ENSMUSG00000005763	Cd247	4930549J05Rik|A430104F18Rik|AW552088|Cd3|Cd3-eta|Cd3-zeta|Cd3h|Cd3z|Cd3zeta|T3z|Tcrk|Tcrz	CD247 antigen	protein-coding
mm_72534.1	chr8	83995727	83995744	+	1	NA	3' UTR (NM_008854, exon 10 of 10)	3' UTR (NM_008854, exon 10 of 10)	-1937	NM_001081415	666704	Mm.298091	NM_001081415	ENSMUSG00000079003	Samd1	AA589507	sterile alpha motif domain containing 1	protein-coding
mm_67356.1	chr7	79836398	79836408	-	1	NA	exon (NM_008486, exon 10 of 20)	exon (NM_008486, exon 10 of 20)	5949	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_20716.1	chr2	134644126	134644143	-	1	NA	promoter-TSS (NM_029148)	promoter-TSS (NM_029148)	-13	NM_029148	52837	Mm.264096	NM_029148	ENSMUSG00000034723	Tmx4	2810417D04Rik|4930500L08Rik|AI843224|AW046784|D2Bwg1356e|Txndc13|mKIAA1162	thioredoxin-related transmembrane protein 4	protein-coding
mm_122433.1	chr14	45173584	45173612	-	1	NA	intron (NM_001310534, intron 7 of 20)	RMER17D|LTR|ERVK	45827	NM_172597	70561	Mm.28129	NM_172597	ENSMUSG00000021830	Txndc16	5730420B22Rik|C77647	thioredoxin domain containing 16	protein-coding
mm_67822.1	chr7	98236509	98236530	-	1	NA	intron (NM_025408, intron 7 of 10)	L1MD1|LINE|L1	-37044	NM_001081167	272411	Mm.98333	NM_001081167	ENSMUSG00000074004	B3gnt6	BC039789|Core-3|Core3	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 6 (core 3 synthase)	protein-coding
mm_56330.1	chr6	92565603	92565640	-	1	NA	intron (NM_001081146, intron 2 of 8)	intron (NM_001081146, intron 2 of 8)	1745	NM_001134461	243548	Mm.248820	NM_001081146	ENSMUSG00000030020	Prickle2	6230400G14Rik|6720451F06Rik|mpk2	prickle planar cell polarity protein 2	protein-coding
mm_15262.1	chr2	155019149	155019157	+	1	NA	intron (NM_015770, intron 1 of 3)	ERVB4_1-I_MM-int|LTR|ERVK	5583	NM_015770	50518	Mm.315593	NM_015770	ENSMUSG00000027596	a	A<y>|ASIP|ASP|As	nonagouti	protein-coding
mm_136311.1	chr16	91688710	91688774	-	1	NA	promoter-TSS (NM_021720)	promoter-TSS (NM_021720)	-14	NM_021720	60364	Mm.328698	NM_021720	ENSMUSG00000022960	Donson	1110025J21Rik|AI845729|ORF60	downstream neighbor of SON	protein-coding
mm_63956.1	chr7	139914615	139914629	+	1	NA	intron (NM_177261, intron 9 of 30)	intron (NM_177261, intron 9 of 30)	19926	NM_177261	76484	Mm.44442	NM_177261	ENSMUSG00000066129	Kndc1	2410012C07Rik|B830014K08Rik|VKIND|very-kind	kinase non-catalytic C-lobe domain (KIND) containing 1	protein-coding
mm_107582.1	chr12	44525739	44525741	+	1	NA	intron (NM_001146031, intron 3 of 27)	intron (NM_001146031, intron 3 of 27)	196855	NM_001146031	319504	Mm.208439	NM_176930	ENSMUSG00000020598	Nrcam	Bravo|C030017F07Rik|C130076O07Rik|mKIAA0343	neuronal cell adhesion molecule	protein-coding
mm_1565.1	chr1	74155695	74155705	+	1	NA	intron (NM_009909, intron 1 of 1)	intron (NM_009909, intron 1 of 1)	1706	NM_009909	12765	Mm.234466	NM_009909	ENSMUSG00000026180	Cxcr2	CD128|CDw128|Cmkar2|Gpcr16|IL-8Rh|IL-8rb|IL8RA|Il8rb|mIL-8RH	chemokine (C-X-C motif) receptor 2	protein-coding
mm_89181.1	chr10	86345852	86345867	+	1	NA	exon (NM_011595, exon 5 of 5)	exon (NM_011595, exon 5 of 5)	45447	NM_011595	21859	Mm.4871	NM_011595	ENSMUSG00000020044	Timp3	Timp-3	tissue inhibitor of metalloproteinase 3	protein-coding
mm_97.1	chr1	8936406	8936416	+	1	NA	intron (NM_027671, intron 3 of 20)	RLTR9E|LTR|ERVK	363466	NM_001290390	71096	Mm.336395	NM_027671	ENSMUSG00000025909	Sntg1	4933426D16Rik|G1SYN|SYN4	syntrophin, gamma 1	protein-coding
mm_81594.1	chr9	110510242	110510251	+	1	NA	intron (NM_010628, intron 13 of 20)	(T)n|Simple_repeat|Simple_repeat	-22351	NM_001081340	235626	Mm.288949	NM_001081340	ENSMUSG00000044791	Setd2	4921524K10Rik|BC031601|KMT3A	SET domain containing 2	protein-coding
mm_84991.1	chr9	86587614	86587619	-	1	NA	intron (NM_008615, intron 12 of 13)	intron (NM_008615, intron 12 of 13)	15563	NM_027100	69519	Mm.272517	NM_027100	ENSMUSG00000032417	Rwdd2a	1700030C20Rik|AI848608|Rwdd2	RWD domain containing 2A	protein-coding
mm_1575.1	chr1	74267807	74267849	+	1	NA	3' UTR (NM_029711, exon 10 of 10)	3' UTR (NM_029711, exon 10 of 10)	-10772	NM_174985	227289	Mm.246587	NM_174985	ENSMUSG00000064272	Gpbar1	BG37|GPCR|GPR131|M-BAR|TGR5	G protein-coupled bile acid receptor 1	protein-coding
mm_48583.1	chr5	143613422	143613434	-	1	NA	Intergenic	Intergenic	-9019	NM_011182	19159	Mm.281003	NM_011182	ENSMUSG00000018001	Cyth3	AI648983|ARNO3|CLM3|Grp1|Pscd3	cytohesin 3	protein-coding
mm_105987.1	chr11	115627728	115627738	-	1	NA	5' UTR (NM_001252384, exon 2 of 8)	5' UTR (NM_001252384, exon 2 of 8)	562	NM_001252394	67283	Mm.383426	NM_026071	ENSMUSG00000020744	Slc25a19	2900089E13Rik|DNC|MUP1|TPC	solute carrier family 25 (mitochondrial thiamine pyrophosphate carrier), member 19	protein-coding
mm_119375.1	chr14	41123546	41123562	+	1	NA	3' UTR (NM_133653, exon 10 of 10)	3' UTR (NM_133653, exon 10 of 10)	-8234	NM_023134	20387	Mm.46062	NM_023134	ENSMUSG00000021789	Sftpa1	SP-A|Sftp-1|Sftp1	surfactant associated protein A1	protein-coding
mm_37388.1	chr4	121016981	121017008	-	1	NA	5' UTR (NM_133716, exon 1 of 10)	5' UTR (NM_133716, exon 1 of 10)	253	NM_133716	69780	Mm.271819	NM_133716	ENSMUSG00000032870	Smap2	1810031K02Rik|AA408614|Smap1l	small ArfGAP 2	protein-coding
mm_45564.1	chr5	73212568	73212605	-	1	NA	intron (NM_028194, intron 2 of 62)	intron (NM_028194, intron 2 of 62)	44032	NM_028194	72313	Mm.260594	NM_028194	ENSMUSG00000070733	Fryl	2010313D22Rik|2310004H21Rik|2510002A14Rik|9030227G01Rik|mKIAA0826	FRY like transcription coactivator	protein-coding
mm_16110.1	chr2	169641122	169641146	+	1	NA	intron (NM_080455, intron 1 of 1)	intron (NM_080455, intron 1 of 1)	7488	NM_080455	228911	Mm.315789	NM_080455	ENSMUSG00000047907	Tshz2	2900073F20Rik|B830045G17|Mtsh2|Sdccag33l|Tsh2|Zfp218|mKIAA4248|teashirt2	teashirt zinc finger family member 2	protein-coding
mm_56432.1	chr6	97352316	97352323	-	1	NA	intron (NM_001346639, intron 7 of 22)	intron (NM_001346639, intron 7 of 22)	-99539	NM_001081157	320502	Mm.68163	NM_001081157	ENSMUSG00000044086	Lmod3	5430424A14Rik	leiomodin 3 (fetal)	protein-coding
mm_162750.1	chr10	59136978	59136989	+	1	NA	3' UTR (NM_172788, exon 10 of 10)	3' UTR (NM_172788, exon 10 of 10)	84864	NM_001024911	103080	Mm.346842	NM_001024910	ENSMUSG00000019917	Sept10	4921515A04Rik|9430099J10Rik|AA408298|AI874685	septin 10	protein-coding
mm_103697.1	chr11	79516352	79516363	-	1	NA	exon (NM_001077496, exon 2 of 2)	exon (NM_001077496, exon 2 of 2)	7405	NM_001077496	216984	Mm.439665	NM_001077496	ENSMUSG00000093938	Evi2b	Evi-2|Evi2	ecotropic viral integration site 2b	protein-coding
mm_21328.1	chr2	157101324	157101334	-	1	NA	3' UTR (NM_001139520, exon 16 of 17)	3' UTR (NM_001139520, exon 16 of 17)	14274	NM_001177439	383766	Mm.480305	NM_001177439	ENSMUSG00000074628	Tldc2	Gm1332	TBC/LysM associated domain containing 2	protein-coding
mm_34949.1	chr4	155944038	155944048	+	1	NA	promoter-TSS (NM_001284312)	promoter-TSS (NM_001284312)	-115	NM_001284312	140499	Mm.371673	NM_021402	ENSMUSG00000023286	Ube2j2	1200007B18Rik|2400008G19Rik|5730472G04Rik|AL022923|NCUBE-2|Ubc6|Ubc6p	ubiquitin-conjugating enzyme E2J 2	protein-coding
mm_45729.1	chr5	86197882	86197895	-	1	NA	promoter-TSS (NM_001310651)	promoter-TSS (NM_001310651)	13	NM_001310653	14715	Mm.26791	NM_010323	ENSMUSG00000029255	Gnrhr	-	gonadotropin releasing hormone receptor	protein-coding
mm_29837.1	chr3	129822426	129822432	-	1	NA	promoter-TSS (NM_009102)	promoter-TSS (NM_009102)	76	NM_009102	20132	Mm.278758	NM_009102	ENSMUSG00000028012	Rrh	-	retinal pigment epithelium derived rhodopsin homolog	protein-coding
mm_122007.1	chr14	26970559	26970596	-	1	NA	promoter-TSS (NM_145221)	promoter-TSS (NM_145221)	-26	NM_145221	72993	Mm.202322	NM_145221	ENSMUSG00000040760	Appl1	2900057D21Rik|7330406P05Rik|AI585782|AW209077|BB022931|C88264|DIP13	adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 1	protein-coding
mm_46045.1	chr5	92043000	92043051	-	1	NA	promoter-TSS (NM_016912)	promoter-TSS (NM_016912)	17	NM_177270	53886	Mm.44963	NM_016912	ENSMUSG00000029403	Cdkl2	5330436L21Rik|AI505225|KKIAMRE|Kkm	cyclin-dependent kinase-like 2 (CDC2-related kinase)	protein-coding
mm_62555.1	chr7	102483114	102483115	+	1	NA	TTS (NM_020289)	TTS (NM_020289)	5193	NM_020289	257926	Mm.103733	NM_020289	ENSMUSG00000043925	Olfr544	MOR42-3|Ors6	olfactory receptor 544	protein-coding
mm_1039.1	chr1	58795372	58795447	+	1	NA	promoter-TSS (NM_009812)	promoter-TSS (NM_009812)	35	NM_009812	12370	Mm.336851	NM_009812	ENSMUSG00000026029	Casp8	CASP-8|FLICE|MACH|Mch5	caspase 8	protein-coding
mm_104002.1	chr11	84880250	84880299	-	1	NA	promoter-TSS (NM_001077636)	promoter-TSS (NM_001077636)	11	NM_001077636	70325	Mm.390414	NM_027388	ENSMUSG00000045140	Pigw	2610044A17Rik|Gwt1	phosphatidylinositol glycan anchor biosynthesis, class W	protein-coding
mm_72776.1	chr8	86615400	86615401	+	1	NA	Intergenic	Intergenic	-8643	NM_025827	66887	Mm.324550	NM_025827	ENSMUSG00000047866	Lonp2	1300002A08Rik|AU015403|Lonp	lon peptidase 2, peroxisomal	protein-coding
mm_67178.1	chr7	73612657	73612690	-	1	NA	Intergenic	B1_Mur3|SINE|Alu	-54278	NR_037569	69170	Mm.34539	NR_037569	ENSMUSG00000101970	1810026B05Rik	-	RIKEN cDNA 1810026B05 gene	ncRNA
mm_20538.1	chr2	131055827	131055830	-	1	NA	intron (NR_136922, intron 7 of 21)	intron (NR_136922, intron 7 of 21)	7986	NR_136922	110751	Mm.108550	NM_033615	ENSMUSG00000027318	Adam33	Adaml	a disintegrin and metallopeptidase domain 33	protein-coding
mm_1738.1	chr1	75439228	75439238	+	1	NA	intron (NM_133708, intron 5 of 12)	intron (NM_133708, intron 5 of 12)	3290	NM_133708	69080	Mm.23951	NM_133708	ENSMUSG00000033021	Gmppa	1810012N01Rik	GDP-mannose pyrophosphorylase A	protein-coding
mm_146748.1	chr18	16640586	16640595	-	1	NA	exon (NM_007664, exon 7 of 16)	exon (NM_007664, exon 7 of 16)	168656	NM_007664	12558	Mm.257437	NM_007664	ENSMUSG00000024304	Cdh2	CDHN|N-CAD|Ncad	cadherin 2	protein-coding
mm_135020.1	chr16	32487874	32487895	-	1	NA	promoter-TSS (NM_145932)	promoter-TSS (NM_145932)	-5	NM_145932	106407	Mm.476915	NM_145932	ENSMUSG00000035699	Slc51a	AV001382|AW261577|D630035O19Rik|OSTalpha|Osta	solute carrier family 51, alpha subunit	protein-coding
mm_153134.1	chr19	34243458	34243500	-	1	NA	exon (NM_007392, exon 8 of 9)	exon (NM_007392, exon 8 of 9)	11894	NM_007392	11475	Mm.213025	NM_007392	ENSMUSG00000035783	Acta2	0610041G09Rik|Actvs|SMalphaA|a-SMA|alphaSMA	actin, alpha 2, smooth muscle, aorta	protein-coding
mm_5286.1	chr1	20804815	20804817	-	1	NA	intron (NM_008563, intron 16 of 16)	intron (NM_008563, intron 16 of 16)	15397	NM_008563	17215	Mm.4502	NM_008563	ENSMUSG00000041859	Mcm3	AL033361|C80350|Mcmd|P1|p1.m	minichromosome maintenance complex component 3	protein-coding
mm_92262.1	chr10	71069838	71069839	-	1	NA	intron (NM_031397, intron 2 of 20)	B1F|SINE|Alu	89852	NM_031397	83675	Mm.286834	NM_031397	ENSMUSG00000014329	Bicc1	Bic-C|bpk|jcpk	BicC family RNA binding protein 1	protein-coding
mm_113794.1	chr13	46340228	46340244	+	1	NA	Intergenic	ORR1D2|LTR|ERVL-MaLR	66515	NM_001005422	380842	Mm.188108	NM_001005422	ENSMUSG00000063529	Stmnd1	Gm1574	stathmin domain containing 1	protein-coding
mm_35317.1	chr4	25792902	25792905	-	1	NA	intron (NM_010243, intron 1 of 2)	intron (NM_010243, intron 1 of 2)	7100	NM_010243	14348	Mm.39101	NM_010243	ENSMUSG00000055373	Fut9	AI746471|AU067636|mFUT9|mFuc-TIX	fucosyltransferase 9	protein-coding
mm_134525.1	chr16	19236847	19236856	-	1	NA	Intergenic	RMER17B|LTR|ERVK	49890	NM_146451	258443	Mm.377506	NM_146451	ENSMUSG00000050742	Olfr164	MOR279-2	olfactory receptor 164	protein-coding
mm_24293.1	chr3	89271908	89271908	+	1	NA	3' UTR (NM_001162425, exon 5 of 5)	3' UTR (NM_001162425, exon 5 of 5)	-1338	NM_009057	19729	Mm.17958	NM_009057	ENSMUSG00000027953	Slc50a1	MmSWEET1|Rag1ap1|Rga	solute carrier family 50 (sugar transporter), member 1	protein-coding
mm_3235.1	chr1	135850678	135850686	+	1	NA	intron (NM_001130174, intron 10 of 13)	intron (NM_001130174, intron 10 of 13)	9821	NM_001130176	21956	Mm.247470	NM_011619	ENSMUSG00000026414	Tnnt2	Tnt|cTnT	troponin T2, cardiac	protein-coding
mm_150656.1	chr19	41933909	41933912	+	1	NA	promoter-TSS (NM_001320233)	promoter-TSS (NM_001320233)	438	NM_023740	74168	Mm.20387	NM_023740	ENSMUSG00000025157	Zdhhc16	1500015N03Rik|Aph2	zinc finger, DHHC domain containing 16	protein-coding
mm_102943.1	chr11	69603539	69603562	-	1	NA	exon (NM_013415, exon 2 of 7)	exon (NM_013415, exon 2 of 7)	2410	NM_013415	11932	Mm.235204	NM_013415	ENSMUSG00000041329	Atp1b2	Amog|Atpb-2	ATPase, Na+/K+ transporting, beta 2 polypeptide	protein-coding
mm_31154.1	chr4	43416150	43416174	+	1	NA	exon (NM_001037709, exon 2 of 12)	exon (NM_001037709, exon 2 of 12)	9660	NM_199057	100213	Mm.235730	NM_199057	ENSMUSG00000035969	Rusc2	AI840675|mKIAA0375	RUN and SH3 domain containing 2	protein-coding
mm_922.1	chr1	55131254	55131302	+	1	NA	promoter-TSS (NM_025283)	promoter-TSS (NM_025283)	33	NM_025283	19070	Mm.291037	NM_025283	ENSMUSG00000025979	Mob4	2610109B12Rik|Mobkl3|Phocn|Prei3	MOB family member 4, phocein	protein-coding
mm_76776.1	chr8	95888511	95888520	-	1	NA	promoter-TSS (NM_010325)	promoter-TSS (NM_010325)	-150	NM_010325	14719	Mm.230169	NM_010325	ENSMUSG00000031672	Got2	AL022787|FABP-pm|Got-2|Kyat4|mAspAT	glutamatic-oxaloacetic transaminase 2, mitochondrial	protein-coding
mm_60988.1	chr7	49160717	49160723	+	1	NA	intron (NM_001111016, intron 2 of 38)	intron (NM_001111016, intron 2 of 38)	-85469	NM_175272	78286	Mm.333881	NM_175272	ENSMUSG00000052512	Nav2	5330421F07Rik|AU067780|BQ960892|HELAD1|POMFIL2|RAINB1|RAINB2|Unc53H2|mKIAA3015	neuron navigator 2	protein-coding
mm_24109.1	chr3	88142548	88142585	+	1	NA	5' UTR (NM_001310593, exon 1 of 11)	5' UTR (NM_001310593, exon 1 of 11)	194	NM_001310593	17261	Mm.28184	NM_133665	ENSMUSG00000001419	Mef2d	C80750	myocyte enhancer factor 2D	protein-coding
mm_96154.1	chr11	61485439	61485452	+	1	NA	promoter-TSS (NM_029568)	promoter-TSS (NM_029568)	1	NM_029568	76293	Mm.272278	NM_029568	ENSMUSG00000042436	Mfap4	1110007F23Rik	microfibrillar-associated protein 4	protein-coding
mm_88024.1	chr10	67215299	67215310	+	1	NA	exon (NM_207221, exon 4 of 26)	exon (NM_207221, exon 4 of 26)	29554	NM_001242396	108829	Mm.23846	NM_207221	ENSMUSG00000037876	Jmjd1c	5430433L24Rik|D630035I23Rik|Jmjdic|TRIP8	jumonji domain containing 1C	protein-coding
mm_63832.1	chr7	135300938	135300941	+	1	NA	Intergenic	Intergenic	32320	NM_001163611	100043254	Mm.192092	NM_001163611	ENSMUSG00000073804	Nps	ENSMUSG00000073804	neuropeptide S	protein-coding
mm_47679.1	chr5	128820054	128820082	-	1	NA	intron (NM_001310733, intron 3 of 20)	intron (NM_001310733, intron 3 of 20)	83822	NM_021311	57749	Mm.272720	NM_021311	ENSMUSG00000029423	Piwil1	MIWI	piwi-like RNA-mediated gene silencing 1	protein-coding
mm_4889.1	chr1	188654684	188654692	+	1	NA	exon (NM_021408, exon 36 of 71)	exon (NM_021408, exon 36 of 71)	353152	NM_172650	226823	Mm.209880	NM_172650	ENSMUSG00000026608	Kctd3	4930438A20Rik|9330185B06|E330032J19Rik|NY-REN-45	potassium channel tetramerisation domain containing 3	protein-coding
mm_75751.1	chr8	69901662	69901672	-	1	NA	promoter-TSS (NM_032004)	promoter-TSS (NM_032004)	-517	NM_032004	83984	Mm.432504	NM_032004	ENSMUSG00000047654	Tssk6	Sstk|TSK-6|TSSK-6	testis-specific serine kinase 6	protein-coding
mm_100674.1	chr11	3409080	3409088	-	1	NA	5' UTR (NM_010718, exon 1 of 16)	5' UTR (NM_010718, exon 1 of 16)	154	NM_010718	16886	Mm.124176	NM_010718	ENSMUSG00000020451	Limk2	Limk-2|whe	LIM motif-containing protein kinase 2	protein-coding
mm_87258.1	chr10	41519818	41519833	+	1	NA	intron (NM_016898, intron 1 of 5)	CpG	325	NM_016898	53599	Mm.269815	NM_016898	ENSMUSG00000019818	Cd164	A115|A24|AA589639|AW540279|MGC-24|MSSP	CD164 antigen	protein-coding
mm_127867.1	chr15	8398019	8398021	-	1	NA	intron (NM_201232, intron 1 of 45)	L1MEc|LINE|L1	46443	NM_027707	71175	Mm.240329	NM_027707	ENSMUSG00000022141	Nipbl	Idn3	Nipped-B homolog (Drosophila)	protein-coding
mm_102178.1	chr11	54028138	54028148	-	1	NA	promoter-TSS (NM_001330304)	promoter-TSS (NM_001330304)	-39	NM_001330304	30805	Mm.274590	NM_019687	ENSMUSG00000020334	Slc22a4	Octn1	solute carrier family 22 (organic cation transporter), member 4	protein-coding
mm_67974.1	chr7	100656858	100656868	-	1	NA	5' UTR (NM_001163187, exon 1 of 6)	5' UTR (NM_001163187, exon 1 of 6)	102	NM_001163187	27276	Mm.491216	NM_013746	ENSMUSG00000030701	Plekhb1	AI315628|PHR1|Phret1|evt-1	pleckstrin homology domain containing, family B (evectins) member 1	protein-coding
mm_93659.1	chr10	117690500	117690517	-	1	NA	exon (NM_010786, exon 12 of 12)	exon (NM_010786, exon 12 of 12)	20250	NM_010786	17246	Mm.22670	NM_010786	ENSMUSG00000020184	Mdm2	1700007J15Rik|AA415488|Mdm-2	transformed mouse 3T3 cell double minute 2	protein-coding
mm_132774.1	chr16	44773280	44773290	+	1	NA	intron (NM_021325, intron 1 of 6)	B1_Mur4|SINE|Alu	7549	NM_021325	57781	Mm.416152	NM_021325	ENSMUSG00000022667	Cd200r1	CD200R|Mox2r|OX2R	CD200 receptor 1	protein-coding
mm_98428.1	chr11	94654033	94654053	+	1	NA	promoter-TSS (NM_177752)	promoter-TSS (NM_177752)	252	NM_053161	94064	Mm.34951	NM_053161	ENSMUSG00000024414	Mrpl27	A630055F16Rik|D11Moh47|D18Ertd643e	mitochondrial ribosomal protein L27	protein-coding
mm_164697.1	chr17	48605398	48605402	+	1	NA	Intergenic	MTE2b|LTR|ERVL-MaLR	150499	NM_152823	76589	Mm.311629	NM_152823	ENSMUSG00000043592	Unc5cl	2510009H09Rik|BB155270|Zud	unc-5 family C-terminal like	protein-coding
mm_131763.1	chr16	22892036	22892051	+	1	NA	promoter-TSS (NM_001276450)	promoter-TSS (NM_001276450)	28	NM_001276449	11625	Mm.197554	NM_013465	ENSMUSG00000022868	Ahsg	-	alpha-2-HS-glycoprotein	protein-coding
mm_155399.1	chrX	72997249	72997255	+	1	NA	intron (NM_009549, intron 2 of 18)	intron (NM_009549, intron 2 of 18)	5173	NR_035517	100316779		NR_035517	ENSMUSG00000089357	Mir2137	mmu-mir-2137	microRNA 2137	ncRNA
mm_98581.1	chr11	95716430	95716439	+	1	NA	Intergenic	Intergenic	-3680	NR_045780	432396	Mm.426849	NR_045780	ENSMUSG00000086191	Zfp652os	1110035M17Rik	zinc finger protein 652, opposite strand	ncRNA
mm_48984.1	chr6	4755580	4755590	+	1	NA	exon (NM_130877, exon 2 of 2)	exon (NM_130877, exon 2 of 2)	8279	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_27785.1	chr3	75143713	75143759	-	1	NA	promoter-TSS (NM_172515)	promoter-TSS (NM_172515)	36	NM_001310529	213234	Mm.80075	NM_172515	ENSMUSG00000034151	Zbbx	4931432L23	zinc finger, B-box domain containing	protein-coding
mm_92957.1	chr10	85541604	85541616	-	1	NA	intron (NM_028709, intron 1 of 16)	RMER17C|LTR|ERVK	-56801	NM_001017525	74007	Mm.36544	NM_028709	ENSMUSG00000020042	Btbd11	6330404E16Rik	BTB (POZ) domain containing 11	protein-coding
mm_56695.1	chr6	114474996	114474996	-	1	NA	intron (NM_001317124, intron 1 of 1)	intron (NM_001317124, intron 1 of 1)	16474	NM_001317124	15465	Mm.333327	NM_008285	ENSMUSG00000053004	Hrh1	Bphs|H1R|HH1R|Hir	histamine receptor H1	protein-coding
mm_6131.1	chr1	64617154	64617238	-	1	NA	promoter-TSS (NM_025964)	promoter-TSS (NM_025964)	-28	NM_025964	67099	Mm.46394	NM_025964	ENSMUSG00000025956	Mettl21a	2310038H17Rik|AI464204|Fam119a	methyltransferase like 21A	protein-coding
mm_90531.1	chr10	128086293	128086306	+	1	NA	TTS (NR_030442)	TTS (NR_030442)	1013	NR_030442	751518		NR_030442	ENSMUSG00000093245	Mir677	Mirn677|mir-677|mmu-mir-677	microRNA 677	ncRNA
mm_72727.1	chr8	85071738	85071769	+	1	NA	promoter-TSS (NM_001039514)	promoter-TSS (NM_001039514)	-4	NM_001039514	330817	Mm.193086	NM_201408	ENSMUSG00000060038	Dhps	Dhs	deoxyhypusine synthase	protein-coding
mm_153135.1	chr19	34244947	34244965	-	1	NA	exon (NM_007392, exon 7 of 9)	exon (NM_007392, exon 7 of 9)	10417	NM_007392	11475	Mm.213025	NM_007392	ENSMUSG00000035783	Acta2	0610041G09Rik|Actvs|SMalphaA|a-SMA|alphaSMA	actin, alpha 2, smooth muscle, aorta	protein-coding
mm_6181.1	chr1	65103150	65103172	-	1	NA	exon (NM_007774, exon 2 of 3)	exon (NM_007774, exon 2 of 3)	202	NM_007774	12964	Mm.26904	NM_007774	ENSMUSG00000044429	Cryga	Cryg-4|DGcry-4	crystallin, gamma A	protein-coding
mm_6709.1	chr1	82287240	82287247	-	1	NA	exon (NM_010570, exon 1 of 2)	exon (NM_010570, exon 1 of 2)	4196	NM_010570	16367	Mm.4952	NM_010570	ENSMUSG00000055980	Irs1	G972R|IRS-1	insulin receptor substrate 1	protein-coding
mm_145750.1	chr18	64519943	64519956	+	1	NA	Intergenic	ORR1D2|LTR|ERVL-MaLR	-3392	NM_001142950	70223	Mm.29192	NM_027350	ENSMUSG00000024587	Nars	3010001M15Rik|AA960128|ASNRS|C78150	asparaginyl-tRNA synthetase	protein-coding
mm_157499.1	chrX	48513386	48513438	-	1	NA	5' UTR (NM_001290364, exon 1 of 16)	5' UTR (NM_001290364, exon 1 of 16)	151	NM_001290364	26926	Mm.240434	NM_012019	ENSMUSG00000036932	Aifm1	AIF|AIFsh2|Hq|Pdcd8	apoptosis-inducing factor, mitochondrion-associated 1	protein-coding
mm_168708.1	chr11	99932420	99932420	+	1	NA	Intergenic	Intergenic	-3871	NM_001025244	432602	Mm.246878	NM_001025244	ENSMUSG00000051481	Krtap31-2	OTTMUSG00000002177	keratin associated protein 31-2	protein-coding
mm_154777.1	chrX	12840415	12840433	+	1	NA	Intergenic	Intergenic	78146	NR_045852	552913	Mm.216846	NR_045852	ENSMUSG00000085891	Gm14634	OTTMUSG00000017535	predicted gene 14634	ncRNA
mm_115951.1	chr13	23746497	23746522	-	1	NA	promoter-TSS (NM_175664)	promoter-TSS (NM_175664)	-225	NM_175664	319178	Mm.390567	NM_175664	ENSMUSG00000075031	Hist1h2bb	H2b-143	histone cluster 1, H2bb	protein-coding
mm_136966.1	chr17	15706552	15706561	+	1	NA	intron (NM_007690, intron 1 of 35)	intron (NM_007690, intron 1 of 35)	1589	NM_007690	12648	Mm.8137	NM_007690	ENSMUSG00000023852	Chd1	4930525N21Rik|AI851787|AW555109	chromodomain helicase DNA binding protein 1	protein-coding
mm_87742.1	chr10	60266908	60266916	+	1	NA	Intergenic	Intergenic	-10716	NM_001146123	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_105137.1	chr11	101459357	101459369	-	1	NA	TTS (NM_027320)	TTS (NM_027320)	6836	NM_012037	26949	Mm.29210	NM_012037	ENSMUSG00000034993	Vat1	VAT-1	vesicle amine transport 1	protein-coding
mm_152073.1	chr19	6840568	6840582	-	1	NA	promoter-TSS (NM_019924)	promoter-TSS (NM_019924)	52	NM_019924	56613	Mm.20914	NM_019924	ENSMUSG00000024952	Rps6ka4	1110069D02Rik|90kDa|AI848992|Msk2|mMSK2	ribosomal protein S6 kinase, polypeptide 4	protein-coding
mm_66322.1	chr7	41682995	41683004	-	1	NA	intron (NR_004441, intron 1 of 6)	intron (NR_004441, intron 1 of 6)	14985	NR_004441	75835	Mm.159597	NM_029460	ENSMUSG00000074164	Vmn2r-ps54	1700108E19Rik|4930562N12Rik|Casr-rs5|ENSMUSG00000078527|Gm10948|Gprc2a-rs5	vomeronasal 2, receptor, pseudogene 54	pseudo
mm_108095.1	chr12	74346212	74346216	+	1	NA	Intergenic	Intergenic	48740	NM_198866	386753	Mm.341686	NM_198866	ENSMUSG00000029878	Dbpht2	Spot2	DNA binding protein with his-thr domain	protein-coding
mm_111446.1	chr12	98259248	98259338	-	1	NA	exon (NM_008079, exon 1 of 17)	exon (NM_008079, exon 1 of 17)	166	NM_008079	14420	Mm.5120	NM_008079	ENSMUSG00000021003	Galc	2310068B06Rik|A930008M05Rik|AW212969|AW413532|Gacy|twi|twitcher	galactosylceramidase	protein-coding
mm_60289.1	chr7	43995834	43995862	+	1	NA	promoter-TSS (NM_010640)	promoter-TSS (NM_010640)	-29	NM_010640	16613	Mm.443378	NM_010640	ENSMUSG00000044485	Klk1b11	Klk11|mGK-11	kallikrein 1-related peptidase b11	protein-coding
mm_12038.1	chr2	58769637	58769637	+	1	NA	intron (NM_029692, intron 2 of 6)	intron (NM_029692, intron 2 of 6)	14453	NM_029692	76654	Mm.200370	NM_029692	ENSMUSG00000026839	Upp2	1700124F02Rik|AI266885|UDRPASE2|UP2|UPASE2	uridine phosphorylase 2	protein-coding
mm_15294.1	chr2	155382285	155382299	+	1	NA	intron (NM_178111, intron 1 of 3)	CpG	436	NM_178111	68728	Mm.293605	NM_178111	ENSMUSG00000038375	Trp53inp2	1110029F20Rik|Tp53inp2	transformation related protein 53 inducible nuclear protein 2	protein-coding
mm_16614.1	chr2	5379337	5379360	-	1	NA	promoter-TSS (NR_030601)	promoter-TSS (NR_030601)	-42	NR_030601	100124465		NR_030601	ENSMUSG00000078031	Mir466d	Mirn466d	microRNA 466d	ncRNA
mm_44541.1	chr5	24540941	24540950	-	1	NA	promoter-TSS (NM_080444)	promoter-TSS (NM_080444)	33	NM_001310476	117590	Mm.207071	NM_080444	ENSMUSG00000038204	Asb10	Asb-10|BB137407	ankyrin repeat and SOCS box-containing 10	protein-coding
mm_103106.1	chr11	69980219	69980229	-	1	NA	promoter-TSS (NM_026017)	promoter-TSS (NM_026017)	106	NM_001253700	54351	Mm.13430	NM_018740	ENSMUSG00000018565	Elp5	Derp6|Rai12	elongator acetyltransferase complex subunit 5	protein-coding
mm_76820.1	chr8	104549989	104550014	-	1	NA	3' UTR (NM_053070, exon 7 of 7)	3' UTR (NM_053070, exon 7 of 7)	8692	NM_001301165	12354	Mm.129265	NM_053070	ENSMUSG00000031883	Car7	AV343731|Ca7	carbonic anhydrase 7	protein-coding
mm_6684.1	chr1	80631449	80631467	-	1	NA	intron (NM_175291, intron 3 of 55)	intron (NM_175291, intron 3 of 55)	33894	NM_001285927	210293	Mm.133473	NM_175291	ENSMUSG00000038608	Dock10	9330153B10Rik|A630054M16Rik|Jr4|Jr5|R75174|ZIZ3|Zizimin3|mKIAA0694	dedicator of cytokinesis 10	protein-coding
mm_171074.1	chr3	117868895	117868895	-	1	NA	promoter-TSS (NM_029655)	promoter-TSS (NM_029655)	41	NM_001190156	76561	Mm.33824	NM_029655	ENSMUSG00000028007	Snx7	2510028H01Rik	sorting nexin 7	protein-coding
mm_85478.1	chr9	105960643	105960659	-	1	NA	promoter-TSS (NM_001167923)	promoter-TSS (NM_001167923)	-8	NM_001167923	665033	Mm.39826	NM_001167923	ENSMUSG00000091345	Col6a5	Col29a1|EG665033|Gm7455	collagen, type VI, alpha 5	protein-coding
mm_143456.1	chr17	70990508	70990548	-	1	NA	promoter-TSS (NM_023402)	promoter-TSS (NM_023402)	-12	NM_023402	67938	Mm.261329	NM_023402	ENSMUSG00000034868	Myl12b	1500001M02Rik|C77744|Mylc2b|RLC-B	myosin, light chain 12B, regulatory	protein-coding
mm_102330.1	chr11	57829018	57829020	-	1	NA	3' UTR (NM_008213, exon 2 of 2)	3' UTR (NM_008213, exon 2 of 2)	3128	NM_008213	15110	Mm.4746	NM_008213	ENSMUSG00000037335	Hand1	Ehand1|Hxt|Th1|Thing1|bHLHa27|eHAND	heart and neural crest derivatives expressed transcript 1	protein-coding
mm_144132.1	chr18	4921663	4921690	+	1	NA	Intergenic	Intergenic	109190	NR_045881	100038439	Mm.387569	NR_045881	ENSMUSG00000097043	Gm10556	ENSMUSG00000073646	predicted gene 10556	ncRNA
mm_115317.1	chr13	112367875	112367879	+	1	NA	exon (NM_029898, exon 9 of 11)	exon (NM_029898, exon 9 of 11)	79359	NM_001168404	77318	Mm.159895	NM_029898	ENSMUSG00000049985	Ankrd55	C030011J08Rik	ankyrin repeat domain 55	protein-coding
mm_52369.1	chr6	113046373	113046389	+	1	NA	promoter-TSS (NM_008188)	promoter-TSS (NM_008188)	54	NM_008188	14911	Mm.781	NM_008188	ENSMUSG00000030264	Thumpd3	AW556087|Gt(ROSA)26asSor|Gtrosa26as	THUMP domain containing 3	protein-coding
mm_123118.1	chr14	56100714	56100723	-	1	NA	exon (NM_007800, exon 4 of 5)	exon (NM_007800, exon 4 of 5)	1856	NM_007800	13035	Mm.4858	NM_007800	ENSMUSG00000040314	Ctsg	CatG|VSP	cathepsin G	protein-coding
mm_152309.1	chr19	9744121	9744126	-	1	NA	Intergenic	Intergenic	155410	NM_016692	16319	Mm.29755	NM_016692	ENSMUSG00000024660	Incenp	2700067E22Rik|AU019509|C130081E20|C77457	inner centromere protein	protein-coding
mm_36445.1	chr4	82422531	82422534	-	1	NA	intron (NM_001113210, intron 2 of 11)	intron (NM_001113210, intron 2 of 11)	83247	NM_001286127	18028	Mm.317947	NM_008687	ENSMUSG00000008575	Nfib	6720429L07Rik|CTF|E030026I10Rik|NF-I/B|NF1-B|NFI-B	nuclear factor I/B	protein-coding
mm_151942.1	chr19	5800914	5800921	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	1755	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_60021.1	chr7	30789705	30789708	+	1	NA	intron (NM_001033131, intron 2 of 5)	(T)n|Simple_repeat|Simple_repeat	1801	NM_001033131	64661	Mm.268157	NM_001033131	ENSMUSG00000074199	Krtdap	Kdap|sk221	keratinocyte differentiation associated protein	protein-coding
mm_46293.1	chr5	100416086	100416109	-	1	NA	intron (NM_026969, intron 1 of 27)	CpG	137	NM_026969	69162	Mm.18634	NM_026969	ENSMUSG00000035325	Sec31a	1810024J13Rik|ABP125|ABP130|AU042160|HSPC275|Sec31l1	Sec31 homolog A (S. cerevisiae)	protein-coding
mm_10216.1	chr2	5895457	5895475	+	1	NA	promoter-TSS (NM_021305)	promoter-TSS (NM_021305)	-113	NM_021305	57743	Mm.21435	NM_021305	ENSMUSG00000025816	Sec61a2	-	Sec61, alpha subunit 2 (S. cerevisiae)	protein-coding
mm_148906.1	chr19	6942594	6942607	+	1	NA	promoter-TSS (NM_001285453)	promoter-TSS (NM_001285453)	38	NM_001285453	12015	Mm.4387	NM_007522	ENSMUSG00000024959	Bad	AI325008|Bbc2	BCL2-associated agonist of cell death	protein-coding
mm_23070.1	chr3	36151064	36151112	+	1	NA	promoter-TSS (NM_001101478)	promoter-TSS (NM_001101478)	8	NM_001101478	241944	Mm.260056	NM_001101478	ENSMUSG00000033883	D3Ertd254e	-	DNA segment, Chr 3, ERATO Doi 254, expressed	protein-coding
mm_134996.1	chr16	32164473	32164488	-	1	NA	intron (NM_146069, intron 1 of 3)	intron (NM_146069, intron 1 of 3)	996	NM_146069	224109	Mm.33498	NM_146069	ENSMUSG00000052384	Nrros	E430025L02Rik|Lrcc33|Lrrc33	negative regulator of reactive oxygen species	protein-coding
mm_139826.1	chr17	68314596	68314609	+	1	NA	5' UTR (NM_177278, exon 2 of 21)	5' UTR (NM_177278, exon 2 of 21)	40805	NM_177278	320858	Mm.137356	NM_177278	ENSMUSG00000041565	L3mbtl4	A730037L19Rik|D930040M24Rik	l(3)mbt-like 4 (Drosophila)	protein-coding
mm_46087.1	chr5	92346993	92346995	-	1	NA	3' UTR (NM_021274, exon 4 of 4)	3' UTR (NM_021274, exon 4 of 4)	1895	NM_021274	15945	Mm.877	NM_021274	ENSMUSG00000034855	Cxcl10	C7|CRG-2|INP10|IP-10|IP10|Ifi10|Scyb10|gIP-10|mob-1	chemokine (C-X-C motif) ligand 10	protein-coding
mm_29745.1	chr3	126942816	126942827	-	1	NA	exon (NM_001034168, exon 1 of 10)	exon (NM_001034168, exon 1 of 10)	565	NM_001034168	109676	Mm.220242	NM_178655	ENSMUSG00000032826	Ank2	100043364|AI835472|AW491075|Ank-2|Gm4392	ankyrin 2, brain	protein-coding
mm_151028.1	chr19	47014478	47014486	+	1	NA	promoter-TSS (NM_146100)	promoter-TSS (NM_146100)	-216	NM_146100	226180	Mm.276251	NM_146100	ENSMUSG00000034336	Ina	AV028420|NF-66|NF66	internexin neuronal intermediate filament protein, alpha	protein-coding
mm_114516.1	chr13	73260474	73260487	+	1	NA	promoter-TSS (NM_018885)	promoter-TSS (NM_018885)	-17	NM_018885	50916	Mm.103784	NM_018885	ENSMUSG00000021604	Irx4	-	Iroquois related homeobox 4 (Drosophila)	protein-coding
mm_109744.1	chr12	117533921	117533942	+	1	NA	intron (NM_175930, intron 3 of 27)	CpG	17452	NM_175930	217944	Mm.227642	NM_175930	ENSMUSG00000041992	Rapgef5	4932413M22|C86120|D030051B22Rik|GFR|Mrgef|mKIAA0277|mmr-gef	Rap guanine nucleotide exchange factor (GEF) 5	protein-coding
mm_153607.1	chr19	43940169	43940199	-	1	NA	promoter-TSS (NM_028029)	promoter-TSS (NM_028029)	14	NM_028029	71972	Mm.159024	NM_028029	ENSMUSG00000025195	Dnmbp	2410003L07Rik|2410003M15Rik|TUBA	dynamin binding protein	protein-coding
mm_136759.1	chr17	8800662	8800682	+	1	NA	intron (NM_001290707, intron 2 of 22)	intron (NM_001290707, intron 2 of 22)	-1073	NM_011866	23984	Mm.87161	NM_011866	ENSMUSG00000023868	Pde10a	-	phosphodiesterase 10A	protein-coding
mm_6443.1	chr1	73998546	73998548	-	1	NA	intron (NM_027884, intron 6 of 34)	intron (NM_027884, intron 6 of 34)	125900	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_132037.1	chr16	27422770	27422785	+	1	NA	intron (NM_001025615, intron 5 of 9)	intron (NM_001025615, intron 5 of 9)	33821	NM_001289436	67501	Mm.258985	NM_026202	ENSMUSG00000038127	Ccdc50	C3orf6	coiled-coil domain containing 50	protein-coding
mm_26869.1	chr3	16257254	16257254	-	1	NA	Intergenic	MMERVK9E_I-int|LTR|ERVK	74071	NM_001145919	229096	Mm.23834	NM_172677	ENSMUSG00000047213	Ythdf3	9130022A11Rik	YTH domain family 3	protein-coding
mm_79276.1	chr9	50774220	50774227	+	1	NA	Intergenic	MIRb|SINE|MIR	-1002	NM_133981	102580	Mm.160035	NM_133981	ENSMUSG00000032059	Alg9	8230402H15Rik|AI747665|B430313H07Rik|Dibd1	asparagine-linked glycosylation 9 (alpha 1,2 mannosyltransferase)	protein-coding
mm_2768.1	chr1	130717085	130717098	+	1	NA	promoter-TSS (NM_178691)	promoter-TSS (NM_178691)	-236	NM_178691	226418	Mm.106553	NM_178691	ENSMUSG00000046404	Yod1	6330564D18Rik|9930028C20Rik|Hshin7	YOD1 deubiquitinase	protein-coding
mm_66104.1	chr7	31040209	31040263	-	1	NA	promoter-TSS (NR_106017)	promoter-TSS (NR_106017)	81	NR_106017	102465635		NR_106017	ENSMUSG00000098783	Mir7050	Gm27578|mmu-mir-7050	microRNA 7050	ncRNA
mm_3663.1	chr1	153425166	153425177	+	1	NA	promoter-TSS (NM_001033162)	promoter-TSS (NM_001033162)	-38	NM_001033162	71836	Mm.49460	NM_001033162	ENSMUSG00000042708	Shcbp1l	1700012A16Rik	Shc SH2-domain binding protein 1-like	protein-coding
mm_161969.1	chr19	10634341	10634341	+	1	NA	5' UTR (NM_027913, exon 1 of 20)	5' UTR (NM_027913, exon 1 of 20)	108	NM_027913	71768	Mm.169261	NM_027913	ENSMUSG00000043789	Vwce	1300015B04Rik	von Willebrand factor C and EGF domains	protein-coding
mm_116851.1	chr13	54759434	54759441	-	1	NA	3' UTR (NM_033610, exon 6 of 6)	3' UTR (NM_033610, exon 6 of 6)	7003	NM_033610	104069	Mm.200843	NM_033610	ENSMUSG00000034891	Sncb	AI838531|betaSYN	synuclein, beta	protein-coding
mm_56451.1	chr6	97617628	97617642	-	1	NA	promoter-TSS (NM_145148)	promoter-TSS (NM_145148)	22	NM_145148	232288	Mm.27789	NM_145148	ENSMUSG00000030064	Frmd4b	6030440G05Rik|C87375|GOBLIN|GRSP1|R74720	FERM domain containing 4B	protein-coding
mm_97740.1	chr11	80456956	80456981	+	1	NA	intron (NM_178616, intron 6 of 13)	intron (NM_178616, intron 6 of 13)	-20078	NM_009871	12569	Mm.142275	NM_009871	ENSMUSG00000048895	Cdk5r1	Cdk5r|D11Bwg0379e|p25|p35	cyclin-dependent kinase 5, regulatory subunit 1 (p35)	protein-coding
mm_95012.1	chr11	31935045	31935069	+	1	NA	3' UTR (NM_026252, exon 10 of 10)	3' UTR (NM_026252, exon 10 of 10)	-30576	NM_026262	67592	Mm.78654	NM_026262	ENSMUSG00000020299	4930524B15Rik	-	RIKEN cDNA 4930524B15 gene	protein-coding
mm_66202.1	chr7	34233991	34234017	-	1	NA	Intergenic	Intergenic	-3668	NM_008155	14751	Mm.589	NM_008155	ENSMUSG00000036427	Gpi1	Amf|Gpi|Gpi-1|Gpi-1r|Gpi-1s|Gpi-1t|Gpi1-r|Gpi1-s|Gpi1-t|Gpi1s|MF|NK|NK/GPI|Nlk|Org|Pgi|Phi	glucose phosphate isomerase 1	protein-coding
mm_61942.1	chr7	90182950	90182962	+	1	NA	intron (NM_001252520, intron 13 of 20)	intron (NM_001252520, intron 13 of 20)	52724	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_40472.1	chr5	53998473	53998488	+	1	NA	promoter-TSS (NM_001081103)	promoter-TSS (NM_001081103)	-43	NM_001081103	116873	Mm.265985	NM_054083	ENSMUSG00000039156	Stim2	-	stromal interaction molecule 2	protein-coding
mm_546.1	chr1	38019028	38019049	+	1	NA	exon (NM_198303, exon 4 of 24)	exon (NM_198303, exon 4 of 24)	21028	NM_198303	226982	Mm.260943	NM_198303	ENSMUSG00000026083	Eif5b	A030003E17Rik|BC018347|IF2	eukaryotic translation initiation factor 5B	protein-coding
mm_113278.1	chr13	30003392	30003400	+	1	NA	Intergenic	Intergenic	-17333	NM_010093	13557	Mm.268356	NM_010093	ENSMUSG00000016477	E2f3	E2F3b|E2f3a	E2F transcription factor 3	protein-coding
mm_116349.1	chr13	38960479	38960496	-	1	NA	promoter-TSS (NM_001170430)	promoter-TSS (NM_001170430)	50	NM_001170430	108652	Mm.255506	NM_134060	ENSMUSG00000021432	Slc35b3	4921526O06Rik|AI428480|CGI-19|PABST2|PAPST2	solute carrier family 35, member B3	protein-coding
mm_46721.1	chr5	110682158	110682163	-	1	NA	intron (NM_173066, intron 37 of 50)	intron (NM_173066, intron 37 of 50)	-16019	NR_105993	102466216		NR_105993	ENSMUSG00000099284	Mir7026	Gm27988|mmu-mir-7026	microRNA 7026	ncRNA
mm_115685.1	chr13	13558922	13558935	-	1	NA	Intergenic	Intergenic	-31481	NM_010748	17101	Mm.342337	NM_010748	ENSMUSG00000019726	Lyst	D13Sfk13|beige|bg	lysosomal trafficking regulator	protein-coding
mm_74096.1	chr8	122574806	122574810	+	1	NA	3' UTR (NM_009698, exon 5 of 5)	3' UTR (NM_009698, exon 5 of 5)	2099	NM_009698	11821	Mm.1786	NM_009698	ENSMUSG00000006589	Aprt	C85684	adenine phosphoribosyl transferase	protein-coding
mm_15522.1	chr2	158376256	158376295	+	1	NA	exon (NM_175692, exon 2 of 5)	exon (NM_175692, exon 2 of 5)	637	NM_175692	319317	Mm.294494	NM_175692	ENSMUSG00000044349	Snhg11	A930034L06Rik|AI854265|AL022637|AW319638|E130013N09Rik	small nucleolar RNA host gene 11	protein-coding
mm_112957.1	chr13	21179951	21179966	+	1	NA	promoter-TSS (NM_009054)	promoter-TSS (NM_009054)	27	NM_009054	19720	Mm.314056	NM_009054	ENSMUSG00000021326	Trim27	AW538890|Gm19403|Rfp	tripartite motif-containing 27	protein-coding
mm_89820.1	chr10	105238124	105238157	+	1	NA	intron (NM_177368, intron 11 of 11)	LSU-rRNA_Hsa|rRNA|rRNA	336339	NM_177368	278279	Mm.25225	NM_177368	ENSMUSG00000036019	Tmtc2	8430438D04Rik|D330034A10Rik	transmembrane and tetratricopeptide repeat containing 2	protein-coding
mm_158635.1	chrX	155128410	155128440	-	1	NA	intron (NM_001081671, intron 2 of 2)	intron (NM_001081671, intron 2 of 2)	19424	NM_001081671	73347	Mm.63848	NM_001081671	ENSMUSG00000057402	Cldn34b2	1700042B14Rik	claudin 34B2	protein-coding
mm_131450.1	chr16	16870708	16870718	+	1	NA	promoter-TSS (NM_011624)	promoter-TSS (NM_011624)	-23	NM_001326576	21976	Mm.326089	NM_011624	ENSMUSG00000022779	Top3b	-	topoisomerase (DNA) III beta	protein-coding
mm_150494.1	chr19	39011762	39011804	+	1	NA	exon (NM_028089, exon 3 of 9)	exon (NM_028089, exon 3 of 9)	4764	NM_028089	72082	Mm.142581	NM_028089	ENSMUSG00000025002	Cyp2c55	2010318C06Rik	cytochrome P450, family 2, subfamily c, polypeptide 55	protein-coding
mm_152218.1	chr19	8262603	8262649	-	1	NA	Intergenic	Intergenic	-43726	NM_001347426	236293	Mm.440581	NM_172776	ENSMUSG00000075044	Slc22a29	D630002G06Rik	solute carrier family 22. member 29	protein-coding
mm_8646.1	chr1	156430849	156430859	-	1	NA	3' UTR (NM_009230, exon 16 of 16)	3' UTR (NM_009230, exon 16 of 16)	-9939	NM_001346967	77352	Mm.428709	NM_001033180	ENSMUSG00000026601	Axdnd1	9430070O13Rik|Gm979	axonemal dynein light chain domain containing 1	protein-coding
mm_109497.1	chr12	111449890	111449894	+	1	NA	intron (NM_009396, intron 8 of 11)	intron (NM_009396, intron 8 of 11)	7231	NM_009396	21928	Mm.255332	NM_009396	ENSMUSG00000021281	Tnfaip2	B94|Exoc3l3|M-sec|Tnfip2|tnfb94	tumor necrosis factor, alpha-induced protein 2	protein-coding
mm_85070.1	chr9	91130478	91130488	-	1	NA	Intergenic	Intergenic	235316	NM_009573	22771	Mm.335350	NM_009573	ENSMUSG00000032368	Zic1	ZIC|ZNF201	zinc finger protein of the cerebellum 1	protein-coding
mm_166018.1	chr4	122008549	122008556	-	1	NA	Intergenic	Intergenic	-386427	NM_001099309	666927	Mm.465133	NM_001099309	ENSMUSG00000078575	Gm12887	OTTMUSG00000008910	predicted gene 12887	protein-coding
mm_93129.1	chr10	92073391	92073418	-	1	NA	Intergenic	Intergenic	-1219	NR_029812	723955		NR_029812	ENSMUSG00000065524	Mir135a-2	Mirn135a-2|mir-135a-2	microRNA 135a-2	ncRNA
mm_90991.1	chr10	13965663	13965675	-	1	NA	promoter-TSS (NM_010437)	promoter-TSS (NM_010437)	-710	NM_010437	15273	Mm.42157	NM_010437	ENSMUSG00000015501	Hivep2	Gm20114|MIBP1|Schnurri-2|Shn-2	human immunodeficiency virus type I enhancer binding protein 2	protein-coding
mm_134765.1	chr16	23500489	23500489	-	1	NA	intron (NM_008555, intron 2 of 15)	intron (NM_008555, intron 2 of 15)	20101	NM_008555	17174	Mm.1213	NM_008555	ENSMUSG00000022887	Masp1	AW048060|CCPII|Crarf|Masp1/3	mannan-binding lectin serine peptidase 1	protein-coding
mm_89338.1	chr10	87934670	87934686	+	1	NA	3' UTR (NM_010512, exon 5 of 5)	3' UTR (NM_010512, exon 5 of 5)	-31993	NR_000040	22172	Mm.391420	NR_000040		Tyms-ps	-	thymidylate synthase, pseudogene	pseudo
mm_63802.1	chr7	133001618	133001624	+	1	NA	intron (NM_001347623, intron 1 of 8)	intron (NM_001347623, intron 1 of 8)	13626	NM_001170744	13017	Mm.246240	NM_009980	ENSMUSG00000030970	Ctbp2	AA407280|D7Ertd45e|Gtrgeo6|Ribeye	C-terminal binding protein 2	protein-coding
mm_109660.1	chr12	113014547	113014557	+	1	NA	promoter-TSS (NM_001291445)	promoter-TSS (NM_001291445)	44	NM_001291444	217893	Mm.35754	NM_198165	ENSMUSG00000021143	Pacs2	6720425G15Rik|AW208651|AW489976|E230011J22|Pacs1l|mKIAA0602	phosphofurin acidic cluster sorting protein 2	protein-coding
mm_150702.1	chr19	42255891	42255903	+	1	NA	5' UTR (NM_001141983, exon 3 of 7)	5' UTR (NM_001141983, exon 3 of 7)	158	NM_027694	71146	Mm.329851	NM_027694	ENSMUSG00000042532	Golga7b	4933417O08Rik|AI839934	golgi autoantigen, golgin subfamily a, 7B	protein-coding
mm_130125.1	chr15	89841804	89841814	-	1	NA	promoter-TSS (NM_018803)	promoter-TSS (NM_018803)	51	NM_018803	54526	Mm.261601	NM_018803	ENSMUSG00000063260	Syt10	-	synaptotagmin X	protein-coding
mm_52284.1	chr6	108661748	108661777	+	1	NA	promoter-TSS (NR_104577)	promoter-TSS (NR_104577)	-828	NR_104577	75394	Mm.395061	NR_040757	ENSMUSG00000087341	0610040F04Rik	-	RIKEN cDNA 0610040F04 gene	ncRNA
mm_95284.1	chr11	45893880	45893890	+	1	NA	exon (NM_001045520, exon 7 of 12)	exon (NM_001045520, exon 7 of 12)	41921	NM_001045520	216705	Mm.169673	NM_001045520	ENSMUSG00000006169	Clint1	AI642036|AW537616|C530049I24Rik|Enth|Epn4|F630206G17Rik|mKIAA0171	clathrin interactor 1	protein-coding
mm_42630.1	chr5	118435841	118435848	+	1	NA	Intergenic	Intergenic	-124875	NM_001347445	76199	Mm.206238	NM_172424	ENSMUSG00000018076	Med13l	2210413I17Rik|6330591G05Rik|9030618F05Rik|Thrap2|Trap240L|mKIAA1025	mediator complex subunit 13-like	protein-coding
mm_20768.1	chr2	142879586	142879604	-	1	NA	intron (NM_001081133, intron 1 of 25)	intron (NM_001081133, intron 1 of 25)	21869	NM_001081133	16558	Mm.251934	NM_001081133	ENSMUSG00000038844	Kif16b	8430434E15Rik|AA623607|AI789011|C80253|C80902|mKIAA1590	kinesin family member 16B	protein-coding
mm_112589.1	chr13	13784371	13784414	+	1	NA	promoter-TSS (NM_010317)	promoter-TSS (NM_010317)	85	NM_010317	14706	Mm.215394	NM_010317	ENSMUSG00000021303	Gng4	-	guanine nucleotide binding protein (G protein), gamma 4	protein-coding
mm_79341.1	chr9	53384018	53384030	+	1	NA	promoter-TSS (NM_212445)	promoter-TSS (NM_212445)	1	NM_212445	68304	Mm.427519	NM_212445	ENSMUSG00000034487	Kdelc2	2010004J24Rik|4833410J10Rik|AW549401	KDEL (Lys-Asp-Glu-Leu) containing 2	protein-coding
mm_64385.1	chr7	142475173	142475205	+	1	NA	intron (NM_001271508, intron 1 of 10)	intron (NM_001271508, intron 1 of 10)	-1824	NM_001271523	16985	Mm.234003	NM_019391	ENSMUSG00000018819	Lsp1	Lsp-1|WP34|p50|pp52	lymphocyte specific 1	protein-coding
mm_49661.1	chr6	31216688	31216700	+	1	NA	intron (NR_110469, intron 1 of 3)	CpG	1780	NR_110470	232685	Mm.443019	NM_144555	ENSMUSG00000044471	Lncpint	Lincpint|MNCb-1768|Pint|linc-Pint	long non-protein coding RNA, Trp53 induced transcript	ncRNA
mm_109052.1	chr12	104339340	104339358	+	1	NA	intron (NM_011458, intron 1 of 4)	CT-rich|Low_complexity|Low_complexity	863	NM_011458	20714	Mm.291569	NM_011458	ENSMUSG00000058207	Serpina3k	1300001I07Rik|D12Rp54|MMCM2|MMSpi2|RP54|Spi-2|Spi2|contrapsin	serine (or cysteine) peptidase inhibitor, clade A, member 3K	protein-coding
mm_117996.1	chr13	100492357	100492388	-	1	NA	intron (NM_022011, intron 1 of 15)	CpG	237	NM_022011	23894	Mm.272533	NM_022011	ENSMUSG00000021639	Gtf2h2	44kDa|BTF2 p44|BTF2-p44|Btf2p44|p44	general transcription factor II H, polypeptide 2	protein-coding
mm_104824.1	chr11	99024180	99024197	-	1	NA	promoter-TSS (NM_011623)	promoter-TSS (NM_011623)	1	NM_011623	21973	Mm.4237	NM_011623	ENSMUSG00000020914	Top2a	Top-2	topoisomerase (DNA) II alpha	protein-coding
mm_152553.1	chr19	11484521	11484544	-	1	NA	Intergenic	Intergenic	-7506	NM_001164202	666926	Mm.486382	NM_001164202	ENSMUSG00000058470	Gm8369	EG666926	predicted gene 8369	protein-coding
mm_59070.1	chr7	19508715	19508741	+	1	NA	promoter-TSS (NM_177692)	promoter-TSS (NM_177692)	58	NM_025960	67091	Mm.44213	NM_025960	ENSMUSG00000002043	Trappc6a	1810073E21Rik|4930519D19Rik|AI480686|TRS33|mhyp	trafficking protein particle complex 6A	protein-coding
mm_2374.1	chr1	93305945	93305961	+	1	NA	promoter-TSS (NM_001310756)	promoter-TSS (NM_001310756)	-74	NM_001310756	69821	Mm.52809	NM_178051	ENSMUSG00000026273	Mterf4	1810059A23Rik|4933412H03Rik|Mterfd2	mitochondrial transcription termination factor 4	protein-coding
mm_169458.1	chr1	46383536	46383536	+	1	NA	Intergenic	L1Md_T|LINE|L1	-41982	NM_001310335	100101919	Mm.383402	NM_001310335	ENSMUSG00000101337	Dnah7c	Dnahc7c	dynein, axonemal, heavy chain 7C	protein-coding
mm_147508.1	chr18	50568664	50568706	-	1	NA	promoter-TSS (NM_026108)	promoter-TSS (NM_026108)	14	NM_026108	67365	Mm.158150	NM_026108	ENSMUSG00000048875	Hdhd1a	1700121L12Rik|GS1|Hdhd1|Pudp	haloacid dehalogenase-like hydrolase domain containing 1A	protein-coding
mm_46807.1	chr5	113077171	113077182	-	1	NA	intron (NM_001159650, intron 5 of 5)	GA-rich|Low_complexity|Low_complexity	4408	NM_001159650	12962	Mm.378899	NM_021352	ENSMUSG00000029352	Crybb3	AI852419	crystallin, beta B3	protein-coding
mm_38309.1	chr4	136956572	136956578	-	1	NA	intron (NM_007939, intron 1 of 16)	intron (NM_007939, intron 1 of 16)	241	NM_007939	13842	Mm.1390	NM_007939	ENSMUSG00000028661	Epha8	AW047546|Eek|Hek3|mKIAA1459	Eph receptor A8	protein-coding
mm_26484.1	chr3	144727792	144727809	+	1	NA	Intergenic	Intergenic	-7465	NM_001282037	54673	Mm.271775	NM_019464	ENSMUSG00000037062	Sh3glb1	AA409932|AI314629|AU015566|Bif-1|mKIAA0491	SH3-domain GRB2-like B1 (endophilin)	protein-coding
mm_171258.1	chr3	8245522	8245535	-	1	NA	Intergenic	B2_Mm2|SINE|B2	217570	NR_033512	620966	Mm.301719	NR_033512		Gm6194	1700003N22Rik|EG620966	transmembrane protein 189 pseudogene	pseudo
mm_102271.1	chr11	55394849	55394964	-	1	NA	3' UTR (NM_009242, exon 10 of 10)	3' UTR (NM_009242, exon 10 of 10)	25174	NM_009242	20692	Mm.291442	NM_009242	ENSMUSG00000018593	Sparc	BM-40|ON	secreted acidic cysteine rich glycoprotein	protein-coding
mm_122855.1	chr14	54870914	54870947	-	1	NA	Intergenic	Intergenic	6608	NM_001167908	105651	Mm.297365	NM_001167908	ENSMUSG00000072494	Ppp1r3e	A630071A11Rik|AW049239|Gm1211	protein phosphatase 1, regulatory (inhibitor) subunit 3E	protein-coding
mm_2008.1	chr1	87127536	87127541	+	1	NA	exon (NM_007432, exon 11 of 11)	exon (NM_007432, exon 11 of 11)	2530	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_50973.1	chr6	61180444	61180488	+	1	NA	5' UTR (NM_183310, exon 1 of 11)	5' UTR (NM_183310, exon 1 of 11)	141	NM_183310	232035	Mm.150324	NM_183310	ENSMUSG00000039578	Ccser1	6230405M12Rik|C130092O11Rik|Fam190a	coiled-coil serine rich 1	protein-coding
mm_38038.1	chr4	133899470	133899493	-	1	NA	Intergenic	Intergenic	-11684	NM_009097	20111	Mm.301827	NM_009097	ENSMUSG00000003644	Rps6ka1	Mapkapk-1a|Rsk|Rsk-1|Rsk1|S6K-alpha-1|p90-Rsk1|p90Rsk1|p90S6K|p90rsk	ribosomal protein S6 kinase polypeptide 1	protein-coding
mm_43065.1	chr5	124328196	124328209	+	1	NA	promoter-TSS (NM_001277867)	promoter-TSS (NM_001277867)	113	NM_001134717	72650	Mm.121658	NM_028310	ENSMUSG00000047635	2810006K23Rik	-	RIKEN cDNA 2810006K23 gene	protein-coding
mm_114620.1	chr13	75967705	75967753	+	1	NA	promoter-TSS (NM_029343)	promoter-TSS (NM_029343)	-10	NM_029343	75571	Mm.443291	NM_029343	ENSMUSG00000021590	Spata9	1700030K01Rik|4930599C08Rik|A930023H06Rik	spermatogenesis associated 9	protein-coding
mm_54398.1	chr6	31480164	31480180	-	1	NA	intron (NM_013791, intron 12 of 17)	intron (NM_013791, intron 12 of 17)	81344	NM_013791	27418	Mm.238038	NM_013791	ENSMUSG00000025609	Mkln1	A130067F06Rik|AU015903|BB154892	muskelin 1, intracellular mediator containing kelch motifs	protein-coding
mm_136281.1	chr16	91069167	91069192	-	1	NA	promoter-TSS (NM_028905)	promoter-TSS (NM_028905)	-34	NM_028905	74387	Mm.236220	NM_028905	ENSMUSG00000039851	4932438H23Rik	4931406G06Rik|AI550392	RIKEN cDNA 4932438H23 gene	protein-coding
mm_18470.1	chr2	62411839	62411864	-	1	NA	5' UTR (NM_010074, exon 1 of 26)	5' UTR (NM_010074, exon 1 of 26)	380	NM_010074	13482	Mm.1151	NM_010074	ENSMUSG00000035000	Dpp4	Cd26|Dpp-4|THAM	dipeptidylpeptidase 4	protein-coding
mm_50722.1	chr6	52235121	52235127	+	1	NA	promoter-TSS (NM_008263)	promoter-TSS (NM_008263)	-185	NM_008263	15395	Mm.5	NM_008263	ENSMUSG00000000938	Hoxa10	Hox-1.8|Hoxa-10	homeobox A10	protein-coding
mm_15689.1	chr2	163658516	163658526	+	1	NA	promoter-TSS (NM_001164053)	promoter-TSS (NM_001164053)	63	NM_001164053	18769	Mm.10091	NM_011106	ENSMUSG00000035268	Pkig	PKIgamma	protein kinase inhibitor, gamma	protein-coding
mm_123235.1	chr14	60121718	60121749	-	1	NA	Intergenic	Intergenic	-34899	NM_015803	50769	Mm.319599	NM_015803	ENSMUSG00000021983	Atp8a2	AI415030|Atpc1b|agil|wl	ATPase, aminophospholipid transporter-like, class I, type 8A, member 2	protein-coding
mm_110575.1	chr12	56497398	56497430	-	1	NA	intron (NR_045082, intron 5 of 6)	B3|SINE|B2	32006	NR_045082	104798	Mm.310950	NR_045082		E030019B13Rik	AI413669	RIKEN cDNA E030019B13 gene	ncRNA
mm_162098.1	chrX	37651289	37651289	-	1	NA	promoter-TSS (NM_001039698)	promoter-TSS (NM_001039698)	38	NM_001039698	664608	Mm.491809	NM_001039698	ENSMUSG00000079628	Rhox4g	Rhox4.6|Rhox4.7|Rhox4f	reproductive homeobox 4G	protein-coding
mm_31213.1	chr4	43965551	43965555	+	1	NA	intron (NM_027450, intron 1 of 4)	MLTR14|LTR|ERV1	7851	NM_027450	384009	Mm.22213	NM_027450	ENSMUSG00000028480	Glipr2	5730414A08Rik|C77180|GAPR-1	GLI pathogenesis-related 2	protein-coding
mm_56723.1	chr6	115592572	115592599	-	1	NA	promoter-TSS (NM_001101431)	promoter-TSS (NM_001101431)	-9	NM_001101431	70291	Mm.133694	NM_001101431	ENSMUSG00000068011	Mkrn2os	2510049J12Rik	makorin, ring finger protein 2, opposite strand	protein-coding
mm_37771.1	chr4	129810974	129810987	-	1	NA	Intergenic	CpG	-9499	NM_008974	19244	Mm.193688	NM_008974	ENSMUSG00000028788	Ptp4a2	Prl-2	protein tyrosine phosphatase 4a2	protein-coding
mm_123888.1	chr14	72709987	72710027	-	1	NA	promoter-TSS (NM_207636)	promoter-TSS (NM_207636)	-4	NM_207636	319448	Mm.205421	NM_207636	ENSMUSG00000033487	Fndc3a	1700094E19Rik|D14Ertd453e|F730017H24Rik|Fndc3|sys	fibronectin type III domain containing 3A	protein-coding
mm_84215.1	chr9	61913424	61913473	-	1	NA	exon (NM_018853, exon 3 of 3)	exon (NM_018853, exon 3 of 3)	1062	NM_018853	56040	Mm.3158	NM_018853	ENSMUSG00000007892	Rplp1	2410042H16Rik|Arpp1|C430017H15Rik	ribosomal protein, large, P1	protein-coding
mm_71748.1	chr8	65209166	65209185	+	1	NA	Intergenic	RLTR9A3A|LTR|ERVK	-79638	NR_033217	407795	Mm.387876	NR_033217	ENSMUSG00000074300	BC030870	-	cDNA sequence BC030870	ncRNA
mm_54196.1	chr6	24619595	24619609	-	1	NA	exon (NM_028459, exon 9 of 11)	exon (NM_028459, exon 9 of 11)	21831	NM_053098	93677	Mm.332941	NM_053098	ENSMUSG00000029683	Lmod2	C-Lmod	leiomodin 2 (cardiac)	protein-coding
mm_56711.1	chr6	115252168	115252203	-	1	NA	promoter-TSS (NM_080639)	promoter-TSS (NM_080639)	-336	NM_080639	110595	Mm.255607	NM_080639	ENSMUSG00000030317	Timp4	TIMP-4	tissue inhibitor of metalloproteinase 4	protein-coding
mm_6954.1	chr1	85961030	85961073	-	1	NA	promoter-TSS (NM_001033290)	promoter-TSS (NM_001033290)	4	NM_001033290	227326	Mm.244158	NM_001033290	ENSMUSG00000049608	Gpr55	CTFL|Gm218|Lpir1	G protein-coupled receptor 55	protein-coding
mm_71999.1	chr8	70649645	70649665	+	1	NA	3' UTR (NM_023217, exon 5 of 5)	3' UTR (NM_023217, exon 5 of 5)	10083	NM_023217	66522	Mm.154906	NM_023217	ENSMUSG00000056204	Pgpep1	2810003H13Rik|Gm19458|PAP-I|PGP|PGP-I|PGPI|Pcp	pyroglutamyl-peptidase I	protein-coding
mm_58334.1	chr6	146634508	146634518	-	1	NA	promoter-TSS (NM_026281)	promoter-TSS (NM_026281)	79	NM_026281	67623	Mm.278037	NM_026281	ENSMUSG00000040234	Tm7sf3	2010003B14Rik|NARP1	transmembrane 7 superfamily member 3	protein-coding
mm_48131.1	chr5	137149944	137149950	-	1	NA	Intergenic	Intergenic	-33740	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_35436.1	chr4	38804017	38804018	-	1	NA	Intergenic	L1_Mus2|LINE|L1	-646276	NM_001081095	75471	Mm.23522	NM_001081095	ENSMUSG00000028287	1700009N14Rik	AI429145	RIKEN cDNA 1700009N14 gene	protein-coding
mm_159216.1	chr2	126374701	126374701	-	1	NA	intron (NM_001080944, intron 18 of 27)	intron (NM_001080944, intron 18 of 27)	116852	NM_001080944	241633	Mm.222235	NM_001080944	ENSMUSG00000060131	Atp8b4	A530043E15|Im	ATPase, class I, type 8B, member 4	protein-coding
mm_86832.1	chr10	21252397	21252424	+	1	NA	Intergenic	Intergenic	-43569	NM_001042593	56422	Mm.25527	NM_019702	ENSMUSG00000019977	Hbs1l	2810035F15Rik|AI326327|eRFS	Hbs1-like (S. cerevisiae)	protein-coding
mm_16656.1	chr2	6583717	6583725	-	1	NA	intron (NM_001347094, intron 9 of 12)	(TCCC)n|Simple_repeat|Simple_repeat	137941	NM_001310447	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_47487.1	chr5	123880031	123880039	-	1	NA	promoter-TSS (NM_175520)	promoter-TSS (NM_175520)	-15	NM_175520	243270	Mm.33362	NM_175520	ENSMUSG00000049241	Hcar1	Gpr81	hydrocarboxylic acid receptor 1	protein-coding
mm_165133.1	chr2	10080489	10080499	-	1	NA	promoter-TSS (NM_001112738)	promoter-TSS (NM_001112738)	16	NM_020615	11949	Mm.12677	NM_020615	ENSMUSG00000025781	Atp5c1	1700094F02Rik	ATP synthase, H+ transporting, mitochondrial F1 complex, gamma polypeptide 1	protein-coding
mm_59715.1	chr7	28766838	28766849	+	1	NA	promoter-TSS (NM_001122766)	promoter-TSS (NM_001122766)	91	NM_001122766	64383	Mm.272443	NM_022432	ENSMUSG00000015149	Sirt2	5730427M03Rik|SIR2L2|Sir2l	sirtuin 2	protein-coding
mm_35514.1	chr4	41114683	41114700	-	1	NA	3' UTR (NM_139236, exon 26 of 26)	3' UTR (NM_139236, exon 26 of 26)	9648	NM_139236	230082	Mm.285797	NM_139236	ENSMUSG00000028430	Nol6	AA410091|Nrap	nucleolar protein family 6 (RNA-associated)	protein-coding
mm_169472.1	chr1	4689407	4689420	-	1	NA	Intergenic	Intergenic	96313	NR_033530	27395	Mm.182927	NM_025300	ENSMUSG00000033845	Mrpl15	HSPC145|MRP-L7|Rpml7	mitochondrial ribosomal protein L15	protein-coding
mm_26257.1	chr3	142496925	142496939	+	1	NA	promoter-TSS (NM_153564)	promoter-TSS (NM_153564)	-2	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_48595.1	chr5	143992711	143992722	-	1	NA	intron (NM_177682, intron 11 of 14)	intron (NM_177682, intron 11 of 14)	22137	NM_177682	231874	Mm.320432	NM_177682	ENSMUSG00000029617	Ccz1	AU022870	CCZ1 vacuolar protein trafficking and biogenesis associated	protein-coding
mm_39418.1	chr5	15934707	15934719	+	1	NA	promoter-TSS (NM_001110843)	promoter-TSS (NM_001110843)	22	NM_001110844	12293	Mm.159842	NM_009784	ENSMUSG00000040118	Cacna2d1	Ca(v)alpha2delta1|Cacna2|Cchl2a	calcium channel, voltage-dependent, alpha2/delta subunit 1	protein-coding
mm_65690.1	chr7	28372549	28372557	-	1	NA	5' UTR (NM_001083912, exon 1 of 19)	5' UTR (NM_001083912, exon 1 of 19)	109	NM_138752	101497	Mm.235700	NM_138752	ENSMUSG00000037552	Plekhg2	AI194308|Clg|Cslg	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	protein-coding
mm_107657.1	chr12	52783289	52783299	+	1	NA	intron (NM_198111, intron 1 of 13)	intron (NM_198111, intron 1 of 13)	83911	NM_198111	238161	Mm.310822	NM_198111	ENSMUSG00000061603	Akap6	AI482140|Akapalpha|Akapbeta|PRKA	A kinase (PRKA) anchor protein 6	protein-coding
mm_133244.1	chr16	77111623	77111636	+	1	NA	intron (NM_013918, intron 21 of 23)	T-rich|Low_complexity|Low_complexity	97560	NM_013918	30940	Mm.40986	NM_013918	ENSMUSG00000022867	Usp25	-	ubiquitin specific peptidase 25	protein-coding
mm_143618.1	chr17	78773596	78773604	-	1	NA	exon (NM_001081179, exon 27 of 36)	exon (NM_001081179, exon 27 of 36)	-37040	NM_011500	268980	Mm.311915	NM_011500	ENSMUSG00000024077	Strn	AU022939|D130055P19	striatin, calmodulin binding protein	protein-coding
mm_74513.1	chr8	8689839	8689871	-	1	NA	TTS (NR_106114)	TTS (NR_106114)	307	NR_106114	102465762		NR_106114	ENSMUSG00000098917	Mir7654	Gm27748|mmu-mir-7654	microRNA 7654	ncRNA
mm_32198.1	chr4	101419697	101419732	+	1	NA	promoter-TSS (NM_009647)	promoter-TSS (NM_009647)	11	NM_009647	11639	Mm.42040	NM_009647	ENSMUSG00000028527	Ak4	AK 4|Ak-3|Ak-4|Ak3|Ak3l1|D4Ertd274e	adenylate kinase 4	protein-coding
mm_110209.1	chr12	27342697	27342726	-	1	NA	promoter-TSS (NM_009234)	promoter-TSS (NM_009234)	7	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding
mm_2030.1	chr1	87190625	87190640	+	1	NA	promoter-TSS (NM_021600)	promoter-TSS (NM_021600)	35	NM_021600	11447	Mm.2811	NM_021600	ENSMUSG00000026251	Chrnd	Achr-4|Acrd|L10076	cholinergic receptor, nicotinic, delta polypeptide	protein-coding
mm_3407.1	chr1	144001585	144001616	+	1	NA	3' UTR (NM_009061, exon 5 of 5)	3' UTR (NM_009061, exon 5 of 5)	2549	NM_009061	19735	Mm.28262	NM_009061	ENSMUSG00000026360	Rgs2	GOS8	regulator of G-protein signaling 2	protein-coding
mm_4572.1	chr1	177740832	177740855	+	1	NA	intron (NM_027077, intron 2 of 5)	intron (NM_027077, intron 2 of 5)	11029	NM_027077	69428	Mm.84467	NM_027077	ENSMUSG00000015962	1700016C15Rik	-	RIKEN cDNA 1700016C15 gene	protein-coding
mm_76988.1	chr8	107056651	107056691	-	1	NA	promoter-TSS (NM_139229)	promoter-TSS (NM_139229)	66	NM_139229	97484	Mm.288641	NM_139229	ENSMUSG00000031916	Cog8	BB235941|C87832	component of oligomeric golgi complex 8	protein-coding
mm_99227.1	chr11	101055081	101055095	+	1	NA	exon (NM_001243049, exon 19 of 21)	exon (NM_001243049, exon 19 of 21)	-15006	NM_013792	27419	Mm.95452	NM_013792	ENSMUSG00000001751	Naglu	-	alpha-N-acetylglucosaminidase (Sanfilippo disease IIIB)	protein-coding
mm_59538.1	chr7	27804820	27804872	+	1	NA	Intergenic	Intergenic	-2350	NM_027703	71163	Mm.440493	NM_027703	ENSMUSG00000030604	Zfp626	4833408D11Rik|4933426I21Rik|7630402I04Rik	zinc finger protein 626	protein-coding
mm_37074.1	chr4	116163756	116163771	-	1	NA	exon (NM_133681, exon 6 of 8)	exon (NM_133681, exon 6 of 8)	3835	NM_133681	66805	Mm.45994	NM_133681	ENSMUSG00000028699	Tspan1	9030418M05Rik	tetraspanin 1	protein-coding
mm_128224.1	chr15	36496723	36496808	-	1	NA	promoter-TSS (NM_175134)	promoter-TSS (NM_175134)	26	NM_175134	68839	Mm.396537	NM_175134	ENSMUSG00000048307	Ankrd46	1110054N06Rik|AI314978|AI987733	ankyrin repeat domain 46	protein-coding
mm_32087.1	chr4	98436908	98436961	+	1	NA	intron (NM_001005784, intron 11 of 19)	intron (NM_001005784, intron 11 of 19)	41108	NM_172696	12695	Mm.90218	NM_007704	ENSMUSG00000061859	Patj	Cipp|Inadl	PATJ, crumbs cell polarity complex component	protein-coding
mm_31924.1	chr4	85388819	85388822	+	1	NA	3' UTR (NM_019535, exon 9 of 9)	3' UTR (NM_019535, exon 9 of 9)	183364	NM_019535	20404	Mm.143603	NM_019535	ENSMUSG00000028488	Sh3gl2	9530001L19Rik|AI120490|AW555077|B930049H17Rik|EEN-B1|SH3PA|Sh3d2a	SH3-domain GRB2-like 2	protein-coding
mm_152874.1	chr19	24508250	24508258	-	1	NA	intron (NM_008846, intron 1 of 14)	intron (NM_008846, intron 1 of 14)	-30780	NM_026520	68034	Mm.440181	NM_026520	ENSMUSG00000074922	Fam122a	2410124L17Rik|2900009I07Rik|ENSMUSG00000051082|Gm9849	family with sequence similarity 122, member A	protein-coding
mm_70871.1	chr8	25068460	25068470	+	1	NA	intron (NM_031257, intron 3 of 11)	intron (NM_031257, intron 3 of 11)	-29503	NM_001081187	330723	Mm.334452	NM_001081187	ENSMUSG00000037406	Htra4	B430206E18Rik	HtrA serine peptidase 4	protein-coding
mm_42691.1	chr5	119835153	119835167	+	1	NA	5' UTR (NM_011537, exon 1 of 9)	5' UTR (NM_011537, exon 1 of 9)	497	NM_011537	21388	Mm.103636	NM_011537	ENSMUSG00000018263	Tbx5	-	T-box 5	protein-coding
mm_150169.1	chr19	32491273	32491293	+	1	NA	intron (NM_010799, intron 1 of 4)	intron (NM_010799, intron 1 of 4)	5514	NM_010799	17330	Mm.255116	NM_010799	ENSMUSG00000024896	Minpp1	AA408516	multiple inositol polyphosphate histidine phosphatase 1	protein-coding
mm_7152.1	chr1	91406078	91406083	-	1	NA	promoter-TSS (NR_026924)	promoter-TSS (NR_026924)	-51	NR_026924	67086	Mm.396158	NR_026924	ENSMUSG00000100253	1700020N18Rik	-	RIKEN cDNA 1700020N18 gene	ncRNA
mm_69664.1	chr7	139980774	139980776	-	1	NA	intron (NM_007403, intron 22 of 23)	B1_Mur1|SINE|Alu	-2020	NM_001347613	381933	Mm.440431	NM_001033465	ENSMUSG00000073795	6430531B16Rik	Gm1093	RIKEN cDNA 6430531B16 gene	protein-coding
mm_31821.1	chr4	66841953	66841965	+	1	NA	3' UTR (NM_021297, exon 3 of 3)	3' UTR (NM_021297, exon 3 of 3)	14408	NM_021297	21898	Mm.38049	NM_021297	ENSMUSG00000039005	Tlr4	Lps|Ly87|Ran/M1|Rasl2-8	toll-like receptor 4	protein-coding
mm_170935.1	chr2	47128709	47128715	-	1	NA	Intergenic	L1Md_T|LINE|L1	1432107	NR_040497	69405	Mm.396184	NR_040497	ENSMUSG00000086202	1700019E08Rik	-	RIKEN cDNA 1700019E08 gene	ncRNA
mm_131013.1	chr15	103563282	103563292	-	1	NA	exon (NM_008134, exon 3 of 4)	exon (NM_008134, exon 3 of 4)	1794	NM_001289587	14663	Mm.219621	NM_008134	ENSMUSG00000022491	Glycam1	MC26|Sgp50|glyCAM-1	glycosylation dependent cell adhesion molecule 1	protein-coding
mm_21337.1	chr2	157106257	157106290	-	1	NA	exon (NM_001139520, exon 13 of 17)	exon (NM_001139520, exon 13 of 17)	19218	NM_001177439	383766	Mm.480305	NM_001177439	ENSMUSG00000074628	Tldc2	Gm1332	TBC/LysM associated domain containing 2	protein-coding
mm_6351.1	chr1	71649290	71649313	-	1	NA	exon (NM_001276413, exon 4 of 44)	exon (NM_001276413, exon 4 of 44)	3933	NM_010233	14268	Mm.193099	NM_010233	ENSMUSG00000026193	Fn1	E330027I09|Fn|Fn-1	fibronectin 1	protein-coding
mm_107317.1	chr12	31266263	31266309	+	1	NA	intron (NM_008482, intron 1 of 32)	CpG	992	NM_008482	16777	Mm.172674	NM_008482	ENSMUSG00000002900	Lamb1	C77966|C80098|C81607|D130003D08Rik|Lamb-1|Lamb1-1	laminin B1	protein-coding
mm_122968.1	chr14	54974190	54974227	-	1	NA	non-coding (NR_033497, exon 5 of 5)	non-coding (NR_033497, exon 5 of 5)	1568	NR_030607	100124433		NR_030607	ENSMUSG00000077928	Mir208b	Mirn208b|mir-208b	microRNA 208b	ncRNA
mm_13252.1	chr2	98663856	98663873	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	1196207	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_119648.1	chr14	51989038	51989064	+	1	NA	promoter-TSS (NR_045728)	promoter-TSS (NR_045728)	-222	NR_045728	100502764	Mm.437219	NR_045728	ENSMUSG00000097633	Gm16617	-	predicted gene, 16617	ncRNA
mm_102401.1	chr11	59084248	59084250	-	1	NA	intron (NM_001171512, intron 18 of 103)	MTEb|LTR|ERVL-MaLR	52126	NM_001171512	380698	Mm.339542	NM_199152	ENSMUSG00000061462	Obscn	BC046431|Gm878|OTTMUSG00000005786|UNC89	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	protein-coding
mm_120028.1	chr14	55824945	55824963	+	1	NA	5' UTR (NM_001168346, exon 1 of 9)	5' UTR (NM_001168346, exon 1 of 9)	159	NM_023699	73181	Mm.27908	NM_023699	ENSMUSG00000023411	Nfatc4	3110041H08Rik|AW107667|AW546455|Nfat3	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 4	protein-coding
mm_151654.1	chr19	4121537	4121581	-	1	NA	promoter-TSS (NM_001276284)	promoter-TSS (NM_001276284)	16	NM_001276284	11632	Mm.10433	NM_016666	ENSMUSG00000024847	Aip	AA408703|AW476050|Ara9|D19Bwg1412e|Fkbp16|Xap2	aryl-hydrocarbon receptor-interacting protein	protein-coding
mm_22932.1	chr3	31163139	31163151	+	1	NA	exon (NM_008770, exon 3 of 3)	exon (NM_008770, exon 3 of 3)	13225	NM_008770	18417	Mm.4425	NM_008770	ENSMUSG00000037625	Cldn11	Claudin-11|Claudin11|Osp|Otm	claudin 11	protein-coding
mm_153560.1	chr19	42202132	42202140	-	1	NA	5' UTR (NM_018780, exon 1 of 3)	5' UTR (NM_018780, exon 1 of 3)	116	NM_018780	54612	Mm.470071	NM_018780	ENSMUSG00000018822	Sfrp5	AI605071|SARP3	secreted frizzled-related sequence protein 5	protein-coding
mm_105571.1	chr11	106587938	106587948	-	1	NA	intron (NM_198292, intron 1 of 11)	intron (NM_198292, intron 1 of 11)	24987	NM_198292	21763	Mm.102407	NM_198292	ENSMUSG00000040548	Tex2	4930568E07Rik|AI553404|Def-5|Taz4	testis expressed gene 2	protein-coding
mm_38061.1	chr4	134018786	134018792	-	1	NA	promoter-TSS (NM_145833)	promoter-TSS (NM_145833)	27	NM_145833	83557	Mm.302567	NM_145833	ENSMUSG00000050966	Lin28a	AL024421|ENSMUSG00000070700|Gm10299|Lin-28|Lin28|Tex17|lin-28A	lin-28 homolog A (C. elegans)	protein-coding
mm_92907.1	chr10	83534050	83534061	-	1	NA	promoter-TSS (NM_153543)	promoter-TSS (NM_153543)	85	NM_153543	216188	Mm.263138	NM_153543	ENSMUSG00000020256	Aldh1l2	D330038I09Rik|mtFDH	aldehyde dehydrogenase 1 family, member L2	protein-coding
mm_142553.1	chr17	46629421	46629500	-	1	NA	promoter-TSS (NM_175168)	promoter-TSS (NM_175168)	44	NM_175168	71461	Mm.181833	NM_175168	ENSMUSG00000023972	Ptk7	8430404F20Rik|chz|mPTK7/CCK4	PTK7 protein tyrosine kinase 7	protein-coding
mm_36659.1	chr4	94979064	94979106	-	1	NA	promoter-TSS (NM_177239)	promoter-TSS (NM_177239)	15	NM_177239	320713	Mm.208868	NM_177239	ENSMUSG00000062627	Mysm1	C130067A03Rik|C530050H10Rik	myb-like, SWIRM and MPN domains 1	protein-coding
mm_163827.1	chr14	19417386	19417404	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	185192	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_77481.1	chr8	122476004	122476026	-	1	NA	promoter-TSS (NM_153775)	promoter-TSS (NM_153775)	49	NM_001033142	68718	Mm.34356	NM_001033142	ENSMUSG00000014470	Rnf166	1110031E24Rik|AW555115|Zfp313l	ring finger protein 166	protein-coding
mm_80818.1	chr9	96637429	96637429	+	1	NA	Intergenic	Intergenic	-5926	NM_053268	114713	Mm.124502	NM_053268	ENSMUSG00000032413	Rasa2	5430433H21Rik|AA517451|AU023900|GAP1m	RAS p21 protein activator 2	protein-coding
mm_16482.1	chr2	180890700	180890712	+	1	NA	Intergenic	Intergenic	-3334	NR_029538	723951		NR_029538	ENSMUSG00000065454	Mir124a-3	Mirn124a-3|mir-124-3|mir-124a-3	microRNA 124a-3	ncRNA
mm_90753.1	chr10	5548685	5548723	-	1	NA	intron (NM_001347732, intron 1 of 145)	intron (NM_001347732, intron 1 of 145)	1988	NM_153399	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_138002.1	chr17	33817706	33817716	+	1	NA	exon (NM_030697, exon 3 of 11)	exon (NM_030697, exon 3 of 11)	6787	NM_016844	54127	Mm.352374	NM_016844	ENSMUSG00000067288	Rps28	-	ribosomal protein S28	protein-coding
mm_132728.1	chr16	43626646	43626657	+	1	NA	Intergenic	Intergenic	-14004	NR_030576	100124467		NR_030576	ENSMUSG00000076372	Mir568	Mirn568|mmu-mir-568	microRNA 568	ncRNA
mm_1806.1	chr1	81077218	81077252	+	1	NA	promoter-TSS (NM_172849)	promoter-TSS (NM_172849)	-82	NM_172849	241134	Mm.313904	NM_172849	ENSMUSG00000054976	Nyap2	9430031J16Rik|Jr6|Kiaa1486	neuronal tyrosine-phophorylated phosphoinositide 3-kinase adaptor 2	protein-coding
mm_27594.1	chr3	59131063	59131081	-	1	NA	promoter-TSS (NM_001287124)	promoter-TSS (NM_001287124)	46	NM_001287122	140795	Mm.439021	NM_133200	ENSMUSG00000036381	P2ry14	A330108O13Rik|Gpr105|P2Y14	purinergic receptor P2Y, G-protein coupled, 14	protein-coding
mm_88520.1	chr10	78054855	78054876	+	1	NA	promoter-TSS (NM_001284200)	promoter-TSS (NM_001284200)	-470	NM_001284198	54427	Mm.13433	NM_019448	ENSMUSG00000000730	Dnmt3l	D6Ertd14e|ecat7	DNA (cytosine-5-)-methyltransferase 3-like	protein-coding
mm_110865.1	chr12	73546384	73546411	-	1	NA	promoter-TSS (NM_178715)	promoter-TSS (NM_178715)	-2	NM_178715	238257	Mm.251196	NM_178715	ENSMUSG00000034435	Tmem30b	9130011B11Rik	transmembrane protein 30B	protein-coding
mm_48798.1	chr5	148928917	148928927	-	1	NA	promoter-TSS (NM_153572)	promoter-TSS (NM_153572)	-275	NM_153572	231912	Mm.397405	NM_153572	ENSMUSG00000041298	Katnal1	-	katanin p60 subunit A-like 1	protein-coding
mm_26672.1	chr3	154718093	154718110	+	1	NA	intron (NM_175176, intron 2 of 6)	L1_Mur3|LINE|L1	6968	NM_175176	209601	Mm.331454	NM_175176	ENSMUSG00000078161	Erich3	1700013E18Rik|4922501L14Rik|5031409G23Rik|AI596448|Gm133	glutamate rich 3	protein-coding
mm_155924.1	chrX	103356492	103356513	+	1	NA	promoter-TSS (NM_009767)	promoter-TSS (NM_009767)	26	NM_009767	12212	Mm.42223	NM_009767	ENSMUSG00000031327	Chic1	Brx|ENSMUSG00000073019|Gm10454	cysteine-rich hydrophobic domain 1	protein-coding
mm_82619.1	chr9	21795012	21795022	-	1	NA	exon (NM_145611, exon 3 of 12)	exon (NM_145611, exon 3 of 12)	3529	NM_145611	235041	Mm.257371	NM_145611	ENSMUSG00000032194	Kank2	AI504612|Ankrd25|BC010245	KN motif and ankyrin repeat domains 2	protein-coding
mm_102266.1	chr11	55337785	55337793	-	1	NA	Intergenic	Intergenic	-25532	NM_001029988	245827	Mm.339363	NM_001029988	ENSMUSG00000055333	Fat2	EMI2|Fath2|Gm523|mKIAA0811	FAT atypical cadherin 2	protein-coding
mm_159705.1	chr5	28237873	28237873	-	1	NA	intron (NM_001310512, intron 1 of 3)	intron (NM_001310512, intron 1 of 3)	7915	NM_001310512	269637	Mm.68286	NM_175651	ENSMUSG00000044681	Cnpy1	1500012D20Rik|9630008K15Rik|AI853839	canopy FGF signaling regulator 1	protein-coding
mm_119912.1	chr14	54953025	54953078	+	1	NA	exon (NM_010856, exon 23 of 39)	exon (NM_010856, exon 23 of 39)	-3909	NR_029724	387204		NR_029724	ENSMUSG00000065432	Mir208a	Mirn208|Mirn208a|mir-208|mir-208a|mmu-mir-208	microRNA 208a	ncRNA
mm_34904.1	chr4	155669667	155669674	+	1	NA	promoter-TSS (NM_001256107)	promoter-TSS (NM_001256107)	-416	NM_001256107	76580	Mm.235738	NM_145124	ENSMUSG00000029060	Mib2	2210008I11Rik|Zzank1|skd	mindbomb E3 ubiquitin protein ligase 2	protein-coding
mm_83268.1	chr9	42944480	42944510	-	1	NA	promoter-TSS (NM_175481)	promoter-TSS (NM_175481)	-124	NM_175481	110637	Mm.370291	NM_175481	ENSMUSG00000032017	Grik4	6330551K01Rik|GluK4|GluRgamma1|KA-1|KA1	glutamate receptor, ionotropic, kainate 4	protein-coding
mm_13912.1	chr2	120501819	120501829	+	1	NA	intron (NM_007601, intron 16 of 23)	intron (NM_007601, intron 16 of 23)	24915	NM_001109761	12335	Mm.458021	NM_007601	ENSMUSG00000079110	Capn3	AI323605|Capa-3|Capa3|Lp82|p94	calpain 3	protein-coding
mm_160689.1	chr10	22361909	22361909	+	1	NA	promoter-TSS (NM_020030)	promoter-TSS (NM_020030)	15	NM_020030	56554	Mm.458004	NM_020030	ENSMUSG00000078452	Raet1d	RAE-1delta	retinoic acid early transcript delta	protein-coding
mm_108118.1	chr12	75669836	75669878	+	1	NA	promoter-TSS (NM_028203)	promoter-TSS (NM_028203)	-320	NM_028203	72338	Mm.341719	NM_028203	ENSMUSG00000045690	Wdr89	2600001A11Rik	WD repeat domain 89	protein-coding
mm_61408.1	chr7	73537948	73537970	+	1	NA	intron (NM_001081345, intron 2 of 38)	CpG	3787	NM_001081345	244059	Mm.34539	NM_001081345	ENSMUSG00000078671	Chd2	2810013C04Rik|2810040A01Rik|5630401D06Rik|AI851092|BC029703|CHD-2	chromodomain helicase DNA binding protein 2	protein-coding
mm_149202.1	chr19	9978927	9978957	+	1	NA	Intergenic	Intergenic	-1658	NR_073181	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
mm_115548.1	chr13	8871000	8871058	-	1	NA	promoter-TSS (NM_172445)	promoter-TSS (NM_172445)	15	NM_001039389	207615	Mm.284654	NM_172445	ENSMUSG00000021147	Wdr37	-	WD repeat domain 37	protein-coding
mm_125060.1	chr15	25940697	25940732	+	1	NA	promoter-TSS (NM_001277316)	promoter-TSS (NM_001277316)	12	NM_001277315	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_171844.1	chr5	16755727	16755732	+	1	NA	Intergenic	L1Md_T|LINE|L1	201828	NM_001289461	15234	Mm.267078	NM_010427	ENSMUSG00000028864	Hgf	C230052L06Rik|HGF/SF|NK1|NK2|SF|SF/HGF	hepatocyte growth factor	protein-coding
mm_158535.1	chrX	143931434	143931469	-	1	NA	intron (NM_001110224, intron 1 of 6)	intron (NM_001110224, intron 1 of 6)	1673	NM_001110222	13193	Mm.12871	NM_010025	ENSMUSG00000031285	Dcx	Dbct	doublecortin	protein-coding
mm_40543.1	chr5	58014607	58014626	+	1	NA	intron (NM_001310608, intron 3 of 3)	intron (NM_001310608, intron 3 of 3)	296535	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_76438.1	chr8	84990871	84990901	-	1	NA	intron (NM_133255, intron 1 of 21)	intron (NM_133255, intron 1 of 21)	291	NM_001167991	170833	Mm.247775	NM_133255	ENSMUSG00000052566	Hook2	A630054I03Rik	hook microtubule tethering protein 2	protein-coding
mm_166017.1	chr4	121608996	121608997	+	1	NA	Intergenic	Intergenic	13129	NM_001099309	666927	Mm.465133	NM_001099309	ENSMUSG00000078575	Gm12887	OTTMUSG00000008910	predicted gene 12887	protein-coding
mm_65447.1	chr7	25398698	25398719	-	1	NA	intron (NR_015569, intron 3 of 6)	intron (NR_015569, intron 3 of 6)	-2721	NM_010719	16890	Mm.158548	NM_010719	ENSMUSG00000003123	Lipe	4933403G17Rik|HSL	lipase, hormone sensitive	protein-coding
mm_105969.1	chr11	115491647	115491666	-	1	NA	exon (NM_015807, exon 1 of 5)	exon (NM_015807, exon 1 of 5)	127	NR_136931	102634812	Mm.390379	NR_136931		LOC102634812	-	ribosomal protein L39 pseudogene	pseudo
mm_7908.1	chr1	133689926	133689936	-	1	NA	promoter-TSS (NM_172842)	promoter-TSS (NM_172842)	85	NM_172842	240754	Mm.36534	NM_172842	ENSMUSG00000051998	Lax1	A530029E09|E430019B13Rik	lymphocyte transmembrane adaptor 1	protein-coding
mm_104068.1	chr11	86585442	86585454	-	1	NA	exon (NM_029478, exon 12 of 12)	exon (NM_029478, exon 12 of 12)	-1290	NR_029738	387140		NR_029738	ENSMUSG00000065455	Mir21a	Mir21|Mirn21|mmu-mir-21|mmu-mir-21a	microRNA 21a	ncRNA
mm_32186.1	chr4	101069036	101069074	+	1	NA	promoter-TSS (NM_183024)	promoter-TSS (NM_183024)	17	NM_183024	242570	Mm.185636	NM_183024	ENSMUSG00000035275	Raver2	A430091O22Rik	ribonucleoprotein, PTB-binding 2	protein-coding
mm_51311.1	chr6	72314182	72314201	+	1	NA	3' UTR (NM_001282071, exon 11 of 11)	3' UTR (NM_001282071, exon 11 of 11)	9581	NM_147779	20388	Mm.46033	NM_147779	ENSMUSG00000056370	Sftpb	AI562151|SF-B|SP-B|Sftp-3|Sftp3	surfactant associated protein B	protein-coding
mm_377.1	chr1	34011551	34011559	+	1	NA	promoter-TSS (NM_134448)	promoter-TSS (NM_134448)	-270	NM_133833	13518	Mm.336625	NM_010081	ENSMUSG00000026131	Dst	2310001O04Rik|A830042E19Rik|AW554249|BP230|BPAG1-n|Bpag|Bpag1|Macf2|ah|athetoid|dt|mKIAA0728|nmf203|nmf339	dystonin	protein-coding
mm_93385.1	chr10	105841324	105841372	-	1	NA	promoter-TSS (NM_207522)	promoter-TSS (NM_207522)	32	NM_207522	216292	Mm.250875	NM_207522	ENSMUSG00000036009	Mettl25	-	methyltransferase like 25	protein-coding
mm_60801.1	chr7	45627483	45627493	+	1	NA	promoter-TSS (NM_028544)	promoter-TSS (NM_028544)	-49	NM_028544	69903	Mm.181396	NM_028544	ENSMUSG00000044562	Rasip1	1110025D03Rik|2610025P08Rik|AI853551|Rain	Ras interacting protein 1	protein-coding
mm_132754.1	chr16	44173240	44173270	+	1	NA	promoter-TSS (NM_001029889)	promoter-TSS (NM_001029889)	-142	NM_001029889	207806	Mm.310566	NM_001029889	ENSMUSG00000068284	Usf3	5530400K22Rik|Gm1779|Gm608|mKIAA2018	upstream transcription factor family member 3	protein-coding
mm_33053.1	chr4	123116247	123116265	+	1	NA	promoter-TSS (NM_181859)	promoter-TSS (NM_181859)	8	NM_181859	353371	Mm.189660	NM_181859	ENSMUSG00000076438	Oxct2b	Scot-t2	3-oxoacid CoA transferase 2B	protein-coding
mm_150217.1	chr19	33115414	33115416	+	1	NA	Intergenic	Intergenic	276880	NM_001167818	67795	Mm.204591	NM_001146342	ENSMUSG00000071573	Rnls	6530404N21Rik|AI452315|AW060440|C10orf59	renalase, FAD-dependent amine oxidase	protein-coding
mm_48023.1	chr5	136244849	136244859	-	1	NA	promoter-TSS (NM_018825)	promoter-TSS (NM_018825)	86	NM_001302939	23921	Mm.425294	NM_018825	ENSMUSG00000005057	Sh2b2	Aps	SH2B adaptor protein 2	protein-coding
mm_75501.1	chr8	53446880	53446891	-	1	NA	Intergenic	Intergenic	-64817	NM_001205054	11593	Mm.334535	NM_001005847	ENSMUSG00000031521	Aga	AW060726	aspartylglucosaminidase	protein-coding
mm_14087.1	chr2	125151835	125151846	+	1	NA	promoter-TSS (NM_001079690)	promoter-TSS (NM_001079690)	-760	NM_183354	20495	Mm.3914	NM_011389	ENSMUSG00000027202	Slc12a1	AI788571|D630042G03Rik|Nkcc2|mBSC1|urehr3	solute carrier family 12, member 1	protein-coding
mm_10748.1	chr2	23156174	23156188	+	1	NA	promoter-TSS (NM_013771)	promoter-TSS (NM_013771)	-157	NM_025979	67121	Mm.253721	NM_025979	ENSMUSG00000026779	Mastl	2700091H24Rik|C88295|GW|GWL|MAST-L|THC2	microtubule associated serine/threonine kinase-like	protein-coding
mm_609.1	chr1	39971367	39971367	+	1	NA	intron (NM_001252200, intron 3 of 31)	intron (NM_001252200, intron 3 of 31)	70454	NM_008696	26921	Mm.491139	NM_008696	ENSMUSG00000026074	Map4k4	9430080K19Rik|AU043147|AU045934|AW046177|HGK|Nik	mitogen-activated protein kinase kinase kinase kinase 4	protein-coding
mm_59390.1	chr7	26757154	26757171	+	1	NA	promoter-TSS (NM_007814)	promoter-TSS (NM_007814)	20	NM_007814	13090	Mm.14098	NM_007814	ENSMUSG00000066704	Cyp2b19	CYPIIB19	cytochrome P450, family 2, subfamily b, polypeptide 19	protein-coding
mm_58451.1	chr7	3330254	3330263	+	1	NA	exon (NM_011102, exon 18 of 18)	exon (NM_011102, exon 18 of 18)	-6327	NM_133189	81904	Mm.214994	NM_133189	ENSMUSG00000069806	Cacng7	-	calcium channel, voltage-dependent, gamma subunit 7	protein-coding
mm_75387.1	chr8	45410986	45411003	-	1	NA	promoter-TSS (NM_126166)	promoter-TSS (NM_126166)	-455	NM_126166	142980	Mm.33874	NM_126166	ENSMUSG00000031639	Tlr3	AI957183	toll-like receptor 3	protein-coding
mm_28924.1	chr3	98858244	98858265	-	1	NA	5' UTR (NM_008293, exon 2 of 5)	5' UTR (NM_008293, exon 2 of 5)	1540	NM_001304800	15492	Mm.140811	NM_008293	ENSMUSG00000027871	Hsd3b1	3-beta-HSD I|D3Ertd383e	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1	protein-coding
mm_81937.1	chr9	120303897	120303960	+	1	NA	promoter-TSS (NM_144557)	promoter-TSS (NM_144557)	-145	NM_144557	245049	Mm.100936	NM_144557	ENSMUSG00000041794	Myrip	A230081N12Rik|Slac2-c|Slac2c	myosin VIIA and Rab interacting protein	protein-coding
mm_156486.1	chrX	144335937	144335999	+	1	NA	intron (NR_037145, intron 3 of 26)	intron (NR_037145, intron 3 of 26)	18002	NM_026247	67574	Mm.249084	NM_026247	ENSMUSG00000041718	Alg13	2810046O15Rik|4833435D08Rik|Glt28d1|MDS031|OTTMUSG00000018917	asparagine-linked glycosylation 13	protein-coding
mm_28744.1	chr3	95739555	95739576	-	1	NA	promoter-TSS (NM_007899)	promoter-TSS (NM_007899)	4	NM_007899	13601	Mm.3433	NM_007899	ENSMUSG00000028108	Ecm1	AI663821|p85	extracellular matrix protein 1	protein-coding
mm_39107.1	chr4	154925260	154925263	-	1	NA	intron (NM_178931, intron 4 of 7)	intron (NM_178931, intron 4 of 7)	2816	NM_178931	230979	Mm.215147	NM_178931	ENSMUSG00000042333	Tnfrsf14	Atar|HveA|Hvem|Tnfrs14	tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)	protein-coding
mm_160419.1	chr8	84148028	84148028	+	1	NA	promoter-TSS (NM_029045)	promoter-TSS (NM_029045)	-10	NM_001163752	74666	Mm.33625	NM_029045	ENSMUSG00000008129	4930432K21Rik	-	RIKEN cDNA 4930432K21 gene	protein-coding
mm_54357.1	chr6	31088439	31088445	-	1	NA	Intergenic	Intergenic	-25349	NR_029532	387223		NR_029532	ENSMUSG00000065604	Mir29b-1	Mirn29b|Mirn29b-1|mir-29b-1	microRNA 29b-1	ncRNA
mm_107292.1	chr12	30019639	30019641	+	1	NA	Intergenic	Intergenic	81604	NM_181395	69675	Mm.251774	NM_181395	ENSMUSG00000020674	Pxdn	2310075M15Rik|C85409|E330004E07|VPO1|mKIAA0230	peroxidasin	protein-coding
mm_148876.1	chr19	6497950	6497979	+	1	NA	intron (NM_001205234, intron 17 of 22)	CpG	45106	NM_009203	20521	Mm.391146	NM_009203	ENSMUSG00000061742	Slc22a12	AI987855|OAT4L|Rst|Slc22al2|URAT1	solute carrier family 22 (organic anion/cation transporter), member 12	protein-coding
mm_128341.1	chr15	38709788	38709801	-	1	NA	Intergenic	Intergenic	18722	NR_131206	105463124	Mm.432448	NR_131206		Borg	-	BMP/OP-responsive gene	ncRNA
mm_161490.1	chr15	85735526	85735526	+	1	NA	promoter-TSS (NM_011144)	promoter-TSS (NM_011144)	-38	NM_001113418	19013	Mm.212789	NM_011144	ENSMUSG00000022383	Ppara	4933429D07Rik|AW742785|Nr1c1|PPAR-alpha|PPARalpha|Ppar	peroxisome proliferator activated receptor alpha	protein-coding
mm_100203.1	chr11	116843573	116843603	+	1	NA	promoter-TSS (NM_028865)	promoter-TSS (NM_028865)	73	NM_028865	74319	Mm.429312	NM_028865	ENSMUSG00000090266	Mettl23	1110005A03Rik|1500035B17Rik|4933424L15Rik	methyltransferase like 23	protein-coding
mm_61502.1	chr7	76457286	76457288	+	1	NA	intron (NM_001199224, intron 17 of 22)	Lx8|LINE|L1	227400	NM_001199224	244071	Mm.322829	NM_172902	ENSMUSG00000025754	Agbl1	Ccp4|D430020F16|EG244071|Nna1-l1	ATP/GTP binding protein-like 1	protein-coding
mm_53918.1	chr6	4069759	4069770	-	1	NA	Intergenic	Intergenic	17163	NM_009748	12068	Mm.286457	NM_009748	ENSMUSG00000032757	Bet1	AW555236|Bet-1	Bet1 golgi vesicular membrane trafficking protein	protein-coding
mm_63904.1	chr7	139213240	139213304	+	1	NA	promoter-TSS (NM_001143755)	promoter-TSS (NM_001143755)	-3	NM_001143755	76612	Mm.17757	NM_027164	ENSMUSG00000015980	Lrrc27	1700071K18Rik|2310044E02Rik	leucine rich repeat containing 27	protein-coding
mm_129564.1	chr15	79546580	79546588	-	1	NA	promoter-TSS (NM_199079)	promoter-TSS (NM_199079)	-25	NM_199079	67040	Mm.29644	NM_152806	ENSMUSG00000055065	Ddx17	2610007K22Rik|A430025E01Rik|AI047725|C80929|Gm926|p72	DEAD (Asp-Glu-Ala-Asp) box polypeptide 17	protein-coding
mm_107371.1	chr12	32850781	32850800	+	1	NA	3' UTR (NM_021524, exon 11 of 11)	3' UTR (NM_021524, exon 11 of 11)	26674	NR_045032	100504486	Mm.440246	NR_045032		Gdap10	Gdap-ps	ganglioside-induced differentiation-associated-protein 10	ncRNA
mm_163513.1	chr12	113427467	113427473	-	1	NA	Intergenic	Intergenic	-62095	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_68655.1	chr7	118578367	118578394	-	1	NA	intron (NM_172476, intron 1 of 15)	intron (NM_172476, intron 1 of 15)	6306	NM_172476	209760	Mm.69380	NM_172476	ENSMUSG00000042246	Tmc7	1700030H01Rik|C230064B05|C630024K23Rik	transmembrane channel-like gene family 7	protein-coding
mm_62316.1	chr7	100285479	100285564	+	1	NA	promoter-TSS (NM_177161)	promoter-TSS (NM_177161)	1	NM_177161	320452	Mm.150294	NM_177161	ENSMUSG00000051048	P4ha3	D930031A02Rik	procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide III	protein-coding
mm_139710.1	chr17	57460027	57460036	+	1	NA	intron (NM_010130, intron 17 of 21)	Lx9|LINE|L1	85283	NM_001104591	224916	Mm.469889	NM_001104591	ENSMUSG00000090655	Vmn2r120	EG224916	vomeronasal 2, receptor 120	protein-coding
mm_23225.1	chr3	49062449	49062460	+	1	NA	Intergenic	RLTR20C2_MM|LTR|ERVK	-453354	NR_003617	66332	Mm.46124	NM_025493		1700018B24Rik	-	enhancer of rudimentary homolog pseudogene	pseudo
mm_132336.1	chr16	33819708	33819719	+	1	NA	3' UTR (NM_010739, exon 13 of 13)	3' UTR (NM_010739, exon 13 of 13)	-9952	NM_010580	16419	Mm.6424	NM_010580	ENSMUSG00000022817	Itgb5	AA475909|AI874634|ESTM23|[b]-5|[b]5|[b]5A|[b]5B|beta-5|beta5	integrin beta 5	protein-coding
mm_68834.1	chr7	126200510	126200525	-	1	NA	promoter-TSS (NM_028816)	promoter-TSS (NM_028816)	-18	NM_001311143	74204	Mm.235663	NM_028816	ENSMUSG00000000131	Xpo6	2610005L19Rik|AL022631|C230091E20Rik|R75304|Ranbp20|mKIAA0370	exportin 6	protein-coding
mm_87853.1	chr10	61171931	61171943	+	1	NA	promoter-TSS (NM_001017419)	promoter-TSS (NM_001017419)	-27	NM_001017419	65971	Mm.30227	NM_023064	ENSMUSG00000020096	Tbata	1700021K02Rik|AI428928|Spatial|Titest	thymus, brain and testes associated	protein-coding
mm_107580.1	chr12	44525693	44525702	+	1	NA	intron (NM_001146031, intron 3 of 27)	intron (NM_001146031, intron 3 of 27)	196812	NM_001146031	319504	Mm.208439	NM_176930	ENSMUSG00000020598	Nrcam	Bravo|C030017F07Rik|C130076O07Rik|mKIAA0343	neuronal cell adhesion molecule	protein-coding
mm_169444.1	chr14	56998232	56998232	-	1	NA	Intergenic	L1Md_T|LINE|L1	-16902	NM_001256060	432860	Mm.390718	NM_001256060	ENSMUSG00000096144	B020004C17Rik	-	RIKEN cDNA B020004C17 gene	protein-coding
mm_79441.1	chr9	56090076	56090089	+	1	NA	5' UTR (NM_011193, exon 1 of 15)	5' UTR (NM_011193, exon 1 of 15)	106	NM_011193	19200	Mm.2534	NM_011193	ENSMUSG00000032322	Pstpip1	CD2BP1|def-2	proline-serine-threonine phosphatase-interacting protein 1	protein-coding
mm_99575.1	chr11	104132842	104132852	+	1	NA	promoter-TSS (NM_007762)	promoter-TSS (NM_007762)	66	NM_001313929	12921	Mm.1892	NM_007762	ENSMUSG00000018634	Crhr1	CRF1R|CRFR1|Crhr	corticotropin releasing hormone receptor 1	protein-coding
mm_126207.1	chr15	78889802	78889817	+	1	NA	exon (NM_145929, exon 11 of 17)	exon (NM_145929, exon 11 of 17)	-2031	NR_105920	102466210		NR_105920	ENSMUSG00000099267	Mir6955	Gm27769|mmu-mir-6955	microRNA 6955	ncRNA
mm_127455.1	chr15	101271735	101271749	+	1	NA	exon (NM_010444, exon 3 of 7)	exon (NM_010444, exon 3 of 7)	4896	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_151561.1	chr19	60581247	60581263	+	1	NA	promoter-TSS (NM_001172096)	promoter-TSS (NM_001172096)	-232	NM_001172096	78832	Mm.259026	NM_030197	ENSMUSG00000033417	Cacul1	2700078E11Rik|2810417M16Rik|9830127L17Rik|AI450346|D130033C15Rik	CDK2 associated, cullin domain 1	protein-coding
mm_130353.1	chr15	97750886	97750913	-	1	NA	intron (NM_144850, intron 18 of 27)	intron (NM_144850, intron 18 of 27)	16767	NM_001177810	223864	Mm.24028	NM_144850	ENSMUSG00000022469	Rapgef3	2310016P22Rik|9330170P05Rik|Epac|Epac1	Rap guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_121315.1	chr14	109247795	109247842	+	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-212412	NR_039542	100628607		NR_039542	ENSMUSG00000092639	Mir3964	mmu-mir-3964|mu-mir-3964	microRNA 3964	ncRNA
mm_44833.1	chr5	34105782	34105803	-	1	NA	intron (NM_181857, intron 13 of 24)	RMER19B|LTR|ERVK	-12948	NR_040703	75357	Mm.410806	NR_040703	ENSMUSG00000106902	4930557J02Rik	-	RIKEN cDNA 4930557J02 gene	ncRNA
mm_118746.1	chr14	22325410	22325418	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	217384	NR_046307	74896	Mm.444661	NR_046307		4930405A10Rik	4930456G20Rik	RIKEN cDNA 4930405A10 gene	ncRNA
mm_40928.1	chr5	76205864	76205878	+	1	NA	TTS (NR_035422)	TTS (NR_035422)	21991	NM_011626	21982	Mm.790	NM_011626	ENSMUSG00000029234	Tmem165	AV026557|Tpardl|Tparl|pFT27	transmembrane protein 165	protein-coding
mm_141197.1	chr17	27021273	27021304	-	1	NA	exon (NM_007523, exon 5 of 6)	exon (NM_007523, exon 5 of 6)	3253	NM_001251881	70772	Mm.440437	NM_027544	ENSMUSG00000048731	Ggnbp1	0610031G08Rik|mdf	gametogenetin binding protein 1	protein-coding
mm_104565.1	chr11	96916379	96916406	-	1	NA	5' UTR (NM_030248, exon 1 of 14)	5' UTR (NM_030248, exon 1 of 14)	122	NM_001308183	80280	Mm.28297	NM_030248	ENSMUSG00000018669	Cdk5rap3	1810007E24Rik|BC002318|C53|C81486|HSF-27|IC53|LZAP|MST016	CDK5 regulatory subunit associated protein 3	protein-coding
mm_2156.1	chr1	88200606	88200631	+	1	NA	promoter-TSS (NM_013701)	promoter-TSS (NM_013701)	7	NM_013701	22236	Mm.300095	NM_013701	ENSMUSG00000090171	Ugt1a2	UDPGT 1-2|Ugt1	UDP glucuronosyltransferase 1 family, polypeptide A2	protein-coding
mm_80791.1	chr9	96043606	96043608	+	1	NA	intron (NM_011916, intron 37 of 41)	intron (NM_011916, intron 37 of 41)	-75822	NM_177352	235533	Mm.213651	NM_177352	ENSMUSG00000041440	Gk5	AV095337|C330018K18Rik|G630067D24Rik	glycerol kinase 5 (putative)	protein-coding
mm_29162.1	chr3	106166211	106166245	-	1	NA	intron (NM_009892, intron 1 of 10)	intron (NM_009892, intron 1 of 10)	1336	NM_009892	12655	Mm.387173	NM_009892	ENSMUSG00000040809	Chil3	AI505981|Chi3l3|ECF-L|Ym1	chitinase-like 3	protein-coding
mm_132307.1	chr16	33684481	33684498	+	1	NA	promoter-TSS (NM_175256)	promoter-TSS (NM_175256)	23	NM_175256	77446	Mm.245741	NM_172934	ENSMUSG00000075254	Heg1	4632417D23Rik|5530401I02Rik|9530025L16Rik|BC038614|Gm629|OTTMUSG00000027315	heart development protein with EGF-like domains 1	protein-coding
mm_165802.1	chr3	143017211	143017220	+	1	NA	Intergenic	Intergenic	-135211	NM_178654	109333	Mm.244236	NM_178654	ENSMUSG00000004591	Pkn2	6030436C20Rik|AI507382|PRK2|Prkcl2|Stk7	protein kinase N2	protein-coding
mm_54621.1	chr6	38551213	38551256	-	1	NA	promoter-TSS (NM_001170849)	promoter-TSS (NM_001170849)	-100	NM_138680	192196	Mm.276133	NM_138680	ENSMUSG00000029823	Luc7l2	4930471C18Rik|AA522013|AU015269|CGI59|Cgi74	LUC7-like 2 (S. cerevisiae)	protein-coding
mm_44183.1	chr5	151368993	151369013	+	1	NA	intron (NR_045699, intron 1 of 3)	CpG	328	NR_045699	625175	Mm.443286	NR_045699	ENSMUSG00000097321	1700028E10Rik	A630054D14|Gm6561	RIKEN cDNA 1700028E10 gene	ncRNA
mm_59331.1	chr7	25396178	25396193	+	1	NA	promoter-TSS (NM_010719)	promoter-TSS (NM_010719)	-198	NM_010719	16890	Mm.158548	NM_010719	ENSMUSG00000003123	Lipe	4933403G17Rik|HSL	lipase, hormone sensitive	protein-coding
mm_10709.1	chr2	22774374	22774424	+	1	NA	promoter-TSS (NM_019456)	promoter-TSS (NM_019456)	72	NM_019456	54519	Mm.14255	NM_019456	ENSMUSG00000026786	Apbb1ip	9930118P07Rik|Prp48	amyloid beta (A4) precursor protein-binding, family B, member 1 interacting protein	protein-coding
mm_57631.1	chr6	128300504	128300525	-	1	NA	5' UTR (NM_001080979, exon 1 of 11)	5' UTR (NM_001080979, exon 1 of 11)	299	NM_001080979	21679	Mm.14774	NM_011567	ENSMUSG00000030353	Tead4	ETFR-2|Etfr2|FR-19|Rtef1|TEAD-4|TEF-3|Tcf13r1|Tef3|Tefr|Tefr1|Tefr1a	TEA domain family member 4	protein-coding
mm_57199.1	chr6	122850460	122850504	-	1	NA	exon (NM_009779, exon 2 of 2)	exon (NM_009779, exon 2 of 2)	5675	NM_009779	12267	Mm.2408	NM_009779	ENSMUSG00000040552	C3ar1	AZ3B|C3AR|HNFAG09	complement component 3a receptor 1	protein-coding
mm_46787.1	chr5	112590018	112590022	-	1	NA	promoter-TSS (NR_045397)	promoter-TSS (NR_045397)	-24	NR_045397	67325	Mm.490791	NR_045396	ENSMUSG00000097962	1700034G24Rik	-	RIKEN cDNA 1700034G24 gene	ncRNA
mm_161108.1	chr12	103828012	103828012	-	1	NA	Intergenic	Intergenic	35607	NM_001252569	20700	Mm.439692	NM_009243	ENSMUSG00000066366	Serpina1a	Aat-2|Aat2|Dom1|PI1|Spi1-1|Spi1-3	serine (or cysteine) peptidase inhibitor, clade A, member 1A	protein-coding
mm_46404.1	chr5	104093065	104093107	-	1	NA	exon (NM_010097, exon 4 of 11)	exon (NM_010097, exon 4 of 11)	-15478	NM_001163772	100271704	Mm.366664	NM_001163772	ENSMUSG00000091034	Gm17660	Scpppq1	predicted gene, 17660	protein-coding
mm_51133.1	chr6	68518982	68518997	+	1	NA	Intergenic	Intergenic	808185	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_130075.1	chr15	89373811	89373829	-	1	NA	promoter-TSS (NM_001111288)	promoter-TSS (NM_001111288)	-2	NM_001111288	100126824	Mm.287977	NM_001111288	ENSMUSG00000091780	Sco2	-	SCO2 cytochrome c oxidase assembly protein	protein-coding
mm_83317.1	chr9	44135186	44135210	-	1	NA	intron (NM_023061, intron 1 of 15)	CpG	540	NM_023061	84004	Mm.275003	NM_023061	ENSMUSG00000032135	Mcam	1-gicerin|AV025631|CD146|CD149|Muc18|s-endo|s-gicerin	melanoma cell adhesion molecule	protein-coding
mm_6547.1	chr1	75133479	75133483	-	1	NA	exon (NM_194333, exon 2 of 12)	exon (NM_194333, exon 2 of 12)	409	NM_194333	22626	Mm.68157	NM_194333	ENSMUSG00000026205	Slc23a3	SVCT3|Yspl1	solute carrier family 23 (nucleobase transporters), member 3	protein-coding
mm_38139.1	chr4	134757640	134757648	-	1	NA	intron (NM_145554, intron 2 of 8)	MTD|LTR|ERVL-MaLR	10360	NM_145554	100017	Mm.27486	NM_145554	ENSMUSG00000037295	Ldlrap1	AA691260|ARH2|Arh|Arh1|FHCB1|FHCB2	low density lipoprotein receptor adaptor protein 1	protein-coding
mm_51272.1	chr6	72115266	72115276	+	1	NA	intron (NM_011375, intron 1 of 6)	intron (NM_011375, intron 1 of 6)	7669	NR_045163	71265	Mm.442035	NR_045163	ENSMUSG00000108709	4933431G14Rik	4930565C19Rik	RIKEN cDNA 4933431G14 gene	ncRNA
mm_87538.1	chr10	53595912	53595914	+	1	NA	intron (NM_027830, intron 8 of 13)	intron (NM_027830, intron 8 of 13)	-1048	NM_025541	66403	Mm.272989	NM_025541	ENSMUSG00000019857	Asf1a	2310079C17Rik|C79052	anti-silencing function 1A histone chaperone	protein-coding
mm_116541.1	chr13	45925405	45925418	-	1	NA	intron (NM_001199304, intron 2 of 6)	MTD|LTR|ERVL-MaLR	39580	NM_001199304	20238	Mm.342683	NM_009124	ENSMUSG00000046876	Atxn1	2900016G23Rik|Atx1|C85907|ENSMUSG00000074917|Gm10786|Sca1	ataxin 1	protein-coding
mm_25618.1	chr3	118456320	118456325	+	1	NA	Intergenic	Intergenic	22465	NR_029551	387155		NR_029551	ENSMUSG00000065569	Mir137	Mirn137|mir-137|mmu-mir-137	microRNA 137	ncRNA
mm_128625.1	chr15	59024284	59024288	-	1	NA	intron (NM_001146180, intron 3 of 13)	intron (NM_001146180, intron 3 of 13)	57740	NM_001146180	211401	Mm.215481	NM_144800	ENSMUSG00000022353	Mtss1	2310003N14Rik|BC024131|D130001D01Rik|Mim|mKIAA0429	metastasis suppressor 1	protein-coding
mm_12508.1	chr2	71980987	71980995	+	1	NA	promoter-TSS (NM_001204167)	promoter-TSS (NM_001204167)	-224	NM_001204167	56508	Mm.196153	NM_019688	ENSMUSG00000049044	Rapgef4	1300003D15Rik|5730402K07Rik|6330581N18Rik|EPAC 2|Epac-2|Epac2|mKIAA4040	Rap guanine nucleotide exchange factor (GEF) 4	protein-coding
mm_138972.1	chr17	45298098	45298115	+	1	NA	Intergenic	Intergenic	135601	NM_152810	71702	Mm.28270	NM_152810	ENSMUSG00000023932	Cdc5l	1200002I02Rik|AA408004|PCDC5RP	cell division cycle 5-like (S. pombe)	protein-coding
mm_114984.1	chr13	97482696	97482706	+	1	NA	promoter-TSS (NR_110431)	promoter-TSS (NR_110431)	0	NR_110430	100039691	Mm.219358	NR_110430	ENSMUSG00000078952	Lncenc1	ENSMUSG00000078952|Gm11019|Gm2373|Lincenc1|Platr18|linc-Enc1	long non-coding RNA, embryonic stem cells expressed 1	ncRNA
mm_91778.1	chr10	52195277	52195288	-	1	NA	promoter-TSS (NM_011282)	promoter-TSS (NM_011282)	-38	NM_011282	19886	Mm.236163	NM_011282	ENSMUSG00000019893	Ros1	Ros-1|c-ros	Ros1 proto-oncogene	protein-coding
mm_143407.1	chr17	70819898	70819907	-	1	NA	3' UTR (NM_177639, exon 12 of 12)	3' UTR (NM_177639, exon 12 of 12)	26875	NM_001164077	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_84936.1	chr9	82951467	82951475	-	1	NA	intron (NM_001081216, intron 6 of 39)	ORR1C2-int|LTR|ERVL-MaLR	24018	NM_001081216	83946	Mm.221688	NM_031879	ENSMUSG00000032253	Phip	2810004D21Rik|4632404O06Rik|Ndrp|Wdr11	pleckstrin homology domain interacting protein	protein-coding
mm_139801.1	chr17	66111606	66111665	+	1	NA	promoter-TSS (NM_026833)	promoter-TSS (NM_026833)	-10	NM_001037757	68767	Mm.296545	NM_026833	ENSMUSG00000024101	Washc1	1110049F14Rik|ORF19|Wash|Wash1	WASH complex subunit 1	protein-coding
mm_131646.1	chr16	20531856	20531870	+	1	NA	3' UTR (NM_007889, exon 15 of 15)	3' UTR (NM_007889, exon 15 of 15)	-3617	NM_001302970	11773	Mm.18946	NM_009679	ENSMUSG00000022841	Ap2m1	-	adaptor-related protein complex 2, mu 1 subunit	protein-coding
mm_71953.1	chr8	70501117	70501172	+	1	NA	exon (NM_018827, exon 6 of 9)	exon (NM_018827, exon 6 of 9)	5595	NM_025577	66462	Mm.28242	NM_025577	ENSMUSG00000058833	2810428I15Rik	-	RIKEN cDNA 2810428I15 gene	protein-coding
mm_117015.1	chr13	58126780	58126792	-	1	NA	3' UTR (NM_029872, exon 1 of 1)	3' UTR (NM_029872, exon 1 of 1)	1770	NM_029872	77134	Mm.490274	NM_029872	ENSMUSG00000007836	Hnrnpa0	1110055B05Rik|3010025E17Rik|Hnrpa0|hnRNP A0	heterogeneous nuclear ribonucleoprotein A0	protein-coding
mm_38023.1	chr4	133757401	133757435	-	1	NA	Intergenic	Intergenic	-3807	NM_001080819	93760	Mm.22478	NM_001080819	ENSMUSG00000007880	Arid1a	1110030E03Rik|BAF250a|Osa1|Smarcf1	AT rich interactive domain 1A (SWI-like)	protein-coding
mm_12775.1	chr2	79328365	79328385	+	1	NA	3' UTR (NM_010576, exon 28 of 28)	3' UTR (NM_010576, exon 28 of 28)	72949	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D|Itga4B	integrin alpha 4	protein-coding
mm_50607.1	chr6	49395533	49395558	+	1	NA	promoter-TSS (NM_029916)	promoter-TSS (NM_029916)	-59	NM_029916	77485	Mm.128054	NM_029916	ENSMUSG00000023403	Stk31	C330007K24Rik	serine threonine kinase 31	protein-coding
mm_42235.1	chr5	113589131	113589146	+	1	NA	3' UTR (NM_177292, exon 8 of 8)	3' UTR (NM_177292, exon 8 of 8)	38718	NM_177292	320916	Mm.102783	NM_177292	ENSMUSG00000063430	Wscd2	4933413A10Rik|C530024P05Rik|Gm450	WSC domain containing 2	protein-coding
mm_141696.1	chr17	33978854	33978860	-	1	NA	promoter-TSS (NR_004446)	promoter-TSS (NR_004446)	-66	NR_004446	630499	Mm.440940	NM_001081015		H2-K2	EG630499|Gm7035|H-2K1|H-2K1K|H-2K2|H2-K1	histocompatibility 2, K region locus 2	pseudo
mm_156256.1	chrX	136741822	136741864	+	1	NA	promoter-TSS (NM_019768)	promoter-TSS (NM_019768)	-234	NM_019768	56397	Mm.27218	NM_019768	ENSMUSG00000031422	Morf4l2	2410017O14Rik|Mrgx|Sid393p|mKIAA0026	mortality factor 4 like 2	protein-coding
mm_21472.1	chr2	160989304	160989305	-	1	NA	intron (NR_126509, intron 18 of 35)	PB1D9|SINE|Alu	-76965	NM_182840	280635	Mm.330747	NM_182840	ENSMUSG00000050700	Emilin3	1110013O17Rik|EMILIN-3|EMILIN-5|EMILIN-T|Emilin5	elastin microfibril interfacer 3	protein-coding
mm_124649.1	chr15	5153153	5153156	+	1	NA	intron (NM_001013367, intron 1 of 8)	B1_Mus2|SINE|Alu	9293	NM_001013367	105787	Mm.207004	NM_001013367	ENSMUSG00000050697	Prkaa1	AI194361|AI450832|AL024255|AMPKalpha1|C130083N04Rik	protein kinase, AMP-activated, alpha 1 catalytic subunit	protein-coding
mm_99283.1	chr11	101316918	101316927	+	1	NA	intron (NM_011192, intron 1 of 10)	intron (NM_011192, intron 1 of 10)	671	NM_011192	19192	Mm.288477	NM_011192	ENSMUSG00000078652	Psme3	AA410043|AU020960|Ki|PA28gamma|REGgamma|pa28g	proteaseome (prosome, macropain) activator subunit 3 (PA28 gamma, Ki)	protein-coding
mm_116941.1	chr13	56089157	56089192	-	1	NA	intron (NM_001159514, intron 5 of 8)	intron (NM_001159514, intron 5 of 8)	46376	NM_012015	26914	Mm.283802	NM_012015	ENSMUSG00000015937	H2afy	H2AF12M|mH2a1|macroH2A1	H2A histone family, member Y	protein-coding
mm_91731.1	chr10	45486364	45486384	-	1	NA	Intergenic	CpG	-16173	NM_001031772	380669	Mm.440328	NM_001031772	ENSMUSG00000063804	Lin28b	2810403D23Rik|D030047M17Rik|Lin-28.2	lin-28 homolog B (C. elegans)	protein-coding
mm_88422.1	chr10	77202198	77202213	+	1	NA	Intergenic	Intergenic	-35675	NM_009929	12822	Mm.4352	NM_009929	ENSMUSG00000001435	Col18a1	-	collagen, type XVIII, alpha 1	protein-coding
mm_129705.1	chr15	81729834	81729844	-	1	NA	promoter-TSS (NM_011241)	promoter-TSS (NM_011241)	80	NM_011241	19387	Mm.270975	NM_011241	ENSMUSG00000022391	Rangap1	C79654|Fug1|mKIAA1835	RAN GTPase activating protein 1	protein-coding
mm_128771.1	chr15	66560998	66561067	-	1	NA	promoter-TSS (NM_172514)	promoter-TSS (NM_172514)	14	NM_172514	213068	Mm.132299	NM_172514	ENSMUSG00000036944	Tmem71	AI661017|E430024D12	transmembrane protein 71	protein-coding
mm_73052.1	chr8	94365895	94365900	+	1	NA	exon (NM_001205311, exon 25 of 25)	exon (NM_001205311, exon 25 of 25)	-20603	NM_022331	64209	Mm.29151	NM_022331	ENSMUSG00000031770	Herpud1	Herp|Mifl|SUP	homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1	protein-coding
mm_70764.1	chr8	21776568	21776595	+	1	NA	promoter-TSS (NM_007843)	promoter-TSS (NM_007843)	26	NM_007843	13214	Mm.431316	NM_007843	ENSMUSG00000044748	Defb1	AW260221|BD-1	defensin beta 1	protein-coding
mm_44981.1	chr5	36988923	36988970	-	1	NA	promoter-TSS (NM_011716)	promoter-TSS (NM_011716)	36	NM_011716	22393	Mm.20916	NM_011716	ENSMUSG00000039474	Wfs1	AI481085|wolframin	Wolfram syndrome 1 homolog (human)	protein-coding
mm_49951.1	chr6	40471362	40471511	+	1	NA	promoter-TSS (NM_028358)	promoter-TSS (NM_028358)	21	NM_028358	381760	Mm.276356	NM_028358	ENSMUSG00000029911	Ssbp1	2810480P10Rik|G630031O20Rik|MtSSB|mtDBP	single-stranded DNA binding protein 1	protein-coding
mm_93061.1	chr10	88788382	88788388	-	1	NA	intron (NM_175158, intron 25 of 61)	intron (NM_175158, intron 25 of 61)	38429	NM_175158	70683	Mm.29631	NM_175158	ENSMUSG00000004356	Utp20	3830408P06Rik|AA617408|Drim|mDRIM|mDRIN	UTP20 small subunit processome component	protein-coding
mm_47673.1	chr5	127783161	127783189	-	1	NA	TTS (NM_172885)	TTS (NM_172885)	150913	NM_177005	319804	Mm.237888	NM_177005	ENSMUSG00000049971	Glt1d1	5730455A04Rik	glycosyltransferase 1 domain containing 1	protein-coding
mm_28673.1	chr3	95306795	95306810	-	1	NA	promoter-TSS (NM_001085383)	promoter-TSS (NM_001085383)	2	NM_001085383	71790	Mm.218844	NM_023628	ENSMUSG00000015702	Anxa9	1110003P15Rik|2310069F17Rik	annexin A9	protein-coding
mm_141159.1	chr17	26508215	26508247	-	1	NA	exon (NM_013642, exon 1 of 4)	exon (NM_013642, exon 1 of 4)	241	NM_013642	19252	Mm.239041	NM_013642	ENSMUSG00000024190	Dusp1	3CH134|MKP1|Ptpn16|U19515|erp|mkp-1	dual specificity phosphatase 1	protein-coding
mm_50662.1	chr6	51523925	51523941	+	1	NA	promoter-TSS (NM_001127349)	promoter-TSS (NM_001127349)	30	NM_001127349	71982	Mm.294166	NM_028035	ENSMUSG00000038301	Snx10	2410004M09Rik	sorting nexin 10	protein-coding
mm_19275.1	chr2	85198739	85198780	-	1	NA	Intergenic	Intergenic	-2060	NM_001033346	241528	Mm.291095	NM_001033346	ENSMUSG00000075224	Lrrc55	A330097E02Rik|Gm351	leucine rich repeat containing 55	protein-coding
mm_69550.1	chr7	135697908	135697928	-	1	NA	exon (NM_001081117, exon 12 of 14)	exon (NM_001081117, exon 12 of 14)	18461	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_98197.1	chr11	87795287	87795300	+	1	NA	exon (NM_010824, exon 4 of 14)	exon (NM_010824, exon 4 of 14)	1509	NM_010824	17523	Mm.4668	NM_010824	ENSMUSG00000009350	Mpo	mKIAA4033	myeloperoxidase	protein-coding
mm_27538.1	chr3	57576439	57576445	-	1	NA	promoter-TSS (NM_133784)	promoter-TSS (NM_133784)	-532	NM_001168281	97064	Mm.405029	NM_133784	ENSMUSG00000027803	Wwtr1	2310058J06Rik|2610021I22Rik|C78399|Taz	WW domain containing transcription regulator 1	protein-coding
mm_104568.1	chr11	96936368	96936395	-	1	NA	TTS (NM_146026)	TTS (NM_146026)	7057	NM_146026	217138	Mm.342551	NM_146026	ENSMUSG00000047040	Prr15l	Atad4|BC022765|E230006A12Rik	proline rich 15-like	protein-coding
mm_104681.1	chr11	97699701	97699709	-	1	NA	promoter-TSS (NM_001163308)	promoter-TSS (NM_001163308)	-57	NM_001163308	22658	Mm.2418	NM_009545	ENSMUSG00000018537	Pcgf2	Mel18|Rnf110|Zfp144|mel-18	polycomb group ring finger 2	protein-coding
mm_93548.1	chr10	116113935	116113941	-	1	NA	promoter-TSS (NM_001161855)	promoter-TSS (NM_001161855)	-21	NM_001161855	619332	Mm.391427	NM_001033821	ENSMUSG00000074734	4933416C03Rik	-	RIKEN cDNA 4933416C03 gene	protein-coding
mm_93048.1	chr10	88503929	88503950	-	1	NA	promoter-TSS (NM_001146690)	promoter-TSS (NM_001146690)	31	NR_027477	212862	Mm.288897	NM_144807	ENSMUSG00000060002	Chpt1	-	choline phosphotransferase 1	protein-coding
mm_69905.1	chr7	141639942	141639950	-	1	NA	intron (NM_001330001, intron 31 of 33)	intron (NM_001330001, intron 31 of 33)	15373	NM_001330001	353328	Mm.246621	NM_181729	ENSMUSG00000048191	Muc6	-	mucin 6, gastric	protein-coding
mm_54020.1	chr6	8735310	8735314	-	1	NA	intron (NM_001252266, intron 5 of 11)	intron (NM_001252266, intron 5 of 11)	23146	NM_001252266	15893	Mm.275683	NM_010492	ENSMUSG00000062995	Ica1	69kDa|ICA69	islet cell autoantigen 1	protein-coding
mm_161691.1	chr17	22361385	22361385	-	1	NA	promoter-TSS (NM_176962)	promoter-TSS (NM_176962)	15	NM_176962	319615	Mm.442162	NM_176962	ENSMUSG00000033972	Zfp944	6330416L07Rik	zinc finger protein 944	protein-coding
mm_135559.1	chr16	50046244	50046251	-	1	NA	intron (NR_045935, intron 1 of 3)	intron (NR_045935, intron 1 of 3)	26605	NR_045935	224180	Mm.146439	NM_175010		Gm4827	B130050K08|EG224180	predicted gene 4827	ncRNA
mm_73259.1	chr8	104340665	104340704	+	1	NA	promoter-TSS (NM_024217)	promoter-TSS (NM_024217)	90	NM_024217	68119	Mm.390108	NM_024217	ENSMUSG00000031875	Cmtm3	9430096L06Rik|AI413895|BNAS2|Cklfsf3	CKLF-like MARVEL transmembrane domain containing 3	protein-coding
mm_35746.1	chr4	45409451	45409462	-	1	NA	promoter-TSS (NM_001009949)	promoter-TSS (NM_001009949)	-690	NM_001009949	230125	Mm.260210	NM_001009949	ENSMUSG00000045973	Slc25a51	9130208E07Rik|D130005A03Rik|Gm138|Mcart1	solute carrier family 25, member 51	protein-coding
mm_83118.1	chr9	40392436	40392482	-	1	NA	intron (NM_172768, intron 2 of 19)	intron (NM_172768, intron 2 of 19)	58987	NR_040728	73558	Mm.398307	NR_040728		1700110K17Rik	-	RIKEN cDNA 1700110K17 gene	ncRNA
mm_63165.1	chr7	123993335	123993348	+	1	NA	intron (NM_001252072, intron 1 of 1)	intron (NM_001252072, intron 1 of 1)	10160	NM_001252072	628779	Mm.40210	NM_001252072	ENSMUSG00000078591	Hs3st4	EG628779|Gm6915	heparan sulfate (glucosamine) 3-O-sulfotransferase 4	protein-coding
mm_126603.1	chr15	82454119	82454157	+	1	NA	exon (NM_010006, exon 3 of 9)	exon (NM_010006, exon 3 of 9)	1761	NM_010006	13105	Mm.226708	NM_010006	ENSMUSG00000068086	Cyp2d9	Cyp2d|P450-2D	cytochrome P450, family 2, subfamily d, polypeptide 9	protein-coding
mm_71370.1	chr8	45763874	45763933	+	1	NA	intron (NM_172752, intron 8 of 22)	intron (NM_172752, intron 8 of 22)	55394	NR_045739	319940	Mm.441720	NR_045739	ENSMUSG00000085440	Sorbs2os	D330022K07Rik	sorbin and SH3 domain containing 2, opposite strand	ncRNA
mm_137118.1	chr17	22497441	22497460	+	1	NA	Intergenic	Intergenic	73248	NM_001331198	74149	Mm.30767	NM_198003	ENSMUSG00000071266	Zfp946	1300003B13Rik	zinc finger protein 946	protein-coding
mm_13310.1	chr2	102658753	102658764	+	1	NA	promoter-TSS (NM_001077514)	promoter-TSS (NM_001077514)	75	NM_001077514	20511	Mm.267547	NM_011393	ENSMUSG00000005089	Slc1a2	1700091C19Rik|2900019G14Rik|AI159670|Eaat2|GLT-1|GLT1|MGLT1	solute carrier family 1 (glial high affinity glutamate transporter), member 2	protein-coding
mm_49366.1	chr6	23248620	23248628	+	1	NA	promoter-TSS (NM_028462)	promoter-TSS (NM_028462)	-360	NM_028462	73191	Mm.55115	NM_028462	ENSMUSG00000029697	Fezf1	3110069A13Rik|Fez|Zfp312-like|fez-like	Fez family zinc finger 1	protein-coding
mm_91023.1	chr10	17920038	17920042	-	1	NA	intron (NM_001033432, intron 1 of 3)	intron (NM_001033432, intron 1 of 3)	28027	NM_001033432	380629	Mm.276430	NM_001033432	ENSMUSG00000039879	Heca	Gm869|HDC|HDCL	hdc homolog, cell cycle regulator	protein-coding
mm_19292.1	chr2	90457571	90457591	-	1	NA	intron (NM_001135657, intron 10 of 25)	intron (NM_001135657, intron 10 of 25)	21593	NM_001135657	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_130336.1	chr15	97731202	97731213	-	1	NA	intron (NM_001168693, intron 1 of 9)	intron (NM_001168693, intron 1 of 9)	198	NM_001168693	19011	Mm.1001	NM_008902	ENSMUSG00000022468	Endou	Pp11r|Tcl-30	endonuclease, polyU-specific	protein-coding
mm_105429.1	chr11	103901116	103901120	-	1	NA	intron (NM_008740, intron 8 of 20)	intron (NM_008740, intron 8 of 20)	52938	NM_008740	18195	Mm.260117	NM_008740	ENSMUSG00000034187	Nsf	AI316878|AU020090|AU067812|SKD2	N-ethylmaleimide sensitive fusion protein	protein-coding
mm_62933.1	chr7	118712574	118712616	+	1	NA	promoter-TSS (NM_182995)	promoter-TSS (NM_182995)	-16	NM_182995	101565	Mm.23279	NM_182995	ENSMUSG00000033904	Ccp110	6330503K22Rik|AA415922|AI427129|AW557948|CP110	centriolar coiled coil protein 110	protein-coding
mm_121627.1	chr14	8317819	8317829	-	1	NA	Intergenic	Intergenic	-8048	NM_183187	268709	Mm.256058	NM_183187	ENSMUSG00000021750	Fam107a	DRR1	family with sequence similarity 107, member A	protein-coding
mm_155582.1	chrX	78446636	78446637	+	1	NA	Intergenic	Intergenic	76993	NM_001177966	74910	Mm.159364	NM_001177966	ENSMUSG00000035651	4930480E11Rik	-	RIKEN cDNA 4930480E11 gene	protein-coding
mm_101765.1	chr11	43747964	43748015	-	1	NA	promoter-TSS (NM_133795)	promoter-TSS (NM_133795)	-16	NM_133795	66827	Mm.271974	NM_133795	ENSMUSG00000041278	Ttc1	4833412C19Rik|C79328|TPR1	tetratricopeptide repeat domain 1	protein-coding
mm_169059.1	chr13	23803681	23803685	-	1	NA	Intergenic	U5|snRNA|snRNA	-3344	NM_144836	218103	Mm.24030	NM_144836	ENSMUSG00000036110	Slc17a2	C730032N17Rik|NPT3	solute carrier family 17 (sodium phosphate), member 2	protein-coding
mm_31876.1	chr4	80910671	80910685	+	1	NA	promoter-TSS (NM_026821)	promoter-TSS (NM_026821)	-8	NM_026821	52829	Mm.273986	NM_026821	ENSMUSG00000048706	Lurap1l	1110029A09Rik|AV077978|AV175137|D4Bwg0951e|WI-13707|bM350F23.1	leucine rich adaptor protein 1-like	protein-coding
mm_34843.1	chr4	155409271	155409280	+	1	NA	promoter-TSS (NM_001166029)	promoter-TSS (NM_001166029)	85	NM_001166029	544678	Mm.472798	NM_177674	ENSMUSG00000078490	Cfap74	2010015L04Rik|A530045M11	cilia and flagella associated protein 74	protein-coding
mm_64886.1	chr7	15920668	15920692	-	1	NA	intron (NM_009156, intron 1 of 5)	intron (NM_009156, intron 1 of 5)	1691	NM_009156	20364	Mm.42829	NM_009156	ENSMUSG00000041571	Selenow	Sepw1|selW	selenoprotein W	protein-coding
mm_162314.1	chr1	37998188	37998199	+	1	NA	promoter-TSS (NM_172054)	promoter-TSS (NM_172054)	183	NM_198303	226982	Mm.260943	NM_198303	ENSMUSG00000026083	Eif5b	A030003E17Rik|BC018347|IF2	eukaryotic translation initiation factor 5B	protein-coding
mm_5644.1	chr1	40515216	40515230	-	1	NA	promoter-TSS (NM_010553)	promoter-TSS (NM_010553)	-139	NM_010553	16174	Mm.20466	NM_010553	ENSMUSG00000026068	Il18rap	AcPL|IL-18R-beta|IL-18RAcP|IL-18Rbeta|IL-1RAcPL	interleukin 18 receptor accessory protein	protein-coding
mm_18014.1	chr2	38290403	38290416	-	1	NA	Intergenic	MIRc|SINE|MIR	-3025	NM_146122	227801	Mm.314245	NM_146122	ENSMUSG00000035392	Dennd1a	6030446I19Rik|connecdenn	DENN/MADD domain containing 1A	protein-coding
mm_97266.1	chr11	75765093	75765104	+	1	NA	3' UTR (NM_009536, exon 6 of 6)	3' UTR (NM_009536, exon 6 of 6)	-30711	NR_136933	102641247	Mm.411386	NR_136932		Gm12339	OTTMUSG00000006218	predicted gene 12339	ncRNA
mm_101961.1	chr11	50300951	50301012	-	1	NA	exon (NM_001110500, exon 10 of 15)	exon (NM_001110500, exon 10 of 15)	-8645	NM_175334	103806	Mm.51116	NM_175334	ENSMUSG00000050567	Maml1	AI644666|AW743257|D930008C07Rik|Mam-1|Mam1|mKIAA0200	mastermind like 1 (Drosophila)	protein-coding
mm_125361.1	chr15	39434352	39434357	+	1	NA	intron (NM_001256382, intron 3 of 26)	intron (NM_001256382, intron 3 of 26)	-225157	NM_001256384	116838	Mm.309296	NM_053271	ENSMUSG00000037386	Rims2	2810036I15Rik|AW048769|RIM2|Rab3ip2|Rim2(+40A)|Rim2(+44A)|Rim2(+4A)|Serg2|Syt3-rs|mKIAA0751	regulating synaptic membrane exocytosis 2	protein-coding
mm_27337.1	chr3	50406890	50406893	-	1	NA	intron (NM_011990, intron 6 of 11)	intron (NM_011990, intron 6 of 11)	36722	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_95139.1	chr11	35078564	35078572	+	1	NA	Intergenic	RLTR17|LTR|ERVK	-42888	NM_011412	20564	Mm.478604	NM_011412	ENSMUSG00000056427	Slit3	Slil2|Slit1|b2b2362.1Clo	slit homolog 3 (Drosophila)	protein-coding
mm_87573.1	chr10	56388095	56388143	+	1	NA	exon (NM_010288, exon 2 of 2)	exon (NM_010288, exon 2 of 2)	10819	NM_010288	14609	Mm.378921	NM_010288	ENSMUSG00000050953	Gja1	AU042049|AW546267|Cnx43|Cx43|Cx43alpha1|Gja-1|Npm1|connexin43	gap junction protein, alpha 1	protein-coding
mm_151201.1	chr19	53539374	53539391	+	1	NA	intron (NM_001085390, intron 3 of 3)	intron (NM_001085390, intron 3 of 3)	10064	NM_001085390	240672	Mm.482424	NM_001085390	ENSMUSG00000034765	Dusp5	Gm337	dual specificity phosphatase 5	protein-coding
mm_116305.1	chr13	36734372	36734385	-	1	NA	promoter-TSS (NM_153529)	promoter-TSS (NM_153529)	99	NM_153529	68404	Mm.232930	NM_153529	ENSMUSG00000039114	Nrn1	0710008J23Rik|Cpg15|Nrn	neuritin 1	protein-coding
mm_19611.1	chr2	102746740	102746751	-	1	NA	intron (NM_001077515, intron 5 of 10)	intron (NM_001077515, intron 5 of 10)	40307	NM_001077515	20511	Mm.267547	NM_011393	ENSMUSG00000005089	Slc1a2	1700091C19Rik|2900019G14Rik|AI159670|Eaat2|GLT-1|GLT1|MGLT1	solute carrier family 1 (glial high affinity glutamate transporter), member 2	protein-coding
mm_82316.1	chr9	7873158	7873192	-	1	NA	promoter-TSS (NM_007464)	promoter-TSS (NM_007464)	-5	NM_007464	11796	Mm.2026	NM_007464	ENSMUSG00000032000	Birc3	AW107670|Api1|Api2|Birc2|C-IAP2|HIAP2|IAP1|IAP2|MIAP1|MIAP2|MIHB|MIHC|RNF49|cIAP-1|cIAP-2|cIAP1|cIAP2	baculoviral IAP repeat-containing 3	protein-coding
mm_42133.1	chr5	111124089	111124099	+	1	NA	intron (NM_001267622, intron 5 of 22)	intron (NM_001267622, intron 5 of 22)	119950	NR_030482	735278		NR_030482	ENSMUSG00000076163	Mir701	Mirn701|mir-701|mmu-mir-701	microRNA 701	ncRNA
mm_126359.1	chr15	80024486	80024490	+	1	NA	Intergenic	Intergenic	-9680	NM_011057	18591	Mm.144089	NM_011057	ENSMUSG00000000489	Pdgfb	PDGF-B|Sis	platelet derived growth factor, B polypeptide	protein-coding
mm_40027.1	chr5	33378730	33378798	+	1	NA	promoter-TSS (NM_001081101)	promoter-TSS (NM_001081101)	68	NM_001081101	71101	Mm.132178	NM_001081101	ENSMUSG00000037355	Uvssa	4933407H18Rik|D330017J19Rik|Kiaa1530|mKIAA1530	UV stimulated scaffold protein A	protein-coding
mm_54310.1	chr6	30135955	30135957	-	1	NA	intron (NM_010938, intron 11 of 11)	intron (NM_010938, intron 11 of 11)	30036	NR_029569	387177		NR_029569	ENSMUSG00000076361	Mir182	Mirn182|mir-182|mmu-mir-182	microRNA 182	ncRNA
mm_90983.1	chr10	13678988	13679011	-	1	NA	intron (NM_001347362, intron 4 of 5)	A-rich|Low_complexity|Low_complexity	-125857	NM_001347361	56535	Mm.282711	NM_019961	ENSMUSG00000019809	Pex3	1700014F15Rik|2810027F19Rik|2900010N04Rik	peroxisomal biogenesis factor 3	protein-coding
mm_132138.1	chr16	31933969	31934006	+	1	NA	5' UTR (NM_172822, exon 1 of 3)	5' UTR (NM_172822, exon 1 of 3)	136	NM_172822	239827	Mm.440388	NM_172822	ENSMUSG00000045625	Pigz	F630022B06Rik	phosphatidylinositol glycan anchor biosynthesis, class Z	protein-coding
mm_57583.1	chr6	127151045	127151055	-	1	NA	promoter-TSS (NM_009829)	promoter-TSS (NM_009829)	-2	NM_009829	12444	Mm.333406	NM_009829	ENSMUSG00000000184	Ccnd2	2600016F06Rik|AI256817|BF642806|C86853|Vin-1|Vin1|cD2	cyclin D2	protein-coding
mm_51326.1	chr6	72351842	72351885	+	1	NA	3' UTR (NM_026696, exon 4 of 4)	3' UTR (NM_026696, exon 4 of 4)	-3620	NM_144916	232086	Mm.491165	NM_144916	ENSMUSG00000055912	Tmem150a	BC014685|Tmem150	transmembrane protein 150A	protein-coding
mm_26161.1	chr3	138277643	138277659	+	1	NA	promoter-TSS (NM_007409)	promoter-TSS (NM_007409)	6	NM_007409	11522	Mm.2409	NM_007409	ENSMUSG00000074207	Adh1	ADH-AA|AI194826|Adh-1|Adh-1-t|Adh-1e|Adh-1t|Adh-3e|Adh1-e|Adh1-t|Adh1tl|Adh3-e	alcohol dehydrogenase 1 (class I)	protein-coding
mm_102442.1	chr11	59542504	59542543	-	1	NA	promoter-TSS (NM_145827)	promoter-TSS (NM_145827)	-163	NM_145827	216799	Mm.54174	NM_145827	ENSMUSG00000032691	Nlrp3	AGTAVPRL|AII/AVP|Cias1|FCAS|FCU|MWS|Mmig1|NALP3|Pypaf1	NLR family, pyrin domain containing 3	protein-coding
mm_34336.1	chr4	143389686	143389712	+	1	NA	Intergenic	Intergenic	-4742	NM_031377	83491	Mm.190607	NM_031377	ENSMUSG00000041805	Pramel1	-	preferentially expressed antigen in melanoma-like 1	protein-coding
mm_131736.1	chr16	22009451	22009466	+	1	NA	promoter-TSS (NM_029457)	promoter-TSS (NM_029457)	-26	NM_029457	75826	Mm.297431	NM_029457	ENSMUSG00000022855	Senp2	2310007L05Rik|4930538C18Rik|AI646780|AW554757|Smt3ip2|SuPr-1|mKIAA1331	SUMO/sentrin specific peptidase 2	protein-coding
mm_111733.1	chr12	103828032	103828062	-	1	NA	Intergenic	Intergenic	35572	NM_001252569	20700	Mm.439692	NM_009243	ENSMUSG00000066366	Serpina1a	Aat-2|Aat2|Dom1|PI1|Spi1-1|Spi1-3	serine (or cysteine) peptidase inhibitor, clade A, member 1A	protein-coding
mm_77832.1	chr9	4309828	4309842	+	1	NA	promoter-TSS (NM_026962)	promoter-TSS (NM_026962)	19	NM_026962	69149	Mm.25946	NM_026962	ENSMUSG00000025893	Kbtbd3	2200003A07Rik|Bklhd3	kelch repeat and BTB (POZ) domain containing 3	protein-coding
mm_159610.1	chr4	131968076	131968076	-	1	NA	intron (NM_001128606, intron 11 of 17)	intron (NM_001128606, intron 11 of 17)	46305	NM_001201367	623230	Mm.421179	NM_001201367	ENSMUSG00000070720	Tmem200b	EG623230	transmembrane protein 200B	protein-coding
mm_158691.1	chrX	160976489	160976499	-	1	NA	intron (NM_001024624, intron 1 of 18)	intron (NM_001024624, intron 1 of 18)	18187	NM_001024624	382253	Mm.443717	NM_001024624	ENSMUSG00000031292	Cdkl5	BC038161|Stk9	cyclin-dependent kinase-like 5	protein-coding
mm_68035.1	chr7	101301724	101301744	-	1	NA	intron (NM_001111111, intron 1 of 17)	intron (NM_001111111, intron 1 of 17)	354	NM_001111111	73683	Mm.275744	NM_001111111	ENSMUSG00000047767	Atg16l2	2410118P20Rik	autophagy related 16-like 2 (S. cerevisiae)	protein-coding
mm_43317.1	chr5	134966844	134966863	+	1	NA	Intergenic	Intergenic	-19361	NM_009902	12739	Mm.158662	NM_009902	ENSMUSG00000070473	Cldn3	AI182374|Cpetr2|mRVP1	claudin 3	protein-coding
mm_118477.1	chr14	11640121	11640121	+	1	NA	intron (NM_008981, intron 1 of 29)	intron (NM_008981, intron 1 of 29)	86568	NM_008981	19270	Mm.431266	NM_008981	ENSMUSG00000021745	Ptprg	5430405N12Rik|AW046354|AW549872|RPTPgamma	protein tyrosine phosphatase, receptor type, G	protein-coding
mm_59599.1	chr7	28139914	28139921	+	1	NA	exon (NM_001164655, exon 5 of 20)	exon (NM_001164655, exon 5 of 20)	10451	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_14740.1	chr2	144368909	144368953	+	1	NA	promoter-TSS (NM_001166640)	promoter-TSS (NM_001166640)	-52	NM_001164813	100048644	Mm.227925	NM_001164813	ENSMUSG00000098387	Pet117	Gm20571	PET117 homolog	protein-coding
mm_112699.1	chr13	17700347	17700350	+	1	NA	Intergenic	Intergenic	4935	NM_025479	66308	Mm.291109	NM_025479	ENSMUSG00000012429	Mplkip	2810021B07Rik|C330007M08Rik|Ttdn1	M-phase specific PLK1 intereacting protein	protein-coding
mm_136469.1	chr16	95586586	95586595	-	1	NA	promoter-TSS (NM_001302152)	promoter-TSS (NM_001302152)	3	NM_001302152	13876	Mm.164531	NM_133659	ENSMUSG00000040732	Erg	D030036I24Rik	avian erythroblastosis virus E-26 (v-ets) oncogene related	protein-coding
mm_51094.1	chr6	67238116	67238129	+	1	NA	Intergenic	Intergenic	-28857	NM_001113564	66870	Mm.240490	NM_025814	ENSMUSG00000036371	Serbp1	1200009K13Rik|9330147J08Rik|AL022786|Pairbp1	serpine1 mRNA binding protein 1	protein-coding
mm_141020.1	chr17	25136469	25136479	-	1	NA	promoter-TSS (NM_001317404)	promoter-TSS (NM_001317404)	-157	NM_001317404	26373	Mm.270587	NM_011930	ENSMUSG00000036636	Clcn7	ClC-7|D17Wsu51e	chloride channel, voltage-sensitive 7	protein-coding
mm_40157.1	chr5	35583690	35583711	+	1	NA	intron (NR_045807, intron 3 of 3)	intron (NR_045807, intron 3 of 3)	640	NM_030721	80911	Mm.291503	NM_030721	ENSMUSG00000029098	Acox3	BI685180|EST-s59|PCOX	acyl-Coenzyme A oxidase 3, pristanoyl	protein-coding
mm_75734.1	chr8	69522958	69522994	-	1	NA	Intergenic	Intergenic	102199	NM_001045553	234362	Mm.458487	NM_172754	ENSMUSG00000060427	Zfp868	AI449175|AW108241|C530032E20|mszf62	zinc finger protein 868	protein-coding
mm_82509.1	chr9	20492724	20492765	-	1	NA	promoter-TSS (NM_001110309)	promoter-TSS (NM_001110309)	2	NM_146221	235028	Mm.297660	NM_146221	ENSMUSG00000059475	Zfp426	2900057C04Rik|KRAB1|Zfo61|Zfp68-rs1|Znf426|mKIAA4237	zinc finger protein 426	protein-coding
mm_108419.1	chr12	81971223	81971245	+	1	NA	intron (NM_018814, intron 19 of 35)	intron (NM_018814, intron 19 of 35)	111204	NM_018814	54604	Mm.86584	NM_018814	ENSMUSG00000021140	Pcnx	2900024E21Rik|3526401J03Rik|AF096286|AI327143|AI413187|Pcnx1|Pcnxl1	pecanex homolog (Drosophila)	protein-coding
mm_24472.1	chr3	90669534	90669574	+	1	NA	exon (NM_013650, exon 2 of 3)	exon (NM_013650, exon 2 of 3)	483	NM_013650	20201	Mm.21567	NM_013650	ENSMUSG00000056054	S100a8	60B8Ag|AI323541|B8Ag|CFAg|CP-10|Caga|MRP8|p8	S100 calcium binding protein A8 (calgranulin A)	protein-coding
mm_60290.1	chr7	43998849	43998866	+	1	NA	exon (NM_010640, exon 3 of 5)	exon (NM_010640, exon 3 of 5)	2980	NM_010640	16613	Mm.443378	NM_010640	ENSMUSG00000044485	Klk1b11	Klk11|mGK-11	kallikrein 1-related peptidase b11	protein-coding
mm_120194.1	chr14	61599551	61599569	+	1	NA	promoter-TSS (NM_023233)	promoter-TSS (NM_023233)	48	NM_023233	66597	Mm.491258	NM_023233	ENSMUSG00000035235	Trim13	3110001L12Rik|CAR|LEU5|RNF77|Rfp2	tripartite motif-containing 13	protein-coding
mm_141652.1	chr17	33685387	33685410	-	1	NA	promoter-TSS (NM_001109913)	promoter-TSS (NM_001109913)	60	NM_001109913	76936	Mm.311439	NM_029804	ENSMUSG00000059208	Hnrnpm	2610023M21Rik|AA409009|Hnrpm|mKIAA4193	heterogeneous nuclear ribonucleoprotein M	protein-coding
mm_157792.1	chrX	73854538	73854548	-	1	NA	3' UTR (NM_008478, exon 29 of 29)	3' UTR (NM_008478, exon 29 of 29)	26291	NM_008478	16728	Mm.260568	NM_008478	ENSMUSG00000031391	L1cam	CD171|L1|N-CAM-L1|NCAM-L1	L1 cell adhesion molecule	protein-coding
mm_63767.1	chr7	131223348	131223359	+	1	NA	intron (NM_175166, intron 8 of 22)	intron (NM_175166, intron 8 of 22)	48951	NM_175166	71395	Mm.118845	NM_175166	ENSMUSG00000006204	5430419D17Rik	-	RIKEN cDNA 5430419D17 gene	protein-coding
mm_61337.1	chr7	68277748	68277755	+	1	NA	intron (NM_001013811, intron 1 of 8)	intron (NM_001013811, intron 1 of 8)	-1157	NR_040340	100504026	Mm.426764	NR_040340	ENSMUSG00000086628	Gm16157	OTTMUSG00000031023	predicted gene 16157	ncRNA
mm_82372.1	chr9	14615298	14615309	-	1	NA	promoter-TSS (NM_001081395)	promoter-TSS (NM_001081395)	-303	NM_001081395	75723	Mm.159552	NM_001081395	ENSMUSG00000013076	Amotl1	2310010G08Rik|2310067L22Rik|4932416D09Rik|JEAP|mFLJ00155	angiomotin-like 1	protein-coding
mm_75213.1	chr8	39605495	39605511	-	1	NA	3' UTR (NM_031195, exon 9 of 9)	3' UTR (NM_031195, exon 9 of 9)	37175	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_112829.1	chr13	20818334	20818354	+	1	NA	intron (NM_012054, intron 2 of 20)	B2_Mm2|SINE|B2	24231	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_91051.1	chr10	18786779	18786789	-	1	NA	promoter-TSS (NM_177706)	promoter-TSS (NM_177706)	9	NM_177706	237300	Mm.444821	NM_177706	ENSMUSG00000044624	Gm4922	4933423E17|EG237300	predicted gene 4922	protein-coding
mm_396.1	chr1	34121404	34121425	+	1	NA	intron (NM_001276764, intron 8 of 102)	intron (NM_001276764, intron 8 of 102)	4055	NR_105861	102466987		NR_105861	ENSMUSG00000105982	Mir6896	mmu-mir-6896	microRNA 6896	ncRNA
mm_64700.1	chr7	4547417	4547425	-	1	NA	promoter-TSS (NM_016908)	promoter-TSS (NM_016908)	-854	NM_016908	53420	Mm.358663	NM_016908	ENSMUSG00000004961	Syt5	SytV	synaptotagmin V	protein-coding
mm_33698.1	chr4	133584356	133584415	+	1	NA	promoter-TSS (NM_001290742)	promoter-TSS (NM_001290742)	12	NM_133884	100210	Mm.274001	NM_133884	ENSMUSG00000028848	Gpn2	AI838661|Atpbd1b|R74630	GPN-loop GTPase 2	protein-coding
mm_32478.1	chr4	107879746	107879796	+	1	NA	promoter-TSS (NM_001282737)	promoter-TSS (NM_001282737)	16	NM_001282737	17149	Mm.808	NM_001282737	ENSMUSG00000028609	Magoh	Mago-m|Mos2	mago homolog, exon junction complex core component	protein-coding
mm_165436.1	chr2	153875039	153875045	+	1	NA	promoter-TSS (NM_025631)	promoter-TSS (NM_025631)	-3	NM_025631	66557	Mm.46448	NM_025631	ENSMUSG00000027481	Bpifb2	2310034L21Rik|2310069A01Rik|AV089125|Bpil1|LPLUNC2|RYSR	BPI fold containing family B, member 2	protein-coding
mm_121549.1	chr14	122475372	122475388	+	1	NA	promoter-TSS (NR_045046)	promoter-TSS (NR_045046)	-4	NM_009574	22772	Mm.308936	NM_009574	ENSMUSG00000061524	Zic2	HPE5|Ku	zinc finger protein of the cerebellum 2	protein-coding
mm_97807.1	chr11	82961518	82961544	+	1	NA	promoter-TSS (NR_045932)	promoter-TSS (NR_045932)	-850	NR_045932	76392	Mm.295205	NR_045932	ENSMUSG00000086327	Slfn5os	1700003F17Rik	schlafen 5, opposite strand	ncRNA
mm_133297.1	chr16	77500543	77500563	+	1	NA	intron (NR_015543, intron 3 of 4)	intron (NR_015543, intron 3 of 4)	-98383	NR_029535	387229		NR_029535	ENSMUSG00000065530	Mir99a	Mirn99a|mir-99a|mmu-mir-99a	microRNA 99a	ncRNA
mm_117582.1	chr13	89384820	89384825	-	1	NA	Intergenic	RLTR44B|LTR|ERVK	-155814	NM_013500	12950	Mm.266790	NM_013500	ENSMUSG00000021613	Hapln1	BB099155|CLP|Crtl1|Crtl1l|LP|LP-1	hyaluronan and proteoglycan link protein 1	protein-coding
mm_135651.1	chr16	52394785	52394824	-	1	NA	intron (NM_009655, intron 1 of 15)	intron (NM_009655, intron 1 of 15)	58277	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_67003.1	chr7	65213365	65213373	-	1	NA	Intergenic	Intergenic	-56841	NM_183087	70638	Mm.441986	NM_183087	ENSMUSG00000030518	Fam189a1	5730507A09Rik|AW047451	family with sequence similarity 189, member A1	protein-coding
mm_33467.1	chr4	130812563	130812570	+	1	NA	intron (NM_011520, intron 1 of 4)	intron (NM_011520, intron 1 of 4)	20029	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_35691.1	chr4	44073017	44073021	-	1	NA	promoter-TSS (NM_001190414)	promoter-TSS (NM_001190414)	-346	NM_001190414	50798	Mm.256718	NM_015828	ENSMUSG00000028479	Gne	2310066H07Rik|DMRV|GLCNE|IBM2|NM|Uae1	glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase	protein-coding
mm_90365.1	chr10	127166689	127166700	+	1	NA	intron (NR_045166, intron 2 of 9)	intron (NR_045166, intron 2 of 9)	863	NM_001244618	14421	Mm.386762	NM_008080	ENSMUSG00000006731	B4galnt1	4933429D13Rik|Gal-NAc-T|GalNAc-T|GalNAcT|Galgt1|Ggm-2|Ggm2	beta-1,4-N-acetyl-galactosaminyl transferase 1	protein-coding
mm_4050.1	chr1	165788747	165788769	+	1	NA	promoter-TSS (NM_031162)	promoter-TSS (NM_031162)	77	NM_001113392	12503	Mm.217308	NM_031162	ENSMUSG00000005763	Cd247	4930549J05Rik|A430104F18Rik|AW552088|Cd3|Cd3-eta|Cd3-zeta|Cd3h|Cd3z|Cd3zeta|T3z|Tcrk|Tcrz	CD247 antigen	protein-coding
mm_7576.1	chr1	124846069	124846075	-	1	NA	Intergenic	Intergenic	589655	NM_023735	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding
mm_19284.1	chr2	89946995	89947017	-	1	NA	Intergenic	Intergenic	-2893	NM_146341	258338	Mm.354180	NM_146341	ENSMUSG00000068806	Olfr1259	MOR232-9	olfactory receptor 1259	protein-coding
mm_34993.1	chr4	156030962	156030974	+	1	NA	Intergenic	Intergenic	4626	NM_021985	21936	Mm.3180	NM_009400	ENSMUSG00000041954	Tnfrsf18	AITR|Gitr	tumor necrosis factor receptor superfamily, member 18	protein-coding
mm_164296.1	chr15	103895998	103896004	+	1	NA	3' UTR (NM_009267, exon 4 of 4)	3' UTR (NM_009267, exon 4 of 4)	3299	NM_009268	20771	Mm.30276	NM_009268		Mucl1	Spt-2|Spt2	mucin-like 1	protein-coding
mm_151898.1	chr19	5799104	5799137	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	-3139	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_168935.1	chr12	69095285	69095294	+	1	NA	Intergenic	Intergenic	63897	NM_009093	20090	Mm.379006	NM_009093	ENSMUSG00000034892	Rps29	-	ribosomal protein S29	protein-coding
mm_149947.1	chr19	27335529	27335534	+	1	NA	3' UTR (NM_183179, exon 2 of 2)	3' UTR (NM_183179, exon 2 of 2)	12912	NM_183179	240595	Mm.269759	NM_183179	ENSMUSG00000047298	Kcnv2	KV11.1	potassium channel, subfamily V, member 2	protein-coding
mm_139976.1	chr17	71781288	71781306	+	1	NA	promoter-TSS (NM_030179)	promoter-TSS (NM_030179)	-2	NM_001271483	78785	Mm.196382	NM_030179	ENSMUSG00000024059	Clip4	1700024K14Rik|1700074B05Rik|4833417L20Rik|5830409B12Rik|Rsnl2	CAP-GLY domain containing linker protein family, member 4	protein-coding
mm_13687.1	chr2	117120758	117120794	+	1	NA	promoter-TSS (NM_001277256)	promoter-TSS (NM_001277256)	-295	NM_001277256	114715	Mm.245890	NM_033524	ENSMUSG00000027351	Spred1	5730461F13Rik|AL024345|AW047647	sprouty protein with EVH-1 domain 1, related sequence	protein-coding
mm_66415.1	chr7	44524643	44524663	-	1	NA	promoter-TSS (NM_146189)	promoter-TSS (NM_146189)	16	NM_146189	233199	Mm.358888	NM_146189	ENSMUSG00000038670	Mybpc2	-	myosin binding protein C, fast-type	protein-coding
mm_32657.1	chr4	115088991	115089149	+	1	NA	exon (NM_001164557, exon 1 of 4)	exon (NM_001164557, exon 1 of 4)	362	NM_001164557	67182	Mm.30181	NM_026018	ENSMUSG00000028716	Pdzk1ip1	0610007F13Rik|2700030M23Rik|AU046042|Map17	PDZK1 interacting protein 1	protein-coding
mm_102610.1	chr11	62457558	62457571	-	1	NA	promoter-TSS (NM_177229)	promoter-TSS (NM_177229)	-232	NM_177229	20185	Mm.271814	NM_011308	ENSMUSG00000018501	Ncor1	5730405M06Rik|A230020K14Rik|N-CoR|RIP13|Rxrip13|mKIAA1047	nuclear receptor co-repressor 1	protein-coding
mm_74177.1	chr8	123454241	123454286	+	1	NA	exon (NM_054046, exon 5 of 12)	exon (NM_054046, exon 5 of 12)	11004	NM_001281803	23854	Mm.275127	NM_054046	ENSMUSG00000001482	Def8	AI449518|D8Ertd713e|DEF-8	differentially expressed in FDCP 8	protein-coding
mm_46477.1	chr5	105131739	105131741	-	1	NA	intron (NM_008620, intron 3 of 10)	A-rich|Low_complexity|Low_complexity	7812	NM_008620	17472	Mm.440525	NM_008620	ENSMUSG00000079363	Gbp4	AW228052|Mag-2|Mpa-2|Mpa2	guanylate binding protein 4	protein-coding
mm_103098.1	chr11	69936149	69936161	-	1	NA	promoter-TSS (NM_001347634)	promoter-TSS (NM_001347634)	-173	NM_001347634	53422	Mm.29286	NM_016875	ENSMUSG00000018554	Ybx2	Msy2	Y box protein 2	protein-coding
mm_168543.1	chr1	162706581	162706581	+	1	NA	exon (NM_001081290, exon 16 of 35)	exon (NM_001081290, exon 16 of 35)	33975	NM_001081290	226562	Mm.245446	NM_001081290	ENSMUSG00000040225	Prrc2c	1810043M20Rik|9630039I18Rik|A630006J20|Bat2d|Bat2d1|Bat2l2|E130112L15Rik|Prrc3|mKIAA1096	proline-rich coiled-coil 2C	protein-coding
mm_123739.1	chr14	70185054	70185066	-	1	NA	exon (NM_001271407, exon 18 of 21)	exon (NM_001271407, exon 18 of 21)	7186	NM_001271409	20410	Mm.5068	NM_011366	ENSMUSG00000022091	Sorbs3	SCAM-1|SH3P3|Sh3d4|vinexin-g	sorbin and SH3 domain containing 3	protein-coding
mm_69711.1	chr7	140116396	140116428	-	1	NA	promoter-TSS (NM_053119)	promoter-TSS (NM_053119)	11	NM_053119	93747	Mm.24452	NM_053119	ENSMUSG00000025465	Echs1	C80529	enoyl Coenzyme A hydratase, short chain, 1, mitochondrial	protein-coding
mm_94230.1	chr11	3290301	3290348	+	1	NA	promoter-TSS (NM_001253691)	promoter-TSS (NM_001253691)	-133	NM_001253690	56218	Mm.275563	NM_019574	ENSMUSG00000020453	Patz1	8430401L15Rik|AI447519|Mazr|Patz|Zfp278	POZ (BTB) and AT hook containing zinc finger 1	protein-coding
mm_41315.1	chr5	90470124	90470127	+	1	NA	intron (NM_009654, intron 9 of 14)	intron (NM_009654, intron 9 of 14)	9255	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_90419.1	chr10	127476522	127476532	+	1	NA	exon (NM_001168293, exon 13 of 24)	exon (NM_001168293, exon 13 of 24)	-25190	NM_177707	237611	Mm.32087	NM_177707	ENSMUSG00000040287	Stac3	9830125E18	SH3 and cysteine rich domain 3	protein-coding
mm_39778.1	chr5	30155244	30155311	+	1	NA	promoter-TSS (NM_001289798)	promoter-TSS (NM_001289798)	24	NM_001289798	231086	Mm.291463	NM_145558	ENSMUSG00000059447	Hadhb	4930479F15Rik|Mtpb|TP-beta	hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), beta subunit	protein-coding
mm_85606.1	chr9	107597023	107597082	-	1	NA	TTS (NM_001291539)	TTS (NM_001291539)	8350	NM_009153	20347	Mm.4083	NM_009153	ENSMUSG00000057969	Sema3b	SemA|Semaa|sema5|semaV	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B	protein-coding
mm_134879.1	chr16	28930014	28930080	-	1	NA	promoter-TSS (NM_177718)	promoter-TSS (NM_177718)	-349	NM_177718	239796	Mm.155887	NM_177718	ENSMUSG00000051065	Mb21d2	1600021P15Rik|A430031N04|C87006	Mab-21 domain containing 2	protein-coding
mm_33465.1	chr4	130811663	130811673	+	1	NA	intron (NM_011520, intron 1 of 4)	intron (NM_011520, intron 1 of 4)	19131	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_36141.1	chr4	59438651	59438679	-	1	NA	promoter-TSS (NM_001163288)	promoter-TSS (NM_001163288)	-32	NM_001163288	634731	Mm.483589	NM_001163288	ENSMUSG00000038578	Susd1	A530080P10|Gm12528|OTTMUSG00000007332	sushi domain containing 1	protein-coding
mm_26453.1	chr3	142701045	142701065	+	1	NA	promoter-TSS (NM_001293560)	promoter-TSS (NM_001293560)	7	NM_001293560	229905	Mm.289643	NM_173763	ENSMUSG00000040213	Kyat3	Ccbl2|KATIII|Kat3	kynurenine aminotransferase 3	protein-coding
mm_1461.1	chr1	67437200	67437200	+	1	NA	Intergenic	Intergenic	314173	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_46321.1	chr5	100719664	100719674	-	1	NA	promoter-TSS (NM_152803)	promoter-TSS (NM_152803)	47	NM_152803	15442	Mm.265786	NM_152803	ENSMUSG00000035273	Hpse	HSE1|Hpa|Hpr1	heparanase	protein-coding
mm_18264.1	chr2	52308340	52308351	-	1	NA	exon (NM_010889, exon 16 of 157)	exon (NM_010889, exon 16 of 157)	17343	NR_040620	78049	Mm.243883	NR_040620		4930573O16Rik	-	RIKEN cDNA 4930573O16 gene	ncRNA
mm_148221.1	chr18	80257439	80257447	-	1	NA	intron (NM_001164420, intron 2 of 4)	intron (NM_001164420, intron 2 of 4)	1137	NM_001164423	66943	Mm.29247	NM_025861	ENSMUSG00000034006	Pqlc1	2310009N05Rik|4933425L21Rik|5730564E11Rik|C78974	PQ loop repeat containing 1	protein-coding
mm_162491.1	chr1	135849441	135849445	-	1	NA	exon (NM_001130176, exon 9 of 13)	exon (NM_001130176, exon 9 of 13)	8582	NM_001130176	21956	Mm.247470	NM_011619	ENSMUSG00000026414	Tnnt2	Tnt|cTnT	troponin T2, cardiac	protein-coding
mm_102929.1	chr11	69600782	69600795	-	1	NA	3' UTR (NM_013415, exon 7 of 7)	3' UTR (NM_013415, exon 7 of 7)	5172	NM_013415	11932	Mm.235204	NM_013415	ENSMUSG00000041329	Atp1b2	Amog|Atpb-2	ATPase, Na+/K+ transporting, beta 2 polypeptide	protein-coding
mm_140334.1	chr17	86760437	86760447	+	1	NA	intron (NM_010137, intron 1 of 15)	(GGGTG)n|Simple_repeat|Simple_repeat	6578	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_33906.1	chr4	136310937	136310947	+	1	NA	promoter-TSS (NM_001277123)	promoter-TSS (NM_001277123)	0	NM_001277122	74326	Mm.31051	NM_028871	ENSMUSG00000066037	Hnrnpr	2610003J05Rik|2610528B01Rik|Hnrpr	heterogeneous nuclear ribonucleoprotein R	protein-coding
mm_133152.1	chr16	70314668	70314680	+	1	NA	intron (NM_028803, intron 1 of 15)	intron (NM_028803, intron 1 of 15)	725	NM_028803	74185	Mm.396102	NM_028803	ENSMUSG00000022707	Gbe1	2310045H19Rik|2810426P10Rik|D16Ertd536e	glucan (1,4-alpha-), branching enzyme 1	protein-coding
mm_72193.1	chr8	72493016	72493024	+	1	NA	promoter-TSS (NM_177766)	promoter-TSS (NM_177766)	-406	NM_177766	270066	Mm.291461	NM_177766	ENSMUSG00000019731	Slc35e1	6030458H05|AA408278	solute carrier family 35, member E1	protein-coding
mm_159272.1	chr2	164486151	164486151	+	1	NA	promoter-TSS (NM_001048227)	promoter-TSS (NM_001048227)	11	NM_001048227	52840	Mm.256927	NM_026797	ENSMUSG00000017734	Dbndd2	1110017A21Rik|2900022J10Rik|AU041050|AW048677|D2Bwg0891e|Nkip|R74724	dysbindin (dystrobrevin binding protein 1) domain containing 2	protein-coding
mm_28145.1	chr3	87330857	87330866	-	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-27020	NM_009690	11801	Mm.6676	NM_009690	ENSMUSG00000015854	Cd5l	1/6|AAC-11|AI047839|Api6|CT2|Pdp|Sp-alpha|mAIM	CD5 antigen-like	protein-coding
mm_143791.1	chr17	81738372	81738400	-	1	NA	promoter-TSS (NM_001112798)	promoter-TSS (NM_001112798)	1	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_84169.1	chr9	59941022	59941045	-	1	NA	Intergenic	Intergenic	9046	NM_013708	23958	Mm.103641	NM_013708	ENSMUSG00000032292	Nr2e3	A930035N01Rik|PNR|RNR|rd7	nuclear receptor subfamily 2, group E, member 3	protein-coding
mm_63689.1	chr7	130575040	130575052	+	1	NA	Intergenic	Intergenic	-2438	NM_001004468	57752	Mm.86322	NM_021314	ENSMUSG00000030852	Tacc2	mKIAA4180	transforming, acidic coiled-coil containing protein 2	protein-coding
mm_138672.1	chr17	35887873	35888023	+	1	NA	exon (NM_026987, exon 14 of 20)	exon (NM_026987, exon 14 of 20)	8170	NM_026987	69192	Mm.390986	NM_026987	ENSMUSG00000024422	Dhx16	2410006N22Rik|DBP2|Ddx16|mKIAA0577	DEAH (Asp-Glu-Ala-His) box polypeptide 16	protein-coding
mm_22622.1	chr3	14649834	14649839	+	1	NA	intron (NM_024495, intron 2 of 6)	intron (NM_024495, intron 2 of 6)	8109	NM_024495	71934	Mm.158776	NM_024495	ENSMUSG00000027555	Car13	2310075C21Rik|Ca13	carbonic anhydrase 13	protein-coding
mm_157512.1	chrX	49288196	49288218	-	1	NA	promoter-TSS (NM_145951)	promoter-TSS (NM_145951)	35	NM_001271449	209224	Mm.327730	NM_145951	ENSMUSG00000031109	Enox2	APK1|Cova1|tNOX	ecto-NOX disulfide-thiol exchanger 2	protein-coding
mm_35804.1	chr4	46630068	46630078	-	1	NA	intron (NM_198664, intron 3 of 12)	intron (NM_198664, intron 3 of 12)	20126	NM_198664	381605	Mm.331595	NM_198664	ENSMUSG00000039813	Tbc1d2	A630005A06Rik|BC022630|Gm1037|PARIS-1|PARIS1	TBC1 domain family, member 2	protein-coding
mm_119630.1	chr14	51220276	51220303	+	1	NA	Intergenic	Intergenic	16594	NM_017389	503847	Mm.377124	NM_017389	ENSMUSG00000050766	Ear14	-	eosinophil-associated, ribonuclease A family, member 14	protein-coding
mm_52630.1	chr6	117174308	117174324	+	1	NA	3' UTR (NM_021704, exon 3 of 3)	3' UTR (NM_021704, exon 3 of 3)	5781	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_19897.1	chr2	114052200	114052203	-	1	NA	intron (NM_009608, intron 1 of 6)	intron (NM_009608, intron 1 of 6)	674	NM_009608	11464	Mm.686	NM_009608	ENSMUSG00000068614	Actc1	Actc-1	actin, alpha, cardiac muscle 1	protein-coding
mm_99456.1	chr11	102434479	102434489	+	1	NA	exon (NM_008175, exon 7 of 13)	exon (NM_008175, exon 7 of 13)	4162	NM_008175	14824	Mm.1568	NM_008175	ENSMUSG00000034708	Grn	Pgrn|epithelin	granulin	protein-coding
mm_67233.1	chr7	75199277	75199279	-	1	NA	intron (NM_001109753, intron 2 of 12)	Lx|LINE|L1	109108	NM_001109753	64176	Mm.273082	NM_153579	ENSMUSG00000053025	Sv2b	A830038F04Rik|AI850768|mKIAA0735	synaptic vesicle glycoprotein 2 b	protein-coding
mm_10227.1	chr2	6322752	6322783	+	1	NA	promoter-TSS (NM_001080548)	promoter-TSS (NM_001080548)	10	NM_001080548	98910	Mm.40673	NM_181399	ENSMUSG00000039046	Usp6nl	AI316785|RNTRE|TRE2NL|mKIAA0019	USP6 N-terminal like	protein-coding
mm_106613.1	chr11	120816405	120816424	-	1	NA	exon (NM_007988, exon 16 of 43)	exon (NM_007988, exon 16 of 43)	8133	NM_007988	14104	Mm.236443	NM_007988	ENSMUSG00000025153	Fasn	A630082H08Rik|FAS	fatty acid synthase	protein-coding
mm_51826.1	chr6	89294940	89294955	+	1	NA	Intergenic	Intergenic	-9222	NR_131021	75131	Mm.391482	NR_131021	ENSMUSG00000107622	4930512J16Rik	-	RIKEN cDNA 4930512J16 gene	ncRNA
mm_119393.1	chr14	41137808	41137823	+	1	NA	Intergenic	Intergenic	6027	NM_023134	20387	Mm.46062	NM_023134	ENSMUSG00000021789	Sftpa1	SP-A|Sftp-1|Sftp1	surfactant associated protein A1	protein-coding
mm_119730.1	chr14	54075018	54075024	+	1	NA	Intergenic	Intergenic	178908	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_11280.1	chr2	30062552	30062570	+	1	NA	intron (NM_023871, intron 1 of 7)	intron (NM_023871, intron 1 of 7)	565	NM_023871	56086	Mm.326055	NM_023871	ENSMUSG00000054766	Set	2610030F17Rik|5730420M11Rik|AA407739|I-2PP2A|StF-IT-1|TAF-I	SET nuclear oncogene	protein-coding
mm_7945.1	chr1	133914971	133914982	-	1	NA	exon (NM_054077, exon 2 of 3)	exon (NM_054077, exon 2 of 3)	6425	NM_054077	116847	Mm.214514	NM_054077	ENSMUSG00000041577	Prelp	7330409J17Rik|SLRR2A	proline arginine-rich end leucine-rich repeat	protein-coding
mm_24309.1	chr3	89418547	89418572	+	1	NA	promoter-TSS (NM_011368)	promoter-TSS (NM_011368)	8	NM_011368	20416	Mm.86595	NM_011368	ENSMUSG00000042626	Shc1	Shc|ShcA|p66|p66shc	src homology 2 domain-containing transforming protein C1	protein-coding
mm_1352.1	chr1	66321810	66321820	+	1	NA	promoter-TSS (NM_001310634)	promoter-TSS (NM_001310634)	91	NM_001310634	17756	Mm.256966	NM_008632	ENSMUSG00000015222	Map2	G1-397-34|MAP-2|Mtap-2|Mtap2|repro4	microtubule-associated protein 2	protein-coding
mm_4949.1	chr1	191201472	191201499	+	1	NA	Intergenic	Intergenic	-18152	NM_007498	11910	Mm.2706	NM_007498	ENSMUSG00000026628	Atf3	LRG-21	activating transcription factor 3	protein-coding
mm_107354.1	chr12	32821318	32821334	+	1	NA	intron (NM_021524, intron 1 of 10)	GC_rich|Low_complexity|Low_complexity	991	NM_021524	59027	Mm.202727	NM_021524	ENSMUSG00000020572	Nampt	1110035O14Rik|AI314458|AI480535|NAmPRTase|Pbef|Pbef1|Visfatin	nicotinamide phosphoribosyltransferase	protein-coding
mm_171480.1	chr4	145868791	145868791	+	1	NA	Intergenic	Intergenic	31572	NR_033612	236069	Mm.276881	NR_033612	ENSMUSG00000096233	Gm13238	OTTMUSG00000011065	carnitine deficiency-associated gene expressed in ventricle 3 pseudogene	pseudo
mm_11265.1	chr2	29999998	30000012	+	1	NA	exon (NM_001177668, exon 22 of 56)	exon (NM_001177668, exon 22 of 56)	4055	NR_105963	102465603		NR_105963	ENSMUSG00000098453	Mir6997	Gm27310|mmu-mir-6997	microRNA 6997	ncRNA
mm_124204.1	chr14	98920898	98920900	-	1	NA	Intergenic	Intergenic	125237	NM_175245	76789	Mm.38912	NM_175245	ENSMUSG00000033186	Mzt1	2410129H14Rik|AI120158|Mozart1	mitotic spindle organizing protein 1	protein-coding
mm_74173.1	chr8	123443289	123443339	+	1	NA	promoter-TSS (NM_001281803)	promoter-TSS (NM_001281803)	55	NM_001281803	23854	Mm.275127	NM_054046	ENSMUSG00000001482	Def8	AI449518|D8Ertd713e|DEF-8	differentially expressed in FDCP 8	protein-coding
mm_119569.1	chr14	50061358	50061361	+	1	NA	Intergenic	RLTR46A2|LTR|ERVK	23320	NM_146316	258313	Mm.463727	NM_146316	ENSMUSG00000060523	Olfr726	MOR246-4	olfactory receptor 726	protein-coding
mm_74054.1	chr8	122306975	122306975	+	1	NA	intron (NM_009569, intron 2 of 9)	intron (NM_009569, intron 2 of 9)	24834	NM_009569	22761	Mm.3105	NM_009569	ENSMUSG00000049577	Zfpm1	FOG|Fog1	zinc finger protein, multitype 1	protein-coding
mm_126394.1	chr15	80193054	80193070	+	1	NA	intron (NM_010795, intron 1 of 1)	intron (NM_010795, intron 1 of 1)	19341	NM_010795	17309	Mm.299693	NM_010795	ENSMUSG00000042428	Mgat3	1110038J12Rik|AI848272|GnT-III	mannoside acetylglucosaminyltransferase 3	protein-coding
mm_148615.1	chr19	5388815	5388831	+	1	NA	promoter-TSS (NM_016882)	promoter-TSS (NM_016882)	-120	NM_016882	20227	Mm.34562	NM_016882	ENSMUSG00000039148	Sart1	U5-110K	squamous cell carcinoma antigen recognized by T cells 1	protein-coding
mm_149096.1	chr19	8932450	8932487	+	1	NA	intron (NM_144872, intron 4 of 21)	intron (NM_144872, intron 4 of 21)	2774	NM_144872	225898	Mm.31008	NM_144872	ENSMUSG00000071647	Eml3	BC022146	echinoderm microtubule associated protein like 3	protein-coding
mm_74168.1	chr8	123420725	123420763	+	1	NA	exon (NM_023279, exon 4 of 4)	exon (NM_023279, exon 4 of 4)	9180	NM_023279	22152	Mm.40068	NM_023279	ENSMUSG00000062380	Tubb3	3200002H15Rik|M(beta)3|M(beta)6	tubulin, beta 3 class III	protein-coding
mm_4583.1	chr1	178299500	178299514	+	1	NA	Intergenic	Intergenic	-19646	NM_025511	66359	Mm.489720	NM_025511	ENSMUSG00000026500	Cox20	2310005N03Rik|Fam36a	COX20 Cox2 chaperone	protein-coding
mm_24210.1	chr3	88621916	88621940	+	1	NA	intron (NM_001198912, intron 1 of 21)	intron (NM_001198912, intron 1 of 21)	534	NM_001198912	16800	Mm.239329	NM_008487	ENSMUSG00000028059	Arhgef2	AA408978|GEF|GEF-H1|GEFH1|LFP40|Lbcl1|Lfc|P40|mKIAA0651	rho/rac guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_139096.1	chr17	46910453	46910464	+	1	NA	promoter-TSS (NM_008938)	promoter-TSS (NM_008938)	-27	NM_008938	19133	Mm.291370	NM_008938	ENSMUSG00000023978	Prph2	AOFMD|AVMD|Nmf193|PRPH|RP7|Rd-2|Rd2|Rds|Tspan22|rds	peripherin 2	protein-coding
mm_51873.1	chr6	90552303	90552324	+	1	NA	intron (NM_027406, intron 1 of 22)	(CA)n|Simple_repeat|Simple_repeat	1465	NM_027406	107747	Mm.30035	NM_027406	ENSMUSG00000030088	Aldh1l1	1810048F20Rik|FDH|Fthfd|Neut2	aldehyde dehydrogenase 1 family, member L1	protein-coding
mm_21971.1	chr2	167313167	167313178	-	1	NA	exon (NM_019835, exon 2 of 9)	exon (NM_019835, exon 2 of 9)	36006	NM_019835	56336	Mm.200886	NM_019835	ENSMUSG00000017929	B4galt5	9430078I07Rik|AW049941|AW539721	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 5	protein-coding
mm_145344.1	chr18	56470963	56470966	+	1	NA	intron (NM_026240, intron 2 of 13)	intron (NM_026240, intron 2 of 13)	38832	NM_026240	107022	Mm.24356	NM_026240	ENSMUSG00000001700	Gramd3	9030613F08Rik|9130427A09Rik|AW061306|NS3TP2	GRAM domain containing 3	protein-coding
mm_89339.1	chr10	87934821	87934850	+	1	NA	3' UTR (NM_010512, exon 5 of 5)	3' UTR (NM_010512, exon 5 of 5)	-31836	NR_000040	22172	Mm.391420	NR_000040		Tyms-ps	-	thymidylate synthase, pseudogene	pseudo
mm_10098.1	chr2	3441033	3441044	+	1	NA	intron (NM_001302684, intron 9 of 14)	intron (NM_001302684, intron 9 of 14)	16907	NM_001302684	227525	Mm.23483	NM_146114	ENSMUSG00000026648	Dclre1c	9930121L06Rik|AI661365|Art|Snm1l	DNA cross-link repair 1C	protein-coding
mm_153345.1	chr19	39463068	39463081	-	1	NA	promoter-TSS (NM_010002)	promoter-TSS (NM_010002)	1	NM_010002	13097	Mm.42100	NM_010002	ENSMUSG00000032808	Cyp2c38	-	cytochrome P450, family 2, subfamily c, polypeptide 38	protein-coding
mm_160884.1	chr11	69761874	69761874	-	1	NA	promoter-TSS (NM_019871)	promoter-TSS (NM_019871)	-30	NM_019871	56293	Mm.6211	NM_019871	ENSMUSG00000018776	Slc35g3	Amac1	solute carrier family 35, member G3	protein-coding
mm_88755.1	chr10	80323504	80323521	+	1	NA	exon (NM_008793, exon 11 of 15)	exon (NM_008793, exon 11 of 15)	-2964	NM_025521	66374	Mm.383824	NM_025521	ENSMUSG00000020133	2310011J03Rik	AI452186|AW545358	RIKEN cDNA 2310011J03 gene	protein-coding
mm_21777.1	chr2	164847788	164847799	-	1	NA	intron (NM_011125, intron 8 of 15)	intron (NM_011125, intron 8 of 15)	9915	NM_011125	18830	Mm.6105	NM_011125	ENSMUSG00000017754	Pltp	Bpife|OD107	phospholipid transfer protein	protein-coding
mm_49045.1	chr6	4760281	4760287	+	1	NA	3' UTR (NM_130877, exon 2 of 2)	3' UTR (NM_130877, exon 2 of 2)	12978	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_13389.1	chr2	103969607	103969625	+	1	NA	promoter-TSS (NM_008505)	promoter-TSS (NM_008505)	59	NM_001142336	16909	Mm.29266	NM_008505	ENSMUSG00000032698	Lmo2	Rbtn-2|Rbtn2|Rhom-2|Ttg2	LIM domain only 2	protein-coding
mm_30892.1	chr4	32268319	32268348	+	1	NA	Intergenic	Intergenic	-149102	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_87566.1	chr10	56377414	56377424	+	1	NA	5' UTR (NM_010288, exon 1 of 2)	5' UTR (NM_010288, exon 1 of 2)	119	NM_010288	14609	Mm.378921	NM_010288	ENSMUSG00000050953	Gja1	AU042049|AW546267|Cnx43|Cx43|Cx43alpha1|Gja-1|Npm1|connexin43	gap junction protein, alpha 1	protein-coding
mm_46465.1	chr5	105121133	105121143	-	1	NA	intron (NM_008620, intron 7 of 10)	intron (NM_008620, intron 7 of 10)	-10846	NM_172777	236573	Mm.425261	NM_172777	ENSMUSG00000029298	Gbp9	-	guanylate-binding protein 9	protein-coding
mm_96894.1	chr11	70437614	70437658	+	1	NA	promoter-TSS (NR_106064)	promoter-TSS (NR_106064)	-619	NR_106064	102465670		NR_106064	ENSMUSG00000099109	Mir7115	Gm27902|mmu-mir-7115	microRNA 7115	ncRNA
mm_110226.1	chr12	28750366	28750418	-	1	NA	promoter-TSS (NM_001161411)	promoter-TSS (NM_001161411)	2	NM_001161410	217449	Mm.132006	NM_178811	ENSMUSG00000020628	Trappc12	CGI-87|D930014A20Rik|Ttc15	trafficking protein particle complex 12	protein-coding
mm_103790.1	chr11	82845908	82845923	-	1	NA	intron (NM_001164569, intron 1 of 7)	intron (NM_001164569, intron 1 of 7)	-16872	NM_026097	67338	Mm.341608	NM_026097	ENSMUSG00000020696	Rffl	1700051E09Rik|4930516L10Rik|BG080975|Carp2	ring finger and FYVE like domain containing protein	protein-coding
mm_142895.1	chr17	51899584	51899627	-	1	NA	intron (NR_045095, intron 1 of 2)	intron (NR_045095, intron 1 of 2)	16878	NR_045095	100504169	Mm.417731	NR_045095		Gm20098	-	predicted gene, 20098	ncRNA
mm_120061.1	chr14	56864874	56864912	+	1	NA	Intergenic	Intergenic	-22902	NM_029498	76007	Mm.31417	NM_029498	ENSMUSG00000021945	Zmym2	5830413P05Rik|FIM|MYM|RAMP|SCLL|Zfp198|Znf198	zinc finger, MYM-type 2	protein-coding
mm_140634.1	chr17	12507397	12507408	-	1	NA	5' UTR (NM_011395, exon 1 of 11)	5' UTR (NM_011395, exon 1 of 11)	302	NM_011395	20519	Mm.99252	NM_011395	ENSMUSG00000023828	Slc22a3	EMT|Oct3|Orct3|Slca22a3	solute carrier family 22 (organic cation transporter), member 3	protein-coding
mm_75267.1	chr8	40656021	40656026	-	1	NA	Intergenic	Intergenic	-19054	NM_010086	13526	Mm.67403	NM_010086	ENSMUSG00000046723	Adam24	Dtgn5	a disintegrin and metallopeptidase domain 24 (testase 1)	protein-coding
mm_101860.1	chr11	48871279	48871300	-	1	NA	promoter-TSS (NM_008326)	promoter-TSS (NM_008326)	57	NM_008326	15944	Mm.29938	NM_008326	ENSMUSG00000046879	Irgm1	Ifggd3|Ifi1|Iigp3|Iipg3|Irgm|LRG-47	immunity-related GTPase family M member 1	protein-coding
mm_90485.1	chr10	127902001	127902034	+	1	NA	intron (NM_027301, intron 1 of 3)	intron (NM_027301, intron 1 of 3)	3482	NM_027301	70061	Mm.158320	NM_027301	ENSMUSG00000040127	Sdr9c7	1810054F20Rik|Rdh20|Rdhs|SDR-O|Sdro	4short chain dehydrogenase/reductase family 9C, member 7	protein-coding
mm_81130.1	chr9	106499955	106499965	+	1	NA	promoter-TSS (NM_001146701)	promoter-TSS (NM_001146701)	-7	NM_028843	74267	Mm.116682	NM_028843	ENSMUSG00000066383	Iqcf1	1700055J15Rik	IQ motif containing F1	protein-coding
mm_124498.1	chr14	121879029	121879078	-	1	NA	promoter-TSS (NR_131002)	promoter-TSS (NR_131002)	355	NR_130999	78312	Mm.188743	NR_130999	ENSMUSG00000102112	1810041H14Rik	-	RIKEN cDNA 1810041H14 gene	ncRNA
mm_136456.1	chr16	94997707	94997727	-	1	NA	promoter-TSS (NM_010606)	promoter-TSS (NM_010606)	-21	NM_010606	16522	Mm.328720	NM_010606	ENSMUSG00000043301	Kcnj6	BIR1|GIRK2|KATP2|KCNJ7|Kir3.2|weaver|wv	potassium inwardly-rectifying channel, subfamily J, member 6	protein-coding
mm_75001.1	chr8	27228513	27228519	-	1	NA	5' UTR (NM_013462, exon 2 of 4)	5' UTR (NM_013462, exon 2 of 4)	1072	NM_013462	11556	Mm.278475	NM_013462	ENSMUSG00000031489	Adrb3	Adrb-3	adrenergic receptor, beta 3	protein-coding
mm_125818.1	chr15	74955641	74955660	+	1	NA	5' UTR (NM_001164036, exon 1 of 4)	5' UTR (NM_001164036, exon 1 of 4)	544	NM_001164040	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_84230.1	chr9	61976578	61976597	-	1	NA	intron (NM_028748, intron 2 of 7)	intron (NM_028748, intron 2 of 7)	-29788	NM_024245	71819	Mm.259374	NM_024245	ENSMUSG00000032254	Kif23	3110001D19Rik|C87313|CHO1|Knsl5|MKLP-1|MKLP1	kinesin family member 23	protein-coding
mm_104488.1	chr11	95824406	95824416	-	1	NA	promoter-TSS (NM_153104)	promoter-TSS (NM_153104)	-89	NM_153104	237928	Mm.133075	NM_153104	ENSMUSG00000050860	Phospho1	D11Moh36|Phospo1	phosphatase, orphan 1	protein-coding
mm_163868.1	chr14	19419085	19419100	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	183495	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_18615.1	chr2	68426934	68426954	-	1	NA	intron (NM_016866, intron 1 of 17)	intron (NM_016866, intron 1 of 17)	45037	NM_016866	53416	Mm.198414	NM_016866	ENSMUSG00000027030	Stk39	AW227544|AW556857|DCHT|RF005|Rnl5|SPAK	serine/threonine kinase 39	protein-coding
mm_149452.1	chr19	11492066	11492082	+	1	NA	promoter-TSS (NM_001164202)	promoter-TSS (NM_001164202)	36	NM_001164202	666926	Mm.486382	NM_001164202	ENSMUSG00000058470	Gm8369	EG666926	predicted gene 8369	protein-coding
mm_87638.1	chr10	58352103	58352120	+	1	NA	intron (NM_026148, intron 1 of 9)	intron (NM_026148, intron 1 of 9)	-19343	NM_201242	110829	Mm.57734	NM_026148	ENSMUSG00000019920	Lims1	2310016J22Rik|4921524A02Rik|AI507642|AU021743|AW551584|C430041B13Rik|Lims1l|PINCH|PINCH1	LIM and senescent cell antigen-like domains 1	protein-coding
mm_166563.1	chr6	48699168	48699182	+	1	NA	Intergenic	Intergenic	9069	NM_153175	231931	Mm.321047	NM_153175	ENSMUSG00000047867	Gimap6	4833419H03Rik|Ian6|mFLJ00102	GTPase, IMAP family member 6	protein-coding
mm_67038.1	chr7	67152722	67152757	-	1	NA	TTS (NM_001033877)	TTS (NM_001033877)	69719	NR_131044	76628	Mm.384589	NR_131043	ENSMUSG00000097527	1700112J16Rik	-	RIKEN cDNA 1700112J16 gene	ncRNA
mm_15745.1	chr2	164237473	164237492	+	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	859	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_87663.1	chr10	58493770	58493820	+	1	NA	exon (NM_011240, exon 29 of 29)	exon (NM_011240, exon 29 of 29)	-4142	NM_001162956	76138	Mm.211744	NM_001162956	ENSMUSG00000038010	Ccdc138	6230424H07Rik|BC042726	coiled-coil domain containing 138	protein-coding
mm_26008.1	chr3	135298873	135298917	+	1	NA	intron (NM_001172055, intron 7 of 9)	intron (NM_001172055, intron 7 of 9)	-8805	NM_178877	97086	Mm.441764	NM_178877	ENSMUSG00000037994	Slc9b2	C80638|NHA2|NHE10|Nhedc2|nha-oc|nhaoc	solute carrier family 9, subfamily B (NHA2, cation proton antiporter 2), member 2	protein-coding
mm_57410.1	chr6	124865794	124865804	-	1	NA	3' UTR (NM_013488, exon 10 of 10)	3' UTR (NM_013488, exon 10 of 10)	-1882	NM_013533	14788	Mm.2514	NM_013533	ENSMUSG00000038390	Gpr162	A-2|BC031437|Grca	G protein-coupled receptor 162	protein-coding
mm_172051.1	chr6	128760784	128760802	-	1	NA	Intergenic	4.5SRNA|scRNA|scRNA	27848	NM_008527	17059	Mm.480764	NM_008527	ENSMUSG00000030325	Klrb1c	AI462337|CD161|Ly-59|Ly55c|Ly59|NK-RP1|NK1.1|NKR-P1.9|NKRP1|NKRP140|Nk-1|Nk-1.2|Nk1|Nk1.2|Nkrp1c|ly-55c	killer cell lectin-like receptor subfamily B member 1C	protein-coding
mm_146282.1	chr18	77938422	77938451	+	1	NA	promoter-TSS (NM_001195633)	promoter-TSS (NM_001195633)	-31	NM_001195633	100502841	Mm.297782	NM_001195633	ENSMUSG00000039840	Epg5	4732475F16|5430411K18Rik|AI661957|AW456499|mKIAA1632	ectopic P-granules autophagy protein 5 homolog (C. elegans)	protein-coding
mm_30780.1	chr4	19280921	19280931	+	1	NA	promoter-TSS (NM_013927)	promoter-TSS (NM_013927)	76	NM_013927	30952	Mm.445778	NM_013927	ENSMUSG00000056494	Cngb3	CCNC2|CNG6|Cngbeta2	cyclic nucleotide gated channel beta 3	protein-coding
mm_100885.1	chr11	6018605	6018641	-	1	NA	intron (NM_007595, intron 2 of 20)	intron (NM_007595, intron 2 of 20)	47125	NM_001174054	12323	Mm.439733	NM_007595	ENSMUSG00000057897	Camk2b	CaMKII	calcium/calmodulin-dependent protein kinase II, beta	protein-coding
mm_72333.1	chr8	79028566	79028613	+	1	NA	5' UTR (NM_178267, exon 1 of 15)	5' UTR (NM_178267, exon 1 of 15)	152	NM_178267	622675	Mm.48724	NM_178267	ENSMUSG00000071064	Zfp827	2810449M09Rik|D630040G17Rik|Znf827	zinc finger protein 827	protein-coding
mm_75933.1	chr8	71534300	71534316	-	1	NA	TTS (NM_198095)	TTS (NM_198095)	3129	NM_198095	69550	Mm.260325	NM_198095	ENSMUSG00000046718	Bst2	2310015I10Rik|Bst-2|C87040|CD317|DAMP-1|GREG	bone marrow stromal cell antigen 2	protein-coding
mm_27897.1	chr3	79457010	79457038	-	1	NA	3' UTR (NM_001162999, exon 17 of 17)	3' UTR (NM_001162999, exon 17 of 17)	110655	NM_001162999	329679	Mm.244005	NM_001162999	ENSMUSG00000061175	Fnip2	D630023B12Rik|mKIAA1450	folliculin interacting protein 2	protein-coding
mm_90923.1	chr10	12634078	12634123	-	1	NA	intron (NM_011682, intron 48 of 73)	intron (NM_011682, intron 48 of 73)	227635	NM_011682	22288	Mm.331784	NM_011682	ENSMUSG00000019820	Utrn	AA589569|DRP|Dmdl	utrophin	protein-coding
mm_170418.1	chr18	68692259	68692260	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-47141	NR_105774	102465183		NR_105774	ENSMUSG00000099300	Mir6356	Gm27461|mmu-mir-6356	microRNA 6356	ncRNA
mm_163972.1	chr14	55510496	55510514	+	1	NA	promoter-TSS (NM_009947)	promoter-TSS (NM_009947)	57	NM_001136057	12891	Mm.5249	NM_009947	ENSMUSG00000022212	Cpne6	AU067659|BB076446	copine VI	protein-coding
mm_137201.1	chr17	23898718	23898722	+	1	NA	promoter-TSS (NM_001039238)	promoter-TSS (NM_001039238)	-2	NM_001039238	630537	Mm.436677	NM_001039238	ENSMUSG00000096278	Dcpp2	Dcpp-2|EG630537|SPT-2	demilune cell and parotid protein 2	protein-coding
mm_116769.1	chr13	52843433	52843433	-	1	NA	intron (NM_016709, intron 6 of 9)	intron (NM_016709, intron 6 of 9)	-86228	NR_027893	105404	Mm.184173	NR_027893		BB123696	-	expressed sequence BB123696	ncRNA
mm_16651.1	chr2	6323156	6323171	-	1	NA	intron (NM_001080548, intron 1 of 14)	CpG	406	NM_001080548	98910	Mm.40673	NM_181399	ENSMUSG00000039046	Usp6nl	AI316785|RNTRE|TRE2NL|mKIAA0019	USP6 N-terminal like	protein-coding
mm_113157.1	chr13	24802870	24802893	+	1	NA	5' UTR (NM_024473, exon 1 of 5)	5' UTR (NM_024473, exon 1 of 5)	1224	NM_024473	79555	Mm.266668	NM_024473	ENSMUSG00000019132	BC005537	8030460C05Rik|C78201	cDNA sequence BC005537	protein-coding
mm_158197.1	chrX	105070054	105070103	-	1	NA	promoter-TSS (NR_015467)	promoter-TSS (NR_015467)	46	NR_015467	71445	Mm.242968	NR_015467	ENSMUSG00000087174	5530601H04Rik	AI835882	RIKEN cDNA 5530601H04 gene	ncRNA
mm_95591.1	chr11	53332156	53332171	+	1	NA	intron (NM_026479, intron 3 of 3)	intron (NM_026479, intron 3 of 3)	7474	NM_026479	67966	Mm.288072	NM_026479	ENSMUSG00000018239	Zcchc10	2410141K03Rik|AA675321|D11Ertd416e	zinc finger, CCHC domain containing 10	protein-coding
mm_50221.1	chr6	42350001	42350076	+	1	NA	5' UTR (NM_001289618, exon 1 of 10)	5' UTR (NM_001289618, exon 1 of 10)	210	NM_001289619	22793	Mm.282303	NM_011777	ENSMUSG00000029860	Zyx	9530098H06Rik|R75157	zyxin	protein-coding
mm_84361.1	chr9	64737656	64737661	-	1	NA	promoter-TSS (NM_017382)	promoter-TSS (NM_017382)	98	NM_017382	53869	Mm.1387	NM_017382	ENSMUSG00000004771	Rab11a	-	RAB11A, member RAS oncogene family	protein-coding
mm_41721.1	chr5	102481347	102481357	+	1	NA	promoter-TSS (NM_029270)	promoter-TSS (NM_029270)	-39	NM_146161	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding
mm_5799.1	chr1	52164664	52164679	-	1	NA	3' UTR (NM_001081081, exon 18 of 18)	3' UTR (NM_001081081, exon 18 of 18)	45049	NM_001205313	20846	Mm.277406	NM_009283	ENSMUSG00000026104	Stat1	2010005J02Rik|AA408197	signal transducer and activator of transcription 1	protein-coding
mm_150128.1	chr19	30030616	30030634	+	1	NA	5' UTR (NM_144873, exon 1 of 16)	5' UTR (NM_144873, exon 1 of 16)	112	NM_144873	109113	Mm.313364	NM_144873	ENSMUSG00000024817	Uhrf2	2310065A22Rik|AI426270|AW214556|D130071B19Rik|Nirf	ubiquitin-like, containing PHD and RING finger domains 2	protein-coding
mm_102777.1	chr11	68386900	68386917	-	1	NA	promoter-TSS (NM_008744)	promoter-TSS (NM_008744)	-82	NM_008744	18208	Mm.39095	NM_008744	ENSMUSG00000020902	Ntn1	AI561871|BC019633|Netrin-1	netrin 1	protein-coding
mm_95385.1	chr11	49212025	49212036	+	1	NA	intron (NM_009562, intron 1 of 3)	intron (NM_009562, intron 1 of 3)	8530	NM_009562	22720	Mm.16650	NM_009562	ENSMUSG00000046311	Zfp62	-	zinc finger protein 62	protein-coding
mm_110554.1	chr12	55491307	55491317	-	1	NA	TTS (NR_035430)	TTS (NR_035430)	1335	NM_010907	18035	Mm.170515	NM_010907	ENSMUSG00000021025	Nfkbia	AI462015|Nfkbi	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, alpha	protein-coding
mm_104249.1	chr11	88863822	88863834	-	1	NA	intron (NR_126433, intron 3 of 4)	intron (NR_126433, intron 3 of 4)	758	NM_001042541	11640	Mm.2969	NM_009648	ENSMUSG00000018428	Akap1	AKAP121|AKAP84|Akap|C76494|C81186|DAKAP1|S-AKAP84	A kinase (PRKA) anchor protein 1	protein-coding
mm_73270.1	chr8	104540801	104540816	+	1	NA	promoter-TSS (NM_053070)	promoter-TSS (NM_053070)	1	NM_053070	12354	Mm.129265	NM_053070	ENSMUSG00000031883	Car7	AV343731|Ca7	carbonic anhydrase 7	protein-coding
mm_163060.1	chr11	65009944	65009974	-	1	NA	exon (NM_001099288, exon 18 of 20)	exon (NM_001099288, exon 18 of 20)	30924	NM_023479	68626	Mm.157711	NM_023479	ENSMUSG00000020549	Elac2	1110017O07Rik|D11Wsu80e|Hpc2	elaC ribonuclease Z 2	protein-coding
mm_43223.1	chr5	129787391	129787413	+	1	NA	promoter-TSS (NM_009838)	promoter-TSS (NM_009838)	46	NM_009838	12466	Mm.153159	NM_009838		Cct6a	CCT-zeta|CCT-zeta-1|Cct6|Cctz-1|TCP-1-zeta	chaperonin containing Tcp1, subunit 6a (zeta)	protein-coding
mm_31673.1	chr4	62208035	62208041	+	1	NA	intron (NM_001290351, intron 1 of 3)	intron (NM_001290351, intron 1 of 3)	164	NM_001290353	22696	Mm.5011	NM_009554	ENSMUSG00000028389	Zfp37	Tzn|Zfp-37	zinc finger protein 37	protein-coding
mm_86818.1	chr10	20907395	20907412	+	1	NA	Intergenic	Intergenic	-45144	NM_026203	52906	Mm.253280	NM_026203	ENSMUSG00000019986	Ahi1	1700015F03Rik|Ahi-1|D10Bwg0629e	Abelson helper integration site 1	protein-coding
mm_172822.1	chr9	15279939	15279940	-	1	NA	promoter-TSS (NM_144933)	promoter-TSS (NM_144933)	-72	NM_144933	234959	Mm.44151	NM_144933	ENSMUSG00000031935	Med17	77kDa|C330002H14Rik|Crsp6|Trap80	mediator complex subunit 17	protein-coding
mm_162041.1	chr19	57215987	57215987	-	1	NA	promoter-TSS (NM_178688)	promoter-TSS (NM_178688)	45	NM_001290813	226251	Mm.217161	NM_178688	ENSMUSG00000025085	Ablim1	2210411C18Rik|2610209L21Rik|4833406P10Rik|9330196J19Rik|AV079770|AW060987|AW215784|Limab1|mKIAA0059	actin-binding LIM protein 1	protein-coding
mm_50549.1	chr6	49047293	49047299	+	1	NA	exon (NM_053110, exon 5 of 11)	exon (NM_053110, exon 5 of 11)	10778	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_99131.1	chr11	100319881	100319905	+	1	NA	promoter-TSS (NM_011508)	promoter-TSS (NM_011508)	-56	NM_011508	20918	Mm.13886	NM_011508	ENSMUSG00000035530	Eif1	Sui1-rs1	eukaryotic translation initiation factor 1	protein-coding
mm_31978.1	chr4	89050241	89050248	+	1	NA	promoter-TSS (NR_033533)	promoter-TSS (NR_033533)	-63	NR_033533	100040617	Mm.171720	NR_033533	ENSMUSG00000085183	Gm12603	OTTMUSG00000007693	predicted gene 12603	ncRNA
mm_171019.1	chr2	83978131	83978148	+	1	NA	Intergenic	CpG	-36913	NM_027964	71861	Mm.116957	NM_027964	ENSMUSG00000034552	Zswim2	1700025P14Rik|4933437F18Rik|MEX	zinc finger SWIM-type containing 2	protein-coding
mm_52544.1	chr6	115933994	115934001	+	1	NA	exon (NM_145383, exon 2 of 5)	exon (NM_145383, exon 2 of 5)	2070	NM_145383	212541	Mm.2965	NM_145383	ENSMUSG00000030324	Rho	Noerg1|Opn2|Ops|RP4	rhodopsin	protein-coding
mm_22167.1	chr2	173033610	173033656	-	1	NA	exon (NM_019547, exon 4 of 4)	exon (NM_019547, exon 4 of 4)	11731	NM_019547	56190	Mm.485782	NM_019547	ENSMUSG00000027510	Rbm38	Rnpc1|Seb4|Seb4l	RNA binding motif protein 38	protein-coding
mm_146438.1	chr18	84934626	84934634	+	1	NA	promoter-TSS (NM_015798)	promoter-TSS (NM_015798)	-395	NM_015798	50764	Mm.28369	NM_015798	ENSMUSG00000034391	Fbxo15	AU019763|Fbx15|ecat3	F-box protein 15	protein-coding
mm_172721.1	chr8	72284151	72284170	-	1	NA	Intergenic	Intergenic	-34902	NM_008452	16598	Mm.26938	NM_008452	ENSMUSG00000055148	Klf2	Lklf	Kruppel-like factor 2 (lung)	protein-coding
mm_97277.1	chr11	76000007	76000011	+	1	NA	promoter-TSS (NM_198637)	promoter-TSS (NM_198637)	97	NM_198637	74230	Mm.271247	NM_198637	ENSMUSG00000053783	1700016K19Rik	Liat1	RIKEN cDNA 1700016K19 gene	protein-coding
mm_171322.1	chr3	96360113	96360119	-	1	NA	Intergenic	U1|snRNA|snRNA	54717	NR_001579	21748		NR_001579	ENSMUSG00000064796	Terc	mTER|mTR	telomerase RNA component	ncRNA
mm_171957.1	chr5	8056526	8056530	+	1	NA	promoter-TSS (NM_001080974)	promoter-TSS (NM_001080974)	-14	NM_001080974	109552	Mm.96211	NM_025618	ENSMUSG00000003161	Sri	2210417O06Rik|2900070H08Rik|Sor	sorcin	protein-coding
mm_30509.1	chr3	158031649	158031691	-	1	NA	promoter-TSS (NM_001093753)	promoter-TSS (NM_001093753)	84	NM_001093753	69207	Mm.223946	NM_026989	ENSMUSG00000055436	Srsf11	0610009J05Rik|2610019N13Rik|BF642805|Sfrs11	serine/arginine-rich splicing factor 11	protein-coding
mm_150769.1	chr19	44281040	44281051	+	1	NA	Intergenic	Intergenic	-12631	NM_009128	20250	Mm.487021	NM_009128	ENSMUSG00000025203	Scd2	Mir5114|Scd-2|mir-5114|swty	stearoyl-Coenzyme A desaturase 2	protein-coding
mm_14144.1	chr2	126552736	126552747	+	1	NA	promoter-TSS (NM_011978)	promoter-TSS (NM_011978)	-283	NM_011978	26458	Mm.290044	NM_011978	ENSMUSG00000027359	Slc27a2	ACSVL1|FATP2|VLCS|Vlac|Vlacs	solute carrier family 27 (fatty acid transporter), member 2	protein-coding
mm_45500.1	chr5	72264598	72264606	-	1	NA	non-coding (NR_003966, exon 12 of 23)	non-coding (NR_003966, exon 12 of 23)	61259	NM_153389	231287	Mm.32775	NM_153389	ENSMUSG00000046808	Atp10d	9830145H18Rik|ATPVD|D5Buc24e	ATPase, class V, type 10D	protein-coding
mm_11967.1	chr2	53605135	53605141	+	1	NA	Intergenic	Intergenic	413054	NM_022989	65103	Mm.37623	NM_022989	ENSMUSG00000026960	Arl6ip6	2310057C01Rik|2610529A11Rik|Aip-6	ADP-ribosylation factor-like 6 interacting protein 6	protein-coding
mm_161861.1	chr18	31886012	31886012	+	1	NA	intron (NM_028866, intron 12 of 21)	intron (NM_028866, intron 12 of 21)	25891	NM_026006	67158	Mm.31537	NM_026006	ENSMUSG00000044982	Sft2d3	2610206C24Rik|AI847965|AW046173	SFT2 domain containing 3	protein-coding
mm_26331.1	chr3	142544318	142544326	+	1	NA	intron (NM_145545, intron 8 of 10)	intron (NM_145545, intron 8 of 10)	13986	NM_145545	229900	Mm.45740	NM_145545	ENSMUSG00000040253	Gbp7	9830147J24Rik	guanylate binding protein 7	protein-coding
mm_20408.1	chr2	129299992	129300050	-	1	NA	3' UTR (NM_010554, exon 7 of 7)	3' UTR (NM_010554, exon 7 of 7)	2651	NR_040371	100503468	Mm.446943	NR_040371	ENSMUSG00000085498	Gm14023	OTTMUSG00000015408	predicted gene 14023	ncRNA
mm_104825.1	chr11	99051467	99051504	-	1	NA	exon (NM_010517, exon 4 of 4)	exon (NM_010517, exon 4 of 4)	10225	NM_010517	16010	Mm.233799	NM_010517	ENSMUSG00000017493	Igfbp4	AI875747|Deb2|IGFBP-4	insulin-like growth factor binding protein 4	protein-coding
mm_136499.1	chr16	96419214	96419214	-	1	NA	intron (NM_001177886, intron 8 of 8)	intron (NM_001177886, intron 8 of 8)	24400	NM_008405	16415	Mm.12872	NM_008405	ENSMUSG00000000157	Itgb2l	5033406G21Rik|pactolus	integrin beta 2-like	protein-coding
mm_124942.1	chr15	12321510	12321520	+	1	NA	promoter-TSS (NM_025673)	promoter-TSS (NM_025673)	19	NM_025673	66629	Mm.157655	NM_025673	ENSMUSG00000022200	Golph3	4733401N08Rik|5730410D03Rik|AW413496	golgi phosphoprotein 3	protein-coding
mm_33314.1	chr4	129070545	129070569	+	1	NA	intron (NM_029219, intron 1 of 8)	B3|SINE|B2	12286	NM_029219	75234	Mm.259672	NM_029219	ENSMUSG00000028793	Rnf19b	4930534K13Rik|4930555L03Rik|Ibrdc3	ring finger protein 19B	protein-coding
mm_74755.1	chr8	19114831	19114838	-	1	NA	promoter-TSS (NM_152802)	promoter-TSS (NM_152802)	-1	NM_152802	77674	Mm.281961	NM_152802	ENSMUSG00000043787	Defb12	9230103N16Rik|BD-12	defensin beta 12	protein-coding
mm_95124.1	chr11	34091215	34091226	+	1	NA	3' UTR (NM_010696, exon 21 of 21)	3' UTR (NM_010696, exon 21 of 21)	44019	NM_010696	16822	Mm.265350	NM_010696	ENSMUSG00000002699	Lcp2	AI323664|BB161688|SLP-76|SLP76|m1Khoe|twm	lymphocyte cytosolic protein 2	protein-coding
mm_82391.1	chr9	14676037	14676041	-	1	NA	Intergenic	Intergenic	-61039	NM_001081395	75723	Mm.159552	NM_001081395	ENSMUSG00000013076	Amotl1	2310010G08Rik|2310067L22Rik|4932416D09Rik|JEAP|mFLJ00155	angiomotin-like 1	protein-coding
mm_70560.1	chr8	13074244	13074263	+	1	NA	3' UTR (NM_025834, exon 8 of 8)	3' UTR (NM_025834, exon 8 of 8)	13345	NM_025834	66901	Mm.441140	NM_025834	ENSMUSG00000031445	Proz	1300015B06Rik	protein Z, vitamin K-dependent plasma glycoprotein	protein-coding
mm_85748.1	chr9	108578678	108578691	-	1	NA	promoter-TSS (NM_031392)	promoter-TSS (NM_031392)	-14	NM_031392	83669	Mm.335454	NM_031392	ENSMUSG00000066357	Wdr6	mWDR6	WD repeat domain 6	protein-coding
mm_127974.1	chr15	12196608	12196612	-	1	NA	Intergenic	Intergenic	-8484	NM_172958	268783	Mm.54460	NM_172958	ENSMUSG00000039458	Mtmr12	3Pap|4932703C11|C730015A02Rik|Pip3ap|mKIAA1682	myotubularin related protein 12	protein-coding
mm_168660.1	chr11	88966974	88966993	-	1	NA	promoter-TSS (NR_003564)	promoter-TSS (NR_003564)	-66	NR_003564	217066	Mm.347543	NM_001025564	ENSMUSG00000057534	Gm15698	OTTMUSG00000001305|OTTMUSG00000025408	transcription elongation factor B (SIII), polypeptide 2 pseudogene	pseudo
mm_70278.1	chr8	3599522	3599571	+	1	NA	intron (NM_001347113, intron 5 of 17)	PB1D10|SINE|Alu	12096	NM_001347111	69697	Mm.390010	NM_027171	ENSMUSG00000044433	Camsap3	2310057J16Rik|Kiaa1543|Nezha	calmodulin regulated spectrin-associated protein family, member 3	protein-coding
mm_104463.1	chr11	95076804	95076818	-	1	NA	promoter-TSS (NM_001306162)	promoter-TSS (NM_001306162)	0	NM_001306162	16400	Mm.57035	NM_013565	ENSMUSG00000001507	Itga3	AA407068|CD49C|GAPB3	integrin alpha 3	protein-coding
mm_19702.1	chr2	103773046	103773061	-	1	NA	exon (NM_016739, exon 13 of 19)	exon (NM_016739, exon 13 of 19)	-11803	NM_153126	98956	Mm.288005	NM_153126	ENSMUSG00000027185	Nat10	AI429152	N-acetyltransferase 10	protein-coding
mm_49280.1	chr6	17637800	17637812	+	1	NA	intron (NM_007604, intron 1 of 9)	intron (NM_007604, intron 1 of 9)	708	NM_007604	12343	Mm.392504	NM_007604	ENSMUSG00000015733	Capza2	1110053K06Rik|AW208808|Cappa2	capping protein (actin filament) muscle Z-line, alpha 2	protein-coding
mm_159155.1	chr2	89249586	89249586	-	1	NA	exon (NM_146971, exon 1 of 1)	exon (NM_146971, exon 1 of 1)	106	NM_146971	258973	Mm.463734	NM_146971	ENSMUSG00000099486	Olfr1228	MOR233-1	olfactory receptor 1228	protein-coding
mm_70840.1	chr8	23411273	23411300	+	1	NA	promoter-TSS (NM_013834)	promoter-TSS (NM_013834)	-216	NM_013834	20377	Mm.281691	NM_013834	ENSMUSG00000031548	Sfrp1	2210415K03Rik|AW011917|AW107218|AW742929|sFRP-1	secreted frizzled-related protein 1	protein-coding
mm_113351.1	chr13	31807393	31807410	+	1	NA	exon (NM_008592, exon 1 of 1)	exon (NM_008592, exon 1 of 1)	755	NM_008592	17300	Mm.12949	NM_008592	ENSMUSG00000050295	Foxc1	FREAC3|Fkh1|Mf1|Mf4|ch|fkh-1|frkhda	forkhead box C1	protein-coding
mm_123120.1	chr14	56105134	56105140	-	1	NA	Intergenic	Intergenic	-2563	NM_007800	13035	Mm.4858	NM_007800	ENSMUSG00000040314	Ctsg	CatG|VSP	cathepsin G	protein-coding
mm_70708.1	chr8	15059000	15059010	+	1	NA	intron (NM_008664, intron 1 of 36)	intron (NM_008664, intron 1 of 36)	1352	NM_008664	17930	Mm.272115	NM_008664	ENSMUSG00000031461	Myom2	AW146149	myomesin 2	protein-coding
mm_142980.1	chr17	56218882	56218922	-	1	NA	promoter-TSS (NM_172624)	promoter-TSS (NM_172624)	-13	NM_172624	224897	Mm.205535	NM_172624	ENSMUSG00000001229	Dpp9	6430584G11Rik|A330078I11|DPP IX|DPRP2	dipeptidylpeptidase 9	protein-coding
mm_51800.1	chr6	88724428	88724430	+	1	NA	promoter-TSS (NM_001166251)	promoter-TSS (NM_001166251)	17	NM_011844	23945	Mm.272197	NM_011844	ENSMUSG00000033174	Mgll	AA589436|Magl|Mgl	monoglyceride lipase	protein-coding
mm_13693.1	chr2	117121041	117121045	+	1	NA	promoter-TSS (NM_001277256)	promoter-TSS (NM_001277256)	-28	NM_001277256	114715	Mm.245890	NM_033524	ENSMUSG00000027351	Spred1	5730461F13Rik|AL024345|AW047647	sprouty protein with EVH-1 domain 1, related sequence	protein-coding
mm_6306.1	chr1	71414931	71414941	-	1	NA	promoter-TSS (NM_175210)	promoter-TSS (NM_175210)	-26	NM_175210	74591	Mm.159251	NM_175210	ENSMUSG00000050296	Abca12	4832428G11Rik|4833417A11Rik	ATP-binding cassette, sub-family A (ABC1), member 12	protein-coding
mm_21653.1	chr2	164334389	164334395	-	1	NA	TTS (NM_009301)	TTS (NM_009301)	1627	NM_009301	20944	Mm.140154	NM_009301	ENSMUSG00000017004	Svs5	BB115186|Semg1|Svp-1|Svp1|Svp5	seminal vesicle secretory protein 5	protein-coding
mm_150998.1	chr19	46652723	46652740	+	1	NA	intron (NM_146099, intron 3 of 3)	intron (NM_146099, intron 3 of 3)	20269	NM_007809	13074	Mm.1262	NM_007809	ENSMUSG00000003555	Cyp17a1	Cyp17|p450c17	cytochrome P450, family 17, subfamily a, polypeptide 1	protein-coding
mm_90028.1	chr10	115422334	115422338	+	1	NA	intron (NM_001033261, intron 24 of 34)	intron (NM_001033261, intron 24 of 34)	37377	NM_001033261	216345	Mm.207621	NM_001033261	ENSMUSG00000034163	Zfc3h1	BC033596|Ccdc131|Psrc2	zinc finger, C3H1-type containing	protein-coding
mm_138814.1	chr17	39846875	39846894	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	3887	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_149242.1	chr19	10195235	10195257	+	1	NA	3' UTR (NM_146094, exon 12 of 12)	3' UTR (NM_146094, exon 12 of 12)	3871	NR_105959	102465600		NR_105959	ENSMUSG00000098363	Mir6993	Gm27642|mmu-mir-6993	microRNA 6993	ncRNA
mm_39631.1	chr5	24430772	24430779	+	1	NA	intron (NM_009207, intron 5 of 22)	intron (NM_009207, intron 5 of 22)	3254	NM_001253892	20535	Mm.4580	NM_009207	ENSMUSG00000028962	Slc4a2	Ae2|B3RP	solute carrier family 4 (anion exchanger), member 2	protein-coding
mm_143845.1	chr17	84135390	84135402	-	1	NA	Intergenic	Intergenic	52551	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_119426.1	chr14	45389029	45389076	+	1	NA	promoter-TSS (NM_019425)	promoter-TSS (NM_019425)	-256	NM_019425	54342	Mm.312945	NM_019425	ENSMUSG00000037722	Gnpnat1	AU017428|AU040593|EMeg32|Gpnat1|Gsnpat	glucosamine-phosphate N-acetyltransferase 1	protein-coding
mm_85446.1	chr9	104262901	104262949	-	1	NA	promoter-TSS (NM_001163026)	promoter-TSS (NM_001163026)	5	NM_001163026	235567	Mm.217256	NM_001163026	ENSMUSG00000032560	Dnajc13	D030002L11Rik|Gm1124|RME-8|Rme8|mKIAA0678	DnaJ heat shock protein family (Hsp40) member C13	protein-coding
mm_159772.1	chr5	100498578	100498578	-	1	NA	promoter-TSS (NM_001115010)	promoter-TSS (NM_001115010)	-5	NM_001115010	231506	Mm.212568	NM_172714	ENSMUSG00000035310	Lin54	AI461788	lin-54 homolog (C. elegans)	protein-coding
mm_162033.1	chr19	53987443	53987443	+	1	NA	intron (NM_019658, intron 1 of 8)	intron (NM_019658, intron 1 of 8)	42567	NM_019658	56392	Mm.228669	NM_019658	ENSMUSG00000024976	Shoc2	AU017287|Sur8|mKIAA0862	soc-2 (suppressor of clear) homolog (C. elegans)	protein-coding
mm_102184.1	chr11	54225208	54225228	-	1	NA	Intergenic	Intergenic	-11930	NR_045506	71056	Mm.56332	NR_045506	ENSMUSG00000086209	4933405E24Rik	-	RIKEN cDNA 4933405E24 gene	ncRNA
mm_123456.1	chr14	65425170	65425188	-	1	NA	5' UTR (NM_010932, exon 1 of 4)	5' UTR (NM_010932, exon 1 of 4)	293	NM_001205075	18155	Mm.16347	NM_010932	ENSMUSG00000045731	Pnoc	N/OFQ|Npnc1|OFQ/N	prepronociceptin	protein-coding
mm_167773.1	chr9	111216719	111216722	+	1	NA	intron (NM_027742, intron 10 of 13)	intron (NM_027742, intron 10 of 13)	54888	NM_026810	17350	Mm.486383	NM_026810	ENSMUSG00000032498	Mlh1	1110035C23Rik|AI317206|AI325952|AI561766	mutL homolog 1	protein-coding
mm_158194.1	chrX	104671049	104671071	-	1	NA	promoter-TSS (NM_175358)	promoter-TSS (NM_175358)	4	NM_175358	108672	Mm.30574	NM_175358	ENSMUSG00000033906	Zdhhc15	6030457O13Rik	zinc finger, DHHC domain containing 15	protein-coding
mm_168291.1	chr11	102124047	102124047	+	1	NA	Intergenic	Intergenic	-16215	NM_001346771	217212	Mm.46248	NM_145435	ENSMUSG00000017311	Pyy	-	peptide YY	protein-coding
mm_102628.1	chr11	62539024	62539032	-	1	NA	exon (NM_028448, exon 1 of 5)	exon (NM_028448, exon 1 of 5)	233	NM_028448	73139	Mm.390409	NM_028448	ENSMUSG00000018509	Cenpv	3110013H01Rik|AA671303|Prr6	centromere protein V	protein-coding
mm_89937.1	chr10	111260143	111260148	+	1	NA	intron (NM_175489, intron 5 of 23)	intron (NM_175489, intron 5 of 23)	-38534	NM_027914	71769	Mm.45256	NM_027914	ENSMUSG00000035759	Bbs10	1300007O09Rik|AI452285	Bardet-Biedl syndrome 10 (human)	protein-coding
mm_162358.1	chr1	59548875	59548880	+	1	NA	intron (NM_001013771, intron 4 of 19)	intron (NM_001013771, intron 4 of 19)	32613	NM_001013771	381260	Mm.486706	NM_001013771	ENSMUSG00000047361	Gm973	AW554518	predicted gene 973	protein-coding
mm_28607.1	chr3	94658844	94658878	-	1	NA	promoter-TSS (NM_011656)	promoter-TSS (NM_011656)	11	NM_001293728	22156	Mm.10214	NM_011656	ENSMUSG00000005968	Tuft1	-	tuftelin 1	protein-coding
mm_122399.1	chr14	41004227	41004260	-	1	NA	intron (NM_001316735, intron 1 of 5)	intron (NM_001316735, intron 1 of 5)	2677	NM_001316739	70564	Mm.27227	NM_027464	ENSMUSG00000021792	Fam213a	5730469M10Rik|AU040822|Adrx|Pamm	family with sequence similarity 213, member A	protein-coding
mm_85609.1	chr9	107605248	107605259	-	1	NA	intron (NR_111986, intron 1 of 17)	intron (NR_111986, intron 1 of 17)	149	NM_009153	20347	Mm.4083	NM_009153	ENSMUSG00000057969	Sema3b	SemA|Semaa|sema5|semaV	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B	protein-coding
mm_65154.1	chr7	19628670	19628675	-	1	NA	intron (NM_001290457, intron 1 of 10)	intron (NM_001290457, intron 1 of 10)	766	NM_001290457	19698	Mm.1741	NM_009046	ENSMUSG00000002983	Relb	shep	avian reticuloendotheliosis viral (v-rel) oncogene related B	protein-coding
mm_15869.1	chr2	164834077	164834097	+	1	NA	promoter-TSS (NM_001082974)	promoter-TSS (NM_001082974)	314	NM_008906	19025	Mm.359633	NM_008906	ENSMUSG00000017760	Ctsa	AU019505|PPCA|Ppgb	cathepsin A	protein-coding
mm_7176.1	chr1	92432170	92432195	-	1	NA	Intergenic	RLTR12E|LTR|ERVK	32360	NR_105865	102465542		NR_105865	ENSMUSG00000098288	Mir6900	Gm27708|mmu-mir-6900	microRNA 6900	ncRNA
mm_121705.1	chr14	15438840	15438848	-	1	NA	5' UTR (NM_146052, exon 1 of 2)	5' UTR (NM_146052, exon 1 of 2)	143	NM_146052	218763	Mm.138039	NM_146052	ENSMUSG00000045201	Lrrc3b	BC019794|LRP15	leucine rich repeat containing 3B	protein-coding
mm_27364.1	chr3	50435421	50435447	-	1	NA	exon (NM_011990, exon 3 of 12)	exon (NM_011990, exon 3 of 12)	8179	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_37045.1	chr4	115847456	115847457	-	1	NA	intron (NM_001285487, intron 2 of 14)	intron (NM_001285487, intron 2 of 14)	8258	NM_001285487	17346	Mm.209327	NM_021461	ENSMUSG00000028708	Mknk1	2410048M24Rik|Mnk1	MAP kinase-interacting serine/threonine kinase 1	protein-coding
mm_100303.1	chr11	117878557	117878563	+	1	NA	Intergenic	Intergenic	-5034	NM_027919	71776	Mm.3200	NM_027919	ENSMUSG00000017713	Tha1	1300017K07Rik|GLY1	threonine aldolase 1	protein-coding
mm_67847.1	chr7	98656516	98656524	-	1	NA	promoter-TSS (NM_172280)	promoter-TSS (NM_172280)	49	NM_172280	233545	Mm.387819	NM_172280	ENSMUSG00000035401	Emsy	2210018M11Rik|2310016L09Rik|AU019521|AU019557	EMSY, BRCA2-interacting transcriptional repressor	protein-coding
mm_139873.1	chr17	70694460	70694463	+	1	NA	intron (NM_001347412, intron 8 of 13)	intron (NM_001347412, intron 8 of 13)	132714	NM_001128181	224997	Mm.311840	NM_027712	ENSMUSG00000003279	Dlgap1	4933422O14Rik|9630002F18|AI845682|AI848168|BB075781|D17Bwg0511e|GKAP/SAPAP|GKPA/SAPAP|Gkap|Sapap1|mKIAA4162	discs, large (Drosophila) homolog-associated protein 1	protein-coding
mm_14203.1	chr2	127238418	127238440	+	1	NA	intron (NM_177214, intron 41 of 44)	intron (NM_177214, intron 41 of 44)	9387	NM_025296	26371	Mm.45179	NM_025296	ENSMUSG00000003662	Ciao1	AW210570|Wdr39	cytosolic iron-sulfur protein assembly 1	protein-coding
mm_13024.1	chr2	91042550	91042567	+	1	NA	intron (NM_009023, intron 3 of 7)	intron (NM_009023, intron 3 of 7)	6931	NM_009023	19400	Mm.1272	NM_009023	ENSMUSG00000002104	Rapsn	43kDa|Nraps|Raps|rapsyn	receptor-associated protein of the synapse	protein-coding
mm_117026.1	chr13	58215616	58215662	-	1	NA	promoter-TSS (NM_152234)	promoter-TSS (NM_152234)	14	NM_152234	56085	Mm.182053	NM_026842	ENSMUSG00000005312	Ubqln1	1110046H03Rik|1810030E05Rik|AU019746|C77538|D13Ertd372e|Da41|Dsk2|Plic-1|Plic1|Xdrp1	ubiquilin 1	protein-coding
mm_76579.1	chr8	89007280	89007321	-	1	NA	Intergenic	Intergenic	-17435	NR_106190	102465899		NR_106190	ENSMUSG00000099078	Mir8110	Gm27571|mmu-mir-8110	microRNA 8110	ncRNA
mm_20394.1	chr2	129180639	129180659	-	1	NA	promoter-TSS (NR_045264)	promoter-TSS (NR_045264)	24	NR_045264	100048701	Mm.428544	NR_045264	ENSMUSG00000084826	AI847159	OTTMUSG00000015420	expressed sequence AI847159	ncRNA
mm_133638.1	chr16	91676480	91676483	+	1	NA	intron (NM_178880, intron 9 of 11)	intron (NM_178880, intron 9 of 11)	12247	NM_021720	60364	Mm.328698	NM_021720	ENSMUSG00000022960	Donson	1110025J21Rik|AI845729|ORF60	downstream neighbor of SON	protein-coding
mm_21936.1	chr2	167056921	167056943	-	1	NA	exon (NM_001033196, exon 3 of 14)	exon (NM_001033196, exon 3 of 14)	-6002	NR_138563	68949	Mm.391959	NM_001081005		Zfas1	1500012F01Rik|Zfos1	zinc finger, NFX1-type containing 1, antisense RNA 1	ncRNA
mm_62867.1	chr7	114722245	114722259	+	1	NA	intron (NM_054084, intron 4 of 4)	intron (NM_054084, intron 4 of 4)	3609	NM_054084	116903	Mm.273838	NM_054084	ENSMUSG00000030666	Calcb	CGRP2|Calc2	calcitonin-related polypeptide, beta	protein-coding
mm_93880.1	chr10	125308806	125308806	-	1	NA	intron (NM_011391, intron 1 of 6)	intron (NM_011391, intron 1 of 6)	19729	NM_011391	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|Mct2	solute carrier family 16 (monocarboxylic acid transporters), member 7	protein-coding
mm_48376.1	chr5	139716417	139716427	-	1	NA	exon (NM_174850, exon 6 of 17)	exon (NM_174850, exon 6 of 17)	19911	NM_174850	231830	Mm.240510	NM_174850	ENSMUSG00000036718	Micall2	A930021H16Rik|JRAB|MICAL-L2|mFLJ00139	MICAL-like 2	protein-coding
mm_94456.1	chr11	6415775	6415783	+	1	NA	promoter-TSS (NM_008907)	promoter-TSS (NM_008907)	-91	NM_008907	268373	Mm.5246	NM_008907	ENSMUSG00000071866	Ppia	2700098C05|Cphn|CyP-18|CypA	peptidylprolyl isomerase A	protein-coding
mm_93961.1	chr10	127288416	127288430	-	1	NA	intron (NM_033072, intron 1 of 12)	intron (NM_033072, intron 1 of 12)	595	NM_001347171	110962	Mm.372826	NM_033072	ENSMUSG00000025409	Mbd6	D10Wsu93e	methyl-CpG binding domain protein 6	protein-coding
mm_78572.1	chr9	36693218	36693221	+	1	NA	promoter-TSS (NM_007391)	promoter-TSS (NM_007391)	-1	NM_007391	11451	Mm.4776	NM_007391	ENSMUSG00000032110	Acrv1	Msa63|SP-10	acrosomal vesicle protein 1	protein-coding
mm_76505.1	chr8	86883313	86883329	-	1	NA	intron (NM_030563, intron 1 of 6)	intron (NM_030563, intron 1 of 6)	1937	NM_030563	80750	Mm.25117	NM_030563	ENSMUSG00000031652	N4bp1	AI481586|C81621	NEDD4 binding protein 1	protein-coding
mm_153990.1	chr19	50030520	50030529	-	1	NA	Intergenic	Intergenic	648122	NM_001252501	58178	Mm.313672	NM_021377	ENSMUSG00000043531	Sorcs1	Sorcs|mSorCS	sortilin-related VPS10 domain containing receptor 1	protein-coding
mm_146150.1	chr18	74796993	74797040	+	1	NA	intron (NM_177470, intron 5 of 9)	B4A|SINE|B4	17804	NM_177470	52538	Mm.245724	NM_177470	ENSMUSG00000036880	Acaa2	0610011L04Rik|AI255831|AI265397|D18Ertd240e	acetyl-Coenzyme A acyltransferase 2 (mitochondrial 3-oxoacyl-Coenzyme A thiolase)	protein-coding
mm_98768.1	chr11	96658635	96658679	+	1	NA	intron (NM_001033186, intron 4 of 12)	intron (NM_001033186, intron 4 of 12)	118898	NM_028965	74479	Mm.270781	NM_028965	ENSMUSG00000020876	Snx11	4933439F10Rik|A930041K09Rik|AI117694	sorting nexin 11	protein-coding
mm_50665.1	chr6	51524729	51524743	+	1	NA	intron (NM_001127349, intron 1 of 6)	intron (NM_001127349, intron 1 of 6)	833	NM_001127349	71982	Mm.294166	NM_028035	ENSMUSG00000038301	Snx10	2410004M09Rik	sorting nexin 10	protein-coding
mm_114144.1	chr13	55321992	55322053	+	1	NA	promoter-TSS (NM_025596)	promoter-TSS (NM_025596)	-33	NM_025596	66494	Mm.439805	NM_025596	ENSMUSG00000021486	Prelid1	2610524G07Rik|Preli	PRELI domain containing 1	protein-coding
mm_42964.1	chr5	123135618	123135632	+	1	NA	Intergenic	CpG	-2996	NM_175092	23912	Mm.253876	NM_175092	ENSMUSG00000029449	Rhof	AI845056|AV026554|Arhf|Ifld1|Rif	ras homolog family member F (in filopodia)	protein-coding
mm_109673.1	chr12	113074765	113074775	+	1	NA	TTS (NM_001291445)	TTS (NM_001291445)	268	NM_029381	75671	Mm.23377	NM_029381	ENSMUSG00000012211	Tex22	1700028O09Rik|AV210422|Tep22	testis expressed gene 22	protein-coding
mm_36915.1	chr4	108074462	108074476	-	1	NA	intron (NM_011327, intron 10 of 15)	intron (NM_011327, intron 10 of 15)	-12888	NR_105823	102465213		NR_105823	ENSMUSG00000098980	Mir6397	Gm28004|mmu-mir-6397	microRNA 6397	ncRNA
mm_144593.1	chr18	32163043	32163053	+	1	NA	promoter-TSS (NM_011946)	promoter-TSS (NM_011946)	-41	NM_011946	26405	Mm.211762	NM_011946	ENSMUSG00000024383	Map3k2	9630061B06Rik|AI585793|Mekk2|Mekk2b	mitogen-activated protein kinase kinase kinase 2	protein-coding
mm_123124.1	chr14	56174590	56174602	-	1	NA	promoter-TSS (NM_001305808)	promoter-TSS (NM_001305808)	3	NM_001305808	245839	Mm.207063	NM_153052	ENSMUSG00000015443	Gzmn	GrN	granzyme N	protein-coding
mm_27573.1	chr3	58692057	58692123	-	1	NA	promoter-TSS (NR_045167)	promoter-TSS (NR_045167)	298	NM_009174	20439	Mm.2847	NM_009174	ENSMUSG00000036432	Siah2	AA415433|Sinh2	seven in absentia 2	protein-coding
mm_149688.1	chr19	20640055	20640086	+	1	NA	exon (NM_013467, exon 12 of 13)	exon (NM_013467, exon 12 of 13)	38088	NM_013467	11668	Mm.250866	NM_013467	ENSMUSG00000053279	Aldh1a1	Ahd-2|Ahd2|Aldh1|Aldh1a2|E1|Raldh1	aldehyde dehydrogenase family 1, subfamily A1	protein-coding
mm_164851.1	chr18	46525337	46525365	-	1	NA	intron (NM_173423, intron 1 of 2)	CpG	620	NM_173423	240263	Mm.38249	NM_173423	ENSMUSG00000033319	Fem1c	2610312A07Rik|3632443A22Rik|AI646567	fem-1 homolog c (C.elegans)	protein-coding
mm_99141.1	chr11	100386180	100386205	+	1	NA	exon (NM_010593, exon 2 of 14)	exon (NM_010593, exon 2 of 14)	11598	NM_010593	16480	Mm.299774	NM_010593	ENSMUSG00000001552	Jup	Ctnng|D930025P04Rik|PG	junction plakoglobin	protein-coding
mm_67571.1	chr7	81934571	81934592	-	1	NA	promoter-TSS (NM_013886)	promoter-TSS (NM_013886)	-122	NM_013886	29877	Mm.392934	NM_013886	ENSMUSG00000025104	Hdgfrp3	2700022B06Rik|HRP-3	hepatoma-derived growth factor, related protein 3	protein-coding
mm_20931.1	chr2	150856049	150856070	-	1	NA	intron (NM_024465, intron 2 of 12)	B1_Mur1|SINE|Alu	48672	NM_024465	76192	Mm.112632	NM_024465	ENSMUSG00000032046	Abhd12	1500011G07Rik|6330583M11Rik|AI431047|AW547313	abhydrolase domain containing 12	protein-coding
mm_128904.1	chr15	73423036	73423055	-	1	NA	5' UTR (NM_007982, exon 1 of 32)	5' UTR (NM_007982, exon 1 of 32)	146	NM_007982	14083	Mm.254494	NM_007982	ENSMUSG00000022607	Ptk2	FAK|FRNK|Fadk|mKIAA4203|p125FAK	PTK2 protein tyrosine kinase 2	protein-coding
mm_140751.1	chr17	16921324	16921362	-	1	NA	Intergenic	RLTR1B-int|LTR|ERV1	-142760	NM_001005358	449000	Mm.483718	NM_001005358	ENSMUSG00000096696	Zfp960	-	zinc finger protein 960	protein-coding
mm_43131.1	chr5	125385977	125385979	+	1	NA	TTS (NM_019639)	TTS (NM_019639)	4039	NM_019639	22190	Mm.331	NM_019639	ENSMUSG00000008348	Ubc	2700054O04Rik|AI194771|Rps27a|TI-225|Uba52|Ubb	ubiquitin C	protein-coding
mm_4770.1	chr1	182522413	182522415	+	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-4931	NM_009794	12334	Mm.19306	NM_009794	ENSMUSG00000026509	Capn2	AI326419|Capa-2|Capa2|m-calpain|m-calpin	calpain 2	protein-coding
mm_105095.1	chr11	100939308	100939319	-	1	NA	5' UTR (NM_011486, exon 1 of 24)	5' UTR (NM_011486, exon 1 of 24)	227	NM_213660	20848	Mm.249934	NM_011486	ENSMUSG00000004040	Stat3	1110034C02Rik|AW109958|Aprf	signal transducer and activator of transcription 3	protein-coding
mm_54935.1	chr6	48445679	48445689	-	1	NA	promoter-TSS (NM_001085415)	promoter-TSS (NM_001085415)	141	NM_020589	68910	Mm.2464	NM_020589	ENSMUSG00000068551	Zfp467	1190001I08Rik|AB041616|AI426952|AV017623|EZI|MNCb-3350|Znf467	zinc finger protein 467	protein-coding
mm_79584.1	chr9	58253176	58253272	+	1	NA	promoter-TSS (NM_026942)	promoter-TSS (NM_026942)	60	NM_026942	69106	Mm.216502	NM_026942	ENSMUSG00000032333	Stoml1	1810015E19Rik|AI847431|SLP1|STORP|UNC24|WPB72	stomatin-like 1	protein-coding
mm_143478.1	chr17	71256886	71256930	-	1	NA	intron (NM_145158, intron 4 of 7)	intron (NM_145158, intron 4 of 7)	52254	NM_001164885	64898	Mm.227924	NM_022882	ENSMUSG00000024052	Lpin2	2610511G02Rik|AI481352|AW742896	lipin 2	protein-coding
mm_44371.1	chr5	17814192	17814200	-	1	NA	exon (NM_001159558, exon 7 of 16)	exon (NM_001159558, exon 7 of 16)	21700	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_85250.1	chr9	99140148	99140226	-	1	NA	promoter-TSS (NM_029094)	promoter-TSS (NM_029094)	24	NM_029094	74769	Mm.213128	NM_029094	ENSMUSG00000032462	Pik3cb	1110001J02Rik|AI447572|p110beta	phosphatidylinositol 3-kinase, catalytic, beta polypeptide	protein-coding
mm_149067.1	chr19	8842986	8843035	+	1	NA	exon (NM_008144, exon 3 of 11)	exon (NM_008144, exon 3 of 11)	2507	NM_001290823	14705	Mm.345134	NM_008144	ENSMUSG00000071657	Bscl2	2900097C17Rik|AI046355|Gng3lg	Berardinelli-Seip congenital lipodystrophy 2 (seipin)	protein-coding
mm_71413.1	chr8	46472398	46472412	+	1	NA	intron (NM_007981, intron 1 of 20)	intron (NM_007981, intron 1 of 20)	1368	NM_007981	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_20244.1	chr2	126498162	126498174	-	1	NA	Intergenic	Intergenic	-6615	NM_001080944	241633	Mm.222235	NM_001080944	ENSMUSG00000060131	Atp8b4	A530043E15|Im	ATPase, class I, type 8B, member 4	protein-coding
mm_103632.1	chr11	78945903	78945919	-	1	NA	exon (NM_010927, exon 15 of 27)	exon (NM_010927, exon 15 of 27)	20620	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_102385.1	chr11	58904220	58904236	-	1	NA	promoter-TSS (NM_011758)	promoter-TSS (NM_011758)	-3	NM_011758	22698	Mm.127646	NM_011758	ENSMUSG00000037001	Zfp39	CTfin33|Zfp-39	zinc finger protein 39	protein-coding
mm_58614.1	chr7	5062184	5062241	+	1	NA	promoter-TSS (NM_001205231)	promoter-TSS (NM_001205231)	69	NM_001205231	22185	Mm.360389	NM_133671	ENSMUSG00000030435	U2af2	65kDa	U2 small nuclear ribonucleoprotein auxiliary factor (U2AF) 2	protein-coding
mm_38031.1	chr4	133874659	133874669	-	1	NA	promoter-TSS (NM_001285506)	promoter-TSS (NM_001285506)	67	NM_001285506	20111	Mm.301827	NM_009097	ENSMUSG00000003644	Rps6ka1	Mapkapk-1a|Rsk|Rsk-1|Rsk1|S6K-alpha-1|p90-Rsk1|p90Rsk1|p90S6K|p90rsk	ribosomal protein S6 kinase polypeptide 1	protein-coding
mm_129447.1	chr15	78561002	78561048	-	1	NA	3' UTR (NM_009008, exon 7 of 7)	3' UTR (NM_009008, exon 7 of 7)	11758	NM_009008	19354	Mm.1972	NM_009008	ENSMUSG00000033220	Rac2	AI323801|AI452260	RAS-related C3 botulinum substrate 2	protein-coding
mm_165734.1	chr3	106788013	106788027	-	1	NA	intron (NM_007651, intron 1 of 7)	intron (NM_007651, intron 1 of 7)	2129	NM_007651	12508	Mm.316861	NM_007651	ENSMUSG00000040747	Cd53	AI323659|Ox-44|Tspan25	CD53 antigen	protein-coding
mm_154175.1	chr19	58734677	58734700	-	1	NA	exon (NM_018874, exon 7 of 13)	exon (NM_018874, exon 7 of 13)	5801	NM_018874	18946	Mm.10753	NM_018874	ENSMUSG00000042179	Pnliprp1	Plrp1	pancreatic lipase related protein 1	protein-coding
mm_19659.1	chr2	102968583	102968590	-	1	NA	Intergenic	Intergenic	-66921	NM_001039150	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_72999.1	chr8	93810573	93810651	+	1	NA	promoter-TSS (NM_010308)	promoter-TSS (NM_010308)	-226	NM_010308	14681	Mm.251445	NM_010308	ENSMUSG00000031748	Gnao1	AW050213|Galphao|Gnao|alphaO	guanine nucleotide binding protein, alpha O	protein-coding
mm_153050.1	chr19	32102851	32102861	-	1	NA	intron (NM_018830, intron 1 of 23)	intron (NM_018830, intron 1 of 23)	284	NM_018830	54447	Mm.491229	NM_018830	ENSMUSG00000024887	Asah2	AI585898	N-acylsphingosine amidohydrolase 2	protein-coding
mm_122438.1	chr14	45219365	45219428	-	1	NA	promoter-TSS (NM_027518)	promoter-TSS (NM_027518)	29	NM_172597	70561	Mm.28129	NM_172597	ENSMUSG00000021830	Txndc16	5730420B22Rik|C77647	thioredoxin domain containing 16	protein-coding
mm_23403.1	chr3	58117116	58117129	+	1	NA	Intergenic	Intergenic	46685	NR_040538	67850	Mm.416968	NR_040538	ENSMUSG00000100666	1700007F19Rik	-	RIKEN cDNA 1700007F19 gene	ncRNA
mm_101570.1	chr11	34227354	34227380	-	1	NA	3' UTR (NM_033374, exon 52 of 52)	3' UTR (NM_033374, exon 52 of 52)	-19278	NM_023907	14233	Mm.32926	NM_023907	ENSMUSG00000047861	Foxi1	5830401E05Rik|FREAC6|Fkh10|HFH-3|Hfh3	forkhead box I1	protein-coding
mm_119724.1	chr14	53960955	53960981	+	1	NA	Intergenic	Intergenic	292961	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_112511.1	chr13	8965777	8965780	+	1	NA	Intergenic	RLTR48A|LTR|ERV1	12915	NM_177197	320581	Mm.313743	NM_177197	ENSMUSG00000033520	Idi2	4833405L16Rik|IPPI2	isopentenyl-diphosphate delta isomerase 2	protein-coding
mm_114964.1	chr13	97088484	97088489	+	1	NA	intron (NM_001100458, intron 1 of 12)	intron (NM_001100458, intron 1 of 12)	16843	NM_001100458	320557	Mm.458280	NM_001100458	ENSMUSG00000041817	Fam169a	B230112C05Rik|SLAP75	family with sequence similarity 169, member A	protein-coding
mm_73993.1	chr8	120685844	120685870	+	1	NA	Intergenic	Intergenic	17537	NM_001293559	12857	Mm.386758	NM_009941	ENSMUSG00000031818	Cox4i1	AL024441|COX|COX IV-1|COXIV|Cox4|Cox4a|IV-1	cytochrome c oxidase subunit IV isoform 1	protein-coding
mm_100185.1	chr11	116657514	116657536	+	1	NA	intron (NM_001163318, intron 1 of 4)	intron (NM_001163318, intron 1 of 4)	417	NM_001163318	100038570	Mm.390349	NM_001163318	ENSMUSG00000075410	Prcd	Gm11744|OTTMUSG00000003947	progressive rod cone degeneration protein	protein-coding
mm_31491.1	chr4	53011895	53011907	+	1	NA	promoter-TSS (NM_001347099)	promoter-TSS (NM_001347099)	21	NM_025623	66536	Mm.38244	NM_025623	ENSMUSG00000015247	Nipsnap3b	2700063N13Rik|Nipsnap3a	nipsnap homolog 3B (C. elegans)	protein-coding
mm_27653.1	chr3	63964607	63964624	-	1	NA	5' UTR (NM_001272035, exon 1 of 7)	5' UTR (NM_001272035, exon 1 of 7)	118	NM_001331067	11416	Mm.135619	NM_015728	ENSMUSG00000027822	Slc33a1	AI315656|AI788741|Acatn|D630022N01Rik	solute carrier family 33 (acetyl-CoA transporter), member 1	protein-coding
mm_930.1	chr1	55406164	55406243	+	1	NA	5' UTR (NM_001114663, exon 1 of 6)	5' UTR (NM_001114663, exon 1 of 6)	257	NM_001114663	227120	Mm.194183	NM_001114663	ENSMUSG00000038349	Plcl1	C230017K02Rik|PLC-L|PLC-L1|PLCE|PLCL|PLDL1|PRIP|PRIP-1	phospholipase C-like 1	protein-coding
mm_60064.1	chr7	31213299	31213311	+	1	NA	Intergenic	Intergenic	-50431	NM_001310660	100043827		NM_001310660		Scgb2b1	Abpbg1|Gm4677	secretoglobin, family 2B, member 1	protein-coding
mm_113305.1	chr13	30750653	30750675	+	1	NA	exon (NM_013674, exon 2 of 9)	exon (NM_013674, exon 2 of 9)	1431	NM_013674	16364	Mm.4677	NM_013674	ENSMUSG00000021356	Irf4	AI385587|IRF-4|LSIRF|NF-EM5|Spip	interferon regulatory factor 4	protein-coding
mm_60703.1	chr7	45216672	45216695	+	1	NA	intron (NM_001285498, intron 1 of 11)	intron (NM_001285498, intron 1 of 11)	930	NM_001285498	21677	Mm.3019	NM_011565	ENSMUSG00000030796	Tead2	ETF|Etdf|TEAD-2|TEF-4|TEF4	TEA domain family member 2	protein-coding
mm_42877.1	chr5	122275427	122275456	+	1	NA	Intergenic	Intergenic	-8957	NM_177242	320717	Mm.489670	NM_177242	ENSMUSG00000038582	Pptc7	9130017A15Rik|AA672638|AI848390|TA-PP2C	PTC7 protein phosphatase homolog	protein-coding
mm_35407.1	chr4	34756223	34756233	-	1	NA	promoter-TSS (NM_001033255)	promoter-TSS (NM_001033255)	31	NM_001033255	214568	Mm.297405	NM_001033255	ENSMUSG00000071015	Gm136	-	predicted gene 136	protein-coding
mm_169996.1	chr1	71629749	71629751	-	1	NA	exon (NM_001276413, exon 14 of 44)	exon (NM_001276413, exon 14 of 44)	23484	NM_010233	14268	Mm.193099	NM_010233	ENSMUSG00000026193	Fn1	E330027I09|Fn|Fn-1	fibronectin 1	protein-coding
mm_152371.1	chr19	10203857	10203870	-	1	NA	promoter-TSS (NM_001271614)	promoter-TSS (NM_001271614)	80	NM_007999	14156	Mm.2952	NM_007999	ENSMUSG00000024742	Fen1	AW538437|FEN-1	flap structure specific endonuclease 1	protein-coding
mm_30862.1	chr4	30794948	30794949	+	1	NA	intron (NR_040655, intron 4 of 6)	intron (NR_040655, intron 4 of 6)	130352	NR_040655	75332	Mm.108636	NR_040655		4930556G01Rik	-	RIKEN cDNA 4930556G01 gene	ncRNA
mm_1865.1	chr1	85199596	85199622	+	1	NA	promoter-TSS (NM_001081746)	promoter-TSS (NM_001081746)	-2	NM_001081746	665378	Mm.440912	NM_001081746		Gm7609	EG665378	predicted pseudogene 7609	protein-coding
mm_371.1	chr1	33975922	33975924	+	1	NA	intron (NM_001276764, intron 3 of 102)	intron (NM_001276764, intron 3 of 102)	-35902	NM_133833	13518	Mm.336625	NM_010081	ENSMUSG00000026131	Dst	2310001O04Rik|A830042E19Rik|AW554249|BP230|BPAG1-n|Bpag|Bpag1|Macf2|ah|athetoid|dt|mKIAA0728|nmf203|nmf339	dystonin	protein-coding
mm_126053.1	chr15	76949509	76949543	+	1	NA	intron (NM_001347540, intron 3 of 4)	T-rich|Low_complexity|Low_complexity	982	NM_054099	117171	Mm.322968	NM_054099	ENSMUSG00000063236	1110038F14Rik	-	RIKEN cDNA 1110038F14 gene	protein-coding
mm_67733.1	chr7	90130128	90130175	-	1	NA	promoter-TSS (NM_001252521)	promoter-TSS (NM_001252521)	-81	NM_001252523	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_66731.1	chr7	46349049	46349059	-	1	NA	Intergenic	CpG	-22349	NR_131190	105447647		NR_131190		Munc	DRReRNA	MyoD upstream noncoding	ncRNA
mm_30989.1	chr4	35226224	35226242	+	1	NA	promoter-TSS (NM_001081343)	promoter-TSS (NM_001081343)	-353	NM_001081343	73205	Mm.331544	NM_001081343	ENSMUSG00000028300	3110043O21Rik	AI840585	RIKEN cDNA 3110043O21 gene	protein-coding
mm_136373.1	chr16	92825562	92825572	-	1	NA	intron (NM_001111022, intron 2 of 6)	intron (NM_001111022, intron 2 of 6)	507	NM_001111021	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_148028.1	chr18	69779723	69779771	-	1	NA	Intergenic	Intergenic	-145812	NM_201362	381175	Mm.266831	NM_201362	ENSMUSG00000038903	Ccdc68	BC046343	coiled-coil domain containing 68	protein-coding
mm_169545.1	chr15	102409263	102409268	+	1	NA	exon (NM_013672, exon 3 of 6)	exon (NM_013672, exon 3 of 6)	2949	NM_013672	20683	Mm.4618	NM_013672	ENSMUSG00000001280	Sp1	1110003E12Rik|AA450830|AI845540|Sp1-1	trans-acting transcription factor 1	protein-coding
mm_21529.1	chr2	163645082	163645096	-	1	NA	promoter-TSS (NM_012032)	promoter-TSS (NM_012032)	54	NM_012032	26943	Mm.218473	NM_012032	ENSMUSG00000017707	Serinc3	AA959945|AA960047|AIGP1|DIFF33|TMS-1|Tde1	serine incorporator 3	protein-coding
mm_118428.1	chr14	7957290	7957304	+	1	NA	Intergenic	Intergenic	36885	NM_007870	13421	Mm.272258	NM_007870	ENSMUSG00000025279	Dnase1l3	DNasegamma|Dhp2|Lsd	deoxyribonuclease 1-like 3	protein-coding
mm_70581.1	chr8	13167326	13167335	+	1	NA	exon (NM_010684, exon 3 of 9)	exon (NM_010684, exon 3 of 9)	8169	NM_010684	16783	Mm.16716	NM_010684	ENSMUSG00000031447	Lamp1	CD107a|LGP-120|LGP-A|Lamp-1|P2B	lysosomal-associated membrane protein 1	protein-coding
mm_103437.1	chr11	75925902	75925946	-	1	NA	promoter-TSS (NM_001291159)	promoter-TSS (NM_001291159)	-33	NM_001291159	380714	Mm.425697	NM_029548	ENSMUSG00000020847	Rph3al	Gm1753|Noc2	rabphilin 3A-like (without C2 domains)	protein-coding
mm_75598.1	chr8	61732350	61732392	-	1	NA	intron (NM_001081390, intron 2 of 19)	intron (NM_001081390, intron 2 of 19)	27727	NM_001293773	72333	Mm.29933	NM_001081390	ENSMUSG00000058056	Palld	2410003B16Rik|6030492A02	palladin, cytoskeletal associated protein	protein-coding
mm_101874.1	chr11	48892157	48892166	-	1	NA	intron (NM_001024230, intron 4 of 4)	intron (NM_001024230, intron 4 of 4)	9991	NM_001024230	432555	Mm.338931	NM_001024230	ENSMUSG00000058163	Gm5431	EG432555|Irgb9b8	predicted gene 5431	protein-coding
mm_18943.1	chr2	76766335	76766357	-	1	NA	exon (NM_011652, exon 253 of 313)	exon (NM_011652, exon 253 of 313)	91031	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_110828.1	chr12	72628897	72628907	-	1	NA	Intergenic	Intergenic	35926	NM_025522	66375	Mm.289653	NM_025522	ENSMUSG00000021094	Dhrs7	2310016E22Rik|5730564L20Rik|AW061210|Retdsr4|Retsdr4	dehydrogenase/reductase (SDR family) member 7	protein-coding
mm_67812.1	chr7	98145473	98145479	-	1	NA	promoter-TSS (NM_011010)	promoter-TSS (NM_011010)	-29	NM_011010	18378	Mm.440368	NM_011010	ENSMUSG00000074006	Omp	-	olfactory marker protein	protein-coding
mm_51305.1	chr6	72310709	72310747	+	1	NA	exon (NM_001282071, exon 8 of 11)	exon (NM_001282071, exon 8 of 11)	6118	NM_147779	20388	Mm.46033	NM_147779	ENSMUSG00000056370	Sftpb	AI562151|SF-B|SP-B|Sftp-3|Sftp3	surfactant associated protein B	protein-coding
mm_88642.1	chr10	79930420	79930428	+	1	NA	intron (NM_001288625, intron 1 of 8)	intron (NM_001288625, intron 1 of 8)	3083	NM_001288625	13496	Mm.301282	NM_007880	ENSMUSG00000019564	Arid3a	Bright|Dri1|Dril1	AT rich interactive domain 3A (BRIGHT-like)	protein-coding
mm_16551.1	chr2	181767118	181767129	+	1	NA	promoter-TSS (NM_008665)	promoter-TSS (NM_008665)	94	NM_001171616	17932	Mm.458718	NM_008665	ENSMUSG00000010505	Myt1	Nzf2|Nzf2a|Nzf2b|Nztf2	myelin transcription factor 1	protein-coding
mm_62256.1	chr7	99269180	99269200	+	1	NA	exon (NM_001043355, exon 1 of 3)	exon (NM_001043355, exon 1 of 3)	844	NM_001043355	17760	Mm.154087	NM_010837	ENSMUSG00000055407	Map6	2810411E12Rik|Map-6|Mtap6|STOP	microtubule-associated protein 6	protein-coding
mm_113179.1	chr13	24845123	24845186	+	1	NA	promoter-TSS (NM_001081051)	promoter-TSS (NM_001081051)	23	NR_131787	210108	Mm.261514	NM_001081051	ENSMUSG00000006711	D130043K22Rik	4930451E12Rik|Kiaa0319	RIKEN cDNA D130043K22 gene	protein-coding
mm_44072.1	chr5	148866875	148866883	+	1	NA	Intergenic	Intergenic	61768	NM_153572	231912	Mm.397405	NM_153572	ENSMUSG00000041298	Katnal1	-	katanin p60 subunit A-like 1	protein-coding
mm_126118.1	chr15	78317048	78317059	+	1	NA	Intergenic	Intergenic	-8937	NM_007780	12983	Mm.235324	NM_007780	ENSMUSG00000071713	Csf2rb	AI848964|AIC2B|Bc|CDw131|Csf2rb1|Csfgmrb|Il3r|Il3rb|Il3rb1|Il5rb	colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage)	protein-coding
mm_104579.1	chr11	96956194	96956221	-	1	NA	exon (NM_030220, exon 5 of 7)	exon (NM_030220, exon 5 of 7)	12061	NR_003293	319371	Mm.436865	NR_003293	ENSMUSG00000078700	D030028A08Rik	-	RIKEN cDNA D030028A08 gene	ncRNA
mm_124725.1	chr15	6580212	6580218	+	1	NA	exon (NM_001278269, exon 1 of 17)	exon (NM_001278269, exon 1 of 17)	368	NM_011815	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_22915.1	chr3	31094695	31094712	+	1	NA	promoter-TSS (NM_001039090)	promoter-TSS (NM_001039090)	-355	NM_011386	20482	Mm.15406	NM_011386	ENSMUSG00000027660	Skil	Skir|SnoN|sno	SKI-like	protein-coding
mm_111509.1	chr12	99563920	99563935	-	1	NA	promoter-TSS (NR_136760)	promoter-TSS (NR_136760)	86	NR_136760	102639404	Mm.396324	NR_136760	ENSMUSG00000097917	Gm26839	-	predicted gene, 26839	ncRNA
mm_121142.1	chr14	101898441	101898446	+	1	NA	intron (NM_001347628, intron 9 of 26)	intron (NM_001347628, intron 9 of 26)	57820	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_3022.1	chr1	133424311	133424320	+	1	NA	promoter-TSS (NM_011439)	promoter-TSS (NM_011439)	-103	NM_011439	20668	Mm.8575	NM_011439	ENSMUSG00000070643	Sox13	AA407916|AW259412|AW540933|Sox-13	SRY (sex determining region Y)-box 13	protein-coding
mm_70964.1	chr8	27023365	27023380	+	1	NA	promoter-TSS (NM_153592)	promoter-TSS (NM_153592)	-427	NM_153592	244373	Mm.277699	NM_153592	ENSMUSG00000031483	Erlin2	BC036333|C87251|Spfh2	ER lipid raft associated 2	protein-coding
mm_104650.1	chr11	97574041	97574064	-	1	NA	intron (NM_018873, intron 1 of 19)	intron (NM_018873, intron 1 of 19)	1074	NM_018873	56013	Mm.342665	NM_018873	ENSMUSG00000038453	Srcin1	P140|SNIP|mKIAA1684|p140Cap	SRC kinase signaling inhibitor 1	protein-coding
mm_103867.1	chr11	83522127	83522140	-	1	NA	promoter-TSS (NM_001045543)	promoter-TSS (NM_001045543)	-34	NM_001045543	629303	Mm.390417	NM_001045543	ENSMUSG00000018925	Heatr9	Gm11435|OTTMUSG00000000990	HEAT repeat containing 9	protein-coding
mm_90267.1	chr10	122679012	122679022	+	1	NA	promoter-TSS (NR_106182)	promoter-TSS (NR_106182)	255	NM_001110218	319468	Mm.489703	NM_176919	ENSMUSG00000034613	Ppm1h	A430075L18Rik|ARHCL1|C030002B11Rik	protein phosphatase 1H (PP2C domain containing)	protein-coding
mm_160970.1	chr11	99837861	99837861	-	1	NA	exon (NM_001195383, exon 1 of 1)	exon (NM_001195383, exon 1 of 1)	205	NM_001195383	100502865	Mm.476649	NM_001195383	ENSMUSG00000078257	2300003K06Rik	-	RIKEN cDNA 2300003K06 gene	protein-coding
mm_80390.1	chr9	75625968	75625981	+	1	NA	exon (NM_027309, exon 1 of 3)	exon (NM_027309, exon 1 of 3)	242	NM_027309	70082	Mm.19119	NM_027309	ENSMUSG00000032184	Lysmd2	2210402C18Rik|AV033872|AW538442	LysM, putative peptidoglycan-binding, domain containing 2	protein-coding
mm_143891.1	chr17	84466187	84466245	-	1	NA	promoter-TSS (NM_183021)	promoter-TSS (NM_183021)	-8	NM_183021	240174	Mm.246767	NM_177826	ENSMUSG00000024251	Thada	6530405K19|A930021O22|AU019899|BC052885|GITA	thyroid adenoma associated	protein-coding
mm_94830.1	chr11	23306911	23306937	+	1	NA	promoter-TSS (NM_001190401)	promoter-TSS (NM_001190401)	29	NM_001190401	17847	Mm.119155	NM_001190401	ENSMUSG00000056342	Usp34	A530081C03Rik|Murr2	ubiquitin specific peptidase 34	protein-coding
mm_118703.1	chr14	22163457	22163478	+	1	NA	intron (NM_028275, intron 2 of 6)	L1MA9|LINE|L1	143755	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_155782.1	chrX	96456345	96456356	+	1	NA	promoter-TSS (NM_001159627)	promoter-TSS (NM_001159627)	4	NM_001159627	15203	Mm.277092	NM_010417	ENSMUSG00000031209	Heph	C130006F04Rik|Cpl|mKIAA0698|sla	hephaestin	protein-coding
mm_66478.1	chr7	45008892	45008913	-	1	NA	exon (NM_001008422, exon 7 of 11)	exon (NM_001008422, exon 7 of 11)	3585	NR_106021	102466218		NR_106021	ENSMUSG00000098839	Mir7054	Gm27557|mmu-mir-7054	microRNA 7054	ncRNA
mm_110861.1	chr12	73444922	73444938	-	1	NA	Intergenic	Intergenic	-35367	NR_046013	380765	Mm.490476	NR_046013		D830013O20Rik	Gm891	RIKEN cDNA D830013O20 gene	ncRNA
mm_72981.1	chr8	92911720	92911728	+	1	NA	intron (NM_173014, intron 12 of 13)	intron (NM_173014, intron 12 of 13)	10329	NM_027112	69543	Mm.440514	NM_027112	ENSMUSG00000078144	Capns2	2310005G05Rik|30K-2	calpain, small subunit 2	protein-coding
mm_24391.1	chr3	90265920	90265938	+	1	NA	promoter-TSS (NM_201407)	promoter-TSS (NM_201407)	-585	NM_201407	229541	Mm.30571	NM_201407	ENSMUSG00000042404	Dennd4b	-	DENN/MADD domain containing 4B	protein-coding
mm_42703.1	chr5	120076669	120076670	+	1	NA	Intergenic	Intergenic	-39844	NM_028762	74111	Mm.41022	NM_028762	ENSMUSG00000029594	Rbm19	1200009A02Rik|AV302714|NPO	RNA binding motif protein 19	protein-coding
mm_8506.1	chr1	154117848	154117856	-	1	NA	Intergenic	Intergenic	-83335	NM_001204908	100503355	Mm.484410	NM_001204908	ENSMUSG00000066797	Zfp648	ENSMUSG00000066797|Gm10178|Gm203	zinc finger protein 648	protein-coding
mm_147253.1	chr18	38631538	38631548	-	1	NA	Intergenic	Intergenic	-30275	NM_011898	24066	Mm.42038	NM_011898	ENSMUSG00000024427	Spry4	A030006O18Rik|sprouty4	sprouty homolog 4 (Drosophila)	protein-coding
mm_118966.1	chr14	27622434	27622543	+	1	NA	promoter-TSS (NM_001347497)	promoter-TSS (NM_001347497)	81	NM_177814	238988	Mm.318004	NM_177814	ENSMUSG00000040640	Erc2	6430531D06|CAST|CAST1/ERC2|D14Ertd171e|ELKS2alpha	ELKS/RAB6-interacting/CAST family member 2	protein-coding
mm_27633.1	chr3	61364363	61364410	-	1	NA	promoter-TSS (NM_028712)	promoter-TSS (NM_028712)	-121	NM_028712	74012	Mm.422674	NM_028712	ENSMUSG00000036894	Rap2b	4021402C18Rik|AA408554	RAP2B, member of RAS oncogene family	protein-coding
mm_40966.1	chr5	76995850	76995860	+	1	NA	exon (NM_025691, exon 16 of 19)	exon (NM_025691, exon 16 of 19)	-8200	NM_206935	384185	Mm.451858	NM_206935	ENSMUSG00000063820	Arl9	1700110A09Rik	ADP-ribosylation factor-like 9	protein-coding
mm_110938.1	chr12	76596702	76596722	-	1	NA	intron (NM_013675, intron 32 of 35)	intron (NM_013675, intron 32 of 35)	-48787	NR_046044	100504549	Mm.440349	NR_046044		AI463170	-	expressed sequence AI463170	ncRNA
mm_32734.1	chr4	116596638	116596665	+	1	NA	promoter-TSS (NM_001037916)	promoter-TSS (NM_001037916)	-79	NM_001037916	622665	Mm.388905	NM_001037916	ENSMUSG00000034035	Ccdc17	-	coiled-coil domain containing 17	protein-coding
mm_162636.1	chr1	191224848	191224856	-	1	NA	Intergenic	CpG	-41519	NM_007498	11910	Mm.2706	NM_007498	ENSMUSG00000026628	Atf3	LRG-21	activating transcription factor 3	protein-coding
mm_63652.1	chr7	128748902	128748911	+	1	NA	intron (NM_001029982, intron 1 of 18)	intron (NM_001029982, intron 1 of 18)	4036	NM_001029982	207352	Mm.297105	NM_001029982	ENSMUSG00000055319	Sec23ip	D7Ertd373e|p125	Sec23 interacting protein	protein-coding
mm_47534.1	chr5	124209458	124209463	-	1	NA	intron (NM_011256, intron 2 of 24)	intron (NM_011256, intron 2 of 24)	-20265	NR_045369	75927	Mm.410803	NR_045369	ENSMUSG00000090220	Pitpnm2os1	4930568K20Rik	phosphatidylinositol transfer protein, membrane-associated 2, opposite strand 1	ncRNA
mm_91191.1	chr10	21146336	21146347	-	1	NA	exon (NM_001198914, exon 9 of 16)	exon (NM_001198914, exon 9 of 16)	14643	NM_001198914	17863	Mm.52109	NM_010848	ENSMUSG00000019982	Myb	AI550390|M16449|c-myb	myeloblastosis oncogene	protein-coding
mm_157427.1	chrX	38564954	38564962	-	1	NA	exon (NM_028288, exon 3 of 23)	exon (NM_028288, exon 3 of 23)	11238	NM_028288	72584	Mm.327675	NM_028288	ENSMUSG00000031095	Cul4b	2700050M05Rik|AA409770|CUL-4B|mKIAA0695	cullin 4B	protein-coding
mm_167190.1	chr7	142533136	142533142	+	1	NA	promoter-TSS (NM_011288)	promoter-TSS (NM_011288)	22	NM_011288	19935	Mm.12144	NM_011288	ENSMUSG00000037772	Mrpl23	L23mrp|Rpl23|Rpl23l	mitochondrial ribosomal protein L23	protein-coding
mm_81263.1	chr9	108023927	108023952	+	1	NA	intron (NM_013785, intron 1 of 5)	intron (NM_013785, intron 1 of 5)	21291	NM_013785	27399	Mm.276155	NM_013785	ENSMUSG00000032594	Ip6k1	1200016D08Rik|AU022776|Ihpk1|InsP6|InsP6k1|Itpk6	inositol hexaphosphate kinase 1	protein-coding
mm_150188.1	chr19	32665606	32665612	+	1	NA	3' UTR (NM_011864, exon 13 of 13)	3' UTR (NM_011864, exon 13 of 13)	45604	NM_011864	23972	Mm.203916	NM_011864	ENSMUSG00000024899	Papss2	1810018P12Rik|AI159688|AtpsU2|Atpsk2|Sk2|bm	3'-phosphoadenosine 5'-phosphosulfate synthase 2	protein-coding
mm_70922.1	chr8	25808495	25808513	+	1	NA	promoter-TSS (NM_011485)	promoter-TSS (NM_011485)	30	NM_011485	20845	Mm.293314	NM_011485	ENSMUSG00000031574	Star	AV363654|D8Ertd419e|stARD1	steroidogenic acute regulatory protein	protein-coding
mm_65858.1	chr7	29339217	29339252	-	1	NA	intron (NM_001081028, intron 16 of 22)	intron (NM_001081028, intron 16 of 22)	35229	NM_013874	29861	Mm.101885	NM_013874	ENSMUSG00000030584	Dpf1	Neud4	D4, zinc and double PHD fingers family 1	protein-coding
mm_19093.1	chr2	79370856	79370892	-	1	NA	intron (NM_001048176, intron 2 of 12)	intron (NM_001048176, intron 2 of 12)	58114	NM_001048176	228094	Mm.440704	NM_001033295	ENSMUSG00000075256	Cerkl	Gm1958|Rp26	ceramide kinase-like	protein-coding
mm_29521.1	chr3	116561543	116561543	-	1	NA	Intergenic	LTRIS_Mus|LTR|ERV1	-1430	NM_027321	109245	Mm.216027	NM_027321	ENSMUSG00000027961	Lrrc39	2010005E21Rik|9430028I06Rik|Myomasp	leucine rich repeat containing 39	protein-coding
mm_92635.1	chr10	80329516	80329530	-	1	NA	promoter-TSS (NM_139292)	promoter-TSS (NM_139292)	-50	NM_008793	18551	Mm.299916	NM_008793	ENSMUSG00000020131	Pcsk4	AI647044|L21221|NEC 3|NEC3|PC4|SPC5	proprotein convertase subtilisin/kexin type 4	protein-coding
mm_21877.1	chr2	166117053	166117071	-	1	NA	exon (NM_028072, exon 3 of 21)	exon (NM_028072, exon 3 of 21)	38223	NM_001252578	72043	Mm.1011	NM_028072	ENSMUSG00000006800	Sulf2	2010004N24Rik|AU020235|MSulf-2|mKIAA1247	sulfatase 2	protein-coding
mm_40715.1	chr5	65934911	65934921	+	1	NA	Intergenic	Intergenic	-32208	NM_001081104	231252	Mm.140015	NM_001081104	ENSMUSG00000029205	Chrna9	2410015I05Rik|Acra9|EG666827|Gm8311	cholinergic receptor, nicotinic, alpha polypeptide 9	protein-coding
mm_32420.1	chr4	107067013	107067027	+	1	NA	promoter-TSS (NM_025500)	promoter-TSS (NM_025500)	32	NM_175471	230582	Mm.44608	NM_175471	ENSMUSG00000028621	Cyb5rl	2810410C14Rik	cytochrome b5 reductase-like	protein-coding
mm_24549.1	chr3	93398214	93398226	+	1	NA	exon (NM_009100, exon 3 of 3)	exon (NM_009100, exon 3 of 3)	4521	NM_009100	20129	Mm.1417	NM_009100	ENSMUSG00000041984	Rptn	-	repetin	protein-coding
mm_5630.1	chr1	40398452	40398455	-	1	NA	Intergenic	ORR1A1|LTR|ERVL-MaLR	-31117	NM_001294171	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_98579.1	chr11	95713119	95713137	+	1	NA	promoter-TSS (NR_045780)	promoter-TSS (NR_045780)	-374	NR_045780	432396	Mm.426849	NR_045780	ENSMUSG00000086191	Zfp652os	1110035M17Rik	zinc finger protein 652, opposite strand	ncRNA
mm_68212.1	chr7	104404567	104404579	-	1	NA	Intergenic	Intergenic	-45927	NM_175648	244183	Mm.347647	NM_175648	ENSMUSG00000052749	Trim30b	A530023O14Rik|Trim30-1	tripartite motif-containing 30B	protein-coding
mm_19261.1	chr2	84800443	84800457	-	1	NA	intron (NM_019949, intron 1 of 3)	MIRb|SINE|MIR	1622	NM_019949	56791	Mm.38261	NM_019949	ENSMUSG00000027078	Ube2l6	2810489I21Rik|RIG-B|UBCH8|Ubce8|Ubcm8	ubiquitin-conjugating enzyme E2L 6	protein-coding
mm_2354.1	chr1	92934720	92934791	+	1	NA	non-coding (NR_015525, exon 2 of 2)	non-coding (NR_015525, exon 2 of 2)	347	NM_011796	23830	Mm.294315	NM_011796	ENSMUSG00000026270	Capn10	AW049679|Capn8|mKIAA1845	calpain 10	protein-coding
mm_111866.1	chr12	107991540	107991554	-	1	NA	intron (NM_001079883, intron 1 of 3)	(A)n|Simple_repeat|Simple_repeat	11867	NM_001079883	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_12848.1	chr2	83644525	83644547	+	1	NA	promoter-TSS (NM_026934)	promoter-TSS (NM_026934)	-42	NM_026934	69082	Mm.27804	NM_026934	ENSMUSG00000027091	Zc3h15	1700006A17Rik|1810012H02Rik|2610312B22Rik|FM22|Ierepo4	zinc finger CCCH-type containing 15	protein-coding
mm_48548.1	chr5	142905763	142905796	-	1	NA	intron (NM_007393, intron 1 of 5)	CpG	975	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_62014.1	chr7	91354221	91354225	+	1	NA	intron (NM_011807, intron 1 of 22)	intron (NM_011807, intron 1 of 22)	263437	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_5810.1	chr1	52498943	52498945	-	1	NA	intron (NM_008667, intron 1 of 7)	intron (NM_008667, intron 1 of 7)	1504	NM_008667	17936	Mm.25903	NM_008667	ENSMUSG00000002881	Nab1	-	Ngfi-A binding protein 1	protein-coding
mm_140775.1	chr17	17876707	17876718	-	1	NA	exon (NM_013521, exon 2 of 2)	exon (NM_013521, exon 2 of 2)	7227	NM_013521	14293	Mm.56951	NM_013521	ENSMUSG00000045551	Fpr1	FPR|LXA4R|fMLF-R	formyl peptide receptor 1	protein-coding
mm_125831.1	chr15	74957746	74957756	+	1	NA	intron (NM_001164039, intron 2 of 4)	intron (NM_001164039, intron 2 of 4)	2645	NM_001164040	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_27447.1	chr3	51964967	51964982	-	1	NA	intron (NM_001004176, intron 1 of 4)	intron (NM_001004176, intron 1 of 4)	140032	NM_001004176	433586	Mm.234972	NM_001004176	ENSMUSG00000061143	Maml3	AV234550|BC049812|Mam-2|mKIAA1816	mastermind like 3 (Drosophila)	protein-coding
mm_17959.1	chr2	37374666	37374669	-	1	NA	3' UTR (NM_001100591, exon 22 of 22)	3' UTR (NM_001100591, exon 22 of 22)	-15335	NM_026176	67466	Mm.30709	NM_026176	ENSMUSG00000009030	Pdcl	1200011E13Rik|AW108059|PhLP1	phosducin-like	protein-coding
mm_100618.1	chr11	121559750	121559761	+	1	NA	intron (NM_029878, intron 16 of 38)	intron (NM_029878, intron 16 of 38)	-40413	NM_178763	319530	Mm.11395	NM_178763	ENSMUSG00000039238	Zfp750	A030007D23Rik|Znf750	zinc finger protein 750	protein-coding
mm_79040.1	chr9	46210597	46210607	+	1	NA	exon (NM_027498, exon 20 of 25)	exon (NM_027498, exon 20 of 25)	-18028	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2|apo-AI|apoA-I	apolipoprotein A-I	protein-coding
mm_155569.1	chrX	77368074	77368074	+	1	NA	intron (NR_035475, intron 1 of 3)	MTD|LTR|ERVL-MaLR	107862	NR_035475	100316834		NR_035475	ENSMUSG00000088980	Mir669m-2	mmu-mir-669m-2	microRNA 669m-2	ncRNA
mm_43678.1	chr5	138799640	138799650	+	1	NA	intron (NM_030565, intron 5 of 9)	B4|SINE|B4	-20435	NM_001195128	384244	Mm.485002	NM_001195128	ENSMUSG00000094504	Gm5294	EG384244	predicted gene 5294	protein-coding
mm_85251.1	chr9	99158452	99158454	-	1	NA	Intergenic	Intergenic	-18242	NM_029094	74769	Mm.213128	NM_029094	ENSMUSG00000032462	Pik3cb	1110001J02Rik|AI447572|p110beta	phosphatidylinositol 3-kinase, catalytic, beta polypeptide	protein-coding
mm_108313.1	chr12	79559746	79559766	+	1	NA	intron (NM_009014, intron 7 of 10)	intron (NM_009014, intron 7 of 10)	262405	NM_001252562	19363	Mm.341756	NM_009014	ENSMUSG00000059060	Rad51b	AI553500|R51H2|Rad51l1|mREC2	RAD51 paralog B	protein-coding
mm_76222.1	chr8	83572596	83572627	-	1	NA	TTS (NM_025843)	TTS (NM_025843)	5853	NM_025843	66916	Mm.29683	NM_025843	ENSMUSG00000033938	Ndufb7	1110002H15Rik	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 7	protein-coding
mm_14794.1	chr2	145860892	145860904	+	1	NA	exon (NM_028724, exon 9 of 13)	exon (NM_028724, exon 9 of 13)	-42343	NM_026425	67877	Mm.151168	NM_026425	ENSMUSG00000002728	Naa20	1500004D14Rik|2900026I01Rik|AU041458|D2Ertd186e|Nat5	N(alpha)-acetyltransferase 20, NatB catalytic subunit	protein-coding
mm_130310.1	chr15	97050084	97050099	-	1	NA	intron (NM_027052, intron 1 of 15)	intron (NM_027052, intron 1 of 15)	5865	NM_027052	69354	Mm.250980	NM_027052	ENSMUSG00000022464	Slc38a4	1110012E16Rik|1700012A18Rik|Ata3|mATA3|mNAT3	solute carrier family 38, member 4	protein-coding
mm_38395.1	chr4	138836463	138836473	-	1	NA	intron (NM_001122954, intron 1 of 5)	intron (NM_001122954, intron 1 of 5)	4592	NM_001082531	18780	Mm.4675	NM_011108	ENSMUSG00000058908	Pla2g2a	EF|Mom1|Pla2|sPLA2|sPla2-IIA	phospholipase A2, group IIA (platelets, synovial fluid)	protein-coding
mm_161983.1	chr19	27427143	27427143	-	1	NA	intron (NR_131940, intron 1 of 17)	intron (NR_131940, intron 1 of 17)	2765	NM_177474	52874	Mm.261027	NM_177474	ENSMUSG00000041360	Pum3	1110069H02Rik|AA675048|D19Bwg1357e|Kiaa0020	pumilio RNA-binding family member 3	protein-coding
mm_147912.1	chr18	65476368	65476383	-	1	NA	exon (NM_172833, exon 16 of 16)	exon (NM_172833, exon 16 of 16)	45378	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_143301.1	chr17	65985597	65985617	-	1	NA	exon (NM_001025572, exon 9 of 13)	exon (NM_001025572, exon 9 of 13)	-34420	NM_023053	65960	Mm.10153	NM_023053	ENSMUSG00000024098	Twsg1	1810013J15Rik|9030422N06Rik|AW552143|D17Ertd403e|Tsg|Twg	twisted gastrulation BMP signaling modulator 1	protein-coding
mm_106106.1	chr11	116300321	116300337	-	1	NA	exon (NM_001162872, exon 6 of 18)	exon (NM_001162872, exon 6 of 18)	6409	NM_016857	53413	Mm.22530	NM_016857	ENSMUSG00000020792	Exoc7	Exo70|sec70	exocyst complex component 7	protein-coding
mm_55089.1	chr6	49236510	49236551	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-21576	NM_023670	140488	Mm.281018	NM_023670	ENSMUSG00000029814	Igf2bp3	2610101N11Rik|AA522010|AL022933|AU045931|IMP-3|IMP3|Koc13|Neilsen|mimp3	insulin-like growth factor 2 mRNA binding protein 3	protein-coding
mm_12089.1	chr2	60232521	60232525	+	1	NA	intron (NM_020575, intron 4 of 9)	intron (NM_020575, intron 4 of 9)	22587	NM_020575	57438	Mm.260635	NM_020575	ENSMUSG00000026977	March7	Axo|Axot|Gtrgeo17	membrane-associated ring finger (C3HC4) 7	protein-coding
mm_129962.1	chr15	85578120	85578132	-	1	NA	promoter-TSS (NM_001163634)	promoter-TSS (NM_001163634)	-56	NM_001163634	22422	Mm.306946	NM_009528	ENSMUSG00000022382	Wnt7b	Wnt-7b	wingless-type MMTV integration site family, member 7B	protein-coding
mm_78093.1	chr9	18478338	18478344	+	1	NA	promoter-TSS (NM_028557)	promoter-TSS (NM_028557)	-54	NM_028557	73503	Mm.160088	NM_028557	ENSMUSG00000038691	Mbd3l1	1700070G05Rik|1700095H13Rik|Mbd3l	methyl-CpG binding domain protein 3-like 1	protein-coding
mm_35056.1	chr4	6355480	6355490	-	1	NA	Intergenic	Intergenic	-10195	NM_016807	53378	Mm.247473	NM_016807	ENSMUSG00000028249	Sdcbp	MDA-9|Sycl|syntenin-1	syndecan binding protein	protein-coding
mm_145553.1	chr18	60811307	60811357	+	1	NA	promoter-TSS (NR_039567)	promoter-TSS (NR_039567)	-744	NR_039567	100628611		NR_039567	ENSMUSG00000093327	Mir5107	mir-5107|mmu-mir-5107|mu-mir-5107	microRNA 5107	ncRNA
mm_156132.1	chrX	120718866	120718871	+	1	NA	intron (NR_073451, intron 5 of 7)	L1Md_F|LINE|L1	-405642	NM_001281531	624957		NM_001281531	ENSMUSG00000083616	H2afb3	EG624957|H2A.Bbd3|H2afb3-ps	H2A histone family, member B3	protein-coding
mm_75182.1	chr8	36952346	36952394	-	1	NA	promoter-TSS (NM_001194940)	promoter-TSS (NM_001194940)	72	NM_001194940	50768	Mm.125155	NM_015802	ENSMUSG00000031523	Dlc1	A730069N07Rik|Arhgap7|HP|STARD12|dlc-1	deleted in liver cancer 1	protein-coding
mm_112838.1	chr13	20826509	20826520	+	1	NA	intron (NM_012054, intron 2 of 20)	RMER10B|LTR|ERVL	32401	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_158198.1	chrX	105070105	105070123	-	1	NA	promoter-TSS (NR_015467)	promoter-TSS (NR_015467)	10	NR_015467	71445	Mm.242968	NR_015467	ENSMUSG00000087174	5530601H04Rik	AI835882	RIKEN cDNA 5530601H04 gene	ncRNA
mm_117924.1	chr13	99434096	99434125	-	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-21284	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_128379.1	chr15	42676899	42676931	-	1	NA	promoter-TSS (NM_001286062)	promoter-TSS (NM_001286062)	62	NM_001286062	11600	Mm.309336	NM_009640	ENSMUSG00000022309	Angpt1	1110046O21Rik|Ang-1|Ang1	angiopoietin 1	protein-coding
mm_29604.1	chr3	121206333	121206364	-	1	NA	3' UTR (NM_178936, exon 8 of 8)	3' UTR (NM_178936, exon 8 of 8)	-34653	NM_025637	66568	Mm.263163	NM_025637	ENSMUSG00000028133	Rwdd3	2510027J23Rik|3110037C01Rik|AI035684|AI662458|Rsume|X2CR1	RWD domain containing 3	protein-coding
mm_134391.1	chr16	17405799	17405876	-	1	NA	promoter-TSS (NM_023348)	promoter-TSS (NM_023348)	-163	NM_023348	67474	Mm.271992	NM_023348	ENSMUSG00000022765	Snap29	1300018G05Rik|AI891940|AU020222|BB131856|Gs32	synaptosomal-associated protein 29	protein-coding
mm_131453.1	chr16	16870830	16870844	+	1	NA	5' UTR (NM_011624, exon 1 of 18)	5' UTR (NM_011624, exon 1 of 18)	101	NM_011624	21976	Mm.326089	NM_011624	ENSMUSG00000022779	Top3b	-	topoisomerase (DNA) III beta	protein-coding
mm_44934.1	chr5	36376939	36376981	-	1	NA	intron (NM_030889, intron 1 of 26)	intron (NM_030889, intron 1 of 26)	21179	NM_030889	81840	Mm.34113	NM_030889	ENSMUSG00000029093	Sorcs2	N28137|mKIAA1329	sortilin-related VPS10 domain containing receptor 2	protein-coding
mm_14266.1	chr2	128698823	128698833	+	1	NA	promoter-TSS (NM_008587)	promoter-TSS (NM_008587)	-169	NM_008587	17289	Mm.239655	NM_008587	ENSMUSG00000014361	Mertk	Eyk|Mer|Nyk|nmf12	c-mer proto-oncogene tyrosine kinase	protein-coding
mm_54738.1	chr6	40999467	40999468	-	1	NA	promoter-TSS (NM_001102660)	promoter-TSS (NM_001102660)	12	NM_001102660	100040208	Mm.333011	NM_001102660	ENSMUSG00000096525	Gm2663	-	predicted gene 2663	protein-coding
mm_160592.1	chr9	70561506	70561506	+	1	NA	intron (NM_026337, intron 3 of 20)	intron (NM_026337, intron 3 of 20)	18636	NM_025690	66660	Mm.22379	NM_025690	ENSMUSG00000032212	Sltm	5730455C01Rik|5730555F13Rik|9130215G10Rik|Met	SAFB-like, transcription modulator	protein-coding
mm_59349.1	chr7	25659149	25659157	+	1	NA	promoter-TSS (NM_007533)	promoter-TSS (NM_007533)	0	NM_138586	27998	Mm.27853	NM_138586	ENSMUSG00000061286	Exosc5	D7Wsu180e	exosome component 5	protein-coding
mm_126282.1	chr15	79209384	79209412	+	1	NA	intron (NR_029470, intron 2 of 4)	intron (NR_029470, intron 2 of 4)	-19775	NM_008837	18693	Mm.259464	NM_008837	ENSMUSG00000068206	Pick1	Prkcabp	protein interacting with C kinase 1	protein-coding
mm_32472.1	chr4	107783702	107783720	+	1	NA	Intergenic	Intergenic	-18548	NR_033496	16975	Mm.442134	NM_053073	ENSMUSG00000028613	Lrp8	4932703M08Rik|AA921429|AI848122|ApoER2|Lr8b	low density lipoprotein receptor-related protein 8, apolipoprotein e receptor	protein-coding
mm_44081.1	chr5	149144258	149144283	+	1	NA	promoter-TSS (NR_137278)	promoter-TSS (NR_137278)	7	NR_137278	105242579	Mm.445929	NR_137278	ENSMUSG00000107388	Gm42788	-	predicted gene 42788	ncRNA
mm_127564.1	chr15	102204080	102204118	+	1	NA	promoter-TSS (NM_001289690)	promoter-TSS (NM_001289690)	454	NM_001289691	68744	Mm.352945	NM_153194	ENSMUSG00000046897	Zfp740	1110034O07Rik|AW548228|Znf740	zinc finger protein 740	protein-coding
mm_131726.1	chr16	21794385	21794391	+	1	NA	promoter-TSS (NR_037958)	promoter-TSS (NR_037958)	41	NR_037957	100043489	Mm.326535	NR_037957	ENSMUSG00000097290	1300002E11Rik	1500026P21Rik	RIKEN cDNA 1300002E11 gene	ncRNA
mm_141033.1	chr17	25273367	25273383	-	1	NA	promoter-TSS (NR_027452)	promoter-TSS (NR_027452)	56	NM_001177610	22196	Mm.240044	NM_011665	ENSMUSG00000015120	Ube2i	5830467E05Rik|F830028O17Rik|UBC9|Ubce2i|Ubce9	ubiquitin-conjugating enzyme E2I	protein-coding
mm_107346.1	chr12	32820232	32820245	+	1	NA	promoter-TSS (NM_021524)	promoter-TSS (NM_021524)	-97	NM_021524	59027	Mm.202727	NM_021524	ENSMUSG00000020572	Nampt	1110035O14Rik|AI314458|AI480535|NAmPRTase|Pbef|Pbef1|Visfatin	nicotinamide phosphoribosyltransferase	protein-coding
mm_38684.1	chr4	145096827	145096837	-	1	NA	intron (NM_001276502, intron 41 of 68)	intron (NM_001276502, intron 41 of 68)	93834	NM_001276502	230895	Mm.240310	NM_001033190	ENSMUSG00000020220	Vps13d	-	vacuolar protein sorting 13D	protein-coding
mm_19102.1	chr2	79454386	79454392	-	1	NA	exon (NM_010894, exon 2 of 2)	exon (NM_010894, exon 2 of 2)	2247	NM_010894	18012	Mm.4636	NM_010894	ENSMUSG00000034701	Neurod1	BETA2|BHF-1|Nd1|Neurod|bHLHa3	neurogenic differentiation 1	protein-coding
mm_156608.1	chrX	153305704	153305735	+	1	NA	intron (NM_173780, intron 1 of 6)	ORR1A2|LTR|ERVL-MaLR	67674	NM_173780	245671	Mm.260751	NM_173780	ENSMUSG00000041649	Klf8	A830097P10Rik|BKLF3|ZNF74	Kruppel-like factor 8	protein-coding
mm_172784.1	chr9	100073853	100073854	-	1	NA	Intergenic	L1Md_T|LINE|L1	51553	NR_040763	108970	Mm.390215	NR_040763	ENSMUSG00000101584	4930519F24Rik	-	RIKEN cDNA 4930519F24 gene	ncRNA
mm_9780.1	chr1	181211173	181211196	-	1	NA	exon (NM_145514, exon 1 of 14)	exon (NM_145514, exon 1 of 14)	794	NM_145514	226757	Mm.289082	NM_145514	ENSMUSG00000038733	Wdr26	1600024A01Rik|AA693241|AI447817|AU044014|C77982|Gid7	WD repeat domain 26	protein-coding
mm_46505.1	chr5	105136088	105136108	-	1	NA	intron (NM_008620, intron 2 of 10)	A-rich|Low_complexity|Low_complexity	3454	NM_008620	17472	Mm.440525	NM_008620	ENSMUSG00000079363	Gbp4	AW228052|Mag-2|Mpa-2|Mpa2	guanylate binding protein 4	protein-coding
mm_26092.1	chr3	136775719	136775721	+	1	NA	intron (NM_008913, intron 1 of 13)	intron (NM_008913, intron 1 of 13)	105654	NM_001293622	19055	Mm.331389	NM_008913	ENSMUSG00000028161	Ppp3ca	2900074D19Rik|CN|Caln|Calna|CnA	protein phosphatase 3, catalytic subunit, alpha isoform	protein-coding
mm_88571.1	chr10	79669499	79669507	+	1	NA	promoter-TSS (NM_148934)	promoter-TSS (NM_148934)	93	NM_148934	110012	Mm.22623	NM_148934	ENSMUSG00000020308	Tpgs1	AV005629|Gm16517|Gtrgeo22|PGs1	tubulin polyglutamylase complex subunit 1	protein-coding
mm_31937.1	chr4	86575741	86575751	+	1	NA	promoter-TSS (NM_178376)	promoter-TSS (NM_178376)	73	NM_178376	68441	Mm.31178	NM_178376	ENSMUSG00000070934	Rraga	1300010C19Rik|AI255374|FIP-1|RAGA	Ras-related GTP binding A	protein-coding
mm_149262.1	chr19	10554965	10554973	+	1	NA	intron (NM_001277860, intron 2 of 4)	intron (NM_001277860, intron 2 of 4)	794	NM_001277861	68642	Mm.31236	NM_026798	ENSMUSG00000024667	Tmem216	1110017C22Rik|2810441K11Rik|4921533J23Rik|A930021F15Rik|AI482550	transmembrane protein 216	protein-coding
mm_149398.1	chr19	11389191	11389229	+	1	NA	intron (NM_001310331, intron 5 of 6)	MER45C|DNA|hAT-Tip100	13722	NM_001310331	666907		NM_001310331	ENSMUSG00000101389	Ms4a4a	EG666907	membrane-spanning 4-domains, subfamily A, member 4A	protein-coding
mm_5250.1	chr1	16615503	16615506	-	1	NA	intron (NM_025773, intron 1 of 5)	intron (NM_025773, intron 1 of 5)	3834	NM_025773	66799	Mm.122430	NM_025773	ENSMUSG00000025939	Ube2w	6130401J04Rik	ubiquitin-conjugating enzyme E2W (putative)	protein-coding
mm_120605.1	chr14	70100163	70100179	+	1	NA	promoter-TSS (NM_021328)	promoter-TSS (NM_021328)	26	NM_021328	57784	Mm.24186	NM_021328	ENSMUSG00000022089	Bin3	1700015F07Rik	bridging integrator 3	protein-coding
mm_170941.1	chr2	4954674	4954678	+	1	NA	Intergenic	BGLII|LTR|ERVK	-21446	NM_001311208	68527	Mm.27791	NM_026754	ENSMUSG00000026668	Ucma	1110017I16Rik|AW121955|Grp	upper zone of growth plate and cartilage matrix associated	protein-coding
mm_151438.1	chr19	57360961	57360980	+	1	NA	promoter-TSS (NM_145505)	promoter-TSS (NM_145505)	-39	NM_145505	226252	Mm.358870	NM_145505	ENSMUSG00000033478	Fam160b1	AI450540|mKIAA1600	family with sequence similarity 160, member B1	protein-coding
mm_109549.1	chr12	111712424	111712429	+	1	NA	promoter-TSS (NM_026511)	promoter-TSS (NM_026511)	527	NM_001324481	70369	Mm.44239	NM_027404	ENSMUSG00000049792	Bag5	1600025G07Rik|4930405J06Rik|Bag-5	BCL2-associated athanogene 5	protein-coding
mm_102959.1	chr11	69665059	69665120	-	1	NA	non-coding (NR_110993, exon 3 of 5)	non-coding (NR_110993, exon 3 of 5)	1081	NM_001291058	12514	Mm.15819	NM_009853	ENSMUSG00000018774	Cd68	Lamp4|Scard1|gp110	CD68 antigen	protein-coding
mm_127098.1	chr15	97790994	97791007	+	1	NA	3' UTR (NM_026353, exon 3 of 3)	3' UTR (NM_026353, exon 3 of 3)	6635	NM_026353	67739	Mm.28955	NM_026353	ENSMUSG00000081534	Slc48a1	4930570C03Rik	solute carrier family 48 (heme transporter), member 1	protein-coding
mm_94057.1	chr10	128298067	128298101	-	1	NA	promoter-TSS (NM_031252)	promoter-TSS (NM_031252)	0	NM_031252	83430	Mm.125482	NM_031252	ENSMUSG00000025383	Il23a	IL-23|p19	interleukin 23, alpha subunit p19	protein-coding
mm_6000.1	chr1	58962558	58962561	-	1	NA	intron (NM_172406, intron 1 of 15)	intron (NM_172406, intron 1 of 15)	10923	NM_172406	70827	Mm.222887	NM_172406	ENSMUSG00000026028	Trak2	2900022D04Rik|4733401O11Rik|AI480836|AW046271|Als2cr3|CALS-C|GRIF-1|GRIF1|OIP98|mKIAA0549	trafficking protein, kinesin binding 2	protein-coding
mm_17790.1	chr2	33086268	33086284	-	1	NA	intron (NM_178888, intron 1 of 28)	intron (NM_178888, intron 1 of 28)	928	NM_178888	99326	Mm.41290	NM_178888	ENSMUSG00000038860	Garnl3	AW120551	GTPase activating RANGAP domain-like 3	protein-coding
mm_30806.1	chr4	20041987	20041997	+	1	NA	promoter-TSS (NM_010281)	promoter-TSS (NM_010281)	-60	NM_010281	14590	Mm.20461	NM_010281	ENSMUSG00000073987	Ggh	gamma-GH	gamma-glutamyl hydrolase	protein-coding
mm_51665.1	chr6	86334010	86334011	+	1	NA	Intergenic	Intergenic	-31673	NM_025591	66488	Mm.422972	NM_025591	ENSMUSG00000057497	Fam136a	2010309E21Rik|AW124904|Hyccin	family with sequence similarity 136, member A	protein-coding
mm_153536.1	chr19	41916909	41916909	-	1	NA	intron (NM_023418, intron 3 of 3)	intron (NM_023418, intron 3 of 3)	5038	NM_023418	18648	Mm.16783	NM_023418	ENSMUSG00000011752	Pgam1	2310050F24Rik|Pgam-1	phosphoglycerate mutase 1	protein-coding
mm_7462.1	chr1	120476722	120476734	-	1	NA	exon (NM_010766, exon 16 of 17)	exon (NM_010766, exon 16 of 17)	28356	NM_010766	17167	Mm.1856	NM_010766	ENSMUSG00000026390	Marco	AI323439|Ly112|Scara2	macrophage receptor with collagenous structure	protein-coding
mm_102258.1	chr11	55311056	55311090	-	1	NA	exon (NM_001029988, exon 1 of 23)	exon (NM_001029988, exon 1 of 23)	1184	NM_001029988	245827	Mm.339363	NM_001029988	ENSMUSG00000055333	Fat2	EMI2|Fath2|Gm523|mKIAA0811	FAT atypical cadherin 2	protein-coding
mm_137075.1	chr17	20965581	20965624	+	1	NA	3' UTR (NM_016891, exon 15 of 15)	3' UTR (NM_016891, exon 15 of 15)	20148	NM_016891	51792	Mm.294138	NM_016891	ENSMUSG00000007564	Ppp2r1a	6330556D22Rik|PP2A|PR65	protein phosphatase 2, regulatory subunit A, alpha	protein-coding
mm_62593.1	chr7	105642338	105642342	+	1	NA	TTS (NM_019502)	TTS (NM_019502)	1800	NM_019502	14356	Mm.220330	NM_019502	ENSMUSG00000089847	Timm10b	Fxc1|Tim10b|Tim9b	translocase of inner mitochondrial membrane 10B	protein-coding
mm_49055.1	chr6	5048297	5048306	+	1	NA	intron (NM_181595, intron 3 of 15)	intron (NM_181595, intron 3 of 15)	144981	NM_181595	243725	Mm.332901	NM_181595	ENSMUSG00000032827	Ppp1r9a	2810430P21Rik|4930518N04Rik|5330407E15|A230094E16Rik|BB181831|NRB|mKIAA1222|neurabin-I	protein phosphatase 1, regulatory (inhibitor) subunit 9A	protein-coding
mm_109297.1	chr12	109559867	109559890	+	1	NA	non-coding (NR_003633, exon 5 of 5)	non-coding (NR_003633, exon 5 of 5)	-3814	NR_030427	791079		NR_030427	ENSMUSG00000076451	Mir770	Mirn770|mir-770|mmu-mir-770	microRNA 770	ncRNA
mm_81664.1	chr9	111021973	111021991	+	1	NA	exon (NM_008522, exon 3 of 17)	exon (NM_008522, exon 3 of 17)	2690	NM_008522	17002	Mm.282359	NM_008522	ENSMUSG00000032496	Ltf	Csp82|Lf|MMS10R|Ms10r	lactotransferrin	protein-coding
mm_110890.1	chr12	75583433	75583436	-	1	NA	intron (NM_012024, intron 2 of 13)	PB1|SINE|Alu	12766	NM_012024	26932	Mm.259626	NM_012024	ENSMUSG00000021051	Ppp2r5e	4633401M22Rik|AI449017|B56beta	protein phosphatase 2, regulatory subunit B', epsilon	protein-coding
mm_43137.1	chr5	125390372	125390407	+	1	NA	promoter-TSS (NM_019639)	promoter-TSS (NM_019639)	-372	NM_019639	22190	Mm.331	NM_019639	ENSMUSG00000008348	Ubc	2700054O04Rik|AI194771|Rps27a|TI-225|Uba52|Ubb	ubiquitin C	protein-coding
mm_150215.1	chr19	32975548	32975551	+	1	NA	Intergenic	Intergenic	217972	NM_008960	19211	Mm.245395	NM_008960	ENSMUSG00000013663	Pten	2310035O07Rik|A130070J02Rik|AI463227|B430203M17Rik|MMAC1|TEP1	phosphatase and tensin homolog	protein-coding
mm_99924.1	chr11	110968017	110968042	+	1	NA	promoter-TSS (NM_001252207)	promoter-TSS (NM_001252207)	-4	NM_010604	16517	Mm.30176	NM_010604	ENSMUSG00000051497	Kcnj16	6430410F18Rik|AI132396|Kir5.1	potassium inwardly-rectifying channel, subfamily J, member 16	protein-coding
mm_81885.1	chr9	119357575	119357604	+	1	NA	5' UTR (NM_001199568, exon 1 of 20)	5' UTR (NM_001199568, exon 1 of 20)	208	NM_001199568	102448	Mm.219497	NM_001033209	ENSMUSG00000035769	Xylb	AI132223|AI327421	xylulokinase homolog (H. influenzae)	protein-coding
mm_89602.1	chr10	95990279	95990287	+	1	NA	exon (NM_001001932, exon 4 of 29)	exon (NM_001001932, exon 4 of 29)	49620	NM_001001932	216238	Mm.210035	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding
mm_166613.1	chr6	71325427	71325436	+	1	NA	intron (NM_009858, intron 1 of 5)	intron (NM_009858, intron 1 of 5)	2619	NM_009858	12526	Mm.333148	NM_009858	ENSMUSG00000053044	Cd8b1	Cd8b|Ly-3|Ly-C|Lyt-3	CD8 antigen, beta chain 1	protein-coding
mm_35686.1	chr4	44025523	44025571	-	1	NA	exon (NM_001080385, exon 4 of 7)	exon (NM_001080385, exon 4 of 7)	12897	NM_001290470	12757	Mm.298875	NM_016760	ENSMUSG00000028478	Clta	AV026556|Lca	clathrin, light polypeptide (Lca)	protein-coding
mm_38161.1	chr4	135216384	135216396	-	1	NA	3' UTR (NM_013885, exon 6 of 6)	3' UTR (NM_013885, exon 6 of 6)	56370	NM_013885	29876	Mm.257765	NM_013885	ENSMUSG00000037242	Clic4	D0Jmb3|TU-74|mc3s5|mtCLIC	chloride intracellular channel 4 (mitochondrial)	protein-coding
mm_86519.1	chr10	7726062	7726083	+	1	NA	promoter-TSS (NM_011835)	promoter-TSS (NM_011835)	72	NM_011835	23924	Mm.28127	NM_011835	ENSMUSG00000019794	Katna1	-	katanin p60 (ATPase-containing) subunit A1	protein-coding
mm_66023.1	chr7	30606927	30606942	-	1	NA	exon (NM_026815, exon 5 of 8)	exon (NM_026815, exon 5 of 8)	5800	NM_026815	109637	Mm.25471	NM_026815	ENSMUSG00000006313	Upk1a	1110031P12Rik|AU019298|C87192|Tspan21|Upk1	uroplakin 1A	protein-coding
mm_173237.1	chrX	8145687	8145687	-	1	NA	non-coding (NR_033561, exon 1 of 3)	non-coding (NR_033561, exon 1 of 3)	193	NM_001166410	19652	Mm.128512	NM_016809	ENSMUSG00000031167	Rbm3	2600016C11Rik	RNA binding motif protein 3	protein-coding
mm_11929.1	chr2	52163726	52163728	+	1	NA	intron (NM_010889, intron 140 of 156)	intron (NM_010889, intron 140 of 156)	90890	NM_175238	51869	Mm.254530	NM_175238	ENSMUSG00000036202	Rif1	5730435J01Rik|6530403D07Rik|AU016181|AW549474|D2Ertd145e	replication timing regulatory factor 1	protein-coding
mm_140793.1	chr17	19629400	19629401	-	1	NA	Intergenic	RLTR50A|LTR|ERVK	-30999	NM_001104564	224572	Mm.469856	NM_001104564	ENSMUSG00000095961	Vmn2r102	EG224572	vomeronasal 2, receptor 102	protein-coding
mm_91201.1	chr10	21160893	21160911	-	1	NA	promoter-TSS (NM_001198914)	promoter-TSS (NM_001198914)	82	NM_001198914	17863	Mm.52109	NM_010848	ENSMUSG00000019982	Myb	AI550390|M16449|c-myb	myeloblastosis oncogene	protein-coding
mm_48207.1	chr5	137600651	137600740	-	1	NA	promoter-TSS (NM_001254762)	promoter-TSS (NM_001254762)	13	NM_001254762	68929	Mm.41355	NM_030037	ENSMUSG00000037221	Mospd3	1190005J19Rik|5133401H10Rik|Gtig2|R124	motile sperm domain containing 3	protein-coding
mm_58209.1	chr6	143947093	143947111	-	1	NA	promoter-TSS (NM_001347506)	promoter-TSS (NM_001347506)	4	NM_001347506	20678	Mm.1752	NM_011444	ENSMUSG00000041540	Sox5	A730017D01Rik|AI528773	SRY (sex determining region Y)-box 5	protein-coding
mm_86844.1	chr10	21571728	21571737	+	1	NA	Intergenic	Intergenic	-21413	NR_027968	67692	Mm.54306	NM_183266	ENSMUSG00000050844	1700020N01Rik	-	RIKEN cDNA 1700020N01 gene	ncRNA
mm_92522.1	chr10	78591936	78591942	-	1	NA	promoter-TSS (NM_027875)	promoter-TSS (NM_027875)	25	NM_027875	71709	Mm.86439	NM_027875	ENSMUSG00000032714	Syde1	1200008N06Rik|BB043000|mSYD1A	synapse defective 1, Rho GTPase, homolog 1 (C. elegans)	protein-coding
mm_53651.1	chr6	141138027	141138037	+	1	NA	Intergenic	Intergenic	-111237	NM_018779	54611	Mm.103728	NM_018779	ENSMUSG00000041741	Pde3a	A930022O17Rik|C87899	phosphodiesterase 3A, cGMP inhibited	protein-coding
mm_8290.1	chr1	143093797	143093807	-	1	NA	Intergenic	Intergenic	-546895	NM_020025	26878	Mm.285580	NM_020025	ENSMUSG00000033849	B3galt2	-	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 2	protein-coding
mm_6367.1	chr1	72236347	72236391	-	1	NA	Intergenic	Intergenic	-24062	NM_001005423	381269	Mm.422636	NM_001005423	ENSMUSG00000039395	Mreg	Gm974|Wdt2|dsu	melanoregulin	protein-coding
mm_66110.1	chr7	31041778	31041809	-	1	NA	promoter-TSS (NM_001111073)	promoter-TSS (NM_001111073)	46	NM_001111073	18301	Mm.1870	NM_008761	ENSMUSG00000009687	Fxyd5	EF-8|Oit2|RIC	FXYD domain-containing ion transport regulator 5	protein-coding
mm_167922.1	chrX	102189404	102189408	-	1	NA	promoter-TSS (NM_009094)	promoter-TSS (NM_009094)	-15	NM_009094	20102	Mm.66	NM_009094	ENSMUSG00000031320	Rps4x	Rps4|Rps4-1	ribosomal protein S4, X-linked	protein-coding
mm_44935.1	chr5	36397672	36397706	-	1	NA	exon (NM_030889, exon 1 of 27)	exon (NM_030889, exon 1 of 27)	450	NM_030889	81840	Mm.34113	NM_030889	ENSMUSG00000029093	Sorcs2	N28137|mKIAA1329	sortilin-related VPS10 domain containing receptor 2	protein-coding
mm_102345.1	chr11	58093111	58093151	-	1	NA	Intergenic	Intergenic	-11022	NM_026949	69125	Mm.28910	NM_026949	ENSMUSG00000020515	Cnot8	1500015I04Rik|1810022F04Rik|AA536816|AU015770|AU043059	CCR4-NOT transcription complex, subunit 8	protein-coding
mm_83139.1	chr9	40450251	40450259	-	1	NA	intron (NM_172768, intron 1 of 19)	intron (NM_172768, intron 1 of 19)	5509	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_44701.1	chr5	30588467	30588479	-	1	NA	exon (NM_010608, exon 1 of 2)	exon (NM_010608, exon 1 of 2)	146	NR_040427	100502829	Mm.39944	NR_040427	ENSMUSG00000053214	Gm9899	ENSMUSG00000053214	predicted gene 9899	ncRNA
mm_117785.1	chr13	97034342	97034365	-	1	NA	promoter-TSS (NM_001284205)	promoter-TSS (NM_001284205)	9	NM_025585	66479	Mm.390629	NM_025585	ENSMUSG00000052075	1700029F12Rik	-	RIKEN cDNA 1700029F12 gene	protein-coding
mm_96638.1	chr11	69326318	69326339	+	1	NA	promoter-TSS (NM_010599)	promoter-TSS (NM_010599)	70	NM_010599	16499	Mm.232472	NM_010599	ENSMUSG00000018470	Kcnab3	C330022D06Rik|Kcnab4|mKv(beta)4	potassium voltage-gated channel, shaker-related subfamily, beta member 3	protein-coding
mm_77303.1	chr8	117423089	117423125	-	1	NA	intron (NM_028941, intron 6 of 20)	intron (NM_028941, intron 6 of 20)	-29916	NR_106045	102466801		NR_106045	ENSMUSG00000099062	Mir7077	Gm27774|mmu-mir-7077	microRNA 7077	ncRNA
mm_154853.1	chrX	20549781	20549796	+	1	NA	promoter-TSS (NM_009060)	promoter-TSS (NM_009060)	-30	NM_009060	19733	Mm.2118	NM_009060	ENSMUSG00000023070	Rgn	AI265316|GNL|SMP30	regucalcin	protein-coding
mm_82354.1	chr9	14380974	14381033	-	1	NA	5' UTR (NM_028013, exon 1 of 2)	5' UTR (NM_028013, exon 1 of 2)	239	NM_028013	71946	Mm.41423	NM_028013	ENSMUSG00000037419	Endod1	2210414F18Rik|2310067E08Rik|C85344	endonuclease domain containing 1	protein-coding
mm_58948.1	chr7	18647074	18647094	+	1	NA	3' UTR (NM_027403, exon 5 of 5)	3' UTR (NM_027403, exon 5 of 5)	9641	NM_027403	72242	Mm.326858	NM_027403	ENSMUSG00000070796	Psg21	1600019C01Rik|1600025N01Rik|1600026N13Rik|cea8	pregnancy-specific glycoprotein 21	protein-coding
mm_63575.1	chr7	128117829	128117848	+	1	NA	3' UTR (NM_008401, exon 30 of 30)	3' UTR (NM_008401, exon 30 of 30)	-11730	NM_021334	16411	Mm.22378	NM_021334	ENSMUSG00000030789	Itgax	AI449405|Cd11c|Cr4|N418	integrin alpha X	protein-coding
mm_85613.1	chr9	107609183	107609214	-	1	NA	promoter-TSS (NM_001291539)	promoter-TSS (NM_001291539)	43	NM_001042779	20347	Mm.4083	NM_009153	ENSMUSG00000057969	Sema3b	SemA|Semaa|sema5|semaV	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B	protein-coding
mm_43212.1	chr5	129501224	129501253	+	1	NA	promoter-TSS (NM_172276)	promoter-TSS (NM_172276)	7	NM_172276	231769	Mm.288714	NM_172276	ENSMUSG00000029439	Sfswap	1190005N23Rik|6330437E22Rik|AI197402|AW212079|SWAP|Sfrs8|Srsf8	splicing factor, suppressor of white-apricot homolog (Drosophila)	protein-coding
mm_30730.1	chr4	13785082	13785120	+	1	NA	5' UTR (NM_009822, exon 1 of 11)	5' UTR (NM_009822, exon 1 of 11)	319	NM_009822	12395	Mm.4909	NM_009822	ENSMUSG00000006586	Runx1t1	Cbfa2t1h|ETO|MTG8	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	protein-coding
mm_46768.1	chr5	112269530	112269551	-	1	NA	TTS (NM_001312894)	TTS (NM_001312894)	-7151	NM_001326590	22022	Mm.250631	NM_009419	ENSMUSG00000029344	Tpst2	AI448750|D5Ucla3|Tango13b|grm|grt	protein-tyrosine sulfotransferase 2	protein-coding
mm_158859.1	chrY	897783	897800	+	1	NA	promoter-TSS (NM_011419)	promoter-TSS (NM_011419)	3	NM_011419	20592	Mm.262676	NM_011419	ENSMUSG00000056673	Kdm5d	HY|Jarid1d|Smcy	lysine (K)-specific demethylase 5D	protein-coding
mm_39594.1	chr5	23501560	23501574	+	1	NA	exon (NM_026984, exon 26 of 26)	exon (NM_026984, exon 26 of 26)	67138	NM_026984	69188	Mm.205190	NM_026984	ENSMUSG00000029004	Kmt2e	1810033J14Rik|9530077A04Rik|D230038D11Rik|Mll5|NKp44L	lysine (K)-specific methyltransferase 2E	protein-coding
mm_151482.1	chr19	58676274	58676289	+	1	NA	exon (NM_026925, exon 7 of 13)	exon (NM_026925, exon 7 of 13)	5916	NM_026925	69060	Mm.20407	NM_026925	ENSMUSG00000046008	Pnlip	1810007A24Rik|PL|PTL	pancreatic lipase	protein-coding
mm_160210.1	chr7	96550172	96550172	+	1	NA	exon (NM_011858, exon 4 of 33)	exon (NM_011858, exon 4 of 33)	-208208	NR_046043	670727	Mm.421352	NR_046043	ENSMUSG00000085751	Gm15412	OTTMUSG00000021245	predicted gene 15412	ncRNA
mm_157449.1	chrX	42113842	42113845	-	1	NA	Intergenic	RMER4B|LTR|ERVK	-35569	NM_001077712	20843	Mm.290422	NM_021465	ENSMUSG00000025862	Stag2	9230105L23Rik|B230112I07Rik|SA-2|SAP2	stromal antigen 2	protein-coding
mm_87564.1	chr10	56224981	56224984	+	1	NA	intron (NM_001033385, intron 1 of 32)	PB1D10|SINE|Alu	3707	NM_001033385	544696	Mm.411188	NM_001033385	ENSMUSG00000038122	Tbc1d32	Bromi|D630037F22Rik|b2b2284Clo	TBC1 domain family, member 32	protein-coding
mm_66273.1	chr7	37423049	37423052	-	1	NA	Intergenic	PB1D10|SINE|Alu	346702	NM_172385	243937	Mm.322505	NM_172385	ENSMUSG00000043456	Zfp536	9630010P11Rik|Znf536|mKIAA0390	zinc finger protein 536	protein-coding
mm_110903.1	chr12	75735634	75735712	-	1	NA	promoter-TSS (NM_030750)	promoter-TSS (NM_030750)	56	NM_030750	81535	Mm.280199	NM_030750	ENSMUSG00000021054	Sgpp1	AI463453|SPP|SPP1|Spph1	sphingosine-1-phosphate phosphatase 1	protein-coding
mm_62552.1	chr7	102441912	102441963	+	1	NA	5' UTR (NM_009103, exon 1 of 19)	5' UTR (NM_009103, exon 1 of 19)	242	NM_009103	20133	Mm.197486	NM_009103	ENSMUSG00000030978	Rrm1	RnrM1	ribonucleotide reductase M1	protein-coding
mm_81581.1	chr9	110422509	110422529	+	1	NA	3' UTR (NM_008694, exon 4 of 4)	3' UTR (NM_008694, exon 4 of 4)	2711	NM_008694	18054	Mm.236225	NM_008694	ENSMUSG00000032484	Ngp	bectenecin	neutrophilic granule protein	protein-coding
mm_147793.1	chr18	61652387	61652397	-	1	NA	non-coding (NR_045402, exon 3 of 5)	non-coding (NR_045402, exon 3 of 5)	-3134	NR_029601	387161		NR_029601	ENSMUSG00000065445	Mir143	Mirn143|mir-143|mmu-mir-143	microRNA 143	ncRNA
mm_115085.1	chr13	102693650	102693660	+	1	NA	promoter-TSS (NM_008533)	promoter-TSS (NM_008533)	97	NM_008533	17079	Mm.373974	NM_008533	ENSMUSG00000021624	Cd180	F630107B15|Ly78|RP105	CD180 antigen	protein-coding
mm_157635.1	chrX	57181480	57181486	-	1	NA	Intergenic	Intergenic	-19154	NR_038463	100502842	Mm.164733	NR_038463	ENSMUSG00000085808	Gm14718	OTTMUSG00000017790	predicted gene 14718	ncRNA
mm_40382.1	chr5	52368792	52368808	+	1	NA	3' UTR (NM_011435, exon 2 of 2)	3' UTR (NM_011435, exon 2 of 2)	4996	NM_011435	20657	Mm.2407	NM_011435	ENSMUSG00000072941	Sod3	AI314465|EC-SOD	superoxide dismutase 3, extracellular	protein-coding
mm_16334.1	chr2	174330013	174330047	+	1	NA	promoter-TSS (NM_001077510)	promoter-TSS (NM_001077510)	-40	NM_201616	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_100868.1	chr11	5898618	5898632	-	1	NA	intron (NM_022879, intron 1 of 6)	intron (NM_022879, intron 1 of 6)	157	NM_022879	17898	Mm.46514	NM_022879	ENSMUSG00000020469	Myl7	MLC-2alpha|MLC2a|MYL2A|Mylc2a|RLC-A	myosin, light polypeptide 7, regulatory	protein-coding
mm_154556.1	chrM	15631	15667	-	1	NA	NA	Intergenic	NA	NA								
mm_16187.1	chr2	172977683	172977695	+	1	NA	Intergenic	Intergenic	-2153	NM_012046	26972	Mm.23495	NM_012046	ENSMUSG00000005883	Spo11	AI449549|Spo11a|Spo11b	SPO11 meiotic protein covalently bound to DSB	protein-coding
mm_8534.1	chr1	155054803	155054811	-	1	NA	Intergenic	Intergenic	44829	NM_010500	15939	Mm.12246	NM_010500	ENSMUSG00000056708	Ier5	-	immediate early response 5	protein-coding
mm_31858.1	chr4	78773815	78773846	+	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	179783	NR_131142	623726		NR_131142		A430085M09Rik	EG623726	RIKEN cDNA A430085M09 gene	ncRNA
mm_21311.1	chr2	157098504	157098521	-	1	NA	3' UTR (NM_001139520, exon 17 of 17)	3' UTR (NM_001139520, exon 17 of 17)	11457	NM_001177439	383766	Mm.480305	NM_001177439	ENSMUSG00000074628	Tldc2	Gm1332	TBC/LysM associated domain containing 2	protein-coding
mm_11310.1	chr2	30267369	30267400	+	1	NA	intron (NM_172267, intron 2 of 11)	intron (NM_172267, intron 2 of 11)	565	NM_001252570	227696	Mm.297949	NM_172267	ENSMUSG00000079484	Phyhd1	-	phytanoyl-CoA dioxygenase domain containing 1	protein-coding
mm_132218.1	chr16	32630843	32630987	+	1	NA	3' UTR (NM_011638, exon 19 of 19)	3' UTR (NM_011638, exon 19 of 19)	-13728	NM_001110147	51789	Mm.251115	NM_016788	ENSMUSG00000022791	Tnk2	Ack|Ack-1|Ack1|Cdgip|Pyk1	tyrosine kinase, non-receptor, 2	protein-coding
mm_74121.1	chr8	123117388	123117404	+	1	NA	promoter-TSS (NM_170684)	promoter-TSS (NM_170684)	22	NM_170684	102278	Mm.36434	NM_170684	ENSMUSG00000034796	Cpne7	AW047065	copine VII	protein-coding
mm_17124.1	chr2	24763157	24763178	-	1	NA	promoter-TSS (NM_001042528)	promoter-TSS (NM_001042528)	-15	NM_007579	12287	Mm.4424	NM_007579	ENSMUSG00000004113	Cacna1b	AW050276|AW060892|AW822256|BIII|Cav2.2|Cchn1a|alpha(1B)	calcium channel, voltage-dependent, N type, alpha 1B subunit	protein-coding
mm_163740.1	chr13	119707247	119707370	+	1	NA	3' UTR (NM_001291439, exon 10 of 10)	3' UTR (NM_001291439, exon 10 of 10)	16957	NM_001291439	208715	Mm.61526	NM_145942	ENSMUSG00000093930	Hmgcs1	B130032C06Rik	3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1	protein-coding
mm_16891.1	chr2	13219057	13219071	-	1	NA	exon (NM_009105, exon 5 of 9)	exon (NM_009105, exon 5 of 9)	52351	NM_009105	20163	Mm.905	NM_009105	ENSMUSG00000026727	Rsu1	RsuI|rsp-1	Ras suppressor protein 1	protein-coding
mm_17152.1	chr2	25214617	25214623	-	1	NA	promoter-TSS (NM_028961)	promoter-TSS (NM_028961)	10	NM_028961	74472	Mm.176944	NM_028961	ENSMUSG00000036770	Stpg3	4933433C11Rik	sperm tail PG rich repeat containing 3	protein-coding
mm_96400.1	chr11	67250748	67250754	+	1	NA	intron (NM_010855, intron 21 of 39)	intron (NM_010855, intron 21 of 39)	12939	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_17448.1	chr2	28539760	28539771	-	1	NA	intron (NM_001145836, intron 1 of 17)	intron (NM_001145836, intron 1 of 17)	6301	NM_001145836	19730	Mm.5236	NM_009058	ENSMUSG00000026821	Ralgds	Gnds|Rgds|mKIAA1308	ral guanine nucleotide dissociation stimulator	protein-coding
mm_77301.1	chr8	117258028	117258031	-	1	NA	intron (NM_001163262, intron 1 of 20)	intron (NM_001163262, intron 1 of 20)	1010	NM_001163262	74440	Mm.233181	NM_028941	ENSMUSG00000034390	Cmip	4933407C03Rik|5830471E12Rik|AI314065|AI464126	c-Maf inducing protein	protein-coding
mm_109032.1	chr12	104100983	104100998	+	1	NA	promoter-TSS (NM_172953)	promoter-TSS (NM_172953)	-123	NM_172953	268591	Mm.73172	NM_172953	ENSMUSG00000041550	Serpina5	4933415L04|PAI-3|Pci	serine (or cysteine) peptidase inhibitor, clade A, member 5	protein-coding
mm_138469.1	chr17	35187957	35187964	+	1	NA	intron (NM_010734, intron 1 of 3)	ID_B1|SINE|B4	480	NM_010734	16988	Mm.19379	NM_010734	ENSMUSG00000073412	Lst1	B144	leukocyte specific transcript 1	protein-coding
mm_133488.1	chr16	90220709	90220725	+	1	NA	promoter-TSS (NM_011434)	promoter-TSS (NM_011434)	-25	NM_011434	20655	Mm.276325	NM_011434	ENSMUSG00000022982	Sod1	B430204E11Rik|Cu/Zn-SOD|CuZnSOD|Ipo-1|Ipo1|SODC|Sod-1	superoxide dismutase 1, soluble	protein-coding
mm_62630.1	chr7	107595240	107595263	+	1	NA	5' UTR (NM_008905, exon 1 of 25)	5' UTR (NM_008905, exon 1 of 25)	200	NM_008905	19024	Mm.2817	NM_008905	ENSMUSG00000036528	Ppfibp2	Cclp1	PTPRF interacting protein, binding protein 2 (liprin beta 2)	protein-coding
mm_136886.1	chr17	13010315	13010321	+	1	NA	intron (NM_013671, intron 2 of 4)	intron (NM_013671, intron 2 of 4)	2479	NM_013671	20656	Mm.290876	NM_013671	ENSMUSG00000006818	Sod2	MnSOD|Sod-2	superoxide dismutase 2, mitochondrial	protein-coding
mm_167111.1	chr7	114152606	114152610	+	1	NA	Intergenic	(GA)n|Simple_repeat|Simple_repeat	-34827	NM_025846	66922	Mm.276572	NM_025846	ENSMUSG00000055723	Rras2	2610016H24Rik|C86394|TC21	related RAS viral (r-ras) oncogene 2	protein-coding
mm_53941.1	chr6	5054635	5054636	-	1	NA	intron (NM_181595, intron 3 of 15)	intron (NM_181595, intron 3 of 15)	139311	NM_011134	18979	Mm.237657	NM_011134	ENSMUSG00000002588	Pon1	Pon	paraoxonase 1	protein-coding
mm_40848.1	chr5	73380583	73380592	+	1	NA	Intergenic	Intergenic	-25491	NM_181323	231293	Mm.280211	NM_181323	ENSMUSG00000029154	Cwh43	C130090K23Rik|imds-60	cell wall biogenesis 43 C-terminal homolog	protein-coding
mm_22966.1	chr3	32529639	32529643	+	1	NA	5' UTR (NM_024200, exon 1 of 18)	5' UTR (NM_024200, exon 1 of 18)	159	NM_024200	67414	Mm.290414	NM_024200	ENSMUSG00000027668	Mfn1	2310002F04Rik|6330416C07Rik|D3Ertd265e|HR2|mKIAA4032	mitofusin 1	protein-coding
mm_106970.1	chr12	8947963	8947980	+	1	NA	promoter-TSS (NM_010770)	promoter-TSS (NM_010770)	42	NM_010770	17182	Mm.42226	NM_010770	ENSMUSG00000020583	Matn3	AV009181	matrilin 3	protein-coding
mm_138365.1	chr17	35000934	35000944	+	1	NA	promoter-TSS (NM_011690)	promoter-TSS (NM_011690)	32	NM_011690	22321	Mm.28420	NM_011690	ENSMUSG00000007029	Vars	Bat6|D17H6S56E|G7a|Vars2	valyl-tRNA synthetase	protein-coding
mm_40146.1	chr5	35279186	35279218	+	1	NA	5' UTR (NM_007418, exon 1 of 1)	5' UTR (NM_007418, exon 1 of 1)	636	NM_007418	11553	Mm.57205	NM_007418	ENSMUSG00000045318	Adra2c	Adra-2c|[a]2C|alpha2-C4|alpha2C	adrenergic receptor, alpha 2c	protein-coding
mm_104889.1	chr11	99566496	99566498	-	1	NA	exon (NM_023511, exon 1 of 1)	exon (NM_023511, exon 1 of 1)	133	NM_023511	69473	Mm.158281	NM_023511	ENSMUSG00000047564	Krtap3-1	2310003K17Rik|KAP3.1|KRTAP3.1	keratin associated protein 3-1	protein-coding
mm_75036.1	chr8	32454851	32454874	-	1	NA	Intergenic	Intergenic	302967	NR_046039	666589	Mm.367675	NR_046039		Gm8179	EG666589	predicted gene 8179	ncRNA
mm_23566.1	chr3	63295525	63295598	+	1	NA	promoter-TSS (NM_008604)	promoter-TSS (NM_008604)	126	NM_001289462	17380	Mm.296022	NM_008604	ENSMUSG00000027820	Mme	6030454K05Rik|C85356|CALLA|CD10|NEP|SFE	membrane metallo endopeptidase	protein-coding
mm_81796.1	chr9	115200886	115200889	+	1	NA	intron (NM_148958, intron 4 of 9)	intron (NM_148958, intron 4 of 9)	81183	NR_029430	111186	Mm.484753	NR_029430		Stmn1-rs1	Lag-rs1|Lap18-rs1	stathmin 1, related sequence 1	pseudo
mm_125633.1	chr15	62037997	62038058	+	1	NA	promoter-TSS (NR_003368)	promoter-TSS (NR_003368)	41	NR_003368	19296	Mm.4608	NM_011222	ENSMUSG00000097039	Pvt1	Ayu21-84Imeg|Gt(pU21)84Imeg|Mis-1|Mlvi-1|Pvt-1	plasmacytoma variant translocation 1	ncRNA
mm_17004.1	chr2	18767054	18767066	-	1	NA	Intergenic	CpG	-6198	NR_126079	100041479	Mm.393659	NR_126079	ENSMUSG00000092353	Gm3363	-	predicted gene 3363	ncRNA
mm_42980.1	chr5	123228217	123228227	+	1	NA	promoter-TSS (NM_026000)	promoter-TSS (NM_026000)	32	NM_026000	67151	Mm.278997	NM_026000	ENSMUSG00000029440	Psmd9	1500011J20Rik|2610202L11Rik|Bridge-1|P27	proteasome (prosome, macropain) 26S subunit, non-ATPase, 9	protein-coding
mm_61838.1	chr7	88288944	88288955	+	1	NA	3' UTR (NM_001311790, exon 4 of 4)	3' UTR (NM_001311790, exon 4 of 4)	10864	NM_001311790	13032	Mm.89295	NM_009982	ENSMUSG00000030560	Ctsc	AI047818|CatC|DPP1|DPPI	cathepsin C	protein-coding
mm_88658.1	chr10	79996516	79996524	+	1	NA	intron (NR_038088, intron 1 of 4)	intron (NR_038088, intron 1 of 4)	-1088	NM_001347081	27403	Mm.103351	NM_013850	ENSMUSG00000035722	Abca7	ABCX|Abc51	ATP-binding cassette, sub-family A (ABC1), member 7	protein-coding
mm_161625.1	chr16	74411113	74411113	-	1	NA	promoter-TSS (NM_175549)	promoter-TSS (NM_175549)	-201	NM_175549	268902	Mm.171736	NM_175549	ENSMUSG00000052516	Robo2	2600013A04Rik|9430089E08Rik|BB097918|D230004I22Rik|mKIAA1568	roundabout guidance receptor 2	protein-coding
mm_113910.1	chr13	49421230	49421303	+	1	NA	promoter-TSS (NM_199056)	promoter-TSS (NM_199056)	43	NM_199056	75678	Mm.390586	NM_199056	ENSMUSG00000021385	Ippk	1810043M15Rik|InsP6	inositol 1,3,4,5,6-pentakisphosphate 2-kinase	protein-coding
mm_127103.1	chr15	97821761	97821776	+	1	NA	intron (NM_001204275, intron 1 of 24)	intron (NM_001204275, intron 1 of 24)	-6905	NM_001204281	56233	Mm.384027	NM_019572	ENSMUSG00000022475	Hdac7	5830434K02Rik|HD7|HD7a|Hdac7a|mFLJ00062	histone deacetylase 7	protein-coding
mm_104517.1	chr11	96050220	96050253	-	1	NA	3' UTR (NM_172300, exon 7 of 7)	3' UTR (NM_172300, exon 7 of 7)	15128	NM_172300	268470	Mm.38802	NM_172300	ENSMUSG00000014349	Ube2z	AW049199|C030047H17Rik|D11Moh35	ubiquitin-conjugating enzyme E2Z	protein-coding
mm_134776.1	chr16	23976245	23976294	-	1	NA	intron (NM_009744, intron 3 of 9)	RSINE1|SINE|B4	12343	NM_009744	12053	Mm.347398	NM_009744	ENSMUSG00000022508	Bcl6	Bcl5	B cell leukemia/lymphoma 6	protein-coding
mm_141539.1	chr17	31856592	31856613	-	1	NA	promoter-TSS (NM_010831)	promoter-TSS (NM_010831)	-810	NM_010831	17691	Mm.290941	NM_010831	ENSMUSG00000024042	Sik1	Msk|Sik|Snf1lk	salt inducible kinase 1	protein-coding
mm_16530.1	chr2	181557350	181557360	+	1	NA	Intergenic	B2_Mm2|SINE|B2	-21125	NR_027289	100271841	Mm.438007	NR_027289	ENSMUSG00000010492	Uckl1os	Gm16119|OTTMUSG00000030649	uridine-cytidine kinase 1-like 1, opposite strand	ncRNA
mm_160457.1	chr8	107551311	107551311	+	1	NA	promoter-TSS (NR_029553)	promoter-TSS (NR_029553)	67	NR_029553	387158		NR_029553	ENSMUSG00000065439	Mir140	Mirn140|mir-140|mmu-mir-140	microRNA 140	ncRNA
mm_48464.1	chr5	140829760	140829771	-	1	NA	intron (NM_010302, intron 1 of 3)	intron (NM_010302, intron 1 of 3)	666	NM_010302	14673	Mm.370185	NM_010302	ENSMUSG00000000149	Gna12	AI414047|AI504261|Galpha12	guanine nucleotide binding protein, alpha 12	protein-coding
mm_115466.1	chr13	119429670	119429680	+	1	NA	intron (NM_145457, intron 1 of 10)	CpG	773	NM_145457	218693	Mm.490243	NM_145457	ENSMUSG00000025451	Paip1	PAIP-1	polyadenylate binding protein-interacting protein 1	protein-coding
mm_71842.1	chr8	68904867	68904880	+	1	NA	3' UTR (NM_008509, exon 10 of 10)	3' UTR (NM_008509, exon 10 of 10)	24318	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_114775.1	chr13	88821709	88821719	+	1	NA	5' UTR (NM_001037987, exon 1 of 11)	5' UTR (NM_001037987, exon 1 of 11)	242	NM_001037987	13612	Mm.125580	NM_010103	ENSMUSG00000034488	Edil3	Del-1|Del1	EGF-like repeats and discoidin I-like domains 3	protein-coding
mm_47721.1	chr5	130013440	130013473	-	1	NA	exon (NM_133768, exon 11 of 17)	exon (NM_133768, exon 11 of 17)	-10628	NM_010368	110006	Mm.3317	NM_010368	ENSMUSG00000025534	Gusb	AI747421|Gur|Gus|Gus-r|Gus-s|Gus-t|Gus-u|Gut|asd|g	glucuronidase, beta	protein-coding
mm_145849.1	chr18	65450699	65450709	+	1	NA	intron (NM_172833, intron 6 of 15)	intron (NM_172833, intron 6 of 15)	19707	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_55727.1	chr6	76210622	76210623	-	1	NA	Intergenic	B1_Mus1|SINE|Alu	-1032095	NM_028880	74342	Mm.292568	NM_028880	ENSMUSG00000060780	Lrrtm1	4632401D06Rik|AW125451	leucine rich repeat transmembrane neuronal 1	protein-coding
mm_15868.1	chr2	164834016	164834048	+	1	NA	promoter-TSS (NM_001082974)	promoter-TSS (NM_001082974)	259	NM_008906	19025	Mm.359633	NM_008906	ENSMUSG00000017760	Ctsa	AU019505|PPCA|Ppgb	cathepsin A	protein-coding
mm_121852.1	chr14	20663653	20663671	-	1	NA	intron (NM_001310431, intron 3 of 3)	intron (NM_001310431, intron 3 of 3)	912	NM_001310432	68760	Mm.35789	NM_175132	ENSMUSG00000039376	Synpo2l	1110054M18Rik|Chap	synaptopodin 2-like	protein-coding
mm_157719.1	chrX	70344287	70344311	-	1	NA	3' UTR (NM_010498, exon 9 of 9)	3' UTR (NM_010498, exon 9 of 9)	20786	NM_010498	15931	Mm.233083	NM_010498	ENSMUSG00000035847	Ids	AW214631	iduronate 2-sulfatase	protein-coding
mm_40748.1	chr5	66745833	66745837	+	1	NA	promoter-TSS (NM_001001980)	promoter-TSS (NM_001001980)	-5	NM_001001980	77569	Mm.374778	NM_001001980	ENSMUSG00000037736	Limch1	3732412D22Rik|mKIAA1102	LIM and calponin homology domains 1	protein-coding
mm_82482.1	chr9	18299382	18299400	-	1	NA	intron (NM_025844, intron 2 of 10)	intron (NM_025844, intron 2 of 10)	7124	NM_025844	66917	Mm.103534	NM_025844	ENSMUSG00000001774	Chordc1	1110001O09Rik|AA409036|Chp-1|morgana	cysteine and histidine-rich domain (CHORD)-containing, zinc-binding protein 1	protein-coding
mm_5046.1	chr1	194620102	194620110	+	1	NA	5' UTR (NM_008882, exon 1 of 32)	5' UTR (NM_008882, exon 1 of 32)	277	NM_008882	18845	Mm.2251	NM_008882	ENSMUSG00000026640	Plxna2	2810428A13Rik|AA589422|AW457381|OCT|PlexA2|Plxn2|mKIAA0463	plexin A2	protein-coding
mm_32128.1	chr4	99037536	99037544	+	1	NA	exon (NM_013913, exon 6 of 7)	exon (NM_013913, exon 6 of 7)	6586	NM_013913	30924	Mm.28341	NM_013913	ENSMUSG00000028553	Angptl3	hypl	angiopoietin-like 3	protein-coding
mm_142619.1	chr17	47010412	47010430	-	1	NA	5' UTR (NM_001177374, exon 1 of 47)	5' UTR (NM_001177374, exon 1 of 47)	111	NM_146078	224826	Mm.28234	NM_146078	ENSMUSG00000023977	Ubr2	9930021A08Rik|AI462103|AW540746|E130209G04Rik|ENSMUSG00000043296|mKIAA0349	ubiquitin protein ligase E3 component n-recognin 2	protein-coding
mm_136439.1	chr16	94526831	94526839	-	1	NA	promoter-TSS (NM_007834)	promoter-TSS (NM_007834)	-206	NM_007834	13185	Mm.7472	NM_007834	ENSMUSG00000022898	Dscr3	AW538125|Dcra	Down syndrome critical region gene 3	protein-coding
mm_162714.1	chr10	29357771	29357777	+	1	NA	promoter-TSS (NM_001284279)	promoter-TSS (NM_001284279)	-61	NM_001284279	68031	Mm.28930	NM_026518	ENSMUSG00000038876	Rnf146	2610509H23Rik|Iduna	ring finger protein 146	protein-coding
mm_122732.1	chr14	52328450	52328473	-	1	NA	5' UTR (NM_015772, exon 1 of 2)	5' UTR (NM_015772, exon 1 of 2)	209	NM_015772	50524	Mm.39487	NM_015772	ENSMUSG00000049532	Sall2	AI225809|AW559097|Msal-2|Sal-2|mKIAA0360|p150(Sal2)	sal-like 2 (Drosophila)	protein-coding
mm_129574.1	chr15	79733751	79733760	-	1	NA	intron (NM_001205346, intron 8 of 17)	intron (NM_001205346, intron 8 of 17)	8781	NM_194342	223697	Mm.202715	NM_194342	ENSMUSG00000042524	Sun2	B230369L08Rik|C030011B15|Unc84b	Sad1 and UNC84 domain containing 2	protein-coding
mm_76599.1	chr8	90298405	90298409	-	1	NA	intron (NM_172913, intron 1 of 6)	ORR1B1|LTR|ERVL-MaLR	49845	NM_172913	244579	Mm.302755	NM_172913	ENSMUSG00000043668	Tox3	500-9|BC052044|C230068E13|CAGF9|Tnrc9	TOX high mobility group box family member 3	protein-coding
mm_42335.1	chr5	114903375	114903389	+	1	NA	intron (NM_011854, intron 3 of 5)	intron (NM_011854, intron 3 of 5)	6448	NM_011854	23962	Mm.228363	NM_011854	ENSMUSG00000029561	Oasl2	M1204|Mmu-OASL|Oasl	2'-5' oligoadenylate synthetase-like 2	protein-coding
mm_26465.1	chr3	144155925	144155935	+	1	NA	Intergenic	LTR50|LTR|ERVL	46402	NM_001161770	16911	Mm.29187	NM_010723	ENSMUSG00000028266	Lmo4	A730077C12Rik|Crp3|Etohi4	LIM domain only 4	protein-coding
mm_108224.1	chr12	77208288	77208304	+	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	-29808	NM_001252614	53618	Mm.35628	NM_016893	ENSMUSG00000021065	Fut8	-	fucosyltransferase 8	protein-coding
mm_21438.1	chr2	158610629	158610648	-	1	NA	promoter-TSS (NM_009508)	promoter-TSS (NM_009508)	85	NR_040358	100045469	Mm.143404	NR_040358	ENSMUSG00000086496	Gm14204	OTTMUSG00000015935	predicted gene 14204	ncRNA
mm_35702.1	chr4	44167619	44167654	-	1	NA	promoter-TSS (NM_175201)	promoter-TSS (NM_175201)	-98	NM_175201	73469	Mm.262859	NM_175201	ENSMUSG00000035696	Rnf38	1700065B19Rik|2610202O07Rik|AA673263|Oip1	ring finger protein 38	protein-coding
mm_111164.1	chr12	83570927	83570929	-	1	NA	intron (NM_183154, intron 3 of 11)	intron (NM_183154, intron 3 of 11)	26219	NM_183154	217695	Mm.59257	NM_183154	ENSMUSG00000042628	Zfyve1	DFCP1|G630053K23|TAFF1|ZNFN2A1|mKIAA1589	zinc finger, FYVE domain containing 1	protein-coding
mm_169797.1	chr16	16507191	16507199	+	1	NA	intron (NM_001301817, intron 1 of 16)	L1Md_T|LINE|L1	20216	NM_001301818	224014	Mm.256131	NM_139232	ENSMUSG00000022788	Fgd4	9030023J02Rik|9330209B17Rik|Frabp|ZFYVE6	FYVE, RhoGEF and PH domain containing 4	protein-coding
mm_114164.1	chr13	55422424	55422438	+	1	NA	exon (NM_021489, exon 4 of 14)	exon (NM_021489, exon 4 of 14)	4373	NM_021489	58992	Mm.42224	NM_021489	ENSMUSG00000021492	F12	FXII|HAF	coagulation factor XII (Hageman factor)	protein-coding
mm_94642.1	chr11	16914740	16914743	+	1	NA	TTS (NM_207655)	TTS (NM_207655)	36541	NR_110421	72735	Mm.268598	NR_015469		Eldr	2810442I21Rik|4930500E12Rik|Fabl	Egfr long non-coding downstream RNA	ncRNA
mm_40147.1	chr5	35361550	35361565	+	1	NA	promoter-TSS (NR_046060)	promoter-TSS (NR_046060)	4	NR_046060	74429	Mm.399502	NR_046060	ENSMUSG00000106762	4930478P22Rik	4933405A14Rik	RIKEN cDNA 4930478P22 gene	ncRNA
mm_42569.1	chr5	117161994	117162019	+	1	NA	intron (NM_001081308, intron 1 of 19)	(TTTG)n|Simple_repeat|Simple_repeat	28418	NM_183306	330177	Mm.24343	NM_183306	ENSMUSG00000061288	Taok3	2900006A08Rik|A130052D22|A430105I05Rik	TAO kinase 3	protein-coding
mm_154216.1	chr19	59345225	59345236	-	1	NA	exon (NM_001033222, exon 1 of 5)	exon (NM_001033222, exon 1 of 5)	550	NM_001033222	107368	Mm.27250	NM_001033222	ENSMUSG00000074746	Pdzd8	A630041P07Rik|AV329468|AW228944|Pdzk8	PDZ domain containing 8	protein-coding
mm_2324.1	chr1	92379625	92379640	+	1	NA	Intergenic	Intergenic	84910	NR_105865	102465542		NR_105865	ENSMUSG00000098288	Mir6900	Gm27708|mmu-mir-6900	microRNA 6900	ncRNA
mm_1299.1	chr1	64532892	64532900	+	1	NA	promoter-TSS (NM_009952)	promoter-TSS (NM_009952)	92	NM_001037726	12912	Mm.422634	NM_009952	ENSMUSG00000025958	Creb1	2310001E10Rik|3526402H21Rik|AV083133|Creb|Creb-1	cAMP responsive element binding protein 1	protein-coding
mm_102843.1	chr11	69366460	69366470	-	1	NA	intron (NM_146019, intron 1 of 39)	intron (NM_146019, intron 1 of 39)	2961	NM_146019	216848	Mm.178246	NM_146019	ENSMUSG00000018474	Chd3	2600010P09Rik|AF020312|Chd7|Prp7|Prp9-1	chromodomain helicase DNA binding protein 3	protein-coding
mm_77626.1	chr8	123982808	123982880	-	1	NA	5' UTR (NM_019552, exon 1 of 13)	5' UTR (NM_019552, exon 1 of 13)	278	NM_019552	56199	Mm.274243	NM_019552	ENSMUSG00000031974	Abcb10	Abc-me|Abcb12	ATP-binding cassette, sub-family B (MDR/TAP), member 10	protein-coding
mm_18276.1	chr2	52399784	52399807	-	1	NA	3' UTR (NM_182994, exon 6 of 6)	3' UTR (NM_182994, exon 6 of 6)	25079	NM_182994	75423	Mm.314378	NM_182994	ENSMUSG00000036093	Arl5a	2410015N24Rik|2810410P22Rik|AA408731|AW610751|Arl5|T25534	ADP-ribosylation factor-like 5A	protein-coding
mm_151583.1	chr19	61224553	61224610	+	1	NA	3' UTR (NM_009970, exon 12 of 12)	3' UTR (NM_009970, exon 12 of 12)	3837	NM_009970	12982	Mm.287228	NM_009970	ENSMUSG00000059326	Csf2ra	CD116|Csfgmra|GM-CSF-Ra|GM-CSFR	colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)	protein-coding
mm_67182.1	chr7	73816447	73816453	-	1	NA	promoter-TSS (NR_077222)	promoter-TSS (NR_077222)	53	NR_077222	100579147	Mm.109205	NR_077222	ENSMUSG00000074067	Gm10619	4932443D20|ENSMUSG00000074067	predicted gene 10619	ncRNA
mm_20542.1	chr2	131067287	131067331	-	1	NA	Intergenic	Intergenic	-3495	NM_001163529	110751	Mm.108550	NM_033615	ENSMUSG00000027318	Adam33	Adaml	a disintegrin and metallopeptidase domain 33	protein-coding
mm_131733.1	chr16	21896463	21896475	+	1	NA	intron (NM_172821, intron 1 of 12)	intron (NM_172821, intron 1 of 12)	4500	NM_172821	71751	Mm.420837	NM_172821	ENSMUSG00000033618	Map3k13	C130026N12Rik|LZK	mitogen-activated protein kinase kinase kinase 13	protein-coding
mm_30615.1	chr4	8461428	8461461	+	1	NA	Intergenic	Intergenic	-74200	NM_021518	59021	Mm.397471	NM_021518	ENSMUSG00000047187	Rab2a	9330148M11Rik|C80220|Rab2	RAB2A, member RAS oncogene family	protein-coding
mm_95542.1	chr11	52299808	52299819	+	1	NA	Intergenic	Intergenic	-16799	NM_001313981	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_156457.1	chrX	142825668	142825690	+	1	NA	intron (NM_001199360, intron 5 of 6)	L2a|LINE|L2	86679	NR_030523	723976		NR_030523	ENSMUSG00000076011	Mir652	Mirn652|miRX|mmu-mir-652	microRNA 652	ncRNA
mm_110541.1	chr12	55302768	55302778	-	1	NA	5' UTR (NM_021529, exon 2 of 14)	5' UTR (NM_021529, exon 2 of 14)	136	NM_025373	66132	Mm.383213	NM_025373	ENSMUSG00000021023	1110008L16Rik	Kiaa0391|Mrpp3|mKIAA0391	RIKEN cDNA 1110008L16 gene	protein-coding
mm_166789.1	chr6	145276306	145276320	-	1	NA	Intergenic	Intergenic	25761	NR_045598	100039495	Mm.121014	NR_045598	ENSMUSG00000086013	Gm15706	OTTMUSG00000025463	predicted gene 15706	ncRNA
mm_107651.1	chr12	52607639	52607643	+	1	NA	Intergenic	Intergenic	-5319	NR_045910	73278	Mm.396209	NR_045910	ENSMUSG00000100315	1700031P21Rik	-	RIKEN cDNA 1700031P21 gene	ncRNA
mm_153102.1	chr19	32739741	32739756	-	1	NA	Intergenic	Intergenic	-17829	NM_008960	19211	Mm.245395	NM_008960	ENSMUSG00000013663	Pten	2310035O07Rik|A130070J02Rik|AI463227|B430203M17Rik|MMAC1|TEP1	phosphatase and tensin homolog	protein-coding
mm_119879.1	chr14	54883571	54883594	+	1	NA	intron (NM_007537, intron 1 of 3)	intron (NM_007537, intron 1 of 3)	157	NM_007537	12050	Mm.6967	NM_007537	ENSMUSG00000089682	Bcl2l2	AW048834|Bcl-w|Gtrgal2|Gtrosa41|bclw|c98	BCL2-like 2	protein-coding
mm_112252.1	chr12	113702652	113702662	-	1	NA	Intergenic	Intergenic	158749	NM_174885	238406	Mm.188683	NM_174885	ENSMUSG00000043945	Adam6a	Adam6|tMDCIV	a disintegrin and metallopeptidase domain 6A	protein-coding
mm_81002.1	chr9	103426622	103426631	+	1	NA	non-coding (NR_040466, exon 2 of 6)	non-coding (NR_040466, exon 2 of 6)	3048	NR_040466	100529079	Mm.437003	NR_040466	ENSMUSG00000086236	5830418P13Rik	-	RIKEN cDNA 5830418P13 gene	ncRNA
mm_13352.1	chr2	103073670	103073755	+	1	NA	promoter-TSS (NM_019735)	promoter-TSS (NM_019735)	37	NM_019735	56369	Mm.24772	NM_019735	ENSMUSG00000010911	Apip	APIP2|CGI-29|Mmrp19	APAF1 interacting protein	protein-coding
mm_90711.1	chr10	4386987	4386995	-	1	NA	intron (NM_001033466, intron 1 of 2)	CpG	1117	NM_001033466	381990	Mm.262466	NM_001033466	ENSMUSG00000075327	Zbtb2	Gm1103	zinc finger and BTB domain containing 2	protein-coding
mm_130771.1	chr15	101418372	101418397	-	1	NA	exon (NM_033073, exon 4 of 9)	exon (NM_033073, exon 4 of 9)	5981	NM_033073	110310	Mm.486285	NM_033073	ENSMUSG00000023039	Krt7	D15Wsu77e|K7|Krt2-7	keratin 7	protein-coding
mm_63780.1	chr7	131560714	131560734	+	1	NA	exon (NM_009774, exon 2 of 8)	exon (NM_009774, exon 2 of 8)	230	NM_001317350	12237	Mm.927	NM_009774	ENSMUSG00000066979	Bub3	AU019800|AU021329|AU043350|AW146323|C78067	BUB3 mitotic checkpoint protein	protein-coding
mm_13328.1	chr2	102784414	102784427	+	1	NA	3' UTR (NM_001077514, exon 11 of 11)	3' UTR (NM_001077514, exon 11 of 11)	77982	NM_001077515	20511	Mm.267547	NM_011393	ENSMUSG00000005089	Slc1a2	1700091C19Rik|2900019G14Rik|AI159670|Eaat2|GLT-1|GLT1|MGLT1	solute carrier family 1 (glial high affinity glutamate transporter), member 2	protein-coding
mm_77375.1	chr8	119834223	119834252	-	1	NA	intron (NM_028071, intron 2 of 3)	intron (NM_028071, intron 2 of 3)	6342	NM_028071	72042	Mm.393405	NM_028071	ENSMUSG00000031827	Cotl1	1810074P22Rik|2010004C08Rik|Clp	coactosin-like 1 (Dictyostelium)	protein-coding
mm_85031.1	chr9	88476692	88476694	-	1	NA	intron (NM_001311113, intron 5 of 10)	intron (NM_001311113, intron 5 of 10)	5704	NM_019666	56403	Mm.260545	NM_019666	ENSMUSG00000032423	Syncrip	2610109K23Rik|4632417O19Rik|GRY-RBP|Nsap1|Nsap1l|hnRNP Q|pp68	synaptotagmin binding, cytoplasmic RNA interacting protein	protein-coding
mm_19771.1	chr2	105675282	105675300	-	1	NA	promoter-TSS (NM_013627)	promoter-TSS (NM_013627)	-453	NM_001244200	18508	Mm.3608	NM_013627	ENSMUSG00000027168	Pax6	1500038E17Rik|AEY11|Dey|Gsfaey11|Pax-6|Sey	paired box 6	protein-coding
mm_169855.1	chr16	3345330	3345339	+	1	NA	Intergenic	Intergenic	-247064	NM_146860	258859	Mm.377723	NM_146860	ENSMUSG00000051003	Olfr161	MOR131-1|OR912-47M6	olfactory receptor 161	protein-coding
mm_51214.1	chr6	71352982	71353002	+	1	NA	Intergenic	Intergenic	-20435	NM_009857	12525	Mm.1858	NM_009857	ENSMUSG00000053977	Cd8a	BB154331|Ly-2|Ly-35|Ly-B|Lyt-2	CD8 antigen, alpha chain	protein-coding
mm_49830.1	chr6	37870709	37870720	+	1	NA	promoter-TSS (NM_145076)	promoter-TSS (NM_145076)	-97	NM_001272064	21848	Mm.41063	NM_145076	ENSMUSG00000029833	Trim24	A130082H20Rik|AI447469|D430004I05Rik|TIF1|TIF1-alpha|TIF1alpha|Tif1a	tripartite motif-containing 24	protein-coding
mm_34054.1	chr4	138304724	138304743	+	1	NA	promoter-TSS (NM_007838)	promoter-TSS (NM_007838)	-5	NM_007838	13200	Mm.7236	NM_007838	ENSMUSG00000028757	Ddost	-	dolichyl-di-phosphooligosaccharide-protein glycotransferase	protein-coding
mm_119773.1	chr14	54176209	54176219	+	1	NA	Intergenic	Intergenic	77715	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_1412.1	chr1	67156200	67156225	+	1	NA	exon (NM_001080809, exon 8 of 38)	exon (NM_001080809, exon 8 of 38)	33185	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_21399.1	chr2	157571436	157571447	-	1	NA	Intergenic	Intergenic	-5080	NM_016916	53619	Mm.480461	NM_016916	ENSMUSG00000067787	Blcap	AI462828|Bc10	bladder cancer associated protein	protein-coding
mm_95905.1	chr11	58204939	58204957	+	1	NA	intron (NM_018738, intron 2 of 2)	B4|SINE|B4	5392	NM_018738	16145	Mm.33902	NM_018738	ENSMUSG00000078853	Igtp	AW558444|Irgm3	interferon gamma induced GTPase	protein-coding
mm_11391.1	chr2	31453788	31453800	+	1	NA	Intergenic	Intergenic	-16476	NM_007494	11898	Mm.3217	NM_007494	ENSMUSG00000076441	Ass1	AA408052|ASS|Ass-1|fold	argininosuccinate synthetase 1	protein-coding
mm_135096.1	chr16	34958869	34958882	-	1	NA	promoter-TSS (NR_045722)	promoter-TSS (NR_045722)	-11	NR_045722	278725	Mm.436927	NR_045722		E130310I04Rik	A930019C19Rik	RIKEN cDNA E130310I04 gene	ncRNA
mm_16843.1	chr2	11502093	11502126	-	1	NA	promoter-TSS (NM_001177754)	promoter-TSS (NM_001177754)	-19	NM_001177757	170768	Mm.19669	NM_133232	ENSMUSG00000026773	Pfkfb3	E330010H22Rik|iPFK-2|uPFK-2	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	protein-coding
mm_109674.1	chr12	113074778	113074801	+	1	NA	TTS (NM_001291445)	TTS (NM_001291445)	287	NM_029381	75671	Mm.23377	NM_029381	ENSMUSG00000012211	Tex22	1700028O09Rik|AV210422|Tep22	testis expressed gene 22	protein-coding
mm_35301.1	chr4	22488454	22488469	-	1	NA	promoter-TSS (NM_008899)	promoter-TSS (NM_008899)	-95	NM_008899	18992	Mm.129387	NM_008899	ENSMUSG00000095139	Pou3f2	9430075J19Rik|A230098E07Rik|Brn-2|Brn2|OTF-7|Otf7|oct-7	POU domain, class 3, transcription factor 2	protein-coding
mm_80683.1	chr9	91368336	91368382	+	1	NA	promoter-TSS (NM_009576)	promoter-TSS (NM_009576)	-613	NM_009576	22774	Mm.8062	NM_009576	ENSMUSG00000036972	Zic4	-	zinc finger protein of the cerebellum 4	protein-coding
mm_155864.1	chrX	101383727	101383741	+	1	NA	promoter-TSS (NM_001302497)	promoter-TSS (NM_001302497)	2	NM_001302497	14618	Mm.21198	NM_008124	ENSMUSG00000047797	Gjb1	Cnx32|Cx32|connexin-32	gap junction protein, beta 1	protein-coding
mm_36397.1	chr4	77787164	77787178	-	1	NA	intron (NM_011211, intron 2 of 39)	intron (NM_011211, intron 2 of 39)	424724	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding
mm_141660.1	chr17	33760358	33760395	-	1	NA	5' UTR (NM_008997, exon 1 of 5)	5' UTR (NM_008997, exon 1 of 5)	110	NM_008997	19326	Mm.387587	NM_008997	ENSMUSG00000077450	Rab11b	A730055L17Rik	RAB11B, member RAS oncogene family	protein-coding
mm_121597.1	chr14	7994223	7994227	-	1	NA	promoter-TSS (NM_007870)	promoter-TSS (NM_007870)	-43	NM_007870	13421	Mm.272258	NM_007870	ENSMUSG00000025279	Dnase1l3	DNasegamma|Dhp2|Lsd	deoxyribonuclease 1-like 3	protein-coding
mm_51557.1	chr6	83351236	83351248	+	1	NA	intron (NM_175277, intron 1 of 3)	intron (NM_175277, intron 1 of 3)	1758	NM_175277	78653	Mm.391470	NM_175277	ENSMUSG00000045160	Bola3	1810056O20Rik	bolA-like 3 (E. coli)	protein-coding
mm_315.1	chr1	24612003	24612039	+	1	NA	Intergenic	Intergenic	-24584	NM_007733	12823	Mm.329196	NM_007733	ENSMUSG00000026141	Col19a1	-	collagen, type XIX, alpha 1	protein-coding
mm_136377.1	chr16	92825792	92825821	-	1	NA	intron (NM_001111022, intron 1 of 6)	intron (NM_001111022, intron 1 of 6)	268	NM_001111021	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_111825.1	chr12	106716347	106716366	-	1	NA	promoter-TSS (NR_015512)	promoter-TSS (NR_015512)	-32	NR_015512	71033	Mm.159404	NR_015512	ENSMUSG00000085820	4933406K04Rik	4930426M03Rik|4930485I22Rik|4933427G14Rik	RIKEN cDNA 4933406K04 gene	ncRNA
mm_167450.1	chr8	122694220	122694221	+	1	NA	intron (NM_009824, intron 1 of 11)	intron (NM_009824, intron 1 of 11)	4889	NM_009824	12398	Mm.194339	NM_009824	ENSMUSG00000006362	Cbfa2t3	A630044F12Rik|AI465270|AW229127|Cbfa2t3h|ETO-2|Eto2|MTGR2	core-binding factor, runt domain, alpha subunit 2, translocated to, 3 (human)	protein-coding
mm_71212.1	chr8	40890740	40890752	+	1	NA	intron (NM_007514, intron 1 of 11)	intron (NM_007514, intron 1 of 11)	28379	NM_001044740	11988	Mm.4676	NM_007514	ENSMUSG00000031596	Slc7a2	20.5|AI158848|Atrc2|CAT-2|Cat2|Tea	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	protein-coding
mm_45176.1	chr5	51553863	51553888	-	1	NA	promoter-TSS (NR_027710)	promoter-TSS (NR_027710)	46	NR_027710	19017	Mm.259072	NM_008904	ENSMUSG00000029167	Ppargc1a	A830037N07Rik|ENSMUSG00000079510|Gm11133|PGC-1|PPARGC-1-alpha|Pgc-1alpha|Pgc1|Pgco1|Ppargc1	peroxisome proliferative activated receptor, gamma, coactivator 1 alpha	protein-coding
mm_118942.1	chr14	27335643	27335654	+	1	NA	promoter-TSS (NM_001289687)	promoter-TSS (NM_001289687)	-389	NM_001289687	71704	Mm.248606	NM_027871	ENSMUSG00000021895	Arhgef3	1200004I24Rik|9830169H03Rik|C76747|Xpln	Rho guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_48298.1	chr5	138263943	138263988	-	1	NA	promoter-TSS (NM_153161)	promoter-TSS (NM_153161)	-80	NR_045821	69004	Mm.439868	NR_045821	ENSMUSG00000085227	6330418K02Rik	-	RIKEN cDNA 6330418K02 gene	ncRNA
mm_104893.1	chr11	99583676	99583682	-	1	NA	promoter-TSS (NM_001039502)	promoter-TSS (NM_001039502)	-2	NM_001039502	629873	Mm.423246	NM_001039502	ENSMUSG00000075567	Krtap1-4	OTTMUSG00000004966	keratin associated protein 1-4	protein-coding
mm_161387.1	chr14	76488562	76488562	+	1	NA	5' UTR (NM_001177751, exon 1 of 3)	5' UTR (NM_001177751, exon 1 of 3)	126	NM_001177751	21807	Mm.153272	NM_009366	ENSMUSG00000022010	Tsc22d1	AA589566|AW105905|Egr5|TSC-22|Tgfb1i4|Tsc|Tsc22	TSC22 domain family, member 1	protein-coding
mm_27330.1	chr3	50377638	50377659	-	1	NA	exon (NM_011990, exon 11 of 12)	exon (NM_011990, exon 11 of 12)	65965	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_108855.1	chr12	98628208	98628235	+	1	NA	promoter-TSS (NM_178914)	promoter-TSS (NM_178914)	79	NM_001289574	104871	Mm.210053	NM_178914	ENSMUSG00000021007	Spata7	AI661438|B230306G18Rik|HSD3	spermatogenesis associated 7	protein-coding
mm_7229.1	chr1	93425287	93425317	-	1	NA	exon (NM_133808, exon 12 of 28)	exon (NM_133808, exon 12 of 28)	20399	NM_001301364	110611	Mm.30012	NM_133808	ENSMUSG00000034088	Hdlbp	1110005P14Rik|AA960365|AI118566|D1Ertd101e	high density lipoprotein (HDL) binding protein	protein-coding
mm_47732.1	chr5	130172411	130172440	-	1	NA	intron (NM_001199059, intron 1 of 8)	intron (NM_001199059, intron 1 of 8)	606	NM_001199059	56715	Mm.288639	NM_019983	ENSMUSG00000025340	Rabgef1	Rab5ef|Rabex5|Rin2	RAB guanine nucleotide exchange factor (GEF) 1	protein-coding
mm_12487.1	chr2	71644299	71644318	+	1	NA	intron (NR_039557, intron 2 of 3).2	intron (NR_039557, intron 2 of 3).2	-75109	NR_037979	381371	Mm.330284	NM_201366	ENSMUSG00000064263	Platr26	Gm1631	pluripotency associated transcript 26	ncRNA
mm_100046.1	chr11	115163334	115163348	+	1	NA	promoter-TSS (NM_012030)	promoter-TSS (NM_012030)	0	NM_012030	26941	Mm.27842	NM_012030	ENSMUSG00000020733	Slc9a3r1	EBP-50|NHE-RF|NHERF-1|NHERF1	solute carrier family 9 (sodium/hydrogen exchanger), member 3 regulator 1	protein-coding
mm_98149.1	chr11	87592945	87593006	+	1	NA	intron (NM_133215, intron 1 of 18)	intron (NM_133215, intron 1 of 18)	758	NM_133215	170749	Mm.399376	NM_133215	ENSMUSG00000018401	Mtmr4	AA596759|ESTM44|FYVE-DSP2|ZFYVE11|mKIAA0647	myotubularin related protein 4	protein-coding
mm_28180.1	chr3	88000895	88000905	-	1	NA	promoter-TSS (NM_001109758)	promoter-TSS (NM_001109758)	-544	NM_001109758	12032	Mm.4598	NM_007529	ENSMUSG00000004892	Bcan	Cspg7	brevican	protein-coding
mm_111923.1	chr12	108882742	108882768	-	1	NA	exon (NM_001164488, exon 3 of 10)	exon (NM_001164488, exon 3 of 10)	10443	NM_001164488	22375	Mm.38433	NM_011710	ENSMUSG00000021266	Wars	TrpRS|WRS	tryptophanyl-tRNA synthetase	protein-coding
mm_119474.1	chr14	47310671	47310704	+	1	NA	exon (NM_178684, exon 3 of 4)	exon (NM_178684, exon 3 of 4)	12373	NM_178684	218975	Mm.212297	NM_178684	ENSMUSG00000021840	Mapk1ip1l	9130202B12|C130032J12Rik	mitogen-activated protein kinase 1 interacting protein 1-like	protein-coding
mm_141778.1	chr17	34293424	34293430	-	1	NA	Intergenic	Intergenic	-5656	NM_010378	14960	Mm.235338	NM_010378	ENSMUSG00000036594	H2-Aa	Aalpha|H-2Aa|H2Aa|I-Aalpha|IAalpha|Ia-1|Ia1	histocompatibility 2, class II antigen A, alpha	protein-coding
mm_17986.1	chr2	37843927	37843944	-	1	NA	intron (NM_146122, intron 19 of 21)	intron (NM_146122, intron 19 of 21)	67686	NM_001163566	241324	Mm.392369	NM_001163566	ENSMUSG00000035403	Crb2	5930402A21|BC043114	crumbs family member 2	protein-coding
mm_117083.1	chr13	59675755	59675814	-	1	NA	promoter-TSS (NM_001035122)	promoter-TSS (NM_001035122)	0	NM_001035122	105348	Mm.171335	NM_027307	ENSMUSG00000021556	Golm1	2310001L02Rik|AW125446|D030064E01Rik|GP73|Golph2|PSEC0257	golgi membrane protein 1	protein-coding
mm_131355.1	chr16	13703101	13703114	+	1	NA	3' UTR (NM_001177552, exon 6 of 6)	3' UTR (NM_001177552, exon 6 of 6)	-26729	NR_040574	76684	Mm.491043	NR_040574		Pla2g10os	1810007I06Rik	phospholipase A2, group X, opposite strand	ncRNA
mm_48492.1	chr5	142608786	142608808	-	1	NA	promoter-TSS (NM_175217)	promoter-TSS (NM_175217)	-45	NM_175217	75104	Mm.48712	NM_175217	ENSMUSG00000039533	Mmd2	4930518M15Rik|C88001	monocyte to macrophage differentiation-associated 2	protein-coding
mm_35442.1	chr4	40214357	40214366	-	1	NA	intron (NM_172689, intron 12 of 17)	intron (NM_172689, intron 12 of 17)	25464	NM_172689	230073	Mm.86382	NM_172689	ENSMUSG00000040296	Ddx58	6430573D20Rik|C330021E21|RIG-I|RLR-1	DEAD (Asp-Glu-Ala-Asp) box polypeptide 58	protein-coding
mm_140542.1	chr17	6785441	6785461	-	1	NA	Intergenic	Intergenic	-2671	NM_009510	22350	Mm.277812	NM_009510	ENSMUSG00000052397	Ezr	AW146364|R75297|Vil2|p81	ezrin	protein-coding
mm_143238.1	chr17	63500330	63500378	-	1	NA	5' UTR (NM_015794, exon 1 of 9)	5' UTR (NM_015794, exon 1 of 9)	226	NM_015794	50758	Mm.136366	NM_015794	ENSMUSG00000023965	Fbxl17	6330576B01Rik|AI452053|BB073797|C130023C01Rik|Fbx13|Fbxo13	F-box and leucine-rich repeat protein 17	protein-coding
mm_66417.1	chr7	44529644	44529660	-	1	NA	intron (NM_019866, intron 3 of 5)	intron (NM_019866, intron 3 of 5)	2419	NM_019866	272382	Mm.8012	NM_019866	ENSMUSG00000008193	Spib	Spi-B	Spi-B transcription factor (Spi-1/PU.1 related)	protein-coding
mm_24649.1	chr3	94388254	94388290	+	1	NA	intron (NR_121656, intron 3 of 9)	intron (NR_121656, intron 3 of 9)	10840	NR_121656	19885	Mm.4372	NM_011281	ENSMUSG00000028150	Rorc	Nr1f3|RORgamma|TOR|Thor	RAR-related orphan receptor gamma	protein-coding
mm_23907.1	chr3	83032125	83032132	+	1	NA	3' UTR (NM_010196, exon 5 of 5)	3' UTR (NM_010196, exon 5 of 5)	5975	NM_001111048	14161	Mm.88793	NM_010196	ENSMUSG00000028001	Fga	ENSMUSG00000059807|Fib	fibrinogen alpha chain	protein-coding
mm_144596.1	chr18	32240310	32240342	+	1	NA	promoter-TSS (NM_133658)	promoter-TSS (NM_133658)	-5	NM_133658	13872	Mm.282335	NM_133658	ENSMUSG00000024382	Ercc3	BTF2 p89|Ercc-3|XPB	excision repair cross-complementing rodent repair deficiency, complementation group 3	protein-coding
mm_134982.1	chr16	32099621	32099635	-	1	NA	promoter-TSS (NM_025892)	promoter-TSS (NM_025892)	99	NM_001111025	72084	Mm.37613	NM_024464	ENSMUSG00000023791	Pigx	2010319C14Rik|PIG-X	phosphatidylinositol glycan anchor biosynthesis, class X	protein-coding
mm_95405.1	chr11	49846765	49846799	+	1	NA	promoter-TSS (NM_001163671)	promoter-TSS (NM_001163671)	31	NM_016961	26420	Mm.68933	NM_016961	ENSMUSG00000020366	Mapk9	AI851083|JNK2|Prkm9|p54aSAPK	mitogen-activated protein kinase 9	protein-coding
mm_82187.1	chr9	123938224	123938232	+	1	NA	Intergenic	Intergenic	30464	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_172121.1	chr6	3201219	3201222	+	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	-87299	NR_036696	667335	Mm.380219	NR_036696	ENSMUSG00000106779	Gm8579	EG667335	spermatogenesis associated glutamate (E)-rich protein 4a pseudogene	pseudo
mm_38348.1	chr4	137769989	137770003	-	1	NA	intron (NM_007431, intron 1 of 11)	intron (NM_007431, intron 1 of 11)	-3521	NM_001287172	11647	Mm.288186	NM_007431	ENSMUSG00000028766	Alpl	ALP|APTNAP|Akp-2|Akp2|TNAP|TNSALP	alkaline phosphatase, liver/bone/kidney	protein-coding
mm_127037.1	chr15	96638491	96638512	+	1	NA	intron (NM_001166458, intron 1 of 15)	intron (NM_001166458, intron 1 of 15)	3461	NM_134086	105727	Mm.103568	NM_134086	ENSMUSG00000023169	Slc38a1	AA408026|AA409865|AL022800|AU015942|NAT2	solute carrier family 38, member 1	protein-coding
mm_91279.1	chr10	24692448	24692457	-	1	NA	intron (NM_001308327, intron 1 of 24)	intron (NM_001308327, intron 1 of 24)	19707	NM_001308327	18605	Mm.27254	NM_008813	ENSMUSG00000037370	Enpp1	4833416E15Rik|AI428932|C76301|CD203c|E-NPP 1|E-NPP1|Ly-41|M6S1|NPP1|Npps|PC-1|Pca|Pca-1|Pdnp1|ttw|twy	ectonucleotide pyrophosphatase/phosphodiesterase 1	protein-coding
mm_149353.1	chr19	10895421	10895425	+	1	NA	5' UTR (NM_134129, exon 1 of 16)	5' UTR (NM_134129, exon 1 of 16)	192	NM_001253843	28000	Mm.491104	NM_134129	ENSMUSG00000024735	Prpf19	AA617263|AL024362|D19Wsu55e|NMP200|PSO4|Prp19|Snev	pre-mRNA processing factor 19	protein-coding
mm_144875.1	chr18	36753434	36753455	+	1	NA	exon (NM_011879, exon 12 of 20)	exon (NM_011879, exon 12 of 20)	-6795	NM_026464	67936	Mm.271719	NM_026464	ENSMUSG00000042660	Wdr55	2410080P20Rik|C80692	WD repeat domain 55	protein-coding
mm_98339.1	chr11	93098038	93098056	+	1	NA	Intergenic	Intergenic	-1243	NM_028296	72605	Mm.342160	NM_028296	ENSMUSG00000056158	Car10	2700029L05Rik|BB085816|Ca10	carbonic anhydrase 10	protein-coding
mm_26573.1	chr3	146618665	146618675	+	1	NA	intron (NM_009474, intron 4 of 7)	intron (NM_009474, intron 4 of 7)	-3072	NM_019957	56629	Mm.25853	NM_019957	ENSMUSG00000028185	Dnase2b	AI526873|Dlad|DnaseIIb	deoxyribonuclease II beta	protein-coding
mm_67758.1	chr7	92669918	92669943	-	1	NA	promoter-TSS (NM_029078)	promoter-TSS (NM_029078)	-18	NM_029078	74737	Mm.288645	NM_029078	ENSMUSG00000041328	Pcf11	2500001H09Rik|5730417B17Rik|C77803	PCF11 cleavage and polyadenylation factor subunit	protein-coding
mm_120062.1	chr14	56886573	56886602	+	1	NA	Intergenic	CpG	-1208	NM_029498	76007	Mm.31417	NM_029498	ENSMUSG00000021945	Zmym2	5830413P05Rik|FIM|MYM|RAMP|SCLL|Zfp198|Znf198	zinc finger, MYM-type 2	protein-coding
mm_87353.1	chr10	43603383	43603387	+	1	NA	intron (NR_033558, intron 1 of 2)	intron (NR_033558, intron 1 of 2)	9958	NR_033558	414125	Mm.244305	NR_033558	ENSMUSG00000075184	F830002L21Rik	F930017D23Rik	RIKEN cDNA F830002L21 gene	ncRNA
mm_136758.1	chr17	8782264	8782265	+	1	NA	intron (NM_001290707, intron 2 of 22)	B4A|SINE|B4	-19481	NM_011866	23984	Mm.87161	NM_011866	ENSMUSG00000023868	Pde10a	-	phosphodiesterase 10A	protein-coding
mm_101513.1	chr11	32347727	32347732	-	1	NA	promoter-TSS (NM_177364)	promoter-TSS (NM_177364)	-82	NM_177364	268396	Mm.227616	NM_177364	ENSMUSG00000040711	Sh3pxd2b	G431001E03Rik|TSK4|fad49	SH3 and PX domains 2B	protein-coding
mm_74472.1	chr8	4258328	4258367	-	1	NA	3' UTR (NM_183315, exon 2 of 2)	3' UTR (NM_183315, exon 2 of 2)	927	NM_183315	330695	Mm.34210	NM_183315	ENSMUSG00000048644	Ctxn1	BC028881|Ctxn	cortexin 1	protein-coding
mm_80101.1	chr9	70317184	70317204	+	1	NA	intron (NM_181072, intron 5 of 27)	ID_B1|SINE|B4	88559	NR_049200	100885839		NR_049200	ENSMUSG00000093763	Mir5626	Gm25590|mir-5626|mmu-mir-5626	microRNA 5626	ncRNA
mm_160046.1	chr6	145808604	145808604	+	1	NA	intron (NM_027760, intron 1 of 3)	intron (NM_027760, intron 1 of 3)	221	NM_027760	71323	Mm.158669	NM_027760	ENSMUSG00000030259	Rassf8	5133400D11Rik|AA815821|AW123240|Hoj1|mHoj-1	Ras association (RalGDS/AF-6) domain family (N-terminal) member 8	protein-coding
mm_11962.1	chr2	53132812	53132825	+	1	NA	3' UTR (NM_172409, exon 27 of 27)	3' UTR (NM_172409, exon 27 of 27)	58369	NM_018785	56194	Mm.257474	NM_018785	ENSMUSG00000061136	Prpf40a	2810012K09Rik|FBP-11|FBP11|Fnbp11|Fnbp3	pre-mRNA processing factor 40A	protein-coding
mm_112052.1	chr12	111713186	111713218	-	1	NA	promoter-TSS (NM_026511)	promoter-TSS (NM_026511)	54	NM_027404	70369	Mm.44239	NM_027404	ENSMUSG00000049792	Bag5	1600025G07Rik|4930405J06Rik|Bag-5	BCL2-associated athanogene 5	protein-coding
mm_96360.1	chr11	67078294	67078307	+	1	NA	promoter-TSS (NM_001099635)	promoter-TSS (NM_001099635)	0	NM_001099635	17883	Mm.340090	NM_001099635	ENSMUSG00000020908	Myh3	MyHC-emb|Myhs-e|Myhse	myosin, heavy polypeptide 3, skeletal muscle, embryonic	protein-coding
mm_1673.1	chr1	74792138	74792157	+	1	NA	5' UTR (NM_009518, exon 1 of 4)	5' UTR (NM_009518, exon 1 of 4)	128	NM_009518	22409	Mm.5130	NM_009518	ENSMUSG00000026167	Wnt10a	-	wingless-type MMTV integration site family, member 10A	protein-coding
mm_67123.1	chr7	70361751	70361777	-	1	NA	intron (NM_183261, intron 1 of 2)	intron (NM_183261, intron 1 of 2)	-1171	NM_009697	11819	Mm.158143	NM_009697	ENSMUSG00000030551	Nr2f2	2700033K02Rik|9430015G03Rik|ARP-1|Aporp1|COUP-TF2|COUP-TFII|COUPTFB|EAR3|SVP40|Tcfcoup2	nuclear receptor subfamily 2, group F, member 2	protein-coding
mm_106370.1	chr11	118398530	118398540	-	1	NA	exon (NM_011150, exon 3 of 6)	exon (NM_011150, exon 3 of 6)	3396	NM_011150	19039	Mm.3152	NM_011150	ENSMUSG00000033880	Lgals3bp	90K|CyCAP|MAC-2BP|Ppicap|Tango10b	lectin, galactoside-binding, soluble, 3 binding protein	protein-coding
mm_62193.1	chr7	97696646	97696725	+	1	NA	promoter-TSS (NM_023671)	promoter-TSS (NM_023671)	28	NM_023671	12729	Mm.21482	NM_023671	ENSMUSG00000025439	Clns1a	2610036D06Rik|2610100O04Rik|Clci|Clcni|ICLN	chloride channel, nucleotide-sensitive, 1A	protein-coding
mm_42221.1	chr5	113340170	113340186	+	1	NA	Intergenic	Intergenic	-2533	NR_106089	102466821		NR_106089	ENSMUSG00000104840	Mir7230	mmu-mir-7230	microRNA 7230	ncRNA
mm_126893.1	chr15	89498049	89498069	+	1	NA	Intergenic	Intergenic	-1798	NM_021423	58234	Mm.146855	NM_021423	ENSMUSG00000022623	Shank3	AI841104|SHANK3c-3|SHANK3c-4|Shank3b	SH3/ankyrin domain gene 3	protein-coding
mm_112526.1	chr13	9276670	9276714	+	1	NA	5' UTR (NM_001081426, exon 1 of 37)	5' UTR (NM_001081426, exon 1 of 37)	167	NM_001081426	208440	Mm.217326	NM_172459	ENSMUSG00000048264	Dip2c	2900024P20Rik|9630044M06|mKIAA0934	disco interacting protein 2 homolog C	protein-coding
mm_56819.1	chr6	116716889	116716923	-	1	NA	promoter-TSS (NM_178768)	promoter-TSS (NM_178768)	-148	NM_178768	319776	Mm.133120	NM_178768	ENSMUSG00000048108	Tmem72	C230095G01Rik	transmembrane protein 72	protein-coding
mm_165428.1	chr2	152911647	152911681	+	1	NA	intron (NM_001081044, intron 1 of 11)	intron (NM_001081044, intron 1 of 11)	312	NM_001081044	228785	Mm.250604	NM_001081044	ENSMUSG00000027470	Mylk2	9830004H17Rik|BB138278	myosin, light polypeptide kinase 2, skeletal muscle	protein-coding
mm_10431.1	chr2	14074092	14074146	+	1	NA	promoter-TSS (NM_011484)	promoter-TSS (NM_011484)	7	NM_011484	20844	Mm.273174	NM_011484	ENSMUSG00000026718	Stam	STAM1	signal transducing adaptor molecule (SH3 domain and ITAM motif) 1	protein-coding
mm_101138.1	chr11	14120420	14120425	-	1	NA	intron (NR_131011, intron 2 of 3)	L1_Mur1|LINE|L1	58619	NR_131011	75280	Mm.108492	NR_131011	ENSMUSG00000085452	4930554G24Rik	-	RIKEN cDNA 4930554G24 gene	ncRNA
mm_74206.1	chr8	123893225	123893247	+	1	NA	exon (NM_009606, exon 3 of 7)	exon (NM_009606, exon 3 of 7)	1539	NM_001272041	11459	Mm.214950	NM_009606	ENSMUSG00000031972	Acta1	AA959943|Acta-2|Acts|Actsk-1	actin, alpha 1, skeletal muscle	protein-coding
mm_32048.1	chr4	97581699	97581711	+	1	NA	promoter-TSS (NM_001122952)	promoter-TSS (NM_001122952)	-238	NM_001122952	18027	Mm.31274	NM_010905	ENSMUSG00000028565	Nfia	1110047K16Rik|9430022M17Rik|CTF|NF1-A|NF1A	nuclear factor I/A	protein-coding
mm_113542.1	chr13	37873042	37873042	+	1	NA	intron (NM_001039188, intron 1 of 9)	intron (NM_001039188, intron 1 of 9)	-15392	NR_033218	68750	Mm.491109	NM_026830	ENSMUSG00000039087	Rreb1	1110037N09Rik|AA414966|B930013M22Rik	ras responsive element binding protein 1	protein-coding
mm_139213.1	chr17	47728797	47728824	+	1	NA	exon (NM_025973, exon 2 of 9)	exon (NM_025973, exon 2 of 9)	1968	NM_025973	109820	Mm.22957	NM_025973	ENSMUSG00000023987	Pgc	2210410L06Rik|Upg-1|Upg1	progastricsin (pepsinogen C)	protein-coding
mm_109106.1	chr12	105337161	105337170	+	1	NA	intron (NR_125773, intron 1 of 3)	CpG	172	NR_125773	69952	Mm.158311	NR_045047	ENSMUSG00000097929	Tunar	2810011L19Rik|Tuna	Tcl1 upstream neural differentiation associated RNA	ncRNA
mm_128164.1	chr15	34068241	34068251	-	1	NA	Intergenic	RMER10B|LTR|ERVL	-14473	NM_026002	67154	Mm.130883	NM_026002	ENSMUSG00000022255	Mtdh	2610103J23Rik|3D3|3D3/Lyric|AEG-1|AV353288|D8Bwg1112e|Lyric	metadherin	protein-coding
mm_65298.1	chr7	24587613	24587665	-	1	NA	promoter-TSS (NM_023154)	promoter-TSS (NM_023154)	2	NM_001033205	101544	Mm.20117	NM_001033205	ENSMUSG00000066721	Zfp575	AI326876|Znf575	zinc finger protein 575	protein-coding
mm_64947.1	chr7	16370385	16370417	-	1	NA	exon (NM_019748, exon 3 of 9)	exon (NM_019748, exon 3 of 9)	17495	NM_001285892	56459	Mm.258530	NM_019748	ENSMUSG00000052833	Sae1	2400010M20Rik|2610044L12Rik|AL033372|AOS1|AW743391|D7Ertd177e|HSPC140|Sua1|Uble1a	SUMO1 activating enzyme subunit 1	protein-coding
mm_121003.1	chr14	79515696	79515707	+	1	NA	promoter-TSS (NM_001286412)	promoter-TSS (NM_001286412)	27	NM_001286411	13709	Mm.20938	NM_007920	ENSMUSG00000036461	Elf1	Elf-1|Sts1|mElf-1|p70	E74-like factor 1	protein-coding
mm_46763.1	chr5	112252451	112252463	-	1	NA	promoter-TSS (NM_021351)	promoter-TSS (NM_021351)	61	NM_001312884	12959	Mm.40324	NM_021351	ENSMUSG00000066975	Cryba4	-	crystallin, beta A4	protein-coding
mm_65265.1	chr7	19935438	19935456	-	1	NA	Intergenic	RMER19A|LTR|ERVK	-14304	NM_027514	52118	Mm.227506	NM_027514	ENSMUSG00000040511	Pvr	3830421F03Rik|CD155|D7Ertd458e|HVED|PVS|Taa1|Tage4|mE4|necl-5	poliovirus receptor	protein-coding
mm_30211.1	chr3	144889774	144889779	-	1	NA	non-coding (NR_126537, exon 2 of 4)	non-coding (NR_126537, exon 2 of 4)	6235	NR_126537	622139	Mm.447150	NM_001039222	ENSMUSG00000074196	Clca4c-ps	Clca4c|EG622139|Gm18718|Gm6289	chloride channel accessory 4C, pseudogene	pseudo
mm_42183.1	chr5	112263561	112263575	+	1	NA	exon (NM_001312894, exon 4 of 6)	exon (NM_001312894, exon 4 of 6)	7748	NM_001312893	12960	Mm.29488	NM_023695	ENSMUSG00000029343	Crybb1	3110006K12Rik|BB1CRY	crystallin, beta B1	protein-coding
mm_11301.1	chr2	30171558	30171564	+	1	NA	promoter-TSS (NM_007931)	promoter-TSS (NM_007931)	37	NM_007931	13804	Mm.474473	NM_007931	ENSMUSG00000015337	Endog	-	endonuclease G	protein-coding
mm_42033.1	chr5	108388406	108388411	+	1	NA	promoter-TSS (NM_008806)	promoter-TSS (NM_008806)	35	NM_008806	18587	Mm.1372	NM_008806	ENSMUSG00000029491	Pde6b	Pdeb|r|rd|rd-1|rd1|rd10	phosphodiesterase 6B, cGMP, rod receptor, beta polypeptide	protein-coding
mm_127093.1	chr15	97786891	97786929	+	1	NA	intron (NM_026353, intron 1 of 2)	intron (NM_026353, intron 1 of 2)	2545	NM_026353	67739	Mm.28955	NM_026353	ENSMUSG00000081534	Slc48a1	4930570C03Rik	solute carrier family 48 (heme transporter), member 1	protein-coding
mm_112374.1	chr12	119210451	119210455	-	1	NA	intron (NM_177290, intron 1 of 13)	intron (NM_177290, intron 1 of 13)	27823	NM_177290	320910	Mm.217000	NM_177290	ENSMUSG00000025321	Itgb8	4832412O06Rik	integrin beta 8	protein-coding
mm_132413.1	chr16	35068522	35068526	+	1	NA	intron (NM_023587, intron 3 of 6)	intron (NM_023587, intron 3 of 6)	46103	NM_023587	70757	Mm.27286	NM_023587	ENSMUSG00000035376	Hacd2	6330408J20Rik|AI255777|AI481689|Hcad2|Ptplb	3-hydroxyacyl-CoA dehydratase 2	protein-coding
mm_78200.1	chr9	21368508	21368524	+	1	NA	promoter-TSS (NM_001277322)	promoter-TSS (NM_001277322)	-16	NM_001277322	16201	Mm.440026	NM_010561	ENSMUSG00000032178	Ilf3	MBII-26|MPHOSPH4|NF90|NFAR	interleukin enhancer binding factor 3	protein-coding
mm_55441.1	chr6	67037379	67037394	-	1	NA	promoter-TSS (NM_007836)	promoter-TSS (NM_007836)	21	NM_007836	13197	Mm.72235	NM_007836	ENSMUSG00000036390	Gadd45a	AA545191|Ddit1|GADD45	growth arrest and DNA-damage-inducible 45 alpha	protein-coding
mm_162161.1	chrX	94235256	94235256	+	1	NA	5' UTR (NM_153165, exon 2 of 5)	5' UTR (NM_153165, exon 2 of 5)	326	NM_001039061	236904	Mm.115533	NM_153165	ENSMUSG00000043929	Klhl15	6330500C13Rik	kelch-like 15	protein-coding
mm_89998.1	chr10	112270010	112270029	+	1	NA	Intergenic	Intergenic	-1104	NM_001025581	268345	Mm.336242	NM_001025581	ENSMUSG00000035681	Kcnc2	AW047325|B230117I07|KShIIIA|Kv3.2	potassium voltage gated channel, Shaw-related subfamily, member 2	protein-coding
mm_168860.1	chr12	28631645	28631650	-	1	NA	exon (NM_011300, exon 6 of 7)	exon (NM_011300, exon 6 of 7)	4306	NM_011300	20115	Mm.279839	NM_011300	ENSMUSG00000061477	Rps7	Mtu|Rps7A|S7	ribosomal protein S7	protein-coding
mm_91015.1	chr10	15521521	15521526	-	1	NA	Intergenic	Intergenic	-270254	NR_131087	77538	Mm.128235	NR_131087		C330004P14Rik	-	RIKEN cDNA C330004P14 gene	ncRNA
mm_119500.1	chr14	47380211	47380266	+	1	NA	exon (NM_010705, exon 3 of 6)	exon (NM_010705, exon 3 of 6)	6378	NM_001145953	16854	Mm.248615	NM_010705	ENSMUSG00000050335	Lgals3	GBP|L-34|Mac-2|gal3	lectin, galactose binding, soluble 3	protein-coding
mm_147409.1	chr18	44662319	44662338	-	1	NA	promoter-TSS (NM_001085374)	promoter-TSS (NM_001085374)	-62	NM_001085374	328949	Mm.312511	NM_001033406	ENSMUSG00000071856	Mcc	D18Ertd451e|E330037C19	mutated in colorectal cancers	protein-coding
mm_107337.1	chr12	32378912	32378929	+	1	NA	5' UTR (NM_001162903, exon 1 of 1)	5' UTR (NM_001162903, exon 1 of 1)	131	NM_001162903	72123	Mm.341352	NM_028111	ENSMUSG00000090946	Ccdc71l	2010109K11Rik|AV375874	coiled-coil domain containing 71 like	protein-coding
mm_119525.1	chr14	47569407	47569410	+	1	NA	promoter-TSS (NM_172599)	promoter-TSS (NM_172599)	-974	NM_172599	100504663	Mm.287279	NM_172599	ENSMUSG00000037526	Atg14	4832427M01|Atg14L|D14Ertd114e|D14Ertd436e	autophagy related 14	protein-coding
mm_60381.1	chr7	44473590	44473603	+	1	NA	Intergenic	Intergenic	3249	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_15211.1	chr2	154214093	154214118	+	1	NA	exon (NM_153418, exon 11 of 16)	exon (NM_153418, exon 11 of 16)	-9637	NM_144890	228802	Mm.167411	NM_144890	ENSMUSG00000038572	Bpifb5	Lplunc5	BPI fold containing family B, member 5	protein-coding
mm_104606.1	chr11	97187837	97187850	-	1	NA	promoter-TSS (NM_008379)	promoter-TSS (NM_008379)	49	NM_008379	16211	Mm.251013	NM_008379	ENSMUSG00000001440	Kpnb1	AA409963|IPOB|Impnb	karyopherin (importin) beta 1	protein-coding
mm_118511.1	chr14	14067871	14067885	+	1	NA	intron (NM_139227, intron 4 of 11)	intron (NM_139227, intron 4 of 11)	53026	NM_025550	66413	Mm.27591	NM_025550	ENSMUSG00000021737	Psmd6	2400006A19Rik	proteasome (prosome, macropain) 26S subunit, non-ATPase, 6	protein-coding
mm_154599.1	chrX	7593454	7593460	+	1	NA	TTS (NM_138603)	TTS (NM_138603)	11963	NM_138603	54638	Mm.288192	NM_138603	ENSMUSG00000031143	Ccdc22	AI481216|DXImx40e|Ppp1r3f|Sfc22	coiled-coil domain containing 22	protein-coding
mm_102775.1	chr11	68386842	68386860	-	1	NA	promoter-TSS (NM_008744)	promoter-TSS (NM_008744)	-25	NM_008744	18208	Mm.39095	NM_008744	ENSMUSG00000020902	Ntn1	AI561871|BC019633|Netrin-1	netrin 1	protein-coding
mm_116887.1	chr13	55211558	55211571	-	1	NA	intron (NM_008739, intron 1 of 22)	CpG	1782	NM_008739	18193	Mm.12964	NM_008739	ENSMUSG00000021488	Nsd1	AI528500|KMT3B	nuclear receptor-binding SET-domain protein 1	protein-coding
mm_88320.1	chr10	75564182	75564197	+	1	NA	Intergenic	Intergenic	-3859	NM_198860	192734	Mm.259320	NM_198860	ENSMUSG00000046807	Lrrc75b	AI646023|Fam211b	leucine rich repeat containing 75B	protein-coding
mm_3321.1	chr1	137916574	137916580	+	1	NA	Intergenic	Intergenic	-49878	NR_029795	735252		NR_029795	ENSMUSG00000065565	Mir181a-1	Mirn181a-1|Mirn213|miR-213|mir-181a-1|mmu-mir-213	microRNA 181a-1	ncRNA
mm_24982.1	chr3	96832143	96832181	+	1	NA	promoter-TSS (NM_001146001)	promoter-TSS (NM_001146001)	-92	NR_015596	67583	Mm.444284	NR_015596	ENSMUSG00000087223	4930442L01Rik	-	RIKEN cDNA 4930442L01 gene	ncRNA
mm_22879.1	chr3	29377857	29377860	+	1	NA	intron (NM_029412, intron 5 of 14)	intron (NM_029412, intron 5 of 14)	-38965	NR_030422	791072		NR_030422	ENSMUSG00000076120	Mir551b	Mirn551b|mir-551b	microRNA 551b	ncRNA
mm_168892.1	chr12	47954848	47954849	+	1	NA	Intergenic	RLTR1F_Mm|LTR|ERVK	346614	NR_039586	100628593		NR_039586	ENSMUSG00000092981	Mir5125	mmu-mir-5125|mu-mir-5125	microRNA 5125	ncRNA
mm_167592.1	chr9	46241457	46241463	+	1	NA	intron (NM_007468, intron 1 of 2)	intron (NM_007468, intron 1 of 2)	616	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_172615.1	chr8	19695006	19695010	+	1	NA	Intergenic	B3A|SINE|B2	-34568	NM_001270553	100861668	Mm.491087	NM_001270553	ENSMUSG00000095294	Gm21119	-	predicted gene, 21119	protein-coding
mm_60022.1	chr7	30831203	30831203	+	1	NA	Intergenic	RLTR1B|LTR|ERV1	-7428	NM_146187	233079	Mm.97338	NM_146187	ENSMUSG00000051314	Ffar2	GPCR43|Gpr43	free fatty acid receptor 2	protein-coding
mm_86610.1	chr10	13964828	13964847	+	1	NA	Intergenic	CpG	-1542	NM_010437	15273	Mm.42157	NM_010437	ENSMUSG00000015501	Hivep2	Gm20114|MIBP1|Schnurri-2|Shn-2	human immunodeficiency virus type I enhancer binding protein 2	protein-coding
mm_45306.1	chr5	65422908	65422918	-	1	NA	intron (NM_009466, intron 5 of 11)	intron (NM_009466, intron 5 of 11)	12929	NM_009466	22235	Mm.344831	NM_009466	ENSMUSG00000029201	Ugdh	Udpgdh	UDP-glucose dehydrogenase	protein-coding
mm_42775.1	chr5	121367208	121367211	+	1	NA	3' UTR (NM_181421, exon 76 of 76)	3' UTR (NM_181421, exon 76 of 76)	18406	NM_001163470	231712	Mm.20488	NM_172275	ENSMUSG00000042726	Trafd1	1110008K06Rik|Fln29	TRAF type zinc finger domain containing 1	protein-coding
mm_57145.1	chr6	122654373	122654387	-	1	NA	Intergenic	MLT1D|LTR|ERVL-MaLR	27956	NM_139218	73708	Mm.27982	NM_139218	ENSMUSG00000046323	Dppa3	2410075G02Rik|PCG7|PGC7|Stella	developmental pluripotency-associated 3	protein-coding
mm_139779.1	chr17	65782985	65783104	+	1	NA	promoter-TSS (NM_001114131)	promoter-TSS (NM_001114131)	-311	NM_001114131	70351	Mm.48686	NM_146081	ENSMUSG00000061950	Ppp4r1	3110001J10Rik|Pp4r1	protein phosphatase 4, regulatory subunit 1	protein-coding
mm_93629.1	chr10	117280668	117280704	-	1	NA	exon (NM_017372, exon 2 of 4)	exon (NM_017372, exon 2 of 4)	1586	NM_017372	17105	Mm.45436	NM_017372	ENSMUSG00000069516	Lyz2	AI326280|Lys|Lysm|Lyzf2|Lyzs|Lzm|Lzm-s1|Lzp	lysozyme 2	protein-coding
mm_89086.1	chr10	83597345	83597352	+	1	NA	TTS (NM_001033375)	TTS (NM_001033375)	51316	NM_145220	216190	Mm.282985	NM_145220	ENSMUSG00000020263	Appl2	Dip3b	adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 2	protein-coding
mm_119551.1	chr14	48580622	48580625	+	1	NA	Intergenic	Intergenic	82249	NM_144841	18424	Mm.134516	NM_144841	ENSMUSG00000021848	Otx2	E130306E05Rik	orthodenticle homeobox 2	protein-coding
mm_62706.1	chr7	110627651	110627666	+	1	NA	promoter-TSS (NM_009627)	promoter-TSS (NM_009627)	-11	NM_009627	11535	Mm.1408	NM_009627	ENSMUSG00000030790	Adm	AM	adrenomedullin	protein-coding
mm_48545.1	chr5	142905594	142905625	-	1	NA	exon (NM_007393, exon 2 of 6)	exon (NM_007393, exon 2 of 6)	1145	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_85132.1	chr9	95750296	95750333	-	1	NA	promoter-TSS (NM_011643)	promoter-TSS (NM_011643)	44	NM_001311123	22063	Mm.149633	NM_011643	ENSMUSG00000032839	Trpc1	Mtrp1|Trp1|Trrp1	transient receptor potential cation channel, subfamily C, member 1	protein-coding
mm_17322.1	chr2	26476131	26476165	-	1	NA	exon (NM_008714, exon 15 of 34)	exon (NM_008714, exon 15 of 34)	-6029	NR_105962	102465602		NR_105962	ENSMUSG00000098548	Mir6996	Gm27531|mmu-mir-6996	microRNA 6996	ncRNA
mm_93967.1	chr10	127288966	127288997	-	1	NA	promoter-TSS (NM_001347171)	promoter-TSS (NM_001347171)	37	NM_001347171	110962	Mm.372826	NM_033072	ENSMUSG00000025409	Mbd6	D10Wsu93e	methyl-CpG binding domain protein 6	protein-coding
mm_94248.1	chr11	3330778	3330780	+	1	NA	promoter-TSS (NM_178149)	promoter-TSS (NM_178149)	48	NM_178149	216505	Mm.390323	NM_178149	ENSMUSG00000034614	Pik3ip1	1500004A08Rik|5830455E04Rik|Crkd|Hgfl	phosphoinositide-3-kinase interacting protein 1	protein-coding
mm_154408.1	chrM	14668	14678	+	1	NA	NA	Intergenic	NA	NA								
mm_80694.1	chr9	91404501	91404531	+	1	NA	Intergenic	Intergenic	35544	NM_009576	22774	Mm.8062	NM_009576	ENSMUSG00000036972	Zic4	-	zinc finger protein of the cerebellum 4	protein-coding
mm_54008.1	chr6	7983043	7983062	-	1	NA	Intergenic	Intergenic	137828	NM_052993	94192	Mm.102752	NM_052993	ENSMUSG00000042460	C1galt1	2210410E06Rik|AV284120|T-synthase	core 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase, 1	protein-coding
mm_31844.1	chr4	74251993	74252009	+	1	NA	5' UTR (NM_144787, exon 1 of 22)	5' UTR (NM_144787, exon 1 of 22)	122	NM_144787	76804	Mm.209059	NM_144787	ENSMUSG00000028397	Kdm4c	2410141F18Rik|AA517467|Gasc1|Jmjd2c	lysine (K)-specific demethylase 4C	protein-coding
mm_59709.1	chr7	28735050	28735063	+	1	NA	intron (NM_001310687, intron 4 of 6)	intron (NM_001310687, intron 4 of 6)	6725	NM_011885	24030	Mm.358650	NM_011885	ENSMUSG00000045948	Mrps12	AI327385|Rpms12|rps12	mitochondrial ribosomal protein S12	protein-coding
mm_138521.1	chr17	35238343	35238371	+	1	NA	3' UTR (NM_023179, exon 3 of 3)	3' UTR (NM_023179, exon 3 of 3)	1761	NM_023179	66237	Mm.396107	NM_023179	ENSMUSG00000024403	Atp6v1g2	1500002D01Rik|Atp6g2|NG38|VAG2	ATPase, H+ transporting, lysosomal V1 subunit G2	protein-coding
mm_52788.1	chr6	121260963	121260989	+	1	NA	intron (NM_011909, intron 4 of 10)	intron (NM_011909, intron 4 of 10)	15070	NM_011909	24110	Mm.326911	NM_011909	ENSMUSG00000030107	Usp18	1110058H21Rik|AW047653|UBP43|Ubp15	ubiquitin specific peptidase 18	protein-coding
mm_34712.1	chr4	152116435	152116443	+	1	NA	promoter-TSS (NM_033042)	promoter-TSS (NM_033042)	96	NM_033042	85030	Mm.101198	NM_033042	ENSMUSG00000024793	Tnfrsf25	APO-3|DDR3|DR3|LARD|TR3|TRAMP|Tnfrsf12|WSL-1|WSL-LR|Wsl	tumor necrosis factor receptor superfamily, member 25	protein-coding
mm_9830.1	chr1	182517741	182517774	-	1	NA	promoter-TSS (NM_009794)	promoter-TSS (NM_009794)	-274	NM_009794	12334	Mm.19306	NM_009794	ENSMUSG00000026509	Capn2	AI326419|Capa-2|Capa2|m-calpain|m-calpin	calpain 2	protein-coding
mm_79708.1	chr9	61225605	61225622	+	1	NA	Intergenic	Intergenic	68196	NR_045334	622037	Mm.126243	NR_045334	ENSMUSG00000111658	B930092H01Rik	-	RIKEN cDNA B930092H01 gene	ncRNA
mm_143710.1	chr17	80702008	80702020	-	1	NA	intron (NM_001290345, intron 1 of 33)	intron (NM_001290345, intron 1 of 33)	26011	NM_001290345	225028	Mm.311948	NM_001081357	ENSMUSG00000024242	Map4k3	4833416M01Rik|4833416M07Rik|9530052P13Rik|Glk|MAPKKKK3|MEKKK 3|MEKKK3|RAB8IPL1	mitogen-activated protein kinase kinase kinase kinase 3	protein-coding
mm_59826.1	chr7	29289301	29289324	+	1	NA	promoter-TSS (NM_026731)	promoter-TSS (NM_026731)	-8	NM_026731	68458	Mm.2343	NM_026731	ENSMUSG00000037166	Ppp1r14a	1110001M11Rik|Cpi17	protein phosphatase 1, regulatory (inhibitor) subunit 14A	protein-coding
mm_121813.1	chr14	20393474	20393572	-	1	NA	promoter-TSS (NM_025440)	promoter-TSS (NM_025440)	32	NM_025440	66242	Mm.23747	NM_025440	ENSMUSG00000049960	Mrps16	1500011E11Rik|Mprs16	mitochondrial ribosomal protein S16	protein-coding
mm_52120.1	chr6	97929824	97929863	+	1	NA	promoter-TSS (NM_001178049)	promoter-TSS (NM_001178049)	26	NM_001178049	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_70531.1	chr8	13037293	13037303	+	1	NA	promoter-TSS (NM_007972)	promoter-TSS (NM_007972)	-10	NM_007972	14058	Mm.262589	NM_007972	ENSMUSG00000031444	F10	Cf10|fX	coagulation factor X	protein-coding
mm_68455.1	chr7	110121580	110121593	-	1	NA	promoter-TSS (NM_009516)	promoter-TSS (NM_009516)	-473	NM_009516	22390	Mm.287173	NM_009516	ENSMUSG00000031016	Wee1	Wee1A	WEE 1 homolog 1 (S. pombe)	protein-coding
mm_144725.1	chr18	35215077	35215130	+	1	NA	promoter-TSS (NM_178005)	promoter-TSS (NM_178005)	-79	NM_178005	107065	Mm.39900	NM_178005	ENSMUSG00000071862	Lrrtm2	AI851755|BB129880|C630011A14Rik|mKIAA0416	leucine rich repeat transmembrane neuronal 2	protein-coding
mm_8057.1	chr1	135375100	135375110	-	1	NA	promoter-TSS (NM_175259)	promoter-TSS (NM_175259)	-42	NM_175259	77552	Mm.41407	NM_175259	ENSMUSG00000041889	Shisa4	9330132O05Rik|Tmem58|mShisa4	shisa family member 4	protein-coding
mm_122748.1	chr14	54171351	54171356	-	1	NA	Intergenic	Intergenic	82576	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_75733.1	chr8	69453538	69453582	-	1	NA	Intergenic	Intergenic	-58016	NR_038043	378466	Mm.37846	NM_194351	ENSMUSG00000110444	Gm10033	9330175B10Rik|ENSMUSG00000057924|Gm10311	predicted gene 10033	ncRNA
mm_91810.1	chr10	53993785	53993804	-	1	NA	intron (NM_008548, intron 5 of 12)	intron (NM_008548, intron 5 of 12)	82002	NM_008548	17155	Mm.117294	NM_008548	ENSMUSG00000003746	Man1a	Man1a1|PCR1	mannosidase 1, alpha	protein-coding
mm_115923.1	chr13	23556115	23556123	-	1	NA	TTS (NM_145713)	TTS (NM_145713)	1087	NM_145713	14957	Mm.247046	NM_145713	ENSMUSG00000052565	Hist1h1d	H1.3|H1D|H1f3|H1s-4	histone cluster 1, H1d	protein-coding
mm_142008.1	chr17	35200314	35200333	-	1	NA	exon (NM_013693, exon 4 of 4)	exon (NM_013693, exon 4 of 4)	1684	NM_013693	21926	Mm.1293	NM_013693	ENSMUSG00000024401	Tnf	DIF|TNF-a|TNF-alpha|TNFSF2|TNFalpha|Tnfa|Tnfsf1a|Tnlg1f	tumor necrosis factor	protein-coding
mm_163048.1	chr11	57829271	57829271	-	1	NA	3' UTR (NM_008213, exon 2 of 2)	3' UTR (NM_008213, exon 2 of 2)	2876	NM_008213	15110	Mm.4746	NM_008213	ENSMUSG00000037335	Hand1	Ehand1|Hxt|Th1|Thing1|bHLHa27|eHAND	heart and neural crest derivatives expressed transcript 1	protein-coding
mm_26529.1	chr3	146117452	146117462	+	1	NA	Intergenic	Intergenic	-4334	NM_134160	171166	Mm.114683	NM_134160	ENSMUSG00000036853	Mcoln3	6720490O21Rik|TRPML3|Va	mucolipin 3	protein-coding
mm_27833.1	chr3	79129423	79129430	-	1	NA	intron (NM_001099624, intron 1 of 23)	intron (NM_001099624, intron 1 of 23)	15461	NM_001310536	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_25282.1	chr3	105558484	105558497	+	1	NA	intron (NM_001039347, intron 2 of 6)	intron (NM_001039347, intron 2 of 6)	99674	NM_019931	56543	Mm.44530	NM_019931	ENSMUSG00000040896	Kcnd3	AW045978|Kncd3|Kv4.3	potassium voltage-gated channel, Shal-related family, member 3	protein-coding
mm_35583.1	chr4	41741302	41741346	-	1	NA	promoter-TSS (NM_001286551)	promoter-TSS (NM_001286551)	35	NM_001286540	18391	Mm.425181	NM_011014	ENSMUSG00000036078	Sigmar1	Oprs1|Sig1R|sigma1R	sigma non-opioid intracellular receptor 1	protein-coding
mm_156861.1	chrX	164419783	164419824	+	1	NA	promoter-TSS (NM_011081)	promoter-TSS (NM_011081)	16	NM_011081	18700	Mm.3781	NM_011081	ENSMUSG00000031381	Piga	AI194334|Pig-a	phosphatidylinositol glycan anchor biosynthesis, class A	protein-coding
mm_24071.1	chr3	87919568	87919576	+	1	NA	promoter-TSS (NM_026591)	promoter-TSS (NM_026591)	28	NM_026591	67707	Mm.393802	NM_026591	ENSMUSG00000019710	Mrpl24	2010005E08Rik|2810470K06Rik|6720473G22Rik|AA407670	mitochondrial ribosomal protein L24	protein-coding
mm_118948.1	chr14	27360718	27360744	+	1	NA	promoter-TSS (NM_001289688)	promoter-TSS (NM_001289688)	-658	NM_001289688	71704	Mm.248606	NM_027871	ENSMUSG00000021895	Arhgef3	1200004I24Rik|9830169H03Rik|C76747|Xpln	Rho guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_57947.1	chr6	134897862	134897907	-	1	NA	promoter-TSS (NM_001167694)	promoter-TSS (NM_001167694)	41	NR_072990	14760	Mm.4787	NM_008157	ENSMUSG00000032641	Gpr19	-	G protein-coupled receptor 19	protein-coding
mm_5330.1	chr1	23891910	23891926	-	1	NA	exon (NM_028534, exon 2 of 10)	exon (NM_028534, exon 2 of 10)	17818	NR_110972	98366	Mm.329963	NM_028534	ENSMUSG00000026155	Smap1	1700056O10Rik|4921514B13Rik|4921525H11Rik|AI462175	small ArfGAP 1	protein-coding
mm_38376.1	chr4	138459920	138459932	-	1	NA	3' UTR (NM_025451, exon 2 of 2)	3' UTR (NM_025451, exon 2 of 2)	4778	NM_025451	66259	Mm.41603	NM_025451	ENSMUSG00000046447	Camk2n1	1810006K23Rik|AI848599|AI891706	calcium/calmodulin-dependent protein kinase II inhibitor 1	protein-coding
mm_168267.1	chr10	93665870	93665880	-	1	NA	promoter-TSS (NR_027478)	promoter-TSS (NR_027478)	-21	NR_027478	667338	Mm.454582	NR_027478		Gm8580	EG667338	ribosomal protein L29 pseudogene	pseudo
mm_45345.1	chr5	65858133	65858141	-	1	NA	Intergenic	Intergenic	-5432	NM_001081105	74734	Mm.20323	NM_001081105	ENSMUSG00000029204	Rhoh	5830400A04Rik|AU019774|Arhh	ras homolog family member H	protein-coding
mm_61069.1	chr7	51510992	51511000	+	1	NA	promoter-TSS (NM_177694)	promoter-TSS (NM_177694)	-33	NR_073508	233246	Mm.254431	NM_177694	ENSMUSG00000055489	Ano5	9330162L24|Gdd1|Tmem16e	anoctamin 5	protein-coding
mm_5122.1	chr1	9298822	9298878	-	1	NA	5' UTR (NM_001290390, exon 1 of 21)	5' UTR (NM_001290390, exon 1 of 21)	1027	NM_001290390	71096	Mm.336395	NM_027671	ENSMUSG00000025909	Sntg1	4933426D16Rik|G1SYN|SYN4	syntrophin, gamma 1	protein-coding
mm_113777.1	chr13	45389735	45389750	+	1	NA	promoter-TSS (NM_153789)	promoter-TSS (NM_153789)	0	NM_153789	218203	Mm.212855	NM_153789	ENSMUSG00000038175	Mylip	9430057C20Rik|Mir	myosin regulatory light chain interacting protein	protein-coding
mm_92246.1	chr10	70364698	70364709	-	1	NA	Intergenic	Intergenic	-75965	NM_001143777	71721	Mm.477813	NM_024244	ENSMUSG00000043259	Fam13c	1200015N20Rik|C030038O19Rik|mKIAA1796	family with sequence similarity 13, member C	protein-coding
mm_20230.1	chr2	125831346	125831349	-	1	NA	3' UTR (NM_001285513, exon 12 of 12)	3' UTR (NM_001285513, exon 12 of 12)	27735	NM_009939	12848	Mm.3596	NM_009939	ENSMUSG00000027206	Cops2	AI315723|C85265|Csn2|Sgn2|TRIP-15|Trip15	COP9 signalosome subunit 2	protein-coding
mm_30701.1	chr4	11758225	11758234	+	1	NA	promoter-TSS (NM_019753)	promoter-TSS (NM_019753)	72	NM_019753	12557	Mm.33402	NM_019753	ENSMUSG00000028217	Cdh17	HPT-1|HPT-1/LI	cadherin 17	protein-coding
mm_29309.1	chr3	107943706	107943741	-	1	NA	promoter-TSS (NM_008184)	promoter-TSS (NM_008184)	26	NM_008184	14867	Mm.458154	NM_008184	ENSMUSG00000068762	Gstm6	-	glutathione S-transferase, mu 6	protein-coding
mm_2078.1	chr1	87653332	87653342	+	1	NA	intron (NM_010566, intron 2 of 26)	intron (NM_010566, intron 2 of 26)	33025	NM_001110193	16331	Mm.15105	NM_010566	ENSMUSG00000026288	Inpp5d	SHIP|SHIP-1|SHIP1|SIP-145|p150Ship|s-SHIP	inositol polyphosphate-5-phosphatase D	protein-coding
mm_160420.1	chr8	84176554	84176554	-	1	NA	promoter-TSS (NM_194059)	promoter-TSS (NM_194059)	-2	NM_194059	244551	Mm.216740	NM_194059	ENSMUSG00000056155	Nanos3	nos3	nanos homolog 3 (Drosophila)	protein-coding
mm_69561.1	chr7	135700385	135700395	-	1	NA	exon (NM_001081117, exon 12 of 14)	exon (NM_001081117, exon 12 of 14)	15989	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_30847.1	chr4	24898081	24898158	+	1	NA	promoter-TSS (NM_026742)	promoter-TSS (NM_026742)	36	NM_026742	68493	Mm.204831	NM_026742	ENSMUSG00000028261	Ndufaf4	1110007M04Rik|3000003G13Rik|AW214064	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, assembly factor 4	protein-coding
mm_53861.1	chr6	149309783	149309824	+	1	NA	5' UTR (NM_001289662, exon 1 of 5)	5' UTR (NM_001289662, exon 1 of 5)	389	NM_001289662	67246	Mm.333515	NM_026054	ENSMUSG00000032712	2810474O19Rik	6720435I21Rik|AA536804|AU020969|GET|Kiaa1551	RIKEN cDNA 2810474O19 gene	protein-coding
mm_87255.1	chr10	41519456	41519480	+	1	NA	promoter-TSS (NM_016898)	promoter-TSS (NM_016898)	-32	NM_016898	53599	Mm.269815	NM_016898	ENSMUSG00000019818	Cd164	A115|A24|AA589639|AW540279|MGC-24|MSSP	CD164 antigen	protein-coding
mm_144272.1	chr18	11633341	11633357	+	1	NA	promoter-TSS (NM_001252495)	promoter-TSS (NM_001252495)	73	NR_045527	225182	Mm.154275	NM_175458	ENSMUSG00000041238	Rbbp8	9930104E21Rik|CtIP|RBBP-8|RIM|SAE2	retinoblastoma binding protein 8	protein-coding
mm_91599.1	chr10	40985684	40985688	-	1	NA	Intergenic	RLTR26_Mus|LTR|ERVK	85898	NM_199058	140741	Mm.290693	NM_199058	ENSMUSG00000046922	Gpr6	AI852874|Gm233	G protein-coupled receptor 6	protein-coding
mm_20882.1	chr2	148771557	148771569	-	1	NA	promoter-TSS (NM_030059)	promoter-TSS (NM_030059)	-66	NM_030059	78240	Mm.99424	NM_030059	ENSMUSG00000036958	Cst11	9230101F08Rik|BB067629|CRES2|mCSTE1	cystatin 11	protein-coding
mm_139527.1	chr17	56659694	56659698	+	1	NA	intron (NM_175350, intron 17 of 21)	intron (NM_175350, intron 17 of 21)	-13529	NM_001252466	71810	Mm.29608	NM_027933	ENSMUSG00000002372	Ranbp3	2610024N24Rik|AA408221	RAN binding protein 3	protein-coding
mm_47075.1	chr5	116591812	116591830	-	1	NA	promoter-TSS (NM_026886)	promoter-TSS (NM_026886)	-4	NM_026886	68955	Mm.146779	NM_026886	ENSMUSG00000063919	Srrm4	1500001A10Rik|B230202K19Rik|bv|mKIAA1853|nSR100	serine/arginine repetitive matrix 4	protein-coding
mm_116039.1	chr13	26787797	26787810	-	1	NA	Intergenic	Intergenic	-17638	NM_008232	15192	Mm.7411	NM_008232	ENSMUSG00000045835	Hdgfl1	4921520N01Rik|HRP-1|Hdgfrp1|Pwwp1	hepatoma derived growth factor-like 1	protein-coding
mm_63927.1	chr7	139403748	139403765	+	1	NA	intron (NM_183144, intron 1 of 15)	L1MB5|LINE|L1	14647	NM_001127363	212111	Mm.28308	NM_183144	ENSMUSG00000025477	Inpp5a	-	inositol polyphosphate-5-phosphatase A	protein-coding
mm_26889.1	chr3	18243268	18243276	-	1	NA	promoter-TSS (NM_007825)	promoter-TSS (NM_007825)	66	NM_007825	13123	Mm.316000	NM_007825	ENSMUSG00000039519	Cyp7b1	AW261589|D3Ertd552e|hct-1	cytochrome P450, family 7, subfamily b, polypeptide 1	protein-coding
mm_113535.1	chr13	37846340	37846350	+	1	NA	intron (NM_001039188, intron 1 of 9)	intron (NM_001039188, intron 1 of 9)	18952	NM_001039188	68750	Mm.491109	NM_026830	ENSMUSG00000039087	Rreb1	1110037N09Rik|AA414966|B930013M22Rik	ras responsive element binding protein 1	protein-coding
mm_62410.1	chr7	101219283	101219317	+	1	NA	intron (NM_199012, intron 8 of 20)	L1MB7|LINE|L1	82788	NM_001111111	73683	Mm.275744	NM_001111111	ENSMUSG00000047767	Atg16l2	2410118P20Rik	autophagy related 16-like 2 (S. cerevisiae)	protein-coding
mm_17313.1	chr2	26409214	26409236	-	1	NA	promoter-TSS (NM_033134)	promoter-TSS (NM_033134)	-6	NR_110957	64436	Mm.330070	NM_033134	ENSMUSG00000026925	Inpp5e	1200002L24Rik|72kDa|mKIAA0123	inositol polyphosphate-5-phosphatase E	protein-coding
mm_59035.1	chr7	19319026	19319043	+	1	NA	Intergenic	Intergenic	-8989	NM_001347586	14282	Mm.248335	NM_008036	ENSMUSG00000003545	Fosb	-	FBJ osteosarcoma oncogene B	protein-coding
mm_107482.1	chr12	38036777	38036778	+	1	NA	intron (NM_178681, intron 2 of 24)	intron (NM_178681, intron 2 of 24)	156072	NM_178681	217480	Mm.126525	NM_178681	ENSMUSG00000036095	Dgkb	6430574F24|90kda|C630029D13Rik|DAGK2|DGK|DGK-beta|mKIAA0718	diacylglycerol kinase, beta	protein-coding
mm_103063.1	chr11	69837737	69837764	-	1	NA	promoter-TSS (NM_026982)	promoter-TSS (NM_026982)	-775	NM_026982	69186	Mm.248772	NM_026982	ENSMUSG00000070394	Tmem256	1810027O10Rik|3110009M16Rik	transmembrane protein 256	protein-coding
mm_158092.1	chrX	101419789	101419859	-	1	NA	promoter-TSS (NM_001177986)	promoter-TSS (NM_001177986)	90	NM_001177986	56364	Mm.23458	NM_019831	ENSMUSG00000031310	Zmym3	9030216B10Rik|AW122925|DXS6673El|Zfp261	zinc finger, MYM-type 3	protein-coding
mm_81564.1	chr9	110415835	110415871	+	1	NA	Intergenic	Intergenic	-3955	NM_008694	18054	Mm.236225	NM_008694	ENSMUSG00000032484	Ngp	bectenecin	neutrophilic granule protein	protein-coding
mm_170479.1	chr19	12272991	12272993	+	1	NA	intron (NR_030566, intron 2 of 3)	intron (NR_030566, intron 2 of 3)	4760	NM_146686	258681	Mm.271522	NM_146686	ENSMUSG00000060049	Olfr235	MOR214-3|Olfr232|Olfr232-ps1|Olfr235-ps1|Olfr245|Olfr245-ps1	olfactory receptor 235	protein-coding
mm_6290.1	chr1	69759706	69759713	-	1	NA	Intergenic	Intergenic	-67261	NM_029160	66722	Mm.440554	NM_025728	ENSMUSG00000053153	Spag16	4921511D23Rik|4930524F24Rik|4930585K05Rik|AV261009|Pf20|Wdr29	sperm associated antigen 16	protein-coding
mm_168754.1	chr12	115964300	115964300	-	1	NA	Intergenic	Intergenic	-83424	NM_001004066	56220	Mm.254997	NM_019565	ENSMUSG00000042063	Zfp386	Kzf1|mKIAA4205	zinc finger protein 386 (Kruppel-like)	protein-coding
mm_80491.1	chr9	78427687	78427707	+	1	NA	Intergenic	CpG	15540	NR_125721	214763	Mm.101559	NM_173386	ENSMUSG00000032344	Mb21d1	E330016A19Rik|cGAS	Mab-21 domain containing 1	protein-coding
mm_115870.1	chr13	21531049	21531083	-	1	NA	promoter-TSS (NM_001251834)	promoter-TSS (NM_001251834)	48	NM_139141	93681	Mm.290601	NM_139141	ENSMUSG00000063894	Zkscan8	2510038J07Rik|D430019P06Rik|LD5-1|Zfp192	zinc finger with KRAB and SCAN domains 8	protein-coding
mm_121317.1	chr14	110239915	110239919	+	1	NA	Intergenic	Intergenic	515232	NM_175499	239250	Mm.49728	NM_175499	ENSMUSG00000045871	Slitrk6	4832410J21Rik|Sltk6	SLIT and NTRK-like family, member 6	protein-coding
mm_31769.1	chr4	63545396	63545398	+	1	NA	intron (NM_024173, intron 1 of 2)	intron (NM_024173, intron 1 of 2)	632	NM_024173	66290	Mm.371615	NM_024173	ENSMUSG00000039105	Atp6v1g1	1810024D14Rik|AA960677|ATP6J|Atp6g1|VAG1|Vma10	ATPase, H+ transporting, lysosomal V1 subunit G1	protein-coding
mm_16987.1	chr2	18050982	18050987	-	1	NA	Intergenic	Intergenic	-2535	NM_028317	72668	Mm.102183	NM_028317	ENSMUSG00000054074	Skida1	2810030E01Rik|5730507N06Rik|BB088113	SKI/DACH domain containing 1	protein-coding
mm_69134.1	chr7	127028121	127028129	-	1	NA	exon (NM_145588, exon 12 of 14)	exon (NM_145588, exon 12 of 14)	-1646	NM_010772	17188	Mm.378964	NM_010772	ENSMUSG00000030678	Maz	MAZI|PUR1|Pur-1|SAF-1|SAF-2	MYC-associated zinc finger protein (purine-binding transcription factor)	protein-coding
mm_41020.1	chr5	81461241	81461250	+	1	NA	intron (NM_001347371, intron 4 of 23)	(T)n|Simple_repeat|Simple_repeat	439652	NM_198702	319387	Mm.273631	NM_198702	ENSMUSG00000037605	Adgrl3	5430402I23Rik|CIRL-3|D130075K09Rik|Gm1379|LEC3|Lphn3|mKIAA0768	adhesion G protein-coupled receptor L3	protein-coding
mm_163101.1	chr11	69735407	69735412	-	1	NA	exon (NM_001291068, exon 29 of 29)	exon (NM_001291068, exon 29 of 29)	23224	NM_001291068	20020	Mm.16533	NM_009089	ENSMUSG00000005198	Polr2a	220kDa|Rpb1|Rpo2-1	polymerase (RNA) II (DNA directed) polypeptide A	protein-coding
mm_116501.1	chr13	44982848	44982858	-	1	NA	exon (NM_025772, exon 5 of 10)	exon (NM_025772, exon 5 of 10)	19243	NM_025772	94245	Mm.352311	NM_025772	ENSMUSG00000057531	Dtnbp1	5430437B18Rik|AW048963|Bloc1s8|dysbindin|sdy	dystrobrevin binding protein 1	protein-coding
mm_58963.1	chr7	18958580	18958594	+	1	NA	exon (NM_001029877, exon 4 of 4)	exon (NM_001029877, exon 4 of 4)	-28937	NM_194064	378430	Mm.277153	NM_194064	ENSMUSG00000051965	Nanos2	nos2	nanos homolog 2 (Drosophila)	protein-coding
mm_155754.1	chrX	96167433	96167443	+	1	NA	3' UTR (NM_010833, exon 13 of 13)	3' UTR (NM_010833, exon 13 of 13)	71393	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_6331.1	chr1	71626040	71626064	-	1	NA	exon (NM_001276413, exon 19 of 44)	exon (NM_001276413, exon 19 of 44)	27182	NM_010233	14268	Mm.193099	NM_010233	ENSMUSG00000026193	Fn1	E330027I09|Fn|Fn-1	fibronectin 1	protein-coding
mm_91054.1	chr10	18805067	18805070	-	1	NA	intron (NR_102728, intron 2 of 3)	MYSERV6-int|LTR|ERVK	-18275	NM_177706	237300	Mm.444821	NM_177706	ENSMUSG00000044624	Gm4922	4933423E17|EG237300	predicted gene 4922	protein-coding
mm_149904.1	chr19	25603191	25603195	+	1	NA	exon (NM_015826, exon 5 of 5)	exon (NM_015826, exon 5 of 5)	-7344	NM_177360	240590	Mm.62785	NM_177360	ENSMUSG00000042372	Dmrt3	-	doublesex and mab-3 related transcription factor 3	protein-coding
mm_90470.1	chr10	127849904	127849914	+	1	NA	promoter-TSS (NM_147222)	promoter-TSS (NM_147222)	-19	NM_147222	216453	Mm.222953	NM_147222	ENSMUSG00000054052	Rdh19	RDH-S|RDH-S2|Rdhs	retinol dehydrogenase 19	protein-coding
mm_111873.1	chr12	108003582	108003592	-	1	NA	promoter-TSS (NM_021399)	promoter-TSS (NM_021399)	-173	NM_021399	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_23064.1	chr3	36000418	36000440	+	1	NA	non-coding (NR_029456, exon 1 of 3)	non-coding (NR_029456, exon 1 of 3)	249	NM_023644	72039	Mm.249016	NM_023644	ENSMUSG00000027709	Mccc1	1810045E08Rik|2310058B18Rik|MCCalpha|Mcca|R75106	methylcrotonoyl-Coenzyme A carboxylase 1 (alpha)	protein-coding
mm_19015.1	chr2	76906315	76906321	-	1	NA	exon (NM_011652, exon 46 of 313)	exon (NM_011652, exon 46 of 313)	76229	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_33932.1	chr4	136890002	136890113	+	1	NA	exon (NM_007574, exon 3 of 3)	exon (NM_007574, exon 3 of 3)	2857	NM_007574	12262	Mm.439732	NM_007574	ENSMUSG00000036896	C1qc	AI385742|C1qg|Ciqc	complement component 1, q subcomponent, C chain	protein-coding
mm_161478.1	chr15	82082421	82082421	+	1	NA	promoter-TSS (NM_001310435)	promoter-TSS (NM_001310435)	-55	NM_001310435	74369	Mm.289351	NM_028897	ENSMUSG00000068117	Mei1	4932408F18Rik|mei1	meiotic double-stranded break formation protein 1	protein-coding
mm_33278.1	chr4	128727569	128727579	+	1	NA	promoter-TSS (NM_001195083)	promoter-TSS (NM_001195083)	3	NM_001195083	54383	Mm.473738	NM_018774	ENSMUSG00000028796	Phc2	A3galt2|AA415044|D130050K19Rik|D4Ertd810e|Edr2|Mph2|p36	polyhomeotic-like 2 (Drosophila)	protein-coding
mm_147392.1	chr18	44175215	44175228	-	1	NA	promoter-TSS (NM_183123)	promoter-TSS (NM_183123)	-148	NM_183123	77424	Mm.99224	NM_183123	ENSMUSG00000053729	Spinkl	9530002K18Rik	serine protease inhibitor, Kazal type-like	protein-coding
mm_132277.1	chr16	32973896	32973907	+	1	NA	exon (NM_001310673, exon 7 of 19)	exon (NM_001310673, exon 7 of 19)	59801	NM_001310672	70144	Mm.491178	NM_001081255	ENSMUSG00000022801	Lrch3	2210409B11Rik|AW215594|Gm1742	leucine-rich repeats and calponin homology (CH) domain containing 3	protein-coding
mm_78673.1	chr9	40780335	40780365	+	1	NA	intron (NM_133733, intron 5 of 6)	L2|LINE|L2	-20923	NM_031165	15481	Mm.290774	NM_031165	ENSMUSG00000015656	Hspa8	2410008N15Rik|Hsc70|Hsc71|Hsc73|Hsp73|Hspa10	heat shock protein 8	protein-coding
mm_82368.1	chr9	14614800	14614808	-	1	NA	5' UTR (NM_001081395, exon 1 of 13)	5' UTR (NM_001081395, exon 1 of 13)	196	NM_001081395	75723	Mm.159552	NM_001081395	ENSMUSG00000013076	Amotl1	2310010G08Rik|2310067L22Rik|4932416D09Rik|JEAP|mFLJ00155	angiomotin-like 1	protein-coding
mm_171325.1	chr3	96460191	96460193	-	1	NA	Intergenic	Intergenic	-7886	NM_001256180	329716	Mm.275223	NM_183223	ENSMUSG00000046317	BC107364	D730018G16	cDNA sequence BC107364	protein-coding
mm_13005.1	chr2	90904790	90904798	+	1	NA	promoter-TSS (NM_025991)	promoter-TSS (NM_025991)	8	NM_025991	67136	Mm.330394	NM_025991	ENSMUSG00000005505	Kbtbd4	2510026C23Rik	kelch repeat and BTB (POZ) domain containing 4	protein-coding
mm_4785.1	chr1	184034454	184034473	+	1	NA	promoter-TSS (NM_028516)	promoter-TSS (NM_028516)	2	NM_022019	63953	Mm.404024	NM_022019	ENSMUSG00000039384	Dusp10	2610306G15Rik|AI158871|MKP-5|MKP5	dual specificity phosphatase 10	protein-coding
mm_82334.1	chr9	9239053	9239095	-	1	NA	promoter-TSS (NM_027823)	promoter-TSS (NM_027823)	-61	NM_027823	71544	Mm.334955	NM_027823	ENSMUSG00000050730	Arhgap42	9030420J04Rik|BE136619	Rho GTPase activating protein 42	protein-coding
mm_114032.1	chr13	52648109	52648128	+	1	NA	3' UTR (NM_011518, exon 14 of 14)	3' UTR (NM_011518, exon 14 of 14)	51236	NM_011518	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_105152.1	chr11	101465191	101465222	-	1	NA	intron (NM_012037, intron 1 of 5)	intron (NM_012037, intron 1 of 5)	993	NM_012037	26949	Mm.29210	NM_012037	ENSMUSG00000034993	Vat1	VAT-1	vesicle amine transport 1	protein-coding
mm_85286.1	chr9	99710070	99710085	-	1	NA	promoter-TSS (NM_001194922)	promoter-TSS (NM_001194922)	-14	NM_001194922	56492	Mm.386784	NM_019815	ENSMUSG00000032473	Cldn18	-	claudin 18	protein-coding
mm_38170.1	chr4	135217255	135217262	-	1	NA	exon (NM_013885, exon 6 of 6)	exon (NM_013885, exon 6 of 6)	55502	NM_013885	29876	Mm.257765	NM_013885	ENSMUSG00000037242	Clic4	D0Jmb3|TU-74|mc3s5|mtCLIC	chloride intracellular channel 4 (mitochondrial)	protein-coding
mm_35487.1	chr4	40931291	40931318	-	1	NA	TTS (NM_011463)	TTS (NM_011463)	11248	NM_011463	20731	Mm.25246	NM_011463	ENSMUSG00000028415	Spink4	MPGC60	serine peptidase inhibitor, Kazal type 4	protein-coding
mm_63062.1	chr7	122078996	122079012	+	1	NA	3' UTR (NM_138589, exon 7 of 7)	3' UTR (NM_138589, exon 7 of 7)	11806	NM_138589	28018	Mm.282122	NM_138589	ENSMUSG00000030870	Ubfd1	AI467302|D7Wsu105e|D7Wsu128e|Ubph	ubiquitin family domain containing 1	protein-coding
mm_46322.1	chr5	100719676	100719706	-	1	NA	promoter-TSS (NM_152803)	promoter-TSS (NM_152803)	25	NM_152803	15442	Mm.265786	NM_152803	ENSMUSG00000035273	Hpse	HSE1|Hpa|Hpr1	heparanase	protein-coding
mm_57628.1	chr6	128300431	128300435	-	1	NA	5' UTR (NM_001080979, exon 1 of 11)	5' UTR (NM_001080979, exon 1 of 11)	380	NM_001080979	21679	Mm.14774	NM_011567	ENSMUSG00000030353	Tead4	ETFR-2|Etfr2|FR-19|Rtef1|TEAD-4|TEF-3|Tcf13r1|Tef3|Tefr|Tefr1|Tefr1a	TEA domain family member 4	protein-coding
mm_103938.1	chr11	83737308	83737319	-	1	NA	Intergenic	Intergenic	-9627	NM_183249	66107	Mm.902	NM_183249	ENSMUSG00000051748	Wfdc21	1100001G20Rik|Wdnm1-like	WAP four-disulfide core domain 21	protein-coding
mm_172719.1	chr8	70897382	70897383	-	1	NA	promoter-TSS (NM_029751)	promoter-TSS (NM_029751)	61	NM_029751	76808	Mm.379251	NM_029751	ENSMUSG00000045128	Rpl18a	2510019J09Rik	ribosomal protein L18A	protein-coding
mm_66079.1	chr7	30956606	30956624	-	1	NA	intron (NM_011680, intron 1 of 9)	CpG-12986	188	NM_011680	22282	Mm.322453	NM_011680	ENSMUSG00000058239	Usf2	Usf-2|bHLHb12	upstream transcription factor 2	protein-coding
mm_68022.1	chr7	100964372	100964395	-	1	NA	promoter-TSS (NM_183168)	promoter-TSS (NM_183168)	-17	NM_183168	233571	Mm.235193	NM_183168	ENSMUSG00000048779	P2ry6	2010204J23Rik|P2Y6	pyrimidinergic receptor P2Y, G-protein coupled, 6	protein-coding
mm_163342.1	chr12	16532779	16532791	+	1	NA	Intergenic	Intergenic	56985	NM_015763	14245	Mm.153625	NM_015763	ENSMUSG00000020593	Lpin1	4631420P06|Kiaa0188|Lipin1|fld|mKIAA0188	lipin 1	protein-coding
mm_148074.1	chr18	72350985	72350993	-	1	NA	promoter-TSS (NM_007831)	promoter-TSS (NM_007831)	80	NM_007831	13176	Mm.167882	NM_007831	ENSMUSG00000060534	Dcc	C030036D22Rik|Igdcc1	deleted in colorectal carcinoma	protein-coding
mm_42332.1	chr5	114902789	114902822	+	1	NA	intron (NM_011854, intron 3 of 5)	B4|SINE|B4	5871	NM_011854	23962	Mm.228363	NM_011854	ENSMUSG00000029561	Oasl2	M1204|Mmu-OASL|Oasl	2'-5' oligoadenylate synthetase-like 2	protein-coding
mm_46107.1	chr5	92348175	92348201	-	1	NA	exon (NM_021274, exon 2 of 4)	exon (NM_021274, exon 2 of 4)	701	NM_021274	15945	Mm.877	NM_021274	ENSMUSG00000034855	Cxcl10	C7|CRG-2|INP10|IP-10|IP10|Ifi10|Scyb10|gIP-10|mob-1	chemokine (C-X-C motif) ligand 10	protein-coding
mm_109782.1	chr12	119946105	119946133	+	1	NA	5' UTR (NM_001160385, exon 1 of 4)	5' UTR (NM_001160385, exon 1 of 4)	157	NM_001160385	217951	Mm.387395	NM_001160385	ENSMUSG00000048004	Tmem196	Gm528	transmembrane protein 196	protein-coding
mm_137915.1	chr17	32284462	32284484	+	1	NA	promoter-TSS (NM_001286630)	promoter-TSS (NM_001286630)	-340	NM_020508	57261	Mm.253518	NM_020508	ENSMUSG00000024002	Brd4	Brd5|HUNK1|MCAP|WI-11513	bromodomain containing 4	protein-coding
mm_133718.1	chr16	93683004	93683024	+	1	NA	promoter-TSS (NM_173047)	promoter-TSS (NM_173047)	-205	NM_173047	109857	Mm.4512	NM_173047	ENSMUSG00000022947	Cbr3	1110001J05Rik|C81353	carbonyl reductase 3	protein-coding
mm_36516.1	chr4	84456183	84456199	-	1	NA	intron (NM_172870, intron 2 of 5)	intron (NM_172870, intron 2 of 5)	218895	NM_172870	242509	Mm.190774	NM_172870	ENSMUSG00000028487	Bnc2	5031434M05Rik|8430420F16Rik	basonuclin 2	protein-coding
mm_47948.1	chr5	135460445	135460452	-	1	NA	exon (NM_146001, exon 2 of 31)	exon (NM_146001, exon 2 of 31)	-65902	NM_148932	107939	Mm.28399	NM_148932	ENSMUSG00000053293	Pom121	2610027A18Rik|C80273|mKIAA0618	nuclear pore membrane protein 121	protein-coding
mm_127557.1	chr15	102151079	102151098	+	1	NA	intron (NM_146064, intron 1 of 14)	intron (NM_146064, intron 1 of 14)	513	NM_146064	223920	Mm.358862	NM_146064	ENSMUSG00000023045	Soat2	ACAT2|D15Wsu97e	sterol O-acyltransferase 2	protein-coding
mm_73994.1	chr8	120697717	120697721	+	1	NA	Intergenic	Intergenic	29399	NM_001293559	12857	Mm.386758	NM_009941	ENSMUSG00000031818	Cox4i1	AL024441|COX|COX IV-1|COXIV|Cox4|Cox4a|IV-1	cytochrome c oxidase subunit IV isoform 1	protein-coding
mm_67801.1	chr7	98097673	98097689	-	1	NA	exon (NM_001256082, exon 6 of 49)	exon (NM_001256082, exon 6 of 49)	11567	NM_001256082	17921	Mm.1403	NM_008663	ENSMUSG00000030761	Myo7a	Hdb|Myo7|USH1B|nmf371|polka|sh-1|sh1	myosin VIIA	protein-coding
mm_113901.1	chr13	49215638	49215654	+	1	NA	intron (NM_026738, intron 1 of 5)	CpG	380	NM_026738	68480	Mm.3336	NM_026738	ENSMUSG00000037960	Card19	1110007C09Rik|AI851695|Bincard	caspase recruitment domain family, member 19	protein-coding
mm_54424.1	chr6	33060173	33060252	-	1	NA	promoter-TSS (NM_025336)	promoter-TSS (NM_025336)	-60	NM_025336	66075	Mm.21501	NM_025336	ENSMUSG00000053768	Chchd3	0610041L09Rik|1700039J09Rik|AW558177	coiled-coil-helix-coiled-coil-helix domain containing 3	protein-coding
mm_165803.1	chr3	144110793	144110801	-	1	NA	Intergenic	Intergenic	91535	NM_001161770	16911	Mm.29187	NM_010723	ENSMUSG00000028266	Lmo4	A730077C12Rik|Crp3|Etohi4	LIM domain only 4	protein-coding
mm_51980.1	chr6	91939002	91939003	+	1	NA	intron (NM_198668, intron 14 of 19)	intron (NM_198668, intron 14 of 19)	34769	NM_198668	381798	Mm.444785	NM_198668	ENSMUSG00000034063	4930590J08Rik	Gm1071	RIKEN cDNA 4930590J08 gene	protein-coding
mm_42524.1	chr5	115605643	115605651	+	1	NA	intron (NM_172719, intron 37 of 57)	ID_B1|SINE|B4	24698	NR_105996	102466790		NR_105996	ENSMUSG00000099047	Mir7029	Gm27293|mmu-mir-7029	microRNA 7029	ncRNA
mm_39587.1	chr5	23485355	23485367	+	1	NA	exon (NM_026984, exon 13 of 26)	exon (NM_026984, exon 13 of 26)	50932	NM_026984	69188	Mm.205190	NM_026984	ENSMUSG00000029004	Kmt2e	1810033J14Rik|9530077A04Rik|D230038D11Rik|Mll5|NKp44L	lysine (K)-specific methyltransferase 2E	protein-coding
mm_66053.1	chr7	30737844	30737867	-	1	NA	exon (NM_001290631, exon 2 of 11)	exon (NM_001290631, exon 2 of 11)	1552	NM_008085	14447	Mm.436562	NM_008085	ENSMUSG00000061099	Gapdhs	Gapd-s|Gapds	glyceraldehyde-3-phosphate dehydrogenase, spermatogenic	protein-coding
mm_21418.1	chr2	158128666	158128693	-	1	NA	exon (NM_009373, exon 8 of 13)	exon (NM_009373, exon 8 of 13)	17713	NM_009373	21817	Mm.330731	NM_009373	ENSMUSG00000037820	Tgm2	G[a]h|TG2|TGase2|tTG|tTGas	transglutaminase 2, C polypeptide	protein-coding
mm_130188.1	chr15	93679951	93679961	-	1	NA	Intergenic	Intergenic	-84065	NM_001033217	106042	Mm.150314	NM_001033217	ENSMUSG00000036158	Prickle1	1110058P22Rik|AW215793|Prickle|b2b019Clo|mpk1	prickle planar cell polarity protein 1	protein-coding
mm_1924.1	chr1	86053044	86053072	+	1	NA	exon (NM_001144992, exon 3 of 3)	exon (NM_001144992, exon 3 of 3)	7195	NM_001144992	72792	Mm.54981	NM_001144992	ENSMUSG00000026227	2810459M11Rik	-	RIKEN cDNA 2810459M11 gene	protein-coding
mm_81652.1	chr9	110953809	110953863	+	1	NA	intron (NM_028838, intron 1 of 8)	CpG	2291	NM_028838	74249	Mm.307615	NM_028838	ENSMUSG00000032495	Lrrc2	2400002D05Rik|4933431K03Rik	leucine rich repeat containing 2	protein-coding
mm_120002.1	chr14	55619039	55619063	+	1	NA	intron (NM_020002, intron 4 of 19)	intron (NM_020002, intron 4 of 19)	885	NM_020002	56739	Mm.23149	NM_020002	ENSMUSG00000002324	Rec8	Rec8L1|mrec	REC8 meiotic recombination protein	protein-coding
mm_39064.1	chr4	154026061	154026092	-	1	NA	promoter-TSS (NM_001163722)	promoter-TSS (NM_001163722)	-32	NM_001163721	68859	Mm.477488	NM_001033144	ENSMUSG00000078350	Smim1	0610011H04Rik|1190007F08Rik|2700009I11Rik	small integral membrane protein 1	protein-coding
mm_142860.1	chr17	51813569	51813579	-	1	NA	intron (NM_001163632, intron 1 of 10)	CpG	-1520	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_42346.1	chr5	114911046	114911056	+	1	NA	exon (NM_011854, exon 6 of 6)	exon (NM_011854, exon 6 of 6)	-12189	NM_145209	231655	Mm.95479	NM_145209	ENSMUSG00000041827	Oasl1	7530414C13Rik|oasl9	2'-5' oligoadenylate synthetase-like 1	protein-coding
mm_39755.1	chr5	29735838	29735850	+	1	NA	promoter-TSS (NM_001037941)	promoter-TSS (NM_001037941)	-54	NM_001037940	23950	Mm.290110	NM_011847	ENSMUSG00000029131	Dnajb6	Mrj|mDj4	DnaJ heat shock protein family (Hsp40) member B6	protein-coding
mm_167570.1	chr9	42776969	42777012	-	1	NA	intron (NM_175481, intron 3 of 20)	intron (NM_175481, intron 3 of 20)	167381	NM_175481	110637	Mm.370291	NM_175481	ENSMUSG00000032017	Grik4	6330551K01Rik|GluK4|GluRgamma1|KA-1|KA1	glutamate receptor, ionotropic, kainate 4	protein-coding
mm_135985.1	chr16	75092709	75092734	-	1	NA	Intergenic	Intergenic	493340	NM_001252513	320355	Mm.99517	NM_177142	ENSMUSG00000032948	Lipi	D930038D03Rik|lpd1	lipase, member I	protein-coding
mm_23274.1	chr3	51660373	51660375	+	1	NA	promoter-TSS (NM_174995)	promoter-TSS (NM_174995)	-805	NM_174995	211666	Mm.24679	NM_174995	ENSMUSG00000074604	Mgst2	GST2|MGST-II	microsomal glutathione S-transferase 2	protein-coding
mm_105691.1	chr11	107770025	107770049	-	1	NA	intron (NM_019431, intron 1 of 3)	B3A|SINE|B2	24427	NM_019431	54377	Mm.103724	NM_019431	ENSMUSG00000020723	Cacng4	AI413107|AW491861	calcium channel, voltage-dependent, gamma subunit 4	protein-coding
mm_45596.1	chr5	74711085	74711100	-	1	NA	Intergenic	Intergenic	-8189	NM_001159577	16924	Mm.440403	NM_010727	ENSMUSG00000029228	Lnx1	Lnx	ligand of numb-protein X 1	protein-coding
mm_159118.1	chr2	65670508	65670508	+	1	NA	exon (NM_001346679, exon 2 of 27)	exon (NM_001346679, exon 2 of 27)	1822	NM_001346680	110876	Mm.220329	NM_001099298	ENSMUSG00000075318	Scn2a	6430408L10|A230052E19Rik|Nav1.2|Scn2a1	sodium channel, voltage-gated, type II, alpha	protein-coding
mm_107901.1	chr12	70852934	70852937	+	1	NA	intron (NM_028127, intron 1 of 13)	intron (NM_028127, intron 1 of 13)	27421	NM_028127	319710	Mm.2962	NM_028127	ENSMUSG00000048285	Frmd6	2610019M19Rik|4930488L10Rik|AW212977|Willin	FERM domain containing 6	protein-coding
mm_116380.1	chr13	41036043	41036064	-	1	NA	intron (NM_001145802, intron 10 of 11)	Lx9|LINE|L1	19803	NM_025387	66154	Mm.30005	NM_025387	ENSMUSG00000021361	Tmem14c	1110021D01Rik|AU020193|HSPC194	transmembrane protein 14C	protein-coding
mm_32717.1	chr4	116221622	116221632	+	1	NA	promoter-TSS (NM_181585)	promoter-TSS (NM_181585)	-287	NM_181585	18710	Mm.253819	NM_181585	ENSMUSG00000028698	Pik3r3	AA414954|p55pik	phosphatidylinositol 3 kinase, regulatory subunit, polypeptide 3 (p55)	protein-coding
mm_129546.1	chr15	79403249	79403309	-	1	NA	promoter-TSS (NM_001253819)	promoter-TSS (NM_001253819)	-1	NM_001253819	223693	Mm.323358	NM_172608	ENSMUSG00000009035	Tmem184b	2610507A11|4732495E13Rik	transmembrane protein 184b	protein-coding
mm_49523.1	chr6	29985297	29985308	+	1	NA	promoter-TSS (NR_040264)	promoter-TSS (NR_040264)	-27	NR_040264	76419	Mm.84522	NR_040263	ENSMUSG00000045709	Smkr-ps	1700023L04Rik	smal lysine rich protein 1, pseudogene	ncRNA
mm_5485.1	chr1	36891615	36891636	-	1	NA	intron (NM_018872, intron 1 of 40)	intron (NM_018872, intron 1 of 40)	47902	NM_018872	56030	Mm.186943	NM_018872	ENSMUSG00000026116	Tmem131	2610524E03Rik|CC28|D1Bwg0491e|Neg|RW1|YR-23|mKIAA0257	transmembrane protein 131	protein-coding
mm_17390.1	chr2	27072204	27072216	-	1	NA	promoter-TSS (NM_025376)	promoter-TSS (NM_025376)	-49	NM_025376	66139	Mm.330087	NM_025376	ENSMUSG00000009214	Tmem8c	1110002H13Rik|AI131587	transmembrane protein 8C	protein-coding
mm_120899.1	chr14	75849563	75849563	+	1	NA	Intergenic	Intergenic	1640	NR_028481	100303751	Mm.484707	NR_028481	ENSMUSG00000065147	Snora31	MBI-161	small nucleolar RNA, H/ACA box 31	snoRNA
mm_59226.1	chr7	24638777	24638783	+	1	NA	intron (NM_133743, intron 3 of 4)	intron (NM_133743, intron 3 of 4)	2210	NM_133743	72434	Mm.281093	NM_133743	ENSMUSG00000057454	Lypd3	2310061G07Rik|C4.4a	Ly6/Plaur domain containing 3	protein-coding
mm_108667.1	chr12	86504761	86504767	+	1	NA	intron (NM_001159500, intron 3 of 6)	intron (NM_001159500, intron 3 of 6)	83120	NM_011934	26380	Mm.235550	NM_011934	ENSMUSG00000021255	Esrrb	Err2|Errb|Estrrb|Nr3b2	estrogen related receptor, beta	protein-coding
mm_146172.1	chr18	75367356	75367373	+	1	NA	promoter-TSS (NM_001042660)	promoter-TSS (NM_001042660)	-1	NM_001042660	17131	Mm.34407	NM_008543	ENSMUSG00000025880	Smad7	Madh7	SMAD family member 7	protein-coding
mm_120687.1	chr14	70774357	70774370	+	1	NA	promoter-TSS (NM_010071)	promoter-TSS (NM_010071)	-18	NM_010071	13449	Mm.243323	NM_010071	ENSMUSG00000022102	Dok2	DokR|Frip	docking protein 2	protein-coding
mm_156562.1	chrX	151803409	151803419	+	1	NA	5' UTR (NM_021523, exon 1 of 83)	5' UTR (NM_021523, exon 1 of 83)	132	NM_021523	59026	Mm.27372	NM_021523	ENSMUSG00000025261	Huwe1	5430439H10Rik|AU041296|Arf-bp1|C430014N20Rik|C80292|Gm1718|Ib772|LASU1|Mule|Ureb1	HECT, UBA and WWE domain containing 1	protein-coding
mm_28758.1	chr3	95871471	95871511	-	1	NA	promoter-TSS (NR_040446)	promoter-TSS (NR_040446)	-31	NR_040446	100042889	Mm.440109	NR_040446	ENSMUSG00000080727	C920021L13Rik	-	RIKEN cDNA C920021L13 gene	ncRNA
mm_107277.1	chr12	29534848	29534913	+	1	NA	promoter-TSS (NM_001093776)	promoter-TSS (NM_001093776)	-25	NM_001093776	17933	Mm.253067	NM_008666	ENSMUSG00000061911	Myt1l	2900046C06Rik|2900093J19Rik|C630034G21Rik|Nztf1|Pmng1|Png-1|mKIAA1106	myelin transcription factor 1-like	protein-coding
mm_172916.1	chr9	65196685	65196689	-	1	NA	Intergenic	U5|snRNA|snRNA	-18003	NM_177460	214424	Mm.31129	NM_177460	ENSMUSG00000032392	Parp16	ARTD15|BC055447|C79952|PARP-16	poly (ADP-ribose) polymerase family, member 16	protein-coding
mm_172592.1	chr8	12873938	12873947	+	1	NA	Intergenic	Intergenic	-41951	NM_178076	17207	Mm.334413	NM_178076	ENSMUSG00000031442	Mcf2l	C130040G20Rik|Dbs|Ost|mKIAA0362	mcf.2 transforming sequence-like	protein-coding
mm_13947.1	chr2	121298593	121298608	+	1	NA	exon (NM_032393, exon 3 of 7)	exon (NM_032393, exon 3 of 7)	3146	NM_001173506	17754	Mm.36501	NM_032393	ENSMUSG00000027254	Map1a	6330416M19Rik|AI853608|Mtap-1|Mtap1|Mtap1a|moth1	microtubule-associated protein 1 A	protein-coding
mm_101963.1	chr11	50301789	50301827	-	1	NA	exon (NM_001110500, exon 9 of 15)	exon (NM_001110500, exon 9 of 15)	-9472	NM_175334	103806	Mm.51116	NM_175334	ENSMUSG00000050567	Maml1	AI644666|AW743257|D930008C07Rik|Mam-1|Mam1|mKIAA0200	mastermind like 1 (Drosophila)	protein-coding
mm_5969.1	chr1	57098886	57098896	-	1	NA	Intergenic	Intergenic	116105	NR_037990	407809	Mm.134505	NR_037990	ENSMUSG00000101429	BC055402	-	cDNA sequence BC055402	ncRNA
mm_81257.1	chr9	107995729	107995738	+	1	NA	Intergenic	Intergenic	-6915	NM_013785	27399	Mm.276155	NM_013785	ENSMUSG00000032594	Ip6k1	1200016D08Rik|AU022776|Ihpk1|InsP6|InsP6k1|Itpk6	inositol hexaphosphate kinase 1	protein-coding
mm_82917.1	chr9	35055786	35055808	-	1	NA	intron (NM_009178, intron 1 of 10)	intron (NM_009178, intron 1 of 10)	-60931	NR_029475	78934	Mm.391688	NR_029475	ENSMUSG00000070315	4930581F22Rik	-	RIKEN cDNA 4930581F22 gene	ncRNA
mm_60201.1	chr7	43427645	43427652	+	1	NA	Intergenic	Intergenic	-2453	NM_177693	233187	Mm.267027	NM_177693	ENSMUSG00000004613	Lim2	19kDa|4833403J20|MP19|To3	lens intrinsic membrane protein 2	protein-coding
mm_51989.1	chr6	92091529	92091537	+	1	NA	promoter-TSS (NM_001347342)	promoter-TSS (NM_001347342)	115	NM_011630	22026	Mm.87062	NM_011630	ENSMUSG00000005893	Nr2c2	TAK1|Tr4|mKIAA4145	nuclear receptor subfamily 2, group C, member 2	protein-coding
mm_157872.1	chrX	75416563	75416591	-	1	NA	promoter-TSS (NM_001166459)	promoter-TSS (NM_001166459)	7	NM_010839	105886298	Mm.16366	NM_010839	ENSMUSG00000090110	Cmc4	Mtcp1nb|p8MTCP1	C-x(9)-C motif containing 4	protein-coding
mm_151744.1	chr19	5001848	5001875	-	1	NA	Intergenic	CpG	-11890	NM_153553	225872	Mm.287867	NM_153553	ENSMUSG00000045903	Npas4	LE-PAS|Nxf	neuronal PAS domain protein 4	protein-coding
mm_22436.1	chr2	181691772	181691801	-	1	NA	promoter-TSS (NM_001291205)	promoter-TSS (NM_001291205)	31	NM_001291205	56470	Mm.274366	NM_026446	ENSMUSG00000002458	Rgs19	2610042F04Rik|AI324841|AW547781|GAIP	regulator of G-protein signaling 19	protein-coding
mm_169689.1	chr15	74530068	74530077	-	1	NA	intron (NM_174991, intron 2 of 30)	intron (NM_174991, intron 2 of 30)	13876	NM_174991	107831	Mm.43133	NM_174991	ENSMUSG00000034730	Adgrb1	B830018M07Rik|Bai1|R75078|mKIAA4089	adhesion G protein-coupled receptor B1	protein-coding
mm_88210.1	chr10	70204633	70204639	+	1	NA	promoter-TSS (NM_001304739)	promoter-TSS (NM_001304739)	-28	NM_001304739	69563	Mm.64672	NM_001304739	ENSMUSG00000019933	Mrln	2310015B20Rik|Mln	myoregulin	protein-coding
mm_63968.1	chr7	139944649	139944655	+	1	NA	exon (NM_009482, exon 2 of 2)	exon (NM_009482, exon 2 of 2)	796	NM_009482	22286	Mm.10205	NM_009482	ENSMUSG00000047751	Utf1	AI505934	undifferentiated embryonic cell transcription factor 1	protein-coding
mm_10784.1	chr2	24345262	24345272	+	1	NA	promoter-TSS (NM_001039701)	promoter-TSS (NM_001039701)	-24	NM_001159562	16181	Mm.882	NM_031167	ENSMUSG00000026981	Il1rn	F630041P17Rik|IL-1ra	interleukin 1 receptor antagonist	protein-coding
mm_160426.1	chr8	86862011	86862011	-	1	NA	exon (NM_030563, exon 2 of 7)	exon (NM_030563, exon 2 of 7)	23247	NM_030563	80750	Mm.25117	NM_030563	ENSMUSG00000031652	N4bp1	AI481586|C81621	NEDD4 binding protein 1	protein-coding
mm_87660.1	chr10	58485881	58485885	+	1	NA	intron (NM_011240, intron 24 of 28)	intron (NM_011240, intron 24 of 28)	-12054	NM_001162956	76138	Mm.211744	NM_001162956	ENSMUSG00000038010	Ccdc138	6230424H07Rik|BC042726	coiled-coil domain containing 138	protein-coding
mm_2813.1	chr1	130875983	130876008	+	1	NA	exon (NM_026976, exon 4 of 8)	exon (NM_026976, exon 4 of 8)	10218	NM_026976	69169	Mm.46042	NM_026976	ENSMUSG00000042474	Fcmr	1810037B05Rik|Faim3|FcmuR|Toso	Fc fragment of IgM receptor	protein-coding
mm_124095.1	chr14	79199201	79199227	-	1	NA	intron (NM_027906, intron 44 of 44)	ORR1C2|LTR|ERVL-MaLR	48153	NM_001033215	105590	Mm.486536	NM_001033215	ENSMUSG00000071262	Zfp957	AU017455	zinc finger protein 957	protein-coding
mm_85398.1	chr9	103358621	103358624	-	1	NA	intron (NM_175565, intron 3 of 4)	intron (NM_175565, intron 3 of 4)	6357	NM_001134427	321022	Mm.261025	NM_175565	ENSMUSG00000032803	Cdv3	2510010F10Rik|C230084J24Rik|C79446|TPP36	carnitine deficiency-associated gene expressed in ventricle 3	protein-coding
mm_73058.1	chr8	94377912	94377938	+	1	NA	Intergenic	Intergenic	-8575	NM_022331	64209	Mm.29151	NM_022331	ENSMUSG00000031770	Herpud1	Herp|Mifl|SUP	homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1	protein-coding
mm_138262.1	chr17	34593389	34593417	+	1	NA	intron (NM_017463, intron 1 of 8)	intron (NM_017463, intron 1 of 8)	932	NM_017463	18515	Mm.390957	NM_017463	ENSMUSG00000034673	Pbx2	AU043397|G17	pre B cell leukemia homeobox 2	protein-coding
mm_72848.1	chr8	88309733	88309750	+	1	NA	exon (NM_001037724, exon 6 of 28)	exon (NM_001037724, exon 6 of 28)	15537	NM_001037724	11513	Mm.288206	NM_007406	ENSMUSG00000031659	Adcy7	AA407758	adenylate cyclase 7	protein-coding
mm_170595.1	chr19	5802213	5802213	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	459	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_128404.1	chr15	44619911	44619912	-	1	NA	5' UTR (NM_019480, exon 1 of 7)	5' UTR (NM_019480, exon 1 of 7)	270	NM_019480	55960	Mm.287896	NM_019480	ENSMUSG00000022339	Ebag9	AI835379|Rcas1	estrogen receptor-binding fragment-associated gene 9	protein-coding
mm_84121.1	chr9	58555220	58555246	-	1	NA	Intergenic	CpG	-14293	NM_133983	102657	Mm.5356	NM_133983	ENSMUSG00000035914	Cd276	6030411F23Rik|AU016588|B7RP-2|B7h3	CD276 antigen	protein-coding
mm_36454.1	chr4	82505223	82505229	-	1	NA	5' UTR (NM_001113209, exon 1 of 12)	5' UTR (NM_001113209, exon 1 of 12)	553	NM_001286127	18028	Mm.317947	NM_008687	ENSMUSG00000008575	Nfib	6720429L07Rik|CTF|E030026I10Rik|NF-I/B|NF1-B|NFI-B	nuclear factor I/B	protein-coding
mm_89434.1	chr10	91116788	91116809	+	1	NA	3' UTR (NM_133668, exon 8 of 8)	3' UTR (NM_133668, exon 8 of 8)	7165	NM_133668	18674	Mm.298	NM_133668	ENSMUSG00000061904	Slc25a3	5730556H19Rik|PTP|Phc	solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 3	protein-coding
mm_116739.1	chr13	51756663	51756691	-	1	NA	intron (NM_001281880, intron 2 of 16)	intron (NM_001281880, intron 2 of 16)	37070	NM_001281880	20354	Mm.33903	NM_013660	ENSMUSG00000021451	Sema4d	CD100|Semacl2|Semaj|Semcl2|coll-4	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D	protein-coding
mm_39839.1	chr5	30887519	30887531	+	1	NA	Intergenic	Intergenic	-1327	NM_174849	231093	Mm.440364	NM_174849	ENSMUSG00000029165	Agbl5	9430057O19Rik|CCP5	ATP/GTP binding protein-like 5	protein-coding
mm_33916.1	chr4	136469756	136469815	+	1	NA	promoter-TSS (NM_024452)	promoter-TSS (NM_024452)	24	NM_024452	269593	Mm.485824	NM_024452	ENSMUSG00000001089	Luzp1	2700072H04Rik|AI266952|Luzp|mFLJ00226	leucine zipper protein 1	protein-coding
mm_148387.1	chr19	3377582	3377620	+	1	NA	intron (NM_013495, intron 14 of 18)	intron (NM_013495, intron 14 of 18)	-11256	NM_001039658	17771	Mm.209941	NM_010841	ENSMUSG00000024905	Mtl5	tesmin	metallothionein-like 5, testis-specific (tesmin)	protein-coding
mm_73868.1	chr8	118733385	118733388	+	1	NA	intron (NM_019707, intron 3 of 13)	intron (NM_019707, intron 3 of 13)	449775	NM_019707	12554	Mm.334841	NM_019707	ENSMUSG00000031841	Cdh13	4932416G01Rik|Cdht|Tcad	cadherin 13	protein-coding
mm_91767.1	chr10	51522433	51522458	-	1	NA	Intergenic	Intergenic	31547	NM_013532	14728	Mm.34408	NM_013532	ENSMUSG00000062593	Lilrb4a	CD85K|Gp49b|HM18|ILT3|LIR-5|Lilrb4|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4A	protein-coding
mm_67546.1	chr7	81493726	81493741	-	1	NA	TTS (NM_183143)	TTS (NM_183143)	192	NM_021492	11775	Mm.322894	NM_021492	ENSMUSG00000062444	Ap3b2	AI549966|AU042881|Naptb|[b]-NAP|beta-NAP|beta3B	adaptor-related protein complex 3, beta 2 subunit	protein-coding
mm_20906.1	chr2	150306802	150306813	-	1	NA	Intergenic	Intergenic	49290	NM_001142410	100216455	Mm.484816	NM_001142410	ENSMUSG00000079008	Gm14124	EG640962|ENSMUSG00000074735|Gm10749|OTTMUSG00000015734	predicted gene 14124	protein-coding
mm_1337.1	chr1	66062807	66062856	+	1	NA	Intergenic	Intergenic	-112498	NM_008632	17756	Mm.256966	NM_008632	ENSMUSG00000015222	Map2	G1-397-34|MAP-2|Mtap-2|Mtap2|repro4	microtubule-associated protein 2	protein-coding
mm_108814.1	chr12	95692314	95692324	+	1	NA	promoter-TSS (NM_201518)	promoter-TSS (NM_201518)	93	NM_201518	399558	Mm.341948	NM_201518	ENSMUSG00000047414	Flrt2	-	fibronectin leucine rich transmembrane protein 2	protein-coding
mm_106635.1	chr11	120938125	120938156	-	1	NA	Intergenic	Intergenic	-5268	NM_027745	71276	Mm.275751	NM_027745	ENSMUSG00000048445	Ccdc57	4933434G05Rik	coiled-coil domain containing 57	protein-coding
mm_162502.1	chr1	143093627	143093688	+	1	NA	Intergenic	Intergenic	-547040	NM_020025	26878	Mm.285580	NM_020025	ENSMUSG00000033849	B3galt2	-	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 2	protein-coding
mm_9771.1	chr1	181001900	181001917	-	1	NA	exon (NM_010145, exon 2 of 9)	exon (NM_010145, exon 2 of 9)	15661	NM_010145	13849	Mm.9075	NM_010145	ENSMUSG00000038776	Ephx1	EH|Eph-1|Eph1|Epxh1|mEH	epoxide hydrolase 1, microsomal	protein-coding
mm_70299.1	chr8	4087446	4087454	+	1	NA	Intergenic	CpG	18314	NM_026956	69142	Mm.171061	NM_026956	ENSMUSG00000051906	Cd209f	1810029C22Rik|AI647041|SIGNR8	CD209f antigen	protein-coding
mm_144506.1	chr18	24653830	24653844	+	1	NA	5' UTR (NM_026779, exon 1 of 15)	5' UTR (NM_026779, exon 1 of 15)	146	NM_026779	68591	Mm.28252	NM_026779	ENSMUSG00000039616	Mocos	1110018O12Rik|HMCS|MCS|MOS	molybdenum cofactor sulfurase	protein-coding
mm_113090.1	chr13	23967282	23967287	+	1	NA	intron (NM_145399, intron 6 of 10)	intron (NM_145399, intron 6 of 10)	23930	NM_145399	214189	Mm.255667	NM_145399	ENSMUSG00000021337	Scgn	-	secretagogin, EF-hand calcium binding protein	protein-coding
mm_110520.1	chr12	54862784	54862921	-	1	NA	promoter-TSS (NM_007688)	promoter-TSS (NM_007688)	25	NM_007688	12632	Mm.276826	NM_007688	ENSMUSG00000062929	Cfl2	-	cofilin 2, muscle	protein-coding
mm_75015.1	chr8	29219578	29219623	-	1	NA	promoter-TSS (NM_001347499)	promoter-TSS (NM_001347499)	36	NM_001347499	210801	Mm.248433	NM_153135	ENSMUSG00000063626	Unc5d	D930029E11Rik|Unc5h4|mKIAA1777	unc-5 netrin receptor D	protein-coding
mm_132189.1	chr16	32431044	32431054	+	1	NA	promoter-TSS (NM_001163160)	promoter-TSS (NM_001163160)	29	NM_001163159	13026	Mm.98775	NM_009981	ENSMUSG00000005615	Pcyt1a	CTalpha|Cctalpha|Ctpct|Cttalpha	phosphate cytidylyltransferase 1, choline, alpha isoform	protein-coding
mm_54056.1	chr6	13839520	13839534	-	1	NA	intron (NM_145066, intron 1 of 3)	intron (NM_145066, intron 1 of 3)	415	NM_001330666	64450	Mm.167625	NM_145066	ENSMUSG00000048216	Gpr85	2900026B03Rik	G protein-coupled receptor 85	protein-coding
mm_35165.1	chr4	14621771	14621786	-	1	NA	promoter-TSS (NM_145947)	promoter-TSS (NM_145947)	0	NM_145947	208890	Mm.483839	NM_145947	ENSMUSG00000040569	Slc26a7	-	solute carrier family 26, member 7	protein-coding
mm_120555.1	chr14	68086639	68086653	+	1	NA	exon (NM_010910, exon 3 of 4)	exon (NM_010910, exon 3 of 4)	2762	NM_010910	18039	Mm.1956	NM_010910	ENSMUSG00000022055	Nefl	AI847934|CMT2E|NF-L|NF68|Nfl	neurofilament, light polypeptide	protein-coding
mm_144460.1	chr18	23415569	23415583	+	1	NA	5' UTR (NM_207650, exon 1 of 21)	5' UTR (NM_207650, exon 1 of 21)	167	NM_001285811	13527	Mm.94371	NM_010087	ENSMUSG00000024302	Dtna	2210407P21Rik|DTN-A|Dtn|Gm19389|a-DB-1|adbn	dystrobrevin alpha	protein-coding
mm_134342.1	chr16	16560147	16560197	-	1	NA	promoter-TSS (NM_139232)	promoter-TSS (NM_139232)	47	NM_139232	224014	Mm.256131	NM_139232	ENSMUSG00000022788	Fgd4	9030023J02Rik|9330209B17Rik|Frabp|ZFYVE6	FYVE, RhoGEF and PH domain containing 4	protein-coding
mm_113540.1	chr13	37857962	37857992	+	1	NA	intron (NM_001039188, intron 1 of 9)	intron (NM_001039188, intron 1 of 9)	-30457	NR_033218	68750	Mm.491109	NM_026830	ENSMUSG00000039087	Rreb1	1110037N09Rik|AA414966|B930013M22Rik	ras responsive element binding protein 1	protein-coding
mm_141146.1	chr17	26505987	26505997	-	1	NA	3' UTR (NM_013642, exon 4 of 4)	3' UTR (NM_013642, exon 4 of 4)	2480	NM_013642	19252	Mm.239041	NM_013642	ENSMUSG00000024190	Dusp1	3CH134|MKP1|Ptpn16|U19515|erp|mkp-1	dual specificity phosphatase 1	protein-coding
mm_69143.1	chr7	127051949	127051987	-	1	NA	promoter-TSS (NM_026918)	promoter-TSS (NM_026918)	9	NM_026918	69036	Mm.21835	NM_026918	ENSMUSG00000049350	Zg16	1810010M01Rik|AI593689|ZG16p	zymogen granule protein 16	protein-coding
mm_171586.1	chr4	147641801	147641808	-	1	NA	intron (NM_145078, intron 1 of 4)	intron (NM_145078, intron 1 of 4)	704	NM_145078	112422	Mm.327194	NM_145078	ENSMUSG00000066000	Zfp979	2610305D13Rik|Ssm1b	zinc finger protein 979	protein-coding
mm_120607.1	chr14	70159316	70159320	+	1	NA	intron (NM_001004155, intron 1 of 6)	intron (NM_001004155, intron 1 of 6)	184	NM_001112735	268759	Mm.12148	NM_001004155	ENSMUSG00000044551	9930012K11Rik	-	RIKEN cDNA 9930012K11 gene	protein-coding
mm_24198.1	chr3	88615405	88615434	+	1	NA	promoter-TSS (NM_001198911)	promoter-TSS (NM_001198911)	-788	NM_001198911	16800	Mm.239329	NM_008487	ENSMUSG00000028059	Arhgef2	AA408978|GEF|GEF-H1|GEFH1|LFP40|Lbcl1|Lfc|P40|mKIAA0651	rho/rac guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_89334.1	chr10	87933375	87933393	+	1	NA	3' UTR (NM_010512, exon 5 of 5)	3' UTR (NM_010512, exon 5 of 5)	-33287	NR_000040	22172	Mm.391420	NR_000040		Tyms-ps	-	thymidylate synthase, pseudogene	pseudo
mm_158124.1	chrX	102505394	102505412	-	1	NA	promoter-TSS (NM_001313742)	promoter-TSS (NM_001313742)	-245	NM_027382	70315	Mm.328128	NM_027382	ENSMUSG00000067567	Hdac8	2610007D20Rik	histone deacetylase 8	protein-coding
mm_22012.1	chr2	167777270	167777282	-	1	NA	Intergenic	Intergenic	86099	NR_015500	329562	Mm.123101	NM_177851	ENSMUSG00000006462	A530013C23Rik	-	RIKEN cDNA A530013C23 gene	ncRNA
mm_141546.1	chr17	32034494	32034523	-	1	NA	promoter-TSS (NM_028902)	promoter-TSS (NM_028902)	0	NM_028902	74377	Mm.75856	NM_028902	ENSMUSG00000002076	Hsf2bp	4932437G14Rik	heat shock transcription factor 2 binding protein	protein-coding
mm_147330.1	chr18	42862636	42862639	-	1	NA	intron (NM_028392, intron 1 of 8)	intron (NM_028392, intron 1 of 8)	36869	NR_073583	72930	Mm.26134	NM_027531	ENSMUSG00000024500	Ppp2r2b	2900026H06Rik|6330404L05Rik|E130009M08Rik|PP2A-PR55B|PR55-BETA|SCA12	protein phosphatase 2, regulatory subunit B, beta	protein-coding
mm_84259.1	chr9	62536947	62536951	-	1	NA	promoter-TSS (NM_175484)	promoter-TSS (NM_175484)	95	NM_175484	235431	Mm.335229	NM_175484	ENSMUSG00000041729	Coro2b	CLIPINC|E130012P22Rik	coronin, actin binding protein, 2B	protein-coding
mm_41619.1	chr5	96831475	96831489	+	1	NA	intron (NM_013470, intron 10 of 12)	intron (NM_013470, intron 10 of 12)	38097	NM_013470	11745	Mm.7214	NM_013470	ENSMUSG00000029484	Anxa3	Anx3	annexin A3	protein-coding
mm_61939.1	chr7	90182368	90182384	+	1	NA	intron (NM_001252520, intron 13 of 20)	intron (NM_001252520, intron 13 of 20)	52144	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_41975.1	chr5	107431566	107431571	+	1	NA	promoter-TSS (NM_027599)	promoter-TSS (NM_027599)	19	NM_027599	70902	Mm.55870	NM_027599	ENSMUSG00000033794	Lpcat2b	4921521K07Rik|Aytl1b	lysophosphatidylcholine acyltransferase 2B	protein-coding
mm_153455.1	chr19	41077107	41077118	-	1	NA	promoter-TSS (NM_153520)	promoter-TSS (NM_153520)	1	NM_153520	226115	Mm.54119	NM_153520	ENSMUSG00000050121	Opalin	Tmem10|Tmp10	oligodendrocytic myelin paranodal and inner loop protein	protein-coding
mm_121423.1	chr14	120275760	120275769	+	1	NA	promoter-TSS (NM_207515)	promoter-TSS (NM_207515)	95	NM_175341	105559	Mm.238266	NM_175341	ENSMUSG00000022139	Mbnl2	1110002M11Rik|AI047808|AI837313|AI849185|AL118326|MBLL|R75232|mKIAA4072	muscleblind-like 2	protein-coding
mm_11486.1	chr2	32396255	32396280	+	1	NA	5' UTR (NM_133783, exon 1 of 7)	5' UTR (NM_133783, exon 1 of 7)	377	NM_133783	96979	Mm.28048	NM_133783	ENSMUSG00000026820	Ptges2	0610038H10Rik|C79137|Gbf1|Mpges2|Pges2	prostaglandin E synthase 2	protein-coding
mm_161070.1	chr12	76385949	76385949	+	1	NA	exon (NM_178744, exon 2 of 2)	exon (NM_178744, exon 2 of 2)	15683	NM_178744	268564	Mm.77065	NM_178744	ENSMUSG00000033454	Zbtb1	9430077A12|AI256369|Bsg2|C430003J21Rik	zinc finger and BTB domain containing 1	protein-coding
mm_148261.1	chr18	80901406	80901409	-	1	NA	intron (NM_001201569, intron 4 of 29)	L1_Mur3|LINE|L1	32651	NM_001201569	50771	Mm.247138	NM_015805	ENSMUSG00000024566	Atp9b	AA934181|Atpc2b|IIb|MMR	ATPase, class II, type 9B	protein-coding
mm_33310.1	chr4	129058319	129058342	+	1	NA	promoter-TSS (NM_029219)	promoter-TSS (NM_029219)	59	NM_029219	75234	Mm.259672	NM_029219	ENSMUSG00000028793	Rnf19b	4930534K13Rik|4930555L03Rik|Ibrdc3	ring finger protein 19B	protein-coding
mm_169128.1	chr13	58064042	58064048	-	1	NA	intron (NM_001195075, intron 6 of 16)	intron (NM_001195075, intron 6 of 16)	38383	NM_001195075	100503085	Mm.379256	NM_001195075	ENSMUSG00000014164	Klhl3	7530408C15Rik|AI430941|EG627648	kelch-like 3	protein-coding
mm_143350.1	chr17	67095390	67095393	-	1	NA	intron (NM_008984, intron 3 of 30)	intron (NM_008984, intron 3 of 30)	-69156	NR_049205	100885844		NR_049205	ENSMUSG00000093508	Mir5709	Gm22041|mir-5709|mmu-mir-5709	microRNA 5709	ncRNA
mm_87183.1	chr10	39198434	39198442	+	1	NA	Intergenic	Intergenic	-34644	NM_001127376	327743	Mm.208111	NM_001127376	ENSMUSG00000062074	Wisp3	CCN6|ENSMUSG00000062074|Gm735|WISP-3	WNT1 inducible signaling pathway protein 3	protein-coding
mm_168414.1	chr11	3202324	3202324	-	1	NA	promoter-TSS (NM_001166549)	promoter-TSS (NM_001166549)	-29	NM_001166548	74203	Mm.255649	NM_023743	ENSMUSG00000020454	Eif4enif1	2610509L04Rik|A930019J01Rik|AA410001|AU021239|Clast4|D11Ertd166e	eukaryotic translation initiation factor 4E nuclear import factor 1	protein-coding
mm_129675.1	chr15	81392312	81392316	-	1	NA	exon (NM_133726, exon 2 of 12)	exon (NM_133726, exon 2 of 12)	7380	NM_133726	70356	Mm.180337	NM_133726	ENSMUSG00000022403	St13	1110007I03Rik|3110002K08Rik|AW555194|HIP|HOP|HSPABP|HSPABP1|PRO0786|SNC6|p48	suppression of tumorigenicity 13	protein-coding
mm_3594.1	chr1	151454198	151454201	+	1	NA	intron (NM_026876, intron 12 of 14)	PB1D10|SINE|Alu	11806	NR_106150	102466847		NR_106150	ENSMUSG00000106406	Mir7682	mmu-mir-7682	microRNA 7682	ncRNA
mm_82039.1	chr9	122128935	122128950	+	1	NA	intron (NM_001164572, intron 1 of 5)	intron (NM_001164572, intron 1 of 5)	11676	NM_133741	20623	Mm.257989	NM_133741	ENSMUSG00000038145	Snrk	2010012F07Rik|AI448042|AW547029|E030034B15|R74830|mKIAA0096	SNF related kinase	protein-coding
mm_165351.1	chr2	120480293	120480307	+	1	NA	intron (NM_001109761, intron 1 of 20)	intron (NM_001109761, intron 1 of 20)	3391	NM_001109761	12335	Mm.458021	NM_007601	ENSMUSG00000079110	Capn3	AI323605|Capa-3|Capa3|Lp82|p94	calpain 3	protein-coding
mm_65355.1	chr7	24999013	24999019	-	1	NA	intron (NM_001290469, intron 4 of 22)	intron (NM_001290469, intron 4 of 22)	6921	NM_001290469	232975	Mm.44101	NM_144921	ENSMUSG00000040907	Atp1a3	Atpa-2	ATPase, Na+/K+ transporting, alpha 3 polypeptide	protein-coding
mm_151585.1	chr19	61224707	61224762	+	1	NA	3' UTR (NM_009970, exon 12 of 12)	3' UTR (NM_009970, exon 12 of 12)	3684	NM_009970	12982	Mm.287228	NM_009970	ENSMUSG00000059326	Csf2ra	CD116|Csfgmra|GM-CSF-Ra|GM-CSFR	colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)	protein-coding
mm_95074.1	chr11	32636449	32636451	+	1	NA	Intergenic	Intergenic	-6105	NM_001271348	103583	Mm.28017	NM_134015	ENSMUSG00000020271	Fbxw11	2310065A07Rik|AA536858|BTRC2|BTRCP2|Fbxw1b|HOS	F-box and WD-40 domain protein 11	protein-coding
mm_168441.1	chr1	138110542	138110544	-	1	NA	intron (NM_001111316, intron 10 of 31)	intron (NM_001111316, intron 10 of 31)	64583	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_128540.1	chr15	54952610	54952622	-	1	NA	Intergenic	CpG	-32470	NM_001285994	18606	Mm.250256	NM_015744	ENSMUSG00000022425	Enpp2	ATX|E-NPP 2|Npps2|PD-Ialpha|Pdnp2|lysoPLD	ectonucleotide pyrophosphatase/phosphodiesterase 2	protein-coding
mm_132464.1	chr16	36277146	36277182	+	1	NA	promoter-TSS (NM_001082543)	promoter-TSS (NM_001082543)	16	NM_001082543	20861	Mm.327618	NM_001082543	ENSMUSG00000071562	Stfa1	Stefin-3|Stf-3|Stf1|Stf3|Stfa3	stefin A1	protein-coding
mm_158688.1	chrX	160751287	160751299	-	1	NA	Intergenic	Intergenic	-16720	NM_011302	20147	Mm.41982	NM_011302	ENSMUSG00000031293	Rs1	Rs1h|Xlrs1|tmgc1	retinoschisis (X-linked, juvenile) 1 (human)	protein-coding
mm_34768.1	chr4	153694247	153694258	+	1	NA	Intergenic	Intergenic	-211422	NM_001099299	230959	Mm.318874	NM_001099299	ENSMUSG00000039546	Ajap1	Gm573	adherens junction associated protein 1	protein-coding
mm_74107.1	chr8	122870607	122870622	+	1	NA	Intergenic	CpG	22240	NM_007662	12555	Mm.1976	NM_007662	ENSMUSG00000031962	Cdh15	AI323380|Cdh14|Mcad	cadherin 15	protein-coding
mm_115190.1	chr13	108670577	108670581	+	1	NA	intron (NM_011056, intron 1 of 16)	intron (NM_011056, intron 1 of 16)	16402	NM_011056	238871	Mm.434429	NM_011056	ENSMUSG00000021699	Pde4d	9630011N22Rik|Dpde3	phosphodiesterase 4D, cAMP specific	protein-coding
mm_36087.1	chr4	58436853	58436864	-	1	NA	3' UTR (NM_010336, exon 4 of 4)	3' UTR (NM_010336, exon 4 of 4)	4240	NR_037278	100526502		NR_037278	ENSMUSG00000093293	Mir3095	mir-3095|mmu-mir-3095	microRNA 3095	ncRNA
mm_146328.1	chr18	80715075	80715088	+	1	NA	Intergenic	Intergenic	-2010	NM_001164109	18018	Mm.329560	NM_016791	ENSMUSG00000033016	Nfatc1	2210017P03Rik|AI449492|AV076380|NF-ATc|NFAT2|NFATc|Nfatcb	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 1	protein-coding
mm_28999.1	chr3	101582077	101582103	-	1	NA	exon (NM_144900, exon 16 of 23)	exon (NM_144900, exon 16 of 23)	22617	NM_144900	11928	Mm.193670	NM_144900	ENSMUSG00000033161	Atp1a1	Atpa-1|BC010319	ATPase, Na+/K+ transporting, alpha 1 polypeptide	protein-coding
mm_80834.1	chr9	97103945	97103953	+	1	NA	intron (NM_138756, intron 1 of 6)	MTD|LTR|ERVL-MaLR	7092	NM_138756	192287	Mm.228067	NM_138756	ENSMUSG00000032449	Slc25a36	C330005L02Rik	solute carrier family 25, member 36	protein-coding
mm_67280.1	chr7	78578135	78578154	-	1	NA	promoter-TSS (NM_182809)	promoter-TSS (NM_182809)	-306	NM_182809	18213	Mm.33496	NM_008746	ENSMUSG00000059146	Ntrk3	AW125844|Ntrk3_tv3|TrkC	neurotrophic tyrosine kinase, receptor, type 3	protein-coding
mm_20640.1	chr2	132021194	132021204	-	1	NA	intron (NM_175445, intron 1 of 10)	intron (NM_175445, intron 1 of 10)	8789	NM_175445	215653	Mm.204737	NM_175445	ENSMUSG00000027339	Rassf2	3830431H01Rik|9030412M04Rik|AI852669|AW495050	Ras association (RalGDS/AF-6) domain family member 2	protein-coding
mm_101673.1	chr11	37236231	37236314	-	1	NA	Intergenic	CpG	-292031	NM_011856	23964	Mm.439889	NM_011856	ENSMUSG00000049336	Tenm2	Odz2|Odz3|Ten-2|Ten-m2	teneurin transmembrane protein 2	protein-coding
mm_22372.1	chr2	181155366	181155377	-	1	NA	exon (NM_007906, exon 2 of 8)	exon (NM_007906, exon 2 of 8)	1644	NM_007906	13628	Mm.2645	NM_007906	ENSMUSG00000016349	Eef1a2	Eef1a|S1|wasted|wst	eukaryotic translation elongation factor 1 alpha 2	protein-coding
mm_16476.1	chr2	180732291	180732297	+	1	NA	intron (NM_183161, intron 2 of 12)	intron (NM_183161, intron 2 of 12)	6955	NM_183161	228993	Mm.87189	NM_183161	ENSMUSG00000023393	Slc17a9	1700019H03Rik|BC019537|Vnut	solute carrier family 17, member 9	protein-coding
mm_141418.1	chr17	29434676	29434694	-	1	NA	Intergenic	Intergenic	-56360	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_70415.1	chr8	11449035	11449045	+	1	NA	3' UTR (NM_009932, exon 48 of 48)	3' UTR (NM_009932, exon 48 of 48)	-28889	NR_126558	102132	Mm.37632	NR_126558	ENSMUSG00000096957	E230013L22Rik	AI645545	RIKEN cDNA E230013L22 gene	ncRNA
mm_120921.1	chr14	76433179	76433182	+	1	NA	intron (NM_001310646, intron 3 of 4)	B1F|SINE|Alu	17359	NM_207652	21807	Mm.153272	NM_009366	ENSMUSG00000022010	Tsc22d1	AA589566|AW105905|Egr5|TSC-22|Tgfb1i4|Tsc|Tsc22	TSC22 domain family, member 1	protein-coding
mm_62664.1	chr7	108938037	108938063	+	1	NA	exon (NM_025344, exon 3 of 8)	exon (NM_025344, exon 3 of 8)	3635	NM_025344	66085	Mm.182962	NM_025344	ENSMUSG00000031029	Eif3f	0610037M02Rik|AA409853|Eif3s5	eukaryotic translation initiation factor 3, subunit F	protein-coding
mm_49146.1	chr6	11925870	11925941	+	1	NA	promoter-TSS (NM_001168382)	promoter-TSS (NM_001168382)	24	NM_001168382	75725	Mm.212411	NM_029404	ENSMUSG00000029629	Phf14	1110001C23Rik|4932409F11Rik|5730446A07Rik|AA623952|AV297001|mKIAA0783	PHD finger protein 14	protein-coding
mm_67871.1	chr7	99170042	99170045	-	1	NA	intron (NM_026384, intron 1 of 7)	intron (NM_026384, intron 1 of 7)	12670	NM_026384	67800	Mm.180189	NM_026384	ENSMUSG00000030747	Dgat2	0610010B06Rik|ARAT|DGAT-2	diacylglycerol O-acyltransferase 2	protein-coding
mm_32814.1	chr4	117210826	117210832	+	1	NA	Intergenic	Intergenic	-28205	NM_134471	73804	Mm.247651	NM_134471	ENSMUSG00000028678	Kif2c	4930402F02Rik|ESTM5|Knsl6|MCAK|X83316	kinesin family member 2C	protein-coding
mm_81863.1	chr9	118926499	118926568	+	1	NA	promoter-TSS (NM_133710)	promoter-TSS (NM_133710)	-3	NM_133710	69274	Mm.439928	NM_133710	ENSMUSG00000047409	Ctdspl	2810418J22Rik|AI426263|HYA22|SCP3	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase-like	protein-coding
mm_162292.1	chr1	31020057	31020057	+	1	NA	intron (NR_136907, intron 3 of 3)	ORR1E|LTR|ERVL-MaLR	-70302	NM_011200	19243	Mm.491181	NM_011200	ENSMUSG00000026064	Ptp4a1	AA415290|AU019864|C130021B01|Prl-1	protein tyrosine phosphatase 4a1	protein-coding
mm_128677.1	chr15	60819717	60819720	-	1	NA	3' UTR (NM_001162926, exon 2 of 2)	3' UTR (NM_001162926, exon 2 of 2)	-3247	NR_030696	320469	Mm.230853	NM_177166		9930014A18Rik	-	RIKEN cDNA 9930014A18 gene	ncRNA
mm_42656.1	chr5	119625940	119625966	+	1	NA	promoter-TSS (NR_046178)	promoter-TSS (NR_046178)	11	NR_046178	330183	Mm.413133	NR_046178	ENSMUSG00000085708	Gm16063	G630008E18|OTTMUSG00000029664	predicted gene 16063	ncRNA
mm_34340.1	chr4	143413003	143413014	+	1	NA	5' UTR (NM_172877, exon 1 of 5)	5' UTR (NM_172877, exon 1 of 5)	582	NM_172877	242736	Mm.275953	NM_172877	ENSMUSG00000046862	Pramef8	4732496O08Rik|AU023234	PRAME family member 8	protein-coding
mm_33111.1	chr4	124737695	124737706	+	1	NA	Intergenic	Intergenic	-4150	NM_008385	16330	Mm.296202	NM_008385	ENSMUSG00000028894	Inpp5b	5PTase|AW260155|INPP5P	inositol polyphosphate-5-phosphatase B	protein-coding
mm_77531.1	chr8	123013459	123013473	-	1	NA	intron (NM_001081379, intron 1 of 12)	B3|SINE|B2	28818	NR_037865	77087	Mm.31567	NM_001081379	ENSMUSG00000035569	Ankrd11	2410104C19Rik|3010027A04Rik|6330578C09Rik|9530048I21Rik|AA930108|Gm176|Yod	ankyrin repeat domain 11	protein-coding
mm_102075.1	chr11	52264973	52265018	-	1	NA	intron (NM_001313981, intron 3 of 10)	intron (NM_001313981, intron 3 of 10)	17600	NM_009331	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_100923.1	chr11	6444385	6444439	-	1	NA	promoter-TSS (NM_029938)	promoter-TSS (NM_029938)	31	NM_029938	77605	Mm.27624	NM_029938	ENSMUSG00000041126	H2afv	C530002L11Rik|H2a.z-2|H2av	H2A histone family, member V	protein-coding
mm_149131.1	chr19	9002406	9002417	+	1	NA	exon (NM_009643, exon 5 of 5)	exon (NM_009643, exon 5 of 5)	13127	NM_001286518	66395	Mm.203866	NM_009643	ENSMUSG00000069833	Ahnak	DY6	AHNAK nucleoprotein (desmoyokin)	protein-coding
mm_47620.1	chr5	125245807	125245815	-	1	NA	Intergenic	CpG	-66597	NM_001253904	20602	Mm.278646	NM_011424	ENSMUSG00000029478	Ncor2	N-CoR|SMRT|SMRTe	nuclear receptor co-repressor 2	protein-coding
mm_49474.1	chr6	29526685	29526685	+	1	NA	promoter-TSS (NM_012057)	promoter-TSS (NM_012057)	60	NM_012057	27056	Mm.6479	NM_012057	ENSMUSG00000029771	Irf5	AW491843|mirf5	interferon regulatory factor 5	protein-coding
mm_94437.1	chr11	6292653	6292663	+	1	NA	promoter-TSS (NM_001252288)	promoter-TSS (NM_001252288)	100	NM_001252288	18293	Mm.276348	NM_010956	ENSMUSG00000020456	Ogdh	2210403E04Rik|2210412K19Rik|AA409584|d1401|mKIAA4192	oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)	protein-coding
mm_158657.1	chrX	156295947	156295949	-	1	NA	Intergenic	Intergenic	-243535	NR_033598	74941	Mm.484588	NR_033598		4930503H13Rik	-	gem (nuclear organelle) associated protein 8 pseudogene	pseudo
mm_107414.1	chr12	34653800	34653803	+	1	NA	intron (NM_001271386, intron 3 of 27)	intron (NM_001271386, intron 3 of 27)	-124912	NM_024124	79221	Mm.310551	NM_024124	ENSMUSG00000004698	Hdac9	AV022454|D030072B18Rik|HD7B|HD9|HDRP|Hdac7b|Mitr|mKIAA0744	histone deacetylase 9	protein-coding
mm_82091.1	chr9	123051327	123051347	+	1	NA	exon (NM_177911, exon 8 of 14)	exon (NM_177911, exon 8 of 14)	16596	NM_177911	331046	Mm.195309	NM_177911	ENSMUSG00000025787	Tgm4	9530008N10Rik|Eapa1|TGP	transglutaminase 4 (prostate)	protein-coding
mm_71381.1	chr8	45934611	45934661	+	1	NA	promoter-TSS (NM_001033246)	promoter-TSS (NM_001033246)	-13	NM_001033246	212392	Mm.296649	NM_001033246	ENSMUSG00000071104	Ccdc110	Gm172	coiled-coil domain containing 110	protein-coding
mm_92822.1	chr10	81461628	81461643	-	1	NA	3' UTR (NM_176954, exon 12 of 12)	3' UTR (NM_176954, exon 12 of 12)	11496	NM_001311127	319586	Mm.152689	NM_176954	ENSMUSG00000034818	Celf5	4930565A21Rik|Brunol5	CUGBP, Elav-like family member 5	protein-coding
mm_143082.1	chr17	57061990	57061995	-	1	NA	promoter-TSS (NM_177638)	promoter-TSS (NM_177638)	-239	NM_001347408	224912	Mm.284447	NM_177638	ENSMUSG00000044279	Crb3	5730439B18|AU015179|AU041752	crumbs family member 3	protein-coding
mm_9855.1	chr1	184792824	184792829	-	1	NA	intron (NM_001290273, intron 6 of 6)	A-rich|Low_complexity|Low_complexity	18474	NM_001290273	66112	Mm.272457	NM_001081361	ENSMUSG00000026621	Marc1	1300013F15Rik|Mosc1	mitochondrial amidoxime reducing component 1	protein-coding
mm_22764.1	chr3	20057879	20057885	+	1	NA	promoter-TSS (NR_105046)	promoter-TSS (NR_105046)	71	NM_009210	20585	Mm.209650	NM_009210	ENSMUSG00000002428	Hltf	AF010600|BC057116|P113|Smarca3|Snf2l3	helicase-like transcription factor	protein-coding
mm_42645.1	chr5	118628942	118628953	+	1	NA	intron (NM_001347445, intron 2 of 30)	intron (NM_001347445, intron 2 of 30)	68228	NM_172424	76199	Mm.206238	NM_172424	ENSMUSG00000018076	Med13l	2210413I17Rik|6330591G05Rik|9030618F05Rik|Thrap2|Trap240L|mKIAA1025	mediator complex subunit 13-like	protein-coding
mm_120961.1	chr14	77520218	77520232	+	1	NA	intron (NM_001253759, intron 7 of 19)	RLTR25A|LTR|ERVK	-13357	NR_033141	629678	Mm.390721	NM_001037935	ENSMUSG00000067973	Gm6994	EG629678	predicted gene 6994	ncRNA
mm_27975.1	chr3	80802680	80802730	-	1	NA	promoter-TSS (NM_013540)	promoter-TSS (NM_013540)	86	NM_013540	14800	Mm.220224	NM_013540	ENSMUSG00000033981	Gria2	GluA2|GluR-B|Glur-2|Glur2	glutamate receptor, ionotropic, AMPA2 (alpha 2)	protein-coding
mm_155130.1	chrX	49470556	49470579	+	1	NA	5' UTR (NM_001081123, exon 1 of 13)	5' UTR (NM_001081123, exon 1 of 13)	117	NM_001081123	75404	Mm.44305	NM_001081123	ENSMUSG00000036198	Arhgap36	1100001E04Rik|rho-gap	Rho GTPase activating protein 36	protein-coding
mm_132895.1	chr16	48844172	48844183	+	1	NA	exon (NM_020509, exon 4 of 4)	exon (NM_020509, exon 4 of 4)	1625	NM_020509	57262	Mm.441868	NM_020509	ENSMUSG00000061100	Retnla	1810019L16Rik|Fizz-1|Fizz1|HIMF|RELM-alpha|RELMa|RELMalpha|Xcp2	resistin like alpha	protein-coding
mm_8370.1	chr1	150797220	150797222	-	1	NA	intron (NM_001024720, intron 11 of 106)	L1VL2|LINE|L1	196214	NM_001024720	545370	Mm.379425	NM_001024720	ENSMUSG00000066842	Hmcn1	EG545370|FIBL-6|Gm201	hemicentin 1	protein-coding
mm_97167.1	chr11	75510078	75510104	+	1	NA	promoter-TSS (NM_001029938)	promoter-TSS (NM_001029938)	-3	NM_001029938	280408	Mm.41416	NM_001029938	ENSMUSG00000038195	Rilp	AI835553|Gm857	Rab interacting lysosomal protein	protein-coding
mm_165275.1	chr2	76807345	76807347	-	1	NA	intron (NM_028004, intron 67 of 191)	intron (NM_028004, intron 67 of 191)	132031	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_155823.1	chrX	100706842	100706842	+	1	NA	intron (NM_008446, intron 19 of 29)	ID_B1|SINE|B4	-23005	NM_023608	71584	Mm.283495	NM_023608	ENSMUSG00000019359	Gdpd2	9130017L10Rik|Gde3|Obdpf	glycerophosphodiester phosphodiesterase domain containing 2	protein-coding
mm_54760.1	chr6	41163554	41163576	-	1	NA	Intergenic	Intergenic	-128056	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_150678.1	chr19	42052822	42052833	+	1	NA	exon (NM_025752, exon 1 of 1)	exon (NM_025752, exon 1 of 1)	599	NM_025752	66765	Mm.440412	NM_025752	ENSMUSG00000090369	4933411K16Rik	-	RIKEN cDNA 4933411K16 gene	protein-coding
mm_72489.1	chr8	83702095	83702104	+	1	NA	Intergenic	ORR1D1|LTR|ERVL-MaLR	-2920	NM_177262	320795	Mm.213000	NM_177262	ENSMUSG00000057672	Pkn1	DBK|F730027O18Rik|PAK1|PRK1|Pkn|Prkcl1|Stk3	protein kinase N1	protein-coding
mm_101258.1	chr11	20881488	20881508	-	1	NA	Intergenic	MTE2a|LTR|ERVL-MaLR	-50390	NM_173752	216551	Mm.76694	NM_173752	ENSMUSG00000042363	Lgalsl	1110067D22Rik|A530071M23|Grpa|Hspc159|Lgalsla	lectin, galactoside binding-like	protein-coding
mm_156099.1	chrX	112558125	112558133	+	1	NA	3' UTR (NM_026333, exon 7 of 7)	3' UTR (NM_026333, exon 7 of 7)	-42397	NM_177747	245595	Mm.259846	NM_177747	ENSMUSG00000025529	Zfp711	2810409C01Rik|A230078I01Rik|Znf711	zinc finger protein 711	protein-coding
mm_163994.1	chr14	64176437	64176440	+	1	NA	intron (NM_001347639, intron 5 of 5)	MIRc|SINE|MIR	72115	NM_028525	73382	Mm.481055	NM_028525	ENSMUSG00000021966	Prss52	1700049K14Rik|Tesp3	protease, serine 52	protein-coding
mm_111179.1	chr12	83921810	83921898	-	1	NA	promoter-TSS (NR_073564)	promoter-TSS (NR_073564)	80	NR_073563	18222	Mm.4390	NM_010949	ENSMUSG00000021224	Numb	Nb	numb homolog (Drosophila)	protein-coding
mm_43238.1	chr5	130029346	130029378	+	1	NA	promoter-TSS (NM_007761)	promoter-TSS (NM_007761)	56	NM_007761	12909	Mm.18072	NM_007761	ENSMUSG00000025532	Crcp	AL022669	calcitonin gene-related peptide-receptor component protein	protein-coding
mm_146849.1	chr18	24020308	24020364	-	1	NA	intron (NM_021559, intron 1 of 3)	CpG	435	NM_021559	59057	Mm.417427	NM_021559	ENSMUSG00000051469	Zfp24	3526401F17Rik|5033419P20Rik|AI480505|AI642085|AL024422|KOX17|ZF-12|Zfp191|Znf191|Znf24|Znp191	zinc finger protein 24	protein-coding
mm_6335.1	chr1	71628102	71628130	-	1	NA	exon (NM_001276413, exon 17 of 44)	exon (NM_001276413, exon 17 of 44)	25118	NM_010233	14268	Mm.193099	NM_010233	ENSMUSG00000026193	Fn1	E330027I09|Fn|Fn-1	fibronectin 1	protein-coding
mm_57934.1	chr6	134632389	134632404	-	1	NA	promoter-TSS (NM_026345)	promoter-TSS (NM_026345)	92	NM_026345	67729	Mm.57648	NM_026345	ENSMUSG00000032718	Mansc1	9130403P13Rik	MANSC domain containing 1	protein-coding
mm_70951.1	chr8	26977107	26977127	+	1	NA	promoter-TSS (NM_001110508)	promoter-TSS (NM_001110508)	-219	NM_001101502	353310	Mm.212469	NM_001101502	ENSMUSG00000085795	Zfp703	1110032O19Rik|AI430822|AL022941|Csmn1|End2|Zeppo1|Znf703|Zpo1	zinc finger protein 703	protein-coding
mm_62071.1	chr7	92705249	92705261	+	1	NA	Intergenic	MIRb|SINE|MIR	-35343	NM_029078	74737	Mm.288645	NM_029078	ENSMUSG00000041328	Pcf11	2500001H09Rik|5730417B17Rik|C77803	PCF11 cleavage and polyadenylation factor subunit	protein-coding
mm_111627.1	chr12	102437183	102437185	-	1	NA	intron (NM_011175, intron 1 of 13)	RSINE1|SINE|B4	2629	NM_011175	19141	Mm.17185	NM_011175	ENSMUSG00000021190	Lgmn	AEP|AI746452|AU022324|Prsc1	legumain	protein-coding
mm_128646.1	chr15	59525576	59525588	-	1	NA	intron (NM_026746, intron 4 of 6)	intron (NM_026746, intron 4 of 6)	-123072	NM_144549	211770	Mm.40298	NM_144549	ENSMUSG00000032501	Trib1	A530090O15Rik|TRB-1|Trb1	tribbles pseudokinase 1	protein-coding
mm_131804.1	chr16	22899389	22899399	+	1	NA	TTS (NM_001276450)	TTS (NM_001276450)	-5008	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_69701.1	chr7	140050893	140050903	-	1	NA	Intergenic	Intergenic	-1810	NM_001347609	17703	Mm.4816	NM_010836	ENSMUSG00000025469	Msx3	AI323377	msh homeobox 3	protein-coding
mm_17205.1	chr2	25470032	25470094	-	1	NA	promoter-TSS (NM_008963)	promoter-TSS (NM_008963)	-314	NM_008963	19215	Mm.1008	NM_008963	ENSMUSG00000015090	Ptgds	21kDa|L-PGDS|PGD2|PGDS|PGDS2|Ptgs3	prostaglandin D2 synthase (brain)	protein-coding
mm_75941.1	chr8	71566628	71566632	-	1	NA	promoter-TSS (NM_145598)	promoter-TSS (NM_145598)	19	NM_145598	234404	Mm.213208	NM_145598	ENSMUSG00000034829	Nxnl1	A930031O08Rik|RdCVF|Txnl6	nucleoredoxin-like 1	protein-coding
mm_28023.1	chr3	83046154	83046189	-	1	NA	exon (NM_181849, exon 3 of 8)	exon (NM_181849, exon 3 of 8)	3692	NM_181849	110135	Mm.30063	NM_181849	ENSMUSG00000033831	Fgb	2510049G14Rik	fibrinogen beta chain	protein-coding
mm_107535.1	chr12	40560241	40560260	+	1	NA	intron (NM_172803, intron 1 of 52)	intron (NM_172803, intron 1 of 52)	114197	NM_172803	238130	Mm.341423	NM_172803	ENSMUSG00000035954	Dock4	5330406C03|6330411N01Rik|AF263288|C030023J22|mKIAA0716	dedicator of cytokinesis 4	protein-coding
mm_61450.1	chr7	75586225	75586235	+	1	NA	exon (NM_029332, exon 5 of 37)	exon (NM_029332, exon 5 of 37)	130696	NM_029332	75547	Mm.216107	NM_029332	ENSMUSG00000066406	Akap13	1700026G02Rik|5730522G15Rik|5830460E08Rik|AKAP-13|AKAP-Lbc|BRX|Ht31|LBC|PROTO-LB|PROTO-LBC	A kinase (PRKA) anchor protein 13	protein-coding
mm_143353.1	chr17	67143440	67143457	-	1	NA	intron (NM_008984, intron 2 of 30)	(TGGA)n|Simple_repeat|Simple_repeat	-117213	NR_049205	100885844		NR_049205	ENSMUSG00000093508	Mir5709	Gm22041|mir-5709|mmu-mir-5709	microRNA 5709	ncRNA
mm_150409.1	chr19	36917068	36917075	+	1	NA	TTS (NM_028263)	TTS (NM_028263)	2528	NM_028263	72514	Mm.41674	NM_028263	ENSMUSG00000047632	Fgfbp3	2610306H15Rik|Fgf-bp3	fibroblast growth factor binding protein 3	protein-coding
mm_112819.1	chr13	20799093	20799104	+	1	NA	intron (NM_012054, intron 1 of 20)	RMER17C|LTR|ERVK	4985	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_53412.1	chr6	132595910	132595913	+	1	NA	promoter-TSS (NM_031499)	promoter-TSS (NM_031499)	-35	NM_031499	83380	Mm.333439	NM_031499	ENSMUSG00000058295	Prp2	MP14	proline rich protein 2	protein-coding
mm_21708.1	chr2	164593515	164593526	-	1	NA	promoter-TSS (NM_029325)	promoter-TSS (NM_029325)	51	NM_029325	75526	Mm.159533	NM_029325	ENSMUSG00000017733	Eppin	1700024E17Rik|Spinlw1	epididymal peptidase inhibitor	protein-coding
mm_59015.1	chr7	19256121	19256129	+	1	NA	TTS (NM_001282022)	TTS (NM_001282022)	15729	NM_001282021	22323	Mm.9684	NM_009499	ENSMUSG00000030403	Vasp	-	vasodilator-stimulated phosphoprotein	protein-coding
mm_128056.1	chr15	26062514	26062537	-	1	NA	Intergenic	RLTR51A_Mm|LTR|ERVK?	78159	NM_144523	52521	Mm.29145	NM_144523	ENSMUSG00000052253	Zfp622	1110033B05Rik|D15Ertd806e|ZPR9|Znf622	zinc finger protein 622	protein-coding
mm_54631.1	chr6	38693490	38693520	-	1	NA	Intergenic	Intergenic	30436	NM_001101507	665180	Mm.349066	NM_001101507	ENSMUSG00000079598	Clec2l	AI414054|AW122724|Gm1064	C-type lectin domain family 2, member L	protein-coding
mm_18910.1	chr2	76734795	76734819	-	1	NA	exon (NM_011652, exon 277 of 313)	exon (NM_011652, exon 277 of 313)	59492	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_62720.1	chr7	110772842	110772857	+	1	NA	5' UTR (NM_009667, exon 1 of 15)	5' UTR (NM_009667, exon 1 of 15)	245	NM_009667	11717	Mm.3238	NM_009667	ENSMUSG00000005686	Ampd3	-	adenosine monophosphate deaminase 3	protein-coding
mm_121839.1	chr14	20546518	20546582	-	1	NA	promoter-TSS (NM_008914)	promoter-TSS (NM_008914)	23	NM_001310426	19056	Mm.274432	NM_008914	ENSMUSG00000021816	Ppp3cb	1110063J16Rik|Calnb|CnAbeta|Cnab	protein phosphatase 3, catalytic subunit, beta isoform	protein-coding
mm_48391.1	chr5	139814199	139814229	-	1	NA	promoter-TSS (NM_001161548)	promoter-TSS (NM_001161548)	69	NM_001161548	231832	Mm.482655	NM_144914	ENSMUSG00000036687	Tmem184a	Sdmg1	transmembrane protein 184a	protein-coding
mm_51349.1	chr6	72555816	72555829	+	1	NA	exon (NM_001042534, exon 4 of 10)	exon (NM_001042534, exon 4 of 10)	6175	NM_001271395	12332	Mm.18626	NM_007599	ENSMUSG00000056737	Capg	gCap39|mbh1	capping protein (actin filament), gelsolin-like	protein-coding
mm_30542.1	chr4	3678109	3678134	+	1	NA	promoter-TSS (NM_001111096)	promoter-TSS (NM_001111096)	0	NM_001111096	17096	Mm.317331	NM_010747	ENSMUSG00000042228	Lyn	AA407514|Hck-2|p53Lyn|p56Lyn	LYN proto-oncogene, Src family tyrosine kinase	protein-coding
mm_16480.1	chr2	180890676	180890686	+	1	NA	Intergenic	Intergenic	-3359	NR_029538	723951		NR_029538	ENSMUSG00000065454	Mir124a-3	Mirn124a-3|mir-124-3|mir-124a-3	microRNA 124a-3	ncRNA
mm_51734.1	chr6	87073075	87073085	+	1	NA	intron (NM_013528, intron 11 of 18)	intron (NM_013528, intron 11 of 18)	30234	NM_013528	14583	Mm.19893	NM_013528	ENSMUSG00000029992	Gfpt1	2810423A18Rik|AI324119|AI449986|GFA|GFAT|GFAT1|GFAT1m|Gfpt	glutamine fructose-6-phosphate transaminase 1	protein-coding
mm_99362.1	chr11	101665555	101665572	+	1	NA	promoter-TSS (NM_025404)	promoter-TSS (NM_025404)	22	NM_025404	80981	Mm.266840	NM_025404	ENSMUSG00000034936	Arl4d	1110036H21Rik|ARL6|AW456149|Arf4l|Arfl4|Arl5	ADP-ribosylation factor-like 4D	protein-coding
mm_3182.1	chr1	135766219	135766225	+	1	NA	5' UTR (NM_013750, exon 1 of 2)	5' UTR (NM_013750, exon 1 of 2)	137	NM_013750	27280	Mm.34346	NM_013750	ENSMUSG00000041801	Phlda3	Tih1	pleckstrin homology like domain, family A, member 3	protein-coding
mm_24904.1	chr3	96195429	96195436	+	1	NA	TTS (NM_022030)	TTS (NM_022030)	2154	NM_026975	69168	Mm.104531	NM_026975	ENSMUSG00000015943	Bola1	1810037G04Rik	bolA-like 1 (E. coli)	protein-coding
mm_118048.1	chr13	101702121	101702127	-	1	NA	intron (NM_001077495, intron 5 of 15)	intron (NM_001077495, intron 5 of 15)	-9494	NM_001024955	18708	Mm.259333	NM_001024955	ENSMUSG00000041417	Pik3r1	PI3K|p50alpha|p55alpha|p85alpha	phosphatidylinositol 3-kinase, regulatory subunit, polypeptide 1 (p85 alpha)	protein-coding
mm_42649.1	chr5	118707407	118707409	+	1	NA	intron (NM_001347445, intron 4 of 30)	intron (NM_001347445, intron 4 of 30)	146689	NM_172424	76199	Mm.206238	NM_172424	ENSMUSG00000018076	Med13l	2210413I17Rik|6330591G05Rik|9030618F05Rik|Thrap2|Trap240L|mKIAA1025	mediator complex subunit 13-like	protein-coding
mm_133589.1	chr16	91425054	91425077	+	1	NA	exon (NM_008349, exon 7 of 7)	exon (NM_008349, exon 7 of 7)	18830	NM_008349	16155	Mm.4154	NM_008349	ENSMUSG00000022969	Il10rb	6620401D04Rik|AI528744|CRF2-4|Crfb4|D16H21S58|D21S58h|IL-10R2|Il10r2	interleukin 10 receptor, beta	protein-coding
mm_5809.1	chr1	52472934	52472937	-	1	NA	intron (NM_008667, intron 4 of 7)	intron (NM_008667, intron 4 of 7)	27513	NM_008667	17936	Mm.25903	NM_008667	ENSMUSG00000002881	Nab1	-	Ngfi-A binding protein 1	protein-coding
mm_110119.1	chr12	26443972	26443980	-	1	NA	3' UTR (NM_021384, exon 6 of 6)	3' UTR (NM_021384, exon 6 of 6)	12476	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_136256.1	chr16	90988752	90988770	-	1	NA	intron (NM_001164483, intron 4 of 31)	intron (NM_001164483, intron 4 of 31)	22334	NM_001045515	104015	Mm.187079	NM_001045515	ENSMUSG00000022973	Synj1	A930006D20Rik|AA675315|mKIAA0910	synaptojanin 1	protein-coding
mm_172699.1	chr8	63933293	63933293	-	1	NA	intron (NM_001195687, intron 5 of 7)	intron (NM_001195687, intron 5 of 7)	18877	NM_001195687	244495	Mm.485331	NM_001195687	ENSMUSG00000094443	Sgol2b	EG244495|Gm4975|Sgo2B	shugoshin like 2b (S. pombe)	protein-coding
mm_134631.1	chr16	21651032	21651051	-	1	NA	3' UTR (NM_001001881, exon 2 of 2)	3' UTR (NM_001001881, exon 2 of 2)	43624	NM_001001881	72190	Mm.131606	NM_001001881	ENSMUSG00000043391	2510009E07Rik	AI194952	RIKEN cDNA 2510009E07 gene	protein-coding
mm_92214.1	chr10	68239594	68239607	-	1	NA	intron (NM_023598, intron 3 of 9)	intron (NM_023598, intron 3 of 9)	39126	NM_023598	71371	Mm.440357	NM_023598	ENSMUSG00000019947	Arid5b	4930580B11|5430435G07Rik|AI467247|Desrt|Mrf2|Mrf2alpha|Mrf2beta	AT rich interactive domain 5B (MRF1-like)	protein-coding
mm_41970.1	chr5	107359607	107359618	+	1	NA	exon (NM_054054, exon 12 of 19)	exon (NM_054054, exon 12 of 19)	28418	NM_054054	114642	Mm.182836	NM_054054	ENSMUSG00000029279	Brdt	7420412D09Rik|Brd6|Fsrg3	bromodomain, testis-specific	protein-coding
mm_28654.1	chr3	95230395	95230419	-	1	NA	intron (NM_001038708, intron 1 of 4)	intron (NM_001038708, intron 1 of 4)	1464	NM_001038708	57912	Mm.28189	NM_172395	ENSMUSG00000046722	Cdc42se1	1300002M12Rik|AW558204|Cdcse1|SCIP1|Spec1	CDC42 small effector 1	protein-coding
mm_169464.1	chr14	65790723	65790724	-	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	-15188	NM_023209	52033	Mm.24337	NM_023209	ENSMUSG00000022033	Pbk	2810434B10Rik|AW538537|D14Ertd732e|TOPK	PDZ binding kinase	protein-coding
mm_98445.1	chr11	94943581	94943614	+	1	NA	exon (NM_007742, exon 24 of 51)	exon (NM_007742, exon 24 of 51)	7373	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_95578.1	chr11	52569219	52569219	+	1	NA	Intergenic	Intergenic	172791	NM_153117	213673	Mm.291979	NM_153117	ENSMUSG00000036275	9530068E07Rik	C85061|Kct2	RIKEN cDNA 9530068E07 gene	protein-coding
mm_81319.1	chr9	108479850	108479916	+	1	NA	promoter-TSS (NM_008483)	promoter-TSS (NM_008483)	21	NM_008483	16779	Mm.27560	NM_008483	ENSMUSG00000052911	Lamb2	AW211941|Lamb-2|Lams|npht	laminin, beta 2	protein-coding
mm_156885.1	chrX	166346610	166346612	+	1	NA	intron (NM_001177960, intron 1 of 7)	intron (NM_001177960, intron 1 of 7)	2058	NM_001177960	14758	Mm.222320	NM_023122	ENSMUSG00000031342	Gpm6b	AI593561|Gpm6|M6B	glycoprotein m6b	protein-coding
mm_86875.1	chr10	21997014	21997026	+	1	NA	exon (NM_001161847, exon 8 of 12)	exon (NM_001161847, exon 8 of 12)	2354	NM_011361	20393	Mm.28405	NM_011361	ENSMUSG00000019970	Sgk1	Sgk	serum/glucocorticoid regulated kinase 1	protein-coding
mm_122822.1	chr14	54653733	54653743	-	1	NA	promoter-TSS (NM_001242606)	promoter-TSS (NM_001242606)	-37	NM_001085472	56215	Mm.297078	NM_019567	ENSMUSG00000022185	Acin1	2610036I19Rik|2610510L13Rik|Acinus|Acn|C79325|acinusL|acinusS|mKIAA0670	apoptotic chromatin condensation inducer 1	protein-coding
mm_63631.1	chr7	128461938	128461974	+	1	NA	promoter-TSS (NM_009383)	promoter-TSS (NM_009383)	-283	NM_001347640	21843	Mm.242072	NM_009383	ENSMUSG00000030846	Tial1	5330433G13Rik|AL033329|TIAR|mTIAR	Tia1 cytotoxic granule-associated RNA binding protein-like 1	protein-coding
mm_67362.1	chr7	79838726	79838756	-	1	NA	exon (NM_008486, exon 7 of 20)	exon (NM_008486, exon 7 of 20)	3611	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_20722.1	chr2	136387741	136387798	-	1	NA	5' UTR (NM_172858, exon 1 of 10)	5' UTR (NM_172858, exon 1 of 10)	198	NM_172858	241656	Mm.131572	NM_172858	ENSMUSG00000039913	Pak7	2900083L08Rik|6430627N20|Pak5	p21 protein (Cdc42/Rac)-activated kinase 7	protein-coding
mm_150843.1	chr19	44957396	44957399	+	1	NA	intron (NM_001081225, intron 9 of 19)	B4|SINE|B4	26278	NM_001081225	226151	Mm.212609	NM_172638	ENSMUSG00000036097	Fam178a	3632432H19|6030443O07Rik|AU014917|Slf2	family with sequence similarity 178, member A	protein-coding
mm_17811.1	chr2	33641093	33641112	-	1	NA	promoter-TSS (NM_010725)	promoter-TSS (NM_010725)	-91	NR_046275	100504399	Mm.72070	NM_177842		C130021I20Rik	-	Riken cDNA C130021I20 gene	ncRNA
mm_6363.1	chr1	72212250	72212267	-	1	NA	promoter-TSS (NM_001005423)	promoter-TSS (NM_001005423)	49	NM_001005423	381269	Mm.422636	NM_001005423	ENSMUSG00000039395	Mreg	Gm974|Wdt2|dsu	melanoregulin	protein-coding
mm_68287.1	chr7	105633480	105633521	-	1	NA	promoter-TSS (NM_001285871)	promoter-TSS (NM_001285871)	71	NM_018880	55992	Mm.29290	NM_018880	ENSMUSG00000036989	Trim3	BERP1|HAC1|Rnf22	tripartite motif-containing 3	protein-coding
mm_27066.1	chr3	27863457	27863471	-	1	NA	Intergenic	Intergenic	32904	NM_001164437	208613	Mm.59189	NM_001164437	ENSMUSG00000043164	Tmem212	E030011K20Rik|Gm564	transmembrane protein 212	protein-coding
mm_98471.1	chr11	94950336	94950355	+	1	NA	exon (NM_007742, exon 48 of 51)	exon (NM_007742, exon 48 of 51)	14121	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_93227.1	chr10	95298638	95298642	-	1	NA	intron (NM_009950, intron 2 of 2)	intron (NM_009950, intron 2 of 2)	25069	NM_001330138	12905	Mm.473739	NM_009950	ENSMUSG00000045867	Cradd	RAIDD	CASP2 and RIPK1 domain containing adaptor with death domain	protein-coding
mm_1000.1	chr1	58714165	58714200	+	1	NA	intron (NM_009805, intron 1 of 4)	intron (NM_009805, intron 1 of 4)	896	NM_207653	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_1559.1	chr1	74125536	74125568	+	1	NA	promoter-TSS (NM_001170641)	promoter-TSS (NM_001170641)	11	NM_001170641	435626	Mm.240447	NM_001034060	ENSMUSG00000061815	Rufy4	F930048N03Rik	RUN and FYVE domain containing 4	protein-coding
mm_105112.1	chr11	100984869	100984878	-	1	NA	Intergenic	Intergenic	-14256	NM_008986	19285	Mm.21864	NM_008986	ENSMUSG00000004044	Ptrf	2310075E07Rik|AW546441|Cav-p60|Cavin	polymerase I and transcript release factor	protein-coding
mm_131319.1	chr16	11984157	11984170	+	1	NA	promoter-TSS (NM_028277)	promoter-TSS (NM_028277)	50	NM_001174086	72555	Mm.310139	NM_028277	ENSMUSG00000022494	Shisa9	2700045P11Rik|Ckamp44	shisa family member 9	protein-coding
mm_81888.1	chr9	119402082	119402153	+	1	NA	promoter-TSS (NM_007397)	promoter-TSS (NM_007397)	-61	NM_001313757	11481	Mm.8940	NM_007397	ENSMUSG00000061393	Acvr2b	4930516B21Rik|ActRIIB	activin receptor IIB	protein-coding
mm_56252.1	chr6	90763938	90763951	-	1	NA	intron (NM_001134384, intron 1 of 13)	intron (NM_001134384, intron 1 of 13)	46179	NM_001134384	232227	Mm.196943	NM_182784	ENSMUSG00000034312	Iqsec1	AW561907|BC026481|BRAG2|D6Ertd349e|cI-43	IQ motif and Sec7 domain 1	protein-coding
mm_168611.1	chr11	76357626	76357643	-	1	NA	intron (NM_008750, intron 1 of 7)	MLTR14|LTR|ERV1	41507	NM_008750	18230	Mm.27915	NM_008750	ENSMUSG00000020844	Nxn	l11Jus13	nucleoredoxin	protein-coding
mm_116827.1	chr13	54611310	54611326	-	1	NA	promoter-TSS (NM_028870)	promoter-TSS (NM_028870)	55	NM_028870	74325	Mm.290026	NM_028870	ENSMUSG00000047547	Cltb	2310046E19Rik|lcb	clathrin, light polypeptide (Lcb)	protein-coding
mm_55748.1	chr6	78371858	78371877	-	1	NA	exon (NM_011036, exon 3 of 6)	exon (NM_011036, exon 3 of 6)	982	NM_011036	18489	Mm.2553	NM_011036	ENSMUSG00000071356	Reg3b	HIP|PAP1|Pap|REG-III	regenerating islet-derived 3 beta	protein-coding
mm_156718.1	chrX	159706094	159706101	+	1	NA	intron (NM_001135727, intron 2 of 17)	MTD|LTR|ERVL-MaLR	-2504	NM_021389	58194	Mm.286495	NM_021389	ENSMUSG00000040990	Sh3kbp1	1200007H22Rik|1700125L08Rik|5830464D22Rik|AI447724|Cin85|IN85|Ruk|Seta	SH3-domain kinase binding protein 1	protein-coding
mm_100378.1	chr11	119270166	119270182	+	1	NA	exon (NM_008064, exon 2 of 20)	exon (NM_008064, exon 2 of 20)	2211	NM_008064	14387	Mm.4793	NM_008064	ENSMUSG00000025579	Gaa	E430018M07Rik	glucosidase, alpha, acid	protein-coding
mm_15008.1	chr2	152518248	152518269	+	1	NA	promoter-TSS (NM_001037502)	promoter-TSS (NM_001037502)	3	NM_001037502	545475	Mm.389378	NM_001037502	ENSMUSG00000074679	Defb28	Gm1635|OTTMUSG00000015852	defensin beta 28	protein-coding
mm_162303.1	chr1	36345106	36345120	-	1	NA	intron (NM_001310513, intron 17 of 21)	intron (NM_001310513, intron 17 of 21)	3645	NR_105863	102465541		NR_105863	ENSMUSG00000098680	Mir6898	Gm27816|mmu-mir-6898	microRNA 6898	ncRNA
mm_138935.1	chr17	43908630	43908651	+	1	NA	intron (NM_001286653, intron 2 of 4)	intron (NM_001286653, intron 2 of 4)	-44359	NM_001286654	53901	Mm.251242	NM_030598	ENSMUSG00000039601	Rcan2	Csp2|Dscr1l1|MCIP2|ZAKI-4	regulator of calcineurin 2	protein-coding
mm_75425.1	chr8	47166086	47166087	-	1	NA	Intergenic	B1_Mm|SINE|Alu	123316	NM_001286376	71069	Mm.23973	NM_175162	ENSMUSG00000038143	Stox2	4933409N07Rik|AI449080|AI835114|mKIAA1392	storkhead box 2	protein-coding
mm_167623.1	chr9	59355873	59355873	+	1	NA	Intergenic	Intergenic	-2365	NM_175325	102774	Mm.200714	NM_175325	ENSMUSG00000025235	Bbs4	AW537059|AW742241|D9Ertd464e	Bardet-Biedl syndrome 4 (human)	protein-coding
mm_95213.1	chr11	43682012	43682036	+	1	NA	promoter-TSS (NM_001164231)	promoter-TSS (NM_001164231)	26	NM_001164231	70802	Mm.397449	NM_027557	ENSMUSG00000044950	Pwwp2a	4631424J17Rik|AI891583|AU024105|D930040F23Rik	PWWP domain containing 2A	protein-coding
mm_32331.1	chr4	104367550	104367592	+	1	NA	promoter-TSS (NM_177259)	promoter-TSS (NM_177259)	33	NM_177259	13131	Mm.289682	NM_010014	ENSMUSG00000028519	Dab1	AI956902|C630028C02Rik|scm|scr|scrambler|yot	disabled 1	protein-coding
mm_36803.1	chr4	103173445	103173458	-	1	NA	3' UTR (NM_177732, exon 10 of 10)	3' UTR (NM_177732, exon 10 of 10)	41433	NM_177732	242585	Mm.281800	NM_177732	ENSMUSG00000028521	Slc35d1	AI834976|C330011J09|UGTREL7|mKIAA0260	solute carrier family 35 (UDP-glucuronic acid/UDP-N-acetylgalactosamine dual transporter), member D1	protein-coding
mm_30112.1	chr3	139075099	139075109	-	1	NA	promoter-TSS (NM_001286759)	promoter-TSS (NM_001286759)	97	NM_145544	229877	Mm.28893	NM_145544	ENSMUSG00000028149	Rap1gds1	BC011279|GDS1	RAP1, GTP-GDP dissociation stimulator 1	protein-coding
mm_27324.1	chr3	50367706	50367723	-	1	NA	3' UTR (NM_011990, exon 12 of 12)	3' UTR (NM_011990, exon 12 of 12)	75899	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_27193.1	chr3	34757955	34757965	-	1	NA	Intergenic	Intergenic	-14115	NR_110488	102638436	Mm.261793	NR_110488	ENSMUSG00000106519	Gm38509	Peril	predicted gene, 38509	ncRNA
mm_120324.1	chr14	63143063	63143068	+	1	NA	3' UTR (NM_007798, exon 10 of 10)	3' UTR (NM_007798, exon 10 of 10)	20603	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_132825.1	chr16	45224583	45224593	+	1	NA	intron (NM_177584, intron 1 of 5)	intron (NM_177584, intron 1 of 5)	251	NM_177584	208154	Mm.38199	NM_177584	ENSMUSG00000052013	Btla	A630002H24	B and T lymphocyte associated	protein-coding
mm_96129.1	chr11	60830659	60830686	+	1	NA	promoter-TSS (NM_001172112)	promoter-TSS (NM_001172112)	41	NM_145428	216820	Mm.21475	NM_145428	ENSMUSG00000042569	Dhrs7b	BC003479|C79874|C80074|PexRAP	dehydrogenase/reductase (SDR family) member 7B	protein-coding
mm_12233.1	chr2	68568593	68568649	+	1	NA	Intergenic	Intergenic	-13792	NM_177651	227998	Mm.67562	NM_177651	ENSMUSG00000053896	4933409G03Rik	-	RIKEN cDNA 4933409G03 gene	protein-coding
mm_24290.1	chr3	89245953	89245978	+	1	NA	promoter-TSS (NM_025327)	promoter-TSS (NM_025327)	-68	NM_183037	360213	Mm.331156	NM_183037	ENSMUSG00000042766	Trim46	TRIFIC	tripartite motif-containing 46	protein-coding
mm_150908.1	chr19	45998144	45998153	+	1	NA	intron (NM_198296, intron 1 of 25)	CpG	340	NM_198296	71617	Mm.210949	NM_198296	ENSMUSG00000039901	9130011E15Rik	AI431055|AW050122	RIKEN cDNA 9130011E15 gene	protein-coding
mm_106150.1	chr11	116598458	116598477	-	1	NA	TTS (NM_009591)	TTS (NM_009591)	4780	NM_009591	11298	Mm.42233	NM_009591	ENSMUSG00000020804	Aanat	AA-NAT|Nat-2|Nat4|Snat	arylalkylamine N-acetyltransferase	protein-coding
mm_115835.1	chr13	21287059	21287063	-	1	NA	3' UTR (NM_010343, exon 5 of 5)	3' UTR (NM_010343, exon 5 of 5)	5625	NM_010343	14780	Mm.1332	NM_010343	ENSMUSG00000004344	Gpx5	AV379049|Arep	glutathione peroxidase 5	protein-coding
mm_68427.1	chr7	109807956	109807962	-	1	NA	intron (NM_020052, intron 18 of 21)	intron (NM_020052, intron 18 of 21)	-26414	NM_020610	78593	Mm.275374	NM_020610	ENSMUSG00000034825	Nrip3	A330103B05Rik|D7H11orf14|ICRFP703B1614Q5.2	nuclear receptor interacting protein 3	protein-coding
mm_73662.1	chr8	111034099	111034165	+	1	NA	5' UTR (NM_146217, exon 1 of 21)	5' UTR (NM_146217, exon 1 of 21)	290	NM_146217	234734	Mm.24174	NM_146217	ENSMUSG00000031960	Aars	AI316495|C76919|sti	alanyl-tRNA synthetase	protein-coding
mm_166445.1	chr5	137264398	137264407	+	1	NA	Intergenic	Intergenic	-23852	NM_009599	11423	Mm.255464	NM_009599	ENSMUSG00000023328	Ache	-	acetylcholinesterase	protein-coding
mm_145927.1	chr18	67133479	67133496	+	1	NA	promoter-TSS (NM_010307)	promoter-TSS (NM_010307)	-73	NM_010307	14680	Mm.440746	NM_010307	ENSMUSG00000024524	Gnal	2610011C15Rik|9630020G10Rik|Galphaolf|Gna10|Golf	guanine nucleotide binding protein, alpha stimulating, olfactory type	protein-coding
mm_152410.1	chr19	10605366	10605405	-	1	NA	promoter-TSS (NM_015735)	promoter-TSS (NM_015735)	-240	NM_015735	13194	Mm.289915	NM_015735	ENSMUSG00000024740	Ddb1	127kDa|AA408517|p127-Ddb1	damage specific DNA binding protein 1	protein-coding
mm_83823.1	chr9	53936101	53936105	-	1	NA	intron (NM_177769, intron 2 of 10)	intron (NM_177769, intron 2 of 10)	39198	NM_177769	270162	Mm.259791	NM_177769	ENSMUSG00000041986	Elmod1	4831417L10|AI428506|AI834991	ELMO/CED-12 domain containing 1	protein-coding
mm_165890.1	chr4	43966351	43966379	+	1	NA	intron (NM_027450, intron 1 of 4)	intron (NM_027450, intron 1 of 4)	8663	NM_027450	384009	Mm.22213	NM_027450	ENSMUSG00000028480	Glipr2	5730414A08Rik|C77180|GAPR-1	GLI pathogenesis-related 2	protein-coding
mm_100724.1	chr11	3914138	3914149	-	1	NA	5' UTR (NM_153142, exon 1 of 2)	5' UTR (NM_153142, exon 1 of 2)	521	NM_153142	103710	Mm.171514	NM_153142	ENSMUSG00000048807	Slc35e4	A330108F03Rik|AI414849|AI536442	solute carrier family 35, member E4	protein-coding
mm_38330.1	chr4	137409778	137409778	-	1	NA	promoter-TSS (NM_001126318)	promoter-TSS (NM_001126318)	13	NM_001126318	242711	Mm.475541	NM_001126318	ENSMUSG00000078520	Cela3a	Gm13011|OTTMUSG00000009877	chymotrypsin-like elastase family, member 3A	protein-coding
mm_47205.1	chr5	120941287	120941296	-	1	NA	3' UTR (NM_011286, exon 22 of 22)	3' UTR (NM_011286, exon 22 of 22)	26473	NM_133893	100535	Mm.247620	NM_133893	ENSMUSG00000032623	Oas1d	AA536864|C85127|oasl8	2'-5' oligoadenylate synthetase 1D	protein-coding
mm_26805.1	chr3	10137461	10137493	-	1	NA	Intergenic	ORR1D1|LTR|ERVL-MaLR	46408	NM_001030305	18857	Mm.371777	NM_001030305	ENSMUSG00000052468	Pmp2	P2	peripheral myelin protein 2	protein-coding
mm_137610.1	chr17	28239124	28239124	+	1	NA	intron (NM_011145, intron 2 of 7)	intron (NM_011145, intron 2 of 7)	6370	NM_011145	19015	Mm.328914	NM_011145	ENSMUSG00000002250	Ppard	NUC-1|NUC1|Nr1c2|PPAR-beta|PPAR-delta|PPAR[b]|PPARdelta|Pparb|Pparb/d	peroxisome proliferator activator receptor delta	protein-coding
mm_153652.1	chr19	44394583	44394593	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	13121	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_118184.1	chr13	107022384	107022394	-	1	NA	promoter-TSS (NM_008442)	promoter-TSS (NM_008442)	-181	NR_015471	100040322	Mm.133867	NR_015471		3830408C21Rik	-	RIKEN cDNA 3830408C21 gene	ncRNA
mm_157516.1	chrX	49788205	49788236	-	1	NA	promoter-TSS (NM_183336)	promoter-TSS (NM_183336)	23	NM_183336	209268	Mm.110505	NM_177591	ENSMUSG00000031111	Igsf1	5330413N23|5530402E03|AI747649|InhBP/p120|mKIAA0364	immunoglobulin superfamily, member 1	protein-coding
mm_133020.1	chr16	56477868	56477891	+	1	NA	promoter-TSS (NM_178790)	promoter-TSS (NM_178790)	33	NM_001014424	320712	Mm.209236	NM_178790	ENSMUSG00000035258	Abi3bp	5033411B22Rik|AI506287|BG172926|D930038M13Rik|TARSH|eratin	ABI gene family, member 3 (NESH) binding protein	protein-coding
mm_67710.1	chr7	89980247	89980259	-	1	NA	intron (NM_021876, intron 1 of 11)	CpG	723	NM_021876	13626	Mm.380914	NM_021876	ENSMUSG00000030619	Eed	ENSMUSG00000039373|l(7)5Rn|l7Rn5|lusk	embryonic ectoderm development	protein-coding
mm_49476.1	chr6	29526742	29526752	+	1	NA	5' UTR (NM_012057, exon 1 of 9)	5' UTR (NM_012057, exon 1 of 9)	122	NM_012057	27056	Mm.6479	NM_012057	ENSMUSG00000029771	Irf5	AW491843|mirf5	interferon regulatory factor 5	protein-coding
mm_32715.1	chr4	116173412	116173422	+	1	NA	promoter-TSS (NM_001099295)	promoter-TSS (NM_001099295)	45	NM_001099295	67323	Mm.45442	NM_001099295	ENSMUSG00000078593	1700042G07Rik	-	RIKEN cDNA 1700042G07 gene	protein-coding
mm_9515.1	chr1	173748079	173748092	-	1	NA	intron (NM_008329, intron 8 of 8)	intron (NM_008329, intron 8 of 8)	-6276	NM_001204910	226691	Mm.440876	NM_001204910	ENSMUSG00000073490	Ifi207	AI607873|Pyhin-A	interferon activated gene 207	protein-coding
mm_110742.1	chr12	69791354	69791364	-	1	NA	promoter-TSS (NM_183294)	promoter-TSS (NM_183294)	-652	NM_183294	71091	Mm.132325	NM_183294	ENSMUSG00000020990	Cdkl1	4933411O17Rik	cyclin-dependent kinase-like 1 (CDC2-related kinase)	protein-coding
mm_16847.1	chr2	11553894	11553961	-	1	NA	promoter-TSS (NM_001177758)	promoter-TSS (NM_001177758)	2	NM_001177758	170768	Mm.19669	NM_133232	ENSMUSG00000026773	Pfkfb3	E330010H22Rik|iPFK-2|uPFK-2	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	protein-coding
mm_101621.1	chr11	35879470	35879474	-	1	NA	intron (NM_170779, intron 9 of 22)	intron (NM_170779, intron 9 of 22)	-44944	NM_025936	104458	Mm.284906	NM_025936	ENSMUSG00000018848	Rars	2610011N19Rik|2610037E21Rik|AL033339|AW985894	arginyl-tRNA synthetase	protein-coding
mm_121573.1	chr14	122876836	122876853	+	1	NA	exon (NM_144844, exon 22 of 24)	exon (NM_144844, exon 22 of 24)	36321	NM_145466	223267	Mm.379358	NM_145466	ENSMUSG00000041625	Ggact	A2ld1	gamma-glutamylamine cyclotransferase	protein-coding
mm_146464.1	chr18	86711709	86711740	+	1	NA	promoter-TSS (NM_172633)	promoter-TSS (NM_172633)	-341	NM_172633	12405	Mm.70775	NM_172633	ENSMUSG00000024647	Cbln2	6330593N19Rik|A730004O05	cerebellin 2 precursor protein	protein-coding
mm_135786.1	chr16	57071349	57071388	-	1	NA	promoter-TSS (NM_183281)	promoter-TSS (NM_183281)	-22	NM_183281	69457	Mm.58105	NM_183281	ENSMUSG00000046748	Tmem45a2	2310005G13Rik	transmembrane protein 45A2	protein-coding
mm_47972.1	chr5	135910141	135910166	-	1	NA	3' UTR (NM_018871, exon 2 of 2)	3' UTR (NM_018871, exon 2 of 2)	22234	NM_013560	15507	Mm.13849	NM_013560	ENSMUSG00000004951	Hspb1	27kDa|Hsp25	heat shock protein 1	protein-coding
mm_135894.1	chr16	65105714	65105727	-	1	NA	promoter-TSS (NM_008310)	promoter-TSS (NM_008310)	64	NM_008310	15557	Mm.5040	NM_008310	ENSMUSG00000050783	Htr1f	Htr1eb	5-hydroxytryptamine (serotonin) receptor 1F	protein-coding
mm_108751.1	chr12	88953417	88953434	+	1	NA	promoter-TSS (NM_172544)	promoter-TSS (NM_172544)	35	NM_172544	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding
mm_169190.1	chr13	66032196	66032208	+	1	NA	Intergenic	Intergenic	-81251	NM_001177832	628709	Mm.390595	NM_001177832	ENSMUSG00000095909	Gm10324	ENSMUSG00000071302	predicted gene 10324	protein-coding
mm_32226.1	chr4	101776239	101776245	+	1	NA	intron (NM_146146, intron 13 of 18)	RSINE1|SINE|B4	58835	NM_010704	16847	Mm.259282	NM_010704	ENSMUSG00000057722	Lepr	LEPROT|Leprb|Modb1|OB-RGRP|Obr|db|diabetes|obese-like|obl	leptin receptor	protein-coding
mm_138503.1	chr17	35220297	35220317	+	1	NA	3' UTR (NM_010909, exon 4 of 4)	3' UTR (NM_010909, exon 4 of 4)	-14703	NM_001347351	66237	Mm.396107	NM_023179	ENSMUSG00000024403	Atp6v1g2	1500002D01Rik|Atp6g2|NG38|VAG2	ATPase, H+ transporting, lysosomal V1 subunit G2	protein-coding
mm_170050.1	chr17	27354832	27354843	-	1	NA	promoter-TSS (NR_106076)	promoter-TSS (NR_106076)	-901	NR_106076	102465701		NR_106076	ENSMUSG00000106578	Mir7217	mmu-mir-7217	microRNA 7217	ncRNA
mm_21664.1	chr2	164425301	164425318	-	1	NA	3' UTR (NM_011521, exon 5 of 5)	3' UTR (NM_011521, exon 5 of 5)	17879	NM_011521	20971	Mm.3815	NM_011521	ENSMUSG00000017009	Sdc4	AA959608|AW108331|S4|Synd4|ryudocan|syndecan-4	syndecan 4	protein-coding
mm_16895.1	chr2	13257912	13257917	-	1	NA	intron (NM_009105, intron 2 of 8)	intron (NM_009105, intron 2 of 8)	13501	NM_009105	20163	Mm.905	NM_009105	ENSMUSG00000026727	Rsu1	RsuI|rsp-1	Ras suppressor protein 1	protein-coding
mm_102418.1	chr11	59212512	59212535	-	1	NA	3' UTR (NM_007476, exon 5 of 5)	3' UTR (NM_007476, exon 5 of 5)	4162	NM_024210	67862	Mm.358708	NM_024210	ENSMUSG00000020441	2310033P09Rik	Mmtag2	RIKEN cDNA 2310033P09 gene	protein-coding
mm_115715.1	chr13	15908747	15908764	-	1	NA	Intergenic	Lx9|LINE|L1	101512	NR_046131	328190	Mm.446957	NR_046131		A530046M15Rik	A530046M15	RIKEN cDNA A530046M15 gene	ncRNA
mm_147220.1	chr18	37999518	37999540	-	1	NA	promoter-TSS (NM_001205336)	promoter-TSS (NM_001205336)	-560	NM_001205336	106952	Mm.247642	NM_139206	ENSMUSG00000024451	Arap3	Centd3|Drag1|E030006K04Rik|cnt-d3	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3	protein-coding
mm_102382.1	chr11	58904146	58904157	-	1	NA	promoter-TSS (NM_011758)	promoter-TSS (NM_011758)	74	NM_011758	22698	Mm.127646	NM_011758	ENSMUSG00000037001	Zfp39	CTfin33|Zfp-39	zinc finger protein 39	protein-coding
mm_122625.1	chr14	51145661	51145677	-	1	NA	exon (NM_011271, exon 2 of 2)	exon (NM_011271, exon 2 of 2)	1098	NM_011271	19752	Mm.235538	NM_011271	ENSMUSG00000035896	Rnase1	AI574248|Rib-1|Rib1	ribonuclease, RNase A family, 1 (pancreatic)	protein-coding
mm_25966.1	chr3	132743646	132743648	+	1	NA	intron (NM_001163455, intron 20 of 25)	intron (NM_001163455, intron 20 of 25)	59503	NM_001163455	271981	Mm.257864	NM_173032	ENSMUSG00000028030	Tbck	1700120J03Rik|9430001M19|A630047E20Rik|C030007I09Rik|Tbckl	TBC1 domain containing kinase	protein-coding
mm_172421.1	chr7	26387340	26387340	+	1	NA	intron (NM_001042612, intron 1 of 8)	MMERVK9C_I-int|LTR|ERVK	6903	NM_001042612	330490	Mm.212174	NM_194062	ENSMUSG00000040614	Nlrp9c	AA636537|BB062542|Nalp-zeta|Nalp9c	NLR family, pyrin domain containing 9C	protein-coding
mm_62823.1	chr7	113512818	113512820	+	1	NA	Intergenic	Intergenic	-1015	NM_001285831	67420	Mm.206919	NM_026143	ENSMUSG00000030759	Far1	2600011M19Rik|2900034E22Rik|3732409C05Rik|AI850429|Mlstd2	fatty acyl CoA reductase 1	protein-coding
mm_141969.1	chr17	35131764	35131785	-	1	NA	promoter-TSS (NM_018816)	promoter-TSS (NM_018816)	-22	NM_018816	55938	Mm.2161	NM_018816	ENSMUSG00000024391	Apom	1190010O19Rik|G3a|NG20	apolipoprotein M	protein-coding
mm_100065.1	chr11	115381907	115381933	+	1	NA	promoter-TSS (NM_001080929)	promoter-TSS (NM_001080929)	4	NM_001080929	237988	Mm.102872	NM_001080929	ENSMUSG00000050910	Cdr2l	D030068L24Rik|Gm21	cerebellar degeneration-related protein 2-like	protein-coding
mm_150199.1	chr19	32757605	32757637	+	1	NA	promoter-TSS (NM_008960)	promoter-TSS (NM_008960)	44	NM_008960	19211	Mm.245395	NM_008960	ENSMUSG00000013663	Pten	2310035O07Rik|A130070J02Rik|AI463227|B430203M17Rik|MMAC1|TEP1	phosphatase and tensin homolog	protein-coding
mm_156237.1	chrX	136139040	136139053	+	1	NA	promoter-TSS (NM_212457)	promoter-TSS (NM_212457)	1	NM_212457	406217	Mm.336245	NM_212457	ENSMUSG00000047844	Bex4	-	brain expressed X-linked 4	protein-coding
mm_36816.1	chr4	104816416	104816424	-	1	NA	3' UTR (NM_146148, exon 11 of 11)	3' UTR (NM_146148, exon 11 of 11)	50103	NM_001316671	110382	Mm.87072	NM_133882	ENSMUSG00000029656	C8b	4930439B20Rik|AI595927	complement component 8, beta polypeptide	protein-coding
mm_143457.1	chr17	70990550	70990562	-	1	NA	promoter-TSS (NM_023402)	promoter-TSS (NM_023402)	-40	NM_023402	67938	Mm.261329	NM_023402	ENSMUSG00000034868	Myl12b	1500001M02Rik|C77744|Mylc2b|RLC-B	myosin, light chain 12B, regulatory	protein-coding
mm_4831.1	chr1	186587296	186587310	+	1	NA	Intergenic	MIR|SINE|MIR	-28622	NR_131158	320449	Mm.404477	NR_131124	ENSMUSG00000103690	A730004F24Rik	-	RIKEN cDNA A730004F24 gene	ncRNA
mm_131835.1	chr16	22960829	22960838	+	1	NA	exon (NM_053176, exon 7 of 7)	exon (NM_053176, exon 7 of 7)	9761	NM_053176	94175	Mm.358794	NM_053176	ENSMUSG00000022877	Hrg	AI265597|AW413091|D16jh2|D18020|Hprg|Hrgp	histidine-rich glycoprotein	protein-coding
mm_69133.1	chr7	127027147	127027197	-	1	NA	promoter-TSS (NM_010772)	promoter-TSS (NM_010772)	-693	NM_010772	17188	Mm.378964	NM_010772	ENSMUSG00000030678	Maz	MAZI|PUR1|Pur-1|SAF-1|SAF-2	MYC-associated zinc finger protein (purine-binding transcription factor)	protein-coding
mm_67762.1	chr7	92741449	92741473	-	1	NA	promoter-TSS (NM_029494)	promoter-TSS (NM_029494)	-2	NR_015510	666737	Mm.473620	NR_015510	ENSMUSG00000074024	4632427E13Rik	AU015482	RIKEN cDNA 4632427E13 gene	ncRNA
mm_145095.1	chr18	43207680	43207700	+	1	NA	promoter-TSS (NM_178749)	promoter-TSS (NM_178749)	-7	NM_178749	269019	Mm.150401	NM_178749	ENSMUSG00000039954	Stk32a	A930015B13Rik|YANK1	serine/threonine kinase 32A	protein-coding
mm_137213.1	chr17	24165259	24165269	+	1	NA	intron (NR_037854, intron 1 of 2)	intron (NR_037854, intron 1 of 2)	-1531	NM_172935	245847	Mm.87319	NM_172935	ENSMUSG00000036820	Amdhd2	5730457F11Rik	amidohydrolase domain containing 2	protein-coding
mm_3431.1	chr1	150101172	150101182	+	1	NA	intron (NM_011198, intron 2 of 9)	intron (NM_011198, intron 2 of 9)	1146	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_15882.1	chr2	164839300	164839319	+	1	NA	TTS (NM_011125)	TTS (NM_011125)	5536	NM_008906	19025	Mm.359633	NM_008906	ENSMUSG00000017760	Ctsa	AU019505|PPCA|Ppgb	cathepsin A	protein-coding
mm_73233.1	chr8	104112969	104112980	+	1	NA	exon (NM_009868, exon 2 of 12)	exon (NM_009868, exon 2 of 12)	-7101	NR_131138	546096	Mm.252264	NR_131138	ENSMUSG00000110053	Gm29682	-	predicted gene, 29682	ncRNA
mm_125061.1	chr15	25940833	25940843	+	1	NA	promoter-TSS (NM_001277316)	promoter-TSS (NM_001277316)	12	NM_025459	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_116737.1	chr13	51748776	51748821	-	1	NA	intron (NM_001281880, intron 2 of 16)	intron (NM_001281880, intron 2 of 16)	44949	NM_001281880	20354	Mm.33903	NM_013660	ENSMUSG00000021451	Sema4d	CD100|Semacl2|Semaj|Semcl2|coll-4	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D	protein-coding
mm_125724.1	chr15	73149023	73149030	+	1	NA	intron (NM_153178, intron 1 of 18)	intron (NM_153178, intron 1 of 18)	35921	NM_153178	239528	Mm.23095	NM_153178	ENSMUSG00000036698	Ago2	1110029L17Rik|2310051F07Rik|AI225898|AL022874|AW546247|ENSMUSG00000072493|Eif2c2|Gerp95|Gm10365|mKIAA4215	argonaute RISC catalytic subunit 2	protein-coding
mm_80063.1	chr9	69453677	69453704	+	1	NA	promoter-TSS (NM_007585)	promoter-TSS (NM_007585)	7	NM_007585	12306	Mm.238343	NM_007585	ENSMUSG00000032231	Anxa2	AW215814|Cal1h	annexin A2	protein-coding
mm_93684.1	chr10	117815292	117815304	-	1	NA	3' UTR (NM_024457, exon 8 of 8)	3' UTR (NM_024457, exon 8 of 8)	-22593	NM_134010	103468	Mm.12568	NM_134010	ENSMUSG00000052798	Nup107	AW541137|C76801	nucleoporin 107	protein-coding
mm_115051.1	chr13	100576292	100576298	+	1	NA	Intergenic	Intergenic	-23797	NM_008756	18260	Mm.4807	NM_008756	ENSMUSG00000021638	Ocln	AI503564|Ocl	occludin	protein-coding
mm_51717.1	chr6	86849489	86849594	+	1	NA	promoter-TSS (NM_177762)	promoter-TSS (NM_177762)	24	NM_001040106	269774	Mm.221038	NM_177762	ENSMUSG00000057230	Aak1	5530400K14Rik|9630042K20|AU067724|AU067726|BC028270|C79663|D6Ertd245e|R75501|mKIAA1048	AP2 associated kinase 1	protein-coding
mm_45595.1	chr5	74702954	74702966	-	1	NA	promoter-TSS (NM_001159577)	promoter-TSS (NM_001159577)	-57	NM_001159577	16924	Mm.440403	NM_010727	ENSMUSG00000029228	Lnx1	Lnx	ligand of numb-protein X 1	protein-coding
mm_9694.1	chr1	178337649	178337652	-	1	NA	5' UTR (NM_016805, exon 1 of 14)	5' UTR (NM_016805, exon 1 of 14)	134	NM_016805	51810	Mm.86589	NM_016805	ENSMUSG00000039630	Hnrnpu	AA408410|AI256620|AL024194|AL024437|AW557595|C86794|Hnrpu|SAFA|Sp120|hnRNP U	heterogeneous nuclear ribonucleoprotein U	protein-coding
mm_118719.1	chr14	22203206	22203208	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	183495	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_27769.1	chr3	72903643	72903678	-	1	NA	exon (NM_001081137, exon 43 of 47)	exon (NM_001081137, exon 43 of 47)	63206	NM_001081137	69983	Mm.261054	NM_001081137	ENSMUSG00000027790	Sis	2010204N08Rik|SI|Si-s	sucrase isomaltase (alpha-glucosidase)	protein-coding
mm_33326.1	chr4	129106770	129106779	+	1	NA	intron (NM_025452, intron 1 of 5)	intron (NM_025452, intron 1 of 5)	1226	NM_001290706	66260	Mm.25295	NM_025452	ENSMUSG00000028786	Tmem54	1810017F10Rik|AI507302	transmembrane protein 54	protein-coding
mm_140613.1	chr17	10840252	10840263	-	1	NA	promoter-TSS (NM_016694)	promoter-TSS (NM_016694)	-66	NM_027032	69310	Mm.18889	NM_027032	ENSMUSG00000037196	Pacrg	1700008H23Rik	PARK2 co-regulated	protein-coding
mm_165103.1	chr19	55893211	55893214	+	1	NA	intron (NR_138565, intron 4 of 15)	intron (NR_138565, intron 4 of 15)	-2109	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_148089.1	chr18	73754458	73754503	-	1	NA	promoter-TSS (NM_053255)	promoter-TSS (NM_053255)	-1	NM_053255	114615	Mm.50642	NM_053255	ENSMUSG00000036941	Elac1	2610018O07Rik|8430417G19Rik	elaC ribonuclease Z 1	protein-coding
mm_93667.1	chr10	117710016	117710032	-	1	NA	5' UTR (NM_010786, exon 2 of 12)	5' UTR (NM_010786, exon 2 of 12)	734	NM_010786	17246	Mm.22670	NM_010786	ENSMUSG00000020184	Mdm2	1700007J15Rik|AA415488|Mdm-2	transformed mouse 3T3 cell double minute 2	protein-coding
mm_165366.1	chr2	126602271	126602280	-	1	NA	intron (NM_008230, intron 7 of 11)	intron (NM_008230, intron 7 of 11)	16403	NM_008230	15186	Mm.18603	NM_008230	ENSMUSG00000027360	Hdc	AW108189|Hdc-a|Hdc-c|Hdc-e|Hdc-s	histidine decarboxylase	protein-coding
mm_119432.1	chr14	46221106	46221124	+	1	NA	Intergenic	MLT1A1|LTR|ERVL-MaLR	137088	NR_002875	218963	Mm.282093	NR_002875		Gm1821	-	ubiquitin pseudogene	pseudo
mm_27451.1	chr3	52009228	52009240	-	1	NA	intron (NM_001004176, intron 1 of 4)	intron (NM_001004176, intron 1 of 4)	95772	NM_001004176	433586	Mm.234972	NM_001004176	ENSMUSG00000061143	Maml3	AV234550|BC049812|Mam-2|mKIAA1816	mastermind like 3 (Drosophila)	protein-coding
mm_168509.1	chr1	156366049	156366071	+	1	NA	intron (NM_001198597, intron 10 of 10)	intron (NM_001198597, intron 10 of 10)	33930	NM_001198597	77352	Mm.428709	NM_001033180	ENSMUSG00000026601	Axdnd1	9430070O13Rik|Gm979	axonemal dynein light chain domain containing 1	protein-coding
mm_6794.1	chr1	84147391	84147400	-	1	NA	intron (NM_001003948, intron 2 of 2)	intron (NM_001003948, intron 2 of 2)	71566	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_80870.1	chr9	98563743	98563775	+	1	NA	promoter-TSS (NM_015827)	promoter-TSS (NM_015827)	28	NM_015827	50797	Mm.400464	NM_015827	ENSMUSG00000032458	Copb2	AI256832	coatomer protein complex, subunit beta 2 (beta prime)	protein-coding
mm_135835.1	chr16	58523615	58523624	-	1	NA	promoter-TSS (NM_018784)	promoter-TSS (NM_018784)	-307	NM_018784	54613	Mm.212742	NM_018784	ENSMUSG00000022747	St3gal6	1700023B24Rik|AI930218|AW552396|Siat10|St3galVI	ST3 beta-galactoside alpha-2,3-sialyltransferase 6	protein-coding
mm_16583.1	chr2	3713316	3713350	-	1	NA	promoter-TSS (NM_025626)	promoter-TSS (NM_025626)	-125	NM_025626	66540	Mm.277864	NM_025626	ENSMUSG00000026655	Fam107b	3110001A13Rik|AA589595|AA959793|AI132312	family with sequence similarity 107, member B	protein-coding
mm_118692.1	chr14	22123874	22123890	+	1	NA	intron (NM_028275, intron 2 of 6)	B4A|SINE|B4	104170	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_62350.1	chr7	100498815	100498827	+	1	NA	exon (NM_011671, exon 7 of 8)	exon (NM_011671, exon 7 of 8)	5463	NM_011671	22228	Mm.171378	NM_011671	ENSMUSG00000033685	Ucp2	Slc25a8	uncoupling protein 2 (mitochondrial, proton carrier)	protein-coding
mm_158987.1	chr1	132642698	132642698	-	1	NA	exon (NM_001160317, exon 3 of 28)	exon (NM_001160317, exon 3 of 28)	160	NM_001160316	269116	Mm.326702	NM_182716	ENSMUSG00000026442	Nfasc	AA387016|D430023G06Rik|NF|mKIAA0756	neurofascin	protein-coding
mm_13211.1	chr2	95481448	95481448	+	1	NA	Intergenic	ORR1G|LTR|ERVL-MaLR	-836721	NM_001289742	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_147403.1	chr18	44633755	44633758	-	1	NA	intron (NM_001085373, intron 3 of 18)	intron (NM_001085373, intron 3 of 18)	-27909	NR_026853	626275	Mm.427116	NR_026853	ENSMUSG00000097610	A930012L18Rik	-	RIKEN cDNA A930012L18 gene	ncRNA
mm_115184.1	chr13	108449901	108449913	+	1	NA	Intergenic	Intergenic	133570	NM_178683	218581	Mm.32318	NM_178683	ENSMUSG00000021697	Depdc1b	9830132O03|AW260467|XTP1	DEP domain containing 1B	protein-coding
mm_122985.1	chr14	54984754	54984762	-	1	NA	exon (NM_080728, exon 23 of 41)	exon (NM_080728, exon 23 of 41)	-8982	NR_030607	100124433		NR_030607	ENSMUSG00000077928	Mir208b	Mirn208b|mir-208b	microRNA 208b	ncRNA
mm_54818.1	chr6	42351306	42351322	-	1	NA	exon (NM_011777, exon 4 of 10)	exon (NM_011777, exon 4 of 10)	1486	NM_001289619	22793	Mm.282303	NM_011777	ENSMUSG00000029860	Zyx	9530098H06Rik|R75157	zyxin	protein-coding
mm_127648.1	chr15	102487062	102487107	+	1	NA	intron (NM_001103165, intron 9 of 14)	intron (NM_001103165, intron 9 of 14)	16452	NM_001174073	18521	Mm.236513	NM_011042	ENSMUSG00000056851	Pcbp2	AW412548|Hnrpx|alphaCP-2	poly(rC) binding protein 2	protein-coding
mm_71275.1	chr8	40919616	40919634	+	1	NA	3' UTR (NM_001044740, exon 12 of 12)	3' UTR (NM_001044740, exon 12 of 12)	-6608	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_78036.1	chr9	13835502	13835504	+	1	NA	intron (NM_176836, intron 5 of 9)	intron (NM_176836, intron 5 of 9)	7776	NM_176836	72826	Mm.246174	NM_176836	ENSMUSG00000037808	Fam76b	2810485I05Rik|C78303	family with sequence similarity 76, member B	protein-coding
mm_31682.1	chr4	62298029	62298042	+	1	NA	3' UTR (NM_025286, exon 4 of 4)	3' UTR (NM_025286, exon 4 of 4)	6488	NM_001290518	20530	Mm.292539	NM_025286	ENSMUSG00000066152	Slc31a2	AI604396|CTR2	solute carrier family 31, member 2	protein-coding
mm_93486.1	chr10	111997120	111997126	-	1	NA	5' UTR (NM_028608, exon 1 of 6)	5' UTR (NM_028608, exon 1 of 6)	141	NM_028608	73690	Mm.173790	NM_028608	ENSMUSG00000056888	Glipr1	2410114O14Rik|RTVP-1|RTVP1|mRTVP-1	GLI pathogenesis-related 1 (glioma)	protein-coding
mm_20420.1	chr2	129302956	129302971	-	1	NA	exon (NM_010554, exon 6 of 7)	exon (NM_010554, exon 6 of 7)	5593	NR_040371	100503468	Mm.446943	NR_040371	ENSMUSG00000085498	Gm14023	OTTMUSG00000015408	predicted gene 14023	ncRNA
mm_1578.1	chr1	74281183	74281202	+	1	NA	intron (NM_001190444, intron 8 of 10)	intron (NM_001190444, intron 8 of 10)	2592	NM_174985	227289	Mm.246587	NM_174985	ENSMUSG00000064272	Gpbar1	BG37|GPCR|GPR131|M-BAR|TGR5	G protein-coupled bile acid receptor 1	protein-coding
mm_138997.1	chr17	45555806	45555817	+	1	NA	5' UTR (NM_008690, exon 1 of 6)	5' UTR (NM_008690, exon 1 of 6)	111	NM_001304956	18037	Mm.57043	NM_008690	ENSMUSG00000023947	Nfkbie	I-kappa-B-epsilon|IKBE|IkB-E|NF-kappa-BIE|ikB-epsilon	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, epsilon	protein-coding
mm_81639.1	chr9	110880402	110880410	+	1	NA	promoter-TSS (NM_001146060)	promoter-TSS (NM_001146060)	84	NM_001146060	235633	Mm.86338	NM_146228	ENSMUSG00000044037	Als2cl	79H19D|79H19E|BC022645|D930044G19Rik|mRn.49018	ALS2 C-terminal like	protein-coding
mm_113666.1	chr13	42704084	42704085	+	1	NA	intron (NM_001302635, intron 2 of 13)	intron (NM_001302635, intron 2 of 13)	-5497	NM_001005740	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding
mm_59374.1	chr7	25719179	25719181	+	1	NA	promoter-TSS (NM_028771)	promoter-TSS (NM_028771)	-127	NM_028771	52132	Mm.278798	NM_028771	ENSMUSG00000002608	Ccdc97	1200014H14Rik|2810446P04Rik|AA545218|D7Ertd462e	coiled-coil domain containing 97	protein-coding
mm_154523.1	chrM	13408	13433	-	1	NA	NA	Intergenic	NA	NA								
mm_172677.1	chr8	51347254	51347254	+	1	NA	Intergenic	L1Md_T|LINE|L1	979142	NR_046067	100039954	Mm.400419	NR_046067	ENSMUSG00000110281	Gm2516	-	predicted gene 2516	ncRNA
mm_110357.1	chr12	40037388	40037411	-	1	NA	promoter-TSS (NM_007487)	promoter-TSS (NM_007487)	-23	NM_007487	11861	Mm.12723	NM_007487	ENSMUSG00000047446	Arl4a	AI467555|Arl4	ADP-ribosylation factor-like 4A	protein-coding
mm_149783.1	chr19	23136866	23136877	+	1	NA	Intergenic	Intergenic	-4355	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_139691.1	chr17	57424878	57424888	+	1	NA	intron (NM_010130, intron 12 of 21)	L1Md_F2|LINE|L1	66197	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_3661.1	chr1	153376962	153376978	+	1	NA	Intergenic	Intergenic	37263	NR_033736	626058	Mm.31556	NM_001177359		E330020D12Rik	EG626058|F430003O07Rik|Gm6648	Riken cDNA E330020D12 gene	ncRNA
mm_81011.1	chr9	104063377	104063415	+	1	NA	promoter-TSS (NM_175324)	promoter-TSS (NM_175324)	-275	NM_025692	66663	Mm.224935	NM_025692	ENSMUSG00000032557	Uba5	5730525G14Rik|AW240750|Ube1dc1	ubiquitin-like modifier activating enzyme 5	protein-coding
mm_34983.1	chr4	156022547	156022550	+	1	NA	intron (NR_040563, intron 2 of 2)	intron (NR_040563, intron 2 of 2)	1276	NR_040563	100038526	Mm.191866	NR_040563		Gm10560	ENSMUSG00000073673	predicted gene 10560	ncRNA
mm_144918.1	chr18	37644317	37644345	+	1	NA	promoter-TSS (NM_175770)	promoter-TSS (NM_175770)	-127	NM_175770	24074	Mm.236009	NM_175770	ENSMUSG00000051316	Taf7	55kDa|AI607308|BB007175|TAFII55|Taf2f	TATA-box binding protein associated factor 7	protein-coding
mm_14658.1	chr2	137663425	137663436	+	1	NA	Intergenic	Intergenic	-546910	NM_013822	16449	Mm.22398	NM_013822	ENSMUSG00000027276	Jag1	ABE2|Gsfabe2|Htu|Ozz|Ser-1	jagged 1	protein-coding
mm_71617.1	chr8	57322195	57322257	+	1	NA	exon (NM_010402, exon 1 of 2)	exon (NM_010402, exon 1 of 2)	1243	NM_010402	15111	Mm.430844	NM_010402	ENSMUSG00000038193	Hand2	AI225906|AI661148|Ehand2|Hed|Th2|Thing2|bHLHa26|dHAND	heart and neural crest derivatives expressed transcript 2	protein-coding
mm_1576.1	chr1	74277105	74277120	+	1	NA	Intergenic	Intergenic	-1488	NM_174985	227289	Mm.246587	NM_174985	ENSMUSG00000064272	Gpbar1	BG37|GPCR|GPR131|M-BAR|TGR5	G protein-coupled bile acid receptor 1	protein-coding
mm_88881.1	chr10	81123819	81123825	+	1	NA	3' UTR (NM_001347144, exon 11 of 11)	3' UTR (NM_001347144, exon 11 of 11)	-12449	NM_010731	16969	Mm.20920	NM_010731	ENSMUSG00000035011	Zbtb7a	9030619K07Rik|9130006G12Rik|AI452336|FBI-1|Lrf|Pokemon|Zbtb7	zinc finger and BTB domain containing 7a	protein-coding
mm_121758.1	chr14	19643189	19643195	-	1	NA	Intergenic	MER5B|DNA|hAT-Charlie	-40605	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_147946.1	chr18	66292649	66292667	-	1	NA	promoter-TSS (NM_178793)	promoter-TSS (NM_178793)	-820	NM_178793	320924	Mm.442049	NM_178793	ENSMUSG00000046318	Ccbe1	4933426F18Rik|9430093N24Rik|mKIAA1983	collagen and calcium binding EGF domains 1	protein-coding
mm_138449.1	chr17	35135696	35135781	+	1	NA	promoter-TSS (NM_001252469)	promoter-TSS (NM_001252469)	24	NM_001252469	224727	Mm.203962	NM_057171	ENSMUSG00000024392	Bag6	2410045D21Rik|AA408914|BAG-6|Bat3|D17H6S52E|G3|Scythe	BCL2-associated athanogene 6	protein-coding
mm_86998.1	chr10	26772524	26772569	+	1	NA	promoter-TSS (NM_176837)	promoter-TSS (NM_176837)	34	NM_176837	73910	Mm.356496	NM_176837	ENSMUSG00000039031	Arhgap18	4833419J07Rik|AI314906|AI843501	Rho GTPase activating protein 18	protein-coding
mm_117900.1	chr13	99425913	99425927	-	1	NA	exon (NM_008634, exon 7 of 7)	exon (NM_008634, exon 7 of 7)	-13094	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_86782.1	chr10	20171004	20171045	+	1	NA	intron (NM_001198635, intron 1 of 17)	intron (NM_001198635, intron 1 of 17)	22104	NM_001198635	17761	Mm.20928	NM_008635	ENSMUSG00000019996	Map7	E-MAP-115|MAP-7|Mtap7|R75000|mshi|mste|ste	microtubule-associated protein 7	protein-coding
mm_126796.1	chr15	86436101	86436107	+	1	NA	intron (NM_145476, intron 11 of 12)	Lx7|LINE|L1	221645	NM_145476	223754	Mm.28904	NM_145476	ENSMUSG00000051864	Tbc1d22a	BC023106|D15Ertd781e	TBC1 domain family, member 22a	protein-coding
mm_96879.1	chr11	70215031	70215058	+	1	NA	exon (NM_153081, exon 3 of 5)	exon (NM_153081, exon 3 of 5)	1134	NM_153081	216867	Mm.289238	NM_153081	ENSMUSG00000040938	Slc16a11	AB041591|MCT 11|MNCb-2717	solute carrier family 16 (monocarboxylic acid transporters), member 11	protein-coding
mm_151700.1	chr19	4440448	4440458	-	1	NA	intron (NR_045989, intron 1 of 4)	intron (NR_045989, intron 1 of 4)	894	NR_045989	319314	Mm.393810	NR_045989	ENSMUSG00000087132	A930001C03Rik	-	RIKEN cDNA A930001C03 gene	ncRNA
mm_23056.1	chr3	35754156	35754166	+	1	NA	promoter-TSS (NM_029570)	promoter-TSS (NM_029570)	23	NM_029570	76295	Mm.239416	NM_029570	ENSMUSG00000037400	Atp11b	1110019I14Rik|ATPIF|ATPIR|mKIAA0956	ATPase, class VI, type 11B	protein-coding
mm_1832.1	chr1	82724965	82724968	+	1	NA	promoter-TSS (NM_029409)	promoter-TSS (NM_029409)	76	NM_001310699	75734	Mm.396863	NM_029409	ENSMUSG00000026150	Mff	5230400G24Rik|AI314724	mitochondrial fission factor	protein-coding
mm_77363.1	chr8	119809954	119809968	-	1	NA	3' UTR (NM_028071, exon 4 of 4)	3' UTR (NM_028071, exon 4 of 4)	30618	NM_028071	72042	Mm.393405	NM_028071	ENSMUSG00000031827	Cotl1	1810074P22Rik|2010004C08Rik|Clp	coactosin-like 1 (Dictyostelium)	protein-coding
mm_149611.1	chr19	16385792	16385806	+	1	NA	3' UTR (NM_008139, exon 7 of 7)	3' UTR (NM_008139, exon 7 of 7)	-49868	NM_008137	14675	Mm.313181	NM_008137	ENSMUSG00000024697	Gna14	AU023208	guanine nucleotide binding protein, alpha 14	protein-coding
mm_115691.1	chr13	14026715	14026726	-	1	NA	intron (NR_130788, intron 3 of 16)	intron (NR_130788, intron 3 of 16)	12918	NR_130788	70430	Mm.260209	NM_178337	ENSMUSG00000039233	Tbce	2610206D02Rik|C530005D02Rik|pmn	tubulin-specific chaperone E	protein-coding
mm_141235.1	chr17	27436869	27436877	-	1	NA	intron (NM_001013385, intron 7 of 8)	(TCTG)n|Simple_repeat|Simple_repeat	66660	NM_001013385	268934	Mm.358940	NM_001013385	ENSMUSG00000063239	Grm4	Gprc1d|mGluR4	glutamate receptor, metabotropic 4	protein-coding
mm_7756.1	chr1	131136296	131136321	-	1	NA	exon (NM_145508, exon 2 of 3)	exon (NM_145508, exon 2 of 3)	1926	NM_145508	226419	Mm.39299	NM_145508	ENSMUSG00000016526	Dyrk3	BC006704	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 3	protein-coding
mm_5779.1	chr1	51513173	51513183	-	1	NA	Intergenic	Intergenic	-34779	NM_001310549	109019	Mm.196290	NM_028696	ENSMUSG00000026107	Nabp1	4930434H03Rik|4930442A21Rik|4930488J04Rik|4933440J18Rik|5830411E10Rik|AI852561|Nbp1|Obfc2a|Ssb2	nucleic acid binding protein 1	protein-coding
mm_10239.1	chr2	8026902	8026906	+	1	NA	Intergenic	B4A|SINE|B4	-630706	NM_001110231	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_18610.1	chr2	68378291	68378333	-	1	NA	intron (NM_016866, intron 5 of 17)	intron (NM_016866, intron 5 of 17)	93669	NM_016866	53416	Mm.198414	NM_016866	ENSMUSG00000027030	Stk39	AW227544|AW556857|DCHT|RF005|Rnl5|SPAK	serine/threonine kinase 39	protein-coding
mm_150627.1	chr19	41339682	41339716	+	1	NA	intron (NM_031376, intron 2 of 16)	intron (NM_031376, intron 2 of 16)	45371	NM_031376	83490	Mm.222266	NM_031376	ENSMUSG00000025017	Pik3ap1	1810044J04Rik|BCAP	phosphoinositide-3-kinase adaptor protein 1	protein-coding
mm_76924.1	chr8	105933929	105933937	-	1	NA	promoter-TSS (NM_023182)	promoter-TSS (NM_023182)	-71	NM_023182	109660	Mm.2745	NM_023182	ENSMUSG00000031896	Ctrl	0910001G08Rik|1810004D15Rik|AV005227|Ctra-1|Ctra1|chymopasin|mFLJ00366	chymotrypsin-like	protein-coding
mm_105689.1	chr11	107734051	107734059	-	1	NA	TTS (NM_019431)	TTS (NM_019431)	-17579	NM_007582	12299	Mm.57093	NM_007582	ENSMUSG00000020722	Cacng1	-	calcium channel, voltage-dependent, gamma subunit 1	protein-coding
mm_120890.1	chr14	75834954	75834967	+	1	NA	Intergenic	Intergenic	10004	NR_045294	100043189	Mm.426329	NR_045294		Gm4285	-	predicted gene 4285	ncRNA
mm_65302.1	chr7	24672055	24672066	-	1	NA	promoter-TSS (NM_019981)	promoter-TSS (NM_019981)	-10	NM_019981	56746	Mm.23385	NM_019981	ENSMUSG00000062773	Tex101	1700008H15Rik|AI429076|TES101RP	testis expressed gene 101	protein-coding
mm_161814.1	chr17	68273827	68273827	+	1	NA	promoter-TSS (NM_177278)	promoter-TSS (NM_177278)	30	NM_177278	320858	Mm.137356	NM_177278	ENSMUSG00000041565	L3mbtl4	A730037L19Rik|D930040M24Rik	l(3)mbt-like 4 (Drosophila)	protein-coding
mm_133649.1	chr16	91798440	91798477	+	1	NA	intron (NM_001110275, intron 5 of 28)	intron (NM_001110275, intron 5 of 28)	69087	NM_010587	16443	Mm.40546	NM_010587	ENSMUSG00000022957	Itsn1	AA517634|AA545208|AI316805|AI839402|AI848451|Ehsh1|Ese1|Itsn|Sh3p17	intersectin 1 (SH3 domain protein 1A)	protein-coding
mm_141523.1	chr17	31766942	31766945	-	1	NA	Intergenic	Intergenic	88849	NM_010831	17691	Mm.290941	NM_010831	ENSMUSG00000024042	Sik1	Msk|Sik|Snf1lk	salt inducible kinase 1	protein-coding
mm_74648.1	chr8	13389694	13389702	-	1	NA	exon (NM_009724, exon 4 of 7)	exon (NM_009724, exon 4 of 7)	7080	NM_009724	11945	Mm.154039	NM_009724	ENSMUSG00000031449	Atp4b	AV080843	ATPase, H+/K+ exchanging, beta polypeptide	protein-coding
mm_163822.1	chr14	19416787	19416825	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	185781	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_54042.1	chr6	13650970	13650988	-	1	NA	intron (NM_175312, intron 2 of 4)	MER21B|LTR|ERVL	26987	NM_175312	101148	Mm.354863	NM_175312	ENSMUSG00000042742	Bmt2	AI666701|B630005N14Rik	base methyltransferase of 25S rRNA 2	protein-coding
mm_149382.1	chr19	11381814	11381827	+	1	NA	intron (NM_001310331, intron 3 of 6)	RMER6A|LTR|ERVK	6332	NM_001310331	666907		NM_001310331	ENSMUSG00000101389	Ms4a4a	EG666907	membrane-spanning 4-domains, subfamily A, member 4A	protein-coding
mm_124261.1	chr14	102978127	102978137	-	1	NA	3' UTR (NM_177715, exon 1 of 1)	3' UTR (NM_177715, exon 1 of 1)	4500	NR_039592	100628599		NR_039592	ENSMUSG00000092901	Mir5130	mir-5130|mmu-mir-5130|mu-mir-5130	microRNA 5130	ncRNA
mm_63200.1	chr7	125707894	125707929	+	1	NA	promoter-TSS (NM_207239)	promoter-TSS (NM_207239)	35	NM_001081022	233865	Mm.274389	NM_001081022	ENSMUSG00000032743	D430042O09Rik	Kiaa0556	RIKEN cDNA D430042O09 gene	protein-coding
mm_104354.1	chr11	94299978	94300068	-	1	NA	exon (NM_026313, exon 6 of 11)	exon (NM_026313, exon 6 of 11)	21888	NM_026313	67684	Mm.30927	NM_026313	ENSMUSG00000020863	Luc7l3	3300001P08Rik|Luc7a	LUC7-like 3 (S. cerevisiae)	protein-coding
mm_98699.1	chr11	96303615	96303633	+	1	NA	exon (NM_008268, exon 1 of 2)	exon (NM_008268, exon 1 of 2)	112	NM_008268	15413	Mm.207	NM_008268	ENSMUSG00000038700	Hoxb5	AI385717|Hox-2.1	homeobox B5	protein-coding
mm_171338.1	chr4	102875773	102875773	-	1	NA	intron (NM_001285862, intron 6 of 19)	IAPLTR1_Mm|LTR|ERVK	-110606	NM_001163767	67344	Mm.111346	NM_026100	ENSMUSG00000028523	Tctex1d1	1700055O19Rik	Tctex1 domain containing 1	protein-coding
mm_102535.1	chr11	61174982	61175010	-	1	NA	promoter-TSS (NM_001004143)	promoter-TSS (NM_001004143)	63	NM_001004143	216825	Mm.30602	NM_001004143	ENSMUSG00000042506	Usp22	AI427806	ubiquitin specific peptidase 22	protein-coding
mm_77444.1	chr8	121792201	121792210	-	1	NA	Intergenic	Intergenic	37364	NM_145605	234825	Mm.209329	NM_145605	ENSMUSG00000040263	Klhdc4	AA408426|AV352552|BC012312|G430025P05Rik	kelch domain containing 4	protein-coding
mm_19637.1	chr2	102829171	102829176	-	1	NA	intron (NM_001039151, intron 5 of 8)	intron (NM_001039151, intron 5 of 8)	72492	NM_001177785	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_29853.1	chr3	130007548	130007560	-	1	NA	exon (NM_207209, exon 7 of 24)	exon (NM_207209, exon 7 of 24)	-37348	NM_001293644	66815	Mm.31056	NM_025779	ENSMUSG00000027994	Ccdc109b	9030408N13Rik|MCUb	coiled-coil domain containing 109B	protein-coding
mm_27355.1	chr3	50417496	50417507	-	1	NA	intron (NM_011990, intron 6 of 11)	intron (NM_011990, intron 6 of 11)	26112	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_70544.1	chr8	13052286	13052289	+	1	NA	intron (NM_001242368, intron 7 of 8)	PB1D9|SINE|Alu	-8621	NM_025834	66901	Mm.441140	NM_025834	ENSMUSG00000031445	Proz	1300015B06Rik	protein Z, vitamin K-dependent plasma glycoprotein	protein-coding
mm_60913.1	chr7	46796089	46796134	+	1	NA	promoter-TSS (NM_001167864)	promoter-TSS (NM_001167864)	17	NM_008186	14884	Mm.22700	NM_008186	ENSMUSG00000006599	Gtf2h1	62kDa|AW743425|AW822074|BTF2 p62|C77871|p62	general transcription factor II H, polypeptide 1	protein-coding
mm_149642.1	chr19	17400237	17400290	+	1	NA	3' UTR (NM_019437, exon 4 of 4)	3' UTR (NM_019437, exon 4 of 4)	6220	NM_019437	54391	Mm.7013	NM_019437	ENSMUSG00000024712	Rfk	0610038L10Rik|AF031381|KOI-4	riboflavin kinase	protein-coding
mm_69730.1	chr7	140856255	140856325	-	1	NA	promoter-TSS (NM_018742)	promoter-TSS (NM_018742)	93	NM_018742	54399	Mm.155696	NM_018742	ENSMUSG00000025484	Bet1l	2610021K23Rik|Gs15	Bet1 golgi vesicular membrane trafficking protein like	protein-coding
mm_123185.1	chr14	57826186	57826203	-	1	NA	promoter-TSS (NM_198605)	promoter-TSS (NM_198605)	-31	NM_198605	219114	Mm.30173	NM_198605	ENSMUSG00000021965	Ska3	F630043A04Rik	spindle and kinetochore associated complex subunit 3	protein-coding
mm_97964.1	chr11	83746990	83747006	+	1	NA	promoter-TSS (NM_183249)	promoter-TSS (NM_183249)	58	NM_183249	66107	Mm.902	NM_183249	ENSMUSG00000051748	Wfdc21	1100001G20Rik|Wdnm1-like	WAP four-disulfide core domain 21	protein-coding
mm_15776.1	chr2	164333358	164333368	+	1	NA	exon (NM_009301, exon 2 of 3)	exon (NM_009301, exon 2 of 3)	598	NM_009301	20944	Mm.140154	NM_009301	ENSMUSG00000017004	Svs5	BB115186|Semg1|Svp-1|Svp1|Svp5	seminal vesicle secretory protein 5	protein-coding
mm_71988.1	chr8	70616667	70616684	+	1	NA	promoter-TSS (NM_153074)	promoter-TSS (NM_153074)	-169	NM_153074	211228	Mm.132939	NM_153074	ENSMUSG00000049988	Lrrc25	Mapa	leucine rich repeat containing 25	protein-coding
mm_154454.1	chrM	2340	2354	-	1	NA	NA	Intergenic	NA	NA								
mm_40824.1	chr5	72647811	72647853	+	1	NA	promoter-TSS (NM_001081205)	promoter-TSS (NM_001081205)	36	NM_001081205	70701	Mm.38884	NM_001081205	ENSMUSG00000067219	Nipal1	3830408G10Rik|Npal1	NIPA-like domain containing 1	protein-coding
mm_51015.1	chr6	65023382	65023390	+	1	NA	Intergenic	RLTR19A2|LTR|ERVK	-19281	NM_007958	13990	Mm.99113	NM_007958	ENSMUSG00000029920	Smarcad1	AV081750|AW226546|D6Pas1|Etl1|mKIAA1122	SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1	protein-coding
mm_97635.1	chr11	78962069	78962078	+	1	NA	TTS (NM_010708)	TTS (NM_010708)	22851	NM_001159301	16859	Mm.341434	NM_010708	ENSMUSG00000001123	Lgals9	AA407335|AI194909|AI265545|LGALS35|Lgals5|gal-9|galectin-9	lectin, galactose binding, soluble 9	protein-coding
mm_115343.1	chr13	112509002	112509017	+	1	NA	Intergenic	Intergenic	44939	NM_010560	16195	Mm.4364	NM_010560	ENSMUSG00000021756	Il6st	5133400A03Rik|AA389424|BB405851|CD130|D13Ertd699e|gp130	interleukin 6 signal transducer	protein-coding
mm_149343.1	chr19	10850454	10850464	+	1	NA	intron (NM_023044, intron 2 of 7)	intron (NM_023044, intron 2 of 7)	7915	NM_023044	65221	Mm.27387	NM_023044	ENSMUSG00000024737	Slc15a3	Ci1|cI-1	solute carrier family 15, member 3	protein-coding
mm_158953.1	chr1	87584055	87584055	+	1	NA	promoter-TSS (NM_001160165)	promoter-TSS (NM_001160165)	33	NM_001160165	23956	Mm.143717	NM_015750	ENSMUSG00000079434	Neu2	MBS|MSS|MTS	neuraminidase 2	protein-coding
mm_9979.1	chr1	191225273	191225286	-	1	NA	Intergenic	Intergenic	-41946	NM_007498	11910	Mm.2706	NM_007498	ENSMUSG00000026628	Atf3	LRG-21	activating transcription factor 3	protein-coding
mm_85322.1	chr9	101251842	101251852	-	1	NA	promoter-TSS (NM_001161362)	promoter-TSS (NM_001161362)	-15	NM_001161362	235542	Mm.335386	NM_172144	ENSMUSG00000043154	Ppp2r3a	3222402P14Rik|A730042E07	protein phosphatase 2, regulatory subunit B'', alpha	protein-coding
mm_92072.1	chr10	62602262	62602291	-	1	NA	promoter-TSS (NM_019553)	promoter-TSS (NM_019553)	22	NM_019553	56200	Mm.413275	NM_019553	ENSMUSG00000020075	Ddx21	AI255159|AL022742|D10Ertd645e|D10Wsu42e	DEAD (Asp-Glu-Ala-Asp) box polypeptide 21	protein-coding
mm_111243.1	chr12	84787151	84787158	-	1	NA	intron (NM_013589, intron 29 of 34)	intron (NM_013589, intron 29 of 34)	13884	NM_028863	74316	Mm.25719	NM_028863	ENSMUSG00000021241	Isca2	0710001C05Rik|5730594E03Rik|Hbld1	iron-sulfur cluster assembly 2	protein-coding
mm_85290.1	chr9	99876199	99876212	-	1	NA	promoter-TSS (NM_011440)	promoter-TSS (NM_011440)	-35	NM_011440	20669	Mm.261595	NM_011440	ENSMUSG00000053747	Sox14	-	SRY (sex determining region Y)-box 14	protein-coding
mm_125901.1	chr15	75969169	75969189	+	1	NA	promoter-TSS (NM_001081065)	promoter-TSS (NM_001081065)	-6	NM_001081065	69020	Mm.294295	NM_001081065	ENSMUSG00000034429	Zfp707	1500031N24Rik|AI451708|AW495315	zinc finger protein 707	protein-coding
mm_51745.1	chr6	87375809	87375822	+	1	NA	exon (NM_025467, exon 3 of 6)	exon (NM_025467, exon 3 of 6)	2450	NM_025467	66284	Mm.46446	NM_025467	ENSMUSG00000030049	Gkn2	1810036H07Rik|Bricd1b	gastrokine 2	protein-coding
mm_164214.1	chr15	83474087	83474106	-	1	NA	Intergenic	Intergenic	-9490	NM_001159509	23970	Mm.23978	NM_011862	ENSMUSG00000016664	Pacsin2	AI197433	protein kinase C and casein kinase substrate in neurons 2	protein-coding
mm_168506.1	chr1	153620718	153620727	-	1	NA	Intergenic	Intergenic	-32315	NM_026380	67792	Mm.379143	NM_026380	ENSMUSG00000042671	Rgs8	6530413N01Rik	regulator of G-protein signaling 8	protein-coding
mm_105358.1	chr11	103101589	103101595	-	1	NA	promoter-TSS (NM_025988)	promoter-TSS (NM_025988)	66	NM_152813	72469	Mm.264743	NM_152813	ENSMUSG00000020937	Plcd3	2610205J15Rik|mKIAA1964	phospholipase C, delta 3	protein-coding
mm_106028.1	chr11	116076987	116077027	-	1	NA	intron (NM_001009573, intron 2 of 32)	intron (NM_001009573, intron 2 of 32)	954	NM_001009573	70450	Mm.259460	NM_001009573	ENSMUSG00000057948	Unc13d	2610108D09Rik|Jinx|Munc13-4|mFLJ00067	unc-13 homolog D (C. elegans)	protein-coding
mm_78448.1	chr9	32224306	32224320	+	1	NA	promoter-TSS (NM_177379)	promoter-TSS (NM_177379)	64	NM_177379	330914	Mm.46683	NM_177379	ENSMUSG00000041444	Arhgap32	3426406O18Rik|Gc-gap|Grit|Px-rics|Rics|mKIAA0712|p200Rhogap|p250Gap	Rho GTPase activating protein 32	protein-coding
mm_11804.1	chr2	43895210	43895223	+	1	NA	intron (NM_001301832, intron 7 of 14)	intron (NM_001301832, intron 7 of 14)	146392	NM_001301831	76117	Mm.217350	NM_153820	ENSMUSG00000049744	Arhgap15	5830480G12Rik	Rho GTPase activating protein 15	protein-coding
mm_87867.1	chr10	61297810	61297824	+	1	NA	promoter-TSS (NM_011073)	promoter-TSS (NM_011073)	-19	NM_011073	18646	Mm.240313	NM_011073	ENSMUSG00000037202	Prf1	Pfn|Pfp|Prf-1	perforin 1 (pore forming protein)	protein-coding
mm_141124.1	chr17	26099258	26099259	-	1	NA	Intergenic	Intergenic	-3788	NM_019731	56520	Mm.41787	NM_019731	ENSMUSG00000024177	Nme4	2610027N22Rik|2810024O08Rik|5730493H09Rik|NM23-M4|Nm23M4	NME/NM23 nucleoside diphosphate kinase 4	protein-coding
mm_136926.1	chr17	13850051	13850055	+	1	NA	intron (NM_010806, intron 17 of 32)	B3|SINE|B2	-88659	NM_022311	21646	Mm.486358	NM_022311	ENSMUSG00000038347	Tcte2	AI429268|Tcte-2	t-complex-associated testis expressed 2	protein-coding
mm_116805.1	chr13	54189977	54190008	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-2137	NM_001010973	15466	Mm.57243	NM_008286	ENSMUSG00000034987	Hrh2	-	histamine receptor H2	protein-coding
mm_22124.1	chr2	170252794	170252807	-	1	NA	Intergenic	Intergenic	-103561	NR_040610	73303	Mm.443297	NR_040610	ENSMUSG00000086999	Bcas1os2	1700040N02Rik	breast carcinoma amplified sequence 1, opposite strand 2	ncRNA
mm_146065.1	chr18	69925543	69925571	+	1	NA	promoter-TSS (NM_201362)	promoter-TSS (NM_201362)	-2	NM_201362	381175	Mm.266831	NM_201362	ENSMUSG00000038903	Ccdc68	BC046343	coiled-coil domain containing 68	protein-coding
mm_64616.1	chr7	3578245	3578248	-	1	NA	Intergenic	Intergenic	37911	NM_175632	232790	Mm.358882	NM_175632	ENSMUSG00000054594	Oscar	mOSCAR|mOSCAR-M1|mOSCAR-M2|mOSCAR-M3	osteoclast associated receptor	protein-coding
mm_167863.1	chrX	20239388	20239391	+	1	NA	intron (NM_177353, intron 1 of 16)	intron (NM_177353, intron 1 of 16)	52375	NM_177353	236727	Mm.132983	NM_177353	ENSMUSG00000037341	Slc9a7	A530087D17Rik|NHE7	solute carrier family 9 (sodium/hydrogen exchanger), member 7	protein-coding
mm_11945.1	chr2	52892119	52892123	+	1	NA	intron (NM_172409, intron 1 of 26)	intron (NM_172409, intron 1 of 26)	34253	NM_172409	71409	Mm.394427	NM_172409	ENSMUSG00000036053	Fmnl2	5430425K04Rik|Man	formin-like 2	protein-coding
mm_95586.1	chr11	53299885	53299895	+	1	NA	intron (NM_008300, intron 1 of 18)	CpG	589	NM_008300	15525	Mm.239865	NM_008300	ENSMUSG00000020361	Hspa4	70kDa|AI317151|APG-2|Hsp110|Hsp70RY|mKIAA4025	heat shock protein 4	protein-coding
mm_130733.1	chr15	101248718	101248726	-	1	NA	Intergenic	Intergenic	-18124	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_163712.1	chr13	109726448	109726448	-	1	NA	intron (NM_011056, intron 3 of 16)	intron (NM_011056, intron 3 of 16)	-177361	NR_035442	100316683		NR_035442	ENSMUSG00000084651	Mir1904	Mirn1904|mmu-mir-1904	microRNA 1904	ncRNA
mm_134253.1	chr16	13730448	13730456	-	1	NA	promoter-TSS (NM_011987)	promoter-TSS (NM_011987)	32	NR_110990	26565	Mm.4214	NM_011987	ENSMUSG00000022683	Pla2g10	GX sPLA2|PLA2GX|sPLA2-X	phospholipase A2, group X	protein-coding
mm_133145.1	chr16	70313968	70313976	+	1	NA	promoter-TSS (NM_028803)	promoter-TSS (NM_028803)	23	NM_028803	74185	Mm.396102	NM_028803	ENSMUSG00000022707	Gbe1	2310045H19Rik|2810426P10Rik|D16Ertd536e	glucan (1,4-alpha-), branching enzyme 1	protein-coding
mm_106649.1	chr11	121063527	121063531	-	1	NA	promoter-TSS (NM_026907)	promoter-TSS (NM_026907)	40	NM_026907	58210	Mm.116986	NM_026907	ENSMUSG00000039364	Sectm1b	1810003C24Rik|K12|Sectm1	secreted and transmembrane 1B	protein-coding
mm_129035.1	chr15	74994937	74994947	-	1	NA	TTS (NM_001271446)	TTS (NM_001271446)	3089	NM_001271417	110454	Mm.425949	NM_010738	ENSMUSG00000075602	Ly6a	Ly-6A.2|Ly-6A/E|Ly-6E.1|Sca-1|Sca1|TAP	lymphocyte antigen 6 complex, locus A	protein-coding
mm_91577.1	chr10	40129303	40129306	-	1	NA	intron (NM_001114332, intron 1 of 5)	PB1D11|SINE|Alu	12950	NM_028247	72472	Mm.186778	NM_028247	ENSMUSG00000019838	Slc16a10	2610103N14Rik|9830169E08|Mct10|PRO0813|TAT1	solute carrier family 16 (monocarboxylic acid transporters), member 10	protein-coding
mm_168204.1	chr10	69912066	69912072	+	1	NA	intron (NM_170689, intron 23 of 41)	B2_Mm2|SINE|B2	-13463	NM_170687	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_28456.1	chr3	90678727	90678738	-	1	NA	Intergenic	Intergenic	9661	NM_013650	20201	Mm.21567	NM_013650	ENSMUSG00000056054	S100a8	60B8Ag|AI323541|B8Ag|CFAg|CP-10|Caga|MRP8|p8	S100 calcium binding protein A8 (calgranulin A)	protein-coding
mm_2547.1	chr1	107589958	107589978	+	1	NA	promoter-TSS (NM_001159748)	promoter-TSS (NM_001159748)	-38	NM_011459	20725	Mm.83909	NM_011459	ENSMUSG00000026315	Serpinb8	CAP-2|CAP2|NK10|Spi8|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 8	protein-coding
mm_158854.1	chrX	169994214	169994226	-	1	NA	Intergenic	CpG	-15303	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_21860.1	chr2	165884693	165884697	-	1	NA	5' UTR (NM_001252584, exon 1 of 23)	5' UTR (NM_001252584, exon 1 of 23)	143	NM_001252584	228880	Mm.227598	NM_027230	ENSMUSG00000039671	Zmynd8	1110013E22Rik|2010005I16Rik|3632413B07Rik|AI316811|AL024039|Prkcbp1|RACK7	zinc finger, MYND-type containing 8	protein-coding
mm_14099.1	chr2	125235853	125235854	+	1	NA	Intergenic	Intergenic	-11395	NM_001159646	110074	Mm.282499	NM_023595	ENSMUSG00000027203	Dut	5031412I06Rik|5133400F09Rik|D2Bwg0749e|Dutp|dUTPase	deoxyuridine triphosphatase	protein-coding
mm_168669.1	chr11	91706206	91706206	-	1	NA	Intergenic	RLTR51A_Mm|LTR|ERVK?	-128651	NM_028547	73470	Mm.67677	NM_028547	ENSMUSG00000046755	Kif2b	1700063D03Rik	kinesin family member 2B	protein-coding
mm_160807.1	chr11	11489281	11489281	+	1	NA	promoter-TSS (NM_028669)	promoter-TSS (NM_028669)	15	NM_028669	73862	Mm.159077	NM_028669	ENSMUSG00000020191	4930415F15Rik	-	RIKEN cDNA 4930415F15 gene	protein-coding
mm_141504.1	chr17	31636584	31636594	-	1	NA	intron (NM_178224, intron 1 of 15)	CpG	616	NM_144855	12411	Mm.206417	NM_144855	ENSMUSG00000024039	Cbs	AI047524|AI303044|HIP4	cystathionine beta-synthase	protein-coding
mm_48747.1	chr5	147894788	147894798	-	1	NA	promoter-TSS (NM_027872)	promoter-TSS (NM_027872)	9	NM_027872	71706	Mm.153218	NM_027872	ENSMUSG00000029650	Slc46a3	1200006F02Rik	solute carrier family 46, member 3	protein-coding
mm_46488.1	chr5	105132172	105132176	-	1	NA	intron (NM_008620, intron 3 of 10)	intron (NM_008620, intron 3 of 10)	7378	NM_008620	17472	Mm.440525	NM_008620	ENSMUSG00000079363	Gbp4	AW228052|Mag-2|Mpa-2|Mpa2	guanylate binding protein 4	protein-coding
mm_67718.1	chr7	90024621	90024624	-	1	NA	Intergenic	Intergenic	-4537	NR_110365	319711	Mm.31753	NR_015614	ENSMUSG00000097585	E230029C05Rik	AI452102|B230337J15	RIKEN cDNA E230029C05 gene	ncRNA
mm_89639.1	chr10	96621387	96621395	+	1	NA	3' UTR (NM_007569, exon 2 of 2)	3' UTR (NM_007569, exon 2 of 2)	4390	NM_007569	12226	Mm.23811	NM_007569	ENSMUSG00000036478	Btg1	AI426953|AW546738	B cell translocation gene 1, anti-proliferative	protein-coding
mm_149988.1	chr19	29251861	29251867	+	1	NA	promoter-TSS (NM_008413)	promoter-TSS (NM_008413)	61	NM_008413	16452	Mm.275839	NM_008413	ENSMUSG00000024789	Jak2	Fd17	Janus kinase 2	protein-coding
mm_74630.1	chr8	13175328	13175337	-	1	NA	TTS (NM_010684)	TTS (NM_010684)	13766	NR_035494	100316713		NR_035494	ENSMUSG00000088054	Mir1968	mir-1968|mmu-mir-1968	microRNA 1968	ncRNA
mm_101371.1	chr11	23770751	23770789	-	1	NA	5' UTR (NM_009044, exon 1 of 10)	5' UTR (NM_009044, exon 1 of 10)	200	NM_009044	19696	Mm.4869	NM_009044	ENSMUSG00000020275	Rel	c-Rel	reticuloendotheliosis oncogene	protein-coding
mm_85624.1	chr9	107615079	107615084	-	1	NA	3' UTR (NM_008138, exon 9 of 9)	3' UTR (NM_008138, exon 9 of 9)	-5840	NM_001291539	20347	Mm.4083	NM_009153	ENSMUSG00000057969	Sema3b	SemA|Semaa|sema5|semaV	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B	protein-coding
mm_53483.1	chr6	135011610	135011640	+	1	NA	promoter-TSS (NM_026360)	promoter-TSS (NM_026360)	13	NM_026360	67755	Mm.166524	NM_026360	ENSMUSG00000030204	Ddx47	4930588A18Rik|C77285	DEAD (Asp-Glu-Ala-Asp) box polypeptide 47	protein-coding
mm_30689.1	chr4	11486003	11486045	+	1	NA	promoter-TSS (NM_001347055)	promoter-TSS (NM_001347055)	66	NM_001347055	66185	Mm.331487	NM_001081183	ENSMUSG00000040720	1110037F02Rik	4930422M05Rik|Kiaa1429|mKIAA1429	RIKEN cDNA 1110037F02 gene	protein-coding
mm_91164.1	chr10	20665415	20665420	-	1	NA	intron (NM_013875, intron 1 of 12)	intron (NM_013875, intron 1 of 12)	59661	NM_013875	29863	Mm.425617	NM_013875	ENSMUSG00000019990	Pde7b	-	phosphodiesterase 7B	protein-coding
mm_147867.1	chr18	64457877	64457886	-	1	NA	3' UTR (NM_007998, exon 11 of 11)	3' UTR (NM_007998, exon 11 of 11)	31185	NM_007998	14151	Mm.1070	NM_007998	ENSMUSG00000024588	Fech	AI894116|Fcl|fch	ferrochelatase	protein-coding
mm_135042.1	chr16	33023912	33023948	-	1	NA	intron (NM_178378, intron 8 of 10)	LTR41B|LTR|ERVL	32256	NM_178378	69707	Mm.227918	NM_178378	ENSMUSG00000035578	Iqcg	2400003L07Rik|G1-374-12|esgd12d|repro1|stubby12d	IQ motif containing G	protein-coding
mm_155454.1	chrX	73495877	73495888	+	1	NA	TTS (NM_007542)	TTS (NM_007542)	-7204	NM_001310537	320707	Mm.210095	NM_177236	ENSMUSG00000031376	Atp2b3	6430519O13Rik|Pmca3	ATPase, Ca++ transporting, plasma membrane 3	protein-coding
mm_146188.1	chr18	76035396	76035430	+	1	NA	intron (NM_145356, intron 3 of 4)	intron (NM_145356, intron 3 of 4)	63058	NR_045365	73009	Mm.443541	NR_045365		2900057B20Rik	-	RIKEN cDNA 2900057B20 gene	ncRNA
mm_133030.1	chr16	57331951	57331960	+	1	NA	intron (NM_025599, intron 1 of 9)	B4|SINE|B4	-21322	NM_001040397	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding
mm_125097.1	chr15	27571583	27571592	+	1	NA	promoter-TSS (NR_106065)	promoter-TSS (NR_106065)	93	NR_106065	102466808		NR_106065	ENSMUSG00000098416	Mir7117	Gm27729|mmu-mir-7117	microRNA 7117	ncRNA
mm_157464.1	chrX	44790320	44790328	-	1	NA	promoter-TSS (NM_178739)	promoter-TSS (NM_178739)	-127	NM_178739	245404	Mm.55685	NM_178739	ENSMUSG00000045284	Dcaf12l1	9330180J20|A230038L21Rik|Decaf12l1|Wdr40b	DDB1 and CUL4 associated factor 12-like 1	protein-coding
mm_113258.1	chr13	28257591	28257600	+	1	NA	Intergenic	Intergenic	115111	NM_023746	28078	Mm.155058	NM_023746	ENSMUSG00000017064	Prl5a1	1600013P04Rik|D13Wsu14e|Ghd24|PLP-L|Prlpl	prolactin family 5, subfamily a, member 1	protein-coding
mm_78234.1	chr9	21616167	21616177	+	1	NA	promoter-TSS (NM_001174078)	promoter-TSS (NM_001174078)	3	NM_001174078	20586	Mm.286593	NM_011417	ENSMUSG00000032187	Smarca4	Brg1|HP1-BP72|SNF2beta|SW1/SNF|b2b508.1Clo|b2b692Clo	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	protein-coding
mm_102603.1	chr11	62392606	62392618	-	1	NA	exon (NM_001252313, exon 11 of 45)	exon (NM_001252313, exon 11 of 45)	45903	NM_001252313	20185	Mm.271814	NM_011308	ENSMUSG00000018501	Ncor1	5730405M06Rik|A230020K14Rik|N-CoR|RIP13|Rxrip13|mKIAA1047	nuclear receptor co-repressor 1	protein-coding
mm_35546.1	chr4	41498222	41498243	-	1	NA	exon (NM_001085515, exon 2 of 2)	exon (NM_001085515, exon 2 of 2)	4843	NM_001085515	329828	Mm.27054	NM_001085515	ENSMUSG00000046312	AI464131	AA408153|AI604836|Gm762|Kiaa1161|NET37	expressed sequence AI464131	protein-coding
mm_24026.1	chr3	87535719	87535730	+	1	NA	exon (NM_012051, exon 5 of 5)	exon (NM_012051, exon 5 of 5)	10146	NM_012051	27049	Mm.219460	NM_012051	ENSMUSG00000003382	Etv3	AI414410|METS|Pe1	ets variant 3	protein-coding
mm_55143.1	chr6	51464454	51464471	-	1	NA	exon (NM_016806, exon 8 of 11)	exon (NM_016806, exon 8 of 11)	5432	NM_182650	53379	Mm.155896	NM_016806	ENSMUSG00000004980	Hnrnpa2b1	9130414A06Rik|Hnrpa2|Hnrpa2b1|hnrnp-A	heterogeneous nuclear ribonucleoprotein A2/B1	protein-coding
mm_152374.1	chr19	10223567	10223572	-	1	NA	intron (NM_001033481, intron 5 of 25)	intron (NM_001033481, intron 5 of 25)	17179	NM_001033481	225908	Mm.329716	NM_001033481	ENSMUSG00000036098	Myrf	6030439E18|Gm1804|Gm98|Mrf	myelin regulatory factor	protein-coding
mm_107390.1	chr12	33314263	33314288	+	1	NA	intron (NM_001033436, intron 1 of 7)	intron (NM_001033436, intron 1 of 7)	11760	NM_001033436	380753	Mm.41540	NM_028139	ENSMUSG00000020564	Atxn7l1	2810423G08Rik|Atxn7l4	ataxin 7-like 1	protein-coding
mm_25346.1	chr3	106785405	106785426	+	1	NA	intron (NM_007651, intron 1 of 7)	intron (NM_007651, intron 1 of 7)	4734	NM_007651	12508	Mm.316861	NM_007651	ENSMUSG00000040747	Cd53	AI323659|Ox-44|Tspan25	CD53 antigen	protein-coding
mm_52757.1	chr6	120773634	120773636	+	1	NA	promoter-TSS (NM_001081048)	promoter-TSS (NM_001081048)	-133	NM_001081048	71803	Mm.425340	NM_001081048	ENSMUSG00000004902	Slc25a18	1500015I14Rik|AW125787	solute carrier family 25 (mitochondrial carrier), member 18	protein-coding
mm_95200.1	chr11	43444752	43444770	+	1	NA	exon (NM_198936, exon 13 of 16)	exon (NM_198936, exon 13 of 16)	11030	NM_198936	193116	Mm.28200	NM_148673	ENSMUSG00000020409	Slu7	AU018913|D11Ertd730e|D3Bwg0878e	SLU7 splicing factor homolog (S. cerevisiae)	protein-coding
mm_143219.1	chr17	63141169	63141172	-	1	NA	intron (NM_015794, intron 7 of 8)	intron (NM_015794, intron 7 of 8)	171803	NR_130176	414079	Mm.444282	NR_130176	ENSMUSG00000090565	4930405O22Rik	-	RIKEN cDNA 4930405O22 gene	ncRNA
mm_59093.1	chr7	19696562	19696572	+	1	NA	exon (NM_009696, exon 4 of 4)	exon (NM_009696, exon 4 of 4)	1831	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_71245.1	chr8	40913959	40914000	+	1	NA	exon (NM_001044740, exon 10 of 12)	exon (NM_001044740, exon 10 of 12)	-12254	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_38081.1	chr4	134128681	134128700	-	1	NA	promoter-TSS (NM_080559)	promoter-TSS (NM_080559)	63	NM_080559	73723	Mm.22240	NM_080559	ENSMUSG00000028843	Sh3bgrl3	1110004L05Rik|AU022188	SH3 domain binding glutamic acid-rich protein-like 3	protein-coding
mm_146104.1	chr18	74216119	74216145	+	1	NA	promoter-TSS (NM_028868)	promoter-TSS (NM_028868)	-80	NM_028868	74322	Mm.17537	NM_028868	ENSMUSG00000024560	Cxxc1	2410002I16Rik|5830420C16Rik|AI426635|Cfp1|Cgbp|PHF18	CXXC finger 1 (PHD domain)	protein-coding
mm_60648.1	chr7	44854590	44854615	+	1	NA	exon (NM_001290695, exon 4 of 4)	exon (NM_001290695, exon 4 of 4)	-2544	NM_021549	59047	Mm.238254	NM_021549	ENSMUSG00000002963	Pnkp	1810009G08Rik|PNK	polynucleotide kinase 3'- phosphatase	protein-coding
mm_57715.1	chr6	128788498	128788534	-	1	NA	exon (NM_001159904, exon 1 of 6)	exon (NM_001159904, exon 1 of 6)	125	NM_008527	17059	Mm.480764	NM_008527	ENSMUSG00000030325	Klrb1c	AI462337|CD161|Ly-59|Ly55c|Ly59|NK-RP1|NK1.1|NKR-P1.9|NKRP1|NKRP140|Nk-1|Nk-1.2|Nk1|Nk1.2|Nkrp1c|ly-55c	killer cell lectin-like receptor subfamily B member 1C	protein-coding
mm_105842.1	chr11	113683977	113684132	-	1	NA	promoter-TSS (NM_138598)	promoter-TSS (NM_138598)	97	NM_138598	28081	Mm.351688	NM_138598	ENSMUSG00000041629	Fam104a	D11Wsu99e	family with sequence similarity 104, member A	protein-coding
mm_136553.1	chr17	3114931	3114939	+	1	NA	promoter-TSS (NM_134123)	promoter-TSS (NM_134123)	-37	NM_134123	106583	Mm.124373	NM_134123	ENSMUSG00000046201	Scaf8	A630086M08Rik|A930036P18Rik|AA408306|AI447644|AI448652|AU015035|Rbm16|mKIAA1116	SR-related CTD-associated factor 8	protein-coding
mm_146958.1	chr18	33213772	33213783	-	1	NA	promoter-TSS (NM_001347624)	promoter-TSS (NM_001347624)	85	NM_001347624	170459	Mm.127058	NM_133774	ENSMUSG00000024378	Stard4	4632419C16Rik|9030213J02Rik	StAR-related lipid transfer (START) domain containing 4	protein-coding
mm_135864.1	chr16	60605546	60605559	-	1	NA	promoter-TSS (NM_007938)	promoter-TSS (NM_007938)	-21	NM_007938	13840	Mm.455790	NM_007938	ENSMUSG00000055540	Epha6	Ehk2|Hek12|m-ehk2	Eph receptor A6	protein-coding
mm_49559.1	chr6	30560508	30560512	+	1	NA	intron (NM_001024698, intron 10 of 10)	PB1D9|SINE|Alu	-7859	NM_027926	71791	Mm.105759	NM_027926	ENSMUSG00000039070	Cpa4	1110019K20Rik|AV009555	carboxypeptidase A4	protein-coding
mm_151403.1	chr19	56510681	56510691	+	1	NA	Intergenic	Intergenic	37536	NM_018831	55947	Mm.2805	NM_018831	ENSMUSG00000025077	Dclre1a	2810043H12Rik|AU022226|Pso2|Smn1a|Snm1|mKIAA0086	DNA cross-link repair 1A	protein-coding
mm_55871.1	chr6	83506831	83506835	-	1	NA	exon (NM_001162521, exon 1 of 6)	exon (NM_001162521, exon 1 of 6)	136	NM_013764	27369	Mm.42234	NM_013764	ENSMUSG00000014554	Dguok	dGK|dGK1|dGK2|dGK3	deoxyguanosine kinase	protein-coding
mm_77276.1	chr8	116673161	116673186	-	1	NA	intron (NM_029441, intron 1 of 6)	RLTR15|LTR|ERVK	59818	NM_029441	75796	Mm.159575	NM_029441	ENSMUSG00000031758	Cdyl2	1700029M19Rik|4930453I21Rik|Gm20194	chromodomain protein, Y chromosome-like 2	protein-coding
mm_48241.1	chr5	137741602	137741617	-	1	NA	promoter-TSS (NM_001347505)	promoter-TSS (NM_001347505)	-441	NM_001347505	243300	Mm.74750	NM_175521	ENSMUSG00000045348	Nyap1	6430598A04Rik	neuronal tyrosine-phosphorylated phosphoinositide 3-kinase adaptor 1	protein-coding
mm_25888.1	chr3	131106181	131106191	+	1	NA	Intergenic	CpG	-4111	NM_010703	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_47291.1	chr5	122240847	122240863	-	1	NA	non-coding (NR_104441, exon 13 of 13)	non-coding (NR_104441, exon 13 of 13)	23605	NR_104441	654470	Mm.28804	NM_001039153	ENSMUSG00000038593	Tctn1	G730031O11Rik|Tect1	tectonic family member 1	protein-coding
mm_23030.1	chr3	34650175	34650189	+	1	NA	5' UTR (NM_011443, exon 1 of 1)	5' UTR (NM_011443, exon 1 of 1)	187	NM_011443	20674	Mm.65396	NM_011443	ENSMUSG00000074637	Sox2	Sox-2|lcc|ysb	SRY (sex determining region Y)-box 2	protein-coding
mm_114365.1	chr13	62129895	62129923	+	1	NA	promoter-TSS (NM_001039239)	promoter-TSS (NM_001039239)	19	NM_001039239	630579	Mm.440905	NM_001039239	ENSMUSG00000074867	Zfp808	EG630579|Gm7036	zinc finger protein 80	protein-coding
mm_30991.1	chr4	36952931	36952970	+	1	NA	Intergenic	Intergenic	-1206	NM_001165999	242384	Mm.132507	NM_175516	ENSMUSG00000045083	Lingo2	B230217C06Rik|Lern3|Lrrn6c	leucine rich repeat and Ig domain containing 2	protein-coding
mm_50152.1	chr6	41544821	41544833	+	1	NA	Intergenic	Intergenic	23051	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_31669.1	chr4	60004835	60004865	+	1	NA	exon (NM_001081285, exon 3 of 6)	exon (NM_001081285, exon 3 of 6)	1301	NM_001081285	620807	Mm.464562	NM_001081285	ENSMUSG00000078689	Mup6	Gm12544|Mup2|OTTMUSG00000007423	major urinary protein 6	protein-coding
mm_43878.1	chr5	143755742	143755747	+	1	NA	Intergenic	Intergenic	-2610	NR_015486	320064	Mm.332820	NR_015486		D130017N08Rik	1700012G11Rik	RIKEN cDNA D130017N08 gene	ncRNA
mm_11722.1	chr2	36251741	36251751	+	1	NA	3' UTR (NM_008969, exon 11 of 11)	3' UTR (NM_008969, exon 11 of 11)	21320	NM_008969	19224	Mm.275434	NM_008969	ENSMUSG00000047250	Ptgs1	COX1|Cox-1|Cox-3|PGHS-1|PHS 1|Pghs1	prostaglandin-endoperoxide synthase 1	protein-coding
mm_137014.1	chr17	17831299	17831316	+	1	NA	TTS (NR_029539)	TTS (NR_029539)	332	NM_001162909	75202	Mm.227456	NM_029205	ENSMUSG00000080316	Spaca6	4930546H06Rik|9530079D04Rik|B230206P06Rik|Ncrna00085|SPACA6A|let-7e|mir-125a|mir-99b	sperm acrosome associated 6	protein-coding
mm_998.1	chr1	58713379	58713381	+	1	NA	promoter-TSS (NM_207653)	promoter-TSS (NM_207653)	94	NM_207653	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_86226.1	chr9	120135831	120135851	-	1	NA	Intergenic	Intergenic	5407	NR_002902	104433	Mm.453530	NR_002902	ENSMUSG00000064925	Snora62	E2|MBI-13|MBI-136|Rnu108	small nucleolar RNA, H/ACA box 62	snoRNA
mm_22365.1	chr2	181043592	181043604	-	1	NA	Intergenic	Intergenic	-4421	NM_015730	11438	Mm.252369	NM_015730	ENSMUSG00000027577	Chrna4	Acra-4|Acra4|EBN1|ENFL1	cholinergic receptor, nicotinic, alpha polypeptide 4	protein-coding
mm_101909.1	chr11	49671256	49671256	-	1	NA	TTS (NM_001290741)	TTS (NM_001290741)	7661	NM_170727	68662	Mm.22802	NM_054037	ENSMUSG00000064057	Scgb3a1	HIN-1|LuLeu2|Pnsp2|UGRP2|Utgrp2	secretoglobin, family 3A, member 1	protein-coding
mm_155466.1	chrX	73635563	73635570	+	1	NA	Intergenic	Intergenic	-3875	NM_029352	75590	Mm.16479	NM_029352	ENSMUSG00000031383	Dusp9	Dusp4|Mpk4|Pyst3	dual specificity phosphatase 9	protein-coding
mm_143532.1	chr17	73913932	73913963	-	1	NA	exon (NM_011723, exon 17 of 36)	exon (NM_011723, exon 17 of 36)	36249	NM_011723	22436	Mm.11223	NM_011723	ENSMUSG00000024066	Xdh	XO|Xor|Xox-1|Xox1	xanthine dehydrogenase	protein-coding
mm_29970.1	chr3	133544251	133544264	-	1	NA	5' UTR (NM_001346736, exon 1 of 12)	5' UTR (NM_001346736, exon 1 of 12)	133	NM_001346736	214133	Mm.347816	NM_145989	ENSMUSG00000040943	Tet2	Ayu17-449|E130014J05Rik|mKIAA1546	tet methylcytosine dioxygenase 2	protein-coding
mm_145977.1	chr18	67935990	67935995	+	1	NA	intron (NM_172631, intron 1 of 5)	intron (NM_172631, intron 1 of 5)	2735	NM_172631	52662	Mm.440183	NM_172631	ENSMUSG00000024544	Ldlrad4	8230401C20Rik|A430083H02|A430108L08Rik|C18orf1|D18Ertd653e|D330030L18Rik	low density lipoprotein receptor class A domain containing 4	protein-coding
mm_99619.1	chr11	104632276	104632310	+	1	NA	exon (NM_016780, exon 3 of 15)	exon (NM_016780, exon 3 of 15)	24293	NM_016780	16416	Mm.87150	NM_016780	ENSMUSG00000020689	Itgb3	CD61|GP3A|INGRB3	integrin beta 3	protein-coding
mm_103349.1	chr11	74770713	74770743	-	1	NA	promoter-TSS (NM_026197)	promoter-TSS (NM_026197)	-135	NM_026197	67493	Mm.45748	NM_026197	ENSMUSG00000010554	Mettl16	2610100D03Rik|2810013M15Rik|A830095F14Rik|AI846133|Mett10d	methyltransferase like 16	protein-coding
mm_126972.1	chr15	93398428	93398438	+	1	NA	promoter-TSS (NM_026025)	promoter-TSS (NM_026025)	-31	NM_001285863	223828	Mm.74208	NM_146062	ENSMUSG00000036167	Pphln1	CR|HSPC206|HSPC232	periphilin 1	protein-coding
mm_19082.1	chr2	77946332	77946373	-	1	NA	promoter-TSS (NM_001290740)	promoter-TSS (NM_001290740)	4	NM_001290740	80744	Mm.288151	NM_030560	ENSMUSG00000027014	Cwc22	AA684037|AI173004|AL022752|B230213M24|mKIAA1604	CWC22 spliceosome-associated protein	protein-coding
mm_79707.1	chr9	61200380	61200381	+	1	NA	Intergenic	Intergenic	61865	NR_045705	619328	Mm.325722	NR_045705	ENSMUSG00000110998	I730028E13Rik	-	RIKEN cDNA I730028E13 gene	ncRNA
mm_68376.1	chr7	109083285	109083337	-	1	NA	promoter-TSS (NM_178780)	promoter-TSS (NM_178780)	13	NM_001038624	320360	Mm.71007	NM_178780	ENSMUSG00000048330	Ric3	E130307J04Rik	RIC3 acetylcholine receptor chaperone	protein-coding
mm_84873.1	chr9	79718570	79718572	-	1	NA	5' UTR (NM_001290308, exon 1 of 66)	5' UTR (NM_001290308, exon 1 of 66)	151	NM_001290308	12816	Mm.3819	NM_007730	ENSMUSG00000032332	Col12a1	-	collagen, type XII, alpha 1	protein-coding
mm_35428.1	chr4	35795201	35795204	-	1	NA	intron (NM_175516, intron 1 of 2)	intron (NM_175516, intron 1 of 2)	50002	NM_001166001	242384	Mm.132507	NM_175516	ENSMUSG00000045083	Lingo2	B230217C06Rik|Lern3|Lrrn6c	leucine rich repeat and Ig domain containing 2	protein-coding
mm_166221.1	chr5	64864767	64864788	-	1	NA	Intergenic	Intergenic	61254	NM_008453	16599	Mm.392759	NM_008453	ENSMUSG00000029178	Klf3	9930027G08Rik|AL024007|Bklf|Tef-2	Kruppel-like factor 3 (basic)	protein-coding
mm_157675.1	chrX	59166081	59166101	-	1	NA	promoter-TSS (NM_001290415)	promoter-TSS (NM_001290415)	-3	NM_001290415	14168	Mm.7995	NM_010200	ENSMUSG00000031137	Fgf13	Fhf2	fibroblast growth factor 13	protein-coding
mm_52671.1	chr6	117907103	117907153	+	1	NA	promoter-TSS (NM_001166429)	intron (NM_133834, intron 1 of 3)	346	NM_133834	98758	Mm.422979	NM_133834	ENSMUSG00000042079	Hnrnpf	4833420I20Rik|AA407306|Hnrpf	heterogeneous nuclear ribonucleoprotein F	protein-coding
mm_74688.1	chr8	14994486	14994500	-	1	NA	intron (NM_172751, intron 27 of 28)	intron (NM_172751, intron 27 of 28)	-16532	NM_029116	74901	Mm.46675	NM_029116	ENSMUSG00000055675	Kbtbd11	2900016B01Rik|4930465M17Rik|mKIAA0711	kelch repeat and BTB (POZ) domain containing 11	protein-coding
mm_50664.1	chr6	51523980	51523997	+	1	NA	promoter-TSS (NM_001127349)	promoter-TSS (NM_001127349)	85	NM_001127349	71982	Mm.294166	NM_028035	ENSMUSG00000038301	Snx10	2410004M09Rik	sorting nexin 10	protein-coding
mm_10354.1	chr2	11690061	11690091	+	1	NA	3' UTR (NM_008367, exon 8 of 8)	3' UTR (NM_008367, exon 8 of 8)	-15217	NM_001271498	16169	Mm.200196	NM_008358	ENSMUSG00000023206	Il15ra	AA690181|IL-15RA	interleukin 15 receptor, alpha chain	protein-coding
mm_138108.1	chr17	34121391	34121405	+	1	NA	intron (NM_001204973, intron 1 of 12)	CpG-6274	349	NM_010238	14312	Mm.3444	NM_010238	ENSMUSG00000024335	Brd2	AW228947|D17H6S113E|Frg-1|Fsrg-1|Fsrg1|Nat|Ring3|Rnf3|mKIAA4005	bromodomain containing 2	protein-coding
mm_154660.1	chrX	7842528	7842612	+	1	NA	exon (NM_001290536, exon 1 of 9)	exon (NM_001290536, exon 1 of 9)	488	NM_001290537	54644	Mm.142827	NM_138604	ENSMUSG00000031154	Otud5	AA407879|AI553596|BB114028|DUBA|DXImx46e|Sfc7	OTU domain containing 5	protein-coding
mm_67932.1	chr7	99980409	99980417	-	1	NA	promoter-TSS (NM_175388)	promoter-TSS (NM_175388)	45	NM_175388	108937	Mm.323087	NM_175388	ENSMUSG00000058761	Rnf169	2900057K09Rik	ring finger protein 169	protein-coding
mm_171755.1	chr5	105022511	105022515	+	1	NA	intron (NM_029509, intron 5 of 9)	L1Md_T|LINE|L1	31048	NM_029509	76074	Mm.458519	NM_029509	ENSMUSG00000034438	Gbp8	5830443L24Rik|mGBP8	guanylate-binding protein 8	protein-coding
mm_59414.1	chr7	27121623	27121635	+	1	NA	exon (NM_007817, exon 2 of 10)	exon (NM_007817, exon 2 of 10)	1674	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_27195.1	chr3	34761417	34761431	-	1	NA	Intergenic	Intergenic	-10651	NR_110488	102638436	Mm.261793	NR_110488	ENSMUSG00000106519	Gm38509	Peril	predicted gene, 38509	ncRNA
mm_150100.1	chr19	29474235	29474267	+	1	NA	Intergenic	Intergenic	47736	NR_015567	77779	Mm.458738	NR_015567	ENSMUSG00000097855	A930007I19Rik	-	RIKEN cDNA A930007I19 gene	ncRNA
mm_14558.1	chr2	134786176	134786196	+	1	NA	promoter-TSS (NM_001145830)	promoter-TSS (NM_001145830)	22	NM_001145830	18795	Mm.330607	NM_019677	ENSMUSG00000051177	Plcb1	3110043I21Rik|AI132408|Plcb|mKIAA0581	phospholipase C, beta 1	protein-coding
mm_14341.1	chr2	129593096	129593127	+	1	NA	promoter-TSS (NM_001291022)	promoter-TSS (NM_001291022)	-58	NM_001291019	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_30042.1	chr3	135696843	135696847	-	1	NA	Intergenic	Intergenic	-5298	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_153185.1	chr19	34499338	34499350	-	1	NA	intron (NM_001111100, intron 8 of 9)	intron (NM_001111100, intron 8 of 9)	-24209	NM_009890	12642	Mm.30824	NM_009890	ENSMUSG00000050370	Ch25h	AI462618|m25OH	cholesterol 25-hydroxylase	protein-coding
mm_159482.1	chr4	40473091	40473091	+	1	NA	promoter-TSS (NM_001166009)	promoter-TSS (NM_001166009)	-39	NM_001166009	320500	Mm.156365	NM_177175	ENSMUSG00000046593	Tmem215	A930001M12Rik	transmembrane protein 215	protein-coding
mm_8139.1	chr1	136260368	136260439	-	1	NA	exon (NM_001101516, exon 1 of 1)	exon (NM_001101516, exon 1 of 1)	470	NM_001101516	383563	Mm.40367	NM_001101516	ENSMUSG00000052759	Gpr25	Gm1300	G protein-coupled receptor 25	protein-coding
mm_56309.1	chr6	92026449	92026450	-	1	NA	intron (NM_172731, intron 3 of 20)	intron (NM_172731, intron 3 of 20)	47484	NM_172731	232237	Mm.295740	NM_172731	ENSMUSG00000034037	Fgd5	C330025N11Rik|ZFYVE23|mFLJ00274	FYVE, RhoGEF and PH domain containing 5	protein-coding
mm_149265.1	chr19	10577440	10577461	+	1	NA	promoter-TSS (NM_028411)	promoter-TSS (NM_028411)	-64	NR_126092	72982	Mm.391194	NM_028411	ENSMUSG00000024666	Tmem138	1700113I01Rik|2900055D14Rik	transmembrane protein 138	protein-coding
mm_141786.1	chr17	34304863	34304871	-	1	NA	promoter-TSS (NM_010382)	promoter-TSS (NM_010382)	-1000	NM_010382	14969	Mm.22564	NM_010382	ENSMUSG00000060586	H2-Eb1	Eb|H-2Eb|H2Eb|Ia-4|Ia4	histocompatibility 2, class II antigen E beta	protein-coding
mm_15149.1	chr2	153988499	153988525	+	1	NA	intron (NM_001080811, intron 5 of 10)	B4A|SINE|B4	13567	NM_001080811	545477	Mm.379973	NM_001080811	ENSMUSG00000078998	Bpifa6	EG545477|Gm5840|Splunc6	BPI fold containing family A, member 6	protein-coding
mm_161907.1	chr18	62324204	62324204	+	1	NA	promoter-TSS (NM_008313)	promoter-TSS (NM_008313)	0	NM_008313	15562	Mm.20440	NM_008313	ENSMUSG00000026322	Htr4	5-HT-4|5-HT4|5-HT<4L>|5HTR4	5 hydroxytryptamine (serotonin) receptor 4	protein-coding
mm_124483.1	chr14	121698384	121698412	-	1	NA	promoter-TSS (NM_001081039)	promoter-TSS (NM_001081039)	19	NM_001347596	105445	Mm.378591	NM_134074	ENSMUSG00000025558	Dock9	AA959601|AW538057|B230309H04Rik|D14Wsu89e|Zizimin1|mKIAA1058	dedicator of cytokinesis 9	protein-coding
mm_31555.1	chr4	56802571	56802613	+	1	NA	promoter-TSS (NM_026079)	promoter-TSS (NM_026079)	-261	NM_026079	230233	Mm.282743	NM_026079	ENSMUSG00000028431	Ikbkap	3110040G09Rik|6030413P05|C78473|Elp1|IKAP	inhibitor of kappa light polypeptide enhancer in B cells, kinase complex-associated protein	protein-coding
mm_53479.1	chr6	134939429	134939433	+	1	NA	intron (NR_037956, intron 1 of 1)	intron (NR_037956, intron 1 of 1)	10339	NR_037955	381822	Mm.5935	NR_037955	ENSMUSG00000098318	Lockd	1190002F15Rik|AI120476|Droc	lncRNA downstream of Cdkn1b	ncRNA
mm_59545.1	chr7	27899027	27899033	+	1	NA	Intergenic	RMER4B|LTR|ERVK	30400	NM_028538	73430	Mm.379224	NM_028538	ENSMUSG00000070709	Zfp974	1700049G17Rik|AV321011|BB026409	zinc finger protein 974	protein-coding
mm_51097.1	chr6	67271194	67271230	+	1	NA	exon (NM_025814, exon 2 of 8)	exon (NM_025814, exon 2 of 8)	4233	NM_025814	66870	Mm.240490	NM_025814	ENSMUSG00000036371	Serbp1	1200009K13Rik|9330147J08Rik|AL022786|Pairbp1	serpine1 mRNA binding protein 1	protein-coding
mm_151144.1	chr19	53128699	53128708	+	1	NA	Intergenic	Intergenic	-11740	NM_001164099	27360	Mm.426080	NM_013758	ENSMUSG00000025026	Add3	AI463285|R75380	adducin 3 (gamma)	protein-coding
mm_97429.1	chr11	78094668	78094678	+	1	NA	promoter-TSS (NM_145430)	promoter-TSS (NM_145430)	0	NM_145430	216971	Mm.119387	NM_145430	ENSMUSG00000037750	Fam222b	9630020I17Rik	family with sequence similarity 222, member B	protein-coding
mm_139451.1	chr17	55750018	55750028	+	1	NA	promoter-TSS (NM_139138)	promoter-TSS (NM_139138)	39	NM_139138	52614	Mm.210497	NM_139138	ENSMUSG00000032915	Adgre4	D17Ertd479e|Egf-tm7|Emr4|Fire|Gpr127	adhesion G protein-coupled receptor E4	protein-coding
mm_139966.1	chr17	71673256	71673271	+	1	NA	promoter-TSS (NM_177087)	promoter-TSS (NM_177087)	2	NM_177087	320159	Mm.187372	NM_177087	ENSMUSG00000045761	Fam179a	4632412N22Rik	family with sequence similarity 179, member A	protein-coding
mm_7673.1	chr1	128588888	128588900	-	1	NA	exon (NM_009911, exon 2 of 2)	exon (NM_009911, exon 2 of 2)	3405	NM_009911	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding
mm_119101.1	chr14	30898749	30898757	+	1	NA	intron (NM_001159299, intron 19 of 22)	intron (NM_001159299, intron 19 of 22)	12277	NM_001289632	16427	Mm.34819	NM_018746	ENSMUSG00000021922	Itih4	ITI-HC4|Itih-4|PK-120	inter alpha-trypsin inhibitor, heavy chain 4	protein-coding
mm_62406.1	chr7	101164196	101164200	+	1	NA	intron (NM_199012, intron 3 of 20)	ORR1C2|LTR|ERVL-MaLR	55423	NM_199012	207278	Mm.263041	NM_199012	ENSMUSG00000030691	Fchsd2	BC034086|R74866|Sh3md3|mKIAA0769	FCH and double SH3 domains 2	protein-coding
mm_34285.1	chr4	141444658	141444714	+	1	NA	promoter-TSS (NM_009541)	promoter-TSS (NM_009541)	13	NM_009541	22642	Mm.389590	NM_009541	ENSMUSG00000006215	Zbtb17	AA589413|Lp-1|Miz1|Zfp100|mZ13	zinc finger and BTB domain containing 17	protein-coding
mm_122250.1	chr14	34015176	34015187	-	1	NA	Intergenic	Intergenic	-25897	NM_001034880	432838	Mm.318383	NM_001034880	ENSMUSG00000072624	Gm5460	EG432838	predicted gene 5460	protein-coding
mm_2847.1	chr1	131661869	131661879	+	1	NA	intron (NM_007799, intron 1 of 9)	intron (NM_007799, intron 1 of 9)	23560	NM_007799	13034	Mm.230249	NM_007799	ENSMUSG00000004552	Ctse	A430072O03Rik|C920004C08Rik|CE|CatE	cathepsin E	protein-coding
mm_130820.1	chr15	101818166	101818170	-	1	NA	promoter-TSS (NM_010668)	promoter-TSS (NM_010668)	1	NM_010668	16681	Mm.358616	NM_010668	ENSMUSG00000064201	Krt2	BB005427|Krt2-17|Krt2-2|Krt2e	keratin 2	protein-coding
mm_135291.1	chr16	38528050	38528050	-	1	NA	intron (NM_001300827, intron 9 of 10)	intron (NM_001300827, intron 9 of 10)	-5387	NM_024273	76916	Mm.132231	NM_024273	ENSMUSG00000002846	Timmdc1	2810021C21Rik|4930455C21Rik|AV135763	translocase of inner mitochondrial membrane domain containing 1	protein-coding
mm_54415.1	chr6	32656981	32656985	-	1	NA	Intergenic	ID_B1|SINE|B4	-68791	NM_175750	243743	Mm.444029	NM_175750	ENSMUSG00000029765	Plxna4	9330117B14|Plxa4|mKIAA1550	plexin A4	protein-coding
mm_37246.1	chr4	118179955	118180035	-	1	NA	promoter-TSS (NM_001161823)	promoter-TSS (NM_001161823)	48	NM_172382	230674	Mm.234234	NM_172382	ENSMUSG00000033326	Kdm4a	D4Ertd222e|JHDM3A|Jmjd2|Jmjd2a|mKIAA0677	lysine (K)-specific demethylase 4A	protein-coding
mm_69507.1	chr7	134364860	134364881	-	1	NA	promoter-TSS (NM_001199941)	promoter-TSS (NM_001199941)	14	NM_001199941	71007	Mm.334285	NM_001081331	ENSMUSG00000030994	D7Ertd443e	4933400E14Rik|FATS|Gm497	DNA segment, Chr 7, ERATO Doi 443, expressed	protein-coding
mm_60868.1	chr7	45923535	45923556	+	1	NA	Intergenic	Intergenic	-2119	NM_010129	13732	Mm.20829	NM_010129	ENSMUSG00000040212	Emp3	H-4|H4|HNMP-1|MI-35|Ymp	epithelial membrane protein 3	protein-coding
mm_33372.1	chr4	129515341	129515350	+	1	NA	TTS (NM_008228)	TTS (NM_008228)	1764	NM_010807	17357	Mm.424974	NM_010807	ENSMUSG00000047945	Marcksl1	AL022768|AW215397|AW536807|D4Bc1|F52|MacMARCKS|Macs2|Macs3|Mlp|Mrp	MARCKS-like 1	protein-coding
mm_49165.1	chr6	14512589	14512601	+	1	NA	Intergenic	RMER17A2|LTR|ERVK	242679	NM_080464	140491	Mm.209429	NM_080464	ENSMUSG00000042717	Ppp1r3a	GM|RG1|RGL	protein phosphatase 1, regulatory (inhibitor) subunit 3A	protein-coding
mm_114276.1	chr13	58263941	58263969	+	1	NA	exon (NM_019832, exon 2 of 12)	exon (NM_019832, exon 2 of 12)	10233	NM_019832	56278	Mm.296625	NM_019832	ENSMUSG00000021552	Gkap1	42kDa|4933400B15Rik|D13Ertd340e|Gkap42	G kinase anchoring protein 1	protein-coding
mm_48711.1	chr5	147305450	147305459	-	1	NA	intron (NM_007673, intron 1 of 2)	intron (NM_007673, intron 1 of 2)	1795	NM_007673	12591	Mm.20358	NM_007673	ENSMUSG00000029646	Cdx2	Cdx-2	caudal type homeobox 2	protein-coding
mm_49972.1	chr6	40778684	40778733	+	1	NA	intron (NR_035473, intron 2 of 3)	intron (NR_035473, intron 2 of 3)	108786	NM_139296	194357	Mm.207087	NM_139296	ENSMUSG00000029885	Moxd2	Dbhl1	monooxygenase, DBH-like 2	protein-coding
mm_23398.1	chr3	57833853	57833882	+	1	NA	TTS (NM_011883)	TTS (NM_011883)	13890	NM_019410	18645	Mm.271744	NM_019410	ENSMUSG00000027805	Pfn2	Pfn	profilin 2	protein-coding
mm_107497.1	chr12	38784368	38784411	+	1	NA	intron (NM_001163154, intron 1 of 9)	intron (NM_001163154, intron 1 of 9)	678	NM_001163154	14009	Mm.4866	NM_007960	ENSMUSG00000004151	Etv1	ER81|Etsrp81	ets variant 1	protein-coding
mm_150275.1	chr19	34246171	34246212	+	1	NA	exon (NM_007392, exon 6 of 9)	exon (NM_007392, exon 6 of 9)	9182	NM_007392	11475	Mm.213025	NM_007392	ENSMUSG00000035783	Acta2	0610041G09Rik|Actvs|SMalphaA|a-SMA|alphaSMA	actin, alpha 2, smooth muscle, aorta	protein-coding
mm_23771.1	chr3	75557577	75557587	+	1	NA	promoter-TSS (NM_009250)	promoter-TSS (NM_009250)	49	NM_009250	20713	Mm.41560	NM_009250	ENSMUSG00000027834	Serpini1	AI837402|Ns|PI-12|PI12|Spi17	serine (or cysteine) peptidase inhibitor, clade I, member 1	protein-coding
mm_112056.1	chr12	111875656	111875659	-	1	NA	intron (NM_011625, intron 1 of 16)	intron (NM_011625, intron 1 of 16)	32398	NM_011625	21981	Mm.313076	NM_011625	ENSMUSG00000021285	Ppp1r13b	AI449786|ASPP1|AW545810|Tp53bp2|Trp53bp2|p85	protein phosphatase 1, regulatory (inhibitor) subunit 13B	protein-coding
mm_98257.1	chr11	88728062	88728076	+	1	NA	intron (NR_038058, intron 3 of 3)	intron (NR_038058, intron 3 of 3)	9426	NR_038058	193280	Mm.396842	NR_038058		C030037D09Rik	9330160M04	RIKEN cDNA C030037D09 gene	ncRNA
mm_79839.1	chr9	64806211	64806214	+	1	NA	Intergenic	Intergenic	-4799	NM_001162917	102442	Mm.222473	NM_176935	ENSMUSG00000053641	Dennd4a	AI115600|AI851943|F730015K02Rik	DENN/MADD domain containing 4A	protein-coding
mm_106643.1	chr11	121039382	121039392	-	1	NA	promoter-TSS (NM_009854)	promoter-TSS (NM_009854)	91	NM_009854	12516	Mm.4100	NM_009854	ENSMUSG00000025163	Cd7	-	CD7 antigen	protein-coding
mm_111726.1	chr12	103765809	103765836	-	1	NA	exon (NM_009246, exon 3 of 5)	exon (NM_009246, exon 3 of 5)	7811	NM_009246	20703	Mm.439695	NM_009246	ENSMUSG00000071177	Serpina1d	AI118301|Dom4|PI4|Spi1-4	serine (or cysteine) peptidase inhibitor, clade A, member 1D	protein-coding
mm_2576.1	chr1	118481967	118481979	+	1	NA	intron (NM_001293300, intron 8 of 40)	intron (NM_001293300, intron 8 of 40)	-22708	NR_027901	68204	Mm.443536	NR_027901	ENSMUSG00000107722	2900060B14Rik	-	RIKEN cDNA 2900060B14 gene	ncRNA
mm_119200.1	chr14	32786005	32786023	+	1	NA	promoter-TSS (NM_001163616)	promoter-TSS (NM_001163616)	51	NM_001163616	69069	Mm.261609	NM_001163616	ENSMUSG00000041707	1810011H11Rik	4733401I05Rik	RIKEN cDNA 1810011H11 gene	protein-coding
mm_22774.1	chr3	20275421	20275436	+	1	NA	exon (NM_029706, exon 2 of 11)	exon (NM_029706, exon 2 of 11)	305	NM_029706	76703	Mm.34692	NM_029706	ENSMUSG00000011463	Cpb1	0910001A18Rik|1810063F02Rik|2210008M23Rik|AI504870	carboxypeptidase B1 (tissue)	protein-coding
mm_144631.1	chr18	32939299	32939397	+	1	NA	5' UTR (NM_009793, exon 1 of 11)	5' UTR (NM_009793, exon 1 of 11)	307	NM_009793	12326	Mm.222329	NM_009793	ENSMUSG00000038128	Camk4	A430110E23Rik|AI666733|CaMKIV|CaMKIV/Gr|D18Bwg0362e	calcium/calmodulin-dependent protein kinase IV	protein-coding
mm_3315.1	chr1	137906784	137906792	+	1	NA	Intergenic	Intergenic	-59667	NR_029795	735252		NR_029795	ENSMUSG00000065565	Mir181a-1	Mirn181a-1|Mirn213|miR-213|mir-181a-1|mmu-mir-213	microRNA 181a-1	ncRNA
mm_61023.1	chr7	49507301	49507330	+	1	NA	intron (NM_175272, intron 11 of 37)	intron (NM_175272, intron 11 of 37)	129520	NM_001005232	13172	Mm.307176	NM_001005232	ENSMUSG00000030507	Dbx1	AI426026|Dbx	developing brain homeobox 1	protein-coding
mm_69419.1	chr7	132720645	132720664	-	1	NA	intron (NM_001347630, intron 3 of 3)	intron (NM_001347630, intron 3 of 3)	56262	NM_001347630	77938	Mm.225649	NM_175268	ENSMUSG00000030956	Fam53b	A930008G19Rik|mKIAA0140	family with sequence similarity 53, member B	protein-coding
mm_39072.1	chr4	154160636	154160696	-	1	NA	promoter-TSS (NM_026388)	promoter-TSS (NM_026388)	18	NM_026388	67808	Mm.288737	NM_026388	ENSMUSG00000029030	Tprgl	1200015A19Rik|Svap30|Tprg1l|mover	transformation related protein 63 regulated like	protein-coding
mm_19503.1	chr2	93520719	93520723	-	1	NA	Intergenic	Intergenic	-57771	NM_001136055	12521	Mm.4261	NM_007656	ENSMUSG00000027215	Cd82	AA682076|AL023070|C33|IA4|Kai1|Tspan27	CD82 antigen	protein-coding
mm_10070.1	chr1	194620865	194620881	-	1	NA	intron (NM_008882, intron 1 of 31)	CpG	1044	NM_008882	18845	Mm.2251	NM_008882	ENSMUSG00000026640	Plxna2	2810428A13Rik|AA589422|AW457381|OCT|PlexA2|Plxn2|mKIAA0463	plexin A2	protein-coding
mm_113834.1	chr13	47106414	47106430	+	1	NA	promoter-TSS (NM_025900)	promoter-TSS (NM_025900)	-201	NM_025900	110052	Mm.131150	NM_025900	ENSMUSG00000021377	Dek	1810019E15Rik|D13H6S231E	DEK oncogene (DNA binding)	protein-coding
mm_101048.1	chr11	8624901	8624918	-	1	NA	intron (NM_001083587, intron 1 of 30)	intron (NM_001083587, intron 1 of 30)	39626	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_68970.1	chr7	126584799	126584817	-	1	NA	promoter-TSS (NM_138310)	promoter-TSS (NM_138310)	-200	NM_138310	171504	Mm.170665	NM_138310	ENSMUSG00000042759	Apobr	Apob-48r|Apob48r	apolipoprotein B receptor	protein-coding
mm_120803.1	chr14	74922106	74922115	+	1	NA	intron (NM_001252132, intron 1 of 18)	intron (NM_001252132, intron 1 of 18)	25767	NM_001252132	380916	Mm.288868	NM_001033439	ENSMUSG00000068015	Lrch1	4832412D13Rik|AI552548|AW215503|Chdc1|mKIAA1016	leucine-rich repeats and calponin homology (CH) domain containing 1	protein-coding
mm_133326.1	chr16	78301776	78301804	+	1	NA	5' UTR (NM_009988, exon 1 of 8)	5' UTR (NM_009988, exon 1 of 8)	119	NM_001276263	13052	Mm.66222	NM_009988	ENSMUSG00000022865	Cxadr	2610206D03Rik|AU016810|AW553441|CAR|MCAR|MCVADR	coxsackie virus and adenovirus receptor	protein-coding
mm_8362.1	chr1	150456229	150456252	-	1	NA	exon (NM_021400, exon 7 of 13)	exon (NM_021400, exon 7 of 13)	9925	NM_021400	96875	Mm.174256	NM_021400	ENSMUSG00000006014	Prg4	CACP|DOL54|JCAP|MSF|SZP|lubricin	proteoglycan 4 (megakaryocyte stimulating factor, articular superficial zone protein)	protein-coding
mm_115667.1	chr13	12475497	12475546	-	1	NA	3' UTR (NM_133643, exon 6 of 6)	3' UTR (NM_133643, exon 6 of 6)	-13783	NM_001291057	56048	Mm.474138	NM_018886	ENSMUSG00000057554	Lgals8	1200015E08Rik|AI326142|D13Ertd524e|Lgals-8	lectin, galactose binding, soluble 8	protein-coding
mm_115150.1	chr13	105308061	105308086	+	1	NA	Intergenic	LTR82B|LTR|ERVL	-15059	NM_027934	71816	Mm.317015	NM_027934	ENSMUSG00000021720	Rnf180	3110001E11Rik|Rines	ring finger protein 180	protein-coding
mm_8482.1	chr1	153549698	153549724	-	1	NA	promoter-TSS (NM_028749)	promoter-TSS (NM_028749)	3	NM_028749	74091	Mm.24887	NM_028749	ENSMUSG00000042684	Npl	0610033B02Rik	N-acetylneuraminate pyruvate lyase	protein-coding
mm_107624.1	chr12	51593366	51593381	+	1	NA	promoter-TSS (NM_001198835)	promoter-TSS (NM_001198835)	32	NM_001198835	12810	Mm.21325	NM_007728	ENSMUSG00000020953	Coch	AW122937|Coch-5B2|D12H14S564E	cochlin	protein-coding
mm_58420.1	chr7	3293028	3293061	+	1	NA	promoter-TSS (NM_001093766)	promoter-TSS (NM_001093766)	16	NM_001093766	50918	Mm.29874	NM_016969	ENSMUSG00000068566	Myadm	D7Wsu62e	myeloid-associated differentiation marker	protein-coding
mm_137076.1	chr17	21008922	21009013	+	1	NA	promoter-TSS (NM_145483)	promoter-TSS (NM_145483)	26	NM_145483	224585	Mm.296036	NM_145483	ENSMUSG00000067942	Zfp160	6720480D16Rik|F11|HKr18|HZF5|KR18|mKIAA1611|mszf47	zinc finger protein 160	protein-coding
mm_55892.1	chr6	83536400	83536434	-	1	NA	promoter-TSS (NM_009610)	promoter-TSS (NM_009610)	-166	NM_009610	11468	Mm.292865	NM_009610	ENSMUSG00000059430	Actg2	ACTA3|Act-4|Act4|SMGA	actin, gamma 2, smooth muscle, enteric	protein-coding
mm_31300.1	chr4	45998990	45998998	+	1	NA	intron (NM_146142, intron 6 of 16)	MIRb|SINE|MIR	26697	NM_146142	100121	Mm.275413	NM_146142	ENSMUSG00000035517	Tdrd7	5730495N10Rik|AI447470|PCTAIRE2BP	tudor domain containing 7	protein-coding
mm_129433.1	chr15	78495038	78495048	-	1	NA	promoter-TSS (NM_008368)	promoter-TSS (NM_008368)	23	NM_008368	16185	Mm.35287	NM_008368	ENSMUSG00000068227	Il2rb	CD122|IL-15Rbeta|IL15Rbeta|Il-2/15Rbeta|Il-2Rbeta|p70	interleukin 2 receptor, beta chain	protein-coding
mm_149814.1	chr19	23893590	23893609	+	1	NA	exon (NM_177034, exon 2 of 13)	exon (NM_177034, exon 2 of 13)	134723	NM_177034	319924	Mm.22879	NM_177034	ENSMUSG00000024897	Apba1	6430513E09Rik|Lin-10|Mint|Mint1|Urop11|X11|X11alpha	amyloid beta (A4) precursor protein binding, family A, member 1	protein-coding
mm_162598.1	chr1	183147503	183147514	-	1	NA	promoter-TSS (NM_001278220)	promoter-TSS (NM_001278220)	49	NM_001278220	68897	Mm.327216	NM_026866	ENSMUSG00000030768	Disp1	1190008H24Rik|DispA	dispatched RND transporter family member 1	protein-coding
mm_130128.1	chr15	90224110	90224159	-	1	NA	promoter-TSS (NM_001033441)	promoter-TSS (NM_001033441)	-177	NM_001033441	380959	Mm.17853	NM_001033441	ENSMUSG00000075470	Alg10b	AA469671|AU045404|AW123895|C85569|Deaf1|Gm917|nse5	asparagine-linked glycosylation 10B (alpha-1,2-glucosyltransferase)	protein-coding
mm_118932.1	chr14	27114848	27114894	+	1	NA	Intergenic	CpG	-29122	NM_001289686	71704	Mm.248606	NM_027871	ENSMUSG00000021895	Arhgef3	1200004I24Rik|9830169H03Rik|C76747|Xpln	Rho guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_80269.1	chr9	72959012	72959021	+	1	NA	intron (NM_026314, intron 1 of 8)	CpG	231	NM_001163725	67685	Mm.31817	NM_026314	ENSMUSG00000089865	Dyx1c1	1700010I24Rik|Dnaaf4|EKN1|b2b811.1Clo|b2b811Clo	dyslexia susceptibility 1 candidate 1	protein-coding
mm_66897.1	chr7	59930801	59930811	-	1	NA	Intergenic	Intergenic	43625	NR_015456	52480	Mm.482346	NR_015456	ENSMUSG00000100826	Snhg14	AU018661|D7Ertd715e|Lncat	small nucleolar RNA host gene 14	ncRNA
mm_46178.1	chr5	97095807	97095822	-	1	NA	intron (NM_198422, intron 6 of 6)	intron (NM_198422, intron 6 of 6)	15782	NM_198422	231474	Mm.332505	NM_198422	ENSMUSG00000055725	Paqr3	6330415A20Rik|AY424292|RKTG	progestin and adipoQ receptor family member III	protein-coding
mm_105494.1	chr11	106159461	106159467	-	1	NA	intron (NM_172397, intron 1 of 4)	intron (NM_172397, intron 1 of 4)	678	NM_172397	67803	Mm.21687	NM_172397	ENSMUSG00000040699	Limd2	0610025L06Rik|AI413966	LIM domain containing 2	protein-coding
mm_9750.1	chr1	180734431	180734441	-	1	NA	exon (NM_133225, exon 3 of 8)	exon (NM_133225, exon 3 of 8)	8393	NM_133225	170760	Mm.272981	NM_133225	ENSMUSG00000026499	Acbd3	60kDa|8430407O11Rik|D1Ertd10e|GCP60|GOLPH1|Gocap1|Pap7	acyl-Coenzyme A binding domain containing 3	protein-coding
mm_82441.1	chr9	15284644	15284658	-	1	NA	3' UTR (NM_001199485, exon 9 of 9)	3' UTR (NM_001199485, exon 9 of 9)	-4784	NM_144933	234959	Mm.44151	NM_144933	ENSMUSG00000031935	Med17	77kDa|C330002H14Rik|Crsp6|Trap80	mediator complex subunit 17	protein-coding
mm_142502.1	chr17	46032142	46032152	-	1	NA	5' UTR (NM_001025250, exon 1 of 8)	5' UTR (NM_001025250, exon 1 of 8)	230	NM_001287058	22339	Mm.282184	NM_009505	ENSMUSG00000023951	Vegfa	Vegf|Vpf	vascular endothelial growth factor A	protein-coding
mm_63215.1	chr7	126272590	126272609	+	1	NA	promoter-TSS (NM_145587)	promoter-TSS (NM_145587)	-20	NM_145587	104175	Mm.29660	NM_145587	ENSMUSG00000042978	Sbk1	Sbk	SH3-binding kinase 1	protein-coding
mm_60107.1	chr7	35448764	35448802	+	1	NA	promoter-TSS (NM_001199016)	promoter-TSS (NM_001199016)	-309	NM_001199015	30962	Mm.45874	NM_021291	ENSMUSG00000030492	Slc7a9	CSNU3	solute carrier family 7 (cationic amino acid transporter, y+ system), member 9	protein-coding
mm_31909.1	chr4	84884367	84884407	+	1	NA	promoter-TSS (NM_177385)	promoter-TSS (NM_177385)	78	NM_177385	338349	Mm.440562	NM_175275	ENSMUSG00000038070	Cntln	AI448092|B430108F07Rik|D530005L17Rik	centlein, centrosomal protein	protein-coding
mm_36272.1	chr4	63729358	63729368	-	1	NA	3' UTR (NM_177371, exon 4 of 4)	3' UTR (NM_177371, exon 4 of 4)	15750	NM_177371	326623	Mm.208152	NM_177371	ENSMUSG00000050395	Tnfsf15	Tl1|Tl1a|Tnlg1b|Vegi	tumor necrosis factor (ligand) superfamily, member 15	protein-coding
mm_107416.1	chr12	34984749	34984758	+	1	NA	promoter-TSS (NM_029294)	promoter-TSS (NM_029294)	-8	NM_029294	75456	Mm.79179	NM_029294	ENSMUSG00000092305	Prps1l1	1700011K15Rik	phosphoribosyl pyrophosphate synthetase 1-like 1	protein-coding
mm_147769.1	chr18	61398981	61399031	-	1	NA	intron (NM_133249, intron 1 of 11)	CpG	1425	NM_133249	170826	Mm.415302	NM_133249	ENSMUSG00000033871	Ppargc1b	4631412G21Rik|Perc	peroxisome proliferative activated receptor, gamma, coactivator 1 beta	protein-coding
mm_6665.1	chr1	80289739	80289757	-	1	NA	intron (NM_001313728, intron 5 of 16)	AT_rich|Low_complexity|Low_complexity	50942	NM_001313728	26554	Mm.12665	NM_016716	ENSMUSG00000004364	Cul3	KIAA0617	cullin 3	protein-coding
mm_119232.1	chr14	33317311	33317321	+	1	NA	intron (NM_153800, intron 4 of 10)	(TCCA)n|Simple_repeat|Simple_repeat	93708	NM_001310452	26419	Mm.21495	NM_016700	ENSMUSG00000021936	Mapk8	AI849689|JNK|JNK1|Prkm8|SAPK1	mitogen-activated protein kinase 8	protein-coding
mm_81379.1	chr9	108914623	108914635	+	1	NA	promoter-TSS (NM_027066)	promoter-TSS (NM_027066)	10	NM_027066	69384	Mm.158271	NM_027066	ENSMUSG00000025652	Tmem89	1700024B07Rik	transmembrane protein 89	protein-coding
mm_173268.1	chrX	95956874	95956875	-	1	NA	promoter-TSS (NM_152822)	promoter-TSS (NM_152822)	100	NM_152822	76130	Mm.274318	NM_152822	ENSMUSG00000057421	Las1l	1810030A06Rik|5830482G23Rik	LAS1-like (S. cerevisiae)	protein-coding
mm_170860.1	chr2	180725320	180725321	+	1	NA	promoter-TSS (NM_183161)	promoter-TSS (NM_183161)	-19	NM_183161	228993	Mm.87189	NM_183161	ENSMUSG00000023393	Slc17a9	1700019H03Rik|BC019537|Vnut	solute carrier family 17, member 9	protein-coding
mm_116047.1	chr13	27249500	27249504	-	1	NA	exon (NM_008865, exon 5 of 5)	exon (NM_008865, exon 5 of 5)	7072	NM_008865	18776	Mm.37203	NM_008865	ENSMUSG00000038891	Prl3b1	Csh2|Ghd8|PL|Pl-2|Pl2|mPL-II|mplII	prolactin family 3, subfamily b, member 1	protein-coding
mm_23251.1	chr3	51224913	51224941	+	1	NA	5' UTR (NM_009834, exon 1 of 3)	5' UTR (NM_009834, exon 1 of 3)	480	NM_009834	12457	Mm.86541	NM_009834	ENSMUSG00000023087	Noct	AU043840|Ccr4|Ccrn4l	nocturnin	protein-coding
mm_105495.1	chr11	106159777	106159788	-	1	NA	intron (NM_172397, intron 1 of 4)	intron (NM_172397, intron 1 of 4)	360	NM_172397	67803	Mm.21687	NM_172397	ENSMUSG00000040699	Limd2	0610025L06Rik|AI413966	LIM domain containing 2	protein-coding
mm_104972.1	chr11	100207320	100207354	-	1	NA	exon (NM_016958, exon 1 of 8)	exon (NM_016958, exon 1 of 8)	173	NM_016958	16664	Mm.439898	NM_016958	ENSMUSG00000045545	Krt14	AI626930|CK-14|K14|Krt-1.14|Krt1-14	keratin 14	protein-coding
mm_156041.1	chrX	108056225	108056229	+	1	NA	Intergenic	LTRIS3|LTR|ERV1	-107791	NM_001033252	213450	Mm.300779	NM_001033252	ENSMUSG00000073006	Gm732	-	predicted gene 732	protein-coding
mm_33845.1	chr4	135856088	135856124	+	1	NA	promoter-TSS (NM_001284196)	promoter-TSS (NM_001284196)	35	NM_010178	14105	Mm.10229	NM_010178	ENSMUSG00000028676	Srsf10	FUSIP2|Fusip1|NSSR1|NSSR2|Nssr|SRrp40|Sfrs13a|Srsf13a|TASR|TASR1|TASR2	serine/arginine-rich splicing factor 10	protein-coding
mm_151507.1	chr19	58732063	58732094	+	1	NA	exon (NM_018874, exon 5 of 13)	exon (NM_018874, exon 5 of 13)	3191	NM_018874	18946	Mm.10753	NM_018874	ENSMUSG00000042179	Pnliprp1	Plrp1	pancreatic lipase related protein 1	protein-coding
mm_116296.1	chr13	36117485	36117587	-	1	NA	promoter-TSS (NM_024274)	promoter-TSS (NM_024274)	-107	NM_024274	69955	Mm.70690	NM_024274	ENSMUSG00000021420	Fars2	Fars1|pheRS	phenylalanine-tRNA synthetase 2 (mitochondrial)	protein-coding
mm_77114.1	chr8	111082019	111082021	-	1	NA	promoter-TSS (NM_181549)	promoter-TSS (NM_181549)	-312	NM_181549	353287	Mm.135495	NM_181549	ENSMUSG00000033633	Clec18a	Mrcl	C-type lectin domain family 18, member A	protein-coding
mm_101801.1	chr11	46266026	46266036	-	1	NA	intron (NM_133769, intron 12 of 30)	intron (NM_133769, intron 12 of 30)	30474	NM_177075	320116	Mm.39600	NM_177075	ENSMUSG00000048721	Fndc9	C030019I05Rik	fibronectin type III domain containing 9	protein-coding
mm_69699.1	chr7	140049084	140049089	-	1	NA	promoter-TSS (NM_010836)	promoter-TSS (NM_010836)	2	NM_010836	17703	Mm.4816	NM_010836	ENSMUSG00000025469	Msx3	AI323377	msh homeobox 3	protein-coding
mm_23074.1	chr3	36453883	36453941	+	1	NA	intron (NM_009673, intron 8 of 12)	intron (NM_009673, intron 8 of 12)	21612	NR_105976	102466786		NR_105976	ENSMUSG00000098808	Mir7009	Gm27472|mmu-mir-7009	microRNA 7009	ncRNA
mm_47974.1	chr5	135910619	135910655	-	1	NA	3' UTR (NM_018871, exon 2 of 2)	3' UTR (NM_018871, exon 2 of 2)	22718	NM_013560	15507	Mm.13849	NM_013560	ENSMUSG00000004951	Hspb1	27kDa|Hsp25	heat shock protein 1	protein-coding
mm_35291.1	chr4	21848365	21848374	-	1	NA	promoter-TSS (NR_028384)	promoter-TSS (NR_028384)	79	NR_028384	67735	Mm.391650	NR_028384		4930528A17Rik	-	RIKEN cDNA 4930528A17 gene	ncRNA
mm_92646.1	chr10	80387643	80387666	-	1	NA	promoter-TSS (NM_198615)	promoter-TSS (NM_198615)	-3	NM_198615	237400	Mm.268389	NM_198615	ENSMUSG00000048696	Mex3d	BC059858|Rkhd1	mex3 RNA binding family member D	protein-coding
mm_25868.1	chr3	129901432	129901466	+	1	NA	promoter-TSS (NM_009811)	promoter-TSS (NM_009811)	34	NM_009811	12368	Mm.281379	NM_009811	ENSMUSG00000027997	Casp6	CASP-6|Mch2	caspase 6	protein-coding
mm_8624.1	chr1	156270738	156270746	-	1	NA	intron (NM_001134741, intron 12 of 17)	intron (NM_001134741, intron 12 of 17)	32606	NM_001134741	214575	Mm.252800	NM_001134741	ENSMUSG00000060985	Tdrd5	Gm103	tudor domain containing 5	protein-coding
mm_4360.1	chr1	171919434	171919441	+	1	NA	intron (NM_001347187, intron 1 of 7)	intron (NM_001347187, intron 1 of 7)	1900	NM_030710	30925	Mm.486404	NM_030710	ENSMUSG00000015314	Slamf6	KAL1|KAL1b|Ly108|NTB-A|NTBA|SF2000	SLAM family member 6	protein-coding
mm_152646.1	chr19	12531931	12531980	-	1	NA	Intergenic	Intergenic	-29959	NM_172442	207521	Mm.247695	NM_172442	ENSMUSG00000039982	Dtx4	AI449438|BC044798|D930042H13|RNF155	deltex 4, E3 ubiquitin ligase	protein-coding
mm_2536.1	chr1	107399483	107399488	+	1	NA	Intergenic	Intergenic	-23204	NM_027548	116872	Mm.66015	NM_027548	ENSMUSG00000067001	Serpinb7	4631416M05Rik|megsin|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 7	protein-coding
mm_50891.1	chr6	56832100	56832160	+	1	NA	promoter-TSS (NM_012056)	promoter-TSS (NM_012056)	71	NM_012056	27055	Mm.20943	NM_012056	ENSMUSG00000029781	Fkbp9	1810014L23|AW549641|FKBP-63|FKBP-9|FKBP60|FKBP63|FKBP65RS	FK506 binding protein 9	protein-coding
mm_156037.1	chrX	107667957	107667985	+	1	NA	promoter-TSS (NM_181319)	promoter-TSS (NM_181319)	7	NM_181319	245572	Mm.137011	NM_145224	ENSMUSG00000031241	Tbx22	D230020M15Rik	T-box 22	protein-coding
mm_23356.1	chr3	55116175	55116195	+	1	NA	intron (NM_001144987, intron 1 of 8)	intron (NM_001144987, intron 1 of 8)	4019	NM_001144987	229285	Mm.235523	NM_144895	ENSMUSG00000036580	Spg20	AI840044|C79168|SPARTIN|TAHCCP1|mKIAA0610	spastic paraplegia 20, spartin (Troyer syndrome) homolog (human)	protein-coding
mm_2835.1	chr1	131527859	131527871	+	1	NA	promoter-TSS (NM_001081011)	promoter-TSS (NM_001081011)	-38	NM_175382	108900	Mm.31278	NM_175382	ENSMUSG00000055184	Fam72a	2700049P18Rik|P17	family with sequence similarity 72, member A	protein-coding
mm_49749.1	chr6	34746273	34746291	+	1	NA	intron (NM_001347100, intron 5 of 13)	intron (NM_001347100, intron 5 of 13)	-34150	NM_001289657	76223	Mm.150047	NM_178630	ENSMUSG00000038836	Agbl3	2900053G10Rik|4930431N21Rik|6530406M24Rik|CCP3	ATP/GTP binding protein-like 3	protein-coding
mm_77812.1	chr9	3038183	3038198	+	1	NA	TTS (NR_039546)	TTS (NR_039546)	553	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_26106.1	chr3	137341148	137341154	+	1	NA	promoter-TSS (NM_016885)	promoter-TSS (NM_016885)	73	NM_016885	59308	Mm.27343	NM_016885	ENSMUSG00000054690	Emcn	0610012K22Rik|AI315669|Muc14	endomucin	protein-coding
mm_119362.1	chr14	41116654	41116669	+	1	NA	intron (NM_133653, intron 6 of 9)	intron (NM_133653, intron 6 of 9)	11628	NM_133653	11720	Mm.14064	NM_133653	ENSMUSG00000037798	Mat1a	AI046368|AdoMet|Ams|MAT|MATA1|SAMS|SAMS1	methionine adenosyltransferase I, alpha	protein-coding
mm_72994.1	chr8	93159076	93159079	+	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	-27794	NM_007954	13884	Mm.88078	NM_007954	ENSMUSG00000057400	Ces1c	Ces-N|Ee-1|Ee1|Es-4|Es-N|Es1|Es4|EsN|PESN	carboxylesterase 1C	protein-coding
mm_74361.1	chr8	128359090	128359102	+	1	NA	promoter-TSS (NM_008737)	promoter-TSS (NM_008737)	23	NM_008737	18186	Mm.271745	NM_008737	ENSMUSG00000025810	Nrp1	C530029I03|NP-1|NPN-1|Npn1|Nrp	neuropilin 1	protein-coding
mm_130339.1	chr15	97731328	97731346	-	1	NA	promoter-TSS (NM_001168693)	promoter-TSS (NM_001168693)	68	NM_001168693	19011	Mm.1001	NM_008902	ENSMUSG00000022468	Endou	Pp11r|Tcl-30	endonuclease, polyU-specific	protein-coding
mm_50893.1	chr6	56832899	56832901	+	1	NA	intron (NM_012056, intron 1 of 9)	intron (NM_012056, intron 1 of 9)	841	NM_012056	27055	Mm.20943	NM_012056	ENSMUSG00000029781	Fkbp9	1810014L23|AW549641|FKBP-63|FKBP-9|FKBP60|FKBP63|FKBP65RS	FK506 binding protein 9	protein-coding
mm_32406.1	chr4	106937322	106937325	+	1	NA	intron (NM_023672, intron 4 of 17)	B3|SINE|B2	25853	NM_023672	72475	Mm.195635	NM_023672	ENSMUSG00000061887	Ssbp3	2610021L12Rik|2610200M23Rik|5730488C10Rik|AI854733|AW551939|LAST|SSDP1	single-stranded DNA binding protein 3	protein-coding
mm_58032.1	chr6	136662269	136662278	-	1	NA	promoter-TSS (NM_025806)	promoter-TSS (NM_025806)	-380	NM_025806	66857	Mm.3311	NM_025806	ENSMUSG00000030214	Plbd1	1100001H23Rik	phospholipase B domain containing 1	protein-coding
mm_90868.1	chr10	8886232	8886245	-	1	NA	promoter-TSS (NM_175155)	promoter-TSS (NM_175155)	-168	NM_175155	70097	Mm.338275	NM_175155	ENSMUSG00000015305	Sash1	1100001C18Rik|2500002E12Rik|A330076K04Rik|mKIAA0790	SAM and SH3 domain containing 1	protein-coding
mm_49287.1	chr6	17666133	17666154	+	1	NA	3' UTR (NM_007604, exon 10 of 10)	3' UTR (NM_007604, exon 10 of 10)	-27851	NM_001289624	64213	Mm.12051	NM_022332	ENSMUSG00000029534	St7	9430001H04Rik|Fam4a2|HELG|RAY1|SEN4|TSG7	suppression of tumorigenicity 7	protein-coding
mm_34694.1	chr4	152009073	152009083	+	1	NA	exon (NM_001033352, exon 1 of 4)	exon (NM_001033352, exon 1 of 4)	187	NM_001033352	242785	Mm.22306	NM_001033352	ENSMUSG00000073700	Klhl21	1810045K06Rik|D330008A20|mKIAA0469	kelch-like 21	protein-coding
mm_145039.1	chr18	39496734	39496744	+	1	NA	Intergenic	Intergenic	-9494	NM_008173	14815	Mm.129481	NM_008173	ENSMUSG00000024431	Nr3c1	GR|Grl-1|Grl1	nuclear receptor subfamily 3, group C, member 1	protein-coding
mm_119538.1	chr14	47898856	47898863	+	1	NA	promoter-TSS (NR_045959)	promoter-TSS (NR_045959)	-5	NR_045959	73961	Mm.390702	NR_045959		4930447J18Rik	4930425M13Rik	RIKEN cDNA 4930447J18 gene	ncRNA
mm_139141.1	chr17	47510630	47510638	+	1	NA	intron (NM_001081635, intron 1 of 6)	B1F1|SINE|Alu	5583	NM_001081635	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_130167.1	chr15	93232024	93232024	-	1	NA	Intergenic	LTR104_Mam|LTR|Gypsy	43060	NM_001033275	223827	Mm.22819	NM_001033275	ENSMUSG00000036197	Gxylt1	Glt8d3|Gm1228|Gm87	glucoside xylosyltransferase 1	protein-coding
mm_133282.1	chr16	77421723	77421737	+	1	NA	intron (NR_015543, intron 2 of 4)	intron (NR_015543, intron 2 of 4)	92402	NR_015543	77994	Mm.394688	NR_015543	ENSMUSG00000090386	Mir99ahg	2810055G20Rik|D730043B02Rik	Mir99a and Mirlet7c-1 host gene (non-protein coding)	ncRNA
mm_54712.1	chr6	39725449	39725478	-	1	NA	promoter-TSS (NM_139294)	promoter-TSS (NM_139294)	0	NM_139294	109880	Mm.245513	NM_139294	ENSMUSG00000002413	Braf	9930012E13Rik|AA120551|AA387315|AA473386|B-raf|Braf-2|Braf2|C230098H17|C87398|D6Ertd631e	Braf transforming gene	protein-coding
mm_98084.1	chr11	86577524	86577537	+	1	NA	Intergenic	Intergenic	6628	NR_029738	387140		NR_029738	ENSMUSG00000065455	Mir21a	Mir21|Mirn21|mmu-mir-21|mmu-mir-21a	microRNA 21a	ncRNA
mm_50833.1	chr6	54816594	54816624	+	1	NA	promoter-TSS (NM_199143)	promoter-TSS (NM_199143)	-307	NM_199143	387524	Mm.286149	NM_199143	ENSMUSG00000058446	Znrf2	1190002C14Rik|AU044205|D6Ertd365e	zinc and ring finger 2	protein-coding
mm_73491.1	chr8	107056932	107056934	+	1	NA	promoter-TSS (NM_139229)	promoter-TSS (NM_139229)	56	NR_028367	66164	Mm.334789	NM_025391	ENSMUSG00000031917	Nip7	1110017C15Rik|6330509M23Rik|AA408773|AA410017|PEachy	NIP7, nucleolar pre-rRNA processing protein	protein-coding
mm_165994.1	chr4	111515608	111515609	+	1	NA	intron (NM_001048189, intron 6 of 12)	intron (NM_001048189, intron 6 of 12)	100602	NM_026279	67621	Mm.45533	NM_026279	ENSMUSG00000028545	Bend5	2310026E23Rik	BEN domain containing 5	protein-coding
mm_99082.1	chr11	99391215	99391220	+	1	NA	Intergenic	Intergenic	-1853	NM_010660	16661	Mm.22662	NM_010660	ENSMUSG00000019761	Krt10	D130054E02Rik|K10|K1C1|Krt-1.10|Krt1-10	keratin 10	protein-coding
mm_94821.1	chr11	23256567	23256580	+	1	NA	5' UTR (NM_134014, exon 2 of 26)	5' UTR (NM_134014, exon 2 of 26)	532	NM_134014	103573	Mm.217547	NM_134014	ENSMUSG00000020290	Xpo1	AA420417|Crm1|Exp1	exportin 1	protein-coding
mm_94583.1	chr11	11690834	11690848	+	1	NA	intron (NM_001301866, intron 1 of 5)	intron (NM_001301866, intron 1 of 5)	664	NM_001301863	22778	Mm.103545	NM_009578	ENSMUSG00000018654	Ikzf1	5832432G11Rik|Ikaros|LyF-1|Zfpn1a1|Znfn1a1|hlk-1|mKIAA4227	IKAROS family zinc finger 1	protein-coding
mm_27973.1	chr3	80802634	80802644	-	1	NA	5' UTR (NM_013540, exon 1 of 16)	5' UTR (NM_013540, exon 1 of 16)	152	NM_013540	14800	Mm.220224	NM_013540	ENSMUSG00000033981	Gria2	GluA2|GluR-B|Glur-2|Glur2	glutamate receptor, ionotropic, AMPA2 (alpha 2)	protein-coding
mm_21547.1	chr2	164060947	164060968	-	1	NA	exon (NM_001291155, exon 4 of 7)	exon (NM_001291155, exon 4 of 7)	10145	NM_025996	67145	Mm.23173	NM_025996	ENSMUSG00000018322	Tomm34	2610100K07Rik|TOM34	translocase of outer mitochondrial membrane 34	protein-coding
mm_69013.1	chr7	126704737	126704762	-	1	NA	promoter-TSS (NM_009898)	promoter-TSS (NM_009898)	67	NM_009898	12721	Mm.290482	NM_009898	ENSMUSG00000030707	Coro1a	Clabp|Lmb3|TACO|p57	coronin, actin binding protein 1A	protein-coding
mm_43201.1	chr5	129096656	129096671	+	1	NA	promoter-TSS (NM_001081342)	promoter-TSS (NM_001081342)	-87	NM_001081342	243277	Mm.440501	NM_177734	ENSMUSG00000044017	Adgrd1	E230012M21Rik|Gpr133	adhesion G protein-coupled receptor D1	protein-coding
mm_26279.1	chr3	142505588	142505604	+	1	NA	exon (NM_153564, exon 7 of 11)	exon (NM_153564, exon 7 of 11)	8662	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_54576.1	chr6	38109549	38109574	-	1	NA	intron (NM_029921, intron 1 of 2)	intron (NM_029921, intron 1 of 2)	208	NM_029921	77522	Mm.387207	NM_029921	ENSMUSG00000029829	Tmem213	D630002J15Rik	transmembrane protein 213	protein-coding
mm_21228.1	chr2	155945283	155945306	-	1	NA	promoter-TSS (NM_008109)	promoter-TSS (NM_008109)	73	NM_008109	14563	Mm.4744	NM_008109	ENSMUSG00000038259	Gdf5	BMP-14|Cdmp-1|bp|brp	growth differentiation factor 5	protein-coding
mm_173278.1	chrY	12439706	12439708	+	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	57718	NM_001199332	100041550	Mm.485768	NM_001199332	ENSMUSG00000095520	Gm20877	-	predicted gene, 20877	protein-coding
mm_25619.1	chr3	118522036	118522039	+	1	NA	Intergenic	Intergenic	-40141	NM_170778	99586	Mm.27907	NM_170778	ENSMUSG00000033308	Dpyd	AI315208|DPD|E330028L06Rik	dihydropyrimidine dehydrogenase	protein-coding
mm_115199.1	chr13	109116174	109116202	+	1	NA	intron (NM_011056, intron 3 of 16)	intron (NM_011056, intron 3 of 16)	-208556	NR_030644	100124489		NR_030644	ENSMUSG00000076946	Mir582	Mirn582|mir-582|mmu-mir-582	microRNA 582	ncRNA
mm_51123.1	chr6	68151855	68151856	+	1	NA	Intergenic	Intergenic	-586156	NR_003100	75070	Mm.463364	NR_003100		4930515G16Rik	-	myc induced nuclear antigen pseudogene	pseudo
mm_92882.1	chr10	82690609	82690636	-	1	NA	promoter-TSS (NM_029102)	promoter-TSS (NM_029102)	28	NM_029102	74782	Mm.191281	NM_029102	ENSMUSG00000020251	Glt8d2	1110021D20Rik	glycosyltransferase 8 domain containing 2	protein-coding
mm_107362.1	chr12	32840937	32840949	+	1	NA	exon (NM_021524, exon 7 of 11)	exon (NM_021524, exon 7 of 11)	16827	NR_045032	100504486	Mm.440246	NR_045032		Gdap10	Gdap-ps	ganglioside-induced differentiation-associated-protein 10	ncRNA
mm_54086.1	chr6	15836628	15836673	-	1	NA	Intergenic	Lx7|LINE|L1	115989	NM_175088	16543	Mm.1314	NM_175088	ENSMUSG00000041390	Mdfic	Kdt1|Mdfid	MyoD family inhibitor domain containing	protein-coding
mm_34171.1	chr4	140131855	140131862	+	1	NA	intron (NM_198610, intron 2 of 9)	intron (NM_198610, intron 2 of 9)	114953	NM_198610	230868	Mm.298731	NM_198610	ENSMUSG00000040972	Igsf21	BC055811|Gm141	immunoglobulin superfamily, member 21	protein-coding
mm_100287.1	chr11	117813414	117813421	+	1	NA	exon (NM_009304, exon 4 of 4)	exon (NM_009304, exon 4 of 4)	3750	NM_009304	20973	Mm.468228	NM_009304	ENSMUSG00000048277	Syngr2	Clast2|cellugyrin	synaptogyrin 2	protein-coding
mm_70320.1	chr8	4250308	4250319	+	1	NA	exon (NM_001195258, exon 4 of 7)	exon (NM_001195258, exon 4 of 7)	2099	NM_001195258	100044509	Mm.439193	NM_001195258	ENSMUSG00000089736	Tgfbr3l	Gm14378|OTTMUSG00000016477	transforming growth factor, beta receptor III-like	protein-coding
mm_170245.1	chr17	93046439	93046457	+	1	NA	Intergenic	(TTAGGG)n|Simple_repeat|Simple_repeat	-152569	NM_001315503	11516	Mm.3407	NM_009625	ENSMUSG00000024256	Adcyap1	PACAP	adenylate cyclase activating polypeptide 1	protein-coding
mm_87836.1	chr10	60380588	60380596	+	1	NA	intron (NR_045556, intron 33 of 68)	intron (NR_045556, intron 33 of 68)	-19134	NM_001164374	100302688	Mm.444135	NM_001164374	ENSMUSG00000090439	Gm17455	-	predicted gene, 17455	protein-coding
mm_154622.1	chrX	7723279	7723282	+	1	NA	intron (NM_001290794, intron 1 of 10)	intron (NM_001290794, intron 1 of 10)	353	NM_001290794	54636	Mm.305725	NM_172372	ENSMUSG00000039382	Wdr45	C79260|DXImx38e|JM5|Sfc19|WIPI-4|Wdrx1	WD repeat domain 45	protein-coding
mm_170017.1	chr17	18476818	18476824	-	1	NA	Intergenic	Intergenic	52717	NM_001102581	328759	Mm.469839	NM_001102581	ENSMUSG00000091631	Vmn2r95	-	vomeronasal 2, receptor 95	protein-coding
mm_153451.1	chr19	41031183	41031193	-	1	NA	intron (NM_009345, intron 1 of 11)	intron (NM_009345, intron 1 of 11)	1913	NM_009345	21673	Mm.25620	NM_009345	ENSMUSG00000025014	Dntt	Tdt	deoxynucleotidyltransferase, terminal	protein-coding
mm_65818.1	chr7	29155718	29155730	-	1	NA	exon (NM_001146023, exon 3 of 8)	exon (NM_001146023, exon 3 of 8)	486	NM_001146023	73833	Mm.260890	NM_028661	ENSMUSG00000030590	Fam98c	1110006G06Rik|AI836081|AV026483|B230110F21Rik	family with sequence similarity 98, member C	protein-coding
mm_77791.1	chr9	3027120	3027145	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	11611	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_172028.1	chr6	123014132	123014134	-	1	NA	intron (NM_001005860, intron 5 of 5)	ORR1A1|LTR|ERVL-MaLR	23766	NM_001005860	474145	Mm.263483	NM_001005860	ENSMUSG00000059639	Clec4a4	Dcir2	C-type lectin domain family 4, member a4	protein-coding
mm_150089.1	chr19	29454218	29454238	+	1	NA	intron (NM_021396, intron 4 of 5)	intron (NM_021396, intron 4 of 5)	43309	NM_021396	58205	Mm.116737	NM_021396	ENSMUSG00000016498	Pdcd1lg2	B7-DC|Btdc|F730015O22Rik|PD-L2	programmed cell death 1 ligand 2	protein-coding
mm_17573.1	chr2	30406403	30406415	-	1	NA	exon (NM_007760, exon 8 of 14)	exon (NM_007760, exon 8 of 14)	9339	NM_007760	12908	Mm.20396	NM_007760	ENSMUSG00000026853	Crat	AW107812|CARAT	carnitine acetyltransferase	protein-coding
mm_112031.1	chr12	111500837	111500850	-	1	NA	Intergenic	MERVK26-int|LTR|ERVK	-15020	NM_001033248	212539	Mm.81916	NM_001033248	ENSMUSG00000010529	Gm266	-	predicted gene 266	protein-coding
mm_130162.1	chr15	91573182	91573245	-	1	NA	promoter-TSS (NM_001033633)	promoter-TSS (NM_001033633)	48	NM_001033633	239606	Mm.360596	NM_001033633	ENSMUSG00000036298	Slc2a13	6530403A04|A630029G22Rik|AI505012|Gm308	solute carrier family 2 (facilitated glucose transporter), member 13	protein-coding
mm_155137.1	chrX	50827559	50827585	+	1	NA	Intergenic	Intergenic	-13799	NM_133729	70415	Mm.46254	NM_133729	ENSMUSG00000031112	Stk26	2610018G03Rik|Mst4	serine/threonine kinase 26	protein-coding
mm_104487.1	chr11	95808597	95808619	-	1	NA	Intergenic	Intergenic	-15892	NM_153104	237928	Mm.133075	NM_153104	ENSMUSG00000050860	Phospho1	D11Moh36|Phospo1	phosphatase, orphan 1	protein-coding
mm_69378.1	chr7	131316212	131316221	-	1	NA	exon (NM_008411, exon 5 of 9)	exon (NM_008411, exon 5 of 9)	6076	NM_008411	16433	Mm.142717	NM_008411	ENSMUSG00000040205	Cuzd1	Erg-1|Itmap1|Uo-44|Usg|Utczp	CUB and zona pellucida-like domains 1	protein-coding
mm_159357.1	chr3	84155724	84155724	-	1	NA	promoter-TSS (NM_029797)	promoter-TSS (NM_029797)	62	NM_029797	76915	Mm.274829	NM_029797	ENSMUSG00000033752	Mnd1	2610034E18Rik|AI591601|Gaj	meiotic nuclear divisions 1	protein-coding
mm_144418.1	chr18	20962870	20962876	+	1	NA	intron (NM_026301, intron 1 of 5)	intron (NM_026301, intron 1 of 5)	18248	NM_026301	67664	Mm.45980	NM_026301	ENSMUSG00000033107	Rnf125	4930553F04Rik	ring finger protein 125	protein-coding
mm_49806.1	chr6	36388056	36388070	+	1	NA	promoter-TSS (NM_203491)	promoter-TSS (NM_203491)	-21	NM_203491	243764	Mm.448632	NM_203491	ENSMUSG00000045613	Chrm2	AChR-M2|Chrm-2|M2	cholinergic receptor, muscarinic 2, cardiac	protein-coding
mm_47339.1	chr5	122502193	122502244	-	1	NA	promoter-TSS (NM_009722)	promoter-TSS (NM_009722)	7	NM_001110140	11938	Mm.227583	NM_009722	ENSMUSG00000029467	Atp2a2	9530097L16Rik|D5Wsu150e|SERCA2|SERCA2B|Serca2a|mKIAA4195	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	protein-coding
mm_5117.1	chr1	7088712	7088718	-	1	NA	promoter-TSS (NM_183028)	promoter-TSS (NM_183028)	-205	NM_183028	319263	Mm.21539	NM_183028	ENSMUSG00000051285	Pcmtd1	8430411F12Rik|A030012M09Rik	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding
mm_123011.1	chr14	55091931	55091934	-	1	NA	intron (NM_001039198, intron 1 of 9)	intron (NM_001039198, intron 1 of 9)	116	NM_001039198	239102	Mm.441113	NM_001039198	ENSMUSG00000040721	Zfhx2	ZFH-5	zinc finger homeobox 2	protein-coding
mm_153145.1	chr19	34249257	34249260	-	1	NA	intron (NM_007392, intron 3 of 8)	intron (NM_007392, intron 3 of 8)	6115	NM_007392	11475	Mm.213025	NM_007392	ENSMUSG00000035783	Acta2	0610041G09Rik|Actvs|SMalphaA|a-SMA|alphaSMA	actin, alpha 2, smooth muscle, aorta	protein-coding
mm_55955.1	chr6	85374584	85374592	-	1	NA	promoter-TSS (NM_177466)	promoter-TSS (NM_177466)	46	NM_177466	52055	Mm.220334	NM_177466	ENSMUSG00000051343	Rab11fip5	9130206P09Rik|C75969|D6Ertd32e|GAF1|RIP11	RAB11 family interacting protein 5 (class I)	protein-coding
mm_113531.1	chr13	37833820	37833843	+	1	NA	intron (NM_001039188, intron 1 of 9)	intron (NM_001039188, intron 1 of 9)	6438	NM_001039188	68750	Mm.491109	NM_026830	ENSMUSG00000039087	Rreb1	1110037N09Rik|AA414966|B930013M22Rik	ras responsive element binding protein 1	protein-coding
mm_112682.1	chr13	16029028	16029040	+	1	NA	3' UTR (NM_008380, exon 5 of 5)	3' UTR (NM_008380, exon 5 of 5)	17183	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_12061.1	chr2	59380887	59380888	+	1	NA	Intergenic	L1MA6|LINE|L1	5795	NR_040510	76676	Mm.110038	NR_040510	ENSMUSG00000087455	5330411J11Rik	-	RIKEN cDNA 5330411J11 gene	ncRNA
mm_71363.1	chr8	45695380	45695394	+	1	NA	intron (NM_001310708, intron 1 of 19)	intron (NM_001310708, intron 1 of 19)	33394	NM_001310708	234214	Mm.211096	NM_172752	ENSMUSG00000031626	Sorbs2	2010203O03Rik|9430041O17Rik|A530071H08|Argbp2|mKIAA0777|nArgBP2	sorbin and SH3 domain containing 2	protein-coding
mm_171349.1	chr4	109118000	109118000	-	1	NA	promoter-TSS (NM_173350)	promoter-TSS (NM_173350)	36	NM_173350	100273	Mm.366315	NM_133885	ENSMUSG00000028559	Osbpl9	2600011I06Rik|AU015843|Orp-9	oxysterol binding protein-like 9	protein-coding
mm_120366.1	chr14	64574365	64574426	+	1	NA	Intergenic	Intergenic	-13720	NR_040709	268755	Mm.194050	NR_040709	ENSMUSG00000097545	Mir124a-1hg	A930011O12Rik|Rncr3|mir-124-1|mir-3078	Mir124-1 host gene (non-protein coding)	ncRNA
mm_85756.1	chr9	108649310	108649323	-	1	NA	promoter-TSS (NM_011790)	promoter-TSS (NM_011790)	64	NM_011790	23807	Mm.290447	NM_011790	ENSMUSG00000064145	Arih2	AI843547|ARI2|TRIAD1|UIP48	ariadne RBR E3 ubiquitin protein ligase 2	protein-coding
mm_2635.1	chr1	121486971	121486980	+	1	NA	intron (NM_001025156, intron 18 of 23)	B3A|SINE|B2	41490	NM_010483	15564	Mm.4833	NM_010483	ENSMUSG00000050534	Htr5b	5-Ht5b	5-hydroxytryptamine (serotonin) receptor 5B	protein-coding
mm_130443.1	chr15	98482687	98482705	-	1	NA	promoter-TSS (NM_010679)	promoter-TSS (NM_010679)	-13	NM_010679	16770	Mm.5074	NM_010679	ENSMUSG00000022991	Lalba	AW208827|Lyzg	lactalbumin, alpha	protein-coding
mm_134948.1	chr16	31297504	31297525	-	1	NA	exon (NM_007470, exon 6 of 6)	exon (NM_007470, exon 6 of 6)	17294	NM_001301353	11815	Mm.2082	NM_007470	ENSMUSG00000022548	Apod	-	apolipoprotein D	protein-coding
mm_9785.1	chr1	181212352	181212375	-	1	NA	promoter-TSS (NM_145514)	promoter-TSS (NM_145514)	-385	NM_145514	226757	Mm.289082	NM_145514	ENSMUSG00000038733	Wdr26	1600024A01Rik|AA693241|AI447817|AU044014|C77982|Gid7	WD repeat domain 26	protein-coding
mm_79889.1	chr9	65294396	65294417	+	1	NA	5' UTR (NM_011802, exon 1 of 14)	5' UTR (NM_011802, exon 1 of 14)	146	NM_011802	270166	Mm.30088	NM_011802	ENSMUSG00000015357	Clpx	AU014732|E330029I21	caseinolytic mitochondrial matrix peptidase chaperone subunit	protein-coding
mm_35789.1	chr4	46503459	46503462	-	1	NA	TTS (NM_053179)	TTS (NM_053179)	14131	NM_053179	94181	Mm.249349	NM_053179	ENSMUSG00000028334	Nans	4632418E04Rik|BB056474|Sas	N-acetylneuraminic acid synthase (sialic acid synthase)	protein-coding
mm_153449.1	chr19	41031153	41031163	-	1	NA	intron (NM_009345, intron 1 of 11)	intron (NM_009345, intron 1 of 11)	1883	NM_009345	21673	Mm.25620	NM_009345	ENSMUSG00000025014	Dntt	Tdt	deoxynucleotidyltransferase, terminal	protein-coding
mm_29020.1	chr3	101924421	101924454	-	1	NA	promoter-TSS (NM_001039371)	promoter-TSS (NM_001039371)	16	NM_001039371	242126	Mm.90204	NM_001039371	ENSMUSG00000033147	Slc22a15	2610034P21Rik|4930477M19|A530052I06Rik|BB219042	solute carrier family 22 (organic anion/cation transporter), member 15	protein-coding
mm_112431.1	chr13	4436095	4436132	+	1	NA	intron (NM_030611, intron 1 of 8)	intron (NM_030611, intron 1 of 8)	1770	NM_030611	83702	Mm.196666	NM_030611	ENSMUSG00000021210	Akr1c6	3alpha-HSD|Akr1c1|Hsd17b5	aldo-keto reductase family 1, member C6	protein-coding
mm_29570.1	chr3	116968713	116968768	-	1	NA	5' UTR (NM_023245, exon 1 of 8)	5' UTR (NM_023245, exon 1 of 8)	212	NM_023245	114301	Mm.253736	NM_023245	ENSMUSG00000033377	Palmd	4631423C22Rik|PALML	palmdelphin	protein-coding
mm_123977.1	chr14	75178402	75178436	-	1	NA	intron (NM_008879, intron 2 of 16)	intron (NM_008879, intron 2 of 16)	41994	NM_008879	18826	Mm.153911	NM_008879	ENSMUSG00000021998	Lcp1	AW536232|D14Ertd310e|LCP-1|Pls2|pp65	lymphocyte cytosolic protein 1	protein-coding
mm_172543.1	chr7	97647769	97647784	-	1	NA	intron (NM_001081267, intron 4 of 15)	RLTR11B|LTR|ERVK	-2664	NR_126461	75448	Mm.439818	NR_126461	ENSMUSG00000086433	Rsf1os1	1700006D18Rik	remodeling and spacing factor 1, opposite strand 1	ncRNA
mm_107517.1	chr12	40446051	40446099	+	1	NA	promoter-TSS (NM_178845)	promoter-TSS (NM_178845)	22	NM_172803	238130	Mm.341423	NM_172803	ENSMUSG00000035954	Dock4	5330406C03|6330411N01Rik|AF263288|C030023J22|mKIAA0716	dedicator of cytokinesis 4	protein-coding
mm_53160.1	chr6	125321259	125321273	+	1	NA	promoter-TSS (NM_011324)	promoter-TSS (NM_011324)	-74	NM_011324	20276	Mm.144114	NM_011324	ENSMUSG00000030340	Scnn1a	ENaC|SCNEA|Scnn1|mENaC	sodium channel, nonvoltage-gated 1 alpha	protein-coding
mm_31512.1	chr4	53779695	53779706	+	1	NA	promoter-TSS (NM_009317)	promoter-TSS (NM_009317)	-5	NM_009317	21350	Mm.56955	NM_009317	ENSMUSG00000028417	Tal2	bHLHa19	T cell acute lymphocytic leukemia 2	protein-coding
mm_41025.1	chr5	81794336	81794348	+	1	NA	exon (NM_198702, exon 28 of 28)	exon (NM_198702, exon 28 of 28)	330371	NR_138557	67327	Mm.87058	NR_138557		1700031L13Rik	-	RIKEN cDNA 1700031L13 gene	ncRNA
mm_105485.1	chr11	105944479	105944518	-	1	NA	promoter-TSS (NM_007805)	promoter-TSS (NM_007805)	-351	NM_007805	13056	Mm.149403	NM_007805	ENSMUSG00000019590	Cyb561	-	cytochrome b-561	protein-coding
mm_170030.1	chr17	21921029	21921032	-	1	NA	Intergenic	CpG	-11104	NM_001256493	70081	Mm.245648	NM_001256493	ENSMUSG00000078546	Zfp995	2210404O09Rik	zinc finger protein 995	protein-coding
mm_87879.1	chr10	61648674	61648686	+	1	NA	promoter-TSS (NM_026438)	promoter-TSS (NM_026438)	59	NM_026438	67895	Mm.28897	NM_026438	ENSMUSG00000020089	Ppa1	2010317E03Rik|Pyp	pyrophosphatase (inorganic) 1	protein-coding
mm_107190.1	chr12	25099692	25099719	+	1	NA	Intergenic	Intergenic	-3613	NM_010496	15902	Mm.34871	NM_010496	ENSMUSG00000020644	Id2	AI255428|C78922|Idb2|bHLHb26	inhibitor of DNA binding 2	protein-coding
mm_118416.1	chr14	7791515	7791515	+	1	NA	Intergenic	CpG	-26442	NM_001081427	286940	Mm.489652	NM_134080	ENSMUSG00000025278	Flnb	AL024016|Fln-b	filamin, beta	protein-coding
mm_106010.1	chr11	115813622	115813654	-	1	NA	promoter-TSS (NM_080643)	promoter-TSS (NM_080643)	-46	NM_080643	140721	Mm.383737	NM_080643	ENSMUSG00000034471	Caskin2	1600028L06Rik|mKIAA1139	CASK-interacting protein 2	protein-coding
mm_112726.1	chr13	19192665	19192674	+	1	NA	Intergenic	Intergenic	203144	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_152436.1	chr19	10726294	10726297	-	1	NA	intron (NM_007650, intron 3 of 10)	intron (NM_007650, intron 3 of 10)	12679	NM_007650	12507	Mm.779	NM_007650	ENSMUSG00000024669	Cd5	Ly-1|Ly-12|Ly-A|Lyt-1	CD5 antigen	protein-coding
mm_18541.1	chr2	64916925	64916947	-	1	NA	intron (NM_016719, intron 11 of 13)	intron (NM_016719, intron 11 of 13)	105830	NM_016719	50915	Mm.214554	NM_016719	ENSMUSG00000026888	Grb14	AI505286	growth factor receptor bound protein 14	protein-coding
mm_120584.1	chr14	69775158	69775193	+	1	NA	exon (NM_020275, exon 4 of 8)	exon (NM_020275, exon 4 of 8)	7703	NM_020275	21933	Mm.193430	NM_020275	ENSMUSG00000022074	Tnfrsf10b	DR5|KILLER|Ly98|MK|TRAILR2|TRICK2A|TRICK2B|TRICKB	tumor necrosis factor receptor superfamily, member 10b	protein-coding
mm_44415.1	chr5	17888885	17888893	-	1	NA	promoter-TSS (NM_001159558)	promoter-TSS (NM_001159558)	70	NM_001159558	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_112078.1	chr12	112668045	112668092	-	1	NA	intron (NM_001331107, intron 2 of 13)	intron (NM_001331107, intron 2 of 13)	6208	NM_001165894	11651	Mm.6645	NM_009652	ENSMUSG00000001729	Akt1	Akt|LTR-akt|PKB|PKB/Akt|PKBalpha|Rac	thymoma viral proto-oncogene 1	protein-coding
mm_132271.1	chr16	32904840	32904844	+	1	NA	intron (NM_027226, intron 8 of 8)	B1F2|SINE|Alu	-9258	NM_001310673	70144	Mm.491178	NM_001081255	ENSMUSG00000022801	Lrch3	2210409B11Rik|AW215594|Gm1742	leucine-rich repeats and calponin homology (CH) domain containing 3	protein-coding
mm_58895.1	chr7	17095085	17095095	+	1	NA	exon (NM_007676, exon 4 of 5)	exon (NM_007676, exon 4 of 5)	21050	NM_007676	26436	Mm.143686	NM_007676	ENSMUSG00000066760	Psg16	Cea11|PSG|bCEA	pregnancy specific glycoprotein 16	protein-coding
mm_96029.1	chr11	59549641	59549648	+	1	NA	exon (NM_145827, exon 4 of 10)	exon (NM_145827, exon 4 of 10)	6958	NM_145827	216799	Mm.54174	NM_145827	ENSMUSG00000032691	Nlrp3	AGTAVPRL|AII/AVP|Cias1|FCAS|FCU|MWS|Mmig1|NALP3|Pypaf1	NLR family, pyrin domain containing 3	protein-coding
mm_109799.1	chr12	3309349	3309398	-	1	NA	exon (NM_016676, exon 1 of 6)	exon (NM_016676, exon 1 of 6)	596	NM_016676	19325	Mm.378993	NM_016676	ENSMUSG00000020671	Rab10	AW107754	RAB10, member RAS oncogene family	protein-coding
mm_110150.1	chr12	26450676	26450684	-	1	NA	exon (NM_021384, exon 3 of 6)	exon (NM_021384, exon 3 of 6)	5772	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_156009.1	chrX	106920644	106920699	+	1	NA	promoter-TSS (NM_175271)	promoter-TSS (NM_175271)	46	NM_175271	78134	Mm.90147	NM_175271	ENSMUSG00000049929	Lpar4	5730485F04Rik|Gpr23|LPA4|p2y9	lysophosphatidic acid receptor 4	protein-coding
mm_70349.1	chr8	4861128	4861135	+	1	NA	Intergenic	Intergenic	-81597	NM_011369	20419	Mm.37801	NM_011369	ENSMUSG00000022322	Shcbp1	mPAL	Shc SH2-domain binding protein 1	protein-coding
mm_130294.1	chr15	97013476	97013495	-	1	NA	exon (NM_027052, exon 5 of 16)	exon (NM_027052, exon 5 of 16)	42471	NM_027052	69354	Mm.250980	NM_027052	ENSMUSG00000022464	Slc38a4	1110012E16Rik|1700012A18Rik|Ata3|mATA3|mNAT3	solute carrier family 38, member 4	protein-coding
mm_75832.1	chr8	70510553	70510584	-	1	NA	promoter-TSS (NM_019883)	promoter-TSS (NM_019883)	-201	NM_019883	22186	Mm.297372	NM_019883	ENSMUSG00000090137	Uba52	D8Ertd21e|Gm1863|Rps27a|Ubb|Ubc	ubiquitin A-52 residue ribosomal protein fusion product 1	protein-coding
mm_21793.1	chr2	164857635	164857652	-	1	NA	promoter-TSS (NM_011125)	promoter-TSS (NM_011125)	65	NM_011125	18830	Mm.6105	NM_011125	ENSMUSG00000017754	Pltp	Bpife|OD107	phospholipid transfer protein	protein-coding
mm_58831.1	chr7	16782304	16782391	+	1	NA	exon (NM_009201, exon 1 of 9)	exon (NM_009201, exon 1 of 9)	1001	NM_009201	20514	Mm.1056	NM_009201	ENSMUSG00000001918	Slc1a5	AAAT|ASCT2|ATBO|M7V1|M7VS1|R16|RDRC|Slc1a7	solute carrier family 1 (neutral amino acid transporter), member 5	protein-coding
mm_54092.1	chr6	16836725	16836733	-	1	NA	intron (NM_031198, intron 5 of 6)	IMPB_01|Satellite|Satellite	61712	NM_031198	21426	Mm.36217	NM_031198	ENSMUSG00000029553	Tfec	BB107417|Tcfec|bHLHe34	transcription factor EC	protein-coding
mm_13236.1	chr2	98662323	98662345	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	1194677	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_77946.1	chr9	7358442	7358460	+	1	NA	3' UTR (NM_008605, exon 10 of 10)	3' UTR (NM_008605, exon 10 of 10)	11077	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_133444.1	chr16	87731522	87731525	+	1	NA	3' UTR (NM_007520, exon 5 of 5)	3' UTR (NM_007520, exon 5 of 5)	32569	NM_007520	12013	Mm.26147	NM_007520	ENSMUSG00000025612	Bach1	6230421P05Rik|AI323795	BTB and CNC homology 1, basic leucine zipper transcription factor 1	protein-coding
mm_18288.1	chr2	52615298	52615301	-	1	NA	intron (NM_001285426, intron 2 of 13)	intron (NM_001285426, intron 2 of 13)	-56688	NM_001285427	12298	Mm.330223	NM_146123	ENSMUSG00000017412	Cacnb4	3110038O15Rik|Cchb4|lh	calcium channel, voltage-dependent, beta 4 subunit	protein-coding
mm_4432.1	chr1	172506625	172506642	+	1	NA	exon (NM_178598, exon 5 of 5)	exon (NM_178598, exon 5 of 5)	6387	NM_178598	21346	Mm.271711	NM_178598	ENSMUSG00000026547	Tagln2	2700094C18Rik|SM22beta|Sm22B|Sm22a	transgelin 2	protein-coding
mm_4609.1	chr1	178528854	178528867	+	1	NA	promoter-TSS (NM_001161665)	promoter-TSS (NM_001161665)	-265	NM_001161665	269152	Mm.129727	NM_177724	ENSMUSG00000026494	Kif26b	4832420M10|BC056349|D230039L06Rik	kinesin family member 26B	protein-coding
mm_157978.1	chrX	94122321	94122326	-	1	NA	intron (NM_001044386, intron 1 of 8)	CpG	1084	NM_011768	22764	Mm.919	NM_011768	ENSMUSG00000079509	Zfx	Zfx5|Zfx5,6|Zfx6	zinc finger protein X-linked	protein-coding
mm_50003.1	chr6	41055902	41055927	+	1	NA	Intergenic	Intergenic	-20405	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_8494.1	chr1	153851049	153851061	-	1	NA	exon (NM_178243, exon 1 of 1)	exon (NM_178243, exon 1 of 1)	140	NM_178243	240817	Mm.439405	NM_178243	ENSMUSG00000045968	Teddm2	5830403L16Rik|AJ554213|Me9|e92	transmembrane epididymal family member 2	protein-coding
mm_171136.1	chr3	149052784	149052784	+	1	NA	Intergenic	(TTAGGG)n|Simple_repeat|Simple_repeat	-98149	NM_001081298	99633	Mm.9776	NM_001081298	ENSMUSG00000028184	Adgrl2	AI450192|CIRL-2|Gm619|Lec1|Lphh1|Lphn2|mKIAA0786	adhesion G protein-coupled receptor L2	protein-coding
mm_57637.1	chr6	128362503	128362523	-	1	NA	promoter-TSS (NM_008021)	promoter-TSS (NM_008021)	309	NM_001326583	72440	Mm.143908	NM_197981	ENSMUSG00000048668	Rhno1	2510047L19Rik|5930416I19Rik	RAD9-HUS1-RAD1 interacting nuclear orphan 1	protein-coding
mm_16674.1	chr2	6825357	6825357	-	1	NA	intron (NM_001110229, intron 2 of 14)	intron (NM_001110229, intron 2 of 14)	46678	NM_001347094	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_120455.1	chr14	65969802	65969821	+	1	NA	intron (NM_013492, intron 1 of 8)	MER5A|DNA|hAT-Charlie	1328	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_116384.1	chr13	41079629	41079662	-	1	NA	promoter-TSS (NM_001145803)	promoter-TSS (NM_001145803)	61	NM_001145803	17152	Mm.8149	NM_008547	ENSMUSG00000021363	Mak	A930010O05Rik	male germ cell-associated kinase	protein-coding
mm_80476.1	chr9	78192007	78192023	+	1	NA	promoter-TSS (NM_010357)	promoter-TSS (NM_010357)	49	NM_010357	14860	Mm.2662	NM_010357	ENSMUSG00000032348	Gsta4	GST5.7|mGsta4	glutathione S-transferase, alpha 4	protein-coding
mm_127416.1	chr15	101260428	101260455	+	1	NA	Intergenic	LFSINE_Vert|SINE|tRNA	-6405	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_160693.1	chr10	26375146	26375146	-	1	NA	promoter-TSS (NM_172787)	promoter-TSS (NM_172787)	73	NM_172787	237339	Mm.338439	NM_172787	ENSMUSG00000039089	L3mbtl3	AI481284|MBT-1	l(3)mbt-like 3 (Drosophila)	protein-coding
mm_106973.1	chr12	8974829	8974857	+	1	NA	intron (NM_001159527, intron 1 of 26)	intron (NM_001159527, intron 1 of 26)	842	NM_172470	74682	Mm.87389	NM_172470	ENSMUSG00000066643	Wdr35	4930459M12Rik|4931430C06|mKIAA1336	WD repeat domain 35	protein-coding
mm_124948.1	chr15	12350218	12350237	+	1	NA	3' UTR (NM_025673, exon 4 of 4)	3' UTR (NM_025673, exon 4 of 4)	28731	NM_025673	66629	Mm.157655	NM_025673	ENSMUSG00000022200	Golph3	4733401N08Rik|5730410D03Rik|AW413496	golgi phosphoprotein 3	protein-coding
mm_85925.1	chr9	111690314	111690344	-	1	NA	promoter-TSS (NM_001324546)	promoter-TSS (NM_001324546)	19	NM_016853	20840	Mm.1414	NM_016853	ENSMUSG00000032502	Stac	-	src homology three (SH3) and cysteine rich domain	protein-coding
mm_20404.1	chr2	129297225	129297231	-	1	NA	promoter-TSS (NM_181589)	promoter-TSS (NM_181589)	-16	NM_181589	70466	Mm.45785	NM_181589	ENSMUSG00000048327	Ckap2l	2010016H04Rik|2610318C08Rik|AV070319|radmis|rdm	cytoskeleton associated protein 2-like	protein-coding
mm_17616.1	chr2	30930091	30930105	-	1	NA	Intergenic	Intergenic	-22903	NM_133673	30934	Mm.249164	NM_133673	ENSMUSG00000026848	Tor1b	2610016F05Rik|DQ1|torsinB	torsin family 1, member B	protein-coding
mm_102095.1	chr11	52306614	52306624	-	1	NA	Intergenic	Intergenic	-23605	NM_001313981	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_94633.1	chr11	16846355	16846389	+	1	NA	intron (NM_207655, intron 1 of 27)	intron (NM_207655, intron 1 of 27)	94169	NM_007912	13649	Mm.8534	NM_007912	ENSMUSG00000020122	Egfr	9030024J15Rik|AI552599|Erbb|Errb1|Errp|Wa5|wa-2|wa2	epidermal growth factor receptor	protein-coding
mm_83559.1	chr9	46242932	46242973	-	1	NA	exon (NM_007468, exon 3 of 3)	exon (NM_007468, exon 3 of 3)	2108	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_152323.1	chr19	9938763	9938808	-	1	NA	Intergenic	Intergenic	-39252	NM_016692	16319	Mm.29755	NM_016692	ENSMUSG00000024660	Incenp	2700067E22Rik|AU019509|C130081E20|C77457	inner centromere protein	protein-coding
mm_65411.1	chr7	25245108	25245144	-	1	NA	exon (NM_010155, exon 4 of 4)	exon (NM_010155, exon 4 of 4)	5632	NM_010155	13875	Mm.8068	NM_010155	ENSMUSG00000040857	Erf	-	Ets2 repressor factor	protein-coding
mm_40415.1	chr5	53267104	53267127	+	1	NA	promoter-TSS (NM_001145433)	promoter-TSS (NM_001145433)	9	NM_001145433	66278	Mm.27900	NM_001145433	ENSMUSG00000061461	Smim20	1110067B18Rik|1810013D10Rik|N28078	small integral membrane protein 20	protein-coding
mm_19793.1	chr2	109278275	109278305	-	1	NA	promoter-TSS (NM_029790)	promoter-TSS (NM_029790)	0	NM_029790	76894	Mm.330451	NM_029790	ENSMUSG00000057234	Mettl15	0610027B03Rik|AI303697|AW049952|Mett5d1	methyltransferase like 15	protein-coding
mm_24338.1	chr3	89730736	89730786	+	1	NA	promoter-TSS (NM_001146296)	promoter-TSS (NM_001146296)	43	NM_019655	56417	Mm.316628	NM_019655	ENSMUSG00000027951	Adar	AV242451|Adar1|Adar1p110|Adar1p150|mZaADAR	adenosine deaminase, RNA-specific	protein-coding
mm_156305.1	chrX	136837990	136838000	+	1	NA	3' UTR (NM_011123, exon 7 of 7)	3' UTR (NM_011123, exon 7 of 7)	15249	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_50499.1	chr6	49035988	49036003	+	1	NA	promoter-TSS (NM_053110)	promoter-TSS (NM_053110)	-523	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_95858.1	chr11	58008862	58008935	+	1	NA	promoter-TSS (NM_028451)	promoter-TSS (NM_028451)	-166	NM_028451	73158	Mm.248843	NM_028451	ENSMUSG00000037331	Larp1	1810024J12Rik|3110040D16Rik|Larp|mKIAA0731	La ribonucleoprotein domain family, member 1	protein-coding
mm_89769.1	chr10	100099065	100099082	+	1	NA	3' UTR (NM_013598, exon 10 of 10)	3' UTR (NM_013598, exon 10 of 10)	83252	NM_013598	17311	Mm.45124	NM_013598	ENSMUSG00000019966	Kitl	Clo|Con|Gb|Kitlg|Mgf|SCF|SF|SLF|Sl|blz|contrasted	kit ligand	protein-coding
mm_118066.1	chr13	102905901	102905916	-	1	NA	intron (NM_175171, intron 4 of 28)	intron (NM_175171, intron 4 of 28)	145653	NR_130171	76624	Mm.426384	NR_130171	ENSMUSG00000091906	1700099I09Rik	-	RIKEN cDNA 1700099I09 gene	ncRNA
mm_124968.1	chr15	18818701	18818726	+	1	NA	promoter-TSS (NM_001316758)	promoter-TSS (NM_001316758)	-234	NM_001316758	320873	Mm.117794	NM_009865	ENSMUSG00000022321	Cdh10	A830016G23Rik|C030003B10Rik|C030011H18Rik	cadherin 10	protein-coding
mm_52919.1	chr6	122850632	122850658	+	1	NA	exon (NM_009779, exon 2 of 2)	exon (NM_009779, exon 2 of 2)	5512	NM_009779	12267	Mm.2408	NM_009779	ENSMUSG00000040552	C3ar1	AZ3B|C3AR|HNFAG09	complement component 3a receptor 1	protein-coding
mm_4714.1	chr1	180945899	180945925	+	1	NA	intron (NM_144794, intron 1 of 22)	intron (NM_144794, intron 1 of 22)	3394	NM_144794	208795	Mm.185518	NM_144794	ENSMUSG00000026519	Tmem63a	BC014795|Tmem64a	transmembrane protein 63a	protein-coding
mm_86602.1	chr10	13501077	13501095	+	1	NA	promoter-TSS (NM_001330198)	promoter-TSS (NM_001330198)	58	NM_025799	66848	Mm.26625	NM_025799	ENSMUSG00000019810	Fuca2	0610025O11Rik|5530401P20Rik	fucosidase, alpha-L- 2, plasma	protein-coding
mm_163589.1	chr13	38464636	38464647	+	1	NA	intron (NM_007556, intron 1 of 6)	intron (NM_007556, intron 1 of 6)	-2848	NR_131033	75854	Mm.417810	NR_131033		4930579J19Rik	-	RIKEN cDNA 4930579J19 gene	ncRNA
mm_29777.1	chr3	127408881	127408887	-	1	NA	5' UTR (NM_001327939, exon 1 of 46)	5' UTR (NM_001327939, exon 1 of 46)	174	NM_001327939	109676	Mm.220242	NM_178655	ENSMUSG00000032826	Ank2	100043364|AI835472|AW491075|Ank-2|Gm4392	ankyrin 2, brain	protein-coding
mm_137074.1	chr17	20965553	20965556	+	1	NA	3' UTR (NM_016891, exon 15 of 15)	3' UTR (NM_016891, exon 15 of 15)	20100	NM_016891	51792	Mm.294138	NM_016891	ENSMUSG00000007564	Ppp2r1a	6330556D22Rik|PP2A|PR65	protein phosphatase 2, regulatory subunit A, alpha	protein-coding
mm_143997.1	chr17	88029488	88029491	-	1	NA	intron (NM_001081034, intron 1 of 22)	intron (NM_001081034, intron 1 of 22)	35796	NM_001081034	225055	Mm.386857	NM_001081034	ENSMUSG00000005371	Fbxo11	C80048|Jf	F-box protein 11	protein-coding
mm_166636.1	chr6	82780929	82780971	-	1	NA	Intergenic	Zaphod3|DNA|hAT-Tip100	-6496	NM_013820	15277	Mm.255848	NM_013820	ENSMUSG00000000628	Hk2	AI642394|HKII	hexokinase 2	protein-coding
mm_116065.1	chr13	27582169	27582172	-	1	NA	promoter-TSS (NM_028477)	promoter-TSS (NM_028477)	1	NM_028477	73244	Mm.215193	NM_028477	ENSMUSG00000019756	Prl8a1	1600017L04Rik|3830403L08Rik|Ghd16|PLP-Cd|Plpcd|Prlpc4	prolactin family 8, subfamily a, member 1	protein-coding
mm_153406.1	chr19	40513834	40513880	-	1	NA	promoter-TSS (NM_009166)	promoter-TSS (NM_009166)	-45	NM_009166	20411	Mm.210815	NM_009166	ENSMUSG00000025006	Sorbs1	2310065E01Rik|9530001P15Rik|CAP|SH3P12|Sh3d5|mKIAA1296	sorbin and SH3 domain containing 1	protein-coding
mm_156503.1	chrX	146414224	146414224	+	1	NA	Intergenic	Intergenic	-548289	NM_008312	15560	Mm.439670	NM_008312	ENSMUSG00000041380	Htr2c	5-HT2C|5-HT2cR|5-HTR2C|5HT1c|Htr1c|SR1	5-hydroxytryptamine (serotonin) receptor 2C	protein-coding
mm_170505.1	chr19	24620170	24620170	+	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	-53838	NM_183160	226040	Mm.391170	NM_183160	ENSMUSG00000048572	Tmem252	E030010A14Rik	transmembrane protein 252	protein-coding
mm_123781.1	chr14	70331442	70331447	-	1	NA	intron (NM_001135151, intron 1 of 9)	intron (NM_001135151, intron 1 of 9)	16989	NM_001135152	213053	Mm.270647	NM_144808	ENSMUSG00000022094	Slc39a14	FAD-123|ZIP-14|Zip14|fad123	solute carrier family 39 (zinc transporter), member 14	protein-coding
mm_133348.1	chr16	81623759	81623762	+	1	NA	3' UTR (NM_001113208, exon 18 of 18)	3' UTR (NM_001113208, exon 18 of 18)	423063	NM_010954	17968	Mm.433941	NM_010954	ENSMUSG00000022762	Ncam2	Ncam-2|Ocam|RNCAM	neural cell adhesion molecule 2	protein-coding
mm_98517.1	chr11	94952618	94952633	+	1	NA	3' UTR (NM_007742, exon 51 of 51)	3' UTR (NM_007742, exon 51 of 51)	-14968	NM_018792	54388	Mm.30482	NM_018792	ENSMUSG00000038994	Hils1	H1.9|TISP64	histone H1-like protein in spermatids 1	protein-coding
mm_129406.1	chr15	78291657	78291682	-	1	NA	exon (NM_007781, exon 8 of 14)	exon (NM_007781, exon 8 of 14)	-6820	NR_106137	102465776		NR_106137	ENSMUSG00000098996	Mir7676-1	Gm27600|mmu-mir-7676-1	microRNA 7676-1	ncRNA
mm_98773.1	chr11	96747075	96747106	+	1	NA	intron (NM_001177898, intron 10 of 10)	intron (NM_001177898, intron 10 of 10)	30465	NM_028965	74479	Mm.270781	NM_028965	ENSMUSG00000020876	Snx11	4933439F10Rik|A930041K09Rik|AI117694	sorting nexin 11	protein-coding
mm_74529.1	chr8	9559295	9559334	-	1	NA	intron (NM_001347127, intron 1 of 3)	B4A|SINE|B4	211709	NM_173446	270028	Mm.268163	NM_173446	ENSMUSG00000079157	Fam155a	6430500D16|AW121567|Tmem28	family with sequence similarity 155, member A	protein-coding
mm_59766.1	chr7	28834005	28834014	+	1	NA	promoter-TSS (NM_010707)	promoter-TSS (NM_010707)	-161	NM_010707	16857	Mm.210336	NM_010707		Lgals6	galectin-6	lectin, galactose binding, soluble 6	protein-coding
mm_49605.1	chr6	30744347	30744376	+	1	NA	exon (NM_001252293, exon 7 of 12)	exon (NM_001252293, exon 7 of 12)	3062	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_153228.1	chr19	34879248	34879268	-	1	NA	5' UTR (NM_001114339, exon 1 of 7)	5' UTR (NM_001114339, exon 1 of 7)	197	NM_001114339	75735	Mm.24742	NM_023792	ENSMUSG00000033610	Pank1	Pank|Pank1b	pantothenate kinase 1	protein-coding
mm_131567.1	chr16	18213968	18214008	+	1	NA	promoter-TSS (NR_027843)	promoter-TSS (NR_027843)	-125	NR_015575	66779	Mm.387525	NR_015575		4933432I09Rik	-	RIKEN cDNA 4933432I09 gene	ncRNA
mm_151989.1	chr19	5848112	5848124	-	1	NA	Intergenic	Intergenic	-2638	NR_003513	66961	Mm.281895	NR_003513	ENSMUSG00000092274	Neat1	2310043N10Rik|VINC	nuclear paraspeckle assembly transcript 1 (non-protein coding)	ncRNA
mm_122626.1	chr14	51145683	51145698	-	1	NA	exon (NM_011271, exon 2 of 2)	exon (NM_011271, exon 2 of 2)	1077	NM_011271	19752	Mm.235538	NM_011271	ENSMUSG00000035896	Rnase1	AI574248|Rib-1|Rib1	ribonuclease, RNase A family, 1 (pancreatic)	protein-coding
mm_29759.1	chr3	127162329	127162360	-	1	NA	intron (NR_105029, intron 2 of 3)	intron (NR_105029, intron 2 of 3)	1039	NR_105029	100862268	Mm.444603	NR_105029	ENSMUSG00000097456	LOC100862268	-	uncharacterized LOC100862268	ncRNA
mm_12989.1	chr2	90885476	90885501	+	1	NA	promoter-TSS (NM_026161)	promoter-TSS (NM_026161)	-298	NM_026161	67445	Mm.258993	NM_026161	ENSMUSG00000040794	C1qtnf4	0710001E10Rik|9430004J15Rik|CTRP4	C1q and tumor necrosis factor related protein 4	protein-coding
mm_93552.1	chr10	116114265	116114279	-	1	NA	promoter-TSS (NM_001161855)	promoter-TSS (NM_001161855)	-355	NM_001161855	619332	Mm.391427	NM_001033821	ENSMUSG00000074734	4933416C03Rik	-	RIKEN cDNA 4933416C03 gene	protein-coding
mm_102788.1	chr11	68432012	68432032	-	1	NA	promoter-TSS (NM_177320)	promoter-TSS (NM_177320)	-103	NM_177320	320207	Mm.244960	NM_177320	ENSMUSG00000020901	Pik3r5	AV230647|F730038I15Rik	phosphoinositide-3-kinase, regulatory subunit 5, p101	protein-coding
mm_75065.1	chr8	33801686	33801688	-	1	NA	intron (NM_001286168, intron 5 of 7)	intron (NM_001286168, intron 5 of 7)	-53917	NM_001206849	72632	Mm.443483	NM_001206849	ENSMUSG00000094500	Smim18	2700090O03Rik|AI835723	small integral membrane protein 18	protein-coding
mm_53958.1	chr6	5491679	5491684	-	1	NA	intron (NM_013743, intron 4 of 10)	intron (NM_013743, intron 4 of 10)	4597	NM_013743	27273	Mm.235547	NM_013743	ENSMUSG00000019577	Pdk4	AV005916	pyruvate dehydrogenase kinase, isoenzyme 4	protein-coding
mm_112688.1	chr13	16031049	16031059	+	1	NA	3' UTR (NM_008380, exon 5 of 5)	3' UTR (NM_008380, exon 5 of 5)	19203	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_24590.1	chr3	93445065	93445067	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	2736	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_35565.1	chr4	41640179	41640233	-	1	NA	promoter-TSS (NM_027147)	promoter-TSS (NM_027147)	96	NM_027147	69638	Mm.372459	NM_027147	ENSMUSG00000028445	Enho	1110065P19Rik|2310040A07Rik	energy homeostasis associated	protein-coding
mm_50484.1	chr6	48988509	48988527	+	1	NA	exon (NM_172888, exon 1 of 5)	exon (NM_172888, exon 1 of 5)	1657	NM_172888	243377	Mm.446302	NM_172888	ENSMUSG00000039215	Svs1	9530003A11	seminal vesicle secretory protein 1	protein-coding
mm_61720.1	chr7	81835586	81835615	+	1	NA	Intergenic	Intergenic	-6169	NM_146193	83962	Mm.439893	NM_146193	ENSMUSG00000025103	Btbd1	1190005H08Rik	BTB (POZ) domain containing 1	protein-coding
mm_112608.1	chr13	14522512	14522519	+	1	NA	intron (NM_001081348, intron 1 of 28)	intron (NM_001081348, intron 1 of 28)	711	NM_001081348	94253	Mm.125298	NM_153130	ENSMUSG00000021301	Hecw1	9330116H24Rik|AV273951|E130207I19Rik|Nedl1	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	protein-coding
mm_61538.1	chr7	79273278	79273295	+	1	NA	promoter-TSS (NM_018811)	promoter-TSS (NM_018811)	20	NM_018811	54608	Mm.365490	NM_018811	ENSMUSG00000039202	Abhd2	2210009N18Rik|LABH2|Labh-2	abhydrolase domain containing 2	protein-coding
mm_75106.1	chr8	34146754	34146768	-	1	NA	promoter-TSS (NM_026609)	promoter-TSS (NM_026609)	-22	NM_026609	68192	Mm.34212	NM_026609	ENSMUSG00000031513	Leprotl1	1110067H13Rik|1520402O14Rik|AI854296	leptin receptor overlapping transcript-like 1	protein-coding
mm_101154.1	chr11	16951084	16951131	-	1	NA	promoter-TSS (NM_176982)	promoter-TSS (NM_176982)	175	NR_110421	72735	Mm.268598	NR_015469		Eldr	2810442I21Rik|4930500E12Rik|Fabl	Egfr long non-coding downstream RNA	ncRNA
mm_107598.1	chr12	49382677	49382691	+	1	NA	promoter-TSS (NM_008241)	promoter-TSS (NM_008241)	-199	NM_001160112	15228	Mm.4704	NM_008241	ENSMUSG00000020950	Foxg1	2900064B05Rik|BF-1|Bf1|Hfh9|Hfhbf1	forkhead box G1	protein-coding
mm_114092.1	chr13	54687310	54687323	+	1	NA	intron (NR_027395, intron 1 of 10)	CpG	492	NM_001146025	105239	Mm.25366	NM_134064	ENSMUSG00000034928	Rnf44	AI854545|mKIAA1100	ring finger protein 44	protein-coding
mm_154240.1	chr19	60581160	60581191	-	1	NA	promoter-TSS (NM_001172096)	promoter-TSS (NM_001172096)	-152	NM_001172096	78832	Mm.259026	NM_030197	ENSMUSG00000033417	Cacul1	2700078E11Rik|2810417M16Rik|9830127L17Rik|AI450346|D130033C15Rik	CDK2 associated, cullin domain 1	protein-coding
mm_85034.1	chr9	88482533	88482587	-	1	NA	promoter-TSS (NM_001284328)	promoter-TSS (NM_001284328)	-163	NM_001284328	56403	Mm.260545	NM_019666	ENSMUSG00000032423	Syncrip	2610109K23Rik|4632417O19Rik|GRY-RBP|Nsap1|Nsap1l|hnRNP Q|pp68	synaptotagmin binding, cytoplasmic RNA interacting protein	protein-coding
mm_27916.1	chr3	79531759	79531784	-	1	NA	intron (NM_001162999, intron 1 of 16)	intron (NM_001162999, intron 1 of 16)	35908	NM_001162999	329679	Mm.244005	NM_001162999	ENSMUSG00000061175	Fnip2	D630023B12Rik|mKIAA1450	folliculin interacting protein 2	protein-coding
mm_25038.1	chr3	98281476	98281492	+	1	NA	intron (NM_008256, intron 1 of 9)	intron (NM_008256, intron 1 of 9)	1053	NM_008256	15360	Mm.289131	NM_008256	ENSMUSG00000027875	Hmgcs2	1300002P16|mHS	3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2	protein-coding
mm_146374.1	chr18	82584817	82584831	+	1	NA	3' UTR (NM_010777, exon 7 of 7)	3' UTR (NM_010777, exon 7 of 7)	30316	NM_001025254	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_23570.1	chr3	63296165	63296171	+	1	NA	promoter-TSS (NM_001289463)	promoter-TSS (NM_001289463)	73	NM_001289463	17380	Mm.296022	NM_008604	ENSMUSG00000027820	Mme	6030454K05Rik|C85356|CALLA|CD10|NEP|SFE	membrane metallo endopeptidase	protein-coding
mm_19145.1	chr2	80524673	80524684	-	1	NA	intron (NM_016965, intron 18 of 30)	intron (NM_016965, intron 18 of 30)	56504	NM_001290745	50884	Mm.25203	NM_016965	ENSMUSG00000027002	Nckap1	C79304|H19|Hem-2|Hem2|Nap1|mKIAA0587|mh19|p125Nap1	NCK-associated protein 1	protein-coding
mm_26437.1	chr3	142620740	142620750	+	1	NA	promoter-TSS (NM_010260)	promoter-TSS (NM_010260)	82	NM_010260	14469	Mm.24038	NM_010260	ENSMUSG00000028270	Gbp2	-	guanylate binding protein 2	protein-coding
mm_112117.1	chr12	112829026	112829106	-	1	NA	5' UTR (NM_028023, exon 1 of 2)	5' UTR (NM_028023, exon 1 of 2)	323	NM_028023	71963	Mm.313185	NM_028023	ENSMUSG00000047832	Cdca4	2410018C03Rik|HEPP|SEI-3	cell division cycle associated 4	protein-coding
mm_31204.1	chr4	43727277	43727313	+	1	NA	promoter-TSS (NM_027511)	promoter-TSS (NM_027511)	97	NM_027511	100039781	Mm.18796	NM_027511	ENSMUSG00000071001	Hrct1	3830408D24Rik	histidine rich carboxyl terminus 1	protein-coding
mm_165018.1	chr19	29812983	29812991	-	1	NA	promoter-TSS (NM_177721)	promoter-TSS (NM_177721)	-13	NM_177721	240614	Mm.125503	NM_177721	ENSMUSG00000074909	Ranbp6	C630001B19	RAN binding protein 6	protein-coding
mm_106178.1	chr11	116694556	116694560	-	1	NA	exon (NM_009180, exon 1 of 9)	exon (NM_009180, exon 1 of 9)	102	NM_009180	20446	Mm.3947	NM_009180	ENSMUSG00000057286	St6galnac2	II|ST6GalNAc|Siat7|Siat7b	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2	protein-coding
mm_163537.1	chr13	13529272	13529307	+	1	NA	Intergenic	Intergenic	-61120	NM_010748	17101	Mm.342337	NM_010748	ENSMUSG00000019726	Lyst	D13Sfk13|beige|bg	lysosomal trafficking regulator	protein-coding
mm_95177.1	chr11	41498694	41498727	+	1	NA	Intergenic	Intergenic	502004	NM_177408	14406	Mm.5309	NM_008073	ENSMUSG00000020436	Gabrg2	GABAA-R|Gabrg-2|gamma2	gamma-aminobutyric acid (GABA) A receptor, subunit gamma 2	protein-coding
mm_93354.1	chr10	102836360	102836377	-	1	NA	Intergenic	AT_rich|Low_complexity|Low_complexity	192409	NM_172553	216285	Mm.19287	NM_172553	ENSMUSG00000036602	Alx1	AI314867|C130005I02|Cart1	ALX homeobox 1	protein-coding
mm_17371.1	chr2	26916324	26916365	-	1	NA	promoter-TSS (NM_013678)	promoter-TSS (NM_013678)	-77	NM_013678	20931	Mm.389260	NM_013678	ENSMUSG00000014873	Surf2	Surf-2	surfeit gene 2	protein-coding
mm_107652.1	chr12	52699234	52699242	+	1	NA	promoter-TSS (NM_198111)	promoter-TSS (NM_198111)	-145	NM_198111	238161	Mm.310822	NM_198111	ENSMUSG00000061603	Akap6	AI482140|Akapalpha|Akapbeta|PRKA	A kinase (PRKA) anchor protein 6	protein-coding
mm_636.1	chr1	40381280	40381295	+	1	NA	Intergenic	Intergenic	-48283	NM_001294171	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_93440.1	chr10	109833196	109833220	-	1	NA	intron (NM_001081035, intron 9 of 38)	intron (NM_001081035, intron 9 of 38)	167011	NM_001081035	260315	Mm.225050	NM_177797	ENSMUSG00000020181	Nav3	4732483H20Rik|9630020C08Rik|POMFIL1|Pomfil1p|mKIAA0938|unc53H3	neuron navigator 3	protein-coding
mm_109280.1	chr12	109547838	109547850	+	1	NA	intron (NR_027651, intron 5 of 8)	intron (NR_027651, intron 5 of 8)	2446	NR_003633	17263	Mm.289645	NM_144513	ENSMUSG00000021268	Meg3	2900016C05Rik|3110050O07Rik|6330408G06Rik|AI425946|AW108224|D12Bwg1266e|Gtl2|R74756|R75394	maternally expressed 3	ncRNA
mm_106575.1	chr11	120713726	120713748	-	1	NA	promoter-TSS (NM_016665)	promoter-TSS (NM_016665)	30	NM_016665	20892	Mm.259716	NM_016665	ENSMUSG00000025144	Cenpx	Stra13	centromere protein X	protein-coding
mm_46778.1	chr5	112419975	112419980	-	1	NA	3' UTR (NM_001253916, exon 17 of 17)	3' UTR (NM_001253916, exon 17 of 17)	-27764	NM_028386	72898	Mm.151745	NM_028386	ENSMUSG00000029348	Asphd2	2900006N09Rik|9230106G13Rik	aspartate beta-hydroxylase domain containing 2	protein-coding
mm_19470.1	chr2	92459590	92459602	-	1	NA	5' UTR (NM_211358, exon 1 of 2)	5' UTR (NM_211358, exon 1 of 2)	198	NM_211358	228368	Mm.273990	NM_145832	ENSMUSG00000049922	Slc35c1	E430007K15Rik|fuct1	solute carrier family 35, member C1	protein-coding
mm_74011.1	chr8	121127828	121127848	+	1	NA	5' UTR (NM_008024, exon 1 of 1)	5' UTR (NM_008024, exon 1 of 1)	153	NM_008024	14241	Mm.5111	NM_008024	ENSMUSG00000097084	Foxl1	FREAC7|Fkh6|fkh-6	forkhead box L1	protein-coding
mm_96287.1	chr11	63128974	63128990	+	1	NA	promoter-TSS (NM_001302258)	promoter-TSS (NM_001302258)	0	NM_001302258	18858	Mm.1237	NM_008885	ENSMUSG00000018217	Pmp22	22kDa|Gas-3|HNPP|Tr|trembler	peripheral myelin protein 22	protein-coding
mm_68337.1	chr7	106505173	106505215	-	1	NA	Intergenic	Intergenic	-64121	NR_003967	209380	Mm.461779	NM_001001318		Gm4759	EG209380	GTPase, very large interferon inducible 1 pseudogene	pseudo
mm_133489.1	chr16	90220748	90220771	+	1	NA	promoter-TSS (NM_011434)	promoter-TSS (NM_011434)	17	NM_011434	20655	Mm.276325	NM_011434	ENSMUSG00000022982	Sod1	B430204E11Rik|Cu/Zn-SOD|CuZnSOD|Ipo-1|Ipo1|SODC|Sod-1	superoxide dismutase 1, soluble	protein-coding
mm_79477.1	chr9	56950965	56950973	+	1	NA	promoter-TSS (NM_178374)	promoter-TSS (NM_178374)	45	NM_178374	66069	Mm.220984	NM_178374	ENSMUSG00000055334	Snupn	0610031A09Rik|Rnut1|Snupn1	snurportin 1	protein-coding
mm_60962.1	chr7	47700030	47700045	+	1	NA	Intergenic	Intergenic	-98665	NM_153067	233222	Mm.240142	NM_153067	ENSMUSG00000078698	Mrgpra3	Mrga3	MAS-related GPR, member A3	protein-coding
mm_118787.1	chr14	24108820	24108821	+	1	NA	Intergenic	T-rich|Low_complexity|Low_complexity	19943	NR_106069	102465697		NR_106069	ENSMUSG00000105723	Mir7210	mir-7210|mmu-mir-7210	microRNA 7210	ncRNA
mm_164439.1	chr16	49775237	49775240	+	1	NA	Intergenic	Intergenic	75944	NM_028680	73916	Mm.241276	NM_028680	ENSMUSG00000032965	Ift57	4833420A15Rik|Esrrbl1|Hippi|MHS4R2	intraflagellar transport 57	protein-coding
mm_46326.1	chr5	100820353	100820355	-	1	NA	intron (NM_172405, intron 1 of 8)	intron (NM_172405, intron 1 of 8)	581	NM_172405	70681	Mm.486560	NM_172405	ENSMUSG00000035234	Fam175a	3830405G04Rik|5630400M01Rik|AI506069|AL024423|AV118690|Ccdc98	family with sequence similarity 175, member A	protein-coding
mm_23961.1	chr3	84952270	84952291	+	1	NA	promoter-TSS (NM_080428)	promoter-TSS (NM_080428)	69	NM_080428	50754	Mm.196475	NM_080428	ENSMUSG00000028086	Fbxw7	1110001A17Rik|AGO|Cdc4|Fbw7|Fbwd6|Fbx30|Fbxo30|Fbxw6|SEL-10	F-box and WD-40 domain protein 7	protein-coding
mm_154389.1	chrM	12690	12701	+	1	NA	NA	Intergenic	NA	NA								
mm_53644.1	chr6	140623832	140623861	+	1	NA	exon (NM_009637, exon 1 of 9)	exon (NM_009637, exon 1 of 9)	344	NM_001005605	11569	Mm.86453	NM_009637	ENSMUSG00000030232	Aebp2	AU023766|B230313N05Rik	AE binding protein 2	protein-coding
mm_108241.1	chr12	78197051	78197061	+	1	NA	Intergenic	Intergenic	-29599	NM_172952	268566	Mm.341742	NM_145965	ENSMUSG00000047454	Gphn	5730552E08Rik|AI662856|BC027112|C230040D23|GPH|GPHRYN|geph	gephyrin	protein-coding
mm_82683.1	chr9	22186260	22186260	-	1	NA	intron (NR_030448, intron 1 of 4)	intron (NR_030448, intron 1 of 4)	-1906	NM_001033813	619310	Mm.335016	NM_001033813	ENSMUSG00000074472	Zfp872	9530015I07Rik	zinc finger protein 872	protein-coding
mm_86631.1	chr10	13993816	13993828	+	1	NA	intron (NM_010437, intron 1 of 8)	intron (NM_010437, intron 1 of 8)	27443	NM_010437	15273	Mm.42157	NM_010437	ENSMUSG00000015501	Hivep2	Gm20114|MIBP1|Schnurri-2|Shn-2	human immunodeficiency virus type I enhancer binding protein 2	protein-coding
mm_40106.1	chr5	34761647	34761660	+	1	NA	promoter-TSS (NM_010414)	promoter-TSS (NM_010414)	-87	NM_010414	15194	Mm.209071	NM_010414	ENSMUSG00000029104	Htt	AI256365|C430023I11Rik|Hd|Hdh|IT15	huntingtin	protein-coding
mm_64556.1	chr7	144742076	144742083	+	1	NA	Intergenic	Intergenic	-3487	NM_001242349	101772	Mm.26700	NM_178642	ENSMUSG00000031075	Ano1	Tmem16a	anoctamin 1, calcium activated chloride channel	protein-coding
mm_30459.1	chr3	153944462	153944514	-	1	NA	5' UTR (NM_007382, exon 1 of 12)	5' UTR (NM_007382, exon 1 of 12)	155	NM_007382	11364	Mm.10530	NM_007382	ENSMUSG00000062908	Acadm	AU018656|MCAD	acyl-Coenzyme A dehydrogenase, medium chain	protein-coding
mm_132965.1	chr16	50732826	50732866	+	1	NA	promoter-TSS (NR_028300)	promoter-TSS (NR_028300)	-73	NR_028300	68190	Mm.139089	NR_028300		Dubr	5330426P16Rik|Dum	Dppa2 upstream binding RNA	ncRNA
mm_28902.1	chr3	98335653	98335656	-	1	NA	intron (NM_016966, intron 1 of 11)	intron (NM_016966, intron 1 of 11)	4315	NM_016966	236539	Mm.16898	NM_016966	ENSMUSG00000053398	Phgdh	3-PGDH|3PGDH|4930479N23|A10|PGAD|PGD|PGDH|SERA	3-phosphoglycerate dehydrogenase	protein-coding
mm_126615.1	chr15	83100282	83100303	+	1	NA	promoter-TSS (NM_023475)	promoter-TSS (NM_023475)	87	NM_023475	68607	Mm.30056	NM_023475	ENSMUSG00000058586	Serhl	0610008B10Rik|1110019M09Rik|AU019786	serine hydrolase-like	protein-coding
mm_67270.1	chr7	75780760	75780770	-	1	NA	Intergenic	Intergenic	-67573	NM_001122780	207952	Mm.206223	NM_029652	ENSMUSG00000055652	Klhl25	2810402K13Rik|BC027373|Enc-1	kelch-like 25	protein-coding
mm_20630.1	chr2	131994185	131994207	-	1	NA	3' UTR (NM_175445, exon 11 of 11)	3' UTR (NM_175445, exon 11 of 11)	35792	NM_175445	215653	Mm.204737	NM_175445	ENSMUSG00000027339	Rassf2	3830431H01Rik|9030412M04Rik|AI852669|AW495050	Ras association (RalGDS/AF-6) domain family member 2	protein-coding
mm_15469.1	chr2	157471009	157471037	+	1	NA	3' UTR (NM_001025395, exon 14 of 14)	3' UTR (NM_001025395, exon 14 of 14)	46730	NM_001025395	20779	Mm.22845	NM_009271	ENSMUSG00000027646	Src	AW259666|pp60c-src	Rous sarcoma oncogene	protein-coding
mm_75454.1	chr8	47713896	47713908	-	1	NA	promoter-TSS (NM_172407)	promoter-TSS (NM_172407)	29	NM_172407	70925	Mm.393807	NM_172407	ENSMUSG00000038069	Cdkn2aip	4921511I16Rik|AW208986|CARF	CDKN2A interacting protein	protein-coding
mm_24331.1	chr3	89459326	89459360	+	1	NA	promoter-TSS (NM_027348)	promoter-TSS (NM_027348)	225	NM_026784	68603	Mm.34242	NM_026784	ENSMUSG00000027952	Pmvk	1110011E12Rik|2900002L22Rik|AV001327|PMK|PMKA|PMKASE	phosphomevalonate kinase	protein-coding
mm_96882.1	chr11	70432553	70432557	+	1	NA	promoter-TSS (NM_001271358)	promoter-TSS (NM_001271358)	-25	NM_001271360	216869	Mm.203747	NM_145429	ENSMUSG00000060216	Arrb2	AI326910|AW122872	arrestin, beta 2	protein-coding
mm_6694.1	chr1	80726354	80726357	-	1	NA	intron (NM_175291, intron 1 of 55)	intron (NM_175291, intron 1 of 55)	32198	NM_175291	210293	Mm.133473	NM_175291	ENSMUSG00000038608	Dock10	9330153B10Rik|A630054M16Rik|Jr4|Jr5|R75174|ZIZ3|Zizimin3|mKIAA0694	dedicator of cytokinesis 10	protein-coding
mm_18890.1	chr2	76709833	76709841	-	1	NA	exon (NM_011652, exon 307 of 313)	exon (NM_011652, exon 307 of 313)	34522	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_163161.1	chr11	84160922	84160923	+	1	NA	intron (NM_001037932, intron 3 of 6)	intron (NM_001037932, intron 3 of 6)	6554	NM_001037932	628813	Mm.390389	NM_001037932	ENSMUSG00000051452	Gm11437	AI463690|OTTMUSG00000000997	predicted gene 11437	protein-coding
mm_39947.1	chr5	31912290	31912297	+	1	NA	intron (NM_144541, intron 7 of 11)	intron (NM_144541, intron 7 of 11)	214243	NM_144541	107976	Mm.482126	NM_144541	ENSMUSG00000052139	Bre	6030405P19Rik|AI429776|B830038C02Rik	brain and reproductive organ-expressed protein	protein-coding
mm_30970.1	chr4	34485770	34485780	+	1	NA	Intergenic	Intergenic	-64840	NM_001007589	433693	Mm.389532	NM_026019	ENSMUSG00000028291	Akirin2	2700059D21Rik|AA114675|AA522011|AU019887|Akirin-2	akirin 2	protein-coding
mm_86515.1	chr10	7681186	7681196	+	1	NA	promoter-TSS (NR_033219)	promoter-TSS (NR_033219)	-18	NM_010690	16798	Mm.34083	NM_010690	ENSMUSG00000040021	Lats1	AW208599	large tumor suppressor	protein-coding
mm_70136.1	chr7	143250466	143250472	-	1	NA	non-coding (NR_001461, exon 1 of 1)	non-coding (NR_001461, exon 1 of 1)	46078	NR_001461	63830	Mm.356096	NR_001461	ENSMUSG00000101609	Kcnq1ot1	Kvlqt1-as|Lit1|Tssc8	KCNQ1 overlapping transcript 1	ncRNA
mm_132309.1	chr16	33684539	33684554	+	1	NA	promoter-TSS (NM_175256)	promoter-TSS (NM_175256)	80	NM_175256	77446	Mm.245741	NM_172934	ENSMUSG00000075254	Heg1	4632417D23Rik|5530401I02Rik|9530025L16Rik|BC038614|Gm629|OTTMUSG00000027315	heart development protein with EGF-like domains 1	protein-coding
mm_12213.1	chr2	67445976	67445983	+	1	NA	promoter-TSS (NM_001083919)	promoter-TSS (NM_001083919)	-23	NM_001083919	241431	Mm.261043	NM_001024618	ENSMUSG00000027022	Xirp2	2310003D02Rik|2310008C07Rik|A530024P18Rik|AI452089|Cmya3|Gm352|Xin2	xin actin-binding repeat containing 2	protein-coding
mm_149363.1	chr19	11292424	11292437	+	1	NA	intron (NR_045317, intron 1 of 2)	RLTR9E|LTR|ERVK	-8617	NM_183190	269063	Mm.268940	NM_183190	ENSMUSG00000054523	Ms4a5	-	membrane-spanning 4-domains, subfamily A, member 5	protein-coding
mm_79573.1	chr9	58134354	58134360	+	1	NA	promoter-TSS (NM_001162479)	promoter-TSS (NM_001162479)	282	NM_001162476	20897	Mm.10801	NM_009291	ENSMUSG00000032327	Stra6	AI891933	stimulated by retinoic acid gene 6	protein-coding
mm_56756.1	chr6	116073150	116073163	-	1	NA	intron (NM_177412, intron 3 of 5)	intron (NM_177412, intron 3 of 5)	-78151	NM_026376	67784	Mm.3085	NM_026376	ENSMUSG00000030123	Plxnd1	6230425C21Rik|b2b1863Clo|b2b553Clo	plexin D1	protein-coding
mm_165758.1	chr3	114030474	114030480	+	1	NA	promoter-TSS (NM_007729)	promoter-TSS (NM_007729)	-63	NM_007729	12814	Mm.209715	NM_007729	ENSMUSG00000027966	Col11a1	C530001D20Rik|cho	collagen, type XI, alpha 1	protein-coding
mm_113345.1	chr13	31806628	31806650	+	1	NA	promoter-TSS (NM_008592)	promoter-TSS (NM_008592)	-7	NM_008592	17300	Mm.12949	NM_008592	ENSMUSG00000050295	Foxc1	FREAC3|Fkh1|Mf1|Mf4|ch|fkh-1|frkhda	forkhead box C1	protein-coding
mm_172285.1	chr6	93376741	93376749	+	1	NA	Intergenic	L1Md_Gf|LINE|L1	436163	NR_015530	330385	Mm.483472	NR_015530	ENSMUSG00000097462	9530026P05Rik	B430306B02	RIKEN cDNA 9530026P05 gene	ncRNA
mm_82260.1	chr9	5311490	5311504	-	1	NA	intron (NM_007609, intron 1 of 8)	RLTR17|LTR|ERVK	2648	NM_007609	12363	Mm.1569	NM_007609	ENSMUSG00000033538	Casp4	CASP-11|CASP-4|Casp11|Caspl|ich-3	caspase 4, apoptosis-related cysteine peptidase	protein-coding
mm_72990.1	chr8	93011569	93011590	+	1	NA	Intergenic	Intergenic	36613	NM_001013764	244595	Mm.390089	NM_001013764	ENSMUSG00000071047	Ces1a	Ces1l|EG244595|Gm4976	carboxylesterase 1A	protein-coding
mm_14362.1	chr2	129616438	129616451	+	1	NA	exon (NM_007547, exon 4 of 8)	exon (NM_007547, exon 4 of 8)	23275	NM_001291022	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_96238.1	chr11	62551739	62551739	+	1	NA	promoter-TSS (NM_001313984)	promoter-TSS (NM_001313984)	8	NM_001313984	22187	Mm.371592	NM_011664	ENSMUSG00000019505	Ubb	AL033289|Rps27a|Uba52|Ubb2|Ubc	ubiquitin B	protein-coding
mm_118420.1	chr14	7818056	7818064	+	1	NA	5' UTR (NM_001081427, exon 1 of 46)	5' UTR (NM_001081427, exon 1 of 46)	103	NM_134080	286940	Mm.489652	NM_134080	ENSMUSG00000025278	Flnb	AL024016|Fln-b	filamin, beta	protein-coding
mm_63063.1	chr7	122079770	122079773	+	1	NA	3' UTR (NM_138589, exon 7 of 7)	3' UTR (NM_138589, exon 7 of 7)	12573	NM_138589	28018	Mm.282122	NM_138589	ENSMUSG00000030870	Ubfd1	AI467302|D7Wsu105e|D7Wsu128e|Ubph	ubiquitin family domain containing 1	protein-coding
mm_60747.1	chr7	45459662	45459688	+	1	NA	5' UTR (NM_010240, exon 1 of 4)	5' UTR (NM_010240, exon 1 of 4)	211	NM_010240	14325	Mm.30357	NM_010240	ENSMUSG00000050708	Ftl1	Ftl|Ftl-1|L-ferritin	ferritin light polypeptide 1	protein-coding
mm_137890.1	chr17	31681003	31681020	+	1	NA	exon (NM_001278570, exon 3 of 3)	exon (NM_001278570, exon 3 of 3)	3080	NM_001278570	12954	Mm.1228	NM_013501	ENSMUSG00000024041	Cryaa	Acry-1|Crya-1|Crya1|DAcry-1|lop18	crystallin, alpha A	protein-coding
mm_152835.1	chr19	23273865	23273884	-	1	NA	promoter-TSS (NM_001252684)	promoter-TSS (NM_001252684)	23	NM_153808	226026	Mm.23267	NM_153808	ENSMUSG00000024943	Smc5	MLZ-453|SMC-5|Smc5l1|mKIAA0594|mSMC5	structural maintenance of chromosomes 5	protein-coding
mm_1809.1	chr1	81077485	81077499	+	1	NA	5' UTR (NM_172849, exon 1 of 5)	5' UTR (NM_172849, exon 1 of 5)	175	NM_172849	241134	Mm.313904	NM_172849	ENSMUSG00000054976	Nyap2	9430031J16Rik|Jr6|Kiaa1486	neuronal tyrosine-phophorylated phosphoinositide 3-kinase adaptor 2	protein-coding
mm_145545.1	chr18	60808232	60808286	+	1	NA	exon (NM_010545, exon 3 of 8)	exon (NM_010545, exon 3 of 8)	-3817	NR_039567	100628611		NR_039567	ENSMUSG00000093327	Mir5107	mir-5107|mmu-mir-5107|mu-mir-5107	microRNA 5107	ncRNA
mm_85140.1	chr9	95795975	95795988	-	1	NA	intron (NM_001033210, intron 1 of 15)	intron (NM_001033210, intron 1 of 15)	-45623	NM_011643	22063	Mm.149633	NM_011643	ENSMUSG00000032839	Trpc1	Mtrp1|Trp1|Trrp1	transient receptor potential cation channel, subfamily C, member 1	protein-coding
mm_128246.1	chr15	36609135	36609139	-	1	NA	promoter-TSS (NM_008774)	promoter-TSS (NM_008774)	-164	NM_008774	18458	Mm.371570	NM_008774	ENSMUSG00000022283	Pabpc1	PABP|Pabp1|PabpI|Pabpl1|ePAB	poly(A) binding protein, cytoplasmic 1	protein-coding
mm_4187.1	chr1	171160644	171160652	+	1	NA	3' UTR (NM_008623, exon 8 of 8)	3' UTR (NM_008623, exon 8 of 8)	5130	NM_001315500	17528	Mm.9986	NM_008623	ENSMUSG00000056569	Mpz	Mpp|P-zero|P0	myelin protein zero	protein-coding
mm_143049.1	chr17	56905800	56905805	-	1	NA	exon (NM_022328, exon 4 of 12)	exon (NM_022328, exon 4 of 12)	29586	NM_022328	64144	Mm.148748	NM_022328	ENSMUSG00000024212	Mllt1	AA407901|BAM11|ENL|LTG19	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 1	protein-coding
mm_31992.1	chr4	89688039	89688085	+	1	NA	promoter-TSS (NM_175647)	promoter-TSS (NM_175647)	-136	NM_175647	242523	Mm.130167	NM_175647	ENSMUSG00000043753	Dmrta1	Dmrt4	doublesex and mab-3 related transcription factor like family A1	protein-coding
mm_100869.1	chr11	5898772	5898788	-	1	NA	promoter-TSS (NM_022879)	promoter-TSS (NM_022879)	2	NM_022879	17898	Mm.46514	NM_022879	ENSMUSG00000020469	Myl7	MLC-2alpha|MLC2a|MYL2A|Mylc2a|RLC-A	myosin, light polypeptide 7, regulatory	protein-coding
mm_38498.1	chr4	141060537	141060567	-	1	NA	promoter-TSS (NM_001145958)	promoter-TSS (NM_001145958)	-7	NM_001145958	230872	Mm.80685	NM_172122	ENSMUSG00000040860	Crocc	-	ciliary rootlet coiled-coil, rootletin	protein-coding
mm_16430.1	chr2	180392035	180392037	+	1	NA	intron (NR_045331, intron 3 of 3)	intron (NR_045331, intron 3 of 3)	2988	NR_029528	387136		NR_029528	ENSMUSG00000070144	Mir1a-1	Mir1-1|Mirn1-1|Mirn1b|Mirn1c|Mirn1d|mir-1a-1|mmu-mir-1-1|mmu-mir-1a-1	microRNA 1a-1	ncRNA
mm_64979.1	chr7	16910043	16910074	-	1	NA	3' UTR (NM_008967, exon 2 of 2)	3' UTR (NM_008967, exon 2 of 2)	3568	NM_008967	19222	Mm.287572	NM_008967	ENSMUSG00000043017	Ptgir	IP|PGI2	prostaglandin I receptor (IP)	protein-coding
mm_103470.1	chr11	76479169	76479199	-	1	NA	intron (NM_001346670, intron 2 of 21)	intron (NM_001346670, intron 2 of 21)	-10719	NM_001291186	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_162355.1	chr1	58393367	58393373	-	1	NA	intron (NM_025824, intron 1 of 11)	CpG	234	NM_025824	66882	Mm.21848	NM_025824	ENSMUSG00000051223	Bzw1	1200015E15Rik|mKIAA0005	basic leucine zipper and W2 domains 1	protein-coding
mm_53015.1	chr6	123283393	123283417	+	1	NA	3' UTR (NM_019948, exon 6 of 6)	3' UTR (NM_019948, exon 6 of 6)	6466	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_22574.1	chr3	10350973	10350981	+	1	NA	intron (NM_025512, intron 1 of 7)	intron (NM_025512, intron 1 of 7)	340	NM_001331015	66361	Mm.371617	NM_025512	ENSMUSG00000039795	Zfand1	2310008M20Rik|AW048890	zinc finger, AN1-type domain 1	protein-coding
mm_7937.1	chr1	133914698	133914717	-	1	NA	exon (NM_054077, exon 2 of 3)	exon (NM_054077, exon 2 of 3)	6694	NM_054077	116847	Mm.214514	NM_054077	ENSMUSG00000041577	Prelp	7330409J17Rik|SLRR2A	proline arginine-rich end leucine-rich repeat	protein-coding
mm_10401.1	chr2	13575534	13575557	+	1	NA	exon (NM_011701, exon 2 of 9)	exon (NM_011701, exon 2 of 9)	1234	NM_011701	22352	Mm.268000	NM_011701	ENSMUSG00000026728	Vim	-	vimentin	protein-coding
mm_170927.1	chr2	40127904	40127905	-	1	NA	Intergenic	Intergenic	-901566	NM_024209	67857	Mm.389242	NM_024209	ENSMUSG00000026753	Ppp6c	2310003C10Rik	protein phosphatase 6, catalytic subunit	protein-coding
mm_57544.1	chr6	126645785	126645800	-	1	NA	promoter-TSS (NM_010595)	promoter-TSS (NM_010595)	9	NM_010595	16485	Mm.40424	NM_010595	ENSMUSG00000047976	Kcna1	AI840627|Kca1-1|Kv1.1|MBK1|Mk-1|Shak|mceph	potassium voltage-gated channel, shaker-related subfamily, member 1	protein-coding
mm_40485.1	chr5	55624932	55624953	+	1	NA	Intergenic	Intergenic	1274950	NR_038045	330086	Mm.254449	NM_177871	ENSMUSG00000105912	Gm10440	D130065D13|ENSMUSG00000072936	predicted gene 10440	ncRNA
mm_81793.1	chr9	115088835	115088847	+	1	NA	intron (NM_148958, intron 1 of 9)	intron (NM_148958, intron 1 of 9)	21562	NM_148958	74486	Mm.458474	NM_148958	ENSMUSG00000040875	Osbpl10	4933433D06Rik|C820004B04Rik|OPR-10|ORP-10	oxysterol binding protein-like 10	protein-coding
mm_120076.1	chr14	57524735	57524804	+	1	NA	promoter-TSS (NM_145837)	promoter-TSS (NM_145837)	-60	NM_145837	239114	Mm.390726	NM_145837	ENSMUSG00000050222	Il17d	AI462269|IL-17D	interleukin 17D	protein-coding
mm_16632.1	chr2	5714464	5714487	-	1	NA	5' UTR (NM_001290375, exon 1 of 11)	5' UTR (NM_001290375, exon 1 of 11)	287	NM_001290374	227541	Mm.191949	NM_177343	ENSMUSG00000039145	Camk1d	A630059D12Rik|CKLiK|CaMKIdelta|E030025C11Rik|mCKLiK	calcium/calmodulin-dependent protein kinase ID	protein-coding
mm_53919.1	chr6	4086804	4086819	-	1	NA	5' UTR (NM_009748, exon 1 of 4)	5' UTR (NM_009748, exon 1 of 4)	116	NM_009748	12068	Mm.286457	NM_009748	ENSMUSG00000032757	Bet1	AW555236|Bet-1	Bet1 golgi vesicular membrane trafficking protein	protein-coding
mm_165503.1	chr2	167775156	167775163	-	1	NA	Intergenic	Intergenic	83982	NR_015500	329562	Mm.123101	NM_177851	ENSMUSG00000006462	A530013C23Rik	-	RIKEN cDNA A530013C23 gene	ncRNA
mm_100231.1	chr11	117199704	117199729	+	1	NA	promoter-TSS (NM_001113486)	promoter-TSS (NM_001113486)	55	NM_001113486	53860	Mm.38450	NM_017380	ENSMUSG00000059248	Sept9	MSF1|Msf|PNUTL4|Sint1	septin 9	protein-coding
mm_99327.1	chr11	101460001	101460013	+	1	NA	3' UTR (NM_012037, exon 6 of 6)	3' UTR (NM_012037, exon 6 of 6)	6192	NM_012037	26949	Mm.29210	NM_012037	ENSMUSG00000034993	Vat1	VAT-1	vesicle amine transport 1	protein-coding
mm_96322.1	chr11	64079479	64079527	+	1	NA	promoter-TSS (NM_178379)	promoter-TSS (NM_178379)	19	NR_033780	66456	Mm.124828	NR_033780	ENSMUSG00000087497	2810001G20Rik	AW045514	RIKEN cDNA 2810001G20 gene	ncRNA
mm_79481.1	chr9	56994890	56994918	+	1	NA	promoter-TSS (NM_019651)	promoter-TSS (NM_019651)	-64	NM_019651	56294	Mm.325643	NM_019651	ENSMUSG00000032290	Ptpn9	MEG2	protein tyrosine phosphatase, non-receptor type 9	protein-coding
mm_39500.1	chr5	21186344	21186354	+	1	NA	promoter-TSS (NM_175437)	promoter-TSS (NM_175437)	82	NM_175437	212167	Mm.121705	NM_175437	ENSMUSG00000039934	Gsap	A530088I07Rik|Pion	gamma-secretase activating protein	protein-coding
mm_105622.1	chr11	106789136	106789152	-	1	NA	promoter-TSS (NM_177088)	promoter-TSS (NM_177088)	-108	NM_177088	320162	Mm.30524	NM_177088	ENSMUSG00000018372	Cep95	4732496G21Rik|AI118346|AI448335|Ccdc45|D330027A14Rik|F630025I20Rik	centrosomal protein 95	protein-coding
mm_107543.1	chr12	40651991	40652010	+	1	NA	intron (NM_172803, intron 8 of 52)	MTD|LTR|ERVL-MaLR	205947	NM_172803	238130	Mm.341423	NM_172803	ENSMUSG00000035954	Dock4	5330406C03|6330411N01Rik|AF263288|C030023J22|mKIAA0716	dedicator of cytokinesis 4	protein-coding
mm_132650.1	chr16	41533000	41533069	+	1	NA	promoter-TSS (NM_175548)	promoter-TSS (NM_175548)	208	NM_001347236	268890	Mm.310524	NM_175548	ENSMUSG00000061080	Lsamp	5430428I19|AW046674|B130007O04Rik|D930023J12Rik|Lam|Lamp	limbic system-associated membrane protein	protein-coding
mm_44992.1	chr5	38158985	38158995	-	1	NA	exon (NM_010942, exon 2 of 5)	exon (NM_010942, exon 2 of 5)	477	NM_010942	18196	Mm.7414	NM_010942	ENSMUSG00000029126	Nsg1	Neep21|m234|p21	neuron specific gene family member 1	protein-coding
mm_127056.1	chr15	97044172	97044189	+	1	NA	intron (NM_027052, intron 1 of 15)	intron (NM_027052, intron 1 of 15)	11776	NM_027052	69354	Mm.250980	NM_027052	ENSMUSG00000022464	Slc38a4	1110012E16Rik|1700012A18Rik|Ata3|mATA3|mNAT3	solute carrier family 38, member 4	protein-coding
mm_145388.1	chr18	57133448	57133462	+	1	NA	5' UTR (NM_001001979, exon 1 of 25)	5' UTR (NM_001001979, exon 1 of 25)	365	NM_001001979	70417	Mm.297863	NM_001001979	ENSMUSG00000024593	Megf10	3000002B06Rik|Gm331	multiple EGF-like-domains 10	protein-coding
mm_106037.1	chr11	116078427	116078464	-	1	NA	promoter-TSS (NM_001009573)	promoter-TSS (NM_001009573)	-484	NM_001009573	70450	Mm.259460	NM_001009573	ENSMUSG00000057948	Unc13d	2610108D09Rik|Jinx|Munc13-4|mFLJ00067	unc-13 homolog D (C. elegans)	protein-coding
mm_97648.1	chr11	79412058	79412105	+	1	NA	exon (NM_010897, exon 10 of 58)	exon (NM_010897, exon 10 of 58)	71950	NR_045305	104522	Mm.436987	NR_045305	ENSMUSG00000091523	AU040972	AU040954	expressed sequence AU040972	ncRNA
mm_132185.1	chr16	32430608	32430618	+	1	NA	promoter-TSS (NM_009981)	promoter-TSS (NM_009981)	-308	NM_009981	13026	Mm.98775	NM_009981	ENSMUSG00000005615	Pcyt1a	CTalpha|Cctalpha|Ctpct|Cttalpha	phosphate cytidylyltransferase 1, choline, alpha isoform	protein-coding
mm_54785.1	chr6	41544835	41544857	-	1	NA	Intergenic	MIRb|SINE|MIR	23070	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_159763.1	chr5	93148403	93148403	+	1	NA	exon (NM_001310669, exon 3 of 11)	exon (NM_001310669, exon 3 of 11)	54987	NM_001347377	52398	Mm.394184	NM_001009818	ENSMUSG00000058013	Sept11	6230410I01Rik|AW548875|D5Ertd606e	septin 11	protein-coding
mm_99748.1	chr11	106674963	106675000	+	1	NA	intron (NM_001305157, intron 13 of 15)	intron (NM_001305157, intron 13 of 15)	40300	NM_001305158	18613	Mm.343951	NM_008816	ENSMUSG00000020717	Pecam1	C85791|Cd31|PECAM-1|Pecam	platelet/endothelial cell adhesion molecule 1	protein-coding
mm_98726.1	chr11	96351870	96351874	+	1	NA	exon (NM_134032, exon 1 of 2)	exon (NM_134032, exon 1 of 2)	240	NM_134032	103889	Mm.281153	NM_134032	ENSMUSG00000075588	Hoxb2	AI894218|Hox-2.8|Hoxbes2	homeobox B2	protein-coding
mm_139946.1	chr17	71204532	71204554	+	1	NA	promoter-TSS (NM_001164885)	promoter-TSS (NM_001164885)	-111	NM_001164885	64898	Mm.227924	NM_022882	ENSMUSG00000024052	Lpin2	2610511G02Rik|AI481352|AW742896	lipin 2	protein-coding
mm_8262.1	chr1	139255712	139255728	-	1	NA	intron (NM_133239, intron 5 of 11)	intron (NM_133239, intron 5 of 11)	121356	NM_133239	170788	Mm.95700	NM_133239	ENSMUSG00000063681	Crb1	7530426H14Rik|A930008G09Rik	crumbs family member 1, photoreceptor morphogenesis associated	protein-coding
mm_117576.1	chr13	86046902	86046904	-	1	NA	promoter-TSS (NM_007749)	promoter-TSS (NM_007749)	-108	NM_007749	12867	Mm.378898	NM_007749	ENSMUSG00000017778	Cox7c	COXVIIc|Cox7c1	cytochrome c oxidase subunit VIIc	protein-coding
mm_168308.1	chr11	107512308	107512308	-	1	NA	Intergenic	B1_Mus2|SINE|Alu	32780	NM_025894	66997	Mm.491171	NM_025894	ENSMUSG00000020720	Psmd12	1500002F15Rik|AI480719|P55	proteasome (prosome, macropain) 26S subunit, non-ATPase, 12	protein-coding
mm_102773.1	chr11	68386806	68386819	-	1	NA	promoter-TSS (NM_008744)	promoter-TSS (NM_008744)	14	NM_008744	18208	Mm.39095	NM_008744	ENSMUSG00000020902	Ntn1	AI561871|BC019633|Netrin-1	netrin 1	protein-coding
mm_14982.1	chr2	152160136	152160136	+	1	NA	Intergenic	B4|SINE|B4	16527	NM_009328	21407	Mm.3881	NM_009328	ENSMUSG00000068079	Tcf15	Meso1|bHLH-EC2	transcription factor 15	protein-coding
mm_145917.1	chr18	66975045	66975056	+	1	NA	Intergenic	RMER17C|LTR|ERVK	-25089	NR_040461	100503582	Mm.329508	NR_040461		Gm19784	-	predicted gene, 19784	ncRNA
mm_119609.1	chr14	51104951	51105041	+	1	NA	exon (NM_201239, exon 2 of 2)	exon (NM_201239, exon 2 of 2)	8996	NM_201239	58809	Mm.202665	NM_021472	ENSMUSG00000021876	Rnase4	C730049F20Rik|Rab1	ribonuclease, RNase A family 4	protein-coding
mm_121154.1	chr14	102720811	102720815	+	1	NA	Intergenic	Intergenic	261819	NR_039592	100628599		NR_039592	ENSMUSG00000092901	Mir5130	mir-5130|mmu-mir-5130|mu-mir-5130	microRNA 5130	ncRNA
mm_57785.1	chr6	129269568	129269579	-	1	NA	intron (NM_001033122, intron 4 of 4)	intron (NM_001033122, intron 4 of 4)	5796	NM_001033122	12515	Mm.74745	NM_001033122	ENSMUSG00000030156	Cd69	5830438K24Rik|AI452015|AIM|VEA	CD69 antigen	protein-coding
mm_166090.1	chr4	139821645	139821645	+	1	NA	intron (NM_011039, intron 4 of 8)	CpG	11323	NM_011039	18509	Mm.218760	NM_011039	ENSMUSG00000028736	Pax7	Pax-7	paired box 7	protein-coding
mm_103590.1	chr11	78245675	78245716	-	1	NA	promoter-TSS (NM_009143)	promoter-TSS (NM_009143)	8	NM_009297	20926	Mm.20755	NM_009297	ENSMUSG00000002052	Supt6	5131400N11Rik|AI132449|SPT6|Supt6h|mKIAA0162	suppressor of Ty 6	protein-coding
mm_55747.1	chr6	77979731	77979735	-	1	NA	promoter-TSS (NM_145732)	promoter-TSS (NM_145732)	-66	NM_009819	12386	Mm.34637	NM_009819	ENSMUSG00000063063	Ctnna2	AI481747|Catna|Catna2|cdf|chp	catenin (cadherin associated protein), alpha 2	protein-coding
mm_51946.1	chr6	91726111	91726132	+	1	NA	exon (NM_009320, exon 5 of 15)	exon (NM_009320, exon 5 of 15)	42054	NM_009320	21366	Mm.395650	NM_009320	ENSMUSG00000030096	Slc6a6	AA589629|C80501|Taut	solute carrier family 6 (neurotransmitter transporter, taurine), member 6	protein-coding
mm_115263.1	chr13	110563225	110563229	+	1	NA	Intergenic	Intergenic	168183	NM_152804	20620	Mm.380	NM_152804	ENSMUSG00000021701	Plk2	Snk	polo-like kinase 2	protein-coding
mm_164665.1	chr17	44247488	44247490	+	1	NA	intron (NM_172621, intron 3 of 5)	B4|SINE|B4	58917	NM_172621	224796	Mm.37666	NM_172621	ENSMUSG00000023959	Clic5	5730531E12Rik|B330005L24|Gm322|jbg	chloride intracellular channel 5	protein-coding
mm_129148.1	chr15	76206310	76206357	-	1	NA	promoter-TSS (NM_201389)	promoter-TSS (NM_201389)	-12	NM_001163540	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
mm_21886.1	chr2	166155243	166155251	-	1	NA	promoter-TSS (NM_001252578)	promoter-TSS (NM_001252578)	38	NM_001252578	72043	Mm.1011	NM_028072	ENSMUSG00000006800	Sulf2	2010004N24Rik|AU020235|MSulf-2|mKIAA1247	sulfatase 2	protein-coding
mm_112364.1	chr12	119160578	119160589	-	1	NA	Intergenic	Intergenic	77693	NM_177290	320910	Mm.217000	NM_177290	ENSMUSG00000025321	Itgb8	4832412O06Rik	integrin beta 8	protein-coding
mm_42800.1	chr5	121712069	121712071	+	1	NA	exon (NM_009125, exon 1 of 25)	exon (NM_009125, exon 1 of 25)	461	NM_009125	20239	Mm.260900	NM_009125	ENSMUSG00000042605	Atxn2	9630045M23Rik|ATX2|AW544490|Sca2	ataxin 2	protein-coding
mm_103492.1	chr11	76571264	76571273	-	1	NA	5' UTR (NM_198895, exon 1 of 23)	5' UTR (NM_198895, exon 1 of 23)	116	NM_198895	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_92886.1	chr10	82764037	82764080	-	1	NA	promoter-TSS (NM_010914)	promoter-TSS (NM_010914)	83	NM_010914	18045	Mm.245998	NM_010914	ENSMUSG00000020248	Nfyb	AA985999|Cbf-A	nuclear transcription factor-Y beta	protein-coding
mm_91354.1	chr10	27616930	27616937	-	1	NA	promoter-TSS (NM_008481)	promoter-TSS (NM_008481)	9	NM_008481	16773	Mm.256087	NM_008481	ENSMUSG00000019899	Lama2	5830440B04|dy|mKIAA4087|mer|merosin	laminin, alpha 2	protein-coding
mm_26912.1	chr3	20035286	20035325	-	1	NA	promoter-TSS (NM_001146323)	promoter-TSS (NM_001146323)	5	NM_001146323	12807	Mm.291533	NM_080634	ENSMUSG00000027615	Hps3	coa	Hermansky-Pudlak syndrome 3	protein-coding
mm_15626.1	chr2	162931521	162931536	+	1	NA	promoter-TSS (NM_026499)	promoter-TSS (NM_026499)	20	NM_026499	67996	Mm.24042	NM_026499	ENSMUSG00000016921	Srsf6	1210001E11Rik|AI314910|AW146126|Sfrs6	serine/arginine-rich splicing factor 6	protein-coding
mm_161488.1	chr15	85042850	85042850	+	1	NA	intron (NM_133750, intron 1 of 8)	intron (NM_133750, intron 1 of 8)	5788	NM_133750	73225	Mm.247535	NM_133750	ENSMUSG00000022434	Fam118a	-	family with sequence similarity 118, member A	protein-coding
mm_87803.1	chr10	60300532	60300582	+	1	NA	exon (NM_011179, exon 13 of 15)	exon (NM_011179, exon 13 of 15)	16096	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_46573.1	chr5	107289433	107289443	-	1	NA	5' UTR (NM_011578, exon 1 of 17)	5' UTR (NM_011578, exon 1 of 17)	157	NM_011578	21814	Mm.200775	NM_011578	ENSMUSG00000029287	Tgfbr3	1110036H20Rik|AU015626|AW215636|TBRIII	transforming growth factor, beta receptor III	protein-coding
mm_7078.1	chr1	88274182	88274184	-	1	NA	intron (NM_198652, intron 3 of 7)	B1F|SINE|Alu	3374	NM_172505	212427	Mm.384762	NM_172505		A730008H23Rik	mFleg1	RIKEN cDNA A730008H23 gene	protein-coding
mm_130624.1	chr15	100403438	100403456	-	1	NA	intron (NM_008732, intron 9 of 16)	intron (NM_008732, intron 9 of 16)	19608	NM_001146161	18174	Mm.234608	NM_008732	ENSMUSG00000023030	Slc11a2	DCT1|DMT1|Nramp2|mk|van	solute carrier family 11 (proton-coupled divalent metal ion transporters), member 2	protein-coding
mm_163167.1	chr11	86757837	86757876	+	1	NA	promoter-TSS (NM_001003908)	promoter-TSS (NM_001003908)	-364	NM_001003908	67300	Mm.254588	NM_001003908	ENSMUSG00000047126	Cltc	3110065L21Rik|CHC|R74732	clathrin, heavy polypeptide (Hc)	protein-coding
mm_136031.1	chr16	77010870	77010888	-	1	NA	promoter-TSS (NR_040573)	promoter-TSS (NR_040573)	2	NR_040573	76601	Mm.396217	NR_040573	ENSMUSG00000100857	1700041M19Rik	-	RIKEN cDNA 1700041M19 gene	ncRNA
mm_121803.1	chr14	20181809	20181809	-	1	NA	promoter-TSS (NM_021542)	promoter-TSS (NM_021542)	-27	NM_021542	16529	Mm.68998	NM_021542	ENSMUSG00000023243	Kcnk5	KCNK5b|TASK-2	potassium channel, subfamily K, member 5	protein-coding
mm_166494.1	chr5	150985624	150985641	+	1	NA	intron (NM_013823, intron 3 of 4)	Lx8b|LINE|L1	33025	NM_013823	16591	Mm.6500	NM_013823	ENSMUSG00000058488	Kl	alpha-kl	klotho	protein-coding
mm_56269.1	chr6	90988771	90988826	-	1	NA	Intergenic	Intergenic	128028	NM_018815	54563	Mm.28162	NM_018815	ENSMUSG00000030091	Nup210	9830001L10|AI836801|Pom210|gp190|gp210	nucleoporin 210	protein-coding
mm_115569.1	chr13	10360811	10360853	-	1	NA	promoter-TSS (NM_033269)	promoter-TSS (NM_033269)	-29	NM_033269	12671	Mm.342315	NM_033269	ENSMUSG00000046159	Chrm3	Chrm-3|M3|M3R	cholinergic receptor, muscarinic 3, cardiac	protein-coding
mm_144534.1	chr18	25234302	25234316	+	1	NA	intron (NM_001033532, intron 5 of 10)	MLT1A|LTR|ERVL-MaLR	65289	NM_001033532	225289	Mm.391081	NM_001033532	ENSMUSG00000033632	AW554918	4921538P22|AI461742|Kiaa1328|mKIAA1328	expressed sequence AW554918	protein-coding
mm_129750.1	chr15	82338802	82338854	-	1	NA	promoter-TSS (NM_008669)	promoter-TSS (NM_008669)	-2	NM_008669	17939	Mm.20325	NM_008669	ENSMUSG00000022453	Naga	-	N-acetyl galactosaminidase, alpha	protein-coding
mm_137854.1	chr17	31106092	31106105	+	1	NA	exon (NM_009593, exon 8 of 15)	exon (NM_009593, exon 8 of 15)	23513	NM_011575	21786	Mm.4641	NM_011575	ENSMUSG00000024029	Tff3	ITF|mITF	trefoil factor 3, intestinal	protein-coding
mm_122013.1	chr14	27336645	27336648	-	1	NA	intron (NM_001289687, intron 1 of 9)	intron (NM_001289687, intron 1 of 9)	609	NM_001289687	71704	Mm.248606	NM_027871	ENSMUSG00000021895	Arhgef3	1200004I24Rik|9830169H03Rik|C76747|Xpln	Rho guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_123452.1	chr14	65255880	65255883	-	1	NA	intron (NM_021458, intron 1 of 6)	(A)n|Simple_repeat|Simple_repeat	6582	NM_021458	14365	Mm.214687	NM_021458	ENSMUSG00000007989	Fzd3	AU020229|D930050A07Rik|Fz3	frizzled class receptor 3	protein-coding
mm_68070.1	chr7	101868725	101868725	-	1	NA	intron (NM_001252552, intron 2 of 6)	intron (NM_001252552, intron 2 of 6)	2063	NM_001252554	14275	Mm.2135	NM_008034	ENSMUSG00000001827	Folr1	FBP1|Folbp-1|Folbp1	folate receptor 1 (adult)	protein-coding
mm_36286.1	chr4	63861297	63861318	-	1	NA	promoter-TSS (NM_009403)	promoter-TSS (NM_009403)	-23	NM_009403	21949	Mm.4664	NM_009403	ENSMUSG00000028362	Tnfsf8	CD153|CD30LG|Cd30l|Tnlg3a	tumor necrosis factor (ligand) superfamily, member 8	protein-coding
mm_173359.1	chrY	90819444	90819454	+	1	NA	Intergenic	Intergenic	19957	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_13584.1	chr2	112379267	112379284	+	1	NA	promoter-TSS (NM_024254)	promoter-TSS (NM_024254)	64	NM_024254	72425	Mm.425091	NM_024254	ENSMUSG00000027132	Katnbl1	2410042D21Rik|AA166487|AA473307|AI467442	katanin p80 subunit B like 1	protein-coding
mm_150953.1	chr19	46341119	46341122	+	1	NA	Intergenic	Intergenic	-1642	NR_030468	751550		NR_030468	ENSMUSG00000070127	Mir146b	Mirn146b|mir-146b	microRNA 146b	ncRNA
mm_12006.1	chr2	57268519	57268536	+	1	NA	intron (NM_001145820, intron 2 of 16)	(TTCC)n|Simple_repeat|Simple_repeat	30145	NM_010274	14571	Mm.3711	NM_010274	ENSMUSG00000026827	Gpd2	AA408484|AI448216|AU021455|AW494132|GPDH|Gdm1|Gpd-m|Gpdh-m|TISP38	glycerol phosphate dehydrogenase 2, mitochondrial	protein-coding
mm_132389.1	chr16	34994946	34994959	+	1	NA	intron (NM_139300, intron 29 of 31)	intron (NM_139300, intron 29 of 31)	-27469	NM_023587	70757	Mm.27286	NM_023587	ENSMUSG00000035376	Hacd2	6330408J20Rik|AI255777|AI481689|Hcad2|Ptplb	3-hydroxyacyl-CoA dehydratase 2	protein-coding
mm_157489.1	chrX	48284269	48284276	-	1	NA	intron (NR_045916, intron 1 of 3)	intron (NR_045916, intron 1 of 3)	1154	NR_045916	100500713	Mm.396609	NR_045916	ENSMUSG00000097197	9530027J09Rik	-	RIKEN cDNA 9530027J09 gene	ncRNA
mm_29324.1	chr3	108017878	108017884	-	1	NA	promoter-TSS (NM_010358)	promoter-TSS (NM_010358)	92	NM_010358	14862	Mm.37199	NM_010358	ENSMUSG00000058135	Gstm1	Gstb-1|Gstb1	glutathione S-transferase, mu 1	protein-coding
mm_19529.1	chr2	94264714	94264734	-	1	NA	Intergenic	Intergenic	-3325	NR_030431	735259		NR_030431	ENSMUSG00000076335	Mir670	Mirn670|mir-670|mmu-mir-670	microRNA 670	ncRNA
mm_36099.1	chr4	58553188	58553261	-	1	NA	promoter-TSS (NM_172989)	promoter-TSS (NM_172989)	69	NM_172989	14745	Mm.4772	NM_010336	ENSMUSG00000038668	Lpar1	AI326300|Edg2|Gpcr26|Kdt2|lpA1|vzg-1	lysophosphatidic acid receptor 1	protein-coding
mm_121484.1	chr14	121107472	121107472	+	1	NA	intron (NM_134082, intron 2 of 26)	intron (NM_134082, intron 2 of 26)	71898	NM_134082	223254	Mm.223980	NM_134082	ENSMUSG00000025555	Farp1	AW228844|BC030329|Cdep	FERM, RhoGEF (Arhgef) and pleckstrin domain protein 1 (chondrocyte-derived)	protein-coding
mm_58683.1	chr7	12603574	12603600	+	1	NA	intron (NM_001104644, intron 1 of 4)	intron (NM_001104644, intron 1 of 4)	2957	NM_001104644	637908	Mm.469871	NM_001104644	ENSMUSG00000096002	Vmn2r53	EG637908|Gm471	vomeronasal 2, receptor 53	protein-coding
mm_158577.1	chrX	150655579	150655596	-	1	NA	exon (NM_019548, exon 3 of 14)	exon (NM_019548, exon 3 of 14)	1849	NM_019548	56191	Mm.3597	NM_019548	ENSMUSG00000025272	Tro	AA409408|Maged3|Maged3l|Tnn|Trol|magphinin	trophinin	protein-coding
mm_125556.1	chr15	58888921	58888969	+	1	NA	promoter-TSS (NM_175226)	promoter-TSS (NM_175226)	-284	NM_175226	75841	Mm.4537	NM_175226	ENSMUSG00000037075	Rnf139	4930555P18Rik	ring finger protein 139	protein-coding
mm_44801.1	chr5	32907643	32907664	-	1	NA	intron (NM_177786, intron 17 of 32)	RLTR40|LTR|ERVK	43932	NM_001170567	277854	Mm.101524	NM_177786	ENSMUSG00000037426	Depdc5	AV016528	DEP domain containing 5	protein-coding
mm_70664.1	chr8	14888023	14888037	+	1	NA	promoter-TSS (NM_012000)	promoter-TSS (NM_012000)	-506	NM_012000	26889	Mm.254027	NM_012000	ENSMUSG00000026317	Cln8	mnd	ceroid-lipofuscinosis, neuronal 8	protein-coding
mm_109915.1	chr12	8482121	8482129	-	1	NA	Intergenic	Intergenic	17860	NM_007483	11852	Mm.687	NM_007483	ENSMUSG00000054364	Rhob	AA017882|Arh6|Arhb	ras homolog family member B	protein-coding
mm_135574.1	chr16	50364249	50364298	-	1	NA	intron (NM_001347240, intron 2 of 16)	intron (NM_001347240, intron 2 of 16)	68116	NM_027444	70508	Mm.28940	NM_027444	ENSMUSG00000022641	Bbx	5530401J07Rik|5730403O13Rik	bobby sox HMG box containing	protein-coding
mm_28955.1	chr3	100489235	100489248	-	1	NA	promoter-TSS (NM_001142952)	promoter-TSS (NM_001142952)	-49	NM_001142952	74645	Mm.226900	NM_001142952	ENSMUSG00000044468	Fam46c	4930431B09Rik|AI449797	family with sequence similarity 46, member C	protein-coding
mm_122817.1	chr14	54632285	54632289	-	1	NA	exon (NM_199470, exon 12 of 12)	exon (NM_199470, exon 12 of 12)	6977	NM_175204	73902	Mm.32009	NM_175204	ENSMUSG00000072423	Psmb11	5830406J20Rik|beta5t	proteasome (prosome, macropain) subunit, beta type, 11	protein-coding
mm_99960.1	chr11	113649578	113649584	+	1	NA	promoter-TSS (NM_013581)	promoter-TSS (NM_013581)	52	NM_013581	16834	Mm.261620	NM_013581	ENSMUSG00000018661	Cog1	6030445I15|Ldlb|mKIAA1381	component of oligomeric golgi complex 1	protein-coding
mm_155971.1	chrX	106105159	106105183	+	1	NA	exon (NM_009726, exon 15 of 23)	exon (NM_009726, exon 15 of 23)	-38104	NM_205820	279572	Mm.336203	NM_205820	ENSMUSG00000033777	Tlr13	AI666735|Gm713	toll-like receptor 13	protein-coding
mm_78570.1	chr9	36475581	36475585	+	1	NA	promoter-TSS (NM_001128510)	promoter-TSS (NM_001128510)	-55	NM_001128510	671003	Mm.475847	NM_001128510	ENSMUSG00000090710	Gm9513	Pate-P|Pate11	predicted gene 9513	protein-coding
mm_89575.1	chr10	95527167	95527169	+	1	NA	intron (NM_080560, intron 1 of 3)	intron (NM_080560, intron 1 of 3)	12006	NM_080560	93765	Mm.371667	NM_080560	ENSMUSG00000074781	Ube2n	1500026J17Rik|AL022654|BB101821|UBC13	ubiquitin-conjugating enzyme E2N	protein-coding
mm_3444.1	chr1	150102772	150102793	+	1	NA	intron (NM_011198, intron 5 of 9)	intron (NM_011198, intron 5 of 9)	2751	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_7348.1	chr1	105990278	105990296	-	1	NA	promoter-TSS (NM_001122675)	promoter-TSS (NM_001122675)	-119	NM_001122676	227449	Mm.210188	NM_001122675	ENSMUSG00000038866	Zcchc2	9930114B20Rik|AW212015	zinc finger, CCHC domain containing 2	protein-coding
mm_99651.1	chr11	105589971	105590028	+	1	NA	promoter-TSS (NM_181071)	promoter-TSS (NM_181071)	13	NM_181071	77097	Mm.22501	NM_175492	ENSMUSG00000053580	Tanc2	3526402J09Rik|5730590C14Rik	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2	protein-coding
mm_138655.1	chr17	35868383	35868449	+	1	NA	exon (NM_001146711, exon 2 of 4)	exon (NM_001146711, exon 2 of 4)	1801	NM_175242	76448	Mm.359982	NM_175242	ENSMUSG00000034595	Ppp1r18	2310014H01Rik|AA407849|AI450394	protein phosphatase 1, regulatory subunit 18	protein-coding
mm_134978.1	chr16	32079125	32079159	-	1	NA	5' UTR (NM_177326, exon 1 of 15)	5' UTR (NM_177326, exon 1 of 15)	200	NM_177326	224105	Mm.234204	NM_177326	ENSMUSG00000022781	Pak2	5330420P17Rik|A130002K10Rik|AI836325|D16Ertd269e|PAK-2|mKIAA4182	p21 protein (Cdc42/Rac)-activated kinase 2	protein-coding
mm_39801.1	chr5	30622944	30622954	+	1	NA	3' UTR (NM_010608, exon 2 of 2)	3' UTR (NM_010608, exon 2 of 2)	-24987	NR_049199	100885838		NR_049199	ENSMUSG00000093710	Mir5625	Gm23930|mmu-mir-5625	microRNA 5625	ncRNA
mm_43480.1	chr5	136697830	136697882	+	1	NA	intron (NM_001303019, intron 4 of 6)	intron (NM_001303019, intron 4 of 6)	3679	NM_001085387	59310	Mm.5178	NM_021611	ENSMUSG00000005474	Myl10	1700027I08Rik|Mylc2pl|PLRLC	myosin, light chain 10, regulatory	protein-coding
mm_33889.1	chr4	136180199	136180211	+	1	NA	promoter-TSS (NM_001305399)	promoter-TSS (NM_001305399)	-577	NM_001305399	242705	Mm.307932	NM_177733	ENSMUSG00000018983	E2f2	E2F-2	E2F transcription factor 2	protein-coding
mm_166499.1	chr6	3570560	3570564	-	1	NA	intron (NM_001167750, intron 19 of 27)	L1_Rod|LINE|L1	72169	NM_001167750	73288	Mm.45539	NM_024260	ENSMUSG00000001376	Vps50	1700034M03Rik|8430415E05Rik|BLM|C87205|Ccdc132|mKIAA1861	VPS50 EARP/GARPII complex subunit	protein-coding
mm_58886.1	chr7	17088060	17088082	+	1	NA	intron (NM_001310628, intron 1 of 5)	intron (NM_001310628, intron 1 of 5)	14031	NM_007676	26436	Mm.143686	NM_007676	ENSMUSG00000066760	Psg16	Cea11|PSG|bCEA	pregnancy specific glycoprotein 16	protein-coding
mm_40380.1	chr5	52368750	52368756	+	1	NA	3' UTR (NM_011435, exon 2 of 2)	3' UTR (NM_011435, exon 2 of 2)	4949	NM_011435	20657	Mm.2407	NM_011435	ENSMUSG00000072941	Sod3	AI314465|EC-SOD	superoxide dismutase 3, extracellular	protein-coding
mm_63862.1	chr7	135684038	135684048	+	1	NA	3' UTR (NM_011212, exon 21 of 21)	3' UTR (NM_011212, exon 21 of 21)	-31729	NR_015548	67765	Mm.445272	NR_015548	ENSMUSG00000097471	5830432E09Rik	-	RIKEN cDNA 5830432E09 gene	ncRNA
mm_22593.1	chr3	13748928	13748930	+	1	NA	intron (NM_178631, intron 2 of 9)	intron (NM_178631, intron 2 of 9)	-96064	NR_040598	75203	Mm.490940	NR_040598		4930539N22Rik	-	RIKEN cDNA 4930539N22 gene	ncRNA
mm_4776.1	chr1	182954771	182954828	+	1	NA	promoter-TSS (NM_016928)	promoter-TSS (NM_016928)	11	NM_016928	53791	Mm.116894	NM_016928	ENSMUSG00000079164	Tlr5	-	toll-like receptor 5	protein-coding
mm_107681.1	chr12	54622531	54622575	+	1	NA	Intergenic	Intergenic	23459	NR_035439	100316682		NR_035439	ENSMUSG00000106344	Mir1892	Mirn1892|mir-1892|mmu-mir-1892	microRNA 1892	ncRNA
mm_67164.1	chr7	73546095	73546098	-	1	NA	intron (NR_037569, intron 4 of 4)	PB1D11|SINE|Alu	-4350	NM_001081345	244059	Mm.34539	NM_001081345	ENSMUSG00000078671	Chd2	2810013C04Rik|2810040A01Rik|5630401D06Rik|AI851092|BC029703|CHD-2	chromodomain helicase DNA binding protein 2	protein-coding
mm_20524.1	chr2	130840084	130840088	-	1	NA	promoter-TSS (NM_001311147)	promoter-TSS (NM_001311147)	59	NM_029432	228602	Mm.271990	NM_028367	ENSMUSG00000027309	4930402H24Rik	2810487F15Rik|AI413763|C78926	RIKEN cDNA 4930402H24 gene	protein-coding
mm_153552.1	chr19	42128912	42128941	-	1	NA	promoter-TSS (NM_027106)	promoter-TSS (NM_027106)	67	NM_027106	69534	Mm.30060	NM_027106	ENSMUSG00000018821	Avpi1	2310008N12Rik|AA410041|VIT32|esu|mVIT32	arginine vasopressin-induced 1	protein-coding
mm_163991.1	chr14	63177787	63177795	-	1	NA	5' UTR (NM_010191, exon 3 of 10)	5' UTR (NM_010191, exon 3 of 10)	1787	NM_010191	14137	Mm.474432	NM_010191	ENSMUSG00000021273	Fdft1	SQS|SS	farnesyl diphosphate farnesyl transferase 1	protein-coding
mm_67518.1	chr7	80905013	80905026	-	1	NA	promoter-TSS (NM_001291280)	promoter-TSS (NM_001291280)	43	NM_026523	68039	Mm.22246	NM_026523	ENSMUSG00000025723	Nmb	3110023K12Rik	neuromedin B	protein-coding
mm_29243.1	chr3	107216103	107216131	-	1	NA	exon (NM_001111143, exon 5 of 9)	exon (NM_001111143, exon 5 of 9)	5615	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_53199.1	chr6	125552954	125552980	+	1	NA	promoter-TSS (NM_011708)	promoter-TSS (NM_011708)	19	NM_011708	22371	Mm.22339	NM_011708	ENSMUSG00000001930	Vwf	6820430P06Rik|AI551257|B130011O06Rik|C630030D09|F8VWF|VWD	Von Willebrand factor	protein-coding
mm_18490.1	chr2	62602924	62602935	-	1	NA	intron (NM_001164477, intron 11 of 14)	intron (NM_001164477, intron 11 of 14)	-28908	NM_007986	14089	Mm.41816	NM_007986	ENSMUSG00000000392	Fap	SIMP	fibroblast activation protein	protein-coding
mm_125489.1	chr15	54745903	54745916	+	1	NA	promoter-TSS (NM_010930)	promoter-TSS (NM_010930)	-19	NM_010930	18133	Mm.5167	NM_010930	ENSMUSG00000037362	Nov	C130088N23Rik|CCN3	nephroblastoma overexpressed gene	protein-coding
mm_48901.1	chr6	3201463	3201521	+	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	-87027	NR_036696	667335	Mm.380219	NR_036696	ENSMUSG00000106779	Gm8579	EG667335	spermatogenesis associated glutamate (E)-rich protein 4a pseudogene	pseudo
mm_36635.1	chr4	93335381	93335423	-	1	NA	exon (NM_026954, exon 1 of 1)	exon (NM_026954, exon 1 of 1)	109	NM_026954	69136	Mm.171558	NM_026954	ENSMUSG00000054000	Tusc1	2200001D17Rik|TSG-9	tumor suppressor candidate 1	protein-coding
mm_124037.1	chr14	77033351	77033361	-	1	NA	intron (NM_172488, intron 4 of 7)	intron (NM_172488, intron 4 of 7)	3261	NM_172488	210808	Mm.89278	NM_172488	ENSMUSG00000044350	Lacc1	9030625A04Rik	laccase (multicopper oxidoreductase) domain containing 1	protein-coding
mm_127424.1	chr15	101267855	101267874	+	1	NA	intron (NM_010444, intron 1 of 6)	intron (NM_010444, intron 1 of 6)	1018	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_134659.1	chr16	22121269	22121285	-	1	NA	intron (NM_183029, intron 2 of 15)	L1MA5|LINE|L1	42022	NM_183029	319765	Mm.489442	NM_183029	ENSMUSG00000033581	Igf2bp2	C330012H03Rik|IMP-2|Imp2|Neilsen	insulin-like growth factor 2 mRNA binding protein 2	protein-coding
mm_172935.1	chr9	78480273	78480286	+	1	NA	exon (NM_010106, exon 3 of 8)	exon (NM_010106, exon 3 of 8)	1445	NM_010106	13627	Mm.138471	NM_010106	ENSMUSG00000037742	Eef1a1	-	eukaryotic translation elongation factor 1 alpha 1	protein-coding
mm_94385.1	chr11	5520952	5520966	+	1	NA	5' UTR (NM_001271730, exon 1 of 6)	5' UTR (NM_001271730, exon 1 of 6)	318	NM_001271730	22433	Mm.469937	NM_013842	ENSMUSG00000020484	Xbp1	D11Ertd39e|TREB-5|TREB5|XBP-1	X-box binding protein 1	protein-coding
mm_17065.1	chr2	22590298	22590305	-	1	NA	Intergenic	Intergenic	-32026	NM_008078	14417	Mm.4784	NM_008078	ENSMUSG00000026787	Gad2	6330404F12Rik|GAD(65)|GAD65|Gad-2	glutamic acid decarboxylase 2	protein-coding
mm_93775.1	chr10	120476223	120476242	-	1	NA	5' UTR (NM_010441, exon 1 of 5)	5' UTR (NM_010441, exon 1 of 5)	237	NM_001347170	15364	Mm.157190	NM_010441	ENSMUSG00000056758	Hmga2	9430083A20Rik|HMGI-C|Hmgic|pg|pygmy	high mobility group AT-hook 2	protein-coding
mm_31376.1	chr4	47412765	47412800	+	1	NA	3' UTR (NM_009370, exon 9 of 9)	3' UTR (NM_009370, exon 9 of 9)	26566	NM_001312869	21812	Mm.197552	NM_009370	ENSMUSG00000007613	Tgfbr1	ALK5|AU017191|Alk-5|ESK2|TGFR-1|TbetaR-I|TbetaRI	transforming growth factor, beta receptor I	protein-coding
mm_72786.1	chr8	86884331	86884341	+	1	NA	intron (NM_030563, intron 1 of 6)	intron (NM_030563, intron 1 of 6)	922	NM_030563	80750	Mm.25117	NM_030563	ENSMUSG00000031652	N4bp1	AI481586|C81621	NEDD4 binding protein 1	protein-coding
mm_97793.1	chr11	82911280	82911294	+	1	NA	promoter-TSS (NM_178680)	promoter-TSS (NM_178680)	34	NM_178680	217012	Mm.295205	NM_178680	ENSMUSG00000018845	Unc45b	AA445617|Cmya4|D230041A13Rik|Unc45	unc-45 myosin chaperone B	protein-coding
mm_46085.1	chr5	92346901	92346914	-	1	NA	3' UTR (NM_021274, exon 4 of 4)	3' UTR (NM_021274, exon 4 of 4)	1982	NM_021274	15945	Mm.877	NM_021274	ENSMUSG00000034855	Cxcl10	C7|CRG-2|INP10|IP-10|IP10|Ifi10|Scyb10|gIP-10|mob-1	chemokine (C-X-C motif) ligand 10	protein-coding
mm_159312.1	chr2	181797147	181797147	+	1	NA	exon (NM_008665, exon 7 of 23)	exon (NM_008665, exon 7 of 23)	840	NM_001171680	17932	Mm.458718	NM_008665	ENSMUSG00000010505	Myt1	Nzf2|Nzf2a|Nzf2b|Nztf2	myelin transcription factor 1	protein-coding
mm_170920.1	chr2	37261867	37261877	-	1	NA	Intergenic	RLTR9D|LTR|ERVK	-5079	NM_001081010	545417	Mm.379955	NM_001081010		Olfr367-ps	EG545417|MOR128-1|ORL1283|OTTMUSG00000012147|Olfr367	olfactory receptor 367, pseudogene	protein-coding
mm_167968.1	chrX	152178965	152178967	+	1	NA	promoter-TSS (NM_001005475)	promoter-TSS (NM_001005475)	-43	NM_001005475	245666	Mm.33027	NM_001005475	ENSMUSG00000041115	Iqsec2	Brag1	IQ motif and Sec7 domain 2	protein-coding
mm_165713.1	chr3	98858328	98858328	-	1	NA	5' UTR (NM_008293, exon 2 of 5)	5' UTR (NM_008293, exon 2 of 5)	1466	NM_001304800	15492	Mm.140811	NM_008293	ENSMUSG00000027871	Hsd3b1	3-beta-HSD I|D3Ertd383e	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1	protein-coding
mm_49979.1	chr6	40891432	40891451	+	1	NA	intron (NR_035473, intron 2 of 3)	intron (NR_035473, intron 2 of 3)	-3947	NM_139296	194357	Mm.207087	NM_139296	ENSMUSG00000029885	Moxd2	Dbhl1	monooxygenase, DBH-like 2	protein-coding
mm_76908.1	chr8	105851966	105851979	-	1	NA	promoter-TSS (NM_177150)	promoter-TSS (NM_177150)	36	NM_177150	320394	Mm.334775	NM_177150	ENSMUSG00000036672	Cenpt	G630055P03Rik	centromere protein T	protein-coding
mm_68092.1	chr7	101921187	101921230	-	1	NA	promoter-TSS (NM_001162974)	promoter-TSS (NM_001162974)	-434	NM_001162974	69358	Mm.214841	NM_027053	ENSMUSG00000064307	Lrrc51	1700008D07Rik|Lrtomt	leucine rich repeat containing 51	protein-coding
mm_2800.1	chr1	130851663	130851682	+	1	NA	3' UTR (NM_011082, exon 11 of 11)	3' UTR (NM_011082, exon 11 of 11)	-14105	NM_026976	69169	Mm.46042	NM_026976	ENSMUSG00000042474	Fcmr	1810037B05Rik|Faim3|FcmuR|Toso	Fc fragment of IgM receptor	protein-coding
mm_15539.1	chr2	158383851	158383859	+	1	NA	3' UTR (NM_175692, exon 5 of 5)	3' UTR (NM_175692, exon 5 of 5)	8217	NM_175692	319317	Mm.294494	NM_175692	ENSMUSG00000044349	Snhg11	A930034L06Rik|AI854265|AL022637|AW319638|E130013N09Rik	small nucleolar RNA host gene 11	protein-coding
mm_81630.1	chr9	110849540	110849554	+	1	NA	intron (NM_183103, intron 1 of 4)	intron (NM_183103, intron 1 of 4)	5041	NM_183103	74306	Mm.87419	NM_183103	ENSMUSG00000049719	Prss46	1700112C13Rik|79H19B|Tessp6	protease, serine 46	protein-coding
mm_45428.1	chr5	67095995	67095996	-	1	NA	3' UTR (NM_008888, exon 3 of 3)	3' UTR (NM_008888, exon 3 of 3)	3131	NM_008888	18935	Mm.62505	NM_008888	ENSMUSG00000012520	Phox2b	Dilp1|NBPhox|Pmx2b|Px2b	paired-like homeobox 2b	protein-coding
mm_61665.1	chr7	80779684	80779695	+	1	NA	intron (NM_016721, intron 2 of 37)	intron (NM_016721, intron 2 of 37)	23642	NM_016721	29875	Mm.207619	NM_016721	ENSMUSG00000030536	Iqgap1	AA682088|D7Ertd237e|D7Ertd257e|mKIAA0051	IQ motif containing GTPase activating protein 1	protein-coding
mm_38753.1	chr4	147778328	147778338	-	1	NA	intron (NM_001127189, intron 3 of 5)	AT_rich|Low_complexity|Low_complexity	31455	NM_001127189	100041677	Mm.327194	NM_001127189	ENSMUSG00000078495	Zfp984	Gm13157|OTTMUSG00000010679	zinc finger protein 984	protein-coding
mm_94169.1	chr10	128804376	128804395	-	1	NA	promoter-TSS (NM_178066)	promoter-TSS (NM_178066)	-15	NM_178066	73827	Mm.24630	NM_178066	ENSMUSG00000047090	Tmem198b	1110012D08Rik	transmembrane protein 198b	protein-coding
mm_22532.1	chr3	8509553	8509557	+	1	NA	promoter-TSS (NM_025285)	promoter-TSS (NM_025285)	28	NM_025285	20257	Mm.29580	NM_025285	ENSMUSG00000027500	Stmn2	AI159727|SCG10|Scgn10|Stmb2	stathmin-like 2	protein-coding
mm_133090.1	chr16	62854318	62854333	+	1	NA	promoter-TSS (NM_011173)	promoter-TSS (NM_011173)	18	NM_011173	19128	Mm.127156	NM_011173	ENSMUSG00000022912	Pros1	AW214361	protein S (alpha)	protein-coding
mm_39886.1	chr5	31116603	31116618	+	1	NA	promoter-TSS (NM_021447)	promoter-TSS (NM_021447)	-2	NM_021447	58522	Mm.143796	NM_021447	ENSMUSG00000062077	Trim54	4930486E09Rik|4930566I02Rik|MURF|MURF-3|MuRF3|Rnf30	tripartite motif-containing 54	protein-coding
mm_156873.1	chrX	164907033	164907033	+	1	NA	Intergenic	BC1_Mm|scRNA|scRNA	73342	NM_001290523	76763	Mm.291758	NM_029730	ENSMUSG00000061778	Mospd2	2410013I23Rik	motile sperm domain containing 2	protein-coding
mm_148432.1	chr19	3941951	3941971	+	1	NA	exon (NM_019449, exon 5 of 11)	exon (NM_019449, exon 5 of 11)	6775	NM_001161428	54445	Mm.262094	NM_019449	ENSMUSG00000036908	Unc93b1	Unc-93B1|Unc93b	unc-93 homolog B1 (C. elegans)	protein-coding
mm_2429.1	chr1	95667692	95667728	+	1	NA	promoter-TSS (NM_001159745)	promoter-TSS (NM_001159745)	-116	NM_001159745	20452	Mm.306228	NM_009183	ENSMUSG00000040710	St8sia4	PST|PST-1|SIAT8-D|ST8SiaIV|Siat8d	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4	protein-coding
mm_147540.1	chr18	53744510	53744629	-	1	NA	promoter-TSS (NM_178686)	promoter-TSS (NM_178686)	-22	NM_178686	225523	Mm.193678	NM_178686	ENSMUSG00000048799	Cep120	A230075C01|AU016693|Ccdc100	centrosomal protein 120	protein-coding
mm_10764.1	chr2	24186454	24186464	+	1	NA	promoter-TSS (NM_153511)	promoter-TSS (NM_153511)	-17	NM_153511	215257	Mm.249379	NM_153511	ENSMUSG00000044103	Il1f9	Il36g	interleukin 1 family, member 9	protein-coding
mm_132935.1	chr16	49855625	49855722	+	1	NA	promoter-TSS (NM_010581)	promoter-TSS (NM_010581)	19	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_139392.1	chr17	52282543	52282552	+	1	NA	Intergenic	Intergenic	-320162	NM_001031811	211468	Mm.399068	NM_001031811	ENSMUSG00000035580	Kcnh8	C130090D05Rik|ELK|ELK1|ELK3|Kv12.1	potassium voltage-gated channel, subfamily H (eag-related), member 8	protein-coding
mm_150697.1	chr19	42247545	42247586	+	1	NA	promoter-TSS (NM_001141983)	promoter-TSS (NM_001141983)	-13	NM_001141983	71146	Mm.329851	NM_027694	ENSMUSG00000042532	Golga7b	4933417O08Rik|AI839934	golgi autoantigen, golgin subfamily a, 7B	protein-coding
mm_101523.1	chr11	32824567	32824586	-	1	NA	promoter-TSS (NM_027050)	promoter-TSS (NM_027050)	18	NM_027050	69351	Mm.65488	NM_027050	ENSMUSG00000020270	Smim23	1700008A04Rik	small integral membrane protein 23	protein-coding
mm_6070.1	chr1	60908876	60908879	-	1	NA	promoter-TSS (NM_009843)	promoter-TSS (NM_009843)	-148	NM_009843	12477	Mm.390	NM_009843	ENSMUSG00000026011	Ctla4	Cd152|Ctla-4|Ly-56	cytotoxic T-lymphocyte-associated protein 4	protein-coding
mm_122431.1	chr14	45102328	45102356	-	1	NA	Intergenic	RMER1C|Other|Other	114231	NM_008964	19217	Mm.4630	NM_008964	ENSMUSG00000037759	Ptger2	EP2|Ptgerep2	prostaglandin E receptor 2 (subtype EP2)	protein-coding
mm_10501.1	chr2	15526472	15526516	+	1	NA	promoter-TSS (NM_001310455)	promoter-TSS (NM_001310455)	15	NM_001310455	102635496		NM_001310455	ENSMUSG00000075520	Malrd1	-	MAM and LDL receptor class A domain containing 1	protein-coding
mm_22997.1	chr3	34020084	34020110	+	1	NA	promoter-TSS (NM_001113188)	promoter-TSS (NM_001113188)	18	NM_001113188	14359	Mm.259021	NM_008053	ENSMUSG00000027680	Fxr1	1110050J02Rik|9530073J07Rik|AI851072|Fxr1h|Fxr1p	fragile X mental retardation gene 1, autosomal homolog	protein-coding
mm_147363.1	chr18	43393262	43393275	-	1	NA	5' UTR (NM_009468, exon 1 of 14)	5' UTR (NM_009468, exon 1 of 14)	109	NM_009468	22240	Mm.8180	NM_009468	ENSMUSG00000024501	Dpysl3	CRMP-4|DRP-3|TUC4|ULIP-1|Ulip|Ulip1	dihydropyrimidinase-like 3	protein-coding
mm_5323.1	chr1	22806148	22806166	-	1	NA	promoter-TSS (NM_001012625)	promoter-TSS (NM_001012625)	-433	NM_001012624	116837	Mm.60061	NM_053270	ENSMUSG00000041670	Rims1	C030033M19Rik|RIM1|RIM1a|RIM1alpha|Rab3ip1|Rim|Serg1|mKIAA0340	regulating synaptic membrane exocytosis 1	protein-coding
mm_150284.1	chr19	34307025	34307049	+	1	NA	intron (NM_007987, intron 1 of 8)	intron (NM_007987, intron 1 of 8)	16378	NM_001146708	14102	Mm.1626	NM_007987	ENSMUSG00000024778	Fas	AI196731|APO1|APT1|CD95|TNFR6|Tnfrsf6|lpr	Fas (TNF receptor superfamily member 6)	protein-coding
mm_159690.1	chr5	19226860	19226860	+	1	NA	promoter-TSS (NR_102342)	promoter-TSS (NR_102342)	-186	NM_001170746	50791	Mm.332231	NM_015823	ENSMUSG00000040003	Magi2	AIP-1|Acvri1|Acvrinp1|Acvrip1|Magi-2|S-SCAM|mKIAA0705	membrane associated guanylate kinase, WW and PDZ domain containing 2	protein-coding
mm_160975.1	chr11	101011871	101011871	+	1	NA	exon (NM_016920, exon 2 of 22)	exon (NM_016920, exon 2 of 22)	2419	NM_001243051	11975	Mm.340818	NM_016920	ENSMUSG00000019302	Atp6v0a1	AA959968|ATP6a1|Atp6n1|Atp6n1a|Atpv0a1|Vpp-1|Vpp1	ATPase, H+ transporting, lysosomal V0 subunit A1	protein-coding
mm_103297.1	chr11	72489954	72489979	-	1	NA	promoter-TSS (NM_153060)	promoter-TSS (NM_153060)	-46	NM_153060	216892	Mm.212812	NM_153060	ENSMUSG00000040447	Spns2	-	spinster homolog 2	protein-coding
mm_112432.1	chr13	4439401	4439408	+	1	NA	intron (NM_030611, intron 3 of 8)	B3A|SINE|B2	5061	NM_030611	83702	Mm.196666	NM_030611	ENSMUSG00000021210	Akr1c6	3alpha-HSD|Akr1c1|Hsd17b5	aldo-keto reductase family 1, member C6	protein-coding
mm_42519.1	chr5	115557313	115557316	+	1	NA	Intergenic	MT2_Mm|LTR|ERVL	-2153	NM_007475	11837	Mm.5286	NM_007475	ENSMUSG00000067274	Rplp0	36B4|Arbp|L10E	ribosomal protein, large, P0	protein-coding
mm_16189.1	chr2	172977732	172977751	+	1	NA	Intergenic	Intergenic	-2101	NM_012046	26972	Mm.23495	NM_012046	ENSMUSG00000005883	Spo11	AI449549|Spo11a|Spo11b	SPO11 meiotic protein covalently bound to DSB	protein-coding
mm_90948.1	chr10	13060386	13060400	-	1	NA	Intergenic	Intergenic	-30395	NM_009538	22634	Mm.287857	NM_009538	ENSMUSG00000019817	Plagl1	Lot1|Zac1	pleiomorphic adenoma gene-like 1	protein-coding
mm_161435.1	chr15	60016450	60016450	-	1	NA	exon (NM_027668, exon 1 of 1)	exon (NM_027668, exon 1 of 1)	168	NM_027668	71088	Mm.425950	NM_027668	ENSMUSG00000071749	4933412E24Rik	-	RIKEN cDNA 4933412E24 gene	protein-coding
mm_125570.1	chr15	59315089	59315128	+	1	NA	promoter-TSS (NM_009270)	promoter-TSS (NM_009270)	16	NM_009270	20775	Mm.296169	NM_009270	ENSMUSG00000022351	Sqle	AI323792	squalene epoxidase	protein-coding
mm_74367.1	chr8	128418118	128418125	+	1	NA	intron (NM_008737, intron 2 of 16)	intron (NM_008737, intron 2 of 16)	58880	NR_035436	100316680		NR_035436	ENSMUSG00000084523	Mir1903	Mirn1903|mmu-mir-1903	microRNA 1903	ncRNA
mm_101915.1	chr11	50128132	50128140	-	1	NA	Intergenic	Intergenic	-3224	NM_001290759	76795	Mm.290975	NM_029745	ENSMUSG00000036644	Tbc1d9b	-	TBC1 domain family, member 9B	protein-coding
mm_120669.1	chr14	70552256	70552264	+	1	NA	Intergenic	Intergenic	-1796	NM_021877	15460	Mm.7598	NM_021877	ENSMUSG00000022096	Hr	ALUNC|AU|N|ba|bldy|hr|rh|rh-bmh|rhino	hairless	protein-coding
mm_103948.1	chr11	84068326	84068345	-	1	NA	promoter-TSS (NM_019819)	promoter-TSS (NM_019819)	22	NM_019819	56405	Mm.240885	NM_019819	ENSMUSG00000018648	Dusp14	1110014C10Rik|2310042C07Rik|D11Ertd395e|MKP-L|Mkp6	dual specificity phosphatase 14	protein-coding
mm_97618.1	chr11	78952984	78952992	+	1	NA	exon (NM_010927, exon 22 of 27)	exon (NM_010927, exon 22 of 27)	27697	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_102263.1	chr11	55336562	55336590	-	1	NA	Intergenic	Intergenic	-24319	NM_001029988	245827	Mm.339363	NM_001029988	ENSMUSG00000055333	Fat2	EMI2|Fath2|Gm523|mKIAA0811	FAT atypical cadherin 2	protein-coding
mm_72550.1	chr8	84021445	84021475	+	1	NA	promoter-TSS (NM_028877)	promoter-TSS (NM_028877)	-14	NM_028877	74337	Mm.250943	NM_028877	ENSMUSG00000047986	Palm3	4432412L15Rik|AL024300	paralemmin 3	protein-coding
mm_148550.1	chr19	4711428	4711438	+	1	NA	5' UTR (NM_021287, exon 1 of 37)	5' UTR (NM_021287, exon 1 of 37)	210	NM_021287	20743	Mm.329668	NM_021287	ENSMUSG00000067889	Sptbn2	Spnb3|mKIAA0302	spectrin beta, non-erythrocytic 2	protein-coding
mm_7282.1	chr1	97661669	97661699	-	1	NA	intron (NM_133825, intron 1 of 2)	CpG	334	NM_133825	52392	Mm.12309	NM_133825	ENSMUSG00000044768	D1Ertd622e	AI987691|AW047450	DNA segment, Chr 1, ERATO Doi 622, expressed	protein-coding
mm_124903.1	chr15	10723915	10723956	+	1	NA	intron (NR_045063, intron 2 of 6)	intron (NR_045063, intron 2 of 6)	9035	NR_045065	75259	Mm.33928	NR_045063	ENSMUSG00000097058	4930556M19Rik	1700009D01Rik|C130022M03Rik	RIKEN cDNA 4930556M19 gene	ncRNA
mm_48194.1	chr5	137530742	137530794	-	1	NA	5' UTR (NM_010312, exon 2 of 10)	5' UTR (NM_010312, exon 2 of 10)	-1174	NR_105846	102465227		NR_105846	ENSMUSG00000098597	Mir6418	Gm27629|mir-6418|mmu-mir-6418	microRNA 6418	ncRNA
mm_9276.1	chr1	171634203	171634218	-	1	NA	3' UTR (NM_144539, exon 8 of 8)	3' UTR (NM_144539, exon 8 of 8)	7690	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_88894.1	chr10	81148412	81148427	+	1	NA	exon (NM_010731, exon 3 of 3)	exon (NM_010731, exon 3 of 3)	12148	NM_010731	16969	Mm.20920	NM_010731	ENSMUSG00000035011	Zbtb7a	9030619K07Rik|9130006G12Rik|AI452336|FBI-1|Lrf|Pokemon|Zbtb7	zinc finger and BTB domain containing 7a	protein-coding
mm_152037.1	chr19	6118469	6118479	-	1	NA	TTS (NM_026912)	TTS (NM_026912)	112	NM_133678	66406	Mm.303924	NM_133678	ENSMUSG00000024790	Sac3d1	2410004C24Rik|AU015683|shd1	SAC3 domain containing 1	protein-coding
mm_82118.1	chr9	123462097	123462103	+	1	NA	3' UTR (NM_153168, exon 21 of 21)	3' UTR (NM_153168, exon 21 of 21)	-16601	NM_013860	29806	Mm.10987	NM_013860	ENSMUSG00000025239	Limd1	AW822033|D9Ertd192e	LIM domains containing 1	protein-coding
mm_89519.1	chr10	94354527	94354530	+	1	NA	Intergenic	Intergenic	-55825	NR_033209	215472	Mm.255656	NM_174999	ENSMUSG00000053420	Gm4792	E130012K09|EG215472	predicted gene 4792	ncRNA
mm_8136.1	chr1	136247538	136247551	-	1	NA	Intergenic	Intergenic	-13264	NM_028872	67313	Mm.36763	NM_028872	ENSMUSG00000041605	5730559C18Rik	1700034M08Rik|4933426C09Rik|AI586180|D1Mgi54	RIKEN cDNA 5730559C18 gene	protein-coding
mm_153944.1	chr19	47508761	47508777	-	1	NA	intron (NM_175360, intron 8 of 9)	intron (NM_175360, intron 8 of 9)	-4213	NR_045322	100503104	Mm.442735	NR_045322	ENSMUSG00000097990	Gm19557	-	predicted gene, 19557	ncRNA
mm_159631.1	chr4	138125988	138125988	+	1	NA	exon (NM_001256198, exon 12 of 33)	exon (NM_001256198, exon 12 of 33)	12530	NR_126429	73563	Mm.444294	NR_126429	ENSMUSG00000084804	1700095J12Rik	-	RIKEN cDNA 1700095J12 gene	ncRNA
mm_92871.1	chr10	82241294	82241304	-	1	NA	promoter-TSS (NM_001105557)	promoter-TSS (NM_001105557)	-24	NM_001105557	237411		NM_172789	ENSMUSG00000062931	Zfp938	B230315N10Rik	zinc finger protein 938	protein-coding
mm_63579.1	chr7	128118018	128118045	+	1	NA	3' UTR (NM_008401, exon 30 of 30)	3' UTR (NM_008401, exon 30 of 30)	-11537	NM_021334	16411	Mm.22378	NM_021334	ENSMUSG00000030789	Itgax	AI449405|Cd11c|Cr4|N418	integrin alpha X	protein-coding
mm_103162.1	chr11	70455222	70455266	-	1	NA	3' UTR (NM_023158, exon 5 of 5)	3' UTR (NM_023158, exon 5 of 5)	3313	NM_025397	66172	Mm.46424	NM_025397	ENSMUSG00000018923	Med11	1110030J09Rik|AI465144|AW545069	mediator complex subunit 11	protein-coding
mm_15362.1	chr2	156420721	156420751	+	1	NA	promoter-TSS (NM_001291121)	promoter-TSS (NM_001291121)	-173	NM_001291122	13821	Mm.20852	NM_013510	ENSMUSG00000027624	Epb41l1	4.1N|Epb4.1l1|NBL1|mKIAA0338	erythrocyte membrane protein band 4.1 like 1	protein-coding
mm_166215.1	chr5	57718139	57718150	+	1	NA	promoter-TSS (NM_001310606)	promoter-TSS (NM_001310606)	63	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_91371.1	chr10	29535808	29535849	-	1	NA	promoter-TSS (NM_028351)	promoter-TSS (NM_028351)	39	NM_028351	72780	Mm.45191	NM_028351	ENSMUSG00000019880	Rspo3	2810459H04Rik|AW742308|Cristin1|Thsd2	R-spondin 3	protein-coding
mm_109601.1	chr12	112679557	112679561	+	1	NA	exon (NM_001100460, exon 2 of 2)	exon (NM_001100460, exon 2 of 2)	719	NM_001100460	382639	Mm.11350	NM_001100460	ENSMUSG00000037638	Zbtb42	EG382639|Gm5188|simiRP58	zinc finger and BTB domain containing 42	protein-coding
mm_2715.1	chr1	128142864	128142871	+	1	NA	intron (NM_181750, intron 1 of 26)	intron (NM_181750, intron 1 of 26)	39561	NM_181750	226412	Mm.221041	NM_181750	ENSMUSG00000056211	R3hdm1	R3hdm	R3H domain containing 1	protein-coding
mm_113221.1	chr13	27059383	27059391	+	1	NA	exon (NM_011164, exon 2 of 5)	exon (NM_011164, exon 2 of 5)	1817	NM_011164	19109	Mm.1270	NM_011164	ENSMUSG00000021342	Prl	AV290867|Gha1|Prl1a1	prolactin	protein-coding
mm_33734.1	chr4	134118090	134118110	+	1	NA	intron (NR_045571, intron 8 of 13)	intron (NR_045571, intron 8 of 13)	10653	NM_080559	73723	Mm.22240	NM_080559	ENSMUSG00000028843	Sh3bgrl3	1110004L05Rik|AU022188	SH3 domain binding glutamic acid-rich protein-like 3	protein-coding
mm_37267.1	chr4	118490031	118490063	-	1	NA	promoter-TSS (NM_011587)	promoter-TSS (NM_011587)	-198	NM_011587	21846	Mm.4345	NM_011587	ENSMUSG00000033191	Tie1	D430008P04Rik|TIE|tie-1	tyrosine kinase with immunoglobulin-like and EGF-like domains 1	protein-coding
mm_70829.1	chr8	23143091	23143095	+	1	NA	promoter-TSS (NR_037293)	promoter-TSS (NR_037293)	-431	NR_037293	100526510		NR_037293	ENSMUSG00000106471	Mir3107	mir-486b|mmu-mir-3107|mmu-mir-486b	microRNA 3107	ncRNA
mm_118155.1	chr13	105250439	105250447	-	1	NA	exon (NM_027934, exon 4 of 8)	exon (NM_027934, exon 4 of 8)	42571	NM_027934	71816	Mm.317015	NM_027934	ENSMUSG00000021720	Rnf180	3110001E11Rik|Rines	ring finger protein 180	protein-coding
mm_19287.1	chr2	90450727	90450729	-	1	NA	intron (NM_001135657, intron 15 of 25)	intron (NM_001135657, intron 15 of 25)	28446	NM_001135657	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_28989.1	chr3	101287898	101287957	-	1	NA	promoter-TSS (NM_013486)	promoter-TSS (NM_013486)	12	NM_013486	12481	Mm.22842	NM_013486	ENSMUSG00000027863	Cd2	LFA-2|Ly-37|Ly37	CD2 antigen	protein-coding
mm_140980.1	chr17	24718007	24718018	-	1	NA	promoter-TSS (NM_026205)	promoter-TSS (NM_026205)	45	NM_026205	67504	Mm.46159	NM_026205	ENSMUSG00000008482	Rnf151	1700010O16Rik|AV047371	ring finger protein 151	protein-coding
mm_142803.1	chr17	50420149	50420195	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-89375	NM_013880	224860	Mm.217362	NM_013880	ENSMUSG00000038910	Plcl2	PLC-L2|PRIP-2|Plce2|mKIAA1092	phospholipase C-like 2	protein-coding
mm_99182.1	chr11	100860327	100860344	+	1	NA	promoter-TSS (NM_001164062)	promoter-TSS (NM_001164062)	-149	NM_001164062	20850	Mm.277403	NM_011488	ENSMUSG00000004043	Stat5a	AA959963|STAT5	signal transducer and activator of transcription 5A	protein-coding
mm_163129.1	chr11	78268093	78268136	+	1	NA	exon (NM_001002004, exon 12 of 39)	exon (NM_001002004, exon 12 of 39)	6360	NM_001002004	72503	Mm.237103	NM_001002004	ENSMUSG00000010277	2610507B11Rik	AU022687|D11Bhm178e|D11Bhm179e|E1|Kiaa0100|mKIAA0100	RIKEN cDNA 2610507B11 gene	protein-coding
mm_102166.1	chr11	53837649	53837657	-	1	NA	intron (NR_033332, intron 2 of 3)	intron (NR_033332, intron 2 of 3)	21603	NR_033332	622459	Mm.479656	NR_033332	ENSMUSG00000081769	Gm12216	602-19-115|OTTMUSG00000005650	predicted gene 12216	ncRNA
mm_113835.1	chr13	47122689	47122715	+	1	NA	promoter-TSS (NM_146042)	promoter-TSS (NM_146042)	-18	NM_146042	218215	Mm.287609	NM_146042	ENSMUSG00000038068	Rnf144b	BC025007|E130105P19Rik|Ibrdc2|Pir2	ring finger protein 144B	protein-coding
mm_24386.1	chr3	90254260	90254332	+	1	NA	promoter-TSS (NM_028881)	promoter-TSS (NM_028881)	15	NM_028881	74343	Mm.35627	NM_028881	ENSMUSG00000027936	Crtc2	4632407F12Rik|Torc2|mTORC2	CREB regulated transcription coactivator 2	protein-coding
mm_70653.1	chr8	14381728	14381745	+	1	NA	intron (NM_172910, intron 3 of 15)	intron (NM_172910, intron 3 of 15)	285861	NM_172910	244310	Mm.404697	NM_172910	ENSMUSG00000047495	Dlgap2	6430596N04Rik|Dap-2|Dap2|Sapap2	discs, large (Drosophila) homolog-associated protein 2	protein-coding
mm_56354.1	chr6	93717589	93717598	-	1	NA	intron (NM_001083321, intron 11 of 21)	intron (NM_001083321, intron 11 of 21)	195370	NR_104594	14924	Mm.217216	NM_010367	ENSMUSG00000045095	Magi1	AIP3|BAP1|Baiap1|Gukmi1|MAGI1c|Magi-1|TNRC19|WWP3|mKIAA4129	membrane associated guanylate kinase, WW and PDZ domain containing 1	protein-coding
mm_131399.1	chr16	14361553	14361601	+	1	NA	promoter-TSS (NM_008576)	promoter-TSS (NM_008576)	19	NM_008576	17250	Mm.196634	NM_008576	ENSMUSG00000023088	Abcc1	Abcc1a|Abcc1b|MRP|Mdrap|Mrp1	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	protein-coding
mm_90220.1	chr10	121034060	121034074	+	1	NA	promoter-TSS (NM_011915)	promoter-TSS (NM_011915)	63	NM_011915	24117	Mm.32831	NM_011915	ENSMUSG00000020218	Wif1	AW107799|WIF-1	Wnt inhibitory factor 1	protein-coding
mm_156756.1	chrX	160438244	160438253	+	1	NA	exon (NM_178712, exon 3 of 28)	exon (NM_178712, exon 3 of 28)	47558	NM_001290445	237175	Mm.213016	NM_178712	ENSMUSG00000031298	Adgrg2	AW212196|B830041D06Rik|Gpr64|Me6	adhesion G protein-coupled receptor G2	protein-coding
mm_132799.1	chr16	45094097	45094117	+	1	NA	promoter-TSS (NM_026439)	promoter-TSS (NM_026439)	54	NM_026439	67896	Mm.181074	NM_026439	ENSMUSG00000022665	Ccdc80	2610001E17Rik|DRO1|Ssg1|Urb	coiled-coil domain containing 80	protein-coding
mm_101993.1	chr11	50943762	50943765	-	1	NA	Intergenic	Intergenic	9869	NM_008936	19127	Mm.1386	NM_008936	ENSMUSG00000044542	Prop1	Prop-1|df	paired like homeodomain factor 1	protein-coding
mm_67555.1	chr7	81706858	81706869	-	1	NA	promoter-TSS (NM_001164086)	promoter-TSS (NM_001164086)	62	NM_011983	26557	Mm.228	NM_011983	ENSMUSG00000025813	Homer2	9330120H11Rik|AW539445|CPD|Vesl-2	homer scaffolding protein 2	protein-coding
mm_20915.1	chr2	150608503	150608561	-	1	NA	promoter-TSS (NM_027977)	promoter-TSS (NM_027977)	-9	NM_027977	71881	Mm.26599	NM_027977	ENSMUSG00000033096	Apmap	2310001A20Rik|AI314817	adipocyte plasma membrane associated protein	protein-coding
mm_78343.1	chr9	25297828	25297846	+	1	NA	exon (NM_001205367, exon 8 of 13)	exon (NM_001205367, exon 8 of 13)	45398	NM_001205367	235072	Mm.270259	NM_009859	ENSMUSG00000001833	Sept7	Cdc10|E430034N22	septin 7	protein-coding
mm_154313.1	chrM	488	498	+	1	NA	NA	Intergenic	NA	NA								
mm_127984.1	chr15	12548587	12548595	-	1	NA	intron (NM_001081064, intron 1 of 23)	L1M5|LINE|L1	43965	NM_001081064	68070	Mm.423205	NM_001081064	ENSMUSG00000022197	Pdzd2	4930537L06Rik|A930022H17Rik|Gm21706|Gm82|Pdzk3|mKIAA0300	PDZ domain containing 2	protein-coding
mm_147857.1	chr18	63694873	63694879	-	1	NA	Intergenic	RLTR1C|LTR|ERV1	-2517	NM_016792	53382	Mm.19169	NM_016792	ENSMUSG00000024583	Txnl1	32kDa|TRP32|Txnl	thioredoxin-like 1	protein-coding
mm_152036.1	chr19	6118235	6118268	-	1	NA	exon (NM_133678, exon 1 of 2)	exon (NM_133678, exon 1 of 2)	335	NM_133678	66406	Mm.303924	NM_133678	ENSMUSG00000024790	Sac3d1	2410004C24Rik|AU015683|shd1	SAC3 domain containing 1	protein-coding
mm_5030.1	chr1	193301971	193301990	+	1	NA	promoter-TSS (NM_001277928)	promoter-TSS (NM_001277928)	-14	NM_008484	16780	Mm.435441	NM_008484	ENSMUSG00000026639	Lamb3	-	laminin, beta 3	protein-coding
mm_45371.1	chr5	66025064	66025090	-	1	NA	exon (NM_139065, exon 5 of 7)	exon (NM_139065, exon 5 of 7)	-20792	NR_027961	231253	Mm.436542	NM_177679	ENSMUSG00000054598	9130230L23Rik	-	RIKEN cDNA 9130230L23 gene	ncRNA
mm_75146.1	chr8	35589013	35589037	-	1	NA	promoter-TSS (NR_040376)	promoter-TSS (NR_040376)	-5	NR_040376	100504714	Mm.381744	NR_040376	ENSMUSG00000097357	Gm16793	-	predicted gene, 16793	ncRNA
mm_58505.1	chr7	3981132	3981134	+	1	NA	Intergenic	Intergenic	-65632	NR_028115	18726	Mm.440989	NM_011090	ENSMUSG00000030427	Lilra6	7M1|Pira3	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	protein-coding
mm_2431.1	chr1	95667834	95667845	+	1	NA	promoter-TSS (NM_001159745)	promoter-TSS (NM_001159745)	-245	NM_001159745	20452	Mm.306228	NM_009183	ENSMUSG00000040710	St8sia4	PST|PST-1|SIAT8-D|ST8SiaIV|Siat8d	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4	protein-coding
mm_91880.1	chr10	59616668	59616695	-	1	NA	promoter-TSS (NM_001033259)	promoter-TSS (NM_001033259)	11	NM_001033259	215999	Mm.296470	NM_001033259	ENSMUSG00000009647	Mcu	2010012O16Rik|AV064928|C10orf42|Ccdc109a|D130073L02Rik|Gm64	mitochondrial calcium uniporter	protein-coding
mm_99100.1	chr11	100052105	100052115	+	1	NA	Intergenic	Intergenic	-1559	NM_010659	16660	Mm.439673	NM_010659	ENSMUSG00000048981	Krt31	Ha1|Kha1|Krt1-1|MKHA-1	keratin 31	protein-coding
mm_46411.1	chr5	104093305	104093320	-	1	NA	exon (NM_010097, exon 4 of 11)	exon (NM_010097, exon 4 of 11)	-15704	NM_001163772	100271704	Mm.366664	NM_001163772	ENSMUSG00000091034	Gm17660	Scpppq1	predicted gene, 17660	protein-coding
mm_34539.1	chr4	149504638	149504677	+	1	NA	Intergenic	B1_Mur1|SINE|Alu	-13584	NM_023465	67087	Mm.299735	NM_023465	ENSMUSG00000028988	Ctnnbip1	1110008O09Rik|2310001I19Rik|AW457332|Catnbip1|Icat	catenin beta interacting protein 1	protein-coding
mm_28042.1	chr3	83859743	83859748	-	1	NA	Intergenic	Intergenic	-18137	NM_011905	24088	Mm.87596	NM_011905	ENSMUSG00000027995	Tlr2	Ly105	toll-like receptor 2	protein-coding
mm_106217.1	chr11	117040169	117040180	-	1	NA	Intergenic	Intergenic	-36609	NR_027059	76972	Mm.309167	NR_027059	ENSMUSG00000086859	Snhg20	2810008D09Rik	small nucleolar RNA host gene 20	ncRNA
mm_139126.1	chr17	47505074	47505084	+	1	NA	promoter-TSS (NM_001081636)	promoter-TSS (NM_001081636)	28	NM_001081635	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_117354.1	chr13	69772607	69772618	-	1	NA	Intergenic	MLTR73|LTR|ERV1	-32715	NM_001145162	76980	Mm.23960	NM_001145162	ENSMUSG00000052981	Ube2ql1	3110006E14Rik	ubiquitin-conjugating enzyme E2Q family-like 1	protein-coding
mm_169626.1	chr15	41234295	41234295	+	1	NA	Intergenic	LTRIS2|LTR|ERV1	-213187	NM_001130166	170719	Mm.254267	NM_130885	ENSMUSG00000022307	Oxr1	2210416C20Rik|C7|C7B	oxidation resistance 1	protein-coding
mm_66407.1	chr7	44478931	44478951	-	1	NA	Intergenic	L1M4c|LINE|L1	-5576	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_36391.1	chr4	77454177	77454184	-	1	NA	intron (NM_011211, intron 4 of 39)	intron (NM_011211, intron 4 of 39)	757715	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding
mm_75672.1	chr8	67862070	67862073	-	1	NA	intron (NM_030263, intron 6 of 12)	intron (NM_030263, intron 6 of 12)	-43776	NM_027626	234353	Mm.32525	NM_027626	ENSMUSG00000030465	Psd3	4931420C21Rik|AI661273|BC003498|D430018P08|EFA6D	pleckstrin and Sec7 domain containing 3	protein-coding
mm_64006.1	chr7	140203692	140203715	+	1	NA	promoter-TSS (NM_001011814)	promoter-TSS (NM_001011814)	-935	NM_001011814	258055	Mm.377339	NM_001011814	ENSMUSG00000050366	Olfr524	MOR103-14P	olfactory receptor 524	protein-coding
mm_110055.1	chr12	20921046	20921083	-	1	NA	Intergenic	CpG	-105285	NR_015521	69513	Mm.273972	NR_015521	ENSMUSG00000099759	1700030C10Rik	-	RIKEN cDNA 1700030C10 gene	ncRNA
mm_106675.1	chr11	121744068	121744092	-	1	NA	Intergenic	Intergenic	41653	NM_144797	210029	Mm.153566	NM_144797	ENSMUSG00000039208	Metrnl	9430048M07Rik|BC019776	meteorin, glial cell differentiation regulator-like	protein-coding
mm_86973.1	chr10	25404567	25404570	+	1	NA	intron (NM_001199265, intron 1 of 19)	intron (NM_001199265, intron 1 of 19)	-3800	NM_013511	13822	Mm.306026	NM_013511	ENSMUSG00000019978	Epb41l2	4.1G|AW555191|D10Ertd398e|Epb4.1l2|NBL2	erythrocyte membrane protein band 4.1 like 2	protein-coding
mm_168751.1	chr12	115834438	115834452	-	1	NA	Intergenic	Intergenic	-138651	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
mm_126985.1	chr15	94205320	94205326	+	1	NA	Intergenic	Intergenic	-41879	NR_045629	328594	Mm.135523	NR_045629		D630010B17Rik	Gm811	RIKEN cDNA D630010B17 gene	ncRNA
mm_136104.1	chr16	85163038	85163041	-	1	NA	intron (NM_007471, intron 1 of 15)	MTEa|LTR|ERVL-MaLR	10668	NM_001198825	11820	Mm.277585	NM_007471	ENSMUSG00000022892	App	Abeta|Abpp|Adap|Ag|Cvap|E030013M08Rik|betaApp	amyloid beta (A4) precursor protein	protein-coding
mm_54803.1	chr6	41701910	41701913	-	1	NA	intron (NM_032540, intron 6 of 18)	intron (NM_032540, intron 6 of 18)	2414	NM_032540	23925	Mm.19958	NM_032540	ENSMUSG00000029866	Kel	CD238|Ece3	Kell blood group	protein-coding
mm_143679.1	chr17	80061000	80061011	-	1	NA	intron (NM_144802, intron 1 of 12)	intron (NM_144802, intron 1 of 12)	1263	NM_144802	72692	Mm.64579	NM_144802	ENSMUSG00000024095	Hnrnpll	2510028H02Rik|2810036L13Rik|AI256697|AI852082|Hnrpll	heterogeneous nuclear ribonucleoprotein L-like	protein-coding
mm_113041.1	chr13	23571383	23571392	+	1	NA	promoter-TSS (NM_178196)	promoter-TSS (NM_178196)	-13	NM_178196	319181	Mm.261673	NM_178196	ENSMUSG00000058385	Hist1h2bg	-	histone cluster 1, H2bg	protein-coding
mm_72757.1	chr8	85492569	85492626	+	1	NA	promoter-TSS (NM_173866)	promoter-TSS (NM_173866)	-20	NM_173866	108682	Mm.200423	NM_173866	ENSMUSG00000031700	Gpt2	4631422C05Rik|ALT2|AU014768|AU041193|C87201	glutamic pyruvate transaminase (alanine aminotransferase) 2	protein-coding
mm_19460.1	chr2	92392336	92392396	-	1	NA	5' UTR (NM_001202446, exon 1 of 12)	5' UTR (NM_001202446, exon 1 of 12)	317	NM_001202446	19099	Mm.2720	NM_011162	ENSMUSG00000027223	Mapk8ip1	IB1|JIP-1|Jip1|Prkm8ip|Skip|mjip-2a	mitogen-activated protein kinase 8 interacting protein 1	protein-coding
mm_91001.1	chr10	14545207	14545225	-	1	NA	promoter-TSS (NM_001002268)	promoter-TSS (NM_001002268)	-180	NM_001002268	215798	Mm.440142	NM_001002268	ENSMUSG00000039116	Adgrg6	1190004A11Rik|AI449247|AW045736|DREG|Gm222|Gpr126	adhesion G protein-coupled receptor G6	protein-coding
mm_127729.1	chr15	103272889	103272892	+	1	NA	promoter-TSS (NM_019817)	promoter-TSS (NM_019817)	-28	NM_019817	56447	Mm.29473	NM_019817	ENSMUSG00000060992	Copz1	5930435A22Rik|AA407760|D4Ertd360e	coatomer protein complex, subunit zeta 1	protein-coding
mm_24148.1	chr3	88336257	88336304	+	1	NA	promoter-TSS (NM_178246)	promoter-TSS (NM_178246)	20	NM_178246	229512	Mm.439830	NM_173188	ENSMUSG00000001415	Smg5	BC024683|mKIAA1089	Smg-5 homolog, nonsense mediated mRNA decay factor (C. elegans)	protein-coding
mm_13248.1	chr2	98663721	98663740	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	1196073	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_11687.1	chr2	35622199	35622200	+	1	NA	exon (NM_001114124, exon 1 of 16)	exon (NM_001114124, exon 1 of 16)	218	NM_001114124	69601	Mm.29629	NM_001001602	ENSMUSG00000026883	Dab2ip	2310011D08Rik|AI480459|Aip1|mKIAA1743	disabled 2 interacting protein	protein-coding
mm_38525.1	chr4	141425569	141425603	-	1	NA	TTS (NM_013868)	TTS (NM_013868)	4807	NM_013868	29818	Mm.46181	NM_013868	ENSMUSG00000006221	Hspb7	27kDa|Hsp25-2|cvHsp	heat shock protein family, member 7 (cardiovascular)	protein-coding
mm_92741.1	chr10	80941899	80941906	-	1	NA	Intergenic	Intergenic	11811	NM_008655	17873	Mm.1360	NM_008655	ENSMUSG00000015312	Gadd45b	AI323528|Myd118	growth arrest and DNA-damage-inducible 45 beta	protein-coding
mm_82317.1	chr9	7965812	7965820	-	1	NA	intron (NM_009534, intron 3 of 7)	B3A|SINE|B2	38780	NM_001171147	22601	Mm.221992	NM_009534	ENSMUSG00000053110	Yap1	AI325207|Yap|Yap65|Yki|Yorkie	yes-associated protein 1	protein-coding
mm_31139.1	chr4	43382035	43382084	+	1	NA	promoter-TSS (NM_001037709)	promoter-TSS (NM_001037709)	77	NM_001037709	100213	Mm.235730	NM_199057	ENSMUSG00000035969	Rusc2	AI840675|mKIAA0375	RUN and SH3 domain containing 2	protein-coding
mm_3272.1	chr1	136566676	136566687	+	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-58220	NM_177643	226442	Mm.62521	NM_177643	ENSMUSG00000041483	Zfp281	Znf281	zinc finger protein 281	protein-coding
mm_42203.1	chr5	112326429	112326442	+	1	NA	promoter-TSS (NM_018783)	promoter-TSS (NM_018783)	66	NM_018783	54723	Mm.172947	NM_018783	ENSMUSG00000029345	Tfip11	2810002G02Rik|AF097181|AW046167|Srr1|TIP33|Tip39	tuftelin interacting protein 11	protein-coding
mm_30930.1	chr4	32982984	32983003	+	1	NA	promoter-TSS (NM_027491)	promoter-TSS (NM_027491)	-5	NM_027491	52187	Mm.300814	NM_027491	ENSMUSG00000028278	Rragd	5730543C08Rik|AI467523|C030003H22Rik|D4Ertd174e	Ras-related GTP binding D	protein-coding
mm_114514.1	chr13	72632615	72632625	+	1	NA	exon (NM_010574, exon 4 of 5)	exon (NM_010574, exon 4 of 5)	3823	NM_010574	16372	Mm.28888	NM_010574	ENSMUSG00000001504	Irx2	-	Iroquois related homeobox 2 (Drosophila)	protein-coding
mm_39036.1	chr4	152317749	152317759	-	1	NA	exon (NM_001033489, exon 2 of 17)	exon (NM_001033489, exon 2 of 17)	871	NM_001033489	433809	Mm.156205	NM_001033489	ENSMUSG00000058498	Rnf207	D330010C22Rik|Gm143	ring finger protein 207	protein-coding
mm_28556.1	chr3	93433849	93433854	-	1	NA	Intergenic	Intergenic	5360	NR_039585	100628630		NR_039585	ENSMUSG00000093269	Mir5124a	Mir5124|mmu-mir-5124|mmu-mir-5124a|mu-mir-5124	microRNA 5124a	ncRNA
mm_87521.1	chr10	53280257	53280263	+	1	NA	promoter-TSS (NR_038015)	promoter-TSS (NR_038015)	-10	NR_038015	100502820	Mm.55827	NR_038015		Gm19395	-	predicted gene, 19395	ncRNA
mm_159333.1	chr3	40894246	40894246	+	1	NA	promoter-TSS (NM_026622)	promoter-TSS (NM_026622)	-31	NM_026622	269423	Mm.32373	NM_026622	ENSMUSG00000037818	Abhd18	2310068E01Rik|3110057O12Rik|AI645591	abhydrolase domain containing 18	protein-coding
mm_95094.1	chr11	33963282	33963297	+	1	NA	5' UTR (NM_031169, exon 1 of 4)	5' UTR (NM_031169, exon 1 of 4)	276	NM_031169	16533	Mm.6206	NM_031169	ENSMUSG00000020155	Kcnmb1	BKbeta1	potassium large conductance calcium-activated channel, subfamily M, beta member 1	protein-coding
mm_18680.1	chr2	71342841	71342854	-	1	NA	intron (NM_172436, intron 3 of 17)	intron (NM_172436, intron 3 of 17)	24707	NM_172436	78830	Mm.30928	NM_172436	ENSMUSG00000027010	Slc25a12	2610002D09Rik|AI839531|B230107K20Rik|BB129864	solute carrier family 25 (mitochondrial carrier, Aralar), member 12	protein-coding
mm_98122.1	chr11	87127268	87127279	+	1	NA	5' UTR (NM_197987, exon 1 of 24)	5' UTR (NM_197987, exon 1 of 24)	198	NM_197987	68729	Mm.17436	NM_197987	ENSMUSG00000018548	Trim37	1110032A10Rik|2810004E07Rik|AI848587|AU043018|MUL|TEF3|mKIAA0898	tripartite motif-containing 37	protein-coding
mm_60845.1	chr7	45785571	45785607	+	1	NA	non-coding (NR_110987, exon 2 of 16)	non-coding (NR_110987, exon 2 of 16)	209	NM_001290990	381983	Mm.44928	NM_001005511	ENSMUSG00000062044	Lmtk3	BC059845|aatyk3	lemur tyrosine kinase 3	protein-coding
mm_25339.1	chr3	106721793	106721803	+	1	NA	5' UTR (NM_001039488, exon 1 of 4)	5' UTR (NM_001039488, exon 1 of 4)	116	NM_001286685	321000	Mm.259638	NM_028081	ENSMUSG00000056260	Lrif1	2010012G17Rik|4933421E11Rik|AI450568	ligand dependent nuclear receptor interacting factor 1	protein-coding
mm_84880.1	chr9	79718792	79718801	-	1	NA	promoter-TSS (NM_001290308)	promoter-TSS (NM_001290308)	-74	NM_001290308	12816	Mm.3819	NM_007730	ENSMUSG00000032332	Col12a1	-	collagen, type XII, alpha 1	protein-coding
mm_44359.1	chr5	17797015	17797068	-	1	NA	exon (NM_001159558, exon 11 of 16)	exon (NM_001159558, exon 11 of 16)	38855	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_157459.1	chrX	43429056	43429069	-	1	NA	Intergenic	Intergenic	-154278	NM_011855	23963	Mm.327698	NM_011855	ENSMUSG00000016150	Tenm1	Odz1|Odz2|TCAP-1|Ten-m1|ten-1	teneurin transmembrane protein 1	protein-coding
mm_128803.1	chr15	66943114	66943136	-	1	NA	exon (NM_008681, exon 8 of 16)	exon (NM_008681, exon 8 of 16)	26516	NM_008681	17988	Mm.30837	NM_008681	ENSMUSG00000005125	Ndrg1	CAP43|CMT4D|DRG1|HMSNL|NMSL|Ndr1|Ndrl|PROXY1|RTP|TDD5	N-myc downstream regulated gene 1	protein-coding
mm_114122.1	chr13	55190451	55190465	+	1	NA	Intergenic	CpG	-19324	NM_008739	18193	Mm.12964	NM_008739	ENSMUSG00000021488	Nsd1	AI528500|KMT3B	nuclear receptor-binding SET-domain protein 1	protein-coding
mm_102913.1	chr11	69579321	69579352	-	1	NA	promoter-TSS (NM_144824)	promoter-TSS (NM_144824)	-12	NM_144824	216853	Mm.31586	NM_144824	ENSMUSG00000041346	Wrap53	BC021790|Wdr79	WD repeat containing, antisense to Trp53	protein-coding
mm_172351.1	chr7	114120218	114120227	+	1	NA	Intergenic	L1Md_T|LINE|L1	-2441	NM_025846	66922	Mm.276572	NM_025846	ENSMUSG00000055723	Rras2	2610016H24Rik|C86394|TC21	related RAS viral (r-ras) oncogene 2	protein-coding
mm_146750.1	chr18	16745267	16745275	-	1	NA	intron (NM_007664, intron 2 of 15)	intron (NM_007664, intron 2 of 15)	63975	NM_007664	12558	Mm.257437	NM_007664	ENSMUSG00000024304	Cdh2	CDHN|N-CAD|Ncad	cadherin 2	protein-coding
mm_27347.1	chr3	50414903	50414913	-	1	NA	intron (NM_011990, intron 6 of 11)	intron (NM_011990, intron 6 of 11)	28705	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_141238.1	chr17	27437032	27437039	-	1	NA	intron (NM_001013385, intron 7 of 8)	intron (NM_001013385, intron 7 of 8)	66498	NM_001013385	268934	Mm.358940	NM_001013385	ENSMUSG00000063239	Grm4	Gprc1d|mGluR4	glutamate receptor, metabotropic 4	protein-coding
mm_36292.1	chr4	64276596	64276604	-	1	NA	Intergenic	Intergenic	-229585	NM_011607	21923	Mm.980	NM_011607	ENSMUSG00000028364	Tnc	AI528729|C130033P17Rik|Hxb|TN|TN-C|Ten|cytotactin|tenascin-C	tenascin C	protein-coding
mm_89824.1	chr10	105574539	105574566	+	1	NA	promoter-TSS (NM_177368)	promoter-TSS (NM_177368)	1	NR_038032	327812	Mm.191660	NR_038032	ENSMUSG00000085282	Gm15663	9330159K06|OTTMUSG00000025047	predicted gene 15663	ncRNA
mm_144573.1	chr18	31857075	31857085	+	1	NA	intron (NM_028866, intron 7 of 21)	intron (NM_028866, intron 7 of 21)	53023	NM_001170966	74320	Mm.277705	NM_028866	ENSMUSG00000024400	Wdr33	1110001N06Rik|2310011G05Rik|2810021O11Rik|8430413N20Rik|WDC146	WD repeat domain 33	protein-coding
mm_54370.1	chr6	31131718	31131726	-	1	NA	intron (NR_110471, intron 3 of 3)	intron (NR_110471, intron 3 of 3)	-68629	NR_029532	387223		NR_029532	ENSMUSG00000065604	Mir29b-1	Mirn29b|Mirn29b-1|mir-29b-1	microRNA 29b-1	ncRNA
mm_113928.1	chr13	49609056	49609096	+	1	NA	intron (NM_008760, intron 1 of 6)	intron (NM_008760, intron 1 of 6)	1005	NM_008760	18295	Mm.4258	NM_008760	ENSMUSG00000021390	Ogn	3110079A16Rik|OG|OIF|SLRR3A|mimecan|mimican	osteoglycin	protein-coding
mm_144048.1	chr17	90447651	90447659	-	1	NA	intron (NM_001346957, intron 14 of 18)	intron (NM_001346957, intron 14 of 18)	8225	NM_001346958	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_15581.1	chr2	158723440	158723450	+	1	NA	intron (NM_153089, intron 2 of 10)	intron (NM_153089, intron 2 of 10)	-44654	NM_027975	71878	Mm.85162	NM_027975	ENSMUSG00000027654	Fam83d	2310007D09Rik|BB104611	family with sequence similarity 83, member D	protein-coding
mm_89457.1	chr10	93162113	93162127	+	1	NA	promoter-TSS (NR_035452)	promoter-TSS (NR_035452)	-665	NR_035452	100316689		NR_035452	ENSMUSG00000089214	Mir1931	mir-1931|mmu-mir-1931	microRNA 1931	ncRNA
mm_123725.1	chr14	70153818	70153846	-	1	NA	promoter-TSS (NM_146055)	promoter-TSS (NM_146055)	-41	NM_146055	219158	Mm.218284	NM_146055	ENSMUSG00000033712	Ccar2	2610301G19Rik|Dbc1|mKIAA1967	cell cycle activator and apoptosis regulator 2	protein-coding
mm_120374.1	chr14	64587479	64587489	+	1	NA	promoter-TSS (NR_040709)	promoter-TSS (NR_040709)	-631	NR_040709	268755	Mm.194050	NR_040709	ENSMUSG00000097545	Mir124a-1hg	A930011O12Rik|Rncr3|mir-124-1|mir-3078	Mir124-1 host gene (non-protein coding)	ncRNA
mm_80333.1	chr9	75052074	75052082	+	1	NA	intron (NM_021548, intron 1 of 2)	intron (NM_021548, intron 1 of 2)	14346	NM_021548	59046	Mm.247837	NM_021548	ENSMUSG00000007656	Arpp19	19kDa|2700024H10Rik|ARPP-19|AW559096|Arpp12	cAMP-regulated phosphoprotein 19	protein-coding
mm_133159.1	chr16	70402779	70402781	+	1	NA	intron (NM_028803, intron 3 of 15)	B2_Mm2|SINE|B2	88831	NM_028803	74185	Mm.396102	NM_028803	ENSMUSG00000022707	Gbe1	2310045H19Rik|2810426P10Rik|D16Ertd536e	glucan (1,4-alpha-), branching enzyme 1	protein-coding
mm_65756.1	chr7	28629723	28629741	-	1	NA	intron (NM_175319, intron 1 of 12)	intron (NM_175319, intron 1 of 12)	1283	NM_175319	101744	Mm.26022	NM_175319	ENSMUSG00000037469	Acp7	AU017076|C330005M16Rik|Papl	acid phosphatase 7, tartrate resistant	protein-coding
mm_105273.1	chr11	102406784	102406828	-	1	NA	intron (NM_026542, intron 1 of 11)	intron (NM_026542, intron 1 of 11)	711	NM_026542	68066	Mm.44226	NM_026542	ENSMUSG00000018677	Slc25a39	3010027G13Rik|D11Ertd333e	solute carrier family 25, member 39	protein-coding
mm_85472.1	chr9	105819468	105819496	-	1	NA	intron (NM_001102607, intron 1 of 36)	LSU-rRNA_Hsa|rRNA|rRNA	8603	NM_001102607	245026	Mm.482507	NM_172927	ENSMUSG00000043719	Col6a6	E330019B14|E330026B02Rik	collagen, type VI, alpha 6	protein-coding
mm_117677.1	chr13	93674301	93674309	-	1	NA	promoter-TSS (NM_022884)	promoter-TSS (NM_022884)	-3	NM_022884	64918	Mm.29981	NM_022884	ENSMUSG00000042118	Bhmt2	C81077|D13Ucla2	betaine-homocysteine methyltransferase 2	protein-coding
mm_11683.1	chr2	35581603	35581651	+	1	NA	intron (NM_001114125, intron 1 of 16)	CpG	-1213	NM_001290637	69601	Mm.29629	NM_001001602	ENSMUSG00000026883	Dab2ip	2310011D08Rik|AI480459|Aip1|mKIAA1743	disabled 2 interacting protein	protein-coding
mm_121093.1	chr14	99301900	99301913	+	1	NA	exon (NM_009769, exon 2 of 4)	exon (NM_009769, exon 2 of 4)	3215	NM_009769	12224	Mm.30262	NM_009769	ENSMUSG00000005148	Klf5	4930520J07Rik|Bteb2|CKLF|IKLF	Kruppel-like factor 5	protein-coding
mm_49132.1	chr6	8948571	8948602	+	1	NA	Intergenic	CpG	-1433	NM_008751	18231	Mm.46954	NM_008751	ENSMUSG00000046178	Nxph1	C130005L03Rik	neurexophilin 1	protein-coding
mm_116818.1	chr13	54565300	54565362	-	1	NA	promoter-TSS (NM_001252648)	promoter-TSS (NM_001252648)	51	NM_001252647	97820	Mm.24593	NM_133797	ENSMUSG00000025871	4833439L19Rik	4930558H15Rik|C81457|Kiaa1191|P33monox	RIKEN cDNA 4833439L19 gene	protein-coding
mm_101976.1	chr11	50326096	50326107	-	1	NA	promoter-TSS (NM_001110500)	promoter-TSS (NM_001110500)	-428	NM_001110500	12330	Mm.248827	NM_007597	ENSMUSG00000020368	Canx	1110069N15Rik|AI988026|Cnx|D11Ertd153e	calnexin	protein-coding
mm_24441.1	chr3	90601774	90601809	+	1	NA	exon (NM_011310, exon 2 of 3)	exon (NM_011310, exon 2 of 3)	1576	NM_011310	20197	Mm.440044	NM_011310	ENSMUSG00000001021	S100a3	S100E	S100 calcium binding protein A3	protein-coding
mm_171877.1	chr5	3236388	3236403	+	1	NA	Intergenic	Intergenic	-107498	NM_009873	12571	Mm.31672	NM_009873	ENSMUSG00000040274	Cdk6	AI504062|Crk2	cyclin-dependent kinase 6	protein-coding
mm_42542.1	chr5	115974855	115974856	+	1	NA	intron (NM_007708, intron 27 of 46)	intron (NM_007708, intron 27 of 46)	49573	NM_031869	19079	Mm.458152	NM_031869	ENSMUSG00000029513	Prkab1	1300015D22Rik|AU021155|E430008F22	protein kinase, AMP-activated, beta 1 non-catalytic subunit	protein-coding
mm_84442.1	chr9	66124852	66124871	-	1	NA	promoter-TSS (NM_019727)	promoter-TSS (NM_019727)	25	NM_019727	56440	Mm.271891	NM_019727	ENSMUSG00000032382	Snx1	-	sorting nexin 1	protein-coding
mm_126525.1	chr15	81949214	81949221	+	1	NA	exon (NM_145473, exon 4 of 4)	exon (NM_145473, exon 4 of 4)	11713	NM_001282040	29858	Mm.18939	NM_013872	ENSMUSG00000022474	Pmm1	C77612	phosphomannomutase 1	protein-coding
mm_145752.1	chr18	64661159	64661183	+	1	NA	promoter-TSS (NM_001001488)	promoter-TSS (NM_001001488)	-171	NM_001001488	54670	Mm.270043	NM_001001488	ENSMUSG00000039529	Atp8b1	AI451886|FIC1|Ic	ATPase, class I, type 8B, member 1	protein-coding
mm_41802.1	chr5	103753945	103753963	+	1	NA	promoter-TSS (NM_133919)	promoter-TSS (NM_133919)	-208	NM_133919	17355	Mm.6949	NM_133919	ENSMUSG00000029313	Aff1	9630032B01Rik|AW319193|Af4|Mllt2h|Rob	AF4/FMR2 family, member 1	protein-coding
mm_56680.1	chr6	113843482	113843493	-	1	NA	intron (NM_001347365, intron 2 of 23)	intron (NM_001347365, intron 2 of 23)	48052	NM_001036684	11941	Mm.321755	NM_009723	ENSMUSG00000030302	Atp2b2	D6Abb2e|Gena300|PMCA2|Tmy|dfw|jog|wms|wri	ATPase, Ca++ transporting, plasma membrane 2	protein-coding
mm_137063.1	chr17	19435332	19435334	+	1	NA	Intergenic	RLTR50A|LTR|ERVK	-69478	NM_001104562	627537	Mm.469858	NM_001104562	ENSMUSG00000091859	Vmn2r100	EG627537	vomeronasal 2, receptor 100	protein-coding
mm_120569.1	chr14	69029380	69029414	+	1	NA	exon (NM_009285, exon 1 of 4)	exon (NM_009285, exon 1 of 4)	108	NM_009285	20855	Mm.20911	NM_009285	ENSMUSG00000014813	Stc1	Stc	stanniocalcin 1	protein-coding
mm_9615.1	chr1	176214016	176214024	-	1	NA	promoter-TSS (NM_001195816)	promoter-TSS (NM_001195816)	-78	NM_001195816	319455	Mm.338001	NM_176916	ENSMUSG00000055214	Pld5	B230365F16Rik	phospholipase D family, member 5	protein-coding
mm_129934.1	chr15	84855094	84855127	-	1	NA	intron (NR_030731, intron 1 of 11)	CpG-5189	1019	NM_001081166	271305	Mm.101022	NM_001081166	ENSMUSG00000016624	Phf21b	A730032D07Rik	PHD finger protein 21B	protein-coding
mm_93006.1	chr10	87057905	87057913	-	1	NA	promoter-TSS (NM_029685)	promoter-TSS (NM_029685)	-137	NM_029685	76640	Mm.78423	NM_029685	ENSMUSG00000047129	1700113H08Rik	-	RIKEN cDNA 1700113H08 gene	protein-coding
mm_142250.1	chr17	37483571	37483581	-	1	NA	promoter-TSS (NM_008204)	promoter-TSS (NM_008204)	-22	NM_001347387	14990	Mm.329041	NM_008204	ENSMUSG00000016283	H2-M2	H-2M2|Thy19.4	histocompatibility 2, M region locus 2	protein-coding
mm_98914.1	chr11	98210797	98210828	+	1	NA	exon (NM_026952, exon 2 of 13)	exon (NM_026952, exon 2 of 13)	7507	NM_001109626	69131	Mm.260516	NM_026952	ENSMUSG00000003119	Cdk12	1810022J16Rik|AI646528|Crk7|Crkrs|D11Ertd752e|Pksc	cyclin-dependent kinase 12	protein-coding
mm_170137.1	chr17	39847873	39847875	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	4877	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_29643.1	chr3	121847087	121847090	-	1	NA	Intergenic	Lx5b|LINE|L1	-31873	NM_008991	19299	Mm.399042	NM_008991	ENSMUSG00000028127	Abcd3	AI313901|AU018866|AW146054|PMP68|PMP70|Pxmp1	ATP-binding cassette, sub-family D (ALD), member 3	protein-coding
mm_47482.1	chr5	123865445	123865451	-	1	NA	promoter-TSS (NM_030701)	promoter-TSS (NM_030701)	68	NM_030701	80885	Mm.440567	NM_030701	ENSMUSG00000045502	Hcar2	Gpr109a|Gpr109b|HM74|Niacr1|PUMA-G|Pumag|mHM74b	hydroxycarboxylic acid receptor 2	protein-coding
mm_74108.1	chr8	122879275	122879281	+	1	NA	Intergenic	B1F|SINE|Alu	30904	NM_007662	12555	Mm.1976	NM_007662	ENSMUSG00000031962	Cdh15	AI323380|Cdh14|Mcad	cadherin 15	protein-coding
mm_27757.1	chr3	69598931	69598943	-	1	NA	promoter-TSS (NM_020026)	promoter-TSS (NM_020026)	23	NM_020026	26879	Mm.153710	NM_020026	ENSMUSG00000043300	B3galnt1	B3galt3|b3GT3	UDP-GalNAc:betaGlcNAc beta 1,3-galactosaminyltransferase, polypeptide 1	protein-coding
mm_50242.1	chr6	42351751	42351759	+	1	NA	exon (NM_001289618, exon 4 of 10)	exon (NM_001289618, exon 4 of 10)	1927	NM_001289619	22793	Mm.282303	NM_011777	ENSMUSG00000029860	Zyx	9530098H06Rik|R75157	zyxin	protein-coding
mm_71868.1	chr8	69112452	69112497	+	1	NA	exon (NM_007509, exon 14 of 14)	exon (NM_007509, exon 14 of 14)	-23252	NM_153054	110877	Mm.19301	NM_153054	ENSMUSG00000036330	Slc18a1	4832416I10Rik|Vat1|Vmat1	solute carrier family 18 (vesicular monoamine), member 1	protein-coding
mm_93172.1	chr10	93311074	93311161	-	1	NA	promoter-TSS (NM_001322268)	promoter-TSS (NM_001322268)	42	NM_001322268	13713	Mm.4454	NM_013508	ENSMUSG00000008398	Elk3	D430049E23Rik|Erp|Etrp|Net|Sap-2	ELK3, member of ETS oncogene family	protein-coding
mm_136680.1	chr17	6659182	6659186	+	1	NA	Intergenic	Intergenic	-3245	NM_001166627	100040531	Mm.457987	NM_001166627	ENSMUSG00000095677	Dynlt1f	100040631|Dynlt1e	dynein light chain Tctex-type 1F	protein-coding
mm_120701.1	chr14	70941910	70941916	+	1	NA	intron (NM_001302094, intron 3 of 7)	intron (NM_001302094, intron 3 of 7)	51806	NM_001302094	14586	Mm.32619	NM_008115	ENSMUSG00000022103	Gfra2	-	glial cell line derived neurotrophic factor family receptor alpha 2	protein-coding
mm_110327.1	chr12	34917090	34917100	-	1	NA	promoter-TSS (NM_001271386)	promoter-TSS (NM_001271386)	0	NM_001271386	79221	Mm.310551	NM_024124	ENSMUSG00000004698	Hdac9	AV022454|D030072B18Rik|HD7B|HD9|HDRP|Hdac7b|Mitr|mKIAA0744	histone deacetylase 9	protein-coding
mm_19078.1	chr2	77817492	77817494	-	1	NA	promoter-TSS (NM_178723)	promoter-TSS (NM_178723)	-677	NM_178723	241494	Mm.490320	NM_178723	ENSMUSG00000027016	Zfp385b	B830010L13Rik|C130013B13Rik|Zfp533|Znf385b	zinc finger protein 385B	protein-coding
mm_12767.1	chr2	79284804	79284808	+	1	NA	exon (NM_010576, exon 10 of 28)	exon (NM_010576, exon 10 of 28)	29380	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D|Itga4B	integrin alpha 4	protein-coding
mm_134456.1	chr16	18411894	18411904	-	1	NA	exon (NM_001111062, exon 3 of 6)	exon (NM_001111062, exon 3 of 6)	1595	NM_001111063	12846	Mm.100940	NM_007744	ENSMUSG00000000326	Comt	Comt1|D16Wsu103e|D330014B15Rik	catechol-O-methyltransferase	protein-coding
mm_171544.1	chr4	147021859	147021863	+	1	NA	promoter-TSS (NM_001177767)	promoter-TSS (NM_001177767)	11	NM_001177767	100043034	Mm.422606	NM_001177767	ENSMUSG00000067919	Rex2	Gm13138|OTTMUSG00000010655	reduced expression 2	protein-coding
mm_47317.1	chr5	122459626	122459636	-	1	NA	exon (NM_009722, exon 16 of 21)	exon (NM_009722, exon 16 of 21)	37187	NM_019805	56317	Mm.37341	NM_019805	ENSMUSG00000029466	Anapc7	APC7|AW545589	anaphase promoting complex subunit 7	protein-coding
mm_9988.1	chr1	191318091	191318126	-	1	NA	promoter-TSS (NM_025424)	promoter-TSS (NM_025424)	10	NM_025424	66208	Mm.46444	NM_025424	ENSMUSG00000037499	Nenf	1110060M21Rik|SCIRP10|Spuf	neuron derived neurotrophic factor	protein-coding
mm_68131.1	chr7	102210271	102210277	-	1	NA	promoter-TSS (NM_001291358)	promoter-TSS (NM_001291358)	-61	NM_001291358	233575	Mm.302013	NM_145583	ENSMUSG00000030990	Pgap2	1810006G21Rik|C76649|Frag1	post-GPI attachment to proteins 2	protein-coding
mm_167928.1	chrX	103706042	103706042	+	1	NA	intron (NM_009197, intron 4 of 5)	intron (NM_009197, intron 4 of 5)	75456	NM_029158	75064	Mm.159414	NM_029158	ENSMUSG00000031330	Zcchc13	4930513O09Rik|Cnbp2	zinc finger, CCHC domain containing 13	protein-coding
mm_128882.1	chr15	73102880	73102881	-	1	NA	3' UTR (NM_153178, exon 19 of 19)	3' UTR (NM_153178, exon 19 of 19)	12468	NM_053068	93696	Mm.23095	NM_053068	ENSMUSG00000068391	Chrac1	2410152E03Rik|2810406L04Rik|YCL1	chromatin accessibility complex 1	protein-coding
mm_131394.1	chr16	14317442	14317473	+	1	NA	promoter-TSS (NM_025345)	promoter-TSS (NM_025345)	-125	NM_025345	66086	Mm.42072	NM_025345	ENSMUSG00000022677	Fopnl	0610037P05Rik	Fgfr1op N-terminal like	protein-coding
mm_167043.1	chr7	80285121	80285131	+	1	NA	intron (NM_178070, intron 12 of 22)	intron (NM_178070, intron 12 of 22)	-9325	NM_145150	233406	Mm.227274	NM_145150	ENSMUSG00000038943	Prc1	D7Ertd348e	protein regulator of cytokinesis 1	protein-coding
mm_21662.1	chr2	164425177	164425215	-	1	NA	3' UTR (NM_011521, exon 5 of 5)	3' UTR (NM_011521, exon 5 of 5)	17992	NM_011521	20971	Mm.3815	NM_011521	ENSMUSG00000017009	Sdc4	AA959608|AW108331|S4|Synd4|ryudocan|syndecan-4	syndecan 4	protein-coding
mm_152337.1	chr19	9982426	9982435	-	1	NA	promoter-TSS (NM_010239)	promoter-TSS (NM_010239)	-216	NM_010239	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
mm_52701.1	chr6	119267462	119267505	+	1	NA	intron (NM_001347427, intron 6 of 36)	intron (NM_001347427, intron 6 of 36)	30957	NM_001347427	319734	Mm.440773	NM_001033382	ENSMUSG00000041460	Cacna2d4	5730412N02Rik|BE686333	calcium channel, voltage-dependent, alpha 2/delta subunit 4	protein-coding
mm_42282.1	chr5	114248261	114248288	+	1	NA	exon (NM_133904, exon 49 of 52)	exon (NM_133904, exon 49 of 52)	25487	NM_148935	116810	Mm.17709	NM_148935	ENSMUSG00000042002	Foxn4	-	forkhead box N4	protein-coding
mm_108386.1	chr12	80945524	80945541	+	1	NA	promoter-TSS (NM_001079694)	promoter-TSS (NM_001079694)	33	NM_001347415	20384	Mm.43331	NM_009159	ENSMUSG00000021134	Srsf5	Sfrs5	serine/arginine-rich splicing factor 5	protein-coding
mm_150964.1	chr19	46500168	46500197	+	1	NA	Intergenic	CpG	-1466	NM_053100	93679	Mm.392177	NM_053100	ENSMUSG00000025034	Trim8	AA408830|BB006755|GERP|Rnf27	tripartite motif-containing 8	protein-coding
mm_52253.1	chr6	107059631	107059640	+	1	NA	Intergenic	RMER17C|LTR|ERVK	-259548	NM_175357	58799	Mm.290085	NM_021449	ENSMUSG00000005362	Crbn	2610203G15Rik|2900045O07Rik|AF229032|AW108261|piL	cereblon	protein-coding
mm_105032.1	chr11	100516373	100516380	-	1	NA	intron (NM_001199296, intron 7 of 28)	intron (NM_001199296, intron 7 of 28)	11624	NM_134037	104112	Mm.282039	NM_134037	ENSMUSG00000020917	Acly	A730098H14Rik|AW538652	ATP citrate lyase	protein-coding
mm_132898.1	chr16	48870942	48870949	+	1	NA	Intergenic	RMER15-int|LTR|ERVL	-1663	NM_181596	245195	Mm.231288	NM_181596	ENSMUSG00000022651	Retnlg	Fizz3|Relmg|Xcp1	resistin like gamma	protein-coding
mm_100156.1	chr11	116210964	116211006	+	1	NA	intron (NM_027107, intron 3 of 3)	intron (NM_027107, intron 3 of 3)	-5017	NR_004853	69681	Mm.33677	NR_004853	ENSMUSG00000092300	Cdk3-ps	2310050O10Rik|Cdk3	cyclin-dependent kinase 3, pseudogene	pseudo
mm_26712.1	chr3	157993627	157993652	+	1	NA	intron (NM_001013806, intron 8 of 12)	intron (NM_001013806, intron 8 of 12)	38115	NM_001093753	69207	Mm.223946	NM_026989	ENSMUSG00000055436	Srsf11	0610009J05Rik|2610019N13Rik|BF642805|Sfrs11	serine/arginine-rich splicing factor 11	protein-coding
mm_29415.1	chr3	108972617	108972631	-	1	NA	3' UTR (NM_001163567, exon 11 of 11)	3' UTR (NM_001163567, exon 11 of 11)	32067	NM_001078646	66715	Mm.158124	NM_025723	ENSMUSG00000045662	Henmt1	4921515J06Rik|Hen1|mHEN1	HEN1 methyltransferase homolog 1 (Arabidopsis)	protein-coding
mm_45985.1	chr5	90476587	90476605	-	1	NA	TTS (NM_009654)	TTS (NM_009654)	-14118	NM_007423	11576	Mm.358570	NM_007423	ENSMUSG00000054932	Afp	-	alpha fetoprotein	protein-coding
mm_156443.1	chrX	142390719	142390731	+	1	NA	promoter-TSS (NM_207625)	promoter-TSS (NM_207625)	-190	NM_019477	50790	Mm.391337	NM_019477	ENSMUSG00000031278	Acsl4	9430020A05Rik|ACS4|AU018108|Facl4|Lacs4	acyl-CoA synthetase long-chain family member 4	protein-coding
mm_170908.1	chr2	31236590	31236595	+	1	NA	Intergenic	B1_Mur3|SINE|Alu	-9331	NM_019681	14299	Mm.249318	NM_019681	ENSMUSG00000062661	Ncs1	9430075O15Rik|A730032G13Rik|AI836659|Freq|Mfreq|NCS-1	neuronal calcium sensor 1	protein-coding
mm_39484.1	chr5	20882176	20882180	+	1	NA	promoter-TSS (NM_177601)	promoter-TSS (NM_177601)	-54	NM_172992	68770	Mm.86410	NM_172992	ENSMUSG00000039987	Phtf2	1110054G21Rik|9530062N20Rik|AI447096|C77923	putative homeodomain transcription factor 2	protein-coding
mm_140703.1	chr17	14676236	14676239	-	1	NA	exon (NM_011581, exon 15 of 22)	exon (NM_011581, exon 15 of 22)	18025	NM_011581	21826	Mm.26688	NM_011581	ENSMUSG00000023885	Thbs2	TSP2|Thbs-2	thrombospondin 2	protein-coding
mm_25217.1	chr3	103851243	103851249	+	1	NA	intron (NM_001142960, intron 3 of 3)	intron (NM_001142960, intron 3 of 3)	-8549	NR_104070	19260	Mm.395	NM_008979	ENSMUSG00000027843	Ptpn22	70zpep|PEP|Ptpn8	protein tyrosine phosphatase, non-receptor type 22 (lymphoid)	protein-coding
mm_76457.1	chr8	85299484	85299535	-	1	NA	promoter-TSS (NM_019716)	promoter-TSS (NM_019716)	-12	NM_022997	65114	Mm.296520	NM_022997	ENSMUSG00000031696	Vps35	AI647796|Mem3	VPS35 retromer complex component	protein-coding
mm_2089.1	chr1	87700398	87700406	+	1	NA	intron (NM_010566, intron 15 of 26)	intron (NM_010566, intron 15 of 26)	-55609	NM_029846	77040	Mm.272972	NM_029846	ENSMUSG00000026289	Atg16l1	1500009K01Rik|Apg16l|Atg16l|WDR30	autophagy related 16-like 1 (S. cerevisiae)	protein-coding
mm_48588.1	chr5	143759753	143759794	-	1	NA	intron (NR_015486, intron 1 of 1)	intron (NR_015486, intron 1 of 1)	1419	NR_015486	320064	Mm.332820	NR_015486		D130017N08Rik	1700012G11Rik	RIKEN cDNA D130017N08 gene	ncRNA
mm_13931.1	chr2	121008417	121008481	+	1	NA	promoter-TSS (NM_010761)	promoter-TSS (NM_010761)	41	NM_010761	17151	Mm.7838	NM_010761	ENSMUSG00000023572	Ccndbp1	AU022347|DIP1|GCIP|Maid|SECC-8|SSEC-8	cyclin D-type binding-protein 1	protein-coding
mm_123081.1	chr14	55745454	55745483	-	1	NA	promoter-TSS (NM_026403)	promoter-TSS (NM_026403)	216	NM_026819	52585	Mm.21623	NM_026819	ENSMUSG00000002332	Dhrs1	1110029G07Rik|AW112170|D14Ertd484e	dehydrogenase/reductase (SDR family) member 1	protein-coding
mm_131786.1	chr16	22898166	22898181	+	1	NA	exon (NM_001276450, exon 6 of 7)	exon (NM_001276450, exon 6 of 7)	-3787	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_35657.1	chr4	43558138	43558149	-	1	NA	intron (NM_011602, intron 1 of 56)	intron (NM_011602, intron 1 of 56)	4440	NM_011602	21894	Mm.208601	NM_011602	ENSMUSG00000028465	Tln1	Tln	talin 1	protein-coding
mm_8556.1	chr1	155232677	155232704	-	1	NA	Intergenic	Intergenic	73987	NM_021433	58244	Mm.66264	NM_021433	ENSMUSG00000026470	Stx6	2310039E05Rik|2410005I16Rik|AA437559|AI415714|AI845861	syntaxin 6	protein-coding
mm_54819.1	chr6	42351333	42351362	-	1	NA	exon (NM_011777, exon 4 of 10)	exon (NM_011777, exon 4 of 10)	1519	NM_001289619	22793	Mm.282303	NM_011777	ENSMUSG00000029860	Zyx	9530098H06Rik|R75157	zyxin	protein-coding
mm_172230.1	chr6	67508707	67508708	-	1	NA	Intergenic	Intergenic	-16852	NM_144548	209590	Mm.221227	NM_144548	ENSMUSG00000049093	Il23r	IL-23R	interleukin 23 receptor	protein-coding
mm_105585.1	chr11	106715204	106715214	-	1	NA	promoter-TSS (NM_008816)	promoter-TSS (NM_008816)	72	NM_001305158	18613	Mm.343951	NM_008816	ENSMUSG00000020717	Pecam1	C85791|Cd31|PECAM-1|Pecam	platelet/endothelial cell adhesion molecule 1	protein-coding
mm_34952.1	chr4	155962412	155962420	+	1	NA	5' UTR (NM_026125, exon 1 of 8)	5' UTR (NM_026125, exon 1 of 8)	104	NM_026125	67389	Mm.29140	NM_026125	ENSMUSG00000023571	Fam132a	1110035L05Rik|C1qdc2|CTRP12|alipolin	family with sequence similarity 132, member A	protein-coding
mm_104459.1	chr11	95065938	95065962	-	1	NA	exon (NM_001306162, exon 5 of 26)	exon (NM_001306162, exon 5 of 26)	3248	NM_001306071	16400	Mm.57035	NM_013565	ENSMUSG00000001507	Itga3	AA407068|CD49C|GAPB3	integrin alpha 3	protein-coding
mm_130289.1	chr15	97008726	97008744	-	1	NA	exon (NM_027052, exon 11 of 16)	exon (NM_027052, exon 11 of 16)	47221	NM_027052	69354	Mm.250980	NM_027052	ENSMUSG00000022464	Slc38a4	1110012E16Rik|1700012A18Rik|Ata3|mATA3|mNAT3	solute carrier family 38, member 4	protein-coding
mm_2249.1	chr1	91057934	91057943	+	1	NA	intron (NM_001310732, intron 1 of 24)	intron (NM_001310732, intron 1 of 24)	4494	NM_008515	16978	Mm.45039	NM_008515	ENSMUSG00000026305	Lrrfip1	AU024550|Fliiap1	leucine rich repeat (in FLII) interacting protein 1	protein-coding
mm_124505.1	chr14	121879671	121879683	-	1	NA	promoter-TSS (NR_130999)	promoter-TSS (NR_130999)	-269	NR_130999	78312	Mm.188743	NR_130999	ENSMUSG00000102112	1810041H14Rik	-	RIKEN cDNA 1810041H14 gene	ncRNA
mm_130148.1	chr15	91048106	91048111	-	1	NA	intron (NM_001109040, intron 1 of 36)	intron (NM_001109040, intron 1 of 36)	1843	NM_001109041	16564	Mm.41379	NM_016705	ENSMUSG00000022629	Kif21a	-	kinesin family member 21A	protein-coding
mm_16880.1	chr2	12979610	12979610	-	1	NA	intron (NM_001305437, intron 3 of 5)	U3|snRNA|snRNA	31254	NM_153155	227580	Mm.229322	NM_153155	ENSMUSG00000049630	C1ql3	1110065A22Rik|AI661623|C1ql|C1qtnf13|CTRP13|K100	C1q-like 3	protein-coding
mm_125463.1	chr15	52712402	52712429	+	1	NA	promoter-TSS (NM_027212)	promoter-TSS (NM_027212)	-30	NM_027212	69790	Mm.195562	NM_027212	ENSMUSG00000038622	Med30	1810038N03Rik|2510044J04Rik|TRAP25|Thrap6	mediator complex subunit 30	protein-coding
mm_22186.1	chr2	173218962	173218975	-	1	NA	promoter-TSS (NM_021394)	promoter-TSS (NM_021394)	-46	NM_001139519	58203	Mm.116687	NM_021394	ENSMUSG00000027514	Zbp1	2010010H03Rik|Dai|Dlm1|mZaDLM	Z-DNA binding protein 1	protein-coding
mm_58653.1	chr7	6383311	6383358	+	1	NA	promoter-TSS (NM_175247)	promoter-TSS (NM_175247)	16	NM_175247	22690	Mm.127014	NM_175247	ENSMUSG00000062861	Zfp28	2810438M17Rik|Zfp-28|mkr-5	zinc finger protein 28	protein-coding
mm_91734.1	chr10	45578101	45578111	-	1	NA	exon (NM_172473, exon 1 of 24)	exon (NM_172473, exon 1 of 24)	277	NM_172473	209462	Mm.458633	NM_172473	ENSMUSG00000038822	Hace1	1700042J16Rik|A730034A22Rik|BC025474	HECT domain and ankyrin repeat containing, E3 ubiquitin protein ligase 1	protein-coding
mm_1421.1	chr1	67172827	67172836	+	1	NA	exon (NM_001080809, exon 18 of 38)	exon (NM_001080809, exon 18 of 38)	49804	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_84955.1	chr9	83254461	83254519	-	1	NA	Intergenic	Intergenic	-107883	NM_026122	94353	Mm.244426	NM_026122	ENSMUSG00000066456	Hmgn3	1110002A15Rik|6330514M13Rik|BB071015|TRIP7	high mobility group nucleosomal binding domain 3	protein-coding
mm_85737.1	chr9	108518205	108518229	-	1	NA	intron (NM_175143, intron 1 of 9)	intron (NM_175143, intron 1 of 9)	1130	NM_175143	69232	Mm.335449	NM_175143	ENSMUSG00000006673	Qrich1	2610028H07Rik	glutamine-rich 1	protein-coding
mm_146780.1	chr18	20061573	20061590	-	1	NA	Intergenic	Intergenic	-2027	NM_001317365	13506	Mm.280547	NM_013505	ENSMUSG00000024331	Dsc2	AW228162	desmocollin 2	protein-coding
mm_53885.1	chr6	3346041	3346053	-	1	NA	Intergenic	Intergenic	53524	NM_010156	209086	Mm.196013	NM_010156	ENSMUSG00000047735	Samd9l	AA175286|ESTM25|mKIAA2005	sterile alpha motif domain containing 9-like	protein-coding
mm_61441.1	chr7	75457331	75457342	+	1	NA	intron (NM_029332, intron 1 of 36)	intron (NM_029332, intron 1 of 36)	1802	NM_029332	75547	Mm.216107	NM_029332	ENSMUSG00000066406	Akap13	1700026G02Rik|5730522G15Rik|5830460E08Rik|AKAP-13|AKAP-Lbc|BRX|Ht31|LBC|PROTO-LB|PROTO-LBC	A kinase (PRKA) anchor protein 13	protein-coding
mm_12592.1	chr2	74133502	74133526	+	1	NA	Intergenic	Intergenic	174203	NR_040501	73962	Mm.50289	NR_040501	ENSMUSG00000085405	4930441J16Rik	Astx1a|Astx1b|Astx1c	RIKEN cDNA 4930441J16 gene	ncRNA
mm_44433.1	chr5	21055855	21055868	-	1	NA	promoter-TSS (NM_011203)	promoter-TSS (NM_011203)	-64	NM_011203	19248	Mm.319117	NM_011203	ENSMUSG00000028771	Ptpn12	P19-PTP|PTP-P19|PTP-PEST|PTPG1	protein tyrosine phosphatase, non-receptor type 12	protein-coding
mm_120012.1	chr14	55745679	55745776	+	1	NA	promoter-TSS (NM_026403)	promoter-TSS (NM_026403)	34	NM_026403	67842	Mm.180338	NM_026403	ENSMUSG00000019297	Nop9	2610027L16Rik	NOP9 nucleolar protein	protein-coding
mm_62833.1	chr7	113765907	113765911	+	1	NA	promoter-TSS (NM_145584)	promoter-TSS (NM_145584)	-89	NM_145584	233744	Mm.334160	NM_145584	ENSMUSG00000038156	Spon1	AI666765|AW455831|BC020531|D330035F22Rik|FSP	spondin 1, (f-spondin) extracellular matrix protein	protein-coding
mm_129046.1	chr15	75216188	75216198	-	1	NA	Intergenic	Intergenic	-52228	NM_008530	17071	Mm.377095	NM_008530	ENSMUSG00000022583	Ly6f	-	lymphocyte antigen 6 complex, locus F	protein-coding
mm_46829.1	chr5	113219552	113219591	-	1	NA	Intergenic	Intergenic	-7338	NM_001033428	333048	Mm.332586	NM_001033428	ENSMUSG00000066964	Tmem211	Gm854	transmembrane protein 211	protein-coding
mm_149224.1	chr19	10022770	10022799	+	1	NA	intron (NM_001347430, intron 1 of 8)	intron (NM_001347430, intron 1 of 8)	4556	NM_144538	74760	Mm.281969	NM_144538	ENSMUSG00000024663	Rab3il1	1200014K04Rik|AI115013|C76746|Rab3ail1	RAB3A interacting protein (rabin3)-like 1	protein-coding
mm_146465.1	chr18	86914110	86914115	+	1	NA	Intergenic	Intergenic	202047	NM_172633	12405	Mm.70775	NM_172633	ENSMUSG00000024647	Cbln2	6330593N19Rik|A730004O05	cerebellin 2 precursor protein	protein-coding
mm_161356.1	chr14	55971429	55971429	+	1	NA	promoter-TSS (NM_001024714)	promoter-TSS (NM_001024714)	1	NM_001024714	545055	Mm.378966	NM_001024714	ENSMUSG00000068289	Cma2	Mcp10	chymase 2, mast cell	protein-coding
mm_48722.1	chr5	147326357	147326381	-	1	NA	Intergenic	Intergenic	-3929	NM_001039678	231903	Mm.291286	NM_001039678	ENSMUSG00000075543	Urad	EG231903|Prhoxnb	ureidoimidazoline (2-oxo-4-hydroxy-4-carboxy-5) decarboxylase	protein-coding
mm_102482.1	chr11	60176614	60176660	-	1	NA	intron (NM_001037764, intron 1 of 4)	CpG	23980	NR_105886	102465555		NR_105886	ENSMUSG00000098547	Mir6921	Gm27352|mmu-mir-6921	microRNA 6921	ncRNA
mm_68613.1	chr7	116443413	116443436	-	1	NA	promoter-TSS (NM_011083)	promoter-TSS (NM_011083)	34	NM_011083	18704	Mm.3810	NM_011083	ENSMUSG00000030660	Pik3c2a	Cpk-m|PI3KC2	phosphatidylinositol 3-kinase, C2 domain containing, alpha polypeptide	protein-coding
mm_132319.1	chr16	33793979	33793985	+	1	NA	promoter-TSS (NM_010739)	promoter-TSS (NM_010739)	-55	NM_010739	17063	Mm.3177	NM_010739	ENSMUSG00000022824	Muc13	114/A10|14/A10|AI159736|Lrrp|Ly64|NJ-1	mucin 13, epithelial transmembrane	protein-coding
mm_81482.1	chr9	109958601	109958605	+	1	NA	intron (NM_001205330, intron 1 of 18)	L1MC3|LINE|L1	26829	NM_008633	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_93963.1	chr10	127288611	127288633	-	1	NA	intron (NM_033072, intron 1 of 12)	intron (NM_033072, intron 1 of 12)	396	NM_001347171	110962	Mm.372826	NM_033072	ENSMUSG00000025409	Mbd6	D10Wsu93e	methyl-CpG binding domain protein 6	protein-coding
mm_88230.1	chr10	70837680	70837683	+	1	NA	Intergenic	RLTR9E|LTR|ERVK	-181718	NR_045292	319646	Mm.483039	NR_045291	ENSMUSG00000037747	D630013N20Rik	-	RIKEN cDNA D630013N20 gene	ncRNA
mm_128296.1	chr15	37381617	37381621	-	1	NA	intron (NM_001170866, intron 5 of 6)	L1MEg|LINE|L1	-43935	NM_029113	74892	Mm.107630	NM_029113	ENSMUSG00000022288	4930447A16Rik	-	RIKEN cDNA 4930447A16 gene	protein-coding
mm_36441.1	chr4	82314195	82314197	-	1	NA	intron (NM_001286131, intron 8 of 9)	intron (NM_001286131, intron 8 of 9)	191583	NM_001286127	18028	Mm.317947	NM_008687	ENSMUSG00000008575	Nfib	6720429L07Rik|CTF|E030026I10Rik|NF-I/B|NF1-B|NFI-B	nuclear factor I/B	protein-coding
mm_8692.1	chr1	157256704	157256725	-	1	NA	intron (NM_177644, intron 3 of 17)	intron (NM_177644, intron 3 of 17)	-148034	NM_001305063	73435	Mm.116705	NM_028540	ENSMUSG00000026592	Tex35	1700057K13Rik	testis expressed 35	protein-coding
mm_44441.1	chr5	21645527	21645527	-	1	NA	promoter-TSS (NM_026034)	promoter-TSS (NM_026034)	78	NM_001199632	320118	Mm.442295	NM_177076	ENSMUSG00000048520	Fbxl13	4921539K22Rik	F-box and leucine-rich repeat protein 13	protein-coding
mm_160432.1	chr8	92674294	92674294	+	1	NA	promoter-TSS (NM_022428)	promoter-TSS (NM_022428)	5	NM_001301137	64379	Mm.137247	NM_022428	ENSMUSG00000031738	Irx6	-	Iroquois related homeobox 6 (Drosophila)	protein-coding
mm_22667.1	chr3	14872202	14872210	+	1	NA	3' UTR (NM_007606, exon 7 of 7)	3' UTR (NM_007606, exon 7 of 7)	8668	NM_007606	12350	Mm.300	NM_007606	ENSMUSG00000027559	Car3	BB219044|Ca3|Car-3	carbonic anhydrase 3	protein-coding
mm_106112.1	chr11	116334209	116334234	-	1	NA	exon (NM_008240, exon 2 of 3)	exon (NM_008240, exon 2 of 3)	1133	NM_008240	15223	Mm.378938	NM_008240	ENSMUSG00000034227	Foxj1	FKHL-13|HFH-4|Hfh4	forkhead box J1	protein-coding
mm_37820.1	chr4	131873368	131873405	-	1	NA	promoter-TSS (NM_020587)	promoter-TSS (NM_020587)	-253	NM_020587	57317	Mm.2478	NM_020587	ENSMUSG00000028911	Srsf4	5730499P16Rik|AW550192|MNCb-2616|SRp75|Sfrs4	serine/arginine-rich splicing factor 4	protein-coding
mm_129368.1	chr15	77994899	77994904	-	1	NA	3' UTR (NM_007583, exon 4 of 4)	3' UTR (NM_007583, exon 4 of 4)	-24077	NM_018749	55944	Mm.3955	NM_018749	ENSMUSG00000016554	Eif3d	66/67kDa|AA407891|Eif3s7|eIF3p66	eukaryotic translation initiation factor 3, subunit D	protein-coding
mm_137710.1	chr17	29099495	29099540	+	1	NA	3' UTR (NM_007669, exon 3 of 3)	3' UTR (NM_007669, exon 3 of 3)	5748	NM_007669	12575	Mm.195663	NM_007669	ENSMUSG00000023067	Cdkn1a	CAP20|CDKI|CIP1|Cdkn1|P21|SDI1|Waf1|mda6|p21Cip1|p21WAF	cyclin-dependent kinase inhibitor 1A (P21)	protein-coding
mm_17617.1	chr2	30932023	30932071	-	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-20954	NM_133673	30934	Mm.249164	NM_133673	ENSMUSG00000026848	Tor1b	2610016F05Rik|DQ1|torsinB	torsin family 1, member B	protein-coding
mm_162425.1	chr1	92730737	92730747	-	1	NA	Intergenic	Intergenic	-81901	NM_153114	260301	Mm.219545	NM_153114	ENSMUSG00000044055	Otos	OTOSP	otospiralin	protein-coding
mm_13972.1	chr2	121433976	121434011	+	1	NA	exon (NM_007952, exon 9 of 13)	exon (NM_007952, exon 9 of 13)	8608	NM_145973	269344	Mm.330522	NM_145973	ENSMUSG00000027246	Ell3	A930015D22Rik	elongation factor RNA polymerase II-like 3	protein-coding
mm_13411.1	chr2	104095813	104095879	+	1	NA	promoter-TSS (NM_001111060)	promoter-TSS (NM_001111060)	45	NM_001111060	12509	Mm.247265	NM_007652	ENSMUSG00000032679	Cd59a	AA987121|Cd59|protectin	CD59a antigen	protein-coding
mm_48680.1	chr5	146221427	146221444	-	1	NA	promoter-TSS (NM_001256087)	promoter-TSS (NM_001256087)	22	NM_028774	74132	Mm.26696	NM_028774	ENSMUSG00000029634	Rnf6	1200013I08Rik|5730419H05Rik|AA537053	ring finger protein (C3H2C3 type) 6	protein-coding
mm_73028.1	chr8	94172775	94172792	+	1	NA	5' UTR (NM_008630, exon 1 of 3)	5' UTR (NM_008630, exon 1 of 3)	165	NM_008630	17750	Mm.147226	NM_008630	ENSMUSG00000031762	Mt2	AA409533|MT-II|Mt-2	metallothionein 2	protein-coding
mm_118381.1	chr13	117025547	117025557	-	1	NA	promoter-TSS (NM_001081009)	promoter-TSS (NM_001081009)	-36	NM_001081009	52552	Mm.274466	NM_027272	ENSMUSG00000021725	Parp8	2810430O08Rik|ARTD16|D13Ertd275e	poly (ADP-ribose) polymerase family, member 8	protein-coding
mm_149928.1	chr19	26749884	26749918	+	1	NA	exon (NM_001347439, exon 2 of 8)	exon (NM_001347439, exon 2 of 8)	1498	NM_026003	67155	Mm.342988	NM_011416	ENSMUSG00000024921	Smarca2	2610209L14Rik|SNF2alpha|Snf2l2|brahma|brm	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	protein-coding
mm_97243.1	chr11	75732909	75732975	+	1	NA	promoter-TSS (NM_009536)	promoter-TSS (NM_009536)	55	NM_009536	22627	Mm.234700	NM_009536	ENSMUSG00000020849	Ywhae	AU019196	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide	protein-coding
mm_46184.1	chr5	97392356	97392365	-	1	NA	promoter-TSS (NM_001033191)	promoter-TSS (NM_001033191)	-30	NM_001033191	97243	Mm.11746	NM_001033191	ENSMUSG00000046000	Naa11	Ard1b|Ard2|C80008	N(alpha)-acetyltransferase 11, NatA catalytic subunit	protein-coding
mm_102763.1	chr11	67922137	67922158	-	1	NA	promoter-TSS (NM_173754)	promoter-TSS (NM_173754)	6	NM_001291049	216835	Mm.158885	NM_173754	ENSMUSG00000020905	Usp43	-	ubiquitin specific peptidase 43	protein-coding
mm_129159.1	chr15	76242646	76242657	-	1	NA	intron (NM_001163576, intron 2 of 9)	intron (NM_001163576, intron 2 of 9)	789	NM_001163576	671535	Mm.373750	NM_001163575	ENSMUSG00000063268	Parp10	-	poly (ADP-ribose) polymerase family, member 10	protein-coding
mm_72925.1	chr8	91106522	91106545	+	1	NA	exon (NM_001282001, exon 15 of 22)	exon (NM_001282001, exon 15 of 22)	27494	NM_001302337	14339	Mm.324588	NM_010241	ENSMUSG00000031667	Aktip	AL023020|Fif|Ft|Ft1|Fts	thymoma viral proto-oncogene 1 interacting protein	protein-coding
mm_37743.1	chr4	129600587	129600595	-	1	NA	promoter-TSS (NM_029748)	promoter-TSS (NM_029748)	57	NM_018799	54709	Mm.250874	NM_018799	ENSMUSG00000028798	Eif3i	36kDa|D4Ertd632e|Eif3s2|Trip1	eukaryotic translation initiation factor 3, subunit I	protein-coding
mm_4230.1	chr1	171370053	171370091	+	1	NA	promoter-TSS (NM_027893)	promoter-TSS (NM_027893)	-101	NM_027893	71740	Mm.263414	NM_027893	ENSMUSG00000006411	Nectin4	1200017F15Rik|Prr4|Pvrl4	nectin cell adhesion molecule 4	protein-coding
mm_37444.1	chr4	123342894	123342918	-	1	NA	5' UTR (NM_001256019, exon 1 of 7)	5' UTR (NM_001256019, exon 1 of 7)	346	NM_001256019	12163	Mm.439749	NM_007558	ENSMUSG00000032726	Bmp8a	Bmp7r1|OP-2|OP2	bone morphogenetic protein 8a	protein-coding
mm_13953.1	chr2	121303410	121303421	+	1	NA	exon (NM_001173506, exon 4 of 6)	exon (NM_001173506, exon 4 of 6)	7961	NM_001173506	17754	Mm.36501	NM_032393	ENSMUSG00000027254	Map1a	6330416M19Rik|AI853608|Mtap-1|Mtap1|Mtap1a|moth1	microtubule-associated protein 1 A	protein-coding
mm_29602.1	chr3	121171679	121171717	-	1	NA	promoter-TSS (NM_025637)	promoter-TSS (NM_025637)	-3	NM_025637	66568	Mm.263163	NM_025637	ENSMUSG00000028133	Rwdd3	2510027J23Rik|3110037C01Rik|AI035684|AI662458|Rsume|X2CR1	RWD domain containing 3	protein-coding
mm_100430.1	chr11	119457257	119457274	+	1	NA	Intergenic	Intergenic	-34082	NM_001164636	338371	Mm.271946	NM_177394	ENSMUSG00000039850	Endov	A730011L01Rik	endonuclease V	protein-coding
mm_147482.1	chr18	47248184	47248202	-	1	NA	3' UTR (NM_018744, exon 19 of 19)	3' UTR (NM_018744, exon 19 of 19)	120675	NM_018744	20358	Mm.40909	NM_018744	ENSMUSG00000019647	Sema6a	A730020P05Rik|AI851735|Sema6A-1|Semaq|VIa	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A	protein-coding
mm_130866.1	chr15	102204192	102204221	-	1	NA	promoter-TSS (NM_001289690)	promoter-TSS (NM_001289690)	-365	NM_001289690	68744	Mm.352945	NM_153194	ENSMUSG00000046897	Zfp740	1110034O07Rik|AW548228|Znf740	zinc finger protein 740	protein-coding
mm_135757.1	chr16	56029667	56029720	-	1	NA	promoter-TSS (NM_001024622)	promoter-TSS (NM_001024622)	24	NM_001024622	76302	Mm.310642	NM_001024622	ENSMUSG00000071533	Pcnp	1110018D06Rik|AI647035	PEST proteolytic signal containing nuclear protein	protein-coding
mm_56320.1	chr6	92418056	92418058	-	1	NA	intron (NM_001081146, intron 6 of 8)	L1MB7|LINE|L1	63335	NM_001134460	243548	Mm.248820	NM_001081146	ENSMUSG00000030020	Prickle2	6230400G14Rik|6720451F06Rik|mpk2	prickle planar cell polarity protein 2	protein-coding
mm_32481.1	chr4	107883068	107883074	+	1	NA	exon (NM_001282737, exon 3 of 5)	exon (NM_001282737, exon 3 of 5)	3316	NM_001282737	17149	Mm.808	NM_001282737	ENSMUSG00000028609	Magoh	Mago-m|Mos2	mago homolog, exon junction complex core component	protein-coding
mm_35013.1	chr4	3574823	3574840	-	1	NA	promoter-TSS (NM_028097)	promoter-TSS (NM_028097)	-48	NM_054089	116940	Mm.171323	NM_054089	ENSMUSG00000028233	Tgs1	D4Ertd800e|Ncoa6ip|Pimt	trimethylguanosine synthase 1	protein-coding
mm_15927.1	chr2	165067230	165067240	+	1	NA	intron (NM_170702, intron 6 of 7)	(CACAG)n|Simple_repeat|Simple_repeat	11599	NM_011611	21939	Mm.271833	NM_011611	ENSMUSG00000017652	Cd40	AI326936|Bp50|GP39|HIGM1|IGM|IMD3|T-BAM|TRAP|Tnfrsf5|p50	CD40 antigen	protein-coding
mm_90687.1	chr10	128933777	128933781	+	1	NA	promoter-TSS (NM_008398)	promoter-TSS (NM_008398)	-34	NM_008398	16404	Mm.179747	NM_008398	ENSMUSG00000025348	Itga7	[a]7|alpha7	integrin alpha 7	protein-coding
mm_23073.1	chr3	36453512	36453542	+	1	NA	exon (NM_009673, exon 9 of 13)	exon (NM_009673, exon 9 of 13)	21997	NR_105976	102466786		NR_105976	ENSMUSG00000098808	Mir7009	Gm27472|mmu-mir-7009	microRNA 7009	ncRNA
mm_10861.1	chr2	25062812	25062825	+	1	NA	TTS (NM_020276)	TTS (NM_020276)	3007	NR_106124	102465989		NR_106124	ENSMUSG00000099320	Mir7664	Gm28015|mmu-mir-7664	microRNA 7664	ncRNA
mm_3889.1	chr1	161175602	161175620	+	1	NA	Intergenic	Intergenic	-16297	NM_001195189	100502590	Mm.449990	NM_001195189		4930469G21Rik	-	RIKEN cDNA 4930469G21 gene	protein-coding
mm_113358.1	chr13	32860961	32860967	+	1	NA	Intergenic	Intergenic	-9779	NM_025429	66222	Mm.20144	NM_025429	ENSMUSG00000044734	Serpinb1a	1190005M04Rik|AI325983|EI|EIA|ELANH2|LEI|M/NEI|MNEI|PI2	serine (or cysteine) peptidase inhibitor, clade B, member 1a	protein-coding
mm_47136.1	chr5	120516498	120516523	-	1	NA	intron (NM_001177594, intron 2 of 14)	intron (NM_001177594, intron 2 of 14)	5318	NM_001177594	170756	Mm.291070	NM_133221	ENSMUSG00000032754	Slc8b1	AF261233|NCKX6|NCLX|Slc24a6	solute carrier family 8 (sodium/lithium/calcium exchanger), member B1	protein-coding
mm_124640.1	chr15	4375659	4375679	+	1	NA	5' UTR (NM_177355, exon 1 of 3)	5' UTR (NM_177355, exon 1 of 3)	178	NM_177355	239318	Mm.308996	NM_177355	ENSMUSG00000049148	Plcxd3	B130016O10Rik	phosphatidylinositol-specific phospholipase C, X domain containing 3	protein-coding
mm_159087.1	chr2	31053365	31053365	-	1	NA	3' UTR (NM_019406, exon 9 of 9)	3' UTR (NM_019406, exon 9 of 9)	43135	NM_001177650	14269	Mm.52297	NM_019406	ENSMUSG00000075415	Fnbp1	1110057E06Rik|2210010H06Rik|FBP1|Fbp17	formin binding protein 1	protein-coding
mm_138650.1	chr17	35867150	35867166	+	1	NA	5' UTR (NM_175242, exon 1 of 3)	5' UTR (NM_175242, exon 1 of 3)	543	NM_175242	76448	Mm.359982	NM_175242	ENSMUSG00000034595	Ppp1r18	2310014H01Rik|AA407849|AI450394	protein phosphatase 1, regulatory subunit 18	protein-coding
mm_134753.1	chr16	23171015	23171028	-	1	NA	Intergenic	RMER19C|LTR|ERVK	24485	NM_009605	11450	Mm.3969	NM_009605	ENSMUSG00000022878	Adipoq	30kDa|APN|Acdc|Acrp30|Ad|GBP28|adipo|apM1	adiponectin, C1Q and collagen domain containing	protein-coding
mm_160925.1	chr11	86730280	86730280	-	1	NA	exon (NM_001003908, exon 6 of 32)	exon (NM_001003908, exon 6 of 32)	27212	NM_001003908	67300	Mm.254588	NM_001003908	ENSMUSG00000047126	Cltc	3110065L21Rik|CHC|R74732	clathrin, heavy polypeptide (Hc)	protein-coding
mm_126708.1	chr15	85232555	85232580	+	1	NA	exon (NM_010180, exon 8 of 17)	exon (NM_010180, exon 8 of 17)	26559	NM_010180	14114	Mm.297992	NM_010180	ENSMUSG00000006369	Fbln1	-	fibulin 1	protein-coding
mm_170934.1	chr2	4657116	4657135	+	1	NA	Intergenic	RLTR10C|LTR|ERVK	-5039	NM_026045	67229	Mm.38529	NM_026045	ENSMUSG00000039449	Prpf18	2810441A10Rik	pre-mRNA processing factor 18	protein-coding
mm_40438.1	chr5	53590674	53590703	+	1	NA	5' UTR (NM_001080927, exon 1 of 11)	5' UTR (NM_001080927, exon 1 of 11)	202	NM_001080927	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_41519.1	chr5	92392731	92392743	+	1	NA	exon (NM_001310664, exon 4 of 11)	exon (NM_001310664, exon 4 of 11)	4603	NM_001310665	109979	Mm.263514	NM_181728	ENSMUSG00000034842	Art3	4930569O04Rik|ARTC3	ADP-ribosyltransferase 3	protein-coding
mm_145211.1	chr18	50030978	50031043	+	1	NA	intron (NM_001177759, intron 1 of 1)	intron (NM_001177759, intron 1 of 1)	-22272	NM_134131	106869	Mm.27740	NM_134131	ENSMUSG00000062210	Tnfaip8	AA987150|E130304C20Rik|ENSMUSG00000073567|Gg2-1|Gm10539|Nded|Ssc-2|Tipe	tumor necrosis factor, alpha-induced protein 8	protein-coding
mm_147956.1	chr18	67057179	67057182	-	1	NA	Intergenic	Intergenic	-31118	NM_177137	14680	Mm.440746	NM_010307	ENSMUSG00000024524	Gnal	2610011C15Rik|9630020G10Rik|Galphaolf|Gna10|Golf	guanine nucleotide binding protein, alpha stimulating, olfactory type	protein-coding
mm_31765.1	chr4	63409606	63409627	+	1	NA	Intergenic	Intergenic	-6171	NM_001045514	100182	Mm.387725	NM_001045514	ENSMUSG00000039158	Akna	AI597013	AT-hook transcription factor	protein-coding
mm_171689.1	chr4	64455067	64455071	+	1	NA	Intergenic	L1Md_T|LINE|L1	-408054	NM_011607	21923	Mm.980	NM_011607	ENSMUSG00000028364	Tnc	AI528729|C130033P17Rik|Hxb|TN|TN-C|Ten|cytotactin|tenascin-C	tenascin C	protein-coding
mm_82628.1	chr9	21926361	21926386	-	1	NA	intron (NM_001253867, intron 1 of 3)	intron (NM_001253867, intron 1 of 3)	915	NM_001253869	235043	Mm.253329	NM_178577	ENSMUSG00000040883	Tmem205	-	transmembrane protein 205	protein-coding
mm_129248.1	chr15	76669670	76669681	-	1	NA	exon (NM_007989, exon 1 of 3)	exon (NM_007989, exon 1 of 3)	273	NM_007989	14106	Mm.42011	NM_007989	ENSMUSG00000033837	Foxh1	Fast1|Fast2|fast-1|fast-2	forkhead box H1	protein-coding
mm_148228.1	chr18	80363623	80363667	-	1	NA	intron (NM_001190373, intron 1 of 3)	CpG	609	NM_001190373	240444	Mm.279568	NM_001190373	ENSMUSG00000059852	Kcng2	AA591524	potassium voltage-gated channel, subfamily G, member 2	protein-coding
mm_31069.1	chr4	41349306	41349322	+	1	NA	intron (NM_023305, intron 1 of 6)	CpG	318	NM_023305	67123	Mm.289795	NM_023305	ENSMUSG00000028437	Ubap1	2700092A01Rik|NAG20|UBAP-1|Ubap	ubiquitin-associated protein 1	protein-coding
mm_140699.1	chr17	14204258	14204281	-	1	NA	promoter-TSS (NM_172826)	promoter-TSS (NM_172826)	-438	NM_172826	240025	Mm.79993	NM_172826	ENSMUSG00000048826	Dact2	2900084M21Rik|A630024E20|Dpr2|Frd2|dapper2	dishevelled-binding antagonist of beta-catenin 2	protein-coding
mm_114765.1	chr13	88390577	88390580	+	1	NA	Intergenic	RMER17D|LTR|ERVK	-430894	NM_010103	13612	Mm.125580	NM_010103	ENSMUSG00000034488	Edil3	Del-1|Del1	EGF-like repeats and discoidin I-like domains 3	protein-coding
mm_80492.1	chr9	78429061	78429076	+	1	NA	Intergenic	Intergenic	14169	NR_125721	214763	Mm.101559	NM_173386	ENSMUSG00000032344	Mb21d1	E330016A19Rik|cGAS	Mab-21 domain containing 1	protein-coding
mm_80644.1	chr9	89450039	89450041	+	1	NA	Intergenic	Intergenic	172946	NM_153509	209743	Mm.242899	NM_153509	ENSMUSG00000039313	AF529169	DD1|Kiaa1024	cDNA sequence AF529169	protein-coding
mm_46773.1	chr5	112342972	112342986	-	1	NA	promoter-TSS (NM_027323)	promoter-TSS (NM_027323)	61	NM_027323	70118	Mm.172947	NM_027323	ENSMUSG00000029346	Srrd	2810002G02Rik|Srr1	SRR1 domain containing	protein-coding
mm_129511.1	chr15	79029125	79029174	-	1	NA	exon (NM_008197, exon 1 of 1)	exon (NM_008197, exon 1 of 1)	937	NM_008197	14958	Mm.24350	NM_008197	ENSMUSG00000096210	H1f0	D130017D06Rik|H1(0)|H1fv	H1 histone family, member 0	protein-coding
mm_151690.1	chr19	4333195	4333200	-	1	NA	intron (NM_001001984, intron 12 of 20)	intron (NM_001001984, intron 12 of 20)	-26975	NM_001290818	110355	Mm.254144	NM_130863	ENSMUSG00000024858	Grk2	Adrbk-1|Adrbk1|Bark-1|beta ARK|betaARK1	G protein-coupled receptor kinase 2	protein-coding
mm_123350.1	chr14	63142395	63142410	-	1	NA	3' UTR (NM_007798, exon 10 of 10)	3' UTR (NM_007798, exon 10 of 10)	19940	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_34632.1	chr4	150613810	150613829	+	1	NA	exon (NM_001085492, exon 16 of 23)	exon (NM_001085492, exon 16 of 23)	38355	NM_173774	242773	Mm.29280	NM_173774	ENSMUSG00000039838	Slc45a1	C230078B22|Dnb5	solute carrier family 45, member 1	protein-coding
mm_53899.1	chr6	3487480	3487484	-	1	NA	intron (NM_178899, intron 1 of 9)	intron (NM_178899, intron 1 of 9)	7016	NM_178899	101202	Mm.206911	NM_178899	ENSMUSG00000044156	Hepacam2	AI987662	HEPACAM family member 2	protein-coding
mm_141673.1	chr17	33909196	33909246	-	1	NA	promoter-TSS (NM_001199733)	promoter-TSS (NM_001199733)	-43	NR_045146	407803	Mm.250393	NR_045146	ENSMUSG00000092564	BC051226	-	cDNA sequence BC051226	ncRNA
mm_26559.1	chr3	146499851	146499886	+	1	NA	promoter-TSS (NM_001316756)	promoter-TSS (NM_001316756)	32	NM_010318	14707	Mm.140804	NM_010318	ENSMUSG00000068523	Gng5	G(y)5	guanine nucleotide binding protein (G protein), gamma 5	protein-coding
mm_115991.1	chr13	24375963	24375972	-	1	NA	intron (NM_001284519, intron 2 of 17)	intron (NM_001284519, intron 2 of 17)	-39155	NM_007717	12763	Mm.8396	NM_007717	ENSMUSG00000016756	Cmah	-	cytidine monophospho-N-acetylneuraminic acid hydroxylase	protein-coding
mm_54723.1	chr6	40436105	40436151	-	1	NA	promoter-TSS (NM_175528)	promoter-TSS (NM_175528)	5	NM_175528	243780	Mm.333006	NM_175528	ENSMUSG00000037172	E330009J07Rik	AI841796|Lchn|mKIAA1147	RIKEN cDNA E330009J07 gene	protein-coding
mm_4788.1	chr1	184358324	184358344	+	1	NA	Intergenic	Intergenic	199357	NR_040472	73590	Mm.82792	NR_040472	ENSMUSG00000101574	1700112H15Rik	-	RIKEN cDNA 1700112H15 gene	ncRNA
mm_62315.1	chr7	100276649	100276650	+	1	NA	3' UTR (NM_027629, exon 14 of 14)	3' UTR (NM_027629, exon 14 of 14)	-8871	NM_177161	320452	Mm.150294	NM_177161	ENSMUSG00000051048	P4ha3	D930031A02Rik	procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide III	protein-coding
mm_131722.1	chr16	21568363	21568403	+	1	NA	intron (NM_001285893, intron 40 of 46)	intron (NM_001285893, intron 40 of 46)	126282	NM_001001881	72190	Mm.131606	NM_001001881	ENSMUSG00000043391	2510009E07Rik	AI194952	RIKEN cDNA 2510009E07 gene	protein-coding
mm_90754.1	chr10	5550129	5550138	-	1	NA	intron (NM_001347732, intron 1 of 145)	intron (NM_001347732, intron 1 of 145)	559	NM_153399	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_151515.1	chr19	58737060	58737080	+	1	NA	exon (NM_018874, exon 9 of 13)	exon (NM_018874, exon 9 of 13)	8183	NM_018874	18946	Mm.10753	NM_018874	ENSMUSG00000042179	Pnliprp1	Plrp1	pancreatic lipase related protein 1	protein-coding
mm_28982.1	chr3	101276176	101276223	-	1	NA	exon (NM_013486, exon 5 of 5)	exon (NM_013486, exon 5 of 5)	11740	NM_013486	12481	Mm.22842	NM_013486	ENSMUSG00000027863	Cd2	LFA-2|Ly-37|Ly37	CD2 antigen	protein-coding
mm_49063.1	chr6	5390502	5390517	+	1	NA	intron (NM_023048, intron 1 of 5)	intron (NM_023048, intron 1 of 5)	7123	NM_023048	65255	Mm.51340	NM_023048	ENSMUSG00000042607	Asb4	8430401O13Rik|AV117194|AW060255	ankyrin repeat and SOCS box-containing 4	protein-coding
mm_172702.1	chr8	63933368	63933368	-	1	NA	intron (NM_001195687, intron 5 of 7)	intron (NM_001195687, intron 5 of 7)	18802	NM_001195687	244495	Mm.485331	NM_001195687	ENSMUSG00000094443	Sgol2b	EG244495|Gm4975|Sgo2B	shugoshin like 2b (S. pombe)	protein-coding
mm_168482.1	chr11	49051169	49051177	-	1	NA	promoter-TSS (NM_173434)	promoter-TSS (NM_173434)	69	NM_173434	245240	Mm.452996	NM_173434	ENSMUSG00000069892	9930111J21Rik2	9930111J21Rik|Irgb5|OTTMUSG00000005540	RIKEN cDNA 9930111J21 gene 2	protein-coding
mm_90427.1	chr10	127501708	127501726	+	1	NA	promoter-TSS (NM_177707)	promoter-TSS (NM_177707)	0	NM_177707	237611	Mm.32087	NM_177707	ENSMUSG00000040287	Stac3	9830125E18	SH3 and cysteine rich domain 3	protein-coding
mm_46716.1	chr5	110448487	110448519	-	1	NA	promoter-TSS (NM_001142642)	promoter-TSS (NM_001142642)	0	NM_001317042	381668	Mm.348782	NM_028596	ENSMUSG00000043323	Fbrsl1	2410025L10Rik|AI467568|Gm1049|Gm29766|mKIAA1545	fibrosin-like 1	protein-coding
mm_47235.1	chr5	121450136	121450152	-	1	NA	intron (NM_026129, intron 1 of 2)	intron (NM_026129, intron 1 of 2)	2330	NM_026129	67397	Mm.154570	NM_026129	ENSMUSG00000029616	Erp29	1200015M03Rik|2810446M09Rik|AW209030|Erp28|Erp31|PDI-Db	endoplasmic reticulum protein 29	protein-coding
mm_7783.1	chr1	131279516	131279529	-	1	NA	promoter-TSS (NM_019777)	promoter-TSS (NM_019777)	41	NM_019777	56489	Mm.386783	NM_019777	ENSMUSG00000042349	Ikbke	AW558201|IKK-i|IKKepsilon|Ikki	inhibitor of kappaB kinase epsilon	protein-coding
mm_18721.1	chr2	72813666	72813685	-	1	NA	promoter-TSS (NR_102349)	promoter-TSS (NR_102349)	42	NR_102348	76218	Mm.75260	NR_102348	ENSMUSG00000085427	6430710C18Rik	5033406J01Rik	RIKEN cDNA 6430710C18 gene	ncRNA
mm_100955.1	chr11	6625806	6625822	-	1	NA	intron (NM_001130457, intron 1 of 12)	CpG	253	NM_001130457	21379	Mm.247761	NM_134011	ENSMUSG00000000384	Tbrg4	2310042P22Rik|AA120735|AA408001|AI527316|Cpr2|R74877|Tb-12|mKIAA0948	transforming growth factor beta regulated gene 4	protein-coding
mm_6217.1	chr1	66863255	66863259	-	1	NA	promoter-TSS (NM_007381)	promoter-TSS (NM_007381)	52	NM_007381	11363	Mm.2445	NM_007381	ENSMUSG00000026003	Acadl	AA960361|AU018452|C79855|LCAD	acyl-Coenzyme A dehydrogenase, long-chain	protein-coding
mm_138010.1	chr17	33843138	33843156	+	1	NA	promoter-TSS (NM_019421)	promoter-TSS (NM_019421)	56	NM_019421	54219	Mm.11175	NM_019421	ENSMUSG00000002308	Cd320	425O18-1|8D6|D17Ertd716e|NG29|TCblR|VLDL	CD320 antigen	protein-coding
mm_42321.1	chr5	114897754	114897764	+	1	NA	exon (NM_011854, exon 1 of 6)	exon (NM_011854, exon 1 of 6)	825	NM_011854	23962	Mm.228363	NM_011854	ENSMUSG00000029561	Oasl2	M1204|Mmu-OASL|Oasl	2'-5' oligoadenylate synthetase-like 2	protein-coding
mm_10276.1	chr2	9882623	9882646	+	1	NA	TTS (NR_040511)	TTS (NR_040511)	1388	NR_024257	381347	Mm.441450	NR_024257		4930412O13Rik	ENSMUSG00000075535|Gm10853	RIKEN cDNA 4930412O13 gene	ncRNA
mm_135783.1	chr16	56886132	56886176	-	1	NA	promoter-TSS (NM_019631)	promoter-TSS (NM_019631)	9	NM_019631	56277	Mm.262328	NM_019631	ENSMUSG00000022754	Tmem45a	C630002M10Rik|M32486|p19.5	transmembrane protein 45a	protein-coding
mm_87568.1	chr10	56379159	56379189	+	1	NA	intron (NM_010288, intron 1 of 1)	intron (NM_010288, intron 1 of 1)	1874	NM_010288	14609	Mm.378921	NM_010288	ENSMUSG00000050953	Gja1	AU042049|AW546267|Cnx43|Cx43|Cx43alpha1|Gja-1|Npm1|connexin43	gap junction protein, alpha 1	protein-coding
mm_135993.1	chr16	75187184	75187187	-	1	NA	Intergenic	Intergenic	398876	NM_001252513	320355	Mm.99517	NM_177142	ENSMUSG00000032948	Lipi	D930038D03Rik|lpd1	lipase, member I	protein-coding
mm_39858.1	chr5	30950047	30950133	+	1	NA	promoter-TSS (NR_003522)	promoter-TSS (NR_003522)	-16	NM_021304	57742	Mm.389615	NM_021304	ENSMUSG00000006638	Abhd1	LABH-1|LABH1	abhydrolase domain containing 1	protein-coding
mm_69781.1	chr7	141072184	141072196	-	1	NA	TTS (NM_177897)	TTS (NM_177897)	-6039	NM_001162924	56460	Mm.350037	NM_019762	ENSMUSG00000054065	Pkp3	2310056L12Rik	plakophilin 3	protein-coding
mm_96793.1	chr11	69980752	69980762	+	1	NA	promoter-TSS (NM_026017)	promoter-TSS (NM_026017)	-411	NM_026017	67181	Mm.41678	NM_026017	ENSMUSG00000018559	Ctdnep1	2610507E10Rik|Dullard	CTD nuclear envelope phosphatase 1	protein-coding
mm_11367.1	chr2	30982329	30982348	+	1	NA	promoter-TSS (NM_028846)	promoter-TSS (NM_028846)	59	NM_028846	74270	Mm.346654	NM_028846	ENSMUSG00000026854	Usp20	1700055M05Rik|AI467231|Vdu2	ubiquitin specific peptidase 20	protein-coding
mm_45379.1	chr5	66084697	66084700	-	1	NA	intron (NM_178446, intron 2 of 6)	intron (NM_178446, intron 2 of 6)	13481	NM_139065	245945	Mm.36863	NM_139065	ENSMUSG00000070780	Rbm47	9530077J19Rik	RNA binding motif protein 47	protein-coding
mm_7197.1	chr1	92997050	92997072	-	1	NA	Intergenic	Intergenic	-9273	NM_177587	208760	Mm.235537	NM_177587	ENSMUSG00000045091	Aqp12	AB084104|mAQP12	aquaporin 12	protein-coding
mm_98367.1	chr11	93996058	93996066	+	1	NA	promoter-TSS (NM_001199204)	promoter-TSS (NM_001199204)	-29	NM_001199203	70834	Mm.260737	NM_027569	ENSMUSG00000020859	Spag9	3110018C07Rik|4733401I23Rik|4831406C20Rik|AW552012|JLP|JSAP2|JSAP2a|Jip4|Mapk8ip4|syd1	sperm associated antigen 9	protein-coding
mm_111596.1	chr12	101976266	101976279	-	1	NA	intron (NM_016856, intron 1 of 14)	CpG	298	NM_016856	51786	Mm.716	NM_016856	ENSMUSG00000041781	Cpsf2	100kDa|2610024B04Rik|AI662483|Cpsf|MCPSF|mKIAA1367	cleavage and polyadenylation specific factor 2	protein-coding
mm_136313.1	chr16	91728600	91728637	-	1	NA	promoter-TSS (NM_001110276)	promoter-TSS (NM_001110276)	184	NM_026994	66609	Mm.109823	NM_026994	ENSMUSG00000058240	Cryzl1	2210407J23Rik|2410006O11Rik|QOH-1	crystallin, zeta (quinone reductase)-like 1	protein-coding
mm_36926.1	chr4	108225380	108225388	-	1	NA	Intergenic	RLTR16|LTR|ERVK	-7462	NM_001167936	230590	Mm.301798	NM_001167936	ENSMUSG00000034645	Zyg11a	BC022150	zyg-11 family member A, cell cycle regulator	protein-coding
mm_7514.1	chr1	124025540	124025570	-	1	NA	intron (NM_199021, intron 1 of 25)	intron (NM_199021, intron 1 of 25)	20004	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_27495.1	chr3	54915868	54915884	-	1	NA	promoter-TSS (NM_177854)	promoter-TSS (NM_177854)	11	NM_177854	329641	Mm.51187	NM_177854	ENSMUSG00000056306	Sertm1	6030405A18Rik	serine rich and transmembrane domain containing 1	protein-coding
mm_27212.1	chr3	35932837	35932854	-	1	NA	promoter-TSS (NM_001205362)	promoter-TSS (NM_001205362)	121	NM_001205361	114893	Mm.374810	NM_033623	ENSMUSG00000027708	Dcun1d1	Rp42|SCCRO|Tes3|pTes3	DCN1, defective in cullin neddylation 1, domain containing 1 (S. cerevisiae)	protein-coding
mm_31276.1	chr4	45799017	45799056	+	1	NA	promoter-TSS (NM_028270)	promoter-TSS (NM_028270)	14	NM_028270	72535	Mm.331583	NM_028270	ENSMUSG00000035561	Aldh1b1	2700007F14Rik	aldehyde dehydrogenase 1 family, member B1	protein-coding
mm_39460.1	chr5	17694656	17694657	+	1	NA	exon (NM_013657, exon 12 of 18)	exon (NM_013657, exon 12 of 18)	119840	NM_013657	20348	Mm.5071	NM_013657	ENSMUSG00000028780	Sema3c	1110036B02Rik|SemE|Semae	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	protein-coding
mm_148103.1	chr18	74064946	74064963	-	1	NA	promoter-TSS (NM_172632)	promoter-TSS (NM_172632)	-5	NM_172632	225724	Mm.254517	NM_172632	ENSMUSG00000024558	Mapk4	A330097D03Rik|Erk3|Prkm4|p63Mapk	mitogen-activated protein kinase 4	protein-coding
mm_169042.1	chr13	14402157	14402159	+	1	NA	intron (NM_001081348, intron 2 of 28)	RLTR10|LTR|ERVK	121068	NM_001081348	94253	Mm.125298	NM_153130	ENSMUSG00000021301	Hecw1	9330116H24Rik|AV273951|E130207I19Rik|Nedl1	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	protein-coding
mm_71220.1	chr8	40899096	40899148	+	1	NA	exon (NM_001044740, exon 2 of 12)	exon (NM_001044740, exon 2 of 12)	-27111	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_8341.1	chr1	150164944	150164964	-	1	NA	promoter-TSS (NR_110420)	promoter-TSS (NR_110420)	-6	NR_110420	102639566	Mm.417208	NR_110420	ENSMUSG00000097754	Ptgs2os2	Gm26687|Linc-cox2|Lincrna-cox2	prostaglandin-endoperoxide synthase 2, opposite strand 2	ncRNA
mm_98841.1	chr11	97539897	97539899	+	1	NA	intron (NM_018873, intron 4 of 19)	intron (NM_018873, intron 4 of 19)	35228	NM_018873	56013	Mm.342665	NM_018873	ENSMUSG00000038453	Srcin1	P140|SNIP|mKIAA1684|p140Cap	SRC kinase signaling inhibitor 1	protein-coding
mm_91635.1	chr10	42264203	42264212	-	1	NA	intron (NM_019740, intron 2 of 3)	(A)n|Simple_repeat|Simple_repeat	12535	NM_019740	56484	Mm.338613	NM_019740	ENSMUSG00000048756	Foxo3	1110048B16Rik|2010203A17Rik|C76856|FKHRL1|Fkhr2|Foxo3a	forkhead box O3	protein-coding
mm_142456.1	chr17	45595504	45595575	-	1	NA	promoter-TSS (NM_001199116)	promoter-TSS (NM_001199116)	33	NM_001199116	63959	Mm.29744	NM_022880	ENSMUSG00000023942	Slc29a1	1200014D21Rik|AA407560|ENT1	solute carrier family 29 (nucleoside transporters), member 1	protein-coding
mm_112461.1	chr13	5867568	5867604	+	1	NA	3' UTR (NM_011803, exon 4 of 4)	3' UTR (NM_011803, exon 4 of 4)	6097	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_88537.1	chr10	78427342	78427401	+	1	NA	exon (NM_007793, exon 3 of 3)	exon (NM_007793, exon 3 of 3)	1701	NM_007793	13014	Mm.6095	NM_007793	ENSMUSG00000005054	Cstb	AA960480|Stfb	cystatin B	protein-coding
mm_140910.1	chr17	24167431	24167437	-	1	NA	intron (NR_037854, intron 1 of 2)	intron (NR_037854, intron 1 of 2)	1961	NR_037854	100039636	Mm.30155	NR_037854		Atp6v0c-ps2	Atp6l-ps2|Gm15487	ATPase, H+ transporting, lysosomal V0 subunit C, pseudogene 2	pseudo
mm_9696.1	chr1	178337707	178337733	-	1	NA	promoter-TSS (NM_016805)	promoter-TSS (NM_016805)	64	NM_016805	51810	Mm.86589	NM_016805	ENSMUSG00000039630	Hnrnpu	AA408410|AI256620|AL024194|AL024437|AW557595|C86794|Hnrpu|SAFA|Sp120|hnRNP U	heterogeneous nuclear ribonucleoprotein U	protein-coding
mm_129885.1	chr15	83489576	83489585	-	1	NA	exon (NM_178869, exon 11 of 12)	exon (NM_178869, exon 11 of 12)	21327	NM_178869	319953	Mm.235007	NM_178869	ENSMUSG00000022442	Ttll1	6330444E16Rik|AV014541	tubulin tyrosine ligase-like 1	protein-coding
mm_5055.1	chr1	194976401	194976431	+	1	NA	non-coding (NR_033564, exon 1 of 5)	non-coding (NR_033564, exon 1 of 5)	543	NR_033564	320400	Mm.417608	NR_033564	ENSMUSG00000097325	Gm16897	C030002c11rik	predicted gene, 16897	ncRNA
mm_77863.1	chr9	5323794	5323806	+	1	NA	intron (NM_007609, intron 4 of 8)	intron (NM_007609, intron 4 of 8)	14951	NM_007609	12363	Mm.1569	NM_007609	ENSMUSG00000033538	Casp4	CASP-11|CASP-4|Casp11|Caspl|ich-3	caspase 4, apoptosis-related cysteine peptidase	protein-coding
mm_39536.1	chr5	21381229	21381278	+	1	NA	intron (NM_029195, intron 2 of 18)	intron (NM_029195, intron 2 of 18)	8580	NM_008013	14190	Mm.292100	NM_008013	ENSMUSG00000039899	Fgl2	AI385601|musfiblp	fibrinogen-like protein 2	protein-coding
mm_61316.1	chr7	68133786	68133792	+	1	NA	intron (NM_010513, intron 2 of 20)	intron (NM_010513, intron 2 of 20)	130444	NM_030101	78444	Mm.425468	NM_030101	ENSMUSG00000030553	Pgpep1l	C330024D12Rik	pyroglutamyl-peptidase I-like	protein-coding
mm_9073.1	chr1	168395560	168395563	-	1	NA	intron (NM_008783, intron 2 of 7)	intron (NM_008783, intron 2 of 7)	36608	NM_001291508	18514	Mm.43358	NM_008783	ENSMUSG00000052534	Pbx1	2310056B04Rik|D230003C07Rik|Pbx-1	pre B cell leukemia homeobox 1	protein-coding
mm_154329.1	chrM	3049	3059	+	1	NA	NA	Intergenic	NA	NA								
mm_149514.1	chr19	12427905	12427928	+	1	NA	promoter-TSS (NM_019540)	promoter-TSS (NM_019540)	11	NM_019540	56093	Mm.285849	NM_019540	ENSMUSG00000040065	Pfpl	Epcs5|Epcs50	pore forming protein-like	protein-coding
mm_23848.1	chr3	83008420	83008444	+	1	NA	exon (NM_133862, exon 3 of 10)	exon (NM_133862, exon 3 of 10)	708	NM_001317105	99571	Mm.16422	NM_133862	ENSMUSG00000033860	Fgg	3010002H13Rik|AI256424	fibrinogen gamma chain	protein-coding
mm_32488.1	chr4	107968401	107968424	+	1	NA	promoter-TSS (NM_146255)	promoter-TSS (NM_146255)	78	NM_146255	242607	Mm.192040	NM_146255	ENSMUSG00000008932	Slc1a7	A930031E15Rik|Eaat5	solute carrier family 1 (glutamate transporter), member 7	protein-coding
mm_50282.1	chr6	47244419	47244437	+	1	NA	promoter-TSS (NM_025771)	promoter-TSS (NM_025771)	32	NM_025771	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding
mm_106384.1	chr11	118510666	118510666	-	1	NA	intron (NM_001024931, intron 5 of 14)	intron (NM_001024931, intron 5 of 14)	33706	NM_172573	217364	Mm.473963	NM_172573	ENSMUSG00000033857	Engase	C130099A03|D230014K01Rik	endo-beta-N-acetylglucosaminidase	protein-coding
mm_50367.1	chr6	48675202	48675209	+	1	NA	promoter-TSS (NM_174960)	promoter-TSS (NM_174960)	-930	NM_174960	317758	Mm.116971	NM_174960	ENSMUSG00000051124	Gimap9	A630002K24|BB145400	GTPase, IMAP family member 9	protein-coding
mm_91334.1	chr10	25536092	25536111	-	1	NA	promoter-TSS (NR_136909)	promoter-TSS (NR_136909)	171	NM_001195596	100504474	Mm.46323	NM_001195596	ENSMUSG00000096546	Smlr1	2010003K15Rik	small leucine-rich protein 1	protein-coding
mm_81044.1	chr9	105470489	105470499	+	1	NA	intron (NM_001253831, intron 1 of 26)	intron (NM_001253831, intron 1 of 26)	24639	NM_175025	235574	Mm.326247	NM_175025	ENSMUSG00000032570	Atp2c1	1700121J11Rik|ATP2C1A|AW061228|BCPM|D930003G21Rik|HHD|SPCA|pmr1	ATPase, Ca++-sequestering	protein-coding
mm_160410.1	chr8	72212828	72212828	-	1	NA	promoter-TSS (NM_001080812)	promoter-TSS (NM_001080812)	9	NM_001080812	234421	Mm.211247	NM_001080812	ENSMUSG00000074240	Cib3	C730014M21Rik|Gm1107|KIP3	calcium and integrin binding family member 3	protein-coding
mm_22801.1	chr3	25330909	25330911	+	1	NA	Intergenic	Lx9|LINE|L1	-546904	NM_001326288	635702	Mm.448351	NM_001326288	ENSMUSG00000102758	Naaladl2	2810043G22Rik|EG635702|Gm1021	N-acetylated alpha-linked acidic dipeptidase-like 2	protein-coding
mm_27508.1	chr3	55784341	55784352	-	1	NA	3' UTR (NM_010750, exon 1 of 1)	3' UTR (NM_010750, exon 1 of 1)	1836	NM_010750	17116	Mm.440209	NM_010750	ENSMUSG00000056947	Mab21l1	AW047968	mab-21-like 1 (C. elegans)	protein-coding
mm_119727.1	chr14	54074899	54074945	+	1	NA	Intergenic	Intergenic	179007	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_139574.1	chr17	57062354	57062360	+	1	NA	promoter-TSS (NM_177638)	promoter-TSS (NM_177638)	80	NM_177638	224912	Mm.284447	NM_177638	ENSMUSG00000044279	Crb3	5730439B18|AU015179|AU041752	crumbs family member 3	protein-coding
mm_134191.1	chr16	10983689	10983709	-	1	NA	intron (NM_019980, intron 1 of 3)	intron (NM_019980, intron 1 of 3)	9422	NM_019980	56722	Mm.294753	NM_019980	ENSMUSG00000022500	Litaf	3222402J11Rik|C85531|N4WBP3|TBX1	LPS-induced TN factor	protein-coding
mm_125049.1	chr15	25843243	25843249	+	1	NA	promoter-TSS (NM_001034851)	promoter-TSS (NM_001034851)	-52	NM_001034851	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_123307.1	chr14	62292960	62293019	-	1	NA	promoter-TSS (NM_173419)	promoter-TSS (NM_173419)	-10	NM_173419	239133	Mm.127330	NM_173419	ENSMUSG00000048281	Dleu7	BC038059	deleted in lymphocytic leukemia, 7	protein-coding
mm_88970.1	chr10	81409573	81409602	+	1	NA	intron (NM_026756, intron 3 of 8)	intron (NM_026756, intron 3 of 8)	6710	NR_106141	102465778		NR_106141	ENSMUSG00000105379	Mir1191b	mmu-mir-1191b	microRNA 1191b	ncRNA
mm_16485.1	chr2	180929001	180929046	+	1	NA	promoter-TSS (NM_001163247)	promoter-TSS (NM_001163247)	0	NM_001163247	329581	Mm.187879	NM_001163247	ENSMUSG00000038840	Birc7	E130019N06|KIAP|Livin|ML-IAP	baculoviral IAP repeat-containing 7 (livin)	protein-coding
mm_916.1	chr1	55052764	55052777	+	1	NA	promoter-TSS (NM_001039710)	promoter-TSS (NM_001039710)	0	NM_026424	67876	Mm.281019	NM_026424	ENSMUSG00000025981	Coq10b	1500041J02Rik|1700030I21Rik|9530077A17Rik|AV002237|AW742641	coenzyme Q10B	protein-coding
mm_152010.1	chr19	5952184	5952220	-	1	NA	intron (NM_001164057, intron 7 of 17)	PB1D10|SINE|Alu	12004	NM_001164057	18969	Mm.209931	NM_008893	ENSMUSG00000024833	Pola2	AI573378	polymerase (DNA directed), alpha 2	protein-coding
mm_145315.1	chr18	54422287	54422340	+	1	NA	promoter-TSS (NR_040338)	promoter-TSS (NR_040338)	18	NR_040338	77433	Mm.159919	NR_040338		Redrum	9430076G02Rik	Redrum, erythroid developmental long intergenic non-protein coding transcript	ncRNA
mm_72060.1	chr8	71402783	71402800	+	1	NA	exon (NM_026636, exon 7 of 9)	exon (NM_026636, exon 7 of 9)	-3221	NM_001310502	234396	Mm.216549	NM_172756	ENSMUSG00000046295	Ankle1	8430438L13Rik|Ankrd41|C430003I23|Lem3	ankyrin repeat and LEM domain containing 1	protein-coding
mm_104139.1	chr11	86993683	86993705	-	1	NA	promoter-TSS (NM_001005341)	promoter-TSS (NM_001005341)	68	NM_001005341	77864	Mm.191894	NM_001005341	ENSMUSG00000018427	Ypel2	6430570G24|E130113K08Rik	yippee-like 2 (Drosophila)	protein-coding
mm_33894.1	chr4	136192909	136192920	+	1	NA	exon (NM_177733, exon 7 of 7)	exon (NM_177733, exon 7 of 7)	12132	NM_001305399	242705	Mm.307932	NM_177733	ENSMUSG00000018983	E2f2	E2F-2	E2F transcription factor 2	protein-coding
mm_22499.1	chr3	7366599	7366641	+	1	NA	promoter-TSS (NM_008862)	promoter-TSS (NM_008862)	16	NM_008862	18767	Mm.3193	NM_008862	ENSMUSG00000027499	Pkia	AI415001|PKIalpha	protein kinase inhibitor, alpha	protein-coding
mm_93232.1	chr10	95323994	95324008	-	1	NA	promoter-TSS (NM_001330138)	promoter-TSS (NM_001330138)	136	NM_001330141	12905	Mm.473739	NM_009950	ENSMUSG00000045867	Cradd	RAIDD	CASP2 and RIPK1 domain containing adaptor with death domain	protein-coding
mm_83723.1	chr9	50768110	50768186	-	1	NA	promoter-TSS (NM_198675)	promoter-TSS (NM_198675)	4	NM_023483	68721	Mm.171374	NM_023483	ENSMUSG00000037971	1110032A03Rik	4930500N06Rik|c11orf1	RIKEN cDNA 1110032A03 gene	protein-coding
mm_144126.1	chr18	4908966	4908974	+	1	NA	Intergenic	L1MC4a|LINE|L1	96484	NR_045881	100038439	Mm.387569	NR_045881	ENSMUSG00000097043	Gm10556	ENSMUSG00000073646	predicted gene 10556	ncRNA
mm_22629.1	chr3	14767413	14767418	+	1	NA	exon (NM_001083957, exon 6 of 7)	exon (NM_001083957, exon 6 of 7)	11045	NM_001083957	12346	Mm.273195	NM_009799	ENSMUSG00000027556	Car1	AW555628|Ca1|Car-1	carbonic anhydrase 1	protein-coding
mm_44844.1	chr5	34187629	34187643	-	1	NA	promoter-TSS (NM_010753)	promoter-TSS (NM_010753)	74	NM_010753	17122	Mm.259260	NM_010753	ENSMUSG00000037235	Mxd4	2810410A03Rik|Mad4|bHLHc12	Max dimerization protein 4	protein-coding
mm_114083.1	chr13	54581127	54581170	+	1	NA	TTS (NM_019968)	TTS (NM_019968)	6135	NM_019968	56795	Mm.89484	NM_019968	ENSMUSG00000025870	Arl10	Arl10a|Arm1	ADP-ribosylation factor-like 10	protein-coding
mm_113685.1	chr13	42866314	42866337	+	1	NA	promoter-TSS (NM_001302636)	promoter-TSS (NM_001302636)	78	NM_001302636	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding
mm_72651.1	chr8	84832258	84832295	+	1	NA	promoter-TSS (NM_183358)	promoter-TSS (NM_183358)	-6	NM_183358	102060	Mm.489649	NM_183358	ENSMUSG00000033751	Gadd45gip1	2310040G17Rik|AI425883|Crif1|MRP-L59|Plinp1	growth arrest and DNA-damage-inducible, gamma interacting protein 1	protein-coding
mm_53406.1	chr6	131837446	131837488	+	1	NA	Intergenic	L1VL1|LINE|L1	-147404	NM_207019	387346	Mm.377908	NM_207019	ENSMUSG00000063478	Tas2r114	T2R14|Tas2r14|mGR14|mt2r46	taste receptor, type 2, member 114	protein-coding
mm_73397.1	chr8	105850835	105850842	+	1	NA	intron (NM_177150, intron 1 of 12)	ID_B1|SINE|B4	1170	NM_177150	320394	Mm.334775	NM_177150	ENSMUSG00000036672	Cenpt	G630055P03Rik	centromere protein T	protein-coding
mm_103961.1	chr11	84167467	84167508	-	1	NA	promoter-TSS (NM_001037932)	promoter-TSS (NM_001037932)	-11	NM_001037932	628813	Mm.390389	NM_001037932	ENSMUSG00000051452	Gm11437	AI463690|OTTMUSG00000000997	predicted gene 11437	protein-coding
mm_108380.1	chr12	80877378	80877399	+	1	NA	3' UTR (NM_178682, exon 6 of 6)	3' UTR (NM_178682, exon 6 of 6)	47059	NR_033786	67340	Mm.386790	NR_033786	ENSMUSG00000101912	1700052I22Rik	-	RIKEN cDNA 1700052I22 gene	ncRNA
mm_89638.1	chr10	96621195	96621208	+	1	NA	3' UTR (NM_007569, exon 2 of 2)	3' UTR (NM_007569, exon 2 of 2)	4200	NM_007569	12226	Mm.23811	NM_007569	ENSMUSG00000036478	Btg1	AI426953|AW546738	B cell translocation gene 1, anti-proliferative	protein-coding
mm_59069.1	chr7	19507321	19507360	+	1	NA	exon (NM_177692, exon 2 of 2)	exon (NM_177692, exon 2 of 2)	991	NM_177692	232946	Mm.64557	NM_177692	ENSMUSG00000057667	Bloc1s3	BC043666|Blos3|E230011O18|rp	biogenesis of lysosomal organelles complex-1, subunit 3	protein-coding
mm_98092.1	chr11	86602362	86602386	+	1	NA	intron (NM_029478, intron 9 of 11)	intron (NM_029478, intron 9 of 11)	-18216	NR_029738	387140		NR_029738	ENSMUSG00000065455	Mir21a	Mir21|Mirn21|mmu-mir-21|mmu-mir-21a	microRNA 21a	ncRNA
mm_123597.1	chr14	67715586	67715640	-	1	NA	promoter-TSS (NM_001111028)	promoter-TSS (NM_001111028)	-3	NM_001110162	108912	Mm.33831	NM_175384	ENSMUSG00000048922	Cdca2	2610311M19Rik|AI586158	cell division cycle associated 2	protein-coding
mm_97220.1	chr11	75636760	75636814	+	1	NA	intron (NM_008916, intron 3 of 11)	intron (NM_008916, intron 3 of 11)	5767	NM_008916	19062	Mm.1458	NM_008916	ENSMUSG00000006127	Inpp5k	C62|Pps|SKIP	inositol polyphosphate 5-phosphatase K	protein-coding
mm_58894.1	chr7	17095007	17095011	+	1	NA	intron (NM_001310628, intron 3 of 5)	intron (NM_001310628, intron 3 of 5)	20969	NM_007676	26436	Mm.143686	NM_007676	ENSMUSG00000066760	Psg16	Cea11|PSG|bCEA	pregnancy specific glycoprotein 16	protein-coding
mm_99377.1	chr11	101987051	101987069	+	1	NA	promoter-TSS (NM_029287)	promoter-TSS (NM_029287)	4	NM_029287	75437	Mm.108632	NM_029287	ENSMUSG00000010841	1700006E09Rik	-	RIKEN cDNA 1700006E09 gene	protein-coding
mm_130284.1	chr15	96996298	96996324	-	1	NA	3' UTR (NM_027052, exon 16 of 16)	3' UTR (NM_027052, exon 16 of 16)	59645	NM_027052	69354	Mm.250980	NM_027052	ENSMUSG00000022464	Slc38a4	1110012E16Rik|1700012A18Rik|Ata3|mATA3|mNAT3	solute carrier family 38, member 4	protein-coding
mm_54178.1	chr6	23824797	23824798	-	1	NA	intron (NM_001252107, intron 1 of 13)	intron (NM_001252107, intron 1 of 13)	14624	NM_001252106	320405	Mm.259632	NM_153163	ENSMUSG00000017978	Cadps2	A230044C21Rik|Caps-2|Caps2|Cpd2	Ca2+-dependent activator protein for secretion 2	protein-coding
mm_69070.1	chr7	126949895	126949939	-	1	NA	promoter-TSS (NM_001039645)	promoter-TSS (NM_001039645)	-336	NM_001039645	233879	Mm.444143	NM_001039645	ENSMUSG00000046378	Asphd1	A830007L07Rik|Gm168	aspartate beta-hydroxylase domain containing 1	protein-coding
mm_74375.1	chr8	128504938	128504966	+	1	NA	3' UTR (NM_008737, exon 17 of 17)	3' UTR (NM_008737, exon 17 of 17)	145711	NR_035436	100316680		NR_035436	ENSMUSG00000084523	Mir1903	Mirn1903|mmu-mir-1903	microRNA 1903	ncRNA
mm_111160.1	chr12	83520290	83520332	-	1	NA	promoter-TSS (NM_030246)	promoter-TSS (NM_030246)	-155	NM_030246	73828	Mm.38238	NM_030246	ENSMUSG00000021222	Dcaf4	1110018E21Rik|Wdr21	DDB1 and CUL4 associated factor 4	protein-coding
mm_102490.1	chr11	60229767	60229780	-	1	NA	3' UTR (NM_001039092, exon 14 of 14)	3' UTR (NM_001039092, exon 14 of 14)	-9146	NM_001313979	20787	Mm.278701	NM_011480	ENSMUSG00000020538	Srebf1	ADD1|SREBP-1a|SREBP1|SREBP1c|bHLHd1	sterol regulatory element binding transcription factor 1	protein-coding
mm_26525.1	chr3	145987836	145987901	+	1	NA	promoter-TSS (NM_001166064)	promoter-TSS (NM_001166064)	-2	NM_001166064	214804	Mm.268854	NM_001166064	ENSMUSG00000036863	Syde2	C430017H16Rik	synapse defective 1, Rho GTPase, homolog 2 (C. elegans)	protein-coding
mm_71702.1	chr8	61913060	61913063	+	1	NA	Intergenic	RMER1C|Other|Other	-10367	NM_001293772	72333	Mm.29933	NM_001081390	ENSMUSG00000058056	Palld	2410003B16Rik|6030492A02	palladin, cytoskeletal associated protein	protein-coding
mm_33466.1	chr4	130811679	130811699	+	1	NA	intron (NM_011520, intron 1 of 4)	intron (NM_011520, intron 1 of 4)	19152	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_82811.1	chr9	30781366	30781371	-	1	NA	Intergenic	Intergenic	139582	NM_001329420	235130	Mm.65867	NM_001024139	ENSMUSG00000033453	Adamts15	-	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 15	protein-coding
mm_104388.1	chr11	94485291	94485327	-	1	NA	promoter-TSS (NM_144827)	promoter-TSS (NM_144827)	1	NM_144827	217116	Mm.156123	NM_144827	ENSMUSG00000020867	Spata20	Tisp78	spermatogenesis associated 20	protein-coding
mm_56425.1	chr6	97309307	97309320	-	1	NA	intron (NM_001346639, intron 12 of 22)	intron (NM_001346639, intron 12 of 22)	-56533	NM_001081157	320502	Mm.68163	NM_001081157	ENSMUSG00000044086	Lmod3	5430424A14Rik	leiomodin 3 (fetal)	protein-coding
mm_117800.1	chr13	97207075	97207080	-	1	NA	Intergenic	RMER5|LTR|ERV1	-8720	NM_010422	15212	Mm.27816	NM_010422	ENSMUSG00000021665	Hexb	-	hexosaminidase B	protein-coding
mm_155984.1	chrX	106127268	106127298	+	1	NA	3' UTR (NM_009726, exon 23 of 23)	3' UTR (NM_009726, exon 23 of 23)	-15992	NM_205820	279572	Mm.336203	NM_205820	ENSMUSG00000033777	Tlr13	AI666735|Gm713	toll-like receptor 13	protein-coding
mm_91313.1	chr10	24924259	24924285	-	1	NA	intron (NM_007482, intron 1 of 7)	intron (NM_007482, intron 1 of 7)	3198	NM_007482	11846	Mm.154144	NM_007482	ENSMUSG00000019987	Arg1	AI|AI256583|Arg-1|PGIF	arginase, liver	protein-coding
mm_18788.1	chr2	73721939	73721969	-	1	NA	intron (NM_001166603, intron 1 of 11)	intron (NM_001166603, intron 1 of 11)	53392	NM_001166603	108699	Mm.257073	NM_029716	ENSMUSG00000056486	Chn1	0610007I19Rik|0710001E19Rik|1700112L09Rik|2900046J01Rik|AI413815|ARHGAP2	chimerin 1	protein-coding
mm_26499.1	chr3	145652408	145652456	+	1	NA	Intergenic	Intergenic	-2447	NM_010516	16007	Mm.1231	NM_010516	ENSMUSG00000028195	Cyr61	AI325051|CCN1|Igfbp10	cysteine rich protein 61	protein-coding
mm_45798.1	chr5	87567384	87567403	-	1	NA	intron (NM_016771, intron 1 of 7)	ORR1B1|LTR|ERVL-MaLR	1613	NM_016771	53315	Mm.6824	NM_016771	ENSMUSG00000029273	Sult1d1	5033411P13Rik|AI987815|ST1d1|SULT-N|Sultn	sulfotransferase family 1D, member 1	protein-coding
mm_151425.1	chr19	56851945	56851954	+	1	NA	exon (NM_031387, exon 16 of 26)	exon (NM_031387, exon 16 of 26)	21237	NM_001002241	83561	Mm.247541	NM_031387	ENSMUSG00000025081	Tdrd1	MTR-1	tudor domain containing 1	protein-coding
mm_27660.1	chr3	65295894	65295905	-	1	NA	intron (NM_010597, intron 3 of 13)	intron (NM_010597, intron 3 of 13)	6786	NR_126080	102637797	Mm.446731	NR_126080	ENSMUSG00000104093	A330015K06Rik	-	RIKEN cDNA A330015K06 gene	ncRNA
mm_2263.1	chr1	91145105	91145115	+	1	NA	promoter-TSS (NM_001033408)	promoter-TSS (NM_001033408)	7	NM_001033408	329207	Mm.295940	NM_001033408	ENSMUSG00000070732	Rbm44	Gm817	RNA binding motif protein 44	protein-coding
mm_14100.1	chr2	125247227	125247287	+	1	NA	promoter-TSS (NM_001159646)	promoter-TSS (NM_001159646)	9	NM_001159646	110074	Mm.282499	NM_023595	ENSMUSG00000027203	Dut	5031412I06Rik|5133400F09Rik|D2Bwg0749e|Dutp|dUTPase	deoxyuridine triphosphatase	protein-coding
mm_883.1	chr1	52568496	52568504	+	1	NA	Intergenic	RLTR51A_Mm|LTR|ERVK?	-62205	NR_024590	227094	Mm.83541	NM_172654	ENSMUSG00000043015	Nemp2	5330401P04Rik|9830163O08|Tmem194b	nuclear envelope integral membrane protein 2	protein-coding
mm_4127.1	chr1	170214827	170214863	+	1	NA	intron (NM_010633, intron 1 of 7)	intron (NM_010633, intron 1 of 7)	548	NM_010633	16589	Mm.209150	NM_010633	ENSMUSG00000026667	Uhmk1	4732477C12Rik|4930500M09Rik|AA673513|AI449218|AU021979|C820018A03Rik|KIS|Kist|OTTMUSG00000021542|P-CIP2	U2AF homology motif (UHM) kinase 1	protein-coding
mm_169795.1	chr16	16049146	16049163	-	1	NA	intron (NM_146068, intron 6 of 19)	intron (NM_146068, intron 6 of 19)	97697	NM_146068	224008	Mm.244703	NM_146068	ENSMUSG00000041974	Spidr	2310008H04Rik|Kiaa0146	scaffolding protein involved in DNA repair	protein-coding
mm_102066.1	chr11	52257062	52257087	-	1	NA	exon (NM_009331, exon 7 of 10)	exon (NM_009331, exon 7 of 10)	25079	NM_011543	21402	Mm.42944	NM_011543	ENSMUSG00000036309	Skp1a	15kDa|2610043E24Rik|2610206H23Rik|EMC19|OCP-II|OCP2|SKP1|Tceb1l|p19A|p19Skp1	S-phase kinase-associated protein 1A	protein-coding
mm_152824.1	chr19	23136525	23136535	-	1	NA	Intergenic	Intergenic	-4696	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_123406.1	chr14	63543915	63543925	-	1	NA	promoter-TSS (NM_177594)	promoter-TSS (NM_177594)	33	NM_177594	210376	Mm.441613	NM_177594	ENSMUSG00000035078	Mtmr9	9430075G12Rik|AA516943|AF073881|LIP-STYX|MTMR8|mMTMH3	myotubularin related protein 9	protein-coding
mm_97486.1	chr11	78324714	78324762	+	1	NA	exon (NM_009657, exon 2 of 8)	exon (NM_009657, exon 2 of 8)	540	NM_009657	11676	Mm.7729	NM_009657	ENSMUSG00000017390	Aldoc	AI847350|AU040929|Aldo3|Scrg2	aldolase C, fructose-bisphosphate	protein-coding
mm_28546.1	chr3	92926243	92926247	-	1	NA	promoter-TSS (NM_001039594)	promoter-TSS (NM_001039594)	-15	NM_001039594	545548	Mm.387664	NM_001039594	ENSMUSG00000054325	Lce3a	EG545548	late cornified envelope 3A	protein-coding
mm_120568.1	chr14	69029124	69029127	+	1	NA	promoter-TSS (NM_009285)	promoter-TSS (NM_009285)	-164	NM_009285	20855	Mm.20911	NM_009285	ENSMUSG00000014813	Stc1	Stc	stanniocalcin 1	protein-coding
mm_17969.1	chr2	37585880	37585882	-	1	NA	intron (NM_009261, intron 16 of 16)	intron (NM_009261, intron 16 of 16)	61404	NM_009261	20744	Mm.237095	NM_009261	ENSMUSG00000026915	Strbp	6430510M02Rik|AI852513|C230082I21Rik|C86322|Spnr	spermatid perinuclear RNA binding protein	protein-coding
mm_103255.1	chr11	70982988	70983024	-	1	NA	promoter-TSS (NM_007573)	promoter-TSS (NM_007573)	20	NM_007573	12261	Mm.30049	NM_007573	ENSMUSG00000018446	C1qbp	AA407365|AA986492|D11Wsu182e|HABP1|P32|gC1qBP	complement component 1, q subcomponent binding protein	protein-coding
mm_47448.1	chr5	123482634	123482644	-	1	NA	promoter-TSS (NM_029594)	promoter-TSS (NM_029594)	-538	NM_029594	76399	Mm.75049	NM_029594	ENSMUSG00000029437	Il31	1700013B14Rik	interleukin 31	protein-coding
mm_39399.1	chr5	14025610	14025625	+	1	NA	5' UTR (NM_011348, exon 1 of 17)	5' UTR (NM_011348, exon 1 of 17)	341	NM_011348	20349	Mm.134093	NM_011348	ENSMUSG00000063531	Sema3e	6430702L12|AA408817|Semah|mKIAA0331	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	protein-coding
mm_156961.1	chrX	169989854	169989869	+	1	NA	3' UTR (NM_001290504, exon 10 of 10)	3' UTR (NM_001290504, exon 10 of 10)	-10944	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_37894.1	chr4	132567465	132567475	-	1	NA	intron (NM_001081211, intron 1 of 1)	intron (NM_001081211, intron 1 of 1)	3403	NM_001081211	19204	Mm.89389	NM_001081211	ENSMUSG00000056529	Ptafr	PAFR	platelet-activating factor receptor	protein-coding
mm_89955.1	chr10	111293649	111293674	+	1	NA	3' UTR (NM_001003717, exon 23 of 23)	3' UTR (NM_001003717, exon 23 of 23)	-5018	NM_027914	71769	Mm.45256	NM_027914	ENSMUSG00000035759	Bbs10	1300007O09Rik|AI452285	Bardet-Biedl syndrome 10 (human)	protein-coding
mm_7024.1	chr1	87098540	87098558	-	1	NA	3' UTR (NM_001081082, exon 11 of 11)	3' UTR (NM_001081082, exon 11 of 11)	3057	NM_001081082	76768	Mm.58068	NM_001081082	ENSMUSG00000079440	Alpi	2010001C14Rik|Akp6|gIAP	alkaline phosphatase, intestinal	protein-coding
mm_25352.1	chr3	106790165	106790176	+	1	NA	promoter-TSS (NM_007651)	promoter-TSS (NM_007651)	-21	NM_007651	12508	Mm.316861	NM_007651	ENSMUSG00000040747	Cd53	AI323659|Ox-44|Tspan25	CD53 antigen	protein-coding
mm_81061.1	chr9	106170886	106170892	+	1	NA	promoter-TSS (NM_029896)	promoter-TSS (NM_029896)	-40	NM_029896	77305	Mm.265125	NM_029896	ENSMUSG00000020257	Wdr82	9430077D24Rik|CDW5/WDR82	WD repeat domain containing 82	protein-coding
mm_171572.1	chr4	147361392	147361396	+	1	NA	intron (NM_001039209, intron 1 of 2)	intron (NM_001039209, intron 1 of 2)	185528	NM_001039209	195531	Mm.270762	NM_001039209	ENSMUSG00000078496	Zfp982	Gm13152|OTTMUSG00000010671	zinc finger protein 982	protein-coding
mm_49991.1	chr6	41047404	41047416	+	1	NA	Intergenic	Intergenic	-11901	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_145593.1	chr18	60986103	60986110	+	1	NA	3' UTR (NM_001286809, exon 6 of 6)	3' UTR (NM_001286809, exon 6 of 6)	22552	NM_001286809	12322	Mm.131530	NM_009792	ENSMUSG00000024617	Camk2a	CaMKII|R74975|mKIAA0968	calcium/calmodulin-dependent protein kinase II alpha	protein-coding
mm_36501.1	chr4	83417554	83417577	-	1	NA	promoter-TSS (NM_029949)	promoter-TSS (NM_029949)	-179	NM_029949	77634	Mm.271985	NM_029949	ENSMUSG00000028483	Snapc3	1810020H02Rik|4930558A07Rik|5031401C21Rik|AI414457|E030018J20Rik	small nuclear RNA activating complex, polypeptide 3	protein-coding
mm_47121.1	chr5	119691212	119691254	-	1	NA	promoter-TSS (NR_040416)	promoter-TSS (NR_040416)	-15	NR_040416	433944	Mm.491053	NR_040416	ENSMUSG00000086847	Tbx3os2	Gm16065|OTTMUSG00000029666	T-box 3, opposite strand 2	ncRNA
mm_83051.1	chr9	37545043	37545052	-	1	NA	TTS (NM_020518)	TTS (NM_020518)	5792	NM_020518	57276	Mm.27478	NM_020518	ENSMUSG00000001943	Vsig2	1190004B15Rik|2210413P10Rik|AU040484|CTX|Ctm	V-set and immunoglobulin domain containing 2	protein-coding
mm_166860.1	chr7	24442537	24442559	+	1	NA	intron (NM_199013, intron 1 of 2)	intron (NM_199013, intron 1 of 2)	3134	NM_199013	210145	Mm.33811	NM_199013	ENSMUSG00000062028	Irgc1	F630044M05Rik|Gm1102|Gm474|Ifgge|Iigp5|Irgc	immunity-related GTPase family, cinema 1	protein-coding
mm_145692.1	chr18	62137546	62137551	+	1	NA	Intergenic	MIRb|SINE|MIR	42433	NM_007420	11555	Mm.5598	NM_007420	ENSMUSG00000045730	Adrb2	Adrb-2|Badm|Gpcr7	adrenergic receptor, beta 2	protein-coding
mm_144345.1	chr18	15150677	15150681	+	1	NA	intron (NM_134112, intron 1 of 4)	CpG	767	NM_134112	106931	Mm.329299	NM_134112	ENSMUSG00000036225	Kctd1	4933402K10Rik|AI661543|AW553000	potassium channel tetramerisation domain containing 1	protein-coding
mm_100640.1	chr11	121830194	121830198	+	1	NA	promoter-TSS (NM_029049)	promoter-TSS (NM_029049)	-22	NM_029049	74675	Mm.61213	NM_029049	ENSMUSG00000039198	Ptchd3	4930451E13Rik|4933440L20Rik|RNDEu-3	patched domain containing 3	protein-coding
mm_400.1	chr1	34160149	34160161	+	1	NA	promoter-TSS (NM_010081)	promoter-TSS (NM_010081)	-175	NM_010081	13518	Mm.336625	NM_010081	ENSMUSG00000026131	Dst	2310001O04Rik|A830042E19Rik|AW554249|BP230|BPAG1-n|Bpag|Bpag1|Macf2|ah|athetoid|dt|mKIAA0728|nmf203|nmf339	dystonin	protein-coding
mm_145616.1	chr18	61105663	61105667	+	1	NA	promoter-TSS (NM_001037859)	promoter-TSS (NM_001037859)	93	NM_001037859	12978	Mm.22574	NM_007779	ENSMUSG00000024621	Csf1r	AI323359|CD115|CSF-1R|Csfmr|Fim-2|Fim2|Fms|M-CSF-R|M-CSFR	colony stimulating factor 1 receptor	protein-coding
mm_64089.1	chr7	140968067	140968102	+	1	NA	promoter-TSS (NM_001112715)	promoter-TSS (NM_001112715)	8	NM_001112715	68713	Mm.175661	NM_026820	ENSMUSG00000025491	Ifitm1	1110036C17Rik|DSPA2a|Mil-2|Mil2	interferon induced transmembrane protein 1	protein-coding
mm_166896.1	chr7	28379490	28379502	-	1	NA	promoter-TSS (NM_011756)	promoter-TSS (NM_011756)	-268	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_27672.1	chr3	65529356	65529384	-	1	NA	promoter-TSS (NR_027955)	promoter-TSS (NR_027955)	44	NR_027955	71004	Mm.475465	NM_001033527	ENSMUSG00000074580	4931440P22Rik	-	RIKEN cDNA 4931440P22 gene	ncRNA
mm_25261.1	chr3	104782364	104782380	+	1	NA	intron (NM_027982, intron 1 of 9)	intron (NM_027982, intron 1 of 9)	1316	NM_027982	71887	Mm.379204	NM_027982	ENSMUSG00000002228	Ppm1j	2310008J22Rik|PP2Czeta|Ppp2cz	protein phosphatase 1J	protein-coding
mm_46664.1	chr5	108693969	108694005	-	1	NA	promoter-TSS (NM_001164259)	promoter-TSS (NM_001164259)	-242	NM_001164259	116701	Mm.35691	NM_054071	ENSMUSG00000008090	Fgfrl1	FGFR5|FGFR5beta|FGFR5gamma	fibroblast growth factor receptor-like 1	protein-coding
mm_107373.1	chr12	32859351	32859353	+	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	35236	NR_045032	100504486	Mm.440246	NR_045032		Gdap10	Gdap-ps	ganglioside-induced differentiation-associated-protein 10	ncRNA
mm_39742.1	chr5	29569343	29569354	+	1	NA	5' UTR (NM_133907, exon 1 of 23)	5' UTR (NM_133907, exon 1 of 23)	106	NM_133907	100763	Mm.137746	NM_133907	ENSMUSG00000039000	Ube3c	AI853514|mKIAA0010	ubiquitin protein ligase E3C	protein-coding
mm_64995.1	chr7	16923876	16923891	-	1	NA	5' UTR (NM_007590, exon 1 of 6)	5' UTR (NM_007590, exon 1 of 6)	149	NM_007590	12315	Mm.288630	NM_007590	ENSMUSG00000019370	Calm3	CaMA|R75142	calmodulin 3	protein-coding
mm_92989.1	chr10	86701953	86701973	-	1	NA	exon (NM_011631, exon 5 of 18)	exon (NM_011631, exon 5 of 18)	3481	NM_011631	22027	Mm.87773	NM_011631	ENSMUSG00000020048	Hsp90b1	ERp99|GRP94|TA-3|Targ2|Tra-1|Tra1|endoplasmin|gp96	heat shock protein 90, beta (Grp94), member 1	protein-coding
mm_49331.1	chr6	21215473	21215484	+	1	NA	promoter-TSS (NM_019697)	promoter-TSS (NM_019697)	-631	NM_019697	16508	Mm.425316	NM_019697	ENSMUSG00000060882	Kcnd2	AI839615|AW555701|Kv4.2|R75121|mKIAA1044	potassium voltage-gated channel, Shal-related family, member 2	protein-coding
mm_156346.1	chrX	139179208	139179232	+	1	NA	Intergenic	Intergenic	-30824	NM_175541	245631	Mm.131001	NM_175541	ENSMUSG00000042515	Mum1l1	9430086K21Rik	melanoma associated antigen (mutated) 1-like 1	protein-coding
mm_22732.1	chr3	19690018	19690020	+	1	NA	intron (NM_001081281, intron 9 of 9)	intron (NM_001081281, intron 9 of 9)	5377	NM_205769	12918	Mm.290689	NM_205769	ENSMUSG00000049796	Crh	CRF|Gm1347	corticotropin releasing hormone	protein-coding
mm_80411.1	chr9	77754527	77754541	+	1	NA	promoter-TSS (NM_010295)	promoter-TSS (NM_010295)	-1	NM_010295	14629	Mm.89888	NM_010295	ENSMUSG00000032350	Gclc	D9Wsu168e|GLCL-H|Ggcs-hs|Glclc	glutamate-cysteine ligase, catalytic subunit	protein-coding
mm_9016.1	chr1	166127182	166127221	-	1	NA	5' UTR (NM_001033344, exon 2 of 6)	5' UTR (NM_001033344, exon 2 of 6)	697	NM_001033344	240892	Mm.35315	NM_001033344	ENSMUSG00000026564	Dusp27	C130085G02Rik|Gm209	dual specificity phosphatase 27 (putative)	protein-coding
mm_48054.1	chr5	136549594	136549601	-	1	NA	intron (NM_001291234, intron 1 of 22)	B1_Mur1|SINE|Alu	16384	NM_001291239	13047	Mm.320317	NM_009986	ENSMUSG00000029705	Cux1	CDP|Cutl1|Cux|Cux-1	cut-like homeobox 1	protein-coding
mm_92985.1	chr10	86695714	86695743	-	1	NA	exon (NM_011631, exon 10 of 18)	exon (NM_011631, exon 10 of 18)	9716	NM_011631	22027	Mm.87773	NM_011631	ENSMUSG00000020048	Hsp90b1	ERp99|GRP94|TA-3|Targ2|Tra-1|Tra1|endoplasmin|gp96	heat shock protein 90, beta (Grp94), member 1	protein-coding
mm_35142.1	chr4	11393887	11393915	-	1	NA	Intergenic	Intergenic	-7118	NM_194055	207920	Mm.387719	NM_194055	ENSMUSG00000040728	Esrp1	2210008M09Rik|A630065D16|BC031468|Rbm35a	epithelial splicing regulatory protein 1	protein-coding
mm_43144.1	chr5	125442112	125442123	+	1	NA	intron (NM_029752, intron 1 of 2)	intron (NM_029752, intron 1 of 2)	549	NM_029752	76809	Mm.290720	NM_029752	ENSMUSG00000037905	Bri3bp	2410150I18Rik|AI841257|AW742481	Bri3 binding protein	protein-coding
mm_90330.1	chr10	127078989	127078991	+	1	NA	promoter-TSS (NM_001301014)	promoter-TSS (NM_001301014)	83	NM_001033263	216439	Mm.336761	NM_001033263	ENSMUSG00000025422	Agap2	AGAP-2|Centg1|PIKE|cnt-g1|mKIAA0167	ArfGAP with GTPase domain, ankyrin repeat and PH domain 2	protein-coding
mm_140596.1	chr17	10286691	10286697	-	1	NA	intron (NM_021881, intron 1 of 6)	intron (NM_021881, intron 1 of 6)	32667	NM_021881	19317	Mm.130694	NM_021881	ENSMUSG00000062078	Qk	1110003F05Rik|1500005P18|QkI|l(17)-1Wis|l17Wis1	quaking	protein-coding
mm_63661.1	chr7	129591842	129591852	+	1	NA	promoter-TSS (NM_172255)	promoter-TSS (NM_172255)	-16	NM_172255	207425	Mm.229323	NM_172255	ENSMUSG00000042055	Wdr11	2900055P10Rik|AW489876|Brwd2|mKIAA1351	WD repeat domain 11	protein-coding
mm_12248.1	chr2	68883551	68883570	+	1	NA	intron (NM_172856, intron 1 of 9)	MTC|LTR|ERVL-MaLR	22119	NM_001347161	241447	Mm.222222	NM_172856	ENSMUSG00000027035	Cers6	4732462C07Rik|AW544719|Lass6|T1L	ceramide synthase 6	protein-coding
mm_88062.1	chr10	67646939	67646954	+	1	NA	Intergenic	Intergenic	-97991	NM_001005419	211488	Mm.297250	NM_001005419	ENSMUSG00000057134	Ado	Gm237	2-aminoethanethiol (cysteamine) dioxygenase	protein-coding
mm_111574.1	chr12	101818906	101818920	-	1	NA	5' UTR (NM_011812, exon 1 of 11)	5' UTR (NM_011812, exon 1 of 11)	206	NM_011812	23876	Mm.288381	NM_011812	ENSMUSG00000021186	Fbln5	A55|DANCE|EVEC	fibulin 5	protein-coding
mm_114325.1	chr13	60608465	60608467	+	1	NA	intron (NM_029653, intron 2 of 25)	intron (NM_029653, intron 2 of 25)	6255	NM_134062	69635	Mm.24103	NM_029653	ENSMUSG00000021559	Dapk1	D13Ucla1|DAP-Kinase	death associated protein kinase 1	protein-coding
mm_137876.1	chr17	31520134	31520169	+	1	NA	promoter-TSS (NM_001083891)	promoter-TSS (NM_001083891)	36	NM_001083891	78330	Mm.28349	NM_030087	ENSMUSG00000024038	Ndufv3	1500032D16Rik	NADH dehydrogenase (ubiquinone) flavoprotein 3	protein-coding
mm_148966.1	chr19	7494523	7494598	+	1	NA	5' UTR (NM_146091, exon 1 of 13)	5' UTR (NM_146091, exon 1 of 13)	122	NM_146091	109168	Mm.264016	NM_146091	ENSMUSG00000024759	Atl3	4633402C03Rik|5730596K20Rik|AI465397|AW228836	atlastin GTPase 3	protein-coding
mm_68045.1	chr7	101379885	101379898	-	1	NA	intron (NM_001040112, intron 1 of 30)	intron (NM_001040112, intron 1 of 30)	1769	NM_001040112	69710	Mm.277687	NM_027180	ENSMUSG00000032812	Arap1	2410002L19Rik|Centd2|mKIAA0782	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	protein-coding
mm_154512.1	chrM	12357	12383	-	1	NA	NA	Intergenic	NA	NA								
mm_157773.1	chrX	73739240	73739245	-	1	NA	TTS (NM_007435)	TTS (NM_007435)	-17861	NM_019587	140571	Mm.275600	NM_019587	ENSMUSG00000031385	Plxnb3	AI451018|Plxn6	plexin B3	protein-coding
mm_106688.1	chr12	3365109	3365142	+	1	NA	promoter-TSS (NM_008445)	promoter-TSS (NM_008445)	-7	NM_008445	16570	Mm.7688	NM_008445	ENSMUSG00000020668	Kif3c	mKIAA4058	kinesin family member 3C	protein-coding
mm_82686.1	chr9	22259888	22259949	-	1	NA	promoter-TSS (NM_181419)	promoter-TSS (NM_181419)	-23	NM_181419	235048	Mm.292381	NM_181419	ENSMUSG00000062794	Zfp599	6720416P20	zinc finger protein 599	protein-coding
mm_88365.1	chr10	75943021	75943028	+	1	NA	Intergenic	MER65D|LTR|ERV1	-2352	NM_001277132	333670	Mm.291320	NM_001037714	ENSMUSG00000050157	Gm867	Gm736	predicted gene 867	protein-coding
mm_113255.1	chr13	28020244	28020252	+	1	NA	exon (NM_011165, exon 3 of 5)	exon (NM_011165, exon 3 of 5)	4025	NM_011165	19110	Mm.18607	NM_011165	ENSMUSG00000005891	Prl4a1	AA409771|Ghd23|PLP-A|Prlpa	prolactin family 4, subfamily a, member 1	protein-coding
mm_168256.1	chr10	86705434	86705436	-	1	NA	promoter-TSS (NM_011631)	promoter-TSS (NM_011631)	9	NM_011631	22027	Mm.87773	NM_011631	ENSMUSG00000020048	Hsp90b1	ERp99|GRP94|TA-3|Targ2|Tra-1|Tra1|endoplasmin|gp96	heat shock protein 90, beta (Grp94), member 1	protein-coding
mm_26323.1	chr3	142530330	142530386	+	1	NA	promoter-TSS (NM_001083312)	promoter-TSS (NM_001083312)	22	NM_145545	229900	Mm.45740	NM_145545	ENSMUSG00000040253	Gbp7	9830147J24Rik	guanylate binding protein 7	protein-coding
mm_73773.1	chr8	116504974	116505023	+	1	NA	promoter-TSS (NM_029297)	promoter-TSS (NM_029297)	-17	NM_029297	75465	Mm.23114	NM_029297	ENSMUSG00000034467	Dynlrb2	1700009A04Rik|DNLC2B|Dncl2b	dynein light chain roadblock-type 2	protein-coding
mm_96488.1	chr11	67695315	67695326	+	1	NA	promoter-TSS (NM_009038)	promoter-TSS (NM_009038)	-6	NM_009038	19674	Mm.439726	NM_009038	ENSMUSG00000020907	Rcvrn	CAR|S-modulin	recoverin	protein-coding
mm_16284.1	chr2	174077046	174077059	+	1	NA	promoter-TSS (NM_001102425)	promoter-TSS (NM_001102425)	1	NM_001102423	228960	Mm.277977	NM_172675	ENSMUSG00000027522	Stx16	4930401D03|5430410K23Rik|6330500A18Rik|AI648908|AW553605|Syn16	syntaxin 16	protein-coding
mm_115481.1	chr13	3537665	3537667	-	1	NA	promoter-TSS (NM_008112)	promoter-TSS (NM_008112)	-409	NM_008112	14569	Mm.153226	NM_008112	ENSMUSG00000021218	Gdi2	GDI-B|GDIB|Gdi3	guanosine diphosphate (GDP) dissociation inhibitor 2	protein-coding
mm_57017.1	chr6	121272701	121272727	-	1	NA	Intergenic	Intergenic	26808	NM_011909	24110	Mm.326911	NM_011909	ENSMUSG00000030107	Usp18	1110058H21Rik|AW047653|UBP43|Ubp15	ubiquitin specific peptidase 18	protein-coding
mm_132091.1	chr16	31141511	31141514	+	1	NA	intron (NM_030138, intron 5 of 22)	intron (NM_030138, intron 5 of 22)	59726	NM_030138	78618	Mm.274646	NM_030138	ENSMUSG00000049076	Acap2	4832442G16|9530039J15Rik|CNT-B2|Centb2|mKIAA0041	ArfGAP with coiled-coil, ankyrin repeat and PH domains 2	protein-coding
mm_37568.1	chr4	126242057	126242077	-	1	NA	exon (NM_144941, exon 2 of 17)	exon (NM_144941, exon 2 of 17)	14252	NM_144941	245877	Mm.266716	NM_144941	ENSMUSG00000028849	Map7d1	AV028413|BC019977|Mtap7d1|Parcc1|Rprc1|mKIAA1187	MAP7 domain containing 1	protein-coding
mm_55593.1	chr6	71609046	71609081	-	1	NA	intron (NM_001038695, intron 11 of 26)	intron (NM_001038695, intron 11 of 26)	23623	NM_173001	104263	Mm.260479	NM_173001	ENSMUSG00000053470	Kdm3a	1700105C21Rik|C230043E16Rik|JHDM2a|Jmjd1|Jmjd1a|KDM2A|TGSA|Tsga	lysine (K)-specific demethylase 3A	protein-coding
mm_3731.1	chr1	155098194	155098231	+	1	NA	3' UTR (NM_010500, exon 1 of 1)	3' UTR (NM_010500, exon 1 of 1)	1424	NM_010500	15939	Mm.12246	NM_010500	ENSMUSG00000056708	Ier5	-	immediate early response 5	protein-coding
mm_7577.1	chr1	124846085	124846091	-	1	NA	Intergenic	Intergenic	589639	NM_023735	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding
mm_108506.1	chr12	83987654	83987676	+	1	NA	promoter-TSS (NM_134188)	promoter-TSS (NM_134188)	-196	NM_134188	171210	Mm.371675	NM_134188	ENSMUSG00000021226	Acot2	AA571646|MTE-I|Mte1	acyl-CoA thioesterase 2	protein-coding
mm_48666.1	chr5	145981322	145981331	-	1	NA	intron (NR_030782, intron 11 of 11)	intron (NR_030782, intron 11 of 11)	28291	NM_019792	56388	Mm.301900	NM_019792	ENSMUSG00000029630	Cyp3a25	AI327008	cytochrome P450, family 3, subfamily a, polypeptide 25	protein-coding
mm_766.1	chr1	44118952	44119009	+	1	NA	promoter-TSS (NM_144558)	promoter-TSS (NM_144558)	-207	NM_023645	72050	Mm.281714	NM_023645	ENSMUSG00000026047	Kdelc1	1810049A15Rik|5730416C13Rik|EP58|Kdel1	KDEL (Lys-Asp-Glu-Leu) containing 1	protein-coding
mm_7948.1	chr1	133915169	133915198	-	1	NA	exon (NM_054077, exon 2 of 3)	exon (NM_054077, exon 2 of 3)	6218	NM_054077	116847	Mm.214514	NM_054077	ENSMUSG00000041577	Prelp	7330409J17Rik|SLRR2A	proline arginine-rich end leucine-rich repeat	protein-coding
mm_97615.1	chr11	78952852	78952866	+	1	NA	exon (NM_010927, exon 22 of 27)	exon (NM_010927, exon 22 of 27)	27568	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_169514.1	chr1	4857821	4857822	+	1	NA	promoter-TSS (NM_001159751)	promoter-TSS (NM_001159751)	127	NM_011541	21399	Mm.207263	NM_011541	ENSMUSG00000033813	Tcea1	S-II	transcription elongation factor A (SII) 1	protein-coding
mm_10960.1	chr2	25682785	25682794	+	1	NA	promoter-TSS (NM_178036)	promoter-TSS (NM_178036)	63	NM_178036	332578	Mm.246797	NM_178036	ENSMUSG00000047356	Lcn10	9230112J07Rik	lipocalin 10	protein-coding
mm_117657.1	chr13	93192240	93192263	-	1	NA	promoter-TSS (NM_133905)	promoter-TSS (NM_133905)	32	NM_133905	100715	Mm.242865	NM_133905	ENSMUSG00000042167	Papd4	8030446C20Rik|AI649009|GLD-2|Gld2	PAP associated domain containing 4	protein-coding
mm_142409.1	chr17	45488584	45488588	-	1	NA	Intergenic	Intergenic	-13648	NM_027649	71020	Mm.44257	NM_027649	ENSMUSG00000023935	Spats1	1700011H05Rik|4933400B06Rik|Daip2|Ddip|Srsp1	spermatogenesis associated, serine-rich 1	protein-coding
mm_52195.1	chr6	100451027	100451042	+	1	NA	Intergenic	Intergenic	-76366	NR_040525	73395	Mm.69413	NR_040525	ENSMUSG00000101553	1700049E22Rik	-	RIKEN cDNA 1700049E22 gene	ncRNA
mm_33457.1	chr4	130792135	130792148	+	1	NA	promoter-TSS (NM_011520)	promoter-TSS (NM_011520)	-396	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_40489.1	chr5	57716166	57716173	+	1	NA	intron (NR_015588, intron 1 of 4)	CpG	1750	NR_015588	319216	Mm.332387	NR_015588	ENSMUSG00000097216	4932441J04Rik	-	RIKEN cDNA 4932441J04 gene	ncRNA
mm_92123.1	chr10	63429436	63429437	-	1	NA	promoter-TSS (NM_177612)	promoter-TSS (NM_177612)	-662	NM_177612	216033	Mm.444692	NM_177612	ENSMUSG00000060843	Ctnna3	4930429L08Rik|4933408A16|Catna3|Vr22	catenin (cadherin associated protein), alpha 3	protein-coding
mm_159579.1	chr4	118709243	118709243	+	1	NA	promoter-TSS (NM_146853)	promoter-TSS (NM_146853)	-166	NM_146853	258852	Mm.377720	NM_146853	ENSMUSG00000046790	Olfr1341	MOR258-1	olfactory receptor 1341	protein-coding
mm_171695.1	chr4	67840980	67840980	+	1	NA	Intergenic	L1Md_T|LINE|L1	1013429	NM_021297	21898	Mm.38049	NM_021297	ENSMUSG00000039005	Tlr4	Lps|Ly87|Ran/M1|Rasl2-8	toll-like receptor 4	protein-coding
mm_49156.1	chr6	13069751	13069755	+	1	NA	promoter-TSS (NM_027992)	promoter-TSS (NM_027992)	-6	NM_027992	71900	Mm.27742	NM_027992	ENSMUSG00000029571	Tmem106b	2310036D22Rik|5830455K21Rik|6430519M21Rik|AI428776|AI661344	transmembrane protein 106B	protein-coding
mm_94128.1	chr10	128673897	128673925	-	1	NA	promoter-TSS (NM_173733)	promoter-TSS (NM_173733)	7	NM_173733	211389	Mm.23352	NM_173733	ENSMUSG00000049858	Suox	SO	sulfite oxidase	protein-coding
mm_20356.1	chr2	128127401	128127412	-	1	NA	promoter-TSS (NM_001284410)	promoter-TSS (NM_001284410)	-169	NM_001284410	12125	Mm.141083	NM_009754	ENSMUSG00000027381	Bcl2l11	1500006F24Rik|Bim|Bod|bcl2-L-11	BCL2-like 11 (apoptosis facilitator)	protein-coding
mm_50044.1	chr6	41151199	41151203	+	1	NA	Intergenic	Intergenic	-115692	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_50674.1	chr6	51544651	51544661	+	1	NA	5' UTR (NM_028035, exon 1 of 7)	5' UTR (NM_028035, exon 1 of 7)	133	NM_001127348	71982	Mm.294166	NM_028035	ENSMUSG00000038301	Snx10	2410004M09Rik	sorting nexin 10	protein-coding
mm_79056.1	chr9	46230042	46230064	+	1	NA	exon (NM_009692, exon 4 of 4)	exon (NM_009692, exon 4 of 4)	1423	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2|apo-AI|apoA-I	apolipoprotein A-I	protein-coding
mm_160895.1	chr11	73063701	73063701	+	1	NA	intron (NM_025818, intron 3 of 12)	IAPLTR2a2_Mm|LTR|ERVK	15834	NM_025818	66874	Mm.41903	NM_025818	ENSMUSG00000020783	Ncbp3	1200014J11Rik|C130061O14Rik|C78393	nuclear cap binding subunit 3	protein-coding
mm_68024.1	chr7	100974645	100974669	-	1	NA	Intergenic	CpG	-10291	NM_183168	233571	Mm.235193	NM_183168	ENSMUSG00000048779	P2ry6	2010204J23Rik|P2Y6	pyrimidinergic receptor P2Y, G-protein coupled, 6	protein-coding
mm_83410.1	chr9	44802884	44802926	-	1	NA	promoter-TSS (NM_138951)	promoter-TSS (NM_138951)	46	NM_138951	192653	Mm.325487	NM_138951	ENSMUSG00000039438	Ttc36	-	tetratricopeptide repeat domain 36	protein-coding
mm_5112.1	chr1	6214575	6214605	-	1	NA	promoter-TSS (NM_009826)	promoter-TSS (NM_009826)	-72	NM_009826	12421	Mm.293811	NM_009826	ENSMUSG00000025907	Rb1cc1	2900055E04Rik|5930404L04Rik|Cc1|FIP200|LaXp180	RB1-inducible coiled-coil 1	protein-coding
mm_113117.1	chr13	24501540	24501576	+	1	NA	Intergenic	Intergenic	-80631	NM_001286100	193385	Mm.217319	NM_029679	ENSMUSG00000036006	Fam65b	-	family with sequence similarity 65, member B	protein-coding
mm_108215.1	chr12	77055137	77055160	+	1	NA	Intergenic	MLT1A1|LTR|ERVL-MaLR	-92900	NM_001146176	17187	Mm.268548	NM_008558	ENSMUSG00000059436	Max	AA960152|AI875693|bHLHd4|bHLHd5|bHLHd6|bHLHd7|bHLHd8	Max protein	protein-coding
mm_73942.1	chr8	120101551	120101592	+	1	NA	promoter-TSS (NM_133967)	promoter-TSS (NM_133967)	-99	NM_133967	102193	Mm.240076	NM_133967	ENSMUSG00000031823	Zdhhc7	AL024087|Gramp2	zinc finger, DHHC domain containing 7	protein-coding
mm_130540.1	chr15	98953476	98953519	-	1	NA	promoter-TSS (NM_011653)	promoter-TSS (NM_011653)	4	NM_011653	22142	Mm.405359	NM_011653	ENSMUSG00000072235	Tuba1a	Tuba-1|Tuba1	tubulin, alpha 1A	protein-coding
mm_38089.1	chr4	134187020	134187090	-	1	NA	promoter-TSS (NM_144527)	promoter-TSS (NM_144527)	30	NM_144527	70012	Mm.26542	NM_144527	ENSMUSG00000037443	Cep85	2410030J07Rik|AI173272|AI173504|Ccdc21	centrosomal protein 85	protein-coding
mm_75490.1	chr8	49430629	49430632	-	1	NA	Intergenic	RMER6D|LTR|ERVK	-755940	NM_011857	23965	Mm.42191	NM_011857	ENSMUSG00000031561	Tenm3	2610100B16Rik|Odz1|Odz3|Ten-m3|mKIAA1455	teneurin transmembrane protein 3	protein-coding
mm_169602.1	chr15	3583143	3583143	-	1	NA	5' UTR (NM_010284, exon 1 of 11)	5' UTR (NM_010284, exon 1 of 11)	209	NM_001048178	14600	Mm.3986	NM_010284	ENSMUSG00000055737	Ghr	GHBP|GHR/BP	growth hormone receptor	protein-coding
mm_160122.1	chr7	27689434	27689434	+	1	NA	promoter-TSS (NM_001112731)	promoter-TSS (NM_001112731)	94	NM_001112731	112415	Mm.145362	NM_198417	ENSMUSG00000057093	Zfp607b	C030039L03Rik	zinc finger protein 607B	protein-coding
mm_104665.1	chr11	97629686	97629715	-	1	NA	promoter-TSS (NM_175332)	promoter-TSS (NM_175332)	16	NM_175332	103551	Mm.24506	NM_175332	ENSMUSG00000043439	Epop	AA409164|AI413509|AW539173|E13|E130012A19Rik|esPRC2p48	elongin BC and polycomb repressive complex 2 associated protein	protein-coding
mm_131116.1	chr16	5375098	5375106	+	1	NA	Intergenic	Intergenic	-119146	NM_027446	70511	Mm.45780	NM_027446	ENSMUSG00000022544	Eef2kmt	5730409G15Rik|Fam86|Fam86a|eEF2-KMT	eukaryotic elongation factor 2 lysine methyltransferase	protein-coding
mm_69115.1	chr7	127025844	127025852	-	1	NA	exon (NM_010772, exon 2 of 5)	exon (NM_010772, exon 2 of 5)	631	NM_010772	17188	Mm.378964	NM_010772	ENSMUSG00000030678	Maz	MAZI|PUR1|Pur-1|SAF-1|SAF-2	MYC-associated zinc finger protein (purine-binding transcription factor)	protein-coding
mm_142264.1	chr17	39845744	39845755	-	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	2752	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_103968.1	chr11	84513392	84513402	-	1	NA	5' UTR (NM_019816, exon 1 of 13)	5' UTR (NM_019816, exon 1 of 13)	104	NM_019816	56321	Mm.257482	NM_019816	ENSMUSG00000018697	Aatf	4933415H02Rik|5830465M17Rik|Che-1|Trb	apoptosis antagonizing transcription factor	protein-coding
mm_72740.1	chr8	85085467	85085519	+	1	NA	exon (NM_010764, exon 4 of 24)	exon (NM_010764, exon 4 of 24)	2224	NM_010764	17159	Mm.4219	NM_010764	ENSMUSG00000005142	Man2b1	AW107687|LAMAN	mannosidase 2, alpha B1	protein-coding
mm_480.1	chr1	36714525	36714576	+	1	NA	promoter-TSS (NR_040290)	promoter-TSS (NR_040290)	12	NR_040290	71166	Mm.157049	NR_040290	ENSMUSG00000102416	4933424G06Rik	1700104I15Rik	RIKEN cDNA 4933424G06 gene	ncRNA
mm_65416.1	chr7	25245708	25245710	-	1	NA	exon (NM_010155, exon 3 of 4)	exon (NM_010155, exon 3 of 4)	5049	NM_010155	13875	Mm.8068	NM_010155	ENSMUSG00000040857	Erf	-	Ets2 repressor factor	protein-coding
mm_27245.1	chr3	36613340	36613367	-	1	NA	promoter-TSS (NM_027810)	promoter-TSS (NM_027810)	36	NM_027810	71492	Mm.286187	NM_027810	ENSMUSG00000037325	Bbs7	8430406N16Rik	Bardet-Biedl syndrome 7 (human)	protein-coding
mm_92353.1	chr10	75909930	75909934	-	1	NA	intron (NM_011418, intron 5 of 8)	MLT1A1|LTR|ERVL-MaLR	11682	NM_011418	20587	Mm.279751	NM_011418	ENSMUSG00000000902	Smarcb1	AU020204|Baf47|Ini1|SNF5/INI1|Snf5	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1	protein-coding
mm_123565.1	chr14	66869191	66869221	-	1	NA	promoter-TSS (NM_009955)	promoter-TSS (NM_009955)	356	NM_001034881	432870	Mm.425890	NM_001034881	ENSMUSG00000075553	Gm5464	EG432870	predicted gene 5464	protein-coding
mm_25238.1	chr3	103908036	103908083	+	1	NA	intron (NR_104070, intron 21 of 22)	intron (NR_104070, intron 21 of 22)	-6061	NM_172684	229675	Mm.29366	NM_172684	ENSMUSG00000044098	Rsbn1	C230004D03Rik|E330004N01|Rosbin|Rsbn|Rsbp|mKIAA3002	rosbin, round spermatid basic protein 1	protein-coding
mm_116946.1	chr13	56135428	56135438	-	1	NA	5' UTR (NM_001159515, exon 1 of 9)	5' UTR (NM_001159515, exon 1 of 9)	117	NM_012015	26914	Mm.283802	NM_012015	ENSMUSG00000015937	H2afy	H2AF12M|mH2a1|macroH2A1	H2A histone family, member Y	protein-coding
mm_136361.1	chr16	92776873	92776885	-	1	NA	intron (NM_001111022, intron 2 of 6)	intron (NM_001111022, intron 2 of 6)	49195	NM_001111021	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_137155.1	chr17	23726429	23726474	+	1	NA	5' UTR (NM_023058, exon 1 of 8)	5' UTR (NM_023058, exon 1 of 8)	115	NM_023058	268930	Mm.182193	NM_023058	ENSMUSG00000023908	Pkmyt1	6230424P17|AW209059|Myt1	protein kinase, membrane associated tyrosine/threonine 1	protein-coding
mm_98127.1	chr11	87331641	87331647	+	1	NA	intron (NR_106195, intron 6 of 8)	L1M4|LINE|L1	27350	NM_177167	320472	Mm.341988	NM_177167	ENSMUSG00000046442	Ppm1e	AW049266|B930008A12Rik|POPX1|PP2CH|mKIAA1072	protein phosphatase 1E (PP2C domain containing)	protein-coding
mm_147351.1	chr18	43345145	43345156	-	1	NA	exon (NM_001291455, exon 7 of 14)	exon (NM_001291455, exon 7 of 14)	28122	NM_001136086	22240	Mm.8180	NM_009468	ENSMUSG00000024501	Dpysl3	CRMP-4|DRP-3|TUC4|ULIP-1|Ulip|Ulip1	dihydropyrimidinase-like 3	protein-coding
mm_36217.1	chr4	62514179	62514220	-	1	NA	5' UTR (NM_001276446, exon 2 of 12)	5' UTR (NM_001276446, exon 2 of 12)	5710	NM_001276446	17025	Mm.6988	NM_008525	ENSMUSG00000028393	Alad	ALADH|Lv	aminolevulinate, delta-, dehydratase	protein-coding
mm_46951.1	chr5	114950823	114950853	-	1	NA	exon (NM_009327, exon 9 of 10)	exon (NM_009327, exon 9 of 10)	8636	NM_028211	72357	Mm.292672	NM_028211	ENSMUSG00000029559	2210016L21Rik	-	RIKEN cDNA 2210016L21 gene	protein-coding
mm_56356.1	chr6	93769634	93769637	-	1	NA	intron (NM_001083321, intron 5 of 21)	intron (NM_001083321, intron 5 of 21)	143328	NR_104594	14924	Mm.217216	NM_010367	ENSMUSG00000045095	Magi1	AIP3|BAP1|Baiap1|Gukmi1|MAGI1c|Magi-1|TNRC19|WWP3|mKIAA4129	membrane associated guanylate kinase, WW and PDZ domain containing 1	protein-coding
mm_29859.1	chr3	130060674	130060733	-	1	NA	5' UTR (NM_207209, exon 1 of 24)	5' UTR (NM_207209, exon 1 of 24)	204	NM_207209	99683	Mm.192303	NM_207209	ENSMUSG00000001052	Sec24b	AI605202|SEC24	Sec24 related gene family, member B (S. cerevisiae)	protein-coding
mm_13383.1	chr2	103957927	103957937	+	1	NA	promoter-TSS (NM_001142337)	promoter-TSS (NM_001142337)	-63	NM_001142337	16909	Mm.29266	NM_008505	ENSMUSG00000032698	Lmo2	Rbtn-2|Rbtn2|Rhom-2|Ttg2	LIM domain only 2	protein-coding
mm_24473.1	chr3	90669930	90669940	+	1	NA	TTS (NM_013650)	TTS (NM_013650)	864	NM_013650	20201	Mm.21567	NM_013650	ENSMUSG00000056054	S100a8	60B8Ag|AI323541|B8Ag|CFAg|CP-10|Caga|MRP8|p8	S100 calcium binding protein A8 (calgranulin A)	protein-coding
mm_157065.1	chrX	8175891	8175956	-	1	NA	exon (NM_172478, exon 1 of 6)	exon (NM_172478, exon 1 of 6)	258	NM_001166437	209815	Mm.122963	NM_172478	ENSMUSG00000039201	Tbc1d25	6330576A08Rik|DXHXS7927e|Oatl1	TBC1 domain family, member 25	protein-coding
mm_63113.1	chr7	122671209	122671218	+	1	NA	promoter-TSS (NM_019430)	promoter-TSS (NM_019430)	-531	NM_019430	54376	Mm.444212	NM_019430	ENSMUSG00000066189	Cacng3	-	calcium channel, voltage-dependent, gamma subunit 3	protein-coding
mm_99322.1	chr11	101442523	101442531	+	1	NA	intron (NM_011289, intron 1 of 4)	CpG	282	NM_011289	19942	Mm.340658	NM_011289	ENSMUSG00000063316	Rpl27	-	ribosomal protein L27	protein-coding
mm_46811.1	chr5	113080567	113080578	-	1	NA	5' UTR (NM_021352, exon 2 of 6)	5' UTR (NM_021352, exon 2 of 6)	1012	NM_001159650	12962	Mm.378899	NM_021352	ENSMUSG00000029352	Crybb3	AI852419	crystallin, beta B3	protein-coding
mm_141291.1	chr17	28068474	28068501	-	1	NA	intron (NM_001085555, intron 8 of 9)	intron (NM_001085555, intron 8 of 9)	12097	NM_013687	21463	Mm.29758	NM_013687	ENSMUSG00000062859	Tcp11	D17Ken1|Tcp-11	t-complex protein 11	protein-coding
mm_59559.1	chr7	28085192	28085212	+	1	NA	exon (NM_001122603, exon 4 of 20)	exon (NM_001122603, exon 4 of 20)	13966	NM_001122603	215384	Mm.292276	NM_175444	ENSMUSG00000047730	Fcgbp	A430096B05Rik	Fc fragment of IgG binding protein	protein-coding
mm_97565.1	chr11	78936430	78936464	+	1	NA	exon (NM_010927, exon 7 of 27)	exon (NM_010927, exon 7 of 27)	11156	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_85662.1	chr9	107675190	107675196	-	1	NA	3' UTR (NM_008140, exon 9 of 9)	3' UTR (NM_008140, exon 9 of 9)	4399	NM_008140	14685	Mm.284853	NM_008140	ENSMUSG00000034837	Gnat1	Gnat-1|Ird1|Ird2|Tralpha|irdc|irdr|transducin	guanine nucleotide binding protein, alpha transducing 1	protein-coding
mm_39243.1	chr5	3341523	3341547	+	1	NA	Intergenic	CpG	-2358	NM_009873	12571	Mm.31672	NM_009873	ENSMUSG00000040274	Cdk6	AI504062|Crk2	cyclin-dependent kinase 6	protein-coding
mm_148213.1	chr18	80200598	80200669	-	1	NA	promoter-TSS (NM_199197)	promoter-TSS (NM_199197)	-14	NM_199197	68731	Mm.186936	NM_199197	ENSMUSG00000024570	Rbfa	1110032A13Rik|AI595940	ribosome binding factor A	protein-coding
mm_71123.1	chr8	36249624	36249636	+	1	NA	promoter-TSS (NM_001081150)	promoter-TSS (NM_001081150)	-114	NM_001081150	244421	Mm.324032	NM_001081150	ENSMUSG00000039633	Lonrf1	-	LON peptidase N-terminal domain and ring finger 1	protein-coding
mm_172518.1	chr7	80803321	80803326	-	1	NA	promoter-TSS (NM_016721)	promoter-TSS (NM_016721)	8	NM_016721	29875	Mm.207619	NM_016721	ENSMUSG00000030536	Iqgap1	AA682088|D7Ertd237e|D7Ertd257e|mKIAA0051	IQ motif containing GTPase activating protein 1	protein-coding
mm_32491.1	chr4	108165433	108165441	+	1	NA	promoter-TSS (NM_026728)	promoter-TSS (NM_026728)	0	NM_026728	52430	Mm.270783	NM_026728	ENSMUSG00000028601	Echdc2	1300017C12Rik|2610009M20Rik|D4Ertd765e	enoyl Coenzyme A hydratase domain containing 2	protein-coding
mm_2314.1	chr1	91801492	91801508	+	1	NA	promoter-TSS (NM_007855)	promoter-TSS (NM_007855)	39	NM_007855	13345	Mm.9474	NM_007855	ENSMUSG00000007805	Twist2	Dermo1|bHLHa39	twist basic helix-loop-helix transcription factor 2	protein-coding
mm_55755.1	chr6	78378883	78378891	-	1	NA	promoter-TSS (NM_001161741)	promoter-TSS (NM_001161741)	-22	NM_013893	30053	Mm.33691	NM_013893	ENSMUSG00000068341	Reg3d	INGAP|Ingaprp	regenerating islet-derived 3 delta	protein-coding
mm_97064.1	chr11	72796258	72796268	+	1	NA	promoter-TSS (NM_001045536)	promoter-TSS (NM_001045536)	37	NM_001045536	195018	Mm.272030	NM_001045536	ENSMUSG00000055670	Zzef1	8430405D05Rik|BC051585|C130099L13Rik|C85424|NSPA|mKIAA0399	zinc finger, ZZ-type with EF hand domain 1	protein-coding
mm_107011.1	chr12	11882467	11882487	+	1	NA	non-coding (NR_003964, exon 1 of 1)	non-coding (NR_003964, exon 1 of 1)	422	NR_003964	627110	Mm.194735	NR_003964		Tubb2a-ps2	C79445	tubulin, beta 2a, pseudogene 2	pseudo
mm_34995.1	chr4	156064340	156064351	+	1	NA	Intergenic	Intergenic	-4543	NR_132444	100415901	Mm.437006	NR_132444	ENSMUSG00000086549	Gm13648	OTTMUSG00000013217	predicted gene 13648	ncRNA
mm_58588.1	chr7	5013373	5013388	+	1	NA	promoter-TSS (NM_001110330)	promoter-TSS (NM_001110330)	-138	NM_001110330	23877	Mm.38911	NM_011813	ENSMUSG00000061374	Fiz1	AI790204|mFLJ00416	Flt3 interacting zinc finger protein 1	protein-coding
mm_31256.1	chr4	45013532	45013536	+	1	NA	Intergenic	BGLII_B|LTR|ERVK	-1122	NM_173399	230119	Mm.44222	NM_173399	ENSMUSG00000049657	Zbtb5	5930421I10|9430083K24Rik|AI646847|mKIAA0354	zinc finger and BTB domain containing 5	protein-coding
mm_121476.1	chr14	121035464	121035479	+	1	NA	promoter-TSS (NM_134082)	promoter-TSS (NM_134082)	-103	NM_134082	223254	Mm.223980	NM_134082	ENSMUSG00000025555	Farp1	AW228844|BC030329|Cdep	FERM, RhoGEF (Arhgef) and pleckstrin domain protein 1 (chondrocyte-derived)	protein-coding
mm_62297.1	chr7	100006067	100006085	+	1	NA	promoter-TSS (NM_133709)	promoter-TSS (NM_133709)	-328	NM_133709	69121	Mm.285295	NM_133709	ENSMUSG00000030732	Chrdl2	1810022C01Rik|Chl2	chordin-like 2	protein-coding
mm_102026.1	chr11	51650859	51650877	-	1	NA	promoter-TSS (NR_027958)	promoter-TSS (NR_027958)	-86	NR_027958	97775	Mm.220299	NM_175289	ENSMUSG00000052563	D930048N14Rik	AI315703|R75254	RIKEN cDNA D930048N14 gene	ncRNA
mm_131802.1	chr16	22899309	22899323	+	1	NA	non-coding (NR_075099, exon 6 of 6)	non-coding (NR_075099, exon 6 of 6)	-4930	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_1351.1	chr1	66321796	66321806	+	1	NA	promoter-TSS (NM_001310634)	promoter-TSS (NM_001310634)	77	NM_001310634	17756	Mm.256966	NM_008632	ENSMUSG00000015222	Map2	G1-397-34|MAP-2|Mtap-2|Mtap2|repro4	microtubule-associated protein 2	protein-coding
mm_93916.1	chr10	127067633	127067660	-	1	NA	TTS (NM_009870)	TTS (NM_009870)	2615	NM_025982	67125	Mm.35650	NM_025982	ENSMUSG00000006736	Tspan31	2700085A14Rik|AW742554|Sas	tetraspanin 31	protein-coding
mm_43819.1	chr5	142960349	142960363	+	1	NA	promoter-TSS (NM_007984)	promoter-TSS (NM_007984)	1	NM_007984	14086	Mm.289707	NM_007984	ENSMUSG00000029581	Fscn1	AI663989|Fan1|fascin-1	fascin actin-bundling protein 1	protein-coding
mm_114589.1	chr13	75754613	75754652	+	1	NA	intron (NM_138953, intron 4 of 11)	intron (NM_138953, intron 4 of 11)	47148	NM_138953	192657	Mm.21288	NM_138953	ENSMUSG00000001542	Ell2	-	elongation factor RNA polymerase II 2	protein-coding
mm_60580.1	chr7	44482627	44482633	+	1	NA	Intergenic	Intergenic	-1887	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_111091.1	chr12	80436572	80436603	-	1	NA	promoter-TSS (NM_177267)	promoter-TSS (NM_177267)	14	NM_177267	320808	Mm.220310	NM_177267	ENSMUSG00000049106	Dcaf5	9430020B07Rik|AI325023|AI430035|AI848110|AW124614|BCRG2|BCRP2|Wdr22	DDB1 and CUL4 associated factor 5	protein-coding
mm_167809.1	chr9	123929160	123929182	+	1	NA	Intergenic	Intergenic	39521	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_133815.1	chr16	95709191	95709193	+	1	NA	intron (NM_011809, intron 2 of 9)	intron (NM_011809, intron 2 of 9)	6785	NM_011809	23872	Mm.290207	NM_011809	ENSMUSG00000022895	Ets2	AU022856|Ets-2	E26 avian leukemia oncogene 2, 3' domain	protein-coding
mm_164907.1	chr18	70390789	70390793	+	1	NA	Intergenic	Intergenic	-81663	NM_029019	170461	Mm.83623	NM_029019	ENSMUSG00000079608	Stard6	1700011K09Rik|4833424I06Rik|4933429L05Rik|AI644424	StAR-related lipid transfer (START) domain containing 6	protein-coding
mm_135427.1	chr16	45382623	45382633	-	1	NA	3' UTR (NM_010818, exon 6 of 6)	3' UTR (NM_010818, exon 6 of 6)	26425	NM_010818	17470	Mm.245851	NM_010818	ENSMUSG00000022661	Cd200	Mox2|OX2	CD200 antigen	protein-coding
mm_153333.1	chr19	38125246	38125254	-	1	NA	promoter-TSS (NM_011255)	promoter-TSS (NM_011255)	71	NM_001159487	19662	Mm.2605	NM_011255	ENSMUSG00000024990	Rbp4	Rbp-4	retinol binding protein 4, plasma	protein-coding
mm_131300.1	chr16	11406778	11406789	+	1	NA	intron (NM_001290148, intron 1 of 13)	intron (NM_001290148, intron 1 of 13)	1135	NM_001290148	74478	Mm.325831	NM_028964	ENSMUSG00000071669	Snx29	4933437K13Rik|ENSMUSG00000079738|Gm11170|Gm1737|Gm930|Rundc2a	sorting nexin 29	protein-coding
mm_150805.1	chr19	44333423	44333427	+	1	NA	promoter-TSS (NM_183216)	promoter-TSS (NM_183216)	99	NM_183216	329065	Mm.313583	NM_183216	ENSMUSG00000050195	Scd4	ACOD4	stearoyl-coenzyme A desaturase 4	protein-coding
mm_832.1	chr1	51476656	51476687	+	1	NA	intron (NM_001310548, intron 2 of 5)	intron (NM_001310548, intron 2 of 5)	1728	NM_028696	109019	Mm.196290	NM_028696	ENSMUSG00000026107	Nabp1	4930434H03Rik|4930442A21Rik|4930488J04Rik|4933440J18Rik|5830411E10Rik|AI852561|Nbp1|Obfc2a|Ssb2	nucleic acid binding protein 1	protein-coding
mm_172828.1	chr9	19093720	19093724	+	1	NA	Intergenic	RLTR9D|LTR|ERVK	-27235	NM_146564	258557	Mm.377566	NM_146564	ENSMUSG00000059303	Olfr836	MOR152-3	olfactory receptor 836	protein-coding
mm_99244.1	chr11	101079190	101079201	+	1	NA	exon (NM_010475, exon 4 of 6)	exon (NM_010475, exon 4 of 6)	784	NM_010475	15485	Mm.188939	NM_010475	ENSMUSG00000019301	Hsd17b1	17HSDB1|17beta-HSD|E2DH|Hsd17ba	hydroxysteroid (17-beta) dehydrogenase 1	protein-coding
mm_24841.1	chr3	95661760	95661816	+	1	NA	3' UTR (NM_008562, exon 3 of 3)	3' UTR (NM_008562, exon 3 of 3)	3067	NM_008562	17210	Mm.1639	NM_008562	ENSMUSG00000038612	Mcl1	AW556805|Mcl-1	myeloid cell leukemia sequence 1	protein-coding
mm_157858.1	chrX	75110602	75110638	-	1	NA	TTS (NM_001030307)	TTS (NM_001030307)	14766	NM_001030307	245474	Mm.291062	NM_001030307	ENSMUSG00000031403	Dkc1	BC068171	dyskeratosis congenita 1, dyskerin	protein-coding
mm_4728.1	chr1	181352619	181352641	+	1	NA	promoter-TSS (NM_001160212)	promoter-TSS (NM_001160212)	2	NM_001160211	72978	Mm.338083	NM_028408	ENSMUSG00000026514	Cnih3	2900075G08Rik|CNIH-3	cornichon family AMPA receptor auxiliary protein 3	protein-coding
mm_150596.1	chr19	40705914	40705926	+	1	NA	intron (NM_009848, intron 1 of 9)	RSINE1|SINE|B4	46150	NM_009848	12495	Mm.2824	NM_009848	ENSMUSG00000048120	Entpd1	2610206B08Rik|AA408691|Cd39|NTPDase-1	ectonucleoside triphosphate diphosphohydrolase 1	protein-coding
mm_30931.1	chr4	32983009	32983039	+	1	NA	promoter-TSS (NM_027491)	promoter-TSS (NM_027491)	26	NM_027491	52187	Mm.300814	NM_027491	ENSMUSG00000028278	Rragd	5730543C08Rik|AI467523|C030003H22Rik|D4Ertd174e	Ras-related GTP binding D	protein-coding
mm_66481.1	chr7	45016225	45016296	-	1	NA	promoter-TSS (NM_001008422)	promoter-TSS (NM_001008422)	-11	NM_001008422	233208	Mm.28298	NM_001008422	ENSMUSG00000038406	Scaf1	AI480556|SR-A1	SR-related CTD-associated factor 1	protein-coding
mm_164085.1	chr15	5446496	5446504	-	1	NA	Intergenic	Intergenic	-49818	NR_045274	71432	Mm.291087	NR_045274		5430437J10Rik	-	RIKEN cDNA 5430437J10 gene	ncRNA
mm_134594.1	chr16	20548433	20548460	-	1	NA	promoter-TSS (NM_013852)	promoter-TSS (NM_013852)	110	NR_030670	100042948	Mm.406754	NR_030670		Gm15760	ENSMUSG00000075326|OTTMUSG00000026040	mitochondrial ribosomal protein S18B pseudogene	pseudo
mm_144616.1	chr18	32837246	32837266	+	1	NA	promoter-TSS (NM_001110015)	promoter-TSS (NM_001110015)	31	NM_001110016	225348	Mm.38816	NM_144863	ENSMUSG00000038299	Wdr36	5730444A13Rik|Ta-wdrp	WD repeat domain 36	protein-coding
mm_150598.1	chr19	40736803	40736825	+	1	NA	exon (NM_009848, exon 9 of 10)	exon (NM_009848, exon 9 of 10)	77044	NM_009848	12495	Mm.2824	NM_009848	ENSMUSG00000048120	Entpd1	2610206B08Rik|AA408691|Cd39|NTPDase-1	ectonucleoside triphosphate diphosphohydrolase 1	protein-coding
mm_31463.1	chr4	49059467	49059550	+	1	NA	promoter-TSS (NM_178756)	promoter-TSS (NM_178756)	46	NM_178756	272031	Mm.299460	NM_178756	ENSMUSG00000063446	Plppr1	E130309F12Rik|Lppr1|PRG-3|mKIAA4247	phospholipid phosphatase related 1	protein-coding
mm_107622.1	chr12	51378287	51378294	+	1	NA	intron (NM_029825, intron 1 of 24)	intron (NM_029825, intron 1 of 24)	777	NM_029825	76983	Mm.216511	NM_029825	ENSMUSG00000020952	Scfd1	3110021P21Rik|RA410|STXBP1L2	Sec1 family domain containing 1	protein-coding
mm_166228.1	chr5	65934713	65934717	+	1	NA	Intergenic	Intergenic	-32409	NM_001081104	231252	Mm.140015	NM_001081104	ENSMUSG00000029205	Chrna9	2410015I05Rik|Acra9|EG666827|Gm8311	cholinergic receptor, nicotinic, alpha polypeptide 9	protein-coding
mm_22837.1	chr3	27557397	27557410	+	1	NA	intron (NM_173182, intron 3 of 25)	intron (NM_173182, intron 3 of 25)	27592	NR_037275	100526525		NR_037275	ENSMUSG00000092695	Mir3092	mir-3092|mmu-mir-3092	microRNA 3092	ncRNA
mm_67989.1	chr7	100856313	100856326	-	1	NA	intron (NM_177073, intron 1 of 10)	L2b|LINE|L2	7094	NM_177073	320100	Mm.40336	NM_177073	ENSMUSG00000008318	Relt	E430021K24Rik|Tnfrsf19l	RELT tumor necrosis factor receptor	protein-coding
mm_107768.1	chr12	59130768	59130786	+	1	NA	promoter-TSS (NM_001165253)	promoter-TSS (NM_001165253)	-676	NM_001165253	338320	Mm.213215	NM_146034	ENSMUSG00000021000	Mia2	Ctage5|D12Bwg0579e|Mea6|Mgea|Mgea6	melanoma inhibitory activity 2	protein-coding
mm_67305.1	chr7	79386842	79386867	-	1	NA	5' UTR (NM_020599, exon 1 of 9)	5' UTR (NM_020599, exon 1 of 9)	173	NM_020599	19771	Mm.41653	NM_020599	ENSMUSG00000039194	Rlbp1	3110056M11Rik|CRALBP	retinaldehyde binding protein 1	protein-coding
mm_113360.1	chr13	32956784	32956816	+	1	NA	Intergenic	Intergenic	-8713	NM_011454	20708	Mm.36526	NM_011454	ENSMUSG00000042842	Serpinb6b	NK13|Spi12|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 6b	protein-coding
mm_169685.1	chr15	73701516	73701523	-	1	NA	intron (NM_173365, intron 1 of 1)	(TTCC)n|Simple_repeat|Simple_repeat	5986	NM_173365	239530	Mm.122997	NM_173365	ENSMUSG00000045281	Gpr20	A430106B11Rik	G protein-coupled receptor 20	protein-coding
mm_163111.1	chr11	70459604	70459607	+	1	NA	promoter-TSS (NM_001029929)	promoter-TSS (NM_001029929)	-17	NM_001029929	574428	Mm.472771	NM_001029929	ENSMUSG00000040829	Zmynd15	-	zinc finger, MYND-type containing 15	protein-coding
mm_159182.1	chr2	111873780	111873780	-	1	NA	promoter-TSS (NM_146401)	promoter-TSS (NM_146401)	73	NM_146401	258396	Mm.377480	NM_146401	ENSMUSG00000074955	Olfr1305	MOR245-8	olfactory receptor 1305	protein-coding
mm_144663.1	chr18	34316482	34316520	+	1	NA	exon (NM_007462, exon 16 of 16)	exon (NM_007462, exon 16 of 16)	-14644	NM_025527	66384	Mm.29452	NM_025527	ENSMUSG00000014504	Srp19	2310020D23Rik	signal recognition particle 19	protein-coding
mm_78857.1	chr9	44392202	44392205	+	1	NA	3' UTR (NM_021395, exon 26 of 26)	3' UTR (NM_021395, exon 26 of 26)	-4724	NM_001293631	14385	Mm.30087	NM_008063	ENSMUSG00000032114	Slc37a4	100043178|G6PT|G6pt1|GSD-1b|mG6PT	solute carrier family 37 (glucose-6-phosphate transporter), member 4	protein-coding
mm_92054.1	chr10	62506298	62506309	-	1	NA	intron (NM_011157, intron 1 of 2)	intron (NM_011157, intron 1 of 2)	1452	NM_011157	19073	Mm.338790	NM_011157	ENSMUSG00000020077	Srgn	Prg|Prg1|Sgc	serglycin	protein-coding
mm_97688.1	chr11	80137954	80137983	+	1	NA	exon (NM_183275, exon 3 of 4)	exon (NM_183275, exon 3 of 4)	4185	NM_183275	68550	Mm.18466	NM_183275	ENSMUSG00000046909	Tefm	1110002N22Rik	transcription elongation factor, mitochondrial	protein-coding
mm_91059.1	chr10	18848064	18848070	-	1	NA	intron (NM_022032, intron 1 of 2)	intron (NM_022032, intron 1 of 2)	2996	NM_022032	64058	Mm.28209	NM_022032	ENSMUSG00000019851	Perp	1110017A08Rik|KCP1|KRTCAP1|PIGPC1|THW	PERP, TP53 apoptosis effector	protein-coding
mm_27068.1	chr3	27896361	27896390	-	1	NA	promoter-TSS (NM_001164437)	promoter-TSS (NM_001164437)	-7	NM_001164437	208613	Mm.59189	NM_001164437	ENSMUSG00000043164	Tmem212	E030011K20Rik|Gm564	transmembrane protein 212	protein-coding
mm_31312.1	chr4	46097032	46097036	+	1	NA	exon (NM_021883, exon 8 of 10)	exon (NM_021883, exon 8 of 10)	41441	NM_173033	272027	Mm.331588	NM_173033	ENSMUSG00000035495	Tstd2	3010020C06	thiosulfate sulfurtransferase (rhodanese)-like domain containing 2	protein-coding
mm_45766.1	chr5	86917041	86917044	-	1	NA	3' UTR (NM_152811, exon 6 of 6)	3' UTR (NM_152811, exon 6 of 6)	9461	NM_152811	71773	Mm.26741	NM_152811	ENSMUSG00000035836	Ugt2b1	1300012D20Rik	UDP glucuronosyltransferase 2 family, polypeptide B1	protein-coding
mm_135787.1	chr16	57163720	57163726	-	1	NA	intron (NM_023175, intron 3 of 9)	intron (NM_023175, intron 3 of 9)	3609	NM_023175	52633	Mm.383203	NM_023175	ENSMUSG00000022751	Nit2	1190017B19Rik|D16Ertd502e	nitrilase family, member 2	protein-coding
mm_142997.1	chr17	56412762	56412773	-	1	NA	3' UTR (NM_001252453, exon 29 of 29)	3' UTR (NM_001252453, exon 29 of 29)	6142	NR_105943	102465590		NR_105943	ENSMUSG00000098339	Mir6977	Gm27922|mmu-mir-6977	microRNA 6977	ncRNA
mm_21168.1	chr2	154657973	154657988	-	1	NA	intron (NM_029362, intron 1 of 4)	intron (NM_029362, intron 1 of 4)	954	NM_029362	75608	Mm.262480	NM_029362	ENSMUSG00000038467	Chmp4b	2010012F05Rik|C76846|Snf7-2	charged multivesicular body protein 4B	protein-coding
mm_603.1	chr1	39901077	39901100	+	1	NA	5' UTR (NM_001252202, exon 1 of 30)	5' UTR (NM_001252202, exon 1 of 30)	175	NM_008696	26921	Mm.491139	NM_008696	ENSMUSG00000026074	Map4k4	9430080K19Rik|AU043147|AU045934|AW046177|HGK|Nik	mitogen-activated protein kinase kinase kinase kinase 4	protein-coding
mm_9115.1	chr1	170174901	170174951	-	1	NA	promoter-TSS (NM_133806)	promoter-TSS (NM_133806)	38	NM_001305046	107652	Mm.27969	NM_133806	ENSMUSG00000026670	Uap1	AA420407|AA437972|AGX-1|AGX-2|AGX1|AgX|ESTM38|SPAG2	UDP-N-acetylglucosamine pyrophosphorylase 1	protein-coding
mm_21830.1	chr2	165400368	165400386	-	1	NA	promoter-TSS (NM_029021)	promoter-TSS (NM_029021)	17	NM_029021	74614	Mm.72179	NM_029021	ENSMUSG00000027670	Ocstamp	4833422F24Rik|OC-STAMP	osteoclast stimulatory transmembrane protein	protein-coding
mm_5096.1	chr1	4857565	4857601	-	1	NA	promoter-TSS (NM_011541)	promoter-TSS (NM_011541)	-111	NM_001159750	21399	Mm.207263	NM_011541	ENSMUSG00000033813	Tcea1	S-II	transcription elongation factor A (SII) 1	protein-coding
mm_50458.1	chr6	48907729	48907755	+	1	NA	exon (NM_001161622, exon 3 of 5)	exon (NM_001161622, exon 3 of 5)	2756	NM_001161621	76507	Mm.213898	NM_029638	ENSMUSG00000029811	Aoc1	1600012D06Rik|Abp1|DAO	amine oxidase, copper-containing 1	protein-coding
mm_89359.1	chr10	88379128	88379169	+	1	NA	promoter-TSS (NM_001004164)	promoter-TSS (NM_001004164)	-264	NM_001004164	432486	Mm.335190	NM_001004164	ENSMUSG00000035311	Gnptab	EG432486|mKIAA1208	N-acetylglucosamine-1-phosphate transferase, alpha and beta subunits	protein-coding
mm_69225.1	chr7	127615209	127615219	-	1	NA	promoter-TSS (NM_177226)	promoter-TSS (NM_177226)	-781	NM_177226	320683	Mm.156718	NM_177226	ENSMUSG00000045639	Zfp629	9330199A09Rik|Znf629	zinc finger protein 629	protein-coding
mm_38842.1	chr4	149166687	149166703	-	1	NA	promoter-TSS (NM_001081274)	promoter-TSS (NM_001081274)	12	NM_001081274	110208	Mm.252080	NM_025801	ENSMUSG00000028961	Pgd	0610042A05Rik|AU019875|C78335	phosphogluconate dehydrogenase	protein-coding
mm_2514.1	chr1	106244982	106244987	+	1	NA	intron (NM_133821, intron 1 of 16)	L1VL2|LINE|L1	73115	NM_133821	98432	Mm.24115	NM_133821	ENSMUSG00000044340	Phlpp1	AI836256|Phlpp|Plekhe1|SCOP|mKIAA0606	PH domain and leucine rich repeat protein phosphatase 1	protein-coding
mm_50902.1	chr6	57581541	57581556	+	1	NA	intron (NM_025992, intron 1 of 22)	intron (NM_025992, intron 1 of 22)	556	NM_025992	67138	Mm.297393	NM_025992	ENSMUSG00000029798	Herc6	1700121D12Rik|2510038N07Rik|4930427L17Rik|AI451296|CEB1|Herc5	hect domain and RLD 6	protein-coding
mm_145215.1	chr18	50051703	50051717	+	1	NA	intron (NM_001177759, intron 1 of 1)	intron (NM_001177759, intron 1 of 1)	-1572	NM_134131	106869	Mm.27740	NM_134131	ENSMUSG00000062210	Tnfaip8	AA987150|E130304C20Rik|ENSMUSG00000073567|Gg2-1|Gm10539|Nded|Ssc-2|Tipe	tumor necrosis factor, alpha-induced protein 8	protein-coding
mm_34104.1	chr4	139131117	139131163	+	1	NA	promoter-TSS (NR_033745)	promoter-TSS (NR_033745)	-27	NM_001163006	433771	Mm.305990	NM_001163006	ENSMUSG00000050608	Minos1	2310028O11Rik	mitochondrial inner membrane organizing system 1	protein-coding
mm_21185.1	chr2	155130044	155130055	-	1	NA	Intergenic	Intergenic	-3432	NM_001243712	16396	Mm.208286	NM_008395	ENSMUSG00000027598	Itch	6720481N21Rik|8030492O04Rik|A130065M08|AIP4|C230047C07Rik	itchy, E3 ubiquitin protein ligase	protein-coding
mm_80270.1	chr9	72962162	72962195	+	1	NA	intron (NM_026314, intron 4 of 8)	intron (NM_026314, intron 4 of 8)	3393	NM_001163725	67685	Mm.31817	NM_026314	ENSMUSG00000089865	Dyx1c1	1700010I24Rik|Dnaaf4|EKN1|b2b811.1Clo|b2b811Clo	dyslexia susceptibility 1 candidate 1	protein-coding
mm_109973.1	chr12	12938443	12938458	-	1	NA	intron (NM_008709, intron 2 of 2)	intron (NM_008709, intron 2 of 2)	3386	NM_008709	18109	Mm.16469	NM_008709	ENSMUSG00000037169	Mycn	N-myc|Nmyc|Nmyc-1|Nmyc1|bHLHe37|c-nmyc	v-myc avian myelocytomatosis viral related oncogene, neuroblastoma derived	protein-coding
mm_89803.1	chr10	102540262	102540281	+	1	NA	intron (NM_146240, intron 1 of 1)	intron (NM_146240, intron 1 of 1)	28049	NM_146240	237504	Mm.282672	NM_146240	ENSMUSG00000044921	Rassf9	AW322107|Pamci	Ras association (RalGDS/AF-6) domain family (N-terminal) member 9	protein-coding
mm_87903.1	chr10	62133083	62133098	+	1	NA	promoter-TSS (NM_009719)	promoter-TSS (NM_009719)	0	NM_009719	11925	Mm.57236	NM_009719	ENSMUSG00000044312	Neurog3	Atoh5|Math4B|bHLHa7|ngn3	neurogenin 3	protein-coding
mm_29739.1	chr3	126922850	126922859	-	1	NA	3' UTR (NM_178655, exon 25 of 25)	3' UTR (NM_178655, exon 25 of 25)	20532	NM_001034168	109676	Mm.220242	NM_178655	ENSMUSG00000032826	Ank2	100043364|AI835472|AW491075|Ank-2|Gm4392	ankyrin 2, brain	protein-coding
mm_52034.1	chr6	96115250	96115271	+	1	NA	intron (NM_182808, intron 1 of 4)	intron (NM_182808, intron 1 of 4)	2106	NM_182808	320265	Mm.489890	NM_182808	ENSMUSG00000059187	Fam19a1	C630007B19Rik|FAM19A1 TAFA-1|TAFA1|Tafa-1	family with sequence similarity 19, member A1	protein-coding
mm_21385.1	chr2	157514355	157514366	-	1	NA	Intergenic	Intergenic	-45718	NM_001291129	18111	Mm.34330	NM_010923	ENSMUSG00000067786	Nnat	5730414I02Rik|AW107673|Peg5	neuronatin	protein-coding
mm_77321.1	chr8	118906605	118906606	-	1	NA	intron (NM_019707, intron 5 of 13)	B4A|SINE|B4	-437933	NM_024219	68196	Mm.358714	NM_024219	ENSMUSG00000031839	Hsbp1	0610007A03Rik|AA408769|Hsp25	heat shock factor binding protein 1	protein-coding
mm_64550.1	chr7	144422940	144422959	+	1	NA	TTS (NM_001081370)	TTS (NM_001081370)	20484	NR_037302	100499519		NR_037302	ENSMUSG00000093912	Mir3470b	mmu-mir-3470b	microRNA 3470b	ncRNA
mm_3908.1	chr1	161896369	161896381	+	1	NA	Intergenic	Intergenic	-19714	NM_172645	226551	Mm.170002	NM_172645	ENSMUSG00000040297	Suco	4732491B11|AI848100|AU016931|Opt	SUN domain containing ossification factor	protein-coding
mm_138059.1	chr17	33928476	33928477	+	1	NA	3' UTR (NM_009318, exon 8 of 8)	3' UTR (NM_009318, exon 8 of 8)	-1418	NM_009059	19732	Mm.43777	NM_009059	ENSMUSG00000041354	Rgl2	KE1.5|Rab2l|Rgt2|Rlf	ral guanine nucleotide dissociation stimulator-like 2	protein-coding
mm_17156.1	chr2	25224654	25224659	-	1	NA	promoter-TSS (NM_146116)	promoter-TSS (NM_146116)	46	NM_146116	227613	Mm.227260	NM_146116	ENSMUSG00000036752	Tubb4b	4930542G03Rik|Tubb2c|Tubb2c1	tubulin, beta 4B class IVB	protein-coding
mm_35463.1	chr4	40757824	40757890	-	1	NA	promoter-TSS (NM_021535)	promoter-TSS (NM_021535)	28	NM_021535	74255	Mm.289929	NM_021535	ENSMUSG00000028409	Smu1	2600001O03Rik|2610203K23Rik|AB044414|AI845086|AW556129|Bwd	smu-1 suppressor of mec-8 and unc-52 homolog (C. elegans)	protein-coding
mm_108471.1	chr12	83644388	83644425	+	1	NA	exon (NM_027349, exon 3 of 19)	exon (NM_027349, exon 3 of 19)	12172	NM_027349	67039	Mm.46005	NM_027349	ENSMUSG00000010608	Rbm25	2600011C06Rik|2610015J01Rik|A130095G20Rik|AI159652|AL023075|AU043498|RNPC7	RNA binding motif protein 25	protein-coding
mm_65565.1	chr7	27174582	27174603	-	1	NA	intron (NM_029391, intron 4 of 7)	intron (NM_029391, intron 4 of 7)	1501	NR_037283	100526505		NR_037283	ENSMUSG00000093348	Mir3101	mir-3101|mmu-mir-3101	microRNA 3101	ncRNA
mm_18792.1	chr2	73775342	73775378	-	1	NA	promoter-TSS (NM_001113246)	promoter-TSS (NM_001113246)	-14	NM_001113246	108699	Mm.257073	NM_029716	ENSMUSG00000056486	Chn1	0610007I19Rik|0710001E19Rik|1700112L09Rik|2900046J01Rik|AI413815|ARHGAP2	chimerin 1	protein-coding
mm_56860.1	chr6	118197733	118197743	-	1	NA	promoter-TSS (NM_009050)	promoter-TSS (NM_009050)	6	NM_009050	19713	Mm.57199	NM_009050	ENSMUSG00000030110	Ret	PTC|RET51|RET9|c-Ret	ret proto-oncogene	protein-coding
mm_23214.1	chr3	43082887	43082893	+	1	NA	Intergenic	IAPEY3-int|LTR|ERVK	1340272	NM_027271	73852	Mm.29006	NM_027271	ENSMUSG00000025766	D3Ertd751e	2810009O15Rik|4930415G15Rik	DNA segment, Chr 3, ERATO Doi 751, expressed	protein-coding
mm_103850.1	chr11	83116591	83116592	-	1	NA	promoter-TSS (NM_011407)	promoter-TSS (NM_011407)	-254	NM_011407	20555	Mm.10948	NM_011407	ENSMUSG00000078763	Slfn1	AV316259	schlafen 1	protein-coding
mm_53577.1	chr6	137410836	137410838	+	1	NA	5' UTR (NM_001164403, exon 1 of 15)	5' UTR (NM_001164403, exon 1 of 15)	116	NM_001164403	19277	Mm.186361	NM_011216	ENSMUSG00000030223	Ptpro	D28|GLEPP1|PTPBK|PTPROt|PTPU2|PTPoc|PTPphi|Ptpn15|R-PTP-O	protein tyrosine phosphatase, receptor type, O	protein-coding
mm_19331.1	chr2	90577866	90577888	-	1	NA	intron (NM_008982, intron 1 of 23)	(GA)n|Simple_repeat|Simple_repeat	2770	NM_008982	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_33189.1	chr4	126202996	126203012	+	1	NA	promoter-TSS (NM_146153)	promoter-TSS (NM_146153)	-294	NM_146153	230753	Mm.29813	NM_146153	ENSMUSG00000043962	Thrap3	9330151F09Rik|B230333E16Rik|Trap150	thyroid hormone receptor associated protein 3	protein-coding
mm_1505.1	chr1	72307414	72307450	+	1	NA	promoter-TSS (NM_009533)	promoter-TSS (NM_009533)	11	NM_009533	22596	Mm.246952	NM_009533	ENSMUSG00000026187	Xrcc5	AI314015|Ku80|Ku86	X-ray repair complementing defective repair in Chinese hamster cells 5	protein-coding
mm_96899.1	chr11	70451906	70451950	+	1	NA	promoter-TSS (NM_025397)	promoter-TSS (NM_025397)	-3	NM_025397	66172	Mm.46424	NM_025397	ENSMUSG00000018923	Med11	1110030J09Rik|AI465144|AW545069	mediator complex subunit 11	protein-coding
mm_113306.1	chr13	30751091	30751096	+	1	NA	intron (NM_001347508, intron 2 of 8)	intron (NM_001347508, intron 2 of 8)	1860	NM_013674	16364	Mm.4677	NM_013674	ENSMUSG00000021356	Irf4	AI385587|IRF-4|LSIRF|NF-EM5|Spip	interferon regulatory factor 4	protein-coding
mm_973.1	chr1	58392967	58392986	+	1	NA	promoter-TSS (NM_025824)	promoter-TSS (NM_025824)	-160	NM_025824	66882	Mm.21848	NM_025824	ENSMUSG00000051223	Bzw1	1200015E15Rik|mKIAA0005	basic leucine zipper and W2 domains 1	protein-coding
mm_5697.1	chr1	43187088	43187097	-	1	NA	intron (NM_001289533, intron 1 of 5)	RMER10A|LTR|ERVL	9669	NM_001289533	14200	Mm.6799	NM_010212	ENSMUSG00000008136	Fhl2	FHL-2|SLIM-3|SLIM3	four and a half LIM domains 2	protein-coding
mm_143343.1	chr17	66594574	66594591	-	1	NA	promoter-TSS (NM_028998)	promoter-TSS (NM_028998)	40	NM_028998	74556	Mm.218634	NM_028998	ENSMUSG00000024105	Themis3	9130404H23Rik	thymocyte selection associated family member 3	protein-coding
mm_44255.1	chr5	5479041	5479060	-	1	NA	promoter-TSS (NM_001200025)	promoter-TSS (NM_001200025)	93	NM_001200025	381716	Mm.276086	NM_001200025	ENSMUSG00000079666	1700015F17Rik	Gm1686	RIKEN cDNA 1700015F17 gene	protein-coding
mm_2420.1	chr1	95313608	95313677	+	1	NA	promoter-TSS (NM_026321)	promoter-TSS (NM_026321)	14	NM_026321	67698	Mm.272705	NM_026321	ENSMUSG00000051185	Fam174a	2310044D20Rik|Fam174|Naa6|Tmem157	family with sequence similarity 174, member A	protein-coding
mm_31618.1	chr4	59189203	59189213	+	1	NA	promoter-TSS (NM_011673)	promoter-TSS (NM_011673)	-342	NM_011673	22234	Mm.198803	NM_011673	ENSMUSG00000028381	Ugcg	AU043821|C80537|Epcs21|GlcT-1|Ugcgl	UDP-glucose ceramide glucosyltransferase	protein-coding
mm_93033.1	chr10	88323131	88323151	-	1	NA	3' UTR (NM_027878, exon 7 of 7)	3' UTR (NM_027878, exon 7 of 7)	33934	NM_027878	71712	Mm.35450	NM_027878	ENSMUSG00000020057	Dram1	1200002N14Rik|Dram	DNA-damage regulated autophagy modulator 1	protein-coding
mm_111536.1	chr12	100887837	100887864	-	1	NA	5' UTR (NM_175493, exon 2 of 3)	5' UTR (NM_175493, exon 2 of 3)	11674	NM_001177674	238377	Mm.32160	NM_175493	ENSMUSG00000047415	Gpr68	BB131428|Ogr1	G protein-coupled receptor 68	protein-coding
mm_90878.1	chr10	9675400	9675416	-	1	NA	promoter-TSS (NM_177271)	promoter-TSS (NM_177271)	-200	NM_177271	320825	Mm.101115	NM_177271	ENSMUSG00000060487	Samd5	E130306M17Rik	sterile alpha motif domain containing 5	protein-coding
mm_21880.1	chr2	166154999	166155055	-	1	NA	5' UTR (NM_001252578, exon 1 of 21)	5' UTR (NM_001252578, exon 1 of 21)	258	NM_001252578	72043	Mm.1011	NM_028072	ENSMUSG00000006800	Sulf2	2010004N24Rik|AU020235|MSulf-2|mKIAA1247	sulfatase 2	protein-coding
mm_124006.1	chr14	76050206	76050206	-	1	NA	Intergenic	Intergenic	-39341	NM_026816	68705	Mm.20415	NM_026816	ENSMUSG00000067995	Gtf2f2	1110031C13Rik|AI326315	general transcription factor IIF, polypeptide 2	protein-coding
mm_128242.1	chr15	36608746	36608772	-	1	NA	5' UTR (NM_008774, exon 1 of 15)	5' UTR (NM_008774, exon 1 of 15)	214	NM_008774	18458	Mm.371570	NM_008774	ENSMUSG00000022283	Pabpc1	PABP|Pabp1|PabpI|Pabpl1|ePAB	poly(A) binding protein, cytoplasmic 1	protein-coding
mm_136549.1	chr16	97997215	97997226	-	1	NA	promoter-TSS (NR_130962)	promoter-TSS (NR_130962)	-127	NR_130962	245305	Mm.148033	NR_130962		B230307C23Rik	EG245305|OTTMUSG00000028475	RIKEN cDNA B230307C23 gene	ncRNA
mm_133429.1	chr16	87553403	87553413	+	1	NA	promoter-TSS (NM_144854)	promoter-TSS (NM_144854)	78	NM_144854	224419	Mm.194466	NM_144854	ENSMUSG00000025610	Map3k7cl	C21orf7|ORF63|Tak1l	Map3k7 C-terminal like	protein-coding
mm_25073.1	chr3	99885426	99885439	+	1	NA	promoter-TSS (NM_028892)	promoter-TSS (NM_028892)	15	NM_028892	74362	Mm.55847	NM_028892	ENSMUSG00000027867	Spag17	4931427F14Rik|PF6|Spag17-ps	sperm associated antigen 17	protein-coding
mm_94815.1	chr11	23152116	23152124	+	1	NA	promoter-TSS (NR_131065)	promoter-TSS (NR_131065)	-20	NR_131065	76993	Mm.59224	NR_131065	ENSMUSG00000086366	1700061J23Rik	-	RIKEN cDNA 1700061J23 gene	ncRNA
mm_169133.1	chr13	59107953	59107958	-	1	NA	intron (NM_001025074, intron 16 of 17)	intron (NM_001025074, intron 16 of 17)	300258	NM_001025074	18212	Mm.130054	NM_008745	ENSMUSG00000055254	Ntrk2	GP145-TrkB/GP95-TrkB|Tkrb|trk-B|trkB	neurotrophic tyrosine kinase, receptor, type 2	protein-coding
mm_140234.1	chr17	84108183	84108223	+	1	NA	Intergenic	Intergenic	29543	NR_045458	74473	Mm.399575	NR_045458		4933433H22Rik	-	RIKEN cDNA 4933433H22 gene	ncRNA
mm_52427.1	chr6	113483330	113483366	+	1	NA	promoter-TSS (NM_133930)	promoter-TSS (NM_133930)	-221	NM_133930	171508	Mm.41593	NM_133930	ENSMUSG00000030284	Creld1	AI843811	cysteine-rich with EGF-like domains 1	protein-coding
mm_147965.1	chr18	67134195	67134203	-	1	NA	intron (NM_010307, intron 1 of 11)	intron (NM_010307, intron 1 of 11)	639	NM_010307	14680	Mm.440746	NM_010307	ENSMUSG00000024524	Gnal	2610011C15Rik|9630020G10Rik|Galphaolf|Gna10|Golf	guanine nucleotide binding protein, alpha stimulating, olfactory type	protein-coding
mm_83403.1	chr9	44743798	44743837	-	1	NA	3' UTR (NM_145985, exon 10 of 10)	3' UTR (NM_145985, exon 10 of 10)	-8619	NM_153537	102693	Mm.28639	NM_153537	ENSMUSG00000048537	Phldb1	AU041016|D330037A14Rik|Ll5a	pleckstrin homology like domain, family B, member 1	protein-coding
mm_153076.1	chr19	32276944	32276956	-	1	NA	intron (NM_001168525, intron 2 of 9)	intron (NM_001168525, intron 2 of 9)	-65937	NM_001168526	208449	Mm.329810	NM_144792	ENSMUSG00000040451	Sgms1	9530058O11Rik|AI841905|C80702|Mob|Sms1|Sor1|Tmem23	sphingomyelin synthase 1	protein-coding
mm_54395.1	chr6	31398735	31398766	-	1	NA	promoter-TSS (NM_013791)	promoter-TSS (NM_013791)	23	NR_040300	100503869	Mm.370532	NR_040300	ENSMUSG00000086212	Mkln1os	Gm13845|OTTMUSG00000014733	muskelin 1, intracellular mediator containing kelch motifs, opposite strand	ncRNA
mm_106829.1	chr12	7998610	7998630	+	1	NA	exon (NM_009693, exon 20 of 29)	exon (NM_009693, exon 20 of 29)	20943	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_24229.1	chr3	88950032	88950082	+	1	NA	5' UTR (NM_022994, exon 1 of 13)	5' UTR (NM_022994, exon 1 of 13)	225	NM_022994	65111	Mm.29028	NM_022994	ENSMUSG00000068921	Dap3	4921514D13Rik|DAP-3|MRP-S29|S29mt	death associated protein 3	protein-coding
mm_24621.1	chr3	93520370	93520391	+	1	NA	promoter-TSS (NM_016740)	promoter-TSS (NM_016740)	-116	NM_016740	20195	Mm.280038	NM_016740	ENSMUSG00000027907	S100a11	EMAPI|Emap1|S100a14|S100c|cal	S100 calcium binding protein A11	protein-coding
mm_60009.1	chr7	30729710	30729759	+	1	NA	promoter-TSS (NM_027215)	promoter-TSS (NM_027215)	-200	NM_027215	69804	Mm.27499	NM_027215	ENSMUSG00000006315	Tmem147	2010004E11Rik|5033425B17Rik|Nifie14	transmembrane protein 147	protein-coding
mm_94727.1	chr11	20740588	20740645	+	1	NA	intron (NM_001290545, intron 1 of 9)	intron (NM_001290545, intron 1 of 9)	940	NM_001290545	216549	Mm.356580	NM_181411	ENSMUSG00000049659	Aftph	-	aftiphilin	protein-coding
mm_86411.1	chr10	3366210	3366220	+	1	NA	promoter-TSS (NM_133485)	promoter-TSS (NM_133485)	65	NM_133485	76142	Mm.308126	NM_133485	ENSMUSG00000040653	Ppp1r14c	6330514J04Rik|KEPI	protein phosphatase 1, regulatory (inhibitor) subunit 14c	protein-coding
mm_30653.1	chr4	8854199	8854204	+	1	NA	exon (NM_001277149, exon 29 of 38)	exon (NM_001277149, exon 29 of 38)	163795	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_113307.1	chr13	30751707	30751730	+	1	NA	exon (NM_013674, exon 3 of 9)	exon (NM_013674, exon 3 of 9)	2485	NM_013674	16364	Mm.4677	NM_013674	ENSMUSG00000021356	Irf4	AI385587|IRF-4|LSIRF|NF-EM5|Spip	interferon regulatory factor 4	protein-coding
mm_145449.1	chr18	60213071	60213105	+	1	NA	intron (NM_001033767, intron 2 of 2)	Lx8|LINE|L1	1011	NM_001033767	240327	Mm.357104	NM_001033767	ENSMUSG00000073555	Gm4951	EG240327|Ifgga2	predicted gene 4951	protein-coding
mm_96148.1	chr11	61126748	61126762	+	1	NA	Intergenic	Intergenic	-14080	NM_021349	57916	Mm.265915	NM_021349	ENSMUSG00000010142	Tnfrsf13b	1200009E08Rik|Taci	tumor necrosis factor receptor superfamily, member 13b	protein-coding
mm_34829.1	chr4	155221678	155221681	+	1	NA	exon (NM_011385, exon 1 of 7)	exon (NM_011385, exon 1 of 7)	856	NM_011385	20481	Mm.28520	NM_011385	ENSMUSG00000029050	Ski	2310012I02Rik|2610001A11Rik|AA062172|AA589460|BC004088	ski sarcoma viral oncogene homolog (avian)	protein-coding
mm_89976.1	chr10	111595874	111595880	+	1	NA	Intergenic	Intergenic	-1604	NR_045344	71321	Mm.410785	NR_045344	ENSMUSG00000097082	4933440J02Rik	-	RIKEN cDNA 4933440J02 gene	ncRNA
mm_90272.1	chr10	122725358	122725360	+	1	NA	intron (NM_176919, intron 1 of 8)	intron (NM_176919, intron 1 of 8)	46044	NR_106182	102466884		NR_106182	ENSMUSG00000099225	Mir8104	Gm27380|mmu-mir-8104	microRNA 8104	ncRNA
mm_109976.1	chr12	12939862	12939878	-	1	NA	exon (NM_008709, exon 2 of 3)	exon (NM_008709, exon 2 of 3)	1966	NM_008709	18109	Mm.16469	NM_008709	ENSMUSG00000037169	Mycn	N-myc|Nmyc|Nmyc-1|Nmyc1|bHLHe37|c-nmyc	v-myc avian myelocytomatosis viral related oncogene, neuroblastoma derived	protein-coding
mm_40787.1	chr5	67426786	67426801	+	1	NA	intron (NM_001164806, intron 1 of 4)	CpG	1006	NM_001164806	666938	Mm.101339	NM_001164806	ENSMUSG00000092060	Bend4	D330027G24Rik|EG666938	BEN domain containing 4	protein-coding
mm_14571.1	chr2	135336376	135336379	+	1	NA	intron (NM_019677, intron 17 of 32)	intron (NM_019677, intron 17 of 32)	-69453	NR_039540	100628568		NR_039540	ENSMUSG00000092830	Mir3963	mmu-mir-3963|mu-mir-3963	microRNA 3963	ncRNA
mm_80183.1	chr9	72305871	72305876	+	1	NA	intron (NM_001311105, intron 6 of 20)	intron (NM_001311105, intron 6 of 20)	30985	NM_001311105	235469	Mm.242791	NM_146224	ENSMUSG00000038535	Zfp280d	A930005F02Rik|BC027163|Suhw4|ZNF634|Znf280d	zinc finger protein 280D	protein-coding
mm_11003.1	chr2	26475315	26475323	+	1	NA	intron (NM_008714, intron 15 of 33)	intron (NM_008714, intron 15 of 33)	-5200	NR_105962	102465602		NR_105962	ENSMUSG00000098548	Mir6996	Gm27531|mmu-mir-6996	microRNA 6996	ncRNA
mm_116346.1	chr13	38635037	38635119	-	1	NA	promoter-TSS (NM_139063)	promoter-TSS (NM_139063)	31	NM_139063	17828	Mm.261554	NM_139063	ENSMUSG00000038982	Bloc1s5	1810074A19Rik|Muted|mu	biogenesis of lysosomal organelles complex-1, subunit 5, muted	protein-coding
mm_144896.1	chr18	37020098	37020138	+	1	NA	promoter-TSS (NM_138663)	promoter-TSS (NM_138663)	-112	NM_138663	192164	Mm.308500	NM_138663	ENSMUSG00000103310	Pcdha12	Cnr5|Crnr5|Pcdha13	protocadherin alpha 12	protein-coding
mm_96791.1	chr11	69966897	69966911	+	1	NA	intron (NM_016887, intron 1 of 3)	intron (NM_016887, intron 1 of 3)	1483	NM_016887	53624	Mm.281896	NM_016887	ENSMUSG00000018569	Cldn7	-	claudin 7	protein-coding
mm_158329.1	chrX	133961722	133961730	-	1	NA	exon (NM_001290718, exon 3 of 14)	exon (NM_001290718, exon 3 of 14)	20086	NM_001290718	27359	Mm.38674	NM_013757	ENSMUSG00000031255	Sytl4	Gph|Slp4	synaptotagmin-like 4	protein-coding
mm_142155.1	chr17	36032683	36032742	-	1	NA	promoter-TSS (NM_010398)	promoter-TSS (NM_010398)	-11	NM_010398	15040	Mm.439648	NM_010398	ENSMUSG00000067212	H2-T23	37b|37c|H-2T23|H2-Qa1|Qa-1|Qa-1(b)|Qa1|Qed-1|T18c|T18c(37)|T23b|T23d	histocompatibility 2, T region locus 23	protein-coding
mm_24158.1	chr3	88483333	88483382	+	1	NA	exon (NM_019390, exon 10 of 10)	exon (NM_019390, exon 10 of 10)	9955	NM_019390	16905	Mm.243014	NM_019390	ENSMUSG00000028063	Lmna	Dhe	lamin A	protein-coding
mm_75240.1	chr8	39631333	39631369	-	1	NA	exon (NM_031195, exon 3 of 9)	exon (NM_031195, exon 3 of 9)	11327	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_152486.1	chr19	11050414	11050433	-	1	NA	non-coding (NR_102366, exon 1 of 3)	non-coding (NR_102366, exon 1 of 3)	143	NR_102366	107350	Mm.6381	NM_001177351	ENSMUSG00000075010	AW112010	-	expressed sequence AW112010	ncRNA
mm_93453.1	chr10	110098316	110098327	-	1	NA	Intergenic	Intergenic	-98102	NM_001081035	260315	Mm.225050	NM_177797	ENSMUSG00000020181	Nav3	4732483H20Rik|9630020C08Rik|POMFIL1|Pomfil1p|mKIAA0938|unc53H3	neuron navigator 3	protein-coding
mm_114173.1	chr13	55593138	55593177	+	1	NA	promoter-TSS (NM_026211)	promoter-TSS (NM_026211)	22	NM_026211	67511	Mm.45233	NM_026211	ENSMUSG00000058569	Tmed9	2400003B06Rik	transmembrane p24 trafficking protein 9	protein-coding
mm_103755.1	chr11	80789864	80789864	-	1	NA	Intergenic	Intergenic	-9839	NM_177390	338367	Mm.151948	NM_177390	ENSMUSG00000035441	Myo1d	9930104H07Rik|AW544947|D11Ertd9e|myosin-1d	myosin ID	protein-coding
mm_145371.1	chr18	56733230	56733249	+	1	NA	exon (NM_010721, exon 5 of 11)	exon (NM_010721, exon 5 of 11)	25426	NM_010721	16906	Mm.4105	NM_010721	ENSMUSG00000024590	Lmnb1	-	lamin B1	protein-coding
mm_15145.1	chr2	153986363	153986369	+	1	NA	exon (NM_001080811, exon 4 of 11)	exon (NM_001080811, exon 4 of 11)	11421	NM_001080811	545477	Mm.379973	NM_001080811	ENSMUSG00000078998	Bpifa6	EG545477|Gm5840|Splunc6	BPI fold containing family A, member 6	protein-coding
mm_82989.1	chr9	36533853	36533868	-	1	NA	3' UTR (NM_001033783, exon 3 of 3)	3' UTR (NM_001033783, exon 3 of 3)	8103	NM_001033783	434396	Mm.118836	NM_001033783	ENSMUSG00000074448	Gm5615	EG434396|Pate-H|Pate9	predicted gene 5615	protein-coding
mm_153072.1	chr19	32255095	32255109	-	1	NA	intron (NM_144792, intron 3 of 9)	intron (NM_144792, intron 3 of 9)	-44089	NM_001168526	208449	Mm.329810	NM_144792	ENSMUSG00000040451	Sgms1	9530058O11Rik|AI841905|C80702|Mob|Sms1|Sor1|Tmem23	sphingomyelin synthase 1	protein-coding
mm_39265.1	chr5	3571677	3571692	+	1	NA	promoter-TSS (NM_029843)	promoter-TSS (NM_029843)	-32	NM_029843	77036	Mm.389069	NM_029843	ENSMUSG00000008307	1700109H08Rik	-	RIKEN cDNA 1700109H08 gene	protein-coding
mm_47057.1	chr5	116381642	116381644	-	1	NA	Intergenic	MLT1B|LTR|ERVL-MaLR	41221	NM_030704	80888	Mm.21549	NM_030704	ENSMUSG00000041548	Hspb8	AU018630|AW413033|Cryac|D5Ucla4|E2IG1|H11|H11K|HSP20-like|HSP22	heat shock protein 8	protein-coding
mm_103066.1	chr11	69838004	69838038	-	1	NA	promoter-TSS (NM_026982)	promoter-TSS (NM_026982)	-504	NM_026982	69186	Mm.248772	NM_026982	ENSMUSG00000070394	Tmem256	1810027O10Rik|3110009M16Rik	transmembrane protein 256	protein-coding
mm_142108.1	chr17	35835932	35835966	-	1	NA	exon (NM_011655, exon 4 of 4)	exon (NM_011655, exon 4 of 4)	2352	NM_011655	22154	Mm.273538	NM_011655	ENSMUSG00000001525	Tubb5	AA408537|AI596182|B130022C14Rik|M(beta)5	tubulin, beta 5 class I	protein-coding
mm_117705.1	chr13	95050567	95050569	-	1	NA	intron (NM_001346782, intron 11 of 21)	intron (NM_001346782, intron 11 of 21)	74224	NM_172590	218460	Mm.33856	NM_172590	ENSMUSG00000042015	Wdr41	B830029I03Rik|MSTP048	WD repeat domain 41	protein-coding
mm_28832.1	chr3	96556251	96556257	-	1	NA	intron (NR_040409, intron 3 of 3)	intron (NR_040409, intron 3 of 3)	-1703	NM_001009935	56338	Mm.410189	NM_023719	ENSMUSG00000038393	Txnip	1200008J08Rik|AA682105|Hyplip1|THIF|Tbp-2|VDUP1	thioredoxin interacting protein	protein-coding
mm_98854.1	chr11	97663078	97663084	+	1	NA	promoter-TSS (NM_139311)	promoter-TSS (NM_139311)	-331	NM_139311	246198	Mm.23685	NM_139311	ENSMUSG00000038437	Mllt6	AI315037|Af17	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 6	protein-coding
mm_148700.1	chr19	5742461	5742472	+	1	NA	exon (NM_008520, exon 2 of 28)	exon (NM_008520, exon 2 of 28)	1562	NM_008520	16998	Mm.182396	NM_008520	ENSMUSG00000024940	Ltbp3	Ltbp2|mFLJ00070	latent transforming growth factor beta binding protein 3	protein-coding
mm_55855.1	chr6	83442699	83442724	-	1	NA	intron (NR_028382, intron 2 of 2)	intron (NR_028382, intron 2 of 2)	956	NR_028382	320775	Mm.434334	NR_028382	ENSMUSG00000051844	B230319C09Rik	-	RIKEN cDNA B230319C09 gene	ncRNA
mm_147910.1	chr18	65416392	65416407	-	1	NA	intron (NR_105742, intron 3 of 6)	intron (NR_105742, intron 3 of 6)	-14598	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_52075.1	chr6	97827280	97827302	+	1	NA	intron (NM_001113198, intron 1 of 9)	intron (NM_001113198, intron 1 of 9)	20233	NM_001113198	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_24183.1	chr3	88593091	88593113	+	1	NA	Intergenic	Intergenic	13431	NM_025448	66256	Mm.7091	NM_025448	ENSMUSG00000041355	Ssr2	1500032E05Rik|AI315033|AU020133|TLAP|TRAPB|TRAPbeta	signal sequence receptor, beta	protein-coding
mm_44993.1	chr5	38159408	38159454	-	1	NA	promoter-TSS (NM_010942)	promoter-TSS (NM_010942)	36	NM_010942	18196	Mm.7414	NM_010942	ENSMUSG00000029126	Nsg1	Neep21|m234|p21	neuron specific gene family member 1	protein-coding
mm_135406.1	chr16	44746279	44746300	-	1	NA	promoter-TSS (NM_025332)	promoter-TSS (NM_025332)	74	NM_001159329	66067	Mm.34520	NM_025332	ENSMUSG00000022668	Gtpbp8	0610037H22Rik	GTP-binding protein 8 (putative)	protein-coding
mm_147295.1	chr18	39496586	39496600	-	1	NA	Intergenic	Intergenic	-9348	NM_008173	14815	Mm.129481	NM_008173	ENSMUSG00000024431	Nr3c1	GR|Grl-1|Grl1	nuclear receptor subfamily 3, group C, member 1	protein-coding
mm_35750.1	chr4	45514119	45514121	-	1	NA	intron (NM_001033306, intron 1 of 5)	intron (NM_001033306, intron 1 of 5)	16708	NM_001033306	230126	Mm.251716	NM_001033306	ENSMUSG00000044813	Shb	BC028832	src homology 2 domain-containing transforming protein B	protein-coding
mm_84846.1	chr9	78442854	78442869	-	1	NA	exon (NM_173386, exon 1 of 5)	exon (NM_173386, exon 1 of 5)	376	NR_125721	214763	Mm.101559	NM_173386	ENSMUSG00000032344	Mb21d1	E330016A19Rik|cGAS	Mab-21 domain containing 1	protein-coding
mm_1395.1	chr1	67131698	67131745	+	1	NA	intron (NM_001080809, intron 1 of 37)	B4A|SINE|B4	8694	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_12207.1	chr2	66440914	66440929	+	1	NA	promoter-TSS (NR_033495)	promoter-TSS (NR_033495)	41	NR_033495	100038743	Mm.330264	NR_033495		Gm13629	OTTMUSG00000013098	predicted gene 13629	ncRNA
mm_103851.1	chr11	83122267	83122268	-	1	NA	3' UTR (NM_011407, exon 2 of 2)	3' UTR (NM_011407, exon 2 of 2)	5422	NM_011407	20555	Mm.10948	NM_011407	ENSMUSG00000078763	Slfn1	AV316259	schlafen 1	protein-coding
mm_102543.1	chr11	61267178	61267198	-	1	NA	promoter-TSS (NM_007437)	promoter-TSS (NM_007437)	-2	NM_007437	11671	Mm.398221	NM_007437	ENSMUSG00000010025	Aldh3a2	AI194803|Ahd-3|Ahd-3r|Ahd3|Ahd3-r|Aldh4|Aldh4-r|FALDH	aldehyde dehydrogenase family 3, subfamily A2	protein-coding
mm_47460.1	chr5	123666683	123666695	-	1	NA	intron (NM_001347468, intron 1 of 24)	intron (NM_001347468, intron 1 of 24)	17672	NM_019765	56430	Mm.241109	NM_019765	ENSMUSG00000049550	Clip1	1110007I12Rik|4631429H07Rik|AV017631|C81039|CLIP-170|CLIP170|CYLN1|Clip50|Rsn|mKIAA4046|restin	CAP-GLY domain containing linker protein 1	protein-coding
mm_52414.1	chr6	113392418	113392484	+	1	NA	promoter-TSS (NM_133923)	promoter-TSS (NM_133923)	-46	NM_133923	101100	Mm.388573	NM_133923	ENSMUSG00000030276	Ttll3	4833441J24Rik|AI450050	tubulin tyrosine ligase-like family, member 3	protein-coding
mm_159851.1	chr5	137365490	137365490	+	1	NA	exon (NM_010144, exon 10 of 17)	exon (NM_010144, exon 10 of 17)	15381	NM_010144	13846	Mm.34533	NM_010144	ENSMUSG00000029710	Ephb4	AI042935|Htk|MDK2|Myk1|Tyro11	Eph receptor B4	protein-coding
mm_21528.1	chr2	163645052	163645056	-	1	NA	promoter-TSS (NM_012032)	promoter-TSS (NM_012032)	89	NM_012032	26943	Mm.218473	NM_012032	ENSMUSG00000017707	Serinc3	AA959945|AA960047|AIGP1|DIFF33|TMS-1|Tde1	serine incorporator 3	protein-coding
mm_1381.1	chr1	66816208	66816219	+	1	NA	intron (NM_177645, intron 1 of 13)	MIR|SINE|MIR	1382	NM_177645	68691	Mm.240912	NM_177645	ENSMUSG00000026004	Kansl1l	1110028C15Rik|1190030G24|AI427598|C430010P07Rik|mKIAA4189	KAT8 regulatory NSL complex subunit 1-like	protein-coding
mm_124819.1	chr15	9071394	9071471	+	1	NA	5' UTR (NM_001085410, exon 1 of 14)	5' UTR (NM_001085410, exon 1 of 14)	172	NM_001040395	68646	Mm.244226	NM_001040395	ENSMUSG00000022253	Nadk2	MNADK|Nadkd1	NAD kinase 2, mitochondrial	protein-coding
mm_125557.1	chr15	58888974	58889010	+	1	NA	promoter-TSS (NM_175226)	promoter-TSS (NM_175226)	-237	NM_175226	75841	Mm.4537	NM_175226	ENSMUSG00000037075	Rnf139	4930555P18Rik	ring finger protein 139	protein-coding
mm_140543.1	chr17	6827271	6827282	-	1	NA	Intergenic	B3|SINE|B2	-44496	NM_009510	22350	Mm.277812	NM_009510	ENSMUSG00000052397	Ezr	AW146364|R75297|Vil2|p81	ezrin	protein-coding
mm_132008.1	chr16	25824934	25824941	+	1	NA	intron (NM_001127259, intron 4 of 13)	intron (NM_001127259, intron 4 of 13)	23021	NM_001127264	22061	Mm.20894	NM_011641	ENSMUSG00000022510	Trp63	AI462811|Ket|P51/P63|P63|P73l|Tp63|Trp53rp1	transformation related protein 63	protein-coding
mm_26250.1	chr3	141631965	141631972	+	1	NA	intron (NM_001293561, intron 1 of 16)	Lx8|LINE|L1	166404	NM_001293561	22253	Mm.24430	NM_009472	ENSMUSG00000059921	Unc5c	B130051O18Rik|Unc5h3|rcm	unc-5 netrin receptor C	protein-coding
mm_3129.1	chr1	134962572	134962627	+	1	NA	promoter-TSS (NM_026024)	promoter-TSS (NM_026024)	34	NM_001278115	67196	Mm.284587	NM_026024	ENSMUSG00000026429	Ube2t	2700084L22Rik|C80607	ubiquitin-conjugating enzyme E2T	protein-coding
mm_14188.1	chr2	127080512	127080530	+	1	NA	intron (NM_026678, intron 1 of 7)	intron (NM_026678, intron 1 of 7)	9864	NM_026678	109778	Mm.22028	NM_026678	ENSMUSG00000001999	Blvra	0610006A11Rik|2500001N03Rik|Blvr	biliverdin reductase A	protein-coding
mm_5549.1	chr1	38627587	38627605	-	1	NA	promoter-TSS (NM_001290814)	promoter-TSS (NM_001290814)	-352	NM_001290814	16764	Mm.336679	NM_010678	ENSMUSG00000037138	Aff3	3222402O04Rik|A730046J16|LAF-4|Laf4	AF4/FMR2 family, member 3	protein-coding
mm_145723.1	chr18	63926541	63926551	+	1	NA	intron (NM_001014981, intron 23 of 27)	intron (NM_001014981, intron 23 of 27)	217851	NM_001014981	104082	Mm.30850	NM_001014981	ENSMUSG00000040560	Wdr7	AI462727|TRAG|mKIAA0541	WD repeat domain 7	protein-coding
mm_168522.1	chr11	58215038	58215038	+	1	NA	promoter-TSS (NM_019440)	promoter-TSS (NM_019440)	61	NM_019440	54396	Mm.458517	NM_019440	ENSMUSG00000069874	Irgm2	AI481100|GTPI|Ifggd2|Iigp2	immunity-related GTPase family M member 2	protein-coding
mm_122563.1	chr14	49783328	49783394	-	1	NA	promoter-TSS (NM_026142)	promoter-TSS (NM_026142)	6	NM_026142	67419	Mm.318710	NM_026142	ENSMUSG00000036242	3632451O06Rik	AU067705	RIKEN cDNA 3632451O06 gene	protein-coding
mm_151265.1	chr19	54045252	54045267	+	1	NA	promoter-TSS (NM_007417)	promoter-TSS (NM_007417)	77	NM_007417	11551	Mm.235195	NM_007417	ENSMUSG00000033717	Adra2a	AW122659|Adra-2|Adra-2a|alpha(2A)AR|alpha2-C10|alpha2A|alpha2A-AR	adrenergic receptor, alpha 2a	protein-coding
mm_137482.1	chr17	26933071	26933158	+	1	NA	promoter-TSS (NM_009343)	promoter-TSS (NM_009343)	-13	NM_001302397	21652	Mm.258953	NM_009343	ENSMUSG00000024193	Phf1	AW557215|D17Ertd455e|Pcl1|Phf2|Tctex3	PHD finger protein 1	protein-coding
mm_24599.1	chr3	93445359	93445359	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	3029	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_65185.1	chr7	19696489	19696491	-	1	NA	exon (NM_009696, exon 4 of 4)	exon (NM_009696, exon 4 of 4)	1908	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_86606.1	chr10	13553246	13553258	+	1	NA	promoter-TSS (NM_019961)	promoter-TSS (NM_019961)	-110	NM_001347361	56535	Mm.282711	NM_019961	ENSMUSG00000019809	Pex3	1700014F15Rik|2810027F19Rik|2900010N04Rik	peroxisomal biogenesis factor 3	protein-coding
mm_52542.1	chr6	115933939	115933949	+	1	NA	exon (NM_145383, exon 2 of 5)	exon (NM_145383, exon 2 of 5)	2017	NM_145383	212541	Mm.2965	NM_145383	ENSMUSG00000030324	Rho	Noerg1|Opn2|Ops|RP4	rhodopsin	protein-coding
mm_37781.1	chr4	130177165	130177186	-	1	NA	Intergenic	Intergenic	-2053	NM_023476	94242	Mm.15801	NM_023476	ENSMUSG00000028776	Tinagl1	1110021J17Rik|AZ-1|AZ1|Arg1|Lcn7|TARP|Tinagl	tubulointerstitial nephritis antigen-like 1	protein-coding
mm_92331.1	chr10	75789931	75789957	-	1	NA	intron (NM_008185, intron 3 of 4)	intron (NM_008185, intron 3 of 4)	-8522	NM_001346523	103140	Mm.5731	NM_133994	ENSMUSG00000001665	Gstt3	AI118089	glutathione S-transferase, theta 3	protein-coding
mm_15386.1	chr2	156613644	156613661	+	1	NA	promoter-TSS (NM_146128)	promoter-TSS (NM_146128)	-45	NM_146128	228836	Mm.22094	NM_146128	ENSMUSG00000061689	Dlgap4	AI225853|BC024558|DAP-4|DAP4|SAPAP-4|Sapap4|WBP16	discs, large homolog-associated protein 4 (Drosophila)	protein-coding
mm_33644.1	chr4	133011795	133011822	+	1	NA	intron (NM_146155, intron 1 of 6)	CpG	302	NM_146155	230793	Mm.31816	NM_146155	ENSMUSG00000037692	Ahdc1	D030015G18Rik	AT hook, DNA binding motif, containing 1	protein-coding
mm_93663.1	chr10	117693275	117693281	-	1	NA	intron (NM_001288586, intron 8 of 10)	intron (NM_001288586, intron 8 of 10)	17480	NM_010786	17246	Mm.22670	NM_010786	ENSMUSG00000020184	Mdm2	1700007J15Rik|AA415488|Mdm-2	transformed mouse 3T3 cell double minute 2	protein-coding
mm_158186.1	chrX	104348482	104348499	-	1	NA	intron (NM_009592, intron 1 of 15)	CpG	65356	NM_009592	11306	Mm.426128	NM_009592	ENSMUSG00000031333	Abcb7	AA517758|AU019072|Abc7	ATP-binding cassette, sub-family B (MDR/TAP), member 7	protein-coding
mm_122796.1	chr14	54464054	54464067	-	1	NA	promoter-TSS (NM_022993)	promoter-TSS (NM_022993)	-87	NM_022993	65107	Mm.472719	NM_022993	ENSMUSG00000022175	Lrp10	Lrp9	low-density lipoprotein receptor-related protein 10	protein-coding
mm_46157.1	chr5	96131216	96131238	-	1	NA	exon (NM_178854, exon 3 of 12)	exon (NM_178854, exon 3 of 12)	30320	NM_001285511	231464	Mm.28374	NM_144910	ENSMUSG00000034724	Cnot6l	4932442K20Rik	CCR4-NOT transcription complex, subunit 6-like	protein-coding
mm_166233.1	chr5	67260717	67260720	+	1	NA	5' UTR (NM_030108, exon 1 of 9)	5' UTR (NM_030108, exon 1 of 9)	153	NM_030108	67878	Mm.23217	NM_028975	ENSMUSG00000037720	Tmem33	1110006G02Rik|1600019D15Rik|2410089A21Rik|2700052H22Rik|5430406L04Rik|AA388285|AI314185|AI426615|db83	transmembrane protein 33	protein-coding
mm_145564.1	chr18	60812436	60812458	+	1	NA	TTS (NR_039567)	TTS (NR_039567)	371	NR_039567	100628611		NR_039567	ENSMUSG00000093327	Mir5107	mir-5107|mmu-mir-5107|mu-mir-5107	microRNA 5107	ncRNA
mm_158658.1	chrX	157017543	157017560	-	1	NA	Intergenic	Intergenic	397735	NM_011077	18675	Mm.2529	NM_011077	ENSMUSG00000057457	Phex	Gy|HPDR|HPDR1|Hyp|PEX	phosphate regulating endopeptidase homolog, X-linked	protein-coding
mm_74034.1	chr8	121829671	121829689	+	1	NA	promoter-TSS (NM_145605)	promoter-TSS (NM_145605)	-111	NM_145605	234825	Mm.209329	NM_145605	ENSMUSG00000040263	Klhdc4	AA408426|AV352552|BC012312|G430025P05Rik	kelch domain containing 4	protein-coding
mm_42128.1	chr5	110956079	110956081	+	1	NA	intron (NM_001267622, intron 2 of 22)	intron (NM_001267622, intron 2 of 22)	-48064	NR_030482	735278		NR_030482	ENSMUSG00000076163	Mir701	Mirn701|mir-701|mmu-mir-701	microRNA 701	ncRNA
mm_72444.1	chr8	83165449	83165499	+	1	NA	5' UTR (NM_001111304, exon 1 of 21)	5' UTR (NM_001111304, exon 1 of 21)	122	NM_027758	71310	Mm.24031	NM_027758	ENSMUSG00000031709	Tbc1d9	4933431N12Rik|AI847101|AW490653|C76116	TBC1 domain family, member 9	protein-coding
mm_166734.1	chr6	122901588	122901588	+	1	NA	Intergenic	Lx2A1|LINE|L1	-20260	NM_199311	269799	Mm.297275	NM_199311	ENSMUSG00000049037	Clec4a1	BC049354|Dcir4	C-type lectin domain family 4, member a1	protein-coding
mm_138390.1	chr17	35050285	35050291	+	1	NA	promoter-TSS (NM_033444)	promoter-TSS (NM_033444)	45	NM_033444	114584	Mm.29524	NM_033444	ENSMUSG00000007041	Clic1	Clcp|G6	chloride intracellular channel 1	protein-coding
mm_52350.1	chr6	112273801	112273816	+	1	NA	promoter-TSS (NM_144799)	promoter-TSS (NM_144799)	50	NM_144799	30937	Mm.234441	NM_144799	ENSMUSG00000057604	Lmcd1	AW455500|AW553074|dyxin	LIM and cysteine-rich domains 1	protein-coding
mm_160649.1	chr9	110857744	110857744	+	1	NA	promoter-TSS (NM_146227)	promoter-TSS (NM_146227)	-223	NM_146227	235631	Mm.102265	NM_146227	ENSMUSG00000048752	Prss50	79H19C|Tsp50	protease, serine 50	protein-coding
mm_141027.1	chr17	25224694	25224701	-	1	NA	intron (NM_028789, intron 1 of 4)	RLTR14|LTR|ERV1	2115	NM_028789	74154	Mm.267353	NM_028789	ENSMUSG00000015127	Unkl	1300004G08Rik	unkempt family like zinc finger	protein-coding
mm_85996.1	chr9	112217319	112217337	-	1	NA	promoter-TSS (NM_001177623)	promoter-TSS (NM_001177623)	23	NM_001177623	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_87264.1	chr10	41520530	41520534	+	1	NA	intron (NM_016898, intron 1 of 5)	intron (NM_016898, intron 1 of 5)	1032	NM_016898	53599	Mm.269815	NM_016898	ENSMUSG00000019818	Cd164	A115|A24|AA589639|AW540279|MGC-24|MSSP	CD164 antigen	protein-coding
mm_1907.1	chr1	85894532	85894655	+	1	NA	promoter-TSS (NM_022417)	promoter-TSS (NM_022417)	83	NM_022417	64294	Mm.29870	NM_022417	ENSMUSG00000026223	Itm2c	3110038L02Rik|BRI3|Bricd2c|E25|E25C|ITM3	integral membrane protein 2C	protein-coding
mm_86506.1	chr10	7589886	7589902	+	1	NA	promoter-TSS (NM_172784)	promoter-TSS (NM_172784)	94	NM_172784	237253	Mm.206759	NM_172784	ENSMUSG00000019796	Lrp11	1700034J19Rik|6330533B21|9830160H19Rik	low density lipoprotein receptor-related protein 11	protein-coding
mm_138209.1	chr17	34305069	34305075	+	1	NA	promoter-TSS (NM_010382)	promoter-TSS (NM_010382)	-795	NM_010382	14969	Mm.22564	NM_010382	ENSMUSG00000060586	H2-Eb1	Eb|H-2Eb|H2Eb|Ia-4|Ia4	histocompatibility 2, class II antigen E beta	protein-coding
mm_141226.1	chr17	27325049	27325056	-	1	NA	Intergenic	Intergenic	-3333	NR_106075	102466818		NR_106075	ENSMUSG00000099237	Mir7216	Gm27555|mmu-mir-7216	microRNA 7216	ncRNA
mm_87762.1	chr10	60291724	60291736	+	1	NA	exon (NM_011179, exon 2 of 15)	exon (NM_011179, exon 2 of 15)	7269	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_86070.1	chr9	114775464	114775483	-	1	NA	intron (NM_001252479, intron 1 of 3)	intron (NM_001252479, intron 1 of 3)	6520	NM_133978	102545	Mm.35600	NM_133978	ENSMUSG00000032436	Cmtm7	AI481279|Cklfsf7|LNV	CKLF-like MARVEL transmembrane domain containing 7	protein-coding
mm_43430.1	chr5	136060089	136060102	+	1	NA	exon (NM_027158, exon 3 of 6)	exon (NM_027158, exon 3 of 6)	2828	NM_027158	69665	Mm.75713	NM_027158	ENSMUSG00000006143	Upk3bl	2310043J07Rik	uroplakin 3B-like	protein-coding
mm_146564.1	chr18	6490779	6490793	-	1	NA	promoter-TSS (NM_001276350)	promoter-TSS (NM_001276350)	71	NM_001276350	13831	Mm.312133	NM_007935	ENSMUSG00000024240	Epc1	2400007E14Rik|5730566F07Rik|A930032N02Rik|mir-1893	enhancer of polycomb homolog 1 (Drosophila)	protein-coding
mm_5718.1	chr1	44101654	44101659	-	1	NA	intron (NM_029368, intron 2 of 7)	intron (NM_029368, intron 2 of 7)	732	NM_029368	75623	Mm.348017	NM_029368	ENSMUSG00000026049	Tex30	1700029F09Rik|3110030D08Rik	testis expressed 30	protein-coding
mm_27685.1	chr3	65958510	65958534	-	1	NA	promoter-TSS (NM_019937)	promoter-TSS (NM_019937)	-297	NM_019937	56706	Mm.175612	NM_019937	ENSMUSG00000027829	Ccnl1	2610030E23Rik|AU018493|Ccnl|ania-6a	cyclin L1	protein-coding
mm_118408.1	chr13	119488403	119488411	-	1	NA	promoter-TSS (NR_027974)	promoter-TSS (NR_027974)	-23	NR_027974	67304	Mm.474382	NM_026084	ENSMUSG00000074635	3110070M22Rik	-	RIKEN cDNA 3110070M22 gene	ncRNA
mm_125977.1	chr15	76309867	76309877	+	1	NA	Intergenic	Intergenic	-2627	NM_153122	75475	Mm.322738	NM_153122	ENSMUSG00000022562	Oplah	1700010G02Rik	5-oxoprolinase (ATP-hydrolysing)	protein-coding
mm_141356.1	chr17	28691146	28691182	-	1	NA	promoter-TSS (NM_011951)	promoter-TSS (NM_011951)	-178	NM_001168508	26416	Mm.311337	NM_011951	ENSMUSG00000053436	Mapk14	CSBP2|Crk1|Csbp1|Mxi2|PRKM14|PRKM15|p38|p38-alpha|p38MAPK|p38a|p38alpha	mitogen-activated protein kinase 14	protein-coding
mm_129043.1	chr15	75135039	75135070	-	1	NA	Intergenic	Intergenic	-20207	NM_001310438	546644		NM_008531	ENSMUSG00000022582	Ly6g	Gr-1|Gr1|Ly-6G	lymphocyte antigen 6 complex, locus G	protein-coding
mm_118325.1	chr13	113618529	113618539	-	1	NA	promoter-TSS (NM_130796)	promoter-TSS (NM_130796)	30	NM_130796	170625	Mm.33721	NM_130796	ENSMUSG00000042364	Snx18	Snag1	sorting nexin 18	protein-coding
mm_152195.1	chr19	7483200	7483210	-	1	NA	promoter-TSS (NM_053076)	promoter-TSS (NM_053076)	86	NM_001271486	20168	Mm.246990	NM_053076	ENSMUSG00000024758	Rtn3	RTN3-A1	reticulon 3	protein-coding
mm_136922.1	chr17	13846154	13846160	+	1	NA	intron (NM_010806, intron 13 of 32)	intron (NM_010806, intron 13 of 32)	-84763	NM_022311	21646	Mm.486358	NM_022311	ENSMUSG00000038347	Tcte2	AI429268|Tcte-2	t-complex-associated testis expressed 2	protein-coding
mm_72004.1	chr8	70673769	70673784	+	1	NA	intron (NM_015816, intron 1 of 4)	intron (NM_015816, intron 1 of 4)	545	NM_015816	50783	Mm.248188	NM_015816	ENSMUSG00000031848	Lsm4	-	LSM4 homolog, U6 small nuclear RNA and mRNA degradation associated	protein-coding
mm_58462.1	chr7	3366194	3366213	+	1	NA	intron (NM_133189, intron 4 of 4)	intron (NM_133189, intron 4 of 4)	-27839	NM_133190	81905	Mm.357990	NM_133190	ENSMUSG00000053395	Cacng8	-	calcium channel, voltage-dependent, gamma subunit 8	protein-coding
mm_24261.1	chr3	89187432	89187457	+	1	NA	exon (NM_001014995, exon 9 of 12)	exon (NM_001014995, exon 9 of 12)	4219	NM_001014995	68521	Mm.274708	NM_001014995	ENSMUSG00000032657	Fam189b	1110013L07Rik	family with sequence similarity 189, member B	protein-coding
mm_56097.1	chr6	87458098	87458123	-	1	NA	TTS (NM_001286610)	TTS (NM_001286610)	29116	NM_009756	12154	Mm.483321	NM_009756	ENSMUSG00000030046	Bmp10	-	bone morphogenetic protein 10	protein-coding
mm_38956.1	chr4	150652126	150652181	-	1	NA	promoter-TSS (NM_173774)	promoter-TSS (NM_173774)	21	NM_173774	242773	Mm.29280	NM_173774	ENSMUSG00000039838	Slc45a1	C230078B22|Dnb5	solute carrier family 45, member 1	protein-coding
mm_56945.1	chr6	119963835	119963836	-	1	NA	intron (NM_001199084, intron 8 of 27)	intron (NM_001199084, intron 8 of 27)	61137	NM_001166381	19365	Mm.149	NM_011236	ENSMUSG00000030166	Rad52	Rad52yh	RAD52 homolog, DNA repair protein	protein-coding
mm_4663.1	chr1	180368098	180368109	+	1	NA	intron (NM_001081175, intron 2 of 7)	intron (NM_001081175, intron 2 of 7)	-37554	NR_003623	277333	Mm.389223	NM_199472		Gm5069	EG277333	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_90624.1	chr10	128459210	128459220	+	1	NA	promoter-TSS (NM_001114096)	promoter-TSS (NM_001114096)	-21	NM_001114096	68094	Mm.417338	NM_198160	ENSMUSG00000025369	Smarcc2	5930405J04Rik	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2	protein-coding
mm_141129.1	chr17	26201329	26201350	-	1	NA	promoter-TSS (NM_008113)	promoter-TSS (NM_008113)	11	NM_008113	14570	Mm.1383	NM_008113	ENSMUSG00000073433	Arhgdig	Gdi5|RIP2|Rho-GDI-3|Rho-GDI2	Rho GDP dissociation inhibitor (GDI) gamma	protein-coding
mm_57526.1	chr6	126166727	126166761	-	1	NA	promoter-TSS (NM_001164034)	promoter-TSS (NM_001164034)	0	NM_001164034	18205	Mm.267570	NM_008742	ENSMUSG00000049107	Ntf3	AI316846|AI835689|HDNF|NGF-2|Nt3|Ntf-3	neurotrophin 3	protein-coding
mm_27657.1	chr3	64757469	64757470	-	1	NA	intron (NR_003962, intron 2 of 8)	Lx5|LINE|L1	-37867	NM_175674	319217	Mm.246646	NM_175674	ENSMUSG00000062200	Vmn2r7	4933425M15Rik	vomeronasal 2, receptor 7	protein-coding
mm_115042.1	chr13	99641952	99641957	+	1	NA	Intergenic	Intergenic	-125352	NM_008634	17755	Mm.4173	NM_008634	ENSMUSG00000052727	Map1b	A230055D22|AI843217|LC1|MAP5|Mtap-5|Mtap1b|Mtap5	microtubule-associated protein 1B	protein-coding
mm_136623.1	chr17	5538505	5538510	+	1	NA	intron (NM_146073, intron 1 of 8)	URR1A|DNA|hAT-Charlie	45907	NM_146073	224454	Mm.487663	NM_146073	ENSMUSG00000034265	Zdhhc14	B530001K09Rik|New1cp	zinc finger, DHHC domain containing 14	protein-coding
mm_13006.1	chr2	90905044	90905058	+	1	NA	promoter-TSS (NM_026688)	promoter-TSS (NM_026688)	265	NM_025991	67136	Mm.330394	NM_025991	ENSMUSG00000005505	Kbtbd4	2510026C23Rik	kelch repeat and BTB (POZ) domain containing 4	protein-coding
mm_101834.1	chr11	47988963	47988980	-	1	NA	intron (NR_105801, intron 3 of 3)	CpG	85612	NR_105801	102466638		NR_105801	ENSMUSG00000099011	Mir6380	Gm27356|mmu-mir-6380	microRNA 6380	ncRNA
mm_116885.1	chr13	55211355	55211370	-	1	NA	intron (NM_008739, intron 1 of 22)	CpG	1580	NM_008739	18193	Mm.12964	NM_008739	ENSMUSG00000021488	Nsd1	AI528500|KMT3B	nuclear receptor-binding SET-domain protein 1	protein-coding
mm_123064.1	chr14	55672137	55672147	-	1	NA	promoter-TSS (NM_177992)	promoter-TSS (NM_177992)	-93	NM_177992	105446	Mm.390685	NM_177992	ENSMUSG00000002326	Gmpr2	1810008P16Rik|5730544D12Rik|AA959850|GMPR 2	guanosine monophosphate reductase 2	protein-coding
mm_104307.1	chr11	90687573	90687606	-	1	NA	promoter-TSS (NM_028011)	promoter-TSS (NM_028011)	12	NM_028011	71943	Mm.167868	NM_028011	ENSMUSG00000020541	Tom1l1	2310045L10Rik|C80573|Srcasm	target of myb1-like 1 (chicken)	protein-coding
mm_135712.1	chr16	55523782	55523784	-	1	NA	Intergenic	Intergenic	29052	NR_039578	100628589		NR_039578	ENSMUSG00000093292	Mir5118	mmu-mir-5118|mu-mir-5118	microRNA 5118	ncRNA
mm_32474.1	chr4	107802282	107802297	+	1	NA	promoter-TSS (NM_001080926)	promoter-TSS (NM_001080926)	30	NM_001080926	16975	Mm.442134	NM_053073	ENSMUSG00000028613	Lrp8	4932703M08Rik|AA921429|AI848122|ApoER2|Lr8b	low density lipoprotein receptor-related protein 8, apolipoprotein e receptor	protein-coding
mm_137157.1	chr17	23726507	23726514	+	1	NA	5' UTR (NM_023058, exon 1 of 8)	5' UTR (NM_023058, exon 1 of 8)	174	NM_023058	268930	Mm.182193	NM_023058	ENSMUSG00000023908	Pkmyt1	6230424P17|AW209059|Myt1	protein kinase, membrane associated tyrosine/threonine 1	protein-coding
mm_98191.1	chr11	87794044	87794057	+	1	NA	5' UTR (NM_010824, exon 1 of 14)	5' UTR (NM_010824, exon 1 of 14)	266	NM_010824	17523	Mm.4668	NM_010824	ENSMUSG00000009350	Mpo	mKIAA4033	myeloperoxidase	protein-coding
mm_164672.1	chr17	45571463	45571484	-	1	NA	exon (NM_008302, exon 3 of 11)	exon (NM_008302, exon 3 of 11)	1788	NM_008302	15516	Mm.2180	NM_008302	ENSMUSG00000023944	Hsp90ab1	90kDa|AL022974|C81438|Hsp84|Hsp84-1|Hsp90|Hspcb	heat shock protein 90 alpha (cytosolic), class B member 1	protein-coding
mm_32971.1	chr4	120032877	120032907	+	1	NA	intron (NM_010657, intron 2 of 8)	CpG	-128314	NM_007902	13615	Mm.284855	NM_007902	ENSMUSG00000028635	Edn2	ET-2|PPET2|VIC	endothelin 2	protein-coding
mm_80171.1	chr9	71698917	71698925	+	1	NA	intron (NM_001304362, intron 8 of 18)	(CA)n|Simple_repeat|Simple_repeat	72681	NM_026599	68178	Mm.99961	NM_026599	ENSMUSG00000032232	Cgnl1	4933421H10Rik|9930020M10Rik|AI503810|Jacop	cingulin-like 1	protein-coding
mm_149158.1	chr19	9017589	9017591	+	1	NA	promoter-TSS (NR_105786)	promoter-TSS (NR_105786)	-314	NR_105786	102465190		NR_105786	ENSMUSG00000099308	Mir6367	Gm27467|mmu-mir-6367	microRNA 6367	ncRNA
mm_82900.1	chr9	32718109	32718113	-	1	NA	intron (NM_011808, intron 1 of 7)	intron (NM_011808, intron 1 of 7)	22069	NM_001038642	23871	Mm.292415	NM_011808	ENSMUSG00000032035	Ets1	AI196000|AI448617|D230050P06|Ets-1|Tpl1|vs	E26 avian leukemia oncogene 1, 5' domain	protein-coding
mm_21346.1	chr2	157112519	157112535	-	1	NA	intron (NM_018851, intron 9 of 15)	intron (NM_018851, intron 9 of 15)	22695	NM_001139520	56045	Mm.248478	NM_018851	ENSMUSG00000027639	Samhd1	E330031J07Rik|Mg11	SAM domain and HD domain, 1	protein-coding
mm_81366.1	chr9	108786089	108786092	+	1	NA	Intergenic	Intergenic	-9904	NM_029634	76500	Mm.276336	NM_029634	ENSMUSG00000032599	Ip6k2	1500005N04Rik|AW050208|Ihpk2	inositol hexaphosphate kinase 2	protein-coding
mm_69186.1	chr7	127260678	127260706	-	1	NA	promoter-TSS (NM_023203)	promoter-TSS (NM_023203)	-25	NM_023203	66422	Mm.29898	NM_023203	ENSMUSG00000042462	Dctpp1	2410015N17Rik|AI854235|RS21-C6	dCTP pyrophosphatase 1	protein-coding
mm_21162.1	chr2	154603659	154603693	-	1	NA	promoter-TSS (NM_021534)	promoter-TSS (NM_021534)	-3	NM_021534	59038	Mm.24673	NM_021534	ENSMUSG00000000876	Pxmp4	3010018P03Rik|Pmp24	peroxisomal membrane protein 4	protein-coding
mm_169679.1	chr1	56782377	56782377	-	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	-144926	NM_027661	71066	Mm.152656	NM_027661	ENSMUSG00000045336	Hsfy2	4933413G11Rik|Hspy2l	heat shock transcription factor, Y-linked 2	protein-coding
mm_11524.1	chr2	32621751	32621774	+	1	NA	promoter-TSS (NM_001198790)	promoter-TSS (NM_001198790)	4	NM_001198790	11636	Mm.29189	NM_021515	ENSMUSG00000026817	Ak1	Ak-1|B430205N08Rik	adenylate kinase 1	protein-coding
mm_139058.1	chr17	46410887	46410896	+	1	NA	exon (NM_207671, exon 10 of 10)	exon (NM_207671, exon 10 of 10)	-18051	NM_053250	114570	Mm.25168	NM_053250	ENSMUSG00000023968	Crip3	TLP|TLP-A|TLP-B|Tlmp	cysteine-rich protein 3	protein-coding
mm_60268.1	chr7	43841967	43841975	+	1	NA	promoter-TSS (NM_026806)	promoter-TSS (NM_026806)	-298	NM_026806	68668	Mm.458122	NM_026806	ENSMUSG00000074155	Klk5	1110030O19Rik	kallikrein related-peptidase 5	protein-coding
mm_167008.1	chr7	52005779	52005791	-	1	NA	promoter-TSS (NR_027704)	promoter-TSS (NR_027704)	-71	NR_027704	75744	Mm.386823	NM_001160345	ENSMUSG00000074093	Svip	1700006C13Rik|6620401M08Rik	small VCP/p97-interacting protein	protein-coding
mm_104757.1	chr11	98463895	98463905	-	1	NA	TTS (NM_011771)	TTS (NM_011771)	17066	NM_010346	14786	Mm.276702	NM_010346	ENSMUSG00000019312	Grb7	mKIAA4028	growth factor receptor bound protein 7	protein-coding
mm_108282.1	chr12	79069810	79069813	+	1	NA	intron (NM_181073, intron 17 of 28)	intron (NM_181073, intron 17 of 28)	19859	NM_029988	110417	Mm.268317	NM_029988	ENSMUSG00000021120	Pigh	2210416H01Rik|A930028P05Rik	phosphatidylinositol glycan anchor biosynthesis, class H	protein-coding
mm_170441.1	chr18	80186209	80186211	+	1	NA	promoter-TSS (NR_131039)	promoter-TSS (NR_131039)	-29	NR_131039	105246506	Mm.392326	NR_131039		LOC105246506	-	uncharacterized LOC105246506	ncRNA
mm_60162.1	chr7	39588526	39588545	+	1	NA	Intergenic	Intergenic	70769	NM_001004139	70227	Mm.333800	NM_001004139	ENSMUSG00000068959	Zfp619	3000002G13Rik	zinc finger protein 619	protein-coding
mm_153737.1	chr19	44545837	44545871	-	1	NA	promoter-TSS (NM_001033343)	promoter-TSS (NM_001033343)	-6	NM_001033343	240667	Mm.329873	NM_001033343	ENSMUSG00000051984	Sec31b	Gm341|Sec31l2	Sec31 homolog B (S. cerevisiae)	protein-coding
mm_132265.1	chr16	32822088	32822088	+	1	NA	3' UTR (NM_001200038, exon 20 of 20)	3' UTR (NM_001200038, exon 20 of 20)	-11642	NM_001256309	381043	Mm.303864	NM_001256309	ENSMUSG00000094430	Gm933	Gm1743	predicted gene 933	protein-coding
mm_152900.1	chr19	25096456	25096470	-	1	NA	intron (NM_028785, intron 11 of 47)	intron (NM_028785, intron 11 of 47)	96934	NM_028785	76088	Mm.102485	NM_028785	ENSMUSG00000052085	Dock8	1200017A24Rik|5830472H07Rik|A130095G14Rik|AI461977	dedicator of cytokinesis 8	protein-coding
mm_4682.1	chr1	180579291	180579310	+	1	NA	exon (NM_007415, exon 4 of 23)	exon (NM_007415, exon 4 of 23)	-7901	NR_105869	102466761		NR_105869	ENSMUSG00000098926	Mir6904	Gm27426|mmu-mir-6904	microRNA 6904	ncRNA
mm_110296.1	chr12	32208610	32208683	-	1	NA	promoter-TSS (NM_001146201)	promoter-TSS (NM_001146201)	3	NM_001146200	30955	Mm.101369	NM_020272	ENSMUSG00000020573	Pik3cg	5830428L06Rik|PI3Kgamma|p110gamma	phosphoinositide-3-kinase, catalytic, gamma polypeptide	protein-coding
mm_116949.1	chr13	56135630	56135655	-	1	NA	promoter-TSS (NM_001159515)	promoter-TSS (NM_001159515)	-92	NM_001159513	26914	Mm.283802	NM_012015	ENSMUSG00000015937	H2afy	H2AF12M|mH2a1|macroH2A1	H2A histone family, member Y	protein-coding
mm_20017.1	chr2	119278005	119278015	-	1	NA	Intergenic	Intergenic	-6784	NM_145530	228543	Mm.120274	NM_145530	ENSMUSG00000034226	Rhov	A030005A06Rik|Arhv	ras homolog family member V	protein-coding
mm_156791.1	chrX	162760389	162760415	+	1	NA	promoter-TSS (NM_009031)	promoter-TSS (NM_009031)	30	NM_009031	245688	Mm.270186	NM_009031	ENSMUSG00000031353	Rbbp7	AA409861|AI173248|AU019541|BB114024|mRbAp46	retinoblastoma binding protein 7	protein-coding
mm_84276.1	chr9	62811427	62811476	-	1	NA	5' UTR (NM_010193, exon 1 of 2)	5' UTR (NM_010193, exon 1 of 2)	197	NM_010193	14155	Mm.24069	NM_010193	ENSMUSG00000032244	Fem1b	mKIAA0396	feminization 1 homolog b (C. elegans)	protein-coding
mm_69721.1	chr7	140357083	140357110	-	1	NA	Intergenic	L1MA4|LINE|L1	-11109	NM_146955	18361	Mm.222844	NM_146955	ENSMUSG00000060112	Olfr60	IH6|MOR253-6	olfactory receptor 60	protein-coding
mm_56683.1	chr6	113910472	113910484	-	1	NA	intron (NM_001347365, intron 2 of 23)	intron (NM_001347365, intron 2 of 23)	-18939	NM_001036684	11941	Mm.321755	NM_009723	ENSMUSG00000030302	Atp2b2	D6Abb2e|Gena300|PMCA2|Tmy|dfw|jog|wms|wri	ATPase, Ca++ transporting, plasma membrane 2	protein-coding
mm_103074.1	chr11	69892112	69892115	-	1	NA	intron (NM_153788, intron 2 of 21)	B1_Mur1|SINE|Alu	3426	NM_153788	216859	Mm.288671	NM_153788	ENSMUSG00000001588	Acap1	Centb1	ArfGAP with coiled-coil, ankyrin repeat and PH domains 1	protein-coding
mm_41636.1	chr5	97264745	97264750	+	1	NA	Intergenic	7SK|RNA|RNA	127583	NM_001033191	97243	Mm.11746	NM_001033191	ENSMUSG00000046000	Naa11	Ard1b|Ard2|C80008	N(alpha)-acetyltransferase 11, NatA catalytic subunit	protein-coding
mm_157649.1	chrX	57326149	57326206	-	1	NA	intron (NM_152801, intron 2 of 21)	intron (NM_152801, intron 2 of 21)	12552	NM_152801	73341	Mm.261443	NM_152801	ENSMUSG00000031133	Arhgef6	1600028C08Rik|1700038J06Rik|4930592P22Rik|alpha-PIX	Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_52774.1	chr6	121210772	121210786	+	1	NA	promoter-TSS (NM_017379)	promoter-TSS (NM_017379)	45	NM_017379	53857	Mm.32884	NM_017379	ENSMUSG00000030137	Tuba8	-	tubulin, alpha 8	protein-coding
mm_36585.1	chr4	88416088	88416100	-	1	NA	intron (NM_025760, intron 6 of 6)	L1MA6|LINE|L1	22832	NM_025760	66775	Mm.386788	NM_025760	ENSMUSG00000028497	Hacd4	4933428I03Rik|Hcad4|Ptplad2	3-hydroxyacyl-CoA dehydratase 4	protein-coding
mm_8518.1	chr1	154816932	154816955	-	1	NA	Intergenic	MIR|SINE|MIR	-91023	NM_009782	12290	Mm.267517	NM_009782	ENSMUSG00000004110	Cacna1e	A430040I15|BII|Cach6|Cacnl1a6|Cav2.3|Cchra1|alpha1E	calcium channel, voltage-dependent, R type, alpha 1E subunit	protein-coding
mm_45218.1	chr5	53213269	53213290	-	1	NA	exon (NM_172710, exon 1 of 24)	exon (NM_172710, exon 1 of 24)	173	NM_172710	231238	Mm.235020	NM_172710	ENSMUSG00000029189	Sel1l3	2310045A20Rik|AI429585|mKIAA0746	sel-1 suppressor of lin-12-like 3 (C. elegans)	protein-coding
mm_133192.1	chr16	72765071	72765076	+	1	NA	intron (NM_019413, intron 2 of 28)	intron (NM_019413, intron 2 of 28)	101924	NM_019413	19876	Mm.310772	NM_019413	ENSMUSG00000022883	Robo1	AW494633|AW742721|DUTT1|Gm310	roundabout guidance receptor 1	protein-coding
mm_137287.1	chr17	24736674	24736695	+	1	NA	promoter-TSS (NM_001346668)	promoter-TSS (NM_001346668)	91	NM_001346668	27361	Mm.28212	NM_013759	ENSMUSG00000075705	Msrb1	D17Wsu82e|SELX|SelR|Sepr|Sepx1	methionine sulfoxide reductase B1	protein-coding
mm_44540.1	chr5	24540440	24540451	-	1	NA	promoter-TSS (NM_080444)	promoter-TSS (NM_080444)	12	NM_080444	117590	Mm.207071	NM_080444	ENSMUSG00000038204	Asb10	Asb-10|BB137407	ankyrin repeat and SOCS box-containing 10	protein-coding
mm_95773.1	chr11	54909464	54909476	+	1	NA	exon (NM_008161, exon 5 of 5)	exon (NM_008161, exon 5 of 5)	6616	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_44129.1	chr5	149678225	149678241	+	1	NA	promoter-TSS (NM_001081204)	promoter-TSS (NM_001081204)	-24	NM_001081204	381694	Mm.45060	NM_001081204	ENSMUSG00000051950	B3glct	B3galtl|Gm1057	beta-3-glucosyltransferase	protein-coding
mm_72621.1	chr8	84638597	84638611	+	1	NA	intron (NM_001252059, intron 44 of 45)	intron (NM_001252059, intron 44 of 45)	24248	NM_010499	15936	Mm.399	NM_010499	ENSMUSG00000053560	Ier2	AI317238|Ch1|Pip92	immediate early response 2	protein-coding
mm_134797.1	chr16	24216494	24216531	-	1	NA	Intergenic	Intergenic	-176838	NM_178665	210126	Mm.209385	NM_178665	ENSMUSG00000033306	Lpp	9430020K16Rik|AA959454|AU024130|B130055L10Rik|C79715|D630048H16	LIM domain containing preferred translocation partner in lipoma	protein-coding
mm_128840.1	chr15	68393044	68393066	-	1	NA	Intergenic	Intergenic	-51766	NR_029718	387228		NR_029718	ENSMUSG00000065437	Mir30d	Mirn30d|mir-30d|mmu-mir-30d	microRNA 30d	ncRNA
mm_45435.1	chr5	67099236	67099255	-	1	NA	promoter-TSS (NM_008888)	promoter-TSS (NM_008888)	-119	NM_008888	18935	Mm.62505	NM_008888	ENSMUSG00000012520	Phox2b	Dilp1|NBPhox|Pmx2b|Px2b	paired-like homeobox 2b	protein-coding
mm_52994.1	chr6	123267142	123267149	+	1	NA	exon (NM_010819, exon 3 of 6)	exon (NM_010819, exon 3 of 6)	5038	NM_010819	17474	Mm.441101	NM_010819	ENSMUSG00000030144	Clec4d	Clecsf8|Mpcl|mcl	C-type lectin domain family 4, member d	protein-coding
mm_60461.1	chr7	44477767	44477777	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-6745	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_154366.1	chrM	8619	8619	+	1	NA	NA	Intergenic	NA	NA								
mm_164741.1	chr17	73637025	73637031	-	1	NA	intron (NM_027864, intron 1 of 14)	intron (NM_027864, intron 1 of 14)	73423	NM_027864	71685	Mm.271953	NM_027864	ENSMUSG00000024064	Galnt14	0610033M06Rik	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 14	protein-coding
mm_3941.1	chr1	163779710	163779744	+	1	NA	5' UTR (NM_010629, exon 1 of 21)	5' UTR (NM_010629, exon 1 of 21)	144	NM_010629	16579	Mm.4651	NM_010629	ENSMUSG00000026585	Kifap3	KAP-3|KAP3|SMAP	kinesin-associated protein 3	protein-coding
mm_103513.1	chr11	76726908	76726912	-	1	NA	3' UTR (NM_016810, exon 9 of 9)	3' UTR (NM_016810, exon 9 of 9)	36645	NM_016810	53334	Mm.20931	NM_016810	ENSMUSG00000010392	Gosr1	AI414660|AI426320|BB145494|GOS-28|GOSRI|GS28	golgi SNAP receptor complex member 1	protein-coding
mm_29956.1	chr3	133234837	133234839	-	1	NA	promoter-TSS (NM_029953)	promoter-TSS (NM_029953)	51	NM_029953	77669	Mm.98630	NM_029953	ENSMUSG00000040969	Arhgef38	9130221D24Rik|D630013G24Rik	Rho guanine nucleotide exchange factor (GEF) 38	protein-coding
mm_104194.1	chr11	87875525	87875534	-	1	NA	promoter-TSS (NM_007946)	promoter-TSS (NM_007946)	7	NM_007946	13861	Mm.1315	NM_007946	ENSMUSG00000052234	Epx	EPO	eosinophil peroxidase	protein-coding
mm_127610.1	chr15	102459484	102459510	+	1	NA	5' UTR (NM_025385, exon 2 of 5)	5' UTR (NM_025385, exon 2 of 5)	327	NM_025385	66151	Mm.393955	NM_025385	ENSMUSG00000023048	Prr13	1110020C13Rik|2010324E22Rik	proline rich 13	protein-coding
mm_45943.1	chr5	90254771	90254812	-	1	NA	exon (NM_030886, exon 25 of 34)	exon (NM_030886, exon 25 of 34)	-30795	NM_001163456	231430	Mm.319697	NM_001033310	ENSMUSG00000035505	Cox18	BC038311	cytochrome c oxidase assembly protein 18	protein-coding
mm_62744.1	chr7	111080176	111080193	+	1	NA	exon (NM_013507, exon 4 of 22)	exon (NM_013507, exon 4 of 22)	2846	NM_001040131	13690	Mm.185453	NM_013507	ENSMUSG00000005610	Eif4g2	DAP-5|E130105L11Rik|Nat1|Natm1|p97	eukaryotic translation initiation factor 4, gamma 2	protein-coding
mm_60152.1	chr7	39449480	39449523	+	1	NA	promoter-TSS (NM_001243021)	promoter-TSS (NM_001243021)	-17	NM_001243021	233147	Mm.148946	NM_001243021	ENSMUSG00000030424	Zfp939	9430025M13Rik	zinc finger protein 939	protein-coding
mm_66667.1	chr7	45717959	45717974	-	1	NA	promoter-TSS (NM_001172561)	promoter-TSS (NM_001172561)	36	NM_203280	56632	Mm.24222	NM_020011	ENSMUSG00000057342	Sphk2	C76851	sphingosine kinase 2	protein-coding
mm_29458.1	chr3	113565012	113565022	-	1	NA	exon (NM_007446, exon 4 of 11)	exon (NM_007446, exon 4 of 11)	9745	NM_007446	11722	Mm.439727	NM_007446	ENSMUSG00000074264	Amy1	Amy-1|Amy1a|C030014B17Rik	amylase 1, salivary	protein-coding
mm_68345.1	chr7	106506549	106506575	-	1	NA	Intergenic	Intergenic	-65489	NR_003967	209380	Mm.461779	NM_001001318		Gm4759	EG209380	GTPase, very large interferon inducible 1 pseudogene	pseudo
mm_9660.1	chr1	177796452	177796514	-	1	NA	promoter-TSS (NM_007422)	promoter-TSS (NM_007422)	26	NM_007422	11566	Mm.338021	NM_007422	ENSMUSG00000015961	Adss	AI314886|AS|Adss2	adenylosuccinate synthetase, non muscle	protein-coding
mm_157562.1	chrX	52165346	52165362	-	1	NA	promoter-TSS (NM_008150)	promoter-TSS (NM_008150)	-431	NM_008150	14735	Mm.1528	NM_008150	ENSMUSG00000031119	Gpc4	9530073D23Rik|AF311610|AI385680|AI661372|K-glypican	glypican 4	protein-coding
mm_64964.1	chr7	16614850	16614860	-	1	NA	5' UTR (NM_172739, exon 1 of 7)	5' UTR (NM_172739, exon 1 of 7)	138	NM_172739	232906	Mm.28646	NM_172739	ENSMUSG00000058230	Arhgap35	6430596G11Rik|AI841135|Grlf1|mKIAA1722|p190A|p190RhoGAP	Rho GTPase activating protein 35	protein-coding
mm_3352.1	chr1	138163115	138163127	+	1	NA	intron (NM_001111316, intron 1 of 31)	intron (NM_001111316, intron 1 of 31)	12005	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_168577.1	chr1	171503161	171503171	-	1	NA	promoter-TSS (NM_019484)	promoter-TSS (NM_019484)	-312	NM_019484	56009	Mm.389208	NM_019484	ENSMUSG00000060244	Alyref2	C130042O11Rik|REF2|Refbp2	Aly/REF export factor 2	protein-coding
mm_106240.1	chr11	117780589	117780606	-	1	NA	promoter-TSS (NM_181321)	promoter-TSS (NM_181321)	24	NM_181321	217353	Mm.286963	NM_145439	ENSMUSG00000025572	Tmc6	D11Ertd204e|EVER1	transmembrane channel-like gene family 6	protein-coding
mm_155073.1	chrX	45090883	45090893	+	1	NA	promoter-TSS (NM_026841)	promoter-TSS (NM_026841)	-16	NM_026841	68800	Mm.336041	NM_026841	ENSMUSG00000037086	Prr32	1110059M19Rik	proline rich 32	protein-coding
mm_138455.1	chr17	35136092	35136123	+	1	NA	intron (NM_001252469, intron 1 of 23)	intron (NM_001252469, intron 1 of 23)	393	NM_001252469	224727	Mm.203962	NM_057171	ENSMUSG00000024392	Bag6	2410045D21Rik|AA408914|BAG-6|Bat3|D17H6S52E|G3|Scythe	BCL2-associated athanogene 6	protein-coding
mm_87489.1	chr10	51494723	51494748	+	1	NA	intron (NM_001291894, intron 6 of 8)	intron (NM_001291894, intron 6 of 8)	3837	NM_013532	14728	Mm.34408	NM_013532	ENSMUSG00000062593	Lilrb4a	CD85K|Gp49b|HM18|ILT3|LIR-5|Lilrb4|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4A	protein-coding
mm_134457.1	chr16	18411920	18411930	-	1	NA	exon (NM_001111062, exon 3 of 6)	exon (NM_001111062, exon 3 of 6)	1569	NM_001111063	12846	Mm.100940	NM_007744	ENSMUSG00000000326	Comt	Comt1|D16Wsu103e|D330014B15Rik	catechol-O-methyltransferase	protein-coding
mm_147598.1	chr18	56708863	56708892	-	1	NA	intron (NM_010721, intron 1 of 10)	CpG	1064	NM_010721	16906	Mm.4105	NM_010721	ENSMUSG00000024590	Lmnb1	-	lamin B1	protein-coding
mm_15153.1	chr2	154008257	154008274	+	1	NA	promoter-TSS (NM_008953)	promoter-TSS (NM_008953)	-11	NM_008953	19194	Mm.29197	NM_008953	ENSMUSG00000042459	Bpifa2	Bpifa2e|Psp	BPI fold containing family A, member 2	protein-coding
mm_124460.1	chr14	120774607	120774609	-	1	NA	Intergenic	RLTR9A3B|LTR|ERVK	-136586	NM_023579	70572	Mm.221452	NM_023579	ENSMUSG00000030662	Ipo5	1110011C18Rik|5730478E03Rik|AA409333|C76941|IMB3|Kpnb3|Ranbp5	importin 5	protein-coding
mm_65180.1	chr7	19696339	19696362	-	1	NA	3' UTR (NM_009696, exon 4 of 4)	3' UTR (NM_009696, exon 4 of 4)	2048	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_31597.1	chr4	57892998	57893008	+	1	NA	3' UTR (NM_001035533, exon 4 of 4)	3' UTR (NM_001035533, exon 4 of 4)	23261	NM_178727	242484	Mm.23214	NM_178727	ENSMUSG00000052117	D630039A03Rik	-	RIKEN cDNA D630039A03 gene	protein-coding
mm_132885.1	chr16	48818876	48818898	+	1	NA	TTS (NM_023881)	TTS (NM_023881)	2031	NM_023881	57263	Mm.21123	NM_023881	ENSMUSG00000022650	Retnlb	9030012B21Rik|Fizz2|RELMbeta|Relmb|Xcp3	resistin like beta	protein-coding
mm_79990.1	chr9	67031449	67031482	+	1	NA	exon (NM_001164251, exon 7 of 10)	exon (NM_001164251, exon 7 of 10)	12406	NM_001164252	22003	Mm.121878	NM_024427	ENSMUSG00000032366	Tpm1	AA986836|AI854628|TM2|Tm3|Tmpa|Tpm-1|alpha-TM	tropomyosin 1, alpha	protein-coding
mm_157058.1	chrX	8132398	8132424	-	1	NA	5' UTR (NM_026137, exon 1 of 9)	5' UTR (NM_026137, exon 1 of 9)	447	NM_001290783	73447	Mm.284162	NM_026137	ENSMUSG00000031166	Wdr13	1700060B08Rik|5730411P10Rik|DXHXS7467e|W51679|mMg21	WD repeat domain 13	protein-coding
mm_96476.1	chr11	67652836	67652858	+	1	NA	intron (NM_001109657, intron 4 of 13)	intron (NM_001109657, intron 4 of 13)	-42479	NM_009038	19674	Mm.439726	NM_009038	ENSMUSG00000020907	Rcvrn	CAR|S-modulin	recoverin	protein-coding
mm_34763.1	chr4	152477733	152477766	+	1	NA	promoter-TSS (NM_010598)	promoter-TSS (NM_010598)	-200	NM_010598	16498	Mm.388924	NM_010598	ENSMUSG00000028931	Kcnab2	F5|I2rf5|Kcnb3|kv-beta-2	potassium voltage-gated channel, shaker-related subfamily, beta member 2	protein-coding
mm_99585.1	chr11	104296012	104296059	+	1	NA	intron (NM_001038609, intron 5 of 11)	intron (NM_001038609, intron 5 of 11)	64599	NM_001285454	17762	Mm.1287	NM_010838	ENSMUSG00000018411	Mapt	AI413597|AW045860|Mtapt|Tau	microtubule-associated protein tau	protein-coding
mm_91826.1	chr10	56355099	56355100	-	1	NA	Intergenic	Intergenic	-22201	NM_010288	14609	Mm.378921	NM_010288	ENSMUSG00000050953	Gja1	AU042049|AW546267|Cnx43|Cx43|Cx43alpha1|Gja-1|Npm1|connexin43	gap junction protein, alpha 1	protein-coding
mm_77309.1	chr8	117671527	117671555	-	1	NA	promoter-TSS (NM_028725)	promoter-TSS (NM_028725)	-26	NM_028725	74032	Mm.296302	NM_028725	ENSMUSG00000034308	Sdr42e1	4632417N05Rik|AI117603	short chain dehydrogenase/reductase family 42E, member 1	protein-coding
mm_52786.1	chr6	121257196	121257214	+	1	NA	intron (NM_011909, intron 4 of 10)	B1F2|SINE|Alu	11299	NM_011909	24110	Mm.326911	NM_011909	ENSMUSG00000030107	Usp18	1110058H21Rik|AW047653|UBP43|Ubp15	ubiquitin specific peptidase 18	protein-coding
mm_160859.1	chr11	59228197	59228197	-	1	NA	promoter-TSS (NM_007476)	promoter-TSS (NM_007476)	-35	NM_001130408	11840	Mm.371546	NM_007476	ENSMUSG00000048076	Arf1	-	ADP-ribosylation factor 1	protein-coding
mm_125196.1	chr15	32778935	32778959	+	1	NA	Intergenic	Intergenic	-141776	NM_008304	15529	Mm.234266	NM_008304	ENSMUSG00000022261	Sdc2	4833414L08Rik|AA960457|Hspg1|Synd2|syndecan-2	syndecan 2	protein-coding
mm_125797.1	chr15	74835388	74835404	+	1	NA	3' UTR (NM_001033229, exon 9 of 9)	3' UTR (NM_001033229, exon 9 of 9)	6247	NM_001033229	110115	Mm.322606	NM_001033229	ENSMUSG00000075604	Cyp11b1	AA389061|CPN1|Cyp11b|Cyp11b-1|FHI	cytochrome P450, family 11, subfamily b, polypeptide 1	protein-coding
mm_150502.1	chr19	39022105	39022124	+	1	NA	intron (NM_028089, intron 4 of 8)	B3|SINE|B2	15095	NM_028089	72082	Mm.142581	NM_028089	ENSMUSG00000025002	Cyp2c55	2010318C06Rik	cytochrome P450, family 2, subfamily c, polypeptide 55	protein-coding
mm_45348.1	chr5	65858219	65858240	-	1	NA	Intergenic	Intergenic	-5340	NM_001081105	74734	Mm.20323	NM_001081105	ENSMUSG00000029204	Rhoh	5830400A04Rik|AU019774|Arhh	ras homolog family member H	protein-coding
mm_44843.1	chr5	34187086	34187105	-	1	NA	intron (NM_010753, intron 2 of 5)	CpG	615	NM_010753	17122	Mm.259260	NM_010753	ENSMUSG00000037235	Mxd4	2810410A03Rik|Mad4|bHLHc12	Max dimerization protein 4	protein-coding
mm_30128.1	chr3	141931878	141931880	-	1	NA	promoter-TSS (NM_001277220)	promoter-TSS (NM_001277220)	-291	NM_001277220	12167	Mm.39089	NM_007560	ENSMUSG00000052430	Bmpr1b	AI385617|ALK-6|AV355320|Acvrlk6|Alk6|BMPR-1B|BMPR-IB|CFK-43a|SKR6	bone morphogenetic protein receptor, type 1B	protein-coding
mm_103563.1	chr11	77801216	77801250	-	1	NA	promoter-TSS (NM_001291215)	promoter-TSS (NM_001291215)	-65	NM_001291214	360013	Mm.341248	NM_011586	ENSMUSG00000000631	Myo18a	MAJN|MyoPDZ|MysPDZ|SP-R210	myosin XVIIIA	protein-coding
mm_95281.1	chr11	45890595	45890637	+	1	NA	intron (NM_001346760, intron 5 of 11)	intron (NM_001346760, intron 5 of 11)	38652	NM_001045520	216705	Mm.169673	NM_001045520	ENSMUSG00000006169	Clint1	AI642036|AW537616|C530049I24Rik|Enth|Epn4|F630206G17Rik|mKIAA0171	clathrin interactor 1	protein-coding
mm_119273.1	chr14	34170641	34170641	+	1	NA	Intergenic	Intergenic	-18222	NM_008919	19065	Mm.57059	NM_008919	ENSMUSG00000048337	Npy4r	NYYR-D|Ppyr1|Y4	neuropeptide Y receptor Y4	protein-coding
mm_121646.1	chr14	9529352	9529368	-	1	NA	Intergenic	Intergenic	-354735	NR_030680	100042415	Mm.235938	NR_030680		Mnd1-ps	Gm3833	Mnd1 retrotransposed pseudogene	pseudo
mm_154991.1	chrX	38320478	38320479	+	1	NA	intron (NM_133690, intron 1 of 7)	intron (NM_133690, intron 1 of 7)	4356	NM_133690	67821	Mm.60134	NM_133690	ENSMUSG00000016327	Atp1b4	1110020B02Rik	ATPase, (Na+)/K+ transporting, beta 4 polypeptide	protein-coding
mm_103391.1	chr11	75422525	75422561	-	1	NA	promoter-TSS (NM_011340)	promoter-TSS (NM_011340)	80	NM_011340	20317	Mm.2044	NM_011340	ENSMUSG00000000753	Serpinf1	AI195227|EPC-1|Pedf|Pedfl|Sdf3	serine (or cysteine) peptidase inhibitor, clade F, member 1	protein-coding
mm_156682.1	chrX	159364922	159364931	+	1	NA	3' UTR (NM_148945, exon 22 of 22)	3' UTR (NM_148945, exon 22 of 22)	-7269	NM_025437	66235	Mm.294623	NM_025437	ENSMUSG00000067194	Eif1ax	1500010B24Rik|AI426898|Eif1ay	eukaryotic translation initiation factor 1A, X-linked	protein-coding
mm_2364.1	chr1	93135245	93135256	+	1	NA	promoter-TSS (NM_016702)	promoter-TSS (NM_016702)	10	NM_001276710	11611	Mm.7457	NM_016702	ENSMUSG00000026272	Agxt	AGT|Agt1|Agxt1|SPT	alanine-glyoxylate aminotransferase	protein-coding
mm_93856.1	chr10	122097043	122097073	-	1	NA	promoter-TSS (NM_153059)	promoter-TSS (NM_153059)	44	NM_153059	216395	Mm.236764	NM_153059	ENSMUSG00000034620	Tmem5	6330415D21Rik	transmembrane protein 5	protein-coding
mm_154562.1	chrX	6400028	6400061	+	1	NA	promoter-TSS (NM_001040459)	promoter-TSS (NM_001040459)	12	NM_001040459	208431	Mm.23208	NM_001040459	ENSMUSG00000068270	Shroom4	D430043L16Rik|Gm724|Shrm4	shroom family member 4	protein-coding
mm_132807.1	chr16	45158955	45159001	+	1	NA	promoter-TSS (NM_028756)	promoter-TSS (NM_028756)	149	NM_026402	67841	Mm.41775	NM_026402	ENSMUSG00000022663	Atg3	2610016C12Rik|APG3|Apg3l|Atg3l|PC3-96	autophagy related 3	protein-coding
mm_15616.1	chr2	160880729	160880747	+	1	NA	promoter-TSS (NM_022883)	promoter-TSS (NM_022883)	68	NM_022883	64899	Mm.292111	NM_022883	ENSMUSG00000027412	Lpin3	9130206L11Rik|AA438110|AV236139|mKIAA4023	lipin 3	protein-coding
mm_94703.1	chr11	20227922	20227945	+	1	NA	3' UTR (NM_172260, exon 7 of 7)	3' UTR (NM_172260, exon 7 of 7)	21491	NM_172260	216543	Mm.260314	NM_172260	ENSMUSG00000044066	Cep68	6030463E10Rik|AI481761|BC027174|Kiaa0582	centrosomal protein 68	protein-coding
mm_18612.1	chr2	68389485	68389488	-	1	NA	intron (NM_016866, intron 5 of 17)	B1_Mm|SINE|Alu	82495	NM_016866	53416	Mm.198414	NM_016866	ENSMUSG00000027030	Stk39	AW227544|AW556857|DCHT|RF005|Rnl5|SPAK	serine/threonine kinase 39	protein-coding
mm_25545.1	chr3	115887872	115887882	+	1	NA	promoter-TSS (NM_027193)	promoter-TSS (NM_027193)	182	NR_027894	68161	Mm.392043	NR_015487	ENSMUSG00000054426	A930005H10Rik	-	RIKEN cDNA A930005H10 gene	ncRNA
mm_65898.1	chr7	30187393	30187409	-	1	NA	3' UTR (NM_009795, exon 11 of 11)	3' UTR (NM_009795, exon 11 of 11)	3230	NM_009944	12865	Mm.423030	NM_009944	ENSMUSG00000074218	Cox7a1	COX7A|COX7AH|COX7AM	cytochrome c oxidase subunit VIIa 1	protein-coding
mm_154705.1	chrX	8272274	8272304	+	1	NA	intron (NM_172479, intron 3 of 15)	intron (NM_172479, intron 3 of 15)	908	NM_172479	209837	Mm.6055	NM_172479	ENSMUSG00000031170	Slc38a5	C81234|E330031E14|JM24|SN2	solute carrier family 38, member 5	protein-coding
mm_129359.1	chr15	77945873	77945894	-	1	NA	intron (NM_001168260, intron 7 of 8)	intron (NM_001168260, intron 7 of 8)	10839	NM_001168260	239554	Mm.295605	NM_001017983	ENSMUSG00000016552	Foxred2	A430097D04Rik|D15Bwg0759e|Gm304	FAD-dependent oxidoreductase domain containing 2	protein-coding
mm_128497.1	chr15	51978125	51978139	-	1	NA	exon (NM_009009, exon 3 of 14)	exon (NM_009009, exon 3 of 14)	13628	NM_009009	19357	Mm.182628	NM_009009	ENSMUSG00000022314	Rad21	SCC1|mKIAA0078	RAD21 cohesin complex component	protein-coding
mm_107137.1	chr12	21316409	21316435	+	1	NA	promoter-TSS (NM_026347)	promoter-TSS (NM_026347)	30	NM_026347	67732	Mm.335830	NM_026347	ENSMUSG00000062054	Iah1	1500019E20Rik|4833421E05Rik	isoamyl acetate-hydrolyzing esterase 1 homolog	protein-coding
mm_139094.1	chr17	46890654	46890692	+	1	NA	promoter-TSS (NM_178385)	promoter-TSS (NM_178385)	52	NM_178385	72726	Mm.33780	NM_178385	ENSMUSG00000036430	Tbcc	2810055C19Rik	tubulin-specific chaperone C	protein-coding
mm_68277.1	chr7	105599287	105599291	-	1	NA	exon (NM_017371, exon 4 of 10)	exon (NM_017371, exon 4 of 10)	827	NM_017371	15458	Mm.3485	NM_017371	ENSMUSG00000030895	Hpx	Hpxn|hx	hemopexin	protein-coding
mm_69694.1	chr7	139999090	139999103	-	1	NA	intron (NM_133755, intron 14 of 17)	intron (NM_133755, intron 14 of 17)	-6534	NM_001291066	11501	Mm.15969	NM_007403	ENSMUSG00000025473	Adam8	ADAM 8|CD156|CD156a|E430039A18Rik|MS2	a disintegrin and metallopeptidase domain 8	protein-coding
mm_17842.1	chr2	34371927	34371991	-	1	NA	promoter-TSS (NM_001290576)	promoter-TSS (NM_001290576)	86	NM_001290576	18516	Mm.239941	NM_016768	ENSMUSG00000038718	Pbx3	-	pre B cell leukemia homeobox 3	protein-coding
mm_107338.1	chr12	32379071	32379101	+	1	NA	exon (NM_001162903, exon 1 of 1)	exon (NM_001162903, exon 1 of 1)	297	NM_001162903	72123	Mm.341352	NM_028111	ENSMUSG00000090946	Ccdc71l	2010109K11Rik|AV375874	coiled-coil domain containing 71 like	protein-coding
mm_142846.1	chr17	51797030	51797038	-	1	NA	intron (NM_009122, intron 5 of 10)	intron (NM_009122, intron 5 of 10)	15020	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_57106.1	chr6	122591489	122591502	-	1	NA	intron (NM_031159, intron 3 of 7)	intron (NM_031159, intron 3 of 7)	10949	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_76574.1	chr8	89006613	89006623	-	1	NA	Intergenic	CpG	-18117	NR_106190	102465899		NR_106190	ENSMUSG00000099078	Mir8110	Gm27571|mmu-mir-8110	microRNA 8110	ncRNA
mm_120644.1	chr14	70528506	70528546	+	1	NA	Intergenic	Intergenic	-2295	NM_145219	213469	Mm.41708	NM_145219	ENSMUSG00000033595	Lgi3	AI841179|AW049851	leucine-rich repeat LGI family, member 3	protein-coding
mm_159625.1	chr4	135965140	135965140	+	1	NA	promoter-TSS (NM_178389)	promoter-TSS (NM_178389)	-25	NM_178389	74246	Mm.247946	NM_178389	ENSMUSG00000028671	Gale	2310002A12Rik|AI323962	galactose-4-epimerase, UDP	protein-coding
mm_95644.1	chr11	53721904	53721929	+	1	NA	intron (NM_010558, intron 2 of 3)	intron (NM_010558, intron 2 of 3)	1122	NM_010558	16191	Mm.4461	NM_010558	ENSMUSG00000036117	Il5	Il-5	interleukin 5	protein-coding
mm_149308.1	chr19	10740936	10740949	+	1	NA	promoter-TSS (NR_027805)	promoter-TSS (NR_027805)	-5	NR_027805	403202	Mm.34482	NM_207529	ENSMUSG00000067577	A430093F15Rik	Gm674	RIKEN cDNA A430093F15 gene	ncRNA
mm_17311.1	chr2	26409101	26409133	-	1	NA	promoter-TSS (NM_001290437)	promoter-TSS (NM_001290437)	10	NM_001290437	64436	Mm.330070	NM_033134	ENSMUSG00000026925	Inpp5e	1200002L24Rik|72kDa|mKIAA0123	inositol polyphosphate-5-phosphatase E	protein-coding
mm_81716.1	chr9	111351962	111351970	+	1	NA	intron (NM_001164659, intron 7 of 21)	intron (NM_001164659, intron 7 of 21)	40227	NM_001164659	320429	Mm.270754	NM_001164659	ENSMUSG00000062296	Trank1	A230061D21Rik|C030048J01Rik|Gm187|Lba1	tetratricopeptide repeat and ankyrin repeat containing 1	protein-coding
mm_94070.1	chr10	128401240	128401252	-	1	NA	promoter-TSS (NM_028092)	promoter-TSS (NM_028092)	-22	NM_001136237	72002	Mm.22983	NM_028051	ENSMUSG00000039878	Slc39a5	1810013D05Rik|2010205A06Rik|Zip5	solute carrier family 39 (metal ion transporter), member 5	protein-coding
mm_110664.1	chr12	59219730	59219776	-	1	NA	promoter-TSS (NM_001033156)	promoter-TSS (NM_001033156)	-270	NM_001033156	70611	Mm.311026	NM_001033156	ENSMUSG00000035329	Fbxo33	5730501N20Rik|AI642135	F-box protein 33	protein-coding
mm_142651.1	chr17	47595768	47595771	-	1	NA	intron (NM_001081635, intron 4 of 6)	intron (NM_001081635, intron 4 of 6)	2302	NM_007632	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_80211.1	chr9	72448702	72448712	+	1	NA	exon (NM_008613, exon 5 of 10)	exon (NM_008613, exon 5 of 10)	10178	NM_008613	17427	Mm.387671	NM_008613	ENSMUSG00000032221	Mns1	AW546487	meiosis-specific nuclear structural protein 1	protein-coding
mm_145093.1	chr18	43207552	43207563	+	1	NA	promoter-TSS (NM_178749)	promoter-TSS (NM_178749)	-140	NM_178749	269019	Mm.150401	NM_178749	ENSMUSG00000039954	Stk32a	A930015B13Rik|YANK1	serine/threonine kinase 32A	protein-coding
mm_47275.1	chr5	122002341	122002368	-	1	NA	intron (NM_001312908, intron 2 of 22)	intron (NM_001312908, intron 2 of 22)	45471	NM_007804	13048	Mm.156172	NM_007804	ENSMUSG00000042589	Cux2	1700051K22Rik|Cutl2|Cux-2|ENSMUSG00000072641	cut-like homeobox 2	protein-coding
mm_138430.1	chr17	35077081	35077153	+	1	NA	5' UTR (NM_027366, exon 1 of 3)	5' UTR (NM_027366, exon 1 of 3)	175	NM_027366	70274	Mm.250491	NM_027366	ENSMUSG00000013766	Ly6g6e	2310011I02Rik|G6e	lymphocyte antigen 6 complex, locus G6E	protein-coding
mm_47081.1	chr5	117004727	117004738	-	1	NA	Intergenic	Intergenic	111261	NM_001122666	71954	Mm.34456	NM_178622	ENSMUSG00000066900	Suds3	2400003N08Rik|2410008L21Rik|AU067672|mSds3	suppressor of defective silencing 3 homolog (S. cerevisiae)	protein-coding
mm_58985.1	chr7	19080707	19080723	+	1	NA	exon (NM_010058, exon 3 of 5)	exon (NM_010058, exon 3 of 5)	-3134	NR_126095	13400	Mm.6529	NM_032418	ENSMUSG00000030409	Dmpk	DM|DMK|Dm15|MDPK|MT-PK	dystrophia myotonica-protein kinase	protein-coding
mm_43689.1	chr5	138996226	138996263	+	1	NA	Intergenic	Intergenic	-1291	NM_008808	18590	Mm.2675	NM_008808	ENSMUSG00000025856	Pdgfa	-	platelet derived growth factor, alpha	protein-coding
mm_151271.1	chr19	55181884	55181894	+	1	NA	exon (NM_009348, exon 2 of 10)	exon (NM_009348, exon 2 of 10)	1004	NM_009348	21684	Mm.42139	NM_009348	ENSMUSG00000024979	Tectb	Tctnb	tectorin beta	protein-coding
mm_98760.1	chr11	96567487	96567490	+	1	NA	intron (NM_001033186, intron 4 of 12)	intron (NM_001033186, intron 4 of 12)	102897	NM_001177898	78473	Mm.395840	NM_001033186	ENSMUSG00000057058	Skap1	1700091G21Rik|Scap1|Skap-55	src family associated phosphoprotein 1	protein-coding
mm_146717.1	chr18	15063630	15063655	-	1	NA	promoter-TSS (NM_001142731)	promoter-TSS (NM_001142731)	-60	NM_001142731	106931	Mm.329299	NM_134112	ENSMUSG00000036225	Kctd1	4933402K10Rik|AI661543|AW553000	potassium channel tetramerisation domain containing 1	protein-coding
mm_101461.1	chr11	30268172	30268191	-	1	NA	Intergenic	CpG	-48409	NM_175836	20742	Mm.123110	NM_009260	ENSMUSG00000020315	Sptbn1	9930031C03Rik|AL033301|SPTB2|Spnb-2|Spnb2|elf1|elf3|mKIAA4049	spectrin beta, non-erythrocytic 1	protein-coding
mm_21476.1	chr2	161519864	161519867	-	1	NA	Intergenic	Intergenic	-410779	NR_126509	71389	Mm.122738	NM_173368	ENSMUSG00000057133	Chd6	5430439G14Rik|6330406J24Rik|CHD-6	chromodomain helicase DNA binding protein 6	protein-coding
mm_7711.1	chr1	130462681	130462771	-	1	NA	promoter-TSS (NM_010016)	promoter-TSS (NM_010016)	18	NM_010016	13136	Mm.101591	NM_010016	ENSMUSG00000026399	Cd55	Daf|Daf-GPI|Daf1|GPI-DAF	CD55 molecule, decay accelerating factor for complement	protein-coding
mm_77997.1	chr9	8900460	8900489	+	1	NA	exon (NM_008829, exon 1 of 8)	exon (NM_008829, exon 1 of 8)	641	NM_008829	18667	Mm.12798	NM_008829	ENSMUSG00000031870	Pgr	9930019P03Rik|BB114106|ENSMUSG00000074510|NR3C3|PR|PR-A|PR-B	progesterone receptor	protein-coding
mm_150073.1	chr19	29386771	29386789	+	1	NA	3' UTR (NM_021893, exon 7 of 7)	3' UTR (NM_021893, exon 7 of 7)	19342	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_85300.1	chr9	100506816	100506833	-	1	NA	promoter-TSS (NM_001324530)	promoter-TSS (NM_001324530)	32	NM_001324530	17973	Mm.181485	NM_010878	ENSMUSG00000032475	Nck1	6330586M15Rik|D230010O13Rik|Nck|Nck-1	non-catalytic region of tyrosine kinase adaptor protein 1	protein-coding
mm_6654.1	chr1	79858628	79858643	-	1	NA	promoter-TSS (NM_009255)	promoter-TSS (NM_009255)	30	NM_009255	20720	Mm.3093	NM_009255	ENSMUSG00000026249	Serpine2	B230326M24Rik|PAI-1|PI-7|PI7|PN-1|Spi4	serine (or cysteine) peptidase inhibitor, clade E, member 2	protein-coding
mm_158731.1	chrX	163958603	163958618	-	1	NA	promoter-TSS (NM_009453)	promoter-TSS (NM_009453)	56	NM_009453	22184	Mm.426178	NM_009453	ENSMUSG00000031370	Zrsr2	35kDa|5031411E02Rik|A230052C13Rik|C77286|U2af1-rs2|URP	zinc finger (CCCH type), RNA binding motif and serine/arginine rich 2	protein-coding
mm_131478.1	chr16	17137295	17137327	+	1	NA	Intergenic	Intergenic	-4928	NM_022324	64136	Mm.30222	NM_022324	ENSMUSG00000022769	Sdf2l1	-	stromal cell-derived factor 2-like 1	protein-coding
mm_33997.1	chr4	137913488	137913539	+	1	NA	intron (NM_199307, intron 2 of 19)	CpG	51276	NM_199307	230857	Mm.401062	NM_199307	ENSMUSG00000057530	Ece1	AW322500|ECE-1|ECE-1a|ECE-1b|ECE-1d	endothelin converting enzyme 1	protein-coding
mm_75416.1	chr8	46617168	46617225	-	1	NA	promoter-TSS (NM_009810)	promoter-TSS (NM_009810)	4	NM_001001184	408022	Mm.217385	NM_001001184	ENSMUSG00000038225	Primpol	BC065112|Ccdc111	primase and polymerase (DNA-directed)	protein-coding
mm_109306.1	chr12	109560729	109560746	+	1	NA	non-coding (NR_003633, exon 5 of 5)	non-coding (NR_003633, exon 5 of 5)	-2955	NR_030427	791079		NR_030427	ENSMUSG00000076451	Mir770	Mirn770|mir-770|mmu-mir-770	microRNA 770	ncRNA
mm_117673.1	chr13	93637718	93637733	-	1	NA	promoter-TSS (NM_016668)	promoter-TSS (NM_016668)	33	NM_016668	12116	Mm.329582	NM_016668	ENSMUSG00000074768	Bhmt	-	betaine-homocysteine methyltransferase	protein-coding
mm_162861.1	chr10	93124206	93124253	+	1	NA	Intergenic	Intergenic	-36647	NM_146239	237459	Mm.217404	NM_146239	ENSMUSG00000020015	Cdk17	6430598J10Rik|Pctk2	cyclin-dependent kinase 17	protein-coding
mm_101252.1	chr11	20831010	20831053	-	1	NA	promoter-TSS (NM_173752)	promoter-TSS (NM_173752)	77	NM_173752	216551	Mm.76694	NM_173752	ENSMUSG00000042363	Lgalsl	1110067D22Rik|A530071M23|Grpa|Hspc159|Lgalsla	lectin, galactoside binding-like	protein-coding
mm_69595.1	chr7	135716307	135716309	-	1	NA	promoter-TSS (NM_001081117)	promoter-TSS (NM_001081117)	71	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_98925.1	chr11	98348765	98348779	+	1	NA	5' UTR (NM_144828, exon 1 of 7)	5' UTR (NM_144828, exon 1 of 7)	366	NM_144828	19049	Mm.45372	NM_144828	ENSMUSG00000061718	Ppp1r1b	AU040756|DARPP-32|Darpp32	protein phosphatase 1, regulatory (inhibitor) subunit 1B	protein-coding
mm_66436.1	chr7	44815620	44815657	-	1	NA	promoter-TSS (NM_030693)	promoter-TSS (NM_030693)	20	NM_030693	107503	Mm.389890	NM_030693	ENSMUSG00000038539	Atf5	AFTA|Atf7|Atfx|ODA-10	activating transcription factor 5	protein-coding
mm_117665.1	chr13	93499717	93499801	-	1	NA	promoter-TSS (NM_021310)	promoter-TSS (NM_021310)	49	NM_021310	57748	Mm.100273	NM_021310	ENSMUSG00000021690	Jmy	-	junction-mediating and regulatory protein	protein-coding
mm_2681.1	chr1	127306545	127306594	+	1	NA	intron (NM_145128, intron 2 of 17)	intron (NM_145128, intron 2 of 17)	101583	NM_145128	107895	Mm.214682	NM_145128	ENSMUSG00000036155	Mgat5	4930471A21Rik|5330407H02Rik|AI480971|GlcNAc-TV	mannoside acetylglucosaminyltransferase 5	protein-coding
mm_108058.1	chr12	73927413	73927423	+	1	NA	intron (NM_001313920, intron 2 of 14)	intron (NM_001313920, intron 2 of 14)	19551	NM_001313919	15251	Mm.3879	NM_010431	ENSMUSG00000021109	Hif1a	AA959795|HIF-1-alpha|HIF1-alpha|HIF1alpha|MOP1|bHLHe78	hypoxia inducible factor 1, alpha subunit	protein-coding
mm_56713.1	chr6	115317067	115317082	-	1	NA	Intergenic	Intergenic	-43877	NM_001127330	19016	Mm.3020	NM_011146	ENSMUSG00000000440	Pparg	Nr1c3|PPAR-gamma|PPAR-gamma2|PPARgamma|PPARgamma2	peroxisome proliferator activated receptor gamma	protein-coding
mm_166948.1	chr7	43952829	43952870	+	1	NA	exon (NM_008457, exon 2 of 5)	exon (NM_008457, exon 2 of 5)	2183	NM_008457	16624	Mm.435488	NM_008457	ENSMUSG00000063089	Klk1b8	Klk8|Nrpn|TADG14|kallikrein|mGK-8	kallikrein 1-related peptidase b8	protein-coding
mm_107736.1	chr12	57576141	57576166	+	1	NA	exon (NM_001312644, exon 2 of 32)	exon (NM_001312644, exon 2 of 32)	12038	NM_001312644	70846	Mm.84118	NM_001037743	ENSMUSG00000046782	Ttc6	4921506M07Rik|EG639426|ENSMUSG00000046782|Gm69|Gm9813	tetratricopeptide repeat domain 6	protein-coding
mm_18452.1	chr2	60963096	60963104	-	1	NA	5' UTR (NM_020296, exon 1 of 14)	5' UTR (NM_020296, exon 1 of 14)	104	NM_020296	56878	Mm.259667	NM_020296	ENSMUSG00000026970	Rbms1	2600014B10Rik|AI255215|MSSP-1|MSSP-2|MSSP-3|YC1	RNA binding motif, single stranded interacting protein 1	protein-coding
mm_97482.1	chr11	78324405	78324415	+	1	NA	exon (NM_009657, exon 1 of 8)	exon (NM_009657, exon 1 of 8)	212	NM_009657	11676	Mm.7729	NM_009657	ENSMUSG00000017390	Aldoc	AI847350|AU040929|Aldo3|Scrg2	aldolase C, fructose-bisphosphate	protein-coding
mm_73737.1	chr8	114133570	114133597	+	1	NA	promoter-TSS (NM_024446)	promoter-TSS (NM_024446)	9	NM_024437	67528	Mm.27889	NM_024437	ENSMUSG00000031767	Nudt7	1300007B24Rik|2210404C19Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 7	protein-coding
mm_152684.1	chr19	16060046	16060052	-	1	NA	Intergenic	Intergenic	-72782	NM_008139	14682	Mm.439701	NM_008139	ENSMUSG00000024639	Gnaq	1110005L02Rik|6230401I02Rik|AA408290|AW060788|Dsk1|Dsk10|Galphaq|Gq|GqI	guanine nucleotide binding protein, alpha q polypeptide	protein-coding
mm_98398.1	chr11	94328038	94328064	+	1	NA	promoter-TSS (NM_027799)	promoter-TSS (NM_027799)	50	NM_146024	71452	Mm.141054	NM_027799	ENSMUSG00000020864	Ankrd40	1110011C06Rik|5530600A18Rik|Gcap15	ankyrin repeat domain 40	protein-coding
mm_72590.1	chr8	84338812	84338828	+	1	NA	Intergenic	Intergenic	-68418	NM_026350	67736	Mm.30095	NM_026350	ENSMUSG00000004994	Ccdc130	4930527D15Rik|C77430	coiled-coil domain containing 130	protein-coding
mm_135137.1	chr16	35848022	35848033	-	1	NA	intron (NM_001039530, intron 8 of 16)	intron (NM_001039530, intron 8 of 16)	23355	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_4890.1	chr1	188680500	188680501	+	1	NA	intron (NM_021408, intron 37 of 70)	B4A|SINE|B4	327340	NM_172650	226823	Mm.209880	NM_172650	ENSMUSG00000026608	Kctd3	4930438A20Rik|9330185B06|E330032J19Rik|NY-REN-45	potassium channel tetramerisation domain containing 3	protein-coding
mm_130834.1	chr15	101848132	101848160	-	1	NA	exon (NM_008473, exon 4 of 9)	exon (NM_008473, exon 4 of 9)	2640	NM_008473	16678	Mm.183137	NM_008473	ENSMUSG00000046834	Krt1	Krt-2.1|Krt2-1|Krt86	keratin 1	protein-coding
mm_129802.1	chr15	82912144	82912190	-	1	NA	promoter-TSS (NM_013836)	promoter-TSS (NM_013836)	-33	NM_001114140	21411	Mm.252156	NM_013836	ENSMUSG00000041852	Tcf20	2810438H08Rik|SPBP|mKIAA0292	transcription factor 20	protein-coding
mm_121786.1	chr14	19977104	19977126	-	1	NA	promoter-TSS (NM_001285911)	promoter-TSS (NM_001285911)	134	NM_001038637	14702	Mm.41737	NM_010315	ENSMUSG00000043004	Gng2	-	guanine nucleotide binding protein (G protein), gamma 2	protein-coding
mm_77265.1	chr8	115707806	115707822	-	1	NA	promoter-TSS (NM_001025577)	promoter-TSS (NM_001025577)	-920	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_66228.1	chr7	35056468	35056556	-	1	NA	promoter-TSS (NM_009884)	promoter-TSS (NM_009884)	54	NM_009884	12611	Mm.273090	NM_009884	ENSMUSG00000056216	Cebpg	C/EBP[g]|C/EBPgamma|GPE1-BP|Gpe1bp|Ig/EBP	CCAAT/enhancer binding protein (C/EBP), gamma	protein-coding
mm_149660.1	chr19	18730613	18730617	+	1	NA	Intergenic	Intergenic	17379	NM_177640	225995	Mm.28101	NM_177640	ENSMUSG00000047044	D030056L22Rik	-	RIKEN cDNA D030056L22 gene	protein-coding
mm_13569.1	chr2	112281625	112281628	+	1	NA	intron (NM_133649, intron 1 of 24)	intron (NM_133649, intron 1 of 24)	-3062	NM_133648	107723	Mm.491155	NM_133648	ENSMUSG00000027130	Slc12a6	9530023I19Rik|KCC3|gaxp	solute carrier family 12, member 6	protein-coding
mm_20288.1	chr2	126925828	126925838	-	1	NA	exon (NM_023220, exon 5 of 15)	exon (NM_023220, exon 5 of 15)	7402	NM_023220	66552	Mm.269928	NM_023220	ENSMUSG00000027366	Sppl2a	2010106G01Rik|C130089K23Rik	signal peptide peptidase like 2A	protein-coding
mm_30966.1	chr4	33929587	33929590	+	1	NA	intron (NM_007726, intron 1 of 1)	intron (NM_007726, intron 1 of 1)	4956	NM_007726	12801	Mm.7992	NM_007726	ENSMUSG00000044288	Cnr1	CB-R|CB1|CB1R	cannabinoid receptor 1 (brain)	protein-coding
mm_146435.1	chr18	84932883	84932886	+	1	NA	Intergenic	Intergenic	-2141	NM_015798	50764	Mm.28369	NM_015798	ENSMUSG00000034391	Fbxo15	AU019763|Fbx15|ecat3	F-box protein 15	protein-coding
mm_93349.1	chr10	100589206	100589269	-	1	NA	promoter-TSS (NM_175128)	promoter-TSS (NM_175128)	22	NM_175128	68281	Mm.268474	NM_175128	ENSMUSG00000046567	4930430F08Rik	4930571E09Rik|A730088G13Rik|AW551239|C430008C19Rik	RIKEN cDNA 4930430F08 gene	protein-coding
mm_169430.1	chr14	53757335	53757357	+	1	NA	Intergenic	Intergenic	496583	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_123898.1	chr14	73117047	73117055	-	1	NA	Intergenic	Intergenic	-25459	NM_001170694	105670	Mm.280068	NM_134083	ENSMUSG00000022106	Rcbtb2	2610028E02Rik|2810420M18Rik|AI448345|AW240694|Chc1l|RC/BTB2	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 2	protein-coding
mm_141174.1	chr17	26716223	26716260	-	1	NA	intron (NM_029870, intron 1 of 8)	CpG	591	NM_029870	77128	Mm.275414	NM_029870	ENSMUSG00000048249	Crebrf	A930001N09Rik|LRF	CREB3 regulatory factor	protein-coding
mm_42120.1	chr5	110879847	110879887	+	1	NA	promoter-TSS (NM_001267622)	promoter-TSS (NM_001267622)	64	NM_001267622	209683	Mm.295660	NM_024477	ENSMUSG00000033209	Ttc28	2310015L07Rik|6030435N04|AI428795|AI851761|BC002262|TPRBK	tetratricopeptide repeat domain 28	protein-coding
mm_63346.1	chr7	126974366	126974369	+	1	NA	Intergenic	Intergenic	-1547	NM_026638	52858	Mm.28219	NM_026638	ENSMUSG00000030682	Cdipt	9530042F15Rik|D7Bwg0575e|Pis|Pis1	CDP-diacylglycerol--inositol 3-phosphatidyltransferase (phosphatidylinositol synthase)	protein-coding
mm_130783.1	chr15	101558400	101558422	-	1	NA	intron (NM_177717, intron 3 of 8)	intron (NM_177717, intron 3 of 8)	4539	NM_177717	239673	Mm.461267	NM_177717	ENSMUSG00000048699	Krt90	4732456N10Rik|Ket90	keratin 90	protein-coding
mm_137285.1	chr17	24736640	24736658	+	1	NA	promoter-TSS (NM_001346668)	promoter-TSS (NM_001346668)	56	NM_001346668	27361	Mm.28212	NM_013759	ENSMUSG00000075705	Msrb1	D17Wsu82e|SELX|SelR|Sepr|Sepx1	methionine sulfoxide reductase B1	protein-coding
mm_113328.1	chr13	30792621	30792627	+	1	NA	Intergenic	Intergenic	43391	NM_013674	16364	Mm.4677	NM_013674	ENSMUSG00000021356	Irf4	AI385587|IRF-4|LSIRF|NF-EM5|Spip	interferon regulatory factor 4	protein-coding
mm_90094.1	chr10	116962445	116962460	+	1	NA	non-coding (NR_038026, exon 3 of 3)	non-coding (NR_038026, exon 3 of 3)	-2288	NR_027847	103175	Mm.27138	NR_027846	ENSMUSG00000031294	D630029K05Rik	AI314111|AI875589	RIKEN cDNA D630029K05 gene	ncRNA
mm_131669.1	chr16	20657910	20657927	+	1	NA	intron (NM_134101, intron 11 of 20)	intron (NM_134101, intron 11 of 20)	6266	NM_134101	21762	Mm.243234	NM_134101	ENSMUSG00000006998	Psmd2	9430095H01Rik|AA407121|TEG-190|Tex190	proteasome (prosome, macropain) 26S subunit, non-ATPase, 2	protein-coding
mm_79457.1	chr9	56257480	56257517	+	1	NA	intron (NM_172924, intron 4 of 6)	intron (NM_172924, intron 4 of 6)	-96428	NM_019793	56434	Mm.28484	NM_019793	ENSMUSG00000032324	Tspan3	1700055K04Rik|TM4-A|Tm4sf8	tetraspanin 3	protein-coding
mm_68615.1	chr7	116444591	116444601	-	1	NA	Intergenic	Intergenic	-1138	NM_011083	18704	Mm.3810	NM_011083	ENSMUSG00000030660	Pik3c2a	Cpk-m|PI3KC2	phosphatidylinositol 3-kinase, C2 domain containing, alpha polypeptide	protein-coding
mm_2734.1	chr1	128244433	128244443	+	1	NA	5' UTR (NM_026390, exon 1 of 13)	5' UTR (NM_026390, exon 1 of 13)	257	NM_026390	67812	Mm.293321	NM_026390	ENSMUSG00000026353	Ubxn4	1300013G12Rik|Ubxd2|mKIAA0242	UBX domain protein 4	protein-coding
mm_22347.1	chr2	180909824	180909827	-	1	NA	intron (NM_173761, intron 4 of 4)	intron (NM_173761, intron 4 of 4)	11111	NM_173761	228994	Mm.30205	NM_173761	ENSMUSG00000038848	Ythdf1	2210410K23Rik|8030473O16	YTH domain family 1	protein-coding
mm_168327.1	chr11	116357457	116357459	+	1	NA	intron (NM_027258, intron 8 of 18)	B1_Mus1|SINE|Alu	-22104	NM_008240	15223	Mm.378938	NM_008240	ENSMUSG00000034227	Foxj1	FKHL-13|HFH-4|Hfh4	forkhead box J1	protein-coding
mm_108183.1	chr12	76533614	76533625	+	1	NA	promoter-TSS (NR_039597)	promoter-TSS (NR_039597)	59	NM_153804	263406	Mm.291854	NM_153804	ENSMUSG00000052609	Plekhg3	BC030417	pleckstrin homology domain containing, family G (with RhoGef domain) member 3	protein-coding
mm_10654.1	chr2	20671837	20671854	+	1	NA	intron (NM_029895, intron 4 of 18)	intron (NM_029895, intron 4 of 18)	152332	NM_001177631	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding
mm_23081.1	chr3	36616893	36616901	+	1	NA	Intergenic	L1M2|LINE|L1	-3508	NM_027810	71492	Mm.286187	NM_027810	ENSMUSG00000037325	Bbs7	8430406N16Rik	Bardet-Biedl syndrome 7 (human)	protein-coding
mm_50771.1	chr6	53629740	53629763	+	1	NA	intron (NM_001327821, intron 7 of 10)	intron (NM_001327821, intron 7 of 10)	56377	NM_172728	231991	Mm.227444	NM_172728	ENSMUSG00000053007	Creb5	9430076C15Rik|CRE-BPa|Crebpa|D430026C09Rik	cAMP responsive element binding protein 5	protein-coding
mm_39603.1	chr5	23850576	23850589	+	1	NA	promoter-TSS (NR_045042)	promoter-TSS (NR_045042)	-15	NR_045042	67194	Mm.423733	NR_045040	ENSMUSG00000097180	2700038G22Rik	-	RIKEN cDNA 2700038G22 gene	ncRNA
mm_65639.1	chr7	27929444	27929465	-	1	NA	promoter-TSS (NM_028538)	promoter-TSS (NM_028538)	-24	NM_028538	73430	Mm.379224	NM_028538	ENSMUSG00000070709	Zfp974	1700049G17Rik|AV321011|BB026409	zinc finger protein 974	protein-coding
mm_146153.1	chr18	75000490	75000499	+	1	NA	promoter-TSS (NR_028552)	promoter-TSS (NR_028552)	17	NM_001002239	319195	Mm.276337	NM_001002239	ENSMUSG00000062328	Rpl17	-	ribosomal protein L17	protein-coding
mm_30082.1	chr3	138114141	138114159	-	1	NA	exon (NM_001163457, exon 10 of 20)	exon (NM_001163457, exon 10 of 20)	17227	NM_008642	17777	Mm.2941	NM_008642	ENSMUSG00000028158	Mttp	1810043K16Rik|MTP	microsomal triglyceride transfer protein	protein-coding
mm_42741.1	chr5	120678570	120678576	+	1	NA	intron (NM_013832, intron 20 of 21)	intron (NM_013832, intron 20 of 21)	29385	NM_001281999	19415	Mm.41209	NM_013832	ENSMUSG00000029602	Rasal1	MRASAL	RAS protein activator like 1 (GAP1 like)	protein-coding
mm_107276.1	chr12	29534717	29534725	+	1	NA	promoter-TSS (NM_001093776)	promoter-TSS (NM_001093776)	-184	NM_001093776	17933	Mm.253067	NM_008666	ENSMUSG00000061911	Myt1l	2900046C06Rik|2900093J19Rik|C630034G21Rik|Nztf1|Pmng1|Png-1|mKIAA1106	myelin transcription factor 1-like	protein-coding
mm_22320.1	chr2	180589347	180589397	-	1	NA	promoter-TSS (NM_031373)	promoter-TSS (NM_031373)	-35	NM_031373	72075	Mm.250418	NM_031373	ENSMUSG00000049401	Ogfr	2010013E17Rik	opioid growth factor receptor	protein-coding
mm_9966.1	chr1	191177362	191177379	-	1	NA	exon (NM_007498, exon 2 of 4)	exon (NM_007498, exon 2 of 4)	5963	NM_007498	11910	Mm.2706	NM_007498	ENSMUSG00000026628	Atf3	LRG-21	activating transcription factor 3	protein-coding
mm_41577.1	chr5	93172995	93173019	+	1	NA	3' UTR (NM_001009818, exon 10 of 10)	3' UTR (NM_001009818, exon 10 of 10)	33488	NM_017367	12453	Mm.250419	NM_017367	ENSMUSG00000063015	Ccni	-	cyclin I	protein-coding
mm_138020.1	chr17	33910318	33910335	+	1	NA	intron (NM_001199733, intron 1 of 7)	intron (NM_001199733, intron 1 of 7)	725	NM_001199733	13163	Mm.271809	NM_007829	ENSMUSG00000002307	Daxx	-	Fas death domain-associated protein	protein-coding
mm_143410.1	chr17	70829982	70830011	-	1	NA	Intergenic	Intergenic	16781	NM_001164077	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_44208.1	chr5	4104448	4104462	-	1	NA	5' UTR (NM_020010, exon 1 of 10)	5' UTR (NM_020010, exon 1 of 10)	242	NM_020010	13121	Mm.140158	NM_020010	ENSMUSG00000001467	Cyp51	AI426508|CYPLI|Cyp51a1|Ldm|P450-14DM|P450LI	cytochrome P450, family 51	protein-coding
mm_426.1	chr1	34472715	34472757	+	1	NA	intron (NM_011206, intron 12 of 14)	intron (NM_011206, intron 12 of 14)	12990	NM_011206	19253	Mm.361	NM_011206	ENSMUSG00000026126	Ptpn18	FLP1|HSCF|PTP-HSCF|PTP-K1|Ptpk1	protein tyrosine phosphatase, non-receptor type 18	protein-coding
mm_65448.1	chr7	25400262	25400298	-	1	NA	3' UTR (NM_153576, exon 4 of 4)	3' UTR (NM_153576, exon 4 of 4)	-4293	NM_010719	16890	Mm.158548	NM_010719	ENSMUSG00000003123	Lipe	4933403G17Rik|HSL	lipase, hormone sensitive	protein-coding
mm_19021.1	chr2	76945384	76945394	-	1	NA	exon (NM_011652, exon 28 of 313)	exon (NM_011652, exon 28 of 313)	37158	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_70334.1	chr8	4493497	4493511	+	1	NA	promoter-TSS (NM_026058)	promoter-TSS (NM_026058)	99	NM_026058	67260	Mm.35511	NM_026058	ENSMUSG00000008206	Cers4	2900019C14Rik|Lass4|Trh1	ceramide synthase 4	protein-coding
mm_2261.1	chr1	91144971	91144988	+	1	NA	promoter-TSS (NM_001033408)	promoter-TSS (NM_001033408)	-124	NM_001033408	329207	Mm.295940	NM_001033408	ENSMUSG00000070732	Rbm44	Gm817	RNA binding motif protein 44	protein-coding
mm_94962.1	chr11	30771844	30771854	+	1	NA	promoter-TSS (NM_134013)	promoter-TSS (NM_134013)	74	NM_134013	103554	Mm.240066	NM_134013	ENSMUSG00000040850	Psme4	AA409398|AU041366|TEMO|mKIAA0077	proteasome (prosome, macropain) activator subunit 4	protein-coding
mm_88447.1	chr10	77548625	77548636	+	1	NA	exon (NM_008404, exon 6 of 16)	exon (NM_008404, exon 6 of 16)	18282	NM_008404	16414	Mm.1137	NM_008404	ENSMUSG00000000290	Itgb2	2E6|AI528527|Cd18|LAD|LCAMB|Lfa1|MF17	integrin beta 2	protein-coding
mm_60875.1	chr7	46033827	46033846	+	1	NA	exon (NM_153057, exon 1 of 31)	exon (NM_153057, exon 1 of 31)	140	NM_153057	211548	Mm.274811	NM_153057	ENSMUSG00000030835	Nomo1	D7Ertd156e|Nomo|pM5	nodal modulator 1	protein-coding
mm_39157.1	chr4	155491203	155491215	-	1	NA	promoter-TSS (NM_008142)	promoter-TSS (NM_008142)	-152	NM_001160017	14688	Mm.2344	NM_008142	ENSMUSG00000029064	Gnb1	AA409223|C77571|Gnb-1	guanine nucleotide binding protein (G protein), beta 1	protein-coding
mm_19846.1	chr2	113685003	113685035	-	1	NA	promoter-TSS (NM_001287818)	promoter-TSS (NM_001287818)	-71	NM_001287818	14260	Mm.4938	NM_010230	ENSMUSG00000044042	Fmn1	Fmn|formin-1|ld	formin 1	protein-coding
mm_100867.1	chr11	5898561	5898574	-	1	NA	intron (NM_022879, intron 1 of 6)	intron (NM_022879, intron 1 of 6)	215	NM_022879	17898	Mm.46514	NM_022879	ENSMUSG00000020469	Myl7	MLC-2alpha|MLC2a|MYL2A|Mylc2a|RLC-A	myosin, light polypeptide 7, regulatory	protein-coding
mm_151819.1	chr19	5510468	5510518	-	1	NA	promoter-TSS (NM_001024560)	promoter-TSS (NM_001024560)	-4	NM_001024560	225861	Mm.20071	NM_001024560	ENSMUSG00000056185	Snx32	B930037P14Rik|Snx6b	sorting nexin 32	protein-coding
mm_16283.1	chr2	174076297	174076356	+	1	NA	promoter-TSS (NM_001102425)	promoter-TSS (NM_001102425)	-725	NM_172675	228960	Mm.277977	NM_172675	ENSMUSG00000027522	Stx16	4930401D03|5430410K23Rik|6330500A18Rik|AI648908|AW553605|Syn16	syntaxin 16	protein-coding
mm_79155.1	chr9	47789780	47789814	+	1	NA	exon (NM_018770, exon 3 of 10)	exon (NM_018770, exon 3 of 10)	28411	NR_046048	100038460	Mm.447649	NR_046048		Gm10677	ENSMUSG00000074363	predicted gene 10677	ncRNA
mm_116130.1	chr13	28953306	28953319	-	1	NA	5' UTR (NM_009238, exon 1 of 1)	5' UTR (NM_009238, exon 1 of 1)	370	NM_009238	20677	Mm.240627	NM_009238	ENSMUSG00000076431	Sox4	AA682046|Sox-4	SRY (sex determining region Y)-box 4	protein-coding
mm_56981.1	chr6	120357441	120357489	-	1	NA	promoter-TSS (NM_026028)	promoter-TSS (NM_026028)	4	NM_026028	67200	Mm.45767	NM_026028	ENSMUSG00000030177	Ccdc77	2400002C23Rik|2700091N06Rik|AV168274	coiled-coil domain containing 77	protein-coding
mm_160286.1	chr7	126377995	126377995	-	1	NA	promoter-TSS (NM_023712)	promoter-TSS (NM_023712)	-61	NR_045537	73658	Mm.11112	NM_023712	ENSMUSG00000030741	Spns1	2210013K02Rik|Spin1|Spinl	spinster homolog 1	protein-coding
mm_113159.1	chr13	24802992	24803008	+	1	NA	5' UTR (NM_024473, exon 1 of 5)	5' UTR (NM_024473, exon 1 of 5)	1343	NM_024473	79555	Mm.266668	NM_024473	ENSMUSG00000019132	BC005537	8030460C05Rik|C78201	cDNA sequence BC005537	protein-coding
mm_64224.1	chr7	141625414	141625422	+	1	NA	intron (NM_007459, intron 15 of 21)	intron (NM_007459, intron 15 of 21)	4717	NR_106030	102466798		NR_106030	ENSMUSG00000098759	Mir7063	Gm27654|mmu-mir-7063	microRNA 7063	ncRNA
mm_8248.1	chr1	138619200	138619207	-	1	NA	intron (NM_001311148, intron 1 of 7)	CpG	554	NM_021605	59125	Mm.143817	NM_021605	ENSMUSG00000026393	Nek7	2810460C19Rik|AU020186	NIMA (never in mitosis gene a)-related expressed kinase 7	protein-coding
mm_88589.1	chr10	79711577	79711675	+	1	NA	3' UTR (NM_001077184, exon 7 of 7)	3' UTR (NM_001077184, exon 7 of 7)	-5008	NM_008226	15166	Mm.12956	NM_008226	ENSMUSG00000020331	Hcn2	BCNG2|HAC1|trls	hyperpolarization-activated, cyclic nucleotide-gated K+ 2	protein-coding
mm_13040.1	chr2	91082363	91082387	+	1	NA	Intergenic	Intergenic	-12060	NM_001290765	68427	Mm.192375	NM_026721	ENSMUSG00000002105	Slc39a13	1100001L14Rik|AA387663|ZIP-13|ZIP13	solute carrier family 39 (metal ion transporter), member 13	protein-coding
mm_91213.1	chr10	21753920	21753930	-	1	NA	Intergenic	Intergenic	63080	NR_045843	432436	Mm.244553	NM_001004162		Gm5420	EG432436	predicted gene 5420	ncRNA
mm_121661.1	chr14	12345246	12345255	-	1	NA	intron (NM_080433, intron 1 of 4)	CpG	615	NM_080433	54713	Mm.34644	NM_080433	ENSMUSG00000021743	Fezf2	AI451466|AI852056|Fez|Fezl|Zfp312	Fez family zinc finger 2	protein-coding
mm_143264.1	chr17	65638947	65638950	-	1	NA	exon (NM_153519, exon 2 of 2)	exon (NM_153519, exon 2 of 2)	808	NM_153519	213272	Mm.255732	NM_153519	ENSMUSG00000050612	Txndc2	AU021712|Sptrx-1|Sptrx1|Trx4	thioredoxin domain containing 2 (spermatozoa)	protein-coding
mm_121579.1	chr14	123660116	123660209	+	1	NA	promoter-TSS (NM_145467)	promoter-TSS (NM_145467)	22	NM_145467	223272	Mm.383176	NM_145467	ENSMUSG00000032925	Itgbl1	B930011D01Rik	integrin, beta-like 1	protein-coding
mm_147925.1	chr18	65939020	65939030	-	1	NA	promoter-TSS (NM_013833)	promoter-TSS (NM_013833)	64	NM_013833	19434	Mm.431047	NM_013833	ENSMUSG00000024518	Rax	7530406A22Rik|E130303K03Rik|Rx|ey-1|ey1	retina and anterior neural fold homeobox	protein-coding
mm_105820.1	chr11	112711470	112711479	-	1	NA	promoter-TSS (NR_024085)	promoter-TSS (NR_024085)	-118	NR_024085	217294	Mm.297761	NM_146031	ENSMUSG00000041674	BC006965	-	cDNA sequence BC006965	ncRNA
mm_122349.1	chr14	38710438	38710440	-	1	NA	intron (NM_001190187, intron 2 of 9)	intron (NM_001190187, intron 2 of 9)	-187863	NR_045713	75170	Mm.372967	NR_045713	ENSMUSG00000093528	Nrg3os	4930529F24Rik	neuregulin 3, opposite strand	ncRNA
mm_116479.1	chr13	43560175	43560231	-	1	NA	promoter-TSS (NM_001081059)	promoter-TSS (NM_001081059)	-12	NM_001081059	76137	Mm.426290	NM_001081059	ENSMUSG00000021371	Mcur1	6230416A05Rik|AU015498|AV136929|AW554392|C88263|Ccdc90a	mitochondrial calcium uniporter regulator 1	protein-coding
mm_150337.1	chr19	34575723	34575743	+	1	NA	3' UTR (NM_008332, exon 3 of 3)	3' UTR (NM_008332, exon 3 of 3)	-7796	NM_010501	15959	Mm.426079	NM_010501	ENSMUSG00000074896	Ifit3	Ifi49|P49	interferon-induced protein with tetratricopeptide repeats 3	protein-coding
mm_82296.1	chr9	7836890	7836910	-	1	NA	promoter-TSS (NM_001291503)	promoter-TSS (NM_001291503)	-94	NM_001291503	11797	Mm.335659	NM_007465	ENSMUSG00000057367	Birc2	AW146227|Api1|Api2|Birc3|C-IAP1|C330006D17Rik|HIAP1|HIAP2|IAP1|IAP2|MIAP1|MIAP2|MIHB|MIHC|RNF48|cIAP1|cIAP2|mcIAP1	baculoviral IAP repeat-containing 2	protein-coding
mm_172264.1	chr6	75297045	75297048	-	1	NA	Intergenic	Intergenic	-1826025	NR_108032	73408	Mm.233629	NR_108032	ENSMUSG00000107408	1700065L07Rik	-	RIKEN cDNA 1700065L07 gene	ncRNA
mm_34568.1	chr4	150033559	150033565	+	1	NA	Intergenic	Intergenic	-24539	NM_173371	100198	Mm.22183	NM_173371	ENSMUSG00000028980	H6pd	AI785303|G6pd1|Gpd-1|Gpd1	hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase)	protein-coding
mm_35001.1	chr4	156203293	156203310	+	1	NA	promoter-TSS (NR_030671)	promoter-TSS (NR_030671)	17	NR_030671	100382	Mm.461024	NR_030671		AW011738	-	expressed sequence AW011738	ncRNA
mm_108534.1	chr12	84218575	84218615	+	1	NA	intron (NM_001163501, intron 1 of 12)	CpG	286	NM_001163501	238317	Mm.31256	NM_001163501	ENSMUSG00000042507	Elmsan1	9430029N19Rik|C130039O16Rik|Gm260	ELM2 and Myb/SANT-like domain containing 1	protein-coding
mm_165127.1	chr2	6570523	6570524	+	1	NA	intron (NM_001347094, intron 9 of 12)	intron (NM_001347094, intron 9 of 12)	151139	NM_001310447	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_3078.1	chr1	134302974	134302999	+	1	NA	intron (NM_001144855, intron 25 of 28)	X7A_LINE|LINE|CR1	12982	NM_031189	17928	Mm.16528	NM_031189	ENSMUSG00000026459	Myog	MYF4|bHLHc3|myo	myogenin	protein-coding
mm_166262.1	chr5	87781776	87781776	+	1	NA	exon (NM_001304768, exon 8 of 13)	exon (NM_001304768, exon 8 of 13)	7326	NM_007785	12993	Mm.4908	NM_007785	ENSMUSG00000061937	Csn1s2a	Csng|PP22	casein alpha s2-like A	protein-coding
mm_46947.1	chr5	114922011	114922023	-	1	NA	Intergenic	Intergenic	-1223	NM_145209	231655	Mm.95479	NM_145209	ENSMUSG00000041827	Oasl1	7530414C13Rik|oasl9	2'-5' oligoadenylate synthetase-like 1	protein-coding
mm_76577.1	chr8	89006672	89006680	-	1	NA	Intergenic	CpG	-18059	NR_106190	102465899		NR_106190	ENSMUSG00000099078	Mir8110	Gm27571|mmu-mir-8110	microRNA 8110	ncRNA
mm_139066.1	chr17	46556422	46556429	+	1	NA	promoter-TSS (NM_020493)	promoter-TSS (NM_020493)	-263	NM_020493	20807	Mm.45044	NM_020493	ENSMUSG00000015605	Srf	AW049942|AW240594	serum response factor	protein-coding
mm_24865.1	chr3	95933999	95934022	+	1	NA	exon (NM_001253757, exon 2 of 7)	exon (NM_001253757, exon 2 of 7)	4753	NM_023210	66471	Mm.218657	NM_023210	ENSMUSG00000015749	Anp32e	2810018A15Rik|AI047746|AI326868|CPD1|LANP-L|LANPL|mLANP-L	acidic (leucine-rich) nuclear phosphoprotein 32 family, member E	protein-coding
mm_32288.1	chr4	103114386	103114394	+	1	NA	promoter-TSS (NM_027696)	promoter-TSS (NM_027696)	0	NM_027696	71148	Mm.288721	NM_027696	ENSMUSG00000028522	Mier1	4933425I22Rik|5830411K19Rik|er1	MEIR1 treanscription regulator	protein-coding
mm_129525.1	chr15	79258615	79258647	-	1	NA	exon (NM_177580, exon 14 of 14)	exon (NM_177580, exon 14 of 14)	-3883	NM_020516	57274	Mm.441697	NM_020516	ENSMUSG00000032988	Slc16a8	Mct3	solute carrier family 16 (monocarboxylic acid transporters), member 8	protein-coding
mm_58148.1	chr6	142322968	142322977	-	1	NA	promoter-TSS (NM_130861)	promoter-TSS (NM_130861)	9	NM_130861	108096	Mm.206599	NM_130861	ENSMUSG00000063975	Slco1a5	Oatp-3|Oatp3|Slc21a7	solute carrier organic anion transporter family, member 1a5	protein-coding
mm_14288.1	chr2	128818296	128818351	+	1	NA	promoter-TSS (NM_028248)	promoter-TSS (NM_028248)	20	NM_028248	72477	Mm.259688	NM_028248	ENSMUSG00000014353	Tmem87b	2610301K12Rik|2810431I02Rik|AU014804	transmembrane protein 87B	protein-coding
mm_78137.1	chr9	20888302	20888312	+	1	NA	exon (NM_145610, exon 1 of 11)	exon (NM_145610, exon 1 of 11)	132	NM_145610	235036	Mm.2930	NM_145610	ENSMUSG00000004100	Ppan	A230087P06Rik|SSF1	peter pan homolog (Drosophila)	protein-coding
mm_45753.1	chr5	86783170	86783178	-	1	NA	Intergenic	Intergenic	-21092	NM_001347375	231386	Mm.196325	NM_177680	ENSMUSG00000035851	Ythdc1	A730098D12Rik|C80342|mKIAA1966	YTH domain containing 1	protein-coding
mm_50734.1	chr6	52714004	52714049	+	1	NA	intron (NM_025816, intron 1 of 17)	CpG	297	NM_025816	52440	Mm.389757	NM_025816	ENSMUSG00000004535	Tax1bp1	1200003J11Rik|1700069J21Rik|AA930106|D6Ertd404e|D6Ertd772e|T6bp|TXBP151	Tax1 (human T cell leukemia virus type I) binding protein 1	protein-coding
mm_110123.1	chr12	26444156	26444162	-	1	NA	3' UTR (NM_021384, exon 6 of 6)	3' UTR (NM_021384, exon 6 of 6)	12293	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_29030.1	chr3	102166970	102167006	-	1	NA	intron (NM_177545, intron 4 of 7)	intron (NM_177545, intron 4 of 7)	37705	NM_177545	229658	Mm.118004	NM_177545	ENSMUSG00000027860	Vangl1	Kitenin|Lpp2|Stb2|Stbm	vang-like 1 (van gogh, Drosophila)	protein-coding
mm_47698.1	chr5	129787159	129787173	-	1	NA	promoter-TSS (NM_009838)	promoter-TSS (NM_009838)	87	NM_133900	100678	Mm.271784	NM_133900	ENSMUSG00000029446	Psph	AI480570|PSP|PSPase	phosphoserine phosphatase	protein-coding
mm_124244.1	chr14	101594458	101594460	-	1	NA	intron (NM_001081278, intron 1 of 18)	intron (NM_001081278, intron 1 of 18)	14732	NM_001081278	210789	Mm.320639	NM_173380	ENSMUSG00000033083	Tbc1d4	5930406J04Rik|A930035N22|AV295684|As160	TBC1 domain family, member 4	protein-coding
mm_62887.1	chr7	115020324	115020336	+	1	NA	Intergenic	MER21C|LTR|ERVL	69056	NR_040319	101786	Mm.395157	NR_040317	ENSMUSG00000108379	A730082K24Rik	AU044236	RIKEN cDNA A730082K24 gene	ncRNA
mm_32022.1	chr4	95075753	95075791	+	1	NA	Intergenic	Intergenic	-23550	NM_010591	16476	Mm.275071	NM_010591	ENSMUSG00000052684	Jun	AP-1|Junc|c-jun	jun proto-oncogene	protein-coding
mm_131397.1	chr16	14352843	14352889	+	1	NA	Intergenic	Intergenic	-8692	NM_008576	17250	Mm.196634	NM_008576	ENSMUSG00000023088	Abcc1	Abcc1a|Abcc1b|MRP|Mdrap|Mrp1	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	protein-coding
mm_66243.1	chr7	35555291	35555353	-	1	NA	exon (NM_033080, exon 1 of 3)	exon (NM_033080, exon 1 of 3)	606	NM_033080	110959	Mm.410206	NM_033080	ENSMUSG00000034875	Nudt19	D7Rp2|D7Rp2-r|D7Rp2-s|D7Rp2e|RP2-r|RP2-s	nudix (nucleoside diphosphate linked moiety X)-type motif 19	protein-coding
mm_45006.1	chr5	38480284	38480295	-	1	NA	promoter-TSS (NM_001102415)	promoter-TSS (NM_001102415)	17	NM_001102414	117591	Mm.260137	NM_145559	ENSMUSG00000005107	Slc2a9	Glut9|SLC2A9B|SLC2a9A	solute carrier family 2 (facilitated glucose transporter), member 9	protein-coding
mm_56801.1	chr6	116656938	116656987	-	1	NA	intron (NM_178045, intron 3 of 10)	IMPB_01|Satellite|Satellite	6278	NM_001166580	213393	Mm.38231	NM_145980	ENSMUSG00000048489	8430408G22Rik	Depp|Fseg	RIKEN cDNA 8430408G22 gene	protein-coding
mm_4479.1	chr1	173436015	173436023	+	1	NA	intron (NM_001013779, intron 2 of 8)	B4A|SINE|B4	15415	NM_001013779	383619	Mm.131453	NM_001013779	ENSMUSG00000037860	Aim2	Gm1313|Ifi210	absent in melanoma 2	protein-coding
mm_34219.1	chr4	140977387	140977419	+	1	NA	exon (NM_023374, exon 7 of 8)	exon (NM_023374, exon 7 of 8)	-9470	NM_029097	74772	Mm.205625	NM_029097	ENSMUSG00000036622	Atp13a2	1110012E06Rik|AA589443	ATPase type 13A2	protein-coding
mm_77415.1	chr8	120634380	120634398	-	1	NA	promoter-TSS (NM_197988)	promoter-TSS (NM_197988)	-7	NM_197988	68918	Mm.473736	NM_197988	ENSMUSG00000043687	1190005I06Rik	-	RIKEN cDNA 1190005I06 gene	protein-coding
mm_51435.1	chr6	79818253	79818273	+	1	NA	exon (NM_001190732, exon 1 of 1)	exon (NM_001190732, exon 1 of 1)	232	NM_001190732	100463512	Mm.461086	NM_001190732	ENSMUSG00000096887	Gm20594	Mtrnr2l	predicted gene, 20594	protein-coding
mm_95185.1	chr11	42420830	42420855	+	1	NA	promoter-TSS (NM_001347314)	promoter-TSS (NM_001347314)	-508	NM_001347314	14401	Mm.338723	NM_008070	ENSMUSG00000007653	Gabrb2	AI834970|C030002O17Rik|C030021G16Rik|Gabrab2|Gabrb-2	gamma-aminobutyric acid (GABA) A receptor, subunit beta 2	protein-coding
mm_168444.1	chr1	140649058	140649058	-	1	NA	intron (NR_040604, intron 1 of 3)	intron (NR_040604, intron 1 of 3)	7344	NR_040604	75910	Mm.483845	NR_040604	ENSMUSG00000102368	4930590L20Rik	-	RIKEN cDNA 4930590L20 gene	ncRNA
mm_163881.1	chr14	21499731	21499775	+	1	NA	promoter-TSS (NM_001205241)	promoter-TSS (NM_001205241)	-17	NM_001205241	54169	Mm.248967	NM_017479	ENSMUSG00000021767	Kat6b	AI507552|B130044K16Rik|MYST-4|Morf|Myst4|mKIAA0383|qkf|querkopf	K(lysine) acetyltransferase 6B	protein-coding
mm_88451.1	chr10	77553856	77553878	+	1	NA	intron (NM_008404, intron 8 of 15)	intron (NM_008404, intron 8 of 15)	23519	NM_008404	16414	Mm.1137	NM_008404	ENSMUSG00000000290	Itgb2	2E6|AI528527|Cd18|LAD|LCAMB|Lfa1|MF17	integrin beta 2	protein-coding
mm_13904.1	chr2	120484332	120484342	+	1	NA	intron (NM_001109761, intron 3 of 20)	intron (NM_001109761, intron 3 of 20)	7428	NM_001109761	12335	Mm.458021	NM_007601	ENSMUSG00000079110	Capn3	AI323605|Capa-3|Capa3|Lp82|p94	calpain 3	protein-coding
mm_96777.1	chr11	69939903	69939913	+	1	NA	exon (NM_016875, exon 5 of 9)	exon (NM_016875, exon 5 of 9)	3580	NM_001347634	53422	Mm.29286	NM_016875	ENSMUSG00000018554	Ybx2	Msy2	Y box protein 2	protein-coding
mm_139582.1	chr17	57106633	57106643	+	1	NA	promoter-TSS (NR_033508)	promoter-TSS (NR_033508)	-696	NR_033508	100169874	Mm.76700	NR_033508	ENSMUSG00000079414	Gm11110	ENSMUSG00000079414	predicted gene 11110	ncRNA
mm_14668.1	chr2	139493915	139493923	+	1	NA	promoter-TSS (NM_175467)	promoter-TSS (NM_175467)	-1	NM_175467	228677	Mm.100450	NM_175467	ENSMUSG00000039092	Sptlc3	C130053K05Rik	serine palmitoyltransferase, long chain base subunit 3	protein-coding
mm_28829.1	chr3	96402011	96402017	-	1	NA	Intergenic	CpG	12819	NR_001579	21748		NR_001579	ENSMUSG00000064796	Terc	mTER|mTR	telomerase RNA component	ncRNA
mm_112201.1	chr12	113426768	113426780	-	1	NA	Intergenic	Intergenic	-62791	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_14522.1	chr2	132691885	132691903	+	1	NA	intron (NM_028637, intron 1 of 2)	intron (NM_028637, intron 1 of 2)	1611	NM_028637	73747	Mm.284114	NM_028637	ENSMUSG00000044991	1110034G24Rik	-	RIKEN cDNA 1110034G24 gene	protein-coding
mm_105797.1	chr11	110095956	110095969	-	1	NA	promoter-TSS (NM_153145)	promoter-TSS (NM_153145)	-25	NM_153145	217258	Mm.344148	NM_153145	ENSMUSG00000041828	Abca8a	-	ATP-binding cassette, sub-family A (ABC1), member 8a	protein-coding
mm_126444.1	chr15	80711242	80711265	+	1	NA	promoter-TSS (NM_144812)	promoter-TSS (NM_144812)	-60	NM_144812	213988	Mm.131328	NM_144812	ENSMUSG00000047888	Tnrc6b	2700090M07Rik|A730065C02Rik|AI848765|D230019K20Rik	trinucleotide repeat containing 6b	protein-coding
mm_139817.1	chr17	67521162	67521167	+	1	NA	Intergenic	Intergenic	111559	NM_001033340	240131	Mm.295736	NM_001033340	ENSMUSG00000073375	Lrrc30	Gm326	leucine rich repeat containing 30	protein-coding
mm_17595.1	chr2	30796632	30796639	-	1	NA	intron (NR_028486, intron 4 of 6)	intron (NR_028486, intron 4 of 6)	5102	NM_198000	73598	Mm.34166	NM_198000	ENSMUSG00000044320	1700001O22Rik	1700113K14Rik|4930549G18Rik	RIKEN cDNA 1700001O22 gene	protein-coding
mm_152225.1	chr19	8707794	8707806	-	1	NA	exon (NM_008577, exon 9 of 9)	exon (NM_008577, exon 9 of 9)	6097	NM_008577	17254	Mm.4114	NM_008577	ENSMUSG00000010095	Slc3a2	4F2|4F2HC|AI314110|Cd98|Ly-10|Ly-m10|Ly10|Mdu1|Mgp-2hc|NACAE	solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2	protein-coding
mm_159635.1	chr4	138877969	138877969	+	1	NA	promoter-TSS (NM_012044)	promoter-TSS (NM_012044)	27	NM_012044	26970	Mm.296007	NM_012044	ENSMUSG00000028751	Pla2g2e	-	phospholipase A2, group IIE	protein-coding
mm_62628.1	chr7	107595069	107595085	+	1	NA	promoter-TSS (NM_008905)	promoter-TSS (NM_008905)	26	NM_008905	19024	Mm.2817	NM_008905	ENSMUSG00000036528	Ppfibp2	Cclp1	PTPRF interacting protein, binding protein 2 (liprin beta 2)	protein-coding
mm_164849.1	chr18	45559014	45559022	+	1	NA	intron (NM_001312905, intron 3 of 10)	intron (NM_001312905, intron 3 of 10)	-1136	NM_080465	140492	Mm.411614	NM_080465	ENSMUSG00000054477	Kcnn2	KCa2.2|SK2|SKCA2|bc|fri	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2	protein-coding
mm_116874.1	chr13	55021197	55021239	-	1	NA	promoter-TSS (NM_001206391)	promoter-TSS (NM_001206391)	167	NM_001206392	212032	Mm.267479	NM_001033245	ENSMUSG00000025877	Hk3	HK III|HK-III	hexokinase 3	protein-coding
mm_81907.1	chr9	120002346	120002357	+	1	NA	Intergenic	Intergenic	-17693	NM_153287	215418	Mm.491094	NM_153287	ENSMUSG00000032515	Csrnp1	4931429D10Rik|Axud1|CSRNP-1|URAX1|taip-3	cysteine-serine-rich nuclear protein 1	protein-coding
mm_91049.1	chr10	18743692	18743760	-	1	NA	promoter-TSS (NM_001033258)	promoter-TSS (NM_001033258)	32	NM_001033258	215821	Mm.40491	NM_001033258	ENSMUSG00000019852	Arfgef3	9630004D11|B930094H20Rik|BIG3|D10Bwg1379e|mKIAA1244	ARFGEF family member 3	protein-coding
mm_32691.1	chr4	115884335	115884340	+	1	NA	promoter-TSS (NM_001039124)	promoter-TSS (NM_001039124)	-63	NM_001039124	654462	Mm.388913	NM_001039124	ENSMUSG00000073774	Kncn	Kino|L5	kinocilin	protein-coding
mm_112654.1	chr13	16026448	16026458	+	1	NA	exon (NM_008380, exon 5 of 5)	exon (NM_008380, exon 5 of 5)	14602	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_156775.1	chrX	161082505	161082537	+	1	NA	Intergenic	Intergenic	-80229	NM_001290652	107815	Mm.159173	NM_133194	ENSMUSG00000000037	Scml2	4932420G07Rik	sex comb on midleg-like 2 (Drosophila)	protein-coding
mm_96812.1	chr11	69991699	69991712	+	1	NA	5' UTR (NM_019749, exon 1 of 4)	5' UTR (NM_019749, exon 1 of 4)	335	NM_019749	56486	Mm.272460	NM_019749	ENSMUSG00000018567	Gabarap	-	gamma-aminobutyric acid receptor associated protein	protein-coding
mm_120443.1	chr14	65968492	65968510	+	1	NA	promoter-TSS (NM_013492)	promoter-TSS (NM_013492)	18	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_72812.1	chr8	87521374	87521378	+	1	NA	intron (NR_125722, intron 1 of 3)	B3|SINE|B2	-42531	NM_177901	330820	Mm.212913	NM_177901	ENSMUSG00000069971	4933402J07Rik	-	RIKEN cDNA 4933402J07 gene	protein-coding
mm_134126.1	chr16	10395269	10395339	-	1	NA	exon (NM_001099275, exon 1 of 6)	exon (NM_001099275, exon 1 of 6)	144	NM_001099275	70426	Mm.142181	NM_001099275	ENSMUSG00000039179	Tekt5	3300001K11Rik	tektin 5	protein-coding
mm_154152.1	chr19	58455260	58455324	-	1	NA	non-coding (NR_104342, exon 1 of 12)	non-coding (NR_104342, exon 1 of 12)	106	NM_001285457	14585	Mm.88367	NM_010279	ENSMUSG00000025089	Gfra1	AU042498	glial cell line derived neurotrophic factor family receptor alpha 1	protein-coding
mm_139807.1	chr17	66235747	66235753	+	1	NA	Intergenic	Intergenic	112230	NM_001003919	320209	Mm.259605	NM_001003919	ENSMUSG00000035842	Ddx11	4732462I11Rik|CHL1|CHLR1|KRG2|essa15a	DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11	protein-coding
mm_75153.1	chr8	36182277	36182301	-	1	NA	Intergenic	Intergenic	67227	NM_001081150	244421	Mm.324032	NM_001081150	ENSMUSG00000039633	Lonrf1	-	LON peptidase N-terminal domain and ring finger 1	protein-coding
mm_70446.1	chr8	11728170	11728256	+	1	NA	5' UTR (NM_001113517, exon 1 of 19)	5' UTR (NM_001113517, exon 1 of 19)	108	NM_001113517	54126	Mm.244068	NM_017402	ENSMUSG00000031511	Arhgef7	Cool|PIX|Pak3bp|betaPix|betaPix-b|betaPix-c|cool-1|mKIAA0142|p85Cool1|p85SPR	Rho guanine nucleotide exchange factor (GEF7)	protein-coding
mm_106002.1	chr11	115699428	115699438	-	1	NA	5' UTR (NM_001313937, exon 1 of 5)	5' UTR (NM_001313937, exon 1 of 5)	101	NM_001313937	14784	Mm.439649	NM_008163	ENSMUSG00000059923	Grb2	AA408164|Ash	growth factor receptor bound protein 2	protein-coding
mm_40872.1	chr5	74093062	74093072	+	1	NA	promoter-TSS (NR_145131)	promoter-TSS (NR_145131)	7	NR_145131	70036	Mm.46547	NR_015531	ENSMUSG00000053656	Dancr	2700023E23Rik	differentiation antagonizing non-protein coding RNA	ncRNA
mm_142319.1	chr17	43157872	43157903	-	1	NA	non-coding (NR_045155, exon 1 of 6)	non-coding (NR_045155, exon 1 of 6)	404	NR_045155	545207	Mm.329050	NR_045153		E130008D07Rik	-	RIKEN cDNA E130008D07 gene	ncRNA
mm_151272.1	chr19	55195880	55195904	+	1	NA	3' UTR (NM_009348, exon 10 of 10)	3' UTR (NM_009348, exon 10 of 10)	3214	NR_106146	102465990		NR_106146	ENSMUSG00000098289	Mir6715	Gm27474|mmu-mir-6715	microRNA 6715	ncRNA
mm_8031.1	chr1	135133194	135133226	-	1	NA	promoter-TSS (NM_007955)	promoter-TSS (NM_007955)	485	NM_177081	320139	Mm.258388	NM_177081	ENSMUSG00000031506	Ptpn7	BPTP-4|C920001D21Rik|HEPTP|LC-PTP|LPTP	protein tyrosine phosphatase, non-receptor type 7	protein-coding
mm_105656.1	chr11	107319247	107319269	-	1	NA	intron (NM_145823, intron 4 of 9)	intron (NM_145823, intron 4 of 9)	-129877	NM_001161329	68979	Mm.294617	NM_133702	ENSMUSG00000018433	Nol11	1500002M01Rik|AU015220|AU019874	nucleolar protein 11	protein-coding
mm_47744.1	chr5	130255381	130255391	-	1	NA	promoter-TSS (NM_178897)	promoter-TSS (NM_178897)	144	NM_023248	66711	Mm.280484	NM_023248	ENSMUSG00000025337	Sbds	4733401P19Rik|AI836084|CGI-97|SDS	Shwachman-Bodian-Diamond syndrome homolog (human)	protein-coding
mm_85093.1	chr9	92250473	92250486	-	1	NA	intron (NM_011636, intron 1 of 8)	CpG	285	NM_011636	22038	Mm.421956	NM_011636	ENSMUSG00000032369	Plscr1	MmTRA1a|MmTRA1b|Nor1|Tra1|Tra1a|Tra1b|Tras1|Tras2	phospholipid scramblase 1	protein-coding
mm_1114.1	chr1	59874761	59874763	+	1	NA	3' UTR (NM_007561, exon 13 of 13)	3' UTR (NM_007561, exon 13 of 13)	-38244	NM_001037725	72750	Mm.258250	NM_001037725	ENSMUSG00000041040	Fam117b	2810425F24Rik|6330416D14Rik|Als2cr13	family with sequence similarity 117, member B	protein-coding
mm_73974.1	chr8	120525352	120525371	+	1	NA	intron (NM_198671, intron 1 of 15)	intron (NM_198671, intron 1 of 15)	-10496	NM_001145897	382034	Mm.334856	NM_198671	ENSMUSG00000031822	Gse1	2210013I18Rik|mKIAA0182	genetic suppressor element 1, coiled-coil protein	protein-coding
mm_70715.1	chr8	15077719	15077725	+	1	NA	intron (NM_008664, intron 6 of 36)	intron (NM_008664, intron 6 of 36)	20069	NM_008664	17930	Mm.272115	NM_008664	ENSMUSG00000031461	Myom2	AW146149	myomesin 2	protein-coding
mm_44491.1	chr5	23675928	23675938	-	1	NA	Intergenic	CpG	36734	NR_038090	433855	Mm.205125	NR_015554	ENSMUSG00000105987	AI506816	-	expressed sequence AI506816	ncRNA
mm_50582.1	chr6	49056555	49056565	+	1	NA	3' UTR (NM_053110, exon 11 of 11)	3' UTR (NM_053110, exon 11 of 11)	-17235	NM_029353	75593	Mm.439947	NM_029353	ENSMUSG00000029815	Malsu1	2410003K15Rik|Matsu1	mitochondrial assembly of ribosomal large subunit 1	protein-coding
mm_12498.1	chr2	71866128	71866132	+	1	NA	intron (NR_039557, intron 3 of 3).2	intron (NR_039557, intron 3 of 3).2	-7094	NM_172665	228026	Mm.34411	NM_172665	ENSMUSG00000006494	Pdk1	B830012B01|D530020C15Rik	pyruvate dehydrogenase kinase, isoenzyme 1	protein-coding
mm_36339.1	chr4	72200834	72200928	-	1	NA	promoter-TSS (NM_001285532)	promoter-TSS (NM_001285532)	12	NM_011599	21885	Mm.278444	NM_011599	ENSMUSG00000008305	Tle1	C230057C06Rik|Estm14|Grg-1|Grg1|Tle4l	transducin-like enhancer of split 1	protein-coding
mm_43593.1	chr5	137761677	137761679	+	1	NA	intron (NM_029805, intron 4 of 5)	intron (NM_029805, intron 4 of 5)	15709	NM_029805	78829	Mm.286399	NM_023910	ENSMUSG00000029723	Tsc22d4	0610009M14Rik|1700023B23Rik|AI415410|Thg-1pit|Tilz2	TSC22 domain family, member 4	protein-coding
mm_8864.1	chr1	162813244	162813291	-	1	NA	promoter-TSS (NM_144878)	promoter-TSS (NM_144878)	-718	NM_144878	226564	Mm.155164	NM_144878	ENSMUSG00000026692	Fmo4	D1Ertd532e	flavin containing monooxygenase 4	protein-coding
mm_151546.1	chr19	59322288	59322288	+	1	NA	intron (NM_001033222, intron 2 of 4)	intron (NM_001033222, intron 2 of 4)	23492	NM_001033222	107368	Mm.27250	NM_001033222	ENSMUSG00000074746	Pdzd8	A630041P07Rik|AV329468|AW228944|Pdzk8	PDZ domain containing 8	protein-coding
mm_154304.1	chr19	61226077	61226102	-	1	NA	intron (NM_009970, intron 6 of 11)	CpG-7695	2329	NM_009970	12982	Mm.287228	NM_009970	ENSMUSG00000059326	Csf2ra	CD116|Csfgmra|GM-CSF-Ra|GM-CSFR	colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)	protein-coding
mm_120046.1	chr14	56575641	56575665	+	1	NA	promoter-TSS (NM_001145978)	promoter-TSS (NM_001145978)	34	NM_001145978	328417	Mm.379357	NM_001145978	ENSMUSG00000054509	Parp4	Adprtl1|C030027K23Rik|E230037B21Rik|Gm743|PARPL|PH5P|VAULT3|VPARP|p193	poly (ADP-ribose) polymerase family, member 4	protein-coding
mm_95946.1	chr11	58386788	58386806	+	1	NA	exon (NM_001083884, exon 6 of 7)	exon (NM_001083884, exon 6 of 7)	6151	NM_001330197	70163	Mm.24119	NM_027339	ENSMUSG00000013643	Lypd8	2210415F13Rik	LY6/PLAUR domain containing 8	protein-coding
mm_164342.1	chr16	14708337	14708337	+	1	NA	3' UTR (NM_011415, exon 3 of 3)	3' UTR (NM_011415, exon 3 of 3)	2478	NM_011415	20583	Mm.4272	NM_011415	ENSMUSG00000022676	Snai2	Slug|Slugh|Snail2	snail family zinc finger 2	protein-coding
mm_79234.1	chr9	50499175	50499186	+	1	NA	exon (NM_029639, exon 2 of 4)	exon (NM_029639, exon 2 of 4)	4655	NM_029639	76509	Mm.29959	NM_029639	ENSMUSG00000032068	Plet1	0610037B23Rik|1600029D21Rik|AA407923|AU043048	placenta expressed transcript 1	protein-coding
mm_164574.1	chr17	24169624	24169646	-	1	NA	promoter-TSS (NM_009729)	promoter-TSS (NM_009729)	-206	NM_009729	11984	Mm.30155	NM_009729	ENSMUSG00000024121	Atp6v0c	Atp6c|Atp6c2|Atp6l|Atpl|Atpl-rs1|PL16|VATL|Vma3	ATPase, H+ transporting, lysosomal V0 subunit C	protein-coding
mm_166596.1	chr6	65042705	65042707	+	1	NA	promoter-TSS (NM_007958)	promoter-TSS (NM_007958)	39	NM_007958	13990	Mm.99113	NM_007958	ENSMUSG00000029920	Smarcad1	AV081750|AW226546|D6Pas1|Etl1|mKIAA1122	SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1	protein-coding
mm_20488.1	chr2	130048534	130048550	-	1	NA	3' UTR (NM_009374, exon 13 of 13)	3' UTR (NM_009374, exon 13 of 13)	-32134	NR_105757	102466628		NR_105757	ENSMUSG00000098347	Mir6339	Gm27848|mmu-mir-6339	microRNA 6339	ncRNA
mm_21578.1	chr2	164237204	164237210	-	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	1134	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_61410.1	chr7	73538065	73538092	+	1	NA	intron (NM_001081345, intron 2 of 38)	intron (NM_001081345, intron 2 of 38)	3668	NM_001081345	244059	Mm.34539	NM_001081345	ENSMUSG00000078671	Chd2	2810013C04Rik|2810040A01Rik|5630401D06Rik|AI851092|BC029703|CHD-2	chromodomain helicase DNA binding protein 2	protein-coding
mm_110574.1	chr12	56373844	56373885	-	1	NA	Intergenic	Intergenic	-27970	NM_145442	217588	Mm.25656	NM_145442	ENSMUSG00000021028	Mbip	4933408E06Rik	MAP3K12 binding inhibitory protein 1	protein-coding
mm_170732.1	chr2	152226904	152226904	+	1	NA	promoter-TSS (NM_007788)	promoter-TSS (NM_007788)	64	NM_007788	12995	Mm.23692	NM_007788	ENSMUSG00000074698	Csnk2a1	Csnk2a1-rs4	casein kinase 2, alpha 1 polypeptide	protein-coding
mm_65030.1	chr7	18524757	18524764	-	1	NA	exon (NM_054060, exon 4 of 5)	exon (NM_054060, exon 4 of 5)	7467	NM_054060	114868	Mm.389809	NM_054060	ENSMUSG00000070798	Psg25	cea13	pregnancy-specific glycoprotein 25	protein-coding
mm_123228.1	chr14	59677543	59677586	-	1	NA	intron (NM_015803, intron 34 of 35)	intron (NM_015803, intron 34 of 35)	52283	NM_145463	219134	Mm.275409	NM_145463	ENSMUSG00000044461	Shisa2	9430059P22Rik|MAd2|Tmem46|mShisa|shisa	shisa family member 2	protein-coding
mm_151736.1	chr19	4927314	4927326	-	1	NA	intron (NM_133803, intron 1 of 17)	intron (NM_133803, intron 1 of 17)	967	NM_133803	75221	Mm.234769	NM_133803	ENSMUSG00000063904	Dpp3	4930533O14Rik|C86324	dipeptidylpeptidase 3	protein-coding
mm_17783.1	chr2	32966875	32966894	-	1	NA	Intergenic	CpG	3583	NR_002898	104367	Mm.250030	NR_002898	ENSMUSG00000065124	Snora65	MBII-351|Rnu65	small nucleolar RNA, H/ACA box 65	snoRNA
mm_8134.1	chr1	136246754	136246756	-	1	NA	Intergenic	Intergenic	-12475	NM_028872	67313	Mm.36763	NM_028872	ENSMUSG00000041605	5730559C18Rik	1700034M08Rik|4933426C09Rik|AI586180|D1Mgi54	RIKEN cDNA 5730559C18 gene	protein-coding
mm_97198.1	chr11	75588154	75588177	+	1	NA	promoter-TSS (NM_008850)	promoter-TSS (NM_008850)	86	NM_008850	18738	Mm.3128	NM_008850	ENSMUSG00000017781	Pitpna	Pitpn|vb|vibrator	phosphatidylinositol transfer protein, alpha	protein-coding
mm_131285.1	chr16	11176196	11176220	+	1	NA	intron (NM_145931, intron 1 of 22)	CpG	185	NR_027502	106205	Mm.226860	NM_145931	ENSMUSG00000037965	Zc3h7a	A430104C18Rik|AI447294|AW556219|HSPC055|Zc3h7|Zc3hdc7	zinc finger CCCH type containing 7 A	protein-coding
mm_128666.1	chr15	60186887	60186897	-	1	NA	Intergenic	Intergenic	-170274	NM_027668	71088	Mm.425950	NM_027668	ENSMUSG00000071749	4933412E24Rik	-	RIKEN cDNA 4933412E24 gene	protein-coding
mm_65450.1	chr7	25412833	25412841	-	1	NA	promoter-TSS (NM_153576)	promoter-TSS (NM_153576)	49	NM_153576	232983	Mm.10545	NM_153576	ENSMUSG00000060188	Cxcl17	VCC-1|Vcc1	chemokine (C-X-C motif) ligand 17	protein-coding
mm_34261.1	chr4	141421688	141421689	+	1	NA	5' UTR (NM_013868, exon 1 of 3)	5' UTR (NM_013868, exon 1 of 3)	909	NM_013868	29818	Mm.46181	NM_013868	ENSMUSG00000006221	Hspb7	27kDa|Hsp25-2|cvHsp	heat shock protein family, member 7 (cardiovascular)	protein-coding
mm_46413.1	chr5	104093364	104093377	-	1	NA	exon (NM_010097, exon 4 of 11)	exon (NM_010097, exon 4 of 11)	-15762	NM_001163772	100271704	Mm.366664	NM_001163772	ENSMUSG00000091034	Gm17660	Scpppq1	predicted gene, 17660	protein-coding
mm_156502.1	chrX	145729914	145729917	+	1	NA	Intergenic	(TAG)n|Simple_repeat|Simple_repeat	-242276	NM_153319	27494	Mm.100068	NM_153319	ENSMUSG00000041688	Amot	CAG-2|D0Kist1|Sii6	angiomotin	protein-coding
mm_51774.1	chr6	88090129	88090154	+	1	NA	exon (NM_133933, exon 3 of 10)	exon (NM_133933, exon 3 of 10)	5668	NM_133933	103963	Mm.188544	NM_133933	ENSMUSG00000030062	Rpn1	AU018702|D6Wsu137e|Rpn-1	ribophorin I	protein-coding
mm_13070.1	chr2	91119040	91119052	+	1	NA	intron (NM_008653, intron 1 of 31)	intron (NM_008653, intron 1 of 31)	902	NM_008653	17868	Mm.10728	NM_008653	ENSMUSG00000002100	Mybpc3	-	myosin binding protein C, cardiac	protein-coding
mm_139345.1	chr17	50239203	50239213	+	1	NA	promoter-TSS (NR_131975)	promoter-TSS (NR_131975)	0	NR_131975	446210	Mm.378184	NM_001004437	ENSMUSG00000067103	AY702103	STDP2	cDNA sequence AY702103	ncRNA
mm_167802.1	chr9	123928185	123928207	+	1	NA	Intergenic	MLT1F|LTR|ERVL-MaLR	40496	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_85821.1	chr9	110419969	110419997	-	1	NA	exon (NM_008694, exon 1 of 4)	exon (NM_008694, exon 1 of 4)	175	NM_008694	18054	Mm.236225	NM_008694	ENSMUSG00000032484	Ngp	bectenecin	neutrophilic granule protein	protein-coding
mm_147284.1	chr18	39488725	39488752	-	1	NA	Intergenic	Intergenic	-1493	NM_008173	14815	Mm.129481	NM_008173	ENSMUSG00000024431	Nr3c1	GR|Grl-1|Grl1	nuclear receptor subfamily 3, group C, member 1	protein-coding
mm_85384.1	chr9	103227946	103227982	-	1	NA	exon (NM_133977, exon 2 of 17)	exon (NM_133977, exon 2 of 17)	2322	NM_133977	22041	Mm.37214	NM_133977	ENSMUSG00000032554	Trf	AI266983|Cd176|HP|Tf|Tfn|hpx	transferrin	protein-coding
mm_110512.1	chr12	54734716	54734719	-	1	NA	Intergenic	U1|snRNA|snRNA	-38823	NM_025456	66266	Mm.156440	NM_025456	ENSMUSG00000054302	Eapp	1810011O16Rik	E2F-associated phosphoprotein	protein-coding
mm_102123.1	chr11	53324591	53324612	-	1	NA	promoter-TSS (NM_026479)	promoter-TSS (NM_026479)	-88	NM_026479	67966	Mm.288072	NM_026479	ENSMUSG00000018239	Zcchc10	2410141K03Rik|AA675321|D11Ertd416e	zinc finger, CCHC domain containing 10	protein-coding
mm_169062.1	chr13	26441732	26441736	+	1	NA	Intergenic	L1Md_T|LINE|L1	-129328	NR_045933	73576	Mm.45473	NR_045933		1700092E19Rik	-	RIKEN cDNA 1700092E19 gene	ncRNA
mm_85139.1	chr9	95795948	95795961	-	1	NA	intron (NM_001033210, intron 1 of 15)	intron (NM_001033210, intron 1 of 15)	-45596	NM_011643	22063	Mm.149633	NM_011643	ENSMUSG00000032839	Trpc1	Mtrp1|Trp1|Trrp1	transient receptor potential cation channel, subfamily C, member 1	protein-coding
mm_43786.1	chr5	142629538	142629589	+	1	NA	promoter-TSS (NM_178398)	promoter-TSS (NM_178398)	-21	NM_178398	74781	Mm.29432	NM_178398	ENSMUSG00000029578	Wipi2	1110018O08Rik|2510001I10Rik	WD repeat domain, phosphoinositide interacting 2	protein-coding
mm_102676.1	chr11	65243657	65243668	-	1	NA	intron (NM_146386, intron 1 of 12)	intron (NM_146386, intron 1 of 12)	26327	NM_145136	214384	Mm.32257	NM_145136	ENSMUSG00000020542	Myocd	BSAC2A|Srfcp	myocardin	protein-coding
mm_108139.1	chr12	76215443	76215451	+	1	NA	intron (NM_001159532, intron 5 of 8)	RMER10B|LTR|ERVL	31299	NM_019784	80384	Mm.78551	NM_019784	ENSMUSG00000021056	Tex21	4931406F04Rik|4931412D23Rik|4931421K24Rik|tsec-2	testis expressed gene 21	protein-coding
mm_123206.1	chr14	59365435	59365461	-	1	NA	promoter-TSS (NM_199015)	promoter-TSS (NM_199015)	42	NM_199015	219132	Mm.479285	NM_199015	ENSMUSG00000068245	Phf11d	D14Ertd668e|Phf11|Phf11l	PHD finger protein 11D	protein-coding
mm_66527.1	chr7	45128726	45128747	-	1	NA	promoter-TSS (NM_009438)	promoter-TSS (NM_009438)	9	NM_009438	22121	Mm.180458	NM_009438	ENSMUSG00000074129	Rpl13a	1810026N22Rik|Tstap198-7|tum-antigen	ribosomal protein L13A	protein-coding
mm_49697.1	chr6	33973287	33973320	+	1	NA	TTS (NM_009148)	TTS (NM_009148)	-56145	NM_028886	74354	Mm.127952	NM_028886	ENSMUSG00000056215	Lrguk	4921528H16Rik	leucine-rich repeats and guanylate kinase domain containing	protein-coding
mm_165469.1	chr2	164237504	164237506	+	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	836	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_66254.1	chr7	35647052	35647107	-	1	NA	intron (NM_019746, intron 1 of 5)	CpG	403	NM_019746	56330	Mm.371609	NM_019746	ENSMUSG00000030417	Pdcd5	2200003D22Rik|AA408513|Tfar19	programmed cell death 5	protein-coding
mm_110108.1	chr12	26442858	26442870	-	1	NA	3' UTR (NM_021384, exon 6 of 6)	3' UTR (NM_021384, exon 6 of 6)	13588	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_26037.1	chr3	135544692	135544705	+	1	NA	intron (NM_027288, intron 8 of 16)	intron (NM_027288, intron 8 of 16)	59087	NM_027288	110173	Mm.280536	NM_027288	ENSMUSG00000028164	Manba	2410030O07Rik|B930014J03Rik|Bmn	mannosidase, beta A, lysosomal	protein-coding
mm_2026.1	chr1	87181241	87181254	+	1	NA	Intergenic	Intergenic	-2067	NM_027084	69453	Mm.84618	NM_027084	ENSMUSG00000036480	Prss56	1700027L20Rik	protease, serine 56	protein-coding
mm_89696.1	chr10	97607104	97607115	+	1	NA	promoter-TSS (NM_008438)	promoter-TSS (NM_008438)	-96	NM_008438	16545	Mm.6228	NM_008438	ENSMUSG00000019932	Kera	CNA2|SLRR2B	keratocan	protein-coding
mm_33508.1	chr4	130913265	130913348	+	1	NA	promoter-TSS (NM_010686)	promoter-TSS (NM_010686)	-28	NM_010686	16792	Mm.271868	NM_010686	ENSMUSG00000028581	Laptm5	E3	lysosomal-associated protein transmembrane 5	protein-coding
mm_147394.1	chr18	44253430	44253459	-	1	NA	Intergenic	Intergenic	-16683	NM_010935	18169	Mm.57234	NM_010935	ENSMUSG00000038071	Npy6r	-	neuropeptide Y receptor Y6	protein-coding
mm_94714.1	chr11	20542914	20542922	+	1	NA	promoter-TSS (NM_021372)	promoter-TSS (NM_021372)	-335	NM_021372	58172	Mm.339676	NM_021372	ENSMUSG00000049800	Sertad2	AB041541|AU021878|Kiaa0127|MNCb-1504|SEI-2|Sei2|TRIP-Br2|mKIAA0127	SERTA domain containing 2	protein-coding
mm_68564.1	chr7	115312915	115312919	-	1	NA	Intergenic	Intergenic	361643	NR_040319	101786	Mm.395157	NR_040317	ENSMUSG00000108379	A730082K24Rik	AU044236	RIKEN cDNA A730082K24 gene	ncRNA
mm_93638.1	chr10	117282433	117282441	-	1	NA	promoter-TSS (NM_017372)	promoter-TSS (NM_017372)	-165	NM_017372	17105	Mm.45436	NM_017372	ENSMUSG00000069516	Lyz2	AI326280|Lys|Lysm|Lyzf2|Lyzs|Lzm|Lzm-s1|Lzp	lysozyme 2	protein-coding
mm_98316.1	chr11	90249427	90249448	+	1	NA	promoter-TSS (NM_026178)	promoter-TSS (NM_026178)	-39	NM_026178	67468	Mm.277518	NM_026178	ENSMUSG00000003948	Mmd	1200017E07Rik|1810073C06Rik|AA690185	monocyte to macrophage differentiation-associated	protein-coding
mm_18034.1	chr2	38714492	38714514	-	1	NA	promoter-TSS (NM_139051)	promoter-TSS (NM_139051)	39	NM_139051	26423	Mm.31387	NM_139051	ENSMUSG00000026751	Nr5a1	Ad4BP|ELP|ELP-3|Ftz-F1|Ftzf1|SF-1|SF1|STF-1	nuclear receptor subfamily 5, group A, member 1	protein-coding
mm_56907.1	chr6	119196718	119196728	-	1	NA	promoter-TSS (NM_009781)	promoter-TSS (NM_009781)	-314	NM_001255999	12288	Mm.41628	NM_009781	ENSMUSG00000051331	Cacna1c	Cav1.2|Cchl1a1|D930026N18Rik|MBC|MELC-CC	calcium channel, voltage-dependent, L type, alpha 1C subunit	protein-coding
mm_6942.1	chr1	85727240	85727254	-	1	NA	intron (NM_177055, intron 1 of 5)	PB1D7|SINE|Alu	9359	NM_177055	319997	Mm.116691	NM_177055	ENSMUSG00000052760	A630001G21Rik	-	RIKEN cDNA A630001G21 gene	protein-coding
mm_79449.1	chr9	56114084	56114119	+	1	NA	intron (NM_011193, intron 1 of 14)	intron (NM_011193, intron 1 of 14)	24125	NM_011193	19200	Mm.2534	NM_011193	ENSMUSG00000032322	Pstpip1	CD2BP1|def-2	proline-serine-threonine phosphatase-interacting protein 1	protein-coding
mm_53490.1	chr6	135196881	135196906	+	1	NA	Intergenic	Intergenic	-1094	NM_028982	74525	Mm.34182	NM_028982	ENSMUSG00000030207	Fam234b	8430419L09Rik|Kiaa1467|mKIAA1467	family with sequence similarity 234, member B	protein-coding
mm_78858.1	chr9	44396930	44396955	+	1	NA	promoter-TSS (NM_001293631)	promoter-TSS (NM_001293631)	15	NM_001293631	14385	Mm.30087	NM_008063	ENSMUSG00000032114	Slc37a4	100043178|G6PT|G6pt1|GSD-1b|mG6PT	solute carrier family 37 (glucose-6-phosphate transporter), member 4	protein-coding
mm_152961.1	chr19	29360934	29360950	-	1	NA	intron (NM_026362, intron 1 of 5)	intron (NM_026362, intron 1 of 5)	929	NM_026362	67759	Mm.275511	NM_026362	ENSMUSG00000016495	Plgrkt	1110007H22Rik|5033414D02Rik|AI852040|Plg-R(KT)|Plg-RKT	plasminogen receptor, C-terminal lysine transmembrane protein	protein-coding
mm_55010.1	chr6	48840488	48840492	-	1	NA	promoter-TSS (NM_025326)	promoter-TSS (NM_025326)	498	NM_023056	65963	Mm.28385	NM_023056	ENSMUSG00000029810	Tmem176b	1810009M01Rik|Clast1|Lr8	transmembrane protein 176B	protein-coding
mm_154399.1	chrM	13640	13659	+	1	NA	NA	Intergenic	NA	NA								
mm_89795.1	chr10	102512033	102512063	+	1	NA	promoter-TSS (NM_146240)	promoter-TSS (NM_146240)	-174	NM_146240	237504	Mm.282672	NM_146240	ENSMUSG00000044921	Rassf9	AW322107|Pamci	Ras association (RalGDS/AF-6) domain family (N-terminal) member 9	protein-coding
mm_144084.1	chr17	94749875	94749887	-	1	NA	promoter-TSS (NM_176917)	promoter-TSS (NM_176917)	11	NM_176917	76781	Mm.139146	NM_176917	ENSMUSG00000055660	Mettl4	2410198H06Rik|A730091E08Rik|AV296509|HsT661	methyltransferase like 4	protein-coding
mm_50235.1	chr6	42351271	42351290	+	1	NA	exon (NM_011777, exon 4 of 10)	exon (NM_011777, exon 4 of 10)	1452	NM_001289619	22793	Mm.282303	NM_011777	ENSMUSG00000029860	Zyx	9530098H06Rik|R75157	zyxin	protein-coding
mm_55339.1	chr6	56369626	56369639	-	1	NA	promoter-TSS (NM_001159957)	promoter-TSS (NM_001159957)	2	NM_001159957	18575	Mm.5145	NM_011054	ENSMUSG00000004347	Pde1c	-	phosphodiesterase 1C	protein-coding
mm_23522.1	chr3	60617095	60617116	+	1	NA	intron (NM_001310514, intron 7 of 8)	intron (NM_001310514, intron 7 of 8)	115926	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_121031.1	chr14	79769899	79769910	+	1	NA	exon (NM_021543, exon 1 of 3)	exon (NM_021543, exon 1 of 3)	1408	NM_001042726	18530	Mm.390715	NM_021543	ENSMUSG00000036422	Pcdh8	1700080P15Rik|Papc	protocadherin 8	protein-coding
mm_128473.1	chr15	50889044	50889054	-	1	NA	promoter-TSS (NR_035444)	promoter-TSS (NR_035444)	0	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_94968.1	chr11	30883731	30883737	+	1	NA	Intergenic	Intergenic	-1624	NM_175490	237716	Mm.338361	NM_175490	ENSMUSG00000043999	Gpr75	-	G protein-coupled receptor 75	protein-coding
mm_114035.1	chr13	52985975	52985981	+	1	NA	Intergenic	Intergenic	-4939	NM_017373	18030	Mm.136604	NM_017373	ENSMUSG00000056749	Nfil3	AV225605|E4BP4	nuclear factor, interleukin 3, regulated	protein-coding
mm_118257.1	chr13	112438040	112438062	-	1	NA	Intergenic	RCHARR1|DNA|hAT-Charlie	-26019	NM_010560	16195	Mm.4364	NM_010560	ENSMUSG00000021756	Il6st	5133400A03Rik|AA389424|BB405851|CD130|D13Ertd699e|gp130	interleukin 6 signal transducer	protein-coding
mm_169745.1	chr15	86195202	86195219	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-9069	NM_145475	223753	Mm.222685	NM_145475	ENSMUSG00000035891	Cerk	AI848610|D330016D08Rik|mKIAA1646	ceramide kinase	protein-coding
mm_146254.1	chr18	77789912	77789922	+	1	NA	Intergenic	RLTR31B_Mm|LTR|ERVK	-4633	NM_013831	19201	Mm.57174	NM_013831	ENSMUSG00000025429	Pstpip2	MAYP|cmo	proline-serine-threonine phosphatase-interacting protein 2	protein-coding
mm_73134.1	chr8	94974705	94974721	+	1	NA	Intergenic	Intergenic	-2396	NM_001198894	14766	Mm.290834	NM_018882	ENSMUSG00000031785	Adgrg1	Cyt28|Gpr56|TM7LN4|TM7XN1	adhesion G protein-coupled receptor G1	protein-coding
mm_88057.1	chr10	67547961	67547985	+	1	NA	3' UTR (NM_001005419, exon 1 of 1)	3' UTR (NM_001005419, exon 1 of 1)	982	NM_001005419	211488	Mm.297250	NM_001005419	ENSMUSG00000057134	Ado	Gm237	2-aminoethanethiol (cysteamine) dioxygenase	protein-coding
mm_24306.1	chr3	89393860	89393864	+	1	NA	promoter-TSS (NM_009565)	promoter-TSS (NM_009565)	-428	NR_040404	545539	Mm.393389	NR_040403	ENSMUSG00000074466	Gm15417	ENSMUSG00000074466|OTTMUSG00000021274	predicted gene 15417	ncRNA
mm_68637.1	chr7	118243670	118243686	-	1	NA	promoter-TSS (NM_001031814)	promoter-TSS (NM_001031814)	-41	NM_001031814	233789	Mm.309053	NM_177180	ENSMUSG00000030655	Smg1	2610207I05Rik|5430435M13Rik|C130002K18Rik|mKIAA0421	SMG1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)	protein-coding
mm_149955.1	chr19	28835102	28835116	+	1	NA	promoter-TSS (NM_009199)	promoter-TSS (NM_009199)	-57	NM_009199	20510	Mm.246670	NM_009199	ENSMUSG00000024935	Slc1a1	D130048G10Rik|EAAC1|EAAC2|EAAT3|MEAAC1	solute carrier family 1 (neuronal/epithelial high affinity glutamate transporter, system Xag), member 1	protein-coding
mm_34456.1	chr4	148085853	148085876	+	1	NA	intron (NM_001301281, intron 1 of 4)	intron (NM_001301281, intron 1 of 4)	2200	NM_009642	11610	Mm.46247	NM_009642	ENSMUSG00000029007	Agtrap	3300002E14Rik|AT1R|Atrap|D4Wsu124e	angiotensin II, type I receptor-associated protein	protein-coding
mm_117387.1	chr13	73347256	73347264	-	1	NA	non-coding (NR_045293, exon 1 of 3)	non-coding (NR_045293, exon 1 of 3)	124	NR_045293	432777	Mm.415319	NR_045293		D630045M09Rik	AU019512	RIKEN cDNA D630045M09 gene	ncRNA
mm_72858.1	chr8	88428811	88428823	+	1	NA	Intergenic	Intergenic	-66626	NM_012047	26992	Mm.5400	NM_012047	ENSMUSG00000031660	Brd7	BP75|CELTIX1|Ptpn13ip	bromodomain containing 7	protein-coding
mm_118172.1	chr13	106836348	106836380	-	1	NA	intron (NM_029665, intron 27 of 29)	intron (NM_029665, intron 27 of 29)	100551	NM_029665	76582	Mm.132208	NM_029665	ENSMUSG00000042590	Ipo11	1700081H05Rik|2510001A17Rik|AI314624|AW555235|E330021B14Rik|Ranbp11	importin 11	protein-coding
mm_49049.1	chr6	4903299	4903346	+	1	NA	promoter-TSS (NM_181595)	promoter-TSS (NM_181595)	2	NM_181595	243725	Mm.332901	NM_181595	ENSMUSG00000032827	Ppp1r9a	2810430P21Rik|4930518N04Rik|5330407E15|A230094E16Rik|BB181831|NRB|mKIAA1222|neurabin-I	protein phosphatase 1, regulatory (inhibitor) subunit 9A	protein-coding
mm_132393.1	chr16	35000637	35000656	+	1	NA	3' UTR (NM_139300, exon 32 of 32)	3' UTR (NM_139300, exon 32 of 32)	-21775	NM_023587	70757	Mm.27286	NM_023587	ENSMUSG00000035376	Hacd2	6330408J20Rik|AI255777|AI481689|Hcad2|Ptplb	3-hydroxyacyl-CoA dehydratase 2	protein-coding
mm_170784.1	chr2	174437396	174437409	-	1	NA	intron (NM_022325, intron 2 of 5)	intron (NM_022325, intron 2 of 5)	1637	NM_022325	64138	Mm.156919	NM_022325	ENSMUSG00000016256	Ctsz	AI787083|AU019819|CTSX|D2Wsu143e	cathepsin Z	protein-coding
mm_61352.1	chr7	68289547	68289550	+	1	NA	intron (NM_001013811, intron 1 of 8)	intron (NM_001013811, intron 1 of 8)	-12954	NR_040340	100504026	Mm.426764	NR_040340	ENSMUSG00000086628	Gm16157	OTTMUSG00000031023	predicted gene 16157	ncRNA
mm_55017.1	chr6	48840772	48840786	-	1	NA	promoter-TSS (NM_025326)	promoter-TSS (NM_025326)	209	NM_023056	65963	Mm.28385	NM_023056	ENSMUSG00000029810	Tmem176b	1810009M01Rik|Clast1|Lr8	transmembrane protein 176B	protein-coding
mm_106873.1	chr12	8010533	8010550	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	32864	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_88916.1	chr10	81182401	81182410	+	1	NA	promoter-TSS (NM_001190474)	promoter-TSS (NM_001190474)	-602	NM_001190474	13144	Mm.10294	NM_007828	ENSMUSG00000034974	Dapk3	ZIPK|dlk	death-associated protein kinase 3	protein-coding
mm_27194.1	chr3	34761196	34761243	-	1	NA	Intergenic	Intergenic	-10856	NR_110488	102638436	Mm.261793	NR_110488	ENSMUSG00000106519	Gm38509	Peril	predicted gene, 38509	ncRNA
mm_108063.1	chr12	73937660	73937671	+	1	NA	exon (NM_010431, exon 8 of 15)	exon (NM_010431, exon 8 of 15)	-26865	NM_178392	75627	Mm.25937	NM_178392	ENSMUSG00000021113	Snapc1	2700033G17Rik|AU015787	small nuclear RNA activating complex, polypeptide 1	protein-coding
mm_112484.1	chr13	5869640	5869718	+	1	NA	3' UTR (NM_011803, exon 4 of 4)	3' UTR (NM_011803, exon 4 of 4)	8190	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_125441.1	chr15	44787747	44787769	+	1	NA	promoter-TSS (NR_040309)	promoter-TSS (NR_040309)	-5	NR_040309	69659	Mm.352401	NR_040309	ENSMUSG00000097102	2310069G16Rik	-	RIKEN cDNA 2310069G16 gene	ncRNA
mm_63296.1	chr7	126807815	126807825	+	1	NA	Intergenic	Intergenic	-7373	NM_001177308	11674	Mm.275831	NM_007438	ENSMUSG00000030695	Aldoa	Aldo-1|Aldo1	aldolase A, fructose-bisphosphate	protein-coding
mm_95979.1	chr11	58963824	58963829	+	1	NA	promoter-TSS (NM_031172)	promoter-TSS (NM_031172)	45	NM_031172	56631	Mm.179733	NM_031172	ENSMUSG00000036964	Trim17	Rnf16|terf	tripartite motif-containing 17	protein-coding
mm_127898.1	chr15	9469446	9469456	-	1	NA	Intergenic	Intergenic	33423	NM_029341	75568	Mm.82143	NM_029341	ENSMUSG00000039676	Capsl	1700028N11Rik|AW125205	calcyphosine-like	protein-coding
mm_129599.1	chr15	79834289	79834314	-	1	NA	promoter-TSS (NM_001013360)	promoter-TSS (NM_001013360)	32	NM_001013360	504193	Mm.38438	NM_029079	ENSMUSG00000089837	Npcd	Cbx6-Nptxr	neuronal pentraxin chromo domain	protein-coding
mm_114042.1	chr13	54071816	54071859	+	1	NA	promoter-TSS (NM_027324)	promoter-TSS (NM_027324)	-8	NM_027324	14057	Mm.134191	NM_027324	ENSMUSG00000021474	Sfxn1	2810002O05Rik|A930015P12Rik|f	sideroflexin 1	protein-coding
mm_79187.1	chr9	48418310	48418328	+	1	NA	Intergenic	Intergenic	-36025	NR_026561	667933	Mm.491076	NR_026561		Gm8884	EG667933	predicted gene 8884	ncRNA
mm_153935.1	chr19	47460609	47460623	-	1	NA	intron (NM_001164717, intron 1 of 13)	intron (NM_001164717, intron 1 of 13)	3795	NM_001164717	14218	Mm.127560	NM_008018	ENSMUSG00000053617	Sh3pxd2a	2310014D11Rik|AA589508|AI256723|AI413738|C230050L11|EG329070|Fish|Gm5098|Sh3md1|TSK5|Tks5	SH3 and PX domains 2A	protein-coding
mm_51724.1	chr6	86946920	86946942	+	1	NA	exon (NM_177762, exon 7 of 20)	exon (NM_177762, exon 7 of 20)	-62905	NM_001170591	56748	Mm.23809	NM_020045	ENSMUSG00000029993	Nfu1	0610006G17Rik|CGI-33|Hirip5	NFU1 iron-sulfur cluster scaffold	protein-coding
mm_23525.1	chr3	60617440	60617472	+	1	NA	intron (NM_001310514, intron 7 of 8)	intron (NM_001310514, intron 7 of 8)	116277	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_129720.1	chr15	81955704	81955732	-	1	NA	exon (NM_001282040, exon 4 of 7)	exon (NM_001282040, exon 4 of 7)	5212	NM_001282040	29858	Mm.18939	NM_013872	ENSMUSG00000022474	Pmm1	C77612	phosphomannomutase 1	protein-coding
mm_39100.1	chr4	154920058	154920069	-	1	NA	Intergenic	L1_Mus2|LINE|L1	8014	NM_178931	230979	Mm.215147	NM_178931	ENSMUSG00000042333	Tnfrsf14	Atar|HveA|Hvem|Tnfrs14	tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)	protein-coding
mm_111240.1	chr12	84773074	84773083	-	1	NA	promoter-TSS (NM_028863)	promoter-TSS (NM_028863)	34	NM_023409	67963	Mm.282556	NM_023409	ENSMUSG00000021242	Npc2	2700012J19Rik|AA408070|AU045843|HE1	Niemann-Pick type C2	protein-coding
mm_42273.1	chr5	114146526	114146550	+	1	NA	Intergenic	Intergenic	15382	NM_011677	22256	Mm.1393	NM_011677	ENSMUSG00000029591	Ung	UNG1|UNG2	uracil DNA glycosylase	protein-coding
mm_160754.1	chr10	81812134	81812134	+	1	NA	promoter-TSS (NM_001142963).2	promoter-TSS (NM_001142963).2	-52	NM_001142963	100233208	Mm.327168	NM_001142963	ENSMUSG00000096856	Gm10778	ENSMUSG00000074860	predicted gene 10778	protein-coding
mm_131610.1	chr16	19241215	19241259	+	1	NA	Intergenic	Intergenic	45504	NM_146451	258443	Mm.377506	NM_146451	ENSMUSG00000050742	Olfr164	MOR279-2	olfactory receptor 164	protein-coding
mm_43870.1	chr5	143503633	143503635	+	1	NA	3' UTR (NM_144915, exon 15 of 15)	3' UTR (NM_144915, exon 15 of 15)	24359	NM_009007	19353	Mm.292510	NM_009007	ENSMUSG00000001847	Rac1	AL023026|D5Ertd559e	RAS-related C3 botulinum substrate 1	protein-coding
mm_126943.1	chr15	92051177	92051225	+	1	NA	promoter-TSS (NM_001159648)	promoter-TSS (NM_001159648)	36	NM_001159648	12805	Mm.4911	NM_007727	ENSMUSG00000055022	Cntn1	AW495098|CNTN|F3cam|usl	contactin 1	protein-coding
mm_46986.1	chr5	115313761	115313772	-	1	NA	intron (NR_131932, intron 1 of 1)	intron (NR_131932, intron 1 of 1)	12646	NR_131932	102639268	Mm.319998	NR_131932		Gm13830	OTTMUSG00000014646	predicted gene 13830	ncRNA
mm_57459.1	chr6	125172056	125172064	-	1	NA	intron (NM_146171, intron 22 of 31)	B1_Mur2|SINE|Alu	-5593	NM_001289726	14433	Mm.304088	NM_008084	ENSMUSG00000057666	Gapdh	Gapd	glyceraldehyde-3-phosphate dehydrogenase	protein-coding
mm_162299.1	chr1	34459725	34459740	+	1	NA	promoter-TSS (NM_011206)	promoter-TSS (NM_011206)	-14	NM_011206	19253	Mm.361	NM_011206	ENSMUSG00000026126	Ptpn18	FLP1|HSCF|PTP-HSCF|PTP-K1|Ptpk1	protein tyrosine phosphatase, non-receptor type 18	protein-coding
mm_126520.1	chr15	81912260	81912280	+	1	NA	exon (NM_080633, exon 14 of 18)	exon (NM_080633, exon 14 of 18)	13943	NM_030229	78929	Mm.215115	NM_030229	ENSMUSG00000022476	Polr3h	5031409G22Rik|RPC8	polymerase (RNA) III (DNA directed) polypeptide H	protein-coding
mm_42107.1	chr5	110544327	110544370	+	1	NA	promoter-TSS (NM_198306)	promoter-TSS (NM_198306)	-7	NM_198306	231605	Mm.275748	NM_198306	ENSMUSG00000033316	Galnt9	GalNAc-T9	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 9	protein-coding
mm_28165.1	chr3	87846788	87846801	-	1	NA	promoter-TSS (NM_021309)	promoter-TSS (NM_021309)	39	NM_021309	27371	Mm.86361	NM_021309	ENSMUSG00000028071	Sh2d2a	Lad|Ribp|Tsad	SH2 domain containing 2A	protein-coding
mm_166000.1	chr4	115563621	115563631	+	1	NA	promoter-TSS (NM_001252539)	promoter-TSS (NM_001252539)	-23	NM_001252539	666168	Mm.482086	NM_201640	ENSMUSG00000028712	Cyp4a31	-	cytochrome P450, family 4, subfamily a, polypeptide 31	protein-coding
mm_132694.1	chr16	43253702	43253704	+	1	NA	intron (NM_181058, intron 1 of 6)	intron (NM_181058, intron 1 of 6)	6419	NM_019778	56490	Mm.136238	NM_019778	ENSMUSG00000022708	Zbtb20	1300017A20Rik|7330412A13Rik|A930017C21Rik|D16Wsu73e|DPZF|HOF|ODA-8S|Oda8|Zfp288	zinc finger and BTB domain containing 20	protein-coding
mm_148016.1	chr18	68427880	68427913	-	1	NA	promoter-TSS (NM_001271717)	promoter-TSS (NM_001271717)	-56	NM_001271717	17200	Mm.426053	NM_008560	ENSMUSG00000045569	Mc2r	ACTH-R|ACTHR|MC2-R	melanocortin 2 receptor	protein-coding
mm_44798.1	chr5	32785610	32785648	-	1	NA	promoter-TSS (NM_177298)	promoter-TSS (NM_177298)	-3	NM_177298	320951	Mm.273765	NM_177298	ENSMUSG00000023452	Pisd	9030221M09Rik	phosphatidylserine decarboxylase	protein-coding
mm_172122.1	chr6	3201231	3201240	+	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	-87284	NR_036696	667335	Mm.380219	NR_036696	ENSMUSG00000106779	Gm8579	EG667335	spermatogenesis associated glutamate (E)-rich protein 4a pseudogene	pseudo
mm_128333.1	chr15	38455121	38455139	-	1	NA	Intergenic	Intergenic	35417	NR_105916	102465574		NR_105916	ENSMUSG00000099110	Mir6951	Gm27765|mmu-mir-6951	microRNA 6951	ncRNA
mm_87505.1	chr10	52381494	52381499	+	1	NA	intron (NM_001199272, intron 1 of 8)	intron (NM_001199272, intron 1 of 8)	628	NM_053187	94221	Mm.390258	NM_053187	ENSMUSG00000019861	Gopc	2210402P09Rik|AI844555|CAL|FIG|GOPC1|PIST	golgi associated PDZ and coiled-coil motif containing	protein-coding
mm_141857.1	chr17	34803498	34803512	-	1	NA	intron (NM_009995, intron 3 of 9)	intron (NM_009995, intron 3 of 9)	921	NM_009995	13079	Mm.440407	NM_009995	ENSMUSG00000024365	Cyp21a1	21-OH|21OH|21OHA|21OHB|CYP21OH-A|Cyp21|Cyp21-ps1|Cyp21B|Cyp21a2-ps|Cyp21a2ps|Oh21-1|Oh21-2	cytochrome P450, family 21, subfamily a, polypeptide 1	protein-coding
mm_20026.1	chr2	119462236	119462256	-	1	NA	intron (NM_026574, intron 1 of 35)	ORR1C2|LTR|ERVL-MaLR	15383	NM_026574	68142	Mm.330496	NM_026574	ENSMUSG00000034154	Ino80	2310079N15Rik|4632409L19Rik|Inoc1	INO80 complex subunit	protein-coding
mm_484.1	chr1	36761794	36761843	+	1	NA	promoter-TSS (NM_009539)	promoter-TSS (NM_009539)	20	NM_009539	22637	Mm.8038	NM_009539	ENSMUSG00000026117	Zap70	Srk|ZAP-70|mrtle|mur	zeta-chain (TCR) associated protein kinase	protein-coding
mm_125666.1	chr15	65805006	65805012	+	1	NA	intron (NM_133766, intron 1 of 22)	intron (NM_133766, intron 1 of 22)	17968	NM_133766	76740	Mm.260647	NM_133766	ENSMUSG00000015002	Efr3a	A130089M23Rik|BB071175|C76891|C920006C10Rik|D030063F01Rik|mKIAA0143	EFR3 homolog A	protein-coding
mm_15531.1	chr2	158382965	158382975	+	1	NA	3' UTR (NM_175692, exon 5 of 5)	3' UTR (NM_175692, exon 5 of 5)	7332	NM_175692	319317	Mm.294494	NM_175692	ENSMUSG00000044349	Snhg11	A930034L06Rik|AI854265|AL022637|AW319638|E130013N09Rik	small nucleolar RNA host gene 11	protein-coding
mm_29517.1	chr3	116424135	116424146	-	1	NA	promoter-TSS (NM_001173553)	promoter-TSS (NM_001173553)	-108	NM_001173553	229776	Mm.17647	NM_001080818	ENSMUSG00000033502	Cdc14a	A830059A17Rik|CDC14A2|CDC14a1|Cdc14	CDC14 cell division cycle 14A	protein-coding
mm_34158.1	chr4	139431119	139431129	+	1	NA	intron (NM_001160319, intron 48 of 105)	intron (NM_001160319, intron 48 of 105)	50465	NM_001160319	69116	Mm.271956	NM_001160319	ENSMUSG00000066036	Ubr4	1810009A16Rik|A930005E13Rik|D930005K06Rik|Gm1032|Gm1666|N28143|RBAF600|Zubr1|mKIAA0462|p600	ubiquitin protein ligase E3 component n-recognin 4	protein-coding
mm_103267.1	chr11	71285307	71285321	-	1	NA	promoter-TSS (NR_027858)	promoter-TSS (NR_027858)	-82	NR_027858	627984	Mm.390378	NM_001039234	ENSMUSG00000092528	Nlrp1c-ps	Nalp1c|Nlrp1c|OTTMUSG00000006090	NLR family, pyrin domain containing 1C, pseudogene	pseudo
mm_105292.1	chr11	102470102	102470110	-	1	NA	promoter-TSS (NM_010575)	promoter-TSS (NM_010575)	-223	NM_010575	16399	Mm.26646	NM_010575	ENSMUSG00000034664	Itga2b	AI172977|CD41|CD41B|GpIIb|alphaIIb	integrin alpha 2b	protein-coding
mm_59716.1	chr7	28767222	28767226	+	1	NA	promoter-TSS (NM_010908)	promoter-TSS (NM_010908)	472	NM_001122766	64383	Mm.272443	NM_022432	ENSMUSG00000015149	Sirt2	5730427M03Rik|SIR2L2|Sir2l	sirtuin 2	protein-coding
mm_107086.1	chr12	17354872	17354892	+	1	NA	promoter-TSS (NR_037226)	promoter-TSS (NR_037226)	-510	NR_037226	100526470		NR_037226	ENSMUSG00000093037	Mir3066	mir-3066|mmu-mir-3066	microRNA 3066	ncRNA
mm_60028.1	chr7	30973787	30973816	+	1	NA	promoter-TSS (NM_017405)	promoter-TSS (NM_017405)	-3	NR_038860	76415	Mm.259739	NM_175240	ENSMUSG00000046826	Fam187b	1700020B09Rik|Tmem162	family with sequence similarity 187, member B	protein-coding
mm_105061.1	chr11	100715885	100715894	-	1	NA	3' UTR (NM_001305003, exon 6 of 6)	3' UTR (NM_001305003, exon 6 of 6)	2039	NM_029307	75482	Mm.46175	NM_029307	ENSMUSG00000017832	Hspb9	1700007H20Rik	heat shock protein, alpha-crystallin-related, B9	protein-coding
mm_119852.1	chr14	54441057	54441115	+	1	NA	3' UTR (NM_008608, exon 10 of 10)	3' UTR (NM_008608, exon 10 of 10)	9488	NM_008608	17387	Mm.280175	NM_008608	ENSMUSG00000000957	Mmp14	AI325305|MMP-X1|MT-MMP-1|MT1-MMP|sabe	matrix metallopeptidase 14 (membrane-inserted)	protein-coding
mm_124853.1	chr15	9528491	9528503	+	1	NA	intron (NM_008372, intron 1 of 7)	intron (NM_008372, intron 1 of 7)	1379	NM_008372	16197	Mm.389	NM_008372	ENSMUSG00000003882	Il7r	CD127|IL-7Ralpha	interleukin 7 receptor	protein-coding
mm_38445.1	chr4	139967584	139967618	-	1	NA	promoter-TSS (NR_035519)	promoter-TSS (NR_035519)	19	NR_035519	100316727		NR_035519	ENSMUSG00000089294	Mir2139	mmu-mir-2139	microRNA 2139	ncRNA
mm_127384.1	chr15	100952423	100952424	+	1	NA	intron (NM_001077499, intron 2 of 26)	intron (NM_001077499, intron 2 of 26)	16152	NM_011323	20273	Mm.385012	NM_011323	ENSMUSG00000023033	Scn8a	AI853486|C630029C19Rik|NaCh6|Nav1.6|dmu|med|mnd-2|mnd2|nmf2|nmf335|nmf58|nur14|seal	sodium channel, voltage-gated, type VIII, alpha	protein-coding
mm_36514.1	chr4	84357043	84357045	-	1	NA	intron (NM_172870, intron 4 of 5)	intron (NM_172870, intron 4 of 5)	-312165	NR_130998	78238	Mm.243903	NR_130998	ENSMUSG00000085217	6030471H07Rik	-	RIKEN cDNA 6030471H07 gene	ncRNA
mm_42647.1	chr5	118639525	118639528	+	1	NA	intron (NM_001347445, intron 2 of 30)	intron (NM_001347445, intron 2 of 30)	78807	NM_172424	76199	Mm.206238	NM_172424	ENSMUSG00000018076	Med13l	2210413I17Rik|6330591G05Rik|9030618F05Rik|Thrap2|Trap240L|mKIAA1025	mediator complex subunit 13-like	protein-coding
mm_31367.1	chr4	47306054	47306081	+	1	NA	intron (NM_009928, intron 34 of 39)	intron (NM_009928, intron 34 of 39)	-47155	NM_001312868	21812	Mm.197552	NM_009370	ENSMUSG00000007613	Tgfbr1	ALK5|AU017191|Alk-5|ESK2|TGFR-1|TbetaR-I|TbetaRI	transforming growth factor, beta receptor I	protein-coding
mm_5341.1	chr1	24587414	24587425	-	1	NA	promoter-TSS (NM_007733)	promoter-TSS (NM_007733)	18	NM_007733	12823	Mm.329196	NM_007733	ENSMUSG00000026141	Col19a1	-	collagen, type XIX, alpha 1	protein-coding
mm_42328.1	chr5	114901851	114901866	+	1	NA	intron (NM_011854, intron 3 of 5)	intron (NM_011854, intron 3 of 5)	4924	NM_011854	23962	Mm.228363	NM_011854	ENSMUSG00000029561	Oasl2	M1204|Mmu-OASL|Oasl	2'-5' oligoadenylate synthetase-like 2	protein-coding
mm_38788.1	chr4	148089182	148089190	-	1	NA	Intergenic	Intergenic	-1122	NM_001301281	11610	Mm.46247	NM_009642	ENSMUSG00000029007	Agtrap	3300002E14Rik|AT1R|Atrap|D4Wsu124e	angiotensin II, type I receptor-associated protein	protein-coding
mm_115363.1	chr13	112987823	112987838	+	1	NA	promoter-TSS (NM_001081062)	promoter-TSS (NM_001081062)	28	NM_001081062	218630	Mm.25457	NM_001081062	ENSMUSG00000042417	Ccno	C86987|Ccnu|E130318K11|Ung2	cyclin O	protein-coding
mm_19678.1	chr2	103454552	103454580	-	1	NA	3' UTR (NM_009804, exon 13 of 13)	3' UTR (NM_009804, exon 13 of 13)	30498	NM_010125	13711	Mm.20888	NM_010125	ENSMUSG00000027186	Elf5	ESE-2|ESE-5|ESE-5.	E74-like factor 5	protein-coding
mm_41368.1	chr5	90518942	90518956	+	1	NA	promoter-TSS (NM_145146)	promoter-TSS (NM_145146)	0	NM_145146	280662	Mm.348786	NM_145146	ENSMUSG00000029369	Afm	Alf|alpha-Alb	afamin	protein-coding
mm_153894.1	chr19	46985373	46985398	-	1	NA	intron (NM_001164363, intron 1 of 17)	intron (NM_001164363, intron 1 of 17)	-15818	NM_001164365	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_93356.1	chr10	103028772	103028782	-	1	NA	promoter-TSS (NM_172553)	promoter-TSS (NM_172553)	0	NM_172553	216285	Mm.19287	NM_172553	ENSMUSG00000036602	Alx1	AI314867|C130005I02|Cart1	ALX homeobox 1	protein-coding
mm_124471.1	chr14	121378939	121378998	-	1	NA	5' UTR (NM_145465, exon 1 of 11)	5' UTR (NM_145465, exon 1 of 11)	262	NM_145465	223255	Mm.390756	NM_145465	ENSMUSG00000063410	Stk24	1810013H02Rik|C76483|MST-3|Mst3|STE20	serine/threonine kinase 24	protein-coding
mm_10864.1	chr2	25080482	25080492	+	1	NA	5' UTR (NM_028093, exon 1 of 10)	5' UTR (NM_028093, exon 1 of 10)	164	NM_028093	72090	Mm.33403	NM_028093	ENSMUSG00000036813	Entpd8	-	ectonucleoside triphosphate diphosphohydrolase 8	protein-coding
mm_168167.1	chr10	5289485	5289485	-	1	NA	exon (NM_001347711, exon 55 of 146)	exon (NM_001347711, exon 55 of 146)	-94778	NM_001079686	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_153380.1	chr19	40376740	40376750	-	1	NA	exon (NM_178362, exon 7 of 29)	exon (NM_178362, exon 7 of 29)	25565	NM_001034964	20411	Mm.210815	NM_009166	ENSMUSG00000025006	Sorbs1	2310065E01Rik|9530001P15Rik|CAP|SH3P12|Sh3d5|mKIAA1296	sorbin and SH3 domain containing 1	protein-coding
mm_114257.1	chr13	56706555	56706559	+	1	NA	intron (NM_001164042, intron 1 of 6)	B1_Mur2|SINE|Alu	2889	NM_001164042	17129	Mm.272920	NM_008541	ENSMUSG00000021540	Smad5	1110051M15Rik|AI451355|Dwf-C|Madh5|MusMLP	SMAD family member 5	protein-coding
mm_47607.1	chr5	125102903	125102913	-	1	NA	intron (NM_011424, intron 6 of 46)	intron (NM_011424, intron 6 of 46)	76306	NM_001253905	20602	Mm.278646	NM_011424	ENSMUSG00000029478	Ncor2	N-CoR|SMRT|SMRTe	nuclear receptor co-repressor 2	protein-coding
mm_57633.1	chr6	128340304	128340308	-	1	NA	intron (NM_011657, intron 1 of 10)	B1F2|SINE|Alu	15545	NM_011657	22158	Mm.291783	NM_011657	ENSMUSG00000001521	Tulp3	2310022L06Rik|AI316887	tubby-like protein 3	protein-coding
mm_30401.1	chr3	152253071	152253076	-	1	NA	exon (NM_199465, exon 3 of 13)	exon (NM_199465, exon 3 of 13)	13247	NM_199465	68810	Mm.200188	NM_199465	ENSMUSG00000039103	Nexn	1110046H09Rik|AA553326|NELIN	nexilin	protein-coding
mm_98955.1	chr11	98470536	98470554	+	1	NA	intron (NM_011771, intron 7 of 7)	intron (NM_011771, intron 7 of 7)	23711	NM_010346	14786	Mm.276702	NM_010346	ENSMUSG00000019312	Grb7	mKIAA4028	growth factor receptor bound protein 7	protein-coding
mm_29127.1	chr3	105426591	105426601	-	1	NA	Intergenic	Intergenic	-25734	NM_001039347	56543	Mm.44530	NM_019931	ENSMUSG00000040896	Kcnd3	AW045978|Kncd3|Kv4.3	potassium voltage-gated channel, Shal-related family, member 3	protein-coding
mm_86940.1	chr10	24595490	24595520	+	1	NA	promoter-TSS (NM_010217)	promoter-TSS (NM_010217)	63	NM_010217	14219	Mm.390287	NM_010217	ENSMUSG00000019997	Ctgf	Ccn2|Fisp12|Hcs24|fisp-12	connective tissue growth factor	protein-coding
mm_119611.1	chr14	51105329	51105408	+	1	NA	3' UTR (NM_201239, exon 2 of 2)	3' UTR (NM_201239, exon 2 of 2)	9368	NM_201239	58809	Mm.202665	NM_021472	ENSMUSG00000021876	Rnase4	C730049F20Rik|Rab1	ribonuclease, RNase A family 4	protein-coding
mm_55253.1	chr6	52909619	52909621	-	1	NA	promoter-TSS (NM_001168277)	promoter-TSS (NM_001168277)	0	NM_001168277	231986	Mm.386865	NM_173406	ENSMUSG00000063568	Jazf1	AI591476|C820002C15|Jaz1|Tip27	JAZF zinc finger 1	protein-coding
mm_158282.1	chrX	111536386	111536388	-	1	NA	intron (NM_025949, intron 1 of 24)	intron (NM_025949, intron 1 of 24)	1572	NM_025949	67071	Mm.37617	NM_025949	ENSMUSG00000025665	Rps6ka6	2610524K04Rik|RSK4|S6K-alpha-6	ribosomal protein S6 kinase polypeptide 6	protein-coding
mm_157123.1	chrX	9445842	9445861	-	1	NA	intron (NM_007807, intron 9 of 12)	RMER4A|LTR|ERVK	23473	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_87420.1	chr10	50666287	50666291	+	1	NA	intron (NM_198007, intron 13 of 41)	intron (NM_198007, intron 13 of 41)	73620	NM_198007	77987	Mm.222497	NM_198007	ENSMUSG00000038774	Ascc3	ASC1p200|B630009I04Rik|BC023451|D430001L07Rik|D630041L21|Helic1|RNAH	activating signal cointegrator 1 complex subunit 3	protein-coding
mm_88079.1	chr10	67981795	67981797	+	1	NA	intron (NM_001081346, intron 1 of 12)	B1_Mm|SINE|Alu	2198	NM_001081346	170799	Mm.209844	NM_133244	ENSMUSG00000037846	Rtkn2	B130039D23Rik|Mbf|Plekhk1	rhotekin 2	protein-coding
mm_5284.1	chr1	20626821	20626842	-	1	NA	Intergenic	L1_Mus3|LINE|L1	-8774	NM_153179	241035	Mm.249253	NM_153179	ENSMUSG00000043760	Pkhd1	AI118496|AI182499|FPC|Tigm1	polycystic kidney and hepatic disease 1	protein-coding
mm_62128.1	chr7	96951553	96951597	+	1	NA	promoter-TSS (NM_153591)	promoter-TSS (NM_153591)	48	NM_153591	244141	Mm.274864	NM_153591	ENSMUSG00000018995	Nars2	AI875199	asparaginyl-tRNA synthetase 2 (mitochondrial)(putative)	protein-coding
mm_90769.1	chr10	5805413	5805454	-	1	NA	promoter-TSS (NM_025995)	promoter-TSS (NM_025995)	32	NM_025995	67141	Mm.197520	NM_025995	ENSMUSG00000019773	Fbxo5	2510044I10Rik|C85305|Emi1|Fbxo31	F-box protein 5	protein-coding
mm_138260.1	chr17	34592249	34592329	+	1	NA	promoter-TSS (NM_017463)	promoter-TSS (NM_017463)	-182	NM_017463	18515	Mm.390957	NM_017463	ENSMUSG00000034673	Pbx2	AU043397|G17	pre B cell leukemia homeobox 2	protein-coding
mm_103096.1	chr11	69921330	69921347	-	1	NA	promoter-TSS (NM_001166592)	promoter-TSS (NM_001166592)	48	NM_001166591	276770	Mm.18026	NM_181582	ENSMUSG00000078812	Eif5a	AA410058|D19Wsu54e|Eif4d|Eif5a1|eIF-4D|eIF-5A|eIF-5A-1|eIF-5A1	eukaryotic translation initiation factor 5A	protein-coding
mm_117463.1	chr13	75943675	75943696	-	1	NA	5' UTR (NM_028493, exon 1 of 12)	5' UTR (NM_028493, exon 1 of 12)	139	NM_028493	73296	Mm.276200	NM_028493	ENSMUSG00000021589	Rhobtb3	1700040C17Rik|2610033K01Rik|4930503C18Rik|AI317148|AW208826|mKIAA0878	Rho-related BTB domain containing 3	protein-coding
mm_46171.1	chr5	96921153	96921160	-	1	NA	promoter-TSS (NR_131152)	promoter-TSS (NR_131152)	-116	NR_131152	666266	Mm.32442	NR_131152	ENSMUSG00000106357	Gm8013	EG666266	predicted gene 8013	ncRNA
mm_49027.1	chr6	4759652	4759663	+	1	NA	3' UTR (NM_130877, exon 2 of 2)	3' UTR (NM_130877, exon 2 of 2)	12351	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_54755.1	chr6	41034322	41034371	-	1	NA	exon (NM_023333, exon 2 of 5)	exon (NM_023333, exon 2 of 5)	1163	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_93795.1	chr10	120783311	120783316	-	1	NA	3' UTR (NM_177092, exon 7 of 7)	3' UTR (NM_177092, exon 7 of 7)	17581	NR_038003	70874	Mm.427286	NR_038000	ENSMUSG00000044544	4921513I03Rik	-	RIKEN cDNA 4921513I03 gene	ncRNA
mm_28119.1	chr3	86920334	86920348	-	1	NA	5' UTR (NM_001195500, exon 1 of 12)	5' UTR (NM_001195500, exon 1 of 12)	543	NM_001195496	70762	Mm.44490	NM_027539	ENSMUSG00000028078	Dclk2	6330415M09Rik|AU044875|CL2|CLICK2|Click-II|Dcamkl2	doublecortin-like kinase 2	protein-coding
mm_7555.1	chr1	124688040	124688043	-	1	NA	Intergenic	Intergenic	-642482	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_2995.1	chr1	133223041	133223048	+	1	NA	Intergenic	Intergenic	-23053	NM_001160268	240753	Mm.253559	NM_182930	ENSMUSG00000041757	Plekha6	9530028L01Rik|AU042621|Pepp3	pleckstrin homology domain containing, family A member 6	protein-coding
mm_167005.1	chr7	51861806	51861834	+	1	NA	promoter-TSS (NM_001330608)	promoter-TSS (NM_001330608)	-195	NM_001330608	14453	Mm.207360	NM_008087	ENSMUSG00000030498	Gas2	Gas-2	growth arrest specific 2	protein-coding
mm_151854.1	chr19	5796712	5796737	-	1	NA	promoter-TSS (NR_144621)	promoter-TSS (NR_144621)	-743	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_38861.1	chr4	149426604	149426638	-	1	NA	promoter-TSS (NM_022022)	promoter-TSS (NM_022022)	10	NM_022022	63958	Mm.415260	NM_022022	ENSMUSG00000028960	Ube4b	4930551I19Rik|4933406G05Rik|AU014668|D4Bwg0973e|UFD2|UFD2a|Ufd2p|mKIAA0684	ubiquitination factor E4B	protein-coding
mm_41201.1	chr5	88328342	88328373	+	1	NA	exon (NM_008644, exon 3 of 3)	exon (NM_008644, exon 3 of 3)	11045	NM_008644	17830	Mm.200411	NM_008644	ENSMUSG00000064156	Prol1	Muc10	proline rich, lacrimal 1	protein-coding
mm_74164.1	chr8	123411545	123411562	+	1	NA	promoter-TSS (NM_023279)	promoter-TSS (NM_023279)	-11	NM_023279	22152	Mm.40068	NM_023279	ENSMUSG00000062380	Tubb3	3200002H15Rik|M(beta)3|M(beta)6	tubulin, beta 3 class III	protein-coding
mm_159075.1	chr2	25737009	25737009	+	1	NA	promoter-TSS (NM_001099301)	promoter-TSS (NM_001099301)	0	NM_001099301	383678	Mm.464561	NM_001099301	ENSMUSG00000079539	Obp2b	Lcn14|OTTMUSG00000012631	odorant binding protein 2B	protein-coding
mm_33036.1	chr4	122836237	122836259	+	1	NA	promoter-TSS (NM_008917)	promoter-TSS (NM_008917)	21	NM_008917	19063	Mm.277719	NM_008917	ENSMUSG00000028657	Ppt1	9530043G02Rik|AA960502|C77813|CLN1|D4Ertd184e|INCL|PPT	palmitoyl-protein thioesterase 1	protein-coding
mm_142026.1	chr17	35219587	35219593	-	1	NA	TTS (NM_010909)	TTS (NM_010909)	-14239	NM_010735	16992	Mm.87787	NM_010735	ENSMUSG00000024402	Lta	LT|LT-[a]|LT-alpha|LT[a]|LTalpha|Ltx|TNF-beta|TNFSF1|Tnfb|Tnfsf1b|Tnlg1e|hlb382	lymphotoxin A	protein-coding
mm_63555.1	chr7	128077773	128077775	+	1	NA	intron (NM_001082960, intron 6 of 29)	Lx3A|LINE|L1	15134	NM_008401	16409	Mm.262106	NM_008401	ENSMUSG00000030786	Itgam	CD11b/CD18|CR3|CR3A|Cd11b|F730045J24Rik|Ly-40|MAC1|Mac-1|Mac-1a	integrin alpha M	protein-coding
mm_130247.1	chr15	96640790	96640825	-	1	NA	intron (NM_001166458, intron 1 of 15)	intron (NM_001166458, intron 1 of 15)	1155	NM_134086	105727	Mm.103568	NM_134086	ENSMUSG00000023169	Slc38a1	AA408026|AA409865|AL022800|AU015942|NAT2	solute carrier family 38, member 1	protein-coding
mm_61767.1	chr7	82867305	82867313	+	1	NA	promoter-TSS (NM_175366)	promoter-TSS (NM_175366)	-24	NM_175366	108797	Mm.306789	NM_175366	ENSMUSG00000057706	Mex3b	4931439A04Rik|M-04814|Rkhd3|mKIAA2009	mex3 RNA binding family member B	protein-coding
mm_143553.1	chr17	74173762	74173774	-	1	NA	Intergenic	Intergenic	121095	NM_133771	76890	Mm.311874	NM_133771	ENSMUSG00000058704	Memo1	0610016J10Rik|D930048L02Rik	mediator of cell motility 1	protein-coding
mm_168081.1	chr10	121628794	121628804	-	1	NA	Intergenic	RMER6B|LTR|ERVK	-2483	NM_001081056	73192	Mm.25042	NM_001081056	ENSMUSG00000034667	Xpot	1110004L07Rik|3110065H13Rik|AI452076|C79645|EXPORTIN-T	exportin, tRNA (nuclear export receptor for tRNAs)	protein-coding
mm_56720.1	chr6	115592511	115592529	-	1	NA	promoter-TSS (NM_001101431)	promoter-TSS (NM_001101431)	56	NM_001101431	70291	Mm.133694	NM_001101431	ENSMUSG00000068011	Mkrn2os	2510049J12Rik	makorin, ring finger protein 2, opposite strand	protein-coding
mm_145541.1	chr18	60807909	60807924	+	1	NA	exon (NM_010545, exon 2 of 8)	exon (NM_010545, exon 2 of 8)	4067	NM_010545	16149	Mm.439737	NM_010545	ENSMUSG00000024610	Cd74	CLIP|DHLAG|HLADG|Ia-GAMMA|Ii	CD74 antigen (invariant polypeptide of major histocompatibility complex, class II antigen-associated)	protein-coding
mm_18566.1	chr2	65293539	65293546	-	1	NA	Intergenic	MT2A|LTR|ERVL	-54916	NM_027225	319876	Mm.34159	NM_027225	ENSMUSG00000034903	Cobll1	1810047P18Rik|Coblr1|D430044D16Rik	Cobl-like 1	protein-coding
mm_73452.1	chr8	106400044	106400061	+	1	NA	Intergenic	Intergenic	-15287	NM_011764	22751	Mm.295582	NM_011764	ENSMUSG00000031907	Zfp90	6430515L01Rik|KRAB17|NK10|Zfp64|Zfp83|mKIAA1954	zinc finger protein 90	protein-coding
mm_116030.1	chr13	25269921	25270025	-	1	NA	promoter-TSS (NM_009513)	promoter-TSS (NM_009513)	23	NM_009513	22360	Mm.4766	NM_009513	ENSMUSG00000048978	Nrsn1	Neurensin-1|Neuro-p24|Vmp	neurensin 1	protein-coding
mm_147155.1	chr18	36679286	36679349	-	1	NA	promoter-TSS (NM_146085)	promoter-TSS (NM_146085)	49	NM_146085	225372	Mm.89673	NM_146085	ENSMUSG00000006050	Apbb3	Fe65l2|Rirl2|TR2S	amyloid beta (A4) precursor protein-binding, family B, member 3	protein-coding
mm_80569.1	chr9	83925184	83925194	+	1	NA	promoter-TSS (NM_001305935)	promoter-TSS (NM_001305935)	52	NM_001305935	12040	Mm.12819	NM_199195	ENSMUSG00000032263	Bckdhb	BCKDE1B|BCKDH E1-beta	branched chain ketoacid dehydrogenase E1, beta polypeptide	protein-coding
mm_88647.1	chr10	79954402	79954445	+	1	NA	3' UTR (NM_001288626, exon 9 of 9)	3' UTR (NM_001288626, exon 9 of 9)	-5729	NM_175450	216156	Mm.35828	NM_175450	ENSMUSG00000035754	Wdr18	2310012I10Rik|AU044733|AW122032	WD repeat domain 18	protein-coding
mm_55718.1	chr6	73221693	73221701	-	1	NA	promoter-TSS (NM_001164669)	promoter-TSS (NM_001164669)	-66	NM_001164669	330355	Mm.333166	NM_001164669	ENSMUSG00000052861	Dnah6	9830168K20|A730004I20Rik|Dnahc6|mKIAA1697|mdhc6	dynein, axonemal, heavy chain 6	protein-coding
mm_7697.1	chr1	129680639	129680643	-	1	NA	intron (NM_172485, intron 7 of 27)	intron (NM_172485, intron 7 of 27)	407337	NM_172485	210417	Mm.380518	NM_172485	ENSMUSG00000042581	Thsd7b	1700074E13Rik|B930082A18|D130067I03Rik	thrombospondin, type I, domain containing 7B	protein-coding
mm_76215.1	chr8	83458387	83458397	-	1	NA	promoter-TSS (NM_001039137)	promoter-TSS (NM_001039137)	4	NM_001039137	56367	Mm.246911	NM_019708	ENSMUSG00000063253	Scoc	0610011C06Rik|2810002J11Rik|AA415030|SCOCO	short coiled-coil protein	protein-coding
mm_143250.1	chr17	65366829	65366830	-	1	NA	intron (NM_001008973, intron 13 of 14)	B1_Mur2|SINE|Alu	173953	NM_001008973	381107	Mm.141275	NM_001008973	ENSMUSG00000045036	Tmem232	E130009J12Rik|Gm940|Tes13-L|Tes13-S	transmembrane protein 232	protein-coding
mm_49571.1	chr6	30640582	30640667	+	1	NA	exon (NM_025350, exon 3 of 10)	exon (NM_025350, exon 3 of 10)	1406	NM_025350	109697	Mm.25377	NM_025350	ENSMUSG00000054446	Cpa1	0910001L12Rik|Cpa	carboxypeptidase A1, pancreatic	protein-coding
mm_111999.1	chr12	110702643	110702670	-	1	NA	Intergenic	Intergenic	-6261	NM_010480	15519	Mm.1843	NM_010480	ENSMUSG00000021270	Hsp90aa1	86kDa|89kDa|AL024080|AL024147|Hsp86-1|Hsp89|Hsp90|Hspca|hsp4	heat shock protein 90, alpha (cytosolic), class A member 1	protein-coding
mm_20.1	chr1	5083561	5083587	+	1	NA	intron (NM_001310442, intron 1 of 12)	intron (NM_001310442, intron 1 of 12)	488	NM_001310442	108664	Mm.27082	NM_133826	ENSMUSG00000033793	Atp6v1h	0710001F19Rik|AU022349|CGI-11|SFD|SFDalpha|SFDbeta|VMA13	ATPase, H+ transporting, lysosomal V1 subunit H	protein-coding
mm_163059.1	chr11	62648156	62648188	+	1	NA	promoter-TSS (NM_175002)	promoter-TSS (NM_175002)	351	NM_198861	192976	Mm.339972	NM_198861	ENSMUSG00000046417	Lrrc75a	Fam211a	leucine rich repeat containing 75A	protein-coding
mm_122939.1	chr14	54965322	54965331	-	1	NA	exon (NM_010856, exon 3 of 39)	exon (NM_010856, exon 3 of 39)	1281	NM_001164171	17888	Mm.290003	NM_010856	ENSMUSG00000040752	Myh6	A830009F23Rik|AA517445|Myhc-a|Myhca|alpha-MHC	myosin, heavy polypeptide 6, cardiac muscle, alpha	protein-coding
mm_129187.1	chr15	76350192	76350239	-	1	NA	exon (NM_025340, exon 2 of 9)	exon (NM_025340, exon 2 of 9)	895	NM_025340	106025	Mm.41463	NM_025340	ENSMUSG00000022552	Sharpin	0610041B22Rik|AW121341|RBCKL1|SIPL1|cpdm	SHANK-associated RH domain interacting protein	protein-coding
mm_22348.1	chr2	180911544	180911571	-	1	NA	exon (NM_173761, exon 4 of 5)	exon (NM_173761, exon 4 of 5)	9379	NM_173761	228994	Mm.30205	NM_173761	ENSMUSG00000038848	Ythdf1	2210410K23Rik|8030473O16	YTH domain family 1	protein-coding
mm_74927.1	chr8	25601821	25601849	-	1	NA	promoter-TSS (NM_001308482)	promoter-TSS (NM_001308482)	234	NM_001308481	234135	Mm.217337	NM_001001735	ENSMUSG00000054823	Whsc1l1	6720429E03|A530023P05|AI528490|NSD3|WHISTLE	Wolf-Hirschhorn syndrome candidate 1-like 1 (human)	protein-coding
mm_70233.1	chr8	3221172	3221187	+	1	NA	intron (NM_010568, intron 2 of 20)	CpG	58438	NM_010568	16337	Mm.268003	NM_010568	ENSMUSG00000005534	Insr	4932439J01Rik|CD220|D630014A15Rik|IR|IR-A|IR-B	insulin receptor	protein-coding
mm_147324.1	chr18	42262054	42262140	-	1	NA	promoter-TSS (NM_134137)	promoter-TSS (NM_134137)	-26	NM_134137	107045	Mm.312170	NM_134137	ENSMUSG00000024493	Lars	2310045K21Rik|3110009L02Rik|AW536573|mKIAA1352	leucyl-tRNA synthetase	protein-coding
mm_72677.1	chr8	84913370	84913414	+	1	NA	promoter-TSS (NR_103491)	promoter-TSS (NR_103491)	57	NR_103491	100503676	Mm.437155	NR_103491	ENSMUSG00000003812	Gm38426	-	predicted gene, 38426	ncRNA
mm_19681.1	chr2	103454632	103454688	-	1	NA	3' UTR (NM_009804, exon 13 of 13)	3' UTR (NM_009804, exon 13 of 13)	30493	NM_009804	12359	Mm.4215	NM_009804	ENSMUSG00000027187	Cat	2210418N07|Cas-1|Cas1|Cs-1	catalase	protein-coding
mm_61362.1	chr7	68860243	68860249	+	1	NA	Intergenic	Intergenic	-111008	NM_025549	66412	Mm.251199	NM_025549	ENSMUSG00000042659	Arrdc4	2410003C09Rik|AV216361	arrestin domain containing 4	protein-coding
mm_113899.1	chr13	49197060	49197068	+	1	NA	TTS (NM_013610)	TTS (NM_013610)	9517	NM_013610	18081	Mm.18503	NM_013610	ENSMUSG00000037966	Ninj1	AU024536	ninjurin 1	protein-coding
mm_115461.1	chr13	119428491	119428504	+	1	NA	promoter-TSS (NM_001079849)	promoter-TSS (NM_001079849)	-103	NM_001079849	218693	Mm.490243	NM_145457	ENSMUSG00000025451	Paip1	PAIP-1	polyadenylate binding protein-interacting protein 1	protein-coding
mm_101978.1	chr11	50377604	50377647	-	1	NA	promoter-TSS (NM_021510)	promoter-TSS (NM_021510)	-94	NM_021510	59013	Mm.21740	NM_021510	ENSMUSG00000007850	Hnrnph1	AI642080|E430005G16Rik|Hnrnph|Hnrph1	heterogeneous nuclear ribonucleoprotein H1	protein-coding
mm_160817.1	chr11	29173527	29173527	+	1	NA	intron (NM_134034, intron 1 of 15)	intron (NM_134034, intron 1 of 15)	620	NM_134034	104570	Mm.276386	NM_134034	ENSMUSG00000020463	Smek2	AW011752|AW557776|Ppp4r3b|mKIAA1387	SMEK homolog 2, suppressor of mek1 (Dictyostelium)	protein-coding
mm_84327.1	chr9	64021899	64021906	-	1	NA	5' UTR (NM_008542, exon 1 of 4)	5' UTR (NM_008542, exon 1 of 4)	157	NM_008542	17130	Mm.325757	NM_008542	ENSMUSG00000036867	Smad6	Madh6|b2b390Clo	SMAD family member 6	protein-coding
mm_115177.1	chr13	108316367	108316387	+	1	NA	promoter-TSS (NM_178683)	promoter-TSS (NM_178683)	40	NM_178683	218581	Mm.32318	NM_178683	ENSMUSG00000021697	Depdc1b	9830132O03|AW260467|XTP1	DEP domain containing 1B	protein-coding
mm_29608.1	chr3	121262952	121262969	-	1	NA	intron (NM_178936, intron 1 of 7)	CpG	356	NM_178936	99887	Mm.26088	NM_178936	ENSMUSG00000028132	Tmem56	4930577M16Rik|AU018104|AW109744|C730036B01Rik	transmembrane protein 56	protein-coding
mm_28455.1	chr3	90670028	90670033	-	1	NA	TTS (NM_013650)	TTS (NM_013650)	959	NM_013650	20201	Mm.21567	NM_013650	ENSMUSG00000056054	S100a8	60B8Ag|AI323541|B8Ag|CFAg|CP-10|Caga|MRP8|p8	S100 calcium binding protein A8 (calgranulin A)	protein-coding
mm_128830.1	chr15	67176825	67176841	-	1	NA	promoter-TSS (NM_009177)	promoter-TSS (NM_009177)	49	NM_009177	20442	Mm.248334	NM_009177	ENSMUSG00000013846	St3gal1	5330418N22Rik|AI467004|ST3GalI|Siat4|Siat4a|St3gal-1	ST3 beta-galactoside alpha-2,3-sialyltransferase 1	protein-coding
mm_63771.1	chr7	131371139	131371182	+	1	NA	promoter-TSS (NM_001039534)	promoter-TSS (NM_001039534)	14	NM_001039534	214580	Mm.272948	NM_177609	ENSMUSG00000063179	Pstk	5430423O14Rik|5730458D16Rik|Gm1099|R75284	phosphoseryl-tRNA kinase	protein-coding
mm_102587.1	chr11	61855302	61855339	-	1	NA	promoter-TSS (NM_013881)	promoter-TSS (NM_013881)	-228	NM_013881	29869	Mm.162025	NM_013881	ENSMUSG00000004798	Ulk2	A830085I22Rik|AU015340|Unc51.2|mKIAA0623	unc-51 like kinase 2	protein-coding
mm_105253.1	chr11	102353317	102353344	-	1	NA	exon (NM_011403, exon 16 of 20)	exon (NM_011403, exon 16 of 20)	11951	NM_011403	20533	Mm.7248	NM_011403	ENSMUSG00000006574	Slc4a1	Ae1|CD233|Empb3|l11Jus51	solute carrier family 4 (anion exchanger), member 1	protein-coding
mm_38869.1	chr4	149657926	149657945	-	1	NA	intron (NM_001164051, intron 8 of 23)	intron (NM_001164051, intron 8 of 23)	-2368	NR_105990	102465983		NR_105990	ENSMUSG00000098580	Mir7023	Gm27912|mmu-mir-7023	microRNA 7023	ncRNA
mm_160197.1	chr7	79143551	79143551	-	1	NA	intron (NM_008594, intron 3 of 9)	ID4_|SINE|ID	5509	NM_001045489	17304	Mm.1451	NM_008594	ENSMUSG00000030605	Mfge8	AA408458|AI325141|MFG-E8|MP47|Mfgm|P47|SED1|lactadherin	milk fat globule-EGF factor 8 protein	protein-coding
mm_60632.1	chr7	44815930	44815940	+	1	NA	promoter-TSS (NM_030693)	promoter-TSS (NM_030693)	-153	NM_053074	18226	Mm.2565	NM_053074	ENSMUSG00000109511	Nup62	D7Ertd649e|Nupc1|p62	nucleoporin 62	protein-coding
mm_108346.1	chr12	80463183	80463200	+	1	NA	promoter-TSS (NM_133798)	promoter-TSS (NM_133798)	96	NM_133798	97827	Mm.206631	NM_133798	ENSMUSG00000032705	Exd2	4930539P14Rik|C85658|Exdl2	exonuclease 3'-5' domain containing 2	protein-coding
mm_152146.1	chr19	7206233	7206242	-	1	NA	promoter-TSS (NM_134150)	promoter-TSS (NM_134150)	47	NM_134150	107260	Mm.203921	NM_134150	ENSMUSG00000024767	Otub1	AI850305	OTU domain, ubiquitin aldehyde binding 1	protein-coding
mm_158290.1	chrX	112698388	112698399	-	1	NA	exon (NM_181579, exon 2 of 17)	exon (NM_181579, exon 2 of 17)	258	NM_181579	69693	Mm.34964	NM_181579	ENSMUSG00000034607	Pof1b	2310066B14Rik	premature ovarian failure 1B	protein-coding
mm_78359.1	chr9	25570611	25570621	+	1	NA	intron (NM_026189, intron 3 of 7)	intron (NM_026189, intron 3 of 7)	89019	NM_026189	67484	Mm.112977	NM_026189	ENSMUSG00000036611	Eepd1	2310005P05Rik|AI481005	endonuclease/exonuclease/phosphatase family domain containing 1	protein-coding
mm_110442.1	chr12	50649191	50649281	-	1	NA	promoter-TSS (NM_008858)	promoter-TSS (NM_008858)	-13	NM_008858	18760	Mm.133719	NM_008858	ENSMUSG00000002688	Prkd1	PKD|PKD1|Pkcm|Prkcm	protein kinase D1	protein-coding
mm_81283.1	chr9	108306270	108306276	+	1	NA	promoter-TSS (NM_133986)	promoter-TSS (NM_133986)	113	NM_016802	11848	Mm.757	NM_016802	ENSMUSG00000007815	Rhoa	Arha|Arha1|Arha2	ras homolog family member A	protein-coding
mm_121253.1	chr14	103057606	103057622	+	1	NA	Intergenic	B4A|SINE|B4	10602	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_85602.1	chr9	107566868	107566897	-	1	NA	TTS (NM_019742)	TTS (NM_019742)	-2281	NM_010489	15587	Mm.4834	NM_010489	ENSMUSG00000010047	Hyal2	AI256841|AU020858|AW555733	hyaluronoglucosaminidase 2	protein-coding
mm_127490.1	chr15	101322884	101322916	+	1	NA	Intergenic	Intergenic	29688	NR_033803	77717	Mm.391998	NR_033803	ENSMUSG00000075408	6030408B16Rik	AI225877	RIKEN cDNA 6030408B16 gene	ncRNA
mm_18366.1	chr2	59470016	59470023	-	1	NA	Intergenic	Intergenic	-14634	NM_029723	76747	Mm.275769	NM_029723	ENSMUSG00000026989	Dapl1	2310032F03Rik|EEDA	death associated protein-like 1	protein-coding
mm_13504.1	chr2	108948769	108948780	+	1	NA	Intergenic	Intergenic	329516	NM_029790	76894	Mm.330451	NM_029790	ENSMUSG00000057234	Mettl15	0610027B03Rik|AI303697|AW049952|Mett5d1	methyltransferase like 15	protein-coding
mm_120719.1	chr14	73107310	73107311	+	1	NA	Intergenic	Intergenic	-35200	NM_001170694	105670	Mm.280068	NM_134083	ENSMUSG00000022106	Rcbtb2	2610028E02Rik|2810420M18Rik|AI448345|AW240694|Chc1l|RC/BTB2	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 2	protein-coding
mm_80115.1	chr9	70542849	70542870	+	1	NA	promoter-TSS (NM_025690)	promoter-TSS (NM_025690)	-11	NM_025690	66660	Mm.22379	NM_025690	ENSMUSG00000032212	Sltm	5730455C01Rik|5730555F13Rik|9130215G10Rik|Met	SAFB-like, transcription modulator	protein-coding
mm_169600.1	chr15	35371378	35371378	+	1	NA	promoter-TSS (NM_177151)	promoter-TSS (NM_177151)	-168	NM_177151	666173	Mm.309250	NM_177151	ENSMUSG00000037646	Vps13b	1810042B05Rik|2310042E16Rik|4732488H20|C330002D13Rik|C87206|Coh1|D230005K13|mKIAA0532|mKIAA5032	vacuolar protein sorting 13B	protein-coding
mm_127041.1	chr15	96641309	96641328	+	1	NA	5' UTR (NM_134086, exon 1 of 16)	5' UTR (NM_134086, exon 1 of 16)	644	NM_134086	105727	Mm.103568	NM_134086	ENSMUSG00000023169	Slc38a1	AA408026|AA409865|AL022800|AU015942|NAT2	solute carrier family 38, member 1	protein-coding
mm_153344.1	chr19	39042065	39042068	-	1	NA	exon (NM_028089, exon 9 of 9)	exon (NM_028089, exon 9 of 9)	-18940	NM_028191	72303	Mm.482578	NM_028191	ENSMUSG00000067231	Cyp2c65	2210009K14Rik	cytochrome P450, family 2, subfamily c, polypeptide 65	protein-coding
mm_24997.1	chr3	97628845	97628864	+	1	NA	promoter-TSS (NM_001161763)	promoter-TSS (NM_001161763)	16	NM_010232	14263	Mm.385180	NM_010232	ENSMUSG00000028088	Fmo5	5033418D19Rik|AI195026	flavin containing monooxygenase 5	protein-coding
mm_102621.1	chr11	62466480	62466498	-	1	NA	intron (NM_001039536, intron 1 of 6)	intron (NM_001039536, intron 1 of 6)	8029	NM_001039536	327942	Mm.390358	NM_199026	ENSMUSG00000014245	Pigl	Gm737	phosphatidylinositol glycan anchor biosynthesis, class L	protein-coding
mm_77521.1	chr8	122914145	122914172	-	1	NA	intron (NM_001081379, intron 3 of 12)	intron (NM_001081379, intron 3 of 12)	65784	NM_007662	12555	Mm.1976	NM_007662	ENSMUSG00000031962	Cdh15	AI323380|Cdh14|Mcad	cadherin 15	protein-coding
mm_55041.1	chr6	48987981	48987989	-	1	NA	exon (NM_172888, exon 1 of 5)	exon (NM_172888, exon 1 of 5)	1124	NM_172888	243377	Mm.446302	NM_172888	ENSMUSG00000039215	Svs1	9530003A11	seminal vesicle secretory protein 1	protein-coding
mm_156140.1	chrX	128375379	128375390	+	1	NA	Intergenic	Intergenic	-638830	NM_001281537	73934	Mm.159093	NM_001281537	ENSMUSG00000043569	Cldn34c4	4930412D23Rik	claudin 34C4	protein-coding
mm_136997.1	chr17	17402927	17402941	+	1	NA	5' UTR (NM_025681, exon 1 of 6)	5' UTR (NM_025681, exon 1 of 6)	248	NM_025681	66643	Mm.268018	NM_025681	ENSMUSG00000047786	Lix1	5730466L18Rik	limb and CNS expressed 1	protein-coding
mm_165005.1	chr19	22942304	22942306	+	1	NA	intron (NM_001035239, intron 21 of 24)	Lx|LINE|L1	191700	NR_029591	387200		NR_029591	ENSMUSG00000065507	Mir204	Mirn204|mir-204|mmu-mir-204	microRNA 204	ncRNA
mm_104018.1	chr11	85546642	85546642	-	1	NA	intron (NM_138681, intron 18 of 25)	intron (NM_138681, intron 18 of 25)	173102	NR_045875	71489	Mm.442482	NR_045875	ENSMUSG00000086199	Bcas3os1	8430403D17Rik	breast carcinoma amplified sequence 3, opposite strand 1	ncRNA
mm_32539.1	chr4	109033857	109033872	+	1	NA	intron (NM_001347169, intron 11 of 32)	intron (NM_001347169, intron 11 of 32)	16209	NR_030432	791075		NR_030432	ENSMUSG00000076444	Mir761	Mirn761|mir-761|mmu-mir-761	microRNA 761	ncRNA
mm_156978.1	chrX	7188661	7188671	-	1	NA	promoter-TSS (NM_016691)	promoter-TSS (NM_016691)	48	NM_016691	12728	Mm.486257	NM_016691	ENSMUSG00000004317	Clcn5	5430408K11Rik|ClC-5|Clc4-1|Clc5|Clcn4-1|D930009B12Rik|DXImx42e|Sfc13|T25545	chloride channel, voltage-sensitive 5	protein-coding
mm_56780.1	chr6	116633568	116633595	-	1	NA	3' UTR (NM_178045, exon 11 of 11)	3' UTR (NM_178045, exon 11 of 11)	-4582	NM_026057	67255	Mm.18810	NM_026057	ENSMUSG00000059878	Zfp422	2900028O21Rik|AU041373|KOX15|Krox-25-2|Krox-26|Krox25|Krox26|Znf22	zinc finger protein 422	protein-coding
mm_61991.1	chr7	91090933	91090951	+	1	NA	5' UTR (NM_011807, exon 1 of 23)	5' UTR (NM_011807, exon 1 of 23)	156	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_119801.1	chr14	54211449	54211466	+	1	NA	Intergenic	Intergenic	42472	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_49316.1	chr6	18848572	18848582	+	1	NA	promoter-TSS (NM_133939)	promoter-TSS (NM_133939)	-58	NM_133939	76522	Mm.275158	NM_133939	ENSMUSG00000044155	Lsm8	2010003I05Rik|AW214405|Naa38	LSM8 homolog, U6 small nuclear RNA associated	protein-coding
mm_105344.1	chr11	102997557	102997568	-	1	NA	intron (NM_026551, intron 3 of 4)	intron (NM_026551, intron 3 of 4)	2359	NR_105896	102466988		NR_105896	ENSMUSG00000098613	Mir6931	Gm27303|mmu-mir-6931	microRNA 6931	ncRNA
mm_23027.1	chr3	34649924	34649934	+	1	NA	promoter-TSS (NM_011443)	promoter-TSS (NM_011443)	-66	NM_011443	20674	Mm.65396	NM_011443	ENSMUSG00000074637	Sox2	Sox-2|lcc|ysb	SRY (sex determining region Y)-box 2	protein-coding
mm_63840.1	chr7	135650361	135650376	+	1	NA	intron (NR_015548, intron 2 of 2)	intron (NR_015548, intron 2 of 2)	-1531	NM_001316681	19267	Mm.945	NM_011212	ENSMUSG00000041836	Ptpre	PTPe|PTPepsilon|RPTPepsilon	protein tyrosine phosphatase, receptor type, E	protein-coding
mm_8930.1	chr1	164098044	164098074	-	1	NA	Intergenic	Intergenic	-17205	NM_011347	20344	Mm.3337	NM_011347	ENSMUSG00000026580	Selp	CD62P|GMP-140|Grmp|LECAM3|PADGEM	selectin, platelet	protein-coding
mm_88067.1	chr10	67703024	67703046	+	1	NA	Intergenic	Intergenic	-154080	NM_001005419	211488	Mm.297250	NM_001005419	ENSMUSG00000057134	Ado	Gm237	2-aminoethanethiol (cysteamine) dioxygenase	protein-coding
mm_99627.1	chr11	105092195	105092201	+	1	NA	promoter-TSS (NM_001081046)	promoter-TSS (NM_001081046)	-21	NM_001081046	70894	Mm.87320	NM_001081046	ENSMUSG00000020690	Efcab3	4921510J17Rik	EF-hand calcium binding domain 3	protein-coding
mm_136724.1	chr17	8236062	8236075	+	1	NA	promoter-TSS (NM_001190333)	promoter-TSS (NM_001190333)	25	NM_001190333	12458	Mm.8007	NM_009835	ENSMUSG00000040899	Ccr6	CC-CKR-6|CCR-6|Cmkbr6|KY411	chemokine (C-C motif) receptor 6	protein-coding
mm_75594.1	chr8	61663798	61663845	-	1	NA	intron (NM_001293772, intron 10 of 21)	ID_B1|SINE|B4	-72652	NM_001293774	72333	Mm.29933	NM_001081390	ENSMUSG00000058056	Palld	2410003B16Rik|6030492A02	palladin, cytoskeletal associated protein	protein-coding
mm_132004.1	chr16	25752098	25752117	+	1	NA	intron (NM_001127259, intron 1 of 13)	intron (NM_001127259, intron 1 of 13)	-49809	NM_001127263	22061	Mm.20894	NM_011641	ENSMUSG00000022510	Trp63	AI462811|Ket|P51/P63|P63|P73l|Tp63|Trp53rp1	transformation related protein 63	protein-coding
mm_4854.1	chr1	187608756	187608764	+	1	NA	promoter-TSS (NM_001243792)	promoter-TSS (NM_001243792)	-246	NM_001243792	26381	Mm.89989	NM_011935	ENSMUSG00000026610	Esrrg	ERR3|Errg|NR3B3|mKIAA0832	estrogen-related receptor gamma	protein-coding
mm_24470.1	chr3	90659652	90659660	+	1	NA	Intergenic	Intergenic	5354	NM_199422	381493	Mm.291525	NM_199422	ENSMUSG00000063767	S100a7a	AY465109|Gm1020|S100A7L1|S100A7f|S100a15|S100a15a|S100a17l1	S100 calcium binding protein A7A	protein-coding
mm_79177.1	chr9	47893311	47893320	+	1	NA	Intergenic	MLT1J1|LTR|ERVL-MaLR	-75107	NR_046048	100038460	Mm.447649	NR_046048		Gm10677	ENSMUSG00000074363	predicted gene 10677	ncRNA
mm_6346.1	chr1	71641272	71641314	-	1	NA	exon (NM_001276413, exon 9 of 44)	exon (NM_001276413, exon 9 of 44)	11941	NM_010233	14268	Mm.193099	NM_010233	ENSMUSG00000026193	Fn1	E330027I09|Fn|Fn-1	fibronectin 1	protein-coding
mm_58707.1	chr7	12965963	12965973	+	1	NA	5' UTR (NM_178732, exon 1 of 4)	5' UTR (NM_178732, exon 1 of 4)	104	NM_178732	243834	Mm.133086	NM_178732	ENSMUSG00000004500	Zfp324	A930002M05|D430030K24Rik|ZF5128	zinc finger protein 324	protein-coding
mm_106951.1	chr12	8790701	8790740	+	1	NA	exon (NM_011519, exon 3 of 5)	exon (NM_011519, exon 3 of 5)	19324	NM_011519	20969	Mm.2580	NM_011519	ENSMUSG00000020592	Sdc1	AA408134|AA409076|CD138|Sstn|Synd|Synd1|syn-1	syndecan 1	protein-coding
mm_2262.1	chr1	91145058	91145101	+	1	NA	promoter-TSS (NM_001033408)	promoter-TSS (NM_001033408)	-24	NM_001033408	329207	Mm.295940	NM_001033408	ENSMUSG00000070732	Rbm44	Gm817	RNA binding motif protein 44	protein-coding
mm_64237.1	chr7	141700502	141700512	+	1	NA	exon (NM_023566, exon 23 of 46)	exon (NM_023566, exon 23 of 46)	10167	NM_023566	17831	Mm.2041	NM_023566		Muc2	2010015E03Rik|MCM|wnn	mucin 2	protein-coding
mm_169788.1	chr16	13780422	13780423	-	1	NA	promoter-TSS (NM_001039521)	promoter-TSS (NM_001039521)	-277	NM_001039521	106298	Mm.288606	NM_001039521	ENSMUSG00000022682	Rrn3	AL023001|E130302O19Rik|R75565|TIF-1A|Tif1a	RRN3 RNA polymerase I transcription factor homolog (yeast)	protein-coding
mm_105808.1	chr11	110252411	110252423	-	1	NA	promoter-TSS (NM_147218)	promoter-TSS (NM_147218)	-641	NM_001166557	76184	Mm.159704	NM_147218	ENSMUSG00000044749	Abca6	6330565N06Rik	ATP-binding cassette, sub-family A (ABC1), member 6	protein-coding
mm_109599.1	chr12	112678804	112678823	+	1	NA	promoter-TSS (NM_001100460)	promoter-TSS (NM_001100460)	-27	NM_001100460	382639	Mm.11350	NM_001100460	ENSMUSG00000037638	Zbtb42	EG382639|Gm5188|simiRP58	zinc finger and BTB domain containing 42	protein-coding
mm_23896.1	chr3	83031672	83031680	+	1	NA	exon (NM_010196, exon 5 of 5)	exon (NM_010196, exon 5 of 5)	5523	NM_001111048	14161	Mm.88793	NM_010196	ENSMUSG00000028001	Fga	ENSMUSG00000059807|Fib	fibrinogen alpha chain	protein-coding
mm_83137.1	chr9	40437265	40437294	-	1	NA	intron (NM_172768, intron 1 of 19)	B3|SINE|B2	18485	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_26870.1	chr3	17326364	17326378	-	1	NA	Intergenic	Intergenic	-463550	NR_033490	70441	Mm.458192	NR_033490	ENSMUSG00000100252	Mir124-2hg	100040120|2610100L16Rik|6430547I21Rik|A930005K07Rik|AW125202|Gm2612	Mir124-2 host gene (non-protein coding)	ncRNA
mm_292.1	chr1	23256266	23256289	+	1	NA	Intergenic	CpG	-15992	NR_029533	387225		NR_029533	ENSMUSG00000065405	Mir30a	Mirn30a|mir-30a|mmu-mir-30a	microRNA 30a	ncRNA
mm_168169.1	chr10	53900365	53900368	-	1	NA	Intergenic	Lx8b|LINE|L1	-149457	NM_001081428	75906	Mm.436785	NM_001081428	ENSMUSG00000019856	Fam184a	3110012E06Rik|4930438C08Rik|4930589M24Rik	family with sequence similarity 184, member A	protein-coding
mm_131944.1	chr16	24179426	24179427	+	1	NA	Intergenic	Intergenic	-190814	NM_009744	12053	Mm.347398	NM_009744	ENSMUSG00000022508	Bcl6	Bcl5	B cell leukemia/lymphoma 6	protein-coding
mm_22070.1	chr2	168741851	168741870	-	1	NA	promoter-TSS (NM_015731)	promoter-TSS (NM_015731)	-60	NM_015731	11981	Mm.330819	NM_015731	ENSMUSG00000027546	Atp9a	IIa	ATPase, class II, type 9A	protein-coding
mm_146241.1	chr18	77196179	77196206	+	1	NA	intron (NM_153124, intron 1 of 6)	intron (NM_153124, intron 1 of 6)	10345	NM_013666	225742	Mm.365178	NM_013666	ENSMUSG00000025425	St8sia5	ST8SiaV|Siat8e	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 5	protein-coding
mm_166557.1	chr6	42597457	42597461	-	1	NA	promoter-TSS (NM_203396)	promoter-TSS (NM_203396)	-87	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_125183.1	chr15	32244866	32244874	+	1	NA	promoter-TSS (NM_009154)	promoter-TSS (NM_009154)	57	NM_009154	20356	Mm.260374	NM_009154	ENSMUSG00000022231	Sema5a	5930434A13|9130201M22Rik|AI464145|Semaf|semF	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A	protein-coding
mm_105883.1	chr11	114930608	114930622	-	1	NA	intron (NM_199221, intron 1 of 3)	intron (NM_199221, intron 1 of 3)	3771	NM_001347651	217304	Mm.185355	NM_199221	ENSMUSG00000063193	Cd300lb	CLM-7|Clm7|Gm253|LMIR5	CD300 molecule like family member B	protein-coding
mm_152568.1	chr19	11589059	11589081	-	1	NA	intron (NM_026835, intron 5 of 6)	intron (NM_026835, intron 5 of 6)	15734	NM_026835	68774	Mm.290390	NM_026835	ENSMUSG00000024679	Ms4a6d	1110058E16Rik|AI447446|Ms4a11	membrane-spanning 4-domains, subfamily A, member 6D	protein-coding
mm_50014.1	chr6	41113369	41113379	+	1	NA	Intergenic	Intergenic	-77865	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_83528.1	chr9	46230162	46230210	-	1	NA	exon (NM_009692, exon 4 of 4)	exon (NM_009692, exon 4 of 4)	1556	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2|apo-AI|apoA-I	apolipoprotein A-I	protein-coding
mm_83278.1	chr9	43071369	43071382	-	1	NA	intron (NM_027144, intron 1 of 40)	intron (NM_027144, intron 1 of 40)	34343	NM_027144	69632	Mm.275266	NM_027144	ENSMUSG00000059495	Arhgef12	2310014B11Rik|AU019857|Larg|mKIAA0382	Rho guanine nucleotide exchange factor (GEF) 12	protein-coding
mm_46571.1	chr5	107289290	107289300	-	1	NA	5' UTR (NM_011578, exon 1 of 17)	5' UTR (NM_011578, exon 1 of 17)	300	NM_011578	21814	Mm.200775	NM_011578	ENSMUSG00000029287	Tgfbr3	1110036H20Rik|AU015626|AW215636|TBRIII	transforming growth factor, beta receptor III	protein-coding
mm_124736.1	chr15	6580986	6580996	+	1	NA	exon (NM_001278269, exon 1 of 17)	exon (NM_001278269, exon 1 of 17)	1144	NM_011815	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_129176.1	chr15	76273826	76273839	-	1	NA	intron (NM_028852, intron 1 of 4)	B3|SINE|B2	-3993	NR_045747	100038659	Mm.448549	NR_045747		Mirt2	ENSMUSG00000075583|Gm10872|Gm24562	myocardial infraction associated transcript 2	ncRNA
mm_80035.1	chr9	68882849	68882849	+	1	NA	intron (NM_013646, intron 1 of 10)	intron (NM_013646, intron 1 of 10)	117503	NR_033299	320440	Mm.483129	NM_177159		9530091C08Rik	-	RIKEN cDNA 9530091C08 gene	ncRNA
mm_106515.1	chr11	120531778	120531791	-	1	NA	intron (NM_008101, intron 1 of 13)	intron (NM_008101, intron 1 of 13)	1057	NM_008101	14527	Mm.22329	NM_008101	ENSMUSG00000025127	Gcgr	GR	glucagon receptor	protein-coding
mm_160547.1	chr9	44726088	44726088	-	1	NA	exon (NM_153537, exon 4 of 22)	exon (NM_153537, exon 4 of 22)	9110	NM_153537	102693	Mm.28639	NM_153537	ENSMUSG00000048537	Phldb1	AU041016|D330037A14Rik|Ll5a	pleckstrin homology like domain, family B, member 1	protein-coding
mm_15500.1	chr2	157914619	157914653	+	1	NA	promoter-TSS (NM_198627)	promoter-TSS (NM_198627)	-17	NM_198627	277432	Mm.441156	NM_198627	ENSMUSG00000037843	Vstm2l	Gm691	V-set and transmembrane domain containing 2-like	protein-coding
mm_117204.1	chr13	64066285	64066287	-	1	NA	intron (NM_008291, intron 6 of 10)	intron (NM_008291, intron 6 of 10)	22915	NM_008291	15487	Mm.5109	NM_008291	ENSMUSG00000033122	Hsd17b3	-	hydroxysteroid (17-beta) dehydrogenase 3	protein-coding
mm_124420.1	chr14	118052236	118052253	-	1	NA	promoter-TSS (NM_010024)	promoter-TSS (NM_010024)	2	NM_010024	13190	Mm.19987	NM_010024	ENSMUSG00000022129	Dct	DT|TRP-2|TRP2|Tyrp-2|Tyrp2|slaty|slt	dopachrome tautomerase	protein-coding
mm_144889.1	chr18	36939121	36939128	+	1	NA	promoter-TSS (NM_198117)	promoter-TSS (NM_198117)	-81	NM_198117	353234	Mm.308500	NM_198117	ENSMUSG00000104148	Pcdha2	-	protocadherin alpha 2	protein-coding
mm_61070.1	chr7	51511006	51511046	+	1	NA	promoter-TSS (NM_177694)	promoter-TSS (NM_177694)	-3	NR_073508	233246	Mm.254431	NM_177694	ENSMUSG00000055489	Ano5	9330162L24|Gdd1|Tmem16e	anoctamin 5	protein-coding
mm_49463.1	chr6	29419993	29420002	+	1	NA	exon (NM_001347071, exon 17 of 18)	exon (NM_001347071, exon 17 of 18)	-13156	NM_001081185	68794	Mm.39046	NM_026839	ENSMUSG00000068699	Flnc	1110055E19Rik|ABP-280|ABPL|Fln2	filamin C, gamma	protein-coding
mm_95857.1	chr11	57973403	57973429	+	1	NA	Intergenic	Intergenic	-35648	NM_028451	73158	Mm.248843	NM_028451	ENSMUSG00000037331	Larp1	1810024J12Rik|3110040D16Rik|Larp|mKIAA0731	La ribonucleoprotein domain family, member 1	protein-coding
mm_39456.1	chr5	17574696	17574714	+	1	NA	promoter-TSS (NM_013657)	promoter-TSS (NM_013657)	-111	NM_013657	20348	Mm.5071	NM_013657	ENSMUSG00000028780	Sema3c	1110036B02Rik|SemE|Semae	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	protein-coding
mm_64482.1	chr7	143065785	143065794	+	1	NA	intron (NM_133655, intron 3 of 7)	intron (NM_133655, intron 3 of 7)	-3579	NM_020285	56844	Mm.139675	NM_020285	ENSMUSG00000045752	Tssc4	AA241958|ESTM671070	tumor-suppressing subchromosomal transferable fragment 4	protein-coding
mm_67025.1	chr7	66377214	66377252	-	1	NA	intron (NM_146191, intron 2 of 33)	intron (NM_146191, intron 2 of 33)	4491	NR_106024	102465640		NR_106024	ENSMUSG00000098353	Mir7057	Gm27550|mmu-mir-7057	microRNA 7057	ncRNA
mm_110942.1	chr12	76612648	76612660	-	1	NA	exon (NM_013675, exon 16 of 36)	exon (NM_013675, exon 16 of 36)	-64729	NR_046044	100504549	Mm.440349	NR_046044		AI463170	-	expressed sequence AI463170	ncRNA
mm_16737.1	chr2	9304861	9304863	-	1	NA	Intergenic	Tigger7|DNA|TcMar-Tigger	115347	NR_038180	73438	Mm.23558	NR_038180	ENSMUSG00000085580	1700061F12Rik	-	RIKEN cDNA 1700061F12 gene	ncRNA
mm_134677.1	chr16	22411748	22411784	-	1	NA	exon (NM_023794, exon 7 of 13)	exon (NM_023794, exon 7 of 13)	27804	NM_023794	104156	Mm.155708	NM_023794	ENSMUSG00000013089	Etv5	1110005E01Rik|8430401F14Rik|ERM	ets variant 5	protein-coding
mm_5820.1	chr1	52727256	52727268	-	1	NA	promoter-TSS (NM_133829)	promoter-TSS (NM_133829)	56	NM_178081	98682	Mm.491173	NM_133829	ENSMUSG00000041439	Mfsd6	2210010L05Rik|9630025I22Rik|AI836200|AW212394|MMR2	major facilitator superfamily domain containing 6	protein-coding
mm_11786.1	chr2	40958330	40958335	+	1	NA	intron (NM_053011, intron 43 of 90)	intron (NM_053011, intron 43 of 90)	1489236	NR_105754	102465171		NR_105754	ENSMUSG00000098660	Mir6336	Gm27584|mmu-mir-6336	microRNA 6336	ncRNA
mm_85574.1	chr9	107289470	107289480	-	1	NA	promoter-TSS (NM_001316691)	promoter-TSS (NM_001316691)	-79	NM_001316691	102626	Mm.222612	NM_178907	ENSMUSG00000032577	Mapkapk3	3PK|AI874665|MAPKAP-K3|MAPKAP3|MK-3|MK3|MapkKapk3	mitogen-activated protein kinase-activated protein kinase 3	protein-coding
mm_120549.1	chr14	67716239	67716285	+	1	NA	promoter-TSS (NM_175384)	promoter-TSS (NM_175384)	164	NM_001285933	105440	Mm.6720	NM_134073	ENSMUSG00000034327	Kctd9	-	potassium channel tetramerisation domain containing 9	protein-coding
mm_31501.1	chr4	53341416	53341423	+	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	-71187	NR_033139	381524	Mm.23351	NM_001033454	ENSMUSG00000086712	AI427809	Gm1659	expressed sequence AI427809	ncRNA
mm_27963.1	chr3	80688269	80688305	-	1	NA	3' UTR (NM_013540, exon 16 of 16)	3' UTR (NM_013540, exon 16 of 16)	114504	NM_013540	14800	Mm.220224	NM_013540	ENSMUSG00000033981	Gria2	GluA2|GluR-B|Glur-2|Glur2	glutamate receptor, ionotropic, AMPA2 (alpha 2)	protein-coding
mm_128690.1	chr15	61985158	61985174	-	1	NA	promoter-TSS (NM_001177354)	promoter-TSS (NM_001177354)	-175	NM_001177354	17869	Mm.2444	NM_010849	ENSMUSG00000022346	Myc	AU016757|Myc2|Niard|Nird|bHLHe39	myelocytomatosis oncogene	protein-coding
mm_102025.1	chr11	51650814	51650851	-	1	NA	promoter-TSS (NR_027958)	promoter-TSS (NR_027958)	-122	NR_027958	97775	Mm.220299	NM_175289	ENSMUSG00000052563	D930048N14Rik	AI315703|R75254	RIKEN cDNA D930048N14 gene	ncRNA
mm_72488.1	chr8	83691041	83691087	+	1	NA	exon (NM_001199593, exon 3 of 22)	exon (NM_001199593, exon 3 of 22)	2997	NM_001199593	320795	Mm.213000	NM_177262	ENSMUSG00000057672	Pkn1	DBK|F730027O18Rik|PAK1|PRK1|Pkn|Prkcl1|Stk3	protein kinase N1	protein-coding
mm_151786.1	chr19	5388630	5388641	-	1	NA	promoter-TSS (NM_016882)	promoter-TSS (NM_016882)	68	NM_016882	20227	Mm.34562	NM_016882	ENSMUSG00000039148	Sart1	U5-110K	squamous cell carcinoma antigen recognized by T cells 1	protein-coding
mm_51519.1	chr6	83156402	83156451	+	1	NA	promoter-TSS (NM_023790)	promoter-TSS (NM_023790)	22	NM_027948	71837	Mm.17621	NM_027948	ENSMUSG00000030030	1700003E16Rik	AU041756	RIKEN cDNA 1700003E16 gene	protein-coding
mm_139512.1	chr17	56469049	56469078	+	1	NA	intron (NM_001252455, intron 1 of 27)	intron (NM_001252455, intron 1 of 27)	-6842	NM_001252456	19280	Mm.258771	NM_011218	ENSMUSG00000013236	Ptprs	AL022616|PTP|PTP-NU3|PTPNU-3|PTPsigma|Ptpt9|R-PTP-S|RPTPsigma	protein tyrosine phosphatase, receptor type, S	protein-coding
mm_148453.1	chr19	4000396	4000430	+	1	NA	promoter-TSS (NM_025529)	promoter-TSS (NM_025529)	-167	NM_025529	66387	Mm.259222	NM_025529	ENSMUSG00000024869	Nudt8	2310039H17Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 8	protein-coding
mm_46932.1	chr5	114744832	114744832	-	1	NA	intron (NM_001347400, intron 13 of 19)	intron (NM_001347400, intron 13 of 19)	25317	NR_105995	102465622		NR_105995	ENSMUSG00000098656	Mir7028	Gm27674|mmu-mir-7028	microRNA 7028	ncRNA
mm_15305.1	chr2	155386999	155387011	+	1	NA	3' UTR (NM_178111, exon 4 of 4)	3' UTR (NM_178111, exon 4 of 4)	5149	NM_178111	68728	Mm.293605	NM_178111	ENSMUSG00000038375	Trp53inp2	1110029F20Rik|Tp53inp2	transformation related protein 53 inducible nuclear protein 2	protein-coding
mm_43119.1	chr5	124725120	124725137	+	1	NA	promoter-TSS (NM_019536)	promoter-TSS (NM_019536)	43	NM_019536	56087	Mm.261014	NM_019536	ENSMUSG00000038011	Dnah10	Dnahc10	dynein, axonemal, heavy chain 10	protein-coding
mm_80369.1	chr9	75338335	75338365	+	1	NA	intron (NR_073186, intron 8 of 11)	B3A|SINE|B2	-9408	NM_013479	12049	Mm.25988	NM_013479	ENSMUSG00000032191	Bcl2l10	AA420380|AU023065|Boo|C85687|Diva	Bcl2-like 10	protein-coding
mm_142228.1	chr17	37480771	37480781	-	1	NA	TTS (NM_008204)	TTS (NM_008204)	2753	NM_008204	14990	Mm.329041	NM_008204	ENSMUSG00000016283	H2-M2	H-2M2|Thy19.4	histocompatibility 2, M region locus 2	protein-coding
mm_83394.1	chr9	44713197	44713218	-	1	NA	intron (NM_153537, intron 6 of 21)	intron (NM_153537, intron 6 of 21)	21991	NM_153537	102693	Mm.28639	NM_153537	ENSMUSG00000048537	Phldb1	AU041016|D330037A14Rik|Ll5a	pleckstrin homology like domain, family B, member 1	protein-coding
mm_45921.1	chr5	89441653	89441670	-	1	NA	exon (NM_008096, exon 5 of 13)	exon (NM_008096, exon 5 of 13)	16237	NM_008096	14473	Mm.196595	NM_008096	ENSMUSG00000035540	Gc	DBP|VDB	group specific component	protein-coding
mm_58122.1	chr6	140041410	140041466	-	1	NA	promoter-TSS (NM_054066)	promoter-TSS (NM_054066)	-21	NM_054066	114875	Mm.50808	NM_054066	ENSMUSG00000030230	Plcz1	1700041H07Rik|PLCzeta	phospholipase C, zeta 1	protein-coding
mm_125617.1	chr15	61987493	61987521	+	1	NA	exon (NM_010849, exon 2 of 3)	exon (NM_010849, exon 2 of 3)	2166	NM_001177352	17869	Mm.2444	NM_010849	ENSMUSG00000022346	Myc	AU016757|Myc2|Niard|Nird|bHLHe39	myelocytomatosis oncogene	protein-coding
mm_145386.1	chr18	57133367	57133369	+	1	NA	5' UTR (NM_001001979, exon 1 of 25)	5' UTR (NM_001001979, exon 1 of 25)	278	NM_001001979	70417	Mm.297863	NM_001001979	ENSMUSG00000024593	Megf10	3000002B06Rik|Gm331	multiple EGF-like-domains 10	protein-coding
mm_110900.1	chr12	75669497	75669544	-	1	NA	promoter-TSS (NM_028203)	promoter-TSS (NM_028203)	17	NM_028203	72338	Mm.341719	NM_028203	ENSMUSG00000045690	Wdr89	2600001A11Rik	WD repeat domain 89	protein-coding
mm_40804.1	chr5	69556937	69557018	+	1	NA	promoter-TSS (NM_001310631)	promoter-TSS (NM_001310631)	53	NM_001310631	231279	Mm.21105	NM_172711	ENSMUSG00000029208	Guf1	4631409J12|AA407526|EF-4	GUF1 homolog, GTPase	protein-coding
mm_116284.1	chr13	34993874	34993914	-	1	NA	5' UTR (NM_011868, exon 1 of 10)	5' UTR (NM_011868, exon 1 of 10)	250	NM_011868	23986	Mm.491141	NM_011868	ENSMUSG00000021417	Eci2	Acbd2|Drs1|Hca88|Peci	enoyl-Coenzyme A delta isomerase 2	protein-coding
mm_26014.1	chr3	135348089	135348095	+	1	NA	promoter-TSS (NM_028946)	promoter-TSS (NM_028946)	55	NM_028946	74446	Mm.85000	NM_028946	ENSMUSG00000050150	Slc9b1	1700094G20Rik|4933424B12Rik|4933425K02Rik|Nhedc1|mtsNHE	solute carrier family 9, subfamily B (NHA1, cation proton antiporter 1), member 1	protein-coding
mm_72524.1	chr8	83976880	83976899	+	1	NA	promoter-TSS (NM_001277898)	promoter-TSS (NM_001277898)	6	NM_001277898	18747	Mm.19111	NM_008854	ENSMUSG00000005469	Prkaca	PKCD|Pkaca	protein kinase, cAMP dependent, catalytic, alpha	protein-coding
mm_50403.1	chr6	48728080	48728086	+	1	NA	Intergenic	Intergenic	9462	NM_146167	231932	Mm.30479	NM_146167	ENSMUSG00000043931	Gimap7	IAN7|Ian3	GTPase, IMAP family member 7	protein-coding
mm_158043.1	chrX	98890567	98890583	-	1	NA	5' UTR (NM_052976, exon 1 of 25)	5' UTR (NM_052976, exon 1 of 25)	450	NM_052976	94190	Mm.33536	NM_052976	ENSMUSG00000031214	Ophn1	C130037N19Rik|Wtgr	oligophrenin 1	protein-coding
mm_147619.1	chr18	57552338	57552348	-	1	NA	promoter-TSS (NR_015494)	promoter-TSS (NR_015494)	52	NR_027944	75084	Mm.243841	NR_015494	ENSMUSG00000086607	4930511M06Rik	-	RIKEN cDNA 4930511M06 gene	ncRNA
mm_78741.1	chr9	41600133	41600150	+	1	NA	intron (NR_131930, intron 3 of 3)	intron (NR_131930, intron 3 of 3)	18215	NR_029822	387236		NR_029822	ENSMUSG00000093354	Mir125b-1	Mirn125b|Mirn125b-1|mir-125b-1	microRNA 125b-1	ncRNA
mm_58358.1	chr6	148212338	148212343	-	1	NA	promoter-TSS (NM_026168)	promoter-TSS (NM_026168)	34	NM_026168	67456	Mm.59812	NM_026168	ENSMUSG00000030304	Ergic2	1200009B18Rik|4930572C01Rik|AA408438|Ptx1	ERGIC and golgi 2	protein-coding
mm_55709.1	chr6	72958435	72958446	-	1	NA	promoter-TSS (NM_025284)	promoter-TSS (NM_025284)	43	NM_025284	19240	Mm.3532	NM_025284	ENSMUSG00000079523	Tmsb10	Ptmb10|Tb10	thymosin, beta 10	protein-coding
mm_118959.1	chr14	27428791	27428874	+	1	NA	promoter-TSS (NM_001114879)	promoter-TSS (NM_001114879)	-15	NM_028945	218850	Mm.247767	NM_028945	ENSMUSG00000040651	Fam208a	4732418E12|4933409E02Rik|D14Abb1e|MommeD6	family with sequence similarity 208, member A	protein-coding
mm_101234.1	chr11	20542896	20542907	-	1	NA	promoter-TSS (NM_021372)	promoter-TSS (NM_021372)	-352	NM_021372	58172	Mm.339676	NM_021372	ENSMUSG00000049800	Sertad2	AB041541|AU021878|Kiaa0127|MNCb-1504|SEI-2|Sei2|TRIP-Br2|mKIAA0127	SERTA domain containing 2	protein-coding
mm_124426.1	chr14	118236119	118236145	-	1	NA	promoter-TSS (NR_131969)	promoter-TSS (NR_131969)	-100	NR_131969	105245869	Mm.460408	NR_131969	ENSMUSG00000090534	LOC105245869	-	uncharacterized LOC105245869	ncRNA
mm_160850.1	chr11	53634858	53634858	-	1	NA	promoter-TSS (NM_008355)	promoter-TSS (NM_008355)	-156	NM_008355	16163	Mm.1284	NM_008355	ENSMUSG00000020383	Il13	Il-13	interleukin 13	protein-coding
mm_171454.1	chr4	145510774	145510774	+	1	NA	promoter-TSS (NM_001324553)	promoter-TSS (NM_001324553)	15	NM_001324553	101056073	Mm.276881	NM_001324553	ENSMUSG00000078503	LOC101056073	-	zinc finger protein 501-like	protein-coding
mm_36114.1	chr4	58893670	58893673	-	1	NA	intron (NM_172381, intron 1 of 48)	intron (NM_172381, intron 1 of 48)	19054	NM_172381	230249	Mm.234801	NM_172381	ENSMUSG00000050812	AI314180	AW558785|BB181316|mKIAA0368	expressed sequence AI314180	protein-coding
mm_28835.1	chr3	96579913	96579941	-	1	NA	intron (NM_001293701, intron 5 of 6)	intron (NM_001293701, intron 5 of 6)	-13126	NR_040409	100038464	Mm.475126	NR_040409	ENSMUSG00000074398	Gm15441	ENSMUSG00000074398|OTTMUSG00000021867	predicted gene 15441	ncRNA
mm_3893.1	chr1	161396632	161396640	+	1	NA	intron (NM_009452, intron 1 of 2)	intron (NM_009452, intron 1 of 2)	1198	NM_009452	22164	Mm.4994	NM_009452	ENSMUSG00000026700	Tnfsf4	Ath-1|Ath1|CD134L|OX-40L|Ox40l|TXGP1|Tnlg2b|Txgp1l|gp34	tumor necrosis factor (ligand) superfamily, member 4	protein-coding
mm_93749.1	chr10	120170333	120170343	-	1	NA	exon (NM_028679, exon 6 of 12)	exon (NM_028679, exon 6 of 12)	31199	NM_028679	73914	Mm.146194	NM_028679	ENSMUSG00000020227	Irak3	4833428C18Rik|AI563835|IRAK-M	interleukin-1 receptor-associated kinase 3	protein-coding
mm_37136.1	chr4	116820906	116820906	-	1	NA	exon (NM_146256, exon 1 of 1)	exon (NM_146256, exon 1 of 1)	602	NM_146256	242642	Mm.279897	NM_146256	ENSMUSG00000043155	Hpdl	A830048M07Rik|BC034099|Gloxd1	4-hydroxyphenylpyruvate dioxygenase-like	protein-coding
mm_170182.1	chr17	60985121	60985129	-	1	NA	Intergenic	(A)n|Simple_repeat|Simple_repeat	1896192	NM_207654	13640	Mm.7978	NM_010109	ENSMUSG00000048915	Efna5	AL-1|AV158822|EFL-5|Ephrin-A5|Epl7|LERK-7|RAGS	ephrin A5	protein-coding
mm_51847.1	chr6	90363384	90363392	+	1	NA	3' UTR (NM_144940, exon 20 of 20)	3' UTR (NM_144940, exon 20 of 20)	-6106	NM_173002	80292	Mm.100116	NM_030260	ENSMUSG00000034430	Zxdc	A930012H20|B930086F11Rik|BC003332	ZXD family zinc finger C	protein-coding
mm_101107.1	chr11	11932844	11932855	-	1	NA	3' UTR (NM_010345, exon 17 of 17)	3' UTR (NM_010345, exon 17 of 17)	-34705	NM_001190448	13195	Mm.12906	NM_016672	ENSMUSG00000020182	Ddc	Aadc	dopa decarboxylase	protein-coding
mm_139338.1	chr17	49454938	49454954	+	1	NA	3' UTR (NM_020042, exon 11 of 11)	3' UTR (NM_020042, exon 11 of 11)	26582	NM_020042	56738	Mm.22256	NM_020042	ENSMUSG00000064120	Mocs1	3110045D15Rik|AI043170|AW536397	molybdenum cofactor synthesis 1	protein-coding
mm_49353.1	chr6	21986888	21986917	+	1	NA	exon (NM_001081351, exon 1 of 22)	exon (NM_001081351, exon 1 of 22)	992	NM_001081351	214642	Mm.221404	NM_001081351	ENSMUSG00000062980	Cped1	6720481P07|A430107O13Rik|AI552584	cadherin-like and PC-esterase domain containing 1	protein-coding
mm_6242.1	chr1	67038750	67038760	-	1	NA	promoter-TSS (NM_001190984)	promoter-TSS (NM_001190984)	79	NM_001190984	14768	Mm.20522	NM_021295	ENSMUSG00000026000	Lancl1	AW124738|Gpr69|Gpr69a|p40	LanC (bacterial lantibiotic synthetase component C)-like 1	protein-coding
mm_26489.1	chr3	145118884	145118934	+	1	NA	intron (NM_001162538, intron 1 of 16)	CpG	309	NM_025714	52184	Mm.259105	NM_025714	ENSMUSG00000028256	Odf2l	4733401D09Rik|9630045K08Rik|D3Ertd250e	outer dense fiber of sperm tails 2-like	protein-coding
mm_98896.1	chr11	97921445	97921446	+	1	NA	Intergenic	Intergenic	-37291	NM_001081435	72973	Mm.245939	NM_001081435	ENSMUSG00000070336	Fbxo47	2900052P03Rik|Gm1562	F-box protein 47	protein-coding
mm_41683.1	chr5	100205924	100205949	+	1	NA	Intergenic	Intergenic	-4756	NR_040679	69571	Mm.396412	NR_040679	ENSMUSG00000100157	2310034O05Rik	-	RIKEN cDNA 2310034O05 gene	ncRNA
mm_145661.1	chr18	61130833	61130847	+	1	NA	TTS (NM_178277)	TTS (NM_178277)	13372	NR_105949	102466212		NR_105949	ENSMUSG00000098389	Mir6983	Gm27496|mmu-mir-6983	microRNA 6983	ncRNA
mm_20329.1	chr2	127511136	127511140	-	1	NA	intron (NR_110989, intron 1 of 8)	intron (NR_110989, intron 1 of 8)	10254	NM_001291005	56461	Mm.315292	NM_019789	ENSMUSG00000079056	Kcnip3	4933407H12Rik|AI413860|Csen|DREAM|KChIP3|R74849	Kv channel interacting protein 3, calsenilin	protein-coding
mm_157081.1	chrX	9435911	9435927	-	1	NA	3' UTR (NM_007807, exon 13 of 13)	3' UTR (NM_007807, exon 13 of 13)	33405	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_607.1	chr1	39904123	39904164	+	1	NA	intron (NM_001252200, intron 2 of 31)	intron (NM_001252200, intron 2 of 31)	3230	NM_008696	26921	Mm.491139	NM_008696	ENSMUSG00000026074	Map4k4	9430080K19Rik|AU043147|AU045934|AW046177|HGK|Nik	mitogen-activated protein kinase kinase kinase kinase 4	protein-coding
mm_110365.1	chr12	40107109	40107129	-	1	NA	intron (NM_009132, intron 3 of 13)	Lx8|LINE|L1	27109	NM_009132	20259	Mm.2416	NM_009132	ENSMUSG00000002565	Scin	AW545522|adseverin	scinderin	protein-coding
mm_142617.1	chr17	46858686	46858707	-	1	NA	Intergenic	Intergenic	-27283	NM_001100452	210982	Mm.37642	NM_001100452	ENSMUSG00000036568	Gltscr1l	mKIAA0240	GLTSCR1-like	protein-coding
mm_110849.1	chr12	73102547	73102550	-	1	NA	3' UTR (NM_011382, exon 3 of 3)	3' UTR (NM_011382, exon 3 of 3)	10697	NM_011382	20474	Mm.249575	NM_011382	ENSMUSG00000034460	Six4	AI047561|AREC3|TrexBF	sine oculis-related homeobox 4	protein-coding
mm_22995.1	chr3	34019948	34019963	+	1	NA	promoter-TSS (NM_001113188)	promoter-TSS (NM_001113188)	-124	NM_001113189	14359	Mm.259021	NM_008053	ENSMUSG00000027680	Fxr1	1110050J02Rik|9530073J07Rik|AI851072|Fxr1h|Fxr1p	fragile X mental retardation gene 1, autosomal homolog	protein-coding
mm_100990.1	chr11	7232190	7232192	-	1	NA	Intergenic	Intergenic	-18268	NM_008343	16009	Mm.29254	NM_008343	ENSMUSG00000020427	Igfbp3	AI649005|IGFBP-3|IGgfbp3	insulin-like growth factor binding protein 3	protein-coding
mm_64022.1	chr7	140315762	140315785	+	1	NA	Intergenic	Intergenic	-6928	NM_146956	258958	Mm.347648	NM_146956	ENSMUSG00000061489	Olfr525	MOR251-2	olfactory receptor 525	protein-coding
mm_80367.1	chr9	75337411	75337412	+	1	NA	intron (NR_073186, intron 8 of 11)	intron (NR_073186, intron 8 of 11)	-10347	NM_013479	12049	Mm.25988	NM_013479	ENSMUSG00000032191	Bcl2l10	AA420380|AU023065|Boo|C85687|Diva	Bcl2-like 10	protein-coding
mm_117860.1	chr13	98815409	98815431	-	1	NA	promoter-TSS (NM_172591)	promoter-TSS (NM_172591)	29	NM_172591	218503	Mm.23928	NM_172591	ENSMUSG00000041685	Fcho2	5832424M12Rik|AA387320	FCH domain only 2	protein-coding
mm_14545.1	chr2	132846851	132846854	+	1	NA	promoter-TSS (NM_025646)	promoter-TSS (NM_025646)	186	NM_001024385	66586	Mm.357342	NM_025646	ENSMUSG00000027357	Crls1	0610009I22Rik|4930557M15Rik|5730490M08Rik	cardiolipin synthase 1	protein-coding
mm_75303.1	chr8	41112853	41112867	-	1	NA	intron (NM_001005863, intron 1 of 13)	MT2B1|LTR|ERVL	1807	NM_001286413	102103	Mm.149438	NM_001005863	ENSMUSG00000045636	Mtus1	AI481402|ATBP135|Atip1|B430010I23Rik|B430305I03Rik|C85752|Cctsg1-440|MD44|MTSG1|mKIAA1288	mitochondrial tumor suppressor 1	protein-coding
mm_123937.1	chr14	73368401	73368403	-	1	NA	exon (NM_008410, exon 2 of 6)	exon (NM_008410, exon 2 of 6)	16869	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_153215.1	chr19	34747292	34747313	-	1	NA	promoter-TSS (NM_172838)	promoter-TSS (NM_172838)	-191	NM_172838	240638	Mm.74636	NM_172838	ENSMUSG00000009378	Slc16a12	3230401A21|AW210596	solute carrier family 16 (monocarboxylic acid transporters), member 12	protein-coding
mm_73070.1	chr8	94434379	94434403	+	1	NA	non-coding (NR_015514, exon 2 of 3)	non-coding (NR_015514, exon 2 of 3)	712	NR_015514	320377	Mm.486022	NR_015514		9330175E14Rik	A630085K21	RIKEN cDNA 9330175E14 gene	ncRNA
mm_58844.1	chr7	16842971	16843016	+	1	NA	promoter-TSS (NM_178900)	promoter-TSS (NM_178900)	-72	NM_178900	101540	Mm.1881	NM_178900	ENSMUSG00000041187	Prkd2	AI325941|PKD2	protein kinase D2	protein-coding
mm_2684.1	chr1	127306657	127306667	+	1	NA	5' UTR (NM_145128, exon 3 of 18)	5' UTR (NM_145128, exon 3 of 18)	101676	NM_145128	107895	Mm.214682	NM_145128	ENSMUSG00000036155	Mgat5	4930471A21Rik|5330407H02Rik|AI480971|GlcNAc-TV	mannoside acetylglucosaminyltransferase 5	protein-coding
mm_84530.1	chr9	67049201	67049220	-	1	NA	promoter-TSS (NM_001164251)	promoter-TSS (NM_001164251)	3	NM_001164255	22003	Mm.121878	NM_024427	ENSMUSG00000032366	Tpm1	AA986836|AI854628|TM2|Tm3|Tmpa|Tpm-1|alpha-TM	tropomyosin 1, alpha	protein-coding
mm_66377.1	chr7	43672246	43672252	-	1	NA	intron (NM_145582, intron 1 of 2)	intron (NM_145582, intron 1 of 2)	218	NM_145582	233189	Mm.26514	NM_145582	ENSMUSG00000038888	Ctu1	Atpbd3|BC005752	cytosolic thiouridylase subunit 1	protein-coding
mm_119199.1	chr14	32771557	32771557	+	1	NA	Intergenic	Intergenic	-14406	NM_001163616	69069	Mm.261609	NM_001163616	ENSMUSG00000041707	1810011H11Rik	4733401I05Rik	RIKEN cDNA 1810011H11 gene	protein-coding
mm_32330.1	chr4	104367331	104367360	+	1	NA	promoter-TSS (NM_177259)	promoter-TSS (NM_177259)	-193	NR_104385	13131	Mm.289682	NM_010014	ENSMUSG00000028519	Dab1	AI956902|C630028C02Rik|scm|scr|scrambler|yot	disabled 1	protein-coding
mm_149108.1	chr19	8953862	8953884	+	1	NA	promoter-TSS (NM_197993)	promoter-TSS (NM_197993)	41	NM_197993	70044	Mm.165979	NM_197993	ENSMUSG00000071645	Tut1	2700038E08Rik|PAPD2|Rbm21|TUTase6|U6-TUTase|star-PAP	terminal uridylyl transferase 1, U6 snRNA-specific	protein-coding
mm_100504.1	chr11	120491867	120491889	+	1	NA	promoter-TSS (NM_013770)	promoter-TSS (NM_013770)	41	NM_013770	27376	Mm.3991	NM_013770	ENSMUSG00000025792	Slc25a10	Dic	solute carrier family 25 (mitochondrial carrier, dicarboxylate transporter), member 10	protein-coding
mm_39680.1	chr5	25759941	25759984	+	1	NA	promoter-TSS (NM_001004365)	promoter-TSS (NM_001004365)	-11	NM_001310504	242894	Mm.150319	NM_001004365	ENSMUSG00000056367	Actr3b	9630005C02|ARP11|AW047569|Arp3b|Arp3beta	ARP3 actin-related protein 3B	protein-coding
mm_132255.1	chr16	32752225	32752259	+	1	NA	exon (NM_080457, exon 2 of 27)	exon (NM_080457, exon 2 of 27)	16356	NM_080457	140474	Mm.214599	NM_080457	ENSMUSG00000079620	Muc4	4933405I11Rik|Asgp	mucin 4	protein-coding
mm_129869.1	chr15	83385778	83385795	-	1	NA	intron (NM_011862, intron 6 of 10)	intron (NM_011862, intron 6 of 10)	-18489	NR_027980	69291	Mm.66794	NM_001033147		1700001L05Rik	-	RIKEN cDNA 1700001L05 gene	ncRNA
mm_73333.1	chr8	105302549	105302552	+	1	NA	intron (NM_148952, intron 7 of 9)	B1_Mur3|SINE|Alu	-3051	NM_172760	234683	Mm.237966	NM_172760	ENSMUSG00000014791	Elmo3	9930107J06|BC058752|CED-12|Ced12	engulfment and cell motility 3	protein-coding
mm_140957.1	chr17	24632584	24632603	-	1	NA	promoter-TSS (NM_008743)	promoter-TSS (NM_008743)	34	NM_011647	22084	Mm.30435	NM_011647	ENSMUSG00000002496	Tsc2	Nafld|Tcs2	tuberous sclerosis 2	protein-coding
mm_10906.1	chr2	25341716	25341719	+	1	NA	intron (NM_001029983, intron 5 of 12)	intron (NM_001029983, intron 5 of 12)	8974	NM_001029983	227619	Mm.270798	NM_001029983	ENSMUSG00000036646	Man1b1	E430019H13Rik|ERMan1|Gm108|MANA-ER	mannosidase, alpha, class 1B, member 1	protein-coding
mm_42439.1	chr5	115429697	115429707	+	1	NA	promoter-TSS (NM_008629)	promoter-TSS (NM_008629)	17	NM_008629	17690	Mm.5077	NM_008629	ENSMUSG00000054256	Msi1	Msi1h|Musahi1|m-Msi-1	musashi RNA-binding protein 1	protein-coding
mm_168518.1	chr11	58199614	58199624	+	1	NA	promoter-TSS (NM_018738)	promoter-TSS (NM_018738)	63	NM_018738	16145	Mm.33902	NM_018738	ENSMUSG00000078853	Igtp	AW558444|Irgm3	interferon gamma induced GTPase	protein-coding
mm_122405.1	chr14	41006883	41006912	-	1	NA	promoter-TSS (NM_001316739)	promoter-TSS (NM_001316739)	23	NM_001316739	70564	Mm.27227	NM_027464	ENSMUSG00000021792	Fam213a	5730469M10Rik|AU040822|Adrx|Pamm	family with sequence similarity 213, member A	protein-coding
mm_164620.1	chr17	31162796	31162811	-	1	NA	exon (NM_009362, exon 2 of 3)	exon (NM_009362, exon 2 of 3)	2250	NM_009362	21784	Mm.2854	NM_009362	ENSMUSG00000024032	Tff1	Bcei|PS2	trefoil factor 1	protein-coding
mm_43112.1	chr5	124552906	124552918	+	1	NA	promoter-TSS (NM_001190795)	promoter-TSS (NM_001190795)	48	NM_026409	67848	Mm.281601	NM_026409	ENSMUSG00000029389	Ddx55	2810021H22Rik|mKIAA1595	DEAD (Asp-Glu-Ala-Asp) box polypeptide 55	protein-coding
mm_71526.1	chr8	46852736	46852744	+	1	NA	Intergenic	LTR67B|LTR|ERVL	112995	NM_008391	16363	Mm.1149	NM_008391	ENSMUSG00000031627	Irf2	9830146E22Rik|AI646973|Irf-2	interferon regulatory factor 2	protein-coding
mm_45040.1	chr5	40439957	40439959	-	1	NA	Intergenic	Lx4A|LINE|L1	-795327	NM_010474	15476	Mm.12559	NM_010474	ENSMUSG00000051022	Hs3st1	3-Ost|D5Wsu110e|Hsg3ost	heparan sulfate (glucosamine) 3-O-sulfotransferase 1	protein-coding
mm_130725.1	chr15	101122336	101122339	-	1	NA	Intergenic	Intergenic	-6185	NM_001277258	11482	Mm.279542	NM_009612	ENSMUSG00000000530	Acvrl1	AI115505|AI427544|Acvrlk1|Alk1	activin A receptor, type II-like 1	protein-coding
mm_2819.1	chr1	131019844	131019852	+	1	NA	promoter-TSS (NM_010548)	promoter-TSS (NM_010548)	3	NM_010548	16153	Mm.874	NM_010548	ENSMUSG00000016529	Il10	CSIF|Il-10	interleukin 10	protein-coding
mm_132866.1	chr16	48611657	48611671	+	1	NA	intron (NM_010816, intron 20 of 26)	intron (NM_010816, intron 20 of 26)	160292	NM_198297	77647	Mm.167298	NM_198297	ENSMUSG00000030775	Trat1	C030046M14Rik|Tcrim|Trim	T cell receptor associated transmembrane adaptor 1	protein-coding
mm_47130.1	chr5	120467297	120467351	-	1	NA	intron (NM_133902, intron 1 of 7)	intron (NM_133902, intron 1 of 7)	5439	NM_133902	257635	Mm.5162	NM_133902	ENSMUSG00000029596	Sdsl	4432411H13Rik|AI504310|SDH1|SDS-RS1|TDH	serine dehydratase-like	protein-coding
mm_172147.1	chr6	37741369	37741374	+	1	NA	Intergenic	RLTR9E|LTR|ERVK	-129440	NM_001272064	21848	Mm.41063	NM_145076	ENSMUSG00000029833	Trim24	A130082H20Rik|AI447469|D430004I05Rik|TIF1|TIF1-alpha|TIF1alpha|Tif1a	tripartite motif-containing 24	protein-coding
mm_124418.1	chr14	118052042	118052063	-	1	NA	5' UTR (NM_010024, exon 1 of 8)	5' UTR (NM_010024, exon 1 of 8)	194	NM_010024	13190	Mm.19987	NM_010024	ENSMUSG00000022129	Dct	DT|TRP-2|TRP2|Tyrp-2|Tyrp2|slaty|slt	dopachrome tautomerase	protein-coding
mm_43193.1	chr5	128755128	128755143	+	1	NA	3' UTR (NM_021311, exon 22 of 22)	3' UTR (NM_021311, exon 22 of 22)	18889	NM_021311	57749	Mm.272720	NM_021311	ENSMUSG00000029423	Piwil1	MIWI	piwi-like RNA-mediated gene silencing 1	protein-coding
mm_7750.1	chr1	131097536	131097576	-	1	NA	5' UTR (NM_008551, exon 1 of 10)	5' UTR (NM_008551, exon 1 of 10)	287	NM_008551	17164	Mm.221235	NM_008551	ENSMUSG00000016528	Mapkapk2	AA960234|MAPKAP-K2|MK-2|MK2|Rps6kc1	MAP kinase-activated protein kinase 2	protein-coding
mm_86951.1	chr10	24904197	24904201	+	1	NA	intron (NM_027347, intron 21 of 28)	intron (NM_027347, intron 21 of 28)	-6465	NR_105870	102465545		NR_105870	ENSMUSG00000099181	Mir6905	Gm27879|mmu-mir-6905	microRNA 6905	ncRNA
mm_165520.1	chr2	174115975	174115980	+	1	NA	intron (NM_213733, intron 5 of 11)	intron (NM_213733, intron 5 of 11)	5626	NM_213733	228961	Mm.295629	NM_213733	ENSMUSG00000039263	Npepl1	BC023239|C85514|mKIAA1974	aminopeptidase-like 1	protein-coding
mm_102280.1	chr11	55395837	55395877	-	1	NA	exon (NM_009242, exon 9 of 10)	exon (NM_009242, exon 9 of 10)	24223	NM_009242	20692	Mm.291442	NM_009242	ENSMUSG00000018593	Sparc	BM-40|ON	secreted acidic cysteine rich glycoprotein	protein-coding
mm_82488.1	chr9	18469683	18469700	-	1	NA	intron (NM_028935, intron 2 of 7)	MER21B|LTR|ERVL	3868	NM_028935	72230	Mm.289689	NM_028935	ENSMUSG00000074500	Zfp558	1700007A21Rik|4932704I17Rik|Zfp558-ps	zinc finger protein 558	protein-coding
mm_85877.1	chr9	110989736	110989748	-	1	NA	promoter-TSS (NM_153100)	promoter-TSS (NM_153100)	-29	NM_153100	235636	Mm.441138	NM_153100	ENSMUSG00000066319	Rtp3	Tmem7	receptor transporter protein 3	protein-coding
mm_110588.1	chr12	56529501	56529511	-	1	NA	promoter-TSS (NR_045082)	promoter-TSS (NR_045082)	-86	NR_045082	104798	Mm.310950	NR_045082		E030019B13Rik	AI413669	RIKEN cDNA E030019B13 gene	ncRNA
mm_139990.1	chr17	72871723	72871744	+	1	NA	Intergenic	Intergenic	35029	NM_027166	383295	Mm.277533	NM_027166	ENSMUSG00000039770	Ypel5	2310076K21Rik|CGI-127	yippee-like 5 (Drosophila)	protein-coding
mm_12518.1	chr2	72137125	72137142	+	1	NA	intron (NM_001204166, intron 1 of 27)	intron (NM_001204166, intron 1 of 27)	82516	NM_001204166	56508	Mm.196153	NM_019688	ENSMUSG00000049044	Rapgef4	1300003D15Rik|5730402K07Rik|6330581N18Rik|EPAC 2|Epac-2|Epac2|mKIAA4040	Rap guanine nucleotide exchange factor (GEF) 4	protein-coding
mm_114743.1	chr13	83801729	83801729	+	1	NA	Intergenic	RMER12C|LTR|ERVK	62915	NR_029545	723967		NR_029545	ENSMUSG00000065424	Mir9-2	Mirn9-2|mir-9-2|mmu-mir-9-2	microRNA 9-2	ncRNA
mm_74221.1	chr8	124021569	124021579	+	1	NA	promoter-TSS (NM_133966)	promoter-TSS (NM_133966)	-265	NM_133966	102162	Mm.291777	NM_133966	ENSMUSG00000038697	Taf5l	1110005N04Rik|AI849020	TATA-box binding protein associated factor 5 like	protein-coding
mm_52403.1	chr6	113327244	113327264	+	1	NA	exon (NM_010957, exon 1 of 7)	exon (NM_010957, exon 1 of 7)	278	NM_010957	18294	Mm.43612	NM_010957	ENSMUSG00000030271	Ogg1	Mmh	8-oxoguanine DNA-glycosylase 1	protein-coding
mm_44037.1	chr5	147500722	147500724	+	1	NA	intron (NM_028291, intron 5 of 18)	intron (NM_028291, intron 5 of 18)	70143	NM_028291	72587	Mm.320469	NM_028291	ENSMUSG00000029647	Pan3	2700050F09Rik|A430027N15Rik|AU014670	PAN3 poly(A) specific ribonuclease subunit	protein-coding
mm_66410.1	chr7	44480776	44480788	-	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-3735	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_64933.1	chr7	16286796	16286810	-	1	NA	promoter-TSS (NM_001136471)	promoter-TSS (NM_001136471)	-8	NM_001136471	243846	Mm.482401	NM_172297	ENSMUSG00000041375	Ccdc9	2600011L02Rik	coiled-coil domain containing 9	protein-coding
mm_154067.1	chr19	55718967	55718970	-	1	NA	Intergenic	L1MA8|LINE|L1	-16764	NR_045318	77594	Mm.329924	NR_045318	ENSMUSG00000097632	4930552P12Rik	-	RIKEN cDNA 4930552P12 gene	ncRNA
mm_78465.1	chr9	32541613	32541656	+	1	NA	promoter-TSS (NM_008026)	promoter-TSS (NM_008026)	-182	NM_008026	14247	Mm.258908	NM_008026	ENSMUSG00000016087	Fli1	EWSR2|Fli-1|SIC-1|Sic1	Friend leukemia integration 1	protein-coding
mm_39974.1	chr5	32247450	32247468	+	1	NA	5' UTR (NM_001081407, exon 2 of 59)	5' UTR (NM_001081407, exon 2 of 59)	8375	NM_001081407	665270	Mm.160067	NM_030072	ENSMUSG00000029134	Plb1	4632413E21Rik|4930433E17Rik|4930539A06Rik|BC033606	phospholipase B1	protein-coding
mm_5386.1	chr1	31016884	31016888	-	1	NA	Intergenic	Intergenic	-67131	NM_011200	19243	Mm.491181	NM_011200	ENSMUSG00000026064	Ptp4a1	AA415290|AU019864|C130021B01|Prl-1	protein tyrosine phosphatase 4a1	protein-coding
mm_33158.1	chr4	125609947	125609962	+	1	NA	intron (NM_001081097, intron 1 of 15)	L1MC1|LINE|L1	105205	NR_035409	100124641		NR_035409	ENSMUSG00000076033	Mir692-3	Mir692-2b|Mirn692-2b|mmu-mir-692-3	microRNA 692-3	ncRNA
mm_128933.1	chr15	74636756	74636775	-	1	NA	promoter-TSS (NM_001177437)	promoter-TSS (NM_001177437)	-447	NM_001177437	69439	Mm.263708	NM_001177437	ENSMUSG00000022603	Mroh4	1700016M24Rik	maestro heat-like repeat family member 4	protein-coding
mm_118622.1	chr14	21104419	21104421	+	1	NA	intron (NM_001243041, intron 3 of 10)	intron (NM_001243041, intron 3 of 10)	28268	NM_001243041	11534	Mm.188734	NM_134079	ENSMUSG00000039197	Adk	2310026J05Rik|5033405D03Rik|AI255373|AI987814|Ak	adenosine kinase	protein-coding
mm_131131.1	chr16	5902158	5902201	+	1	NA	intron (NM_021477, intron 1 of 16)	Lx8b|LINE|L1	17386	NM_021477	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_118078.1	chr13	103129621	103129623	-	1	NA	intron (NM_175171, intron 3 of 28)	ORR1E|LTR|ERVL-MaLR	204870	NM_175171	328329	Mm.202606	NM_175171	ENSMUSG00000034751	Mast4	4930420O11Rik|AI642422|mKIAA0303	microtubule associated serine/threonine kinase family member 4	protein-coding
mm_131426.1	chr16	14708361	14708411	+	1	NA	3' UTR (NM_011415, exon 3 of 3)	3' UTR (NM_011415, exon 3 of 3)	2527	NM_011415	20583	Mm.4272	NM_011415	ENSMUSG00000022676	Snai2	Slug|Slugh|Snail2	snail family zinc finger 2	protein-coding
mm_95770.1	chr11	54908624	54908637	+	1	NA	exon (NM_008161, exon 3 of 5)	exon (NM_008161, exon 3 of 5)	5776	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_104689.1	chr11	97775877	97775899	-	1	NA	promoter-TSS (NM_028156)	promoter-TSS (NM_028156)	30	NM_028156	72215	Mm.269049	NM_028156	ENSMUSG00000018543	1700001P01Rik	-	RIKEN cDNA 1700001P01 gene	protein-coding
mm_48564.1	chr5	143180799	143180814	-	1	NA	promoter-TSS (NM_177880)	promoter-TSS (NM_177880)	-31	NM_001045482	57782	Mm.320419	NM_021326	ENSMUSG00000061898	Rbak	-	RB-associated KRAB zinc finger	protein-coding
mm_130065.1	chr15	89196415	89196430	-	1	NA	promoter-TSS (NM_027081)	promoter-TSS (NM_027081)	52	NM_027081	69440	Mm.482128	NM_027081	ENSMUSG00000015377	Dennd6b	1700027J05Rik|AI414881|Fam116b	DENN/MADD domain containing 6B	protein-coding
mm_132899.1	chr16	48870970	48870979	+	1	NA	Intergenic	RMER15-int|LTR|ERVL	-1634	NM_181596	245195	Mm.231288	NM_181596	ENSMUSG00000022651	Retnlg	Fizz3|Relmg|Xcp1	resistin like gamma	protein-coding
mm_56128.1	chr6	87579926	87579938	-	1	NA	3' UTR (NM_021381, exon 3 of 3)	3' UTR (NM_021381, exon 3 of 3)	10769	NM_021381	58182	Mm.333226	NM_021381	ENSMUSG00000049409	Prokr1	EG-VEGFR1|Gpr73|Pkr1	prokineticin receptor 1	protein-coding
mm_103854.1	chr11	83237447	83237450	-	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	13872	NR_015519	100043636	Mm.295569	NR_015519	ENSMUSG00000087107	AI662270	AW496474	expressed sequence AI662270	ncRNA
mm_34150.1	chr4	139375819	139375836	+	1	NA	3' UTR (NM_146157, exon 24 of 24)	3' UTR (NM_146157, exon 24 of 24)	-4832	NM_001160319	69116	Mm.271956	NM_001160319	ENSMUSG00000066036	Ubr4	1810009A16Rik|A930005E13Rik|D930005K06Rik|Gm1032|Gm1666|N28143|RBAF600|Zubr1|mKIAA0462|p600	ubiquitin protein ligase E3 component n-recognin 4	protein-coding
mm_99329.1	chr11	101460084	101460098	+	1	NA	3' UTR (NM_012037, exon 6 of 6)	3' UTR (NM_012037, exon 6 of 6)	6108	NM_012037	26949	Mm.29210	NM_012037	ENSMUSG00000034993	Vat1	VAT-1	vesicle amine transport 1	protein-coding
mm_115082.1	chr13	102691966	102691971	+	1	NA	Intergenic	Intergenic	-1590	NM_008533	17079	Mm.373974	NM_008533	ENSMUSG00000021624	Cd180	F630107B15|Ly78|RP105	CD180 antigen	protein-coding
mm_42517.1	chr5	115544399	115544424	+	1	NA	exon (NM_011223, exon 2 of 11)	exon (NM_011223, exon 2 of 11)	-15056	NM_007475	11837	Mm.5286	NM_007475	ENSMUSG00000067274	Rplp0	36B4|Arbp|L10E	ribosomal protein, large, P0	protein-coding
mm_112149.1	chr12	113260029	113260039	-	1	NA	Intergenic	Intergenic	74131	NM_153776	69195	Mm.313244	NM_153776	ENSMUSG00000049036	Tmem121	2410008J05Rik|Hole	transmembrane protein 121	protein-coding
mm_119483.1	chr14	47360782	47360794	+	1	NA	Intergenic	RSINE1|SINE|B4	-13072	NM_010705	16854	Mm.248615	NM_010705	ENSMUSG00000050335	Lgals3	GBP|L-34|Mac-2|gal3	lectin, galactose binding, soluble 3	protein-coding
mm_62056.1	chr7	92447562	92447570	+	1	NA	3' UTR (NM_001243047, exon 11 of 11)	3' UTR (NM_001243047, exon 11 of 11)	-113583	NM_025515	66365	Mm.21173	NM_025515	ENSMUSG00000030613	Ccdc90b	2310015N07Rik|C86558	coiled-coil domain containing 90B	protein-coding
mm_87691.1	chr10	59403677	59403687	+	1	NA	promoter-TSS (NM_023530)	promoter-TSS (NM_023530)	-3	NM_023530	69836	Mm.30268	NM_023530	ENSMUSG00000009646	Pla2g12b	2010002E04Rik|Fksg71|Pla2g13|hlb218	phospholipase A2, group XIIB	protein-coding
mm_73814.1	chr8	117401166	117401183	+	1	NA	intron (NM_028941, intron 3 of 20)	MTD|LTR|ERVL-MaLR	-51849	NR_106045	102466801		NR_106045	ENSMUSG00000099062	Mir7077	Gm27774|mmu-mir-7077	microRNA 7077	ncRNA
mm_96558.1	chr11	68967642	68967652	+	1	NA	promoter-TSS (NM_028048)	promoter-TSS (NM_028048)	-484	NM_028048	71998	Mm.298622	NM_028048	ENSMUSG00000018740	Slc25a35	1810012H11Rik	solute carrier family 25, member 35	protein-coding
mm_169822.1	chr16	22295027	22295031	+	1	NA	Intergenic	Intergenic	-29024	NM_001330555	20462	Mm.210352	NM_009186	ENSMUSG00000022858	Tra2b	5730405G21Rik|D16Ertd266e|SIG-41|Sfrs10|Silg41|TRA2beta	transformer 2 beta homolog (Drosophila)	protein-coding
mm_167100.1	chr7	110166227	110166259	-	1	NA	Intergenic	Intergenic	44184	NM_009516	22390	Mm.287173	NM_009516	ENSMUSG00000031016	Wee1	Wee1A	WEE 1 homolog 1 (S. pombe)	protein-coding
mm_37990.1	chr4	133632236	133632268	-	1	NA	intron (NM_001017968, intron 1 of 7)	intron (NM_001017968, intron 1 of 7)	1177	NM_001017968	503610	Mm.331948	NM_001017968	ENSMUSG00000037553	Zdhhc18	-	zinc finger, DHHC domain containing 18	protein-coding
mm_26636.1	chr3	153078275	153078291	+	1	NA	Intergenic	Intergenic	73825	NR_108044	75001		NR_108044		4930482G09Rik	-	RIKEN cDNA 4930482G09 gene	ncRNA
mm_171472.1	chr4	145781522	145781522	+	1	NA	promoter-TSS (NM_001083918)	promoter-TSS (NM_001083918)	-21	NM_001083918	666532	Mm.392861	NM_001083918	ENSMUSG00000067916	Zfp991	Gm13139|OTTMUSG00000010657	zinc finger protein 991	protein-coding
mm_37946.1	chr4	133159292	133159300	-	1	NA	intron (NM_153423, intron 1 of 8)	intron (NM_153423, intron 1 of 8)	28663	NM_153423	242687	Mm.23566	NM_153423	ENSMUSG00000028868	Wasf2	AW742646|D4Ertd13e|WAVE2	WAS protein family, member 2	protein-coding
mm_54691.1	chr6	39445409	39445416	-	1	NA	Intergenic	B1_Mur1|SINE|Alu	-25043	NM_018810	54484	Mm.270484	NM_018810	ENSMUSG00000029922	Mkrn1	RFP	makorin, ring finger protein, 1	protein-coding
mm_63945.1	chr7	139834307	139834318	+	1	NA	5' UTR (NM_177469, exon 1 of 8)	5' UTR (NM_177469, exon 1 of 8)	138	NM_177469	52389	Mm.39863	NM_177469	ENSMUSG00000025475	Adgra1	2900059M17Rik|D7Ertd680e|Gpr123	adhesion G protein-coupled receptor A1	protein-coding
mm_57428.1	chr6	124914112	124914130	-	1	NA	3' UTR (NM_026988, exon 5 of 5)	3' UTR (NM_026988, exon 5 of 5)	-2416	NM_008479	16768	Mm.4528	NM_008479	ENSMUSG00000030124	Lag3	CD223|LAG-3|Ly66	lymphocyte-activation gene 3	protein-coding
mm_133356.1	chr16	84677600	84677604	+	1	NA	Intergenic	Intergenic	-2187	NR_040537	78023	Mm.243853	NR_040537		4930529L06Rik	-	RIKEN cDNA 4930529L06 gene	ncRNA
mm_81547.1	chr9	110281281	110281338	+	1	NA	promoter-TSS (NR_105744)	promoter-TSS (NR_105744)	22	NR_105744	102465959		NR_105744	ENSMUSG00000098973	Mir6236	Gm27547|mmu-mir-6236	microRNA 6236	ncRNA
mm_81690.1	chr9	111148034	111148039	+	1	NA	intron (NM_027742, intron 3 of 13)	(T)n|Simple_repeat|Simple_repeat	29925	NM_001164838	71268	Mm.302287	NM_027742	ENSMUSG00000032497	Lrrfip2	5133400F20Rik|AI850587	leucine rich repeat (in FLII) interacting protein 2	protein-coding
mm_104332.1	chr11	93996751	93996763	-	1	NA	intron (NM_001199203, intron 1 of 29)	intron (NM_001199203, intron 1 of 29)	666	NM_027569	70834	Mm.260737	NM_027569	ENSMUSG00000020859	Spag9	3110018C07Rik|4733401I23Rik|4831406C20Rik|AW552012|JLP|JSAP2|JSAP2a|Jip4|Mapk8ip4|syd1	sperm associated antigen 9	protein-coding
mm_50615.1	chr6	49823732	49823740	+	1	NA	exon (NM_023456, exon 2 of 4)	exon (NM_023456, exon 2 of 4)	1026	NM_023456	109648	Mm.154796	NM_023456	ENSMUSG00000029819	Npy	0710005A05Rik	neuropeptide Y	protein-coding
mm_102363.1	chr11	58386771	58386804	-	1	NA	exon (NM_001083884, exon 6 of 7)	exon (NM_001083884, exon 6 of 7)	6141	NM_001330197	70163	Mm.24119	NM_027339	ENSMUSG00000013643	Lypd8	2210415F13Rik	LY6/PLAUR domain containing 8	protein-coding
mm_124633.1	chr15	4035466	4035466	+	1	NA	intron (NM_024188, intron 2 of 16)	intron (NM_024188, intron 2 of 16)	-8060	NR_028266	414066	Mm.394461	NR_028266		BC037032	-	cDNA Sequence BC037032	ncRNA
mm_74957.1	chr8	26058062	26058100	-	1	NA	intron (NM_207659, intron 15 of 21)	PB1D9|SINE|Alu	-24528	NR_110583	76604	Mm.437190	NR_110583	ENSMUSG00000085437	1700047A11Rik	4930554C15Rik	RIKEN cDNA 1700047A11 gene	ncRNA
mm_11689.1	chr2	35661297	35661369	+	1	NA	intron (NM_001290641, intron 2 of 15)	CpG	-30661	NM_001001602	69601	Mm.29629	NM_001001602	ENSMUSG00000026883	Dab2ip	2310011D08Rik|AI480459|Aip1|mKIAA1743	disabled 2 interacting protein	protein-coding
mm_111300.1	chr12	85485981	85485994	-	1	NA	Intergenic	Intergenic	12086	NM_010234	14281	Mm.246513	NM_010234	ENSMUSG00000021250	Fos	D12Rfj1|c-fos|cFos	FBJ osteosarcoma oncogene	protein-coding
mm_49615.1	chr6	30747627	30747641	+	1	NA	TTS (NM_017478)	TTS (NM_017478)	6335	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_39649.1	chr5	24685816	24685819	+	1	NA	promoter-TSS (NM_001305264)	promoter-TSS (NM_001305264)	2	NM_001305264	53312	Mm.5856	NM_016736	ENSMUSG00000028954	Nub1	4931404D21Rik|6330412F12Rik|BS4|NY-REN-18	negative regulator of ubiquitin-like proteins 1	protein-coding
mm_103986.1	chr11	84828936	84828944	-	1	NA	promoter-TSS (NR_046281)	promoter-TSS (NR_046281)	63	NM_177564	192970	Mm.192213	NM_177564	ENSMUSG00000034449	Dhrs11	-	dehydrogenase/reductase (SDR family) member 11	protein-coding
mm_132886.1	chr16	48842478	48842487	+	1	NA	promoter-TSS (NM_020509)	promoter-TSS (NM_020509)	-70	NM_020509	57262	Mm.441868	NM_020509	ENSMUSG00000061100	Retnla	1810019L16Rik|Fizz-1|Fizz1|HIMF|RELM-alpha|RELMa|RELMalpha|Xcp2	resistin like alpha	protein-coding
mm_252.1	chr1	19237407	19237417	+	1	NA	3' UTR (NM_009334, exon 7 of 7)	3' UTR (NM_009334, exon 7 of 7)	25358	NM_001025305	21419	Mm.137021	NM_009334	ENSMUSG00000025927	Tfap2b	AI606113|AP-2(beta)|E130018K07Rik|Tcfap2b	transcription factor AP-2 beta	protein-coding
mm_122272.1	chr14	34363229	34363248	-	1	NA	Intergenic	Intergenic	-7845	NM_183278	69134	Mm.27156	NM_183278	ENSMUSG00000043681	Fam25c	2200001I15Rik|Fam25	family with sequence similarity 25, member C	protein-coding
mm_67562.1	chr7	81862524	81862530	-	1	NA	promoter-TSS (NM_001291282)	promoter-TSS (NM_001291282)	-160	NM_001291282	107769	Mm.221412	NM_145375	ENSMUSG00000038623	Tm6sf1	AI428514|BC023123|C630016D09Rik	transmembrane 6 superfamily member 1	protein-coding
mm_20922.1	chr2	150840168	150840179	-	1	NA	intron (NM_024465, intron 6 of 12)	intron (NM_024465, intron 6 of 12)	53377	NM_153781	110078	Mm.222584	NM_153781	ENSMUSG00000033059	Pygb	-	brain glycogen phosphorylase	protein-coding
mm_136036.1	chr16	77421732	77421743	-	1	NA	intron (NR_015543, intron 2 of 4)	intron (NR_015543, intron 2 of 4)	92409	NR_015543	77994	Mm.394688	NR_015543	ENSMUSG00000090386	Mir99ahg	2810055G20Rik|D730043B02Rik	Mir99a and Mirlet7c-1 host gene (non-protein coding)	ncRNA
mm_76238.1	chr8	83574830	83574850	-	1	NA	intron (NM_134118, intron 1 of 12)	intron (NM_134118, intron 1 of 12)	8082	NM_025843	66916	Mm.29683	NM_025843	ENSMUSG00000033938	Ndufb7	1110002H15Rik	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 7	protein-coding
mm_98423.1	chr11	94644396	94644410	+	1	NA	TTS (NM_177752)	TTS (NM_177752)	9351	NM_177752	268465	Mm.358937	NM_177752	ENSMUSG00000039055	Eme1	6820428D13	essential meiotic structure-specific endonuclease 1	protein-coding
mm_94305.1	chr11	4175055	4175078	+	1	NA	exon (NM_026175, exon 8 of 16)	exon (NM_026175, exon 8 of 16)	-11767	NM_134023	103724	Mm.28140	NM_134023	ENSMUSG00000034412	Tbc1d10a	AI447804|EPI64|Tbc1d10|mFLJ00288	TBC1 domain family, member 10a	protein-coding
mm_74525.1	chr8	9545191	9545200	-	1	NA	intron (NM_001347127, intron 1 of 3)	intron (NM_001347127, intron 1 of 3)	225828	NM_173446	270028	Mm.268163	NM_173446	ENSMUSG00000079157	Fam155a	6430500D16|AW121567|Tmem28	family with sequence similarity 155, member A	protein-coding
mm_131159.1	chr16	6935599	6935606	+	1	NA	intron (NM_021477, intron 5 of 16)	L1MC4a|LINE|L1	-134233	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_169085.1	chr13	35991529	35991548	-	1	NA	intron (NM_201358, intron 2 of 2)	CpG	23632	NM_029628	76487	Mm.44745	NM_029628	ENSMUSG00000050423	Ppp1r3g	1600032L17Rik	protein phosphatase 1, regulatory (inhibitor) subunit 3G	protein-coding
mm_32147.1	chr4	99715621	99715635	+	1	NA	promoter-TSS (NM_001081264)	promoter-TSS (NM_001081264)	-2	NM_001081264	320438	Mm.32408	NM_001081264	ENSMUSG00000073792	Alg6	E230028F23Rik	asparagine-linked glycosylation 6 (alpha-1,3,-glucosyltransferase)	protein-coding
mm_14192.1	chr2	127086455	127086490	+	1	NA	intron (NM_026678, intron 4 of 7)	B1_Mur2|SINE|Alu	15815	NM_026678	109778	Mm.22028	NM_026678	ENSMUSG00000001999	Blvra	0610006A11Rik|2500001N03Rik|Blvr	biliverdin reductase A	protein-coding
mm_23925.1	chr3	83766301	83766331	+	1	NA	promoter-TSS (NM_009144)	promoter-TSS (NM_009144)	-5	NM_009144	20319	Mm.19155	NM_009144	ENSMUSG00000027996	Sfrp2	AI851596|Sdf5	secreted frizzled-related protein 2	protein-coding
mm_120709.1	chr14	71856711	71856717	+	1	NA	promoter-TSS (NR_046274)	promoter-TSS (NR_046274)	5	NR_046274	74667	Mm.159286	NR_046274		4930434J06Rik	-	RIKEN cDNA 4930434J06 gene	ncRNA
mm_139985.1	chr17	72837625	72837656	+	1	NA	intron (NM_027166, intron 1 of 2)	CpG	936	NM_027166	383295	Mm.277533	NM_027166	ENSMUSG00000039770	Ypel5	2310076K21Rik|CGI-127	yippee-like 5 (Drosophila)	protein-coding
mm_158838.1	chrX	168673829	168673896	-	1	NA	promoter-TSS (NM_010832)	promoter-TSS (NM_010832)	40	NM_010832	17692	Mm.24248	NM_010832	ENSMUSG00000031358	Msl3	AU018931|Msl31|Msl3l1	male-specific lethal 3 homolog (Drosophila)	protein-coding
mm_24672.1	chr3	94786723	94786738	+	1	NA	promoter-TSS (NM_001293727)	promoter-TSS (NM_001293727)	-215	NM_001037711	70737	Mm.87634	NM_001037711	ENSMUSG00000068876	Cgn	6330408J11Rik	cingulin	protein-coding
mm_7400.1	chr1	118982552	118982606	-	1	NA	intron (NM_001081125, intron 2 of 13)	intron (NM_001081125, intron 2 of 13)	28359	NR_105764	102465176		NR_105764	ENSMUSG00000098273	Mir6346	Gm27829|mmu-mir-6346	microRNA 6346	ncRNA
mm_103049.1	chr11	69805618	69805673	-	1	NA	promoter-TSS (NM_001033433)	promoter-TSS (NM_001033433)	-21	NM_001033433	380705	Mm.490673	NM_001033433	ENSMUSG00000089876	Tmem102	4632403M07Rik|Cbap|Tmem102-ps	transmembrane protein 102	protein-coding
mm_14235.1	chr2	127691832	127691842	+	1	NA	Intergenic	Intergenic	-35142	NM_001171187	17153	Mm.39040	NM_010762	ENSMUSG00000027375	Mal	Mpv17|Vip17	myelin and lymphocyte protein, T cell differentiation protein	protein-coding
mm_67205.1	chr7	74302782	74302787	-	1	NA	intron (NM_001038643, intron 8 of 10)	B4|SINE|B4	251996	NM_023908	108116	Mm.425467	NM_023908	ENSMUSG00000025790	Slco3a1	5830414C08Rik|Anr1|MJAM|OATP-D|R75096|Slc21a11	solute carrier organic anion transporter family, member 3a1	protein-coding
mm_147934.1	chr18	66006089	66006089	-	1	NA	Intergenic	Lx9|LINE|L1	-3454	NM_001172062	70361	Mm.290857	NM_027400	ENSMUSG00000041891	Lman1	2610020P13Rik|AI326273|AU043785|C730041J05|ERGIC53|F5F8D|MCFD1|MR60|P58|gp58	lectin, mannose-binding, 1	protein-coding
mm_78527.1	chr9	34647564	34647571	+	1	NA	intron (NM_001190912, intron 1 of 15)	intron (NM_001190912, intron 1 of 15)	158836	NM_001190911	67703	Mm.220710	NM_026324	ENSMUSG00000032036	Kirrel3	1500010O20Rik|2900036G11Rik|NEPH2|SST4|mKIAA1867	kin of IRRE like 3 (Drosophila)	protein-coding
mm_77026.1	chr8	108876985	108877009	-	1	NA	intron (NM_007496, intron 4 of 9)	intron (NM_007496, intron 4 of 9)	-59863	NR_037295	100526511		NR_037295	ENSMUSG00000093241	Mir3108	mir-3108|mmu-mir-3108	microRNA 3108	ncRNA
mm_151586.1	chr19	61227493	61227503	+	1	NA	intron (NM_009970, intron 1 of 11)	CpG-7695	920	NM_009970	12982	Mm.287228	NM_009970	ENSMUSG00000059326	Csf2ra	CD116|Csfgmra|GM-CSF-Ra|GM-CSFR	colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)	protein-coding
mm_69992.1	chr7	142383500	142383536	-	1	NA	exon (NM_009983, exon 3 of 9)	exon (NM_009983, exon 3 of 9)	4352	NM_009983	13033	Mm.231395	NM_009983	ENSMUSG00000007891	Ctsd	CD|CatD	cathepsin D	protein-coding
mm_119364.1	chr14	41117093	41117104	+	1	NA	intron (NM_133653, intron 6 of 9)	intron (NM_133653, intron 6 of 9)	12065	NM_133653	11720	Mm.14064	NM_133653	ENSMUSG00000037798	Mat1a	AI046368|AdoMet|Ams|MAT|MATA1|SAMS|SAMS1	methionine adenosyltransferase I, alpha	protein-coding
mm_162655.1	chr10	4266118	4266135	+	1	NA	promoter-TSS (NM_031185)	promoter-TSS (NM_031185)	-203	NM_031185	83397	Mm.27481	NM_031185	ENSMUSG00000038587	Akap12	AI317366|SSeCKS|Srcs5|Tsga12	A kinase (PRKA) anchor protein (gravin) 12	protein-coding
mm_132577.1	chr16	38244947	38244956	+	1	NA	3' UTR (NM_019827, exon 11 of 11)	3' UTR (NM_019827, exon 11 of 11)	49873	NM_010936	18171	Mm.8509	NM_010936	ENSMUSG00000022809	Nr1i2	PXR|PXR.1|PXR.2|PXR1|SXR|mPXR	nuclear receptor subfamily 1, group I, member 2	protein-coding
mm_116962.1	chr13	56152899	56152909	-	1	NA	Intergenic	MLT1J1|LTR|ERVL-MaLR	-17354	NM_001159513	26914	Mm.283802	NM_012015	ENSMUSG00000015937	H2afy	H2AF12M|mH2a1|macroH2A1	H2A histone family, member Y	protein-coding
mm_86646.1	chr10	16584237	16584247	+	1	NA	Intergenic	Intergenic	511540	NR_038020	100504235	Mm.84044	NR_038020	ENSMUSG00000101969	Gm20125	-	predicted gene, 20125	ncRNA
mm_21844.1	chr2	165852067	165852086	-	1	NA	exon (NM_001281926, exon 3 of 23)	exon (NM_001281926, exon 3 of 23)	6097	NM_001252585	228880	Mm.227598	NM_027230	ENSMUSG00000039671	Zmynd8	1110013E22Rik|2010005I16Rik|3632413B07Rik|AI316811|AL024039|Prkcbp1|RACK7	zinc finger, MYND-type containing 8	protein-coding
mm_69086.1	chr7	127017003	127017032	-	1	NA	TTS (NM_001102563)	TTS (NM_001102563)	335	NM_030240	67278	Mm.345385	NM_030240	ENSMUSG00000030680	Pagr1a	2900092E17Rik|C77040|PA1|PAGR1	PAXIP1 associated glutamate rich protein 1A	protein-coding
mm_137899.1	chr17	31681685	31681699	+	1	NA	TTS (NM_001278570)	TTS (NM_001278570)	3761	NM_001278570	12954	Mm.1228	NM_013501	ENSMUSG00000024041	Cryaa	Acry-1|Crya-1|Crya1|DAcry-1|lop18	crystallin, alpha A	protein-coding
mm_98981.1	chr11	98740890	98740952	+	1	NA	promoter-TSS (NM_001313983)	promoter-TSS (NM_001313983)	-864	NM_178060	21833	Mm.265917	NM_178060	ENSMUSG00000058756	Thra	6430529J03Rik|AW259572|Erba|Nr1a1|Rvr|T3R[a]|T3Ralpha|Thra1|Thra2|c-erbA-1|c-erbA-alpha|c-erbAalpha	thyroid hormone receptor alpha	protein-coding
mm_24227.1	chr3	88914002	88914035	+	1	NA	promoter-TSS (NM_144898)	promoter-TSS (NM_144898)	-68	NM_144898	229524	Mm.440405	NM_144898	ENSMUSG00000068922	Msto1	BC008103|mst	misato 1, mitochondrial distribution and morphology regulator	protein-coding
mm_41491.1	chr5	92137897	92137939	+	1	NA	promoter-TSS (NM_019490)	promoter-TSS (NM_019490)	-20	NM_019490	56041	Mm.15868	NM_019490	ENSMUSG00000029407	Uso1	115kDa|TAP|Vdp	USO1 vesicle docking factor	protein-coding
mm_148234.1	chr18	80469659	80469662	-	1	NA	promoter-TSS (NM_026295)	promoter-TSS (NM_026295)	7	NM_026295	67655	Mm.312893	NM_026295	ENSMUSG00000033323	Ctdp1	4930563P03Rik|AW553592	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) phosphatase, subunit 1	protein-coding
mm_101689.1	chr11	40695207	40695223	-	1	NA	promoter-TSS (NM_001199274)	promoter-TSS (NM_001199274)	-12	NM_001199274	108645	Mm.293771	NM_134017	ENSMUSG00000042032	Mat2b	1110064C04Rik|2410018D16Rik|AI182287|AU022853|MAT-II|MATIIbeta|TGR	methionine adenosyltransferase II, beta	protein-coding
mm_156227.1	chrX	135800895	135800905	+	1	NA	exon (NM_026081, exon 11 of 11)	exon (NM_026081, exon 11 of 11)	-38134	NM_001163016	245607	Mm.489763	NM_001163015	ENSMUSG00000072966	Gprasp2	5330440H13Rik|GASP-2|GASP2|Prpl5	G protein-coupled receptor associated sorting protein 2	protein-coding
mm_38256.1	chr4	136819534	136819548	-	1	NA	intron (NM_001290753, intron 1 of 15)	intron (NM_001290753, intron 1 of 15)	16471	NM_001290753	13844	Mm.250981	NM_010142	ENSMUSG00000028664	Ephb2	Cek5|Drt|ETECK|Erk|Hek5|Nuk|Prkm5|Qek5|Sek3|Tyro5	Eph receptor B2	protein-coding
mm_9462.1	chr1	172895026	172895044	-	1	NA	promoter-TSS (NM_011318)	promoter-TSS (NM_011318)	19	NM_011318	20219	Mm.330510	NM_011318	ENSMUSG00000026542	Apcs	Sap	serum amyloid P-component	protein-coding
mm_19307.1	chr2	90523110	90523117	-	1	NA	intron (NM_008982, intron 1 of 23)	A-rich|Low_complexity|Low_complexity	-43939	NM_001135657	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_7544.1	chr1	124504168	124504179	-	1	NA	Intergenic	RSINE1|SINE|B4	-458614	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_170155.1	chr17	45596176	45596195	-	1	NA	promoter-TSS (NM_001199116)	promoter-TSS (NM_001199116)	-283	NM_001199114	63959	Mm.29744	NM_022880	ENSMUSG00000023942	Slc29a1	1200014D21Rik|AA407560|ENT1	solute carrier family 29 (nucleoside transporters), member 1	protein-coding
mm_58105.1	chr6	137630282	137630282	-	1	NA	intron (NM_007945, intron 1 of 21)	intron (NM_007945, intron 1 of 21)	19003	NM_001271588	13860	Mm.235346	NM_007945	ENSMUSG00000015766	Eps8	AW261790	epidermal growth factor receptor pathway substrate 8	protein-coding
mm_8271.1	chr1	139560214	139560229	-	1	NA	promoter-TSS (NM_015780)	promoter-TSS (NM_015780)	1	NM_015780	50702	Mm.220362	NM_015780	ENSMUSG00000057037	Cfhr1	AI194696|CFHRB|Cfhl1	complement factor H-related 1	protein-coding
mm_7168.1	chr1	92113328	92113334	-	1	NA	intron (NM_207225, intron 2 of 26)	intron (NM_207225, intron 2 of 26)	67010	NM_207225	208727	Mm.318567	NM_207225	ENSMUSG00000026313	Hdac4	4932408F19Rik|HD4	histone deacetylase 4	protein-coding
mm_166385.1	chr5	132383860	132383861	+	1	NA	intron (NM_177047, intron 1 of 18)	PB1D10|SINE|Alu	158483	NM_177047	319974	Mm.409595	NM_177047	ENSMUSG00000029673	Auts2	2700063G02Rik|A730011F23Rik|D830032G16Rik	autism susceptibility candidate 2	protein-coding
mm_30547.1	chr4	3684836	3684846	+	1	NA	intron (NM_010747, intron 1 of 12)	Lx9|LINE|L1	6720	NM_010747	17096	Mm.317331	NM_010747	ENSMUSG00000042228	Lyn	AA407514|Hck-2|p53Lyn|p56Lyn	LYN proto-oncogene, Src family tyrosine kinase	protein-coding
mm_59964.1	chr7	30428361	30428369	+	1	NA	3' UTR (NM_172142, exon 11 of 11)	3' UTR (NM_172142, exon 11 of 11)	5061	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_144297.1	chr18	12256221	12256242	+	1	NA	intron (NM_001190371, intron 9 of 9)	intron (NM_001190371, intron 9 of 9)	-19845	NM_008720	18145	Mm.3484	NM_008720	ENSMUSG00000024413	Npc1	A430089E03Rik|C85354|D18Ertd139e|D18Ertd723e|lcsd|nmf164|spm	Niemann-Pick type C1	protein-coding
mm_158700.1	chrX	162069466	162069469	-	1	NA	intron (NM_001081052, intron 1 of 7)	U6|snRNA|snRNA	89974	NM_001081052	195727	Mm.336313	NM_001081052	ENSMUSG00000059493	Nhs	Gm389|Gm48|Nhs1|Xcat	Nance-Horan syndrome (human)	protein-coding
mm_103022.1	chr11	69735035	69735039	-	1	NA	exon (NM_001291068, exon 29 of 29)	exon (NM_001291068, exon 29 of 29)	23596	NM_001291068	20020	Mm.16533	NM_009089	ENSMUSG00000005198	Polr2a	220kDa|Rpb1|Rpo2-1	polymerase (RNA) II (DNA directed) polypeptide A	protein-coding
mm_152067.1	chr19	6541666	6541670	-	1	NA	intron (NM_009203, intron 1 of 9)	(TG)n|Simple_repeat|Simple_repeat	1402	NM_009203	20521	Mm.391146	NM_009203	ENSMUSG00000061742	Slc22a12	AI987855|OAT4L|Rst|Slc22al2|URAT1	solute carrier family 22 (organic anion/cation transporter), member 12	protein-coding
mm_60562.1	chr7	44481353	44481363	+	1	NA	Intergenic	Intergenic	-3159	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_162832.1	chr10	81628683	81628689	+	1	NA	intron (NM_027480, intron 1 of 19)	intron (NM_027480, intron 1 of 19)	146	NM_027480	70615	Mm.304382	NM_027480	ENSMUSG00000054708	Ankrd24	4631433D01Rik|5730519E19Rik|D10Bur2e	ankyrin repeat domain 24	protein-coding
mm_54181.1	chr6	23839323	23839333	-	1	NA	promoter-TSS (NM_153163)	promoter-TSS (NM_153163)	93	NM_001252106	320405	Mm.259632	NM_153163	ENSMUSG00000017978	Cadps2	A230044C21Rik|Caps-2|Caps2|Cpd2	Ca2+-dependent activator protein for secretion 2	protein-coding
mm_54274.1	chr6	29160171	29160195	-	1	NA	exon (NM_133925, exon 2 of 19)	exon (NM_133925, exon 2 of 19)	4541	NM_133925	68272	Mm.40802	NM_026650	ENSMUSG00000029701	Rbm28	2810480G15Rik|AI503051	RNA binding motif protein 28	protein-coding
mm_144015.1	chr17	88791979	88791996	-	1	NA	promoter-TSS (NM_013582)	promoter-TSS (NM_013582)	-11	NM_013582	16867	Mm.1644	NM_013582	ENSMUSG00000024107	Lhcgr	Gpcr19-rs1|LH-R|Lhr	luteinizing hormone/choriogonadotropin receptor	protein-coding
mm_171335.1	chr3	99907592	99907608	-	1	NA	intron (NM_028892, intron 1 of 48)	L1Md_T|LINE|L1	22183	NM_028892	74362	Mm.55847	NM_028892	ENSMUSG00000027867	Spag17	4931427F14Rik|PF6|Spag17-ps	sperm associated antigen 17	protein-coding
mm_5637.1	chr1	40439496	40439506	-	1	NA	promoter-TSS (NM_010743)	promoter-TSS (NM_010743)	-128	NM_001025602	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_57284.1	chr6	124364480	124364495	-	1	NA	promoter-TSS (NR_131162)	promoter-TSS (NR_131162)	-1	NR_131162	72268	Mm.420740	NR_131162		1700027F06Rik	-	RIKEN cDNA 1700027F06 gene	ncRNA
mm_137414.1	chr17	26116793	26116803	+	1	NA	exon (NM_021793, exon 2 of 13)	exon (NM_021793, exon 2 of 13)	3482	NM_021793	60455	Mm.304656	NM_021793	ENSMUSG00000024180	Tmem8	AW490096|M83|Tmem8a	transmembrane protein 8 (five membrane-spanning domains)	protein-coding
mm_25118.1	chr3	102010139	102010171	+	1	NA	promoter-TSS (NM_178777)	promoter-TSS (NM_178777)	10	NM_178777	18072	Mm.137286	NM_178777	ENSMUSG00000048540	Nhlh2	6230401I09Rik|Hen2|NSCL2|Nscl-2|bHLHa34	nescient helix loop helix 2	protein-coding
mm_171053.1	chr3	103646062	103646071	-	1	NA	promoter-TSS (NM_174875)	promoter-TSS (NM_174875)	2	NM_174875	666468	Mm.102230	NM_174875	ENSMUSG00000079418	Atg4a	AI627006|AV169859|Apg4a|Atg4al|Autl2	autophagy related 4A, cysteine peptidase	protein-coding
mm_100598.1	chr11	121204421	121204441	+	1	NA	promoter-TSS (NM_001001333)	promoter-TSS (NM_001001333)	-2	NM_001001333	238023	Mm.275130	NM_001001333	ENSMUSG00000039307	Hexdc	BC069960	hexosaminidase (glycosyl hydrolase family 20, catalytic domain) containing	protein-coding
mm_47910.1	chr5	134946897	134946906	-	1	NA	promoter-TSS (NM_009903)	promoter-TSS (NM_009903)	33	NM_009903	12740	Mm.7339	NM_009903	ENSMUSG00000047501	Cldn4	Cep-r|Cpetr|Cpetr1	claudin 4	protein-coding
mm_73864.1	chr8	118443637	118443638	+	1	NA	intron (NM_019707, intron 1 of 13)	PB1D7|SINE|Alu	160026	NM_019707	12554	Mm.334841	NM_019707	ENSMUSG00000031841	Cdh13	4932416G01Rik|Cdht|Tcad	cadherin 13	protein-coding
mm_120266.1	chr14	63122481	63122495	+	1	NA	promoter-TSS (NM_007798)	promoter-TSS (NM_007798)	26	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_146129.1	chr18	74625075	74625084	+	1	NA	intron (NM_201600, intron 5 of 38)	intron (NM_201600, intron 5 of 38)	-93955	NR_045368	73606	Mm.444734	NR_045368		1700120E14Rik	-	RIKEN cDNA 1700120E14 gene	ncRNA
mm_81301.1	chr9	108339289	108339299	+	1	NA	5' UTR (NM_008160, exon 1 of 2)	5' UTR (NM_008160, exon 1 of 2)	214	NM_001329528	14775	Mm.1090	NM_008160	ENSMUSG00000063856	Gpx1	AI195024|AL033363|CGPx|GPx-1|GSHPx-1|Gpx	glutathione peroxidase 1	protein-coding
mm_58138.1	chr6	141778102	141778124	-	1	NA	Intergenic	Intergenic	78058	NM_030687	28250	Mm.255586	NM_030687	ENSMUSG00000030237	Slco1a4	AI785519|Oatp1a4|Oatp2|Slc21a5	solute carrier organic anion transporter family, member 1a4	protein-coding
mm_17765.1	chr2	32788711	32788731	-	1	NA	3' UTR (NM_001113569, exon 20 of 20)	3' UTR (NM_001113569, exon 20 of 20)	-4316	NM_025619	227736	Mm.441499	NM_025619	ENSMUSG00000038987	Cfap157	1700019L03Rik	cilia and flagella associated protein 157	protein-coding
mm_70769.1	chr8	21969829	21969833	+	1	NA	promoter-TSS (NM_026459)	promoter-TSS (NM_026459)	-765	NM_026459	67929	Mm.60688	NM_026459	ENSMUSG00000017049	Ccdc70	1700112P19Rik	coiled-coil domain containing 70	protein-coding
mm_15364.1	chr2	156421039	156421043	+	1	NA	5' UTR (NM_001291121, exon 1 of 22)	5' UTR (NM_001291121, exon 1 of 22)	132	NM_001291123	13821	Mm.20852	NM_013510	ENSMUSG00000027624	Epb41l1	4.1N|Epb4.1l1|NBL1|mKIAA0338	erythrocyte membrane protein band 4.1 like 1	protein-coding
mm_146766.1	chr18	17829337	17829338	-	1	NA	Intergenic	ERVB4_1B-I_MM-int|LTR|ERVK	-248347	NR_045374	75162	Mm.60874	NR_045374		4930545E07Rik	-	RIKEN cDNA 4930545E07 gene	ncRNA
mm_92636.1	chr10	80335335	80335370	-	1	NA	3' UTR (NM_139292, exon 6 of 6)	3' UTR (NM_139292, exon 6 of 6)	5207	NM_139292	70335	Mm.28147	NM_139292	ENSMUSG00000035504	Reep6	0610011M24Rik|Dp1l1	receptor accessory protein 6	protein-coding
mm_70307.1	chr8	4172872	4172876	+	1	NA	intron (NM_001346730, intron 1 of 19)	B1_Mus1|SINE|Alu	6307	NM_001346730	213027	Mm.437106	NM_153536	ENSMUSG00000011832	Evi5l	1700084G18Rik|2310039H16Rik|3110007G05Rik|B130050I23Rik	ecotropic viral integration site 5 like	protein-coding
mm_62855.1	chr7	114494564	114494576	+	1	NA	exon (NM_011055, exon 3 of 16)	exon (NM_011055, exon 3 of 16)	68402	NR_110407	244209	Mm.108037	NM_177382	ENSMUSG00000030670	Cyp2r1	-	cytochrome P450, family 2, subfamily r, polypeptide 1	protein-coding
mm_91032.1	chr10	18094362	18094366	-	1	NA	intron (NM_009048, intron 5 of 19)	intron (NM_009048, intron 5 of 19)	38424	NM_001111065	19707	Mm.4479	NM_009048	ENSMUSG00000019854	Reps1	BB161292	RalBP1 associated Eps domain containing protein	protein-coding
mm_48878.1	chr5	151127536	151127544	-	1	NA	intron (NM_146258, intron 1 of 13)	intron (NM_146258, intron 1 of 13)	62653	NM_001163493	243362	Mm.209272	NM_146258	ENSMUSG00000016128	Stard13	DLC2|GT650	StAR-related lipid transfer (START) domain containing 13	protein-coding
mm_615.1	chr1	40028794	40028801	+	1	NA	Intergenic	Intergenic	-55971	NM_010555	16178	Mm.1349	NM_010555	ENSMUSG00000026073	Il1r2	CD121b|Il1r-2	interleukin 1 receptor, type II	protein-coding
mm_126856.1	chr15	89243316	89243330	+	1	NA	5' UTR (NM_026813, exon 3 of 25)	5' UTR (NM_026813, exon 3 of 25)	31764	NM_027805	71474	Mm.184055	NM_026813	ENSMUSG00000036561	Ppp6r2	1110033O10Rik|8430411H09Rik|B230107H12Rik|Pp6r2|Saps2	protein phosphatase 6, regulatory subunit 2	protein-coding
mm_24032.1	chr3	87617542	87617613	+	1	NA	Intergenic	CpG	-1174	NM_001003912	213498	Mm.287267	NM_001003912	ENSMUSG00000041977	Arhgef11	B930073M02|E130307F09|PDZ-RhoGEF|Prg|RhoGEF|mKIAA0380	Rho guanine nucleotide exchange factor (GEF) 11	protein-coding
mm_86569.1	chr10	11356124	11356128	+	1	NA	intron (NM_010146, intron 1 of 3)	intron (NM_010146, intron 1 of 3)	12681	NM_010146	13853	Mm.89946	NM_010146	ENSMUSG00000055493	Epm2a	TG-B|Tg(TcraK,TcrbK)TG-BFlv	epilepsy, progressive myoclonic epilepsy, type 2 gene alpha	protein-coding
mm_120834.1	chr14	75177135	75177154	+	1	NA	intron (NM_008879, intron 2 of 16)	intron (NM_008879, intron 2 of 16)	40719	NM_008879	18826	Mm.153911	NM_008879	ENSMUSG00000021998	Lcp1	AW536232|D14Ertd310e|LCP-1|Pls2|pp65	lymphocyte cytosolic protein 1	protein-coding
mm_24932.1	chr3	96559698	96559711	+	1	NA	exon (NM_023719, exon 5 of 8)	exon (NM_023719, exon 5 of 8)	1747	NM_023719	56338	Mm.410189	NM_023719	ENSMUSG00000038393	Txnip	1200008J08Rik|AA682105|Hyplip1|THIF|Tbp-2|VDUP1	thioredoxin interacting protein	protein-coding
mm_52938.1	chr6	122934077	122934126	+	1	NA	3' UTR (NM_199311, exon 6 of 6)	3' UTR (NM_199311, exon 6 of 6)	12253	NM_199311	269799	Mm.297275	NM_199311	ENSMUSG00000049037	Clec4a1	BC049354|Dcir4	C-type lectin domain family 4, member a1	protein-coding
mm_83745.1	chr9	51105833	51105851	-	1	NA	Intergenic	Intergenic	-2197	NR_029655	723849		NR_029655	ENSMUSG00000065492	Mir34b	Mirn34b|mir-34b|mmu-mir-34b	microRNA 34b	ncRNA
mm_124974.1	chr15	20449034	20449078	+	1	NA	Intergenic	Intergenic	217694	NM_022816	64833	Mm.352763	NM_022816	ENSMUSG00000047565	Acot10	Acate3|MT-ACT48|p48	acyl-CoA thioesterase 10	protein-coding
mm_101604.1	chr11	34833585	34833596	-	1	NA	promoter-TSS (NM_027411)	promoter-TSS (NM_027411)	51	NM_027411	70385	Mm.194368	NM_027411	ENSMUSG00000069910	Spdl1	1700018I02Rik|2600001J17Rik|2810049B11Rik|AA409762|Ccdc99	spindle apparatus coiled-coil protein 1	protein-coding
mm_36015.1	chr4	56916141	56916151	-	1	NA	intron (NM_175518, intron 7 of 17)	L1M3|LINE|L1	-20848	NR_029789	723837		NR_029789	ENSMUSG00000065544	Mir32	Mirn32|mir-32|mmu-mir-32	microRNA 32	ncRNA
mm_163569.1	chr13	29151996	29152000	+	1	NA	Intergenic	Intergenic	135743	NR_045075	77920	Mm.197051	NR_045073	ENSMUSG00000086363	A330102I10Rik	-	RIKEN cDNA A330102I10 gene	ncRNA
mm_65256.1	chr7	19880429	19880440	-	1	NA	intron (NM_177036, intron 5 of 6)	B3A|SINE|B2	7531	NM_177036	319930	Mm.215839	NM_177036	ENSMUSG00000049848	Ceacam19	C130022P09Rik|CEAL1	carcinoembryonic antigen-related cell adhesion molecule 19	protein-coding
mm_164947.1	chr19	4238786	4238788	+	1	NA	Intergenic	Intergenic	6372	NR_132280	69745	Mm.32518	NM_027196	ENSMUSG00000024854	Pold4	2410012M21Rik|AI463381|AW060307|Polds|p12	polymerase (DNA-directed), delta 4	protein-coding
mm_89155.1	chr10	86033023	86033030	+	1	NA	intron (NM_001347151, intron 4 of 8)	intron (NM_001347151, intron 4 of 8)	10872	NM_001347151	69754	Mm.44236	NM_153195	ENSMUSG00000001786	Fbxo7	2410015K21Rik|A230052G17Rik|AI117679|AW260462|C85118	F-box protein 7	protein-coding
mm_50922.1	chr6	57606879	57606896	+	1	NA	intron (NM_025992, intron 6 of 22)	intron (NM_025992, intron 6 of 22)	25895	NM_025992	67138	Mm.297393	NM_025992	ENSMUSG00000029798	Herc6	1700121D12Rik|2510038N07Rik|4930427L17Rik|AI451296|CEB1|Herc5	hect domain and RLD 6	protein-coding
mm_171357.1	chr4	115791802	115791803	+	1	NA	intron (NM_181040, intron 4 of 8)	B1_Mur3|SINE|Alu	6988	NM_181040	230649	Mm.109600	NM_181040	ENSMUSG00000028710	Atpaf1	6330547J17Rik|AI593252|ATP11|ATP11p	ATP synthase mitochondrial F1 complex assembly factor 1	protein-coding
mm_111397.1	chr12	90738563	90738568	-	1	NA	5' UTR (NM_010050, exon 1 of 2)	5' UTR (NM_010050, exon 1 of 2)	472	NM_010050	13371	Mm.21389	NM_010050	ENSMUSG00000007682	Dio2	5DII|AI324267|DIOII	deiodinase, iodothyronine, type II	protein-coding
mm_60872.1	chr7	45942280	45942292	+	1	NA	intron (NM_001033243, intron 7 of 12)	intron (NM_001033243, intron 7 of 12)	13888	NM_001033243	211535	Mm.227539	NM_001033243	ENSMUSG00000040189	Ccdc114	-	coiled-coil domain containing 114	protein-coding
mm_28515.1	chr3	92584431	92584437	-	1	NA	exon (NM_008574, exon 2 of 2)	exon (NM_008574, exon 2 of 2)	4590	NM_008574	17235	Mm.331192	NM_008574		Smcp	Mcs|Mcsp	sperm mitochondria-associated cysteine-rich protein	protein-coding
mm_79970.1	chr9	66468620	66468623	+	1	NA	intron (NM_145617, intron 50 of 77)	intron (NM_145617, intron 50 of 77)	45972	NM_175206	74165	Mm.297998	NM_175206	ENSMUSG00000050503	Fbxl22	1110004B15Rik	F-box and leucine-rich repeat protein 22	protein-coding
mm_51517.1	chr6	83145889	83145937	+	1	NA	intron (NM_009106, intron 2 of 12)	intron (NM_009106, intron 2 of 12)	8829	NM_009106	20166	Mm.4139	NM_009106	ENSMUSG00000034930	Rtkn	-	rhotekin	protein-coding
mm_156050.1	chrX	109095416	109095426	+	1	NA	promoter-TSS (NM_019989)	promoter-TSS (NM_019989)	14	NM_019989	56726	Mm.260760	NM_019989	ENSMUSG00000031246	Sh3bgrl	1190008F14Rik	SH3-binding domain glutamic acid-rich protein like	protein-coding
mm_169383.1	chr14	41336699	41336718	+	1	NA	Intergenic	Intergenic	-151510	NM_009160	20390	Mm.1321	NM_009160	ENSMUSG00000021795	Sftpd	AI573415|SP-D|Sfpd|Sftp4	surfactant associated protein D	protein-coding
mm_19293.1	chr2	90458174	90458189	-	1	NA	exon (NM_008982, exon 10 of 24)	exon (NM_008982, exon 10 of 24)	20993	NM_001135657	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_107799.1	chr12	64917946	64917989	+	1	NA	promoter-TSS (NM_001025605)	promoter-TSS (NM_001025605)	56	NM_001025605	217648	Mm.341586	NM_001025605	ENSMUSG00000047227	Gm527	-	predicted gene 527	protein-coding
mm_36993.1	chr4	110286582	110286617	-	1	NA	5' UTR (NM_010488, exon 1 of 7)	5' UTR (NM_010488, exon 1 of 7)	235	NM_010488	15572	Mm.3970	NM_010488	ENSMUSG00000028546	Elavl4	Elav|Hud|PNEM	ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4 (Hu antigen D)	protein-coding
mm_36273.1	chr4	63729501	63729509	-	1	NA	3' UTR (NM_177371, exon 4 of 4)	3' UTR (NM_177371, exon 4 of 4)	15608	NM_177371	326623	Mm.208152	NM_177371	ENSMUSG00000050395	Tnfsf15	Tl1|Tl1a|Tnlg1b|Vegi	tumor necrosis factor (ligand) superfamily, member 15	protein-coding
mm_126692.1	chr15	85017164	85017200	+	1	NA	promoter-TSS (NM_023478)	promoter-TSS (NM_023478)	41	NM_023478	22270	Mm.46214	NM_023478	ENSMUSG00000022435	Upk3a	1110017C07Rik|UP3a|UPIII|Upk3	uroplakin 3A	protein-coding
mm_86344.1	chr9	123307977	123307989	-	1	NA	Intergenic	Intergenic	-47194	NM_001002267	72309	Mm.8569	NM_001002267	ENSMUSG00000054871	Tmem158	2310037P21Rik|Ris1	transmembrane protein 158	protein-coding
mm_136413.1	chr16	93833004	93833049	-	1	NA	intron (NM_001045529, intron 1 of 16)	PB1D11|SINE|Alu	905	NM_001045529	338467	Mm.287329	NM_001045529	ENSMUSG00000039456	Morc3	1110051N18Rik|AI452146|BF318192|D16Jhu32e|NXP2|Zcwcc3	microrchidia 3	protein-coding
mm_43704.1	chr5	139256633	139256636	+	1	NA	intron (NM_001163316, intron 1 of 8)	B4A|SINE|B4	3137	NM_001163316	67604	Mm.270137	NM_026269	ENSMUSG00000025858	Get4	1110007L15Rik|AW412535|Cee	golgi to ER traffic protein 4	protein-coding
mm_140571.1	chr17	8923951	8923997	-	1	NA	intron (NM_001347321, intron 3 of 21)	MTE2b|LTR|ERVL-MaLR	-64359	NM_025851	66931	Mm.67591	NM_025851	ENSMUSG00000023873	1700010I14Rik	-	RIKEN cDNA 1700010I14 gene	protein-coding
mm_50298.1	chr6	47510175	47510175	+	1	NA	intron (NM_012042, intron 9 of 21)	intron (NM_012042, intron 9 of 21)	55851	NM_012042	26965	Mm.87611	NM_012042	ENSMUSG00000029686	Cul1	-	cullin 1	protein-coding
mm_3564.1	chr1	150431223	150431241	+	1	NA	exon (NM_133780, exon 34 of 52)	exon (NM_133780, exon 34 of 52)	34933	NM_021400	96875	Mm.174256	NM_021400	ENSMUSG00000006014	Prg4	CACP|DOL54|JCAP|MSF|SZP|lubricin	proteoglycan 4 (megakaryocyte stimulating factor, articular superficial zone protein)	protein-coding
mm_166154.1	chr5	12719663	12719696	+	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	336513	NM_028882	108151	Mm.89313	NM_028882	ENSMUSG00000040254	Sema3d	4631426B19Rik	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D	protein-coding
mm_21330.1	chr2	157101393	157101439	-	1	NA	exon (NM_001139520, exon 16 of 17)	exon (NM_001139520, exon 16 of 17)	14361	NM_001177439	383766	Mm.480305	NM_001177439	ENSMUSG00000074628	Tldc2	Gm1332	TBC/LysM associated domain containing 2	protein-coding
mm_102092.1	chr11	52283249	52283270	-	1	NA	promoter-TSS (NM_009331)	promoter-TSS (NM_009331)	-245	NM_001313981	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_146663.1	chr18	12128627	12128644	-	1	NA	promoter-TSS (NM_024182)	promoter-TSS (NM_024182)	-215	NM_024182	66878	Mm.28551	NM_024182	ENSMUSG00000024404	Riok3	1200013N13Rik|D18Ertd331e|E130306C24Rik|Sudd	RIO kinase 3	protein-coding
mm_147354.1	chr18	43361064	43361072	-	1	NA	exon (NM_001291455, exon 3 of 14)	exon (NM_001291455, exon 3 of 14)	12204	NM_001136086	22240	Mm.8180	NM_009468	ENSMUSG00000024501	Dpysl3	CRMP-4|DRP-3|TUC4|ULIP-1|Ulip|Ulip1	dihydropyrimidinase-like 3	protein-coding
mm_105501.1	chr11	106160505	106160545	-	1	NA	promoter-TSS (NM_172397)	promoter-TSS (NM_172397)	-383	NM_172397	67803	Mm.21687	NM_172397	ENSMUSG00000040699	Limd2	0610025L06Rik|AI413966	LIM domain containing 2	protein-coding
mm_111362.1	chr12	87147419	87147476	-	1	NA	promoter-TSS (NM_001252556)	promoter-TSS (NM_001252556)	-260	NM_001252556	14874	Mm.29652	NM_010363	ENSMUSG00000021033	Gstz1	MAAI	glutathione transferase zeta 1 (maleylacetoacetate isomerase)	protein-coding
mm_140085.1	chr17	75435887	75435937	+	1	NA	promoter-TSS (NM_001166493)	promoter-TSS (NM_001166493)	7	NM_001166493	240168	Mm.329203	NM_207246	ENSMUSG00000071042	Rasgrp3	BC066069|Gm327	RAS, guanyl releasing protein 3	protein-coding
mm_102445.1	chr11	59787193	59787201	-	1	NA	promoter-TSS (NR_110894)	promoter-TSS (NR_110894)	25	NR_110894	194908	Mm.344651	NM_183139	ENSMUSG00000043648	Pld6	4933433K01Rik|Gm10|Zuc|mZuc|mitoPLD	phospholipase D family, member 6	protein-coding
mm_124497.1	chr14	121878450	121878463	-	1	NA	promoter-TSS (NM_026861)	promoter-TSS (NM_026861)	48	NR_131000	78312	Mm.188743	NR_130999	ENSMUSG00000102112	1810041H14Rik	-	RIKEN cDNA 1810041H14 gene	ncRNA
mm_84523.1	chr9	67043870	67043945	-	1	NA	promoter-TSS (NM_001164256)	promoter-TSS (NM_001164256)	-36	NM_001164253	22003	Mm.121878	NM_024427	ENSMUSG00000032366	Tpm1	AA986836|AI854628|TM2|Tm3|Tmpa|Tpm-1|alpha-TM	tropomyosin 1, alpha	protein-coding
mm_96639.1	chr11	69326347	69326355	+	1	NA	promoter-TSS (NM_010599)	promoter-TSS (NM_010599)	93	NM_010599	16499	Mm.232472	NM_010599	ENSMUSG00000018470	Kcnab3	C330022D06Rik|Kcnab4|mKv(beta)4	potassium voltage-gated channel, shaker-related subfamily, beta member 3	protein-coding
mm_55851.1	chr6	83429087	83429104	-	1	NA	intron (NM_001347313, intron 3 of 11)	(A)n|Simple_repeat|Simple_repeat	12583	NM_183138	194388	Mm.211030	NM_183138	ENSMUSG00000034832	Tet3	B430006D22Rik|BC037432|D230004J03Rik	tet methylcytosine dioxygenase 3	protein-coding
mm_130306.1	chr15	97020324	97020336	-	1	NA	intron (NM_027052, intron 1 of 15)	intron (NM_027052, intron 1 of 15)	35626	NM_027052	69354	Mm.250980	NM_027052	ENSMUSG00000022464	Slc38a4	1110012E16Rik|1700012A18Rik|Ata3|mATA3|mNAT3	solute carrier family 38, member 4	protein-coding
mm_83523.1	chr9	46230049	46230055	-	1	NA	exon (NM_009692, exon 4 of 4)	exon (NM_009692, exon 4 of 4)	1422	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2|apo-AI|apoA-I	apolipoprotein A-I	protein-coding
mm_8056.1	chr1	135374956	135375098	-	1	NA	promoter-TSS (NM_175259)	promoter-TSS (NM_175259)	36	NM_175259	77552	Mm.41407	NM_175259	ENSMUSG00000041889	Shisa4	9330132O05Rik|Tmem58|mShisa4	shisa family member 4	protein-coding
mm_22741.1	chr3	19956987	19956993	+	1	NA	promoter-TSS (NM_007752)	promoter-TSS (NM_007752)	-64	NM_001276250	12870	Mm.13787	NM_007752	ENSMUSG00000003617	Cp	D3Ertd555e	ceruloplasmin	protein-coding
mm_94244.1	chr11	3311033	3311059	+	1	NA	non-coding (NR_045708, exon 2 of 6)	non-coding (NR_045708, exon 2 of 6)	2046	NR_045708	100302648	Mm.458664	NR_045708	ENSMUSG00000084941	Gm11944	OTTMUSG00000005017	predicted gene 11944	ncRNA
mm_28428.1	chr3	90464656	90464663	-	1	NA	intron (NM_008727, intron 1 of 21)	intron (NM_008727, intron 1 of 21)	1207	NM_008727	18160	Mm.4627	NM_008727	ENSMUSG00000027931	Npr1	AI893888|GC-A|NPR-A|NPRA|Pndr	natriuretic peptide receptor 1	protein-coding
mm_157452.1	chrX	42365459	42365468	-	1	NA	Intergenic	MLT1D|LTR|ERVL-MaLR	-137102	NM_011364	20400	Mm.441197	NM_011364	ENSMUSG00000005696	Sh2d1a	Gm686|SAP	SH2 domain containing 1A	protein-coding
mm_105809.1	chr11	110337613	110337704	-	1	NA	promoter-TSS (NM_147219)	promoter-TSS (NM_147219)	58	NM_147219	217265	Mm.41942	NM_147219	ENSMUSG00000018800	Abca5	ABC13|B930033A02Rik|mKIAA1888	ATP-binding cassette, sub-family A (ABC1), member 5	protein-coding
mm_13243.1	chr2	98662757	98662778	+	1	NA	Intergenic	SYNREP_MM|Satellite|Satellite	1195110	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_62464.1	chr7	101663615	101663617	+	1	NA	promoter-TSS (NM_009191)	promoter-TSS (NM_009191)	-152	NM_009191	20480	Mm.3990	NM_009191	ENSMUSG00000001829	Clpb	AL118244|Skd3	ClpB caseinolytic peptidase B	protein-coding
mm_102993.1	chr11	69686829	69686840	-	1	NA	3' UTR (NM_011614, exon 7 of 7)	3' UTR (NM_011614, exon 7 of 7)	-1280	NM_023517	69583	Mm.8983	NM_023517	ENSMUSG00000089669	Tnfsf13	2310026N09Rik|April|Tall2|Tnlg7b|Trdl1	tumor necrosis factor (ligand) superfamily, member 13	protein-coding
mm_57961.1	chr6	135253300	135253314	-	1	NA	5' UTR (NM_010352, exon 2 of 7)	5' UTR (NM_010352, exon 2 of 7)	1029	NM_010352	14840	Mm.272306	NM_010352	ENSMUSG00000030206	Gsg1	-	germ cell associated 1	protein-coding
mm_94279.1	chr11	3963971	3963983	+	1	NA	promoter-TSS (NM_022889)	promoter-TSS (NM_022889)	2	NM_022889	64934	Mm.28659	NM_022889	ENSMUSG00000020430	Pes1	-	pescadillo ribosomal biogenesis factor 1	protein-coding
mm_109589.1	chr12	112620068	112620084	+	1	NA	promoter-TSS (NM_007421)	promoter-TSS (NM_007421)	29	NM_007421	11565	Mm.3440	NM_007421	ENSMUSG00000011148	Adssl1	AI528595|Adss|Adss1	adenylosuccinate synthetase like 1	protein-coding
mm_100397.1	chr11	119392256	119392269	+	1	NA	Intergenic	Intergenic	1790	NR_035453	100316690		NR_035453	ENSMUSG00000088015	Mir1932	mir-1932|mmu-mir-1932	microRNA 1932	ncRNA
mm_172846.1	chr9	3532721	3532723	+	1	NA	5' UTR (NM_001033322, exon 1 of 8)	5' UTR (NM_001033322, exon 1 of 8)	373	NM_001033322	234889	Mm.91240	NM_001033322	ENSMUSG00000041624	Gucy1a2	6330407I18Rik|A230060L24Rik	guanylate cyclase 1, soluble, alpha 2	protein-coding
mm_17155.1	chr2	25224231	25224268	-	1	NA	intron (NM_146116, intron 1 of 3)	CpG-7809	453	NM_146116	227613	Mm.227260	NM_146116	ENSMUSG00000036752	Tubb4b	4930542G03Rik|Tubb2c|Tubb2c1	tubulin, beta 4B class IVB	protein-coding
mm_34229.1	chr4	141077945	141077984	+	1	NA	intron (NM_025383, intron 1 of 7)	CpG	381	NM_025383	66147	Mm.21187	NM_025383	ENSMUSG00000028923	Necap2	1110005F07Rik|AA409105|C78898	NECAP endocytosis associated 2	protein-coding
mm_12157.1	chr2	62046615	62046621	+	1	NA	5' UTR (NM_001242379, exon 1 of 25)	5' UTR (NM_001242379, exon 1 of 25)	103	NM_033552	94229	Mm.314497	NM_033552	ENSMUSG00000026904	Slc4a10	NCBE|mKIAA4136	solute carrier family 4, sodium bicarbonate cotransporter-like, member 10	protein-coding
mm_23422.1	chr3	58595716	58595719	+	1	NA	Intergenic	RLTR22_Mus|LTR|ERVK	19059	NM_001040396	69227	Mm.270950	NM_001040396	ENSMUSG00000075700	Selenot	2810407C02Rik|5730408P04Rik|Selt	selenoprotein T	protein-coding
mm_166571.1	chr6	48990172	48990173	+	1	NA	exon (NM_172888, exon 2 of 5)	exon (NM_172888, exon 2 of 5)	3311	NM_172888	243377	Mm.446302	NM_172888	ENSMUSG00000039215	Svs1	9530003A11	seminal vesicle secretory protein 1	protein-coding
mm_140071.1	chr17	75005736	75005786	+	1	NA	5' UTR (NM_019919, exon 1 of 34)	5' UTR (NM_019919, exon 1 of 34)	232	NM_019919	268977	Mm.269747	NM_019919	ENSMUSG00000001870	Ltbp1	9430031G15Rik|9830146M04|Ltbp-1|Ltbp1L|TGF-beta1-BP-1|Tgfb|b2b1000Clo	latent transforming growth factor beta binding protein 1	protein-coding
mm_100627.1	chr11	121702576	121702586	+	1	NA	5' UTR (NM_144797, exon 1 of 4)	5' UTR (NM_144797, exon 1 of 4)	154	NM_144797	210029	Mm.153566	NM_144797	ENSMUSG00000039208	Metrnl	9430048M07Rik|BC019776	meteorin, glial cell differentiation regulator-like	protein-coding
mm_56948.1	chr6	119969520	119969534	-	1	NA	exon (NM_001185020, exon 7 of 26)	exon (NM_001185020, exon 7 of 26)	64784	NR_030487	735290		NR_030487	ENSMUSG00000076217	Mir706	Mirn706|mir-706|mmu-mir-706	microRNA 706	ncRNA
mm_48600.1	chr5	144221400	144221407	-	1	NA	intron (NM_027410, intron 1 of 24)	intron (NM_027410, intron 1 of 24)	2175	NM_027410	70381	Mm.239412	NM_027410	ENSMUSG00000066621	Tecpr1	2210010N04Rik|mKIAA1358	tectonin beta-propeller repeat containing 1	protein-coding
mm_26981.1	chr3	25599070	25599073	-	1	NA	intron (NM_001163387, intron 3 of 5)	intron (NM_001163387, intron 3 of 5)	554236	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_49837.1	chr6	37900503	37900520	+	1	NA	promoter-TSS (NM_001272076)	promoter-TSS (NM_001272076)	24	NM_001272076	21848	Mm.41063	NM_145076	ENSMUSG00000029833	Trim24	A130082H20Rik|AI447469|D430004I05Rik|TIF1|TIF1-alpha|TIF1alpha|Tif1a	tripartite motif-containing 24	protein-coding
mm_115414.1	chr13	114932206	114932222	+	1	NA	promoter-TSS (NM_008396)	promoter-TSS (NM_008396)	-173	NM_008396	16398	Mm.5007	NM_008396	ENSMUSG00000015533	Itga2	CD49B|DX5	integrin alpha 2	protein-coding
mm_38444.1	chr4	139967148	139967161	-	1	NA	TTS (NR_035519)	TTS (NR_035519)	466	NR_035519	100316727		NR_035519	ENSMUSG00000089294	Mir2139	mmu-mir-2139	microRNA 2139	ncRNA
mm_124969.1	chr15	18818896	18818942	+	1	NA	promoter-TSS (NM_001316758)	promoter-TSS (NM_001316758)	-28	NM_001316758	320873	Mm.117794	NM_009865	ENSMUSG00000022321	Cdh10	A830016G23Rik|C030003B10Rik|C030011H18Rik	cadherin 10	protein-coding
mm_70863.1	chr8	24503141	24503144	+	1	NA	Intergenic	Intergenic	-18156	NR_035483	100316707		NR_035483	ENSMUSG00000088552	Mir1957a	Mir1957|mmu-mir-1957|mmu-mir-1957a	microRNA 1957a	ncRNA
mm_104905.1	chr11	99643982	99643999	-	1	NA	promoter-TSS (NM_029613)	promoter-TSS (NM_029613)	99	NM_029613	76444	Mm.348022	NM_029613	ENSMUSG00000045109	Krtap4-7	2310037K05Rik|KAP4.7|KRTAP4.7	keratin associated protein 4-7	protein-coding
mm_79007.1	chr9	45431330	45431339	+	1	NA	promoter-TSS (NR_040732)	promoter-TSS (NR_040732)	-102	NR_040732	74602	Mm.394117	NR_040732	ENSMUSG00000097074	4833428L15Rik	-	RIKEN cDNA 4833428L15 gene	ncRNA
mm_4404.1	chr1	172475372	172475384	+	1	NA	promoter-TSS (NM_029612)	promoter-TSS (NM_029612)	18	NM_029612	98365	Mm.150050	NM_029612	ENSMUSG00000026548	Slamf9	2310026I04Rik|AI462096|CD2F-10|CD84-H1|Cd2f10|SF2001	SLAM family member 9	protein-coding
mm_68516.1	chr7	111736018	111736044	-	1	NA	intron (NM_173739, intron 1 of 10)	intron (NM_173739, intron 1 of 10)	43946	NM_173739	233733	Mm.323322	NM_173739	ENSMUSG00000038296	Galnt18	2900011G21Rik|BC024988|Galntl4	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 18	protein-coding
mm_131648.1	chr16	20535436	20535439	+	1	NA	promoter-TSS (NM_009679)	promoter-TSS (NM_009679)	-43	NM_001302970	11773	Mm.18946	NM_009679	ENSMUSG00000022841	Ap2m1	-	adaptor-related protein complex 2, mu 1 subunit	protein-coding
mm_161728.1	chr17	29135251	29135251	+	1	NA	5' UTR (NM_001002786, exon 1 of 8)	5' UTR (NM_001002786, exon 1 of 8)	195	NM_001002786	442827	Mm.440341	NM_001002786	ENSMUSG00000064147	Rab44	9830134C10Rik	RAB44, member RAS oncogene family	protein-coding
mm_87077.1	chr10	29211776	29211805	+	1	NA	5' UTR (NM_001162537, exon 1 of 6)	5' UTR (NM_001162537, exon 1 of 6)	147	NM_001162537	212448	Mm.132789	NM_001162537	ENSMUSG00000004360	9330159F19Rik	-	RIKEN cDNA 9330159F19 gene	protein-coding
mm_114137.1	chr13	55247906	55247953	+	1	NA	exon (NM_008739, exon 5 of 23)	exon (NM_008739, exon 5 of 23)	38147	NM_008739	18193	Mm.12964	NM_008739	ENSMUSG00000021488	Nsd1	AI528500|KMT3B	nuclear receptor-binding SET-domain protein 1	protein-coding
mm_78844.1	chr9	44327545	44327560	+	1	NA	exon (NM_007875, exon 2 of 9)	exon (NM_007875, exon 2 of 9)	707	NM_007875	13478	Mm.18353	NM_007875	ENSMUSG00000032123	Dpagt1	AU021132|Dpagt2|GPT|Gnpta	dolichyl-phosphate (UDP-N-acetylglucosamine) acetylglucosaminephosphotransferase 1 (GlcNAc-1-P transferase)	protein-coding
mm_152804.1	chr19	21737655	21737662	-	1	NA	Intergenic	Intergenic	-40682	NM_001033759	83921	Mm.329776	NM_031997	ENSMUSG00000024754	Tmem2	-	transmembrane protein 2	protein-coding
mm_121353.1	chr14	116925546	116925554	+	1	NA	5' UTR (NM_011821, exon 1 of 9)	5' UTR (NM_011821, exon 1 of 9)	253	NM_011821	23888	Mm.440025	NM_011821	ENSMUSG00000058571	Gpc6	-	glypican 6	protein-coding
mm_171703.1	chr4	72579204	72579204	-	1	NA	Intergenic	L1Md_A|LINE|L1	273430	NM_001199270	353204	Mm.317892	NM_001199270	ENSMUSG00000059343	Aldoart1	4921524E03Rik|Aldo1-ps|Aldo1-ps2|Aldoa-ps2	aldolase 1 A, retrogene 1	protein-coding
mm_43867.1	chr5	143503413	143503431	+	1	NA	3' UTR (NM_144915, exon 15 of 15)	3' UTR (NM_144915, exon 15 of 15)	24571	NM_009007	19353	Mm.292510	NM_009007	ENSMUSG00000001847	Rac1	AL023026|D5Ertd559e	RAS-related C3 botulinum substrate 1	protein-coding
mm_112869.1	chr13	20851390	20851401	+	1	NA	intron (NM_012054, intron 4 of 20)	intron (NM_012054, intron 4 of 20)	57282	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_28568.1	chr3	93445023	93445033	-	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	2698	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_45598.1	chr5	74983580	74983580	-	1	NA	Intergenic	Intergenic	34386	NR_045866	619945	Mm.359372	NM_001037908	ENSMUSG00000072874	Gm6116	EG619945	predicted gene 6116	ncRNA
mm_75633.1	chr8	64718967	64719001	-	1	NA	3' UTR (NM_025436, exon 6 of 6)	3' UTR (NM_025436, exon 6 of 6)	14594	NM_025436	66234	Mm.30119	NM_025436	ENSMUSG00000031604	Msmo1	1500001G16Rik|C78600|DESP4|ERG25|Sc4mol	methylsterol monoxygenase 1	protein-coding
mm_24310.1	chr3	89418616	89418630	+	1	NA	promoter-TSS (NM_011368)	promoter-TSS (NM_011368)	72	NM_011368	20416	Mm.86595	NM_011368	ENSMUSG00000042626	Shc1	Shc|ShcA|p66|p66shc	src homology 2 domain-containing transforming protein C1	protein-coding
mm_36907.1	chr4	108027308	108027343	-	1	NA	intron (NM_001285958, intron 3 of 12)	intron (NM_001285958, intron 3 of 12)	3661	NM_001285956	242608	Mm.74710	NM_172874	ENSMUSG00000028600	Podn	9430070G18|Pcan|SLRR5A	podocan	protein-coding
mm_170793.1	chr2	175275104	175275113	+	1	NA	promoter-TSS (NM_001199308)	promoter-TSS (NM_001199308)	-16	NM_001033123	13999		NM_001033123	ENSMUSG00000078889	Gm14288	OTTMUSG00000016199	predicted gene 14288	protein-coding
mm_103001.1	chr11	69693538	69693552	-	1	NA	intron (NM_001034097, intron 4 of 12)	intron (NM_001034097, intron 4 of 12)	2553	NM_011614	21944	Mm.8983	NM_011614	ENSMUSG00000097328	Tnfsf12	Apo3l|Dr3l|Dr3lg|Tweak	tumor necrosis factor (ligand) superfamily, member 12	protein-coding
mm_52563.1	chr6	116226259	116226264	+	1	NA	intron (NM_026585, intron 13 of 30)	B1F1|SINE|Alu	18228	NM_026585	28006	Mm.28524	NM_026585	ENSMUSG00000024104	Washc2	A130095H06|C530005J20Rik|D6Wsu116e|Fam21	WASH complex subunit 2	protein-coding
mm_53557.1	chr6	136938997	136939015	+	1	NA	intron (NM_001301301, intron 1 of 5)	intron (NM_001301301, intron 1 of 5)	521	NM_001301303	11857	Mm.2241	NM_007486	ENSMUSG00000030220	Arhgdib	D4|Gdid4|Ly-GDI	Rho, GDP dissociation inhibitor (GDI) beta	protein-coding
mm_163815.1	chr14	19416408	19416414	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	186176	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_8417.1	chr1	152090309	152090332	-	1	NA	promoter-TSS (NM_197990)	promoter-TSS (NM_197990)	0	NM_197990	69399	Mm.278031	NM_197990	ENSMUSG00000032666	1700025G04Rik	2610510E02Rik|2900042O04Rik|ENSMUSG00000073540	RIKEN cDNA 1700025G04 gene	protein-coding
mm_30699.1	chr4	11704440	11704454	+	1	NA	promoter-TSS (NM_010276)	promoter-TSS (NM_010276)	0	NM_010276	14579	Mm.247486	NM_010276	ENSMUSG00000028214	Gem	AV020497	GTP binding protein (gene overexpressed in skeletal muscle)	protein-coding
mm_25723.1	chr3	122729919	122729929	+	1	NA	intron (NM_153422, intron 1 of 20)	CpG	766	NM_153422	242202	Mm.134911	NM_153422	ENSMUSG00000053965	Pde5a	Cgbpde|Cn5n|PDE5a2|Pde5|Pde5a1	phosphodiesterase 5A, cGMP-specific	protein-coding
mm_8399.1	chr1	151500767	151500777	-	1	NA	promoter-TSS (NM_011277)	promoter-TSS (NM_011277)	51	NM_011277	19821	Mm.474038	NM_011277	ENSMUSG00000026484	Rnf2	AI326319|AI450156|AU019207|Ring1B|dinG	ring finger protein 2	protein-coding
mm_158380.1	chrX	135693784	135693795	-	1	NA	promoter-TSS (NM_027952)	promoter-TSS (NM_027952)	1	NM_027952	71841	Mm.371643	NM_027952	ENSMUSG00000058252	Tcp11x2	1700008I05Rik|C77164|TCP11|Tcp11l3	t-complex 11 family, X-linked 2	protein-coding
mm_61494.1	chr7	75752361	75752384	+	1	NA	3' UTR (NM_029332, exon 37 of 37)	3' UTR (NM_029332, exon 37 of 37)	-95966	NM_001122780	207952	Mm.206223	NM_029652	ENSMUSG00000055652	Klhl25	2810402K13Rik|BC027373|Enc-1	kelch-like 25	protein-coding
mm_62798.1	chr7	112809798	112809810	+	1	NA	intron (NM_009346, intron 2 of 12)	B1_Mus1|SINE|Alu	50420	NM_001166585	21676	Mm.24685	NM_009346	ENSMUSG00000055320	Tead1	2610024B07Rik|B230114H05Rik|Gtrgeo5|TEAD-1|TEF-1|Tcf13|mTEF-1	TEA domain family member 1	protein-coding
mm_90288.1	chr10	123360767	123360805	+	1	NA	intron (NR_045514, intron 1 of 5)	intron (NR_045514, intron 1 of 5)	96710	NM_001252387	268354	Mm.51939	NM_182807	ENSMUSG00000044071	Fam19a2	6330575M02|FAM19A2 TAFA-2|TAFA2|Tafa-2	family with sequence similarity 19, member A2	protein-coding
mm_72072.1	chr8	71542912	71542973	+	1	NA	promoter-TSS (NM_028617)	promoter-TSS (NM_028617)	12	NM_028617	73711	Mm.307770	NM_028617	ENSMUSG00000031813	Mvb12a	1110012M11Rik|Fam125a	multivesicular body subunit 12A	protein-coding
mm_55532.1	chr6	70726854	70726861	-	1	NA	Intergenic	Intergenic	65318	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_91766.1	chr10	51496588	51496600	-	1	NA	TTS (NM_013532)	TTS (NM_013532)	5696	NM_013532	14728	Mm.34408	NM_013532	ENSMUSG00000062593	Lilrb4a	CD85K|Gp49b|HM18|ILT3|LIR-5|Lilrb4|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4A	protein-coding
mm_87909.1	chr10	62253112	62253121	+	1	NA	exon (NM_009314, exon 1 of 5)	exon (NM_009314, exon 1 of 5)	678	NM_009314	21337	Mm.8054	NM_009314	ENSMUSG00000020081	Tacr2	Nk2r|Skr|Tac2r	tachykinin receptor 2	protein-coding
mm_52637.1	chr6	117174623	117174634	+	1	NA	3' UTR (NM_021704, exon 3 of 3)	3' UTR (NM_021704, exon 3 of 3)	6093	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_35726.1	chr4	44710688	44710721	-	1	NA	promoter-TSS (NM_008782)	promoter-TSS (NM_008782)	-264	NM_008782	18507	Mm.439659	NM_008782	ENSMUSG00000014030	Pax5	BSAP|EBB-1|KLP|Pax-5	paired box 5	protein-coding
mm_40474.1	chr5	53998665	53998680	+	1	NA	5' UTR (NM_001081103, exon 1 of 12)	5' UTR (NM_001081103, exon 1 of 12)	149	NM_001081103	116873	Mm.265985	NM_054083	ENSMUSG00000039156	Stim2	-	stromal interaction molecule 2	protein-coding
mm_1477.1	chr1	71327301	71327317	+	1	NA	intron (NM_175210, intron 11 of 52)	intron (NM_175210, intron 11 of 52)	87601	NM_175210	74591	Mm.159251	NM_175210	ENSMUSG00000050296	Abca12	4832428G11Rik|4833417A11Rik	ATP-binding cassette, sub-family A (ABC1), member 12	protein-coding
mm_123793.1	chr14	70443220	70443238	-	1	NA	promoter-TSS (NR_029802)	promoter-TSS (NR_029802)	-2	NM_001164082	67065	Mm.20420	NM_025945	ENSMUSG00000000776	Polr3d	2810426M17Rik|44kDa|AI326118|AW489084|BN51T|RPC4|TSBN51	polymerase (RNA) III (DNA directed) polypeptide D	protein-coding
mm_101301.1	chr11	22286996	22287005	-	1	NA	promoter-TSS (NM_153078)	promoter-TSS (NM_153078)	-205	NM_001252515	216565	Mm.491265	NM_153078	ENSMUSG00000042302	Ehbp1	AF424697|Flj21950|NACSIN	EH domain binding protein 1	protein-coding
mm_35470.1	chr4	40806061	40806085	-	1	NA	3' UTR (NM_022305, exon 6 of 6)	3' UTR (NM_022305, exon 6 of 6)	44065	NR_039584	100628614		NR_039584	ENSMUSG00000096377	Mir5123	mmu-mir-5123|mu-mir-5123	microRNA 5123	ncRNA
mm_57168.1	chr6	122802170	122802232	-	1	NA	Intergenic	Intergenic	-17983	NM_021899	60611	Mm.87142	NM_021899	ENSMUSG00000003154	Foxj2	Fhx	forkhead box J2	protein-coding
mm_41790.1	chr5	103753012	103753034	+	1	NA	Intergenic	Charlie1a|DNA|hAT-Charlie	-1139	NM_133919	17355	Mm.6949	NM_133919	ENSMUSG00000029313	Aff1	9630032B01Rik|AW319193|Af4|Mllt2h|Rob	AF4/FMR2 family, member 1	protein-coding
mm_158788.1	chrX	167208566	167208615	-	1	NA	intron (NM_021278, intron 1 of 2)	intron (NM_021278, intron 1 of 2)	628	NM_021278	19241	Mm.142729	NM_021278	ENSMUSG00000049775	Tmsb4x	Ptmb4|Tb4	thymosin, beta 4, X chromosome	protein-coding
mm_160703.1	chr10	51490974	51490974	+	1	NA	promoter-TSS (NM_013532)	promoter-TSS (NM_013532)	76	NM_013532	14728	Mm.34408	NM_013532	ENSMUSG00000062593	Lilrb4a	CD85K|Gp49b|HM18|ILT3|LIR-5|Lilrb4|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4A	protein-coding
mm_92168.1	chr10	67570004	67570052	-	1	NA	Intergenic	Intergenic	-21073	NM_001005419	211488	Mm.297250	NM_001005419	ENSMUSG00000057134	Ado	Gm237	2-aminoethanethiol (cysteamine) dioxygenase	protein-coding
mm_79800.1	chr9	64121502	64121504	+	1	NA	intron (NM_145835, intron 5 of 13)	B1_Mus1|SINE|Alu	4356	NM_145835	235435	Mm.436581	NM_145835	ENSMUSG00000032401	Lctl	E130104I05Rik|KLPH	lactase-like	protein-coding
mm_72548.1	chr8	84003107	84003118	+	1	NA	intron (NM_183097, intron 2 of 5)	intron (NM_183097, intron 2 of 5)	1406	NM_183097	73453	Mm.75101	NM_183097	ENSMUSG00000046408	1700067K01Rik	-	RIKEN cDNA 1700067K01 gene	protein-coding
mm_10217.1	chr2	5895490	5895513	+	1	NA	promoter-TSS (NM_021305)	promoter-TSS (NM_021305)	-148	NM_021305	57743	Mm.21435	NM_021305	ENSMUSG00000025816	Sec61a2	-	Sec61, alpha subunit 2 (S. cerevisiae)	protein-coding
mm_67114.1	chr7	70361456	70361464	-	1	NA	promoter-TSS (NM_009697)	promoter-TSS (NM_009697)	-867	NM_009697	11819	Mm.158143	NM_009697	ENSMUSG00000030551	Nr2f2	2700033K02Rik|9430015G03Rik|ARP-1|Aporp1|COUP-TF2|COUP-TFII|COUPTFB|EAR3|SVP40|Tcfcoup2	nuclear receptor subfamily 2, group F, member 2	protein-coding
mm_172091.1	chr6	21014226	21014226	+	1	NA	Intergenic	Intergenic	-201883	NM_019697	16508	Mm.425316	NM_019697	ENSMUSG00000060882	Kcnd2	AI839615|AW555701|Kv4.2|R75121|mKIAA1044	potassium voltage-gated channel, Shal-related family, member 2	protein-coding
mm_48800.1	chr5	148928982	148929044	-	1	NA	promoter-TSS (NM_153572)	promoter-TSS (NM_153572)	-366	NM_153572	231912	Mm.397405	NM_153572	ENSMUSG00000041298	Katnal1	-	katanin p60 subunit A-like 1	protein-coding
mm_147287.1	chr18	39489521	39489542	-	1	NA	Intergenic	CpG	-2286	NM_008173	14815	Mm.129481	NM_008173	ENSMUSG00000024431	Nr3c1	GR|Grl-1|Grl1	nuclear receptor subfamily 3, group C, member 1	protein-coding
mm_11117.1	chr2	28205172	28205182	+	1	NA	promoter-TSS (NM_019498)	promoter-TSS (NM_019498)	-512	NM_001038612	56177	Mm.43278	NM_019498	ENSMUSG00000026833	Olfm1	AMY|AW742568|Noe1|OlfA|Pancortin|Pancortin3	olfactomedin 1	protein-coding
mm_11254.1	chr2	29903543	29903557	+	1	NA	intron (NM_013615, intron 7 of 16)	intron (NM_013615, intron 7 of 16)	13487	NM_013615	18286	Mm.330116	NM_013615	ENSMUSG00000026790	Odf2	AI848335|MMTEST29	outer dense fiber of sperm tails 2	protein-coding
mm_83400.1	chr9	44735185	44735187	-	1	NA	promoter-TSS (NM_153537)	promoter-TSS (NM_153537)	12	NM_153537	102693	Mm.28639	NM_153537	ENSMUSG00000048537	Phldb1	AU041016|D330037A14Rik|Ll5a	pleckstrin homology like domain, family B, member 1	protein-coding
mm_164769.1	chr17	86667964	86667969	+	1	NA	Intergenic	L1M2|LINE|L1	-85898	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_46510.1	chr5	105136829	105136849	-	1	NA	exon (NM_001256005, exon 2 of 11)	exon (NM_001256005, exon 2 of 11)	2713	NM_008620	17472	Mm.440525	NM_008620	ENSMUSG00000079363	Gbp4	AW228052|Mag-2|Mpa-2|Mpa2	guanylate binding protein 4	protein-coding
mm_49917.1	chr6	39118269	39118342	+	1	NA	promoter-TSS (NM_172893)	promoter-TSS (NM_172893)	44	NM_172893	243771	Mm.268462	NM_172893	ENSMUSG00000038507	Parp12	9930021O16|AA409132|AA536654|ARTD12|PARP-12|Zc3hdc1	poly (ADP-ribose) polymerase family, member 12	protein-coding
mm_169090.1	chr13	38656220	38656228	-	1	NA	exon (NM_025380, exon 2 of 4)	exon (NM_025380, exon 2 of 4)	2804	NM_025380	66143	Mm.490319	NM_025380	ENSMUSG00000001707	Eef1e1	1110003A02Rik	eukaryotic translation elongation factor 1 epsilon 1	protein-coding
mm_141301.1	chr17	28080570	28080589	-	1	NA	promoter-TSS (NM_013687)	promoter-TSS (NM_013687)	5	NM_013687	21463	Mm.29758	NM_013687	ENSMUSG00000062859	Tcp11	D17Ken1|Tcp-11	t-complex protein 11	protein-coding
mm_34379.1	chr4	144898703	144898707	+	1	NA	intron (NM_011303, intron 1 of 5)	intron (NM_011303, intron 1 of 5)	5568	NM_011303	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding
mm_158795.1	chrX	167241235	167241258	-	1	NA	3' UTR (NM_001313760, exon 2 of 2)	3' UTR (NM_001313760, exon 2 of 2)	23083	NM_001313761	170744	Mm.196676	NM_133212	ENSMUSG00000040522	Tlr8	-	toll-like receptor 8	protein-coding
mm_134620.1	chr16	21333296	21333367	-	1	NA	promoter-TSS (NR_131983)	promoter-TSS (NR_131983)	25	NR_131983	76222	Mm.86031	NR_131983		Magef1	6430590I03Rik	melanoma antigen family F, 1	pseudo
mm_53255.1	chr6	127796483	127796491	+	1	NA	Intergenic	Intergenic	-8344	NR_106092	102466996		NR_106092	ENSMUSG00000104804	Mir7233	mmu-mir-7233	microRNA 7233	ncRNA
mm_71503.1	chr8	46807233	46807243	+	1	NA	exon (NM_008391, exon 4 of 9)	exon (NM_008391, exon 4 of 9)	67493	NM_008391	16363	Mm.1149	NM_008391	ENSMUSG00000031627	Irf2	9830146E22Rik|AI646973|Irf-2	interferon regulatory factor 2	protein-coding
mm_61189.1	chr7	63452966	63452967	+	1	NA	intron (NM_130880, intron 1 of 13)	B1F|SINE|Alu	8194	NM_130880	170711	Mm.156872	NM_130880	ENSMUSG00000033510	Otud7a	AJ430384|Otud7	OTU domain containing 7A	protein-coding
mm_152246.1	chr19	8714327	8714336	-	1	NA	promoter-TSS (NM_008577)	promoter-TSS (NM_008577)	-434	NM_008577	17254	Mm.4114	NM_008577	ENSMUSG00000010095	Slc3a2	4F2|4F2HC|AI314110|Cd98|Ly-10|Ly-m10|Ly10|Mdu1|Mgp-2hc|NACAE	solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2	protein-coding
mm_161993.1	chr19	34938255	34938255	+	1	NA	exon (NM_183046, exon 13 of 32)	exon (NM_183046, exon 13 of 32)	15897	NM_183046	240641	Mm.278471	NM_183046	ENSMUSG00000024795	Kif20b	33cex|B130024C23|C330014J10Rik|Mphosph1|magoo	kinesin family member 20B	protein-coding
mm_22466.1	chr3	3657069	3657079	+	1	NA	exon (NM_013920, exon 10 of 10)	exon (NM_013920, exon 10 of 10)	149044	NM_013920	30942	Mm.330897	NM_013920	ENSMUSG00000017688	Hnf4g	NR2A2	hepatocyte nuclear factor 4, gamma	protein-coding
mm_55524.1	chr6	70458052	70458055	-	1	NA	Intergenic	Intergenic	334122	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_100166.1	chr11	116531098	116531103	+	1	NA	promoter-TSS (NM_001172475)	promoter-TSS (NM_001172475)	-811	NM_001172475	20698	Mm.20944	NM_011451	ENSMUSG00000061878	Sphk1	1110006G24Rik|Sk1|Spk1	sphingosine kinase 1	protein-coding
mm_165567.1	chr3	17948460	17948468	+	1	NA	promoter-TSS (NM_029289)	promoter-TSS (NM_029289)	20	NM_029289	75439	Mm.27023	NM_029289	ENSMUSG00000027564	Cypt12	1700001F04Rik|AV209098	cysteine-rich perinuclear theca 12	protein-coding
mm_105402.1	chr11	103413071	103413093	-	1	NA	promoter-TSS (NM_183034)	promoter-TSS (NM_183034)	-418	NM_183034	353047	Mm.18556	NM_183034	ENSMUSG00000034247	Plekhm1	AP162|B2|BC038943|D330036J23Rik	pleckstrin homology domain containing, family M (with RUN domain) member 1	protein-coding
mm_56067.1	chr6	86785548	86785559	-	1	NA	intron (NM_013471, intron 1 of 12)	intron (NM_013471, intron 1 of 12)	8031	NM_013471	11746	Mm.259702	NM_013471	ENSMUSG00000029994	Anxa4	AI265406|AIV|AW106930|Anx4|Xanx-4	annexin A4	protein-coding
mm_74658.1	chr8	13548976	13548982	-	1	NA	Intergenic	Intergenic	13482	NM_025601	66501	Mm.46136	NM_025601	ENSMUSG00000031452	1700029H14Rik	-	RIKEN cDNA 1700029H14 gene	protein-coding
mm_147625.1	chr18	58097059	58097061	-	1	NA	intron (NM_010181, intron 15 of 64)	MTB_Mm|LTR|ERVL-MaLR	112866	NM_010181	14119	Mm.20271	NM_010181	ENSMUSG00000024598	Fbn2	BC063774|Fib-2|mKIAA4226|sne|sy	fibrillin 2	protein-coding
mm_4268.1	chr1	171558913	171558930	+	1	NA	promoter-TSS (NM_018729)	promoter-TSS (NM_018729)	-272	NM_018729	18106	Mm.2299	NM_018729	ENSMUSG00000004709	Cd244	2B4|C9.1|F730046O15Rik|Ly90|NAIL|NKR2B4|Nmrk|SLAMF4	CD244 natural killer cell receptor 2B4	protein-coding
mm_51802.1	chr6	88724463	88724478	+	1	NA	promoter-TSS (NM_001166251)	promoter-TSS (NM_001166251)	58	NM_011844	23945	Mm.272197	NM_011844	ENSMUSG00000033174	Mgll	AA589436|Magl|Mgl	monoglyceride lipase	protein-coding
mm_117872.1	chr13	98891037	98891063	-	1	NA	promoter-TSS (NM_001048267)	promoter-TSS (NM_001048267)	-8	NM_001048267	238799	Mm.173286	NM_178716	ENSMUSG00000009470	Tnpo1	AU021749|D13Ertd688e|IPO2|Kpnb2|MIP|MIP1|TRN	transportin 1	protein-coding
mm_154371.1	chrM	9976	9987	+	1	NA	NA	Intergenic	NA	NA								
mm_148799.1	chr19	6241683	6241694	+	1	NA	promoter-TSS (NM_194348)	promoter-TSS (NM_194348)	20	NM_194348	329015	Mm.277384	NM_194348	ENSMUSG00000024773	Atg2a	1810013C15Rik|A830054M12|BC023754|mKIAA0404	autophagy related 2A	protein-coding
mm_141350.1	chr17	28622086	28622102	-	1	NA	intron (NM_016795, intron 1 of 15)	CpG-6184	360	NM_016795	20815	Mm.15252	NM_016795	ENSMUSG00000004865	Srpk1	AU017960	serine/arginine-rich protein specific kinase 1	protein-coding
mm_27775.1	chr3	73047949	73047958	-	1	NA	TTS (NM_198864)	TTS (NM_198864)	8990	NM_198864	386750	Mm.331076	NM_198864	ENSMUSG00000048304	Slitrk3	-	SLIT and NTRK-like family, member 3	protein-coding
mm_120925.1	chr14	76476889	76476905	+	1	NA	intron (NM_001310646, intron 3 of 4)	intron (NM_001310646, intron 3 of 4)	-11539	NM_001177751	21807	Mm.153272	NM_009366	ENSMUSG00000022010	Tsc22d1	AA589566|AW105905|Egr5|TSC-22|Tgfb1i4|Tsc|Tsc22	TSC22 domain family, member 1	protein-coding
mm_69454.1	chr7	133122739	133122762	-	1	NA	intron (NM_009980, intron 1 of 10)	CpG	733	NM_009980	13017	Mm.246240	NM_009980	ENSMUSG00000030970	Ctbp2	AA407280|D7Ertd45e|Gtrgeo6|Ribeye	C-terminal binding protein 2	protein-coding
mm_60354.1	chr7	44384638	44384674	+	1	NA	intron (NM_001114116, intron 1 of 10)	intron (NM_001114116, intron 1 of 10)	530	NM_016663	20981	Mm.4824	NM_016663	ENSMUSG00000030731	Syt3	AI385753|sytIII	synaptotagmin III	protein-coding
mm_25231.1	chr3	103860379	103860389	+	1	NA	5' UTR (NM_008979, exon 1 of 21)	5' UTR (NM_008979, exon 1 of 21)	107	NM_008979	19260	Mm.395	NM_008979	ENSMUSG00000027843	Ptpn22	70zpep|PEP|Ptpn8	protein tyrosine phosphatase, non-receptor type 22 (lymphoid)	protein-coding
mm_81604.1	chr9	110656467	110656477	+	1	NA	promoter-TSS (NM_028312)	promoter-TSS (NM_028312)	-31	NM_028312	72654	Mm.249115	NM_028312	ENSMUSG00000019659	Ccdc12	2700094L05Rik|C76605	coiled-coil domain containing 12	protein-coding
mm_59364.1	chr7	25687572	25687583	+	1	NA	5' UTR (NM_011577, exon 1 of 7)	5' UTR (NM_011577, exon 1 of 7)	575	NM_011577	21803	Mm.248380	NM_011577	ENSMUSG00000002603	Tgfb1	TGF-beta1|TGFbeta1|Tgfb|Tgfb-1	transforming growth factor, beta 1	protein-coding
mm_51647.1	chr6	86028754	86028768	+	1	NA	promoter-TSS (NM_001271860)	promoter-TSS (NM_001271860)	80	NM_001271860	11519	Mm.104155	NM_013458	ENSMUSG00000030000	Add2	2900072M03Rik|add97	adducin 2 (beta)	protein-coding
mm_10521.1	chr2	16362437	16362440	+	1	NA	intron (NM_026162, intron 1 of 13)	intron (NM_026162, intron 1 of 13)	6134	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding
mm_162267.1	chr1	7130808	7130811	+	1	NA	intron (NM_183028, intron 2 of 5)	RMER16-int|LTR|ERVK	41889	NM_183028	319263	Mm.21539	NM_183028	ENSMUSG00000051285	Pcmtd1	8430411F12Rik|A030012M09Rik	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding
mm_99331.1	chr11	101460224	101460237	+	1	NA	exon (NM_012037, exon 6 of 6)	exon (NM_012037, exon 6 of 6)	5969	NM_012037	26949	Mm.29210	NM_012037	ENSMUSG00000034993	Vat1	VAT-1	vesicle amine transport 1	protein-coding
mm_83833.1	chr9	54209941	54209944	-	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-16500	NM_007810	13075	Mm.5199	NM_007810	ENSMUSG00000032274	Cyp19a1	Ar|ArKO|Cyp19|Int-5|Int5|p450arom	cytochrome P450, family 19, subfamily a, polypeptide 1	protein-coding
mm_9364.1	chr1	172199143	172199168	-	1	NA	exon (NM_001329871, exon 3 of 4)	exon (NM_001329871, exon 3 of 4)	7649	NM_001329871	18611	Mm.544	NM_011063	ENSMUSG00000013698	Pea15a	Mat1|PEA-15|Pea15|Pkcs15	phosphoprotein enriched in astrocytes 15A	protein-coding
mm_50968.1	chr6	60485972	60485992	+	1	NA	Intergenic	Intergenic	-82275	NR_015565	208079	Mm.131226	NM_177329	ENSMUSG00000046764	A530053G22Rik	-	RIKEN cDNA A530053G22 gene	ncRNA
mm_104977.1	chr11	100246213	100246226	-	1	NA	3' UTR (NM_008470, exon 8 of 8)	3' UTR (NM_008470, exon 8 of 8)	2683	NM_001313958	16666	Mm.422799	NM_008470	ENSMUSG00000053797	Krt16	AI324768|CK-16|K16|Krt1-16	keratin 16	protein-coding
mm_154586.1	chrX	7572797	7572809	+	1	NA	promoter-TSS (NR_029473)	promoter-TSS (NR_029473)	-797	NR_029473	78185	Mm.160055	NR_029473	ENSMUSG00000039545	Ppp1r3fos	4930524L23Rik	protein phosphatase 1, regulatory subunit 3F, opposite strand	ncRNA
mm_135701.1	chr16	52453018	52453028	-	1	NA	promoter-TSS (NM_001331110)	promoter-TSS (NM_001331110)	58	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_50850.1	chr6	54878404	54878417	+	1	NA	exon (NM_199143, exon 3 of 5)	exon (NM_199143, exon 3 of 5)	61494	NM_199143	387524	Mm.286149	NM_199143	ENSMUSG00000058446	Znrf2	1190002C14Rik|AU044205|D6Ertd365e	zinc and ring finger 2	protein-coding
mm_58864.1	chr7	16910479	16910490	+	1	NA	3' UTR (NM_008967, exon 2 of 2)	3' UTR (NM_008967, exon 2 of 2)	3994	NM_008967	19222	Mm.287572	NM_008967	ENSMUSG00000043017	Ptgir	IP|PGI2	prostaglandin I receptor (IP)	protein-coding
mm_97318.1	chr11	76902175	76902180	+	1	NA	Intergenic	Intergenic	-2368	NM_025655	66601	Mm.25138	NM_025655	ENSMUSG00000020839	Tmigd1	2010002A20Rik|Tmigd	transmembrane and immunoglobulin domain containing 1	protein-coding
mm_7077.1	chr1	88274134	88274139	-	1	NA	intron (NM_198652, intron 3 of 7)	B1F|SINE|Alu	3421	NM_172505	212427	Mm.384762	NM_172505		A730008H23Rik	mFleg1	RIKEN cDNA A730008H23 gene	protein-coding
mm_75014.1	chr8	29150544	29150587	-	1	NA	intron (NM_001347498, intron 1 of 14)	intron (NM_001347498, intron 1 of 14)	69071	NM_001347499	210801	Mm.248433	NM_153135	ENSMUSG00000063626	Unc5d	D930029E11Rik|Unc5h4|mKIAA1777	unc-5 netrin receptor D	protein-coding
mm_124618.1	chr15	3279722	3279739	+	1	NA	TTS (NM_001166063)	TTS (NM_001166063)	8753	NM_009155	20363	Mm.392203	NM_009155	ENSMUSG00000064373	Selenop	AU018766|D15Ucla1|Se-P|Sepp1|selp	selenoprotein P	protein-coding
mm_142883.1	chr17	51829524	51829537	-	1	NA	intron (NM_001163632, intron 1 of 10)	intron (NM_001163632, intron 1 of 10)	-2942	NM_001163631	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_137625.1	chr17	28328170	28328179	+	1	NA	promoter-TSS (NM_011287)	promoter-TSS (NM_011287)	-297	NM_011287	19896	Mm.336955	NM_011287	ENSMUSG00000037805	Rpl10a	CsA-19|Nedd6	ribosomal protein L10A	protein-coding
mm_68661.1	chr7	118781299	118781328	-	1	NA	intron (NM_027815, intron 14 of 30)	intron (NM_027815, intron 14 of 30)	41042	NM_027815	71517	Mm.213298	NM_027815	ENSMUSG00000030982	9030624J02Rik	2610029J22Rik	RIKEN cDNA 9030624J02 gene	protein-coding
mm_135451.1	chr16	45724345	45724454	-	1	NA	5' UTR (NM_019754, exon 1 of 4)	5' UTR (NM_019754, exon 1 of 4)	132	NM_019754	56370	Mm.24183	NM_019754	ENSMUSG00000022658	Tagln3	2700038H05Rik|2900005O10Rik|AI426007|Np25	transgelin 3	protein-coding
mm_119913.1	chr14	54953080	54953110	+	1	NA	exon (NM_010856, exon 23 of 39)	exon (NM_010856, exon 23 of 39)	-3953	NR_029724	387204		NR_029724	ENSMUSG00000065432	Mir208a	Mirn208|Mirn208a|mir-208|mir-208a|mmu-mir-208	microRNA 208a	ncRNA
mm_81721.1	chr9	112227428	112227442	+	1	NA	promoter-TSS (NR_131053)	promoter-TSS (NR_131053)	-21	NR_131053	70194	Mm.452769	NR_131053		2310075C17Rik	-	RIKEN cDNA 2310075C17 gene	ncRNA
mm_102977.1	chr11	69672379	69672398	-	1	NA	promoter-TSS (NM_144958)	promoter-TSS (NM_144958)	35	NM_144958	13681	Mm.26680	NM_144958	ENSMUSG00000059796	Eif4a1	BM-010|Ddx2a|Eif4	eukaryotic translation initiation factor 4A1	protein-coding
mm_16708.1	chr2	7083858	7083876	-	1	NA	intron (NM_001110231, intron 3 of 15)	intron (NM_001110231, intron 3 of 15)	-2565	NM_001160292	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_89514.1	chr10	94199028	94199043	+	1	NA	promoter-TSS (NM_025551)	promoter-TSS (NM_025551)	26	NM_025551	66414	Mm.27886	NM_025551	ENSMUSG00000020022	Ndufa12	2410011G03Rik|AW112974	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 12	protein-coding
mm_40234.1	chr5	37338456	37338551	+	1	NA	promoter-TSS (NM_145920)	promoter-TSS (NM_145920)	25	NM_145920	68525	Mm.25506	NM_145920	ENSMUSG00000050248	Evc2	1110017L09Rik|Lbn|limbin	Ellis van Creveld syndrome 2	protein-coding
mm_165535.1	chr2	180381147	180381147	-	1	NA	intron (NR_040745, intron 4 of 6)	intron (NR_040745, intron 4 of 6)	-4457	NR_045331	622283	Mm.447602	NR_045331		Mir1a-1hg	EG622283|Gm6307	Mir1a-1 and Mir133a-2 host gene	ncRNA
mm_153954.1	chr19	47691910	47691912	-	1	NA	5' UTR (NM_007732, exon 1 of 53)	5' UTR (NM_007732, exon 1 of 53)	131	NM_007732	12821	Mm.1225	NM_007732	ENSMUSG00000025064	Col17a1	BP180|Bpag|Bpag2	collagen, type XVII, alpha 1	protein-coding
mm_111723.1	chr12	103763796	103763840	-	1	NA	exon (NM_009246, exon 5 of 5)	exon (NM_009246, exon 5 of 5)	9815	NM_009246	20703	Mm.439695	NM_009246	ENSMUSG00000071177	Serpina1d	AI118301|Dom4|PI4|Spi1-4	serine (or cysteine) peptidase inhibitor, clade A, member 1D	protein-coding
mm_75103.1	chr8	34146582	34146587	-	1	NA	intron (NM_026609, intron 1 of 3)	CpG	155	NM_026609	68192	Mm.34212	NM_026609	ENSMUSG00000031513	Leprotl1	1110067H13Rik|1520402O14Rik|AI854296	leptin receptor overlapping transcript-like 1	protein-coding
mm_39229.1	chr4	156228541	156228570	-	1	NA	promoter-TSS (NM_001008233)	promoter-TSS (NM_001008233)	-13	NM_001008233	231002	Mm.423124	NM_001008233	ENSMUSG00000078485	Plekhn1	BC025458	pleckstrin homology domain containing, family N member 1	protein-coding
mm_138606.1	chr17	35649757	35649768	+	1	NA	promoter-TSS (NM_001163194)	promoter-TSS (NM_001163194)	54	NM_001163194	433102	Mm.136760	NM_001163194	ENSMUSG00000090509	Sfta2	EG433102	surfactant associated 2	protein-coding
mm_98736.1	chr11	96353156	96353164	+	1	NA	exon (NM_134032, exon 2 of 2)	exon (NM_134032, exon 2 of 2)	1528	NM_134032	103889	Mm.281153	NM_134032	ENSMUSG00000075588	Hoxb2	AI894218|Hox-2.8|Hoxbes2	homeobox B2	protein-coding
mm_167072.1	chr7	99625515	99625515	+	1	NA	exon (NM_001195529, exon 1 of 1)	exon (NM_001195529, exon 1 of 1)	1588	NM_001195529	100503386	Mm.180719	NM_001195529	ENSMUSG00000096606	Tpbgl	EG245190|Gm4980	trophoblast glycoprotein-like	protein-coding
mm_46684.1	chr5	109690820	109690857	-	1	NA	Intergenic	Intergenic	-131845	NM_001310694	57914	Mm.35771	NM_016715	ENSMUSG00000033467	Crlf2	CRLM2|Ly114|Tpte2|Tslpr	cytokine receptor-like factor 2	protein-coding
mm_118564.1	chr14	18034344	18034347	+	1	NA	3' UTR (NM_001113417, exon 10 of 10)	3' UTR (NM_001113417, exon 10 of 10)	52701	NM_009380	21834	Mm.32563	NM_009380	ENSMUSG00000021779	Thrb	Nr1a2|T3R[b]|T3Rbeta|Thrb1|Thrb2|c-erbAbeta	thyroid hormone receptor beta	protein-coding
mm_45651.1	chr5	77095019	77095039	-	1	NA	5' UTR (NM_001159901, exon 1 of 2)	5' UTR (NM_001159901, exon 1 of 2)	238	NM_001159901	74318	Mm.181852	NM_175606	ENSMUSG00000059325	Hopx	1110018K11Rik|1200015P04Rik|2300002F06Rik|AI848177|AW490897|Cameo|Hdop|Hod|Hop|Ob1|Obl|Toto	HOP homeobox	protein-coding
mm_126341.1	chr15	79900318	79900334	+	1	NA	intron (NM_001160415, intron 5 of 8)	intron (NM_001160415, intron 5 of 8)	5303	NM_001347041	80287	Mm.284059	NM_030255	ENSMUSG00000009585	Apobec3	Apobec|Arp3|BC003314|Cem15|Rfv3	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 3	protein-coding
mm_157526.1	chrX	51017909	51017923	-	1	NA	5' UTR (NM_172413, exon 1 of 3)	5' UTR (NM_172413, exon 1 of 3)	102	NM_172413	72065	Mm.43152	NM_172413	ENSMUSG00000050029	Rap2c	2010200P20Rik|AI194294|AL022976	RAP2C, member of RAS oncogene family	protein-coding
mm_81023.1	chr9	104361894	104361899	+	1	NA	Intergenic	Intergenic	-24174	NM_207668	56318	Mm.19941	NM_019807	ENSMUSG00000032561	Acpp	5'-NT|A030005E02Rik|FRAP|Lap|PAP|Ppal	acid phosphatase, prostate	protein-coding
mm_141770.1	chr17	34283307	34283315	-	1	NA	exon (NM_010378, exon 4 of 5)	exon (NM_010378, exon 4 of 5)	4460	NM_010378	14960	Mm.235338	NM_010378	ENSMUSG00000036594	H2-Aa	Aalpha|H-2Aa|H2Aa|I-Aalpha|IAalpha|Ia-1|Ia1	histocompatibility 2, class II antigen A, alpha	protein-coding
mm_58794.1	chr7	16160196	16160210	+	1	NA	3' UTR (NM_148946, exon 10 of 10)	3' UTR (NM_148946, exon 10 of 10)	-15192	NM_001277988	17537	Mm.360516	NM_008627	ENSMUSG00000041420	Meis3	AI573393|Mrg2	Meis homeobox 3	protein-coding
mm_150497.1	chr19	39018470	39018498	+	1	NA	intron (NM_028089, intron 3 of 8)	intron (NM_028089, intron 3 of 8)	11465	NM_028089	72082	Mm.142581	NM_028089	ENSMUSG00000025002	Cyp2c55	2010318C06Rik	cytochrome P450, family 2, subfamily c, polypeptide 55	protein-coding
mm_95827.1	chr11	55417225	55417232	+	1	NA	intron (NM_001290817, intron 1 of 9)	(TG)n|Simple_repeat|Simple_repeat	2852	NM_009242	20692	Mm.291442	NM_009242	ENSMUSG00000018593	Sparc	BM-40|ON	secreted acidic cysteine rich glycoprotein	protein-coding
mm_145128.1	chr18	44556803	44556807	+	1	NA	intron (NM_001085373, intron 3 of 18)	RLTR1|LTR|ERV1	-104860	NR_026853	626275	Mm.427116	NR_026853	ENSMUSG00000097610	A930012L18Rik	-	RIKEN cDNA A930012L18 gene	ncRNA
mm_147687.1	chr18	60727523	60727572	-	1	NA	Intergenic	Intergenic	-14158	NM_008306	15531	Mm.181862	NM_008306	ENSMUSG00000054008	Ndst1	1200015G06Rik|HSNST|HSNST 1|Hsst|N-HSST|N-HSST 1|NDST-1|b2b2230Clo	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 1	protein-coding
mm_96253.1	chr11	62583899	62583921	+	1	NA	intron (NM_011706, intron 5 of 15)	intron (NM_011706, intron 5 of 15)	9424	NM_011706	22368	Mm.288064	NM_011706	ENSMUSG00000018507	Trpv2	GRC|OTRPC2|VRL-1|Vrl1	transient receptor potential cation channel, subfamily V, member 2	protein-coding
mm_135375.1	chr16	44138976	44138994	-	1	NA	promoter-TSS (NM_007508)	promoter-TSS (NM_007508)	34	NM_007508	11964	Mm.217787	NM_007508	ENSMUSG00000052459	Atp6v1a	AI647066|Atp6a1|Atp6a2|Atp6v1a1|VA68|VPP2	ATPase, H+ transporting, lysosomal V1 subunit A	protein-coding
mm_67232.1	chr7	74853806	74853837	-	1	NA	Intergenic	Intergenic	-176390	NR_131122	75205	Mm.399304	NR_131122	ENSMUSG00000108803	4930533N22Rik	-	RIKEN cDNA 4930533N22 gene	ncRNA
mm_169912.1	chr16	55819694	55819707	-	1	NA	exon (NM_030612, exon 4 of 14)	exon (NM_030612, exon 4 of 14)	2438	NM_001159394	80859	Mm.247272	NM_030612	ENSMUSG00000035356	Nfkbiz	AA408868|INAP|Mail	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, zeta	protein-coding
mm_152496.1	chr19	11081089	11081111	-	1	NA	promoter-TSS (NM_022430)	promoter-TSS (NM_022430)	3	NM_022430	64381	Mm.34460	NM_022430	ENSMUSG00000024730	Ms4a8a	2010004L09Rik|AI481240|CD20L5|Ms4a8	membrane-spanning 4-domains, subfamily A, member 8A	protein-coding
mm_25911.1	chr3	131113882	131113892	+	1	NA	exon (NM_001276402, exon 2 of 10)	exon (NM_001276402, exon 2 of 10)	1096	NM_001276403	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_40666.1	chr5	65391524	65391565	+	1	NA	promoter-TSS (NM_024471)	promoter-TSS (NM_024471)	47	NM_001310612	79464	Mm.195776	NM_024471	ENSMUSG00000029199	Lias	2900022L22Rik|4933425M12Rik|7a5ex|C77512|LS|lip-syn	lipoic acid synthetase	protein-coding
mm_172409.1	chr7	18108415	18108432	+	1	NA	Intergenic	L1Md_T|LINE|L1	42494	NM_001162523	67315	Mm.46089	NM_026087	ENSMUSG00000030366	Ceacam12	1600031J20Rik|Ceacam12-C1|Ceacam12-C3|Ceacam12C1|Ceacam12C3	carcinoembryonic antigen-related cell adhesion molecule 12	protein-coding
mm_145596.1	chr18	60987747	60987785	+	1	NA	3' UTR (NM_001286809, exon 6 of 6)	3' UTR (NM_001286809, exon 6 of 6)	24212	NM_001286809	12322	Mm.131530	NM_009792	ENSMUSG00000024617	Camk2a	CaMKII|R74975|mKIAA0968	calcium/calmodulin-dependent protein kinase II alpha	protein-coding
mm_106269.1	chr11	117969906	117969938	-	1	NA	promoter-TSS (NM_007707)	promoter-TSS (NM_007707)	-556	NM_007707	12702	Mm.3468	NM_007707	ENSMUSG00000053113	Socs3	Cis3|Cish3|EF-10|Ef10|SSI-3|Ssi3	suppressor of cytokine signaling 3	protein-coding
mm_124673.1	chr15	6417479	6417482	+	1	NA	intron (NM_001310446, intron 2 of 13)	intron (NM_001310446, intron 2 of 13)	-27853	NM_013485	12279	Mm.29095	NM_013485	ENSMUSG00000022149	C9	-	complement component 9	protein-coding
mm_11674.1	chr2	35331071	35331073	+	1	NA	intron (NM_013515, intron 1 of 6)	intron (NM_013515, intron 1 of 6)	5937	NM_013515	13830	Mm.295284	NM_013515	ENSMUSG00000026880	Stom	Epb7.2	stomatin	protein-coding
mm_109375.1	chr12	109650978	109650997	+	1	NA	promoter-TSS (NR_046305)	promoter-TSS (NR_046305)	278	NR_028434	100303647		NR_028434		AF357359	MBII-426	snoRNA AF357359	snoRNA
mm_135372.1	chr16	44086095	44086110	-	1	NA	3' UTR (NM_007508, exon 15 of 15)	3' UTR (NM_007508, exon 15 of 15)	52917	NM_007508	11964	Mm.217787	NM_007508	ENSMUSG00000052459	Atp6v1a	AI647066|Atp6a1|Atp6a2|Atp6v1a1|VA68|VPP2	ATPase, H+ transporting, lysosomal V1 subunit A	protein-coding
mm_70462.1	chr8	11854332	11854335	+	1	NA	exon (NM_029326, exon 5 of 7)	exon (NM_029326, exon 5 of 7)	13812	NM_029326	75528	Mm.440342	NM_029326	ENSMUSG00000031512	Tex29	1700018L24Rik	testis expressed 29	protein-coding
mm_160546.1	chr9	44483204	44483204	+	1	NA	Intergenic	CpG	-15932	NM_030256	80288	Mm.370270	NM_030256	ENSMUSG00000063382	Bcl9l	B9L|BC003321|BCL9-2|DLNB11	B cell CLL/lymphoma 9-like	protein-coding
mm_105881.1	chr11	114930308	114930350	-	1	NA	intron (NM_199221, intron 1 of 3)	B1F2|SINE|Alu	4057	NM_001347651	217304	Mm.185355	NM_199221	ENSMUSG00000063193	Cd300lb	CLM-7|Clm7|Gm253|LMIR5	CD300 molecule like family member B	protein-coding
mm_52668.1	chr6	117906937	117907008	+	1	NA	promoter-TSS (NM_001166429)	intron (NM_133834, intron 1 of 3)	190	NM_133834	98758	Mm.422979	NM_133834	ENSMUSG00000042079	Hnrnpf	4833420I20Rik|AA407306|Hnrpf	heterogeneous nuclear ribonucleoprotein F	protein-coding
mm_97070.1	chr11	72991968	72991979	+	1	NA	3' UTR (NM_001163337, exon 22 of 22)	3' UTR (NM_001163337, exon 22 of 22)	-7172	NM_008771	18436	Mm.25722	NM_008771	ENSMUSG00000020787	P2rx1	AI323649|BB122383|P2x|Pdcd3|RP-2	purinergic receptor P2X, ligand-gated ion channel, 1	protein-coding
mm_89341.1	chr10	87935908	87935930	+	1	NA	3' UTR (NM_010512, exon 5 of 5)	3' UTR (NM_010512, exon 5 of 5)	-30752	NR_000040	22172	Mm.391420	NR_000040		Tyms-ps	-	thymidylate synthase, pseudogene	pseudo
mm_6030.1	chr1	59537196	59537231	-	1	NA	intron (NM_001013771, intron 2 of 19)	intron (NM_001013771, intron 2 of 19)	20949	NM_001013771	381260	Mm.486706	NM_001013771	ENSMUSG00000047361	Gm973	AW554518	predicted gene 973	protein-coding
mm_94105.1	chr10	128578470	128578505	-	1	NA	exon (NM_010153, exon 12 of 28)	exon (NM_010153, exon 12 of 28)	6010	NR_105882	102465553		NR_105882	ENSMUSG00000098592	Mir6917	Gm27633|mmu-mir-6917	microRNA 6917	ncRNA
mm_129530.1	chr15	79285451	79285465	-	1	NA	promoter-TSS (NM_177580)	promoter-TSS (NM_177580)	51	NM_177580	207495	Mm.309647	NM_177580	ENSMUSG00000018126	Baiap2l2	BC048937	BAI1-associated protein 2-like 2	protein-coding
mm_96670.1	chr11	69410826	69410854	+	1	NA	intron (NM_001017426, intron 1 of 22)	CpG	2835	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_72255.1	chr8	75096840	75096876	+	1	NA	exon (NM_010442, exon 3 of 5)	exon (NM_010442, exon 3 of 5)	3240	NM_010442	15368	Mm.276389	NM_010442	ENSMUSG00000005413	Hmox1	D8Wsu38e|HO-1|HO1|Hemox|Hmox|Hsp32	heme oxygenase 1	protein-coding
mm_31322.1	chr4	46343638	46343655	+	1	NA	promoter-TSS (NM_183298)	promoter-TSS (NM_183298)	-548	NM_183298	110805	Mm.354634	NM_183298	ENSMUSG00000070990	Foxe1	Titf2	forkhead box E1	protein-coding
mm_6102.1	chr1	64030184	64030198	-	1	NA	Intergenic	Intergenic	12310	NR_105864	102466760		NR_105864	ENSMUSG00000098487	Mir6899	Gm27384|mmu-mir-6899	microRNA 6899	ncRNA
mm_39807.1	chr5	30628030	30628043	+	1	NA	Intergenic	Intergenic	-19900	NR_049199	100885838		NR_049199	ENSMUSG00000093710	Mir5625	Gm23930|mmu-mir-5625	microRNA 5625	ncRNA
mm_81005.1	chr9	103427487	103427501	+	1	NA	intron (NR_040466, intron 3 of 5)	L2b|LINE|L2	3916	NR_040466	100529079	Mm.437003	NR_040466	ENSMUSG00000086236	5830418P13Rik	-	RIKEN cDNA 5830418P13 gene	ncRNA
mm_86186.1	chr9	119339850	119339860	-	1	NA	exon (NM_010851, exon 1 of 6)	exon (NM_010851, exon 1 of 6)	185	NM_010851	17874	Mm.213003	NM_010851	ENSMUSG00000032508	Myd88	-	myeloid differentiation primary response gene 88	protein-coding
mm_43546.1	chr5	137553602	137553608	+	1	NA	promoter-TSS (NM_031404)	promoter-TSS (NM_031404)	50	NM_031404	83766	Mm.31646	NM_031404	ENSMUSG00000029712	Actl6b	Actl6|ArpNa|Baf53b	actin-like 6B	protein-coding
mm_4996.1	chr1	191821493	191821568	+	1	NA	promoter-TSS (NM_010892)	promoter-TSS (NM_010892)	57	NM_010892	18005	Mm.33773	NM_010892	ENSMUSG00000026622	Nek2	AA617254|C77054	NIMA (never in mitosis gene a)-related expressed kinase 2	protein-coding
mm_112281.1	chr12	114392215	114392226	-	1	NA	Intergenic	Intergenic	77246	NR_106062	102465663		NR_106062	ENSMUSG00000105438	Mir7094-1	mmu-mir-7094-1	microRNA 7094-1	ncRNA
mm_133965.1	chr16	4211457	4211464	-	1	NA	intron (NM_001025432, intron 1 of 30)	intron (NM_001025432, intron 1 of 30)	1944	NM_001025432	12914	Mm.132238	NM_001025432	ENSMUSG00000022521	Crebbp	AW558298|CBP|CBP/p300|KAT3A|p300/CBP	CREB binding protein	protein-coding
mm_121176.1	chr14	103037404	103037431	+	1	NA	Intergenic	MTE2a|LTR|ERVL-MaLR	-3614	NR_045657	71264	Mm.399572	NR_045657		4933432I03Rik	-	RIKEN cDNA 4933432I03 gene	ncRNA
mm_87692.1	chr10	59540851	59540857	+	1	NA	intron (NM_001033259, intron 1 of 7)	intron (NM_001033259, intron 1 of 7)	75838	NM_001033259	215999	Mm.296470	NM_001033259	ENSMUSG00000009647	Mcu	2010012O16Rik|AV064928|C10orf42|Ccdc109a|D130073L02Rik|Gm64	mitochondrial calcium uniporter	protein-coding
mm_131702.1	chr16	20717821	20717851	+	1	NA	promoter-TSS (NM_145632)	promoter-TSS (NM_145632)	10	NM_145632	245841	Mm.288730	NM_145632	ENSMUSG00000021018	Polr2h	-	polymerase (RNA) II (DNA directed) polypeptide H	protein-coding
mm_65921.1	chr7	30231723	30231790	-	1	NA	promoter-TSS (NM_027259)	promoter-TSS (NM_027259)	273	NM_025548	66411	Mm.27947	NM_025548	ENSMUSG00000006095	Tbcb	2410007D12Rik|AU041393|CG22|CKAPI|Ckap1	tubulin folding cofactor B	protein-coding
mm_35689.1	chr4	44072579	44072693	-	1	NA	promoter-TSS (NM_001190414)	promoter-TSS (NM_001190414)	37	NM_001190414	50798	Mm.256718	NM_015828	ENSMUSG00000028479	Gne	2310066H07Rik|DMRV|GLCNE|IBM2|NM|Uae1	glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase	protein-coding
mm_36833.1	chr4	106464078	106464120	-	1	NA	5' UTR (NM_153565, exon 1 of 12)	5' UTR (NM_153565, exon 1 of 12)	226	NM_153565	100102	Mm.133268	NM_153565	ENSMUSG00000044254	Pcsk9	AI415265|AI747682|FH3|HCHOLA3|Narc1|PC9	proprotein convertase subtilisin/kexin type 9	protein-coding
mm_168429.1	chr11	33754852	33754852	-	1	NA	intron (NM_001190885, intron 1 of 8)	LSU-rRNA_Hsa|rRNA|rRNA	88733	NM_027398	70357	Mm.252514	NM_027398	ENSMUSG00000053519	Kcnip1	KCHIP1|Kchip1.2	Kv channel-interacting protein 1	protein-coding
mm_109833.1	chr12	4038906	4038957	-	1	NA	promoter-TSS (NM_001082483)	promoter-TSS (NM_001082483)	-16	NM_001082483	668212	Mm.210266	NM_001082483	ENSMUSG00000020658	Efr3b	AI852640|C030014M07Rik|mKIAA0953	EFR3 homolog B	protein-coding
mm_105545.1	chr11	106324964	106324985	-	1	NA	intron (NM_133199, intron 18 of 23)	intron (NM_133199, intron 18 of 23)	-10412	NM_001313939	15985	Mm.2987	NM_008339	ENSMUSG00000040592	Cd79b	B29|Ig-beta|Igb|Igbeta	CD79B antigen	protein-coding
mm_15005.1	chr2	152477051	152477073	+	1	NA	promoter-TSS (NM_176950)	promoter-TSS (NM_176950)	-1	NM_176950	319579	Mm.190454	NM_176950	ENSMUSG00000049560	Defb20	9230107O10Rik|BD-20|mBD-20	defensin beta 20	protein-coding
mm_41532.1	chr5	92809333	92809371	+	1	NA	promoter-TSS (NM_001077595)	promoter-TSS (NM_001077595)	-30	NM_001077595	27428	Mm.46014	NM_015756	ENSMUSG00000029381	Shroom3	AL022960|D5Ertd287e|Shrm|Shrm3	shroom family member 3	protein-coding
mm_85403.1	chr9	103365422	103365480	-	1	NA	promoter-TSS (NM_001134427)	promoter-TSS (NM_001134427)	329	NM_175833	321022	Mm.261025	NM_175565	ENSMUSG00000032803	Cdv3	2510010F10Rik|C230084J24Rik|C79446|TPP36	carnitine deficiency-associated gene expressed in ventricle 3	protein-coding
mm_110565.1	chr12	55821138	55821149	-	1	NA	5' UTR (NM_019994, exon 1 of 41)	5' UTR (NM_019994, exon 1 of 41)	373	NM_019994	56784	Mm.292180	NM_019994	ENSMUSG00000021027	Ralgapa1	2310003F20Rik|4930400K19Rik|AI563624|GRIPE|Garnl1|Tulip1|mKIAA0884	Ral GTPase activating protein, alpha subunit 1	protein-coding
mm_47717.1	chr5	130002654	130002689	-	1	NA	exon (NM_010368, exon 1 of 12)	exon (NM_010368, exon 1 of 12)	157	NM_010368	110006	Mm.3317	NM_010368	ENSMUSG00000025534	Gusb	AI747421|Gur|Gus|Gus-r|Gus-s|Gus-t|Gus-u|Gut|asd|g	glucuronidase, beta	protein-coding
mm_54734.1	chr6	40940528	40940554	-	1	NA	promoter-TSS (NM_028550)	promoter-TSS (NM_028550)	16	NM_028550	73481	Mm.333010	NM_028550	ENSMUSG00000029883	1700074P13Rik	AV047902|Tryx5	RIKEN cDNA 1700074P13 gene	protein-coding
mm_56932.1	chr6	119673804	119673807	-	1	NA	intron (NR_104484, intron 16 of 20)	intron (NR_104484, intron 16 of 20)	-129458	NM_009525	22419	Mm.321818	NM_009525	ENSMUSG00000030170	Wnt5b	AW545702|Wnt-5b	wingless-type MMTV integration site family, member 5B	protein-coding
mm_168963.1	chr12	80441414	80441424	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-4818	NM_177267	320808	Mm.220310	NM_177267	ENSMUSG00000049106	Dcaf5	9430020B07Rik|AI325023|AI430035|AI848110|AW124614|BCRG2|BCRP2|Wdr22	DDB1 and CUL4 associated factor 5	protein-coding
mm_78270.1	chr9	22003036	22003037	+	1	NA	promoter-TSS (NM_029939)	promoter-TSS (NM_029939)	48	NM_008925	19089	Mm.214593	NM_008925	ENSMUSG00000003402	Prkcsh	80K-H|PKCSH	protein kinase C substrate 80K-H	protein-coding
mm_46513.1	chr5	105239541	105239545	-	1	NA	promoter-TSS (NM_001039646)	promoter-TSS (NM_001039646)	-10	NM_001039646	626578	Mm.275893	NM_001039646	ENSMUSG00000105096	Gbp10	-	guanylate-binding protein 10	protein-coding
mm_116667.1	chr13	49205458	49205483	-	1	NA	intron (NM_026738, intron 2 of 5)	intron (NM_026738, intron 2 of 5)	10556	NM_026738	68480	Mm.3336	NM_026738	ENSMUSG00000037960	Card19	1110007C09Rik|AI851695|Bincard	caspase recruitment domain family, member 19	protein-coding
mm_112425.1	chr13	4191229	4191242	+	1	NA	promoter-TSS (NM_013778)	promoter-TSS (NM_013778)	48	NM_013778	27384	Mm.27447	NM_013778	ENSMUSG00000021213	Akr1c13	mKIAA4014	aldo-keto reductase family 1, member C13	protein-coding
mm_37539.1	chr4	125116672	125116714	-	1	NA	Intergenic	Intergenic	11188	NM_153159	230738	Mm.402	NM_153159	ENSMUSG00000042677	Zc3h12a	BC036563|MCPIP|MCPIP-1|Mcpip1|Reg1	zinc finger CCCH type containing 12A	protein-coding
mm_109759.1	chr12	117843847	117843871	+	1	NA	promoter-TSS (NM_146040)	promoter-TSS (NM_146040)	-2	NM_146040	217946	Mm.281149	NM_146040	ENSMUSG00000021175	Cdca7l	BC006933|JPO2	cell division cycle associated 7 like	protein-coding
mm_89261.1	chr10	87859482	87859492	+	1	NA	intron (NM_001314010, intron 2 of 4)	intron (NM_001314010, intron 2 of 4)	435	NM_010512	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_88340.1	chr10	75589424	75589437	+	1	NA	promoter-TSS (NM_011820)	promoter-TSS (NM_011820)	49	NM_011820	23887	Mm.257927	NM_011820	ENSMUSG00000006344	Ggt5	AI551243|GGL|GGT-REL|Ggtla1	gamma-glutamyltransferase 5	protein-coding
mm_145923.1	chr18	67088288	67088345	+	1	NA	promoter-TSS (NM_177137)	promoter-TSS (NM_177137)	18	NM_177137	14680	Mm.440746	NM_010307	ENSMUSG00000024524	Gnal	2610011C15Rik|9630020G10Rik|Galphaolf|Gna10|Golf	guanine nucleotide binding protein, alpha stimulating, olfactory type	protein-coding
mm_115840.1	chr13	21287257	21287275	-	1	NA	3' UTR (NM_010343, exon 5 of 5)	3' UTR (NM_010343, exon 5 of 5)	5420	NM_010343	14780	Mm.1332	NM_010343	ENSMUSG00000004344	Gpx5	AV379049|Arep	glutathione peroxidase 5	protein-coding
mm_111925.1	chr12	108882785	108882800	-	1	NA	exon (NM_001164488, exon 3 of 10)	exon (NM_001164488, exon 3 of 10)	10406	NM_001164488	22375	Mm.38433	NM_011710	ENSMUSG00000021266	Wars	TrpRS|WRS	tryptophanyl-tRNA synthetase	protein-coding
mm_122048.1	chr14	30056380	30056384	-	1	NA	intron (NM_001302637, intron 41 of 48)	intron (NM_001302637, intron 41 of 48)	33749	NM_175343	218865	Mm.259916	NM_172264	ENSMUSG00000015970	Chdh	AU041472|D630034H06Rik	choline dehydrogenase	protein-coding
mm_27383.1	chr3	50607218	50607227	-	1	NA	Intergenic	Intergenic	-163609	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_74076.1	chr8	122444057	122444059	+	1	NA	promoter-TSS (NM_138656)	promoter-TSS (NM_138656)	402	NR_045696	100689703	Mm.271989	NR_045696		9330133O14Rik	-	RIKEN cDNA 9330133O14 gene	ncRNA
mm_95708.1	chr11	54455752	54455753	+	1	NA	intron (NM_173753, intron 1 of 17)	intron (NM_173753, intron 1 of 17)	17573	NM_173753	216742	Mm.34087	NM_173753	ENSMUSG00000035992	Fnip1	A730024A03Rik|AI838773|AW557298	folliculin interacting protein 1	protein-coding
mm_161760.1	chr17	35847199	35847199	+	1	NA	intron (NM_001010833, intron 4 of 15)	intron (NM_001010833, intron 4 of 15)	5701	NM_001010833	240087	Mm.218511	NM_001010833	ENSMUSG00000061607	Mdc1	6820401C03|AA413496|Nfbd1|mKIAA0170	mediator of DNA damage checkpoint 1	protein-coding
mm_72995.1	chr8	93175570	93175570	+	1	NA	intron (NM_053200, intron 10 of 13)	intron (NM_053200, intron 10 of 13)	22234	NM_053200	104158	Mm.292803	NM_053200	ENSMUSG00000056973	Ces1d	Ces3|TGH	carboxylesterase 1D	protein-coding
mm_163541.1	chr13	15103779	15103782	+	1	NA	Intergenic	Lx8b|LINE|L1	-359943	NM_008130	14634	Mm.5098	NM_008130	ENSMUSG00000021318	Gli3	AI854843|AU023367|Bph|GLI3-190|GLI3FL|Pdn|Xt|add	GLI-Kruppel family member GLI3	protein-coding
mm_155406.1	chrX	73342651	73342661	+	1	NA	promoter-TSS (NM_031494)	promoter-TSS (NM_031494)	35	NM_001160229	27081	Mm.26595	NM_031494	ENSMUSG00000031365	Zfp275	5430431L06Rik|AI593314|DXBay20|DXHXS52|DXPas8	zinc finger protein 275	protein-coding
mm_151636.1	chr19	3935801	3935815	-	1	NA	exon (NM_019449, exon 2 of 11)	exon (NM_019449, exon 2 of 11)	622	NM_001161428	54445	Mm.262094	NM_019449	ENSMUSG00000036908	Unc93b1	Unc-93B1|Unc93b	unc-93 homolog B1 (C. elegans)	protein-coding
mm_171828.1	chr5	144679210	144679212	+	1	NA	Intergenic	BGLII|LTR|ERVK	82367	NM_177735	243339	Mm.126793	NM_177735	ENSMUSG00000043388	Tmem130	BC067004|C130036G08	transmembrane protein 130	protein-coding
mm_112137.1	chr12	113000625	113000656	-	1	NA	promoter-TSS (NM_028193)	promoter-TSS (NM_028193)	-19	NM_028193	72308	Mm.196721	NM_028193	ENSMUSG00000011158	Brf1	2510002F24Rik|GTF3B|TAF3C|TAFIII90|TFIIIB90|mTFIIIB90	BRF1, RNA polymerase III transcription initiation factor 90 kDa subunit	protein-coding
mm_151372.1	chr19	55932376	55932379	+	1	NA	non-coding (NR_138565, exon 16 of 16)	non-coding (NR_138565, exon 16 of 16)	37056	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_155152.1	chrX	52912233	52912361	+	1	NA	promoter-TSS (NM_027642)	promoter-TSS (NM_027642)	83	NM_001290546	70998	Mm.26870	NM_027642	ENSMUSG00000025626	Phf6	2700007B13Rik|4931428F02Rik|mKIAA1823	PHD finger protein 6	protein-coding
mm_59144.1	chr7	24280663	24280700	+	1	NA	Intergenic	Intergenic	10263	NM_009567	22755	Mm.383535	NM_009567	ENSMUSG00000055305	Zfp93	Znf235	zinc finger protein 93	protein-coding
mm_88045.1	chr10	67538564	67538569	+	1	NA	intron (NM_001347458, intron 2 of 2)	CpG	636	NM_001347458	13654	Mm.290421	NM_010118	ENSMUSG00000037868	Egr2	Egr-2|Krox-20|Krox20|NGF1-B|Zfp-25|Zfp-6	early growth response 2	protein-coding
mm_84465.1	chr9	66592994	66593024	-	1	NA	5' UTR (NM_144937, exon 1 of 15)	5' UTR (NM_144937, exon 1 of 15)	106	NM_144937	235441	Mm.32465	NM_144937	ENSMUSG00000032376	Usp3	AA409661|BC017156	ubiquitin specific peptidase 3	protein-coding
mm_17829.1	chr2	33913709	33913739	-	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	-25778	NM_175184	72543	Mm.254914	NM_175184	ENSMUSG00000038740	Mvb12b	2610200O14Rik|2610528K11Rik|AI414895|Fam125b	multivesicular body subunit 12B	protein-coding
mm_41825.1	chr5	104046908	104046914	+	1	NA	promoter-TSS (NM_028794)	promoter-TSS (NM_028794)	47	NM_028794	74167	Mm.241484	NM_028794	ENSMUSG00000029310	Nudt9	1190002C07Rik|ADPR-PPase|AI462474	nudix (nucleoside diphosphate linked moiety X)-type motif 9	protein-coding
mm_40133.1	chr5	35042555	35042568	+	1	NA	intron (NM_019447, intron 2 of 13)	intron (NM_019447, intron 2 of 13)	1052	NM_019447	54426	Mm.27369	NM_019447	ENSMUSG00000029102	Hgfac	HGFA	hepatocyte growth factor activator	protein-coding
mm_131044.1	chr16	3907777	3907820	+	1	NA	intron (NM_028484, intron 1 of 2)	intron (NM_028484, intron 1 of 2)	891	NM_028484	73261	Mm.486226	NM_028484	ENSMUSG00000005983	1700037C18Rik	2810022L20Rik	RIKEN cDNA 1700037C18 gene	protein-coding
mm_114524.1	chr13	73467215	73467316	+	1	NA	promoter-TSS (NM_145376)	promoter-TSS (NM_145376)	-118	NM_145376	210992	Mm.284649	NM_145376	ENSMUSG00000021608	Lpcat1	2900035H07Rik|Aytl2|BB137372|BC005662|C87117|LPCAT|rd11	lysophosphatidylcholine acyltransferase 1	protein-coding
mm_58338.1	chr6	146954384	146954396	-	1	NA	promoter-TSS (NM_028509)	promoter-TSS (NM_028509)	31	NM_001164236	73344	Mm.391543	NM_028509	ENSMUSG00000040163	1700034J05Rik	-	RIKEN cDNA 1700034J05 gene	protein-coding
mm_160357.1	chr8	21618138	21618138	+	1	NA	promoter-TSS (NM_001079933)	promoter-TSS (NM_001079933)	-30	NM_001079933	626708	Mm.305275	NM_001079933	ENSMUSG00000060070	Defa26	Defcr26	defensin, alpha, 26	protein-coding
mm_107542.1	chr12	40648281	40648289	+	1	NA	intron (NM_172803, intron 7 of 52)	ID4|SINE|ID	202232	NM_172803	238130	Mm.341423	NM_172803	ENSMUSG00000035954	Dock4	5330406C03|6330411N01Rik|AF263288|C030023J22|mKIAA0716	dedicator of cytokinesis 4	protein-coding
mm_79527.1	chr9	57652720	57652742	+	1	NA	intron (NM_001304761, intron 1 of 14)	intron (NM_001304761, intron 1 of 14)	900	NM_001304761	12988	Mm.21974	NM_007783	ENSMUSG00000032312	Csk	AW212630|p50CSK	c-src tyrosine kinase	protein-coding
mm_1327.1	chr1	65186661	65186674	+	1	NA	promoter-TSS (NM_001310624)	promoter-TSS (NM_001310624)	-18	NM_011086	18711	Mm.38370	NM_011086	ENSMUSG00000025949	Pikfyve	5230400C17Rik|Pip5k|Pip5k3|Pipk5k3|PipkIII|p235	phosphoinositide kinase, FYVE finger containing	protein-coding
mm_170671.1	chr2	121230367	121230379	+	1	NA	intron (NM_001290830, intron 12 of 26)	(ACTG)n|Simple_repeat|Simple_repeat	41034	NM_001290830	27223	Mm.215389	NM_013735	ENSMUSG00000043909	Trp53bp1	53BP1|Tp53bp1|m53BP1|p53BP1	transformation related protein 53 binding protein 1	protein-coding
mm_74520.1	chr8	9207277	9207295	-	1	NA	3' UTR (NM_173446, exon 3 of 3)	3' UTR (NM_173446, exon 3 of 3)	62617	NR_073360	74688	Mm.159298	NR_073360	ENSMUSG00000109215	4930453L07Rik	-	RIKEN cDNA 4930453L07 gene	ncRNA
mm_75833.1	chr8	70522948	70522983	-	1	NA	intron (NM_029366, intron 1 of 4)	CpG	215	NM_029366	75620	Mm.482129	NM_029366	ENSMUSG00000055553	Kxd1	0610030B01Rik|2810422J05Rik|C78305	KxDL motif containing 1	protein-coding
mm_114959.1	chr13	97071409	97071424	+	1	NA	promoter-TSS (NM_001100458)	promoter-TSS (NM_001100458)	-227	NM_001100458	320557	Mm.458280	NM_001100458	ENSMUSG00000041817	Fam169a	B230112C05Rik|SLAP75	family with sequence similarity 169, member A	protein-coding
mm_51698.1	chr6	86594887	86594903	+	1	NA	Intergenic	MTEa|LTR|ERVL-MaLR	-33279	NM_026414	67855	Mm.183043	NM_026414	ENSMUSG00000033508	Asprv1	2300003P22Rik|AA986851|SASP|SASPase|Taps	aspartic peptidase, retroviral-like 1	protein-coding
mm_10252.1	chr2	9193479	9193505	+	1	NA	non-coding (NR_038180, exon 3 of 4)	non-coding (NR_038180, exon 3 of 4)	3977	NR_038180	73438	Mm.23558	NR_038180	ENSMUSG00000085580	1700061F12Rik	-	RIKEN cDNA 1700061F12 gene	ncRNA
mm_15832.1	chr2	164656044	164656113	+	1	NA	promoter-TSS (NM_001039501)	promoter-TSS (NM_001039501)	32	NM_001039501	629756	Mm.189007	NM_001039501	ENSMUSG00000070529	Wfdc10	Gm120|OTTMUSG00000016289	WAP four-disulfide core domain 10	protein-coding
mm_9657.1	chr1	177776593	177776607	-	1	NA	intron (NM_007422, intron 5 of 12)	intron (NM_007422, intron 5 of 12)	19909	NM_007422	11566	Mm.338021	NM_007422	ENSMUSG00000015961	Adss	AI314886|AS|Adss2	adenylosuccinate synthetase, non muscle	protein-coding
mm_91526.1	chr10	37140803	37140831	-	1	NA	Intergenic	Intergenic	-1891	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_91528.1	chr10	37141276	37141289	-	1	NA	Intergenic	Intergenic	-2356	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_91691.1	chr10	43997344	43997361	-	1	NA	exon (NM_172393, exon 2 of 20)	exon (NM_172393, exon 2 of 20)	7494	NM_172393	11630	Mm.292082	NM_172393	ENSMUSG00000019866	Aim1	AI462491|AI463325	absent in melanoma 1	protein-coding
mm_60757.1	chr7	45514620	45514642	+	1	NA	promoter-TSS (NM_001290998)	promoter-TSS (NM_001290998)	29	NM_001290998	56734	Mm.439742	NM_008807	ENSMUSG00000023467	Tulp2	Pdet	tubby-like protein 2	protein-coding
mm_77479.1	chr8	122474777	122474781	-	1	NA	intron (NM_001033142, intron 1 of 5)	intron (NM_001033142, intron 1 of 5)	1285	NM_001033142	68718	Mm.34356	NM_001033142	ENSMUSG00000014470	Rnf166	1110031E24Rik|AW555115|Zfp313l	ring finger protein 166	protein-coding
mm_32737.1	chr4	116596779	116596782	+	1	NA	promoter-TSS (NM_001037916)	promoter-TSS (NM_001037916)	50	NM_001037916	622665	Mm.388905	NM_001037916	ENSMUSG00000034035	Ccdc17	-	coiled-coil domain containing 17	protein-coding
mm_83967.1	chr9	57158190	57158200	-	1	NA	intron (NM_025417, intron 1 of 7)	intron (NM_025417, intron 1 of 7)	104	NM_025417	66199	Mm.41687	NM_025417	ENSMUSG00000032299	Commd4	1110039H05Rik	COMM domain containing 4	protein-coding
mm_85795.1	chr9	109849441	109849454	-	1	NA	promoter-TSS (NM_009921)	promoter-TSS (NM_009921)	9	NM_009921	12796	Mm.3834	NM_009921	ENSMUSG00000038357	Camp	CAP18|Cnlp|Cramp|FALL39|MCLP	cathelicidin antimicrobial peptide	protein-coding
mm_133047.1	chr16	57569766	57569779	+	1	NA	exon (NM_001040397, exon 5 of 5)	exon (NM_001040397, exon 5 of 5)	20530	NM_001177871	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding
mm_12314.1	chr2	69219990	69220005	+	1	NA	promoter-TSS (NM_021331)	promoter-TSS (NM_021331)	48	NM_001289857	14378	Mm.140768	NM_021331	ENSMUSG00000005232	G6pc2	G6pc-rs|IGRP	glucose-6-phosphatase, catalytic, 2	protein-coding
mm_141811.1	chr17	34603676	34603702	-	1	NA	promoter-TSS (NM_019403)	promoter-TSS (NM_019403)	-128	NM_019403	54197	Mm.274542	NM_019403	ENSMUSG00000015478	Rnf5	2410131O05Rik|AA407576|NG2	ring finger protein 5	protein-coding
mm_121537.1	chr14	122375796	122375815	+	1	NA	intron (NM_029556, intron 3 of 7)	intron (NM_029556, intron 3 of 7)	75310	NR_033325	328479	Mm.86095	NR_033325	ENSMUSG00000064052	Gm5089	6530402A20|C030005G22Rik|EG328479	predicted gene 5089	ncRNA
mm_69494.1	chr7	134225089	134225104	-	1	NA	promoter-TSS (NM_007400)	promoter-TSS (NM_007400)	1	NM_007400	11489	Mm.439714	NM_007400	ENSMUSG00000054555	Adam12	Mltna	a disintegrin and metallopeptidase domain 12 (meltrin alpha)	protein-coding
mm_3443.1	chr1	150102743	150102762	+	1	NA	exon (NM_011198, exon 5 of 10)	exon (NM_011198, exon 5 of 10)	2721	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_146535.1	chr18	5404499	5404502	-	1	NA	Intergenic	Intergenic	-70061	NM_178722	240186	Mm.118257	NM_178722	ENSMUSG00000050945	Zfp438	9430031G09|9430091M14Rik|B830013J05Rik	zinc finger protein 438	protein-coding
mm_38735.1	chr4	145245623	145245642	-	1	NA	intron (NM_011610, intron 1 of 9)	intron (NM_011610, intron 1 of 9)	1238	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_164518.1	chr16	96443711	96443735	+	1	NA	promoter-TSS (NM_008405)	promoter-TSS (NM_008405)	-109	NM_008405	16415	Mm.12872	NM_008405	ENSMUSG00000000157	Itgb2l	5033406G21Rik|pactolus	integrin beta 2-like	protein-coding
mm_116589.1	chr13	48273866	48273909	-	1	NA	promoter-TSS (NR_045162)	promoter-TSS (NR_045162)	-3	NR_045162	320315	Mm.185120	NR_045162	ENSMUSG00000097326	A330048O09Rik	-	RIKEN cDNA A330048O09 gene	ncRNA
mm_164634.1	chr17	34055061	34055082	+	1	NA	intron (NM_001317722, intron 28 of 64)	intron (NM_001317722, intron 28 of 64)	15933	NM_001317722	12815	Mm.20230	NM_009926	ENSMUSG00000024330	Col11a2	-	collagen, type XI, alpha 2	protein-coding
mm_74844.1	chr8	24571211	24571218	-	1	NA	intron (NM_145949, intron 1 of 9)	intron (NM_145949, intron 1 of 9)	5119	NM_145949	209176	Mm.219580	NM_145949	ENSMUSG00000031549	Ido2	AI265623|C230043N17Rik|Ido-2|Indol1	indoleamine 2,3-dioxygenase 2	protein-coding
mm_44028.1	chr5	147430378	147430401	+	1	NA	promoter-TSS (NM_028291)	promoter-TSS (NM_028291)	-191	NM_028291	72587	Mm.320469	NM_028291	ENSMUSG00000029647	Pan3	2700050F09Rik|A430027N15Rik|AU014670	PAN3 poly(A) specific ribonuclease subunit	protein-coding
mm_48845.1	chr5	149367163	149367171	-	1	NA	Intergenic	Intergenic	-44639	NM_027519	70717	Mm.252139	NM_027519	ENSMUSG00000029659	Medag	6330406I15Rik|Awms3|MEDA-4|Meda4|mAWMS3	mesenteric estrogen dependent adipogenesis	protein-coding
mm_63265.1	chr7	126759614	126759651	+	1	NA	promoter-TSS (NM_011952)	promoter-TSS (NM_011952)	6	NM_011952	26417	Mm.8385	NM_011952	ENSMUSG00000063065	Mapk3	Erk-1|Erk1|Ert2|Esrk1|Mnk1|Mtap2k|Prkm3|p44|p44erk1|p44mapk	mitogen-activated protein kinase 3	protein-coding
mm_164195.1	chr15	78959929	78959939	+	1	NA	exon (NM_001039155, exon 6 of 8)	exon (NM_001039155, exon 6 of 8)	12210	NM_001039155	110253	Mm.123714	NM_138579	ENSMUSG00000033088	Triobp	AI428493|EST478828|Tara|mKIAA1662	TRIO and F-actin binding protein	protein-coding
mm_94198.1	chr11	3101413	3101433	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	-22598	NR_003517	236604	Mm.247625	NM_001004146		Pisd-ps1	-	phosphatidylserine decarboxylase, pseudogene 1	pseudo
mm_89396.1	chr10	90071012	90071015	+	1	NA	intron (NM_001128086, intron 5 of 24)	intron (NM_001128086, intron 5 of 24)	197504	NM_001128086	77531	Mm.440605	NM_181398	ENSMUSG00000058589	Anks1b	AIDA-1b|C030032C09Rik|E530015N03Rik|ENSMUSG00000078431|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding
mm_103937.1	chr11	83657418	83657426	-	1	NA	Intergenic	Intergenic	-5162	NM_013652	20303	Mm.244263	NM_013652	ENSMUSG00000018930	Ccl4	AT744.1|Act-2|MIP-1B|Mip1b|Scya4	chemokine (C-C motif) ligand 4	protein-coding
mm_95137.1	chr11	34833787	34833791	+	1	NA	promoter-TSS (NM_027411)	promoter-TSS (NM_027411)	-148	NM_027411	70385	Mm.194368	NM_027411	ENSMUSG00000069910	Spdl1	1700018I02Rik|2600001J17Rik|2810049B11Rik|AA409762|Ccdc99	spindle apparatus coiled-coil protein 1	protein-coding
mm_121300.1	chr14	105589617	105589623	+	1	NA	promoter-TSS (NR_102319)	promoter-TSS (NR_102319)	71	NR_102319	380930	Mm.427836	NR_102319		9330188P03Rik	Gm1589|mgt-6	RIKEN cDNA 9330188P03 gene	ncRNA
mm_79428.1	chr9	55938223	55938264	+	1	NA	promoter-TSS (NM_001081341)	promoter-TSS (NM_001081341)	-128	NM_001081341	244891	Mm.86588	NM_175536	ENSMUSG00000034007	Scaper	C430017I08|D530014O03Rik|Zfp291	S phase cyclin A-associated protein in the ER	protein-coding
mm_56926.1	chr6	119467192	119467202	-	1	NA	promoter-TSS (NM_001271758)	promoter-TSS (NM_001271758)	14	NM_001271758	22419	Mm.321818	NM_009525	ENSMUSG00000030170	Wnt5b	AW545702|Wnt-5b	wingless-type MMTV integration site family, member 5B	protein-coding
mm_95584.1	chr11	53267046	53267065	+	1	NA	exon (NM_008300, exon 14 of 19)	exon (NM_008300, exon 14 of 19)	33424	NM_008300	15525	Mm.239865	NM_008300	ENSMUSG00000020361	Hspa4	70kDa|AI317151|APG-2|Hsp110|Hsp70RY|mKIAA4025	heat shock protein 4	protein-coding
mm_119419.1	chr14	45329801	45329811	+	1	NA	promoter-TSS (NM_025959)	promoter-TSS (NM_025959)	-18	NM_025959	67089	Mm.18472	NM_025959	ENSMUSG00000021832	Psmc6	2300001E01Rik|AI451058	proteasome (prosome, macropain) 26S subunit, ATPase, 6	protein-coding
mm_37423.1	chr4	122885906	122885919	-	1	NA	5' UTR (NM_007598, exon 1 of 13)	5' UTR (NM_007598, exon 1 of 13)	145	NM_007598	12331	Mm.8687	NM_007598	ENSMUSG00000028656	Cap1	-	CAP, adenylate cyclase-associated protein 1 (yeast)	protein-coding
mm_146346.1	chr18	82537650	82537705	+	1	NA	intron (NM_001025245, intron 3 of 3)	(CCA)n|Simple_repeat|Simple_repeat	-16786	NM_001025256	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_145993.1	chr18	68337546	68337546	+	1	NA	promoter-TSS (NM_013596)	promoter-TSS (NM_013596)	-57	NM_013596	17203	Mm.8003	NM_013596	ENSMUSG00000007480	Mc5r	-	melanocortin 5 receptor	protein-coding
mm_67597.1	chr7	83732402	83732437	-	1	NA	intron (NM_010551, intron 1 of 18)	intron (NM_010551, intron 1 of 18)	3071	NM_010551	16170	Mm.10137	NM_010551	ENSMUSG00000001741	Il16	mKIAA4048	interleukin 16	protein-coding
mm_20957.1	chr2	151741237	151741309	-	1	NA	promoter-TSS (NM_001305244)	promoter-TSS (NM_001305244)	37	NM_212446	228769	Mm.146984	NM_144889	ENSMUSG00000032869	Psmf1	AW048666|BC012260|PI31	proteasome (prosome, macropain) inhibitor subunit 1	protein-coding
mm_165806.1	chr3	144720005	144720033	-	1	NA	exon (NM_019464, exon 1 of 9)	exon (NM_019464, exon 1 of 9)	316	NM_001282042	54673	Mm.271775	NM_019464	ENSMUSG00000037062	Sh3glb1	AA409932|AI314629|AU015566|Bif-1|mKIAA0491	SH3-domain GRB2-like B1 (endophilin)	protein-coding
mm_29265.1	chr3	107333025	107333069	-	1	NA	exon (NM_001045807, exon 1 of 2)	exon (NM_001045807, exon 1 of 2)	242	NM_001045807	229700	Mm.27966	NM_001045807	ENSMUSG00000048109	Rbm15	C230088J01Rik|mKIAA1438	RNA binding motif protein 15	protein-coding
mm_121749.1	chr14	18893750	18893816	-	1	NA	promoter-TSS (NM_144839)	promoter-TSS (NM_144839)	-156	NM_144839	218793	Mm.23551	NM_144839	ENSMUSG00000058317	Ube2e2	BC016265	ubiquitin-conjugating enzyme E2E 2	protein-coding
mm_120428.1	chr14	65694829	65694833	+	1	NA	intron (NM_028903, intron 3 of 8)	intron (NM_028903, intron 3 of 8)	28428	NM_001168318	71145	Mm.83840	NM_028903	ENSMUSG00000022032	Scara5	4932433F15Rik|4933425F03Rik|AV278087|Tesr	scavenger receptor class A, member 5	protein-coding
mm_5796.1	chr1	52140429	52140432	-	1	NA	intron (NM_001205313, intron 10 of 24)	intron (NM_001205313, intron 10 of 24)	20808	NM_001205313	20846	Mm.277406	NM_009283	ENSMUSG00000026104	Stat1	2010005J02Rik|AA408197	signal transducer and activator of transcription 1	protein-coding
mm_46490.1	chr5	105132309	105132319	-	1	NA	intron (NM_008620, intron 3 of 10)	L1M2|LINE|L1	7238	NM_008620	17472	Mm.440525	NM_008620	ENSMUSG00000079363	Gbp4	AW228052|Mag-2|Mpa-2|Mpa2	guanylate binding protein 4	protein-coding
mm_111960.1	chr12	109597094	109597097	-	1	NA	Intergenic	Intergenic	-1692	NM_184109	353326	Mm.23062	NM_184109	ENSMUSG00000085925	Rtl1	6430411K18Rik|Mar|Mart1|Mor1|Peg11	retrotransposon-like 1	protein-coding
mm_98164.1	chr11	87745194	87745205	+	1	NA	Intergenic	Intergenic	7634	NM_009296	20922	Mm.622	NM_009296	ENSMUSG00000020485	Supt4a	AL022777|Supt4h|Supt4h1|Supt4h1a	suppressor of Ty 4A	protein-coding
mm_105350.1	chr11	103001892	103001895	-	1	NA	intron (NM_026551, intron 1 of 4)	PB1D10|SINE|Alu	-1972	NR_105896	102466988		NR_105896	ENSMUSG00000098613	Mir6931	Gm27303|mmu-mir-6931	microRNA 6931	ncRNA
mm_127405.1	chr15	101232404	101232433	+	1	NA	3' UTR (NM_019518, exon 8 of 8)	3' UTR (NM_019518, exon 8 of 8)	-7232	NR_045328	380977	Mm.399924	NR_045326	ENSMUSG00000097915	A330009N23Rik	-	RIKEN cDNA A330009N23 gene	ncRNA
mm_47572.1	chr5	124480039	124480063	-	1	NA	Intergenic	Intergenic	-1816	NM_030259	80291	Mm.425280	NM_030259	ENSMUSG00000029401	Rilpl2	-	Rab interacting lysosomal protein-like 2	protein-coding
mm_49259.1	chr6	17463827	17463829	+	1	NA	promoter-TSS (NM_008591)	promoter-TSS (NM_008591)	-129	NM_008591	17295	Mm.86844	NM_008591	ENSMUSG00000009376	Met	AI838057|HGF|HGFR|Par4|c-Met	met proto-oncogene	protein-coding
mm_68313.1	chr7	105787545	105787555	-	1	NA	promoter-TSS (NM_001162943)	promoter-TSS (NM_001162943)	0	NM_001162943	233651	Mm.334108	NM_001162943	ENSMUSG00000036862	Dchs1	3110041P15Rik|C130033F22Rik|CDH25|FIB1|Gm165|PCDH16	dachsous 1 (Drosophila)	protein-coding
mm_171558.1	chr4	147132235	147132247	+	1	NA	Intergenic	Intergenic	-43625	NM_001039209	195531	Mm.270762	NM_001039209	ENSMUSG00000078496	Zfp982	Gm13152|OTTMUSG00000010671	zinc finger protein 982	protein-coding
mm_170361.1	chr1	85270178	85270185	-	1	NA	5' UTR (NM_001037909, exon 1 of 7)	5' UTR (NM_001037909, exon 1 of 7)	385	NM_175219	620078	Mm.386456	NM_175219	ENSMUSG00000052477	C130026I21Rik	4930565N07Rik|OTTMUSG00000029174	RIKEN cDNA C130026I21 gene	protein-coding
mm_146159.1	chr18	75018924	75018934	+	1	NA	5' UTR (NM_027727, exon 1 of 17)	5' UTR (NM_027727, exon 1 of 17)	157	NM_027727	69190	Mm.173826	NM_027727	ENSMUSG00000035765	Dym	1810041M12Rik|4933427L07Rik|C030019K18Rik	dymeclin	protein-coding
mm_115114.1	chr13	104109753	104109782	+	1	NA	promoter-TSS (NM_029447)	promoter-TSS (NM_029447)	-23	NM_144838	218544	Mm.44416	NM_144838	ENSMUSG00000042743	Sgtb	C630001O05Rik	small glutamine-rich tetratricopeptide repeat (TPR)-containing, beta	protein-coding
mm_6919.1	chr1	84840232	84840246	-	1	NA	promoter-TSS (NM_133975)	promoter-TSS (NM_133975)	398	NM_025386	66153	Mm.381192	NM_025386	ENSMUSG00000073633	Fbxo36	0610008D19Rik|1110020F21Rik|2410002G19Rik|D1Ertd757e	F-box protein 36	protein-coding
mm_78705.1	chr9	41376413	41376434	+	1	NA	promoter-TSS (NR_040725)	promoter-TSS (NR_040725)	-103	NR_040725	73144	Mm.38166	NM_001033153	ENSMUSG00000074415	3110039I08Rik	2610203C20Rik|AI848448|D230004N17Rik|D3Mgi9|Mir100hg	RIKEN cDNA 3110039I08 gene	ncRNA
mm_91720.1	chr10	44458770	44458784	-	1	NA	promoter-TSS (NM_007548)	promoter-TSS (NM_007548)	-29	NM_007548	12142	Mm.4800	NM_007548	ENSMUSG00000038151	Prdm1	Blimp-1|Blimp1|PRDI-BF1|ZNFPR1A1|b2b1765Clo	PR domain containing 1, with ZNF domain	protein-coding
mm_43215.1	chr5	129715489	129715539	+	1	NA	promoter-TSS (NM_025450)	promoter-TSS (NM_025450)	-14	NM_025450	66258	Mm.249809	NM_025450	ENSMUSG00000034211	Mrps17	1810006P02Rik|Mprs17	mitochondrial ribosomal protein S17	protein-coding
mm_160316.1	chr7	142229976	142229976	-	1	NA	promoter-TSS (NM_001037822)	promoter-TSS (NM_001037822)	-5	NM_001037822	114666	Mm.444495	NM_001037822	ENSMUSG00000073785	Krtap5-5	A030001H12Rik|AI586182|BB149782	keratin associated protein 5-5	protein-coding
mm_108850.1	chr12	98420143	98420153	+	1	NA	Intergenic	Intergenic	-103696	NR_136759	105245437	Mm.446375	NR_136759		Gm40893	-	predicted gene, 40893	ncRNA
mm_144069.1	chr17	90995539	90995543	-	1	NA	intron (NM_001346957, intron 1 of 18)	intron (NM_001346957, intron 1 of 18)	94064	NM_001346957	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_115438.1	chr13	117602332	117602338	+	1	NA	promoter-TSS (NM_010408)	promoter-TSS (NM_010408)	15	NM_010408	15165	Mm.343429	NM_010408	ENSMUSG00000021730	Hcn1	Bcng1|C630013B14Rik|HAC2	hyperpolarization-activated, cyclic nucleotide-gated K+ 1	protein-coding
mm_52983.1	chr6	123263717	123263748	+	1	NA	intron (NM_001163161, intron 1 of 5)	ID4|SINE|ID	1625	NM_010819	17474	Mm.441101	NM_010819	ENSMUSG00000030144	Clec4d	Clecsf8|Mpcl|mcl	C-type lectin domain family 4, member d	protein-coding
mm_109434.1	chr12	110694260	110694281	+	1	NA	exon (NM_010480, exon 5 of 11)	exon (NM_010480, exon 5 of 11)	2125	NM_010480	15519	Mm.1843	NM_010480	ENSMUSG00000021270	Hsp90aa1	86kDa|89kDa|AL024080|AL024147|Hsp86-1|Hsp89|Hsp90|Hspca|hsp4	heat shock protein 90, alpha (cytosolic), class A member 1	protein-coding
mm_115949.1	chr13	23745512	23745526	-	1	NA	promoter-TSS (NM_175653)	promoter-TSS (NM_175653)	2	NM_175653	319148	Mm.262517	NM_175653	ENSMUSG00000069310	Hist1h3c	H3-143	histone cluster 1, H3c	protein-coding
mm_172223.1	chr6	66734067	66734072	-	1	NA	Intergenic	Intergenic	2677	NM_134165	171183	Mm.377164	NM_134165	ENSMUSG00000057612	Vmn1r37	V1rc10	vomeronasal 1 receptor 37	protein-coding
mm_121880.1	chr14	21052453	21052510	-	1	NA	promoter-TSS (NM_134079)	promoter-TSS (NM_134079)	-39	NM_018829	55946	Mm.376269	NM_018829	ENSMUSG00000021824	Ap3m1	1200013D09Rik|C78982|R75378	adaptor-related protein complex 3, mu 1 subunit	protein-coding
mm_37530.1	chr4	124851120	124851147	-	1	NA	promoter-TSS (NM_001142727)	promoter-TSS (NM_001142727)	374	NM_153566	230734	Mm.258568	NM_153566	ENSMUSG00000028889	Yrdc	AV303379|BC023823|IRIP|ITIP	yrdC domain containing (E.coli)	protein-coding
mm_77668.1	chr8	124862973	124863006	-	1	NA	promoter-TSS (NM_025615)	promoter-TSS (NM_025615)	40	NM_025615	66523	Mm.436864	NM_025615	ENSMUSG00000031984	2810004N23Rik	3110004G14Rik|Ayu21-55|Gt(pU21)55Imeg|GtAyu21-55	RIKEN cDNA 2810004N23 gene	protein-coding
mm_114617.1	chr13	75849416	75849432	+	1	NA	3' UTR (NM_053108, exon 3 of 3)	3' UTR (NM_053108, exon 3 of 3)	9538	NM_053108	93692	Mm.25844	NM_053108	ENSMUSG00000021591	Glrx	C86710|D13Wsu156e|Glrx1|Grx1|TTase	glutaredoxin	protein-coding
mm_154078.1	chr19	56548123	56548127	-	1	NA	promoter-TSS (NM_018831)	promoter-TSS (NM_018831)	97	NM_018831	55947	Mm.2805	NM_018831	ENSMUSG00000025077	Dclre1a	2810043H12Rik|AU022226|Pso2|Smn1a|Snm1|mKIAA0086	DNA cross-link repair 1A	protein-coding
mm_97841.1	chr11	83065232	83065237	+	1	NA	5' UTR (NM_011408, exon 1 of 2)	5' UTR (NM_011408, exon 1 of 2)	122	NM_011408	20556	Mm.278689	NM_011408	ENSMUSG00000072620	Slfn2	Shlf2	schlafen 2	protein-coding
mm_666.1	chr1	40444907	40444921	+	1	NA	intron (NM_001025602, intron 6 of 10)	intron (NM_001025602, intron 6 of 10)	5285	NM_010743	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_29829.1	chr3	129754879	129754912	-	1	NA	exon (NM_010113, exon 1 of 24)	exon (NM_010113, exon 1 of 24)	427	NM_010113	13645	Mm.252481	NM_010113	ENSMUSG00000028017	Egf	AI790464	epidermal growth factor	protein-coding
mm_102559.1	chr11	61453891	61453910	-	1	NA	promoter-TSS (NM_009548)	promoter-TSS (NM_009548)	92	NM_009548	22671	Mm.89201	NM_009548	ENSMUSG00000010086	Rnf112	ZNF179|Zfp179|bfp|neurolastin	ring finger protein 112	protein-coding
mm_37228.1	chr4	117953576	117953583	-	1	NA	intron (NM_009176, intron 9 of 11)	intron (NM_009176, intron 9 of 11)	-23816	NM_001284192	11876	Mm.56897	NM_009711	ENSMUSG00000028539	Artn	neublastin	artemin	protein-coding
mm_125232.1	chr15	34142523	34142530	+	1	NA	TTS (NM_026002)	TTS (NM_026002)	59807	NM_026002	67154	Mm.130883	NM_026002	ENSMUSG00000022255	Mtdh	2610103J23Rik|3D3|3D3/Lyric|AEG-1|AV353288|D8Bwg1112e|Lyric	metadherin	protein-coding
mm_24738.1	chr3	95283324	95283333	+	1	NA	5' UTR (NM_133858, exon 1 of 10)	5' UTR (NM_133858, exon 1 of 10)	393	NM_199475	75007	Mm.279287	NM_133858	ENSMUSG00000038712	Fam63a	1810005H09Rik|4930504E06Rik|AA562754|AA960384|AW561904|cI-40|mKIAA1390|ni	family with sequence similarity 63, member A	protein-coding
mm_51194.1	chr6	71270875	71270929	+	1	NA	promoter-TSS (NR_106192)	promoter-TSS (NR_106192)	-769	NR_106192	102465900		NR_106192	ENSMUSG00000098623	Mir8112	Gm27739|mmu-mir-8112	microRNA 8112	ncRNA
mm_20577.1	chr2	131086855	131086867	-	1	NA	promoter-TSS (NM_011426)	promoter-TSS (NM_011426)	-96	NM_011426	20612	Mm.1374	NM_011426	ENSMUSG00000027322	Siglec1	Cd169|Siglec-1|Sn	sialic acid binding Ig-like lectin 1, sialoadhesin	protein-coding
mm_51744.1	chr6	87375789	87375796	+	1	NA	exon (NM_025467, exon 3 of 6)	exon (NM_025467, exon 3 of 6)	2427	NM_025467	66284	Mm.46446	NM_025467	ENSMUSG00000030049	Gkn2	1810036H07Rik|Bricd1b	gastrokine 2	protein-coding
mm_149212.1	chr19	9984179	9984219	+	1	NA	TTS (NM_011913)	TTS (NM_011913)	1553	NM_010239	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
mm_8987.1	chr1	165700930	165700941	-	1	NA	intron (NM_178593, intron 1 of 6)	intron (NM_178593, intron 1 of 6)	7159	NM_178593	226594	Mm.265552	NM_178593	ENSMUSG00000040723	Rcsd1	A430105K13Rik|BC025872|CapZIP	RCSD domain containing 1	protein-coding
mm_99700.1	chr11	106159973	106159981	+	1	NA	intron (NM_172397, intron 1 of 4)	CpG	165	NM_172397	67803	Mm.21687	NM_172397	ENSMUSG00000040699	Limd2	0610025L06Rik|AI413966	LIM domain containing 2	protein-coding
mm_18842.1	chr2	75137492	75137506	-	1	NA	Intergenic	CpG	306680	NR_040635	77269	Mm.389278	NR_040635		9430019J16Rik	-	RIKEN cDNA 9430019J16 gene	ncRNA
mm_19833.1	chr2	112268004	112268017	-	1	NA	intron (NM_133649, intron 1 of 24)	intron (NM_133649, intron 1 of 24)	1696	NM_133649	107723	Mm.491155	NM_133648	ENSMUSG00000027130	Slc12a6	9530023I19Rik|KCC3|gaxp	solute carrier family 12, member 6	protein-coding
mm_77889.1	chr9	7346109	7346154	+	1	NA	intron (NM_001320077, intron 1 of 10)	intron (NM_001320077, intron 1 of 10)	-1243	NM_001320076	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_98454.1	chr11	94946310	94946317	+	1	NA	exon (NM_007742, exon 33 of 51)	exon (NM_007742, exon 33 of 51)	10089	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_83843.1	chr9	54474098	54474123	-	1	NA	intron (NM_172771, intron 3 of 43)	intron (NM_172771, intron 3 of 43)	27516	NM_172771	235380	Mm.93636	NM_172771	ENSMUSG00000041268	Dmxl2	6330586A12|6430411K14Rik|E130119P06Rik|mKIAA0856	Dmx-like 2	protein-coding
mm_30536.1	chr4	3574938	3574955	+	1	NA	promoter-TSS (NM_028097)	promoter-TSS (NM_028097)	67	NM_054089	116940	Mm.171323	NM_054089	ENSMUSG00000028233	Tgs1	D4Ertd800e|Ncoa6ip|Pimt	trimethylguanosine synthase 1	protein-coding
mm_172303.1	chr7	104315342	104315346	-	1	NA	intron (NR_040749, intron 1 of 6)	intron (NR_040749, intron 1 of 6)	151	NM_023835	76681	Mm.458309	NM_023835	ENSMUSG00000066258	Trim12a	2310043C01Rik|Trim12	tripartite motif-containing 12A	protein-coding
mm_87825.1	chr10	60350696	60350705	+	1	NA	intron (NM_028732, intron 1 of 6)	MER113|DNA|hAT-Charlie	3849	NM_028732	74048	Mm.273584	NM_028732	ENSMUSG00000020101	Vsir	4632428N05Rik|Dies1|PD-1H|VISTA	V-set immunoregulatory receptor	protein-coding
mm_25821.1	chr3	127916165	127916169	+	1	NA	promoter-TSS (NR_040552)	promoter-TSS (NR_040552)	-4	NR_040552	329753	Mm.119720	NR_040552	ENSMUSG00000104763	9830132P13Rik	9830132P13	RIKEN cDNA 9830132P13 gene	ncRNA
mm_124215.1	chr14	100189577	100189587	-	1	NA	Intergenic	Intergenic	-39786	NM_010636	16597	Mm.396499	NM_010636	ENSMUSG00000072294	Klf12	2700063E05Rik|AI225908|AI315654|AP-2rep|B130052C06Rik|D530033K05Rik	Kruppel-like factor 12	protein-coding
mm_140292.1	chr17	85620776	85620788	+	1	NA	promoter-TSS (NM_011381)	promoter-TSS (NM_011381)	-52	NM_011381	20473	Mm.370208	NM_011381	ENSMUSG00000038805	Six3	E130112M24Rik|Six3a|Six3alpha|Six3b|Six3beta	sine oculis-related homeobox 3	protein-coding
mm_142374.1	chr17	44716741	44716744	-	1	NA	intron (NR_073392, intron 4 of 7)	intron (NR_073392, intron 4 of 7)	19434	NR_073425	12393	Mm.391013	NM_009820	ENSMUSG00000039153	Runx2	AML3|Cbf|Cbfa-1|Cbfa1|LS3|Osf2|PEBP2aA|Pebp2a1|Pebpa2a	runt related transcription factor 2	protein-coding
mm_157659.1	chrX	57339236	57339240	-	1	NA	promoter-TSS (NM_152801)	promoter-TSS (NM_152801)	-509	NM_152801	73341	Mm.261443	NM_152801	ENSMUSG00000031133	Arhgef6	1600028C08Rik|1700038J06Rik|4930592P22Rik|alpha-PIX	Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_134289.1	chr16	14218899	14218912	-	1	NA	exon (NM_013607, exon 23 of 42)	exon (NM_013607, exon 23 of 42)	55630	NM_001114085	67203	Mm.24105	NM_023317	ENSMUSG00000022678	Nde1	2810027M15Rik|AU042936|AW822251|Nude|mNudE	nudE neurodevelopment protein 1	protein-coding
mm_150259.1	chr19	34192796	34192808	+	1	NA	intron (NM_029682, intron 1 of 10)	intron (NM_029682, intron 1 of 10)	532	NM_029682	76630	Mm.130952	NM_029682	ENSMUSG00000024776	Stambpl1	1700095N21Rik|8230401J17Rik|ALMalpha|AMSH-FP	STAM binding protein like 1	protein-coding
mm_90516.1	chr10	128043444	128043454	+	1	NA	exon (NM_001113199, exon 3 of 9)	exon (NM_001113199, exon 3 of 9)	8103	NM_001113199	17938	Mm.3746	NM_013608	ENSMUSG00000061315	Naca	AL022831|AL024382|Gm1878|mKIAA0363|skNAC	nascent polypeptide-associated complex alpha polypeptide	protein-coding
mm_46872.1	chr5	113832497	113832512	-	1	NA	Intergenic	Intergenic	-2003	NM_009151	20345	Mm.332590	NM_009151	ENSMUSG00000048163	Selplg	CD162|Psgl-1|Psgl1|Selp1|Selpl	selectin, platelet (p-selectin) ligand	protein-coding
mm_15894.1	chr2	164947062	164947075	+	1	NA	Intergenic	Intergenic	-1151	NM_013599	17395	Mm.4406	NM_013599	ENSMUSG00000017737	Mmp9	AW743869|B/MMP9|Clg4b|Gel B|MMP-9|pro-MMP-9	matrix metallopeptidase 9	protein-coding
mm_51262.1	chr6	72097703	72097713	+	1	NA	promoter-TSS (NM_011375)	promoter-TSS (NM_011375)	100	NM_011375	20454	Mm.38248	NM_011375	ENSMUSG00000056091	St3gal5	3S-T|Siat9|[a]2	ST3 beta-galactoside alpha-2,3-sialyltransferase 5	protein-coding
mm_160043.1	chr6	140041495	140041495	+	1	NA	promoter-TSS (NM_054066)	promoter-TSS (NM_054066)	-30	NM_007605	12344	Mm.12817	NM_007605	ENSMUSG00000041791	Capza3	510-4|Cappa3|Gsg3|Tex8|repro32	capping protein (actin filament) muscle Z-line, alpha 3	protein-coding
mm_69124.1	chr7	127026464	127026474	-	1	NA	promoter-TSS (NM_010772)	promoter-TSS (NM_010772)	10	NM_010772	17188	Mm.378964	NM_010772	ENSMUSG00000030678	Maz	MAZI|PUR1|Pur-1|SAF-1|SAF-2	MYC-associated zinc finger protein (purine-binding transcription factor)	protein-coding
mm_8266.1	chr1	139377020	139377034	-	1	NA	promoter-TSS (NM_133239)	promoter-TSS (NM_133239)	49	NM_133239	170788	Mm.95700	NM_133239	ENSMUSG00000063681	Crb1	7530426H14Rik|A930008G09Rik	crumbs family member 1, photoreceptor morphogenesis associated	protein-coding
mm_89425.1	chr10	90934777	90934780	+	1	NA	intron (NM_001347053, intron 5 of 8)	intron (NM_001347053, intron 5 of 8)	104935	NM_001347053	77531	Mm.440605	NM_181398	ENSMUSG00000058589	Anks1b	AIDA-1b|C030032C09Rik|E530015N03Rik|ENSMUSG00000078431|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding
mm_161213.1	chr13	64758490	64758490	-	1	NA	intron (NM_001081129, intron 15 of 23)	intron (NM_001081129, intron 15 of 23)	145398	NM_001081129	238680	Mm.390590	NM_001081129	ENSMUSG00000033063	Cntnap3	-	contactin associated protein-like 3	protein-coding
mm_165777.1	chr3	129332525	129332536	-	1	NA	5' UTR (NM_007934, exon 1 of 20)	5' UTR (NM_007934, exon 1 of 20)	219	NM_007934	13809	Mm.1193	NM_007934	ENSMUSG00000028024	Enpep	6030431M22Rik|APA|Bp-1/6C3|Ly-51|Ly51	glutamyl aminopeptidase	protein-coding
mm_165039.1	chr19	38481015	38481033	+	1	NA	Intergenic	CpG	-43173	NM_019588	74055	Mm.34031	NM_019588	ENSMUSG00000024998	Plce1	4933403A21Rik|PLCepsilon|Plce|mKIAA1516	phospholipase C, epsilon 1	protein-coding
mm_163682.1	chr13	93563306	93563313	+	1	NA	Intergenic	MTC|LTR|ERVL-MaLR	-63501	NM_021310	57748	Mm.100273	NM_021310	ENSMUSG00000021690	Jmy	-	junction-mediating and regulatory protein	protein-coding
mm_41087.1	chr5	87682185	87682224	+	1	NA	3' UTR (NM_007784, exon 34 of 34)	3' UTR (NM_007784, exon 34 of 34)	15996	NM_001286016	12990	Mm.427467	NM_007784	ENSMUSG00000070702	Csn1s1	AA959832|AW212882|Csna	casein alpha s1	protein-coding
mm_31710.1	chr4	62619721	62619740	+	1	NA	promoter-TSS (NM_001081650)	promoter-TSS (NM_001081650)	58	NM_134257	50780	Mm.286753	NM_019492	ENSMUSG00000059810	Rgs3	4930506N09Rik|C2PA-RGS3|C2pa|PDZ-RGS3|RGS3S	regulator of G-protein signaling 3	protein-coding
mm_45017.1	chr5	38546464	38546472	-	1	NA	intron (NM_011715, intron 4 of 14)	U4|snRNA|snRNA	15127	NM_011715	22388	Mm.2654	NM_011715	ENSMUSG00000005103	Wdr1	Aip1|D5Wsu185e|rede	WD repeat domain 1	protein-coding
mm_35140.1	chr4	11386735	11386754	-	1	NA	promoter-TSS (NM_001290383)	promoter-TSS (NM_001290383)	34	NM_001347052	207920	Mm.387719	NM_194055	ENSMUSG00000040728	Esrp1	2210008M09Rik|A630065D16|BC031468|Rbm35a	epithelial splicing regulatory protein 1	protein-coding
mm_107557.1	chr12	41263235	41263238	+	1	NA	intron (NM_053122, intron 4 of 6)	intron (NM_053122, intron 4 of 6)	222821	NM_001271708	16981	Mm.404786	NM_010733	ENSMUSG00000036295	Lrrn3	NLRR-3	leucine rich repeat protein 3, neuronal	protein-coding
mm_162887.1	chr10	107705217	107705219	+	1	NA	intron (NM_001081432, intron 8 of 44)	intron (NM_001081432, intron 8 of 44)	14809	NM_001081432	237523	Mm.391418	NM_001081432	ENSMUSG00000035916	Ptprq	-	protein tyrosine phosphatase, receptor type, Q	protein-coding
mm_81983.1	chr9	121380659	121380678	+	1	NA	intron (NM_175114, intron 1 of 15)	intron (NM_175114, intron 1 of 15)	13710	NM_175114	67095	Mm.491112	NM_175114	ENSMUSG00000032536	Trak1	2310001H13Rik|AI413908|AI467545|hyrt|mKIAA1042	trafficking protein, kinesin binding 1	protein-coding
mm_136150.1	chr16	87612560	87612564	-	1	NA	Intergenic	Intergenic	59232	NM_144854	224419	Mm.194466	NM_144854	ENSMUSG00000025610	Map3k7cl	C21orf7|ORF63|Tak1l	Map3k7 C-terminal like	protein-coding
mm_12243.1	chr2	68863290	68863309	+	1	NA	intron (NM_172856, intron 1 of 9)	intron (NM_172856, intron 1 of 9)	1858	NM_001347161	241447	Mm.222222	NM_172856	ENSMUSG00000027035	Cers6	4732462C07Rik|AW544719|Lass6|T1L	ceramide synthase 6	protein-coding
mm_157298.1	chrX	20928099	20928117	-	1	NA	exon (NM_008823, exon 6 of 9)	exon (NM_008823, exon 6 of 9)	3447	NM_008823	18636	Mm.3064	NM_008823	ENSMUSG00000001128	Cfp	BCFG|Pfc	complement factor properdin	protein-coding
mm_147434.1	chr18	46465781	46465819	-	1	NA	promoter-TSS (NR_045438)	promoter-TSS (NR_045438)	16	NR_045438	72076	Mm.82766	NM_028086		Mospd4	2010013H21Rik	motile sperm domain containing 4	pseudo
mm_24216.1	chr3	88646863	88646888	+	1	NA	3' UTR (NM_001198913, exon 22 of 22)	3' UTR (NM_001198913, exon 22 of 22)	6267	NM_181817	242093	Mm.269130	NM_181817	ENSMUSG00000049741	Rxfp4	GPCR142|Gpr100|Rln3r2|SALPR	relaxin family peptide receptor 4	protein-coding
mm_158522.1	chrX	143827392	143827402	-	1	NA	promoter-TSS (NM_007603)	promoter-TSS (NM_007603)	15	NM_007603	12338	Mm.30290	NM_007603	ENSMUSG00000067276	Capn6	-	calpain 6	protein-coding
mm_79219.1	chr9	49340388	49340408	+	1	NA	promoter-TSS (NM_010077)	promoter-TSS (NM_010077)	-264	NM_010077	13489	Mm.41970	NM_010077	ENSMUSG00000032259	Drd2	D2R|Drd-2	dopamine receptor D2	protein-coding
mm_62050.1	chr7	92420788	92420791	+	1	NA	intron (NM_001243046, intron 9 of 14)	intron (NM_001243046, intron 9 of 14)	-140360	NM_025515	66365	Mm.21173	NM_025515	ENSMUSG00000030613	Ccdc90b	2310015N07Rik|C86558	coiled-coil domain containing 90B	protein-coding
mm_11724.1	chr2	36254690	36254697	+	1	NA	Intergenic	(GTGTG)n|Simple_repeat|Simple_repeat	24267	NM_008969	19224	Mm.275434	NM_008969	ENSMUSG00000047250	Ptgs1	COX1|Cox-1|Cox-3|PGHS-1|PHS 1|Pghs1	prostaglandin-endoperoxide synthase 1	protein-coding
mm_40436.1	chr5	53590454	53590529	+	1	NA	promoter-TSS (NM_001080927)	promoter-TSS (NM_001080927)	5	NM_001080927	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_101386.1	chr11	23895209	23895280	-	1	NA	promoter-TSS (NM_172555)	promoter-TSS (NM_172555)	26	NM_172555	216578	Mm.470599	NM_172555	ENSMUSG00000020273	Papolg	9630006B20Rik	poly(A) polymerase gamma	protein-coding
mm_6459.1	chr1	74026924	74026955	-	1	NA	intron (NM_027884, intron 3 of 34)	intron (NM_027884, intron 3 of 34)	97508	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_114300.1	chr13	59419585	59419590	+	1	NA	Intergenic	Intergenic	124864	NM_001284221	67269	Mm.153008	NM_023328	ENSMUSG00000021557	Agtpbp1	1700020N17Rik|2310001G17Rik|2900054O13Rik|4930445M19Rik|5730402G09Rik|CCP1|Nna1|nmf243|pcd	ATP/GTP binding protein 1	protein-coding
mm_120145.1	chr14	60386518	60386520	+	1	NA	Intergenic	Intergenic	8233	NM_001164705	72125	Mm.275499	NM_028113	ENSMUSG00000021986	Amer2	2600011E07Rik|Fam123a	APC membrane recruitment 2	protein-coding
mm_79655.1	chr9	59653602	59653624	+	1	NA	Intergenic	Intergenic	-2755	NM_011099	18746	Mm.326167	NM_011099	ENSMUSG00000032294	Pkm	AA414905|AL024370|AL024424|Pk-2|Pk-3|Pk3|Pkm2	pyruvate kinase, muscle	protein-coding
mm_159166.1	chr2	92230834	92230834	+	1	NA	intron (NM_001346704, intron 6 of 18)	intron (NM_001346704, intron 6 of 18)	9272	NM_001109690	192285	Mm.330408	NM_138755	ENSMUSG00000058318	Phf21a	80kDa|Bhc|Bhc80|D030065N23Rik|PFTF1	PHD finger protein 21A	protein-coding
mm_31014.1	chr4	40721140	40721148	+	1	NA	non-coding (NR_077226, exon 3 of 3)	non-coding (NR_077226, exon 3 of 3)	1173	NR_077221	622208	Mm.471544	NR_077221		Gm6297	-	predicted gene 6297	ncRNA
mm_102163.1	chr11	53769748	53769780	-	1	NA	promoter-TSS (NM_001159396)	promoter-TSS (NM_001159396)	-250	NM_001159393	16362	Mm.105218	NM_008390	ENSMUSG00000018899	Irf1	AU020929|Irf-1	interferon regulatory factor 1	protein-coding
mm_85951.1	chr9	112118641	112118643	-	1	NA	promoter-TSS (NR_029823)	promoter-TSS (NR_029823)	69	NR_029823	723815		NR_029823	ENSMUSG00000065441	Mir128-2	Mirn128-2|Mirn128b|mir-128-2|mir-128b	microRNA 128-2	ncRNA
mm_160892.1	chr11	70654562	70654562	-	1	NA	promoter-TSS (NM_011072)	promoter-TSS (NM_011072)	88	NM_011072	18643	Mm.2647	NM_011072	ENSMUSG00000018293	Pfn1	Pfn	profilin 1	protein-coding
mm_64091.1	chr7	140968221	140968237	+	1	NA	5' UTR (NM_001112715, exon 1 of 2)	5' UTR (NM_001112715, exon 1 of 2)	153	NM_001112715	68713	Mm.175661	NM_026820	ENSMUSG00000025491	Ifitm1	1110036C17Rik|DSPA2a|Mil-2|Mil2	interferon induced transmembrane protein 1	protein-coding
mm_2866.1	chr1	131744012	131744029	+	1	NA	promoter-TSS (NM_177243)	promoter-TSS (NM_177243)	-2	NM_177243	320718	Mm.482704	NM_177243	ENSMUSG00000042268	Slc26a9	E030002L01Rik	solute carrier family 26, member 9	protein-coding
mm_128802.1	chr15	66940217	66940229	-	1	NA	exon (NM_008681, exon 10 of 16)	exon (NM_008681, exon 10 of 16)	29418	NM_008681	17988	Mm.30837	NM_008681	ENSMUSG00000005125	Ndrg1	CAP43|CMT4D|DRG1|HMSNL|NMSL|Ndr1|Ndrl|PROXY1|RTP|TDD5	N-myc downstream regulated gene 1	protein-coding
mm_161774.1	chr17	37530187	37530187	+	1	NA	exon (NM_001005485, exon 1 of 1)	exon (NM_001005485, exon 1 of 1)	230	NM_001005485	545205	Mm.383371	NM_001005485	ENSMUSG00000090675	Olfr111	-	olfactory receptor 111	protein-coding
mm_85494.1	chr9	106136359	106136362	-	1	NA	Intergenic	Intergenic	-17764	NR_029549	387153		NR_029549	ENSMUSG00000065407	Mir135a-1	Mir135a01|Mirn135|Mirn135a-1|mir-135a-1	microRNA 135a-1	ncRNA
mm_151645.1	chr19	4042244	4042273	-	1	NA	promoter-TSS (NM_181796)	promoter-TSS (NM_181796)	-37	NM_181796	14869	Mm.441542	NM_181796	ENSMUSG00000038155	Gstp2	GSTpiA|Gst-3|Gst3	glutathione S-transferase, pi 2	protein-coding
mm_3113.1	chr1	134574471	134574474	+	1	NA	intron (NM_152895, intron 1 of 26)	B1F|SINE|Alu	14294	NM_152895	75605	Mm.28995	NM_152895	ENSMUSG00000042207	Kdm5b	2010009J12Rik|2210016I17Rik|AW556288|D1Ertd202e|Jarid1b|PLU-1|PUT1|Plu1|RBBP2H1A|Rb-Bp2|mKIAA4034	lysine (K)-specific demethylase 5B	protein-coding
mm_126486.1	chr15	81616760	81616776	+	1	NA	exon (NM_177821, exon 8 of 31)	exon (NM_177821, exon 8 of 31)	30554	NM_177821	328572	Mm.258397	NM_177821	ENSMUSG00000055024	Ep300	A430090G16|A730011L11|KAT3B|p300|p300 HAT	E1A binding protein p300	protein-coding
mm_92607.1	chr10	80117987	80117990	-	1	NA	intron (NR_126043, intron 1 of 10)	intron (NR_126043, intron 1 of 10)	2185	NM_001301854	20869	Mm.44231	NM_011492	ENSMUSG00000003068	Stk11	AA408040|Lkb1|Par-4|R75140	serine/threonine kinase 11	protein-coding
mm_170745.1	chr2	155531049	155531050	-	1	NA	intron (NM_019811, intron 2 of 17)	B1_Mus2|SINE|Alu	13006	NM_019811	60525	Mm.255026	NM_019811	ENSMUSG00000027605	Acss2	1110017C11Rik|ACAS|Acas1|Acas2|AceCS1|Acs1	acyl-CoA synthetase short-chain family member 2	protein-coding
mm_49962.1	chr6	40643528	40643529	+	1	NA	intron (NM_001171003, intron 2 of 47)	intron (NM_001171003, intron 2 of 47)	14697	NM_001171003	232714	Mm.33401	NM_001171003	ENSMUSG00000068587	Mgam	6030407P20Rik|MGA	maltase-glucoamylase	protein-coding
mm_13084.1	chr2	91207811	91207825	+	1	NA	exon (NM_007387, exon 8 of 11)	exon (NM_007387, exon 8 of 11)	4906	NM_007387	11432	Mm.45570	NM_007387	ENSMUSG00000002103	Acp2	Acp-2|LAP	acid phosphatase 2, lysosomal	protein-coding
mm_25250.1	chr3	104456624	104456625	+	1	NA	3' UTR (NM_001025067, exon 18 of 18)	3' UTR (NM_001025067, exon 18 of 18)	55294	NM_001310698	269473	Mm.34855	NM_001025067	ENSMUSG00000032913	Lrig2	4632419I10Rik|BB096938|LIG-2	leucine-rich repeats and immunoglobulin-like domains 2	protein-coding
mm_100690.1	chr11	3526452	3526477	-	1	NA	exon (NM_001284429, exon 13 of 22)	exon (NM_001284429, exon 13 of 22)	11780	NM_053267	114679	Mm.34046	NM_053267	ENSMUSG00000075702	Selenom	1500040L08Rik|A230103K18|Selm|Sepm	selenoprotein M	protein-coding
mm_91823.1	chr10	56115554	56115565	-	1	NA	exon (NM_001163833, exon 2 of 2)	exon (NM_001163833, exon 2 of 2)	8642	NM_001163833	73390	Mm.181475	NM_133751	ENSMUSG00000047669	Msl3l2	1700060H10Rik	male-specific lethal 3-like 2 (Drosophila)	protein-coding
mm_42834.1	chr5	122102849	122102881	+	1	NA	intron (NM_010861, intron 3 of 6)	intron (NM_010861, intron 3 of 6)	1885	NM_010861	17906	Mm.1529	NM_010861	ENSMUSG00000013936	Myl2	MLC-2|MLC-2s/v|MLC-2v|Mlc2v|Mylpc	myosin, light polypeptide 2, regulatory, cardiac, slow	protein-coding
mm_5515.1	chr1	37541004	37541046	-	1	NA	promoter-TSS (NM_173870)	promoter-TSS (NM_173870)	-9	NM_173870	269181	Mm.25861	NM_173870	ENSMUSG00000026110	Mgat4a	9530018I07Rik|GnT-IVa|glcNAc-T-IVa	mannoside acetylglucosaminyltransferase 4, isoenzyme A	protein-coding
mm_95328.1	chr11	46739828	46739840	+	1	NA	promoter-TSS (NM_001166632)	promoter-TSS (NM_001166632)	-389	NM_001166632	171283	Mm.17771	NM_134248	ENSMUSG00000040405	Havcr1	AI503787|KIM-1|TIM-1|Tim1|Timd1	hepatitis A virus cellular receptor 1	protein-coding
mm_51893.1	chr6	90619102	90619115	+	1	NA	promoter-TSS (NM_001037493)	promoter-TSS (NM_001037493)	-138	NM_001037493	71699	Mm.272633	NM_027868	ENSMUSG00000030089	Slc41a3	1010001P06Rik|AI480742|SLC41A1-L2	solute carrier family 41, member 3	protein-coding
mm_112802.1	chr13	20473095	20473109	+	1	NA	5' UTR (NM_198093, exon 1 of 7)	5' UTR (NM_198093, exon 1 of 7)	112	NM_198093	140580	Mm.342392	NM_080288	ENSMUSG00000041112	Elmo1	6330578D22Rik|C230095H21Rik|CED-12	engulfment and cell motility 1	protein-coding
mm_149949.1	chr19	27344770	27344782	+	1	NA	Intergenic	L2|LINE|L2	22157	NM_183179	240595	Mm.269759	NM_183179	ENSMUSG00000047298	Kcnv2	KV11.1	potassium channel, subfamily V, member 2	protein-coding
mm_17167.1	chr2	25291667	25291682	-	1	NA	TTS (NM_146117)	TTS (NM_146117)	454	NM_001242940	320354	Mm.445875	NM_001242940		Grin1os	E130003G02Rik	glutamate receptor, ionotropic, NMDA1 (zeta 1), opposite strand	protein-coding
mm_56028.1	chr6	86607661	86607678	-	1	NA	Intergenic	Intergenic	-20505	NM_026414	67855	Mm.183043	NM_026414	ENSMUSG00000033508	Asprv1	2300003P22Rik|AA986851|SASP|SASPase|Taps	aspartic peptidase, retroviral-like 1	protein-coding
mm_1609.1	chr1	74382468	74382480	+	1	NA	intron (NM_013612, intron 9 of 14)	intron (NM_013612, intron 9 of 14)	7271	NM_013612	18173	Mm.2913	NM_013612	ENSMUSG00000026177	Slc11a1	Bcg|Ity|Ity1|Lsh|Nramp|Nramp1|ity	solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1	protein-coding
mm_78347.1	chr9	25303734	25303766	+	1	NA	exon (NM_001205367, exon 11 of 13)	exon (NM_001205367, exon 11 of 13)	51311	NM_001205367	235072	Mm.270259	NM_009859	ENSMUSG00000001833	Sept7	Cdc10|E430034N22	septin 7	protein-coding
mm_65681.1	chr7	28338705	28338715	-	1	NA	promoter-TSS (NM_013676)	promoter-TSS (NM_013676)	9	NM_013676	20924	Mm.285906	NM_013676	ENSMUSG00000003435	Supt5	AL033283|AL033321|AU019549|Spt5|Supt5h	suppressor of Ty 5	protein-coding
mm_148536.1	chr19	4603075	4603079	+	1	NA	exon (NM_001162946, exon 8 of 21)	exon (NM_001162946, exon 8 of 21)	8758	NM_008797	18563	Mm.1845	NM_008797	ENSMUSG00000024892	Pcx	Pc|Pcb	pyruvate carboxylase	protein-coding
mm_83468.1	chr9	45272361	45272373	-	1	NA	Intergenic	Intergenic	-3218	NM_001324486	16154	Mm.379327	NM_008348	ENSMUSG00000032089	Il10ra	AW553859|CDw210|CDw210a|IL-10R1|IL-10RA|Il10r|mIL-10R	interleukin 10 receptor, alpha	protein-coding
mm_127224.1	chr15	99393952	99393988	+	1	NA	intron (NM_001171036, intron 2 of 10)	intron (NM_001171036, intron 2 of 10)	751	NM_001171035	110213	Mm.16769	NM_026669	ENSMUSG00000023010	Tmbim6	5031406P05Rik|Bi1|Tegt	transmembrane BAX inhibitor motif containing 6	protein-coding
mm_153678.1	chr19	44396582	44396597	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	11120	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_130368.1	chr15	97808416	97808431	-	1	NA	exon (NM_001204278, exon 8 of 24)	exon (NM_001204278, exon 8 of 24)	6440	NM_001204281	56233	Mm.384027	NM_019572	ENSMUSG00000022475	Hdac7	5830434K02Rik|HD7|HD7a|Hdac7a|mFLJ00062	histone deacetylase 7	protein-coding
mm_33184.1	chr4	126103941	126104020	+	1	NA	promoter-TSS (NM_028800)	promoter-TSS (NM_028800)	23	NM_001145827	74178	Mm.440269	NM_028800	ENSMUSG00000042608	Stk40	2310004N11Rik|AI428792	serine/threonine kinase 40	protein-coding
mm_47901.1	chr5	134915471	134915486	-	1	NA	promoter-TSS (NM_020504)	promoter-TSS (NM_020504)	52	NM_020504	57255	Mm.86652	NM_020504	ENSMUSG00000008843	Cldn13	2500004B14Rik	claudin 13	protein-coding
mm_139768.1	chr17	64634557	64634560	+	1	NA	intron (NM_008549, intron 3 of 21)	intron (NM_008549, intron 3 of 21)	32909	NM_008549	17158	Mm.2433	NM_008549	ENSMUSG00000024085	Man2a1	Mana-2|Mana2|Map-2	mannosidase 2, alpha 1	protein-coding
mm_62223.1	chr7	98490558	98490596	+	1	NA	Intergenic	Intergenic	-3645	NM_001113379	434215	Mm.323057	NM_001113379	ENSMUSG00000090958	Lrrc32	AI426318|D11S833Eh|D7H11S833E|EG434215|Garp	leucine rich repeat containing 32	protein-coding
mm_18499.1	chr2	62610499	62610536	-	1	NA	exon (NM_027835, exon 7 of 16)	exon (NM_027835, exon 7 of 16)	35738	NM_027835	71586	Mm.136224	NM_027835	ENSMUSG00000026896	Ifih1	9130009C22Rik|Helicard|Hlcd|MDA5|RLR-2	interferon induced with helicase C domain 1	protein-coding
mm_14165.1	chr2	126607753	126607807	+	1	NA	intron (NM_008230, intron 2 of 11)	intron (NM_008230, intron 2 of 11)	10898	NM_008230	15186	Mm.18603	NM_008230	ENSMUSG00000027360	Hdc	AW108189|Hdc-a|Hdc-c|Hdc-e|Hdc-s	histidine decarboxylase	protein-coding
mm_41470.1	chr5	91450032	91450040	+	1	NA	Intergenic	Intergenic	-47042	NM_007568	12223	Mm.2024	NM_007568	ENSMUSG00000082361	Btc	Bcn	betacellulin, epidermal growth factor family member	protein-coding
mm_159037.1	chr1	179961156	179961156	+	1	NA	promoter-TSS (NM_001033285)	promoter-TSS (NM_001033285)	67	NM_001033285	226751	Mm.259655	NM_001033285	ENSMUSG00000026490	Cdc42bpa	A930014J19Rik|DMPK-like	CDC42 binding protein kinase alpha	protein-coding
mm_105175.1	chr11	101784814	101784833	-	1	NA	intron (NM_008815, intron 1 of 12)	CpG-2651	487	NM_008815	18612	Mm.5025	NM_008815	ENSMUSG00000017724	Etv4	AW414408|Pea-3|Pea3	ets variant 4	protein-coding
mm_18843.1	chr2	75191855	75191855	-	1	NA	Intergenic	Intergenic	252324	NR_040635	77269	Mm.389278	NR_040635		9430019J16Rik	-	RIKEN cDNA 9430019J16 gene	ncRNA
mm_153042.1	chr19	32061439	32061465	-	1	NA	intron (NM_018830, intron 2 of 23)	intron (NM_018830, intron 2 of 23)	41688	NM_018830	54447	Mm.491229	NM_018830	ENSMUSG00000024887	Asah2	AI585898	N-acylsphingosine amidohydrolase 2	protein-coding
mm_153878.1	chr19	46908646	46908649	-	1	NA	intron (NM_001164365, intron 3 of 17)	B1_Mur1|SINE|Alu	53704	NM_029810	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_4780.1	chr1	183600763	183600771	+	1	NA	Intergenic	Intergenic	181519	NM_001308052	78772	Mm.29003	NM_030175	ENSMUSG00000053461	Hhipl2	4930507C10Rik|AW208802|Hhip3	hedgehog interacting protein-like 2	protein-coding
mm_105206.1	chr11	102101318	102101321	-	1	NA	promoter-TSS (NM_008918)	promoter-TSS (NM_008918)	-19	NM_008918	19064	Mm.1269	NM_008918	ENSMUSG00000017316	Ppy	AV061413|IGSPP|PP	pancreatic polypeptide	protein-coding
mm_161417.1	chr15	33090253	33090253	+	1	NA	intron (NM_176073, intron 1 of 7)	(TTTTTG)n|Simple_repeat|Simple_repeat	7124	NM_176073	54381	Mm.158251	NM_018755	ENSMUSG00000039007	Cpq	1190003P12Rik|2610034C17Rik|Hls2|Lal-1|Pgcp	carboxypeptidase Q	protein-coding
mm_26179.1	chr3	138290595	138290630	+	1	NA	TTS (NM_007409)	TTS (NM_007409)	12967	NM_007409	11522	Mm.2409	NM_007409	ENSMUSG00000074207	Adh1	ADH-AA|AI194826|Adh-1|Adh-1-t|Adh-1e|Adh-1t|Adh-3e|Adh1-e|Adh1-t|Adh1tl|Adh3-e	alcohol dehydrogenase 1 (class I)	protein-coding
mm_5489.1	chr1	36932061	36932065	-	1	NA	intron (NM_018872, intron 1 of 40)	PB1D10|SINE|Alu	7464	NM_018872	56030	Mm.186943	NM_018872	ENSMUSG00000026116	Tmem131	2610524E03Rik|CC28|D1Bwg0491e|Neg|RW1|YR-23|mKIAA0257	transmembrane protein 131	protein-coding
mm_161523.1	chr15	100551758	100551758	-	1	NA	intron (NM_033476, intron 1 of 15)	CpG	250	NM_033476	21422	Mm.219040	NM_033476	ENSMUSG00000009733	Tfcp2	CP-2|CP2|D230015P20Rik|LBP-1c|LBP-1d|LBP1|LSF|Tcfcp2|UBP-1	transcription factor CP2	protein-coding
mm_37080.1	chr4	116371725	116371743	-	1	NA	intron (NM_008641, intron 4 of 28)	intron (NM_008641, intron 4 of 28)	92447	NM_001042743	17776	Mm.9287	NM_008641	ENSMUSG00000003810	Mast2	MAST205|Mtssk	microtubule associated serine/threonine kinase 2	protein-coding
mm_151141.1	chr19	53062316	53062326	+	1	NA	Intergenic	B3A|SINE|B2	-13931	NR_045320	78457	Mm.76932	NR_045320	ENSMUSG00000099988	1700054A03Rik	-	RIKEN cDNA 1700054A03 gene	ncRNA
mm_122215.1	chr14	32201888	32201908	-	1	NA	promoter-TSS (NM_011960)	promoter-TSS (NM_011960)	-7	NM_016897	53600	Mm.303703	NM_016897	ENSMUSG00000013701	Timm23	Tim23	translocase of inner mitochondrial membrane 23	protein-coding
mm_171415.1	chr4	130360148	130360149	+	1	NA	promoter-TSS (NM_025645)	promoter-TSS (NM_025645)	16	NM_025645	66585	Mm.423019	NM_025645	ENSMUSG00000074088	Snrnp40	0610009C03Rik|Prp8bp|Wdr57	small nuclear ribonucleoprotein 40 (U5)	protein-coding
mm_86536.1	chr10	7862091	7862103	+	1	NA	intron (NM_172785, intron 3 of 5)	intron (NM_172785, intron 3 of 5)	25716	NR_039563	100628581		NR_039563	ENSMUSG00000093060	Mir5104	mir-5104|mmu-mir-5104|mu-mir-5104	microRNA 5104	ncRNA
mm_54639.1	chr6	38819284	38819294	-	1	NA	exon (NM_010433, exon 2 of 15)	exon (NM_010433, exon 2 of 15)	18022	NM_001136065	15258	Mm.23790	NM_010433	ENSMUSG00000061436	Hipk2	1110014O20Rik|B230339E18Rik|Stank	homeodomain interacting protein kinase 2	protein-coding
mm_2059.1	chr1	87470309	87470330	+	1	NA	promoter-TSS (NM_028473)	promoter-TSS (NM_028473)	55	NM_028473	73234	Mm.7310	NM_028473	ENSMUSG00000026258	3110079O15Rik	Snorc	RIKEN cDNA 3110079O15 gene	protein-coding
mm_122594.1	chr14	50930262	50930283	-	1	NA	exon (NM_001033271, exon 2 of 7)	exon (NM_001033271, exon 2 of 7)	577	NM_001310506	219024	Mm.239117	NM_001033271	ENSMUSG00000035953	Tmem55b	BC039161	transmembrane protein 55b	protein-coding
mm_55830.1	chr6	83124830	83124843	-	1	NA	intron (NM_023547, intron 1 of 4)	intron (NM_023547, intron 1 of 4)	193	NM_023547	70020	Mm.27814	NM_023547	ENSMUSG00000030034	Ino80b	2510009I23Rik|HMG1YL4|Hmga1l4|Papa1|Znhit4	INO80 complex subunit B	protein-coding
mm_119894.1	chr14	54938432	54938437	+	1	NA	intron (NM_026066, intron 2 of 4)	intron (NM_026066, intron 2 of 4)	1937	NM_029390	67272	Mm.41614	NM_026066	ENSMUSG00000040759	Cmtm5	1500005P16Rik|2900052H21Rik|Cklfsf5	CKLF-like MARVEL transmembrane domain containing 5	protein-coding
mm_127277.1	chr15	99725770	99725815	+	1	NA	TTS (NM_010271)	TTS (NM_010271)	174	NM_183256	66379	Mm.5265	NM_183256	ENSMUSG00000023020	Cox14	2310016M24Rik|AA959804	cytochrome c oxidase assembly protein 14	protein-coding
mm_28621.1	chr3	95025347	95025367	-	1	NA	Intergenic	RMER17A2|LTR|ERVK	-10119	NM_030074	78266	Mm.389478	NM_030074	ENSMUSG00000019338	Zfp687	4931408L03Rik|Znf687|mKIAA1441	zinc finger protein 687	protein-coding
mm_110385.1	chr12	40248020	40248067	-	1	NA	Intergenic	Intergenic	24679	NR_045157	629820	Mm.435540	NR_045157	ENSMUSG00000035983	Gm7008	EG629820	predicted gene 7008	ncRNA
mm_102709.1	chr11	67011653	67011665	-	1	NA	Intergenic	Intergenic	-13495	NM_001291042	338369	Mm.128138	NM_177392	ENSMUSG00000050270	Tmem220	-	transmembrane protein 220	protein-coding
mm_109253.1	chr12	109459639	109459684	+	1	NA	exon (NM_010052, exon 5 of 5)	exon (NM_010052, exon 5 of 5)	6206	NM_010052	13386	Mm.157069	NM_010052	ENSMUSG00000040856	Dlk1	AW742678|DLK-1|DlkI|FA1|Ly107|Peg9|SCP1|ZOG|pG2|pref-1	delta-like 1 homolog (Drosophila)	protein-coding
mm_171117.1	chr3	138844792	138844800	-	1	NA	intron (NM_019571, intron 1 of 7)	intron (NM_019571, intron 1 of 7)	102588	NM_019571	56224	Mm.31927	NM_019571	ENSMUSG00000028152	Tspan5	2810455A09Rik|4930505M03Rik|NET-4|Tm4sf9	tetraspanin 5	protein-coding
mm_80384.1	chr9	75441519	75441575	+	1	NA	promoter-TSS (NM_001039522)	promoter-TSS (NM_001039522)	23	NM_001039522	235497	Mm.41508	NM_001006122	ENSMUSG00000042487	Leo1	Gm185	Leo1, Paf1/RNA polymerase II complex component	protein-coding
mm_37517.1	chr4	124299862	124299877	-	1	NA	Intergenic	Intergenic	186090	NR_040774	78460	Mm.452060	NR_040774		1700057H15Rik	-	RIKEN cDNA 1700057H15 gene	ncRNA
mm_123282.1	chr14	61436800	61436810	-	1	NA	intron (NM_008466, intron 1 of 16)	(A)n|Simple_repeat|Simple_repeat	3142	NM_008466	16648	Mm.25548	NM_008466	ENSMUSG00000021929	Kpna3	IPOA4	karyopherin (importin) alpha 3	protein-coding
mm_44053.1	chr5	147957311	147957357	+	1	NA	promoter-TSS (NM_029920)	promoter-TSS (NM_029920)	14	NM_029920	77521	Mm.244177	NM_029920	ENSMUSG00000029651	Mtus2	5730592G18Rik|A730013O20Rik|AU067634|C130038G02Rik|Cazip|Gm763|mKIAA0774	microtubule associated tumor suppressor candidate 2	protein-coding
mm_101176.1	chr11	16994738	16994776	-	1	NA	exon (NM_019549, exon 3 of 10)	exon (NM_019549, exon 3 of 10)	13961	NM_019549	56193	Mm.98232	NM_019549	ENSMUSG00000020120	Plek	2010300B13Rik	pleckstrin	protein-coding
mm_105706.1	chr11	108273686	108273727	-	1	NA	intron (NM_011101, intron 2 of 16)	intron (NM_011101, intron 2 of 16)	70182	NM_011101	18750	Mm.222178	NM_011101	ENSMUSG00000050965	Prkca	AI875142|Pkca	protein kinase C, alpha	protein-coding
mm_78710.1	chr9	41396280	41396280	+	1	NA	intron (NR_131929, intron 3 of 4)	intron (NR_131929, intron 3 of 4)	19754	NR_131928	73144	Mm.38166	NM_001033153	ENSMUSG00000074415	3110039I08Rik	2610203C20Rik|AI848448|D230004N17Rik|D3Mgi9|Mir100hg	RIKEN cDNA 3110039I08 gene	ncRNA
mm_82464.1	chr9	15710214	15710235	-	1	NA	intron (NM_172289, intron 1 of 10)	(TCTG)n|Simple_repeat|Simple_repeat	455	NM_172289	234967	Mm.138815	NM_172289	ENSMUSG00000043885	Slc36a4	6330573I15Rik|PAT4	solute carrier family 36 (proton/amino acid symporter), member 4	protein-coding
mm_59868.1	chr7	30193930	30193957	+	1	NA	exon (NM_009795, exon 2 of 11)	exon (NM_009795, exon 2 of 11)	1105	NM_009795	12336	Mm.439782	NM_009795	ENSMUSG00000001794	Capns1	Capa-4|Capa4|Capn4|D7Ertd146e	calpain, small subunit 1	protein-coding
mm_77925.1	chr9	7352958	7352985	+	1	NA	exon (NM_008605, exon 5 of 10)	exon (NM_008605, exon 5 of 10)	5597	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_109937.1	chr12	11204376	11204387	-	1	NA	non-coding (NR_131085, exon 1 of 3)	non-coding (NR_131085, exon 1 of 3)	121	NR_131084	77442	Mm.159922	NR_131083		9530020I12Rik	-	RIKEN cDNA 9530020I12 gene	ncRNA
mm_170892.1	chr2	27407018	27407036	-	1	NA	intron (NM_009500, intron 1 of 27)	intron (NM_009500, intron 1 of 27)	20581	NR_133905	22325	Mm.179011	NM_009500	ENSMUSG00000009621	Vav2	2810040F13Rik|AI847175|Vav-2	vav 2 oncogene	protein-coding
mm_32524.1	chr4	108847898	108847925	+	1	NA	promoter-TSS (NM_029571)	promoter-TSS (NM_029571)	54	NM_029571	100087	Mm.440007	NM_029571	ENSMUSG00000073775	Kti12	1110001A12Rik|AI326810|AU014758	KTI12 homolog, chromatin associated	protein-coding
mm_34352.1	chr4	144529538	144529563	+	1	NA	TTS (NM_198662)	TTS (NM_198662)	9728	NM_198662	381572	Mm.184290	NM_198662	ENSMUSG00000028593	9430007A20Rik	Aadacl4|Gm1034	RIKEN cDNA 9430007A20 gene	protein-coding
mm_110714.1	chr12	69475511	69475555	-	1	NA	promoter-TSS (NR_038060)	promoter-TSS (NR_038060)	17	NR_038060	76062	Mm.380755	NR_038060		5830428M24Rik	100040862|Gm3007	RIKEN cDNA 5830428M24 gene	ncRNA
mm_131584.1	chr16	18429809	18429820	+	1	NA	exon (NM_013711, exon 2 of 18)	exon (NM_013711, exon 2 of 18)	-3098	NM_001111062	12846	Mm.100940	NM_007744	ENSMUSG00000000326	Comt	Comt1|D16Wsu103e|D330014B15Rik	catechol-O-methyltransferase	protein-coding
mm_42390.1	chr5	114937028	114937045	+	1	NA	exon (NM_145209, exon 7 of 7)	exon (NM_145209, exon 7 of 7)	-5166	NM_028211	72357	Mm.292672	NM_028211	ENSMUSG00000029559	2210016L21Rik	-	RIKEN cDNA 2210016L21 gene	protein-coding
mm_452.1	chr1	36104860	36104873	+	1	NA	3' UTR (NM_015818, exon 2 of 2)	3' UTR (NM_015818, exon 2 of 2)	36466	NM_015818	50785	Mm.213566	NM_015818	ENSMUSG00000045216	Hs6st1	6Ost1	heparan sulfate 6-O-sulfotransferase 1	protein-coding
mm_56178.1	chr6	88161045	88161053	-	1	NA	Intergenic	Intergenic	-37615	NM_008090	14461	Mm.491156	NM_008090	ENSMUSG00000015053	Gata2	Gata-2	GATA binding protein 2	protein-coding
mm_81461.1	chr9	109849303	109849311	+	1	NA	exon (NM_009921, exon 1 of 4)	exon (NM_009921, exon 1 of 4)	149	NM_009921	12796	Mm.3834	NM_009921	ENSMUSG00000038357	Camp	CAP18|Cnlp|Cramp|FALL39|MCLP	cathelicidin antimicrobial peptide	protein-coding
mm_25395.1	chr3	107219708	107219730	+	1	NA	exon (NM_001111143, exon 2 of 9)	exon (NM_001111143, exon 2 of 9)	2013	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_83925.1	chr9	56621330	56621338	-	1	NA	intron (NM_181074, intron 3 of 3)	intron (NM_181074, intron 3 of 3)	14314	NM_001311076	235402	Mm.246605	NM_181074	ENSMUSG00000049556	Lingo1	4930471K13Rik|AV148400|LERN1|LINGO-1|Lrrn6a|UNQ201	leucine rich repeat and Ig domain containing 1	protein-coding
mm_7798.1	chr1	131525312	131525351	-	1	NA	5' UTR (NM_001081011, exon 2 of 23)	5' UTR (NM_001081011, exon 2 of 23)	2030	NM_001081011	14270	Mm.276259	NM_019520	ENSMUSG00000026425	Srgap2	9930124L22Rik|AI448945|FBP2|Fnbp2|srGAP3	SLIT-ROBO Rho GTPase activating protein 2	protein-coding
mm_21396.1	chr2	157569505	157569515	-	1	NA	Intergenic	(A)n|Simple_repeat|Simple_repeat	-3149	NM_016916	53619	Mm.480461	NM_016916	ENSMUSG00000067787	Blcap	AI462828|Bc10	bladder cancer associated protein	protein-coding
mm_25507.1	chr3	109574002	109574017	+	1	NA	promoter-TSS (NM_146139)	promoter-TSS (NM_146139)	2	NM_146139	57257	Mm.282257	NM_020505	ENSMUSG00000033721	Vav3	A530094I06Rik|AA986410|Idd18.1	vav 3 oncogene	protein-coding
mm_38663.1	chr4	144438763	144438763	-	1	NA	promoter-TSS (NM_027056)	promoter-TSS (NM_027056)	9	NM_027056	69364	Mm.158267	NM_027056	ENSMUSG00000028589	1700012P22Rik	-	RIKEN cDNA 1700012P22 gene	protein-coding
mm_102331.1	chr11	57829050	57829065	-	1	NA	3' UTR (NM_008213, exon 2 of 2)	3' UTR (NM_008213, exon 2 of 2)	3090	NM_008213	15110	Mm.4746	NM_008213	ENSMUSG00000037335	Hand1	Ehand1|Hxt|Th1|Thing1|bHLHa27|eHAND	heart and neural crest derivatives expressed transcript 1	protein-coding
mm_63786.1	chr7	132405967	132405977	+	1	NA	Intergenic	Intergenic	-88817	NM_029935	77590	Mm.213582	NM_029935	ENSMUSG00000030930	Chst15	4631426J05Rik|BRAG|GalNAcS-6ST|MAd5|mKIAA0598	carbohydrate (N-acetylgalactosamine 4-sulfate 6-O) sulfotransferase 15	protein-coding
mm_53372.1	chr6	129416744	129416768	+	1	NA	intron (NM_001205363, intron 4 of 6)	RMER17C|LTR|ERVK	7894	NM_172732	232414	Mm.391518	NM_172732	ENSMUSG00000046080	Clec9a	9830005G06Rik|DNGR-1	C-type lectin domain family 9, member a	protein-coding
mm_147580.1	chr18	56468996	56469007	-	1	NA	intron (NM_026240, intron 1 of 13)	MIRb|SINE|MIR	36869	NM_026240	107022	Mm.24356	NM_026240	ENSMUSG00000001700	Gramd3	9030613F08Rik|9130427A09Rik|AW061306|NS3TP2	GRAM domain containing 3	protein-coding
mm_173060.1	chrX	127548087	127548096	-	1	NA	Intergenic	RLTR9E|LTR|ERVK	153798	NR_003646	245598	Mm.72281	NM_207250	ENSMUSG00000049815	4921511C20Rik	Gm383	high density lipoprotein (HDL) binding protein pseudogene	pseudo
mm_39916.1	chr5	31485859	31485865	+	1	NA	promoter-TSS (NM_026296)	promoter-TSS (NM_026296)	3	NM_026296	67656	Mm.23355	NM_026296	ENSMUSG00000029138	4930548H24Rik	AI427865	RIKEN cDNA 4930548H24 gene	protein-coding
mm_149707.1	chr19	21653105	21653109	+	1	NA	promoter-TSS (NM_025423)	promoter-TSS (NM_025423)	-202	NM_146096	226016	Mm.28796	NM_146096	ENSMUSG00000047368	Abhd17b	5730446C15Rik|Cgi67|Fam108b|Fam108b1	abhydrolase domain containing 17B	protein-coding
mm_48209.1	chr5	137601044	137601075	-	1	NA	promoter-TSS (NM_030037)	promoter-TSS (NM_030037)	0	NM_030037	68929	Mm.41355	NM_030037	ENSMUSG00000037221	Mospd3	1190005J19Rik|5133401H10Rik|Gtig2|R124	motile sperm domain containing 3	protein-coding
mm_122018.1	chr14	27428656	27428682	-	1	NA	promoter-TSS (NM_001114879)	promoter-TSS (NM_001114879)	-178	NM_028945	218850	Mm.247767	NM_028945	ENSMUSG00000040651	Fam208a	4732418E12|4933409E02Rik|D14Abb1e|MommeD6	family with sequence similarity 208, member A	protein-coding
mm_50610.1	chr6	49586820	49586842	+	1	NA	Intergenic	Intergenic	191227	NM_029916	77485	Mm.128054	NM_029916	ENSMUSG00000023403	Stk31	C330007K24Rik	serine threonine kinase 31	protein-coding
mm_126146.1	chr15	78349169	78349193	+	1	NA	TTS (NR_106138)	TTS (NR_106138)	582	NR_106138	102466845		NR_106138	ENSMUSG00000099059	Mir7676-2	Gm27790|mmu-mir-7676-2	microRNA 7676-2	ncRNA
mm_50760.1	chr6	53573353	53573359	+	1	NA	promoter-TSS (NM_172728)	promoter-TSS (NM_172728)	-18	NM_172728	231991	Mm.227444	NM_172728	ENSMUSG00000053007	Creb5	9430076C15Rik|CRE-BPa|Crebpa|D430026C09Rik	cAMP responsive element binding protein 5	protein-coding
mm_89161.1	chr10	86123475	86123482	+	1	NA	intron (NM_013722, intron 7 of 13)	intron (NM_013722, intron 7 of 13)	27624	NR_038024	78170	Mm.444790	NR_038024		4930486F22Rik	-	RIKEN cDNA 4930486F22 gene	ncRNA
mm_44972.1	chr5	36815526	36815557	-	1	NA	exon (NM_008550, exon 11 of 19)	exon (NM_008550, exon 11 of 19)	15108	NM_008550	17160	Mm.761	NM_008550	ENSMUSG00000029119	Man2b2	mKIAA0935	mannosidase 2, alpha B2	protein-coding
mm_121987.1	chr14	26442623	26442691	-	1	NA	intron (NM_001347494, intron 10 of 19)	intron (NM_001347494, intron 10 of 19)	85110	NR_038005	71106	Mm.158564	NR_038005	ENSMUSG00000021874	4933413J09Rik	GCSE	RIKEN cDNA 4933413J09 gene	ncRNA
mm_123321.1	chr14	62760889	62760901	-	1	NA	5' UTR (NM_008715, exon 1 of 19)	5' UTR (NM_008715, exon 1 of 19)	217	NM_008715	18130	Mm.319684	NM_008715	ENSMUSG00000035161	Ints6	2900075H24Rik|AI480962|DICE1|Ddx26|HDB|Notch2l	integrator complex subunit 6	protein-coding
mm_106337.1	chr11	118393092	118393120	-	1	NA	exon (NM_011150, exon 6 of 6)	exon (NM_011150, exon 6 of 6)	8825	NM_011150	19039	Mm.3152	NM_011150	ENSMUSG00000033880	Lgals3bp	90K|CyCAP|MAC-2BP|Ppicap|Tango10b	lectin, galactoside-binding, soluble, 3 binding protein	protein-coding
mm_3599.1	chr1	151571430	151571440	+	1	NA	promoter-TSS (NM_022018)	promoter-TSS (NM_022018)	62	NM_022018	63913	Mm.157700	NM_022018	ENSMUSG00000026483	Fam129a	AI256368|AU019833|Niban	family with sequence similarity 129, member A	protein-coding
mm_32040.1	chr4	95967118	95967145	+	1	NA	promoter-TSS (NR_045777)	promoter-TSS (NR_045777)	-96	NR_045777	319247	Mm.473527	NM_175680	ENSMUSG00000044125	9530080O11Rik	-	RIKEN cDNA 9530080O11 gene	ncRNA
mm_108683.1	chr12	86832675	86832722	+	1	NA	Intergenic	Intergenic	52116	NM_145836	238330	Mm.248358	NM_145836	ENSMUSG00000034168	Irf2bpl	6430527G18Rik|Eap1	interferon regulatory factor 2 binding protein-like	protein-coding
mm_152775.1	chr19	21170950	21170956	-	1	NA	Intergenic	Intergenic	66243	NR_126458	75354	Mm.243873	NR_126458		4930554I06Rik	-	RIKEN cDNA 4930554I06 gene	ncRNA
mm_83894.1	chr9	56136246	56136286	-	1	NA	3' UTR (NM_019793, exon 7 of 7)	3' UTR (NM_019793, exon 7 of 7)	24804	NM_019793	56434	Mm.28484	NM_019793	ENSMUSG00000032324	Tspan3	1700055K04Rik|TM4-A|Tm4sf8	tetraspanin 3	protein-coding
mm_21137.1	chr2	154214044	154214056	-	1	NA	exon (NM_153418, exon 11 of 16)	exon (NM_153418, exon 11 of 16)	-9692	NM_144890	228802	Mm.167411	NM_144890	ENSMUSG00000038572	Bpifb5	Lplunc5	BPI fold containing family B, member 5	protein-coding
mm_57374.1	chr6	124812891	124812916	-	1	NA	exon (NM_009415, exon 2 of 7)	exon (NM_009415, exon 2 of 7)	1393	NM_009415	21991	Mm.4222	NM_009415	ENSMUSG00000023456	Tpi1	AI255506|Tpi|Tpi-1	triosephosphate isomerase 1	protein-coding
mm_107878.1	chr12	69986413	69986429	+	1	NA	intron (NM_022028, intron 1 of 4)	intron (NM_022028, intron 1 of 4)	581	NM_022028	64010	Mm.390480	NM_022028	ENSMUSG00000021067	Sav1	1700040G09Rik|Salv|Sav|WW45|Wwp3|Wwp4	salvador family WW domain containing 1	protein-coding
mm_11010.1	chr2	26581051	26581061	+	1	NA	promoter-TSS (NM_178444)	promoter-TSS (NM_178444)	0	NM_178444	353156	Mm.268933	NM_178444	ENSMUSG00000026921	Egfl7	VE-statin|Zneu1	EGF-like domain 7	protein-coding
mm_158450.1	chrX	140543144	140543153	-	1	NA	promoter-TSS (NM_010286)	promoter-TSS (NM_010286)	39	NM_010286	14605	Mm.22216	NM_010286	ENSMUSG00000031431	Tsc22d3	DIP|Dsip1|Gilz|TSC-22R|Tilz3	TSC22 domain family, member 3	protein-coding
mm_60026.1	chr7	30957135	30957137	+	1	NA	promoter-TSS (NM_011680)	promoter-TSS (NM_011680)	-333	NM_011680	22282	Mm.322453	NM_011680	ENSMUSG00000058239	Usf2	Usf-2|bHLHb12	upstream transcription factor 2	protein-coding
mm_11248.1	chr2	29890535	29890545	+	1	NA	intron (NM_013615, intron 1 of 16)	CpG	477	NM_013615	18286	Mm.330116	NM_013615	ENSMUSG00000026790	Odf2	AI848335|MMTEST29	outer dense fiber of sperm tails 2	protein-coding
mm_53169.1	chr6	125342529	125342545	+	1	NA	intron (NM_011324, intron 7 of 11)	intron (NM_011324, intron 7 of 11)	-7186	NM_011609	21937	Mm.1258	NM_011609	ENSMUSG00000030341	Tnfrsf1a	CD120a|FPF|TNF-R|TNF-R-I|TNF-R1|TNF-R55|TNF-alphaR1|TNFAR|TNFR60|TNFRI|TNFRp55|TNFalpha-R1|Tnfr-2|Tnfr1|p55|p55-R	tumor necrosis factor receptor superfamily, member 1a	protein-coding
mm_143236.1	chr17	63500251	63500268	-	1	NA	5' UTR (NM_015794, exon 1 of 9)	5' UTR (NM_015794, exon 1 of 9)	321	NM_015794	50758	Mm.136366	NM_015794	ENSMUSG00000023965	Fbxl17	6330576B01Rik|AI452053|BB073797|C130023C01Rik|Fbx13|Fbxo13	F-box and leucine-rich repeat protein 17	protein-coding
mm_3844.1	chr1	160044898	160044923	+	1	NA	intron (NM_001162896, intron 1 of 2)	intron (NM_001162896, intron 1 of 2)	530	NM_001162896	67647	Mm.171518	NM_001024470	ENSMUSG00000090394	4930523C07Rik	-	RIKEN cDNA 4930523C07 gene	protein-coding
mm_50638.1	chr6	51329891	51329920	+	1	NA	Intergenic	Intergenic	-49805	NR_110455	625167	Mm.389772	NR_110455	ENSMUSG00000107660	Gm6559	EG625167	predicted gene 6559	ncRNA
mm_84074.1	chr9	58201903	58201913	-	1	NA	promoter-TSS (NM_001161540)	promoter-TSS (NM_001161540)	-109	NM_001161540	320563	Mm.186499	NM_177193	ENSMUSG00000051243	Islr2	B930052A04Rik|Linx|Mbu-3|mKIAA1465	immunoglobulin superfamily containing leucine-rich repeat 2	protein-coding
mm_94138.1	chr10	128704979	128705049	-	1	NA	promoter-TSS (NM_016756)	promoter-TSS (NM_016756)	37	NM_183417	12566	Mm.111326	NM_016756	ENSMUSG00000025358	Cdk2	A630093N05Rik	cyclin-dependent kinase 2	protein-coding
mm_170096.1	chr17	39842992	39843006	+	1	NA	promoter-TSS (NR_046233)	promoter-TSS (NR_046233)	2	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_58780.1	chr7	16061902	16061913	+	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	-9938	NM_001347559	666528	Mm.290718	NM_001099277	ENSMUSG00000078796	Zfp541	EG666528|Znf541	zinc finger protein 541	protein-coding
mm_28545.1	chr3	92870216	92870224	-	1	NA	promoter-TSS (NM_025621)	promoter-TSS (NM_025621)	-15	NM_025621	66533	Mm.144259	NM_025621	ENSMUSG00000090314	2310050C09Rik	-	RIKEN cDNA 2310050C09 gene	protein-coding
mm_168915.1	chr1	25662049	25662054	+	1	NA	intron (NM_175642, intron 2 of 30)	intron (NM_175642, intron 2 of 30)	167656	NM_175642	210933	Mm.336569	NM_175642	ENSMUSG00000033569	Adgrb3	A830096D10Rik|Bai3	adhesion G protein-coupled receptor B3	protein-coding
mm_107856.1	chr12	69538287	69538299	+	1	NA	Intergenic	Intergenic	44735	NM_001033236	207965	Mm.102487	NM_001033236	ENSMUSG00000049882	Vcpkmt	Gm71|Mettl21d|Mettl221d|VCP-KMT	valosin containing protein lysine (K) methyltransferase	protein-coding
mm_96432.1	chr11	67294550	67294564	+	1	NA	exon (NM_177369, exon 22 of 40)	exon (NM_177369, exon 22 of 40)	17433	NM_177369	17885	Mm.340163	NM_177369	ENSMUSG00000055775	Myh8	4832426G23Rik|AI327267|MHCp|MyHC-pn|Myhs-p|Myhsp	myosin, heavy polypeptide 8, skeletal muscle, perinatal	protein-coding
mm_91797.1	chr10	53398746	53398756	-	1	NA	Intergenic	Intergenic	-18900	NM_001204983	100038725	Mm.441403	NM_001204983	ENSMUSG00000038594	Cep85l	ENSMUSG00000038594|Gm9766	centrosomal protein 85-like	protein-coding
mm_152660.1	chr19	12796109	12796146	-	1	NA	promoter-TSS (NM_053009)	promoter-TSS (NM_053009)	-4	NM_053009	109910	Mm.290924	NM_053009	ENSMUSG00000024695	Zfp91	9130014I08Rik|A530054C17Rik|AL024263|AW545902|Pzf|Zfp-91	zinc finger protein 91	protein-coding
mm_79852.1	chr9	64947705	64947711	+	1	NA	intron (NM_144813, intron 2 of 9)	intron (NM_144813, intron 2 of 9)	3899	NM_144813	214111	Mm.156124	NM_144813	ENSMUSG00000034452	Slc24a1	-	solute carrier family 24 (sodium/potassium/calcium exchanger), member 1	protein-coding
mm_75275.1	chr8	40899043	40899068	-	1	NA	exon (NM_001044740, exon 2 of 12)	exon (NM_001044740, exon 2 of 12)	-27178	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_11424.1	chr2	31887263	31887310	+	1	NA	promoter-TSS (NM_011836)	promoter-TSS (NM_011836)	5	NM_011836	23928	Mm.302362	NM_011836	ENSMUSG00000026840	Lamc3	AI562206|AW240805	laminin gamma 3	protein-coding
mm_28583.1	chr3	94369634	94369637	-	1	NA	Intergenic	Intergenic	-3159	NM_011281	19885	Mm.4372	NM_011281	ENSMUSG00000028150	Rorc	Nr1f3|RORgamma|TOR|Thor	RAR-related orphan receptor gamma	protein-coding
mm_62267.1	chr7	99535301	99535311	+	1	NA	promoter-TSS (NM_178220)	promoter-TSS (NM_178220)	-180	NM_178220	109689	Mm.260193	NM_177231	ENSMUSG00000018909	Arrb1	1200006I17Rik|AW208571|G430100A01Rik	arrestin, beta 1	protein-coding
mm_153023.1	chr19	31451562	31451562	-	1	NA	intron (NM_011160, intron 2 of 17)	intron (NM_011160, intron 2 of 17)	212808	NM_011160	19091	Mm.381170	NM_011160	ENSMUSG00000052920	Prkg1	AW125416|CGKI|Gm19690|Prkg1b|Prkgr1b	protein kinase, cGMP-dependent, type I	protein-coding
mm_80955.1	chr9	103007981	103007987	+	1	NA	promoter-TSS (NM_033314)	promoter-TSS (NM_033314)	-505	NM_033314	24059	Mm.207106	NM_033314	ENSMUSG00000032548	Slco2a1	2310021C19Rik|Pgt|Slc21a2|mPgt	solute carrier organic anion transporter family, member 2a1	protein-coding
mm_22925.1	chr3	31120451	31120463	+	1	NA	3' UTR (NM_001039090, exon 7 of 7)	3' UTR (NM_001039090, exon 7 of 7)	25399	NM_001039090	20482	Mm.15406	NM_011386	ENSMUSG00000027660	Skil	Skir|SnoN|sno	SKI-like	protein-coding
mm_103426.1	chr11	75626718	75626733	-	1	NA	3' UTR (NM_008850, exon 12 of 12)	3' UTR (NM_008850, exon 12 of 12)	-4295	NM_008916	19062	Mm.1458	NM_008916	ENSMUSG00000006127	Inpp5k	C62|Pps|SKIP	inositol polyphosphate 5-phosphatase K	protein-coding
mm_163746.1	chr13	119755814	119755826	-	1	NA	promoter-TSS (NM_175538)	promoter-TSS (NM_175538)	62	NM_175538	245269	Mm.403943	NM_175538	ENSMUSG00000095930	Nim1k	E130304F04Rik|Nim1	NIM1 serine/threonine protein kinase	protein-coding
mm_47012.1	chr5	115479645	115479651	-	1	NA	exon (NM_001167691, exon 4 of 5)	exon (NM_001167691, exon 4 of 5)	4649	NM_001167691	75387	Mm.332616	NM_133760	ENSMUSG00000029524	Sirt4	4930596O17Rik	sirtuin 4	protein-coding
mm_133140.1	chr16	69863686	69863687	+	1	NA	promoter-TSS (NM_173069)	promoter-TSS (NM_173069)	58	NM_173069	224318	Mm.212743	NM_173069	ENSMUSG00000063163	Speer2	SPEER-2	spermatogenesis associated glutamate (E)-rich protein 2	protein-coding
mm_120693.1	chr14	70776223	70776231	+	1	NA	intron (NM_010071, intron 3 of 4)	intron (NM_010071, intron 3 of 4)	1846	NM_010071	13449	Mm.243323	NM_010071	ENSMUSG00000022102	Dok2	DokR|Frip	docking protein 2	protein-coding
mm_17735.1	chr2	32576261	32576265	-	1	NA	intron (NM_198191, intron 1 of 9)	intron (NM_198191, intron 1 of 9)	545	NM_198191	227733	Mm.78923	NM_198191	ENSMUSG00000046854	Pip5kl1	BC028795	phosphatidylinositol-4-phosphate 5-kinase-like 1	protein-coding
mm_96181.1	chr11	61653359	61653370	+	1	NA	promoter-TSS (NM_027817)	promoter-TSS (NM_027817)	43	NM_027817	71520	Mm.202760	NM_027817	ENSMUSG00000004837	Grap	8430435N19Rik|BB233594	GRB2-related adaptor protein	protein-coding
mm_153028.1	chr19	31664607	31664618	-	1	NA	promoter-TSS (NM_011160)	promoter-TSS (NM_011160)	-242	NM_011160	19091	Mm.381170	NM_011160	ENSMUSG00000052920	Prkg1	AW125416|CGKI|Gm19690|Prkg1b|Prkgr1b	protein kinase, cGMP-dependent, type I	protein-coding
mm_50781.1	chr6	53698025	53698036	+	1	NA	3' UTR (NM_001327821, exon 11 of 11)	3' UTR (NM_001327821, exon 11 of 11)	122795	NM_025817	66873	Mm.422727	NM_025817	ENSMUSG00000043496	Tril	1200009O22Rik|AI316813|mKIAA0644	TLR4 interactor with leucine-rich repeats	protein-coding
mm_147174.1	chr18	36734900	36734906	-	1	NA	promoter-TSS (NM_028036)	promoter-TSS (NM_028036)	-167	NM_028036	71983	Mm.135188	NM_028036	ENSMUSG00000006850	Tmco6	2410015B03Rik	transmembrane and coiled-coil domains 6	protein-coding
mm_116038.1	chr13	26770158	26770174	-	1	NA	promoter-TSS (NM_008232)	promoter-TSS (NM_008232)	-1	NM_008232	15192	Mm.7411	NM_008232	ENSMUSG00000045835	Hdgfl1	4921520N01Rik|HRP-1|Hdgfrp1|Pwwp1	hepatoma derived growth factor-like 1	protein-coding
mm_48129.1	chr5	137149892	137149899	-	1	NA	Intergenic	Intergenic	-33688	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_63329.1	chr7	126950021	126950055	+	1	NA	promoter-TSS (NM_001039645)	promoter-TSS (NM_001039645)	-457	NM_001039645	233879	Mm.444143	NM_001039645	ENSMUSG00000046378	Asphd1	A830007L07Rik|Gm168	aspartate beta-hydroxylase domain containing 1	protein-coding
mm_93080.1	chr10	89506632	89506650	-	1	NA	promoter-TSS (NM_001163700)	promoter-TSS (NM_001163700)	17	NM_001163700	20186	Mm.3095	NM_009108	ENSMUSG00000047638	Nr1h4	AI957360|Fxr|HRR1|RIP14|Rxrip14	nuclear receptor subfamily 1, group H, member 4	protein-coding
mm_96414.1	chr11	67255592	67255603	+	1	NA	exon (NM_010855, exon 32 of 40)	exon (NM_010855, exon 32 of 40)	17785	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_133651.1	chr16	91804614	91804650	+	1	NA	intron (NM_001110275, intron 7 of 28)	intron (NM_001110275, intron 7 of 28)	75261	NM_010587	16443	Mm.40546	NM_010587	ENSMUSG00000022957	Itsn1	AA517634|AA545208|AI316805|AI839402|AI848451|Ehsh1|Ese1|Itsn|Sh3p17	intersectin 1 (SH3 domain protein 1A)	protein-coding
mm_167329.1	chr8	70523171	70523178	-	1	NA	promoter-TSS (NM_029366)	promoter-TSS (NM_029366)	6	NM_029366	75620	Mm.482129	NM_029366	ENSMUSG00000055553	Kxd1	0610030B01Rik|2810422J05Rik|C78305	KxDL motif containing 1	protein-coding
mm_53613.1	chr6	139896712	139896714	+	1	NA	intron (NM_011084, intron 10 of 15)	intron (NM_011084, intron 10 of 15)	55268	NM_011084	18705	Mm.333471	NM_011084	ENSMUSG00000030228	Pik3c2g	C80387|PI3K-C2-gamma	phosphatidylinositol 3-kinase, C2 domain containing, gamma polypeptide	protein-coding
mm_90292.1	chr10	125308969	125308975	+	1	NA	intron (NM_011391, intron 1 of 6)	intron (NM_011391, intron 1 of 6)	19563	NM_011391	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|Mct2	solute carrier family 16 (monocarboxylic acid transporters), member 7	protein-coding
mm_47682.1	chr5	128953304	128953331	-	1	NA	5' UTR (NM_001081388, exon 1 of 22)	5' UTR (NM_001081388, exon 1 of 22)	169	NM_001081388	231760	Mm.233996	NM_001081388	ENSMUSG00000029420	Rimbp2	A930033C01Rik|mKIAA0318	RIMS binding protein 2	protein-coding
mm_169544.1	chr15	102100215	102100231	-	1	NA	Intergenic	CpG	-2765	NM_153533	209039	Mm.29389	NM_153533	ENSMUSG00000037003	Tns2	C1-ten|Tenc1|nep|nph	tensin 2	protein-coding
mm_89468.1	chr10	93468137	93468158	+	1	NA	intron (NM_001313897, intron 6 of 17)	intron (NM_001313897, intron 6 of 17)	14751	NM_008517	16993	Mm.271071	NM_008517	ENSMUSG00000015889	Lta4h	-	leukotriene A4 hydrolase	protein-coding
mm_96084.1	chr11	60139958	60140025	+	1	NA	promoter-TSS (NM_001037764)	promoter-TSS (NM_001037764)	-91	NM_001037764	19377	Mm.296366	NM_009021	ENSMUSG00000062115	Rai1	Gt1	retinoic acid induced 1	protein-coding
mm_98715.1	chr11	96318651	96318718	+	1	NA	5' UTR (NM_010459, exon 1 of 2)	5' UTR (NM_010459, exon 1 of 2)	417	NM_010459	15412	Mm.3546	NM_010459	ENSMUSG00000038692	Hoxb4	Hox-2.6	homeobox B4	protein-coding
mm_93538.1	chr10	115384389	115384435	-	1	NA	promoter-TSS (NM_025780)	promoter-TSS (NM_025780)	23	NM_025780	66816	Mm.32314	NM_025780	ENSMUSG00000020137	Thap2	2900040O07Rik|9030625G08Rik|AI450385|AI649097	THAP domain containing, apoptosis associated protein 2	protein-coding
mm_101297.1	chr11	22246685	22246690	-	1	NA	intron (NM_001252515, intron 3 of 24)	intron (NM_001252515, intron 3 of 24)	40108	NM_153078	216565	Mm.491265	NM_153078	ENSMUSG00000042302	Ehbp1	AF424697|Flj21950|NACSIN	EH domain binding protein 1	protein-coding
mm_156349.1	chrX	139217169	139217190	+	1	NA	promoter-TSS (NM_001164633)	promoter-TSS (NM_001164633)	13	NM_001164632	245631	Mm.131001	NM_175541	ENSMUSG00000042515	Mum1l1	9430086K21Rik	melanoma associated antigen (mutated) 1-like 1	protein-coding
mm_89672.1	chr10	97507706	97507717	+	1	NA	exon (NM_007833, exon 5 of 8)	exon (NM_007833, exon 5 of 8)	25380	NM_007833	13179	Mm.56769	NM_007833	ENSMUSG00000019929	Dcn	DC|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding
mm_112212.1	chr12	113428556	113428578	-	1	NA	Intergenic	Intergenic	-60998	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_103929.1	chr11	83648283	83648293	-	1	NA	exon (NM_011337, exon 3 of 3)	exon (NM_011337, exon 3 of 3)	1090	NM_011337	20302	Mm.1282	NM_011337	ENSMUSG00000000982	Ccl3	AI323804|G0S19-1|LD78alpha|MIP-1alpha|MIP1-(a)|MIP1-alpha|Mip1a|Scya3	chemokine (C-C motif) ligand 3	protein-coding
mm_117517.1	chr13	80960833	80960841	-	1	NA	Intergenic	Intergenic	-3237	NR_015587	319983	Mm.343027	NR_015587	ENSMUSG00000097098	9330111N05Rik	-	RIKEN cDNA 9330111N05 gene	ncRNA
mm_113206.1	chr13	25056045	25056054	+	1	NA	promoter-TSS (NM_177577)	promoter-TSS (NM_177577)	45	NM_177577	195208	Mm.284719	NM_177577	ENSMUSG00000035910	Dcdc2a	AW492955|Dcdc2|RU2	doublecortin domain containing 2a	protein-coding
mm_170085.1	chr17	35479983	35479991	+	1	NA	Intergenic	MMVL30-int|LTR|ERV1	9898	NM_010391	15007	Mm.88795	NM_010391	ENSMUSG00000067235	H2-Q10	H-2Q10|Q10|Qa10	histocompatibility 2, Q region locus 10	protein-coding
mm_34548.1	chr4	149586421	149586427	+	1	NA	promoter-TSS (NM_023051)	promoter-TSS (NM_023051)	-44	NM_001290989	65945	Mm.38993	NM_023051	ENSMUSG00000039953	Clstn1	1810034E21Rik|Cst-1|Cstn1	calsyntenin 1	protein-coding
mm_76393.1	chr8	84844185	84844215	-	1	NA	exon (NM_007591, exon 7 of 9)	exon (NM_007591, exon 7 of 9)	2731	NM_007591	12317	Mm.1971	NM_007591	ENSMUSG00000003814	Calr	CRT|Calregulin	calreticulin	protein-coding
mm_21723.1	chr2	164654966	164654971	-	1	NA	promoter-TSS (NM_001160414)	promoter-TSS (NM_001160414)	-2	NM_001160414	629754	Mm.190489	NM_001160414	ENSMUSG00000074594	Wfdc9	OTTMUSG00000001088	WAP four-disulfide core domain 9	protein-coding
mm_34912.1	chr4	155705273	155705320	+	1	NA	5' UTR (NM_026899, exon 1 of 5)	5' UTR (NM_026899, exon 1 of 5)	481	NM_026899	68991	Mm.294770	NM_026899	ENSMUSG00000029038	Ssu72	1190002E22Rik|1500011L16Rik|2610101M12Rik	Ssu72 RNA polymerase II CTD phosphatase homolog (yeast)	protein-coding
mm_137728.1	chr17	29274140	29274162	+	1	NA	intron (NM_030561, intron 1 of 8)	intron (NM_030561, intron 1 of 8)	5363	NM_030561	80748	Mm.290116	NM_030561	ENSMUSG00000052712	BC004004	2400006G15Rik	cDNA sequence BC004004	protein-coding
mm_98340.1	chr11	93098358	93098397	+	1	NA	promoter-TSS (NM_028296)	promoter-TSS (NM_028296)	-913	NM_028296	72605	Mm.342160	NM_028296	ENSMUSG00000056158	Car10	2700029L05Rik|BB085816|Ca10	carbonic anhydrase 10	protein-coding
mm_121439.1	chr14	120429811	120429831	+	1	NA	3' UTR (NM_207515, exon 8 of 8)	3' UTR (NM_207515, exon 8 of 8)	-48640	NM_029519	76108	Mm.261448	NM_029519	ENSMUSG00000051615	Rap2a	5830461H18Rik	RAS related protein 2a	protein-coding
mm_151483.1	chr19	58676515	58676522	+	1	NA	exon (NM_026925, exon 8 of 13)	exon (NM_026925, exon 8 of 13)	6153	NM_026925	69060	Mm.20407	NM_026925	ENSMUSG00000046008	Pnlip	1810007A24Rik|PL|PTL	pancreatic lipase	protein-coding
mm_154155.1	chr19	58455482	58455495	-	1	NA	promoter-TSS (NM_010279)	promoter-TSS (NM_010279)	-90	NM_010279	14585	Mm.88367	NM_010279	ENSMUSG00000025089	Gfra1	AU042498	glial cell line derived neurotrophic factor family receptor alpha 1	protein-coding
mm_165200.1	chr2	32713476	32713488	+	1	NA	promoter-TSS (NM_130860)	promoter-TSS (NM_130860)	-510	NR_039536	100628606		NR_039536	ENSMUSG00000105841	Mir3960	mmu-mir-3960	microRNA 3960	ncRNA
mm_71016.1	chr8	32160218	32160233	+	1	NA	intron (NR_046039, intron 1 of 2)	intron (NR_046039, intron 1 of 2)	8330	NR_046039	666589	Mm.367675	NR_046039		Gm8179	EG666589	predicted gene 8179	ncRNA
mm_92291.1	chr10	71980671	71980681	-	1	NA	promoter-TSS (NR_003644)	promoter-TSS (NR_003644)	14	NR_003644	108950	Mm.212793	NM_175390	ENSMUSG00000043859	1700049L16Rik	-	hematological and neurological expressed 1-like pseudogene	pseudo
mm_23507.1	chr3	60529429	60529453	+	1	NA	5' UTR (NM_001253708, exon 2 of 9)	5' UTR (NM_001253708, exon 2 of 9)	28262	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_111814.1	chr12	105683563	105683566	-	1	NA	intron (NM_029654, intron 1 of 41)	B1F1|SINE|Alu	1677	NM_029654	76559	Mm.114362	NM_029654	ENSMUSG00000041341	Atg2b	2410024A21Rik|AI047755|AI503411|AW558123|C030004M05Rik|C630028L02Rik|mKIAA4067	autophagy related 2B	protein-coding
mm_27614.1	chr3	59220092	59220116	-	1	NA	intron (NM_027571, intron 2 of 3)	intron (NM_027571, intron 2 of 3)	-9222	NM_028808	74191	Mm.90067	NM_028808	ENSMUSG00000036362	P2ry13	2010001L06Rik|GPCR1|GPR94|Gpr86|P2Y13|P2yr13|SP174	purinergic receptor P2Y, G-protein coupled 13	protein-coding
mm_103988.1	chr11	84828982	84829023	-	1	NA	promoter-TSS (NR_046281)	promoter-TSS (NR_046281)	1	NM_177564	192970	Mm.192213	NM_177564	ENSMUSG00000034449	Dhrs11	-	dehydrogenase/reductase (SDR family) member 11	protein-coding
mm_126507.1	chr15	81802710	81802722	+	1	NA	promoter-TSS (NM_153484)	promoter-TSS (NM_153484)	43	NM_153484	21685	Mm.270278	NM_017376	ENSMUSG00000022389	Tef	2310028D20Rik	thyrotroph embryonic factor	protein-coding
mm_161416.1	chr15	30172640	30172640	+	1	NA	promoter-TSS (NM_008729)	promoter-TSS (NM_008729)	47	NM_008729	18163	Mm.321648	NM_008729	ENSMUSG00000022240	Ctnnd2	Catnd2|Nprap|neurojugin	catenin (cadherin associated protein), delta 2	protein-coding
mm_2119.1	chr1	87882696	87882701	+	1	NA	intron (NM_177646, intron 3 of 29)	(T)n|Simple_repeat|Simple_repeat	-28399	NR_136921	100503175	Mm.426422	NR_136921	ENSMUSG00000101942	Gm19582	-	predicted gene, 19582	ncRNA
mm_27387.1	chr3	50628486	50628508	-	1	NA	Intergenic	Intergenic	-184884	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_114752.1	chr13	84348426	84348455	+	1	NA	Intergenic	Intergenic	126144	NM_175187	72745	Mm.295063	NM_175187	ENSMUSG00000035762	Tmem161b	2810446P07Rik|AI843389	transmembrane protein 161B	protein-coding
mm_14549.1	chr2	132847820	132847831	+	1	NA	promoter-TSS (NM_025646)	promoter-TSS (NM_025646)	91	NM_025646	66586	Mm.357342	NM_025646	ENSMUSG00000027357	Crls1	0610009I22Rik|4930557M15Rik|5730490M08Rik	cardiolipin synthase 1	protein-coding
mm_2360.1	chr1	92973177	92973192	+	1	NA	promoter-TSS (NM_001104529)	promoter-TSS (NM_001104529)	65	NM_001104529	64095	Mm.152780	NM_022320	ENSMUSG00000026271	Gpr35	KPG_007	G protein-coupled receptor 35	protein-coding
mm_95312.1	chr11	46386821	46386829	+	1	NA	intron (NM_010583, intron 1 of 16)	intron (NM_010583, intron 1 of 16)	2690	NM_001281968	16428	Mm.339927	NM_010583	ENSMUSG00000020395	Itk	Emt|Tcsk|Tsk	IL2 inducible T cell kinase	protein-coding
mm_165330.1	chr2	113996510	113996510	+	1	NA	Intergenic	Intergenic	-17055	NR_028423	320846	Mm.441458	NR_028423	ENSMUSG00000087694	A530058N18Rik	-	RIKEN cDNA A530058N18 gene	ncRNA
mm_79497.1	chr9	57117710	57117713	+	1	NA	intron (NM_001110350, intron 17 of 20)	B3|SINE|B2	-13066	NM_028636	73744	Mm.30110	NM_028636	ENSMUSG00000032295	Man2c1	1110025H24Rik	mannosidase, alpha, class 2C, member 1	protein-coding
mm_124232.1	chr14	101200350	101200418	-	1	NA	promoter-TSS (NM_029680)	promoter-TSS (NM_029680)	-315	NM_029680	76627	Mm.31415	NM_029680	ENSMUSG00000042888	Prr30	1700110M21Rik	proline rich 30	protein-coding
mm_60302.1	chr7	44055702	44055715	+	1	NA	exon (NM_020268, exon 3 of 5)	exon (NM_020268, exon 3 of 5)	3418	NM_020268	16619	Mm.445911	NM_020268	ENSMUSG00000063177	Klk1b27	Gk27|Klk21l|Klk27|mGK-27	kallikrein 1-related peptidase b27	protein-coding
mm_163582.1	chr13	34355404	34355415	-	1	NA	Intergenic	Intergenic	-10227	NM_001033167	73102	Mm.23932	NM_001033167	ENSMUSG00000038267	Slc22a23	3110004L20Rik	solute carrier family 22, member 23	protein-coding
mm_86786.1	chr10	20172002	20172012	+	1	NA	intron (NM_001198635, intron 1 of 17)	intron (NM_001198635, intron 1 of 17)	23087	NM_001198635	17761	Mm.20928	NM_008635	ENSMUSG00000019996	Map7	E-MAP-115|MAP-7|Mtap7|R75000|mshi|mste|ste	microtubule-associated protein 7	protein-coding
mm_85845.1	chr9	110645296	110645302	-	1	NA	intron (NM_183276, intron 1 of 53)	intron (NM_183276, intron 1 of 53)	8862	NM_183276	235627	Mm.335481	NM_183276	ENSMUSG00000056724	Nbeal2	1110014F23Rik|BC042396|mKIAA0540	neurobeachin-like 2	protein-coding
mm_116260.1	chr13	34182666	34182683	-	1	NA	3' UTR (NM_001033167, exon 11 of 11)	3' UTR (NM_001033167, exon 11 of 11)	19710	NM_001110515	69666	Mm.24788	NM_001101430	ENSMUSG00000071451	Psmg4	PAC-4|mPAC4	proteasome (prosome, macropain) assembly chaperone 4	protein-coding
mm_103740.1	chr11	80081118	80081142	-	1	NA	promoter-TSS (NM_018776)	promoter-TSS (NM_018776)	-139	NM_018776	54394	Mm.272093	NM_018776	ENSMUSG00000017561	Crlf3	BB164954|Creme9|Cytor4	cytokine receptor-like factor 3	protein-coding
mm_17030.1	chr2	20339402	20339403	-	1	NA	intron (NM_001081006, intron 1 of 21)	intron (NM_001081006, intron 1 of 21)	49489	NM_001081006	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding
mm_16553.1	chr2	181767344	181767385	+	1	NA	intron (NM_001171616, intron 1 of 21)	intron (NM_001171616, intron 1 of 21)	335	NM_001171616	17932	Mm.458718	NM_008665	ENSMUSG00000010505	Myt1	Nzf2|Nzf2a|Nzf2b|Nztf2	myelin transcription factor 1	protein-coding
mm_51925.1	chr6	91270031	91270054	+	1	NA	exon (NM_001081437, exon 16 of 17)	exon (NM_001081437, exon 16 of 17)	57278	NM_007992	14115	Mm.249146	NM_007992	ENSMUSG00000064080	Fbln2	5730577E14Rik|FIBL-2	fibulin 2	protein-coding
mm_104308.1	chr11	91577514	91577574	-	1	NA	promoter-TSS (NM_028547)	promoter-TSS (NM_028547)	11	NM_028547	73470	Mm.67677	NM_028547	ENSMUSG00000046755	Kif2b	1700063D03Rik	kinesin family member 2B	protein-coding
mm_98151.1	chr11	87595647	87595659	+	1	NA	intron (NM_133215, intron 2 of 18)	CpG	3436	NM_133215	170749	Mm.399376	NM_133215	ENSMUSG00000018401	Mtmr4	AA596759|ESTM44|FYVE-DSP2|ZFYVE11|mKIAA0647	myotubularin related protein 4	protein-coding
mm_131009.1	chr15	103562931	103562941	-	1	NA	exon (NM_008134, exon 4 of 4)	exon (NM_008134, exon 4 of 4)	2145	NM_001289587	14663	Mm.219621	NM_008134	ENSMUSG00000022491	Glycam1	MC26|Sgp50|glyCAM-1	glycosylation dependent cell adhesion molecule 1	protein-coding
mm_20361.1	chr2	128295036	128295044	-	1	NA	Intergenic	Intergenic	134311	NR_028591	100043424	Mm.297222	NR_028589		Gm14005	OTTMUSG00000015351	predicted gene 14005	ncRNA
mm_167103.1	chr7	110863015	110863024	-	1	NA	promoter-TSS (NM_053247)	promoter-TSS (NM_053247)	-66	NM_053247	114332	Mm.396078	NM_053247	ENSMUSG00000030787	Lyve1	1200012G08Rik|Crsbp-1|Lyve-1|Xlkd1	lymphatic vessel endothelial hyaluronan receptor 1	protein-coding
mm_54306.1	chr6	29609609	29609642	-	1	NA	promoter-TSS (NM_177296)	promoter-TSS (NM_177296)	-18	NM_177296	320938	Mm.276381	NM_177296	ENSMUSG00000012535	Tnpo3	5730544L10Rik|C430013M08Rik|C81142|D6Ertd313e|Trn-SR|mKIAA4133	transportin 3	protein-coding
mm_66063.1	chr7	30820243	30820257	-	1	NA	5' UTR (NM_146187, exon 3 of 3)	5' UTR (NM_146187, exon 3 of 3)	727	NM_001168512	233079	Mm.97338	NM_146187	ENSMUSG00000051314	Ffar2	GPCR43|Gpr43	free fatty acid receptor 2	protein-coding
mm_106999.1	chr12	11279652	11279664	+	1	NA	exon (NM_025695, exon 5 of 27)	exon (NM_025695, exon 5 of 27)	13772	NM_025695	67241	Mm.173953	NM_025695	ENSMUSG00000020608	Smc6	2810489L22Rik|3830418C19Rik|AA990493|AU018782|AW742439|SMC-6|Smc6l1|mKIAA4103	structural maintenance of chromosomes 6	protein-coding
mm_22707.1	chr3	19187322	19187351	+	1	NA	promoter-TSS (NM_001253391)	promoter-TSS (NM_001253391)	7	NM_001253391	67472	Mm.45125	NM_026182	ENSMUSG00000027601	Mtfr1	1300002C08Rik|1700080D04Rik|2810026O10Rik|4930579E05Rik|Chppr|Fam54a2	mitochondrial fission regulator 1	protein-coding
mm_28790.1	chr3	95995937	95995955	-	1	NA	promoter-TSS (NM_023320)	promoter-TSS (NM_023320)	-107	NM_023320	67220	Mm.458147	NM_023320	ENSMUSG00000015745	Plekho1	2810052M02Rik|CKIP-1|Ckip1|JZA-20|Jza2	pleckstrin homology domain containing, family O member 1	protein-coding
mm_93932.1	chr10	127166984	127167003	-	1	NA	intron (NR_045166, intron 3 of 9)	intron (NR_045166, intron 3 of 9)	1162	NM_001244618	14421	Mm.386762	NM_008080	ENSMUSG00000006731	B4galnt1	4933429D13Rik|Gal-NAc-T|GalNAc-T|GalNAcT|Galgt1|Ggm-2|Ggm2	beta-1,4-N-acetyl-galactosaminyl transferase 1	protein-coding
mm_94290.1	chr11	4035069	4035101	+	1	NA	intron (NM_146013, intron 1 of 11)	MLTR14|LTR|ERV1	3303	NM_146013	103655	Mm.337476	NM_146013	ENSMUSG00000019368	Sec14l4	AI256582|AW536553|SPF|TAP	SEC14-like lipid binding 4	protein-coding
mm_165997.1	chr4	113999516	113999518	-	1	NA	promoter-TSS (NM_001167878)	promoter-TSS (NM_001167878)	-14	NM_001167876	242627	Mm.484115	NM_001167876	ENSMUSG00000078598	Skint5	OTTMUSG00000008560|Skint-5	selection and upkeep of intraepithelial T cells 5	protein-coding
mm_80767.1	chr9	95559600	95559652	+	1	NA	promoter-TSS (NM_198414)	promoter-TSS (NM_198414)	-191	NM_198414	75552	Mm.151485	NM_198414	ENSMUSG00000064225	Paqr9	1700020G04Rik	progestin and adipoQ receptor family member IX	protein-coding
mm_102802.1	chr11	68860023	68860063	-	1	NA	Intergenic	Intergenic	-6912	NM_023668	83431	Mm.31979	NM_023668	ENSMUSG00000018736	Ndel1	2600006O07Rik|MITAP1|NUDEL|mNudel	nudE neurodevelopment protein 1 like 1	protein-coding
mm_166019.1	chr4	122673803	122673806	+	1	NA	Intergenic	L2|LINE|L2	-15455	NM_023865	77432	Mm.491436	NM_023865	ENSMUSG00000023263	9530002B09Rik	Aump|Vpp1|Vppl	RIKEN cDNA 9530002B09 gene	protein-coding
mm_7428.1	chr1	119837320	119837328	-	1	NA	promoter-TSS (NM_019933)	promoter-TSS (NM_019933)	-253	NM_019933	19258	Mm.458796	NM_019933	ENSMUSG00000026384	Ptpn4	PTPMEG|Ptn4|TEP|TEP/mPTPMEG|hPTP-MEG	protein tyrosine phosphatase, non-receptor type 4	protein-coding
mm_121770.1	chr14	19874755	19874788	-	1	NA	3' UTR (NM_001285911, exon 4 of 4)	3' UTR (NM_001285911, exon 4 of 4)	35846	NR_105025	52512	Mm.483998	NR_105025		D14Ertd670e	-	DNA segment, Chr 14, ERATO Doi 670, expressed	ncRNA
mm_23093.1	chr3	37063632	37063639	+	1	NA	promoter-TSS (NM_009350)	promoter-TSS (NM_009350)	-21	NM_009350	21744	Mm.8122	NM_009350	ENSMUSG00000027719	Adad1	Tenr	adenosine deaminase domain containing 1 (testis specific)	protein-coding
mm_55187.1	chr6	52184128	52184151	-	1	NA	intron (NM_010452, intron 2 of 4)	intron (NM_010452, intron 2 of 4)	7564	NM_008265	15401	Mm.439647	NM_008265	ENSMUSG00000000942	Hoxa4	AV206827|Hox-1.4	homeobox A4	protein-coding
mm_59299.1	chr7	25152457	25152462	+	1	NA	promoter-TSS (NR_045847)	promoter-TSS (NR_045847)	2	NR_045847	434147	Mm.59171	NM_001033781	ENSMUSG00000074274	D930028M14Rik	EG434147	RIKEN cDNA D930028M14 gene	ncRNA
mm_145982.1	chr18	68227839	68227880	+	1	NA	intron (NM_172631, intron 3 of 5)	intron (NM_172631, intron 3 of 5)	33114	NR_106078	102465702		NR_106078	ENSMUSG00000098253	Mir7219	Gm27613|mmu-mir-7219	microRNA 7219	ncRNA
mm_92951.1	chr10	85185004	85185069	-	1	NA	promoter-TSS (NM_007771)	promoter-TSS (NM_007771)	18	NM_007771	12952	Mm.26237	NM_007771	ENSMUSG00000020038	Cry1	AU020726|AU021000|Phll1	cryptochrome 1 (photolyase-like)	protein-coding
mm_89134.1	chr10	85386814	85386846	+	1	NA	promoter-TSS (NM_028709)	promoter-TSS (NM_028709)	16	NM_028709	74007	Mm.36544	NM_028709	ENSMUSG00000020042	Btbd11	6330404E16Rik	BTB (POZ) domain containing 11	protein-coding
mm_145192.1	chr18	49835888	49835915	+	1	NA	intron (NM_001081371, intron 1 of 42)	RLTR20C1_MM|LTR|ERVK	2904	NM_001081371	240283	Mm.257790	NM_001081371	ENSMUSG00000037416	Dmxl1	C630007L23Rik|D030030C22	Dmx-like 1	protein-coding
mm_32805.1	chr4	117120741	117120751	+	1	NA	non-coding (NR_024078, exon 7 of 7)	non-coding (NR_024078, exon 7 of 7)	4979	NR_024078	78611	Mm.446227	NM_001033187		Btbd19	9530048O09Rik|BB115071	BTB (POZ) domain containing 19	ncRNA
mm_51535.1	chr6	83195810	83195825	+	1	NA	intron (NM_001347310, intron 20 of 26)	intron (NM_001347310, intron 20 of 26)	9871	NM_001347310	13191	Mm.6919	NM_007835	ENSMUSG00000031865	Dctn1	AL022633|DAP-150|DP-150|Glued|p150|p150-glued|p150<glued>	dynactin 1	protein-coding
mm_91966.1	chr10	61383375	61383391	-	1	NA	5' UTR (NM_013753, exon 1 of 20)	5' UTR (NM_013753, exon 1 of 20)	140	NM_013753	27355	Mm.269699	NM_013753	ENSMUSG00000020092	Pald1	MMPAL|Pald|mKIAA1274	phosphatase domain containing, paladin 1	protein-coding
mm_124841.1	chr15	9370398	9370407	+	1	NA	3' UTR (NM_144845, exon 7 of 7)	3' UTR (NM_144845, exon 7 of 7)	34804	NM_144845	223337	Mm.422853	NM_144845	ENSMUSG00000049152	Ugt3a2	AI313915	UDP glycosyltransferases 3 family, polypeptide A2	protein-coding
mm_142185.1	chr17	36867117	36867159	-	1	NA	promoter-TSS (NM_001024134)	promoter-TSS (NM_001024134)	49	NM_001024134	69097	Mm.307027	NM_001024134	ENSMUSG00000050747	Trim15	1810012B10Rik	tripartite motif-containing 15	protein-coding
mm_156534.1	chrX	151047334	151047357	+	1	NA	5' UTR (NM_008001, exon 1 of 18)	5' UTR (NM_008001, exon 1 of 18)	175	NM_008001	14163	Mm.8142	NM_008001	ENSMUSG00000025265	Fgd1	ZFYVE3	FYVE, RhoGEF and PH domain containing 1	protein-coding
mm_90633.1	chr10	128488011	128488023	+	1	NA	exon (NM_001114096, exon 28 of 29)	exon (NM_001114096, exon 28 of 29)	4992	NM_001317220	17904	Mm.337074	NM_010860	ENSMUSG00000090841	Myl6	ESMLC|LC17|LC17-GI|MLC-3|MLC1SM|Myln	myosin, light polypeptide 6, alkali, smooth muscle and non-muscle	protein-coding
mm_71601.1	chr8	55059110	55059124	+	1	NA	3' UTR (NM_001253754, exon 7 of 7)	3' UTR (NM_001253754, exon 7 of 7)	104389	NM_001253756	234267	Mm.241700	NM_153581	ENSMUSG00000031517	Gpm6a	Gpm6|M6A	glycoprotein m6a	protein-coding
mm_66419.1	chr7	44531387	44531399	-	1	NA	intron (NM_019866, intron 1 of 5)	intron (NM_019866, intron 1 of 5)	678	NM_019866	272382	Mm.8012	NM_019866	ENSMUSG00000008193	Spib	Spi-B	Spi-B transcription factor (Spi-1/PU.1 related)	protein-coding
mm_55232.1	chr6	52240762	52240768	-	1	NA	promoter-TSS (NM_001122950)	promoter-TSS (NM_001122950)	89	NM_001122950	15395	Mm.5	NM_008263	ENSMUSG00000000938	Hoxa10	Hox-1.8|Hoxa-10	homeobox A10	protein-coding
mm_128969.1	chr15	74832211	74832215	-	1	NA	Intergenic	B3|SINE|B2	9430	NM_001033229	110115	Mm.322606	NM_001033229	ENSMUSG00000075604	Cyp11b1	AA389061|CPN1|Cyp11b|Cyp11b-1|FHI	cytochrome P450, family 11, subfamily b, polypeptide 1	protein-coding
mm_73146.1	chr8	94985524	94985568	+	1	NA	intron (NM_018882, intron 1 of 13)	intron (NM_018882, intron 1 of 13)	1147	NM_018882	14766	Mm.290834	NM_018882	ENSMUSG00000031785	Adgrg1	Cyt28|Gpr56|TM7LN4|TM7XN1	adhesion G protein-coupled receptor G1	protein-coding
mm_122762.1	chr14	54236097	54236130	-	1	NA	intron (NM_001113358, intron 2 of 2)	intron (NM_001113358, intron 2 of 2)	17816	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_12462.1	chr2	71348508	71348544	+	1	NA	intron (NM_172436, intron 2 of 17)	ID_B1|SINE|B4	19028	NM_172436	78830	Mm.30928	NM_172436	ENSMUSG00000027010	Slc25a12	2610002D09Rik|AI839531|B230107K20Rik|BB129864	solute carrier family 25 (mitochondrial carrier, Aralar), member 12	protein-coding
mm_165439.1	chr2	154010547	154010550	+	1	NA	exon (NM_008953, exon 4 of 9)	exon (NM_008953, exon 4 of 9)	2272	NM_008953	19194	Mm.29197	NM_008953	ENSMUSG00000042459	Bpifa2	Bpifa2e|Psp	BPI fold containing family A, member 2	protein-coding
mm_166120.1	chr4	151848139	151848139	-	1	NA	intron (NM_001081557, intron 1 of 23)	intron (NM_001081557, intron 1 of 23)	13629	NM_001081557	100072	Mm.318846	NM_001081557	ENSMUSG00000014592	Camta1	1810059M14Rik|2310058O09Rik|AI316882|AW987475|mKIAA0833	calmodulin binding transcription activator 1	protein-coding
mm_100076.1	chr11	115462711	115462731	+	1	NA	exon (NM_001080934, exon 1 of 4)	exon (NM_001080934, exon 1 of 4)	248	NM_001080934	217316	Mm.25773	NM_001080934	ENSMUSG00000045775	Slc16a5	A130015N09Rik|MCT 5|MCT 6|MCT5	solute carrier family 16 (monocarboxylic acid transporters), member 5	protein-coding
mm_109779.1	chr12	119260931	119260936	+	1	NA	Intergenic	MLT1A0|LTR|ERVL-MaLR	-22657	NM_177290	320910	Mm.217000	NM_177290	ENSMUSG00000025321	Itgb8	4832412O06Rik	integrin beta 8	protein-coding
mm_70971.1	chr8	27085584	27085592	+	1	NA	promoter-TSS (NM_054044)	promoter-TSS (NM_054044)	-253	NM_054044	78560	Mm.87046	NM_054044	ENSMUSG00000031486	Adgra2	8430414O08Rik|9530074E10Rik|Gpr124|Tem5|mKIAA1531	adhesion G protein-coupled receptor A2	protein-coding
mm_53504.1	chr6	135363005	135363022	+	1	NA	promoter-TSS (NM_001288628)	promoter-TSS (NM_001288628)	82	NM_001288628	13730	Mm.182785	NM_010128	ENSMUSG00000030208	Emp1	I-8-09|TMP	epithelial membrane protein 1	protein-coding
mm_43857.1	chr5	143420996	143421010	+	1	NA	3' UTR (NM_025841, exon 5 of 5)	3' UTR (NM_025841, exon 5 of 5)	17183	NM_025841	66913	Mm.181880	NM_025841	ENSMUSG00000079111	Kdelr2	1110007A14Rik	KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 2	protein-coding
mm_96779.1	chr11	69940384	69940390	+	1	NA	exon (NM_016875, exon 6 of 9)	exon (NM_016875, exon 6 of 9)	4059	NM_001347634	53422	Mm.29286	NM_016875	ENSMUSG00000018554	Ybx2	Msy2	Y box protein 2	protein-coding
mm_111175.1	chr12	83731448	83731473	-	1	NA	intron (NM_008943, intron 10 of 11)	PB1|SINE|Alu	-32174	NM_001205343	170721	Mm.133443	NM_130887	ENSMUSG00000021223	Papln	E030033C16Rik	papilin, proteoglycan-like sulfated glycoprotein	protein-coding
mm_18710.1	chr2	72156427	72156441	-	1	NA	intron (NM_019688, intron 6 of 29)	intron (NM_019688, intron 6 of 29)	101817	NM_001204166	56508	Mm.196153	NM_019688	ENSMUSG00000049044	Rapgef4	1300003D15Rik|5730402K07Rik|6330581N18Rik|EPAC 2|Epac-2|Epac2|mKIAA4040	Rap guanine nucleotide exchange factor (GEF) 4	protein-coding
mm_40360.1	chr5	48011141	48011151	+	1	NA	intron (NR_111900, intron 4 of 35)	intron (NR_111900, intron 4 of 35)	27991	NM_001291228	20563	Mm.289739	NM_178804	ENSMUSG00000031558	Slit2	Drad-1|E030015M03Rik|E130320P19Rik|Slil3|mKIAA4141|slit-2	slit homolog 2 (Drosophila)	protein-coding
mm_146569.1	chr18	6515135	6515140	-	1	NA	intron (NM_007935, intron 1 of 13)	intron (NM_007935, intron 1 of 13)	971	NM_007935	13831	Mm.312133	NM_007935	ENSMUSG00000024240	Epc1	2400007E14Rik|5730566F07Rik|A930032N02Rik|mir-1893	enhancer of polycomb homolog 1 (Drosophila)	protein-coding
mm_139962.1	chr17	71654052	71654056	+	1	NA	intron (NM_175639, intron 16 of 17)	B2_Mm2|SINE|B2	12415	NR_028551	100217456		NR_028551	ENSMUSG00000092887	Snord53	MBII-35	small nucleolar RNA, C/D box 53	snoRNA
mm_67168.1	chr7	73554978	73554992	-	1	NA	intron (NR_037569, intron 3 of 4)	intron (NR_037569, intron 3 of 4)	3410	NR_037569	69170	Mm.34539	NR_037569	ENSMUSG00000101970	1810026B05Rik	-	RIKEN cDNA 1810026B05 gene	ncRNA
mm_20528.1	chr2	130906339	130906393	-	1	NA	promoter-TSS (NR_015523)	promoter-TSS (NR_015523)	30	NR_015523	613258	Mm.271990	NR_015523		A730017L22Rik	-	RIKEN cDNA A730017L22 gene	ncRNA
mm_172226.1	chr6	67266979	67266981	+	1	NA	promoter-TSS (NM_025814)	promoter-TSS (NM_025814)	1	NM_025814	66870	Mm.240490	NM_025814	ENSMUSG00000036371	Serbp1	1200009K13Rik|9330147J08Rik|AL022786|Pairbp1	serpine1 mRNA binding protein 1	protein-coding
mm_166791.1	chr6	145341465	145341470	+	1	NA	Intergenic	CpG	-46158	NR_003625	381827	Mm.179075	NM_001001987		1700073E17Rik	-	ribosomal protein L7 pseudogene	pseudo
mm_3061.1	chr1	134099438	134099483	+	1	NA	Intergenic	Intergenic	-11782	NM_001284524	71884	Mm.328268	NM_027979	ENSMUSG00000026450	Chit1	2300002L19Rik	chitinase 1 (chitotriosidase)	protein-coding
mm_13592.1	chr2	112506979	112506984	+	1	NA	intron (NM_028844, intron 1 of 5)	intron (NM_028844, intron 1 of 5)	14017	NM_028844	74268	Mm.315125	NM_028844	ENSMUSG00000003604	Aven	1700013A01Rik|1700056A21Rik|mAven-L|mAven-S	apoptosis, caspase activation inhibitor	protein-coding
mm_173327.1	chrY	90775804	90775817	-	1	NA	Intergenic	Intergenic	-9632	NR_137282	170942	Mm.76062	NM_133362	ENSMUSG00000096768	Erdr1	edr	erythroid differentiation regulator 1	protein-coding
mm_44236.1	chr5	5265724	5265728	-	1	NA	5' UTR (NM_001310448, exon 1 of 14)	5' UTR (NM_001310448, exon 1 of 14)	342	NM_001310448	18647	Mm.389061	NM_011074	ENSMUSG00000028926	Cdk14	Pftk1|mKIAA0834	cyclin-dependent kinase 14	protein-coding
mm_54650.1	chr6	38876519	38876529	-	1	NA	promoter-TSS (NM_010433)	promoter-TSS (NM_010433)	-334	NM_001294143	15258	Mm.23790	NM_010433	ENSMUSG00000061436	Hipk2	1110014O20Rik|B230339E18Rik|Stank	homeodomain interacting protein kinase 2	protein-coding
mm_483.1	chr1	36761775	36761777	+	1	NA	promoter-TSS (NM_009539)	promoter-TSS (NM_009539)	-22	NM_009539	22637	Mm.8038	NM_009539	ENSMUSG00000026117	Zap70	Srk|ZAP-70|mrtle|mur	zeta-chain (TCR) associated protein kinase	protein-coding
mm_124106.1	chr14	79389418	79389421	-	1	NA	intron (NM_025832, intron 1 of 19)	ID_B1|SINE|B4	1249	NM_025832	66897	Mm.24425	NM_025832	ENSMUSG00000022020	Naa16	1300019C06Rik|Narg1l	N(alpha)-acetyltransferase 16, NatA auxiliary subunit	protein-coding
mm_169941.1	chr16	65000200	65000201	-	1	NA	intron (NM_008310, intron 2 of 2)	intron (NM_008310, intron 2 of 2)	105584	NM_008310	15557	Mm.5040	NM_008310	ENSMUSG00000050783	Htr1f	Htr1eb	5-hydroxytryptamine (serotonin) receptor 1F	protein-coding
mm_101577.1	chr11	34361060	34361075	-	1	NA	intron (NM_001025382, intron 1 of 3)	MTD|LTR|ERVL-MaLR	46245	NM_001025382	574403	Mm.444796	NM_001025382	ENSMUSG00000069911	Fam196b	EG574403|Gm6041	family with sequence similarity 196, member B	protein-coding
mm_90186.1	chr10	120162211	120162220	+	1	NA	intron (NM_028679, intron 8 of 11)	RMER17C|LTR|ERVK	39322	NM_028679	73914	Mm.146194	NM_028679	ENSMUSG00000020227	Irak3	4833428C18Rik|AI563835|IRAK-M	interleukin-1 receptor-associated kinase 3	protein-coding
mm_133009.1	chr16	55975173	55975207	+	1	NA	promoter-TSS (NR_027965)	promoter-TSS (NR_027965)	-573	NR_027965	66391	Mm.472722	NM_133677	ENSMUSG00000102101	Zbtb11os1	2310061J03Rik	zinc finger and BTB domain containing 11, opposite strand 1	ncRNA
mm_118783.1	chr14	24099571	24099603	+	1	NA	Intergenic	B3A|SINE|B2	10710	NR_106069	102465697		NR_106069	ENSMUSG00000105723	Mir7210	mir-7210|mmu-mir-7210	microRNA 7210	ncRNA
mm_151409.1	chr19	56548633	56548684	+	1	NA	promoter-TSS (NM_018831)	promoter-TSS (NM_018831)	397	NM_025811	66866	Mm.46346	NM_025811	ENSMUSG00000025078	Nhlrc2	1200003G01Rik|AI835049|AV002846|AW496455	NHL repeat containing 2	protein-coding
mm_30855.1	chr4	28813126	28813136	+	1	NA	promoter-TSS (NM_010141)	promoter-TSS (NM_010141)	0	NM_001290434	13841	Mm.257266	NM_010141	ENSMUSG00000028289	Epha7	Cek11|Ebk|Ehk3|Hek11|Mdk1	Eph receptor A7	protein-coding
mm_155646.1	chrX	85574019	85574039	+	1	NA	promoter-TSS (NM_025729)	promoter-TSS (NM_025729)	7	NM_025729	66724	Mm.119646	NM_025729	ENSMUSG00000035476	Tab3	4921526G09Rik|Map3k7ip3|mKIAA4135	TGF-beta activated kinase 1/MAP3K7 binding protein 3	protein-coding
mm_161779.1	chr17	38305584	38305584	-	1	NA	promoter-TSS (NM_146488)	promoter-TSS (NM_146488)	-125	NM_146488	258481	Mm.377526	NM_146488	ENSMUSG00000054940	Olfr137	MOR256-18	olfactory receptor 137	protein-coding
mm_160188.1	chr7	54835274	54835274	+	1	NA	promoter-TSS (NM_178705)	promoter-TSS (NM_178705)	29	NM_178705	233271	Mm.387344	NM_178705	ENSMUSG00000063297	Luzp2	9330154K17Rik|D130073E01	leucine zipper protein 2	protein-coding
mm_122630.1	chr14	51145804	51145823	-	1	NA	exon (NM_011271, exon 2 of 2)	exon (NM_011271, exon 2 of 2)	954	NM_011271	19752	Mm.235538	NM_011271	ENSMUSG00000035896	Rnase1	AI574248|Rib-1|Rib1	ribonuclease, RNase A family, 1 (pancreatic)	protein-coding
mm_157796.1	chrX	73880832	73880840	-	1	NA	promoter-TSS (NM_008478)	promoter-TSS (NM_008478)	-2	NM_008478	16728	Mm.260568	NM_008478	ENSMUSG00000031391	L1cam	CD171|L1|N-CAM-L1|NCAM-L1	L1 cell adhesion molecule	protein-coding
mm_89265.1	chr10	87859699	87859707	+	1	NA	intron (NM_001314010, intron 2 of 4)	intron (NM_001314010, intron 2 of 4)	651	NM_010512	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_89508.1	chr10	94133349	94133360	+	1	NA	exon (NM_053072, exon 15 of 21)	exon (NM_053072, exon 15 of 21)	-14577	NM_011629	22025	Mm.107483	NM_011629	ENSMUSG00000005897	Nr2c1	4831444H07Rik|80.3|Eenr|TR2|Tr2-11	nuclear receptor subfamily 2, group C, member 1	protein-coding
mm_140303.1	chr17	85623970	85624035	+	1	NA	3' UTR (NM_011381, exon 2 of 2)	3' UTR (NM_011381, exon 2 of 2)	3168	NM_011381	20473	Mm.370208	NM_011381	ENSMUSG00000038805	Six3	E130112M24Rik|Six3a|Six3alpha|Six3b|Six3beta	sine oculis-related homeobox 3	protein-coding
mm_115701.1	chr13	14318955	14318986	-	1	NA	exon (NM_001081348, exon 9 of 29)	exon (NM_001081348, exon 9 of 29)	204256	NM_001081348	94253	Mm.125298	NM_153130	ENSMUSG00000021301	Hecw1	9330116H24Rik|AV273951|E130207I19Rik|Nedl1	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	protein-coding
mm_107258.1	chr12	28751799	28751868	+	1	NA	promoter-TSS (NM_201357)	promoter-TSS (NM_201357)	5	NM_201357	380752	Mm.273724	NM_201357	ENSMUSG00000036613	Tssc1	D12Ertd604e|Eipr1	tumor suppressing subtransferable candidate 1	protein-coding
mm_170658.1	chr2	108334135	108334136	-	1	NA	Intergenic	L1Md_A|LINE|L1	944155	NM_029790	76894	Mm.330451	NM_029790	ENSMUSG00000057234	Mettl15	0610027B03Rik|AI303697|AW049952|Mett5d1	methyltransferase like 15	protein-coding
mm_51809.1	chr6	88820158	88820169	+	1	NA	intron (NM_001166249, intron 6 of 7)	intron (NM_001166249, intron 6 of 7)	21772	NM_030251	80283	Mm.166858	NM_030251	ENSMUSG00000030083	Abtb1	AI847549|BC003234|BPOZ|EF1ABP	ankyrin repeat and BTB (POZ) domain containing 1	protein-coding
mm_94110.1	chr10	128589926	128589946	-	1	NA	promoter-TSS (NM_010153)	promoter-TSS (NM_010153)	-435	NM_010153	13867	Mm.373043	NM_010153	ENSMUSG00000018166	Erbb3	C76256|Erbb-3|Erbb3r|Her3	erb-b2 receptor tyrosine kinase 3	protein-coding
mm_105388.1	chr11	103363629	103363639	-	1	NA	promoter-TSS (NM_183288)	promoter-TSS (NM_183288)	58	NM_183288	544817	Mm.259113	NM_133715	ENSMUSG00000034255	Arhgap27	2310069I04Rik|5730442P18Rik|Gm21552|Sh3d20	Rho GTPase activating protein 27	protein-coding
mm_41186.1	chr5	88327826	88327837	+	1	NA	exon (NM_008644, exon 3 of 3)	exon (NM_008644, exon 3 of 3)	10519	NM_008644	17830	Mm.200411	NM_008644	ENSMUSG00000064156	Prol1	Muc10	proline rich, lacrimal 1	protein-coding
mm_86055.1	chr9	114564289	114564295	-	1	NA	promoter-TSS (NM_001042503)	promoter-TSS (NM_001042503)	77	NM_001042503	636931	Mm.17857	NM_001042503	ENSMUSG00000079259	Trim71	2610206G21Rik|AL022943|Gm1127|Lin41|lin-41|mLin41|mlin-41	tripartite motif-containing 71	protein-coding
mm_129179.1	chr15	76280972	76280978	-	1	NA	intron (NM_028852, intron 1 of 4)	ORR1D1|LTR|ERVL-MaLR	-11136	NR_045747	100038659	Mm.448549	NR_045747		Mirt2	ENSMUSG00000075583|Gm10872|Gm24562	myocardial infraction associated transcript 2	ncRNA
mm_43415.1	chr5	135980105	135980108	+	1	NA	promoter-TSS (NM_011776)	promoter-TSS (NM_011776)	1	NM_011776	22788	Mm.1381	NM_011776	ENSMUSG00000004948	Zp3	Zp-3	zona pellucida glycoprotein 3	protein-coding
mm_80245.1	chr9	72746433	72746452	+	1	NA	exon (NM_010890, exon 28 of 29)	exon (NM_010890, exon 28 of 29)	-60832	NM_175485	235472	Mm.31696	NM_175485	ENSMUSG00000036030	Prtg	A230098A12Rik|Igdcc5	protogenin	protein-coding
mm_126695.1	chr15	85037080	85037143	+	1	NA	promoter-TSS (NM_133750)	promoter-TSS (NM_133750)	49	NM_133750	73225	Mm.247535	NM_133750	ENSMUSG00000022434	Fam118a	-	family with sequence similarity 118, member A	protein-coding
mm_169557.1	chr15	103827239	103827251	+	1	NA	intron (NM_009268, intron 2 of 4)	CpG	-71747	NR_126081	20771	Mm.30276	NM_009268		Mucl1	Spt-2|Spt2	mucin-like 1	protein-coding
mm_138450.1	chr17	35135798	35135802	+	1	NA	promoter-TSS (NM_001252469)	promoter-TSS (NM_001252469)	86	NM_001252469	224727	Mm.203962	NM_057171	ENSMUSG00000024392	Bag6	2410045D21Rik|AA408914|BAG-6|Bat3|D17H6S52E|G3|Scythe	BCL2-associated athanogene 6	protein-coding
mm_170866.1	chr2	18453679	18453680	+	1	NA	Intergenic	RLTR9E|LTR|ERVK	-60849	NM_007869	13418	Mm.246674	NM_007869	ENSMUSG00000026740	Dnajc1	4733401K02Rik|AA960110|D230036H06Rik|Dnajl1|ERdj1|ERj1p|MTJ1	DnaJ heat shock protein family (Hsp40) member C1	protein-coding
mm_173155.1	chrX	35745896	35745898	-	1	NA	Intergenic	(CTA)n|Simple_repeat|Simple_repeat	-142935	NM_001009947	75974	Mm.32873	NM_177745	ENSMUSG00000031093	Dock11	5033414A21Rik|8030476J24|Zizimin2|sph238	dedicator of cytokinesis 11	protein-coding
mm_116947.1	chr13	56135473	56135508	-	1	NA	promoter-TSS (NM_001159515)	promoter-TSS (NM_001159515)	60	NM_012015	26914	Mm.283802	NM_012015	ENSMUSG00000015937	H2afy	H2AF12M|mH2a1|macroH2A1	H2A histone family, member Y	protein-coding
mm_77585.1	chr8	123859399	123859415	-	1	NA	exon (NM_028536, exon 2 of 4)	exon (NM_028536, exon 2 of 4)	802	NM_028536	73420	Mm.157746	NM_028536	ENSMUSG00000031971	Ccsap	1700054N08Rik|AI853424	centriole, cilia and spindle associated protein	protein-coding
mm_57450.1	chr6	125131787	125131819	-	1	NA	promoter-TSS (NM_138747)	promoter-TSS (NM_138747)	-80	NM_138747	110109	Mm.29203	NM_138747	ENSMUSG00000038279	Nop2	120kDa|A530002O17|Nol1	NOP2 nucleolar protein	protein-coding
mm_42891.1	chr5	122392271	122392274	+	1	NA	intron (NM_019824, intron 1 of 6)	intron (NM_019824, intron 1 of 6)	394	NM_019824	56378	Mm.275942	NM_019824	ENSMUSG00000029465	Arpc3	1110006A04Rik|p21-ARC|p21-Ar|p21Arc	actin related protein 2/3 complex, subunit 3	protein-coding
mm_112545.1	chr13	12156340	12156376	+	1	NA	Intergenic	RLTR26C_MM|LTR|ERVK	30130	NR_045170	328186	Mm.188154	NM_183202		Gm10336	B330003H21|ENSMUSG00000071543	predicted gene 10336	ncRNA
mm_122919.1	chr14	54960429	54960460	-	1	NA	exon (NM_010856, exon 13 of 39)	exon (NM_010856, exon 13 of 39)	6163	NM_001164171	17888	Mm.290003	NM_010856	ENSMUSG00000040752	Myh6	A830009F23Rik|AA517445|Myhc-a|Myhca|alpha-MHC	myosin, heavy polypeptide 6, cardiac muscle, alpha	protein-coding
mm_26440.1	chr3	142623806	142623834	+	1	NA	TTS (NR_105802)	TTS (NR_105802)	126	NR_105802	102465200		NR_105802	ENSMUSG00000098871	Mir6381	Gm27963|mmu-mir-6381	microRNA 6381	ncRNA
mm_46007.1	chr5	90770059	90770062	-	1	NA	TTS (NM_023785)	TTS (NM_023785)	1542	NM_023785	57349	Mm.293614	NM_023785	ENSMUSG00000029372	Ppbp	2400003M24Rik|AI854500|CTAP3|CTAPIII|Cxcl7|LA-PF4|LDGF|MDGF|NAP-2|NAP-2-L1|Scyb7|TGB|TGB1|THBGB1|b-TG1|beta-TG	pro-platelet basic protein	protein-coding
mm_154860.1	chrX	20658451	20658479	+	1	NA	promoter-TSS (NM_001276317)	promoter-TSS (NM_001276317)	-39	NM_001276317	22201	Mm.1104	NM_009457	ENSMUSG00000001924	Uba1	A1S9|Sbx|Ube-1|Ube1x	ubiquitin-like modifier activating enzyme 1	protein-coding
mm_91193.1	chr10	21146425	21146443	-	1	NA	exon (NM_001198914, exon 9 of 16)	exon (NM_001198914, exon 9 of 16)	14550	NM_001198914	17863	Mm.52109	NM_010848	ENSMUSG00000019982	Myb	AI550390|M16449|c-myb	myeloblastosis oncogene	protein-coding
mm_18777.1	chr2	73529726	73529736	-	1	NA	promoter-TSS (NM_153138)	promoter-TSS (NM_153138)	-244	NM_153138	215280	Mm.223504	NM_153138	ENSMUSG00000075284	Wipf1	AI115543|D2Ertd120e|WIP|Waspip	WAS/WASL interacting protein family, member 1	protein-coding
mm_2280.1	chr1	91308634	91308642	+	1	NA	intron (NM_016717, intron 5 of 11)	intron (NM_016717, intron 5 of 11)	10300	NM_016717	50880	Mm.25724	NM_016717	ENSMUSG00000026307	Scly	9830169H08|A930015N15Rik|SCL|Scly1|Scly2	selenocysteine lyase	protein-coding
mm_59277.1	chr7	24904385	24904411	+	1	NA	promoter-TSS (NM_001130152)	promoter-TSS (NM_001130152)	52	NM_001130152	16801	Mm.3181	NM_008488	ENSMUSG00000040940	Arhgef1	Lbcl2|Lsc	Rho guanine nucleotide exchange factor (GEF) 1	protein-coding
mm_38567.1	chr4	141723402	141723436	-	1	NA	promoter-TSS (NM_001017966)	promoter-TSS (NM_001017966)	0	NM_001017966	68817	Mm.393721	NM_001017966	ENSMUSG00000078515	Ddi2	1110056G13Rik|1700027M01Rik|9130022E05Rik|AI604911|AU040698	DNA-damage inducible protein 2	protein-coding
mm_5043.1	chr1	194619851	194619872	+	1	NA	promoter-TSS (NM_008882)	promoter-TSS (NM_008882)	32	NM_008882	18845	Mm.2251	NM_008882	ENSMUSG00000026640	Plxna2	2810428A13Rik|AA589422|AW457381|OCT|PlexA2|Plxn2|mKIAA0463	plexin A2	protein-coding
mm_143092.1	chr17	57080635	57080646	-	1	NA	3' UTR (NM_009451, exon 4 of 4)	3' UTR (NM_009451, exon 4 of 4)	-2130	NM_153551	70785	Mm.284447	NM_153551	ENSMUSG00000002668	Dennd1c	4432409M07Rik	DENN/MADD domain containing 1C	protein-coding
mm_82951.1	chr9	35569741	35569748	-	1	NA	intron (NM_029762, intron 1 of 3)	CpG	325	NM_029762	76832	Mm.482285	NM_029762	ENSMUSG00000050555	Hyls1	3010015K02Rik	hydrolethalus syndrome 1	protein-coding
mm_40185.1	chr5	36237742	36237782	+	1	NA	intron (NM_030889, intron 1 of 26)	Lx5c|LINE|L1	33741	NM_175249	76943	Mm.44242	NM_175249	ENSMUSG00000043430	Psapl1	2310020A21Rik	prosaposin-like 1	protein-coding
mm_117587.1	chr13	89690732	89690735	-	1	NA	exon (NM_019389, exon 7 of 14)	exon (NM_019389, exon 7 of 14)	51779	NM_001081249	13003	Mm.158700	NM_019389	ENSMUSG00000021614	Vcan	5430420N07Rik|9430051N09|Cspg2|DPEAAE|NG2|PG-M|PG-M(V0)|PG-M(V1)|hdf	versican	protein-coding
mm_46626.1	chr5	108434374	108434409	-	1	NA	promoter-TSS (NM_007507)	promoter-TSS (NM_007507)	-13	NM_007507	11958	Mm.136093	NM_007507	ENSMUSG00000050856	Atp5k	2610008D24Rik|Atp5i|Lfm1	ATP synthase, H+ transporting, mitochondrial F1F0 complex, subunit E	protein-coding
mm_144442.1	chr18	22171432	22171435	+	1	NA	promoter-TSS (NM_027616)	promoter-TSS (NM_027616)	-37	NM_027616	70950	Mm.235716	NM_027616	ENSMUSG00000024306	Ccdc178	4921528I01Rik	coiled coil domain containing 178	protein-coding
mm_52148.1	chr6	97980127	97980156	+	1	NA	intron (NM_001113198, intron 2 of 9)	intron (NM_001113198, intron 2 of 9)	-11642	NM_008601	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_136323.1	chr16	92321394	92321400	-	1	NA	promoter-TSS (NM_029252)	promoter-TSS (NM_029252)	44	NM_029252	75328	Mm.72970	NM_029252	ENSMUSG00000051728	4930563D23Rik	-	RIKEN cDNA 4930563D23 gene	protein-coding
mm_41553.1	chr5	92955055	92955058	+	1	NA	intron (NM_001077595, intron 7 of 9)	intron (NM_001077595, intron 7 of 9)	57063	NM_001077596	27428	Mm.46014	NM_015756	ENSMUSG00000029381	Shroom3	AL022960|D5Ertd287e|Shrm|Shrm3	shroom family member 3	protein-coding
mm_35045.1	chr4	4529438	4529464	-	1	NA	promoter-TSS (NM_001277919)	promoter-TSS (NM_001277919)	7	NM_001277919	622019	Mm.246123	NM_001277919		Gm11780	OTTMUSG00000004194	predicted gene 11780	protein-coding
mm_52015.1	chr6	94500358	94500371	+	1	NA	promoter-TSS (NM_026255)	promoter-TSS (NM_026255)	50	NM_026255	67582	Mm.280725	NM_026255	ENSMUSG00000045100	Slc25a26	4930433D19Rik|4933433F13Rik|AW557176|D6Bwg0781e|Slc25a6	solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 26	protein-coding
mm_168876.1	chr12	40884277	40884295	-	1	NA	Intergenic	Intergenic	-139804	NM_053122	93757	Mm.363813	NM_053122	ENSMUSG00000056899	Immp2l	AI853880|IMP2	IMP2 inner mitochondrial membrane peptidase-like (S. cerevisiae)	protein-coding
mm_171719.1	chr4	84675081	84675089	-	1	NA	promoter-TSS (NM_172870)	promoter-TSS (NM_172870)	1	NM_172870	242509	Mm.190774	NM_172870	ENSMUSG00000028487	Bnc2	5031434M05Rik|8430420F16Rik	basonuclin 2	protein-coding
mm_76326.1	chr8	84705268	84705278	-	1	NA	TTS (NM_008535)	TTS (NM_008535)	3816	NM_008535	17095	Mm.4925	NM_008535	ENSMUSG00000034041	Lyl1	Lyl-1|bHLHa18	lymphoblastomic leukemia 1	protein-coding
mm_93021.1	chr10	87860356	87860365	-	1	NA	promoter-TSS (NM_001111276)	promoter-TSS (NM_001111276)	-751	NM_001111274	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_66434.1	chr7	44754035	44754047	-	1	NA	intron (NM_133945, intron 3 of 14)	intron (NM_133945, intron 3 of 14)	5412	NM_133945	101568	Mm.28816	NM_133945	ENSMUSG00000002205	Vrk3	AI428238	vaccinia related kinase 3	protein-coding
mm_125649.1	chr15	62730822	62730841	+	1	NA	Intergenic	Intergenic	-511380	NR_003523	67552	Mm.484027	NM_026230		H2afy3	4933432H23Rik	H2A histone family, member Y3	pseudo
mm_19754.1	chr2	105017016	105017075	-	1	NA	promoter-TSS (NM_145380)	promoter-TSS (NM_145380)	-18	NM_145380	98221	Mm.379278	NM_145380	ENSMUSG00000027170	Eif3m	Ga17|Pcid1|Tango7	eukaryotic translation initiation factor 3, subunit M	protein-coding
mm_166195.1	chr5	37154336	37154345	+	1	NA	Intergenic	Intergenic	69104	NM_001347348	76071	Mm.85280	NM_178394	ENSMUSG00000063646	Jakmip1	5830437M04Rik|C330021K24Rik|Gababrbp|Marlin-1	janus kinase and microtubule interacting protein 1	protein-coding
mm_9798.1	chr1	181845275	181845302	-	1	NA	Intergenic	Intergenic	-2887	NM_133815	98386	Mm.4538	NM_133815	ENSMUSG00000004880	Lbr	AI505894|ic	lamin B receptor	protein-coding
mm_127389.1	chr15	101077882	101077920	+	1	NA	Intergenic	CpG	-23502	NM_001214911	668225	Mm.385011	NM_001214911	ENSMUSG00000095440	Fignl2	EG668225	fidgetin-like 2	protein-coding
mm_110132.1	chr12	26445148	26445160	-	1	NA	3' UTR (NM_021384, exon 6 of 6)	3' UTR (NM_021384, exon 6 of 6)	11298	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_76737.1	chr8	95143191	95143213	-	1	NA	promoter-TSS (NM_010631)	promoter-TSS (NM_010631)	-662	NM_001145831	16582	Mm.378951	NM_010631	ENSMUSG00000031788	Kifc3	AI325457|BB123200	kinesin family member C3	protein-coding
mm_132360.1	chr16	34690549	34690559	+	1	NA	promoter-TSS (NM_172824)	promoter-TSS (NM_172824)	-62	NM_172824	239839	Mm.272045	NM_172824	ENSMUSG00000022833	Ccdc14	G630039H03Rik	coiled-coil domain containing 14	protein-coding
mm_28610.1	chr3	94783109	94783118	-	1	NA	intron (NM_001037711, intron 1 of 20)	intron (NM_001037711, intron 1 of 20)	3402	NM_001293727	70737	Mm.87634	NM_001037711	ENSMUSG00000068876	Cgn	6330408J11Rik	cingulin	protein-coding
mm_165321.1	chr2	107793230	107793233	+	1	NA	Intergenic	Lx5|LINE|L1	502642	NM_021275	16492	Mm.142718	NM_021275	ENSMUSG00000042604	Kcna4	Kv1.4	potassium voltage-gated channel, shaker-related subfamily, member 4	protein-coding
mm_130898.1	chr15	102399667	102399716	-	1	NA	Intergenic	Intergenic	-6625	NM_013672	20683	Mm.4618	NM_013672	ENSMUSG00000001280	Sp1	1110003E12Rik|AA450830|AI845540|Sp1-1	trans-acting transcription factor 1	protein-coding
mm_54184.1	chr6	23839526	23839547	-	1	NA	promoter-TSS (NM_153163)	promoter-TSS (NM_153163)	-115	NM_001252105	320405	Mm.259632	NM_153163	ENSMUSG00000017978	Cadps2	A230044C21Rik|Caps-2|Caps2|Cpd2	Ca2+-dependent activator protein for secretion 2	protein-coding
mm_132077.1	chr16	30093994	30093999	+	1	NA	Intergenic	Intergenic	28639	NM_008235	15205	Mm.390859	NM_008235	ENSMUSG00000022528	Hes1	Hry|bHLHb39	hairy and enhancer of split 1 (Drosophila)	protein-coding
mm_41571.1	chr5	93169951	93169966	+	1	NA	intron (NM_001310671, intron 9 of 9)	intron (NM_001310671, intron 9 of 9)	36537	NM_017367	12453	Mm.250419	NM_017367	ENSMUSG00000063015	Ccni	-	cyclin I	protein-coding
mm_169914.1	chr16	56116292	56116310	-	1	NA	intron (NM_001003972, intron 5 of 6)	RLTR17|LTR|ERVK	40821	NM_001304503	66315	Mm.255784	NM_025483	ENSMUSG00000052917	Senp7	2410152H17Rik|2810413I22Rik|2900036C23Rik|6030449K19Rik|AI790676	SUMO1/sentrin specific peptidase 7	protein-coding
mm_143179.1	chr17	57247633	57247694	-	1	NA	promoter-TSS (NM_030084)	promoter-TSS (NM_030084)	26	NM_001308072	78308	Mm.28468	NM_030084	ENSMUSG00000005823	Gpr108	1810015L19Rik|AA589464|C79132|Lustr2	G protein-coupled receptor 108	protein-coding
mm_2112.1	chr1	87853339	87853343	+	1	NA	promoter-TSS (NM_177646)	promoter-TSS (NM_177646)	54	NM_177646	227333	Mm.277217	NM_177646	ENSMUSG00000070738	Dgkd	AI841987|D330025K09|DGKdelta|dgkd-2	diacylglycerol kinase, delta	protein-coding
mm_105203.1	chr11	102097605	102097607	-	1	NA	Intergenic	Intergenic	3694	NM_008918	19064	Mm.1269	NM_008918	ENSMUSG00000017316	Ppy	AV061413|IGSPP|PP	pancreatic polypeptide	protein-coding
mm_1451.1	chr1	67230611	67230628	+	1	NA	3' UTR (NM_001080809, exon 38 of 38)	3' UTR (NM_001080809, exon 38 of 38)	107592	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_148782.1	chr19	6112925	6112937	+	1	NA	exon (NM_001009546, exon 13 of 18)	exon (NM_001009546, exon 13 of 18)	5655	NM_133678	66406	Mm.303924	NM_133678	ENSMUSG00000024790	Sac3d1	2410004C24Rik|AU015683|shd1	SAC3 domain containing 1	protein-coding
mm_81356.1	chr9	108650135	108650145	+	1	NA	promoter-TSS (NM_011790)	promoter-TSS (NM_011790)	-760	NM_011790	23807	Mm.290447	NM_011790	ENSMUSG00000064145	Arih2	AI843547|ARI2|TRIAD1|UIP48	ariadne RBR E3 ubiquitin protein ligase 2	protein-coding
mm_71706.1	chr8	61931585	61931596	+	1	NA	intron (NM_001293783, intron 1 of 37)	Lx7|LINE|L1	3503	NM_001293783	234311	Mm.275233	NM_144928	ENSMUSG00000037921	Ddx60	9830118M07	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	protein-coding
mm_64194.1	chr7	141464094	141464113	+	1	NA	intron (NM_001025103, intron 3 of 9)	intron (NM_001025103, intron 3 of 9)	3009	NM_001025103	213573	Mm.386851	NM_001025103	ENSMUSG00000048200	Cracr2b	6330520A15Rik|BC026645|Cracr2a|Efcab4|Efcab4a	calcium release activated channel regulator 2B	protein-coding
mm_77715.1	chr8	126593947	126593971	-	1	NA	promoter-TSS (NM_001164598)	promoter-TSS (NM_001164598)	-523	NM_001164598	270110	Mm.334918	NM_001164598	ENSMUSG00000051495	Irf2bp2	E130305N23Rik|IRF-2BP2	interferon regulatory factor 2 binding protein 2	protein-coding
mm_88694.1	chr10	80142280	80142290	+	1	NA	promoter-TSS (NM_025313)	promoter-TSS (NM_025313)	10	NM_001347092	66043	Mm.278560	NM_025313	ENSMUSG00000003072	Atp5d	0610008F14Rik|1500000I11Rik|AA960090|AI876556|AU020773|C85518	ATP synthase, H+ transporting, mitochondrial F1 complex, delta subunit	protein-coding
mm_73984.1	chr8	120627470	120627475	+	1	NA	intron (NM_001308449, intron 2 of 3)	intron (NM_001308449, intron 2 of 3)	6910	NM_197988	68918	Mm.473736	NM_197988	ENSMUSG00000043687	1190005I06Rik	-	RIKEN cDNA 1190005I06 gene	protein-coding
mm_60498.1	chr7	44478909	44478924	+	1	NA	Intergenic	L1M4c|LINE|L1	-5601	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_39688.1	chr5	26904458	26904481	+	1	NA	promoter-TSS (NM_001198886)	promoter-TSS (NM_001198886)	-309	NM_001198886	13483	Mm.42078	NM_010075	ENSMUSG00000061576	Dpp6	B930011P16Rik|D5Buc3|D5Buc4|D5Buc5|DPP VI|Dpp-6|Gm1377|In(5)6H-p|Peplb|Rw	dipeptidylpeptidase 6	protein-coding
mm_102591.1	chr11	61915194	61915208	-	1	NA	exon (NM_019921, exon 4 of 15)	exon (NM_019921, exon 4 of 15)	15056	NM_019921	56697	Mm.274404	NM_019921	ENSMUSG00000047804	Akap10	1500031L16Rik|B130049N18Rik|D-AKAP-2|D-AKAP2|PRKA10	A kinase (PRKA) anchor protein 10	protein-coding
mm_55194.1	chr6	52191676	52191685	-	1	NA	promoter-TSS (NM_008265)	promoter-TSS (NM_008265)	23	NM_008265	15401	Mm.439647	NM_008265	ENSMUSG00000000942	Hoxa4	AV206827|Hox-1.4	homeobox A4	protein-coding
mm_74829.1	chr8	23191179	23191198	-	1	NA	5' UTR (NM_018743, exon 2 of 13)	5' UTR (NM_018743, exon 2 of 13)	17265	NM_018743	102247	Mm.200898	NM_018743	ENSMUSG00000031545	Gpat4	AU041707|AW545732|Agpat6|Tsarg7	glycerol-3-phosphate acyltransferase 4	protein-coding
mm_59735.1	chr7	28813276	28813294	+	1	NA	exon (NM_177301, exon 2 of 13)	exon (NM_177301, exon 2 of 13)	2395	NM_177301	15388	Mm.9043	NM_177301	ENSMUSG00000015165	Hnrnpl	C79783|D830027H13Rik|Hnrpl	heterogeneous nuclear ribonucleoprotein L	protein-coding
mm_42048.1	chr5	108520282	108520300	+	1	NA	exon (NM_007756, exon 4 of 4)	exon (NM_007756, exon 4 of 4)	29736	NM_007756	12889	Mm.5195	NM_007756	ENSMUSG00000033615	Cplx1	921-S	complexin 1	protein-coding
mm_25285.1	chr3	105704658	105704680	+	1	NA	promoter-TSS (NM_001163356)	promoter-TSS (NM_001163356)	70	NM_175398	109050	Mm.212591	NM_175398	ENSMUSG00000048458	Fam212b	6530418L21Rik|inka2	family with sequence similarity 212, member B	protein-coding
mm_125913.1	chr15	76033046	76033055	+	1	NA	Intergenic	Intergenic	-18714	NM_134087	105732	Mm.267178	NM_134087	ENSMUSG00000046761	Fam83h	AA409316	family with sequence similarity 83, member H	protein-coding
mm_85123.1	chr9	95489803	95489819	-	1	NA	exon (NM_001114977, exon 12 of 28)	exon (NM_001114977, exon 12 of 28)	22185	NM_026476	67958	Mm.292742	NM_026476	ENSMUSG00000032407	U2surp	2610101N10Rik|AU023006|Sr140	U2 snRNP-associated SURP domain containing	protein-coding
mm_93822.1	chr10	121476249	121476275	-	1	NA	promoter-TSS (NM_138956)	promoter-TSS (NM_138956)	-12	NM_138956	192678	Mm.41265	NM_138956	ENSMUSG00000025795	Rassf3	AW212023|AW322379	Ras association (RalGDS/AF-6) domain family member 3	protein-coding
mm_32396.1	chr4	106836901	106836905	+	1	NA	Intergenic	Intergenic	-31896	NM_001347159	329910	Mm.222956	NM_025590	ENSMUSG00000034853	Acot11	1110020M10Rik|2010309H15Rik|AW060409|BFIT|BFIT1|Thea|Them1|mKIAA0707	acyl-CoA thioesterase 11	protein-coding
mm_2892.1	chr1	131910484	131910539	+	1	NA	promoter-TSS (NM_001145804)	promoter-TSS (NM_001145804)	53	NM_001145804	98415	Mm.246869	NM_175294	ENSMUSG00000026434	Nucks1	2700010L10Rik|8430423A01Rik|AI647518|C78391|Nucks	nuclear casein kinase and cyclin-dependent kinase substrate 1	protein-coding
mm_60392.1	chr7	44474764	44474776	+	1	NA	Intergenic	Intergenic	4423	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_57661.1	chr6	128487452	128487481	-	1	NA	exon (NM_007376, exon 31 of 36)	exon (NM_007376, exon 31 of 36)	39254	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_133092.1	chr16	62854348	62854361	+	1	NA	promoter-TSS (NM_011173)	promoter-TSS (NM_011173)	47	NM_011173	19128	Mm.127156	NM_011173	ENSMUSG00000022912	Pros1	AW214361	protein S (alpha)	protein-coding
mm_60059.1	chr7	31162061	31162072	+	1	NA	promoter-TSS (NR_046062)	promoter-TSS (NR_046062)	-292	NR_046062	100038516	Mm.387223	NR_046062	ENSMUSG00000100985	Gm10640	EG668322|ENSMUSG00000074193	predicted gene 10640	ncRNA
mm_157630.1	chrX	56731874	56731875	-	1	NA	promoter-TSS (NM_001077361)	promoter-TSS (NM_001077361)	-83	NM_001077361	14199	Mm.3126	NM_010211	ENSMUSG00000023092	Fhl1	FHL-1|KyoT|RAM14-1|SLIM|SLIM-1	four and a half LIM domains 1	protein-coding
mm_157485.1	chrX	48208698	48208708	-	1	NA	promoter-TSS (NM_172465)	promoter-TSS (NM_172465)	-1	NM_172465	208884	Mm.207367	NM_172465	ENSMUSG00000036985	Zdhhc9	6430508G22|9530098M12Rik	zinc finger, DHHC domain containing 9	protein-coding
mm_122053.1	chr14	30206128	30206131	-	1	NA	intron (NM_001302637, intron 3 of 48)	intron (NM_001302637, intron 3 of 48)	147357	NM_001302637	12289	Mm.9772	NM_028981	ENSMUSG00000015968	Cacna1d	8430418G19Rik|C79217|Cach3|Cacn4|Cacnl1a2|Cav1.3|Cchl1a|Cchl1a2|D-LTCC	calcium channel, voltage-dependent, L type, alpha 1D subunit	protein-coding
mm_66398.1	chr7	44306904	44306953	-	1	NA	promoter-TSS (NM_009131)	promoter-TSS (NM_009131)	31	NM_009131	20256	Mm.20428	NM_009131	ENSMUSG00000004473	Clec11a	AW457320|Clecsf3|Scgf	C-type lectin domain family 11, member a	protein-coding
mm_122303.1	chr14	34674641	34674674	-	1	NA	intron (NM_001004436, intron 1 of 18)	CpG	729	NM_001301330	218914	Mm.27957	NM_001004436	ENSMUSG00000041408	Wapl	A530089A20Rik|BC037674|DIF-2|FOE|Wapal	WAPL cohesin release factor	protein-coding
mm_105606.1	chr11	106782113	106782117	-	1	NA	TTS (NR_037224)	TTS (NR_037224)	644	NR_037224	100526469		NR_037224	ENSMUSG00000093273	Mir3064	mir-3064|mmu-mir-3064	microRNA 3064	ncRNA
mm_147592.1	chr18	56572889	56572945	-	1	NA	promoter-TSS (NM_001127338)	promoter-TSS (NM_001127338)	22	NM_001127338	110695	Mm.30250	NM_138600	ENSMUSG00000053644	Aldh7a1	Atq1|D18Wsu181e	aldehyde dehydrogenase family 7, member A1	protein-coding
mm_114857.1	chr13	93304923	93304935	+	1	NA	5' UTR (NM_011982, exon 1 of 5)	5' UTR (NM_011982, exon 1 of 5)	1172	NM_011982	26556	Mm.37533	NM_011982	ENSMUSG00000007617	Homer1	PSD-Zip45|SYN47|Ves-1|homer-1|vesl-1	homer scaffolding protein 1	protein-coding
mm_41314.1	chr5	90469583	90469617	+	1	NA	exon (NM_009654, exon 9 of 15)	exon (NM_009654, exon 9 of 15)	8730	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_109404.1	chr12	110444717	110444748	+	1	NA	Intergenic	RMER15|LTR|ERVL	-2447	NM_001135001	26931	Mm.240396	NM_012023	ENSMUSG00000017843	Ppp2r5c	2610043M05Rik|2700063L20Rik|AI060890|AW545884|C85228|D12Bwg0916e|mKIAA0044	protein phosphatase 2, regulatory subunit B', gamma	protein-coding
mm_125153.1	chr15	30647009	30647084	+	1	NA	exon (NM_008729, exon 7 of 23)	exon (NM_008729, exon 7 of 23)	-392080	NR_045186	73784	Mm.66947	NR_045186		4930430F21Rik	-	RIKEN cDNA 4930430F21 gene	ncRNA
mm_23342.1	chr3	54693060	54693079	+	1	NA	promoter-TSS (NM_019995)	promoter-TSS (NM_019995)	-36	NM_019995	56790	Mm.486375	NM_019995	ENSMUSG00000027751	Supt20	AA667204|AI450544|D3Ertd300e|Fam48a|Supt20h|p38IP	suppressor of Ty 20	protein-coding
mm_3556.1	chr1	150423541	150423557	+	1	NA	exon (NM_133780, exon 26 of 52)	exon (NM_133780, exon 26 of 52)	-30494	NM_145511	226499	Mm.222093	NM_145511	ENSMUSG00000006010	BC003331	1810053E15Rik|Odr4|odr-4	cDNA sequence BC003331	protein-coding
mm_114754.1	chr13	85126691	85126702	+	1	NA	Intergenic	Intergenic	-62689	NM_001347587	66671	Mm.18474	NM_023243	ENSMUSG00000021548	Ccnh	6330408H09Rik|AI661354|AV102684|AW538719	cyclin H	protein-coding
mm_74158.1	chr8	123397790	123397825	+	1	NA	intron (NM_001286362, intron 12 of 16)	intron (NM_001286362, intron 12 of 16)	-9275	NM_008559	17199	Mm.324942	NM_008559	ENSMUSG00000074037	Mc1r	Mcr1|Mshra|Tob|e	melanocortin 1 receptor	protein-coding
mm_155375.1	chrX	71556875	71556904	+	1	NA	intron (NM_001293623, intron 1 of 4)	CpG	972	NM_001293625	15354	Mm.336087	NM_008253	ENSMUSG00000015217	Hmgb3	Hmg2a|Hmg4	high mobility group box 3	protein-coding
mm_90731.1	chr10	5289398	5289436	-	1	NA	exon (NM_001347711, exon 55 of 146)	exon (NM_001347711, exon 55 of 146)	-94710	NM_001079686	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_57286.1	chr6	124415038	124415078	-	1	NA	promoter-TSS (NM_008995)	promoter-TSS (NM_008995)	9	NM_008995	19305	Mm.22418	NM_008995	ENSMUSG00000005069	Pex5	AW212715|ESTM1|PTS1R|Pxr1|X83306	peroxisomal biogenesis factor 5	protein-coding
mm_1901.1	chr1	85793412	85793517	+	1	NA	promoter-TSS (NM_133781)	promoter-TSS (NM_133781)	17	NM_133781	12283	Mm.26135	NM_133781	ENSMUSG00000036707	Cab39	AA408805|AA960512|C78372|MO25|MO25alpha	calcium binding protein 39	protein-coding
mm_81873.1	chr9	119102464	119102530	+	1	NA	promoter-TSS (NM_177117)	promoter-TSS (NM_177117)	19	NM_177117	320256	Mm.110648	NM_177117	ENSMUSG00000038060	Dlec1	D630005C06Rik	deleted in lung and esophageal cancer 1	protein-coding
mm_99800.1	chr11	107548836	107548841	+	1	NA	intron (NM_198298, intron 1 of 31)	intron (NM_198298, intron 1 of 31)	878	NM_198298	78455	Mm.272047	NM_198298	ENSMUSG00000020721	Helz	3110078M01Rik|9430093I07Rik|9630002H22Rik|AI851979|DRHC	helicase with zinc finger domain	protein-coding
mm_16067.1	chr2	168080883	168080910	+	1	NA	promoter-TSS (NM_021409)	promoter-TSS (NM_021409)	-108	NM_021409	58220	Mm.292834	NM_021409	ENSMUSG00000044641	Pard6b	AV025615|Par6b	par-6 family cell polarity regulator beta	protein-coding
mm_28506.1	chr3	92534503	92534519	-	1	NA	Intergenic	Intergenic	-34018	NM_173070	229562	Mm.246590	NM_173070	ENSMUSG00000045566	Sprr4	-	small proline-rich protein 4	protein-coding
mm_61140.1	chr7	57419646	57419658	+	1	NA	intron (NM_176942, intron 7 of 9)	intron (NM_176942, intron 7 of 9)	32380	NR_033504	791383	Mm.403104	NR_033504	ENSMUSG00000055048	Gm9962	ENSMUSG00000055048	predicted gene 9962	ncRNA
mm_50470.1	chr6	48987846	48987855	+	1	NA	exon (NM_172888, exon 1 of 5)	exon (NM_172888, exon 1 of 5)	989	NM_172888	243377	Mm.446302	NM_172888	ENSMUSG00000039215	Svs1	9530003A11	seminal vesicle secretory protein 1	protein-coding
mm_114231.1	chr13	56609234	56609257	+	1	NA	promoter-TSS (NM_009369)	promoter-TSS (NM_009369)	-358	NM_009369	21810	Mm.14455	NM_009369	ENSMUSG00000035493	Tgfbi	68kDa|AI181842|AI747162|Beta-ig|big-h3	transforming growth factor, beta induced	protein-coding
mm_31794.1	chr4	63979881	63979883	+	1	NA	intron (NM_011607, intron 15 of 25)	intron (NM_011607, intron 15 of 25)	67133	NM_011607	21923	Mm.980	NM_011607	ENSMUSG00000028364	Tnc	AI528729|C130033P17Rik|Hxb|TN|TN-C|Ten|cytotactin|tenascin-C	tenascin C	protein-coding
mm_115426.1	chr13	117229353	117229362	+	1	NA	intron (NM_010330, intron 1 of 8)	intron (NM_010330, intron 1 of 8)	8784	NM_010330	13723	Mm.274926	NM_010330	ENSMUSG00000021728	Emb	AL022799|Gp70	embigin	protein-coding
mm_171199.1	chr3	51415961	51415961	+	1	NA	promoter-TSS (NM_053089)	promoter-TSS (NM_053089)	-55	NM_053089	74838	Mm.275281	NM_053089	ENSMUSG00000063273	Naa15	5730450D16Rik|6330400I15|ASTBDN|Narg1|Tbdn-1|mNAT1	N(alpha)-acetyltransferase 15, NatA auxiliary subunit	protein-coding
mm_92723.1	chr10	80812564	80812584	-	1	NA	intron (NM_028001, intron 1 of 6)	MIRc|SINE|MIR	924	NM_028001	71912	Mm.45137	NM_028001	ENSMUSG00000020216	Jsrp1	2300003C06Rik|2310032K21Rik|JP-45|JP45	junctional sarcoplasmic reticulum protein 1	protein-coding
mm_141121.1	chr17	26095452	26095461	-	1	NA	promoter-TSS (NM_019731)	promoter-TSS (NM_019731)	14	NM_019731	56520	Mm.41787	NM_019731	ENSMUSG00000024177	Nme4	2610027N22Rik|2810024O08Rik|5730493H09Rik|NM23-M4|Nm23M4	NME/NM23 nucleoside diphosphate kinase 4	protein-coding
mm_36734.1	chr4	99122486	99122497	-	1	NA	Intergenic	Intergenic	-1576	NM_026082	67299	Mm.260623	NM_026082	ENSMUSG00000028556	Dock7	3110056M06Rik|Gm430	dedicator of cytokinesis 7	protein-coding
mm_1525.1	chr1	72828632	72828642	+	1	NA	intron (NM_001310659, intron 1 of 3)	B1_Mur4|SINE|Alu	3250	NM_001310659	16008	Mm.141936	NM_008342	ENSMUSG00000039323	Igfbp2	AI255832|IBP-2|Igfbp-2|mIGFBP-2	insulin-like growth factor binding protein 2	protein-coding
mm_82830.1	chr9	31149927	31149956	-	1	NA	3' UTR (NM_009691, exon 16 of 16)	3' UTR (NM_009691, exon 16 of 16)	-18142	NM_011176	19143	Mm.243926	NM_011176	ENSMUSG00000031995	St14	Epithin|MT-SP1|Prss14|Tmprss14|mCAP3|matriptase	suppression of tumorigenicity 14 (colon carcinoma)	protein-coding
mm_155186.1	chrX	56322977	56322989	+	1	NA	Intergenic	Intergenic	5375	NR_038168	72030	Mm.426148	NR_038168	ENSMUSG00000085114	1600025M17Rik	Gm394	RIKEN cDNA 1600025M17 gene	ncRNA
mm_112531.1	chr13	9350077	9350080	+	1	NA	intron (NM_001081426, intron 1 of 36)	intron (NM_001081426, intron 1 of 36)	73553	NM_001081426	208440	Mm.217326	NM_172459	ENSMUSG00000048264	Dip2c	2900024P20Rik|9630044M06|mKIAA0934	disco interacting protein 2 homolog C	protein-coding
mm_75675.1	chr8	67920998	67921012	-	1	NA	intron (NM_177698, intron 3 of 14)	intron (NM_177698, intron 3 of 14)	-10059	NM_030263	234353	Mm.32525	NM_027626	ENSMUSG00000030465	Psd3	4931420C21Rik|AI661273|BC003498|D430018P08|EFA6D	pleckstrin and Sec7 domain containing 3	protein-coding
mm_96675.1	chr11	69411398	69411412	+	1	NA	intron (NM_001017426, intron 1 of 22)	CpG	2270	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_91081.1	chr10	19012169	19012184	-	1	NA	promoter-TSS (NM_001166402)	promoter-TSS (NM_001166402)	-213	NM_001166402	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_6545.1	chr1	75128602	75128621	-	1	NA	exon (NM_194333, exon 10 of 12)	exon (NM_194333, exon 10 of 12)	5279	NM_194333	22626	Mm.68157	NM_194333	ENSMUSG00000026205	Slc23a3	SVCT3|Yspl1	solute carrier family 23 (nucleobase transporters), member 3	protein-coding
mm_120377.1	chr14	64588113	64588120	+	1	NA	promoter-TSS (NR_040709)	promoter-TSS (NR_040709)	1	NR_040709	268755	Mm.194050	NR_040709	ENSMUSG00000097545	Mir124a-1hg	A930011O12Rik|Rncr3|mir-124-1|mir-3078	Mir124-1 host gene (non-protein coding)	ncRNA
mm_92426.1	chr10	77088914	77088951	-	1	NA	exon (NM_001109991, exon 3 of 41)	exon (NM_001109991, exon 3 of 41)	24773	NM_001109991	12822	Mm.4352	NM_009929	ENSMUSG00000001435	Col18a1	-	collagen, type XVIII, alpha 1	protein-coding
mm_23203.1	chr3	41539241	41539243	+	1	NA	Intergenic	Intergenic	-10768	NR_130791	78648	Mm.366093	NR_130791		2400006E01Rik	lncRNA-JADE	RIKEN cDNA 2400006E01 gene	ncRNA
mm_65686.1	chr7	28367713	28367722	-	1	NA	exon (NM_001083912, exon 9 of 19)	exon (NM_001083912, exon 9 of 19)	4945	NM_138752	101497	Mm.235700	NM_138752	ENSMUSG00000037552	Plekhg2	AI194308|Clg|Cslg	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	protein-coding
mm_29502.1	chr3	116114557	116114569	-	1	NA	exon (NM_011693, exon 8 of 9)	exon (NM_011693, exon 8 of 9)	15125	NM_011693	22329	Mm.76649	NM_011693	ENSMUSG00000027962	Vcam1	CD106|Vcam-1	vascular cell adhesion molecule 1	protein-coding
mm_52134.1	chr6	97946834	97946855	+	1	NA	intron (NM_001113198, intron 2 of 9)	intron (NM_001113198, intron 2 of 9)	17027	NM_001178049	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_9542.1	chr1	173912905	173912932	-	1	NA	5' UTR (NM_001301745, exon 1 of 7)	5' UTR (NM_001301745, exon 1 of 7)	128	NM_001301745	381308	Mm.490248	NM_001033450	ENSMUSG00000026536	Ifi211	A730048F03|Ifi205b|Mnda|ifi-205-B	interferon activated gene 211	protein-coding
mm_169264.1	chr13	84222357	84222358	+	1	NA	promoter-TSS (NR_138587)	promoter-TSS (NR_138587)	61	NM_175187	72745	Mm.295063	NM_175187	ENSMUSG00000035762	Tmem161b	2810446P07Rik|AI843389	transmembrane protein 161B	protein-coding
mm_114827.1	chr13	91930665	91930671	+	1	NA	intron (NM_009027, intron 5 of 14)	ORR1A4|LTR|ERVL-MaLR	-53783	NM_198415	76722	Mm.316438	NM_198415	ENSMUSG00000021622	Ckmt2	2300008A19Rik|ScCKmit	creatine kinase, mitochondrial 2	protein-coding
mm_164299.1	chr15	103896049	103896050	-	1	NA	exon (NM_009267, exon 4 of 4)	exon (NM_009267, exon 4 of 4)	3251	NM_009268	20771	Mm.30276	NM_009268		Mucl1	Spt-2|Spt2	mucin-like 1	protein-coding
mm_14751.1	chr2	144594057	144594083	+	1	NA	promoter-TSS (NM_001033297)	promoter-TSS (NM_001033297)	5	NM_001033297	228715	Mm.27391	NM_001033297	ENSMUSG00000074754	Gm561	-	predicted gene 561	protein-coding
mm_169280.1	chr13	94858491	94858504	+	1	NA	Intergenic	RLTR9D|LTR|ERVK	-17130	NM_011021	18420	Mm.42051	NM_011021	ENSMUSG00000021685	Otp	-	orthopedia homeobox	protein-coding
mm_64373.1	chr7	142442377	142442421	+	1	NA	promoter-TSS (NM_009405)	promoter-TSS (NM_009405)	-69	NM_009405	21953	Mm.39469	NM_009405	ENSMUSG00000031097	Tnni2	-	troponin I, skeletal, fast 2	protein-coding
mm_80480.1	chr9	78206017	78206029	+	1	NA	exon (NM_010357, exon 5 of 7)	exon (NM_010357, exon 5 of 7)	14057	NM_010357	14860	Mm.2662	NM_010357	ENSMUSG00000032348	Gsta4	GST5.7|mGsta4	glutathione S-transferase, alpha 4	protein-coding
mm_7112.1	chr1	89968275	89968315	-	1	NA	exon (NM_139152, exon 4 of 6)	exon (NM_139152, exon 4 of 6)	-37119	NM_010262	14472	Mm.204730	NM_010262	ENSMUSG00000034486	Gbx2	D130058E05Rik|Gbx-2|MMoxA|Stra7	gastrulation brain homeobox 2	protein-coding
mm_39034.1	chr4	152305264	152305270	-	1	NA	non-coding (NR_037908, exon 6 of 6)	non-coding (NR_037908, exon 6 of 6)	8053	NM_133788	57295	Mm.277464	NM_133788	ENSMUSG00000039662	Icmt	1700008E11Rik|C80758|Gm13095|HSTE14|OTTMUSG00000010406|PPMT|STE14|pcCMT	isoprenylcysteine carboxyl methyltransferase	protein-coding
mm_53221.1	chr6	126939958	126939988	+	1	NA	promoter-TSS (NM_001347455)	promoter-TSS (NM_001347455)	7	NM_138594	28040	Mm.44228	NM_138594	ENSMUSG00000030347	D6Wsu163e	C12orf4	DNA segment, Chr 6, Wayne State University 163, expressed	protein-coding
mm_90883.1	chr10	9886708	9886725	-	1	NA	intron (NM_001081344, intron 2 of 25)	L1MC1|LINE|L1	14324	NM_001081344	78808	Mm.331751	NM_030191	ENSMUSG00000019790	Stxbp5	0710001E20Rik|4930565N16Rik|AW742610|LGL3|mKIAA1006	syntaxin binding protein 5 (tomosyn)	protein-coding
mm_127289.1	chr15	100060246	100060258	+	1	NA	intron (NM_001159361, intron 1 of 37)	intron (NM_001159361, intron 1 of 37)	21588	NM_001159361	239667	Mm.243658	NM_172819	ENSMUSG00000023026	Dip2b	4932422C22|AI317237|AI854602|mKIAA1463	disco interacting protein 2 homolog B	protein-coding
mm_139721.1	chr17	57472561	57472579	+	1	NA	intron (NM_010130, intron 18 of 21)	L1_Mus3|LINE|L1	72744	NM_001104591	224916	Mm.469889	NM_001104591	ENSMUSG00000090655	Vmn2r120	EG224916	vomeronasal 2, receptor 120	protein-coding
mm_96028.1	chr11	59549210	59549218	+	1	NA	exon (NM_145827, exon 4 of 10)	exon (NM_145827, exon 4 of 10)	6528	NM_145827	216799	Mm.54174	NM_145827	ENSMUSG00000032691	Nlrp3	AGTAVPRL|AII/AVP|Cias1|FCAS|FCU|MWS|Mmig1|NALP3|Pypaf1	NLR family, pyrin domain containing 3	protein-coding
mm_158024.1	chrX	96166809	96166820	-	1	NA	3' UTR (NM_010833, exon 13 of 13)	3' UTR (NM_010833, exon 13 of 13)	70769	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_125711.1	chr15	68928381	68928393	+	1	NA	promoter-TSS (NM_010158)	promoter-TSS (NM_010158)	-33	NM_010158	13992	Mm.17964	NM_010158	ENSMUSG00000022332	Khdrbs3	Etle|SLM-2|Salp|Slm2|T-STAR	KH domain containing, RNA binding, signal transduction associated 3	protein-coding
mm_127072.1	chr15	97376689	97376702	+	1	NA	intron (NM_172293, intron 5 of 5)	intron (NM_172293, intron 5 of 5)	-129408	NM_001164602	105827	Mm.24005	NM_178114	ENSMUSG00000048218	Amigo2	AI415330|AMIGO-2|AW208913|Ali1	adhesion molecule with Ig like domain 2	protein-coding
mm_65295.1	chr7	24512434	24512438	-	1	NA	intron (NR_110958, intron 2 of 2)	intron (NR_110958, intron 2 of 2)	5349	NR_110958	232969	Mm.181332	NM_146183	ENSMUSG00000064264	Zfp428	2410005H09Rik|AV271806|AW047854|Znf428	zinc finger protein 428	protein-coding
mm_85792.1	chr9	109832668	109832680	-	1	NA	promoter-TSS (NM_018757)	promoter-TSS (NM_018757)	-120	NM_018757	54369	Mm.12951	NM_018757	ENSMUSG00000032478	Nme6	nm23-M6	NME/NM23 nucleoside diphosphate kinase 6	protein-coding
mm_95166.1	chr11	40692775	40692802	+	1	NA	promoter-TSS (NM_134017)	promoter-TSS (NM_134017)	-106	NM_134017	108645	Mm.293771	NM_134017	ENSMUSG00000042032	Mat2b	1110064C04Rik|2410018D16Rik|AI182287|AU022853|MAT-II|MATIIbeta|TGR	methionine adenosyltransferase II, beta	protein-coding
mm_10828.1	chr2	24386334	24386369	+	1	NA	intron (NM_177611, intron 1 of 16)	intron (NM_177611, intron 1 of 16)	954	NM_177611	215632	Mm.490434	NM_177611	ENSMUSG00000026979	Psd4	BC046518|EFA6B	pleckstrin and Sec7 domain containing 4	protein-coding
mm_53755.1	chr6	145387604	145387621	+	1	NA	promoter-TSS (NR_003625)	promoter-TSS (NR_003625)	-13	NR_003625	381827	Mm.179075	NM_001001987		1700073E17Rik	-	ribosomal protein L7 pseudogene	pseudo
mm_53002.1	chr6	123270344	123270376	+	1	NA	exon (NM_010819, exon 5 of 6)	exon (NM_010819, exon 5 of 6)	8253	NM_010819	17474	Mm.441101	NM_010819	ENSMUSG00000030144	Clec4d	Clecsf8|Mpcl|mcl	C-type lectin domain family 4, member d	protein-coding
mm_158933.1	chr1	72536392	72536392	-	1	NA	5' UTR (NM_001045533, exon 1 of 4)	5' UTR (NM_001045533, exon 1 of 4)	172	NM_001045533	381270	Mm.337023	NM_001045533	ENSMUSG00000039372	March4	BC056494|mKIAA1399	membrane-associated ring finger (C3HC4) 4	protein-coding
mm_18500.1	chr2	62610569	62610579	-	1	NA	exon (NM_027835, exon 7 of 16)	exon (NM_027835, exon 7 of 16)	35681	NM_027835	71586	Mm.136224	NM_027835	ENSMUSG00000026896	Ifih1	9130009C22Rik|Helicard|Hlcd|MDA5|RLR-2	interferon induced with helicase C domain 1	protein-coding
mm_172556.1	chr8	105594036	105594036	+	1	NA	Intergenic	Intergenic	-11193	NM_001081241	75687	Mm.41261	NM_001081241	ENSMUSG00000038604	Fam65a	2310066E14Rik|AI837433	family with sequence similarity 65, member A	protein-coding
mm_124323.1	chr14	103815751	103815763	-	1	NA	3' UTR (NM_001136061, exon 8 of 8)	3' UTR (NM_001136061, exon 8 of 8)	27944	NM_007904	13618	Mm.229532	NM_007904	ENSMUSG00000022122	Ednrb	ET-B|ET-BR|ETR-b|ETb|Sox10m1	endothelin receptor type B	protein-coding
mm_139374.1	chr17	51832816	51832825	+	1	NA	promoter-TSS (NM_009122)	promoter-TSS (NM_009122)	-173	NM_009122	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_148950.1	chr19	7268714	7268732	+	1	NA	5' UTR (NM_001320554, exon 1 of 12)	5' UTR (NM_001320554, exon 1 of 12)	444	NM_001320554	104383	Mm.283859	NM_054048	ENSMUSG00000024968	Rcor2	1A13|AW122124|CoREST|Rcor|Rcor1	REST corepressor 2	protein-coding
mm_21601.1	chr2	164238243	164238248	-	1	NA	promoter-TSS (NM_017390)	promoter-TSS (NM_017390)	96	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_73125.1	chr8	94781171	94781177	+	1	NA	3' UTR (NM_009142, exon 3 of 3)	3' UTR (NM_009142, exon 3 of 3)	8994	NM_009142	20312	Mm.103711	NM_009142	ENSMUSG00000031778	Cx3cl1	AB030188|ABCD-3|AI848747|CX3C|Cxc3|D8Bwg0439e|Scyd1	chemokine (C-X3-C motif) ligand 1	protein-coding
mm_97974.1	chr11	83860614	83860631	+	1	NA	intron (NM_001291268, intron 2 of 8)	intron (NM_001291268, intron 2 of 8)	7662	NM_001291269	21410	Mm.7226	NM_009330	ENSMUSG00000020679	Hnf1b	HNF-1-beta|HNF-1B|HNF-1Beta|Hnf1beta|LFB3|Tcf-2|Tcf2|vHNF1	HNF1 homeobox B	protein-coding
mm_40639.1	chr5	64910223	64910233	+	1	NA	Intergenic	RSINE1|SINE|B4	22471	NM_030682	21897	Mm.273024	NM_030682	ENSMUSG00000044827	Tlr1	-	toll-like receptor 1	protein-coding
mm_94043.1	chr10	128176469	128176489	-	1	NA	promoter-TSS (NM_019711)	promoter-TSS (NM_019711)	89	NM_019711	56516	Mm.42247	NM_019711	ENSMUSG00000040043	Rbms2	2610315E04Rik|Scr3	RNA binding motif, single stranded interacting protein 2	protein-coding
mm_36170.1	chr4	61855789	61855793	-	1	NA	Intergenic	RLTR1F_Mm|LTR|ERVK	-20611	NM_008649	17844	Mm.445286	NM_008649	ENSMUSG00000058523	Mup5	Mup18	major urinary protein 5	protein-coding
mm_63838.1	chr7	135605777	135605784	+	1	NA	promoter-TSS (NM_001316679)	promoter-TSS (NM_001316679)	-48	NM_001316679	19267	Mm.945	NM_011212	ENSMUSG00000041836	Ptpre	PTPe|PTPepsilon|RPTPepsilon	protein tyrosine phosphatase, receptor type, E	protein-coding
mm_149881.1	chr19	25300571	25300582	+	1	NA	intron (NM_181404, intron 2 of 13)	intron (NM_181404, intron 2 of 13)	63374	NM_181404	107351	Mm.260722	NM_181404	ENSMUSG00000032702	Kank1	A930031B09Rik|AU015049|AW121052|Ankrd15|D330024H06Rik|mKIAA0172	KN motif and ankyrin repeat domains 1	protein-coding
mm_171370.1	chr4	119282299	119282300	-	1	NA	exon (NM_011732, exon 5 of 8)	exon (NM_011732, exon 5 of 8)	12214	NM_011732	22608	Mm.258204	NM_011732	ENSMUSG00000028639	Ybx1	1700102N10Rik|C79409|EF1A|MSY1|Nsep1|YB-1|dbpB|mYB-1a	Y box protein 1	protein-coding
mm_28860.1	chr3	97227384	97227421	-	1	NA	promoter-TSS (NM_029933)	promoter-TSS (NM_029933)	-38	NM_029933	77578	Mm.226175	NM_029933	ENSMUSG00000038256	Bcl9	2610202E01Rik|8030475K17Rik|A330041G23Rik|Gm130	B cell CLL/lymphoma 9	protein-coding
mm_49199.1	chr6	15208075	15208080	+	1	NA	intron (NM_053242, intron 4 of 18)	intron (NM_053242, intron 4 of 18)	22571	NM_001286607	114142	Mm.332919	NM_053242	ENSMUSG00000029563	Foxp2	2810043D05Rik|AI449000|CAG-16|D0Kist7	forkhead box P2	protein-coding
mm_51115.1	chr6	67759667	67759672	+	1	NA	Intergenic	Intergenic	-193970	NR_003100	75070	Mm.463364	NR_003100		4930515G16Rik	-	myc induced nuclear antigen pseudogene	pseudo
mm_157636.1	chrX	57182630	57182636	-	1	NA	Intergenic	Intergenic	-18004	NR_038463	100502842	Mm.164733	NR_038463	ENSMUSG00000085808	Gm14718	OTTMUSG00000017790	predicted gene 14718	ncRNA
mm_72189.1	chr8	72491848	72491862	+	1	NA	exon (NM_177766, exon 2 of 6)	exon (NM_177766, exon 2 of 6)	759	NM_177766	270066	Mm.291461	NM_177766	ENSMUSG00000019731	Slc35e1	6030458H05|AA408278	solute carrier family 35, member E1	protein-coding
mm_131204.1	chr16	8619798	8619811	+	1	NA	3' UTR (NM_001170978, exon 15 of 15)	3' UTR (NM_001170978, exon 15 of 15)	17897	NM_025708	66690	Mm.10068	NM_025708	ENSMUSG00000043140	Tmem186	2810440M13Rik|4432406C05Rik|AI648175|AW210586	transmembrane protein 186	protein-coding
mm_160292.1	chr7	128154363	128154363	+	1	NA	Intergenic	Intergenic	-19583	NM_001029872	381924	Mm.334257	NM_001029872	ENSMUSG00000070369	Itgad	Cd11d	integrin, alpha D	protein-coding
mm_101097.1	chr11	11897702	11897708	-	1	NA	intron (NM_001190448, intron 1 of 14)	intron (NM_001190448, intron 1 of 14)	439	NM_001190448	13195	Mm.12906	NM_016672	ENSMUSG00000020182	Ddc	Aadc	dopa decarboxylase	protein-coding
mm_122687.1	chr14	52020035	52020078	-	1	NA	promoter-TSS (NM_001253694)	promoter-TSS (NM_001253694)	-343	NM_001253694	69890	Mm.475652	NM_027248	ENSMUSG00000049295	Zfp219	2010302A17Rik	zinc finger protein 219	protein-coding
mm_78360.1	chr9	25570624	25570633	+	1	NA	intron (NM_026189, intron 3 of 7)	intron (NM_026189, intron 3 of 7)	89031	NM_026189	67484	Mm.112977	NM_026189	ENSMUSG00000036611	Eepd1	2310005P05Rik|AI481005	endonuclease/exonuclease/phosphatase family domain containing 1	protein-coding
mm_111465.1	chr12	98572367	98572370	-	1	NA	intron (NM_029911, intron 1 of 6)	intron (NM_029911, intron 1 of 6)	2344	NM_001316666	72258	Mm.196158	NM_029911	ENSMUSG00000033854	Kcnk10	1700024D23Rik|3010005K24Rik|Trek2	potassium channel, subfamily K, member 10	protein-coding
mm_141283.1	chr17	27909207	27909264	-	1	NA	promoter-TSS (NM_001286041)	promoter-TSS (NM_001286041)	-71	NM_001286040	224650	Mm.32556	NM_181413	ENSMUSG00000024219	Anks1	Anks1a|mKIAA0229	ankyrin repeat and SAM domain containing 1	protein-coding
mm_40219.1	chr5	37242026	37242081	+	1	NA	promoter-TSS (NM_001136058)	promoter-TSS (NM_001136058)	-5	NM_001136058	12933	Mm.290995	NM_007765	ENSMUSG00000029121	Crmp1	CRMP-1|DRP-1|Dpysl1|ULIP-3|Ulip3	collapsin response mediator protein 1	protein-coding
mm_115243.1	chr13	110394599	110394633	+	1	NA	promoter-TSS (NM_152804)	promoter-TSS (NM_152804)	-428	NM_152804	20620	Mm.380	NM_152804	ENSMUSG00000021701	Plk2	Snk	polo-like kinase 2	protein-coding
mm_75878.1	chr8	70766655	70766671	-	1	NA	promoter-TSS (NM_023065)	promoter-TSS (NM_023065)	0	NM_023065	65972	Mm.30241	NM_023065	ENSMUSG00000031838	Ifi30	GILT|IP30	interferon gamma inducible protein 30	protein-coding
mm_96528.1	chr11	68503082	68503113	+	1	NA	promoter-TSS (NM_001081566)	promoter-TSS (NM_001081566)	78	NR_126154	104709	Mm.234573	NM_001004435	ENSMUSG00000046207	Pik3r6	BB220380|p84|p84 PIKAP|p87(PIKAP)|p87PIKAP	phosphoinositide-3-kinase, regulatory subunit 6	protein-coding
mm_96593.1	chr11	69090844	69090859	+	1	NA	3' UTR (NM_009497, exon 5 of 5)	3' UTR (NM_009497, exon 5 of 5)	2323	NM_009497	22318	Mm.28643	NM_009497	ENSMUSG00000020894	Vamp2	Syb-2|Syb2|sybII	vesicle-associated membrane protein 2	protein-coding
mm_75528.1	chr8	57310383	57310393	-	1	NA	intron (NR_110474, intron 2 of 4)	intron (NR_110474, intron 2 of 4)	10471	NR_110474	102636514		NR_110474	ENSMUSG00000100510	Uph	-	upperhand	ncRNA
mm_71124.1	chr8	36458081	36458093	+	1	NA	Intergenic	CpG	-31104	NM_176952	319582	Mm.180924	NM_176952	ENSMUSG00000039620	6430573F11Rik	Kiaa1456|TRM9L	RIKEN cDNA 6430573F11 gene	protein-coding
mm_116738.1	chr13	51756606	51756636	-	1	NA	intron (NM_001281880, intron 2 of 16)	intron (NM_001281880, intron 2 of 16)	37126	NM_001281880	20354	Mm.33903	NM_013660	ENSMUSG00000021451	Sema4d	CD100|Semacl2|Semaj|Semcl2|coll-4	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D	protein-coding
mm_148353.1	chr18	84685616	84685671	-	1	NA	promoter-TSS (NM_023149)	promoter-TSS (NM_023149)	59	NM_023149	66054	Mm.29646	NM_023149	ENSMUSG00000024644	Cndp2	0610010E05Rik|C76600|Cn2|Dip-2|Pep-1|Pep1	CNDP dipeptidase 2 (metallopeptidase M20 family)	protein-coding
mm_89513.1	chr10	94162279	94162297	+	1	NA	exon (NM_011629, exon 3 of 14)	exon (NM_011629, exon 3 of 14)	14357	NM_011629	22025	Mm.107483	NM_011629	ENSMUSG00000005897	Nr2c1	4831444H07Rik|80.3|Eenr|TR2|Tr2-11	nuclear receptor subfamily 2, group C, member 1	protein-coding
mm_52361.1	chr6	112489225	112489256	+	1	NA	exon (NM_001081147, exon 1 of 2)	exon (NM_001081147, exon 1 of 2)	568	NM_001081147	18430	Mm.333310	NM_001081147	ENSMUSG00000049112	Oxtr	OTR	oxytocin receptor	protein-coding
mm_82980.1	chr9	35934366	35934366	-	1	NA	Intergenic	L1MCa|LINE|L1	-84486	NR_030730	100041605	Mm.99350	NR_030730	ENSMUSG00000098705	Gm3428	-	predicted gene 3428	ncRNA
mm_46227.1	chr5	99037149	99037206	-	1	NA	promoter-TSS (NM_008926)	promoter-TSS (NM_008926)	-98	NM_008926	19092	Mm.263002	NM_008926	ENSMUSG00000029334	Prkg2	AW212535|CGKII|Prkgr2|cGK-II	protein kinase, cGMP-dependent, type II	protein-coding
mm_84084.1	chr9	58202351	58202363	-	1	NA	promoter-TSS (NM_177193)	promoter-TSS (NM_177193)	-13	NM_001161539	320563	Mm.186499	NM_177193	ENSMUSG00000051243	Islr2	B930052A04Rik|Linx|Mbu-3|mKIAA1465	immunoglobulin superfamily containing leucine-rich repeat 2	protein-coding
mm_102901.1	chr11	69433106	69433114	-	1	NA	intron (NM_001081330, intron 72 of 85)	intron (NM_001081330, intron 72 of 85)	-19435	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_76632.1	chr8	92059692	92059695	-	1	NA	Intergenic	MIRb|SINE|MIR	-258039	NM_008393	16373	Mm.238044	NM_008393	ENSMUSG00000031734	Irx3	AI894186	Iroquois related homeobox 3	protein-coding
mm_163396.1	chr12	69197165	69197197	+	1	NA	promoter-TSS (NR_033222)	promoter-TSS (NR_033222)	-30	NR_033222	414085	Mm.256223	NR_033222	ENSMUSG00000097061	9330151L19Rik	-	RIKEN cDNA 9330151L19 gene	ncRNA
mm_11638.1	chr2	34871090	34871113	+	1	NA	promoter-TSS (NM_080554)	promoter-TSS (NM_080554)	-139	NM_080554	66998	Mm.270632	NM_080554	ENSMUSG00000026869	Psmd5	1500032A03Rik|AW475925|S5b|W91691|mKIAA0072	proteasome (prosome, macropain) 26S subunit, non-ATPase, 5	protein-coding
mm_25557.1	chr3	116184669	116184680	+	1	NA	Intergenic	Intergenic	-54986	NM_011693	22329	Mm.76649	NM_011693	ENSMUSG00000027962	Vcam1	CD106|Vcam-1	vascular cell adhesion molecule 1	protein-coding
mm_26380.1	chr3	142568426	142568439	+	1	NA	intron (NM_001289493, intron 7 of 10)	intron (NM_001289493, intron 7 of 10)	7936	NM_001289493	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_122290.1	chr14	34552211	34552222	-	1	NA	exon (NM_001039071, exon 8 of 13)	exon (NM_001039071, exon 8 of 13)	-29415	NM_030062	78243	Mm.117483	NM_030062	ENSMUSG00000021797	9230112D13Rik	-	RIKEN cDNA 9230112D13 gene	protein-coding
mm_128978.1	chr15	74833485	74833497	-	1	NA	Intergenic	B3|SINE|B2	8152	NM_001033229	110115	Mm.322606	NM_001033229	ENSMUSG00000075604	Cyp11b1	AA389061|CPN1|Cyp11b|Cyp11b-1|FHI	cytochrome P450, family 11, subfamily b, polypeptide 1	protein-coding
mm_151639.1	chr19	4012739	4012749	-	1	NA	promoter-TSS (NM_133666)	promoter-TSS (NM_133666)	11	NM_133666	17995	Mm.29842	NM_133666	ENSMUSG00000037916	Ndufv1	CI-51kD	NADH dehydrogenase (ubiquinone) flavoprotein 1	protein-coding
mm_75516.1	chr8	54718665	54718689	-	1	NA	promoter-TSS (NM_028220)	promoter-TSS (NM_028220)	1	NM_028220	244484	Mm.95281	NM_028220	ENSMUSG00000039375	Wdr17	3010002I12Rik|B230207L18Rik	WD repeat domain 17	protein-coding
mm_88348.1	chr10	75841963	75841965	+	1	NA	Intergenic	Intergenic	-7083	NM_010361	14872	Mm.24118	NM_010361	ENSMUSG00000033318	Gstt2	AI266894|Yrs|mGSTT2	glutathione S-transferase, theta 2	protein-coding
mm_118568.1	chr14	18330039	18330040	+	1	NA	intron (NM_009455, intron 2 of 5)	intron (NM_009455, intron 2 of 5)	1805	NM_009455	22194	Mm.4429	NM_009455	ENSMUSG00000021774	Ube2e1	UbcM3|Ubce5|ubcM2	ubiquitin-conjugating enzyme E2E 1	protein-coding
mm_107188.1	chr12	25097429	25097439	+	1	NA	Intergenic	Intergenic	-1342	NM_010496	15902	Mm.34871	NM_010496	ENSMUSG00000020644	Id2	AI255428|C78922|Idb2|bHLHb26	inhibitor of DNA binding 2	protein-coding
mm_158534.1	chrX	143923424	143923432	-	1	NA	exon (NM_010025, exon 3 of 7)	exon (NM_010025, exon 3 of 7)	9696	NM_001110222	13193	Mm.12871	NM_010025	ENSMUSG00000031285	Dcx	Dbct	doublecortin	protein-coding
mm_2552.1	chr1	108373106	108373111	+	1	NA	Intergenic	Lx8b|LINE|L1	455849	NR_102307	319596	Mm.136054	NR_102306	ENSMUSG00000100457	D830032E09Rik	-	RIKEN cDNA D830032E09 gene	ncRNA
mm_72402.1	chr8	81770112	81770121	+	1	NA	intron (NM_001024617, intron 6 of 24)	intron (NM_001024617, intron 6 of 24)	427554	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_170083.1	chr17	35400675	35400692	+	1	NA	Intergenic	Intergenic	6584	NR_051981	15016	Mm.439648	NR_051981	ENSMUSG00000055413	H2-Q5	H-2Q5|Qa-5|Qa5|Qat-5	histocompatibility 2, Q region locus 5	pseudo
mm_82017.1	chr9	121720567	121720569	+	1	NA	intron (NM_010918, intron 2 of 16)	intron (NM_010918, intron 2 of 16)	1387	NM_010918	18087	Mm.32842	NM_010918	ENSMUSG00000032525	Nktr	5330401F18Rik|D9Wsu172e	natural killer tumor recognition sequence	protein-coding
mm_135683.1	chr16	52424437	52424454	-	1	NA	intron (NM_009655, intron 1 of 15)	intron (NM_009655, intron 1 of 15)	28636	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_152432.1	chr19	10685176	10685209	-	1	NA	non-coding (NR_131163, exon 2 of 2)	non-coding (NR_131163, exon 2 of 2)	399	NR_131163	72305	Mm.383489	NR_131163		2210404E10Rik	-	RIKEN cDNA 2210404E10 gene	ncRNA
mm_157981.1	chrX	94123360	94123412	-	1	NA	promoter-TSS (NM_011768)	promoter-TSS (NM_011768)	21	NM_011768	22764	Mm.919	NM_011768	ENSMUSG00000079509	Zfx	Zfx5|Zfx5,6|Zfx6	zinc finger protein X-linked	protein-coding
mm_55702.1	chr6	72900131	72900216	-	1	NA	promoter-TSS (NM_019715)	promoter-TSS (NM_019715)	-194	NM_019715	74287	Mm.29194	NM_019715	ENSMUSG00000055239	Kcmf1	1700094M07Rik|Debt91|Pmcf	potassium channel modulatory factor 1	protein-coding
mm_6494.1	chr1	74236652	74236681	-	1	NA	5' UTR (NM_029711, exon 1 of 10)	5' UTR (NM_029711, exon 1 of 10)	116	NM_029711	76709	Mm.337038	NM_029711	ENSMUSG00000006304	Arpc2	2210023N03Rik|34kDa|p34-Arc	actin related protein 2/3 complex, subunit 2	protein-coding
mm_168095.1	chr10	128705067	128705069	-	1	NA	promoter-TSS (NM_016756)	promoter-TSS (NM_016756)	-17	NM_016756	12566	Mm.111326	NM_016756	ENSMUSG00000025358	Cdk2	A630093N05Rik	cyclin-dependent kinase 2	protein-coding
mm_168392.1	chr11	27233915	27233915	+	1	NA	Intergenic	Intergenic	448807	NR_002890	654472	Mm.347777	NR_002890		Gm12070	OTTMUSG00000005300	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_167303.1	chr8	57511882	57511884	+	1	NA	promoter-TSS (NM_008252)	promoter-TSS (NM_008252)	40	NM_008252	97165	Mm.276881	NM_008252	ENSMUSG00000054717	Hmgb2	C80539|HMG-2|Hmg2	high mobility group box 2	protein-coding
mm_160978.1	chr11	102317246	102317246	-	1	NA	promoter-TSS (NM_001044383)	promoter-TSS (NM_001044383)	41	NM_001044383	21429	Mm.2845	NM_011551	ENSMUSG00000020923	Ubtf	A930005G04Rik|NOR-90|Tcfubf|UBF|UBF-1|UBF1	upstream binding transcription factor, RNA polymerase I	protein-coding
mm_109419.1	chr12	110497615	110497626	+	1	NA	intron (NM_012023, intron 1 of 13)	intron (NM_012023, intron 1 of 13)	11881	NM_012023	26931	Mm.240396	NM_012023	ENSMUSG00000017843	Ppp2r5c	2610043M05Rik|2700063L20Rik|AI060890|AW545884|C85228|D12Bwg0916e|mKIAA0044	protein phosphatase 2, regulatory subunit B', gamma	protein-coding
mm_162609.1	chr1	183297030	183297073	+	1	NA	promoter-TSS (NM_027861)	promoter-TSS (NM_027861)	-9	NM_181732	108909	Mm.290502	NM_145626	ENSMUSG00000042901	Aida	2610208M17Rik|BC004835	axin interactor, dorsalization associated	protein-coding
mm_113756.1	chr13	44734035	44734069	+	1	NA	intron (NM_001205044, intron 2 of 18)	CpG	2781	NM_001205043	16468	Mm.25059	NM_021878	ENSMUSG00000038518	Jarid2	Jmj|jumonji	jumonji, AT rich interactive domain 2	protein-coding
mm_112826.1	chr13	20805182	20805190	+	1	NA	intron (NM_012054, intron 1 of 20)	Lx8b|LINE|L1	11073	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_52465.1	chr6	113697402	113697412	+	1	NA	5' UTR (NM_001347356, exon 1 of 8)	5' UTR (NM_001347356, exon 1 of 8)	357	NM_001033463	381801	Mm.333322	NM_001033463	ENSMUSG00000056952	Tatdn2	AI646012|mKIAA0218	TatD DNase domain containing 2	protein-coding
mm_15583.1	chr2	158762119	158762137	+	1	NA	3' UTR (NM_001159662, exon 11 of 11)	3' UTR (NM_001159662, exon 11 of 11)	-5971	NM_027975	71878	Mm.85162	NM_027975	ENSMUSG00000027654	Fam83d	2310007D09Rik|BB104611	family with sequence similarity 83, member D	protein-coding
mm_139723.1	chr17	57476296	57476315	+	1	NA	intron (NM_010130, intron 19 of 21)	intron (NM_010130, intron 19 of 21)	69009	NM_001104591	224916	Mm.469889	NM_001104591	ENSMUSG00000090655	Vmn2r120	EG224916	vomeronasal 2, receptor 120	protein-coding
mm_23002.1	chr3	34057065	34057071	+	1	NA	TTS (NM_001026211)	TTS (NM_001026211)	24286	NM_001286972	67713	Mm.274266	NM_026332	ENSMUSG00000027679	Dnajc19	1810055D05Rik|AA959924|Tim14	DnaJ heat shock protein family (Hsp40) member C19	protein-coding
mm_109087.1	chr12	104414058	104414076	+	1	NA	3' UTR (NM_009252, exon 5 of 5)	3' UTR (NM_009252, exon 5 of 5)	7359	NM_009252	20716	Mm.482074	NM_009252	ENSMUSG00000021091	Serpina3n	Spi2-2|Spi2.2|Spi2/eb.4	serine (or cysteine) peptidase inhibitor, clade A, member 3N	protein-coding
mm_89581.1	chr10	95730335	95730337	+	1	NA	Intergenic	Intergenic	-166169	NM_027722	71207	Mm.24397	NM_027722	ENSMUSG00000020029	Nudt4	4933436C10Rik|DIPP2|DIPP2alpha|DIPP2beta|HDCMB47P	nudix (nucleoside diphosphate linked moiety X)-type motif 4	protein-coding
mm_158203.1	chrX	105391771	105391781	-	1	NA	promoter-TSS (NR_015552)	promoter-TSS (NR_015552)	-22	NR_015552	100043213	Mm.388967	NR_015552	ENSMUSG00000087620	5330434G04Rik	-	RIKEN cDNA 5330434G04 gene	ncRNA
mm_55364.1	chr6	57535423	57535447	-	1	NA	promoter-TSS (NM_175523)	promoter-TSS (NM_175523)	-9	NM_175523	243382	Mm.396893	NM_175523	ENSMUSG00000037826	Ppm1k	2900063A19Rik|A930026L03Rik|PP2Cm	protein phosphatase 1K (PP2C domain containing)	protein-coding
mm_77838.1	chr9	5298768	5298781	+	1	NA	intron (NM_009807, intron 1 of 9)	intron (NM_009807, intron 1 of 9)	257	NM_009807	12362	Mm.1051	NM_009807	ENSMUSG00000025888	Casp1	ICE|Il1bc	caspase 1	protein-coding
mm_138334.1	chr17	34896959	34896977	+	1	NA	TTS (NM_198886)	TTS (NM_198886)	-1524	NM_001286575	110147	Mm.35345	NM_145830	ENSMUSG00000013787	Ehmt2	Bat8|D17Ertd710e|G9a|KMT1C|NG36	euchromatic histone lysine N-methyltransferase 2	protein-coding
mm_115671.1	chr13	12527012	12527015	-	1	NA	Intergenic	Intergenic	-6563	NM_133643	171211	Mm.159671	NM_133643	ENSMUSG00000095105	Edaradd	1810032E07Rik|5830469M23Rik|A630043P06|cr	EDAR (ectodysplasin-A receptor)-associated death domain	protein-coding
mm_69553.1	chr7	135698059	135698076	-	1	NA	exon (NM_001081117, exon 12 of 14)	exon (NM_001081117, exon 12 of 14)	18312	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_2788.1	chr1	130849047	130849079	+	1	NA	exon (NM_011082, exon 8 of 11)	exon (NM_011082, exon 8 of 11)	-16714	NM_026976	69169	Mm.46042	NM_026976	ENSMUSG00000042474	Fcmr	1810037B05Rik|Faim3|FcmuR|Toso	Fc fragment of IgM receptor	protein-coding
mm_111337.1	chr12	86883946	86884034	-	1	NA	5' UTR (NM_145836, exon 1 of 1)	5' UTR (NM_145836, exon 1 of 1)	824	NM_145836	238330	Mm.248358	NM_145836	ENSMUSG00000034168	Irf2bpl	6430527G18Rik|Eap1	interferon regulatory factor 2 binding protein-like	protein-coding
mm_102228.1	chr11	54910117	54910156	-	1	NA	TTS (NM_021327)	TTS (NM_021327)	7282	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_111071.1	chr12	80132275	80132278	-	1	NA	intron (NR_033514, intron 1 of 2)	intron (NR_033514, intron 1 of 2)	568	NR_033514	69548	Mm.269712	NR_033514	ENSMUSG00000097729	2310015A10Rik	5330419I17Rik	RIKEN cDNA 2310015A10 gene	ncRNA
mm_145416.1	chr18	58408901	58408947	+	1	NA	Intergenic	Intergenic	-147316	NM_001081072	225579	Mm.258517	NM_001081072	ENSMUSG00000024600	Slc27a6	4732438L20Rik|FACVL2|FATP6|VLCS-H1	solute carrier family 27 (fatty acid transporter), member 6	protein-coding
mm_52622.1	chr6	117174060	117174072	+	1	NA	3' UTR (NM_021704, exon 3 of 3)	3' UTR (NM_021704, exon 3 of 3)	5531	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_134958.1	chr16	31311329	31311341	-	1	NA	intron (NM_001301354, intron 1 of 4)	intron (NM_001301354, intron 1 of 4)	3473	NM_001301353	11815	Mm.2082	NM_007470	ENSMUSG00000022548	Apod	-	apolipoprotein D	protein-coding
mm_95825.1	chr11	55405239	55405265	+	1	NA	exon (NM_009242, exon 5 of 10)	exon (NM_009242, exon 5 of 10)	14828	NM_009242	20692	Mm.291442	NM_009242	ENSMUSG00000018593	Sparc	BM-40|ON	secreted acidic cysteine rich glycoprotein	protein-coding
mm_1134.1	chr1	60490202	60490220	+	1	NA	exon (NM_001045513, exon 14 of 14)	exon (NM_001045513, exon 14 of 14)	76554	NM_001045513	77300	Mm.440325	NM_001045513	ENSMUSG00000026014	Raph1	9430025M21Rik|C730009O10Rik|Lpd	Ras association (RalGDS/AF-6) and pleckstrin homology domains 1	protein-coding
mm_130345.1	chr15	97731635	97731643	-	1	NA	promoter-TSS (NM_001168693)	promoter-TSS (NM_001168693)	-234	NM_001168693	19011	Mm.1001	NM_008902	ENSMUSG00000022468	Endou	Pp11r|Tcl-30	endonuclease, polyU-specific	protein-coding
mm_89825.1	chr10	105841065	105841132	+	1	NA	promoter-TSS (NM_025602)	promoter-TSS (NM_025602)	282	NM_207522	216292	Mm.250875	NM_207522	ENSMUSG00000036009	Mettl25	-	methyltransferase like 25	protein-coding
mm_10477.1	chr2	14603827	14603859	+	1	NA	promoter-TSS (NM_023116)	promoter-TSS (NM_023116)	-463	NM_023116	12296	Mm.313930	NM_023116	ENSMUSG00000057914	Cacnb2	AW060387|CAB2|Cavbeta2|Cchb2	calcium channel, voltage-dependent, beta 2 subunit	protein-coding
mm_43987.1	chr5	146455562	146455566	+	1	NA	exon (NM_145155, exon 6 of 10)	exon (NM_145155, exon 6 of 10)	-26379	NM_001243104	623198	Mm.489582	NM_001243104	ENSMUSG00000096344	Gm6408	-	predicted gene 6408	protein-coding
mm_133091.1	chr16	62854335	62854345	+	1	NA	promoter-TSS (NM_011173)	promoter-TSS (NM_011173)	33	NM_011173	19128	Mm.127156	NM_011173	ENSMUSG00000022912	Pros1	AW214361	protein S (alpha)	protein-coding
mm_92797.1	chr10	81350390	81350466	-	1	NA	promoter-TSS (NM_001163166)	promoter-TSS (NM_001163166)	-1	NM_010440	15353	Mm.38474	NM_010440	ENSMUSG00000020232	Hmg20b	AW610687|BRAF35|Hmgx2|Hmgxb2|Smarce1r	high mobility group 20B	protein-coding
mm_50865.1	chr6	55376285	55376351	+	1	NA	promoter-TSS (NM_001003685)	promoter-TSS (NM_001003685)	23	NM_001003685	14602	Mm.89928	NM_001003685	ENSMUSG00000004654	Ghrhr	Ghrfr|lit|little	growth hormone releasing hormone receptor	protein-coding
mm_138223.1	chr17	34330052	34330066	+	1	NA	intron (NM_001033978, intron 1 of 4)	ORR1E|LTR|ERVL-MaLR	4384	NM_001033978	381091	Mm.139204	NM_001033978	ENSMUSG00000067341	H2-Eb2	A130038H09Rik|H-2Eb2|Ia-5|Ia5|Iebeta2	histocompatibility 2, class II antigen E beta2	protein-coding
mm_111009.1	chr12	78980602	78980624	-	1	NA	intron (NM_178745, intron 1 of 2)	intron (NM_178745, intron 1 of 2)	2865	NM_001170401	268567	Mm.341747	NM_178745	ENSMUSG00000046157	Tmem229b	6330442E10Rik|9830138K24|AU019070	transmembrane protein 229B	protein-coding
mm_94826.1	chr11	23306429	23306472	+	1	NA	promoter-TSS (NM_001190401)	promoter-TSS (NM_001190401)	-445	NM_001190401	17847	Mm.119155	NM_001190401	ENSMUSG00000056342	Usp34	A530081C03Rik|Murr2	ubiquitin specific peptidase 34	protein-coding
mm_26568.1	chr3	146598984	146598989	+	1	NA	intron (NM_009474, intron 1 of 7)	intron (NM_009474, intron 1 of 7)	1837	NM_009474	22262	Mm.10865	NM_009474	ENSMUSG00000028186	Uox	AI663847	urate oxidase	protein-coding
mm_134177.1	chr16	10960459	10960461	-	1	NA	3' UTR (NM_019980, exon 4 of 4)	3' UTR (NM_019980, exon 4 of 4)	32661	NM_019980	56722	Mm.294753	NM_019980	ENSMUSG00000022500	Litaf	3222402J11Rik|C85531|N4WBP3|TBX1	LPS-induced TN factor	protein-coding
mm_111667.1	chr12	103336918	103336936	-	1	NA	intron (NM_023049, intron 3 of 9)	intron (NM_023049, intron 3 of 9)	19074	NM_023049	65256	Mm.27159	NM_023049	ENSMUSG00000021200	Asb2	1110008E15Rik	ankyrin repeat and SOCS box-containing 2	protein-coding
mm_44266.1	chr5	5663264	5663294	-	1	NA	intron (NM_172447, intron 1 of 22)	intron (NM_172447, intron 1 of 22)	953	NM_172447	207686	Mm.319007	NM_172447	ENSMUSG00000040473	Cfap69	4921525K03|A330021E22Rik|AI427898	cilia and flagella associated protein 69	protein-coding
mm_152751.1	chr19	20010140	20010148	-	1	NA	Intergenic	Intergenic	380527	NM_010730	16952	Mm.248360	NM_010730	ENSMUSG00000024659	Anxa1	Anx-1|Anx-A1|C430014K04Rik|Lpc-1|Lpc1	annexin A1	protein-coding
mm_69675.1	chr7	139984764	139984832	-	1	NA	exon (NM_001291066, exon 19 of 24)	exon (NM_001291066, exon 19 of 24)	2076	NR_106029	102465643		NR_106029	ENSMUSG00000099092	Mir7062	Gm27339|mmu-mir-7062	microRNA 7062	ncRNA
mm_106932.1	chr12	8572153	8572166	+	1	NA	intron (NM_177802, intron 1 of 6)	ERVB7_2-LTR_MM|LTR|ERVK	26907	NM_177802	328059	Mm.46326	NM_177802	ENSMUSG00000020600	Slc7a15	Arpat	solute carrier family 7 (cationic amino acid transporter, y+ system), member 15	protein-coding
mm_42196.1	chr5	112286123	112286141	+	1	NA	intron (NM_001326590, intron 1 of 5)	B2_Mm2|SINE|B2	9441	NM_009419	22022	Mm.250631	NM_009419	ENSMUSG00000029344	Tpst2	AI448750|D5Ucla3|Tango13b|grm|grt	protein-tyrosine sulfotransferase 2	protein-coding
mm_142414.1	chr17	45549688	45549719	-	1	NA	promoter-TSS (NM_001013749)	promoter-TSS (NM_001013749)	-26	NM_001013749	210573	Mm.329064	NM_001013749	ENSMUSG00000096847	Tmem151b	Gm323	transmembrane protein 151B	protein-coding
mm_37639.1	chr4	127971715	127971723	-	1	NA	promoter-TSS (NM_001134733)	promoter-TSS (NM_001134733)	-878	NM_001134733	635169	Mm.346755	NM_001134733	ENSMUSG00000028813	CK137956	-	cDNA sequence CK137956	protein-coding
mm_165662.1	chr3	87971146	87971150	+	1	NA	promoter-TSS (NM_016701)	promoter-TSS (NM_016701)	55	NM_016701	18008	Mm.331129	NM_016701	ENSMUSG00000004891	Nes	AA166324|C78523|ESTM46	nestin	protein-coding
mm_98244.1	chr11	88201425	88201435	+	1	NA	intron (NM_001291270, intron 1 of 4)	intron (NM_001291270, intron 1 of 4)	-2958	NM_024174	64656	Mm.168680	NM_024174	ENSMUSG00000023723	Mrps23	D11Bwg1153e|MRP-S23|Rpms23|S23mt	mitochondrial ribosomal protein S23	protein-coding
mm_144002.1	chr17	88065772	88065831	-	1	NA	promoter-TSS (NM_001081034)	promoter-TSS (NM_001081034)	-516	NM_001081034	225055	Mm.386857	NM_001081034	ENSMUSG00000005371	Fbxo11	C80048|Jf	F-box protein 11	protein-coding
mm_131983.1	chr16	25040254	25040278	+	1	NA	Intergenic	Intergenic	-19373	NR_040374	319487	Mm.137341	NR_040374	ENSMUSG00000096960	A230028O05Rik	-	RIKEN cDNA A230028O05 gene	ncRNA
mm_103454.1	chr11	76263092	76263103	-	1	NA	exon (NM_008750, exon 6 of 8)	exon (NM_008750, exon 6 of 8)	19361	NM_183263	67390	Mm.24886	NM_183263	ENSMUSG00000038046	Rnmtl1	4833420N02Rik|AI255153|HC90|Mrm3	RNA methyltransferase like 1	protein-coding
mm_108599.1	chr12	85455566	85455606	+	1	NA	Intergenic	Intergenic	-18315	NM_010234	14281	Mm.246513	NM_010234	ENSMUSG00000021250	Fos	D12Rfj1|c-fos|cFos	FBJ osteosarcoma oncogene	protein-coding
mm_23372.1	chr3	55467194	55467197	+	1	NA	3' UTR (NM_001195540, exon 3 of 3)	3' UTR (NM_001195540, exon 3 of 3)	5437	NM_001195540	13175	Mm.393242	NM_019978	ENSMUSG00000027797	Dclk1	1700113D08Rik|2810480F11Rik|AI836758|Click-I|Cpg16|Dcamkl1|Dcl|Dclk|mKIAA0369	doublecortin-like kinase 1	protein-coding
mm_81152.1	chr9	107278846	107278858	+	1	NA	intron (NM_001316691, intron 1 of 7)	intron (NM_001316691, intron 1 of 7)	10544	NM_001316691	102626	Mm.222612	NM_178907	ENSMUSG00000032577	Mapkapk3	3PK|AI874665|MAPKAP-K3|MAPKAP3|MK-3|MK3|MapkKapk3	mitogen-activated protein kinase-activated protein kinase 3	protein-coding
mm_67876.1	chr7	99183841	99183860	-	1	NA	Intergenic	B1_Mur4|SINE|Alu	-1137	NM_026384	67800	Mm.180189	NM_026384	ENSMUSG00000030747	Dgat2	0610010B06Rik|ARAT|DGAT-2	diacylglycerol O-acyltransferase 2	protein-coding
mm_100228.1	chr11	117156367	117156385	+	1	NA	exon (NM_001166506, exon 15 of 16)	exon (NM_001166506, exon 15 of 16)	41204	NM_001166506	74136	Mm.272312	NM_028777	ENSMUSG00000020823	Sec14l1	1200017E04Rik|2810012L19Rik|Naa-35	SEC14-like lipid binding 1	protein-coding
mm_103115.1	chr11	69997245	69997258	-	1	NA	promoter-TSS (NM_001291127)	promoter-TSS (NM_001291127)	-211	NM_001291127	78246	Mm.20805	NM_030064	ENSMUSG00000018572	Phf23	JUNE-1	PHD finger protein 23	protein-coding
mm_25177.1	chr3	103263061	103263067	+	1	NA	Intergenic	RMER19C|LTR|ERVK	-16229	NM_053170	94093	Mm.195036	NM_053170	ENSMUSG00000033014	Trim33	8030451N04Rik|AI413936|Ecto|Tif1g	tripartite motif-containing 33	protein-coding
mm_30133.1	chr3	142150092	142150097	-	1	NA	intron (NM_001277216, intron 1 of 11)	intron (NM_001277216, intron 1 of 11)	19134	NM_001277217	12167	Mm.39089	NM_007560	ENSMUSG00000052430	Bmpr1b	AI385617|ALK-6|AV355320|Acvrlk6|Alk6|BMPR-1B|BMPR-IB|CFK-43a|SKR6	bone morphogenetic protein receptor, type 1B	protein-coding
mm_116098.1	chr13	28836090	28836094	-	1	NA	intron (NR_045053, intron 2 of 8)	ORR1E|LTR|ERVL-MaLR	49330	NR_045054	72518	Mm.37454	NR_045053		2610307P16Rik	AI666457	RIKEN cDNA 2610307P16 gene	ncRNA
mm_169303.1	chr14	103371520	103371521	-	1	NA	Intergenic	Intergenic	-24720	NM_207215	105689	Mm.6478	NM_207215	ENSMUSG00000033004	Mycbp2	AU023734|AW107953|AW546647|C130061D10Rik|Pam|Phr1|R75243	MYC binding protein 2	protein-coding
mm_115261.1	chr13	110538432	110538434	+	1	NA	Intergenic	Intergenic	143389	NM_152804	20620	Mm.380	NM_152804	ENSMUSG00000021701	Plk2	Snk	polo-like kinase 2	protein-coding
mm_76984.1	chr8	106935575	106935604	-	1	NA	promoter-TSS (NM_009229)	promoter-TSS (NM_009229)	-161	NM_009229	20650	Mm.30228	NM_009229	ENSMUSG00000041308	Sntb2	Snt2	syntrophin, basic 2	protein-coding
mm_64211.1	chr7	141476393	141476402	+	1	NA	promoter-TSS (NM_001252588)	promoter-TSS (NM_001252588)	17	NM_001252588	64540	Mm.489619	NM_053082	ENSMUSG00000025511	Tspan4	AI325509|AI746565|D130042I01Rik|NAG-2|Tm4sf7|Tspan-4	tetraspanin 4	protein-coding
mm_29097.1	chr3	104794457	104794459	-	1	NA	TTS (NM_008619)	TTS (NM_008619)	5424	NM_007484	11853	Mm.262	NM_007484	ENSMUSG00000002233	Rhoc	AI324259|Arh9|Arhc	ras homolog family member C	protein-coding
mm_83864.1	chr9	54803014	54803025	-	1	NA	Intergenic	Intergenic	38271	NM_013496	12903	Mm.34797	NM_013496	ENSMUSG00000032291	Crabp1	AI326249|CRABP-I|Crabp-1|CrabpI|Rbp-5	cellular retinoic acid binding protein I	protein-coding
mm_116829.1	chr13	54611528	54611540	-	1	NA	promoter-TSS (NM_028870)	promoter-TSS (NM_028870)	-161	NM_001347512	74325	Mm.290026	NM_028870	ENSMUSG00000047547	Cltb	2310046E19Rik|lcb	clathrin, light polypeptide (Lcb)	protein-coding
mm_118263.1	chr13	112463917	112463966	-	1	NA	promoter-TSS (NM_010560)	promoter-TSS (NM_010560)	-129	NM_010560	16195	Mm.4364	NM_010560	ENSMUSG00000021756	Il6st	5133400A03Rik|AA389424|BB405851|CD130|D13Ertd699e|gp130	interleukin 6 signal transducer	protein-coding
mm_166083.1	chr4	138262480	138262504	+	1	NA	5' UTR (NM_001190978, exon 1 of 12)	5' UTR (NM_001190978, exon 1 of 12)	241	NM_010623	16559	Mm.271936	NM_010623	ENSMUSG00000028758	Kif17	5930435E01Rik|AW492270|Kif17b|mKIAA1405	kinesin family member 17	protein-coding
mm_154623.1	chrX	7728432	7728442	+	1	NA	promoter-TSS (NM_138602)	promoter-TSS (NM_138602)	-134	NM_138602	54637	Mm.28850	NM_138602	ENSMUSG00000031149	Praf2	AA986329|C78013|DXImx39e|JM4|Sfc20	PRA1 domain family 2	protein-coding
mm_65816.1	chr7	29155598	29155616	-	1	NA	intron (NM_001146023, intron 3 of 7)	CpG	603	NM_001146023	73833	Mm.260890	NM_028661	ENSMUSG00000030590	Fam98c	1110006G06Rik|AI836081|AV026483|B230110F21Rik	family with sequence similarity 98, member C	protein-coding
mm_101554.1	chr11	33843527	33843629	-	1	NA	promoter-TSS (NM_001290690)	promoter-TSS (NM_001290690)	7	NM_027398	70357	Mm.252514	NM_027398	ENSMUSG00000053519	Kcnip1	KCHIP1|Kchip1.2	Kv channel-interacting protein 1	protein-coding
mm_131152.1	chr16	6824769	6824772	+	1	NA	intron (NM_021477, intron 5 of 16)	intron (NM_021477, intron 5 of 16)	-245065	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_21471.1	chr2	160982738	160982764	-	1	NA	intron (NR_126509, intron 22 of 35)	intron (NR_126509, intron 22 of 35)	-70412	NM_182840	280635	Mm.330747	NM_182840	ENSMUSG00000050700	Emilin3	1110013O17Rik|EMILIN-3|EMILIN-5|EMILIN-T|Emilin5	elastin microfibril interfacer 3	protein-coding
mm_8082.1	chr1	135603217	135603223	-	1	NA	Intergenic	Intergenic	-17865	NM_173437	215690	Mm.34977	NM_173437	ENSMUSG00000009418	Nav1	9530089B19|9930003A20Rik|C230080M11Rik|Pomfil3|Unc53h1|mKIAA1151|steerin-1	neuron navigator 1	protein-coding
mm_84128.1	chr9	58979136	58979148	-	1	NA	intron (NM_001042752, intron 4 of 27)	intron (NM_001042752, intron 4 of 27)	57299	NM_008684	18007	Mm.42249	NM_008684	ENSMUSG00000032340	Neo1	2610028H22Rik|AI327052|D930014N22Rik|Igdcc2	neogenin	protein-coding
mm_108295.1	chr12	79208905	79208923	+	1	NA	promoter-TSS (NM_030017)	promoter-TSS (NM_030017)	1	NM_030017	77974	Mm.274373	NM_030017	ENSMUSG00000021123	Rdh12	-	retinol dehydrogenase 12	protein-coding
mm_119818.1	chr14	54226051	54226060	+	1	NA	Intergenic	Intergenic	27874	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_54110.1	chr6	17171568	17171578	-	1	NA	Intergenic	Intergenic	-26178	NR_102305	319682	Mm.136046	NR_102304	ENSMUSG00000085171	D830026I12Rik	-	RIKEN cDNA D830026I12 gene	ncRNA
mm_50613.1	chr6	49823616	49823629	+	1	NA	exon (NM_023456, exon 2 of 4)	exon (NM_023456, exon 2 of 4)	912	NM_023456	109648	Mm.154796	NM_023456	ENSMUSG00000029819	Npy	0710005A05Rik	neuropeptide Y	protein-coding
mm_65118.1	chr7	19399860	19399909	-	1	NA	promoter-TSS (NM_001286038)	promoter-TSS (NM_001286038)	37	NM_001286038	232943	Mm.213403	NM_146182	ENSMUSG00000040714	Klc3	BC017147|Klct	kinesin light chain 3	protein-coding
mm_118429.1	chr14	8002891	8002946	+	1	NA	promoter-TSS (NM_001331065)	promoter-TSS (NM_001331065)	30	NM_001331065	66082	Mm.181473	NM_025341	ENSMUSG00000025277	Abhd6	0610041D24Rik|AA673485|AV065425	abhydrolase domain containing 6	protein-coding
mm_114567.1	chr13	74639835	74639864	+	1	NA	promoter-TSS (NM_030711)	promoter-TSS (NM_030711)	-23	NM_030711	80898	Mm.83526	NM_030711	ENSMUSG00000021583	Erap1	Arts1|ERAAP|PILSA|PILSAP	endoplasmic reticulum aminopeptidase 1	protein-coding
mm_128245.1	chr15	36608960	36608983	-	1	NA	promoter-TSS (NM_008774)	promoter-TSS (NM_008774)	2	NM_008774	18458	Mm.371570	NM_008774	ENSMUSG00000022283	Pabpc1	PABP|Pabp1|PabpI|Pabpl1|ePAB	poly(A) binding protein, cytoplasmic 1	protein-coding
mm_27903.1	chr3	79483189	79483203	-	1	NA	intron (NM_001162999, intron 12 of 16)	Lx8b|LINE|L1	84483	NM_001162999	329679	Mm.244005	NM_001162999	ENSMUSG00000061175	Fnip2	D630023B12Rik|mKIAA1450	folliculin interacting protein 2	protein-coding
mm_26101.1	chr3	136955275	136955284	+	1	NA	Intergenic	RMER17B|LTR|ERVK	285213	NM_001293622	19055	Mm.331389	NM_008913	ENSMUSG00000028161	Ppp3ca	2900074D19Rik|CN|Caln|Calna|CnA	protein phosphatase 3, catalytic subunit, alpha isoform	protein-coding
mm_35650.1	chr4	43533245	43533253	-	1	NA	intron (NM_011602, intron 53 of 56)	intron (NM_011602, intron 53 of 56)	-9695	NM_001277875	22004	Mm.646	NM_009416	ENSMUSG00000028464	Tpm2	Tpm-2|Trop-2	tropomyosin 2, beta	protein-coding
mm_23185.1	chr3	40949946	40949956	+	1	NA	promoter-TSS (NM_001040399)	promoter-TSS (NM_001040399)	-680	NM_001040399	214048	Mm.46782	NM_027663	ENSMUSG00000025762	Larp1b	1700108L22Rik|4933421B21Rik|AA690246|Larp2	La ribonucleoprotein domain family, member 1B	protein-coding
mm_36859.1	chr4	106859599	106859620	-	1	NA	Intergenic	Intergenic	-51861	NM_198438	72475	Mm.195635	NM_023672	ENSMUSG00000061887	Ssbp3	2610021L12Rik|2610200M23Rik|5730488C10Rik|AI854733|AW551939|LAST|SSDP1	single-stranded DNA binding protein 3	protein-coding
mm_12530.1	chr2	72205646	72205646	+	1	NA	intron (NM_001204165, intron 15 of 30)	(T)n|Simple_repeat|Simple_repeat	-79991	NM_023057	65964	Mm.304143	NM_023057	ENSMUSG00000004085	Map3k20	AV006891|B230120H23Rik|MLTK|MLTKalpha|MLTKbeta|Zak	mitogen-activated protein kinase kinase kinase 20	protein-coding
mm_29466.1	chr3	113577744	113577756	-	1	NA	promoter-TSS (NM_001110505)	promoter-TSS (NM_001110505)	0	NM_001110505	11722	Mm.439727	NM_007446	ENSMUSG00000074264	Amy1	Amy-1|Amy1a|C030014B17Rik	amylase 1, salivary	protein-coding
mm_100101.1	chr11	115765421	115765466	+	1	NA	promoter-TSS (NM_028014)	promoter-TSS (NM_028014)	10	NM_028014	71947	Mm.23168	NM_028014	ENSMUSG00000020747	Tmem94	2310067B10Rik|Kiaa0195|mKIAA0195	transmembrane protein 94	protein-coding
mm_162011.1	chr19	44192419	44192419	-	1	NA	promoter-TSS (NM_181422)	promoter-TSS (NM_181422)	23	NM_181422	329064	Mm.308481	NM_181422	ENSMUSG00000037578	Pkd2l1	B830002B15|BC046386|PCL|PKD2L|Pkdl|TRPP3	polycystic kidney disease 2-like 1	protein-coding
mm_21737.1	chr2	164777974	164777984	-	1	NA	exon (NM_009394, exon 3 of 6)	exon (NM_009394, exon 3 of 6)	1755	NM_009394	21925	Mm.1716	NM_009394	ENSMUSG00000017300	Tnnc2	Tncs	troponin C2, fast	protein-coding
mm_93008.1	chr10	87057938	87057947	-	1	NA	promoter-TSS (NM_029685)	promoter-TSS (NM_029685)	-104	NM_029685	76640	Mm.78423	NM_029685	ENSMUSG00000047129	1700113H08Rik	-	RIKEN cDNA 1700113H08 gene	protein-coding
mm_68788.1	chr7	123329470	123329495	-	1	NA	intron (NM_001122641, intron 2 of 18)	MLTR25A|LTR|ERVK	40433	NM_001122643	70497	Mm.403318	NM_144529	ENSMUSG00000030766	Arhgap17	5730403H17Rik|Nadrin|Nadrin2|Rich1|Wbp15	Rho GTPase activating protein 17	protein-coding
mm_28167.1	chr3	87849106	87849126	-	1	NA	exon (NM_021309, exon 4 of 7)	exon (NM_021309, exon 4 of 7)	2361	NM_021309	27371	Mm.86361	NM_021309	ENSMUSG00000028071	Sh2d2a	Lad|Ribp|Tsad	SH2 domain containing 2A	protein-coding
mm_3579.1	chr1	151132968	151132978	+	1	NA	Intergenic	RLTR20A1|LTR|ERVK	-5061	NR_038011	402734	Mm.337666	NR_038011		C730036E19Rik	lncLSTR	RIKEN cDNA C730036E19 gene	ncRNA
mm_57139.1	chr6	122609965	122609979	-	1	NA	5' UTR (NM_008108, exon 1 of 2)	5' UTR (NM_008108, exon 1 of 2)	115	NM_008108	14562	Mm.299742	NM_008108	ENSMUSG00000030117	Gdf3	C78318|Gdf-3|Vgr-2|Vgr2|ecat9	growth differentiation factor 3	protein-coding
mm_149061.1	chr19	8839560	8839580	+	1	NA	promoter-TSS (NM_010316)	promoter-TSS (NM_010316)	242	NM_008144	14705	Mm.345134	NM_008144	ENSMUSG00000071657	Bscl2	2900097C17Rik|AI046355|Gng3lg	Berardinelli-Seip congenital lipodystrophy 2 (seipin)	protein-coding
mm_35076.1	chr4	6990617	6990635	-	1	NA	promoter-TSS (NM_145711)	promoter-TSS (NM_145711)	97	NM_145711	252838	Mm.435828	NM_145711	ENSMUSG00000041272	Tox	1700007F02Rik	thymocyte selection-associated high mobility group box	protein-coding
mm_58185.1	chr6	142964369	142964403	-	1	NA	promoter-TSS (NM_011374)	promoter-TSS (NM_011374)	66	NM_011374	20449	Mm.260838	NM_011374	ENSMUSG00000030283	St8sia1	9330109E03Rik|GD3S|Sia-T|Siat8|Siat8a	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 1	protein-coding
mm_12513.1	chr2	72054599	72054640	+	1	NA	promoter-TSS (NM_001204166)	promoter-TSS (NM_001204166)	2	NM_001204166	56508	Mm.196153	NM_019688	ENSMUSG00000049044	Rapgef4	1300003D15Rik|5730402K07Rik|6330581N18Rik|EPAC 2|Epac-2|Epac2|mKIAA4040	Rap guanine nucleotide exchange factor (GEF) 4	protein-coding
mm_65078.1	chr7	19149190	19149273	-	1	NA	promoter-TSS (NM_026943)	promoter-TSS (NM_026943)	-35	NM_026111	67369	Mm.234876	NM_026111	ENSMUSG00000030407	Qpctl	1810019P04Rik|BB101812|gQC	glutaminyl-peptide cyclotransferase-like	protein-coding
mm_47933.1	chr5	135078315	135078346	-	1	NA	promoter-TSS (NM_177574)	promoter-TSS (NM_177574)	-64	NM_001199677	194309	Mm.44356	NM_177574	ENSMUSG00000043614	Vps37d	Wbscr24	vacuolar protein sorting 37D	protein-coding
mm_85201.1	chr9	96737606	96737611	-	1	NA	intron (NR_015511, intron 2 of 3)	BGLII_Mur|LTR|ERVK	-5933	NM_175537	245007	Mm.485954	NM_175537	ENSMUSG00000040433	Zbtb38	A930014K01Rik|CIBZ	zinc finger and BTB domain containing 38	protein-coding
mm_126437.1	chr15	80623471	80623491	+	1	NA	promoter-TSS (NM_010815)	promoter-TSS (NM_010815)	-2	NM_010815	17444	Mm.12947	NM_010815	ENSMUSG00000042351	Grap2	GRAP-2|GRB2L|GRBLG|GRID|Gads|GrbX|Grf40|GrpL|Mona|P38	GRB2-related adaptor protein 2	protein-coding
mm_145389.1	chr18	57133467	57133504	+	1	NA	5' UTR (NM_001001979, exon 1 of 25)	5' UTR (NM_001001979, exon 1 of 25)	395	NM_001001979	70417	Mm.297863	NM_001001979	ENSMUSG00000024593	Megf10	3000002B06Rik|Gm331	multiple EGF-like-domains 10	protein-coding
mm_33809.1	chr4	135152703	135152748	+	1	NA	intron (NM_019732, intron 1 of 5)	CpG	32080	NM_019732	12399	Mm.378894	NM_019732	ENSMUSG00000070691	Runx3	AML2|Cbfa3|Pebp2a3	runt related transcription factor 3	protein-coding
mm_17938.1	chr2	36049278	36049357	-	1	NA	promoter-TSS (NM_029309)	promoter-TSS (NM_029309)	-25	NM_026703	68375	Mm.19834	NM_026703	ENSMUSG00000026895	Ndufa8	0610033L03Rik|AW261656	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 8	protein-coding
mm_130050.1	chr15	89149558	89149650	-	1	NA	promoter-TSS (NM_011161)	promoter-TSS (NM_011161)	2	NM_011161	19094	Mm.91969	NM_011161	ENSMUSG00000053137	Mapk11	P38b|Prkm11|Sapk2|Sapk2b|p38-2|p38beta|p38beta2	mitogen-activated protein kinase 11	protein-coding
mm_159030.1	chr1	174448833	174448833	+	1	NA	exon (NM_207694, exon 1 of 1)	exon (NM_207694, exon 1 of 1)	208	NM_207694	546747	Mm.380253	NM_207694	ENSMUSG00000066671	Olfr220	EG546747|MOR103-13P|MOR103-17|Olfr220-ps1|Olfr413-ps1	olfactory receptor 220	protein-coding
mm_57110.1	chr6	122594228	122594264	-	1	NA	intron (NM_031159, intron 3 of 7)	L1M5|LINE|L1	8198	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_103080.1	chr11	69900897	69900929	-	1	NA	promoter-TSS (NM_001291119)	promoter-TSS (NM_001291119)	73	NM_001316696	70419	Mm.272859	NM_027419	ENSMUSG00000018570	2810408A11Rik	1700019L01Rik|4930470J18Rik	RIKEN cDNA 2810408A11 gene	protein-coding
mm_159719.1	chr5	33843320	33843320	+	1	NA	exon (NM_175231, exon 1 of 21)	exon (NM_175231, exon 1 of 21)	208	NM_001177884	107823	Mm.19892	NM_175231	ENSMUSG00000057406	Whsc1	5830445G22Rik|9430010A17Rik|AW555663|C130020C13Rik|D030027O06Rik|D930023B08Rik|MMSET|NSD2|Whsc1l|mKIAA1090	Wolf-Hirschhorn syndrome candidate 1 (human)	protein-coding
mm_98681.1	chr11	96286639	96286653	+	1	NA	promoter-TSS (NM_010460)	promoter-TSS (NM_010460)	0	NM_010460	15415	Mm.390366	NM_010460	ENSMUSG00000038721	Hoxb7	AI325018|Hox-2.3	homeobox B7	protein-coding
mm_109190.1	chr12	108554702	108554723	+	1	NA	promoter-TSS (NM_007965)	promoter-TSS (NM_007965)	-8	NM_001163394	14026	Mm.238841	NM_007965	ENSMUSG00000021262	Evl	AI528774	Ena-vasodilator stimulated phosphoprotein	protein-coding
mm_102455.1	chr11	59836924	59836941	-	1	NA	exon (NM_011991, exon 2 of 12)	exon (NM_011991, exon 2 of 12)	2835	NM_011991	26572	Mm.40	NM_011991	ENSMUSG00000019373	Cops3	Csn3|Sgn3	COP9 signalosome subunit 3	protein-coding
mm_21110.1	chr2	153444390	153444407	-	1	NA	promoter-TSS (NM_001001986)	promoter-TSS (NM_001001986)	81	NM_001001986	329540	Mm.50600	NM_001001986	ENSMUSG00000061411	Nol4l	4931410H15|8430427H17Rik|AI429157|Gm1636	nucleolar protein 4-like	protein-coding
mm_73881.1	chr8	119344718	119344731	+	1	NA	intron (NM_024219, intron 1 of 3)	CpG	186	NM_024219	68196	Mm.358714	NM_024219	ENSMUSG00000031839	Hsbp1	0610007A03Rik|AA408769|Hsp25	heat shock factor binding protein 1	protein-coding
mm_169269.1	chr13	86046752	86046755	-	1	NA	promoter-TSS (NM_007749)	promoter-TSS (NM_007749)	42	NM_007749	12867	Mm.378898	NM_007749	ENSMUSG00000017778	Cox7c	COXVIIc|Cox7c1	cytochrome c oxidase subunit VIIc	protein-coding
mm_85308.1	chr9	101034858	101034867	-	1	NA	promoter-TSS (NM_001311149)	promoter-TSS (NM_001311149)	22	NM_001311149	66904	Mm.335385	NM_025835	ENSMUSG00000032527	Pccb	1300012P06Rik|AI314687|R74805	propionyl Coenzyme A carboxylase, beta polypeptide	protein-coding
mm_28486.1	chr3	92457491	92457514	-	1	NA	exon (NM_011478, exon 2 of 2)	exon (NM_011478, exon 2 of 2)	1218	NM_001204427	20766	Mm.57092	NM_011478	ENSMUSG00000045539	Sprr3	SPR3	small proline-rich protein 3	protein-coding
mm_63181.1	chr7	125491113	125491130	+	1	NA	intron (NM_026330, intron 1 of 7)	intron (NM_026330, intron 1 of 7)	421	NM_026330	67711	Mm.4467	NM_026330	ENSMUSG00000030750	Nsmce1	2510027N19Rik	NSE1 homolog, SMC5-SMC6 complex component	protein-coding
mm_170584.1	chr19	5798880	5798883	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	-2900	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_11485.1	chr2	32396227	32396250	+	1	NA	5' UTR (NM_133783, exon 1 of 7)	5' UTR (NM_133783, exon 1 of 7)	348	NM_133783	96979	Mm.28048	NM_133783	ENSMUSG00000026820	Ptges2	0610038H10Rik|C79137|Gbf1|Mpges2|Pges2	prostaglandin E synthase 2	protein-coding
mm_144469.1	chr18	23796840	23796840	+	1	NA	intron (NM_001162941, intron 2 of 7)	intron (NM_001162941, intron 2 of 7)	-7130	NM_153058	212307	Mm.132237	NM_153058	ENSMUSG00000024277	Mapre2	AI314113|C820009F03Rik|D18Abb1e|EB1|EB2|RP1	microtubule-associated protein, RP/EB family, member 2	protein-coding
mm_1121.1	chr1	59959192	59959195	+	1	NA	intron (NM_001037725, intron 4 of 7)	B1_Mur4|SINE|Alu	46187	NM_001037725	72750	Mm.258250	NM_001037725	ENSMUSG00000041040	Fam117b	2810425F24Rik|6330416D14Rik|Als2cr13	family with sequence similarity 117, member B	protein-coding
mm_91579.1	chr10	40134129	40134132	-	1	NA	intron (NM_001114332, intron 1 of 5)	intron (NM_001114332, intron 1 of 5)	8124	NM_028247	72472	Mm.186778	NM_028247	ENSMUSG00000019838	Slc16a10	2610103N14Rik|9830169E08|Mct10|PRO0813|TAT1	solute carrier family 16 (monocarboxylic acid transporters), member 10	protein-coding
mm_44353.1	chr5	17795576	17795582	-	1	NA	exon (NM_001159558, exon 12 of 16)	exon (NM_001159558, exon 12 of 16)	40317	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_80519.1	chr9	80067010	80067047	+	1	NA	5' UTR (NM_146003, exon 1 of 23)	5' UTR (NM_146003, exon 1 of 23)	125	NM_146003	215351	Mm.28232	NM_146003	ENSMUSG00000034252	Senp6	2810017C20Rik|E130319N12Rik|Susp1|mKIAA0797	SUMO/sentrin specific peptidase 6	protein-coding
mm_28899.1	chr3	98069340	98069351	-	1	NA	intron (NM_010928, intron 2 of 33)	intron (NM_010928, intron 2 of 33)	55807	NM_010928	18129	Mm.485843	NM_010928	ENSMUSG00000027878	Notch2	AI853703|N2	notch 2	protein-coding
mm_96299.1	chr11	63146643	63146646	+	1	NA	intron (NM_001302261, intron 2 of 3)	intron (NM_001302261, intron 2 of 3)	13841	NM_001302260	18858	Mm.1237	NM_008885	ENSMUSG00000018217	Pmp22	22kDa|Gas-3|HNPP|Tr|trembler	peripheral myelin protein 22	protein-coding
mm_3650.1	chr1	153085617	153085624	+	1	NA	intron (NM_175460, intron 4 of 10)	intron (NM_175460, intron 4 of 10)	100827	NM_008485	16782	Mm.329272	NM_008485	ENSMUSG00000026479	Lamc2	AA589349	laminin, gamma 2	protein-coding
mm_129299.1	chr15	77306963	77306969	-	1	NA	promoter-TSS (NM_175387)	promoter-TSS (NM_175387)	87	NM_001110827	93686	Mm.202774	NM_053104	ENSMUSG00000033565	Rbfox2	Fbm2|Fxh|Hrnbp2|Rbm9	RNA binding protein, fox-1 homolog (C. elegans) 2	protein-coding
mm_1948.1	chr1	86350646	86350666	+	1	NA	TTS (NR_028478)	TTS (NR_028478)	629	NR_028478	100303740	Mm.154378	NR_028478	ENSMUSG00000064837	Snora75	MBI-55	small nucleolar RNA, H/ACA box 75	snoRNA
mm_28038.1	chr3	83836855	83836867	-	1	NA	exon (NM_011905, exon 3 of 3)	exon (NM_011905, exon 3 of 3)	4747	NM_011905	24088	Mm.87596	NM_011905	ENSMUSG00000027995	Tlr2	Ly105	toll-like receptor 2	protein-coding
mm_50690.1	chr6	51589078	51589094	+	1	NA	3' UTR (NM_001127349, exon 7 of 7)	3' UTR (NM_001127349, exon 7 of 7)	44563	NM_001127348	71982	Mm.294166	NM_028035	ENSMUSG00000038301	Snx10	2410004M09Rik	sorting nexin 10	protein-coding
mm_118065.1	chr13	102905805	102905814	-	1	NA	intron (NM_175171, intron 4 of 28)	intron (NM_175171, intron 4 of 28)	145554	NR_130171	76624	Mm.426384	NR_130171	ENSMUSG00000091906	1700099I09Rik	-	RIKEN cDNA 1700099I09 gene	ncRNA
mm_156150.1	chrX	129891641	129891653	+	1	NA	intron (NM_172493, intron 4 of 26)	Lx9|LINE|L1	141905	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diaph2	Dia3|Diap2|Drf2|E430022I22Rik	diaphanous related formin 2	protein-coding
mm_144364.1	chr18	20436013	20436043	+	1	NA	promoter-TSS (NM_181564)	promoter-TSS (NM_181564)	-147	NM_181564	16769	Mm.358619	NM_181564	ENSMUSG00000001804	Dsg4	CDHF13|lah	desmoglein 4	protein-coding
mm_115641.1	chr13	12274071	12274108	-	1	NA	intron (NM_033268, intron 18 of 20)	intron (NM_033268, intron 18 of 20)	-15976	NM_001081128	238505	Mm.40335	NM_001081128	ENSMUSG00000021311	Mtr	AI894170|D830038K18Rik|MS	5-methyltetrahydrofolate-homocysteine methyltransferase	protein-coding
mm_165584.1	chr3	31126522	31126528	+	1	NA	Intergenic	Intergenic	-23395	NM_008770	18417	Mm.4425	NM_008770	ENSMUSG00000037625	Cldn11	Claudin-11|Claudin11|Osp|Otm	claudin 11	protein-coding
mm_162931.1	chr10	123264976	123265001	+	1	NA	non-coding (NR_045514, exon 1 of 6)	non-coding (NR_045514, exon 1 of 6)	912	NM_001252387	268354	Mm.51939	NM_182807	ENSMUSG00000044071	Fam19a2	6330575M02|FAM19A2 TAFA-2|TAFA2|Tafa-2	family with sequence similarity 19, member A2	protein-coding
mm_129668.1	chr15	81327303	81327328	-	1	NA	exon (NM_011399, exon 6 of 9)	exon (NM_011399, exon 6 of 9)	33450	NM_011399	20524	Mm.222536	NM_011399	ENSMUSG00000022404	Slc25a17	34kDa|47kDa|PMP34|Pmp47	solute carrier family 25 (mitochondrial carrier, peroxisomal membrane protein), member 17	protein-coding
mm_76623.1	chr8	91801375	91801389	-	1	NA	5' UTR (NM_001253822, exon 1 of 4)	5' UTR (NM_001253822, exon 1 of 4)	272	NM_001253822	16373	Mm.238044	NM_008393	ENSMUSG00000031734	Irx3	AI894186	Iroquois related homeobox 3	protein-coding
mm_8062.1	chr1	135375283	135375285	-	1	NA	promoter-TSS (NM_175259)	promoter-TSS (NM_175259)	-221	NM_175259	77552	Mm.41407	NM_175259	ENSMUSG00000041889	Shisa4	9330132O05Rik|Tmem58|mShisa4	shisa family member 4	protein-coding
mm_75561.1	chr8	58701004	58701024	-	1	NA	promoter-TSS (NM_001177534)	promoter-TSS (NM_001177534)	-218	NM_001177534	100271928	Mm.484123	NM_001177534		Gm15881	OTTMUSG00000027193	predicted gene 15881	protein-coding
mm_75370.1	chr8	45307079	45307089	-	1	NA	exon (NM_133969, exon 11 of 11)	exon (NM_133969, exon 11 of 11)	-12249	NM_008455	16621	Mm.482691	NM_008455	ENSMUSG00000109764	Klkb1	APS|Kal-3|Kal3|Klk3|PSA	kallikrein B, plasma 1	protein-coding
mm_8800.1	chr1	161816707	161816709	-	1	NA	3' UTR (NM_172645, exon 24 of 24)	3' UTR (NM_172645, exon 24 of 24)	-28213	NM_010177	14103	Mm.3355	NM_010177	ENSMUSG00000000817	Fasl	APT1LG1|CD178|CD95-L|CD95L|Fas-L|Faslg|Tnfsf6|Tnlg1a|gld	Fas ligand (TNF superfamily, member 6)	protein-coding
mm_131422.1	chr16	14708172	14708181	+	1	NA	exon (NM_011415, exon 3 of 3)	exon (NM_011415, exon 3 of 3)	2317	NM_011415	20583	Mm.4272	NM_011415	ENSMUSG00000022676	Snai2	Slug|Slugh|Snail2	snail family zinc finger 2	protein-coding
mm_33752.1	chr4	134315113	134315126	+	1	NA	promoter-TSS (NM_001039048)	promoter-TSS (NM_001039048)	-1	NM_001039048	433766	Mm.331961	NM_001039048	ENSMUSG00000028834	Trim63	MuRF1|RF1|Rnf28	tripartite motif-containing 63	protein-coding
mm_69161.1	chr7	127196050	127196058	-	1	NA	promoter-TSS (NM_027353)	promoter-TSS (NM_027353)	23	NM_001285907	70233	Mm.28050	NM_027353	ENSMUSG00000042502	Cd2bp2	1500011B02Rik|2410024K20Rik|AW048183	CD2 antigen (cytoplasmic tail) binding protein 2	protein-coding
mm_112775.1	chr13	20090258	20090285	+	1	NA	promoter-TSS (NM_080288)	promoter-TSS (NM_080288)	-236	NM_080288	140580	Mm.342392	NM_080288	ENSMUSG00000041112	Elmo1	6330578D22Rik|C230095H21Rik|CED-12	engulfment and cell motility 1	protein-coding
mm_27548.1	chr3	57847725	57847835	-	1	NA	promoter-TSS (NM_019410)	promoter-TSS (NM_019410)	-23	NM_019410	18645	Mm.271744	NM_019410	ENSMUSG00000027805	Pfn2	Pfn	profilin 2	protein-coding
mm_144420.1	chr18	20963125	20963128	+	1	NA	intron (NM_026301, intron 1 of 5)	intron (NM_026301, intron 1 of 5)	18501	NM_026301	67664	Mm.45980	NM_026301	ENSMUSG00000033107	Rnf125	4930553F04Rik	ring finger protein 125	protein-coding
mm_118386.1	chr13	117267480	117267496	-	1	NA	exon (NM_010330, exon 6 of 9)	exon (NM_010330, exon 6 of 9)	46915	NM_010330	13723	Mm.274926	NM_010330	ENSMUSG00000021728	Emb	AL022799|Gp70	embigin	protein-coding
mm_138809.1	chr17	39846453	39846504	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	3481	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_14227.1	chr2	127462991	127462994	+	1	NA	intron (NM_001291005, intron 5 of 8)	intron (NM_001291005, intron 5 of 8)	-18427	NM_029629	68126	Mm.288676	NM_029629	ENSMUSG00000027371	Fahd2a	1500003K14Rik|B430104H02Rik|Cgi-105|Fahd2	fumarylacetoacetate hydrolase domain containing 2A	protein-coding
mm_21883.1	chr2	166155136	166155162	-	1	NA	5' UTR (NM_001252578, exon 1 of 21)	5' UTR (NM_001252578, exon 1 of 21)	136	NM_001252578	72043	Mm.1011	NM_028072	ENSMUSG00000006800	Sulf2	2010004N24Rik|AU020235|MSulf-2|mKIAA1247	sulfatase 2	protein-coding
mm_93502.1	chr10	112928908	112928927	-	1	NA	5' UTR (NM_001033474, exon 1 of 1)	5' UTR (NM_001033474, exon 1 of 1)	109	NM_001033474	382423	Mm.431239	NM_001033474	ENSMUSG00000074748	Atxn7l3b	4921506J03Rik|6230409E21Rik|AI315132|ENSMUSG00000074747	ataxin 7-like 3B	protein-coding
mm_159323.1	chr3	17948499	17948499	+	1	NA	promoter-TSS (NM_029289)	promoter-TSS (NM_029289)	55	NM_029289	75439	Mm.27023	NM_029289	ENSMUSG00000027564	Cypt12	1700001F04Rik|AV209098	cysteine-rich perinuclear theca 12	protein-coding
mm_166670.1	chr6	91706258	91706267	-	1	NA	intron (NM_009320, intron 2 of 14)	intron (NM_009320, intron 2 of 14)	22195	NM_009320	21366	Mm.395650	NM_009320	ENSMUSG00000030096	Slc6a6	AA589629|C80501|Taut	solute carrier family 6 (neurotransmitter transporter, taurine), member 6	protein-coding
mm_121075.1	chr14	98874573	98874575	+	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	171562	NM_175245	76789	Mm.38912	NM_175245	ENSMUSG00000033186	Mzt1	2410129H14Rik|AI120158|Mozart1	mitotic spindle organizing protein 1	protein-coding
mm_100318.1	chr11	117987469	117987479	+	1	NA	intron (NM_133757, intron 1 of 9)	intron (NM_133757, intron 1 of 9)	617	NM_133757	74451	Mm.28864	NM_133757	ENSMUSG00000017715	Pgs1	2610019F11Rik|4933424M23Rik|SAF	phosphatidylglycerophosphate synthase 1	protein-coding
mm_49704.1	chr6	34358125	34358169	+	1	NA	exon (NM_008012, exon 4 of 10)	exon (NM_008012, exon 4 of 10)	3983	NM_008012	14187	Mm.5378	NM_008012	ENSMUSG00000029762	Akr1b8	FR-1|Fgfrp|Fgrp	aldo-keto reductase family 1, member B8	protein-coding
mm_24595.1	chr3	93445233	93445249	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	2911	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_42725.1	chr5	120613093	120613131	+	1	NA	promoter-TSS (NM_029096)	promoter-TSS (NM_029096)	-18	NM_028041	71990	Mm.24495	NM_028041	ENSMUSG00000029599	Ddx54	2410015A15Rik|AI414901|DP97	DEAD (Asp-Glu-Ala-Asp) box polypeptide 54	protein-coding
mm_54630.1	chr6	38693040	38693041	-	1	NA	Intergenic	Intergenic	29971	NM_001101507	665180	Mm.349066	NM_001101507	ENSMUSG00000079598	Clec2l	AI414054|AW122724|Gm1064	C-type lectin domain family 2, member L	protein-coding
mm_106893.1	chr12	8012412	8012419	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	34738	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_144898.1	chr18	37143715	37143729	+	1	NA	promoter-TSS (NM_001003672)	promoter-TSS (NM_001003672)	-247	NM_001003672	353237	Mm.308500	NM_001003672	ENSMUSG00000102697	Pcdhac2	CNRc2	protocadherin alpha subfamily C, 2	protein-coding
mm_117038.1	chr13	58275701	58275703	-	1	NA	Intergenic	B4|SINE|B4	-1514	NM_019832	56278	Mm.296625	NM_019832	ENSMUSG00000021552	Gkap1	42kDa|4933400B15Rik|D13Ertd340e|Gkap42	G kinase anchoring protein 1	protein-coding
mm_42577.1	chr5	117252539	117252551	+	1	NA	exon (NM_001199685, exon 16 of 21)	exon (NM_001199685, exon 16 of 21)	35019	NM_018858	23980	Mm.195898	NM_018858	ENSMUSG00000032959	Pebp1	HCNP|Pbp|Pbp1|Pbpr|Rkip	phosphatidylethanolamine binding protein 1	protein-coding
mm_157403.1	chrX	38431979	38432058	-	1	NA	exon (NM_001017959, exon 5 of 9)	exon (NM_001017959, exon 5 of 9)	24442	NM_010685	16784	Mm.486	NM_010685	ENSMUSG00000016534	Lamp2	CD107b|LGP-B|Lamp II|Lamp-2|Lamp-2a|Lamp-2b|Lamp-2c|Mac3	lysosomal-associated membrane protein 2	protein-coding
mm_7915.1	chr1	133736366	133736414	-	1	NA	intron (NM_213616, intron 6 of 19)	intron (NM_213616, intron 6 of 19)	-9745	NR_105868	102466206		NR_105868	ENSMUSG00000098606	Mir6903	Gm27797|mmu-mir-6903	microRNA 6903	ncRNA
mm_149027.1	chr19	8770984	8771019	+	1	NA	promoter-TSS (NM_025791)	promoter-TSS (NM_025791)	5	NM_025791	66836	Mm.440071	NM_025791	ENSMUSG00000010097	Tmem223	0610006I08Rik	transmembrane protein 223	protein-coding
mm_36094.1	chr4	58499399	58499409	-	1	NA	promoter-TSS (NM_001290486)	promoter-TSS (NM_001290486)	-1	NM_001290486	14745	Mm.4772	NM_010336	ENSMUSG00000038668	Lpar1	AI326300|Edg2|Gpcr26|Kdt2|lpA1|vzg-1	lysophosphatidic acid receptor 1	protein-coding
mm_140210.1	chr17	83795365	83795383	+	1	NA	intron (NM_054082, intron 14 of 16)	intron (NM_054082, intron 14 of 16)	51416	NM_025325	107766	Mm.30100	NM_025325	ENSMUSG00000000673	Haao	0610007K21Rik|0610012J07Rik|3-HAO|3-HAOxase|3HAO	3-hydroxyanthranilate 3,4-dioxygenase	protein-coding
mm_66301.1	chr7	38227962	38227972	-	1	NA	promoter-TSS (NM_024413)	promoter-TSS (NM_024413)	27	NM_024413	72287	Mm.333798	NM_024413	ENSMUSG00000074170	Plekhf1	1810013P09Rik|APPD|LAPF|PHAFIN1|ZFYVE15	pleckstrin homology domain containing, family F (with FYVE domain) member 1	protein-coding
mm_6224.1	chr1	66928826	66928839	-	1	NA	intron (NM_021285, intron 3 of 6)	intron (NM_021285, intron 3 of 6)	6534	NM_001113387	17901	Mm.1000	NM_021285	ENSMUSG00000061816	Myl1	AI325107|MLC1f|MLC3f|Mylf	myosin, light polypeptide 1	protein-coding
mm_161634.1	chr16	89837891	89837891	-	1	NA	intron (NM_009384, intron 13 of 27)	intron (NM_009384, intron 13 of 27)	-19539	NM_001145887	21844	Mm.310902	NM_009384	ENSMUSG00000002489	Tiam1	AI847750|D16Ium10|D16Ium10e	T cell lymphoma invasion and metastasis 1	protein-coding
mm_49050.1	chr6	4903351	4903367	+	1	NA	promoter-TSS (NM_181595)	promoter-TSS (NM_181595)	39	NM_181595	243725	Mm.332901	NM_181595	ENSMUSG00000032827	Ppp1r9a	2810430P21Rik|4930518N04Rik|5330407E15|A230094E16Rik|BB181831|NRB|mKIAA1222|neurabin-I	protein phosphatase 1, regulatory (inhibitor) subunit 9A	protein-coding
mm_48083.1	chr5	136956700	136956709	-	1	NA	intron (NM_001347504, intron 1 of 3)	intron (NM_001347504, intron 1 of 3)	3429	NM_001347504	66437	Mm.25849	NM_025562	ENSMUSG00000019054	Fis1	2010003O14Rik|Ttc11	fission, mitochondrial 1	protein-coding
mm_114344.1	chr13	60902102	60902106	+	1	NA	exon (NM_026429, exon 3 of 5)	exon (NM_026429, exon 3 of 5)	2743	NM_026429	116913	Mm.443229	NM_026429	ENSMUSG00000062705	Tpbpb	1600012N09Rik	trophoblast specific protein beta	protein-coding
mm_24061.1	chr3	87915485	87915512	+	1	NA	3' UTR (NM_008231, exon 6 of 6)	3' UTR (NM_008231, exon 6 of 6)	-4046	NM_026591	67707	Mm.393802	NM_026591	ENSMUSG00000019710	Mrpl24	2010005E08Rik|2810470K06Rik|6720473G22Rik|AA407670	mitochondrial ribosomal protein L24	protein-coding
mm_113984.1	chr13	52582695	52582705	+	1	NA	promoter-TSS (NM_001198977)	promoter-TSS (NM_001198977)	-737	NM_001198977	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_11856.1	chr2	47545328	47545330	+	1	NA	Intergenic	L1_Mur1|LINE|L1	-1268780	NM_007396	11480	Mm.314338	NM_007396	ENSMUSG00000052155	Acvr2a	ActrIIa|Acvr2|TactrII	activin receptor IIA	protein-coding
mm_38398.1	chr4	138863602	138863605	-	1	NA	promoter-TSS (NM_001122954)	promoter-TSS (NM_001122954)	-134	NM_001122954	18784	Mm.486532	NM_011110	ENSMUSG00000041193	Pla2g5	PLA2|sPLA2	phospholipase A2, group V	protein-coding
mm_64320.1	chr7	141949675	141949687	+	1	NA	promoter-TSS (NM_029426)	promoter-TSS (NM_029426)	-70	NM_001009930	75770	Mm.274868	NM_029426	ENSMUSG00000053046	Brsk2	4833424K13Rik|SAD-A|SADA	BR serine/threonine kinase 2	protein-coding
mm_165108.1	chr19	57245353	57245366	-	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-28601	NR_045319	78120	Mm.445892	NR_045319		4930449E18Rik	-	RIKEN cDNA 4930449E18 gene	ncRNA
mm_19118.1	chr2	80010118	80010129	-	1	NA	intron (NM_001159582, intron 2 of 15)	intron (NM_001159582, intron 2 of 15)	-101724	NM_001009978	18573	Mm.40678	NM_016744	ENSMUSG00000059173	Pde1a	AI987702|AW125737	phosphodiesterase 1A, calmodulin-dependent	protein-coding
mm_53037.1	chr6	124570321	124570323	+	1	NA	promoter-TSS (NM_001113356)	promoter-TSS (NM_001113356)	-108	NM_001113356	667277	Mm.481484	NM_001113356	ENSMUSG00000098470	C1rb	Gm8551|mC1rB	complement component 1, r subcomponent B	protein-coding
mm_91982.1	chr10	61783922	61783959	-	1	NA	promoter-TSS (NM_207000)	promoter-TSS (NM_207000)	-76	NM_207000	404634	Mm.272870	NM_207000	ENSMUSG00000020086	H2afy2	macroH2A2	H2A histone family, member Y2	protein-coding
mm_93628.1	chr10	117278906	117278918	-	1	NA	intron (NM_017372, intron 2 of 3)	intron (NM_017372, intron 2 of 3)	3360	NM_017372	17105	Mm.45436	NM_017372	ENSMUSG00000069516	Lyz2	AI326280|Lys|Lysm|Lyzf2|Lyzs|Lzm|Lzm-s1|Lzp	lysozyme 2	protein-coding
mm_136287.1	chr16	91372675	91372699	-	1	NA	promoter-TSS (NM_010509)	promoter-TSS (NM_010509)	-96	NM_010509	15976	Mm.6834	NM_010509	ENSMUSG00000022971	Ifnar2	AI747302|Ifnar-2	interferon (alpha and beta) receptor 2	protein-coding
mm_51632.1	chr6	85587563	85587573	+	1	NA	promoter-TSS (NM_145223)	promoter-TSS (NM_145223)	37	NM_145223	236266	Mm.246967	NM_145223	ENSMUSG00000063810	Alms1	bbb	Alstrom syndrome 1	protein-coding
mm_89168.1	chr10	86310935	86310955	+	1	NA	intron (NM_011595, intron 1 of 4)	intron (NM_011595, intron 1 of 4)	10533	NM_011595	21859	Mm.4871	NM_011595	ENSMUSG00000020044	Timp3	Timp-3	tissue inhibitor of metalloproteinase 3	protein-coding
mm_151327.1	chr19	55893353	55893388	+	1	NA	intron (NR_138565, intron 4 of 15)	intron (NR_138565, intron 4 of 15)	-1951	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_20035.1	chr2	119787505	119787533	-	1	NA	promoter-TSS (NM_177294)	promoter-TSS (NM_177294)	18	NM_177294	68925	Mm.30496	NM_177294	ENSMUSG00000034032	Rpap1	1190005L06Rik|A730023M06Rik|AU041788|AW107702|mKIAA1403	RNA polymerase II associated protein 1	protein-coding
mm_137961.1	chr17	33432190	33432205	+	1	NA	promoter-TSS (NM_183282)	promoter-TSS (NM_183282)	-702	NM_183282	69481	Mm.154333	NM_183282	ENSMUSG00000092519	Actl9	1700029I08Rik|AV259599	actin-like 9	protein-coding
mm_31752.1	chr4	63345153	63345180	+	1	NA	exon (NM_008768, exon 2 of 6)	exon (NM_008768, exon 2 of 6)	610	NM_008768	18405	Mm.4777	NM_008768	ENSMUSG00000039196	Orm1	Agp-1|Agp-2|Orm-1	orosomucoid 1	protein-coding
mm_28135.1	chr3	87174633	87174655	-	1	NA	5' UTR (NM_130867, exon 1 of 16)	5' UTR (NM_130867, exon 1 of 16)	103	NM_001170985	170643	Mm.89552	NM_130867	ENSMUSG00000041734	Kirrel	6720469N11Rik|Kirrel1|Neph1	kin of IRRE like (Drosophila)	protein-coding
mm_122235.1	chr14	33193928	33193938	-	1	NA	Intergenic	Intergenic	-8867	NM_001146022	545030	Mm.318345	NM_001146022	ENSMUSG00000051506	Wdfy4	Gm18810	WD repeat and FYVE domain containing 4	protein-coding
mm_6932.1	chr1	85112465	85112507	-	1	NA	Intergenic	Intergenic	-2633	NM_213615	381287	Mm.487565	NM_213615	ENSMUSG00000089844	A530032D15Rik	Gm1888	RIKEN cDNA A530032D15Rik gene	protein-coding
mm_154400.1	chrM	13833	13844	+	1	NA	NA	Intergenic	NA	NA								
mm_15724.1	chr2	164078450	164078452	+	1	NA	intron (NM_021420, intron 1 of 10)	intron (NM_021420, intron 1 of 10)	4273	NM_021420	58231	Mm.234472	NM_021420	ENSMUSG00000018209	Stk4	AI447339|AU020804|Kas-2|Mst1|Ysk3	serine/threonine kinase 4	protein-coding
mm_40688.1	chr5	65763765	65763776	+	1	NA	intron (NM_001024917, intron 1 of 19)	CpG	249	NM_001024917	333789	Mm.332398	NM_001024917	ENSMUSG00000037795	N4bp2	B3bp|E430014I16|Gm1791|Gm868	NEDD4 binding protein 2	protein-coding
mm_7405.1	chr1	119053621	119053638	-	1	NA	promoter-TSS (NM_001081125)	promoter-TSS (NM_001081125)	-10	NM_001081125	14633	Mm.273292	NM_001081125	ENSMUSG00000048402	Gli2	-	GLI-Kruppel family member GLI2	protein-coding
mm_120575.1	chr14	69172009	69172013	+	1	NA	promoter-TSS (NR_045931)	promoter-TSS (NR_045931)	-168	NR_045931	73554	Mm.320005	NR_045931	ENSMUSG00000092499	1700092C10Rik	-	RIKEN cDNA 1700092C10 gene	ncRNA
mm_165170.1	chr2	26911456	26911474	+	1	NA	promoter-TSS (NM_001033908)	promoter-TSS (NM_001033908)	658	NM_013721	27176	Mm.328601	NM_013721	ENSMUSG00000062647	Rpl7a	Surf3	ribosomal protein L7A	protein-coding
mm_116011.1	chr13	24635917	24635924	-	1	NA	intron (NM_178658, intron 1 of 13)	intron (NM_178658, intron 1 of 13)	-2728	NM_001080381	193385	Mm.217319	NM_029679	ENSMUSG00000036006	Fam65b	-	family with sequence similarity 65, member B	protein-coding
mm_160347.1	chr8	20363174	20363174	-	1	NA	promoter-TSS (NM_001177408)	promoter-TSS (NM_001177408)	28	NM_001177408	100040599	Mm.491087	NM_001177408	ENSMUSG00000074449	Gm15319	OTTMUSG00000020118	predicted gene 15319	protein-coding
mm_32867.1	chr4	118429703	118429725	+	1	NA	promoter-TSS (NM_001039176)	promoter-TSS (NM_001039176)	13	NM_001039176	54325	Mm.282096	NM_019422	ENSMUSG00000006390	Elovl1	AA407424|BB151133|Ssc1	elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 1	protein-coding
mm_59330.1	chr7	25394288	25394307	+	1	NA	promoter-TSS (NR_015569)	promoter-TSS (NR_015569)	-416	NR_015569	654804	Mm.389841	NM_001039540	ENSMUSG00000053714	4732471J01Rik	-	RIKEN cDNA 4732471J01 gene	ncRNA
mm_4992.1	chr1	191817386	191817401	+	1	NA	Intergenic	Lx10|LINE|L1	-4080	NM_010892	18005	Mm.33773	NM_010892	ENSMUSG00000026622	Nek2	AA617254|C77054	NIMA (never in mitosis gene a)-related expressed kinase 2	protein-coding
mm_160447.1	chr8	104831616	104831616	+	1	NA	promoter-TSS (NM_198171)	promoter-TSS (NM_198171)	-28	NM_198171	234669	Mm.443387	NM_198171	ENSMUSG00000050097	Ces2b	-	carboxyesterase 2B	protein-coding
mm_103548.1	chr11	77685979	77686009	-	1	NA	promoter-TSS (NM_001024205)	promoter-TSS (NM_001024205)	-145	NM_001024205	68564	Mm.428996	NM_001024205	ENSMUSG00000037857	Nufip2	1110001M19Rik|9530056D24Rik|AI256692|AI461731|PIG1|mKIAA1321	nuclear fragile X mental retardation protein interacting protein 2	protein-coding
mm_156062.1	chrX	109160367	109160405	+	1	NA	3' UTR (NM_019989, exon 4 of 4)	3' UTR (NM_019989, exon 4 of 4)	-36370	NM_001037917	622976	Mm.482747	NM_001037917	ENSMUSG00000048621	Gm6377	EG622976	predicted gene 6377	protein-coding
mm_160982.1	chr11	102946673	102946673	-	1	NA	promoter-TSS (NM_011795)	promoter-TSS (NM_011795)	-212	NM_011795	23829	Mm.57154	NM_011795	ENSMUSG00000045532	C1ql1	C1qrf|CRF|CTRP14|gliacolin	complement component 1, q subcomponent-like 1	protein-coding
mm_158042.1	chrX	98890539	98890561	-	1	NA	5' UTR (NM_052976, exon 1 of 25)	5' UTR (NM_052976, exon 1 of 25)	475	NM_052976	94190	Mm.33536	NM_052976	ENSMUSG00000031214	Ophn1	C130037N19Rik|Wtgr	oligophrenin 1	protein-coding
mm_101329.1	chr11	22972883	22972936	-	1	NA	5' UTR (NM_011663, exon 1 of 1)	5' UTR (NM_011663, exon 1 of 1)	904	NM_011663	22183	Mm.29542	NM_011663	ENSMUSG00000044068	Zrsr1	D11Ncvs75|Irlgs2|SP2|U2af1-rs1|U2afbp-rs	zinc finger (CCCH type), RNA binding motif and serine/arginine rich 1	protein-coding
mm_53332.1	chr6	129233812	129233833	+	1	NA	intron (NR_040265, intron 1 of 2)	intron (NR_040265, intron 1 of 2)	4223	NR_040265	76432	Mm.261738	NR_040265	ENSMUSG00000097354	2310001H17Rik	AI646108	RIKEN cDNA 2310001H17 gene	ncRNA
mm_157002.1	chrX	7572849	7572858	-	1	NA	promoter-TSS (NR_029473)	promoter-TSS (NR_029473)	-747	NR_029473	78185	Mm.160055	NR_029473	ENSMUSG00000039545	Ppp1r3fos	4930524L23Rik	protein phosphatase 1, regulatory subunit 3F, opposite strand	ncRNA
mm_55442.1	chr6	67037400	67037417	-	1	NA	promoter-TSS (NM_007836)	promoter-TSS (NM_007836)	-1	NM_007836	13197	Mm.72235	NM_007836	ENSMUSG00000036390	Gadd45a	AA545191|Ddit1|GADD45	growth arrest and DNA-damage-inducible 45 alpha	protein-coding
mm_124754.1	chr15	6643688	6643706	+	1	NA	exon (NM_001278269, exon 10 of 17)	exon (NM_001278269, exon 10 of 17)	63850	NM_011815	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_90608.1	chr10	128337740	128337759	+	1	NA	promoter-TSS (NM_026444)	promoter-TSS (NM_026444)	22	NM_026444	12974	Mm.58836	NM_026444	ENSMUSG00000005683	Cs	2610511A05Rik|9030605P22Rik|Ahl4|BB234005|Cis	citrate synthase	protein-coding
mm_138607.1	chr17	35649770	35649797	+	1	NA	promoter-TSS (NM_001163194)	promoter-TSS (NM_001163194)	75	NM_001163194	433102	Mm.136760	NM_001163194	ENSMUSG00000090509	Sfta2	EG433102	surfactant associated 2	protein-coding
mm_104265.1	chr11	88994317	88994323	-	1	NA	Intergenic	Intergenic	-5083	NM_009546	217069	Mm.248445	NM_009546	ENSMUSG00000000275	Trim25	AA960166|AL022677|EFP|Zfp147	tripartite motif-containing 25	protein-coding
mm_81841.1	chr9	118506227	118506289	+	1	NA	promoter-TSS (NM_018748)	promoter-TSS (NM_018748)	-60	NM_018748	54214	Mm.10409	NM_018748	ENSMUSG00000038708	Golga4	AI225887|AU019508|Olp-1	golgi autoantigen, golgin subfamily a, 4	protein-coding
mm_120212.1	chr14	62555621	62555633	+	1	NA	promoter-TSS (NM_001243857)	promoter-TSS (NM_001243857)	-110	NM_001243857	629059	Mm.291864	NM_001243857	ENSMUSG00000035184	Fam124a	EG629059	family with sequence similarity 124, member A	protein-coding
mm_172163.1	chr6	44793020	44793022	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-267040	NM_001004357	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding
mm_79197.1	chr9	48495262	48495266	+	1	NA	promoter-TSS (NM_001004191)	promoter-TSS (NM_001004191)	66	NM_001326355	67010	Mm.76911	NM_144948	ENSMUSG00000042396	Rbm7	1200007M24Rik|1500011D06Rik|AU041934|AW554393	RNA binding motif protein 7	protein-coding
mm_42888.1	chr5	122391891	122391928	+	1	NA	promoter-TSS (NM_019824)	promoter-TSS (NM_019824)	31	NM_019824	56378	Mm.275942	NM_019824	ENSMUSG00000029465	Arpc3	1110006A04Rik|p21-ARC|p21-Ar|p21Arc	actin related protein 2/3 complex, subunit 3	protein-coding
mm_108949.1	chr12	102313119	102313148	+	1	NA	exon (NM_177620, exon 2 of 10)	exon (NM_177620, exon 2 of 10)	29492	NM_001161365	217835	Mm.24145	NM_177620	ENSMUSG00000044456	Rin3	6430500K07|C86933	Ras and Rab interactor 3	protein-coding
mm_124472.1	chr14	121379127	121379137	-	1	NA	promoter-TSS (NM_145465)	promoter-TSS (NM_145465)	98	NM_145465	223255	Mm.390756	NM_145465	ENSMUSG00000063410	Stk24	1810013H02Rik|C76483|MST-3|Mst3|STE20	serine/threonine kinase 24	protein-coding
mm_28373.1	chr3	89913187	89913202	-	1	NA	promoter-TSS (NM_010559)	promoter-TSS (NM_010559)	2	NM_001310676	16194	Mm.2856	NM_010559	ENSMUSG00000027947	Il6ra	CD126|IL-6R|IL-6R-alpha|IL-6RA|Il6r	interleukin 6 receptor, alpha	protein-coding
mm_80088.1	chr9	70220716	70220736	+	1	NA	intron (NM_181072, intron 1 of 27)	B4|SINE|B4	13376	NM_181072	71602	Mm.249311	NM_181072	ENSMUSG00000032220	Myo1e	2310020N23Rik|9130023P14Rik|AA407778|myosin-1e|myr 3	myosin IE	protein-coding
mm_322.1	chr1	24678642	24678676	+	1	NA	promoter-TSS (NM_001310483)	promoter-TSS (NM_001310483)	115	NM_026719	68421	Mm.336563	NM_026719	ENSMUSG00000073725	Lmbrd1	0910001K20Rik|AV347960	LMBR1 domain containing 1	protein-coding
mm_51695.1	chr6	86571109	86571122	+	1	NA	Intergenic	Intergenic	43714	NR_037961	72012	Mm.349174	NR_037960	ENSMUSG00000097048	1600020E01Rik	-	RIKEN cDNA 1600020E01 gene	ncRNA
mm_90165.1	chr10	119413433	119413439	+	1	NA	promoter-TSS (NR_040578)	promoter-TSS (NR_040578)	-8	NR_040578	67081	Mm.72644	NR_040578	ENSMUSG00000100558	1700025F24Rik	-	RIKEN cDNA 1700025F24 gene	ncRNA
mm_148364.1	chr18	85698214	85698215	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-696738	NM_144946	246317	Mm.329578	NM_144946	ENSMUSG00000050321	Neto1	AI851453|Btcl1|C130005O10Rik	neuropilin (NRP) and tolloid (TLL)-like 1	protein-coding
mm_155852.1	chrX	101276183	101276196	+	1	NA	exon (NM_021521, exon 5 of 45)	exon (NM_021521, exon 5 of 45)	2098	NM_021521	59024	Mm.20873	NM_021521	ENSMUSG00000079487	Med12	230kDa|Mopa|OPA-1|Tnrc11|Trap230	mediator complex subunit 12	protein-coding
mm_93819.1	chr10	121474083	121474095	-	1	NA	intron (NM_138956, intron 1 of 4)	intron (NM_138956, intron 1 of 4)	2161	NM_138956	192678	Mm.41265	NM_138956	ENSMUSG00000025795	Rassf3	AW212023|AW322379	Ras association (RalGDS/AF-6) domain family member 3	protein-coding
mm_11388.1	chr2	31446327	31446365	+	1	NA	Intergenic	Intergenic	-23924	NM_007494	11898	Mm.3217	NM_007494	ENSMUSG00000076441	Ass1	AA408052|ASS|Ass-1|fold	argininosuccinate synthetase 1	protein-coding
mm_103702.1	chr11	79516486	79516504	-	1	NA	exon (NM_001077496, exon 2 of 2)	exon (NM_001077496, exon 2 of 2)	7267	NM_001077496	216984	Mm.439665	NM_001077496	ENSMUSG00000093938	Evi2b	Evi-2|Evi2	ecotropic viral integration site 2b	protein-coding
mm_76903.1	chr8	105827618	105827637	-	1	NA	promoter-TSS (NM_024445)	promoter-TSS (NM_024445)	-117	NM_024445	72236	Mm.386810	NM_024445	ENSMUSG00000031893	Tsnaxip1	1700016K08Rik|TXI1	translin-associated factor X (Tsnax) interacting protein 1	protein-coding
mm_51445.1	chr6	80174104	80174112	+	1	NA	intron (NM_001347261, intron 2 of 2)	RLTR12A|LTR|ERVK	154465	NM_178731	243499	Mm.483425	NM_178731	ENSMUSG00000052581	Lrrtm4	7530419J18Rik|A230052N11	leucine rich repeat transmembrane neuronal 4	protein-coding
mm_106700.1	chr12	3572380	3572524	+	1	NA	promoter-TSS (NM_007886)	promoter-TSS (NM_007886)	61	NR_027870	13528	Mm.286202	NM_007886	ENSMUSG00000071454	Dtnb	-	dystrobrevin, beta	protein-coding
mm_102060.1	chr11	52253823	52253836	-	1	NA	3' UTR (NM_009331, exon 10 of 10)	3' UTR (NM_009331, exon 10 of 10)	21834	NM_011543	21402	Mm.42944	NM_011543	ENSMUSG00000036309	Skp1a	15kDa|2610043E24Rik|2610206H23Rik|EMC19|OCP-II|OCP2|SKP1|Tceb1l|p19A|p19Skp1	S-phase kinase-associated protein 1A	protein-coding
mm_83259.1	chr9	42439550	42439586	-	1	NA	intron (NM_173038, intron 5 of 7)	intron (NM_173038, intron 5 of 7)	32658	NM_173038	272589	Mm.34483	NM_173038	ENSMUSG00000037287	Tbcel	D330014K23|E130107N23Rik|Lrrc35	tubulin folding cofactor E-like	protein-coding
mm_141386.1	chr17	29090884	29090894	-	1	NA	promoter-TSS (NM_001111099)	promoter-TSS (NM_001111099)	-90	NM_001111099	12575	Mm.195663	NM_007669	ENSMUSG00000023067	Cdkn1a	CAP20|CDKI|CIP1|Cdkn1|P21|SDI1|Waf1|mda6|p21Cip1|p21WAF	cyclin-dependent kinase inhibitor 1A (P21)	protein-coding
mm_130889.1	chr15	102350635	102350690	-	1	NA	promoter-TSS (NM_153416)	promoter-TSS (NM_153416)	97	NM_153416	223921	Mm.352946	NM_153416	ENSMUSG00000036678	Aaas	AAA|ADRACALA|D030041N15Rik|GL003	achalasia, adrenocortical insufficiency, alacrimia	protein-coding
mm_105404.1	chr11	103504894	103504903	-	1	NA	Intergenic	Intergenic	-92234	NM_183034	353047	Mm.18556	NM_183034	ENSMUSG00000034247	Plekhm1	AP162|B2|BC038943|D330036J23Rik	pleckstrin homology domain containing, family M (with RUN domain) member 1	protein-coding
mm_81087.1	chr9	106313434	106313441	+	1	NA	intron (NM_027354, intron 9 of 10)	intron (NM_027354, intron 9 of 10)	32376	NM_027354	70235	Mm.23054	NM_027354	ENSMUSG00000023345	Poc1a	2510040D07Rik|Wdr51a|cha	POC1 centriolar protein A	protein-coding
mm_115324.1	chr13	112438228	112438232	+	1	NA	Intergenic	RCHARR1|DNA|hAT-Charlie	-25840	NM_010560	16195	Mm.4364	NM_010560	ENSMUSG00000021756	Il6st	5133400A03Rik|AA389424|BB405851|CD130|D13Ertd699e|gp130	interleukin 6 signal transducer	protein-coding
mm_95563.1	chr11	52361050	52361064	+	1	NA	5' UTR (NM_011694, exon 1 of 9)	5' UTR (NM_011694, exon 1 of 9)	195	NM_011694	22333	Mm.3555	NM_011694	ENSMUSG00000020402	Vdac1	AL033343|Vdac5|mVDAC1|mVDAC5	voltage-dependent anion channel 1	protein-coding
mm_91698.1	chr10	44003833	44003898	-	1	NA	exon (NM_172393, exon 1 of 20)	exon (NM_172393, exon 1 of 20)	981	NM_172393	11630	Mm.292082	NM_172393	ENSMUSG00000019866	Aim1	AI462491|AI463325	absent in melanoma 1	protein-coding
mm_79030.1	chr9	46022447	46022457	+	1	NA	intron (NM_027498, intron 1 of 24)	intron (NM_027498, intron 1 of 24)	9632	NM_027498	70661	Mm.219459	NM_027498	ENSMUSG00000034135	Sik3	5730525O22Rik|9030204A07Rik|AI447252|AI846254|AI849445|Qsk|SIK-3|mKIAA0999	SIK family kinase 3	protein-coding
mm_19055.1	chr2	77280570	77280580	-	1	NA	promoter-TSS (NM_175465)	promoter-TSS (NM_175465)	17	NM_175465	228071	Mm.27120	NM_175465	ENSMUSG00000042272	Sestd1	1500031J16Rik|A930010O20|Solo/Trio8	SEC14 and spectrin domains 1	protein-coding
mm_58989.1	chr7	19094616	19094633	+	1	NA	promoter-TSS (NM_011383)	promoter-TSS (NM_011383)	80	NM_011383	20475	Mm.3410	NM_011383	ENSMUSG00000040841	Six5	Dmahp|MDMAHP|TrexBF	sine oculis-related homeobox 5	protein-coding
mm_100182.1	chr11	116624453	116624458	+	1	NA	promoter-TSS (NM_001167680)	promoter-TSS (NM_001167680)	-203	NM_001167680	217344	Mm.89695	NM_172572	ENSMUSG00000020806	Rhbdf2	4732465I17Rik|Rhbdl6|cub	rhomboid 5 homolog 2	protein-coding
mm_61386.1	chr7	73105296	73105304	+	1	NA	Intergenic	Intergenic	-3232	NR_046024	625243	Mm.261798	NR_046024	ENSMUSG00000108383	Gm6567	-	predicted gene 6567	ncRNA
mm_89957.1	chr10	111295118	111295123	+	1	NA	3' UTR (NM_001003717, exon 23 of 23)	3' UTR (NM_001003717, exon 23 of 23)	-3559	NM_027914	71769	Mm.45256	NM_027914	ENSMUSG00000035759	Bbs10	1300007O09Rik|AI452285	Bardet-Biedl syndrome 10 (human)	protein-coding
mm_29284.1	chr3	107696206	107696216	-	1	NA	exon (NM_145542, exon 1 of 17)	exon (NM_145542, exon 1 of 17)	337	NM_145542	229709	Mm.220328	NM_145542	ENSMUSG00000027893	Ahcyl1	1110034F20Rik|AA409031|AA414901|Ahcy-rs3|DCAL|Irbit	S-adenosylhomocysteine hydrolase-like 1	protein-coding
mm_110662.1	chr12	59219447	59219494	-	1	NA	promoter-TSS (NM_001033156)	promoter-TSS (NM_001033156)	13	NM_001033156	70611	Mm.311026	NM_001033156	ENSMUSG00000035329	Fbxo33	5730501N20Rik|AI642135	F-box protein 33	protein-coding
mm_62047.1	chr7	92348217	92348246	+	1	NA	intron (NM_011807, intron 14 of 22)	intron (NM_011807, intron 14 of 22)	113261	NM_001243047	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_35068.1	chr4	6494243	6494269	-	1	NA	Intergenic	RLTR47|LTR|ERVK	-39985	NM_010945	18201	Mm.3059	NM_010945	ENSMUSG00000028245	Nsmaf	AA959567|C630007J05|Fan	neutral sphingomyelinase (N-SMase) activation associated factor	protein-coding
mm_169330.1	chr14	117547588	117547589	+	1	NA	intron (NM_001079844, intron 3 of 9)	L1Md_A|LINE|L1	406259	NR_105747	102465148		NR_105747	ENSMUSG00000098648	Mir6239	Gm28025|mmu-mir-6239	microRNA 6239	ncRNA
mm_128832.1	chr15	68252709	68252717	-	1	NA	intron (NM_001145888, intron 1 of 15)	L1ME2|LINE|L1	6143	NM_001145888	380993	Mm.309526	NM_198644	ENSMUSG00000022335	Zfat	Gm922|Zfat1|Zfp406	zinc finger and AT hook domain containing	protein-coding
mm_140724.1	chr17	15434852	15434867	-	1	NA	Intergenic	L1M4c|LINE|L1	38613	NM_024203	67544	Mm.35039	NM_024203	ENSMUSG00000014763	Fam120b	4932442K08Rik|AW049283|AW413338|CCPG|Pgcc1|mKIAA1838	family with sequence similarity 120, member B	protein-coding
mm_12702.1	chr2	76537490	76537502	+	1	NA	intron (NM_001290733, intron 4 of 26)	intron (NM_001290733, intron 4 of 26)	38490	NM_001290735	99031	Mm.240435	NM_145525	ENSMUSG00000042359	Osbpl6	1110062M20Rik|AI596402|ORP-6|mKIAA4128	oxysterol binding protein-like 6	protein-coding
mm_25895.1	chr3	131110807	131110815	+	1	NA	5' UTR (NM_001276402, exon 1 of 10)	5' UTR (NM_001276402, exon 1 of 10)	514	NM_001276402	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_15985.1	chr2	166827070	166827072	+	1	NA	intron (NM_001085495, intron 2 of 38)	intron (NM_001085495, intron 2 of 38)	21490	NM_001085495	99371	Mm.297192	NM_001085495	ENSMUSG00000074582	Arfgef2	AI463430|AW493672|BIG2|E230011G24Rik	ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited)	protein-coding
mm_166344.1	chr5	117414426	117414504	+	1	NA	5' UTR (NM_001312914, exon 1 of 20)	5' UTR (NM_001312914, exon 1 of 20)	463	NM_001312914	333050	Mm.437947	NM_001034873	ENSMUSG00000061578	Ksr2	-	kinase suppressor of ras 2	protein-coding
mm_138026.1	chr17	33915906	33915916	+	1	NA	promoter-TSS (NM_020625)	promoter-TSS (NM_020625)	-265	NM_020625	81630	Mm.482096	NM_020625	ENSMUSG00000051390	Zbtb22	1110008J20Rik|AI265210|AI415166|Bing1|Zfp297	zinc finger and BTB domain containing 22	protein-coding
mm_15507.1	chr2	158153185	158153226	+	1	NA	Intergenic	Intergenic	-6813	NM_009373	21817	Mm.330731	NM_009373	ENSMUSG00000037820	Tgm2	G[a]h|TG2|TGase2|tTG|tTGas	transglutaminase 2, C polypeptide	protein-coding
mm_89166.1	chr10	86301187	86301188	+	1	NA	intron (NM_011595, intron 1 of 4)	intron (NM_011595, intron 1 of 4)	775	NM_011595	21859	Mm.4871	NM_011595	ENSMUSG00000020044	Timp3	Timp-3	tissue inhibitor of metalloproteinase 3	protein-coding
mm_104075.1	chr11	86586818	86586848	-	1	NA	intron (NM_029478, intron 10 of 11)	intron (NM_029478, intron 10 of 11)	-2675	NR_029738	387140		NR_029738	ENSMUSG00000065455	Mir21a	Mir21|Mirn21|mmu-mir-21|mmu-mir-21a	microRNA 21a	ncRNA
mm_91376.1	chr10	30200595	30200605	-	1	NA	promoter-TSS (NM_001109747)	promoter-TSS (NM_001109747)	-60	NM_001109747	66311	Mm.251779	NM_001109747	ENSMUSG00000075266	Cenpw	2610036L11Rik|Cug2	centromere protein W	protein-coding
mm_114861.1	chr13	93340283	93340293	+	1	NA	intron (NM_152134, intron 1 of 8)	Tigger17a|DNA|TcMar-Tigger	32254	NM_152134	26556	Mm.37533	NM_011982	ENSMUSG00000007617	Homer1	PSD-Zip45|SYN47|Ves-1|homer-1|vesl-1	homer scaffolding protein 1	protein-coding
mm_97620.1	chr11	78956525	78956533	+	1	NA	exon (NM_010927, exon 25 of 27)	exon (NM_010927, exon 25 of 27)	28395	NM_001159301	16859	Mm.341434	NM_010708	ENSMUSG00000001123	Lgals9	AA407335|AI194909|AI265545|LGALS35|Lgals5|gal-9|galectin-9	lectin, galactose binding, soluble 9	protein-coding
mm_147083.1	chr18	35627264	35627274	-	1	NA	promoter-TSS (NM_011397)	promoter-TSS (NM_011397)	-42	NM_011397	20522	Mm.22702	NM_011397	ENSMUSG00000024354	Slc23a1	D18Ucla2|SVCT1|Slc23a2|YSPL3	solute carrier family 23 (nucleobase transporters), member 1	protein-coding
mm_17699.1	chr2	32353313	32353324	-	1	NA	promoter-TSS (NR_125959)	promoter-TSS (NR_125959)	11	NM_001301737	13429	Mm.44736	NM_010065	ENSMUSG00000026825	Dnm1	AI838169|Dnm|Ftfl|mKIAA4093	dynamin 1	protein-coding
mm_85456.1	chr9	105395238	105395289	-	1	NA	promoter-TSS (NM_025651)	promoter-TSS (NM_025651)	24	NM_172461	208583	Mm.347509	NM_172461	ENSMUSG00000035032	Nek11	4932416N14Rik	NIMA (never in mitosis gene a)-related expressed kinase 11	protein-coding
mm_136739.1	chr17	8340493	8340513	+	1	NA	promoter-TSS (NM_178774)	promoter-TSS (NM_178774)	97	NR_028280	320111	Mm.442510	NM_178774	ENSMUSG00000055945	Prr18	9630019K15Rik	proline rich 18	protein-coding
mm_168526.1	chr11	6011371	6011378	+	1	NA	intron (NM_007595, intron 3 of 20)	RLTR4_Mm|LTR|ERV1	54374	NM_001174054	12323	Mm.439733	NM_007595	ENSMUSG00000057897	Camk2b	CaMKII	calcium/calmodulin-dependent protein kinase II, beta	protein-coding
mm_136076.1	chr16	84834877	84834885	-	1	NA	promoter-TSS (NM_008065)	promoter-TSS (NM_008065)	117	NM_001302216	11957	Mm.353	NM_016755	ENSMUSG00000022890	Atp5j	CF6	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit F	protein-coding
mm_122549.1	chr14	48667433	48667450	-	1	NA	5' UTR (NM_001286482, exon 1 of 5)	5' UTR (NM_001286482, exon 1 of 5)	203	NM_001286482	18424	Mm.134516	NM_144841	ENSMUSG00000021848	Otx2	E130306E05Rik	orthodenticle homeobox 2	protein-coding
mm_87293.1	chr10	42502185	42502195	+	1	NA	5' UTR (NM_017472, exon 1 of 4)	5' UTR (NM_017472, exon 1 of 4)	136	NM_017472	54198	Mm.277870	NM_017472	ENSMUSG00000019804	Snx3	SDP3	sorting nexin 3	protein-coding
mm_44276.1	chr5	5749286	5749315	-	1	NA	promoter-TSS (NM_027399)	promoter-TSS (NM_027399)	17	NM_027399	70358	Mm.85429	NM_027399	ENSMUSG00000015652	Steap1	2410007B19Rik|Prss24|Steap	six transmembrane epithelial antigen of the prostate 1	protein-coding
mm_93743.1	chr10	120158806	120158836	-	1	NA	intron (NM_028679, intron 8 of 11)	IAPLTR3|LTR|ERVK	42716	NM_028679	73914	Mm.146194	NM_028679	ENSMUSG00000020227	Irak3	4833428C18Rik|AI563835|IRAK-M	interleukin-1 receptor-associated kinase 3	protein-coding
mm_129825.1	chr15	83122757	83122782	-	1	NA	promoter-TSS (NM_029101)	promoter-TSS (NM_029101)	32	NM_029101	74778	Mm.30056	NM_029101	ENSMUSG00000018040	Rrp7a	1110014J01Rik|AA408146|Kheg1	ribosomal RNA processing 7 homolog A (S. cerevisiae)	protein-coding
mm_112855.1	chr13	20840862	20840897	+	1	NA	intron (NM_012054, intron 3 of 20)	MLTR14|LTR|ERV1	46766	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_87148.1	chr10	34898223	34898229	+	1	NA	Intergenic	Intergenic	414826	NM_010237	14302	Mm.332432	NM_010237	ENSMUSG00000019779	Frk	BSK|BSK/IYK|C85044|GTK|RAK	fyn-related kinase	protein-coding
mm_128790.1	chr15	66810614	66810627	-	1	NA	intron (NM_001029841, intron 1 of 7)	intron (NM_001029841, intron 1 of 7)	21209	NM_001029841	20491	Mm.7601	NM_009192	ENSMUSG00000022372	Sla	Slap|Slap-1	src-like adaptor	protein-coding
mm_167543.1	chr9	26760384	26760392	+	1	NA	3' UTR (NM_001310766, exon 7 of 7)	3' UTR (NM_001310766, exon 7 of 7)	8826	NM_029792	76898	Mm.218788	NM_029792	ENSMUSG00000045994	B3gat1	0710007K08Rik|AI846286|GlcAT-P|Glcatp|Hnk1	beta-1,3-glucuronyltransferase 1 (glucuronosyltransferase P)	protein-coding
mm_71466.1	chr8	46534630	46534645	+	1	NA	3' UTR (NM_007981, exon 21 of 21)	3' UTR (NM_007981, exon 21 of 21)	-17432	NM_027973	71876	Mm.22108	NM_027973	ENSMUSG00000031629	Cenpu	1700029A22Rik|Mlf1ip	centromere protein U	protein-coding
mm_15929.1	chr2	165072464	165072466	+	1	NA	TTS (NR_027852)	TTS (NR_027852)	16829	NM_011611	21939	Mm.271833	NM_011611	ENSMUSG00000017652	Cd40	AI326936|Bp50|GP39|HIGM1|IGM|IMD3|T-BAM|TRAP|Tnfrsf5|p50	CD40 antigen	protein-coding
mm_158340.1	chrX	134111853	134111873	-	1	NA	promoter-TSS (NM_172203)	promoter-TSS (NM_172203)	-9	NM_172203	237038	Mm.67938	NM_172203	ENSMUSG00000031257	Nox1	GP91-2|MOX1|NOH-1|NOH1|NOX1a|NOX1alpha|Nox-1	NADPH oxidase 1	protein-coding
mm_62059.1	chr7	92447613	92447633	+	1	NA	3' UTR (NM_001243047, exon 11 of 11)	3' UTR (NM_001243047, exon 11 of 11)	-113526	NM_025515	66365	Mm.21173	NM_025515	ENSMUSG00000030613	Ccdc90b	2310015N07Rik|C86558	coiled-coil domain containing 90B	protein-coding
mm_152901.1	chr19	25096488	25096503	-	1	NA	intron (NM_028785, intron 11 of 47)	intron (NM_028785, intron 11 of 47)	96966	NM_028785	76088	Mm.102485	NM_028785	ENSMUSG00000052085	Dock8	1200017A24Rik|5830472H07Rik|A130095G14Rik|AI461977	dedicator of cytokinesis 8	protein-coding
mm_118825.1	chr14	25586543	25586559	+	1	NA	promoter-TSS (NR_033492)	promoter-TSS (NR_033492)	-253	NR_033492	77592	Mm.444871	NM_175264		4931406H21Rik	-	RIKEN cDNA 4931406H21 gene	ncRNA
mm_8250.1	chr1	138619666	138619683	-	1	NA	promoter-TSS (NM_021605)	promoter-TSS (NM_021605)	83	NM_021605	59125	Mm.143817	NM_021605	ENSMUSG00000026393	Nek7	2810460C19Rik|AU020186	NIMA (never in mitosis gene a)-related expressed kinase 7	protein-coding
mm_155103.1	chrX	48343703	48343723	+	1	NA	intron (NM_178782, intron 2 of 14)	CpG	2355	NM_178782	320376	Mm.210146	NM_178782	ENSMUSG00000036959	Bcorl1	6720425J07Rik|B930011H20Rik	BCL6 co-repressor-like 1	protein-coding
mm_160073.1	chr7	6515340	6515340	-	1	NA	promoter-TSS (NM_207136)	promoter-TSS (NM_207136)	87	NM_207136	269862	Mm.377869	NM_207136	ENSMUSG00000048067	Olfr1349	MOR232-8	olfactory receptor 1349	protein-coding
mm_51005.1	chr6	63913432	63913440	+	1	NA	intron (NM_008167, intron 3 of 15)	MIRb|SINE|MIR	656579	NM_008167	14804	Mm.439651	NM_008167	ENSMUSG00000071424	Grid2	B230104L07Rik|GluD2|GluRdelta2|Lc|Lc<J>|MMS10-AC|Ms10ac|cpr|ho|nmf408|tpr	glutamate receptor, ionotropic, delta 2	protein-coding
mm_166965.1	chr7	44480875	44480887	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-3636	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_13761.1	chr2	118388616	118388640	+	1	NA	promoter-TSS (NM_013719)	promoter-TSS (NM_013719)	11	NM_013719	27103	Mm.217616	NM_013719	ENSMUSG00000005102	Eif2ak4	2610011M03|GCN2|MGCN2	eukaryotic translation initiation factor 2 alpha kinase 4	protein-coding
mm_48869.1	chr5	150566421	150566425	-	1	NA	intron (NM_001081001, intron 24 of 26)	L1MC5a|LINE|L1	28102	NM_133898	100637	Mm.279932	NM_133898	ENSMUSG00000041132	N4bp2l1	2410024N18Rik|AI428195|B230342M21Rik	NEDD4 binding protein 2-like 1	protein-coding
mm_99019.1	chr11	98907828	98907866	+	1	NA	promoter-TSS (NM_011799)	promoter-TSS (NM_011799)	-42	NM_001025779	23834	Mm.20912	NM_011799	ENSMUSG00000017499	Cdc6	CDC18L	cell division cycle 6	protein-coding
mm_19685.1	chr2	103455135	103455164	-	1	NA	exon (NM_009804, exon 12 of 13)	exon (NM_009804, exon 12 of 13)	30004	NM_009804	12359	Mm.4215	NM_009804	ENSMUSG00000027187	Cat	2210418N07|Cas-1|Cas1|Cs-1	catalase	protein-coding
mm_144935.1	chr18	37730993	37731010	+	1	NA	promoter-TSS (NM_033577)	promoter-TSS (NM_033577)	-153	NM_033577	93702	Mm.247203	NM_033577	ENSMUSG00000103749	Pcdhgb5	-	protocadherin gamma subfamily B, 5	protein-coding
mm_48553.1	chr5	143018171	143018177	-	1	NA	intron (NM_080561, intron 14 of 16)	B4A|SINE|B4	57819	NM_007984	14086	Mm.289707	NM_007984	ENSMUSG00000029581	Fscn1	AI663989|Fan1|fascin-1	fascin actin-bundling protein 1	protein-coding
mm_116095.1	chr13	28784315	28784319	-	1	NA	intron (NR_045053, intron 2 of 8)	(A)n|Simple_repeat|Simple_repeat	-73444	NR_105787	102466635		NR_105787	ENSMUSG00000099158	Mir6368	Gm27800|mmu-mir-6368	microRNA 6368	ncRNA
mm_171951.1	chr5	77260346	77260347	+	1	NA	Intergenic	Intergenic	-5148	NM_011263	19712	Mm.28840	NM_011263	ENSMUSG00000029249	Rest	2610008J04Rik|AA407358|NRSF|REST4	RE1-silencing transcription factor	protein-coding
mm_168163.1	chr10	46804754	46804754	-	1	NA	Intergenic	LTRIS3|LTR|ERV1	560005	NR_028276	108637		NR_028276	ENSMUSG00000096263	Snord14c	Gm23107|Rnu14|U14	small nucleolar RNA, C/D box 14C	snoRNA
mm_130888.1	chr15	102350594	102350605	-	1	NA	exon (NM_153416, exon 1 of 16)	exon (NM_153416, exon 1 of 16)	160	NM_153416	223921	Mm.352946	NM_153416	ENSMUSG00000036678	Aaas	AAA|ADRACALA|D030041N15Rik|GL003	achalasia, adrenocortical insufficiency, alacrimia	protein-coding
mm_23799.1	chr3	79860614	79860645	+	1	NA	Intergenic	Intergenic	-17967	NM_027495	70652	Mm.46635	NM_027495	ENSMUSG00000027956	Tmem144	1110057I03Rik|5730537D05Rik	transmembrane protein 144	protein-coding
mm_30819.1	chr4	21862141	21862151	+	1	NA	exon (NM_025669, exon 6 of 12)	exon (NM_025669, exon 6 of 12)	-13698	NR_028384	67735	Mm.391650	NR_028384		4930528A17Rik	-	RIKEN cDNA 4930528A17 gene	ncRNA
mm_89436.1	chr10	91123420	91123433	+	1	NA	intron (NM_133668, intron 2 of 7)	intron (NM_133668, intron 2 of 7)	537	NM_133668	18674	Mm.298	NM_133668	ENSMUSG00000061904	Slc25a3	5730556H19Rik|PTP|Phc	solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 3	protein-coding
mm_164721.1	chr17	57024821	57024831	+	1	NA	exon (NM_010613, exon 11 of 18)	exon (NM_010613, exon 11 of 18)	6681	NM_010613	16549	Mm.34296	NM_010613	ENSMUSG00000007670	Khsrp	6330409F21Rik|Fbp2|Fubp2|Ksrp	KH-type splicing regulatory protein	protein-coding
mm_10202.1	chr2	4936040	4936056	+	1	NA	exon (NM_010726, exon 7 of 9)	exon (NM_010726, exon 7 of 9)	17052	NM_010726	16922	Mm.391704	NM_010726	ENSMUSG00000026664	Phyh	AI256161|AI265699|Lnap1|PAHX	phytanoyl-CoA hydroxylase	protein-coding
mm_118265.1	chr13	112552119	112552132	-	1	NA	intron (NM_139299, intron 4 of 16)	URR1A|DNA|hAT-Charlie	28537	NM_139299	218624	Mm.380801	NM_139299	ENSMUSG00000050377	Il31ra	CRL3|GLM-R|GPL|Glmr|NR10	interleukin 31 receptor A	protein-coding
mm_166592.1	chr6	56902100	56902144	-	1	NA	promoter-TSS (NM_001252374)	promoter-TSS (NM_001252374)	-236	NM_001252374	107569	Mm.158936	NM_026004	ENSMUSG00000029780	Nt5c3	1600024P05Rik|2610206B05Rik|3110004A18Rik|AI842776|Nt5c3a|Nt5y|PN-1|PN-I|PSN1|UMPH|Umph-1|Umph1|cN-III|lupin|p36	5'-nucleotidase, cytosolic III	protein-coding
mm_57194.1	chr6	122850109	122850119	-	1	NA	exon (NM_009779, exon 2 of 2)	exon (NM_009779, exon 2 of 2)	6043	NM_009779	12267	Mm.2408	NM_009779	ENSMUSG00000040552	C3ar1	AZ3B|C3AR|HNFAG09	complement component 3a receptor 1	protein-coding
mm_2949.1	chr1	132342364	132342372	+	1	NA	Intergenic	Intergenic	25580	NM_001311108	68875	Mm.273785	NM_178874	ENSMUSG00000042066	Tmcc2	1110063G11Rik	transmembrane and coiled-coil domains 2	protein-coding
mm_150642.1	chr19	41848513	41848515	+	1	NA	promoter-TSS (NM_177603)	promoter-TSS (NM_177603)	-382	NM_177603	212398	Mm.222723	NM_177603	ENSMUSG00000047604	Frat2	-	frequently rearranged in advanced T cell lymphomas 2	protein-coding
mm_45070.1	chr5	43786108	43786123	-	1	NA	Intergenic	RMER19B|LTR|ERVK	-3966	NM_178729	242960	Mm.25794	NM_178729	ENSMUSG00000039753	Fbxl5	Fbl4|Fir4	F-box and leucine-rich repeat protein 5	protein-coding
mm_85730.1	chr9	108347722	108347745	-	1	NA	promoter-TSS (NM_011678)	promoter-TSS (NM_011678)	-98	NM_001311157	22258	Mm.3974	NM_011678	ENSMUSG00000032612	Usp4	F730026I20Rik|Unp|mKIAA4155	ubiquitin specific peptidase 4 (proto-oncogene)	protein-coding
mm_50438.1	chr6	48860340	48860358	+	1	NA	Intergenic	Intergenic	18693	NM_001098271	66058	Mm.27061	NM_025326	ENSMUSG00000023367	Tmem176a	0610011I04Rik|AU040201|AU041743|Keg2	transmembrane protein 176A	protein-coding
mm_116487.1	chr13	44477052	44477060	-	1	NA	Intergenic	Intergenic	37329	NR_045489	69491	Mm.392410	NR_045489	ENSMUSG00000098144	1700029N11Rik	-	RIKEN cDNA 1700029N11 gene	ncRNA
mm_25747.1	chr3	123264792	123264818	+	1	NA	Intergenic	ORR1D1-int|LTR|ERVL-MaLR	-2691	NM_027135	69608	Mm.29293	NM_027135	ENSMUSG00000039234	Sec24d	2310020L09Rik|Gm1349	Sec24 related gene family, member D (S. cerevisiae)	protein-coding
mm_58274.1	chr6	145434080	145434090	-	1	NA	intron (NM_028742, intron 1 of 9)	intron (NM_028742, intron 1 of 9)	840	NM_028742	74071	Mm.441497	NM_028742	ENSMUSG00000054966	Lmntd1	4933403M22Rik|AI482300|Ifltd1|Lmna-rs1|Lmna1|OTTMUSG00000022798	lamin tail domain containing 1	protein-coding
mm_101580.1	chr11	34406975	34406986	-	1	NA	intron (NM_001025382, intron 3 of 3)	intron (NM_001025382, intron 3 of 3)	92158	NM_001025382	574403	Mm.444796	NM_001025382	ENSMUSG00000069911	Fam196b	EG574403|Gm6041	family with sequence similarity 196, member B	protein-coding
mm_139535.1	chr17	56709907	56709934	+	1	NA	intron (NR_045519, intron 14 of 16)	intron (NR_045519, intron 14 of 16)	7001	NM_178926	106639	Mm.37290	NM_178926	ENSMUSG00000054723	Vmac	AI662250	vimentin-type intermediate filament associated coiled-coil protein	protein-coding
mm_78952.1	chr9	45138792	45138798	+	1	NA	promoter-TSS (NM_001013390)	promoter-TSS (NM_001013390)	-247	NM_001013390	399548	Mm.335112	NM_001013390	ENSMUSG00000046480	Scn4b	Gm1471	sodium channel, type IV, beta	protein-coding
mm_70867.1	chr8	25015099	25015112	+	1	NA	intron (NM_001270996, intron 1 of 21)	intron (NM_001270996, intron 1 of 21)	1817	NM_001270996	11502	Mm.28908	NM_007404	ENSMUSG00000031555	Adam9	AU020942|MDC9|Mltng|mKIAA0021	a disintegrin and metallopeptidase domain 9 (meltrin gamma)	protein-coding
mm_143157.1	chr17	57223897	57223922	-	1	NA	exon (NM_009778, exon 11 of 41)	exon (NM_009778, exon 11 of 41)	4227	NM_009778	12266	Mm.19131	NM_009778	ENSMUSG00000024164	C3	AI255234|ASP|HSE-MSF|Plp	complement component 3	protein-coding
mm_167090.1	chr7	105640417	105640421	+	1	NA	promoter-TSS (NM_019502)	promoter-TSS (NM_019502)	-3	NM_029802	76932	Mm.41637	NM_029802	ENSMUSG00000030881	Arfip2	2310002N04Rik|POR|Por1	ADP-ribosylation factor interacting protein 2	protein-coding
mm_99757.1	chr11	106751610	106751647	+	1	NA	intron (NM_001033435, intron 1 of 6)	intron (NM_001033435, intron 1 of 6)	402	NM_001033435	380732	Mm.343952	NM_001033435	ENSMUSG00000040528	Milr1	Allergin-1|Gm885|Mca32	mast cell immunoglobulin like receptor 1	protein-coding
mm_75214.1	chr8	39605605	39605612	-	1	NA	3' UTR (NM_031195, exon 9 of 9)	3' UTR (NM_031195, exon 9 of 9)	37070	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_28730.1	chr3	95735974	95735985	-	1	NA	exon (NM_007899, exon 8 of 11)	exon (NM_007899, exon 8 of 11)	-1006	NR_105981	102466787		NR_105981	ENSMUSG00000098737	Mir7014	Gm27837|mmu-mir-7014	microRNA 7014	ncRNA
mm_71936.1	chr8	70315760	70315835	+	1	NA	promoter-TSS (NM_001163282)	promoter-TSS (NM_001163282)	22	NM_001163282	14559	Mm.258280	NM_008107	ENSMUSG00000087408	Gdf1	AI385651|Gdf-1	growth differentiation factor 1	protein-coding
mm_64801.1	chr7	6691141	6691160	-	1	NA	intron (NM_011769, intron 2 of 7)	B4A|SINE|B4	5282	NM_011769	22776	Mm.89976	NM_011769	ENSMUSG00000002266	Zim1	-	zinc finger, imprinted 1	protein-coding
mm_104623.1	chr11	97309454	97309468	-	1	NA	Intergenic	Intergenic	-6255	NM_025927	67036	Mm.5381	NM_025927	ENSMUSG00000018882	Mrpl45	2600005P05Rik|AU043542|R75241	mitochondrial ribosomal protein L45	protein-coding
mm_86310.1	chr9	122843977	122843985	-	1	NA	Intergenic	Intergenic	22025	NM_173364	235682	Mm.326477	NM_173364	ENSMUSG00000047036	Zfp445	AW610627|ZNF168|Znf445|mszf29|mszf50	zinc finger protein 445	protein-coding
mm_130671.1	chr15	100674674	100674682	-	1	NA	3' UTR (NM_033612, exon 8 of 8)	3' UTR (NM_033612, exon 8 of 8)	-5178	NM_001270537	668218	Mm.451225	NM_001270537	ENSMUSG00000098112	Bin2	-	bridging integrator 2	protein-coding
mm_154946.1	chrX	36328421	36328441	+	1	NA	promoter-TSS (NM_028894)	promoter-TSS (NM_028894)	22	NM_028894	74365	Mm.327654	NM_028894	ENSMUSG00000016239	Lonrf3	4932412G04Rik|5730439E01Rik|A830039N02Rik|AU023707|Rnf127	LON peptidase N-terminal domain and ring finger 3	protein-coding
mm_84280.1	chr9	62811836	62811846	-	1	NA	promoter-TSS (NM_010193)	promoter-TSS (NM_010193)	-193	NM_010193	14155	Mm.24069	NM_010193	ENSMUSG00000032244	Fem1b	mKIAA0396	feminization 1 homolog b (C. elegans)	protein-coding
mm_116775.1	chr13	52981014	52981024	-	1	NA	promoter-TSS (NM_017373)	promoter-TSS (NM_017373)	20	NM_017373	18030	Mm.136604	NM_017373	ENSMUSG00000056749	Nfil3	AV225605|E4BP4	nuclear factor, interleukin 3, regulated	protein-coding
mm_41640.1	chr5	98030726	98030736	+	1	NA	5' UTR (NM_133738, exon 1 of 17)	5' UTR (NM_133738, exon 1 of 17)	231	NM_133738	71914	Mm.24842	NM_133738	ENSMUSG00000029338	Antxr2	2310046B19Rik|AW561899|CMG-2|CMG2|cI-35	anthrax toxin receptor 2	protein-coding
mm_67277.1	chr7	78432597	78432600	-	1	NA	intron (NM_008746, intron 11 of 16)	intron (NM_008746, intron 11 of 16)	145240	NM_008746	18213	Mm.33496	NM_008746	ENSMUSG00000059146	Ntrk3	AW125844|Ntrk3_tv3|TrkC	neurotrophic tyrosine kinase, receptor, type 3	protein-coding
mm_20637.1	chr2	132020732	132020779	-	1	NA	intron (NM_175445, intron 1 of 10)	intron (NM_175445, intron 1 of 10)	9233	NM_175445	215653	Mm.204737	NM_175445	ENSMUSG00000027339	Rassf2	3830431H01Rik|9030412M04Rik|AI852669|AW495050	Ras association (RalGDS/AF-6) domain family member 2	protein-coding
mm_150319.1	chr19	34573909	34573930	+	1	NA	exon (NM_008332, exon 3 of 3)	exon (NM_008332, exon 3 of 3)	-9610	NM_010501	15959	Mm.426079	NM_010501	ENSMUSG00000074896	Ifit3	Ifi49|P49	interferon-induced protein with tetratricopeptide repeats 3	protein-coding
mm_131003.1	chr15	103538311	103538341	-	1	NA	promoter-TSS (NM_021391)	promoter-TSS (NM_021391)	-334	NM_021391	58200	Mm.143788	NM_021391	ENSMUSG00000022490	Ppp1r1a	0610038N18Rik|I-1	protein phosphatase 1, regulatory (inhibitor) subunit 1A	protein-coding
mm_165115.1	chr19	58860002	58860026	+	1	NA	intron (NM_001327998, intron 2 of 12)	intron (NM_001327998, intron 2 of 12)	970	NM_175199	73442	Mm.39739	NM_175199	ENSMUSG00000025092	Hspa12a	1700063D12Rik|AI118035|AI840429|AW048913|AW556406|D5Mgi40|Gm19925|mKIAA0417	heat shock protein 12A	protein-coding
mm_67921.1	chr7	99862665	99862665	-	1	NA	intron (NM_001164258, intron 2 of 18)	MTD|LTR|ERVL-MaLR	3447	NM_001164258	446101	Mm.440757	NM_001164258	ENSMUSG00000035211	Xrra1	AI449753	X-ray radiation resistance associated 1	protein-coding
mm_139044.1	chr17	46248070	46248139	+	1	NA	promoter-TSS (NM_009085)	promoter-TSS (NM_009085)	24	NM_145353	28064	Mm.248769	NM_145353	ENSMUSG00000071074	Yipf3	C6orf109|D17Wsu94e|KLIP1	Yip1 domain family, member 3	protein-coding
mm_141607.1	chr17	32805699	32805710	-	1	NA	intron (NM_183177, intron 1 of 3)	B3|SINE|B2	4227	NM_001267583	240063	Mm.30675	NM_183177	ENSMUSG00000055202	Zfp811	BC052046	zinc finger protein 811	protein-coding
mm_117223.1	chr13	64152411	64152455	-	1	NA	intron (NM_175494, intron 1 of 4)	CpG	766	NM_175494	238673	Mm.300065	NM_175494	ENSMUSG00000044934	Zfp367	8030486J21Rik|ZFF29a|ZFF29b|Znf367	zinc finger protein 367	protein-coding
mm_152393.1	chr19	10525152	10525181	-	1	NA	promoter-TSS (NM_025333)	promoter-TSS (NM_025333)	43	NM_025333	66072	Mm.180063	NM_025333	ENSMUSG00000024668	Sdhaf2	0610038F07Rik|AA407634|AW049997	succinate dehydrogenase complex assembly factor 2	protein-coding
mm_117855.1	chr13	98813299	98813302	-	1	NA	intron (NM_172591, intron 1 of 25)	B1_Mus1|SINE|Alu	2149	NM_172591	218503	Mm.23928	NM_172591	ENSMUSG00000041685	Fcho2	5832424M12Rik|AA387320	FCH domain only 2	protein-coding
mm_134726.1	chr16	22898909	22898915	-	1	NA	exon (NM_001276450, exon 7 of 7)	exon (NM_001276450, exon 7 of 7)	-4526	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_1611.1	chr1	74391391	74391397	+	1	NA	promoter-TSS (NM_153088)	promoter-TSS (NM_153088)	-215	NM_153088	227292	Mm.165042	NM_153088	ENSMUSG00000026176	Ctdsp1	GIP|NLIIF|Nif3|SCP1	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 1	protein-coding
mm_127589.1	chr15	102365228	102365235	+	1	NA	intron (NM_130458, intron 1 of 1)	B1_Mur3|SINE|Alu	1040	NM_130458	170574	Mm.263284	NM_130458	ENSMUSG00000060284	Sp7	6430578P22Rik|C22|Osx	Sp7 transcription factor 7	protein-coding
mm_73816.1	chr8	117401427	117401482	+	1	NA	intron (NM_028941, intron 3 of 20)	(CA)n|Simple_repeat|Simple_repeat	-51569	NR_106045	102466801		NR_106045	ENSMUSG00000099062	Mir7077	Gm27774|mmu-mir-7077	microRNA 7077	ncRNA
mm_59486.1	chr7	27473762	27473773	+	1	NA	promoter-TSS (NM_133210)	promoter-TSS (NM_133210)	-73	NM_133210	170742	Mm.200120	NM_133210	ENSMUSG00000055200	Sertad3	AW124805|D1Mgi51|Rbt1|Sei3	SERTA domain containing 3	protein-coding
mm_160612.1	chr9	85842389	85842389	+	1	NA	promoter-TSS (NM_001164792)	promoter-TSS (NM_001164792)	9	NM_011627	21983	Mm.20864	NM_011627	ENSMUSG00000035274	Tpbg	5T4|AW495680|WAIF1	trophoblast glycoprotein	protein-coding
mm_6259.1	chr1	69108259	69108275	-	1	NA	promoter-TSS (NM_010154)	promoter-TSS (NM_010154)	-208	NM_010154	13869	Mm.442420	NM_010154	ENSMUSG00000062209	Erbb4	Her4|c-erbB-4	erb-b2 receptor tyrosine kinase 4	protein-coding
mm_91512.1	chr10	37138497	37138502	-	1	NA	exon (NM_008538, exon 1 of 2)	exon (NM_008538, exon 1 of 2)	427	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_131822.1	chr16	22929184	22929195	+	1	NA	exon (NM_021564, exon 2 of 8)	exon (NM_021564, exon 2 of 8)	8967	NM_001083904	59083	Mm.28461	NM_021564	ENSMUSG00000022871	Fetub	2310011O17Rik|AI255764|D17980|Gugu	fetuin beta	protein-coding
mm_127354.1	chr15	100619900	100619912	+	1	NA	3' UTR (NM_011873, exon 4 of 4)	3' UTR (NM_011873, exon 4 of 4)	4244	NM_011873	23994	Mm.486175	NM_011873	ENSMUSG00000000346	Dazap2	AI314727|Brbp|Gcap28|Prtb|gt6-12|mKIAA0058	DAZ associated protein 2	protein-coding
mm_30462.1	chr3	154091786	154091789	-	1	NA	intron (NM_001081263, intron 1 of 21)	intron (NM_001081263, intron 1 of 21)	118351	NM_001081263	242259	Mm.239962	NM_001081263	ENSMUSG00000028360	Slc44a5	AA117069|Gm422	solute carrier family 44, member 5	protein-coding
mm_5347.1	chr1	25027262	25027271	-	1	NA	Intergenic	MTE2b|LTR|ERVL-MaLR	250688	NM_001204913	100504323	Mm.484176	NM_001204913		Gm20172	-	predicted gene, 20172	protein-coding
mm_39873.1	chr5	31077041	31077047	+	1	NA	intron (NM_023525, intron 39 of 43)	intron (NM_023525, intron 39 of 43)	16483	NM_011773	22784	Mm.1396	NM_011773	ENSMUSG00000029151	Slc30a3	Znt3	solute carrier family 30 (zinc transporter), member 3	protein-coding
mm_171196.1	chr3	46936099	46936103	-	1	NA	Intergenic	L1Md_A|LINE|L1	-35319	NR_105800	102465199		NR_105800	ENSMUSG00000098417	Mir6379	Gm27730|mmu-mir-6379	microRNA 6379	ncRNA
mm_42851.1	chr5	122209919	122209921	+	1	NA	promoter-TSS (NM_028752)	promoter-TSS (NM_028752)	191	NM_001042489	74096	Mm.28804	NM_028752	ENSMUSG00000064267	Hvcn1	0610039P13Rik|AI450555|BTS|HV1|Vsop.|mVSOP	hydrogen voltage-gated channel 1	protein-coding
mm_65223.1	chr7	19700405	19700434	-	1	NA	TTS (NM_001109748)	TTS (NM_001109748)	-1231	NM_009696	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_121475.1	chr14	121035437	121035447	+	1	NA	promoter-TSS (NM_134082)	promoter-TSS (NM_134082)	-132	NM_134082	223254	Mm.223980	NM_134082	ENSMUSG00000025555	Farp1	AW228844|BC030329|Cdep	FERM, RhoGEF (Arhgef) and pleckstrin domain protein 1 (chondrocyte-derived)	protein-coding
mm_75892.1	chr8	70892753	70892758	-	1	NA	promoter-TSS (NM_053248)	promoter-TSS (NM_053248)	2	NM_053248	114479	Mm.172923	NM_053248	ENSMUSG00000000792	Slc5a5	NIS	solute carrier family 5 (sodium iodide symporter), member 5	protein-coding
mm_147978.1	chr18	67489417	67489421	-	1	NA	3' UTR (NM_176832, exon 14 of 14)	3' UTR (NM_176832, exon 14 of 14)	24570	NM_144867	225655	Mm.221420	NM_144867	ENSMUSG00000024530	Slmo1	A230074A19Rik|BC019561|Prelid3a	slowmo homolog 1 (Drosophila)	protein-coding
mm_113503.1	chr13	37578394	37578394	+	1	NA	Intergenic	MER5A|DNA|hAT-Charlie	233049	NM_010745	17084	Mm.2639	NM_010745	ENSMUSG00000021423	Ly86	MD-1|MD1|ly86_tv2	lymphocyte antigen 86	protein-coding
mm_134443.1	chr16	18248728	18248744	-	1	NA	promoter-TSS (NM_011239)	promoter-TSS (NM_011239)	-42	NM_011239	19385	Mm.235287	NM_011239	ENSMUSG00000005732	Ranbp1	Htf9a	RAN binding protein 1	protein-coding
mm_15923.1	chr2	165066847	165066861	+	1	NA	intron (NM_170702, intron 6 of 7)	intron (NM_170702, intron 6 of 7)	11218	NM_011611	21939	Mm.271833	NM_011611	ENSMUSG00000017652	Cd40	AI326936|Bp50|GP39|HIGM1|IGM|IMD3|T-BAM|TRAP|Tnfrsf5|p50	CD40 antigen	protein-coding
mm_127922.1	chr15	9748813	9748874	-	1	NA	promoter-TSS (NM_001305042)	promoter-TSS (NM_001305042)	25	NM_177123	320277	Mm.127822	NM_177123	ENSMUSG00000072663	Spef2	C230086A09Rik	sperm flagellar 2	protein-coding
mm_123004.1	chr14	54993386	54993421	-	1	NA	intron (NM_080728, intron 2 of 40)	intron (NM_080728, intron 2 of 40)	1146	NM_080728	140781	Mm.457983	NM_080728	ENSMUSG00000053093	Myh7	B-MHC|MyHC-I|Myhc-b|Myhcb|beta-MHC	myosin, heavy polypeptide 7, cardiac muscle, beta	protein-coding
mm_49910.1	chr6	39021666	39021676	+	1	NA	intron (NM_011539, intron 7 of 12)	intron (NM_011539, intron 7 of 12)	45915	NR_040523	69986	Mm.490941	NR_040523	ENSMUSG00000100121	1700025N23Rik	-	RIKEN cDNA 1700025N23 gene	ncRNA
mm_136828.1	chr17	12614750	12614755	+	1	NA	exon (NM_013667, exon 8 of 11)	exon (NM_013667, exon 8 of 11)	30563	NM_013667	20518	Mm.17322	NM_013667	ENSMUSG00000040966	Slc22a2	Oct2|Orct2	solute carrier family 22 (organic cation transporter), member 2	protein-coding
mm_80091.1	chr9	70221075	70221088	+	1	NA	intron (NM_181072, intron 1 of 27)	intron (NM_181072, intron 1 of 27)	13731	NM_181072	71602	Mm.249311	NM_181072	ENSMUSG00000032220	Myo1e	2310020N23Rik|9130023P14Rik|AA407778|myosin-1e|myr 3	myosin IE	protein-coding
mm_97274.1	chr11	75999929	75999946	+	1	NA	promoter-TSS (NM_198637)	promoter-TSS (NM_198637)	25	NM_198637	74230	Mm.271247	NM_198637	ENSMUSG00000053783	1700016K19Rik	Liat1	RIKEN cDNA 1700016K19 gene	protein-coding
mm_19020.1	chr2	76945245	76945252	-	1	NA	exon (NM_011652, exon 28 of 313)	exon (NM_011652, exon 28 of 313)	37299	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_142538.1	chr17	46552863	46552868	-	1	NA	TTS (NR_105942)	TTS (NR_105942)	1024	NR_105942	102466778		NR_105942	ENSMUSG00000106514	Mir6976	mmu-mir-6976	microRNA 6976	ncRNA
mm_27369.1	chr3	50438800	50438810	-	1	NA	exon (NM_011990, exon 2 of 12)	exon (NM_011990, exon 2 of 12)	4808	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_78568.1	chr9	36431823	36431836	+	1	NA	promoter-TSS (NM_001167586)	promoter-TSS (NM_001167586)	-55	NM_001167586	639025	Mm.386535	NM_001167586	ENSMUSG00000023093	Gm7257	EG639025|Pate-q|Pate12	predicted gene 7257	protein-coding
mm_703.1	chr1	40681572	40681606	+	1	NA	promoter-TSS (NM_001033289)	promoter-TSS (NM_001033289)	-123	NM_001033289	226999	Mm.256414	NM_001033289	ENSMUSG00000026062	Slc9a2	2210416H12Rik|4932415O19Rik|AV333884|NHE2	solute carrier family 9 (sodium/hydrogen exchanger), member 2	protein-coding
mm_113696.1	chr13	43125870	43125878	+	1	NA	intron (NM_001005740, intron 9 of 12)	intron (NM_001005740, intron 9 of 12)	3035	NM_001005748	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding
mm_143398.1	chr17	70747708	70747731	-	1	NA	intron (NM_001347411, intron 9 of 14)	intron (NM_001347411, intron 9 of 14)	99058	NM_001164077	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_141122.1	chr17	26095465	26095480	-	1	NA	promoter-TSS (NM_019731)	promoter-TSS (NM_019731)	-2	NM_019731	56520	Mm.41787	NM_019731	ENSMUSG00000024177	Nme4	2610027N22Rik|2810024O08Rik|5730493H09Rik|NM23-M4|Nm23M4	NME/NM23 nucleoside diphosphate kinase 4	protein-coding
mm_87099.1	chr10	33139113	33139124	+	1	NA	exon (NM_029726, exon 2 of 38)	exon (NM_029726, exon 2 of 38)	55635	NM_029726	76757	Mm.338508	NM_029726	ENSMUSG00000019787	Trdn	2310045H21Rik|EG432451|TDN	triadin	protein-coding
mm_102884.1	chr11	69410713	69410736	-	1	NA	intron (NM_001017426, intron 1 of 22)	CpG	2951	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_77261.1	chr8	115707451	115707485	-	1	NA	promoter-TSS (NM_001025577)	promoter-TSS (NM_001025577)	-574	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_108513.1	chr12	83993401	83993413	+	1	NA	3' UTR (NM_134188, exon 3 of 3)	3' UTR (NM_134188, exon 3 of 3)	5546	NM_134188	171210	Mm.371675	NM_134188	ENSMUSG00000021226	Acot2	AA571646|MTE-I|Mte1	acyl-CoA thioesterase 2	protein-coding
mm_89112.1	chr10	84646607	84646655	+	1	NA	intron (NM_027423, intron 9 of 27)	intron (NM_027423, intron 9 of 27)	24194	NM_027423	70428	Mm.335007	NM_027423	ENSMUSG00000034453	Polr3b	2700078H01Rik|A330032P03Rik|C85372|RPC2	polymerase (RNA) III (DNA directed) polypeptide B	protein-coding
mm_26901.1	chr3	19290037	19290041	-	1	NA	intron (NM_001122759, intron 1 of 12)	intron (NM_001122759, intron 1 of 12)	21283	NM_001122759	18583	Mm.355614	NM_008802	ENSMUSG00000069094	Pde7a	AU015378|AW047537	phosphodiesterase 7A	protein-coding
mm_9459.1	chr1	172894969	172894980	-	1	NA	promoter-TSS (NM_011318)	promoter-TSS (NM_011318)	80	NM_011318	20219	Mm.330510	NM_011318	ENSMUSG00000026542	Apcs	Sap	serum amyloid P-component	protein-coding
mm_85469.1	chr9	105764161	105764161	-	1	NA	intron (NM_001102607, intron 10 of 36)	intron (NM_001102607, intron 10 of 36)	45487	NM_172927	245026	Mm.482507	NM_172927	ENSMUSG00000043719	Col6a6	E330019B14|E330026B02Rik	collagen, type VI, alpha 6	protein-coding
mm_87547.1	chr10	53597111	53597119	+	1	NA	5' UTR (NM_025541, exon 1 of 4)	5' UTR (NM_025541, exon 1 of 4)	154	NM_025541	66403	Mm.272989	NM_025541	ENSMUSG00000019857	Asf1a	2310079C17Rik|C79052	anti-silencing function 1A histone chaperone	protein-coding
mm_108571.1	chr12	84855442	84855471	+	1	NA	intron (NM_013589, intron 2 of 34)	intron (NM_013589, intron 2 of 34)	-20346	NR_028577	100303738	Mm.479389	NR_028577		D030025P21Rik	-	RIKEN cDNA D030025P21 gene	ncRNA
mm_123040.1	chr14	55585251	55585317	-	1	NA	promoter-TSS (NM_033146)	promoter-TSS (NM_033146)	-30	NM_033146	85308	Mm.40667	NM_033146	ENSMUSG00000022217	Emc9	1500005A01Rik|Cgi112|Fam158a	ER membrane protein complex subunit 9	protein-coding
mm_131792.1	chr16	22898973	22898988	+	1	NA	exon (NM_001276450, exon 7 of 7)	exon (NM_001276450, exon 7 of 7)	-4594	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_23280.1	chr3	51661210	51661250	+	1	NA	promoter-TSS (NM_174995)	promoter-TSS (NM_174995)	51	NM_001310482	211666	Mm.24679	NM_174995	ENSMUSG00000074604	Mgst2	GST2|MGST-II	microsomal glutathione S-transferase 2	protein-coding
mm_35754.1	chr4	45811307	45811310	-	1	NA	3' UTR (NM_018741, exon 5 of 5)	3' UTR (NM_018741, exon 5 of 5)	12286	NM_028270	72535	Mm.331583	NM_028270	ENSMUSG00000035561	Aldh1b1	2700007F14Rik	aldehyde dehydrogenase 1 family, member B1	protein-coding
mm_167633.1	chr9	62846971	62846989	+	1	NA	exon (NM_001033175, exon 4 of 7)	exon (NM_001033175, exon 4 of 7)	8193	NM_001033175	76524	Mm.283636	NM_001033175	ENSMUSG00000032245	Cln6	1810065L06Rik|AW743417|D9Bwg1455e|nclf	ceroid-lipofuscinosis, neuronal 6	protein-coding
mm_33749.1	chr4	134246943	134246969	+	1	NA	Intergenic	Intergenic	-1365	NM_024215	68040	Mm.300404	NM_024215	ENSMUSG00000028840	Zfp593	3110024A21Rik|AV062409|E130106C14Rik|ZNF593	zinc finger protein 593	protein-coding
mm_28598.1	chr3	94501272	94501281	-	1	NA	3' UTR (NM_029721, exon 12 of 12)	3' UTR (NM_029721, exon 12 of 12)	18554	NR_110353	78784	Mm.44292	NM_172434	ENSMUSG00000028137	Celf3	4930415M08Rik|BRUNOL1|CAGH4|ERDA4|Tnrc4	CUGBP, Elav-like family member 3	protein-coding
mm_61063.1	chr7	50599152	50599154	+	1	NA	promoter-TSS (NM_172901)	promoter-TSS (NM_172901)	-37	NM_172901	243996	Mm.443270	NM_172901	ENSMUSG00000084234	4933405O20Rik	-	RIKEN cDNA 4933405O20 gene	protein-coding
mm_60208.1	chr7	43437601	43437624	+	1	NA	exon (NM_024253, exon 2 of 4)	exon (NM_024253, exon 2 of 4)	474	NM_024253	72310	Mm.34613	NM_024253	ENSMUSG00000004612	Nkg7	2500004F03Rik	natural killer cell group 7 sequence	protein-coding
mm_6473.1	chr1	74068866	74068908	-	1	NA	intron (NM_027884, intron 2 of 34)	CpG-274	55560	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_10658.1	chr2	20722468	20722473	+	1	NA	intron (NM_029895, intron 6 of 18)	intron (NM_029895, intron 6 of 18)	202957	NM_001177631	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding
mm_159905.1	chr6	42405673	42405673	+	1	NA	exon (NM_199159, exon 1 of 1)	exon (NM_199159, exon 1 of 1)	144	NM_199159	387512	Mm.377919	NM_199159	ENSMUSG00000056203	Tas2r135	Tas2r35|mt2r38	taste receptor, type 2, member 135	protein-coding
mm_66328.1	chr7	42692748	42692773	-	1	NA	promoter-TSS (NM_001008427)	promoter-TSS (NM_001008427)	-42	NM_001008427	434179	Mm.284947	NM_001008427	ENSMUSG00000069727	Zfp975	EG434179|Gm5595|mszf88	zinc finger protein 975	protein-coding
mm_160834.1	chr11	48826136	48826136	+	1	NA	promoter-TSS (NM_053166)	promoter-TSS (NM_053166)	-2	NM_053166	94089	Mm.390335	NM_053166	ENSMUSG00000040350	Trim7	AI790312	tripartite motif-containing 7	protein-coding
mm_125462.1	chr15	52712388	52712394	+	1	NA	promoter-TSS (NM_027212)	promoter-TSS (NM_027212)	-54	NM_027212	69790	Mm.195562	NM_027212	ENSMUSG00000038622	Med30	1810038N03Rik|2510044J04Rik|TRAP25|Thrap6	mediator complex subunit 30	protein-coding
mm_124039.1	chr14	77036553	77036561	-	1	NA	promoter-TSS (NM_172488)	promoter-TSS (NM_172488)	60	NM_172488	210808	Mm.89278	NM_172488	ENSMUSG00000044350	Lacc1	9030625A04Rik	laccase (multicopper oxidoreductase) domain containing 1	protein-coding
mm_128887.1	chr15	73157205	73157227	-	1	NA	intron (NM_153178, intron 1 of 18)	intron (NM_153178, intron 1 of 18)	27731	NM_153178	239528	Mm.23095	NM_153178	ENSMUSG00000036698	Ago2	1110029L17Rik|2310051F07Rik|AI225898|AL022874|AW546247|ENSMUSG00000072493|Eif2c2|Gerp95|Gm10365|mKIAA4215	argonaute RISC catalytic subunit 2	protein-coding
mm_127623.1	chr15	102462219	102462243	+	1	NA	3' UTR (NM_025385, exon 5 of 5)	3' UTR (NM_025385, exon 5 of 5)	3061	NM_025385	66151	Mm.393955	NM_025385	ENSMUSG00000023048	Prr13	1110020C13Rik|2010324E22Rik	proline rich 13	protein-coding
mm_121228.1	chr14	103055645	103055655	+	1	NA	3' UTR (NM_008392, exon 5 of 5)	3' UTR (NM_008392, exon 5 of 5)	8638	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_70404.1	chr8	11325582	11325600	+	1	NA	intron (NM_009932, intron 3 of 47)	B4A|SINE|B4	-12765	NM_009931	12826	Mm.738	NM_009931	ENSMUSG00000031502	Col4a1	Bru|Col4a-1|Raw|Svc	collagen, type IV, alpha 1	protein-coding
mm_146170.1	chr18	75297589	75297594	+	1	NA	promoter-TSS (NR_045394)	promoter-TSS (NR_045394)	-262	NR_045393	100503117	Mm.250517	NR_045393	ENSMUSG00000102047	2010010A06Rik	5033420E22Rik	RIKEN cDNA 2010010A06 gene	ncRNA
mm_12386.1	chr2	69870380	69870393	+	1	NA	TTS (NR_110977)	TTS (NR_110977)	8824	NM_009278	20823	Mm.10508	NM_009278	ENSMUSG00000068882	Ssb	SS-B	Sjogren syndrome antigen B	protein-coding
mm_62278.1	chr7	99594606	99594630	+	1	NA	intron (NM_177231, intron 10 of 15)	intron (NM_177231, intron 10 of 15)	32485	NM_001195529	100503386	Mm.180719	NM_001195529	ENSMUSG00000096606	Tpbgl	EG245190|Gm4980	trophoblast glycoprotein-like	protein-coding
mm_4866.1	chr1	187692207	187692215	+	1	NA	intron (NM_001243792, intron 1 of 7)	(T)n|Simple_repeat|Simple_repeat	83205	NM_001243792	26381	Mm.89989	NM_011935	ENSMUSG00000026610	Esrrg	ERR3|Errg|NR3B3|mKIAA0832	estrogen-related receptor gamma	protein-coding
mm_57054.1	chr6	122472699	122472710	-	1	NA	exon (NM_027664, exon 2 of 6)	exon (NM_027664, exon 2 of 6)	13601	NM_027664	108653	Mm.277939	NM_027664	ENSMUSG00000040649	Rimklb	4931417E21Rik|4933426K21Rik|AA097693|AI325948|AU015629|Naags	ribosomal modification protein rimK-like family member B	protein-coding
mm_102492.1	chr11	60239980	60240002	-	1	NA	TTS (NM_001039093)	TTS (NM_001039093)	-19364	NM_001313979	20787	Mm.278701	NM_011480	ENSMUSG00000020538	Srebf1	ADD1|SREBP-1a|SREBP1|SREBP1c|bHLHd1	sterol regulatory element binding transcription factor 1	protein-coding
mm_83857.1	chr9	54647200	54647222	-	1	NA	intron (NM_053178, intron 1 of 13)	intron (NM_053178, intron 1 of 13)	14674	NM_053178	94180	Mm.20592	NM_053178	ENSMUSG00000032281	Acsbg1	BG1|Bgm|E230019G03Rik|GR-LACS|Lpd|R75185	acyl-CoA synthetase bubblegum family member 1	protein-coding
mm_65907.1	chr7	30193339	30193367	-	1	NA	intron (NM_009795, intron 2 of 10)	intron (NM_009795, intron 2 of 10)	1695	NM_009795	12336	Mm.439782	NM_009795	ENSMUSG00000001794	Capns1	Capa-4|Capa4|Capn4|D7Ertd146e	calpain, small subunit 1	protein-coding
mm_129348.1	chr15	77915369	77915413	-	1	NA	3' UTR (NM_019913, exon 4 of 4)	3' UTR (NM_019913, exon 4 of 4)	13603	NM_019913	56551	Mm.291917	NM_019913	ENSMUSG00000005354	Txn2	2510006J11Rik|AI788873|Trx2	thioredoxin 2	protein-coding
mm_114506.1	chr13	70650183	70650219	+	1	NA	Intergenic	L2a|LINE|L2	-12567	NM_144837	218333	Mm.139738	NM_144837	ENSMUSG00000034525	Ice1	C77245|mKIAA0947	interactor of little elongation complex ELL subunit 1	protein-coding
mm_85681.1	chr9	107872688	107872747	-	1	NA	5' UTR (NM_029169, exon 1 of 21)	5' UTR (NM_029169, exon 1 of 21)	102	NM_011251	19654	Mm.139926	NM_011251	ENSMUSG00000032582	Rbm6	4930506F14Rik|Def-3|NY-LU-12|g16|mKIAA4015	RNA binding motif protein 6	protein-coding
mm_126287.1	chr15	79247151	79247152	+	1	NA	intron (NM_001045558, intron 10 of 12)	intron (NM_001045558, intron 10 of 12)	7597	NM_020516	57274	Mm.441697	NM_020516	ENSMUSG00000032988	Slc16a8	Mct3	solute carrier family 16 (monocarboxylic acid transporters), member 8	protein-coding
mm_55220.1	chr6	52230526	52230538	-	1	NA	promoter-TSS (NR_029912)	promoter-TSS (NR_029912)	-367	NR_029912	723820		NR_029912	ENSMUSG00000065443	Mir196b	Mirn196b|mir-196b	microRNA 196b	ncRNA
mm_128556.1	chr15	55906801	55906821	-	1	NA	5' UTR (NM_016667, exon 1 of 7)	5' UTR (NM_016667, exon 1 of 7)	138	NM_016667	20649	Mm.309425	NM_016667	ENSMUSG00000060429	Sntb1	-	syntrophin, basic 1	protein-coding
mm_162411.1	chr1	87127941	87127945	-	1	NA	TTS (NM_007432)	TTS (NM_007432)	2935	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_116461.1	chr13	43398183	43398186	-	1	NA	promoter-TSS (NM_023554)	promoter-TSS (NM_023554)	-192	NM_023554	70078	Mm.439927	NM_023554	ENSMUSG00000063200	Nol7	2210008F15Rik|5730556I21Rik|NOP27|RARG-1	nucleolar protein 7	protein-coding
mm_46499.1	chr5	105133578	105133601	-	1	NA	intron (NM_008620, intron 3 of 10)	Lx|LINE|L1	5963	NM_008620	17472	Mm.440525	NM_008620	ENSMUSG00000079363	Gbp4	AW228052|Mag-2|Mpa-2|Mpa2	guanylate binding protein 4	protein-coding
mm_78138.1	chr9	20889825	20889844	+	1	NA	exon (NM_145610, exon 5 of 11)	exon (NM_145610, exon 5 of 11)	1659	NM_145610	235036	Mm.2930	NM_145610	ENSMUSG00000004100	Ppan	A230087P06Rik|SSF1	peter pan homolog (Drosophila)	protein-coding
mm_173149.1	chrX	24008507	24008517	+	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	115749	NM_001034864	236749	Mm.296422	NM_001034864	ENSMUSG00000068113	Gm4907	EG236749	predicted gene 4907	protein-coding
mm_91391.1	chr10	30655860	30655868	-	1	NA	promoter-TSS (NM_001111267)	promoter-TSS (NM_001111267)	3	NM_001111267	211329	Mm.297903	NM_172495	ENSMUSG00000039697	Ncoa7	9030406N13Rik	nuclear receptor coactivator 7	protein-coding
mm_164843.1	chr18	43059565	43059569	-	1	NA	promoter-TSS (NM_028392)	promoter-TSS (NM_028392)	-96	NM_028392	72930	Mm.26134	NM_027531	ENSMUSG00000024500	Ppp2r2b	2900026H06Rik|6330404L05Rik|E130009M08Rik|PP2A-PR55B|PR55-BETA|SCA12	protein phosphatase 2, regulatory subunit B, beta	protein-coding
mm_67436.1	chr7	80385674	80385684	-	1	NA	intron (NM_010194, intron 3 of 18)	RSINE1|SINE|B4	2267	NM_010194	14159	Mm.48757	NM_010194	ENSMUSG00000053158	Fes	AI586313|BB137047|FPS|c-fes	feline sarcoma oncogene	protein-coding
mm_65097.1	chr7	19272553	19272562	-	1	NA	promoter-TSS (NM_001282022)	promoter-TSS (NM_001282022)	-703	NM_001282022	22323	Mm.9684	NM_009499	ENSMUSG00000030403	Vasp	-	vasodilator-stimulated phosphoprotein	protein-coding
mm_53269.1	chr6	128399882	128399919	+	1	NA	5' UTR (NM_021717, exon 1 of 6)	5' UTR (NM_021717, exon 1 of 6)	134	NM_001162858	60345	Mm.269883	NM_021717	ENSMUSG00000001520	Nrip2	AW491344|NIX1	nuclear receptor interacting protein 2	protein-coding
mm_121959.1	chr14	24617484	24617492	-	1	NA	Intergenic	Intergenic	126807	NM_011297	20088	Mm.16775	NM_011297	ENSMUSG00000025290	Rps24	-	ribosomal protein S24	protein-coding
mm_164364.1	chr16	23060376	23060378	+	1	NA	intron (NM_023125, intron 1 of 10)	intron (NM_023125, intron 1 of 10)	2077	NM_001102412	16644	Mm.2160	NM_023125	ENSMUSG00000022875	Kng1	Kng	kininogen 1	protein-coding
mm_25335.1	chr3	106574029	106574040	+	1	NA	3' UTR (NM_026013, exon 9 of 9)	3' UTR (NM_026013, exon 9 of 9)	-26232	NM_133869	99712	Mm.429443	NM_133869	ENSMUSG00000040774	Cept1	9930118K05Rik|mCEPT1	choline/ethanolaminephosphotransferase 1	protein-coding
mm_32588.1	chr4	111415137	111415218	+	1	NA	exon (NM_026279, exon 1 of 6)	exon (NM_026279, exon 1 of 6)	171	NM_026279	67621	Mm.45533	NM_026279	ENSMUSG00000028545	Bend5	2310026E23Rik	BEN domain containing 5	protein-coding
mm_13105.1	chr2	91513026	91513030	+	1	NA	3' UTR (NM_172668, exon 38 of 38)	3' UTR (NM_172668, exon 38 of 38)	-33294	NM_001165989	75786	Mm.168478	NM_029437	ENSMUSG00000040549	Ckap5	3110043H24Rik|4930432B04Rik|D730027C18Rik|T25636|mKIAA0097	cytoskeleton associated protein 5	protein-coding
mm_9141.1	chr1	170867804	170867814	-	1	NA	promoter-TSS (NM_001081304)	promoter-TSS (NM_001081304)	-38	NM_001081304	226641	Mm.377046	NM_001081304	ENSMUSG00000026663	Atf6	9130025P16Rik|9630036G24|AA789574|Atf6alpha|ESTM49	activating transcription factor 6	protein-coding
mm_89241.1	chr10	87858256	87858294	+	1	NA	promoter-TSS (NM_010512)	promoter-TSS (NM_010512)	10	NM_001314010	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_120151.1	chr14	60634720	60634776	+	1	NA	promoter-TSS (NM_001033272)	promoter-TSS (NM_001033272)	43	NM_001033272	219140	Mm.149776	NM_001033272	ENSMUSG00000021990	Spata13	C79050|ESTM11|X83327|mFLJ00298	spermatogenesis associated 13	protein-coding
mm_15809.1	chr2	164492033	164492034	+	1	NA	3' UTR (NM_001048229, exon 3 of 3)	3' UTR (NM_001048229, exon 3 of 3)	3922	NM_001048229	52840	Mm.256927	NM_026797	ENSMUSG00000017734	Dbndd2	1110017A21Rik|2900022J10Rik|AU041050|AW048677|D2Bwg0891e|Nkip|R74724	dysbindin (dystrobrevin binding protein 1) domain containing 2	protein-coding
mm_143108.1	chr17	57149634	57149637	-	1	NA	5' UTR (NM_011617, exon 1 of 3)	5' UTR (NM_011617, exon 1 of 3)	142	NM_011617	21948	Mm.42228	NM_011617	ENSMUSG00000019489	Cd70	CD27LG|Cd27l|Tnfsf7|Tnlg8a	CD70 antigen	protein-coding
mm_44837.1	chr5	34169025	34169035	-	1	NA	intron (NM_146159, intron 1 of 4)	intron (NM_146159, intron 1 of 4)	394	NM_146159	231123	Mm.319286	NM_146159	ENSMUSG00000079555	Haus3	D4S43h|D5H4S43|D5H4S43E	HAUS augmin-like complex, subunit 3	protein-coding
mm_107357.1	chr12	32830261	32830282	+	1	NA	exon (NM_021524, exon 2 of 11)	exon (NM_021524, exon 2 of 11)	6155	NR_045032	100504486	Mm.440246	NR_045032		Gdap10	Gdap-ps	ganglioside-induced differentiation-associated-protein 10	ncRNA
mm_144831.1	chr18	36365813	36365823	+	1	NA	intron (NM_001081365, intron 1 of 2)	intron (NM_001081365, intron 1 of 2)	17194	NM_001081365	66060	Mm.272527	NM_001081365	ENSMUSG00000046727	Cystm1	0610010O12Rik	cysteine-rich transmembrane module containing 1	protein-coding
mm_89278.1	chr10	87863785	87863798	+	1	NA	intron (NM_001111274, intron 1 of 4)	intron (NM_001111274, intron 1 of 4)	2680	NM_001111276	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_106528.1	chr11	120572906	120572908	-	1	NA	promoter-TSS (NM_011032)	promoter-TSS (NM_011032)	29	NM_011032	18453	Mm.16660	NM_011032	ENSMUSG00000025130	P4hb	ERp59|PDI|Pdia1|Thbp	prolyl 4-hydroxylase, beta polypeptide	protein-coding
mm_9487.1	chr1	173729143	173729196	-	1	NA	exon (NM_001204910, exon 5 of 8)	exon (NM_001204910, exon 5 of 8)	12640	NM_001204910	226691	Mm.440876	NM_001204910	ENSMUSG00000073490	Ifi207	AI607873|Pyhin-A	interferon activated gene 207	protein-coding
mm_33868.1	chr4	135963721	135963733	+	1	NA	Intergenic	CpG	-1438	NM_178389	74246	Mm.247946	NM_178389	ENSMUSG00000028671	Gale	2310002A12Rik|AI323962	galactose-4-epimerase, UDP	protein-coding
mm_86559.1	chr10	11281026	11281041	+	1	NA	promoter-TSS (NM_027968)	promoter-TSS (NM_027968)	-297	NM_027968	71865	Mm.276229	NM_027968	ENSMUSG00000047648	Fbxo30	1700026A16Rik|MUSA1	F-box protein 30	protein-coding
mm_71391.1	chr8	46162256	46162262	+	1	NA	Intergenic	Intergenic	-7297	NM_025747	66756	Mm.133623	NM_025747	ENSMUSG00000031631	Cfap97	1110068E21Rik|4933411K20Rik|AW049273|Kiaa1430|mKIAA1430	cilia and flagella associated protein 97	protein-coding
mm_23653.1	chr3	67582771	67582816	+	1	NA	promoter-TSS (NM_025813)	promoter-TSS (NM_025813)	25	NM_025813	66868	Mm.491153	NM_025813	ENSMUSG00000027775	Mfsd1	1200003O06Rik	major facilitator superfamily domain containing 1	protein-coding
mm_101079.1	chr11	11694270	11694284	-	1	NA	intron (NM_001301866, intron 1 of 5)	B4A|SINE|B4	4100	NM_001301863	22778	Mm.103545	NM_009578	ENSMUSG00000018654	Ikzf1	5832432G11Rik|Ikaros|LyF-1|Zfpn1a1|Znfn1a1|hlk-1|mKIAA4227	IKAROS family zinc finger 1	protein-coding
mm_95534.1	chr11	52253713	52253758	+	1	NA	3' UTR (NM_009331, exon 10 of 10)	3' UTR (NM_009331, exon 10 of 10)	21740	NM_011543	21402	Mm.42944	NM_011543	ENSMUSG00000036309	Skp1a	15kDa|2610043E24Rik|2610206H23Rik|EMC19|OCP-II|OCP2|SKP1|Tceb1l|p19A|p19Skp1	S-phase kinase-associated protein 1A	protein-coding
mm_134545.1	chr16	19883862	19883872	-	1	NA	non-coding (NR_015488, exon 1 of 2)	non-coding (NR_015488, exon 1 of 2)	407	NR_027896	68162	Mm.35159	NR_015488		A930003A15Rik	AI853191	RIKEN cDNA A930003A15 gene	ncRNA
mm_97135.1	chr11	75172472	75172478	+	1	NA	promoter-TSS (NR_029794)	promoter-TSS (NR_029794)	-913	NR_029794	387208		NR_029794	ENSMUSG00000065590	Mir212	Mirn212|mir-212|mmu-mir-212	microRNA 212	ncRNA
mm_26886.1	chr3	18125717	18125720	-	1	NA	intron (NM_007825, intron 1 of 5)	intron (NM_007825, intron 1 of 5)	71393	NM_021560	59058	Mm.149938	NM_021560	ENSMUSG00000025128	Bhlhe22	Beta3|Beta3a|Bhlhb5	basic helix-loop-helix family, member e22	protein-coding
mm_72759.1	chr8	85492677	85492687	+	1	NA	promoter-TSS (NM_173866)	promoter-TSS (NM_173866)	65	NM_173866	108682	Mm.200423	NM_173866	ENSMUSG00000031700	Gpt2	4631422C05Rik|ALT2|AU014768|AU041193|C87201	glutamic pyruvate transaminase (alanine aminotransferase) 2	protein-coding
mm_87904.1	chr10	62231420	62231424	+	1	NA	promoter-TSS (NM_197996)	promoter-TSS (NM_197996)	-204	NM_197996	70423	Mm.416781	NM_197996	ENSMUSG00000037031	Tspan15	1110036D12Rik|2700063A19Rik|AW048364|Tm4sf15	tetraspanin 15	protein-coding
mm_133210.1	chr16	74828358	74828359	+	1	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	-417446	NM_175549	268902	Mm.171736	NM_175549	ENSMUSG00000052516	Robo2	2600013A04Rik|9430089E08Rik|BB097918|D230004I22Rik|mKIAA1568	roundabout guidance receptor 2	protein-coding
mm_153926.1	chr19	47320380	47320440	-	1	NA	intron (NM_001164717, intron 6 of 13)	intron (NM_001164717, intron 6 of 13)	-46821	NR_105961	102466782		NR_105961	ENSMUSG00000098786	Mir6995	Gm27576|mmu-mir-6995	microRNA 6995	ncRNA
mm_81334.1	chr9	108517517	108517527	+	1	NA	intron (NM_175143, intron 1 of 9)	CpG	435	NM_175143	69232	Mm.335449	NM_175143	ENSMUSG00000006673	Qrich1	2610028H07Rik	glutamine-rich 1	protein-coding
mm_147424.1	chr18	46212596	46212634	-	1	NA	promoter-TSS (NM_178872)	promoter-TSS (NM_178872)	-8	NM_178872	28105	Mm.277382	NM_178872	ENSMUSG00000033949	Trim36	D18Wsu100e|haprin	tripartite motif-containing 36	protein-coding
mm_10773.1	chr2	24277264	24277277	+	1	NA	promoter-TSS (NM_019451)	promoter-TSS (NM_019451)	-1	NM_019451	54450	Mm.29261	NM_019451	ENSMUSG00000026983	Il1f5	AI413231|Fil1delta|IL-36Ra|IL36RN|Il-1h3|Il1hy1	interleukin 1 family, member 5 (delta)	protein-coding
mm_88054.1	chr10	67547823	67547838	+	1	NA	3' UTR (NM_001005419, exon 1 of 1)	3' UTR (NM_001005419, exon 1 of 1)	1125	NM_001005419	211488	Mm.297250	NM_001005419	ENSMUSG00000057134	Ado	Gm237	2-aminoethanethiol (cysteamine) dioxygenase	protein-coding
mm_100766.1	chr11	4594826	4594828	-	1	NA	promoter-TSS (NM_028860)	promoter-TSS (NM_028860)	-12	NM_028860	74302	Mm.425669	NM_028860	ENSMUSG00000034354	Mtmr3	1700092A20Rik|AI255150|AW557713|FYVE-DSP1|ZFYVE10|mKIAA0371	myotubularin related protein 3	protein-coding
mm_2254.1	chr1	91093525	91093536	+	1	NA	intron (NM_001310732, intron 11 of 24)	intron (NM_001310732, intron 11 of 24)	40086	NM_008515	16978	Mm.45039	NM_008515	ENSMUSG00000026305	Lrrfip1	AU024550|Fliiap1	leucine rich repeat (in FLII) interacting protein 1	protein-coding
mm_32916.1	chr4	119136623	119136642	+	1	NA	3' UTR (NM_011400, exon 10 of 10)	3' UTR (NM_011400, exon 10 of 10)	27887	NM_011400	20525	Mm.21002	NM_011400	ENSMUSG00000028645	Slc2a1	Glut-1|Glut1	solute carrier family 2 (facilitated glucose transporter), member 1	protein-coding
mm_1051.1	chr1	58802595	58802637	+	1	NA	5' UTR (NM_001277926, exon 1 of 10)	5' UTR (NM_001277926, exon 1 of 10)	114	NM_001080126	12370	Mm.336851	NM_009812	ENSMUSG00000026029	Casp8	CASP-8|FLICE|MACH|Mch5	caspase 8	protein-coding
mm_104188.1	chr11	87814323	87814335	-	1	NA	exon (NM_080420, exon 9 of 13)	exon (NM_080420, exon 9 of 13)	11785	NM_080420	76113	Mm.41236	NM_080420	ENSMUSG00000009356	Lpo	5830499B15Rik	lactoperoxidase	protein-coding
mm_124240.1	chr14	101477488	101477514	-	1	NA	intron (NM_001081278, intron 9 of 18)	intron (NM_001081278, intron 9 of 18)	131690	NM_001081278	210789	Mm.320639	NM_173380	ENSMUSG00000033083	Tbc1d4	5930406J04Rik|A930035N22|AV295684|As160	TBC1 domain family, member 4	protein-coding
mm_28371.1	chr3	89913103	89913111	-	1	NA	promoter-TSS (NM_010559)	promoter-TSS (NM_010559)	89	NM_001310676	16194	Mm.2856	NM_010559	ENSMUSG00000027947	Il6ra	CD126|IL-6R|IL-6R-alpha|IL-6RA|Il6r	interleukin 6 receptor, alpha	protein-coding
mm_127134.1	chr15	98167924	98167934	+	1	NA	5' UTR (NM_177716, exon 1 of 1)	5' UTR (NM_177716, exon 1 of 1)	123	NM_177716	239650	Mm.54140	NM_177716	ENSMUSG00000029875	Ccdc184	5630400A08|AI836003	coiled-coil domain containing 184	protein-coding
mm_159098.1	chr2	36376842	36376842	+	1	NA	promoter-TSS (NM_146947)	promoter-TSS (NM_146947)	64	NM_146947	258949	Mm.377765	NM_146947	ENSMUSG00000068950	Olfr338	MOR136-5	olfactory receptor 338	protein-coding
mm_155.1	chr1	12692406	12692419	+	1	NA	promoter-TSS (NM_001198566)	promoter-TSS (NM_001198566)	-18	NM_001198565	240725	Mm.45563	NM_172294	ENSMUSG00000016918	Sulf1	AI467640|AW121680|mKIAA1077	sulfatase 1	protein-coding
mm_81431.1	chr9	109094836	109094850	+	1	NA	promoter-TSS (NM_172775)	promoter-TSS (NM_172775)	-593	NM_172775	235611	Mm.53862	NM_172775	ENSMUSG00000053646	Plxnb1	2900002G15Rik|AU042020|mKIAA0407	plexin B1	protein-coding
mm_168988.1	chr12	99645126	99645130	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-17154	NR_045288	73457	Mm.383439	NR_045288	ENSMUSG00000100211	1700064M15Rik	-	RIKEN cDNA 1700064M15 gene	ncRNA
mm_37528.1	chr4	124850653	124850664	-	1	NA	promoter-TSS (NM_001142727)	promoter-TSS (NM_001142727)	72	NM_001142727	68920	Mm.272397	NM_001142727	ENSMUSG00000078570	1110065P20Rik	C530005M16Rik	RIKEN cDNA 1110065P20 gene	protein-coding
mm_155654.1	chrX	85870379	85870389	+	1	NA	5' UTR (NM_001163539, exon 1 of 2)	5' UTR (NM_001163539, exon 1 of 2)	111	NM_001163539	71398	Mm.185296	NM_001163539	ENSMUSG00000025058	5430427O19Rik	-	RIKEN cDNA 5430427O19 gene	protein-coding
mm_78868.1	chr9	44407091	44407161	+	1	NA	promoter-TSS (NM_024266)	promoter-TSS (NM_024266)	422	NM_021789	60409	Mm.29814	NM_021789	ENSMUSG00000032112	Trappc4	1500017G03Rik|AI303617|HSPC172|PTD009|Sbd|Sbdn|Sdcbp2|TRS23	trafficking protein particle complex 4	protein-coding
mm_78304.1	chr9	22643247	22643257	+	1	NA	intron (NM_178415, intron 13 of 22)	Lx8|LINE|L1	167537	NM_178415	319845	Mm.176725	NM_178415	ENSMUSG00000035919	Bbs9	E130103I17Rik	Bardet-Biedl syndrome 9 (human)	protein-coding
mm_14091.1	chr2	125158921	125158937	+	1	NA	intron (NM_183354, intron 3 of 27)	B4|SINE|B4	6329	NM_001079690	20495	Mm.3914	NM_011389	ENSMUSG00000027202	Slc12a1	AI788571|D630042G03Rik|Nkcc2|mBSC1|urehr3	solute carrier family 12, member 1	protein-coding
mm_137247.1	chr17	24488738	24488771	+	1	NA	promoter-TSS (NM_027937)	promoter-TSS (NM_027937)	-29	NM_027937	268932	Mm.70989	NM_027937	ENSMUSG00000033597	Caskin1	3300002N10Rik|C130061I24|C630036E02Rik|mKIAA1306	CASK interacting protein 1	protein-coding
mm_60389.1	chr7	44474081	44474095	+	1	NA	Intergenic	Intergenic	3741	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_42945.1	chr5	122990776	122990780	+	1	NA	intron (NR_045820, intron 1 of 2)	intron (NR_045820, intron 1 of 2)	1424	NR_045820	109202	Mm.30769	NM_175405	ENSMUSG00000056735	A930024E05Rik	-	RIKEN cDNA A930024E05 gene	ncRNA
mm_146966.1	chr18	33462539	33462544	-	1	NA	intron (NM_053078, intron 1 of 3)	intron (NM_053078, intron 1 of 3)	1093	NM_001267717	27528	Mm.407415	NM_053078	ENSMUSG00000042834	Nrep	AI325076|D0H4S114|Harp|P311|PTZ17|SEZ17	neuronal regeneration related protein	protein-coding
mm_35515.1	chr4	41124225	41124285	-	1	NA	promoter-TSS (NM_139236)	promoter-TSS (NM_139236)	84	NM_139236	230082	Mm.285797	NM_139236	ENSMUSG00000028430	Nol6	AA410091|Nrap	nucleolar protein family 6 (RNA-associated)	protein-coding
mm_117605.1	chr13	90886719	90886723	-	1	NA	exon (NM_001145879, exon 6 of 7)	exon (NM_001145879, exon 6 of 7)	18634	NM_001145879	435376	Mm.292579	NM_001145879	ENSMUSG00000078958	Atp6ap1l	EG435376	ATPase, H+ transporting, lysosomal accessory protein 1-like	protein-coding
mm_118454.1	chr14	8368257	8368265	+	1	NA	intron (NM_146050, intron 1 of 9)	intron (NM_146050, intron 1 of 9)	10502	NM_146050	18300	Mm.25351	NM_146050	ENSMUSG00000021749	Oit1	2310076N21Rik|AV067083|EF-7|Fam3d	oncoprotein induced transcript 1	protein-coding
mm_117007.1	chr13	57908325	57908339	-	1	NA	promoter-TSS (NM_001166463)	promoter-TSS (NM_001166463)	0	NM_009262	20745	Mm.379020	NM_009262	ENSMUSG00000056222	Spock1	Spock|Ticn1|testican	sparc/osteonectin, cwcv and kazal-like domains proteoglycan 1	protein-coding
mm_123500.1	chr14	66213720	66213730	-	1	NA	promoter-TSS (NM_001162366)	promoter-TSS (NM_001162366)	-173	NM_001162366	19229	Mm.21613	NM_172498	ENSMUSG00000059456	Ptk2b	CADTK|CAKB|CAKbeta|E430023O05Rik|FADK2|FAK2|PYK2|Raftk	PTK2 protein tyrosine kinase 2 beta	protein-coding
mm_57775.1	chr6	129238005	129238015	-	1	NA	promoter-TSS (NR_040265)	promoter-TSS (NR_040265)	35	NR_040265	76432	Mm.261738	NR_040265	ENSMUSG00000097354	2310001H17Rik	AI646108	RIKEN cDNA 2310001H17 gene	ncRNA
mm_105156.1	chr11	101466223	101466237	-	1	NA	promoter-TSS (NM_012037)	promoter-TSS (NM_012037)	-31	NM_012037	26949	Mm.29210	NM_012037	ENSMUSG00000034993	Vat1	VAT-1	vesicle amine transport 1	protein-coding
mm_95496.1	chr11	51763655	51763669	+	1	NA	promoter-TSS (NM_025535)	promoter-TSS (NM_025535)	-1	NM_025535	66397	Mm.196592	NM_025535	ENSMUSG00000020386	Sar1b	2310075M17Rik|2900019I22Rik|CMRD|Sara1b|Sara2|Sarb	secretion associated Ras related GTPase 1B	protein-coding
mm_35093.1	chr4	8642813	8642816	-	1	NA	Intergenic	ID_B1|SINE|B4	-47592	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_93665.1	chr10	117699036	117699041	-	1	NA	intron (NM_001288586, intron 5 of 10)	AT_rich|Low_complexity|Low_complexity	11720	NM_010786	17246	Mm.22670	NM_010786	ENSMUSG00000020184	Mdm2	1700007J15Rik|AA415488|Mdm-2	transformed mouse 3T3 cell double minute 2	protein-coding
mm_117864.1	chr13	98840390	98840399	-	1	NA	Intergenic	Intergenic	-24945	NM_172591	218503	Mm.23928	NM_172591	ENSMUSG00000041685	Fcho2	5832424M12Rik|AA387320	FCH domain only 2	protein-coding
mm_17500.1	chr2	28840259	28840269	-	1	NA	promoter-TSS (NM_001166033)	promoter-TSS (NM_001166033)	96	NM_172977	269252	Mm.26043	NM_172977	ENSMUSG00000035666	Gtf3c4	5330400C03|AI426938|AU014771|AU017413|KAT12|TFIIIC90	general transcription factor IIIC, polypeptide 4	protein-coding
mm_110544.1	chr12	55376020	55376022	-	1	NA	intron (NR_035430, intron 1 of 3)	RLTR1B|LTR|ERV1	5326	NR_035430	100316807		NR_035430	ENSMUSG00000080645	Mir1198	Mirn1198|mmu-mir-1198	microRNA 1198	ncRNA
mm_94162.1	chr10	128746234	128746252	-	1	NA	Intergenic	Intergenic	-1636	NM_030100	78428	Mm.27358	NM_030100	ENSMUSG00000064030	Pym1	A030010B05Rik|Pym|Wibg	PYM homolog 1, exon junction complex associated factor	protein-coding
mm_99591.1	chr11	104310329	104310341	+	1	NA	exon (NM_010838, exon 6 of 10)	exon (NM_010838, exon 6 of 10)	78899	NM_001285454	17762	Mm.1287	NM_010838	ENSMUSG00000018411	Mapt	AI413597|AW045860|Mtapt|Tau	microtubule-associated protein tau	protein-coding
mm_85035.1	chr9	88482594	88482600	-	1	NA	promoter-TSS (NM_001284328)	promoter-TSS (NM_001284328)	-200	NM_001284328	56403	Mm.260545	NM_019666	ENSMUSG00000032423	Syncrip	2610109K23Rik|4632417O19Rik|GRY-RBP|Nsap1|Nsap1l|hnRNP Q|pp68	synaptotagmin binding, cytoplasmic RNA interacting protein	protein-coding
mm_51788.1	chr6	88200580	88200593	+	1	NA	exon (NM_008090, exon 3 of 6)	exon (NM_008090, exon 3 of 6)	1922	NM_008090	14461	Mm.491156	NM_008090	ENSMUSG00000015053	Gata2	Gata-2	GATA binding protein 2	protein-coding
mm_24947.1	chr3	96618598	96618628	+	1	NA	exon (NM_001163170, exon 3 of 6)	exon (NM_001163170, exon 3 of 6)	11206	NR_003619	229613	Mm.445135	NM_175469	ENSMUSG00000045327	6330549D23Rik	-	RIKEN cDNA 6330549D23 gene	pseudo
mm_57186.1	chr6	122848850	122848861	-	1	NA	3' UTR (NM_009779, exon 2 of 2)	3' UTR (NM_009779, exon 2 of 2)	7302	NM_009779	12267	Mm.2408	NM_009779	ENSMUSG00000040552	C3ar1	AZ3B|C3AR|HNFAG09	complement component 3a receptor 1	protein-coding
mm_36606.1	chr4	88942038	88942053	-	1	NA	promoter-TSS (NR_132734)	promoter-TSS (NR_132734)	-3	NR_132735	106557447	Mm.484668	NR_132734		LOC106557447	-	uncharacterized LOC106557447	ncRNA
mm_140989.1	chr17	24849994	24850018	-	1	NA	promoter-TSS (NM_024284)	promoter-TSS (NM_024284)	296	NM_023480	68636	Mm.347964	NM_023480	ENSMUSG00000045316	Fahd1	1110025H10Rik|AV002085	fumarylacetoacetate hydrolase domain containing 1	protein-coding
mm_49031.1	chr6	4759789	4759799	+	1	NA	3' UTR (NM_130877, exon 2 of 2)	3' UTR (NM_130877, exon 2 of 2)	12488	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_28925.1	chr3	98858290	98858296	-	1	NA	5' UTR (NM_008293, exon 2 of 5)	5' UTR (NM_008293, exon 2 of 5)	1501	NM_001304800	15492	Mm.140811	NM_008293	ENSMUSG00000027871	Hsd3b1	3-beta-HSD I|D3Ertd383e	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1	protein-coding
mm_65736.1	chr7	28385760	28385764	-	1	NA	3' UTR (NM_026042, exon 4 of 4)	3' UTR (NM_026042, exon 4 of 4)	-6534	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_6518.1	chr1	74397027	74397057	-	1	NA	3' UTR (NM_153088, exon 7 of 7)	3' UTR (NM_153088, exon 7 of 7)	2732	NR_029743	387219		NR_029743	ENSMUSG00000065468	Mir26b	Mirn26b|mir-26b|mmu-mir-26b	microRNA 26b	ncRNA
mm_169684.1	chr15	72913311	72913330	+	1	NA	intron (NM_029640, intron 15 of 21)	intron (NM_029640, intron 15 of 21)	-102996	NR_002864	353342	Mm.440245	NR_002864	ENSMUSG00000106847	Peg13	-	paternally expressed 13	ncRNA
mm_25312.1	chr3	106131926	106131960	+	1	NA	exon (NM_023186, exon 11 of 11)	exon (NM_023186, exon 11 of 11)	18561	NM_023186	81600	Mm.46418	NM_023186	ENSMUSG00000062778	Chia1	2200003E03Rik|AMCase|Chia|YNL	chitinase, acidic 1	protein-coding
mm_110536.1	chr12	55080099	55080121	-	1	NA	promoter-TSS (NM_011899)	promoter-TSS (NM_011899)	0	NR_030764	72658	Mm.434380	NM_028314	ENSMUSG00000062198	2700097O09Rik	AW552125	RIKEN cDNA 2700097O09 gene	protein-coding
mm_156396.1	chrX	139808254	139808267	+	1	NA	intron (NM_016675, intron 1 of 1)	intron (NM_016675, intron 1 of 1)	7452	NM_016675	12738	Mm.117068	NM_016675	ENSMUSG00000047230	Cldn2	AL022813	claudin 2	protein-coding
mm_82859.1	chr9	31913162	31913177	-	1	NA	5' UTR (NM_013800, exon 1 of 4)	5' UTR (NM_013800, exon 1 of 4)	116	NM_013800	12023	Mm.261044	NM_013800	ENSMUSG00000032033	Barx2	2310006E12Rik|Barx2b	BarH-like homeobox 2	protein-coding
mm_94832.1	chr11	23497736	23497740	+	1	NA	intron (NM_001290655, intron 1 of 8)	CpG	301	NM_001290655	268390	Mm.13148	NM_172391	ENSMUSG00000020288	Ahsa2	-	AHA1, activator of heat shock protein ATPase 2	protein-coding
mm_83281.1	chr9	43105823	43105874	-	1	NA	promoter-TSS (NM_027144)	promoter-TSS (NM_027144)	-130	NM_027144	69632	Mm.275266	NM_027144	ENSMUSG00000059495	Arhgef12	2310014B11Rik|AU019857|Larg|mKIAA0382	Rho guanine nucleotide exchange factor (GEF) 12	protein-coding
mm_110162.1	chr12	26834872	26834882	-	1	NA	Intergenic	RMER17B|LTR|ERVK	280118	NR_045052	100504347	Mm.130500	NR_045052		Gm20187	-	predicted gene, 20187	ncRNA
mm_9625.1	chr1	176756899	176756901	-	1	NA	exon (NM_001099637, exon 13 of 20)	exon (NM_001099637, exon 13 of 20)	15523	NR_029775	723921		NR_029775	ENSMUSG00000065573	Mir350	Mirn350|mir-350|mmu-mir-350	microRNA 350	ncRNA
mm_38743.1	chr4	145267595	145267618	-	1	NA	Intergenic	B1F|SINE|Alu	-20736	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_1214.1	chr1	62726974	62727002	+	1	NA	intron (NM_001077405, intron 2 of 15)	intron (NM_001077405, intron 2 of 15)	23671	NM_001077405	18187	Mm.266341	NM_010939	ENSMUSG00000025969	Nrp2	1110048P06Rik|Np-2|Np2|Npn-2|Npn2	neuropilin 2	protein-coding
mm_17059.1	chr2	21205644	21205677	-	1	NA	promoter-TSS (NM_027728)	promoter-TSS (NM_027728)	-64	NM_001001297	208967	Mm.268841	NM_177588	ENSMUSG00000048550	Thnsl1	AW413632	threonine synthase-like 1 (bacterial)	protein-coding
mm_45283.1	chr5	64959118	64959175	-	1	NA	intron (NM_011604, intron 1 of 1)	intron (NM_011604, intron 1 of 1)	888	NM_011604	21899	Mm.42146	NM_011604	ENSMUSG00000051498	Tlr6	-	toll-like receptor 6	protein-coding
mm_6313.1	chr1	71595725	71595754	-	1	NA	exon (NM_001276413, exon 39 of 44)	exon (NM_001276413, exon 39 of 44)	38583	NM_026195	108147	Mm.38010	NM_026195	ENSMUSG00000026192	Atic	2610509C24Rik|AA536954|AW212393	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	protein-coding
mm_39601.1	chr5	23787692	23787751	+	1	NA	promoter-TSS (NM_177323)	promoter-TSS (NM_177323)	10	NM_001310467	72772	Mm.133300	NM_177323	ENSMUSG00000028999	Rint1	1500019C06Rik|2810450M21Rik|Rint-1	RAD50 interactor 1	protein-coding
mm_58512.1	chr7	4129266	4129285	+	1	NA	intron (NR_033548, intron 2 of 2)	intron (NR_033548, intron 2 of 2)	7651	NR_033548	100037396	Mm.447887	NR_033548	ENSMUSG00000085886	D030047H15Rik	Gm15924|OTTMUSG00000027889	RIKEN cDNA D030047H15 gene	ncRNA
mm_70808.1	chr8	23035102	23035106	+	1	NA	promoter-TSS (NM_001277281)	promoter-TSS (NM_001277281)	5	NM_001277284	11733	Mm.334444	NM_031158	ENSMUSG00000031543	Ank1	Ank-1|nb|pale	ankyrin 1, erythroid	protein-coding
mm_38510.1	chr4	141184029	141184041	-	1	NA	intron (NM_172518, intron 4 of 9)	intron (NM_172518, intron 4 of 9)	-29921	NM_001081174	76166	Mm.271064	NM_001081174	ENSMUSG00000073733	Rsg1	6330545A04Rik|Gm723	REM2 and RAB-like small GTPase 1	protein-coding
mm_153648.1	chr19	44294800	44294805	-	1	NA	intron (NM_009128, intron 1 of 5)	intron (NM_009128, intron 1 of 5)	1126	NM_009128	20250	Mm.487021	NM_009128	ENSMUSG00000025203	Scd2	Mir5114|Scd-2|mir-5114|swty	stearoyl-Coenzyme A desaturase 2	protein-coding
mm_146135.1	chr18	74714766	74714774	+	1	NA	intron (NM_201600, intron 23 of 38)	intron (NM_201600, intron 23 of 38)	63685	NR_028560	100217466		NR_028560		Scarna17	MBII-119	small Cajal body-specific RNA 17	ncRNA
mm_98957.1	chr11	98545659	98545681	+	1	NA	intron (NM_011771, intron 1 of 7)	intron (NM_011771, intron 1 of 7)	361	NM_011771	22780	Mm.133367	NM_011771	ENSMUSG00000018168	Ikzf3	5830411O07Rik|Aiolos|Zfpn1a3|Znfn1a3	IKAROS family zinc finger 3	protein-coding
mm_35258.1	chr4	19880032	19880045	-	1	NA	exon (NM_175406, exon 7 of 8)	exon (NM_175406, exon 7 of 8)	42528	NM_175406	242341	Mm.19298	NM_175406	ENSMUSG00000028238	Atp6v0d2	1620401A02Rik|AI324824|V-ATPase	ATPase, H+ transporting, lysosomal V0 subunit D2	protein-coding
mm_105452.1	chr11	104503233	104503253	-	1	NA	3' UTR (NM_145436, exon 19 of 19)	3' UTR (NM_145436, exon 19 of 19)	47377	NM_001285990	217232	Mm.89845	NM_145436	ENSMUSG00000020687	Cdc27	AI452358|APC3|BC023187	cell division cycle 27	protein-coding
mm_43974.1	chr5	146231164	146231186	+	1	NA	promoter-TSS (NM_153599)	promoter-TSS (NM_153599)	-500	NM_153599	264064	Mm.260576	NM_153599	ENSMUSG00000029635	Cdk8	-	cyclin-dependent kinase 8	protein-coding
mm_49545.1	chr6	30460981	30460989	+	1	NA	promoter-TSS (NR_131049)	promoter-TSS (NR_131049)	0	NR_131049	69337	Mm.396168	NR_131049	ENSMUSG00000085470	1700012C14Rik	-	RIKEN cDNA 1700012C14 gene	ncRNA
mm_57337.1	chr6	124745601	124745619	-	1	NA	intron (NM_007881, intron 6 of 9)	CpG	-4531	NM_013535	14790	Mm.439877	NM_013535	ENSMUSG00000072772	Grcc10	2310033H05Rik|C10	gene rich cluster, C10 gene	protein-coding
mm_43356.1	chr5	135187349	135187359	+	1	NA	promoter-TSS (NM_011714)	promoter-TSS (NM_011714)	31	NM_011714	22385	Mm.40331	NM_011714	ENSMUSG00000002748	Baz1b	C87820|WSTF|Wbscr9	bromodomain adjacent to zinc finger domain, 1B	protein-coding
mm_152811.1	chr19	23075881	23075904	-	1	NA	Intergenic	MTEb-int|LTR|ERVL-MaLR	-65334	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_158740.1	chrX	164229177	164229178	-	1	NA	intron (NM_009759, intron 9 of 18)	intron (NM_009759, intron 9 of 18)	29016	NM_009759	12169	Mm.504	NM_009759	ENSMUSG00000031377	Bmx	Etk|Etk/Bmx|Tyro8	BMX non-receptor tyrosine kinase	protein-coding
mm_25076.1	chr3	99981266	99981303	+	1	NA	intron (NM_028892, intron 4 of 48)	GSAT_MM|Satellite|Satellite	95867	NM_028892	74362	Mm.55847	NM_028892	ENSMUSG00000027867	Spag17	4931427F14Rik|PF6|Spag17-ps	sperm associated antigen 17	protein-coding
mm_128154.1	chr15	32244622	32244630	-	1	NA	promoter-TSS (NM_009154)	promoter-TSS (NM_009154)	36	NR_038186	100616095	Mm.391938	NR_038186	ENSMUSG00000096956	Snhg18	0610007N19Rik|Snord123	small nucleolar RNA host gene 18	ncRNA
mm_81579.1	chr9	110422450	110422484	+	1	NA	3' UTR (NM_008694, exon 4 of 4)	3' UTR (NM_008694, exon 4 of 4)	2659	NM_008694	18054	Mm.236225	NM_008694	ENSMUSG00000032484	Ngp	bectenecin	neutrophilic granule protein	protein-coding
mm_163242.1	chr11	105589963	105589966	+	1	NA	promoter-TSS (NM_181071)	promoter-TSS (NM_181071)	-22	NM_181071	77097	Mm.22501	NM_175492	ENSMUSG00000053580	Tanc2	3526402J09Rik|5730590C14Rik	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2	protein-coding
mm_160684.1	chr10	19712571	19712571	+	1	NA	promoter-TSS (NM_172786)	promoter-TSS (NM_172786)	-16	NM_172786	237313	Mm.234667	NM_172786	ENSMUSG00000020007	Il20ra	E230031K19	interleukin 20 receptor, alpha	protein-coding
mm_150798.1	chr19	44303814	44303833	+	1	NA	TTS (NR_039574)	TTS (NR_039574)	652	NR_039574	100628619		NR_039574	ENSMUSG00000093315	Mir5114	mmu-mir-5114|mu-mir-5114	microRNA 5114	ncRNA
mm_17378.1	chr2	27019979	27019993	-	1	NA	intron (NM_029862, intron 5 of 5)	intron (NM_029862, intron 5 of 5)	8012	NM_172659	227659	Mm.41203	NM_172659	ENSMUSG00000036067	Slc2a6	A330096C23|F630103L12Rik|Glut6|Glut9	solute carrier family 2 (facilitated glucose transporter), member 6	protein-coding
mm_155548.1	chrX	74329059	74329076	+	1	NA	promoter-TSS (NM_008883)	promoter-TSS (NM_008883)	1	NM_008883	18846	Mm.1685	NM_008883	ENSMUSG00000031398	Plxna3	PlexA3|Plxa3|Plxn3|Plxn4|SEX|mKIAA4078	plexin A3	protein-coding
mm_3097.1	chr1	134424756	134424775	+	1	NA	exon (NM_001306069, exon 4 of 8)	exon (NM_001306069, exon 4 of 8)	9101	NM_001306069	72674	Mm.259976	NM_028320	ENSMUSG00000026457	Adipor1	2810031L11Rik|ACDCR1|CGI-45|Paqr1	adiponectin receptor 1	protein-coding
mm_117134.1	chr13	60939430	60939434	-	1	NA	3' UTR (NM_009411, exon 5 of 5)	3' UTR (NM_009411, exon 5 of 5)	2503	NM_009411	21984	Mm.2372	NM_009411	ENSMUSG00000033834	Tpbpa	AV033951|Tb-1|Tb1|Tpbp|b2b1247Clo	trophoblast specific protein alpha	protein-coding
mm_83915.1	chr9	56418100	56418110	-	1	NA	promoter-TSS (NM_025812)	promoter-TSS (NM_025812)	-55	NM_172924	244895	Mm.490331	NM_172924	ENSMUSG00000074305	Peak1	1110049L02Rik|9530046P14|AA690169|BE132841|C230081A13Rik|SGK269|mKIAA2002	pseudopodium-enriched atypical kinase 1	protein-coding
mm_33848.1	chr4	135856637	135856680	+	1	NA	intron (NM_010178, intron 1 of 5)	PB1D7|SINE|Alu	587	NM_010178	14105	Mm.10229	NM_010178	ENSMUSG00000028676	Srsf10	FUSIP2|Fusip1|NSSR1|NSSR2|Nssr|SRrp40|Sfrs13a|Srsf13a|TASR|TASR1|TASR2	serine/arginine-rich splicing factor 10	protein-coding
mm_30845.1	chr4	24799895	24799895	+	1	NA	intron (NM_001033531, intron 2 of 9)	intron (NM_001033531, intron 2 of 9)	51191	NM_001163020	212390	Mm.412074	NM_001033531	ENSMUSG00000040387	Klhl32	6430524H05Rik|D4Ertd389e|Gm1356|mKIAA1900	kelch-like 32	protein-coding
mm_136773.1	chr17	10001605	10001609	+	1	NA	Intergenic	Intergenic	-225741	NR_045433	71092	Mm.243827	NR_045433		4930452A19Rik	4933424P20Rik	RIKEN cDNA 4930452A19 gene	ncRNA
mm_166673.1	chr6	95149867	95149872	+	1	NA	Intergenic	Intergenic	31989	NM_001008785	243574	Mm.333275	NM_001008785	ENSMUSG00000030031	Kbtbd8	AU040152|SSEC-51|SSEC51|Takrp|mKIAA1842	kelch repeat and BTB (POZ) domain containing 8	protein-coding
mm_160561.1	chr9	53706204	53706204	-	1	NA	promoter-TSS (NM_175562)	promoter-TSS (NM_175562)	28	NM_175562	270160	Mm.290285	NM_175562	ENSMUSG00000055069	Rab39	C230094F14Rik|Rab39a	RAB39, member RAS oncogene family	protein-coding
mm_127044.1	chr15	96642460	96642497	+	1	NA	promoter-TSS (NM_001166456)	promoter-TSS (NM_001166456)	-135	NM_001166456	105727	Mm.103568	NM_134086	ENSMUSG00000023169	Slc38a1	AA408026|AA409865|AL022800|AU015942|NAT2	solute carrier family 38, member 1	protein-coding
mm_156988.1	chrX	7412757	7412772	-	1	NA	intron (NR_027924, intron 1 of 1)	intron (NR_027924, intron 1 of 1)	8283	NR_027925	68355	Mm.45111	NR_027924		2010204K13Rik	0610010M13Rik|Cip7	RIKEN cDNA 2010204K13 gene	ncRNA
mm_168668.1	chr11	9150630	9150648	-	1	NA	Intergenic	CpG	32132	NM_001159402	22271	Mm.4610	NM_009477	ENSMUSG00000020407	Upp1	AI325217|UPase|UdRPase|Up|Upp	uridine phosphorylase 1	protein-coding
mm_146393.1	chr18	82902043	82902051	+	1	NA	Intergenic	Intergenic	-8832	NM_183033	329003	Mm.326526	NM_183033	ENSMUSG00000058881	Zfp516	C330029B10Rik|D230016L03|Zfp26l|Znf516|mKIAA0222	zinc finger protein 516	protein-coding
mm_131834.1	chr16	22960774	22960786	+	1	NA	exon (NM_053176, exon 7 of 7)	exon (NM_053176, exon 7 of 7)	9708	NM_053176	94175	Mm.358794	NM_053176	ENSMUSG00000022877	Hrg	AI265597|AW413091|D16jh2|D18020|Hprg|Hrgp	histidine-rich glycoprotein	protein-coding
mm_129312.1	chr15	77755267	77755281	-	1	NA	promoter-TSS (NM_001081970)	promoter-TSS (NM_001081970)	-45	NM_001081970	239552	Mm.125650	NM_001081970	ENSMUSG00000056656	Apol8	9830006J20Rik|APOL-II|Apol2	apolipoprotein L 8	protein-coding
mm_38297.1	chr4	136896139	136896152	-	1	NA	3' UTR (NM_007572, exon 3 of 3)	3' UTR (NM_007572, exon 3 of 3)	2699	NM_007572	12259	Mm.439957	NM_007572	ENSMUSG00000036887	C1qa	AI255395|C1q	complement component 1, q subcomponent, alpha polypeptide	protein-coding
mm_62884.1	chr7	114768882	114768891	+	1	NA	intron (NM_173767, intron 1 of 12)	intron (NM_173767, intron 1 of 12)	23120	NM_173767	233752	Mm.83037	NM_173767	ENSMUSG00000048782	Insc	3830422K02Rik|C730020D23	inscuteable homolog (Drosophila)	protein-coding
mm_101859.1	chr11	48871260	48871273	-	1	NA	promoter-TSS (NM_008326)	promoter-TSS (NM_008326)	80	NM_008326	15944	Mm.29938	NM_008326	ENSMUSG00000046879	Irgm1	Ifggd3|Ifi1|Iigp3|Iipg3|Irgm|LRG-47	immunity-related GTPase family M member 1	protein-coding
mm_128491.1	chr15	51790280	51790297	-	1	NA	intron (NM_080635, intron 5 of 7)	intron (NM_080635, intron 5 of 7)	75173	NM_080635	68135	Mm.289800	NM_080635	ENSMUSG00000022312	Eif3h	1110008A16Rik|40kD|9430017H16Rik|EIF3-P40|EIF3-gamma|Eif3s3	eukaryotic translation initiation factor 3, subunit H	protein-coding
mm_8204.1	chr1	138123598	138123615	-	1	NA	intron (NM_001111316, intron 2 of 31)	intron (NM_001111316, intron 2 of 31)	51520	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_142401.1	chr17	45433683	45433709	-	1	NA	promoter-TSS (NM_152810)	promoter-TSS (NM_152810)	11	NM_152810	71702	Mm.28270	NM_152810	ENSMUSG00000023932	Cdc5l	1200002I02Rik|AA408004|PCDC5RP	cell division cycle 5-like (S. pombe)	protein-coding
mm_97704.1	chr11	80178021	80178045	+	1	NA	intron (NM_172133, intron 10 of 10)	B1_Mur2|SINE|Alu	-5839	NM_028019	71956	Mm.22985	NM_028019	ENSMUSG00000020707	Rnf135	0610037N03Rik|2410006N06Rik	ring finger protein 135	protein-coding
mm_36867.1	chr4	107058924	107058929	-	1	NA	intron (NM_025500, intron 5 of 6)	intron (NM_025500, intron 5 of 6)	7940	NM_025500	56280	Mm.29517	NM_025500	ENSMUSG00000028622	Mrpl37	2300004O14Rik|AI132596|MRP-L2|Rpml2	mitochondrial ribosomal protein L37	protein-coding
mm_75084.1	chr8	33916847	33916851	-	1	NA	intron (NM_001042674, intron 1 of 7)	AT_rich|Low_complexity|Low_complexity	13014	NM_019733	19663	Mm.323997	NM_019733	ENSMUSG00000031586	Rbpms	2010300K22Rik|2700019M19Rik|AU017537|RBP-MS|hermes	RNA binding protein gene with multiple splicing	protein-coding
mm_142342.1	chr17	43591503	43591514	-	1	NA	promoter-TSS (NR_045445)	promoter-TSS (NR_045445)	1	NR_045445	73504	Mm.9277	NR_045444	ENSMUSG00000090307	1700071M16Rik	-	RIKEN cDNA 1700071M16 gene	ncRNA
mm_13304.1	chr2	102658229	102658239	+	1	NA	promoter-TSS (NM_001077514)	promoter-TSS (NM_001077514)	-449	NM_001077514	20511	Mm.267547	NM_011393	ENSMUSG00000005089	Slc1a2	1700091C19Rik|2900019G14Rik|AI159670|Eaat2|GLT-1|GLT1|MGLT1	solute carrier family 1 (glial high affinity glutamate transporter), member 2	protein-coding
mm_47201.1	chr5	120898192	120898209	-	1	NA	intron (NM_145211, intron 5 of 6)	intron (NM_145211, intron 5 of 6)	9325	NM_145211	246730	Mm.14301	NM_145211	ENSMUSG00000052776	Oas1a	L3	2'-5' oligoadenylate synthetase 1A	protein-coding
mm_155938.1	chrX	103672664	103672690	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	42091	NM_029158	75064	Mm.159414	NM_029158	ENSMUSG00000031330	Zcchc13	4930513O09Rik|Cnbp2	zinc finger, CCHC domain containing 13	protein-coding
mm_51856.1	chr6	90465257	90465277	+	1	NA	intron (NM_023184, intron 1 of 2)	intron (NM_023184, intron 1 of 2)	2641	NM_023184	66277	Mm.38343	NM_023184	ENSMUSG00000030087	Klf15	1810013I09Rik|AV048136|AW494632|CKLF|KKLF	Kruppel-like factor 15	protein-coding
mm_130859.1	chr15	102188953	102188971	-	1	NA	promoter-TSS (NM_144942)	promoter-TSS (NM_144942)	81	NM_144942	246277	Mm.296382	NM_144942	ENSMUSG00000023044	Csad	Csd	cysteine sulfinic acid decarboxylase	protein-coding
mm_159980.1	chr6	113472605	113472605	+	1	NA	intron (NM_134159, intron 3 of 16)	intron (NM_134159, intron 3 of 16)	1150	NM_134159	171095	Mm.213397	NM_134159	ENSMUSG00000030281	Il17rc	1110025H02Rik|Gm19850|IL-17RC|IL17-RC|IL17-RL|Il17rl	interleukin 17 receptor C	protein-coding
mm_120030.1	chr14	55853979	55853989	+	1	NA	promoter-TSS (NM_001040072)	promoter-TSS (NM_001040072)	-131	NM_001040072	277154	Mm.319347	NM_001040072	ENSMUSG00000075592	Nynrin	AA409373|C80530|mKIAA1305	NYN domain and retroviral integrase containing	protein-coding
mm_124005.1	chr14	76010864	76010931	-	1	NA	promoter-TSS (NM_026816)	promoter-TSS (NM_026816)	-32	NM_026816	68705	Mm.20415	NM_026816	ENSMUSG00000067995	Gtf2f2	1110031C13Rik|AI326315	general transcription factor IIF, polypeptide 2	protein-coding
mm_18732.1	chr2	72980403	72980471	-	1	NA	promoter-TSS (NM_001018042)	promoter-TSS (NM_001018042)	9	NM_001018042	20687	Mm.124328	NM_011450	ENSMUSG00000027109	Sp3	D130027J01Rik	trans-acting transcription factor 3	protein-coding
mm_22325.1	chr2	180642627	180642639	-	1	NA	promoter-TSS (NM_178254)	promoter-TSS (NM_178254)	58	NM_178254	277353	Mm.473700	NM_178254	ENSMUSG00000038932	Tcfl5	AV260129|Figlb|Sosf1	transcription factor-like 5 (basic helix-loop-helix)	protein-coding
mm_55482.1	chr6	68991324	68991347	-	1	NA	Intergenic	Intergenic	335839	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_128301.1	chr15	37459409	37459411	-	1	NA	promoter-TSS (NM_001170868)	promoter-TSS (NM_001170868)	-28	NM_001170868	52589	Mm.283370	NM_134094	ENSMUSG00000051359	Ncald	AI848120|D030020D09Rik|D15Ertd412e	neurocalcin delta	protein-coding
mm_70744.1	chr8	19157880	19157893	+	1	NA	promoter-TSS (NM_153115)	promoter-TSS (NM_153115)	-1	NM_153115	78128	Mm.229357	NM_153115	ENSMUSG00000079842	Spag11a	9230111C08Rik|Bin1b|EP2Q|EP2e|Spag11	sperm associated antigen 11A	protein-coding
mm_93198.1	chr10	94433073	94433074	-	1	NA	Intergenic	Intergenic	-81784	NM_172051	319880	Mm.23047	NM_172051	ENSMUSG00000020023	Tmcc3	AW488095|C630016B22Rik|C88213|Tmcc1	transmembrane and coiled coil domains 3	protein-coding
mm_15107.1	chr2	153376329	153376332	+	1	NA	intron (NM_001039939, intron 3 of 11)	L1MEf|LINE|L1	30191	NM_001039939	228790	Mm.330677	NM_001039939	ENSMUSG00000042548	Asxl1	mKIAA0978	additional sex combs like 1	protein-coding
mm_39993.1	chr5	32610306	32610314	+	1	NA	promoter-TSS (NM_009535)	promoter-TSS (NM_009535)	-861	NM_001205133	22612	Mm.4558	NM_009535	ENSMUSG00000014932	Yes1	Yes|p61-Yes	YES proto-oncogene 1, Src family tyrosine kinase	protein-coding
mm_9947.1	chr1	190978955	190978998	-	1	NA	promoter-TSS (NM_144879)	promoter-TSS (NM_144879)	22	NM_144879	226841	Mm.22856	NM_144879	ENSMUSG00000037568	Vash2	B130052G07Rik	vasohibin 2	protein-coding
mm_61242.1	chr7	65693440	65693446	+	1	NA	promoter-TSS (NM_178056)	promoter-TSS (NM_178056)	26	NM_026795	68634	Mm.476828	NM_026795	ENSMUSG00000078681	Tm2d3	1110025I09Rik|5930422O05Rik|Blp2	TM2 domain containing 3	protein-coding
mm_35757.1	chr4	45826803	45826813	-	1	NA	promoter-TSS (NM_018741)	promoter-TSS (NM_018741)	19	NM_018741	75426	Mm.3919	NM_018741	ENSMUSG00000035551	Igfbpl1	2810011G06Rik|2810453O06Rik|IGFBPL	insulin-like growth factor binding protein-like 1	protein-coding
mm_47603.1	chr5	125058334	125058345	-	1	NA	intron (NM_011424, intron 17 of 46)	intron (NM_011424, intron 17 of 46)	54864	NM_028443	73121	Mm.296138	NM_028443	ENSMUSG00000037962	Rflna	3110032G18Rik|Fam101a|cfm|cfm2	refilin A	protein-coding
mm_80915.1	chr9	100719402	100719405	+	1	NA	intron (NM_009282, intron 3 of 33)	Lx8b|LINE|L1	75780	NM_009282	20842	Mm.42135	NM_009282	ENSMUSG00000037286	Stag1	AU045003|SA-1|Scc3	stromal antigen 1	protein-coding
mm_111236.1	chr12	84772889	84772910	-	1	NA	promoter-TSS (NM_028863)	promoter-TSS (NM_028863)	213	NM_023409	67963	Mm.282556	NM_023409	ENSMUSG00000021242	Npc2	2700012J19Rik|AA408070|AU045843|HE1	Niemann-Pick type C2	protein-coding
mm_17495.1	chr2	28621903	28621913	-	1	NA	promoter-TSS (NM_001160406)	promoter-TSS (NM_001160406)	74	NM_008114	14582	Mm.373385	NM_008114	ENSMUSG00000026815	Gfi1b	Gfi-1B	growth factor independent 1B	protein-coding
mm_152995.1	chr19	29812953	29812974	-	1	NA	promoter-TSS (NM_177721)	promoter-TSS (NM_177721)	11	NM_177721	240614	Mm.125503	NM_177721	ENSMUSG00000074909	Ranbp6	C630001B19	RAN binding protein 6	protein-coding
mm_77927.1	chr9	7353239	7353249	+	1	NA	intron (NM_001320077, intron 6 of 10)	intron (NM_001320077, intron 6 of 10)	5870	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_36572.1	chr4	87944664	87944667	-	1	NA	intron (NM_027326, intron 2 of 10)	L1ME3A|LINE|L1	88742	NM_027326	70122	Mm.288898	NM_027326	ENSMUSG00000028496	Mllt3	2210011H10Rik|2610012I03Rik|3830408D16Rik|Af9|D4Ertd321e	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 3	protein-coding
mm_32037.1	chr4	95738410	95738424	+	1	NA	intron (NM_001113412, intron 6 of 15)	intron (NM_001113412, intron 6 of 15)	158996	NM_029347	75578	Mm.276098	NM_029347	ENSMUSG00000028573	Fggy	2310009E04Rik	FGGY carbohydrate kinase domain containing	protein-coding
mm_86066.1	chr9	114775382	114775392	-	1	NA	intron (NM_001252479, intron 1 of 3)	intron (NM_001252479, intron 1 of 3)	6606	NM_133978	102545	Mm.35600	NM_133978	ENSMUSG00000032436	Cmtm7	AI481279|Cklfsf7|LNV	CKLF-like MARVEL transmembrane domain containing 7	protein-coding
mm_43426.1	chr5	136057305	136057346	+	1	NA	promoter-TSS (NM_027158)	promoter-TSS (NM_027158)	58	NM_027158	69665	Mm.75713	NM_027158	ENSMUSG00000006143	Upk3bl	2310043J07Rik	uroplakin 3B-like	protein-coding
mm_63536.1	chr7	127974394	127974407	+	1	NA	exon (NM_139149, exon 7 of 15)	exon (NM_139149, exon 7 of 15)	6921	NM_139149	233908	Mm.277680	NM_139149	ENSMUSG00000030795	Fus	D430004D17Rik|D930039C12Rik|Fus1|Tls	fused in sarcoma	protein-coding
mm_23646.1	chr3	67472850	67472855	+	1	NA	intron (NM_138591, intron 15 of 17)	intron (NM_138591, intron 15 of 17)	-8945	NM_016753	17035	Mm.2632	NM_016753	ENSMUSG00000047557	Lxn	-	latexin	protein-coding
mm_118578.1	chr14	19751277	19751292	+	1	NA	promoter-TSS (NM_008695)	promoter-TSS (NM_008695)	27	NM_008695	18074	Mm.20348	NM_008695	ENSMUSG00000021806	Nid2	AW547149|Ly111|NID-2|entactin-2|nidogen-2	nidogen 2	protein-coding
mm_11289.1	chr2	30066833	30066843	+	1	NA	exon (NM_001204875, exon 1 of 8)	exon (NM_001204875, exon 1 of 8)	364	NM_001204875	56086	Mm.326055	NM_023871	ENSMUSG00000054766	Set	2610030F17Rik|5730420M11Rik|AA407739|I-2PP2A|StF-IT-1|TAF-I	SET nuclear oncogene	protein-coding
mm_110214.1	chr12	28623314	28623329	-	1	NA	promoter-TSS (NM_027866)	promoter-TSS (NM_027866)	9	NM_001313978	71693	Mm.30724	NM_027866	ENSMUSG00000036655	Colec11	CL-K1	collectin sub-family member 11	protein-coding
mm_130304.1	chr15	97019941	97019972	-	1	NA	intron (NM_027052, intron 1 of 15)	intron (NM_027052, intron 1 of 15)	36000	NM_027052	69354	Mm.250980	NM_027052	ENSMUSG00000022464	Slc38a4	1110012E16Rik|1700012A18Rik|Ata3|mATA3|mNAT3	solute carrier family 38, member 4	protein-coding
mm_136628.1	chr17	5575005	5575032	+	1	NA	intron (NM_146073, intron 1 of 8)	MLT1H1|LTR|ERVL-MaLR	82418	NM_146073	224454	Mm.487663	NM_146073	ENSMUSG00000034265	Zdhhc14	B530001K09Rik|New1cp	zinc finger, DHHC domain containing 14	protein-coding
mm_61757.1	chr7	82771543	82771561	+	1	NA	intron (NM_175317, intron 18 of 19)	intron (NM_175317, intron 18 of 19)	-15908	NR_046004	77800	Mm.444811	NR_046004	ENSMUSG00000086690	4933406J10Rik	A930009F24Rik	RIKEN cDNA 4933406J10 gene	ncRNA
mm_106580.1	chr11	120729521	120729529	-	1	NA	TTS (NM_007621)	TTS (NM_007621)	-2241	NM_001347608	67880	Mm.231091	NM_026428	ENSMUSG00000039450	Dcxr	0610038K04Rik|1810027P18Rik|XR	dicarbonyl L-xylulose reductase	protein-coding
mm_19141.1	chr2	80447360	80447376	-	1	NA	promoter-TSS (NM_011356)	promoter-TSS (NM_011356)	28	NM_011356	20378	Mm.427436	NM_011356	ENSMUSG00000027004	Frzb	Frp|Sfrp3|frezzled|fritz|frzb-1	frizzled-related protein	protein-coding
mm_127030.1	chr15	96288906	96288916	+	1	NA	intron (NM_175251, intron 2 of 20)	intron (NM_175251, intron 2 of 20)	1389	NM_175251	77044	Mm.17166	NM_175251	ENSMUSG00000033237	Arid2	1700124K17Rik|4432409D24Rik|zipzap/p200	AT rich interactive domain 2 (ARID, RFX-like)	protein-coding
mm_82462.1	chr9	15709346	15709357	-	1	NA	promoter-TSS (NM_172289)	promoter-TSS (NM_172289)	-418	NM_172289	234967	Mm.138815	NM_172289	ENSMUSG00000043885	Slc36a4	6330573I15Rik|PAT4	solute carrier family 36 (proton/amino acid symporter), member 4	protein-coding
mm_48272.1	chr5	137963030	137963040	-	1	NA	promoter-TSS (NM_080450)	promoter-TSS (NM_080450)	-76	NM_080450	118446	Mm.332771	NM_080450	ENSMUSG00000056966	Gjc3	Cx29|Gje1	gap junction protein, gamma 3	protein-coding
mm_50333.1	chr6	48448101	48448122	+	1	NA	promoter-TSS (NM_173428)	promoter-TSS (NM_173428)	-118	NM_173428	243369	Mm.25039	NM_173428	ENSMUSG00000029797	Sspo	C79529|Scospondin	SCO-spondin	protein-coding
mm_69983.1	chr7	142380851	142380886	-	1	NA	exon (NM_009983, exon 5 of 9)	exon (NM_009983, exon 5 of 9)	7002	NM_009983	13033	Mm.231395	NM_009983	ENSMUSG00000007891	Ctsd	CD|CatD	cathepsin D	protein-coding
mm_111264.1	chr12	85177289	85177306	-	1	NA	promoter-TSS (NM_008827)	promoter-TSS (NM_008827)	16	NM_008827	18654	Mm.4809	NM_008827	ENSMUSG00000004791	Pgf	AI854365|PIGF|Plgf	placental growth factor	protein-coding
mm_151917.1	chr19	5799782	5799796	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	2883	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_104670.1	chr11	97660354	97660401	-	1	NA	Intergenic	CpG	-3035	NM_139311	246198	Mm.23685	NM_139311	ENSMUSG00000038437	Mllt6	AI315037|Af17	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 6	protein-coding
mm_142792.1	chr17	50180632	50180646	-	1	NA	intron (NM_181397, intron 1 of 9)	intron (NM_181397, intron 1 of 9)	9858	NM_181397	76438	Mm.41854	NM_181397	ENSMUSG00000039316	Rftn1	2310015N21Rik|AI853526	raftlin lipid raft linker 1	protein-coding
mm_22681.1	chr3	16183298	16183308	+	1	NA	non-coding (NR_027375, exon 1 of 6)	non-coding (NR_027375, exon 1 of 6)	120	NM_001145919	229096	Mm.23834	NM_172677	ENSMUSG00000047213	Ythdf3	9130022A11Rik	YTH domain family 3	protein-coding
mm_36403.1	chr4	77891699	77891699	-	1	NA	intron (NM_011211, intron 2 of 39)	intron (NM_011211, intron 2 of 39)	320196	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding
mm_103866.1	chr11	83522103	83522109	-	1	NA	promoter-TSS (NM_001045543)	promoter-TSS (NM_001045543)	-7	NM_001045543	629303	Mm.390417	NM_001045543	ENSMUSG00000018925	Heatr9	Gm11435|OTTMUSG00000000990	HEAT repeat containing 9	protein-coding
mm_90008.1	chr10	114737267	114737274	+	1	NA	intron (NM_146241, intron 2 of 18)	(CCCTAA)n|Simple_repeat|Simple_repeat	64100	NM_146241	237553	Mm.445550	NM_146241	ENSMUSG00000050663	Trhde	9330155P21Rik	TRH-degrading enzyme	protein-coding
mm_85040.1	chr9	88845617	88845629	-	1	NA	intron (NM_001177858, intron 6 of 6)	intron (NM_001177858, intron 6 of 6)	6459	NM_001177858	666731	Mm.446951	NM_001177858	ENSMUSG00000067399	Trim43c	EG666731|Trim43	tripartite motif-containing 43C	protein-coding
mm_52804.1	chr6	121342505	121342515	+	1	NA	promoter-TSS (NM_001347433)	promoter-TSS (NM_001347433)	-566	NM_001347433	14411	Mm.274506	NM_133661	ENSMUSG00000030109	Slc6a12	BGT1|GAT-2|GAT2|Gabt2	solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12	protein-coding
mm_121694.1	chr14	13961627	13961640	-	1	NA	promoter-TSS (NM_025435)	promoter-TSS (NM_025435)	-320	NM_025435	66231	Mm.295875	NM_025435	ENSMUSG00000053453	Thoc7	Nif3l1bp1	THO complex 7	protein-coding
mm_78179.1	chr9	21184349	21184384	+	1	NA	5' UTR (NM_001310750, exon 1 of 15)	5' UTR (NM_001310750, exon 1 of 15)	265	NM_001310750	18577	Mm.191749	NM_019798	ENSMUSG00000032177	Pde4a	D9Ertd60e|Dpde2	phosphodiesterase 4A, cAMP specific	protein-coding
mm_3532.1	chr1	150180671	150180682	+	1	NA	Intergenic	L1M2|LINE|L1	-15728	NR_110420	102639566	Mm.417208	NR_110420	ENSMUSG00000097754	Ptgs2os2	Gm26687|Linc-cox2|Lincrna-cox2	prostaglandin-endoperoxide synthase 2, opposite strand 2	ncRNA
mm_164611.1	chr17	31152865	31152875	+	1	NA	non-coding (NR_110503, exon 1 of 6)	non-coding (NR_110503, exon 1 of 6)	118	NR_110502	102631757	Mm.373036	NR_110502	ENSMUSG00000086010	LOC102631757	-	uncharacterized LOC102631757	ncRNA
mm_103019.1	chr11	69734948	69734959	-	1	NA	exon (NM_001291068, exon 29 of 29)	exon (NM_001291068, exon 29 of 29)	23680	NM_001291068	20020	Mm.16533	NM_009089	ENSMUSG00000005198	Polr2a	220kDa|Rpb1|Rpo2-1	polymerase (RNA) II (DNA directed) polypeptide A	protein-coding
mm_112862.1	chr13	20846765	20846774	+	1	NA	intron (NM_012054, intron 3 of 20)	Lx7|LINE|L1	52656	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_71509.1	chr8	46843115	46843126	+	1	NA	intron (NM_008391, intron 7 of 8)	intron (NM_008391, intron 7 of 8)	103375	NM_008391	16363	Mm.1149	NM_008391	ENSMUSG00000031627	Irf2	9830146E22Rik|AI646973|Irf-2	interferon regulatory factor 2	protein-coding
mm_164943.1	chr19	4037893	4037906	-	1	NA	promoter-TSS (NM_013541)	promoter-TSS (NM_013541)	13	NM_013541	14870	Mm.299292	NM_013541	ENSMUSG00000060803	Gstp1	GstpiB	glutathione S-transferase, pi 1	protein-coding
mm_150029.1	chr19	29373782	29373813	+	1	NA	exon (NM_021893, exon 3 of 7)	exon (NM_021893, exon 3 of 7)	6359	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_13881.1	chr2	119972436	119972449	+	1	NA	promoter-TSS (NM_011941)	promoter-TSS (NM_011941)	-257	NM_011941	26390	Mm.330501	NM_011941	ENSMUSG00000033902	Mapkbp1	2810483F24Rik|AW123212|JNKBP-1|Jnkbp1|mKIAA0596	mitogen-activated protein kinase binding protein 1	protein-coding
mm_125087.1	chr15	27466648	27466696	+	1	NA	promoter-TSS (NM_020332)	promoter-TSS (NM_020332)	-5	NM_020332	11732	Mm.265264	NM_020332	ENSMUSG00000022265	Ank	Ankh|D15Ertd221e|ank|mKIAA1581	progressive ankylosis	protein-coding
mm_12931.1	chr2	85048488	85048503	+	1	NA	Intergenic	CpG	-1965	NM_001081260	228140	Mm.23606	NM_001081260	ENSMUSG00000033955	Tnks1bp1	Tab182|mKIAA1741	tankyrase 1 binding protein 1	protein-coding
mm_39942.1	chr5	31821526	31821545	+	1	NA	intron (NM_144541, intron 5 of 11)	intron (NM_144541, intron 5 of 11)	123485	NM_144541	107976	Mm.482126	NM_144541	ENSMUSG00000052139	Bre	6030405P19Rik|AI429776|B830038C02Rik	brain and reproductive organ-expressed protein	protein-coding
mm_21405.1	chr2	158028424	158028440	-	1	NA	promoter-TSS (NM_027434)	promoter-TSS (NM_027434)	-65	NM_001291134	70470	Mm.290810	NM_027434	ENSMUSG00000027651	Rprd1b	2610304G08Rik|2810446G03Rik|Crept	regulation of nuclear pre-mRNA domain containing 1B	protein-coding
mm_34410.1	chr4	145245739	145245768	+	1	NA	intron (NM_011610, intron 1 of 9)	intron (NM_011610, intron 1 of 9)	1117	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_67918.1	chr7	99858873	99858906	-	1	NA	promoter-TSS (NM_001164258)	promoter-TSS (NM_001164258)	-6	NM_025668	66624	Mm.30043	NM_025668	ENSMUSG00000035227	Spcs2	5730406I15Rik|AA408713|mKIAA0102	signal peptidase complex subunit 2 homolog (S. cerevisiae)	protein-coding
mm_95818.1	chr11	55204397	55204412	+	1	NA	promoter-TSS (NM_153139)	promoter-TSS (NM_153139)	64	NM_153139	215335	Mm.35732	NM_153139	ENSMUSG00000020261	Slc36a1	5830411H19Rik|AI839897|Pat1	solute carrier family 36 (proton/amino acid symporter), member 1	protein-coding
mm_133762.1	chr16	94527038	94527094	+	1	NA	promoter-TSS (NM_007834)	promoter-TSS (NM_007834)	-437	NM_007834	13185	Mm.7472	NM_007834	ENSMUSG00000022898	Dscr3	AW538125|Dcra	Down syndrome critical region gene 3	protein-coding
mm_84937.1	chr9	82971863	82971866	-	1	NA	intron (NM_001081216, intron 4 of 39)	intron (NM_001081216, intron 4 of 39)	3625	NM_001081216	83946	Mm.221688	NM_031879	ENSMUSG00000032253	Phip	2810004D21Rik|4632404O06Rik|Ndrp|Wdr11	pleckstrin homology domain interacting protein	protein-coding
mm_24367.1	chr3	90088094	90088097	+	1	NA	intron (NM_001293749, intron 4 of 7)	intron (NM_001293749, intron 4 of 7)	8574	NM_001293749	59069	Mm.240839	NM_022314	ENSMUSG00000027940	Tpm3	TM30nm|TMnm|Tm5NM|Tpm-5|Tpm5|Trop-5|gamma-TM|hTM30nm|hTMnm	tropomyosin 3, gamma	protein-coding
mm_19941.1	chr2	116067156	116067185	-	1	NA	5' UTR (NM_001346047, exon 1 of 14)	5' UTR (NM_001346047, exon 1 of 14)	274	NM_001346047	17536	Mm.247566	NM_010825	ENSMUSG00000027210	Meis2	A430109D20Rik|Mrg1|Stra10	Meis homeobox 2	protein-coding
mm_162464.1	chr1	130832065	130832068	-	1	NA	intron (NM_011082, intron 1 of 10)	intron (NM_011082, intron 1 of 10)	5382	NM_011082	18703	Mm.276414	NM_011082	ENSMUSG00000026417	Pigr	-	polymeric immunoglobulin receptor	protein-coding
mm_73682.1	chr8	111543008	111543030	+	1	NA	intron (NM_001168623, intron 1 of 4)	intron (NM_001168623, intron 1 of 4)	4676	NM_001168623	170737	Mm.271578	NM_133206	ENSMUSG00000033545	Znrf1	B830022L21Rik|Rnf42|Zrfp1|nin283	zinc and ring finger 1	protein-coding
mm_149766.1	chr19	22959955	22959981	+	1	NA	intron (NM_001035239, intron 21 of 24)	intron (NM_001035239, intron 21 of 24)	-181258	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_117512.1	chr13	80884727	80884745	-	1	NA	intron (NM_001042591, intron 1 of 7)	intron (NM_001042591, intron 1 of 7)	1314	NM_001042591	105171	Mm.423137	NM_001042591	ENSMUSG00000074794	Arrdc3	AI450344|mKIAA1376	arrestin domain containing 3	protein-coding
mm_52383.1	chr6	113212835	113212836	+	1	NA	Intergenic	L1MB8|LINE|L1	-17451	NM_177763	269788	Mm.37943	NM_177763	ENSMUSG00000042873	Lhfpl4	1190004M23Rik|AI604880|B230384L07|mKIAA4027	lipoma HMGIC fusion partner-like protein 4	protein-coding
mm_169356.1	chr14	26638811	26638815	-	1	NA	intron (NM_007479, intron 1 of 5)	intron (NM_007479, intron 1 of 5)	616	NM_007479	11843	Mm.297768	NM_007479	ENSMUSG00000021877	Arf4	AA407803	ADP-ribosylation factor 4	protein-coding
mm_128868.1	chr15	72925603	72925611	-	1	NA	exon (NM_001164642, exon 15 of 17)	exon (NM_001164642, exon 15 of 17)	-115283	NR_002864	353342	Mm.440245	NR_002864	ENSMUSG00000106847	Peg13	-	paternally expressed 13	ncRNA
mm_128490.1	chr15	51790251	51790268	-	1	NA	intron (NM_080635, intron 5 of 7)	intron (NM_080635, intron 5 of 7)	75202	NM_080635	68135	Mm.289800	NM_080635	ENSMUSG00000022312	Eif3h	1110008A16Rik|40kD|9430017H16Rik|EIF3-P40|EIF3-gamma|Eif3s3	eukaryotic translation initiation factor 3, subunit H	protein-coding
mm_13502.1	chr2	107320082	107320083	+	1	NA	Intergenic	Intergenic	29493	NM_021275	16492	Mm.142718	NM_021275	ENSMUSG00000042604	Kcna4	Kv1.4	potassium voltage-gated channel, shaker-related subfamily, member 4	protein-coding
mm_6167.1	chr1	65063438	65063440	-	1	NA	promoter-TSS (NM_007776)	promoter-TSS (NM_007776)	1	NM_007776	12967	Mm.425031	NM_007776	ENSMUSG00000067299	Crygd	Aey4|Cryg-1|DGcry-1|Lop12	crystallin, gamma D	protein-coding
mm_10039.1	chr1	192855724	192855736	-	1	NA	promoter-TSS (NM_198247)	promoter-TSS (NM_198247)	22	NM_198247	214791	Mm.22806	NM_198247	ENSMUSG00000016262	Sertad4	4833404A09|C130018M11Rik	SERTA domain containing 4	protein-coding
mm_11745.1	chr2	38351225	38351246	+	1	NA	promoter-TSS (NM_010710)	promoter-TSS (NM_010710)	-73	NM_010710	16870	Mm.142856	NM_010710	ENSMUSG00000000247	Lhx2	LH2A|Lh-2|Lim2|ap|apterous	LIM homeobox protein 2	protein-coding
mm_29792.1	chr3	127688539	127688552	-	1	NA	intron (NM_027808, intron 4 of 13)	intron (NM_027808, intron 4 of 13)	55400	NM_009718	11924	Mm.42017	NM_009718	ENSMUSG00000027967	Neurog2	Atoh4|Math4A|bHLHa8|ngn-2|ngn2	neurogenin 2	protein-coding
mm_92193.1	chr10	68126268	68126270	-	1	NA	intron (NM_023598, intron 7 of 9)	intron (NM_023598, intron 7 of 9)	146671	NM_001081346	170799	Mm.209844	NM_133244	ENSMUSG00000037846	Rtkn2	B130039D23Rik|Mbf|Plekhk1	rhotekin 2	protein-coding
mm_46307.1	chr5	100562867	100562880	-	1	NA	intron (NM_139198, intron 1 of 4)	intron (NM_139198, intron 1 of 4)	9332	NM_139198	231507	Mm.34609	NM_139198	ENSMUSG00000029322	Plac8	C15|D5Wsu111e	placenta-specific 8	protein-coding
mm_59289.1	chr7	24990488	24990507	+	1	NA	exon (NM_001290469, exon 12 of 23)	exon (NM_001290469, exon 12 of 23)	-2830	NR_106014	102465634		NR_106014	ENSMUSG00000099258	Mir7047	Gm27270|mmu-mir-7047	microRNA 7047	ncRNA
mm_68872.1	chr7	126446937	126446973	-	1	NA	exon (NM_007504, exon 21 of 23)	exon (NM_007504, exon 21 of 23)	16118	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_69060.1	chr7	126897363	126897415	-	1	NA	intron (NM_026827, intron 1 of 5)	MIRc|SINE|MIR	889	NM_026827	68742	Mm.248646	NM_026827	ENSMUSG00000060538	Tmem219	1110032O16Rik|2900045G02Rik|IGFBP-3R	transmembrane protein 219	protein-coding
mm_156407.1	chrX	140456619	140456632	+	1	NA	promoter-TSS (NM_021463)	promoter-TSS (NM_021463)	22	NM_021463	19139	Mm.287178	NM_021463	ENSMUSG00000031432	Prps1	2310010D17Rik|C76571|C76678|PRS-I|Prps-1	phosphoribosyl pyrophosphate synthetase 1	protein-coding
mm_169606.1	chr15	36771963	36771965	-	1	NA	3' UTR (NM_001253807, exon 5 of 5)	3' UTR (NM_001253807, exon 5 of 5)	18968	NM_001253807	22631	Mm.3360	NM_011740	ENSMUSG00000022285	Ywhaz	1110013I11Rik|14-3-3zeta|AI596267|AL022924|AU020854	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide	protein-coding
mm_75919.1	chr8	71485955	71485981	-	1	NA	promoter-TSS (NM_001164679)	promoter-TSS (NM_001164679)	99	NM_001164679	382014	Mm.260360	NM_001164679	ENSMUSG00000034863	Ano8	BC053460|Tmem16h	anoctamin 8	protein-coding
mm_702.1	chr1	40681362	40681380	+	1	NA	promoter-TSS (NM_001033289)	promoter-TSS (NM_001033289)	-341	NM_001033289	226999	Mm.256414	NM_001033289	ENSMUSG00000026062	Slc9a2	2210416H12Rik|4932415O19Rik|AV333884|NHE2	solute carrier family 9 (sodium/hydrogen exchanger), member 2	protein-coding
mm_13568.1	chr2	112270818	112270821	+	1	NA	intron (NM_133649, intron 1 of 24)	PB1|SINE|Alu	4505	NM_133649	107723	Mm.491155	NM_133648	ENSMUSG00000027130	Slc12a6	9530023I19Rik|KCC3|gaxp	solute carrier family 12, member 6	protein-coding
mm_19843.1	chr2	113217053	113217094	-	1	NA	promoter-TSS (NM_001319156)	promoter-TSS (NM_001319156)	10	NM_001319156	20192	Mm.436657	NM_177652	ENSMUSG00000057378	Ryr3	AI851294|C230090H21|RYR-3	ryanodine receptor 3	protein-coding
mm_117568.1	chr13	85289000	85289058	-	1	NA	5' UTR (NM_145452, exon 1 of 25)	5' UTR (NM_145452, exon 1 of 25)	457	NM_145452	218397	Mm.259653	NM_145452	ENSMUSG00000021549	Rasa1	Gap|RasGAP|Rasa	RAS p21 protein activator 1	protein-coding
mm_5058.1	chr1	194986520	194986544	+	1	NA	Intergenic	Intergenic	-9573	NR_033564	320400	Mm.417608	NR_033564	ENSMUSG00000097325	Gm16897	C030002c11rik	predicted gene, 16897	ncRNA
mm_138344.1	chr17	34914433	34914446	+	1	NA	promoter-TSS (NM_023557)	promoter-TSS (NM_023557)	-27	NM_023557	70129	Mm.183126	NM_023557	ENSMUSG00000007034	Slc44a4	2210409B01Rik|NG22	solute carrier family 44, member 4	protein-coding
mm_31819.1	chr4	66841859	66841870	+	1	NA	3' UTR (NM_021297, exon 3 of 3)	3' UTR (NM_021297, exon 3 of 3)	14313	NM_021297	21898	Mm.38049	NM_021297	ENSMUSG00000039005	Tlr4	Lps|Ly87|Ran/M1|Rasl2-8	toll-like receptor 4	protein-coding
mm_133954.1	chr16	4003751	4003828	-	1	NA	Intergenic	CpG	-2111	NM_177472	52864	Mm.29935	NM_177472	ENSMUSG00000039738	Slx4	AI256635|AI426760|Btbd12|D16Bwg1016e	SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)	protein-coding
mm_2337.1	chr1	92848584	92848617	+	1	NA	intron (NM_016696, intron 1 of 8)	CpG	-1778	NR_029559	387167		NR_029559	ENSMUSG00000065470	Mir149	Mirn149|mir-149|mmu-mir-149	microRNA 149	ncRNA
mm_7432.1	chr1	119899854	119899870	-	1	NA	Intergenic	Intergenic	13306	NM_175106	66343	Mm.49942	NM_175106	ENSMUSG00000036975	Tmem177	2300008B03Rik	transmembrane protein 177	protein-coding
mm_19207.1	chr2	84531317	84531331	-	1	NA	Intergenic	MTEa|LTR|ERVL-MaLR	-24451	NR_046046	672763	Mm.491046	NR_046046	ENSMUSG00000087362	Gm13710	OTTMUSG00000013441	predicted gene 13710	ncRNA
mm_12793.1	chr2	79635417	79635441	+	1	NA	promoter-TSS (NM_080558)	promoter-TSS (NM_080558)	4	NM_080558	70599	Mm.272881	NM_080558	ENSMUSG00000027007	Ssfa2	5730488C15Rik|CS-1|CS1|KRAP|SPAG13|mKIAA1927	sperm specific antigen 2	protein-coding
mm_5332.1	chr1	23909735	23909740	-	1	NA	promoter-TSS (NM_001290683)	promoter-TSS (NM_001290683)	-1	NM_001290683	98366	Mm.329963	NM_028534	ENSMUSG00000026155	Smap1	1700056O10Rik|4921514B13Rik|4921525H11Rik|AI462175	small ArfGAP 1	protein-coding
mm_5069.1	chr1	195037115	195037118	+	1	NA	promoter-TSS (NR_029809)	promoter-TSS (NR_029809)	76	NR_029809	723963		NR_029809	ENSMUSG00000065412	Mir29b-2	Mirn29b-2|mir-29b-2	microRNA 29b-2	ncRNA
mm_128809.1	chr15	66969939	66969953	-	1	NA	promoter-TSS (NM_008681)	promoter-TSS (NM_008681)	-305	NM_008681	17988	Mm.30837	NM_008681	ENSMUSG00000005125	Ndrg1	CAP43|CMT4D|DRG1|HMSNL|NMSL|Ndr1|Ndrl|PROXY1|RTP|TDD5	N-myc downstream regulated gene 1	protein-coding
mm_34057.1	chr4	138311866	138311892	+	1	NA	exon (NM_007838, exon 11 of 11)	exon (NM_007838, exon 11 of 11)	4321	NR_105986	102466788		NR_105986	ENSMUSG00000099200	Mir7019	Gm27947|mmu-mir-7019	microRNA 7019	ncRNA
mm_142898.1	chr17	51945721	51945729	-	1	NA	intron (NR_045095, intron 2 of 2)	L2a|LINE|L2	62998	NR_045095	100504169	Mm.417731	NR_045095		Gm20098	-	predicted gene, 20098	ncRNA
mm_165554.1	chr3	14504458	14504461	+	1	NA	intron (NM_080852, intron 3 of 3)	L1_Mur3|LINE|L1	23760	NM_080852	140918	Mm.215250	NM_080852	ENSMUSG00000039710	Slc7a12	Asc-2|XAT1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 12	protein-coding
mm_44250.1	chr5	5380155	5380169	-	1	NA	promoter-TSS (NM_011074)	promoter-TSS (NM_011074)	89	NM_011074	18647	Mm.389061	NM_011074	ENSMUSG00000028926	Cdk14	Pftk1|mKIAA0834	cyclin-dependent kinase 14	protein-coding
mm_171662.1	chr4	44704184	44704188	-	1	NA	non-coding (NR_073462, exon 1 of 1)	non-coding (NR_073462, exon 1 of 1)	1386	NR_073462	70602	Mm.491142	NR_073462	ENSMUSG00000103995	5730488B01Rik	-	RIKEN cDNA 5730488B01 gene	ncRNA
mm_87532.1	chr10	53344991	53345007	+	1	NA	3' UTR (NM_001141927, exon 3 of 3)	3' UTR (NM_001141927, exon 3 of 3)	7313	NM_001141927	18821	Mm.34145	NM_023129	ENSMUSG00000038583	Pln	Plb	phospholamban	protein-coding
mm_134099.1	chr16	9994548	9994567	-	1	NA	Intergenic	Intergenic	-2024	NM_008170	14811	Mm.2953	NM_008170	ENSMUSG00000059003	Grin2a	GluN2A|NMDAR2A|NR2A	glutamate receptor, ionotropic, NMDA2A (epsilon 1)	protein-coding
mm_170627.1	chr1	97423505	97423505	+	1	NA	Intergenic	L1Md_Gf|LINE|L1	238513	NM_133825	52392	Mm.12309	NM_133825	ENSMUSG00000044768	D1Ertd622e	AI987691|AW047450	DNA segment, Chr 1, ERATO Doi 622, expressed	protein-coding
mm_163298.1	chr11	120349279	120349290	+	1	NA	promoter-TSS (NM_009609)	promoter-TSS (NM_009609)	606	NR_038126	66838	Mm.375010	NR_038126	ENSMUSG00000043644	0610009L18Rik	-	RIKEN cDNA 0610009L18 gene	ncRNA
mm_36380.1	chr4	76877574	76877576	-	1	NA	intron (NM_011211, intron 8 of 39)	intron (NM_011211, intron 8 of 39)	1334320	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding
mm_100604.1	chr11	121259984	121260055	+	1	NA	promoter-TSS (NM_001080932)	promoter-TSS (NM_001080932)	32	NM_001080932	68837	Mm.209750	NM_001080932	ENSMUSG00000039275	Foxk2	1110054H05Rik|5730434B08Rik|6230415M23Rik|ILF|Ilf1	forkhead box K2	protein-coding
mm_36539.1	chr4	86657370	86657387	-	1	NA	exon (NM_007408, exon 8 of 8)	exon (NM_007408, exon 8 of 8)	12681	NM_007408	11520	Mm.381	NM_007408	ENSMUSG00000028494	Plin2	AA407157|ADPH|Adfp|Adrp	perilipin 2	protein-coding
mm_91069.1	chr10	19007887	19007900	-	1	NA	intron (NM_001166402, intron 2 of 7)	intron (NM_001166402, intron 2 of 7)	4070	NM_001166402	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_29186.1	chr3	106546162	106546172	-	1	NA	intron (NM_133869, intron 1 of 8)	intron (NM_133869, intron 1 of 8)	-1631	NM_001286986	67171	Mm.290488	NM_026013	ENSMUSG00000027900	Dram2	2010305N14Rik|2610318G18Rik|AI647667|Tmem77	DNA-damage regulated autophagy modulator 2	protein-coding
mm_74317.1	chr8	126758178	126758190	+	1	NA	Intergenic	Intergenic	-164748	NM_001164598	270110	Mm.334918	NM_001164598	ENSMUSG00000051495	Irf2bp2	E130305N23Rik|IRF-2BP2	interferon regulatory factor 2 binding protein 2	protein-coding
mm_170444.1	chr18	82618897	82618900	-	1	NA	exon (NM_177832, exon 23 of 30)	exon (NM_177832, exon 23 of 30)	64390	NM_001025254	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_61233.1	chr7	64511785	64511791	+	1	NA	intron (NM_001291166, intron 1 of 14)	intron (NM_001291166, intron 1 of 14)	9650	NM_001291167	11784	Mm.4657	NM_007461	ENSMUSG00000030519	Apba2	X11-like|X11L|XllL|mXllL	amyloid beta (A4) precursor protein-binding, family A, member 2	protein-coding
mm_5642.1	chr1	40448436	40448442	-	1	NA	TTS (NM_010743)	TTS (NM_010743)	8810	NM_010743	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_140056.1	chr17	74599212	74599232	+	1	NA	intron (NM_007566, intron 17 of 72)	intron (NM_007566, intron 17 of 72)	70927	NM_007566	12211	Mm.442564	NM_007566	ENSMUSG00000024073	Birc6	A430032G04Rik|A430040A19Rik|AA501170|Bruce|D630005A10Rik|mKIAA1289	baculoviral IAP repeat-containing 6	protein-coding
mm_146825.1	chr18	21421990	21421993	-	1	NA	Intergenic	RLTR17|LTR|ERVK	-121852	NM_001033445	381126	Mm.312276	NM_001033445	ENSMUSG00000042680	Garem1	C86169|Fam59a|Garem|Gm944|mKIAA4238	GRB2 associated regulator of MAPK1 subtype 1	protein-coding
mm_23801.1	chr3	79877285	79877306	+	1	NA	Intergenic	Intergenic	-8635	NM_133187	68659	Mm.427274	NM_133187	ENSMUSG00000027955	Fam198b	1110032E23Rik|2210419I08Rik|AV011458|Ened	family with sequence similarity 198, member B	protein-coding
mm_130588.1	chr15	99633962	99633965	-	1	NA	intron (NM_012025, intron 7 of 17)	intron (NM_012025, intron 7 of 17)	17693	NM_001253808	26934	Mm.273804	NM_012025	ENSMUSG00000023015	Racgap1	AI227039|AI327394|Band25|GTPase|MgcRacGAP|gtl11|mKIAA1478	Rac GTPase-activating protein 1	protein-coding
mm_65499.1	chr7	25721719	25721728	-	1	NA	TTS (NM_144922)	TTS (NM_144922)	-2670	NM_028771	52132	Mm.278798	NM_028771	ENSMUSG00000002608	Ccdc97	1200014H14Rik|2810446P04Rik|AA545218|D7Ertd462e	coiled-coil domain containing 97	protein-coding
mm_126998.1	chr15	95790832	95790859	+	1	NA	promoter-TSS (NM_001253813)	promoter-TSS (NM_001253813)	2	NM_001253813	105722	Mm.38087	NM_175344	ENSMUSG00000064210	Ano6	2900059G15Rik|AA407480|AW554778|F730003B03Rik|Tmem16f	anoctamin 6	protein-coding
mm_55341.1	chr6	56568943	56568995	-	1	NA	Intergenic	CpG	135730	NM_025520	66373	Mm.25642	NM_025520	ENSMUSG00000091625	Lsm5	2010208O10Rik|2310034K10Rik	LSM5 homolog, U6 small nuclear RNA and mRNA degradation associated	protein-coding
mm_92327.1	chr10	75773351	75773434	-	1	NA	promoter-TSS (NM_010027)	promoter-TSS (NM_010027)	-18	NM_010027	13202	Mm.298947	NM_010027	ENSMUSG00000001666	Ddt	C78655	D-dopachrome tautomerase	protein-coding
mm_148084.1	chr18	73572346	73572360	-	1	NA	promoter-TSS (NM_001039214)	promoter-TSS (NM_001039214)	-352	NM_001039214	240396	Mm.24131	NM_001039214	ENSMUSG00000037253	Mex3c	A130001D14Rik|BC035207|BM-013|Rkhd2	mex3 RNA binding family member C	protein-coding
mm_54002.1	chr6	7692905	7692914	-	1	NA	intron (NM_012055, intron 1 of 11)	intron (NM_012055, intron 1 of 11)	273	NM_012055	27053	Mm.2942	NM_012055	ENSMUSG00000029752	Asns	-	asparagine synthetase	protein-coding
mm_76247.1	chr8	83594406	83594432	-	1	NA	promoter-TSS (NM_027179)	promoter-TSS (NM_027179)	72	NM_027179	106529	Mm.352239	NM_027179	ENSMUSG00000031708	Tecr	2410016D23Rik|A230102P12Rik|AI173355|D17Ertd178e|Gpsn2|SC2	trans-2,3-enoyl-CoA reductase	protein-coding
mm_2597.1	chr1	119648381	119648389	+	1	NA	intron (NM_145506, intron 1 of 24)	CpG	615	NM_001113416	226352	Mm.253156	NM_145506	ENSMUSG00000026383	Epb41l5	1700030C16Rik|AL022914|BE37|E230025E14Rik|Epb4.1l5|Lulu1|NBL5	erythrocyte membrane protein band 4.1 like 5	protein-coding
mm_42822.1	chr5	122093548	122093561	+	1	NA	Intergenic	Intergenic	-7426	NM_010861	17906	Mm.1529	NM_010861	ENSMUSG00000013936	Myl2	MLC-2|MLC-2s/v|MLC-2v|Mlc2v|Mylpc	myosin, light polypeptide 2, regulatory, cardiac, slow	protein-coding
mm_7696.1	chr1	129616193	129616246	-	1	NA	intron (NM_172485, intron 4 of 27)	intron (NM_172485, intron 4 of 27)	342915	NM_172485	210417	Mm.380518	NM_172485	ENSMUSG00000042581	Thsd7b	1700074E13Rik|B930082A18|D130067I03Rik	thrombospondin, type I, domain containing 7B	protein-coding
mm_95362.1	chr11	48901315	48901339	+	1	NA	intron (NM_001024230, intron 2 of 4)	B1_Mur1|SINE|Alu	825	NM_001024230	432555	Mm.338931	NM_001024230	ENSMUSG00000058163	Gm5431	EG432555|Irgb9b8	predicted gene 5431	protein-coding
mm_31645.1	chr4	59581698	59581714	+	1	NA	5' UTR (NM_024255, exon 1 of 11)	5' UTR (NM_024255, exon 1 of 11)	143	NM_024255	72479	Mm.272905	NM_024255	ENSMUSG00000028383	Hsdl2	2610207I16Rik	hydroxysteroid dehydrogenase like 2	protein-coding
mm_69368.1	chr7	130624889	130624901	-	1	NA	exon (NM_001004468, exon 3 of 22)	exon (NM_001004468, exon 3 of 22)	47411	NM_206856	57752	Mm.86322	NM_021314	ENSMUSG00000030852	Tacc2	mKIAA4180	transforming, acidic coiled-coil containing protein 2	protein-coding
mm_40696.1	chr5	65851059	65851070	+	1	NA	Intergenic	Helitron1Na_Mam|RC|Helitron	-12505	NM_001081105	74734	Mm.20323	NM_001081105	ENSMUSG00000029204	Rhoh	5830400A04Rik|AU019774|Arhh	ras homolog family member H	protein-coding
mm_133601.1	chr16	91475877	91475897	+	1	NA	Intergenic	RLTR16|LTR|ERVK	-9328	NM_010508	15975	Mm.502	NM_010508	ENSMUSG00000022967	Ifnar1	CD118|Ifar|Ifnar|Ifrc|Infar	interferon (alpha and beta) receptor 1	protein-coding
mm_24526.1	chr3	93197271	93197284	+	1	NA	promoter-TSS (NM_001013804)	promoter-TSS (NM_001013804)	4	NM_001013804	229574	Mm.10755	NM_001013804		Flg2	EG229574	filaggrin family member 2	protein-coding
mm_57602.1	chr6	127796333	127796337	-	1	NA	Intergenic	Intergenic	-8192	NR_106092	102466996		NR_106092	ENSMUSG00000104804	Mir7233	mmu-mir-7233	microRNA 7233	ncRNA
mm_19203.1	chr2	84501302	84501332	-	1	NA	non-coding (NR_046046, exon 3 of 3)	non-coding (NR_046046, exon 3 of 3)	5556	NR_046046	672763	Mm.491046	NR_046046	ENSMUSG00000087362	Gm13710	OTTMUSG00000013441	predicted gene 13710	ncRNA
mm_130969.1	chr15	103323218	103323267	-	1	NA	intron (NM_013866, intron 2 of 7)	CpG	-12804	NM_030720	80910	Mm.160369	NM_030720	ENSMUSG00000063234	Gpr84	EX33	G protein-coupled receptor 84	protein-coding
mm_85466.1	chr9	105521238	105521265	-	1	NA	promoter-TSS (NM_001253831)	promoter-TSS (NM_001253831)	6	NM_001253831	235574	Mm.326247	NM_175025	ENSMUSG00000032570	Atp2c1	1700121J11Rik|ATP2C1A|AW061228|BCPM|D930003G21Rik|HHD|SPCA|pmr1	ATPase, Ca++-sequestering	protein-coding
mm_150066.1	chr19	29386363	29386376	+	1	NA	3' UTR (NM_021893, exon 7 of 7)	3' UTR (NM_021893, exon 7 of 7)	18931	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_57460.1	chr6	125186676	125186688	-	1	NA	promoter-TSS (NR_028517)	promoter-TSS (NR_028517)	-251	NR_028517	100217413		NR_028517		Scarna10	MBI-52	small Cajal body-specific RNA 10	ncRNA
mm_46914.1	chr5	114380506	114380520	-	1	NA	promoter-TSS (NM_001159941)	promoter-TSS (NM_001159941)	-8	NM_026145	330171	Mm.238285	NM_026145	ENSMUSG00000001098	Kctd10	AW536343|C87062|mBACURD3	potassium channel tetramerisation domain containing 10	protein-coding
mm_145738.1	chr18	64265343	64265365	+	1	NA	5' UTR (NM_009182, exon 3 of 6)	5' UTR (NM_009182, exon 3 of 6)	10995	NM_009182	20451	Mm.252110	NM_009182	ENSMUSG00000056812	St8sia3	AI847333|ST8SiaIII|Siat8c	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3	protein-coding
mm_164283.1	chr15	102928155	102928200	+	1	NA	3' UTR (NM_010464, exon 2 of 2)	3' UTR (NM_010464, exon 2 of 2)	7046	NM_010464	15422	Mm.207062	NM_010464	ENSMUSG00000001655	Hoxc13	-	homeobox C13	protein-coding
mm_20372.1	chr2	128429178	128429226	-	1	NA	non-coding (NR_028591, exon 1 of 2)	non-coding (NR_028591, exon 1 of 2)	149	NR_028591	100043424	Mm.297222	NR_028589		Gm14005	OTTMUSG00000015351	predicted gene 14005	ncRNA
mm_84920.1	chr9	80265408	80265416	-	1	NA	intron (NM_001039546, intron 15 of 32)	intron (NM_001039546, intron 15 of 32)	100378	NM_001039546	17920	Mm.4040	NM_008662	ENSMUSG00000033577	Myo6	BC029719|Tlc|sv	myosin VI	protein-coding
mm_93650.1	chr10	117376923	117376954	-	1	NA	promoter-TSS (NM_001013391)	promoter-TSS (NM_001013391)	35	NM_001013391	432508	Mm.478881	NM_001013391	ENSMUSG00000055531	Cpsf6	4733401N12Rik|AI256641|CFIM|CFIM68|HPBRII-4|HPBRII-7	cleavage and polyadenylation specific factor 6	protein-coding
mm_118577.1	chr14	19750962	19750968	+	1	NA	promoter-TSS (NM_008695)	promoter-TSS (NM_008695)	-292	NM_008695	18074	Mm.20348	NM_008695	ENSMUSG00000021806	Nid2	AW547149|Ly111|NID-2|entactin-2|nidogen-2	nidogen 2	protein-coding
mm_5216.1	chr1	13660746	13660755	-	1	NA	promoter-TSS (NM_145381)	promoter-TSS (NM_145381)	-241	NM_145381	212442	Mm.89572	NM_145381	ENSMUSG00000025937	Lactb2	Cgi-83|E430032H21Rik	lactamase, beta 2	protein-coding
mm_80136.1	chr9	70679130	70679140	+	1	NA	5' UTR (NM_007399, exon 1 of 16)	5' UTR (NM_007399, exon 1 of 16)	153	NM_007399	11487	Mm.3037	NM_007399	ENSMUSG00000054693	Adam10	1700031C13Rik|MADM|kuz|kuzbanian	a disintegrin and metallopeptidase domain 10	protein-coding
mm_25315.1	chr3	106482428	106482477	+	1	NA	promoter-TSS (NM_001278941)	promoter-TSS (NM_001278941)	2	NM_001278941	72121	Mm.14816	NM_028110	ENSMUSG00000027901	Dennd2d	2010308M01Rik|AI451421	DENN/MADD domain containing 2D	protein-coding
mm_59134.1	chr7	23974685	23974695	+	1	NA	Intergenic	RLTR10B|LTR|ERVK	-9271	NM_207546	404289	Mm.279185	NM_207546	ENSMUSG00000097425	Vmn1r181	V1rd20	vomeronasal 1 receptor 181	protein-coding
mm_151514.1	chr19	58737029	58737045	+	1	NA	exon (NM_018874, exon 9 of 13)	exon (NM_018874, exon 9 of 13)	8150	NM_018874	18946	Mm.10753	NM_018874	ENSMUSG00000042179	Pnliprp1	Plrp1	pancreatic lipase related protein 1	protein-coding
mm_105277.1	chr11	102407900	102407913	-	1	NA	promoter-TSS (NM_026542)	promoter-TSS (NM_026542)	-389	NM_026542	68066	Mm.44226	NM_026542	ENSMUSG00000018677	Slc25a39	3010027G13Rik|D11Ertd333e	solute carrier family 25, member 39	protein-coding
mm_45929.1	chr5	89445372	89445389	-	1	NA	exon (NM_008096, exon 3 of 13)	exon (NM_008096, exon 3 of 13)	12518	NM_008096	14473	Mm.196595	NM_008096	ENSMUSG00000035540	Gc	DBP|VDB	group specific component	protein-coding
mm_137869.1	chr17	31386219	31386238	+	1	NA	promoter-TSS (NM_001163748)	promoter-TSS (NM_001163748)	-6	NM_008804	18585	Mm.10812	NM_008804	ENSMUSG00000041119	Pde9a	PDE9A1	phosphodiesterase 9A	protein-coding
mm_5249.1	chr1	16579122	16579132	-	1	NA	intron (NM_025773, intron 5 of 5)	BC1_Mm|scRNA|scRNA	40211	NM_025773	66799	Mm.122430	NM_025773	ENSMUSG00000025939	Ube2w	6130401J04Rik	ubiquitin-conjugating enzyme E2W (putative)	protein-coding
mm_93212.1	chr10	94944836	94944862	-	1	NA	promoter-TSS (NM_018797)	promoter-TSS (NM_018797)	-271	NM_018797	54712	Mm.256712	NM_018797	ENSMUSG00000074785	Plxnc1	2510048K12Rik|AW742158|CD232|Vespr	plexin C1	protein-coding
mm_92057.1	chr10	62507738	62507764	-	1	NA	promoter-TSS (NM_011157)	promoter-TSS (NM_011157)	4	NM_011157	19073	Mm.338790	NM_011157	ENSMUSG00000020077	Srgn	Prg|Prg1|Sgc	serglycin	protein-coding
mm_164857.1	chr18	52056261	52056263	-	1	NA	Intergenic	Lx5b|LINE|L1	67284	NR_029788	723830		NR_029788	ENSMUSG00000065494	Mir28a	Mir28|Mirn28|mmu-mir-28|mmu-mir-28a	microRNA 28a	ncRNA
mm_62171.1	chr7	97332639	97332651	+	1	NA	intron (NM_001039039, intron 1 of 1)	intron (NM_001039039, intron 1 of 1)	322	NM_001039039	622320	Mm.334029	NM_001039039	ENSMUSG00000044952	Kctd21	EG622320	potassium channel tetramerisation domain containing 21	protein-coding
mm_112712.1	chr13	19184928	19184981	+	1	NA	Intergenic	Intergenic	210859	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_53308.1	chr6	129181344	129181361	+	1	NA	intron (NM_053109, intron 1 of 4)	intron (NM_053109, intron 1 of 4)	737	NM_053109	93694	Mm.197536	NM_053109	ENSMUSG00000030157	Clec2d	Clr-b|Clrb|Ocil	C-type lectin domain family 2, member d	protein-coding
mm_43365.1	chr5	135404894	135404906	+	1	NA	Intergenic	Intergenic	-10354	NM_148932	107939	Mm.28399	NM_148932	ENSMUSG00000053293	Pom121	2610027A18Rik|C80273|mKIAA0618	nuclear pore membrane protein 121	protein-coding
mm_12086.1	chr2	60210640	60210664	+	1	NA	intron (NM_020575, intron 1 of 9)	intron (NM_020575, intron 1 of 9)	716	NM_020575	57438	Mm.260635	NM_020575	ENSMUSG00000026977	March7	Axo|Axot|Gtrgeo17	membrane-associated ring finger (C3HC4) 7	protein-coding
mm_104848.1	chr11	99244059	99244136	-	1	NA	promoter-TSS (NM_172946)	promoter-TSS (NM_172946)	-30	NM_172946	268481	Mm.133193	NM_172946	ENSMUSG00000035849	Krt222	6330509G02Rik	keratin 222	protein-coding
mm_156451.1	chrX	142720393	142720403	+	1	NA	intron (NM_001199360, intron 2 of 6)	intron (NM_001199360, intron 2 of 6)	-18602	NR_030523	723976		NR_030523	ENSMUSG00000076011	Mir652	Mirn652|miRX|mmu-mir-652	microRNA 652	ncRNA
mm_87880.1	chr10	61680303	61680361	+	1	NA	promoter-TSS (NM_009120)	promoter-TSS (NM_009120)	11	NM_009120	20224	Mm.391794	NM_009120	ENSMUSG00000020088	Sar1a	1600019H17Rik|Sara|Sara1	secretion associated Ras related GTPase 1A	protein-coding
mm_161218.1	chr13	67306461	67306461	-	1	NA	promoter-TSS (NM_001003666)	promoter-TSS (NM_001003666)	-49	NM_001003666	431706	Mm.439456	NM_001003666	ENSMUSG00000055341	Zfp457	Rslcan-6	zinc finger protein 457	protein-coding
mm_85199.1	chr9	96732272	96732284	-	1	NA	promoter-TSS (NM_175537)	promoter-TSS (NM_175537)	-603	NM_175537	245007	Mm.485954	NM_175537	ENSMUSG00000040433	Zbtb38	A930014K01Rik|CIBZ	zinc finger and BTB domain containing 38	protein-coding
mm_31059.1	chr4	41275701	41275749	+	1	NA	promoter-TSS (NM_026872)	promoter-TSS (NM_026872)	-590	NM_026872	68926	Mm.41864	NM_026872	ENSMUSG00000028433	Ubap2	1190005K07Rik|AA408600|AU045235|UBAP-2|mKIAA1491	ubiquitin-associated protein 2	protein-coding
mm_97089.1	chr11	73138440	73138482	+	1	NA	promoter-TSS (NM_010353)	promoter-TSS (NM_010353)	-167	NM_010353	14841	Mm.42045	NM_010353	ENSMUSG00000050107	Gsg2	Haspin	germ cell associated 2, haspin	protein-coding
mm_83526.1	chr9	46230094	46230102	-	1	NA	exon (NM_009692, exon 4 of 4)	exon (NM_009692, exon 4 of 4)	1468	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2|apo-AI|apoA-I	apolipoprotein A-I	protein-coding
mm_151405.1	chr19	56548436	56548512	+	1	NA	promoter-TSS (NM_018831)	promoter-TSS (NM_018831)	213	NM_025811	66866	Mm.46346	NM_025811	ENSMUSG00000025078	Nhlrc2	1200003G01Rik|AI835049|AV002846|AW496455	NHL repeat containing 2	protein-coding
mm_68602.1	chr7	116237801	116237821	-	1	NA	promoter-TSS (NM_001305186)	promoter-TSS (NM_001305186)	-35	NM_001305186	233765	Mm.3741	NM_172743	ENSMUSG00000045659	Plekha7	A430081P20Rik|AI414265	pleckstrin homology domain containing, family A member 7	protein-coding
mm_121663.1	chr14	12345728	12345740	-	1	NA	5' UTR (NM_080433, exon 1 of 5)	5' UTR (NM_080433, exon 1 of 5)	131	NM_080433	54713	Mm.34644	NM_080433	ENSMUSG00000021743	Fezf2	AI451466|AI852056|Fez|Fezl|Zfp312	Fez family zinc finger 2	protein-coding
mm_22323.1	chr2	180642318	180642335	-	1	NA	exon (NM_178254, exon 1 of 6)	exon (NM_178254, exon 1 of 6)	365	NM_178254	277353	Mm.473700	NM_178254	ENSMUSG00000038932	Tcfl5	AV260129|Figlb|Sosf1	transcription factor-like 5 (basic helix-loop-helix)	protein-coding
mm_90001.1	chr10	112270257	112270267	+	1	NA	promoter-TSS (NM_001025581)	promoter-TSS (NM_001025581)	-861	NM_001025581	268345	Mm.336242	NM_001025581	ENSMUSG00000035681	Kcnc2	AW047325|B230117I07|KShIIIA|Kv3.2	potassium voltage gated channel, Shaw-related subfamily, member 2	protein-coding
mm_113105.1	chr13	24397427	24397436	+	1	NA	intron (NM_001284519, intron 3 of 17)	intron (NM_001284519, intron 3 of 17)	-17691	NM_007717	12763	Mm.8396	NM_007717	ENSMUSG00000016756	Cmah	-	cytidine monophospho-N-acetylneuraminic acid hydroxylase	protein-coding
mm_171656.1	chr4	4242257	4242258	-	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	-103812	NM_001002927	18619	Mm.475097	NM_001002927	ENSMUSG00000045573	Penk	AI326464|ENK|PPA|Penk1	preproenkephalin	protein-coding
mm_90048.1	chr10	116018427	116018440	+	1	NA	promoter-TSS (NM_011217)	promoter-TSS (NM_011217)	70	NM_011217	19279	Mm.336316	NM_011217	ENSMUSG00000020151	Ptprr	Gmcp1|PTP-SL|PTPBR7|RPTPRR|mPTP213	protein tyrosine phosphatase, receptor type, R	protein-coding
mm_32160.1	chr4	99978509	99978533	+	1	NA	intron (NM_028132, intron 7 of 10)	intron (NM_028132, intron 7 of 10)	49070	NM_028132	72157	Mm.217764	NM_028132	ENSMUSG00000025791	Pgm2	2610020G18Rik|AA407108|AI098105|Pgm-2|Pgm1	phosphoglucomutase 2	protein-coding
mm_22534.1	chr3	8545616	8545628	+	1	NA	exon (NM_025285, exon 3 of 5)	exon (NM_025285, exon 3 of 5)	36095	NM_025285	20257	Mm.29580	NM_025285	ENSMUSG00000027500	Stmn2	AI159727|SCG10|Scgn10|Stmb2	stathmin-like 2	protein-coding
mm_270.1	chr1	21218576	21218617	+	1	NA	promoter-TSS (NM_001290679)	promoter-TSS (NM_001290679)	21	NM_029398	75712	Mm.304763	NM_029398	ENSMUSG00000025933	Tmem14a	5730496E24Rik|C85783|PTD011	transmembrane protein 14A	protein-coding
mm_99518.1	chr11	103133304	103133332	+	1	NA	promoter-TSS (NM_027658)	promoter-TSS (NM_027658)	-21	NM_001130516	71059	Mm.273871	NM_027658	ENSMUSG00000043372	Hexim2	4933402L21Rik	hexamethylene bis-acetamide inducible 2	protein-coding
mm_125339.1	chr15	39006273	39006365	+	1	NA	promoter-TSS (NM_008056)	promoter-TSS (NM_008056)	-14	NM_008056	14368	Mm.4769	NM_008056	ENSMUSG00000022297	Fzd6	Fz6	frizzled class receptor 6	protein-coding
mm_152232.1	chr19	8709069	8709128	-	1	NA	exon (NM_008577, exon 7 of 9)	exon (NM_008577, exon 7 of 9)	4799	NM_008577	17254	Mm.4114	NM_008577	ENSMUSG00000010095	Slc3a2	4F2|4F2HC|AI314110|Cd98|Ly-10|Ly-m10|Ly10|Mdu1|Mgp-2hc|NACAE	solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2	protein-coding
mm_88090.1	chr10	68723635	68723650	+	1	NA	promoter-TSS (NM_177794)	promoter-TSS (NM_177794)	-104	NM_177794	327766	Mm.2479	NM_177794	ENSMUSG00000060044	Tmem26	3230401A06|AI195372	transmembrane protein 26	protein-coding
mm_7053.1	chr1	87128281	87128302	-	1	NA	TTS (NM_007432)	TTS (NM_007432)	3283	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_155879.1	chrX	101449104	101449135	+	1	NA	promoter-TSS (NM_013712)	promoter-TSS (NM_013712)	10	NM_013712	26549	Mm.46232	NM_013712	ENSMUSG00000031312	Itgb1bp2	Chordc3	integrin beta 1 binding protein 2	protein-coding
mm_45979.1	chr5	90474612	90474645	-	1	NA	exon (NM_009654, exon 13 of 15)	exon (NM_009654, exon 13 of 15)	13758	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_38126.1	chr4	134563436	134563438	-	1	NA	3' UTR (NM_207237, exon 12 of 12)	3' UTR (NM_207237, exon 12 of 12)	4414	NR_105829	102465216		NR_105829	ENSMUSG00000099289	Mir6403	Gm27992|mmu-mir-6403	microRNA 6403	ncRNA
mm_65927.1	chr7	30280336	30280424	-	1	NA	promoter-TSS (NM_146186)	promoter-TSS (NM_146186)	41	NM_146186	233064	Mm.271677	NM_146186	ENSMUSG00000037020	Wdr62	2310038K02Rik	WD repeat domain 62	protein-coding
mm_53336.1	chr6	129237001	129237016	+	1	NA	intron (NR_040265, intron 1 of 2)	MTE2a|LTR|ERVL-MaLR	1037	NR_040265	76432	Mm.261738	NR_040265	ENSMUSG00000097354	2310001H17Rik	AI646108	RIKEN cDNA 2310001H17 gene	ncRNA
mm_111262.1	chr12	85151214	85151260	-	1	NA	promoter-TSS (NM_146244)	promoter-TSS (NM_146244)	27	NM_146244	238323	Mm.44829	NM_146244	ENSMUSG00000019235	Rps6kl1	A830084F09Rik|AW046440	ribosomal protein S6 kinase-like 1	protein-coding
mm_131972.1	chr16	24934146	24934151	+	1	NA	intron (NM_001145954, intron 5 of 7)	intron (NM_001145954, intron 5 of 7)	-125491	NR_040374	319487	Mm.137341	NR_040374	ENSMUSG00000096960	A230028O05Rik	-	RIKEN cDNA A230028O05 gene	ncRNA
mm_3854.1	chr1	160941136	160941141	+	1	NA	intron (NM_001024952, intron 5 of 19)	intron (NM_001024952, intron 5 of 19)	34727	NM_001024952	381305	Mm.329667	NM_001024952	ENSMUSG00000040423	Rc3h1	5730557L09Rik|Gm551|N28103|mKIAA2025	RING CCCH (C3H) domains 1	protein-coding
mm_14899.1	chr2	149830895	149830907	+	1	NA	5' UTR (NM_001085521, exon 1 of 4)	5' UTR (NM_001085521, exon 1 of 4)	118	NM_001085521	433485	Mm.330649	NM_001085521	ENSMUSG00000074736	Syndig1	AW123113|DSPC2|Gm14134|H2C20orf39|OTTMUSG00000015750|Tmem90b	synapse differentiation inducing 1	protein-coding
mm_12392.1	chr2	69930529	69930536	+	1	NA	intron (NM_001303033, intron 5 of 38)	B3|SINE|B2	33286	NM_177783	68795	Mm.314576	NM_177783	ENSMUSG00000044308	Ubr3	1110059H15Rik|4833421P10Rik|A130030D10Rik|AA409735|AA414972|AA422631|AI646861|AU016126|Zfp650|Znf650	ubiquitin protein ligase E3 component n-recognin 3	protein-coding
mm_21011.1	chr2	152396193	152396196	-	1	NA	3' UTR (NM_011438, exon 1 of 1)	3' UTR (NM_011438, exon 1 of 1)	1852	NM_011438	20667	Mm.28424	NM_011438	ENSMUSG00000051817	Sox12	2010205A02Rik	SRY (sex determining region Y)-box 12	protein-coding
mm_138713.1	chr17	36143169	36143187	+	1	NA	Intergenic	Intergenic	-1840	NR_033517	675325	Mm.75890	NR_033517	ENSMUSG00000038311	2410017I17Rik	-	RIKEN cDNA 2410017I17 gene	ncRNA
mm_121507.1	chr14	121950048	121950078	+	1	NA	intron (NM_026861, intron 4 of 8)	intron (NM_026861, intron 4 of 8)	15130	NM_183031	321019	Mm.265618	NM_183031	ENSMUSG00000051212	Gpr183	Ebi2	G protein-coupled receptor 183	protein-coding
mm_113551.1	chr13	38149487	38149492	+	1	NA	Intergenic	Intergenic	-1805	NM_023842	109620	Mm.355327	NM_023842	ENSMUSG00000054889	Dsp	2300002E22Rik|5730453H04Rik|AA407887|AA407888|AW109828|DP|rul	desmoplakin	protein-coding
mm_162269.1	chr1	10232934	10232938	-	1	NA	promoter-TSS (NM_001102430)	promoter-TSS (NM_001102430)	-266	NM_001102430	211673	Mm.229141	NM_001102430	ENSMUSG00000067851	Arfgef1	ARFGEP1|BIG1|D130059B05Rik|D730028O18Rik|P200	ADP-ribosylation factor guanine nucleotide-exchange factor 1(brefeldin A-inhibited)	protein-coding
mm_60112.1	chr7	35449155	35449167	+	1	NA	promoter-TSS (NM_001199016)	promoter-TSS (NM_001199016)	-18	NM_021291	30962	Mm.45874	NM_021291	ENSMUSG00000030492	Slc7a9	CSNU3	solute carrier family 7 (cationic amino acid transporter, y+ system), member 9	protein-coding
mm_106042.1	chr11	116079355	116079383	-	1	NA	3' UTR (NM_016852, exon 8 of 8)	3' UTR (NM_016852, exon 8 of 8)	-1408	NM_001009573	70450	Mm.259460	NM_001009573	ENSMUSG00000057948	Unc13d	2610108D09Rik|Jinx|Munc13-4|mFLJ00067	unc-13 homolog D (C. elegans)	protein-coding
mm_33588.1	chr4	132563492	132563510	+	1	NA	promoter-TSS (NM_001081211)	promoter-TSS (NM_001081211)	-566	NM_001081211	19204	Mm.89389	NM_001081211	ENSMUSG00000056529	Ptafr	PAFR	platelet-activating factor receptor	protein-coding
mm_145424.1	chr18	58572016	58572033	+	1	NA	intron (NM_001081072, intron 1 of 9)	intron (NM_001081072, intron 1 of 9)	15784	NM_001081072	225579	Mm.258517	NM_001081072	ENSMUSG00000024600	Slc27a6	4732438L20Rik|FACVL2|FATP6|VLCS-H1	solute carrier family 27 (fatty acid transporter), member 6	protein-coding
mm_137487.1	chr17	26941421	26941464	+	1	NA	promoter-TSS (NM_001281491)	promoter-TSS (NM_001281491)	-10	NM_001281491	240057	Mm.328888	NM_001281491	ENSMUSG00000067629	Syngap1	Gm1963|Syngap	synaptic Ras GTPase activating protein 1 homolog (rat)	protein-coding
mm_104378.1	chr11	94451836	94451863	-	1	NA	intron (NM_001177888, intron 9 of 34)	intron (NM_001177888, intron 9 of 34)	22349	NM_001177888	12291	Mm.29585	NM_009783	ENSMUSG00000020866	Cacna1g	Cav3.1d|[a]1G|a1G|alpha-1G|mKIAA1123	calcium channel, voltage-dependent, T type, alpha 1G subunit	protein-coding
mm_82080.1	chr9	122999466	122999487	+	1	NA	intron (NM_010620, intron 21 of 34)	intron (NM_010620, intron 21 of 34)	-21850	NM_025339	66079	Mm.482265	NM_025339	ENSMUSG00000066233	Tmem42	0610027O18Rik|4933429E06Rik|AV003444|D9Ertd662e	transmembrane protein 42	protein-coding
mm_63777.1	chr7	131560409	131560419	+	1	NA	promoter-TSS (NM_009774)	promoter-TSS (NM_009774)	44	NM_009774	12237	Mm.927	NM_009774	ENSMUSG00000066979	Bub3	AU019800|AU021329|AU043350|AW146323|C78067	BUB3 mitotic checkpoint protein	protein-coding
mm_63588.1	chr7	128134751	128134776	+	1	NA	intron (NM_021334, intron 8 of 29)	intron (NM_021334, intron 8 of 29)	5195	NM_021334	16411	Mm.22378	NM_021334	ENSMUSG00000030789	Itgax	AI449405|Cd11c|Cr4|N418	integrin alpha X	protein-coding
mm_61322.1	chr7	68189913	68189923	+	1	NA	intron (NM_010513, intron 9 of 20)	intron (NM_010513, intron 9 of 20)	74315	NM_030101	78444	Mm.425468	NM_030101	ENSMUSG00000030553	Pgpep1l	C330024D12Rik	pyroglutamyl-peptidase I-like	protein-coding
mm_101653.1	chr11	36631370	36631373	-	1	NA	intron (NM_011856, intron 2 of 28)	RMER4A|LTR|ERVK	312870	NM_001290702	23964	Mm.439889	NM_011856	ENSMUSG00000049336	Tenm2	Odz2|Odz3|Ten-2|Ten-m2	teneurin transmembrane protein 2	protein-coding
mm_120292.1	chr14	63136403	63136499	+	1	NA	exon (NM_007798, exon 5 of 10)	exon (NM_007798, exon 5 of 10)	13989	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_77803.1	chr9	3034198	3034209	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	4540	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_156543.1	chrX	151169674	151169689	+	1	NA	Intergenic	CpG	-28397	NM_001271679	279561	Mm.441474	NM_001271678	ENSMUSG00000041245	Wnk3	Prkwnk3|Wnk3-ps	WNK lysine deficient protein kinase 3	protein-coding
mm_27153.1	chr3	33082980	33082988	-	1	NA	promoter-TSS (NM_021483)	promoter-TSS (NM_021483)	76	NM_021483	58869	Mm.151332	NM_021483	ENSMUSG00000027674	Pex5l	1700016J08Rik|PXR2|Pex2|TRIP8b|pex5Rp	peroxisomal biogenesis factor 5-like	protein-coding
mm_37935.1	chr4	132922591	132922601	-	1	NA	promoter-TSS (NM_145553)	promoter-TSS (NM_145553)	-45	NM_001163792	230789	Mm.11473	NM_145553	ENSMUSG00000028878	Fam76a	-	family with sequence similarity 76, member A	protein-coding
mm_152176.1	chr19	7382945	7382976	-	1	NA	promoter-TSS (NM_001033139)	promoter-TSS (NM_001033139)	-43	NR_045703	654802	Mm.414924	NR_045703		1700105P06Rik	-	RIKEN cDNA 1700105P06 gene	ncRNA
mm_90363.1	chr10	127166025	127166043	+	1	NA	exon (NM_027739, exon 1 of 10)	exon (NM_027739, exon 1 of 10)	203	NM_001244618	14421	Mm.386762	NM_008080	ENSMUSG00000006731	B4galnt1	4933429D13Rik|Gal-NAc-T|GalNAc-T|GalNAcT|Galgt1|Ggm-2|Ggm2	beta-1,4-N-acetyl-galactosaminyl transferase 1	protein-coding
mm_109383.1	chr12	109721913	109721916	+	1	NA	promoter-TSS (NR_030270)	promoter-TSS (NR_030270)	-804	NR_030270	723856		NR_030270	ENSMUSG00000076006	Mir376c	Mirn376c|mir-376c	microRNA 376c	ncRNA
mm_53806.1	chr6	146888482	146888588	+	1	NA	promoter-TSS (NM_001170433)	promoter-TSS (NM_001170433)	41	NM_026221	67533	Mm.103382	NM_026221	ENSMUSG00000016487	Ppfibp1	4632409B19Rik|AW214454|AW261454	PTPRF interacting protein, binding protein 1 (liprin beta 1)	protein-coding
mm_133516.1	chr16	90816520	90816522	+	1	NA	Intergenic	Lx8|LINE|L1	-6108	NM_029497	207932	Mm.328688	NM_029497	ENSMUSG00000039929	Urb1	4921511H13Rik|5730405K23Rik|AA670781|AI645590|mKIAA0539	URB1 ribosome biogenesis 1 homolog (S. cerevisiae)	protein-coding
mm_170260.1	chr18	14732801	14732819	+	1	NA	intron (NM_001163609, intron 4 of 6)	MT2B1|LTR|ERVL	26659	NM_001163609	73677	Mm.87277	NM_001163609	ENSMUSG00000036743	Psma8	2410072D24Rik	proteasome (prosome, macropain) subunit, alpha type, 8	protein-coding
mm_93018.1	chr10	87809473	87809484	-	1	NA	Intergenic	Lx5c|LINE|L1	-48787	NM_001314010	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_69157.1	chr7	127144604	127144632	-	1	NA	Intergenic	Intergenic	-6795	NM_001037810	20737	Mm.283714	NM_009259	ENSMUSG00000051457	Spn	A630014B01Rik|Cd43|Galgp|Ly-48|Ly48	sialophorin	protein-coding
mm_111796.1	chr12	104865190	104865198	-	1	NA	promoter-TSS (NR_104437)	promoter-TSS (NR_104437)	-118	NR_104435	94040	Mm.244078	NM_053155	ENSMUSG00000021097	Clmn	9330188N17Rik|AI428889|AI788815|mKIAA1188	calmin	protein-coding
mm_88782.1	chr10	80602906	80602912	+	1	NA	promoter-TSS (NM_019575)	promoter-TSS (NM_019575)	27	NM_019575	56214	Mm.273170	NM_019575	ENSMUSG00000078441	Scamp4	2410022D05Rik|AI448940|AU022392|AW742369|Sc4	secretory carrier membrane protein 4	protein-coding
mm_69504.1	chr7	134266203	134266204	-	1	NA	TTS (NM_001081331)	TTS (NM_001081331)	-41106	NM_007400	11489	Mm.439714	NM_007400	ENSMUSG00000054555	Adam12	Mltna	a disintegrin and metallopeptidase domain 12 (meltrin alpha)	protein-coding
mm_38136.1	chr4	134704236	134704295	-	1	NA	promoter-TSS (NM_207237)	promoter-TSS (NM_207237)	25	NM_207237	230815	Mm.18905	NM_207237	ENSMUSG00000037306	Man1c1	AI593348	mannosidase, alpha, class 1C, member 1	protein-coding
mm_84939.1	chr9	82974953	82974987	-	1	NA	intron (NM_001081216, intron 2 of 39)	intron (NM_001081216, intron 2 of 39)	519	NM_001081216	83946	Mm.221688	NM_031879	ENSMUSG00000032253	Phip	2810004D21Rik|4632404O06Rik|Ndrp|Wdr11	pleckstrin homology domain interacting protein	protein-coding
mm_105420.1	chr11	103697062	103697063	-	1	NA	promoter-TSS (NR_102389)	promoter-TSS (NR_102389)	648	NM_019650	56494	Mm.195451	NM_019650	ENSMUSG00000020946	Gosr2	2310032N09Rik|C76855|Gs27|SNARE|membrin	golgi SNAP receptor complex member 2	protein-coding
mm_14304.1	chr2	129101075	129101083	+	1	NA	promoter-TSS (NM_009086)	promoter-TSS (NM_009086)	83	NM_009086	20017	Mm.259078	NM_009086	ENSMUSG00000027395	Polr1b	128kDa|D630020H17Rik|RPA116|RPA135|RPA2|Rpo1-2	polymerase (RNA) I polypeptide B	protein-coding
mm_24973.1	chr3	96757932	96757942	+	1	NA	intron (NM_026406, intron 2 of 8)	intron (NM_026406, intron 2 of 8)	30326	NM_026406	67845	Mm.386792	NM_026406	ENSMUSG00000028098	Rnf115	2610028E05Rik|AU042696|Zfp364	ring finger protein 115	protein-coding
mm_26169.1	chr3	138282786	138282805	+	1	NA	exon (NM_007409, exon 5 of 9)	exon (NM_007409, exon 5 of 9)	5150	NM_007409	11522	Mm.2409	NM_007409	ENSMUSG00000074207	Adh1	ADH-AA|AI194826|Adh-1|Adh-1-t|Adh-1e|Adh-1t|Adh-3e|Adh1-e|Adh1-t|Adh1tl|Adh3-e	alcohol dehydrogenase 1 (class I)	protein-coding
mm_112735.1	chr13	19256863	19256909	+	1	NA	Intergenic	Intergenic	138927	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_109771.1	chr12	118847306	118847311	+	1	NA	intron (NM_177082, intron 1 of 2)	intron (NM_177082, intron 1 of 2)	979	NM_177082	320145	Mm.51682	NM_177082	ENSMUSG00000048562	Sp8	D930049B17Rik|mBtd	trans-acting transcription factor 8	protein-coding
mm_26131.1	chr3	137868122	137868129	+	1	NA	intron (NM_001033155, intron 1 of 7)	intron (NM_001033155, intron 1 of 7)	450	NM_001033155	70604	Mm.256488	NM_001033155	ENSMUSG00000074212	Dnajb14	5730496F10Rik	DnaJ heat shock protein family (Hsp40) member B14	protein-coding
mm_44269.1	chr5	5664197	5664253	-	1	NA	promoter-TSS (NM_172447)	promoter-TSS (NM_172447)	7	NM_172447	207686	Mm.319007	NM_172447	ENSMUSG00000040473	Cfap69	4921525K03|A330021E22Rik|AI427898	cilia and flagella associated protein 69	protein-coding
mm_63878.1	chr7	136894599	136894639	+	1	NA	promoter-TSS (NM_008598)	promoter-TSS (NM_008598)	8	NM_008598	17314	Mm.440219	NM_008598	ENSMUSG00000054612	Mgmt	AGT|AI267024|Agat	O-6-methylguanine-DNA methyltransferase	protein-coding
mm_106361.1	chr11	118393934	118393940	-	1	NA	exon (NM_011150, exon 6 of 6)	exon (NM_011150, exon 6 of 6)	7994	NM_011150	19039	Mm.3152	NM_011150	ENSMUSG00000033880	Lgals3bp	90K|CyCAP|MAC-2BP|Ppicap|Tango10b	lectin, galactoside-binding, soluble, 3 binding protein	protein-coding
mm_114187.1	chr13	55714625	55714642	+	1	NA	promoter-TSS (NM_175150)	promoter-TSS (NM_175150)	-17	NM_175150	69672	Mm.294457	NM_175150	ENSMUSG00000021497	Txndc15	2310047H23Rik|AI854086|C5orf14|UNQ335	thioredoxin domain containing 15	protein-coding
mm_50731.1	chr6	52492502	52492508	+	1	NA	promoter-TSS (NR_046049)	promoter-TSS (NR_046049)	54	NR_046049	74304	Mm.490579	NR_046049	ENSMUSG00000107895	1700094M24Rik	-	RIKEN cDNA 1700094M24 gene	ncRNA
mm_99335.1	chr11	101468165	101468175	+	1	NA	promoter-TSS (NM_009708)	promoter-TSS (NM_009708)	-168	NM_009708	11858	Mm.378883	NM_009708	ENSMUSG00000001313	Rnd2	Arhn|Rohn	Rho family GTPase 2	protein-coding
mm_5149.1	chr1	9798986	9798996	-	1	NA	intron (NM_177547, intron 1 of 16)	intron (NM_177547, intron 1 of 16)	861	NM_177547	170755	Mm.336410	NM_133220	ENSMUSG00000025915	Sgk3	2510015P22Rik|A330005P07Rik|Cisk|fy|fz	serum/glucocorticoid regulated kinase 3	protein-coding
mm_63678.1	chr7	130546982	130547014	+	1	NA	exon (NM_001162855, exon 1 of 11)	exon (NM_001162855, exon 1 of 11)	383	NM_001162855	67872	Mm.21714	NM_001162855	ENSMUSG00000040331	Nsmce4a	2410003A14Rik	NSE4 homolog A, SMC5-SMC6 complex component	protein-coding
mm_68909.1	chr7	126457176	126457198	-	1	NA	exon (NM_007504, exon 7 of 23)	exon (NM_007504, exon 7 of 23)	5886	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_59092.1	chr7	19696530	19696554	+	1	NA	exon (NM_009696, exon 4 of 4)	exon (NM_009696, exon 4 of 4)	1856	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_147567.1	chr18	54990595	54990654	-	1	NA	promoter-TSS (NM_175751)	promoter-TSS (NM_175751)	-444	NM_175751	269023	Mm.192984	NM_175751	ENSMUSG00000052713	Zfp608	4932417D18Rik|D430007A19Rik|Znf608	zinc finger protein 608	protein-coding
mm_15613.1	chr2	160797167	160797176	+	1	NA	intron (NM_177263, intron 2 of 3)	intron (NM_177263, intron 2 of 3)	65861	NM_021280	18803	Mm.44463	NM_021280	ENSMUSG00000016933	Plcg1	AI894140|Cded|Plc-1|Plc-gamma1|Plcg-1	phospholipase C, gamma 1	protein-coding
mm_78830.1	chr9	44134207	44134254	+	1	NA	promoter-TSS (NM_023061)	promoter-TSS (NM_023061)	-428	NM_023061	84004	Mm.275003	NM_023061	ENSMUSG00000032135	Mcam	1-gicerin|AV025631|CD146|CD149|Muc18|s-endo|s-gicerin	melanoma cell adhesion molecule	protein-coding
mm_28175.1	chr3	88000234	88000240	-	1	NA	5' UTR (NM_001109758, exon 1 of 8)	5' UTR (NM_001109758, exon 1 of 8)	119	NM_007529	12032	Mm.4598	NM_007529	ENSMUSG00000004892	Bcan	Cspg7	brevican	protein-coding
mm_28147.1	chr3	87512577	87512585	-	1	NA	Intergenic	Intergenic	-12997	NM_001083318	27049	Mm.219460	NM_012051	ENSMUSG00000003382	Etv3	AI414410|METS|Pe1	ets variant 3	protein-coding
mm_113829.1	chr13	47066432	47066442	+	1	NA	intron (NM_172262, intron 11 of 20)	intron (NM_172262, intron 11 of 20)	22938	NM_172262	218214	Mm.31259	NM_172262	ENSMUSG00000038080	Kdm1b	4632428N09Rik|AI482520|Aof1	lysine (K)-specific demethylase 1B	protein-coding
mm_88394.1	chr10	76562257	76562267	+	1	NA	promoter-TSS (NM_029661)	promoter-TSS (NM_029661)	-10	NM_029661	76573	Mm.45611	NM_029661	ENSMUSG00000009115	Spatc1l	1700022B01Rik|1700027D21Rik|AA062323	spermatogenesis and centriole associated 1 like	protein-coding
mm_103777.1	chr11	82763875	82763885	-	1	NA	promoter-TSS (NM_025884)	promoter-TSS (NM_025884)	441	NM_009839	12467	Mm.4126	NM_009839	ENSMUSG00000020698	Cct6b	CCT-zeta-2|CCTzeta-2|Cctz-2|TCP-1-zeta-2	chaperonin containing Tcp1, subunit 6b (zeta)	protein-coding
mm_88222.1	chr10	70365360	70365391	+	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	-75293	NM_001143777	71721	Mm.477813	NM_024244	ENSMUSG00000043259	Fam13c	1200015N20Rik|C030038O19Rik|mKIAA1796	family with sequence similarity 13, member C	protein-coding
mm_4548.1	chr1	177258797	177258808	+	1	NA	Intergenic	CpG	-10035	NM_011785	23797	Mm.235194	NM_011785	ENSMUSG00000019699	Akt3	AI851531|D930002M15Rik|Nmf350	thymoma viral proto-oncogene 3	protein-coding
mm_166550.1	chr6	41216087	41216097	+	1	NA	Intergenic	Intergenic	-86180	NM_011646	22074	Mm.383263	NM_011646	ENSMUSG00000054106	Try4	0910001B19Rik|Td	trypsin 4	protein-coding
mm_15422.1	chr2	156863176	156863186	+	1	NA	promoter-TSS (NM_026124)	promoter-TSS (NM_026124)	59	NM_026124	67388	Mm.29264	NM_026124	ENSMUSG00000027637	1110008F13Rik	AI316789	RIKEN cDNA 1110008F13 gene	protein-coding
mm_9435.1	chr1	172522672	172522682	-	1	NA	intron (NM_027972, intron 1 of 11)	intron (NM_027972, intron 1 of 11)	1547	NM_027972	71870	Mm.78373	NM_027972	ENSMUSG00000026546	Cfap45	1700028D05Rik|Ccdc19|Nesg1	cilia and flagella associated protein 45	protein-coding
mm_101491.1	chr11	31671864	31671881	-	1	NA	promoter-TSS (NM_001024919)	promoter-TSS (NM_001024919)	-10	NM_001024919	69556	Mm.34183	NM_001024919	ENSMUSG00000044502	Bod1	2310022M17Rik|BOD2.1|Fam44b	biorientation of chromosomes in cell division 1	protein-coding
mm_49570.1	chr6	30640554	30640570	+	1	NA	exon (NM_025350, exon 3 of 10)	exon (NM_025350, exon 3 of 10)	1344	NM_025350	109697	Mm.25377	NM_025350	ENSMUSG00000054446	Cpa1	0910001L12Rik|Cpa	carboxypeptidase A1, pancreatic	protein-coding
mm_67806.1	chr7	98117756	98117766	-	1	NA	5' UTR (NM_008663, exon 2 of 49)	5' UTR (NM_008663, exon 2 of 49)	1732	NM_001256081	17921	Mm.1403	NM_008663	ENSMUSG00000030761	Myo7a	Hdb|Myo7|USH1B|nmf371|polka|sh-1|sh1	myosin VIIA	protein-coding
mm_105905.1	chr11	114983125	114983137	-	1	NA	3' UTR (NM_145437, exon 4 of 4)	3' UTR (NM_145437, exon 4 of 4)	6755	NM_145437	217305	Mm.275986	NM_145437	ENSMUSG00000034641	Cd300ld	4732429D16Rik|CLM5|Cd300ld1|LMIR4|MAIR-IV|clm-5	CD300 molecule like family member d	protein-coding
mm_18833.1	chr2	74716125	74716135	-	1	NA	promoter-TSS (NR_027899)	promoter-TSS (NR_027899)	0	NR_027899	73429	Mm.443313	NR_027899		Hoxd3os1	1700064D17Rik|1700109F18Rik	homeobox D3, opposite strand 1	ncRNA
mm_92183.1	chr10	68026712	68026718	-	1	NA	intron (NM_001081346, intron 10 of 12)	intron (NM_001081346, intron 10 of 12)	47117	NM_001081346	170799	Mm.209844	NM_133244	ENSMUSG00000037846	Rtkn2	B130039D23Rik|Mbf|Plekhk1	rhotekin 2	protein-coding
mm_25252.1	chr3	104645033	104645036	+	1	NA	intron (NM_009196, intron 1 of 4)	ID_B1|SINE|B4	6370	NM_009196	20501	Mm.9086	NM_009196	ENSMUSG00000032902	Slc16a1	AL022710|Mct1	solute carrier family 16 (monocarboxylic acid transporters), member 1	protein-coding
mm_104570.1	chr11	96943787	96943797	-	1	NA	promoter-TSS (NR_003293)	promoter-TSS (NR_003293)	227	NM_134021	103711	Mm.254704	NM_134021	ENSMUSG00000018659	Pnpo	AI415282	pyridoxine 5'-phosphate oxidase	protein-coding
mm_51906.1	chr6	91157084	91157099	+	1	NA	intron (NM_144919, intron 1 of 9)	intron (NM_144919, intron 1 of 9)	276	NM_144919	232232	Mm.206218	NM_144919	ENSMUSG00000034245	Hdac11	-	histone deacetylase 11	protein-coding
mm_46168.1	chr5	96210006	96210026	-	1	NA	promoter-TSS (NM_053158)	promoter-TSS (NM_053158)	-99	NM_001039084	94061	Mm.295499	NM_053158	ENSMUSG00000029486	Mrpl1	2410002L03Rik|5830418D04Rik|AI462572|L1mt	mitochondrial ribosomal protein L1	protein-coding
mm_154093.1	chr19	56822162	56822220	-	1	NA	Intergenic	CpG	-4018	NM_001002238	83561	Mm.247541	NM_031387	ENSMUSG00000025081	Tdrd1	MTR-1	tudor domain containing 1	protein-coding
mm_31481.1	chr4	52439236	52439287	+	1	NA	promoter-TSS (NR_045175)	promoter-TSS (NR_045175)	40	NM_001301412	14211	Mm.2999	NM_008017	ENSMUSG00000028312	Smc2	5730502P04Rik|AI255214|AW545314|CAP-E|CAPE|Fin16|SMC-2|Smc2l1	structural maintenance of chromosomes 2	protein-coding
mm_56418.1	chr6	97252724	97252737	-	1	NA	promoter-TSS (NM_001081157)	promoter-TSS (NM_001081157)	50	NM_001081157	320502	Mm.68163	NM_001081157	ENSMUSG00000044086	Lmod3	5430424A14Rik	leiomodin 3 (fetal)	protein-coding
mm_165914.1	chr4	57916508	57916533	-	1	NA	promoter-TSS (NM_178727)	promoter-TSS (NM_178727)	-256	NM_178727	242484	Mm.23214	NM_178727	ENSMUSG00000052117	D630039A03Rik	-	RIKEN cDNA D630039A03 gene	protein-coding
mm_97596.1	chr11	78948343	78948357	+	1	NA	exon (NM_010927, exon 17 of 27)	exon (NM_010927, exon 17 of 27)	23059	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_117.1	chr1	9797796	9797809	+	1	NA	promoter-TSS (NM_133220)	promoter-TSS (NM_133220)	-328	NM_133220	170755	Mm.336410	NM_133220	ENSMUSG00000025915	Sgk3	2510015P22Rik|A330005P07Rik|Cisk|fy|fz	serum/glucocorticoid regulated kinase 3	protein-coding
mm_120132.1	chr14	60209419	60209425	+	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	19493	NR_030458	751526		NR_030458	ENSMUSG00000076270	Mir719	Mirn719|mmu-mir-719	microRNA 719	ncRNA
mm_14984.1	chr2	152177728	152177739	+	1	NA	Intergenic	Intergenic	34124	NM_009328	21407	Mm.3881	NM_009328	ENSMUSG00000068079	Tcf15	Meso1|bHLH-EC2	transcription factor 15	protein-coding
mm_90872.1	chr10	8945282	8945294	-	1	NA	Intergenic	Intergenic	-59218	NM_175155	70097	Mm.338275	NM_175155	ENSMUSG00000015305	Sash1	1100001C18Rik|2500002E12Rik|A330076K04Rik|mKIAA0790	SAM and SH3 domain containing 1	protein-coding
mm_128240.1	chr15	36608651	36608661	-	1	NA	5' UTR (NM_008774, exon 1 of 15)	5' UTR (NM_008774, exon 1 of 15)	317	NM_008774	18458	Mm.371570	NM_008774	ENSMUSG00000022283	Pabpc1	PABP|Pabp1|PabpI|Pabpl1|ePAB	poly(A) binding protein, cytoplasmic 1	protein-coding
mm_50568.1	chr6	49050111	49050133	+	1	NA	intron (NM_053110, intron 6 of 10)	ID_B1|SINE|B4	13604	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_73395.1	chr8	105827754	105827769	+	1	NA	promoter-TSS (NM_024445)	promoter-TSS (NM_024445)	17	NM_024445	72236	Mm.386810	NM_024445	ENSMUSG00000031893	Tsnaxip1	1700016K08Rik|TXI1	translin-associated factor X (Tsnax) interacting protein 1	protein-coding
mm_165422.1	chr2	151302013	151302035	+	1	NA	promoter-TSS (NR_040747)	promoter-TSS (NR_040747)	-15	NR_040747	74660	Mm.170672	NR_040747	ENSMUSG00000087609	4930442J19Rik	1700029E19Rik|Gm14152|OTTMUSG00000015807	RIKEN cDNA 4930442J19 gene	ncRNA
mm_52836.1	chr6	121636259	121636265	+	1	NA	promoter-TSS (NM_175628)	promoter-TSS (NM_175628)	89	NM_175628	232345	Mm.30151	NM_175628	ENSMUSG00000030111	A2m	A2mp	alpha-2-macroglobulin	protein-coding
mm_162818.1	chr10	79984657	79984659	+	1	NA	promoter-TSS (NM_001003949)	promoter-TSS (NM_001003949)	-328	NM_001003949	216157	Mm.29442	NM_001003949	ENSMUSG00000013858	Tmem259	AC087114.7gm2|ORF61|R32184_3|mFLJ00277	transmembrane protein 259	protein-coding
mm_118070.1	chr13	102906995	102907000	-	1	NA	intron (NM_175171, intron 4 of 28)	intron (NM_175171, intron 4 of 28)	146742	NR_130171	76624	Mm.426384	NR_130171	ENSMUSG00000091906	1700099I09Rik	-	RIKEN cDNA 1700099I09 gene	ncRNA
mm_65303.1	chr7	24672069	24672077	-	1	NA	promoter-TSS (NM_019981)	promoter-TSS (NM_019981)	-23	NM_019981	56746	Mm.23385	NM_019981	ENSMUSG00000062773	Tex101	1700008H15Rik|AI429076|TES101RP	testis expressed gene 101	protein-coding
mm_28686.1	chr3	95402796	95402851	-	1	NA	promoter-TSS (NR_015490)	promoter-TSS (NR_015490)	18	NR_015490	67654	Mm.75066	NR_015490	ENSMUSG00000105734	4930558C23Rik	-	RIKEN cDNA 4930558C23 gene	ncRNA
mm_75452.1	chr8	47710621	47710624	-	1	NA	3' UTR (NM_172407, exon 3 of 3)	3' UTR (NM_172407, exon 3 of 3)	3309	NM_172407	70925	Mm.393807	NM_172407	ENSMUSG00000038069	Cdkn2aip	4921511I16Rik|AW208986|CARF	CDKN2A interacting protein	protein-coding
mm_127744.1	chr15	103453783	103453860	+	1	NA	promoter-TSS (NM_153505)	promoter-TSS (NM_153505)	-4	NM_153505	105855	Mm.30805	NM_153505	ENSMUSG00000022488	Nckap1l	4930568P13Rik|AI463083|Hem1|Hemp1	NCK associated protein 1 like	protein-coding
mm_62890.1	chr7	115465343	115465348	+	1	NA	Intergenic	(CAGTG)n|Simple_repeat|Simple_repeat	336264	NM_001277328	20679	Mm.323365	NM_011445	ENSMUSG00000051910	Sox6	AI987981|SOX-LZ	SRY (sex determining region Y)-box 6	protein-coding
mm_122916.1	chr14	54958679	54958695	-	1	NA	exon (NM_010856, exon 15 of 39)	exon (NM_010856, exon 15 of 39)	7920	NM_001164171	17888	Mm.290003	NM_010856	ENSMUSG00000040752	Myh6	A830009F23Rik|AA517445|Myhc-a|Myhca|alpha-MHC	myosin, heavy polypeptide 6, cardiac muscle, alpha	protein-coding
mm_145577.1	chr18	60963616	60963626	+	1	NA	promoter-TSS (NM_001286809)	promoter-TSS (NM_001286809)	67	NM_001286809	12322	Mm.131530	NM_009792	ENSMUSG00000024617	Camk2a	CaMKII|R74975|mKIAA0968	calcium/calmodulin-dependent protein kinase II alpha	protein-coding
mm_153820.1	chr19	46304543	46304564	-	1	NA	promoter-TSS (NM_001177369)	promoter-TSS (NM_001177369)	-184	NM_001177369	18034	Mm.102365	NM_019408	ENSMUSG00000025225	Nfkb2	NF-kappaB2|lyt|p49|p49/p100|p50B|p52	nuclear factor of kappa light polypeptide gene enhancer in B cells 2, p49/p100	protein-coding
mm_106905.1	chr12	8015469	8015496	+	1	NA	exon (NM_009693, exon 29 of 29)	exon (NM_009693, exon 29 of 29)	37805	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_135158.1	chr16	35858659	35858670	-	1	NA	exon (NM_001039530, exon 6 of 17)	exon (NM_001039530, exon 6 of 17)	12718	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_42204.1	chr5	112326803	112326816	+	1	NA	intron (NM_018783, intron 1 of 13)	intron (NM_018783, intron 1 of 13)	440	NM_018783	54723	Mm.172947	NM_018783	ENSMUSG00000029345	Tfip11	2810002G02Rik|AF097181|AW046167|Srr1|TIP33|Tip39	tuftelin interacting protein 11	protein-coding
mm_102812.1	chr11	68956196	68956229	-	1	NA	intron (NM_177566, intron 1 of 15)	intron (NM_177566, intron 1 of 15)	646	NM_177566	442801	Mm.376147	NM_177566	ENSMUSG00000052921	Arhgef15	D130071N09|D530030K12Rik|E5	Rho guanine nucleotide exchange factor (GEF) 15	protein-coding
mm_170538.1	chr19	38874784	38874813	-	1	NA	intron (NM_145952, intron 2 of 12)	RLTRETN_Mm|LTR|ERVK	38219	NM_145952	209478	Mm.391153	NM_145952	ENSMUSG00000048720	Tbc1d12	BC033574	TBC1D12: TBC1 domain family, member 12	protein-coding
mm_35386.1	chr4	33248501	33248518	-	1	NA	5' UTR (NM_001033225, exon 1 of 2)	5' UTR (NM_001033225, exon 1 of 2)	278	NM_001033225	108767	Mm.27769	NM_001033225	ENSMUSG00000040128	Pnrc1	5730463C12Rik|B4-2|PRR2|Prol2	proline-rich nuclear receptor coactivator 1	protein-coding
mm_149384.1	chr19	11381971	11381993	+	1	NA	intron (NM_001310331, intron 3 of 6)	RMER6A|LTR|ERVK	6494	NM_001310331	666907		NM_001310331	ENSMUSG00000101389	Ms4a4a	EG666907	membrane-spanning 4-domains, subfamily A, member 4A	protein-coding
mm_21113.1	chr2	153444587	153444615	-	1	NA	promoter-TSS (NM_001001986)	promoter-TSS (NM_001001986)	-122	NM_001001986	329540	Mm.50600	NM_001001986	ENSMUSG00000061411	Nol4l	4931410H15|8430427H17Rik|AI429157|Gm1636	nucleolar protein 4-like	protein-coding
mm_155276.1	chrX	61120489	61120499	+	1	NA	intron (NR_030706, intron 4 of 7)	intron (NR_030706, intron 4 of 7)	4116	NR_030706	331424	Mm.127263	NM_177916	ENSMUSG00000071753	C230004F18Rik	-	RIKEN cDNA C230004F18 gene	ncRNA
mm_98532.1	chr11	95006351	95006369	+	1	NA	3' UTR (NM_172261, exon 10 of 10)	3' UTR (NM_172261, exon 10 of 10)	-3519	NM_146025	217125	Mm.297199	NM_146025	ENSMUSG00000047181	Samd14	AI839049|AI854782|BC034054	sterile alpha motif domain containing 14	protein-coding
mm_29275.1	chr3	107554992	107555043	-	1	NA	promoter-TSS (NM_026261)	promoter-TSS (NM_026261)	56	NM_026261	67591	Mm.55982	NM_026261	ENSMUSG00000055891	Ubl4b	4930522D07Rik	ubiquitin-like 4B	protein-coding
mm_115327.1	chr13	112464522	112464529	+	1	NA	intron (NM_010560, intron 1 of 16)	CpG	455	NM_010560	16195	Mm.4364	NM_010560	ENSMUSG00000021756	Il6st	5133400A03Rik|AA389424|BB405851|CD130|D13Ertd699e|gp130	interleukin 6 signal transducer	protein-coding
mm_32924.1	chr4	119195280	119195293	+	1	NA	promoter-TSS (NM_024462)	promoter-TSS (NM_024462)	-24	NM_024462	69216	Mm.36697	NM_024462	ENSMUSG00000028643	Svbp	2410005K17Rik|AI851162|Ccdc23	small vasohibin binding protein	protein-coding
mm_10359.1	chr2	11697994	11697997	+	1	NA	Intergenic	Lx8|LINE|L1	-7298	NM_001271498	16169	Mm.200196	NM_008358	ENSMUSG00000023206	Il15ra	AA690181|IL-15RA	interleukin 15 receptor, alpha chain	protein-coding
mm_44704.1	chr5	30623476	30623485	-	1	NA	3' UTR (NM_010608, exon 2 of 2)	3' UTR (NM_010608, exon 2 of 2)	-24456	NR_049199	100885838		NR_049199	ENSMUSG00000093710	Mir5625	Gm23930|mmu-mir-5625	microRNA 5625	ncRNA
mm_100424.1	chr11	119444254	119444263	+	1	NA	Intergenic	Intergenic	-47089	NM_001164636	338371	Mm.271946	NM_177394	ENSMUSG00000039850	Endov	A730011L01Rik	endonuclease V	protein-coding
mm_169876.1	chr16	37719019	37719036	+	1	NA	Intergenic	RLTR16|LTR|ERVK	-58028	NM_008047	14314	Mm.182434	NM_008047	ENSMUSG00000022816	Fstl1	AI316791|AW107808|Fstl|TSC-36	follistatin-like 1	protein-coding
mm_86490.1	chr10	5593719	5593739	+	1	NA	promoter-TSS (NM_026793)	promoter-TSS (NM_026793)	1	NM_026793	68632	Mm.338242	NM_026793	ENSMUSG00000046916	Myct1	1110020B04Rik|AI225941|AI642973|Mtmc1	myc target 1	protein-coding
mm_118493.1	chr14	13284754	13284764	+	1	NA	promoter-TSS (NM_028052)	promoter-TSS (NM_028052)	-21	NM_028052	72003	Mm.317515	NM_028052	ENSMUSG00000056296	Synpr	1500003F20Rik|SPO	synaptoporin	protein-coding
mm_58095.1	chr6	137519881	137519900	-	1	NA	promoter-TSS (NM_001271589)	promoter-TSS (NM_001271589)	5	NM_001271589	13860	Mm.235346	NM_007945	ENSMUSG00000015766	Eps8	AW261790	epidermal growth factor receptor pathway substrate 8	protein-coding
mm_97105.1	chr11	74619595	74619643	+	1	NA	promoter-TSS (NM_001013784)	promoter-TSS (NM_001013784)	14	NM_001013784	432582	Mm.274369	NM_001013784	ENSMUSG00000069814	Ccdc92b	E130309D14Rik	coiled-coil domain containing 92B	protein-coding
mm_40046.1	chr5	33983091	33983100	+	1	NA	promoter-TSS (NM_001310547)	promoter-TSS (NM_001310547)	-338	NM_001033458	381633	Mm.4923	NM_001033458	ENSMUSG00000070858	Gm1673	-	predicted gene 1673	protein-coding
mm_20221.1	chr2	125775608	125775629	-	1	NA	exon (NM_177608, exon 2 of 18)	exon (NM_177608, exon 2 of 18)	7252	NM_177608	70354	Mm.138091	NM_133725	ENSMUSG00000035093	Secisbp2l	3110001I20Rik|AI504340|C630011I23	SECIS binding protein 2-like	protein-coding
mm_23395.1	chr3	57779454	57779468	+	1	NA	exon (NM_011883, exon 4 of 9)	exon (NM_011883, exon 4 of 9)	43399	NR_130743	24017	Mm.274360	NM_011883	ENSMUSG00000036503	Rnf13	2010001H16Rik|Rzf	ring finger protein 13	protein-coding
mm_30201.1	chr3	144720277	144720307	-	1	NA	promoter-TSS (NM_019464)	promoter-TSS (NM_019464)	43	NM_001282042	54673	Mm.271775	NM_019464	ENSMUSG00000037062	Sh3glb1	AA409932|AI314629|AU015566|Bif-1|mKIAA0491	SH3-domain GRB2-like B1 (endophilin)	protein-coding
mm_33592.1	chr4	132564052	132564076	+	1	NA	promoter-TSS (NM_001081211)	promoter-TSS (NM_001081211)	-3	NM_001081211	19204	Mm.89389	NM_001081211	ENSMUSG00000056529	Ptafr	PAFR	platelet-activating factor receptor	protein-coding
mm_81218.1	chr9	107587867	107587889	+	1	NA	TTS (NM_178020)	TTS (NM_178020)	160	NM_025903	15983	Mm.215335	NM_025903	ENSMUSG00000010048	Ifrd2	1810034A24Rik|AA470234|AI838527|SKMc15	interferon-related developmental regulator 2	protein-coding
mm_131039.1	chr16	3884658	3884680	+	1	NA	promoter-TSS (NM_001290689)	promoter-TSS (NM_001290689)	50	NM_001290689	74763	Mm.28403	NM_029090	ENSMUSG00000005982	Naa60	1200013P24Rik|AI315146|Nat15	N(alpha)-acetyltransferase 60, NatF catalytic subunit	protein-coding
mm_67686.1	chr7	89404145	89404149	-	1	NA	promoter-TSS (NM_008055)	promoter-TSS (NM_008055)	-219	NM_008055	14366	Mm.86755	NM_008055	ENSMUSG00000049791	Fzd4	Fz4	frizzled class receptor 4	protein-coding
mm_16459.1	chr2	180589424	180589479	+	1	NA	promoter-TSS (NM_031373)	promoter-TSS (NM_031373)	44	NM_031373	72075	Mm.250418	NM_031373	ENSMUSG00000049401	Ogfr	2010013E17Rik	opioid growth factor receptor	protein-coding
mm_114783.1	chr13	88827495	88827495	+	1	NA	intron (NM_010103, intron 1 of 9)	intron (NM_010103, intron 1 of 9)	6023	NM_001037987	13612	Mm.125580	NM_010103	ENSMUSG00000034488	Edil3	Del-1|Del1	EGF-like repeats and discoidin I-like domains 3	protein-coding
mm_35585.1	chr4	41774165	41774176	-	1	NA	promoter-TSS (NM_001164045)	promoter-TSS (NM_001164045)	6	NM_001164044	20301	Mm.335946	NM_011336	ENSMUSG00000073888	Ccl27a	ALP|AW558992|CTACK|CTAK|Ccl27|ESkine|ILC|PESKY|Scya27|Scya27a	chemokine (C-C motif) ligand 27A	protein-coding
mm_151993.1	chr19	5874975	5874993	-	1	NA	intron (NM_026169, intron 1 of 10)	intron (NM_026169, intron 1 of 10)	224	NM_026169	67457	Mm.202092	NM_026169	ENSMUSG00000024816	Frmd8	1200004M23Rik|2310035N23Rik|4931429L16Rik|AU018809	FERM domain containing 8	protein-coding
mm_75379.1	chr8	45382109	45382130	-	1	NA	5' UTR (NM_153535, exon 1 of 14)	5' UTR (NM_153535, exon 1 of 14)	172	NM_153535	212326	Mm.51259	NM_153535	ENSMUSG00000070044	Fam149a	AW213256|mKIAA4166	family with sequence similarity 149, member A	protein-coding
mm_1971.1	chr1	86504612	86504626	+	1	NA	Intergenic	Intergenic	-22117	NM_008972	19231	Mm.19187	NM_008972	ENSMUSG00000026238	Ptma	Thym	prothymosin alpha	protein-coding
mm_104646.1	chr11	97540358	97540382	-	1	NA	intron (NM_018873, intron 4 of 19)	intron (NM_018873, intron 4 of 19)	34756	NM_018873	56013	Mm.342665	NM_018873	ENSMUSG00000038453	Srcin1	P140|SNIP|mKIAA1684|p140Cap	SRC kinase signaling inhibitor 1	protein-coding
mm_106164.1	chr11	116654039	116654068	-	1	NA	5' UTR (NM_030206, exon 1 of 4)	5' UTR (NM_030206, exon 1 of 4)	260	NM_030206	114886	Mm.34598	NM_030206	ENSMUSG00000020810	Cygb	3110001K20Rik|HGb|Staap	cytoglobin	protein-coding
mm_55490.1	chr6	69500816	69500841	-	1	NA	Intergenic	Intergenic	-173654	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_144965.1	chr18	37824091	37824103	+	1	NA	intron (NM_033583, intron 1 of 3)	intron (NM_033583, intron 1 of 3)	4551	NM_033583	93708	Mm.247203	NM_033583	ENSMUSG00000102543	Pcdhgc5	-	protocadherin gamma subfamily C, 5	protein-coding
mm_166796.1	chr7	3330805	3330816	+	1	NA	3' UTR (NM_011102, exon 18 of 18)	3' UTR (NM_011102, exon 18 of 18)	-5775	NM_133189	81904	Mm.214994	NM_133189	ENSMUSG00000069806	Cacng7	-	calcium channel, voltage-dependent, gamma subunit 7	protein-coding
mm_64769.1	chr7	4995299	4995319	-	1	NA	intron (NM_026741, intron 1 of 1)	intron (NM_026741, intron 1 of 1)	792	NM_026741	68490	Mm.76400	NM_026741	ENSMUSG00000051550	Zfp579	1110003A17Rik|Znf579	zinc finger protein 579	protein-coding
mm_65853.1	chr7	29281939	29281973	-	1	NA	promoter-TSS (NM_001082548)	promoter-TSS (NM_001082548)	21	NM_001082548	20733	Mm.295230	NM_011464	ENSMUSG00000074227	Spint2	AL024025|C76321|HAI-2	serine protease inhibitor, Kunitz type 2	protein-coding
mm_68721.1	chr7	120145287	120145292	-	1	NA	promoter-TSS (NM_011775)	promoter-TSS (NM_011775)	2	NM_011775	22787	Mm.6510	NM_011775	ENSMUSG00000030911	Zp2	Zp-2	zona pellucida glycoprotein 2	protein-coding
mm_74807.1	chr8	22633196	22633258	-	1	NA	intron (NM_011130, intron 11 of 13)	intron (NM_011130, intron 11 of 13)	3582	NR_027886	68074	Mm.463136	NR_027886		A930013F10Rik	-	RIKEN cDNA A930013F10 gene	ncRNA
mm_83757.1	chr9	51943372	51943375	-	1	NA	3' UTR (NM_007996, exon 4 of 4)	3' UTR (NM_007996, exon 4 of 4)	20229	NM_007996	14148	Mm.1061	NM_007996	ENSMUSG00000032051	Fdx1	-	ferredoxin 1	protein-coding
mm_50037.1	chr6	41141145	41141182	+	1	NA	Intergenic	Intergenic	-105654	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_61001.1	chr7	49304282	49304288	+	1	NA	intron (NM_175272, intron 1 of 37)	intron (NM_175272, intron 1 of 37)	58096	NM_175272	78286	Mm.333881	NM_175272	ENSMUSG00000052512	Nav2	5330421F07Rik|AU067780|BQ960892|HELAD1|POMFIL2|RAINB1|RAINB2|Unc53H2|mKIAA3015	neuron navigator 2	protein-coding
mm_159935.1	chr6	71912395	71912395	+	1	NA	intron (NM_009088, intron 1 of 33)	intron (NM_009088, intron 1 of 33)	3342	NM_009088	20019	Mm.135581	NM_009088	ENSMUSG00000049553	Polr1a	194kDa|3010014K16Rik|RPA194|Rpo1-4|mRPA1	polymerase (RNA) I polypeptide A	protein-coding
mm_77819.1	chr9	3335471	3335501	+	1	NA	intron (NM_026303, intron 1 of 11)	intron (NM_026303, intron 1 of 11)	255	NM_026303	67667	Mm.116968	NM_026303	ENSMUSG00000025899	Alkbh8	4930562C03Rik|8030431D03Rik|9430088N01Rik|Abh8	alkB homolog 8, tRNA methyltransferase	protein-coding
mm_142321.1	chr17	43361352	43361356	-	1	NA	Intergenic	Intergenic	-28112	NM_001081178	224792	Mm.23478	NM_001081178	ENSMUSG00000056492	Adgrf5	8430401C09Rik|9330185D23|AI528491|Gpr116|mKIAA0758	adhesion G protein-coupled receptor F5	protein-coding
mm_63322.1	chr7	126942038	126942053	+	1	NA	intron (NM_172747, intron 4 of 5)	intron (NM_172747, intron 4 of 5)	7536	NM_001347657	233879	Mm.444143	NM_001039645	ENSMUSG00000046378	Asphd1	A830007L07Rik|Gm168	aspartate beta-hydroxylase domain containing 1	protein-coding
mm_96049.1	chr11	59559731	59559742	+	1	NA	intron (NM_145827, intron 7 of 9)	intron (NM_145827, intron 7 of 9)	12002	NM_001011789	257962	Mm.377316	NM_001011789	ENSMUSG00000059610	Olfr222	MOR256-45P	olfactory receptor 222	protein-coding
mm_99919.1	chr11	110399162	110399173	+	1	NA	promoter-TSS (NM_011943)	promoter-TSS (NM_011943)	45	NM_011943	26399	Mm.14487	NM_011943	ENSMUSG00000020623	Map2k6	MEK6|MKK6|Prkmk6|SAPKK3	mitogen-activated protein kinase kinase 6	protein-coding
mm_118115.1	chr13	103921903	103921914	-	1	NA	Intergenic	Intergenic	-1322	NM_001005868	59079	Mm.277354	NM_021563	ENSMUSG00000021709	Erbin	1700028E05Rik|Erbb2ip|mKIAA1225	Erbb2 interacting protein	protein-coding
mm_92566.1	chr10	79874566	79874587	-	1	NA	promoter-TSS (NM_001170935)	promoter-TSS (NM_001170935)	58	NM_181681	216152	Mm.29678	NM_181681	ENSMUSG00000035835	Plppr3	Lppr3|Prg2	phospholipid phosphatase related 3	protein-coding
mm_52761.1	chr6	120836202	120836257	+	1	NA	promoter-TSS (NM_153516)	promoter-TSS (NM_153516)	-1	NM_153516	94044	Mm.27990	NM_153516	ENSMUSG00000009112	Bcl2l13	BCL-RAMBO|E430016C20Rik|Mil-1|Mil1	BCL2-like 13 (apoptosis facilitator)	protein-coding
mm_128027.1	chr15	25149073	25149100	-	1	NA	Intergenic	RSINE1|SINE|B4	264678	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	brain abundant, membrane attached signal protein 1	protein-coding
mm_55066.1	chr6	49050496	49050510	-	1	NA	exon (NM_053110, exon 7 of 11)	exon (NM_053110, exon 7 of 11)	13985	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_131670.1	chr16	20672717	20672859	+	1	NA	promoter-TSS (NM_145941)	promoter-TSS (NM_145941)	61	NM_001304432	208643	Mm.260256	NM_145941	ENSMUSG00000045983	Eif4g1	E030015G23Rik|eIF-4-gamma 1|eIF-4G 1|eIF-4G1|eIF4GI	eukaryotic translation initiation factor 4, gamma 1	protein-coding
mm_26947.1	chr3	20266524	20266524	-	1	NA	intron (NM_029706, intron 3 of 10)	intron (NM_029706, intron 3 of 10)	9209	NM_029706	76703	Mm.34692	NM_029706	ENSMUSG00000011463	Cpb1	0910001A18Rik|1810063F02Rik|2210008M23Rik|AI504870	carboxypeptidase B1 (tissue)	protein-coding
mm_31475.1	chr4	50789616	50789622	+	1	NA	Intergenic	Lx7|LINE|L1	-427059	NM_001162865	74914	Mm.159368	NM_001162865	ENSMUSG00000039555	Cylc2	4930488P18Rik	cylicin, basic protein of sperm head cytoskeleton 2	protein-coding
mm_120315.1	chr14	63142707	63142750	+	1	NA	3' UTR (NM_007798, exon 10 of 10)	3' UTR (NM_007798, exon 10 of 10)	20266	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_78898.1	chr9	44641353	44641355	+	1	NA	TTS (NM_001110826)	TTS (NM_001110826)	-31879	NM_001277851	58866	Mm.45380	NM_021481	ENSMUSG00000032098	Treh	2210412M19Rik	trehalase (brush-border membrane glycoprotein)	protein-coding
mm_88275.1	chr10	75037245	75037288	+	1	NA	5' UTR (NM_029781, exon 1 of 11)	5' UTR (NM_029781, exon 1 of 11)	177	NM_029781	76877	Mm.133593	NM_029781	ENSMUSG00000020175	Rab36	6330593L16Rik|AW047545	RAB36, member RAS oncogene family	protein-coding
mm_113564.1	chr13	38204929	38204962	+	1	NA	promoter-TSS (NM_026382)	promoter-TSS (NM_026382)	6	NM_026382	67797	Mm.250783	NM_026382	ENSMUSG00000021431	Snrnp48	1110050F08Rik|6530403A03Rik|C6orf151	small nuclear ribonucleoprotein 48 (U11/U12)	protein-coding
mm_166590.1	chr6	56569152	56569181	-	1	NA	Intergenic	Intergenic	135533	NM_025520	66373	Mm.25642	NM_025520	ENSMUSG00000091625	Lsm5	2010208O10Rik|2310034K10Rik	LSM5 homolog, U6 small nuclear RNA and mRNA degradation associated	protein-coding
mm_79236.1	chr9	50499255	50499266	+	1	NA	exon (NM_029639, exon 2 of 4)	exon (NM_029639, exon 2 of 4)	4735	NM_029639	76509	Mm.29959	NM_029639	ENSMUSG00000032068	Plet1	0610037B23Rik|1600029D21Rik|AA407923|AU043048	placenta expressed transcript 1	protein-coding
mm_113149.1	chr13	24741211	24741237	+	1	NA	Intergenic	Intergenic	20713	NM_020567	57441	Mm.12239	NM_020567	ENSMUSG00000006715	Gmnn	AW546347|Gem	geminin	protein-coding
mm_143848.1	chr17	84140957	84140985	-	1	NA	Intergenic	Intergenic	46976	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_129337.1	chr15	77836242	77836268	-	1	NA	intron (NM_022410, intron 1 of 40)	intron (NM_022410, intron 1 of 40)	5920	NM_022410	17886	Mm.29677	NM_022410	ENSMUSG00000022443	Myh9	Fltn|Myhn-1|Myhn1|NMHCIIA|NMMHC-A|NMMHC-IIA|TU72.6	myosin, heavy polypeptide 9, non-muscle	protein-coding
mm_34585.1	chr4	150148906	150148916	+	1	NA	promoter-TSS (NM_001085529)	promoter-TSS (NM_001085529)	-61	NM_001085529	435818	Mm.359648	NM_001085529	ENSMUSG00000062064	Slc2a7	OTTMUSG00000010396	solute carrier family 2 (facilitated glucose transporter), member 7	protein-coding
mm_105226.1	chr11	102296619	102296681	-	1	NA	promoter-TSS (NM_001098836)	promoter-TSS (NM_001098836)	-21	NM_001098837	217218	Mm.390381	NM_001098836	ENSMUSG00000059995	Atxn7l3	E030022H21Rik	ataxin 7-like 3	protein-coding
mm_155769.1	chrX	96242907	96242911	+	1	NA	promoter-TSS (NR_029801)	promoter-TSS (NR_029801)	92	NR_029801	723814		NR_029801	ENSMUSG00000076066	Mir223	Mirn223|miR-223|mmu-mir-223	microRNA 223	ncRNA
mm_28043.1	chr3	83863065	83863075	-	1	NA	Intergenic	Intergenic	-21462	NM_011905	24088	Mm.87596	NM_011905	ENSMUSG00000027995	Tlr2	Ly105	toll-like receptor 2	protein-coding
mm_97789.1	chr11	82827761	82827766	+	1	NA	intron (NM_001164571, intron 1 of 5)	RLTR1B|LTR|ERV1	1280	NM_026097	67338	Mm.341608	NM_026097	ENSMUSG00000020696	Rffl	1700051E09Rik|4930516L10Rik|BG080975|Carp2	ring finger and FYVE like domain containing protein	protein-coding
mm_37316.1	chr4	119359787	119359810	-	1	NA	promoter-TSS (NM_001270446)	promoter-TSS (NM_001270446)	96	NM_001270446	73332	Mm.425204	NM_028506	ENSMUSG00000028637	Ccdc30	1700001O02Rik|1700041C02Rik|1700111D19Rik|4930445I03Rik	coiled-coil domain containing 30	protein-coding
mm_72765.1	chr8	85602025	85602037	+	1	NA	Intergenic	Intergenic	-46760	NM_019794	56445	Mm.475573	NM_019794	ENSMUSG00000031701	Dnaja2	1500017M13Rik|2010206B19Rik|DNAJ|DNJ3|Dnaj3|HIRIP4|PRO3015|mDj3	DnaJ heat shock protein family (Hsp40) member A2	protein-coding
mm_154281.1	chr19	60791011	60791053	-	1	NA	promoter-TSS (NM_010123)	promoter-TSS (NM_010123)	-339	NM_010123	13669	Mm.2238	NM_010123	ENSMUSG00000024991	Eif3a	A830012B05Rik|Csma|Eif3|Eif3s10|mKIAA0139	eukaryotic translation initiation factor 3, subunit A	protein-coding
mm_12404.1	chr2	70476052	70476092	+	1	NA	exon (NM_022435, exon 2 of 2)	exon (NM_022435, exon 2 of 2)	1149	NM_022435	64406	Mm.423397	NM_022435	ENSMUSG00000075304	Sp5	-	trans-acting transcription factor 5	protein-coding
mm_94196.1	chr11	3100425	3100465	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	-23576	NR_003517	236604	Mm.247625	NM_001004146		Pisd-ps1	-	phosphatidylserine decarboxylase, pseudogene 1	pseudo
mm_155335.1	chrX	66653004	66653031	+	1	NA	promoter-TSS (NM_198863)	promoter-TSS (NM_198863)	-142	NM_198863	245450	Mm.336081	NM_198863	ENSMUSG00000036790	Slitrk2	A930040J07	SLIT and NTRK-like family, member 2	protein-coding
mm_97450.1	chr11	78193364	78193369	+	1	NA	promoter-TSS (NM_001045516)	promoter-TSS (NM_001045516)	-26	NM_001045516	216974	Mm.50974	NM_001045516	ENSMUSG00000044122	Proca1	4933404M19Rik	protein interacting with cyclin A1	protein-coding
mm_103703.1	chr11	79516525	79516555	-	1	NA	exon (NM_001077496, exon 2 of 2)	exon (NM_001077496, exon 2 of 2)	7222	NM_001077496	216984	Mm.439665	NM_001077496	ENSMUSG00000093938	Evi2b	Evi-2|Evi2	ecotropic viral integration site 2b	protein-coding
mm_142452.1	chr17	45592898	45592911	-	1	NA	promoter-TSS (NM_022880)	promoter-TSS (NM_022880)	-511	NM_022880	63959	Mm.29744	NM_022880	ENSMUSG00000023942	Slc29a1	1200014D21Rik|AA407560|ENT1	solute carrier family 29 (nucleoside transporters), member 1	protein-coding
mm_142715.1	chr17	47924636	47924652	-	1	NA	promoter-TSS (NM_028767)	promoter-TSS (NM_028767)	-12	NM_001110825	74123	Mm.240062	NM_028767	ENSMUSG00000023991	Foxp4	1200010K03Rik|2310007G05Rik|mFKHLA	forkhead box P4	protein-coding
mm_135218.1	chr16	36666045	36666055	-	1	NA	promoter-TSS (NM_019388)	promoter-TSS (NM_019388)	27	NM_019388	12524	Mm.1452	NM_019388	ENSMUSG00000022901	Cd86	B7|B7-2|B7.2|B70|CLS1|Cd28l2|ETC-1|Ly-58|Ly58|MB7|MB7-2|TS/A-2	CD86 antigen	protein-coding
mm_44919.1	chr5	35729049	35729078	-	1	NA	5' UTR (NM_194344, exon 1 of 18)	5' UTR (NM_194344, exon 1 of 18)	213	NM_194344	231147	Mm.290429	NM_194344	ENSMUSG00000036553	Sh3tc1	4631428G15|BC024909	SH3 domain and tetratricopeptide repeats 1	protein-coding
mm_103317.1	chr11	73176985	73176999	-	1	NA	promoter-TSS (NM_025318)	promoter-TSS (NM_025318)	16	NM_001168470	66048	Mm.73608	NM_025318	ENSMUSG00000047260	Emc6	0610009E20Rik|0610025L18Rik|Tmem93	ER membrane protein complex subunit 6	protein-coding
mm_4307.1	chr1	171840852	171840869	+	1	NA	intron (NM_001289470, intron 2 of 8)	intron (NM_001289470, intron 2 of 8)	1163	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_105903.1	chr11	114983076	114983092	-	1	NA	3' UTR (NM_145437, exon 4 of 4)	3' UTR (NM_145437, exon 4 of 4)	6802	NM_145437	217305	Mm.275986	NM_145437	ENSMUSG00000034641	Cd300ld	4732429D16Rik|CLM5|Cd300ld1|LMIR4|MAIR-IV|clm-5	CD300 molecule like family member d	protein-coding
mm_39468.1	chr5	19697039	19697044	+	1	NA	intron (NM_001170746, intron 2 of 22)	MER20|DNA|hAT-Charlie	-210477	NM_001170745	50791	Mm.332231	NM_015823	ENSMUSG00000040003	Magi2	AIP-1|Acvri1|Acvrinp1|Acvrip1|Magi-2|S-SCAM|mKIAA0705	membrane associated guanylate kinase, WW and PDZ domain containing 2	protein-coding
mm_77091.1	chr8	110793608	110793614	-	1	NA	intron (NM_029646, intron 1 of 7)	intron (NM_029646, intron 1 of 7)	12313	NM_029646	76527	Mm.77697	NM_029646	ENSMUSG00000031750	Il34	2010004A03Rik|AI593503	interleukin 34	protein-coding
mm_132995.1	chr16	55818094	55818128	+	1	NA	exon (NM_030612, exon 7 of 14)	exon (NM_030612, exon 7 of 14)	4027	NM_001159394	80859	Mm.247272	NM_030612	ENSMUSG00000035356	Nfkbiz	AA408868|INAP|Mail	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, zeta	protein-coding
mm_23965.1	chr3	84952490	84952500	+	1	NA	exon (NM_080428, exon 1 of 11)	exon (NM_080428, exon 1 of 11)	284	NM_080428	50754	Mm.196475	NM_080428	ENSMUSG00000028086	Fbxw7	1110001A17Rik|AGO|Cdc4|Fbw7|Fbwd6|Fbx30|Fbxo30|Fbxw6|SEL-10	F-box and WD-40 domain protein 7	protein-coding
mm_64557.1	chr7	144742088	144742099	+	1	NA	Intergenic	Intergenic	-3501	NM_001242349	101772	Mm.26700	NM_178642	ENSMUSG00000031075	Ano1	Tmem16a	anoctamin 1, calcium activated chloride channel	protein-coding
mm_160675.1	chr10	11082438	11082438	-	1	NA	promoter-TSS (NM_001114333)	promoter-TSS (NM_001114333)	-107	NM_016976	14816	Mm.391904	NM_016976	ENSMUSG00000019828	Grm1	4930455H15Rik|ENSMUSG00000075319|Gm10828|Gprc1a|mGluR1|nmf373|rcw|wobl	glutamate receptor, metabotropic 1	protein-coding
mm_99635.1	chr11	105181638	105181663	+	1	NA	promoter-TSS (NR_027956)	promoter-TSS (NR_027956)	123	NM_001294329	24086	Mm.126976	NM_011903	ENSMUSG00000020694	Tlk2	4933403M19Rik|PKU-alpha|PKUalpha|Tlk	tousled-like kinase 2 (Arabidopsis)	protein-coding
mm_137967.1	chr17	33524110	33524118	+	1	NA	promoter-TSS (NM_001329152)	promoter-TSS (NM_001329152)	29	NM_001329147	224697	Mm.29304	NM_172619	ENSMUSG00000024299	Adamts10	9430006O18|AW045948|Adam-ts10|Adamts-10|Znmp	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 10	protein-coding
mm_168826.1	chr12	22558920	22558920	+	1	NA	Intergenic	Intergenic	-402274	NR_136920	100043416		NM_001004167	ENSMUSG00000093846	Gm4425	EG432637|Gm5433	KRAB-domain protein pseudogene	pseudo
mm_102512.1	chr11	60777436	60777460	-	1	NA	promoter-TSS (NM_001085440)	promoter-TSS (NM_001085440)	-77	NM_001085440	237782	Mm.57726	NM_175491	ENSMUSG00000049323	Smcr8	2310076G09Rik|AI642055|D030073L15Rik	Smith-Magenis syndrome chromosome region, candidate 8 homolog (human)	protein-coding
mm_113515.1	chr13	37787221	37787225	+	1	NA	Intergenic	Intergenic	-38815	NM_026830	68750	Mm.491109	NM_026830	ENSMUSG00000039087	Rreb1	1110037N09Rik|AA414966|B930013M22Rik	ras responsive element binding protein 1	protein-coding
mm_113606.1	chr13	41249842	41249863	+	1	NA	promoter-TSS (NM_001135577)	promoter-TSS (NM_001135577)	8	NM_001135577	108934	Mm.38578	NM_001135577	ENSMUSG00000091264	Smim13	2900036K02Rik	small integral membrane protein 13	protein-coding
mm_164823.1	chr18	36195679	36195679	+	1	NA	intron (NM_001167891, intron 1 of 9)	(CCA)n|Simple_repeat|Simple_repeat	1481	NM_001167891	100042150	Mm.380390	NM_001167891	ENSMUSG00000060275	Nrg2	Don1|NTAK	neuregulin 2	protein-coding
mm_171384.1	chr4	120825696	120825711	-	1	NA	promoter-TSS (NM_001277095)	promoter-TSS (NM_001277095)	38	NM_001277095	18046	Mm.435590	NM_008692	ENSMUSG00000032897	Nfyc	-	nuclear transcription factor-Y gamma	protein-coding
mm_117896.1	chr13	99425132	99425146	-	1	NA	3' UTR (NM_008634, exon 7 of 7)	3' UTR (NM_008634, exon 7 of 7)	-12313	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_152689.1	chr19	16780827	16780835	-	1	NA	5' UTR (NM_173028, exon 1 of 72)	5' UTR (NM_173028, exon 1 of 72)	102	NM_173028	271564	Mm.211963	NM_173028	ENSMUSG00000046230	Vps13a	4930425F11|4930516E05Rik|4930543C13Rik|9930023P20|Chac|Chorein|D330038K10Rik|mKIAA0986	vacuolar protein sorting 13A	protein-coding
mm_119741.1	chr14	54122143	54122147	+	1	NA	Intergenic	Intergenic	131784	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_121488.1	chr14	121239726	121239737	+	1	NA	intron (NM_134082, intron 10 of 26)	intron (NM_134082, intron 10 of 26)	139499	NM_145465	223255	Mm.390756	NM_145465	ENSMUSG00000063410	Stk24	1810013H02Rik|C76483|MST-3|Mst3|STE20	serine/threonine kinase 24	protein-coding
mm_12067.1	chr2	59612035	59612109	+	1	NA	promoter-TSS (NM_198294)	promoter-TSS (NM_198294)	30	NM_198294	66860	Mm.27917	NM_198294	ENSMUSG00000035168	Tanc1	1200003E16Rik|Tanc|mKIAA1728	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	protein-coding
mm_138157.1	chr17	34239872	34239881	+	1	NA	intron (NM_010389, intron 1 of 5)	intron (NM_010389, intron 1 of 5)	971	NM_010389	15002	Mm.327358	NM_010389	ENSMUSG00000041538	H2-Ob	A-beta-2|A-beta2|H-2Ab|H-2I|H-2Ob|H2-Ab|H2-Ab2|H2-IAb2|Ob	histocompatibility 2, O region beta locus	protein-coding
mm_36404.1	chr4	77893398	77893401	-	1	NA	intron (NM_011211, intron 2 of 39)	intron (NM_011211, intron 2 of 39)	318496	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding
mm_168048.1	chrY	90811765	90811782	+	1	NA	intron (NM_133362, intron 2 of 3)	IMPB_01|Satellite|Satellite	26331	NM_133362	170942	Mm.76062	NM_133362	ENSMUSG00000096768	Erdr1	edr	erythroid differentiation regulator 1	protein-coding
mm_56846.1	chr6	117907662	117907671	-	1	NA	promoter-TSS (NM_001166429)	intron (NM_133834, intron 1 of 3)	-138	NM_001166428	98758	Mm.422979	NM_133834	ENSMUSG00000042079	Hnrnpf	4833420I20Rik|AA407306|Hnrpf	heterogeneous nuclear ribonucleoprotein F	protein-coding
mm_117199.1	chr13	64059812	64059815	-	1	NA	intron (NM_008291, intron 9 of 10)	intron (NM_008291, intron 9 of 10)	29388	NM_008291	15487	Mm.5109	NM_008291	ENSMUSG00000033122	Hsd17b3	-	hydroxysteroid (17-beta) dehydrogenase 3	protein-coding
mm_155430.1	chrX	73493011	73493036	+	1	NA	exon (NM_007542, exon 6 of 8)	exon (NM_007542, exon 6 of 8)	9422	NM_007542	12111	Mm.2608	NM_007542	ENSMUSG00000031375	Bgn	BG|DSPG1|PG-S1|PGI|SLRR1A	biglycan	protein-coding
mm_91211.1	chr10	21342051	21342059	-	1	NA	promoter-TSS (NR_045352)	promoter-TSS (NR_045352)	0	NR_045352	73990	Mm.399240	NR_045352		4930455C13Rik	-	RIKEN cDNA 4930455C13 gene	ncRNA
mm_1070.1	chr1	59298921	59298939	+	1	NA	intron (NM_001033373, intron 8 of 13)	intron (NM_001033373, intron 8 of 13)	42023	NM_001033373	271697	Mm.297713	NM_001033373	ENSMUSG00000026023	Cdk15	Als2cr7|Pftk2	cyclin-dependent kinase 15	protein-coding
mm_163517.1	chr12	114479492	114479496	-	1	NA	Intergenic	Intergenic	-10028	NR_106062	102465663		NR_106062	ENSMUSG00000105438	Mir7094-1	mmu-mir-7094-1	microRNA 7094-1	ncRNA
mm_83500.1	chr9	45954967	45954987	-	1	NA	5' UTR (NM_001289668, exon 1 of 27)	5' UTR (NM_001289668, exon 1 of 27)	272	NM_172257	214597	Mm.379345	NM_172257	ENSMUSG00000034908	Sidt2	B930096O19|BC023957|CGI-40	SID1 transmembrane family, member 2	protein-coding
mm_145746.1	chr18	64340570	64340586	+	1	NA	exon (NM_194268, exon 1 of 2)	exon (NM_194268, exon 1 of 2)	214	NM_194268	225631	Mm.234723	NM_194268	ENSMUSG00000045991	Onecut2	C730009D12|OC-2|Oc2	one cut domain, family member 2	protein-coding
mm_159707.1	chr5	30205721	30205721	-	1	NA	promoter-TSS (NM_001014394)	promoter-TSS (NM_001014394)	1	NM_001014394	381628	Mm.291148	NM_001014394	ENSMUSG00000067642	Adgrf3	Gm1041|Gpr113|Pgr23	adhesion G protein-coupled receptor F3	protein-coding
mm_26633.1	chr3	152928890	152928900	+	1	NA	intron (NM_012028, intron 2 of 4)	intron (NM_012028, intron 2 of 4)	53312	NM_012028	26938	Mm.40915	NM_012028	ENSMUSG00000039037	St6galnac5	AI851940|Siat7e	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 5	protein-coding
mm_77203.1	chr8	113848729	113848774	-	1	NA	promoter-TSS (NM_172466)	promoter-TSS (NM_172466)	88	NM_172466	208936	Mm.167471	NM_172466	ENSMUSG00000053399	Adamts18	9630038L21|ADAMTS21|E130314N14Rik	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 18	protein-coding
mm_100355.1	chr11	118433827	118433863	+	1	NA	promoter-TSS (NM_019959)	promoter-TSS (NM_019959)	44	NM_019959	56745	Mm.23845	NM_019959	ENSMUSG00000017446	C1qtnf1	1600017K21Rik|CTRP1|Zsig37	C1q and tumor necrosis factor related protein 1	protein-coding
mm_117618.1	chr13	91807637	91807655	-	1	NA	promoter-TSS (NM_145453)	promoter-TSS (NM_145453)	50	NM_145453	69085	Mm.52356	NM_145453	ENSMUSG00000021621	Zcchc9	1810019C21Rik	zinc finger, CCHC domain containing 9	protein-coding
mm_16173.1	chr2	172549637	172549649	+	1	NA	promoter-TSS (NM_009335)	promoter-TSS (NM_009335)	50	NM_009335	21420	Mm.3629	NM_009335	ENSMUSG00000028640	Tfap2c	AA409384|AP2gamma|Ap-2.2|Stra2|Tcfap2c	transcription factor AP-2, gamma	protein-coding
mm_16063.1	chr2	167932384	167932400	+	1	NA	promoter-TSS (NM_011201)	promoter-TSS (NM_011201)	65	NM_011201	19246	Mm.277916	NM_011201	ENSMUSG00000027540	Ptpn1	PTP-1B|PTP-HA2|PTP1B	protein tyrosine phosphatase, non-receptor type 1	protein-coding
mm_151694.1	chr19	4388199	4388203	-	1	NA	intron (NM_001001984, intron 2 of 20)	intron (NM_001001984, intron 2 of 20)	8876	NM_001001984	225876	Mm.31941	NM_001001984	ENSMUSG00000054611	Kdm2a	100043628|5530401A10Rik|AA589516|AW536790|Cxxc8|Fbl11|Fbl7|Fbxl11|Gm4560|Jhdm1|Jhdm1a|lalina	lysine (K)-specific demethylase 2A	protein-coding
mm_146169.1	chr18	75279472	75279475	+	1	NA	intron (NM_027727, intron 16 of 16)	intron (NM_027727, intron 16 of 16)	17844	NR_045394	100503117	Mm.250517	NR_045393	ENSMUSG00000102047	2010010A06Rik	5033420E22Rik	RIKEN cDNA 2010010A06 gene	ncRNA
mm_23496.1	chr3	60516952	60516962	+	1	NA	intron (NM_001253710, intron 1 of 7)	intron (NM_001253710, intron 1 of 7)	15778	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_154747.1	chrX	10518625	10518627	+	1	NA	intron (NM_019634, intron 1 of 7)	intron (NM_019634, intron 1 of 7)	33510	NM_019634	21912	Mm.18590	NM_019634	ENSMUSG00000058254	Tspan7	1200014P11Rik|A15|AI323365|Cd231|Mxs1|PE31|R74651|TALLA|Tm4sf2	tetraspanin 7	protein-coding
mm_102681.1	chr11	65269079	65269089	-	1	NA	intron (NM_146386, intron 1 of 12)	intron (NM_146386, intron 1 of 12)	905	NM_145136	214384	Mm.32257	NM_145136	ENSMUSG00000020542	Myocd	BSAC2A|Srfcp	myocardin	protein-coding
mm_133592.1	chr16	91458406	91458427	+	1	NA	Intergenic	Intergenic	-6688	NR_077219	100503120	Mm.387130	NR_077219	ENSMUSG00000084866	A930006K02Rik	-	RIKEN cDNA A930006K02 gene	ncRNA
mm_85415.1	chr9	103449171	103449181	-	1	NA	intron (NM_001002896, intron 3 of 6)	intron (NM_001002896, intron 3 of 6)	25598	NR_040466	100529079	Mm.437003	NR_040466	ENSMUSG00000086236	5830418P13Rik	-	RIKEN cDNA 5830418P13 gene	ncRNA
mm_26874.1	chr3	17691937	17691940	-	1	NA	Intergenic	Intergenic	-97983	NR_033490	70441	Mm.458192	NR_033490	ENSMUSG00000100252	Mir124-2hg	100040120|2610100L16Rik|6430547I21Rik|A930005K07Rik|AW125202|Gm2612	Mir124-2 host gene (non-protein coding)	ncRNA
mm_53095.1	chr6	125009262	125009317	+	1	NA	promoter-TSS (NM_175557)	promoter-TSS (NM_175557)	51	NM_001252083	269800	Mm.108677	NM_175557	ENSMUSG00000038346	Zfp384	BB163993|C130073D16Rik|Ciz|NP|Nmp4	zinc finger protein 384	protein-coding
mm_136268.1	chr16	91044383	91044458	-	1	NA	promoter-TSS (NM_026110)	promoter-TSS (NM_026110)	-41	NM_026110	67367	Mm.347	NM_026110	ENSMUSG00000022974	Paxbp1	1810007M14Rik|C21orf66|Gcfc|Gcfc1|Pax3/7bp	PAX3 and PAX7 binding protein 1	protein-coding
mm_109906.1	chr12	8301982	8301995	-	1	NA	promoter-TSS (NM_013527)	promoter-TSS (NM_013527)	-34	NM_013527	238057	Mm.271308	NM_013527	ENSMUSG00000037660	Gdf7	BMP12	growth differentiation factor 7	protein-coding
mm_137391.1	chr17	25819824	25819835	+	1	NA	3' UTR (NM_001164225, exon 6 of 6)	3' UTR (NM_001164225, exon 6 of 6)	-3798	NM_173741	268933	Mm.95512	NM_173741	ENSMUSG00000025737	Wdr24	BC037651	WD repeat domain 24	protein-coding
mm_153589.1	chr19	43524370	43524373	-	1	NA	exon (NM_010324, exon 1 of 9)	exon (NM_010324, exon 1 of 9)	234	NM_010324	14718	Mm.19039	NM_010324	ENSMUSG00000025190	Got1	AI789014|Got-1|cAspAT|cCAT	glutamic-oxaloacetic transaminase 1, soluble	protein-coding
mm_167430.1	chr8	117794757	117794761	+	1	NA	intron (NM_026758, intron 2 of 4)	intron (NM_026758, intron 2 of 4)	7170	NM_026758	68533	Mm.181836	NM_026758	ENSMUSG00000031843	Mphosph6	1110001M01Rik|AA536809|C86426	M phase phosphoprotein 6	protein-coding
mm_168005.1	chrY	4453591	4453600	+	1	NA	Intergenic	MURVY-int|LTR|ERV1	681922	NM_011253	19657	Mm.4711	NM_011253	ENSMUSG00000094658	Rbmy	RBM|Rbm1|Rbm1-rs1|Rbmy1a1|Rbmy1a1-rs1|Rbmy1b	RNA binding motif protein, Y chromosome	protein-coding
mm_155126.1	chrX	48885018	48885029	+	1	NA	Intergenic	Intergenic	-7310	NM_001085499	209005	Mm.336054	NM_001085499	ENSMUSG00000079606	Gm595	-	predicted gene 595	protein-coding
mm_167466.1	chr8	125569496	125569498	+	1	NA	Intergenic	CpG	-15141	NR_015535	75930	Mm.195663	NR_015535	ENSMUSG00000110629	4930567H12Rik	4930579P07Rik	RIKEN cDNA 4930567H12 gene	ncRNA
mm_153561.1	chr19	42202151	42202164	-	1	NA	promoter-TSS (NM_018780)	promoter-TSS (NM_018780)	95	NM_018780	54612	Mm.470071	NM_018780	ENSMUSG00000018822	Sfrp5	AI605071|SARP3	secreted frizzled-related sequence protein 5	protein-coding
mm_23642.1	chr3	67374092	67374102	+	1	NA	promoter-TSS (NM_010801)	promoter-TSS (NM_010801)	0	NM_010801	17349	Mm.10414	NM_010801	ENSMUSG00000048416	Mlf1	HLS7	myeloid leukemia factor 1	protein-coding
mm_61115.1	chr7	54835628	54835667	+	1	NA	5' UTR (NM_178705, exon 1 of 12)	5' UTR (NM_178705, exon 1 of 12)	402	NM_178705	233271	Mm.387344	NM_178705	ENSMUSG00000063297	Luzp2	9330154K17Rik|D130073E01	leucine zipper protein 2	protein-coding
mm_89740.1	chr10	99023676	99023687	+	1	NA	3' UTR (NM_026482, exon 21 of 21)	3' UTR (NM_026482, exon 21 of 21)	-83490	NM_027740	382406	Mm.440656	NM_027740	ENSMUSG00000019952	Poc1b	4933430F16Rik|Wdr51b	POC1 centriolar protein B	protein-coding
mm_30515.1	chr3	158282206	158282209	-	1	NA	intron (NM_001081358, intron 8 of 27)	intron (NM_001081358, intron 8 of 27)	245525	NM_001289524	67144	Mm.358704	NM_024194	ENSMUSG00000063052	Lrrc40	2610040E16Rik|AI837674	leucine rich repeat containing 40	protein-coding
mm_134737.1	chr16	23025228	23025240	-	1	NA	intron (NM_001102410, intron 2 of 10)	B3|SINE|B2	3867	NM_201375	385643	Mm.440414	NM_201375	ENSMUSG00000060459	Kng2	-	kininogen 2	protein-coding
mm_167676.1	chr9	77097053	77097082	+	1	NA	Intergenic	Intergenic	-51286	NM_012033	26944	Mm.23199	NM_012033	ENSMUSG00000032357	Tinag	AI452335|TIN-ag	tubulointerstitial nephritis antigen	protein-coding
mm_99739.1	chr11	106375301	106375316	+	1	NA	intron (NM_029345, intron 2 of 5)	intron (NM_029345, intron 2 of 5)	482	NM_029345	75573	Mm.159539	NM_029345	ENSMUSG00000009210	Prr29	2310007L24Rik	proline rich 29	protein-coding
mm_156844.1	chrX	164385928	164385938	+	1	NA	exon (NM_010216, exon 2 of 7)	exon (NM_010216, exon 2 of 7)	12411	NM_010216	14205	Mm.297978	NM_010216	ENSMUSG00000031380	Vegfd	AI325264|Figf|VEGF-D	vascular endothelial growth factor D	protein-coding
mm_129004.1	chr15	74876659	74876659	-	1	NA	Intergenic	Intergenic	5045	NM_025929	67038	Mm.154566	NM_025929	ENSMUSG00000063522	2010109I03Rik	Ly6m	RIKEN cDNA 2010109I03 gene	protein-coding
mm_129540.1	chr15	79357735	79357751	-	1	NA	exon (NM_001304830, exon 3 of 3)	exon (NM_001304830, exon 3 of 3)	9341	NM_001304832	17133	Mm.86646	NM_010755	ENSMUSG00000042622	Maff	-	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein F (avian)	protein-coding
mm_78696.1	chr9	41137399	41137413	+	1	NA	intron (NM_176860, intron 1 of 13)	ID4|SINE|ID	20088	NM_176860	72828	Mm.133615	NM_176860	ENSMUSG00000032020	Ubash3b	2810457I06Rik|BB125008|TULA-2|p70	ubiquitin associated and SH3 domain containing, B	protein-coding
mm_51944.1	chr6	91724931	91724944	+	1	NA	exon (NM_009320, exon 4 of 15)	exon (NM_009320, exon 4 of 15)	40870	NM_009320	21366	Mm.395650	NM_009320	ENSMUSG00000030096	Slc6a6	AA589629|C80501|Taut	solute carrier family 6 (neurotransmitter transporter, taurine), member 6	protein-coding
mm_164192.1	chr15	78774881	78774889	-	1	NA	TTS (NM_130859)	TTS (NM_130859)	-1440	NM_008595	17305	Mm.149235	NM_008595	ENSMUSG00000018169	Mfng	AW546563	MFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	protein-coding
mm_163635.1	chr13	59640216	59640237	-	1	NA	exon (NM_001035122, exon 8 of 10)	exon (NM_001035122, exon 8 of 10)	35558	NM_001035122	105348	Mm.171335	NM_027307	ENSMUSG00000021556	Golm1	2310001L02Rik|AW125446|D030064E01Rik|GP73|Golph2|PSEC0257	golgi membrane protein 1	protein-coding
mm_149531.1	chr19	12461173	12461183	+	1	NA	5' UTR (NM_010821, exon 2 of 2)	5' UTR (NM_010821, exon 2 of 2)	399	NM_010821	17476	Mm.3999	NM_010821	ENSMUSG00000046805	Mpeg1	MPS1|Mpg-1	macrophage expressed gene 1	protein-coding
mm_170243.1	chr17	92057451	92057452	+	1	NA	Intergenic	Lx3C|LINE|L1	-964649	NM_020252	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_45291.1	chr5	65019195	65019207	-	1	NA	intron (NM_026667, intron 7 of 13)	intron (NM_026667, intron 7 of 13)	48883	NR_030577	100124451		NR_030577	ENSMUSG00000077042	Mir574	Mirn574|mir-574|mmu-mir-574	microRNA 574	ncRNA
mm_65668.1	chr7	28291106	28291112	-	1	NA	promoter-TSS (NM_175033)	promoter-TSS (NM_175033)	25	NM_175033	280621	Mm.212777	NM_175033	ENSMUSG00000046750	Selenov	Selv	selenoprotein V	protein-coding
mm_94816.1	chr11	23152126	23152133	+	1	NA	promoter-TSS (NR_131065)	promoter-TSS (NR_131065)	-11	NR_131065	76993	Mm.59224	NR_131065	ENSMUSG00000086366	1700061J23Rik	-	RIKEN cDNA 1700061J23 gene	ncRNA
mm_38645.1	chr4	143245888	143245890	-	1	NA	Intergenic	RMER17C|LTR|ERVK	-33180	NM_001256380	110593	Mm.332020	NM_001081355	ENSMUSG00000057637	Prdm2	4833427P12Rik|E330024L24Rik|Gm1033|Gm19732|KMT8|Riz|Riz1|Znfpr1c1	PR domain containing 2, with ZNF domain	protein-coding
mm_111127.1	chr12	81456927	81456927	-	1	NA	intron (NM_001309810, intron 3 of 4)	MurERV4_19-int|LTR|ERVK	27924	NR_132135	66272	Mm.439970	NM_025461	ENSMUSG00000091803	Cox16	1810020G14Rik|1810055I05Rik|BB388670	cytochrome c oxidase assembly protein 16	protein-coding
mm_27280.1	chr3	41467359	41467397	-	1	NA	Intergenic	Lx6|LINE|L1	25821	NR_040385	78706	Mm.366094	NR_040385	ENSMUSG00000097639	Platr4	C430002E04Rik	pluripotency associated transcript 4	ncRNA
mm_21814.1	chr2	165283600	165283620	-	1	NA	intron (NM_144893, intron 1 of 9)	intron (NM_144893, intron 1 of 9)	4177	NM_001252574	228875	Mm.21184	NM_144893	ENSMUSG00000017664	Slc35c2	C85957|CGI-15|D2Wsu58e|Ovcov1	solute carrier family 35, member C2	protein-coding
mm_89578.1	chr10	95708145	95708150	+	1	NA	Intergenic	Intergenic	-143980	NM_027722	71207	Mm.24397	NM_027722	ENSMUSG00000020029	Nudt4	4933436C10Rik|DIPP2|DIPP2alpha|DIPP2beta|HDCMB47P	nudix (nucleoside diphosphate linked moiety X)-type motif 4	protein-coding
mm_155681.1	chrX	93654971	93654981	+	1	NA	5' UTR (NM_177546, exon 1 of 8)	5' UTR (NM_177546, exon 1 of 8)	113	NM_177546	236899	Mm.166467	NM_177546	ENSMUSG00000035246	Pcyt1b	AW045697|CTTbeta	phosphate cytidylyltransferase 1, choline, beta isoform	protein-coding
mm_67350.1	chr7	79835406	79835416	-	1	NA	exon (NM_008486, exon 12 of 20)	exon (NM_008486, exon 12 of 20)	6941	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_20710.1	chr2	134554349	134554369	-	1	NA	promoter-TSS (NM_010403)	promoter-TSS (NM_010403)	-7	NM_010403	15112	Mm.26634	NM_010403	ENSMUSG00000027261	Hao1	GOX|Gox1|Hao-1	hydroxyacid oxidase 1, liver	protein-coding
mm_49383.1	chr6	24733252	24733295	+	1	NA	promoter-TSS (NM_028920)	promoter-TSS (NM_028920)	28	NM_028920	74409	Mm.87331	NM_028920	ENSMUSG00000029679	Hyal6	4932701A20Rik|Hyal-ps1|Hyalp1	hyaluronoglucosaminidase 6	protein-coding
mm_102736.1	chr11	67250960	67250960	-	1	NA	exon (NM_010855, exon 22 of 40)	exon (NM_010855, exon 22 of 40)	13148	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_155148.1	chrX	52791180	52791201	+	1	NA	promoter-TSS (NM_001034059)	promoter-TSS (NM_001034059)	-10	NM_001034059	434778	Mm.23411	NM_001034059	ENSMUSG00000073207	Ccdc160	6330534C20Rik	coiled-coil domain containing 160	protein-coding
mm_95655.1	chr11	53763821	53763856	+	1	NA	promoter-TSS (NR_106131)	promoter-TSS (NR_106131)	-184	NR_106131	102465772		NR_106131	ENSMUSG00000099153	Mir7671	Gm27802|mmu-mir-7671	microRNA 7671	ncRNA
mm_63422.1	chr7	127471485	127471551	+	1	NA	promoter-TSS (NM_145589)	promoter-TSS (NM_145589)	-96	NM_145589	233895	Mm.44183	NM_145589	ENSMUSG00000030822	Prr14	BC006909	proline rich 14	protein-coding
mm_134175.1	chr16	10838548	10838575	-	1	NA	intron (NM_001162932, intron 1 of 1)	intron (NM_001162932, intron 1 of 1)	3502	NM_001162932	223970	Mm.325777	NM_001033278	ENSMUSG00000037991	Rmi2	A630055G03Rik|Gm537|Gm929	RecQ mediated genome instability 2	protein-coding
mm_37503.1	chr4	123750231	123750235	-	1	NA	promoter-TSS (NM_023423)	promoter-TSS (NM_023423)	66	NM_023423	68050	Mm.27903	NM_023423	ENSMUSG00000023075	Akirin1	6330407G11Rik	akirin 1	protein-coding
mm_3670.1	chr1	153665283	153665325	+	1	NA	promoter-TSS (NM_001347115)	promoter-TSS (NM_001347115)	-369	NM_001347115	67792	Mm.379143	NM_026380	ENSMUSG00000042671	Rgs8	6530413N01Rik	regulator of G-protein signaling 8	protein-coding
mm_104834.1	chr11	99154017	99154027	-	1	NA	intron (NM_007719, intron 1 of 2)	intron (NM_007719, intron 1 of 2)	1055	NM_001301713	12775	Mm.2932	NM_007719	ENSMUSG00000037944	Ccr7	CC-CKR-7|CCR-7|CD197|Cdw197|Cmkbr7|EBI1|Ebi1h	chemokine (C-C motif) receptor 7	protein-coding
mm_129253.1	chr15	76695976	76695979	-	1	NA	promoter-TSS (NM_182805)	promoter-TSS (NM_182805)	-749	NM_182805	76282	Mm.30130	NM_182805	ENSMUSG00000022546	Gpt	1300007J06Rik|2310022B03Rik|ALT|ALT1|Gpt-1|Gpt1	glutamic pyruvic transaminase, soluble	protein-coding
mm_5547.1	chr1	38627539	38627549	-	1	NA	promoter-TSS (NM_001290814)	promoter-TSS (NM_001290814)	-300	NM_001290814	16764	Mm.336679	NM_010678	ENSMUSG00000037138	Aff3	3222402O04Rik|A730046J16|LAF-4|Laf4	AF4/FMR2 family, member 3	protein-coding
mm_131695.1	chr16	20695001	20695009	+	1	NA	promoter-TSS (NM_133778)	promoter-TSS (NM_133778)	-52	NM_133778	78408	Mm.196512	NM_133778	ENSMUSG00000050821	Fam131a	2900046G09Rik	family with sequence similarity 131, member A	protein-coding
mm_79883.1	chr9	65265174	65265187	+	1	NA	promoter-TSS (NM_173385)	promoter-TSS (NM_173385)	0	NM_173385	214425	Mm.138455	NM_173385	ENSMUSG00000042254	Cilp	9830114D16|C130036G17Rik	cartilage intermediate layer protein, nucleotide pyrophosphohydrolase	protein-coding
mm_114828.1	chr13	92354749	92354766	+	1	NA	promoter-TSS (NM_010049)	promoter-TSS (NM_010049)	-26	NM_010049	13361	Mm.23695	NM_010049	ENSMUSG00000021707	Dhfr	8430436I03Rik|AA607882|AI662710|AW555094	dihydrofolate reductase	protein-coding
mm_128856.1	chr15	72547638	72547644	-	1	NA	Intergenic	CpG-4938	-1362	NM_001033876	223604	Mm.386856	NM_001033876	ENSMUSG00000036760	Kcnk9	Task3	potassium channel, subfamily K, member 9	protein-coding
mm_132062.1	chr16	30008658	30008672	+	1	NA	promoter-TSS (NR_033631)	promoter-TSS (NR_033631)	-2	NR_033631	100043102	Mm.30797	NR_033631	ENSMUSG00000097184	4632428C04Rik	Gm4231	RIKEN cDNA 4632428C04 gene	ncRNA
mm_18310.1	chr2	54085408	54085418	-	1	NA	5' UTR (NM_023396, exon 1 of 1)	5' UTR (NM_023396, exon 1 of 1)	139	NM_023396	67874	Mm.27086	NM_023396	ENSMUSG00000075334	Rprm	2410012A13Rik|Reprimo	reprimo, TP53 dependent G2 arrest mediator candidate	protein-coding
mm_33544.1	chr4	130934616	130934626	+	1	NA	3' UTR (NM_010686, exon 8 of 8)	3' UTR (NM_010686, exon 8 of 8)	-9764	NM_010769	17180	Mm.271796	NM_010769	ENSMUSG00000040533	Matn1	CMP|Crtm|Mat1|matrilin-1	matrilin 1, cartilage matrix protein	protein-coding
mm_125738.1	chr15	73512645	73512690	+	1	NA	5' UTR (NM_001081066, exon 1 of 23)	5' UTR (NM_001081066, exon 1 of 23)	107	NM_001081066	105841	Mm.322557	NM_001081066	ENSMUSG00000036661	Dennd3	AI447457|E030003N15Rik	DENN/MADD domain containing 3	protein-coding
mm_99623.1	chr11	104637541	104637547	+	1	NA	intron (NM_016780, intron 5 of 14)	intron (NM_016780, intron 5 of 14)	29544	NM_016780	16416	Mm.87150	NM_016780	ENSMUSG00000020689	Itgb3	CD61|GP3A|INGRB3	integrin beta 3	protein-coding
mm_81440.1	chr9	109103545	109103583	+	1	NA	intron (NM_172775, intron 7 of 37)	intron (NM_172775, intron 7 of 37)	8128	NM_172775	235611	Mm.53862	NM_172775	ENSMUSG00000053646	Plxnb1	2900002G15Rik|AU042020|mKIAA0407	plexin B1	protein-coding
mm_52243.1	chr6	105677749	105677761	+	1	NA	promoter-TSS (NM_173004)	promoter-TSS (NM_173004)	10	NM_173004	269784	Mm.321683	NM_173004	ENSMUSG00000064293	Cntn4	9630050B05|Axcam|BIG-2	contactin 4	protein-coding
mm_68217.1	chr7	104410156	104410183	-	1	NA	3' UTR (NM_009099, exon 8 of 8)	3' UTR (NM_009099, exon 8 of 8)	-51523	NM_175648	244183	Mm.347647	NM_175648	ENSMUSG00000052749	Trim30b	A530023O14Rik|Trim30-1	tripartite motif-containing 30B	protein-coding
mm_129217.1	chr15	76534939	76535010	-	1	NA	TTS (NM_013909)	TTS (NM_013909)	3772	NM_013909	30840	Mm.275279	NM_013909	ENSMUSG00000022559	Fbxl6	AU021795|Fbl6	F-box and leucine-rich repeat protein 6	protein-coding
mm_125795.1	chr15	74819113	74819117	+	1	NA	promoter-TSS (NM_010416)	promoter-TSS (NM_010416)	39	NM_010416	15202	Mm.17336	NM_010416	ENSMUSG00000068600	Gml2	1700057K19Rik|HemT|Hemt1	glycosylphosphatidylinositol anchored molecule like 2	protein-coding
mm_22751.1	chr3	19970916	19970924	+	1	NA	exon (NM_007752, exon 6 of 19)	exon (NM_007752, exon 6 of 19)	13866	NM_007752	12870	Mm.13787	NM_007752	ENSMUSG00000003617	Cp	D3Ertd555e	ceruloplasmin	protein-coding
mm_47519.1	chr5	124095750	124095820	-	1	NA	promoter-TSS (NM_019875)	promoter-TSS (NM_019875)	13	NM_019875	56325	Mm.254839	NM_019875	ENSMUSG00000029408	Abcb9	TAPL|mKIAA1520	ATP-binding cassette, sub-family B (MDR/TAP), member 9	protein-coding
mm_166235.1	chr5	67815845	67815845	-	1	NA	intron (NM_001284345, intron 1 of 36)	L2c|LINE|L2	31586	NM_009727	11980	Mm.153230	NM_009727	ENSMUSG00000037685	Atp8a1	AI481521|AI853962|APLT|AW743152|AW822227|Atp3a2|B230107D19Rik|ClassI	ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1	protein-coding
mm_106029.1	chr11	116077048	116077068	-	1	NA	intron (NM_001009573, intron 2 of 32)	intron (NM_001009573, intron 2 of 32)	903	NM_001009573	70450	Mm.259460	NM_001009573	ENSMUSG00000057948	Unc13d	2610108D09Rik|Jinx|Munc13-4|mFLJ00067	unc-13 homolog D (C. elegans)	protein-coding
mm_164942.1	chr19	3686500	3686506	-	1	NA	promoter-TSS (NM_008513)	promoter-TSS (NM_008513)	61	NM_008513	16973	Mm.274581	NM_008513	ENSMUSG00000024913	Lrp5	BMND1|HBM|LR3|LRP7|OPPG|mKIAA4142	low density lipoprotein receptor-related protein 5	protein-coding
mm_151058.1	chr19	47179360	47179375	+	1	NA	5' UTR (NM_021360, exon 1 of 6)	5' UTR (NM_021360, exon 1 of 6)	547	NM_021360	18011	Mm.313651	NM_021360	ENSMUSG00000006435	Neurl1a	2410129E16Rik|AI450910|AI481072|Neu1|Neur1|Neurl|Neurl1|Nlz|Rnf67	neuralized E3 ubiquitin protein ligase 1A	protein-coding
mm_5432.1	chr1	34816897	34816929	-	1	NA	3' UTR (NM_001160236, exon 7 of 7)	3' UTR (NM_001160236, exon 7 of 7)	15191	NM_183019	226970	Mm.41604	NM_183019	ENSMUSG00000037509	Arhgef4	9330140K16Rik|Asef|ENSMUSG00000070955	Rho guanine nucleotide exchange factor (GEF) 4	protein-coding
mm_135761.1	chr16	56712826	56712838	-	1	NA	5' UTR (NM_001252443, exon 2 of 7)	5' UTR (NM_001252443, exon 2 of 7)	4618	NM_001252443	21787	Mm.425970	NM_019678	ENSMUSG00000022757	Tfg	AI173908	Trk-fused gene	protein-coding
mm_103874.1	chr11	83526026	83526070	-	1	NA	exon (NM_013653, exon 3 of 3)	exon (NM_013653, exon 3 of 3)	-3949	NM_001045543	629303	Mm.390417	NM_001045543	ENSMUSG00000018925	Heatr9	Gm11435|OTTMUSG00000000990	HEAT repeat containing 9	protein-coding
mm_162157.1	chrX	89409697	89409697	-	1	NA	promoter-TSS (NM_008821)	promoter-TSS (NM_008821)	-8	NM_008821	18630	Mm.3086	NM_008821	ENSMUSG00000035395	Pet2	PC231|PC326|Pex3	plasmacytoma expressed transcript 2	protein-coding
mm_24807.1	chr3	95556340	95556346	+	1	NA	TTS (NM_021281)	TTS (NM_021281)	-3334	NM_026489	67981	Mm.179050	NM_026489	ENSMUSG00000028109	Hormad1	4921522K05Rik|Nohma	HORMA domain containing 1	protein-coding
mm_104345.1	chr11	94242906	94242929	-	1	NA	promoter-TSS (NM_181819)	promoter-TSS (NM_181819)	-338	NM_181819	278507	Mm.342216	NM_181819	ENSMUSG00000044177	Wfikkn2	2610304F08Rik|AY100450|Gasp1|WFIKKNRP	WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 2	protein-coding
mm_172623.1	chr8	20270760	20270764	-	1	NA	non-coding (NR_030708, exon 5 of 5)	non-coding (NR_030708, exon 5 of 5)	26670	NR_030708	547150	Mm.359054	NR_030708	ENSMUSG00000071796	6820431F20Rik	-	cadherin 11 pseudogene	pseudo
mm_142340.1	chr17	43591473	43591480	-	1	NA	promoter-TSS (NR_045445)	promoter-TSS (NR_045445)	33	NR_045445	73504	Mm.9277	NR_045444	ENSMUSG00000090307	1700071M16Rik	-	RIKEN cDNA 1700071M16 gene	ncRNA
mm_93483.1	chr10	111995909	111995926	-	1	NA	intron (NM_028608, intron 1 of 5)	intron (NM_028608, intron 1 of 5)	1347	NM_028608	73690	Mm.173790	NM_028608	ENSMUSG00000056888	Glipr1	2410114O14Rik|RTVP-1|RTVP1|mRTVP-1	GLI pathogenesis-related 1 (glioma)	protein-coding
mm_116178.1	chr13	30820743	30820760	-	1	NA	intron (NM_025588, intron 25 of 27)	intron (NM_025588, intron 25 of 27)	71518	NM_013674	16364	Mm.4677	NM_013674	ENSMUSG00000021356	Irf4	AI385587|IRF-4|LSIRF|NF-EM5|Spip	interferon regulatory factor 4	protein-coding
mm_139788.1	chr17	65800064	65800075	+	1	NA	intron (NM_001114131, intron 2 of 19)	intron (NM_001114131, intron 2 of 19)	16714	NR_104465	70351	Mm.48686	NM_146081	ENSMUSG00000061950	Ppp4r1	3110001J10Rik|Pp4r1	protein phosphatase 4, regulatory subunit 1	protein-coding
mm_162230.1	chrX	149941638	149941638	+	1	NA	promoter-TSS (NM_001122735)	promoter-TSS (NM_001122735)	-17	NM_001122735	382244	Mm.359506	NM_001122735	ENSMUSG00000095082	Gm15091	OTTMUSG00000018981	predicted gene 15091	protein-coding
mm_70058.1	chr7	142651584	142651594	-	1	NA	3' UTR (NM_010514, exon 4 of 4)	3' UTR (NM_010514, exon 4 of 4)	3407	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_13054.1	chr2	91102331	91102347	+	1	NA	intron (NM_011355, intron 2 of 4)	URR1A|DNA|hAT-Charlie	5661	NM_011355	20375	Mm.1302	NM_011355	ENSMUSG00000002111	Spi1	Dis-1|Dis1|PU.1|Sfpi-1|Sfpi1|Spi-1|Tcfpu1|Tfpu.1	spleen focus forming virus (SFFV) proviral integration oncogene	protein-coding
mm_55352.1	chr6	56804315	56804315	-	1	NA	Intergenic	B1_Mus2|SINE|Alu	-6502	NM_145958	210973	Mm.57295	NM_145958	ENSMUSG00000059486	Kbtbd2	BC022962|Bklhd1|mKIAA1489	kelch repeat and BTB (POZ) domain containing 2	protein-coding
mm_144099.1	chr18	3446897	3446906	+	1	NA	Intergenic	Intergenic	-61056	NM_026505	68010	Mm.284863	NM_026505	ENSMUSG00000024232	Bambi	2610003H06Rik	BMP and activin membrane-bound inhibitor	protein-coding
mm_91147.1	chr10	20175315	20175322	-	1	NA	intron (NM_001198635, intron 1 of 17)	intron (NM_001198635, intron 1 of 17)	26398	NM_001198635	17761	Mm.20928	NM_008635	ENSMUSG00000019996	Map7	E-MAP-115|MAP-7|Mtap7|R75000|mshi|mste|ste	microtubule-associated protein 7	protein-coding
mm_147557.1	chr18	54985215	54985219	-	1	NA	intron (NM_175751, intron 2 of 9)	intron (NM_175751, intron 2 of 9)	4963	NM_175751	269023	Mm.192984	NM_175751	ENSMUSG00000052713	Zfp608	4932417D18Rik|D430007A19Rik|Znf608	zinc finger protein 608	protein-coding
mm_7893.1	chr1	133382799	133382808	-	1	NA	3' UTR (NM_011439, exon 14 of 14)	3' UTR (NM_011439, exon 14 of 14)	19231	NM_175443	214253	Mm.52111	NM_175443	ENSMUSG00000070644	Etnk2	4933417N20Rik|AI197444|EKI 2|Eki2|Tuc1	ethanolamine kinase 2	protein-coding
mm_124573.1	chr14	124443617	124443650	-	1	NA	intron (NM_207667, intron 1 of 4)	A-rich|Low_complexity|Low_complexity	233494	NM_207667	14169	Mm.206362	NM_010201	ENSMUSG00000025551	Fgf14	FHF-4|Fhf4|mFHF-4(1B)	fibroblast growth factor 14	protein-coding
mm_116319.1	chr13	37743870	37743870	-	1	NA	Intergenic	Intergenic	-82168	NM_026830	68750	Mm.491109	NM_026830	ENSMUSG00000039087	Rreb1	1110037N09Rik|AA414966|B930013M22Rik	ras responsive element binding protein 1	protein-coding
mm_21251.1	chr2	156196524	156196561	-	1	NA	promoter-TSS (NM_172674)	promoter-TSS (NM_172674)	-105	NM_172674	228829	Mm.427078	NM_172674	ENSMUSG00000038116	Phf20	6820402O20Rik	PHD finger protein 20	protein-coding
mm_75187.1	chr8	36953387	36953391	-	1	NA	promoter-TSS (NM_001194940)	promoter-TSS (NM_001194940)	-947	NM_001194940	50768	Mm.125155	NM_015802	ENSMUSG00000031523	Dlc1	A730069N07Rik|Arhgap7|HP|STARD12|dlc-1	deleted in liver cancer 1	protein-coding
mm_54769.1	chr6	41519898	41519912	-	1	NA	Intergenic	Intergenic	-1871	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_51799.1	chr6	88636036	88636039	+	1	NA	Intergenic	ORR1D1-int|LTR|ERVL-MaLR	-8589	NM_001278671	74589	Mm.196226	NM_029013	ENSMUSG00000033182	Kbtbd12	4833415F11Rik|4933428M03Rik|Klhdc6	kelch repeat and BTB (POZ) domain containing 12	protein-coding
mm_78432.1	chr9	31948343	31948345	+	1	NA	Intergenic	Intergenic	-35059	NM_013800	12023	Mm.261044	NM_013800	ENSMUSG00000032033	Barx2	2310006E12Rik|Barx2b	BarH-like homeobox 2	protein-coding
mm_82551.1	chr9	20952839	20952881	-	1	NA	promoter-TSS (NM_001199433)	promoter-TSS (NM_001199433)	119	NM_010066	13433	Mm.128580	NM_010066	ENSMUSG00000004099	Dnmt1	Cxxc9|Dnmt|Dnmt1o|MCMT|MTase|Met-1|Met1|MommeD2|m.MmuI	DNA methyltransferase (cytosine-5) 1	protein-coding
mm_167705.1	chr9	92942348	92942348	+	1	NA	Intergenic	Intergenic	63385	NR_040756	78349	Mm.52612	NR_040756	ENSMUSG00000100294	1700034K08Rik	-	RIKEN cDNA 1700034K08 gene	ncRNA
mm_131334.1	chr16	13348944	13348947	+	1	NA	intron (NM_001122667, intron 3 of 16)	L1MC4|LINE|L1	-9476	NM_153588	239719	Mm.270643	NM_153588	ENSMUSG00000009569	Mkl2	ENSMUSG00000075401|Gt4-1|MRTF-B|Mrtfb|mKIAA1243	MKL/myocardin-like 2	protein-coding
mm_88838.1	chr10	80855324	80855338	+	1	NA	promoter-TSS (NM_025349)	promoter-TSS (NM_025349)	56	NM_175195	73218	Mm.3285	NM_175195	ENSMUSG00000035206	Sppl2b	3110056O03Rik|AW550292|PSL1	signal peptide peptidase like 2B	protein-coding
mm_83321.1	chr9	44163421	44163430	-	1	NA	exon (NM_007619, exon 9 of 16)	exon (NM_007619, exon 9 of 16)	28767	NM_023061	84004	Mm.275003	NM_023061	ENSMUSG00000032135	Mcam	1-gicerin|AV025631|CD146|CD149|Muc18|s-endo|s-gicerin	melanoma cell adhesion molecule	protein-coding
mm_23286.1	chr3	51788976	51788991	+	1	NA	intron (NM_001004176, intron 2 of 4)	intron (NM_001004176, intron 2 of 4)	127804	NM_001310482	211666	Mm.24679	NM_174995	ENSMUSG00000074604	Mgst2	GST2|MGST-II	microsomal glutathione S-transferase 2	protein-coding
mm_92850.1	chr10	81524249	81524259	-	1	NA	promoter-TSS (NM_010304)	promoter-TSS (NM_010304)	-29	NM_010304	14676	Mm.1546	NM_010304	ENSMUSG00000034792	Gna15	G[a]15|Galpha15	guanine nucleotide binding protein, alpha 15	protein-coding
mm_114691.1	chr13	81783309	81783325	+	1	NA	promoter-TSS (NM_007684)	promoter-TSS (NM_007684)	25	NM_007684	12626	Mm.12481	NM_007684	ENSMUSG00000021537	Cetn3	MmCEN3	centrin 3	protein-coding
mm_104296.1	chr11	90390647	90390658	-	1	NA	5' UTR (NM_172563, exon 1 of 4)	5' UTR (NM_172563, exon 1 of 4)	265	NM_172563	217082	Mm.158903	NM_172563	ENSMUSG00000003949	Hlf	E230015K02Rik	hepatic leukemia factor	protein-coding
mm_39240.1	chr5	3341197	3341211	+	1	NA	Intergenic	CpG	-2689	NM_009873	12571	Mm.31672	NM_009873	ENSMUSG00000040274	Cdk6	AI504062|Crk2	cyclin-dependent kinase 6	protein-coding
mm_64217.1	chr7	141540002	141540014	+	1	NA	promoter-TSS (NM_001142681)	promoter-TSS (NM_001142681)	-151	NM_001142681	68038	Mm.245355	NM_026522	ENSMUSG00000025512	Chid1	3110023E09Rik|AI841869	chitinase domain containing 1	protein-coding
mm_86849.1	chr10	21593144	21593146	+	1	NA	promoter-TSS (NR_027968)	promoter-TSS (NR_027968)	0	NR_027968	67692	Mm.54306	NM_183266	ENSMUSG00000050844	1700020N01Rik	-	RIKEN cDNA 1700020N01 gene	ncRNA
mm_30975.1	chr4	34550919	34550929	+	1	NA	5' UTR (NM_001007589, exon 1 of 5)	5' UTR (NM_001007589, exon 1 of 5)	309	NM_001007589	433693	Mm.389532	NM_026019	ENSMUSG00000028291	Akirin2	2700059D21Rik|AA114675|AA522011|AU019887|Akirin-2	akirin 2	protein-coding
mm_76219.1	chr8	83571823	83571866	-	1	NA	TTS (NM_025843)	TTS (NM_025843)	5086	NM_025843	66916	Mm.29683	NM_025843	ENSMUSG00000033938	Ndufb7	1110002H15Rik	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 7	protein-coding
mm_75348.1	chr8	43320595	43320605	-	1	NA	Intergenic	B1_Mur3|SINE|Alu	-13591	NM_009556	22702	Mm.285848	NM_009556	ENSMUSG00000051176	Zfp42	Rex-1|Rex1|Zfp-42	zinc finger protein 42	protein-coding
mm_147223.1	chr18	38203785	38203795	-	1	NA	intron (NM_029357, intron 1 of 2)	intron (NM_029357, intron 1 of 2)	5972	NM_029357	75599	Mm.36560	NM_029357	ENSMUSG00000051375	Pcdh1	2010005A06Rik|AI585920	protocadherin 1	protein-coding
mm_123173.1	chr14	57525500	57525525	-	1	NA	exon (NM_145837, exon 2 of 3)	exon (NM_145837, exon 2 of 3)	683	NM_145837	239114	Mm.390726	NM_145837	ENSMUSG00000050222	Il17d	AI462269|IL-17D	interleukin 17D	protein-coding
mm_20003.1	chr2	119029360	119029389	-	1	NA	promoter-TSS (NM_199310)	promoter-TSS (NM_199310)	19	NM_199310	269336	Mm.292465	NM_199310	ENSMUSG00000039983	Ccdc32	Gm631	coiled-coil domain containing 32	protein-coding
mm_126906.1	chr15	89574188	89574202	+	1	NA	exon (NM_013455, exon 5 of 5)	exon (NM_013455, exon 5 of 5)	5869	NM_001277246	11434	Mm.57	NM_013455	ENSMUSG00000022622	Acr	-	acrosin prepropeptide	protein-coding
mm_130426.1	chr15	98098673	98098677	-	1	NA	intron (NM_001163488, intron 1 of 22)	RLTR31C_MM|LTR|ERVK	-5106	NM_144851	223870	Mm.384023	NM_144851	ENSMUSG00000033075	Senp1	2310046A20Rik|D15Ertd528e|E330036L07Rik|suPr-2	SUMO1/sentrin specific peptidase 1	protein-coding
mm_35077.1	chr4	6990647	6990662	-	1	NA	promoter-TSS (NM_145711)	promoter-TSS (NM_145711)	69	NM_145711	252838	Mm.435828	NM_145711	ENSMUSG00000041272	Tox	1700007F02Rik	thymocyte selection-associated high mobility group box	protein-coding
mm_87177.1	chr10	38966921	38966951	+	1	NA	intron (NM_010681, intron 1 of 37)	intron (NM_010681, intron 1 of 37)	1421	NM_010681	16775	Mm.258065	NM_010681	ENSMUSG00000019846	Lama4	-	laminin, alpha 4	protein-coding
mm_124251.1	chr14	101729691	101729735	-	1	NA	promoter-TSS (NM_201529)	promoter-TSS (NM_201529)	-215	NM_201529	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_107494.1	chr12	38783620	38783662	+	1	NA	promoter-TSS (NM_001163154)	promoter-TSS (NM_001163154)	-70	NM_001163154	14009	Mm.4866	NM_007960	ENSMUSG00000004151	Etv1	ER81|Etsrp81	ets variant 1	protein-coding
mm_14175.1	chr2	126718042	126718058	+	1	NA	5' UTR (NM_001252580, exon 2 of 19)	5' UTR (NM_001252580, exon 2 of 19)	10722	NM_019729	84092	Mm.272629	NM_019729	ENSMUSG00000027363	Usp8	AI574262|AW557536|Ubpy|mKIAA0055	ubiquitin specific peptidase 8	protein-coding
mm_138517.1	chr17	35237924	35237934	+	1	NA	3' UTR (NM_023179, exon 3 of 3)	3' UTR (NM_023179, exon 3 of 3)	1333	NM_023179	66237	Mm.396107	NM_023179	ENSMUSG00000024403	Atp6v1g2	1500002D01Rik|Atp6g2|NG38|VAG2	ATPase, H+ transporting, lysosomal V1 subunit G2	protein-coding
mm_71252.1	chr8	40916538	40916546	+	1	NA	3' UTR (NM_001044740, exon 12 of 12)	3' UTR (NM_001044740, exon 12 of 12)	-9691	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_59920.1	chr7	30421725	30421742	+	1	NA	Intergenic	CpG	-1571	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_126238.1	chr15	78987105	78987120	+	1	NA	intron (NM_001024716, intron 1 of 13)	intron (NM_001024716, intron 1 of 13)	4056	NM_001024716	110253	Mm.123714	NM_138579	ENSMUSG00000033088	Triobp	AI428493|EST478828|Tara|mKIAA1662	TRIO and F-actin binding protein	protein-coding
mm_137666.1	chr17	28699615	28699618	+	1	NA	intron (NM_001168514, intron 2 of 12)	intron (NM_001168514, intron 2 of 12)	7048	NM_001168513	26416	Mm.311337	NM_011951	ENSMUSG00000053436	Mapk14	CSBP2|Crk1|Csbp1|Mxi2|PRKM14|PRKM15|p38|p38-alpha|p38MAPK|p38a|p38alpha	mitogen-activated protein kinase 14	protein-coding
mm_91551.1	chr10	39899162	39899184	-	1	NA	promoter-TSS (NR_033628)	promoter-TSS (NR_033628)	65	NR_033628	213332	Mm.484359	NR_033628		Mfsd4b4	AA474331	major facilitator superfamily domain containing 4B4	pseudo
mm_141203.1	chr17	27038438	27038446	-	1	NA	Intergenic	Intergenic	9183	NM_027544	70772	Mm.440437	NM_027544	ENSMUSG00000048731	Ggnbp1	0610031G08Rik|mdf	gametogenetin binding protein 1	protein-coding
mm_31026.1	chr4	40853302	40853324	+	1	NA	intron (NM_022305, intron 1 of 5)	intron (NM_022305, intron 1 of 5)	1224	NM_022305	14595	Mm.15622	NM_022305	ENSMUSG00000028413	B4galt1	B-1,4-GalT|B-1,4-GalT1|GalT|Ggtb|Ggtb2|b4Gal-T1|beta-1,4-GalT|beta-1,4-GalT1|beta4Gal-T1	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1	protein-coding
mm_48930.1	chr6	4530953	4530966	+	1	NA	exon (NM_007743, exon 35 of 52)	exon (NM_007743, exon 35 of 52)	25341	NM_007743	12843	Mm.277792	NM_007743	ENSMUSG00000029661	Col1a2	AA960264|AI325291|Col1a-2|Cola-2|Cola2|oim	collagen, type I, alpha 2	protein-coding
mm_96710.1	chr11	69655841	69655857	+	1	NA	TTS (NR_125917)	TTS (NR_125917)	812	NM_009235	20670	Mm.347499	NM_009235	ENSMUSG00000041287	Sox15	-	SRY (sex determining region Y)-box 15	protein-coding
mm_35091.1	chr4	8239035	8239047	-	1	NA	promoter-TSS (NM_007592)	promoter-TSS (NM_007592)	0	NM_007592	12319	Mm.119320	NM_007592	ENSMUSG00000041261	Car8	AW546993|Ca8|Cals|Cals1|Carp|wdl	carbonic anhydrase 8	protein-coding
mm_84319.1	chr9	63757934	63757964	-	1	NA	promoter-TSS (NM_016769)	promoter-TSS (NM_016769)	45	NM_016769	17127	Mm.7320	NM_016769	ENSMUSG00000032402	Smad3	AU022421|Madh3	SMAD family member 3	protein-coding
mm_83600.1	chr9	48495267	48495273	-	1	NA	promoter-TSS (NM_001004191)	promoter-TSS (NM_001004191)	60	NM_001326355	67010	Mm.76911	NM_144948	ENSMUSG00000042396	Rbm7	1200007M24Rik|1500011D06Rik|AU041934|AW554393	RNA binding motif protein 7	protein-coding
mm_43110.1	chr5	124541297	124541315	+	1	NA	intron (NM_019770, intron 1 of 3)	CpG	515	NM_019770	56334	Mm.325307	NM_019770	ENSMUSG00000029390	Tmed2	1110032D12Rik|1810020N21Rik|Rnp24|Sid394|p24beta1	transmembrane p24 trafficking protein 2	protein-coding
mm_25971.1	chr3	132865848	132865897	+	1	NA	intron (NR_102297, intron 1 of 3)	intron (NR_102297, intron 1 of 3)	12724	NR_102297	101243624	Mm.306256	NR_102297	ENSMUSG00000106230	Gm29811	-	predicted gene, 29811	ncRNA
mm_55898.1	chr6	83572430	83572472	-	1	NA	promoter-TSS (NM_024239)	promoter-TSS (NM_024239)	53	NM_024239	70527	Mm.32801	NM_024239	ENSMUSG00000006906	Stambp	5330424L14Rik|5730422L11Rik|AW107289|Amsh|mKIAA4198	STAM binding protein	protein-coding
mm_53327.1	chr6	129230503	129230513	+	1	NA	Intergenic	Intergenic	7537	NR_040265	76432	Mm.261738	NR_040265	ENSMUSG00000097354	2310001H17Rik	AI646108	RIKEN cDNA 2310001H17 gene	ncRNA
mm_14101.1	chr2	125247710	125247743	+	1	NA	5' UTR (NM_023595, exon 1 of 6)	5' UTR (NM_023595, exon 1 of 6)	211	NM_023595	110074	Mm.282499	NM_023595	ENSMUSG00000027203	Dut	5031412I06Rik|5133400F09Rik|D2Bwg0749e|Dutp|dUTPase	deoxyuridine triphosphatase	protein-coding
mm_50117.1	chr6	41534889	41534896	+	1	NA	Intergenic	Intergenic	13116	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_99503.1	chr11	103028328	103028368	+	1	NA	promoter-TSS (NM_008707)	promoter-TSS (NM_008707)	-214	NM_008707	18107	Mm.10265	NM_008707	ENSMUSG00000020936	Nmt1	AW536594	N-myristoyltransferase 1	protein-coding
mm_53296.1	chr6	129036744	129036753	+	1	NA	Intergenic	RMER19A|LTR|ERVK	-9153	NR_024262	232408	Mm.259262	NM_153094	ENSMUSG00000030154	Klrb1f	A630024B12Rik|Nkr-p1f|Nkrp1-f|Nkrp1f	killer cell lectin-like receptor subfamily B member 1F	protein-coding
mm_97199.1	chr11	75594911	75594921	+	1	NA	intron (NM_008850, intron 2 of 11)	intron (NM_008850, intron 2 of 11)	5315	NR_110477	654359	Mm.439961	NR_110477		Gm12338	OTTMUSG00000006216	cytochrome c oxidase, subunit VIIc pseudogene	pseudo
mm_146701.1	chr18	13726734	13726737	-	1	NA	intron (NM_145492, intron 5 of 7)	intron (NM_145492, intron 5 of 7)	245998	NM_145492	225207	Mm.40325	NM_145492	ENSMUSG00000024420	Zfp521	B930086A16Rik|Evi3|Znf521	zinc finger protein 521	protein-coding
mm_127036.1	chr15	96474885	96474891	+	1	NA	Intergenic	Intergenic	-14045	NM_028148	72193	Mm.324474	NM_028148	ENSMUSG00000033228	Scaf11	1110061H03Rik|2610510E10Rik|AI462454|CASP11|SIP1|SRRP129|Sfrs2ip|Srsf2ip|mKIAA3013	SR-related CTD-associated factor 11	protein-coding
mm_123579.1	chr14	67008086	67008090	-	1	NA	intron (NM_009761, intron 1 of 5)	ID_B1|SINE|B4	789	NM_009761	12177	Mm.29820	NM_009761	ENSMUSG00000022051	Bnip3l	C86132|D14Ertd719e|Nip3L|Nix	BCL2/adenovirus E1B interacting protein 3-like	protein-coding
mm_8581.1	chr1	155861415	155861429	-	1	NA	intron (NM_001039184, intron 34 of 37)	intron (NM_001039184, intron 34 of 37)	-48523	NM_001024945	104009	Mm.27035	NM_023268	ENSMUSG00000033684	Qsox1	1300003H02Rik|QSOX|Qscn6|SOx	quiescin Q6 sulfhydryl oxidase 1	protein-coding
mm_97708.1	chr11	80178657	80178665	+	1	NA	3' UTR (NM_172133, exon 11 of 11)	3' UTR (NM_172133, exon 11 of 11)	-5211	NM_028019	71956	Mm.22985	NM_028019	ENSMUSG00000020707	Rnf135	0610037N03Rik|2410006N06Rik	ring finger protein 135	protein-coding
mm_4240.1	chr1	171389069	171389099	+	1	NA	TTS (NM_027893)	TTS (NM_027893)	124	NM_001005508	226652	Mm.251048	NM_001005508	ENSMUSG00000048865	Arhgap30	6030405P05Rik|Gm102|mFLJ00267	Rho GTPase activating protein 30	protein-coding
mm_43363.1	chr5	135351900	135351927	+	1	NA	Intergenic	Intergenic	-1382	NM_001346745	215061	Mm.261834	NM_178240	ENSMUSG00000053388	Trim50	-	tripartite motif-containing 50	protein-coding
mm_135490.1	chr16	46120120	46120137	-	1	NA	5' UTR (NM_032465, exon 1 of 15)	5' UTR (NM_032465, exon 1 of 15)	120	NM_032465	84544	Mm.29204	NM_032465	ENSMUSG00000022657	Cd96	1700109I12Rik|Tactile	CD96 antigen	protein-coding
mm_54034.1	chr6	12749071	12749079	-	1	NA	5' UTR (NM_001164805, exon 1 of 27)	5' UTR (NM_001164805, exon 1 of 27)	178	NM_001164805	330267	Mm.11989	NM_001164805	ENSMUSG00000032625	Thsd7a	Gm837	thrombospondin, type I, domain containing 7A	protein-coding
mm_100314.1	chr11	117986901	117986916	+	1	NA	promoter-TSS (NM_133757)	promoter-TSS (NM_133757)	51	NM_133757	74451	Mm.28864	NM_133757	ENSMUSG00000017715	Pgs1	2610019F11Rik|4933424M23Rik|SAF	phosphatidylglycerophosphate synthase 1	protein-coding
mm_109439.1	chr12	110699055	110699104	+	1	NA	Intergenic	RMER17C|LTR|ERVK	-2684	NM_010480	15519	Mm.1843	NM_010480	ENSMUSG00000021270	Hsp90aa1	86kDa|89kDa|AL024080|AL024147|Hsp86-1|Hsp89|Hsp90|Hspca|hsp4	heat shock protein 90, alpha (cytosolic), class A member 1	protein-coding
mm_13335.1	chr2	102786318	102786328	+	1	NA	3' UTR (NM_001077514, exon 11 of 11)	3' UTR (NM_001077514, exon 11 of 11)	79885	NM_001077515	20511	Mm.267547	NM_011393	ENSMUSG00000005089	Slc1a2	1700091C19Rik|2900019G14Rik|AI159670|Eaat2|GLT-1|GLT1|MGLT1	solute carrier family 1 (glial high affinity glutamate transporter), member 2	protein-coding
mm_24969.1	chr3	96727768	96727794	+	1	NA	promoter-TSS (NM_028925)	promoter-TSS (NM_028925)	170	NM_026406	67845	Mm.386792	NM_026406	ENSMUSG00000028098	Rnf115	2610028E05Rik|AU042696|Zfp364	ring finger protein 115	protein-coding
mm_51823.1	chr6	89140993	89141014	+	1	NA	promoter-TSS (NR_121596)	promoter-TSS (NR_121596)	9	NR_121593	434065	Mm.333241	NM_001033491	ENSMUSG00000090254	Gm1965	AU018164|AU021089|AU023851|C86079	predicted gene 1965	ncRNA
mm_130462.1	chr15	98609030	98609046	-	1	NA	Intergenic	Intergenic	-1405	NM_007405	11512	Mm.157091	NM_007405	ENSMUSG00000022994	Adcy6	AC6|mKIAA0422	adenylate cyclase 6	protein-coding
mm_49272.1	chr6	17519759	17519802	+	1	NA	intron (NM_008591, intron 4 of 21)	intron (NM_008591, intron 4 of 21)	55823	NM_008591	17295	Mm.86844	NM_008591	ENSMUSG00000009376	Met	AI838057|HGF|HGFR|Par4|c-Met	met proto-oncogene	protein-coding
mm_94538.1	chr11	9125158	9125170	+	1	NA	intron (NM_001159401, intron 2 of 8)	intron (NM_001159401, intron 2 of 8)	6657	NM_001159402	22271	Mm.4610	NM_009477	ENSMUSG00000020407	Upp1	AI325217|UPase|UdRPase|Up|Upp	uridine phosphorylase 1	protein-coding
mm_2735.1	chr1	128244585	128244593	+	1	NA	intron (NM_026390, intron 1 of 12)	CpG	408	NM_026390	67812	Mm.293321	NM_026390	ENSMUSG00000026353	Ubxn4	1300013G12Rik|Ubxd2|mKIAA0242	UBX domain protein 4	protein-coding
mm_31261.1	chr4	45184816	45184851	+	1	NA	promoter-TSS (NM_001081172)	promoter-TSS (NM_001081172)	-73	NM_001081172	666060	Mm.24783	NM_001081172	ENSMUSG00000035615	Frmpd1	BC031840|mKIAA0967	FERM and PDZ domain containing 1	protein-coding
mm_48377.1	chr5	139716496	139716524	-	1	NA	exon (NM_174850, exon 6 of 17)	exon (NM_174850, exon 6 of 17)	19823	NM_174850	231830	Mm.240510	NM_174850	ENSMUSG00000036718	Micall2	A930021H16Rik|JRAB|MICAL-L2|mFLJ00139	MICAL-like 2	protein-coding
mm_156070.1	chrX	109161305	109161315	+	1	NA	3' UTR (NM_019989, exon 4 of 4)	3' UTR (NM_019989, exon 4 of 4)	-35446	NM_001037917	622976	Mm.482747	NM_001037917	ENSMUSG00000048621	Gm6377	EG622976	predicted gene 6377	protein-coding
mm_30263.1	chr3	146770133	146770146	-	1	NA	promoter-TSS (NM_001164198)	promoter-TSS (NM_001164198)	99	NM_001164198	18749	Mm.16766	NM_011100	ENSMUSG00000005034	Prkacb	CbPKA|Pkacb	protein kinase, cAMP dependent, catalytic, beta	protein-coding
mm_64221.1	chr7	141562286	141562296	+	1	NA	5' UTR (NM_007459, exon 1 of 22)	5' UTR (NM_007459, exon 1 of 22)	111	NM_007459	11772	Mm.253090	NM_007459	ENSMUSG00000002957	Ap2a2	2410074K14Rik|AF006990|AW146353|Adtab|C78001|L25	adaptor-related protein complex 2, alpha 2 subunit	protein-coding
mm_67799.1	chr7	98085474	98085519	-	1	NA	exon (NM_001256082, exon 16 of 49)	exon (NM_001256082, exon 16 of 49)	23752	NM_001256082	17921	Mm.1403	NM_008663	ENSMUSG00000030761	Myo7a	Hdb|Myo7|USH1B|nmf371|polka|sh-1|sh1	myosin VIIA	protein-coding
mm_170086.1	chr17	35506120	35506120	+	1	NA	promoter-TSS (NM_013633)	promoter-TSS (NM_013633)	88	NM_013633	18999	Mm.17031	NM_013633	ENSMUSG00000024406	Pou5f1	NF-A3|Oct-3|Oct-3/4|Oct-4|Oct3|Oct3/4|Oct4|Otf-3|Otf-4|Otf3|Otf3-rs7|Otf3g|Otf4	POU domain, class 5, transcription factor 1	protein-coding
mm_4117.1	chr1	167689635	167689662	+	1	NA	promoter-TSS (NM_033652)	promoter-TSS (NM_033652)	90	NM_033652	110648	Mm.330081	NM_033652	ENSMUSG00000026686	Lmx1a	Lmx1.1|dr|dreher|sst	LIM homeobox transcription factor 1 alpha	protein-coding
mm_156316.1	chrX	136993282	136993308	+	1	NA	promoter-TSS (NM_001114179)	promoter-TSS (NM_001114179)	140	NM_001035509	66995	Mm.440155	NM_025893	ENSMUSG00000031428	Zcchc18	1500031H04Rik|Sizn2	zinc finger, CCHC domain containing 18	protein-coding
mm_102277.1	chr11	55395529	55395546	-	1	NA	3' UTR (NM_009242, exon 10 of 10)	3' UTR (NM_009242, exon 10 of 10)	24543	NM_009242	20692	Mm.291442	NM_009242	ENSMUSG00000018593	Sparc	BM-40|ON	secreted acidic cysteine rich glycoprotein	protein-coding
mm_19951.1	chr2	117331093	117331097	-	1	NA	intron (NM_011246, intron 2 of 16)	intron (NM_011246, intron 2 of 16)	11782	NM_011246	19419	Mm.42150	NM_011246	ENSMUSG00000027347	Rasgrp1	Rasgrp	RAS guanyl releasing protein 1	protein-coding
mm_103170.1	chr11	70459657	70459705	-	1	NA	promoter-TSS (NM_001029929)	promoter-TSS (NM_001029929)	59	NM_001029929	574428	Mm.472771	NM_001029929	ENSMUSG00000040829	Zmynd15	-	zinc finger, MYND-type containing 15	protein-coding
mm_85078.1	chr9	91364874	91364887	-	1	NA	exon (NM_009573, exon 1 of 3)	exon (NM_009573, exon 1 of 3)	919	NM_009573	22771	Mm.335350	NM_009573	ENSMUSG00000032368	Zic1	ZIC|ZNF201	zinc finger protein of the cerebellum 1	protein-coding
mm_105954.1	chr11	115322026	115322064	-	1	NA	promoter-TSS (NM_176847)	promoter-TSS (NM_176847)	-127	NM_176847	16470	Mm.451539	NM_176847	ENSMUSG00000045288	Ush1g	Sans|js	Usher syndrome 1G	protein-coding
mm_19608.1	chr2	102739838	102739858	-	1	NA	exon (NM_011393, exon 4 of 10)	exon (NM_011393, exon 4 of 10)	33410	NM_001077515	20511	Mm.267547	NM_011393	ENSMUSG00000005089	Slc1a2	1700091C19Rik|2900019G14Rik|AI159670|Eaat2|GLT-1|GLT1|MGLT1	solute carrier family 1 (glial high affinity glutamate transporter), member 2	protein-coding
mm_64984.1	chr7	16916009	16916035	-	1	NA	3' UTR (NM_007590, exon 6 of 6)	3' UTR (NM_007590, exon 6 of 6)	8010	NM_007590	12315	Mm.288630	NM_007590	ENSMUSG00000019370	Calm3	CaMA|R75142	calmodulin 3	protein-coding
mm_111690.1	chr12	103609791	103609803	-	1	NA	intron (NM_028980, intron 23 of 24)	intron (NM_028980, intron 23 of 24)	21647	NM_001301404	217847	Mm.29094	NM_144834	ENSMUSG00000061947	Serpina10	PZI|ZPI	serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 10	protein-coding
mm_32542.1	chr4	109280366	109280400	+	1	NA	5' UTR (NM_007943, exon 1 of 25)	5' UTR (NM_007943, exon 1 of 25)	108	NM_007943	13858	Mm.318250	NM_007943	ENSMUSG00000028552	Eps15	2410112D09Rik	epidermal growth factor receptor pathway substrate 15	protein-coding
mm_15156.1	chr2	154009104	154009111	+	1	NA	intron (NM_008953, intron 1 of 8)	intron (NM_008953, intron 1 of 8)	831	NM_008953	19194	Mm.29197	NM_008953	ENSMUSG00000042459	Bpifa2	Bpifa2e|Psp	BPI fold containing family A, member 2	protein-coding
mm_40332.1	chr5	43910889	43910907	+	1	NA	3' UTR (NM_007646, exon 8 of 8)	3' UTR (NM_007646, exon 8 of 8)	42089	NM_007646	12494	Mm.249873	NM_007646	ENSMUSG00000029084	Cd38	ADPRC 1|Cd38-rs1|I-19	CD38 antigen	protein-coding
mm_57579.1	chr6	127149653	127149663	-	1	NA	promoter-TSS (NR_040275)	promoter-TSS (NR_040275)	32	NR_040273	77558	Mm.358918	NR_040273	ENSMUSG00000097166	9330179D12Rik	-	RIKEN cDNA 9330179D12 gene	ncRNA
mm_91203.1	chr10	21161355	21161369	-	1	NA	promoter-TSS (NM_001198914)	promoter-TSS (NM_001198914)	-378	NM_010848	17863	Mm.52109	NM_010848	ENSMUSG00000019982	Myb	AI550390|M16449|c-myb	myeloblastosis oncogene	protein-coding
mm_41869.1	chr5	104459622	104459642	+	1	NA	5' UTR (NM_008861, exon 1 of 15)	5' UTR (NM_008861, exon 1 of 15)	175	NM_008861	18764	Mm.6442	NM_008861	ENSMUSG00000034462	Pkd2	C030034P18Rik|PC2|TRPP2	polycystic kidney disease 2	protein-coding
mm_13507.1	chr2	109692525	109692544	+	1	NA	promoter-TSS (NM_001048141)	promoter-TSS (NM_001048141)	98	NM_001048141	12064	Mm.1442	NM_007540	ENSMUSG00000048482	Bdnf	-	brain derived neurotrophic factor	protein-coding
mm_56876.1	chr6	118968132	118968147	-	1	NA	intron (NM_001256002, intron 3 of 47)	L2b|LINE|L2	87981	NR_046053	74363	Mm.399403	NR_046053		4931430N09Rik	-	RIKEN cDNA 4931430N09 gene	ncRNA
mm_138792.1	chr17	37492267	37492274	+	1	NA	promoter-TSS (NM_146328)	promoter-TSS (NM_146328)	-198	NM_146328	258325	Mm.484339	NM_146328	ENSMUSG00000090894	Olfr110	MOR249-2	olfactory receptor 110	protein-coding
mm_138779.1	chr17	37270215	37270249	+	1	NA	promoter-TSS (NM_013819)	promoter-TSS (NM_013819)	-2	NM_013819	14991	Mm.14437	NM_013819	ENSMUSG00000016206	H2-M3	H-2M3|Hmt|M3a|MuprM3|MuprM301|MuprM302|R4B2	histocompatibility 2, M region locus 3	protein-coding
mm_22529.1	chr3	7686917	7686951	+	1	NA	Intergenic	Intergenic	-73174	NM_001313888	16196	Mm.3825	NM_008371	ENSMUSG00000040329	Il7	A630026I06Rik|Il-7|hlb368	interleukin 7	protein-coding
mm_30863.1	chr4	31616577	31616578	+	1	NA	Intergenic	MLT1B|LTR|ERVL-MaLR	-347530	NM_009316	26409	Mm.258589	NM_009316	ENSMUSG00000028284	Map3k7	B430101B05|C87327|Tak1	mitogen-activated protein kinase kinase kinase 7	protein-coding
mm_50961.1	chr6	59208862	59208878	+	1	NA	promoter-TSS (NM_001081145)	promoter-TSS (NM_001081145)	0	NM_001081145	68140	Mm.25843	NM_001081145	ENSMUSG00000049232	Tigd2	3632410O17Rik	tigger transposable element derived 2	protein-coding
mm_164757.1	chr17	84137885	84137887	-	1	NA	Intergenic	Intergenic	50061	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_74659.1	chr8	13548990	13548998	-	1	NA	Intergenic	Intergenic	13467	NM_025601	66501	Mm.46136	NM_025601	ENSMUSG00000031452	1700029H14Rik	-	RIKEN cDNA 1700029H14 gene	protein-coding
mm_77373.1	chr8	119830614	119830624	-	1	NA	intron (NM_028071, intron 2 of 3)	PB1D10|SINE|Alu	9960	NM_028071	72042	Mm.393405	NM_028071	ENSMUSG00000031827	Cotl1	1810074P22Rik|2010004C08Rik|Clp	coactosin-like 1 (Dictyostelium)	protein-coding
mm_3962.1	chr1	164136203	164136235	+	1	NA	intron (NM_011347, intron 8 of 15)	intron (NM_011347, intron 8 of 15)	-15616	NM_007976	14067	Mm.12900	NM_007976	ENSMUSG00000026579	F5	AI173222|Cf-5|Cf5	coagulation factor V	protein-coding
mm_152409.1	chr19	10604395	10604397	-	1	NA	promoter-TSS (NM_145496)	promoter-TSS (NM_145496)	-138	NM_145496	225913	Mm.374868	NM_145496	ENSMUSG00000034371	Tkfc	BC021917|Dak	triokinase, FMN cyclase	protein-coding
mm_107727.1	chr12	57230515	57230564	+	1	NA	5' UTR (NM_001164370, exon 1 of 10)	5' UTR (NM_001164370, exon 1 of 10)	114	NM_001164370	73490	Mm.268180	NM_001164370	ENSMUSG00000047022	Mipol1	1700081O04Rik|6030439O22Rik|AU021838|AW536152|D12Ertd19e	mirror-image polydactyly 1	protein-coding
mm_42548.1	chr5	116123591	116123637	+	1	NA	Intergenic	Intergenic	-40368	NM_001101546	545798	Mm.483995	NM_001101546	ENSMUSG00000079278	Tmem233	DSPB2|Gm13843|OTTMUSG00000014722	transmembrane protein 233	protein-coding
mm_157632.1	chrX	56822506	56822508	-	1	NA	promoter-TSS (NM_177293)	promoter-TSS (NM_177293)	-182	NM_177293	320923	Mm.186745	NM_177293	ENSMUSG00000067878	Mtap7d3	4933424A10Rik|Map7d3	MAP7 domain containing 3	protein-coding
mm_67953.1	chr7	100499392	100499406	-	1	NA	3' UTR (NM_011671, exon 8 of 8)	3' UTR (NM_011671, exon 8 of 8)	6041	NM_011671	22228	Mm.171378	NM_011671	ENSMUSG00000033685	Ucp2	Slc25a8	uncoupling protein 2 (mitochondrial, proton carrier)	protein-coding
mm_124074.1	chr14	78616351	78616354	-	1	NA	exon (NM_001281794, exon 9 of 28)	exon (NM_001281794, exon 9 of 28)	12938	NM_001253766	380921	Mm.89591	NM_001081336	ENSMUSG00000034731	Dgkh	5930402B05Rik|D130015C16|DGK	diacylglycerol kinase, eta	protein-coding
mm_120833.1	chr14	75176824	75176904	+	1	NA	5' UTR (NM_008879, exon 2 of 17)	5' UTR (NM_008879, exon 2 of 17)	40439	NM_008879	18826	Mm.153911	NM_008879	ENSMUSG00000021998	Lcp1	AW536232|D14Ertd310e|LCP-1|Pls2|pp65	lymphocyte cytosolic protein 1	protein-coding
mm_109186.1	chr12	108488208	108488215	+	1	NA	intron (NM_001043335, intron 3 of 21)	intron (NM_001043335, intron 3 of 21)	65395	NM_001043335	68519	Mm.236645	NM_001043335	ENSMUSG00000058070	Eml1	1110008N23Rik|A930030P13Rik|AA171013|AI847476|AI853955|ELP79|EMAP|EMAPL|heco	echinoderm microtubule associated protein like 1	protein-coding
mm_115703.1	chr13	14521807	14521818	-	1	NA	intron (NM_001081348, intron 1 of 28)	intron (NM_001081348, intron 1 of 28)	1414	NM_001081348	94253	Mm.125298	NM_153130	ENSMUSG00000021301	Hecw1	9330116H24Rik|AV273951|E130207I19Rik|Nedl1	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	protein-coding
mm_29156.1	chr3	106014631	106014643	-	1	NA	promoter-TSS (NM_001200028)	promoter-TSS (NM_001200028)	9	NM_001200028	100503311	Mm.386825	NM_029604	ENSMUSG00000010136	Pifo	1700027A23Rik	primary cilia formation	protein-coding
mm_84307.1	chr9	63666790	63666796	-	1	NA	intron (NM_016769, intron 3 of 8)	intron (NM_016769, intron 3 of 8)	64138	NM_025857	66939	Mm.34338	NM_025857	ENSMUSG00000037257	Aagab	2310007F21Rik|p34	alpha- and gamma-adaptin binding protein	protein-coding
mm_103673.1	chr11	79146464	79146482	-	1	NA	promoter-TSS (NM_013571)	promoter-TSS (NM_013571)	-119	NM_013571	16706	Mm.4745	NM_013571	ENSMUSG00000018334	Ksr1	AW492498|B-KSR1|D11Bhm183e|D11Bhm184e|Ksr|RSU2|hb	kinase suppressor of ras 1	protein-coding
mm_94794.1	chr11	22972089	22972110	+	1	NA	promoter-TSS (NM_011663)	promoter-TSS (NM_011663)	94	NM_011663	22183	Mm.29542	NM_011663	ENSMUSG00000044068	Zrsr1	D11Ncvs75|Irlgs2|SP2|U2af1-rs1|U2afbp-rs	zinc finger (CCCH type), RNA binding motif and serine/arginine rich 1	protein-coding
mm_99755.1	chr11	106751243	106751251	+	1	NA	promoter-TSS (NM_001271373)	promoter-TSS (NM_001271373)	21	NM_001033435	380732	Mm.343952	NM_001033435	ENSMUSG00000040528	Milr1	Allergin-1|Gm885|Mca32	mast cell immunoglobulin like receptor 1	protein-coding
mm_149500.1	chr19	11913124	11913135	+	1	NA	intron (NM_172635, intron 1 of 18)	MIR3|SINE|MIR	730	NM_172635	225929	Mm.42711	NM_172635	ENSMUSG00000046139	Patl1	AV312086|Pat1b	protein associated with topoisomerase II homolog 1 (yeast)	protein-coding
mm_165020.1	chr19	31932358	31932358	+	1	NA	intron (NM_001081074, intron 7 of 11)	intron (NM_001081074, intron 7 of 11)	63597	NM_001081074	69865	Mm.87538	NM_001081074	ENSMUSG00000052595	A1cf	1810073H04Rik|ACF64|ACF65|ASP|Acf|MCM|MerCreMer|Tg(Myh6-cre/Esr1*)1Jmk|mer	APOBEC1 complementation factor	protein-coding
mm_121451.1	chr14	120478323	120478351	+	1	NA	promoter-TSS (NM_029519)	promoter-TSS (NM_029519)	-124	NM_029519	76108	Mm.261448	NM_029519	ENSMUSG00000051615	Rap2a	5830461H18Rik	RAS related protein 2a	protein-coding
mm_139230.1	chr17	47730859	47730868	+	1	NA	intron (NM_025973, intron 5 of 8)	intron (NM_025973, intron 5 of 8)	4021	NM_025973	109820	Mm.22957	NM_025973	ENSMUSG00000023987	Pgc	2210410L06Rik|Upg-1|Upg1	progastricsin (pepsinogen C)	protein-coding
mm_130506.1	chr15	98845604	98845629	-	1	NA	exon (NM_001033276, exon 40 of 55)	exon (NM_001033276, exon 40 of 55)	-14108	NM_016781	19082	Mm.6670	NM_016781	ENSMUSG00000067713	Prkag1	AA571379|BB036179|Prkaac	protein kinase, AMP-activated, gamma 1 non-catalytic subunit	protein-coding
mm_98692.1	chr11	96299138	96299148	+	1	NA	promoter-TSS (NM_008269)	promoter-TSS (NM_008269)	-28	NM_008269	15414	Mm.215	NM_008269	ENSMUSG00000000690	Hoxb6	Hox-2.2	homeobox B6	protein-coding
mm_50131.1	chr6	41542545	41542557	+	1	NA	Intergenic	Intergenic	20775	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_97706.1	chr11	80178274	80178284	+	1	NA	intron (NM_172133, intron 10 of 10)	intron (NM_172133, intron 10 of 10)	-5593	NM_028019	71956	Mm.22985	NM_028019	ENSMUSG00000020707	Rnf135	0610037N03Rik|2410006N06Rik	ring finger protein 135	protein-coding
mm_171194.1	chr3	46141342	46141344	+	1	NA	Intergenic	Lx|LINE|L1	306598	NM_001101479	241989	Mm.119234	NM_001101479	ENSMUSG00000090919	Pabpc4l	C330050A14Rik|EG241989	poly(A) binding protein, cytoplasmic 4-like	protein-coding
mm_93032.1	chr10	88146868	88146936	-	1	NA	promoter-TSS (NM_027191)	promoter-TSS (NM_027191)	39	NM_029249	75317	Mm.179378	NM_029249	ENSMUSG00000035365	Parpbp	4930547N16Rik|AI503644|PARI	PARP1 binding protein	protein-coding
mm_101219.1	chr11	20140363	20140377	-	1	NA	Intergenic	RLTR17|LTR|ERVK	-27419	NM_146243	66713	Mm.259045	NM_146243	ENSMUSG00000020152	Actr2	4921510D23Rik|AA409782|Arp2|D6Ertd746e	ARP2 actin-related protein 2	protein-coding
mm_113217.1	chr13	26769367	26769377	+	1	NA	exon (NM_008232, exon 1 of 1)	exon (NM_008232, exon 1 of 1)	793	NM_008232	15192	Mm.7411	NM_008232	ENSMUSG00000045835	Hdgfl1	4921520N01Rik|HRP-1|Hdgfrp1|Pwwp1	hepatoma derived growth factor-like 1	protein-coding
mm_119819.1	chr14	54226064	54226100	+	1	NA	Intergenic	Intergenic	27847	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_62172.1	chr7	97371593	97371601	+	1	NA	promoter-TSS (NM_199035)	promoter-TSS (NM_199035)	-20	NM_199035	381903	Mm.279683	NM_199035	ENSMUSG00000035704	Alg8	AI447372|Gm1089	asparagine-linked glycosylation 8 (alpha-1,3-glucosyltransferase)	protein-coding
mm_124816.1	chr15	9071253	9071273	+	1	NA	promoter-TSS (NM_001085410)	promoter-TSS (NM_001085410)	3	NM_001040395	68646	Mm.244226	NM_001040395	ENSMUSG00000022253	Nadk2	MNADK|Nadkd1	NAD kinase 2, mitochondrial	protein-coding
mm_161105.1	chr12	102840252	102840252	-	1	NA	5' UTR (NM_172806, exon 3 of 12)	5' UTR (NM_172806, exon 3 of 12)	38154	NM_172806	238386	Mm.63456	NM_172806	ENSMUSG00000041702	Btbd7	5730507E09Rik|8030448M07|E130118E17Rik|FUP1|mKIAA1525	BTB (POZ) domain containing 7	protein-coding
mm_91954.1	chr10	61100090	61100109	-	1	NA	3' UTR (NM_001316673, exon 15 of 15)	3' UTR (NM_001316673, exon 15 of 15)	10768	NM_025273	13180	Mm.39473	NM_025273	ENSMUSG00000020098	Pcbd1	Dcoh|Pcbd|Pcd|Phs	pterin 4 alpha carbinolamine dehydratase/dimerization cofactor of hepatocyte nuclear factor 1 alpha (TCF1) 1	protein-coding
mm_21953.1	chr2	167111690	167111694	-	1	NA	intron (NM_008420, intron 1 of 1)	intron (NM_008420, intron 1 of 1)	46399	NR_028540	100217443		NR_028540		Snord12	MBII-99	small nucleolar RNA, C/D box 12	snoRNA
mm_71675.1	chr8	60863845	60863848	+	1	NA	Intergenic	T-rich|Low_complexity|Low_complexity	-26605	NM_028299	72612	Mm.25263	NM_028299	ENSMUSG00000038005	Hpf1	2700029M09Rik|C230006B22Rik|C4orf27	histone PARylation factor 1	protein-coding
mm_160976.1	chr11	101078169	101078169	+	1	NA	promoter-TSS (NM_010475)	promoter-TSS (NM_010475)	-242	NM_010475	15485	Mm.188939	NM_010475	ENSMUSG00000019301	Hsd17b1	17HSDB1|17beta-HSD|E2DH|Hsd17ba	hydroxysteroid (17-beta) dehydrogenase 1	protein-coding
mm_105650.1	chr11	107137719	107137743	-	1	NA	Intergenic	Intergenic	-5809	NM_176850	207165	Mm.343986	NM_176850	ENSMUSG00000040481	Bptf	9430093H17Rik|Falz	bromodomain PHD finger transcription factor	protein-coding
mm_133634.1	chr16	91659513	91659538	+	1	NA	exon (NM_019973, exon 3 of 5)	exon (NM_019973, exon 3 of 5)	11701	NM_178880	20658	Mm.46401	NM_019973	ENSMUSG00000022961	Son	2900011L12Rik|AA409051|AU067731|C81487|mKIAA1019|nrebp	Son DNA binding protein	protein-coding
mm_137472.1	chr17	26699275	26699318	+	1	NA	3' UTR (NM_025272, exon 4 of 4)	3' UTR (NM_025272, exon 4 of 4)	-16354	NM_029870	77128	Mm.275414	NM_029870	ENSMUSG00000048249	Crebrf	A930001N09Rik|LRF	CREB3 regulatory factor	protein-coding
mm_92367.1	chr10	75994037	75994065	-	1	NA	intron (NM_198635, intron 9 of 13)	intron (NM_198635, intron 9 of 13)	-14875	NR_105836	102466646		NR_105836	ENSMUSG00000098817	Mir6409	Gm27787|mmu-mir-6409	microRNA 6409	ncRNA
mm_67445.1	chr7	80389817	80389827	-	1	NA	3' UTR (NM_001081454, exon 16 of 16)	3' UTR (NM_001081454, exon 16 of 16)	-1876	NM_010194	14159	Mm.48757	NM_010194	ENSMUSG00000053158	Fes	AI586313|BB137047|FPS|c-fes	feline sarcoma oncogene	protein-coding
mm_6758.1	chr1	84059104	84059116	-	1	NA	intron (NM_001003948, intron 2 of 2)	intron (NM_001003948, intron 2 of 2)	159851	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_2094.1	chr1	87701260	87701265	+	1	NA	exon (NM_001110192, exon 16 of 27)	exon (NM_001110192, exon 16 of 27)	-54749	NM_029846	77040	Mm.272972	NM_029846	ENSMUSG00000026289	Atg16l1	1500009K01Rik|Apg16l|Atg16l|WDR30	autophagy related 16-like 1 (S. cerevisiae)	protein-coding
mm_20805.1	chr2	144270853	144270863	-	1	NA	promoter-TSS (NM_024225)	promoter-TSS (NM_024225)	44	NM_001199188	69178	Mm.273379	NM_024225	ENSMUSG00000027423	Snx5	0910001N05Rik|1810032P22Rik|AU019504|D2Ertd52e	sorting nexin 5	protein-coding
mm_83933.1	chr9	56635993	56635998	-	1	NA	promoter-TSS (NM_001311076)	promoter-TSS (NM_001311076)	-347	NM_001311076	235402	Mm.246605	NM_181074	ENSMUSG00000049556	Lingo1	4930471K13Rik|AV148400|LERN1|LINGO-1|Lrrn6a|UNQ201	leucine rich repeat and Ig domain containing 1	protein-coding
mm_55596.1	chr6	71632873	71632877	-	1	NA	promoter-TSS (NM_173001)	promoter-TSS (NM_173001)	42	NM_001038695	104263	Mm.260479	NM_173001	ENSMUSG00000053470	Kdm3a	1700105C21Rik|C230043E16Rik|JHDM2a|Jmjd1|Jmjd1a|KDM2A|TGSA|Tsga	lysine (K)-specific demethylase 3A	protein-coding
mm_114793.1	chr13	89540846	89540865	+	1	NA	5' UTR (NM_013500, exon 1 of 5)	5' UTR (NM_013500, exon 1 of 5)	219	NM_013500	12950	Mm.266790	NM_013500	ENSMUSG00000021613	Hapln1	BB099155|CLP|Crtl1|Crtl1l|LP|LP-1	hyaluronan and proteoglycan link protein 1	protein-coding
mm_52913.1	chr6	122826667	122826681	+	1	NA	intron (NM_021899, intron 1 of 10)	intron (NM_021899, intron 1 of 10)	-4703	NR_106090	102465710		NR_106090	ENSMUSG00000106580	Mir7231	mmu-mir-7231	microRNA 7231	ncRNA
mm_14480.1	chr2	131514532	131514551	+	1	NA	intron (NM_001177836, intron 2 of 7)	intron (NM_001177836, intron 2 of 7)	22679	NM_001177838	228608	Mm.136586	NM_145533	ENSMUSG00000027333	Smox	B130066H01Rik|PAO|PAOh1|SMO	spermine oxidase	protein-coding
mm_40813.1	chr5	71729193	71729195	+	1	NA	intron (NM_008069, intron 3 of 8)	intron (NM_008069, intron 3 of 8)	29178	NM_008069	14400	Mm.38567	NM_008069	ENSMUSG00000029212	Gabrb1	AW061132|B230208N19Rik|Gabrb-1	gamma-aminobutyric acid (GABA) A receptor, subunit beta 1	protein-coding
mm_49313.1	chr6	18170783	18170798	+	1	NA	5' UTR (NM_021050, exon 1 of 27)	5' UTR (NM_021050, exon 1 of 27)	103	NM_021050	12638	Mm.15621	NM_021050	ENSMUSG00000041301	Cftr	AW495489|Abcc7	cystic fibrosis transmembrane conductance regulator	protein-coding
mm_61895.1	chr7	90029154	90029184	+	1	NA	promoter-TSS (NR_110365)	promoter-TSS (NR_110365)	10	NR_110364	319711	Mm.31753	NR_015614	ENSMUSG00000097585	E230029C05Rik	AI452102|B230337J15	RIKEN cDNA E230029C05 gene	ncRNA
mm_20319.1	chr2	127318227	127318230	-	1	NA	Intergenic	Intergenic	-17931	NM_010090	13537	Mm.4729	NM_010090	ENSMUSG00000027368	Dusp2	PAC1	dual specificity phosphatase 2	protein-coding
mm_171529.1	chr4	146611174	146611186	+	1	NA	Intergenic	Intergenic	-64307	NR_045468	67524	Mm.444300	NR_045468	ENSMUSG00000086046	1700095A21Rik	-	RIKEN cDNA 1700095A21 gene	ncRNA
mm_81016.1	chr9	104116105	104116105	+	1	NA	intron (NM_175324, intron 16 of 19)	intron (NM_175324, intron 16 of 19)	10538	NM_145700	252837	Mm.269254	NM_145700	ENSMUSG00000079355	Ackr4	A630091E18Rik|CCBP2|CCR11|CCX-CKR|CCX-CKR1|Ccrl1|Cmkbrl1|PPR1|VSHK1	atypical chemokine receptor 4	protein-coding
mm_163162.1	chr11	85171069	85171073	+	1	NA	promoter-TSS (NM_028589)	promoter-TSS (NM_028589)	-25	NM_028589	73634	Mm.48850	NM_028589	ENSMUSG00000018479	1700125H20Rik	-	RIKEN cDNA 1700125H20 gene	protein-coding
mm_42374.1	chr5	114928171	114928212	+	1	NA	exon (NM_145209, exon 3 of 7)	exon (NM_145209, exon 3 of 7)	4951	NM_145209	231655	Mm.95479	NM_145209	ENSMUSG00000041827	Oasl1	7530414C13Rik|oasl9	2'-5' oligoadenylate synthetase-like 1	protein-coding
mm_100259.1	chr11	117332304	117332328	+	1	NA	promoter-TSS (NM_001113488)	promoter-TSS (NM_001113488)	3	NM_001113488	53860	Mm.38450	NM_017380	ENSMUSG00000059248	Sept9	MSF1|Msf|PNUTL4|Sint1	septin 9	protein-coding
mm_128146.1	chr15	31601507	31601558	-	1	NA	promoter-TSS (NM_026546)	promoter-TSS (NM_026546)	272	NM_007637	12465	Mm.282158	NM_007637	ENSMUSG00000022234	Cct5	CCT-epsilon|Ccte|TCP-1-epsilon|TCPE|mKIAA0098	chaperonin containing Tcp1, subunit 5 (epsilon)	protein-coding
mm_14303.1	chr2	129101001	129101066	+	1	NA	promoter-TSS (NM_009086)	promoter-TSS (NM_009086)	37	NM_009086	20017	Mm.259078	NM_009086	ENSMUSG00000027395	Polr1b	128kDa|D630020H17Rik|RPA116|RPA135|RPA2|Rpo1-2	polymerase (RNA) I polypeptide B	protein-coding
mm_158631.1	chrX	153262876	153262879	-	1	NA	intron (NM_173780, intron 1 of 6)	RMER5|LTR|ERV1	24832	NM_173780	245671	Mm.260751	NM_173780	ENSMUSG00000041649	Klf8	A830097P10Rik|BKLF3|ZNF74	Kruppel-like factor 8	protein-coding
mm_51835.1	chr6	90301232	90301236	+	1	NA	promoter-TSS (NM_177738)	promoter-TSS (NM_177738)	-36	NM_177738	243535	Mm.233854	NM_177738	ENSMUSG00000049694	BC048671	-	cDNA sequence BC048671	protein-coding
mm_76343.1	chr8	84723782	84723794	-	1	NA	exon (NM_001081982, exon 7 of 10)	exon (NM_001081982, exon 7 of 10)	22331	NM_008535	17095	Mm.4925	NM_008535	ENSMUSG00000034041	Lyl1	Lyl-1|bHLHa18	lymphoblastomic leukemia 1	protein-coding
mm_86207.1	chr9	119983763	119983780	-	1	NA	intron (NM_153287, intron 1 of 4)	CpG	887	NM_153287	215418	Mm.491094	NM_153287	ENSMUSG00000032515	Csrnp1	4931429D10Rik|Axud1|CSRNP-1|URAX1|taip-3	cysteine-serine-rich nuclear protein 1	protein-coding
mm_160171.1	chr7	45181274	45181274	+	1	NA	intron (NM_053256, intron 1 of 2)	intron (NM_053256, intron 1 of 2)	279	NM_053256	114640	Mm.207078	NM_053256	ENSMUSG00000038300	Pth2	Tifp39|Tip39	parathyroid hormone 2	protein-coding
mm_153471.1	chr19	41273236	41273251	-	1	NA	TTS (NM_031376)	TTS (NM_031376)	-9239	NM_133352	107358	Mm.246440	NM_133352	ENSMUSG00000025016	Tm9sf3	1810073M23Rik|2810031D16Rik|AI115521|AI413748|AW146116|AW549777|Smbp|mKIAA4036	transmembrane 9 superfamily member 3	protein-coding
mm_65359.1	chr7	25000714	25000746	-	1	NA	exon (NM_001290469, exon 4 of 23)	exon (NM_001290469, exon 4 of 23)	5207	NM_001290469	232975	Mm.44101	NM_144921	ENSMUSG00000040907	Atp1a3	Atpa-2	ATPase, Na+/K+ transporting, alpha 3 polypeptide	protein-coding
mm_164648.1	chr17	35534130	35534138	-	1	NA	exon (NM_020576, exon 2 of 2)	exon (NM_020576, exon 2 of 2)	933	NM_020576	57390	Mm.34201	NM_020576	ENSMUSG00000024409	Psors1c2	AI448740|Pcg|SPR1	psoriasis susceptibility 1 candidate 2 (human)	protein-coding
mm_13932.1	chr2	121008489	121008506	+	1	NA	promoter-TSS (NM_010761)	promoter-TSS (NM_010761)	89	NM_010761	17151	Mm.7838	NM_010761	ENSMUSG00000023572	Ccndbp1	AU022347|DIP1|GCIP|Maid|SECC-8|SSEC-8	cyclin D-type binding-protein 1	protein-coding
mm_145516.1	chr18	60443226	60443239	+	1	NA	Intergenic	Intergenic	58751	NM_134133	106878	Mm.273197	NM_134133	ENSMUSG00000038059	Smim3	2010002N04Rik|AI195350|AW561905|Nid67|cI-41	small integral membrane protein 3	protein-coding
mm_58460.1	chr7	3365958	3365971	+	1	NA	exon (NM_133189, exon 4 of 5)	exon (NM_133189, exon 4 of 5)	-28078	NM_133190	81905	Mm.357990	NM_133190	ENSMUSG00000053395	Cacng8	-	calcium channel, voltage-dependent, gamma subunit 8	protein-coding
mm_170156.1	chr17	47141176	47141184	+	1	NA	5' UTR (NM_001097623, exon 2 of 20)	5' UTR (NM_001097623, exon 2 of 20)	238	NM_001097623	224829	Mm.260989	NM_172622		Trerf1	9430096I18Rik|AI429294|B830015H24|RAPA|Trep-132|Trep132	transcriptional regulating factor 1	protein-coding
mm_6652.1	chr1	79762431	79762443	-	1	NA	promoter-TSS (NM_001111279)	promoter-TSS (NM_001111279)	-668	NM_027057	69368	Mm.293273	NM_027057	ENSMUSG00000073643	Wdfy1	1700013B03Rik|1700120F24Rik|FENS-1|Jr1|WDF1|ZFYVE17|mKIAA1435	WD repeat and FYVE domain containing 1	protein-coding
mm_30981.1	chr4	34893730	34893738	+	1	NA	promoter-TSS (NM_009889)	promoter-TSS (NM_009889)	-45	NM_009889	12640	Mm.1361	NM_009889	ENSMUSG00000028298	Cga	CG-alpha|FSHA|GPHA1|GPHalpha|HCG|LHA|Tsha|aGSU|alpha-GSU|alphaGSU|alphaSU	glycoprotein hormones, alpha subunit	protein-coding
mm_156953.1	chrX	169987666	169987678	+	1	NA	exon (NM_001290504, exon 9 of 10)	exon (NM_001290504, exon 9 of 10)	-8755	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_85267.1	chr9	99426133	99426134	-	1	NA	intron (NM_008624, intron 1 of 5)	intron (NM_008624, intron 1 of 5)	10579	NM_008624	17532	Mm.2045	NM_008624	ENSMUSG00000032470	Mras	2900078C09Rik|AI326250	muscle and microspikes RAS	protein-coding
mm_86492.1	chr10	5593811	5593821	+	1	NA	promoter-TSS (NM_026793)	promoter-TSS (NM_026793)	88	NM_026793	68632	Mm.338242	NM_026793	ENSMUSG00000046916	Myct1	1110020B04Rik|AI225941|AI642973|Mtmc1	myc target 1	protein-coding
mm_171978.1	chr5	89689201	89689206	-	1	NA	intron (NM_001081401, intron 18 of 21)	intron (NM_001081401, intron 18 of 21)	72767	NR_037571	631105	Mm.7732	NR_037571		Gm7056	Gm149	predicted gene 7056	ncRNA
mm_107503.1	chr12	38998543	38998546	+	1	NA	Intergenic	Intergenic	214833	NM_001163154	14009	Mm.4866	NM_007960	ENSMUSG00000004151	Etv1	ER81|Etsrp81	ets variant 1	protein-coding
mm_134414.1	chr16	17722453	17722466	-	1	NA	intron (NM_001285886, intron 1 of 16)	intron (NM_001285886, intron 1 of 16)	441	NM_001285886	94112	Mm.208970	NM_033609	ENSMUSG00000012114	Med15	A230074L19Rik|AW536074|Pcqap|mPcqap	mediator complex subunit 15	protein-coding
mm_135487.1	chr16	46038603	46038623	-	1	NA	intron (NM_032465, intron 13 of 14)	LTRIS2|LTR|ERV1	-28200	NM_001134480	433022	Mm.380993	NM_001134480	ENSMUSG00000087141	Plcxd2	AW494639|EG433022	phosphatidylinositol-specific phospholipase C, X domain containing 2	protein-coding
mm_22458.1	chr3	3188113	3188117	+	1	NA	Intergenic	Intergenic	-319915	NM_013920	30942	Mm.330897	NM_013920	ENSMUSG00000017688	Hnf4g	NR2A2	hepatocyte nuclear factor 4, gamma	protein-coding
mm_95811.1	chr11	55110398	55110417	+	1	NA	3' UTR (NM_010299, exon 4 of 4)	3' UTR (NM_010299, exon 4 of 4)	12422	NM_010299	14667	Mm.287807	NM_010299	ENSMUSG00000000594	Gm2a	AA408702|AW215435|GM2-AP|SAP-3	GM2 ganglioside activator protein	protein-coding
mm_119696.1	chr14	53634822	53634831	+	1	NA	Intergenic	Intergenic	619103	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_154186.1	chr19	58794437	58794455	-	1	NA	promoter-TSS (NM_026208)	promoter-TSS (NM_026208)	-32	NM_026208	67507	Mm.27027	NM_026208	ENSMUSG00000026931	1700019N19Rik	-	RIKEN cDNA 1700019N19 gene	protein-coding
mm_71223.1	chr8	40899271	40899302	+	1	NA	exon (NM_001044740, exon 2 of 12)	exon (NM_001044740, exon 2 of 12)	-26947	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_17745.1	chr2	32713554	32713577	-	1	NA	promoter-TSS (NM_130860)	promoter-TSS (NM_130860)	-593	NR_039536	100628606		NR_039536	ENSMUSG00000105841	Mir3960	mmu-mir-3960	microRNA 3960	ncRNA
mm_84788.1	chr9	77045651	77045670	-	1	NA	exon (NM_012033, exon 1 of 11)	exon (NM_012033, exon 1 of 11)	121	NR_136923	26944	Mm.23199	NM_012033	ENSMUSG00000032357	Tinag	AI452335|TIN-ag	tubulointerstitial nephritis antigen	protein-coding
mm_139241.1	chr17	47733752	47733755	+	1	NA	intron (NM_025973, intron 7 of 8)	intron (NM_025973, intron 7 of 8)	-3284	NM_001161722	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_76673.1	chr8	93535871	93535880	-	1	NA	promoter-TSS (NM_001003951)	promoter-TSS (NM_001003951)	-168	NM_001003951	67935	Mm.65457	NM_001003951	ENSMUSG00000058019	Ces5a	1700081L16Rik|1700122C07Rik|BB081581|Ces7|Gm503|cauxin	carboxylesterase 5A	protein-coding
mm_53694.1	chr6	142751629	142751641	+	1	NA	Intergenic	RLTR41A2|LTR|ERV1	-5051	NM_009908	12764	Mm.3820	NM_009908	ENSMUSG00000030282	Cmas	AW208911|CMPNeu5Ac|D6Bwg0250e	cytidine monophospho-N-acetylneuraminic acid synthetase	protein-coding
mm_168313.1	chr11	109011981	109011983	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	91633	NM_015732	12006	Mm.71710	NM_015732	ENSMUSG00000000142	Axin2	Axi1|Axil|Conductin	axin 2	protein-coding
mm_84738.1	chr9	75373203	75373252	-	1	NA	Intergenic	Intergenic	25469	NM_013479	12049	Mm.25988	NM_013479	ENSMUSG00000032191	Bcl2l10	AA420380|AU023065|Boo|C85687|Diva	Bcl2-like 10	protein-coding
mm_148300.1	chr18	82759782	82759792	-	1	NA	promoter-TSS (NR_045389)	promoter-TSS (NR_045389)	-748	NR_045389	76961	Mm.396392	NR_045389	ENSMUSG00000101773	2210420H20Rik	-	RIKEN cDNA 2210420H20 gene	ncRNA
mm_131708.1	chr16	20812336	20812337	+	1	NA	Intergenic	MERV1_LTR|LTR|ERV1	-77825	NM_009379	21832	Mm.3943	NM_009379	ENSMUSG00000022847	Thpo	Mgdf|Ml|Mpllg|Tpo	thrombopoietin	protein-coding
mm_88357.1	chr10	75936227	75936259	+	1	NA	exon (NM_175329, exon 2 of 4)	exon (NM_175329, exon 2 of 4)	670	NM_175329	103172	Mm.333849	NM_175329	ENSMUSG00000049422	Chchd10	1620401E04Rik|AI267078|Ndg2	coiled-coil-helix-coiled-coil-helix domain containing 10	protein-coding
mm_23199.1	chr3	41493360	41493364	+	1	NA	promoter-TSS (NR_040385)	promoter-TSS (NR_040385)	-163	NR_040385	78706	Mm.366094	NR_040385	ENSMUSG00000097639	Platr4	C430002E04Rik	pluripotency associated transcript 4	ncRNA
mm_72731.1	chr8	85081426	85081468	+	1	NA	promoter-TSS (NM_026399)	promoter-TSS (NM_026399)	484	NM_001001493	414077	Mm.35790	NM_001001493	ENSMUSG00000059355	Wdr83os	-	WD repeat domain 83 opposite strand	protein-coding
mm_110655.1	chr12	59061404	59061412	-	1	NA	promoter-TSS (NM_001306218)	promoter-TSS (NM_001306218)	64	NM_001306218	78232	Mm.290070	NM_030057	ENSMUSG00000020993	Trappc6b	5830498C14Rik|C79212	trafficking protein particle complex 6B	protein-coding
mm_158831.1	chrX	168124318	168124340	-	1	NA	intron (NM_001033330, intron 3 of 19)	intron (NM_001033330, intron 3 of 19)	-1332	NM_001290427	333605	Mm.426168	NM_001033330	ENSMUSG00000049176	Frmpd4	Gm196|PKAP1|Pdzd10|Pdzk10|Preso1|preso	FERM and PDZ domain containing 4	protein-coding
mm_156138.1	chrX	128261718	128261736	+	1	NA	Intergenic	Intergenic	-525173	NM_001281537	73934	Mm.159093	NM_001281537	ENSMUSG00000043569	Cldn34c4	4930412D23Rik	claudin 34C4	protein-coding
mm_147335.1	chr18	42899307	42899317	-	1	NA	non-coding (NR_073583, exon 1 of 9)	non-coding (NR_073583, exon 1 of 9)	194	NR_073583	72930	Mm.26134	NM_027531	ENSMUSG00000024500	Ppp2r2b	2900026H06Rik|6330404L05Rik|E130009M08Rik|PP2A-PR55B|PR55-BETA|SCA12	protein phosphatase 2, regulatory subunit B, beta	protein-coding
mm_34386.1	chr4	144922184	144922194	+	1	NA	intron (NM_011303, intron 4 of 5)	intron (NM_011303, intron 4 of 5)	29052	NM_011303	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding
mm_128217.1	chr15	36276796	36276800	-	1	NA	intron (NM_013923, intron 1 of 9)	intron (NM_013923, intron 1 of 9)	6349	NM_013923	30945	Mm.5181	NM_013923	ENSMUSG00000022280	Rnf19a	AA032313|Dorfin|Rnf19|UIP117|Ubce7ip2|XYbp	ring finger protein 19A	protein-coding
mm_1617.1	chr1	74391633	74391684	+	1	NA	promoter-TSS (NM_153088)	promoter-TSS (NM_153088)	49	NM_153088	227292	Mm.165042	NM_153088	ENSMUSG00000026176	Ctdsp1	GIP|NLIIF|Nif3|SCP1	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 1	protein-coding
mm_111572.1	chr12	101818856	101818866	-	1	NA	5' UTR (NM_011812, exon 1 of 11)	5' UTR (NM_011812, exon 1 of 11)	258	NM_011812	23876	Mm.288381	NM_011812	ENSMUSG00000021186	Fbln5	A55|DANCE|EVEC	fibulin 5	protein-coding
mm_161320.1	chr14	45220144	45220144	-	1	NA	promoter-TSS (NM_172597)	promoter-TSS (NM_172597)	427	NM_027518	70713	Mm.343793	NM_027518	ENSMUSG00000049092	Gpr137c	6330416L11Rik|Gm908|TM7SF1L2	G protein-coupled receptor 137C	protein-coding
mm_165644.1	chr3	82271796	82271816	+	1	NA	Intergenic	L1_Mur3|LINE|L1	-86266	NM_001081230	213582	Mm.271269	NM_001081230	ENSMUSG00000033900	Map9	5033421J10Rik|5330427D05Rik|ASAP|Mtap9	microtubule-associated protein 9	protein-coding
mm_126101.1	chr15	78244854	78244866	+	1	NA	promoter-TSS (NM_008677)	promoter-TSS (NM_008677)	49	NM_008677	17972	Mm.2068	NM_008677	ENSMUSG00000071715	Ncf4	AI451400|p40phox	neutrophil cytosolic factor 4	protein-coding
mm_55318.1	chr6	55133016	55133029	-	1	NA	promoter-TSS (NM_001288618)	promoter-TSS (NM_001288618)	-6	NM_001288618	12922	Mm.236081	NM_009953	ENSMUSG00000003476	Crhr2	CRF-R2|CRFR2alpha|CRFR2beta|Crfr2	corticotropin releasing hormone receptor 2	protein-coding
mm_137511.1	chr17	27057289	27057334	+	1	NA	promoter-TSS (NM_080553)	promoter-TSS (NM_080553)	7	NM_080553	16440	Mm.458106	NM_080553	ENSMUSG00000042644	Itpr3	IP3R 3|Ip3r3|Itpr-3|tf	inositol 1,4,5-triphosphate receptor 3	protein-coding
mm_104879.1	chr11	99438144	99438159	-	1	NA	promoter-TSS (NM_023256)	promoter-TSS (NM_023256)	2	NM_023256	66809	Mm.28042	NM_023256	ENSMUSG00000035775	Krt20	9030623C06Rik|Ck-20|Ck20|K20|Krt21	keratin 20	protein-coding
mm_163575.1	chr13	31625486	31625498	-	1	NA	promoter-TSS (NM_010225)	promoter-TSS (NM_010225)	-324	NM_010225	14238	Mm.125548	NM_010225	ENSMUSG00000038402	Foxf2	FREAC2|Fkh20|LUN	forkhead box F2	protein-coding
mm_33509.1	chr4	130913366	130913370	+	1	NA	promoter-TSS (NM_010686)	promoter-TSS (NM_010686)	34	NM_010686	16792	Mm.271868	NM_010686	ENSMUSG00000028581	Laptm5	E3	lysosomal-associated protein transmembrane 5	protein-coding
mm_166238.1	chr5	71657920	71657921	+	1	NA	5' UTR (NM_010251, exon 1 of 9)	5' UTR (NM_010251, exon 1 of 9)	388	NM_010251	14397	Mm.248731	NM_010251	ENSMUSG00000029211	Gabra4	Gabra-4	gamma-aminobutyric acid (GABA) A receptor, subunit alpha 4	protein-coding
mm_114364.1	chr13	62015919	62015960	+	1	NA	Intergenic	Intergenic	-113951	NM_001039239	630579	Mm.440905	NM_001039239	ENSMUSG00000074867	Zfp808	EG630579|Gm7036	zinc finger protein 80	protein-coding
mm_122854.1	chr14	54864056	54864151	-	1	NA	promoter-TSS (NM_001177705)	promoter-TSS (NM_001177705)	55	NM_001177705	239099	Mm.280994	NM_183174	ENSMUSG00000057156	Homez	mKIAA1443	homeodomain leucine zipper-encoding gene	protein-coding
mm_15546.1	chr2	158409843	158409862	+	1	NA	promoter-TSS (NM_001291138)	promoter-TSS (NM_001291138)	-1	NM_001291137	228850	Mm.398185	NM_177227	ENSMUSG00000027652	Ralgapb	AI507211|B230339M05Rik|p170	Ral GTPase activating protein, beta subunit (non-catalytic)	protein-coding
mm_55271.1	chr6	53820903	53820913	-	1	NA	promoter-TSS (NM_025817)	promoter-TSS (NM_025817)	-83	NM_025817	66873	Mm.422727	NM_025817	ENSMUSG00000043496	Tril	1200009O22Rik|AI316813|mKIAA0644	TLR4 interactor with leucine-rich repeats	protein-coding
mm_141062.1	chr17	25785325	25785343	-	1	NA	promoter-TSS (NM_026897)	promoter-TSS (NM_026897)	4	NM_026897	68977	Mm.29230	NM_026897	ENSMUSG00000061046	Haghl	1500017E18Rik|2810014I23Rik|C330022E15Rik	hydroxyacylglutathione hydrolase-like	protein-coding
mm_17420.1	chr2	27426537	27426563	-	1	NA	non-coding (NR_133905, exon 1 of 30)	non-coding (NR_133905, exon 1 of 30)	1058	NR_133905	22325	Mm.179011	NM_009500	ENSMUSG00000009621	Vav2	2810040F13Rik|AI847175|Vav-2	vav 2 oncogene	protein-coding
mm_32185.1	chr4	101068994	101069029	+	1	NA	promoter-TSS (NM_183024)	promoter-TSS (NM_183024)	-27	NM_183024	242570	Mm.185636	NM_183024	ENSMUSG00000035275	Raver2	A430091O22Rik	ribonucleoprotein, PTB-binding 2	protein-coding
mm_163199.1	chr11	96264318	96264326	+	1	NA	promoter-TSS (NR_029721)	promoter-TSS (NR_029721)	-842	NR_029721	387191		NR_029721	ENSMUSG00000065546	Mir196a-1	Mirn196|Mirn196a-1|miR-196|mir-196a-1	microRNA 196a-1	ncRNA
mm_80531.1	chr9	80165080	80165086	+	1	NA	promoter-TSS (NM_001039546)	promoter-TSS (NM_001039546)	49	NM_001039546	17920	Mm.4040	NM_008662	ENSMUSG00000033577	Myo6	BC029719|Tlc|sv	myosin VI	protein-coding
mm_80508.1	chr9	78615838	78615881	+	1	NA	5' UTR (NM_153098, exon 1 of 33)	5' UTR (NM_153098, exon 1 of 33)	313	NM_153098	235505	Mm.32955	NM_153098	ENSMUSG00000046186	Cd109	9930012E15Rik|AI480638|GARP	CD109 antigen	protein-coding
mm_125889.1	chr15	75863280	75863294	+	1	NA	intron (NM_026960, intron 1 of 10)	intron (NM_026960, intron 1 of 10)	948	NM_026960	69146	Mm.27385	NM_026960	ENSMUSG00000022575	Gsdmd	1810036L03Rik|AW558049|DF5L|Dfna5l|Gsdmdc1|M2-4	gasdermin D	protein-coding
mm_113191.1	chr13	24943145	24943164	+	1	NA	promoter-TSS (NM_008156)	promoter-TSS (NM_008156)	2	NM_008156	14756	Mm.291831	NM_008156	ENSMUSG00000021340	Gpld1	6330541J12Rik|AW546131	glycosylphosphatidylinositol specific phospholipase D1	protein-coding
mm_69765.1	chr7	141009817	141009873	-	1	NA	exon (NM_025378, exon 2 of 2)	exon (NM_025378, exon 2 of 2)	899	NM_025378	66141	Mm.141021	NM_025378	ENSMUSG00000025492	Ifitm3	1110004C05Rik|Cd225|Cdw217|DSPA2b|Fgls|IP15|mil-1	interferon induced transmembrane protein 3	protein-coding
mm_29073.1	chr3	103859898	103859912	-	1	NA	promoter-TSS (NM_008979)	promoter-TSS (NM_008979)	110	NR_104070	19260	Mm.395	NM_008979	ENSMUSG00000027843	Ptpn22	70zpep|PEP|Ptpn8	protein tyrosine phosphatase, non-receptor type 22 (lymphoid)	protein-coding
mm_72260.1	chr8	75097093	75097103	+	1	NA	exon (NM_010442, exon 3 of 5)	exon (NM_010442, exon 3 of 5)	3480	NM_010442	15368	Mm.276389	NM_010442	ENSMUSG00000005413	Hmox1	D8Wsu38e|HO-1|HO1|Hemox|Hmox|Hsp32	heme oxygenase 1	protein-coding
mm_133996.1	chr16	4719129	4719146	-	1	NA	5' UTR (NM_001290761, exon 1 of 5)	5' UTR (NM_001290761, exon 1 of 5)	219	NM_001290763	67824	Mm.28451	NM_026393	ENSMUSG00000063445	Nmral1	1110025F24Rik|AI256624	NmrA-like family domain containing 1	protein-coding
mm_87707.1	chr10	60002801	60002809	+	1	NA	promoter-TSS (NM_001199187)	promoter-TSS (NM_001199187)	0	NM_026937	69090	Mm.155839	NM_026937	ENSMUSG00000044475	Ascc1	1810015P09Rik|AI550520|ASC1p50|CGI-18	activating signal cointegrator 1 complex subunit 1	protein-coding
mm_21320.1	chr2	157099261	157099279	-	1	NA	3' UTR (NM_001139520, exon 17 of 17)	3' UTR (NM_001139520, exon 17 of 17)	12215	NM_001177439	383766	Mm.480305	NM_001177439	ENSMUSG00000074628	Tldc2	Gm1332	TBC/LysM associated domain containing 2	protein-coding
mm_35764.1	chr4	46138399	46138464	-	1	NA	promoter-TSS (NM_173033)	promoter-TSS (NM_173033)	44	NM_173033	272027	Mm.331588	NM_173033	ENSMUSG00000035495	Tstd2	3010020C06	thiosulfate sulfurtransferase (rhodanese)-like domain containing 2	protein-coding
mm_163590.1	chr13	38580884	38580884	+	1	NA	Intergenic	Intergenic	-52060	NM_001289598	105245	Mm.28622	NM_145367	ENSMUSG00000038991	Txndc5	AL022641|ERp46|PC-TRP	thioredoxin domain containing 5	protein-coding
mm_128976.1	chr15	74832832	74832843	-	1	NA	Intergenic	Intergenic	8806	NM_001033229	110115	Mm.322606	NM_001033229	ENSMUSG00000075604	Cyp11b1	AA389061|CPN1|Cyp11b|Cyp11b-1|FHI	cytochrome P450, family 11, subfamily b, polypeptide 1	protein-coding
mm_149504.1	chr19	11943432	11943445	+	1	NA	3' UTR (NM_172635, exon 19 of 19)	3' UTR (NM_172635, exon 19 of 19)	19710	NR_105960	102465601		NR_105960	ENSMUSG00000104979	Mir6994	mmu-mir-6994	microRNA 6994	ncRNA
mm_93925.1	chr10	127145457	127145459	-	1	NA	Intergenic	RMER17C|LTR|ERVK	-19698	NR_045166	14421	Mm.386762	NM_008080	ENSMUSG00000006731	B4galnt1	4933429D13Rik|Gal-NAc-T|GalNAc-T|GalNAcT|Galgt1|Ggm-2|Ggm2	beta-1,4-N-acetyl-galactosaminyl transferase 1	protein-coding
mm_164464.1	chr16	59505826	59505827	+	1	NA	intron (NM_174848, intron 15 of 18)	intron (NM_174848, intron 15 of 18)	34051	NM_025910	67014	Mm.289150	NM_025910	ENSMUSG00000022724	Mina	1810047J07Rik|2410057H13Rik|3830408E23Rik|AI449204	myc induced nuclear antigen	protein-coding
mm_33531.1	chr4	130932360	130932370	+	1	NA	intron (NM_010686, intron 7 of 7)	RMER1C|Other|Other	-12020	NM_010769	17180	Mm.271796	NM_010769	ENSMUSG00000040533	Matn1	CMP|Crtm|Mat1|matrilin-1	matrilin 1, cartilage matrix protein	protein-coding
mm_130648.1	chr15	100620022	100620043	-	1	NA	3' UTR (NM_011873, exon 4 of 4)	3' UTR (NM_011873, exon 4 of 4)	4370	NM_011873	23994	Mm.486175	NM_011873	ENSMUSG00000000346	Dazap2	AI314727|Brbp|Gcap28|Prtb|gt6-12|mKIAA0058	DAZ associated protein 2	protein-coding
mm_137891.1	chr17	31681043	31681068	+	1	NA	exon (NM_001278570, exon 3 of 3)	exon (NM_001278570, exon 3 of 3)	3124	NM_001278570	12954	Mm.1228	NM_013501	ENSMUSG00000024041	Cryaa	Acry-1|Crya-1|Crya1|DAcry-1|lop18	crystallin, alpha A	protein-coding
mm_18464.1	chr2	62343968	62343974	-	1	NA	intron (NM_001159543, intron 23 of 24)	intron (NM_001159543, intron 23 of 24)	68260	NM_010074	13482	Mm.1151	NM_010074	ENSMUSG00000035000	Dpp4	Cd26|Dpp-4|THAM	dipeptidylpeptidase 4	protein-coding
mm_24449.1	chr3	90612833	90612865	+	1	NA	promoter-TSS (NM_011313)	promoter-TSS (NM_011313)	-45	NM_011313	20200	Mm.100144	NM_011313	ENSMUSG00000001025	S100a6	2A9|5B10|CALCYCLIN|Cacy|PRA	S100 calcium binding protein A6 (calcyclin)	protein-coding
mm_27092.1	chr3	30107696	30107700	-	1	NA	Intergenic	Intergenic	-94494	NM_007963	14013	Mm.56965	NM_007963	ENSMUSG00000027684	Mecom	D630039M04Rik|Evi-1|Evi1|Jbo|Mds|Mds1|Mds1-Evi1|Prdm3|Znfpr1b1	MDS1 and EVI1 complex locus	protein-coding
mm_37393.1	chr4	121098141	121098151	-	1	NA	promoter-TSS (NM_172700)	promoter-TSS (NM_172700)	97	NM_172700	230709	Mm.34399	NM_172700	ENSMUSG00000043207	Zmpste24	A530043O15Rik|D030046F19|FACE1|Face-1|MADB|STE24|Ste24p	zinc metallopeptidase, STE24	protein-coding
mm_71297.1	chr8	41239574	41239659	+	1	NA	promoter-TSS (NM_023662)	promoter-TSS (NM_023662)	-143	NM_023662	18536	Mm.117896	NM_023662	ENSMUSG00000031592	Pcm1	2600002H09Rik|9430077F19Rik|C030044G17Rik	pericentriolar material 1	protein-coding
mm_123061.1	chr14	55671859	55671869	-	1	NA	promoter-TSS (NM_177992)	promoter-TSS (NM_177992)	42	NM_008683	18002	Mm.296566	NM_008683	ENSMUSG00000010376	Nedd8	Rub1	neural precursor cell expressed, developmentally down-regulated gene 8	protein-coding
mm_75445.1	chr8	47632811	47632820	-	1	NA	Intergenic	Intergenic	42344	NM_023503	69260	Mm.430733	NM_023503	ENSMUSG00000063049	Ing2	2810011M06Rik|Ing1l|Ing2b|P33ING2	inhibitor of growth family, member 2	protein-coding
mm_131707.1	chr16	20733105	20733158	+	1	NA	promoter-TSS (NM_009893)	promoter-TSS (NM_009893)	4	NM_009893	12667	Mm.20457	NM_009893	ENSMUSG00000006958	Chrd	Chd	chordin	protein-coding
mm_343.1	chr1	30949865	30949882	+	1	NA	promoter-TSS (NR_002688)	promoter-TSS (NR_002688)	-118	NM_011200	19243	Mm.491181	NM_011200	ENSMUSG00000026064	Ptp4a1	AA415290|AU019864|C130021B01|Prl-1	protein tyrosine phosphatase 4a1	protein-coding
mm_7865.1	chr1	132624474	132624490	-	1	NA	intron (NM_001160318, intron 7 of 26)	L1MEg|LINE|L1	18376	NM_001160316	269116	Mm.326702	NM_182716	ENSMUSG00000026442	Nfasc	AA387016|D430023G06Rik|NF|mKIAA0756	neurofascin	protein-coding
mm_22754.1	chr3	19974967	19974979	+	1	NA	exon (NM_007752, exon 9 of 19)	exon (NM_007752, exon 9 of 19)	17919	NM_007752	12870	Mm.13787	NM_007752	ENSMUSG00000003617	Cp	D3Ertd555e	ceruloplasmin	protein-coding
mm_114481.1	chr13	69611533	69611543	+	1	NA	promoter-TSS (NM_175283)	promoter-TSS (NM_175283)	-75	NM_175283	78925	Mm.451912	NM_175283	ENSMUSG00000021594	Srd5a1	0610031P22Rik|4930435F02Rik|S5AR 1|Srd5a-1	steroid 5 alpha-reductase 1	protein-coding
mm_149314.1	chr19	10784224	10784232	+	1	NA	intron (NR_027805, intron 2 of 3)	intron (NR_027805, intron 2 of 3)	43281	NR_027805	403202	Mm.34482	NM_207529	ENSMUSG00000067577	A430093F15Rik	Gm674	RIKEN cDNA A430093F15 gene	ncRNA
mm_69624.1	chr7	137314298	137314327	-	1	NA	5' UTR (NM_001113414, exon 1 of 16)	5' UTR (NM_001113414, exon 1 of 16)	133	NM_001113415	13593	Mm.258708	NM_010096	ENSMUSG00000010476	Ebf3	3110018A08Rik|O/E-2|mKIAA4201	early B cell factor 3	protein-coding
mm_111623.1	chr12	102421442	102421455	-	1	NA	intron (NM_011175, intron 2 of 13)	ORR1C2|LTR|ERVL-MaLR	18365	NM_011175	19141	Mm.17185	NM_011175	ENSMUSG00000021190	Lgmn	AEP|AI746452|AU022324|Prsc1	legumain	protein-coding
mm_159504.1	chr4	44167530	44167530	-	1	NA	promoter-TSS (NM_175201)	promoter-TSS (NM_175201)	8	NM_175201	73469	Mm.262859	NM_175201	ENSMUSG00000035696	Rnf38	1700065B19Rik|2610202O07Rik|AA673263|Oip1	ring finger protein 38	protein-coding
mm_125567.1	chr15	59275413	59275417	+	1	NA	Intergenic	Intergenic	-31533	NR_045613	100416830	Mm.490788	NR_045613	ENSMUSG00000098528	Zfp572	4930472F24Rik	zinc finger protein 572	pseudo
mm_37603.1	chr4	126752778	126752788	-	1	NA	promoter-TSS (NM_001035526)	promoter-TSS (NM_001035526)	646	NM_011986	26562	Mm.206206	NM_011986	ENSMUSG00000028833	Ncdn	AU042419|MMS10-AE|Ms10ae|mKIAA0607|norbin	neurochondrin	protein-coding
mm_122924.1	chr14	54961033	54961091	-	1	NA	exon (NM_010856, exon 12 of 39)	exon (NM_010856, exon 12 of 39)	5545	NM_001164171	17888	Mm.290003	NM_010856	ENSMUSG00000040752	Myh6	A830009F23Rik|AA517445|Myhc-a|Myhca|alpha-MHC	myosin, heavy polypeptide 6, cardiac muscle, alpha	protein-coding
mm_158565.1	chrX	150457377	150457379	-	1	NA	intron (NM_001164683, intron 1 of 2)	ID_B1|SINE|B4	1772	NM_001164683	382245	Mm.277309	NM_001164683	ENSMUSG00000041353	Tmem29	2700081K05Rik|6330540D07Rik|CXorf44-like	transmembrane protein 29	protein-coding
mm_120603.1	chr14	70081156	70081162	+	1	NA	3' UTR (NM_001289927, exon 2 of 2)	3' UTR (NM_001289927, exon 2 of 2)	3364	NM_001289927	13655	Mm.103737	NM_018781	ENSMUSG00000033730	Egr3	Pilot	early growth response 3	protein-coding
mm_26827.1	chr3	10351315	10351342	-	1	NA	promoter-TSS (NM_001331013)	promoter-TSS (NM_001331013)	-11	NM_001331014	66361	Mm.371617	NM_025512	ENSMUSG00000039795	Zfand1	2310008M20Rik|AW048890	zinc finger, AN1-type domain 1	protein-coding
mm_169117.1	chr13	50021716	50021719	-	1	NA	Intergenic	RLTR13D3A1|LTR|ERVK	228591	NM_001033438	380882	Mm.425809	NM_001033438	ENSMUSG00000095300	Gm906	-	predicted gene 906	protein-coding
mm_81410.1	chr9	109052829	109052864	+	1	NA	intron (NM_025858, intron 3 of 5)	intron (NM_025858, intron 3 of 5)	-2020	NM_026381	66940	Mm.196533	NM_025858	ENSMUSG00000025647	Shisa5	2310008D10Rik|6430628I05Rik|Scotin|mShisa5	shisa family member 5	protein-coding
mm_162613.1	chr1	183345354	183345388	-	1	NA	intron (NM_177389, intron 6 of 26)	CpG	24194	NM_177389	338366	Mm.41152	NM_177389		Mia3	9130229H14Rik|A930039G15Rik|AU022327|B230399H06Rik|C80126|Gm1525|TANGO1|Tango	melanoma inhibitory activity 3	protein-coding
mm_31364.1	chr4	47287829	47287835	+	1	NA	intron (NM_009928, intron 22 of 39)	intron (NM_009928, intron 22 of 39)	-65390	NM_001312868	21812	Mm.197552	NM_009370	ENSMUSG00000007613	Tgfbr1	ALK5|AU017191|Alk-5|ESK2|TGFR-1|TbetaR-I|TbetaRI	transforming growth factor, beta receptor I	protein-coding
mm_78713.1	chr9	41447107	41447110	+	1	NA	intron (NR_131928, intron 3 of 4)	intron (NR_131928, intron 3 of 4)	-27785	NR_131931	73144	Mm.38166	NM_001033153	ENSMUSG00000074415	3110039I08Rik	2610203C20Rik|AI848448|D230004N17Rik|D3Mgi9|Mir100hg	RIKEN cDNA 3110039I08 gene	ncRNA
mm_133808.1	chr16	95702045	95702094	+	1	NA	promoter-TSS (NM_011809)	promoter-TSS (NM_011809)	-338	NM_011809	23872	Mm.290207	NM_011809	ENSMUSG00000022895	Ets2	AU022856|Ets-2	E26 avian leukemia oncogene 2, 3' domain	protein-coding
mm_75787.1	chr8	70095174	70095206	-	1	NA	3' UTR (NM_007789, exon 15 of 15)	3' UTR (NM_007789, exon 15 of 15)	7396	NR_106033	102465646		NR_106033	ENSMUSG00000099042	Mir7066	Gm27290|mmu-mir-7066	microRNA 7066	ncRNA
mm_158323.1	chrX	133898400	133898413	-	1	NA	promoter-TSS (NM_019656)	promoter-TSS (NM_019656)	23	NM_019656	56496	Mm.46701	NM_019656	ENSMUSG00000067377	Tspan6	6720473L21Rik|AI316786|T245|TSPAN-6|Tm4sf|Tm4sf6	tetraspanin 6	protein-coding
mm_88975.1	chr10	81461566	81461567	+	1	NA	3' UTR (NM_176954, exon 12 of 12)	3' UTR (NM_176954, exon 12 of 12)	11565	NM_001311127	319586	Mm.152689	NM_176954	ENSMUSG00000034818	Celf5	4930565A21Rik|Brunol5	CUGBP, Elav-like family member 5	protein-coding
mm_31369.1	chr4	47353220	47353224	+	1	NA	promoter-TSS (NM_009370)	promoter-TSS (NM_009370)	0	NM_001312868	21812	Mm.197552	NM_009370	ENSMUSG00000007613	Tgfbr1	ALK5|AU017191|Alk-5|ESK2|TGFR-1|TbetaR-I|TbetaRI	transforming growth factor, beta receptor I	protein-coding
mm_42767.1	chr5	121220406	121220415	+	1	NA	5' UTR (NM_181421, exon 1 of 76)	5' UTR (NM_181421, exon 1 of 76)	191	NM_181421	269700	Mm.184589	NM_181421	ENSMUSG00000042744	Gm15800	A130010L24|AU042671|BC019639|EG545802|OTTMUSG00000026283|mKIAA0614	predicted gene 15800	protein-coding
mm_148892.1	chr19	6906699	6906711	+	1	NA	TTS (NM_012021)	TTS (NM_012021)	2940	NM_012021	54683	Mm.279782	NM_012021	ENSMUSG00000024953	Prdx5	AOEB166|AOPP|Pmp20|Prdx6|PrxV	peroxiredoxin 5	protein-coding
mm_24366.1	chr3	90087416	90087439	+	1	NA	intron (NM_001293749, intron 2 of 7)	intron (NM_001293749, intron 2 of 7)	7906	NM_001293749	59069	Mm.240839	NM_022314	ENSMUSG00000027940	Tpm3	TM30nm|TMnm|Tm5NM|Tpm-5|Tpm5|Trop-5|gamma-TM|hTM30nm|hTMnm	tropomyosin 3, gamma	protein-coding
mm_37567.1	chr4	126237806	126237845	-	1	NA	intron (NM_001145970, intron 5 of 16)	intron (NM_001145970, intron 5 of 16)	18494	NM_144941	245877	Mm.266716	NM_144941	ENSMUSG00000028849	Map7d1	AV028413|BC019977|Mtap7d1|Parcc1|Rprc1|mKIAA1187	MAP7 domain containing 1	protein-coding
mm_48382.1	chr5	139774386	139774409	-	1	NA	exon (NM_026748, exon 2 of 47)	exon (NM_026748, exon 2 of 47)	1281	NM_026748	68510	Mm.292942	NM_026748	ENSMUSG00000029547	Ints1	1110015K06Rik	integrator complex subunit 1	protein-coding
mm_54908.1	chr6	47636892	47636914	-	1	NA	Intergenic	Intergenic	18191	NR_002841	19799		NR_002841		Rn4.5s	-	4.5S RNA	rRNA
mm_12694.1	chr2	76383566	76383576	+	1	NA	3' UTR (NM_153405, exon 10 of 10)	3' UTR (NM_153405, exon 10 of 10)	13587	NM_153405	241490	Mm.33310	NM_153405	ENSMUSG00000042369	Rbm45	Drb1|Drbp1|G430095G15Rik	RNA binding motif protein 45	protein-coding
mm_42828.1	chr5	122100973	122100986	+	1	NA	promoter-TSS (NM_010861)	promoter-TSS (NM_010861)	-1	NM_010861	17906	Mm.1529	NM_010861	ENSMUSG00000013936	Myl2	MLC-2|MLC-2s/v|MLC-2v|Mlc2v|Mylpc	myosin, light polypeptide 2, regulatory, cardiac, slow	protein-coding
mm_150766.1	chr19	44242310	44242337	+	1	NA	3' UTR (NM_024450, exon 6 of 6)	3' UTR (NM_024450, exon 6 of 6)	39035	NM_024450	30049	Mm.480594	NM_024450	ENSMUSG00000025202	Scd3	4930513N16Rik	stearoyl-coenzyme A desaturase 3	protein-coding
mm_19856.1	chr2	113829070	113829110	-	1	NA	promoter-TSS (NM_009162)	promoter-TSS (NM_009162)	1	NM_009162	20394	Mm.4836	NM_009162	ENSMUSG00000023236	Scg5	7B2|AI325031|Sgne-1|Sgne1	secretogranin V	protein-coding
mm_29214.1	chr3	107038044	107038062	-	1	NA	TTS (NM_008418)	TTS (NM_008418)	-1451	NR_033498	229694	Mm.347584	NM_173787	ENSMUSG00000056145	AI504432	A230102G19	expressed sequence AI504432	ncRNA
mm_74693.1	chr8	15018923	15018940	-	1	NA	intron (NM_029116, intron 1 of 1)	intron (NM_029116, intron 1 of 1)	7906	NM_029116	74901	Mm.46675	NM_029116	ENSMUSG00000055675	Kbtbd11	2900016B01Rik|4930465M17Rik|mKIAA0711	kelch repeat and BTB (POZ) domain containing 11	protein-coding
mm_67458.1	chr7	80402771	80402823	-	1	NA	promoter-TSS (NM_011046)	promoter-TSS (NM_011046)	15	NM_011046	18550	Mm.5241	NM_011046	ENSMUSG00000030530	Furin	9130404I01Rik|Fur|PACE|Pcsk3|SPC1	furin (paired basic amino acid cleaving enzyme)	protein-coding
mm_20818.1	chr2	144550778	144550864	-	1	NA	promoter-TSS (NM_015754)	promoter-TSS (NM_015754)	38	NM_015754	26450	Mm.440564	NM_015754	ENSMUSG00000027428	Rbbp9	Bog	retinoblastoma binding protein 9	protein-coding
mm_45520.1	chr5	72587545	72587555	-	1	NA	promoter-TSS (NM_001024147)	promoter-TSS (NM_001024147)	0	NM_001024147	545758	Mm.332426	NM_001024147	ENSMUSG00000060204	Gm5868	EG545758	predicted gene 5868	protein-coding
mm_157071.1	chrX	8203185	8203213	-	1	NA	exon (NM_145907, exon 6 of 14)	exon (NM_145907, exon 6 of 14)	3326	NM_145907	53627	Mm.443425	NM_016913	ENSMUSG00000031169	Porcn	2410004O13Rik|AW045557|DXHXS7465e|Mg61|Mporc|Ppn|mMg61|porc	porcupine homolog (Drosophila)	protein-coding
mm_158530.1	chrX	143861282	143861321	-	1	NA	3' UTR (NM_010025, exon 7 of 7)	3' UTR (NM_010025, exon 7 of 7)	-33889	NM_007603	12338	Mm.30290	NM_007603	ENSMUSG00000067276	Capn6	-	calpain 6	protein-coding
mm_74254.1	chr8	124862659	124862672	+	1	NA	promoter-TSS (NM_010322)	promoter-TSS (NM_010322)	364	NM_025615	66523	Mm.436864	NM_025615	ENSMUSG00000031984	2810004N23Rik	3110004G14Rik|Ayu21-55|Gt(pU21)55Imeg|GtAyu21-55	RIKEN cDNA 2810004N23 gene	protein-coding
mm_2463.1	chr1	105356847	105356857	+	1	NA	promoter-TSS (NM_001160368)	promoter-TSS (NM_001160368)	-142	NM_001160368	320311	Mm.389162	NM_178779	ENSMUSG00000047496	Rnf152	A930029B02Rik	ring finger protein 152	protein-coding
mm_4125.1	chr1	169969429	169969454	+	1	NA	promoter-TSS (NM_010476)	promoter-TSS (NM_010476)	32	NR_040438	67303	Mm.396611	NR_040438	ENSMUSG00000097503	3110045C21Rik	AI838577	RIKEN cDNA 3110045C21 gene	ncRNA
mm_90559.1	chr10	128194603	128194613	+	1	NA	promoter-TSS (NM_001285779)	promoter-TSS (NM_001285779)	-27	NM_001285777	216456	Mm.30102	NM_001033264	ENSMUSG00000044005	Gls2	A330074B06Rik|AI195532|GA|GLS|Lga	glutaminase 2 (liver, mitochondrial)	protein-coding
mm_132651.1	chr16	41533076	41533093	+	1	NA	promoter-TSS (NM_175548)	promoter-TSS (NM_175548)	258	NM_001347236	268890	Mm.310524	NM_175548	ENSMUSG00000061080	Lsamp	5430428I19|AW046674|B130007O04Rik|D930023J12Rik|Lam|Lamp	limbic system-associated membrane protein	protein-coding
mm_66893.1	chr7	59315384	59315388	-	1	NA	intron (NR_015479, intron 2 of 2)	intron (NR_015479, intron 2 of 2)	8763	NR_015479	330544	Mm.9002	NR_015479	ENSMUSG00000100826	C230091D08Rik	-	RIKEN cDNA C230091D08 gene	ncRNA
mm_53375.1	chr6	129471638	129471664	+	1	NA	intron (NR_132130, intron 1 of 5)	intron (NR_132130, intron 1 of 5)	1128	NM_001309637	56644	Mm.239516	NM_020008	ENSMUSG00000079293	Clec7a	BGR|Clecsf12|beta-GR	C-type lectin domain family 7, member a	protein-coding
mm_51210.1	chr6	71338653	71338670	+	1	NA	Intergenic	Intergenic	15849	NM_009858	12526	Mm.333148	NM_009858	ENSMUSG00000053044	Cd8b1	Cd8b|Ly-3|Ly-C|Lyt-3	CD8 antigen, beta chain 1	protein-coding
mm_166141.1	chr4	156327561	156327564	-	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	-3541	NR_028141	22314	Mm.458976	NM_009494	ENSMUSG00000057021	Vmn2r-ps159	V2r8|V2r9|Vmn2r-ps160	vomeronasal 2, receptor, pseudogene 159	pseudo
mm_69400.1	chr7	132317064	132317129	-	1	NA	promoter-TSS (NM_029935)	promoter-TSS (NM_029935)	59	NM_029935	77590	Mm.213582	NM_029935	ENSMUSG00000030930	Chst15	4631426J05Rik|BRAG|GalNAcS-6ST|MAd5|mKIAA0598	carbohydrate (N-acetylgalactosamine 4-sulfate 6-O) sulfotransferase 15	protein-coding
mm_173184.1	chrX	59284105	59284118	+	1	NA	intron (NM_001290414, intron 2 of 6)	L1Md_A|LINE|L1	-118023	NM_001290415	14168	Mm.7995	NM_010200	ENSMUSG00000031137	Fgf13	Fhf2	fibroblast growth factor 13	protein-coding
mm_10048.1	chr1	193197894	193197906	-	1	NA	exon (NM_153137, exon 3 of 16)	exon (NM_153137, exon 3 of 16)	3646	NM_153137	215243	Mm.261259	NM_153137	ENSMUSG00000037318	Traf3ip3	6030423D04Rik|AI115021|T3jam	TRAF3 interacting protein 3	protein-coding
mm_122565.1	chr14	50381362	50381392	-	1	NA	Intergenic	Intergenic	-11381	NM_146666	258660	Mm.377623	NM_146666	ENSMUSG00000047716	Olfr736	MOR106-5	olfactory receptor 736	protein-coding
mm_171690.1	chr4	65124766	65124769	+	1	NA	exon (NM_021362, exon 1 of 22)	exon (NM_021362, exon 1 of 22)	593	NM_021362	18491	Mm.317854	NM_021362	ENSMUSG00000028370	Pappa	8430414N03Rik|IGFBP-4ase|PAG1|PAPP-A	pregnancy-associated plasma protein A	protein-coding
mm_38141.1	chr4	134767925	134767937	-	1	NA	promoter-TSS (NM_145554)	promoter-TSS (NM_145554)	73	NM_145554	100017	Mm.27486	NM_145554	ENSMUSG00000037295	Ldlrap1	AA691260|ARH2|Arh|Arh1|FHCB1|FHCB2	low density lipoprotein receptor adaptor protein 1	protein-coding
mm_7994.1	chr1	134304824	134304848	-	1	NA	intron (NM_001144855, intron 23 of 28)	intron (NM_001144855, intron 23 of 28)	14832	NM_031189	17928	Mm.16528	NM_031189	ENSMUSG00000026459	Myog	MYF4|bHLHc3|myo	myogenin	protein-coding
mm_88843.1	chr10	80900408	80900429	+	1	NA	TTS (NM_010722)	TTS (NM_010722)	551	NM_013895	30055	Mm.142132	NM_013895	ENSMUSG00000020219	Timm13	D10Ertd378e|Tim9|Timm9	translocase of inner mitochondrial membrane 13	protein-coding
mm_139045.1	chr17	46248174	46248176	+	1	NA	promoter-TSS (NM_009085)	promoter-TSS (NM_009085)	95	NM_145353	28064	Mm.248769	NM_145353	ENSMUSG00000071074	Yipf3	C6orf109|D17Wsu94e|KLIP1	Yip1 domain family, member 3	protein-coding
mm_8238.1	chr1	138304163	138304166	-	1	NA	Intergenic	Intergenic	30426	NM_177397	338375	Mm.114424	NM_177397	ENSMUSG00000026394	Atp6v1g3	-	ATPase, H+ transporting, lysosomal V1 subunit G3	protein-coding
mm_165335.1	chr2	114055257	114055266	+	1	NA	non-coding (NR_028422, exon 1 of 3)	non-coding (NR_028422, exon 1 of 3)	865	NR_028422	100303644	Mm.330469	NR_028422	ENSMUSG00000092397	C130080G10Rik	-	RIKEN cDNA C130080G10 gene	ncRNA
mm_100029.1	chr11	114923810	114923836	+	1	NA	3' UTR (NM_199221, exon 4 of 4)	3' UTR (NM_199221, exon 4 of 4)	10563	NM_001347651	217304	Mm.185355	NM_199221	ENSMUSG00000063193	Cd300lb	CLM-7|Clm7|Gm253|LMIR5	CD300 molecule like family member B	protein-coding
mm_113832.1	chr13	47105573	47105592	+	1	NA	exon (NM_025900, exon 2 of 11)	exon (NM_025900, exon 2 of 11)	639	NM_025900	110052	Mm.131150	NM_025900	ENSMUSG00000021377	Dek	1810019E15Rik|D13H6S231E	DEK oncogene (DNA binding)	protein-coding
mm_127896.1	chr15	9155423	9155423	-	1	NA	promoter-TSS (NM_001285980)	promoter-TSS (NM_001285980)	2	NM_001285980	27401	Mm.35584	NM_013787	ENSMUSG00000054115	Skp2	4930500A04Rik|FBXL1|FWD1|p45	S-phase kinase-associated protein 2 (p45)	protein-coding
mm_114746.1	chr13	84222187	84222199	+	1	NA	promoter-TSS (NR_138587)	promoter-TSS (NR_138587)	-18	NR_138587	320919	Mm.131386	NR_138587	ENSMUSG00000097292	A230107N01Rik	-	RIKEN cDNA A230107N01 gene	ncRNA
mm_37588.1	chr4	126440783	126440795	-	1	NA	intron (NM_001317174, intron 16 of 18)	MIRb|SINE|MIR	-11247	NM_153402	214150	Mm.440915	NM_153402	ENSMUSG00000028842	Ago3	AW048688|C130014L07Rik|Eif2c3	argonaute RISC catalytic subunit 3	protein-coding
mm_89873.1	chr10	108268616	108268631	+	1	NA	exon (NM_027892, exon 21 of 26)	exon (NM_027892, exon 21 of 26)	-63566	NM_054056	114774	Mm.391419	NM_054056	ENSMUSG00000035873	Pawr	2310001G03Rik|PAR4|Par-4	PRKC, apoptosis, WT1, regulator	protein-coding
mm_89243.1	chr10	87858640	87858649	+	1	NA	promoter-TSS (NM_010512)	promoter-TSS (NM_010512)	379	NM_001314010	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_10455.1	chr2	14289085	14289104	+	1	NA	exon (NM_008625, exon 12 of 30)	exon (NM_008625, exon 12 of 30)	28091	NR_030609	100124488		NR_030609	ENSMUSG00000077897	Mir511	Mirn511|mir-511|mmu-mir-511	microRNA 511	ncRNA
mm_112866.1	chr13	20849518	20849527	+	1	NA	intron (NM_012054, intron 3 of 20)	MTEa|LTR|ERVL-MaLR	55409	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_53486.1	chr6	135078672	135078709	+	1	NA	exon (NM_181444, exon 2 of 4)	exon (NM_181444, exon 2 of 4)	13028	NM_181444	232431	Mm.23575	NM_181444	ENSMUSG00000046733	Gprc5a	Rai3|Raig1	G protein-coupled receptor, family C, group 5, member A	protein-coding
mm_64037.1	chr7	140770982	140771003	+	1	NA	exon (NM_021282, exon 6 of 9)	exon (NM_021282, exon 6 of 9)	7160	NM_021282	13106	Mm.21758	NM_021282	ENSMUSG00000025479	Cyp2e1	Cyp2e	cytochrome P450, family 2, subfamily e, polypeptide 1	protein-coding
mm_103663.1	chr11	79047484	79047496	-	1	NA	intron (NM_013571, intron 2 of 17)	intron (NM_013571, intron 2 of 17)	23893	NR_045873	790910	Mm.440410	NR_045873		Gm11201	ENSMUSG00000072637|OTTMUSG00000000169	predicted gene 11201	ncRNA
mm_66264.1	chr7	35754386	35754392	-	1	NA	promoter-TSS (NM_178704)	promoter-TSS (NM_178704)	65	NM_178704	233115	Mm.257808	NM_178704	ENSMUSG00000043671	Dpy19l3	6030410G08|9330164H19Rik	dpy-19-like 3 (C. elegans)	protein-coding
mm_23541.1	chr3	61363913	61363948	+	1	NA	promoter-TSS (NM_028712)	promoter-TSS (NM_028712)	-577	NM_028712	74012	Mm.422674	NM_028712	ENSMUSG00000036894	Rap2b	4021402C18Rik|AA408554	RAP2B, member of RAS oncogene family	protein-coding
mm_160466.1	chr8	111082017	111082017	-	1	NA	promoter-TSS (NM_181549)	promoter-TSS (NM_181549)	-309	NM_181549	353287	Mm.135495	NM_181549	ENSMUSG00000033633	Clec18a	Mrcl	C-type lectin domain family 18, member A	protein-coding
mm_66504.1	chr7	45091714	45091734	-	1	NA	intron (NM_026555, intron 1 of 6)	intron (NM_026555, intron 1 of 6)	489	NM_026555	52377	Mm.29997	NM_026555	ENSMUSG00000019539	Rcn3	6030455P07Rik|D530026G20Rik|D7Ertd671e|RLP49	reticulocalbin 3, EF-hand calcium binding domain	protein-coding
mm_35311.1	chr4	25281802	25281830	-	1	NA	promoter-TSS (NM_026194)	promoter-TSS (NM_026194)	5	NM_026194	67490	Mm.226295	NM_026194	ENSMUSG00000040359	Ufl1	1810074P20Rik|AI429228|Kiaa0776|Maxer|Rcad|mKIAA0776	UFM1 specific ligase 1	protein-coding
mm_10042.1	chr1	193035652	193035728	-	1	NA	promoter-TSS (NM_181546)	promoter-TSS (NM_181546)	85	NM_001301370	329324	Mm.76710	NM_181546	ENSMUSG00000016200	Syt14	B230320I09Rik|sytXIV	synaptotagmin XIV	protein-coding
mm_19537.1	chr2	94438082	94438161	-	1	NA	promoter-TSS (NM_001305258)	promoter-TSS (NM_001305258)	65	NM_007466	11800	Mm.181824	NM_007466	ENSMUSG00000027193	Api5	AAC-11|AI196452|API-5	apoptosis inhibitor 5	protein-coding
mm_41266.1	chr5	89050788	89050791	+	1	NA	intron (NM_018760, intron 6 of 25)	intron (NM_018760, intron 6 of 25)	163529	NM_018760	54403	Mm.41044	NM_018760	ENSMUSG00000060961	Slc4a4	AI835705|NBC|NBC1	solute carrier family 4 (anion exchanger), member 4	protein-coding
mm_164107.1	chr15	26610798	26610801	-	1	NA	intron (NM_176959, intron 2 of 3)	intron (NM_176959, intron 2 of 3)	284765	NM_176959	448987	Mm.253378	NM_176959	ENSMUSG00000043556	Fbxl7	AL023057|D230018M15Rik|FBL7|Fbl6	F-box and leucine-rich repeat protein 7	protein-coding
mm_10833.1	chr2	24394791	24394808	+	1	NA	exon (NM_177611, exon 2 of 17)	exon (NM_177611, exon 2 of 17)	9402	NM_177611	215632	Mm.490434	NM_177611	ENSMUSG00000026979	Psd4	BC046518|EFA6B	pleckstrin and Sec7 domain containing 4	protein-coding
mm_30687.1	chr4	11485948	11485964	+	1	NA	promoter-TSS (NM_001347055)	promoter-TSS (NM_001347055)	-2	NM_001081183	66185	Mm.331487	NM_001081183	ENSMUSG00000040720	1110037F02Rik	4930422M05Rik|Kiaa1429|mKIAA1429	RIKEN cDNA 1110037F02 gene	protein-coding
mm_50995.1	chr6	63257914	63257923	+	1	NA	intron (NM_008167, intron 1 of 15)	intron (NM_008167, intron 1 of 15)	1061	NM_008167	14804	Mm.439651	NM_008167	ENSMUSG00000071424	Grid2	B230104L07Rik|GluD2|GluRdelta2|Lc|Lc<J>|MMS10-AC|Ms10ac|cpr|ho|nmf408|tpr	glutamate receptor, ionotropic, delta 2	protein-coding
mm_9994.1	chr1	191396568	191396592	-	1	NA	5' UTR (NM_144880, exon 1 of 13)	5' UTR (NM_144880, exon 1 of 13)	461	NM_144880	226849	Mm.205569	NM_144880	ENSMUSG00000026626	Ppp2r5a	PR61alpha	protein phosphatase 2, regulatory subunit B', alpha	protein-coding
mm_89725.1	chr10	98917554	98917559	+	1	NA	intron (NM_026482, intron 1 of 20)	intron (NM_026482, intron 1 of 20)	2404	NM_026482	67972	Mm.166944	NM_026482	ENSMUSG00000019943	Atp2b1	2810442I22Rik|E130111D10Rik|Pmca1	ATPase, Ca++ transporting, plasma membrane 1	protein-coding
mm_126644.1	chr15	83784327	83784348	+	1	NA	intron (NM_172610, intron 1 of 6)	intron (NM_172610, intron 1 of 6)	4314	NM_172610	223726	Mm.36395	NM_172610	ENSMUSG00000041708	Mpped1	6230403M19|AW456965|D15Bwg0669e	metallophosphoesterase domain containing 1	protein-coding
mm_153037.1	chr19	31914077	31914082	-	1	NA	intron (NM_001081074, intron 4 of 11)	intron (NM_001081074, intron 4 of 11)	45318	NM_001081074	69865	Mm.87538	NM_001081074	ENSMUSG00000052595	A1cf	1810073H04Rik|ACF64|ACF65|ASP|Acf|MCM|MerCreMer|Tg(Myh6-cre/Esr1*)1Jmk|mer	APOBEC1 complementation factor	protein-coding
mm_92523.1	chr10	78591946	78591953	-	1	NA	promoter-TSS (NM_027875)	promoter-TSS (NM_027875)	15	NM_027875	71709	Mm.86439	NM_027875	ENSMUSG00000032714	Syde1	1200008N06Rik|BB043000|mSYD1A	synapse defective 1, Rho GTPase, homolog 1 (C. elegans)	protein-coding
mm_108040.1	chr12	73901371	73901391	+	1	NA	promoter-TSS (NM_001313920)	promoter-TSS (NM_001313920)	57	NM_001313920	15251	Mm.3879	NM_010431	ENSMUSG00000021109	Hif1a	AA959795|HIF-1-alpha|HIF1-alpha|HIF1alpha|MOP1|bHLHe78	hypoxia inducible factor 1, alpha subunit	protein-coding
mm_95670.1	chr11	53980026	53980036	+	1	NA	promoter-TSS (NM_019723)	promoter-TSS (NM_019723)	-4	NM_019723	56517	Mm.154284	NM_019723	ENSMUSG00000063652	Slc22a21	Octn3|Slc22a9	solute carrier family 22 (organic cation transporter), member 21	protein-coding
mm_89728.1	chr10	98931137	98931145	+	1	NA	intron (NM_026482, intron 1 of 20)	B1_Mus1|SINE|Alu	15989	NM_026482	67972	Mm.166944	NM_026482	ENSMUSG00000019943	Atp2b1	2810442I22Rik|E130111D10Rik|Pmca1	ATPase, Ca++ transporting, plasma membrane 1	protein-coding
mm_108297.1	chr12	79209279	79209294	+	1	NA	intron (NM_001313971, intron 1 of 6)	intron (NM_001313971, intron 1 of 6)	373	NM_030017	77974	Mm.274373	NM_030017	ENSMUSG00000021123	Rdh12	-	retinol dehydrogenase 12	protein-coding
mm_108739.1	chr12	88632268	88632280	+	1	NA	Intergenic	Intergenic	-162230	NM_001198587	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding
mm_129528.1	chr15	79283535	79283582	-	1	NA	intron (NM_177580, intron 3 of 13)	intron (NM_177580, intron 3 of 13)	1951	NM_177580	207495	Mm.309647	NM_177580	ENSMUSG00000018126	Baiap2l2	BC048937	BAI1-associated protein 2-like 2	protein-coding
mm_91152.1	chr10	20505490	20505515	-	1	NA	intron (NM_013875, intron 2 of 12)	intron (NM_013875, intron 2 of 12)	42826	NM_001347366	29863	Mm.425617	NM_013875	ENSMUSG00000019990	Pde7b	-	phosphodiesterase 7B	protein-coding
mm_96236.1	chr11	62551494	62551503	+	1	NA	promoter-TSS (NR_002875).2	promoter-TSS (NR_002875).2	-6	NR_002875	218963	Mm.282093	NR_002875		Gm1821	-	ubiquitin pseudogene	pseudo
mm_101561.1	chr11	34008911	34008919	-	1	NA	Intergenic	Intergenic	-15722	NM_001190886	70357	Mm.252514	NM_027398	ENSMUSG00000053519	Kcnip1	KCHIP1|Kchip1.2	Kv channel-interacting protein 1	protein-coding
mm_73080.1	chr8	94478695	94478722	+	1	NA	intron (NM_001033207, intron 4 of 48)	B2_Mm2|SINE|B2	5945	NM_001033207	434341	Mm.334720	NM_001033207	ENSMUSG00000074151	Nlrc5	AI451557|AK220210|NOD27	NLR family, CARD domain containing 5	protein-coding
mm_65573.1	chr7	27195688	27195694	-	1	NA	promoter-TSS (NM_001046637)	promoter-TSS (NM_001046637)	69	NM_001046637	53607	Mm.386890	NM_015782	ENSMUSG00000061479	Snrpa	C430021M15Rik|Rnu1a-1|Rnu1a1|U1-A|U1A	small nuclear ribonucleoprotein polypeptide A	protein-coding
mm_118183.1	chr13	107022314	107022362	-	1	NA	promoter-TSS (NM_008442)	promoter-TSS (NM_008442)	-224	NM_008442	16563	Mm.355686	NM_008442	ENSMUSG00000021693	Kif2a	C530030B14Rik|Kif2|Kns2|M-kinesin	kinesin family member 2A	protein-coding
mm_99427.1	chr11	102399816	102399826	+	1	NA	intron (NM_016759, intron 7 of 10)	CpG-2672	5166	NR_105895	102465561		NR_105895	ENSMUSG00000098774	Mir6930	Gm27436|mmu-mir-6930	microRNA 6930	ncRNA
mm_16495.1	chr2	181187510	181187595	+	1	NA	5' UTR (NM_025598, exon 2 of 5)	5' UTR (NM_025598, exon 2 of 5)	209	NM_025598	66496	Mm.213943	NM_025598	ENSMUSG00000016344	Ppdpf	0610012G23Rik|2610317A05Rik|2700038C09Rik|3110053G12Rik	pancreatic progenitor cell differentiation and proliferation factor	protein-coding
mm_75186.1	chr8	36953219	36953239	-	1	NA	promoter-TSS (NM_001194940)	promoter-TSS (NM_001194940)	-787	NM_001194940	50768	Mm.125155	NM_015802	ENSMUSG00000031523	Dlc1	A730069N07Rik|Arhgap7|HP|STARD12|dlc-1	deleted in liver cancer 1	protein-coding
mm_152808.1	chr19	22992419	22992421	-	1	NA	Intergenic	Intergenic	-148806	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_169972.1	chr17	14057118	14057126	-	1	NA	Intergenic	(CTG)n|Simple_repeat|Simple_repeat	108749	NM_001122977	635895	Mm.388844	NM_001122977	ENSMUSG00000067941	Gm7168	EG635895	predicted gene 7168	protein-coding
mm_154253.1	chr19	60766789	60766813	-	1	NA	exon (NM_010123, exon 19 of 22)	exon (NM_010123, exon 19 of 22)	7584	NR_034047	100217439		NR_034047		Snora19	MBI-51	small nucleolar RNA, H/ACA box 19	snoRNA
mm_102052.1	chr11	52099712	52099739	-	1	NA	intron (NM_019411, intron 1 of 6)	intron (NM_019411, intron 1 of 6)	901	NM_019411	19052	Mm.260288	NM_019411	ENSMUSG00000020349	Ppp2ca	PP2A|R75353	protein phosphatase 2 (formerly 2A), catalytic subunit, alpha isoform	protein-coding
mm_127719.1	chr15	103102216	103102228	+	1	NA	Intergenic	CpG	44606	NR_045743	432989	Mm.383979	NR_045743	ENSMUSG00000097003	D930007P13Rik	-	Riken cDNA D930007P13 gene	ncRNA
mm_92420.1	chr10	77008314	77008322	-	1	NA	Intergenic	Intergenic	-3677	NR_045882	100038479	Mm.387034	NR_045882	ENSMUSG00000074919	Gm10787	ENSMUSG00000074919	predicted gene 10787	ncRNA
mm_54965.1	chr6	48723623	48723660	-	1	NA	exon (NM_146167, exon 2 of 2)	exon (NM_146167, exon 2 of 2)	5020	NM_146167	231932	Mm.30479	NM_146167	ENSMUSG00000043931	Gimap7	IAN7|Ian3	GTPase, IMAP family member 7	protein-coding
mm_65023.1	chr7	18354982	18355016	-	1	NA	promoter-TSS (NM_011963)	promoter-TSS (NM_011963)	-6	NM_001163685	26438	Mm.89991	NM_011963	ENSMUSG00000003505	Psg18	Cea-3|Cea3|mmCGM6	pregnancy specific glycoprotein 18	protein-coding
mm_40387.1	chr5	52741570	52741623	+	1	NA	promoter-TSS (NM_025951)	promoter-TSS (NM_025951)	22	NM_025951	67073	Mm.248647	NM_025951	ENSMUSG00000029186	Pi4k2b	2610042N09Rik|4933409G22Rik	phosphatidylinositol 4-kinase type 2 beta	protein-coding
mm_127951.1	chr15	10723540	10723561	-	1	NA	intron (NR_045063, intron 2 of 6)	ORR1C1|LTR|ERVL-MaLR	8650	NR_045065	75259	Mm.33928	NR_045063	ENSMUSG00000097058	4930556M19Rik	1700009D01Rik|C130022M03Rik	RIKEN cDNA 4930556M19 gene	ncRNA
mm_146291.1	chr18	78827453	78827454	+	1	NA	intron (NM_053099, intron 4 of 5)	MTEa-int|LTR|ERVL-MaLR	-230503	NM_030683	27411	Mm.44158	NM_030683	ENSMUSG00000024552	Slc14a2	UT-A1|UT-A3	solute carrier family 14 (urea transporter), member 2	protein-coding
mm_68824.1	chr7	126181616	126181632	-	1	NA	intron (NM_001311143, intron 1 of 23)	MTE2b|LTR|ERVL-MaLR	18784	NM_028816	74204	Mm.235663	NM_028816	ENSMUSG00000000131	Xpo6	2610005L19Rik|AL022631|C230091E20Rik|R75304|Ranbp20|mKIAA0370	exportin 6	protein-coding
mm_120487.1	chr14	65979673	65979709	+	1	NA	exon (NM_013492, exon 7 of 9)	exon (NM_013492, exon 7 of 9)	11208	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_169465.1	chr1	46583533	46583537	+	1	NA	intron (NM_001310335, intron 19 of 64)	L1Md_T|LINE|L1	158017	NM_001310335	100101919	Mm.383402	NM_001310335	ENSMUSG00000101337	Dnah7c	Dnahc7c	dynein, axonemal, heavy chain 7C	protein-coding
mm_42593.1	chr5	117389116	117389181	+	1	NA	promoter-TSS (NM_028128)	promoter-TSS (NM_028128)	-125	NM_028128	72151	Mm.27997	NM_028128	ENSMUSG00000029363	Rfc5	2610020K06Rik|2610209F07Rik|36.5kDa|36kDa|Recc5	replication factor C (activator 1) 5	protein-coding
mm_20073.1	chr2	120539853	120539866	-	1	NA	intron (NM_011743, intron 3 of 21)	intron (NM_011743, intron 3 of 21)	23972	NM_011743	20402	Mm.485295	NM_011743	ENSMUSG00000027288	Zfp106	Cd-1|D2Dcr28|H3a|Sh3bp3|Znf106|sirm	zinc finger protein 106	protein-coding
mm_150258.1	chr19	34192733	34192743	+	1	NA	intron (NM_029682, intron 1 of 10)	CpG	468	NM_029682	76630	Mm.130952	NM_029682	ENSMUSG00000024776	Stambpl1	1700095N21Rik|8230401J17Rik|ALMalpha|AMSH-FP	STAM binding protein like 1	protein-coding
mm_47409.1	chr5	123132652	123132678	-	1	NA	promoter-TSS (NM_175092)	promoter-TSS (NM_175092)	-36	NM_175092	23912	Mm.253876	NM_175092	ENSMUSG00000029449	Rhof	AI845056|AV026554|Arhf|Ifld1|Rif	ras homolog family member F (in filopodia)	protein-coding
mm_115573.1	chr13	11569416	11569459	-	1	NA	intron (NM_023868, intron 98 of 104)	B3|SINE|B2	47385	NR_027813	664793	Mm.410565	NR_027813		Zp4-ps	EG664793|Zp4|Zpb	zona pellucida glycoprotein 4, pseudogene	pseudo
mm_24828.1	chr3	95653918	95653924	+	1	NA	Intergenic	Intergenic	-4800	NM_008562	17210	Mm.1639	NM_008562	ENSMUSG00000038612	Mcl1	AW556805|Mcl-1	myeloid cell leukemia sequence 1	protein-coding
mm_121419.1	chr14	119875644	119875648	+	1	NA	Intergenic	Intergenic	126419	NR_045621	75432	Mm.443277	NR_045621	ENSMUSG00000100274	1700006F04Rik	-	RIKEN cDNA 1700006F04 gene	ncRNA
mm_35849.1	chr4	48473340	48473356	-	1	NA	promoter-TSS (NM_172304)	promoter-TSS (NM_172304)	74	NM_172304	269536	Mm.272025	NM_172304	ENSMUSG00000028345	Tex10	2610206N19Rik|2810462N03Rik|BC006867	testis expressed gene 10	protein-coding
mm_103689.1	chr11	79503968	79503978	-	1	NA	5' UTR (NM_019409, exon 1 of 2)	5' UTR (NM_019409, exon 1 of 2)	109	NM_019409	18377	Mm.93335	NM_019409	ENSMUSG00000049612	Omg	-	oligodendrocyte myelin glycoprotein	protein-coding
mm_159870.1	chr5	146185304	146185304	-	1	NA	promoter-TSS (NM_001008547)	promoter-TSS (NM_001008547)	0	NM_001008547	69282	Mm.373573	NM_001008547	ENSMUSG00000095040	1700001J03Rik	-	RIKEN cDNA 1700001J03 gene	protein-coding
mm_71308.1	chr8	42247190	42247214	+	1	NA	Intergenic	Intergenic	419935	NR_045497	69966	Mm.416903	NR_045497	ENSMUSG00000102046	2810404M03Rik	-	RIKEN cDNA 2810404M03 gene	ncRNA
mm_7842.1	chr1	132358244	132358256	-	1	NA	intron (NM_001311107, intron 4 of 4)	intron (NM_001311107, intron 4 of 4)	9698	NM_001311108	68875	Mm.273785	NM_178874	ENSMUSG00000042066	Tmcc2	1110063G11Rik	transmembrane and coiled-coil domains 2	protein-coding
mm_138964.1	chr17	44734144	44734175	+	1	NA	intron (NR_073392, intron 2 of 7)	intron (NR_073392, intron 2 of 7)	2017	NR_073425	12393	Mm.391013	NM_009820	ENSMUSG00000039153	Runx2	AML3|Cbf|Cbfa-1|Cbfa1|LS3|Osf2|PEBP2aA|Pebp2a1|Pebpa2a	runt related transcription factor 2	protein-coding
mm_144708.1	chr18	34887520	34887524	+	1	NA	Intergenic	CpG	26315	NM_007913	13653	Mm.181959	NM_007913	ENSMUSG00000038418	Egr1	A530045N19Rik|ETR103|Egr-1|Krox-1|Krox-24|Krox24|NGF1-A|NGFI-A|NGFIA|TIS8|Zenk|Zfp-6|Zif268|egr	early growth response 1	protein-coding
mm_118120.1	chr13	104109577	104109619	-	1	NA	promoter-TSS (NM_029447)	promoter-TSS (NM_029447)	16	NM_029447	75805	Mm.127692	NM_029447	ENSMUSG00000021710	Nln	4930472G13Rik|C79345	neurolysin (metallopeptidase M3 family)	protein-coding
mm_148674.1	chr19	5638212	5638214	+	1	NA	intron (NM_009045, intron 1 of 10)	intron (NM_009045, intron 1 of 10)	723	NM_009045	19697	Mm.249966	NM_009045	ENSMUSG00000024927	Rela	p65	v-rel reticuloendotheliosis viral oncogene homolog A (avian)	protein-coding
mm_171625.1	chr4	16632038	16632042	+	1	NA	Intergenic	LTRIS2|LTR|ERV1	467930	NR_045765	100415915	Mm.387180	NR_045765	ENSMUSG00000085112	A530072M11Rik	-	RIKEN cDNA gene A530072M11	ncRNA
mm_117884.1	chr13	99411921	99411934	-	1	NA	non-coding (NR_015515, exon 1 of 2)	non-coding (NR_015515, exon 1 of 2)	899	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_56446.1	chr6	97487889	97487972	-	1	NA	promoter-TSS (NM_001346637)	promoter-TSS (NM_001346637)	-110	NM_001346637	232288	Mm.27789	NM_145148	ENSMUSG00000030064	Frmd4b	6030440G05Rik|C87375|GOBLIN|GRSP1|R74720	FERM domain containing 4B	protein-coding
mm_159581.1	chr4	118809885	118809885	-	1	NA	promoter-TSS (NM_207703)	promoter-TSS (NM_207703)	-23	NM_207703	435804	Mm.296491	NM_207703	ENSMUSG00000066061	Olfr1335	MOR259-12|MOR259-5|Olfr1334-ps1|Olfr1335-ps1	olfactory receptor 1335	protein-coding
mm_91867.1	chr10	59469454	59469460	-	1	NA	intron (NM_001033259, intron 2 of 7)	L1MEf|LINE|L1	-27678	NM_010959	18302	Mm.123013	NM_010959	ENSMUSG00000009654	Oit3	EF-9|LZP	oncoprotein induced transcript 3	protein-coding
mm_129911.1	chr15	84123175	84123203	-	1	NA	promoter-TSS (NM_029427)	promoter-TSS (NM_029427)	-14	NM_029427	75772	Mm.159565	NM_029427	ENSMUSG00000018868	Pnpla5	4833426H19Rik|GS2L	patatin-like phospholipase domain containing 5	protein-coding
mm_2747.1	chr1	128612807	128612843	+	1	NA	Intergenic	B4|SINE|B4	-20526	NM_009911	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding
mm_52176.1	chr6	99262925	99262928	+	1	NA	intron (NM_001347345, intron 3 of 19)	(CA)n|Simple_repeat|Simple_repeat	3589	NM_001197321	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_25092.1	chr3	100922437	100922473	+	1	NA	promoter-TSS (NM_001165953)	promoter-TSS (NM_001165953)	-38	NM_001165952	229644	Mm.189351	NM_194343	ENSMUSG00000033233	Trim45	4921530N01Rik	tripartite motif-containing 45	protein-coding
mm_58152.1	chr6	142323043	142323062	-	1	NA	promoter-TSS (NM_130861)	promoter-TSS (NM_130861)	-71	NM_130861	108096	Mm.206599	NM_130861	ENSMUSG00000063975	Slco1a5	Oatp-3|Oatp3|Slc21a7	solute carrier organic anion transporter family, member 1a5	protein-coding
mm_86550.1	chr10	10234988	10234994	+	1	NA	Intergenic	Intergenic	237323	NM_001127353	215772	Mm.246573	NM_172547	ENSMUSG00000050994	Adgb	9130014G24Rik	androglobin	protein-coding
mm_156745.1	chrX	159973442	159973460	+	1	NA	non-coding (NR_110970, exon 17 of 17)	non-coding (NR_110970, exon 17 of 17)	-14982	NM_001163085	270672	Mm.386889	NM_001163085	ENSMUSG00000031303	Map3k15	BC031147|MEKK15	mitogen-activated protein kinase kinase kinase 15	protein-coding
mm_152682.1	chr19	15984971	15985018	-	1	NA	promoter-TSS (NM_198019)	promoter-TSS (NM_198019)	-5	NM_198019	208518	Mm.105652	NM_198019	ENSMUSG00000041491	Cep78	5730599I05Rik|D030027P05	centrosomal protein 78	protein-coding
mm_67792.1	chr7	97729371	97729394	-	1	NA	intron (NM_175105, intron 1 of 2)	B4A|SINE|B4	8865	NM_175105	66333	Mm.29756	NM_175105	ENSMUSG00000042797	Aqp11	1700015P13Rik|AI648923|sjds	aquaporin 11	protein-coding
mm_99738.1	chr11	106374836	106374850	+	1	NA	promoter-TSS (NM_029345)	promoter-TSS (NM_029345)	17	NM_029345	75573	Mm.159539	NM_029345	ENSMUSG00000009210	Prr29	2310007L24Rik	proline rich 29	protein-coding
mm_151172.1	chr19	53310459	53310463	+	1	NA	promoter-TSS (NM_001008542)	promoter-TSS (NM_001008542)	-45	NM_001008542	17859	Mm.2154	NM_010847	ENSMUSG00000025025	Mxi1	ENSMUSG00000067085|Gm10197|Mad2|bHLHc11	MAX interactor 1, dimerization protein	protein-coding
mm_104566.1	chr11	96916408	96916426	-	1	NA	promoter-TSS (NM_030248)	promoter-TSS (NM_030248)	97	NM_001308183	80280	Mm.28297	NM_030248	ENSMUSG00000018669	Cdk5rap3	1810007E24Rik|BC002318|C53|C81486|HSF-27|IC53|LZAP|MST016	CDK5 regulatory subunit associated protein 3	protein-coding
mm_19046.1	chr2	77170578	77170589	-	1	NA	promoter-TSS (NM_001025576)	promoter-TSS (NM_001025576)	52	NM_001025576	545428	Mm.26579	NM_001025576	ENSMUSG00000044033	Ccdc141	2610301F02Rik|CAMDI|ENSMUSG00000075261	coiled-coil domain containing 141	protein-coding
mm_49506.1	chr6	29853747	29853790	+	1	NA	promoter-TSS (NM_001347084)	promoter-TSS (NM_001347084)	27	NM_001347084	74340	Mm.210899	NM_021414	ENSMUSG00000029772	Ahcyl2	4631427C17Rik|AI227036|Adohcyase3|mKIAA0828	S-adenosylhomocysteine hydrolase-like 2	protein-coding
mm_167774.1	chr9	112164673	112164683	-	1	NA	intron (NM_001177623, intron 9 of 9)	intron (NM_001177623, intron 9 of 9)	21271	NM_001177618	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_129610.1	chr15	79934408	79934414	-	1	NA	Intergenic	Intergenic	-1765	NM_144811	52609	Mm.323442	NM_144811	ENSMUSG00000053411	Cbx7	1600014J01Rik|AI851678|D15Ertd417e	chromobox 7	protein-coding
mm_19554.1	chr2	98666660	98666693	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	1199019	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_23441.1	chr3	59432060	59432095	+	1	NA	Intergenic	Intergenic	-87821	NM_001162884	242050	Mm.228086	NM_001162884	ENSMUSG00000036334	Igsf10	6530405F15Rik|9030224D03|AA409708|AA536958|AI414626|Adlican2|CMF608	immunoglobulin superfamily, member 10	protein-coding
mm_60772.1	chr7	45557552	45557562	+	1	NA	intron (NM_025330, intron 3 of 8)	intron (NM_025330, intron 3 of 8)	2629	NM_025330	66065	Mm.285710	NM_025330	ENSMUSG00000030825	Hsd17b14	0610039E24Rik|Dhrs10|retSDR3	hydroxysteroid (17-beta) dehydrogenase 14	protein-coding
mm_11853.1	chr2	45696594	45696611	+	1	NA	promoter-TSS (NR_040497)	promoter-TSS (NR_040497)	-3	NR_040497	69405	Mm.396184	NR_040497	ENSMUSG00000086202	1700019E08Rik	-	RIKEN cDNA 1700019E08 gene	ncRNA
mm_15265.1	chr2	155096001	155096014	+	1	NA	Intergenic	Intergenic	4072	NR_040634	100504268	Mm.410858	NR_040634	ENSMUSG00000087254	2310005A03Rik	-	RIKEN cDNA 2310005A03 gene	ncRNA
mm_154296.1	chr19	61224588	61224606	-	1	NA	3' UTR (NM_009970, exon 12 of 12)	3' UTR (NM_009970, exon 12 of 12)	3821	NM_009970	12982	Mm.287228	NM_009970	ENSMUSG00000059326	Csf2ra	CD116|Csfgmra|GM-CSF-Ra|GM-CSFR	colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)	protein-coding
mm_132716.1	chr16	43508119	43508158	+	1	NA	intron (NM_181058, intron 3 of 6)	intron (NM_181058, intron 3 of 6)	-87942	NR_046026	626693	Mm.447083	NR_046026	ENSMUSG00000085499	Gm15713	OTTMUSG00000025617	predicted gene 15713	ncRNA
mm_4275.1	chr1	171559299	171559305	+	1	NA	5' UTR (NM_018729, exon 1 of 9)	5' UTR (NM_018729, exon 1 of 9)	109	NM_018729	18106	Mm.2299	NM_018729	ENSMUSG00000004709	Cd244	2B4|C9.1|F730046O15Rik|Ly90|NAIL|NKR2B4|Nmrk|SLAMF4	CD244 natural killer cell receptor 2B4	protein-coding
mm_163896.1	chr14	27379685	27379693	+	1	NA	exon (NM_027871, exon 4 of 11)	exon (NM_027871, exon 4 of 11)	18300	NM_001289688	71704	Mm.248606	NM_027871	ENSMUSG00000021895	Arhgef3	1200004I24Rik|9830169H03Rik|C76747|Xpln	Rho guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_27345.1	chr3	50414864	50414880	-	1	NA	intron (NM_011990, intron 6 of 11)	AT_rich|Low_complexity|Low_complexity	28741	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_23668.1	chr3	68572382	68572392	+	1	NA	promoter-TSS (NM_013928)	promoter-TSS (NM_013928)	19	NM_013928	30953	Mm.331064	NM_013928	ENSMUSG00000027777	Schip1	Nf2ip|Schip-1	schwannomin interacting protein 1	protein-coding
mm_132246.1	chr16	32751226	32751237	+	1	NA	exon (NM_080457, exon 2 of 27)	exon (NM_080457, exon 2 of 27)	15345	NM_080457	140474	Mm.214599	NM_080457	ENSMUSG00000079620	Muc4	4933405I11Rik|Asgp	mucin 4	protein-coding
mm_63713.1	chr7	130692748	130692788	+	1	NA	5' UTR (NM_021314, exon 1 of 18)	5' UTR (NM_021314, exon 1 of 18)	212	NM_021314	57752	Mm.86322	NM_021314	ENSMUSG00000030852	Tacc2	mKIAA4180	transforming, acidic coiled-coil containing protein 2	protein-coding
mm_153194.1	chr19	34524444	34524467	-	1	NA	intron (NM_001111100, intron 2 of 9)	intron (NM_001111100, intron 2 of 9)	3019	NM_001111100	16889	Mm.157545	NM_021460	ENSMUSG00000024781	Lipa	AA960673|Lal|Lip-1|Lip1	lysosomal acid lipase A	protein-coding
mm_22738.1	chr3	19894904	19894914	+	1	NA	promoter-TSS (NR_027985)	promoter-TSS (NR_027985)	38	NR_027985	70808	Mm.427103	NR_027985	ENSMUSG00000048106	4632415L05Rik	AI662792	RRS1 ribosome biogenesis regulator homolog pseudogene	pseudo
mm_15829.1	chr2	164653841	164653850	+	1	NA	intron (NM_001160414, intron 1 of 3)	intron (NM_001160414, intron 1 of 3)	1121	NM_001160414	629754	Mm.190489	NM_001160414	ENSMUSG00000074594	Wfdc9	OTTMUSG00000001088	WAP four-disulfide core domain 9	protein-coding
mm_137823.1	chr17	30576532	30576559	+	1	NA	promoter-TSS (NM_027060)	promoter-TSS (NM_027060)	-258	NM_027060	224671	Mm.41220	NM_027060	ENSMUSG00000062202	Btbd9	1700023F20Rik|4930402L05|AI464421	BTB (POZ) domain containing 9	protein-coding
mm_11509.1	chr2	32570862	32570913	+	1	NA	promoter-TSS (NM_010073)	promoter-TSS (NM_010073)	29	NM_010073	13481	Mm.22001	NM_010073	ENSMUSG00000026810	Dpm2	AW557993|R75484	dolichol-phosphate (beta-D) mannosyltransferase 2	protein-coding
mm_45174.1	chr5	51534527	51534529	-	1	NA	intron (NR_132764, intron 2 of 12)	intron (NR_132764, intron 2 of 12)	19393	NR_027710	19017	Mm.259072	NM_008904	ENSMUSG00000029167	Ppargc1a	A830037N07Rik|ENSMUSG00000079510|Gm11133|PGC-1|PPARGC-1-alpha|Pgc-1alpha|Pgc1|Pgco1|Ppargc1	peroxisome proliferative activated receptor, gamma, coactivator 1 alpha	protein-coding
mm_145197.1	chr18	49937489	49937495	+	1	NA	intron (NM_001081371, intron 36 of 42)	intron (NM_001081371, intron 36 of 42)	-41935	NM_001177760	106869	Mm.27740	NM_134131	ENSMUSG00000062210	Tnfaip8	AA987150|E130304C20Rik|ENSMUSG00000073567|Gg2-1|Gm10539|Nded|Ssc-2|Tipe	tumor necrosis factor, alpha-induced protein 8	protein-coding
mm_133864.1	chr16	96361712	96361722	+	1	NA	promoter-TSS (NM_028078)	promoter-TSS (NM_028078)	-40	NM_001177887	72058	Mm.119714	NM_028078	ENSMUSG00000000159	Igsf5	2010003D20Rik|JCAM|Jam4	immunoglobulin superfamily, member 5	protein-coding
mm_32661.1	chr4	115090189	115090228	+	1	NA	intron (NM_026018, intron 2 of 4)	intron (NM_026018, intron 2 of 4)	1500	NM_001164557	67182	Mm.30181	NM_026018	ENSMUSG00000028716	Pdzk1ip1	0610007F13Rik|2700030M23Rik|AU046042|Map17	PDZK1 interacting protein 1	protein-coding
mm_90690.1	chr10	128971078	128971086	+	1	NA	Intergenic	L1M4|LINE|L1	-10094	NM_027853	71664	Mm.337232	NM_027853	ENSMUSG00000025347	Mettl7b	0610006F02Rik|AI266817	methyltransferase like 7B	protein-coding
mm_27247.1	chr3	36613419	36613429	-	1	NA	promoter-TSS (NM_027810)	promoter-TSS (NM_027810)	-35	NM_027810	71492	Mm.286187	NM_027810	ENSMUSG00000037325	Bbs7	8430406N16Rik	Bardet-Biedl syndrome 7 (human)	protein-coding
mm_44227.1	chr5	5076243	5076276	-	1	NA	intron (NM_011074, intron 8 of 14)	intron (NM_011074, intron 8 of 14)	189809	NM_001310448	18647	Mm.389061	NM_011074	ENSMUSG00000028926	Cdk14	Pftk1|mKIAA0834	cyclin-dependent kinase 14	protein-coding
mm_60664.1	chr7	44997750	44997760	+	1	NA	promoter-TSS (NM_029410)	promoter-TSS (NM_029410)	107	NM_016849	54131	Mm.3960	NM_016849	ENSMUSG00000003184	Irf3	C920001K05Rik|IRF-3	interferon regulatory factor 3	protein-coding
mm_100273.1	chr11	117762440	117762458	+	1	NA	3' UTR (NM_198022, exon 22 of 22)	3' UTR (NM_198022, exon 22 of 22)	18172	NM_181321	217353	Mm.286963	NM_145439	ENSMUSG00000025572	Tmc6	D11Ertd204e|EVER1	transmembrane channel-like gene family 6	protein-coding
mm_76628.1	chr8	91801881	91801892	-	1	NA	promoter-TSS (NM_001253822)	promoter-TSS (NM_001253822)	-232	NM_008393	16373	Mm.238044	NM_008393	ENSMUSG00000031734	Irx3	AI894186	Iroquois related homeobox 3	protein-coding
mm_99022.1	chr11	98927827	98927854	+	1	NA	Intergenic	Intergenic	-9856	NM_009024	19401	Mm.439744	NM_009024	ENSMUSG00000037992	Rara	Nr1b1|RAR|RARalpha1	retinoic acid receptor, alpha	protein-coding
mm_124997.1	chr15	23036450	23036492	+	1	NA	promoter-TSS (NM_001081299)	promoter-TSS (NM_001081299)	8	NM_001081299	320865	Mm.241965	NM_001081299	ENSMUSG00000040420	Cdh18	B230220E17Rik|Cdh14l	cadherin 18	protein-coding
mm_30214.1	chr3	145009822	145009838	-	1	NA	exon (NM_017474, exon 10 of 14)	exon (NM_017474, exon 10 of 14)	22946	NM_017474	23844	Mm.33483	NM_017474	ENSMUSG00000028255	Clca1	Clca2|Clca3|gob-5|gob5	chloride channel accessory 1	protein-coding
mm_68581.1	chr7	115953299	115953328	-	1	NA	intron (NM_001025559, intron 1 of 15)	intron (NM_001025559, intron 1 of 15)	41773	NM_011445	20679	Mm.323365	NM_011445	ENSMUSG00000051910	Sox6	AI987981|SOX-LZ	SRY (sex determining region Y)-box 6	protein-coding
mm_139487.1	chr17	56079673	56079704	+	1	NA	promoter-TSS (NM_001304785)	promoter-TSS (NM_001304785)	57	NM_001304785	15193	Mm.12966	NM_008233	ENSMUSG00000002833	Hdgfrp2	HRP-2	hepatoma-derived growth factor, related protein 2	protein-coding
mm_75551.1	chr8	57652994	57653013	-	1	NA	promoter-TSS (NM_144731)	promoter-TSS (NM_144731)	52	NM_001167981	108150	Mm.62886	NM_144731	ENSMUSG00000031608	Galnt7	AI225872	UDP-N-acetyl-alpha-D-galactosamine: polypeptide N-acetylgalactosaminyltransferase 7	protein-coding
mm_138625.1	chr17	35841669	35841683	+	1	NA	5' UTR (NM_001010833, exon 1 of 16)	5' UTR (NM_001010833, exon 1 of 16)	178	NM_001010833	240087	Mm.218511	NM_001010833	ENSMUSG00000061607	Mdc1	6820401C03|AA413496|Nfbd1|mKIAA0170	mediator of DNA damage checkpoint 1	protein-coding
mm_159697.1	chr5	26039507	26039507	-	1	NA	promoter-TSS (NM_029376)	promoter-TSS (NM_029376)	-2	NM_029376	75657	Mm.374273	NM_029376	ENSMUSG00000073119	Speer4a	1700027N01Rik|SPEER-4A	spermatogenesis associated glutamate (E)-rich protein 4A	protein-coding
mm_148626.1	chr19	5447860	5447866	+	1	NA	5' UTR (NM_010235, exon 1 of 4)	5' UTR (NM_010235, exon 1 of 4)	165	NM_010235	14283	Mm.6215	NM_010235	ENSMUSG00000024912	Fosl1	AW538199|Fra1|fra-1	fos-like antigen 1	protein-coding
mm_148849.1	chr19	6384454	6384456	+	1	NA	promoter-TSS (NM_011224)	promoter-TSS (NM_011224)	47	NM_011224	19309	Mm.27806	NM_011224	ENSMUSG00000032648	Pygm	AI115133|PG	muscle glycogen phosphorylase	protein-coding
mm_57358.1	chr6	124760826	124760840	-	1	NA	3' UTR (NM_013509, exon 12 of 12)	3' UTR (NM_013509, exon 12 of 12)	-4346	NM_007881	13498	Mm.333380	NM_007881	ENSMUSG00000004263	Atn1	Atr1|Drpla|atrophin-1	atrophin 1	protein-coding
mm_5829.1	chr1	52800419	52800448	-	1	NA	intron (NM_008384, intron 1 of 5)	MT2B|LTR|ERVL	17255	NM_008384	16329	Mm.917	NM_008384	ENSMUSG00000026102	Inpp1	2300002C06Rik|AV137389	inositol polyphosphate-1-phosphatase	protein-coding
mm_2392.1	chr1	93512129	93512156	+	1	NA	promoter-TSS (NM_145519)	promoter-TSS (NM_145519)	38	NM_145519	227377	Mm.243091	NM_145519	ENSMUSG00000034066	Farp2	AI465173|BC009153|D030026M03Rik|Fir|mKIAA0793	FERM, RhoGEF and pleckstrin domain protein 2	protein-coding
mm_45298.1	chr5	65330140	65330148	-	1	NA	intron (NM_001347358, intron 1 of 24)	intron (NM_001347358, intron 1 of 24)	5495	NM_011258	19687	Mm.148877	NM_011258	ENSMUSG00000029191	Rfc1	140kDa|Alp145|RFC140|Recc1	replication factor C (activator 1) 1	protein-coding
mm_172276.1	chr6	85843879	85843884	+	1	NA	Intergenic	Intergenic	-11991	NM_023455	68396	Mm.154782	NM_023455	ENSMUSG00000030004	Nat8	0610037O16Rik|CCNAT|Cml4	N-acetyltransferase 8 (GCN5-related)	protein-coding
mm_113474.1	chr13	36730043	36730055	+	1	NA	intron (NM_153529, intron 2 of 2)	intron (NM_153529, intron 2 of 2)	4428	NM_153529	68404	Mm.232930	NM_153529	ENSMUSG00000039114	Nrn1	0710008J23Rik|Cpg15|Nrn	neuritin 1	protein-coding
mm_168058.1	chrY	90828710	90828750	-	1	NA	Intergenic	CpG	10676	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_90825.1	chr10	7950161	7950167	-	1	NA	intron (NM_138667, intron 1 of 6)	intron (NM_138667, intron 1 of 6)	5959	NM_138667	68652	Mm.193041	NM_138667	ENSMUSG00000015755	Tab2	1110030N06Rik|A530078N03Rik|Map3k7ip2|mKIAA0733	TGF-beta activated kinase 1/MAP3K7 binding protein 2	protein-coding
mm_155403.1	chrX	73228273	73228314	+	1	NA	promoter-TSS (NM_007978)	promoter-TSS (NM_007978)	-13	NM_007978	14070	Mm.165807	NM_007978	ENSMUSG00000078317	F8a	AI852759|DXUcsf1|F8a1	factor 8-associated gene A	protein-coding
mm_80515.1	chr9	80066754	80066764	+	1	NA	promoter-TSS (NM_146003)	promoter-TSS (NM_146003)	-144	NM_001311110	215351	Mm.28232	NM_146003	ENSMUSG00000034252	Senp6	2810017C20Rik|E130319N12Rik|Susp1|mKIAA0797	SUMO/sentrin specific peptidase 6	protein-coding
mm_30994.1	chr4	39450269	39450314	+	1	NA	promoter-TSS (NM_001081095)	promoter-TSS (NM_001081095)	-2	NM_001081095	75471	Mm.23522	NM_001081095	ENSMUSG00000028287	1700009N14Rik	AI429145	RIKEN cDNA 1700009N14 gene	protein-coding
mm_155700.1	chrX	94636101	94636111	+	1	NA	promoter-TSS (NM_008179)	promoter-TSS (NM_008179)	37	NM_008179	14853	Mm.20826	NM_008179	ENSMUSG00000071723	Gspt2	-	G1 to S phase transition 2	protein-coding
mm_65755.1	chr7	28629695	28629713	-	1	NA	exon (NM_175319, exon 2 of 13)	exon (NM_175319, exon 2 of 13)	1311	NM_175319	101744	Mm.26022	NM_175319	ENSMUSG00000037469	Acp7	AU017076|C330005M16Rik|Papl	acid phosphatase 7, tartrate resistant	protein-coding
mm_172624.1	chr8	20270819	20270822	-	1	NA	non-coding (NR_030708, exon 5 of 5)	non-coding (NR_030708, exon 5 of 5)	26612	NR_030708	547150	Mm.359054	NR_030708	ENSMUSG00000071796	6820431F20Rik	-	cadherin 11 pseudogene	pseudo
mm_7964.1	chr1	133930133	133930146	-	1	NA	Intergenic	Intergenic	-8738	NM_054077	116847	Mm.214514	NM_054077	ENSMUSG00000041577	Prelp	7330409J17Rik|SLRR2A	proline arginine-rich end leucine-rich repeat	protein-coding
mm_156730.1	chrX	159924916	159924938	+	1	NA	intron (NM_001135728, intron 7 of 12)	intron (NM_001135728, intron 7 of 12)	-17766	NM_001290661	58194	Mm.286495	NM_021389	ENSMUSG00000040990	Sh3kbp1	1200007H22Rik|1700125L08Rik|5830464D22Rik|AI447724|Cin85|IN85|Ruk|Seta	SH3-domain kinase binding protein 1	protein-coding
mm_116434.1	chr13	42174636	42174636	-	1	NA	intron (NM_007772, intron 7 of 8)	intron (NM_007772, intron 7 of 8)	122615	NM_007772	110521	Mm.4808	NM_007772	ENSMUSG00000021366	Hivep1	Cryabp1	human immunodeficiency virus type I enhancer binding protein 1	protein-coding
mm_1510.1	chr1	72383351	72383367	+	1	NA	exon (NM_009533, exon 18 of 21)	exon (NM_009533, exon 18 of 21)	75938	NM_009533	22596	Mm.246952	NM_009533	ENSMUSG00000026187	Xrcc5	AI314015|Ku80|Ku86	X-ray repair complementing defective repair in Chinese hamster cells 5	protein-coding
mm_118264.1	chr13	112552103	112552117	-	1	NA	intron (NM_139299, intron 4 of 16)	URR1A|DNA|hAT-Charlie	28552	NM_139299	218624	Mm.380801	NM_139299	ENSMUSG00000050377	Il31ra	CRL3|GLM-R|GPL|Glmr|NR10	interleukin 31 receptor A	protein-coding
mm_122859.1	chr14	54893860	54893899	-	1	NA	promoter-TSS (NM_019402)	promoter-TSS (NM_019402)	-264	NM_019402	54196	Mm.7723	NM_019402	ENSMUSG00000022194	Pabpn1	PAB2|Pabp3|mPABII	poly(A) binding protein, nuclear 1	protein-coding
mm_65420.1	chr7	25267409	25267421	-	1	NA	promoter-TSS (NM_001302811)	promoter-TSS (NM_001302811)	-284	NM_001302811	71722	Mm.28833	NM_027882	ENSMUSG00000005442	Cic	1200010B10Rik|mKIAA0306	capicua transcriptional repressor	protein-coding
mm_51185.1	chr6	70849463	70849464	+	1	NA	intron (NM_001313918, intron 1 of 2)	PB1D11|SINE|Alu	4948	NM_001313918	13666	Mm.247167	NM_010121	ENSMUSG00000031668	Eif2ak3	Pek|Perk	eukaryotic translation initiation factor 2 alpha kinase 3	protein-coding
mm_98890.1	chr11	97838132	97838146	+	1	NA	3' UTR (NM_010688, exon 7 of 7)	3' UTR (NM_010688, exon 7 of 7)	-2641	NM_001080935	68127	Mm.110270	NM_001080935	ENSMUSG00000050538	B230217C12Rik	AI840637	RIKEN cDNA B230217C12 gene	protein-coding
mm_151288.1	chr19	55315626	55315636	+	1	NA	promoter-TSS (NM_016862)	promoter-TSS (NM_016862)	401	NM_025883	66980	Mm.386789	NM_025883	ENSMUSG00000024982	Zdhhc6	2400007G07Rik|5930409M18Rik|AI462345|C77369	zinc finger, DHHC domain containing 6	protein-coding
mm_42786.1	chr5	121463194	121463209	+	1	NA	promoter-TSS (NM_001161627)	promoter-TSS (NM_001161627)	20	NM_001161627	77462	Mm.358781	NM_029912	ENSMUSG00000029452	Tmem116	4930406A18Rik|4930513P12Rik|C030022K24Rik	transmembrane protein 116	protein-coding
mm_113243.1	chr13	27345695	27345701	+	1	NA	promoter-TSS (NM_010088)	promoter-TSS (NM_010088)	25	NM_001289919	13529	Mm.291450	NM_010088	ENSMUSG00000018259	Prl8a2	D/tPRP|DPRP|Dtprp|Ghd11|mdPRP	prolactin family 8, subfamily a, member 2	protein-coding
mm_156081.1	chrX	109199569	109199577	+	1	NA	3' UTR (NM_001037917, exon 2 of 2)	3' UTR (NM_001037917, exon 2 of 2)	2817	NM_001037917	622976	Mm.482747	NM_001037917	ENSMUSG00000048621	Gm6377	EG622976	predicted gene 6377	protein-coding
mm_61580.1	chr7	79842524	79842549	+	1	NA	promoter-TSS (NM_008486)	promoter-TSS (NM_008486)	-184	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_158459.1	chrX	140599476	140599490	-	1	NA	intron (NM_001077364, intron 1 of 3)	CpG	1039	NM_001077364	14605	Mm.22216	NM_010286	ENSMUSG00000031431	Tsc22d3	DIP|Dsip1|Gilz|TSC-22R|Tilz3	TSC22 domain family, member 3	protein-coding
mm_90414.1	chr10	127421209	127421235	+	1	NA	5' UTR (NM_001168293, exon 1 of 24)	5' UTR (NM_001168293, exon 1 of 24)	355	NM_001168293	71750	Mm.29342	NM_027900	ENSMUSG00000025404	R3hdm2	1300003K24Rik|AU041262|mKIAA1002	R3H domain containing 2	protein-coding
mm_148259.1	chr18	80860955	80860963	-	1	NA	intron (NM_001201569, intron 7 of 29)	intron (NM_001201569, intron 7 of 29)	73099	NM_001201569	50771	Mm.247138	NM_015805	ENSMUSG00000024566	Atp9b	AA934181|Atpc2b|IIb|MMR	ATPase, class II, type 9B	protein-coding
mm_155734.1	chrX	96166062	96166074	+	1	NA	exon (NM_010833, exon 12 of 13)	exon (NM_010833, exon 12 of 13)	70023	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_80206.1	chr9	72438580	72438598	+	1	NA	promoter-TSS (NM_008613)	promoter-TSS (NM_008613)	60	NM_008613	17427	Mm.387671	NM_008613	ENSMUSG00000032221	Mns1	AW546487	meiosis-specific nuclear structural protein 1	protein-coding
mm_35455.1	chr4	40702894	40702937	-	1	NA	promoter-TSS (NM_025545)	promoter-TSS (NM_025545)	1	NM_025545	66408	Mm.430710	NM_025545	ENSMUSG00000028411	Aptx	2410016G21Rik|AA388047|FHA-HIT	aprataxin	protein-coding
mm_6260.1	chr1	69108419	69108460	-	1	NA	promoter-TSS (NM_010154)	promoter-TSS (NM_010154)	-380	NM_010154	13869	Mm.442420	NM_010154	ENSMUSG00000062209	Erbb4	Her4|c-erbB-4	erb-b2 receptor tyrosine kinase 4	protein-coding
mm_26041.1	chr3	135548604	135548626	+	1	NA	intron (NM_027288, intron 10 of 16)	L2|LINE|L2	63004	NM_027288	110173	Mm.280536	NM_027288	ENSMUSG00000028164	Manba	2410030O07Rik|B930014J03Rik|Bmn	mannosidase, beta A, lysosomal	protein-coding
mm_81463.1	chr9	109861634	109861640	+	1	NA	Intergenic	Intergenic	-12181	NM_009921	12796	Mm.3834	NM_009921	ENSMUSG00000038357	Camp	CAP18|Cnlp|Cramp|FALL39|MCLP	cathelicidin antimicrobial peptide	protein-coding
mm_76520.1	chr8	87472122	87472133	-	1	NA	promoter-TSS (NR_125722)	promoter-TSS (NR_125722)	465	NM_019626	12404	Mm.4880	NM_019626	ENSMUSG00000031654	Cbln1	AI323299	cerebellin 1 precursor protein	protein-coding
mm_64567.1	chr7	144897018	144897037	+	1	NA	intron (NM_008003, intron 1 of 2)	CpG	495	NM_008003	14170	Mm.3904	NM_008003	ENSMUSG00000031073	Fgf15	FGF19	fibroblast growth factor 15	protein-coding
mm_98356.1	chr11	93885272	93885289	+	1	NA	promoter-TSS (NM_134012)	promoter-TSS (NM_134012)	486	NM_001013375	217109	Mm.379350	NM_001013375	ENSMUSG00000054079	Utp18	6230425C22Rik|6430513M13|Wdr50	UTP18 small subunit processome component	protein-coding
mm_107626.1	chr12	51691126	51691140	+	1	NA	5' UTR (NM_001329699, exon 1 of 6)	5' UTR (NM_001329699, exon 1 of 6)	167	NM_001329698	11782	Mm.386749	NM_021710	ENSMUSG00000020955	Ap4s1	AI314282	adaptor-related protein complex AP-4, sigma 1	protein-coding
mm_16596.1	chr2	4956353	4956361	-	1	NA	Intergenic	Intergenic	-19765	NM_001311208	68527	Mm.27791	NM_026754	ENSMUSG00000026668	Ucma	1110017I16Rik|AW121955|Grp	upper zone of growth plate and cartilage matrix associated	protein-coding
mm_26026.1	chr3	135439090	135439098	+	1	NA	promoter-TSS (NR_030689)	promoter-TSS (NR_030689)	335	NM_025356	66105	Mm.49884	NM_025356	ENSMUSG00000078578	Ube2d3	1100001F19Rik|9430029A22Rik|AA414951	ubiquitin-conjugating enzyme E2D 3	protein-coding
mm_102520.1	chr11	60878765	60878812	-	1	NA	5' UTR (NM_001168507, exon 1 of 3)	5' UTR (NM_001168507, exon 1 of 3)	250	NM_173453	216821	Mm.28063	NM_173453	ENSMUSG00000043284	Tmem11	5730466P16Rik|AA409091	transmembrane protein 11	protein-coding
mm_148449.1	chr19	3972508	3972566	+	1	NA	5' UTR (NM_001177438, exon 1 of 10)	5' UTR (NM_001177438, exon 1 of 10)	209	NM_001177438	621603	Mm.34137	NM_001177438	ENSMUSG00000075296	Aldh3b2	AI848594|C130048D07Rik	aldehyde dehydrogenase 3 family, member B2	protein-coding
mm_109561.1	chr12	111814269	111814279	+	1	NA	promoter-TSS (NM_028875)	promoter-TSS (NM_028875)	104	NM_026752	68520	Mm.390497	NM_026752	ENSMUSG00000021286	Zfyve21	1110013H04Rik|AW558780|C85416	zinc finger, FYVE domain containing 21	protein-coding
mm_123726.1	chr14	70159417	70159430	-	1	NA	promoter-TSS (NM_001112735)	promoter-TSS (NM_001112735)	79	NM_001112735	268759	Mm.12148	NM_001004155	ENSMUSG00000044551	9930012K11Rik	-	RIKEN cDNA 9930012K11 gene	protein-coding
mm_48402.1	chr5	140208729	140208747	-	1	NA	intron (NM_010752, intron 10 of 17)	intron (NM_010752, intron 10 of 17)	112814	NM_010752	17120	Mm.27250	NM_010752	ENSMUSG00000029554	Mad1l1	AI173502|AW550425|Mad1	MAD1 mitotic arrest deficient 1-like 1	protein-coding
mm_143064.1	chr17	57011646	57011649	-	1	NA	promoter-TSS (NM_133801)	promoter-TSS (NM_133801)	-359	NM_133801	98053	Mm.24632	NM_133801	ENSMUSG00000002658	Gtf2f1	2810405L04Rik|C76800|RAP74	general transcription factor IIF, polypeptide 1	protein-coding
mm_66470.1	chr7	44974743	44974779	-	1	NA	promoter-TSS (NM_153679)	promoter-TSS (NM_153679)	90	NM_153679	78070	Mm.231465	NM_153679	ENSMUSG00000007783	Cpt1c	6530437J22Rik|9630004I06Rik	carnitine palmitoyltransferase 1c	protein-coding
mm_51301.1	chr6	72309830	72309849	+	1	NA	exon (NM_001282071, exon 7 of 11)	exon (NM_001282071, exon 7 of 11)	5229	NM_147779	20388	Mm.46033	NM_147779	ENSMUSG00000056370	Sftpb	AI562151|SF-B|SP-B|Sftp-3|Sftp3	surfactant associated protein B	protein-coding
mm_117074.1	chr13	59491791	59491794	-	1	NA	intron (NM_023328, intron 17 of 25)	AT_rich|Low_complexity|Low_complexity	52659	NM_001284221	67269	Mm.153008	NM_023328	ENSMUSG00000021557	Agtpbp1	1700020N17Rik|2310001G17Rik|2900054O13Rik|4930445M19Rik|5730402G09Rik|CCP1|Nna1|nmf243|pcd	ATP/GTP binding protein 1	protein-coding
mm_5040.1	chr1	193632697	193632724	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-125180	NR_029592	387201		NR_029592	ENSMUSG00000065533	Mir205	Mirn205|mir-205|mmu-mir-205	microRNA 205	ncRNA
mm_160963.1	chr11	99591238	99591238	-	1	NA	exon (NM_001085526, exon 1 of 1)	exon (NM_001085526, exon 1 of 1)	139	NM_001085526	435273		NM_001085526	ENSMUSG00000078131	Krtap1-3	-	keratin associated protein 1-3	protein-coding
mm_113132.1	chr13	24614609	24614634	+	1	NA	promoter-TSS (NM_001286101)	promoter-TSS (NM_001286101)	15	NM_178658	193385	Mm.217319	NM_029679	ENSMUSG00000036006	Fam65b	-	family with sequence similarity 65, member B	protein-coding
mm_154446.1	chrM	1589	1619	-	1	NA	NA	Intergenic	NA	NA								
mm_142890.1	chr17	51833076	51833103	-	1	NA	promoter-TSS (NM_009122)	promoter-TSS (NM_009122)	201	NM_001163632	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_68128.1	chr7	102210075	102210094	-	1	NA	promoter-TSS (NM_001291358)	promoter-TSS (NM_001291358)	82	NM_001287166	269966	Mm.439800	NM_022979	ENSMUSG00000063550	Nup98	4732457F17|AI849286|Nup96	nucleoporin 98	protein-coding
mm_45066.1	chr5	43782050	43782060	-	1	NA	promoter-TSS (NM_178729)	promoter-TSS (NM_178729)	94	NM_001159963	242960	Mm.25794	NM_178729	ENSMUSG00000039753	Fbxl5	Fbl4|Fir4	F-box and leucine-rich repeat protein 5	protein-coding
mm_7559.1	chr1	124723005	124723020	-	1	NA	Intergenic	Intergenic	-677453	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_106109.1	chr11	116307169	116307190	-	1	NA	promoter-TSS (NM_001162872)	promoter-TSS (NM_001162872)	-429	NM_001347636	53413	Mm.22530	NM_016857	ENSMUSG00000020792	Exoc7	Exo70|sec70	exocyst complex component 7	protein-coding
mm_14561.1	chr2	134855285	134855304	+	1	NA	intron (NM_019677, intron 2 of 32)	intron (NM_019677, intron 2 of 32)	69130	NM_001145830	18795	Mm.330607	NM_019677	ENSMUSG00000051177	Plcb1	3110043I21Rik|AI132408|Plcb|mKIAA0581	phospholipase C, beta 1	protein-coding
mm_254.1	chr1	19606090	19606100	+	1	NA	Intergenic	Intergenic	394041	NM_001025305	21419	Mm.137021	NM_009334	ENSMUSG00000025927	Tfap2b	AI606113|AP-2(beta)|E130018K07Rik|Tcfap2b	transcription factor AP-2 beta	protein-coding
mm_86932.1	chr10	24189030	24189043	+	1	NA	TTS (NM_016797)	TTS (NM_016797)	-34481	NM_021509	59012	Mm.285934	NM_021509	ENSMUSG00000020000	Moxd1	3230402N08Rik|MNCb-5203	monooxygenase, DBH-like 1	protein-coding
mm_23931.1	chr3	83773848	83773860	+	1	NA	3' UTR (NM_009144, exon 3 of 3)	3' UTR (NM_009144, exon 3 of 3)	7533	NM_009144	20319	Mm.19155	NM_009144	ENSMUSG00000027996	Sfrp2	AI851596|Sdf5	secreted frizzled-related protein 2	protein-coding
mm_155363.1	chrX	71050161	71050171	+	1	NA	promoter-TSS (NM_001256048)	promoter-TSS (NM_001256048)	-90	NM_001256048	333639	Mm.371730	NM_001081354	ENSMUSG00000059401	Mamld1	G630014P10Rik	mastermind-like domain containing 1	protein-coding
mm_30037.1	chr3	135691421	135691479	-	1	NA	promoter-TSS (NM_008689)	promoter-TSS (NM_008689)	97	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_93162.1	chr10	93258427	93258429	-	1	NA	intron (NM_001282967, intron 2 of 3)	intron (NM_001282967, intron 2 of 3)	52731	NM_001322268	13713	Mm.4454	NM_013508	ENSMUSG00000008398	Elk3	D430049E23Rik|Erp|Etrp|Net|Sap-2	ELK3, member of ETS oncogene family	protein-coding
mm_94129.1	chr10	128676732	128676740	-	1	NA	TTS (NM_177411)	TTS (NM_177411)	-2818	NM_173733	211389	Mm.23352	NM_173733	ENSMUSG00000049858	Suox	SO	sulfite oxidase	protein-coding
mm_139651.1	chr17	57398582	57398623	+	1	NA	intron (NM_010130, intron 2 of 21)	L1VL2|LINE|L1	39916	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_43948.1	chr5	145135124	145135148	+	1	NA	exon (NM_001033313, exon 3 of 6)	exon (NM_001033313, exon 3 of 6)	4953	NM_001033313	231887	Mm.188851	NM_001033313	ENSMUSG00000029623	Pdap1	HASPP28|PAP|PAP1	PDGFA associated protein 1	protein-coding
mm_162873.1	chr10	95808917	95808917	-	1	NA	Intergenic	Intergenic	-131746	NM_001001932	216238	Mm.210035	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding
mm_165738.1	chr3	107211465	107211469	-	1	NA	exon (NM_001111143, exon 9 of 9)	exon (NM_001111143, exon 9 of 9)	10265	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_91481.1	chr10	34418466	34418567	-	1	NA	promoter-TSS (NM_176968)	promoter-TSS (NM_176968)	35	NM_176968	319638	Mm.73467	NM_176968	ENSMUSG00000039480	Nt5dc1	6030401B09Rik|AW987726|Nt5c2l1	5'-nucleotidase domain containing 1	protein-coding
mm_34206.1	chr4	140945381	140945432	+	1	NA	intron (NM_008812, intron 13 of 15)	intron (NM_008812, intron 13 of 15)	12496	NR_045911	100126227	Mm.404073	NR_045911	ENSMUSG00000087698	Gm13031	OTTMUSG00000010081	predicted gene 13031	ncRNA
mm_104614.1	chr11	97280333	97280407	-	1	NA	exon (NM_008942, exon 1 of 23)	exon (NM_008942, exon 1 of 23)	206	NM_008942	19155	Mm.29824	NM_008942	ENSMUSG00000001441	Npepps	AAP-S|MP100|Psa|R74825|goku	aminopeptidase puromycin sensitive	protein-coding
mm_100550.1	chr11	120721453	120721536	+	1	NA	promoter-TSS (NM_133223)	promoter-TSS (NM_133223)	26	NM_133223	170758	Mm.34008	NM_133223	ENSMUSG00000018012	Rac3	Rac1B	RAS-related C3 botulinum substrate 3	protein-coding
mm_80657.1	chr9	90054508	90054525	+	1	NA	5' UTR (NM_007801, exon 1 of 12)	5' UTR (NM_007801, exon 1 of 12)	249	NM_001312649	13036	Mm.2277	NM_007801	ENSMUSG00000032359	Ctsh	AL022844	cathepsin H	protein-coding
mm_55952.1	chr6	85370099	85370109	-	1	NA	intron (NM_001003955, intron 1 of 5)	intron (NM_001003955, intron 1 of 5)	4530	NM_177466	52055	Mm.220334	NM_177466	ENSMUSG00000051343	Rab11fip5	9130206P09Rik|C75969|D6Ertd32e|GAF1|RIP11	RAB11 family interacting protein 5 (class I)	protein-coding
mm_170478.1	chr19	12153117	12153127	-	1	NA	intron (NR_030566, intron 2 of 3)	intron (NR_030566, intron 2 of 3)	-32448	NM_146682	258677	Mm.261576	NM_146682	ENSMUSG00000067522	Olfr76	MOR215-3|V5	olfactory receptor 76	protein-coding
mm_78509.1	chr9	32754761	32754766	+	1	NA	3' UTR (NM_001038642, exon 7 of 7)	3' UTR (NM_001038642, exon 7 of 7)	58721	NM_001038642	23871	Mm.292415	NM_011808	ENSMUSG00000032035	Ets1	AI196000|AI448617|D230050P06|Ets-1|Tpl1|vs	E26 avian leukemia oncogene 1, 5' domain	protein-coding
mm_87937.1	chr10	62761678	62761683	+	1	NA	intron (NM_026201, intron 15 of 24)	intron (NM_026201, intron 15 of 24)	3926	NR_028557	100217463		NR_028557		Snord98	MBII-419	small nucleolar RNA, C/D box 98	snoRNA
mm_45215.1	chr5	52994428	52994444	-	1	NA	Intergenic	Intergenic	-2144	NR_040413	75954	Mm.258937	NR_040413	ENSMUSG00000106352	5033403H07Rik	-	RIKEN cDNA 5033403H07 gene	ncRNA
mm_33996.1	chr4	137905260	137905295	+	1	NA	intron (NM_199307, intron 2 of 19)	hAT-N1_Mam|DNA|hAT?	43040	NM_199307	230857	Mm.401062	NM_199307	ENSMUSG00000057530	Ece1	AW322500|ECE-1|ECE-1a|ECE-1b|ECE-1d	endothelin converting enzyme 1	protein-coding
mm_87729.1	chr10	60126125	60126154	+	1	NA	promoter-TSS (NR_105871)	promoter-TSS (NR_105871)	-637	NR_105871	102465546		NR_105871	ENSMUSG00000105468	Mir6906	mmu-mir-6906	microRNA 6906	ncRNA
mm_90219.1	chr10	121034041	121034049	+	1	NA	promoter-TSS (NM_011915)	promoter-TSS (NM_011915)	41	NM_011915	24117	Mm.32831	NM_011915	ENSMUSG00000020218	Wif1	AW107799|WIF-1	Wnt inhibitory factor 1	protein-coding
mm_47865.1	chr5	134631786	134631787	-	1	NA	intron (NM_001312867, intron 1 of 5)	intron (NM_001312867, intron 1 of 5)	7623	NM_001312867	22384	Mm.27955	NM_033561	ENSMUSG00000040731	Eif4h	AU018978|D5Ertd355e|E430026L18Rik|Ef4h|Wbscr1|Wscr1|eIF-4H	eukaryotic translation initiation factor 4H	protein-coding
mm_162646.1	chr1	194892233	194892240	+	1	NA	Intergenic	Intergenic	-46585	NM_133654	12490	Mm.29798	NM_133654	ENSMUSG00000016494	Cd34	AU040960	CD34 antigen	protein-coding
mm_142712.1	chr17	47914208	47914211	-	1	NA	intron (NM_001110824, intron 1 of 16)	intron (NM_001110824, intron 1 of 16)	10423	NM_028767	74123	Mm.240062	NM_028767	ENSMUSG00000023991	Foxp4	1200010K03Rik|2310007G05Rik|mFKHLA	forkhead box P4	protein-coding
mm_65714.1	chr7	28378270	28378294	-	1	NA	exon (NM_011756, exon 2 of 2)	exon (NM_011756, exon 2 of 2)	946	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_126142.1	chr15	78348947	78348959	+	1	NA	TTS (NR_106138)	TTS (NR_106138)	354	NR_106138	102466845		NR_106138	ENSMUSG00000099059	Mir7676-2	Gm27790|mmu-mir-7676-2	microRNA 7676-2	ncRNA
mm_56503.1	chr6	99338330	99338350	-	1	NA	intron (NM_001347345, intron 2 of 19)	intron (NM_001347345, intron 2 of 19)	-71825	NM_001197321	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_90211.1	chr10	120775981	120775982	+	1	NA	intron (NR_038000, intron 2 of 2)	ID_B1|SINE|B4	10249	NR_038003	70874	Mm.427286	NR_038000	ENSMUSG00000044544	4921513I03Rik	-	RIKEN cDNA 4921513I03 gene	ncRNA
mm_105990.1	chr11	115628094	115628122	-	1	NA	5' UTR (NM_001252384, exon 1 of 8)	5' UTR (NM_001252384, exon 1 of 8)	187	NM_001252394	67283	Mm.383426	NM_026071	ENSMUSG00000020744	Slc25a19	2900089E13Rik|DNC|MUP1|TPC	solute carrier family 25 (mitochondrial thiamine pyrophosphate carrier), member 19	protein-coding
mm_13409.1	chr2	104069820	104069838	+	1	NA	Intergenic	Intergenic	-1181	NM_181858	333883	Mm.359026	NM_181858	ENSMUSG00000068686	Cd59b	-	CD59b antigen	protein-coding
mm_164229.1	chr15	88891228	88891240	+	1	NA	Intergenic	Intergenic	29040	NM_145478	223775	Mm.400129	NM_145478	ENSMUSG00000035828	Pim3	BC026639|Kid1	proviral integration site 3	protein-coding
mm_21904.1	chr2	166398125	166398143	-	1	NA	Intergenic	Intergenic	-49317	NR_015558	319684	Mm.399746	NR_015558		5031425F14Rik	-	RIKEN cDNA 5031425F14 gene	ncRNA
mm_40785.1	chr5	67395707	67395711	+	1	NA	3' UTR (NM_001164806, exon 5 of 5)	3' UTR (NM_001164806, exon 5 of 5)	32090	NM_001164806	666938	Mm.101339	NM_001164806	ENSMUSG00000092060	Bend4	D330027G24Rik|EG666938	BEN domain containing 4	protein-coding
mm_79795.1	chr9	64084920	64084936	+	1	NA	intron (NR_040743, intron 1 of 2)	CpG	4167	NR_040743	76814	Mm.243771	NR_040743		Scarletltr	2600006L11Rik	Scarletltr, erythroid developmental long intergenic non-protein coding transcript	ncRNA
mm_123022.1	chr14	55116562	55116585	-	1	NA	5' UTR (NM_177049, exon 1 of 6)	5' UTR (NM_177049, exon 1 of 6)	362	NM_177049	319984	Mm.19047	NM_177049	ENSMUSG00000022208	Jph4	9330157P13Rik|JP-4|JPHL1	junctophilin 4	protein-coding
mm_152977.1	chr19	29486569	29486571	-	1	NA	Intergenic	Intergenic	35417	NR_015567	77779	Mm.458738	NR_015567	ENSMUSG00000097855	A930007I19Rik	-	RIKEN cDNA A930007I19 gene	ncRNA
mm_8111.1	chr1	135919165	135919175	-	1	NA	promoter-TSS (NM_019645)	promoter-TSS (NM_019645)	37	NM_001313701	18772	Mm.4494	NM_019645	ENSMUSG00000026413	Pkp1	-	plakophilin 1	protein-coding
mm_137601.1	chr17	28207821	28207893	+	1	NA	promoter-TSS (NM_027185)	promoter-TSS (NM_027185)	79	NM_027185	23853	Mm.204731	NM_027185	ENSMUSG00000002257	Def6	2410003F05Rik|6430538D02Rik|AV094905|Ibp|Slat|Slat2|Slat6	differentially expressed in FDCP 6	protein-coding
mm_141347.1	chr17	28560705	28560718	-	1	NA	promoter-TSS (NM_025469)	promoter-TSS (NM_025469)	55	NM_025469	109791	Mm.21160	NM_025469	ENSMUSG00000024225	Clps	2200003J09Rik	colipase, pancreatic	protein-coding
mm_29101.1	chr3	104818107	104818128	-	1	NA	exon (NM_001163440, exon 2 of 21)	exon (NM_001163440, exon 2 of 21)	188	NM_008619	17454	Mm.1597	NM_008619	ENSMUSG00000002227	Mov10	C77703|Mov-10	Moloney leukemia virus 10	protein-coding
mm_62235.1	chr7	98656146	98656159	+	1	NA	intron (NM_172280, intron 1 of 19)	CpG	417	NM_172280	233545	Mm.387819	NM_172280	ENSMUSG00000035401	Emsy	2210018M11Rik|2310016L09Rik|AU019521|AU019557	EMSY, BRCA2-interacting transcriptional repressor	protein-coding
mm_167754.1	chr9	110421733	110421743	-	1	NA	exon (NM_008694, exon 3 of 4)	exon (NM_008694, exon 3 of 4)	1930	NM_008694	18054	Mm.236225	NM_008694	ENSMUSG00000032484	Ngp	bectenecin	neutrophilic granule protein	protein-coding
mm_26173.1	chr3	138288735	138288777	+	1	NA	exon (NM_007409, exon 7 of 9)	exon (NM_007409, exon 7 of 9)	11111	NM_007409	11522	Mm.2409	NM_007409	ENSMUSG00000074207	Adh1	ADH-AA|AI194826|Adh-1|Adh-1-t|Adh-1e|Adh-1t|Adh-3e|Adh1-e|Adh1-t|Adh1tl|Adh3-e	alcohol dehydrogenase 1 (class I)	protein-coding
mm_158866.1	chrY	1137179	1137181	-	1	NA	intron (NM_009484, intron 20 of 26)	intron (NM_009484, intron 20 of 26)	-78312	NR_027507	22109	Mm.10106	NR_027507	ENSMUSG00000091749	Tspy-ps	-	testis specific protein-Y encoded, pseudogene	pseudo
mm_83390.1	chr9	44604779	44604815	-	1	NA	promoter-TSS (NM_001110826)	promoter-TSS (NM_001110826)	-95	NM_001110826	13209	Mm.267061	NM_007841	ENSMUSG00000032097	Ddx6	1110001P04Rik|E230023J21Rik|HLR2|mRCK/P54|p54|rck	DEAD (Asp-Glu-Ala-Asp) box polypeptide 6	protein-coding
mm_94135.1	chr10	128698102	128698106	-	1	NA	3' UTR (NM_016756, exon 7 of 7)	3' UTR (NM_016756, exon 7 of 7)	-1836	NM_177411	19344	Mm.12815	NM_011229	ENSMUSG00000000711	Rab5b	C030027M18Rik	RAB5B, member RAS oncogene family	protein-coding
mm_52495.1	chr6	114748856	114748868	+	1	NA	intron (NM_001253718, intron 18 of 19)	L1_Mur3|LINE|L1	105765	NM_001253717	74244	Mm.275332	NM_028835	ENSMUSG00000030314	Atg7	1810013K23Rik|Agp7|Apg7l|Atg7l|Gm21553	autophagy related 7	protein-coding
mm_59982.1	chr7	30465736	30465762	+	1	NA	promoter-TSS (NR_004443)	promoter-TSS (NR_004443)	-158	NR_004443	445267	Mm.398140	NR_004443	ENSMUSG00000087009	Nphs1os	Nphs1as	nephrosis 1 homolog, nephrin, opposite strand	ncRNA
mm_116859.1	chr13	54765705	54765720	-	1	NA	intron (NM_033610, intron 1 of 5)	intron (NM_033610, intron 1 of 5)	728	NM_033610	104069	Mm.200843	NM_033610	ENSMUSG00000034891	Sncb	AI838531|betaSYN	synuclein, beta	protein-coding
mm_144050.1	chr17	90455944	90456026	-	1	NA	promoter-TSS (NM_001346961)	promoter-TSS (NM_001346961)	-105	NM_001346959	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_51248.1	chr6	71729859	71729862	+	1	NA	intron (NM_178608, intron 1 of 6)	RMER30|DNA|hAT-Charlie	22179	NM_178608	52250	Mm.146332	NM_178608	ENSMUSG00000052852	Reep1	D6Ertd253e	receptor accessory protein 1	protein-coding
mm_7620.1	chr1	126830787	126830798	-	1	NA	promoter-TSS (NM_176957)	promoter-TSS (NM_176957)	-160	NM_176957	210356	Mm.377234	NM_172484	ENSMUSG00000049690	Nckap5	8430408F21|D130011D22Rik|E030049G20Rik|Erih1|Erih2|Gm1548|Nap5	NCK-associated protein 5	protein-coding
mm_33559.1	chr4	131873609	131873679	+	1	NA	promoter-TSS (NM_020587)	promoter-TSS (NM_020587)	5	NM_020587	57317	Mm.2478	NM_020587	ENSMUSG00000028911	Srsf4	5730499P16Rik|AW550192|MNCb-2616|SRp75|Sfrs4	serine/arginine-rich splicing factor 4	protein-coding
mm_129014.1	chr15	74923564	74923574	-	1	NA	Intergenic	Intergenic	-31482	NM_001164039	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_663.1	chr1	40441317	40441332	+	1	NA	exon (NM_010743, exon 3 of 8)	exon (NM_010743, exon 3 of 8)	1695	NM_010743	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_141748.1	chr17	34214472	34214486	-	1	NA	exon (NM_011530, exon 9 of 12)	exon (NM_011530, exon 9 of 12)	10000	NM_011530	21355	Mm.14814	NM_011530	ENSMUSG00000024339	Tap2	ABC18|AI462429|APT2|Abcb3|Ham-2|Ham2|MTP2|PSF2|RING11|Tap-2|Y1|jas	transporter 2, ATP-binding cassette, sub-family B (MDR/TAP)	protein-coding
mm_20116.1	chr2	121160303	121160324	-	1	NA	3' UTR (NM_001290819, exon 5 of 5)	3' UTR (NM_001290819, exon 5 of 5)	10812	NM_001290819	99334	Mm.188422	NM_178889	ENSMUSG00000050619	Zscan29	AW125441|Zfp690	zinc finger SCAN domains 29	protein-coding
mm_77017.1	chr8	108537845	108537861	-	1	NA	Intergenic	Intergenic	46824	NR_077224	109215	Mm.65282	NR_077224	ENSMUSG00000110613	Lncbate1	3010033K07Rik|Lnc-BATE1	brown adipose tissue enriched long non-coding RNA 1	ncRNA
mm_6831.1	chr1	84208793	84208796	-	1	NA	intron (NM_001003948, intron 1 of 2)	intron (NM_001003948, intron 1 of 2)	10167	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_113578.1	chr13	40859809	40859822	+	1	NA	promoter-TSS (NM_023887)	promoter-TSS (NM_023887)	47	NM_023887	14538	Mm.314757	NM_008105	ENSMUSG00000021360	Gcnt2	5330430K10Rik|IGnT|IGnTA|IGnTB|IGnTC	glucosaminyl (N-acetyl) transferase 2, I-branching enzyme	protein-coding
mm_149641.1	chr19	17400184	17400199	+	1	NA	3' UTR (NM_019437, exon 4 of 4)	3' UTR (NM_019437, exon 4 of 4)	6148	NM_019437	54391	Mm.7013	NM_019437	ENSMUSG00000024712	Rfk	0610038L10Rik|AF031381|KOI-4	riboflavin kinase	protein-coding
mm_165505.1	chr2	167776756	167776765	+	1	NA	Intergenic	MIR|SINE|MIR	85583	NR_015500	329562	Mm.123101	NM_177851	ENSMUSG00000006462	A530013C23Rik	-	RIKEN cDNA A530013C23 gene	ncRNA
mm_9587.1	chr1	174031798	174031827	-	1	NA	promoter-TSS (NM_172648)	promoter-TSS (NM_172648)	-57	NM_172648	226695	Mm.425061	NM_172648	ENSMUSG00000054203	Ifi205	D3|D3cDNA|Ifi205a	interferon activated gene 205	protein-coding
mm_60018.1	chr7	30766574	30766576	+	1	NA	intron (NM_172899, intron 6 of 18)	intron (NM_172899, intron 6 of 18)	2819	NM_001166174	73712	Mm.30138	NM_028618	ENSMUSG00000060962	Dmkn	1110014F24Rik|AW561900|C130074A08|SK30|SK89|cI-36	dermokine	protein-coding
mm_40818.1	chr5	72261422	72261428	+	1	NA	intron (NM_153389, intron 11 of 22)	Lx5b|LINE|L1	58082	NM_153389	231287	Mm.32775	NM_153389	ENSMUSG00000046808	Atp10d	9830145H18Rik|ATPVD|D5Buc24e	ATPase, class V, type 10D	protein-coding
mm_10905.1	chr2	25332796	25332813	+	1	NA	promoter-TSS (NR_027448)	promoter-TSS (NR_027448)	61	NM_001029983	227619	Mm.270798	NM_001029983	ENSMUSG00000036646	Man1b1	E430019H13Rik|ERMan1|Gm108|MANA-ER	mannosidase, alpha, class 1B, member 1	protein-coding
mm_51030.1	chr6	65525309	65525320	+	1	NA	Intergenic	Intergenic	-65084	NM_001001495	414084	Mm.117558	NM_001001495	ENSMUSG00000044162	Tnip3	9030611K07Rik|ABIN-3|LIND	TNFAIP3 interacting protein 3	protein-coding
mm_141551.1	chr17	32166880	32166898	-	1	NA	promoter-TSS (NM_008716)	promoter-TSS (NM_008716)	-37	NM_008716	18131	Mm.439741	NM_008716	ENSMUSG00000038146	Notch3	AW229011|N3|hpbk	notch 3	protein-coding
mm_43034.1	chr5	123973718	123973733	+	1	NA	promoter-TSS (NM_145070)	promoter-TSS (NM_145070)	97	NM_145070	29816	Mm.149954	NM_145070	ENSMUSG00000000915	Hip1r	AA410023|mKIAA0655	huntingtin interacting protein 1 related	protein-coding
mm_132602.1	chr16	38558691	38558737	+	1	NA	promoter-TSS (NM_001205286)	promoter-TSS (NM_001205286)	16	NM_001205286	67846	Mm.310476	NM_026407	ENSMUSG00000002845	Tmem39a	2610033C09Rik	transmembrane protein 39a	protein-coding
mm_151239.1	chr19	53821675	53821709	+	1	NA	intron (NM_001170847, intron 5 of 13)	intron (NM_001170847, intron 5 of 13)	-70539	NM_011050	18569	Mm.1605	NM_011050	ENSMUSG00000024975	Pdcd4	D19Ucla1|Ma3|Tis	programmed cell death 4	protein-coding
mm_152949.1	chr19	29021306	29021324	-	1	NA	3' UTR (NM_021299, exon 5 of 5)	3' UTR (NM_021299, exon 5 of 5)	-26168	NR_028360	67329	Mm.394933	NR_028360		1700018L02Rik	-	RIKEN cDNA 1700018L02 gene	ncRNA
mm_164782.1	chr18	5721378	5721384	+	1	NA	intron (NM_011546, intron 2 of 7)	intron (NM_011546, intron 2 of 7)	-128944	NR_033552	791318	Mm.84339	NR_033552	ENSMUSG00000063087	Gm10125	ENSMUSG00000063087|Zeb1os	predicted gene 10125	ncRNA
mm_170550.1	chr19	4078496	4078513	-	1	NA	Intergenic	U3|snRNA|snRNA	-3984	NM_001160253	29866	Mm.46268	NM_013878	ENSMUSG00000024857	Cabp2	-	calcium binding protein 2	protein-coding
mm_170709.1	chr2	14295697	14295699	+	1	NA	intron (NM_008625, intron 15 of 29)	intron (NM_008625, intron 15 of 29)	34695	NR_030609	100124488		NR_030609	ENSMUSG00000077897	Mir511	Mirn511|mir-511|mmu-mir-511	microRNA 511	ncRNA
mm_52805.1	chr6	121342518	121342526	+	1	NA	promoter-TSS (NM_001347433)	promoter-TSS (NM_001347433)	-554	NM_001347433	14411	Mm.274506	NM_133661	ENSMUSG00000030109	Slc6a12	BGT1|GAT-2|GAT2|Gabt2	solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12	protein-coding
mm_108389.1	chr12	80946290	80946308	+	1	NA	promoter-TSS (NR_045057)	promoter-TSS (NR_045057)	800	NM_001347415	20384	Mm.43331	NM_009159	ENSMUSG00000021134	Srsf5	Sfrs5	serine/arginine-rich splicing factor 5	protein-coding
mm_109613.1	chr12	112760433	112760447	+	1	NA	promoter-TSS (NM_178911)	promoter-TSS (NM_178911)	-215	NM_178911	104759	Mm.203915	NM_178911	ENSMUSG00000052160	Pld4	AI132321|thss	phospholipase D family, member 4	protein-coding
mm_111852.1	chr12	107939131	107939141	-	1	NA	intron (NM_001286343, intron 1 of 1)	intron (NM_001286343, intron 1 of 1)	64278	NM_001079883	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_101687.1	chr11	40694951	40694983	-	1	NA	5' UTR (NM_001199274, exon 1 of 7)	5' UTR (NM_001199274, exon 1 of 7)	236	NM_001199274	108645	Mm.293771	NM_134017	ENSMUSG00000042032	Mat2b	1110064C04Rik|2410018D16Rik|AI182287|AU022853|MAT-II|MATIIbeta|TGR	methionine adenosyltransferase II, beta	protein-coding
mm_31557.1	chr4	57434358	57434368	+	1	NA	Intergenic	CpG	-70071	NR_038178	73349	Mm.393774	NR_038178		1700042G15Rik	-	RIKEN cDNA 1700042G15 gene	ncRNA
mm_39311.1	chr5	8046163	8046184	+	1	NA	promoter-TSS (NM_025618)	promoter-TSS (NM_025618)	95	NM_025618	109552	Mm.96211	NM_025618	ENSMUSG00000003161	Sri	2210417O06Rik|2900070H08Rik|Sor	sorcin	protein-coding
mm_140605.1	chr17	10319749	10319799	-	1	NA	promoter-TSS (NM_001159517)	promoter-TSS (NM_001159517)	-145	NR_037588	100526796	Mm.384135	NR_037588		Cahm	B930003M22Rik	colon adenocarcinoma hypermethylated RNA	ncRNA
mm_100643.1	chr11	121830255	121830279	+	1	NA	promoter-TSS (NM_029049)	promoter-TSS (NM_029049)	49	NM_029049	74675	Mm.61213	NM_029049	ENSMUSG00000039198	Ptchd3	4930451E13Rik|4933440L20Rik|RNDEu-3	patched domain containing 3	protein-coding
mm_147979.1	chr18	67502598	67502601	-	1	NA	intron (NM_194355, intron 9 of 14)	intron (NM_194355, intron 9 of 14)	37750	NM_144867	225655	Mm.221420	NM_144867	ENSMUSG00000024530	Slmo1	A230074A19Rik|BC019561|Prelid3a	slowmo homolog 1 (Drosophila)	protein-coding
mm_106549.1	chr11	120581538	120581548	-	1	NA	promoter-TSS (NM_133796)	promoter-TSS (NM_133796)	77	NM_133796	192662	Mm.30016	NM_133796	ENSMUSG00000025132	Arhgdia	5330430M07Rik|Gdi-1|Rho-GDI|RhoDGI|RhoGDI-1	Rho GDP dissociation inhibitor (GDI) alpha	protein-coding
mm_82219.1	chr9	3018989	3019010	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	19744	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_43122.1	chr5	124862675	124862771	+	1	NA	promoter-TSS (NM_001081750)	promoter-TSS (NM_001081750)	18	NM_001081750	269704	Mm.138617	NM_001081750	ENSMUSG00000079215	Zfp664	AW060232|D930038J03Rik|ZFOC1|Znf664	zinc finger protein 664	protein-coding
mm_8021.1	chr1	135105160	135105170	-	1	NA	5' UTR (NM_001033409, exon 1 of 18)	5' UTR (NM_001033409, exon 1 of 18)	111	NM_001033409	329252	Mm.279594	NM_001033409	ENSMUSG00000042793	Lgr6	A530037C04Rik|D830026M09	leucine-rich repeat-containing G protein-coupled receptor 6	protein-coding
mm_47480.1	chr5	123749375	123749391	-	1	NA	promoter-TSS (NM_001042421)	promoter-TSS (NM_001042421)	31	NM_001005525	208606	Mm.276341	NM_025438	ENSMUSG00000029422	Rsrc2	1500011J06Rik	arginine/serine-rich coiled-coil 2	protein-coding
mm_54595.1	chr6	38254215	38254267	-	1	NA	promoter-TSS (NM_194061)	promoter-TSS (NM_194061)	-232	NM_194061	330286	Mm.277163	NM_194061	ENSMUSG00000063455	D630045J12Rik	Kiaa1549|mKIAA1549	RIKEN cDNA D630045J12 gene	protein-coding
mm_137406.1	chr17	26069636	26069639	+	1	NA	promoter-TSS (NM_001162868)	promoter-TSS (NM_001162868)	-460	NM_001162869	215445	Mm.41191	NM_153140	ENSMUSG00000037098	Rab11fip3	Cart1|D030060O14Rik|Rab11-FIP3|mKIAA0665	RAB11 family interacting protein 3 (class II)	protein-coding
mm_104006.1	chr11	85038349	85038351	-	1	NA	intron (NM_001029934, intron 15 of 33)	intron (NM_001029934, intron 15 of 33)	80596	NM_007607	12351	Mm.1641	NM_007607	ENSMUSG00000000805	Car4	AW456718|Ca4	carbonic anhydrase 4	protein-coding
mm_42544.1	chr5	116006778	116006781	+	1	NA	TTS (NM_007708)	TTS (NM_007708)	17649	NM_031869	19079	Mm.458152	NM_031869	ENSMUSG00000029513	Prkab1	1300015D22Rik|AU021155|E430008F22	protein kinase, AMP-activated, beta 1 non-catalytic subunit	protein-coding
mm_170041.1	chr17	24414692	24414693	+	1	NA	promoter-TSS (NM_001080128)	promoter-TSS (NM_001080128)	17	NM_001080128	19826	Mm.1951	NM_009070	ENSMUSG00000034681	Rnps1	-	ribonucleic acid binding protein S1	protein-coding
mm_153431.1	chr19	40953334	40953354	-	1	NA	intron (NM_008528, intron 6 of 16)	intron (NM_008528, intron 6 of 16)	41191	NM_008528	17060	Mm.9749	NM_008528	ENSMUSG00000061132	Blnk	BASH|Bca|Ly-57|Ly57|Lyw-57|SLP-65	B cell linker	protein-coding
mm_124802.1	chr15	8446189	8446194	+	1	NA	Intergenic	Intergenic	-1728	NM_201232	71175	Mm.240329	NM_027707	ENSMUSG00000022141	Nipbl	Idn3	Nipped-B homolog (Drosophila)	protein-coding
mm_46155.1	chr5	96093352	96093355	-	1	NA	intron (NM_144910, intron 7 of 11)	intron (NM_144910, intron 7 of 11)	68194	NM_001285511	231464	Mm.28374	NM_144910	ENSMUSG00000034724	Cnot6l	4932442K20Rik	CCR4-NOT transcription complex, subunit 6-like	protein-coding
mm_6117.1	chr1	64121372	64121382	-	1	NA	promoter-TSS (NM_033563)	promoter-TSS (NM_033563)	12	NM_033563	93691	Mm.29466	NM_033563	ENSMUSG00000025959	Klf7	9830124P08Rik	Kruppel-like factor 7 (ubiquitous)	protein-coding
mm_69757.1	chr7	140999450	140999460	-	1	NA	Intergenic	Intergenic	11289	NM_025378	66141	Mm.141021	NM_025378	ENSMUSG00000025492	Ifitm3	1110004C05Rik|Cd225|Cdw217|DSPA2b|Fgls|IP15|mil-1	interferon induced transmembrane protein 3	protein-coding
mm_106162.1	chr11	116653937	116653995	-	1	NA	5' UTR (NM_030206, exon 1 of 4)	5' UTR (NM_030206, exon 1 of 4)	347	NM_030206	114886	Mm.34598	NM_030206	ENSMUSG00000020810	Cygb	3110001K20Rik|HGb|Staap	cytoglobin	protein-coding
mm_166365.1	chr5	124450851	124450859	+	1	NA	exon (NM_001310723, exon 3 of 7)	exon (NM_001310723, exon 3 of 7)	4151	NM_001310727	67956	Mm.137966	NM_030241	ENSMUSG00000049327	Kmt5a	2410195B05Rik|AA617402|AW536475|PR-SET7|PR/SET07|Setd8	lysine methyltransferase 5A	protein-coding
mm_80349.1	chr9	75177673	75177692	+	1	NA	intron (NM_010864, intron 23 of 40)	MTD|LTR|ERVL-MaLR	-54332	NM_001081322	208943	Mm.41339	NM_001081322	ENSMUSG00000033590	Myo5c	9130003O20Rik|BB085560|C330029I24	myosin VC	protein-coding
mm_34965.1	chr4	156008659	156008666	+	1	NA	intron (NM_001302468, intron 4 of 6)	intron (NM_001302468, intron 4 of 6)	-5033	NM_011659	22163	Mm.13885	NM_011659	ENSMUSG00000029075	Tnfrsf4	ACT35|CD134|Ly-70|Ox40|TXGP1L|Txgp1	tumor necrosis factor receptor superfamily, member 4	protein-coding
mm_142594.1	chr17	46752171	46752231	-	1	NA	promoter-TSS (NM_001305990)	promoter-TSS (NM_001305990)	13	NM_001305989	72029	Mm.240325	NM_028065	ENSMUSG00000023973	Cnpy3	1600025D17Rik|2410050O22Rik|AI413153|CAG4A|ERDA5|PRAT4A|Tnrc5	canopy FGF signaling regulator 3	protein-coding
mm_29563.1	chr3	116808219	116808268	-	1	NA	promoter-TSS (NM_001081326)	promoter-TSS (NM_001081326)	-77	NM_001081326	77559	Mm.237099	NM_001081326	ENSMUSG00000033400	Agl	1110061O17Rik|9430004C13Rik|9630046L06Rik|AI850929|C77197	amylo-1,6-glucosidase, 4-alpha-glucanotransferase	protein-coding
mm_151175.1	chr19	53310571	53310579	+	1	NA	promoter-TSS (NM_001008542)	promoter-TSS (NM_001008542)	69	NM_001008542	17859	Mm.2154	NM_010847	ENSMUSG00000025025	Mxi1	ENSMUSG00000067085|Gm10197|Mad2|bHLHc11	MAX interactor 1, dimerization protein	protein-coding
mm_155233.1	chrX	57200558	57200571	+	1	NA	promoter-TSS (NR_038463)	promoter-TSS (NR_038463)	-73	NR_038463	100502842	Mm.164733	NR_038463	ENSMUSG00000085808	Gm14718	OTTMUSG00000017790	predicted gene 14718	ncRNA
mm_14308.1	chr2	129129798	129129831	+	1	NA	5' UTR (NM_025395, exon 1 of 4)	5' UTR (NM_025395, exon 1 of 4)	114	NM_025395	66170	Mm.40621	NM_025395	ENSMUSG00000037938	Chchd5	1110027L01Rik|AW045710	coiled-coil-helix-coiled-coil-helix domain containing 5	protein-coding
mm_40538.1	chr5	57965190	57965196	+	1	NA	intron (NM_001310608, intron 3 of 3)	intron (NM_001310608, intron 3 of 3)	247112	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_45307.1	chr5	65424329	65424339	-	1	NA	intron (NM_009466, intron 2 of 11)	B1F1|SINE|Alu	11508	NM_009466	22235	Mm.344831	NM_009466	ENSMUSG00000029201	Ugdh	Udpgdh	UDP-glucose dehydrogenase	protein-coding
mm_19328.1	chr2	90574610	90574624	-	1	NA	intron (NM_008982, intron 1 of 23)	(CCCA)n|Simple_repeat|Simple_repeat	6030	NM_008982	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_28540.1	chr3	92807892	92807904	-	1	NA	promoter-TSS (NM_001254760)	promoter-TSS (NM_001254760)	-7	NM_001254760	631101	Mm.250525	NM_001254760	ENSMUSG00000095870	Lce1k	Gm7055|Sprrl6	late cornified envelope 1K	protein-coding
mm_111142.1	chr12	81781122	81781176	-	1	NA	promoter-TSS (NM_177395)	promoter-TSS (NM_177395)	21	NM_177395	338372	Mm.35284	NM_177395	ENSMUSG00000042724	Map3k9	E130314H24Rik|Mlk1|Prke1	mitogen-activated protein kinase kinase kinase 9	protein-coding
mm_119536.1	chr14	47719788	47719804	+	1	NA	intron (NM_001347524, intron 31 of 38)	intron (NM_001347524, intron 31 of 38)	56040	NM_001347522	16709	Mm.3110	NM_008477	ENSMUSG00000021843	Ktn1	-	kinectin 1	protein-coding
mm_45767.1	chr5	86917282	86917293	-	1	NA	3' UTR (NM_152811, exon 6 of 6)	3' UTR (NM_152811, exon 6 of 6)	9216	NM_152811	71773	Mm.26741	NM_152811	ENSMUSG00000035836	Ugt2b1	1300012D20Rik	UDP glucuronosyltransferase 2 family, polypeptide B1	protein-coding
mm_72901.1	chr8	90876601	90876635	+	1	NA	intron (NM_177224, intron 2 of 39)	intron (NM_177224, intron 2 of 39)	47783	NM_177224	109151	Mm.100615	NM_177224	ENSMUSG00000056608	Chd9	1810014J18Rik|9030205D12Rik|A330063D19Rik|AD013|PRIC320|mKIAA0308	chromodomain helicase DNA binding protein 9	protein-coding
mm_150665.1	chr19	42022200	42022217	+	1	NA	intron (NM_145500, intron 1 of 2)	intron (NM_145500, intron 1 of 2)	-13830	NM_020033	56642	Mm.143737	NM_020033	ENSMUSG00000025172	Ankrd2	Arpp|mArpp	ankyrin repeat domain 2 (stretch responsive muscle)	protein-coding
mm_18881.1	chr2	76647972	76647991	-	1	NA	promoter-TSS (NM_011871)	promoter-TSS (NM_011871)	13	NM_011871	23992	Mm.277250	NM_011871	ENSMUSG00000002731	Prkra	AV120107|PRK|Pact|RAX|lear	protein kinase, interferon inducible double stranded RNA dependent activator	protein-coding
mm_157847.1	chrX	74393181	74393200	-	1	NA	promoter-TSS (NM_001161424)	promoter-TSS (NM_001161424)	84	NM_025473	66294	Mm.166485	NM_025473	ENSMUSG00000031399	Fam3a	1810037C20Rik	family with sequence similarity 3, member A	protein-coding
mm_39627.1	chr5	24428212	24428243	+	1	NA	intron (NM_009207, intron 2 of 22)	intron (NM_009207, intron 2 of 22)	706	NM_001253892	20535	Mm.4580	NM_009207	ENSMUSG00000028962	Slc4a2	Ae2|B3RP	solute carrier family 4 (anion exchanger), member 2	protein-coding
mm_38152.1	chr4	134918367	134918415	-	1	NA	Intergenic	Intergenic	-3475	NM_027935	71817	Mm.88349	NM_027935	ENSMUSG00000028822	Tmem50a	3200001F09Rik|CAM|Smp1	transmembrane protein 50A	protein-coding
mm_49525.1	chr6	29985347	29985353	+	1	NA	promoter-TSS (NR_040264)	promoter-TSS (NR_040264)	21	NR_040263	76419	Mm.84522	NR_040263	ENSMUSG00000045709	Smkr-ps	1700023L04Rik	smal lysine rich protein 1, pseudogene	ncRNA
mm_83220.1	chr9	42124361	42124371	-	1	NA	promoter-TSS (NM_011436)	promoter-TSS (NM_011436)	-77	NM_011436	20660	Mm.121920	NM_011436	ENSMUSG00000049313	Sorl1	2900010L19Rik|AI596264|AW261561|LR11|SorLA|gp250|mSorLA	sortilin-related receptor, LDLR class A repeats-containing	protein-coding
mm_168996.1	chr13	100272156	100272158	+	1	NA	Intergenic	LTRIS2|LTR|ERV1	-24821	NM_010870	17951	Mm.290476	NM_010870	ENSMUSG00000071203	Naip5	Birc1e|Lgn1|Naip-rs3	NLR family, apoptosis inhibitory protein 5	protein-coding
mm_171543.1	chr4	147021795	147021796	+	1	NA	promoter-TSS (NM_001177767)	promoter-TSS (NM_001177767)	-55	NM_001177767	100043034	Mm.422606	NM_001177767	ENSMUSG00000067919	Rex2	Gm13138|OTTMUSG00000010655	reduced expression 2	protein-coding
mm_29731.1	chr3	126746469	126746497	-	1	NA	intron (NM_001346636, intron 4 of 20)	intron (NM_001346636, intron 4 of 20)	149532	NM_023813	108058	Mm.255822	NM_023813	ENSMUSG00000053819	Camk2d	2810011D23Rik|8030469K03Rik|CaMK II|[d]-CaMKII	calcium/calmodulin-dependent protein kinase II, delta	protein-coding
mm_127240.1	chr15	99590651	99590667	+	1	NA	promoter-TSS (NM_009701)	promoter-TSS (NM_009701)	-369	NM_009701	11830	Mm.45580	NM_009701	ENSMUSG00000044217	Aqp5	-	aquaporin 5	protein-coding
mm_104454.1	chr11	95041309	95041330	-	1	NA	promoter-TSS (NM_133667)	promoter-TSS (NM_133667)	52	NM_133667	18604	Mm.29768	NM_133667	ENSMUSG00000038967	Pdk2	-	pyruvate dehydrogenase kinase, isoenzyme 2	protein-coding
mm_119688.1	chr14	53538247	53538258	+	1	NA	Intergenic	Intergenic	715677	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_55351.1	chr6	56800231	56800236	-	1	NA	Intergenic	RLTR13D6|LTR|ERVK	-2420	NM_145958	210973	Mm.57295	NM_145958	ENSMUSG00000059486	Kbtbd2	BC022962|Bklhd1|mKIAA1489	kelch repeat and BTB (POZ) domain containing 2	protein-coding
mm_93011.1	chr10	87491460	87491486	-	1	NA	3' UTR (NM_008553, exon 2 of 2)	3' UTR (NM_008553, exon 2 of 2)	2187	NM_008553	17172	Mm.136217	NM_008553	ENSMUSG00000020052	Ascl1	AI225900|ASH1|Mash1|bHLHa46	achaete-scute family bHLH transcription factor 1	protein-coding
mm_28035.1	chr3	83774670	83774673	-	1	NA	TTS (NM_009144)	TTS (NM_009144)	8350	NM_009144	20319	Mm.19155	NM_009144	ENSMUSG00000027996	Sfrp2	AI851596|Sdf5	secreted frizzled-related protein 2	protein-coding
mm_79793.1	chr9	64022235	64022271	+	1	NA	promoter-TSS (NM_008542)	promoter-TSS (NM_008542)	-194	NM_008542	17130	Mm.325757	NM_008542	ENSMUSG00000036867	Smad6	Madh6|b2b390Clo	SMAD family member 6	protein-coding
mm_120436.1	chr14	65806067	65806084	+	1	NA	5' UTR (NM_023209, exon 1 of 8)	5' UTR (NM_023209, exon 1 of 8)	164	NM_023209	52033	Mm.24337	NM_023209	ENSMUSG00000022033	Pbk	2810434B10Rik|AW538537|D14Ertd732e|TOPK	PDZ binding kinase	protein-coding
mm_135107.1	chr16	35769309	35769327	-	1	NA	promoter-TSS (NM_153550)	promoter-TSS (NM_153550)	38	NM_153550	224132	Mm.24094	NM_153550	ENSMUSG00000022848	Dirc2	RCC4	disrupted in renal carcinoma 2 (human)	protein-coding
mm_71218.1	chr8	40899025	40899055	+	1	NA	exon (NM_001044740, exon 2 of 12)	exon (NM_001044740, exon 2 of 12)	-27193	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_92049.1	chr10	62497858	62497873	-	1	NA	exon (NM_011157, exon 2 of 3)	exon (NM_011157, exon 2 of 3)	9890	NM_011157	19073	Mm.338790	NM_011157	ENSMUSG00000020077	Srgn	Prg|Prg1|Sgc	serglycin	protein-coding
mm_136977.1	chr17	15772290	15772293	+	1	NA	3' UTR (NM_007690, exon 36 of 36)	3' UTR (NM_007690, exon 36 of 36)	54295	NM_178615	68799	Mm.293466	NM_178615	ENSMUSG00000048027	Rgmb	1110059F19Rik|DRAGON	repulsive guidance molecule family member B	protein-coding
mm_70426.1	chr8	11497548	11497616	+	1	NA	promoter-TSS (NM_026995)	promoter-TSS (NM_026995)	14	NM_026995	69225	Mm.64911	NM_026995	ENSMUSG00000031505	Naxd	0710008K08Rik|2810407E01Rik|Carkd	NAD(P)HX dehydratase	protein-coding
mm_80722.1	chr9	92309363	92309386	+	1	NA	promoter-TSS (NM_001033184)	promoter-TSS (NM_001033184)	-3	NM_001033184	78459	Mm.179195	NM_001033184	ENSMUSG00000074139	1700057G04Rik	-	RIKEN cDNA 1700057G04 gene	protein-coding
mm_94679.1	chr11	17953969	17953980	+	1	NA	promoter-TSS (NM_026576)	promoter-TSS (NM_026576)	4	NR_131915	102633673	Mm.396603	NR_131915	ENSMUSG00000086468	Etaa1os	2900053O20Rik|4930542E09Rik	Ewing tumor-associated antigen 1, opposite strand	ncRNA
mm_11811.1	chr2	43954270	43954275	+	1	NA	intron (NM_001301832, intron 7 of 14)	intron (NM_001301832, intron 7 of 14)	111052	NR_040622	320872	Mm.445023	NR_040622	ENSMUSG00000085089	Arhgap15os	A430092G05Rik	Rho GTPase activating protein 15, opposite strand	ncRNA
mm_113010.1	chr13	21910940	21910949	+	1	NA	Intergenic	B1_Mur1|SINE|Alu	-13895	NR_035500	100316716		NR_035500	ENSMUSG00000088148	Mir1983	mmu-mir-1983	microRNA 1983	ncRNA
mm_962.1	chr1	58029956	58029974	+	1	NA	promoter-TSS (NM_009676)	promoter-TSS (NM_009676)	-4	NM_009676	11761	Mm.26787	NM_009676	ENSMUSG00000063558	Aox1	AI196512|AI255253|Ao|Aox-1|Aox-2|Aox2|Moro|Ro	aldehyde oxidase 1	protein-coding
mm_115965.1	chr13	23914999	23915011	-	1	NA	promoter-TSS (NM_177016)	promoter-TSS (NM_177016)	2	NM_177016	319848	Mm.97959	NM_177016	ENSMUSG00000021336	Slc17a4	9130214H05Rik	solute carrier family 17 (sodium phosphate), member 4	protein-coding
mm_94493.1	chr11	7063330	7063338	+	1	NA	promoter-TSS (NM_009622)	promoter-TSS (NM_009622)	-155	NM_009622	432530	Mm.259733	NM_009622	ENSMUSG00000020431	Adcy1	AC1|D11Bwg1392e|I-AC|brl|mKIAA4070	adenylate cyclase 1	protein-coding
mm_27967.1	chr3	80688475	80688488	-	1	NA	3' UTR (NM_013540, exon 16 of 16)	3' UTR (NM_013540, exon 16 of 16)	114310	NM_013540	14800	Mm.220224	NM_013540	ENSMUSG00000033981	Gria2	GluA2|GluR-B|Glur-2|Glur2	glutamate receptor, ionotropic, AMPA2 (alpha 2)	protein-coding
mm_169070.1	chr13	28520076	28520079	+	1	NA	intron (NR_045053, intron 7 of 8)	intron (NR_045053, intron 7 of 8)	190796	NR_105787	102466635		NR_105787	ENSMUSG00000099158	Mir6368	Gm27800|mmu-mir-6368	microRNA 6368	ncRNA
mm_52976.1	chr6	123260485	123260501	+	1	NA	Intergenic	Intergenic	-1614	NM_001163161	17474	Mm.441101	NM_010819	ENSMUSG00000030144	Clec4d	Clecsf8|Mpcl|mcl	C-type lectin domain family 4, member d	protein-coding
mm_33846.1	chr4	135856129	135856160	+	1	NA	promoter-TSS (NM_001284196)	promoter-TSS (NM_001284196)	73	NM_010178	14105	Mm.10229	NM_010178	ENSMUSG00000028676	Srsf10	FUSIP2|Fusip1|NSSR1|NSSR2|Nssr|SRrp40|Sfrs13a|Srsf13a|TASR|TASR1|TASR2	serine/arginine-rich splicing factor 10	protein-coding
mm_53756.1	chr6	145615758	145615772	+	1	NA	promoter-TSS (NM_009449)	promoter-TSS (NM_009449)	-198	NM_009449	22147	Mm.270295	NM_009449	ENSMUSG00000067338	Tuba3b	M[a]7|Tuba7	tubulin, alpha 3B	protein-coding
mm_6662.1	chr1	80276512	80276550	-	1	NA	exon (NM_016716, exon 13 of 16)	exon (NM_016716, exon 13 of 16)	-62587	NM_173425	241128	Mm.145511	NM_173425	ENSMUSG00000043230	Fam124b	A830043J08Rik	family with sequence similarity 124, member B	protein-coding
mm_80126.1	chr9	70580254	70580291	+	1	NA	exon (NM_025690, exon 12 of 21)	exon (NM_025690, exon 12 of 21)	37402	NM_025690	66660	Mm.22379	NM_025690	ENSMUSG00000032212	Sltm	5730455C01Rik|5730555F13Rik|9130215G10Rik|Met	SAFB-like, transcription modulator	protein-coding
mm_52286.1	chr6	108662340	108662343	+	1	NA	intron (NM_011498, intron 3 of 4)	intron (NM_011498, intron 3 of 4)	-1407	NR_104577	75394	Mm.395061	NR_040757	ENSMUSG00000087341	0610040F04Rik	-	RIKEN cDNA 0610040F04 gene	ncRNA
mm_30671.1	chr4	11156469	11156483	+	1	NA	promoter-TSS (NM_001199105)	promoter-TSS (NM_001199105)	35	NM_021897	60599	Mm.393018	NM_021897	ENSMUSG00000028211	Trp53inp1	2700057G22Rik|SIP|SIP18|SIP27|Stinp|Teap	transformation related protein 53 inducible nuclear protein 1	protein-coding
mm_88770.1	chr10	80336021	80336031	+	1	NA	3' UTR (NM_139292, exon 6 of 6)	3' UTR (NM_139292, exon 6 of 6)	5881	NM_139292	70335	Mm.28147	NM_139292	ENSMUSG00000035504	Reep6	0610011M24Rik|Dp1l1	receptor accessory protein 6	protein-coding
mm_113969.1	chr13	51645693	51645727	+	1	NA	intron (NM_025415, intron 1 of 2)	CpG	478	NM_025415	66197	Mm.222228	NM_025415	ENSMUSG00000062248	Cks2	1110038L14Rik|CKSHS2	CDC28 protein kinase regulatory subunit 2	protein-coding
mm_34403.1	chr4	145224342	145224406	+	1	NA	exon (NM_011610, exon 6 of 10)	exon (NM_011610, exon 6 of 10)	22496	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_83144.1	chr9	40455775	40455777	-	1	NA	promoter-TSS (NM_172768)	promoter-TSS (NM_172768)	-12	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_74279.1	chr8	125344342	125344347	+	1	NA	Intergenic	Intergenic	148366	NM_001081337	244668	Mm.271668	NM_001081337	ENSMUSG00000001995	Sipa1l2	BC058408|mKIAA1389	signal-induced proliferation-associated 1 like 2	protein-coding
mm_144677.1	chr18	34751804	34751818	+	1	NA	promoter-TSS (NM_009860)	promoter-TSS (NM_009860)	-278	NM_009860	12532	Mm.286602	NM_009860	ENSMUSG00000044201	Cdc25c	Cdc25	cell division cycle 25C	protein-coding
mm_153636.1	chr19	44069647	44069675	-	1	NA	promoter-TSS (NM_145502)	promoter-TSS (NM_145502)	25	NM_145502	226144	Mm.279865	NM_145502	ENSMUSG00000025198	Erlin1	2810439N09Rik|C80197|Keo4|Spfh1	ER lipid raft associated 1	protein-coding
mm_62917.1	chr7	118129817	118129836	+	1	NA	promoter-TSS (NM_019419)	promoter-TSS (NM_019419)	-201	NM_019419	54208	Mm.29924	NM_019419	ENSMUSG00000030654	Arl6ip1	AIP-6|AL022945|ARMER|AU042858|Aip-1|Arl6ip|C85138|mKIAA0069	ADP-ribosylation factor-like 6 interacting protein 1	protein-coding
mm_9959.1	chr1	191096093	191096098	-	1	NA	Intergenic	Intergenic	-2319	NM_030060	381319	Mm.6922	NM_030060	ENSMUSG00000026630	Batf3	9130211I03Rik|Snft	basic leucine zipper transcription factor, ATF-like 3	protein-coding
mm_168603.1	chr11	74925797	74925797	+	1	NA	promoter-TSS (NM_001163311)	promoter-TSS (NM_001163311)	1	NM_013761	27364	Mm.131443	NM_013761	ENSMUSG00000001323	Srr	M100034|Rgsc34|Srs	serine racemase	protein-coding
mm_14493.1	chr2	131937128	131937146	+	1	NA	exon (NM_001278256, exon 4 of 4)	exon (NM_001278256, exon 4 of 4)	-13724	NM_001278257	26434	Mm.180750	NM_023043	ENSMUSG00000027338	Prnd	AI450264|Dpl|PrPLP|doppel	prion protein dublet	protein-coding
mm_60281.1	chr7	43966740	43966756	+	1	NA	promoter-TSS (NM_010645)	promoter-TSS (NM_010645)	-3	NM_010645	16623	Mm.447819	NM_010645	ENSMUSG00000063133	Klk1b1	Klk1|mGK-1|mK1	kallikrein 1-related peptidase b1	protein-coding
mm_18755.1	chr2	73437311	73437331	-	1	NA	exon (NM_153138, exon 5 of 8)	exon (NM_153138, exon 5 of 8)	16568	NM_001289722	215280	Mm.223504	NM_153138	ENSMUSG00000075284	Wipf1	AI115543|D2Ertd120e|WIP|Waspip	WAS/WASL interacting protein family, member 1	protein-coding
mm_122375.1	chr14	39473842	39473870	-	1	NA	promoter-TSS (NM_008734)	promoter-TSS (NM_008734)	-768	NM_008734	18183	Mm.258705	NM_008734	ENSMUSG00000041014	Nrg3	ska	neuregulin 3	protein-coding
mm_47748.1	chr5	130255526	130255537	-	1	NA	promoter-TSS (NM_178897)	promoter-TSS (NM_178897)	-1	NM_023248	66711	Mm.280484	NM_023248	ENSMUSG00000025337	Sbds	4733401P19Rik|AI836084|CGI-97|SDS	Shwachman-Bodian-Diamond syndrome homolog (human)	protein-coding
mm_26005.1	chr3	135281301	135281332	+	1	NA	promoter-TSS (NM_027208)	promoter-TSS (NM_027208)	95	NM_027208	69772	Mm.45121	NM_027208	ENSMUSG00000028167	Bdh2	1810026B04Rik|Dhrs6	3-hydroxybutyrate dehydrogenase, type 2	protein-coding
mm_139522.1	chr17	56613437	56613477	+	1	NA	promoter-TSS (NM_018730)	promoter-TSS (NM_018730)	62	NM_018730	54217	Mm.11376	NM_018730	ENSMUSG00000057863	Rpl36	-	ribosomal protein L36	protein-coding
mm_151390.1	chr19	56417137	56417158	+	1	NA	intron (NM_007611, intron 2 of 6)	B4|SINE|B4	20018	NM_007611	12369	Mm.35687	NM_007611	ENSMUSG00000025076	Casp7	AI314680|CMH-1|ICE-IAP3|Mch3|caspase-7|mCASP-7	caspase 7	protein-coding
mm_38522.1	chr4	141424118	141424172	-	1	NA	3' UTR (NM_013868, exon 3 of 3)	3' UTR (NM_013868, exon 3 of 3)	3366	NM_013868	29818	Mm.46181	NM_013868	ENSMUSG00000006221	Hspb7	27kDa|Hsp25-2|cvHsp	heat shock protein family, member 7 (cardiovascular)	protein-coding
mm_171606.1	chr4	149143428	149143438	-	1	NA	Intergenic	Intergenic	-5833	NM_027263	69928	Mm.260893	NM_027263	ENSMUSG00000073705	Apitd1	2610040C18Rik|2810407L01Rik|CENP-S	apoptosis-inducing, TAF9-like domain 1	protein-coding
mm_84789.1	chr9	77045720	77045722	-	1	NA	promoter-TSS (NM_012033)	promoter-TSS (NM_012033)	60	NR_136923	26944	Mm.23199	NM_012033	ENSMUSG00000032357	Tinag	AI452335|TIN-ag	tubulointerstitial nephritis antigen	protein-coding
mm_10483.1	chr2	14763113	14763142	+	1	NA	intron (NM_023116, intron 2 of 13)	intron (NM_023116, intron 2 of 13)	42485	NR_028497	625342	Mm.484784	NR_028497		Gm13315	OTTMUSG00000011384	lactate dehydrogenase A pseudogene	pseudo
mm_170056.1	chr17	3044745	3044762	-	1	NA	Intergenic	Intergenic	39430	NR_003519	328734	Mm.335641	NR_003519		Pisd-ps2	D030013I16Rik	phosphatidylserine decarboxylase, pseudogene 2	pseudo
mm_152064.1	chr19	6532265	6532286	-	1	NA	3' UTR (NM_020253, exon 23 of 23)	3' UTR (NM_020253, exon 23 of 23)	10795	NM_009203	20521	Mm.391146	NM_009203	ENSMUSG00000061742	Slc22a12	AI987855|OAT4L|Rst|Slc22al2|URAT1	solute carrier family 22 (organic anion/cation transporter), member 12	protein-coding
mm_99690.1	chr11	106066056	106066100	+	1	NA	promoter-TSS (NM_027346)	promoter-TSS (NM_027346)	-29	NM_027346	70207	Mm.343857	NM_027346	ENSMUSG00000001983	Taco1	2310066I18Rik|Ccdc44	translational activator of mitochondrially encoded cytochrome c oxidase I	protein-coding
mm_119957.1	chr14	55095049	55095100	+	1	NA	5' UTR (NM_153083, exon 1 of 2)	5' UTR (NM_153083, exon 1 of 2)	290	NM_153083	105663	Mm.319204	NM_153083	ENSMUSG00000045691	Thtpa	AW122966	thiamine triphosphatase	protein-coding
mm_146839.1	chr18	23022830	23022841	-	1	NA	intron (NM_001347510, intron 1 of 9)	(A)n|Simple_repeat|Simple_repeat	15828	NM_001161483	319211	Mm.209896	NM_199024	ENSMUSG00000041923	Nol4	1700013J13Rik|4930568N03Rik|Gm1262	nucleolar protein 4	protein-coding
mm_70114.1	chr7	142679702	142679714	-	1	NA	promoter-TSS (NM_001185083)	promoter-TSS (NM_001185083)	18	NM_001185083	16334	Mm.4946	NM_008387	ENSMUSG00000000215	Ins2	AA986540|Ins-2|InsII|Mody|Mody4	insulin II	protein-coding
mm_138093.1	chr17	34039167	34039182	+	1	NA	promoter-TSS (NM_009926)	promoter-TSS (NM_009926)	36	NM_001317722	12815	Mm.20230	NM_009926	ENSMUSG00000024330	Col11a2	-	collagen, type XI, alpha 2	protein-coding
mm_53548.1	chr6	136828813	136828825	+	1	NA	promoter-TSS (NM_021714)	promoter-TSS (NM_021714)	-24	NM_178776	320135	Mm.386899	NM_178776	ENSMUSG00000047515	BC049715	-	cDNA sequence BC049715	protein-coding
mm_164673.1	chr17	45574085	45574087	+	1	NA	promoter-TSS (NM_008302)	promoter-TSS (NM_008302)	-825	NM_008302	15516	Mm.2180	NM_008302	ENSMUSG00000023944	Hsp90ab1	90kDa|AL022974|C81438|Hsp84|Hsp84-1|Hsp90|Hspcb	heat shock protein 90 alpha (cytosolic), class B member 1	protein-coding
mm_57076.1	chr6	122580769	122580800	-	1	NA	exon (NM_031159, exon 7 of 8)	exon (NM_031159, exon 7 of 8)	21660	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_147526.1	chr18	52529848	52529890	-	1	NA	promoter-TSS (NM_010728)	promoter-TSS (NM_010728)	-2	NM_001286182	16948	Mm.172	NM_010728	ENSMUSG00000024529	Lox	AI893619|TSC-160|rrg	lysyl oxidase	protein-coding
mm_85898.1	chr9	111055937	111055956	-	1	NA	exon (NM_017466, exon 2 of 2)	exon (NM_017466, exon 2 of 2)	1298	NM_001302377	54199	Mm.7336	NM_017466	ENSMUSG00000043953	Ccrl2	1810047I05Rik|Ackr5|CCR11|Cmkbr1l2|E01|L-CCR	chemokine (C-C motif) receptor-like 2	protein-coding
mm_1446.1	chr1	67230404	67230425	+	1	NA	3' UTR (NM_001080809, exon 38 of 38)	3' UTR (NM_001080809, exon 38 of 38)	107387	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_25945.1	chr3	131564777	131564788	+	1	NA	promoter-TSS (NM_001289478)	promoter-TSS (NM_001289478)	14	NM_011863	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_111237.1	chr12	84772926	84772951	-	1	NA	promoter-TSS (NM_028863)	promoter-TSS (NM_028863)	174	NM_023409	67963	Mm.282556	NM_023409	ENSMUSG00000021242	Npc2	2700012J19Rik|AA408070|AU045843|HE1	Niemann-Pick type C2	protein-coding
mm_147919.1	chr18	65698489	65698511	-	1	NA	intron (NM_177028, intron 1 of 14)	intron (NM_177028, intron 1 of 14)	232	NM_177028	319888	Mm.183576	NM_177028	ENSMUSG00000046610	Oacyl	5330437I02Rik|Acyl3	O-acyltransferase like	protein-coding
mm_79025.1	chr9	45955328	45955346	+	1	NA	promoter-TSS (NM_001289668)	promoter-TSS (NM_001289668)	-88	NM_001289668	214597	Mm.379345	NM_172257	ENSMUSG00000034908	Sidt2	B930096O19|BC023957|CGI-40	SID1 transmembrane family, member 2	protein-coding
mm_95597.1	chr11	53350735	53350782	+	1	NA	promoter-TSS (NM_033565)	promoter-TSS (NM_033565)	-9	NM_033565	93736	Mm.395281	NM_033565	ENSMUSG00000049470	Aff4	AF5Q31|Alf4|Laf4l|MCEF	AF4/FMR2 family, member 4	protein-coding
mm_26324.1	chr3	142531875	142531885	+	1	NA	intron (NM_001083312, intron 1 of 10)	ID_B1|SINE|B4	1544	NM_145545	229900	Mm.45740	NM_145545	ENSMUSG00000040253	Gbp7	9830147J24Rik	guanylate binding protein 7	protein-coding
mm_137330.1	chr17	25045384	25045396	+	1	NA	intron (NM_134126, intron 13 of 29)	intron (NM_134126, intron 13 of 29)	29304	NM_134126	106633	Mm.32802	NM_134126	ENSMUSG00000024169	Ift140	AI661311|Tce5|Wdtc2|mKIAA0590	intraflagellar transport 140	protein-coding
mm_41356.1	chr5	90506516	90506524	+	1	NA	intron (NM_007423, intron 11 of 14)	intron (NM_007423, intron 11 of 14)	-12429	NM_145146	280662	Mm.348786	NM_145146	ENSMUSG00000029369	Afm	Alf|alpha-Alb	afamin	protein-coding
mm_75074.1	chr8	33844916	33844922	-	1	NA	intron (NM_001042674, intron 4 of 7)	intron (NM_001042674, intron 4 of 7)	84944	NM_019733	19663	Mm.323997	NM_019733	ENSMUSG00000031586	Rbpms	2010300K22Rik|2700019M19Rik|AU017537|RBP-MS|hermes	RNA binding protein gene with multiple splicing	protein-coding
mm_154538.1	chrM	14026	14036	-	1	NA	NA	Intergenic	NA	NA								
mm_51981.1	chr6	91978852	91978913	+	1	NA	promoter-TSS (NM_172731)	promoter-TSS (NM_172731)	-83	NM_172731	232237	Mm.295740	NM_172731	ENSMUSG00000034037	Fgd5	C330025N11Rik|ZFYVE23|mFLJ00274	FYVE, RhoGEF and PH domain containing 5	protein-coding
mm_94469.1	chr11	6521011	6521024	+	1	NA	promoter-TSS (NM_178440)	promoter-TSS (NM_178440)	-59	NM_178440	246177	Mm.239554	NM_178440	ENSMUSG00000020437	Myo1g	E430002D17Rik	myosin IG	protein-coding
mm_19104.1	chr2	79454700	79454710	-	1	NA	exon (NM_010894, exon 2 of 2)	exon (NM_010894, exon 2 of 2)	1931	NM_010894	18012	Mm.4636	NM_010894	ENSMUSG00000034701	Neurod1	BETA2|BHF-1|Nd1|Neurod|bHLHa3	neurogenic differentiation 1	protein-coding
mm_10612.1	chr2	19166953	19166958	+	1	NA	Intergenic	Intergenic	-32163	NM_001271563	70882	Mm.276696	NM_001081083	ENSMUSG00000037683	Armc3	4921513G22Rik	armadillo repeat containing 3	protein-coding
mm_69747.1	chr7	140955818	140955822	-	1	NA	exon (NM_030694, exon 1 of 2)	exon (NM_030694, exon 1 of 2)	141	NM_030694	80876	Mm.379266	NM_030694	ENSMUSG00000060591	Ifitm2	DSPA2c|Ifitm3l|fragilis3|mil-3	interferon induced transmembrane protein 2	protein-coding
mm_104651.1	chr11	97574069	97574082	-	1	NA	intron (NM_018873, intron 1 of 19)	intron (NM_018873, intron 1 of 19)	1051	NM_018873	56013	Mm.342665	NM_018873	ENSMUSG00000038453	Srcin1	P140|SNIP|mKIAA1684|p140Cap	SRC kinase signaling inhibitor 1	protein-coding
mm_168028.1	chrY	90738374	90738385	+	1	NA	Intergenic	IMPB_01|Satellite|Satellite	16671	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_11036.1	chr2	26973469	26973479	+	1	NA	promoter-TSS (NM_001290463)	promoter-TSS (NM_001290463)	58	NM_001290465	279028	Mm.330084	NM_001001322	ENSMUSG00000014852	Adamts13	ADAM-TS13|ADAMTS-13|Gm710|vWF-CP	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 13	protein-coding
mm_91067.1	chr10	19005599	19005609	-	1	NA	exon (NM_009397, exon 6 of 9)	exon (NM_009397, exon 6 of 9)	6359	NM_001166402	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_116128.1	chr13	28953007	28953059	-	1	NA	5' UTR (NM_009238, exon 1 of 1)	5' UTR (NM_009238, exon 1 of 1)	649	NM_009238	20677	Mm.240627	NM_009238	ENSMUSG00000076431	Sox4	AA682046|Sox-4	SRY (sex determining region Y)-box 4	protein-coding
mm_23425.1	chr3	58715506	58715508	+	1	NA	intron (NR_045167, intron 2 of 7)	Charlie1a|DNA|hAT-Charlie	22918	NR_045167	71301	Mm.254475	NR_045167	ENSMUSG00000097725	4930593A02Rik	4933440I01Rik	RIKEN cDNA 4930593A02 gene	ncRNA
mm_6595.1	chr1	75278442	75278455	-	1	NA	promoter-TSS (NR_138251)	promoter-TSS (NR_138251)	-33	NM_009049	19711	Mm.4032	NM_009049	ENSMUSG00000033061	Resp18	AI851012	regulated endocrine-specific protein 18	protein-coding
mm_2310.1	chr1	91626354	91626393	+	1	NA	Intergenic	Intergenic	85293	NM_023046	65247	Mm.234152	NM_023046	ENSMUSG00000026311	Asb1	1700029O08Rik|1700054C17Rik|AI426616|AI851378|mKIAA1146	ankyrin repeat and SOCS box-containing 1	protein-coding
mm_67219.1	chr7	74492647	74492673	-	1	NA	intron (NM_001038643, intron 2 of 10)	B4A|SINE|B4	62120	NM_023908	108116	Mm.425467	NM_023908	ENSMUSG00000025790	Slco3a1	5830414C08Rik|Anr1|MJAM|OATP-D|R75096|Slc21a11	solute carrier organic anion transporter family, member 3a1	protein-coding
mm_149948.1	chr19	27344739	27344768	+	1	NA	Intergenic	L2|LINE|L2	22134	NM_183179	240595	Mm.269759	NM_183179	ENSMUSG00000047298	Kcnv2	KV11.1	potassium channel, subfamily V, member 2	protein-coding
mm_12641.1	chr2	74711959	74712000	+	1	NA	promoter-TSS (NM_010468)	promoter-TSS (NM_010468)	-14	NM_010468	15434	Mm.430708	NM_010468	ENSMUSG00000079277	Hoxd3	Hox-4.1|Hox-5.5	homeobox D3	protein-coding
mm_50025.1	chr6	41121340	41121382	+	1	NA	Intergenic	Intergenic	-85852	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_5154.1	chr1	9944088	9944090	-	1	NA	promoter-TSS (NR_024067)	promoter-TSS (NR_024067)	29	NR_024067	73824	Mm.28311	NR_024067	ENSMUSG00000098234	Snhg6	1110008H02Rik	small nucleolar RNA host gene 6	ncRNA
mm_97836.1	chr11	83065028	83065032	+	1	NA	promoter-TSS (NM_011408)	promoter-TSS (NM_011408)	-82	NM_011408	20556	Mm.278689	NM_011408	ENSMUSG00000072620	Slfn2	Shlf2	schlafen 2	protein-coding
mm_92174.1	chr10	67598460	67598496	-	1	NA	Intergenic	Intergenic	-49523	NM_001005419	211488	Mm.297250	NM_001005419	ENSMUSG00000057134	Ado	Gm237	2-aminoethanethiol (cysteamine) dioxygenase	protein-coding
mm_118824.1	chr14	25581593	25581618	+	1	NA	exon (NM_183208, exon 6 of 24)	exon (NM_183208, exon 6 of 24)	-5199	NR_033492	77592	Mm.444871	NM_175264		4931406H21Rik	-	RIKEN cDNA 4931406H21 gene	ncRNA
mm_99027.1	chr11	98939915	98939944	+	1	NA	intron (NM_001177303, intron 1 of 8)	intron (NM_001177303, intron 1 of 8)	218	NM_001177303	19401	Mm.439744	NM_009024	ENSMUSG00000037992	Rara	Nr1b1|RAR|RARalpha1	retinoic acid receptor, alpha	protein-coding
mm_18696.1	chr2	71546369	71546399	-	1	NA	exon (NM_010054, exon 1 of 3)	exon (NM_010054, exon 1 of 3)	370	NM_010054	13392	Mm.3896	NM_010054	ENSMUSG00000023391	Dlx2	AW121999|Dlx-2|Tes-1	distal-less homeobox 2	protein-coding
mm_84140.1	chr9	59291371	59291384	-	1	NA	promoter-TSS (NM_028121)	promoter-TSS (NM_028121)	-195	NM_028121	72141	Mm.22456	NM_028121	ENSMUSG00000025236	Adpgk	2610017G09Rik|Adp-gk|C77577	ADP-dependent glucokinase	protein-coding
mm_74021.1	chr8	121590425	121590469	+	1	NA	promoter-TSS (NM_026160)	promoter-TSS (NM_026160)	-21	NM_026160	67443	Mm.28357	NM_026160	ENSMUSG00000031812	Map1lc3b	1010001C15Rik|Atg8|LC3b|Map1lc3	microtubule-associated protein 1 light chain 3 beta	protein-coding
mm_80600.1	chr9	86507129	86507132	+	1	NA	intron (NM_177208, intron 14 of 38)	B4A|SINE|B4	39976	NM_177208	320615	Mm.245500	NM_177208	ENSMUSG00000034973	Dopey1	B130005I07Rik|BC035275|C130028L17|D9Ertd809e	dopey family member 1	protein-coding
mm_103448.1	chr11	76174444	76174447	-	1	NA	intron (NM_026664, intron 2 of 21)	intron (NM_026664, intron 2 of 21)	5185	NM_026664	68299	Mm.46397	NM_026664	ENSMUSG00000017288	Vps53	2010002A08Rik|2310040I21Rik|3100002B05Rik|Hccs1	VPS53 GARP complex subunit	protein-coding
mm_85429.1	chr9	103507087	103507126	-	1	NA	intron (NM_178638, intron 3 of 5)	intron (NM_178638, intron 3 of 5)	-26778	NM_001002896	107993	Mm.335403	NM_001002896	ENSMUSG00000032556	Bfsp2	AI448593|CP49	beaded filament structural protein 2, phakinin	protein-coding
mm_65666.1	chr7	28152818	28152824	-	1	NA	exon (NM_001164655, exon 11 of 20)	exon (NM_001164655, exon 11 of 20)	-16927	NM_007991	14113	Mm.4595	NM_007991	ENSMUSG00000046865	Fbl	AL022665|FIB|FLRN|RNU3IP1	fibrillarin	protein-coding
mm_156599.1	chrX	152433056	152433086	+	1	NA	Intergenic	Intergenic	64043	NR_045452	75693	Mm.287381	NR_045451	ENSMUSG00000084885	3010001F23Rik	-	RIKEN cDNA 3010001F23 gene	ncRNA
mm_52167.1	chr6	99003217	99003229	+	1	NA	exon (NM_053202, exon 9 of 19)	exon (NM_053202, exon 9 of 19)	25075	NM_001197322	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_54521.1	chr6	35539766	35539823	-	1	NA	promoter-TSS (NM_008098)	promoter-TSS (NM_008098)	94	NM_008098	14489	Mm.182746	NM_008098	ENSMUSG00000029840	Mtpn	5033418D15Rik|Gcdp|V1	myotrophin	protein-coding
mm_167562.1	chr9	40408087	40408089	-	1	NA	intron (NM_172768, intron 2 of 19)	intron (NM_172768, intron 2 of 19)	47676	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_11104.1	chr2	28192933	28192937	+	1	NA	promoter-TSS (NM_001038613)	promoter-TSS (NM_001038613)	-158	NM_001038613	56177	Mm.43278	NM_019498	ENSMUSG00000026833	Olfm1	AMY|AW742568|Noe1|OlfA|Pancortin|Pancortin3	olfactomedin 1	protein-coding
mm_168272.1	chr10	97479581	97479581	+	1	NA	promoter-TSS (NM_001190451)	promoter-TSS (NM_001190451)	81	NM_001190451	13179	Mm.56769	NM_007833	ENSMUSG00000019929	Dcn	DC|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding
mm_80837.1	chr9	97141114	97141139	+	1	NA	Intergenic	RLTR14|LTR|ERV1	-30085	NM_138756	192287	Mm.228067	NM_138756	ENSMUSG00000032449	Slc25a36	C330005L02Rik	solute carrier family 25, member 36	protein-coding
mm_7520.1	chr1	124045978	124045989	-	1	NA	promoter-TSS (NM_199021)	promoter-TSS (NM_199021)	-424	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_132345.1	chr16	33885051	33885093	+	1	NA	exon (NM_001145884, exon 5 of 15)	exon (NM_001145884, exon 5 of 15)	55407	NM_001145884	16419	Mm.6424	NM_010580	ENSMUSG00000022817	Itgb5	AA475909|AI874634|ESTM23|[b]-5|[b]5|[b]5A|[b]5B|beta-5|beta5	integrin beta 5	protein-coding
mm_133744.1	chr16	94011001	94011011	+	1	NA	Intergenic	PB1D9|SINE|Alu	-2169	NM_019500	56173	Mm.328716	NM_019500	ENSMUSG00000047109	Cldn14	AI851731	claudin 14	protein-coding
mm_34185.1	chr4	140701448	140701463	+	1	NA	promoter-TSS (NM_173867)	promoter-TSS (NM_173867)	-18	NM_173867	108911	Mm.253	NM_173867	ENSMUSG00000040945	Rcc2	2610510H01Rik|2610529N02Rik|AA536646|AA675016|Td60|mKIAA1470	regulator of chromosome condensation 2	protein-coding
mm_143506.1	chr17	71752868	71752891	-	1	NA	promoter-TSS (NM_146082)	promoter-TSS (NM_146082)	6	NM_146082	225004	Mm.134151	NM_146082	ENSMUSG00000044375	BC027072	-	cDNA sequence BC027072	protein-coding
mm_137942.1	chr17	32685656	32685677	+	1	NA	promoter-TSS (NM_134127)	promoter-TSS (NM_134127)	7	NM_134127	106648	Mm.26539	NM_134127	ENSMUSG00000073424	Cyp4f15	AI787289|Cyp4f-15	cytochrome P450, family 4, subfamily f, polypeptide 15	protein-coding
mm_70343.1	chr8	4613212	4613224	+	1	NA	promoter-TSS (NM_145591)	promoter-TSS (NM_145591)	48	NM_145591	233987	Mm.102799	NM_145591	ENSMUSG00000058748	Zfp958	-	zinc finger protein 958	protein-coding
mm_137564.1	chr17	27704473	27704487	+	1	NA	intron (NM_011861, intron 3 of 9)	intron (NM_011861, intron 3 of 9)	19241	NM_178365	23969	Mm.4926	NM_011861	ENSMUSG00000040276	Pacsin1	A830061D09Rik|H74|mKIAA1379|syndapin	protein kinase C and casein kinase substrate in neurons 1	protein-coding
mm_29529.1	chr3	116659336	116659341	-	1	NA	intron (NM_008246, intron 1 of 11)	intron (NM_008246, intron 1 of 11)	3339	NM_008246	15247	Mm.280077	NM_008246	ENSMUSG00000089911	Mfsd14a	Hiat1	major facilitator superfamily domain containing 14A	protein-coding
mm_70465.1	chr8	11913123	11913136	+	1	NA	Intergenic	Intergenic	72608	NM_029326	75528	Mm.440342	NM_029326	ENSMUSG00000031512	Tex29	1700018L24Rik	testis expressed 29	protein-coding
mm_105914.1	chr11	114984246	114984267	-	1	NA	exon (NM_145437, exon 4 of 4)	exon (NM_145437, exon 4 of 4)	5630	NM_145437	217305	Mm.275986	NM_145437	ENSMUSG00000034641	Cd300ld	4732429D16Rik|CLM5|Cd300ld1|LMIR4|MAIR-IV|clm-5	CD300 molecule like family member d	protein-coding
mm_122193.1	chr14	31780929	31780963	-	1	NA	intron (NM_001024604, intron 1 of 27)	intron (NM_001024604, intron 1 of 27)	49469	NM_001024604	105522	Mm.37660	NM_001024604	ENSMUSG00000014496	Ankrd28	AI465466|AI604979|E430019N21Rik|mKIAA0379	ankyrin repeat domain 28	protein-coding
mm_108035.1	chr12	73777412	73777418	+	1	NA	3' UTR (NM_008856, exon 14 of 14)	3' UTR (NM_008856, exon 14 of 14)	-123909	NM_001313920	15251	Mm.3879	NM_010431	ENSMUSG00000021109	Hif1a	AA959795|HIF-1-alpha|HIF1-alpha|HIF1alpha|MOP1|bHLHe78	hypoxia inducible factor 1, alpha subunit	protein-coding
mm_84572.1	chr9	69029133	69029143	-	1	NA	intron (NM_013646, intron 1 of 10)	intron (NM_013646, intron 1 of 10)	-260703	NM_001289916	19883	Mm.378450	NM_013646	ENSMUSG00000032238	Rora	9530021D13Rik|Nr1f1|ROR1|ROR2|ROR3|nmf267|sg|staggerer|tmgc26	RAR-related orphan receptor alpha	protein-coding
mm_41932.1	chr5	105700759	105700835	+	1	NA	promoter-TSS (NM_178701)	promoter-TSS (NM_178701)	-13	NM_178701	231549	Mm.23837	NM_178701	ENSMUSG00000046079	Lrrc8d	2810473G09Rik|4930525N13Rik|A930019F03|Lrrc5	leucine rich repeat containing 8D	protein-coding
mm_120335.1	chr14	63436532	63436548	+	1	NA	5' UTR (NM_177628, exon 1 of 4)	5' UTR (NM_177628, exon 1 of 4)	146	NM_177628	219148	Mm.37882	NM_177628	ENSMUSG00000035095	Fam167a	A030013D21	family with sequence similarity 167, member A	protein-coding
mm_146662.1	chr18	12121507	12121541	-	1	NA	promoter-TSS (NM_001289667)	promoter-TSS (NM_001289667)	13	NR_110356	338363	Mm.271567	NM_178801	ENSMUSG00000049411	Tmem241	6030446N20Rik	transmembrane protein 241	protein-coding
mm_20326.1	chr2	127458308	127458332	-	1	NA	non-coding (NR_110989, exon 9 of 9)	non-coding (NR_110989, exon 9 of 9)	-13755	NM_029629	68126	Mm.288676	NM_029629	ENSMUSG00000027371	Fahd2a	1500003K14Rik|B430104H02Rik|Cgi-105|Fahd2	fumarylacetoacetate hydrolase domain containing 2A	protein-coding
mm_69953.1	chr7	142372343	142372371	-	1	NA	promoter-TSS (NM_177265)	promoter-TSS (NM_177265)	-30	NM_001347542	320802	Mm.154486	NM_177265	ENSMUSG00000045777	Ifitm10	6330512M04Rik|AI848576|DSPA3	interferon induced transmembrane protein 10	protein-coding
mm_119311.1	chr14	36316922	36316928	+	1	NA	Intergenic	Intergenic	221960	NM_175008	218921	Mm.212464	NM_175008	ENSMUSG00000096405	4930474N05Rik	-	RIKEN cDNA 4930474N05 gene	protein-coding
mm_135884.1	chr16	64770917	64770971	-	1	NA	promoter-TSS (NM_026273)	promoter-TSS (NM_026273)	-5	NM_026273	67609	Mm.212157	NM_026273	ENSMUSG00000059920	4930453N24Rik	AI649104|din	RIKEN cDNA 4930453N24 gene	protein-coding
mm_540.1	chr1	37998775	37998777	+	1	NA	intron (NM_198303, intron 1 of 23)	intron (NM_198303, intron 1 of 23)	766	NM_198303	226982	Mm.260943	NM_198303	ENSMUSG00000026083	Eif5b	A030003E17Rik|BC018347|IF2	eukaryotic translation initiation factor 5B	protein-coding
mm_6977.1	chr1	86353253	86353283	-	1	NA	exon (NM_010880, exon 9 of 14)	exon (NM_010880, exon 9 of 14)	-1141	NR_106184	102465895		NR_106184	ENSMUSG00000104627	Gm24148	Mir3535|mir-3535|mmu-mir-3535	predicted gene, 24148	ncRNA
mm_86867.1	chr10	21994002	21994021	+	1	NA	promoter-TSS (NM_011361)	promoter-TSS (NM_011361)	121	NM_001161850	20393	Mm.28405	NM_011361	ENSMUSG00000019970	Sgk1	Sgk	serum/glucocorticoid regulated kinase 1	protein-coding
mm_20971.1	chr2	151973310	151973316	-	1	NA	promoter-TSS (NM_001289151)	promoter-TSS (NM_001289151)	81	NM_001289151	73847	Mm.272444	NM_028666	ENSMUSG00000027459	Fam110a	1700008J10Rik|5430432M24Rik|AI747080	family with sequence similarity 110, member A	protein-coding
mm_47961.1	chr5	135713477	135713497	-	1	NA	intron (NM_008898, intron 1 of 15)	intron (NM_008898, intron 1 of 15)	22402	NR_106001	102466791		NR_106001	ENSMUSG00000099197	Mir7034	Gm27372|mmu-mir-7034	microRNA 7034	ncRNA
mm_79717.1	chr9	61391869	61391877	+	1	NA	intron (NM_001083927, intron 4 of 19)	intron (NM_001083927, intron 4 of 19)	19507	NM_001083927	21887	Mm.24255	NM_009389	ENSMUSG00000032280	Tle3	2610103N05Rik|ESG|Grg3a|Grg3b|mKIAA1547	transducin-like enhancer of split 3	protein-coding
mm_79004.1	chr9	45410129	45410169	+	1	NA	non-coding (NR_028499, exon 6 of 6)	non-coding (NR_028499, exon 6 of 6)	4072	NM_007503	11936	Mm.22742	NM_007503	ENSMUSG00000059412	Fxyd2	Atp1g1	FXYD domain-containing ion transport regulator 2	protein-coding
mm_171299.1	chr3	93520517	93520521	+	1	NA	promoter-TSS (NM_016740)	promoter-TSS (NM_016740)	23	NM_016740	20195	Mm.280038	NM_016740	ENSMUSG00000027907	S100a11	EMAPI|Emap1|S100a14|S100c|cal	S100 calcium binding protein A11	protein-coding
mm_148465.1	chr19	4082519	4082533	+	1	NA	promoter-TSS (NM_001160252)	promoter-TSS (NM_001160252)	38	NM_001160253	29866	Mm.46268	NM_013878	ENSMUSG00000024857	Cabp2	-	calcium binding protein 2	protein-coding
mm_60466.1	chr7	44478006	44478023	+	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	-6503	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_147370.1	chr18	43438301	43438303	-	1	NA	promoter-TSS (NM_001291455)	promoter-TSS (NM_001291455)	-16	NM_001291455	22240	Mm.8180	NM_009468	ENSMUSG00000024501	Dpysl3	CRMP-4|DRP-3|TUC4|ULIP-1|Ulip|Ulip1	dihydropyrimidinase-like 3	protein-coding
mm_121140.1	chr14	101894024	101894037	+	1	NA	intron (NM_001347628, intron 8 of 26)	L2a|LINE|L2	53407	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_10567.1	chr2	18063892	18063913	+	1	NA	promoter-TSS (NM_001252561)	promoter-TSS (NM_001252561)	-683	NM_001252560	17354	Mm.209175	NM_010804	ENSMUSG00000026743	Mllt10	Af10|B130021D15Rik|D630001B22Rik|mKIAA4140	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 10	protein-coding
mm_14932.1	chr2	151542556	151542646	+	1	NA	non-coding (NR_126058, exon 1 of 4)	non-coding (NR_126058, exon 1 of 4)	118	NM_001302078	14225	Mm.278458	NM_008019	ENSMUSG00000032966	Fkbp1a	FKBP12|Fkbp|Fkbp1	FK506 binding protein 1a	protein-coding
mm_153099.1	chr19	32712351	32712359	-	1	NA	promoter-TSS (NM_026487)	promoter-TSS (NM_026487)	-57	NM_026487	67979	Mm.27123	NM_026487	ENSMUSG00000013662	Atad1	4921525H23Rik|AW107648|Thorase	ATPase family, AAA domain containing 1	protein-coding
mm_166486.1	chr5	147860472	147860481	+	1	NA	promoter-TSS (NM_025624)	promoter-TSS (NM_025624)	-152	NM_025624	66537	Mm.332855	NM_025624	ENSMUSG00000029649	Pomp	2510048O06Rik|Ump1	proteasome maturation protein	protein-coding
mm_13666.1	chr2	114200216	114200218	+	1	NA	intron (NM_175466, intron 1 of 1)	intron (NM_175466, intron 1 of 1)	1215	NM_175466	228491	Mm.132523	NM_175466	ENSMUSG00000040321	Zfp770	6430601A21Rik|Znf770	zinc finger protein 770	protein-coding
mm_119787.1	chr14	54192257	54192287	+	1	NA	Intergenic	Intergenic	61657	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_5650.1	chr1	40529312	40529331	-	1	NA	intron (NM_010553, intron 6 of 12)	intron (NM_010553, intron 6 of 12)	13959	NM_010553	16174	Mm.20466	NM_010553	ENSMUSG00000026068	Il18rap	AcPL|IL-18R-beta|IL-18RAcP|IL-18Rbeta|IL-1RAcPL	interleukin 18 receptor accessory protein	protein-coding
mm_36263.1	chr4	63496036	63496065	-	1	NA	promoter-TSS (NM_001008793)	promoter-TSS (NM_001008793)	-59	NM_001008791	73750	Mm.300397	NM_028640	ENSMUSG00000039137	Whrn	1110035G07Rik|AW122018|AW742671|C430046P22Rik|Dfnb31|Ush2d|wi	whirlin	protein-coding
mm_168176.1	chr10	56497246	56497246	+	1	NA	Intergenic	Intergenic	119946	NM_010288	14609	Mm.378921	NM_010288	ENSMUSG00000050953	Gja1	AU042049|AW546267|Cnx43|Cx43|Cx43alpha1|Gja-1|Npm1|connexin43	gap junction protein, alpha 1	protein-coding
mm_49072.1	chr6	5786931	5786933	+	1	NA	intron (NM_001191026, intron 5 of 16)	L1MEc|LINE|L1	61293	NM_001191026	13426	Mm.20893	NM_010063	ENSMUSG00000029757	Dync1i1	DH IC-1|DHIC-1|DIC|Dncic1|IC74	dynein cytoplasmic 1 intermediate chain 1	protein-coding
mm_91088.1	chr10	19015304	19015317	-	1	NA	promoter-TSS (NM_009397)	promoter-TSS (NM_009397)	100	NM_009397	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_25808.1	chr3	127789942	127789983	+	1	NA	promoter-TSS (NM_145133)	promoter-TSS (NM_145133)	49	NM_145133	211550	Mm.31852	NM_145133	ENSMUSG00000046688	Tifa	T2bp	TRAF-interacting protein with forkhead-associated domain	protein-coding
mm_73870.1	chr8	118891177	118891182	+	1	NA	intron (NM_019707, intron 5 of 13)	HAL1ME|LINE|L1	-453359	NM_024219	68196	Mm.358714	NM_024219	ENSMUSG00000031839	Hsbp1	0610007A03Rik|AA408769|Hsp25	heat shock factor binding protein 1	protein-coding
mm_115299.1	chr13	112001435	112001443	+	1	NA	Intergenic	Intergenic	133503	NR_130345	102636620	Mm.402328	NR_130345	ENSMUSG00000086111	Gm15326	OTTMUSG00000020187	predicted gene 15326	ncRNA
mm_35633.1	chr4	43508741	43508753	-	1	NA	exon (NM_139305, exon 3 of 11)	exon (NM_139305, exon 3 of 11)	1721	NM_139305	230099	Mm.283682	NM_139305	ENSMUSG00000028463	Car9	CAIX|Ca9|MN/CA9	carbonic anhydrase 9	protein-coding
mm_83265.1	chr9	42463803	42463822	-	1	NA	intron (NM_173038, intron 1 of 7)	intron (NM_173038, intron 1 of 7)	8414	NM_173038	272589	Mm.34483	NM_173038	ENSMUSG00000037287	Tbcel	D330014K23|E130107N23Rik|Lrrc35	tubulin folding cofactor E-like	protein-coding
mm_158151.1	chrX	103472999	103473002	-	1	NA	intron (NR_001463, intron 1 of 6)	intron (NR_001463, intron 1 of 6)	10233	NR_001570	213742	Mm.274770	NR_001463	ENSMUSG00000086503	Xist	A430022B11|AI314753	inactive X specific transcripts	ncRNA
mm_119494.1	chr14	47378387	47378397	+	1	NA	intron (NM_001145953, intron 1 of 5)	intron (NM_001145953, intron 1 of 5)	4532	NM_001145953	16854	Mm.248615	NM_010705	ENSMUSG00000050335	Lgals3	GBP|L-34|Mac-2|gal3	lectin, galactose binding, soluble 3	protein-coding
mm_31098.1	chr4	41755812	41755852	+	1	NA	promoter-TSS (NM_001302511)	promoter-TSS (NM_001302511)	-378	NM_001302511	14430	Mm.439669	NM_016658	ENSMUSG00000036073	Galt	AW553376	galactose-1-phosphate uridyl transferase	protein-coding
mm_36034.1	chr4	57143748	57143758	-	1	NA	promoter-TSS (NM_019427)	promoter-TSS (NM_019427)	-597	NM_019427	54357	Mm.28217	NM_019427	ENSMUSG00000028434	Epb41l4b	6430543G08Rik|AA589614|AU021054|BB007528|D4Ertd346e|Ehm2|Epb4.1l4b|Lulu2	erythrocyte membrane protein band 4.1 like 4b	protein-coding
mm_116350.1	chr13	38960499	38960539	-	1	NA	promoter-TSS (NM_001170430)	promoter-TSS (NM_001170430)	18	NM_001170430	108652	Mm.255506	NM_134060	ENSMUSG00000021432	Slc35b3	4921526O06Rik|AI428480|CGI-19|PABST2|PAPST2	solute carrier family 35, member B3	protein-coding
mm_20377.1	chr2	128467514	128467522	-	1	NA	Intergenic	Intergenic	-38167	NR_028590	100043424	Mm.297222	NR_028589		Gm14005	OTTMUSG00000015351	predicted gene 14005	ncRNA
mm_38648.1	chr4	143268300	143268307	-	1	NA	3' UTR (NM_010329, exon 6 of 6)	3' UTR (NM_010329, exon 6 of 6)	31261	NM_010329	14726	Mm.2976	NM_010329	ENSMUSG00000028583	Pdpn	Gp38|OTS-8|RANDAM-2|T1-alpha|T1a|T1alpha	podoplanin	protein-coding
mm_157354.1	chrX	37048661	37048671	-	1	NA	promoter-TSS (NM_173779)	promoter-TSS (NM_173779)	-179	NM_173779	245381	Mm.123697	NM_173779	ENSMUSG00000044400	Sowahd	A630014H24Rik|Ankrd58	sosondowah ankyrin repeat domain family member D	protein-coding
mm_100702.1	chr11	3647472	3647508	-	1	NA	promoter-TSS (NR_110490)	promoter-TSS (NR_110490)	46	NR_110490	544752	Mm.390314	NR_002321	ENSMUSG00000056579	Tug1	AI316828	taurine upregulated gene 1	ncRNA
mm_53470.1	chr6	134924544	134924567	+	1	NA	3' UTR (NM_009875, exon 3 of 3)	3' UTR (NM_009875, exon 3 of 3)	4154	NM_009875	12576	Mm.2958	NM_009875	ENSMUSG00000003031	Cdkn1b	AA408329|AI843786|Kip1|p27|p27Kip1	cyclin-dependent kinase inhibitor 1B	protein-coding
mm_139784.1	chr17	65799212	65799215	+	1	NA	intron (NM_001114131, intron 2 of 19)	B1_Mm|SINE|Alu	15858	NR_104465	70351	Mm.48686	NM_146081	ENSMUSG00000061950	Ppp4r1	3110001J10Rik|Pp4r1	protein phosphatase 4, regulatory subunit 1	protein-coding
mm_35915.1	chr4	52814518	52814567	-	1	NA	promoter-TSS (NR_040661)	promoter-TSS (NR_040661)	-62	NR_040661	75367	Mm.159510	NR_040661	ENSMUSG00000070984	4930552N02Rik	-	RIKEN cDNA 4930552N02 gene	ncRNA
mm_110004.1	chr12	15850611	15850630	-	1	NA	Intergenic	Intergenic	-33835	NM_144551	217410	Mm.491136	NM_144551	ENSMUSG00000020601	Trib2	AW319517|TRB-2|TRB2	tribbles pseudokinase 2	protein-coding
mm_151625.1	chr19	3911754	3911759	-	1	NA	intron (NM_001271443, intron 1 of 6)	intron (NM_001271443, intron 1 of 6)	1018	NM_144870	225887	Mm.44227	NM_144870	ENSMUSG00000059734	Ndufs8	BC021616|CI-23kD|TYKY	NADH dehydrogenase (ubiquinone) Fe-S protein 8	protein-coding
mm_104278.1	chr11	89733653	89733671	-	1	NA	Intergenic	Intergenic	-36726	NM_001327810	382543	Mm.60997	NM_172534	ENSMUSG00000047773	Ankfn1	4932411E22Rik|Gm1175|nmf9	ankyrin-repeat and fibronectin type III domain containing 1	protein-coding
mm_28961.1	chr3	100684948	100684951	-	1	NA	5' UTR (NM_010763, exon 1 of 13)	5' UTR (NM_010763, exon 1 of 13)	524	NM_010763	17156	Mm.271617	NM_010763	ENSMUSG00000008763	Man1a2	AI428775|AI528764|AI854422|Man1b|PCR2	mannosidase, alpha, class 1A, member 2	protein-coding
mm_130275.1	chr15	96699122	96699137	-	1	NA	intron (NM_175121, intron 1 of 15)	CpG	569	NM_175121	67760	Mm.46754	NM_175121	ENSMUSG00000022462	Slc38a2	5033402L14Rik|AI316867|ATA2|SAT2|mKIAA1382	solute carrier family 38, member 2	protein-coding
mm_29358.1	chr3	108554738	108554753	-	1	NA	promoter-TSS (NR_028538)	promoter-TSS (NR_028538)	-343	NR_028538	100217438		NR_028538		Scarna2	MBII-382	small Cajal body-specific RNA 2	ncRNA
mm_66656.1	chr7	45714668	45714678	-	1	NA	5' UTR (NM_020011, exon 1 of 6)	5' UTR (NM_020011, exon 1 of 6)	534	NM_020011	56632	Mm.24222	NM_020011	ENSMUSG00000057342	Sphk2	C76851	sphingosine kinase 2	protein-coding
mm_7384.1	chr1	110922355	110922358	-	1	NA	intron (NM_001081386, intron 7 of 11)	Lx9|LINE|L1	55016	NM_001081386	227485	Mm.322070	NM_001081386	ENSMUSG00000047216	Cdh19	-	cadherin 19, type 2	protein-coding
mm_141130.1	chr17	26201364	26201387	-	1	NA	promoter-TSS (NM_008113)	promoter-TSS (NM_008113)	-25	NM_008113	14570	Mm.1383	NM_008113	ENSMUSG00000073433	Arhgdig	Gdi5|RIP2|Rho-GDI-3|Rho-GDI2	Rho GDP dissociation inhibitor (GDI) gamma	protein-coding
mm_54387.1	chr6	31218445	31218465	-	1	NA	promoter-TSS (NR_110471)	promoter-TSS (NR_110471)	19	NR_110470	232685	Mm.443019	NM_144555	ENSMUSG00000044471	Lncpint	Lincpint|MNCb-1768|Pint|linc-Pint	long non-protein coding RNA, Trp53 induced transcript	ncRNA
mm_54686.1	chr6	39420403	39420413	-	1	NA	promoter-TSS (NM_018810)	promoter-TSS (NM_018810)	-39	NM_018810	54484	Mm.270484	NM_018810	ENSMUSG00000029922	Mkrn1	RFP	makorin, ring finger protein, 1	protein-coding
mm_129681.1	chr15	81399796	81399832	-	1	NA	promoter-TSS (NM_133726)	promoter-TSS (NM_133726)	-120	NM_133726	70356	Mm.180337	NM_133726	ENSMUSG00000022403	St13	1110007I03Rik|3110002K08Rik|AW555194|HIP|HOP|HSPABP|HSPABP1|PRO0786|SNC6|p48	suppression of tumorigenicity 13	protein-coding
mm_57976.1	chr6	135721758	135721768	-	1	NA	Intergenic	Intergenic	62850	NR_126088	75024	Mm.399147	NR_126088	ENSMUSG00000107396	4930425L21Rik	4930473P14Rik	RIKEN cDNA 4930425L21 gene	ncRNA
mm_149802.1	chr19	23687664	23687675	+	1	NA	intron (NM_028208, intron 1 of 6)	CpG	269	NM_028208	72351	Mm.474795	NM_028208	ENSMUSG00000074925	Ptar1	1700084D09Rik|2010013L17Rik|4930428J16Rik|AI449677	protein prenyltransferase alpha subunit repeat containing 1	protein-coding
mm_17053.1	chr2	20969572	20969586	-	1	NA	non-coding (NR_033225, exon 2 of 2)	non-coding (NR_033225, exon 2 of 2)	705	NR_033225	433408	Mm.386941	NR_033225		Gm13375	OTTMUSG00000011664	predicted gene 13375	ncRNA
mm_79366.1	chr9	54538985	54538993	+	1	NA	promoter-TSS (NM_173778)	promoter-TSS (NM_173778)	5	NM_173778	244885	Mm.358924	NM_173778	ENSMUSG00000046460	Sh2d7	4933412E14Rik	SH2 domain containing 7	protein-coding
mm_78438.1	chr9	32078232	32078240	+	1	NA	Intergenic	Intergenic	-37900	NM_001195632	330914	Mm.46683	NM_177379	ENSMUSG00000041444	Arhgap32	3426406O18Rik|Gc-gap|Grit|Px-rics|Rics|mKIAA0712|p200Rhogap|p250Gap	Rho GTPase activating protein 32	protein-coding
mm_86570.1	chr10	11492126	11492146	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-117088	NM_013898	30058	Mm.214504	NM_013898	ENSMUSG00000048007	Timm8a1	DXHXS1274E|Ddp1|Fci-12|Tim8a|Timm8a	translocase of inner mitochondrial membrane 8A1	protein-coding
mm_128328.1	chr15	38255292	38255314	-	1	NA	Intergenic	Lx9|LINE|L1	36100	NM_008757	18285	Mm.252830	NM_008757	ENSMUSG00000061923	Odf1	-	outer dense fiber of sperm tails 1	protein-coding
mm_34426.1	chr4	145432422	145432444	+	1	NA	Intergenic	Intergenic	-31777	NR_002888	545700	Mm.389595	NR_002888	ENSMUSG00000052912	Smarca5-ps	9230115A19Rik|OTTMUSG00000011029	SWI/SNF related, matrix associated, actin depenent ragulator of chromatin, subfamily a, member 5, pseudogene	pseudo
mm_135948.1	chr16	74411777	74411792	-	1	NA	promoter-TSS (NM_175549)	promoter-TSS (NM_175549)	-872	NM_175549	268902	Mm.171736	NM_175549	ENSMUSG00000052516	Robo2	2600013A04Rik|9430089E08Rik|BB097918|D230004I22Rik|mKIAA1568	roundabout guidance receptor 2	protein-coding
mm_47321.1	chr5	122465976	122465992	-	1	NA	exon (NM_009722, exon 11 of 21)	exon (NM_009722, exon 11 of 21)	36241	NM_001110140	11938	Mm.227583	NM_009722	ENSMUSG00000029467	Atp2a2	9530097L16Rik|D5Wsu150e|SERCA2|SERCA2B|Serca2a|mKIAA4195	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	protein-coding
mm_7582.1	chr1	125402817	125402839	-	1	NA	intron (NM_001205385, intron 9 of 12)	intron (NM_001205385, intron 9 of 12)	32899	NM_023735	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding
mm_160681.1	chr10	14760112	14760112	+	1	NA	promoter-TSS (NM_008703)	promoter-TSS (NM_008703)	-177	NM_008703	18101	Mm.487342	NM_008703	ENSMUSG00000019865	Nmbr	BB182387	neuromedin B receptor	protein-coding
mm_1852.1	chr1	83836027	83836027	+	1	NA	Intergenic	Intergenic	382934	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_68862.1	chr7	126414834	126414844	-	1	NA	promoter-TSS (NM_009844)	promoter-TSS (NM_009844)	31	NM_009844	12478	Mm.4360	NM_009844	ENSMUSG00000030724	Cd19	AW495831	CD19 antigen	protein-coding
mm_129549.1	chr15	79414716	79414755	-	1	NA	Intergenic	Intergenic	-11432	NM_172608	223693	Mm.323358	NM_172608	ENSMUSG00000009035	Tmem184b	2610507A11|4732495E13Rik	transmembrane protein 184b	protein-coding
mm_86911.1	chr10	22817786	22817796	+	1	NA	exon (NM_011545, exon 2 of 2)	exon (NM_011545, exon 2 of 2)	2337	NM_011545	21412	Mm.16497	NM_011545	ENSMUSG00000045680	Tcf21	Pod-1|Pod1|bHLHa23|capsulin|epc|epicardin	transcription factor 21	protein-coding
mm_62411.1	chr7	101223762	101223771	+	1	NA	intron (NM_199012, intron 8 of 20)	L1_Mur2|LINE|L1	78322	NM_001111111	73683	Mm.275744	NM_001111111	ENSMUSG00000047767	Atg16l2	2410118P20Rik	autophagy related 16-like 2 (S. cerevisiae)	protein-coding
mm_51362.1	chr6	72636245	72636258	+	1	NA	intron (NM_009332, intron 4 of 11)	intron (NM_009332, intron 4 of 11)	6420	NR_040421	100038714	Mm.321330	NR_040421		Gm15401	ENSMUSG00000072999|OTTMUSG00000021199	predicted gene 15401	ncRNA
mm_133982.1	chr16	4558608	4558649	-	1	NA	intron (NM_031182, intron 1 of 6)	CpG	1092	NM_031182	83383	Mm.273210	NM_031182	ENSMUSG00000005718	Tfap4	AI642933|AP-4|D930048N17Rik|Tcfap4|bHLHc41	transcription factor AP4	protein-coding
mm_159522.1	chr4	61594817	61594817	-	1	NA	intron (NM_001200006, intron 2 of 6)	intron (NM_001200006, intron 2 of 6)	1008	NM_001134644	100048885	Mm.422695	NM_001134644		Gm2083	-	major urinary protein LOC100048885	protein-coding
mm_80420.1	chr9	77917186	77917207	+	1	NA	promoter-TSS (NM_134255)	promoter-TSS (NM_134255)	-169	NM_134255	68801	Mm.430736	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	ELOVL family member 5, elongation of long chain fatty acids (yeast)	protein-coding
mm_156965.1	chrX	169990703	169990730	+	1	NA	TTS (NM_001290504)	TTS (NM_001290504)	-11799	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_70903.1	chr8	25640706	25640728	+	1	NA	exon (NM_001081269, exon 1 of 23)	exon (NM_001081269, exon 1 of 23)	140	NM_001081269	234135	Mm.217337	NM_001001735	ENSMUSG00000054823	Whsc1l1	6720429E03|A530023P05|AI528490|NSD3|WHISTLE	Wolf-Hirschhorn syndrome candidate 1-like 1 (human)	protein-coding
mm_72717.1	chr8	85025641	85025649	+	1	NA	promoter-TSS (NM_019652)	promoter-TSS (NM_019652)	-367	NM_019652	56495	Mm.41475	NM_019652	ENSMUSG00000052456	Asna1	1810048H22Rik|ArsA	arsA arsenite transporter, ATP-binding, homolog 1 (bacterial)	protein-coding
mm_100670.1	chr11	3348682	3348696	-	1	NA	intron (NM_173053, intron 10 of 14)	intron (NM_173053, intron 10 of 14)	7452	NM_001034030	16886	Mm.124176	NM_010718	ENSMUSG00000020451	Limk2	Limk-2|whe	LIM motif-containing protein kinase 2	protein-coding
mm_23930.1	chr3	83766980	83766990	+	1	NA	exon (NM_009144, exon 1 of 3)	exon (NM_009144, exon 1 of 3)	664	NM_009144	20319	Mm.19155	NM_009144	ENSMUSG00000027996	Sfrp2	AI851596|Sdf5	secreted frizzled-related protein 2	protein-coding
mm_11796.1	chr2	43555346	43555355	+	1	NA	promoter-TSS (NM_001289593)	promoter-TSS (NM_001289593)	25	NM_027552	70789	Mm.105278	NM_027552	ENSMUSG00000026866	Kynu	4432411A05Rik	kynureninase (L-kynurenine hydrolase)	protein-coding
mm_97715.1	chr11	80183862	80183882	+	1	NA	promoter-TSS (NM_028019)	promoter-TSS (NM_028019)	0	NM_028019	71956	Mm.22985	NM_028019	ENSMUSG00000020707	Rnf135	0610037N03Rik|2410006N06Rik	ring finger protein 135	protein-coding
mm_168899.1	chr12	54729736	54729746	+	1	NA	Intergenic	U1|snRNA|snRNA	-33847	NM_025456	66266	Mm.156440	NM_025456	ENSMUSG00000054302	Eapp	1810011O16Rik	E2F-associated phosphoprotein	protein-coding
mm_25698.1	chr3	122275554	122275580	+	1	NA	exon (NM_153806, exon 2 of 7)	exon (NM_153806, exon 2 of 7)	1153	NM_153806	99480	Mm.398647	NM_153806	ENSMUSG00000039756	Dnttip2	4930588M11Rik|AA408582|AU014960|HSU15552	deoxynucleotidyltransferase, terminal, interacting protein 2	protein-coding
mm_70507.1	chr8	12926193	12926201	+	1	NA	intron (NM_178076, intron 1 of 30)	intron (NM_178076, intron 1 of 30)	10304	NM_178076	17207	Mm.334413	NM_178076	ENSMUSG00000031442	Mcf2l	C130040G20Rik|Dbs|Ost|mKIAA0362	mcf.2 transforming sequence-like	protein-coding
mm_141612.1	chr17	32810697	32810721	-	1	NA	promoter-TSS (NM_001267583)	promoter-TSS (NM_001267583)	-778	NM_183177	240063	Mm.30675	NM_183177	ENSMUSG00000055202	Zfp811	BC052046	zinc finger protein 811	protein-coding
mm_75269.1	chr8	40660418	40660430	-	1	NA	Intergenic	Intergenic	-14653	NM_010086	13526	Mm.67403	NM_010086	ENSMUSG00000046723	Adam24	Dtgn5	a disintegrin and metallopeptidase domain 24 (testase 1)	protein-coding
mm_133937.1	chr16	3884473	3884572	-	1	NA	promoter-TSS (NM_001290689)	promoter-TSS (NM_001290689)	-97	NM_029090	74763	Mm.28403	NM_029090	ENSMUSG00000005982	Naa60	1200013P24Rik|AI315146|Nat15	N(alpha)-acetyltransferase 60, NatF catalytic subunit	protein-coding
mm_147708.1	chr18	60812240	60812262	-	1	NA	TTS (NR_039567)	TTS (NR_039567)	175	NR_039567	100628611		NR_039567	ENSMUSG00000093327	Mir5107	mir-5107|mmu-mir-5107|mu-mir-5107	microRNA 5107	ncRNA
mm_66209.1	chr7	34313490	34313500	-	1	NA	Intergenic	CpG	-27886	NM_172741	233103	Mm.491097	NM_172741	ENSMUSG00000066571	4931406P16Rik	AA553327|mKIAA0355	RIKEN cDNA 4931406P16 gene	protein-coding
mm_172727.1	chr8	75033724	75033726	+	1	NA	promoter-TSS (NM_011622)	promoter-TSS (NM_011622)	39	NM_011622	21968	Mm.1967	NM_011622	ENSMUSG00000042870	Tom1	-	target of myb1 trafficking protein	protein-coding
mm_162904.1	chr10	116177424	116177434	+	1	NA	promoter-TSS (NM_001161838)	promoter-TSS (NM_001161838)	78	NM_001161840	19279	Mm.336316	NM_011217	ENSMUSG00000020151	Ptprr	Gmcp1|PTP-SL|PTPBR7|RPTPRR|mPTP213	protein tyrosine phosphatase, receptor type, R	protein-coding
mm_33192.1	chr4	126260385	126260390	+	1	NA	Intergenic	ID_B1|SINE|B4	-2018	NM_013718	27096	Mm.8392	NM_013718	ENSMUSG00000028847	Trappc3	1110058K12Rik|AI835942|AU019197|Bet3	trafficking protein particle complex 3	protein-coding
mm_63990.1	chr7	140096965	140096978	+	1	NA	TTS (NR_104415)	TTS (NR_104415)	3575	NM_009475	22264	Mm.439707	NM_009475	ENSMUSG00000025467	Prap1	Upa	proline-rich acidic protein 1	protein-coding
mm_149201.1	chr19	9978791	9978803	+	1	NA	Intergenic	Intergenic	-1803	NR_073181	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
mm_26593.1	chr3	151438060	151438074	+	1	NA	intron (NM_133222, intron 1 of 15)	intron (NM_133222, intron 1 of 15)	185	NM_133222	170757	Mm.317261	NM_133222	ENSMUSG00000039167	Adgrl4	1110033N21Rik|ETL1|Eltd1|Etl	adhesion G protein-coupled receptor L4	protein-coding
mm_112902.1	chr13	20899603	20899624	+	1	NA	intron (NM_012054, intron 4 of 20)	intron (NM_012054, intron 4 of 20)	105500	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_77398.1	chr8	120428283	120428287	-	1	NA	Intergenic	Intergenic	-60581	NM_198671	382034	Mm.334856	NM_198671	ENSMUSG00000031822	Gse1	2210013I18Rik|mKIAA0182	genetic suppressor element 1, coiled-coil protein	protein-coding
mm_169421.1	chr1	45311723	45311723	+	1	NA	5' UTR (NM_009930, exon 1 of 51)	5' UTR (NM_009930, exon 1 of 51)	185	NM_009930	12825	Mm.249555	NM_009930	ENSMUSG00000026043	Col3a1	AW550625|Col3a-1|Tsk-2|Tsk2	collagen, type III, alpha 1	protein-coding
mm_100080.1	chr11	115463844	115463852	+	1	NA	intron (NM_001080934, intron 1 of 3)	intron (NM_001080934, intron 1 of 3)	1375	NM_001080934	217316	Mm.25773	NM_001080934	ENSMUSG00000045775	Slc16a5	A130015N09Rik|MCT 5|MCT 6|MCT5	solute carrier family 16 (monocarboxylic acid transporters), member 5	protein-coding
mm_122773.1	chr14	54409371	54409418	-	1	NA	promoter-TSS (NM_001253680)	promoter-TSS (NM_001253680)	78	NM_001253680	20540	Mm.142455	NM_011405	ENSMUSG00000000958	Slc7a7	AI790233|my+lat1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 7	protein-coding
mm_11413.1	chr2	31615515	31615538	+	1	NA	exon (NM_001290548, exon 18 of 19)	exon (NM_001290548, exon 18 of 19)	3105	NR_105964	102466214		NR_105964	ENSMUSG00000098904	Mir6998	Gm28024|mmu-mir-6998	microRNA 6998	ncRNA
mm_72008.1	chr8	70700294	70700298	+	1	NA	3' UTR (NM_001286944, exon 1 of 1)	3' UTR (NM_001286944, exon 1 of 1)	2557	NM_001286944	16478	Mm.419851	NM_010592	ENSMUSG00000071076	Jund	Jund1	jun D proto-oncogene	protein-coding
mm_117696.1	chr13	94295062	94295072	-	1	NA	Intergenic	MTC|LTR|ERVL-MaLR	-9236	NM_001346609	107767	Mm.201455	NM_029153	ENSMUSG00000021687	Scamp1	4930505M11Rik|AI415563|AW122395	secretory carrier membrane protein 1	protein-coding
mm_119209.1	chr14	32991380	32991390	+	1	NA	promoter-TSS (NM_001146021)	promoter-TSS (NM_001146021)	3	NM_026253	67580	Mm.46115	NM_026253	ENSMUSG00000041673	Lrrc18	4930442L21Rik|MTLR1	leucine rich repeat containing 18	protein-coding
mm_170340.1	chr1	84738046	84738050	-	1	NA	intron (NM_133975, intron 32 of 40)	intron (NM_133975, intron 32 of 40)	-41827	NM_152915	227325	Mm.292560	NM_152915	ENSMUSG00000036766	Dner	A930026D19Rik|BET|Bret	delta/notch-like EGF repeat containing	protein-coding
mm_116505.1	chr13	45002046	45002117	-	1	NA	promoter-TSS (NM_025772)	promoter-TSS (NM_025772)	15	NM_025772	94245	Mm.352311	NM_025772	ENSMUSG00000057531	Dtnbp1	5430437B18Rik|AW048963|Bloc1s8|dysbindin|sdy	dystrobrevin binding protein 1	protein-coding
mm_127178.1	chr15	98983408	98983438	+	1	NA	Intergenic	Intergenic	-2542	NR_045991	75951	Mm.441657	NR_045991	ENSMUSG00000097587	4930578M01Rik	3010001K12Rik	RIKEN cDNA 4930578M01 gene	ncRNA
mm_70926.1	chr8	25813037	25813043	+	1	NA	3' UTR (NM_011485, exon 7 of 7)	3' UTR (NM_011485, exon 7 of 7)	4566	NM_011485	20845	Mm.293314	NM_011485	ENSMUSG00000031574	Star	AV363654|D8Ertd419e|stARD1	steroidogenic acute regulatory protein	protein-coding
mm_165233.1	chr2	58780458	58780464	+	1	NA	intron (NM_001289660, intron 7 of 7)	intron (NM_001289660, intron 7 of 7)	25277	NM_029692	76654	Mm.200370	NM_029692	ENSMUSG00000026839	Upp2	1700124F02Rik|AI266885|UDRPASE2|UP2|UPASE2	uridine phosphorylase 2	protein-coding
mm_156029.1	chrX	107255773	107255782	+	1	NA	promoter-TSS (NM_001177781)	promoter-TSS (NM_001177781)	-101	NM_001177781	213439	Mm.383562	NM_001033251	ENSMUSG00000073008	Gpr174	Gm376|Lypsr3	G protein-coupled receptor 174	protein-coding
mm_21686.1	chr2	164431290	164431308	-	1	NA	exon (NM_011521, exon 2 of 5)	exon (NM_011521, exon 2 of 5)	11889	NM_011521	20971	Mm.3815	NM_011521	ENSMUSG00000017009	Sdc4	AA959608|AW108331|S4|Synd4|ryudocan|syndecan-4	syndecan 4	protein-coding
mm_148708.1	chr19	5802104	5802137	+	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	552	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_24776.1	chr3	95536903	95536920	+	1	NA	intron (NM_001267695, intron 2 of 7)	intron (NM_001267695, intron 2 of 7)	10125	NM_001267695	13040	Mm.3619	NM_021281	ENSMUSG00000038642	Ctss	Cats	cathepsin S	protein-coding
mm_28173.1	chr3	88000189	88000193	-	1	NA	5' UTR (NM_001109758, exon 1 of 8)	5' UTR (NM_001109758, exon 1 of 8)	165	NM_007529	12032	Mm.4598	NM_007529	ENSMUSG00000004892	Bcan	Cspg7	brevican	protein-coding
mm_130674.1	chr15	100675355	100675362	-	1	NA	exon (NM_033612, exon 7 of 8)	exon (NM_033612, exon 7 of 8)	-5858	NM_001270537	668218	Mm.451225	NM_001270537	ENSMUSG00000098112	Bin2	-	bridging integrator 2	protein-coding
mm_70089.1	chr7	142656037	142656058	-	1	NA	intron (NM_001315488, intron 1 of 3)	intron (NM_001315488, intron 1 of 3)	-1051	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_57150.1	chr6	122729497	122729544	-	1	NA	3' UTR (NM_011401, exon 10 of 10)	3' UTR (NM_011401, exon 10 of 10)	13225	NM_011401	20527	Mm.395108	NM_011401	ENSMUSG00000003153	Slc2a3	AA408729|AL023014|AL024341|AU040424|C78366|Glut-3|Glut3	solute carrier family 2 (facilitated glucose transporter), member 3	protein-coding
mm_983.1	chr1	58445260	58445307	+	1	NA	5' UTR (NM_027374, exon 1 of 6)	5' UTR (NM_027374, exon 1 of 6)	132	NM_022988	65102	Mm.340248	NM_022988	ENSMUSG00000026036	Nif3l1	1110030G24Rik	Ngg1 interacting factor 3-like 1 (S. pombe)	protein-coding
mm_134880.1	chr16	28930157	28930191	-	1	NA	promoter-TSS (NM_177718)	promoter-TSS (NM_177718)	-476	NM_177718	239796	Mm.155887	NM_177718	ENSMUSG00000051065	Mb21d2	1600021P15Rik|A430031N04|C87006	Mab-21 domain containing 2	protein-coding
mm_142970.1	chr17	56133786	56133797	-	1	NA	promoter-TSS (NM_013662)	promoter-TSS (NM_013662)	61	NM_013662	20359	Mm.8029	NM_013662	ENSMUSG00000001227	Sema6b	Sema|Seman|VIb|semaZ	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B	protein-coding
mm_123351.1	chr14	63142413	63142427	-	1	NA	3' UTR (NM_007798, exon 10 of 10)	3' UTR (NM_007798, exon 10 of 10)	19958	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_5160.1	chr1	10009162	10009166	-	1	NA	promoter-TSS (NM_145692)	promoter-TSS (NM_145692)	-28	NM_145692	69312	Mm.386795	NM_027033	ENSMUSG00000025916	Ppp1r42	1700011J18Rik|4930418G15Rik|Lrrc67|TLRR	protein phosphatase 1, regulatory subunit 42	protein-coding
mm_132117.1	chr16	31664186	31664188	+	1	NA	non-coding (NR_045516, exon 1 of 25)	non-coding (NR_045516, exon 1 of 25)	252	NM_001252434	13383	Mm.382	NM_007862	ENSMUSG00000022770	Dlg1	B130052P05Rik|Dlgh1|E-dlg/SAP97|SAP-97|SAP97|mKIAA4187	discs, large homolog 1 (Drosophila)	protein-coding
mm_20972.1	chr2	151973355	151973372	-	1	NA	promoter-TSS (NM_001289151)	promoter-TSS (NM_001289151)	31	NM_001289151	73847	Mm.272444	NM_028666	ENSMUSG00000027459	Fam110a	1700008J10Rik|5430432M24Rik|AI747080	family with sequence similarity 110, member A	protein-coding
mm_191.1	chr1	15803255	15803264	+	1	NA	Intergenic	RLTR11D|LTR|ERVK	-2387	NM_009352	21749	Mm.4306	NM_009352	ENSMUSG00000025925	Terf1	Pin2|Trbf1|Trf1	telomeric repeat binding factor 1	protein-coding
mm_94417.1	chr11	5863979	5864003	+	1	NA	exon (NM_009636, exon 2 of 21)	exon (NM_009636, exon 2 of 21)	2125	NM_001291857	11568	Mm.3317	NM_009636	ENSMUSG00000020473	Aebp1	ACLP	AE binding protein 1	protein-coding
mm_106923.1	chr12	8332219	8332228	+	1	NA	intron (NM_021429, intron 4 of 6)	intron (NM_021429, intron 4 of 6)	18790	NM_021429	58240	Mm.309954	NM_021429	ENSMUSG00000020605	Hs1bp3	-	HCLS1 binding protein 3	protein-coding
mm_108383.1	chr12	80878478	80878488	+	1	NA	3' UTR (NM_178682, exon 6 of 6)	3' UTR (NM_178682, exon 6 of 6)	45964	NR_033786	67340	Mm.386790	NR_033786	ENSMUSG00000101912	1700052I22Rik	-	RIKEN cDNA 1700052I22 gene	ncRNA
mm_111437.1	chr12	93273737	93273746	-	1	NA	Intergenic	Intergenic	171082	NR_126436	75295	Mm.243878	NR_126436		4930559C10Rik	-	RIKEN cDNA 4930559C10 gene	ncRNA
mm_843.1	chr1	51747099	51747127	+	1	NA	Intergenic	(CACG)n|Simple_repeat|Simple_repeat	168865	NM_001290982	17912	Mm.3390	NM_010863	ENSMUSG00000018417	Myo1b	AA406997|MIH-L|MMIa	myosin IB	protein-coding
mm_11731.1	chr2	37452232	37452286	+	1	NA	promoter-TSS (NM_001033960)	promoter-TSS (NM_001033960)	5	NM_001033960	227800	Mm.383192	NM_146121	ENSMUSG00000035437	Rabgap1	Gapcena|mKIAA4104	RAB GTPase activating protein 1	protein-coding
mm_172965.1	chr9	88833689	88833695	+	1	NA	Intergenic	B1_Mus1|SINE|Alu	-5472	NM_001177858	666731	Mm.446951	NM_001177858	ENSMUSG00000067399	Trim43c	EG666731|Trim43	tripartite motif-containing 43C	protein-coding
mm_70491.1	chr8	12572821	12572831	+	1	NA	promoter-TSS (NM_024279)	promoter-TSS (NM_024279)	-223	NM_024279	78634	Mm.116871	NM_024279	ENSMUSG00000010435	Spaca7	1700094C09Rik	sperm acrosome associated 7	protein-coding
mm_60723.1	chr7	45336904	45336943	+	1	NA	exon (NM_010473, exon 1 of 6)	exon (NM_010473, exon 1 of 6)	1654	NM_010473	15464	Mm.39968	NM_010473	ENSMUSG00000038239	Hrc	-	histidine rich calcium binding protein	protein-coding
mm_92365.1	chr10	75940604	75940623	-	1	NA	promoter-TSS (NM_001277132)	promoter-TSS (NM_001277132)	59	NM_001277132	333670	Mm.291320	NM_001037714	ENSMUSG00000050157	Gm867	Gm736	predicted gene 867	protein-coding
mm_85226.1	chr9	97111028	97111067	-	1	NA	promoter-TSS (NM_138756)	promoter-TSS (NM_138756)	-6	NM_138756	192287	Mm.228067	NM_138756	ENSMUSG00000032449	Slc25a36	C330005L02Rik	solute carrier family 25, member 36	protein-coding
mm_147935.1	chr18	66019960	66019991	-	1	NA	Intergenic	Intergenic	-17340	NM_001172062	70361	Mm.290857	NM_027400	ENSMUSG00000041891	Lman1	2610020P13Rik|AI326273|AU043785|C730041J05|ERGIC53|F5F8D|MCFD1|MR60|P58|gp58	lectin, mannose-binding, 1	protein-coding
mm_95646.1	chr11	53723769	53723790	+	1	NA	exon (NM_010558, exon 3 of 4)	exon (NM_010558, exon 3 of 4)	2985	NM_010558	16191	Mm.4461	NM_010558	ENSMUSG00000036117	Il5	Il-5	interleukin 5	protein-coding
mm_48792.1	chr5	148746810	148746821	-	1	NA	Intergenic	RLTR44D|LTR|ERVK	4975	NR_028285	70138	Mm.417834	NR_028285	ENSMUSG00000086494	2210417A02Rik	AV081004	RIKEN cDNA 2210417A02 gene	ncRNA
mm_123840.1	chr14	70642263	70642285	-	1	NA	promoter-TSS (NM_008004)	promoter-TSS (NM_008004)	-6	NM_008004	14171	Mm.12814	NM_008004	ENSMUSG00000022101	Fgf17	-	fibroblast growth factor 17	protein-coding
mm_125302.1	chr15	37233287	37233306	+	1	NA	5' UTR (NM_026496, exon 1 of 16)	5' UTR (NM_026496, exon 1 of 16)	260	NM_026496	252973	Mm.244612	NM_026496	ENSMUSG00000022286	Grhl2	0610015A08Rik|BOM|Tcfcp2l3|clft3	grainyhead-like 2 (Drosophila)	protein-coding
mm_43248.1	chr5	130171814	130171879	+	1	NA	promoter-TSS (NM_001199059)	promoter-TSS (NM_001199059)	27	NM_001199059	56715	Mm.288639	NM_019983	ENSMUSG00000025340	Rabgef1	Rab5ef|Rabex5|Rin2	RAB guanine nucleotide exchange factor (GEF) 1	protein-coding
mm_24542.1	chr3	93293109	93293119	+	1	NA	Intergenic	Intergenic	-26635	NM_133698	68723	Mm.208047	NM_133698	ENSMUSG00000041991	Hrnr	1110033K19Rik|A530063N20Rik|S100a18	hornerin	protein-coding
mm_143149.1	chr17	57222872	57222886	-	1	NA	exon (NM_009778, exon 13 of 41)	exon (NM_009778, exon 13 of 41)	5257	NM_009778	12266	Mm.19131	NM_009778	ENSMUSG00000024164	C3	AI255234|ASP|HSE-MSF|Plp	complement component 3	protein-coding
mm_9613.1	chr1	176213959	176213967	-	1	NA	promoter-TSS (NM_001195816)	promoter-TSS (NM_001195816)	-21	NM_001195816	319455	Mm.338001	NM_176916	ENSMUSG00000055214	Pld5	B230365F16Rik	phospholipase D family, member 5	protein-coding
mm_12995.1	chr2	90885877	90885902	+	1	NA	5' UTR (NM_026161, exon 1 of 2)	5' UTR (NM_026161, exon 1 of 2)	103	NM_026161	67445	Mm.258993	NM_026161	ENSMUSG00000040794	C1qtnf4	0710001E10Rik|9430004J15Rik|CTRP4	C1q and tumor necrosis factor related protein 4	protein-coding
mm_23015.1	chr3	34560345	34560350	+	1	NA	promoter-TSS (NR_015580)	promoter-TSS (NR_015580)	-34	NR_015580	320478	Mm.444063	NR_015580	ENSMUSG00000105265	Sox2ot	B230215L15Rik	SOX2 overlapping transcript (non-protein coding)	ncRNA
mm_149340.1	chr19	10850372	10850382	+	1	NA	intron (NM_023044, intron 2 of 7)	MTD|LTR|ERVL-MaLR	7833	NM_023044	65221	Mm.27387	NM_023044	ENSMUSG00000024737	Slc15a3	Ci1|cI-1	solute carrier family 15, member 3	protein-coding
mm_125251.1	chr15	35200932	35200974	+	1	NA	Intergenic	Intergenic	-45147	NM_019635	56274	Mm.262330	NM_019635	ENSMUSG00000022329	Stk3	0610042I06Rik|MST|Mst2|Mst3|Ste20|mess1	serine/threonine kinase 3	protein-coding
mm_131697.1	chr16	20695042	20695091	+	1	NA	promoter-TSS (NM_133778)	promoter-TSS (NM_133778)	9	NM_133778	78408	Mm.196512	NM_133778	ENSMUSG00000050821	Fam131a	2900046G09Rik	family with sequence similarity 131, member A	protein-coding
mm_66525.1	chr7	45126943	45126946	-	1	NA	promoter-TSS (NR_039581)	promoter-TSS (NR_039581)	1	NR_001277	27208		NR_001277	ENSMUSG00000065628	Snord33	Rnu33|U33	small nucleolar RNA, C/D box 33	snoRNA
mm_69010.1	chr7	126704180	126704195	-	1	NA	promoter-TSS (NM_001301374)	promoter-TSS (NM_001301374)	33	NM_001301374	12721	Mm.290482	NM_009898	ENSMUSG00000030707	Coro1a	Clabp|Lmb3|TACO|p57	coronin, actin binding protein 1A	protein-coding
mm_135123.1	chr16	35841608	35841638	-	1	NA	exon (NM_001039530, exon 13 of 17)	exon (NM_001039530, exon 13 of 17)	29759	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_38289.1	chr4	136890418	136890422	-	1	NA	exon (NM_007574, exon 3 of 3)	exon (NM_007574, exon 3 of 3)	2494	NM_007574	12262	Mm.439732	NM_007574	ENSMUSG00000036896	C1qc	AI385742|C1qg|Ciqc	complement component 1, q subcomponent, C chain	protein-coding
mm_96622.1	chr11	69126219	69126249	+	1	NA	promoter-TSS (NM_011786)	promoter-TSS (NM_011786)	-143	NM_011786	23801	Mm.41989	NM_011786	ENSMUSG00000020892	Aloxe3	e-LOX-3|eLOX-3	arachidonate lipoxygenase 3	protein-coding
mm_50648.1	chr6	51464467	51464512	+	1	NA	exon (NM_016806, exon 8 of 11)	exon (NM_016806, exon 8 of 11)	5405	NM_182650	53379	Mm.155896	NM_016806	ENSMUSG00000004980	Hnrnpa2b1	9130414A06Rik|Hnrpa2|Hnrpa2b1|hnrnp-A	heterogeneous nuclear ribonucleoprotein A2/B1	protein-coding
mm_118476.1	chr14	11618626	11618629	+	1	NA	intron (NM_008981, intron 1 of 29)	MTD|LTR|ERVL-MaLR	65074	NM_008981	19270	Mm.431266	NM_008981	ENSMUSG00000021745	Ptprg	5430405N12Rik|AW046354|AW549872|RPTPgamma	protein tyrosine phosphatase, receptor type, G	protein-coding
mm_121824.1	chr14	20479863	20479869	-	1	NA	5' UTR (NM_009674, exon 1 of 13)	5' UTR (NM_009674, exon 1 of 13)	267	NM_001110794	11750	Mm.280231	NM_009674	ENSMUSG00000021814	Anxa7	AI265384|AI316497|Anx7|synexin	annexin A7	protein-coding
mm_36877.1	chr4	107177807	107177848	-	1	NA	promoter-TSS (NM_029565)	promoter-TSS (NM_029565)	539	NM_025617	66526	Mm.246956	NM_025617	ENSMUSG00000028619	Tceanc2	2210010B22Rik|2210012G02Rik|6330404A07Rik|AU015593|Tdeanc2	transcription elongation factor A (SII) N-terminal and central domain containing 2	protein-coding
mm_77593.1	chr8	123891925	123891944	-	1	NA	3' UTR (NM_009606, exon 7 of 7)	3' UTR (NM_009606, exon 7 of 7)	2841	NM_001272041	11459	Mm.214950	NM_009606	ENSMUSG00000031972	Acta1	AA959943|Acta-2|Acts|Actsk-1	actin, alpha 1, skeletal muscle	protein-coding
mm_156542.1	chrX	151169621	151169659	+	1	NA	Intergenic	CpG	-28438	NM_001271679	279561	Mm.441474	NM_001271678	ENSMUSG00000041245	Wnk3	Prkwnk3|Wnk3-ps	WNK lysine deficient protein kinase 3	protein-coding
mm_57813.1	chr6	129462446	129462458	-	1	NA	non-coding (NR_132130, exon 6 of 6)	non-coding (NR_132130, exon 6 of 6)	10327	NM_001309637	56644	Mm.239516	NM_020008	ENSMUSG00000079293	Clec7a	BGR|Clecsf12|beta-GR	C-type lectin domain family 7, member a	protein-coding
mm_152072.1	chr19	6571578	6571586	-	1	NA	Intergenic	RMER19B|LTR|ERVK	-28512	NM_009203	20521	Mm.391146	NM_009203	ENSMUSG00000061742	Slc22a12	AI987855|OAT4L|Rst|Slc22al2|URAT1	solute carrier family 22 (organic anion/cation transporter), member 12	protein-coding
mm_165938.1	chr4	74826208	74826209	+	1	NA	Intergenic	L1_Mus4|LINE|L1	452078	NM_025849	66928	Mm.24332	NM_025849	ENSMUSG00000028398	Tmem261	1700027K24Rik|3110001D03Rik	transmembrane protein 261	protein-coding
mm_124556.1	chr14	122913752	122913764	-	1	NA	promoter-TSS (NM_145466)	promoter-TSS (NM_145466)	-593	NM_145466	223267	Mm.379358	NM_145466	ENSMUSG00000041625	Ggact	A2ld1	gamma-glutamylamine cyclotransferase	protein-coding
mm_49572.1	chr6	30640673	30640715	+	1	NA	exon (NM_025350, exon 3 of 10)	exon (NM_025350, exon 3 of 10)	1476	NM_025350	109697	Mm.25377	NM_025350	ENSMUSG00000054446	Cpa1	0910001L12Rik|Cpa	carboxypeptidase A1, pancreatic	protein-coding
mm_117099.1	chr13	59823049	59823057	-	1	NA	promoter-TSS (NM_153538)	promoter-TSS (NM_153538)	94	NM_153538	214290	Mm.233082	NM_153538	ENSMUSG00000035248	Zcchc6	6030448M23Rik|AA420405	zinc finger, CCHC domain containing 6	protein-coding
mm_153663.1	chr19	44395783	44395787	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	11924	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_149878.1	chr19	25236991	25237007	+	1	NA	promoter-TSS (NM_181404)	promoter-TSS (NM_181404)	-203	NM_181404	107351	Mm.260722	NM_181404	ENSMUSG00000032702	Kank1	A930031B09Rik|AU015049|AW121052|Ankrd15|D330024H06Rik|mKIAA0172	KN motif and ankyrin repeat domains 1	protein-coding
mm_107160.1	chr12	24575827	24575829	+	1	NA	intron (NM_001161406, intron 1 of 15)	intron (NM_001161406, intron 1 of 15)	3541	NM_001161406	195733	Mm.263068	NM_145890	ENSMUSG00000020656	Grhl1	LBP-32|MGR|Tcfcp2l2	grainyhead-like 1 (Drosophila)	protein-coding
mm_94926.1	chr11	29526424	29526474	+	1	NA	promoter-TSS (NM_001282119)	promoter-TSS (NM_001282119)	52	NM_133767	76784	Mm.285429	NM_133767	ENSMUSG00000020459	Mtif2	2310038D14Rik|2410112O06Rik|IF-2(Mt)|IF-2mt|IF2(mt)	mitochondrial translational initiation factor 2	protein-coding
mm_78801.1	chr9	44047573	44047583	+	1	NA	3' UTR (NM_009382, exon 4 of 4)	3' UTR (NM_009382, exon 4 of 4)	4194	NM_009382	21838	Mm.3951	NM_009382	ENSMUSG00000032011	Thy1	CD90|T25|Thy-1|Thy-1.2|Thy1.1|Thy1.2	thymus cell antigen 1, theta	protein-coding
mm_163969.1	chr14	55116414	55116416	-	1	NA	5' UTR (NM_177049, exon 1 of 6)	5' UTR (NM_177049, exon 1 of 6)	520	NM_177049	319984	Mm.19047	NM_177049	ENSMUSG00000022208	Jph4	9330157P13Rik|JP-4|JPHL1	junctophilin 4	protein-coding
mm_103142.1	chr11	70239208	70239219	-	1	NA	intron (NM_173742, intron 1 of 2)	intron (NM_173742, intron 1 of 2)	639	NM_173742	52898	Mm.29852	NM_173742	ENSMUSG00000040904	Rnasek	2310033H11Rik|AA571397|D11Bwg0434e	ribonuclease, RNase K	protein-coding
mm_103005.1	chr11	69695803	69695872	-	1	NA	5' UTR (NM_001159503, exon 1 of 13)	5' UTR (NM_001159503, exon 1 of 13)	261	NM_011614	21944	Mm.8983	NM_011614	ENSMUSG00000097328	Tnfsf12	Apo3l|Dr3l|Dr3lg|Tweak	tumor necrosis factor (ligand) superfamily, member 12	protein-coding
mm_21914.1	chr2	166695754	166695757	-	1	NA	intron (NR_105783, intron 2 of 2)	B4|SINE|B4	18077	NM_177782	277360	Mm.34420	NM_177782	ENSMUSG00000039621	Prex1	G630042G04|P-REX1|Setd6	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	protein-coding
mm_85518.1	chr9	106438332	106438391	-	1	NA	promoter-TSS (NM_001276442)	promoter-TSS (NM_001276442)	-125	NM_001276442	109652	Mm.7165	NM_025371	ENSMUSG00000023262	Acy1	1110014J22Rik|Acy-1	aminoacylase 1	protein-coding
mm_130700.1	chr15	100687119	100687126	-	1	NA	intron (NM_033612, intron 2 of 7)	intron (NM_033612, intron 2 of 7)	798	NM_033612	109901	Mm.2131	NM_033612	ENSMUSG00000023031	Cela1	1810009A17Rik|1810062B19Rik|Ela-1|Ela1|PC-TsF	chymotrypsin-like elastase family, member 1	protein-coding
mm_140902.1	chr17	24150867	24150881	-	1	NA	promoter-TSS (NM_001286662)	promoter-TSS (NM_001286662)	48	NM_001286662	18607	Mm.10504	NM_011062	ENSMUSG00000024122	Pdpk1	Pdk1	3-phosphoinositide dependent protein kinase 1	protein-coding
mm_103035.1	chr11	69758362	69758392	-	1	NA	5' UTR (NM_001291068, exon 1 of 29)	5' UTR (NM_001291068, exon 1 of 29)	256	NM_001291068	20020	Mm.16533	NM_009089	ENSMUSG00000005198	Polr2a	220kDa|Rpb1|Rpo2-1	polymerase (RNA) II (DNA directed) polypeptide A	protein-coding
mm_77439.1	chr8	121590300	121590345	-	1	NA	promoter-TSS (NM_026160)	promoter-TSS (NM_026160)	-146	NM_026160	67443	Mm.28357	NM_026160	ENSMUSG00000031812	Map1lc3b	1010001C15Rik|Atg8|LC3b|Map1lc3	microtubule-associated protein 1 light chain 3 beta	protein-coding
mm_120774.1	chr14	73879501	73879535	+	1	NA	Intergenic	Intergenic	326732	NM_011506	20916	Mm.38951	NM_011506	ENSMUSG00000022110	Sucla2	4930547K18Rik|A-SCS	succinate-Coenzyme A ligase, ADP-forming, beta subunit	protein-coding
mm_138965.1	chr17	44735768	44735783	+	1	NA	non-coding (NR_073425, exon 1 of 6)	non-coding (NR_073425, exon 1 of 6)	401	NR_073425	12393	Mm.391013	NM_009820	ENSMUSG00000039153	Runx2	AML3|Cbf|Cbfa-1|Cbfa1|LS3|Osf2|PEBP2aA|Pebp2a1|Pebpa2a	runt related transcription factor 2	protein-coding
mm_58606.1	chr7	5056707	5056741	+	1	NA	promoter-TSS (NM_146178)	promoter-TSS (NM_146178)	-2	NM_001290432	232821	Mm.482157	NM_146178	ENSMUSG00000035228	Ccdc106	BC018462	coiled-coil domain containing 106	protein-coding
mm_49936.1	chr6	39573859	39573887	+	1	NA	promoter-TSS (NM_178873)	promoter-TSS (NM_178873)	-3	NM_178873	57869	Mm.247957	NM_178873	ENSMUSG00000046947	Adck2	AA408112|BB006057	aarF domain containing kinase 2	protein-coding
mm_99458.1	chr11	102435062	102435075	+	1	NA	exon (NM_008175, exon 9 of 13)	exon (NM_008175, exon 9 of 13)	4746	NM_008175	14824	Mm.1568	NM_008175	ENSMUSG00000034708	Grn	Pgrn|epithelin	granulin	protein-coding
mm_26208.1	chr3	138733491	138733514	+	1	NA	Intergenic	Intergenic	-6518	NR_040545	74635	Mm.410825	NR_040545	ENSMUSG00000105838	4930425O10Rik	-	RIKEN cDNA 4930425O10 gene	ncRNA
mm_49702.1	chr6	34354126	34354151	+	1	NA	promoter-TSS (NM_008012)	promoter-TSS (NM_008012)	-26	NM_008012	14187	Mm.5378	NM_008012	ENSMUSG00000029762	Akr1b8	FR-1|Fgfrp|Fgrp	aldo-keto reductase family 1, member B8	protein-coding
mm_59668.1	chr7	28376727	28376738	+	1	NA	TTS (NM_011756)	TTS (NM_011756)	2496	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_22939.1	chr3	31902649	31902659	+	1	NA	promoter-TSS (NM_028231)	promoter-TSS (NM_028231)	-49	NM_028231	72413	Mm.64790	NM_028231	ENSMUSG00000037610	Kcnmb2	2700049B16Rik|3110031N04Rik	potassium large conductance calcium-activated channel, subfamily M, beta member 2	protein-coding
mm_69659.1	chr7	139978710	139978747	-	1	NA	promoter-TSS (NM_001033465)	promoter-TSS (NM_001033465)	27	NM_001347614	381933	Mm.440431	NM_001033465	ENSMUSG00000073795	6430531B16Rik	Gm1093	RIKEN cDNA 6430531B16 gene	protein-coding
mm_84791.1	chr9	77045789	77045824	-	1	NA	promoter-TSS (NM_012033)	promoter-TSS (NM_012033)	-25	NM_012033	26944	Mm.23199	NM_012033	ENSMUSG00000032357	Tinag	AI452335|TIN-ag	tubulointerstitial nephritis antigen	protein-coding
mm_142272.1	chr17	39847835	39847861	-	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	4851	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_88226.1	chr10	70440677	70440720	+	1	NA	promoter-TSS (NM_001143777)	promoter-TSS (NM_001143777)	30	NM_001143777	71721	Mm.477813	NM_024244	ENSMUSG00000043259	Fam13c	1200015N20Rik|C030038O19Rik|mKIAA1796	family with sequence similarity 13, member C	protein-coding
mm_101629.1	chr11	36169062	36169065	-	1	NA	intron (NM_011856, intron 8 of 28)	intron (NM_011856, intron 8 of 28)	-188974	NM_170779	211652	Mm.31267	NM_170779	ENSMUSG00000018849	Wwc1	AA408228|AU017197|BC037006|Kibra|mKIAA0869	WW, C2 and coiled-coil domain containing 1	protein-coding
mm_33352.1	chr4	129382686	129382706	+	1	NA	Intergenic	RMER15|LTR|ERVL	-4668	NM_028603	73680	Mm.32997	NM_028603	ENSMUSG00000028807	Zbtb8a	2410081M15Rik|AI480941	zinc finger and BTB domain containing 8a	protein-coding
mm_18764.1	chr2	73459668	73459682	-	1	NA	intron (NM_153138, intron 1 of 7)	L2b|LINE|L2	-5786	NM_001289722	215280	Mm.223504	NM_153138	ENSMUSG00000075284	Wipf1	AI115543|D2Ertd120e|WIP|Waspip	WAS/WASL interacting protein family, member 1	protein-coding
mm_70071.1	chr7	142653073	142653101	-	1	NA	3' UTR (NM_010514, exon 4 of 4)	3' UTR (NM_010514, exon 4 of 4)	1909	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_26373.1	chr3	142561685	142561746	+	1	NA	intron (NM_001289492, intron 2 of 11)	intron (NM_001289492, intron 2 of 11)	1219	NM_001289493	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_42592.1	chr5	117363514	117363552	+	1	NA	intron (NM_021539, intron 1 of 8)	intron (NM_021539, intron 1 of 8)	6228	NM_021539	59043	Mm.28489	NM_021539	ENSMUSG00000029364	Wsb2	AA673511|Swip2|WSB-2	WD repeat and SOCS box-containing 2	protein-coding
mm_89661.1	chr10	97483408	97483416	+	1	NA	exon (NM_007833, exon 2 of 8)	exon (NM_007833, exon 2 of 8)	1081	NM_007833	13179	Mm.56769	NM_007833	ENSMUSG00000019929	Dcn	DC|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding
mm_157308.1	chrX	20931496	20931517	-	1	NA	promoter-TSS (NM_008823)	promoter-TSS (NM_008823)	49	NM_008823	18636	Mm.3064	NM_008823	ENSMUSG00000001128	Cfp	BCFG|Pfc	complement factor properdin	protein-coding
mm_11955.1	chr2	52982749	52982749	+	1	NA	intron (NM_172409, intron 1 of 26)	intron (NM_172409, intron 1 of 26)	124881	NM_172409	71409	Mm.394427	NM_172409	ENSMUSG00000036053	Fmnl2	5430425K04Rik|Man	formin-like 2	protein-coding
mm_53912.1	chr6	3988901	3988941	-	1	NA	promoter-TSS (NR_138566)	promoter-TSS (NR_138566)	-63	NR_138566	21789	Mm.25612	NM_009364	ENSMUSG00000029664	Tfpi2	AV000670|PP5/TFPI-2	tissue factor pathway inhibitor 2	protein-coding
mm_86430.1	chr10	3863690	3863706	+	1	NA	intron (NM_001159942, intron 2 of 16)	intron (NM_001159942, intron 2 of 16)	-8969	NM_001033253	213783	Mm.150831	NM_001033253	ENSMUSG00000040624	Plekhg1	D10Ertd733e|Gm521|mKIAA1209	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	protein-coding
mm_75382.1	chr8	45382199	45382214	-	1	NA	promoter-TSS (NM_153535)	promoter-TSS (NM_153535)	85	NM_153535	212326	Mm.51259	NM_153535	ENSMUSG00000070044	Fam149a	AW213256|mKIAA4166	family with sequence similarity 149, member A	protein-coding
mm_130498.1	chr15	98808307	98808318	-	1	NA	promoter-TSS (NM_001013741)	promoter-TSS (NM_001013741)	-387	NM_001013741	13199	Mm.390810	NM_001013741	ENSMUSG00000059213	Ddn	Gm748	dendrin	protein-coding
mm_139540.1	chr17	56710065	56710071	+	1	NA	intron (NR_045519, intron 14 of 16)	intron (NR_045519, intron 14 of 16)	6853	NM_178926	106639	Mm.37290	NM_178926	ENSMUSG00000054723	Vmac	AI662250	vimentin-type intermediate filament associated coiled-coil protein	protein-coding
mm_55740.1	chr6	77511842	77511845	-	1	NA	intron (NM_001109764, intron 8 of 19)	intron (NM_001109764, intron 8 of 19)	-129368	NR_045141	70753	Mm.490700	NR_045141	ENSMUSG00000108077	6330415B21Rik	-	RIKEN cDNA 6330415B21 gene	ncRNA
mm_18915.1	chr2	76737000	76737014	-	1	NA	exon (NM_011652, exon 275 of 313)	exon (NM_011652, exon 275 of 313)	61692	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_100548.1	chr11	120713920	120713965	+	1	NA	promoter-TSS (NM_016665)	promoter-TSS (NM_016665)	-11	NM_153545	217366	Mm.347545	NM_153545	ENSMUSG00000025145	Lrrc45	BC023296	leucine rich repeat containing 45	protein-coding
mm_65046.1	chr7	18616499	18616507	-	1	NA	promoter-TSS (NM_020261)	promoter-TSS (NM_020261)	-2	NM_020261	56868	Mm.333617	NM_020261	ENSMUSG00000074359	Psg23	1620401C02Rik|cea11	pregnancy-specific glycoprotein 23	protein-coding
mm_53890.1	chr6	3377014	3377106	-	1	NA	exon (NM_010156, exon 2 of 2)	exon (NM_010156, exon 2 of 2)	22511	NM_010156	209086	Mm.196013	NM_010156	ENSMUSG00000047735	Samd9l	AA175286|ESTM25|mKIAA2005	sterile alpha motif domain containing 9-like	protein-coding
mm_37837.1	chr4	132053460	132053465	-	1	NA	intron (NM_183428, intron 1 of 20)	L1M5|LINE|L1	-4384	NM_001128606	269587	Mm.30038	NM_183428	ENSMUSG00000028906	Epb41	4.1R|AI415518|D4Ertd442e|Elp-1|Elp1|Epb4.1|mKIAA4056	erythrocyte membrane protein band 4.1	protein-coding
mm_158381.1	chrX	135720628	135720641	-	1	NA	promoter-TSS (NM_030106)	promoter-TSS (NM_030106)	39	NM_030106	78478	Mm.391317	NM_030106	ENSMUSG00000060726	Tmsb15a	1700129I15Rik|Tb15a|Tmsbl1|Tmsl8	thymosin beta 15a	protein-coding
mm_71113.1	chr8	35999862	35999867	+	1	NA	Intergenic	L2|LINE|L2	-94964	NM_172911	244418	Mm.244971	NM_172911	ENSMUSG00000050271	Prag1	9830148H23|D8Ertd82e|NACK|Sgk223|mFLJ00269	PEAK1 related kinase activating pseudokinase 1	protein-coding
mm_91425.1	chr10	32890002	32890027	-	1	NA	promoter-TSS (NM_001025286)	promoter-TSS (NM_001025286)	-99	NM_001025286	432450	Mm.49665	NM_001013411	ENSMUSG00000069670	Nkain2	6330571D19Rik|AW455467|Tcba1	Na+/K+ transporting ATPase interacting 2	protein-coding
mm_50577.1	chr6	49052926	49052948	+	1	NA	intron (NM_053110, intron 9 of 10)	B4|SINE|B4	16419	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_94246.1	chr11	3330669	3330694	+	1	NA	promoter-TSS (NM_178149)	promoter-TSS (NM_178149)	-50	NM_178149	216505	Mm.390323	NM_178149	ENSMUSG00000034614	Pik3ip1	1500004A08Rik|5830455E04Rik|Crkd|Hgfl	phosphoinositide-3-kinase interacting protein 1	protein-coding
mm_23028.1	chr3	34649988	34650005	+	1	NA	promoter-TSS (NM_011443)	promoter-TSS (NM_011443)	1	NM_011443	20674	Mm.65396	NM_011443	ENSMUSG00000074637	Sox2	Sox-2|lcc|ysb	SRY (sex determining region Y)-box 2	protein-coding
mm_125903.1	chr15	75969288	75969312	+	1	NA	promoter-TSS (NM_001347040)	promoter-TSS (NM_001347040)	18	NM_001347040	69020	Mm.294295	NM_001081065	ENSMUSG00000034429	Zfp707	1500031N24Rik|AI451708|AW495315	zinc finger protein 707	protein-coding
mm_136562.1	chr17	3199602	3199605	+	1	NA	TTS (NM_134123)	TTS (NM_134123)	84631	NM_134123	106583	Mm.124373	NM_134123	ENSMUSG00000046201	Scaf8	A630086M08Rik|A930036P18Rik|AA408306|AI447644|AI448652|AU015035|Rbm16|mKIAA1116	SR-related CTD-associated factor 8	protein-coding
mm_39584.1	chr5	23482418	23482432	+	1	NA	exon (NM_026984, exon 12 of 26)	exon (NM_026984, exon 12 of 26)	47996	NM_026984	69188	Mm.205190	NM_026984	ENSMUSG00000029004	Kmt2e	1810033J14Rik|9530077A04Rik|D230038D11Rik|Mll5|NKp44L	lysine (K)-specific methyltransferase 2E	protein-coding
mm_1221.1	chr1	62738350	62738379	+	1	NA	exon (NM_001077407, exon 3 of 16)	exon (NM_001077407, exon 3 of 16)	35047	NM_001077405	18187	Mm.266341	NM_010939	ENSMUSG00000025969	Nrp2	1110048P06Rik|Np-2|Np2|Npn-2|Npn2	neuropilin 2	protein-coding
mm_78188.1	chr9	21265288	21265322	+	1	NA	promoter-TSS (NM_153583)	promoter-TSS (NM_153583)	20	NM_153583	235040	Mm.440165	NM_153583	ENSMUSG00000002820	Atg4d	9830134P12Rik|APG4-D|Apg4d|Atg4dl|Autl4	autophagy related 4D, cysteine peptidase	protein-coding
mm_100467.1	chr11	119916648	119916683	+	1	NA	intron (NM_001085498, intron 4 of 7)	intron (NM_001085498, intron 4 of 7)	2855	NM_001085498	208092	Mm.306673	NM_001085498	ENSMUSG00000025371	Chmp6	2400004G01Rik	charged multivesicular body protein 6	protein-coding
mm_104057.1	chr11	86577285	86577290	-	1	NA	Intergenic	Intergenic	6871	NR_029738	387140		NR_029738	ENSMUSG00000065455	Mir21a	Mir21|Mirn21|mmu-mir-21|mmu-mir-21a	microRNA 21a	ncRNA
mm_171103.1	chr3	133544233	133544233	-	1	NA	5' UTR (NM_001346736, exon 1 of 12)	5' UTR (NM_001346736, exon 1 of 12)	157	NM_001346736	214133	Mm.347816	NM_145989	ENSMUSG00000040943	Tet2	Ayu17-449|E130014J05Rik|mKIAA1546	tet methylcytosine dioxygenase 2	protein-coding
mm_111235.1	chr12	84772874	84772881	-	1	NA	promoter-TSS (NM_028863)	promoter-TSS (NM_028863)	235	NM_023409	67963	Mm.282556	NM_023409	ENSMUSG00000021242	Npc2	2700012J19Rik|AA408070|AU045843|HE1	Niemann-Pick type C2	protein-coding
mm_5248.1	chr1	16520107	16520133	-	1	NA	promoter-TSS (NM_025303)	promoter-TSS (NM_025303)	-818	NM_001111272	29819	Mm.216257	NM_025303	ENSMUSG00000025920	Stau2	-	staufen (RNA binding protein) homolog 2 (Drosophila)	protein-coding
mm_134131.1	chr16	10447372	10447389	-	1	NA	promoter-TSS (NM_001013778)	promoter-TSS (NM_001013778)	-30	NM_001013778	383103	Mm.325732	NM_001013778	ENSMUSG00000050908	Tvp23a	Fam18a	trans-golgi network vesicle protein 23A	protein-coding
mm_148904.1	chr19	6941902	6941932	+	1	NA	promoter-TSS (NM_001177360)	promoter-TSS (NM_001177360)	56	NM_007522	12015	Mm.4387	NM_007522	ENSMUSG00000024959	Bad	AI325008|Bbc2	BCL2-associated agonist of cell death	protein-coding
mm_130387.1	chr15	97859241	97859253	-	1	NA	exon (NM_009504, exon 8 of 10)	exon (NM_009504, exon 8 of 10)	-14745	NM_001204278	56233	Mm.384027	NM_019572	ENSMUSG00000022475	Hdac7	5830434K02Rik|HD7|HD7a|Hdac7a|mFLJ00062	histone deacetylase 7	protein-coding
mm_84060.1	chr9	58199687	58199702	-	1	NA	exon (NM_177193, exon 3 of 3)	exon (NM_177193, exon 3 of 3)	2021	NM_001161535	320563	Mm.186499	NM_177193	ENSMUSG00000051243	Islr2	B930052A04Rik|Linx|Mbu-3|mKIAA1465	immunoglobulin superfamily containing leucine-rich repeat 2	protein-coding
mm_171762.1	chr5	105797727	105797747	-	1	NA	intron (NM_001122768, intron 2 of 2)	intron (NM_001122768, intron 2 of 2)	-78831	NR_030777	54367	Mm.248876	NM_018759	ENSMUSG00000029290	Zfp326	5730470H14Rik|ZAN75|Znf326	zinc finger protein 326	protein-coding
mm_21376.1	chr2	157346682	157346684	-	1	NA	promoter-TSS (NM_010285)	promoter-TSS (NM_010285)	-28	NM_010285	14601	Mm.389327	NM_010285	ENSMUSG00000027643	Ghrh	GRF|Ghrf	growth hormone releasing hormone	protein-coding
mm_145688.1	chr18	61726394	61726451	+	1	NA	promoter-TSS (NM_021296)	promoter-TSS (NM_021296)	32	NR_029432	68982	Mm.441992	NR_029432	ENSMUSG00000098702	1500015A07Rik	-	RIKEN cDNA 1500015A07 gene	ncRNA
mm_92728.1	chr10	80844008	80844021	-	1	NA	promoter-TSS (NM_001013758)	promoter-TSS (NM_001013758)	25	NM_001013758	237403	Mm.40213	NM_001013758	ENSMUSG00000051067	Lingo3	AI851712|LERN2	leucine rich repeat and Ig domain containing 3	protein-coding
mm_96293.1	chr11	63132649	63132677	+	1	NA	promoter-TSS (NM_001302260)	promoter-TSS (NM_001302260)	94	NM_001302259	18858	Mm.1237	NM_008885	ENSMUSG00000018217	Pmp22	22kDa|Gas-3|HNPP|Tr|trembler	peripheral myelin protein 22	protein-coding
mm_47749.1	chr5	130256805	130256809	-	1	NA	promoter-TSS (NM_001015876)	promoter-TSS (NM_001015876)	-230	NM_001015876	100929	Mm.271296	NM_178897	ENSMUSG00000056310	Tyw1	AW125391|Rsafd1	tRNA-yW synthesizing protein 1 homolog (S. cerevisiae)	protein-coding
mm_161187.1	chr13	49248740	49248740	-	1	NA	promoter-TSS (NM_028340)	promoter-TSS (NM_028340)	-34	NM_028340	66329	Mm.34308	NM_025491	ENSMUSG00000021384	Susd3	1700017I11Rik|2810440J20Rik	sushi domain containing 3	protein-coding
mm_47153.1	chr5	120612559	120612598	-	1	NA	promoter-TSS (NM_029096)	promoter-TSS (NM_029096)	11	NM_029096	100764	Mm.9654	NM_029096	ENSMUSG00000029600	Rita1	1110008J03Rik|AI853657|C86297|Rita	RBPJ interacting and tubulin associated 1	protein-coding
mm_28015.1	chr3	83043883	83043909	-	1	NA	exon (NM_181849, exon 6 of 8)	exon (NM_181849, exon 6 of 8)	5967	NM_181849	110135	Mm.30063	NM_181849	ENSMUSG00000033831	Fgb	2510049G14Rik	fibrinogen beta chain	protein-coding
mm_161667.1	chr17	13052296	13052296	-	1	NA	promoter-TSS (NM_001013832)	promoter-TSS (NM_001013832)	-16	NM_001013832	436440	Mm.335670	NM_001013832	ENSMUSG00000071311	Gpr31b	12-HETER|GPR31c(t)|Gpr31|Gpr31c	G protein-coupled receptor 31, D17Leh66b region	protein-coding
mm_49080.1	chr6	6330317	6330320	+	1	NA	intron (NR_136905, intron 3 of 3)	ORR1A3-int|LTR|ERVL-MaLR	81659	NR_136905	101056138	Mm.389085	NR_136904	ENSMUSG00000093482	Gm20619	-	predicted gene 20619	ncRNA
mm_117898.1	chr13	99425419	99425440	-	1	NA	3' UTR (NM_008634, exon 7 of 7)	3' UTR (NM_008634, exon 7 of 7)	-12603	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_94517.1	chr11	8708932	8708939	+	1	NA	Intergenic	Intergenic	-44400	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_84718.1	chr9	73968671	73968709	-	1	NA	Intergenic	Intergenic	-35123	NM_001081153	208898	Mm.41035	NM_001081153	ENSMUSG00000062151	Unc13c	1500037O19Rik|AU019458|D9Ertd414e|Munc13-3|Unc13h3	unc-13 homolog C (C. elegans)	protein-coding
mm_13610.1	chr2	113365528	113365539	+	1	NA	exon (NM_010230, exon 2 of 20)	exon (NM_010230, exon 2 of 20)	37797	NM_010230	14260	Mm.4938	NM_010230	ENSMUSG00000044042	Fmn1	Fmn|formin-1|ld	formin 1	protein-coding
mm_32231.1	chr4	102254740	102254761	+	1	NA	promoter-TSS (NM_001177983)	promoter-TSS (NM_001177983)	8	NM_001177983	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_88439.1	chr10	77545149	77545229	+	1	NA	intron (NM_008404, intron 3 of 15)	intron (NM_008404, intron 3 of 15)	14841	NM_008404	16414	Mm.1137	NM_008404	ENSMUSG00000000290	Itgb2	2E6|AI528527|Cd18|LAD|LCAMB|Lfa1|MF17	integrin beta 2	protein-coding
mm_147929.1	chr18	65970085	65970089	-	1	NA	promoter-TSS (NM_145493)	promoter-TSS (NM_145493)	91	NM_145493	225644	Mm.192285	NM_145493	ENSMUSG00000024519	Cplx4	A930004D23Rik|CPXIV|Gm957	complexin 4	protein-coding
mm_124980.1	chr15	20568770	20568776	+	1	NA	Intergenic	Intergenic	97977	NM_022816	64833	Mm.352763	NM_022816	ENSMUSG00000047565	Acot10	Acate3|MT-ACT48|p48	acyl-CoA thioesterase 10	protein-coding
mm_143164.1	chr17	57225104	57225115	-	1	NA	exon (NM_009778, exon 6 of 41)	exon (NM_009778, exon 6 of 41)	3027	NM_009778	12266	Mm.19131	NM_009778	ENSMUSG00000024164	C3	AI255234|ASP|HSE-MSF|Plp	complement component 3	protein-coding
mm_147039.1	chr18	34862708	34862721	-	1	NA	exon (NM_007913, exon 2 of 2)	exon (NM_007913, exon 2 of 2)	1507	NM_007913	13653	Mm.181959	NM_007913	ENSMUSG00000038418	Egr1	A530045N19Rik|ETR103|Egr-1|Krox-1|Krox-24|Krox24|NGF1-A|NGFI-A|NGFIA|TIS8|Zenk|Zfp-6|Zif268|egr	early growth response 1	protein-coding
mm_140847.1	chr17	23676642	23676646	-	1	NA	intron (NM_013749, intron 1 of 3)	CpG	805	NM_001161746	27279	Mm.28518	NM_013749	ENSMUSG00000023905	Tnfrsf12a	AI255180|C87282|Fn14|HPIP|TWEAK-R|TweakR	tumor necrosis factor receptor superfamily, member 12a	protein-coding
mm_74213.1	chr8	123949411	123949437	+	1	NA	promoter-TSS (NM_172288)	promoter-TSS (NM_172288)	-159	NM_172288	234865	Mm.267812	NM_172288	ENSMUSG00000039509	Nup133	mermaid	nucleoporin 133	protein-coding
mm_168157.1	chr10	4253760	4253775	-	1	NA	Intergenic	Intergenic	-12562	NM_031185	83397	Mm.27481	NM_031185	ENSMUSG00000038587	Akap12	AI317366|SSeCKS|Srcs5|Tsga12	A kinase (PRKA) anchor protein (gravin) 12	protein-coding
mm_11655.1	chr2	34963714	34963722	+	1	NA	Intergenic	Intergenic	-1946	NM_001326601	22029	Mm.239514	NM_009421	ENSMUSG00000026875	Traf1	4732496E14Rik	TNF receptor-associated factor 1	protein-coding
mm_6036.1	chr1	59662440	59662441	-	1	NA	intron (NM_009460, intron 1 of 4)	intron (NM_009460, intron 1 of 4)	8394	NM_009460	22218	Mm.362118	NM_009460	ENSMUSG00000026021	Sumo1	GMP1|PIC1|SENTRIN|SMT3|SMT3H3|SMTP3|SUMO-1|Smt3C|Ubl1	small ubiquitin-like modifier 1	protein-coding
mm_163440.1	chr12	85476663	85476692	-	1	NA	3' UTR (NM_010234, exon 4 of 4)	3' UTR (NM_010234, exon 4 of 4)	2776	NM_010234	14281	Mm.246513	NM_010234	ENSMUSG00000021250	Fos	D12Rfj1|c-fos|cFos	FBJ osteosarcoma oncogene	protein-coding
mm_65485.1	chr7	25658727	25658761	-	1	NA	promoter-TSS (NM_007533)	promoter-TSS (NM_007533)	17	NM_007533	12039	Mm.25848	NM_007533	ENSMUSG00000060376	Bckdha	-	branched chain ketoacid dehydrogenase E1, alpha polypeptide	protein-coding
mm_118353.1	chr13	115052758	115052770	-	1	NA	intron (NM_001033228, intron 1 of 28)	intron (NM_001033228, intron 1 of 28)	37394	NM_134058	105083	Mm.486295	NM_134058	ENSMUSG00000042275	Pelo	AA409897|AI852218	pelota homolog (Drosophila)	protein-coding
mm_143295.1	chr17	65885286	65885301	-	1	NA	promoter-TSS (NM_001198949)	promoter-TSS (NM_001198949)	-370	NM_001198949	19765	Mm.17009	NM_009067	ENSMUSG00000024096	Ralbp1	RLIP76|Rip1	ralA binding protein 1	protein-coding
mm_166334.1	chr5	114379079	114379106	-	1	NA	intron (NM_026145, intron 1 of 6)	intron (NM_026145, intron 1 of 6)	1413	NM_001159941	330171	Mm.238285	NM_026145	ENSMUSG00000001098	Kctd10	AW536343|C87062|mBACURD3	potassium channel tetramerisation domain containing 10	protein-coding
mm_131286.1	chr16	11203376	11203448	+	1	NA	promoter-TSS (NM_025546)	promoter-TSS (NM_025546)	29	NR_038156	69918	Mm.440400	NR_038154		2610020C07Rik	-	RIKEN cDNA 2610020C07 gene	ncRNA
mm_124603.1	chr15	3279122	3279130	+	1	NA	exon (NM_009155, exon 5 of 5)	exon (NM_009155, exon 5 of 5)	8149	NM_009155	20363	Mm.392203	NM_009155	ENSMUSG00000064373	Selenop	AU018766|D15Ucla1|Se-P|Sepp1|selp	selenoprotein P	protein-coding
mm_3511.1	chr1	150107360	150107362	+	1	NA	3' UTR (NM_011198, exon 10 of 10)	3' UTR (NM_011198, exon 10 of 10)	7330	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_145931.1	chr18	67205370	67205426	+	1	NA	promoter-TSS (NM_024190)	promoter-TSS (NM_024190)	39	NM_024190	67064	Mm.73777	NM_024190	ENSMUSG00000109901	Chmp1b	2810405I11Rik|Chmp1b1	charged multivesicular body protein 1B	protein-coding
mm_119057.1	chr14	30715689	30715741	+	1	NA	promoter-TSS (NM_001166532)	promoter-TSS (NM_001166532)	100	NM_001166532	54650	Mm.294662	NM_019460	ENSMUSG00000006527	Sfmbt1	4930442N21Rik|9330180L21Rik|AA536974|Sfmbt|Smr	Scm-like with four mbt domains 1	protein-coding
mm_43826.1	chr5	142970542	142970562	+	1	NA	exon (NM_007984, exon 4 of 5)	exon (NM_007984, exon 4 of 5)	10197	NM_007984	14086	Mm.289707	NM_007984	ENSMUSG00000029581	Fscn1	AI663989|Fan1|fascin-1	fascin actin-bundling protein 1	protein-coding
mm_142144.1	chr17	35980239	35980253	-	1	NA	promoter-TSS (NM_001282025)	promoter-TSS (NM_001282025)	291	NM_008136	14670	Mm.335754	NM_008136	ENSMUSG00000024429	Gnl1	Gna-rs1|Gnal1	guanine nucleotide binding protein-like 1	protein-coding
mm_97468.1	chr11	78290870	78290884	+	1	NA	promoter-TSS (NM_001287206)	promoter-TSS (NM_001287206)	36	NM_001287206	216976	Mm.477146	NM_001045522		BC030499	BC037104|Sgk494	cDNA sequence BC030499	protein-coding
mm_99029.1	chr11	98942488	98942499	+	1	NA	intron (NM_001177303, intron 1 of 8)	intron (NM_001177303, intron 1 of 8)	2782	NM_001177303	19401	Mm.439744	NM_009024	ENSMUSG00000037992	Rara	Nr1b1|RAR|RARalpha1	retinoic acid receptor, alpha	protein-coding
mm_21643.1	chr2	164333445	164333469	-	1	NA	exon (NM_009301, exon 2 of 3)	exon (NM_009301, exon 2 of 3)	692	NM_009301	20944	Mm.140154	NM_009301	ENSMUSG00000017004	Svs5	BB115186|Semg1|Svp-1|Svp1|Svp5	seminal vesicle secretory protein 5	protein-coding
mm_161262.1	chr14	3049123	3049123	+	1	NA	promoter-TSS (NM_001177715)	promoter-TSS (NM_001177715)	-162	NM_001177715	100040671	Mm.360540	NM_001177714	ENSMUSG00000079410	Gm2897	ENSMUSG00000079410	predicted gene 2897	protein-coding
mm_10508.1	chr2	16356088	16356099	+	1	NA	promoter-TSS (NM_026162)	promoter-TSS (NM_026162)	-211	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding
mm_98142.1	chr11	87581107	87581125	+	1	NA	promoter-TSS (NM_011129)	promoter-TSS (NM_011129)	55	NM_001284392	18952	Mm.2214	NM_011129	ENSMUSG00000020486	Sept4	ARTS|Bh5|OTTMUSG00000001265|Pnutl2	septin 4	protein-coding
mm_19353.1	chr2	91063117	91063125	-	1	NA	non-coding (NR_110981, exon 7 of 8)	non-coding (NR_110981, exon 7 of 8)	7194	NM_026721	68427	Mm.192375	NM_026721	ENSMUSG00000002105	Slc39a13	1100001L14Rik|AA387663|ZIP-13|ZIP13	solute carrier family 39 (metal ion transporter), member 13	protein-coding
mm_53587.1	chr6	137735183	137735189	+	1	NA	5' UTR (NM_011499, exon 1 of 10)	5' UTR (NM_011499, exon 1 of 10)	104	NM_011499	20901	Mm.22584	NM_011499	ENSMUSG00000030224	Strap	AW557906|C78091|C79202|Unrip	serine/threonine kinase receptor associated protein	protein-coding
mm_131581.1	chr16	18428917	18428934	+	1	NA	intron (NM_013711, intron 1 of 17)	intron (NM_013711, intron 1 of 17)	-2209	NM_001111062	12846	Mm.100940	NM_007744	ENSMUSG00000000326	Comt	Comt1|D16Wsu103e|D330014B15Rik	catechol-O-methyltransferase	protein-coding
mm_12342.1	chr2	69723249	69723278	+	1	NA	5' UTR (NM_001081086, exon 1 of 14)	5' UTR (NM_001081086, exon 1 of 14)	175	NM_001081086	228005	Mm.11815	NM_001081086	ENSMUSG00000042133	Ppig	AU019516|AU022200|B230312B02Rik|CYP|SRCyp	peptidyl-prolyl isomerase G (cyclophilin G)	protein-coding
mm_89306.1	chr10	87916302	87916308	+	1	NA	intron (NM_001111274, intron 4 of 4)	MLT1B|LTR|ERVL-MaLR	-50366	NR_000040	22172	Mm.391420	NR_000040		Tyms-ps	-	thymidylate synthase, pseudogene	pseudo
mm_139007.1	chr17	45570365	45570388	+	1	NA	exon (NM_008302, exon 6 of 11)	exon (NM_008302, exon 6 of 11)	2885	NM_008302	15516	Mm.2180	NM_008302	ENSMUSG00000023944	Hsp90ab1	90kDa|AL022974|C81438|Hsp84|Hsp84-1|Hsp90|Hspcb	heat shock protein 90 alpha (cytosolic), class B member 1	protein-coding
mm_45161.1	chr5	49525077	49525085	-	1	NA	Intergenic	Intergenic	-239422	NM_001199244	80334	Mm.160172	NM_030265	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding
mm_126759.1	chr15	85832302	85832317	+	1	NA	promoter-TSS (NM_001033337)	promoter-TSS (NM_001033337)	5	NM_001033337	239570	Mm.151748	NM_001033337	ENSMUSG00000035944	Ttc38	9030019H09	tetratricopeptide repeat domain 38	protein-coding
mm_35634.1	chr4	43515169	43515190	-	1	NA	3' UTR (NM_009416, exon 9 of 9)	3' UTR (NM_009416, exon 9 of 9)	8153	NM_139305	230099	Mm.283682	NM_139305	ENSMUSG00000028463	Car9	CAIX|Ca9|MN/CA9	carbonic anhydrase 9	protein-coding
mm_10177.1	chr2	4560119	4560148	+	1	NA	5' UTR (NM_001177844, exon 1 of 12)	5' UTR (NM_001177844, exon 1 of 12)	379	NM_001177844	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding
mm_22595.1	chr3	13833437	13833445	+	1	NA	intron (NM_178631, intron 3 of 9)	B1_Mus2|SINE|Alu	-112931	NM_001163329	76897	Mm.422625	NM_178631	ENSMUSG00000039717	Ralyl	0710005M24Rik	RALY RNA binding protein-like	protein-coding
mm_71470.1	chr8	46534815	46534831	+	1	NA	3' UTR (NM_007981, exon 21 of 21)	3' UTR (NM_007981, exon 21 of 21)	-17246	NM_027973	71876	Mm.22108	NM_027973	ENSMUSG00000031629	Cenpu	1700029A22Rik|Mlf1ip	centromere protein U	protein-coding
mm_123116.1	chr14	56062308	56062313	-	1	NA	promoter-TSS (NM_010779)	promoter-TSS (NM_010779)	0	NM_010779	17227	Mm.439684	NM_010779	ENSMUSG00000061068	Mcpt4	MMCP-4|MMCP-4A|MMCP-4B|Mcp-4|Mcp4	mast cell protease 4	protein-coding
mm_11342.1	chr2	30803776	30803783	+	1	NA	promoter-TSS (NR_028487)	promoter-TSS (NR_028487)	-115	NR_028487	73598	Mm.34166	NM_198000	ENSMUSG00000044320	1700001O22Rik	1700113K14Rik|4930549G18Rik	RIKEN cDNA 1700001O22 gene	protein-coding
mm_110152.1	chr12	26453723	26453733	-	1	NA	intron (NM_021384, intron 2 of 5)	intron (NM_021384, intron 2 of 5)	2724	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_2041.1	chr1	87264414	87264444	+	1	NA	promoter-TSS (NM_028889)	promoter-TSS (NM_028889)	65	NM_028889	98363	Mm.247951	NM_028889	ENSMUSG00000026255	Efhd1	4931430I01Rik|AI452351|PP3051|mitocalcin	EF hand domain containing 1	protein-coding
mm_154784.1	chrX	13071060	13071082	+	1	NA	promoter-TSS (NM_009481)	promoter-TSS (NM_009481)	-427	NM_009481	22284	Mm.242646	NM_009481	ENSMUSG00000031010	Usp9x	5730589N07Rik|AA407302|AA407699|AL022658|AL022749|Dffrx|FAF-X|Fafl	ubiquitin specific peptidase 9, X chromosome	protein-coding
mm_57296.1	chr6	124450178	124450210	-	1	NA	intron (NM_001346656, intron 10 of 17)	GA-rich|Low_complexity|Low_complexity	12550	NM_001346656	232370	Mm.193701	NM_153508	ENSMUSG00000008153	Clstn3	CSTN3|Cs3|Cst-3|alc-beta	calsyntenin 3	protein-coding
mm_126246.1	chr15	79005475	79005491	+	1	NA	3' UTR (NM_138579, exon 24 of 24)	3' UTR (NM_138579, exon 24 of 24)	3260	NR_105921	102465577		NR_105921	ENSMUSG00000099180	Mir6956	Gm27880|mmu-mir-6956	microRNA 6956	ncRNA
mm_152790.1	chr19	21471139	21471149	-	1	NA	intron (NM_010266, intron 1 of 13)	intron (NM_010266, intron 1 of 13)	1517	NM_010266	14544	Mm.45054	NM_010266	ENSMUSG00000058624	Gda	AU015411|AW047581|GAH	guanine deaminase	protein-coding
mm_22238.1	chr2	174441351	174441360	-	1	NA	Intergenic	Intergenic	-2316	NM_022325	64138	Mm.156919	NM_022325	ENSMUSG00000016256	Ctsz	AI787083|AU019819|CTSX|D2Wsu143e	cathepsin Z	protein-coding
mm_59329.1	chr7	25392271	25392279	+	1	NA	intron (NM_010719, intron 1 of 9)	intron (NM_010719, intron 1 of 9)	-2163	NM_001039507	16890	Mm.158548	NM_010719	ENSMUSG00000003123	Lipe	4933403G17Rik|HSL	lipase, hormone sensitive	protein-coding
mm_128189.1	chr15	34876331	34876341	-	1	NA	3' UTR (NM_019635, exon 11 of 11)	3' UTR (NM_019635, exon 11 of 11)	38287	NM_001271704	16539	Mm.71045	NM_181317	ENSMUSG00000050963	Kcns2	E130006J24Rik|Kv9.2	K+ voltage-gated channel, subfamily S, 2	protein-coding
mm_135462.1	chr16	45784492	45784504	-	1	NA	intron (NM_001252442, intron 6 of 18)	intron (NM_001252442, intron 6 of 18)	-41543	NM_172511	213012	Mm.247453	NM_172511	ENSMUSG00000033157	Abhd10	-	abhydrolase domain containing 10	protein-coding
mm_66260.1	chr7	35654208	35654223	-	1	NA	Intergenic	Intergenic	-6733	NM_019746	56330	Mm.371609	NM_019746	ENSMUSG00000030417	Pdcd5	2200003D22Rik|AA408513|Tfar19	programmed cell death 5	protein-coding
mm_171698.1	chr4	70468088	70468088	-	1	NA	intron (NM_172694, intron 2 of 5)	B3|SINE|B2	-57653	NM_145990	214444	Mm.370777	NM_145990	ENSMUSG00000039298	Cdk5rap2	2900018K03Rik|an|mKIAA1633	CDK5 regulatory subunit associated protein 2	protein-coding
mm_99912.1	chr11	109936308	109936318	+	1	NA	intron (NM_013851, intron 36 of 38)	intron (NM_013851, intron 36 of 38)	59503	NM_013851	27404	Mm.341004	NM_013851	ENSMUSG00000020620	Abca8b	Abca8	ATP-binding cassette, sub-family A (ABC1), member 8b	protein-coding
mm_115780.1	chr13	19311467	19311475	-	1	NA	Intergenic	Intergenic	84342	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_74039.1	chr8	121947953	121947979	+	1	NA	Intergenic	Intergenic	-2526	NM_016812	53325	Mm.287163	NM_016812	ENSMUSG00000025316	Banp	AA408158|SMAR1	BTG3 associated nuclear protein	protein-coding
mm_113153.1	chr13	24801172	24801184	+	1	NA	promoter-TSS (NM_024473)	promoter-TSS (NM_024473)	-479	NM_024473	79555	Mm.266668	NM_024473	ENSMUSG00000019132	BC005537	8030460C05Rik|C78201	cDNA sequence BC005537	protein-coding
mm_17878.1	chr2	34958713	34958743	-	1	NA	intron (NM_009421, intron 3 of 10)	intron (NM_009421, intron 3 of 10)	3044	NM_009421	22029	Mm.239514	NM_009421	ENSMUSG00000026875	Traf1	4732496E14Rik	TNF receptor-associated factor 1	protein-coding
mm_963.1	chr1	58029985	58029997	+	1	NA	promoter-TSS (NM_009676)	promoter-TSS (NM_009676)	22	NM_009676	11761	Mm.26787	NM_009676	ENSMUSG00000063558	Aox1	AI196512|AI255253|Ao|Aox-1|Aox-2|Aox2|Moro|Ro	aldehyde oxidase 1	protein-coding
mm_136720.1	chr17	8165918	8165922	+	1	NA	intron (NM_001197046, intron 1 of 12)	intron (NM_001197046, intron 1 of 12)	402	NM_201230	75296	Mm.227250	NM_201230	ENSMUSG00000069135	Fgfr1op	4930553O10Rik|FOP	Fgfr1 oncogene partner	protein-coding
mm_132525.1	chr16	37829125	37829136	+	1	NA	exon (NM_008047, exon 9 of 11)	exon (NM_008047, exon 9 of 11)	-39270	NM_177093	320184	Mm.390882	NM_177093	ENSMUSG00000034158	Lrrc58	1810012N18Rik|C330018J07Rik	leucine rich repeat containing 58	protein-coding
mm_13847.1	chr2	119584566	119584584	+	1	NA	exon (NM_019769, exon 6 of 7)	exon (NM_019769, exon 6 of 7)	-9721	NR_027832	66602	Mm.379181	NR_015473	ENSMUSG00000085438	1700020I14Rik	1190006L01Rik|4933437I03Rik|AI451541|AI585852|AW538376|AW558897|Cyrano	RIKEN cDNA 1700020I14 gene	ncRNA
mm_88329.1	chr10	75571504	75571512	+	1	NA	intron (NM_001305992, intron 1 of 13)	intron (NM_001305992, intron 1 of 13)	-1987	NM_008116	14598	Mm.4559	NM_008116	ENSMUSG00000006345	Ggt1	CD224|GGT|GGT 1|GGT-1|Ggtp|dwg	gamma-glutamyltransferase 1	protein-coding
mm_57802.1	chr6	129331806	129331807	-	1	NA	promoter-TSS (NM_199034)	promoter-TSS (NM_199034)	-25	NM_199034	381816	Mm.46114	NM_199034	ENSMUSG00000047720	4922502D21Rik	Clec2m|Gm1074|SPATA78	RIKEN cDNA 4922502D21 gene	protein-coding
mm_5255.1	chr1	16655490	16655528	-	1	NA	intron (NM_001310470, intron 1 of 4)	B1_Mur1|SINE|Alu	1356	NM_026456	67923	Mm.289248	NM_026456	ENSMUSG00000079658	Eloc	2610043E24Rik|2610301I15Rik|AA407206|AI987979|AW049146|Tceb1	elongin C	protein-coding
mm_145070.1	chr18	42053649	42053662	+	1	NA	promoter-TSS (NM_001146299)	promoter-TSS (NM_001146299)	-55	NM_172966	269016	Mm.45472	NM_172966	ENSMUSG00000057719	Sh3rf2	2310046K19|9130023G24Rik|AI452083|Ppp1r39|RNF158	SH3 domain containing ring finger 2	protein-coding
mm_67032.1	chr7	66689552	66689569	-	1	NA	promoter-TSS (NR_003961)	promoter-TSS (NR_003961)	1	NM_080443	117589	Mm.34785	NM_080443	ENSMUSG00000030509	Asb7	AI449039|Asb-7|D030055C23Rik	ankyrin repeat and SOCS box-containing 7	protein-coding
mm_114456.1	chr13	67128220	67128251	+	1	NA	promoter-TSS (NM_172392)	promoter-TSS (NM_172392)	7	NM_172392	268670	Mm.56274	NM_172392	ENSMUSG00000057396	Zfp759	BC028265|Rslcan-8|Rslcan8	zinc finger protein 759	protein-coding
mm_60564.1	chr7	44481379	44481387	+	1	NA	Intergenic	Intergenic	-3134	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_13254.1	chr2	98664016	98664048	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	1196375	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_158864.1	chrY	2390505	2390508	+	1	NA	Intergenic	RLTR44B|LTR|ERVK	-208593	NM_001113395	100042840	Mm.472681	NM_001113395	ENSMUSG00000095573	H2al2b	ENSMUSG00000069034|Gm16501|H2al2y	H2A histone family member L2B	protein-coding
mm_92613.1	chr10	80139160	80139172	-	1	NA	non-coding (NR_036582, exon 1 of 11)	non-coding (NR_036582, exon 1 of 11)	201	NR_036582	100503659	Mm.485395	NM_015761	ENSMUSG00000035640	Cbarp	9630008F14|Dos|R29144/1	calcium channel, voltage-dependent, beta subunit associated regulatory protein	protein-coding
mm_113404.1	chr13	33953232	33953242	+	1	NA	intron (NR_040707, intron 1 of 4)	intron (NR_040707, intron 1 of 4)	-11422	NM_001163239	18105	Mm.264036	NM_020282	ENSMUSG00000046949	Nqo2	NMO2|Nmor2|Ox2	NAD(P)H dehydrogenase, quinone 2	protein-coding
mm_129052.1	chr15	75566311	75566354	-	1	NA	intron (NM_011837, intron 1 of 3)	intron (NM_011837, intron 1 of 3)	316	NM_001135689	23934	Mm.22154	NM_011837	ENSMUSG00000022577	Ly6h	-	lymphocyte antigen 6 complex, locus H	protein-coding
mm_164515.1	chr16	96200716	96200720	+	1	NA	exon (NM_015825, exon 1 of 8)	exon (NM_015825, exon 1 of 8)	248	NM_015825	50795	Mm.28638	NM_015825	ENSMUSG00000040666	Sh3bgr	5430437A18Rik	SH3-binding domain glutamic acid-rich protein	protein-coding
mm_83893.1	chr9	56136138	56136153	-	1	NA	3' UTR (NM_019793, exon 7 of 7)	3' UTR (NM_019793, exon 7 of 7)	24925	NM_019793	56434	Mm.28484	NM_019793	ENSMUSG00000032324	Tspan3	1700055K04Rik|TM4-A|Tm4sf8	tetraspanin 3	protein-coding
mm_9422.1	chr1	172341031	172341045	-	1	NA	promoter-TSS (NM_001039484)	promoter-TSS (NM_001039484)	-172	NM_001039484	16513	Mm.254563	NM_020269	ENSMUSG00000044708	Kcnj10	BIR10|BIRK-1|Kir1.2|Kir4.1	potassium inwardly-rectifying channel, subfamily J, member 10	protein-coding
mm_100401.1	chr11	119393061	119393083	+	1	NA	Intergenic	Intergenic	2600	NR_035453	100316690		NR_035453	ENSMUSG00000088015	Mir1932	mir-1932|mmu-mir-1932	microRNA 1932	ncRNA
mm_122478.1	chr14	45658035	45658050	-	1	NA	promoter-TSS (NR_039593)	promoter-TSS (NR_039593)	11	NR_039593	100628600		NR_039593	ENSMUSG00000093167	Mir5131	mmu-mir-5131|mu-mir-5131	microRNA 5131	ncRNA
mm_53267.1	chr6	128375465	128375512	+	1	NA	promoter-TSS (NM_027697)	promoter-TSS (NM_027697)	-22	NM_027697	71149	Mm.483176	NM_027697	ENSMUSG00000079304	4933413G19Rik	-	RIKEN cDNA 4933413G19 gene	protein-coding
mm_84364.1	chr9	64803439	64803474	-	1	NA	Intergenic	Intergenic	-7555	NM_001162917	102442	Mm.222473	NM_176935	ENSMUSG00000053641	Dennd4a	AI115600|AI851943|F730015K02Rik	DENN/MADD domain containing 4A	protein-coding
mm_41724.1	chr5	102481501	102481542	+	1	NA	5' UTR (NM_029270, exon 1 of 10)	5' UTR (NM_029270, exon 1 of 10)	130	NM_029270	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding
mm_48825.1	chr5	149051901	149051979	-	1	NA	promoter-TSS (NM_001313894)	promoter-TSS (NM_001313894)	-324	NM_001313894	15289	Mm.207047	NM_010439	ENSMUSG00000066551	Hmgb1	HMG-1|Hmg1|SBP-1|p30	high mobility group box 1	protein-coding
mm_72935.1	chr8	91313587	91313591	+	1	NA	promoter-TSS (NM_173431)	promoter-TSS (NM_173431)	64	NM_011936	26383	Mm.4375	NM_011936	ENSMUSG00000055932	Fto	AW743446|mKIAA1752	fat mass and obesity associated	protein-coding
mm_127258.1	chr15	99704137	99704148	+	1	NA	intron (NM_031842, intron 4 of 12)	intron (NM_031842, intron 4 of 12)	1855	NM_031842	83797	Mm.273756	NM_031842	ENSMUSG00000023018	Smarcd1	AA407987|Baf60a|D15Kz1	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1	protein-coding
mm_100423.1	chr11	119442760	119442771	+	1	NA	Intergenic	Intergenic	-48582	NM_001164636	338371	Mm.271946	NM_177394	ENSMUSG00000039850	Endov	A730011L01Rik	endonuclease V	protein-coding
mm_78992.1	chr9	45403175	45403189	+	1	NA	promoter-TSS (NM_052823)	promoter-TSS (NM_052823)	44	NM_052823	11936	Mm.22742	NM_007503	ENSMUSG00000059412	Fxyd2	Atp1g1	FXYD domain-containing ion transport regulator 2	protein-coding
mm_133807.1	chr16	95701980	95701991	+	1	NA	promoter-TSS (NM_011809)	promoter-TSS (NM_011809)	-422	NM_011809	23872	Mm.290207	NM_011809	ENSMUSG00000022895	Ets2	AU022856|Ets-2	E26 avian leukemia oncogene 2, 3' domain	protein-coding
mm_50652.1	chr6	51470406	51470416	+	1	NA	promoter-TSS (NM_007624)	promoter-TSS (NM_007624)	-205	NM_007624	12417	Mm.280968	NM_007624	ENSMUSG00000029836	Cbx3	HP1g|M32	chromobox 3	protein-coding
mm_115304.1	chr13	112263050	112263050	+	1	NA	Intergenic	Intergenic	-25401	NM_001168403	77318	Mm.159895	NM_029898	ENSMUSG00000049985	Ankrd55	C030011J08Rik	ankyrin repeat domain 55	protein-coding
mm_26747.1	chr3	7613578	7613592	-	1	NA	promoter-TSS (NM_001313890)	promoter-TSS (NM_001313890)	175	NM_008371	16196	Mm.3825	NM_008371	ENSMUSG00000040329	Il7	A630026I06Rik|Il-7|hlb368	interleukin 7	protein-coding
mm_83401.1	chr9	44735190	44735213	-	1	NA	promoter-TSS (NM_153537)	promoter-TSS (NM_153537)	-3	NM_153537	102693	Mm.28639	NM_153537	ENSMUSG00000048537	Phldb1	AU041016|D330037A14Rik|Ll5a	pleckstrin homology like domain, family B, member 1	protein-coding
mm_130756.1	chr15	101270648	101270664	-	1	NA	exon (NM_010444, exon 2 of 7)	exon (NM_010444, exon 2 of 7)	3810	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_41589.1	chr5	93268248	93268289	+	1	NA	intron (NM_007635, intron 1 of 7)	CpG	695	NM_007635	12452	Mm.3527	NM_007635	ENSMUSG00000029385	Ccng2	-	cyclin G2	protein-coding
mm_132868.1	chr16	48611726	48611741	+	1	NA	intron (NM_010816, intron 20 of 26)	intron (NM_010816, intron 20 of 26)	160223	NM_198297	77647	Mm.167298	NM_198297	ENSMUSG00000030775	Trat1	C030046M14Rik|Tcrim|Trim	T cell receptor associated transmembrane adaptor 1	protein-coding
mm_27496.1	chr3	54915986	54916021	-	1	NA	promoter-TSS (NM_177854)	promoter-TSS (NM_177854)	-116	NM_177854	329641	Mm.51187	NM_177854	ENSMUSG00000056306	Sertm1	6030405A18Rik	serine rich and transmembrane domain containing 1	protein-coding
mm_164436.1	chr16	48874321	48874327	+	1	NA	exon (NM_181596, exon 4 of 4)	exon (NM_181596, exon 4 of 4)	1716	NM_181596	245195	Mm.231288	NM_181596	ENSMUSG00000022651	Retnlg	Fizz3|Relmg|Xcp1	resistin like gamma	protein-coding
mm_64663.1	chr7	4164797	4164827	-	1	NA	promoter-TSS (NM_021454)	promoter-TSS (NM_021454)	-113	NM_021454	58804	Mm.34268	NM_021454	ENSMUSG00000063838	Cdc42ep5	1700027J19Rik|2010007O02Rik|Borg3|C85526|CEP5	CDC42 effector protein (Rho GTPase binding) 5	protein-coding
mm_141890.1	chr17	34861822	34861837	-	1	NA	TTS (NM_013484)	TTS (NM_013484)	685	NM_001142706	14962	Mm.653	NM_008198	ENSMUSG00000090231	Cfb	AI195813|AI255840|B|Bf|C2|Fb|H2-Bf	complement factor B	protein-coding
mm_21774.1	chr2	164846645	164846664	-	1	NA	intron (NM_011125, intron 9 of 15)	intron (NM_011125, intron 9 of 15)	11054	NM_011125	18830	Mm.6105	NM_011125	ENSMUSG00000017754	Pltp	Bpife|OD107	phospholipid transfer protein	protein-coding
mm_102048.1	chr11	52000722	52000744	-	1	NA	promoter-TSS (NM_009458)	promoter-TSS (NM_009458)	-267	NM_009458	22210	Mm.384918	NM_009458	ENSMUSG00000020390	Ube2b	2610301N02Rik|E2-14k|HR6B|Rad6b|mHR6B	ubiquitin-conjugating enzyme E2B	protein-coding
mm_81614.1	chr9	110766692	110766702	+	1	NA	exon (NM_010859, exon 3 of 7)	exon (NM_010859, exon 3 of 7)	3016	NM_010859	17897	Mm.7353	NM_010859	ENSMUSG00000059741	Myl3	MLC1s|MLC1v|Mylc|VLC1	myosin, light polypeptide 3	protein-coding
mm_60934.1	chr7	46861254	46861281	+	1	NA	promoter-TSS (NM_013580)	promoter-TSS (NM_013580)	4	NM_013580	16833	Mm.16563	NM_013580	ENSMUSG00000030851	Ldhc	LDH-C4|Ldh-3|Ldh-x|Ldh3|Ldhc4	lactate dehydrogenase C	protein-coding
mm_103230.1	chr11	70675588	70675591	-	1	NA	exon (NM_001190378, exon 13 of 22)	exon (NM_001190378, exon 13 of 22)	-6173	NM_001167669	216873	Mm.432524	NM_172561	ENSMUSG00000018287	Spag7	5730443G10|ACRP|FSA-1|Fsa1l	sperm associated antigen 7	protein-coding
mm_123077.1	chr14	55722224	55722264	-	1	NA	promoter-TSS (NM_019519)	promoter-TSS (NM_019519)	-68	NM_019519	56187	Mm.87216	NM_019519	ENSMUSG00000040472	Rabggta	gm	Rab geranylgeranyl transferase, a subunit	protein-coding
mm_33140.1	chr4	125085137	125085173	+	1	NA	promoter-TSS (NM_001290701)	promoter-TSS (NM_001290701)	21	NM_001290701	70088	Mm.291214	NM_027310	ENSMUSG00000028863	Meaf6	2310005N01Rik|2810036M01Rik	MYST/Esa1-associated factor 6	protein-coding
mm_858.1	chr1	52132547	52132561	+	1	NA	exon (NM_001205314, exon 6 of 25)	exon (NM_001205314, exon 6 of 25)	12932	NM_001205313	20846	Mm.277406	NM_009283	ENSMUSG00000026104	Stat1	2010005J02Rik|AA408197	signal transducer and activator of transcription 1	protein-coding
mm_44712.1	chr5	30945394	30945455	-	1	NA	promoter-TSS (NM_026770)	promoter-TSS (NM_026770)	3	NM_001160149	68567	Mm.45127	NM_026770	ENSMUSG00000029161	Cgref1	1110004G24Rik|AW045201|Cgr11	cell growth regulator with EF hand domain 1	protein-coding
mm_27143.1	chr3	32736744	32736777	-	1	NA	promoter-TSS (NM_025316)	promoter-TSS (NM_025316)	-5	NM_029017	74600	Mm.288960	NM_029017	ENSMUSG00000037531	Mrpl47	4833424P18Rik|CGI-204|ENSMUSG00000051761|Gm9859|L47mt|MRP-L47|MTF/L47|NCM1	mitochondrial ribosomal protein L47	protein-coding
mm_118419.1	chr14	7818005	7818018	+	1	NA	promoter-TSS (NM_001081427)	promoter-TSS (NM_001081427)	54	NM_134080	286940	Mm.489652	NM_134080	ENSMUSG00000025278	Flnb	AL024016|Fln-b	filamin, beta	protein-coding
mm_9327.1	chr1	171845537	171845539	-	1	NA	intron (NM_001289470, intron 2 of 8)	B4A|SINE|B4	5841	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_35281.1	chr4	20778710	20778730	-	1	NA	promoter-TSS (NM_172987)	promoter-TSS (NM_172987)	-52	NM_172987	269513	Mm.317473	NM_172987	ENSMUSG00000055761	Nkain3	C530048M05|E130310K16Rik	Na+/K+ transporting ATPase interacting 3	protein-coding
mm_12841.1	chr2	82063886	82063888	+	1	NA	intron (NM_175513, intron 1 of 3)	intron (NM_175513, intron 1 of 3)	10229	NM_175513	241514	Mm.119383	NM_175513	ENSMUSG00000070866	Zfp804a	C630007C17Rik|Znf804a	zinc finger protein 804A	protein-coding
mm_172635.1	chr8	20580077	20580080	+	1	NA	Intergenic	B3A|SINE|B2	-34849	NM_001270553	100861668	Mm.491087	NM_001270553	ENSMUSG00000095294	Gm21119	-	predicted gene, 21119	protein-coding
mm_84533.1	chr9	67155247	67155264	-	1	NA	intron (NR_045748, intron 1 of 2)	intron (NR_045748, intron 1 of 2)	21694	NR_045748	100502636	Mm.412607	NR_045748	ENSMUSG00000111556	Gm19299	-	predicted gene, 19299	ncRNA
mm_119236.1	chr14	33345613	33345636	+	1	NA	intron (NM_153800, intron 5 of 10)	intron (NM_153800, intron 5 of 10)	65400	NM_001310452	26419	Mm.21495	NM_016700	ENSMUSG00000021936	Mapk8	AI849689|JNK|JNK1|Prkm8|SAPK1	mitogen-activated protein kinase 8	protein-coding
mm_67736.1	chr7	90131129	90131138	-	1	NA	intron (NM_001252520, intron 1 of 20)	intron (NM_001252520, intron 1 of 20)	901	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_150116.1	chr19	29805270	29805293	+	1	NA	intron (NM_172836, intron 1 of 7)	CpG	728	NM_172836	240613	Mm.313351	NM_172836	ENSMUSG00000046138	9930021J03Rik	ENSMUSG00000048936|Gm9832|mKIAA2026	RIKEN cDNA 9930021J03 gene	protein-coding
mm_3831.1	chr1	159926054	159926065	+	1	NA	Intergenic	MIR3|SINE|MIR	-118321	NR_028111	67647	Mm.171518	NM_001024470	ENSMUSG00000090394	4930523C07Rik	-	RIKEN cDNA 4930523C07 gene	protein-coding
mm_89855.1	chr10	107421233	107421238	+	1	NA	3' UTR (NM_001039354, exon 6 of 6)	3' UTR (NM_001039354, exon 6 of 6)	64899	NM_008656	17877	Mm.4984	NM_008656	ENSMUSG00000000435	Myf5	B130010J22Rik|Myf-5|bHLHc2	myogenic factor 5	protein-coding
mm_37985.1	chr4	133622559	133622577	-	1	NA	intron (NM_001017968, intron 2 of 7)	intron (NM_001017968, intron 2 of 7)	10861	NM_001017968	503610	Mm.331948	NM_001017968	ENSMUSG00000037553	Zdhhc18	-	zinc finger, DHHC domain containing 18	protein-coding
mm_11999.1	chr2	57237652	57237729	+	1	NA	promoter-TSS (NM_010274)	promoter-TSS (NM_010274)	12	NM_001145820	14571	Mm.3711	NM_010274	ENSMUSG00000026827	Gpd2	AA408484|AI448216|AU021455|AW494132|GPDH|Gdm1|Gpd-m|Gpdh-m|TISP38	glycerol phosphate dehydrogenase 2, mitochondrial	protein-coding
mm_162785.1	chr10	70599310	70599312	-	1	NA	promoter-TSS (NM_178621)	promoter-TSS (NM_178621)	-20	NM_178621	70911	Mm.19825	NM_178621	ENSMUSG00000037747	Phyhipl	4921522K17Rik|AI267048	phytanoyl-CoA hydroxylase interacting protein-like	protein-coding
mm_164493.1	chr16	90708850	90708850	+	1	NA	Intergenic	Intergenic	18521	NM_025642	66578	Mm.180363	NM_025642	ENSMUSG00000022978	Mis18a	2610039C10Rik|2810018N07Rik	MIS18 kinetochore protein A	protein-coding
mm_2250.1	chr1	91062739	91062751	+	1	NA	intron (NM_001310732, intron 1 of 24)	intron (NM_001310732, intron 1 of 24)	9301	NM_008515	16978	Mm.45039	NM_008515	ENSMUSG00000026305	Lrrfip1	AU024550|Fliiap1	leucine rich repeat (in FLII) interacting protein 1	protein-coding
mm_32136.1	chr4	99194750	99194782	+	1	NA	intron (NM_175029, intron 1 of 10)	intron (NM_175029, intron 1 of 10)	619	NM_001145967	242557	Mm.241663	NM_175029	ENSMUSG00000028550	Atg4c	Apg4-C|Apg4c|Atg4cl|Autl1	autophagy related 4C, cysteine peptidase	protein-coding
mm_24021.1	chr3	87527229	87527239	+	1	NA	intron (NM_001286844, intron 1 of 4)	intron (NM_001286844, intron 1 of 4)	1656	NM_012051	27049	Mm.219460	NM_012051	ENSMUSG00000003382	Etv3	AI414410|METS|Pe1	ets variant 3	protein-coding
mm_59351.1	chr7	25659402	25659409	+	1	NA	promoter-TSS (NM_007533)	promoter-TSS (NM_007533)	252	NR_104358	27998	Mm.27853	NM_138586	ENSMUSG00000061286	Exosc5	D7Wsu180e	exosome component 5	protein-coding
mm_115611.1	chr13	12008876	12008880	-	1	NA	intron (NM_023868, intron 1 of 104)	intron (NM_023868, intron 1 of 104)	98067	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding
mm_25782.1	chr3	126607108	126607121	+	1	NA	intron (NM_001346636, intron 2 of 20)	intron (NM_001346636, intron 2 of 20)	10163	NM_023813	108058	Mm.255822	NM_023813	ENSMUSG00000053819	Camk2d	2810011D23Rik|8030469K03Rik|CaMK II|[d]-CaMKII	calcium/calmodulin-dependent protein kinase II, delta	protein-coding
mm_37658.1	chr4	128962429	128962449	-	1	NA	promoter-TSS (NM_172875)	promoter-TSS (NM_172875)	16	NM_172875	242669	Mm.215814	NM_172875	ENSMUSG00000028789	Azin2	4933429I20Rik|Adc|Azi2|B930082O19|ODC-p|Odcp	antizyme inhibitor 2	protein-coding
mm_170046.1	chr17	24720141	24720142	+	1	NA	promoter-TSS (NR_028515)	promoter-TSS (NR_028515)	78	NM_008503	16898	Mm.157452	NM_008503	ENSMUSG00000044533	Rps2	Llrep3|S4	ribosomal protein S2	protein-coding
mm_119532.1	chr14	47664236	47664258	+	1	NA	exon (NM_001293635, exon 2 of 41)	exon (NM_001293635, exon 2 of 41)	491	NM_001347522	16709	Mm.3110	NM_008477	ENSMUSG00000021843	Ktn1	-	kinectin 1	protein-coding
mm_108890.1	chr12	100007073	100007099	+	1	NA	intron (NM_146037, intron 2 of 2)	intron (NM_146037, intron 2 of 2)	42587	NM_001164427	217826	Mm.312335	NM_146037	ENSMUSG00000045404	Kcnk13	BB085247|F730021E22Rik|Gm1570|Gm1685	potassium channel, subfamily K, member 13	protein-coding
mm_155094.1	chrX	48256855	48256865	+	1	NA	promoter-TSS (NM_028276)	promoter-TSS (NM_028276)	-74	NM_028276	72554	Mm.336045	NM_028276	ENSMUSG00000063785	Utp14a	2700066J21Rik|JsdX|NY-CO-16|SDCCAG16|T25628|mKIAA0266	UTP14A small subunit processome component	protein-coding
mm_146983.1	chr18	33891475	33891512	-	1	NA	intron (NM_013512, intron 3 of 23)	intron (NM_013512, intron 3 of 23)	96601	NR_038151	69749	Mm.248787	NR_038151	ENSMUSG00000087590	Epb41l4aos	2410004N09Rik|Epb4.1l4aos	erythrocyte membrane protein band 4.1 like 4a, opposite strand	ncRNA
mm_63449.1	chr7	127511977	127512075	+	1	NA	promoter-TSS (NM_001304266)	promoter-TSS (NM_001304266)	43	NM_001304266	100043597	Mm.428042	NM_175144	ENSMUSG00000053877	Srcap	B930091H02Rik|D030022P06Rik|F630004O05Rik	Snf2-related CREBBP activator protein	protein-coding
mm_144194.1	chr18	7877544	7877584	+	1	NA	intron (NM_153085, intron 3 of 13)	intron (NM_153085, intron 3 of 13)	8367	NM_153085	225131	Mm.204524	NM_153085	ENSMUSG00000024283	Wac	1110067P07Rik|A230035H12Rik|AI256735|AI256776|Wwp4	WW domain containing adaptor with coiled-coil	protein-coding
mm_69050.1	chr7	126861808	126861824	-	1	NA	promoter-TSS (NM_153580)	promoter-TSS (NM_153580)	-156	NM_172746	233876	Mm.363427	NM_172746	ENSMUSG00000042606	Hirip3	B130036O03|C86302	HIRA interacting protein 3	protein-coding
mm_5218.1	chr1	13827533	13827540	-	1	NA	Intergenic	RMER19B|LTR|ERVK	-40607	NR_004447	433273	Mm.304088	NR_004447	ENSMUSG00000097711	Gm5523	EG433273	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_130161.1	chr15	91548705	91548712	-	1	NA	intron (NM_001033633, intron 1 of 9)	intron (NM_001033633, intron 1 of 9)	24553	NM_001033633	239606	Mm.360596	NM_001033633	ENSMUSG00000036298	Slc2a13	6530403A04|A630029G22Rik|AI505012|Gm308	solute carrier family 2 (facilitated glucose transporter), member 13	protein-coding
mm_14789.1	chr2	145860654	145860699	+	1	NA	exon (NM_028724, exon 9 of 13)	exon (NM_028724, exon 9 of 13)	-42565	NM_026425	67877	Mm.151168	NM_026425	ENSMUSG00000002728	Naa20	1500004D14Rik|2900026I01Rik|AU041458|D2Ertd186e|Nat5	N(alpha)-acetyltransferase 20, NatB catalytic subunit	protein-coding
mm_78195.1	chr9	21367866	21367881	+	1	NA	promoter-TSS (NM_001042707)	promoter-TSS (NM_001042707)	2	NM_001042709	16201	Mm.440026	NM_010561	ENSMUSG00000032178	Ilf3	MBII-26|MPHOSPH4|NF90|NFAR	interleukin enhancer binding factor 3	protein-coding
mm_9131.1	chr1	170788654	170788694	-	1	NA	exon (NM_001081304, exon 13 of 16)	exon (NM_001081304, exon 13 of 16)	79097	NM_001081304	226641	Mm.377046	NM_001081304	ENSMUSG00000026663	Atf6	9130025P16Rik|9630036G24|AA789574|Atf6alpha|ESTM49	activating transcription factor 6	protein-coding
mm_153281.1	chr19	37208019	37208067	-	1	NA	promoter-TSS (NM_198300)	promoter-TSS (NM_198300)	498	NM_001164336	69104	Mm.175989	NM_027314	ENSMUSG00000023307	March5	1810015H18Rik|2310008I22Rik|2700055A20Rik|5730499H23Rik|E130202O05Rik|MARCH-V|MITOL|Marchv|Rnf153	membrane-associated ring finger (C3HC4) 5	protein-coding
mm_74036.1	chr8	121906704	121906708	+	1	NA	intron (NM_011404, intron 1 of 9)	intron (NM_011404, intron 1 of 9)	980	NM_011404	20539	Mm.22374	NM_011404	ENSMUSG00000040010	Slc7a5	4F2LC|D0H16S474E|LAT1|TA1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 5	protein-coding
mm_73703.1	chr8	111686664	111686666	+	1	NA	exon (NM_025583, exon 7 of 7)	exon (NM_025583, exon 7 of 7)	3009	NR_106044	102466993		NR_106044	ENSMUSG00000099129	Mir7076	Gm27318|mmu-mir-7076	microRNA 7076	ncRNA
mm_64761.1	chr7	4866162	4866198	-	1	NA	promoter-TSS (NM_026158)	promoter-TSS (NM_026158)	-1	NM_026158	67441	Mm.41385	NM_026158	ENSMUSG00000052605	Isoc2b	0610042E07Rik|AI553388|Isoc2	isochorismatase domain containing 2b	protein-coding
mm_108717.1	chr12	87157601	87157641	+	1	NA	intron (NM_001252555, intron 2 of 9)	intron (NM_001252555, intron 2 of 9)	-2136	NR_136901	625237	Mm.390529	NR_136901		Gm6566	EG625237	predicted gene 6566	ncRNA
mm_60269.1	chr7	43841993	43842003	+	1	NA	promoter-TSS (NM_026806)	promoter-TSS (NM_026806)	-271	NM_026806	68668	Mm.458122	NM_026806	ENSMUSG00000074155	Klk5	1110030O19Rik	kallikrein related-peptidase 5	protein-coding
mm_85728.1	chr9	108340127	108340156	-	1	NA	3' UTR (NM_008160, exon 2 of 2)	3' UTR (NM_008160, exon 2 of 2)	1061	NM_001329528	14775	Mm.1090	NM_008160	ENSMUSG00000063856	Gpx1	AI195024|AL033363|CGPx|GPx-1|GSHPx-1|Gpx	glutathione peroxidase 1	protein-coding
mm_69402.1	chr7	132317165	132317192	-	1	NA	promoter-TSS (NM_029935)	promoter-TSS (NM_029935)	-23	NM_029935	77590	Mm.213582	NM_029935	ENSMUSG00000030930	Chst15	4631426J05Rik|BRAG|GalNAcS-6ST|MAd5|mKIAA0598	carbohydrate (N-acetylgalactosamine 4-sulfate 6-O) sulfotransferase 15	protein-coding
mm_74411.1	chr8	3624660	3624667	-	1	NA	TTS (NM_001195244)	TTS (NM_001195244)	386	NM_001129804	18545	Mm.440882	NM_008790	ENSMUSG00000004630	Pcp2	L7|Pcp-2	Purkinje cell protein 2 (L7)	protein-coding
mm_47285.1	chr5	122130407	122130421	-	1	NA	intron (NM_001289809, intron 1 of 11)	intron (NM_001289809, intron 1 of 11)	4479	NM_001289811	330188	Mm.386907	NM_183307	ENSMUSG00000043036	Ccdc63	4921511C16Rik	coiled-coil domain containing 63	protein-coding
mm_167684.1	chr9	83254534	83254540	-	1	NA	Intergenic	Intergenic	-107930	NM_026122	94353	Mm.244426	NM_026122	ENSMUSG00000066456	Hmgn3	1110002A15Rik|6330514M13Rik|BB071015|TRIP7	high mobility group nucleosomal binding domain 3	protein-coding
mm_109251.1	chr12	109457010	109457012	+	1	NA	intron (NR_033813, intron 4 of 5)	intron (NR_033813, intron 4 of 5)	3556	NM_010052	13386	Mm.157069	NM_010052	ENSMUSG00000040856	Dlk1	AW742678|DLK-1|DlkI|FA1|Ly107|Peg9|SCP1|ZOG|pG2|pref-1	delta-like 1 homolog (Drosophila)	protein-coding
mm_21432.1	chr2	158361473	158361503	-	1	NA	promoter-TSS (NR_015463)	promoter-TSS (NR_015463)	21	NR_015463	68108	Mm.119198	NR_015463		Snhg17	9430008C03Rik	small nucleolar RNA host gene 17	ncRNA
mm_155712.1	chrX	96096083	96096116	+	1	NA	promoter-TSS (NM_010833)	promoter-TSS (NM_010833)	54	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_143424.1	chr17	70846289	70846308	-	1	NA	exon (NM_001164077, exon 1 of 2)	exon (NM_001164077, exon 1 of 2)	479	NM_001164077	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_79672.1	chr9	59679830	59679845	+	1	NA	TTS (NM_011099)	TTS (NM_011099)	23469	NM_001253883	18746	Mm.326167	NM_011099	ENSMUSG00000032294	Pkm	AA414905|AL024370|AL024424|Pk-2|Pk-3|Pk3|Pkm2	pyruvate kinase, muscle	protein-coding
mm_16427.1	chr2	180385600	180385617	+	1	NA	promoter-TSS (NR_045331)	promoter-TSS (NR_045331)	4	NR_045331	622283	Mm.447602	NR_045331		Mir1a-1hg	EG622283|Gm6307	Mir1a-1 and Mir133a-2 host gene	ncRNA
mm_64727.1	chr7	4674539	4674551	-	1	NA	intron (NM_024172, intron 4 of 7)	intron (NM_024172, intron 4 of 7)	10418	NM_024172	66245	Mm.6803	NM_024172	ENSMUSG00000063802	Hspbp1	1500019G21Rik	HSPA (heat shock 70kDa) binding protein, cytoplasmic cochaperone 1	protein-coding
mm_121392.1	chr14	119108471	119108473	+	1	NA	Intergenic	Intergenic	-9038	NM_001081252	66435	Mm.213406	NM_025561	ENSMUSG00000042104	Uggt2	1810064L21Rik|3110001A05Rik|3110027P15Rik|A230065J02Rik|AW047562|Ugcgl2	UDP-glucose glycoprotein glucosyltransferase 2	protein-coding
mm_11874.1	chr2	49308946	49308977	+	1	NA	intron (NM_029924, intron 15 of 16)	intron (NM_029924, intron 15 of 16)	63061	NM_001290656	109241	Mm.440436	NM_029924	ENSMUSG00000036792	Mbd5	9430004D19Rik|AA536666|AI426407|C030040A15Rik|Gm1630|OTTMUSG00000012483	methyl-CpG binding domain protein 5	protein-coding
mm_49002.1	chr6	4756861	4756872	+	1	NA	exon (NM_130877, exon 2 of 2)	exon (NM_130877, exon 2 of 2)	9560	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_25402.1	chr3	107278821	107278829	+	1	NA	promoter-TSS (NM_026774)	promoter-TSS (NM_026774)	-33	NM_026774	68576	Mm.290035	NM_026774	ENSMUSG00000087260	Lamtor5	1110003H18Rik|Hbxip|XIP	late endosomal/lysosomal adaptor, MAPK and MTOR activator 5	protein-coding
mm_70862.1	chr8	24503094	24503106	+	1	NA	Intergenic	Intergenic	-18114	NR_035483	100316707		NR_035483	ENSMUSG00000088552	Mir1957a	Mir1957|mmu-mir-1957|mmu-mir-1957a	microRNA 1957a	ncRNA
mm_24135.1	chr3	88227435	88227438	+	1	NA	Intergenic	Intergenic	11838	NR_029817	387133		NR_029817	ENSMUSG00000106493	Mir9-1	Mirn9|Mirn9-1|mir-9-1|mmu-mir-9-1	microRNA 9-1	ncRNA
mm_142236.1	chr17	37481187	37481206	-	1	NA	3' UTR (NM_008204, exon 4 of 4)	3' UTR (NM_008204, exon 4 of 4)	2333	NM_008204	14990	Mm.329041	NM_008204	ENSMUSG00000016283	H2-M2	H-2M2|Thy19.4	histocompatibility 2, M region locus 2	protein-coding
mm_169390.1	chr14	43271717	43271722	+	1	NA	Intergenic	BGLII|LTR|ERVK	76092	NM_027940	71826	Mm.335855	NM_027940	ENSMUSG00000095384	1700001F09Rik	Gm10377	RIKEN cDNA 1700001F09 gene	protein-coding
mm_142716.1	chr17	47924657	47924680	-	1	NA	promoter-TSS (NM_028767)	promoter-TSS (NM_028767)	-36	NM_001110825	74123	Mm.240062	NM_028767	ENSMUSG00000023991	Foxp4	1200010K03Rik|2310007G05Rik|mFKHLA	forkhead box P4	protein-coding
mm_18857.1	chr2	75679412	75679432	-	1	NA	exon (NM_010902, exon 2 of 5)	exon (NM_010902, exon 2 of 5)	20132	NR_033513	627828	Mm.459502	NR_033513	ENSMUSG00000092086	Gm6793	EG627828	heterogeneous nuclear ribonucleoprotein A3 pseudogene	pseudo
mm_116942.1	chr13	56096175	56096189	-	1	NA	exon (NM_001159515, exon 5 of 9)	exon (NM_001159515, exon 5 of 9)	39368	NM_012015	26914	Mm.283802	NM_012015	ENSMUSG00000015937	H2afy	H2AF12M|mH2a1|macroH2A1	H2A histone family, member Y	protein-coding
mm_154553.1	chrM	15355	15365	-	1	NA	NA	Intergenic	NA	NA								
mm_104028.1	chr11	86201588	86201610	-	1	NA	promoter-TSS (NM_178309)	promoter-TSS (NM_178309)	239	NR_130958	74038	Mm.171304	NR_130958	ENSMUSG00000085208	Brip1os	4632419I22Rik	BRCA1 interacting protein C-terminal helicase 1, opposite strand	ncRNA
mm_92656.1	chr10	80406812	80406819	-	1	NA	promoter-TSS (NM_025650)	promoter-TSS (NM_025650)	6	NM_025650	66594	Mm.379119	NM_025650	ENSMUSG00000020163	Uqcr11	0710008D09Rik|AL022707|Uqcr	ubiquinol-cytochrome c reductase, complex III subunit XI	protein-coding
mm_134757.1	chr16	23225303	23225316	-	1	NA	promoter-TSS (NM_001252505)	promoter-TSS (NM_001252505)	569	NM_145933	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_125111.1	chr15	27968375	27968384	+	1	NA	intron (NM_001081302, intron 1 of 56)	intron (NM_001081302, intron 1 of 56)	57469	NM_001081302	223435	Mm.485422	NM_001081302	ENSMUSG00000022263	Trio	6720464I07Rik|AA408740|Solo	triple functional domain (PTPRF interacting)	protein-coding
mm_96522.1	chr11	68496566	68496582	+	1	NA	3' UTR (NM_177320, exon 19 of 19)	3' UTR (NM_177320, exon 19 of 19)	-6445	NM_001004435	104709	Mm.234573	NM_001004435	ENSMUSG00000046207	Pik3r6	BB220380|p84|p84 PIKAP|p87(PIKAP)|p87PIKAP	phosphoinositide-3-kinase, regulatory subunit 6	protein-coding
mm_154167.1	chr19	58675149	58675170	-	1	NA	exon (NM_026925, exon 6 of 13)	exon (NM_026925, exon 6 of 13)	4794	NM_026925	69060	Mm.20407	NM_026925	ENSMUSG00000046008	Pnlip	1810007A24Rik|PL|PTL	pancreatic lipase	protein-coding
mm_31200.1	chr4	43669667	43669678	+	1	NA	promoter-TSS (NM_175517)	promoter-TSS (NM_175517)	701	NM_001085508	242409	Mm.171489	NM_001085508	ENSMUSG00000078716	Tmem8b	4930500O05Rik	transmembrane protein 8B	protein-coding
mm_60705.1	chr7	45220449	45220459	+	1	NA	exon (NM_001285498, exon 5 of 12)	exon (NM_001285498, exon 5 of 12)	4701	NM_001285498	21677	Mm.3019	NM_011565	ENSMUSG00000030796	Tead2	ETF|Etdf|TEAD-2|TEF-4|TEF4	TEA domain family member 2	protein-coding
mm_46533.1	chr5	105699243	105699250	-	1	NA	promoter-TSS (NM_001122768)	promoter-TSS (NM_001122768)	-723	NM_001122768	231549	Mm.23837	NM_178701	ENSMUSG00000046079	Lrrc8d	2810473G09Rik|4930525N13Rik|A930019F03|Lrrc5	leucine rich repeat containing 8D	protein-coding
mm_159666.1	chr4	152377149	152377149	+	1	NA	intron (NM_029216, intron 24 of 40)	intron (NM_029216, intron 24 of 40)	38498	NM_001081376	269610	Mm.40192	NM_029216	ENSMUSG00000005045	Chd5	4930532L22Rik|AW060752|B230399N07Rik|CHD-5	chromodomain helicase DNA binding protein 5	protein-coding
mm_48952.1	chr6	4540600	4540620	+	1	NA	exon (NM_007743, exon 52 of 52)	exon (NM_007743, exon 52 of 52)	34992	NM_007743	12843	Mm.277792	NM_007743	ENSMUSG00000029661	Col1a2	AA960264|AI325291|Col1a-2|Cola-2|Cola2|oim	collagen, type I, alpha 2	protein-coding
mm_132042.1	chr16	27439817	27439835	+	1	NA	intron (NM_001025615, intron 8 of 9)	B1F1|SINE|Alu	50870	NM_001289436	67501	Mm.258985	NM_026202	ENSMUSG00000038127	Ccdc50	C3orf6	coiled-coil domain containing 50	protein-coding
mm_34212.1	chr4	140961405	140961415	+	1	NA	exon (NM_023374, exon 1 of 8)	exon (NM_023374, exon 1 of 8)	139	NM_023374	67680	Mm.246965	NM_023374	ENSMUSG00000009863	Sdhb	0710008N11Rik	succinate dehydrogenase complex, subunit B, iron sulfur (Ip)	protein-coding
mm_22787.1	chr3	22078767	22078770	+	1	NA	intron (NM_030732, intron 1 of 15)	ID4|SINE|ID	2116	NM_030732	81004	Mm.202966	NM_030732	ENSMUSG00000027630	Tbl1xr1	8030499H02Rik|A630076E03Rik|AW539987|C21|C230089I12Rik|DC42|Ira1|TBLR1	transducin (beta)-like 1X-linked receptor 1	protein-coding
mm_26315.1	chr3	142520117	142520119	+	1	NA	intron (NM_153564, intron 10 of 10)	intron (NM_153564, intron 10 of 10)	-10218	NM_001083312	229900	Mm.45740	NM_145545	ENSMUSG00000040253	Gbp7	9830147J24Rik	guanylate binding protein 7	protein-coding
mm_79666.1	chr9	59661461	59661512	+	1	NA	intron (NM_001253883, intron 1 of 10)	intron (NM_001253883, intron 1 of 10)	5118	NM_001253883	18746	Mm.326167	NM_011099	ENSMUSG00000032294	Pkm	AA414905|AL024370|AL024424|Pk-2|Pk-3|Pk3|Pkm2	pyruvate kinase, muscle	protein-coding
mm_129807.1	chr15	82987834	82987866	-	1	NA	Intergenic	Intergenic	-28554	NR_037241	100526477		NR_037241	ENSMUSG00000092751	Mir3080	mmu-mir-3080	microRNA 3080	ncRNA
mm_49218.1	chr6	15779108	15779118	+	1	NA	intron (NM_175088, intron 4 of 4)	intron (NM_175088, intron 4 of 4)	58452	NM_175088	16543	Mm.1314	NM_175088	ENSMUSG00000041390	Mdfic	Kdt1|Mdfid	MyoD family inhibitor domain containing	protein-coding
mm_86899.1	chr10	22306697	22306732	+	1	NA	promoter-TSS (NR_015465)	promoter-TSS (NR_015465)	-6	NR_015465	606736	Mm.387042	NR_015465	ENSMUSG00000097352	C920009B18Rik	-	RIKEN cDNA C920009B18 gene	ncRNA
mm_75216.1	chr8	39605648	39605665	-	1	NA	3' UTR (NM_031195, exon 9 of 9)	3' UTR (NM_031195, exon 9 of 9)	37022	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_133334.1	chr16	78695023	78695036	+	1	NA	Intergenic	Lx8|LINE|L1	-118341	NM_025967	67102	Mm.37332	NM_025967	ENSMUSG00000022864	D16Ertd472e	1700010I10Rik|2310009O17Rik|E330003K22Rik|Eurl	DNA segment, Chr 16, ERATO Doi 472, expressed	protein-coding
mm_143518.1	chr17	73108637	73108672	-	1	NA	intron (NM_001081071, intron 1 of 5)	intron (NM_001081071, intron 1 of 5)	669	NM_001177967	225010	Mm.329194	NM_001081071	ENSMUSG00000054469	Lclat1	AI181996|Agpat8|Alcat1|Gm91|Lycat	lysocardiolipin acyltransferase 1	protein-coding
mm_60560.1	chr7	44481309	44481320	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-3203	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_85424.1	chr9	103489350	103489376	-	1	NA	intron (NM_178638, intron 4 of 5)	intron (NM_178638, intron 4 of 5)	-9035	NM_001002896	107993	Mm.335403	NM_001002896	ENSMUSG00000032556	Bfsp2	AI448593|CP49	beaded filament structural protein 2, phakinin	protein-coding
mm_38283.1	chr4	136890251	136890255	-	1	NA	exon (NM_007574, exon 3 of 3)	exon (NM_007574, exon 3 of 3)	2661	NM_007574	12262	Mm.439732	NM_007574	ENSMUSG00000036896	C1qc	AI385742|C1qg|Ciqc	complement component 1, q subcomponent, C chain	protein-coding
mm_70399.1	chr8	11312509	11312531	+	1	NA	promoter-TSS (NM_009932)	promoter-TSS (NM_009932)	-285	NM_009932	12827	Mm.181021	NM_009932	ENSMUSG00000031503	Col4a2	Col4a-2	collagen, type IV, alpha 2	protein-coding
mm_148578.1	chr19	4962335	4962362	+	1	NA	promoter-TSS (NM_025553)	promoter-TSS (NM_025553)	42	NM_025553	66419	Mm.28494	NM_025553	ENSMUSG00000024902	Mrpl11	2410001P07Rik|L11mt	mitochondrial ribosomal protein L11	protein-coding
mm_124817.1	chr15	9071290	9071304	+	1	NA	promoter-TSS (NM_001085410)	promoter-TSS (NM_001085410)	37	NM_001040395	68646	Mm.244226	NM_001040395	ENSMUSG00000022253	Nadk2	MNADK|Nadkd1	NAD kinase 2, mitochondrial	protein-coding
mm_117699.1	chr13	94358893	94358931	-	1	NA	promoter-TSS (NM_009680)	promoter-TSS (NM_009680)	11	NR_045619	328309	Mm.174191	NM_183205		Gm9776	A530089L17|ENSMUSG00000042857	predicted gene 9776	ncRNA
mm_170928.1	chr2	40127917	40127928	-	1	NA	Intergenic	Intergenic	-901584	NM_024209	67857	Mm.389242	NM_024209	ENSMUSG00000026753	Ppp6c	2310003C10Rik	protein phosphatase 6, catalytic subunit	protein-coding
mm_72481.1	chr8	83652633	83652633	+	1	NA	promoter-TSS (NM_018771)	promoter-TSS (NM_018771)	-45	NM_018771	67903	Mm.20945	NM_018771	ENSMUSG00000019433	Gipc1	GIPC|Glut1CIP|Rgs19ip1|Semcap1|TIP-2|TaxIP2	GIPC PDZ domain containing family, member 1	protein-coding
mm_124183.1	chr14	93890693	93890716	-	1	NA	promoter-TSS (NM_001271798)	promoter-TSS (NM_001271798)	-25	NM_001346722	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding
mm_170285.1	chr18	28188891	28188891	-	1	NA	Intergenic	Intergenic	-371273	NR_045398	320624	Mm.50107	NR_045398		4930474G06Rik	-	RIKEN cDNA 4930474G06 gene	ncRNA
mm_12760.1	chr2	79255725	79255725	+	1	NA	exon (NM_010576, exon 1 of 28)	exon (NM_010576, exon 1 of 28)	299	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D|Itga4B	integrin alpha 4	protein-coding
mm_42261.1	chr5	114103340	114103370	+	1	NA	intron (NM_001033202, intron 2 of 12)	intron (NM_001033202, intron 2 of 12)	3022	NM_001033202	100756	Mm.240421	NM_001033202	ENSMUSG00000029592	Usp30	6330590F17Rik|AI851327|D5Ertd483e	ubiquitin specific peptidase 30	protein-coding
mm_157684.1	chrX	60147672	60147680	-	1	NA	promoter-TSS (NM_133197)	promoter-TSS (NM_133197)	24	NM_133197	109904	Mm.93796	NM_133197	ENSMUSG00000031139	Mcf2	B230117G22Rik|Dbl|Mcf-2	mcf.2 transforming sequence	protein-coding
mm_90045.1	chr10	115833040	115833042	+	1	NA	intron (NM_146010, intron 2 of 7)	intron (NM_146010, intron 2 of 7)	15757	NM_001168679	216350	Mm.22270	NM_146010	ENSMUSG00000034127	Tspan8	C76990|E330007O21Rik|Tm4sf3	tetraspanin 8	protein-coding
mm_105767.1	chr11	109611354	109611414	-	1	NA	promoter-TSS (NM_145940)	promoter-TSS (NM_145940)	5	NM_145940	52639	Mm.35817	NM_145940	ENSMUSG00000041895	Wipi1	4930533H01Rik|AW411817|D11Ertd498e	WD repeat domain, phosphoinositide interacting 1	protein-coding
mm_59512.1	chr7	27581226	27581258	+	1	NA	3' UTR (NM_175107, exon 10 of 10)	3' UTR (NM_175107, exon 10 of 10)	-10310	NM_001110208	11652	Mm.177194	NM_007434	ENSMUSG00000004056	Akt2	2410016A19Rik|AW554154|PKB|PKBbeta	thymoma viral proto-oncogene 2	protein-coding
mm_82069.1	chr9	122875515	122875521	+	1	NA	Intergenic	Intergenic	-9512	NM_173364	235682	Mm.326477	NM_173364	ENSMUSG00000047036	Zfp445	AW610627|ZNF168|Znf445|mszf29|mszf50	zinc finger protein 445	protein-coding
mm_118631.1	chr14	21272716	21272728	+	1	NA	intron (NM_001243041, intron 6 of 10)	intron (NM_001243041, intron 6 of 10)	196570	NM_001243041	11534	Mm.188734	NM_134079	ENSMUSG00000039197	Adk	2310026J05Rik|5033405D03Rik|AI255373|AI987814|Ak	adenosine kinase	protein-coding
mm_109300.1	chr12	109560291	109560301	+	1	NA	non-coding (NR_003633, exon 5 of 5)	non-coding (NR_003633, exon 5 of 5)	-3396	NR_030427	791079		NR_030427	ENSMUSG00000076451	Mir770	Mirn770|mir-770|mmu-mir-770	microRNA 770	ncRNA
mm_73617.1	chr8	110126407	110126435	+	1	NA	Intergenic	Intergenic	41785	NM_007586	12308	Mm.2755	NM_007586	ENSMUSG00000003657	Calb2	CR	calbindin 2	protein-coding
mm_22609.1	chr3	14530628	14530656	+	1	NA	Intergenic	L1_Mur3|LINE|L1	-3146	NM_001163579	71710	Mm.257449	NM_028915	ENSMUSG00000027550	Lrrcc1	1200008A14Rik|4932441F23Rik|AI195358|AI447421	leucine rich repeat and coiled-coil domain containing 1	protein-coding
mm_95178.1	chr11	41499137	41499140	+	1	NA	Intergenic	Intergenic	501576	NM_177408	14406	Mm.5309	NM_008073	ENSMUSG00000020436	Gabrg2	GABAA-R|Gabrg-2|gamma2	gamma-aminobutyric acid (GABA) A receptor, subunit gamma 2	protein-coding
mm_80809.1	chr9	96392315	96392316	+	1	NA	Intergenic	Intergenic	-28016	NM_007502	11933	Mm.424	NM_007502	ENSMUSG00000032412	Atp1b3	AA409958|AI664000|AW212096	ATPase, Na+/K+ transporting, beta 3 polypeptide	protein-coding
mm_103717.1	chr11	79527675	79527691	-	1	NA	exon (NM_010161, exon 2 of 2)	exon (NM_010161, exon 2 of 2)	2926	NM_146023	101488212	Mm.439665	NM_146023	ENSMUSG00000070354	Gm21975	Evi2a-evi2b	predicted gene 21975	protein-coding
mm_113475.1	chr13	36730069	36730078	+	1	NA	intron (NM_153529, intron 2 of 2)	intron (NM_153529, intron 2 of 2)	4404	NM_153529	68404	Mm.232930	NM_153529	ENSMUSG00000039114	Nrn1	0710008J23Rik|Cpg15|Nrn	neuritin 1	protein-coding
mm_171593.1	chr4	147651842	147651844	-	1	NA	Intergenic	RLTR27|LTR|ERVK	-9335	NM_145078	112422	Mm.327194	NM_145078	ENSMUSG00000066000	Zfp979	2610305D13Rik|Ssm1b	zinc finger protein 979	protein-coding
mm_25502.1	chr3	109509147	109509185	+	1	NA	intron (NM_020505, intron 8 of 26)	B3|SINE|B2	-64841	NM_146139	57257	Mm.282257	NM_020505	ENSMUSG00000033721	Vav3	A530094I06Rik|AA986410|Idd18.1	vav 3 oncogene	protein-coding
mm_93135.1	chr10	92162728	92162740	-	1	NA	intron (NR_028262, intron 2 of 12)	intron (NR_028262, intron 2 of 12)	2444	NR_028262	110333	Mm.429764	NR_028262		Rmst	100041799|AI853140|C230053E11Rik|D930049J19Rik|Dmt2|Gm3515|M2|Ncrms	rhabdomyosarcoma 2 associated transcript (non-coding RNA)	ncRNA
mm_98322.1	chr11	90255141	90255159	+	1	NA	intron (NM_026178, intron 1 of 6)	B4A|SINE|B4	5674	NM_026178	67468	Mm.277518	NM_026178	ENSMUSG00000003948	Mmd	1200017E07Rik|1810073C06Rik|AA690185	monocyte to macrophage differentiation-associated	protein-coding
mm_146422.1	chr18	84721142	84721146	+	1	NA	intron (NM_173770, intron 1 of 4)	intron (NM_173770, intron 1 of 4)	902	NM_173770	240479	Mm.472378	NM_173770	ENSMUSG00000047992	Fam69c	B230399E16Rik	family with sequence similarity 69, member C	protein-coding
mm_23948.1	chr3	84829787	84829790	+	1	NA	intron (NM_001177773, intron 1 of 13)	B1_Mur3|SINE|Alu	14211	NM_001177773	50754	Mm.196475	NM_080428	ENSMUSG00000028086	Fbxw7	1110001A17Rik|AGO|Cdc4|Fbw7|Fbwd6|Fbx30|Fbxo30|Fbxw6|SEL-10	F-box and WD-40 domain protein 7	protein-coding
mm_9215.1	chr1	171231224	171231233	-	1	NA	exon (NM_010185, exon 2 of 5)	exon (NM_010185, exon 2 of 5)	3121	NM_010185	14127	Mm.22673	NM_010185	ENSMUSG00000058715	Fcer1g	AI573376|CD23|FcR-gamma|FcR[g]|FcRgamma|Fce1g|FcepsilonRI|Ly-50	Fc receptor, IgE, high affinity I, gamma polypeptide	protein-coding
mm_159236.1	chr2	144823713	144823713	+	1	NA	promoter-TSS (NM_025490)	promoter-TSS (NM_025490)	47	NM_025490	66328	Mm.45377	NM_025490	ENSMUSG00000027431	Scp2d1	1700010M22Rik	SCP2 sterol-binding domain containing 1	protein-coding
mm_94647.1	chr11	16951372	16951417	+	1	NA	promoter-TSS (NM_176982)	promoter-TSS (NM_176982)	-16	NM_176982	319701	Mm.120672	NM_176982	ENSMUSG00000044966	Fbxo48	A630050E13Rik	F-box protein 48	protein-coding
mm_157518.1	chrX	49797871	49797900	-	1	NA	promoter-TSS (NM_177591)	promoter-TSS (NM_177591)	-140	NM_177591	209268	Mm.110505	NM_177591	ENSMUSG00000031111	Igsf1	5330413N23|5530402E03|AI747649|InhBP/p120|mKIAA0364	immunoglobulin superfamily, member 1	protein-coding
mm_55997.1	chr6	86397099	86397150	-	1	NA	promoter-TSS (NM_025823)	promoter-TSS (NM_025823)	26	NM_025823	66881	Mm.30849	NM_025823	ENSMUSG00000029998	Pcyox1	1200015P13Rik|AI115532|AI448340|PCL1|Pcly	prenylcysteine oxidase 1	protein-coding
mm_118501.1	chr14	13588840	13588841	+	1	NA	intron (NM_001163032, intron 3 of 4)	intron (NM_001163032, intron 3 of 4)	-82036	NM_177624	218739	Mm.39919	NM_177624	ENSMUSG00000044772	Sntn	A430083B19Rik	sentan, cilia apical structure protein	protein-coding
mm_13009.1	chr2	90917256	90917266	+	1	NA	intron (NM_025576, intron 3 of 4)	intron (NM_025576, intron 3 of 4)	789	NM_025576	66461	Mm.23926	NM_025576		Ptpmt1	1110001D10Rik|2810004N20Rik|PLIP	protein tyrosine phosphatase, mitochondrial 1	protein-coding
mm_156508.1	chrX	150147493	150147503	+	1	NA	Intergenic	RLTR9D|LTR|ERVK	165866	NM_001101501	333588	Mm.159296	NM_001101501		Gm15104	OTTMUSG00000018998	predicted gene 15104	protein-coding
mm_49754.1	chr6	34751575	34751578	+	1	NA	intron (NM_001347100, intron 5 of 13)	intron (NM_001347100, intron 5 of 13)	-28856	NM_001289657	76223	Mm.150047	NM_178630	ENSMUSG00000038836	Agbl3	2900053G10Rik|4930431N21Rik|6530406M24Rik|CCP3	ATP/GTP binding protein-like 3	protein-coding
mm_156261.1	chrX	136822848	136822851	+	1	NA	5' UTR (NM_011123, exon 1 of 7)	5' UTR (NM_011123, exon 1 of 7)	103	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_116871.1	chr13	55018548	55018561	-	1	NA	intron (NM_001206392, intron 1 of 17)	intron (NM_001206392, intron 1 of 17)	2265	NM_001206390	212032	Mm.267479	NM_001033245	ENSMUSG00000025877	Hk3	HK III|HK-III	hexokinase 3	protein-coding
mm_113671.1	chr13	42728842	42728842	+	1	NA	intron (NM_001005740, intron 1 of 12)	intron (NM_001005740, intron 1 of 12)	19261	NM_001005740	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding
mm_119095.1	chr14	30895401	30895412	+	1	NA	exon (NM_001289633, exon 13 of 22)	exon (NM_001289633, exon 13 of 22)	8930	NM_001289632	16427	Mm.34819	NM_018746	ENSMUSG00000021922	Itih4	ITI-HC4|Itih-4|PK-120	inter alpha-trypsin inhibitor, heavy chain 4	protein-coding
mm_68122.1	chr7	102120181	102120185	-	1	NA	3' UTR (NM_001287164, exon 33 of 33)	3' UTR (NM_001287164, exon 33 of 33)	-3470	NM_001081424	504186	Mm.334074	NM_001081424	ENSMUSG00000066279	Chrna10	-	cholinergic receptor, nicotinic, alpha polypeptide 10	protein-coding
mm_89926.1	chr10	111232166	111232177	+	1	NA	intron (NM_175489, intron 3 of 23)	B2_Mm2|SINE|B2	-66508	NM_027914	71769	Mm.45256	NM_027914	ENSMUSG00000035759	Bbs10	1300007O09Rik|AI452285	Bardet-Biedl syndrome 10 (human)	protein-coding
mm_38090.1	chr4	134227360	134227388	-	1	NA	promoter-TSS (NM_177866)	promoter-TSS (NM_177866)	9	NM_001130030	329954	Mm.79072	NM_177866	ENSMUSG00000048003	Catsper4	4933412L05	cation channel, sperm associated 4	protein-coding
mm_137429.1	chr17	26270391	26270402	+	1	NA	intron (NR_037906, intron 5 of 8)	intron (NR_037906, intron 5 of 8)	17486	NR_037905	66978	Mm.440216	NM_025881	ENSMUSG00000024188	Luc7l	1810045C04Rik|2410018D03Rik	Luc7-like	protein-coding
mm_13642.1	chr2	114049551	114049582	+	1	NA	exon (NM_009608, exon 4 of 7)	exon (NM_009608, exon 4 of 7)	3309	NM_009608	11464	Mm.686	NM_009608	ENSMUSG00000068614	Actc1	Actc-1	actin, alpha, cardiac muscle 1	protein-coding
mm_171473.1	chr4	145781558	145781559	+	1	NA	promoter-TSS (NM_001083918)	promoter-TSS (NM_001083918)	15	NM_001083918	666532	Mm.392861	NM_001083918	ENSMUSG00000067916	Zfp991	Gm13139|OTTMUSG00000010657	zinc finger protein 991	protein-coding
mm_43979.1	chr5	146261240	146261253	+	1	NA	intron (NM_153599, intron 2 of 12)	LSU-rRNA_Hsa|rRNA|rRNA	29571	NM_153599	264064	Mm.260576	NM_153599	ENSMUSG00000029635	Cdk8	-	cyclin-dependent kinase 8	protein-coding
mm_122062.1	chr14	30378413	30378417	-	1	NA	intron (NM_028981, intron 1 of 46)	intron (NM_028981, intron 1 of 46)	-24929	NM_001083616	12289	Mm.9772	NM_028981	ENSMUSG00000015968	Cacna1d	8430418G19Rik|C79217|Cach3|Cacn4|Cacnl1a2|Cav1.3|Cchl1a|Cchl1a2|D-LTCC	calcium channel, voltage-dependent, L type, alpha 1D subunit	protein-coding
mm_154786.1	chrX	13071262	13071297	+	1	NA	promoter-TSS (NM_009481)	promoter-TSS (NM_009481)	-219	NM_009481	22284	Mm.242646	NM_009481	ENSMUSG00000031010	Usp9x	5730589N07Rik|AA407302|AA407699|AL022658|AL022749|Dffrx|FAF-X|Fafl	ubiquitin specific peptidase 9, X chromosome	protein-coding
mm_78355.1	chr9	25504410	25504424	+	1	NA	intron (NM_026189, intron 2 of 7)	intron (NM_026189, intron 2 of 7)	22820	NM_026189	67484	Mm.112977	NM_026189	ENSMUSG00000036611	Eepd1	2310005P05Rik|AI481005	endonuclease/exonuclease/phosphatase family domain containing 1	protein-coding
mm_95787.1	chr11	54956225	54956240	+	1	NA	intron (NM_001199275, intron 1 of 18)	CpG-1959	6708	NM_021327	57783	Mm.259671	NM_021327	ENSMUSG00000020400	Tnip1	ABIN|ABIN-1|ABIN1|AU018810|Naf1|Nef|VAN	TNFAIP3 interacting protein 1	protein-coding
mm_59296.1	chr7	25088356	25088365	+	1	NA	Intergenic	T-rich|Low_complexity|Low_complexity	8815	NR_105855	102465968		NR_105855	ENSMUSG00000098441	Mir6537	Gm27808|mmu-mir-6537	microRNA 6537	ncRNA
mm_59087.1	chr7	19696321	19696337	+	1	NA	TTS (NM_009696)	TTS (NM_009696)	2069	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_159742.1	chr5	71658308	71658308	-	1	NA	promoter-TSS (NM_010251)	promoter-TSS (NM_010251)	0	NM_010251	14397	Mm.248731	NM_010251	ENSMUSG00000029211	Gabra4	Gabra-4	gamma-aminobutyric acid (GABA) A receptor, subunit alpha 4	protein-coding
mm_25299.1	chr3	105959454	105959541	+	1	NA	promoter-TSS (NM_027432)	promoter-TSS (NM_027432)	-1	NM_027432	70465	Mm.5110	NM_027432	ENSMUSG00000000561	Wdr77	2610003I18Rik|2610312E17Rik|C79984|p44/MEP50	WD repeat domain 77	protein-coding
mm_129083.1	chr15	75894475	75894529	-	1	NA	promoter-TSS (NM_172607)	promoter-TSS (NM_172607)	-21	NM_172607	223646	Mm.288368	NM_172607	ENSMUSG00000022574	Naprt	9130210N20Rik|Naprt1	nicotinate phosphoribosyltransferase	protein-coding
mm_160902.1	chr11	75911079	75911079	-	1	NA	promoter-TSS (NM_029548)	promoter-TSS (NM_029548)	-20	NM_029548	380714	Mm.425697	NM_029548	ENSMUSG00000020847	Rph3al	Gm1753|Noc2	rabphilin 3A-like (without C2 domains)	protein-coding
mm_127482.1	chr15	101274601	101274610	+	1	NA	3' UTR (NM_010444, exon 7 of 7)	3' UTR (NM_010444, exon 7 of 7)	7759	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_51640.1	chr6	86004353	86004354	+	1	NA	Intergenic	Intergenic	-12838	NM_012013	26910	Mm.8024	NM_012013	ENSMUSG00000030001	Figla	FIGalpha|bHLHc8	folliculogenesis specific basic helix-loop-helix	protein-coding
mm_120771.1	chr14	73552781	73552811	+	1	NA	promoter-TSS (NM_011506)	promoter-TSS (NM_011506)	10	NM_011506	20916	Mm.38951	NM_011506	ENSMUSG00000022110	Sucla2	4930547K18Rik|A-SCS	succinate-Coenzyme A ligase, ADP-forming, beta subunit	protein-coding
mm_117414.1	chr13	74220789	74220803	-	1	NA	intron (NM_001317351, intron 6 of 9)	intron (NM_001317351, intron 6 of 9)	-12096	NM_177333	211446	Mm.261859	NM_177333	ENSMUSG00000034152	Exoc3	2810050O03Rik|E430013E20Rik|Sec6|Sec6l1	exocyst complex component 3	protein-coding
mm_118318.1	chr13	113567869	113567871	-	1	NA	Intergenic	Intergenic	50694	NM_130796	170625	Mm.33721	NM_130796	ENSMUSG00000042364	Snx18	Snag1	sorting nexin 18	protein-coding
mm_149139.1	chr19	9003755	9003766	+	1	NA	exon (NM_009643, exon 5 of 5)	exon (NM_009643, exon 5 of 5)	-14144	NR_105786	102465190		NR_105786	ENSMUSG00000099308	Mir6367	Gm27467|mmu-mir-6367	microRNA 6367	ncRNA
mm_119527.1	chr14	47648400	47648427	+	1	NA	promoter-TSS (NM_001293636)	promoter-TSS (NM_001293636)	-898	NM_001347527	16709	Mm.3110	NM_008477	ENSMUSG00000021843	Ktn1	-	kinectin 1	protein-coding
mm_73268.1	chr8	104535054	104535081	+	1	NA	promoter-TSS (NM_144931)	promoter-TSS (NM_144931)	367	NM_001301164	12354	Mm.129265	NM_053070	ENSMUSG00000031883	Car7	AV343731|Ca7	carbonic anhydrase 7	protein-coding
mm_99959.1	chr11	113649520	113649560	+	1	NA	promoter-TSS (NM_013581)	promoter-TSS (NM_013581)	11	NM_013581	16834	Mm.261620	NM_013581	ENSMUSG00000018661	Cog1	6030445I15|Ldlb|mKIAA1381	component of oligomeric golgi complex 1	protein-coding
mm_4817.1	chr1	185431917	185431929	+	1	NA	non-coding (NR_038006, exon 2 of 2)	non-coding (NR_038006, exon 2 of 2)	9896	NR_038006	319562	Mm.184335	NM_176943	ENSMUSG00000051295	9630028B13Rik	-	RIKEN cDNA 9630028B13 gene	ncRNA
mm_27127.1	chr3	32341146	32341164	-	1	NA	3' UTR (NM_009517, exon 6 of 6)	3' UTR (NM_009517, exon 6 of 6)	-24334	NR_027966	67576	Mm.435324	NR_027966		4930429B21Rik	-	RIKEN cDNA 4930429B21 gene	ncRNA
mm_41876.1	chr5	104662336	104662349	+	1	NA	Intergenic	Intergenic	90670	NM_001346671	69623	Mm.69919	NM_027142		Zfp33b	2310012P17Rik	zinc finger protein 33B	protein-coding
mm_113380.1	chr13	33016146	33016163	+	1	NA	3' UTR (NM_009256, exon 7 of 7)	3' UTR (NM_009256, exon 7 of 7)	-11260	NM_011452	20706	Mm.45371	NM_011452	ENSMUSG00000021403	Serpinb9b	1600019A21Rik|R86|SPI-CI|Spi10|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 9b	protein-coding
mm_160404.1	chr8	71487891	71487891	+	1	NA	promoter-TSS (NM_032544)	promoter-TSS (NM_032544)	-212	NM_032544	70359	Mm.142112	NM_032544	ENSMUSG00000007610	Gtpbp3	2410009F13Rik|AI607903	GTP binding protein 3	protein-coding
mm_6203.1	chr1	66765085	66765087	-	1	NA	intron (NM_177645, intron 5 of 13)	intron (NM_177645, intron 5 of 13)	52509	NM_177645	68691	Mm.240912	NM_177645	ENSMUSG00000026004	Kansl1l	1110028C15Rik|1190030G24|AI427598|C430010P07Rik|mKIAA4189	KAT8 regulatory NSL complex subunit 1-like	protein-coding
mm_51853.1	chr6	90462563	90462587	+	1	NA	promoter-TSS (NM_023184)	promoter-TSS (NM_023184)	-51	NM_023184	66277	Mm.38343	NM_023184	ENSMUSG00000030087	Klf15	1810013I09Rik|AV048136|AW494632|CKLF|KKLF	Kruppel-like factor 15	protein-coding
mm_2047.1	chr1	87336609	87336613	+	1	NA	intron (NM_146112, intron 2 of 28)	B1F2|SINE|Alu	9613	NM_001110212	227331	Mm.23065	NM_146112	ENSMUSG00000048000	Gigyf2	2610016F01Rik|A830080H02Rik|AI852361|AW259676|BC006835|Tnrc15|mKIAA0642	GRB10 interacting GYF protein 2	protein-coding
mm_15625.1	chr2	162661305	162661320	+	1	NA	promoter-TSS (NM_021464)	promoter-TSS (NM_021464)	149	NR_033569	77288	Mm.376571	NR_033569		9430021M05Rik	-	RIKEN cDNA 9430021M05 gene	ncRNA
mm_40710.1	chr5	65863776	65863795	+	1	NA	5' UTR (NM_001081105, exon 1 of 3)	5' UTR (NM_001081105, exon 1 of 3)	216	NM_001081105	74734	Mm.20323	NM_001081105	ENSMUSG00000029204	Rhoh	5830400A04Rik|AU019774|Arhh	ras homolog family member H	protein-coding
mm_72866.1	chr8	88650536	88650546	+	1	NA	intron (NM_145857, intron 1 of 12)	intron (NM_145857, intron 1 of 12)	3194	NM_145857	257632	Mm.222633	NM_145857	ENSMUSG00000055994	Nod2	ACUG|BLAU|CD|Card15|F830032C23Rik|IBD1|Nlrc2	nucleotide-binding oligomerization domain containing 2	protein-coding
mm_63376.1	chr7	127212614	127212630	+	1	NA	intron (NM_016754, intron 1 of 6)	ID_B1|SINE|B4	1014	NM_016754	17907	Mm.14526	NM_016754	ENSMUSG00000030672	Mylpf	2410014J02Rik|MLC-2|Mlc2	myosin light chain, phosphorylatable, fast skeletal muscle	protein-coding
mm_139631.1	chr17	57367461	57367471	+	1	NA	intron (NM_010130, intron 2 of 21)	intron (NM_010130, intron 2 of 21)	8780	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_136195.1	chr16	89508314	89508327	-	1	NA	promoter-TSS (NM_027771)	promoter-TSS (NM_027771)	3	NM_027771	71363	Mm.158680	NM_027771	ENSMUSG00000056706	Krtap7-1	5430433J05Rik	keratin associated protein 7-1	protein-coding
mm_28056.1	chr3	84191243	84191315	-	1	NA	intron (NM_001271725, intron 5 of 11)	intron (NM_001271725, intron 5 of 11)	16641	NR_036654	624713	Mm.442604	NR_036654		Gm6525	EG624713	ribosomal protein L36a pseudogene	pseudo
mm_100906.1	chr11	6213874	6213914	-	1	NA	intron (NM_207242, intron 18 of 18)	intron (NM_207242, intron 18 of 18)	-13443	NM_173748	209586	Mm.25321	NM_173748	ENSMUSG00000053838	Nudcd3	AI427847|BC024322|mKIAA1068	NudC domain containing 3	protein-coding
mm_166014.1	chr4	120570308	120570311	-	1	NA	promoter-TSS (NM_016748)	promoter-TSS (NM_016748)	-33	NM_016748	51797	Mm.1815	NM_016748	ENSMUSG00000028633	Ctps	Ctps1	cytidine 5'-triphosphate synthase	protein-coding
mm_40047.1	chr5	33983480	33983529	+	1	NA	promoter-TSS (NM_001310547)	promoter-TSS (NM_001310547)	71	NM_001310546	381633	Mm.4923	NM_001033458	ENSMUSG00000070858	Gm1673	-	predicted gene 1673	protein-coding
mm_69018.1	chr7	126746852	126746890	-	1	NA	Intergenic	Intergenic	-12755	NM_011952	26417	Mm.8385	NM_011952	ENSMUSG00000063065	Mapk3	Erk-1|Erk1|Ert2|Esrk1|Mnk1|Mtap2k|Prkm3|p44|p44erk1|p44mapk	mitogen-activated protein kinase 3	protein-coding
mm_114721.1	chr13	83687193	83687219	+	1	NA	Intergenic	Intergenic	-40900	NR_015561	320203	Mm.245636	NM_177100	ENSMUSG00000050334	C130071C03Rik	2810449C10Rik	RIKEN cDNA C130071C03 gene	ncRNA
mm_140100.1	chr17	78375787	78375799	+	1	NA	3' UTR (NM_015800, exon 17 of 17)	3' UTR (NM_015800, exon 17 of 17)	42359	NM_001285949	225020	Mm.236835	NM_199448	ENSMUSG00000056121	Fez2	9030616F16|D17Ertd315e	fasciculation and elongation protein zeta 2 (zygin II)	protein-coding
mm_105134.1	chr11	101425616	101425642	-	1	NA	promoter-TSS (NM_026865)	promoter-TSS (NM_026865)	-296	NM_026865	73635	Mm.472804	NM_026865	ENSMUSG00000097487	Ptges3l	1110069E20Rik|1700113I22Rik	prostaglandin E synthase 3 (cytosolic)-like	protein-coding
mm_138348.1	chr17	34931905	34931937	+	1	NA	exon (NM_010893, exon 2 of 6)	exon (NM_010893, exon 2 of 6)	668	NM_010893	18010	Mm.8856	NM_010893	ENSMUSG00000007038	Neu1	AA407268|AA407316|Aglp|Apl|Bat-7|Bat7|G9|Map-2|Neu|Neu-1	neuraminidase 1	protein-coding
mm_172529.1	chr7	86118677	86118677	+	1	NA	Intergenic	Intergenic	53047	NM_001102578	546981	Mm.469835	NM_001102578	ENSMUSG00000090436	Vmn2r75	EG546981	vomeronasal 2, receptor 75	protein-coding
mm_127462.1	chr15	101272252	101272264	+	1	NA	exon (NM_010444, exon 4 of 7)	exon (NM_010444, exon 4 of 7)	5412	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_18036.1	chr2	38797172	38797176	-	1	NA	intron (NM_010264, intron 3 of 10)	intron (NM_010264, intron 3 of 10)	-12659	NM_001159549	14536	Mm.439703	NM_010264	ENSMUSG00000063972	Nr6a1	1700113M01Rik|Gcnf|NCNF|RTR	nuclear receptor subfamily 6, group A, member 1	protein-coding
mm_59151.1	chr7	24370085	24370093	+	1	NA	promoter-TSS (NM_001163510)	promoter-TSS (NM_001163510)	-174	NM_001163510	16534	Mm.9911	NM_008433	ENSMUSG00000054342	Kcnn4	IK1|IKCA1|KCA4|KCa3.1|SK4|SKCas|mIKCa1	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4	protein-coding
mm_91916.1	chr10	60299174	60299204	-	1	NA	exon (NM_011179, exon 9 of 15)	exon (NM_011179, exon 9 of 15)	14728	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_106348.1	chr11	118393472	118393482	-	1	NA	exon (NM_011150, exon 6 of 6)	exon (NM_011150, exon 6 of 6)	8454	NM_011150	19039	Mm.3152	NM_011150	ENSMUSG00000033880	Lgals3bp	90K|CyCAP|MAC-2BP|Ppicap|Tango10b	lectin, galactoside-binding, soluble, 3 binding protein	protein-coding
mm_98156.1	chr11	87617227	87617247	+	1	NA	promoter-TSS (NM_001045527)	promoter-TSS (NM_001045527)	73	NM_001045527	327992	Mm.390371	NM_001045527	ENSMUSG00000070345	Hsf5	Gm739|MLZ-220	heat shock transcription factor family member 5	protein-coding
mm_69173.1	chr7	127215684	127215695	-	1	NA	exon (NM_017461, exon 8 of 11)	exon (NM_017461, exon 8 of 11)	2756	NM_017461	54204	Mm.18	NM_017461	ENSMUSG00000000486	Sept1	Diff6|Pnutl3	septin 1	protein-coding
mm_162753.1	chr10	60162413	60162415	-	1	NA	Intergenic	LTRIS2|LTR|ERV1	35638	NR_105871	102465546		NR_105871	ENSMUSG00000105468	Mir6906	mmu-mir-6906	microRNA 6906	ncRNA
mm_13480.1	chr2	106080926	106080930	+	1	NA	Intergenic	Intergenic	-77379	NR_033993	99349	Mm.25661	NM_026992	ENSMUSG00000027166	Dnajc24	1700030A21Rik|2610027M02Rik|AV066965|AW240712|Dph4|MmDjC7|Zcsl3	DnaJ heat shock protein family (Hsp40) member C24	protein-coding
mm_105438.1	chr11	104367245	104367248	-	1	NA	intron (NM_001081045, intron 4 of 13)	intron (NM_001081045, intron 4 of 13)	75045	NM_001081045	76719	Mm.136418	NM_001081045	ENSMUSG00000018412	Kansl1	1700081L11Rik|9430041J06Rik|mKIAA1267	KAT8 regulatory NSL complex subunit 1	protein-coding
mm_111566.1	chr12	101718514	101718530	-	1	NA	promoter-TSS (NM_001082976)	promoter-TSS (NM_001082976)	1	NM_001082976	74413	Mm.275939	NM_028924	ENSMUSG00000021187	Tc2n	4933406D09Rik|Mtac2d1|Tac2-N	tandem C2 domains, nuclear	protein-coding
mm_27895.1	chr3	79287328	79287343	-	1	NA	Intergenic	CpG	-58041	NM_001142953	100233207	Mm.373801	NM_001142953	ENSMUSG00000091685	Gm17359	-	predicted gene, 17359	protein-coding
mm_169268.1	chr1	38577328	38577337	-	1	NA	intron (NM_001290814, intron 1 of 21)	RMER17A2|LTR|ERVK	49912	NM_001290814	16764	Mm.336679	NM_010678	ENSMUSG00000037138	Aff3	3222402O04Rik|A730046J16|LAF-4|Laf4	AF4/FMR2 family, member 3	protein-coding
mm_164726.1	chr17	57236003	57236013	-	1	NA	exon (NM_030084, exon 16 of 17)	exon (NM_030084, exon 16 of 17)	-7872	NM_009778	12266	Mm.19131	NM_009778	ENSMUSG00000024164	C3	AI255234|ASP|HSE-MSF|Plp	complement component 3	protein-coding
mm_32200.1	chr4	101446798	101446803	+	1	NA	intron (NM_001177605, intron 2 of 5)	RLTR13B2|LTR|ERVK	27097	NM_009647	11639	Mm.42040	NM_009647	ENSMUSG00000028527	Ak4	AK 4|Ak-3|Ak-4|Ak3|Ak3l1|D4Ertd274e	adenylate kinase 4	protein-coding
mm_105234.1	chr11	102317761	102317785	-	1	NA	promoter-TSS (NM_001044383)	promoter-TSS (NM_001044383)	-486	NM_001044383	21429	Mm.2845	NM_011551	ENSMUSG00000020923	Ubtf	A930005G04Rik|NOR-90|Tcfubf|UBF|UBF-1|UBF1	upstream binding transcription factor, RNA polymerase I	protein-coding
mm_17096.1	chr2	23068017	23068058	-	1	NA	promoter-TSS (NM_001102436)	promoter-TSS (NM_001102436)	-164	NM_028793	74159	Mm.181973	NM_028793	ENSMUSG00000026781	Acbd5	1300014E15Rik	acyl-Coenzyme A binding domain containing 5	protein-coding
mm_170487.1	chr19	17926750	17926769	+	1	NA	Intergenic	Intergenic	-89127	NM_001190483	18552	Mm.3401	NM_001163144	ENSMUSG00000024713	Pcsk5	PC5|PC6|SPC6|b2b1549Clo|b2b585Clo	proprotein convertase subtilisin/kexin type 5	protein-coding
mm_45733.1	chr5	86373414	86373428	-	1	NA	promoter-TSS (NM_145561)	promoter-TSS (NM_145561)	-34	NM_145561	231382	Mm.240139	NM_145561	ENSMUSG00000061259	Tmprss11d	AST|AsP|BC020151	transmembrane protease, serine 11d	protein-coding
mm_67002.1	chr7	65156506	65156561	-	1	NA	promoter-TSS (NM_183087)	promoter-TSS (NM_183087)	-5	NM_183087	70638	Mm.441986	NM_183087	ENSMUSG00000030518	Fam189a1	5730507A09Rik|AW047451	family with sequence similarity 189, member A1	protein-coding
mm_157987.1	chrX	94212686	94212696	-	1	NA	promoter-TSS (NM_012010)	promoter-TSS (NM_012010)	-40	NM_012010	26905	Mm.218851	NM_012010	ENSMUSG00000035150	Eif2s3x	AA409828|AA547477|AI314668|Eif-2gx	eukaryotic translation initiation factor 2, subunit 3, structural gene X-linked	protein-coding
mm_6511.1	chr1	74337819	74337848	-	1	NA	intron (NM_019999, intron 1 of 8)	intron (NM_019999, intron 1 of 8)	5223	NM_019999	56695	Mm.384726	NM_019999	ENSMUSG00000026179	Pnkd	2210013N15Rik|2810403H05Rik|AI854243|Brp17|MNCb-5687|MR-1|Tahccp2	paroxysmal nonkinesiogenic dyskinesia	protein-coding
mm_77104.1	chr8	111061768	111061773	-	1	NA	Intergenic	Intergenic	5431	NM_028274	72544	Mm.24174	NM_028274	ENSMUSG00000109941	Exosc6	2610510N21Rik|C76919|Mtr3	exosome component 6	protein-coding
mm_53821.1	chr6	147111952	147111959	+	1	NA	3' UTR (NM_001081237, exon 3 of 3)	3' UTR (NM_001081237, exon 3 of 3)	20880	NM_001081237	232539	Mm.491206	NM_001081237	ENSMUSG00000040102	Klhl42	A330079N23Rik|AI450355|C230080I20Rik|Ctb9|Klhdc5|mKIAA1340	kelch-like 42	protein-coding
mm_107285.1	chr12	29800056	29800072	+	1	NA	intron (NM_001093778, intron 8 of 24)	intron (NM_001093778, intron 8 of 24)	-113619	NR_046080	328075	Mm.447832	NR_046080		C630031E19Rik	C630031E19	RIKEN cDNA C630031E19 gene	ncRNA
mm_111209.1	chr12	84399614	84399624	-	1	NA	intron (NM_001026214, intron 2 of 15)	intron (NM_001026214, intron 2 of 15)	1315	NM_001286058	12499	Mm.10211	NM_007647	ENSMUSG00000021236	Entpd5	AI196558|AI987697|Cd39l4|ER-UDPase|NTPDase-5|NTPDase5|Pcph|mNTPase	ectonucleoside triphosphate diphosphohydrolase 5	protein-coding
mm_164103.1	chr15	23196636	23196641	+	1	NA	intron (NM_001081299, intron 2 of 11)	MTE-int|LTR|ERVL-MaLR	160175	NM_001081299	320865	Mm.241965	NM_001081299	ENSMUSG00000040420	Cdh18	B230220E17Rik|Cdh14l	cadherin 18	protein-coding
mm_146263.1	chr18	77832972	77832976	+	1	NA	intron (NM_013831, intron 1 of 14)	intron (NM_013831, intron 1 of 14)	38424	NM_013831	19201	Mm.57174	NM_013831	ENSMUSG00000025429	Pstpip2	MAYP|cmo	proline-serine-threonine phosphatase-interacting protein 2	protein-coding
mm_160113.1	chr7	26173410	26173410	+	1	NA	promoter-TSS (NM_010000)	promoter-TSS (NM_010000)	1	NM_010000	13094	Mm.14413	NM_010000	ENSMUSG00000040660	Cyp2b9	Cyp2b	cytochrome P450, family 2, subfamily b, polypeptide 9	protein-coding
mm_121422.1	chr14	120275699	120275714	+	1	NA	promoter-TSS (NM_207515)	promoter-TSS (NM_207515)	37	NM_175341	105559	Mm.238266	NM_175341	ENSMUSG00000022139	Mbnl2	1110002M11Rik|AI047808|AI837313|AI849185|AL118326|MBLL|R75232|mKIAA4072	muscleblind-like 2	protein-coding
mm_8140.1	chr1	136260917	136260931	-	1	NA	promoter-TSS (NM_001101516)	promoter-TSS (NM_001101516)	-51	NM_001101516	383563	Mm.40367	NM_001101516	ENSMUSG00000052759	Gpr25	Gm1300	G protein-coupled receptor 25	protein-coding
mm_66390.1	chr7	44236087	44236093	-	1	NA	promoter-TSS (NR_029436)	promoter-TSS (NR_029436)	32	NR_029436	70004	Mm.158317	NR_029436	ENSMUSG00000038782	1700028J19Rik	-	RIKEN cDNA 1700028J19 gene	ncRNA
mm_49888.1	chr6	38843439	38843449	+	1	NA	intron (NM_001294144, intron 1 of 14)	intron (NM_001294144, intron 1 of 14)	-6133	NM_001136065	15258	Mm.23790	NM_010433	ENSMUSG00000061436	Hipk2	1110014O20Rik|B230339E18Rik|Stank	homeodomain interacting protein kinase 2	protein-coding
mm_111897.1	chr12	108688511	108688515	-	1	NA	TTS (NM_007965)	TTS (NM_007965)	13793	NM_001171002	70059	Mm.207605	NM_027299	ENSMUSG00000021263	Degs2	2210008A03Rik|AI852933|DES2	delta(4)-desaturase, sphingolipid 2	protein-coding
mm_104530.1	chr11	96280567	96280570	-	1	NA	Intergenic	Intergenic	-1337	NM_010461	15416	Mm.4822	NM_010461	ENSMUSG00000056648	Hoxb8	Hox-2.4	homeobox B8	protein-coding
mm_112044.1	chr12	111671537	111671591	-	1	NA	exon (NM_021273, exon 3 of 8)	exon (NM_021273, exon 3 of 8)	774	NM_021273	12709	Mm.16831	NM_021273	ENSMUSG00000001270	Ckb	B-CK|Bck|Ck-3|Ck3|Ckbb	creatine kinase, brain	protein-coding
mm_19313.1	chr2	90548395	90548407	-	1	NA	intron (NM_008982, intron 1 of 23)	B1_Mur2|SINE|Alu	32246	NM_008982	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_52770.1	chr6	121185457	121185471	+	1	NA	intron (NR_130903, intron 1 of 6)	intron (NR_130903, intron 1 of 6)	1797	NM_001304773	74043	Mm.491240	NM_028730	ENSMUSG00000067825	Pex26	4632428M11Rik	peroxisomal biogenesis factor 26	protein-coding
mm_95942.1	chr11	58384669	58384688	+	1	NA	exon (NM_001083884, exon 5 of 7)	exon (NM_001083884, exon 5 of 7)	4032	NM_001330197	70163	Mm.24119	NM_027339	ENSMUSG00000013643	Lypd8	2210415F13Rik	LY6/PLAUR domain containing 8	protein-coding
mm_86082.1	chr9	114781987	114781998	-	1	NA	promoter-TSS (NM_133978)	promoter-TSS (NM_133978)	1	NM_133978	102545	Mm.35600	NM_133978	ENSMUSG00000032436	Cmtm7	AI481279|Cklfsf7|LNV	CKLF-like MARVEL transmembrane domain containing 7	protein-coding
mm_43442.1	chr5	136099616	136099621	+	1	NA	intron (NM_001039103, intron 8 of 19)	ID_B1|SINE|B4	-5904	NR_106002	102465626		NR_106002	ENSMUSG00000099003	Mir7035	Gm27661|mmu-mir-7035	microRNA 7035	ncRNA
mm_84221.1	chr9	61925457	61925461	-	1	NA	intron (NM_024245, intron 15 of 22)	intron (NM_024245, intron 15 of 22)	-10949	NM_018853	56040	Mm.3158	NM_018853	ENSMUSG00000007892	Rplp1	2410042H16Rik|Arpp1|C430017H15Rik	ribosomal protein, large, P1	protein-coding
mm_139418.1	chr17	53479243	53479303	+	1	NA	promoter-TSS (NM_025887)	promoter-TSS (NM_025887)	39	NM_025887	271457	Mm.329123	NM_025887	ENSMUSG00000017831	Rab5a	2410015H04Rik|AI663973|AU021172|nnyRab5a	RAB5A, member RAS oncogene family	protein-coding
mm_152940.1	chr19	28763538	28763540	-	1	NA	Intergenic	Intergenic	-71627	NM_009199	20510	Mm.246670	NM_009199	ENSMUSG00000024935	Slc1a1	D130048G10Rik|EAAC1|EAAC2|EAAT3|MEAAC1	solute carrier family 1 (neuronal/epithelial high affinity glutamate transporter, system Xag), member 1	protein-coding
mm_50327.1	chr6	48395818	48395828	+	1	NA	5' UTR (NM_133922, exon 1 of 18)	5' UTR (NM_133922, exon 1 of 18)	237	NM_001347153	77827	Mm.107646	NM_133922	ENSMUSG00000042810	Krba1	A930040G15Rik|AI448780	KRAB-A domain containing 1	protein-coding
mm_157712.1	chrX	66778802	66778833	-	1	NA	Intergenic	(CAT)n|Simple_repeat|Simple_repeat	-1485	NR_030535	100124496		NR_030535	ENSMUSG00000094184	Mir743b	Mirn743b|mir-743b	microRNA 743b	ncRNA
mm_36173.1	chr4	62086007	62086032	-	1	NA	exon (NM_001039544, exon 3 of 7)	exon (NM_001039544, exon 3 of 7)	1293	NM_001039544	17842	Mm.250267	NM_010845	ENSMUSG00000066154	Mup3	MUP15|MUPIII|Mup-3|Mup25	major urinary protein 3	protein-coding
mm_162776.1	chr10	69275187	69275190	-	1	NA	intron (NM_001252637, intron 7 of 10)	intron (NM_001252637, intron 7 of 10)	61994	NM_001252638	69288	Mm.26659	NM_001081347	ENSMUSG00000019944	Rhobtb1	1700008H16Rik|3110048G13Rik|AI173445|AI573858|AV350930	Rho-related BTB domain containing 1	protein-coding
mm_55223.1	chr6	52233184	52233194	-	1	NA	intron (NM_001122950, intron 1 of 1)	intron (NM_001122950, intron 1 of 1)	1750	NM_008263	15395	Mm.5	NM_008263	ENSMUSG00000000938	Hoxa10	Hox-1.8|Hoxa-10	homeobox A10	protein-coding
mm_60693.1	chr7	45175064	45175073	+	1	NA	3' UTR (NM_182993, exon 12 of 12)	3' UTR (NM_182993, exon 12 of 12)	1765	NR_106022	102465638		NR_106022	ENSMUSG00000106470	Mir7055	mmu-mir-7055	microRNA 7055	ncRNA
mm_63241.1	chr7	126585534	126585549	+	1	NA	exon (NM_138310, exon 2 of 4)	exon (NM_138310, exon 2 of 4)	276	NM_001146311	12752	Mm.268930	NM_009907	ENSMUSG00000030720	Cln3	AI323623	ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease)	protein-coding
mm_23465.1	chr3	60473099	60473128	+	1	NA	5' UTR (NM_001253713, exon 2 of 10)	5' UTR (NM_001253713, exon 2 of 10)	283	NM_001253713	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_51555.1	chr6	83341580	83341594	+	1	NA	TTS (NM_145571)	TTS (NM_145571)	-7897	NM_175277	78653	Mm.391470	NM_175277	ENSMUSG00000045160	Bola3	1810056O20Rik	bolA-like 3 (E. coli)	protein-coding
mm_92159.1	chr10	67539163	67539172	-	1	NA	intron (NM_001347458, intron 2 of 2)	intron (NM_001347458, intron 2 of 2)	1237	NM_001347458	13654	Mm.290421	NM_010118	ENSMUSG00000037868	Egr2	Egr-2|Krox-20|Krox20|NGF1-B|Zfp-25|Zfp-6	early growth response 2	protein-coding
mm_57712.1	chr6	128707769	128707777	-	1	NA	intron (NM_001099918, intron 5 of 5)	intron (NM_001099918, intron 5 of 5)	15273	NM_001099918	100043861	Mm.66911	NM_001099918	ENSMUSG00000079299	Klrb1	4930431A04Rik|Gm4696|Klrb1g|Klrb6|Ly-55|Ly55|NKR-P1G|Nkrp-1e|Nkrp1g	killer cell lectin-like receptor subfamily B member 1	protein-coding
mm_101347.1	chr11	23633647	23633669	-	1	NA	promoter-TSS (NM_001347242)	promoter-TSS (NM_001347242)	-27	NM_027860	71675	Mm.48031	NM_027860	ENSMUSG00000042208	0610010F05Rik	Kiaa1841|mKIAA1841	RIKEN cDNA 0610010F05 gene	protein-coding
mm_164186.1	chr15	77740752	77740769	+	1	NA	Intergenic	MT2B1|LTR|ERVL	11639	NM_001168660	71898	Mm.422856	NM_173743	ENSMUSG00000068246	Apol9b	2310016F22Rik	apolipoprotein L 9b	protein-coding
mm_127359.1	chr15	100674420	100674431	+	1	NA	TTS (NM_033612)	TTS (NM_033612)	-4925	NM_001270537	668218	Mm.451225	NM_001270537	ENSMUSG00000098112	Bin2	-	bridging integrator 2	protein-coding
mm_164848.1	chr18	45268952	45268965	+	1	NA	promoter-TSS (NM_001312905)	promoter-TSS (NM_001312905)	98	NM_001312905	140492	Mm.411614	NM_080465	ENSMUSG00000054477	Kcnn2	KCa2.2|SK2|SKCA2|bc|fri	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2	protein-coding
mm_22271.1	chr2	178506112	178506127	-	1	NA	Intergenic	Intergenic	75604	NM_198656	381409	Mm.330860	NM_198656	ENSMUSG00000039155	Cdh26	Gm1010	cadherin-like 26	protein-coding
mm_22178.1	chr2	173215808	173215842	-	1	NA	exon (NM_021394, exon 3 of 8)	exon (NM_021394, exon 3 of 8)	3097	NM_021394	58203	Mm.116687	NM_021394	ENSMUSG00000027514	Zbp1	2010010H03Rik|Dai|Dlm1|mZaDLM	Z-DNA binding protein 1	protein-coding
mm_76821.1	chr8	104609342	104609362	-	1	NA	intron (NM_001252628, intron 17 of 17)	intron (NM_001252628, intron 17 of 17)	15044	NM_007663	12556	Mm.19423	NM_007663	ENSMUSG00000031881	Cdh16	-	cadherin 16	protein-coding
mm_60518.1	chr7	44479903	44479919	+	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	-4606	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_117752.1	chr13	95912588	95912610	-	1	NA	Intergenic	Intergenic	-20677	NM_027711	544963	Mm.38878	NM_027711	ENSMUSG00000021676	Iqgap2	4933417J23Rik|A630053O10|AI788777	IQ motif containing GTPase activating protein 2	protein-coding
mm_129213.1	chr15	76522403	76522470	-	1	NA	promoter-TSS (NM_130893)	promoter-TSS (NM_130893)	-307	NM_130893	170729	Mm.218747	NM_130893	ENSMUSG00000048385	Scrt1	-	scratch family zinc finger 1	protein-coding
mm_140935.1	chr17	24415525	24415534	-	1	NA	intron (NM_009070, intron 2 of 8)	intron (NM_009070, intron 2 of 8)	854	NM_001080128	19826	Mm.1951	NM_009070	ENSMUSG00000034681	Rnps1	-	ribonucleic acid binding protein S1	protein-coding
mm_26743.1	chr3	6802684	6802687	-	1	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	-182242	NM_027048	69347	Mm.45822	NM_027048	ENSMUSG00000069118	1700008P02Rik	-	RIKEN cDNA 1700008P02 gene	protein-coding
mm_140075.1	chr17	75178650	75178660	+	1	NA	promoter-TSS (NM_001331237)	promoter-TSS (NM_001331237)	-126	NM_001331236	268977	Mm.269747	NM_019919	ENSMUSG00000001870	Ltbp1	9430031G15Rik|9830146M04|Ltbp-1|Ltbp1L|TGF-beta1-BP-1|Tgfb|b2b1000Clo	latent transforming growth factor beta binding protein 1	protein-coding
mm_126262.1	chr15	79108912	79108982	+	1	NA	promoter-TSS (NM_177461)	promoter-TSS (NM_177461)	-36	NM_177461	27008	Mm.196480	NM_177461	ENSMUSG00000033039	Micall1	AI448246|D15Mit260|D15N2e|EST573322|EST820961|MIRab13|mKIAA1668	microtubule associated monooxygenase, calponin and LIM domain containing -like 1	protein-coding
mm_24406.1	chr3	90363161	90363164	+	1	NA	Intergenic	Intergenic	21508	NM_139304	229542	Mm.270999	NM_139304	ENSMUSG00000042390	Gatad2b	AL118180|C430014D17Rik|P66beta|mKIAA1150	GATA zinc finger domain containing 2B	protein-coding
mm_111798.1	chr12	104930052	104930074	-	1	NA	3' UTR (NM_172500, exon 17 of 17)	3' UTR (NM_172500, exon 17 of 17)	-64987	NR_104435	94040	Mm.244078	NM_053155	ENSMUSG00000021097	Clmn	9330188N17Rik|AI428889|AI788815|mKIAA1188	calmin	protein-coding
mm_127430.1	chr15	101270120	101270124	+	1	NA	exon (NM_010444, exon 2 of 7)	exon (NM_010444, exon 2 of 7)	3276	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_44576.1	chr5	24842457	24842467	-	1	NA	promoter-TSS (NM_053075)	promoter-TSS (NM_053075)	-101	NM_053075	19744	Mm.319175	NM_053075	ENSMUSG00000028945	Rheb	Rheb1	Ras homolog enriched in brain	protein-coding
mm_130951.1	chr15	103255372	103255386	-	1	NA	promoter-TSS (NM_008685)	promoter-TSS (NM_008685)	60	NM_008685	18022	Mm.457989	NM_008685	ENSMUSG00000058794	Nfe2	NF-E2|NF-E2/P45|p45|p45NFE2|p45nf-e2	nuclear factor, erythroid derived 2	protein-coding
mm_43493.1	chr5	136962082	136962129	+	1	NA	promoter-TSS (NM_025562)	promoter-TSS (NM_025562)	28	NM_025562	66437	Mm.25849	NM_025562	ENSMUSG00000019054	Fis1	2010003O14Rik|Ttc11	fission, mitochondrial 1	protein-coding
mm_74321.1	chr8	126849017	126849030	+	1	NA	Intergenic	Intergenic	96898	NM_024214	67952	Mm.6932	NM_024214	ENSMUSG00000093904	Tomm20	1810060K07Rik|BB284719|Gm19268|MAS20|MOM19|TOM20|mKIAA0016	translocase of outer mitochondrial membrane 20 homolog (yeast)	protein-coding
mm_89623.1	chr10	96186206	96186245	+	1	NA	Intergenic	Intergenic	-39982	NR_110448	74881	Mm.410819	NR_110448		4930459C07Rik	-	RIKEN cDNA 4930459C07 gene	ncRNA
mm_150794.1	chr19	44303348	44303412	+	1	NA	TTS (NR_039574)	TTS (NR_039574)	209	NR_039574	100628619		NR_039574	ENSMUSG00000093315	Mir5114	mmu-mir-5114|mu-mir-5114	microRNA 5114	ncRNA
mm_59577.1	chr7	28120508	28120549	+	1	NA	exon (NM_001122603, exon 19 of 20)	exon (NM_001122603, exon 19 of 20)	-8938	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_92118.1	chr10	63338125	63338129	-	1	NA	intron (NM_019812, intron 1 of 8)	intron (NM_019812, intron 1 of 8)	908	NM_019812	93759	Mm.351459	NM_019812	ENSMUSG00000020063	Sirt1	AA673258|SIR2L1|Sir2|Sir2a|Sir2alpha	sirtuin 1	protein-coding
mm_110749.1	chr12	69982742	69982744	-	1	NA	intron (NM_022028, intron 2 of 4)	intron (NM_022028, intron 2 of 4)	4259	NM_022028	64010	Mm.390480	NM_022028	ENSMUSG00000021067	Sav1	1700040G09Rik|Salv|Sav|WW45|Wwp3|Wwp4	salvador family WW domain containing 1	protein-coding
mm_138286.1	chr17	34612689	34612704	+	1	NA	TTS (NM_152922)	TTS (NM_152922)	3275	NM_152922	81701	Mm.231343	NM_152922	ENSMUSG00000015467	Egfl8	Ng3	EGF-like domain 8	protein-coding
mm_22391.1	chr2	181202537	181202563	-	1	NA	5' UTR (NM_009184, exon 1 of 8)	5' UTR (NM_009184, exon 1 of 8)	239	NM_009184	20459	Mm.4497	NM_009184	ENSMUSG00000038751	Ptk6	BRK|Sik|Tksk|tks	PTK6 protein tyrosine kinase 6	protein-coding
mm_147731.1	chr18	61035756	61035764	-	1	NA	exon (NM_009880, exon 1 of 3)	exon (NM_009880, exon 1 of 3)	439	NM_009880	12590	Mm.144448	NM_009880	ENSMUSG00000024619	Cdx1	Cdx|Cdx-1	caudal type homeobox 1	protein-coding
mm_173057.1	chrX	125624873	125624874	+	1	NA	Intergenic	RMER12|LTR|ERVK	1209131	NM_177705	237029	Mm.60998	NM_177705	ENSMUSG00000058670	4932411N23Rik	-	RIKEN cDNA 4932411N23 gene	protein-coding
mm_157142.1	chrX	9459465	9459494	-	1	NA	intron (NM_007807, intron 3 of 12)	B1_Mus1|SINE|Alu	9845	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_115075.1	chr13	101692479	101692499	+	1	NA	5' UTR (NM_001024955, exon 1 of 10)	5' UTR (NM_001024955, exon 1 of 10)	141	NM_001024955	18708	Mm.259333	NM_001024955	ENSMUSG00000041417	Pik3r1	PI3K|p50alpha|p55alpha|p85alpha	phosphatidylinositol 3-kinase, regulatory subunit, polypeptide 1 (p85 alpha)	protein-coding
mm_139101.1	chr17	47141133	47141154	+	1	NA	5' UTR (NM_001097623, exon 2 of 20)	5' UTR (NM_001097623, exon 2 of 20)	201	NM_001097623	224829	Mm.260989	NM_172622		Trerf1	9430096I18Rik|AI429294|B830015H24|RAPA|Trep-132|Trep132	transcriptional regulating factor 1	protein-coding
mm_153830.1	chr19	46318067	46318077	-	1	NA	intron (NM_028627, intron 11 of 17)	CpG	8794	NM_001347454	73728	Mm.268532	NM_028627	ENSMUSG00000037126	Psd	1110007H17Rik|A930015K15|Efa6|Efa6a|Psdl|mKIAA2011	pleckstrin and Sec7 domain containing	protein-coding
mm_39557.1	chr5	22746119	22746130	+	1	NA	promoter-TSS (NM_029990)	promoter-TSS (NM_029990)	-69	NM_001081231	269629	Mm.371712	NM_029990	ENSMUSG00000106379	Lhfpl3	A930031L14Rik	lipoma HMGIC fusion partner-like 3	protein-coding
mm_154154.1	chr19	58455467	58455476	-	1	NA	promoter-TSS (NM_010279)	promoter-TSS (NM_010279)	-73	NM_010279	14585	Mm.88367	NM_010279	ENSMUSG00000025089	Gfra1	AU042498	glial cell line derived neurotrophic factor family receptor alpha 1	protein-coding
mm_1762.1	chr1	75546450	75546514	+	1	NA	intron (NM_009208, intron 1 of 22)	CpG	216	NM_009208	20536	Mm.5053	NM_009208	ENSMUSG00000006576	Slc4a3	A930038D23Rik|Ae3	solute carrier family 4 (anion exchanger), member 3	protein-coding
mm_112530.1	chr13	9281602	9281603	+	1	NA	intron (NM_001081426, intron 1 of 36)	intron (NM_001081426, intron 1 of 36)	5077	NM_001081426	208440	Mm.217326	NM_172459	ENSMUSG00000048264	Dip2c	2900024P20Rik|9630044M06|mKIAA0934	disco interacting protein 2 homolog C	protein-coding
mm_88292.1	chr10	75241156	75241176	+	1	NA	exon (NM_001145826, exon 6 of 19)	exon (NM_001145826, exon 6 of 19)	28776	NM_001145826	74392	Mm.27716	NM_153406	ENSMUSG00000033444	Specc1l	4930470P14Rik|4932439K10Rik|9530057A13Rik|AI317249|Cytsa|mKIAA0376	sperm antigen with calponin homology and coiled-coil domains 1-like	protein-coding
mm_10648.1	chr2	20662131	20662153	+	1	NA	intron (NM_029895, intron 4 of 18)	intron (NM_029895, intron 4 of 18)	142629	NM_001177631	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding
mm_76746.1	chr8	95332181	95332250	-	1	NA	promoter-TSS (NM_024467)	promoter-TSS (NM_024467)	-69	NM_133954	101985	Mm.29069	NM_133954	ENSMUSG00000031792	Usb1	AA960436	U6 snRNA biogenesis 1	protein-coding
mm_152917.1	chr19	28009775	28009782	-	1	NA	intron (NM_011265, intron 1 of 16)	intron (NM_011265, intron 1 of 16)	1388	NM_011265	19726	Mm.313321	NM_011265	ENSMUSG00000040929	Rfx3	C230093O12Rik|MRFX3	regulatory factor X, 3 (influences HLA class II expression)	protein-coding
mm_28291.1	chr3	89091531	89091570	-	1	NA	exon (NM_001083807, exon 2 of 10)	exon (NM_001083807, exon 2 of 10)	-1519	NM_001083808	72296	Mm.27687	NM_028188	ENSMUSG00000041263	Rusc1	2210403N08Rik|AA408288|NESCA	RUN and SH3 domain containing 1	protein-coding
mm_163784.1	chr13	120300281	120300313	+	1	NA	promoter-TSS (NM_001037925)	promoter-TSS (NM_001037925)	-95	NM_001037925	625360	Mm.327506	NM_001037925	ENSMUSG00000094796	BC147527	-	cDNA sequence BC147527	protein-coding
mm_6305.1	chr1	71414923	71414927	-	1	NA	promoter-TSS (NM_175210)	promoter-TSS (NM_175210)	-15	NM_175210	74591	Mm.159251	NM_175210	ENSMUSG00000050296	Abca12	4832428G11Rik|4833417A11Rik	ATP-binding cassette, sub-family A (ABC1), member 12	protein-coding
mm_153112.1	chr19	32980263	32980280	-	1	NA	Intergenic	Intergenic	222694	NM_008960	19211	Mm.245395	NM_008960	ENSMUSG00000013663	Pten	2310035O07Rik|A130070J02Rik|AI463227|B430203M17Rik|MMAC1|TEP1	phosphatase and tensin homolog	protein-coding
mm_4662.1	chr1	180365779	180365782	+	1	NA	intron (NM_001081175, intron 2 of 7)	intron (NM_001081175, intron 2 of 7)	-35231	NR_003623	277333	Mm.389223	NM_199472		Gm5069	EG277333	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_47046.1	chr5	116024476	116024490	-	1	NA	promoter-TSS (NM_031869)	promoter-TSS (NM_031869)	-55	NM_031869	19079	Mm.458152	NM_031869	ENSMUSG00000029513	Prkab1	1300015D22Rik|AU021155|E430008F22	protein kinase, AMP-activated, beta 1 non-catalytic subunit	protein-coding
mm_108446.1	chr12	82451153	82451172	+	1	NA	3' UTR (NM_001167983, exon 24 of 24)	3' UTR (NM_001167983, exon 24 of 24)	139813	NM_172579	217692	Mm.261333	NM_172579	ENSMUSG00000042700	Sipa1l1	4931426N11Rik|AW213287|Spar|mKIAA0440	signal-induced proliferation-associated 1 like 1	protein-coding
mm_36984.1	chr4	109665681	109665711	-	1	NA	promoter-TSS (NM_007671)	promoter-TSS (NM_007671)	-324	NM_007671	12580	Mm.1912	NM_007671	ENSMUSG00000028551	Cdkn2c	C77269|INK4c|p18|p18-INK4c|p18-INK6|p18INK4c	cyclin-dependent kinase inhibitor 2C (p18, inhibits CDK4)	protein-coding
mm_101573.1	chr11	34311740	34311757	-	1	NA	intron (NM_033374, intron 28 of 51)	intron (NM_033374, intron 28 of 51)	-3074	NM_001025382	574403	Mm.444796	NM_001025382	ENSMUSG00000069911	Fam196b	EG574403|Gm6041	family with sequence similarity 196, member B	protein-coding
mm_78973.1	chr9	45370004	45370019	+	1	NA	promoter-TSS (NM_022004)	promoter-TSS (NM_022004)	-174	NM_022004	59095	Mm.208287	NM_022004	ENSMUSG00000066705	Fxyd6	0610030I18Rik|Php	FXYD domain-containing ion transport regulator 6	protein-coding
mm_116909.1	chr13	55482784	55482804	-	1	NA	exon (NM_019813, exon 3 of 14)	exon (NM_019813, exon 3 of 14)	-5018	NR_105909	102465569		NR_105909	ENSMUSG00000098341	Mir6944	Gm27710|mmu-mir-6944	microRNA 6944	ncRNA
mm_12287.1	chr2	69022923	69022933	+	1	NA	intron (NM_172856, intron 4 of 9)	intron (NM_172856, intron 4 of 9)	-112872	NM_181547	329416	Mm.90047	NM_181547	ENSMUSG00000034738	Nostrin	Daip2|mDaIP2	nitric oxide synthase trafficker	protein-coding
mm_23491.1	chr3	60502271	60502279	+	1	NA	intron (NM_001253710, intron 1 of 7)	intron (NM_001253710, intron 1 of 7)	1096	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_133997.1	chr16	4719149	4719164	-	1	NA	5' UTR (NM_001290761, exon 1 of 5)	5' UTR (NM_001290761, exon 1 of 5)	200	NM_001290763	67824	Mm.28451	NM_026393	ENSMUSG00000063445	Nmral1	1110025F24Rik|AI256624	NmrA-like family domain containing 1	protein-coding
mm_68548.1	chr7	114254660	114254733	-	1	NA	promoter-TSS (NM_033370)	promoter-TSS (NM_033370)	-16	NM_033370	70349	Mm.277024	NM_033370	ENSMUSG00000030754	Copb1	2610019B04Rik	coatomer protein complex, subunit beta 1	protein-coding
mm_61241.1	chr7	65644919	65644932	+	1	NA	promoter-TSS (NM_172310)	promoter-TSS (NM_172310)	27	NM_172310	272396	Mm.35127	NM_172310	ENSMUSG00000030515	Tarsl2	A530046H20Rik	threonyl-tRNA synthetase-like 2	protein-coding
mm_40723.1	chr5	65967385	65967401	+	1	NA	5' UTR (NM_001081104, exon 1 of 5)	5' UTR (NM_001081104, exon 1 of 5)	269	NM_001081104	231252	Mm.140015	NM_001081104	ENSMUSG00000029205	Chrna9	2410015I05Rik|Acra9|EG666827|Gm8311	cholinergic receptor, nicotinic, alpha polypeptide 9	protein-coding
mm_45965.1	chr5	90465953	90465970	-	1	NA	exon (NM_009654, exon 6 of 15)	exon (NM_009654, exon 6 of 15)	5091	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_136607.1	chr17	5278454	5278464	+	1	NA	intron (NM_001085355, intron 6 of 19)	intron (NM_001085355, intron 6 of 19)	140308	NM_175349	106557	Mm.432764	NM_175349	ENSMUSG00000101959	Ldhal6b	4933402O15Rik|AI326310|LDHL|Ldhal	lactate dehydrogenase A-like 6B	protein-coding
mm_73638.1	chr8	110737934	110737948	+	1	NA	exon (NM_198625, exon 13 of 14)	exon (NM_198625, exon 13 of 14)	12215	NM_001310591	244654	Mm.490385	NM_198625	ENSMUSG00000033763	Mtss1l	ABBA	metastasis suppressor 1-like	protein-coding
mm_85750.1	chr9	108597559	108597604	-	1	NA	promoter-TSS (NM_028944)	promoter-TSS (NM_028944)	19	NM_028944	74443	Mm.226534	NM_028944	ENSMUSG00000006675	P4htm	4933406E20Rik|AI853847|BB128974|Ph-4	prolyl 4-hydroxylase, transmembrane (endoplasmic reticulum)	protein-coding
mm_151281.1	chr19	55253982	55253992	+	1	NA	5' UTR (NM_027976, exon 1 of 22)	5' UTR (NM_027976, exon 1 of 22)	618	NM_027976	433256	Mm.292056	NM_027976	ENSMUSG00000024981	Acsl5	1700030F05Rik|ACS2|ACS5|Facl5	acyl-CoA synthetase long-chain family member 5	protein-coding
mm_117041.1	chr13	58291734	58291742	-	1	NA	intron (NM_175214, intron 15 of 16)	intron (NM_175214, intron 15 of 16)	-17550	NM_019832	56278	Mm.296625	NM_019832	ENSMUSG00000021552	Gkap1	42kDa|4933400B15Rik|D13Ertd340e|Gkap42	G kinase anchoring protein 1	protein-coding
mm_67759.1	chr7	92670069	92670092	-	1	NA	promoter-TSS (NM_029078)	promoter-TSS (NM_029078)	-168	NM_029078	74737	Mm.288645	NM_029078	ENSMUSG00000041328	Pcf11	2500001H09Rik|5730417B17Rik|C77803	PCF11 cleavage and polyadenylation factor subunit	protein-coding
mm_72806.1	chr8	87472890	87472894	+	1	NA	promoter-TSS (NM_019626)	promoter-TSS (NM_019626)	80	NR_033430	100040294	Mm.213632	NR_033430	ENSMUSG00000097248	Gm2694	C230036H16Rik|linc1582	predicted gene 2694	ncRNA
mm_135252.1	chr16	37621939	37621947	-	1	NA	non-coding (NR_027778, exon 10 of 13)	non-coding (NR_027778, exon 10 of 13)	32425	NM_026610	68194	Mm.379154	NM_026610	ENSMUSG00000022820	Ndufb4	0610006N12Rik|1300010H20Rik	NADH dehydrogenase (ubiquinone) 1 beta subcomplex 4	protein-coding
mm_38365.1	chr4	138326235	138326305	-	1	NA	promoter-TSS (NM_026880)	promoter-TSS (NM_026880)	26	NM_026880	68943	Mm.18539	NM_026880	ENSMUSG00000028756	Pink1	1190006F07Rik|AU042772|AW557854|BRPK|mFLJ00387	PTEN induced putative kinase 1	protein-coding
mm_63810.1	chr7	133709352	133709358	+	1	NA	promoter-TSS (NM_025392)	promoter-TSS (NM_025392)	22	NM_025392	66165	Mm.389983	NM_025392	ENSMUSG00000030983	Bccip	1110013J05Rik|TOK-1	BRCA2 and CDKN1A interacting protein	protein-coding
mm_99260.1	chr11	101245997	101246044	+	1	NA	promoter-TSS (NM_019444)	promoter-TSS (NM_019444)	-314	NM_019444	54409	Mm.260698	NM_019444	ENSMUSG00000001240	Ramp2	-	receptor (calcitonin) activity modifying protein 2	protein-coding
mm_46797.1	chr5	112896414	112896424	-	1	NA	promoter-TSS (NM_028901)	promoter-TSS (NM_028901)	-57	NM_028901	74376	Mm.441903	NM_028901	ENSMUSG00000072720	Myo18b	4932408L24Rik|4933411E19Rik|Gm448	myosin XVIIIb	protein-coding
mm_36326.1	chr4	70410335	70410360	-	1	NA	promoter-TSS (NM_001313762)	promoter-TSS (NM_001313762)	88	NM_001313762	214444	Mm.370777	NM_145990	ENSMUSG00000039298	Cdk5rap2	2900018K03Rik|an|mKIAA1633	CDK5 regulatory subunit associated protein 2	protein-coding
mm_158593.1	chrX	150986085	150986115	-	1	NA	3' UTR (NM_198110, exon 16 of 16)	3' UTR (NM_198110, exon 16 of 16)	31193	NM_001168600	237107	Mm.45987	NM_198110	ENSMUSG00000025266	Gnl3l	BC020354	guanine nucleotide binding protein-like 3 (nucleolar)-like	protein-coding
mm_124822.1	chr15	9071650	9071724	+	1	NA	exon (NM_001085410, exon 1 of 14)	exon (NM_001085410, exon 1 of 14)	427	NM_001040395	68646	Mm.244226	NM_001040395	ENSMUSG00000022253	Nadk2	MNADK|Nadkd1	NAD kinase 2, mitochondrial	protein-coding
mm_12173.1	chr2	62664320	62664335	+	1	NA	promoter-TSS (NM_145523)	promoter-TSS (NM_145523)	0	NM_145523	227960	Mm.219877	NM_145523	ENSMUSG00000026893	Gca	5133401E04Rik|AI573844	grancalcin	protein-coding
mm_135209.1	chr16	36611165	36611165	-	1	NA	intron (NM_019388, intron 5 of 7)	MLT1E2|LTR|ERVL-MaLR	-49031	NM_013803	12374	Mm.103619	NM_013803	ENSMUSG00000051980	Casr	CaR|Gprc2a	calcium-sensing receptor	protein-coding
mm_8224.1	chr1	138174283	138174304	-	1	NA	intron (NM_001111316, intron 1 of 31)	intron (NM_001111316, intron 1 of 31)	833	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_98849.1	chr11	97660470	97660500	+	1	NA	Intergenic	CpG	-2927	NM_139311	246198	Mm.23685	NM_139311	ENSMUSG00000038437	Mllt6	AI315037|Af17	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 6	protein-coding
mm_116513.1	chr13	45670605	45670622	-	1	NA	intron (NM_001199304, intron 5 of 6)	intron (NM_001199304, intron 5 of 6)	163169	NM_025508	66355	Mm.290802	NM_025508	ENSMUSG00000000253	Gmpr	2310004P21Rik|AV028449|GMPR 1	guanosine monophosphate reductase	protein-coding
mm_25734.1	chr3	122856427	122856440	+	1	NA	3' UTR (NM_153422, exon 21 of 21)	3' UTR (NM_153422, exon 21 of 21)	-38639	NM_007980	14079	Mm.28398	NM_007980	ENSMUSG00000023057	Fabp2	Fabpi|I-FABP	fatty acid binding protein 2, intestinal	protein-coding
mm_35190.1	chr4	16013812	16013830	-	1	NA	promoter-TSS (NM_145950)	promoter-TSS (NM_145950)	56	NM_145950	209212	Mm.46455	NM_145950	ENSMUSG00000041153	Osgin2	BC010311|C230027H09Rik	oxidative stress induced growth inhibitor family member 2	protein-coding
mm_39355.1	chr5	9101089	9101107	+	1	NA	intron (NM_001081029, intron 1 of 4)	CpG	361	NM_001081029	652925	Mm.439954	NM_001081029	ENSMUSG00000079659	Tmem243	4930420K17Rik|E030031F02Rik	transmembrane protein 243, mitochondrial	protein-coding
mm_46603.1	chr5	107869013	107869056	-	1	NA	intron (NM_007964, intron 1 of 17)	CpG	6073	NM_007964	14020	Mm.35796	NM_007964	ENSMUSG00000011831	Evi5	NB4S	ecotropic viral integration site 5	protein-coding
mm_94485.1	chr11	6635602	6635609	+	1	NA	3' UTR (NM_011709, exon 4 of 4)	3' UTR (NM_011709, exon 4 of 4)	3044	NM_011709	22373	Mm.268094	NM_011709	ENSMUSG00000000381	Wap	-	whey acidic protein	protein-coding
mm_116476.1	chr13	43559813	43559851	-	1	NA	exon (NM_001081059, exon 1 of 9)	exon (NM_001081059, exon 1 of 9)	359	NM_001081059	76137	Mm.426290	NM_001081059	ENSMUSG00000021371	Mcur1	6230416A05Rik|AU015498|AV136929|AW554392|C88263|Ccdc90a	mitochondrial calcium uniporter regulator 1	protein-coding
mm_1729.1	chr1	75381652	75381663	+	1	NA	promoter-TSS (NM_001085371)	promoter-TSS (NM_001085371)	-457	NM_001085371	11790	Mm.275397	NM_007463	ENSMUSG00000026207	Speg	AW125581|Apeg1|BPEG|D1Bwg1450e|SPEGalpha|SPEGbeta|mKIAA1297	SPEG complex locus	protein-coding
mm_8818.1	chr1	162028711	162028714	-	1	NA	intron (NM_172646, intron 16 of 19)	ID_B1|SINE|B4	23743	NR_040562	72753	Mm.452125	NR_040562	ENSMUSG00000090260	2810442N19Rik	-	RIKEN cDNA 2810442N19 gene	ncRNA
mm_86746.1	chr10	19486689	19486729	+	1	NA	Intergenic	Intergenic	-105240	NM_010511	15979	Mm.549	NM_010511	ENSMUSG00000020009	Ifngr1	CD119|IFN-gammaR|Ifgr|Ifngr|Nktar	interferon gamma receptor 1	protein-coding
mm_53930.1	chr6	4746392	4746395	-	1	NA	promoter-TSS (NM_130877)	promoter-TSS (NM_130877)	811	NM_001130188	20392	Mm.8739	NM_011360	ENSMUSG00000004631	Sgce	e-SG	sarcoglycan, epsilon	protein-coding
mm_82484.1	chr9	18385982	18386068	-	1	NA	promoter-TSS (NM_028279)	promoter-TSS (NM_028279)	-97	NM_028279	72560	Mm.474510	NM_028279	ENSMUSG00000043943	Naalad2	2700022G20Rik|D9Ertd285e|Folh1b|GCP3|GCPIII|NAADALASE2|NAALADASE2	N-acetylated alpha-linked acidic dipeptidase 2	protein-coding
mm_107961.1	chr12	72668368	72668370	+	1	NA	Intergenic	Intergenic	-3541	NM_025522	66375	Mm.289653	NM_025522	ENSMUSG00000021094	Dhrs7	2310016E22Rik|5730564L20Rik|AW061210|Retdsr4|Retsdr4	dehydrogenase/reductase (SDR family) member 7	protein-coding
mm_37926.1	chr4	132853409	132853411	-	1	NA	TTS (NM_133887)	TTS (NM_133887)	-10241	NM_146154	100336	Mm.105230	NM_146154	ENSMUSG00000028882	Ppp1r8	6330548N22Rik|AU044684|NIPP1	protein phosphatase 1, regulatory (inhibitor) subunit 8	protein-coding
mm_137803.1	chr17	29846548	29846558	+	1	NA	exon (NM_001081160, exon 7 of 16)	exon (NM_001081160, exon 7 of 16)	41329	NM_001081160	74762	Mm.40901	NM_001081160	ENSMUSG00000043557	Mdga1	1200011I03Rik|GPIM|Mamdc3	MAM domain containing glycosylphosphatidylinositol anchor 1	protein-coding
mm_113120.1	chr13	24514942	24514944	+	1	NA	Intergenic	Intergenic	-67246	NM_001286100	193385	Mm.217319	NM_029679	ENSMUSG00000036006	Fam65b	-	family with sequence similarity 65, member B	protein-coding
mm_78269.1	chr9	22003003	22003028	+	1	NA	promoter-TSS (NM_029939)	promoter-TSS (NM_029939)	27	NM_008925	19089	Mm.214593	NM_008925	ENSMUSG00000003402	Prkcsh	80K-H|PKCSH	protein kinase C substrate 80K-H	protein-coding
mm_113080.1	chr13	23836927	23836961	+	1	NA	Intergenic	Intergenic	-2490	NM_001164743	105355	Mm.27038	NM_134069	ENSMUSG00000036083	Slc17a3	AW261723|Npt4	solute carrier family 17 (sodium phosphate), member 3	protein-coding
mm_78804.1	chr9	44047972	44047985	+	1	NA	3' UTR (NM_009382, exon 4 of 4)	3' UTR (NM_009382, exon 4 of 4)	4594	NM_009382	21838	Mm.3951	NM_009382	ENSMUSG00000032011	Thy1	CD90|T25|Thy-1|Thy-1.2|Thy1.1|Thy1.2	thymus cell antigen 1, theta	protein-coding
mm_5243.1	chr1	16345474	16345487	-	1	NA	3' UTR (NM_001347044, exon 14 of 14)	3' UTR (NM_001347044, exon 14 of 14)	173635	NM_001347044	29819	Mm.216257	NM_025303	ENSMUSG00000025920	Stau2	-	staufen (RNA binding protein) homolog 2 (Drosophila)	protein-coding
mm_121479.1	chr14	121035539	121035575	+	1	NA	promoter-TSS (NM_134082)	promoter-TSS (NM_134082)	-17	NM_134082	223254	Mm.223980	NM_134082	ENSMUSG00000025555	Farp1	AW228844|BC030329|Cdep	FERM, RhoGEF (Arhgef) and pleckstrin domain protein 1 (chondrocyte-derived)	protein-coding
mm_102120.1	chr11	53300687	53300704	-	1	NA	promoter-TSS (NM_008300)	promoter-TSS (NM_008300)	-216	NM_008300	15525	Mm.239865	NM_008300	ENSMUSG00000020361	Hspa4	70kDa|AI317151|APG-2|Hsp110|Hsp70RY|mKIAA4025	heat shock protein 4	protein-coding
mm_80641.1	chr9	89317121	89317126	+	1	NA	Intergenic	Intergenic	105933	NM_026829	107885	Mm.486274	NM_026829	ENSMUSG00000066442	Mthfs	1110034I12Rik|2310020H23Rik|AI119695	5, 10-methenyltetrahydrofolate synthetase	protein-coding
mm_141919.1	chr17	35000369	35000411	-	1	NA	promoter-TSS (NM_011690)	promoter-TSS (NM_011690)	356	NM_033075	110956	Mm.22506	NM_033075		D17H6S56E-5	G7e	DNA segment, Chr 17, human D6S56E 5	protein-coding
mm_147517.1	chr18	52519089	52519109	-	1	NA	3' UTR (NM_010728, exon 7 of 7)	3' UTR (NM_010728, exon 7 of 7)	10622	NM_001286181	16948	Mm.172	NM_010728	ENSMUSG00000024529	Lox	AI893619|TSC-160|rrg	lysyl oxidase	protein-coding
mm_138129.1	chr17	34187601	34187608	+	1	NA	promoter-TSS (NM_001161730)	promoter-TSS (NM_001161730)	48	NM_013683	21354	Mm.482076	NM_013683	ENSMUSG00000037321	Tap1	ABC17|APT1|Abcb2|Ham-1|Ham1|MTP1|PSF1|RING4|TAP|Tap-1|Y3	transporter 1, ATP-binding cassette, sub-family B (MDR/TAP)	protein-coding
mm_149758.1	chr19	22800496	22800497	+	1	NA	intron (NM_001035243, intron 8 of 23)	intron (NM_001035243, intron 8 of 23)	49891	NR_029591	387200		NR_029591	ENSMUSG00000065507	Mir204	Mirn204|mir-204|mmu-mir-204	microRNA 204	ncRNA
mm_37016.1	chr4	113286956	113287004	-	1	NA	promoter-TSS (NM_001103199)	promoter-TSS (NM_001103199)	-7	NM_001103199	230622	Mm.291107	NM_001103199	ENSMUSG00000087194	Skint6	OTTMUSG00000008519	selection and upkeep of intraepithelial T cells 6	protein-coding
mm_83219.1	chr9	42124277	42124333	-	1	NA	promoter-TSS (NM_011436)	promoter-TSS (NM_011436)	-16	NM_011436	20660	Mm.121920	NM_011436	ENSMUSG00000049313	Sorl1	2900010L19Rik|AI596264|AW261561|LR11|SorLA|gp250|mSorLA	sortilin-related receptor, LDLR class A repeats-containing	protein-coding
mm_75121.1	chr8	34807051	34807061	-	1	NA	promoter-TSS (NM_176933)	promoter-TSS (NM_176933)	-554	NM_176933	319520	Mm.170276	NM_176933	ENSMUSG00000031530	Dusp4	2700078F24Rik|AI844617|BB104621|E130306H24Rik|MKP2	dual specificity phosphatase 4	protein-coding
mm_9880.1	chr1	185451623	185451656	-	1	NA	intron (NR_040305, intron 2 of 2)	intron (NR_040305, intron 2 of 2)	-3209	NM_001033286	226781	Mm.227117	NM_001033286	ENSMUSG00000026614	Slc30a10	E130106K10Rik|Gm212	solute carrier family 30, member 10	protein-coding
mm_155149.1	chrX	52791205	52791231	+	1	NA	promoter-TSS (NM_001034059)	promoter-TSS (NM_001034059)	18	NM_001034059	434778	Mm.23411	NM_001034059	ENSMUSG00000073207	Ccdc160	6330534C20Rik	coiled-coil domain containing 160	protein-coding
mm_143582.1	chr17	74323890	74323895	-	1	NA	promoter-TSS (NM_024428)	promoter-TSS (NM_024428)	52	NM_024428	66310	Mm.28536	NM_024428	ENSMUSG00000024067	Dpy30	2810410M20Rik|C87842	dpy-30, histone methyltransferase complex regulatory subunit	protein-coding
mm_45973.1	chr5	90469610	90469630	-	1	NA	exon (NM_009654, exon 9 of 15)	exon (NM_009654, exon 9 of 15)	8750	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_76128.1	chr8	80880162	80880249	-	1	NA	5' UTR (NM_001301298, exon 1 of 11)	5' UTR (NM_001301298, exon 1 of 11)	274	NM_021356	14388	Mm.277409	NM_021356	ENSMUSG00000031714	Gab1	AA408973|AW107238	growth factor receptor bound protein 2-associated protein 1	protein-coding
mm_11849.1	chr2	45239291	45239304	+	1	NA	Intergenic	Intergenic	-126018	NM_015753	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_82996.1	chr9	36693112	36693123	-	1	NA	promoter-TSS (NM_007391)	promoter-TSS (NM_007391)	72	NR_040741	75567	Mm.426883	NR_040741	ENSMUSG00000098304	1700027I24Rik	-	RIKEN cDNA 1700027I24 gene	ncRNA
mm_161901.1	chr18	56562593	56562593	+	1	NA	promoter-TSS (NM_138600)	promoter-TSS (NM_138600)	24	NM_001162989	56698	Mm.214569	NM_019996	ENSMUSG00000008301	Phax	2810055C14Rik|4933427L19Rik|AU018701|AU018854|D18Ertd65e|Rnuxa|p55	phosphorylated adaptor for RNA export	protein-coding
mm_165479.1	chr2	164333397	164333397	-	1	NA	exon (NM_009301, exon 2 of 3)	exon (NM_009301, exon 2 of 3)	632	NM_009301	20944	Mm.140154	NM_009301	ENSMUSG00000017004	Svs5	BB115186|Semg1|Svp-1|Svp1|Svp5	seminal vesicle secretory protein 5	protein-coding
mm_90960.1	chr10	13304720	13304754	-	1	NA	intron (NM_001195065, intron 1 of 12)	intron (NM_001195065, intron 1 of 12)	19423	NM_001195096	215789	Mm.283359	NM_001033257	ENSMUSG00000062866	Phactr2	AV158170|BC012871	phosphatase and actin regulator 2	protein-coding
mm_103621.1	chr11	78694218	78694221	-	1	NA	intron (NM_008702, intron 1 of 10)	intron (NM_008702, intron 1 of 10)	3206	NM_008702	18099	Mm.9001	NM_008702	ENSMUSG00000017376	Nlk	AI194375	nemo like kinase	protein-coding
mm_14191.1	chr2	127083383	127083398	+	1	NA	intron (NM_026678, intron 3 of 7)	intron (NM_026678, intron 3 of 7)	12733	NM_026678	109778	Mm.22028	NM_026678	ENSMUSG00000001999	Blvra	0610006A11Rik|2500001N03Rik|Blvr	biliverdin reductase A	protein-coding
mm_156845.1	chrX	164391671	164391692	+	1	NA	exon (NM_010216, exon 3 of 7)	exon (NM_010216, exon 3 of 7)	18159	NM_010216	14205	Mm.297978	NM_010216	ENSMUSG00000031380	Vegfd	AI325264|Figf|VEGF-D	vascular endothelial growth factor D	protein-coding
mm_98285.1	chr11	89065828	89065847	+	1	NA	intron (NR_110336, intron 1 of 3)	intron (NR_110336, intron 1 of 3)	5086	NR_110336	414094	Mm.124287	NM_001001497		Dgkeos	A930013B10Rik	diacylglycerol kinase, epsilon, opposite strand	ncRNA
mm_154369.1	chrM	9453	9468	+	1	NA	NA	Intergenic	NA	NA								
mm_74222.1	chr8	124047146	124047162	+	1	NA	exon (NM_001029876, exon 9 of 9)	exon (NM_001029876, exon 9 of 9)	23681	NM_001029876	382038	Mm.334891	NM_001029876	ENSMUSG00000031976	Urb2	C77575|mKIAA0133	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	protein-coding
mm_107037.1	chr12	13559176	13559182	+	1	NA	intron (NM_027706, intron 49 of 51)	Lx8|LINE|L1	68467	NR_136761	102639399	Mm.122052	NR_136761		Gm35725	-	predicted gene, 35725	ncRNA
mm_77137.1	chr8	111393839	111393851	-	1	NA	promoter-TSS (NM_178086)	promoter-TSS (NM_178086)	-24	NM_178086	338521	Mm.41083	NM_178086	ENSMUSG00000033579	Fa2h	FAAH|Faxdc1|G630055L08Rik	fatty acid 2-hydroxylase	protein-coding
mm_45203.1	chr5	52669459	52669477	-	1	NA	intron (NM_172490, intron 1 of 10)	CpG	233	NM_172490	211006	Mm.244719	NM_172490	ENSMUSG00000029173	Sepsecs	AA986712|D5Ertd135e|SLA|SecS	Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase	protein-coding
mm_121899.1	chr14	21848843	21848852	-	1	NA	promoter-TSS (NM_026965)	promoter-TSS (NM_026965)	63	NM_026965	69156	Mm.11827	NM_026965	ENSMUSG00000021773	Comtd1	1810030M08Rik|MT773	catechol-O-methyltransferase domain containing 1	protein-coding
mm_169.1	chr1	13177143	13177145	+	1	NA	exon (NM_008678, exon 10 of 23)	exon (NM_008678, exon 10 of 23)	-49981	NM_001081209	383491	Mm.309380	NM_001081209	ENSMUSG00000042414	Prdm14	-	PR domain containing 14	protein-coding
mm_173256.1	chrX	94775696	94775702	-	1	NA	Intergenic	ORR1C2|LTR|ERVL-MaLR	22590	NR_003292	668171	Mm.426134	NR_003292		Zxda	4933406P09Rik|AW413531	zinc finger, X-linked, duplicated A	pseudo
mm_137226.1	chr17	24273998	24274001	+	1	NA	intron (NM_001031621, intron 25 of 29)	intron (NM_001031621, intron 25 of 29)	-22590	NM_007634	12449	Mm.77695	NM_007634	ENSMUSG00000072082	Ccnf	CycF|Fbxo1	cyclin F	protein-coding
mm_122714.1	chr14	52257698	52257784	-	1	NA	Intergenic	CpG	-20169	NM_201637	67772	Mm.289934	NM_201637	ENSMUSG00000053754	Chd8	5830451P18Rik|AU015341|Duplin|HELSNF1|mKIAA1564	chromodomain helicase DNA binding protein 8	protein-coding
mm_27091.1	chr3	30048239	30048250	-	1	NA	Intergenic	L2|LINE|L2	-35040	NM_007963	14013	Mm.56965	NM_007963	ENSMUSG00000027684	Mecom	D630039M04Rik|Evi-1|Evi1|Jbo|Mds|Mds1|Mds1-Evi1|Prdm3|Znfpr1b1	MDS1 and EVI1 complex locus	protein-coding
mm_149357.1	chr19	10948408	10948427	+	1	NA	exon (NM_023731, exon 1 of 4)	exon (NM_023731, exon 1 of 4)	849	NM_023731	108673	Mm.294908	NM_023731	ENSMUSG00000024732	Ccdc86	4933411H20Rik|6720480F16Rik|D19Ertd678e	coiled-coil domain containing 86	protein-coding
mm_120519.1	chr14	66784501	66784502	+	1	NA	Intergenic	Intergenic	84099	NM_009955	12934	Mm.352648	NM_009955	ENSMUSG00000022048	Dpysl2	AI851130|Crmp2|DRP2|Musunc33|TOAD-64|Ulip2	dihydropyrimidinase-like 2	protein-coding
mm_23232.1	chr3	50439117	50439149	+	1	NA	intron (NM_011990, intron 1 of 11)	B3|SINE|B2	4480	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_107889.1	chr12	70455707	70455710	+	1	NA	intron (NM_028339, intron 1 of 7)	intron (NM_028339, intron 1 of 7)	2554	NM_028339	72736	Mm.204670	NM_028339	ENSMUSG00000021072	Tmx1	2810425A04Rik|AI465319|Txndc1	thioredoxin-related transmembrane protein 1	protein-coding
mm_148935.1	chr19	7018816	7018827	+	1	NA	exon (NM_153795, exon 2 of 15)	exon (NM_153795, exon 2 of 15)	648	NM_153795	108101	Mm.157591	NM_153795	ENSMUSG00000024965	Fermt3	C79673|Kindlin3	fermitin family member 3	protein-coding
mm_64880.1	chr7	14493018	14493041	-	1	NA	promoter-TSS (NM_001184981)	promoter-TSS (NM_001184981)	-103	NM_001184981	638251	Mm.482063	NM_001184981	ENSMUSG00000094156	Sult2a7	EG638251|Gm7231	sulfotransferase family 2A, dehydroepiandrosterone (DHEA)-preferring, member 7	protein-coding
mm_74833.1	chr8	23208320	23208356	-	1	NA	5' UTR (NM_018743, exon 1 of 13)	5' UTR (NM_018743, exon 1 of 13)	115	NM_018743	102247	Mm.200898	NM_018743	ENSMUSG00000031545	Gpat4	AU041707|AW545732|Agpat6|Tsarg7	glycerol-3-phosphate acyltransferase 4	protein-coding
mm_153592.1	chr19	43674845	43674909	-	1	NA	promoter-TSS (NR_045645)	promoter-TSS (NR_045645)	4	NM_145156	246696	Mm.23827	NM_145156	ENSMUSG00000040414	Slc25a28	2210403D18Rik|Mfrn2|Mrs3/4	solute carrier family 25, member 28	protein-coding
mm_30612.1	chr4	6990739	6990766	+	1	NA	promoter-TSS (NM_145711)	promoter-TSS (NM_145711)	-29	NM_145711	252838	Mm.435828	NM_145711	ENSMUSG00000041272	Tox	1700007F02Rik	thymocyte selection-associated high mobility group box	protein-coding
mm_60750.1	chr7	45486260	45486274	+	1	NA	promoter-TSS (NM_001290999)	promoter-TSS (NM_001290999)	4	NM_001290999	56734	Mm.439742	NM_008807	ENSMUSG00000023467	Tulp2	Pdet	tubby-like protein 2	protein-coding
mm_21342.1	chr2	157109453	157109482	-	1	NA	exon (NM_001139520, exon 11 of 17)	exon (NM_001139520, exon 11 of 17)	22412	NM_001177439	383766	Mm.480305	NM_001177439	ENSMUSG00000074628	Tldc2	Gm1332	TBC/LysM associated domain containing 2	protein-coding
mm_36507.1	chr4	83485915	83485934	-	1	NA	5' UTR (NM_001290527, exon 2 of 11)	5' UTR (NM_001290527, exon 2 of 11)	524	NM_001290527	101739	Mm.105331	NM_133948	ENSMUSG00000028484	Psip1	AA408851|AU015605|Dfs70|Ledgfa|Ledgfb|Psip2	PC4 and SFRS1 interacting protein 1	protein-coding
mm_150527.1	chr19	39113903	39113916	+	1	NA	promoter-TSS (NM_001011707)	promoter-TSS (NM_001011707)	11	NM_001011707	69888	Mm.271190	NM_001011707	ENSMUSG00000067229	Cyp2c66	2010301M18Rik	cytochrome P450, family 2, subfamily c, polypeptide 66	protein-coding
mm_68257.1	chr7	105591687	105591697	-	1	NA	TTS (NM_017371)	TTS (NM_017371)	8424	NM_017371	15458	Mm.3485	NM_017371	ENSMUSG00000030895	Hpx	Hpxn|hx	hemopexin	protein-coding
mm_170297.1	chr18	31804066	31804066	+	1	NA	promoter-TSS (NM_028866)	promoter-TSS (NM_028866)	9	NM_001170966	74320	Mm.277705	NM_028866	ENSMUSG00000024400	Wdr33	1110001N06Rik|2310011G05Rik|2810021O11Rik|8430413N20Rik|WDC146	WD repeat domain 33	protein-coding
mm_59778.1	chr7	28837557	28837562	+	1	NA	intron (NM_010706, intron 3 of 9)	intron (NM_010706, intron 3 of 9)	3389	NM_010707	16857	Mm.210336	NM_010707		Lgals6	galectin-6	lectin, galactose binding, soluble 6	protein-coding
mm_46186.1	chr5	97456972	97457007	-	1	NA	promoter-TSS (NM_010294)	promoter-TSS (NM_010294)	19	NM_010294	14626	Mm.61206	NM_010294	ENSMUSG00000050553	Gk2	GKTA|Gk-rs2	glycerol kinase 2	protein-coding
mm_82218.1	chr9	3016906	3016926	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	21827	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_72098.1	chr8	71592125	71592131	+	1	NA	promoter-TSS (NM_025396)	promoter-TSS (NM_025396)	-56	NM_025396	66171	Mm.282284	NM_025396	ENSMUSG00000031807	Pgls	1110030K05Rik|AI447866|Plgs	6-phosphogluconolactonase	protein-coding
mm_23499.1	chr3	60525859	60525869	+	1	NA	intron (NM_001253710, intron 1 of 7)	intron (NM_001253710, intron 1 of 7)	24685	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_166136.1	chr4	155992940	155992946	+	1	NA	promoter-TSS (NM_011341)	promoter-TSS (NM_011341)	38	NM_001302467	20318	Mm.293517	NM_011341	ENSMUSG00000029076	Sdf4	Cab45	stromal cell derived factor 4	protein-coding
mm_29355.1	chr3	108475047	108475066	-	1	NA	intron (NM_001346518, intron 7 of 21)	intron (NM_001346518, intron 7 of 21)	-29797	NM_001204979	20226	Mm.28688	NM_011319	ENSMUSG00000068739	Sars	Sars1|Strs|serRS	seryl-aminoacyl-tRNA synthetase	protein-coding
mm_3295.1	chr1	136683662	136683670	+	1	NA	promoter-TSS (NR_045325)	promoter-TSS (NR_045325)	37	NR_045325	100503460	Mm.30630	NR_045324	ENSMUSG00000097113	Gm19705	-	predicted gene, 19705	ncRNA
mm_132063.1	chr16	30008697	30008703	+	1	NA	promoter-TSS (NR_033631)	promoter-TSS (NR_033631)	33	NR_033631	100043102	Mm.30797	NR_033631	ENSMUSG00000097184	4632428C04Rik	Gm4231	RIKEN cDNA 4632428C04 gene	ncRNA
mm_97894.1	chr11	83305535	83305541	+	1	NA	intron (NM_027915, intron 1 of 20)	ID2|SINE|ID	2841	NM_001035854	71770	Mm.39053	NM_027915	ENSMUSG00000035152	Ap2b1	1300012O03Rik|AI788979	adaptor-related protein complex 2, beta 1 subunit	protein-coding
mm_141492.1	chr17	31296651	31296666	-	1	NA	5' UTR (NM_001242427, exon 1 of 20)	5' UTR (NM_001242427, exon 1 of 20)	434	NM_001242427	224674	Mm.311395	NM_153062	ENSMUSG00000024036	Slc37a1	G3PP	solute carrier family 37 (glycerol-3-phosphate transporter), member 1	protein-coding
mm_90990.1	chr10	13965645	13965650	-	1	NA	promoter-TSS (NM_010437)	promoter-TSS (NM_010437)	-732	NM_010437	15273	Mm.42157	NM_010437	ENSMUSG00000015501	Hivep2	Gm20114|MIBP1|Schnurri-2|Shn-2	human immunodeficiency virus type I enhancer binding protein 2	protein-coding
mm_102769.1	chr11	68199209	68199251	-	1	NA	intron (NM_018768, intron 7 of 7)	intron (NM_018768, intron 7 of 7)	-21662	NR_105833	102465219		NR_105833	ENSMUSG00000099174	Mir6406	Gm27981|mmu-mir-6406	microRNA 6406	ncRNA
mm_7450.1	chr1	120258890	120258898	-	1	NA	intron (NM_001085409, intron 2 of 5)	intron (NM_001085409, intron 2 of 5)	6386	NM_133186	68428	Mm.181033	NM_133186	ENSMUSG00000026389	Steap3	1010001D01Rik|Tsap6|pHyde	STEAP family member 3	protein-coding
mm_95193.1	chr11	43012165	43012187	+	1	NA	Intergenic	Intergenic	-137701	NM_176999	319767	Mm.252339	NM_176999	ENSMUSG00000055415	Atp10b	5930426O13Rik|9030605H24Rik	ATPase, class V, type 10B	protein-coding
mm_33643.1	chr4	133011519	133011546	+	1	NA	promoter-TSS (NM_146155)	promoter-TSS (NM_146155)	26	NM_146155	230793	Mm.31816	NM_146155	ENSMUSG00000037692	Ahdc1	D030015G18Rik	AT hook, DNA binding motif, containing 1	protein-coding
mm_58569.1	chr7	4793104	4793112	+	1	NA	intron (NM_009081, intron 1 of 4)	CpG	143	NM_009081	19943	Mm.379002	NM_009081	ENSMUSG00000030432	Rpl28	D7Wsu21e	ribosomal protein L28	protein-coding
mm_160726.1	chr10	75212370	75212370	+	1	NA	promoter-TSS (NM_001145826)	promoter-TSS (NM_001145826)	-20	NM_001145826	74392	Mm.27716	NM_153406	ENSMUSG00000033444	Specc1l	4930470P14Rik|4932439K10Rik|9530057A13Rik|AI317249|Cytsa|mKIAA0376	sperm antigen with calponin homology and coiled-coil domains 1-like	protein-coding
mm_97507.1	chr11	78499037	78499041	+	1	NA	promoter-TSS (NM_011707)	promoter-TSS (NM_011707)	-81	NM_011707	22370	Mm.3667	NM_011707	ENSMUSG00000017344	Vtn	AI256434|Vn	vitronectin	protein-coding
mm_147681.1	chr18	60691732	60691762	-	1	NA	intron (NM_008306, intron 11 of 13)	intron (NM_008306, intron 11 of 13)	21642	NM_008306	15531	Mm.181862	NM_008306	ENSMUSG00000054008	Ndst1	1200015G06Rik|HSNST|HSNST 1|Hsst|N-HSST|N-HSST 1|NDST-1|b2b2230Clo	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 1	protein-coding
mm_139316.1	chr17	48409174	48409178	+	1	NA	promoter-TSS (NM_001289491)	promoter-TSS (NM_001289491)	644	NM_001110832	18044	Mm.4929	NM_010913	ENSMUSG00000023994	Nfya	AA407810|Cbf-b|SEZ-10|SEZ10	nuclear transcription factor-Y alpha	protein-coding
mm_14096.1	chr2	125218140	125218146	+	1	NA	exon (NM_001079690, exon 24 of 28)	exon (NM_001079690, exon 24 of 28)	-29105	NM_001159646	110074	Mm.282499	NM_023595	ENSMUSG00000027203	Dut	5031412I06Rik|5133400F09Rik|D2Bwg0749e|Dutp|dUTPase	deoxyuridine triphosphatase	protein-coding
mm_32586.1	chr4	111411094	111411103	+	1	NA	intron (NM_001048189, intron 6 of 12)	intron (NM_001048189, intron 6 of 12)	-3908	NR_033793	67621	Mm.45533	NM_026279	ENSMUSG00000028545	Bend5	2310026E23Rik	BEN domain containing 5	protein-coding
mm_60037.1	chr7	31036989	31037008	+	1	NA	intron (NM_008761, intron 5 of 8)	intron (NM_008761, intron 5 of 8)	3319	NR_106017	102465635		NR_106017	ENSMUSG00000098783	Mir7050	Gm27578|mmu-mir-7050	microRNA 7050	ncRNA
mm_19333.1	chr2	90579451	90579463	-	1	NA	intron (NM_008982, intron 1 of 23)	intron (NM_008982, intron 1 of 23)	1190	NM_008982	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_38373.1	chr4	138457051	138457067	-	1	NA	3' UTR (NM_025451, exon 2 of 2)	3' UTR (NM_025451, exon 2 of 2)	1911	NM_025451	66259	Mm.41603	NM_025451	ENSMUSG00000046447	Camk2n1	1810006K23Rik|AI848599|AI891706	calcium/calmodulin-dependent protein kinase II inhibitor 1	protein-coding
mm_81282.1	chr9	108306257	108306267	+	1	NA	promoter-TSS (NM_133986)	promoter-TSS (NM_133986)	102	NM_016802	11848	Mm.757	NM_016802	ENSMUSG00000007815	Rhoa	Arha|Arha1|Arha2	ras homolog family member A	protein-coding
mm_13967.1	chr2	121429450	121429540	+	1	NA	exon (NM_007952, exon 5 of 13)	exon (NM_007952, exon 5 of 13)	13106	NM_145973	269344	Mm.330522	NM_145973	ENSMUSG00000027246	Ell3	A930015D22Rik	elongation factor RNA polymerase II-like 3	protein-coding
mm_90545.1	chr10	128092659	128092700	+	1	NA	promoter-TSS (NM_054078)	promoter-TSS (NM_054078)	-104	NM_054078	116848	Mm.252213	NM_054078	ENSMUSG00000040054	Baz2a	AA415431|C030005G16Rik|C78388|Tip5|Walp3|mKIAA0314	bromodomain adjacent to zinc finger domain, 2A	protein-coding
mm_97674.1	chr11	79711360	79711375	+	1	NA	promoter-TSS (NR_029579)	promoter-TSS (NR_029579)	-602	NR_029579	387188		NR_029579	ENSMUSG00000065395	Mir193a	Mir193|Mirn193|mir-193a|mmu-mir-193|mmu-mir-193a	microRNA 193a	ncRNA
mm_123490.1	chr14	66077785	66077791	-	1	NA	promoter-TSS (NM_009618)	promoter-TSS (NM_009618)	-19	NM_009618	11495	Mm.422850	NM_009618	ENSMUSG00000022039	Adam2	AI323749|Ftnb|Ph30-beta	a disintegrin and metallopeptidase domain 2	protein-coding
mm_87570.1	chr10	56386312	56386314	+	1	NA	intron (NM_010288, intron 1 of 1)	intron (NM_010288, intron 1 of 1)	9013	NM_010288	14609	Mm.378921	NM_010288	ENSMUSG00000050953	Gja1	AU042049|AW546267|Cnx43|Cx43|Cx43alpha1|Gja-1|Npm1|connexin43	gap junction protein, alpha 1	protein-coding
mm_20075.1	chr2	120563796	120563878	-	1	NA	promoter-TSS (NM_011743)	promoter-TSS (NM_011743)	-6	NM_011743	20402	Mm.485295	NM_011743	ENSMUSG00000027288	Zfp106	Cd-1|D2Dcr28|H3a|Sh3bp3|Znf106|sirm	zinc finger protein 106	protein-coding
mm_115583.1	chr13	11768891	11768894	-	1	NA	intron (NM_023868, intron 27 of 104)	intron (NM_023868, intron 27 of 104)	246840	NR_027813	664793	Mm.410565	NR_027813		Zp4-ps	EG664793|Zp4|Zpb	zona pellucida glycoprotein 4, pseudogene	pseudo
mm_19610.1	chr2	102746732	102746736	-	1	NA	intron (NM_001077515, intron 5 of 10)	intron (NM_001077515, intron 5 of 10)	40296	NM_001077515	20511	Mm.267547	NM_011393	ENSMUSG00000005089	Slc1a2	1700091C19Rik|2900019G14Rik|AI159670|Eaat2|GLT-1|GLT1|MGLT1	solute carrier family 1 (glial high affinity glutamate transporter), member 2	protein-coding
mm_167909.1	chrX	84772745	84772747	+	1	NA	intron (NM_007868, intron 55 of 78)	intron (NM_007868, intron 55 of 78)	-275549	NM_001314038	13405	Mm.275608	NM_007868	ENSMUSG00000045103	Dmd	DXSmh7|DXSmh9|Dp427|Dp71|dys|mdx|pke	dystrophin, muscular dystrophy	protein-coding
mm_78005.1	chr9	11104412	11104459	+	1	NA	Intergenic	MMERVK9C_I-int|LTR|ERVK	-199660	NM_001170787	244682	Mm.187021	NM_001033359	ENSMUSG00000039488	Cntn5	6720426O10Rik|A830025P08Rik|Gm507|NB-2	contactin 5	protein-coding
mm_153307.1	chr19	38022793	38022813	-	1	NA	intron (NM_001302140, intron 2 of 53)	intron (NM_001302140, intron 2 of 53)	20774	NM_001099634	226101	Mm.34674	NM_177035	ENSMUSG00000048612	Myof	2310004N10Rik|2310051D19Rik|E030042N20Rik|Fer1l3	myoferlin	protein-coding
mm_32616.1	chr4	114163459	114163470	+	1	NA	promoter-TSS (NM_177669)	promoter-TSS (NM_177669)	80	NM_001166027	230623	Mm.124482	NM_177669	ENSMUSG00000057977	Skint11	A630098G03Rik|Gm569	selection and upkeep of intraepithelial T cells 11	protein-coding
mm_70435.1	chr8	11558413	11558433	+	1	NA	promoter-TSS (NM_001302459)	promoter-TSS (NM_001302459)	13	NM_001302459	26356	Mm.25709	NM_011919	ENSMUSG00000045969	Ing1	2610028J21Rik|AA407184|AI875420|mING1h|p33Ing1|p37Ing1b	inhibitor of growth family, member 1	protein-coding
mm_155807.1	chrX	99136120	99136138	+	1	NA	promoter-TSS (NM_010110)	promoter-TSS (NM_010110)	68	NM_010110	13641	Mm.3374	NM_010110	ENSMUSG00000031217	Efnb1	Cek5-L|EFL-3|Elk-L|Epl2|Eplg2|LERK-2|Lerk2|Stra1	ephrin B1	protein-coding
mm_104187.1	chr11	87801093	87801109	-	1	NA	exon (NM_010824, exon 10 of 14)	exon (NM_010824, exon 10 of 14)	7317	NM_010824	17523	Mm.4668	NM_010824	ENSMUSG00000009350	Mpo	mKIAA4033	myeloperoxidase	protein-coding
mm_150797.1	chr19	44303539	44303560	+	1	NA	TTS (NR_039574)	TTS (NR_039574)	378	NR_039574	100628619		NR_039574	ENSMUSG00000093315	Mir5114	mmu-mir-5114|mu-mir-5114	microRNA 5114	ncRNA
mm_153716.1	chr19	44403242	44403259	-	1	NA	exon (NM_009127, exon 3 of 6)	exon (NM_009127, exon 3 of 6)	4459	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_97641.1	chr11	79276581	79276592	+	1	NA	Intergenic	B1_Mur2|SINE|Alu	-21891	NM_019653	78889	Mm.307022	NM_019653	ENSMUSG00000017677	Wsb1	1110056B13Rik|2700038M07Rik	WD repeat and SOCS box-containing 1	protein-coding
mm_79223.1	chr9	49559226	49559228	+	1	NA	intron (NM_001081445, intron 7 of 17)	intron (NM_001081445, intron 7 of 17)	40939	NR_029465	100036537	Mm.437541	NR_029465	ENSMUSG00000079564	Gm11149	ENSMUSG00000060603|ENSMUSG00000079564	predicted gene 11149	ncRNA
mm_46347.1	chr5	102479984	102480007	-	1	NA	Intergenic	Intergenic	-1396	NM_146161	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding
mm_84787.1	chr9	76582022	76582044	-	1	NA	Intergenic	Intergenic	-36229	NM_001045518	208994	Mm.256929	NM_001045518	ENSMUSG00000032358	Fam83b	C530008M07Rik|Gm516	family with sequence similarity 83, member B	protein-coding
mm_11570.1	chr2	32901798	32901846	+	1	NA	intron (NM_146119, intron 1 of 13)	intron (NM_146119, intron 1 of 13)	25688	NM_146119	227737	Mm.301646	NM_146119	ENSMUSG00000026796	Fam129b	9130404D14Rik	family with sequence similarity 129, member B	protein-coding
mm_55707.1	chr6	72958400	72958411	-	1	NA	promoter-TSS (NM_025284)	promoter-TSS (NM_025284)	78	NM_025284	19240	Mm.3532	NM_025284	ENSMUSG00000079523	Tmsb10	Ptmb10|Tb10	thymosin, beta 10	protein-coding
mm_44364.1	chr5	17806381	17806423	-	1	NA	intron (NM_007643, intron 8 of 14)	ORR1C1-int|LTR|ERVL-MaLR	29494	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_104325.1	chr11	93965958	93965966	-	1	NA	intron (NM_008704, intron 1 of 4)	intron (NM_008704, intron 1 of 4)	2559	NM_008704	18102	Mm.439702	NM_008704	ENSMUSG00000037601	Nme1	AL024257|NDPK-A|NM23-M1|NM23A	NME/NM23 nucleoside diphosphate kinase 1	protein-coding
mm_36781.1	chr4	102989536	102989545	-	1	NA	intron (NM_001163767, intron 2 of 4)	intron (NM_001163767, intron 2 of 4)	215	NR_040444	100504717	Mm.394445	NR_040444	ENSMUSG00000085181	Gm12709	OTTMUSG00000008056	predicted gene 12709	ncRNA
mm_52464.1	chr6	113697377	113697392	+	1	NA	5' UTR (NM_001347356, exon 1 of 8)	5' UTR (NM_001347356, exon 1 of 8)	334	NM_001033463	381801	Mm.333322	NM_001033463	ENSMUSG00000056952	Tatdn2	AI646012|mKIAA0218	TatD DNase domain containing 2	protein-coding
mm_94835.1	chr11	23497811	23497832	+	1	NA	exon (NM_172391, exon 1 of 9)	exon (NM_172391, exon 1 of 9)	218	NM_001290655	268390	Mm.13148	NM_172391	ENSMUSG00000020288	Ahsa2	-	AHA1, activator of heat shock protein ATPase 2	protein-coding
mm_70242.1	chr8	3353688	3353701	+	1	NA	5' UTR (NM_001033378, exon 1 of 11)	5' UTR (NM_001033378, exon 1 of 11)	279	NM_001033378	319493	Mm.234565	NM_001033378	ENSMUSG00000074497	A430078G23Rik	-	RIKEN cDNA A430078G23 gene	protein-coding
mm_124144.1	chr14	87141822	87141830	-	1	NA	promoter-TSS (NM_019670)	promoter-TSS (NM_019670)	-712	NM_019670	56419	Mm.440585	NM_019670	ENSMUSG00000022021	Diaph3	4930417P13Rik|Dia2|Diap3|Drf3|mDia2|mKIAA4117|p134MDia2	diaphanous related formin 3	protein-coding
mm_45504.1	chr5	72501874	72501909	-	1	NA	intron (NM_001122756, intron 1 of 21)	intron (NM_001122756, intron 1 of 21)	2317	NM_016869	53419	Mm.332425	NM_016869	ENSMUSG00000005220	Corin	AV273130|Lrp4	corin	protein-coding
mm_81208.1	chr9	107579901	107579912	+	1	NA	promoter-TSS (NM_019750)	promoter-TSS (NM_019750)	-763	NM_019750	56441	Mm.10305	NM_019750	ENSMUSG00000079334	Nat6	AI225910|Fus2	N-acetyltransferase 6	protein-coding
mm_88636.1	chr10	79916958	79916986	+	1	NA	promoter-TSS (NM_177994)	promoter-TSS (NM_177994)	1	NM_053244	114229	Mm.191035	NM_053244	ENSMUSG00000035773	Kiss1r	Gpr54|KiSS-1	KISS1 receptor	protein-coding
mm_75407.1	chr8	46294593	46294601	-	1	NA	promoter-TSS (NM_173789)	promoter-TSS (NM_173789)	74	NM_173789	234219	Mm.145631	NM_173789	ENSMUSG00000047171	Helt	A830086M02|Hesl|Heslike|Mgn|megane	helt bHLH transcription factor	protein-coding
mm_81981.1	chr9	121350908	121350909	+	1	NA	Intergenic	Intergenic	-16050	NM_175114	67095	Mm.491112	NM_175114	ENSMUSG00000032536	Trak1	2310001H13Rik|AI413908|AI467545|hyrt|mKIAA1042	trafficking protein, kinesin binding 1	protein-coding
mm_33415.1	chr4	129928790	129928800	+	1	NA	Intergenic	Intergenic	22569	NR_045190	319894	Mm.59196	NR_045190	ENSMUSG00000086369	E330017L17Rik	-	RIKEN cDNA E330017L17 gene	ncRNA
mm_69586.1	chr7	135704753	135704778	-	1	NA	exon (NM_001081117, exon 8 of 14)	exon (NM_001081117, exon 8 of 14)	11614	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_113610.1	chr13	41254081	41254082	+	1	NA	intron (NM_001135577, intron 1 of 1)	HAL1|LINE|L1	4237	NM_001135577	108934	Mm.38578	NM_001135577	ENSMUSG00000091264	Smim13	2900036K02Rik	small integral membrane protein 13	protein-coding
mm_80435.1	chr9	77923713	77923740	+	1	NA	intron (NM_134255, intron 1 of 7)	intron (NM_134255, intron 1 of 7)	6361	NM_134255	68801	Mm.430736	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	ELOVL family member 5, elongation of long chain fatty acids (yeast)	protein-coding
mm_169455.1	chr1	46181107	46181110	+	1	NA	intron (NM_001160386, intron 22 of 65)	IAPLTR1_Mm|LTR|ERVK	114370	NM_001160386	227058	Mm.296880	NM_001160386	ENSMUSG00000041144	Dnah7b	Dnahc7b|Gm107	dynein, axonemal, heavy chain 7B	protein-coding
mm_163063.1	chr11	66563536	66563540	+	1	NA	Intergenic	Intergenic	-37412	NM_001034874	380702	Mm.351764	NM_001034874	ENSMUSG00000053930	Shisa6	Gm879|ckamp52	shisa family member 6	protein-coding
mm_3340.1	chr1	137967754	137967762	+	1	NA	Intergenic	Intergenic	1119	NR_029820	723890		NR_029820	ENSMUSG00000065458	Mir181b-1	Mirn181b-1|mir-181b-1	microRNA 181b-1	ncRNA
mm_155377.1	chrX	71638573	71638577	+	1	NA	Intergenic	L1Md_F2|LINE|L1	-25092	NM_010340	14765	Mm.33336	NM_010340	ENSMUSG00000056380	Gpr50	H9	G-protein-coupled receptor 50	protein-coding
mm_145833.1	chr18	65442216	65442227	+	1	NA	intron (NM_172833, intron 2 of 15)	intron (NM_172833, intron 2 of 15)	11224	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_103458.1	chr11	76341635	76341637	-	1	NA	intron (NM_008750, intron 1 of 7)	intron (NM_008750, intron 1 of 7)	57505	NM_008750	18230	Mm.27915	NM_008750	ENSMUSG00000020844	Nxn	l11Jus13	nucleoredoxin	protein-coding
mm_14768.1	chr2	145675507	145675527	+	1	NA	Intergenic	Intergenic	-25678	NR_033220	408057	Mm.486711	NR_033220	ENSMUSG00000087594	BC039771	-	cDNA sequence BC039771	ncRNA
mm_92126.1	chr10	64072878	64072898	-	1	NA	intron (NM_178678, intron 2 of 2)	intron (NM_178678, intron 2 of 2)	17367	NM_178678	216028	Mm.431318	NM_178678	ENSMUSG00000042846	Lrrtm3	9630044H04Rik	leucine rich repeat transmembrane neuronal 3	protein-coding
mm_11699.1	chr2	35979323	35979363	+	1	NA	exon (NM_029774, exon 1 of 10)	exon (NM_029774, exon 1 of 10)	281	NM_029774	74410	Mm.21591	NM_028921	ENSMUSG00000026885	Ttll11	4932702F08Rik|4933424A20Rik|AU043211|D2Ertd624e	tubulin tyrosine ligase-like family, member 11	protein-coding
mm_106742.1	chr12	3907674	3907705	+	1	NA	exon (NM_153743, exon 18 of 18)	exon (NM_153743, exon 18 of 18)	15945	NM_153743	13435	Mm.5001	NM_007872	ENSMUSG00000020661	Dnmt3a	MmuIIIA	DNA methyltransferase 3A	protein-coding
mm_41886.1	chr5	105481580	105481592	+	1	NA	exon (NM_001033550, exon 4 of 5)	exon (NM_001033550, exon 4 of 5)	-37885	NM_133897	100604	Mm.319847	NM_133897	ENSMUSG00000054720	Lrrc8c	AD158|AI326115|E430036I04Rik|fad158	leucine rich repeat containing 8 family, member C	protein-coding
mm_158608.1	chrX	152342434	152342457	-	1	NA	promoter-TSS (NM_029836)	promoter-TSS (NM_029836)	39	NM_029836	52808	Mm.9997	NM_029836	ENSMUSG00000041096	Tspyl2	CDA1|CINAP|DENTT|DXBwg1396e|DXHXS1008E|E130307F10Rik	TSPY-like 2	protein-coding
mm_10573.1	chr2	18064646	18064705	+	1	NA	promoter-TSS (NM_001252561)	promoter-TSS (NM_001252561)	90	NM_001252561	17354	Mm.209175	NM_010804	ENSMUSG00000026743	Mllt10	Af10|B130021D15Rik|D630001B22Rik|mKIAA4140	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 10	protein-coding
mm_156366.1	chrX	139610210	139610238	+	1	NA	promoter-TSS (NM_023270)	promoter-TSS (NM_023270)	-396	NM_023270	66889	Mm.27764	NM_023270	ENSMUSG00000031438	Rnf128	1300002C13Rik|AI987883|GRAIL|Greul1	ring finger protein 128	protein-coding
mm_68818.1	chr7	126082379	126082392	-	1	NA	promoter-TSS (NM_001101488)	promoter-TSS (NM_001101488)	26	NM_001101488	269994	Mm.39599	NM_001101488	ENSMUSG00000046182	Gsg1l	AI852434|C230098I05Rik|G630023A01Rik|Gm637|g1l	GSG1-like	protein-coding
mm_69484.1	chr7	133782777	133782791	-	1	NA	promoter-TSS (NM_001286031)	promoter-TSS (NM_001286031)	1	NM_001286031	101437	Mm.199223	NM_133941	ENSMUSG00000030986	Dhx32	3110079L04Rik|4732469F02Rik|AA408140|Ddx32	DEAH (Asp-Glu-Ala-His) box polypeptide 32	protein-coding
mm_146777.1	chr18	20059593	20059613	-	1	NA	promoter-TSS (NM_013505)	promoter-TSS (NM_013505)	-49	NM_001317365	13506	Mm.280547	NM_013505	ENSMUSG00000024331	Dsc2	AW228162	desmocollin 2	protein-coding
mm_10667.1	chr2	20968666	20968697	+	1	NA	promoter-TSS (NM_001081364)	promoter-TSS (NM_001081364)	-193	NR_033225	433408	Mm.386941	NR_033225		Gm13375	OTTMUSG00000011664	predicted gene 13375	ncRNA
mm_87648.1	chr10	58407674	58407708	+	1	NA	intron (NM_001346676, intron 2 of 9)	B1_Mur2|SINE|Alu	13318	NM_001346676	110829	Mm.57734	NM_026148	ENSMUSG00000019920	Lims1	2310016J22Rik|4921524A02Rik|AI507642|AU021743|AW551584|C430041B13Rik|Lims1l|PINCH|PINCH1	LIM and senescent cell antigen-like domains 1	protein-coding
mm_100777.1	chr11	4807382	4807389	-	1	NA	intron (NM_001252251, intron 5 of 16)	intron (NM_001252251, intron 5 of 16)	25750	NM_001252253	18016	Mm.297109	NM_010898	ENSMUSG00000009073	Nf2	merlin	neurofibromin 2	protein-coding
mm_34566.1	chr4	149854634	149854638	+	1	NA	Intergenic	Intergenic	-80369	NM_027460	70556	Mm.41877	NM_027460	ENSMUSG00000028982	Slc25a33	5730438N18Rik|Pnc1	solute carrier family 25, member 33	protein-coding
mm_148293.1	chr18	82585284	82585308	-	1	NA	3' UTR (NM_010777, exon 7 of 7)	3' UTR (NM_010777, exon 7 of 7)	30788	NM_001025254	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_94694.1	chr11	20039076	20039078	+	1	NA	Intergenic	Intergenic	73874	NM_146243	66713	Mm.259045	NM_146243	ENSMUSG00000020152	Actr2	4921510D23Rik|AA409782|Arp2|D6Ertd746e	ARP2 actin-related protein 2	protein-coding
mm_126682.1	chr15	84765692	84765707	+	1	NA	exon (NM_001164628, exon 8 of 12)	exon (NM_001164628, exon 8 of 12)	-45433	NR_040347	328576	Mm.400211	NR_040347		Gm20556	A430075N02	predicted gene, 20556	ncRNA
mm_127244.1	chr15	99601208	99601221	+	1	NA	promoter-TSS (NM_175087)	promoter-TSS (NM_175087)	-186	NM_175087	11831	Mm.202309	NM_175087	ENSMUSG00000043144	Aqp6	AI790337	aquaporin 6	protein-coding
mm_139427.1	chr17	53566737	53566763	+	1	NA	promoter-TSS (NM_020005)	promoter-TSS (NM_020005)	-221	NM_020005	18519	Mm.255025	NM_020005	ENSMUSG00000000708	Kat2b	A930006P13Rik|AI461839|AW536563|Pcaf|p/CAF	K(lysine) acetyltransferase 2B	protein-coding
mm_127154.1	chr15	98571041	98571045	+	1	NA	promoter-TSS (NM_001201322)	promoter-TSS (NM_001201322)	39	NM_001201322	73863	Mm.66894	NM_001201322	ENSMUSG00000022993	4930415O20Rik	-	RIKEN cDNA 4930415O20 gene	protein-coding
mm_134247.1	chr16	13520430	13520438	-	1	NA	promoter-TSS (NR_037997)	promoter-TSS (NR_037997)	-15	NR_037997	70100	Mm.158330	NR_037997	ENSMUSG00000099411	2310015D24Rik	-	RIKEN cDNA 2310015D24 gene	ncRNA
mm_35089.1	chr4	8142819	8142821	-	1	NA	3' UTR (NM_007592, exon 9 of 9)	3' UTR (NM_007592, exon 9 of 9)	96221	NM_007592	12319	Mm.119320	NM_007592	ENSMUSG00000041261	Car8	AW546993|Ca8|Cals|Cals1|Carp|wdl	carbonic anhydrase 8	protein-coding
mm_142731.1	chr17	48348691	48348736	-	1	NA	exon (NM_031254, exon 2 of 5)	exon (NM_031254, exon 2 of 5)	2312	NM_001272078	83433	Mm.261623	NM_031254	ENSMUSG00000023992	Trem2	TREM-2|Trem2a|Trem2b|Trem2c	triggering receptor expressed on myeloid cells 2	protein-coding
mm_142953.1	chr17	56117266	56117283	-	1	NA	promoter-TSS (NM_001077348)	promoter-TSS (NM_001077348)	24	NM_001077348	66968	Mm.254985	NM_025874	ENSMUSG00000011305	Plin5	2310076L09Rik|AI415325|AW109675|Lsdp5|MLDP|PAT-1	perilipin 5	protein-coding
mm_41308.1	chr5	90468621	90468631	+	1	NA	exon (NM_009654, exon 8 of 15)	exon (NM_009654, exon 8 of 15)	7756	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_48488.1	chr5	142530095	142530100	-	1	NA	promoter-TSS (NM_019943)	promoter-TSS (NM_019943)	-21	NM_019943	56522	Mm.441372	NM_019943	ENSMUSG00000074817	Papolb	PAP|Paplob|Papola-ps|Papt|Plap-ps|Tpap	poly (A) polymerase beta (testis specific)	protein-coding
mm_81896.1	chr9	119894877	119894913	+	1	NA	promoter-TSS (NM_026236)	promoter-TSS (NM_026236)	0	NM_026236	67561	Mm.104789	NM_026236	ENSMUSG00000032512	Wdr48	8430408H12Rik|Uaf1|mKIAA1449	WD repeat domain 48	protein-coding
mm_60486.1	chr7	44478539	44478549	+	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	-5973	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_115690.1	chr13	13968898	13968923	-	1	NA	intron (NM_178640, intron 2 of 11)	intron (NM_178640, intron 2 of 11)	14236	NM_178640	97884	Mm.21686	NM_178640	ENSMUSG00000039242	B3galnt2	A930105D20Rik|C80633|D230016N13Rik	UDP-GalNAc:betaGlcNAc beta 1,3-galactosaminyltransferase, polypeptide 2	protein-coding
mm_159130.1	chr2	74726758	74726758	+	1	NA	TTS (NR_029566)	TTS (NR_029566)	688	NR_029566	387144		NR_029566	ENSMUSG00000065500	Mir10b	Mirn10b|mir-10b|mmu-mir-10b	microRNA 10b	ncRNA
mm_158972.1	chr1	107278373	107278373	-	1	NA	promoter-TSS (NM_201363)	promoter-TSS (NM_201363)	-2	NM_201363	381286	Mm.337362	NM_201363	ENSMUSG00000073601	Serpinb3c	1110001H02Rik|1110013A16Rik|Scca2|Serpinb4	serine (or cysteine) peptidase inhibitor, clade B, member 3C	protein-coding
mm_109025.1	chr12	103895088	103895128	+	1	NA	exon (NM_009245, exon 5 of 5)	exon (NM_009245, exon 5 of 5)	9842	NM_009245	20702	Mm.439692	NM_009245	ENSMUSG00000079015	Serpina1c	Pi3|Pi6|Skalp|Spi1-3|Spi1-6|Wap3	serine (or cysteine) peptidase inhibitor, clade A, member 1C	protein-coding
mm_77552.1	chr8	123278337	123278351	-	1	NA	exon (NM_016925, exon 31 of 43)	exon (NM_016925, exon 31 of 43)	-24122	NM_028200	72325	Mm.276193	NM_028200	ENSMUSG00000001062	Vps9d1	1300018I17Rik|2410004N05Rik|5DOS1|Vsp9d1	VPS9 domain containing 1	protein-coding
mm_163789.1	chr14	9658570	9658570	+	1	NA	intron (NM_001308286, intron 5 of 6)	intron (NM_001308286, intron 5 of 6)	-225525	NR_030680	100042415	Mm.235938	NR_030680		Mnd1-ps	Gm3833	Mnd1 retrotransposed pseudogene	pseudo
mm_31126.1	chr4	43046292	43046315	+	1	NA	promoter-TSS (NM_172691)	promoter-TSS (NM_172691)	-83	NM_172691	230088	Mm.260162	NM_172691	ENSMUSG00000036002	Fam214b	B230312A22Rik	family with sequence similarity 214, member B	protein-coding
mm_169316.1	chr14	106455023	106455030	+	1	NA	intron (NR_045938, intron 1 of 3)	intron (NR_045938, intron 1 of 3)	31494	NR_045938	73631	Mm.48862	NR_045938	ENSMUSG00000099794	1700128A07Rik	-	RIKEN cDNA 1700128A07 gene	ncRNA
mm_102719.1	chr11	67114941	67114952	-	1	NA	non-coding (NR_038055, exon 4 of 5)	non-coding (NR_038055, exon 4 of 5)	5134	NR_038055	74184	Mm.162554	NR_038055	ENSMUSG00000087410	2310065F04Rik	linc-Myh	RIKEN cDNA 2310065F04 gene	ncRNA
mm_67548.1	chr7	81493884	81493947	-	1	NA	promoter-TSS (NM_021492)	promoter-TSS (NM_021492)	10	NM_021492	11775	Mm.322894	NM_021492	ENSMUSG00000062444	Ap3b2	AI549966|AU042881|Naptb|[b]-NAP|beta-NAP|beta3B	adaptor-related protein complex 3, beta 2 subunit	protein-coding
mm_111625.1	chr12	102423742	102423774	-	1	NA	intron (NM_011175, intron 1 of 13)	intron (NM_011175, intron 1 of 13)	16055	NM_011175	19141	Mm.17185	NM_011175	ENSMUSG00000021190	Lgmn	AEP|AI746452|AU022324|Prsc1	legumain	protein-coding
mm_20908.1	chr2	150362709	150362753	-	1	NA	promoter-TSS (NM_027017)	promoter-TSS (NM_027017)	34	NM_027017	69277	Mm.272470	NM_027017	ENSMUSG00000063364	3300002I08Rik	2900016H11Rik	RIKEN cDNA 3300002I08 gene	protein-coding
mm_49402.1	chr6	28426380	28426390	+	1	NA	3' UTR (NM_007480, exon 6 of 6)	3' UTR (NM_007480, exon 6 of 6)	-1516	NM_019569	56223	Mm.31708	NM_019569	ENSMUSG00000029707	Fscn3	-	fascin actin-bundling protein 3	protein-coding
mm_169849.1	chr16	31912124	31912128	+	1	NA	Intergenic	Intergenic	-21725	NM_172822	239827	Mm.440388	NM_172822	ENSMUSG00000045625	Pigz	F630022B06Rik	phosphatidylinositol glycan anchor biosynthesis, class Z	protein-coding
mm_152719.1	chr19	17837621	17837642	-	1	NA	promoter-TSS (NM_001190483)	promoter-TSS (NM_001190483)	1	NM_001163144	18552	Mm.3401	NM_001163144	ENSMUSG00000024713	Pcsk5	PC5|PC6|SPC6|b2b1549Clo|b2b585Clo	proprotein convertase subtilisin/kexin type 5	protein-coding
mm_17742.1	chr2	32713043	32713062	-	1	NA	promoter-TSS (NM_130860)	promoter-TSS (NM_130860)	-80	NR_039536	100628606		NR_039536	ENSMUSG00000105841	Mir3960	mmu-mir-3960	microRNA 3960	ncRNA
mm_75088.1	chr8	33929934	33929977	-	1	NA	promoter-TSS (NM_019733)	promoter-TSS (NM_019733)	-92	NM_001042675	19663	Mm.323997	NM_019733	ENSMUSG00000031586	Rbpms	2010300K22Rik|2700019M19Rik|AU017537|RBP-MS|hermes	RNA binding protein gene with multiple splicing	protein-coding
mm_151677.1	chr19	4201592	4201623	-	1	NA	promoter-TSS (NM_011237)	promoter-TSS (NM_011237)	-4	NM_011237	19367	Mm.277629	NM_011237	ENSMUSG00000024824	Rad9a	Rad9	RAD9 checkpoint clamp component A	protein-coding
mm_60267.1	chr7	43841932	43841950	+	1	NA	promoter-TSS (NM_026806)	promoter-TSS (NM_026806)	-328	NM_026806	68668	Mm.458122	NM_026806	ENSMUSG00000074155	Klk5	1110030O19Rik	kallikrein related-peptidase 5	protein-coding
mm_138544.1	chr17	35263292	35263310	+	1	NA	intron (NM_010380, intron 1 of 7)	CpG	178	NM_001267808	14980	Mm.439675	NM_001267808		H2-L	H-2L	histocompatibility 2, D region locus L	protein-coding
mm_60054.1	chr7	31150007	31150018	+	1	NA	intron (NM_027898, intron 1 of 18)	intron (NM_027898, intron 1 of 18)	1038	NM_027898	52857	Mm.27366	NM_027898	ENSMUSG00000001248	Gramd1a	1300003M23Rik|AI415002|AW547240|D7Bwg0611e	GRAM domain containing 1A	protein-coding
mm_121911.1	chr14	21989476	21989493	-	1	NA	5' UTR (NM_145459, exon 1 of 3)	5' UTR (NM_145459, exon 1 of 3)	117	NM_145459	218820	Mm.292401	NM_145459	ENSMUSG00000039081	Zfp503	AI181838|B830002A16Rik|Nolz-1|Nolz1|Znf503	zinc finger protein 503	protein-coding
mm_1239.1	chr1	62796112	62796200	+	1	NA	3' UTR (NM_001077407, exon 16 of 16)	3' UTR (NM_001077407, exon 16 of 16)	-1424	NR_040601	74992	Mm.401979	NR_040601		4930487H11Rik	-	RIKEN cDNA 4930487H11 gene	ncRNA
mm_78588.1	chr9	37367667	37367672	+	1	NA	promoter-TSS (NM_175189)	promoter-TSS (NM_175189)	63	NM_175189	72927	Mm.266133	NM_175189	ENSMUSG00000046240	Hepacam	2900042E01Rik|Glialcam|Hepn1	hepatocyte cell adhesion molecule	protein-coding
mm_58383.1	chr6	149305466	149305473	-	1	NA	Intergenic	RodERV21-int|LTR|ERV1	-3945	NM_001289661	67246	Mm.333515	NM_026054	ENSMUSG00000032712	2810474O19Rik	6720435I21Rik|AA536804|AU020969|GET|Kiaa1551	RIKEN cDNA 2810474O19 gene	protein-coding
mm_131032.1	chr16	3744163	3744180	+	1	NA	promoter-TSS (NM_148924)	promoter-TSS (NM_148924)	72	NM_148924	74120	Mm.29081	NM_148924	ENSMUSG00000022529	Zfp263	1200014J04Rik|AI326880|AU020888|NT2|mFPM315	zinc finger protein 263	protein-coding
mm_118211.1	chr13	110127732	110127769	-	1	NA	intron (NM_023852, intron 3 of 4)	intron (NM_023852, intron 3 of 4)	152456	NM_023852	67295	Mm.151600	NM_023852	ENSMUSG00000021700	Rab3c	2700062I01Rik|3110015B08Rik|3110037E15Rik|AI850886	RAB3C, member RAS oncogene family	protein-coding
mm_79628.1	chr9	59292599	59292602	+	1	NA	intron (NM_028121, intron 1 of 6)	AT_rich|Low_complexity|Low_complexity	1028	NM_028121	72141	Mm.22456	NM_028121	ENSMUSG00000025236	Adpgk	2610017G09Rik|Adp-gk|C77577	ADP-dependent glucokinase	protein-coding
mm_103266.1	chr11	71285251	71285279	-	1	NA	promoter-TSS (NR_027858)	promoter-TSS (NR_027858)	-33	NR_027858	627984	Mm.390378	NM_001039234	ENSMUSG00000092528	Nlrp1c-ps	Nalp1c|Nlrp1c|OTTMUSG00000006090	NLR family, pyrin domain containing 1C, pseudogene	pseudo
mm_167811.1	chr9	123931108	123931135	-	1	NA	Intergenic	RMER1B|Other|Other	37571	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_43123.1	chr5	125003441	125003466	+	1	NA	promoter-TSS (NM_028443)	promoter-TSS (NM_028443)	-22	NM_028443	73121	Mm.296138	NM_028443	ENSMUSG00000037962	Rflna	3110032G18Rik|Fam101a|cfm|cfm2	refilin A	protein-coding
mm_14621.1	chr2	136770147	136770152	+	1	NA	exon (NM_011428, exon 5 of 8)	exon (NM_011428, exon 5 of 8)	56699	NM_001291056	20614	Mm.45953	NM_011428	ENSMUSG00000027273	Snap25	Bdr|GENA70|SNAP-25|SUP|sp	synaptosomal-associated protein 25	protein-coding
mm_5884.1	chr1	53978541	53978584	-	1	NA	intron (NM_001001883, intron 2 of 28)	intron (NM_001001883, intron 2 of 28)	129138	NR_106149	102465783		NR_106149	ENSMUSG00000098443	Mir7681	Gm27806|mmu-mir-7681	microRNA 7681	ncRNA
mm_107370.1	chr12	32850705	32850728	+	1	NA	3' UTR (NM_021524, exon 11 of 11)	3' UTR (NM_021524, exon 11 of 11)	26600	NR_045032	100504486	Mm.440246	NR_045032		Gdap10	Gdap-ps	ganglioside-induced differentiation-associated-protein 10	ncRNA
mm_24269.1	chr3	89188406	89188410	+	1	NA	exon (NM_001014995, exon 11 of 12)	exon (NM_001014995, exon 11 of 12)	5183	NM_001014995	68521	Mm.274708	NM_001014995	ENSMUSG00000032657	Fam189b	1110013L07Rik	family with sequence similarity 189, member B	protein-coding
mm_33384.1	chr4	129575636	129575651	+	1	NA	Intergenic	Intergenic	-2002	NM_001162433	16818	Mm.293753	NM_010693	ENSMUSG00000000409	Lck	Hck-3|Lsk|Lskt|p56<lck>|p56Lck	lymphocyte protein tyrosine kinase	protein-coding
mm_61795.1	chr7	83964511	83964517	+	1	NA	intron (NM_030728, intron 13 of 28)	intron (NM_030728, intron 13 of 28)	72514	NM_023403	67943	Mm.117365	NM_023403	ENSMUSG00000038503	Mesdc2	2210015O11Rik|AW537813|mKIAA0081|mesd|msd	mesoderm development candidate 2	protein-coding
mm_103045.1	chr11	69797362	69797383	-	1	NA	3' UTR (NM_010198, exon 6 of 6)	3' UTR (NM_010198, exon 6 of 6)	-1435	NM_009601	11443	Mm.86425	NM_009601	ENSMUSG00000041189	Chrnb1	Achr-2|Acrb	cholinergic receptor, nicotinic, beta polypeptide 1 (muscle)	protein-coding
mm_167384.1	chr8	94524845	94524854	+	1	NA	intron (NM_001033207, intron 46 of 48)	intron (NM_001033207, intron 46 of 48)	-8179	NM_153507	234577	Mm.291815	NM_153507	ENSMUSG00000034361	Cpne2	3322401K10Rik	copine II	protein-coding
mm_80268.1	chr9	72958854	72958864	+	1	NA	promoter-TSS (NM_001163725)	promoter-TSS (NM_001163725)	74	NM_001163725	67685	Mm.31817	NM_026314	ENSMUSG00000089865	Dyx1c1	1700010I24Rik|Dnaaf4|EKN1|b2b811.1Clo|b2b811Clo	dyslexia susceptibility 1 candidate 1	protein-coding
mm_87251.1	chr10	41476327	41476392	+	1	NA	promoter-TSS (NM_001164433)	promoter-TSS (NM_001164433)	45	NM_138315	171580	Mm.290431	NM_138315	ENSMUSG00000019823	Mical1	MICAL|MICAL-1|Nical	microtubule associated monooxygenase, calponin and LIM domain containing 1	protein-coding
mm_11827.1	chr2	44957409	44957414	+	1	NA	Intergenic	Intergenic	65766	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_166902.1	chr7	28540820	28540833	+	1	NA	promoter-TSS (NM_026716)	promoter-TSS (NM_026716)	-59	NM_026716	68416	Mm.25210	NM_026716	ENSMUSG00000084174	Sycn	0910001K16Rik|1810038B08Rik|SYL	syncollin	protein-coding
mm_10400.1	chr2	13575518	13575528	+	1	NA	intron (NM_011701, intron 1 of 8)	intron (NM_011701, intron 1 of 8)	1212	NM_011701	22352	Mm.268000	NM_011701	ENSMUSG00000026728	Vim	-	vimentin	protein-coding
mm_136215.1	chr16	89960471	89960481	-	1	NA	intron (NM_001145886, intron 1 of 27)	intron (NM_001145886, intron 1 of 27)	351	NM_009384	21844	Mm.310902	NM_009384	ENSMUSG00000002489	Tiam1	AI847750|D16Ium10|D16Ium10e	T cell lymphoma invasion and metastasis 1	protein-coding
mm_171878.1	chr5	32578867	32578880	+	1	NA	Intergenic	RLTR9D|LTR|ERVK	-32298	NM_001205133	22612	Mm.4558	NM_009535	ENSMUSG00000014932	Yes1	Yes|p61-Yes	YES proto-oncogene 1, Src family tyrosine kinase	protein-coding
mm_157888.1	chrX	75874537	75874590	-	1	NA	promoter-TSS (NM_145629)	promoter-TSS (NM_145629)	11	NM_145629	102866	Mm.28777	NM_145629	ENSMUSG00000016382	Pls3	AI115446|AL024105	plastin 3 (T-isoform)	protein-coding
mm_95481.1	chr11	51262946	51262954	+	1	NA	promoter-TSS (NM_177567)	promoter-TSS (NM_177567)	1	NM_177567	193286	Mm.80975	NM_177567	ENSMUSG00000045942	BC049762	4930503F14	cDNA sequence BC049762	protein-coding
mm_98546.1	chr11	95010367	95010379	+	1	NA	5' UTR (NM_146025, exon 1 of 10)	5' UTR (NM_146025, exon 1 of 10)	494	NM_146025	217125	Mm.297199	NM_146025	ENSMUSG00000047181	Samd14	AI839049|AI854782|BC034054	sterile alpha motif domain containing 14	protein-coding
mm_147044.1	chr18	34908138	34908150	-	1	NA	exon (NM_144866, exon 8 of 11)	exon (NM_144866, exon 8 of 11)	23859	NM_144866	225363	Mm.329353	NM_144866	ENSMUSG00000024360	Etf1	AI463371|D6Ertd109e|ERF|ERF1|SUP45L1|TB3-1	eukaryotic translation termination factor 1	protein-coding
mm_32631.1	chr4	114987325	114987337	+	1	NA	promoter-TSS (NM_025647)	promoter-TSS (NM_025647)	-103	NM_025647	66588	Mm.294159	NM_025647	ENSMUSG00000028719	Cmpk1	0610011D08Rik|CK|Cmpk|UMP-CMPk	cytidine monophosphate (UMP-CMP) kinase 1	protein-coding
mm_70335.1	chr8	4522113	4522124	+	1	NA	intron (NM_026058, intron 9 of 10)	intron (NM_026058, intron 9 of 10)	28713	NM_026058	67260	Mm.35511	NM_026058	ENSMUSG00000008206	Cers4	2900019C14Rik|Lass4|Trh1	ceramide synthase 4	protein-coding
mm_3460.1	chr1	150104019	150104031	+	1	NA	exon (NM_011198, exon 7 of 10)	exon (NM_011198, exon 7 of 10)	3994	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_146592.1	chr18	9400374	9400378	-	1	NA	intron (NM_026484, intron 1 of 9)	intron (NM_026484, intron 1 of 9)	49774	NM_026484	67974	Mm.86523	NM_026484	ENSMUSG00000024286	Ccny	1700025H17Rik|3110050L10Rik|4631402G10Rik|5730405I09Rik	cyclin Y	protein-coding
mm_23223.1	chr3	49062423	49062432	+	1	NA	Intergenic	RLTR20C2_MM|LTR|ERVK	-453327	NR_003617	66332	Mm.46124	NM_025493		1700018B24Rik	-	enhancer of rudimentary homolog pseudogene	pseudo
mm_167870.1	chrX	33560896	33560915	-	1	NA	Intergenic	(A)n|Simple_repeat|Simple_repeat	16409	NM_001145038	100040732	Mm.465135	NM_001145038	ENSMUSG00000078324	Btbd35f14	Gm2933	BTB domain containing 35, family member 14	protein-coding
mm_119996.1	chr14	55604498	55604534	+	1	NA	promoter-TSS (NM_001159418)	promoter-TSS (NM_001159418)	-63	NM_001159418	16391	Mm.2032	NM_008394	ENSMUSG00000002325	Irf9	Irf-9|Isgf3g|p48	interferon regulatory factor 9	protein-coding
mm_106016.1	chr11	116012714	116012724	-	1	NA	promoter-TSS (NM_016905)	promoter-TSS (NM_016905)	0	NM_016905	14635	Mm.2820	NM_016905	ENSMUSG00000020766	Galk1	AA409894|GALK|Gk|Glk|Glk1	galactokinase 1	protein-coding
mm_34914.1	chr4	155705355	155705372	+	1	NA	5' UTR (NM_026899, exon 1 of 5)	5' UTR (NM_026899, exon 1 of 5)	548	NM_026899	68991	Mm.294770	NM_026899	ENSMUSG00000029038	Ssu72	1190002E22Rik|1500011L16Rik|2610101M12Rik	Ssu72 RNA polymerase II CTD phosphatase homolog (yeast)	protein-coding
mm_151913.1	chr19	5799722	5799726	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	2948	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_68915.1	chr7	126460773	126460783	-	1	NA	exon (NM_007504, exon 4 of 23)	exon (NM_007504, exon 4 of 23)	2295	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_58583.1	chr7	4922845	4922896	+	1	NA	TTS (NM_170759)	TTS (NM_170759)	619	NM_201355	269854	Mm.42652	NM_201355	ENSMUSG00000035285	Nat14	BC047219	N-acetyltransferase 14	protein-coding
mm_117499.1	chr13	78199874	78199924	-	1	NA	intron (NR_045195, intron 1 of 2)	intron (NR_045195, intron 1 of 2)	-1026	NM_010151	13865	Mm.439653	NM_010151	ENSMUSG00000069171	Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR-3|EAR3|Erbal3|SVP44|Tcfcoup1	nuclear receptor subfamily 2, group F, member 1	protein-coding
mm_63479.1	chr7	127745786	127745824	+	1	NA	promoter-TSS (NM_172748)	promoter-TSS (NM_172748)	-970	NM_172748	233902	Mm.259353	NM_172748	ENSMUSG00000030811	Fbxl19	6030430O11|BC059812|Fbl19	F-box and leucine-rich repeat protein 19	protein-coding
mm_47212.1	chr5	121009409	121009415	-	1	NA	promoter-TSS (NM_001302345)	promoter-TSS (NM_001302345)	126	NM_011286	19894	Mm.181166	NM_011286	ENSMUSG00000029608	Rph3a	2900002P20Rik|AU022689|AW108370	rabphilin 3A	protein-coding
mm_79006.1	chr9	45430317	45430379	+	1	NA	promoter-TSS (NM_001081270)	promoter-TSS (NM_001081270)	55	NM_001081270	114873	Mm.325499	NM_001081270	ENSMUSG00000032087	Dscaml1	4921507G06Rik|4930435C18Rik|BB239540|mKIAA1132	Down syndrome cell adhesion molecule like 1	protein-coding
mm_84345.1	chr9	64242710	64242717	-	1	NA	intron (NM_008927, intron 1 of 10)	intron (NM_008927, intron 1 of 10)	7512	NM_033607	93841	Mm.390180	NM_033607	ENSMUSG00000035337	Uchl4	-	ubiquitin carboxyl-terminal esterase L4	protein-coding
mm_7360.1	chr1	106711576	106711588	-	1	NA	TTS (NM_177410)	TTS (NM_177410)	2708	NM_009741	12043	Mm.257460	NM_009741	ENSMUSG00000057329	Bcl2	AW986256|Bcl-2|C430015F12Rik|D630044D05Rik|D830018M01Rik	B cell leukemia/lymphoma 2	protein-coding
mm_25287.1	chr3	105803592	105803602	+	1	NA	Intergenic	Intergenic	-2216	NM_145541	109905	Mm.101922	NM_145541	ENSMUSG00000068798	Rap1a	AI848598|G-22K|Krev-1|Rap1	RAS-related protein-1a	protein-coding
mm_32270.1	chr4	102625198	102625208	+	1	NA	Intergenic	Intergenic	35360	NM_001177981	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_41705.1	chr5	101764852	101764864	+	1	NA	promoter-TSS (NM_173370)	promoter-TSS (NM_173370)	-272	NM_173370	74596	Mm.46764	NM_173370	ENSMUSG00000029330	Cds1	4833409J18Rik|AI314024|AW125888	CDP-diacylglycerol synthase 1	protein-coding
mm_122932.1	chr14	54961793	54961822	-	1	NA	exon (NM_010856, exon 10 of 39)	exon (NM_010856, exon 10 of 39)	4800	NM_001164171	17888	Mm.290003	NM_010856	ENSMUSG00000040752	Myh6	A830009F23Rik|AA517445|Myhc-a|Myhca|alpha-MHC	myosin, heavy polypeptide 6, cardiac muscle, alpha	protein-coding
mm_166903.1	chr7	28541004	28541021	+	1	NA	exon (NM_026716, exon 1 of 2)	exon (NM_026716, exon 1 of 2)	127	NM_026716	68416	Mm.25210	NM_026716	ENSMUSG00000084174	Sycn	0910001K16Rik|1810038B08Rik|SYL	syncollin	protein-coding
mm_104830.1	chr11	99132516	99132550	-	1	NA	Intergenic	Intergenic	22544	NM_001301713	12775	Mm.2932	NM_007719	ENSMUSG00000037944	Ccr7	CC-CKR-7|CCR-7|CD197|Cdw197|Cmkbr7|EBI1|Ebi1h	chemokine (C-C motif) receptor 7	protein-coding
mm_71452.1	chr8	46521672	46521686	+	1	NA	intron (NM_001302163, intron 11 of 20)	intron (NM_001302163, intron 11 of 20)	-30390	NM_027973	71876	Mm.22108	NM_027973	ENSMUSG00000031629	Cenpu	1700029A22Rik|Mlf1ip	centromere protein U	protein-coding
mm_40061.1	chr5	33996732	33996745	+	1	NA	5' UTR (NM_001001985, exon 1 of 3)	5' UTR (NM_001001985, exon 1 of 3)	754	NM_001001985	269642	Mm.274610	NM_001001985	ENSMUSG00000048142	Nat8l	1110038O08Rik|Shati	N-acetyltransferase 8-like	protein-coding
mm_158706.1	chrX	162159930	162160009	-	1	NA	promoter-TSS (NM_001290526)	promoter-TSS (NM_001290526)	-528	NM_001290526	195727	Mm.336313	NM_001081052	ENSMUSG00000059493	Nhs	Gm389|Gm48|Nhs1|Xcat	Nance-Horan syndrome (human)	protein-coding
mm_81680.1	chr9	111058191	111058202	+	1	NA	promoter-TSS (NM_017466)	promoter-TSS (NM_017466)	-678	NM_001302376	54199	Mm.7336	NM_017466	ENSMUSG00000043953	Ccrl2	1810047I05Rik|Ackr5|CCR11|Cmkbr1l2|E01|L-CCR	chemokine (C-C motif) receptor-like 2	protein-coding
mm_58770.1	chr7	15896166	15896176	+	1	NA	promoter-TSS (NM_001205274)	promoter-TSS (NM_001205274)	47	NM_001033638	546024	Mm.259041	NM_001033638	ENSMUSG00000074365	Crxos	AA606869|AY590891|Crxos1|Egam1	cone-rod homeobox, opposite strand	protein-coding
mm_50871.1	chr6	55452187	55452198	+	1	NA	5' UTR (NM_001025372, exon 1 of 16)	5' UTR (NM_001025372, exon 1 of 16)	214	NM_007407	11517	Mm.44245	NM_007407	ENSMUSG00000029778	Adcyap1r1	2900024I10Rik|AI846590|PAC1|PAC1R|PACAP1-R	adenylate cyclase activating polypeptide 1 receptor 1	protein-coding
mm_154441.1	chrM	1328	1348	-	1	NA	NA	Intergenic	NA	NA								
mm_10878.1	chr2	25242228	25242284	+	1	NA	promoter-TSS (NM_176834)	promoter-TSS (NM_176834)	-673	NM_176834	68846	Mm.24777	NM_176834	ENSMUSG00000044628	Rnf208	1110061N23Rik	ring finger protein 208	protein-coding
mm_96661.1	chr11	69406854	69406878	+	1	NA	exon (NM_001017426, exon 9 of 23)	exon (NM_001017426, exon 9 of 23)	6809	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_15082.1	chr2	153161929	153161956	+	1	NA	intron (NM_133847, intron 1 of 17)	intron (NM_133847, intron 1 of 17)	641	NM_133847	99237	Mm.330674	NM_133847	ENSMUSG00000068040	Tm9sf4	AA986553|AU045326|B930079E06|mKIAA0255	transmembrane 9 superfamily protein member 4	protein-coding
mm_172914.1	chr9	64176140	64176141	+	1	NA	TTS (NR_028548)	TTS (NR_028548)	708	NR_028548	100217453		NR_028548	ENSMUSG00000094411	Snord16a	MBII-98	small nucleolar RNA, C/D box 16A	snoRNA
mm_11447.1	chr2	32081553	32081562	+	1	NA	intron (NM_175511, intron 1 of 1)	intron (NM_175511, intron 1 of 1)	2148	NM_175511	241303	Mm.250441	NM_175511	ENSMUSG00000050592	Fam78a	A130092J06Rik	family with sequence similarity 78, member A	protein-coding
mm_82342.1	chr9	11108059	11108061	-	1	NA	Intergenic	L1_Mus2|LINE|L1	-203285	NM_001170787	244682	Mm.187021	NM_001033359	ENSMUSG00000039488	Cntn5	6720426O10Rik|A830025P08Rik|Gm507|NB-2	contactin 5	protein-coding
mm_168674.1	chr11	93996539	93996551	+	1	NA	exon (NM_001199204, exon 1 of 30)	exon (NM_001199204, exon 1 of 30)	454	NM_027569	70834	Mm.260737	NM_027569	ENSMUSG00000020859	Spag9	3110018C07Rik|4733401I23Rik|4831406C20Rik|AW552012|JLP|JSAP2|JSAP2a|Jip4|Mapk8ip4|syd1	sperm associated antigen 9	protein-coding
mm_129084.1	chr15	75894539	75894549	-	1	NA	promoter-TSS (NM_172607)	promoter-TSS (NM_172607)	-63	NM_172607	223646	Mm.288368	NM_172607	ENSMUSG00000022574	Naprt	9130210N20Rik|Naprt1	nicotinate phosphoribosyltransferase	protein-coding
mm_91967.1	chr10	61415608	61415632	-	1	NA	Intergenic	Intergenic	-2352	NM_013611	18119	Mm.57195	NM_013611	ENSMUSG00000037171	Nodal	Tg.413d	nodal	protein-coding
mm_82250.1	chr9	4795970	4795987	-	1	NA	5' UTR (NM_001113181, exon 1 of 11)	5' UTR (NM_001113181, exon 1 of 11)	256	NM_001113180	14802	Mm.209263	NM_019691	ENSMUSG00000025892	Gria4	GluA4|GluR-D|Glur-4|Glur4|Gluralpha4|spkw1	glutamate receptor, ionotropic, AMPA4 (alpha 4)	protein-coding
mm_167759.1	chr9	110422610	110422635	-	1	NA	3' UTR (NM_008694, exon 4 of 4)	3' UTR (NM_008694, exon 4 of 4)	2814	NM_008694	18054	Mm.236225	NM_008694	ENSMUSG00000032484	Ngp	bectenecin	neutrophilic granule protein	protein-coding
mm_133591.1	chr16	91425411	91425430	+	1	NA	3' UTR (NM_008349, exon 7 of 7)	3' UTR (NM_008349, exon 7 of 7)	19185	NM_008349	16155	Mm.4154	NM_008349	ENSMUSG00000022969	Il10rb	6620401D04Rik|AI528744|CRF2-4|Crfb4|D16H21S58|D21S58h|IL-10R2|Il10r2	interleukin 10 receptor, beta	protein-coding
mm_22838.1	chr3	27617335	27617368	+	1	NA	intron (NM_173182, intron 3 of 25)	intron (NM_173182, intron 3 of 25)	-32356	NR_037275	100526525		NR_037275	ENSMUSG00000092695	Mir3092	mir-3092|mmu-mir-3092	microRNA 3092	ncRNA
mm_68504.1	chr7	111082027	111082055	-	1	NA	intron (NM_001040131, intron 1 of 20)	CpG	989	NM_001040131	13690	Mm.185453	NM_013507	ENSMUSG00000005610	Eif4g2	DAP-5|E130105L11Rik|Nat1|Natm1|p97	eukaryotic translation initiation factor 4, gamma 2	protein-coding
mm_32502.1	chr4	108460001	108460030	+	1	NA	intron (NM_175472, intron 1 of 30)	CpG	589	NM_175472	230594	Mm.25181	NM_175472	ENSMUSG00000034610	Zcchc11	6030404K05Rik|9230115F04Rik|PPAPD3|mKIAA0191	zinc finger, CCHC domain containing 11	protein-coding
mm_72541.1	chr8	83997317	83997369	+	1	NA	promoter-TSS (NM_001081415)	promoter-TSS (NM_001081415)	-329	NM_001081415	666704	Mm.298091	NM_001081415	ENSMUSG00000079003	Samd1	AA589507	sterile alpha motif domain containing 1	protein-coding
mm_109216.1	chr12	108713774	108713780	+	1	NA	Intergenic	Intergenic	-11471	NM_027299	70059	Mm.207605	NM_027299	ENSMUSG00000021263	Degs2	2210008A03Rik|AI852933|DES2	delta(4)-desaturase, sphingolipid 2	protein-coding
mm_164238.1	chr15	91673339	91673347	+	1	NA	exon (NM_025730, exon 1 of 51)	exon (NM_025730, exon 1 of 51)	119	NM_025730	66725	Mm.37558	NM_025730	ENSMUSG00000036273	Lrrk2	4921513O20Rik|9330188B09Rik|AW561911|D630001M17Rik|Gm927|cI-46	leucine-rich repeat kinase 2	protein-coding
mm_119100.1	chr14	30898712	30898741	+	1	NA	intron (NM_001159299, intron 19 of 22)	intron (NM_001159299, intron 19 of 22)	12250	NM_001289632	16427	Mm.34819	NM_018746	ENSMUSG00000021922	Itih4	ITI-HC4|Itih-4|PK-120	inter alpha-trypsin inhibitor, heavy chain 4	protein-coding
mm_45319.1	chr5	65454719	65454735	-	1	NA	intron (NM_133697, intron 3 of 4)	intron (NM_133697, intron 3 of 4)	-18885	NM_009466	22235	Mm.344831	NM_009466	ENSMUSG00000029201	Ugdh	Udpgdh	UDP-glucose dehydrogenase	protein-coding
mm_156068.1	chrX	109161094	109161161	+	1	NA	3' UTR (NM_019989, exon 4 of 4)	3' UTR (NM_019989, exon 4 of 4)	-35629	NM_001037917	622976	Mm.482747	NM_001037917	ENSMUSG00000048621	Gm6377	EG622976	predicted gene 6377	protein-coding
mm_128701.1	chr15	63479623	63479646	-	1	NA	promoter-TSS (NR_045279)	promoter-TSS (NR_045279)	-26	NR_045279	432958	Mm.255105	NR_045279		Gm20740	-	predicted gene, 20740	ncRNA
mm_139514.1	chr17	56584924	56584932	+	1	NA	promoter-TSS (NM_001163300)	promoter-TSS (NM_001163300)	-54	NM_001163300	224903	Mm.255066	NM_001163300	ENSMUSG00000071054	Safb	3110021E02Rik|5330423C17Rik|AU018122|D18386|E130307D12|HAP|HET|SAF-B1|SAFB1	scaffold attachment factor B	protein-coding
mm_126726.1	chr15	85503906	85503923	+	1	NA	promoter-TSS (NM_001256072)	promoter-TSS (NM_001256072)	-687	NM_001256072	328577	Mm.212960	NM_001256072	ENSMUSG00000096607	7530416G11Rik	-	RIKEN cDNA 7530416G11 gene	protein-coding
mm_139987.1	chr17	72848965	72848975	+	1	NA	3' UTR (NM_027166, exon 3 of 3)	3' UTR (NM_027166, exon 3 of 3)	12266	NM_027166	383295	Mm.277533	NM_027166	ENSMUSG00000039770	Ypel5	2310076K21Rik|CGI-127	yippee-like 5 (Drosophila)	protein-coding
mm_142746.1	chr17	48432724	48432741	-	1	NA	promoter-TSS (NM_009694)	promoter-TSS (NM_009694)	-4	NM_009694	11811	Mm.281793	NM_009694	ENSMUSG00000040694	Apobec2	Arp1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 2	protein-coding
mm_128631.1	chr15	59081878	59081889	-	1	NA	5' UTR (NM_144800, exon 1 of 15)	5' UTR (NM_144800, exon 1 of 15)	143	NM_001146180	211401	Mm.215481	NM_144800	ENSMUSG00000022353	Mtss1	2310003N14Rik|BC024131|D130001D01Rik|Mim|mKIAA0429	metastasis suppressor 1	protein-coding
mm_129547.1	chr15	79403548	79403578	-	1	NA	promoter-TSS (NM_001253819)	promoter-TSS (NM_001253819)	-260	NM_172608	223693	Mm.323358	NM_172608	ENSMUSG00000009035	Tmem184b	2610507A11|4732495E13Rik	transmembrane protein 184b	protein-coding
mm_113119.1	chr13	24501614	24501625	+	1	NA	Intergenic	Intergenic	-80570	NM_001286100	193385	Mm.217319	NM_029679	ENSMUSG00000036006	Fam65b	-	family with sequence similarity 65, member B	protein-coding
mm_7640.1	chr1	127976502	127976518	-	1	NA	exon (NM_001285945, exon 13 of 21)	exon (NM_001285945, exon 13 of 21)	107737	NM_178690	226407	Mm.489713	NM_178690	ENSMUSG00000036104	Rab3gap1	1700003B17Rik|4732493F09Rik|AL117896|Rab3gap|p130	RAB3 GTPase activating protein subunit 1	protein-coding
mm_13992.1	chr2	121866919	121866997	+	1	NA	promoter-TSS (NM_199038)	promoter-TSS (NM_199038)	-12	NM_199038	319996	Mm.292109	NM_177054	ENSMUSG00000060227	Casc4	D130060C09Rik|VGFG2573	cancer susceptibility candidate 4	protein-coding
mm_22230.1	chr2	174433549	174433572	-	1	NA	exon (NM_022325, exon 3 of 6)	exon (NM_022325, exon 3 of 6)	5479	NM_022325	64138	Mm.156919	NM_022325	ENSMUSG00000016256	Ctsz	AI787083|AU019819|CTSX|D2Wsu143e	cathepsin Z	protein-coding
mm_132789.1	chr16	45025658	45025658	+	1	NA	Intergenic	Intergenic	-68395	NM_026439	67896	Mm.181074	NM_026439	ENSMUSG00000022665	Ccdc80	2610001E17Rik|DRO1|Ssg1|Urb	coiled-coil domain containing 80	protein-coding
mm_38951.1	chr4	150569866	150569895	-	1	NA	intron (NM_001085492, intron 11 of 22)	CpG	82294	NM_173774	242773	Mm.29280	NM_173774	ENSMUSG00000039838	Slc45a1	C230078B22|Dnb5	solute carrier family 45, member 1	protein-coding
mm_40907.1	chr5	75574987	75575001	+	1	NA	promoter-TSS (NM_001122733)	promoter-TSS (NM_001122733)	3	NM_021099	16590	Mm.247073	NM_021099	ENSMUSG00000005672	Kit	Bs|CD117|Fdc|Gsfsco1|Gsfsco5|Gsfsow3|SCO1|SCO5|SOW3|Ssm|Tr-kit|W|c-KIT	KIT proto-oncogene receptor tyrosine kinase	protein-coding
mm_48090.1	chr5	136987819	136987829	-	1	NA	promoter-TSS (NM_001310748)	promoter-TSS (NM_001310748)	135	NM_027318	70103	Mm.273147	NM_027318	ENSMUSG00000059518	Znhit1	2700001K05Rik|ZNFN4A1	zinc finger, HIT domain containing 1	protein-coding
mm_94681.1	chr11	18212203	18212205	+	1	NA	Intergenic	Intergenic	116218	NR_131129	327872		NR_131129	ENSMUSG00000085453	Gm12018	OTTMUSG00000005202	predicted gene 12018	ncRNA
mm_32414.1	chr4	107036134	107036152	+	1	NA	intron (NM_023672, intron 9 of 17)	intron (NM_023672, intron 9 of 17)	30723	NM_025500	56280	Mm.29517	NM_025500	ENSMUSG00000028622	Mrpl37	2300004O14Rik|AI132596|MRP-L2|Rpml2	mitochondrial ribosomal protein L37	protein-coding
mm_69667.1	chr7	139983349	139983368	-	1	NA	exon (NM_001291066, exon 21 of 24)	exon (NM_001291066, exon 21 of 24)	3516	NR_106029	102465643		NR_106029	ENSMUSG00000099092	Mir7062	Gm27339|mmu-mir-7062	microRNA 7062	ncRNA
mm_37892.1	chr4	132533570	132533652	-	1	NA	5' UTR (NM_007512, exon 2 of 4)	5' UTR (NM_007512, exon 2 of 4)	1803	NM_007512	11983	Mm.2171	NM_007512	ENSMUSG00000054428	Atpif1	Atpi|IF(1)|If1	ATPase inhibitory factor 1	protein-coding
mm_3860.1	chr1	160978660	160978664	+	1	NA	promoter-TSS (NM_080844)	promoter-TSS (NM_080844)	56	NM_080844	11905	Mm.260770	NM_080844	ENSMUSG00000026715	Serpinc1	AI114908|ATIII|At-3|At3	serine (or cysteine) peptidase inhibitor, clade C (antithrombin), member 1	protein-coding
mm_149600.1	chr19	16320535	16320553	+	1	NA	intron (NM_008139, intron 3 of 6)	(T)n|Simple_repeat|Simple_repeat	-5540	NR_105832	102465218		NR_105832	ENSMUSG00000098718	Mir496b	Gm28028|mmu-mir-496b	microRNA 496b	ncRNA
mm_38933.1	chr4	150192630	150192633	-	1	NA	exon (NM_009802, exon 6 of 8)	exon (NM_009802, exon 6 of 8)	8504	NM_009802	12353	Mm.232523	NM_009802	ENSMUSG00000028972	Car6	Ca6|DOC1	carbonic anhydrase 6	protein-coding
mm_109934.1	chr12	11150306	11150348	-	1	NA	promoter-TSS (NM_173417)	promoter-TSS (NM_173417)	46	NM_173417	238076	Mm.113278	NM_173417	ENSMUSG00000043673	Kcns3	-	potassium voltage-gated channel, delayed-rectifier, subfamily S, member 3	protein-coding
mm_164734.1	chr17	68004063	68004073	-	1	NA	promoter-TSS (NM_172964)	promoter-TSS (NM_172964)	40	NM_172964	268970	Mm.9935	NM_172964	ENSMUSG00000024043	Arhgap28	AU044757|AW550892|E130310N06	Rho GTPase activating protein 28	protein-coding
mm_2193.1	chr1	89120862	89120866	+	1	NA	intron (NM_133816, intron 2 of 5)	(T)n|Simple_repeat|Simple_repeat	50402	NM_133816	98402	Mm.170983	NM_133816	ENSMUSG00000036206	Sh3bp4	AI594717|AW227605|BOG25	SH3-domain binding protein 4	protein-coding
mm_57946.1	chr6	134887784	134887866	-	1	NA	promoter-TSS (NM_008157)	promoter-TSS (NM_008157)	36	NM_001167699	14760	Mm.4787	NM_008157	ENSMUSG00000032641	Gpr19	-	G protein-coupled receptor 19	protein-coding
mm_17934.1	chr2	35882699	35882712	-	1	NA	intron (NM_029774, intron 6 of 9)	intron (NM_029774, intron 6 of 9)	63515	NR_040618	77665	Mm.400558	NR_040618	ENSMUSG00000086449	9030204H09Rik	-	RIKEN cDNA 9030204H09 gene	ncRNA
mm_34668.1	chr4	150919574	150919576	+	1	NA	promoter-TSS (NM_001077508)	promoter-TSS (NM_001077508)	-580	NM_011612	21942	Mm.244187	NM_011612	ENSMUSG00000028965	Tnfrsf9	4-1BB|A930040I11Rik|AA408498|AI325004|CDw137|Cd137|ILA|Ly63	tumor necrosis factor receptor superfamily, member 9	protein-coding
mm_97175.1	chr11	75532128	75532151	+	1	NA	promoter-TSS (NM_001199283)	promoter-TSS (NM_001199283)	27	NM_001199283	215113	Mm.11186	NM_173388	ENSMUSG00000038178	Slc43a2	7630402D21Rik|BC042513|Lat4	solute carrier family 43, member 2	protein-coding
mm_9842.1	chr1	184612910	184612917	-	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	-55222	NR_040472	73590	Mm.82792	NR_040472	ENSMUSG00000101574	1700112H15Rik	-	RIKEN cDNA 1700112H15 gene	ncRNA
mm_169461.1	chr14	6427098	6427104	-	1	NA	Intergenic	CpG	-139851	NM_001270812	100861615	Mm.488431	NM_001270812	ENSMUSG00000079396	LOC100861615	-	alpha takusan-like	protein-coding
mm_28170.1	chr3	87930122	87930182	-	1	NA	promoter-TSS (NM_177663)	promoter-TSS (NM_177663)	43	NM_153562	229503	Mm.296008	NM_153562	ENSMUSG00000004896	Rrnad1	-	ribosomal RNA adenine dimethylase domain containing 1	protein-coding
mm_167876.1	chrX	37754592	37754633	+	1	NA	promoter-TSS (NM_008818)	promoter-TSS (NM_008818)	4	NM_008818	18617	Mm.423066	NM_008818	ENSMUSG00000095180	Rhox5	AA409564|Pem	reproductive homeobox 5	protein-coding
mm_154936.1	chrX	35897834	35897837	+	1	NA	intron (NM_001009947, intron 1 of 52)	intron (NM_001009947, intron 1 of 52)	9003	NM_001009947	75974	Mm.32873	NM_177745	ENSMUSG00000031093	Dock11	5033414A21Rik|8030476J24|Zizimin2|sph238	dedicator of cytokinesis 11	protein-coding
mm_144140.1	chr18	4994601	4994623	+	1	NA	Intergenic	Intergenic	-51977	NM_153153	225115	Mm.136791	NM_153153	ENSMUSG00000024236	Svil	AU024053|B430302E16Rik	supervillin	protein-coding
mm_152955.1	chr19	29252095	29252105	-	1	NA	5' UTR (NM_008413, exon 1 of 25)	5' UTR (NM_008413, exon 1 of 25)	297	NM_008413	16452	Mm.275839	NM_008413	ENSMUSG00000024789	Jak2	Fd17	Janus kinase 2	protein-coding
mm_38973.1	chr4	150907324	150907330	-	1	NA	intron (NM_020569, intron 2 of 6)	intron (NM_020569, intron 2 of 6)	2594	NM_020569	57320	Mm.277349	NM_020569	ENSMUSG00000028964	Park7	DJ-1|Dj1	Parkinson disease (autosomal recessive, early onset) 7	protein-coding
mm_33512.1	chr4	130926105	130926160	+	1	NA	exon (NM_010686, exon 2 of 8)	exon (NM_010686, exon 2 of 8)	12798	NM_010686	16792	Mm.271868	NM_010686	ENSMUSG00000028581	Laptm5	E3	lysosomal-associated protein transmembrane 5	protein-coding
mm_46449.1	chr5	105116752	105116763	-	1	NA	3' UTR (NM_001256005, exon 11 of 11)	3' UTR (NM_001256005, exon 11 of 11)	-6465	NM_172777	236573	Mm.425261	NM_172777	ENSMUSG00000029298	Gbp9	-	guanylate-binding protein 9	protein-coding
mm_126550.1	chr15	82059145	82059158	+	1	NA	promoter-TSS (NM_001166475)	promoter-TSS (NM_001166475)	0	NM_001166475	328573	Mm.399189	NM_001166475	ENSMUSG00000075524	4930407I10Rik	Gm747	RIKEN cDNA 4930407I10 gene	protein-coding
mm_109084.1	chr12	104413769	104413779	+	1	NA	3' UTR (NM_009252, exon 5 of 5)	3' UTR (NM_009252, exon 5 of 5)	7066	NM_009252	20716	Mm.482074	NM_009252	ENSMUSG00000021091	Serpina3n	Spi2-2|Spi2.2|Spi2/eb.4	serine (or cysteine) peptidase inhibitor, clade A, member 3N	protein-coding
mm_18370.1	chr2	59920408	59920421	-	1	NA	exon (NM_001001182, exon 24 of 36)	exon (NM_001001182, exon 24 of 36)	-37808	NM_028118	72137	Mm.288734	NM_028118	ENSMUSG00000026988	Wdsub1	1700048E19Rik|2610014F08Rik	WD repeat, SAM and U-box domain containing 1	protein-coding
mm_130553.1	chr15	98992603	98992613	-	1	NA	Intergenic	Intergenic	6643	NR_045991	75951	Mm.441657	NR_045991	ENSMUSG00000097587	4930578M01Rik	3010001K12Rik	RIKEN cDNA 4930578M01 gene	ncRNA
mm_95774.1	chr11	54909540	54909550	+	1	NA	exon (NM_008161, exon 5 of 5)	exon (NM_008161, exon 5 of 5)	6691	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_142449.1	chr17	45592601	45592611	-	1	NA	promoter-TSS (NM_022880)	promoter-TSS (NM_022880)	-213	NM_022880	63959	Mm.29744	NM_022880	ENSMUSG00000023942	Slc29a1	1200014D21Rik|AA407560|ENT1	solute carrier family 29 (nucleoside transporters), member 1	protein-coding
mm_40092.1	chr5	34549569	34549581	+	1	NA	promoter-TSS (NM_001145859)	promoter-TSS (NM_001145859)	-1	NM_001145859	24055	Mm.5012	NM_011893	ENSMUSG00000054520	Sh3bp2	3BP2	SH3-domain binding protein 2	protein-coding
mm_170408.1	chr1	86529471	86529482	+	1	NA	exon (NM_008972, exon 3 of 5)	exon (NM_008972, exon 3 of 5)	2740	NM_008972	19231	Mm.19187	NM_008972	ENSMUSG00000026238	Ptma	Thym	prothymosin alpha	protein-coding
mm_9680.1	chr1	178332235	178332296	-	1	NA	exon (NM_016805, exon 7 of 14)	exon (NM_016805, exon 7 of 14)	5519	NM_016805	51810	Mm.86589	NM_016805	ENSMUSG00000039630	Hnrnpu	AA408410|AI256620|AL024194|AL024437|AW557595|C86794|Hnrpu|SAFA|Sp120|hnRNP U	heterogeneous nuclear ribonucleoprotein U	protein-coding
mm_56160.1	chr6	87965527	87965530	-	1	NA	Intergenic	Intergenic	15954	NM_198622	243529	Mm.33796	NM_198622	ENSMUSG00000044927	H1fx	Gm461|H1.10|H1X	H1 histone family, member X	protein-coding
mm_118558.1	chr14	17981507	17981509	+	1	NA	promoter-TSS (NM_009380)	promoter-TSS (NM_009380)	-136	NM_009380	21834	Mm.32563	NM_009380	ENSMUSG00000021779	Thrb	Nr1a2|T3R[b]|T3Rbeta|Thrb1|Thrb2|c-erbAbeta	thyroid hormone receptor beta	protein-coding
mm_69968.1	chr7	142376866	142376878	-	1	NA	exon (NM_009983, exon 8 of 9)	exon (NM_009983, exon 8 of 9)	-3126	NM_001347541	320802	Mm.154486	NM_177265	ENSMUSG00000045777	Ifitm10	6330512M04Rik|AI848576|DSPA3	interferon induced transmembrane protein 10	protein-coding
mm_1478.1	chr1	71557150	71557152	+	1	NA	promoter-TSS (NM_026195)	promoter-TSS (NM_026195)	-5	NM_026195	108147	Mm.38010	NM_026195	ENSMUSG00000026192	Atic	2610509C24Rik|AA536954|AW212393	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	protein-coding
mm_111666.1	chr12	103336893	103336911	-	1	NA	intron (NM_023049, intron 3 of 9)	intron (NM_023049, intron 3 of 9)	19099	NM_023049	65256	Mm.27159	NM_023049	ENSMUSG00000021200	Asb2	1110008E15Rik	ankyrin repeat and SOCS box-containing 2	protein-coding
mm_124291.1	chr14	103054786	103054808	-	1	NA	exon (NM_008392, exon 5 of 5)	exon (NM_008392, exon 5 of 5)	7785	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_167777.1	chr9	113793295	113793301	+	1	NA	promoter-TSS (NM_001286603)	promoter-TSS (NM_001286603)	-32	NM_001286603	76499	Mm.222272	NM_029633	ENSMUSG00000033392	Clasp2	1500004F14Rik|8030404L10Rik|C77448|CLASP2beta|mKIAA0627	CLIP associating protein 2	protein-coding
mm_1303.1	chr1	64690444	64690467	+	1	NA	promoter-TSS (NM_001097644)	promoter-TSS (NM_001097644)	204	NR_038009	69941	Mm.69044	NR_038009	ENSMUSG00000087213	2810408I11Rik	-	RIKEN cDNA 2810408I11 gene	ncRNA
mm_19497.1	chr2	93458782	93458791	-	1	NA	intron (NR_040532, intron 2 of 4)	intron (NR_040532, intron 2 of 4)	3065	NM_001271461	12521	Mm.4261	NM_007656	ENSMUSG00000027215	Cd82	AA682076|AL023070|C33|IA4|Kai1|Tspan27	CD82 antigen	protein-coding
mm_67712.1	chr7	89980505	89980586	-	1	NA	5' UTR (NM_021876, exon 1 of 12)	5' UTR (NM_021876, exon 1 of 12)	431	NM_021876	13626	Mm.380914	NM_021876	ENSMUSG00000030619	Eed	ENSMUSG00000039373|l(7)5Rn|l7Rn5|lusk	embryonic ectoderm development	protein-coding
mm_98468.1	chr11	94950091	94950174	+	1	NA	exon (NM_007742, exon 47 of 51)	exon (NM_007742, exon 47 of 51)	13908	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_114596.1	chr13	75764064	75764082	+	1	NA	exon (NM_138953, exon 8 of 12)	exon (NM_138953, exon 8 of 12)	56589	NM_138953	192657	Mm.21288	NM_138953	ENSMUSG00000001542	Ell2	-	elongation factor RNA polymerase II 2	protein-coding
mm_77156.1	chr8	111686713	111686757	-	1	NA	exon (NM_025583, exon 7 of 7)	exon (NM_025583, exon 7 of 7)	2939	NR_106044	102466993		NR_106044	ENSMUSG00000099129	Mir7076	Gm27318|mmu-mir-7076	microRNA 7076	ncRNA
mm_109327.1	chr12	109564700	109564715	+	1	NA	TTS (NR_030427)	TTS (NR_030427)	1015	NR_030427	791079		NR_030427	ENSMUSG00000076451	Mir770	Mirn770|mir-770|mmu-mir-770	microRNA 770	ncRNA
mm_77690.1	chr8	126588479	126588489	-	1	NA	3' UTR (NM_001164598, exon 2 of 2)	3' UTR (NM_001164598, exon 2 of 2)	4952	NM_001164598	270110	Mm.334918	NM_001164598	ENSMUSG00000051495	Irf2bp2	E130305N23Rik|IRF-2BP2	interferon regulatory factor 2 binding protein 2	protein-coding
mm_116193.1	chr13	31442113	31442144	-	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	-116042	NM_008239	15220	Mm.44235	NM_008239	ENSMUSG00000038415	Foxq1	HFH-1|Hfh1|Hfh1l|sa	forkhead box Q1	protein-coding
mm_92498.1	chr10	78351712	78351722	-	1	NA	promoter-TSS (NM_053014)	promoter-TSS (NM_053014)	-17	NM_053014	28169	Mm.141230	NM_053014	ENSMUSG00000001211	Agpat3	AW061257|AW493985|D10Jhu12e|lpaat3	1-acylglycerol-3-phosphate O-acyltransferase 3	protein-coding
mm_47175.1	chr5	120745763	120745783	-	1	NA	exon (NM_145227, exon 3 of 11)	exon (NM_145227, exon 3 of 11)	4075	NM_145227	246728	Mm.260926	NM_145227	ENSMUSG00000032690	Oas2	Oasl11	2'-5' oligoadenylate synthetase 2	protein-coding
mm_105252.1	chr11	102353299	102353313	-	1	NA	exon (NM_011403, exon 16 of 20)	exon (NM_011403, exon 16 of 20)	11975	NM_011403	20533	Mm.7248	NM_011403	ENSMUSG00000006574	Slc4a1	Ae1|CD233|Empb3|l11Jus51	solute carrier family 4 (anion exchanger), member 1	protein-coding
mm_90471.1	chr10	127849918	127849926	+	1	NA	promoter-TSS (NM_147222)	promoter-TSS (NM_147222)	-6	NM_147222	216453	Mm.222953	NM_147222	ENSMUSG00000054052	Rdh19	RDH-S|RDH-S2|Rdhs	retinol dehydrogenase 19	protein-coding
mm_2390.1	chr1	93509163	93509179	+	1	NA	3' UTR (NM_010891, exon 13 of 13)	3' UTR (NM_010891, exon 13 of 13)	-2933	NM_145519	227377	Mm.243091	NM_145519	ENSMUSG00000034066	Farp2	AI465173|BC009153|D030026M03Rik|Fir|mKIAA0793	FERM, RhoGEF and pleckstrin domain protein 2	protein-coding
mm_129198.1	chr15	76509706	76509723	-	1	NA	intron (NM_010046, intron 1 of 16)	intron (NM_010046, intron 1 of 16)	2104	NM_010046	13350	Mm.22633	NM_010046	ENSMUSG00000022555	Dgat1	ARAT|C75990|D15Ertd23e|Dgat	diacylglycerol O-acyltransferase 1	protein-coding
mm_56501.1	chr6	99334333	99334357	-	1	NA	intron (NM_001347345, intron 2 of 19)	intron (NM_001347345, intron 2 of 19)	-67830	NM_001197321	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_11135.1	chr2	28469608	28469620	+	1	NA	exon (NM_001166031, exon 4 of 4)	exon (NM_001166031, exon 4 of 4)	1548	NM_001166031	118451	Mm.294951	NM_080452	ENSMUSG00000035772	Mrps2	1500019M10Rik	mitochondrial ribosomal protein S2	protein-coding
mm_67527.1	chr7	81213126	81213160	-	1	NA	promoter-TSS (NM_008803)	promoter-TSS (NM_008803)	-661	NM_008803	18584	Mm.371577	NM_008803	ENSMUSG00000025584	Pde8a	AI551852|Pde8	phosphodiesterase 8A	protein-coding
mm_158506.1	chrX	142464315	142464320	-	1	NA	Intergenic	Intergenic	-73782	NM_019477	50790	Mm.391337	NM_019477	ENSMUSG00000031278	Acsl4	9430020A05Rik|ACS4|AU018108|Facl4|Lacs4	acyl-CoA synthetase long-chain family member 4	protein-coding
mm_28623.1	chr3	95106819	95106897	-	1	NA	promoter-TSS (NM_008847)	promoter-TSS (NM_008847)	72	NM_001293707	18720	Mm.296409	NM_008847	ENSMUSG00000028126	Pip5k1a	PI4P5K-I[a]|PIP5K1-alpha|PIP5KIalpha|Pipk5a	phosphatidylinositol-4-phosphate 5-kinase, type 1 alpha	protein-coding
mm_46464.1	chr5	105121109	105121120	-	1	NA	exon (NM_001256005, exon 8 of 11)	exon (NM_001256005, exon 8 of 11)	-10822	NM_172777	236573	Mm.425261	NM_172777	ENSMUSG00000029298	Gbp9	-	guanylate-binding protein 9	protein-coding
mm_22402.1	chr2	181241956	181241962	-	1	NA	promoter-TSS (NM_183162)	promoter-TSS (NM_183162)	68	NM_183162	229003	Mm.315872	NM_183162	ENSMUSG00000027580	Helz2	PDIP1|Pric285|mKIAA1769|mPDIP1	helicase with zinc finger 2, transcriptional coactivator	protein-coding
mm_25837.1	chr3	129213921	129213938	+	1	NA	promoter-TSS (NM_001287048)	promoter-TSS (NM_001287048)	-3	NM_001042502	18741	Mm.246804	NM_011098	ENSMUSG00000028023	Pitx2	9430085M16Rik|Brx1|Brx1b|Munc30|Otlx2|Ptx2|Rieg	paired-like homeodomain transcription factor 2	protein-coding
mm_161272.1	chr14	7658632	7658632	-	1	NA	Intergenic	CpG	-90066	NM_001270842	100041874	Mm.350858	NM_001270842	ENSMUSG00000079364	Gm3558	ENSMUSG00000079364	predicted gene 3558	protein-coding
mm_107903.1	chr12	70910641	70910641	+	1	NA	Intergenic	Intergenic	-27216	NM_019785	56444	Mm.29317	NM_019785	ENSMUSG00000021076	Actr10	Actr11|Arp11	ARP10 actin-related protein 10	protein-coding
mm_88385.1	chr10	76449122	76449135	+	1	NA	promoter-TSS (NM_029816)	promoter-TSS (NM_029816)	47	NM_029816	76964	Mm.472489	NM_029816	ENSMUSG00000009114	2610028H24Rik	ORF67	RIKEN cDNA 2610028H24 gene	protein-coding
mm_44737.1	chr5	31179902	31179942	-	1	NA	5' UTR (NM_027901, exon 1 of 19)	5' UTR (NM_027901, exon 1 of 19)	222	NM_027901	71752	Mm.271923	NM_027901	ENSMUSG00000101678	Gtf3c2	1300004C11Rik|2610510G03Rik|AI225816|AU041069|TFIIIC110|mKIAA0011	general transcription factor IIIC, polypeptide 2, beta	protein-coding
mm_66765.1	chr7	46728872	46728894	-	1	NA	3' UTR (NM_011316, exon 4 of 4)	3' UTR (NM_011316, exon 4 of 4)	3720	NM_011316	20211	Mm.3489	NM_011316	ENSMUSG00000040017	Saa4	Saa-4|Saa-5	serum amyloid A 4	protein-coding
mm_94177.1	chr10	128919174	128919184	-	1	NA	TTS (NM_015740)	TTS (NM_015740)	118	NM_134006	19682	Mm.439856	NM_134006	ENSMUSG00000025350	Rdh5	9-cis|AI987873|RDH4|cRDH	retinol dehydrogenase 5	protein-coding
mm_93623.1	chr10	117277999	117278005	-	1	NA	3' UTR (NM_017372, exon 4 of 4)	3' UTR (NM_017372, exon 4 of 4)	4270	NM_017372	17105	Mm.45436	NM_017372	ENSMUSG00000069516	Lyz2	AI326280|Lys|Lysm|Lyzf2|Lyzs|Lzm|Lzm-s1|Lzp	lysozyme 2	protein-coding
mm_47041.1	chr5	116024330	116024340	-	1	NA	promoter-TSS (NM_031869)	promoter-TSS (NM_031869)	93	NM_031869	19079	Mm.458152	NM_031869	ENSMUSG00000029513	Prkab1	1300015D22Rik|AU021155|E430008F22	protein kinase, AMP-activated, beta 1 non-catalytic subunit	protein-coding
mm_92129.1	chr10	64090242	64090262	-	1	NA	promoter-TSS (NM_178678)	promoter-TSS (NM_178678)	3	NM_178678	216028	Mm.431318	NM_178678	ENSMUSG00000042846	Lrrtm3	9630044H04Rik	leucine rich repeat transmembrane neuronal 3	protein-coding
mm_122814.1	chr14	54603377	54603400	-	1	NA	intron (NM_028890, intron 1 of 6)	CpG	2520	NM_028890	74359	Mm.79815	NM_028890	ENSMUSG00000022179	4931414P19Rik	-	RIKEN cDNA 4931414P19 gene	protein-coding
mm_143460.1	chr17	70990752	70990819	-	1	NA	promoter-TSS (NM_023402)	promoter-TSS (NM_023402)	-269	NM_023402	67938	Mm.261329	NM_023402	ENSMUSG00000034868	Myl12b	1500001M02Rik|C77744|Mylc2b|RLC-B	myosin, light chain 12B, regulatory	protein-coding
mm_89648.1	chr10	97479420	97479432	+	1	NA	promoter-TSS (NM_001190451)	promoter-TSS (NM_001190451)	-74	NM_001190451	13179	Mm.56769	NM_007833	ENSMUSG00000019929	Dcn	DC|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding
mm_121773.1	chr14	19875577	19875584	-	1	NA	3' UTR (NM_001285911, exon 4 of 4)	3' UTR (NM_001285911, exon 4 of 4)	36655	NR_105025	52512	Mm.483998	NR_105025		D14Ertd670e	-	DNA segment, Chr 14, ERATO Doi 670, expressed	ncRNA
mm_128785.1	chr15	66804019	66804034	-	1	NA	intron (NM_001029841, intron 1 of 7)	intron (NM_001029841, intron 1 of 7)	27803	NM_001029841	20491	Mm.7601	NM_009192	ENSMUSG00000022372	Sla	Slap|Slap-1	src-like adaptor	protein-coding
mm_48089.1	chr5	136987785	136987801	-	1	NA	promoter-TSS (NM_001310748)	promoter-TSS (NM_001310748)	166	NM_027318	70103	Mm.273147	NM_027318	ENSMUSG00000059518	Znhit1	2700001K05Rik|ZNFN4A1	zinc finger, HIT domain containing 1	protein-coding
mm_146272.1	chr18	77882189	77882204	+	1	NA	3' UTR (NM_013831, exon 15 of 15)	3' UTR (NM_013831, exon 15 of 15)	-56271	NM_001195633	100502841	Mm.297782	NM_001195633	ENSMUSG00000039840	Epg5	4732475F16|5430411K18Rik|AI661957|AW456499|mKIAA1632	ectopic P-granules autophagy protein 5 homolog (C. elegans)	protein-coding
mm_79715.1	chr9	61373506	61373521	+	1	NA	intron (NM_001083927, intron 1 of 19)	CpG	1147	NM_001083927	21887	Mm.24255	NM_009389	ENSMUSG00000032280	Tle3	2610103N05Rik|ESG|Grg3a|Grg3b|mKIAA1547	transducin-like enhancer of split 3	protein-coding
mm_17990.1	chr2	37975367	37975373	-	1	NA	intron (NM_146122, intron 11 of 21)	intron (NM_146122, intron 11 of 21)	199121	NM_001163566	241324	Mm.392369	NM_001163566	ENSMUSG00000035403	Crb2	5930402A21|BC043114	crumbs family member 2	protein-coding
mm_35649.1	chr4	43523837	43523847	-	1	NA	promoter-TSS (NM_009416)	promoter-TSS (NM_009416)	-288	NM_001277875	22004	Mm.646	NM_009416	ENSMUSG00000028464	Tpm2	Tpm-2|Trop-2	tropomyosin 2, beta	protein-coding
mm_132224.1	chr16	32644111	32644145	+	1	NA	promoter-TSS (NM_001110147)	promoter-TSS (NM_001110147)	-515	NM_001110147	51789	Mm.251115	NM_016788	ENSMUSG00000022791	Tnk2	Ack|Ack-1|Ack1|Cdgip|Pyk1	tyrosine kinase, non-receptor, 2	protein-coding
mm_147429.1	chr18	46311859	46311871	-	1	NA	promoter-TSS (NM_001160399)	promoter-TSS (NM_001160399)	63	NM_001160399	240261	Mm.329416	NM_001160399	ENSMUSG00000071855	Ccdc112	8430438M01Rik|AW108467	coiled-coil domain containing 112	protein-coding
mm_107628.1	chr12	51692645	51692646	+	1	NA	promoter-TSS (NM_001172098)	promoter-TSS (NM_001172098)	-731	NM_052973	94186	Mm.65979	NM_052973	ENSMUSG00000020954	Strn3	Gs2na|SG2NA	striatin, calmodulin binding protein 3	protein-coding
mm_118633.1	chr14	21307596	21307598	+	1	NA	intron (NM_001243041, intron 6 of 10)	intron (NM_001243041, intron 6 of 10)	-192173	NM_001205241	54169	Mm.248967	NM_017479	ENSMUSG00000021767	Kat6b	AI507552|B130044K16Rik|MYST-4|Morf|Myst4|mKIAA0383|qkf|querkopf	K(lysine) acetyltransferase 6B	protein-coding
mm_165602.1	chr3	50402697	50402707	+	1	NA	intron (NM_011990, intron 6 of 11)	intron (NM_011990, intron 6 of 11)	40911	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_38940.1	chr4	150198134	150198140	-	1	NA	exon (NM_009802, exon 2 of 8)	exon (NM_009802, exon 2 of 8)	2998	NM_009802	12353	Mm.232523	NM_009802	ENSMUSG00000028972	Car6	Ca6|DOC1	carbonic anhydrase 6	protein-coding
mm_61599.1	chr7	80026371	80026394	+	1	NA	5' UTR (NM_175433, exon 1 of 5)	5' UTR (NM_175433, exon 1 of 5)	154	NM_175433	209225	Mm.290925	NM_175433	ENSMUSG00000048897	Zfp710	5430400N05Rik|9830165K13|AI324798|Znf710	zinc finger protein 710	protein-coding
mm_101793.1	chr11	46166398	46166407	-	1	NA	promoter-TSS (NM_172524)	promoter-TSS (NM_172524)	-43	NM_172524	214112	Mm.225253	NM_172524	ENSMUSG00000020411	Nipal4	9530066K23Rik	NIPA-like domain containing 4	protein-coding
mm_55263.1	chr6	53820450	53820473	-	1	NA	5' UTR (NM_025817, exon 1 of 1)	5' UTR (NM_025817, exon 1 of 1)	364	NM_025817	66873	Mm.422727	NM_025817	ENSMUSG00000043496	Tril	1200009O22Rik|AI316813|mKIAA0644	TLR4 interactor with leucine-rich repeats	protein-coding
mm_98477.1	chr11	94950498	94950550	+	1	NA	exon (NM_007742, exon 48 of 51)	exon (NM_007742, exon 48 of 51)	14300	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_113994.1	chr13	52583251	52583262	+	1	NA	promoter-TSS (NM_001198977)	promoter-TSS (NM_001198977)	-181	NM_001198977	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_6042.1	chr1	59697746	59697779	-	1	NA	intron (NM_018868, intron 4 of 14)	RLTR9D|LTR|ERVK	5804	NR_028554	100217459		NR_028554		Snord70	MBII-234|snoRNA234	small nucleolar RNA, C/D box 70	snoRNA
mm_95087.1	chr11	33529875	33529897	+	1	NA	Intergenic	Intergenic	-16140	NM_023146	66011	Mm.383775	NM_023146	ENSMUSG00000040594	Ranbp17	-	RAN binding protein 17	protein-coding
mm_90579.1	chr10	128255283	128255292	+	1	NA	3' UTR (NM_133996, exon 2 of 2)	3' UTR (NM_133996, exon 2 of 2)	1156	NM_133996	28194	Mm.439846	NM_133996	ENSMUSG00000051716	Apon	AI195275|D10Ucla2	apolipoprotein N	protein-coding
mm_153157.1	chr19	34255326	34255342	-	1	NA	promoter-TSS (NM_007392)	promoter-TSS (NM_007392)	39	NM_007392	11475	Mm.213025	NM_007392	ENSMUSG00000035783	Acta2	0610041G09Rik|Actvs|SMalphaA|a-SMA|alphaSMA	actin, alpha 2, smooth muscle, aorta	protein-coding
mm_172893.1	chr9	56161048	56161048	-	1	NA	promoter-TSS (NM_019793)	promoter-TSS (NM_019793)	22	NM_019793	56434	Mm.28484	NM_019793	ENSMUSG00000032324	Tspan3	1700055K04Rik|TM4-A|Tm4sf8	tetraspanin 3	protein-coding
mm_3210.1	chr1	135827950	135827961	+	1	NA	exon (NM_133664, exon 3 of 10)	exon (NM_133664, exon 3 of 10)	-8379	NM_001130180	21956	Mm.247470	NM_011619	ENSMUSG00000026414	Tnnt2	Tnt|cTnT	troponin T2, cardiac	protein-coding
mm_44393.1	chr5	17830821	17830860	-	1	NA	intron (NM_001159556, intron 1 of 14)	intron (NM_001159556, intron 1 of 14)	5056	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_97650.1	chr11	79450935	79450935	+	1	NA	intron (NM_010897, intron 27 of 57)	B1_Mur1|SINE|Alu	33096	NR_045305	104522	Mm.436987	NR_045305	ENSMUSG00000091523	AU040972	AU040954	expressed sequence AU040972	ncRNA
mm_117537.1	chr13	83575654	83575684	-	1	NA	5' UTR (NM_025282, exon 3 of 11)	5' UTR (NM_025282, exon 3 of 11)	2062	NM_001347569	17260	Mm.24001	NM_025282	ENSMUSG00000005583	Mef2c	5430401D19Rik|9930028G15Rik|AV011172|Mef2	myocyte enhancer factor 2C	protein-coding
mm_150310.1	chr19	34571892	34571935	+	1	NA	intron (NM_008332, intron 2 of 2)	intron (NM_008332, intron 2 of 2)	-11616	NM_010501	15959	Mm.426079	NM_010501	ENSMUSG00000074896	Ifit3	Ifi49|P49	interferon-induced protein with tetratricopeptide repeats 3	protein-coding
mm_115307.1	chr13	112288581	112288594	+	1	NA	promoter-TSS (NM_001168404)	promoter-TSS (NM_001168404)	69	NM_001168404	77318	Mm.159895	NM_029898	ENSMUSG00000049985	Ankrd55	C030011J08Rik	ankyrin repeat domain 55	protein-coding
mm_57692.1	chr6	128521185	128521194	-	1	NA	intron (NM_007376, intron 6 of 35)	intron (NM_007376, intron 6 of 35)	5531	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_5291.1	chr1	20869952	20869954	-	1	NA	Intergenic	Intergenic	20520	NR_040492	77741	Mm.159984	NR_040492	ENSMUSG00000097934	6720483E21Rik	-	RIKEN cDNA 6720483E21 gene	ncRNA
mm_31267.1	chr4	45320386	45320397	+	1	NA	exon (NM_025513, exon 1 of 4)	exon (NM_025513, exon 1 of 4)	212	NM_025513	66362	Mm.275788	NM_025513	ENSMUSG00000028322	Exosc3	2310005D06Rik|AI593501|Rrp40	exosome component 3	protein-coding
mm_173329.1	chrY	90783892	90783905	-	1	NA	Intergenic	Intergenic	-1544	NR_137282	170942	Mm.76062	NM_133362	ENSMUSG00000096768	Erdr1	edr	erythroid differentiation regulator 1	protein-coding
mm_60760.1	chr7	45526431	45526447	+	1	NA	promoter-TSS (NM_008654)	promoter-TSS (NM_008654)	109	NM_148927	69217	Mm.274158	NM_148927	ENSMUSG00000040428	Plekha4	2410005C22Rik|C88169|Pepp1	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 4	protein-coding
mm_110744.1	chr12	69892990	69893082	-	1	NA	promoter-TSS (NM_178628)	promoter-TSS (NM_178628)	-69	NM_178628	73991	Mm.474462	NM_178628	ENSMUSG00000021066	Atl1	4930435M24Rik|Adfsp|Fsp1|Spg3|Spg3a	atlastin GTPase 1	protein-coding
mm_10397.1	chr2	13574300	13574318	+	1	NA	promoter-TSS (NM_011701)	promoter-TSS (NM_011701)	-2	NM_011701	22352	Mm.268000	NM_011701	ENSMUSG00000026728	Vim	-	vimentin	protein-coding
mm_166115.1	chr4	149774289	149774298	-	1	NA	promoter-TSS (NM_027460)	promoter-TSS (NM_027460)	-26	NM_027460	70556	Mm.41877	NM_027460	ENSMUSG00000028982	Slc25a33	5730438N18Rik|Pnc1	solute carrier family 25, member 33	protein-coding
mm_81768.1	chr9	114401502	114401515	+	1	NA	intron (NR_108101, intron 1 of 14)	CpG	413	NM_001200002	100504715	Mm.290516	NM_001200002	ENSMUSG00000079260	Tmppe	-	transmembrane protein with metallophosphoesterase domain	protein-coding
mm_138130.1	chr17	34187691	34187699	+	1	NA	promoter-TSS (NM_013585)	promoter-TSS (NM_013585)	139	NM_013683	21354	Mm.482076	NM_013683	ENSMUSG00000037321	Tap1	ABC17|APT1|Abcb2|Ham-1|Ham1|MTP1|PSF1|RING4|TAP|Tap-1|Y3	transporter 1, ATP-binding cassette, sub-family B (MDR/TAP)	protein-coding
mm_19205.1	chr2	84513646	84513662	-	1	NA	Intergenic	Lx3C|LINE|L1	-6781	NR_046046	672763	Mm.491046	NR_046046	ENSMUSG00000087362	Gm13710	OTTMUSG00000013441	predicted gene 13710	ncRNA
mm_14187.1	chr2	127080470	127080497	+	1	NA	intron (NM_026678, intron 1 of 7)	RMER15|LTR|ERVL	9826	NM_026678	109778	Mm.22028	NM_026678	ENSMUSG00000001999	Blvra	0610006A11Rik|2500001N03Rik|Blvr	biliverdin reductase A	protein-coding
mm_565.1	chr1	38035710	38035716	+	1	NA	intron (NM_198303, intron 9 of 23)	intron (NM_198303, intron 9 of 23)	37703	NM_198303	226982	Mm.260943	NM_198303	ENSMUSG00000026083	Eif5b	A030003E17Rik|BC018347|IF2	eukaryotic translation initiation factor 5B	protein-coding
mm_33177.1	chr4	126057951	126057954	+	1	NA	promoter-TSS (NM_172701)	promoter-TSS (NM_172701)	-613	NM_172701	230751	Mm.38907	NM_172701	ENSMUSG00000042616	Oscp1	1810007P19Rik|5730415O04|6030436A01Rik	organic solute carrier partner 1	protein-coding
mm_104544.1	chr11	96747655	96747660	-	1	NA	intron (NM_001177898, intron 10 of 10)	intron (NM_001177898, intron 10 of 10)	29898	NM_028965	74479	Mm.270781	NM_028965	ENSMUSG00000020876	Snx11	4933439F10Rik|A930041K09Rik|AI117694	sorting nexin 11	protein-coding
mm_66654.1	chr7	45712453	45712469	-	1	NA	exon (NM_001172561, exon 3 of 6)	exon (NM_001172561, exon 3 of 6)	2746	NM_020011	56632	Mm.24222	NM_020011	ENSMUSG00000057342	Sphk2	C76851	sphingosine kinase 2	protein-coding
mm_155698.1	chrX	94636045	94636053	+	1	NA	promoter-TSS (NM_008179)	promoter-TSS (NM_008179)	-20	NM_008179	14853	Mm.20826	NM_008179	ENSMUSG00000071723	Gspt2	-	G1 to S phase transition 2	protein-coding
mm_35159.1	chr4	12562820	12562821	-	1	NA	Intergenic	Intergenic	-344017	NM_173746	208820	Mm.12057	NM_173746	ENSMUSG00000055963	Triqk	C130086A10|Gm11818|OTTMUSG00000004461	triple QxxK/R motif containing	protein-coding
mm_49657.1	chr6	31123857	31123867	+	1	NA	intron (NR_110471, intron 3 of 3)	intron (NR_110471, intron 3 of 3)	-60769	NR_029532	387223		NR_029532	ENSMUSG00000065604	Mir29b-1	Mirn29b|Mirn29b-1|mir-29b-1	microRNA 29b-1	ncRNA
mm_26402.1	chr3	142603668	142603684	+	1	NA	exon (NM_010259, exon 5 of 11)	exon (NM_010259, exon 5 of 11)	8829	NM_010259	14468	Mm.457978	NM_010259	ENSMUSG00000040264	Gbp2b	Gbp-1|Gbp1|Mag-1|Mpa-1|Mpa1	guanylate binding protein 2b	protein-coding
mm_148411.1	chr19	3933474	3933484	+	1	NA	Intergenic	Intergenic	-1707	NM_019449	54445	Mm.262094	NM_019449	ENSMUSG00000036908	Unc93b1	Unc-93B1|Unc93b	unc-93 homolog B1 (C. elegans)	protein-coding
mm_21066.1	chr2	152803207	152803215	-	1	NA	intron (NM_001289717, intron 2 of 2)	intron (NM_001289717, intron 2 of 2)	27506	NM_001289716	12048	Mm.238213	NM_009743	ENSMUSG00000007659	Bcl2l1	Bcl(X)L|Bcl-XL|Bcl2l|BclX|bcl-x|bcl2-L-1	BCL2-like 1	protein-coding
mm_52199.1	chr6	100670689	100670698	+	1	NA	intron (NM_181590, intron 1 of 10)	CpG	464	NM_181590	72171	Mm.256022	NM_181590	ENSMUSG00000035378	Shq1	2810403P18Rik|Grim-1	SHQ1 homolog (S. cerevisiae)	protein-coding
mm_9116.1	chr1	170174960	170175001	-	1	NA	promoter-TSS (NM_133806)	promoter-TSS (NM_133806)	-16	NM_001305045	107652	Mm.27969	NM_133806	ENSMUSG00000026670	Uap1	AA420407|AA437972|AGX-1|AGX-2|AGX1|AgX|ESTM38|SPAG2	UDP-N-acetylglucosamine pyrophosphorylase 1	protein-coding
mm_117460.1	chr13	75930038	75930057	-	1	NA	intron (NM_028493, intron 3 of 11)	intron (NM_028493, intron 3 of 11)	13777	NM_028493	73296	Mm.276200	NM_028493	ENSMUSG00000021589	Rhobtb3	1700040C17Rik|2610033K01Rik|4930503C18Rik|AI317148|AW208826|mKIAA0878	Rho-related BTB domain containing 3	protein-coding
mm_163266.1	chr11	114741713	114741715	+	1	NA	intron (NM_001034878, intron 6 of 12)	intron (NM_001034878, intron 6 of 12)	8035	NR_037269	100526524		NR_037269	ENSMUSG00000077991	Mir466n	mmu-mir-466n	microRNA 466n	ncRNA
mm_112473.1	chr13	5868563	5868573	+	1	NA	3' UTR (NM_011803, exon 4 of 4)	3' UTR (NM_011803, exon 4 of 4)	7079	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_41429.1	chr5	90893125	90893133	+	1	NA	TTS (NM_008176)	TTS (NM_008176)	1884	NM_008176	14825	Mm.21013	NM_008176	ENSMUSG00000029380	Cxcl1	Fsp|Gro1|KC|Mgsa|N51|Scyb1|gro	chemokine (C-X-C motif) ligand 1	protein-coding
mm_25125.1	chr3	102085918	102085936	+	1	NA	promoter-TSS (NM_009814)	promoter-TSS (NM_009814)	-528	NM_009814	12373	Mm.15343	NM_009814	ENSMUSG00000027861	Casq2	AA033488|AW146219|Csq2|ESTM52|cCSQ	calsequestrin 2	protein-coding
mm_71846.1	chr8	68905141	68905162	+	1	NA	3' UTR (NM_008509, exon 10 of 10)	3' UTR (NM_008509, exon 10 of 10)	24596	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_56230.1	chr6	90660335	90660336	-	1	NA	3' UTR (NM_001134384, exon 14 of 14)	3' UTR (NM_001134384, exon 14 of 14)	41089	NM_001037493	71699	Mm.272633	NM_027868	ENSMUSG00000030089	Slc41a3	1010001P06Rik|AI480742|SLC41A1-L2	solute carrier family 41, member 3	protein-coding
mm_55639.1	chr6	72338513	72338528	-	1	NA	exon (NM_138592, exon 4 of 13)	exon (NM_138592, exon 4 of 13)	6655	NM_138592	28035	Mm.281900	NM_138592	ENSMUSG00000056305	Usp39	AA408960|AI894154|CGI-21|D6Wsu157e|SAD1	ubiquitin specific peptidase 39	protein-coding
mm_98466.1	chr11	94948735	94948785	+	1	NA	exon (NM_007742, exon 43 of 51)	exon (NM_007742, exon 43 of 51)	12536	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_83568.1	chr9	46319985	46319990	-	1	NA	promoter-TSS (NM_183104)	promoter-TSS (NM_183104)	-1	NM_183104	74361	Mm.159169	NM_183104	ENSMUSG00000056617	4931429L15Rik	-	RIKEN cDNA 4931429L15 gene	protein-coding
mm_61844.1	chr7	88290898	88290913	+	1	NA	3' UTR (NM_001311790, exon 4 of 4)	3' UTR (NM_001311790, exon 4 of 4)	12820	NM_001311790	13032	Mm.89295	NM_009982	ENSMUSG00000030560	Ctsc	AI047818|CatC|DPP1|DPPI	cathepsin C	protein-coding
mm_15193.1	chr2	154204754	154204769	+	1	NA	exon (NM_153418, exon 3 of 16)	exon (NM_153418, exon 3 of 16)	4381	NM_153418	228801	Mm.3783	NM_153418	ENSMUSG00000027485	Bpifb1	Lplunc1	BPI fold containing family B, member 1	protein-coding
mm_145612.1	chr18	61105562	61105579	+	1	NA	promoter-TSS (NM_001037859)	promoter-TSS (NM_001037859)	-2	NM_001037859	12978	Mm.22574	NM_007779	ENSMUSG00000024621	Csf1r	AI323359|CD115|CSF-1R|Csfmr|Fim-2|Fim2|Fms|M-CSF-R|M-CSFR	colony stimulating factor 1 receptor	protein-coding
mm_82696.1	chr9	22389087	22389099	-	1	NA	5' UTR (NM_028390, exon 1 of 24)	5' UTR (NM_028390, exon 1 of 24)	113	NM_028390	68743	Mm.282751	NM_028390	ENSMUSG00000036777	Anln	1110037A17Rik|2900037I21Rik|C78101|Scraps	anillin, actin binding protein	protein-coding
mm_8729.1	chr1	160077927	160077944	-	1	NA	promoter-TSS (NR_038031)	promoter-TSS (NR_038031)	-17	NR_038030	75255	Mm.414845	NR_038030	ENSMUSG00000026729	4930562F07Rik	-	RIKEN cDNA 4930562F07 gene	ncRNA
mm_87060.1	chr10	28844007	28844019	+	1	NA	intron (NM_001305663, intron 5 of 5)	intron (NM_001305663, intron 5 of 5)	79494	NR_033601	114676	Mm.390292	NR_033601		4930519F09Rik	-	pyruvate dehydrogenase E1 alpha 1 pseudogene	pseudo
mm_102429.1	chr11	59472465	59472488	-	1	NA	promoter-TSS (NM_178417)	promoter-TSS (NM_178417)	-2	NM_178417	237775	Mm.339604	NM_178417	ENSMUSG00000054519	Zfp867	-	zinc finger protein 867	protein-coding
mm_108039.1	chr12	73901349	73901365	+	1	NA	promoter-TSS (NM_001313920)	promoter-TSS (NM_001313920)	33	NM_001313920	15251	Mm.3879	NM_010431	ENSMUSG00000021109	Hif1a	AA959795|HIF-1-alpha|HIF1-alpha|HIF1alpha|MOP1|bHLHe78	hypoxia inducible factor 1, alpha subunit	protein-coding
mm_49327.1	chr6	21214867	21214907	+	1	NA	Intergenic	CpG	-1222	NM_019697	16508	Mm.425316	NM_019697	ENSMUSG00000060882	Kcnd2	AI839615|AW555701|Kv4.2|R75121|mKIAA1044	potassium voltage-gated channel, Shal-related family, member 2	protein-coding
mm_78756.1	chr9	43257404	43257411	+	1	NA	Intergenic	RMER13B|LTR|ERVK	-2472	NM_001243261	235302	Mm.135745	NM_001243261	ENSMUSG00000095385	D630033O11Rik	Gm588	RIKEN cDNA D630033O11 gene	protein-coding
mm_156005.1	chrX	106703906	106703916	+	1	NA	intron (NM_001033541, intron 3 of 3)	intron (NM_001033541, intron 3 of 3)	-100232	NM_001281859	58861	Mm.287166	NM_021476	ENSMUSG00000052821	Cysltr1	BB147369|CysLT1R|Cyslt1	cysteinyl leukotriene receptor 1	protein-coding
mm_73992.1	chr8	120685381	120685410	+	1	NA	Intergenic	Intergenic	17075	NM_001293559	12857	Mm.386758	NM_009941	ENSMUSG00000031818	Cox4i1	AL024441|COX|COX IV-1|COXIV|Cox4|Cox4a|IV-1	cytochrome c oxidase subunit IV isoform 1	protein-coding
mm_124038.1	chr14	77033365	77033394	-	1	NA	intron (NM_172488, intron 4 of 7)	intron (NM_172488, intron 4 of 7)	3238	NM_172488	210808	Mm.89278	NM_172488	ENSMUSG00000044350	Lacc1	9030625A04Rik	laccase (multicopper oxidoreductase) domain containing 1	protein-coding
mm_122404.1	chr14	41004518	41004528	-	1	NA	intron (NM_001316735, intron 1 of 5)	intron (NM_001316735, intron 1 of 5)	2397	NM_001316739	70564	Mm.27227	NM_027464	ENSMUSG00000021792	Fam213a	5730469M10Rik|AU040822|Adrx|Pamm	family with sequence similarity 213, member A	protein-coding
mm_27670.1	chr3	65392547	65392562	-	1	NA	promoter-TSS (NM_026155)	promoter-TSS (NM_026155)	-1	NM_026155	67437	Mm.232728	NM_026155	ENSMUSG00000027828	Ssr3	0610038P07Rik|AL022999|AU022074|AW553833|TRAPG	signal sequence receptor, gamma	protein-coding
mm_138078.1	chr17	33955903	33955926	+	1	NA	promoter-TSS (NM_011296)	promoter-TSS (NM_011296)	32	NM_172620	224705	Mm.448614	NM_172620	ENSMUSG00000024319	Vps52	ARE1|D130068D18|D430041K17Rik|SAC2|Sacm2l|tclw5	VPS52 GARP complex subunit	protein-coding
mm_34139.1	chr4	139291602	139291622	+	1	NA	3' UTR (NM_001271405, exon 9 of 9)	3' UTR (NM_001271405, exon 9 of 9)	19088	NM_145384	212555	Mm.45131	NM_145384	ENSMUSG00000028744	Pqlc2	BC019216	PQ loop repeat containing 2	protein-coding
mm_50544.1	chr6	49046246	49046257	+	1	NA	intron (NM_053110, intron 4 of 10)	intron (NM_053110, intron 4 of 10)	9733	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_126545.1	chr15	82028112	82028133	+	1	NA	intron (NM_010247, intron 7 of 12)	intron (NM_010247, intron 7 of 12)	11753	NM_010247	14375	Mm.288809	NM_010247	ENSMUSG00000022471	Xrcc6	70kDa|G22p1|Ku70	X-ray repair complementing defective repair in Chinese hamster cells 6	protein-coding
mm_17533.1	chr2	29744646	29744649	-	1	NA	Intergenic	Intergenic	-16881	NM_001177392	433416	Mm.330112	NM_001034887	ENSMUSG00000075425	Gm13547	OTTMUSG00000012686	predicted gene 13547	protein-coding
mm_8905.1	chr1	163312522	163312543	-	1	NA	exon (NM_175686, exon 1 of 5)	exon (NM_175686, exon 1 of 5)	1118	NM_011127	18933	Mm.288642	NM_011127	ENSMUSG00000026586	Prrx1	A230024N07Rik|AA755424|AI385634|AI843499|K-2|Pmx|Pmx1|Prx1|mHox	paired related homeobox 1	protein-coding
mm_158869.1	chrY	1245686	1245752	-	1	NA	promoter-TSS (NM_001326682)	promoter-TSS (NM_001326682)	40	NM_001326683	22290	Mm.20477	NM_009484	ENSMUSG00000068457	Uty	Hydb|mKIAA4057	ubiquitously transcribed tetratricopeptide repeat gene, Y chromosome	protein-coding
mm_36491.1	chr4	83256775	83256780	-	1	NA	intron (NM_027238, intron 6 of 19)	intron (NM_027238, intron 6 of 19)	67412	NM_027238	69863	Mm.5540	NM_025782	ENSMUSG00000038172	Ttc39b	1810054D07Rik|9130422G05Rik|AI450603|AV103077|AW215585	tetratricopeptide repeat domain 39B	protein-coding
mm_47731.1	chr5	130172349	130172362	-	1	NA	intron (NM_001199059, intron 1 of 8)	PB1D7|SINE|Alu	536	NM_001199059	56715	Mm.288639	NM_019983	ENSMUSG00000025340	Rabgef1	Rab5ef|Rabex5|Rin2	RAB guanine nucleotide exchange factor (GEF) 1	protein-coding
mm_155502.1	chrX	73787093	73787101	+	1	NA	promoter-TSS (NM_008323)	promoter-TSS (NM_008323)	-46	NM_009279	20832	Mm.831	NM_009279	ENSMUSG00000002014	Ssr4	AW743063|C78062|Trap	signal sequence receptor, delta	protein-coding
mm_38805.1	chr4	148159839	148159930	-	1	NA	promoter-TSS (NM_176848)	promoter-TSS (NM_176848)	210	NM_173401	230903	Mm.220327	NM_173401	ENSMUSG00000029001	Fbxo44	5730411K09|AV001623|FBG3|FBX30|Fbx6a|Fbxo6a	F-box protein 44	protein-coding
mm_37957.1	chr4	133339239	133339263	-	1	NA	promoter-TSS (NM_199306)	promoter-TSS (NM_199306)	64	NM_199306	230796	Mm.226576	NM_199306	ENSMUSG00000037622	Wdtc1	Gm695|adipose|adp	WD and tetratricopeptide repeats 1	protein-coding
mm_33927.1	chr4	136880405	136880417	+	1	NA	exon (NM_009777, exon 3 of 3)	exon (NM_009777, exon 3 of 3)	5766	NM_009777	12260	Mm.2570	NM_009777	ENSMUSG00000036905	C1qb	-	complement component 1, q subcomponent, beta polypeptide	protein-coding
mm_21411.1	chr2	158118970	158118978	-	1	NA	exon (NM_009373, exon 12 of 13)	exon (NM_009373, exon 12 of 13)	-27177	NR_040609	72340	Mm.443395	NR_040609	ENSMUSG00000100860	2010009K17Rik	-	RIKEN cDNA 2010009K17 gene	ncRNA
mm_75278.1	chr8	41006769	41006783	-	1	NA	intron (NM_001005863, intron 7 of 13)	intron (NM_001005863, intron 7 of 13)	-10692	NR_015457	78849	Mm.440930	NR_015457	ENSMUSG00000084960	B430010I23Rik	-	RIKEN cDNA B430010I23 gene	ncRNA
mm_16107.1	chr2	169633300	169633332	+	1	NA	promoter-TSS (NM_080455)	promoter-TSS (NM_080455)	-330	NM_080455	228911	Mm.315789	NM_080455	ENSMUSG00000047907	Tshz2	2900073F20Rik|B830045G17|Mtsh2|Sdccag33l|Tsh2|Zfp218|mKIAA4248|teashirt2	teashirt zinc finger family member 2	protein-coding
mm_89025.1	chr10	82629804	82629818	+	1	NA	promoter-TSS (NR_037190)	promoter-TSS (NR_037190)	-27	NM_011561	21665	Mm.284252	NM_011561	ENSMUSG00000034674	Tdg	E130317C12Rik|JZA-3|Jza1	thymine DNA glycosylase	protein-coding
mm_63784.1	chr7	131966447	131966469	+	1	NA	promoter-TSS (NM_173410)	promoter-TSS (NM_173410)	-2	NM_173410	233919	Mm.208740	NM_173410	ENSMUSG00000040125	Gpr26	9630036A11Rik|A730021D22	G protein-coupled receptor 26	protein-coding
mm_107098.1	chr12	17701994	17702036	+	1	NA	intron (NM_016677, intron 1 of 3)	intron (NM_016677, intron 1 of 3)	11201	NM_016677	53602	Mm.313619	NM_016677	ENSMUSG00000071379	Hpcal1	NVP-3|Nvp3|VILIP3|Vnsl3|Vsnl3	hippocalcin-like 1	protein-coding
mm_125535.1	chr15	58033945	58033967	+	1	NA	intron (NM_029418, intron 1 of 5)	CpG	338	NM_029418	75758	Mm.455792	NM_029418	ENSMUSG00000101892	9130401M01Rik	AI849328	RIKEN cDNA 9130401M01 gene	protein-coding
mm_122975.1	chr14	54976070	54976082	-	1	NA	promoter-TSS (NR_030607)	promoter-TSS (NR_030607)	-300	NR_030607	100124433		NR_030607	ENSMUSG00000077928	Mir208b	Mirn208b|mir-208b	microRNA 208b	ncRNA
mm_15384.1	chr2	156613467	156613491	+	1	NA	promoter-TSS (NM_146128)	promoter-TSS (NM_146128)	-57	NR_040372	100504350	Mm.94426	NR_040372	ENSMUSG00000086118	Gm14169	OTTMUSG00000015869	predicted gene 14169	ncRNA
mm_53940.1	chr6	5019126	5019136	-	1	NA	intron (NM_181595, intron 2 of 15)	intron (NM_181595, intron 2 of 15)	115811	NM_181595	243725	Mm.332901	NM_181595	ENSMUSG00000032827	Ppp1r9a	2810430P21Rik|4930518N04Rik|5330407E15|A230094E16Rik|BB181831|NRB|mKIAA1222|neurabin-I	protein phosphatase 1, regulatory (inhibitor) subunit 9A	protein-coding
mm_95532.1	chr11	52246552	52246559	+	1	NA	3' UTR (NM_011543, exon 6 of 6)	3' UTR (NM_011543, exon 6 of 6)	14560	NM_011543	21402	Mm.42944	NM_011543	ENSMUSG00000036309	Skp1a	15kDa|2610043E24Rik|2610206H23Rik|EMC19|OCP-II|OCP2|SKP1|Tceb1l|p19A|p19Skp1	S-phase kinase-associated protein 1A	protein-coding
mm_49552.1	chr6	30512341	30512345	+	1	NA	promoter-TSS (NM_029373)	promoter-TSS (NM_029373)	57	NM_029373	75647	Mm.46117	NM_027073	ENSMUSG00000029784	Ssmem1	1700016K02Rik|1700025E21Rik	serine-rich single-pass membrane protein 1	protein-coding
mm_88125.1	chr10	69246993	69247004	+	1	NA	intron (NM_001252637, intron 2 of 10)	intron (NM_001252637, intron 2 of 10)	33804	NM_001252638	69288	Mm.26659	NM_001081347	ENSMUSG00000019944	Rhobtb1	1700008H16Rik|3110048G13Rik|AI173445|AI573858|AV350930	Rho-related BTB domain containing 1	protein-coding
mm_141245.1	chr17	27486756	27486760	-	1	NA	intron (NM_001013385, intron 1 of 8)	PB1D10|SINE|Alu	16775	NM_001013385	268934	Mm.358940	NM_001013385	ENSMUSG00000063239	Grm4	Gprc1d|mGluR4	glutamate receptor, metabotropic 4	protein-coding
mm_149110.1	chr19	8953978	8953991	+	1	NA	exon (NM_197993, exon 1 of 9)	exon (NM_197993, exon 1 of 9)	152	NM_197993	70044	Mm.165979	NM_197993	ENSMUSG00000071645	Tut1	2700038E08Rik|PAPD2|Rbm21|TUTase6|U6-TUTase|star-PAP	terminal uridylyl transferase 1, U6 snRNA-specific	protein-coding
mm_34315.1	chr4	141819051	141819079	+	1	NA	exon (NM_007919, exon 6 of 8)	exon (NM_007919, exon 6 of 8)	6940	NM_007919	13706	Mm.45316	NM_007919	ENSMUSG00000058579	Cela2a	Ela-2|Ela2|Ela2a	chymotrypsin-like elastase family, member 2A	protein-coding
mm_104664.1	chr11	97629670	97629676	-	1	NA	promoter-TSS (NM_175332)	promoter-TSS (NM_175332)	43	NM_175332	103551	Mm.24506	NM_175332	ENSMUSG00000043439	Epop	AA409164|AI413509|AW539173|E13|E130012A19Rik|esPRC2p48	elongin BC and polycomb repressive complex 2 associated protein	protein-coding
mm_32272.1	chr4	102625421	102625459	+	1	NA	Intergenic	Intergenic	35597	NM_001177981	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_155495.1	chrX	73757045	73757061	+	1	NA	promoter-TSS (NM_019587)	promoter-TSS (NM_019587)	-50	NM_019587	140571	Mm.275600	NM_019587	ENSMUSG00000031385	Plxnb3	AI451018|Plxn6	plexin B3	protein-coding
mm_24522.1	chr3	92967060	92967062	+	1	NA	promoter-TSS (NM_001254725)	promoter-TSS (NM_001254725)	0	NM_001254725	69514	Mm.440092	NM_001254725	ENSMUSG00000074433	Lce3e	2310001H18Rik	late cornified envelope 3E	protein-coding
mm_103044.1	chr11	69797160	69797179	-	1	NA	3' UTR (NM_010198, exon 6 of 6)	3' UTR (NM_010198, exon 6 of 6)	-1232	NM_009601	11443	Mm.86425	NM_009601	ENSMUSG00000041189	Chrnb1	Achr-2|Acrb	cholinergic receptor, nicotinic, beta polypeptide 1 (muscle)	protein-coding
mm_164351.1	chr16	19983113	19983117	-	1	NA	promoter-TSS (NM_183390)	promoter-TSS (NM_183390)	-66	NM_183390	239743	Mm.86699	NM_183390	ENSMUSG00000043008	Klhl6	-	kelch-like 6	protein-coding
mm_101741.1	chr11	43379151	43379186	-	1	NA	Intergenic	Intergenic	-4707	NR_029558	387164		NR_029558	ENSMUSG00000065601	Mir146	Mirn146|miR-146a|mmu-mir-146	microRNA 146	ncRNA
mm_132775.1	chr16	44774603	44774616	+	1	NA	intron (NM_021325, intron 1 of 6)	intron (NM_021325, intron 1 of 6)	8873	NM_021325	57781	Mm.416152	NM_021325	ENSMUSG00000022667	Cd200r1	CD200R|Mox2r|OX2R	CD200 receptor 1	protein-coding
mm_163577.1	chr13	33078511	33078523	+	1	NA	Intergenic	MLT-int|LTR|ERVL-MaLR	-5586	NM_173052	282663	Mm.314490	NM_173052	ENSMUSG00000051029	Serpinb1b	6330533H24Rik|EIB|Serpin1b1|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 1b	protein-coding
mm_80720.1	chr9	92275896	92275906	+	1	NA	5' UTR (NM_001195084, exon 1 of 8)	5' UTR (NM_001195084, exon 1 of 8)	299	NM_001195084	18828	Mm.10306	NM_008880	ENSMUSG00000032372	Plscr2	-	phospholipid scramblase 2	protein-coding
mm_88653.1	chr10	79995019	79995035	+	1	NA	3' UTR (NM_007725, exon 7 of 7)	3' UTR (NM_007725, exon 7 of 7)	-2581	NM_001347081	27403	Mm.103351	NM_013850	ENSMUSG00000035722	Abca7	ABCX|Abc51	ATP-binding cassette, sub-family A (ABC1), member 7	protein-coding
mm_127433.1	chr15	101270160	101270171	+	1	NA	exon (NM_010444, exon 2 of 7)	exon (NM_010444, exon 2 of 7)	3319	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_104801.1	chr11	98775060	98775073	-	1	NA	5' UTR (NM_145434, exon 1 of 8)	5' UTR (NM_145434, exon 1 of 8)	311	NM_145434	217166	Mm.390397	NM_145434	ENSMUSG00000020889	Nr1d1	A530070C09Rik|R75201	nuclear receptor subfamily 1, group D, member 1	protein-coding
mm_18638.1	chr2	69405852	69405862	-	1	NA	Intergenic	Intergenic	25395	NM_175512	241452	Mm.211655	NM_175512	ENSMUSG00000027068	Dhrs9	C730025I08Rik|Rdh15	dehydrogenase/reductase (SDR family) member 9	protein-coding
mm_13052.1	chr2	91099783	91099824	+	1	NA	intron (NM_011355, intron 2 of 4)	Lx7|LINE|L1	3125	NM_011355	20375	Mm.1302	NM_011355	ENSMUSG00000002111	Spi1	Dis-1|Dis1|PU.1|Sfpi-1|Sfpi1|Spi-1|Tcfpu1|Tfpu.1	spleen focus forming virus (SFFV) proviral integration oncogene	protein-coding
mm_105532.1	chr11	106301124	106301162	-	1	NA	exon (NM_008117, exon 3 of 5)	exon (NM_008117, exon 3 of 5)	753	NM_008117	14599	Mm.343934	NM_008117	ENSMUSG00000020713	Gh	Gh1|Ghb1	growth hormone	protein-coding
mm_102424.1	chr11	59421621	59421636	-	1	NA	exon (NM_144521, exon 4 of 5)	exon (NM_144521, exon 4 of 5)	28328	NM_144521	67826	Mm.26680	NM_144521	ENSMUSG00000009894	Snap47	1110031B06Rik|SNAP-47	synaptosomal-associated protein, 47	protein-coding
mm_90992.1	chr10	13966751	13966763	-	1	NA	intron (NM_010437, intron 1 of 8)	CpG-904	378	NM_010437	15273	Mm.42157	NM_010437	ENSMUSG00000015501	Hivep2	Gm20114|MIBP1|Schnurri-2|Shn-2	human immunodeficiency virus type I enhancer binding protein 2	protein-coding
mm_99947.1	chr11	111075432	111075444	+	1	NA	3' UTR (NM_008425, exon 2 of 2)	3' UTR (NM_008425, exon 2 of 2)	9274	NM_008425	16518	Mm.4951	NM_008425	ENSMUSG00000041695	Kcnj2	IRK1|Kcnf1|Kir2.1	potassium inwardly-rectifying channel, subfamily J, member 2	protein-coding
mm_170515.1	chr19	29367489	29367489	+	1	NA	promoter-TSS (NM_021893)	promoter-TSS (NM_021893)	51	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_12130.1	chr2	61650087	61650098	+	1	NA	exon (NM_001164072, exon 7 of 8)	exon (NM_001164072, exon 7 of 8)	56995	NM_001164071	21353	Mm.244393	NM_011529	ENSMUSG00000064289	Tank	C86182|E430026L09Rik|I-TRAF	TRAF family member-associated Nf-kappa B activator	protein-coding
mm_81376.1	chr9	108855531	108855537	+	1	NA	intron (NM_134420, intron 1 of 17)	intron (NM_134420, intron 1 of 17)	1491	NM_134420	171429	Mm.45201	NM_134420	ENSMUSG00000023259	Slc26a6	B930010B04Rik|CFEX|Pat-1|Pat1	solute carrier family 26, member 6	protein-coding
mm_121394.1	chr14	119137676	119137701	+	1	NA	promoter-TSS (NM_015820)	promoter-TSS (NM_015820)	-577	NM_015820	50787	Mm.445777	NM_015820	ENSMUSG00000053465	Hs6st3	6OST3|HS6ST-3	heparan sulfate 6-O-sulfotransferase 3	protein-coding
mm_130861.1	chr15	102189006	102189030	-	1	NA	promoter-TSS (NM_144942)	promoter-TSS (NM_144942)	25	NM_144942	246277	Mm.296382	NM_144942	ENSMUSG00000023044	Csad	Csd	cysteine sulfinic acid decarboxylase	protein-coding
mm_89448.1	chr10	93124572	93124580	+	1	NA	Intergenic	Intergenic	-36300	NM_146239	237459	Mm.217404	NM_146239	ENSMUSG00000020015	Cdk17	6430598J10Rik|Pctk2	cyclin-dependent kinase 17	protein-coding
mm_84097.1	chr9	58249662	58249672	-	1	NA	exon (NM_008884, exon 1 of 8)	exon (NM_008884, exon 1 of 8)	119	NM_178087	18854	Mm.392123	NM_008884	ENSMUSG00000036986	Pml	1200009E24Rik|AI661194|Trim19	promyelocytic leukemia	protein-coding
mm_67785.1	chr7	97420958	97420980	-	1	NA	Intergenic	ID4|SINE|ID	-3419	NM_009381	21835	Mm.28585	NM_009381	ENSMUSG00000035686	Thrsp	S14|SPOT14	thyroid hormone responsive	protein-coding
mm_137266.1	chr17	24696277	24696320	+	1	NA	promoter-TSS (NM_027988)	promoter-TSS (NM_027988)	64	NM_027988	71893	Mm.390971	NM_027988	ENSMUSG00000019320	Noxo1	2310034C04Rik|P41NOX|P41NOXA|P41NOXB|P41NOXC|Snx28|hslt	NADPH oxidase organizer 1	protein-coding
mm_100666.1	chr11	3332254	3332276	-	1	NA	intron (NM_178149, intron 3 of 5)	CpG-1656	1534	NM_178149	216505	Mm.390323	NM_178149	ENSMUSG00000034614	Pik3ip1	1500004A08Rik|5830455E04Rik|Crkd|Hgfl	phosphoinositide-3-kinase interacting protein 1	protein-coding
mm_99275.1	chr11	101260550	101260560	+	1	NA	promoter-TSS (NM_175638)	promoter-TSS (NM_175638)	-12	NM_175638	69847	Mm.23656	NM_175638	ENSMUSG00000035112	Wnk4	2010002J11Rik|Pha2b|Prkwnk4	WNK lysine deficient protein kinase 4	protein-coding
mm_24751.1	chr3	95320168	95320203	+	1	NA	exon (NM_001320492, exon 2 of 11)	exon (NM_001320492, exon 2 of 11)	1355	NM_001320492	76893	Mm.181009	NM_029789	ENSMUSG00000015714	Cers2	0610013I17Rik|AI225939|Lass2|TRH3	ceramide synthase 2	protein-coding
mm_6538.1	chr1	74951439	74951450	-	1	NA	5' UTR (NM_010544, exon 1 of 3)	5' UTR (NM_010544, exon 1 of 3)	228	NM_001313683	16147	Mm.439736	NM_010544	ENSMUSG00000006538	Ihh	HHG-2	Indian hedgehog	protein-coding
mm_107840.1	chr12	69296965	69296971	+	1	NA	5' UTR (NM_027117, exon 1 of 13)	5' UTR (NM_027117, exon 1 of 13)	287	NM_027117	69554	Mm.234368	NM_027117	ENSMUSG00000020978	Klhdc2	2310022K15Rik|D12Ertd522e|HCLP-1|LCP	kelch domain containing 2	protein-coding
mm_147485.1	chr18	47275757	47275764	-	1	NA	intron (NM_018744, intron 17 of 18)	intron (NM_018744, intron 17 of 18)	93108	NM_018744	20358	Mm.40909	NM_018744	ENSMUSG00000019647	Sema6a	A730020P05Rik|AI851735|Sema6A-1|Semaq|VIa	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A	protein-coding
mm_108434.1	chr12	82256577	82256585	+	1	NA	intron (NM_001167983, intron 2 of 23)	RMER5|LTR|ERV1	-54768	NM_172579	217692	Mm.261333	NM_172579	ENSMUSG00000042700	Sipa1l1	4931426N11Rik|AW213287|Spar|mKIAA0440	signal-induced proliferation-associated 1 like 1	protein-coding
mm_105844.1	chr11	113684189	113684198	-	1	NA	promoter-TSS (NM_138598)	promoter-TSS (NM_138598)	-42	NM_138598	28081	Mm.351688	NM_138598	ENSMUSG00000041629	Fam104a	D11Wsu99e	family with sequence similarity 104, member A	protein-coding
mm_38088.1	chr4	134186993	134187006	-	1	NA	promoter-TSS (NM_144527)	promoter-TSS (NM_144527)	86	NM_144527	70012	Mm.26542	NM_144527	ENSMUSG00000037443	Cep85	2410030J07Rik|AI173272|AI173504|Ccdc21	centrosomal protein 85	protein-coding
mm_152304.1	chr19	9087946	9087962	-	1	NA	promoter-TSS (NM_011681)	promoter-TSS (NM_011681)	2	NM_011681	22287	Mm.2258	NM_011681	ENSMUSG00000024653	Scgb1a1	CC10|CC16|CCSP|PCB-BP|UG|UGB|Utg	secretoglobin, family 1A, member 1 (uteroglobin)	protein-coding
mm_113014.1	chr13	21945085	21945140	+	1	NA	promoter-TSS (NM_183014)	promoter-TSS (NM_183014)	18	NM_183014	193452	Mm.187446	NM_183014	ENSMUSG00000006720	Zfp184	4930500C15Rik	zinc finger protein 184 (Kruppel-like)	protein-coding
mm_105433.1	chr11	104301354	104301366	-	1	NA	intron (NM_001038609, intron 5 of 11)	intron (NM_001038609, intron 5 of 11)	69924	NM_001285454	17762	Mm.1287	NM_010838	ENSMUSG00000018411	Mapt	AI413597|AW045860|Mtapt|Tau	microtubule-associated protein tau	protein-coding
mm_23963.1	chr3	84952428	84952435	+	1	NA	exon (NM_080428, exon 1 of 11)	exon (NM_080428, exon 1 of 11)	220	NM_080428	50754	Mm.196475	NM_080428	ENSMUSG00000028086	Fbxw7	1110001A17Rik|AGO|Cdc4|Fbw7|Fbwd6|Fbx30|Fbxo30|Fbxw6|SEL-10	F-box and WD-40 domain protein 7	protein-coding
mm_137893.1	chr17	31681162	31681174	+	1	NA	exon (NM_001278570, exon 3 of 3)	exon (NM_001278570, exon 3 of 3)	3237	NM_001278570	12954	Mm.1228	NM_013501	ENSMUSG00000024041	Cryaa	Acry-1|Crya-1|Crya1|DAcry-1|lop18	crystallin, alpha A	protein-coding
mm_9627.1	chr1	176808969	176808991	-	1	NA	Intergenic	Intergenic	-1856	NM_001099637	545389	Mm.269991	NM_001024722	ENSMUSG00000057335	Cep170	4933426L22Rik|A330004A13Rik|AI195353	centrosomal protein 170	protein-coding
mm_21666.1	chr2	164425368	164425380	-	1	NA	3' UTR (NM_011521, exon 5 of 5)	3' UTR (NM_011521, exon 5 of 5)	17814	NM_011521	20971	Mm.3815	NM_011521	ENSMUSG00000017009	Sdc4	AA959608|AW108331|S4|Synd4|ryudocan|syndecan-4	syndecan 4	protein-coding
mm_12736.1	chr2	78872401	78872419	+	1	NA	intron (NM_009454, intron 2 of 5)	intron (NM_009454, intron 2 of 5)	3363	NM_009454	22193	Mm.1485	NM_009454	ENSMUSG00000027011	Ube2e3	Ubce4|ubcM2	ubiquitin-conjugating enzyme E2E 3	protein-coding
mm_130842.1	chr15	101892917	101892921	-	1	NA	promoter-TSS (NM_001033177)	promoter-TSS (NM_001033177)	1	NM_001033177	77055	Mm.195788	NM_001033177	ENSMUSG00000075402	Krt76	2310001L23Rik	keratin 76	protein-coding
mm_57556.1	chr6	126921792	126921801	-	1	NA	promoter-TSS (NM_207210)	promoter-TSS (NM_207210)	43	NM_207210	101320	Mm.44896	NM_207210	ENSMUSG00000030345	Dyrk4	AW049118|Dyrk4a|Dyrk4b	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 4	protein-coding
mm_36862.1	chr4	106947905	106947910	-	1	NA	intron (NM_023672, intron 4 of 17)	intron (NM_023672, intron 4 of 17)	36437	NM_023672	72475	Mm.195635	NM_023672	ENSMUSG00000061887	Ssbp3	2610021L12Rik|2610200M23Rik|5730488C10Rik|AI854733|AW551939|LAST|SSDP1	single-stranded DNA binding protein 3	protein-coding
mm_98072.1	chr11	86201426	86201444	+	1	NA	promoter-TSS (NM_178309)	promoter-TSS (NM_178309)	75	NR_130958	74038	Mm.171304	NR_130958	ENSMUSG00000085208	Brip1os	4632419I22Rik	BRCA1 interacting protein C-terminal helicase 1, opposite strand	ncRNA
mm_68129.1	chr7	102210121	102210157	-	1	NA	promoter-TSS (NM_001291358)	promoter-TSS (NM_001291358)	27	NM_001287166	269966	Mm.439800	NM_022979	ENSMUSG00000063550	Nup98	4732457F17|AI849286|Nup96	nucleoporin 98	protein-coding
mm_11730.1	chr2	37452217	37452230	+	1	NA	promoter-TSS (NM_001033960)	promoter-TSS (NM_001033960)	-31	NM_001033960	227800	Mm.383192	NM_146121	ENSMUSG00000035437	Rabgap1	Gapcena|mKIAA4104	RAB GTPase activating protein 1	protein-coding
mm_22898.1	chr3	30801094	30801105	+	1	NA	exon (NM_027016, exon 3 of 8)	exon (NM_027016, exon 3 of 8)	8223	NM_027016	69276	Mm.26017	NM_027016	ENSMUSG00000027706	Sec62	3100002M17Rik|AI844545|AW545092|Dtrp1|HTP1|Tloc1	SEC62 homolog (S. cerevisiae)	protein-coding
mm_26579.1	chr3	147389740	147389754	+	1	NA	Intergenic	Intergenic	537380	NM_001302958	70892	Mm.187793	NM_027594	ENSMUSG00000036745	Ttll7	1110049N09Rik|4921517B04Rik|C630030B20|mTTLL7	tubulin tyrosine ligase-like family, member 7	protein-coding
mm_160299.1	chr7	134938234	134938234	-	1	NA	5' UTR (NM_001143802, exon 1 of 4)	5' UTR (NM_001143802, exon 1 of 4)	196	NM_001143802	627214	Mm.323610	NM_001143802	ENSMUSG00000073805	Fam196a	B830028B13Rik	family with sequence similarity 196, member A	protein-coding
mm_113324.1	chr13	30786510	30786518	+	1	NA	Intergenic	Intergenic	37281	NM_013674	16364	Mm.4677	NM_013674	ENSMUSG00000021356	Irf4	AI385587|IRF-4|LSIRF|NF-EM5|Spip	interferon regulatory factor 4	protein-coding
mm_14681.1	chr2	139678638	139678680	+	1	NA	5' UTR (NM_001276489, exon 1 of 6)	5' UTR (NM_001276489, exon 1 of 6)	481	NM_001276489	319909	Mm.41113	NM_001126490	ENSMUSG00000074766	Ism1	5430433G21Rik|Ism	isthmin 1, angiogenesis inhibitor	protein-coding
mm_36209.1	chr4	62434723	62434738	-	1	NA	promoter-TSS (NM_153504)	promoter-TSS (NM_153504)	-4	NM_153504	76072	Mm.169565	NM_153504	ENSMUSG00000063851	Rnf183	5830442J12Rik	ring finger protein 183	protein-coding
mm_16870.1	chr2	12301895	12301903	-	1	NA	promoter-TSS (NM_001001309)	promoter-TSS (NM_001001309)	45	NR_138462	241226	Mm.329997	NM_001001309	ENSMUSG00000026768	Itga8	AI447669	integrin alpha 8	protein-coding
mm_94077.1	chr10	128410533	128410565	-	1	NA	promoter-TSS (NM_027257)	promoter-TSS (NM_027257)	-753	NM_027257	69917	Mm.46614	NM_027257	ENSMUSG00000025374	Nabp2	2610036N15Rik|Obfc2b|SSB1	nucleic acid binding protein 2	protein-coding
mm_146730.1	chr18	15312694	15312733	-	1	NA	Intergenic	Intergenic	90286	NM_001308647	11829	Mm.250786	NM_009700	ENSMUSG00000024411	Aqp4	WCH4	aquaporin 4	protein-coding
mm_3513.1	chr1	150107376	150107400	+	1	NA	3' UTR (NM_011198, exon 10 of 10)	3' UTR (NM_011198, exon 10 of 10)	7357	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_63428.1	chr7	127478495	127478549	+	1	NA	Intergenic	CpG	-6699	NM_010183	14123	Mm.323505	NM_010183	ENSMUSG00000042423	Fbrs	Fbs|Fbs1	fibrosin	protein-coding
mm_3076.1	chr1	134289998	134290015	+	1	NA	promoter-TSS (NM_031189)	promoter-TSS (NM_031189)	2	NM_031189	17928	Mm.16528	NM_031189	ENSMUSG00000026459	Myog	MYF4|bHLHc3|myo	myogenin	protein-coding
mm_162624.1	chr1	183420370	183420380	-	1	NA	intron (NM_001308052, intron 1 of 8)	intron (NM_001308052, intron 1 of 8)	1127	NM_001308052	78772	Mm.29003	NM_030175	ENSMUSG00000053461	Hhipl2	4930507C10Rik|AW208802|Hhip3	hedgehog interacting protein-like 2	protein-coding
mm_103761.1	chr11	81153604	81153642	-	1	NA	promoter-TSS (NM_007384)	promoter-TSS (NM_007384)	-720	NM_007384	11418	Mm.234998	NM_007384	ENSMUSG00000020704	Asic2	ACIC2|Accn1|BNC1|BNaC1|BNaC1a|Mdeg	acid-sensing (proton-gated) ion channel 2	protein-coding
mm_100268.1	chr11	117523527	117523544	+	1	NA	Intergenic	Intergenic	39167	NR_130966	432615	Mm.126359	NR_130966	ENSMUSG00000069588	Gm11733	OTTMUSG00000003802	predicted gene 11733	ncRNA
mm_117039.1	chr13	58291687	58291689	-	1	NA	intron (NM_175214, intron 15 of 16)	intron (NM_175214, intron 15 of 16)	-17500	NM_019832	56278	Mm.296625	NM_019832	ENSMUSG00000021552	Gkap1	42kDa|4933400B15Rik|D13Ertd340e|Gkap42	G kinase anchoring protein 1	protein-coding
mm_48801.1	chr5	148955758	148955762	-	1	NA	Intergenic	RMER17C|LTR|ERVK	5510	NR_040686	71473	Mm.90306	NR_040686	ENSMUSG00000079069	8430423G03Rik	-	RIKEN cDNA 8430423G03 gene	ncRNA
mm_51638.1	chr6	85915788	85915798	+	1	NA	promoter-TSS (NM_001170488)	promoter-TSS (NM_001170488)	74	NM_001170488	69786	Mm.218434	NM_176842	ENSMUSG00000054226	Tprkb	0610033G21Rik|1810034M08Rik|Cgi-121|DRWMS1|mDRWMS1	Tp53rk binding protein	protein-coding
mm_91563.1	chr10	40025207	40025218	-	1	NA	promoter-TSS (NM_144821)	promoter-TSS (NM_144821)	56	NM_144821	215929	Mm.55513	NM_144821	ENSMUSG00000038522	Mfsd4b1	AI317395|AI482555|Naglt1a	major facilitator superfamily domain containing 4B1	protein-coding
mm_167417.1	chr8	109962072	109962080	-	1	NA	exon (NM_028584, exon 1 of 3)	exon (NM_028584, exon 1 of 3)	129	NM_212447	73608	Mm.86833	NM_028584	ENSMUSG00000001672	Marveld3	1810006A16Rik|AI642133|Marvd3|Mrvldc3	MARVEL (membrane-associating) domain containing 3	protein-coding
mm_7133.1	chr1	91052888	91052898	-	1	NA	promoter-TSS (NM_008515)	promoter-TSS (NM_008515)	-551	NM_001310732	16978	Mm.45039	NM_008515	ENSMUSG00000026305	Lrrfip1	AU024550|Fliiap1	leucine rich repeat (in FLII) interacting protein 1	protein-coding
mm_86531.1	chr10	7832458	7832491	+	1	NA	promoter-TSS (NM_172785)	promoter-TSS (NM_172785)	4	NM_172785	237256	Mm.140055	NM_172785	ENSMUSG00000039981	Zc3h12d	D730019B10Rik|TFL	zinc finger CCCH type containing 12D	protein-coding
mm_14721.1	chr2	143989782	143989824	+	1	NA	exon (NM_133626, exon 2 of 3)	exon (NM_133626, exon 2 of 3)	21460	NM_133626	81910	Mm.13705	NM_024281	ENSMUSG00000027422	Rrbp1	1700087N07Rik|5730465C04Rik|ES/130|mKIAA1398|mRRp0|mRRp1.8|mRRp10|mRRp15a|mRRp15b|mRRp16.8|mRRp2|mRRp41|mRRp47|mRRp5.4|p180	ribosome binding protein 1	protein-coding
mm_63316.1	chr7	126897581	126897599	+	1	NA	intron (NM_026827, intron 1 of 5)	intron (NM_026827, intron 1 of 5)	688	NM_026827	68742	Mm.248646	NM_026827	ENSMUSG00000060538	Tmem219	1110032O16Rik|2900045G02Rik|IGFBP-3R	transmembrane protein 219	protein-coding
mm_38021.1	chr4	133756521	133756539	-	1	NA	Intergenic	Intergenic	-2919	NM_001080819	93760	Mm.22478	NM_001080819	ENSMUSG00000007880	Arid1a	1110030E03Rik|BAF250a|Osa1|Smarcf1	AT rich interactive domain 1A (SWI-like)	protein-coding
mm_160008.1	chr6	124808579	124808579	+	1	NA	promoter-TSS (NM_001306053)	promoter-TSS (NM_001306053)	-82	NM_001306051	14794	Mm.261906	NM_013539	ENSMUSG00000038451	Spsb2	AI461677|C9|Grcc9|SSB2	splA/ryanodine receptor domain and SOCS box containing 2	protein-coding
mm_19311.1	chr2	90542799	90542828	-	1	NA	intron (NM_008982, intron 1 of 23)	intron (NM_008982, intron 1 of 23)	37834	NM_008982	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_141091.1	chr17	25979937	25979950	-	1	NA	intron (NM_001347334, intron 1 of 11)	intron (NM_001347334, intron 1 of 11)	5931	NM_001347334	50817	Mm.216072	NM_015830	ENSMUSG00000037326	Capn15	Solh	calpain 15	protein-coding
mm_98018.1	chr11	84901130	84901146	+	1	NA	intron (NM_025414, intron 16 of 24)	intron (NM_025414, intron 16 of 24)	15218	NM_001005223	448850	Mm.379733	NM_001005223	ENSMUSG00000020526	Znhit3	Myohd1|Trip3	zinc finger, HIT type 3	protein-coding
mm_45155.1	chr5	49473333	49473337	-	1	NA	Intergenic	Intergenic	-187676	NM_001199244	80334	Mm.160172	NM_030265	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding
mm_66847.1	chr7	49636848	49636851	-	1	NA	promoter-TSS (NM_001005232)	promoter-TSS (NM_001005232)	-14	NM_001005232	13172	Mm.307176	NM_001005232	ENSMUSG00000030507	Dbx1	AI426026|Dbx	developing brain homeobox 1	protein-coding
mm_100527.1	chr11	120598536	120598549	+	1	NA	promoter-TSS (NM_011568)	promoter-TSS (NM_011568)	10	NM_001038230	66156	Mm.21645	NM_025389	ENSMUSG00000025135	Anapc11	1110011I19Rik|R75218	anaphase promoting complex subunit 11	protein-coding
mm_7940.1	chr1	133914771	133914781	-	1	NA	exon (NM_054077, exon 2 of 3)	exon (NM_054077, exon 2 of 3)	6625	NM_054077	116847	Mm.214514	NM_054077	ENSMUSG00000041577	Prelp	7330409J17Rik|SLRR2A	proline arginine-rich end leucine-rich repeat	protein-coding
mm_28973.1	chr3	101029525	101029533	-	1	NA	promoter-TSS (NM_001167906)	promoter-TSS (NM_001167906)	-34	NM_001167906	630146	Mm.190915	NM_001099332	ENSMUSG00000086564	Cd101	EWI-101|Gm1016|Gm734|Igsf2	CD101 antigen	protein-coding
mm_136246.1	chr16	90937174	90937191	-	1	NA	3' UTR (NM_001045515, exon 33 of 33)	3' UTR (NM_001045515, exon 33 of 33)	-2333	NM_026502	68001	Mm.45374	NM_026502	ENSMUSG00000022972	1110004E09Rik	-	RIKEN cDNA 1110004E09 gene	protein-coding
mm_52022.1	chr6	94681756	94681791	+	1	NA	intron (NM_008377, intron 1 of 18)	intron (NM_008377, intron 1 of 18)	18372	NM_008377	16206	Mm.245210	NM_008377	ENSMUSG00000030029	Lrig1	D6Bwg0781e|Img|LIG-1	leucine-rich repeats and immunoglobulin-like domains 1	protein-coding
mm_143503.1	chr17	71598699	71598722	-	1	NA	promoter-TSS (NR_015549)	promoter-TSS (NR_015549)	51	NR_015549	68789	Mm.75202	NR_015549	ENSMUSG00000085492	Trmt61b	1110039F03Rik|623451|Gm6431	tRNA methyltransferase 61B	ncRNA
mm_101654.1	chr11	36672052	36672054	-	1	NA	intron (NM_011856, intron 2 of 28)	intron (NM_011856, intron 2 of 28)	272188	NM_001290702	23964	Mm.439889	NM_011856	ENSMUSG00000049336	Tenm2	Odz2|Odz3|Ten-2|Ten-m2	teneurin transmembrane protein 2	protein-coding
mm_107435.1	chr12	36020528	36020546	+	1	NA	exon (NM_025359, exon 5 of 6)	exon (NM_025359, exon 5 of 6)	21941	NM_025359	66109	Mm.254663	NM_025359	ENSMUSG00000020577	Tspan13	1100001I23Rik|NET-6|Tm4sf13	tetraspanin 13	protein-coding
mm_11284.1	chr2	30066539	30066567	+	1	NA	promoter-TSS (NM_001204875)	promoter-TSS (NM_001204875)	79	NM_001204875	56086	Mm.326055	NM_023871	ENSMUSG00000054766	Set	2610030F17Rik|5730420M11Rik|AA407739|I-2PP2A|StF-IT-1|TAF-I	SET nuclear oncogene	protein-coding
mm_20289.1	chr2	126926846	126926865	-	1	NA	exon (NM_023220, exon 3 of 15)	exon (NM_023220, exon 3 of 15)	6380	NM_023220	66552	Mm.269928	NM_023220	ENSMUSG00000027366	Sppl2a	2010106G01Rik|C130089K23Rik	signal peptide peptidase like 2A	protein-coding
mm_39322.1	chr5	8422832	8422906	+	1	NA	promoter-TSS (NM_178766)	promoter-TSS (NM_178766)	31	NM_178766	319653	Mm.146262	NM_178766	ENSMUSG00000054099	Slc25a40	B230315F11Rik	solute carrier family 25, member 40	protein-coding
mm_58350.1	chr6	147264125	147264152	-	1	NA	promoter-TSS (NM_008970)	promoter-TSS (NM_008970)	-125	NM_008970	19227	Mm.28440	NM_008970	ENSMUSG00000048776	Pthlh	PLP|PTH-like|Pthrp	parathyroid hormone-like peptide	protein-coding
mm_93740.1	chr10	120142753	120142777	-	1	NA	exon (NM_028679, exon 12 of 12)	exon (NM_028679, exon 12 of 12)	-29800	NM_080446	117599	Mm.214703	NM_080446	ENSMUSG00000020228	Helb	AI447783|D10Ertd664e	helicase (DNA) B	protein-coding
mm_54219.1	chr6	25809246	25809256	-	1	NA	promoter-TSS (NM_133931)	promoter-TSS (NM_133931)	-25	NM_133931	101185	Mm.274589	NM_133931	ENSMUSG00000029676	Pot1a	1500031H18Rik|AI851169|Pot1	protection of telomeres 1A	protein-coding
mm_132805.1	chr16	45158848	45158862	+	1	NA	promoter-TSS (NM_028756)	promoter-TSS (NM_028756)	26	NM_026402	67841	Mm.41775	NM_026402	ENSMUSG00000022663	Atg3	2610016C12Rik|APG3|Apg3l|Atg3l|PC3-96	autophagy related 3	protein-coding
mm_165292.1	chr2	91096686	91096693	+	1	NA	promoter-TSS (NM_011355)	promoter-TSS (NM_011355)	11	NM_011355	20375	Mm.1302	NM_011355	ENSMUSG00000002111	Spi1	Dis-1|Dis1|PU.1|Sfpi-1|Sfpi1|Spi-1|Tcfpu1|Tfpu.1	spleen focus forming virus (SFFV) proviral integration oncogene	protein-coding
mm_27968.1	chr3	80691138	80691146	-	1	NA	TTS (NM_001039195)	TTS (NM_001039195)	111649	NM_013540	14800	Mm.220224	NM_013540	ENSMUSG00000033981	Gria2	GluA2|GluR-B|Glur-2|Glur2	glutamate receptor, ionotropic, AMPA2 (alpha 2)	protein-coding
mm_158772.1	chrX	166618687	166618693	-	1	NA	Intergenic	MLTR25A|LTR|ERVK	-32974	NM_019397	54156	Mm.37707	NM_019397	ENSMUSG00000000402	Egfl6	Maeg	EGF-like-domain, multiple 6	protein-coding
mm_124609.1	chr15	3279400	3279415	+	1	NA	exon (NM_009155, exon 5 of 5)	exon (NM_009155, exon 5 of 5)	8430	NM_009155	20363	Mm.392203	NM_009155	ENSMUSG00000064373	Selenop	AU018766|D15Ucla1|Se-P|Sepp1|selp	selenoprotein P	protein-coding
mm_83470.1	chr9	45545418	45545418	-	1	NA	intron (NM_001081270, intron 3 of 32)	intron (NM_001081270, intron 3 of 32)	-114186	NR_040732	74602	Mm.394117	NR_040732	ENSMUSG00000097074	4833428L15Rik	-	RIKEN cDNA 4833428L15 gene	ncRNA
mm_64401.1	chr7	142502721	142502728	+	1	NA	intron (NM_001347550, intron 3 of 14)	intron (NM_001347550, intron 3 of 14)	3888	NM_001347551	21957	Mm.389992	NM_011620	ENSMUSG00000061723	Tnnt3	fTnT	troponin T3, skeletal, fast	protein-coding
mm_37666.1	chr4	129111976	129111991	-	1	NA	TTS (NM_001290706)	TTS (NM_001290706)	6435	NM_001290706	66260	Mm.25295	NM_025452	ENSMUSG00000028786	Tmem54	1810017F10Rik|AI507302	transmembrane protein 54	protein-coding
mm_160658.1	chr9	119032866	119032866	+	1	NA	TTS (NR_029742)	TTS (NR_029742)	1070	NR_029742	387218		NR_029742	ENSMUSG00000065513	Mir26a-1	Mirn26a|Mirn26a-1|miR-26a|mir-26a-1	microRNA 26a-1	ncRNA
mm_97717.1	chr11	80209020	80209057	+	1	NA	promoter-TSS (NM_001163354)	promoter-TSS (NM_001163354)	-17	NM_001163354	59040	Mm.489674	NM_021536	ENSMUSG00000017686	Rhot1	2210403N23Rik|AA415293|AF244542|AI834919|Arht1|C430039G08Rik|Miro1	ras homolog family member T1	protein-coding
mm_11483.1	chr2	32387114	32387124	+	1	NA	exon (NM_008491, exon 2 of 6)	exon (NM_008491, exon 2 of 6)	620	NM_008491	16819	Mm.9537	NM_008491	ENSMUSG00000026822	Lcn2	24p3|AW212229|NRL|Sip24	lipocalin 2	protein-coding
mm_26983.1	chr3	25672654	25672658	-	1	NA	intron (NM_001163387, intron 3 of 5)	intron (NM_001163387, intron 3 of 5)	480651	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_116447.1	chr13	43159562	43159569	-	1	NA	intron (NM_001252640, intron 4 of 7)	intron (NM_001252640, intron 4 of 7)	11936	NM_001252639	67046	Mm.269213	NM_025935	ENSMUSG00000021368	Tbc1d7	2610009C09Rik	TBC1 domain family, member 7	protein-coding
mm_1380.1	chr1	66816129	66816147	+	1	NA	intron (NM_177645, intron 1 of 13)	MIR|SINE|MIR	1457	NM_177645	68691	Mm.240912	NM_177645	ENSMUSG00000026004	Kansl1l	1110028C15Rik|1190030G24|AI427598|C430010P07Rik|mKIAA4189	KAT8 regulatory NSL complex subunit 1-like	protein-coding
mm_131337.1	chr16	13358443	13358453	+	1	NA	promoter-TSS (NM_153588)	promoter-TSS (NM_153588)	27	NM_153588	239719	Mm.270643	NM_153588	ENSMUSG00000009569	Mkl2	ENSMUSG00000075401|Gt4-1|MRTF-B|Mrtfb|mKIAA1243	MKL/myocardin-like 2	protein-coding
mm_27575.1	chr3	58692426	58692443	-	1	NA	promoter-TSS (NM_009174)	promoter-TSS (NM_009174)	-46	NM_009174	20439	Mm.2847	NM_009174	ENSMUSG00000036432	Siah2	AA415433|Sinh2	seven in absentia 2	protein-coding
mm_24013.1	chr3	87435765	87435787	+	1	NA	promoter-TSS (NM_183222)	promoter-TSS (NM_183222)	-6	NM_183222	329693	Mm.331122	NM_183222	ENSMUSG00000048031	Fcrl5	Fcrh3|mBXMH2	Fc receptor-like 5	protein-coding
mm_101294.1	chr11	22138804	22138808	-	1	NA	intron (NM_001252515, intron 10 of 24)	intron (NM_001252515, intron 10 of 24)	-137155	NM_011023	18423	Mm.129663	NM_011023	ENSMUSG00000005917	Otx1	A730044F23Rik|jv	orthodenticle homeobox 1	protein-coding
mm_136726.1	chr17	8238331	8238337	+	1	NA	intron (NM_001190333, intron 1 of 2)	Tigger15a|DNA|TcMar-Tigger	2291	NM_001190333	12458	Mm.8007	NM_009835	ENSMUSG00000040899	Ccr6	CC-CKR-6|CCR-6|Cmkbr6|KY411	chemokine (C-C motif) receptor 6	protein-coding
mm_19924.1	chr2	116058789	116058799	-	1	NA	intron (NM_001346047, intron 6 of 13)	intron (NM_001346047, intron 6 of 13)	5825	NM_001346044	17536	Mm.247566	NM_010825	ENSMUSG00000027210	Meis2	A430109D20Rik|Mrg1|Stra10	Meis homeobox 2	protein-coding
mm_95456.1	chr11	50377048	50377063	+	1	NA	promoter-TSS (NM_021510)	promoter-TSS (NM_021510)	-664	NM_021510	59013	Mm.21740	NM_021510	ENSMUSG00000007850	Hnrnph1	AI642080|E430005G16Rik|Hnrnph|Hnrph1	heterogeneous nuclear ribonucleoprotein H1	protein-coding
mm_97469.1	chr11	78297330	78297333	+	1	NA	TTS (NM_001287206)	TTS (NM_001287206)	-4260	NM_017407	54141	Mm.24250	NM_017407	ENSMUSG00000002055	Spag5	AI874642|D11Bhm180e|Deepest|MAP126|Mastrin|S17	sperm associated antigen 5	protein-coding
mm_16849.1	chr2	11603193	11603268	-	1	NA	promoter-TSS (NM_152824)	promoter-TSS (NM_152824)	-31	NM_152824	76938	Mm.182769	NM_152824	ENSMUSG00000037197	Rbm17	2700027J02Rik	RNA binding motif protein 17	protein-coding
mm_34058.1	chr4	138425738	138425740	+	1	NA	Intergenic	Intergenic	-8933	NM_026689	68350	Mm.103413	NM_026689	ENSMUSG00000041241	Mul1	0610009K11Rik|AV000801|Gide	mitochondrial ubiquitin ligase activator of NFKB 1	protein-coding
mm_32844.1	chr4	117849341	117849355	+	1	NA	intron (NM_008135, intron 2 of 13)	intron (NM_008135, intron 2 of 13)	14090	NM_008135	14664	Mm.244549	NM_008135	ENSMUSG00000028542	Slc6a9	Glyt-1|Glyt1	solute carrier family 6 (neurotransmitter transporter, glycine), member 9	protein-coding
mm_13073.1	chr2	91119884	91119888	+	1	NA	intron (NM_008653, intron 2 of 31)	intron (NM_008653, intron 2 of 31)	1742	NM_008653	17868	Mm.10728	NM_008653	ENSMUSG00000002100	Mybpc3	-	myosin binding protein C, cardiac	protein-coding
mm_14090.1	chr2	125158429	125158429	+	1	NA	intron (NM_183354, intron 3 of 27)	intron (NM_183354, intron 3 of 27)	5829	NM_001079690	20495	Mm.3914	NM_011389	ENSMUSG00000027202	Slc12a1	AI788571|D630042G03Rik|Nkcc2|mBSC1|urehr3	solute carrier family 12, member 1	protein-coding
mm_76476.1	chr8	85432844	85432859	-	1	NA	promoter-TSS (NM_025722)	promoter-TSS (NM_025722)	-10	NM_025722	66714	Mm.272748	NM_025722	ENSMUSG00000036934	4921524J17Rik	-	RIKEN cDNA 4921524J17 gene	protein-coding
mm_104739.1	chr11	98399595	98399625	-	1	NA	intron (NM_001033537, intron 1 of 7)	MIRb|SINE|MIR	880	NM_001033537	320655	Mm.86519	NM_001033537	ENSMUSG00000038208	Pgap3	CAB2|D430035D22Rik|Perld1	post-GPI attachment to proteins 3	protein-coding
mm_70232.1	chr7	145289058	145289081	-	1	NA	Intergenic	Intergenic	-5058	NR_132642	233979	Mm.102235	NM_146206	ENSMUSG00000048677	Tpcn2	D830047E22Rik|Gm35086	two pore segment channel 2	protein-coding
mm_169591.1	chr1	52939508	52939514	+	1	NA	intron (NM_144953, intron 1 of 1)	L1Md_T|LINE|L1	13329	NM_144953	67080	Mm.236287	NM_144953	ENSMUSG00000043629	1700019D03Rik	2410136C24Rik|AA410151|smAKAP	RIKEN cDNA 1700019D03 gene	protein-coding
mm_137980.1	chr17	33587331	33587353	+	1	NA	intron (NM_053214, intron 14 of 27)	B1_Mur1|SINE|Alu	31635	NM_053214	17916	Mm.42019	NM_053214	ENSMUSG00000024300	Myo1f	C330006B10Rik	myosin IF	protein-coding
mm_83214.1	chr9	42098010	42098037	-	1	NA	intron (NM_011436, intron 3 of 47)	intron (NM_011436, intron 3 of 47)	26266	NM_011436	20660	Mm.121920	NM_011436	ENSMUSG00000049313	Sorl1	2900010L19Rik|AI596264|AW261561|LR11|SorLA|gp250|mSorLA	sortilin-related receptor, LDLR class A repeats-containing	protein-coding
mm_145810.1	chr18	65414988	65414994	+	1	NA	intron (NR_105742, intron 3 of 6)	intron (NR_105742, intron 3 of 6)	-16006	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_100982.1	chr11	7213415	7213421	-	1	NA	exon (NM_008343, exon 1 of 5)	exon (NM_008343, exon 1 of 5)	505	NM_008343	16009	Mm.29254	NM_008343	ENSMUSG00000020427	Igfbp3	AI649005|IGFBP-3|IGgfbp3	insulin-like growth factor binding protein 3	protein-coding
mm_107315.1	chr12	31265456	31265466	+	1	NA	exon (NM_008482, exon 1 of 33)	exon (NM_008482, exon 1 of 33)	167	NM_008482	16777	Mm.172674	NM_008482	ENSMUSG00000002900	Lamb1	C77966|C80098|C81607|D130003D08Rik|Lamb-1|Lamb1-1	laminin B1	protein-coding
mm_28634.1	chr3	95217691	95217728	-	1	NA	TTS (NM_019914)	TTS (NM_019914)	233	NM_172512	213054	Mm.224820	NM_029885	ENSMUSG00000038766	Gabpb2	1810015F01Rik|5830427M07|9430006E19Rik|A430024B14Rik|AV050852|Gabpb2-1	GA repeat binding protein, beta 2	protein-coding
mm_167659.1	chr9	71165336	71165345	+	1	NA	Intergenic	Intergenic	-2051	NM_022026	64008	Mm.449427	NM_022026	ENSMUSG00000032204	Aqp9	1700020I22Rik|AI266899|AQP-9	aquaporin 9	protein-coding
mm_55739.1	chr6	77478011	77478016	-	1	NA	intron (NM_001109764, intron 8 of 19)	intron (NM_001109764, intron 8 of 19)	-95538	NR_045141	70753	Mm.490700	NR_045141	ENSMUSG00000108077	6330415B21Rik	-	RIKEN cDNA 6330415B21 gene	ncRNA
mm_89572.1	chr10	95515117	95515161	+	1	NA	promoter-TSS (NM_080560)	promoter-TSS (NM_080560)	-23	NM_080560	93765	Mm.371667	NM_080560	ENSMUSG00000074781	Ube2n	1500026J17Rik|AL022654|BB101821|UBC13	ubiquitin-conjugating enzyme E2N	protein-coding
mm_75428.1	chr8	47267939	47267943	-	1	NA	intron (NM_175162, intron 1 of 4)	intron (NM_175162, intron 1 of 4)	21461	NM_001286376	71069	Mm.23973	NM_175162	ENSMUSG00000038143	Stox2	4933409N07Rik|AI449080|AI835114|mKIAA1392	storkhead box 2	protein-coding
mm_127257.1	chr15	99704106	99704124	+	1	NA	intron (NM_031842, intron 4 of 12)	intron (NM_031842, intron 4 of 12)	1828	NM_031842	83797	Mm.273756	NM_031842	ENSMUSG00000023018	Smarcd1	AA407987|Baf60a|D15Kz1	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1	protein-coding
mm_126116.1	chr15	78261352	78261365	+	1	NA	intron (NM_008677, intron 9 of 9)	intron (NM_008677, intron 9 of 9)	16547	NM_008677	17972	Mm.2068	NM_008677	ENSMUSG00000071715	Ncf4	AI451400|p40phox	neutrophil cytosolic factor 4	protein-coding
mm_153523.1	chr19	41774108	41774167	-	1	NA	exon (NM_001163495, exon 10 of 11)	exon (NM_001163495, exon 10 of 11)	27176	NR_040320	100502871	Mm.394485	NR_040320		Gm19424	-	predicted gene, 19424	ncRNA
mm_108150.1	chr12	76307100	76307111	+	1	NA	intron (NM_138745, intron 21 of 27)	intron (NM_138745, intron 21 of 27)	-17786	NM_001101471	238276	Mm.311452	NM_001101471	ENSMUSG00000021057	Akap5	3526401B18Rik|AKAP 150|AKAP-5|AKAP150|BB098886|Gm258|P150	A kinase (PRKA) anchor protein 5	protein-coding
mm_169659.1	chr15	58134859	58134868	-	1	NA	exon (NM_027435, exon 1 of 28)	exon (NM_027435, exon 1 of 28)	219	NM_027435	70472	Mm.221758	NM_027435	ENSMUSG00000022360	Atad2	2610509G12Rik	ATPase family, AAA domain containing 2	protein-coding
mm_34930.1	chr4	155839676	155839684	+	1	NA	promoter-TSS (NM_024263)	promoter-TSS (NM_024263)	0	NM_024263	74761	Mm.159028	NM_024263	ENSMUSG00000029070	Mxra8	1200013A08Rik|1700095D18Rik|AI131686|Asp3|Dicam	matrix-remodelling associated 8	protein-coding
mm_139735.1	chr17	57769165	57769217	+	1	NA	promoter-TSS (NM_001081653)	promoter-TSS (NM_001081653)	-379	NM_001081653	620292	Mm.391030	NM_001081653	ENSMUSG00000038048	Cntnap5c	Caspr5-3|EG620292|Gm325	contactin associated protein-like 5C	protein-coding
mm_6793.1	chr1	84146786	84146790	-	1	NA	intron (NM_001003948, intron 2 of 2)	intron (NM_001003948, intron 2 of 2)	72173	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_10258.1	chr2	9369039	9369053	+	1	NA	Intergenic	Intergenic	179531	NR_038180	73438	Mm.23558	NR_038180	ENSMUSG00000085580	1700061F12Rik	-	RIKEN cDNA 1700061F12 gene	ncRNA
mm_12921.1	chr2	84958863	84958865	+	1	NA	TTS (NM_021398)	TTS (NM_021398)	-21597	NM_008920	19074	Mm.142727	NM_008920	ENSMUSG00000027073	Prg2	EMBP|MBP|mMBP|mMBP-1	proteoglycan 2, bone marrow	protein-coding
mm_18975.1	chr2	76843619	76843620	-	1	NA	intron (NM_011652, intron 145 of 312)	intron (NM_011652, intron 145 of 312)	138928	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_87271.1	chr10	41809999	41810013	+	1	NA	promoter-TSS (NM_001162908)	promoter-TSS (NM_001162908)	-138	NM_026643	103268	Mm.338605	NM_026643	ENSMUSG00000019813	Cep57l1	2410017P07Rik|4930484D11Rik|AI607327|cep57R	centrosomal protein 57-like 1	protein-coding
mm_132850.1	chr16	46958877	46958881	+	1	NA	Intergenic	Intergenic	-461912	NM_021497	58998	Mm.40477	NM_021495	ENSMUSG00000022656	Nectin3	2610301B19Rik|3000002N23Rik|4921513D19Rik|AA407785|AU016832|AW538082|CD113|Pvrl3	nectin cell adhesion molecule 3	protein-coding
mm_167104.1	chr7	111080318	111080322	-	1	NA	exon (NM_013507, exon 4 of 22)	exon (NM_013507, exon 4 of 22)	2710	NM_001040131	13690	Mm.185453	NM_013507	ENSMUSG00000005610	Eif4g2	DAP-5|E130105L11Rik|Nat1|Natm1|p97	eukaryotic translation initiation factor 4, gamma 2	protein-coding
mm_33279.1	chr4	128727590	128727644	+	1	NA	promoter-TSS (NM_001195083)	promoter-TSS (NM_001195083)	46	NM_001195083	54383	Mm.473738	NM_018774	ENSMUSG00000028796	Phc2	A3galt2|AA415044|D130050K19Rik|D4Ertd810e|Edr2|Mph2|p36	polyhomeotic-like 2 (Drosophila)	protein-coding
mm_95189.1	chr11	42421323	42421333	+	1	NA	promoter-TSS (NM_001347314)	promoter-TSS (NM_001347314)	-22	NM_001347314	14401	Mm.338723	NM_008070	ENSMUSG00000007653	Gabrb2	AI834970|C030002O17Rik|C030021G16Rik|Gabrab2|Gabrb-2	gamma-aminobutyric acid (GABA) A receptor, subunit beta 2	protein-coding
mm_126607.1	chr15	82642182	82642194	+	1	NA	promoter-TSS (NR_003552)	promoter-TSS (NR_003552)	-143	NR_003552	68444	Mm.443212	NR_003552		Cyp2d13	1300007K12Rik	cytochrome P450, family 2, subfamily d, polypeptide 13	pseudo
mm_19106.1	chr2	79454966	79454972	-	1	NA	exon (NM_010894, exon 2 of 2)	exon (NM_010894, exon 2 of 2)	1667	NM_010894	18012	Mm.4636	NM_010894	ENSMUSG00000034701	Neurod1	BETA2|BHF-1|Nd1|Neurod|bHLHa3	neurogenic differentiation 1	protein-coding
mm_129853.1	chr15	83172238	83172248	-	1	NA	promoter-TSS (NM_029787)	promoter-TSS (NM_029787)	-35	NM_029787	109754	Mm.22560	NM_029787	ENSMUSG00000018042	Cyb5r3	0610016L08Rik|2500002N19Rik|C85115|Dia-1|Dia1|WU:AL591952.1-001|WU:AL591952.1-002|WU:AL591952.1-003|WU:Cyb5r3	cytochrome b5 reductase 3	protein-coding
mm_8653.1	chr1	156462224	156462247	-	1	NA	intron (NM_009230, intron 2 of 15)	ID_B1|SINE|B4	12093	NM_009230	20652	Mm.28099	NM_009230	ENSMUSG00000026600	Soat1	8430426K15Rik|ACAT-1|AW550831|Acact|ald|hid	sterol O-acyltransferase 1	protein-coding
mm_155214.1	chrX	56787802	56787812	+	1	NA	intron (NM_001287800, intron 1 of 5)	intron (NM_001287800, intron 1 of 5)	1280	NM_001287800	14199	Mm.3126	NM_010211	ENSMUSG00000023092	Fhl1	FHL-1|KyoT|RAM14-1|SLIM|SLIM-1	four and a half LIM domains 1	protein-coding
mm_115666.1	chr13	12473534	12473538	-	1	NA	3' UTR (NM_133643, exon 6 of 6)	3' UTR (NM_133643, exon 6 of 6)	-11798	NM_001291057	56048	Mm.474138	NM_018886	ENSMUSG00000057554	Lgals8	1200015E08Rik|AI326142|D13Ertd524e|Lgals-8	lectin, galactose binding, soluble 8	protein-coding
mm_90723.1	chr10	5069045	5069079	-	1	NA	promoter-TSS (NM_022027)	promoter-TSS (NM_022027)	1	NM_022027	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_83975.1	chr9	57261978	57261981	-	1	NA	intron (NM_028820, intron 1 of 2)	CpG	620	NM_028820	74211	Mm.428905	NM_028820	ENSMUSG00000032300	1700017B05Rik	AA682102|D9Ertd278e	RIKEN cDNA 1700017B05 gene	protein-coding
mm_31398.1	chr4	48045325	48045333	+	1	NA	promoter-TSS (NM_015743)	promoter-TSS (NM_015743)	24	NM_015743	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_72360.1	chr8	80494033	80494065	+	1	NA	promoter-TSS (NM_010369)	promoter-TSS (NM_010369)	4	NM_010369	14934	Mm.13123	NM_010369	ENSMUSG00000051839	Gypa	AI853584|CD235a|GPA	glycophorin A	protein-coding
mm_23705.1	chr3	68786999	68787044	+	1	NA	Intergenic	Intergenic	-82565	NM_001167996	68725	Mm.45741	NM_001167996	ENSMUSG00000046999	1110032F04Rik	AI115547	RIKEN cDNA 1110032F04 gene	protein-coding
mm_7651.1	chr1	128324324	128324327	-	1	NA	intron (NM_001081078, intron 1 of 16)	ID_B1|SINE|B4	3993	NM_001081078	226413	Mm.26930	NM_001081078	ENSMUSG00000026354	Lct	Gm100|LAC|LPH|Lphl	lactase	protein-coding
mm_94614.1	chr11	16752221	16752236	+	1	NA	promoter-TSS (NM_007912)	promoter-TSS (NM_007912)	25	NM_007912	13649	Mm.8534	NM_007912	ENSMUSG00000020122	Egfr	9030024J15Rik|AI552599|Erbb|Errb1|Errp|Wa5|wa-2|wa2	epidermal growth factor receptor	protein-coding
mm_83170.1	chr9	40531317	40531334	-	1	NA	Intergenic	CpG	-75561	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_1602.1	chr1	74380902	74380918	+	1	NA	exon (NM_013612, exon 8 of 15)	exon (NM_013612, exon 8 of 15)	5707	NM_013612	18173	Mm.2913	NM_013612	ENSMUSG00000026177	Slc11a1	Bcg|Ity|Ity1|Lsh|Nramp|Nramp1|ity	solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1	protein-coding
mm_21816.1	chr2	165283657	165283683	-	1	NA	intron (NM_144893, intron 1 of 9)	intron (NM_144893, intron 1 of 9)	4117	NM_001252574	228875	Mm.21184	NM_144893	ENSMUSG00000017664	Slc35c2	C85957|CGI-15|D2Wsu58e|Ovcov1	solute carrier family 35, member C2	protein-coding
mm_134059.1	chr16	7038517	7038520	-	1	NA	intron (NM_021477, intron 5 of 16)	intron (NM_021477, intron 5 of 16)	-31317	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_101305.1	chr11	22610332	22610344	-	1	NA	Intergenic	Intergenic	98055	NM_153596	103765	Mm.221274	NM_153596	ENSMUSG00000049904	Tmem17	AI503894|AW049890	transmembrane protein 17	protein-coding
mm_87335.1	chr10	43221506	43221529	+	1	NA	promoter-TSS (NM_001168289)	promoter-TSS (NM_001168289)	31	NM_001168289	71365	Mm.490430	NM_027772	ENSMUSG00000038240	Pdss2	5430420P03Rik|Gm60|Plmp|kd|mDLP1	prenyl (solanesyl) diphosphate synthase, subunit 2	protein-coding
mm_101908.1	chr11	49590327	49590350	-	1	NA	Intergenic	Intergenic	-19341	NM_008029	14257	Mm.3291	NM_008029	ENSMUSG00000020357	Flt4	AI323512|Chy|Flt-4|VEGFR-3|VEGFR3	FMS-like tyrosine kinase 4	protein-coding
mm_10852.1	chr2	24994386	24994394	+	1	NA	intron (NM_146251, intron 8 of 34)	intron (NM_146251, intron 8 of 34)	18357	NM_146251	241274	Mm.389243	NM_146251	ENSMUSG00000036833	Pnpla7	BC027342|E430013P11Rik|Nre	patatin-like phospholipase domain containing 7	protein-coding
mm_18706.1	chr2	71868307	71868326	-	1	NA	intron (NR_039557, intron 3 of 3).2	RLTR11C_MM|LTR|ERVK	-4908	NM_172665	228026	Mm.34411	NM_172665	ENSMUSG00000006494	Pdk1	B830012B01|D530020C15Rik	pyruvate dehydrogenase kinase, isoenzyme 1	protein-coding
mm_132816.1	chr16	45201728	45201729	+	1	NA	Intergenic	MLTR14|LTR|ERV1	-22609	NM_001037719	208154	Mm.38199	NM_177584	ENSMUSG00000052013	Btla	A630002H24	B and T lymphocyte associated	protein-coding
mm_73986.1	chr8	120628724	120628728	+	1	NA	intron (NM_001308449, intron 1 of 3)	intron (NM_001308449, intron 1 of 3)	5656	NM_197988	68918	Mm.473736	NM_197988	ENSMUSG00000043687	1190005I06Rik	-	RIKEN cDNA 1190005I06 gene	protein-coding
mm_58854.1	chr7	16886423	16886472	+	1	NA	3' UTR (NM_001081655, exon 4 of 4)	3' UTR (NM_001081655, exon 4 of 4)	-5339	NM_010320	14709	Mm.103770	NM_010320	ENSMUSG00000063594	Gng8	G(y)8	guanine nucleotide binding protein (G protein), gamma 8	protein-coding
mm_126097.1	chr15	78044137	78044147	+	1	NA	intron (NM_007583, intron 1 of 3)	intron (NM_007583, intron 1 of 3)	-73318	NM_018749	55944	Mm.3955	NM_018749	ENSMUSG00000016554	Eif3d	66/67kDa|AA407891|Eif3s7|eIF3p66	eukaryotic translation initiation factor 3, subunit D	protein-coding
mm_127507.1	chr15	101469444	101469452	+	1	NA	intron (NM_016879, intron 6 of 9)	intron (NM_016879, intron 6 of 9)	-4030	NM_010667	16679	Mm.383183	NM_010667	ENSMUSG00000067614	Krt86	5430421N21Rik|AI325212|Khb4|Krt2-10|Krt2-11|MHb4	keratin 86	protein-coding
mm_140025.1	chr17	73948429	73948437	+	1	NA	intron (NM_011723, intron 1 of 35)	intron (NM_011723, intron 1 of 35)	1763	NM_011723	22436	Mm.11223	NM_011723	ENSMUSG00000024066	Xdh	XO|Xor|Xox-1|Xox1	xanthine dehydrogenase	protein-coding
mm_151396.1	chr19	56441230	56441238	+	1	NA	3' UTR (NM_007611, exon 7 of 7)	3' UTR (NM_007611, exon 7 of 7)	-20403	NM_001164263	226245	Mm.156742	NM_172641	ENSMUSG00000035818	Plekhs1	9930023K05Rik	pleckstrin homology domain containing, family S member 1	protein-coding
mm_98677.1	chr11	96284773	96284786	+	1	NA	3' UTR (NM_010461, exon 2 of 2)	3' UTR (NM_010461, exon 2 of 2)	-1867	NM_010460	15415	Mm.390366	NM_010460	ENSMUSG00000038721	Hoxb7	AI325018|Hox-2.3	homeobox B7	protein-coding
mm_141328.1	chr17	28467273	28467276	-	1	NA	intron (NM_010220, intron 1 of 10)	B1_Mur2|SINE|Alu	18875	NM_010220	14229	Mm.276405	NM_010220	ENSMUSG00000024222	Fkbp5	D17Ertd592e|Dit1|FKBP-5|FKBP51	FK506 binding protein 5	protein-coding
mm_116185.1	chr13	31077453	31077464	-	1	NA	Intergenic	Intergenic	-103411	NM_025588	66482	Mm.293510	NM_025588	ENSMUSG00000021357	Exoc2	2410030I24Rik|AI648199|Sec5|Sec5l1	exocyst complex component 2	protein-coding
mm_111148.1	chr12	82170579	82170611	-	1	NA	intron (NM_001167983, intron 1 of 23)	intron (NM_001167983, intron 1 of 23)	579	NM_001167983	217692	Mm.261333	NM_172579	ENSMUSG00000042700	Sipa1l1	4931426N11Rik|AW213287|Spar|mKIAA0440	signal-induced proliferation-associated 1 like 1	protein-coding
mm_113295.1	chr13	30614910	30614925	+	1	NA	promoter-TSS (NR_045975)	promoter-TSS (NR_045975)	-126	NR_045975	75090	Mm.292232	NR_045975	ENSMUSG00000086263	4930519D14Rik	-	RIKEN cDNA 4930519D14 gene	ncRNA
mm_77119.1	chr8	111259193	111259221	-	1	NA	promoter-TSS (NM_009149)	promoter-TSS (NM_009149)	-5	NM_009149	20340	Mm.276271	NM_009149	ENSMUSG00000003316	Glg1	AI593353|AW537898|CFR|CFR-1|ESL-1|MG-160|MG160|Selel	golgi apparatus protein 1	protein-coding
mm_127495.1	chr15	101411054	101411095	+	1	NA	Intergenic	Intergenic	-1329	NM_033073	110310	Mm.486285	NM_033073	ENSMUSG00000023039	Krt7	D15Wsu77e|K7|Krt2-7	keratin 7	protein-coding
mm_36966.1	chr4	109374941	109374941	-	1	NA	intron (NM_001159964, intron 9 of 12)	intron (NM_001159964, intron 9 of 12)	31316	NR_131195	102635290	Mm.427859	NR_131195		Ttc39aos1	Gm12750|OTTMUSG00000008290|lincRNA-EPS	Ttc39a opposite strand RNA 1	ncRNA
mm_107250.1	chr12	27339364	27339369	+	1	NA	3' UTR (NM_009234, exon 1 of 1)	3' UTR (NM_009234, exon 1 of 1)	3352	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding
mm_95807.1	chr11	55110168	55110172	+	1	NA	3' UTR (NM_010299, exon 4 of 4)	3' UTR (NM_010299, exon 4 of 4)	12185	NM_010299	14667	Mm.287807	NM_010299	ENSMUSG00000000594	Gm2a	AA408702|AW215435|GM2-AP|SAP-3	GM2 ganglioside activator protein	protein-coding
mm_54814.1	chr6	42349672	42349680	-	1	NA	promoter-TSS (NM_001289618)	promoter-TSS (NM_001289618)	-152	NM_011777	22793	Mm.282303	NM_011777	ENSMUSG00000029860	Zyx	9530098H06Rik|R75157	zyxin	protein-coding
mm_68971.1	chr7	126584823	126584833	-	1	NA	promoter-TSS (NM_138310)	promoter-TSS (NM_138310)	-180	NM_138310	171504	Mm.170665	NM_138310	ENSMUSG00000042759	Apobr	Apob-48r|Apob48r	apolipoprotein B receptor	protein-coding
mm_90932.1	chr10	12869085	12869137	-	1	NA	Intergenic	CpG	-7376	NM_011682	22288	Mm.331784	NM_011682	ENSMUSG00000019820	Utrn	AA589569|DRP|Dmdl	utrophin	protein-coding
mm_61575.1	chr7	79811222	79811266	+	1	NA	exon (NM_008589, exon 1 of 2)	exon (NM_008589, exon 1 of 2)	517	NM_008589	17293	Mm.31472	NM_008589	ENSMUSG00000030543	Mesp2	bHLHc6	mesoderm posterior 2	protein-coding
mm_51705.1	chr6	86668810	86668818	+	1	NA	intron (NM_010751, intron 1 of 5)	CpG	345	NM_010751	17119	Mm.279580	NM_010751	ENSMUSG00000001156	Mxd1	AW122478|Mad|Mad1	MAX dimerization protein 1	protein-coding
mm_105563.1	chr11	106514238	106514241	-	1	NA	intron (NM_198292, intron 8 of 11)	intron (NM_198292, intron 8 of 11)	13248	NR_030703	100216537		NR_030703	ENSMUSG00000065126	Snord104	-	small nucleolar RNA, C/D box 104	snoRNA
mm_90172.1	chr10	119548749	119548752	+	1	NA	intron (NM_133442, intron 1 of 21)	intron (NM_133442, intron 1 of 21)	94716	NM_001277293	74053	Mm.196692	NM_028736	ENSMUSG00000034813	Grip1	4931400F03Rik|GRIP|eb	glutamate receptor interacting protein 1	protein-coding
mm_162009.1	chr19	42078937	42078937	-	1	NA	intron (NM_198108, intron 1 of 4)	intron (NM_198108, intron 1 of 4)	7433	NM_198108	226123	Mm.259441	NM_198108	ENSMUSG00000049670	Morn4	-	MORN repeat containing 4	protein-coding
mm_39469.1	chr5	19766731	19766764	+	1	NA	intron (NM_001170746, intron 2 of 22)	Lx2A|LINE|L1	-140771	NM_001170745	50791	Mm.332231	NM_015823	ENSMUSG00000040003	Magi2	AIP-1|Acvri1|Acvrinp1|Acvrip1|Magi-2|S-SCAM|mKIAA0705	membrane associated guanylate kinase, WW and PDZ domain containing 2	protein-coding
mm_117975.1	chr13	100067917	100067924	-	1	NA	intron (NM_001081061, intron 13 of 38)	PB1D9|SINE|Alu	36150	NM_001081061	544971	Mm.288546	NM_001081061	ENSMUSG00000049658	Bdp1	AI662220|AW049390|AW456745|B130055N23Rik|G630013P12Rik|TAF3B1|TFC5|TFIIIB150|TFIIIB90|Tfnr|mKIAA1241	B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB	protein-coding
mm_105341.1	chr11	102995006	102995041	-	1	NA	exon (NM_026551, exon 5 of 5)	exon (NM_026551, exon 5 of 5)	4898	NR_105896	102466988		NR_105896	ENSMUSG00000098613	Mir6931	Gm27303|mmu-mir-6931	microRNA 6931	ncRNA
mm_132376.1	chr16	34921401	34921405	+	1	NA	intron (NM_139300, intron 15 of 31)	intron (NM_139300, intron 15 of 31)	17926	NR_040536	76649	Mm.420532	NR_040536	ENSMUSG00000100593	1700119H24Rik	-	RIKEN cDNA 1700119H24 gene	ncRNA
mm_34155.1	chr4	139399739	139399753	+	1	NA	intron (NM_001160319, intron 12 of 105)	intron (NM_001160319, intron 12 of 105)	19087	NM_001160319	69116	Mm.271956	NM_001160319	ENSMUSG00000066036	Ubr4	1810009A16Rik|A930005E13Rik|D930005K06Rik|Gm1032|Gm1666|N28143|RBAF600|Zubr1|mKIAA0462|p600	ubiquitin protein ligase E3 component n-recognin 4	protein-coding
mm_123513.1	chr14	66244121	66244123	-	1	NA	intron (NM_001162365, intron 1 of 30)	intron (NM_001162365, intron 1 of 30)	-30570	NM_001162366	19229	Mm.21613	NM_172498	ENSMUSG00000059456	Ptk2b	CADTK|CAKB|CAKbeta|E430023O05Rik|FADK2|FAK2|PYK2|Raftk	PTK2 protein tyrosine kinase 2 beta	protein-coding
mm_59892.1	chr7	30307148	30307169	+	1	NA	3' UTR (NM_001081114, exon 14 of 14)	3' UTR (NM_001081114, exon 14 of 14)	-1595	NM_198027	233065	Mm.276277	NM_198027	ENSMUSG00000042831	Alkbh6	AI839550|Abh6|C130099A02	alkB homolog 6	protein-coding
mm_69807.1	chr7	141215672	141215705	-	1	NA	promoter-TSS (NM_025886)	promoter-TSS (NM_025886)	-172	NM_025886	66985	Mm.21202	NM_025886	ENSMUSG00000038618	Rassf7	2400009B11Rik|AW210608	Ras association (RalGDS/AF-6) domain family (N-terminal) member 7	protein-coding
mm_156693.1	chrX	159459200	159459214	+	1	NA	promoter-TSS (NM_001313752)	promoter-TSS (NM_001313752)	82	NM_001313753	78283	Mm.160079	NM_001081124	ENSMUSG00000041020	Map7d2	1600028E09Rik|2900002G04Rik|5330432J06Rik|C030036K04Rik|Mtap7d2	MAP7 domain containing 2	protein-coding
mm_19169.1	chr2	84342602	84342614	-	1	NA	intron (NM_018782, intron 13 of 15)	intron (NM_018782, intron 13 of 15)	82658	NM_018782	54598	Mm.75467	NM_018782	ENSMUSG00000059588	Calcrl	AV071593|CRLR	calcitonin receptor-like	protein-coding
mm_127128.1	chr15	98131281	98131292	+	1	NA	intron (NM_021514, intron 19 of 21)	intron (NM_021514, intron 19 of 21)	14416	NM_030121	78541	Mm.200766	NM_030121	ENSMUSG00000048175	Asb8	4930539L19Rik|AI788835|C430011H06Rik	ankyrin repeat and SOCS box-containing 8	protein-coding
mm_149978.1	chr19	29101388	29101438	+	1	NA	promoter-TSS (NM_021525)	promoter-TSS (NM_021525)	38	NM_021525	59028	Mm.28630	NM_021525	ENSMUSG00000024785	Rcl1	2310040A02Rik|AI789745|C76567|RPCL1|Rnac	RNA terminal phosphate cyclase-like 1	protein-coding
mm_93470.1	chr10	111157354	111157392	-	1	NA	Intergenic	Intergenic	-7429	NM_001003717	237542	Mm.220204	NM_175489	ENSMUSG00000020189	Osbpl8	AA536976|AA536995|C730029P18Rik|D330025H14Rik|ORP-8	oxysterol binding protein-like 8	protein-coding
mm_164511.1	chr16	95454990	95455026	+	1	NA	intron (NM_001302152, intron 3 of 10)	intron (NM_001302152, intron 3 of 10)	4340	NM_001302154	13876	Mm.164531	NM_133659	ENSMUSG00000040732	Erg	D030036I24Rik	avian erythroblastosis virus E-26 (v-ets) oncogene related	protein-coding
mm_173295.1	chrY	40031563	40031563	-	1	NA	Intergenic	RLTR6_Mm|LTR|ERV1	2073743	NM_207162	382133	Mm.463885	NM_207162	ENSMUSG00000094575	Gm20738	-	predicted gene, 20738	protein-coding
mm_5562.1	chr1	38836534	38836628	-	1	NA	Intergenic	CpG	-15366	NM_001029878	381338	Mm.487137	NM_028403	ENSMUSG00000048814	Lonrf2	2900060P06Rik|AI851349	LON peptidase N-terminal domain and ring finger 2	protein-coding
mm_35907.1	chr4	49682378	49682385	-	1	NA	promoter-TSS (NM_001004025)	promoter-TSS (NM_001004025)	-398	NM_001004025	19059	Mm.46125	NM_001004025	ENSMUSG00000028310	Ppp3r2	CaNB2|CnB2	protein phosphatase 3, regulatory subunit B, alpha isoform (calcineurin B, type II)	protein-coding
mm_97609.1	chr11	78951104	78951135	+	1	NA	exon (NM_010927, exon 21 of 27)	exon (NM_010927, exon 21 of 27)	25828	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_77489.1	chr8	122568349	122568367	-	1	NA	intron (NM_026014, intron 1 of 9)	CpG	343	NM_026014	67177	Mm.21873	NM_026014	ENSMUSG00000006585	Cdt1	2610318F11Rik|AW545653|C76791|Ris2	chromatin licensing and DNA replication factor 1	protein-coding
mm_64276.1	chr7	141808581	141808618	+	1	NA	intron (NM_010844, intron 31 of 49)	intron (NM_010844, intron 31 of 49)	19588	NM_010844	17833	Mm.334332	NM_010844	ENSMUSG00000037974	Muc5ac	2210005L13Rik|MGM	mucin 5, subtypes A and C, tracheobronchial/gastric	protein-coding
mm_2869.1	chr1	131750486	131750494	+	1	NA	intron (NM_177243, intron 1 of 20)	intron (NM_177243, intron 1 of 20)	6468	NM_177243	320718	Mm.482704	NM_177243	ENSMUSG00000042268	Slc26a9	E030002L01Rik	solute carrier family 26, member 9	protein-coding
mm_1341.1	chr1	66175237	66175247	+	1	NA	promoter-TSS (NM_008632)	promoter-TSS (NM_008632)	-87	NM_008632	17756	Mm.256966	NM_008632	ENSMUSG00000015222	Map2	G1-397-34|MAP-2|Mtap-2|Mtap2|repro4	microtubule-associated protein 2	protein-coding
mm_48281.1	chr5	138171217	138171246	-	1	NA	promoter-TSS (NM_021392)	promoter-TSS (NM_021392)	631	NM_008568	17220	Mm.378965	NM_008568	ENSMUSG00000029730	Mcm7	AI747533|Mcmd7|mCDC47	minichromosome maintenance complex component 7	protein-coding
mm_32443.1	chr4	107262366	107262423	+	1	NA	intron (NM_028394, intron 1 of 5)	intron (NM_028394, intron 1 of 5)	8460	NM_028394	72938	Mm.21787	NM_028394	ENSMUSG00000063172	Hspb11	2900042B11Rik|IFT25	heat shock protein family B (small), member 11	protein-coding
mm_51495.1	chr6	83078340	83078389	+	1	NA	promoter-TSS (NM_197992)	promoter-TSS (NM_197992)	-26	NM_197992	69837	Mm.12261	NM_197992	ENSMUSG00000069678	Pcgf1	2010002K04Rik|AU024121|Nspc1	polycomb group ring finger 1	protein-coding
mm_39955.1	chr5	32133826	32133838	+	1	NA	Intergenic	Intergenic	-2640	NM_008037	14284	Mm.24684	NM_008037	ENSMUSG00000029135	Fosl2	Fra-2	fos-like antigen 2	protein-coding
mm_28909.1	chr3	98724555	98724577	-	1	NA	promoter-TSS (NM_153193)	promoter-TSS (NM_153193)	-23	NM_153193	15493	Mm.482364	NM_153193	ENSMUSG00000063730	Hsd3b2	-	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 2	protein-coding
mm_40517.1	chr5	57830133	57830142	+	1	NA	intron (NM_001310608, intron 1 of 3)	intron (NM_001310608, intron 1 of 3)	112056	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_55517.1	chr6	70217450	70217452	-	1	NA	Intergenic	Intergenic	574724	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_33930.1	chr4	136889805	136889815	+	1	NA	TTS (NM_007574)	TTS (NM_007574)	3104	NM_007574	12262	Mm.439732	NM_007574	ENSMUSG00000036896	C1qc	AI385742|C1qg|Ciqc	complement component 1, q subcomponent, C chain	protein-coding
mm_70594.1	chr8	13287888	13287929	+	1	NA	promoter-TSS (NM_172282)	promoter-TSS (NM_172282)	-105	NM_172282	234076	Mm.219813	NM_172282	ENSMUSG00000038497	Tmco3	B230339H12Rik|C87304	transmembrane and coiled-coil domains 3	protein-coding
mm_29513.1	chr3	116423751	116423757	-	1	NA	5' UTR (NM_001173553, exon 1 of 14)	5' UTR (NM_001173553, exon 1 of 14)	278	NM_001080818	229776	Mm.17647	NM_001080818	ENSMUSG00000033502	Cdc14a	A830059A17Rik|CDC14A2|CDC14a1|Cdc14	CDC14 cell division cycle 14A	protein-coding
mm_15377.1	chr2	156475804	156475834	+	1	NA	5' UTR (NM_001006664, exon 1 of 22)	5' UTR (NM_001006664, exon 1 of 22)	285	NM_001006664	13821	Mm.20852	NM_013510	ENSMUSG00000027624	Epb41l1	4.1N|Epb4.1l1|NBL1|mKIAA0338	erythrocyte membrane protein band 4.1 like 1	protein-coding
mm_75758.1	chr8	69911674	69911677	-	1	NA	intron (NM_145596, intron 12 of 12)	intron (NM_145596, intron 12 of 12)	-9117	NM_023312	67184	Mm.21162	NM_023312	ENSMUSG00000036199	Ndufa13	2700054G14Rik|AU022060|CDA016|CGI-39|GRIM-19|Grim19	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 13	protein-coding
mm_57458.1	chr6	125170788	125170824	-	1	NA	exon (NM_146171, exon 27 of 32)	exon (NM_146171, exon 27 of 32)	-4339	NM_001289726	14433	Mm.304088	NM_008084	ENSMUSG00000057666	Gapdh	Gapd	glyceraldehyde-3-phosphate dehydrogenase	protein-coding
mm_125517.1	chr15	57694762	57694777	+	1	NA	5' UTR (NM_199449, exon 1 of 4)	5' UTR (NM_199449, exon 1 of 4)	102	NM_199449	387609	Mm.36557	NM_199449	ENSMUSG00000071757	Zhx2	Afr-1|Afr1|Raf|mKIAA0854	zinc fingers and homeoboxes 2	protein-coding
mm_23227.1	chr3	49325677	49325692	+	1	NA	Intergenic	Intergenic	431632	NM_130448	73173	Mm.87246	NM_130448	ENSMUSG00000037892	Pcdh18	3110038E07Rik|BB095589|PCDH68L	protocadherin 18	protein-coding
mm_39380.1	chr5	13125459	13125470	+	1	NA	Intergenic	Intergenic	-271320	NM_001243072	20346	Mm.372039	NM_009152	ENSMUSG00000028883	Sema3a	Hsema-I|SEMA1|SemD|Semad|coll-1	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	protein-coding
mm_66456.1	chr7	44869821	44869831	-	1	NA	promoter-TSS (NM_133949)	promoter-TSS (NM_133949)	-38	NM_133949	84113	Mm.42855	NM_133949	ENSMUSG00000038502	Ptov1	1110030G05Rik|AU041779|Gcap3	prostate tumor over expressed gene 1	protein-coding
mm_111984.1	chr12	110478602	110478626	-	1	NA	intron (NM_001135001, intron 3 of 13)	intron (NM_001135001, intron 3 of 13)	-7125	NM_001081457	26931	Mm.240396	NM_012023	ENSMUSG00000017843	Ppp2r5c	2610043M05Rik|2700063L20Rik|AI060890|AW545884|C85228|D12Bwg0916e|mKIAA0044	protein phosphatase 2, regulatory subunit B', gamma	protein-coding
mm_102568.1	chr11	61494174	61494261	-	1	NA	promoter-TSS (NM_001291037)	promoter-TSS (NM_001291037)	49	NM_001291037	23939	Mm.38172	NM_011841	ENSMUSG00000001034	Mapk7	BMK-1|BMK1|ERK-5|ERK5|Erk5-T|PRKM7	mitogen-activated protein kinase 7	protein-coding
mm_75900.1	chr8	71272339	71272351	-	1	NA	promoter-TSS (NM_001142322)	promoter-TSS (NM_001142322)	245	NM_001163042	76478	Mm.27355	NM_029621	ENSMUSG00000035439	Haus8	2410004L22Rik|Hice1	4HAUS augmin-like complex, subunit 8	protein-coding
mm_125834.1	chr15	74958187	74958197	+	1	NA	intron (NM_001164037, intron 3 of 4)	intron (NM_001164037, intron 3 of 4)	3086	NM_001164040	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_87923.1	chr10	62508099	62508117	+	1	NA	promoter-TSS (NM_011157)	promoter-TSS (NM_011157)	-353	NM_011157	19073	Mm.338790	NM_011157	ENSMUSG00000020077	Srgn	Prg|Prg1|Sgc	serglycin	protein-coding
mm_84348.1	chr9	64253618	64253635	-	1	NA	promoter-TSS (NM_008927)	promoter-TSS (NM_008927)	-21	NM_008927	26395	Mm.248907	NM_008927	ENSMUSG00000004936	Map2k1	MAPKK1|MEKK1|Mek1|Prkmk1	mitogen-activated protein kinase kinase 1	protein-coding
mm_41708.1	chr5	101765193	101765209	+	1	NA	promoter-TSS (NM_173370)	promoter-TSS (NM_173370)	71	NM_173370	74596	Mm.46764	NM_173370	ENSMUSG00000029330	Cds1	4833409J18Rik|AI314024|AW125888	CDP-diacylglycerol synthase 1	protein-coding
mm_69105.1	chr7	127021078	127021135	-	1	NA	5' UTR (NM_001102563, exon 1 of 4)	5' UTR (NM_001102563, exon 1 of 4)	105	NM_001102563	69017	Mm.392047	NM_001102563	ENSMUSG00000045114	Prrt2	1500031I19Rik|AI195361|DSPB3	proline-rich transmembrane protein 2	protein-coding
mm_3765.1	chr1	156303466	156303470	+	1	NA	promoter-TSS (NM_001134741)	promoter-TSS (NM_001134741)	-120	NM_001134741	214575	Mm.252800	NM_001134741	ENSMUSG00000060985	Tdrd5	Gm103	tudor domain containing 5	protein-coding
mm_38434.1	chr4	139352506	139352527	-	1	NA	promoter-TSS (NM_146157)	promoter-TSS (NM_146157)	60	NM_001290810	69902	Mm.27871	NM_023536	ENSMUSG00000028741	Mrto4	2610012O22Rik|Mg684|Mrt4	mRNA turnover 4, ribosome maturation factor	protein-coding
mm_15646.1	chr2	163063220	163063221	+	1	NA	intron (NM_008652, intron 4 of 13)	ID_B1|SINE|B4	-4870	NR_105970	102465607		NR_105970	ENSMUSG00000099091	Mir7003	Gm27340|mmu-mir-7003	microRNA 7003	ncRNA
mm_120705.1	chr14	70978509	70978545	+	1	NA	3' UTR (NM_008115, exon 9 of 9)	3' UTR (NM_008115, exon 9 of 9)	88420	NM_001302094	14586	Mm.32619	NM_008115	ENSMUSG00000022103	Gfra2	-	glial cell line derived neurotrophic factor family receptor alpha 2	protein-coding
mm_91822.1	chr10	56115540	56115547	-	1	NA	exon (NM_001163833, exon 2 of 2)	exon (NM_001163833, exon 2 of 2)	8626	NM_001163833	73390	Mm.181475	NM_133751	ENSMUSG00000047669	Msl3l2	1700060H10Rik	male-specific lethal 3-like 2 (Drosophila)	protein-coding
mm_67924.1	chr7	99865352	99865367	-	1	NA	intron (NM_001164258, intron 2 of 18)	intron (NM_001164258, intron 2 of 18)	6141	NM_001164258	446101	Mm.440757	NM_001164258	ENSMUSG00000035211	Xrra1	AI449753	X-ray radiation resistance associated 1	protein-coding
mm_143196.1	chr17	62649684	62649688	-	1	NA	intron (NM_010109, intron 2 of 3)	intron (NM_010109, intron 2 of 3)	231631	NM_207654	13640	Mm.7978	NM_010109	ENSMUSG00000048915	Efna5	AL-1|AV158822|EFL-5|Ephrin-A5|Epl7|LERK-7|RAGS	ephrin A5	protein-coding
mm_108005.1	chr12	73584323	73584327	+	1	NA	promoter-TSS (NM_008856)	promoter-TSS (NM_008856)	-471	NM_001313977	18755	Mm.341677	NM_008856	ENSMUSG00000021108	Prkch	Pkch	protein kinase C, eta	protein-coding
mm_60473.1	chr7	44478165	44478184	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-6343	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_125267.1	chr15	35531461	35531468	+	1	NA	intron (NM_177151, intron 17 of 61)	MTD|LTR|ERVL-MaLR	129454	NR_035527	100316736		NR_035527	ENSMUSG00000076333	Mir599	mmu-mir-599	microRNA 599	ncRNA
mm_59480.1	chr7	27461694	27461703	+	1	NA	intron (NM_001290525, intron 3 of 4)	intron (NM_001290525, intron 3 of 4)	9280	NM_001290525	233016	Mm.24021	NM_144923	ENSMUSG00000040466	Blvrb	-	biliverdin reductase B (flavin reductase (NADPH))	protein-coding
mm_70422.1	chr8	11476990	11477002	+	1	NA	promoter-TSS (NR_126558)	promoter-TSS (NR_126558)	-933	NR_126558	102132	Mm.37632	NR_126558	ENSMUSG00000096957	E230013L22Rik	AI645545	RIKEN cDNA E230013L22 gene	ncRNA
mm_90994.1	chr10	13966822	13966871	-	1	NA	intron (NM_010437, intron 1 of 8)	CpG-904	467	NM_010437	15273	Mm.42157	NM_010437	ENSMUSG00000015501	Hivep2	Gm20114|MIBP1|Schnurri-2|Shn-2	human immunodeficiency virus type I enhancer binding protein 2	protein-coding
mm_163979.1	chr14	55900241	55900260	-	1	NA	promoter-TSS (NM_001082975)	promoter-TSS (NM_001082975)	-18	NM_001082975	654795	Mm.486218	NM_001082975	ENSMUSG00000022223	Sdr39u1	2310014G06Rik	short chain dehydrogenase/reductase family 39U, member 1	protein-coding
mm_164957.1	chr19	5796835	5796866	-	1	NA	promoter-TSS (NR_144621)	promoter-TSS (NR_144621)	-869	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_31211.1	chr4	43957502	43957527	+	1	NA	promoter-TSS (NM_027450)	promoter-TSS (NM_027450)	-188	NM_027450	384009	Mm.22213	NM_027450	ENSMUSG00000028480	Glipr2	5730414A08Rik|C77180|GAPR-1	GLI pathogenesis-related 2	protein-coding
mm_132215.1	chr16	32630094	32630106	+	1	NA	exon (NM_011638, exon 19 of 19)	exon (NM_011638, exon 19 of 19)	-14543	NM_001110147	51789	Mm.251115	NM_016788	ENSMUSG00000022791	Tnk2	Ack|Ack-1|Ack1|Cdgip|Pyk1	tyrosine kinase, non-receptor, 2	protein-coding
mm_65183.1	chr7	19696450	19696460	-	1	NA	exon (NM_009696, exon 4 of 4)	exon (NM_009696, exon 4 of 4)	1943	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_37510.1	chr4	123892804	123892807	-	1	NA	Intergenic	Intergenic	-12208	NM_019660	56309	Mm.446553	NM_019660	ENSMUSG00000028647	Mycbp	5730488M09Rik|AW552132|AW742590|Amy-1	MYC binding protein	protein-coding
mm_64272.1	chr7	141805710	141805716	+	1	NA	exon (NM_010844, exon 30 of 50)	exon (NM_010844, exon 30 of 50)	16702	NM_010844	17833	Mm.334332	NM_010844	ENSMUSG00000037974	Muc5ac	2210005L13Rik|MGM	mucin 5, subtypes A and C, tracheobronchial/gastric	protein-coding
mm_107289.1	chr12	29938007	29938021	+	1	NA	promoter-TSS (NM_181395)	promoter-TSS (NM_181395)	-22	NM_181395	69675	Mm.251774	NM_181395	ENSMUSG00000020674	Pxdn	2310075M15Rik|C85409|E330004E07|VPO1|mKIAA0230	peroxidasin	protein-coding
mm_159684.1	chr5	11917985	11917985	+	1	NA	promoter-TSS (NM_001177510)	promoter-TSS (NM_001177510)	-58	NM_001177510	545732	Mm.389066	NM_001177510	ENSMUSG00000067848	4933402N22Rik	-	RIKEN cDNA 4933402N22 gene	protein-coding
mm_76647.1	chr8	93123198	93123211	-	1	NA	exon (NM_007954, exon 5 of 13)	exon (NM_007954, exon 5 of 13)	8079	NM_007954	13884	Mm.88078	NM_007954	ENSMUSG00000057400	Ces1c	Ces-N|Ee-1|Ee1|Es-4|Es-N|Es1|Es4|EsN|PESN	carboxylesterase 1C	protein-coding
mm_71183.1	chr8	40862380	40862430	+	1	NA	promoter-TSS (NM_001044740)	promoter-TSS (NM_001044740)	38	NM_001044740	11988	Mm.4676	NM_007514	ENSMUSG00000031596	Slc7a2	20.5|AI158848|Atrc2|CAT-2|Cat2|Tea	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	protein-coding
mm_92601.1	chr10	80104335	80104376	-	1	NA	intron (NR_038088, intron 1 of 4)	intron (NR_038088, intron 1 of 4)	-1653	NM_183426	216161	Mm.262102	NM_183426	ENSMUSG00000035673	Sbno2	BC019206|F730040C21|Sno|Stno	strawberry notch homolog 2 (Drosophila)	protein-coding
mm_169906.1	chr1	65429036	65429036	-	1	NA	Intergenic	L1Md_T|LINE|L1	117779	NM_139270	213527	Mm.294225	NM_139270	ENSMUSG00000025946	Pth2r	Pthr2	parathyroid hormone 2 receptor	protein-coding
mm_170574.1	chr19	53589047	53589049	-	1	NA	Intergenic	Intergenic	-11348	NM_007790	13006	Mm.14910	NM_007790	ENSMUSG00000024974	Smc3	Bamacan|Cspg6|HCAP|Mmip1|SMC-3|SmcD	structural maintenance of chromosomes 3	protein-coding
mm_171253.1	chr3	8022880	8022889	-	1	NA	Intergenic	RLTR44B|LTR|ERVK	-67997	NR_040587	75476	Mm.491752	NR_040587	ENSMUSG00000100010	1700010I02Rik	-	RIKEN cDNA 1700010I02 gene	ncRNA
mm_52415.1	chr6	113392511	113392517	+	1	NA	promoter-TSS (NM_133923)	promoter-TSS (NM_133923)	17	NM_133923	101100	Mm.388573	NM_133923	ENSMUSG00000030276	Ttll3	4833441J24Rik|AI450050	tubulin tyrosine ligase-like family, member 3	protein-coding
mm_73944.1	chr8	120112875	120112900	+	1	NA	Intergenic	Intergenic	-1265	NM_001163762	234797	Mm.101958	NM_172286	ENSMUSG00000031824	6430548M08Rik	AW049007|Kiaa0513|mKIAA0513	RIKEN cDNA 6430548M08 gene	protein-coding
mm_15963.1	chr2	166020293	166020295	+	1	NA	intron (NM_008679, intron 1 of 22)	intron (NM_008679, intron 1 of 22)	27657	NM_008679	17979	Mm.469663	NM_008679	ENSMUSG00000027678	Ncoa3	2010305B15Rik|AW321064|Actr|Aib1|KAT13B|Rac3|Src3|Tram-1|Tram1|bHLHe42|p/Cip|pCip	nuclear receptor coactivator 3	protein-coding
mm_126997.1	chr15	95654471	95654481	+	1	NA	exon (NM_207533, exon 1 of 4)	exon (NM_207533, exon 1 of 4)	295	NM_207533	223843	Mm.152937	NM_207533	ENSMUSG00000045608	Dbx2	9430056A22Rik|9630005K15|AI846217|Gm1229	developing brain homeobox 2	protein-coding
mm_163608.1	chr13	49223304	49223305	+	1	NA	Intergenic	Intergenic	-7278	NM_026738	68480	Mm.3336	NM_026738	ENSMUSG00000037960	Card19	1110007C09Rik|AI851695|Bincard	caspase recruitment domain family, member 19	protein-coding
mm_20960.1	chr2	151751414	151751418	-	1	NA	promoter-TSS (NR_138568)	promoter-TSS (NR_138568)	49	NR_138568	75283	Mm.195735	NM_029235		4930556L07Rik	1700020P01Rik|4930593I08Rik	RIKEN cDNA 4930556L07 gene	ncRNA
mm_6801.1	chr1	84151304	84151332	-	1	NA	intron (NM_001003948, intron 2 of 2)	L1MA5|LINE|L1	67643	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_43129.1	chr5	125303304	125303314	+	1	NA	intron (NM_001205083, intron 2 of 10)	intron (NM_001205083, intron 2 of 10)	37785	NM_016741	20778	Mm.282242	NM_016741	ENSMUSG00000037936	Scarb1	AI120173|CD36|Cd36l1|Chohd1|Cla-1|Cla1|D5Ertd460e|Hdlq1|Hlb398|SR-B1|SR-BI|SRBI|Srb1|mSR-BI	scavenger receptor class B, member 1	protein-coding
mm_75639.1	chr8	64849878	64849888	-	1	NA	promoter-TSS (NM_178633)	promoter-TSS (NM_178633)	41	NM_178633	77113	Mm.350347	NM_178633	ENSMUSG00000031605	Klhl2	6030411N21Rik|ABP-KELCH|AU020744|Mav	kelch-like 2, Mayven	protein-coding
mm_137757.1	chr17	29472999	29473032	+	1	NA	Intergenic	MTC|LTR|ERVL-MaLR	-18030	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_104264.1	chr11	88966937	88966944	-	1	NA	promoter-TSS (NR_003564)	promoter-TSS (NR_003564)	-23	NR_003564	217066	Mm.347543	NM_001025564	ENSMUSG00000057534	Gm15698	OTTMUSG00000001305|OTTMUSG00000025408	transcription elongation factor B (SIII), polypeptide 2 pseudogene	pseudo
mm_70165.1	chr7	143600050	143600078	-	1	NA	promoter-TSS (NM_001252593)	promoter-TSS (NM_001252593)	26	NM_001252593	27267	Mm.125659	NM_013742	ENSMUSG00000010755	Cars	CA3	cysteinyl-tRNA synthetase	protein-coding
mm_172343.1	chr7	11108249	11108251	-	1	NA	Intergenic	Intergenic	57898	NM_001100186	545913	Mm.380086	NM_001100186	ENSMUSG00000090714	Zscan4d	EG545913	zinc finger and SCAN domain containing 4D	protein-coding
mm_105921.1	chr11	115048329	115048371	-	1	NA	promoter-TSS (NM_199201)	promoter-TSS (NM_199201)	-55	NM_199201	382551	Mm.424732	NM_199201	ENSMUSG00000069607	Cd300ld3	AY457049|Cd300lh|Clm3|Lmir7|clm-3	CD300 molecule like family member D3	protein-coding
mm_9630.1	chr1	176814015	176814025	-	1	NA	promoter-TSS (NM_029756)	promoter-TSS (NM_029756)	-640	NM_029756	76816	Mm.171399	NM_029756	ENSMUSG00000026504	Sdccag8	2700048G21Rik|5730470G24Rik|Cccap	serologically defined colon cancer antigen 8	protein-coding
mm_75714.1	chr8	68905733	68905746	-	1	NA	3' UTR (NM_008509, exon 10 of 10)	3' UTR (NM_008509, exon 10 of 10)	25184	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_39267.1	chr5	3596205	3596256	+	1	NA	5' UTR (NM_172991, exon 1 of 5)	5' UTR (NM_172991, exon 1 of 5)	164	NM_001293806	71382	Mm.379196	NM_027777	ENSMUSG00000005907	Pex1	5430414H02Rik|E330005K07Rik|ZWS1	peroxisomal biogenesis factor 1	protein-coding
mm_132371.1	chr16	34819608	34819608	+	1	NA	intron (NM_139300, intron 2 of 31)	intron (NM_139300, intron 2 of 31)	34658	NM_139300	107589	Mm.33360	NM_139300	ENSMUSG00000022836	Mylk	9530072E15Rik|A930019C19Rik|AW489456|KRP|MLCK108|MLCK210|Mlck|nmMlck|smMLCK	myosin, light polypeptide kinase	protein-coding
mm_9013.1	chr1	166049290	166049299	-	1	NA	Intergenic	Intergenic	-46660	NM_011137	18986	Mm.245261	NM_011137	ENSMUSG00000026565	Pou2f1	2810482H01Rik|NF-A1|Oct-1|Oct1|Otf-1|Otf1	POU domain, class 2, transcription factor 1	protein-coding
mm_103845.1	chr11	83066802	83066823	-	1	NA	intron (NM_011408, intron 1 of 1)	intron (NM_011408, intron 1 of 1)	1700	NM_011408	20556	Mm.278689	NM_011408	ENSMUSG00000072620	Slfn2	Shlf2	schlafen 2	protein-coding
mm_99476.1	chr11	102604371	102604435	+	1	NA	promoter-TSS (NM_020510)	promoter-TSS (NM_020510)	-28	NM_020510	57265	Mm.36416	NM_020510	ENSMUSG00000050288	Fzd2	AL033370|AW456835|Fz10|Fzd10|Mfz10|Mfz10a	frizzled class receptor 2	protein-coding
mm_141126.1	chr17	26199031	26199045	-	1	NA	promoter-TSS (NM_001081070)	promoter-TSS (NM_001081070)	49	NM_001081070	69191	Mm.32631	NM_001081070	ENSMUSG00000024184	Pdia2	1810041F13Rik|AI661267|Pdip|Pdipl	protein disulfide isomerase associated 2	protein-coding
mm_107232.1	chr12	26478142	26478159	+	1	NA	3' UTR (NM_020557, exon 5 of 5)	3' UTR (NM_020557, exon 5 of 5)	8935	NM_020557	22169	Mm.271839	NM_020557	ENSMUSG00000020638	Cmpk2	1200004E04Rik|TDKI|Tyki	cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial	protein-coding
mm_115120.1	chr13	104229367	104229386	+	1	NA	promoter-TSS (NM_021790)	promoter-TSS (NM_021790)	-12	NM_021790	60411	Mm.281498	NM_021790	ENSMUSG00000021714	Cenpk	B130045K24Rik|BB232189|C530004N04Rik|Cenp-K|Solt|Solzt	centromere protein K	protein-coding
mm_132490.1	chr16	36931364	36931390	+	1	NA	intron (NM_030035, intron 20 of 21)	intron (NM_030035, intron 20 of 21)	-3606	NM_008225	15163	Mm.4091	NM_008225	ENSMUSG00000022831	Hcls1	AW213261|HS1	hematopoietic cell specific Lyn substrate 1	protein-coding
mm_52807.1	chr6	121342870	121342880	+	1	NA	promoter-TSS (NM_001347433)	promoter-TSS (NM_001347433)	-201	NM_001347433	14411	Mm.274506	NM_133661	ENSMUSG00000030109	Slc6a12	BGT1|GAT-2|GAT2|Gabt2	solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12	protein-coding
mm_121816.1	chr14	20397349	20397358	-	1	NA	intron (NM_029698, intron 25 of 28)	intron (NM_029698, intron 25 of 28)	-3798	NM_025440	66242	Mm.23747	NM_025440	ENSMUSG00000049960	Mrps16	1500011E11Rik|Mprs16	mitochondrial ribosomal protein S16	protein-coding
mm_2931.1	chr1	132298571	132298600	+	1	NA	promoter-TSS (NM_144810)	promoter-TSS (NM_144810)	-41	NM_144810	213417	Mm.39723	NM_144810	ENSMUSG00000042115	Klhdc8a	A630065K24Rik	kelch domain containing 8A	protein-coding
mm_81472.1	chr9	109931576	109931578	+	1	NA	promoter-TSS (NM_008633)	promoter-TSS (NM_008633)	-197	NM_001205331	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_73768.1	chr8	115830514	115830524	+	1	NA	Intergenic	Intergenic	-123625	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_74756.1	chr8	19141472	19141518	-	1	NA	exon (NM_001034905, exon 2 of 2)	exon (NM_001034905, exon 2 of 2)	736	NM_001286493	546038	Mm.99206	NM_001034905	ENSMUSG00000059463	Spag11b	EG546038|Ep2c/h|Spag11c/h	sperm associated antigen 11B	protein-coding
mm_111351.1	chr12	86950452	86950456	-	1	NA	intron (NM_001289432, intron 1 of 4)	intron (NM_001289432, intron 1 of 4)	3111	NM_001289432	217732	Mm.22337	NM_173735	ENSMUSG00000034157	Cipc	2310044G17Rik|AI842544|AI853744|Kiaa1737|mKIAA1737	CLOCK interacting protein, circadian	protein-coding
mm_69299.1	chr7	128298082	128298138	-	1	NA	promoter-TSS (NM_145590)	promoter-TSS (NM_145590)	21	NM_145590	233913	Mm.220880	NM_145590	ENSMUSG00000030780	BC017158	-	cDNA sequence BC017158	protein-coding
mm_118530.1	chr14	15358178	15358178	+	1	NA	exon (NM_146052, exon 2 of 2)	exon (NM_146052, exon 2 of 2)	80809	NM_146052	218763	Mm.138039	NM_146052	ENSMUSG00000045201	Lrrc3b	BC019794|LRP15	leucine rich repeat containing 3B	protein-coding
mm_65954.1	chr7	30428514	30428519	-	1	NA	3' UTR (NM_172142, exon 11 of 11)	3' UTR (NM_172142, exon 11 of 11)	5212	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_24820.1	chr3	95645655	95645663	+	1	NA	Intergenic	Intergenic	-13062	NM_008562	17210	Mm.1639	NM_008562	ENSMUSG00000038612	Mcl1	AW556805|Mcl-1	myeloid cell leukemia sequence 1	protein-coding
mm_64623.1	chr7	3667191	3667240	-	1	NA	intron (NM_181820, intron 11 of 14)	intron (NM_181820, intron 11 of 14)	-1375	NM_027203	69757	Mm.389782	NM_027203	ENSMUSG00000078813	Leng1	1500001K17Rik	leukocyte receptor cluster (LRC) member 1	protein-coding
mm_82022.1	chr9	121760001	121760061	+	1	NA	promoter-TSS (NM_001166644)	promoter-TSS (NM_001166644)	-2	NM_001166644	270210	Mm.473702	NM_001166644	ENSMUSG00000013419	Zfp651	4732420M22Rik|BC030045|R74626	zinc finger protein 651	protein-coding
mm_30912.1	chr4	32527091	32527113	+	1	NA	intron (NM_001109661, intron 2 of 4)	intron (NM_001109661, intron 2 of 4)	44560	NR_026843	414068	Mm.389550	NR_026843	ENSMUSG00000086150	Bach2os	-	BTB and CNC homology 2, opposite strand	ncRNA
mm_33562.1	chr4	131876064	131876092	+	1	NA	intron (NM_020587, intron 1 of 5)	B3|SINE|B2	2439	NM_020587	57317	Mm.2478	NM_020587	ENSMUSG00000028911	Srsf4	5730499P16Rik|AW550192|MNCb-2616|SRp75|Sfrs4	serine/arginine-rich splicing factor 4	protein-coding
mm_75691.1	chr8	68206062	68206083	-	1	NA	Intergenic	Intergenic	-70456	NM_028182	72281	Mm.40974	NM_028182	ENSMUSG00000053886	Sh2d4a	2210402M20Rik|SH2A	SH2 domain containing 4A	protein-coding
mm_98369.1	chr11	94044101	94044105	+	1	NA	promoter-TSS (NM_001199205)	promoter-TSS (NM_001199205)	-102	NM_001025430	70834	Mm.260737	NM_027569	ENSMUSG00000020859	Spag9	3110018C07Rik|4733401I23Rik|4831406C20Rik|AW552012|JLP|JSAP2|JSAP2a|Jip4|Mapk8ip4|syd1	sperm associated antigen 9	protein-coding
mm_170009.1	chr17	17005210	17005224	+	1	NA	Intergenic	Intergenic	-58886	NM_001005358	449000	Mm.483718	NM_001005358	ENSMUSG00000096696	Zfp960	-	zinc finger protein 960	protein-coding
mm_8912.1	chr1	163313142	163313152	-	1	NA	5' UTR (NM_175686, exon 1 of 5)	5' UTR (NM_175686, exon 1 of 5)	503	NM_011127	18933	Mm.288642	NM_011127	ENSMUSG00000026586	Prrx1	A230024N07Rik|AA755424|AI385634|AI843499|K-2|Pmx|Pmx1|Prx1|mHox	paired related homeobox 1	protein-coding
mm_147093.1	chr18	35649313	35649328	-	1	NA	promoter-TSS (NM_027222)	promoter-TSS (NM_027222)	47	NM_027222	69816	Mm.27252	NM_027222	ENSMUSG00000024353	Mzb1	2010001M09Rik|AV064572|PACAP|pERp1	marginal zone B and B1 cell-specific protein 1	protein-coding
mm_75935.1	chr8	71537403	71537468	-	1	NA	promoter-TSS (NM_198095)	promoter-TSS (NM_198095)	2	NM_198095	69550	Mm.260325	NM_198095	ENSMUSG00000046718	Bst2	2310015I10Rik|Bst-2|C87040|CD317|DAMP-1|GREG	bone marrow stromal cell antigen 2	protein-coding
mm_161442.1	chr15	73055880	73055880	-	1	NA	promoter-TSS (NM_029640)	promoter-TSS (NM_029640)	-68	NM_029640	76510	Mm.158902	NM_029640	ENSMUSG00000047921	Trappc9	1810044A24Rik|2900005P22Rik|4632408O18Rik|Ibp|Nibp|TRS130|mKIAA1882	trafficking protein particle complex 9	protein-coding
mm_147721.1	chr18	60844139	60844153	-	1	NA	intron (NM_001198984, intron 2 of 25)	intron (NM_001198984, intron 2 of 25)	4818	NM_011552	21453	Mm.486251	NM_011552	ENSMUSG00000024613	Tcof1	AA408847|AW209012|treacle	treacle ribosome biogenesis factor 1	protein-coding
mm_121290.1	chr14	105258799	105258816	+	1	NA	exon (NM_029561, exon 1 of 8)	exon (NM_029561, exon 1 of 8)	134	NM_001190989	76273	Mm.290669	NM_029561	ENSMUSG00000053253	Ndfip2	0710001O20Rik|2810436B12Rik|9130207N19Rik|N4wbp5a|mKIAA1165	Nedd4 family interacting protein 2	protein-coding
mm_144984.1	chr18	38244790	38244798	+	1	NA	intron (NR_015475, intron 1 of 3)	intron (NR_015475, intron 1 of 3)	5404	NR_015475	73516	Mm.48776	NR_015475	ENSMUSG00000097080	1700086O06Rik	-	RIKEN cDNA 1700086O06 gene	ncRNA
mm_31580.1	chr4	57742077	57742086	+	1	NA	intron (NM_001304544, intron 5 of 8)	intron (NM_001304544, intron 5 of 8)	-103167	NM_009649	11641	Mm.467752	NM_009649	ENSMUSG00000038729	Akap2	AA959716|AI649048|Akap-2|Akap-kl|B230340M18Rik|Prka2	A kinase (PRKA) anchor protein 2	protein-coding
mm_76150.1	chr8	82353453	82353480	-	1	NA	intron (NM_008357, intron 2 of 7)	intron (NM_008357, intron 2 of 7)	49120	NM_001254747	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_96060.1	chr11	59566417	59566427	+	1	NA	3' UTR (NM_145827, exon 10 of 10)	3' UTR (NM_145827, exon 10 of 10)	5316	NM_001011789	257962	Mm.377316	NM_001011789	ENSMUSG00000059610	Olfr222	MOR256-45P	olfactory receptor 222	protein-coding
mm_160938.1	chr11	94510158	94510158	-	1	NA	intron (NM_170671, intron 7 of 18)	intron (NM_170671, intron 7 of 18)	-10184	NM_027984	71889	Mm.248620	NM_027984	ENSMUSG00000010080	Epn3	2310022G12Rik	epsin 3	protein-coding
mm_44616.1	chr5	25529512	25529524	-	1	NA	promoter-TSS (NR_027388)	promoter-TSS (NR_027388)	-500	NR_027388	73571	Mm.105263	NR_027388	ENSMUSG00000101856	1700096K18Rik	-	RIKEN cDNA 1700096K18 gene	ncRNA
mm_59179.1	chr7	24460150	24460159	+	1	NA	Intergenic	RMER5|LTR|ERV1	-2329	NM_011113	18793	Mm.1359	NM_011113	ENSMUSG00000046223	Plaur	Cd87|u-PAR|uPAR	plasminogen activator, urokinase receptor	protein-coding
mm_40311.1	chr5	43854369	43854398	+	1	NA	Intergenic	Intergenic	-14426	NM_007646	12494	Mm.249873	NM_007646	ENSMUSG00000029084	Cd38	ADPRC 1|Cd38-rs1|I-19	CD38 antigen	protein-coding
mm_55460.1	chr6	67533660	67533663	-	1	NA	TTS (NM_020047)	TTS (NM_020047)	2161	NM_020047	56753	Mm.439913	NM_020047	ENSMUSG00000051397	Tacstd2	C80403|EGP-1|GA733-1|Ly97|TROP2	tumor-associated calcium signal transducer 2	protein-coding
mm_18428.1	chr2	60763281	60763293	-	1	NA	exon (NM_001141932, exon 7 of 15)	exon (NM_001141932, exon 7 of 15)	-40684	NM_001159564	16420	Mm.98193	NM_021359	ENSMUSG00000026971	Itgb6	2210409C20Rik|4831415H04Rik	integrin beta 6	protein-coding
mm_124525.1	chr14	122229205	122229212	-	1	NA	TTS (NR_015532)	TTS (NR_015532)	4430	NR_015532	68245	Mm.443285	NR_015532	ENSMUSG00000100585	1700108J01Rik	-	RIKEN cDNA 1700108J01 gene	ncRNA
mm_32540.1	chr4	109280267	109280315	+	1	NA	promoter-TSS (NM_007943)	promoter-TSS (NM_007943)	16	NM_007943	13858	Mm.318250	NM_007943	ENSMUSG00000028552	Eps15	2410112D09Rik	epidermal growth factor receptor pathway substrate 15	protein-coding
mm_149733.1	chr19	21937298	21937312	+	1	NA	Intergenic	Intergenic	158965	NM_031997	83921	Mm.329776	NM_031997	ENSMUSG00000024754	Tmem2	-	transmembrane protein 2	protein-coding
mm_11766.1	chr2	38536606	38536616	+	1	NA	intron (NM_001159631, intron 1 of 9)	intron (NM_001159631, intron 1 of 9)	24735	NM_001159631	59126	Mm.143818	NM_021606	ENSMUSG00000026749	Nek6	1300007C09Rik	NIMA (never in mitosis gene a)-related expressed kinase 6	protein-coding
mm_119429.1	chr14	45573537	45573538	+	1	NA	Intergenic	Intergenic	29827	NR_045809	67651	Mm.55930	NR_045809		4930527F14Rik	-	RIKEN cDNA 4930527F14 gene	ncRNA
mm_173122.1	chrX	16299357	16299360	-	1	NA	Intergenic	RLTR13D3A|LTR|ERVK	-223511	NM_001310461	66742	Mm.45302	NM_025738	ENSMUSG00000023257	Cypt1	4931420D14Rik|Ckt1r3|Cypt5|Cypt6|TISP55	cysteine-rich perinuclear theca 1	protein-coding
mm_47952.1	chr5	135527717	135527729	-	1	NA	intron (NM_146001, intron 1 of 30)	intron (NM_146001, intron 1 of 30)	17399	NM_146001	215114	Mm.280805	NM_146001	ENSMUSG00000039959	Hip1	2610109B09Rik|A930014B11Rik|E130315I21Rik|mKIAA4113	huntingtin interacting protein 1	protein-coding
mm_54331.1	chr6	30640717	30640741	-	1	NA	exon (NM_025350, exon 3 of 10)	exon (NM_025350, exon 3 of 10)	1511	NM_025350	109697	Mm.25377	NM_025350	ENSMUSG00000054446	Cpa1	0910001L12Rik|Cpa	carboxypeptidase A1, pancreatic	protein-coding
mm_127703.1	chr15	102990995	102991000	+	1	NA	exon (NM_010466, exon 1 of 2)	exon (NM_010466, exon 1 of 2)	458	NM_010466	15426	Mm.6167	NM_010466	ENSMUSG00000001657	Hoxc8	D130011F21Rik|Hox-3.1	homeobox C8	protein-coding
mm_153936.1	chr19	47460759	47460767	-	1	NA	intron (NM_001164717, intron 1 of 13)	intron (NM_001164717, intron 1 of 13)	3648	NM_001164717	14218	Mm.127560	NM_008018	ENSMUSG00000053617	Sh3pxd2a	2310014D11Rik|AA589508|AI256723|AI413738|C230050L11|EG329070|Fish|Gm5098|Sh3md1|TSK5|Tks5	SH3 and PX domains 2A	protein-coding
mm_121166.1	chr14	103012932	103012967	+	1	NA	intron (NR_045657, intron 2 of 2)	intron (NR_045657, intron 2 of 2)	20854	NR_045657	71264	Mm.399572	NR_045657		4933432I03Rik	-	RIKEN cDNA 4933432I03 gene	ncRNA
mm_157404.1	chrX	38435165	38435179	-	1	NA	intron (NM_010685, intron 4 of 8)	intron (NM_010685, intron 4 of 8)	21288	NM_010685	16784	Mm.486	NM_010685	ENSMUSG00000016534	Lamp2	CD107b|LGP-B|Lamp II|Lamp-2|Lamp-2a|Lamp-2b|Lamp-2c|Mac3	lysosomal-associated membrane protein 2	protein-coding
mm_79937.1	chr9	65896434	65896468	+	1	NA	intron (NM_026515, intron 3 of 3)	intron (NM_026515, intron 3 of 3)	6128	NM_026515	68026	Mm.351273	NM_026515	ENSMUSG00000040204	Pclaf	2810417H13Rik|AA409629|Ns5apt9|Ns5atp9|PAF15|Paf|mKIAA0101|p15(PAF)	PCNA clamp associated factor	protein-coding
mm_172523.1	chr7	83755820	83755830	+	1	NA	Intergenic	Intergenic	-20335	NM_010551	16170	Mm.10137	NM_010551	ENSMUSG00000001741	Il16	mKIAA4048	interleukin 16	protein-coding
mm_89286.1	chr10	87880944	87880956	+	1	NA	intron (NM_001314010, intron 3 of 4)	intron (NM_001314010, intron 3 of 4)	19839	NM_001111276	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_68437.1	chr7	109960208	109960218	-	1	NA	5' UTR (NM_021494, exon 1 of 23)	5' UTR (NM_021494, exon 1 of 23)	209	NM_021494	19347	Mm.21904	NM_021494	ENSMUSG00000035901	Dennd5a	1500012B19Rik|AJ245569|AW496491|ORF37|Rab6ip1|mKIAA1091	DENN/MADD domain containing 5A	protein-coding
mm_152805.1	chr19	21942395	21942399	-	1	NA	Intergenic	Intergenic	164057	NM_031997	83921	Mm.329776	NM_031997	ENSMUSG00000024754	Tmem2	-	transmembrane protein 2	protein-coding
mm_99887.1	chr11	109472237	109472247	+	1	NA	intron (NM_001029842, intron 1 of 5)	intron (NM_001029842, intron 1 of 5)	987	NM_134038	104681	Mm.265874	NM_134038	ENSMUSG00000041920	Slc16a6	AW743111|ESTM12|MCT 6|MCT 7|MCT6	solute carrier family 16 (monocarboxylic acid transporters), member 6	protein-coding
mm_73642.1	chr8	110754990	110755004	+	1	NA	intron (NM_029646, intron 2 of 7)	intron (NM_029646, intron 2 of 7)	29271	NM_001310591	244654	Mm.490385	NM_198625	ENSMUSG00000033763	Mtss1l	ABBA	metastasis suppressor 1-like	protein-coding
mm_92757.1	chr10	81037301	81037339	-	1	NA	Intergenic	Intergenic	-3408	NM_134135	106947	Mm.5353	NM_134135	ENSMUSG00000046822	Slc39a3	AI845814|Zip3	solute carrier family 39 (zinc transporter), member 3	protein-coding
mm_108845.1	chr12	98268657	98268677	+	1	NA	promoter-TSS (NM_008152)	promoter-TSS (NM_008152)	32	NM_008152	14744	Mm.378924	NM_008152	ENSMUSG00000021886	Gpr65	Dig1|Gpcr25|TDAG8	G-protein coupled receptor 65	protein-coding
mm_113333.1	chr13	31625680	31625727	+	1	NA	promoter-TSS (NM_010225)	promoter-TSS (NM_010225)	-113	NM_010225	14238	Mm.125548	NM_010225	ENSMUSG00000038402	Foxf2	FREAC2|Fkh20|LUN	forkhead box F2	protein-coding
mm_40586.1	chr5	64160208	64160220	+	1	NA	promoter-TSS (NM_019636)	promoter-TSS (NM_019636)	-46	NM_019636	57915	Mm.286353	NM_019636	ENSMUSG00000029174	Tbc1d1	1110062G02Rik|AI385682|AW555803|Nob1|Nobq1|Tbc1|mKIAA1108	TBC1 domain family, member 1	protein-coding
mm_164923.1	chr18	77415586	77415598	+	1	NA	intron (NM_172834, intron 35 of 38)	(CAGT)n|Simple_repeat|Simple_repeat	133634	NM_172834	240411	Mm.380247	NM_172834	ENSMUSG00000032818	Loxhd1	1700096C21Rik|4932417K07|sba	lipoxygenase homology domains 1	protein-coding
mm_107784.1	chr12	61528679	61528683	+	1	NA	intron (NM_178714, intron 1 of 3)	intron (NM_178714, intron 1 of 3)	5514	NM_001310586	238205	Mm.28802	NM_178714	ENSMUSG00000035653	Lrfn5	AI427653|AI604817|C130061B21|mKIAA4208	leucine rich repeat and fibronectin type III domain containing 5	protein-coding
mm_89274.1	chr10	87861007	87861031	+	1	NA	promoter-TSS (NM_001111276)	promoter-TSS (NM_001111276)	-92	NM_001111274	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_12813.1	chr2	80315517	80315528	+	1	NA	promoter-TSS (NM_024181)	promoter-TSS (NM_024181)	56	NM_024181	66861	Mm.21762	NM_024181	ENSMUSG00000027006	Dnajc10	1200006L06Rik|D2Ertd706e|ERdj5|JPDI	DnaJ heat shock protein family (Hsp40) member C10	protein-coding
mm_68454.1	chr7	110120327	110120332	-	1	NA	Intergenic	Intergenic	-1730	NM_009516	22390	Mm.287173	NM_009516	ENSMUSG00000031016	Wee1	Wee1A	WEE 1 homolog 1 (S. pombe)	protein-coding
mm_123674.1	chr14	69472830	69472850	-	1	NA	Intergenic	B2_Mm2|SINE|B2	39709	NM_173420	239167	Mm.259889	NM_173420	ENSMUSG00000047977	Synb	D930020E02Rik|syncytin-B	syncytin b	protein-coding
mm_170233.1	chr17	84355358	84355364	+	1	NA	intron (NM_183021, intron 26 of 37)	ERVB3_1-LTR_MM|LTR|ERVK	110847	NM_183021	240174	Mm.246767	NM_177826	ENSMUSG00000024251	Thada	6530405K19|A930021O22|AU019899|BC052885|GITA	thyroid adenoma associated	protein-coding
mm_119384.1	chr14	41136432	41136442	+	1	NA	TTS (NM_023134)	TTS (NM_023134)	4649	NM_023134	20387	Mm.46062	NM_023134	ENSMUSG00000021789	Sftpa1	SP-A|Sftp-1|Sftp1	surfactant associated protein A1	protein-coding
mm_164212.1	chr15	82508563	82508570	+	1	NA	Intergenic	RMER17A|LTR|ERVK	-46532	NM_201360	380997	Mm.482248	NM_201360	ENSMUSG00000096852	Cyp2d12	9030605E09Rik	cytochrome P450, family 2, subfamily d, polypeptide 12	protein-coding
mm_99508.1	chr11	103056879	103056891	+	1	NA	intron (NM_008707, intron 6 of 11)	intron (NM_008707, intron 6 of 11)	28323	NM_008707	18107	Mm.10265	NM_008707	ENSMUSG00000020936	Nmt1	AW536594	N-myristoyltransferase 1	protein-coding
mm_7191.1	chr1	92908120	92908130	-	1	NA	TTS (NR_138577)	TTS (NR_138577)	1136	NM_175118	67446	Mm.46179	NM_175118	ENSMUSG00000047067	Dusp28	0710001B24Rik|AV005521	dual specificity phosphatase 28	protein-coding
mm_69682.1	chr7	139988506	139988518	-	1	NA	exon (NM_001291066, exon 9 of 24)	exon (NM_001291066, exon 9 of 24)	-1638	NR_106029	102465643		NR_106029	ENSMUSG00000099092	Mir7062	Gm27339|mmu-mir-7062	microRNA 7062	ncRNA
mm_132407.1	chr16	35022395	35022440	+	1	NA	promoter-TSS (NM_023587)	promoter-TSS (NM_023587)	-4	NM_023587	70757	Mm.27286	NM_023587	ENSMUSG00000035376	Hacd2	6330408J20Rik|AI255777|AI481689|Hcad2|Ptplb	3-hydroxyacyl-CoA dehydratase 2	protein-coding
mm_170313.1	chr18	36560900	36560905	+	1	NA	exon (NM_175375, exon 1 of 34)	exon (NM_175375, exon 1 of 34)	299	NM_175375	108857	Mm.482287	NM_175375	ENSMUSG00000024483	Ankhd1	1110004O12Rik|4933432B13Rik|9130019P20Rik|A530027J04Rik|A630021B20Rik|AA571404|Mask|mFLJ00246|mKIAA1085	ankyrin repeat and KH domain containing 1	protein-coding
mm_43136.1	chr5	125389487	125389493	+	1	NA	intron (NM_019639, intron 1 of 1)	CpG	527	NM_019639	22190	Mm.331	NM_019639	ENSMUSG00000008348	Ubc	2700054O04Rik|AI194771|Rps27a|TI-225|Uba52|Ubb	ubiquitin C	protein-coding
mm_61669.1	chr7	80781555	80781563	+	1	NA	intron (NM_016721, intron 2 of 37)	intron (NM_016721, intron 2 of 37)	21772	NM_016721	29875	Mm.207619	NM_016721	ENSMUSG00000030536	Iqgap1	AA682088|D7Ertd237e|D7Ertd257e|mKIAA0051	IQ motif containing GTPase activating protein 1	protein-coding
mm_61191.1	chr7	63896478	63896499	+	1	NA	intron (NM_021366, intron 1 of 1)	intron (NM_021366, intron 1 of 1)	-20369	NM_001256311	381994	Mm.425466	NM_001256311	ENSMUSG00000095061	E030018B13Rik	Gm1697	RIKEN cDNA E030018B13 gene	protein-coding
mm_12283.1	chr2	69008443	69008455	+	1	NA	intron (NM_172856, intron 4 of 9)	intron (NM_172856, intron 4 of 9)	-127351	NM_181547	329416	Mm.90047	NM_181547	ENSMUSG00000034738	Nostrin	Daip2|mDaIP2	nitric oxide synthase trafficker	protein-coding
mm_171114.1	chr3	13826269	13826284	-	1	NA	intron (NM_178631, intron 3 of 9)	IAPLTR1_Mm|LTR|ERVK	-120096	NM_001163329	76897	Mm.422625	NM_178631	ENSMUSG00000039717	Ralyl	0710005M24Rik	RALY RNA binding protein-like	protein-coding
mm_122895.1	chr14	54949954	54949966	-	1	NA	promoter-TSS (NR_029724)	promoter-TSS (NR_029724)	-818	NR_029724	387204		NR_029724	ENSMUSG00000065432	Mir208a	Mirn208|Mirn208a|mir-208|mir-208a|mmu-mir-208	microRNA 208a	ncRNA
mm_10602.1	chr2	18698999	18699018	+	1	NA	promoter-TSS (NM_001001334)	promoter-TSS (NM_001001334)	-14	NM_001001334	381350	Mm.330024	NM_001001334	ENSMUSG00000037708	Spag6	Spag6l	sperm associated antigen 6	protein-coding
mm_34484.1	chr4	148511475	148511500	+	1	NA	intron (NM_020009, intron 28 of 57)	intron (NM_020009, intron 28 of 57)	-11025	NM_001039554	654812	Mm.388929	NM_001039554	ENSMUSG00000028989	Angptl7	-	angiopoietin-like 7	protein-coding
mm_130644.1	chr15	100599963	100599979	-	1	NA	promoter-TSS (NM_001304965)	promoter-TSS (NM_001304965)	13	NM_001304965	19009	Mm.28825	NM_010127	ENSMUSG00000009739	Pou6f1	2310038G18Rik|C79593|Emb|cns-1	POU domain, class 6, transcription factor 1	protein-coding
mm_35405.1	chr4	34730158	34730232	-	1	NA	promoter-TSS (NM_027041)	promoter-TSS (NM_027041)	11	NM_027041	69329	Mm.389548	NM_027041	ENSMUSG00000028294	Cfap206	1700003M02Rik|AU024269	cilia and flagella associated protein 206	protein-coding
mm_17083.1	chr2	22953535	22953567	-	1	NA	exon (NM_001077190, exon 8 of 11)	exon (NM_001077190, exon 8 of 11)	58029	NM_019501	56075	Mm.249752	NM_019501	ENSMUSG00000026784	Pdss1	2610203G20Rik|2700031G06Rik|TPT|TPT 1|Tprt|mDLP1|mSPS1	prenyl (solanesyl) diphosphate synthase, subunit 1	protein-coding
mm_9801.1	chr1	181860709	181860752	-	1	NA	Intergenic	Intergenic	-18329	NM_133815	98386	Mm.4538	NM_133815	ENSMUSG00000004880	Lbr	AI505894|ic	lamin B receptor	protein-coding
mm_136585.1	chr17	4994287	4994373	+	1	NA	promoter-TSS (NM_001085355)	promoter-TSS (NM_001085355)	-744	NM_001085355	239985	Mm.133401	NM_001085355	ENSMUSG00000069729	Arid1b	8030481M12|9330189K18Rik|AI836955|Ardi1b|B230217J03Rik|mKIAA1235	AT rich interactive domain 1B (SWI-like)	protein-coding
mm_9564.1	chr1	173977287	173977302	-	1	NA	exon (NM_011940, exon 2 of 7)	exon (NM_011940, exon 2 of 7)	5550	NM_008327	26388	Mm.218770	NM_008327	ENSMUSG00000026535	Ifi202b	Ifbip-1|Ifi202|Ifi202a|p202	interferon activated gene 202B	protein-coding
mm_95020.1	chr11	32001655	32001678	+	1	NA	intron (NM_001290681, intron 1 of 4)	intron (NM_001290681, intron 1 of 4)	389	NM_001290681	18197	Mm.3304	NM_008741	ENSMUSG00000020297	Nsg2	-	neuron specific gene family member 2	protein-coding
mm_171342.1	chr4	103563901	103563902	+	1	NA	Intergenic	Intergenic	181401	NR_040673	622167	Mm.244115	NR_040673	ENSMUSG00000086136	Gm12718	OTTMUSG00000008109	predicted gene 12718	ncRNA
mm_166448.1	chr5	137268549	137268578	-	1	NA	Intergenic	Intergenic	-19691	NM_009599	11423	Mm.255464	NM_009599	ENSMUSG00000023328	Ache	-	acetylcholinesterase	protein-coding
mm_79380.1	chr9	54765553	54765564	+	1	NA	exon (NM_001284507, exon 2 of 3)	exon (NM_001284507, exon 2 of 3)	810	NM_013496	12903	Mm.34797	NM_013496	ENSMUSG00000032291	Crabp1	AI326249|CRABP-I|Crabp-1|CrabpI|Rbp-5	cellular retinoic acid binding protein I	protein-coding
mm_131462.1	chr16	17018385	17018399	+	1	NA	exon (NM_001038663, exon 3 of 8)	exon (NM_001038663, exon 3 of 8)	35010	NM_001038663	26413	Mm.196581	NM_011949	ENSMUSG00000063358	Mapk1	9030612K14Rik|AA407128|AU018647|C78273|ERK|Erk2|MAPK2|PRKM2|Prkm1|p41mapk|p42mapk	mitogen-activated protein kinase 1	protein-coding
mm_12926.1	chr2	85037449	85037530	+	1	NA	promoter-TSS (NM_001136081)	promoter-TSS (NM_001136081)	38	NM_001136081	20833	Mm.219793	NM_182990	ENSMUSG00000027067	Ssrp1	C81323|Hmg1-rs1|Hmgi-rs3|Hmgox|T160	structure specific recognition protein 1	protein-coding
mm_158093.1	chrX	101420207	101420225	-	1	NA	promoter-TSS (NM_019831)	promoter-TSS (NM_019831)	6	NM_001177988	56364	Mm.23458	NM_019831	ENSMUSG00000031310	Zmym3	9030216B10Rik|AW122925|DXS6673El|Zfp261	zinc finger, MYM-type 3	protein-coding
mm_53109.1	chr6	125083229	125083240	+	1	NA	TTS (NM_001163269)	TTS (NM_001163269)	11957	NM_001163268	381810	Mm.333386	NM_001163268	ENSMUSG00000067714	Lpar5	GPR93|Gm1072|Gpr92|LPA5	lysophosphatidic acid receptor 5	protein-coding
mm_116308.1	chr13	36734451	36734492	-	1	NA	promoter-TSS (NM_153529)	promoter-TSS (NM_153529)	6	NM_153529	68404	Mm.232930	NM_153529	ENSMUSG00000039114	Nrn1	0710008J23Rik|Cpg15|Nrn	neuritin 1	protein-coding
mm_40765.1	chr5	66997087	66997135	+	1	NA	intron (NM_001256122, intron 4 of 20)	intron (NM_001256122, intron 4 of 20)	28695	NM_001256122	77569	Mm.374778	NM_001001980	ENSMUSG00000037736	Limch1	3732412D22Rik|mKIAA1102	LIM and calponin homology domains 1	protein-coding
mm_53897.1	chr6	3399546	3399574	-	1	NA	promoter-TSS (NM_010156)	promoter-TSS (NM_010156)	11	NM_010156	209086	Mm.196013	NM_010156	ENSMUSG00000047735	Samd9l	AA175286|ESTM25|mKIAA2005	sterile alpha motif domain containing 9-like	protein-coding
mm_150941.1	chr19	46306161	46306171	+	1	NA	intron (NM_001177369, intron 2 of 22)	intron (NM_001177369, intron 2 of 22)	236	NM_001177370	18034	Mm.102365	NM_019408	ENSMUSG00000025225	Nfkb2	NF-kappaB2|lyt|p49|p49/p100|p50B|p52	nuclear factor of kappa light polypeptide gene enhancer in B cells 2, p49/p100	protein-coding
mm_75063.1	chr8	33731794	33731823	-	1	NA	promoter-TSS (NM_001167922)	promoter-TSS (NM_001167922)	-106	NM_001167921	68153	Mm.286104	NM_026584	ENSMUSG00000031585	Gtf2e2	34kDa|AI462509|C330006J08Rik	general transcription factor II E, polypeptide 2 (beta subunit)	protein-coding
mm_3472.1	chr1	150104655	150104663	+	1	NA	intron (NM_011198, intron 8 of 9)	intron (NM_011198, intron 8 of 9)	4628	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_129317.1	chr15	77761079	77761111	-	1	NA	3' UTR (NM_022410, exon 41 of 41)	3' UTR (NM_022410, exon 41 of 41)	-5866	NM_001081970	239552	Mm.125650	NM_001081970	ENSMUSG00000056656	Apol8	9830006J20Rik|APOL-II|Apol2	apolipoprotein L 8	protein-coding
mm_86870.1	chr10	21994675	21994694	+	1	NA	promoter-TSS (NM_011361)	promoter-TSS (NM_011361)	18	NM_011361	20393	Mm.28405	NM_011361	ENSMUSG00000019970	Sgk1	Sgk	serum/glucocorticoid regulated kinase 1	protein-coding
mm_129480.1	chr15	78770827	78770835	-	1	NA	intron (NM_008595, intron 1 of 7)	intron (NM_008595, intron 1 of 7)	2614	NM_008595	17305	Mm.149235	NM_008595	ENSMUSG00000018169	Mfng	AW546563	MFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	protein-coding
mm_83414.1	chr9	44878665	44878671	-	1	NA	intron (NM_001081049, intron 1 of 35)	intron (NM_001081049, intron 1 of 35)	2606	NM_001081049	214162	Mm.2389	NM_001081049	ENSMUSG00000002028	Kmt2a	6430520K01|ALL-1|All1|Cxxc7|HRX|HTRX1|Mll|Mll1|mKIAA4050	lysine (K)-specific methyltransferase 2A	protein-coding
mm_65365.1	chr7	25072258	25072286	-	1	NA	promoter-TSS (NM_008168)	promoter-TSS (NM_008168)	97	NM_008168	14809	Mm.2879	NM_008168	ENSMUSG00000003378	Grik5	GluK5|GluRgamma2|KA2	glutamate receptor, ionotropic, kainate 5 (gamma 2)	protein-coding
mm_71054.1	chr8	33731868	33731946	+	1	NA	promoter-TSS (NM_001167922)	promoter-TSS (NM_001167922)	-7	NM_001167921	68153	Mm.286104	NM_026584	ENSMUSG00000031585	Gtf2e2	34kDa|AI462509|C330006J08Rik	general transcription factor II E, polypeptide 2 (beta subunit)	protein-coding
mm_40587.1	chr5	64160228	64160270	+	1	NA	promoter-TSS (NM_019636)	promoter-TSS (NM_019636)	-11	NM_019636	57915	Mm.286353	NM_019636	ENSMUSG00000029174	Tbc1d1	1110062G02Rik|AI385682|AW555803|Nob1|Nobq1|Tbc1|mKIAA1108	TBC1 domain family, member 1	protein-coding
mm_51778.1	chr6	88189901	88189907	+	1	NA	Intergenic	CpG	-8760	NM_008090	14461	Mm.491156	NM_008090	ENSMUSG00000015053	Gata2	Gata-2	GATA binding protein 2	protein-coding
mm_65049.1	chr7	18647035	18647039	-	1	NA	3' UTR (NM_027403, exon 5 of 5)	3' UTR (NM_027403, exon 5 of 5)	9688	NM_027403	72242	Mm.326858	NM_027403	ENSMUSG00000070796	Psg21	1600019C01Rik|1600025N01Rik|1600026N13Rik|cea8	pregnancy-specific glycoprotein 21	protein-coding
mm_109537.1	chr12	111545328	111545345	+	1	NA	3' UTR (NM_178041, exon 12 of 12)	3' UTR (NM_178041, exon 12 of 12)	4390	NR_033168	100316932	Mm.484709	NR_033168	ENSMUSG00000064493	Snora28	MBI-13	small nucleolar RNA, H/ACA box 28	snoRNA
mm_126469.1	chr15	81301769	81301777	+	1	NA	Intergenic	Intergenic	-49911	NR_077230	78102	Mm.296832	NR_077229		8430426J06Rik	-	RIKEN cDNA 8430426J06 gene	ncRNA
mm_2641.1	chr1	125174904	125174924	+	1	NA	Intergenic	Intergenic	260813	NM_023735	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding
mm_73079.1	chr8	94478645	94478661	+	1	NA	intron (NM_001033207, intron 4 of 48)	intron (NM_001033207, intron 4 of 48)	5890	NM_001033207	434341	Mm.334720	NM_001033207	ENSMUSG00000074151	Nlrc5	AI451557|AK220210|NOD27	NLR family, CARD domain containing 5	protein-coding
mm_60049.1	chr7	31059923	31059941	+	1	NA	promoter-TSS (NM_144556)	promoter-TSS (NM_144556)	-3	NM_144556	243914	Mm.389870	NM_144556	ENSMUSG00000036560	Lgi4	Lgil3|clp	leucine-rich repeat LGI family, member 4	protein-coding
mm_115778.1	chr13	19311425	19311435	-	1	NA	Intergenic	Intergenic	84383	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_14471.1	chr2	131491752	131491760	+	1	NA	promoter-TSS (NM_001177840)	promoter-TSS (NM_001177840)	-106	NM_001177834	228608	Mm.136586	NM_145533	ENSMUSG00000027333	Smox	B130066H01Rik|PAO|PAOh1|SMO	spermine oxidase	protein-coding
mm_95275.1	chr11	45851998	45852019	+	1	NA	promoter-TSS (NM_001045520)	promoter-TSS (NM_001045520)	44	NM_001045520	216705	Mm.169673	NM_001045520	ENSMUSG00000006169	Clint1	AI642036|AW537616|C530049I24Rik|Enth|Epn4|F630206G17Rik|mKIAA0171	clathrin interactor 1	protein-coding
mm_109309.1	chr12	109560824	109560840	+	1	NA	non-coding (NR_003633, exon 5 of 5)	non-coding (NR_003633, exon 5 of 5)	-2860	NR_030427	791079		NR_030427	ENSMUSG00000076451	Mir770	Mirn770|mir-770|mmu-mir-770	microRNA 770	ncRNA
mm_129860.1	chr15	83313583	83313595	-	1	NA	exon (NM_025445, exon 11 of 16)	exon (NM_025445, exon 11 of 16)	36658	NM_025445	66251	Mm.258910	NM_025445	ENSMUSG00000054277	Arfgap3	0610009H19Rik|1810004P07Rik|1810035F16Rik|9130416J18Rik|Arfgap1	ADP-ribosylation factor GTPase activating protein 3	protein-coding
mm_141470.1	chr17	30606628	30606655	-	1	NA	intron (NM_025374, intron 1 of 5)	MER90|LTR|ERV1	6018	NM_025374	109801	Mm.261984	NM_025374	ENSMUSG00000024026	Glo1	0610009E22Rik|1110008E19Rik|2510049H23Rik|AW550643|GLY1|Glo-1|Glo-1r|Glo-1s|Glo1-r|Glo1-s|Qglo	glyoxalase 1	protein-coding
mm_56911.1	chr6	119330669	119330694	-	1	NA	promoter-TSS (NM_172492)	promoter-TSS (NM_172492)	85	NM_172492	211187	Mm.121498	NM_172492	ENSMUSG00000055003	Lrtm2	A230084J22|AI841794	leucine-rich repeats and transmembrane domains 2	protein-coding
mm_27368.1	chr3	50438064	50438076	-	1	NA	intron (NM_011990, intron 2 of 11)	intron (NM_011990, intron 2 of 11)	5543	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_115899.1	chr13	23313388	23313399	-	1	NA	promoter-TSS (NR_126443)	promoter-TSS (NR_126443)	14	NR_126443	75322	Mm.108666	NR_126443	ENSMUSG00000085488	4930557F10Rik	-	RIKEN cDNA 4930557F10 gene	ncRNA
mm_152799.1	chr19	21652715	21652723	-	1	NA	promoter-TSS (NM_025423)	promoter-TSS (NM_025423)	72	NM_025423	66206	Mm.272430	NM_025423	ENSMUSG00000035171	1110059E24Rik	-	RIKEN cDNA 1110059E24 gene	protein-coding
mm_5244.1	chr1	16519202	16519260	-	1	NA	promoter-TSS (NM_025303)	promoter-TSS (NM_025303)	71	NM_025303	29819	Mm.216257	NM_025303	ENSMUSG00000025920	Stau2	-	staufen (RNA binding protein) homolog 2 (Drosophila)	protein-coding
mm_107231.1	chr12	26478117	26478130	+	1	NA	exon (NM_020557, exon 5 of 5)	exon (NM_020557, exon 5 of 5)	8908	NM_020557	22169	Mm.271839	NM_020557	ENSMUSG00000020638	Cmpk2	1200004E04Rik|TDKI|Tyki	cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial	protein-coding
mm_88287.1	chr10	75212048	75212058	+	1	NA	promoter-TSS (NM_001145826)	promoter-TSS (NM_001145826)	-20	NM_153406	74392	Mm.27716	NM_153406	ENSMUSG00000033444	Specc1l	4930470P14Rik|4932439K10Rik|9530057A13Rik|AI317249|Cytsa|mKIAA0376	sperm antigen with calponin homology and coiled-coil domains 1-like	protein-coding
mm_99611.1	chr11	104582094	104582107	+	1	NA	intron (NM_010858, intron 4 of 8)	ID_B1|SINE|B4	-19902	NR_130177	100415912	Mm.446786	NR_130177		Gm11665	Gm11664|OTTMUSG00000003182|OTTMUSG00000003183	predicted gene 11665	ncRNA
mm_26030.1	chr3	135439471	135439500	+	1	NA	promoter-TSS (NR_030689)	promoter-TSS (NR_030689)	726	NM_025356	66105	Mm.49884	NM_025356	ENSMUSG00000078578	Ube2d3	1100001F19Rik|9430029A22Rik|AA414951	ubiquitin-conjugating enzyme E2D 3	protein-coding
mm_109623.1	chr12	112766706	112766724	+	1	NA	exon (NM_178911, exon 7 of 11)	exon (NM_178911, exon 7 of 11)	6060	NM_178911	104759	Mm.203915	NM_178911	ENSMUSG00000052160	Pld4	AI132321|thss	phospholipase D family, member 4	protein-coding
mm_89316.1	chr10	87929243	87929256	+	1	NA	intron (NM_001111274, intron 4 of 4)	intron (NM_001111274, intron 4 of 4)	-37422	NR_000040	22172	Mm.391420	NR_000040		Tyms-ps	-	thymidylate synthase, pseudogene	pseudo
mm_145400.1	chr18	57354734	57354797	+	1	NA	promoter-TSS (NM_028447)	promoter-TSS (NM_028447)	32	NM_028447	73137	Mm.29889	NM_028447	ENSMUSG00000024594	Prrc1	1190002C06Rik|2310058D16Rik|3110038B19Rik|9430085A19Rik	proline-rich coiled-coil 1	protein-coding
mm_169275.1	chr13	91461087	91461088	+	1	NA	promoter-TSS (NM_024186)	promoter-TSS (NM_024186)	-10	NM_024272	66970	Mm.343095	NM_024186	ENSMUSG00000003992	Ssbp2	1500004K09Rik|2310079I02Rik|9330163K02Rik|A830008M03Rik|AU067692|AW558684|Hspc116|SSDP2	single-stranded DNA binding protein 2	protein-coding
mm_25795.1	chr3	127632739	127632765	+	1	NA	promoter-TSS (NM_009718)	promoter-TSS (NM_009718)	-393	NM_009718	11924	Mm.42017	NM_009718	ENSMUSG00000027967	Neurog2	Atoh4|Math4A|bHLHa8|ngn-2|ngn2	neurogenin 2	protein-coding
mm_55289.1	chr6	54566327	54566413	-	1	NA	promoter-TSS (NM_027268)	promoter-TSS (NM_027268)	12	NM_027268	69938	Mm.41557	NM_027268	ENSMUSG00000019124	Scrn1	2810019K23Rik|6330535A03Rik|AI852905|SES1|mKIAA0193	secernin 1	protein-coding
mm_146609.1	chr18	10012788	10012792	-	1	NA	intron (NM_001038589, intron 4 of 14)	intron (NM_001038589, intron 4 of 14)	17359	NM_021522	59025	Mm.329277	NM_021522	ENSMUSG00000047879	Usp14	2610005K12Rik|2610037B11Rik|AW107924|C78769|ax|nmf375	ubiquitin specific peptidase 14	protein-coding
mm_149726.1	chr19	21792778	21792799	+	1	NA	exon (NM_031997, exon 3 of 25)	exon (NM_031997, exon 3 of 25)	14448	NM_031997	83921	Mm.329776	NM_031997	ENSMUSG00000024754	Tmem2	-	transmembrane protein 2	protein-coding
mm_37205.1	chr4	117872564	117872593	-	1	NA	promoter-TSS (NM_001034876)	promoter-TSS (NM_001034876)	-108	NM_001034876	381546	Mm.440118	NM_001034876	ENSMUSG00000078588	Ccdc24	Gm1028	coiled-coil domain containing 24	protein-coding
mm_68808.1	chr7	125492401	125492406	-	1	NA	promoter-TSS (NM_026330)	promoter-TSS (NM_026330)	-861	NM_026330	67711	Mm.4467	NM_026330	ENSMUSG00000030750	Nsmce1	2510027N19Rik	NSE1 homolog, SMC5-SMC6 complex component	protein-coding
mm_172970.1	chr9	90114591	90114592	-	1	NA	5' UTR (NM_024431, exon 1 of 12)	5' UTR (NM_024431, exon 1 of 12)	229	NM_001039147	21761	Mm.426209	NM_024431	ENSMUSG00000062270	Morf4l1	MORFRG15|MRG15|TEG-189|Tex189|mKIAA4002	mortality factor 4 like 1	protein-coding
mm_84285.1	chr9	62980875	62980902	-	1	NA	promoter-TSS (NM_019663)	promoter-TSS (NM_019663)	-9	NM_019663	56469	Mm.431253	NM_019663	ENSMUSG00000032405	Pias1	2900068C24Rik|Ddxbp1|GBP	protein inhibitor of activated STAT 1	protein-coding
mm_41645.1	chr5	98180867	98180881	+	1	NA	promoter-TSS (NM_029947)	promoter-TSS (NM_029947)	5	NM_029947	77630	Mm.332511	NM_029947	ENSMUSG00000035456	Prdm8	4930565F05Rik|PFM5	PR domain containing 8	protein-coding
mm_96472.1	chr11	67652575	67652594	+	1	NA	intron (NM_001109657, intron 4 of 13)	intron (NM_001109657, intron 4 of 13)	-42742	NM_009038	19674	Mm.439726	NM_009038	ENSMUSG00000020907	Rcvrn	CAR|S-modulin	recoverin	protein-coding
mm_33037.1	chr4	122857959	122857996	+	1	NA	3' UTR (NM_008917, exon 9 of 9)	3' UTR (NM_008917, exon 9 of 9)	21750	NM_008917	19063	Mm.277719	NM_008917	ENSMUSG00000028657	Ppt1	9530043G02Rik|AA960502|C77813|CLN1|D4Ertd184e|INCL|PPT	palmitoyl-protein thioesterase 1	protein-coding
mm_50479.1	chr6	48988169	48988177	+	1	NA	exon (NM_172888, exon 1 of 5)	exon (NM_172888, exon 1 of 5)	1312	NM_172888	243377	Mm.446302	NM_172888	ENSMUSG00000039215	Svs1	9530003A11	seminal vesicle secretory protein 1	protein-coding
mm_88626.1	chr10	79881024	79881037	+	1	NA	intron (NM_011178, intron 2 of 4)	intron (NM_011178, intron 2 of 4)	1363	NM_011178	19152	Mm.2364	NM_011178	ENSMUSG00000057729	Prtn3	PR3|mPR3	proteinase 3	protein-coding
mm_159704.1	chr5	27841838	27841838	+	1	NA	promoter-TSS (NM_008314)	promoter-TSS (NM_008314)	-109	NM_008314	15563	Mm.4835	NM_008314	ENSMUSG00000039106	Htr5a	Htr5	5-hydroxytryptamine (serotonin) receptor 5A	protein-coding
mm_89941.1	chr10	111278299	111278302	+	1	NA	intron (NM_175489, intron 15 of 23)	intron (NM_175489, intron 15 of 23)	-20379	NM_027914	71769	Mm.45256	NM_027914	ENSMUSG00000035759	Bbs10	1300007O09Rik|AI452285	Bardet-Biedl syndrome 10 (human)	protein-coding
mm_132667.1	chr16	42258108	42258149	+	1	NA	intron (NM_008083, intron 2 of 2)	intron (NM_008083, intron 2 of 2)	45341	NR_105858	102466172		NR_105858	ENSMUSG00000098300	Mir6540	Gm27780|mir-6540|mmu-mir-6540	microRNA 6540	ncRNA
mm_29899.1	chr3	131466256	131466260	-	1	NA	Intergenic	Intergenic	-98510	NM_001289479	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_137596.1	chr17	28142268	28142321	+	1	NA	promoter-TSS (NM_001004366)	promoter-TSS (NM_001004366)	-232	NM_001004366	268935	Mm.258491	NM_001004366	ENSMUSG00000038677	Scube3	CEGF3|D030038I21Rik	signal peptide, CUB domain, EGF-like 3	protein-coding
mm_140047.1	chr17	74528280	74528288	+	1	NA	promoter-TSS (NM_007566)	promoter-TSS (NM_007566)	-11	NM_007566	12211	Mm.442564	NM_007566	ENSMUSG00000024073	Birc6	A430032G04Rik|A430040A19Rik|AA501170|Bruce|D630005A10Rik|mKIAA1289	baculoviral IAP repeat-containing 6	protein-coding
mm_20103.1	chr2	121085747	121085753	-	1	NA	promoter-TSS (NM_028799)	promoter-TSS (NM_028799)	9	NM_028799	74176	Mm.20187	NM_028799	ENSMUSG00000053675	Tgm5	2310007C07Rik|TGMX|TGx	transglutaminase 5	protein-coding
mm_162779.1	chr10	69563754	69563760	+	1	NA	intron (NM_170730, intron 1 of 17)	intron (NM_170730, intron 1 of 17)	30049	NM_146005	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_54641.1	chr6	38837306	38837316	-	1	NA	promoter-TSS (NM_001136065)	promoter-TSS (NM_001136065)	0	NM_001136065	15258	Mm.23790	NM_010433	ENSMUSG00000061436	Hipk2	1110014O20Rik|B230339E18Rik|Stank	homeodomain interacting protein kinase 2	protein-coding
mm_4116.1	chr1	167689553	167689563	+	1	NA	promoter-TSS (NM_033652)	promoter-TSS (NM_033652)	0	NM_033652	110648	Mm.330081	NM_033652	ENSMUSG00000026686	Lmx1a	Lmx1.1|dr|dreher|sst	LIM homeobox transcription factor 1 alpha	protein-coding
mm_37275.1	chr4	118620799	118620806	-	1	NA	promoter-TSS (NM_026789)	promoter-TSS (NM_026789)	3	NM_026932	69072	Mm.29906	NM_026932	ENSMUSG00000028729	Ebna1bp2	1810014B19Rik|AA537058|B830003A16Rik|C81321|Ebp2|Nobp|p40	EBNA1 binding protein 2	protein-coding
mm_75599.1	chr8	61760021	61760036	-	1	NA	promoter-TSS (NM_001293773)	promoter-TSS (NM_001293773)	70	NM_001293773	72333	Mm.29933	NM_001081390	ENSMUSG00000058056	Palld	2410003B16Rik|6030492A02	palladin, cytoskeletal associated protein	protein-coding
mm_70535.1	chr8	13037803	13037838	+	1	NA	exon (NM_001242368, exon 2 of 9)	exon (NM_001242368, exon 2 of 9)	512	NM_001242368	14058	Mm.262589	NM_007972	ENSMUSG00000031444	F10	Cf10|fX	coagulation factor X	protein-coding
mm_72357.1	chr8	79712913	79712924	+	1	NA	intron (NM_026904, intron 1 of 4)	RMER10B|LTR|ERVL	1098	NM_026904	68999	Mm.257445	NM_026904	ENSMUSG00000036977	Anapc10	1500026N15Rik|A830003M23Rik|APC10	anaphase promoting complex subunit 10	protein-coding
mm_93710.1	chr10	118855865	118855913	-	1	NA	Intergenic	Intergenic	13014	NM_001014390	69181	Mm.45565	NM_001014390	ENSMUSG00000028630	Dyrk2	1810038L18Rik	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 2	protein-coding
mm_126570.1	chr15	82252470	82252475	+	1	NA	promoter-TSS (NR_037697)	promoter-TSS (NR_037697)	75	NR_037697	76505	Mm.23023	NR_037697	ENSMUSG00000068099	1500009C09Rik	-	RIKEN cDNA 1500009C09 gene	ncRNA
mm_155051.1	chrX	42155476	42155498	+	1	NA	intron (NM_021465, intron 1 of 32)	B1_Mus1|SINE|Alu	4786	NM_021465	20843	Mm.290422	NM_021465	ENSMUSG00000025862	Stag2	9230105L23Rik|B230112I07Rik|SA-2|SAP2	stromal antigen 2	protein-coding
mm_162454.1	chr1	126824743	126824747	-	1	NA	intron (NM_001081756, intron 1 of 16)	intron (NM_001081756, intron 1 of 16)	5887	NM_001081756	210356	Mm.377234	NM_172484	ENSMUSG00000049690	Nckap5	8430408F21|D130011D22Rik|E030049G20Rik|Erih1|Erih2|Gm1548|Nap5	NCK-associated protein 5	protein-coding
mm_143925.1	chr17	85618583	85618593	-	1	NA	promoter-TSS (NR_015387)	promoter-TSS (NR_015387)	-192	NR_038082	100043902	Mm.150838	NR_015385	ENSMUSG00000093460	Six3os1	D17Mgi26|E130112H22Rik|Rncr1|Six3os	SIX homeobox 3, opposite strand 1	ncRNA
mm_154724.1	chrX	9435953	9436001	+	1	NA	3' UTR (NM_007807, exon 13 of 13)	3' UTR (NM_007807, exon 13 of 13)	33347	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_30999.1	chr4	40143511	40143521	+	1	NA	5' UTR (NM_007386, exon 1 of 21)	5' UTR (NM_007386, exon 1 of 21)	251	NM_007386	11428	Mm.331547	NM_007386	ENSMUSG00000028405	Aco1	Aco-1|Irebp|Irp1	aconitase 1	protein-coding
mm_91679.1	chr10	43540946	43541024	-	1	NA	promoter-TSS (NM_026411)	promoter-TSS (NM_026411)	9	NM_026411	67851	Mm.209953	NM_026411	ENSMUSG00000019797	1700021F05Rik	-	RIKEN cDNA 1700021F05 gene	protein-coding
mm_90967.1	chr10	13388831	13388845	-	1	NA	5' UTR (NM_001195066, exon 1 of 13)	5' UTR (NM_001195066, exon 1 of 13)	132	NM_001195066	215789	Mm.283359	NM_001033257	ENSMUSG00000062866	Phactr2	AV158170|BC012871	phosphatase and actin regulator 2	protein-coding
mm_134794.1	chr16	24193388	24193404	-	1	NA	Intergenic	Intergenic	-199954	NM_178665	210126	Mm.209385	NM_178665	ENSMUSG00000033306	Lpp	9430020K16Rik|AA959454|AU024130|B130055L10Rik|C79715|D630048H16	LIM domain containing preferred translocation partner in lipoma	protein-coding
mm_72191.1	chr8	72492916	72492951	+	1	NA	promoter-TSS (NM_177766)	promoter-TSS (NM_177766)	-319	NM_177766	270066	Mm.291461	NM_177766	ENSMUSG00000019731	Slc35e1	6030458H05|AA408278	solute carrier family 35, member E1	protein-coding
mm_32634.1	chr4	115000191	115000209	+	1	NA	promoter-TSS (NM_009185)	promoter-TSS (NM_009185)	82	NM_001304555	20460	Mm.3988	NM_009185	ENSMUSG00000028718	Stil	Sil	Scl/Tal1 interrupting locus	protein-coding
mm_105556.1	chr11	106487759	106487765	-	1	NA	promoter-TSS (NM_023913)	promoter-TSS (NM_023913)	34	NM_023913	78943	Mm.340943	NM_023913	ENSMUSG00000020715	Ern1	9030414B18Rik|AI225830|C85377|Ire1a|Ire1alpha|Ire1p	endoplasmic reticulum (ER) to nucleus signalling 1	protein-coding
mm_69505.1	chr7	134341966	134341968	-	1	NA	intron (NM_001199941, intron 3 of 8)	intron (NM_001199941, intron 3 of 8)	22917	NM_001199941	71007	Mm.334285	NM_001081331	ENSMUSG00000030994	D7Ertd443e	4933400E14Rik|FATS|Gm497	DNA segment, Chr 7, ERATO Doi 443, expressed	protein-coding
mm_146731.1	chr18	15312739	15312752	-	1	NA	Intergenic	Intergenic	90254	NM_001308647	11829	Mm.250786	NM_009700	ENSMUSG00000024411	Aqp4	WCH4	aquaporin 4	protein-coding
mm_50947.1	chr6	58640537	58640596	+	1	NA	intron (NM_011920, intron 1 of 15)	CpG	43894	NM_011920	26357	Mm.333096	NM_011920	ENSMUSG00000029802	Abcg2	ABC15|ABCP|AI428558|BCRP|Bcrp1|MXR|MXR1	ATP-binding cassette, sub-family G (WHITE), member 2	protein-coding
mm_19667.1	chr2	103303180	103303210	-	1	NA	promoter-TSS (NM_007914)	promoter-TSS (NM_007914)	1	NM_007914	13661	Mm.10724	NM_007914	ENSMUSG00000012350	Ehf	9030625L19Rik|AU019492	ets homologous factor	protein-coding
mm_22210.1	chr2	174267054	174267057	-	1	NA	promoter-TSS (NR_029646)	promoter-TSS (NR_029646)	70	NR_029646	723906		NR_029646	ENSMUSG00000065521	Mir296	Mirn296|mir-296|mmu-mir-296	microRNA 296	ncRNA
mm_31779.1	chr4	63560628	63560649	+	1	NA	intron (NM_144905, intron 1 of 9)	intron (NM_144905, intron 1 of 9)	278	NM_144905	230279	Mm.41523	NM_144905	ENSMUSG00000045917	Tmem268	6330416G13Rik|AW492431|bM230C2.2	transmembrane protein 268	protein-coding
mm_34627.1	chr4	150569539	150569598	+	1	NA	intron (NM_001085492, intron 11 of 22)	CpG	82606	NM_173774	242773	Mm.29280	NM_173774	ENSMUSG00000039838	Slc45a1	C230078B22|Dnb5	solute carrier family 45, member 1	protein-coding
mm_65488.1	chr7	25681019	25681034	-	1	NA	promoter-TSS (NM_172148)	promoter-TSS (NM_172148)	-132	NM_172148	232987	Mm.22849	NM_172148	ENSMUSG00000063439	B9d2	stumpy	B9 protein domain 2	protein-coding
mm_8781.1	chr1	161241770	161241791	-	1	NA	exon (NM_007453, exon 5 of 5)	exon (NM_007453, exon 5 of 5)	9430	NR_130150	11758	Mm.186185	NM_007453	ENSMUSG00000026701	Prdx6	1-Cys Prx|1-cysPrx|9430088D19Rik|AA690119|Aop2|Brp-12|CP-3|GPx|Ltw-4|Ltw4|Lvtw-4|NSGPx|ORF06|Prdx5|aiPLA2	peroxiredoxin 6	protein-coding
mm_101980.1	chr11	50415727	50415732	-	1	NA	intron (NM_172557, intron 6 of 17)	intron (NM_172557, intron 6 of 17)	15382	NM_172557	216724	Mm.390400	NM_172557	ENSMUSG00000020375	Rufy1	3000002E04Rik|Rabip4|ZFYVE12	RUN and FYVE domain containing 1	protein-coding
mm_104128.1	chr11	86805272	86805275	-	1	NA	intron (NM_026191, intron 2 of 17)	intron (NM_026191, intron 2 of 17)	2387	NM_026191	67487	Mm.260627	NM_026191	ENSMUSG00000018425	Dhx40	2410016C14Rik|ARG147|DDX40|PAD	DEAH (Asp-Glu-Ala-His) box polypeptide 40	protein-coding
mm_60362.1	chr7	44441716	44441756	+	1	NA	promoter-TSS (NM_198250)	promoter-TSS (NM_198250)	-751	NM_198250	272381	Mm.44173	NM_198250	ENSMUSG00000047085	Lrrc4b	A830007M12|Lrig4	leucine rich repeat containing 4B	protein-coding
mm_43051.1	chr5	124116073	124116083	+	1	NA	promoter-TSS (NM_144509)	promoter-TSS (NM_144509)	-30	NM_144509	65105	Mm.29430	NM_144509	ENSMUSG00000029404	Arl6ip4	AA408210|AA408365|Aip-4|Srp25	ADP-ribosylation factor-like 6 interacting protein 4	protein-coding
mm_138895.1	chr17	43568448	43568458	+	1	NA	promoter-TSS (NM_013737)	promoter-TSS (NM_013737)	2	NM_013737	27226	Mm.9277	NM_013737	ENSMUSG00000023913	Pla2g7	PAF-AH|R75400	phospholipase A2, group VII (platelet-activating factor acetylhydrolase, plasma)	protein-coding
mm_45025.1	chr5	38563216	38563234	-	1	NA	Intergenic	Intergenic	-1630	NM_011715	22388	Mm.2654	NM_011715	ENSMUSG00000005103	Wdr1	Aip1|D5Wsu185e|rede	WD repeat domain 1	protein-coding
mm_7322.1	chr1	100180263	100180308	-	1	NA	intron (NM_172851, intron 10 of 23)	L1Md_F2|LINE|L1	407520	NM_172851	241175	Mm.251301	NM_172851	ENSMUSG00000067028	Cntnap5b	C230078M14Rik|Caspr5-2	contactin associated protein-like 5B	protein-coding
mm_28750.1	chr3	95818822	95818877	-	1	NA	5' UTR (NM_001081293, exon 1 of 11)	5' UTR (NM_001081293, exon 1 of 11)	104	NM_001081293	75137	Mm.196275	NM_028328	ENSMUSG00000028106	Rprd2	2810036A19Rik|4930535B03Rik|6720469I21Rik|AL022841|AL022940|AU021304|BB077382|mKIAA0460	regulation of nuclear pre-mRNA domain containing 2	protein-coding
mm_32838.1	chr4	117835279	117835301	+	1	NA	promoter-TSS (NM_008135)	promoter-TSS (NM_008135)	32	NM_008135	14664	Mm.244549	NM_008135	ENSMUSG00000028542	Slc6a9	Glyt-1|Glyt1	solute carrier family 6 (neurotransmitter transporter, glycine), member 9	protein-coding
mm_116843.1	chr13	54693795	54693888	-	1	NA	non-coding (NR_027396, exon 1 of 11)	non-coding (NR_027396, exon 1 of 11)	119	NR_027395	105239	Mm.25366	NM_134064	ENSMUSG00000034928	Rnf44	AI854545|mKIAA1100	ring finger protein 44	protein-coding
mm_78833.1	chr9	44234362	44234374	+	1	NA	promoter-TSS (NM_007619)	promoter-TSS (NM_007619)	-322	NM_007619	12402	Mm.266871	NM_007619	ENSMUSG00000034342	Cbl	4732447J05Rik|Cbl-2|c-Cbl|cbl	Casitas B-lineage lymphoma	protein-coding
mm_22630.1	chr3	14767481	14767489	+	1	NA	exon (NM_001083957, exon 6 of 7)	exon (NM_001083957, exon 6 of 7)	10975	NM_001083957	12346	Mm.273195	NM_009799	ENSMUSG00000027556	Car1	AW555628|Ca1|Car-1	carbonic anhydrase 1	protein-coding
mm_163110.1	chr11	70433969	70433982	+	1	NA	intron (NM_001271359, intron 1 of 15)	intron (NM_001271359, intron 1 of 15)	1395	NM_001271358	216869	Mm.203747	NM_145429	ENSMUSG00000060216	Arrb2	AI326910|AW122872	arrestin, beta 2	protein-coding
mm_126952.1	chr15	92161344	92161366	+	1	NA	promoter-TSS (NM_001159647)	promoter-TSS (NM_001159647)	-2	NM_001159647	12805	Mm.4911	NM_007727	ENSMUSG00000055022	Cntn1	AW495098|CNTN|F3cam|usl	contactin 1	protein-coding
mm_38890.1	chr4	149749453	149749465	-	1	NA	intron (NM_027460, intron 5 of 6)	intron (NM_027460, intron 5 of 6)	-11391	NM_177672	230917	Mm.266704	NM_177672	ENSMUSG00000044700	Tmem201	AV028368|D4Ertd429e|Net5|Samp1	transmembrane protein 201	protein-coding
mm_32232.1	chr4	102254921	102254931	+	1	NA	promoter-TSS (NM_019840)	promoter-TSS (NM_019840)	-13	NM_019840	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_136697.1	chr17	7170086	7170097	+	1	NA	promoter-TSS (NM_011299)	promoter-TSS (NM_011299)	-24	NM_011299	20112	Mm.268383	NM_011299	ENSMUSG00000023809	Rps6ka2	90kDa|D17Wsu134e|Rps6ka-rs1|Rsk3|p90rsk|pp90rsk	ribosomal protein S6 kinase, polypeptide 2	protein-coding
mm_16575.1	chr2	3474990	3475004	-	1	NA	promoter-TSS (NM_022724)	promoter-TSS (NM_022724)	-11	NR_027509	64707	Mm.23483	NM_022724	ENSMUSG00000026646	Suv39h2	4930507K23Rik|AA536750|D030054H19Rik|D2Ertd544e|KMT1B	suppressor of variegation 3-9 homolog 2 (Drosophila)	protein-coding
mm_25784.1	chr3	126746697	126746708	+	1	NA	intron (NM_001346636, intron 4 of 20)	intron (NM_001346636, intron 4 of 20)	149751	NM_023813	108058	Mm.255822	NM_023813	ENSMUSG00000053819	Camk2d	2810011D23Rik|8030469K03Rik|CaMK II|[d]-CaMKII	calcium/calmodulin-dependent protein kinase II, delta	protein-coding
mm_32141.1	chr4	99650436	99650452	+	1	NA	Intergenic	Intergenic	-5855	NM_010425	15221	Mm.4758	NM_010425	ENSMUSG00000067261	Foxd3	CWH3|Genesis|Hfh2	forkhead box D3	protein-coding
mm_50304.1	chr6	47781640	47781678	+	1	NA	Intergenic	HY3|scRNA|scRNA	21993	NR_030485	735289		NR_030485	ENSMUSG00000076060	Mir704	Mirn704|mir-704|mmu-mir-704	microRNA 704	ncRNA
mm_76687.1	chr8	94098432	94098442	-	1	NA	5' UTR (NM_026116, exon 1 of 17)	5' UTR (NM_026116, exon 1 of 17)	374	NM_026116	67378	Mm.292107	NM_026116	ENSMUSG00000031755	Bbs2	2410125H22Rik|AI447581	Bardet-Biedl syndrome 2 (human)	protein-coding
mm_71910.1	chr8	70083492	70083508	+	1	NA	promoter-TSS (NM_177900)	promoter-TSS (NM_177900)	-29	NM_177900	330790	Mm.152048	NM_177900	ENSMUSG00000007594	Hapln4	9330174O11|Bral2|Lpr4	hyaluronan and proteoglycan link protein 4	protein-coding
mm_58546.1	chr7	4657813	4657814	+	1	NA	intron (NM_172894, intron 1 of 23)	intron (NM_172894, intron 1 of 23)	1137	NM_172894	243819	Mm.258670	NM_172894	ENSMUSG00000052296	Ppp6r1	2010309P17Rik|AI836219|B430201G11Rik|D030074N20Rik|Pp6r1|Saps1|mKIAA1115	protein phosphatase 6, regulatory subunit 1	protein-coding
mm_39715.1	chr5	28032094	28032111	+	1	NA	Intergenic	MTEa|LTR|ERVL-MaLR	-39310	NM_153526	231070	Mm.30221	NM_153526	ENSMUSG00000045294	Insig1	1810013C12Rik|Insig-1	insulin induced gene 1	protein-coding
mm_86811.1	chr10	20347789	20347859	+	1	NA	promoter-TSS (NM_027930)	promoter-TSS (NM_027930)	5	NM_027930	71804	Mm.262151	NM_027930	ENSMUSG00000019992	Mtfr2	2610016C23Rik|4933412C16Rik|Dufd1|Fam54a	mitochondrial fission regulator 2	protein-coding
mm_46702.1	chr5	110176498	110176512	-	1	NA	promoter-TSS (NM_008146)	promoter-TSS (NM_008146)	-1	NR_040430	100504007	Mm.441495	NR_040430	ENSMUSG00000086247	Gm15787	OTTMUSG00000026209	predicted gene 15787	ncRNA
mm_12011.1	chr2	57367464	57367474	+	1	NA	exon (NM_010274, exon 17 of 17)	exon (NM_010274, exon 17 of 17)	129087	NM_010274	14571	Mm.3711	NM_010274	ENSMUSG00000026827	Gpd2	AA408484|AI448216|AU021455|AW494132|GPDH|Gdm1|Gpd-m|Gpdh-m|TISP38	glycerol phosphate dehydrogenase 2, mitochondrial	protein-coding
mm_157300.1	chrX	20928505	20928515	-	1	NA	exon (NM_008823, exon 5 of 9)	exon (NM_008823, exon 5 of 9)	3045	NM_008823	18636	Mm.3064	NM_008823	ENSMUSG00000001128	Cfp	BCFG|Pfc	complement factor properdin	protein-coding
mm_140960.1	chr17	24644934	24644976	-	1	NA	promoter-TSS (NM_023449)	promoter-TSS (NM_023449)	2	NM_023449	65962	Mm.21587	NM_023055	ENSMUSG00000002504	Slc9a3r2	0610011L07Rik|1200011K07Rik|2010007A20Rik|E3karp|NHERF-2|Nherf2|Octs2|Sip-1|Sip1|Sryip1|Tka-1	solute carrier family 9 (sodium/hydrogen exchanger), member 3 regulator 2	protein-coding
mm_138696.1	chr17	35980404	35980426	+	1	NA	promoter-TSS (NM_001282025)	promoter-TSS (NM_001282025)	460	NM_008136	14670	Mm.335754	NM_008136	ENSMUSG00000024429	Gnl1	Gna-rs1|Gnal1	guanine nucleotide binding protein-like 1	protein-coding
mm_90408.1	chr10	127420335	127420348	+	1	NA	promoter-TSS (NM_001168293)	promoter-TSS (NM_001168293)	-526	NM_027900	71750	Mm.29342	NM_027900	ENSMUSG00000025404	R3hdm2	1300003K24Rik|AU041262|mKIAA1002	R3H domain containing 2	protein-coding
mm_35542.1	chr4	41464642	41464667	-	1	NA	promoter-TSS (NM_025539)	promoter-TSS (NM_025539)	194	NM_024241	109242	Mm.370288	NM_024241	ENSMUSG00000028438	Kif24	4933425J19Rik|9430029L23Rik	kinesin family member 24	protein-coding
mm_77650.1	chr8	124563942	124563955	-	1	NA	exon (NM_007428, exon 2 of 5)	exon (NM_007428, exon 2 of 5)	5759	NM_007428	11606	Mm.301626	NM_007428	ENSMUSG00000031980	Agt	AI265500|AngI|AngII|Aogen|Serpina8	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	protein-coding
mm_150560.1	chr19	39347345	39347348	+	1	NA	Intergenic	Intergenic	60261	NM_007815	13095	Mm.20764	NM_007815	ENSMUSG00000003053	Cyp2c29	AHOH|AHOHase|AI159681|AI196010|Ah-2|Ahh-1|Cyp2c|P450-2C	cytochrome P450, family 2, subfamily c, polypeptide 29	protein-coding
mm_90891.1	chr10	10296923	10296935	-	1	NA	Intergenic	MTC|LTR|ERVL-MaLR	175385	NM_001127353	215772	Mm.246573	NM_172547	ENSMUSG00000050994	Adgb	9130014G24Rik	androglobin	protein-coding
mm_37476.1	chr4	123565485	123565496	-	1	NA	intron (NM_001199136, intron 1 of 97)	intron (NM_001199136, intron 1 of 97)	-50930	NR_105824	102465214		NR_105824	ENSMUSG00000099005	Mir6398	Gm27657|mmu-mir-6398	microRNA 6398	ncRNA
mm_63319.1	chr7	126928910	126928926	+	1	NA	promoter-TSS (NM_172747)	promoter-TSS (NM_172747)	39	NM_172747	233877	Mm.245897	NM_172747	ENSMUSG00000030685	Kctd13	1500003N18Rik|AV259508|PDIP1alpha|Pdip1|Poldip1	potassium channel tetramerisation domain containing 13	protein-coding
mm_33766.1	chr4	134401304	134401325	+	1	NA	intron (NM_001285872, intron 1 of 10)	intron (NM_001285872, intron 1 of 10)	-1598	NM_001285874	100163	Mm.22116	NM_133880	ENSMUSG00000037366	Pafah2	2310074E22Rik|AI507170	platelet-activating factor acetylhydrolase 2	protein-coding
mm_66745.1	chr7	46712077	46712094	-	1	NA	TTS (NM_011315)	TTS (NM_011315)	-1434	NM_030233	78935	Mm.289866	NM_030233	ENSMUSG00000006763	Saal1	5031425D22Rik|SPACIA1	serum amyloid A-like 1	protein-coding
mm_18605.1	chr2	68238907	68238910	-	1	NA	intron (NM_016866, intron 16 of 17)	intron (NM_016866, intron 16 of 17)	134236	NM_020283	26877	Mm.226435	NM_020283	ENSMUSG00000034780	B3galt1	beta3Gal-T1	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 1	protein-coding
mm_161767.1	chr17	36271386	36271386	-	1	NA	promoter-TSS (NM_178281)	promoter-TSS (NM_178281)	47	NM_178281	79263	Mm.40624	NM_024468	ENSMUSG00000045409	Trim39	1100001D15Rik|E130103K13Rik|RBCC-B30.2|Rnf23|mKIAA4179|tfp	tripartite motif-containing 39	protein-coding
mm_74725.1	chr8	17535206	17535219	-	1	NA	5' UTR (NM_053171, exon 1 of 70)	5' UTR (NM_053171, exon 1 of 70)	173	NM_053171	94109	Mm.436988	NM_053171	ENSMUSG00000060924	Csmd1	B930082H09|mKIAA1890	CUB and Sushi multiple domains 1	protein-coding
mm_140385.1	chr17	87174988	87174992	+	1	NA	Intergenic	Intergenic	19952	NR_046016	399626	Mm.396062	NR_046016		C330024C12Rik	-	RIKEN cDNA C330024C12 gene	ncRNA
mm_39869.1	chr5	31074805	31074811	+	1	NA	intron (NM_023525, intron 34 of 43)	intron (NM_023525, intron 34 of 43)	18719	NM_011773	22784	Mm.1396	NM_011773	ENSMUSG00000029151	Slc30a3	Znt3	solute carrier family 30 (zinc transporter), member 3	protein-coding
mm_130182.1	chr15	93519471	93519483	-	1	NA	intron (NM_001033217, intron 1 of 7)	CpG	76414	NM_001033217	106042	Mm.150314	NM_001033217	ENSMUSG00000036158	Prickle1	1110058P22Rik|AW215793|Prickle|b2b019Clo|mpk1	prickle planar cell polarity protein 1	protein-coding
mm_66692.1	chr7	45896678	45896692	-	1	NA	promoter-TSS (NM_144801)	promoter-TSS (NM_144801)	26	NM_001291064	58867	Mm.214217	NM_021482	ENSMUSG00000040231	Syngr4	1700016O14Rik	synaptogyrin 4	protein-coding
mm_115202.1	chr13	109116249	109116277	+	1	NA	intron (NM_011056, intron 3 of 16)	intron (NM_011056, intron 3 of 16)	-208481	NR_030644	100124489		NR_030644	ENSMUSG00000076946	Mir582	Mirn582|mir-582|mmu-mir-582	microRNA 582	ncRNA
mm_76143.1	chr8	81854687	81854693	-	1	NA	intron (NM_001297591, intron 7 of 24)	intron (NM_001297591, intron 7 of 24)	512128	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_33969.1	chr4	137610672	137610708	+	1	NA	exon (NM_130879, exon 7 of 28)	exon (NM_130879, exon 7 of 28)	16501	NM_130879	170707	Mm.218478	NM_130879	ENSMUSG00000043411	Usp48	2810449C13Rik|AI115503|BC021769|D330022K21Rik|Usp31	ubiquitin specific peptidase 48	protein-coding
mm_133927.1	chr16	3718095	3718097	-	1	NA	promoter-TSS (NM_001161791)	promoter-TSS (NM_001161791)	28	NM_001161790	54483	Mm.143718	NM_019453	ENSMUSG00000022534	Mefv	FMF|TRIM20|pyrin	Mediterranean fever	protein-coding
mm_42999.1	chr5	123414939	123414945	+	1	NA	intron (NM_133917, intron 1 of 16)	ID_B1|SINE|B4	20144	NM_177582	208104	Mm.83277	NM_133917	ENSMUSG00000038342	Mlxip	AW228700|Mir|bHLHe36	MLX interacting protein	protein-coding
mm_149359.1	chr19	11047967	11047992	+	1	NA	non-coding (NR_102366, exon 3 of 3)	non-coding (NR_102366, exon 3 of 3)	2587	NR_102366	107350	Mm.6381	NM_001177351	ENSMUSG00000075010	AW112010	-	expressed sequence AW112010	ncRNA
mm_8954.1	chr1	164458726	164458737	-	1	NA	promoter-TSS (NM_009721)	promoter-TSS (NM_009721)	-376	NM_009721	11931	Mm.4550	NM_009721	ENSMUSG00000026576	Atp1b1	Atp4b|Atpb|Atpb-1|NKbeta1	ATPase, Na+/K+ transporting, beta 1 polypeptide	protein-coding
mm_150820.1	chr19	44408021	44408038	+	1	NA	promoter-TSS (NM_009127)	promoter-TSS (NM_009127)	-320	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_12520.1	chr2	72137216	72137240	+	1	NA	intron (NM_001204166, intron 1 of 27)	intron (NM_001204166, intron 1 of 27)	82611	NM_001204166	56508	Mm.196153	NM_019688	ENSMUSG00000049044	Rapgef4	1300003D15Rik|5730402K07Rik|6330581N18Rik|EPAC 2|Epac-2|Epac2|mKIAA4040	Rap guanine nucleotide exchange factor (GEF) 4	protein-coding
mm_49180.1	chr6	15184571	15184581	+	1	NA	promoter-TSS (NM_001286607)	promoter-TSS (NM_001286607)	-930	NM_212435	114142	Mm.332919	NM_053242	ENSMUSG00000029563	Foxp2	2810043D05Rik|AI449000|CAG-16|D0Kist7	forkhead box P2	protein-coding
mm_56455.1	chr6	97890571	97890575	-	1	NA	intron (NM_001113198, intron 1 of 9)	intron (NM_001113198, intron 1 of 9)	-39244	NM_001178049	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_27547.1	chr3	57847691	57847720	-	1	NA	promoter-TSS (NM_019410)	promoter-TSS (NM_019410)	52	NM_019410	18645	Mm.271744	NM_019410	ENSMUSG00000027805	Pfn2	Pfn	profilin 2	protein-coding
mm_52493.1	chr6	114654816	114654825	+	1	NA	intron (NM_001253718, intron 2 of 19)	B1F1|SINE|Alu	11723	NM_001253717	74244	Mm.275332	NM_028835	ENSMUSG00000030314	Atg7	1810013K23Rik|Agp7|Apg7l|Atg7l|Gm21553	autophagy related 7	protein-coding
mm_119969.1	chr14	55540289	55540315	+	1	NA	promoter-TSS (NM_028994)	promoter-TSS (NM_028994)	36	NM_028994	74551	Mm.29856	NM_028994	ENSMUSG00000040618	Pck2	1810010O14Rik|9130022B02Rik|PEPCK-M	phosphoenolpyruvate carboxykinase 2 (mitochondrial)	protein-coding
mm_128873.1	chr15	73038626	73038636	-	1	NA	intron (NM_180662, intron 4 of 21)	intron (NM_180662, intron 4 of 21)	17181	NM_029640	76510	Mm.158902	NM_029640	ENSMUSG00000047921	Trappc9	1810044A24Rik|2900005P22Rik|4632408O18Rik|Ibp|Nibp|TRS130|mKIAA1882	trafficking protein particle complex 9	protein-coding
mm_135922.1	chr16	69800402	69800416	-	1	NA	promoter-TSS (NR_130991)	promoter-TSS (NR_130991)	-28	NR_130991	78110	Mm.211406	NR_130991	ENSMUSG00000107073	4930428D20Rik	-	RIKEN cDNA 4930428D20 gene	ncRNA
mm_26447.1	chr3	142635868	142635878	+	1	NA	exon (NM_010260, exon 10 of 11)	exon (NM_010260, exon 10 of 11)	-11927	NR_105802	102465200		NR_105802	ENSMUSG00000098871	Mir6381	Gm27963|mmu-mir-6381	microRNA 6381	ncRNA
mm_107685.1	chr12	55080215	55080235	+	1	NA	promoter-TSS (NM_011899)	promoter-TSS (NM_011899)	-115	NM_028314	72658	Mm.434380	NM_028314	ENSMUSG00000062198	2700097O09Rik	AW552125	RIKEN cDNA 2700097O09 gene	protein-coding
mm_12994.1	chr2	90885862	90885872	+	1	NA	promoter-TSS (NM_026161)	promoter-TSS (NM_026161)	81	NM_026161	67445	Mm.258993	NM_026161	ENSMUSG00000040794	C1qtnf4	0710001E10Rik|9430004J15Rik|CTRP4	C1q and tumor necrosis factor related protein 4	protein-coding
mm_138236.1	chr17	34417320	34417331	+	1	NA	5' UTR (NM_001001177, exon 3 of 20)	5' UTR (NM_001001177, exon 3 of 20)	18505	NM_001163855	407788	Mm.73205	NM_001001177	ENSMUSG00000057246	BC051142	NG8|TSBP|Tesb|Tesbp	cDNA sequence BC051142	protein-coding
mm_15154.1	chr2	154008276	154008277	+	1	NA	promoter-TSS (NM_008953)	promoter-TSS (NM_008953)	0	NM_008953	19194	Mm.29197	NM_008953	ENSMUSG00000042459	Bpifa2	Bpifa2e|Psp	BPI fold containing family A, member 2	protein-coding
mm_53292.1	chr6	129036522	129036526	+	1	NA	Intergenic	RMER19A|LTR|ERVK	-9377	NR_024262	232408	Mm.259262	NM_153094	ENSMUSG00000030154	Klrb1f	A630024B12Rik|Nkr-p1f|Nkrp1-f|Nkrp1f	killer cell lectin-like receptor subfamily B member 1F	protein-coding
mm_84670.1	chr9	72010473	72010476	-	1	NA	intron (NM_001253862, intron 4 of 19)	intron (NM_001253862, intron 4 of 19)	47033	NR_029879	723889		NR_029879	ENSMUSG00000105200	Mir378a	Mir378|Mirn378|mmu-mir-378|mmu-mir-378a	microRNA 378a	ncRNA
mm_9659.1	chr1	177796415	177796433	-	1	NA	promoter-TSS (NM_007422)	promoter-TSS (NM_007422)	85	NM_007422	11566	Mm.338021	NM_007422	ENSMUSG00000015961	Adss	AI314886|AS|Adss2	adenylosuccinate synthetase, non muscle	protein-coding
mm_146211.1	chr18	76930483	76930484	+	1	NA	intron (NM_025409, intron 1 of 2)	intron (NM_025409, intron 1 of 2)	456	NM_025409	66191	Mm.28593	NM_025409	ENSMUSG00000090000	Ier3ip1	1110057H19Rik|AI644142|AL022842|AL022863|AV026606	immediate early response 3 interacting protein 1	protein-coding
mm_68612.1	chr7	116443401	116443411	-	1	NA	promoter-TSS (NM_011083)	promoter-TSS (NM_011083)	52	NM_011083	18704	Mm.3810	NM_011083	ENSMUSG00000030660	Pik3c2a	Cpk-m|PI3KC2	phosphatidylinositol 3-kinase, C2 domain containing, alpha polypeptide	protein-coding
mm_82340.1	chr9	10904767	10904835	-	1	NA	promoter-TSS (NM_001170787)	promoter-TSS (NM_001170787)	-26	NM_001170787	244682	Mm.187021	NM_001033359	ENSMUSG00000039488	Cntn5	6720426O10Rik|A830025P08Rik|Gm507|NB-2	contactin 5	protein-coding
mm_163413.1	chr12	78980524	78980524	-	1	NA	intron (NM_178745, intron 1 of 2)	intron (NM_178745, intron 1 of 2)	2954	NM_001170401	268567	Mm.341747	NM_178745	ENSMUSG00000046157	Tmem229b	6330442E10Rik|9830138K24|AU019070	transmembrane protein 229B	protein-coding
mm_30447.1	chr3	153733910	153733929	-	1	NA	Intergenic	B3|SINE|B2	-8786	NM_011372	20447	Mm.296453	NM_011372	ENSMUSG00000052544	St6galnac3	Siat7c	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 3	protein-coding
mm_73889.1	chr8	119404583	119404595	+	1	NA	intron (NM_019966, intron 3 of 4)	intron (NM_019966, intron 3 of 4)	9697	NM_019966	56690	Mm.423037	NM_019966	ENSMUSG00000074064	Mlycd	AI324784|Mcd	malonyl-CoA decarboxylase	protein-coding
mm_50535.1	chr6	49045824	49045834	+	1	NA	intron (NM_053110, intron 4 of 10)	intron (NM_053110, intron 4 of 10)	9311	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_147280.1	chr18	39487027	39487045	-	1	NA	exon (NM_008173, exon 1 of 8)	exon (NM_008173, exon 1 of 8)	209	NM_008173	14815	Mm.129481	NM_008173	ENSMUSG00000024431	Nr3c1	GR|Grl-1|Grl1	nuclear receptor subfamily 3, group C, member 1	protein-coding
mm_142226.1	chr17	37480735	37480747	-	1	NA	TTS (NM_008204)	TTS (NM_008204)	2788	NM_008204	14990	Mm.329041	NM_008204	ENSMUSG00000016283	H2-M2	H-2M2|Thy19.4	histocompatibility 2, M region locus 2	protein-coding
mm_141683.1	chr17	33940300	33940342	-	1	NA	promoter-TSS (NM_010385)	promoter-TSS (NM_010385)	9	NM_001185182	14976	Mm.2948	NM_010385	ENSMUSG00000024309	Pfdn6	H-2Ke2|H2-Ke2|Ke-2	prefoldin subunit 6	protein-coding
mm_19629.1	chr2	102813731	102813741	-	1	NA	3' UTR (NM_009851, exon 19 of 19)	3' UTR (NM_009851, exon 19 of 19)	87929	NM_001177785	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_120387.1	chr14	64590379	64590389	+	1	NA	promoter-TSS (NR_029813)	promoter-TSS (NR_029813)	-273	NR_029813	387233		NR_029813	ENSMUSG00000065597	Mir124a-1	Mirn124a|Mirn124a-1	microRNA 124a-1	ncRNA
mm_11421.1	chr2	31759902	31759921	+	1	NA	promoter-TSS (NM_009594)	promoter-TSS (NM_009594)	-28	NM_009594	11350	Mm.1318	NM_009594	ENSMUSG00000026842	Abl1	AI325092|Abl|E430008G22Rik|c-Abl	c-abl oncogene 1, non-receptor tyrosine kinase	protein-coding
mm_7643.1	chr1	128103017	128103053	-	1	NA	promoter-TSS (NM_001285945)	promoter-TSS (NM_001285945)	12	NM_001285945	226409	Mm.425048	NM_027678	ENSMUSG00000036086	Zranb3	4933425L19Rik|AH2|AI316834|C730006D09	zinc finger, RAN-binding domain containing 3	protein-coding
mm_12550.1	chr2	72405699	72405712	+	1	NA	3' UTR (NM_001164791, exon 12 of 12)	3' UTR (NM_001164791, exon 12 of 12)	-70514	NM_025866	66953	Mm.270676	NM_025866	ENSMUSG00000055612	Cdca7	2310021G01Rik|AU044109|JPO1	cell division cycle associated 7	protein-coding
mm_145911.1	chr18	66458588	66458604	+	1	NA	promoter-TSS (NM_021451)	promoter-TSS (NM_021451)	-8	NM_021451	58801	Mm.271878	NM_021451	ENSMUSG00000024521	Pmaip1	Noxa	phorbol-12-myristate-13-acetate-induced protein 1	protein-coding
mm_12210.1	chr2	67173885	67173894	+	1	NA	promoter-TSS (NM_001033477)	promoter-TSS (NM_001033477)	55	NM_001033477	383709	Mm.244520	NM_001033477		Gm1322	-	predicted gene 1322	protein-coding
mm_76967.1	chr8	106280966	106281008	-	1	NA	intron (NM_021491, intron 2 of 8)	intron (NM_021491, intron 2 of 8)	-1242	NR_126091	75044	Mm.445896	NR_126090		4930506A18Rik	-	RIKEN cDNA 4930506A18 gene	ncRNA
mm_42.1	chr1	6487372	6487378	+	1	NA	5' UTR (NM_001244693, exon 1 of 23)	5' UTR (NM_001244693, exon 1 of 23)	144	NM_001244692	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding
mm_154179.1	chr19	58744159	58744170	-	1	NA	TTS (NM_018874)	TTS (NM_018874)	15277	NM_018874	18946	Mm.10753	NM_018874	ENSMUSG00000042179	Pnliprp1	Plrp1	pancreatic lipase related protein 1	protein-coding
mm_43242.1	chr5	130079440	130079448	+	1	NA	promoter-TSS (NM_001130476)	promoter-TSS (NM_001130476)	74	NM_001130476	22021	Mm.332720	NM_013837	ENSMUSG00000034118	Tpst1	R75054|Tango13a	protein-tyrosine sulfotransferase 1	protein-coding
mm_15582.1	chr2	158723456	158723467	+	1	NA	intron (NM_153089, intron 2 of 10)	intron (NM_153089, intron 2 of 10)	-44638	NM_027975	71878	Mm.85162	NM_027975	ENSMUSG00000027654	Fam83d	2310007D09Rik|BB104611	family with sequence similarity 83, member D	protein-coding
mm_122279.1	chr14	34422752	34422754	-	1	NA	exon (NM_009758, exon 10 of 13)	exon (NM_009758, exon 10 of 13)	47249	NM_153127	105450	Mm.272673	NM_153127	ENSMUSG00000041445	Mmrn2	AA986839|ENDOGLYX1|Emilin3|EndoGlyx-1	multimerin 2	protein-coding
mm_137048.1	chr17	17917789	17917802	+	1	NA	Intergenic	Intergenic	29971	NM_008039	14289	Mm.378918	NM_008039	ENSMUSG00000052270	Fpr2	E330010I07Rik|Fpr-rs2	formyl peptide receptor 2	protein-coding
mm_142673.1	chr17	47730630	47730632	-	1	NA	exon (NM_025973, exon 5 of 9)	exon (NM_025973, exon 5 of 9)	3789	NM_025973	109820	Mm.22957	NM_025973	ENSMUSG00000023987	Pgc	2210410L06Rik|Upg-1|Upg1	progastricsin (pepsinogen C)	protein-coding
mm_13650.1	chr2	114054392	114054415	+	1	NA	promoter-TSS (NR_028422)	promoter-TSS (NR_028422)	7	NR_028422	100303644	Mm.330469	NR_028422	ENSMUSG00000092397	C130080G10Rik	-	RIKEN cDNA C130080G10 gene	ncRNA
mm_73718.1	chr8	112011366	112011388	+	1	NA	promoter-TSS (NM_001286384)	promoter-TSS (NM_001286384)	18	NM_020584	57321	Mm.213064	NM_020584	ENSMUSG00000033430	Terf2ip	Rap1	telomeric repeat binding factor 2, interacting protein	protein-coding
mm_8312.1	chr1	144245175	144245219	-	1	NA	3' UTR (NM_015811, exon 5 of 5)	3' UTR (NM_015811, exon 5 of 5)	3907	NM_015811	50778	Mm.103701	NM_015811	ENSMUSG00000026358	Rgs1	BL34	regulator of G-protein signaling 1	protein-coding
mm_16231.1	chr2	173156139	173156162	+	1	NA	intron (NM_011044, intron 6 of 9)	intron (NM_011044, intron 6 of 9)	3077	NM_011044	18534	Mm.266867	NM_011044	ENSMUSG00000027513	Pck1	AI265463|PEPCK|Pck-1	phosphoenolpyruvate carboxykinase 1, cytosolic	protein-coding
mm_22231.1	chr2	174433628	174433652	-	1	NA	exon (NM_022325, exon 3 of 6)	exon (NM_022325, exon 3 of 6)	5399	NM_022325	64138	Mm.156919	NM_022325	ENSMUSG00000016256	Ctsz	AI787083|AU019819|CTSX|D2Wsu143e	cathepsin Z	protein-coding
mm_62729.1	chr7	110783494	110783496	+	1	NA	intron (NM_001276301, intron 2 of 14)	intron (NM_001276301, intron 2 of 14)	10891	NM_009667	11717	Mm.3238	NM_009667	ENSMUSG00000005686	Ampd3	-	adenosine monophosphate deaminase 3	protein-coding
mm_106020.1	chr11	116023965	116023977	-	1	NA	exon (NM_008211, exon 2 of 4)	exon (NM_008211, exon 2 of 4)	533	NM_008211	15081	Mm.18516	NM_008211	ENSMUSG00000016559	H3f3b	9430068D06Rik|H3.3B	H3 histone, family 3B	protein-coding
mm_42618.1	chr5	118027856	118027860	+	1	NA	promoter-TSS (NM_021344)	promoter-TSS (NM_021344)	34	NM_021344	57816	Mm.273285	NM_021344	ENSMUSG00000029359	Tesc	1010001A17Rik|2410011K10Rik|TE-1	tescalcin	protein-coding
mm_131077.1	chr16	4726375	4726439	+	1	NA	promoter-TSS (NM_001136066)	promoter-TSS (NM_001136066)	46	NM_001136066	15369	Mm.272866	NM_010443	ENSMUSG00000004070	Hmox2	HO-2|HO2	heme oxygenase 2	protein-coding
mm_14356.1	chr2	129615532	129615548	+	1	NA	exon (NM_007547, exon 3 of 8)	exon (NM_007547, exon 3 of 8)	22371	NM_001291022	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_32324.1	chr4	103804863	103804864	+	1	NA	Intergenic	Intergenic	422363	NR_040673	622167	Mm.244115	NR_040673	ENSMUSG00000086136	Gm12718	OTTMUSG00000008109	predicted gene 12718	ncRNA
mm_50777.1	chr6	53681014	53681060	+	1	NA	exon (NM_172728, exon 4 of 7)	exon (NM_172728, exon 4 of 7)	107663	NM_172728	231991	Mm.227444	NM_172728	ENSMUSG00000053007	Creb5	9430076C15Rik|CRE-BPa|Crebpa|D430026C09Rik	cAMP responsive element binding protein 5	protein-coding
mm_56150.1	chr6	87843462	87843539	-	1	NA	3' UTR (NM_013493, exon 5 of 5)	3' UTR (NM_013493, exon 5 of 5)	-4741	NM_133934	57905	Mm.241546	NM_133934	ENSMUSG00000030056	Isy1	5830446M03Rik|AI181014|AU020769	ISY1 splicing factor homolog	protein-coding
mm_3335.1	chr1	137960496	137960503	+	1	NA	Intergenic	Intergenic	-5956	NR_029795	735252		NR_029795	ENSMUSG00000065565	Mir181a-1	Mirn181a-1|Mirn213|miR-213|mir-181a-1|mmu-mir-213	microRNA 181a-1	ncRNA
mm_57866.1	chr6	129623841	129623866	-	1	NA	promoter-TSS (NM_001286018)	promoter-TSS (NM_001286018)	11	NM_001083322	27007	Mm.8217	NM_033078	ENSMUSG00000030149	Klrk1	D6H12S2489E|NKG2-D|Nkg2d	killer cell lectin-like receptor subfamily K, member 1	protein-coding
mm_40174.1	chr5	35950882	35950895	+	1	NA	exon (NM_027373, exon 6 of 17)	exon (NM_027373, exon 6 of 17)	57569	NM_027373	70292	Mm.125167	NM_027373	ENSMUSG00000029094	Afap1	2600003E23Rik|9630044L16Rik|AI848729|Afap|mKIAA3018	actin filament associated protein 1	protein-coding
mm_63633.1	chr7	128523577	128523598	+	1	NA	promoter-TSS (NM_013863)	promoter-TSS (NM_013863)	4	NM_013863	29810	Mm.84073	NM_013863	ENSMUSG00000030847	Bag3	AA407278|Bis|mg638	BCL2-associated athanogene 3	protein-coding
mm_92463.1	chr10	77969809	77969839	-	1	NA	promoter-TSS (NM_138301)	promoter-TSS (NM_138301)	48	NM_138301	28240	Mm.276762	NM_138301	ENSMUSG00000009292	Trpm2	9830168K16Rik|C79133|LTRPC2|TRPC7|Trp7|Trrp7	transient receptor potential cation channel, subfamily M, member 2	protein-coding
mm_42998.1	chr5	123401075	123401084	+	1	NA	intron (NM_133917, intron 1 of 16)	ID_B1|SINE|B4	6281	NM_177582	208104	Mm.83277	NM_133917	ENSMUSG00000038342	Mlxip	AW228700|Mir|bHLHe36	MLX interacting protein	protein-coding
mm_91999.1	chr10	62194200	62194211	-	1	NA	promoter-TSS (NR_106122)	promoter-TSS (NR_106122)	22	NR_106122	102465767		NR_106122	ENSMUSG00000099185	Mir7662	Gm27876|mmu-mir-7662	microRNA 7662	ncRNA
mm_121539.1	chr14	122464148	122464160	+	1	NA	exon (NM_022987, exon 1 of 2)	exon (NM_022987, exon 1 of 2)	1504	NM_022987	65100	Mm.390761	NM_022987	ENSMUSG00000041703	Zic5	1700049L20Rik|Opr	zinc finger protein of the cerebellum 5	protein-coding
mm_169399.1	chr14	47569401	47569405	+	1	NA	promoter-TSS (NM_172599)	promoter-TSS (NM_172599)	-969	NM_172599	100504663	Mm.287279	NM_172599	ENSMUSG00000037526	Atg14	4832427M01|Atg14L|D14Ertd114e|D14Ertd436e	autophagy related 14	protein-coding
mm_107067.1	chr12	16894828	16894887	+	1	NA	promoter-TSS (NM_009072)	promoter-TSS (NM_009072)	-121	NM_009072	19878	Mm.276024	NM_009072	ENSMUSG00000020580	Rock2	B230113H15Rik|ROKalpha|Rho-kinase|Rock-II|Rock2m|mKIAA0619	Rho-associated coiled-coil containing protein kinase 2	protein-coding
mm_147548.1	chr18	54840135	54840137	-	1	NA	Intergenic	Intergenic	150044	NM_175751	269023	Mm.192984	NM_175751	ENSMUSG00000052713	Zfp608	4932417D18Rik|D430007A19Rik|Znf608	zinc finger protein 608	protein-coding
mm_75141.1	chr8	35415391	35415424	-	1	NA	Intergenic	Intergenic	39666	NM_177741	244416	Mm.247126	NM_177741	ENSMUSG00000046794	Ppp1r3b	6430576E21|AW821953|GL|PTG	protein phosphatase 1, regulatory (inhibitor) subunit 3B	protein-coding
mm_151142.1	chr19	53076239	53076247	+	1	NA	promoter-TSS (NR_045320)	promoter-TSS (NR_045320)	-9	NR_045320	78457	Mm.76932	NR_045320	ENSMUSG00000099988	1700054A03Rik	-	RIKEN cDNA 1700054A03 gene	ncRNA
mm_37870.1	chr4	132352215	132352233	-	1	NA	non-coding (NR_003270, exon 3 of 3)	non-coding (NR_003270, exon 3 of 3)	1462	NR_003270	399101	Mm.486919	NR_002904	ENSMUSG00000085241	Snhg3	Rnu17d|U17HG	small nucleolar RNA host gene 3	ncRNA
mm_105869.1	chr11	114237208	114237213	-	1	NA	Intergenic	MTE2a|LTR|ERVL-MaLR	38952	NR_045930	73536	Mm.54275	NR_045930	ENSMUSG00000078600	1700092K14Rik	-	RIKEN cDNA 1700092K14 gene	ncRNA
mm_12886.1	chr2	84742999	84743012	+	1	NA	Intergenic	Intergenic	-1827	NR_029544	387149		NR_029544	ENSMUSG00000065484	Mir130a	Mirn130|Mirn130a|mir-130a	microRNA 130a	ncRNA
mm_37991.1	chr4	133633420	133633525	-	1	NA	promoter-TSS (NM_001017968)	promoter-TSS (NM_001017968)	-43	NM_001017968	503610	Mm.331948	NM_001017968	ENSMUSG00000037553	Zdhhc18	-	zinc finger, DHHC domain containing 18	protein-coding
mm_144455.1	chr18	23352616	23352620	+	1	NA	intron (NM_001285813, intron 1 of 21)	intron (NM_001285813, intron 1 of 21)	42598	NM_001285813	13527	Mm.94371	NM_010087	ENSMUSG00000024302	Dtna	2210407P21Rik|DTN-A|Dtn|Gm19389|a-DB-1|adbn	dystrobrevin alpha	protein-coding
mm_51352.1	chr6	72556162	72556177	+	1	NA	exon (NM_001042534, exon 5 of 10)	exon (NM_001042534, exon 5 of 10)	6522	NM_001271395	12332	Mm.18626	NM_007599	ENSMUSG00000056737	Capg	gCap39|mbh1	capping protein (actin filament), gelsolin-like	protein-coding
mm_13160.1	chr2	92599672	92599724	+	1	NA	promoter-TSS (NM_023850)	promoter-TSS (NM_023850)	-9	NM_023850	76969	Mm.38021	NM_023850	ENSMUSG00000027221	Chst1	2610008E20Rik|AW125896|C6ST|GST-1|Gst1|KSGAL6ST	carbohydrate (keratan sulfate Gal-6) sulfotransferase 1	protein-coding
mm_159677.1	chr4	155992874	155992874	+	1	NA	promoter-TSS (NM_011341)	promoter-TSS (NM_011341)	31	NM_011341	20318	Mm.293517	NM_011341	ENSMUSG00000029076	Sdf4	Cab45	stromal cell derived factor 4	protein-coding
mm_156787.1	chrX	162500432	162500446	+	1	NA	intron (NM_178256, intron 13 of 17)	L1M5|LINE|L1	143219	NM_001290633	194590	Mm.442441	NM_178256	ENSMUSG00000040855	Reps2	POB1	RALBP1 associated Eps domain containing protein 2	protein-coding
mm_110298.1	chr12	32569062	32569069	-	1	NA	Intergenic	Intergenic	190276	NM_001162903	72123	Mm.341352	NM_028111	ENSMUSG00000090946	Ccdc71l	2010109K11Rik|AV375874	coiled-coil domain containing 71 like	protein-coding
mm_42612.1	chr5	117976738	117976748	+	1	NA	promoter-TSS (NM_001346588)	promoter-TSS (NM_001346588)	-27	NM_145564	231670	Mm.21912	NM_145564	ENSMUSG00000032898	Fbxo21	2810425J22Rik|AU016673	F-box protein 21	protein-coding
mm_128044.1	chr15	25396026	25396026	-	1	NA	intron (NM_027395, intron 1 of 1)	intron (NM_027395, intron 1 of 1)	17738	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	brain abundant, membrane attached signal protein 1	protein-coding
mm_110623.1	chr12	57181454	57181461	-	1	NA	intron (NM_172577, intron 1 of 9)	intron (NM_172577, intron 1 of 9)	16015	NM_172577	217593	Mm.32835	NM_172577	ENSMUSG00000035472	Slc25a21	9930033G19Rik|A630030I10|BB158148	solute carrier family 25 (mitochondrial oxodicarboxylate carrier), member 21	protein-coding
mm_121027.1	chr14	79704072	79704082	+	1	NA	intron (NR_045060, intron 1 of 3)	intron (NR_045060, intron 1 of 3)	1157	NR_045060	73989	Mm.107775	NR_045060		4930452G13Rik	-	RIKEN cDNA 4930452G13 gene	ncRNA
mm_39109.1	chr4	154928104	154928147	-	1	NA	promoter-TSS (NM_178931)	promoter-TSS (NM_178931)	-48	NM_178931	230979	Mm.215147	NM_178931	ENSMUSG00000042333	Tnfrsf14	Atar|HveA|Hvem|Tnfrs14	tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)	protein-coding
mm_35146.1	chr4	11738078	11738079	-	1	NA	Intergenic	Intergenic	-20079	NM_019753	12557	Mm.33402	NM_019753	ENSMUSG00000028217	Cdh17	HPT-1|HPT-1/LI	cadherin 17	protein-coding
mm_80209.1	chr9	72442256	72442261	+	1	NA	intron (NM_008613, intron 2 of 9)	intron (NM_008613, intron 2 of 9)	3729	NM_008613	17427	Mm.387671	NM_008613	ENSMUSG00000032221	Mns1	AW546487	meiosis-specific nuclear structural protein 1	protein-coding
mm_89891.1	chr10	110745434	110745533	+	1	NA	promoter-TSS (NM_178609)	promoter-TSS (NM_178609)	18	NM_178609	52679	Mm.11747	NM_178609	ENSMUSG00000020185	E2f7	A630014C11Rik|D10Ertd739e	E2F transcription factor 7	protein-coding
mm_124259.1	chr14	102977858	102977926	-	1	NA	3' UTR (NM_177715, exon 1 of 1)	3' UTR (NM_177715, exon 1 of 1)	4740	NR_039592	100628599		NR_039592	ENSMUSG00000092901	Mir5130	mir-5130|mmu-mir-5130|mu-mir-5130	microRNA 5130	ncRNA
mm_28344.1	chr3	89411841	89411894	-	1	NA	promoter-TSS (NM_177041)	promoter-TSS (NM_177041)	-4	NM_177041	319945	Mm.258142	NM_177041	ENSMUSG00000042642	Flad1	A930017E24Rik|Pp591	flavin adenine dinucleotide synthetase 1	protein-coding
mm_54753.1	chr6	41034289	41034304	-	1	NA	exon (NM_023333, exon 2 of 5)	exon (NM_023333, exon 2 of 5)	1213	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_153556.1	chr19	42129044	42129069	-	1	NA	promoter-TSS (NM_027106)	promoter-TSS (NM_027106)	-63	NM_027106	69534	Mm.30060	NM_027106	ENSMUSG00000018821	Avpi1	2310008N12Rik|AA410041|VIT32|esu|mVIT32	arginine vasopressin-induced 1	protein-coding
mm_132165.1	chr16	32271546	32271559	+	1	NA	promoter-TSS (NM_183283)	promoter-TSS (NM_183283)	-57	NM_183283	69576	Mm.432545	NM_183283	ENSMUSG00000046345	Smco1	2310010M20Rik	single-pass membrane protein with coiled-coil domains 1	protein-coding
mm_16707.1	chr2	7083561	7083576	-	1	NA	intron (NM_001110231, intron 3 of 15)	intron (NM_001110231, intron 3 of 15)	-2266	NM_001160292	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_38251.1	chr4	136688009	136688019	-	1	NA	intron (NM_001290753, intron 5 of 15)	intron (NM_001290753, intron 5 of 15)	65393	NM_001243262	242707	Mm.448979	NM_001243262	ENSMUSG00000070683	Lactbl1	-	lactamase, beta-like 1	protein-coding
mm_36458.1	chr4	82505597	82505601	-	1	NA	5' UTR (NM_001113209, exon 1 of 12)	5' UTR (NM_001113209, exon 1 of 12)	180	NM_001286127	18028	Mm.317947	NM_008687	ENSMUSG00000008575	Nfib	6720429L07Rik|CTF|E030026I10Rik|NF-I/B|NF1-B|NFI-B	nuclear factor I/B	protein-coding
mm_85815.1	chr9	110388352	110388363	-	1	NA	exon (NM_001081043, exon 20 of 25)	exon (NM_001081043, exon 20 of 25)	19853	NM_001081043	104831	Mm.335477	NM_001081043	ENSMUSG00000036057	Ptpn23	AI462446|PTP-TD14	protein tyrosine phosphatase, non-receptor type 23	protein-coding
mm_91937.1	chr10	60738195	60738198	-	1	NA	intron (NM_023596, intron 2 of 5)	intron (NM_023596, intron 2 of 5)	14586	NM_023596	71279	Mm.284462	NM_023596	ENSMUSG00000020100	Slc29a3	4933435C21Rik|AW987637|Ent3	solute carrier family 29 (nucleoside transporters), member 3	protein-coding
mm_126850.1	chr15	89180922	89180943	+	1	NA	promoter-TSS (NM_001284506)	promoter-TSS (NM_001284506)	-144	NM_138749	140570	Mm.267514	NM_138749	ENSMUSG00000036606	Plxnb2	Debt|plexin-B2	plexin B2	protein-coding
mm_88772.1	chr10	80336110	80336122	+	1	NA	3' UTR (NM_139292, exon 6 of 6)	3' UTR (NM_139292, exon 6 of 6)	5971	NM_139292	70335	Mm.28147	NM_139292	ENSMUSG00000035504	Reep6	0610011M24Rik|Dp1l1	receptor accessory protein 6	protein-coding
mm_86488.1	chr10	5548717	5548718	+	1	NA	intron (NM_001347732, intron 1 of 145)	intron (NM_001347732, intron 1 of 145)	1975	NM_153399	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_90460.1	chr10	127743761	127743777	+	1	NA	3' UTR (NM_198035, exon 2 of 2)	3' UTR (NM_198035, exon 2 of 2)	4231	NM_198035	320080	Mm.27258	NM_198035	ENSMUSG00000044617	Zbtb39	7030401O21Rik|mKIAA0352	zinc finger and BTB domain containing 39	protein-coding
mm_30527.1	chr4	3090383	3090428	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	-81678	NM_001167534	100312470	Mm.480297	NM_001167534	ENSMUSG00000094798	Vmn1r2	Gm11776|OTTMUSG00000004179	vomeronasal 1 receptor 2	protein-coding
mm_135163.1	chr16	35869182	35869194	-	1	NA	intron (NM_001039530, intron 1 of 16)	intron (NM_001039530, intron 1 of 16)	2194	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_166637.1	chr6	82805089	82805109	-	1	NA	Intergenic	MER45B|DNA|hAT-Tip100	-30645	NM_013820	15277	Mm.255848	NM_013820	ENSMUSG00000000628	Hk2	AI642394|HKII	hexokinase 2	protein-coding
mm_173072.1	chrX	136139106	136139111	+	1	NA	promoter-TSS (NM_212457)	promoter-TSS (NM_212457)	63	NM_212457	406217	Mm.336245	NM_212457	ENSMUSG00000047844	Bex4	-	brain expressed X-linked 4	protein-coding
mm_101283.1	chr11	21571799	21571827	-	1	NA	promoter-TSS (NM_145425)	promoter-TSS (NM_145425)	121	NM_008618	17449	Mm.212703	NM_008618	ENSMUSG00000020321	Mdh1	B230377B03Rik|D17921|MDH-s|MDHA|Mor-2|Mor2	malate dehydrogenase 1, NAD (soluble)	protein-coding
mm_144862.1	chr18	36720217	36720239	+	1	NA	Intergenic	Intergenic	6587	NM_009841	12475	Mm.3460	NM_009841	ENSMUSG00000051439	Cd14	-	CD14 antigen	protein-coding
mm_96499.1	chr11	68431904	68431916	+	1	NA	promoter-TSS (NM_177320)	promoter-TSS (NM_177320)	-215	NM_177320	320207	Mm.244960	NM_177320	ENSMUSG00000020901	Pik3r5	AV230647|F730038I15Rik	phosphoinositide-3-kinase, regulatory subunit 5, p101	protein-coding
mm_109438.1	chr12	110696594	110696635	+	1	NA	promoter-TSS (NM_010480)	promoter-TSS (NM_010480)	-219	NM_010480	15519	Mm.1843	NM_010480	ENSMUSG00000021270	Hsp90aa1	86kDa|89kDa|AL024080|AL024147|Hsp86-1|Hsp89|Hsp90|Hspca|hsp4	heat shock protein 90, alpha (cytosolic), class A member 1	protein-coding
mm_150646.1	chr19	41911852	41911874	+	1	NA	promoter-TSS (NM_023418)	promoter-TSS (NM_023418)	-8	NM_023418	18648	Mm.16783	NM_023418	ENSMUSG00000011752	Pgam1	2310050F24Rik|Pgam-1	phosphoglycerate mutase 1	protein-coding
mm_32955.1	chr4	119637728	119637739	+	1	NA	promoter-TSS (NM_008190)	promoter-TSS (NM_008190)	1	NM_008190	14915	Mm.2614	NM_008190	ENSMUSG00000023247	Guca2a	Guca2	guanylate cyclase activator 2a (guanylin)	protein-coding
mm_140451.1	chr17	88626570	88626604	+	1	NA	promoter-TSS (NM_029858)	promoter-TSS (NM_029858)	32	NM_029858	77057	Mm.482203	NM_029858	ENSMUSG00000033855	Ston1	4921524J06Rik|C86231|Salf|Sblf	stonin 1	protein-coding
mm_68400.1	chr7	109602653	109602709	-	1	NA	intron (NM_001001326, intron 1 of 19)	intron (NM_001001326, intron 1 of 19)	13887	NR_037617	76954	Mm.252009	NM_029811	ENSMUSG00000031024	St5	2010004M01Rik|2610305K15Rik	suppression of tumorigenicity 5	protein-coding
mm_8749.1	chr1	160307352	160307391	-	1	NA	intron (NM_001038621, intron 2 of 8)	intron (NM_001038621, intron 2 of 8)	-11399	NR_035448	100316784		NR_035448	ENSMUSG00000089204	Mir1927	mmu-mir-1927	microRNA 1927	ncRNA
mm_163880.1	chr14	21276887	21276887	+	1	NA	intron (NM_001243041, intron 6 of 10)	intron (NM_001243041, intron 6 of 10)	200735	NM_001243041	11534	Mm.188734	NM_134079	ENSMUSG00000039197	Adk	2310026J05Rik|5033405D03Rik|AI255373|AI987814|Ak	adenosine kinase	protein-coding
mm_59482.1	chr7	27462580	27462604	+	1	NA	exon (NM_144923, exon 4 of 5)	exon (NM_144923, exon 4 of 5)	10174	NM_001290525	233016	Mm.24021	NM_144923	ENSMUSG00000040466	Blvrb	-	biliverdin reductase B (flavin reductase (NADPH))	protein-coding
mm_102664.1	chr11	64774641	64774644	-	1	NA	Intergenic	Intergenic	-204393	NM_023479	68626	Mm.157711	NM_023479	ENSMUSG00000020549	Elac2	1110017O07Rik|D11Wsu80e|Hpc2	elaC ribonuclease Z 2	protein-coding
mm_98283.1	chr11	89060733	89060754	+	1	NA	promoter-TSS (NM_019505)	promoter-TSS (NM_019505)	5	NM_019505	56077	Mm.153695	NM_019505	ENSMUSG00000000276	Dgke	C87606|DAGK6|DGK	diacylglycerol kinase, epsilon	protein-coding
mm_125309.1	chr15	37517484	37517488	+	1	NA	intron (NM_001170866, intron 4 of 6)	intron (NM_001170866, intron 4 of 6)	-58104	NM_001170868	52589	Mm.283370	NM_134094	ENSMUSG00000051359	Ncald	AI848120|D030020D09Rik|D15Ertd412e	neurocalcin delta	protein-coding
mm_60418.1	chr7	44476297	44476325	+	1	NA	Intergenic	L1MEd|LINE|L1	5964	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_151358.1	chr19	55910560	55910577	+	1	NA	intron (NM_001142924, intron 2 of 11)	intron (NM_001142924, intron 2 of 11)	15247	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_51287.1	chr6	72304627	72304645	+	1	NA	promoter-TSS (NM_001282071)	promoter-TSS (NM_001282071)	26	NM_147779	20388	Mm.46033	NM_147779	ENSMUSG00000056370	Sftpb	AI562151|SF-B|SP-B|Sftp-3|Sftp3	surfactant associated protein B	protein-coding
mm_87875.1	chr10	61595294	61595297	+	1	NA	promoter-TSS (NM_001177511)	promoter-TSS (NM_001177511)	-189	NM_001177511	237362	Mm.131297	NM_001177511	ENSMUSG00000020090	Npffr1	Gm236|Gpr147|NPFF1|NPFF1R|OT7T022	neuropeptide FF receptor 1	protein-coding
mm_159180.1	chr2	111421196	111421196	-	1	NA	promoter-TSS (NM_207254)	promoter-TSS (NM_207254)	-247	NM_207254	277562	Mm.377872	NM_207254	ENSMUSG00000096703	Olfr1286	GA_x5J8B7TU5VU-1563-1372|GA_x6K02T2Q125-72472405-72471488|MOR248-21	olfactory receptor 1286	protein-coding
mm_84961.1	chr9	83779090	83779093	-	1	NA	3' UTR (NM_148941, exon 6 of 6)	3' UTR (NM_148941, exon 6 of 6)	27214	NM_148941	83603	Mm.83949	NM_148941	ENSMUSG00000032262	Elovl4	-	elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 4	protein-coding
mm_8503.1	chr1	154116145	154116171	-	1	NA	Intergenic	Intergenic	-85029	NM_001204908	100503355	Mm.484410	NM_001204908	ENSMUSG00000066797	Zfp648	ENSMUSG00000066797|Gm10178|Gm203	zinc finger protein 648	protein-coding
mm_163925.1	chr14	47064997	47065003	+	1	NA	intron (NM_001037221, intron 5 of 12)	intron (NM_001037221, intron 5 of 12)	-3977	NM_001310544	74480	Mm.214454	NM_028966	ENSMUSG00000021838	Samd4	1700024G08Rik|1700111L17Rik|4933436G17Rik|Samd4a|Smaug|Smaug1|sunk	sterile alpha motif domain containing 4	protein-coding
mm_78747.1	chr9	42142077	42142092	+	1	NA	Intergenic	Intergenic	-17795	NM_011436	20660	Mm.121920	NM_011436	ENSMUSG00000049313	Sorl1	2900010L19Rik|AI596264|AW261561|LR11|SorLA|gp250|mSorLA	sortilin-related receptor, LDLR class A repeats-containing	protein-coding
mm_142723.1	chr17	48146307	48146311	-	1	NA	promoter-TSS (NM_177824)	promoter-TSS (NM_177824)	-2	NM_001177896	328829	Mm.466999	NM_177824	ENSMUSG00000073386	9830107B12Rik	Trem5	RIKEN cDNA 9830107B12 gene	protein-coding
mm_75869.1	chr8	70763763	70763825	-	1	NA	exon (NM_023065, exon 6 of 8)	exon (NM_023065, exon 6 of 8)	2869	NM_023065	65972	Mm.30241	NM_023065	ENSMUSG00000031838	Ifi30	GILT|IP30	interferon gamma inducible protein 30	protein-coding
mm_141454.1	chr17	30398259	30398263	-	1	NA	intron (NM_172618, intron 6 of 11)	intron (NM_172618, intron 6 of 11)	-2081	NR_030688	623169	Mm.440508	NR_030688		Gm6402	EG623169	ribosomal protein S17 pseudogene	pseudo
mm_54239.1	chr6	28243795	28243805	-	1	NA	exon (NM_001081678, exon 5 of 6)	exon (NM_001081678, exon 5 of 6)	17801	NM_001081678	627049	Mm.84441	NM_001081678	ENSMUSG00000039841	Zfp800	AA407452|Znf800	zinc finger protein 800	protein-coding
mm_128086.1	chr15	27755473	27755478	-	1	NA	intron (NM_001081302, intron 42 of 56)	B3|SINE|B2	-73933	NM_001242423	223433	Mm.266485	NM_198301	ENSMUSG00000056069	Fam105a	9830126M18	family with sequence similarity 105, member A	protein-coding
mm_131398.1	chr16	14361447	14361451	+	1	NA	promoter-TSS (NM_008576)	promoter-TSS (NM_008576)	-109	NM_008576	17250	Mm.196634	NM_008576	ENSMUSG00000023088	Abcc1	Abcc1a|Abcc1b|MRP|Mdrap|Mrp1	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	protein-coding
mm_145209.1	chr18	50030660	50030683	+	1	NA	intron (NM_001177759, intron 1 of 1)	intron (NM_001177759, intron 1 of 1)	-22611	NM_134131	106869	Mm.27740	NM_134131	ENSMUSG00000062210	Tnfaip8	AA987150|E130304C20Rik|ENSMUSG00000073567|Gg2-1|Gm10539|Nded|Ssc-2|Tipe	tumor necrosis factor, alpha-induced protein 8	protein-coding
mm_104010.1	chr11	85139940	85139971	-	1	NA	promoter-TSS (NM_001029934)	promoter-TSS (NM_001029934)	0	NM_001029934	237898	Mm.178524	NM_001029934	ENSMUSG00000000804	Usp32	2900074J03Rik|6430526O11Rik|AW045245	ubiquitin specific peptidase 32	protein-coding
mm_113228.1	chr13	27196641	27196646	+	1	NA	promoter-TSS (NM_013766)	promoter-TSS (NM_013766)	-17	NM_013766	27372	Mm.291456	NM_013766	ENSMUSG00000017922	Prl3c1	Ghd7|PLP-J|Prlpi|Prlpj|decidualin	prolactin family 3, subfamily c, member 1	protein-coding
mm_95731.1	chr11	54626499	54626509	+	1	NA	intron (NM_175258, intron 10 of 27)	intron (NM_175258, intron 10 of 27)	30358	NM_001252497	192786	Mm.254404	NM_175258	ENSMUSG00000037533	Rapgef6	A530068K01|AI844632|BB085664|C030018K18Rik|PDZ-GEF2|Pdzgef2|RA-GEF-2|Ragef2|mKIAA4052	Rap guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_128641.1	chr15	59275203	59275246	-	1	NA	Intergenic	Intergenic	-31724	NR_045613	100416830	Mm.490788	NR_045613	ENSMUSG00000098528	Zfp572	4930472F24Rik	zinc finger protein 572	pseudo
mm_135649.1	chr16	52389472	52389491	-	1	NA	intron (NM_009655, intron 1 of 15)	intron (NM_009655, intron 1 of 15)	63600	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_36214.1	chr4	62502177	62502182	-	1	NA	promoter-TSS (NM_024257)	promoter-TSS (NM_024257)	21	NM_024257	72748	Mm.41506	NM_024257	ENSMUSG00000038422	Hdhd3	2810435D12Rik	haloacid dehalogenase-like hydrolase domain containing 3	protein-coding
mm_34469.1	chr4	148160148	148160196	+	1	NA	promoter-TSS (NM_001161852)	promoter-TSS (NM_001161852)	-78	NR_104374	230903	Mm.220327	NM_173401	ENSMUSG00000029001	Fbxo44	5730411K09|AV001623|FBG3|FBX30|Fbx6a|Fbxo6a	F-box protein 44	protein-coding
mm_70497.1	chr8	12757079	12757089	+	1	NA	promoter-TSS (NM_001293667)	promoter-TSS (NM_001293667)	68	NM_001293667	50770	Mm.257837	NM_015804	ENSMUSG00000031441	Atp11a	4930558F19Rik|AU040868|Atpc1h|Ih	ATPase, class VI, type 11A	protein-coding
mm_114995.1	chr13	97589970	97589975	+	1	NA	Intergenic	RLTR41|LTR|ERV1	29972	NR_046157	328314	Mm.138047	NR_046157	ENSMUSG00000110235	Gm5086	B230311A21|EG328314	predicted gene 5086	ncRNA
mm_16505.1	chr2	181292738	181292750	+	1	NA	Intergenic	Intergenic	-4778	NM_198169	229004	Mm.220423	NM_198169	ENSMUSG00000038705	Gmeb2	AI839884	glucocorticoid modulatory element binding protein 2	protein-coding
mm_56531.1	chr6	99523374	99523405	-	1	NA	Intergenic	Intergenic	-2396	NM_001347345	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_168900.1	chr12	55080513	55080514	+	1	NA	promoter-TSS (NM_011899)	promoter-TSS (NM_011899)	17	NM_011899	24067	Mm.471968	NM_011899	ENSMUSG00000073079	Srp54a	54kDa|Srp54	signal recognition particle 54A	protein-coding
mm_99752.1	chr11	106723224	106723239	+	1	NA	Intergenic	Intergenic	-7950	NM_001305157	18613	Mm.343951	NM_008816	ENSMUSG00000020717	Pecam1	C85791|Cd31|PECAM-1|Pecam	platelet/endothelial cell adhesion molecule 1	protein-coding
mm_156708.1	chrX	159627385	159627399	+	1	NA	5' UTR (NM_001135727, exon 1 of 18)	5' UTR (NM_001135727, exon 1 of 18)	120	NM_001135727	58194	Mm.286495	NM_021389	ENSMUSG00000040990	Sh3kbp1	1200007H22Rik|1700125L08Rik|5830464D22Rik|AI447724|Cin85|IN85|Ruk|Seta	SH3-domain kinase binding protein 1	protein-coding
mm_66070.1	chr7	30856188	30856200	-	1	NA	promoter-TSS (NM_001033316)	promoter-TSS (NM_001033316)	-16	NM_001033316	233080	Mm.291167	NM_001033316	ENSMUSG00000019429	Ffar3	Gm478|Gpr41	free fatty acid receptor 3	protein-coding
mm_85813.1	chr9	110388204	110388222	-	1	NA	exon (NM_001081043, exon 20 of 25)	exon (NM_001081043, exon 20 of 25)	19997	NM_001081043	104831	Mm.335477	NM_001081043	ENSMUSG00000036057	Ptpn23	AI462446|PTP-TD14	protein tyrosine phosphatase, non-receptor type 23	protein-coding
mm_40277.1	chr5	41762654	41762664	+	1	NA	intron (NM_007524, intron 1 of 1)	intron (NM_007524, intron 1 of 1)	1561	NM_007524	12020	Mm.2530	NM_007524	ENSMUSG00000049691	Nkx3-2	Bapx1|NKX3.2|Nkx-3.2	NK3 homeobox 2	protein-coding
mm_48752.1	chr5	147957730	147957737	-	1	NA	5' UTR (NM_029920, exon 1 of 15)	5' UTR (NM_029920, exon 1 of 15)	413	NM_029920	77521	Mm.244177	NM_029920	ENSMUSG00000029651	Mtus2	5730592G18Rik|A730013O20Rik|AU067634|C130038G02Rik|Cazip|Gm763|mKIAA0774	microtubule associated tumor suppressor candidate 2	protein-coding
mm_84753.1	chr9	75559605	75559665	-	1	NA	promoter-TSS (NM_016963)	promoter-TSS (NM_016963)	22	NM_016963	50875	Mm.38445	NM_016963	ENSMUSG00000058587	Tmod3	U-Tmod|UTMOD	tropomodulin 3	protein-coding
mm_67217.1	chr7	74473323	74473331	-	1	NA	intron (NM_001038643, intron 2 of 10)	intron (NM_001038643, intron 2 of 10)	81453	NM_023908	108116	Mm.425467	NM_023908	ENSMUSG00000025790	Slco3a1	5830414C08Rik|Anr1|MJAM|OATP-D|R75096|Slc21a11	solute carrier organic anion transporter family, member 3a1	protein-coding
mm_121384.1	chr14	118953215	118953229	+	1	NA	intron (NM_008929, intron 2 of 11)	intron (NM_008929, intron 2 of 11)	15290	NM_008929	100037258	Mm.12616	NM_008929	ENSMUSG00000022136	Dnajc3	AA408985|AU067833|Dnajc3a|Dnajc3b|Prkri|mp58|p58|p58IPK	DnaJ heat shock protein family (Hsp40) member C3	protein-coding
mm_64784.1	chr7	5125971	5125978	-	1	NA	promoter-TSS (NM_009028)	promoter-TSS (NM_009028)	-24	NM_009028	19428	Mm.322186	NM_009028	ENSMUSG00000083649	Rasl2-9	M2|Ran|Ran/M2|Rasl2-9-ps	RAS-like, family 2, locus 9	protein-coding
mm_39260.1	chr5	3554671	3554684	+	1	NA	exon (NM_001042501, exon 2 of 11)	exon (NM_001042501, exon 2 of 11)	10844	NM_001042501	68152	Mm.240265	NM_026583	ENSMUSG00000058503	Fam133b	2900022K02Rik|5830415L20Rik	family with sequence similarity 133, member B	protein-coding
mm_5945.1	chr1	56782217	56782225	-	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	-144770	NM_027661	71066	Mm.152656	NM_027661	ENSMUSG00000045336	Hsfy2	4933413G11Rik|Hspy2l	heat shock transcription factor, Y-linked 2	protein-coding
mm_47978.1	chr5	135910889	135910912	-	1	NA	3' UTR (NM_018871, exon 2 of 2)	3' UTR (NM_018871, exon 2 of 2)	22981	NM_013560	15507	Mm.13849	NM_013560	ENSMUSG00000004951	Hspb1	27kDa|Hsp25	heat shock protein 1	protein-coding
mm_117603.1	chr13	90089514	90089543	-	1	NA	promoter-TSS (NM_025335)	promoter-TSS (NM_025335)	80	NM_028012	108138	Mm.37531	NM_028012	ENSMUSG00000021615	Xrcc4	2310057B22Rik|AW413319|AW545101	X-ray repair complementing defective repair in Chinese hamster cells 4	protein-coding
mm_161586.1	chr16	32644449	32644449	+	1	NA	promoter-TSS (NM_001110147)	promoter-TSS (NM_001110147)	-194	NM_001110147	51789	Mm.251115	NM_016788	ENSMUSG00000022791	Tnk2	Ack|Ack-1|Ack1|Cdgip|Pyk1	tyrosine kinase, non-receptor, 2	protein-coding
mm_118923.1	chr14	27000494	27000507	+	1	NA	5' UTR (NM_010420, exon 1 of 4)	5' UTR (NM_010420, exon 1 of 4)	138	NM_010420	15209	Mm.4802	NM_010420	ENSMUSG00000040726	Hesx1	HES-1|Rpx	homeobox gene expressed in ES cells	protein-coding
mm_115450.1	chr13	118714622	118714676	+	1	NA	promoter-TSS (NM_008002)	promoter-TSS (NM_008002)	-50	NM_008002	14165	Mm.317323	NM_008002	ENSMUSG00000021732	Fgf10	AEY17|BB213776|Fgf-10|Gsfaey17	fibroblast growth factor 10	protein-coding
mm_124423.1	chr14	118132764	118132774	-	1	NA	promoter-TSS (NM_029578)	promoter-TSS (NM_029578)	-4	NM_029578	76355	Mm.251537	NM_029578	ENSMUSG00000022130	Tgds	2610017J16Rik|2610025M23Rik|AI648925	TDP-glucose 4,6-dehydratase	protein-coding
mm_32654.1	chr4	115088864	115088872	+	1	NA	5' UTR (NM_001164557, exon 1 of 4)	5' UTR (NM_001164557, exon 1 of 4)	160	NM_001164557	67182	Mm.30181	NM_026018	ENSMUSG00000028716	Pdzk1ip1	0610007F13Rik|2700030M23Rik|AU046042|Map17	PDZK1 interacting protein 1	protein-coding
mm_37782.1	chr4	130222327	130222349	-	1	NA	promoter-TSS (NM_001034872)	promoter-TSS (NM_001034872)	-43	NM_001034872	332942	Mm.387701	NM_001034872	ENSMUSG00000023120	Gm853	OTTMUSG00000009560	predicted gene 853	protein-coding
mm_172724.1	chr8	73157847	73157848	-	1	NA	intron (NM_001317391, intron 3 of 15)	intron (NM_001317391, intron 3 of 15)	141335	NR_039551	100628574		NR_039551	ENSMUSG00000093140	Mir28b	mmu-mir-28b	microRNA 28b	ncRNA
mm_84160.1	chr9	59542608	59542627	-	1	NA	intron (NM_010421, intron 1 of 13)	intron (NM_010421, intron 1 of 13)	3077	NM_010421	15211	Mm.2284	NM_010421	ENSMUSG00000025232	Hexa	Hex-1	hexosaminidase A	protein-coding
mm_46139.1	chr5	93093120	93093137	-	1	NA	promoter-TSS (NM_001310669)	promoter-TSS (NM_001310669)	-288	NM_001009818	52398	Mm.394184	NM_001009818	ENSMUSG00000058013	Sept11	6230410I01Rik|AW548875|D5Ertd606e	septin 11	protein-coding
mm_43102.1	chr5	124483166	124483185	+	1	NA	promoter-TSS (NM_029532)	promoter-TSS (NM_029532)	20	NM_029532	76167	Mm.156035	NM_029532	ENSMUSG00000029402	Snrnp35	6330548G22Rik	small nuclear ribonucleoprotein 35 (U11/U12)	protein-coding
mm_75830.1	chr8	70506711	70506766	-	1	NA	promoter-TSS (NM_025577)	promoter-TSS (NM_025577)	1	NM_025577	66462	Mm.28242	NM_025577	ENSMUSG00000058833	2810428I15Rik	-	RIKEN cDNA 2810428I15 gene	protein-coding
mm_61908.1	chr7	90137591	90137605	+	1	NA	intron (NM_001252520, intron 1 of 20)	intron (NM_001252520, intron 1 of 20)	7366	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_11106.1	chr2	28192972	28192985	+	1	NA	promoter-TSS (NM_001038613)	promoter-TSS (NM_001038613)	-115	NM_001038613	56177	Mm.43278	NM_019498	ENSMUSG00000026833	Olfm1	AMY|AW742568|Noe1|OlfA|Pancortin|Pancortin3	olfactomedin 1	protein-coding
mm_81426.1	chr9	109057025	109057041	+	1	NA	TTS (NM_011637)	TTS (NM_011637)	2167	NM_026381	66940	Mm.196533	NM_025858	ENSMUSG00000025647	Shisa5	2310008D10Rik|6430628I05Rik|Scotin|mShisa5	shisa family member 5	protein-coding
mm_113845.1	chr13	47195813	47195814	+	1	NA	intron (NM_001170643, intron 1 of 7)	intron (NM_001170643, intron 1 of 7)	1810	NM_001170643	218215	Mm.287609	NM_146042	ENSMUSG00000038068	Rnf144b	BC025007|E130105P19Rik|Ibrdc2|Pir2	ring finger protein 144B	protein-coding
mm_151422.1	chr19	56826203	56826248	+	1	NA	promoter-TSS (NM_031387)	promoter-TSS (NM_031387)	16	NM_001002238	83561	Mm.247541	NM_031387	ENSMUSG00000025081	Tdrd1	MTR-1	tudor domain containing 1	protein-coding
mm_31158.1	chr4	43442403	43442411	+	1	NA	5' UTR (NM_011571, exon 1 of 10)	5' UTR (NM_011571, exon 1 of 10)	130	NM_011571	21754	Mm.485441	NM_011571	ENSMUSG00000028458	Tesk1	AI326901	testis specific protein kinase 1	protein-coding
mm_156036.1	chrX	107542588	107542595	+	1	NA	promoter-TSS (NR_033580)	promoter-TSS (NR_033580)	9	NR_033580	71011	Mm.307348	NR_033580	ENSMUSG00000055700	4933401B06Rik	-	GLE1 RNA export mediator pseudogene	pseudo
mm_66973.1	chr7	63908588	63908610	-	1	NA	intron (NM_021366, intron 1 of 1)	intron (NM_021366, intron 1 of 1)	-8258	NM_001256311	381994	Mm.425466	NM_001256311	ENSMUSG00000095061	E030018B13Rik	Gm1697	RIKEN cDNA E030018B13 gene	protein-coding
mm_28099.1	chr3	86142643	86142658	-	1	NA	promoter-TSS (NM_016959)	promoter-TSS (NM_016959)	18	NM_016959	20091	Mm.391785	NM_016959	ENSMUSG00000028081	Rps3a1	Rps3a	ribosomal protein S3A1	protein-coding
mm_68296.1	chr7	105737340	105737398	-	1	NA	promoter-TSS (NM_025897)	promoter-TSS (NM_025897)	16	NM_133951	101867	Mm.231400	NM_025897	ENSMUSG00000030888	Rrp8	1500003O22Rik|2900001K19Rik|AW538116	ribosomal RNA processing 8, methyltransferase, homolog (yeast)	protein-coding
mm_151197.1	chr19	53537461	53537479	+	1	NA	exon (NM_001085390, exon 3 of 4)	exon (NM_001085390, exon 3 of 4)	8152	NM_001085390	240672	Mm.482424	NM_001085390	ENSMUSG00000034765	Dusp5	Gm337	dual specificity phosphatase 5	protein-coding
mm_32123.1	chr4	99031463	99031474	+	1	NA	exon (NM_013913, exon 1 of 7)	exon (NM_013913, exon 1 of 7)	514	NM_013913	30924	Mm.28341	NM_013913	ENSMUSG00000028553	Angptl3	hypl	angiopoietin-like 3	protein-coding
mm_51419.1	chr6	78405149	78405158	+	1	NA	promoter-TSS (NM_009043)	promoter-TSS (NM_009043)	-2	NM_009043	19693	Mm.46360	NM_009043	ENSMUSG00000023140	Reg2	RegII	regenerating islet-derived 2	protein-coding
mm_106283.1	chr11	118202481	118202503	-	1	NA	intron (NM_001112699, intron 1 of 12)	intron (NM_001112699, intron 1 of 12)	10250	NM_001112700	19157	Mm.86413	NM_011180	ENSMUSG00000017132	Cyth1	CLM1|CTH-1|CYTIP|Pscd1	cytohesin 1	protein-coding
mm_23224.1	chr3	49062435	49062442	+	1	NA	Intergenic	RLTR20C2_MM|LTR|ERVK	-453338	NR_003617	66332	Mm.46124	NM_025493		1700018B24Rik	-	enhancer of rudimentary homolog pseudogene	pseudo
mm_66541.1	chr7	45189555	45189566	-	1	NA	intron (NM_201374, intron 11 of 19)	intron (NM_201374, intron 11 of 19)	8565	NM_053256	114640	Mm.207078	NM_053256	ENSMUSG00000038300	Pth2	Tifp39|Tip39	parathyroid hormone 2	protein-coding
mm_17071.1	chr2	22744976	22745020	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-29329	NM_019456	54519	Mm.14255	NM_019456	ENSMUSG00000026786	Apbb1ip	9930118P07Rik|Prp48	amyloid beta (A4) precursor protein-binding, family B, member 1 interacting protein	protein-coding
mm_45394.1	chr5	66151333	66151343	-	1	NA	promoter-TSS (NM_001291226)	promoter-TSS (NM_001291226)	-360	NM_178446	245945	Mm.36863	NM_139065	ENSMUSG00000070780	Rbm47	9530077J19Rik	RNA binding motif protein 47	protein-coding
mm_143810.1	chr17	83654703	83654750	-	1	NA	Intergenic	Intergenic	-22831	NM_153512	225030	Mm.223506	NM_153512	ENSMUSG00000045053	Kcng3	KV6.3|Kv10.1a|Kv10.1b	potassium voltage-gated channel, subfamily G, member 3	protein-coding
mm_50707.1	chr6	52158466	52158484	+	1	NA	promoter-TSS (NM_010449)	promoter-TSS (NM_010449)	-49	NR_131181	105242658	Mm.372521	NR_131181	ENSMUSG00000087658	Hotairm1	Gm15051|Hoxaas1|OTTMUSG00000018870	Hoxa transcript antisense RNA, myeloid-specific 1	ncRNA
mm_15102.1	chr2	153346634	153346644	+	1	NA	promoter-TSS (NR_040318)	promoter-TSS (NR_040318)	500	NM_001039939	228790	Mm.330677	NM_001039939	ENSMUSG00000042548	Asxl1	mKIAA0978	additional sex combs like 1	protein-coding
mm_46659.1	chr5	108675317	108675383	-	1	NA	promoter-TSS (NM_001310692)	promoter-TSS (NM_001310692)	15	NM_174870	231583	Mm.440571	NM_174870	ENSMUSG00000046959	Slc26a1	Sat1	solute carrier family 26 (sulfate transporter), member 1	protein-coding
mm_33489.1	chr4	130823113	130823127	+	1	NA	3' UTR (NM_011520, exon 5 of 5)	3' UTR (NM_011520, exon 5 of 5)	30583	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_7127.1	chr1	90969430	90969471	-	1	NA	5' UTR (NM_008998, exon 1 of 6)	5' UTR (NM_008998, exon 1 of 6)	170	NM_008998	19329	Mm.279780	NM_008998	ENSMUSG00000026304	Rab17	AW413472	RAB17, member RAS oncogene family	protein-coding
mm_91286.1	chr10	24806011	24806047	-	1	NA	intron (NM_134005, intron 9 of 24)	intron (NM_134005, intron 9 of 24)	30166	NM_134005	209558	Mm.338425	NM_134005	ENSMUSG00000019989	Enpp3	AI876438|CD203c	ectonucleotide pyrophosphatase/phosphodiesterase 3	protein-coding
mm_8974.1	chr1	165377670	165377672	-	1	NA	intron (NM_028759, intron 10 of 18)	intron (NM_028759, intron 10 of 18)	75048	NM_001310430	240888	Mm.329929	NM_001081126	ENSMUSG00000040836	Gpr161	Gm208|Gm208Gpr|vl	G protein-coupled receptor 161	protein-coding
mm_41285.1	chr5	90462747	90462747	+	1	NA	exon (NM_009654, exon 3 of 15)	exon (NM_009654, exon 3 of 15)	1877	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_146526.1	chr18	4353413	4353431	-	1	NA	promoter-TSS (NM_007746)	promoter-TSS (NM_007746)	-125	NR_040328	73915	Mm.482777	NR_040328		4833419F23Rik	-	RIKEN cDNA 4833419F23 gene	ncRNA
mm_157214.1	chrX	12994522	12994530	-	1	NA	Intergenic	B1_Mur2|SINE|Alu	-47489	NR_038158	70489	Mm.383563	NR_038158	ENSMUSG00000087424	5730405O15Rik	-	RIKEN cDNA 5730405O15 gene	ncRNA
mm_53010.1	chr6	123274668	123274684	+	1	NA	exon (NM_010819, exon 6 of 6)	exon (NM_010819, exon 6 of 6)	12569	NM_010819	17474	Mm.441101	NM_010819	ENSMUSG00000030144	Clec4d	Clecsf8|Mpcl|mcl	C-type lectin domain family 4, member d	protein-coding
mm_115.1	chr1	9788397	9788407	+	1	NA	Intergenic	Intergenic	-9728	NM_133220	170755	Mm.336410	NM_133220	ENSMUSG00000025915	Sgk3	2510015P22Rik|A330005P07Rik|Cisk|fy|fz	serum/glucocorticoid regulated kinase 3	protein-coding
mm_23478.1	chr3	60481139	60481273	+	1	NA	intron (NM_001253713, intron 2 of 9)	C-rich|Low_complexity|Low_complexity	8376	NM_001253713	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_31037.1	chr4	40970956	40971027	+	1	NA	promoter-TSS (NM_023739)	promoter-TSS (NM_023739)	48	NM_023739	74164	Mm.247456	NM_023739	ENSMUSG00000028423	Nfx1	1300017N15Rik|3000003M19Rik|NFX.1|TEG-42|Tex42	nuclear transcription factor, X-box binding 1	protein-coding
mm_49096.1	chr6	7844767	7844803	+	1	NA	promoter-TSS (NM_052993)	promoter-TSS (NM_052993)	-439	NM_052993	94192	Mm.102752	NM_052993	ENSMUSG00000042460	C1galt1	2210410E06Rik|AV284120|T-synthase	core 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase, 1	protein-coding
mm_133757.1	chr16	94454412	94454452	+	1	NA	exon (NM_009441, exon 38 of 46)	exon (NM_009441, exon 38 of 46)	72197	NM_007834	13185	Mm.7472	NM_007834	ENSMUSG00000022898	Dscr3	AW538125|Dcra	Down syndrome critical region gene 3	protein-coding
mm_96127.1	chr11	60778905	60778943	+	1	NA	exon (NM_001085440, exon 1 of 2)	exon (NM_001085440, exon 1 of 2)	1399	NM_175491	237782	Mm.57726	NM_175491	ENSMUSG00000049323	Smcr8	2310076G09Rik|AI642055|D030073L15Rik	Smith-Magenis syndrome chromosome region, candidate 8 homolog (human)	protein-coding
mm_30503.1	chr3	158016347	158016359	-	1	NA	exon (NM_001093753, exon 8 of 12)	exon (NM_001093753, exon 8 of 12)	15401	NM_001093753	69207	Mm.223946	NM_026989	ENSMUSG00000055436	Srsf11	0610009J05Rik|2610019N13Rik|BF642805|Sfrs11	serine/arginine-rich splicing factor 11	protein-coding
mm_157546.1	chrX	51220068	51220074	-	1	NA	Intergenic	Intergenic	-14081	NM_134163	171170	Mm.295324	NM_134163	ENSMUSG00000036109	Mbnl3	A530038J18Rik|AI661274|CHCR|E430034C16Rik|MBLX|MBLX39|MBXL	muscleblind-like 3 (Drosophila)	protein-coding
mm_81804.1	chr9	116208579	116208597	+	1	NA	Intergenic	Intergenic	-33225	NM_009371	21813	Mm.172346	NM_009371	ENSMUSG00000032440	Tgfbr2	1110020H15Rik|AU042018|DNIIR|RIIDN|TBR-II|TbetaR-II|TbetaRII	transforming growth factor, beta receptor II	protein-coding
mm_38379.1	chr4	138725211	138725258	-	1	NA	promoter-TSS (NM_178671)	promoter-TSS (NM_178671)	31	NR_104373	212190	Mm.292226	NM_178671	ENSMUSG00000043621	Ubxn10	5730509E04Rik|A830047D02|Ubxd3	UBX domain protein 10	protein-coding
mm_37007.1	chr4	111898696	111898725	-	1	NA	5' UTR (NM_145551, exon 2 of 15)	5' UTR (NM_145551, exon 2 of 15)	4086	NM_145551	230612	Mm.26630	NM_145551	ENSMUSG00000028544	Slc5a9	AI159731|SGLT4	solute carrier family 5 (sodium/glucose cotransporter), member 9	protein-coding
mm_159534.1	chr4	73790639	73790639	-	1	NA	promoter-TSS (NR_046042)	promoter-TSS (NR_046042)	-37	NM_001017427	242505	Mm.389582	NM_001017427	ENSMUSG00000043003	Rasef	BC030882|RAB45	RAS and EF hand domain containing	protein-coding
mm_43478.1	chr5	136697806	136697810	+	1	NA	intron (NM_001303019, intron 4 of 6)	ZP3AR|Satellite|Satellite	3631	NM_001085387	59310	Mm.5178	NM_021611	ENSMUSG00000005474	Myl10	1700027I08Rik|Mylc2pl|PLRLC	myosin, light chain 10, regulatory	protein-coding
mm_138860.1	chr17	42508427	42508430	+	1	NA	TTS (NM_028474)	TTS (NM_028474)	102885	NM_181753	353344	Mm.184937	NM_181753	ENSMUSG00000043972	Opn5	Gpr136|Neuropsin|PGR12|TMEM13	opsin 5	protein-coding
mm_45954.1	chr5	90461749	90461775	-	1	NA	exon (NM_009654, exon 2 of 15)	exon (NM_009654, exon 2 of 15)	892	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_150046.1	chr19	29380372	29380406	+	1	NA	exon (NM_021893, exon 4 of 7)	exon (NM_021893, exon 4 of 7)	12951	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_88433.1	chr10	77530422	77530432	+	1	NA	promoter-TSS (NM_008404)	promoter-TSS (NM_008404)	79	NM_008404	16414	Mm.1137	NM_008404	ENSMUSG00000000290	Itgb2	2E6|AI528527|Cd18|LAD|LCAMB|Lfa1|MF17	integrin beta 2	protein-coding
mm_104532.1	chr11	96295406	96295407	-	1	NA	intron (NR_131758, intron 1 of 2)	intron (NR_131758, intron 1 of 2)	-3765	NM_008269	15414	Mm.215	NM_008269	ENSMUSG00000000690	Hoxb6	Hox-2.2	homeobox B6	protein-coding
mm_136343.1	chr16	92603255	92603265	-	1	NA	3' UTR (NM_001111021, exon 8 of 8)	3' UTR (NM_001111021, exon 8 of 8)	94069	NM_001111023	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_22956.1	chr3	32397269	32397296	+	1	NA	Intergenic	CpG	-31617	NM_009517	22401	Mm.35705	NM_009517	ENSMUSG00000027663	Zmat3	Wig1	zinc finger matrin type 3	protein-coding
mm_57067.1	chr6	122577907	122577944	-	1	NA	3' UTR (NM_031159, exon 8 of 8)	3' UTR (NM_031159, exon 8 of 8)	24116	NM_009645	11628	Mm.391503	NM_009645	ENSMUSG00000040627	Aicda	Aid|Arp2	activation-induced cytidine deaminase	protein-coding
mm_94766.1	chr11	21238690	21238745	+	1	NA	promoter-TSS (NM_001290628)	promoter-TSS (NM_001290628)	-315	NM_139061	245944	Mm.170103	NM_139061	ENSMUSG00000020128	Vps54	Hcc8|Vps54l|mSLP8|wr	VPS54 GARP complex subunit	protein-coding
mm_132967.1	chr16	50783435	50783444	+	1	NA	promoter-TSS (NR_131006)	promoter-TSS (NR_131006)	30	NR_131005	78639	Mm.160109	NR_131005	ENSMUSG00000092276	1700116B05Rik	-	RIKEN cDNA 1700116B05 gene	ncRNA
mm_84318.1	chr9	63757885	63757898	-	1	NA	5' UTR (NM_016769, exon 1 of 9)	5' UTR (NM_016769, exon 1 of 9)	103	NM_016769	17127	Mm.7320	NM_016769	ENSMUSG00000032402	Smad3	AU022421|Madh3	SMAD family member 3	protein-coding
mm_124988.1	chr15	21410787	21410787	+	1	NA	intron (NM_001008420, intron 3 of 11)	intron (NM_001008420, intron 3 of 11)	299335	NM_001008420	215654	Mm.300909	NM_001008420	ENSMUSG00000040452	Cdh12	Cdhb	cadherin 12	protein-coding
mm_161910.1	chr18	62741372	62741372	-	1	NA	promoter-TSS (NM_001168423)	promoter-TSS (NM_001168423)	15	NM_001168423	100038417	Mm.387557	NM_001168423	ENSMUSG00000073551	Spink13	ENSMUSG00000073551|Gm10534|Spink5l3	serine peptidase inhibitor, Kazal type 13	protein-coding
mm_102873.1	chr11	69409393	69409411	-	1	NA	intron (NM_001017426, intron 1 of 22)	intron (NM_001017426, intron 1 of 22)	4273	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_142670.1	chr17	47729357	47729366	-	1	NA	exon (NM_025973, exon 3 of 9)	exon (NM_025973, exon 3 of 9)	2519	NM_025973	109820	Mm.22957	NM_025973	ENSMUSG00000023987	Pgc	2210410L06Rik|Upg-1|Upg1	progastricsin (pepsinogen C)	protein-coding
mm_159389.1	chr3	92316705	92316705	+	1	NA	promoter-TSS (NM_011469)	promoter-TSS (NM_011469)	0	NM_011469	20756	Mm.445310	NM_011469	ENSMUSG00000050092	Sprr2b	-	small proline-rich protein 2B	protein-coding
mm_88688.1	chr10	80116234	80116266	+	1	NA	non-coding (NR_126043, exon 1 of 11)	non-coding (NR_126043, exon 1 of 11)	447	NM_001301854	20869	Mm.44231	NM_011492	ENSMUSG00000003068	Stk11	AA408040|Lkb1|Par-4|R75140	serine/threonine kinase 11	protein-coding
mm_105220.1	chr11	102218824	102218851	-	1	NA	intron (NM_001284248, intron 4 of 28)	intron (NM_001284248, intron 4 of 28)	11313	NR_106179	102465892		NR_106179	ENSMUSG00000098863	Mir8101	Gm27705|mmu-mir-8101	microRNA 8101	ncRNA
mm_105426.1	chr11	103749816	103749829	-	1	NA	promoter-TSS (NM_011719)	promoter-TSS (NM_011719)	-1	NM_011719	22412	Mm.215161	NM_011719	ENSMUSG00000018486	Wnt9b	Wnt14b|Wnt15|clf|clf1|wnt-14b|wnt-15	wingless-type MMTV integration site family, member 9B	protein-coding
mm_17733.1	chr2	32567633	32567669	-	1	NA	3' UTR (NM_153560, exon 11 of 11)	3' UTR (NM_153560, exon 11 of 11)	-3207	NM_010073	13481	Mm.22001	NM_010073	ENSMUSG00000026810	Dpm2	AW557993|R75484	dolichol-phosphate (beta-D) mannosyltransferase 2	protein-coding
mm_135810.1	chr16	57391528	57391557	-	1	NA	intron (NM_001040397, intron 1 of 4)	LSU-rRNA_Hsa|rRNA|rRNA	38265	NM_001040397	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding
mm_26083.1	chr3	136673097	136673099	+	1	NA	intron (NM_008913, intron 1 of 13)	intron (NM_008913, intron 1 of 13)	3032	NM_001293622	19055	Mm.331389	NM_008913	ENSMUSG00000028161	Ppp3ca	2900074D19Rik|CN|Caln|Calna|CnA	protein phosphatase 3, catalytic subunit, alpha isoform	protein-coding
mm_162951.1	chr11	3516056	3516073	+	1	NA	intron (NM_053267, intron 1 of 4)	intron (NM_053267, intron 1 of 4)	1380	NM_053267	114679	Mm.34046	NM_053267	ENSMUSG00000075702	Selenom	1500040L08Rik|A230103K18|Selm|Sepm	selenoprotein M	protein-coding
mm_63139.1	chr7	123124173	123124223	+	1	NA	5' UTR (NM_144925, exon 1 of 24)	5' UTR (NM_144925, exon 1 of 24)	313	NM_144925	233833	Mm.102305	NM_144925	ENSMUSG00000052707	Tnrc6a	2010321I05Rik|3110054G10Rik|AW557223|CAGH26|D130023A07Rik|GW182|Tnrc6	trinucleotide repeat containing 6a	protein-coding
mm_120711.1	chr14	71903641	71903646	+	1	NA	intron (NR_046274, intron 5 of 6)	(T)n|Simple_repeat|Simple_repeat	46934	NR_046274	74667	Mm.159286	NR_046274		4930434J06Rik	-	RIKEN cDNA 4930434J06 gene	ncRNA
mm_144681.1	chr18	34759552	34759558	+	1	NA	intron (NM_175104, intron 1 of 4)	CpG	649	NM_175104	66306	Mm.29424	NM_175104	ENSMUSG00000034300	Fam53c	2810012G03Rik|Gm21179	family with sequence similarity 53, member C	protein-coding
mm_108995.1	chr12	102949235	102949279	+	1	NA	5' UTR (NM_001081017, exon 1 of 49)	5' UTR (NM_001081017, exon 1 of 49)	398	NM_001081017	217843	Mm.387073	NM_177621	ENSMUSG00000021198	Unc79	9030205A07Rik|Mlca3	unc-79 homolog (C. elegans)	protein-coding
mm_141719.1	chr17	34031672	34031674	-	1	NA	promoter-TSS (NM_001205216)	promoter-TSS (NM_001205216)	17	NM_001077709	14977	Mm.18556	NM_008202	ENSMUSG00000024327	Slc39a7	AA408174|AI117660|AL024048|H-2Ke4|H2-Ke4|Ke-4|Ke4|Ring5|Zip7	solute carrier family 39 (zinc transporter), member 7	protein-coding
mm_156727.1	chrX	159901721	159901738	+	1	NA	exon (NM_021389, exon 8 of 17)	exon (NM_021389, exon 8 of 17)	-40964	NM_001290661	58194	Mm.286495	NM_021389	ENSMUSG00000040990	Sh3kbp1	1200007H22Rik|1700125L08Rik|5830464D22Rik|AI447724|Cin85|IN85|Ruk|Seta	SH3-domain kinase binding protein 1	protein-coding
mm_2544.1	chr1	107511528	107511532	+	1	NA	promoter-TSS (NM_011111)	promoter-TSS (NM_011111)	20	NM_011111	18788	Mm.271870	NM_011111	ENSMUSG00000062345	Serpinb2	PAI-2|Planh2|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 2	protein-coding
mm_165277.1	chr2	80025702	80025738	-	1	NA	intron (NM_001159582, intron 2 of 15)	intron (NM_001159582, intron 2 of 15)	103251	NM_016744	18573	Mm.40678	NM_016744	ENSMUSG00000059173	Pde1a	AI987702|AW125737	phosphodiesterase 1A, calmodulin-dependent	protein-coding
mm_36122.1	chr4	58912650	58912662	-	1	NA	promoter-TSS (NM_172381)	promoter-TSS (NM_172381)	69	NM_172381	230249	Mm.234801	NM_172381	ENSMUSG00000050812	AI314180	AW558785|BB181316|mKIAA0368	expressed sequence AI314180	protein-coding
mm_4993.1	chr1	191817440	191817452	+	1	NA	Intergenic	Lx10|LINE|L1	-4027	NM_010892	18005	Mm.33773	NM_010892	ENSMUSG00000026622	Nek2	AA617254|C77054	NIMA (never in mitosis gene a)-related expressed kinase 2	protein-coding
mm_17144.1	chr2	25196580	25196604	-	1	NA	5' UTR (NM_146115, exon 1 of 2)	5' UTR (NM_146115, exon 1 of 2)	221	NM_146115	227612	Mm.119747	NM_146115	ENSMUSG00000059555	Tor4a	A830007P12Rik	torsin family 4, member A	protein-coding
mm_166559.1	chr6	43680403	43680404	+	1	NA	Intergenic	L1MEc|LINE|L1	-14125	NM_013861	29807	Mm.320979	NM_013861	ENSMUSG00000029735	Tpk1	-	thiamine pyrophosphokinase	protein-coding
mm_125544.1	chr15	58415457	58415512	+	1	NA	promoter-TSS (NM_145959)	promoter-TSS (NM_145959)	16	NM_145959	210998	Mm.3224	NM_145959	ENSMUSG00000037119	Fam91a1	AV220772|BC033609|D15Ertd621e|SKIN|mKIAA0493	family with sequence similarity 91, member A1	protein-coding
mm_80146.1	chr9	70914079	70914088	+	1	NA	intron (NM_001324473, intron 1 of 8)	B1_Mus2|SINE|Alu	20725	NM_008280	15450	Mm.390187	NM_008280	ENSMUSG00000032207	Lipc	AI256194|HL|Hpl	lipase, hepatic	protein-coding
mm_8997.1	chr1	165722601	165722610	-	1	NA	Intergenic	Intergenic	-14511	NM_001038846	226594	Mm.265552	NM_178593	ENSMUSG00000040723	Rcsd1	A430105K13Rik|BC025872|CapZIP	RCSD domain containing 1	protein-coding
mm_114033.1	chr13	52677319	52677320	+	1	NA	Intergenic	Intergenic	79886	NR_027893	105404	Mm.184173	NR_027893		BB123696	-	expressed sequence BB123696	ncRNA
mm_49224.1	chr6	15794281	15794295	+	1	NA	intron (NM_175088, intron 4 of 4)	intron (NM_175088, intron 4 of 4)	73627	NM_175088	16543	Mm.1314	NM_175088	ENSMUSG00000041390	Mdfic	Kdt1|Mdfid	MyoD family inhibitor domain containing	protein-coding
mm_95301.1	chr11	46123113	46123131	+	1	NA	exon (NM_009616, exon 10 of 23)	exon (NM_009616, exon 10 of 23)	-4782	NM_001311209	11492	Mm.89940	NM_009616	ENSMUSG00000011256	Adam19	AL024287|MADDAM|MTLNB|Mltnb	a disintegrin and metallopeptidase domain 19 (meltrin beta)	protein-coding
mm_168358.1	chr1	114557302	114557304	+	1	NA	Intergenic	Intergenic	-1127834	NM_001077425	636808	Mm.101576	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding
mm_71346.1	chr8	45628059	45628071	+	1	NA	5' UTR (NM_001310707, exon 1 of 24)	5' UTR (NM_001310707, exon 1 of 24)	314	NM_001310707	234214	Mm.211096	NM_172752	ENSMUSG00000031626	Sorbs2	2010203O03Rik|9430041O17Rik|A530071H08|Argbp2|mKIAA0777|nArgBP2	sorbin and SH3 domain containing 2	protein-coding
mm_42138.1	chr5	111330743	111330768	+	1	NA	promoter-TSS (NM_019640)	promoter-TSS (NM_019640)	58	NM_001301666	56305	Mm.200516	NM_019640	ENSMUSG00000050017	Pitpnb	PI-TP-beta	phosphatidylinositol transfer protein, beta	protein-coding
mm_135068.1	chr16	34223190	34223198	-	1	NA	intron (NM_001164268, intron 16 of 33)	MIRb|SINE|MIR	-256191	NM_009471	22247	Mm.13145	NM_009471	ENSMUSG00000022814	Umps	1700095D23Rik|AA408257|AL033308|BB164745	uridine monophosphate synthetase	protein-coding
mm_160323.1	chr7	145314749	145314749	+	1	NA	promoter-TSS (NM_203490)	promoter-TSS (NM_203490)	-86	NM_203490	211578	Mm.370299	NM_203490	ENSMUSG00000051207	Mrgprd	Gm499|Mgrd|MrgD|TGR7	MAS-related GPR, member D	protein-coding
mm_16236.1	chr2	173156319	173156328	+	1	NA	intron (NM_011044, intron 6 of 9)	RSINE1|SINE|B4	3250	NM_011044	18534	Mm.266867	NM_011044	ENSMUSG00000027513	Pck1	AI265463|PEPCK|Pck-1	phosphoenolpyruvate carboxykinase 1, cytosolic	protein-coding
mm_7258.1	chr1	93801841	93801945	-	1	NA	promoter-TSS (NM_001105667)	promoter-TSS (NM_001105667)	41	NM_023136	21915	Mm.250332	NM_023136	ENSMUSG00000026281	Dtymk	AU044245|CDC8|D10Ertd203e|TMPK|TYPK|Tmk|mtmk	deoxythymidylate kinase	protein-coding
mm_47102.1	chr5	118380485	118380502	-	1	NA	Intergenic	Intergenic	135266	NM_001081236	76792	Mm.103428	NM_001081236	ENSMUSG00000032840	2410131K14Rik	-	RIKEN cDNA 2410131K14 gene	protein-coding
mm_63724.1	chr7	130861243	130861252	+	1	NA	Intergenic	Intergenic	-4477	NM_001346515	101476	Mm.323554	NM_133942	ENSMUSG00000040268	Plekha1	AA960558|C920009D07Rik|TAPP1	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 1	protein-coding
mm_127570.1	chr15	102279447	102279475	+	1	NA	promoter-TSS (NM_134100)	promoter-TSS (NM_134100)	5	NM_134100	106073	Mm.287740	NM_134100	ENSMUSG00000045665	Mfsd5	AA409375|AW556797|D15Mgi27	major facilitator superfamily domain containing 5	protein-coding
mm_168843.1	chr12	23634732	23634734	-	1	NA	Intergenic	CpG	462536	NM_001256489	66808	Mm.379124	NM_001256489	ENSMUSG00000073158	9030624G23Rik	-	RIKEN cDNA 9030624G23 gene	protein-coding
mm_126100.1	chr15	78244782	78244837	+	1	NA	promoter-TSS (NM_008677)	promoter-TSS (NM_008677)	-2	NM_008677	17972	Mm.2068	NM_008677	ENSMUSG00000071715	Ncf4	AI451400|p40phox	neutrophil cytosolic factor 4	protein-coding
mm_48631.1	chr5	145138367	145138376	-	1	NA	intron (NM_001033313, intron 1 of 5)	intron (NM_001033313, intron 1 of 5)	1718	NM_001033313	231887	Mm.188851	NM_001033313	ENSMUSG00000029623	Pdap1	HASPP28|PAP|PAP1	PDGFA associated protein 1	protein-coding
mm_118659.1	chr14	21797974	21797995	+	1	NA	3' UTR (NM_026283, exon 6 of 6)	3' UTR (NM_026283, exon 6 of 6)	-33577	NM_011695	22334	Mm.262327	NM_011695	ENSMUSG00000021771	Vdac2	Vdac6|mVDAC2|mVDAC6	voltage-dependent anion channel 2	protein-coding
mm_24361.1	chr3	90079525	90079537	+	1	NA	promoter-TSS (NM_001253740)	promoter-TSS (NM_001253740)	10	NM_001293749	59069	Mm.240839	NM_022314	ENSMUSG00000027940	Tpm3	TM30nm|TMnm|Tm5NM|Tpm-5|Tpm5|Trop-5|gamma-TM|hTM30nm|hTMnm	tropomyosin 3, gamma	protein-coding
mm_154806.1	chrX	13622915	13622932	+	1	NA	intron (NM_009806, intron 6 of 24)	intron (NM_009806, intron 6 of 24)	-9846	NM_011823	23890	Mm.487326	NM_011823	ENSMUSG00000040229	Gpr34	Lypsr1	G protein-coupled receptor 34	protein-coding
mm_170265.1	chr18	17352673	17352677	-	1	NA	Intergenic	MusHAL1|LINE|L1	-117193	NR_033607	664619	Mm.250005	NR_033607		4921533I20Rik	-	PRP18 pre-mRNA processing factor 18 homolog pseudogene	pseudo
mm_45737.1	chr5	86469073	86469123	-	1	NA	promoter-TSS (NM_001033233)	promoter-TSS (NM_001033233)	-108	NM_001033233	194597	Mm.249106	NM_001033233	ENSMUSG00000072845	Tmprss11a	Gm7	transmembrane protease, serine 11a	protein-coding
mm_15121.1	chr2	153758054	153758081	+	1	NA	exon (NM_007896, exon 4 of 7)	exon (NM_007896, exon 4 of 7)	16780	NM_007896	13589	Mm.143877	NM_007896	ENSMUSG00000027479	Mapre1	5530600P05Rik|AI462499|AI504412|AW260097|BIM1p|D2Ertd459e|Eb1	microtubule-associated protein, RP/EB family, member 1	protein-coding
mm_36834.1	chr4	106464168	106464181	-	1	NA	5' UTR (NM_153565, exon 1 of 12)	5' UTR (NM_153565, exon 1 of 12)	151	NM_153565	100102	Mm.133268	NM_153565	ENSMUSG00000044254	Pcsk9	AI415265|AI747682|FH3|HCHOLA3|Narc1|PC9	proprotein convertase subtilisin/kexin type 9	protein-coding
mm_86109.1	chr9	115310539	115310549	-	1	NA	promoter-TSS (NM_024222)	promoter-TSS (NM_024222)	-123	NM_024222	68292	Mm.296158	NM_024222	ENSMUSG00000032437	Stt3b	1300006C19Rik|Simp	STT3, subunit of the oligosaccharyltransferase complex, homolog B (S. cerevisiae)	protein-coding
mm_120894.1	chr14	75845297	75845307	+	1	NA	promoter-TSS (NM_009429)	promoter-TSS (NM_009429)	46	NM_009429	22070	Mm.297482	NM_009429	ENSMUSG00000060126	Tpt1	TCTP|Trt|p21|p23	tumor protein, translationally-controlled 1	protein-coding
mm_159850.1	chr5	137291347	137291347	+	1	NA	intron (NM_001290010, intron 2 of 4)	(CCCCCA)n|Simple_repeat|Simple_repeat	-2433	NR_106196	102466887		NR_106196	ENSMUSG00000099145	Mir8116	Gm27485|mmu-mir-8116	microRNA 8116	ncRNA
mm_24787.1	chr3	95545332	95545345	+	1	NA	exon (NM_021281, exon 5 of 8)	exon (NM_021281, exon 5 of 8)	-14339	NM_026489	67981	Mm.179050	NM_026489	ENSMUSG00000028109	Hormad1	4921522K05Rik|Nohma	HORMA domain containing 1	protein-coding
mm_159916.1	chr6	49395508	49395508	+	1	NA	promoter-TSS (NM_029916)	promoter-TSS (NM_029916)	-96	NM_029916	77485	Mm.128054	NM_029916	ENSMUSG00000023403	Stk31	C330007K24Rik	serine threonine kinase 31	protein-coding
mm_133856.1	chr16	96273485	96273523	+	1	NA	intron (NM_001122993, intron 2 of 3)	intron (NM_001122993, intron 2 of 3)	-7528	NM_033149	93961	Mm.154783	NM_033149	ENSMUSG00000074892	B3galt5	1190002B21Rik|AU045265|b3Galt-V	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 5	protein-coding
mm_76160.1	chr8	82372155	82372168	-	1	NA	intron (NM_008357, intron 2 of 7)	intron (NM_008357, intron 2 of 7)	30425	NM_001254747	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_15245.1	chr2	154664589	154664614	+	1	NA	intron (NM_029362, intron 1 of 4)	B1F2|SINE|Alu	7575	NM_029362	75608	Mm.262480	NM_029362	ENSMUSG00000038467	Chmp4b	2010012F05Rik|C76846|Snf7-2	charged multivesicular body protein 4B	protein-coding
mm_170660.1	chr2	11180536	11180553	+	1	NA	intron (NM_008859, intron 1 of 17)	GA-rich|Low_complexity|Low_complexity	8162	NM_008859	18761	Mm.329993	NM_008859	ENSMUSG00000026778	Prkcq	A130035A12Rik|AW494342|PKC-0|PKC-theta|PKCtheta|Pkcq	protein kinase C, theta	protein-coding
mm_72849.1	chr8	88320644	88320658	+	1	NA	intron (NM_001037723, intron 17 of 27)	intron (NM_001037723, intron 17 of 27)	26447	NM_001037724	11513	Mm.288206	NM_007406	ENSMUSG00000031659	Adcy7	AA407758	adenylate cyclase 7	protein-coding
mm_102383.1	chr11	58904159	58904168	-	1	NA	promoter-TSS (NM_011758)	promoter-TSS (NM_011758)	62	NM_011758	22698	Mm.127646	NM_011758	ENSMUSG00000037001	Zfp39	CTfin33|Zfp-39	zinc finger protein 39	protein-coding
mm_140700.1	chr17	14252703	14252711	-	1	NA	Intergenic	Intergenic	-26799	NM_022315	64074	Mm.30162	NM_022315	ENSMUSG00000023886	Smoc2	1700056C05Rik|5430426J21Rik|Smoc2l	SPARC related modular calcium binding 2	protein-coding
mm_26244.1	chr3	141491535	141491538	+	1	NA	intron (NM_001293561, intron 1 of 16)	intron (NM_001293561, intron 1 of 16)	25972	NM_001293561	22253	Mm.24430	NM_009472	ENSMUSG00000059921	Unc5c	B130051O18Rik|Unc5h3|rcm	unc-5 netrin receptor C	protein-coding
mm_156389.1	chrX	139800796	139800811	+	1	NA	promoter-TSS (NM_016675)	promoter-TSS (NM_016675)	-5	NM_016675	12738	Mm.117068	NM_016675	ENSMUSG00000047230	Cldn2	AL022813	claudin 2	protein-coding
mm_26462.1	chr3	143973748	143973754	+	1	NA	Intergenic	Intergenic	228581	NM_001161770	16911	Mm.29187	NM_010723	ENSMUSG00000028266	Lmo4	A730077C12Rik|Crp3|Etohi4	LIM domain only 4	protein-coding
mm_53014.1	chr6	123282731	123282780	+	1	NA	3' UTR (NM_019948, exon 6 of 6)	3' UTR (NM_019948, exon 6 of 6)	7116	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_172411.1	chr7	19083971	19083976	+	1	NA	non-coding (NR_126095, exon 1 of 15)	non-coding (NR_126095, exon 1 of 15)	124	NM_001190491	13400	Mm.6529	NM_032418	ENSMUSG00000030409	Dmpk	DM|DMK|Dm15|MDPK|MT-PK	dystrophia myotonica-protein kinase	protein-coding
mm_78340.1	chr9	25288273	25288294	+	1	NA	exon (NM_001205367, exon 5 of 13)	exon (NM_001205367, exon 5 of 13)	35844	NM_001205367	235072	Mm.270259	NM_009859	ENSMUSG00000001833	Sept7	Cdc10|E430034N22	septin 7	protein-coding
mm_95279.1	chr11	45856350	45856391	+	1	NA	intron (NM_001346760, intron 1 of 11)	intron (NM_001346760, intron 1 of 11)	4406	NM_001045520	216705	Mm.169673	NM_001045520	ENSMUSG00000006169	Clint1	AI642036|AW537616|C530049I24Rik|Enth|Epn4|F630206G17Rik|mKIAA0171	clathrin interactor 1	protein-coding
mm_171633.1	chr4	19767069	19767074	-	1	NA	Intergenic	L1Md_F3|LINE|L1	-51656	NM_028746	74087	Mm.173833	NM_028746	ENSMUSG00000041052	Slc7a13	0610009O04Rik|AGT-1|AGT1|XAT2	solute carrier family 7, (cationic amino acid transporter, y+ system) member 13	protein-coding
mm_62841.1	chr7	114139643	114139664	+	1	NA	Intergenic	Intergenic	-21872	NM_025846	66922	Mm.276572	NM_025846	ENSMUSG00000055723	Rras2	2610016H24Rik|C86394|TC21	related RAS viral (r-ras) oncogene 2	protein-coding
mm_71490.1	chr8	46749458	46749461	+	1	NA	intron (NM_008391, intron 1 of 8)	LTR68|LTR|ERV1	9714	NM_008391	16363	Mm.1149	NM_008391	ENSMUSG00000031627	Irf2	9830146E22Rik|AI646973|Irf-2	interferon regulatory factor 2	protein-coding
mm_56725.1	chr6	115644528	115644558	-	1	NA	exon (NM_029780, exon 2 of 17)	exon (NM_029780, exon 2 of 17)	32092	NM_029780	110157	Mm.184163	NM_029780	ENSMUSG00000000441	Raf1	6430402F14Rik|AA990557|BB129353|Craf1|D830050J10Rik|Raf-1|c-Raf|v-Raf	v-raf-leukemia viral oncogene 1	protein-coding
mm_73016.1	chr8	93968856	93968895	+	1	NA	3' UTR (NM_010308, exon 9 of 9)	3' UTR (NM_010308, exon 9 of 9)	43765	NM_011787	23802	Mm.34641	NM_011787	ENSMUSG00000031751	Amfr	gp78	autocrine motility factor receptor	protein-coding
mm_93577.1	chr10	116896676	116896685	-	1	NA	5' UTR (NM_001033333, exon 1 of 25)	5' UTR (NM_001033333, exon 1 of 25)	199	NM_001033333	237558	Mm.336386	NM_001033333	ENSMUSG00000034057	Myrfl	Gm239	myelin regulatory factor-like	protein-coding
mm_141293.1	chr17	28079748	28079775	-	1	NA	intron (NM_001085555, intron 2 of 9)	CpG	823	NM_013687	21463	Mm.29758	NM_013687	ENSMUSG00000062859	Tcp11	D17Ken1|Tcp-11	t-complex protein 11	protein-coding
mm_137559.1	chr17	27658496	27658499	+	1	NA	intron (NM_001286744, intron 1 of 9)	B1_Mur1|SINE|Alu	2906	NM_001286743	23969	Mm.4926	NM_011861	ENSMUSG00000040276	Pacsin1	A830061D09Rik|H74|mKIAA1379|syndapin	protein kinase C and casein kinase substrate in neurons 1	protein-coding
mm_131677.1	chr16	20673535	20673607	+	1	NA	intron (NM_001304432, intron 1 of 31)	intron (NM_001304432, intron 1 of 31)	844	NM_001304432	208643	Mm.260256	NM_145941	ENSMUSG00000045983	Eif4g1	E030015G23Rik|eIF-4-gamma 1|eIF-4G 1|eIF-4G1|eIF4GI	eukaryotic translation initiation factor 4, gamma 1	protein-coding
mm_2567.1	chr1	118389469	118389481	+	1	NA	5' UTR (NM_029709, exon 1 of 37)	5' UTR (NM_029709, exon 1 of 37)	417	NM_001293301	76707	Mm.138740	NM_029709	ENSMUSG00000064302	Clasp1	1700030C23Rik|5730583A19Rik|B130045P17Rik|CLASP1alpha	CLIP associating protein 1	protein-coding
mm_160386.1	chr8	46293778	46293778	-	1	NA	intron (NM_173789, intron 1 of 3)	intron (NM_173789, intron 1 of 3)	893	NM_173789	234219	Mm.145631	NM_173789	ENSMUSG00000047171	Helt	A830086M02|Hesl|Heslike|Mgn|megane	helt bHLH transcription factor	protein-coding
mm_168103.1	chr10	13893418	13893428	+	1	NA	Intergenic	L1Md_Gf|LINE|L1	-24466	NM_001347362	66253	Mm.45755	NM_025446	ENSMUSG00000019806	Aig1	1500031O19Rik|AV064870|AW413422|CGI-103	androgen-induced 1	protein-coding
mm_37026.1	chr4	114926065	114926069	-	1	NA	promoter-TSS (NM_015758)	promoter-TSS (NM_015758)	-54	NM_015758	30923	Mm.377122	NM_015758	ENSMUSG00000044518	Foxe3	FREAC8|dyl|rct	forkhead box E3	protein-coding
mm_167275.1	chr8	34055869	34055877	-	1	NA	Intergenic	Intergenic	51941	NM_001293758	22428	Mm.150373	NM_011722	ENSMUSG00000031516	Dctn6	AU044699|WS-3|p27	dynactin 6	protein-coding
mm_157429.1	chrX	38565035	38565047	-	1	NA	exon (NM_028288, exon 3 of 23)	exon (NM_028288, exon 3 of 23)	11155	NM_028288	72584	Mm.327675	NM_028288	ENSMUSG00000031095	Cul4b	2700050M05Rik|AA409770|CUL-4B|mKIAA0695	cullin 4B	protein-coding
mm_56964.1	chr6	120038622	120038636	-	1	NA	promoter-TSS (NM_001185020)	promoter-TSS (NM_001185020)	26	NM_001199083	232341	Mm.333349	NM_198703	ENSMUSG00000045962	Wnk1	6430573H23Rik|EG406236|Hsn2|Prkwnk1|mKIAA0344	WNK lysine deficient protein kinase 1	protein-coding
mm_48444.1	chr5	140648954	140648964	-	1	NA	promoter-TSS (NM_175274)	promoter-TSS (NM_175274)	72	NM_001308040	78339	Mm.28947	NM_175274	ENSMUSG00000036565	Ttyh3	2900029G13Rik|AI414930|TTY3|mTTY3	tweety family member 3	protein-coding
mm_52876.1	chr6	122365910	122365914	+	1	NA	Intergenic	RMER17C|LTR|ERVK	-25685	NM_001271579	13619	Mm.6822	NM_007905	ENSMUSG00000040669	Phc1	AW557034|Edr|Edr1|Mph1|Rae-28|rae28	polyhomeotic-like 1 (Drosophila)	protein-coding
mm_129651.1	chr15	80743654	80743673	-	1	NA	intron (NM_144812, intron 1 of 24)	intron (NM_144812, intron 1 of 24)	32350	NM_144812	213988	Mm.131328	NM_144812	ENSMUSG00000047888	Tnrc6b	2700090M07Rik|A730065C02Rik|AI848765|D230019K20Rik	trinucleotide repeat containing 6b	protein-coding
mm_41220.1	chr5	88583604	88583606	+	1	NA	promoter-TSS (NM_027530)	promoter-TSS (NM_027530)	92	NM_027530	52822	Mm.270469	NM_027530	ENSMUSG00000029291	Rufy3	2810428M05Rik|6330416M07Rik|AW455998|AW538594|D5Bwg0860e|Ripx|Rpipx	RUN and FYVE domain containing 3	protein-coding
mm_61642.1	chr7	80343166	80343188	+	1	NA	promoter-TSS (NM_026812)	promoter-TSS (NM_026812)	40	NM_026812	68695	Mm.21171	NM_026812	ENSMUSG00000030532	Hddc3	1110033O09Rik|C86475|MESH1	HD domain containing 3	protein-coding
mm_152381.1	chr19	10240763	10240776	-	1	NA	promoter-TSS (NM_001033481)	promoter-TSS (NM_001033481)	-21	NM_001033481	225908	Mm.329716	NM_001033481	ENSMUSG00000036098	Myrf	6030439E18|Gm1804|Gm98|Mrf	myelin regulatory factor	protein-coding
mm_47408.1	chr5	123132578	123132606	-	1	NA	promoter-TSS (NM_175092)	promoter-TSS (NM_175092)	37	NM_175092	23912	Mm.253876	NM_175092	ENSMUSG00000029449	Rhof	AI845056|AV026554|Arhf|Ifld1|Rif	ras homolog family member F (in filopodia)	protein-coding
mm_94463.1	chr11	6474694	6474751	+	1	NA	3' UTR (NM_011221, exon 1 of 1)	3' UTR (NM_011221, exon 1 of 1)	1354	NM_011221	19291	Mm.296150	NM_011221	ENSMUSG00000094483	Purb	2310015K15Rik|AA114818|Cager-2|D11Bwg0414e	purine rich element binding protein B	protein-coding
mm_48499.1	chr5	142815343	142815361	-	1	NA	5' UTR (NM_001122730, exon 2 of 28)	5' UTR (NM_001122730, exon 2 of 28)	2035	NM_178242	231861	Mm.354649	NM_178242	ENSMUSG00000039477	Tnrc18	BC025631|EG381742|Zfp469	trinucleotide repeat containing 18	protein-coding
mm_39082.1	chr4	154471279	154471310	-	1	NA	intron (NM_001177995, intron 3 of 15)	intron (NM_001177995, intron 3 of 15)	165073	NR_045643	320939	Mm.436738	NR_045643		5930403L14Rik	-	RIKEN cDNA 5930403L14 gene	ncRNA
mm_79697.1	chr9	60837697	60837755	+	1	NA	intron (NM_028283, intron 1 of 18)	intron (NM_028283, intron 1 of 18)	43178	NM_028283	72565	Mm.68819	NM_028283	ENSMUSG00000034485	Uaca	2700059D02Rik|nucling	uveal autoantigen with coiled-coil domains and ankyrin repeats	protein-coding
mm_132695.1	chr16	43299315	43299324	+	1	NA	intron (NM_181058, intron 1 of 6)	intron (NM_181058, intron 1 of 6)	52035	NM_019778	56490	Mm.136238	NM_019778	ENSMUSG00000022708	Zbtb20	1300017A20Rik|7330412A13Rik|A930017C21Rik|D16Wsu73e|DPZF|HOF|ODA-8S|Oda8|Zfp288	zinc finger and BTB domain containing 20	protein-coding
mm_54283.1	chr6	29216278	29216292	-	1	NA	promoter-TSS (NM_001302934)	promoter-TSS (NM_001302934)	79	NM_001302933	23917	Mm.260707	NM_011829	ENSMUSG00000003500	Impdh1	B930086D20Rik|IMPDH-I	inosine 5'-phosphate dehydrogenase 1	protein-coding
mm_138325.1	chr17	34850448	34850466	+	1	NA	promoter-TSS (NM_021337)	promoter-TSS (NM_021337)	66	NM_001045864	27632	Mm.653	NM_138580	ENSMUSG00000024369	Nelfe	D17H6S45|NELF-E|RD|Rdbp	negative elongation factor complex member E, Rdbp	protein-coding
mm_93461.1	chr10	110802605	110802613	-	1	NA	intron (NR_045979, intron 2 of 2)	intron (NR_045979, intron 2 of 2)	57144	NM_178609	52679	Mm.11747	NM_178609	ENSMUSG00000020185	E2f7	A630014C11Rik|D10Ertd739e	E2F transcription factor 7	protein-coding
mm_21377.1	chr2	157376446	157376450	-	1	NA	intron (NM_026968, intron 1 of 2)	RSINE1|SINE|B4	8854	NM_026968	69161	Mm.228619	NM_026968	ENSMUSG00000063019	Manbal	1810024K12Rik|AI836500	mannosidase, beta A, lysosomal-like	protein-coding
mm_40420.1	chr5	53414150	53414155	+	1	NA	Intergenic	Intergenic	-141627	NM_001080928	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_156071.1	chrX	109161380	109161408	+	1	NA	3' UTR (NM_019989, exon 4 of 4)	3' UTR (NM_019989, exon 4 of 4)	-35362	NM_001037917	622976	Mm.482747	NM_001037917	ENSMUSG00000048621	Gm6377	EG622976	predicted gene 6377	protein-coding
mm_39209.1	chr4	156050763	156050772	-	1	NA	promoter-TSS (NM_029264)	promoter-TSS (NM_029264)	50	NM_029264	330010	Mm.440232	NM_029264	ENSMUSG00000029074	Ttll10	4833412E22Rik|4930595O22Rik|AU022799|BC042775|Ttll5	tubulin tyrosine ligase-like family, member 10	protein-coding
mm_110169.1	chr12	27336054	27336064	-	1	NA	3' UTR (NM_009234, exon 1 of 1)	3' UTR (NM_009234, exon 1 of 1)	6659	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding
mm_7956.1	chr1	133921394	133921409	-	1	NA	promoter-TSS (NM_054077)	promoter-TSS (NM_054077)	0	NM_054077	116847	Mm.214514	NM_054077	ENSMUSG00000041577	Prelp	7330409J17Rik|SLRR2A	proline arginine-rich end leucine-rich repeat	protein-coding
mm_28127.1	chr3	86999285	86999334	-	1	NA	promoter-TSS (NM_007639)	promoter-TSS (NM_007639)	31	NM_007639	12479	Mm.1894	NM_007639	ENSMUSG00000028076	Cd1d1	AI747460|CD1.1|Cd1a|Cd1d|Ly-38	CD1d1 antigen	protein-coding
mm_147133.1	chr18	36197344	36197403	-	1	NA	promoter-TSS (NM_001167891)	promoter-TSS (NM_001167891)	-213	NM_001167891	100042150	Mm.380390	NM_001167891	ENSMUSG00000060275	Nrg2	Don1|NTAK	neuregulin 2	protein-coding
mm_44708.1	chr5	30888787	30888796	-	1	NA	promoter-TSS (NM_174849)	promoter-TSS (NM_174849)	-61	NM_174849	231093	Mm.440364	NM_174849	ENSMUSG00000029165	Agbl5	9430057O19Rik|CCP5	ATP/GTP binding protein-like 5	protein-coding
mm_62295.1	chr7	100006019	100006023	+	1	NA	promoter-TSS (NM_133709)	promoter-TSS (NM_133709)	-383	NM_133709	69121	Mm.285295	NM_133709	ENSMUSG00000030732	Chrdl2	1810022C01Rik|Chl2	chordin-like 2	protein-coding
mm_30096.1	chr3	138282724	138282743	-	1	NA	exon (NM_007409, exon 5 of 9)	exon (NM_007409, exon 5 of 9)	5088	NM_007409	11522	Mm.2409	NM_007409	ENSMUSG00000074207	Adh1	ADH-AA|AI194826|Adh-1|Adh-1-t|Adh-1e|Adh-1t|Adh-3e|Adh1-e|Adh1-t|Adh1tl|Adh3-e	alcohol dehydrogenase 1 (class I)	protein-coding
mm_77843.1	chr9	5299403	5299415	+	1	NA	exon (NM_009807, exon 2 of 10)	exon (NM_009807, exon 2 of 10)	892	NM_009807	12362	Mm.1051	NM_009807	ENSMUSG00000025888	Casp1	ICE|Il1bc	caspase 1	protein-coding
mm_158976.1	chr1	119836836	119836836	-	1	NA	intron (NM_019933, intron 1 of 26)	CpG	235	NM_019933	19258	Mm.458796	NM_019933	ENSMUSG00000026384	Ptpn4	PTPMEG|Ptn4|TEP|TEP/mPTPMEG|hPTP-MEG	protein tyrosine phosphatase, non-receptor type 4	protein-coding
mm_3571.1	chr1	150496868	150496893	+	1	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	-30715	NM_001110146	96875	Mm.174256	NM_021400	ENSMUSG00000006014	Prg4	CACP|DOL54|JCAP|MSF|SZP|lubricin	proteoglycan 4 (megakaryocyte stimulating factor, articular superficial zone protein)	protein-coding
mm_87012.1	chr10	26885337	26885341	+	1	NA	intron (NM_176837, intron 10 of 14)	intron (NM_176837, intron 10 of 14)	112827	NM_176837	73910	Mm.356496	NM_176837	ENSMUSG00000039031	Arhgap18	4833419J07Rik|AI314906|AI843501	Rho GTPase activating protein 18	protein-coding
mm_25258.1	chr3	104781130	104781143	+	1	NA	promoter-TSS (NM_027982)	promoter-TSS (NM_027982)	80	NM_027982	71887	Mm.379204	NM_027982	ENSMUSG00000002228	Ppm1j	2310008J22Rik|PP2Czeta|Ppp2cz	protein phosphatase 1J	protein-coding
mm_85284.1	chr9	99709953	99709988	-	1	NA	promoter-TSS (NM_001194922)	promoter-TSS (NM_001194922)	93	NM_019815	56492	Mm.386784	NM_019815	ENSMUSG00000032473	Cldn18	-	claudin 18	protein-coding
mm_146848.1	chr18	23987236	23987282	-	1	NA	Intergenic	Intergenic	-2375	NM_011755	22694	Mm.290596	NM_011755	ENSMUSG00000063281	Zfp35	Zfp-35|Znf271|mszf13|mszf20-1|mszf28|mszf68	zinc finger protein 35	protein-coding
mm_70520.1	chr8	12949431	12949469	+	1	NA	promoter-TSS (NM_001159485)	promoter-TSS (NM_001159485)	32	NM_001159485	17207	Mm.334413	NM_178076	ENSMUSG00000031442	Mcf2l	C130040G20Rik|Dbs|Ost|mKIAA0362	mcf.2 transforming sequence-like	protein-coding
mm_107508.1	chr12	40038322	40038335	+	1	NA	promoter-TSS (NM_007487)	promoter-TSS (NM_007487)	-341	NM_001039515	11861	Mm.12723	NM_007487	ENSMUSG00000047446	Arl4a	AI467555|Arl4	ADP-ribosylation factor-like 4A	protein-coding
mm_131176.1	chr16	7069872	7069890	+	1	NA	promoter-TSS (NM_183188)	promoter-TSS (NM_183188)	46	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_95529.1	chr11	52232265	52232286	+	1	NA	intron (NM_011543, intron 1 of 5)	CpG	280	NM_011543	21402	Mm.42944	NM_011543	ENSMUSG00000036309	Skp1a	15kDa|2610043E24Rik|2610206H23Rik|EMC19|OCP-II|OCP2|SKP1|Tceb1l|p19A|p19Skp1	S-phase kinase-associated protein 1A	protein-coding
mm_115942.1	chr13	23698456	23698460	-	1	NA	promoter-TSS (NM_178208)	promoter-TSS (NM_178208)	0	NM_178208	319155	Mm.261662	NM_178208	ENSMUSG00000060678	Hist1h4c	-	histone cluster 1, H4c	protein-coding
mm_148984.1	chr19	8591278	8591300	+	1	NA	promoter-TSS (NM_001164634)	promoter-TSS (NM_001164634)	35	NM_031194	19879	Mm.285294	NM_031194	ENSMUSG00000063796	Slc22a8	Oat3|Roct	solute carrier family 22 (organic anion transporter), member 8	protein-coding
mm_8496.1	chr1	153851168	153851174	-	1	NA	promoter-TSS (NM_178243)	promoter-TSS (NM_178243)	24	NM_178243	240817	Mm.439405	NM_178243	ENSMUSG00000045968	Teddm2	5830403L16Rik|AJ554213|Me9|e92	transmembrane epididymal family member 2	protein-coding
mm_150661.1	chr19	41981624	41981638	+	1	NA	promoter-TSS (NM_028152)	promoter-TSS (NM_028152)	-132	NM_145500	226122	Mm.22948	NM_145500	ENSMUSG00000025171	Ubtd1	BC016129	ubiquitin domain containing 1	protein-coding
mm_54993.1	chr6	48770824	48770830	-	1	NA	promoter-TSS (NM_031247)	promoter-TSS (NM_031247)	24	NM_031247	83408	Mm.333050	NM_031247	ENSMUSG00000039264	Gimap3	2010110D23Rik|Gimap5|Ian4	GTPase, IMAP family member 3	protein-coding
mm_72633.1	chr8	84664539	84664565	+	1	NA	Intergenic	Intergenic	-1700	NM_010499	15936	Mm.399	NM_010499	ENSMUSG00000053560	Ier2	AI317238|Ch1|Pip92	immediate early response 2	protein-coding
mm_17890.1	chr2	35035998	35036013	-	1	NA	exon (NM_010406, exon 11 of 41)	exon (NM_010406, exon 11 of 41)	25436	NM_010406	15139	Mm.2168	NM_010406	ENSMUSG00000026874	Hc	C5|C5a|He	hemolytic complement	protein-coding
mm_22652.1	chr3	14870095	14870137	+	1	NA	exon (NM_007606, exon 6 of 7)	exon (NM_007606, exon 6 of 7)	6578	NM_007606	12350	Mm.300	NM_007606	ENSMUSG00000027559	Car3	BB219044|Ca3|Car-3	carbonic anhydrase 3	protein-coding
mm_133007.1	chr16	55973838	55973864	+	1	NA	promoter-TSS (NM_173026)	promoter-TSS (NM_173026)	47	NM_173026	271377	Mm.282814	NM_173026	ENSMUSG00000022601	Zbtb11	9230110G02Rik|ZNF-U69274	zinc finger and BTB domain containing 11	protein-coding
mm_143670.1	chr17	79896029	79896061	-	1	NA	promoter-TSS (NM_019717)	promoter-TSS (NM_019717)	78	NM_178050	56298	Mm.175403	NM_019717	ENSMUSG00000059811	Atl2	2010110I21Rik|AA407293|AV334690|Aip-2|Arl6ip2	atlastin GTPase 2	protein-coding
mm_147866.1	chr18	64457293	64457309	-	1	NA	3' UTR (NM_007998, exon 11 of 11)	3' UTR (NM_007998, exon 11 of 11)	31765	NM_007998	14151	Mm.1070	NM_007998	ENSMUSG00000024588	Fech	AI894116|Fcl|fch	ferrochelatase	protein-coding
mm_129805.1	chr15	82987679	82987690	-	1	NA	Intergenic	Intergenic	-28388	NR_037241	100526477		NR_037241	ENSMUSG00000092751	Mir3080	mmu-mir-3080	microRNA 3080	ncRNA
mm_164250.1	chr15	97979213	97979239	+	1	NA	exon (NM_001113515, exon 47 of 53)	exon (NM_001113515, exon 47 of 53)	14997	NM_001252153	380967	Mm.196630	NM_201359	ENSMUSG00000052369	Tmem106c	AI046681|BC046621|D15Ertd405e	transmembrane protein 106C	protein-coding
mm_125548.1	chr15	58510038	58510053	+	1	NA	Intergenic	Intergenic	94577	NM_145959	210998	Mm.3224	NM_145959	ENSMUSG00000037119	Fam91a1	AV220772|BC033609|D15Ertd621e|SKIN|mKIAA0493	family with sequence similarity 91, member A1	protein-coding
mm_73021.1	chr8	94010515	94010548	+	1	NA	intron (NM_011787, intron 1 of 13)	intron (NM_011787, intron 1 of 13)	2109	NM_011787	23802	Mm.34641	NM_011787	ENSMUSG00000031751	Amfr	gp78	autocrine motility factor receptor	protein-coding
mm_83686.1	chr9	50528643	50528698	-	1	NA	promoter-TSS (NM_011220)	promoter-TSS (NM_011220)	-29	NM_011220	19286	Mm.35856	NM_011220	ENSMUSG00000032067	Pts	PTPS	6-pyruvoyl-tetrahydropterin synthase	protein-coding
mm_57338.1	chr6	124746688	124746704	-	1	NA	exon (NM_007881, exon 5 of 10)	exon (NM_007881, exon 5 of 10)	-5617	NM_013535	14790	Mm.439877	NM_013535	ENSMUSG00000072772	Grcc10	2310033H05Rik|C10	gene rich cluster, C10 gene	protein-coding
mm_13375.1	chr2	103612363	103612366	+	1	NA	intron (NM_178890, intron 1 of 16)	intron (NM_178890, intron 1 of 16)	46054	NM_178890	99382	Mm.35850	NM_178890	ENSMUSG00000032724	Abtb2	AW539457|BPOZ-2	ankyrin repeat and BTB (POZ) domain containing 2	protein-coding
mm_114297.1	chr13	59133376	59133379	+	1	NA	3' UTR (NM_001282961, exon 18 of 18)	3' UTR (NM_001282961, exon 18 of 18)	325680	NM_001025074	18212	Mm.130054	NM_008745	ENSMUSG00000055254	Ntrk2	GP145-TrkB/GP95-TrkB|Tkrb|trk-B|trkB	neurotrophic tyrosine kinase, receptor, type 2	protein-coding
mm_169942.1	chr16	66559595	66559595	-	1	NA	Intergenic	IAPEY_LTR|LTR|ERVK	-97523	NR_040512	75501	Mm.394300	NR_040512	ENSMUSG00000092599	1700010K23Rik	-	RIKEN cDNA 1700010K23 gene	ncRNA
mm_172854.1	chr9	38637308	38637310	+	1	NA	Intergenic	LTRIS3|LTR|ERV1	10213	NM_146785	258781	Mm.223210	NM_146785	ENSMUSG00000057444	Olfr915	MOR167-4	olfactory receptor 915	protein-coding
mm_105167.1	chr11	101774183	101774191	-	1	NA	exon (NM_001316366, exon 7 of 13)	exon (NM_001316366, exon 7 of 13)	11123	NM_008815	18612	Mm.5025	NM_008815	ENSMUSG00000017724	Etv4	AW414408|Pea-3|Pea3	ets variant 4	protein-coding
mm_48387.1	chr5	139813209	139813220	-	1	NA	promoter-TSS (NM_144914)	promoter-TSS (NM_144914)	29	NM_144914	231832	Mm.482655	NM_144914	ENSMUSG00000036687	Tmem184a	Sdmg1	transmembrane protein 184a	protein-coding
mm_122146.1	chr14	31188838	31188848	-	1	NA	intron (NM_001347583, intron 7 of 13)	intron (NM_001347583, intron 7 of 13)	17983	NM_022656	64652	Mm.298728	NM_022656	ENSMUSG00000021910	Nisch	1200007D05Rik|3202002H23Rik|AW494485|I-1	nischarin	protein-coding
mm_16979.1	chr2	18028742	18028770	-	1	NA	non-coding (NR_028378, exon 1 of 1)	non-coding (NR_028378, exon 1 of 1)	1507	NR_028378	100034739	Mm.401643	NR_028378		Gm17762	-	predicted gene, 17762	ncRNA
mm_49428.1	chr6	29272437	29272462	+	1	NA	promoter-TSS (NM_001190461)	promoter-TSS (NM_001190461)	-39	NM_001190461	69573	Mm.45161	NM_023516	ENSMUSG00000043421	Hilpda	2310016C08Rik|AW049004|Hig2	hypoxia inducible lipid droplet associated	protein-coding
mm_146886.1	chr18	25753583	25753600	-	1	NA	exon (NM_001146295, exon 1 of 2)	exon (NM_001146295, exon 1 of 2)	392	NM_133195	108013	Mm.266435	NM_133195	ENSMUSG00000024268	Celf4	A230070D14Rik|BRUNOL-4|Brul4|Brunol4|C130060B05Rik	CUGBP, Elav-like family member 4	protein-coding
mm_128048.1	chr15	25751612	25751620	-	1	NA	intron (NM_019472, intron 19 of 40)	intron (NM_019472, intron 19 of 40)	-91682	NM_001034851	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_42549.1	chr5	116230449	116230449	+	1	NA	intron (NM_177759, intron 1 of 13)	intron (NM_177759, intron 1 of 13)	58536	NM_177759	269693	Mm.10946	NM_177759	ENSMUSG00000043913	Ccdc60	AU018954|C130098D09	coiled-coil domain containing 60	protein-coding
mm_46032.1	chr5	91807119	91807129	-	1	NA	Intergenic	Intergenic	-39824	NR_045383	73452	Mm.396233	NR_045383	ENSMUSG00000101978	1700063O14Rik	-	RIKEN cDNA 1700063O14 gene	ncRNA
mm_83075.1	chr9	37669159	37669167	-	1	NA	promoter-TSS (NM_172454)	promoter-TSS (NM_172454)	59	NM_172454	208098	Mm.217159	NM_172454	ENSMUSG00000011118	Panx3	3230401P04|4833413G11Rik	pannexin 3	protein-coding
mm_15457.1	chr2	157426365	157426383	+	1	NA	intron (NM_009271, intron 1 of 14)	intron (NM_009271, intron 1 of 14)	2081	NM_001025395	20779	Mm.22845	NM_009271	ENSMUSG00000027646	Src	AW259666|pp60c-src	Rous sarcoma oncogene	protein-coding
mm_96230.1	chr11	62550810	62550857	+	1	NA	promoter-TSS (NR_002875).2	promoter-TSS (NR_002875).2	-338	NM_011664	22187	Mm.371592	NM_011664	ENSMUSG00000019505	Ubb	AL033289|Rps27a|Uba52|Ubb2|Ubc	ubiquitin B	protein-coding
mm_75774.1	chr8	69996091	69996108	-	1	NA	5' UTR (NM_001286450, exon 1 of 13)	5' UTR (NM_001286450, exon 1 of 13)	285	NM_001286450	234366	Mm.270044	NM_145596	ENSMUSG00000036180	Gatad2a	1110066C11Rik|BC031407|C80248	GATA zinc finger domain containing 2A	protein-coding
mm_131861.1	chr16	23107414	23107430	+	1	NA	promoter-TSS (NM_001123037)	promoter-TSS (NM_001123037)	25	NM_001347179	13682	Mm.260084	NM_013506	ENSMUSG00000022884	Eif4a2	4833432N07Rik|BM-010|Ddx2b|Eif4|eIF-4A-II|eIF4A-II	eukaryotic translation initiation factor 4A2	protein-coding
mm_57777.1	chr6	129238053	129238082	-	1	NA	promoter-TSS (NR_040265)	promoter-TSS (NR_040265)	-22	NR_040265	76432	Mm.261738	NR_040265	ENSMUSG00000097354	2310001H17Rik	AI646108	RIKEN cDNA 2310001H17 gene	ncRNA
mm_29396.1	chr3	108904536	108904549	-	1	NA	exon (NM_025845, exon 6 of 6)	exon (NM_025845, exon 6 of 6)	7162	NM_025845	66921	Mm.51049	NM_025845	ENSMUSG00000027881	Prpf38b	1110021E09Rik|AU018955	PRP38 pre-mRNA processing factor 38 (yeast) domain containing B	protein-coding
mm_87223.1	chr10	40386385	40386391	+	1	NA	intron (NM_001291816, intron 1 of 11)	RMER19C|LTR|ERVK	37080	NM_001291816	78334	Mm.200924	NM_198164	ENSMUSG00000038481	Cdk19	2700084L06Rik|AI845279|AW228747|CDK11|Cdc2l6|mKIAA1028	cyclin-dependent kinase 19	protein-coding
mm_64982.1	chr7	16915653	16915672	-	1	NA	3' UTR (NM_007590, exon 6 of 6)	3' UTR (NM_007590, exon 6 of 6)	8370	NM_007590	12315	Mm.288630	NM_007590	ENSMUSG00000019370	Calm3	CaMA|R75142	calmodulin 3	protein-coding
mm_115849.1	chr13	21287526	21287533	-	1	NA	exon (NM_010343, exon 5 of 5)	exon (NM_010343, exon 5 of 5)	5157	NM_010343	14780	Mm.1332	NM_010343	ENSMUSG00000004344	Gpx5	AV379049|Arep	glutathione peroxidase 5	protein-coding
mm_78444.1	chr9	32224112	32224125	+	1	NA	promoter-TSS (NM_177379)	promoter-TSS (NM_177379)	-131	NM_177379	330914	Mm.46683	NM_177379	ENSMUSG00000041444	Arhgap32	3426406O18Rik|Gc-gap|Grit|Px-rics|Rics|mKIAA0712|p200Rhogap|p250Gap	Rho GTPase activating protein 32	protein-coding
mm_104433.1	chr11	94951582	94951590	-	1	NA	exon (NM_007742, exon 51 of 51)	exon (NM_007742, exon 51 of 51)	15362	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_32780.1	chr4	116708576	116708584	+	1	NA	promoter-TSS (NM_026714)	promoter-TSS (NM_026714)	-195	NM_025962	67096	Mm.252785	NM_025962	ENSMUSG00000028690	Mmachc	1810037K07Rik|CblC	methylmalonic aciduria cblC type, with homocystinuria	protein-coding
mm_100790.1	chr11	4939622	4939632	-	1	NA	exon (NM_010904, exon 4 of 4)	exon (NM_010904, exon 4 of 4)	-7894	NM_001243043	11764	Mm.274816	NM_007454	ENSMUSG00000009090	Ap1b1	Adtb1|b2b1660Clo	adaptor protein complex AP-1, beta 1 subunit	protein-coding
mm_155858.1	chrX	101320915	101320930	+	1	NA	3' UTR (NM_172932, exon 7 of 7)	3' UTR (NM_172932, exon 7 of 7)	21743	NM_172932	245537	Mm.121508	NM_172932	ENSMUSG00000031302	Nlgn3	A230085M13Rik|HNL3|NL3	neuroligin 3	protein-coding
mm_110093.1	chr12	25101196	25101226	-	1	NA	Intergenic	Intergenic	-5119	NM_010496	15902	Mm.34871	NM_010496	ENSMUSG00000020644	Id2	AI255428|C78922|Idb2|bHLHb26	inhibitor of DNA binding 2	protein-coding
mm_23287.1	chr3	51879370	51879370	+	1	NA	intron (NM_001004176, intron 1 of 4)	intron (NM_001004176, intron 1 of 4)	218191	NM_001310482	211666	Mm.24679	NM_174995	ENSMUSG00000074604	Mgst2	GST2|MGST-II	microsomal glutathione S-transferase 2	protein-coding
mm_47115.1	chr5	119616685	119616696	-	1	NA	Intergenic	Intergenic	-9252	NR_046178	330183	Mm.413133	NR_046178	ENSMUSG00000085708	Gm16063	G630008E18|OTTMUSG00000029664	predicted gene 16063	ncRNA
mm_31897.1	chr4	83417716	83417758	+	1	NA	promoter-TSS (NM_029949)	promoter-TSS (NM_029949)	-7	NM_029949	77634	Mm.271985	NM_029949	ENSMUSG00000028483	Snapc3	1810020H02Rik|4930558A07Rik|5031401C21Rik|AI414457|E030018J20Rik	small nuclear RNA activating complex, polypeptide 3	protein-coding
mm_127024.1	chr15	96286931	96286939	+	1	NA	promoter-TSS (NM_175251)	promoter-TSS (NM_175251)	-587	NM_175251	77044	Mm.17166	NM_175251	ENSMUSG00000033237	Arid2	1700124K17Rik|4432409D24Rik|zipzap/p200	AT rich interactive domain 2 (ARID, RFX-like)	protein-coding
mm_65082.1	chr7	19227804	19227816	-	1	NA	promoter-TSS (NM_207525)	promoter-TSS (NM_207525)	-579	NM_207525	403187	Mm.239583	NM_207525	ENSMUSG00000052214	Opa3	D630048P19Rik|Gm1425|Gm472	optic atrophy 3	protein-coding
mm_158951.1	chr1	87089928	87089928	-	1	NA	promoter-TSS (NM_007433)	promoter-TSS (NM_007433)	0	NM_007433	11650	Mm.195224	NM_007433	ENSMUSG00000026246	Alppl2	Akp5|C77216|D1Ertd816e|EAP	alkaline phosphatase, placental-like 2	protein-coding
mm_154064.1	chr19	55311887	55311920	-	1	NA	intron (NM_001033573, intron 3 of 10)	intron (NM_001033573, intron 3 of 10)	4129	NM_025883	66980	Mm.386789	NM_025883	ENSMUSG00000024982	Zdhhc6	2400007G07Rik|5930409M18Rik|AI462345|C77369	zinc finger, DHHC domain containing 6	protein-coding
mm_16976.1	chr2	17996925	17996945	-	1	NA	promoter-TSS (NM_026627)	promoter-TSS (NM_026627)	23	NM_026627	68231	Mm.23887	NM_026627	ENSMUSG00000062651	H2afb1	1700113O17Rik|H2A.Bbd|H2al2|TSEG-1|Tseg1	H2A histone family, member B1	protein-coding
mm_89200.1	chr10	86348354	86348368	+	1	NA	3' UTR (NM_011595, exon 5 of 5)	3' UTR (NM_011595, exon 5 of 5)	47949	NM_011595	21859	Mm.4871	NM_011595	ENSMUSG00000020044	Timp3	Timp-3	tissue inhibitor of metalloproteinase 3	protein-coding
mm_169639.1	chr15	49248810	49248812	+	1	NA	Intergenic	Intergenic	-456822	NM_001081391	239420	Mm.309363	NM_001081391	ENSMUSG00000022311	Csmd3	4930500N14Rik|mKIAA1894	CUB and Sushi multiple domains 3	protein-coding
mm_164552.1	chr17	13654843	13654850	+	1	NA	Intergenic	Intergenic	-100752	NR_045437	72578	Mm.46549	NR_045436	ENSMUSG00000038347	2700054A10Rik	-	RIKEN cDNA 2700054A10 gene	ncRNA
mm_130886.1	chr15	102257450	102257496	-	1	NA	promoter-TSS (NM_011244)	promoter-TSS (NM_011244)	49	NM_011244	19411	Mm.1273	NM_011244	ENSMUSG00000001288	Rarg	Nr1b3|RAR-gamma|RARD|RARgamma2	retinoic acid receptor, gamma	protein-coding
mm_18796.1	chr2	73892178	73892188	-	1	NA	intron (NM_001284374, intron 1 of 11)	CpG	456	NM_001284371	11909	Mm.209903	NM_009715	ENSMUSG00000027104	Atf2	Atf-2|CRE-BP|Creb2|D130078H02Rik|D18875|Tg(Gzma-Klra1)7Wum|mXBP	activating transcription factor 2	protein-coding
mm_74115.1	chr8	123062953	123062974	+	1	NA	Intergenic	RLTR31D_MM|LTR|ERVK	-2545	NM_153176	234847	Mm.292075	NM_153176	ENSMUSG00000000738	Spg7	AI452278|AU015315|Cmar|PGN	spastic paraplegia 7 homolog (human)	protein-coding
mm_67919.1	chr7	99858911	99858921	-	1	NA	promoter-TSS (NM_001164258)	promoter-TSS (NM_001164258)	-33	NM_025668	66624	Mm.30043	NM_025668	ENSMUSG00000035227	Spcs2	5730406I15Rik|AA408713|mKIAA0102	signal peptidase complex subunit 2 homolog (S. cerevisiae)	protein-coding
mm_128961.1	chr15	74817289	74817297	-	1	NA	intron (NM_001177524, intron 1 of 3)	intron (NM_001177524, intron 1 of 3)	1522	NM_001177524	625599	Mm.390785	NM_001177524	ENSMUSG00000068349	Gml	EG625599|HemT	glycosylphosphatidylinositol anchored molecule like	protein-coding
mm_56735.1	chr6	115758975	115759000	-	1	NA	promoter-TSS (NM_144805)	promoter-TSS (NM_144805)	12	NM_144805	94346	Mm.29739	NM_144805	ENSMUSG00000059900	Tmem40	9030407H20Rik|AV091463|W64236	transmembrane protein 40	protein-coding
mm_70870.1	chr8	25017326	25017347	+	1	NA	promoter-TSS (NM_007404)	promoter-TSS (NM_007404)	125	NM_027194	69742	Mm.28626	NM_027194	ENSMUSG00000031556	Tm2d2	2410018G23Rik|Blp1	TM2 domain containing 2	protein-coding
mm_74527.1	chr8	9559235	9559251	-	1	NA	intron (NM_001347127, intron 1 of 3)	B4A|SINE|B4	211780	NM_173446	270028	Mm.268163	NM_173446	ENSMUSG00000079157	Fam155a	6430500D16|AW121567|Tmem28	family with sequence similarity 155, member A	protein-coding
mm_136121.1	chr16	85900266	85900280	-	1	NA	5' UTR (NM_011782, exon 1 of 8)	5' UTR (NM_011782, exon 1 of 8)	852	NM_011782	23794	Mm.112933	NM_011782	ENSMUSG00000022894	Adamts5	9530092O11Rik|ADAM-TS5|ADAMTS1|ADAMTS11|ADMP-2|AI481094|ASMP-2	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)	protein-coding
mm_124469.1	chr14	121340202	121340213	-	1	NA	intron (NM_145465, intron 1 of 10)	intron (NM_145465, intron 1 of 10)	39023	NM_145465	223255	Mm.390756	NM_145465	ENSMUSG00000063410	Stk24	1810013H02Rik|C76483|MST-3|Mst3|STE20	serine/threonine kinase 24	protein-coding
mm_82607.1	chr9	21510182	21510203	-	1	NA	promoter-TSS (NM_010744)	promoter-TSS (NM_010744)	42	NR_136912	17083	Mm.196618	NM_010744	ENSMUSG00000032180	Tmed1	Il1rl1l|Ly84l|St2l	transmembrane p24 trafficking protein 1	protein-coding
mm_126546.1	chr15	82028509	82028512	+	1	NA	intron (NM_010247, intron 7 of 12)	intron (NM_010247, intron 7 of 12)	12141	NM_010247	14375	Mm.288809	NM_010247	ENSMUSG00000022471	Xrcc6	70kDa|G22p1|Ku70	X-ray repair complementing defective repair in Chinese hamster cells 6	protein-coding
mm_146677.1	chr18	12819793	12819808	-	1	NA	non-coding (NR_045524, exon 1 of 12)	non-coding (NR_045524, exon 1 of 12)	107	NR_045524	64291	Mm.259470	NM_020573	ENSMUSG00000044252	Osbpl1a	G430090F17Rik|Gm753|ORP-1|Osbpl1b	oxysterol binding protein-like 1A	protein-coding
mm_149495.1	chr19	11912253	11912272	+	1	NA	promoter-TSS (NM_172635)	promoter-TSS (NM_172635)	-137	NM_172635	225929	Mm.42711	NM_172635	ENSMUSG00000046139	Patl1	AV312086|Pat1b	protein associated with topoisomerase II homolog 1 (yeast)	protein-coding
mm_23493.1	chr3	60508465	60508471	+	1	NA	intron (NM_001253710, intron 1 of 7)	intron (NM_001253710, intron 1 of 7)	7289	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_42342.1	chr5	114904906	114904919	+	1	NA	exon (NM_011854, exon 4 of 6)	exon (NM_011854, exon 4 of 6)	7978	NM_011854	23962	Mm.228363	NM_011854	ENSMUSG00000029561	Oasl2	M1204|Mmu-OASL|Oasl	2'-5' oligoadenylate synthetase-like 2	protein-coding
mm_155627.1	chrX	84076589	84076607	+	1	NA	intron (NM_007868, intron 44 of 78)	intron (NM_007868, intron 44 of 78)	-588674	NM_021898	100502723	Mm.383210	NM_021898	ENSMUSG00000035522	Tsga8	Halap-X|Halapx	testis specific gene A8	protein-coding
mm_5076.1	chr1	3671672	3671733	-	1	NA	promoter-TSS (NM_001011874)	promoter-TSS (NM_001011874)	-204	NM_001011874	497097	Mm.454496	NM_001011874	ENSMUSG00000051951	Xkr4	AY534250|Gm210|XRG4|mKIAA1889	X-linked Kx blood group related 4	protein-coding
mm_4001.1	chr1	164796618	164796628	+	1	NA	promoter-TSS (NM_019759)	promoter-TSS (NM_019759)	-109	NM_019759	56429	Mm.28935	NM_019759	ENSMUSG00000026574	Dpt	1810032B19Rik|5033416F05Rik|EQ-1|Eq1	dermatopontin	protein-coding
mm_148678.1	chr19	5638313	5638313	+	1	NA	intron (NM_009045, intron 1 of 10)	intron (NM_009045, intron 1 of 10)	823	NM_009045	19697	Mm.249966	NM_009045	ENSMUSG00000024927	Rela	p65	v-rel reticuloendotheliosis viral oncogene homolog A (avian)	protein-coding
mm_44265.1	chr5	5663208	5663221	-	1	NA	intron (NM_172447, intron 1 of 22)	intron (NM_172447, intron 1 of 22)	1018	NM_172447	207686	Mm.319007	NM_172447	ENSMUSG00000040473	Cfap69	4921525K03|A330021E22Rik|AI427898	cilia and flagella associated protein 69	protein-coding
mm_71940.1	chr8	70352766	70352787	+	1	NA	intron (NM_030680, intron 1 of 23)	CpG	503	NM_030680	19704	Mm.258280	NM_030680	ENSMUSG00000058301	Upf1	B430202H16Rik|NORF1|PNORF-1|Rent1|Upflp	UPF1 regulator of nonsense transcripts homolog (yeast)	protein-coding
mm_163797.1	chr14	17659577	17659582	+	1	NA	Intergenic	Intergenic	-1381	NM_001113417	21834	Mm.32563	NM_009380	ENSMUSG00000021779	Thrb	Nr1a2|T3R[b]|T3Rbeta|Thrb1|Thrb2|c-erbAbeta	thyroid hormone receptor beta	protein-coding
mm_141567.1	chr17	32284089	32284116	-	1	NA	promoter-TSS (NM_001286630)	promoter-TSS (NM_001286630)	21	NM_198094	57261	Mm.253518	NM_020508	ENSMUSG00000024002	Brd4	Brd5|HUNK1|MCAP|WI-11513	bromodomain containing 4	protein-coding
mm_77541.1	chr8	123102261	123102280	-	1	NA	promoter-TSS (NM_016738)	promoter-TSS (NM_016738)	-80	NM_016738	270106	Mm.319719	NM_016738	ENSMUSG00000000740	Rpl13	A52|L13	ribosomal protein L13	protein-coding
mm_104594.1	chr11	97048396	97048415	-	1	NA	3' UTR (NM_026154, exon 5 of 5)	3' UTR (NM_026154, exon 5 of 5)	-2223	NM_001310509	71240	Mm.190450	NM_001081434	ENSMUSG00000038534	Osbpl7	4933437E18Rik	oxysterol binding protein-like 7	protein-coding
mm_160336.1	chr8	13288358	13288358	-	1	NA	promoter-TSS (NM_001042649)	promoter-TSS (NM_001042649)	-232	NM_001042650	102323	Mm.368890	NM_001024504	ENSMUSG00000038506	Dcun1d2	AW495713|mFLJ10704	DCN1, defective in cullin neddylation 1, domain containing 2 (S. cerevisiae)	protein-coding
mm_129397.1	chr15	78247722	78247763	-	1	NA	intron (NM_008677, intron 1 of 9)	intron (NM_008677, intron 1 of 9)	2931	NM_008677	17972	Mm.2068	NM_008677	ENSMUSG00000071715	Ncf4	AI451400|p40phox	neutrophil cytosolic factor 4	protein-coding
mm_46666.1	chr5	108694060	108694109	-	1	NA	promoter-TSS (NM_001164259)	promoter-TSS (NM_001164259)	-145	NM_001164259	116701	Mm.35691	NM_054071	ENSMUSG00000008090	Fgfrl1	FGFR5|FGFR5beta|FGFR5gamma	fibroblast growth factor receptor-like 1	protein-coding
mm_17424.1	chr2	27447914	27447933	-	1	NA	3' UTR (NM_001113574, exon 13 of 13)	3' UTR (NM_001113574, exon 13 of 13)	2707	NR_106102	102466836		NR_106102	ENSMUSG00000098812	Mir7578	Gm27789|mmu-mir-7578	microRNA 7578	ncRNA
mm_120237.1	chr14	62906858	62906895	+	1	NA	intron (NM_175546, intron 3 of 11)	RSINE1|SINE|B4	41334	NR_105860	102465311		NR_105860	ENSMUSG00000098858	Mir6541	Gm27311|mmu-mir-6541	microRNA 6541	ncRNA
mm_91344.1	chr10	26375963	26376002	-	1	NA	promoter-TSS (NM_172787)	promoter-TSS (NM_172787)	-763	NM_172787	237339	Mm.338439	NM_172787	ENSMUSG00000039089	L3mbtl3	AI481284|MBT-1	l(3)mbt-like 3 (Drosophila)	protein-coding
mm_154048.1	chr19	55096742	55096754	-	1	NA	intron (NM_008149, intron 2 of 20)	intron (NM_008149, intron 2 of 20)	2699	NM_008149	14732	Mm.210196	NM_008149	ENSMUSG00000024978	Gpam	GPAT|GPAT1	glycerol-3-phosphate acyltransferase, mitochondrial	protein-coding
mm_155370.1	chrX	71364902	71364920	+	1	NA	5' UTR (NM_016985, exon 1 of 15)	5' UTR (NM_016985, exon 1 of 15)	151	NM_001313706	53332	Mm.219672	NM_016985	ENSMUSG00000015214	Mtmr1	AW049210	myotubularin related protein 1	protein-coding
mm_84394.1	chr9	65536149	65536162	-	1	NA	Intergenic	Intergenic	43932	NM_153119	102595	Mm.247303	NM_153119	ENSMUSG00000050721	Plekho2	AI840980|Plekhq1	pleckstrin homology domain containing, family O member 2	protein-coding
mm_41754.1	chr5	102845331	102845338	+	1	NA	5' UTR (NM_001346585, exon 1 of 7)	5' UTR (NM_001346585, exon 1 of 7)	327	NM_001346585	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding
mm_82217.1	chr9	3015727	3015745	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	23007	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_73998.1	chr8	120739834	120739857	+	1	NA	exon (NM_008320, exon 2 of 9)	exon (NM_008320, exon 2 of 9)	1206	NM_001301811	15900	Mm.334861	NM_008320	ENSMUSG00000041515	Irf8	AI893568|ICSBP|IRF-8|Icsbp1|Myls	interferon regulatory factor 8	protein-coding
mm_78375.1	chr9	27397225	27397234	+	1	NA	promoter-TSS (NM_001305058)	promoter-TSS (NM_001305058)	17	NM_001305058	75469	Mm.45824	NM_029299	ENSMUSG00000031991	Spata19	1700001L23Rik|AV047838|spergen-1	spermatogenesis associated 19	protein-coding
mm_96118.1	chr11	60707272	60707287	+	1	NA	exon (NM_001159405, exon 10 of 22)	exon (NM_001159405, exon 10 of 22)	7589	NM_008502	16897	Mm.285453	NM_008502	ENSMUSG00000020536	Llgl1	AI325176|Lgl1|Llglh|Mgl1	lethal giant larvae homolog 1 (Drosophila)	protein-coding
mm_164291.1	chr15	103895900	103895905	-	1	NA	TTS (NM_009267)	TTS (NM_009267)	3398	NM_009268	20771	Mm.30276	NM_009268		Mucl1	Spt-2|Spt2	mucin-like 1	protein-coding
mm_56321.1	chr6	92427262	92427264	-	1	NA	intron (NM_001081146, intron 3 of 8)	B4A|SINE|B4	54129	NM_001134460	243548	Mm.248820	NM_001081146	ENSMUSG00000030020	Prickle2	6230400G14Rik|6720451F06Rik|mpk2	prickle planar cell polarity protein 2	protein-coding
mm_20975.1	chr2	151973439	151973453	-	1	NA	promoter-TSS (NM_001289151)	promoter-TSS (NM_001289151)	-52	NM_001289151	73847	Mm.272444	NM_028666	ENSMUSG00000027459	Fam110a	1700008J10Rik|5430432M24Rik|AI747080	family with sequence similarity 110, member A	protein-coding
mm_78139.1	chr9	20894350	20894352	+	1	NA	TTS (NM_016876)	TTS (NM_016876)	4239	NM_016876	53356	Mm.427309	NM_016876	ENSMUSG00000070319	Eif3g	44kDa|D0Jmb4|Eif3s4|TU-189B2|eIF3-p44|p44	eukaryotic translation initiation factor 3, subunit G	protein-coding
mm_62191.1	chr7	97590215	97590218	+	1	NA	intron (NM_001081267, intron 1 of 15)	AT_rich|Low_complexity|Low_complexity	10320	NM_001081267	233532	Mm.43977	NM_001081267	ENSMUSG00000035623	Rsf1	4832420A03Rik|C030033M12Rik|Gm164|Hbxap|XAP8|p325	remodeling and spacing factor 1	protein-coding
mm_44387.1	chr5	17828947	17828972	-	1	NA	5' UTR (NM_001159558, exon 4 of 16)	5' UTR (NM_001159558, exon 4 of 16)	6937	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_74912.1	chr8	25256436	25256465	-	1	NA	Intergenic	Intergenic	49820	NR_040352	74489	Mm.256468	NR_040352	ENSMUSG00000110140	5430421F17Rik	-	RIKEN cDNA 5430421F17 gene	ncRNA
mm_28313.1	chr3	89245830	89245899	-	1	NA	promoter-TSS (NM_025327)	promoter-TSS (NM_025327)	33	NM_183037	360213	Mm.331156	NM_183037	ENSMUSG00000042766	Trim46	TRIFIC	tripartite motif-containing 46	protein-coding
mm_116693.1	chr13	49320220	49320289	-	1	NA	Intergenic	Intergenic	-11046	NM_015759	30938	Mm.291089	NM_015759	ENSMUSG00000037946	Fgd3	5830461L01Rik|ZFYVE5	FYVE, RhoGEF and PH domain containing 3	protein-coding
mm_16590.1	chr2	4559672	4559694	-	1	NA	promoter-TSS (NM_001177844)	promoter-TSS (NM_001177844)	-71	NM_001177844	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding
mm_30589.1	chr4	5786674	5786675	+	1	NA	intron (NM_173426, intron 2 of 2)	intron (NM_173426, intron 2 of 2)	142495	NM_173426	242297	Mm.331470	NM_173426	ENSMUSG00000049119	Fam110b	1700012H17Rik|5031405P22|AW049855	family with sequence similarity 110, member B	protein-coding
mm_70565.1	chr8	13105778	13105788	+	1	NA	promoter-TSS (NM_178708)	promoter-TSS (NM_178708)	62	NM_146207	99375	Mm.212861	NM_146207	ENSMUSG00000031446	Cul4a	2810470J21Rik|AW495282	cullin 4A	protein-coding
mm_7421.1	chr1	119637443	119637446	-	1	NA	intron (NM_145506, intron 2 of 24)	Lx7|LINE|L1	11556	NM_001113416	226352	Mm.253156	NM_145506	ENSMUSG00000026383	Epb41l5	1700030C16Rik|AL022914|BE37|E230025E14Rik|Epb4.1l5|Lulu1|NBL5	erythrocyte membrane protein band 4.1 like 5	protein-coding
mm_28059.1	chr3	84259556	84259571	-	1	NA	5' UTR (NM_001271727, exon 1 of 12)	5' UTR (NM_001271727, exon 1 of 12)	216	NM_001271727	80890	Mm.44876	NM_030706	ENSMUSG00000027993	Trim2	mKIAA0517|narf	tripartite motif-containing 2	protein-coding
mm_108572.1	chr12	84922322	84922338	+	1	NA	intron (NM_178065, intron 17 of 19)	intron (NM_178065, intron 17 of 19)	-45835	NM_013589	16997	Mm.3900	NM_013589	ENSMUSG00000002020	Ltbp2	AW208642	latent transforming growth factor beta binding protein 2	protein-coding
mm_48803.1	chr5	148959455	148959489	-	1	NA	Intergenic	Intergenic	9222	NR_040686	71473	Mm.90306	NR_040686	ENSMUSG00000079069	8430423G03Rik	-	RIKEN cDNA 8430423G03 gene	ncRNA
mm_77980.1	chr9	7871937	7871947	+	1	NA	intron (NM_007464, intron 1 of 8)	B1F2|SINE|Alu	1228	NM_007464	11796	Mm.2026	NM_007464	ENSMUSG00000032000	Birc3	AW107670|Api1|Api2|Birc2|C-IAP2|HIAP2|IAP1|IAP2|MIAP1|MIAP2|MIHB|MIHC|RNF49|cIAP-1|cIAP-2|cIAP1|cIAP2	baculoviral IAP repeat-containing 3	protein-coding
mm_160678.1	chr10	13552969	13552969	+	1	NA	promoter-TSS (NM_025748)	promoter-TSS (NM_025748)	62	NM_025748	66757	Mm.331841	NM_025748	ENSMUSG00000019808	Adat2	4933426M09Rik|Deadc1	adenosine deaminase, tRNA-specific 2	protein-coding
mm_140429.1	chr17	88064819	88064829	+	1	NA	intron (NM_001081034, intron 1 of 22)	CpG	461	NM_001081034	225055	Mm.386857	NM_001081034	ENSMUSG00000005371	Fbxo11	C80048|Jf	F-box protein 11	protein-coding
mm_81050.1	chr9	105642958	105643036	+	1	NA	promoter-TSS (NM_001081309)	promoter-TSS (NM_001081309)	2	NM_001081309	75669	Mm.274830	NM_029380	ENSMUSG00000032571	Pik3r4	2210010O15Rik|C730038E05Rik|C85833|D9Ertd418e	phosphatidylinositol 3 kinase, regulatory subunit, polypeptide 4, p150	protein-coding
mm_141589.1	chr17	32418856	32418856	-	1	NA	exon (NM_021319, exon 2 of 5)	exon (NM_021319, exon 2 of 5)	2119	NM_021319	57757	Mm.86752	NM_021319	ENSMUSG00000079563	Pglyrp2	C730002N09Rik|PGRP-L|Pglyrpl|tagL	peptidoglycan recognition protein 2	protein-coding
mm_38390.1	chr4	138819214	138819234	-	1	NA	promoter-TSS (NM_011110)	promoter-TSS (NM_011110)	33	NM_011110	18784	Mm.486532	NM_011110	ENSMUSG00000041193	Pla2g5	PLA2|sPLA2	phospholipase A2, group V	protein-coding
mm_160133.1	chr7	30612496	30612496	-	1	NA	intron (NM_026815, intron 1 of 7)	intron (NM_026815, intron 1 of 7)	238	NM_026815	109637	Mm.25471	NM_026815	ENSMUSG00000006313	Upk1a	1110031P12Rik|AU019298|C87192|Tspan21|Upk1	uroplakin 1A	protein-coding
mm_35811.1	chr4	46677631	46677642	-	1	NA	exon (NM_001081141, exon 16 of 19)	exon (NM_001081141, exon 16 of 19)	-27437	NM_198664	381605	Mm.331595	NM_198664	ENSMUSG00000039813	Tbc1d2	A630005A06Rik|BC022630|Gm1037|PARIS-1|PARIS1	TBC1 domain family, member 2	protein-coding
mm_126720.1	chr15	85354319	85354320	+	1	NA	intron (NM_016843, intron 1 of 11)	intron (NM_016843, intron 1 of 11)	17938	NM_016843	54138	Mm.248906	NM_016843	ENSMUSG00000016541	Atxn10	AI325283|C77170|E46|Sca10|TEG-169|Tex169	ataxin 10	protein-coding
mm_66537.1	chr7	45154505	45154514	-	1	NA	promoter-TSS (NM_145954)	promoter-TSS (NM_145954)	29	NM_145954	69748	Mm.82139	NM_145954	ENSMUSG00000007833	Aldh16a1	2410004H02Rik|AI452234|mFLJ00209	aldehyde dehydrogenase 16 family, member A1	protein-coding
mm_126086.1	chr15	77855544	77855592	+	1	NA	Intergenic	Intergenic	-13393	NM_022410	17886	Mm.29677	NM_022410	ENSMUSG00000022443	Myh9	Fltn|Myhn-1|Myhn1|NMHCIIA|NMMHC-A|NMMHC-IIA|TU72.6	myosin, heavy polypeptide 9, non-muscle	protein-coding
mm_142009.1	chr17	35200340	35200358	-	1	NA	exon (NM_013693, exon 4 of 4)	exon (NM_013693, exon 4 of 4)	1658	NM_013693	21926	Mm.1293	NM_013693	ENSMUSG00000024401	Tnf	DIF|TNF-a|TNF-alpha|TNFSF2|TNFalpha|Tnfa|Tnfsf1a|Tnlg1f	tumor necrosis factor	protein-coding
mm_85243.1	chr9	99017845	99017862	-	1	NA	intron (NM_001080776, intron 3 of 7)	intron (NM_001080776, intron 3 of 7)	17837	NM_001080776	382097	Mm.293727	NM_001080776	ENSMUSG00000044860	Gm1123	AV052824|CLSP	predicted gene 1123	protein-coding
mm_55669.1	chr6	72521711	72521739	-	1	NA	Intergenic	Intergenic	-22666	NM_007599	12332	Mm.18626	NM_007599	ENSMUSG00000056737	Capg	gCap39|mbh1	capping protein (actin filament), gelsolin-like	protein-coding
mm_159259.1	chr2	154551743	154551743	+	1	NA	promoter-TSS (NM_001171640)	promoter-TSS (NM_001171640)	-33	NM_001171640	70362	Mm.479620	NM_001171640	ENSMUSG00000078129	Actl10	1700007I08Rik	actin-like 10	protein-coding
mm_106695.1	chr12	3457561	3457588	+	1	NA	intron (NM_001270988, intron 4 of 11)	(CAGAGA)n|Simple_repeat|Simple_repeat	30717	NM_172421	75302	Mm.120475	NM_172421	ENSMUSG00000037486	Asxl2	4930556B16Rik|mKIAA1685	additional sex combs like 2 (Drosophila)	protein-coding
mm_139325.1	chr17	48454892	48454907	+	1	NA	promoter-TSS (NM_152823)	promoter-TSS (NM_152823)	-2	NM_152823	76589	Mm.311629	NM_152823	ENSMUSG00000043592	Unc5cl	2510009H09Rik|BB155270|Zud	unc-5 family C-terminal like	protein-coding
mm_3471.1	chr1	150104566	150104574	+	1	NA	intron (NM_011198, intron 8 of 9)	intron (NM_011198, intron 8 of 9)	4539	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_103559.1	chr11	77722663	77722673	-	1	NA	exon (NM_009965, exon 3 of 6)	exon (NM_009965, exon 3 of 6)	2625	NM_001313933	12957	Mm.22830	NM_009965	ENSMUSG00000000724	Cryba1	BA3/A1|Cryb	crystallin, beta A1	protein-coding
mm_74777.1	chr8	21932709	21932716	-	1	NA	promoter-TSS (NM_139222)	promoter-TSS (NM_139222)	-2	NM_139222	246082	Mm.390015	NM_139222	ENSMUSG00000048500	Defb15	BD-15	defensin beta 15	protein-coding
mm_23249.1	chr3	51224788	51224807	+	1	NA	5' UTR (NM_009834, exon 1 of 3)	5' UTR (NM_009834, exon 1 of 3)	350	NM_009834	12457	Mm.86541	NM_009834	ENSMUSG00000023087	Noct	AU043840|Ccr4|Ccrn4l	nocturnin	protein-coding
mm_139478.1	chr17	56009200	56009243	+	1	NA	promoter-TSS (NM_026530)	promoter-TSS (NM_026530)	20	NM_026530	68047	Mm.358710	NM_026530	ENSMUSG00000003199	Mpnd	E130307M08Rik	MPN domain containing	protein-coding
mm_73074.1	chr8	94449770	94449796	+	1	NA	Intergenic	B1_Mur4|SINE|Alu	-14680	NR_015514	320377	Mm.486022	NR_015514		9330175E14Rik	A630085K21	RIKEN cDNA 9330175E14 gene	ncRNA
mm_100723.1	chr11	3913796	3913893	-	1	NA	5' UTR (NM_153142, exon 1 of 2)	5' UTR (NM_153142, exon 1 of 2)	820	NM_153142	103710	Mm.171514	NM_153142	ENSMUSG00000048807	Slc35e4	A330108F03Rik|AI414849|AI536442	solute carrier family 35, member E4	protein-coding
mm_75927.1	chr8	71507654	71507741	-	1	NA	exon (NM_032398, exon 3 of 6)	exon (NM_032398, exon 3 of 6)	4072	NM_032398	84094	Mm.260768	NM_032398	ENSMUSG00000034845	Plvap	MECA32|Pv1	plasmalemma vesicle associated protein	protein-coding
mm_24480.1	chr3	91278436	91278439	+	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	-187632	NM_001101461	229550	Mm.98335	NM_001101461	ENSMUSG00000091175	9130204L05Rik	Gm127	RIKEN cDNA 9130204L05 gene	protein-coding
mm_41112.1	chr5	87778164	87778186	+	1	NA	exon (NM_001304768, exon 5 of 13)	exon (NM_001304768, exon 5 of 13)	3725	NM_007785	12993	Mm.4908	NM_007785	ENSMUSG00000061937	Csn1s2a	Csng|PP22	casein alpha s2-like A	protein-coding
mm_82386.1	chr9	14662989	14663006	-	1	NA	Intergenic	Intergenic	-47997	NM_001081395	75723	Mm.159552	NM_001081395	ENSMUSG00000013076	Amotl1	2310010G08Rik|2310067L22Rik|4932416D09Rik|JEAP|mFLJ00155	angiomotin-like 1	protein-coding
mm_31347.1	chr4	46601342	46601374	+	1	NA	intron (NM_001164804, intron 1 of 11)	CpG	571	NM_001164804	107684	Mm.416311	NM_178893	ENSMUSG00000028337	Coro2a	9030208C03Rik|AI563590|IR10	coronin, actin binding protein 2A	protein-coding
mm_54156.1	chr6	23079565	23079607	-	1	NA	intron (NM_013930, intron 18 of 23)	intron (NM_013930, intron 18 of 23)	53400	NM_013930	30956	Mm.18651	NM_013930	ENSMUSG00000029695	Aass	LKR|LKR/SDH|LOR|LOR/SDH|Lorsdh|SDH	aminoadipate-semialdehyde synthase	protein-coding
mm_31663.1	chr4	59964176	59964186	+	1	NA	Intergenic	RLTR9A3A|LTR|ERVK	-3516	NM_008648	17843	Mm.457982	NM_008648	ENSMUSG00000041333	Mup4	Mup-4|Mup1	major urinary protein 4	protein-coding
mm_67402.1	chr7	79935242	79935255	-	1	NA	promoter-TSS (NM_027420)	promoter-TSS (NM_027420)	16	NM_027420	70420	Mm.34266	NM_027420	ENSMUSG00000039043	Arpin	2610034B18Rik	actin-related protein 2/3 complex inhibitor	protein-coding
mm_80343.1	chr9	75134154	75134193	+	1	NA	intron (NM_010864, intron 5 of 40)	intron (NM_010864, intron 5 of 40)	62967	NM_010864	17918	Mm.3645	NM_010864	ENSMUSG00000034593	Myo5a	9630007J19Rik|AI413174|AI661011|Dbv|MVa|Myo5|MyoVA|Sev-1|d|d-120J|flail|flr	myosin VA	protein-coding
mm_100122.1	chr11	115899986	115899999	+	1	NA	promoter-TSS (NM_183259)	promoter-TSS (NM_183259)	-147	NM_183259	66528	Mm.275740	NM_183259	ENSMUSG00000048442	Smim5	2210020M01Rik	small integral membrane protein 5	protein-coding
mm_47678.1	chr5	128819893	128819928	-	1	NA	intron (NM_001310733, intron 3 of 20)	intron (NM_001310733, intron 3 of 20)	83664	NM_021311	57749	Mm.272720	NM_021311	ENSMUSG00000029423	Piwil1	MIWI	piwi-like RNA-mediated gene silencing 1	protein-coding
mm_165290.1	chr2	87218239	87218240	+	1	NA	Intergenic	MTE-int|LTR|ERVL-MaLR	5345	NM_207565	404327	Mm.377941	NM_207565	ENSMUSG00000070857	Olfr1113	MOR264-25	olfactory receptor 1113	protein-coding
mm_8026.1	chr1	135129203	135129215	-	1	NA	5' UTR (NM_007955, exon 2 of 38)	5' UTR (NM_007955, exon 2 of 38)	3366	NM_007955	13924	Mm.4450	NM_007955		Ptprv	Esp|OST|OST-PTP|mOST-PTP	protein tyrosine phosphatase, receptor type, V	protein-coding
mm_45464.1	chr5	67847384	67847398	-	1	NA	promoter-TSS (NM_009727)	promoter-TSS (NM_009727)	40	NM_009727	11980	Mm.153230	NM_009727	ENSMUSG00000037685	Atp8a1	AI481521|AI853962|APLT|AW743152|AW822227|Atp3a2|B230107D19Rik|ClassI	ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1	protein-coding
mm_8909.1	chr1	163312950	163312953	-	1	NA	5' UTR (NM_175686, exon 1 of 5)	5' UTR (NM_175686, exon 1 of 5)	699	NM_011127	18933	Mm.288642	NM_011127	ENSMUSG00000026586	Prrx1	A230024N07Rik|AA755424|AI385634|AI843499|K-2|Pmx|Pmx1|Prx1|mHox	paired related homeobox 1	protein-coding
mm_135157.1	chr16	35858419	35858457	-	1	NA	exon (NM_001039530, exon 6 of 17)	exon (NM_001039530, exon 6 of 17)	12944	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_150137.1	chr19	30587401	30587402	+	1	NA	intron (NM_011160, intron 12 of 17)	intron (NM_011160, intron 12 of 17)	-37905	NM_010051	13380	Mm.214717	NM_010051	ENSMUSG00000024868	Dkk1	mdkk-1	dickkopf WNT signaling pathway inhibitor 1	protein-coding
mm_45999.1	chr5	90640465	90640539	-	1	NA	promoter-TSS (NM_028478)	promoter-TSS (NM_028478)	25	NM_028478	73246	Mm.30172	NM_028478	ENSMUSG00000029370	Rassf6	1600016B17Rik	Ras association (RalGDS/AF-6) domain family member 6	protein-coding
mm_88410.1	chr10	77032259	77032277	+	1	NA	promoter-TSS (NM_031196)	promoter-TSS (NM_031196)	-471	NM_001199271	20509	Mm.265060	NM_031196	ENSMUSG00000001436	Slc19a1	AI323572|RFC|RFC-1|RFC1	solute carrier family 19 (folate transporter), member 1	protein-coding
mm_137914.1	chr17	32201252	32201255	+	1	NA	exon (NM_001286630, exon 15 of 20)	exon (NM_001286630, exon 15 of 20)	-11704	NM_001347341	71932	Mm.176240	NM_001033163	ENSMUSG00000037577	Ephx3	2310063B19Rik|Abhd9	epoxide hydrolase 3	protein-coding
mm_21400.1	chr2	157597309	157597326	-	1	NA	Intergenic	RLTR17|LTR|ERVK	-30956	NM_016916	53619	Mm.480461	NM_016916	ENSMUSG00000067787	Blcap	AI462828|Bc10	bladder cancer associated protein	protein-coding
mm_28061.1	chr3	84259617	84259633	-	1	NA	5' UTR (NM_001271727, exon 1 of 12)	5' UTR (NM_001271727, exon 1 of 12)	154	NM_001271727	80890	Mm.44876	NM_030706	ENSMUSG00000027993	Trim2	mKIAA0517|narf	tripartite motif-containing 2	protein-coding
mm_95613.1	chr11	53501159	53501159	+	1	NA	Intergenic	Intergenic	-18577	NM_033144	20362	Mm.274399	NM_033144	ENSMUSG00000018398	Sept8	AW046166|Sepl	septin 8	protein-coding
mm_11841.1	chr2	45112291	45112304	+	1	NA	promoter-TSS (NR_110571)	promoter-TSS (NR_110571)	37	NR_110571	433424	Mm.441408	NR_110571	ENSMUSG00000052248	Zeb2os	Gm13476|OTTMUSG00000012358|Zeb2nat	zinc finger E-box binding homeobox 2, opposite strand	ncRNA
mm_146860.1	chr18	24477197	24477203	-	1	NA	intron (NM_026529, intron 4 of 4)	intron (NM_026529, intron 4 of 4)	6329	NM_026529	68046	Mm.276574	NM_026529	ENSMUSG00000024273	2700062C07Rik	AI195775|C87515	RIKEN cDNA 2700062C07 gene	protein-coding
mm_137083.1	chr17	21473844	21473866	+	1	NA	Intergenic	Intergenic	-15133	NM_013843	24132	Mm.42140	NM_013843	ENSMUSG00000057409	Zfp53	D030067O06Rik|KRAZ1|Zfp-53|Zfp118|zfas8	zinc finger protein 53	protein-coding
mm_111200.1	chr12	84219067	84219088	-	1	NA	promoter-TSS (NM_001163501)	promoter-TSS (NM_001163501)	-196	NM_001163501	238317	Mm.31256	NM_001163501	ENSMUSG00000042507	Elmsan1	9430029N19Rik|C130039O16Rik|Gm260	ELM2 and Myb/SANT-like domain containing 1	protein-coding
mm_155101.1	chrX	48341345	48341418	+	1	NA	promoter-TSS (NM_178782)	promoter-TSS (NM_178782)	23	NM_178782	320376	Mm.210146	NM_178782	ENSMUSG00000036959	Bcorl1	6720425J07Rik|B930011H20Rik	BCL6 co-repressor-like 1	protein-coding
mm_119464.1	chr14	47276911	47276936	+	1	NA	promoter-TSS (NM_080843)	promoter-TSS (NM_080843)	-66	NM_172598	218973	Mm.265615	NM_172598	ENSMUSG00000037572	Wdhd1	A630092E18|AND-1|D630024B06Rik	WD repeat and HMG-box DNA binding protein 1	protein-coding
mm_107133.1	chr12	21286289	21286299	+	1	NA	promoter-TSS (NM_008403)	promoter-TSS (NM_008403)	-3	NM_018813	54451	Mm.356778	NM_018813	ENSMUSG00000054309	Cpsf3	-	cleavage and polyadenylation specificity factor 3	protein-coding
mm_132652.1	chr16	41533141	41533151	+	1	NA	promoter-TSS (NM_175548)	promoter-TSS (NM_175548)	-196	NM_175548	268890	Mm.310524	NM_175548	ENSMUSG00000061080	Lsamp	5430428I19|AW046674|B130007O04Rik|D930023J12Rik|Lam|Lamp	limbic system-associated membrane protein	protein-coding
mm_168018.1	chrY	90737742	90737777	+	1	NA	Intergenic	Intergenic	17291	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_45286.1	chr5	64960837	64960851	-	1	NA	promoter-TSS (NM_011604)	promoter-TSS (NM_011604)	-810	NM_011604	21899	Mm.42146	NM_011604	ENSMUSG00000051498	Tlr6	-	toll-like receptor 6	protein-coding
mm_61509.1	chr7	78783304	78783341	+	1	NA	promoter-TSS (NM_023331)	promoter-TSS (NM_023331)	191	NM_026498	67994	Mm.297033	NM_026498	ENSMUSG00000030611	Mrps11	0710005I03Rik|C79873	mitochondrial ribosomal protein S11	protein-coding
mm_157311.1	chrX	20950598	20950613	-	1	NA	promoter-TSS (NM_007922)	promoter-TSS (NM_007922)	3	NM_007922	13712	Mm.405823	NM_007922	ENSMUSG00000009406	Elk1	Elk-1	ELK1, member of ETS oncogene family	protein-coding
mm_135318.1	chr16	38713462	38713492	-	1	NA	promoter-TSS (NM_020260)	promoter-TSS (NM_020260)	-442	NM_020260	12549	Mm.370848	NM_020260	ENSMUSG00000022799	Arhgap31	5830477L08Rik|AU041750|Cdgap|D330026I07Rik	Rho GTPase activating protein 31	protein-coding
mm_168238.1	chr10	81812167	81812181	+	1	NA	promoter-TSS (NM_001142963).2	promoter-TSS (NM_001142963).2	-12	NM_001142963	100233208	Mm.327168	NM_001142963	ENSMUSG00000096856	Gm10778	ENSMUSG00000074860	predicted gene 10778	protein-coding
mm_110547.1	chr12	55466366	55466372	-	1	NA	intron (NR_035430, intron 1 of 3)	intron (NR_035430, intron 1 of 3)	26278	NM_010907	18035	Mm.170515	NM_010907	ENSMUSG00000021025	Nfkbia	AI462015|Nfkbi	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, alpha	protein-coding
mm_13759.1	chr2	118329037	118329042	+	1	NA	intron (NM_201367, intron 1 of 2)	intron (NM_201367, intron 1 of 2)	24125	NR_045919	73358	Mm.437192	NR_045919	ENSMUSG00000085889	1700054M17Rik	-	RIKEN cDNA 1700054M17 gene	ncRNA
mm_6407.1	chr1	72874022	72874053	-	1	NA	exon (NM_010518, exon 1 of 4)	exon (NM_010518, exon 1 of 4)	828	NM_010518	16011	Mm.405761	NM_010518	ENSMUSG00000026185	Igfbp5	AI256729|AW208790|IGFBP-5|IGFBP-5P	insulin-like growth factor binding protein 5	protein-coding
mm_119723.1	chr14	53960933	53960949	+	1	NA	Intergenic	Intergenic	292988	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_164808.1	chr18	30524668	30524672	-	1	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	251774	NM_181414	225326	Mm.194127	NM_181414	ENSMUSG00000033628	Pik3c3	5330434F23Rik|Vps34	phosphoinositide-3-kinase, class 3	protein-coding
mm_14835.1	chr2	147365037	147365047	+	1	NA	promoter-TSS (NM_008780)	promoter-TSS (NM_008780)	48	NM_008780	18503	Mm.315502	NM_008780	ENSMUSG00000037034	Pax1	Pax-1|hbs|hunchback|un|undulated|wt	paired box 1	protein-coding
mm_50402.1	chr6	48725782	48725793	+	1	NA	Intergenic	RMER17C|LTR|ERVK	7166	NM_146167	231932	Mm.30479	NM_146167	ENSMUSG00000043931	Gimap7	IAN7|Ian3	GTPase, IMAP family member 7	protein-coding
mm_159805.1	chr5	114568003	114568003	+	1	NA	promoter-TSS (NM_001004180)	promoter-TSS (NM_001004180)	-248	NM_001004180	433940	Mm.194212	NM_001004180	ENSMUSG00000041930	Fam222a	-	family with sequence similarity 222, member A	protein-coding
mm_108200.1	chr12	76896814	76896814	+	1	NA	intron (NM_145927, intron 6 of 11)	intron (NM_145927, intron 6 of 11)	59347	NM_145927	110606	Mm.151174	NM_145927	ENSMUSG00000033373	Fntb	2010013E13Rik|AA409500	farnesyltransferase, CAAX box, beta	protein-coding
mm_31232.1	chr4	44451718	44451720	+	1	NA	Intergenic	Intergenic	150802	NM_010790	17279	Mm.268668	NM_010790	ENSMUSG00000035683	Melk	AI327312|MPK38|mKIAA0175	maternal embryonic leucine zipper kinase	protein-coding
mm_36574.1	chr4	87986263	87986266	-	1	NA	intron (NM_027326, intron 2 of 10)	intron (NM_027326, intron 2 of 10)	47143	NM_027326	70122	Mm.288898	NM_027326	ENSMUSG00000028496	Mllt3	2210011H10Rik|2610012I03Rik|3830408D16Rik|Af9|D4Ertd321e	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 3	protein-coding
mm_16909.1	chr2	13491978	13492025	-	1	NA	promoter-TSS (NM_001081084)	promoter-TSS (NM_001081084)	-125	NM_001081084	65969	Mm.313915	NM_001081084	ENSMUSG00000026726	Cubn	AA408369|AL022750|D2Wsu88e	cubilin (intrinsic factor-cobalamin receptor)	protein-coding
mm_31665.1	chr4	59964210	59964250	+	1	NA	Intergenic	RLTR9A3A|LTR|ERVK	-3565	NM_008648	17843	Mm.457982	NM_008648	ENSMUSG00000041333	Mup4	Mup-4|Mup1	major urinary protein 4	protein-coding
mm_97417.1	chr11	77982878	77982898	+	1	NA	promoter-TSS (NM_174852)	promoter-TSS (NM_174852)	72	NM_174852	268448	Mm.274329	NM_174852	ENSMUSG00000037791	Phf12	2410142K10Rik|F630045O13|PF1|mKIAA1523	PHD finger protein 12	protein-coding
mm_42470.1	chr5	115454269	115454280	+	1	NA	TTS (NM_008629)	TTS (NM_008629)	-11992	NM_011107	18778	Mm.20190	NM_011107	ENSMUSG00000029522	Pla2g1b	Pla2a|sPLA2IB	phospholipase A2, group IB, pancreas	protein-coding
mm_107240.1	chr12	26479035	26479045	+	1	NA	3' UTR (NM_020557, exon 5 of 5)	3' UTR (NM_020557, exon 5 of 5)	9825	NM_020557	22169	Mm.271839	NM_020557	ENSMUSG00000020638	Cmpk2	1200004E04Rik|TDKI|Tyki	cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial	protein-coding
mm_152980.1	chr19	29488580	29488592	-	1	NA	Intergenic	Intergenic	33401	NR_015567	77779	Mm.458738	NR_015567	ENSMUSG00000097855	A930007I19Rik	-	RIKEN cDNA A930007I19 gene	ncRNA
mm_83665.1	chr9	49673943	49673944	-	1	NA	intron (NM_001081445, intron 1 of 17)	intron (NM_001081445, intron 1 of 17)	125126	NM_001081445	17967	Mm.4974	NM_010875	ENSMUSG00000039542	Ncam1	CD56|E-NCAM|NCAM-1|Ncam	neural cell adhesion molecule 1	protein-coding
mm_60963.1	chr7	47700133	47700136	+	1	NA	Intergenic	Intergenic	-98762	NM_153067	233222	Mm.240142	NM_153067	ENSMUSG00000078698	Mrgpra3	Mrga3	MAS-related GPR, member A3	protein-coding
mm_40733.1	chr5	66195600	66195608	+	1	NA	Intergenic	Intergenic	-4269	NR_040695	73639	Mm.48851	NR_040695	ENSMUSG00000107014	1700126H18Rik	-	RIKEN cDNA 1700126H18 gene	ncRNA
mm_155873.1	chrX	101429655	101429708	+	1	NA	promoter-TSS (NM_001252518)	promoter-TSS (NM_001252518)	30	NM_001252518	53610	Mm.280069	NM_023144	ENSMUSG00000031311	Nono	AA407051|AV149256|NRB54|P54NRB|nonA	non-POU-domain-containing, octamer binding protein	protein-coding
mm_108691.1	chr12	86895296	86895315	+	1	NA	Intergenic	Intergenic	-10491	NM_145836	238330	Mm.248358	NM_145836	ENSMUSG00000034168	Irf2bpl	6430527G18Rik|Eap1	interferon regulatory factor 2 binding protein-like	protein-coding
mm_172176.1	chr6	47876030	47876031	-	1	NA	Intergenic	B1_Mm|SINE|Alu	-1525	NM_146175	101095	Mm.440186	NM_146175	ENSMUSG00000025821	Zfp282	AI449432|C81429|E430019K09Rik|HUB1	zinc finger protein 282	protein-coding
mm_114480.1	chr13	69141236	69141258	+	1	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	-141706	NM_153534	210044	Mm.390617	NM_153534	ENSMUSG00000021536	Adcy2	mKIAA1060	adenylate cyclase 2	protein-coding
mm_29054.1	chr3	103741941	103741944	-	1	NA	3' UTR (NM_010432, exon 16 of 16)	3' UTR (NM_010432, exon 16 of 16)	-3941	NM_133859	99543	Mm.211535	NM_133859	ENSMUSG00000027848	Olfml3	2810002E22Rik|AI115209|AW550633|HNOEL-iso|ONT3|mONT3	olfactomedin-like 3	protein-coding
mm_35540.1	chr4	41316744	41316756	-	1	NA	Intergenic	Intergenic	-1849	NM_026893	68970	Mm.28891	NM_026893	ENSMUSG00000028436	Dcaf12	1500001L20Rik|5830424K06Rik|AA420338|AI851081|Wdr40a	DDB1 and CUL4 associated factor 12	protein-coding
mm_64705.1	chr7	4570688	4570691	-	1	NA	intron (NM_207270, intron 8 of 19)	Lx5c|LINE|L1	-24122	NM_016908	53420	Mm.358663	NM_016908	ENSMUSG00000004961	Syt5	SytV	synaptotagmin V	protein-coding
mm_101839.1	chr11	48753509	48753537	-	1	NA	Intergenic	Intergenic	-46837	NM_008143	14694	Mm.5305	NM_008143	ENSMUSG00000020372	Rack1	AL033335|GB-like|Gnb2-rs1|Gnb2l1|p205	receptor for activated C kinase 1	protein-coding
mm_132787.1	chr16	44965250	44965257	+	1	NA	intron (NM_027578, intron 4 of 4)	intron (NM_027578, intron 4 of 4)	21575	NM_001128132	74603	Mm.297337	NM_027578	ENSMUSG00000036172	Cd200r3	4733401I18Rik|4833409J19Rik|AI505817|BB106877|mCD200RLb	CD200 receptor 3	protein-coding
mm_12001.1	chr2	57238428	57238459	+	1	NA	promoter-TSS (NM_010274)	promoter-TSS (NM_010274)	61	NM_010274	14571	Mm.3711	NM_010274	ENSMUSG00000026827	Gpd2	AA408484|AI448216|AU021455|AW494132|GPDH|Gdm1|Gpd-m|Gpdh-m|TISP38	glycerol phosphate dehydrogenase 2, mitochondrial	protein-coding
mm_13032.1	chr2	91054180	91054198	+	1	NA	5' UTR (NM_008948, exon 1 of 12)	5' UTR (NM_008948, exon 1 of 12)	173	NM_008948	19182	Mm.289832	NM_008948	ENSMUSG00000002102	Psmc3	TBP-1	proteasome (prosome, macropain) 26S subunit, ATPase 3	protein-coding
mm_139533.1	chr17	56696728	56696749	+	1	NA	exon (NM_027933, exon 4 of 16)	exon (NM_027933, exon 4 of 16)	20183	NM_178926	106639	Mm.37290	NM_178926	ENSMUSG00000054723	Vmac	AI662250	vimentin-type intermediate filament associated coiled-coil protein	protein-coding
mm_84143.1	chr9	59391545	59391561	-	1	NA	3' UTR (NM_019927, exon 14 of 14)	3' UTR (NM_019927, exon 14 of 14)	-38045	NM_175325	102774	Mm.200714	NM_175325	ENSMUSG00000025235	Bbs4	AW537059|AW742241|D9Ertd464e	Bardet-Biedl syndrome 4 (human)	protein-coding
mm_128231.1	chr15	36600920	36600940	-	1	NA	exon (NM_008774, exon 6 of 15)	exon (NM_008774, exon 6 of 15)	8043	NM_008774	18458	Mm.371570	NM_008774	ENSMUSG00000022283	Pabpc1	PABP|Pabp1|PabpI|Pabpl1|ePAB	poly(A) binding protein, cytoplasmic 1	protein-coding
mm_19612.1	chr2	102746756	102746764	-	1	NA	intron (NM_001077515, intron 5 of 10)	intron (NM_001077515, intron 5 of 10)	40322	NM_001077515	20511	Mm.267547	NM_011393	ENSMUSG00000005089	Slc1a2	1700091C19Rik|2900019G14Rik|AI159670|Eaat2|GLT-1|GLT1|MGLT1	solute carrier family 1 (glial high affinity glutamate transporter), member 2	protein-coding
mm_127579.1	chr15	102300385	102300388	+	1	NA	intron (NM_001014976, intron 5 of 30)	PB1D7|SINE|Alu	4093	NM_001014976	105988	Mm.288324	NM_001014976	ENSMUSG00000058290	Espl1	AL024103|AU045071|Cerp|ESP1|PRCE|SSE	extra spindle pole bodies 1, separase	protein-coding
mm_27796.1	chr3	75650456	75650465	-	1	NA	intron (NR_040539, intron 1 of 2)	RLTR9E|LTR|ERVK	5271	NR_040539	69193	Mm.374088	NR_040539	ENSMUSG00000099370	Platr10	2410007B07Rik	pluripotency associated transcript 10	ncRNA
mm_146976.1	chr18	33809196	33809199	-	1	NA	intron (NM_013512, intron 19 of 23)	intron (NM_013512, intron 19 of 23)	14305	NR_038151	69749	Mm.248787	NR_038151	ENSMUSG00000087590	Epb41l4aos	2410004N09Rik|Epb4.1l4aos	erythrocyte membrane protein band 4.1 like 4a, opposite strand	ncRNA
mm_112017.1	chr12	111377586	111377596	-	1	NA	5' UTR (NM_183016, exon 1 of 37)	5' UTR (NM_183016, exon 1 of 37)	127	NM_183016	217866	Mm.27397	NM_183016	ENSMUSG00000021279	Cdc42bpb	MRCKb	CDC42 binding protein kinase beta	protein-coding
mm_129120.1	chr15	76091685	76091741	-	1	NA	Intergenic	CpG	-1700	NM_144847	223649	Mm.101946	NM_144847	ENSMUSG00000075590	Nrbp2	BC011468	nuclear receptor binding protein 2	protein-coding
mm_88854.1	chr10	80930720	80930733	+	1	NA	intron (NM_008655, intron 2 of 3)	intron (NM_008655, intron 2 of 3)	635	NM_008655	17873	Mm.1360	NM_008655	ENSMUSG00000015312	Gadd45b	AI323528|Myd118	growth arrest and DNA-damage-inducible 45 beta	protein-coding
mm_122027.1	chr14	29432275	29432276	-	1	NA	intron (NM_009785, intron 4 of 37)	intron (NM_009785, intron 4 of 37)	289589	NM_009785	12294	Mm.386754	NM_009785	ENSMUSG00000021991	Cacna2d3	Cacnad3|alapha2delta3	calcium channel, voltage-dependent, alpha2/delta subunit 3	protein-coding
mm_165344.1	chr2	118012464	118012470	+	1	NA	intron (NR_126479, intron 8 of 9)	Lx9|LINE|L1	98735	NR_126479	329496	Mm.235844	NR_126479	ENSMUSG00000087203	Gm13986	C230060E24|OTTMUSG00000015236	predicted gene 13986	ncRNA
mm_158421.1	chrX	139085231	139085247	-	1	NA	promoter-TSS (NM_177920)	promoter-TSS (NM_177920)	-3	NM_177920	331535	Mm.211704	NM_177920	ENSMUSG00000031271	Serpina7	C730040N12Rik|Tbg	serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 7	protein-coding
mm_62583.1	chr7	105480954	105480999	+	1	NA	exon (NM_028444, exon 2 of 2)	exon (NM_028444, exon 2 of 2)	1221	NM_028444	109042	Mm.3124	NM_028444	ENSMUSG00000037060	Prkcdbp	3110015B12Rik|6330514M23Rik|SRBC	protein kinase C, delta binding protein	protein-coding
mm_46771.1	chr5	112276371	112276382	-	1	NA	promoter-TSS (NM_009419)	promoter-TSS (NM_009419)	-315	NM_001326590	22022	Mm.250631	NM_009419	ENSMUSG00000029344	Tpst2	AI448750|D5Ucla3|Tango13b|grm|grt	protein-tyrosine sulfotransferase 2	protein-coding
mm_162665.1	chr10	6979596	6979615	+	1	NA	exon (NM_001170802, exon 2 of 7)	exon (NM_001170802, exon 2 of 7)	676	NM_001347225	320495	Mm.331674	NM_001033391	ENSMUSG00000064065	Ipcef1	A130090K04Rik	interaction protein for cytohesin exchange factors 1	protein-coding
mm_159613.1	chr4	132251840	132251840	-	1	NA	intron (NM_020273, intron 1 of 9)	intron (NM_020273, intron 1 of 9)	9709	NM_020273	56809	Mm.103489	NM_020273	ENSMUSG00000028901	Gmeb1	1110050A04Rik|AI256615|AI481278	glucocorticoid modulatory element binding protein 1	protein-coding
mm_73820.1	chr8	117411057	117411059	+	1	NA	intron (NM_028941, intron 3 of 20)	intron (NM_028941, intron 3 of 20)	-41965	NR_106045	102466801		NR_106045	ENSMUSG00000099062	Mir7077	Gm27774|mmu-mir-7077	microRNA 7077	ncRNA
mm_50546.1	chr6	49046451	49046461	+	1	NA	intron (NM_053110, intron 4 of 10)	intron (NM_053110, intron 4 of 10)	9938	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_111877.1	chr12	108003688	108003705	-	1	NA	promoter-TSS (NM_021399)	promoter-TSS (NM_021399)	-282	NM_021399	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_11620.1	chr2	34772583	34772615	+	1	NA	exon (NM_001163434, exon 3 of 9)	exon (NM_001163434, exon 3 of 9)	509	NM_022310	14828	Mm.330160	NM_022310	ENSMUSG00000026864	Hspa5	AL022860|AU019543|Bip|D2Wsu141e|D2Wsu17e|Grp78|Hsce70|SEZ-7|Sez7|baffled|mBiP	heat shock protein 5	protein-coding
mm_38192.1	chr4	135353165	135353177	-	1	NA	promoter-TSS (NM_001130477)	promoter-TSS (NM_001130477)	43	NM_016799	51796	Mm.1963	NM_016799	ENSMUSG00000028809	Srrm1	AA407769|POP101|Srm160	serine/arginine repetitive matrix 1	protein-coding
mm_150135.1	chr19	30185874	30185885	+	1	NA	Intergenic	RLTR17|LTR|ERVK	-10438	NM_138595	104174	Mm.274852	NM_138595	ENSMUSG00000024827	Gldc	D030049L12Rik|D19Wsu57e	glycine decarboxylase	protein-coding
mm_115969.1	chr13	23991159	23991181	-	1	NA	promoter-TSS (NM_145399)	promoter-TSS (NM_145399)	44	NM_145399	214189	Mm.255667	NM_145399	ENSMUSG00000021337	Scgn	-	secretagogin, EF-hand calcium binding protein	protein-coding
mm_63663.1	chr7	129591898	129591943	+	1	NA	promoter-TSS (NM_172255)	promoter-TSS (NM_172255)	57	NM_172255	207425	Mm.229323	NM_172255	ENSMUSG00000042055	Wdr11	2900055P10Rik|AW489876|Brwd2|mKIAA1351	WD repeat domain 11	protein-coding
mm_144042.1	chr17	90346598	90346601	-	1	NA	intron (NM_001346959, intron 2 of 6)	intron (NM_001346959, intron 2 of 6)	109281	NM_001346958	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_124177.1	chr14	93867199	93867228	-	1	NA	intron (NM_001346722, intron 2 of 4)	intron (NM_001346722, intron 2 of 4)	21675	NM_001271800	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding
mm_126775.1	chr15	86169932	86169954	+	1	NA	intron (NM_145475, intron 1 of 12)	intron (NM_145475, intron 1 of 12)	16198	NM_145475	223753	Mm.222685	NM_145475	ENSMUSG00000035891	Cerk	AI848610|D330016D08Rik|mKIAA1646	ceramide kinase	protein-coding
mm_31496.1	chr4	53246175	53246182	+	1	NA	promoter-TSS (NR_040665)	promoter-TSS (NR_040665)	-18	NR_040665	78180	Mm.243847	NR_040665	ENSMUSG00000086947	4930522O17Rik	-	RIKEN cDNA 4930522O17 gene	ncRNA
mm_80258.1	chr9	72807302	72807314	+	1	NA	promoter-TSS (NM_175485)	promoter-TSS (NM_175485)	34	NM_175485	235472	Mm.31696	NM_175485	ENSMUSG00000036030	Prtg	A230098A12Rik|Igdcc5	protogenin	protein-coding
mm_76355.1	chr8	84772004	84772018	-	1	NA	exon (NM_010906, exon 2 of 9)	exon (NM_010906, exon 2 of 9)	2358	NM_001081981	18032	Mm.9394	NM_010906	ENSMUSG00000001911	Nfix	CTF|NF-I/X|NF1-X|NFI-X	nuclear factor I/X	protein-coding
mm_5655.1	chr1	41533308	41533314	-	1	NA	Intergenic	Intergenic	-352059	NR_040475	74897	Mm.243822	NR_040475	ENSMUSG00000104072	4930448I06Rik	-	RIKEN cDNA 4930448I06 gene	ncRNA
mm_114060.1	chr13	54371501	54371516	+	1	NA	5' UTR (NM_009946, exon 1 of 4)	5' UTR (NM_009946, exon 1 of 4)	159	NM_009946	12890	Mm.268902	NM_009946	ENSMUSG00000025867	Cplx2	921-L|AI413745|AW492120	complexin 2	protein-coding
mm_139012.1	chr17	45595643	45595678	+	1	NA	promoter-TSS (NM_001199116)	promoter-TSS (NM_001199116)	-88	NM_001199116	63959	Mm.29744	NM_022880	ENSMUSG00000023942	Slc29a1	1200014D21Rik|AA407560|ENT1	solute carrier family 29 (nucleoside transporters), member 1	protein-coding
mm_5768.1	chr1	50981091	50981105	-	1	NA	intron (NM_019790, intron 4 of 9)	intron (NM_019790, intron 4 of 9)	53575	NM_019790	56363	Mm.245154	NM_019790	ENSMUSG00000026109	Tmeff2	4832418D20Rik|7630402F16Rik|TR-2	transmembrane protein with EGF-like and two follistatin-like domains 2	protein-coding
mm_49477.1	chr6	29528061	29528116	+	1	NA	intron (NM_001311083, intron 1 of 9)	intron (NM_001311083, intron 1 of 9)	-1194	NM_001252382	27056	Mm.6479	NM_012057	ENSMUSG00000029771	Irf5	AW491843|mirf5	interferon regulatory factor 5	protein-coding
mm_141313.1	chr17	28358705	28358728	-	1	NA	intron (NM_021478, intron 10 of 14)	intron (NM_021478, intron 10 of 14)	6427	NM_021478	22157	Mm.42102	NM_021478	ENSMUSG00000037446	Tulp1	Tulp1l	tubby like protein 1	protein-coding
mm_109365.1	chr12	109636498	109636529	+	1	NA	TTS (NR_046302)	TTS (NR_046302)	501	NR_046302	449562		NR_046302	ENSMUSG00000088294	AF357425	MBII-48	snoRNA AF357425	snoRNA
mm_152681.1	chr19	15984946	15984962	-	1	NA	promoter-TSS (NM_198019)	promoter-TSS (NM_198019)	35	NM_198019	208518	Mm.105652	NM_198019	ENSMUSG00000041491	Cep78	5730599I05Rik|D030027P05	centrosomal protein 78	protein-coding
mm_82167.1	chr9	123834364	123834392	+	1	NA	intron (NM_148925, intron 6 of 18)	intron (NM_148925, intron 6 of 18)	17283	NM_148925	17281	Mm.252941	NM_148925	ENSMUSG00000025241	Fyco1	2810409M01Rik|Mem2|RUFY3|ZFYVE7	FYVE and coiled-coil domain containing 1	protein-coding
mm_115989.1	chr13	24330206	24330218	-	1	NA	intron (NM_001111110, intron 1 of 16)	MuLV-int|LTR|ERV1	2808	NM_001111110	12763	Mm.8396	NM_007717	ENSMUSG00000016756	Cmah	-	cytidine monophospho-N-acetylneuraminic acid hydroxylase	protein-coding
mm_103157.1	chr11	70410011	70410042	-	1	NA	promoter-TSS (NM_029231)	promoter-TSS (NM_029231)	5	NM_029231	75273	Mm.340601	NM_029231	ENSMUSG00000018921	Pelp1	4930563C04Rik|MNAR	proline, glutamic acid and leucine rich protein 1	protein-coding
mm_167047.1	chr7	81859390	81859400	+	1	NA	non-coding (NR_111910, exon 1 of 8)	non-coding (NR_111910, exon 1 of 8)	394	NM_145375	107769	Mm.221412	NM_145375	ENSMUSG00000038623	Tm6sf1	AI428514|BC023123|C630016D09Rik	transmembrane 6 superfamily member 1	protein-coding
mm_58695.1	chr7	12925490	12925504	+	1	NA	exon (NM_009095, exon 3 of 6)	exon (NM_009095, exon 3 of 6)	-1919	NM_029809	381845	Mm.439896	NM_029809	ENSMUSG00000033967	Rnf225	2310014L17Rik|AV237412|C77118	ring finger protein 225	protein-coding
mm_133073.1	chr16	58677834	58677844	+	1	NA	intron (NM_007757, intron 5 of 6)	intron (NM_007757, intron 5 of 6)	7631	NM_007757	12892	Mm.291519	NM_007757	ENSMUSG00000022742	Cpox	CPX|Cpo|HCP|cac|nct	coproporphyrinogen oxidase	protein-coding
mm_48425.1	chr5	140507598	140507601	-	1	NA	intron (NM_021528, intron 1 of 1)	intron (NM_021528, intron 1 of 1)	1990	NM_021528	59031	Mm.28934	NM_021528	ENSMUSG00000036599	Chst12	AI595374|C4S-2|C4ST2	carbohydrate sulfotransferase 12	protein-coding
mm_104103.1	chr11	86705172	86705218	-	1	NA	exon (NM_001003908, exon 23 of 32)	exon (NM_001003908, exon 23 of 32)	21114	NM_001098810	217057	Mm.24868	NM_175004	ENSMUSG00000072582	Ptrh2	A230072I16Rik|Bit1|CGI-147	peptidyl-tRNA hydrolase 2	protein-coding
mm_159372.1	chr3	88835228	88835228	+	1	NA	promoter-TSS (NM_027389)	promoter-TSS (NM_027389)	-3	NM_027389	76022	Mm.126870	NM_027389	ENSMUSG00000054199	Gon4l	1500041I23Rik|2610100B20Rik|3632445O20Rik|5430404N14Rik|AA387005	gon-4-like (C.elegans)	protein-coding
mm_86271.1	chr9	121720089	121720093	-	1	NA	intron (NM_010918, intron 2 of 16)	intron (NM_010918, intron 2 of 16)	910	NM_010918	18087	Mm.32842	NM_010918	ENSMUSG00000032525	Nktr	5330401F18Rik|D9Wsu172e	natural killer tumor recognition sequence	protein-coding
mm_30141.1	chr3	142367293	142367293	-	1	NA	intron (NM_022554, intron 1 of 8)	intron (NM_022554, intron 1 of 8)	24557	NM_022554	56376	Mm.117709	NM_019808	ENSMUSG00000028273	Pdlim5	1110001A05Rik|AI987914|C87059|Enh|Enh1|Enh2|Enh3|LIM	PDZ and LIM domain 5	protein-coding
mm_43631.1	chr5	138187524	138187566	+	1	NA	promoter-TSS (NM_178612)	promoter-TSS (NM_178612)	10	NM_178612	66455	Mm.24592	NM_178612	ENSMUSG00000036968	Cnpy4	2610019P18Rik	canopy FGF signaling regulator 4	protein-coding
mm_159416.1	chr3	105705332	105705332	+	1	NA	promoter-TSS (NM_001163356)	promoter-TSS (NM_001163356)	-126	NM_001163356	109050	Mm.212591	NM_175398	ENSMUSG00000048458	Fam212b	6530418L21Rik|inka2	family with sequence similarity 212, member B	protein-coding
mm_137595.1	chr17	28142183	28142193	+	1	NA	promoter-TSS (NM_001004366)	promoter-TSS (NM_001004366)	-338	NM_001004366	268935	Mm.258491	NM_001004366	ENSMUSG00000038677	Scube3	CEGF3|D030038I21Rik	signal peptide, CUB domain, EGF-like 3	protein-coding
mm_172867.1	chr9	4182760	4182764	+	1	NA	Intergenic	L1Md_T|LINE|L1	126732	NR_136941	67618	Mm.33970	NM_026276	ENSMUSG00000025894	Aasdhppt	2010309J24Rik|2810407B07Rik|AASD-PPT|CGI-80|LYS2|LYS5	aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase	protein-coding
mm_11490.1	chr2	32452175	32452231	+	1	NA	promoter-TSS (NM_001164357)	promoter-TSS (NM_001164357)	-733	NM_146118	227731	Mm.37395	NM_146118	ENSMUSG00000026819	Slc25a25	1110030N17Rik|MCSC|mKIAA1896	solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 25	protein-coding
mm_86054.1	chr9	114564198	114564209	-	1	NA	5' UTR (NM_001042503, exon 1 of 4)	5' UTR (NM_001042503, exon 1 of 4)	166	NM_001042503	636931	Mm.17857	NM_001042503	ENSMUSG00000079259	Trim71	2610206G21Rik|AL022943|Gm1127|Lin41|lin-41|mLin41|mlin-41	tripartite motif-containing 71	protein-coding
mm_43414.1	chr5	135962940	135962960	+	1	NA	exon (NM_001160366, exon 9 of 11)	exon (NM_001160366, exon 9 of 11)	11526	NM_001160366	109267	Mm.332750	NM_001160366	ENSMUSG00000029699	Ssc4d	C330016E03Rik|S4D-SRCRB|SRCRB-S4D|Srcrb4d	scavenger receptor cysteine rich family, 4 domains	protein-coding
mm_16622.1	chr2	5675992	5676025	-	1	NA	promoter-TSS (NM_001290376)	promoter-TSS (NM_001290376)	38	NM_001290376	227541	Mm.191949	NM_177343	ENSMUSG00000039145	Camk1d	A630059D12Rik|CKLiK|CaMKIdelta|E030025C11Rik|mCKLiK	calcium/calmodulin-dependent protein kinase ID	protein-coding
mm_150454.1	chr19	38162181	38162190	+	1	NA	intron (NM_033614, intron 12 of 21)	intron (NM_033614, intron 12 of 21)	29404	NM_001170959	110855	Mm.450141	NM_033614	ENSMUSG00000024992	Pde6c	cpfl1	phosphodiesterase 6C, cGMP specific, cone, alpha prime	protein-coding
mm_48620.1	chr5	144965764	144965786	-	1	NA	promoter-TSS (NM_029438)	promoter-TSS (NM_029438)	55	NM_001038627	75788	Mm.27735	NM_029438	ENSMUSG00000038780	Smurf1	4930431E10Rik|mKIAA1625	SMAD specific E3 ubiquitin protein ligase 1	protein-coding
mm_122785.1	chr14	54413899	54413913	-	1	NA	5' UTR (NM_011405, exon 3 of 12)	5' UTR (NM_011405, exon 3 of 12)	3773	NM_001253679	20540	Mm.142455	NM_011405	ENSMUSG00000000958	Slc7a7	AI790233|my+lat1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 7	protein-coding
mm_49423.1	chr6	29246176	29246184	+	1	NA	Intergenic	B1F2|SINE|Alu	-26308	NM_001190461	69573	Mm.45161	NM_023516	ENSMUSG00000043421	Hilpda	2310016C08Rik|AW049004|Hig2	hypoxia inducible lipid droplet associated	protein-coding
mm_29924.1	chr3	131490748	131490768	-	1	NA	Intergenic	CpG	-74010	NM_001289479	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_55266.1	chr6	53820564	53820578	-	1	NA	5' UTR (NM_025817, exon 1 of 1)	5' UTR (NM_025817, exon 1 of 1)	254	NM_025817	66873	Mm.422727	NM_025817	ENSMUSG00000043496	Tril	1200009O22Rik|AI316813|mKIAA0644	TLR4 interactor with leucine-rich repeats	protein-coding
mm_44379.1	chr5	17820590	17820604	-	1	NA	exon (NM_001159558, exon 5 of 16)	exon (NM_001159558, exon 5 of 16)	15299	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_12573.1	chr2	73085457	73085459	+	1	NA	Intergenic	MER46C|DNA|TcMar-Tigger	-105012	NM_001018042	20687	Mm.124328	NM_011450	ENSMUSG00000027109	Sp3	D130027J01Rik	trans-acting transcription factor 3	protein-coding
mm_72720.1	chr8	85036907	85036925	+	1	NA	promoter-TSS (NM_145390)	promoter-TSS (NM_145390)	1	NM_145390	212999	Mm.220357	NM_145390	ENSMUSG00000031691	Tnpo2	1110034O24Rik|AA414969|AI464345|AI852433|IPO3|Knpb2b|Kpnb2b|TRN2	transportin 2 (importin 3, karyopherin beta 2b)	protein-coding
mm_156539.1	chrX	151169477	151169487	+	1	NA	Intergenic	CpG	-28596	NM_001271679	279561	Mm.441474	NM_001271678	ENSMUSG00000041245	Wnk3	Prkwnk3|Wnk3-ps	WNK lysine deficient protein kinase 3	protein-coding
mm_3652.1	chr1	153093462	153093504	+	1	NA	intron (NM_175460, intron 7 of 10)	intron (NM_175460, intron 7 of 10)	92964	NM_008485	16782	Mm.329272	NM_008485	ENSMUSG00000026479	Lamc2	AA589349	laminin, gamma 2	protein-coding
mm_53988.1	chr6	6871563	6871573	-	1	NA	Intergenic	Intergenic	-2035	NR_015388	320038	Mm.94021	NR_015388		Dlx6os1	A230055N17Rik|Dlx6as1|Evf-1|Evf-2|Evf1|Evf1/2|Evf2|Shhrs|mEvf-1	distal-less homeobox 6, opposite strand 1	ncRNA
mm_98527.1	chr11	94990997	94991012	+	1	NA	promoter-TSS (NM_172261)	promoter-TSS (NM_172261)	-208	NM_172261	217124	Mm.229087	NM_172261	ENSMUSG00000038976	Ppp1r9b	SPL|Spn	protein phosphatase 1, regulatory subunit 9B	protein-coding
mm_118178.1	chr13	106988409	106988414	-	1	NA	intron (NM_001145779, intron 4 of 19)	B1_Mur4|SINE|Alu	33703	NM_001145779	16563	Mm.355686	NM_008442	ENSMUSG00000021693	Kif2a	C530030B14Rik|Kif2|Kns2|M-kinesin	kinesin family member 2A	protein-coding
mm_162759.1	chr10	61783828	61783841	-	1	NA	promoter-TSS (NM_207000)	promoter-TSS (NM_207000)	30	NM_207000	404634	Mm.272870	NM_207000	ENSMUSG00000020086	H2afy2	macroH2A2	H2A histone family, member Y2	protein-coding
mm_142857.1	chr17	51813213	51813227	-	1	NA	intron (NM_001163632, intron 1 of 10)	CpG	-1166	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_48349.1	chr5	139325698	139325752	-	1	NA	promoter-TSS (NM_172723)	promoter-TSS (NM_172723)	-261	NM_172723	231821	Mm.297819	NM_172723	ENSMUSG00000056413	Adap1	4930431P11Rik|Centa1|GC1L|p42IP4	ArfGAP with dual PH domains 1	protein-coding
mm_957.1	chr1	57845535	57845553	+	1	NA	promoter-TSS (NM_001164566)	promoter-TSS (NM_001164566)	-27	NM_001164566	67198	Mm.159989	NM_144882	ENSMUSG00000038305	Spats2l	2810022L02Rik|A230104H11Rik|AA987173|AI480531|AI842453|AW413586	spermatogenesis associated, serine-rich 2-like	protein-coding
mm_60653.1	chr7	44869194	44869225	+	1	NA	intron (NM_133949, intron 1 of 11)	CpG	579	NM_133949	84113	Mm.42855	NM_133949	ENSMUSG00000038502	Ptov1	1110030G05Rik|AU041779|Gcap3	prostate tumor over expressed gene 1	protein-coding
mm_68953.1	chr7	126564588	126564612	-	1	NA	exon (NM_146200, exon 4 of 21)	exon (NM_146200, exon 4 of 21)	1766	NM_146200	56347	Mm.22776	NM_146200	ENSMUSG00000030738	Eif3c	110kDa|3230401O13Rik|Eif3s8|NIPIL(A3)|NipilA3|Xs|Xsl	eukaryotic translation initiation factor 3, subunit C	protein-coding
mm_102525.1	chr11	60931681	60931701	-	1	NA	promoter-TSS (NM_008928)	promoter-TSS (NM_008928)	176	NR_027800	24082	Mm.46270	NM_025293	ENSMUSG00000042549	Map2k3os	F3-1|Gm16516|Gtlf3a	mitogen-activated protein kinase kinase 3, opposite strand	ncRNA
mm_131437.1	chr16	15984478	15984512	+	1	NA	intron (NM_146068, intron 8 of 19)	intron (NM_146068, intron 8 of 19)	97209	NM_007679	12609	Mm.347407	NM_007679	ENSMUSG00000071637	Cebpd	c/EBPdelta	CCAAT/enhancer binding protein (C/EBP), delta	protein-coding
mm_160463.1	chr8	109962049	109962049	-	1	NA	exon (NM_028584, exon 1 of 3)	exon (NM_028584, exon 1 of 3)	156	NM_212447	73608	Mm.86833	NM_028584	ENSMUSG00000001672	Marveld3	1810006A16Rik|AI642133|Marvd3|Mrvldc3	MARVEL (membrane-associating) domain containing 3	protein-coding
mm_7245.1	chr1	93635660	93635674	-	1	NA	promoter-TSS (NM_021537)	promoter-TSS (NM_021537)	60	NM_021537	59041	Mm.28761	NM_021537	ENSMUSG00000026277	Stk25	1500019J11Rik|AU018434|C86992|Ste20-like|Ysk1	serine/threonine kinase 25 (yeast)	protein-coding
mm_17189.1	chr2	25461108	25461112	-	1	NA	promoter-TSS (NM_153557)	promoter-TSS (NM_153557)	-16	NM_153557	227622	Mm.261780	NM_153557	ENSMUSG00000047617	BC029214	D930050G13Rik|Paxx	cDNA sequence BC029214	protein-coding
mm_142020.1	chr17	35201997	35202014	-	1	NA	promoter-TSS (NM_013693)	promoter-TSS (NM_013693)	2	NM_013693	21926	Mm.1293	NM_013693	ENSMUSG00000024401	Tnf	DIF|TNF-a|TNF-alpha|TNFSF2|TNFalpha|Tnfa|Tnfsf1a|Tnlg1f	tumor necrosis factor	protein-coding
mm_128316.1	chr15	37966363	37966366	-	1	NA	TTS (NM_001081359)	TTS (NM_001081359)	-5309	NM_199476	382985	Mm.24738	NM_199476	ENSMUSG00000022292	Rrm2b	p53R2	ribonucleotide reductase M2 B (TP53 inducible)	protein-coding
mm_90062.1	chr10	116289380	116289398	+	1	NA	Intergenic	Intergenic	-11985	NM_029928	19263	Mm.37213	NM_029928	ENSMUSG00000020154	Ptprb	3230402H02Rik|C130094E24|Ptpz|Rptpb|VE-PTP|Veptp	protein tyrosine phosphatase, receptor type, B	protein-coding
mm_26795.1	chr3	9833597	9833611	-	1	NA	promoter-TSS (NM_053182)	promoter-TSS (NM_053182)	75	NM_053182	94212	Mm.23897	NM_053182	ENSMUSG00000027508	Pag1	Cbp|F730007C19Rik|Pag	phosphoprotein associated with glycosphingolipid microdomains 1	protein-coding
mm_27241.1	chr3	36567905	36567928	-	1	NA	exon (NM_009828, exon 5 of 8)	exon (NM_009828, exon 5 of 8)	4080	NM_009828	12428	Mm.4189	NM_009828	ENSMUSG00000027715	Ccna2	AA408589|Ccn-1|Ccn1|Ccna|CycA2|Cyca	cyclin A2	protein-coding
mm_87744.1	chr10	60266957	60266980	+	1	NA	Intergenic	Intergenic	-10660	NM_001146123	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_36453.1	chr4	82504896	82504898	-	1	NA	5' UTR (NM_001113209, exon 1 of 12)	5' UTR (NM_001113209, exon 1 of 12)	882	NM_001286127	18028	Mm.317947	NM_008687	ENSMUSG00000008575	Nfib	6720429L07Rik|CTF|E030026I10Rik|NF-I/B|NF1-B|NFI-B	nuclear factor I/B	protein-coding
mm_110894.1	chr12	75596181	75596194	-	1	NA	promoter-TSS (NM_012024)	promoter-TSS (NM_012024)	13	NM_012024	26932	Mm.259626	NM_012024	ENSMUSG00000021051	Ppp2r5e	4633401M22Rik|AI449017|B56beta	protein phosphatase 2, regulatory subunit B', epsilon	protein-coding
mm_112375.1	chr12	119227629	119227648	-	1	NA	intron (NM_177290, intron 1 of 13)	B1_Mur1|SINE|Alu	10638	NM_177290	320910	Mm.217000	NM_177290	ENSMUSG00000025321	Itgb8	4832412O06Rik	integrin beta 8	protein-coding
mm_45322.1	chr5	65479872	65479881	-	1	NA	intron (NM_133697, intron 1 of 4)	intron (NM_133697, intron 1 of 4)	12959	NM_133697	68552	Mm.10709	NM_133697	ENSMUSG00000037822	Smim14	1110003E01Rik|1700127H04Rik|5430439C17Rik|MAd4	small integral membrane protein 14	protein-coding
mm_80295.1	chr9	73102444	73102469	+	1	NA	promoter-TSS (NM_025890)	promoter-TSS (NM_025890)	58	NM_001311106	66991	Mm.471745	NM_025890	ENSMUSG00000092622	Khdc3	2410004A20Rik|AI467128|FILIA|OEEP48	KH domain containing 3, subcortical maternal complex member	protein-coding
mm_59644.1	chr7	28161163	28161167	+	1	NA	intron (NM_001164655, intron 17 of 19)	intron (NM_001164655, intron 17 of 19)	-8583	NM_007991	14113	Mm.4595	NM_007991	ENSMUSG00000046865	Fbl	AL022665|FIB|FLRN|RNU3IP1	fibrillarin	protein-coding
mm_118283.1	chr13	112760508	112760514	-	1	NA	Intergenic	Intergenic	-40266	NM_008903	19012	Mm.291029	NM_008247	ENSMUSG00000021759	Plpp1	Hic53|Hpic53|LPP-1|LPP1|PAP-2a|PAP2-alpha|PAP2a|Ppap2a|mPAP	phospholipid phosphatase 1	protein-coding
mm_38894.1	chr4	149774239	149774279	-	1	NA	promoter-TSS (NM_027460)	promoter-TSS (NM_027460)	8	NM_027460	70556	Mm.41877	NM_027460	ENSMUSG00000028982	Slc25a33	5730438N18Rik|Pnc1	solute carrier family 25, member 33	protein-coding
mm_119963.1	chr14	55478803	55478807	+	1	NA	promoter-TSS (NM_030686)	promoter-TSS (NM_030686)	47	NM_030686	28200	Mm.27427	NM_030686	ENSMUSG00000022210	Dhrs4	AI043103|AI790593|CR|D14Ucla2|NDRD|PHCR|PSCD|RRD|mouNRDR	dehydrogenase/reductase (SDR family) member 4	protein-coding
mm_152966.1	chr19	29367315	29367370	-	1	NA	promoter-TSS (NM_021893)	promoter-TSS (NM_021893)	-96	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_27934.1	chr3	79568103	79568154	-	1	NA	promoter-TSS (NM_001162999)	promoter-TSS (NM_001162999)	-449	NM_001162999	329679	Mm.244005	NM_001162999	ENSMUSG00000061175	Fnip2	D630023B12Rik|mKIAA1450	folliculin interacting protein 2	protein-coding
mm_8946.1	chr1	164438396	164438420	-	1	NA	exon (NM_009721, exon 6 of 6)	exon (NM_009721, exon 6 of 6)	19947	NM_009721	11931	Mm.4550	NM_009721	ENSMUSG00000026576	Atp1b1	Atp4b|Atpb|Atpb-1|NKbeta1	ATPase, Na+/K+ transporting, beta 1 polypeptide	protein-coding
mm_106186.1	chr11	116806978	116806981	-	1	NA	3' UTR (NM_001347633, exon 5 of 5)	3' UTR (NM_001347633, exon 5 of 5)	21067	NM_026280	67622	Mm.64962	NM_026280	ENSMUSG00000020814	Mxra7	1810057P16Rik|E130302J09Rik	matrix-remodelling associated 7	protein-coding
mm_49408.1	chr6	28480387	28480413	+	1	NA	promoter-TSS (NM_019776)	promoter-TSS (NM_019776)	52	NM_019776	56463	Mm.439987	NM_019776	ENSMUSG00000001424	Snd1	AL033314|Tudor-SN	staphylococcal nuclease and tudor domain containing 1	protein-coding
mm_151771.1	chr19	5293189	5293198	-	1	NA	exon (NM_030109, exon 4 of 21)	exon (NM_030109, exon 4 of 21)	2262	NM_030109	319322	Mm.196532	NM_030109	ENSMUSG00000024853	Sf3b2	145kDa|2610311M13Rik|2810441F20Rik|B230398H18Rik|SAP145|SF3b1|SF3b145|SF3b150	splicing factor 3b, subunit 2	protein-coding
mm_135867.1	chr16	60606468	60606487	-	1	NA	promoter-TSS (NM_007938)	promoter-TSS (NM_007938)	-946	NM_007938	13840	Mm.455790	NM_007938	ENSMUSG00000055540	Epha6	Ehk2|Hek12|m-ehk2	Eph receptor A6	protein-coding
mm_38883.1	chr4	149701615	149701621	-	1	NA	promoter-TSS (NM_001029837)	promoter-TSS (NM_001029837)	11	NM_001029837	18707	Mm.229108	NM_008840	ENSMUSG00000039936	Pik3cd	2410099E07Rik|2610208K16Rik|AW545373|p110delta	phosphatidylinositol 3-kinase catalytic delta polypeptide	protein-coding
mm_112396.1	chr12	119238672	119238691	-	1	NA	promoter-TSS (NM_177290)	promoter-TSS (NM_177290)	-405	NM_177290	320910	Mm.217000	NM_177290	ENSMUSG00000025321	Itgb8	4832412O06Rik	integrin beta 8	protein-coding
mm_159177.1	chr2	111328573	111328573	+	1	NA	exon (NM_001005568, exon 1 of 1)	exon (NM_001005568, exon 1 of 1)	152	NM_001005568	257979	Mm.377322	NM_001005568	ENSMUSG00000095156	Olfr1281	MOR248-14P|MOR248-18	olfactory receptor 1281	protein-coding
mm_49692.1	chr6	33632534	33632544	+	1	NA	intron (NM_009148, intron 10 of 17)	RLTR31B_Mm|LTR|ERVK	383389	NM_009148	20336	Mm.265512	NM_009148	ENSMUSG00000029763	Exoc4	C78892|Sec8|Sec8l1	exocyst complex component 4	protein-coding
mm_41579.1	chr5	93173063	93173104	+	1	NA	3' UTR (NM_001009818, exon 10 of 10)	3' UTR (NM_001009818, exon 10 of 10)	33412	NM_017367	12453	Mm.250419	NM_017367	ENSMUSG00000063015	Ccni	-	cyclin I	protein-coding
mm_11348.1	chr2	30845338	30845353	+	1	NA	promoter-TSS (NM_009116)	promoter-TSS (NM_009116)	-22	NM_009116	20204	Mm.1802	NM_009116	ENSMUSG00000039476	Prrx2	Prx2|S8	paired related homeobox 2	protein-coding
mm_142156.1	chr17	36042722	36042750	-	1	NA	promoter-TSS (NM_001034909)	promoter-TSS (NM_001034909)	6	NM_001347382	15039	Mm.195061	NM_010396	ENSMUSG00000056116	H2-T22	27b|H-2T17|H-2T22|H2-T17|T22b	histocompatibility 2, T region locus 22	protein-coding
mm_47614.1	chr5	125140957	125141042	-	1	NA	intron (NM_011424, intron 1 of 46)	intron (NM_011424, intron 1 of 46)	38215	NM_001253905	20602	Mm.278646	NM_011424	ENSMUSG00000029478	Ncor2	N-CoR|SMRT|SMRTe	nuclear receptor co-repressor 2	protein-coding
mm_136100.1	chr16	85103326	85103341	-	1	NA	exon (NM_001198823, exon 3 of 18)	exon (NM_001198823, exon 3 of 18)	70374	NM_001198825	11820	Mm.277585	NM_007471	ENSMUSG00000022892	App	Abeta|Abpp|Adap|Ag|Cvap|E030013M08Rik|betaApp	amyloid beta (A4) precursor protein	protein-coding
mm_107332.1	chr12	32059972	32059990	+	1	NA	intron (NM_011158, intron 1 of 10)	intron (NM_011158, intron 1 of 10)	1298	NM_011158	19088	Mm.25594	NM_011158	ENSMUSG00000002997	Prkar2b	AI451071|AW061005|PKARIIbeta|Pkarb2|RII(beta)	protein kinase, cAMP dependent regulatory, type II beta	protein-coding
mm_78014.1	chr9	13620978	13620991	+	1	NA	exon (NM_001013813, exon 1 of 4)	exon (NM_001013813, exon 1 of 4)	995	NM_001013813	270118	Mm.116898	NM_173776	ENSMUSG00000031925	Maml2	5930431H10|BC032967	mastermind like 2 (Drosophila)	protein-coding
mm_84624.1	chr9	70641401	70641403	-	1	NA	intron (NM_172772, intron 2 of 8)	L2|LINE|L2	15772	NM_172772	235461	Mm.170855	NM_172772	ENSMUSG00000042444	Fam63b	AI465301|B230380D07Rik|mKIAA1164	family with sequence similarity 63, member B	protein-coding
mm_69717.1	chr7	140164290	140164316	-	1	NA	Intergenic	Intergenic	-1355	NM_146952	258954	Mm.377769	NM_146952	ENSMUSG00000051180	Olfr522	MOR103-5	olfactory receptor 522	protein-coding
mm_72305.1	chr8	77093376	77093378	+	1	NA	intron (NM_001083906, intron 3 of 8)	intron (NM_001083906, intron 3 of 8)	190869	NM_001083906	110784	Mm.324393	NM_001083906	ENSMUSG00000031618	Nr3c2	MR|Mlr	nuclear receptor subfamily 3, group C, member 2	protein-coding
mm_29533.1	chr3	116662555	116662570	-	1	NA	5' UTR (NM_008246, exon 1 of 12)	5' UTR (NM_008246, exon 1 of 12)	115	NM_008246	15247	Mm.280077	NM_008246	ENSMUSG00000089911	Mfsd14a	Hiat1	major facilitator superfamily domain containing 14A	protein-coding
mm_76958.1	chr8	106058699	106058706	-	1	NA	promoter-TSS (NM_010901)	promoter-TSS (NM_010901)	-901	NM_010901	18021	Mm.383185	NM_010901	ENSMUSG00000031902	Nfatc3	C80703|D8Ertd281e|NFAT4|NFATx	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 3	protein-coding
mm_40903.1	chr5	75180135	75180138	+	1	NA	intron (NM_001347718, intron 12 of 15)	intron (NM_001347718, intron 12 of 15)	3305	NR_105992	102465620		NR_105992	ENSMUSG00000099060	Mir7025	Gm27860|mmu-mir-7025	microRNA 7025	ncRNA
mm_73089.1	chr8	94531542	94531548	+	1	NA	Intergenic	L1MB8|LINE|L1	-1483	NM_153507	234577	Mm.291815	NM_153507	ENSMUSG00000034361	Cpne2	3322401K10Rik	copine II	protein-coding
mm_151756.1	chr19	5099677	5099701	-	1	NA	3' UTR (NM_029576, exon 6 of 6)	3' UTR (NM_029576, exon 6 of 6)	-1168	NM_009920	12794	Mm.299737	NM_009920	ENSMUSG00000024873	Cnih2	CNIH-2|Cnil	cornichon family AMPA receptor auxiliary protein 2	protein-coding
mm_131343.1	chr16	13447942	13447967	+	1	NA	Intergenic	Intergenic	-1569	NR_030549	100124432		NR_030549	ENSMUSG00000076972	Mir193b	Mir193|Mirn193b|mir-193b	microRNA 193b	ncRNA
mm_132902.1	chr16	48872051	48872070	+	1	NA	promoter-TSS (NM_181596)	promoter-TSS (NM_181596)	-548	NM_181596	245195	Mm.231288	NM_181596	ENSMUSG00000022651	Retnlg	Fizz3|Relmg|Xcp1	resistin like gamma	protein-coding
mm_144974.1	chr18	37955066	37955122	+	1	NA	promoter-TSS (NM_010411)	promoter-TSS (NM_010411)	-106	NM_010411	15183	Mm.20521	NM_010411	ENSMUSG00000024454	Hdac3	AW537363	histone deacetylase 3	protein-coding
mm_101188.1	chr11	17211505	17211573	-	1	NA	promoter-TSS (NM_178909)	promoter-TSS (NM_178909)	50	NM_025443	66249	Mm.27831	NM_025443	ENSMUSG00000020116	Pno1	1810003N24Rik|AA407421|AU015468|AU019495|AU042323|Emi3|Imi3	partner of NOB1 homolog	protein-coding
mm_140109.1	chr17	78573926	78573940	+	1	NA	intron (NM_028813, intron 4 of 13)	intron (NM_028813, intron 4 of 13)	65870	NM_028813	74199	Mm.292983	NM_028813	ENSMUSG00000024076	Vit	1700052E02Rik|1700110E08Rik|2810429K11Rik	vitrin	protein-coding
mm_73750.1	chr8	114746768	114746771	+	1	NA	intron (NM_019573, intron 8 of 8)	T-rich|Low_complexity|Low_complexity	307117	NM_019573	80707	Mm.440420	NM_019573	ENSMUSG00000004637	Wwox	5330426P09Rik|9030416C10Rik|WOX1	WW domain-containing oxidoreductase	protein-coding
mm_72029.1	chr8	70758184	70758200	+	1	NA	TTS (NM_183170)	TTS (NM_183170)	2729	NM_183170	234384	Mm.213010	NM_183170	ENSMUSG00000035559	Mpv17l2	Fksg24	MPV17 mitochondrial membrane protein-like 2	protein-coding
mm_114366.1	chr13	62263576	62263612	+	1	NA	Intergenic	Intergenic	119580	NM_001162910	100041979	Mm.445930	NM_001162910	ENSMUSG00000094942	Gm3604	-	predicted gene 3604	protein-coding
mm_136209.1	chr16	89837210	89837217	-	1	NA	intron (NM_009384, intron 14 of 27)	intron (NM_009384, intron 14 of 27)	-18861	NM_001145887	21844	Mm.310902	NM_009384	ENSMUSG00000002489	Tiam1	AI847750|D16Ium10|D16Ium10e	T cell lymphoma invasion and metastasis 1	protein-coding
mm_148415.1	chr19	3935769	3935787	+	1	NA	exon (NM_019449, exon 2 of 11)	exon (NM_019449, exon 2 of 11)	592	NM_001161428	54445	Mm.262094	NM_019449	ENSMUSG00000036908	Unc93b1	Unc-93B1|Unc93b	unc-93 homolog B1 (C. elegans)	protein-coding
mm_32490.1	chr4	107968603	107968645	+	1	NA	exon (NM_146255, exon 1 of 11)	exon (NM_146255, exon 1 of 11)	290	NM_146255	242607	Mm.192040	NM_146255	ENSMUSG00000008932	Slc1a7	A930031E15Rik|Eaat5	solute carrier family 1 (glutamate transporter), member 7	protein-coding
mm_138303.1	chr17	34643939	34643947	+	1	NA	promoter-TSS (NM_019873)	promoter-TSS (NM_019873)	-940	NM_019873	56299	Mm.10025	NM_019873	ENSMUSG00000033739	Fkbpl	DIR1|NG7|Ppiase-X|Wisp39	FK506 binding protein-like	protein-coding
mm_70655.1	chr8	14450022	14450045	+	1	NA	intron (NM_172910, intron 3 of 15)	intron (NM_172910, intron 3 of 15)	354158	NM_172910	244310	Mm.404697	NM_172910	ENSMUSG00000047495	Dlgap2	6430596N04Rik|Dap-2|Dap2|Sapap2	discs, large (Drosophila) homolog-associated protein 2	protein-coding
mm_83238.1	chr9	42399695	42399706	-	1	NA	5' UTR (NM_001324548, exon 1 of 24)	5' UTR (NM_001324548, exon 1 of 24)	229	NM_009347	21683	Mm.42209	NM_009347	ENSMUSG00000037705	Tecta	Tctna	tectorin alpha	protein-coding
mm_76879.1	chr8	105606683	105606693	-	1	NA	intron (NM_001081241, intron 1 of 21)	intron (NM_001081241, intron 1 of 21)	1459	NM_001081241	75687	Mm.41261	NM_001081241	ENSMUSG00000038604	Fam65a	2310066E14Rik|AI837433	family with sequence similarity 65, member A	protein-coding
mm_105456.1	chr11	104545923	104545927	-	1	NA	intron (NM_001285988, intron 1 of 18)	AT_rich|Low_complexity|Low_complexity	4695	NM_001285990	217232	Mm.89845	NM_145436	ENSMUSG00000020687	Cdc27	AI452358|APC3|BC023187	cell division cycle 27	protein-coding
mm_164365.1	chr16	23146568	23146578	+	1	NA	promoter-TSS (NM_009605)	promoter-TSS (NM_009605)	37	NM_009605	11450	Mm.3969	NM_009605	ENSMUSG00000022878	Adipoq	30kDa|APN|Acdc|Acrp30|Ad|GBP28|adipo|apM1	adiponectin, C1Q and collagen domain containing	protein-coding
mm_35573.1	chr4	41713492	41713527	-	1	NA	promoter-TSS (NM_027278)	promoter-TSS (NM_027278)	8	NM_027278	69961	Mm.425182	NM_027278	ENSMUSG00000036114	Rpp25l	2810432D09Rik|AW987258|Rppl25	ribonuclease P/MRP 25 subunit-like	protein-coding
mm_99160.1	chr11	100622884	100622920	+	1	NA	promoter-TSS (NM_028024)	promoter-TSS (NM_028024)	-53	NM_028024	71966	Mm.274734	NM_028024	ENSMUSG00000017837	Nkiras2	2410003M04Rik|4930527H08Rik|D630018G21Rik|KBRAS2	NFKB inhibitor interacting Ras-like protein 2	protein-coding
mm_33819.1	chr4	135377113	135377137	+	1	NA	intron (NM_001243305, intron 1 of 3)	intron (NM_001243305, intron 1 of 3)	8547	NM_001168498	230822	Mm.35548	NM_145555	ENSMUSG00000043924	Ncmap	A330049M08Rik|AA545175|Mp11	noncompact myelin associated protein	protein-coding
mm_155871.1	chrX	101384861	101384873	+	1	NA	exon (NM_008124, exon 2 of 2)	exon (NM_008124, exon 2 of 2)	1135	NM_001302497	14618	Mm.21198	NM_008124	ENSMUSG00000047797	Gjb1	Cnx32|Cx32|connexin-32	gap junction protein, beta 1	protein-coding
mm_156816.1	chrX	164139322	164139337	+	1	NA	promoter-TSS (NM_001130513)	promoter-TSS (NM_001130513)	-13	NM_001130513	70008	Mm.13451	NM_027286	ENSMUSG00000015405	Ace2	2010305L05Rik	angiotensin I converting enzyme (peptidyl-dipeptidase A) 2	protein-coding
mm_8876.1	chr1	162860080	162860094	-	1	NA	promoter-TSS (NM_001330291)	promoter-TSS (NM_001330291)	-87	NM_001330318	14261	Mm.976	NM_010231	ENSMUSG00000040181	Fmo1	-	flavin containing monooxygenase 1	protein-coding
mm_98473.1	chr11	94950389	94950434	+	1	NA	exon (NM_007742, exon 48 of 51)	exon (NM_007742, exon 48 of 51)	14187	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_78325.1	chr9	25151993	25152035	+	1	NA	promoter-TSS (NM_020586)	promoter-TSS (NM_020586)	-233	NM_020586	80517	Mm.142843	NM_020586	ENSMUSG00000008429	Herpud2	5031400M07Rik|AB041580	HERPUD family member 2	protein-coding
mm_165376.1	chr2	128406474	128406477	-	1	NA	intron (NR_028591, intron 1 of 1)	intron (NR_028591, intron 1 of 1)	22876	NR_028591	100043424	Mm.297222	NR_028589		Gm14005	OTTMUSG00000015351	predicted gene 14005	ncRNA
mm_116062.1	chr13	27562454	27562454	-	1	NA	exon (NM_023332, exon 2 of 6)	exon (NM_023332, exon 2 of 6)	2152	NM_001316721	67310	Mm.46091	NM_023332	ENSMUSG00000006490	Prl8a9	1600019F10Rik|Ghd15|PLP-C2|PLP-Cbeta|Prlpc2	prolactin family8, subfamily a, member 9	protein-coding
mm_13627.1	chr2	113640547	113640551	+	1	NA	intron (NM_001285458, intron 13 of 16)	intron (NM_001285458, intron 13 of 16)	-44541	NM_001287818	14260	Mm.4938	NM_010230	ENSMUSG00000044042	Fmn1	Fmn|formin-1|ld	formin 1	protein-coding
mm_109263.1	chr12	109544642	109544703	+	1	NA	promoter-TSS (NR_003633)	promoter-TSS (NR_003633)	131	NR_037313	100499530		NR_037313	ENSMUSG00000084559	Mir1906-2	mmu-mir-1906-2	microRNA 1906-2	ncRNA
mm_48613.1	chr5	144479706	144479716	-	1	NA	Intergenic	B4A|SINE|B4	-66176	NM_016789	53324	Mm.10099	NM_016789	ENSMUSG00000059991	Nptx2	Narp|np2	neuronal pentraxin 2	protein-coding
mm_160945.1	chr11	96133656	96133656	+	1	NA	promoter-TSS (NM_172799)	promoter-TSS (NM_172799)	-130	NM_172799	237930	Mm.249912	NM_172799	ENSMUSG00000038756	Ttll6	4932418K24Rik|D11Moh43e|D11Moh44e|t8130b59	tubulin tyrosine ligase-like family, member 6	protein-coding
mm_66637.1	chr7	45538478	45538503	-	1	NA	intron (NM_148927, intron 8 of 19)	intron (NM_148927, intron 8 of 19)	12160	NM_148927	69217	Mm.274158	NM_148927	ENSMUSG00000040428	Plekha4	2410005C22Rik|C88169|Pepp1	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 4	protein-coding
mm_113661.1	chr13	42681590	42681619	+	1	NA	intron (NM_001302635, intron 1 of 13)	intron (NM_001302635, intron 1 of 13)	805	NM_001302635	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding
mm_21975.1	chr2	167349168	167349249	-	1	NA	promoter-TSS (NM_019835)	promoter-TSS (NM_019835)	-30	NM_019835	56336	Mm.200886	NM_019835	ENSMUSG00000017929	B4galt5	9430078I07Rik|AW049941|AW539721	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 5	protein-coding
mm_157725.1	chrX	70346155	70346184	-	1	NA	3' UTR (NM_010498, exon 9 of 9)	3' UTR (NM_010498, exon 9 of 9)	18916	NM_010498	15931	Mm.233083	NM_010498	ENSMUSG00000035847	Ids	AW214631	iduronate 2-sulfatase	protein-coding
mm_160831.1	chr11	46698590	46698590	-	1	NA	5' UTR (NM_001161355, exon 1 of 9)	5' UTR (NM_001161355, exon 1 of 9)	240	NM_001161355	171284	Mm.234654	NM_134249	ENSMUSG00000040413	Timd2	AA816106|AU019358|AU019662|C78111|G9D3|TIM-2|Tim2	T cell immunoglobulin and mucin domain containing 2	protein-coding
mm_96861.1	chr11	70092706	70092749	+	1	NA	promoter-TSS (NM_007493)	promoter-TSS (NM_007493)	83	NM_001313927	11890	Mm.1357	NM_007493	ENSMUSG00000040963	Asgr2	ASGPR2|Asgr|Asgr-2|HL-2	asialoglycoprotein receptor 2	protein-coding
mm_53341.1	chr6	129267995	129268038	+	1	NA	3' UTR (NM_001033122, exon 5 of 5)	3' UTR (NM_001033122, exon 5 of 5)	7353	NM_001033122	12515	Mm.74745	NM_001033122	ENSMUSG00000030156	Cd69	5830438K24Rik|AI452015|AIM|VEA	CD69 antigen	protein-coding
mm_99596.1	chr11	104329768	104329784	+	1	NA	3' UTR (NM_010838, exon 10 of 10)	3' UTR (NM_010838, exon 10 of 10)	98340	NM_001285454	17762	Mm.1287	NM_010838	ENSMUSG00000018411	Mapt	AI413597|AW045860|Mtapt|Tau	microtubule-associated protein tau	protein-coding
mm_123233.1	chr14	60087363	60087382	-	1	NA	promoter-TSS (NM_015803)	promoter-TSS (NM_015803)	-538	NM_015803	50769	Mm.319599	NM_015803	ENSMUSG00000021983	Atp8a2	AI415030|Atpc1b|agil|wl	ATPase, aminophospholipid transporter-like, class I, type 8A, member 2	protein-coding
mm_9243.1	chr1	171344405	171344449	-	1	NA	exon (NM_012049, exon 3 of 7)	exon (NM_012049, exon 3 of 7)	1218	NM_001242580	27045	Mm.12915	NM_012049	ENSMUSG00000013997	Nit1	AI255805|ESTM30|W57327	nitrilase 1	protein-coding
mm_44739.1	chr5	31192699	31192758	-	1	NA	promoter-TSS (NM_153680)	promoter-TSS (NM_153680)	411	NM_001127355	13667	Mm.29394	NM_010122	ENSMUSG00000029145	Eif2b4	Eif2b	eukaryotic translation initiation factor 2B, subunit 4 delta	protein-coding
mm_63749.1	chr7	131037307	131037311	+	1	NA	intron (NM_007769, intron 2 of 46)	intron (NM_007769, intron 2 of 46)	5233	NM_007769	12945	Mm.4138	NM_007769	ENSMUSG00000047517	Dmbt1	CRP|CRP-[a]|CRP-[b]|Crpd|DBMT1|gp300|p80	deleted in malignant brain tumors 1	protein-coding
mm_68450.1	chr7	110060805	110060819	-	1	NA	promoter-TSS (NM_009281)	promoter-TSS (NM_009281)	-890	NM_009281	20841	Mm.10815	NM_009281	ENSMUSG00000061079	Zfp143	AA959806|AU015869|D7Ertd805e|KRAB14|SBF|Staf|Zfp79|Zfp80-rs1|Znf143|pHZ-1	zinc finger protein 143	protein-coding
mm_130613.1	chr15	99931785	99931803	-	1	NA	promoter-TSS (NM_028180)	promoter-TSS (NM_028180)	-136	NM_028180	72277	Mm.272766	NM_028180	ENSMUSG00000045350	1700030F18Rik	FAM186A	RIKEN cDNA 1700030F18 gene	protein-coding
mm_14517.1	chr2	132578023	132578034	+	1	NA	intron (NM_001042672, intron 1 of 18)	CpG	220	NM_001291050	74182	Mm.211211	NM_027096	ENSMUSG00000027346	Gpcpd1	2310004G06Rik|2310032D16Rik|AU015213|Gde5|Prei4|mKIAA1434	glycerophosphocholine phosphodiesterase 1	protein-coding
mm_55529.1	chr6	70726663	70726738	-	1	NA	Intergenic	Intergenic	65475	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_25470.1	chr3	108655575	108655578	+	1	NA	intron (NM_001177771, intron 2 of 12)	intron (NM_001177771, intron 2 of 12)	1586	NM_001177770	229725	Mm.214545	NM_145543	ENSMUSG00000027884	Clcc1	Mclc	chloride channel CLIC-like 1	protein-coding
mm_89392.1	chr10	89873242	89873252	+	1	NA	promoter-TSS (NM_001128086)	promoter-TSS (NM_001128086)	-262	NM_001128086	77531	Mm.440605	NM_181398	ENSMUSG00000058589	Anks1b	AIDA-1b|C030032C09Rik|E530015N03Rik|ENSMUSG00000078431|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding
mm_120248.1	chr14	62992467	62992475	+	1	NA	Intergenic	Intergenic	-5606	NM_001039125	654465	Mm.424929	NM_001039125	ENSMUSG00000075573	Defb47	Defb41|EG654465	defensin beta 47	protein-coding
mm_77673.1	chr8	124897761	124897782	-	1	NA	promoter-TSS (NM_198103)	promoter-TSS (NM_198103)	-66	NM_198103	102058	Mm.347360	NM_198103	ENSMUSG00000074030	Exoc8	AI414418|EXO84|Exo84p|R74783|SEC84	exocyst complex component 8	protein-coding
mm_90457.1	chr10	127728577	127728580	+	1	NA	intron (NM_009312, intron 4 of 6)	intron (NM_009312, intron 4 of 6)	3186	NM_009312	21334	Mm.2374	NM_009312	ENSMUSG00000025400	Tac2	PPT-B|Tac3	tachykinin 2	protein-coding
mm_39699.1	chr5	27181457	27181459	+	1	NA	intron (NM_207282, intron 1 of 25)	B4A|SINE|B4	-80477	NM_001136060	13483	Mm.42078	NM_010075	ENSMUSG00000061576	Dpp6	B930011P16Rik|D5Buc3|D5Buc4|D5Buc5|DPP VI|Dpp-6|Gm1377|In(5)6H-p|Peplb|Rw	dipeptidylpeptidase 6	protein-coding
mm_278.1	chr1	21249805	21249819	+	1	NA	exon (NM_010356, exon 2 of 7)	exon (NM_010356, exon 2 of 7)	9227	NM_010356	14859	Mm.394593	NM_010356	ENSMUSG00000025934	Gsta3	Gst2-3	glutathione S-transferase, alpha 3	protein-coding
mm_140110.1	chr17	78573944	78573946	+	1	NA	intron (NM_028813, intron 4 of 13)	intron (NM_028813, intron 4 of 13)	65882	NM_028813	74199	Mm.292983	NM_028813	ENSMUSG00000024076	Vit	1700052E02Rik|1700110E08Rik|2810429K11Rik	vitrin	protein-coding
mm_65589.1	chr7	27311222	27311235	-	1	NA	TTS (NM_001310678)	TTS (NM_001310678)	22420	NM_001113549	108075	Mm.272251	NM_175641	ENSMUSG00000040488	Ltbp4	2310046A13Rik	latent transforming growth factor beta binding protein 4	protein-coding
mm_93883.1	chr10	125328357	125328369	-	1	NA	5' UTR (NM_011391, exon 1 of 7)	5' UTR (NM_011391, exon 1 of 7)	172	NM_011391	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|Mct2	solute carrier family 16 (monocarboxylic acid transporters), member 7	protein-coding
mm_170357.1	chr18	52529351	52529352	-	1	NA	5' UTR (NM_010728, exon 1 of 7)	5' UTR (NM_010728, exon 1 of 7)	370	NM_001286181	16948	Mm.172	NM_010728	ENSMUSG00000024529	Lox	AI893619|TSC-160|rrg	lysyl oxidase	protein-coding
mm_6450.1	chr1	74013220	74013230	-	1	NA	intron (NM_027884, intron 4 of 34)	intron (NM_027884, intron 4 of 34)	111222	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_97612.1	chr11	78951222	78951226	+	1	NA	exon (NM_010927, exon 21 of 27)	exon (NM_010927, exon 21 of 27)	25933	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_61901.1	chr7	90130111	90130121	+	1	NA	promoter-TSS (NM_001252521)	promoter-TSS (NM_001252521)	-116	NM_001252523	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_15818.1	chr2	164557734	164557747	+	1	NA	Intergenic	Intergenic	-4976	NM_026323	67701	Mm.27289	NM_026323	ENSMUSG00000017723	Wfdc2	1600023A02Rik|HE4|WAP5	WAP four-disulfide core domain 2	protein-coding
mm_164132.1	chr15	43994586	43994587	-	1	NA	Intergenic	Intergenic	-124557	NM_175502	239408	Mm.41219	NM_175502	ENSMUSG00000054409	Tmem74	AA549547|B230382K22Rik	transmembrane protein 74	protein-coding
mm_156379.1	chrX	139672109	139672117	+	1	NA	3' UTR (NM_023270, exon 7 of 7)	3' UTR (NM_023270, exon 7 of 7)	-12883	NM_001081499	245638	Mm.275869	NM_001081499	ENSMUSG00000042473	Tbc1d8b	4921505D17Rik|9030605E16Rik	TBC1 domain family, member 8B	protein-coding
mm_130440.1	chr15	98481968	98481970	-	1	NA	intron (NM_010679, intron 2 of 3)	intron (NM_010679, intron 2 of 3)	714	NM_010679	16770	Mm.5074	NM_010679	ENSMUSG00000022991	Lalba	AW208827|Lyzg	lactalbumin, alpha	protein-coding
mm_114399.1	chr13	63301271	63301276	+	1	NA	promoter-TSS (NR_037235)	promoter-TSS (NR_037235)	10	NR_037235	100526474		NR_037235	ENSMUSG00000092741	Mir3074-1	mmu-mir-3074-1	microRNA 3074-1	ncRNA
mm_6502.1	chr1	74295319	74295404	-	1	NA	exon (NM_027154, exon 2 of 12)	exon (NM_027154, exon 2 of 12)	8975	NM_027154	69660	Mm.261182	NM_027154	ENSMUSG00000006301	Tmbim1	2310061B02Rik|AA960455|AU024746|C78899|RECS1|Tmbib1|mKIAA4161	transmembrane BAX inhibitor motif containing 1	protein-coding
mm_93701.1	chr10	118083056	118083090	-	1	NA	Intergenic	Intergenic	-58714	NM_001162904	17245	Mm.101191	NM_010785	ENSMUSG00000020212	Mdm1	Arrd2|Mdm-1	transformed mouse 3T3 cell double minute 1	protein-coding
mm_10043.1	chr1	193035757	193035830	-	1	NA	promoter-TSS (NM_181546)	promoter-TSS (NM_181546)	-18	NM_181546	329324	Mm.76710	NM_181546	ENSMUSG00000016200	Syt14	B230320I09Rik|sytXIV	synaptotagmin XIV	protein-coding
mm_168253.1	chr10	8559606	8559607	-	1	NA	Intergenic	RLTR9E|LTR|ERVK	-40781	NM_177387	338362	Mm.41163	NM_177387	ENSMUSG00000047712	Ust	D930010O20Rik|UA2OST	uronyl-2-sulfotransferase	protein-coding
mm_134546.1	chr16	19883874	19883915	-	1	NA	non-coding (NR_015488, exon 1 of 2)	non-coding (NR_015488, exon 1 of 2)	380	NR_027896	68162	Mm.35159	NR_015488		A930003A15Rik	AI853191	RIKEN cDNA A930003A15 gene	ncRNA
mm_158913.1	chr1	46012263	46012263	-	1	NA	Intergenic	Intergenic	18174	NR_037690	212225	Mm.78540	NM_172504	ENSMUSG00000044457	Stk-ps2	4930509O22|EG212225|Gm4776	serine/threonine kinase 2	pseudo
mm_16165.1	chr2	172472539	172472553	+	1	NA	promoter-TSS (NM_029608)	promoter-TSS (NM_029608)	-8	NM_029608	76426	Mm.46148	NM_029608	ENSMUSG00000027505	Fam209	1700029J11Rik	family with sequence similarity 209	protein-coding
mm_71916.1	chr8	70139449	70139499	+	1	NA	promoter-TSS (NM_001309841)	promoter-TSS (NM_001309841)	-25	NM_001145552	72368	Mm.644	NM_001145552	ENSMUSG00000002345	Borcs8	2310045N01Rik|Mef2bnb	BLOC-1 related complex subunit 8	protein-coding
mm_12496.1	chr2	71805974	71805985	+	1	NA	intron (NM_001277970, intron 1 of 24)	intron (NM_001277970, intron 1 of 24)	19040	NM_001277970	16403	Mm.225096	NM_008397	ENSMUSG00000027111	Itga6	5033401O05Rik|AI115430|Cd49f|VLA-6	integrin alpha 6	protein-coding
mm_140741.1	chr17	15829826	15829839	-	1	NA	Intergenic	Intergenic	-3246	NM_178615	68799	Mm.293466	NM_178615	ENSMUSG00000048027	Rgmb	1110059F19Rik|DRAGON	repulsive guidance molecule family member B	protein-coding
mm_26928.1	chr3	20259505	20259507	-	1	NA	intron (NM_029706, intron 9 of 10)	Lx6|LINE|L1	16227	NM_029706	76703	Mm.34692	NM_029706	ENSMUSG00000011463	Cpb1	0910001A18Rik|1810063F02Rik|2210008M23Rik|AI504870	carboxypeptidase B1 (tissue)	protein-coding
mm_123476.1	chr14	65975720	65975757	-	1	NA	exon (NM_013492, exon 5 of 9)	exon (NM_013492, exon 5 of 9)	7255	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_28384.1	chr3	90000795	90000804	-	1	NA	3' UTR (NM_001165983, exon 28 of 28)	3' UTR (NM_001165983, exon 28 of 28)	2039	NR_045749	100503469	Mm.440636	NR_045749	ENSMUSG00000105552	Gm19710	-	predicted gene, 19710	ncRNA
mm_154172.1	chr19	58730106	58730133	-	1	NA	exon (NM_018874, exon 3 of 13)	exon (NM_018874, exon 3 of 13)	1232	NM_018874	18946	Mm.10753	NM_018874	ENSMUSG00000042179	Pnliprp1	Plrp1	pancreatic lipase related protein 1	protein-coding
mm_22397.1	chr2	181236120	181236130	-	1	NA	exon (NM_183162, exon 7 of 19)	exon (NM_183162, exon 7 of 19)	5902	NM_183162	229003	Mm.315872	NM_183162	ENSMUSG00000027580	Helz2	PDIP1|Pric285|mKIAA1769|mPDIP1	helicase with zinc finger 2, transcriptional coactivator	protein-coding
mm_41276.1	chr5	89443409	89443445	+	1	NA	exon (NM_008096, exon 4 of 13)	exon (NM_008096, exon 4 of 13)	14471	NM_008096	14473	Mm.196595	NM_008096	ENSMUSG00000035540	Gc	DBP|VDB	group specific component	protein-coding
mm_157678.1	chrX	59567349	59567368	-	1	NA	intron (NM_001290414, intron 1 of 6)	CpG	18214	NM_001290414	14168	Mm.7995	NM_010200	ENSMUSG00000031137	Fgf13	Fhf2	fibroblast growth factor 13	protein-coding
mm_125612.1	chr15	61985541	61985556	+	1	NA	5' UTR (NM_001177354, exon 1 of 3)	5' UTR (NM_001177354, exon 1 of 3)	207	NM_001177352	17869	Mm.2444	NM_010849	ENSMUSG00000022346	Myc	AU016757|Myc2|Niard|Nird|bHLHe39	myelocytomatosis oncogene	protein-coding
mm_12300.1	chr2	69093813	69093820	+	1	NA	intron (NM_172856, intron 8 of 9)	intron (NM_172856, intron 8 of 9)	-41984	NM_181547	329416	Mm.90047	NM_181547	ENSMUSG00000034738	Nostrin	Daip2|mDaIP2	nitric oxide synthase trafficker	protein-coding
mm_116237.1	chr13	33843407	33843410	-	1	NA	promoter-TSS (NM_001045535)	promoter-TSS (NM_001045535)	0	NM_001045535	435350	Mm.263418	NM_001045535	ENSMUSG00000069248	Serpinb6e	Gm11396|OTTMUSG00000000720|SPI3B|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 6e	protein-coding
mm_125434.1	chr15	44457492	44457496	+	1	NA	promoter-TSS (NM_138674)	promoter-TSS (NM_138674)	-59	NM_138674	192190	Mm.211494	NM_138674	ENSMUSG00000038725	Pkhd1l1	AB055648|PKHDL1	polycystic kidney and hepatic disease 1-like 1	protein-coding
mm_139643.1	chr17	57377626	57377636	+	1	NA	intron (NM_010130, intron 2 of 21)	Lx5b|LINE|L1	18945	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_143498.1	chr17	71475892	71475903	-	1	NA	promoter-TSS (NM_028887)	promoter-TSS (NM_028887)	-554	NM_028887	74355	Mm.194450	NM_028887	ENSMUSG00000024054	Smchd1	4931400A14Rik|AW554188|MommeD1|mKIAA0650	SMC hinge domain containing 1	protein-coding
mm_76450.1	chr8	85081320	85081350	-	1	NA	promoter-TSS (NM_026399)	promoter-TSS (NM_026399)	372	NM_001001493	414077	Mm.35790	NM_001001493	ENSMUSG00000059355	Wdr83os	-	WD repeat domain 83 opposite strand	protein-coding
mm_70783.1	chr8	22476721	22476734	+	1	NA	promoter-TSS (NM_011394)	promoter-TSS (NM_011394)	27	NM_011394	20516	Mm.323901	NM_011394	ENSMUSG00000037656	Slc20a2	MolPit2|Pit-2|Pit2|Ram-1|Ram1	solute carrier family 20, member 2	protein-coding
mm_79452.1	chr9	56120559	56120570	+	1	NA	exon (NM_011193, exon 5 of 15)	exon (NM_011193, exon 5 of 15)	30588	NM_011193	19200	Mm.2534	NM_011193	ENSMUSG00000032322	Pstpip1	CD2BP1|def-2	proline-serine-threonine phosphatase-interacting protein 1	protein-coding
mm_38832.1	chr4	149150572	149150605	-	1	NA	3' UTR (NM_001081274, exon 13 of 13)	3' UTR (NM_001081274, exon 13 of 13)	-12988	NM_027263	69928	Mm.260893	NM_027263	ENSMUSG00000073705	Apitd1	2610040C18Rik|2810407L01Rik|CENP-S	apoptosis-inducing, TAF9-like domain 1	protein-coding
mm_59073.1	chr7	19514519	19514542	+	1	NA	non-coding (NR_138584, exon 2 of 4)	non-coding (NR_138584, exon 2 of 4)	-4201	NM_027116	69547	Mm.77325	NM_027116	ENSMUSG00000060621	Nkpd1	2310015G09Rik	NTPase, KAP family P-loop domain containing 1	protein-coding
mm_34256.1	chr4	141382398	141382426	+	1	NA	exon (NM_001085513, exon 5 of 7)	exon (NM_001085513, exon 5 of 7)	14220	NM_001085513	277743	Mm.294614	NM_001085513	ENSMUSG00000006218	Fam131c	Gm693	family with sequence similarity 131, member C	protein-coding
mm_145965.1	chr18	67794578	67794589	+	1	NA	3' UTR (NM_001039088, exon 9 of 9)	3' UTR (NM_001039088, exon 9 of 9)	5360	NR_045376	75286	Mm.307315	NR_045376		4930549G23Rik	-	RIKEN cDNA 4930549G23 gene	ncRNA
mm_102521.1	chr11	60879407	60879426	-	1	NA	promoter-TSS (NM_001168507)	promoter-TSS (NM_001168507)	-378	NM_001168507	216821	Mm.28063	NM_173453	ENSMUSG00000043284	Tmem11	5730466P16Rik|AA409091	transmembrane protein 11	protein-coding
mm_51292.1	chr6	72305931	72305942	+	1	NA	intron (NM_147779, intron 4 of 11)	intron (NM_147779, intron 4 of 11)	1326	NM_147779	20388	Mm.46033	NM_147779	ENSMUSG00000056370	Sftpb	AI562151|SF-B|SP-B|Sftp-3|Sftp3	surfactant associated protein B	protein-coding
mm_30330.1	chr3	151732099	151732114	-	1	NA	3' UTR (NM_133871, exon 8 of 8)	3' UTR (NM_133871, exon 8 of 8)	17853	NM_133871	99899	Mm.30756	NM_133871	ENSMUSG00000028037	Ifi44	A430056A10Rik|AW261460|MTAP44|p44	interferon-induced protein 44	protein-coding
mm_80028.1	chr9	68653743	68653757	+	1	NA	promoter-TSS (NM_001289917)	promoter-TSS (NM_001289917)	-36	NM_001289917	19883	Mm.378450	NM_013646	ENSMUSG00000032238	Rora	9530021D13Rik|Nr1f1|ROR1|ROR2|ROR3|nmf267|sg|staggerer|tmgc26	RAR-related orphan receptor alpha	protein-coding
mm_115205.1	chr13	109116375	109116388	+	1	NA	intron (NM_011056, intron 3 of 16)	intron (NM_011056, intron 3 of 16)	-208363	NR_030644	100124489		NR_030644	ENSMUSG00000076946	Mir582	Mirn582|mir-582|mmu-mir-582	microRNA 582	ncRNA
mm_114119.1	chr13	55105291	55105340	+	1	NA	promoter-TSS (NM_012017)	promoter-TSS (NM_012017)	6	NM_012017	26919	Mm.22795	NM_012017	ENSMUSG00000021481	Zfp346	Jaz|Znf346	zinc finger protein 346	protein-coding
mm_119504.1	chr14	47380368	47380381	+	1	NA	exon (NM_010705, exon 3 of 6)	exon (NM_010705, exon 3 of 6)	6514	NM_001145953	16854	Mm.248615	NM_010705	ENSMUSG00000050335	Lgals3	GBP|L-34|Mac-2|gal3	lectin, galactose binding, soluble 3	protein-coding
mm_146154.1	chr18	75000516	75000559	+	1	NA	promoter-TSS (NR_028552)	promoter-TSS (NR_028552)	60	NM_001002239	319195	Mm.276337	NM_001002239	ENSMUSG00000062328	Rpl17	-	ribosomal protein L17	protein-coding
mm_36599.1	chr4	88880207	88880228	-	1	NA	promoter-TSS (NM_177348)	promoter-TSS (NM_177348)	-16	NM_177348	230405	Mm.246593	NM_177348	ENSMUSG00000045364	Ifne	Ifn-tau-1|Ifne1|Ifnt1|Infe1	interferon epsilon	protein-coding
mm_57189.1	chr6	122849487	122849497	-	1	NA	3' UTR (NM_009779, exon 2 of 2)	3' UTR (NM_009779, exon 2 of 2)	6665	NM_009779	12267	Mm.2408	NM_009779	ENSMUSG00000040552	C3ar1	AZ3B|C3AR|HNFAG09	complement component 3a receptor 1	protein-coding
mm_99378.1	chr11	101987073	101987097	+	1	NA	promoter-TSS (NM_029287)	promoter-TSS (NM_029287)	29	NM_029287	75437	Mm.108632	NM_029287	ENSMUSG00000010841	1700006E09Rik	-	RIKEN cDNA 1700006E09 gene	protein-coding
mm_100237.1	chr11	117232255	117232329	+	1	NA	intron (NM_001113486, intron 2 of 11)	intron (NM_001113486, intron 2 of 11)	32631	NM_001113486	53860	Mm.38450	NM_017380	ENSMUSG00000059248	Sept9	MSF1|Msf|PNUTL4|Sint1	septin 9	protein-coding
mm_117701.1	chr13	95034248	95034288	-	1	NA	exon (NM_001170669, exon 15 of 19)	exon (NM_001170669, exon 15 of 19)	57924	NM_172590	218460	Mm.33856	NM_172590	ENSMUSG00000042015	Wdr41	B830029I03Rik|MSTP048	WD repeat domain 41	protein-coding
mm_78307.1	chr9	22655134	22655142	+	1	NA	intron (NM_178415, intron 15 of 22)	intron (NM_178415, intron 15 of 22)	179423	NM_178415	319845	Mm.176725	NM_178415	ENSMUSG00000035919	Bbs9	E130103I17Rik	Bardet-Biedl syndrome 9 (human)	protein-coding
mm_24323.1	chr3	89436700	89436734	+	1	NA	promoter-TSS (NM_146131)	promoter-TSS (NM_146131)	13	NM_146131	229534	Mm.65906	NM_146131	ENSMUSG00000042613	Pbxip1	4732463H20Rik	pre B cell leukemia transcription factor interacting protein 1	protein-coding
mm_167704.1	chr9	92275799	92275799	+	1	NA	5' UTR (NM_001195084, exon 1 of 8)	5' UTR (NM_001195084, exon 1 of 8)	197	NM_001195084	18828	Mm.10306	NM_008880	ENSMUSG00000032372	Plscr2	-	phospholipid scramblase 2	protein-coding
mm_93368.1	chr10	105296546	105296549	-	1	NA	intron (NM_177368, intron 8 of 11)	intron (NM_177368, intron 8 of 11)	277932	NM_177368	278279	Mm.25225	NM_177368	ENSMUSG00000036019	Tmtc2	8430438D04Rik|D330034A10Rik	transmembrane and tetratricopeptide repeat containing 2	protein-coding
mm_26796.1	chr3	9833618	9833638	-	1	NA	promoter-TSS (NM_053182)	promoter-TSS (NM_053182)	51	NM_053182	94212	Mm.23897	NM_053182	ENSMUSG00000027508	Pag1	Cbp|F730007C19Rik|Pag	phosphoprotein associated with glycosphingolipid microdomains 1	protein-coding
mm_162395.1	chr1	80660358	80660360	+	1	NA	intron (NM_175291, intron 1 of 55)	intron (NM_175291, intron 1 of 55)	4993	NM_001285927	210293	Mm.133473	NM_175291	ENSMUSG00000038608	Dock10	9330153B10Rik|A630054M16Rik|Jr4|Jr5|R75174|ZIZ3|Zizimin3|mKIAA0694	dedicator of cytokinesis 10	protein-coding
mm_104244.1	chr11	88841434	88841475	-	1	NA	intron (NM_001042541, intron 2 of 10)	intron (NM_001042541, intron 2 of 10)	10049	NM_009648	11640	Mm.2969	NM_009648	ENSMUSG00000018428	Akap1	AKAP121|AKAP84|Akap|C76494|C81186|DAKAP1|S-AKAP84	A kinase (PRKA) anchor protein 1	protein-coding
mm_169137.1	chr13	60855841	60855846	+	1	NA	intron (NM_178098, intron 1 of 7)	L1Md_T|LINE|L1	8573	NM_178098	214639	Mm.19839	NM_178098	ENSMUSG00000050345	4930486L24Rik	AW545031	RIKEN cDNA 4930486L24 gene	protein-coding
mm_170725.1	chr2	150500872	150500874	-	1	NA	Intergenic	CpG	-15810	NM_001034900	545471	Mm.451002	NM_001034900	ENSMUSG00000074731	Zfp345	OTTMUSG00000015743	zinc finger protein 345	protein-coding
mm_34322.1	chr4	141821779	141821804	+	1	NA	exon (NM_007919, exon 4 of 8)	exon (NM_007919, exon 4 of 8)	4214	NM_007919	13706	Mm.45316	NM_007919	ENSMUSG00000058579	Cela2a	Ela-2|Ela2|Ela2a	chymotrypsin-like elastase family, member 2A	protein-coding
mm_160723.1	chr10	69987666	69987666	+	1	NA	intron (NM_146005, intron 36 of 42)	intron (NM_146005, intron 36 of 42)	62134	NM_009670	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_148710.1	chr19	5802350	5802404	+	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	295	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_58391.1	chr7	3206939	3206950	+	1	NA	Intergenic	B1F2|SINE|Alu	-11682	NR_029640	100049710		NR_029640	ENSMUSG00000077815	Mir290a	Mir290|Mirn290|mir-290a|mmu-miR-290|mmu-mir-290a	microRNA 290a	ncRNA
mm_54524.1	chr6	35998667	35998674	-	1	NA	Intergenic	Intergenic	-389414	NM_203491	243764	Mm.448632	NM_203491	ENSMUSG00000045613	Chrm2	AChR-M2|Chrm-2|M2	cholinergic receptor, muscarinic 2, cardiac	protein-coding
mm_72766.1	chr8	85602043	85602051	+	1	NA	Intergenic	Intergenic	-46776	NM_019794	56445	Mm.475573	NM_019794	ENSMUSG00000031701	Dnaja2	1500017M13Rik|2010206B19Rik|DNAJ|DNJ3|Dnaj3|HIRIP4|PRO3015|mDj3	DnaJ heat shock protein family (Hsp40) member A2	protein-coding
mm_63900.1	chr7	139086260	139086275	+	1	NA	intron (NM_011993, intron 1 of 13)	CpG	266	NM_011993	26757	Mm.250414	NM_011993	ENSMUSG00000025478	Dpysl4	AI173505|CRMP-3|Crmp3|DPY4|Drp-4|Ulip4	dihydropyrimidinase-like 4	protein-coding
mm_55236.1	chr6	52245765	52245793	-	1	NA	promoter-TSS (NM_010450)	promoter-TSS (NM_010450)	31	NM_010450	15396	Mm.26954	NM_010450	ENSMUSG00000038210	Hoxa11	Hox-1.9|Hoxa-11	homeobox A11	protein-coding
mm_82694.1	chr9	22376245	22376276	-	1	NA	exon (NM_028390, exon 4 of 24)	exon (NM_028390, exon 4 of 24)	2963	NR_030448	751551		NR_030448	ENSMUSG00000076117	Mir680-2	Mirn680-2	microRNA 680-2	ncRNA
mm_26750.1	chr3	7613726	7613732	-	1	NA	promoter-TSS (NM_001313889)	promoter-TSS (NM_001313889)	31	NM_008371	16196	Mm.3825	NM_008371	ENSMUSG00000040329	Il7	A630026I06Rik|Il-7|hlb368	interleukin 7	protein-coding
mm_41779.1	chr5	103715339	103715353	+	1	NA	Intergenic	Intergenic	-38816	NM_133919	17355	Mm.6949	NM_133919	ENSMUSG00000029313	Aff1	9630032B01Rik|AW319193|Af4|Mllt2h|Rob	AF4/FMR2 family, member 1	protein-coding
mm_75977.1	chr8	72160546	72160552	-	1	NA	promoter-TSS (NM_023126)	promoter-TSS (NM_023126)	-651	NM_023126	17274	Mm.162811	NM_023126	ENSMUSG00000003037	Rab8a	AA409338|Mel	RAB8A, member RAS oncogene family	protein-coding
mm_63434.1	chr7	127479015	127479036	+	1	NA	Intergenic	CpG	-6196	NM_010183	14123	Mm.323505	NM_010183	ENSMUSG00000042423	Fbrs	Fbs|Fbs1	fibrosin	protein-coding
mm_3559.1	chr1	150423944	150423954	+	1	NA	exon (NM_133780, exon 27 of 52)	exon (NM_133780, exon 27 of 52)	-30894	NM_145511	226499	Mm.222093	NM_145511	ENSMUSG00000006010	BC003331	1810053E15Rik|Odr4|odr-4	cDNA sequence BC003331	protein-coding
mm_109950.1	chr12	11386873	11386888	-	1	NA	exon (NM_012038, exon 2 of 4)	exon (NM_012038, exon 2 of 4)	49769	NM_012038	26950	Mm.27005	NM_012038	ENSMUSG00000054459	Vsnl1	VILIP|Vnsl1	visinin-like 1	protein-coding
mm_137996.1	chr17	33641200	33641202	+	1	NA	non-coding (NR_028279, exon 2 of 10)	non-coding (NR_028279, exon 2 of 10)	3106	NR_028279	378460	Mm.272606	NM_001002842	ENSMUSG00000032739	Pram1	AY665714	PML-RAR alpha-regulated adaptor molecule 1	protein-coding
mm_140669.1	chr17	12916390	12916408	-	1	NA	promoter-TSS (NM_013686)	promoter-TSS (NM_013686)	70	NM_013686	21454	Mm.229342	NM_013686	ENSMUSG00000068039	Tcp1	AI528772|CCT|Cct1|Ccta|TRic|Tcp-1|Tp63|c-cpn|p63	t-complex protein 1	protein-coding
mm_50349.1	chr6	48589561	48589580	+	1	NA	5' UTR (NM_183309, exon 1 of 2)	5' UTR (NM_183309, exon 1 of 2)	125	NM_183309	330305	Mm.123868	NM_183309	ENSMUSG00000052730	Gm5111	A630038D02|EG330305	predicted gene 5111	protein-coding
mm_130741.1	chr15	101256031	101256039	-	1	NA	Intergenic	Intergenic	-10811	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_168030.1	chrY	90738496	90738548	-	1	NA	Intergenic	IMPB_01|Satellite|Satellite	16528	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_109830.1	chr12	3972870	3972877	-	1	NA	intron (NM_001082483, intron 17 of 22)	L3|LINE|CR1	17928	NM_001278583	18976	Mm.277996	NM_008895	ENSMUSG00000020660	Pomc	ACTH|BE|Beta-LPH|Clip|Gamma-LPH|Npp|Pomc-1|Pomc1|alpha-MSH|alphaMSH|beta-MSH|gamma-MSH	pro-opiomelanocortin-alpha	protein-coding
mm_39754.1	chr5	29735823	29735831	+	1	NA	promoter-TSS (NM_001037941)	promoter-TSS (NM_001037941)	-71	NM_001037940	23950	Mm.290110	NM_011847	ENSMUSG00000029131	Dnajb6	Mrj|mDj4	DnaJ heat shock protein family (Hsp40) member B6	protein-coding
mm_41151.1	chr5	87929779	87929795	+	1	NA	exon (NM_007786, exon 4 of 5)	exon (NM_007786, exon 4 of 5)	4154	NM_007786	12994	Mm.296303	NM_007786	ENSMUSG00000001622	Csn3	AW208918|CSN10|Csnk	casein kappa	protein-coding
mm_103729.1	chr11	79675126	79675130	-	1	NA	promoter-TSS (NR_045898)	promoter-TSS (NR_045898)	-42	NR_045898	72218	Mm.443271	NR_045898	ENSMUSG00000086569	Rab11fip4os2	1700020F10Rik|4930542H20Rik|Rab11fib4os2	RAB11 family interacting protein 4 (class II), opposite strand 2	ncRNA
mm_72968.1	chr8	92855405	92855415	+	1	NA	promoter-TSS (NM_173014)	promoter-TSS (NM_173014)	60	NM_173014	270084	Mm.21463	NM_173014	ENSMUSG00000033192	Lpcat2	A330042H22|Aytl1|Aytl1a|lpafat1	lysophosphatidylcholine acyltransferase 2	protein-coding
mm_40533.1	chr5	57937031	57937050	+	1	NA	intron (NM_001122758, intron 2 of 2)	intron (NM_001122758, intron 2 of 2)	218959	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_74147.1	chr8	123292166	123292170	+	1	NA	intron (NM_016925, intron 20 of 42)	intron (NM_016925, intron 20 of 42)	26408	NM_016925	14087	Mm.6536	NM_016925	ENSMUSG00000032815	Fanca	AW208693|FACA	Fanconi anemia, complementation group A	protein-coding
mm_41500.1	chr5	92326803	92326820	+	1	NA	exon (NM_008599, exon 2 of 4)	exon (NM_008599, exon 2 of 4)	1268	NM_008599	17329	Mm.766	NM_008599	ENSMUSG00000029417	Cxcl9	BB139920|CMK|Mig|MuMIG|Scyb9|crg-10	chemokine (C-X-C motif) ligand 9	protein-coding
mm_106077.1	chr11	116174473	116174486	-	1	NA	exon (NM_015729, exon 13 of 14)	exon (NM_015729, exon 13 of 14)	-6301	NM_172571	217335	Mm.35241	NM_172571	ENSMUSG00000020776	Fbf1	1110033G01Rik|5930413D20|mKIAA1863	Fas (TNFRSF6) binding factor 1	protein-coding
mm_164771.1	chr17	88113362	88113376	-	1	NA	Intergenic	L1M5|LINE|L1	-12143	NM_001190356	225058	Mm.312053	NM_001190356		Gm4832	EG225058	predicted gene 4832	protein-coding
mm_105572.1	chr11	106588871	106588881	-	1	NA	intron (NM_198292, intron 1 of 11)	intron (NM_198292, intron 1 of 11)	24054	NM_198292	21763	Mm.102407	NM_198292	ENSMUSG00000040548	Tex2	4930568E07Rik|AI553404|Def-5|Taz4	testis expressed gene 2	protein-coding
mm_163704.1	chr13	106191410	106191411	-	1	NA	Intergenic	Intergenic	745505	NM_029665	76582	Mm.132208	NM_029665	ENSMUSG00000042590	Ipo11	1700081H05Rik|2510001A17Rik|AI314624|AW555235|E330021B14Rik|Ranbp11	importin 11	protein-coding
mm_31177.1	chr4	43506339	43506360	+	1	NA	promoter-TSS (NM_139305)	promoter-TSS (NM_139305)	-677	NM_139305	230099	Mm.283682	NM_139305	ENSMUSG00000028463	Car9	CAIX|Ca9|MN/CA9	carbonic anhydrase 9	protein-coding
mm_28431.1	chr3	90465794	90465796	-	1	NA	promoter-TSS (NM_008727)	promoter-TSS (NM_008727)	71	NM_008727	18160	Mm.4627	NM_008727	ENSMUSG00000027931	Npr1	AI893888|GC-A|NPR-A|NPRA|Pndr	natriuretic peptide receptor 1	protein-coding
mm_9056.1	chr1	167340516	167340546	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-9460	NM_019993	56752	Mm.292539	NM_019993	ENSMUSG00000026687	Aldh9a1	AA139417|Abaldh|ESTM40|TMABA-DH|Tmabadh	aldehyde dehydrogenase 9, subfamily A1	protein-coding
mm_164790.1	chr18	12741318	12741328	+	1	NA	promoter-TSS (NM_001042420)	promoter-TSS (NM_001042420)	-32	NM_001042419	71132	Mm.179740	NM_027687	ENSMUSG00000024430	Cabyr	1700016C01Rik|4933421A18Rik|CBP86|FSP-2	calcium-binding tyrosine-(Y)-phosphorylation regulated (fibrousheathin 2)	protein-coding
mm_17642.1	chr2	31163564	31163571	-	1	NA	intron (NM_178760, intron 1 of 17)	intron (NM_178760, intron 1 of 17)	11251	NM_178760	277463	Mm.236074	NM_178760	ENSMUSG00000000194	Gpr107	9930033D15Rik|AI790205|C530034M11|mKIAA1624	G protein-coupled receptor 107	protein-coding
mm_1424.1	chr1	67174434	67174447	+	1	NA	exon (NM_001080809, exon 19 of 38)	exon (NM_001080809, exon 19 of 38)	51413	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_51937.1	chr6	91699110	91699121	+	1	NA	intron (NM_009320, intron 2 of 14)	intron (NM_009320, intron 2 of 14)	15048	NM_009320	21366	Mm.395650	NM_009320	ENSMUSG00000030096	Slc6a6	AA589629|C80501|Taut	solute carrier family 6 (neurotransmitter transporter, taurine), member 6	protein-coding
mm_7545.1	chr1	124504182	124504206	-	1	NA	Intergenic	RSINE1|SINE|B4	-458635	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_10997.1	chr2	26380697	26380735	+	1	NA	promoter-TSS (NM_172339)	promoter-TSS (NM_172339)	-63	NM_001290419	227644	Mm.207460	NM_172339	ENSMUSG00000036281	Snapc4	5730436L13Rik	small nuclear RNA activating complex, polypeptide 4	protein-coding
mm_36112.1	chr4	58879082	58879093	-	1	NA	exon (NM_172381, exon 3 of 49)	exon (NM_172381, exon 3 of 49)	33638	NM_172381	230249	Mm.234801	NM_172381	ENSMUSG00000050812	AI314180	AW558785|BB181316|mKIAA0368	expressed sequence AI314180	protein-coding
mm_138370.1	chr17	35001283	35001347	+	1	NA	promoter-TSS (NM_033075)	promoter-TSS (NM_033075)	408	NM_011690	22321	Mm.28420	NM_011690	ENSMUSG00000007029	Vars	Bat6|D17H6S56E|G7a|Vars2	valyl-tRNA synthetase	protein-coding
mm_59872.1	chr7	30263175	30263179	+	1	NA	intron (NM_146186, intron 9 of 32)	intron (NM_146186, intron 9 of 32)	-16917	NR_144498	108167416	Mm.471845	NR_144498		LOC108167416	-	uncharacterized LOC108167416	ncRNA
mm_129207.1	chr15	76518548	76518552	-	1	NA	3' UTR (NM_130893, exon 2 of 2)	3' UTR (NM_130893, exon 2 of 2)	3579	NM_130893	170729	Mm.218747	NM_130893	ENSMUSG00000048385	Scrt1	-	scratch family zinc finger 1	protein-coding
mm_108181.1	chr12	76497976	76497979	+	1	NA	Intergenic	Intergenic	35235	NR_039597	100628604		NR_039597	ENSMUSG00000092738	Mir5135	mir-5135|mmu-mir-5135|mu-mir-5135	microRNA 5135	ncRNA
mm_36385.1	chr4	77154606	77154618	-	1	NA	intron (NM_011211, intron 7 of 39)	RSINE1|SINE|B4	1057283	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding
mm_36428.1	chr4	82293678	82293697	-	1	NA	3' UTR (NM_001113209, exon 12 of 12)	3' UTR (NM_001113209, exon 12 of 12)	212092	NM_001286127	18028	Mm.317947	NM_008687	ENSMUSG00000008575	Nfib	6720429L07Rik|CTF|E030026I10Rik|NF-I/B|NF1-B|NFI-B	nuclear factor I/B	protein-coding
mm_98614.1	chr11	95843227	95843239	+	1	NA	promoter-TSS (NM_001284397)	promoter-TSS (NM_001284397)	-12	NM_001284397	14710	Mm.46299	NM_023121	ENSMUSG00000038811	Gngt2	AV096488	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 2	protein-coding
mm_110822.1	chr12	72408847	72408851	-	1	NA	5' UTR (NM_001286448, exon 1 of 7)	5' UTR (NM_001286448, exon 1 of 7)	205	NM_001286448	104001	Mm.221275	NM_153457	ENSMUSG00000021087	Rtn1	Nsp	reticulon 1	protein-coding
mm_83545.1	chr9	46235683	46235693	-	1	NA	promoter-TSS (NM_001289755)	promoter-TSS (NM_001289755)	-52	NM_001289756	11814	Mm.390161	NM_023114	ENSMUSG00000032081	Apoc3	apo-CIII|apoC-III	apolipoprotein C-III	protein-coding
mm_60085.1	chr7	34388605	34388671	+	1	NA	intron (NM_025948, intron 1 of 10)	intron (NM_025948, intron 1 of 10)	902	NM_025948	67070	Mm.276503	NM_025948	ENSMUSG00000066568	Lsm14a	2700023B17Rik|AA407828|AU017544|Tral	LSM14A mRNA processing body assembly factor	protein-coding
mm_124002.1	chr14	75958429	75958432	-	1	NA	intron (NM_026214, intron 1 of 1)	MER104|DNA|TcMar-Tc2	3427	NM_026214	67516	Mm.390712	NM_026214	ENSMUSG00000046523	Kctd4	2210017A09Rik|AU017169	potassium channel tetramerisation domain containing 4	protein-coding
mm_76811.1	chr8	104442805	104442836	-	1	NA	5' UTR (NM_001013380, exon 1 of 13)	5' UTR (NM_001013380, exon 1 of 13)	227	NM_001013380	234663	Mm.289583	NM_001013380	ENSMUSG00000035770	Dync1li2	AA409702|C920003I06|Dncli2|Dnclic2|LIC2	dynein, cytoplasmic 1 light intermediate chain 2	protein-coding
mm_115039.1	chr13	99434149	99434183	+	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-21340	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_129174.1	chr15	76269828	76269847	-	1	NA	promoter-TSS (NR_045747)	promoter-TSS (NR_045747)	2	NR_045747	100038659	Mm.448549	NR_045747		Mirt2	ENSMUSG00000075583|Gm10872|Gm24562	myocardial infraction associated transcript 2	ncRNA
mm_85137.1	chr9	95785530	95785536	-	1	NA	exon (NM_001033210, exon 4 of 16)	exon (NM_001033210, exon 4 of 16)	-35175	NM_011643	22063	Mm.149633	NM_011643	ENSMUSG00000032839	Trpc1	Mtrp1|Trp1|Trrp1	transient receptor potential cation channel, subfamily C, member 1	protein-coding
mm_159044.1	chr1	181511446	181511446	-	1	NA	promoter-TSS (NM_207280)	promoter-TSS (NM_207280)	5	NM_207280	403180	Mm.220754	NM_207280	ENSMUSG00000050625	Ccdc121	6530421E24Rik|Gm755	coiled-coil domain containing 121	protein-coding
mm_147890.1	chr18	65040694	65040710	-	1	NA	intron (NM_031881, intron 1 of 29)	MTD|LTR|ERVL-MaLR	17175	NM_031881	83814	Mm.98668	NM_031881	ENSMUSG00000024589	Nedd4l	1300012C07Rik|Nedd4-2|Nedd4b	neural precursor cell expressed, developmentally down-regulated gene 4-like	protein-coding
mm_163983.1	chr14	59419198	59419208	-	1	NA	exon (NM_001320721, exon 5 of 13)	exon (NM_001320721, exon 5 of 13)	21677	NM_001320725	107303348		NM_001320725		Setdb2-phf11c	-	Setdb2-Phf11c readthrough	protein-coding
mm_121580.1	chr14	123660222	123660233	+	1	NA	promoter-TSS (NM_145467)	promoter-TSS (NM_145467)	87	NM_145467	223272	Mm.383176	NM_145467	ENSMUSG00000032925	Itgbl1	B930011D01Rik	integrin, beta-like 1	protein-coding
mm_92805.1	chr10	81378381	81378391	-	1	NA	promoter-TSS (NM_019757)	promoter-TSS (NM_019757)	-16	NM_019757	56371	Mm.24202	NM_019757	ENSMUSG00000020235	Fzr1	AW108046|Cdh1|FZR|FZR2|Fyr|HCDH|HCDH1	fizzy/cell division cycle 20 related 1 (Drosophila)	protein-coding
mm_101812.1	chr11	46388550	46388588	-	1	NA	intron (NM_010583, intron 1 of 16)	intron (NM_010583, intron 1 of 16)	946	NM_001281968	16428	Mm.339927	NM_010583	ENSMUSG00000020395	Itk	Emt|Tcsk|Tsk	IL2 inducible T cell kinase	protein-coding
mm_150064.1	chr19	29386314	29386325	+	1	NA	3' UTR (NM_021893, exon 7 of 7)	3' UTR (NM_021893, exon 7 of 7)	18881	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_101134.1	chr11	12464820	12464845	-	1	NA	5' UTR (NM_001282993, exon 1 of 14)	5' UTR (NM_001282993, exon 1 of 14)	128	NM_172496	12808	Mm.22847	NM_172496	ENSMUSG00000020173	Cobl	-	cordon-bleu WH2 repeat	protein-coding
mm_172637.1	chr8	20874667	20874682	-	1	NA	Intergenic	ERVB7_2-LTR_MM|LTR|ERVK	-1825	NR_002880	654455	Mm.424927	NR_002880		Gm21944	Defb48-ps	defensin beta 48 pseudogene	pseudo
mm_86660.1	chr10	17796202	17796226	+	1	NA	promoter-TSS (NM_138628)	promoter-TSS (NM_138628)	-5	NM_138628	378431	Mm.283493	NM_138628	ENSMUSG00000039891	Txlnb	2310001N14Rik|Mdp77	taxilin beta	protein-coding
mm_120263.1	chr14	63082427	63082428	+	1	NA	Intergenic	L2a|LINE|L2	27354	NR_046019	72609	Mm.387101	NR_046019		2700070H01Rik	-	RIKEN cDNA 2700070H01 gene	ncRNA
mm_84275.1	chr9	62809853	62809861	-	1	NA	intron (NM_010193, intron 1 of 1)	(A)n|Simple_repeat|Simple_repeat	1791	NM_010193	14155	Mm.24069	NM_010193	ENSMUSG00000032244	Fem1b	mKIAA0396	feminization 1 homolog b (C. elegans)	protein-coding
mm_41635.1	chr5	97195573	97195598	+	1	NA	Intergenic	Intergenic	-83989	NM_198422	231474	Mm.332505	NM_198422	ENSMUSG00000055725	Paqr3	6330415A20Rik|AY424292|RKTG	progestin and adipoQ receptor family member III	protein-coding
mm_42861.1	chr5	122224413	122224417	+	1	NA	intron (NM_028752, intron 2 of 6)	(T)n|Simple_repeat|Simple_repeat	14128	NM_028752	74096	Mm.28804	NM_028752	ENSMUSG00000064267	Hvcn1	0610039P13Rik|AI450555|BTS|HV1|Vsop.|mVSOP	hydrogen voltage-gated channel 1	protein-coding
mm_22316.1	chr2	180443816	180443834	-	1	NA	Intergenic	Intergenic	-17153	NM_148933	108115	Mm.133687	NM_148933	ENSMUSG00000038963	Slco4a1	OATP-E|Slc21a12	solute carrier organic anion transporter family, member 4a1	protein-coding
mm_23328.1	chr3	53725451	53725461	+	1	NA	Intergenic	Intergenic	-68101	NM_172862	242022	Mm.38378	NM_172862	ENSMUSG00000037016	Frem2	6030440P17Rik|8430406N05Rik|Gm409|b2b1562Clo|my|ne|nv1	Fras1 related extracellular matrix protein 2	protein-coding
mm_80003.1	chr9	67733940	67733952	+	1	NA	Intergenic	Intergenic	-4369	NR_106101	102465716		NR_106101	ENSMUSG00000098446	Mir7242	Gm27809|mmu-mir-7242	microRNA 7242	ncRNA
mm_59222.1	chr7	24611315	24611349	+	1	NA	promoter-TSS (NM_001102613)	promoter-TSS (NM_001102613)	4	NM_001102613	232970	Mm.333663	NM_001102613	ENSMUSG00000074277	Phldb3	EG232970|ENSMUSG00000061511|Gm10102	pleckstrin homology like domain, family B, member 3	protein-coding
mm_32589.1	chr4	111415239	111415259	+	1	NA	exon (NM_026279, exon 1 of 6)	exon (NM_026279, exon 1 of 6)	243	NM_026279	67621	Mm.45533	NM_026279	ENSMUSG00000028545	Bend5	2310026E23Rik	BEN domain containing 5	protein-coding
mm_77621.1	chr8	123952869	123952874	-	1	NA	3' UTR (NM_019552, exon 13 of 13)	3' UTR (NM_019552, exon 13 of 13)	-3606	NM_172288	234865	Mm.267812	NM_172288	ENSMUSG00000039509	Nup133	mermaid	nucleoporin 133	protein-coding
mm_133432.1	chr16	87661411	87661442	+	1	NA	Intergenic	Intergenic	-37528	NM_007520	12013	Mm.26147	NM_007520	ENSMUSG00000025612	Bach1	6230421P05Rik|AI323795	BTB and CNC homology 1, basic leucine zipper transcription factor 1	protein-coding
mm_21890.1	chr2	166155450	166155460	-	1	NA	promoter-TSS (NM_001252578)	promoter-TSS (NM_001252578)	-170	NM_001252578	72043	Mm.1011	NM_028072	ENSMUSG00000006800	Sulf2	2010004N24Rik|AU020235|MSulf-2|mKIAA1247	sulfatase 2	protein-coding
mm_101144.1	chr11	16508150	16508187	-	1	NA	exon (NM_011343, exon 1 of 4)	exon (NM_011343, exon 1 of 4)	316	NM_011343	20335	Mm.325350	NM_011343	ENSMUSG00000078974	Sec61g	-	SEC61, gamma subunit	protein-coding
mm_33718.1	chr4	134052717	134052731	+	1	NA	Intergenic	Intergenic	-15728	NM_001162970	230806	Mm.240080	NM_001162970	ENSMUSG00000012123	Aim1l	-	absent in melanoma 1-like	protein-coding
mm_97531.1	chr11	78512302	78512312	+	1	NA	promoter-TSS (NM_026389)	promoter-TSS (NM_026389)	11	NM_026389	67811	Mm.197493	NM_026389	ENSMUSG00000001100	Poldip2	1300003F06Rik|Pdip38	polymerase (DNA-directed), delta interacting protein 2	protein-coding
mm_22331.1	chr2	180701998	180702046	-	1	NA	promoter-TSS (NM_011805)	promoter-TSS (NM_011805)	80	NM_011805	23856	Mm.253836	NM_011805	ENSMUSG00000038914	Dido1	6720461J16Rik|D130048F08Rik|DATF-1|DIO-1|Datf1|dido	death inducer-obliterator 1	protein-coding
mm_14167.1	chr2	126673597	126673606	+	1	NA	intron (NM_001271470, intron 1 of 8)	intron (NM_001271470, intron 1 of 8)	1991	NM_001271469	14391	Mm.293266	NM_010249	ENSMUSG00000027361	Gabpb1	BABPB2|E4TF1|E4TF1-47|E4TF1-53|E4Tf1B|GABPB|GABPB-1|GABPB-2|GABPB1-1|GABPB1-2|NRF2B1|NRF2B2	GA repeat binding protein, beta 1	protein-coding
mm_42805.1	chr5	121742441	121742446	+	1	NA	intron (NM_009125, intron 1 of 24)	Lx9|LINE|L1	30834	NM_009125	20239	Mm.260900	NM_009125	ENSMUSG00000042605	Atxn2	9630045M23Rik|ATX2|AW544490|Sca2	ataxin 2	protein-coding
mm_16694.1	chr2	6884976	6884991	-	1	NA	promoter-TSS (NM_001110228)	promoter-TSS (NM_001110228)	13	NM_010160	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_43221.1	chr5	129786991	129787058	+	1	NA	promoter-TSS (NM_009838)	promoter-TSS (NM_009838)	229	NM_133900	100678	Mm.271784	NM_133900	ENSMUSG00000029446	Psph	AI480570|PSP|PSPase	phosphoserine phosphatase	protein-coding
mm_79098.1	chr9	46243043	46243047	+	1	NA	exon (NM_007468, exon 3 of 3)	exon (NM_007468, exon 3 of 3)	2201	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_14937.1	chr2	151543878	151543891	+	1	NA	intron (NR_126058, intron 2 of 3)	intron (NR_126058, intron 2 of 3)	1401	NM_001302078	14225	Mm.278458	NM_008019	ENSMUSG00000032966	Fkbp1a	FKBP12|Fkbp|Fkbp1	FK506 binding protein 1a	protein-coding
mm_30795.1	chr4	19818723	19818743	+	1	NA	promoter-TSS (NM_028746)	promoter-TSS (NM_028746)	6	NM_028746	74087	Mm.173833	NM_028746	ENSMUSG00000041052	Slc7a13	0610009O04Rik|AGT-1|AGT1|XAT2	solute carrier family 7, (cationic amino acid transporter, y+ system) member 13	protein-coding
mm_131968.1	chr16	24721843	24721882	+	1	NA	promoter-TSS (NM_001145954)	promoter-TSS (NM_001145954)	7	NM_001145954	210126	Mm.209385	NM_178665	ENSMUSG00000033306	Lpp	9430020K16Rik|AA959454|AU024130|B130055L10Rik|C79715|D630048H16	LIM domain containing preferred translocation partner in lipoma	protein-coding
mm_82043.1	chr9	122349571	122349603	+	1	NA	Intergenic	Intergenic	-2029	NM_026179	67469	Mm.280254	NM_026179	ENSMUSG00000032540	Abhd5	1300003D03Rik|2010002J10Rik|CDS|CGI-58|IECN5|NCIE2	abhydrolase domain containing 5	protein-coding
mm_145539.1	chr18	60807536	60807578	+	1	NA	intron (NM_001042605, intron 1 of 8)	intron (NM_001042605, intron 1 of 8)	3708	NM_010545	16149	Mm.439737	NM_010545	ENSMUSG00000024610	Cd74	CLIP|DHLAG|HLADG|Ia-GAMMA|Ii	CD74 antigen (invariant polypeptide of major histocompatibility complex, class II antigen-associated)	protein-coding
mm_48840.1	chr5	149367060	149367068	-	1	NA	Intergenic	Intergenic	-44742	NM_027519	70717	Mm.252139	NM_027519	ENSMUSG00000029659	Medag	6330406I15Rik|Awms3|MEDA-4|Meda4|mAWMS3	mesenteric estrogen dependent adipogenesis	protein-coding
mm_155257.1	chrX	57224143	57224145	+	1	NA	TTS (NM_011616)	TTS (NM_011616)	12001	NM_011616	21947	Mm.4861	NM_011616	ENSMUSG00000031132	Cd40lg	CD154|CD40-L|Cd40l|HIGM1|IGM|IMD3|Ly-62|Ly62|T-BAM|TRAP|Tnfsf5|Tnlg8b|gp39	CD40 ligand	protein-coding
mm_79364.1	chr9	54469651	54469661	+	1	NA	intron (NM_172771, intron 6 of 43)	L1M2|LINE|L1	31970	NM_172771	235380	Mm.93636	NM_172771	ENSMUSG00000041268	Dmxl2	6330586A12|6430411K14Rik|E130119P06Rik|mKIAA0856	Dmx-like 2	protein-coding
mm_1516.1	chr1	72711260	72711296	+	1	NA	promoter-TSS (NM_009084)	promoter-TSS (NM_009084)	18	NM_009084	19981	Mm.21529	NM_009084	ENSMUSG00000046330	Rpl37a	-	ribosomal protein L37a	protein-coding
mm_138151.1	chr17	34208779	34208792	+	1	NA	exon (NM_011530, exon 4 of 12)	exon (NM_011530, exon 4 of 12)	4306	NM_011530	21355	Mm.14814	NM_011530	ENSMUSG00000024339	Tap2	ABC18|AI462429|APT2|Abcb3|Ham-2|Ham2|MTP2|PSF2|RING11|Tap-2|Y1|jas	transporter 2, ATP-binding cassette, sub-family B (MDR/TAP)	protein-coding
mm_169753.1	chr15	90764696	90764697	-	1	NA	Intergenic	Intergenic	-85308	NM_001033851	66871	Mm.290991	NM_025815	ENSMUSG00000052560	Cpne8	1200003E11Rik|1500031E20Rik	copine VIII	protein-coding
mm_137378.1	chr17	25718226	25718231	+	1	NA	TTS (NM_145409)	TTS (NM_145409)	1056	NM_022422	64337	Mm.171123	NM_022422	ENSMUSG00000025739	Gng13	1500031D04Rik|AB030194|Ggamma13	guanine nucleotide binding protein (G protein), gamma 13	protein-coding
mm_40045.1	chr5	33859912	33859912	+	1	NA	intron (NM_001177884, intron 4 of 8)	intron (NM_001177884, intron 4 of 8)	16800	NM_001177884	107823	Mm.19892	NM_175231	ENSMUSG00000057406	Whsc1	5830445G22Rik|9430010A17Rik|AW555663|C130020C13Rik|D030027O06Rik|D930023B08Rik|MMSET|NSD2|Whsc1l|mKIAA1090	Wolf-Hirschhorn syndrome candidate 1 (human)	protein-coding
mm_50990.1	chr6	63256095	63256104	+	1	NA	promoter-TSS (NM_008167)	promoter-TSS (NM_008167)	-758	NM_008167	14804	Mm.439651	NM_008167	ENSMUSG00000071424	Grid2	B230104L07Rik|GluD2|GluRdelta2|Lc|Lc<J>|MMS10-AC|Ms10ac|cpr|ho|nmf408|tpr	glutamate receptor, ionotropic, delta 2	protein-coding
mm_147994.1	chr18	67669223	67669228	-	1	NA	3' UTR (NM_001127177, exon 9 of 9)	3' UTR (NM_001127177, exon 9 of 9)	27626	NM_134138	107047	Mm.150701	NM_134138	ENSMUSG00000024537	Psmg2	1700017I17Rik|AW545363|Clast3|Tnfsf5ip1	proteasome (prosome, macropain) assembly chaperone 2	protein-coding
mm_23155.1	chr3	40531466	40531470	+	1	NA	Intergenic	Intergenic	-8556	NR_040445	100040882	Mm.272869	NR_040445	ENSMUSG00000037884	1700017G19Rik	-	RIKEN cDNA 1700017G19 gene	ncRNA
mm_23546.1	chr3	61366004	61366024	+	1	NA	3' UTR (NM_028712, exon 1 of 1)	3' UTR (NM_028712, exon 1 of 1)	1507	NM_028712	74012	Mm.422674	NM_028712	ENSMUSG00000036894	Rap2b	4021402C18Rik|AA408554	RAP2B, member of RAS oncogene family	protein-coding
mm_160124.1	chr7	28291042	28291042	-	1	NA	promoter-TSS (NM_175033)	promoter-TSS (NM_175033)	92	NM_175033	280621	Mm.212777	NM_175033	ENSMUSG00000046750	Selenov	Selv	selenoprotein V	protein-coding
mm_124670.1	chr15	6391421	6391460	+	1	NA	intron (NM_001310446, intron 1 of 13)	intron (NM_001310446, intron 1 of 13)	4692	NM_001310446	13132	Mm.240830	NM_023118	ENSMUSG00000022150	Dab2	5730435J12Rik|AA960054|AI957090|D15Wsu122e|D630005B22Rik|Doc-2|Doc2|p96	disabled 2, mitogen-responsive phosphoprotein	protein-coding
mm_36564.1	chr4	87230436	87230476	-	1	NA	promoter-TSS (NM_172426)	promoter-TSS (NM_172426)	84	NM_172426	76376	Mm.490487	NM_172426	ENSMUSG00000037996	Slc24a2	2810021B17Rik|6330417K15Rik|AI847460|Nckx2	solute carrier family 24 (sodium/potassium/calcium exchanger), member 2	protein-coding
mm_167284.1	chr8	40423543	40423557	+	1	NA	promoter-TSS (NM_178395)	promoter-TSS (NM_178395)	-265	NM_178395	70546	Mm.34326	NM_178395	ENSMUSG00000039470	Zdhhc2	5730415P04Rik|6430583A19Rik	zinc finger, DHHC domain containing 2	protein-coding
mm_124227.1	chr14	100619357	100619363	-	1	NA	Intergenic	Intergenic	-469564	NM_010636	16597	Mm.396499	NM_010636	ENSMUSG00000072294	Klf12	2700063E05Rik|AI225908|AI315654|AP-2rep|B130052C06Rik|D530033K05Rik	Kruppel-like factor 12	protein-coding
mm_8676.1	chr1	156718990	156719021	-	1	NA	promoter-TSS (NM_145413)	promoter-TSS (NM_145413)	-95	NM_145413	215015	Mm.229107	NM_145413	ENSMUSG00000033557	Fam20b	C530043G21Rik|mKIAA0475	family with sequence similarity 20, member B	protein-coding
mm_29986.1	chr3	135424097	135424098	-	1	NA	promoter-TSS (NM_025902)	promoter-TSS (NM_025902)	-664	NM_025902	67006	Mm.269993	NM_025902	ENSMUSG00000028165	Cisd2	1500009M05Rik|1500026J14Rik|1500031D15Rik|AI848398|B630006A20Rik|Miner1|Naf-1|Noxp70|Zcd2	CDGSH iron sulfur domain 2	protein-coding
mm_4578.1	chr1	177983467	177983477	+	1	NA	Intergenic	CpG	-7963	NM_001034899	545391	Mm.442974	NM_001034899	ENSMUSG00000091476	Gm16432	EG545391|EG666250	predicted gene 16432	protein-coding
mm_157440.1	chrX	39014109	39014120	-	1	NA	Intergenic	Intergenic	241334	NM_183126	77883	Mm.113311	NM_183126	ENSMUSG00000051361	6030498E09Rik	-	RIKEN cDNA 6030498E09 gene	protein-coding
mm_148380.1	chr19	3283036	3283071	+	1	NA	promoter-TSS (NM_009212)	promoter-TSS (NM_009212)	6	NM_172252	353242	Mm.74084	NM_172252	ENSMUSG00000024829	Mrpl21	BC028768	mitochondrial ribosomal protein L21	protein-coding
mm_43978.1	chr5	146261146	146261177	+	1	NA	intron (NM_153599, intron 2 of 12)	LSU-rRNA_Hsa|rRNA|rRNA	29486	NM_153599	264064	Mm.260576	NM_153599	ENSMUSG00000029635	Cdk8	-	cyclin-dependent kinase 8	protein-coding
mm_138475.1	chr17	35194598	35194602	+	1	NA	promoter-TSS (NM_008518)	promoter-TSS (NM_008518)	93	NM_008518	16994	Mm.1715	NM_008518	ENSMUSG00000024399	Ltb	AI662801|LTbeta|Tnfc|Tnfsf3|Tnlg1c|p33	lymphotoxin B	protein-coding
mm_165152.1	chr2	21178908	21178909	+	1	NA	Intergenic	Intergenic	26457	NM_027728	71233	Mm.27658	NM_027728	ENSMUSG00000026679	Enkur	4933434I06Rik|AU016229	enkurin, TRPC channel interacting protein	protein-coding
mm_157415.1	chrX	38454809	38454810	-	1	NA	intron (NM_010685, intron 1 of 8)	Lx9|LINE|L1	1651	NM_010685	16784	Mm.486	NM_010685	ENSMUSG00000016534	Lamp2	CD107b|LGP-B|Lamp II|Lamp-2|Lamp-2a|Lamp-2b|Lamp-2c|Mac3	lysosomal-associated membrane protein 2	protein-coding
mm_100681.1	chr11	3471497	3471522	-	1	NA	non-coding (NR_028317, exon 2 of 4)	non-coding (NR_028317, exon 2 of 4)	-8519	NR_037301	100499518		NR_037301	ENSMUSG00000095323	Mir3470a	mmu-mir-3470a	microRNA 3470a	ncRNA
mm_77466.1	chr8	122425043	122425056	-	1	NA	exon (NM_007806, exon 6 of 6)	exon (NM_007806, exon 6 of 6)	2964	NM_145834	234836	Mm.222808	NM_145834	ENSMUSG00000046108	Il17c	IL-17C	interleukin 17C	protein-coding
mm_170475.1	chr19	11469440	11469454	+	1	NA	promoter-TSS (NM_028595)	promoter-TSS (NM_028595)	79	NM_028595	73656	Mm.440719	NM_028595	ENSMUSG00000079419	Ms4a6c	2200009H22Rik|2210417N07Rik	membrane-spanning 4-domains, subfamily A, member 6C	protein-coding
mm_12059.1	chr2	59338750	59338760	+	1	NA	exon (NM_026361, exon 14 of 22)	exon (NM_026361, exon 14 of 22)	47927	NR_040510	76676	Mm.110038	NR_040510	ENSMUSG00000087455	5330411J11Rik	-	RIKEN cDNA 5330411J11 gene	ncRNA
mm_29839.1	chr3	129822488	129822510	-	1	NA	promoter-TSS (NM_009102)	promoter-TSS (NM_009102)	6	NM_009102	20132	Mm.278758	NM_009102	ENSMUSG00000028012	Rrh	-	retinal pigment epithelium derived rhodopsin homolog	protein-coding
mm_133411.1	chr16	85056399	85056448	+	1	NA	exon (NM_001198823, exon 6 of 18)	exon (NM_001198823, exon 6 of 18)	84212	NR_045889	100038614	Mm.441351	NR_045889		Gm10791	ENSMUSG00000074933	predicted gene 10791	ncRNA
mm_121487.1	chr14	121239678	121239684	+	1	NA	intron (NM_134082, intron 10 of 26)	intron (NM_134082, intron 10 of 26)	139549	NM_145465	223255	Mm.390756	NM_145465	ENSMUSG00000063410	Stk24	1810013H02Rik|C76483|MST-3|Mst3|STE20	serine/threonine kinase 24	protein-coding
mm_66584.1	chr7	45385799	45385802	-	1	NA	intron (NM_009224, intron 6 of 9)	B3A|SINE|B2	9942	NM_009224	20637	Mm.216386	NM_009224	ENSMUSG00000063511	Snrnp70	2700022N21Rik|3200002N22Rik|AI325098|R74807|Rnu1p70|Rnulp70|Snrp70|Srnp70|U1-70|U1-70K	small nuclear ribonucleoprotein 70 (U1)	protein-coding
mm_117394.1	chr13	73678030	73678040	-	1	NA	promoter-TSS (NM_001168646)	promoter-TSS (NM_001168646)	-12	NM_001168643	22598	Mm.30370	NM_011730	ENSMUSG00000021612	Slc6a18	B0AT3|D630001K16Rik|Xt2|Xtrp2	solute carrier family 6 (neurotransmitter transporter), member 18	protein-coding
mm_135080.1	chr16	34263180	34263208	-	1	NA	intron (NM_001164268, intron 10 of 33)	intron (NM_001164268, intron 10 of 33)	250833	NM_001164268	545156	Mm.82274	NM_177357	ENSMUSG00000061751	Kalrn	2210407G14Rik|AV235988|DUET|E530005C20Rik|Gm539|Hapip|TRAD	kalirin, RhoGEF kinase	protein-coding
mm_129376.1	chr15	78120189	78120241	-	1	NA	promoter-TSS (NM_007583)	promoter-TSS (NM_007583)	-935	NM_007583	12300	Mm.277338	NM_007583	ENSMUSG00000019146	Cacng2	AW060990|B230105C07Rik|B930041E13Rik|stargazer|stargazin|stg|wag|waggler	calcium channel, voltage-dependent, gamma subunit 2	protein-coding
mm_163812.1	chr14	19416326	19416371	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	186239	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_139279.1	chr17	48247784	48247810	+	1	NA	promoter-TSS (NM_021407)	promoter-TSS (NM_021407)	68	NM_021407	58218	Mm.302438	NM_021407	ENSMUSG00000041754	Trem3	BB134760	triggering receptor expressed on myeloid cells 3	protein-coding
mm_23304.1	chr3	52649967	52649973	+	1	NA	Intergenic	MLT1A0|LTR|ERVL-MaLR	-89754	NR_038079	329639	Mm.131245	NR_038079	ENSMUSG00000102785	Gm2447	100039832|A530017F20	predicted gene 2447	ncRNA
mm_105250.1	chr11	102353233	102353255	-	1	NA	exon (NM_011403, exon 16 of 20)	exon (NM_011403, exon 16 of 20)	12037	NM_011403	20533	Mm.7248	NM_011403	ENSMUSG00000006574	Slc4a1	Ae1|CD233|Empb3|l11Jus51	solute carrier family 4 (anion exchanger), member 1	protein-coding
mm_60272.1	chr7	43847056	43847078	+	1	NA	exon (NM_026806, exon 3 of 5)	exon (NM_026806, exon 3 of 5)	4798	NM_026806	68668	Mm.458122	NM_026806	ENSMUSG00000074155	Klk5	1110030O19Rik	kallikrein related-peptidase 5	protein-coding
mm_76455.1	chr8	85261078	85261092	-	1	NA	3' UTR (NM_022997, exon 17 of 17)	3' UTR (NM_022997, exon 17 of 17)	30588	NM_146859	258858	Mm.354727	NM_146859	ENSMUSG00000051952	Olfr371	MOR141-3	olfactory receptor 371	protein-coding
mm_109262.1	chr12	109540980	109541006	+	1	NA	promoter-TSS (NR_027652)	promoter-TSS (NR_027652)	-3	NR_027652	17263	Mm.289645	NM_144513	ENSMUSG00000021268	Meg3	2900016C05Rik|3110050O07Rik|6330408G06Rik|AI425946|AW108224|D12Bwg1266e|Gtl2|R74756|R75394	maternally expressed 3	ncRNA
mm_89515.1	chr10	94311897	94311942	+	1	NA	Intergenic	CpG	-13216	NR_033209	215472	Mm.255656	NM_174999	ENSMUSG00000053420	Gm4792	E130012K09|EG215472	predicted gene 4792	ncRNA
mm_127545.1	chr15	102136266	102136271	+	1	NA	promoter-TSS (NM_001033277)	promoter-TSS (NM_001033277)	-53	NM_001033277	223918	Mm.385009	NM_001033277	ENSMUSG00000036966	Spryd3	BC008150	SPRY domain containing 3	protein-coding
mm_116848.1	chr13	54759209	54759218	-	1	NA	3' UTR (NM_033610, exon 6 of 6)	3' UTR (NM_033610, exon 6 of 6)	7227	NM_033610	104069	Mm.200843	NM_033610	ENSMUSG00000034891	Sncb	AI838531|betaSYN	synuclein, beta	protein-coding
mm_99494.1	chr11	102836426	102836458	+	1	NA	5' UTR (NM_080846, exon 1 of 3)	5' UTR (NM_080846, exon 1 of 3)	146	NM_080846	75689	Mm.44408	NM_080846	ENSMUSG00000020928	Higd1b	2310056K19Rik	HIG1 domain family, member 1B	protein-coding
mm_172150.1	chr6	38376747	38376763	+	1	NA	Intergenic	Intergenic	-4769	NM_153600	264134	Mm.253446	NM_153600	ENSMUSG00000056832	Ttc26	9330141E21Rik|9430097H08Rik|hop|hpy	tetratricopeptide repeat domain 26	protein-coding
mm_148923.1	chr19	6980622	6980638	+	1	NA	promoter-TSS (NM_001166368)	promoter-TSS (NM_001166368)	-169	NM_001166368	14227	Mm.4234	NM_008020	ENSMUSG00000056629	Fkbp2	13kDa|FKBP-2|mFKBP13|mFKBP2	FK506 binding protein 2	protein-coding
mm_357.1	chr1	33719904	33719945	+	1	NA	promoter-TSS (NM_008999)	promoter-TSS (NM_008999)	28	NM_008999	19335	Mm.86744	NM_008999	ENSMUSG00000004768	Rab23	AW545388|opb|opb2	RAB23, member RAS oncogene family	protein-coding
mm_2767.1	chr1	130717061	130717080	+	1	NA	promoter-TSS (NM_178691)	promoter-TSS (NM_178691)	-257	NM_178691	226418	Mm.106553	NM_178691	ENSMUSG00000046404	Yod1	6330564D18Rik|9930028C20Rik|Hshin7	YOD1 deubiquitinase	protein-coding
mm_23310.1	chr3	53054014	53054018	+	1	NA	intron (NM_175386, intron 2 of 3)	intron (NM_175386, intron 2 of 3)	12469	NM_175386	108927	Mm.118617	NM_175386	ENSMUSG00000048332	Lhfp	2810489O06Rik|AI194968	lipoma HMGIC fusion partner	protein-coding
mm_92829.1	chr10	81482115	81482150	-	1	NA	intron (NM_001311124, intron 1 of 11)	G-rich|Low_complexity|Low_complexity	577	NM_176954	319586	Mm.152689	NM_176954	ENSMUSG00000034818	Celf5	4930565A21Rik|Brunol5	CUGBP, Elav-like family member 5	protein-coding
mm_100914.1	chr11	6271641	6271654	-	1	NA	3' UTR (NM_134020, exon 5 of 5)	3' UTR (NM_134020, exon 5 of 5)	3190	NM_134020	103694	Mm.254495	NM_134020	ENSMUSG00000004394	Tmed4	1110014L17Rik|AI326346	transmembrane p24 trafficking protein 4	protein-coding
mm_109368.1	chr12	109646116	109646134	+	1	NA	non-coding (NR_028261, exon 11 of 21)	non-coding (NR_028261, exon 11 of 21)	3287	NR_046303	449561		NR_046303		AF357426	MBII-49	snoRNA AF357426	snoRNA
mm_20051.1	chr2	120245158	120245246	-	1	NA	5' UTR (NM_177845, exon 1 of 20)	5' UTR (NM_177845, exon 1 of 20)	133	NM_177845	329502	Mm.330505	NM_177845	ENSMUSG00000050211	Pla2g4e	2310026J01Rik|C230096D22|Pla2epsilon	phospholipase A2, group IVE	protein-coding
mm_101470.1	chr11	30649418	30649445	-	1	NA	promoter-TSS (NM_029344)	promoter-TSS (NM_029344)	-35	NM_029344	75572	Mm.390319	NM_029344	ENSMUSG00000060923	Acyp2	2310004B09Rik	acylphosphatase 2, muscle type	protein-coding
mm_44323.1	chr5	9725306	9725345	-	1	NA	promoter-TSS (NM_181850)	promoter-TSS (NM_181850)	27	NM_181850	108069	Mm.318966	NM_181850	ENSMUSG00000003974	Grm3	0710001G23Rik|Gprc1c|mGlu3|mGluR3	glutamate receptor, metabotropic 3	protein-coding
mm_98207.1	chr11	87797459	87797471	+	1	NA	exon (NM_010824, exon 8 of 14)	exon (NM_010824, exon 8 of 14)	3681	NM_010824	17523	Mm.4668	NM_010824	ENSMUSG00000009350	Mpo	mKIAA4033	myeloperoxidase	protein-coding
mm_2781.1	chr1	130834396	130834416	+	1	NA	5' UTR (NM_011082, exon 2 of 11)	5' UTR (NM_011082, exon 2 of 11)	7722	NM_011082	18703	Mm.276414	NM_011082	ENSMUSG00000026417	Pigr	-	polymeric immunoglobulin receptor	protein-coding
mm_149503.1	chr19	11923941	11923964	+	1	NA	TTS (NR_105960)	TTS (NR_105960)	224	NR_105960	102465601		NR_105960	ENSMUSG00000104979	Mir6994	mmu-mir-6994	microRNA 6994	ncRNA
mm_127291.1	chr15	100075105	100075122	+	1	NA	intron (NM_001159361, intron 1 of 37)	intron (NM_001159361, intron 1 of 37)	36449	NM_001159361	239667	Mm.243658	NM_172819	ENSMUSG00000023026	Dip2b	4932422C22|AI317237|AI854602|mKIAA1463	disco interacting protein 2 homolog B	protein-coding
mm_139407.1	chr17	52468797	52468809	+	1	NA	Intergenic	Intergenic	-133906	NM_001031811	211468	Mm.399068	NM_001031811	ENSMUSG00000035580	Kcnh8	C130090D05Rik|ELK|ELK1|ELK3|Kv12.1	potassium voltage-gated channel, subfamily H (eag-related), member 8	protein-coding
mm_98182.1	chr11	87764703	87764732	+	1	NA	intron (NM_172449, intron 5 of 31)	CpG-2413	4176	NM_172449	207777	Mm.342019	NM_172449	ENSMUSG00000034156	Bzrap1	D230016K05|PRAX-1|Tspoap1|mKIAA0612	benzodiazepine receptor associated protein 1	protein-coding
mm_680.1	chr1	40500010	40500025	+	1	NA	3' UTR (NM_008365, exon 11 of 11)	3' UTR (NM_008365, exon 11 of 11)	-15345	NM_010553	16174	Mm.20466	NM_010553	ENSMUSG00000026068	Il18rap	AcPL|IL-18R-beta|IL-18RAcP|IL-18Rbeta|IL-1RAcPL	interleukin 18 receptor accessory protein	protein-coding
mm_34953.1	chr4	155962542	155962576	+	1	NA	5' UTR (NM_026125, exon 1 of 8)	5' UTR (NM_026125, exon 1 of 8)	247	NM_026125	67389	Mm.29140	NM_026125	ENSMUSG00000023571	Fam132a	1110035L05Rik|C1qdc2|CTRP12|alipolin	family with sequence similarity 132, member A	protein-coding
mm_157321.1	chrX	21745107	21745114	-	1	NA	Intergenic	Intergenic	30210	NM_020049	56774	Mm.253984	NM_020049	ENSMUSG00000031089	Slc6a14	1110007A17Rik|9030613J17Rik|ATB0plus|CATB0plus	solute carrier family 6 (neurotransmitter transporter), member 14	protein-coding
mm_32235.1	chr4	102255035	102255057	+	1	NA	5' UTR (NM_001177983, exon 1 of 6)	5' UTR (NM_001177983, exon 1 of 6)	107	NM_019840	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_62103.1	chr7	96213393	96213401	+	1	NA	intron (NM_001310760, intron 1 of 32)	AT_rich|Low_complexity|Low_complexity	1726	NM_001310760	23966	Mm.254610	NM_011858	ENSMUSG00000048078	Tenm4	Doc4|ELM2|Odz4|R75022|Ten-m4|l(7)-3Rn|l7Rn3|mKIAA1302	teneurin transmembrane protein 4	protein-coding
mm_29910.1	chr3	131474580	131474596	-	1	NA	Intergenic	Intergenic	-90180	NM_001289479	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_167974.1	chrX	157414827	157414871	-	1	NA	5' UTR (NM_011077, exon 1 of 22)	5' UTR (NM_011077, exon 1 of 22)	437	NM_011077	18675	Mm.2529	NM_011077	ENSMUSG00000057457	Phex	Gy|HPDR|HPDR1|Hyp|PEX	phosphate regulating endopeptidase homolog, X-linked	protein-coding
mm_40346.1	chr5	45524063	45524069	+	1	NA	intron (NM_025895, intron 3 of 3)	intron (NM_025895, intron 3 of 3)	3837	NM_025895	66999	Mm.283045	NM_025895	ENSMUSG00000015804	Med28	1500003D12Rik|AI451633|AU045690|Eg1|FKSG20|magicin	mediator complex subunit 28	protein-coding
mm_114427.1	chr13	64510265	64510277	+	1	NA	Intergenic	Intergenic	-12479	NM_001195435	68880	Mm.390594	NM_001195435	ENSMUSG00000096537	1190003K10Rik	-	RIKEN cDNA 1190003K10 gene	protein-coding
mm_138118.1	chr17	34143342	34143375	+	1	NA	Intergenic	Intergenic	-2058	NM_010388	15000	Mm.195060	NM_010388	ENSMUSG00000037548	H2-DMb2	H-2Mb2|H2-Mb2	histocompatibility 2, class II, locus Mb2	protein-coding
mm_85999.1	chr9	112229986	112229996	-	1	NA	intron (NM_001177619, intron 1 of 10)	intron (NM_001177619, intron 1 of 10)	2510	NM_001177616	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_93244.1	chr10	95416781	95416834	-	1	NA	promoter-TSS (NM_007706)	promoter-TSS (NM_007706)	50	NM_007706	216233	Mm.474283	NM_007706	ENSMUSG00000020027	Socs2	8030460M17|AI527257|AW108012|CIS2|Cish2|D130043N08Rik|JAB|SOCS-2|SSI-2|hg	suppressor of cytokine signaling 2	protein-coding
mm_70642.1	chr8	14090471	14090501	+	1	NA	promoter-TSS (NM_001034862)	promoter-TSS (NM_001034862)	-159	NM_001034862	234086	Mm.268896	NM_001034862	ENSMUSG00000051978	Erich1	-	glutamate rich 1	protein-coding
mm_60835.1	chr7	45718059	45718111	+	1	NA	promoter-TSS (NM_001172561)	promoter-TSS (NM_001172561)	14	NM_009077	19899	Mm.3459	NM_009077	ENSMUSG00000059070	Rpl18	L18|Rpl18a	ribosomal protein L18	protein-coding
mm_158801.1	chrX	167252555	167252566	-	1	NA	intron (NM_001313761, intron 1 of 2)	B4A|SINE|B4	11769	NM_001313761	170744	Mm.196676	NM_133212	ENSMUSG00000040522	Tlr8	-	toll-like receptor 8	protein-coding
mm_152668.1	chr19	14597734	14597749	-	1	NA	promoter-TSS (NM_001302951)	promoter-TSS (NM_001302951)	442	NM_001302950	21888	Mm.103638	NM_011600	ENSMUSG00000024642	Tle4	5730411M05Rik|AA792082|Bce-1|Bce1|ESTM13|ESTM14|Grg4|X83332|X83333|grg-4	transducin-like enhancer of split 4	protein-coding
mm_45986.1	chr5	90492722	90492739	-	1	NA	exon (NM_007423, exon 3 of 15)	exon (NM_007423, exon 3 of 15)	2016	NM_007423	11576	Mm.358570	NM_007423	ENSMUSG00000054932	Afp	-	alpha fetoprotein	protein-coding
mm_39181.1	chr4	155785023	155785039	-	1	NA	intron (NM_001033394, intron 1 of 1)	intron (NM_001033394, intron 1 of 1)	843	NM_001033394	320587	Mm.384382	NM_001033394	ENSMUSG00000073680	Tmem88b	A230069A22Rik	transmembrane protein 88B	protein-coding
mm_40563.1	chr5	61968539	61968542	+	1	NA	Intergenic	Intergenic	159697	NM_019468	14380	Mm.347430	NM_019468	ENSMUSG00000089992	G6pd2	G6pdx-ps1|Gpd-2|Gpd2	glucose-6-phosphate dehydrogenase 2	protein-coding
mm_130259.1	chr15	96642758	96642778	-	1	NA	promoter-TSS (NM_001166456)	promoter-TSS (NM_001166456)	145	NM_001166458	105727	Mm.103568	NM_134086	ENSMUSG00000023169	Slc38a1	AA408026|AA409865|AL022800|AU015942|NAT2	solute carrier family 38, member 1	protein-coding
mm_102224.1	chr11	54909994	54910008	-	1	NA	TTS (NM_021327)	TTS (NM_021327)	7147	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_154384.1	chrM	11426	11457	+	1	NA	NA	Intergenic	NA	NA								
mm_142493.1	chr17	46018253	46018272	-	1	NA	3' UTR (NM_001025250, exon 8 of 8)	3' UTR (NM_001025250, exon 8 of 8)	6901	NM_001110267	22339	Mm.282184	NM_009505	ENSMUSG00000023951	Vegfa	Vegf|Vpf	vascular endothelial growth factor A	protein-coding
mm_147770.1	chr18	61400364	61400449	-	1	NA	promoter-TSS (NM_133249)	promoter-TSS (NM_133249)	25	NM_133249	170826	Mm.415302	NM_133249	ENSMUSG00000033871	Ppargc1b	4631412G21Rik|Perc	peroxisome proliferative activated receptor, gamma, coactivator 1 beta	protein-coding
mm_105524.1	chr11	106300474	106300478	-	1	NA	exon (NM_008117, exon 5 of 5)	exon (NM_008117, exon 5 of 5)	1420	NM_008117	14599	Mm.343934	NM_008117	ENSMUSG00000020713	Gh	Gh1|Ghb1	growth hormone	protein-coding
mm_73524.1	chr8	107545033	107545046	+	1	NA	intron (NM_025830, intron 10 of 23)	intron (NM_025830, intron 10 of 23)	-6205	NR_029553	387158		NR_029553	ENSMUSG00000065439	Mir140	Mirn140|mir-140|mmu-mir-140	microRNA 140	ncRNA
mm_70578.1	chr8	13167126	13167177	+	1	NA	intron (NM_001317353, intron 2 of 8)	intron (NM_001317353, intron 2 of 8)	7990	NM_010684	16783	Mm.16716	NM_010684	ENSMUSG00000031447	Lamp1	CD107a|LGP-120|LGP-A|Lamp-1|P2B	lysosomal-associated membrane protein 1	protein-coding
mm_55546.1	chr6	71144341	71144356	-	1	NA	promoter-TSS (NM_001033929)	promoter-TSS (NM_001033929)	32	NM_001033929	232078	Mm.37547	NM_178413	ENSMUSG00000054474	Thnsl2	BC051244|TSH2	threonine synthase-like 2 (bacterial)	protein-coding
mm_164294.1	chr15	103895975	103895978	-	1	NA	3' UTR (NM_009267, exon 4 of 4)	3' UTR (NM_009267, exon 4 of 4)	3324	NM_009268	20771	Mm.30276	NM_009268		Mucl1	Spt-2|Spt2	mucin-like 1	protein-coding
mm_51038.1	chr6	65596591	65596606	+	1	NA	intron (NM_001001495, intron 3 of 7)	intron (NM_001001495, intron 3 of 7)	6200	NM_001001495	414084	Mm.117558	NM_001001495	ENSMUSG00000044162	Tnip3	9030611K07Rik|ABIN-3|LIND	TNFAIP3 interacting protein 3	protein-coding
mm_92271.1	chr10	71159717	71159734	-	1	NA	promoter-TSS (NM_001347189)	promoter-TSS (NM_001347189)	-35	NM_001347189	83675	Mm.286834	NM_031397	ENSMUSG00000014329	Bicc1	Bic-C|bpk|jcpk	BicC family RNA binding protein 1	protein-coding
mm_139617.1	chr17	57362429	57362445	+	1	NA	intron (NM_010130, intron 2 of 21)	RLTR22_Mur|LTR|ERVK	3751	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_95109.1	chr11	34071100	34071138	+	1	NA	exon (NM_010696, exon 7 of 21)	exon (NM_010696, exon 7 of 21)	23918	NM_010696	16822	Mm.265350	NM_010696	ENSMUSG00000002699	Lcp2	AI323664|BB161688|SLP-76|SLP76|m1Khoe|twm	lymphocyte cytosolic protein 2	protein-coding
mm_145318.1	chr18	54454462	54454466	+	1	NA	Intergenic	Intergenic	32169	NR_040338	77433	Mm.159919	NR_040338		Redrum	9430076G02Rik	Redrum, erythroid developmental long intergenic non-protein coding transcript	ncRNA
mm_153241.1	chr19	36119250	36119262	-	1	NA	exon (NM_013468, exon 2 of 9)	exon (NM_013468, exon 2 of 9)	588	NM_013468	107765	Mm.10279	NM_013468	ENSMUSG00000024803	Ankrd1	Alrp|CARP|Crap|MARP1	ankyrin repeat domain 1 (cardiac muscle)	protein-coding
mm_76080.1	chr8	79294929	79294961	-	1	NA	promoter-TSS (NM_133823)	promoter-TSS (NM_133823)	11	NM_133823	109136	Mm.26510	NM_133823	ENSMUSG00000037022	Mmaa	2810018E08Rik|AI840684	methylmalonic aciduria (cobalamin deficiency) type A	protein-coding
mm_92748.1	chr10	81001339	81001370	-	1	NA	promoter-TSS (NM_001038655)	promoter-TSS (NM_001038655)	11	NM_001038655	14708	Mm.222496	NM_010319	ENSMUSG00000048240	Gng7	AI840417	guanine nucleotide binding protein (G protein), gamma 7	protein-coding
mm_19160.1	chr2	83724330	83724372	-	1	NA	promoter-TSS (NM_008402)	promoter-TSS (NM_008402)	-46	NM_008402	16410	Mm.227	NM_008402	ENSMUSG00000027087	Itgav	1110004F14Rik|2610028E01Rik|CD51|D430040G12Rik	integrin alpha V	protein-coding
mm_166372.1	chr5	125766434	125766447	-	1	NA	intron (NM_001190352, intron 5 of 8)	intron (NM_001190352, intron 5 of 8)	234022	NM_001190352	208151	Mm.40397	NM_001190352	ENSMUSG00000070498	Tmem132b	AK220418|mKIAA1786	transmembrane protein 132B	protein-coding
mm_38077.1	chr4	134128000	134128023	-	1	NA	exon (NM_080559, exon 2 of 3)	exon (NM_080559, exon 2 of 3)	742	NM_080559	73723	Mm.22240	NM_080559	ENSMUSG00000028843	Sh3bgrl3	1110004L05Rik|AU022188	SH3 domain binding glutamic acid-rich protein-like 3	protein-coding
mm_112387.1	chr12	119238220	119238228	-	1	NA	promoter-TSS (NM_177290)	promoter-TSS (NM_177290)	52	NM_177290	320910	Mm.217000	NM_177290	ENSMUSG00000025321	Itgb8	4832412O06Rik	integrin beta 8	protein-coding
mm_73114.1	chr8	94749847	94749853	+	1	NA	exon (NM_009137, exon 3 of 3)	exon (NM_009137, exon 3 of 3)	4166	NM_009137	20299	Mm.12895	NM_009137	ENSMUSG00000031779	Ccl22	ABCD-1|DCBCK|MDC|Scya22	chemokine (C-C motif) ligand 22	protein-coding
mm_6157.1	chr1	65030331	65030333	-	1	NA	intron (NM_001310617, intron 1 of 8)	intron (NM_001310617, intron 1 of 8)	2427	NM_027582	70861	Mm.18725	NM_027582	ENSMUSG00000025955	Akr1cl	4921521F21Rik|AI451536|AI503553	aldo-keto reductase family 1, member C-like	protein-coding
mm_45385.1	chr5	66142457	66142463	-	1	NA	intron (NM_001127382, intron 2 of 7)	intron (NM_001127382, intron 2 of 7)	8518	NM_001291226	245945	Mm.36863	NM_139065	ENSMUSG00000070780	Rbm47	9530077J19Rik	RNA binding motif protein 47	protein-coding
mm_114249.1	chr13	56633249	56633256	+	1	NA	intron (NM_009369, intron 12 of 16)	intron (NM_009369, intron 12 of 16)	23649	NM_009369	21810	Mm.14455	NM_009369	ENSMUSG00000035493	Tgfbi	68kDa|AI181842|AI747162|Beta-ig|big-h3	transforming growth factor, beta induced	protein-coding
mm_151459.1	chr19	58396194	58396201	+	1	NA	intron (NR_104342, intron 4 of 11)	intron (NR_104342, intron 4 of 11)	59201	NM_001285457	14585	Mm.88367	NM_010279	ENSMUSG00000025089	Gfra1	AU042498	glial cell line derived neurotrophic factor family receptor alpha 1	protein-coding
mm_70587.1	chr8	13171333	13171341	+	1	NA	exon (NM_010684, exon 5 of 9)	exon (NM_010684, exon 5 of 9)	12176	NM_010684	16783	Mm.16716	NM_010684	ENSMUSG00000031447	Lamp1	CD107a|LGP-120|LGP-A|Lamp-1|P2B	lysosomal-associated membrane protein 1	protein-coding
mm_161809.1	chr17	63877983	63877983	+	1	NA	promoter-TSS (NM_001286415)	promoter-TSS (NM_001286415)	-83	NM_001286415	14158	Mm.23039	NM_008000	ENSMUSG00000000127	Fer	AV082135|C330004K01Rik|Fert|Fert2	fer (fms/fps related) protein kinase	protein-coding
mm_153481.1	chr19	41276891	41276915	-	1	NA	intron (NM_031376, intron 16 of 16)	intron (NM_031376, intron 16 of 16)	-12899	NM_133352	107358	Mm.246440	NM_133352	ENSMUSG00000025016	Tm9sf3	1810073M23Rik|2810031D16Rik|AI115521|AI413748|AW146116|AW549777|Smbp|mKIAA4036	transmembrane 9 superfamily member 3	protein-coding
mm_95465.1	chr11	50602008	50602067	+	1	NA	promoter-TSS (NM_175643)	promoter-TSS (NM_175643)	-48	NM_175643	216725	Mm.110597	NM_175643	ENSMUSG00000036545	Adamts2	ADAM-TS 2|ADAM-TS2|ADAMTS-2|PC I-NP|PCINP|pNPI	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 2	protein-coding
mm_54670.1	chr6	39207332	39207366	-	1	NA	promoter-TSS (NM_001033430)	promoter-TSS (NM_001033430)	-576	NM_001033430	338523	Mm.293175	NM_001033430	ENSMUSG00000042599	Kdm7a	A630082K20Rik|BB041802|ENSMUSG00000073143|Jhdm1d|mKIAA1718	lysine (K)-specific demethylase 7A	protein-coding
mm_75337.1	chr8	43305921	43305926	-	1	NA	intron (NM_009556, intron 1 of 3)	intron (NM_009556, intron 1 of 3)	1086	NM_009556	22702	Mm.285848	NM_009556	ENSMUSG00000051176	Zfp42	Rex-1|Rex1|Zfp-42	zinc finger protein 42	protein-coding
mm_137948.1	chr17	32878064	32878088	+	1	NA	Intergenic	Intergenic	13527	NM_207245	240066	Mm.26636	NM_207245	ENSMUSG00000095325	Zfp870	AI173952	zinc finger protein 870	protein-coding
mm_129716.1	chr15	81871884	81871916	-	1	NA	promoter-TSS (NM_080633)	promoter-TSS (NM_080633)	-8	NM_026737	68479	Mm.271715	NM_026737	ENSMUSG00000061360	Phf5a	1110007B08Rik	PHD finger protein 5A	protein-coding
mm_57895.1	chr6	131376036	131376055	-	1	NA	exon (NM_139117, exon 6 of 10)	exon (NM_139117, exon 6 of 10)	12405	NM_139117	56449	Mm.458000	NM_011733	ENSMUSG00000030189	Ybx3	Csda|Dpba|MSY3|MSY4|Yb2|dbpA|oxyR	Y box protein 3	protein-coding
mm_66966.1	chr7	62464553	62464573	-	1	NA	promoter-TSS (NM_013788)	promoter-TSS (NM_013788)	-53	NM_013788	27412	Mm.422745	NM_013788	ENSMUSG00000070526	Peg12	Frat3	paternally expressed 12	protein-coding
mm_91885.1	chr10	59899623	59899640	-	1	NA	Intergenic	Intergenic	20040	NM_019965	56709	Mm.103610	NM_019965	ENSMUSG00000020109	Dnajb12	Dj10|mDj10	DnaJ heat shock protein family (Hsp40) member B12	protein-coding
mm_135456.1	chr16	45724601	45724619	-	1	NA	promoter-TSS (NM_019754)	promoter-TSS (NM_019754)	-79	NM_019754	56370	Mm.24183	NM_019754	ENSMUSG00000022658	Tagln3	2700038H05Rik|2900005O10Rik|AI426007|Np25	transgelin 3	protein-coding
mm_32044.1	chr4	95967406	95967426	+	1	NA	promoter-TSS (NR_045777)	promoter-TSS (NR_045777)	37	NM_030014	77963	Mm.49994	NM_030014	ENSMUSG00000028572	Hook1	A930033L17Rik|azh	hook microtubule tethering protein 1	protein-coding
mm_16949.1	chr2	17185479	17185492	-	1	NA	Intergenic	Intergenic	-171759	NR_040632	75069	Mm.50378	NR_040632		4930515L03Rik	-	RIKEN cDNA 4930515L03 gene	ncRNA
mm_66244.1	chr7	35555426	35555513	-	1	NA	exon (NM_033080, exon 1 of 3)	exon (NM_033080, exon 1 of 3)	459	NM_033080	110959	Mm.410206	NM_033080	ENSMUSG00000034875	Nudt19	D7Rp2|D7Rp2-r|D7Rp2-s|D7Rp2e|RP2-r|RP2-s	nudix (nucleoside diphosphate linked moiety X)-type motif 19	protein-coding
mm_67328.1	chr7	79732867	79732882	-	1	NA	promoter-TSS (NM_175640)	promoter-TSS (NM_175640)	-98	NM_001113471	103968	Mm.254917	NM_175640	ENSMUSG00000030546	Plin1	6030432J05Rik|Peri|Plin	perilipin 1	protein-coding
mm_81783.1	chr9	114722311	114722315	+	1	NA	intron (NM_146229, intron 12 of 12)	intron (NM_146229, intron 12 of 12)	-8890	NM_026036	67213	Mm.28858	NM_026036	ENSMUSG00000032434	Cmtm6	2810051A14Rik|AA536733|Cklfsf6	CKLF-like MARVEL transmembrane domain containing 6	protein-coding
mm_165869.1	chr4	38256535	38256535	+	1	NA	Intergenic	Intergenic	-1193758	NM_001081095	75471	Mm.23522	NM_001081095	ENSMUSG00000028287	1700009N14Rik	AI429145	RIKEN cDNA 1700009N14 gene	protein-coding
mm_124011.1	chr14	76110761	76110818	-	1	NA	promoter-TSS (NM_013745)	promoter-TSS (NM_013745)	26	NM_026177	67467	Mm.260767	NM_026177	ENSMUSG00000022008	Gpalpp1	1200011I18Rik|Kiaa1704	GPALPP motifs containing 1	protein-coding
mm_40950.1	chr5	76855051	76855061	+	1	NA	exon (NM_001163793, exon 5 of 9)	exon (NM_001163793, exon 5 of 9)	14457	NM_001163793	320827	Mm.101504	NM_001163793	ENSMUSG00000036377	C530008M17Rik	2810489J07Rik|4930529A19Rik|4931405B09Rik|Kiaa1211|mKIAA1211	RIKEN cDNA C530008M17 gene	protein-coding
mm_67132.1	chr7	71719218	71719221	-	1	NA	Intergenic	RMER19B|LTR|ERVK	-190476	NR_130995	78156	Mm.243818	NR_130995	ENSMUSG00000108669	4930441H08Rik	-	RIKEN cDNA 4930441H08 gene	ncRNA
mm_97691.1	chr11	80154084	80154090	+	1	NA	promoter-TSS (NM_172133)	promoter-TSS (NM_172133)	-75	NM_172133	216991	Mm.341520	NM_172133	ENSMUSG00000020709	Adap2	Centa2	ArfGAP with dual PH domains 2	protein-coding
mm_35098.1	chr4	8912861	8912892	-	1	NA	Intergenic	Intergenic	222470	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_108684.1	chr12	86832754	86832780	+	1	NA	Intergenic	Intergenic	52047	NM_145836	238330	Mm.248358	NM_145836	ENSMUSG00000034168	Irf2bpl	6430527G18Rik|Eap1	interferon regulatory factor 2 binding protein-like	protein-coding
mm_106857.1	chr12	8009217	8009229	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	31546	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_47849.1	chr5	134456703	134456785	-	1	NA	promoter-TSS (NM_001081464)	promoter-TSS (NM_001081464)	-28	NM_001081464	57080	Mm.332735	NM_020331	ENSMUSG00000023079	Gtf2ird1	1700012P16Rik|BEN|Cream1|ESTM9|GTF3|Gtf2il|MusTRD1|Tg(Alb1-Myc)166.8Sst|WBSCR11|X83320	general transcription factor II I repeat domain-containing 1	protein-coding
mm_144812.1	chr18	36287899	36287910	+	1	NA	exon (NM_008989, exon 2 of 2)	exon (NM_008989, exon 2 of 2)	6742	NM_008989	19290	Mm.231802	NM_008989	ENSMUSG00000043991	Pura	CAGER-1|Pur-alpha|ssCRE-BP	purine rich element binding protein A	protein-coding
mm_16363.1	chr2	174614159	174614218	+	1	NA	Intergenic	Intergenic	-29346	NM_001099328	100043757	Mm.48711	NM_001099328	ENSMUSG00000050600	Zfp831	ENSMUSG00000050600|OTTMUSG00000017459	zinc finger protein 831	protein-coding
mm_61056.1	chr7	49910316	49910337	+	1	NA	promoter-TSS (NM_001146013)	promoter-TSS (NM_001146013)	27	NM_001146013	104245	Mm.207053	NM_148931	ENSMUSG00000039728	Slc6a5	Glyt2|prestin	solute carrier family 6 (neurotransmitter transporter, glycine), member 5	protein-coding
mm_62102.1	chr7	96211928	96211938	+	1	NA	5' UTR (NM_001310760, exon 1 of 33)	5' UTR (NM_001310760, exon 1 of 33)	262	NM_001310760	23966	Mm.254610	NM_011858	ENSMUSG00000048078	Tenm4	Doc4|ELM2|Odz4|R75022|Ten-m4|l(7)-3Rn|l7Rn3|mKIAA1302	teneurin transmembrane protein 4	protein-coding
mm_36683.1	chr4	96553471	96553549	-	1	NA	5' UTR (NM_010008, exon 1 of 9)	5' UTR (NM_010008, exon 1 of 9)	141	NM_010008	13110	Mm.98200	NM_010008	ENSMUSG00000052914	Cyp2j6	-	cytochrome P450, family 2, subfamily j, polypeptide 6	protein-coding
mm_115288.1	chr13	111937090	111937095	+	1	NA	Intergenic	(T)n|Simple_repeat|Simple_repeat	69156	NR_130345	102636620	Mm.402328	NR_130345	ENSMUSG00000086111	Gm15326	OTTMUSG00000020187	predicted gene 15326	ncRNA
mm_95042.1	chr11	32277565	32277584	+	1	NA	exon (NM_010405, exon 2 of 3)	exon (NM_010405, exon 2 of 3)	974	NM_010405	15126	Mm.141758	NM_010405	ENSMUSG00000055609	Hba-x	AI450015|Hbz	hemoglobin X, alpha-like embryonic chain in Hba complex	protein-coding
mm_54959.1	chr6	48708130	48708159	-	1	NA	promoter-TSS (NM_153175)	promoter-TSS (NM_153175)	100	NM_153175	231931	Mm.321047	NM_153175	ENSMUSG00000047867	Gimap6	4833419H03Rik|Ian6|mFLJ00102	GTPase, IMAP family member 6	protein-coding
mm_77116.1	chr8	111247288	111247291	-	1	NA	intron (NM_009149, intron 1 of 25)	intron (NM_009149, intron 1 of 25)	11913	NM_009149	20340	Mm.276271	NM_009149	ENSMUSG00000003316	Glg1	AI593353|AW537898|CFR|CFR-1|ESL-1|MG-160|MG160|Selel	golgi apparatus protein 1	protein-coding
mm_65511.1	chr7	25754707	25754750	-	1	NA	promoter-TSS (NM_178089)	promoter-TSS (NM_178089)	-8	NM_144922	232989	Mm.254223	NM_144922	ENSMUSG00000040725	Hnrnpul1	E130317O14Rik|E1B-AP5|E1BAP5|Hnrnpul|Hnrpul1	heterogeneous nuclear ribonucleoprotein U-like 1	protein-coding
mm_60500.1	chr7	44478948	44478970	+	1	NA	Intergenic	L1M4c|LINE|L1	-5558	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_14967.1	chr2	152081869	152081893	+	1	NA	5' UTR (NM_001160410, exon 1 of 2)	5' UTR (NM_001160410, exon 1 of 2)	352	NM_001160410	545474	Mm.214317	NM_001160410	ENSMUSG00000060257	Scrt2	AW060659	scratch family zinc finger 2	protein-coding
mm_127149.1	chr15	98567289	98567328	+	1	NA	promoter-TSS (NR_028442)	promoter-TSS (NR_028442)	-16	NR_028442	100048895	Mm.471074	NR_028442		9330020H09Rik	ENSMUSG00000075426	RIKEN cDNA 9330020H09 gene	ncRNA
mm_130493.1	chr15	98807891	98807908	-	1	NA	promoter-TSS (NM_001013741)	promoter-TSS (NM_001013741)	26	NM_001013741	13199	Mm.390810	NM_001013741	ENSMUSG00000059213	Ddn	Gm748	dendrin	protein-coding
mm_16829.1	chr2	11492095	11492108	-	1	NA	intron (NM_001177756, intron 3 of 16)	B4|SINE|B4	9989	NM_001177754	170768	Mm.19669	NM_133232	ENSMUSG00000026773	Pfkfb3	E330010H22Rik|iPFK-2|uPFK-2	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	protein-coding
mm_158091.1	chrX	101419777	101419787	-	1	NA	5' UTR (NM_001177986, exon 1 of 7)	5' UTR (NM_001177986, exon 1 of 7)	132	NM_001177986	56364	Mm.23458	NM_019831	ENSMUSG00000031310	Zmym3	9030216B10Rik|AW122925|DXS6673El|Zfp261	zinc finger, MYM-type 3	protein-coding
mm_103905.1	chr11	83578468	83578477	-	1	NA	5' UTR (NM_011338, exon 1 of 4)	5' UTR (NM_011338, exon 1 of 4)	164	NM_011338	20308	Mm.416125	NM_011338	ENSMUSG00000019122	Ccl9	CCF18|MRP-2|Scya10|Scya9	chemokine (C-C motif) ligand 9	protein-coding
mm_26590.1	chr3	151386393	151386401	+	1	NA	Intergenic	Intergenic	-51485	NM_133222	170757	Mm.317261	NM_133222	ENSMUSG00000039167	Adgrl4	1110033N21Rik|ETL1|Eltd1|Etl	adhesion G protein-coupled receptor L4	protein-coding
mm_69640.1	chr7	138846203	138846293	-	1	NA	promoter-TSS (NM_026391)	promoter-TSS (NM_026391)	19	NM_001045483	69546	Mm.31598	NM_027115	ENSMUSG00000041775	Mapk1ip1	2310009E07Rik|AU043776|MISS	mitogen-activated protein kinase 1 interacting protein 1	protein-coding
mm_149166.1	chr19	9023510	9023520	+	1	NA	intron (NR_104460, intron 4 of 6)	intron (NR_104460, intron 4 of 6)	5611	NR_105786	102465190		NR_105786	ENSMUSG00000099308	Mir6367	Gm27467|mmu-mir-6367	microRNA 6367	ncRNA
mm_10683.1	chr2	22589032	22589043	+	1	NA	Intergenic	Intergenic	-33290	NM_008078	14417	Mm.4784	NM_008078	ENSMUSG00000026787	Gad2	6330404F12Rik|GAD(65)|GAD65|Gad-2	glutamic acid decarboxylase 2	protein-coding
mm_62950.1	chr7	119596115	119596121	+	1	NA	3' UTR (NM_146197, exon 14 of 14)	3' UTR (NM_146197, exon 14 of 14)	-21710	NM_054094	117147	Mm.427560	NM_054094	ENSMUSG00000033533	Acsm1	Acas3|Bucs1|Macs	acyl-CoA synthetase medium-chain family member 1	protein-coding
mm_19908.1	chr2	114175322	114175344	-	1	NA	promoter-TSS (NM_009702)	promoter-TSS (NM_009702)	6	NM_009702	11834	Mm.2545	NM_009702	ENSMUSG00000040383	Aqr	AW495846|mKIAA0560	aquarius	protein-coding
mm_40969.1	chr5	77001451	77001461	+	1	NA	Intergenic	Intergenic	-2599	NM_206935	384185	Mm.451858	NM_206935	ENSMUSG00000063820	Arl9	1700110A09Rik	ADP-ribosylation factor-like 9	protein-coding
mm_49561.1	chr6	30568368	30568382	+	1	NA	promoter-TSS (NM_027926)	promoter-TSS (NM_027926)	6	NM_027926	71791	Mm.105759	NM_027926	ENSMUSG00000039070	Cpa4	1110019K20Rik|AV009555	carboxypeptidase A4	protein-coding
mm_33470.1	chr4	130816874	130816911	+	1	NA	exon (NM_011520, exon 2 of 5)	exon (NM_011520, exon 2 of 5)	24355	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_169176.1	chr13	65703811	65703814	-	1	NA	Intergenic	Intergenic	-409641	NM_001177832	628709	Mm.390595	NM_001177832	ENSMUSG00000095909	Gm10324	ENSMUSG00000071302	predicted gene 10324	protein-coding
mm_61840.1	chr7	88290452	88290461	+	1	NA	3' UTR (NM_001311790, exon 4 of 4)	3' UTR (NM_001311790, exon 4 of 4)	12371	NM_001311790	13032	Mm.89295	NM_009982	ENSMUSG00000030560	Ctsc	AI047818|CatC|DPP1|DPPI	cathepsin C	protein-coding
mm_146987.1	chr18	34006922	34006989	-	1	NA	5' UTR (NM_013512, exon 1 of 24)	5' UTR (NM_013512, exon 1 of 24)	251	NM_013512	13824	Mm.3465	NM_013512	ENSMUSG00000024376	Epb41l4a	Epb4.1l4|Epb4.1l4a|NBL4	erythrocyte membrane protein band 4.1 like 4a	protein-coding
mm_157862.1	chrX	75126963	75126971	-	1	NA	intron (NM_008621, intron 1 of 11)	intron (NM_008621, intron 1 of 11)	4049	NM_008621	17524	Mm.391267	NM_008621	ENSMUSG00000031402	Mpp1	55kDa|C130070C03Rik|p55	membrane protein, palmitoylated	protein-coding
mm_58666.1	chr7	6977074	6977108	+	1	NA	promoter-TSS (NR_036631)	promoter-TSS (NR_036631)	-429	NR_036631	116811	Mm.381671	NR_036631	ENSMUSG00000108043	Zim3	1700128I23Rik	zinc finger, imprinted 3	ncRNA
mm_97608.1	chr11	78950073	78950096	+	1	NA	exon (NM_010927, exon 20 of 27)	exon (NM_010927, exon 20 of 27)	24793	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_147360.1	chr18	43393139	43393150	-	1	NA	5' UTR (NM_009468, exon 1 of 14)	5' UTR (NM_009468, exon 1 of 14)	233	NM_009468	22240	Mm.8180	NM_009468	ENSMUSG00000024501	Dpysl3	CRMP-4|DRP-3|TUC4|ULIP-1|Ulip|Ulip1	dihydropyrimidinase-like 3	protein-coding
mm_124565.1	chr14	123627156	123627175	-	1	NA	promoter-TSS (NM_177393)	promoter-TSS (NM_177393)	-21	NM_177393	338370	Mm.255348	NM_177393	ENSMUSG00000000197	Nalcn	A530023G15Rik|AI849508|Vgcnl1	sodium leak channel, non-selective	protein-coding
mm_164686.1	chr17	47581143	47581144	+	1	NA	intron (NM_001081635, intron 2 of 6)	intron (NM_001081635, intron 2 of 6)	-12324	NM_007632	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_140509.1	chr17	5492498	5492517	-	1	NA	promoter-TSS (NM_146073)	promoter-TSS (NM_146073)	-93	NM_146073	224454	Mm.487663	NM_146073	ENSMUSG00000034265	Zdhhc14	B530001K09Rik|New1cp	zinc finger, DHHC domain containing 14	protein-coding
mm_17708.1	chr2	32385499	32385511	-	1	NA	exon (NM_008491, exon 5 of 6)	exon (NM_008491, exon 5 of 6)	2234	NM_008491	16819	Mm.9537	NM_008491	ENSMUSG00000026822	Lcn2	24p3|AW212229|NRL|Sip24	lipocalin 2	protein-coding
mm_88420.1	chr10	77197554	77197559	+	1	NA	Intergenic	Intergenic	-31026	NM_009929	12822	Mm.4352	NM_009929	ENSMUSG00000001435	Col18a1	-	collagen, type XVIII, alpha 1	protein-coding
mm_92683.1	chr10	80622522	80622526	-	1	NA	promoter-TSS (NM_134002)	promoter-TSS (NM_134002)	-256	NM_134002	103236	Mm.29873	NM_134002	ENSMUSG00000003345	Csnk1g2	2810429I12Rik|AI463719	casein kinase 1, gamma 2	protein-coding
mm_87460.1	chr10	51484774	51484801	+	1	NA	intron (NM_001291892, intron 7 of 8)	intron (NM_001291892, intron 7 of 8)	4175	NM_001291892	14727	Mm.439661	NM_008147	ENSMUSG00000062593	Lilr4b	Gp49a|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4B	protein-coding
mm_121104.1	chr14	100285178	100285192	+	1	NA	Intergenic	Intergenic	-135389	NM_010636	16597	Mm.396499	NM_010636	ENSMUSG00000072294	Klf12	2700063E05Rik|AI225908|AI315654|AP-2rep|B130052C06Rik|D530033K05Rik	Kruppel-like factor 12	protein-coding
mm_89197.1	chr10	86348078	86348091	+	1	NA	3' UTR (NM_011595, exon 5 of 5)	3' UTR (NM_011595, exon 5 of 5)	47672	NM_011595	21859	Mm.4871	NM_011595	ENSMUSG00000020044	Timp3	Timp-3	tissue inhibitor of metalloproteinase 3	protein-coding
mm_11723.1	chr2	36253316	36253338	+	1	NA	Intergenic	Intergenic	22901	NM_008969	19224	Mm.275434	NM_008969	ENSMUSG00000047250	Ptgs1	COX1|Cox-1|Cox-3|PGHS-1|PHS 1|Pghs1	prostaglandin-endoperoxide synthase 1	protein-coding
mm_72735.1	chr8	85084389	85084412	+	1	NA	intron (NM_010764, intron 1 of 23)	intron (NM_010764, intron 1 of 23)	1131	NM_010764	17159	Mm.4219	NM_010764	ENSMUSG00000005142	Man2b1	AW107687|LAMAN	mannosidase 2, alpha B1	protein-coding
mm_171731.1	chr4	93265578	93265581	-	1	NA	Intergenic	Intergenic	69932	NM_026954	69136	Mm.171558	NM_026954	ENSMUSG00000054000	Tusc1	2200001D17Rik|TSG-9	tumor suppressor candidate 1	protein-coding
mm_163210.1	chr11	99730119	99730121	+	1	NA	Intergenic	Intergenic	42793	NM_001126322	100040276	Mm.475095	NM_001126322	ENSMUSG00000078668	Gm11595	OTTMUSG00000002543	predicted gene 11595	protein-coding
mm_14547.1	chr2	132847708	132847716	+	1	NA	promoter-TSS (NM_025646)	promoter-TSS (NM_025646)	-22	NM_025646	66586	Mm.357342	NM_025646	ENSMUSG00000027357	Crls1	0610009I22Rik|4930557M15Rik|5730490M08Rik	cardiolipin synthase 1	protein-coding
mm_99948.1	chr11	111075452	111075472	+	1	NA	3' UTR (NM_008425, exon 2 of 2)	3' UTR (NM_008425, exon 2 of 2)	9298	NM_008425	16518	Mm.4951	NM_008425	ENSMUSG00000041695	Kcnj2	IRK1|Kcnf1|Kir2.1	potassium inwardly-rectifying channel, subfamily J, member 2	protein-coding
mm_124400.1	chr14	114945941	114945948	-	1	NA	promoter-TSS (NR_126551)	promoter-TSS (NR_126551)	4	NR_126551	74982		NR_126548		1700100I10Rik	1700085D13Rik|4930481K08Rik	RIKEN cDNA 1700100I10 gene	ncRNA
mm_113710.1	chr13	43506054	43506063	+	1	NA	Intergenic	Intergenic	-25085	NM_019930	56705	Mm.148781	NM_019930	ENSMUSG00000038546	Ranbp9	IBAP-1|Ibap1|RanBPM	RAN binding protein 9	protein-coding
mm_90851.1	chr10	8762580	8762616	-	1	NA	intron (NM_175155, intron 8 of 19)	intron (NM_175155, intron 8 of 19)	123472	NM_175155	70097	Mm.338275	NM_175155	ENSMUSG00000015305	Sash1	1100001C18Rik|2500002E12Rik|A330076K04Rik|mKIAA0790	SAM and SH3 domain containing 1	protein-coding
mm_154915.1	chrX	21715035	21715053	+	1	NA	5' UTR (NM_020049, exon 1 of 14)	5' UTR (NM_020049, exon 1 of 14)	144	NM_020049	56774	Mm.253984	NM_020049	ENSMUSG00000031089	Slc6a14	1110007A17Rik|9030613J17Rik|ATB0plus|CATB0plus	solute carrier family 6 (neurotransmitter transporter), member 14	protein-coding
mm_157215.1	chrX	12994554	12994562	-	1	NA	Intergenic	B1_Mur2|SINE|Alu	-47457	NR_038158	70489	Mm.383563	NR_038158	ENSMUSG00000087424	5730405O15Rik	-	RIKEN cDNA 5730405O15 gene	ncRNA
mm_43797.1	chr5	142817884	142817886	+	1	NA	promoter-TSS (NM_001122730)	promoter-TSS (NM_001122730)	-498	NM_001122730	231861	Mm.354649	NM_178242	ENSMUSG00000039477	Tnrc18	BC025631|EG381742|Zfp469	trinucleotide repeat containing 18	protein-coding
mm_130696.1	chr15	100683010	100683031	-	1	NA	exon (NM_033612, exon 5 of 8)	exon (NM_033612, exon 5 of 8)	4900	NM_033612	109901	Mm.2131	NM_033612	ENSMUSG00000023031	Cela1	1810009A17Rik|1810062B19Rik|Ela-1|Ela1|PC-TsF	chymotrypsin-like elastase family, member 1	protein-coding
mm_116982.1	chr13	56295895	56295907	-	1	NA	exon (NM_019568, exon 2 of 4)	exon (NM_019568, exon 2 of 4)	650	NM_019568	57266	Mm.30211	NM_019568	ENSMUSG00000021508	Cxcl14	1110031L23Rik|1200006I23Rik|AI414372|BMAC|BRAK|KS1|Kec|MIP-2g|MIP2gamma|NJAC|Scyb14|bolekine	chemokine (C-X-C motif) ligand 14	protein-coding
mm_13045.1	chr2	91096745	91096788	+	1	NA	promoter-TSS (NM_011355)	promoter-TSS (NM_011355)	88	NM_011355	20375	Mm.1302	NM_011355	ENSMUSG00000002111	Spi1	Dis-1|Dis1|PU.1|Sfpi-1|Sfpi1|Spi-1|Tcfpu1|Tfpu.1	spleen focus forming virus (SFFV) proviral integration oncogene	protein-coding
mm_160128.1	chr7	28693144	28693144	+	1	NA	promoter-TSS (NM_001163702)	promoter-TSS (NM_001163702)	0	NM_001163702	233040	Mm.116116	NM_207238	ENSMUSG00000037463	Fbxo27	E130008B10Rik|FBG5|Gm161	F-box protein 27	protein-coding
mm_158411.1	chrX	136976860	136976883	-	1	NA	promoter-TSS (NM_001081983)	promoter-TSS (NM_001081983)	3	NM_001081983	666244	Mm.381904	NM_001081983	ENSMUSG00000089768	Tmsb15b1	Tm15b	thymosin beta 15b1	protein-coding
mm_63046.1	chr7	121734478	121734489	+	1	NA	promoter-TSS (NM_011326)	promoter-TSS (NM_011326)	4	NM_011326	20278	Mm.35247	NM_011326	ENSMUSG00000000216	Scnn1g	SCNEG	sodium channel, nonvoltage-gated 1 gamma	protein-coding
mm_3139.1	chr1	135133273	135133319	+	1	NA	promoter-TSS (NM_007955)	promoter-TSS (NM_007955)	571	NM_177081	320139	Mm.258388	NM_177081	ENSMUSG00000031506	Ptpn7	BPTP-4|C920001D21Rik|HEPTP|LC-PTP|LPTP	protein tyrosine phosphatase, non-receptor type 7	protein-coding
mm_149795.1	chr19	23165228	23165240	+	1	NA	3' UTR (NM_010638, exon 2 of 2)	3' UTR (NM_010638, exon 2 of 2)	15803	NR_035423	100316672		NR_035423	ENSMUSG00000080626	Mir1192	Mirn1192|mmu-mir-1192	microRNA 1192	ncRNA
mm_39339.1	chr5	8833459	8833460	+	1	NA	intron (NM_011075, intron 19 of 27)	4.5SRNA|scRNA|scRNA	35312	NM_011075	18669	Mm.146649	NM_011075	ENSMUSG00000028970	Abcb1b	Abcb1|Mdr1|Mdr1b|Pgy-1|Pgy1|mdr	ATP-binding cassette, sub-family B (MDR/TAP), member 1B	protein-coding
mm_111344.1	chr12	86884847	86884858	-	1	NA	promoter-TSS (NM_145836)	promoter-TSS (NM_145836)	-38	NM_145836	238330	Mm.248358	NM_145836	ENSMUSG00000034168	Irf2bpl	6430527G18Rik|Eap1	interferon regulatory factor 2 binding protein-like	protein-coding
mm_113053.1	chr13	23685796	23685809	+	1	NA	intron (NM_023422, intron 1 of 1)	intron (NM_023422, intron 1 of 1)	1603	NM_023422	68024	Mm.261676	NM_023422	ENSMUSG00000018102	Hist1h2bc	2610022J01Rik|H2bfs|R74621	histone cluster 1, H2bc	protein-coding
mm_47333.1	chr5	122501216	122501223	-	1	NA	intron (NM_001110140, intron 1 of 19)	intron (NM_001110140, intron 1 of 19)	1006	NM_001110140	11938	Mm.227583	NM_009722	ENSMUSG00000029467	Atp2a2	9530097L16Rik|D5Wsu150e|SERCA2|SERCA2B|Serca2a|mKIAA4195	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	protein-coding
mm_146914.1	chr18	31447384	31447407	-	1	NA	promoter-TSS (NM_009308)	promoter-TSS (NM_009308)	20	NM_009308	20983	Mm.233846	NM_009308	ENSMUSG00000024261	Syt4	SytIV	synaptotagmin IV	protein-coding
mm_136520.1	chr16	97458982	97458991	-	1	NA	intron (NR_003520, intron 2 of 8)	L1MEc|LINE|L1	3919	NM_010846	17857	Mm.33996	NM_010846	ENSMUSG00000000386	Mx1	AI893580|Mx|Mx-1	MX dynamin-like GTPase 1	protein-coding
mm_118267.1	chr13	112578309	112578355	-	1	NA	intron (NM_139299, intron 1 of 16)	LSU-rRNA_Hsa|rRNA|rRNA	2330	NM_139299	218624	Mm.380801	NM_139299	ENSMUSG00000050377	Il31ra	CRL3|GLM-R|GPL|Glmr|NR10	interleukin 31 receptor A	protein-coding
mm_170091.1	chr17	36042697	36042715	-	1	NA	promoter-TSS (NM_001034909)	promoter-TSS (NM_001034909)	-4	NM_010397	15039	Mm.195061	NM_010396	ENSMUSG00000056116	H2-T22	27b|H-2T17|H-2T22|H2-T17|T22b	histocompatibility 2, T region locus 22	protein-coding
mm_32682.1	chr4	115800231	115800254	+	1	NA	intron (NM_181040, intron 7 of 8)	intron (NM_181040, intron 7 of 8)	15428	NM_181040	230649	Mm.109600	NM_181040	ENSMUSG00000028710	Atpaf1	6330547J17Rik|AI593252|ATP11|ATP11p	ATP synthase mitochondrial F1 complex assembly factor 1	protein-coding
mm_7213.1	chr1	93101855	93101879	-	1	NA	promoter-TSS (NM_008440)	promoter-TSS (NM_008440)	7	NM_001294149	16560	Mm.276408	NM_008440	ENSMUSG00000014602	Kif1a	ATSV|C630002N23Rik|Gm1626|Kns1	kinesin family member 1A	protein-coding
mm_27526.1	chr3	57340968	57340971	-	1	NA	Intergenic	MTC|LTR|ERVL-MaLR	-39050	NM_008536	17112	Mm.856	NM_008536	ENSMUSG00000027800	Tm4sf1	L6|M3s1	transmembrane 4 superfamily member 1	protein-coding
mm_70892.1	chr8	25597097	25597127	+	1	NA	intron (NM_173012, intron 1 of 10)	CpG	375	NM_173012	270035	Mm.268349	NM_173012	ENSMUSG00000037363	Letm2	6030453H13|D030041N04Rik	leucine zipper-EF-hand containing transmembrane protein 2	protein-coding
mm_61049.1	chr7	49910071	49910071	+	1	NA	promoter-TSS (NM_001146013)	promoter-TSS (NM_001146013)	-228	NM_001146013	104245	Mm.207053	NM_148931	ENSMUSG00000039728	Slc6a5	Glyt2|prestin	solute carrier family 6 (neurotransmitter transporter, glycine), member 5	protein-coding
mm_94750.1	chr11	21115317	21115354	+	1	NA	intron (NM_023324, intron 1 of 6)	L1MB8|LINE|L1	24011	NM_023324	67245	Mm.28957	NM_023324	ENSMUSG00000020134	Peli1	2810468L03Rik|A930031K15Rik|AA409794|AI586297|D11Ertd676e	pellino 1	protein-coding
mm_45457.1	chr5	67777338	67777374	-	1	NA	intron (NM_001284345, intron 7 of 36)	intron (NM_001284345, intron 7 of 36)	70075	NM_009727	11980	Mm.153230	NM_009727	ENSMUSG00000037685	Atp8a1	AI481521|AI853962|APLT|AW743152|AW822227|Atp3a2|B230107D19Rik|ClassI	ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1	protein-coding
mm_101015.1	chr11	8558400	8558410	-	1	NA	intron (NM_001083587, intron 4 of 30)	intron (NM_001083587, intron 4 of 30)	106130	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_143722.1	chr17	81375885	81375901	-	1	NA	non-coding (NR_104580, exon 9 of 9)	non-coding (NR_104580, exon 9 of 9)	-310808	NM_028138	72167	Mm.273257	NM_028138	ENSMUSG00000024246	Thumpd2	2810025A12Rik	THUMP domain containing 2	protein-coding
mm_46133.1	chr5	92675234	92675249	-	1	NA	promoter-TSS (NM_177230)	promoter-TSS (NM_177230)	-114	NM_177230	320696	Mm.209991	NM_177230	ENSMUSG00000050050	Ccdc158	4932413O14Rik	coiled-coil domain containing 158	protein-coding
mm_124206.1	chr14	99046056	99046098	-	1	NA	promoter-TSS (NM_175245)	promoter-TSS (NM_175245)	59	NM_175245	76789	Mm.38912	NM_175245	ENSMUSG00000033186	Mzt1	2410129H14Rik|AI120158|Mozart1	mitotic spindle organizing protein 1	protein-coding
mm_124352.1	chr14	104521803	104521806	-	1	NA	intron (NM_026047, intron 1 of 5)	intron (NM_026047, intron 1 of 5)	862	NM_026047	72486	Mm.291811	NM_026047	ENSMUSG00000022120	Rnf219	2610206B13Rik|2810449K13Rik|AI451544	ring finger protein 219	protein-coding
mm_32170.1	chr4	100478796	100478802	+	1	NA	promoter-TSS (NM_001033773)	promoter-TSS (NM_001033773)	-68	NM_001033773	381534	Mm.318133	NM_001033773	ENSMUSG00000069733	Ube2u	-	ubiquitin-conjugating enzyme E2U (putative)	protein-coding
mm_127094.1	chr15	97787625	97787642	+	1	NA	intron (NM_026353, intron 1 of 2)	intron (NM_026353, intron 1 of 2)	3268	NM_026353	67739	Mm.28955	NM_026353	ENSMUSG00000081534	Slc48a1	4930570C03Rik	solute carrier family 48 (heme transporter), member 1	protein-coding
mm_65719.1	chr7	28379097	28379101	-	1	NA	intron (NM_011756, intron 1 of 1)	CpG	129	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_168198.1	chr10	65534630	65534647	+	1	NA	Intergenic	Intergenic	589426	NR_038039	69433	Mm.23366	NR_038039	ENSMUSG00000100000	1700023F02Rik	AV205046	RIKEN cDNA 1700023F02 gene	ncRNA
mm_162048.1	chrX	6047438	6047438	+	1	NA	promoter-TSS (NM_021431)	promoter-TSS (NM_021431)	-69	NM_021431	58242	Mm.41198	NM_021431	ENSMUSG00000073295	Nudt11	DIPP3|DIPP3b	nudix (nucleoside diphosphate linked moiety X)-type motif 11	protein-coding
mm_80330.1	chr9	75037798	75037806	+	1	NA	promoter-TSS (NM_021548)	promoter-TSS (NM_021548)	70	NM_021548	59046	Mm.247837	NM_021548	ENSMUSG00000007656	Arpp19	19kDa|2700024H10Rik|ARPP-19|AW559096|Arpp12	cAMP-regulated phosphoprotein 19	protein-coding
mm_55448.1	chr6	67271216	67271288	-	1	NA	exon (NM_025814, exon 2 of 8)	exon (NM_025814, exon 2 of 8)	4273	NM_025814	66870	Mm.240490	NM_025814	ENSMUSG00000036371	Serbp1	1200009K13Rik|9330147J08Rik|AL022786|Pairbp1	serpine1 mRNA binding protein 1	protein-coding
mm_114699.1	chr13	83504234	83504255	+	1	NA	5' UTR (NM_025282, exon 1 of 11)	5' UTR (NM_025282, exon 1 of 11)	210	NM_001347564	17260	Mm.24001	NM_025282	ENSMUSG00000005583	Mef2c	5430401D19Rik|9930028G15Rik|AV011172|Mef2	myocyte enhancer factor 2C	protein-coding
mm_77958.1	chr9	7628201	7628204	+	1	NA	promoter-TSS (NM_013903)	promoter-TSS (NM_013903)	-29	NM_013903	30800	Mm.390121	NM_013903	ENSMUSG00000018620	Mmp20	-	matrix metallopeptidase 20 (enamelysin)	protein-coding
mm_163576.1	chr13	32214148	32214152	-	1	NA	intron (NM_146041, intron 4 of 10)	intron (NM_146041, intron 4 of 10)	124394	NM_146041	218138	Mm.247143	NM_146041	ENSMUSG00000038372	Gmds	BC031788|C87208	GDP-mannose 4, 6-dehydratase	protein-coding
mm_149147.1	chr19	9005937	9005993	+	1	NA	exon (NM_009643, exon 5 of 5)	exon (NM_009643, exon 5 of 5)	-11939	NR_105786	102465190		NR_105786	ENSMUSG00000099308	Mir6367	Gm27467|mmu-mir-6367	microRNA 6367	ncRNA
mm_76806.1	chr8	104340390	104340438	-	1	NA	promoter-TSS (NM_024217)	promoter-TSS (NM_024217)	-180	NM_024217	68119	Mm.390108	NM_024217	ENSMUSG00000031875	Cmtm3	9430096L06Rik|AI413895|BNAS2|Cklfsf3	CKLF-like MARVEL transmembrane domain containing 3	protein-coding
mm_133182.1	chr16	72639608	72639611	+	1	NA	Intergenic	MIRb|SINE|MIR	-23540	NM_019413	19876	Mm.310772	NM_019413	ENSMUSG00000022883	Robo1	AW494633|AW742721|DUTT1|Gm310	roundabout guidance receptor 1	protein-coding
mm_41877.1	chr5	105125511	105125544	+	1	NA	exon (NM_001256005, exon 4 of 11)	exon (NM_001256005, exon 4 of 11)	14025	NM_008620	17472	Mm.440525	NM_008620	ENSMUSG00000079363	Gbp4	AW228052|Mag-2|Mpa-2|Mpa2	guanylate binding protein 4	protein-coding
mm_26178.1	chr3	138290569	138290579	+	1	NA	3' UTR (NM_007409, exon 9 of 9)	3' UTR (NM_007409, exon 9 of 9)	12929	NM_007409	11522	Mm.2409	NM_007409	ENSMUSG00000074207	Adh1	ADH-AA|AI194826|Adh-1|Adh-1-t|Adh-1e|Adh-1t|Adh-3e|Adh1-e|Adh1-t|Adh1tl|Adh3-e	alcohol dehydrogenase 1 (class I)	protein-coding
mm_136386.1	chr16	93127793	93127805	-	1	NA	Intergenic	Intergenic	225390	NR_040486	69857	Mm.81192	NR_040486	ENSMUSG00000100277	1810053B23Rik	1810008L18Rik|1810056K14Rik	RIKEN cDNA 1810053B23 gene	ncRNA
mm_115422.1	chr13	117220307	117220334	+	1	NA	promoter-TSS (NM_010330)	promoter-TSS (NM_010330)	-253	NM_010330	13723	Mm.274926	NM_010330	ENSMUSG00000021728	Emb	AL022799|Gp70	embigin	protein-coding
mm_30358.1	chr3	151764211	151764225	-	1	NA	Intergenic	Intergenic	-1327	NM_031367	15061	Mm.219544	NM_031367	ENSMUSG00000039146	Ifi44l	H-28|H28|H28-1|NS1178	interferon-induced protein 44 like	protein-coding
mm_61477.1	chr7	75643224	75643225	+	1	NA	intron (NM_029332, intron 8 of 36)	intron (NM_029332, intron 8 of 36)	187690	NM_029332	75547	Mm.216107	NM_029332	ENSMUSG00000066406	Akap13	1700026G02Rik|5730522G15Rik|5830460E08Rik|AKAP-13|AKAP-Lbc|BRX|Ht31|LBC|PROTO-LB|PROTO-LBC	A kinase (PRKA) anchor protein 13	protein-coding
mm_74578.1	chr8	11221378	11221392	-	1	NA	exon (NM_009931, exon 30 of 52)	exon (NM_009931, exon 30 of 52)	-91420	NM_009932	12827	Mm.181021	NM_009932	ENSMUSG00000031503	Col4a2	Col4a-2	collagen, type IV, alpha 2	protein-coding
mm_109828.1	chr12	3907836	3907855	-	1	NA	3' UTR (NM_153743, exon 18 of 18)	3' UTR (NM_153743, exon 18 of 18)	16101	NM_153743	13435	Mm.5001	NM_007872	ENSMUSG00000020661	Dnmt3a	MmuIIIA	DNA methyltransferase 3A	protein-coding
mm_147297.1	chr18	39519190	39519205	-	1	NA	Intergenic	Intergenic	-31952	NM_008173	14815	Mm.129481	NM_008173	ENSMUSG00000024431	Nr3c1	GR|Grl-1|Grl1	nuclear receptor subfamily 3, group C, member 1	protein-coding
mm_118389.1	chr13	118387182	118387196	-	1	NA	promoter-TSS (NM_021556)	promoter-TSS (NM_021556)	63	NM_021556	59054	Mm.143810	NM_021556	ENSMUSG00000021731	Mrps30	2610020A16Rik|AA968347|PAP|Pdcd9	mitochondrial ribosomal protein S30	protein-coding
mm_112569.1	chr13	13574125	13574156	+	1	NA	Intergenic	Intergenic	-16269	NM_010748	17101	Mm.342337	NM_010748	ENSMUSG00000019726	Lyst	D13Sfk13|beige|bg	lysosomal trafficking regulator	protein-coding
mm_26609.1	chr3	152234795	152234800	+	1	NA	3' UTR (NM_057172, exon 20 of 20)	3' UTR (NM_057172, exon 20 of 20)	24339	NM_057172	51886	Mm.278922	NM_057172	ENSMUSG00000028034	Fubp1	9530027K12Rik|D3Ertd330e|FBP|Fubp|Fubp4	far upstream element (FUSE) binding protein 1	protein-coding
mm_73579.1	chr8	109781513	109781515	+	1	NA	intron (NM_001301211, intron 1 of 22)	intron (NM_001301211, intron 1 of 22)	2931	NM_001301211	11765	Mm.37210	NM_009677	ENSMUSG00000031731	Ap1g1	AA409002|AU041323|AW551707|Adtg|D8Ertd374e	adaptor protein complex AP-1, gamma 1 subunit	protein-coding
mm_135659.1	chr16	52403303	52403318	-	1	NA	intron (NM_009655, intron 1 of 15)	intron (NM_009655, intron 1 of 15)	49771	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_130768.1	chr15	101406677	101406681	-	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	-5724	NM_033073	110310	Mm.486285	NM_033073	ENSMUSG00000023039	Krt7	D15Wsu77e|K7|Krt2-7	keratin 7	protein-coding
mm_52502.1	chr6	115244184	115244188	+	1	NA	exon (NM_001326560, exon 3 of 9)	exon (NM_001326560, exon 3 of 9)	5192	NM_001326560	20965	Mm.441431	NM_013681	ENSMUSG00000009394	Syn2	2900074L19Rik|AI836018|AI841723	synapsin II	protein-coding
mm_86857.1	chr10	21882301	21882354	+	1	NA	5' UTR (NM_001161845, exon 1 of 14)	5' UTR (NM_001161845, exon 1 of 14)	143	NM_001161845	20393	Mm.28405	NM_011361	ENSMUSG00000019970	Sgk1	Sgk	serum/glucocorticoid regulated kinase 1	protein-coding
mm_112123.1	chr12	112868242	112868259	-	1	NA	Intergenic	Intergenic	-7334	NM_019925	56696	Mm.20455	NM_019925	ENSMUSG00000021298	Gpr132	G2a	G protein-coupled receptor 132	protein-coding
mm_152183.1	chr19	7427142	7427156	-	1	NA	3' UTR (NM_053076, exon 7 of 7)	3' UTR (NM_053076, exon 7 of 7)	4576	NR_105957	102466781		NR_105957	ENSMUSG00000098293	Mir6991	Gm27966|mmu-mir-6991	microRNA 6991	ncRNA
mm_7949.1	chr1	133915217	133915265	-	1	NA	exon (NM_054077, exon 2 of 3)	exon (NM_054077, exon 2 of 3)	6160	NM_054077	116847	Mm.214514	NM_054077	ENSMUSG00000041577	Prelp	7330409J17Rik|SLRR2A	proline arginine-rich end leucine-rich repeat	protein-coding
mm_160460.1	chr8	109614731	109614731	+	1	NA	exon (NM_001286454, exon 1 of 33)	exon (NM_001286454, exon 1 of 33)	214	NM_181544	244646	Mm.436810	NM_181544	ENSMUSG00000048827	Pkd1l3	-	polycystic kidney disease 1 like 3	protein-coding
mm_25673.1	chr3	121989269	121989272	+	1	NA	intron (NM_172525, intron 5 of 22)	intron (NM_172525, intron 5 of 22)	35944	NM_172525	214137	Mm.229287	NM_172525	ENSMUSG00000039831	Arhgap29	6720461J18Rik|A830014I19|AU040217|B130017I01Rik|C76601|Parg1	Rho GTPase activating protein 29	protein-coding
mm_118937.1	chr14	27229873	27229893	+	1	NA	intron (NM_001289686, intron 3 of 12)	intron (NM_001289686, intron 3 of 12)	-8127	NM_027871	71704	Mm.248606	NM_027871	ENSMUSG00000021895	Arhgef3	1200004I24Rik|9830169H03Rik|C76747|Xpln	Rho guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_3825.1	chr1	159310330	159310340	+	1	NA	intron (NM_011931, intron 14 of 19)	intron (NM_011931, intron 14 of 19)	16562	NR_144489	100846986		NR_144489		Pou5f1-rs1	Gm21053|Oct4P2|Otf-3rs|Otf3-rs1|Otf3a	POU domain, class 5, transcription factor 1, related sequence 1	pseudo
mm_87948.1	chr10	63023334	63023352	+	1	NA	intron (NM_001079824, intron 1 of 9)	CpG	506	NM_001079824	432467	Mm.274784	NM_001079824	ENSMUSG00000020069	Hnrnph3	AA693301|AI666703|Hnrph3	heterogeneous nuclear ribonucleoprotein H3	protein-coding
mm_66607.1	chr7	45465255	45465257	-	1	NA	exon (NM_007527, exon 4 of 6)	exon (NM_007527, exon 4 of 6)	1642	NM_007527	12028	Mm.19904	NM_007527	ENSMUSG00000003873	Bax	-	BCL2-associated X protein	protein-coding
mm_34801.1	chr4	154833978	154834014	+	1	NA	Intergenic	Intergenic	-22204	NM_172878	242800	Mm.72944	NM_172878	ENSMUSG00000046637	Ttc34	4932418L02|B230396O12Rik	tetratricopeptide repeat domain 34	protein-coding
mm_155182.1	chrX	53772802	53772816	+	1	NA	3' UTR (NM_001009549, exon 2 of 2)	3' UTR (NM_001009549, exon 2 of 2)	3585	NM_001009549	333473	Mm.327378	NM_001009549	ENSMUSG00000059334	Zfp36l3	AY661338	zinc finger protein 36, C3H type-like 3	protein-coding
mm_39313.1	chr5	8056537	8056551	+	1	NA	promoter-TSS (NM_001080974)	promoter-TSS (NM_001080974)	2	NM_001080974	109552	Mm.96211	NM_025618	ENSMUSG00000003161	Sri	2210417O06Rik|2900070H08Rik|Sor	sorcin	protein-coding
mm_34697.1	chr4	152039359	152039367	+	1	NA	promoter-TSS (NM_028727)	promoter-TSS (NM_028727)	42	NM_028727	74035	Mm.275803	NM_028727	ENSMUSG00000028948	Nol9	4632412I24Rik|6030462G04Rik|AI449622|AW490720	nucleolar protein 9	protein-coding
mm_6870.1	chr1	84282882	84282890	-	1	NA	intron (NM_001003948, intron 1 of 2)	intron (NM_001003948, intron 1 of 2)	1759	NM_001003948	98496	Mm.187470	NM_001003948	ENSMUSG00000045658	Pid1	5033414K04Rik|NYGGF4	phosphotyrosine interaction domain containing 1	protein-coding
mm_132951.1	chr16	49912871	49912875	+	1	NA	Intergenic	Intergenic	57219	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_68634.1	chr7	118243363	118243412	-	1	NA	promoter-TSS (NR_027879)	promoter-TSS (NR_027879)	250	NM_001031814	233789	Mm.309053	NM_177180	ENSMUSG00000030655	Smg1	2610207I05Rik|5430435M13Rik|C130002K18Rik|mKIAA0421	SMG1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)	protein-coding
mm_980.1	chr1	58406800	58406824	+	1	NA	TTS (NM_025824)	TTS (NM_025824)	13676	NM_025824	66882	Mm.21848	NM_025824	ENSMUSG00000051223	Bzw1	1200015E15Rik|mKIAA0005	basic leucine zipper and W2 domains 1	protein-coding
mm_1703.1	chr1	75168747	75168772	+	1	NA	promoter-TSS (NM_026846)	promoter-TSS (NM_026846)	24	NM_026846	68818	Mm.32646	NM_026846	ENSMUSG00000026197	Zfand2b	1110060O18Rik|C81256	zinc finger, AN1 type domain 2B	protein-coding
mm_121259.1	chr14	103070223	103070233	+	1	NA	promoter-TSS (NM_001033242)	promoter-TSS (NM_001033242)	12	NM_001033242	211286	Mm.295289	NM_001033242	ENSMUSG00000022125	Cln5	A730075N08Rik	ceroid-lipofuscinosis, neuronal 5	protein-coding
mm_23006.1	chr3	34104482	34104496	+	1	NA	Intergenic	Intergenic	-23135	NM_026332	67713	Mm.274266	NM_026332	ENSMUSG00000027679	Dnajc19	1810055D05Rik|AA959924|Tim14	DnaJ heat shock protein family (Hsp40) member C19	protein-coding
mm_128183.1	chr15	34678756	34678802	-	1	NA	promoter-TSS (NM_145469)	promoter-TSS (NM_145469)	-73	NM_145469	223473	Mm.258402	NM_145469	ENSMUSG00000038879	Nipal2	9330161F08Rik|Npal2	NIPA-like domain containing 2	protein-coding
mm_145571.1	chr18	60911956	60911973	+	1	NA	promoter-TSS (NM_001038499)	promoter-TSS (NM_001038499)	-276	NM_001038499	545260	Mm.20147	NM_001038499	ENSMUSG00000036412	Arsi	BC020108	arylsulfatase i	protein-coding
mm_163070.1	chr11	67254734	67254743	+	1	NA	exon (NM_010855, exon 30 of 40)	exon (NM_010855, exon 30 of 40)	16926	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_154940.1	chrX	36112115	36112172	+	1	NA	promoter-TSS (NM_133990)	promoter-TSS (NM_133990)	35	NM_133990	16164	Mm.24208	NM_133990	ENSMUSG00000017057	Il13ra1	AI882074|CD213a1|IL-13R-alpha-1|IL-13r[a]|Il13ra|NR4	interleukin 13 receptor, alpha 1	protein-coding
mm_64437.1	chr7	142653554	142653565	+	1	NA	3' UTR (NM_010514, exon 4 of 4)	3' UTR (NM_010514, exon 4 of 4)	1437	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_27842.1	chr3	79156161	79156177	-	1	NA	Intergenic	B4|SINE|B4	-10294	NM_001099624	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_109285.1	chr12	109553904	109553904	+	1	NA	intron (NR_027651, intron 7 of 8)	intron (NR_027651, intron 7 of 8)	8506	NR_003633	17263	Mm.289645	NM_144513	ENSMUSG00000021268	Meg3	2900016C05Rik|3110050O07Rik|6330408G06Rik|AI425946|AW108224|D12Bwg1266e|Gtl2|R74756|R75394	maternally expressed 3	ncRNA
mm_29999.1	chr3	135590622	135590632	-	1	NA	intron (NM_008689, intron 22 of 24)	intron (NM_008689, intron 22 of 24)	100920	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_124713.1	chr15	6574784	6574814	+	1	NA	Intergenic	Intergenic	-5048	NM_001278269	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_142372.1	chr17	44658534	44658559	-	1	NA	exon (NM_009820, exon 6 of 9)	exon (NM_009820, exon 6 of 9)	77630	NR_073425	12393	Mm.391013	NM_009820	ENSMUSG00000039153	Runx2	AML3|Cbf|Cbfa-1|Cbfa1|LS3|Osf2|PEBP2aA|Pebp2a1|Pebpa2a	runt related transcription factor 2	protein-coding
mm_71015.1	chr8	31187400	31187410	+	1	NA	promoter-TSS (NM_001286425)	promoter-TSS (NM_001286425)	74	NM_001286425	171167	Mm.334477	NM_134161	ENSMUSG00000046152	Fut10	fuc-TX|fut10A	fucosyltransferase 10	protein-coding
mm_132289.1	chr16	33185157	33185168	+	1	NA	promoter-TSS (NM_176840)	promoter-TSS (NM_176840)	91	NM_176840	106326	Mm.486405	NM_176840	ENSMUSG00000022807	Osbpl11	9430097N02Rik|AI132306|AU019795|ORP-11	oxysterol binding protein-like 11	protein-coding
mm_144485.1	chr18	24088989	24088992	+	1	NA	Intergenic	Intergenic	32829	NM_172625	225280	Mm.258973	NM_172625	ENSMUSG00000047989	Ino80c	D030070L09Rik	INO80 complex subunit C	protein-coding
mm_92705.1	chr10	80742223	80742280	-	1	NA	promoter-TSS (NM_007460)	promoter-TSS (NM_007460)	-40	NM_007460	11776	Mm.27082	NM_007460	ENSMUSG00000020198	Ap3d1	AA407035|Ap3d|Bolvr|mBLVR1|mh|mocha	adaptor-related protein complex 3, delta 1 subunit	protein-coding
mm_24877.1	chr3	95989349	95989371	+	1	NA	exon (NM_023320, exon 6 of 6)	exon (NM_023320, exon 6 of 6)	3850	NR_045872	668224	Mm.357766	NR_045872		Gm9054	EG668224	predicted gene 9054	ncRNA
mm_154325.1	chrM	2392	2402	+	1	NA	NA	Intergenic	NA	NA								
mm_34503.1	chr4	148664350	148664356	+	1	NA	intron (NM_001085505, intron 5 of 10)	intron (NM_001085505, intron 5 of 10)	21036	NM_001085505	230909	Mm.332067	NM_001085505	ENSMUSG00000070577	Gm572	b2b1167Clo	predicted gene 572	protein-coding
mm_54773.1	chr6	41532869	41532876	-	1	NA	Intergenic	Intergenic	11096	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_55139.1	chr6	51320947	51320967	-	1	NA	Intergenic	Intergenic	-51047	NR_029719	387166		NR_029719	ENSMUSG00000065505	Mir148a	Mirn148|Mirn148a|mir-148a	microRNA 148a	ncRNA
mm_136704.1	chr17	7875378	7875393	+	1	NA	Intergenic	Intergenic	-50615	NM_145968	72536	Mm.119680	NM_145968	ENSMUSG00000033450	Tagap	2610315E15Rik	T cell activation Rho GTPase activating protein	protein-coding
mm_79564.1	chr9	58129477	58129484	+	1	NA	5' UTR (NM_009291, exon 1 of 19)	5' UTR (NM_009291, exon 1 of 19)	131	NM_009291	20897	Mm.10801	NM_009291	ENSMUSG00000032327	Stra6	AI891933	stimulated by retinoic acid gene 6	protein-coding
mm_131240.1	chr16	10489729	10489757	+	1	NA	promoter-TSS (NM_001243761)	promoter-TSS (NM_001243761)	-38	NM_001243761	12265	Mm.249560	NM_007575	ENSMUSG00000022504	Ciita	C2ta|EG669998|Gm9475|Mhc2ta	class II transactivator	protein-coding
mm_170484.1	chr19	14960524	14960531	-	1	NA	Intergenic	Intergenic	-362344	NM_001302947	21888	Mm.103638	NM_011600	ENSMUSG00000024642	Tle4	5730411M05Rik|AA792082|Bce-1|Bce1|ESTM13|ESTM14|Grg4|X83332|X83333|grg-4	transducin-like enhancer of split 4	protein-coding
mm_64073.1	chr7	140907072	140907076	+	1	NA	non-coding (NR_015583, exon 1 of 3)	non-coding (NR_015583, exon 1 of 3)	1010	NR_015583	212965	Mm.387212	NR_015583	ENSMUSG00000109628	BC024386	BC039766	cDNA sequence BC023486	ncRNA
mm_11600.1	chr2	33641328	33641337	+	1	NA	promoter-TSS (NM_010725)	promoter-TSS (NM_010725)	139	NR_046275	100504399	Mm.72070	NM_177842		C130021I20Rik	-	Riken cDNA C130021I20 gene	ncRNA
mm_102751.1	chr11	67257227	67257252	-	1	NA	exon (NM_010855, exon 35 of 40)	exon (NM_010855, exon 35 of 40)	19427	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_115860.1	chr13	21402689	21402748	-	1	NA	promoter-TSS (NM_001145778)	promoter-TSS (NM_001145778)	37	NM_001145778	72739	Mm.296071	NM_023685	ENSMUSG00000021327	Zkscan3	2810435N07Rik|AA408594|AI132359|Skz1|Zf47|Zfp-47|Zfp306|Zfp307|mszf35	zinc finger with KRAB and SCAN domains 3	protein-coding
mm_143328.1	chr17	66449433	66449442	-	1	NA	5' UTR (NM_172963, exon 1 of 14)	5' UTR (NM_172963, exon 1 of 14)	313	NM_172963	68617	Mm.33421	NM_172963	ENSMUSG00000052105	Mtcl1	1110012J17Rik|Ccdc165|D130071O13|Kiaa0802|Soga2|mKIAA0802|t8219b25	microtubule crosslinking factor 1	protein-coding
mm_110000.1	chr12	15816172	15816190	-	1	NA	5' UTR (NM_144551, exon 1 of 3)	5' UTR (NM_144551, exon 1 of 3)	604	NM_144551	217410	Mm.491136	NM_144551	ENSMUSG00000020601	Trib2	AW319517|TRB-2|TRB2	tribbles pseudokinase 2	protein-coding
mm_44596.1	chr5	25059443	25059453	-	1	NA	intron (NM_145401, intron 1 of 15)	intron (NM_145401, intron 1 of 15)	41194	NM_145401	108099	Mm.33649	NM_145401	ENSMUSG00000028944	Prkag2	2410051C13Rik|AAKG|AAKG2|AI854673|H91620p|WPWS	protein kinase, AMP-activated, gamma 2 non-catalytic subunit	protein-coding
mm_2452.1	chr1	101155789	101155804	+	1	NA	promoter-TSS (NR_037989)	promoter-TSS (NR_037989)	28	NR_037989	100504525	Mm.87065	NR_037989	ENSMUSG00000100684	Gm20268	-	predicted gene, 20268	ncRNA
mm_91992.1	chr10	62071820	62071825	-	1	NA	Intergenic	Intergenic	39191	NM_027251	69894	Mm.294126	NM_027251	ENSMUSG00000020083	2010107G23Rik	AA545165	RIKEN cDNA 2010107G23 gene	protein-coding
mm_22608.1	chr3	14507928	14507936	+	1	NA	Intergenic	Intergenic	-25856	NM_001163579	71710	Mm.257449	NM_028915	ENSMUSG00000027550	Lrrcc1	1200008A14Rik|4932441F23Rik|AI195358|AI447421	leucine rich repeat and coiled-coil domain containing 1	protein-coding
mm_165342.1	chr2	118011894	118011907	-	1	NA	intron (NR_126479, intron 8 of 9)	intron (NR_126479, intron 8 of 9)	99302	NR_126479	329496	Mm.235844	NR_126479	ENSMUSG00000087203	Gm13986	C230060E24|OTTMUSG00000015236	predicted gene 13986	ncRNA
mm_66938.1	chr7	61615323	61615349	-	1	NA	promoter-TSS (NR_045727)	promoter-TSS (NR_045727)	-9	NR_045727	319752	Mm.294476	NR_045727		B230209E15Rik	-	RIKEN cDNA B230209E15 gene	ncRNA
mm_38854.1	chr4	149399381	149399398	-	1	NA	intron (NM_022022, intron 1 of 26)	intron (NM_022022, intron 1 of 26)	27242	NM_022022	63958	Mm.415260	NM_022022	ENSMUSG00000028960	Ube4b	4930551I19Rik|4933406G05Rik|AU014668|D4Bwg0973e|UFD2|UFD2a|Ufd2p|mKIAA0684	ubiquitination factor E4B	protein-coding
mm_164968.1	chr19	6980583	6980614	+	1	NA	promoter-TSS (NM_001166368)	promoter-TSS (NM_001166368)	-137	NM_001166368	14227	Mm.4234	NM_008020	ENSMUSG00000056629	Fkbp2	13kDa|FKBP-2|mFKBP13|mFKBP2	FK506 binding protein 2	protein-coding
mm_159045.1	chr1	182442067	182442067	+	1	NA	intron (NM_173378, intron 7 of 17)	intron (NM_173378, intron 7 of 17)	32900	NM_173378	209456	Mm.287450	NM_173378	ENSMUSG00000026510	Trp53bp2	53BP2|AI746547|ASPP2|PPP1R13A|Tp53bp2|X98550	transformation related protein 53 binding protein 2	protein-coding
mm_118278.1	chr13	112652296	112652355	-	1	NA	promoter-TSS (NM_010029)	promoter-TSS (NM_010029)	-15	NM_001145885	13206	Mm.12818	NM_010029	ENSMUSG00000021758	Ddx4	AV206478|Mvh|VASA	DEAD (Asp-Glu-Ala-Asp) box polypeptide 4	protein-coding
mm_12751.1	chr2	79253368	79253397	+	1	NA	Intergenic	MTC|LTR|ERVL-MaLR	-2044	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D|Itga4B	integrin alpha 4	protein-coding
mm_120128.1	chr14	60177643	60177652	+	1	NA	Intergenic	GC_rich|Low_complexity|Low_complexity	51268	NR_030458	751526		NR_030458	ENSMUSG00000076270	Mir719	Mirn719|mmu-mir-719	microRNA 719	ncRNA
mm_145720.1	chr18	63708690	63708730	+	1	NA	promoter-TSS (NM_001014981)	promoter-TSS (NM_001014981)	15	NM_001014981	104082	Mm.30850	NM_001014981	ENSMUSG00000040560	Wdr7	AI462727|TRAG|mKIAA0541	WD repeat domain 7	protein-coding
mm_83585.1	chr9	48340846	48340860	-	1	NA	promoter-TSS (NM_030069)	promoter-TSS (NM_030069)	45	NM_030069	78252	Mm.31626	NM_030069	ENSMUSG00000032028	Nxpe2	4432416J03Rik|AI323362|Fam55b	neurexophilin and PC-esterase domain family, member 2	protein-coding
mm_129537.1	chr15	79334357	79334357	-	1	NA	Intergenic	L2a|LINE|L2	-5986	NM_001199023	53357	Mm.155620	NM_016915	ENSMUSG00000042632	Pla2g6	BB112799|PNPLA9|iPLA(2)beta|iPLA2|iPLA2beta	phospholipase A2, group VI	protein-coding
mm_15762.1	chr2	164289610	164289620	+	1	NA	exon (NM_021363, exon 2 of 3)	exon (NM_021363, exon 2 of 3)	347	NM_021363	64335	Mm.389393	NM_021363	ENSMUSG00000017003	Svs3a	9530026M05Rik|BB121242|Semg2|Svp-3|Svp3|Svs3	seminal vesicle secretory protein 3A	protein-coding
mm_118915.1	chr14	26693268	26693277	+	1	NA	Intergenic	MIR3|SINE|MIR	-23426	NM_178668	211948	Mm.290758	NM_178668	ENSMUSG00000043702	Pde12	2'-PDE|E430028B21Rik	phosphodiesterase 12	protein-coding
mm_6560.1	chr1	75141627	75141648	-	1	NA	intron (NM_026977, intron 1 of 8)	CpG	731	NM_026977	69171	Mm.28193	NM_026977	ENSMUSG00000033159	Cnppd1	1810031K17Rik|AU043960	cyclin Pas1/PHO80 domain containing 1	protein-coding
mm_139134.1	chr17	47509194	47509205	+	1	NA	intron (NM_001081635, intron 1 of 6)	intron (NM_001081635, intron 1 of 6)	4148	NM_001081635	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_79685.1	chr9	59942195	59942204	+	1	NA	TTS (NM_013708)	TTS (NM_013708)	7880	NM_013708	23958	Mm.103641	NM_013708	ENSMUSG00000032292	Nr2e3	A930035N01Rik|PNR|RNR|rd7	nuclear receptor subfamily 2, group E, member 3	protein-coding
mm_47839.1	chr5	134314457	134314473	-	1	NA	5' UTR (NM_010365, exon 1 of 34)	5' UTR (NM_010365, exon 1 of 34)	295	NM_001080746	14886	Mm.261570	NM_010365	ENSMUSG00000060261	Gtf2i	6030441I21Rik|BAP-135|Diws1t|GtfII-I|Spin|TFII-I|WBSCR6	general transcription factor II I	protein-coding
mm_136216.1	chr16	89960728	89960743	-	1	NA	promoter-TSS (NM_009384)	promoter-TSS (NM_009384)	92	NM_009384	21844	Mm.310902	NM_009384	ENSMUSG00000002489	Tiam1	AI847750|D16Ium10|D16Ium10e	T cell lymphoma invasion and metastasis 1	protein-coding
mm_155022.1	chrX	42066530	42066540	+	1	NA	Intergenic	Intergenic	-1301	NM_009688	11798	Mm.259879	NM_009688	ENSMUSG00000025860	Xiap	1110015C02Rik|Aipa|Api3|Birc4|IAP3|ILP-1|MIHA	X-linked inhibitor of apoptosis	protein-coding
mm_21533.1	chr2	163645838	163645847	-	1	NA	promoter-TSS (NM_012032)	promoter-TSS (NM_012032)	-699	NM_012032	26943	Mm.218473	NM_012032	ENSMUSG00000017707	Serinc3	AA959945|AA960047|AIGP1|DIFF33|TMS-1|Tde1	serine incorporator 3	protein-coding
mm_159802.1	chr5	113490669	113490669	+	1	NA	Intergenic	CpG	-59751	NM_177292	320916	Mm.102783	NM_177292	ENSMUSG00000063430	Wscd2	4933413A10Rik|C530024P05Rik|Gm450	WSC domain containing 2	protein-coding
mm_144125.1	chr18	4908945	4908963	+	1	NA	Intergenic	Intergenic	96468	NR_045881	100038439	Mm.387569	NR_045881	ENSMUSG00000097043	Gm10556	ENSMUSG00000073646	predicted gene 10556	ncRNA
mm_26095.1	chr3	136903028	136903069	+	1	NA	intron (NM_008913, intron 8 of 13)	intron (NM_008913, intron 8 of 13)	232982	NM_001293622	19055	Mm.331389	NM_008913	ENSMUSG00000028161	Ppp3ca	2900074D19Rik|CN|Caln|Calna|CnA	protein phosphatase 3, catalytic subunit, alpha isoform	protein-coding
mm_18774.1	chr2	73529392	73529493	-	1	NA	promoter-TSS (NM_153138)	promoter-TSS (NM_153138)	45	NM_153138	215280	Mm.223504	NM_153138	ENSMUSG00000075284	Wipf1	AI115543|D2Ertd120e|WIP|Waspip	WAS/WASL interacting protein family, member 1	protein-coding
mm_35215.1	chr4	19650164	19650184	-	1	NA	exon (NM_177327, exon 9 of 25)	exon (NM_177327, exon 9 of 25)	58830	NM_177327	107568	Mm.78312	NM_177327	ENSMUSG00000041058	Wwp1	8030445B08Rik|AIP5|SDRP1|Tiul1	WW domain containing E3 ubiquitin protein ligase 1	protein-coding
mm_116833.1	chr13	54687217	54687232	-	1	NA	intron (NR_027395, intron 1 of 10)	CpG	584	NM_001146025	105239	Mm.25366	NM_134064	ENSMUSG00000034928	Rnf44	AI854545|mKIAA1100	ring finger protein 44	protein-coding
mm_13536.1	chr2	110601345	110601352	+	1	NA	intron (NM_001177624, intron 1 of 14)	MTD|LTR|ERVL-MaLR	4049	NM_001177624	241612	Mm.277148	NM_001003915	ENSMUSG00000041644	Slc5a12	AI315119|D630015G19|SMCT2	solute carrier family 5 (sodium/glucose cotransporter), member 12	protein-coding
mm_170067.1	chr17	31658713	31658714	-	1	NA	promoter-TSS (NM_001163769)	promoter-TSS (NM_001163769)	41	NM_024187	108121	Mm.379289	NM_024187	ENSMUSG00000061613	U2af1	2010107D16Rik|35kDa	U2 small nuclear ribonucleoprotein auxiliary factor (U2AF) 1	protein-coding
mm_47268.1	chr5	121848839	121848864	-	1	NA	promoter-TSS (NM_175474)	promoter-TSS (NM_175474)	-177	NM_175474	231717	Mm.12654	NM_175474	ENSMUSG00000044134	Fam109a	A230106M15Rik|AU017694|IPIP27A|Ses1	family with sequence similarity 109, member A	protein-coding
mm_171584.1	chr4	147553295	147553305	+	1	NA	promoter-TSS (NM_001014397)	promoter-TSS (NM_001014397)	23	NM_001014397	433804	Mm.332047	NM_001014397	ENSMUSG00000065999	Zfp985	Gm13154|OTTMUSG00000010673	zinc finger protein 985	protein-coding
mm_1210.1	chr1	62726666	62726724	+	1	NA	intron (NM_001077405, intron 2 of 15)	intron (NM_001077405, intron 2 of 15)	23378	NM_001077405	18187	Mm.266341	NM_010939	ENSMUSG00000025969	Nrp2	1110048P06Rik|Np-2|Np2|Npn-2|Npn2	neuropilin 2	protein-coding
mm_122472.1	chr14	45595143	45595172	-	1	NA	3' UTR (NM_001042719, exon 14 of 14)	3' UTR (NM_001042719, exon 14 of 14)	51447	NR_045809	67651	Mm.55930	NR_045809		4930527F14Rik	-	RIKEN cDNA 4930527F14 gene	ncRNA
mm_172707.1	chr8	65711467	65711467	-	1	NA	intron (NM_175188, intron 1 of 7)	L1Md_T|LINE|L1	92942	NM_175188	72925	Mm.380457	NM_175188	ENSMUSG00000036469	March1	2900024D24Rik|BB085186	membrane-associated ring finger (C3HC4) 1	protein-coding
mm_83825.1	chr9	53975121	53975202	-	1	NA	5' UTR (NM_177769, exon 1 of 11)	5' UTR (NM_177769, exon 1 of 11)	140	NM_177769	270162	Mm.259791	NM_177769	ENSMUSG00000041986	Elmod1	4831417L10|AI428506|AI834991	ELMO/CED-12 domain containing 1	protein-coding
mm_24350.1	chr3	89912893	89912898	+	1	NA	intron (NM_001310676, intron 1 of 9)	CpG	301	NM_001310676	16194	Mm.2856	NM_010559	ENSMUSG00000027947	Il6ra	CD126|IL-6R|IL-6R-alpha|IL-6RA|Il6r	interleukin 6 receptor, alpha	protein-coding
mm_80359.1	chr9	75217471	75217483	+	1	NA	intron (NM_010864, intron 39 of 40)	intron (NM_010864, intron 39 of 40)	-14537	NM_001081322	208943	Mm.41339	NM_001081322	ENSMUSG00000033590	Myo5c	9130003O20Rik|BB085560|C330029I24	myosin VC	protein-coding
mm_104050.1	chr11	86358184	86358194	-	1	NA	promoter-TSS (NM_001080931)	promoter-TSS (NM_001080931)	-664	NM_001080931	327987	Mm.341886	NM_001080931	ENSMUSG00000034297	Med13	1110067M05Rik|D030023K18|Thrap1|Trap240	mediator complex subunit 13	protein-coding
mm_94768.1	chr11	21239104	21239147	+	1	NA	promoter-TSS (NM_001290628)	promoter-TSS (NM_001290628)	93	NM_001290628	245944	Mm.170103	NM_139061	ENSMUSG00000020128	Vps54	Hcc8|Vps54l|mSLP8|wr	VPS54 GARP complex subunit	protein-coding
mm_2886.1	chr1	131847563	131847579	+	1	NA	3' UTR (NM_173865, exon 11 of 11)	3' UTR (NM_173865, exon 11 of 11)	19559	NM_173865	98396	Mm.389181	NM_173865	ENSMUSG00000013275	Slc41a1	AI573938|B230315F01Rik	solute carrier family 41, member 1	protein-coding
mm_121516.1	chr14	122030558	122030573	+	1	NA	Intergenic	Intergenic	-4109	NM_001037744	223262	Mm.297637	NM_001037744	ENSMUSG00000071229	Timm8a2	-	translocase of inner mitochondrial membrane 8A2	protein-coding
mm_50953.1	chr6	58831514	58831529	+	1	NA	Intergenic	CpG	-2179	NM_028705	73998	Mm.191892	NM_028705	ENSMUSG00000029804	Herc3	5730409F18Rik|AI646603|mKIAA0032	hect domain and RLD 3	protein-coding
mm_88213.1	chr10	70204676	70204684	+	1	NA	promoter-TSS (NM_001304739)	promoter-TSS (NM_001304739)	16	NM_001304739	69563	Mm.64672	NM_001304739	ENSMUSG00000019933	Mrln	2310015B20Rik|Mln	myoregulin	protein-coding
mm_96307.1	chr11	63158515	63158559	+	1	NA	3' UTR (NM_008885, exon 5 of 5)	3' UTR (NM_008885, exon 5 of 5)	25734	NM_001302260	18858	Mm.1237	NM_008885	ENSMUSG00000018217	Pmp22	22kDa|Gas-3|HNPP|Tr|trembler	peripheral myelin protein 22	protein-coding
mm_112588.1	chr13	13784279	13784365	+	1	NA	promoter-TSS (NM_010317)	promoter-TSS (NM_010317)	15	NM_010317	14706	Mm.215394	NM_010317	ENSMUSG00000021303	Gng4	-	guanine nucleotide binding protein (G protein), gamma 4	protein-coding
mm_85305.1	chr9	100571050	100571128	-	1	NA	promoter-TSS (NM_001101483)	promoter-TSS (NM_001101483)	-4	NM_001101483	245020	Mm.236289	NM_001101483	ENSMUSG00000070287	Slc35g2	Gm519|Tmem22	solute carrier family 35, member G2	protein-coding
mm_29176.1	chr3	106517016	106517020	-	1	NA	intron (NM_133869, intron 4 of 8)	intron (NM_133869, intron 4 of 8)	-30780	NM_001286986	67171	Mm.290488	NM_026013	ENSMUSG00000027900	Dram2	2010305N14Rik|2610318G18Rik|AI647667|Tmem77	DNA-damage regulated autophagy modulator 2	protein-coding
mm_163156.1	chr11	83743824	83743845	+	1	NA	Intergenic	Intergenic	-3106	NM_183249	66107	Mm.902	NM_183249	ENSMUSG00000051748	Wfdc21	1100001G20Rik|Wdnm1-like	WAP four-disulfide core domain 21	protein-coding
mm_30473.1	chr3	154632395	154632407	-	1	NA	Intergenic	Intergenic	-35303	NM_172474	209584	Mm.347513	NM_172474	ENSMUSG00000047583	Tyw3	5230400J09Rik	tRNA-yW synthesizing protein 3 homolog (S. cerevisiae)	protein-coding
mm_108060.1	chr12	73930700	73930711	+	1	NA	exon (NM_010431, exon 5 of 15)	exon (NM_010431, exon 5 of 15)	22838	NM_001313919	15251	Mm.3879	NM_010431	ENSMUSG00000021109	Hif1a	AA959795|HIF-1-alpha|HIF1-alpha|HIF1alpha|MOP1|bHLHe78	hypoxia inducible factor 1, alpha subunit	protein-coding
mm_10879.1	chr2	25242286	25242379	+	1	NA	promoter-TSS (NM_176834)	promoter-TSS (NM_176834)	-597	NM_176834	68846	Mm.24777	NM_176834	ENSMUSG00000044628	Rnf208	1110061N23Rik	ring finger protein 208	protein-coding
mm_168736.1	chr12	115145937	115145937	-	1	NA	Intergenic	Intergenic	549857	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
mm_121776.1	chr14	19890425	19890444	-	1	NA	intron (NM_001038637, intron 4 of 4)	RSINE1|SINE|B4	51509	NR_105025	52512	Mm.483998	NR_105025		D14Ertd670e	-	DNA segment, Chr 14, ERATO Doi 670, expressed	ncRNA
mm_36271.1	chr4	63729164	63729189	-	1	NA	3' UTR (NM_177371, exon 4 of 4)	3' UTR (NM_177371, exon 4 of 4)	15937	NM_177371	326623	Mm.208152	NM_177371	ENSMUSG00000050395	Tnfsf15	Tl1|Tl1a|Tnlg1b|Vegi	tumor necrosis factor (ligand) superfamily, member 15	protein-coding
mm_158457.1	chrX	140599201	140599220	-	1	NA	intron (NM_001077364, intron 1 of 3)	CpG	1312	NM_001077364	14605	Mm.22216	NM_010286	ENSMUSG00000031431	Tsc22d3	DIP|Dsip1|Gilz|TSC-22R|Tilz3	TSC22 domain family, member 3	protein-coding
mm_22825.1	chr3	27241422	27241432	+	1	NA	exon (NM_178772, exon 5 of 5)	exon (NM_178772, exon 5 of 5)	58423	NM_178772	320024	Mm.24576	NM_178772	ENSMUSG00000027698	Nceh1	Aadacl1|B230106I24Rik|CPO-BP|Nceh	neutral cholesterol ester hydrolase 1	protein-coding
mm_152462.1	chr19	10881724	10881766	-	1	NA	promoter-TSS (NM_134142)	promoter-TSS (NM_134142)	-2	NM_134142	68539	Mm.251890	NM_134142	ENSMUSG00000034659	Tmem109	1110006I15Rik|AA958958|C77652	transmembrane protein 109	protein-coding
mm_37211.1	chr4	117887268	117887278	-	1	NA	promoter-TSS (NM_033617)	promoter-TSS (NM_033617)	56	NM_033617	114143	Mm.207052	NM_033617	ENSMUSG00000033379	Atp6v0b	2310024H13Rik|Atp6f|VMA16	ATPase, H+ transporting, lysosomal V0 subunit B	protein-coding
mm_99166.1	chr11	100713955	100713965	+	1	NA	exon (NM_029307, exon 1 of 1)	exon (NM_029307, exon 1 of 1)	110	NM_029307	75482	Mm.46175	NM_029307	ENSMUSG00000017832	Hspb9	1700007H20Rik	heat shock protein, alpha-crystallin-related, B9	protein-coding
mm_18785.1	chr2	73660097	73660110	-	1	NA	5' UTR (NM_175752, exon 1 of 7)	5' UTR (NM_175752, exon 1 of 7)	320	NM_175752	108699	Mm.257073	NM_029716	ENSMUSG00000056486	Chn1	0610007I19Rik|0710001E19Rik|1700112L09Rik|2900046J01Rik|AI413815|ARHGAP2	chimerin 1	protein-coding
mm_139009.1	chr17	45570465	45570469	+	1	NA	exon (NM_008302, exon 6 of 11)	exon (NM_008302, exon 6 of 11)	2794	NM_008302	15516	Mm.2180	NM_008302	ENSMUSG00000023944	Hsp90ab1	90kDa|AL022974|C81438|Hsp84|Hsp84-1|Hsp90|Hspcb	heat shock protein 90 alpha (cytosolic), class B member 1	protein-coding
mm_77125.1	chr8	111333561	111333571	-	1	NA	exon (NM_001310613, exon 2 of 11)	exon (NM_001310613, exon 2 of 11)	4639	NM_001310613	74568	Mm.207971	NM_029005	ENSMUSG00000012519	Mlkl	9130019I15Rik	mixed lineage kinase domain-like	protein-coding
mm_32442.1	chr4	107257119	107257122	+	1	NA	intron (NM_028394, intron 1 of 5)	B2_Mm2|SINE|B2	3186	NM_028394	72938	Mm.21787	NM_028394	ENSMUSG00000063172	Hspb11	2900042B11Rik|IFT25	heat shock protein family B (small), member 11	protein-coding
mm_5516.1	chr1	37559800	37559812	-	1	NA	Intergenic	Intergenic	-18790	NM_173870	269181	Mm.25861	NM_173870	ENSMUSG00000026110	Mgat4a	9530018I07Rik|GnT-IVa|glcNAc-T-IVa	mannoside acetylglucosaminyltransferase 4, isoenzyme A	protein-coding
mm_69382.1	chr7	131322104	131322108	-	1	NA	5' UTR (NM_008411, exon 1 of 9)	5' UTR (NM_008411, exon 1 of 9)	186	NM_008411	16433	Mm.142717	NM_008411	ENSMUSG00000040205	Cuzd1	Erg-1|Itmap1|Uo-44|Usg|Utczp	CUB and zona pellucida-like domains 1	protein-coding
mm_48173.1	chr5	137154088	137154104	-	1	NA	Intergenic	Intergenic	-37889	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_120298.1	chr14	63138987	63139058	+	1	NA	exon (NM_007798, exon 8 of 10)	exon (NM_007798, exon 8 of 10)	16560	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_50028.1	chr6	41122031	41122042	+	1	NA	Intergenic	Intergenic	-86527	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_37524.1	chr4	124708633	124708656	-	1	NA	TTS (NM_010213)	TTS (NM_010213)	-6217	NM_029157	75062	Mm.25779	NM_029157	ENSMUSG00000028902	Sf3a3	4930512K19Rik|60kDa	splicing factor 3a, subunit 3	protein-coding
mm_163172.1	chr11	87719656	87719660	-	1	NA	intron (NM_172448, intron 3 of 9)	intron (NM_172448, intron 3 of 9)	-17907	NM_009296	20922	Mm.622	NM_009296	ENSMUSG00000020485	Supt4a	AL022777|Supt4h|Supt4h1|Supt4h1a	suppressor of Ty 4A	protein-coding
mm_139204.1	chr17	47688993	47689007	+	1	NA	promoter-TSS (NM_001164729)	promoter-TSS (NM_001164729)	-614	NM_001164729	66119	Mm.89912	NM_025365	ENSMUSG00000033475	Tomm6	1110002E23Rik|AI663970	translocase of outer mitochondrial membrane 6 homolog (yeast)	protein-coding
mm_57099.1	chr6	122590661	122590671	-	1	NA	intron (NM_001134391, intron 4 of 7)	B1F|SINE|Alu	11778	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_90434.1	chr10	127621781	127621801	+	1	NA	promoter-TSS (NM_008512)	promoter-TSS (NM_008512)	-643	NM_008512	16971	Mm.271854	NM_008512	ENSMUSG00000040249	Lrp1	A2mr|AI316852|CD91|Lrp|b2b1554Clo	low density lipoprotein receptor-related protein 1	protein-coding
mm_70067.1	chr7	142652444	142652461	-	1	NA	3' UTR (NM_010514, exon 4 of 4)	3' UTR (NM_010514, exon 4 of 4)	2544	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_61315.1	chr7	68104156	68104159	+	1	NA	intron (NM_010513, intron 2 of 20)	intron (NM_010513, intron 2 of 20)	151900	NM_010513	16001	Mm.275742	NM_010513	ENSMUSG00000005533	Igf1r	A330103N21Rik|CD221|D930020L01|IGF-1R|hyft	insulin-like growth factor I receptor	protein-coding
mm_17791.1	chr2	33086431	33086447	-	1	NA	intron (NM_178888, intron 1 of 28)	intron (NM_178888, intron 1 of 28)	765	NM_178888	99326	Mm.41290	NM_178888	ENSMUSG00000038860	Garnl3	AW120551	GTPase activating RANGAP domain-like 3	protein-coding
mm_55295.1	chr6	54681928	54681939	-	1	NA	intron (NM_001289740, intron 1 of 2)	CpG	309	NM_001289740	68235	Mm.233860	NM_026629	ENSMUSG00000038065	Mturn	2410066E13Rik|AI448550|B230212L03Rik	maturin, neural progenitor differentiation regulator homolog (Xenopus)	protein-coding
mm_28977.1	chr3	101110157	101110170	-	1	NA	promoter-TSS (NM_011197)	promoter-TSS (NM_011197)	3	NM_011197	19221	Mm.24807	NM_011197	ENSMUSG00000027864	Ptgfrn	4833445A08Rik|AU042434|CD9P-1|FPRP|Trim45	prostaglandin F2 receptor negative regulator	protein-coding
mm_84185.1	chr9	60141209	60141217	-	1	NA	promoter-TSS (NM_172444)	promoter-TSS (NM_172444)	7	NM_172444	207596	Mm.28791	NM_172444	ENSMUSG00000032289	Thsd4	ADAMTSL-6|ADAMTSL6|AI585901|Adamtsl4|B230114P05Rik	thrombospondin, type I, domain containing 4	protein-coding
mm_46776.1	chr5	112394814	112394832	-	1	NA	Intergenic	CpG	-2610	NM_028386	72898	Mm.151745	NM_028386	ENSMUSG00000029348	Asphd2	2900006N09Rik|9230106G13Rik	aspartate beta-hydroxylase domain containing 2	protein-coding
mm_145074.1	chr18	42141903	42141919	+	1	NA	intron (NM_172966, intron 5 of 7)	L3|LINE|CR1	54798	NM_027072	69401	Mm.34841	NM_027072	ENSMUSG00000059455	Plac8l1	1700009N18Rik|1700015M15Rik	PLAC8-like 1	protein-coding
mm_108958.1	chr12	102368916	102368936	+	1	NA	exon (NM_001161365, exon 6 of 10)	exon (NM_001161365, exon 6 of 10)	70887	NM_011175	19141	Mm.17185	NM_011175	ENSMUSG00000021190	Lgmn	AEP|AI746452|AU022324|Prsc1	legumain	protein-coding
mm_53663.1	chr6	141524569	141524586	+	1	NA	5' UTR (NM_001177772, exon 1 of 15)	5' UTR (NM_001177772, exon 1 of 15)	191	NM_021471	58807	Mm.284495	NM_021471	ENSMUSG00000030235	Slco1c1	OATP-14|OATP-F|Oatp2|Oatpf|Slc21a14	solute carrier organic anion transporter family, member 1c1	protein-coding
mm_57721.1	chr6	128839624	128839648	-	1	NA	Intergenic	Intergenic	-13321	NM_030599	80782	Mm.6180	NM_030599	ENSMUSG00000079298	Klrb1b	Klrb1d|Ly55b|Ly55d|NKR-P1B|NKR-P1D|Nkrp1-b|Nkrp1d|ly-55b|ly-55d	killer cell lectin-like receptor subfamily B member 1B	protein-coding
mm_154673.1	chrX	7884297	7884313	+	1	NA	promoter-TSS (NM_001083937)	promoter-TSS (NM_001083937)	61	NM_078484	22232	Mm.214976	NM_078484	ENSMUSG00000031156	Slc35a2	AI327289|Had-1|Had1|Sfc8|UGT|Ugalt	solute carrier family 35 (UDP-galactose transporter), member A2	protein-coding
mm_110456.1	chr12	51691884	51691925	-	1	NA	promoter-TSS (NM_001172098)	promoter-TSS (NM_001172098)	10	NM_001172098	94186	Mm.65979	NM_052973	ENSMUSG00000020954	Strn3	Gs2na|SG2NA	striatin, calmodulin binding protein 3	protein-coding
mm_127603.1	chr15	102406270	102406333	+	1	NA	promoter-TSS (NM_013672)	promoter-TSS (NM_013672)	-15	NM_013672	20683	Mm.4618	NM_013672	ENSMUSG00000001280	Sp1	1110003E12Rik|AA450830|AI845540|Sp1-1	trans-acting transcription factor 1	protein-coding
mm_152546.1	chr19	11372350	11372373	-	1	NA	Intergenic	Intergenic	-3127	NM_001310331	666907		NM_001310331	ENSMUSG00000101389	Ms4a4a	EG666907	membrane-spanning 4-domains, subfamily A, member 4A	protein-coding
mm_6474.1	chr1	74068917	74068974	-	1	NA	intron (NM_027884, intron 2 of 34)	CpG-274	55502	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_11445.1	chr2	32057607	32057617	+	1	NA	Intergenic	Intergenic	6666	NR_106135	102466844		NR_106135	ENSMUSG00000099075	Mir7674	Gm27563|mmu-mir-7674	microRNA 7674	ncRNA
mm_26416.1	chr3	142610985	142610998	+	1	NA	exon (NM_010259, exon 9 of 11)	exon (NM_010259, exon 9 of 11)	-9672	NM_010260	14469	Mm.24038	NM_010260	ENSMUSG00000028270	Gbp2	-	guanylate binding protein 2	protein-coding
mm_124328.1	chr14	103843541	103843551	-	1	NA	5' UTR (NM_001276296, exon 1 of 8)	5' UTR (NM_001276296, exon 1 of 8)	155	NM_007904	13618	Mm.229532	NM_007904	ENSMUSG00000022122	Ednrb	ET-B|ET-BR|ETR-b|ETb|Sox10m1	endothelin receptor type B	protein-coding
mm_152634.1	chr19	12501814	12501822	-	1	NA	5' UTR (NM_172442, exon 1 of 9)	5' UTR (NM_172442, exon 1 of 9)	178	NM_172442	207521	Mm.247695	NM_172442	ENSMUSG00000039982	Dtx4	AI449438|BC044798|D930042H13|RNF155	deltex 4, E3 ubiquitin ligase	protein-coding
mm_118668.1	chr14	21989933	21989970	+	1	NA	promoter-TSS (NM_145459)	promoter-TSS (NM_145459)	-350	NM_145459	218820	Mm.292401	NM_145459	ENSMUSG00000039081	Zfp503	AI181838|B830002A16Rik|Nolz-1|Nolz1|Znf503	zinc finger protein 503	protein-coding
mm_152178.1	chr19	7383021	7383025	-	1	NA	promoter-TSS (NM_001033139)	promoter-TSS (NM_001033139)	3	NM_001033139	68229	Mm.34766	NM_001033139	ENSMUSG00000024970	AI846148	1700105P06Rik	expressed sequence AI846148	protein-coding
mm_32005.1	chr4	94624727	94624744	+	1	NA	exon (NM_001290568, exon 4 of 14)	exon (NM_001290568, exon 4 of 14)	10244	NM_026319	67694	Mm.240619	NM_026319	ENSMUSG00000028576	Ift74	1700029H06Rik|Ccdc2|Cmg1|b2b796Clo	intraflagellar transport 74	protein-coding
mm_110868.1	chr12	73586457	73586459	-	1	NA	intron (NM_008856, intron 1 of 13)	intron (NM_008856, intron 1 of 13)	1662	NM_008856	18755	Mm.341677	NM_008856	ENSMUSG00000021108	Prkch	Pkch	protein kinase C, eta	protein-coding
mm_26785.1	chr3	9610075	9610086	-	1	NA	promoter-TSS (NM_133218)	promoter-TSS (NM_133218)	5	NM_133218	170753	Mm.212908	NM_133218	ENSMUSG00000040209	Zfp704	C030026M03|C030034L19Rik|Gig1|Znf704	zinc finger protein 704	protein-coding
mm_85449.1	chr9	104320054	104320080	-	1	NA	exon (NM_019807, exon 5 of 11)	exon (NM_019807, exon 5 of 11)	17655	NM_019807	56318	Mm.19941	NM_019807	ENSMUSG00000032561	Acpp	5'-NT|A030005E02Rik|FRAP|Lap|PAP|Ppal	acid phosphatase, prostate	protein-coding
mm_168995.1	chr13	100233906	100233907	+	1	NA	intron (NM_010870, intron 4 of 14)	intron (NM_010870, intron 4 of 14)	13430	NM_010870	17951	Mm.290476	NM_010870	ENSMUSG00000071203	Naip5	Birc1e|Lgn1|Naip-rs3	NLR family, apoptosis inhibitory protein 5	protein-coding
mm_150591.1	chr19	40667608	40667612	+	1	NA	intron (NM_009848, intron 1 of 9)	intron (NM_009848, intron 1 of 9)	7840	NM_009848	12495	Mm.2824	NM_009848	ENSMUSG00000048120	Entpd1	2610206B08Rik|AA408691|Cd39|NTPDase-1	ectonucleoside triphosphate diphosphohydrolase 1	protein-coding
mm_60755.1	chr7	45513719	45513747	+	1	NA	promoter-TSS (NM_008807)	promoter-TSS (NM_008807)	27	NM_001045555	56734	Mm.439742	NM_008807	ENSMUSG00000023467	Tulp2	Pdet	tubby-like protein 2	protein-coding
mm_99605.1	chr11	104576966	104576978	+	1	NA	intron (NM_010858, intron 2 of 8)	intron (NM_010858, intron 2 of 8)	-14774	NR_130177	100415912	Mm.446786	NR_130177		Gm11665	Gm11664|OTTMUSG00000003182|OTTMUSG00000003183	predicted gene 11665	ncRNA
mm_135508.1	chr16	46990349	46990355	-	1	NA	Intergenic	Intergenic	-493385	NM_021497	58998	Mm.40477	NM_021495	ENSMUSG00000022656	Nectin3	2610301B19Rik|3000002N23Rik|4921513D19Rik|AA407785|AU016832|AW538082|CD113|Pvrl3	nectin cell adhesion molecule 3	protein-coding
mm_142407.1	chr17	45474840	45474885	-	1	NA	promoter-TSS (NM_027649)	promoter-TSS (NM_027649)	76	NM_027649	71020	Mm.44257	NM_027649	ENSMUSG00000023935	Spats1	1700011H05Rik|4933400B06Rik|Daip2|Ddip|Srsp1	spermatogenesis associated, serine-rich 1	protein-coding
mm_52230.1	chr6	103664730	103664732	+	1	NA	exon (NM_007697, exon 6 of 27)	exon (NM_007697, exon 6 of 27)	153855	NM_007697	12661	Mm.251288	NM_007697	ENSMUSG00000030077	Chl1	A530023M13Rik|AI465420|CALL|LICAM2	cell adhesion molecule L1-like	protein-coding
mm_133416.1	chr16	85819240	85819244	+	1	NA	promoter-TSS (NR_040506)	promoter-TSS (NR_040506)	31	NR_040506	75310	Mm.108627	NR_040506		4930556C24Rik	-	RIKEN cDNA 4930556C24 gene	ncRNA
mm_46352.1	chr5	102913118	102913154	-	1	NA	3' UTR (NM_001081567, exon 14 of 14)	3' UTR (NM_001081567, exon 14 of 14)	68129	NM_001346585	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding
mm_82643.1	chr9	22015291	22015304	-	1	NA	3' UTR (NM_010487, exon 7 of 7)	3' UTR (NM_010487, exon 7 of 7)	12309	NM_008925	19089	Mm.214593	NM_008925	ENSMUSG00000003402	Prkcsh	80K-H|PKCSH	protein kinase C substrate 80K-H	protein-coding
mm_41445.1	chr5	90905324	90905326	+	1	NA	3' UTR (NM_009140, exon 4 of 4)	3' UTR (NM_009140, exon 4 of 4)	1426	NM_009140	20310	Mm.4979	NM_009140	ENSMUSG00000058427	Cxcl2	CINC-2a|GROb|Gro2|MIP-2|MIP-2a|Mgsa-b|Mip2|Scyb|Scyb2	chemokine (C-X-C motif) ligand 2	protein-coding
mm_155437.1	chrX	73494673	73494691	+	1	NA	exon (NM_007542, exon 8 of 8)	exon (NM_007542, exon 8 of 8)	-8404	NM_001310537	320707	Mm.210095	NM_177236	ENSMUSG00000031376	Atp2b3	6430519O13Rik|Pmca3	ATPase, Ca++ transporting, plasma membrane 3	protein-coding
mm_17244.1	chr2	25621894	25621915	-	1	NA	promoter-TSS (NM_001040130)	promoter-TSS (NM_001040130)	98	NM_001040130	51875	Mm.271147	NM_001040130	ENSMUSG00000026939	Tmem141	1110065P14Rik|AI663999|D2Ertd217e	transmembrane protein 141	protein-coding
mm_33478.1	chr4	130818789	130818804	+	1	NA	exon (NM_011520, exon 3 of 5)	exon (NM_011520, exon 3 of 5)	26259	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_162965.1	chr11	9118099	9118133	+	1	NA	promoter-TSS (NM_009477)	promoter-TSS (NM_009477)	13	NM_009477	22271	Mm.4610	NM_009477	ENSMUSG00000020407	Upp1	AI325217|UPase|UdRPase|Up|Upp	uridine phosphorylase 1	protein-coding
mm_103921.1	chr11	83592982	83592999	-	1	NA	promoter-TSS (NM_009139)	promoter-TSS (NM_009139)	97	NM_009139	20305	Mm.137	NM_009139	ENSMUSG00000018927	Ccl6	MRP-1|Scya6|c10	chemokine (C-C motif) ligand 6	protein-coding
mm_131274.1	chr16	11011511	11011551	+	1	NA	intron (NR_040518, intron 1 of 2)	intron (NR_040518, intron 1 of 2)	2633	NR_040518	100043147	Mm.489001	NR_040518	ENSMUSG00000097056	Gm4262	-	predicted gene 4262	ncRNA
mm_54169.1	chr6	23254078	23254120	-	1	NA	Intergenic	Intergenic	-5835	NM_028462	73191	Mm.55115	NM_028462	ENSMUSG00000029697	Fezf1	3110069A13Rik|Fez|Zfp312-like|fez-like	Fez family zinc finger 1	protein-coding
mm_148158.1	chr18	77632140	77632145	-	1	NA	Intergenic	Intergenic	-67006	NM_001164504	225743	Mm.23293	NM_001164504	ENSMUSG00000025427	Rnf165	2900024M11Rik|AI427432|Akd2|Ark2c|G630064H08Rik|Gm96	ring finger protein 165	protein-coding
mm_1005.1	chr1	58722730	58722747	+	1	NA	intron (NM_009805, intron 1 of 4)	intron (NM_009805, intron 1 of 4)	-7814	NM_001293805	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_172525.1	chr7	84713312	84713315	-	1	NA	intron (NR_038175, intron 1 of 4)	L1Md_T|LINE|L1	23673	NR_038175	72495	Mm.382914	NR_038175	ENSMUSG00000085236	2610206C17Rik	-	RIKEN cDNA 2610206C17 gene	ncRNA
mm_98754.1	chr11	96545571	96545581	+	1	NA	intron (NM_001033186, intron 4 of 12)	intron (NM_001033186, intron 4 of 12)	80985	NM_001177898	78473	Mm.395840	NM_001033186	ENSMUSG00000057058	Skap1	1700091G21Rik|Scap1|Skap-55	src family associated phosphoprotein 1	protein-coding
mm_18257.1	chr2	52272964	52272972	-	1	NA	intron (NM_010889, intron 47 of 156)	intron (NM_010889, intron 47 of 156)	-18034	NR_040620	78049	Mm.243883	NR_040620		4930573O16Rik	-	RIKEN cDNA 4930573O16 gene	ncRNA
mm_68440.1	chr7	109960498	109960504	-	1	NA	promoter-TSS (NM_021494)	promoter-TSS (NM_021494)	-31	NM_001311139	19347	Mm.21904	NM_021494	ENSMUSG00000035901	Dennd5a	1500012B19Rik|AJ245569|AW496491|ORF37|Rab6ip1|mKIAA1091	DENN/MADD domain containing 5A	protein-coding
mm_115054.1	chr13	100651591	100651601	+	1	NA	promoter-TSS (NM_001015889)	promoter-TSS (NM_001015889)	-11	NM_001015889	108143	Mm.301148	NM_027139	ENSMUSG00000052293	Taf9	2310012M09Rik|AA673500|AU045423|TAFII31|TAFII32|Taf2g	TATA-box binding protein associated factor 9	protein-coding
mm_72301.1	chr8	76899774	76899828	+	1	NA	intron (NR_028579, intron 1 of 1)	CpG	372	NR_028579	100039211	Mm.367571	NR_028579	ENSMUSG00000074235	Gm10649	ENSMUSG00000074235	predicted gene 10649	ncRNA
mm_169578.1	chr15	22714206	22714210	-	1	NA	exon (NM_001165971, exon 1 of 1)	exon (NM_001165971, exon 1 of 1)	776	NM_001165971	545091	Mm.475598	NM_001165971		Gm5803	EG545091	predicted gene 5803	protein-coding
mm_45248.1	chr5	59985983	59985997	-	1	NA	promoter-TSS (NR_040683)	promoter-TSS (NR_040683)	12	NR_040683	71057	Mm.50817	NR_040682	ENSMUSG00000106013	4933402J10Rik	-	RIKEN cDNA 4933402J10 gene	ncRNA
mm_71405.1	chr8	46471049	46471078	+	1	NA	promoter-TSS (NM_007981)	promoter-TSS (NM_007981)	26	NM_007981	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_88051.1	chr10	67540017	67540041	+	1	NA	exon (NM_010118, exon 2 of 2)	exon (NM_010118, exon 2 of 2)	2099	NM_001347458	13654	Mm.290421	NM_010118	ENSMUSG00000037868	Egr2	Egr-2|Krox-20|Krox20|NGF1-B|Zfp-25|Zfp-6	early growth response 2	protein-coding
mm_100508.1	chr11	120498086	120498103	+	1	NA	exon (NM_013770, exon 11 of 11)	exon (NM_013770, exon 11 of 11)	6257	NM_013770	27376	Mm.3991	NM_013770	ENSMUSG00000025792	Slc25a10	Dic	solute carrier family 25 (mitochondrial carrier, dicarboxylate transporter), member 10	protein-coding
mm_49511.1	chr6	29859663	29859684	+	1	NA	promoter-TSS (NM_001171001)	promoter-TSS (NM_001171001)	77	NM_001171001	74340	Mm.210899	NM_021414	ENSMUSG00000029772	Ahcyl2	4631427C17Rik|AI227036|Adohcyase3|mKIAA0828	S-adenosylhomocysteine hydrolase-like 2	protein-coding
mm_170872.1	chr2	20899859	20899863	+	1	NA	intron (NM_001128084, intron 3 of 24)	LSU-rRNA_Hsa|rRNA|rRNA	67860	NM_001081364	71435	Mm.28507	NM_001081364	ENSMUSG00000036591	Arhgap21	5530401C11Rik|AA416458|ARHGAP10	Rho GTPase activating protein 21	protein-coding
mm_131727.1	chr16	21826018	21826045	+	1	NA	Intergenic	Intergenic	31684	NR_037957	100043489	Mm.326535	NR_037957	ENSMUSG00000097290	1300002E11Rik	1500026P21Rik	RIKEN cDNA 1300002E11 gene	ncRNA
mm_17538.1	chr2	29772254	29772264	-	1	NA	Intergenic	Intergenic	10731	NM_001177392	433416	Mm.330112	NM_001034887	ENSMUSG00000075425	Gm13547	OTTMUSG00000012686	predicted gene 13547	protein-coding
mm_43595.1	chr5	137778872	137778935	+	1	NA	promoter-TSS (NM_027242)	promoter-TSS (NM_027242)	-15	NM_027242	69871	Mm.276058	NM_027242	ENSMUSG00000029725	Ppp1r35	2010007H12Rik|2010011D20Rik|AL024004	protein phosphatase 1, regulatory subunit 35	protein-coding
mm_130309.1	chr15	97031206	97031221	-	1	NA	intron (NM_027052, intron 1 of 15)	intron (NM_027052, intron 1 of 15)	24743	NM_027052	69354	Mm.250980	NM_027052	ENSMUSG00000022464	Slc38a4	1110012E16Rik|1700012A18Rik|Ata3|mATA3|mNAT3	solute carrier family 38, member 4	protein-coding
mm_163267.1	chr11	114741737	114741742	+	1	NA	intron (NM_001034878, intron 6 of 12)	intron (NM_001034878, intron 6 of 12)	8010	NR_037269	100526524		NR_037269	ENSMUSG00000077991	Mir466n	mmu-mir-466n	microRNA 466n	ncRNA
mm_127803.1	chr15	4027346	4027355	-	1	NA	promoter-TSS (NR_028266)	promoter-TSS (NR_028266)	56	NR_028266	414066	Mm.394461	NR_028266		BC037032	-	cDNA Sequence BC037032	ncRNA
mm_65615.1	chr7	27532625	27532654	-	1	NA	exon (NM_011116, exon 13 of 14)	exon (NM_011116, exon 13 of 14)	9378	NM_001033315	233020	Mm.429716	NM_001033315	ENSMUSG00000040424	Hipk4	Gm162	homeodomain interacting protein kinase 4	protein-coding
mm_95356.1	chr11	48837493	48837513	+	1	NA	promoter-TSS (NM_001347436)	promoter-TSS (NM_001347436)	32	NM_001347446	94089	Mm.390335	NM_053166	ENSMUSG00000040350	Trim7	AI790312	tripartite motif-containing 7	protein-coding
mm_143892.1	chr17	84512122	84512140	-	1	NA	intron (NM_177606, intron 1 of 29)	CpG	236	NM_177606	213556	Mm.215159	NM_177606	ENSMUSG00000040852	Plekhh2	AI256725|E030001K05|mKIAA2028	pleckstrin homology domain containing, family H (with MyTH4 domain) member 2	protein-coding
mm_55146.1	chr6	51466378	51466404	-	1	NA	exon (NM_182650, exon 5 of 10)	exon (NM_182650, exon 5 of 10)	3503	NM_182650	53379	Mm.155896	NM_016806	ENSMUSG00000004980	Hnrnpa2b1	9130414A06Rik|Hnrpa2|Hnrpa2b1|hnrnp-A	heterogeneous nuclear ribonucleoprotein A2/B1	protein-coding
mm_122772.1	chr14	54409301	54409308	-	1	NA	5' UTR (NM_001253680, exon 1 of 10)	5' UTR (NM_001253680, exon 1 of 10)	168	NM_001253680	20540	Mm.142455	NM_011405	ENSMUSG00000000958	Slc7a7	AI790233|my+lat1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 7	protein-coding
mm_119777.1	chr14	54179525	54179530	+	1	NA	Intergenic	Intergenic	74402	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_128807.1	chr15	66949229	66949234	-	1	NA	intron (NM_008681, intron 3 of 15)	intron (NM_008681, intron 3 of 15)	20410	NM_008681	17988	Mm.30837	NM_008681	ENSMUSG00000005125	Ndrg1	CAP43|CMT4D|DRG1|HMSNL|NMSL|Ndr1|Ndrl|PROXY1|RTP|TDD5	N-myc downstream regulated gene 1	protein-coding
mm_15917.1	chr2	165064992	165065002	+	1	NA	intron (NM_170703, intron 5 of 7)	intron (NM_170703, intron 5 of 7)	9361	NM_011611	21939	Mm.271833	NM_011611	ENSMUSG00000017652	Cd40	AI326936|Bp50|GP39|HIGM1|IGM|IMD3|T-BAM|TRAP|Tnfrsf5|p50	CD40 antigen	protein-coding
mm_40467.1	chr5	53671863	53671873	+	1	NA	Intergenic	Intergenic	26720	NR_024201	19866		NR_024201	ENSMUSG00000089083	Rnu7	-	U7 small nuclear RNA	snRNA
mm_66920.1	chr7	60216837	60216858	-	1	NA	Intergenic	Intergenic	-76628	NM_001082962	20646	Mm.274995	NM_013670	ENSMUSG00000102252	Snrpn	2410045I01Rik|HCERN3|Peg4|Pwcr1|SMN	small nuclear ribonucleoprotein N	protein-coding
mm_46956.1	chr5	114971118	114971128	-	1	NA	promoter-TSS (NM_009327)	promoter-TSS (NM_009327)	-61	NM_009327	21405	Mm.332607	NM_009327	ENSMUSG00000029556	Hnf1a	AI323641|HNF1|HNF1-alpha|HNF1[a]|Hnf-1|Hnf1alpha|LFB1|Tcf-1|Tcf1	HNF1 homeobox A	protein-coding
mm_82518.1	chr9	20642281	20642322	-	1	NA	5' UTR (NM_013911, exon 1 of 3)	5' UTR (NM_013911, exon 1 of 3)	505	NM_013911	30843	Mm.24608	NM_013911	ENSMUSG00000066892	Fbxl12	3110048D16Rik|Fbl12	F-box and leucine-rich repeat protein 12	protein-coding
mm_145930.1	chr18	67133714	67133734	+	1	NA	5' UTR (NM_010307, exon 1 of 12)	5' UTR (NM_010307, exon 1 of 12)	164	NM_010307	14680	Mm.440746	NM_010307	ENSMUSG00000024524	Gnal	2610011C15Rik|9630020G10Rik|Galphaolf|Gna10|Golf	guanine nucleotide binding protein, alpha stimulating, olfactory type	protein-coding
mm_87830.1	chr10	60364237	60364265	+	1	NA	exon (NM_001159572, exon 4 of 7)	exon (NM_001159572, exon 4 of 7)	17400	NM_028732	74048	Mm.273584	NM_028732	ENSMUSG00000020101	Vsir	4632428N05Rik|Dies1|PD-1H|VISTA	V-set immunoregulatory receptor	protein-coding
mm_95657.1	chr11	53770459	53770505	+	1	NA	promoter-TSS (NM_001159396)	promoter-TSS (NM_001159396)	9	NM_001159396	16362	Mm.105218	NM_008390	ENSMUSG00000018899	Irf1	AU020929|Irf-1	interferon regulatory factor 1	protein-coding
mm_117595.1	chr13	89742517	89742531	-	1	NA	promoter-TSS (NM_001134474)	promoter-TSS (NM_001134474)	-12	NM_001134475	13003	Mm.158700	NM_019389	ENSMUSG00000021614	Vcan	5430420N07Rik|9430051N09|Cspg2|DPEAAE|NG2|PG-M|PG-M(V0)|PG-M(V1)|hdf	versican	protein-coding
mm_82254.1	chr9	4796142	4796159	-	1	NA	promoter-TSS (NM_001113181)	promoter-TSS (NM_001113181)	84	NM_001113180	14802	Mm.209263	NM_019691	ENSMUSG00000025892	Gria4	GluA4|GluR-D|Glur-4|Glur4|Gluralpha4|spkw1	glutamate receptor, ionotropic, AMPA4 (alpha 4)	protein-coding
mm_34825.1	chr4	155067029	155067064	+	1	NA	promoter-TSS (NM_001042407)	promoter-TSS (NM_001042407)	16	NM_001042407	668173	Mm.133114	NM_001042407	ENSMUSG00000029047	Pex10	AV128229|Gm142	peroxisomal biogenesis factor 10	protein-coding
mm_33740.1	chr4	134124511	134124558	+	1	NA	intron (NR_045571, intron 10 of 13)	intron (NR_045571, intron 10 of 13)	4219	NM_080559	73723	Mm.22240	NM_080559	ENSMUSG00000028843	Sh3bgrl3	1110004L05Rik|AU022188	SH3 domain binding glutamic acid-rich protein-like 3	protein-coding
mm_168599.1	chr1	174172709	174172716	+	1	NA	promoter-TSS (NM_011465)	promoter-TSS (NM_011465)	-64	NM_011465	20739	Mm.200611	NM_011465	ENSMUSG00000026532	Spta1	AF093576|AI451697|Spna-1|Spna1|ha|ihj|nmf4|sph	spectrin alpha, erythrocytic 1	protein-coding
mm_161337.1	chr14	51116600	51116600	+	1	NA	promoter-TSS (NM_203508)	promoter-TSS (NM_203508)	47	NM_203508	219026	Mm.297297	NM_203508	ENSMUSG00000072575	Eddm3b	Fam12|Gm75	epididymal protein 3B	protein-coding
mm_120043.1	chr14	56575510	56575534	+	1	NA	promoter-TSS (NM_001145978)	promoter-TSS (NM_001145978)	-97	NM_001145978	328417	Mm.379357	NM_001145978	ENSMUSG00000054509	Parp4	Adprtl1|C030027K23Rik|E230037B21Rik|Gm743|PARPL|PH5P|VAULT3|VPARP|p193	poly (ADP-ribose) polymerase family, member 4	protein-coding
mm_89372.1	chr10	88732912	88732915	+	1	NA	intron (NM_025859, intron 1 of 5)	intron (NM_025859, intron 1 of 5)	1499	NM_025859	104303	Mm.291247	NM_025859	ENSMUSG00000060904	Arl1	2310008D22Rik|AU019749	ADP-ribosylation factor-like 1	protein-coding
mm_151894.1	chr19	5798895	5798899	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	-2916	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_76038.1	chr8	77433256	77433266	-	1	NA	intron (NM_030113, intron 3 of 22)	intron (NM_030113, intron 3 of 22)	-83795	NR_028125	70345	Mm.411813	NR_028125	ENSMUSG00000097882	0610038B21Rik	-	RIKEN cDNA 0610038B21 gene	ncRNA
mm_74197.1	chr8	123805993	123806037	+	1	NA	promoter-TSS (NM_009003)	promoter-TSS (NM_009003)	19	NM_009003	19341	Mm.9221	NM_009003	ENSMUSG00000019478	Rab4a	AI848268|Rab4	RAB4A, member RAS oncogene family	protein-coding
mm_91168.1	chr10	20697498	20697515	-	1	NA	intron (NM_013875, intron 1 of 12)	intron (NM_013875, intron 1 of 12)	27572	NM_013875	29863	Mm.425617	NM_013875	ENSMUSG00000019990	Pde7b	-	phosphodiesterase 7B	protein-coding
mm_44607.1	chr5	25299578	25299589	-	1	NA	exon (NM_001081383, exon 43 of 59)	exon (NM_001081383, exon 43 of 59)	76690	NM_144908	231050	Mm.21814	NM_144908	ENSMUSG00000038072	Galnt11	A430075I06Rik|AI648252|E430002F06Rik	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 11	protein-coding
mm_159226.1	chr2	130839604	130839604	-	1	NA	promoter-TSS (NM_001311147)	promoter-TSS (NM_001311147)	83	NM_001311147	228602	Mm.271990	NM_028367	ENSMUSG00000027309	4930402H24Rik	2810487F15Rik|AI413763|C78926	RIKEN cDNA 4930402H24 gene	protein-coding
mm_154698.1	chrX	8271169	8271179	+	1	NA	promoter-TSS (NM_172479)	promoter-TSS (NM_172479)	-207	NM_172479	209837	Mm.6055	NM_172479	ENSMUSG00000031170	Slc38a5	C81234|E330031E14|JM24|SN2	solute carrier family 38, member 5	protein-coding
mm_71651.1	chr8	60195884	60195891	+	1	NA	Intergenic	Intergenic	-310237	NM_011834	23923	Mm.35020	NM_011834	ENSMUSG00000057228	Aadat	AI875679|Aadt|KATII|Kat2|Kyat2|mKat-2	aminoadipate aminotransferase	protein-coding
mm_109179.1	chr12	108423139	108423157	+	1	NA	5' UTR (NM_001043335, exon 1 of 22)	5' UTR (NM_001043335, exon 1 of 22)	332	NM_001043335	68519	Mm.236645	NM_001043335	ENSMUSG00000058070	Eml1	1110008N23Rik|A930030P13Rik|AA171013|AI847476|AI853955|ELP79|EMAP|EMAPL|heco	echinoderm microtubule associated protein like 1	protein-coding
mm_13444.1	chr2	105160239	105160244	+	1	NA	intron (NM_144783, intron 5 of 9)	G-rich|Low_complexity|Low_complexity	33712	NM_144783	22431	Mm.389339	NM_144783	ENSMUSG00000016458	Wt1	D630046I19Rik|Wt-1	Wilms tumor 1 homolog	protein-coding
mm_152000.1	chr19	5905490	5905525	-	1	NA	exon (NM_001291078, exon 4 of 12)	exon (NM_001291078, exon 4 of 12)	7364	NM_011262	19708	Mm.2651	NM_011262	ENSMUSG00000024826	Dpf2	2210010M07Rik|BAF45D|Req|ubi-d4	D4, zinc and double PHD fingers family 2	protein-coding
mm_55343.1	chr6	56569184	56569203	-	1	NA	Intergenic	Intergenic	135506	NM_025520	66373	Mm.25642	NM_025520	ENSMUSG00000091625	Lsm5	2010208O10Rik|2310034K10Rik	LSM5 homolog, U6 small nuclear RNA and mRNA degradation associated	protein-coding
mm_38037.1	chr4	133887824	133887824	-	1	NA	promoter-TSS (NM_009097)	promoter-TSS (NM_009097)	-27	NM_009097	20111	Mm.301827	NM_009097	ENSMUSG00000003644	Rps6ka1	Mapkapk-1a|Rsk|Rsk-1|Rsk1|S6K-alpha-1|p90-Rsk1|p90Rsk1|p90S6K|p90rsk	ribosomal protein S6 kinase polypeptide 1	protein-coding
mm_163640.1	chr13	60895607	60895646	-	1	NA	3' UTR (NM_007797, exon 5 of 5)	3' UTR (NM_007797, exon 5 of 5)	1821	NM_007797	13025	Mm.30144	NM_007797	ENSMUSG00000074874	Ctla2b	AW545568|Ctla-2b	cytotoxic T lymphocyte-associated protein 2 beta	protein-coding
mm_68531.1	chr7	113347274	113347293	-	1	NA	intron (NM_133700, intron 4 of 10)	intron (NM_133700, intron 4 of 10)	22056	NM_133700	68815	Mm.238034	NM_133700	ENSMUSG00000038187	Btbd10	1110056N09Rik|Gmrp1	BTB (POZ) domain containing 10	protein-coding
mm_49321.1	chr6	18866310	18866333	+	1	NA	promoter-TSS (NM_029202)	promoter-TSS (NM_029202)	3	NM_001167757	75196	Mm.67665	NM_029202	ENSMUSG00000029517	Ankrd7	4930532L20Rik|AV278427	ankyrin repeat domain 7	protein-coding
mm_164147.1	chr15	60187205	60187209	-	1	NA	Intergenic	Intergenic	-170589	NM_027668	71088	Mm.425950	NM_027668	ENSMUSG00000071749	4933412E24Rik	-	RIKEN cDNA 4933412E24 gene	protein-coding
mm_151257.1	chr19	53944871	53944907	+	1	NA	promoter-TSS (NM_019658)	promoter-TSS (NM_019658)	13	NM_019658	56392	Mm.228669	NM_019658	ENSMUSG00000024976	Shoc2	AU017287|Sur8|mKIAA0862	soc-2 (suppressor of clear) homolog (C. elegans)	protein-coding
mm_74245.1	chr8	124793791	124793821	+	1	NA	5' UTR (NM_198632, exon 1 of 10)	5' UTR (NM_198632, exon 1 of 10)	787	NM_198632	330863	Mm.422769	NM_198632	ENSMUSG00000036913	Trim67	D130049O21Rik|TNL	tripartite motif-containing 67	protein-coding
mm_71190.1	chr8	40869597	40869614	+	1	NA	intron (NM_007514, intron 1 of 11)	intron (NM_007514, intron 1 of 11)	7238	NM_001044740	11988	Mm.4676	NM_007514	ENSMUSG00000031596	Slc7a2	20.5|AI158848|Atrc2|CAT-2|Cat2|Tea	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	protein-coding
mm_99801.1	chr11	107593824	107593826	+	1	NA	intron (NM_198298, intron 5 of 31)	intron (NM_198298, intron 5 of 31)	-43897	NR_105897	102465562		NR_105897	ENSMUSG00000098497	Mir6932	Gm27691|mmu-mir-6932	microRNA 6932	ncRNA
mm_21796.1	chr2	164858179	164858204	-	1	NA	promoter-TSS (NM_011125)	promoter-TSS (NM_011125)	-483	NM_011125	18830	Mm.6105	NM_011125	ENSMUSG00000017754	Pltp	Bpife|OD107	phospholipid transfer protein	protein-coding
mm_74698.1	chr8	15519934	15519937	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	462282	NM_008664	17930	Mm.272115	NM_008664	ENSMUSG00000031461	Myom2	AW146149	myomesin 2	protein-coding
mm_55842.1	chr6	83172743	83172769	-	1	NA	intron (NM_001198866, intron 1 of 31)	intron (NM_001198866, intron 1 of 31)	6832	NM_001198867	13191	Mm.6919	NM_007835	ENSMUSG00000031865	Dctn1	AL022633|DAP-150|DP-150|Glued|p150|p150-glued|p150<glued>	dynactin 1	protein-coding
mm_17651.1	chr2	32017334	32017362	-	1	NA	intron (NM_172268, intron 22 of 35)	intron (NM_172268, intron 22 of 35)	-33598	NR_106135	102466844		NR_106135	ENSMUSG00000099075	Mir7674	Gm27563|mmu-mir-7674	microRNA 7674	ncRNA
mm_96746.1	chr11	69847334	69847380	+	1	NA	exon (NM_001168497, exon 3 of 8)	exon (NM_001168497, exon 3 of 8)	713	NR_033133	70310	Mm.28874	NM_023564	ENSMUSG00000019461	Plscr3	2210403O21Rik|2610037N06Rik|ESTM3|X83310	phospholipid scramblase 3	protein-coding
mm_88103.1	chr10	69096077	69096086	+	1	NA	Intergenic	Intergenic	-112471	NM_001252636	69288	Mm.26659	NM_001081347	ENSMUSG00000019944	Rhobtb1	1700008H16Rik|3110048G13Rik|AI173445|AI573858|AV350930	Rho-related BTB domain containing 1	protein-coding
mm_13017.1	chr2	90987582	90987592	+	1	NA	intron (NM_001244891, intron 2 of 14)	intron (NM_001244891, intron 2 of 14)	47190	NM_017368	13046	Mm.29495	NM_017368	ENSMUSG00000005506	Celf1	1600010O03Rik|AA407467|Brunol2|CUG-BP|CUG-BP1|CUGBP|Cugbp1|D2Wsu101e|HNAB50|NAB50	CUGBP, Elav-like family member 1	protein-coding
mm_68282.1	chr7	105599717	105599743	-	1	NA	exon (NM_017371, exon 3 of 10)	exon (NM_017371, exon 3 of 10)	386	NM_017371	15458	Mm.3485	NM_017371	ENSMUSG00000030895	Hpx	Hpxn|hx	hemopexin	protein-coding
mm_173051.1	chrX	122405558	122405575	+	1	NA	Intergenic	ERVB7_1-LTR_MM|LTR|ERVK	-8181	NM_138742	54561	Mm.490573	NM_138742	ENSMUSG00000055733	Nap1l3	MB20	nucleosome assembly protein 1-like 3	protein-coding
mm_38401.1	chr4	138968996	138969012	-	1	NA	TTS (NM_025786)	TTS (NM_025786)	1892	NM_025786	66825	Mm.252312	NM_025786	ENSMUSG00000070661	Rnf186	9130020G10Rik	ring finger protein 186	protein-coding
mm_62603.1	chr7	105736885	105736908	+	1	NA	promoter-TSS (NM_025897)	promoter-TSS (NM_025897)	171	NM_010562	16202	Mm.274846	NM_010562	ENSMUSG00000030890	Ilk	AA511515|ESTM24	integrin linked kinase	protein-coding
mm_17392.1	chr2	27112002	27112014	-	1	NA	3' UTR (NM_175427, exon 3 of 3)	3' UTR (NM_175427, exon 3 of 3)	30469	NM_175427	109349	Mm.314080	NM_175427	ENSMUSG00000009216	Fam163b	C630035N08Rik	family with sequence similarity 163, member B	protein-coding
mm_48369.1	chr5	139478293	139478309	-	1	NA	intron (NM_133349, intron 4 of 6)	ID_B1|SINE|B4	6190	NM_133349	100494	Mm.24521	NM_133349	ENSMUSG00000053581	Zfand2a	AA407930|AU016206|Airap	zinc finger, AN1-type domain 2A	protein-coding
mm_90014.1	chr10	115315641	115315670	+	1	NA	promoter-TSS (NM_024454)	promoter-TSS (NM_024454)	-64	NM_024454	216344	Mm.21936	NM_024454	ENSMUSG00000020132	Rab21	9630024B22	RAB21, member RAS oncogene family	protein-coding
mm_98079.1	chr11	86544983	86544999	+	1	NA	promoter-TSS (NM_001199045)	promoter-TSS (NM_001199045)	0	NM_001199045	56427	Mm.383207	NM_019756	ENSMUSG00000020513	Tubd1	4930550G19Rik|Tubd	tubulin, delta 1	protein-coding
mm_106781.1	chr12	4703232	4703235	+	1	NA	intron (NM_011365, intron 31 of 38)	BC1_Mm|scRNA|scRNA	35150	NM_029107	74855	Mm.269534	NM_029107	ENSMUSG00000079177	Fam228a	4930417G10Rik	family with sequence similarity 228, member A	protein-coding
mm_132547.1	chr16	37883332	37883346	+	1	NA	3' UTR (NM_177093, exon 4 of 4)	3' UTR (NM_177093, exon 4 of 4)	14939	NM_177093	320184	Mm.390882	NM_177093	ENSMUSG00000034158	Lrrc58	1810012N18Rik|C330018J07Rik	leucine rich repeat containing 58	protein-coding
mm_13882.1	chr2	119972456	119972462	+	1	NA	promoter-TSS (NM_011941)	promoter-TSS (NM_011941)	-240	NM_011941	26390	Mm.330501	NM_011941	ENSMUSG00000033902	Mapkbp1	2810483F24Rik|AW123212|JNKBP-1|Jnkbp1|mKIAA0596	mitogen-activated protein kinase binding protein 1	protein-coding
mm_148339.1	chr18	84518643	84518654	-	1	NA	intron (NM_001033341, intron 3 of 8)	ID_B1|SINE|B4	70856	NM_001033341	240476	Mm.329575	NM_001033341	ENSMUSG00000048410	Zfp407	6430585N13Rik|Gm333|Gm334|Gm948|ZNF407	zinc finger protein 407	protein-coding
mm_120561.1	chr14	68120922	68120997	+	1	NA	exon (NM_008691, exon 3 of 3)	exon (NM_008691, exon 3 of 3)	-2793	NR_045897	100043072	Mm.242832	NR_045897		A230070E04Rik	Gm4210	RIKEN cDNA A230070E04 gene	ncRNA
mm_19195.1	chr2	84442670	84442681	-	1	NA	3' UTR (NM_001177319, exon 8 of 8)	3' UTR (NM_001177319, exon 8 of 8)	-17409	NM_018782	54598	Mm.75467	NM_018782	ENSMUSG00000059588	Calcrl	AV071593|CRLR	calcitonin receptor-like	protein-coding
mm_54142.1	chr6	21924901	21924943	-	1	NA	Intergenic	Intergenic	-24649	NM_001311061	71777	Mm.39999	NM_023626	ENSMUSG00000029670	Ing3	1300013A07Rik|P47ING3	inhibitor of growth family, member 3	protein-coding
mm_85418.1	chr9	103480267	103480269	-	1	NA	promoter-TSS (NM_001002896)	promoter-TSS (NM_001002896)	60	NM_001002896	107993	Mm.335403	NM_001002896	ENSMUSG00000032556	Bfsp2	AI448593|CP49	beaded filament structural protein 2, phakinin	protein-coding
mm_59563.1	chr7	28086471	28086480	+	1	NA	exon (NM_001122603, exon 5 of 20)	exon (NM_001122603, exon 5 of 20)	15239	NM_001122603	215384	Mm.292276	NM_175444	ENSMUSG00000047730	Fcgbp	A430096B05Rik	Fc fragment of IgG binding protein	protein-coding
mm_170917.1	chr2	37261674	37261674	-	1	NA	Intergenic	MMERVK9C_I-int|LTR|ERVK	-5277	NM_001081010	545417	Mm.379955	NM_001081010		Olfr367-ps	EG545417|MOR128-1|ORL1283|OTTMUSG00000012147|Olfr367	olfactory receptor 367, pseudogene	protein-coding
mm_130813.1	chr15	101740353	101740362	-	1	NA	exon (NM_019956, exon 2 of 9)	exon (NM_019956, exon 2 of 9)	2740	NM_019956	56735	Mm.358677	NM_019956	ENSMUSG00000051879	Krt71	AA589543|Ca|Cal4|Cu|Krt2-6g|mK6irs|mK6irs1	keratin 71	protein-coding
mm_62654.1	chr7	107693219	107693244	+	1	NA	intron (NM_001163557, intron 5 of 25)	intron (NM_001163557, intron 5 of 25)	64801	NM_001205227	320635	Mm.132828	NM_177216	ENSMUSG00000048065	Cyb5r2	D630003K02Rik|b5R.2	cytochrome b5 reductase 2	protein-coding
mm_83050.1	chr9	37545025	37545035	-	1	NA	TTS (NM_020518)	TTS (NM_020518)	5775	NM_020518	57276	Mm.27478	NM_020518	ENSMUSG00000001943	Vsig2	1190004B15Rik|2210413P10Rik|AU040484|CTX|Ctm	V-set and immunoglobulin domain containing 2	protein-coding
mm_58204.1	chr6	143535503	143535513	-	1	NA	Intergenic	Intergenic	115780	NR_045732	73425	Mm.417844	NR_045732	ENSMUSG00000086887	1700060C16Rik	-	RIKEN cDNA 1700060C16 gene	ncRNA
mm_52823.1	chr6	121356880	121356892	+	1	NA	intron (NM_001347433, intron 6 of 14)	intron (NM_001347433, intron 6 of 14)	10189	NM_133661	14411	Mm.274506	NM_133661	ENSMUSG00000030109	Slc6a12	BGT1|GAT-2|GAT2|Gabt2	solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12	protein-coding
mm_76321.1	chr8	84687900	84687910	-	1	NA	promoter-TSS (NM_025788)	promoter-TSS (NM_025788)	-43	NM_025788	66830	Mm.289698	NM_025788	ENSMUSG00000001910	Nacc1	2010001H03Rik|4930511N13Rik|Btbd14b|Nac1	nucleus accumbens associated 1, BEN and BTB (POZ) domain containing	protein-coding
mm_108676.1	chr12	86678874	86678886	+	1	NA	5' UTR (NM_177354, exon 1 of 7)	5' UTR (NM_177354, exon 1 of 7)	180	NM_177354	238328	Mm.216101	NM_177354	ENSMUSG00000021256	Vash1	AI834978|D930046M13Rik|G630009D10Rik	vasohibin 1	protein-coding
mm_93175.1	chr10	93516577	93516582	-	1	NA	3' UTR (NM_010401, exon 20 of 20)	3' UTR (NM_010401, exon 20 of 20)	23454	NM_027908	71761	Mm.244518	NM_027908	ENSMUSG00000015890	Amdhd1	1300019J08Rik	amidohydrolase domain containing 1	protein-coding
mm_161145.1	chr13	22278391	22278391	+	1	NA	promoter-TSS (NM_134223)	promoter-TSS (NM_134223)	74	NM_134223	171257	Mm.377211	NM_134223	ENSMUSG00000069296	Vmn1r195	V1ri6	vomeronasal 1 receptor 195	protein-coding
mm_49374.1	chr6	24543317	24543325	+	1	NA	intron (NM_080847, intron 1 of 9)	intron (NM_080847, intron 1 of 9)	15177	NM_080847	78910	Mm.160150	NM_080847	ENSMUSG00000029685	Asb15	4930400E23Rik|Asb-15	ankyrin repeat and SOCS box-containing 15	protein-coding
mm_59406.1	chr7	27029645	27029655	+	1	NA	exon (NM_133657, exon 2 of 9)	exon (NM_133657, exon 2 of 9)	560	NM_133657	13085	Mm.20770	NM_133657	ENSMUSG00000060407	Cyp2a12	-	cytochrome P450, family 2, subfamily a, polypeptide 12	protein-coding
mm_39068.1	chr4	154082100	154082115	-	1	NA	intron (NM_011642, intron 3 of 13)	intron (NM_011642, intron 3 of 13)	15066	NM_001126330	22062	Mm.78015	NM_011642	ENSMUSG00000029026	Trp73	TAp73|Tp73|deltaNp73|p73	transformation related protein 73	protein-coding
mm_118138.1	chr13	104951433	104951451	-	1	NA	3' UTR (NM_029879, exon 6 of 6)	3' UTR (NM_029879, exon 6 of 6)	-87549	NM_029984	77803	Mm.159995	NM_029984	ENSMUSG00000042655	Fam159b	A930021C24Rik	family with sequence similarity 159, member B	protein-coding
mm_11553.1	chr2	32727683	32727712	+	1	NA	promoter-TSS (NM_001252547)	promoter-TSS (NM_001252547)	8	NM_001252547	27387	Mm.9593	NM_013781	ENSMUSG00000059013	Sh2d3c	Chat|Nsp3|Shep1	SH2 domain containing 3C	protein-coding
mm_128063.1	chr15	26743560	26743570	-	1	NA	intron (NM_176959, intron 2 of 3)	intron (NM_176959, intron 2 of 3)	151999	NM_176959	448987	Mm.253378	NM_176959	ENSMUSG00000043556	Fbxl7	AL023057|D230018M15Rik|FBL7|Fbl6	F-box and leucine-rich repeat protein 7	protein-coding
mm_112345.1	chr12	116757210	116757222	-	1	NA	intron (NM_011215, intron 3 of 22)	RMER6C|LTR|ERVK	271496	NM_011215	19276	Mm.206054	NM_011215	ENSMUSG00000056553	Ptprn2	4930425H11Rik|IA2beta|PTP-NP|Phol|mKIAA0387|phogrin	protein tyrosine phosphatase, receptor type, N polypeptide 2	protein-coding
mm_26357.1	chr3	142549344	142549353	+	1	NA	3' UTR (NM_001083312, exon 11 of 11)	3' UTR (NM_001083312, exon 11 of 11)	-10704	NM_018734	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_129649.1	chr15	80701568	80701579	-	1	NA	Intergenic	Intergenic	-3963	NR_045310	106059	Mm.442457	NR_045309		A430088P11Rik	-	RIKEN cDNA A430088P11 gene	ncRNA
mm_21805.1	chr2	165034457	165034488	-	1	NA	intron (NM_144892, intron 1 of 7)	CpG	307	NM_144892	228869	Mm.233080	NM_144892	ENSMUSG00000039804	Ncoa5	CIA	nuclear receptor coactivator 5	protein-coding
mm_61089.1	chr7	51624596	51624608	+	1	NA	intron (NM_080853, intron 1 of 11)	intron (NM_080853, intron 1 of 11)	2772	NM_080853	140919	Mm.256618	NM_080853	ENSMUSG00000030500	Slc17a6	2900073D12Rik|DNPI|VGLUT2	solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 6	protein-coding
mm_9874.1	chr1	185203740	185203743	-	1	NA	promoter-TSS (NM_001163754)	promoter-TSS (NM_001163754)	-427	NM_001163754	98732	Mm.275841	NM_172649	ENSMUSG00000039318	Rab3gap2	1110059F07Rik|2010002H18Rik|5830469C09|AI851069|AW743433|RAB3-GAP150|mKIAA0839	RAB3 GTPase activating protein subunit 2	protein-coding
mm_77277.1	chr8	116677810	116677823	-	1	NA	intron (NM_029441, intron 1 of 6)	intron (NM_029441, intron 1 of 6)	55175	NM_029441	75796	Mm.159575	NM_029441	ENSMUSG00000031758	Cdyl2	1700029M19Rik|4930453I21Rik|Gm20194	chromodomain protein, Y chromosome-like 2	protein-coding
mm_138462.1	chr17	35142300	35142312	+	1	NA	intron (NM_057171, intron 10 of 24)	intron (NM_057171, intron 10 of 24)	6592	NM_001252469	224727	Mm.203962	NM_057171	ENSMUSG00000024392	Bag6	2410045D21Rik|AA408914|BAG-6|Bat3|D17H6S52E|G3|Scythe	BCL2-associated athanogene 6	protein-coding
mm_163518.1	chr12	114844134	114844139	-	1	NA	Intergenic	Intergenic	-330442	NR_106063	102465664		NR_106063	ENSMUSG00000098357	Mir7094-2	Gm27508|mmu-mir-7094-2	microRNA 7094-2	ncRNA
mm_160860.1	chr11	59662551	59662551	+	1	NA	promoter-TSS (NM_201245)	promoter-TSS (NM_201245)	56	NM_012027	26936	Mm.2402	NM_012027	ENSMUSG00000005417	Mprip	9530046C02|AA536749|AI647711|C76423|RIP3|Rhoip3|mKIAA0864|p116Rip	myosin phosphatase Rho interacting protein	protein-coding
mm_53219.1	chr6	126854399	126854403	+	1	NA	intron (NM_009650, intron 1 of 5)	B4A|SINE|B4	1303	NM_009650	11642	Mm.87748	NM_009650	ENSMUSG00000030344	Akap3	Prka3	A kinase (PRKA) anchor protein 3	protein-coding
mm_136433.1	chr16	94370696	94370748	-	1	NA	promoter-TSS (NM_001159620)	promoter-TSS (NM_001159620)	-12	NM_001159616	56176	Mm.474449	NM_019543	ENSMUSG00000022940	Pigp	Dcrc|Dscr5	phosphatidylinositol glycan anchor biosynthesis, class P	protein-coding
mm_171955.1	chr5	8042984	8042994	+	1	NA	Intergenic	ERVB7_1-LTR_MM|LTR|ERVK	-3089	NM_025618	109552	Mm.96211	NM_025618	ENSMUSG00000003161	Sri	2210417O06Rik|2900070H08Rik|Sor	sorcin	protein-coding
mm_163840.1	chr14	19417921	19417944	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	184655	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_84814.1	chr9	77469948	77469963	-	1	NA	intron (NM_172528, intron 3 of 13)	intron (NM_172528, intron 3 of 13)	-70539	NR_040378	70487	Mm.58958	NR_040378	ENSMUSG00000099170	5730403I07Rik	-	RIKEN cDNA 5730403I07 gene	ncRNA
mm_11051.1	chr2	27181569	27181587	+	1	NA	exon (NM_138942, exon 11 of 12)	exon (NM_138942, exon 11 of 12)	16071	NM_138942	13166	Mm.167781	NM_138942	ENSMUSG00000000889	Dbh	-	dopamine beta hydroxylase	protein-coding
mm_33563.1	chr4	131920569	131920600	+	1	NA	promoter-TSS (NR_102393)	promoter-TSS (NR_102393)	-555	NR_102393	545681	Mm.2478	NR_102393	ENSMUSG00000085667	Gm12992	OTTMUSG00000009742	predicted gene 12992	ncRNA
mm_162424.1	chr1	92049086	92049093	-	1	NA	intron (NM_207225, intron 3 of 26)	intron (NM_207225, intron 3 of 26)	131252	NM_207225	208727	Mm.318567	NM_207225	ENSMUSG00000026313	Hdac4	4932408F19Rik|HD4	histone deacetylase 4	protein-coding
mm_72561.1	chr8	84084075	84084093	+	1	NA	exon (NM_009055, exon 7 of 21)	exon (NM_009055, exon 7 of 21)	-2015	NR_030490	735271		NR_030490	ENSMUSG00000076144	Mir709	Mirn709|mir-709|mmu-mir-709	microRNA 709	ncRNA
mm_76646.1	chr8	93121584	93121586	-	1	NA	intron (NM_007954, intron 5 of 12)	intron (NM_007954, intron 5 of 12)	9698	NM_007954	13884	Mm.88078	NM_007954	ENSMUSG00000057400	Ces1c	Ces-N|Ee-1|Ee1|Es-4|Es-N|Es1|Es4|EsN|PESN	carboxylesterase 1C	protein-coding
mm_69300.1	chr7	128346034	128346044	-	1	NA	Intergenic	RSINE1|SINE|B4	-47908	NM_145590	233913	Mm.220880	NM_145590	ENSMUSG00000030780	BC017158	-	cDNA sequence BC017158	protein-coding
mm_130857.1	chr15	102136226	102136230	-	1	NA	promoter-TSS (NM_001033277)	promoter-TSS (NM_001033277)	-13	NM_001033277	223918	Mm.385009	NM_001033277	ENSMUSG00000036966	Spryd3	BC008150	SPRY domain containing 3	protein-coding
mm_27248.1	chr3	36613462	36613471	-	1	NA	promoter-TSS (NM_027810)	promoter-TSS (NM_027810)	-77	NM_027810	71492	Mm.286187	NM_027810	ENSMUSG00000037325	Bbs7	8430406N16Rik	Bardet-Biedl syndrome 7 (human)	protein-coding
mm_84622.1	chr9	70585237	70585262	-	1	NA	intron (NM_026337, intron 16 of 20)	intron (NM_026337, intron 16 of 20)	42379	NM_025690	66660	Mm.22379	NM_025690	ENSMUSG00000032212	Sltm	5730455C01Rik|5730555F13Rik|9130215G10Rik|Met	SAFB-like, transcription modulator	protein-coding
mm_74728.1	chr8	17535609	17535632	-	1	NA	promoter-TSS (NM_053171)	promoter-TSS (NM_053171)	-235	NM_053171	94109	Mm.436988	NM_053171	ENSMUSG00000060924	Csmd1	B930082H09|mKIAA1890	CUB and Sushi multiple domains 1	protein-coding
mm_65321.1	chr7	24954447	24954494	-	1	NA	Intergenic	Intergenic	15605	NR_106013	102465633		NR_106013	ENSMUSG00000098802	Mir7046	Gm27469|mmu-mir-7046	microRNA 7046	ncRNA
mm_155563.1	chrX	75514319	75514340	+	1	NA	promoter-TSS (NM_011692)	promoter-TSS (NM_011692)	32	NM_011692	22327	Mm.8294	NM_011692	ENSMUSG00000031197	Vbp1	VBP-1	von Hippel-Lindau binding protein 1	protein-coding
mm_36876.1	chr4	107177783	107177803	-	1	NA	promoter-TSS (NM_029565)	promoter-TSS (NM_029565)	573	NM_025617	66526	Mm.246956	NM_025617	ENSMUSG00000028619	Tceanc2	2210010B22Rik|2210012G02Rik|6330404A07Rik|AU015593|Tdeanc2	transcription elongation factor A (SII) N-terminal and central domain containing 2	protein-coding
mm_49168.1	chr6	14901213	14901226	+	1	NA	promoter-TSS (NM_053242)	promoter-TSS (NM_053242)	-130	NM_053242	114142	Mm.332919	NM_053242	ENSMUSG00000029563	Foxp2	2810043D05Rik|AI449000|CAG-16|D0Kist7	forkhead box P2	protein-coding
mm_148828.1	chr19	6341122	6341247	+	1	NA	promoter-TSS (NM_001291787)	promoter-TSS (NM_001291787)	24	NR_117093	26412	Mm.25860	NM_009006	ENSMUSG00000024948	Map4k2	AI385662|BL44|GCK|Rab8ip	mitogen-activated protein kinase kinase kinase kinase 2	protein-coding
mm_36596.1	chr4	88722455	88722485	-	1	NA	promoter-TSS (NM_172871)	promoter-TSS (NM_172871)	38	NM_172871	242521	Mm.260601	NM_172871	ENSMUSG00000070923	Klhl9	8030469P05|C530050O22Rik|ENSMUSG00000070923|mKIAA1354	kelch-like 9	protein-coding
mm_155038.1	chrX	42140033	42140064	+	1	NA	Intergenic	Intergenic	-9364	NM_001077712	20843	Mm.290422	NM_021465	ENSMUSG00000025862	Stag2	9230105L23Rik|B230112I07Rik|SA-2|SAP2	stromal antigen 2	protein-coding
mm_108159.1	chr12	76332406	76332409	+	1	NA	3' UTR (NM_001101471, exon 2 of 2)	3' UTR (NM_001101471, exon 2 of 2)	7516	NM_001101471	238276	Mm.311452	NM_001101471	ENSMUSG00000021057	Akap5	3526401B18Rik|AKAP 150|AKAP-5|AKAP150|BB098886|Gm258|P150	A kinase (PRKA) anchor protein 5	protein-coding
mm_81757.1	chr9	113969222	113969229	+	1	NA	intron (NM_013699, intron 11 of 15)	intron (NM_013699, intron 11 of 15)	24575	NR_039590	100628597		NR_039590	ENSMUSG00000092958	Mir5128	mir-5128|mmu-mir-5128|mu-mir-5128	microRNA 5128	ncRNA
mm_139739.1	chr17	60644717	60644718	+	1	NA	Intergenic	Intergenic	-1631395	NM_026497	67993	Mm.36507	NM_026497	ENSMUSG00000024228	Nudt12	0610016O18Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 12	protein-coding
mm_64105.1	chr7	141047993	141048002	+	1	NA	Intergenic	Intergenic	-13277	NM_177897	330671	Mm.133741	NM_177897	ENSMUSG00000055629	B4galnt4	BC038881|Gm1095|beta4GalNAcT4	beta-1,4-N-acetyl-galactosaminyl transferase 4	protein-coding
mm_66812.1	chr7	47752633	47752638	-	1	NA	Intergenic	ERVB4_1B-LTR_MM|LTR|ERVK	-151263	NM_153067	233222	Mm.240142	NM_153067	ENSMUSG00000078698	Mrgpra3	Mrga3	MAS-related GPR, member A3	protein-coding
mm_113057.1	chr13	23710627	23710640	+	1	NA	exon (NM_001347493, exon 1 of 5)	exon (NM_001347493, exon 1 of 5)	221	NM_001347493	15216	Mm.2681	NM_010424	ENSMUSG00000006611	Hfe	MR2	hemochromatosis	protein-coding
mm_3848.1	chr1	160213093	160213147	+	1	NA	promoter-TSS (NM_009786)	promoter-TSS (NM_009786)	-228	NM_009786	12301	Mm.10702	NM_009786	ENSMUSG00000014226	Cacybp	SIP	calcyclin binding protein	protein-coding
mm_69996.1	chr7	142385880	142385901	-	1	NA	intron (NM_009983, intron 1 of 8)	intron (NM_009983, intron 1 of 8)	1980	NM_009983	13033	Mm.231395	NM_009983	ENSMUSG00000007891	Ctsd	CD|CatD	cathepsin D	protein-coding
mm_88487.1	chr10	77706589	77706591	+	1	NA	promoter-TSS (NR_026831)	promoter-TSS (NR_026831)	3	NR_026831	16697	Mm.482251	NR_026831	ENSMUSG00000069584	Gm10272	ENSMUSG00000069584|Krtap12-4	keratin associated protein 12-4	pseudo
mm_129358.1	chr15	77945791	77945800	-	1	NA	intron (NM_001168260, intron 7 of 8)	intron (NM_001168260, intron 7 of 8)	10927	NM_001168260	239554	Mm.295605	NM_001017983	ENSMUSG00000016552	Foxred2	A430097D04Rik|D15Bwg0759e|Gm304	FAD-dependent oxidoreductase domain containing 2	protein-coding
mm_25365.1	chr3	107101552	107101562	+	1	NA	promoter-TSS (NM_008417)	promoter-TSS (NM_008417)	-10	NM_008417	16490	Mm.39285	NM_008417	ENSMUSG00000040724	Kcna2	Akr6a4|ENSMUSG00000074335|Gm10672|Kca1-2|Kv1.2|Mk-2	potassium voltage-gated channel, shaker-related subfamily, member 2	protein-coding
mm_86281.1	chr9	121839508	121839512	-	1	NA	promoter-TSS (NM_028384)	promoter-TSS (NM_028384)	-49	NM_028384	100502861	Mm.335550	NM_028384	ENSMUSG00000079235	Ccdc13	2900041A11Rik|Gm188	coiled-coil domain containing 13	protein-coding
mm_43641.1	chr5	138255728	138255788	+	1	NA	5' UTR (NM_001081108, exon 1 of 4)	5' UTR (NM_001081108, exon 1 of 4)	276	NM_001081108	66096	Mm.206901	NM_001081108	ENSMUSG00000050552	Lamtor4	0910001L09Rik|AV006840	late endosomal/lysosomal adaptor, MAPK and MTOR activator 4	protein-coding
mm_27236.1	chr3	36475605	36475675	-	1	NA	promoter-TSS (NR_105976)	promoter-TSS (NR_105976)	-116	NR_105976	102466786		NR_105976	ENSMUSG00000098808	Mir7009	Gm27472|mmu-mir-7009	microRNA 7009	ncRNA
mm_65973.1	chr7	30440410	30440446	-	1	NA	intron (NM_007467, intron 8 of 16)	intron (NM_007467, intron 8 of 16)	5154	NM_007467	11803	Mm.2381	NM_007467	ENSMUSG00000006651	Aplp1	-	amyloid beta (A4) precursor-like protein 1	protein-coding
mm_148897.1	chr19	6909769	6909804	+	1	NA	promoter-TSS (NM_026306)	promoter-TSS (NM_026306)	88	NM_026306	67674	Mm.318804	NM_026306	ENSMUSG00000038812	Trmt112	0610038D11Rik|Trm112p	tRNA methyltransferase 11-2	protein-coding
mm_31099.1	chr4	41756223	41756293	+	1	NA	promoter-TSS (NM_001302511)	promoter-TSS (NM_001302511)	48	NM_001302511	14430	Mm.439669	NM_016658	ENSMUSG00000036073	Galt	AW553376	galactose-1-phosphate uridyl transferase	protein-coding
mm_37952.1	chr4	133277594	133277674	-	1	NA	non-coding (NR_110978, exon 1 of 5)	non-coding (NR_110978, exon 1 of 5)	156	NM_025667	52174	Mm.244748	NM_025667	ENSMUSG00000028857	Tmem222	5730406H10Rik|AA409341|D4Ertd196e	transmembrane protein 222	protein-coding
mm_149926.1	chr19	26748391	26748474	+	1	NA	promoter-TSS (NM_026003)	promoter-TSS (NM_026003)	29	NM_026003	67155	Mm.342988	NM_011416	ENSMUSG00000024921	Smarca2	2610209L14Rik|SNF2alpha|Snf2l2|brahma|brm	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	protein-coding
mm_125680.1	chr15	66642900	66642924	+	1	NA	3' UTR (NM_001081409, exon 21 of 21)	3' UTR (NM_001081409, exon 21 of 21)	-27858	NM_009375	21819	Mm.441333	NM_009375	ENSMUSG00000053469	Tg	Tgn|cog	thyroglobulin	protein-coding
mm_99343.1	chr11	101552189	101552207	+	1	NA	promoter-TSS (NM_001252222)	promoter-TSS (NM_001252222)	91	NM_001252220	17966	Mm.784	NM_008676	ENSMUSG00000017119	Nbr1	mKIAA0049	neighbor of Brca1 gene 1	protein-coding
mm_52940.1	chr6	122947049	122947090	+	1	NA	Intergenic	Lx8b|LINE|L1	-5446	NM_001204241	73149	Mm.25684	NM_153197	ENSMUSG00000043832	Clec4a3	3110037K17Rik|Dcir3	C-type lectin domain family 4, member a3	protein-coding
mm_146025.1	chr18	69519830	69519835	+	1	NA	intron (NM_013685, intron 5 of 19)	intron (NM_013685, intron 5 of 19)	174111	NM_001083967	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding
mm_53472.1	chr6	134924883	134924926	+	1	NA	3' UTR (NM_009875, exon 3 of 3)	3' UTR (NM_009875, exon 3 of 3)	-4188	NR_037956	381822	Mm.5935	NR_037955	ENSMUSG00000098318	Lockd	1190002F15Rik|AI120476|Droc	lncRNA downstream of Cdkn1b	ncRNA
mm_161623.1	chr16	59148865	59148865	+	1	NA	promoter-TSS (NM_146998)	promoter-TSS (NM_146998)	13	NM_146998	259000	Mm.390872	NM_146998	ENSMUSG00000062608	Olfr195	MOR184-5	olfactory receptor 195	protein-coding
mm_81948.1	chr9	120492738	120492744	+	1	NA	5' UTR (NM_026892, exon 1 of 4)	5' UTR (NM_026892, exon 1 of 4)	135	NM_026892	68969	Mm.28753	NM_026892	ENSMUSG00000006941	Eif1b	1500010M16Rik|3110001N14Rik|Gc20	eukaryotic translation initiation factor 1B	protein-coding
mm_38597.1	chr4	141844658	141844685	-	1	NA	intron (NR_040641, intron 1 of 2)	ID_B1|SINE|B4	350	NR_040641	69139	Mm.491056	NR_040641	ENSMUSG00000086818	Ctrcos	1810035I16Rik	chymotrypsin C (caldecrin), opposite strand	ncRNA
mm_56249.1	chr6	90756770	90756780	-	1	NA	intron (NM_001134384, intron 1 of 13)	intron (NM_001134384, intron 1 of 13)	-40246	NM_001134383	232227	Mm.196943	NM_182784	ENSMUSG00000034312	Iqsec1	AW561907|BC026481|BRAG2|D6Ertd349e|cI-43	IQ motif and Sec7 domain 1	protein-coding
mm_1834.1	chr1	82819656	82819665	+	1	NA	Intergenic	Intergenic	-19800	NM_001310713	15463	Mm.392569	NM_010472	ENSMUSG00000026159	Agfg1	AU045498|C130049H11Rik|C85612|D730048C23Rik|Hrb|RAB|Rip	ArfGAP with FG repeats 1	protein-coding
mm_116954.1	chr13	56135901	56135915	-	1	NA	promoter-TSS (NM_001159515)	promoter-TSS (NM_001159515)	-358	NM_001159513	26914	Mm.283802	NM_012015	ENSMUSG00000015937	H2afy	H2AF12M|mH2a1|macroH2A1	H2A histone family, member Y	protein-coding
mm_118799.1	chr14	24492829	24492832	+	1	NA	intron (NM_207635, intron 3 of 6)	PB1D9|SINE|Alu	2149	NM_011297	20088	Mm.16775	NM_011297	ENSMUSG00000025290	Rps24	-	ribosomal protein S24	protein-coding
mm_13604.1	chr2	113285718	113285719	+	1	NA	promoter-TSS (NM_029232)	promoter-TSS (NM_029232)	-14	NM_029232	75275	Mm.159484	NM_029232	ENSMUSG00000041255	Tmco5b	4930563P21Rik	transmembrane and coiled-coil domains 5B	protein-coding
mm_132305.1	chr16	33684445	33684456	+	1	NA	promoter-TSS (NM_175256)	promoter-TSS (NM_175256)	-16	NM_175256	77446	Mm.245741	NM_172934	ENSMUSG00000075254	Heg1	4632417D23Rik|5530401I02Rik|9530025L16Rik|BC038614|Gm629|OTTMUSG00000027315	heart development protein with EGF-like domains 1	protein-coding
mm_120953.1	chr14	77036747	77036786	+	1	NA	promoter-TSS (NM_172488)	promoter-TSS (NM_172488)	-6	NM_001310648	108811	Mm.102168	NM_175369	ENSMUSG00000034795	Ccdc122	4933415L06Rik	coiled-coil domain containing 122	protein-coding
mm_143612.1	chr17	78736607	78736633	-	1	NA	promoter-TSS (NM_011500)	promoter-TSS (NM_011500)	-60	NM_011500	268980	Mm.311915	NM_011500	ENSMUSG00000024077	Strn	AU022939|D130055P19	striatin, calmodulin binding protein	protein-coding
mm_21696.1	chr2	164497445	164497475	-	1	NA	promoter-TSS (NM_133779)	promoter-TSS (NM_133779)	-65	NM_133779	78928	Mm.28228	NM_133779	ENSMUSG00000017721	Pigt	2510012P17Rik|4930534E15Rik|CGI-06|NDAP|Ndap7	phosphatidylinositol glycan anchor biosynthesis, class T	protein-coding
mm_39702.1	chr5	27262017	27262031	+	1	NA	promoter-TSS (NM_001136060)	promoter-TSS (NM_001136060)	89	NM_001136060	13483	Mm.42078	NM_010075	ENSMUSG00000061576	Dpp6	B930011P16Rik|D5Buc3|D5Buc4|D5Buc5|DPP VI|Dpp-6|Gm1377|In(5)6H-p|Peplb|Rw	dipeptidylpeptidase 6	protein-coding
mm_27380.1	chr3	50443604	50443615	-	1	NA	promoter-TSS (NM_011990)	promoter-TSS (NM_011990)	4	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_1117.1	chr1	59912973	59913027	+	1	NA	promoter-TSS (NM_001037725)	promoter-TSS (NM_001037725)	-6	NM_001037725	72750	Mm.258250	NM_001037725	ENSMUSG00000041040	Fam117b	2810425F24Rik|6330416D14Rik|Als2cr13	family with sequence similarity 117, member B	protein-coding
mm_156332.1	chrX	138999674	138999688	+	1	NA	intron (NM_013724, intron 25 of 27)	intron (NM_013724, intron 25 of 27)	85251	NM_013724	27206	Mm.482319	NM_013724	ENSMUSG00000052854	Nrk	AA407323|AA409510|AI225895|AV168563|AW538185|Nesk	Nik related kinase	protein-coding
mm_57173.1	chr6	122847790	122847831	-	1	NA	3' UTR (NM_009779, exon 2 of 2)	3' UTR (NM_009779, exon 2 of 2)	8347	NM_009779	12267	Mm.2408	NM_009779	ENSMUSG00000040552	C3ar1	AZ3B|C3AR|HNFAG09	complement component 3a receptor 1	protein-coding
mm_138872.1	chr17	43087899	43087912	+	1	NA	exon (NM_178589, exon 6 of 6)	exon (NM_178589, exon 6 of 6)	70386	NR_045155	545207	Mm.329050	NR_045153		E130008D07Rik	-	RIKEN cDNA E130008D07 gene	ncRNA
mm_26063.1	chr3	135826386	135826420	+	1	NA	5' UTR (NM_001135150, exon 2 of 9)	5' UTR (NM_001135150, exon 2 of 9)	613	NM_001135150	67547	Mm.30239	NM_026228	ENSMUSG00000053897	Slc39a8	4933419D20Rik|AA986696|BIGM103|ZIP-8|Zip8	solute carrier family 39 (metal ion transporter), member 8	protein-coding
mm_69895.1	chr7	141637748	141637781	-	1	NA	intron (NM_001330001, intron 31 of 33)	intron (NM_001330001, intron 31 of 33)	17063	NR_106030	102466798		NR_106030	ENSMUSG00000098759	Mir7063	Gm27654|mmu-mir-7063	microRNA 7063	ncRNA
mm_92358.1	chr10	75921563	75921625	-	1	NA	promoter-TSS (NM_001161853)	promoter-TSS (NM_001161853)	20	NM_011418	20587	Mm.279751	NM_011418	ENSMUSG00000000902	Smarcb1	AU020204|Baf47|Ini1|SNF5/INI1|Snf5	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1	protein-coding
mm_56614.1	chr6	112491043	112491044	-	1	NA	Intergenic	Intergenic	-1235	NM_001081147	18430	Mm.333310	NM_001081147	ENSMUSG00000049112	Oxtr	OTR	oxytocin receptor	protein-coding
mm_119587.1	chr14	50930105	50930137	+	1	NA	intron (NM_001310505, intron 2 of 6)	intron (NM_001310505, intron 2 of 6)	728	NM_001310506	219024	Mm.239117	NM_001033271	ENSMUSG00000035953	Tmem55b	BC039161	transmembrane protein 55b	protein-coding
mm_34693.1	chr4	152009032	152009053	+	1	NA	exon (NM_001033352, exon 1 of 4)	exon (NM_001033352, exon 1 of 4)	151	NM_001033352	242785	Mm.22306	NM_001033352	ENSMUSG00000073700	Klhl21	1810045K06Rik|D330008A20|mKIAA0469	kelch-like 21	protein-coding
mm_4727.1	chr1	181352470	181352491	+	1	NA	promoter-TSS (NM_001160212)	promoter-TSS (NM_001160212)	-148	NM_028408	72978	Mm.338083	NM_028408	ENSMUSG00000026514	Cnih3	2900075G08Rik|CNIH-3	cornichon family AMPA receptor auxiliary protein 3	protein-coding
mm_35180.1	chr4	15300081	15300092	-	1	NA	Intergenic	LTR16B|LTR|ERVL	34266	NM_181401	100201	Mm.394111	NM_181401	ENSMUSG00000043252	Tmem64	9630015D15Rik|AI790744|AV300874	transmembrane protein 64	protein-coding
mm_41.1	chr1	6487308	6487338	+	1	NA	promoter-TSS (NM_001244693)	promoter-TSS (NM_001244693)	92	NM_001244692	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding
mm_9620.1	chr1	176735013	176735029	-	1	NA	3' UTR (NM_001099637, exon 20 of 20)	3' UTR (NM_001099637, exon 20 of 20)	37402	NR_029775	723921		NR_029775	ENSMUSG00000065573	Mir350	Mirn350|mir-350|mmu-mir-350	microRNA 350	ncRNA
mm_42463.1	chr5	115443176	115443188	+	1	NA	intron (NM_008629, intron 9 of 14)	intron (NM_008629, intron 9 of 14)	13497	NM_008629	17690	Mm.5077	NM_008629	ENSMUSG00000054256	Msi1	Msi1h|Musahi1|m-Msi-1	musashi RNA-binding protein 1	protein-coding
mm_122187.1	chr14	31640548	31640575	-	1	NA	promoter-TSS (NM_025295)	promoter-TSS (NM_025295)	404	NM_019975	56794	Mm.38887	NM_019975	ENSMUSG00000021884	Hacl1	1600020H07Rik|Hpcl|Phyh2	2-hydroxyacyl-CoA lyase 1	protein-coding
mm_132560.1	chr16	38089115	38089128	+	1	NA	non-coding (NR_033221, exon 1 of 1)	non-coding (NR_033221, exon 1 of 1)	120	NM_019827	56637	Mm.394930	NM_019827	ENSMUSG00000022812	Gsk3b	7330414F15Rik|8430431H08Rik|C86142|GSK-3|GSK-3beta|GSK3	glycogen synthase kinase 3 beta	protein-coding
mm_33528.1	chr4	130932301	130932311	+	1	NA	intron (NM_010686, intron 7 of 7)	RMER1C|Other|Other	-12079	NM_010769	17180	Mm.271796	NM_010769	ENSMUSG00000040533	Matn1	CMP|Crtm|Mat1|matrilin-1	matrilin 1, cartilage matrix protein	protein-coding
mm_86103.1	chr9	115310240	115310250	-	1	NA	5' UTR (NM_024222, exon 1 of 16)	5' UTR (NM_024222, exon 1 of 16)	176	NM_024222	68292	Mm.296158	NM_024222	ENSMUSG00000032437	Stt3b	1300006C19Rik|Simp	STT3, subunit of the oligosaccharyltransferase complex, homolog B (S. cerevisiae)	protein-coding
mm_102989.1	chr11	69685521	69685536	-	1	NA	promoter-TSS (NM_001159505)	promoter-TSS (NM_001159505)	26	NM_001159505	69583	Mm.8983	NM_023517	ENSMUSG00000089669	Tnfsf13	2310026N09Rik|April|Tall2|Tnlg7b|Trdl1	tumor necrosis factor (ligand) superfamily, member 13	protein-coding
mm_133919.1	chr16	97558085	97558099	+	1	NA	intron (NM_013606, intron 12 of 13)	intron (NM_013606, intron 12 of 13)	22009	NM_013606	17858	Mm.14157	NM_013606	ENSMUSG00000023341	Mx2	AI528743|Mx-2	MX dynamin-like GTPase 2	protein-coding
mm_171034.1	chr2	91265323	91265323	+	1	NA	TTS (NM_028733)	TTS (NM_028733)	208	NM_023854	77038	Mm.43636	NM_023854	ENSMUSG00000027255	Arfgap2	2310032E02Rik|Zfp289	ADP-ribosylation factor GTPase activating protein 2	protein-coding
mm_46899.1	chr5	114091359	114091404	-	1	NA	promoter-TSS (NM_026805)	promoter-TSS (NM_026805)	-1	NM_026805	68666	Mm.63584	NM_026805	ENSMUSG00000042078	Svop	1110030H18Rik|AI415691|msvop	SV2 related protein	protein-coding
mm_30964.1	chr4	33925077	33925090	+	1	NA	5' UTR (NM_007726, exon 1 of 2)	5' UTR (NM_007726, exon 1 of 2)	451	NM_007726	12801	Mm.7992	NM_007726	ENSMUSG00000044288	Cnr1	CB-R|CB1|CB1R	cannabinoid receptor 1 (brain)	protein-coding
mm_43323.1	chr5	134986821	134986833	+	1	NA	TTS (NR_026907)	TTS (NR_026907)	613	NM_009902	12739	Mm.158662	NM_009902	ENSMUSG00000070473	Cldn3	AI182374|Cpetr2|mRVP1	claudin 3	protein-coding
mm_77242.1	chr8	115705296	115705306	-	1	NA	3' UTR (NM_001025577, exon 1 of 1)	3' UTR (NM_001025577, exon 1 of 1)	1593	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_110058.1	chr12	21286117	21286162	-	1	NA	promoter-TSS (NM_008403)	promoter-TSS (NM_008403)	98	NM_008403	16413	Mm.273333	NM_008403	ENSMUSG00000062352	Itgb1bp1	AI449260|AU019480|Icap1	integrin beta 1 binding protein 1	protein-coding
mm_112671.1	chr13	16027499	16027509	+	1	NA	3' UTR (NM_008380, exon 5 of 5)	3' UTR (NM_008380, exon 5 of 5)	15653	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_137246.1	chr17	24488672	24488682	+	1	NA	promoter-TSS (NM_027937)	promoter-TSS (NM_027937)	-106	NM_027937	268932	Mm.70989	NM_027937	ENSMUSG00000033597	Caskin1	3300002N10Rik|C130061I24|C630036E02Rik|mKIAA1306	CASK interacting protein 1	protein-coding
mm_61329.1	chr7	68263763	68263769	+	1	NA	intron (NM_030101, intron 1 of 3)	intron (NM_030101, intron 1 of 3)	467	NM_030101	78444	Mm.425468	NM_030101	ENSMUSG00000030553	Pgpep1l	C330024D12Rik	pyroglutamyl-peptidase I-like	protein-coding
mm_4467.1	chr1	173350180	173350206	+	1	NA	intron (NM_053199, intron 1 of 8)	intron (NM_053199, intron 1 of 8)	-16690	NM_010045	13349	Mm.6393	NM_010045	ENSMUSG00000037872	Ackr1	AA162249|CCBP1|CD234|Darc|Dfy|ESTM35|FY|GPD	atypical chemokine receptor 1 (Duffy blood group)	protein-coding
mm_112909.1	chr13	20908550	20908550	+	1	NA	intron (NM_012054, intron 6 of 20)	intron (NM_012054, intron 6 of 20)	114437	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_32538.1	chr4	109015516	109015523	+	1	NA	intron (NM_001346554, intron 2 of 28)	intron (NM_001346554, intron 2 of 28)	-2136	NR_030432	791075		NR_030432	ENSMUSG00000076444	Mir761	Mirn761|mir-761|mmu-mir-761	microRNA 761	ncRNA
mm_149827.1	chr19	24477610	24477627	+	1	NA	promoter-TSS (NM_026520)	promoter-TSS (NM_026520)	-144	NM_026520	68034	Mm.440181	NM_026520	ENSMUSG00000074922	Fam122a	2410124L17Rik|2900009I07Rik|ENSMUSG00000051082|Gm9849	family with sequence similarity 122, member A	protein-coding
mm_164117.1	chr15	34248732	34248737	-	1	NA	intron (NM_033521, intron 1 of 6)	RMER17C|LTR|ERVK	10708	NM_033521	114128	Mm.197518	NM_033521	ENSMUSG00000022257	Laptm4b	C330023P13Rik|LAPTM4beta	lysosomal-associated protein transmembrane 4B	protein-coding
mm_552.1	chr1	38019232	38019243	+	1	NA	exon (NM_198303, exon 4 of 24)	exon (NM_198303, exon 4 of 24)	21227	NM_198303	226982	Mm.260943	NM_198303	ENSMUSG00000026083	Eif5b	A030003E17Rik|BC018347|IF2	eukaryotic translation initiation factor 5B	protein-coding
mm_58631.1	chr7	5089113	5089120	+	1	NA	intron (NM_010147, intron 3 of 11)	intron (NM_010147, intron 3 of 11)	8881	NM_001252454	13854	Mm.3091	NM_010147	ENSMUSG00000035203	Epn1	AA269831|Ibp1	epsin 1	protein-coding
mm_91496.1	chr10	37136004	37136011	-	1	NA	3' UTR (NM_008538, exon 2 of 2)	3' UTR (NM_008538, exon 2 of 2)	2919	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_152622.1	chr19	12464290	12464298	-	1	NA	3' UTR (NM_010821, exon 2 of 2)	3' UTR (NM_010821, exon 2 of 2)	3515	NM_010821	17476	Mm.3999	NM_010821	ENSMUSG00000046805	Mpeg1	MPS1|Mpg-1	macrophage expressed gene 1	protein-coding
mm_86117.1	chr9	115611765	115611775	-	1	NA	Intergenic	Intergenic	229951	NR_130329	100316675		NR_130329	ENSMUSG00000080409	Mir467h	Mirn467h|mmu-mir-467h	microRNA 467h	ncRNA
mm_82432.1	chr9	15045146	15045156	-	1	NA	5' UTR (NM_019482, exon 1 of 5)	5' UTR (NM_019482, exon 1 of 5)	327	NM_019482	55991	Mm.142253	NM_019482	ENSMUSG00000031934	Panx1	AI847747	pannexin 1	protein-coding
mm_75951.1	chr8	71665555	71665581	-	1	NA	intron (NM_001029873, intron 3 of 41)	intron (NM_001029873, intron 3 of 41)	6189	NM_001029873	382018	Mm.334606	NM_001029873	ENSMUSG00000034799	Unc13a	2410078G03Rik|Munc13-1	unc-13 homolog A (C. elegans)	protein-coding
mm_107608.1	chr12	49384561	49384580	+	1	NA	exon (NM_008241, exon 2 of 2)	exon (NM_008241, exon 2 of 2)	1563	NM_008241	15228	Mm.4704	NM_008241	ENSMUSG00000020950	Foxg1	2900064B05Rik|BF-1|Bf1|Hfh9|Hfhbf1	forkhead box G1	protein-coding
mm_50832.1	chr6	54736443	54736484	+	1	NA	Intergenic	Zaphod|DNA|hAT-Tip100	54839	NM_001289740	68235	Mm.233860	NM_026629	ENSMUSG00000038065	Mturn	2410066E13Rik|AI448550|B230212L03Rik	maturin, neural progenitor differentiation regulator homolog (Xenopus)	protein-coding
mm_7823.1	chr1	132041955	132041957	-	1	NA	intron (NM_172510, intron 7 of 10)	intron (NM_172510, intron 7 of 10)	26106	NM_172510	213006	Mm.208445	NM_172510	ENSMUSG00000059149	Mfsd4a	A230072B04|A930031D07Rik|AI850289|Mfsd4	major facilitator superfamily domain containing 4A	protein-coding
mm_99119.1	chr11	100145450	100145474	+	1	NA	exon (NM_008471, exon 1 of 6)	exon (NM_008471, exon 1 of 6)	464	NM_008471	16669	Mm.439699	NM_008471	ENSMUSG00000020911	Krt19	AI663979|CK-19|EndoC|K19|Krt-1.19|Krt1-19	keratin 19	protein-coding
mm_160668.1	chr9	121950872	121950872	+	1	NA	promoter-TSS (NM_001199927)	promoter-TSS (NM_001199927)	-116	NM_177743	245050	Mm.71062	NM_177743	ENSMUSG00000038233	Fam198a	C730027P07Rik	family with sequence similarity 198, member A	protein-coding
mm_114094.1	chr13	54687934	54687955	+	1	NA	promoter-TSS (NM_001146025)	promoter-TSS (NM_001146025)	-136	NM_001146026	105239	Mm.25366	NM_134064	ENSMUSG00000034928	Rnf44	AI854545|mKIAA1100	ring finger protein 44	protein-coding
mm_85266.1	chr9	99423095	99423137	-	1	NA	intron (NM_008624, intron 1 of 5)	intron (NM_008624, intron 1 of 5)	13596	NM_008624	17532	Mm.2045	NM_008624	ENSMUSG00000032470	Mras	2900078C09Rik|AI326250	muscle and microspikes RAS	protein-coding
mm_116235.1	chr13	33569481	33569496	-	1	NA	promoter-TSS (NR_131141)	promoter-TSS (NR_131141)	-171	NR_131141	619715	Mm.390575	NR_131140		Gm6093	EG619715	predicted gene 6093	ncRNA
mm_138931.1	chr17	43801914	43801924	+	1	NA	promoter-TSS (NM_207649)	promoter-TSS (NM_207649)	68	NM_207649	53901	Mm.251242	NM_030598	ENSMUSG00000039601	Rcan2	Csp2|Dscr1l1|MCIP2|ZAKI-4	regulator of calcineurin 2	protein-coding
mm_150004.1	chr19	29288019	29288066	+	1	NA	exon (NM_008413, exon 11 of 25)	exon (NM_008413, exon 11 of 25)	36239	NM_008413	16452	Mm.275839	NM_008413	ENSMUSG00000024789	Jak2	Fd17	Janus kinase 2	protein-coding
mm_66987.1	chr7	63999224	63999228	-	1	NA	Intergenic	Intergenic	-60311	NM_021366	50794	Mm.240473	NM_021366	ENSMUSG00000052040	Klf13	0610043C13Rik|9430029L20Rik|Bteb3|FKLF-2|FKLF2|NSLP1|RFLAT-1|RFLAT1	Kruppel-like factor 13	protein-coding
mm_37858.1	chr4	132270210	132270214	-	1	NA	promoter-TSS (NR_002865)	promoter-TSS (NR_002865)	-26	NR_002865	353373	Mm.424675	NR_002865		Rnu11	MBII-407|Mirn801|mir-801|mmu-mir-801	U11 small nuclear RNA	snRNA
mm_69483.1	chr7	133782722	133782762	-	1	NA	promoter-TSS (NM_001286031)	promoter-TSS (NM_001286031)	43	NM_001286031	101437	Mm.199223	NM_133941	ENSMUSG00000030986	Dhx32	3110079L04Rik|4732469F02Rik|AA408140|Ddx32	DEAH (Asp-Glu-Ala-His) box polypeptide 32	protein-coding
mm_127672.1	chr15	102671950	102671965	+	1	NA	promoter-TSS (NR_030460)	promoter-TSS (NR_030460)	-91	NR_030460	751542		NR_030460	ENSMUSG00000076009	Mir688	Mirn688|mmu-mir-688	microRNA 688	ncRNA
mm_91641.1	chr10	42276666	42276681	-	1	NA	promoter-TSS (NM_019740)	promoter-TSS (NM_019740)	69	NM_019740	56484	Mm.338613	NM_019740	ENSMUSG00000048756	Foxo3	1110048B16Rik|2010203A17Rik|C76856|FKHRL1|Fkhr2|Foxo3a	forkhead box O3	protein-coding
mm_118390.1	chr13	118387225	118387275	-	1	NA	promoter-TSS (NM_021556)	promoter-TSS (NM_021556)	2	NM_021556	59054	Mm.143810	NM_021556	ENSMUSG00000021731	Mrps30	2610020A16Rik|AA968347|PAP|Pdcd9	mitochondrial ribosomal protein S30	protein-coding
mm_66316.1	chr7	40636455	40636457	-	1	NA	Intergenic	Intergenic	-38281	NR_045504	71029	Mm.399496	NR_045504	ENSMUSG00000102004	4933402C06Rik	-	RIKEN cDNA 4933402C06 gene	ncRNA
mm_77183.1	chr8	111732092	111732146	-	1	NA	promoter-TSS (NM_001198839)	promoter-TSS (NM_001198839)	17	NM_001198839	12927	Mm.3758	NM_009954	ENSMUSG00000031955	Bcar1	AI385681|Cas|Crkas	breast cancer anti-estrogen resistance 1	protein-coding
mm_106177.1	chr11	116680875	116680914	-	1	NA	intron (NM_009180, intron 6 of 8)	intron (NM_009180, intron 6 of 8)	6297	NR_028570	100216538		NR_028570	ENSMUSG00000065094	Snord1a	snR38	small nucleolar RNA, C/D box 1A	snoRNA
mm_55660.1	chr6	72394539	72394545	-	1	NA	Intergenic	Intergenic	-3875	NM_016794	22320	Mm.1838	NM_016794	ENSMUSG00000050732	Vamp8	AU041171|Edb|endobrevin	vesicle-associated membrane protein 8	protein-coding
mm_105951.1	chr11	115297511	115297519	-	1	NA	promoter-TSS (NM_178035)	promoter-TSS (NM_178035)	31	NM_178035	328035	Mm.21995	NM_178035	ENSMUSG00000044788	Fads6	BC044804|OTTMUSG00000021749	fatty acid desaturase domain family, member 6	protein-coding
mm_39625.1	chr5	24426843	24426867	+	1	NA	promoter-TSS (NM_001253892)	promoter-TSS (NM_001253892)	-666	NM_001253892	20535	Mm.4580	NM_009207	ENSMUSG00000028962	Slc4a2	Ae2|B3RP	solute carrier family 4 (anion exchanger), member 2	protein-coding
mm_17899.1	chr2	35101543	35101548	-	1	NA	promoter-TSS (NM_178885)	promoter-TSS (NM_178885)	-860	NM_001243103	98870	Mm.415380	NM_178885	ENSMUSG00000035875	AI182371	AI046667	expressed sequence AI182371	protein-coding
mm_26330.1	chr3	142544225	142544282	+	1	NA	intron (NM_145545, intron 8 of 10)	intron (NM_145545, intron 8 of 10)	13917	NM_145545	229900	Mm.45740	NM_145545	ENSMUSG00000040253	Gbp7	9830147J24Rik	guanylate binding protein 7	protein-coding
mm_3305.1	chr1	137898561	137898617	+	1	NA	Intergenic	Intergenic	-67866	NR_029795	735252		NR_029795	ENSMUSG00000065565	Mir181a-1	Mirn181a-1|Mirn213|miR-213|mir-181a-1|mmu-mir-213	microRNA 181a-1	ncRNA
mm_121292.1	chr14	105258836	105258845	+	1	NA	exon (NM_029561, exon 1 of 8)	exon (NM_029561, exon 1 of 8)	167	NM_001190989	76273	Mm.290669	NM_029561	ENSMUSG00000053253	Ndfip2	0710001O20Rik|2810436B12Rik|9130207N19Rik|N4wbp5a|mKIAA1165	Nedd4 family interacting protein 2	protein-coding
mm_127230.1	chr15	99405850	99405877	+	1	NA	exon (NM_026669, exon 6 of 10)	exon (NM_026669, exon 6 of 10)	12644	NM_001171035	110213	Mm.16769	NM_026669	ENSMUSG00000023010	Tmbim6	5031406P05Rik|Bi1|Tegt	transmembrane BAX inhibitor motif containing 6	protein-coding
mm_23297.1	chr3	52268408	52268424	+	1	NA	promoter-TSS (NM_019739)	promoter-TSS (NM_019739)	79	NM_019739	56458	Mm.29891	NM_019739	ENSMUSG00000044167	Foxo1	AI876417|Afxh|FKHR|Fkhr1|Foxo1a	forkhead box O1	protein-coding
mm_172775.1	chr8	95271968	95271971	-	1	NA	intron (NM_001195413, intron 16 of 32)	intron (NM_001195413, intron 16 of 32)	34616	NM_145601	333329	Mm.484049	NM_145601	ENSMUSG00000031789	Cngb1	Cngb1b|Garp2|Gm1959	cyclic nucleotide gated channel beta 1	protein-coding
mm_13783.1	chr2	118779898	118779900	+	1	NA	5' UTR (NM_170593, exon 1 of 8)	5' UTR (NM_170593, exon 1 of 8)	180	NM_170593	214240	Mm.221499	NM_170593	ENSMUSG00000040035	Disp2	AI840597|B230210L08Rik|DispB|mKIAA1742	dispatched RND tramsporter family member 2	protein-coding
mm_132999.1	chr16	55949197	55949225	+	1	NA	Intergenic	Intergenic	-14363	NM_001159365	74201	Mm.178427	NM_028815	ENSMUSG00000022604	Cep97	2810403B08Rik|4932439K18Rik|AA437768|E130116N02Rik|Lrriq2	centrosomal protein 97	protein-coding
mm_136135.1	chr16	86808803	86808825	-	1	NA	Intergenic	Intergenic	-545371	NM_001159331	67768	Mm.296532	NM_026366	ENSMUSG00000044442	N6amt1	5830445C04Rik|Hemk2|Pred28	N-6 adenine-specific DNA methyltransferase 1 (putative)	protein-coding
mm_42458.1	chr5	115435519	115435521	+	1	NA	exon (NM_008629, exon 6 of 15)	exon (NM_008629, exon 6 of 15)	5835	NM_008629	17690	Mm.5077	NM_008629	ENSMUSG00000054256	Msi1	Msi1h|Musahi1|m-Msi-1	musashi RNA-binding protein 1	protein-coding
mm_20355.1	chr2	128054963	128054967	-	1	NA	intron (NM_028765, intron 14 of 17)	intron (NM_028765, intron 14 of 17)	-71073	NM_207681	12125	Mm.141083	NM_009754	ENSMUSG00000027381	Bcl2l11	1500006F24Rik|Bim|Bod|bcl2-L-11	BCL2-like 11 (apoptosis facilitator)	protein-coding
mm_37145.1	chr4	116993740	116993754	-	1	NA	intron (NM_009478, intron 1 of 9)	intron (NM_009478, intron 1 of 9)	666	NM_009478	22275	Mm.46484	NM_009478	ENSMUSG00000028684	Urod	AI323803|UPD|Uro-d	uroporphyrinogen decarboxylase	protein-coding
mm_123014.1	chr14	55106522	55106541	-	1	NA	promoter-TSS (NM_007455)	promoter-TSS (NM_007455)	62	NM_001303502	11766	Mm.238879	NM_007455	ENSMUSG00000040701	Ap1g2	Adtg2|G2ad	adaptor protein complex AP-1, gamma 2 subunit	protein-coding
mm_92716.1	chr10	80797993	80798003	-	1	NA	promoter-TSS (NM_013651)	promoter-TSS (NM_013651)	628	NM_023900	78670	Mm.41479	NM_023900	ENSMUSG00000035278	Plekhj1	9530063M10Rik	pleckstrin homology domain containing, family J member 1	protein-coding
mm_88237.1	chr10	71388502	71388505	+	1	NA	Intergenic	Intergenic	40740	NM_027184	69718	Mm.245867	NM_027184	ENSMUSG00000060733	Ipmk	2410017C19Rik|AA408208|Impk	inositol polyphosphate multikinase	protein-coding
mm_1654.1	chr1	74666263	74666266	+	1	NA	intron (NM_001014974, intron 1 of 19)	intron (NM_001014974, intron 1 of 19)	4510	NM_001014974	67534	Mm.260714	NM_001014974	ENSMUSG00000033257	Ttll4	4632407P03Rik|AI451681|mKIAA0173	tubulin tyrosine ligase-like family, member 4	protein-coding
mm_1849.1	chr1	83116761	83116776	+	1	NA	promoter-TSS (NM_016960)	promoter-TSS (NM_016960)	2	NM_001159738	20297	Mm.116739	NM_016960	ENSMUSG00000026166	Ccl20	CKb4|LARC|MIP-3A|MIP-3[a]|MIP3A|ST38|Scya20|exodus-1	chemokine (C-C motif) ligand 20	protein-coding
mm_46679.1	chr5	109556531	109556553	-	1	NA	exon (NM_001164735, exon 4 of 8)	exon (NM_001164735, exon 4 of 8)	2451	NM_016715	57914	Mm.35771	NM_016715	ENSMUSG00000033467	Crlf2	CRLM2|Ly114|Tpte2|Tslpr	cytokine receptor-like factor 2	protein-coding
mm_157280.1	chrX	20618197	20618218	-	1	NA	promoter-TSS (NM_019435)	promoter-TSS (NM_019435)	448	NM_145627	236732	Mm.279194	NM_145627	ENSMUSG00000031060	Rbm10	E430039K10Rik	RNA binding motif protein 10	protein-coding
mm_104490.1	chr11	95834117	95834131	-	1	NA	intron (NM_025659, intron 4 of 7)	intron (NM_025659, intron 4 of 7)	-8171	NM_023121	14710	Mm.46299	NM_023121	ENSMUSG00000038811	Gngt2	AV096488	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 2	protein-coding
mm_10848.1	chr2	24976181	24976192	+	1	NA	5' UTR (NM_146251, exon 1 of 35)	5' UTR (NM_146251, exon 1 of 35)	153	NM_146251	241274	Mm.389243	NM_146251	ENSMUSG00000036833	Pnpla7	BC027342|E430013P11Rik|Nre	patatin-like phospholipase domain containing 7	protein-coding
mm_156475.1	chrX	143685050	143685073	+	1	NA	intron (NM_001195049, intron 4 of 17)	intron (NM_001195049, intron 4 of 17)	-8226	NM_001195047	18481	Mm.40035	NM_008778	ENSMUSG00000031284	Pak3	PAK-3|Pak65alpha|Pak65beta|Stk4	p21 protein (Cdc42/Rac)-activated kinase 3	protein-coding
mm_79180.1	chr9	48314450	48314505	+	1	NA	Intergenic	L1MB2|LINE|L1	26421	NM_030069	78252	Mm.31626	NM_030069	ENSMUSG00000032028	Nxpe2	4432416J03Rik|AI323362|Fam55b	neurexophilin and PC-esterase domain family, member 2	protein-coding
mm_91793.1	chr10	53376131	53376164	-	1	NA	intron (NM_001204983, intron 1 of 12)	intron (NM_001204983, intron 1 of 12)	3704	NM_001204983	100038725	Mm.441403	NM_001204983	ENSMUSG00000038594	Cep85l	ENSMUSG00000038594|Gm9766	centrosomal protein 85-like	protein-coding
mm_63897.1	chr7	138940364	138940396	+	1	NA	promoter-TSS (NM_028708)	promoter-TSS (NM_028708)	-350	NM_028708	74004	Mm.334298	NM_028708		Jakmip3	6330417G02Rik|AI593226|mKIAA4091	janus kinase and microtubule interacting protein 3	protein-coding
mm_163667.1	chr13	80883359	80883376	+	1	NA	promoter-TSS (NM_001042591)	promoter-TSS (NM_001042591)	-55	NM_001042591	105171	Mm.423137	NM_001042591	ENSMUSG00000074794	Arrdc3	AI450344|mKIAA1376	arrestin domain containing 3	protein-coding
mm_89176.1	chr10	86343939	86343957	+	1	NA	exon (NM_011595, exon 3 of 5)	exon (NM_011595, exon 3 of 5)	43536	NM_011595	21859	Mm.4871	NM_011595	ENSMUSG00000020044	Timp3	Timp-3	tissue inhibitor of metalloproteinase 3	protein-coding
mm_134695.1	chr16	22622322	22622333	-	1	NA	5' UTR (NM_138650, exon 2 of 25)	5' UTR (NM_138650, exon 2 of 25)	34904	NM_138650	110197	Mm.194986	NM_138650	ENSMUSG00000022861	Dgkg	2900055E17Rik|90kDa|AI854428|Dagk3|E430001K23Rik|mKIAA4131	diacylglycerol kinase, gamma	protein-coding
mm_141419.1	chr17	29434709	29434721	-	1	NA	Intergenic	Intergenic	-56330	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_48278.1	chr5	138116852	138116868	-	1	NA	promoter-TSS (NM_011757)	promoter-TSS (NM_011757)	-45	NM_001044703	22697	Mm.2760	NM_011757	ENSMUSG00000037017	Zscan21	AI326272|CTfin51|RU49|Zfp-38|Zfp38|Zipro1	zinc finger and SCAN domain containing 21	protein-coding
mm_3990.1	chr1	164438476	164438507	+	1	NA	exon (NM_009721, exon 6 of 6)	exon (NM_009721, exon 6 of 6)	19864	NM_009721	11931	Mm.4550	NM_009721	ENSMUSG00000026576	Atp1b1	Atp4b|Atpb|Atpb-1|NKbeta1	ATPase, Na+/K+ transporting, beta 1 polypeptide	protein-coding
mm_106205.1	chr11	116850622	116850648	-	1	NA	TTS (NM_028865)	TTS (NM_028865)	2459	NM_011358	20382	Mm.21841	NM_011358	ENSMUSG00000034120	Srsf2	D11Wsu175e|MRF-1|Pr264|SC35|Sfrs10|Sfrs2	serine/arginine-rich splicing factor 2	protein-coding
mm_127834.1	chr15	6708880	6708886	-	1	NA	intron (NM_030168, intron 2 of 37)	CpG-4767	502	NM_030168	78757	Mm.275811	NM_030168	ENSMUSG00000050310	Rictor	4921505C17Rik|6030405M08Rik|AVO3|AW492497|D530039E11Rik	RPTOR independent companion of MTOR, complex 2	protein-coding
mm_30455.1	chr3	153912942	153912960	-	1	NA	promoter-TSS (NR_028525)	promoter-TSS (NR_028525)	15	NM_001163478	19352	Mm.277831	NM_011231	ENSMUSG00000038975	Rabggtb	-	Rab geranylgeranyl transferase, b subunit	protein-coding
mm_160262.1	chr7	109752672	109752672	-	1	NA	promoter-TSS (NM_020050)	promoter-TSS (NM_020050)	-409	NM_020050	56786	Mm.240668	NM_020050	ENSMUSG00000031021	Tmem9b	2310004K06Rik|AW539847|D7H11orf15|ICRFP703B1614Q5.3	TMEM9 domain family, member B	protein-coding
mm_161176.1	chr13	41110274	41110274	-	1	NA	promoter-TSS (NM_008104)	promoter-TSS (NM_008104)	-286	NM_008104	107889	Mm.1399	NM_008104	ENSMUSG00000021362	Gcm2	Gcm-rs1|Gcm1|Gcm1-rs2	glial cells missing homolog 2 (Drosophila)	protein-coding
mm_129113.1	chr15	76071552	76071582	-	1	NA	exon (NM_028364, exon 9 of 12)	exon (NM_028364, exon 9 of 12)	-1783	NM_001310542	105782	Mm.25568	NM_134089	ENSMUSG00000022568	Scrib	AI118201|CRIB|Crc|SCRIB1|Scrb1|mKIAA0147|vartul	scribbled planar cell polarity	protein-coding
mm_137583.1	chr17	28007583	28007596	+	1	NA	intron (NM_001286040, intron 11 of 24)	intron (NM_001286040, intron 11 of 24)	72995	NM_013687	21463	Mm.29758	NM_013687	ENSMUSG00000062859	Tcp11	D17Ken1|Tcp-11	t-complex protein 11	protein-coding
mm_52332.1	chr6	109739838	109739846	+	1	NA	Intergenic	Intergenic	-905670	NM_001346640	108073	Mm.240881	NM_177328	ENSMUSG00000056755	Grm7	6330570A01Rik|BB176677|C030018L03|E130018M02Rik|Gpr1g|Gprc1g|SMN2|Tg(SMN2)89Ahmb|mGluR7	glutamate receptor, metabotropic 7	protein-coding
mm_88979.1	chr10	81559448	81559498	+	1	NA	promoter-TSS (NM_010347)	promoter-TSS (NM_010347)	29	NM_001276288	14797	Mm.180013	NM_010347	ENSMUSG00000054452	Aes	AL024115|Esp1|Grg|Grg-5|Grg5|Tle5	amino-terminal enhancer of split	protein-coding
mm_31145.1	chr4	43384241	43384249	+	1	NA	intron (NM_001037709, intron 1 of 11)	intron (NM_001037709, intron 1 of 11)	2263	NM_001037709	100213	Mm.235730	NM_199057	ENSMUSG00000035969	Rusc2	AI840675|mKIAA0375	RUN and SH3 domain containing 2	protein-coding
mm_154421.1	chrM	16223	16242	+	1	NA	NA	Intergenic	NA	NA								
mm_9447.1	chr1	172590623	172590645	-	1	NA	promoter-TSS (NM_029084)	promoter-TSS (NM_029084)	-66	NM_029084	74748	Mm.179812	NM_029084	ENSMUSG00000053318	Slamf8	5830408F06Rik|Blame|SBBI42	SLAM family member 8	protein-coding
mm_36251.1	chr4	63403362	63403376	-	1	NA	promoter-TSS (NM_001045514)	promoter-TSS (NM_001045514)	76	NM_001045514	100182	Mm.387725	NM_001045514	ENSMUSG00000039158	Akna	AI597013	AT-hook transcription factor	protein-coding
mm_59112.1	chr7	19817718	19817732	+	1	NA	intron (NM_033601, intron 2 of 8)	intron (NM_033601, intron 2 of 8)	5030	NM_033601	12051	Mm.439658	NM_033601	ENSMUSG00000053175	Bcl3	AI528691|Bcl-3	B cell leukemia/lymphoma 3	protein-coding
mm_170924.1	chr2	39005105	39005105	-	1	NA	promoter-TSS (NM_025592)	promoter-TSS (NM_025592)	26	NM_025592	66489	Mm.345333	NM_025592	ENSMUSG00000062997	Rpl35	2410039E09Rik	ribosomal protein L35	protein-coding
mm_23130.1	chr3	37734701	37734712	+	1	NA	Intergenic	Intergenic	-10346	NM_198657	381438	Mm.490549	NM_198657	ENSMUSG00000058174	Gm5148	EG381438	predicted gene 5148	protein-coding
mm_123070.1	chr14	55709476	55709486	-	1	NA	exon (NM_001161715, exon 7 of 15)	exon (NM_001161715, exon 7 of 15)	3607	NM_019984	21816	Mm.41964	NM_019984	ENSMUSG00000022218	Tgm1	2310004J08Rik|Tgase1	transglutaminase 1, K polypeptide	protein-coding
mm_168427.1	chr1	133610246	133610246	-	1	NA	promoter-TSS (NM_009227)	promoter-TSS (NM_009227)	34	NM_009227	20643	Mm.249110	NM_009227	ENSMUSG00000090553	Snrpe	AL022645|C76690|SME	small nuclear ribonucleoprotein E	protein-coding
mm_145690.1	chr18	61953049	61953121	+	1	NA	promoter-TSS (NM_172628)	promoter-TSS (NM_172628)	10	NM_172628	225608	Mm.262320	NM_172628	ENSMUSG00000045629	Sh3tc2	D430044G18Rik	SH3 domain and tetratricopeptide repeats 2	protein-coding
mm_37541.1	chr4	125122506	125122532	-	1	NA	intron (NM_153159, intron 2 of 5)	intron (NM_153159, intron 2 of 5)	5362	NM_153159	230738	Mm.402	NM_153159	ENSMUSG00000042677	Zc3h12a	BC036563|MCPIP|MCPIP-1|Mcpip1|Reg1	zinc finger CCCH type containing 12A	protein-coding
mm_132120.1	chr16	31695884	31695922	+	1	NA	intron (NR_045516, intron 4 of 24)	intron (NR_045516, intron 4 of 24)	31968	NM_001252434	13383	Mm.382	NM_007862	ENSMUSG00000022770	Dlg1	B130052P05Rik|Dlgh1|E-dlg/SAP97|SAP-97|SAP97|mKIAA4187	discs, large homolog 1 (Drosophila)	protein-coding
mm_25912.1	chr3	131123742	131123776	+	1	NA	intron (NM_001276403, intron 3 of 11)	intron (NM_001276403, intron 3 of 11)	10968	NM_001276403	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_156618.1	chrX	153558592	153558594	+	1	NA	promoter-TSS (NM_001310716)	promoter-TSS (NM_001310716)	0	NM_173367	69361	Mm.46095	NM_173367	ENSMUSG00000048573	Cypt3	1700006H02Rik|Ckt1r1	cysteine-rich perinuclear theca 3	protein-coding
mm_113866.1	chr13	48491033	48491047	+	1	NA	exon (NM_026450, exon 5 of 5)	exon (NM_026450, exon 5 of 5)	22370	NM_001164575	67911	Mm.251375	NM_026450	ENSMUSG00000050954	Zfp169	1700025J14Rik|4930429A13Rik|BE688704	zinc finger protein 169	protein-coding
mm_4088.1	chr1	167001458	167001471	+	1	NA	promoter-TSS (NM_175461)	promoter-TSS (NM_175461)	47	NM_001160261	226610	Mm.389217	NM_175461	ENSMUSG00000060568	Fam78b	C030014K22Rik|C030020L09Rik	family with sequence similarity 78, member B	protein-coding
mm_155201.1	chrX	56731421	56731441	+	1	NA	promoter-TSS (NM_010211)	promoter-TSS (NM_010211)	-330	NM_010211	14199	Mm.3126	NM_010211	ENSMUSG00000023092	Fhl1	FHL-1|KyoT|RAM14-1|SLIM|SLIM-1	four and a half LIM domains 1	protein-coding
mm_114896.1	chr13	94394731	94394748	+	1	NA	exon (NM_009680, exon 3 of 27)	exon (NM_009680, exon 3 of 27)	35779	NM_009680	11774	Mm.21185	NM_009680	ENSMUSG00000021686	Ap3b1	AP-3|AU015684|C78395|Hps2|beta3A|pe|pearl|rim2	adaptor-related protein complex 3, beta 1 subunit	protein-coding
mm_156105.1	chrX	114284558	114284571	+	1	NA	Intergenic	Intergenic	-189769	NM_001290478	237010	Mm.132583	NM_172781	ENSMUSG00000025597	Klhl4	B130014A11|C130018J01Rik	kelch-like 4	protein-coding
mm_30832.1	chr4	21931501	21931511	+	1	NA	5' UTR (NM_175234, exon 1 of 6)	5' UTR (NM_175234, exon 1 of 6)	180	NM_175234	76132	Mm.159689	NM_175234	ENSMUSG00000028246	Faxc	6230409E13Rik|AW742931	failed axon connections homolog	protein-coding
mm_166735.1	chr6	122921789	122921799	+	1	NA	promoter-TSS (NM_199311)	promoter-TSS (NM_199311)	-54	NM_199311	269799	Mm.297275	NM_199311	ENSMUSG00000049037	Clec4a1	BC049354|Dcir4	C-type lectin domain family 4, member a1	protein-coding
mm_98526.1	chr11	94990972	94990995	+	1	NA	promoter-TSS (NM_172261)	promoter-TSS (NM_172261)	-229	NM_172261	217124	Mm.229087	NM_172261	ENSMUSG00000038976	Ppp1r9b	SPL|Spn	protein phosphatase 1, regulatory subunit 9B	protein-coding
mm_118613.1	chr14	21032429	21032441	+	1	NA	3' UTR (NM_009502, exon 21 of 21)	3' UTR (NM_009502, exon 21 of 21)	20007	NM_018829	55946	Mm.376269	NM_018829	ENSMUSG00000021824	Ap3m1	1200013D09Rik|C78982|R75378	adaptor-related protein complex 3, mu 1 subunit	protein-coding
mm_90527.1	chr10	128083942	128083985	+	1	NA	exon (NM_016774, exon 2 of 10)	exon (NM_016774, exon 2 of 10)	656	NM_016774	11947	Mm.238973	NM_016774	ENSMUSG00000025393	Atp5b	-	ATP synthase, H+ transporting mitochondrial F1 complex, beta subunit	protein-coding
mm_15600.1	chr2	160670120	160670172	+	1	NA	exon (NM_009408, exon 3 of 21)	exon (NM_009408, exon 3 of 21)	24249	NM_009408	21969	Mm.217233	NM_009408	ENSMUSG00000070544	Top1	AI467334|D130064I21Rik|Top-1	topoisomerase (DNA) I	protein-coding
mm_77263.1	chr8	115707616	115707637	-	1	NA	promoter-TSS (NM_001025577)	promoter-TSS (NM_001025577)	-732	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_65594.1	chr7	27333603	27333640	-	1	NA	promoter-TSS (NM_001113549)	promoter-TSS (NM_001113549)	27	NM_001113549	108075	Mm.272251	NM_175641	ENSMUSG00000040488	Ltbp4	2310046A13Rik	latent transforming growth factor beta binding protein 4	protein-coding
mm_131782.1	chr16	22896001	22896015	+	1	NA	intron (NR_075099, intron 3 of 5)	intron (NR_075099, intron 3 of 5)	-1622	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_67336.1	chr7	79793015	79793047	-	1	NA	exon (NM_008588, exon 1 of 2)	exon (NM_008588, exon 1 of 2)	559	NM_008588	17292	Mm.1404	NM_008588	ENSMUSG00000030544	Mesp1	bHLHc5	mesoderm posterior 1	protein-coding
mm_112768.1	chr13	19358056	19358071	+	1	NA	3' UTR (NM_024270, exon 9 of 9)	3' UTR (NM_024270, exon 9 of 9)	37750	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_155134.1	chrX	49493143	49493174	+	1	NA	intron (NM_001081123, intron 1 of 12)	intron (NM_001081123, intron 1 of 12)	22708	NM_001081123	75404	Mm.44305	NM_001081123	ENSMUSG00000036198	Arhgap36	1100001E04Rik|rho-gap	Rho GTPase activating protein 36	protein-coding
mm_68116.1	chr7	102100203	102100219	-	1	NA	promoter-TSS (NM_007491)	promoter-TSS (NM_007491)	18	NR_111935	11875	Mm.2816	NM_007491	ENSMUSG00000070424	Art5	ARTC5|Yac-2	ADP-ribosyltransferase 5	protein-coding
mm_25119.1	chr3	102012292	102012302	+	1	NA	intron (NM_178777, intron 2 of 2)	CpG	2152	NM_178777	18072	Mm.137286	NM_178777	ENSMUSG00000048540	Nhlh2	6230401I09Rik|Hen2|NSCL2|Nscl-2|bHLHa34	nescient helix loop helix 2	protein-coding
mm_124712.1	chr15	6569559	6569565	+	1	NA	Intergenic	Intergenic	-10285	NM_001278269	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_54885.1	chr6	43266597	43266610	-	1	NA	intron (NM_133674, intron 1 of 14)	intron (NM_133674, intron 1 of 14)	959	NM_133674	54324	Mm.320978	NM_133674	ENSMUSG00000033542	Arhgef5	2210412D05Rik|AA717842|AW495314|Tim1	Rho guanine nucleotide exchange factor (GEF) 5	protein-coding
mm_163857.1	chr14	19418551	19418571	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	184026	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_91335.1	chr10	25536115	25536155	-	1	NA	promoter-TSS (NR_136909)	promoter-TSS (NR_136909)	137	NM_001195596	100504474	Mm.46323	NM_001195596	ENSMUSG00000096546	Smlr1	2010003K15Rik	small leucine-rich protein 1	protein-coding
mm_137571.1	chr17	27840204	27840214	+	1	NA	intron (NM_011432, intron 1 of 5)	CpG	122	NM_011432	20630	Mm.103949	NM_011432	ENSMUSG00000024217	Snrpc	Snrp1c|U1-C|U1C	U1 small nuclear ribonucleoprotein C	protein-coding
mm_47899.1	chr5	134906720	134906724	-	1	NA	promoter-TSS (NM_194065)	promoter-TSS (NM_194065)	11	NM_029681	76629	Mm.159750	NM_029681	ENSMUSG00000040576	Wbscr28	1700111I05Rik	Williams-Beuren syndrome chromosome region 28 (human)	protein-coding
mm_133344.1	chr16	81237734	81237744	+	1	NA	intron (NM_001113208, intron 1 of 17)	B1_Mus1|SINE|Alu	37042	NM_010954	17968	Mm.433941	NM_010954	ENSMUSG00000022762	Ncam2	Ncam-2|Ocam|RNCAM	neural cell adhesion molecule 2	protein-coding
mm_69312.1	chr7	128418380	128418391	-	1	NA	promoter-TSS (NM_026418)	promoter-TSS (NM_026418)	-213	NM_026418	67865	Mm.18635	NM_026418	ENSMUSG00000030844	Rgs10	2310010N19Rik	regulator of G-protein signalling 10	protein-coding
mm_89983.1	chr10	111972751	111972805	+	1	NA	promoter-TSS (NM_178610)	promoter-TSS (NM_178610)	83	NM_178610	52705	Mm.34606	NM_178610	ENSMUSG00000063334	Krr1	2610511F02Rik|AI255219|AI428520|D10Ertd773e|Hrb2	KRR1, small subunit (SSU) processome component, homolog (yeast)	protein-coding
mm_8866.1	chr1	162813943	162813953	-	1	NA	Intergenic	Intergenic	-1399	NM_144878	226564	Mm.155164	NM_144878	ENSMUSG00000026692	Fmo4	D1Ertd532e	flavin containing monooxygenase 4	protein-coding
mm_80080.1	chr9	70012595	70012611	+	1	NA	promoter-TSS (NM_001282084)	promoter-TSS (NM_001282084)	55	NM_001282083	235459	Mm.293117	NM_199151	ENSMUSG00000033543	Gtf2a2	TFIIA-gamma|TfIIg|Tfiia2	general transcription factor II A, 2	protein-coding
mm_148309.1	chr18	83637936	83637943	-	1	NA	Intergenic	(GA)n|Simple_repeat|Simple_repeat	-312055	NR_045361	70960	Mm.410834	NR_045361		4921531P14Rik	1700108N05Rik	RIKEN cDNA 4921531P14 gene	ncRNA
mm_162025.1	chr19	47015243	47015243	-	1	NA	promoter-TSS (NM_001164363)	promoter-TSS (NM_001164363)	-54	NM_001164363	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_17091.1	chr2	23034990	23034994	-	1	NA	intron (NM_001331043, intron 1 of 10)	intron (NM_001331043, intron 1 of 10)	5249	NM_001077192	11308	Mm.205647	NM_007380	ENSMUSG00000058835	Abi1	E3B1|NAP1|Ssh3bp1|abi-1	abl-interactor 1	protein-coding
mm_52620.1	chr6	117174030	117174036	+	1	NA	3' UTR (NM_021704, exon 3 of 3)	3' UTR (NM_021704, exon 3 of 3)	5498	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_108541.1	chr12	84316831	84316865	+	1	NA	promoter-TSS (NM_144833)	promoter-TSS (NM_144833)	-11	NR_045546	52708	Mm.255150	NM_144833	ENSMUSG00000042472	Zfp410	Apa1|D12Ertd748e|Znf410	zinc finger protein 410	protein-coding
mm_70652.1	chr8	14370157	14370181	+	1	NA	intron (NM_172910, intron 3 of 15)	intron (NM_172910, intron 3 of 15)	274294	NM_172910	244310	Mm.404697	NM_172910	ENSMUSG00000047495	Dlgap2	6430596N04Rik|Dap-2|Dap2|Sapap2	discs, large (Drosophila) homolog-associated protein 2	protein-coding
mm_149721.1	chr19	21778326	21778363	+	1	NA	promoter-TSS (NM_031997)	promoter-TSS (NM_031997)	4	NM_031997	83921	Mm.329776	NM_031997	ENSMUSG00000024754	Tmem2	-	transmembrane protein 2	protein-coding
mm_52993.1	chr6	123267093	123267123	+	1	NA	exon (NM_010819, exon 3 of 6)	exon (NM_010819, exon 3 of 6)	5001	NM_010819	17474	Mm.441101	NM_010819	ENSMUSG00000030144	Clec4d	Clecsf8|Mpcl|mcl	C-type lectin domain family 4, member d	protein-coding
mm_163675.1	chr13	83721397	83721401	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-6707	NR_015561	320203	Mm.245636	NM_177100	ENSMUSG00000050334	C130071C03Rik	2810449C10Rik	RIKEN cDNA C130071C03 gene	ncRNA
mm_130905.1	chr15	102510682	102510705	-	1	NA	intron (NM_001163643, intron 1 of 15)	CpG	6311	NM_001163643	26404	Mm.172897	NM_009582	ENSMUSG00000023050	Map3k12	DLK|MUK|Zpk	mitogen-activated protein kinase kinase kinase 12	protein-coding
mm_101009.1	chr11	8503797	8503803	-	1	NA	intron (NM_001083587, intron 16 of 30)	intron (NM_001083587, intron 16 of 30)	160735	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_116860.1	chr13	54765849	54765907	-	1	NA	intron (NM_033610, intron 1 of 5)	CpG	562	NM_033610	104069	Mm.200843	NM_033610	ENSMUSG00000034891	Sncb	AI838531|betaSYN	synuclein, beta	protein-coding
mm_22814.1	chr3	27188414	27188441	+	1	NA	intron (NM_178772, intron 1 of 4)	intron (NM_178772, intron 1 of 4)	5423	NM_178772	320024	Mm.24576	NM_178772	ENSMUSG00000027698	Nceh1	Aadacl1|B230106I24Rik|CPO-BP|Nceh	neutral cholesterol ester hydrolase 1	protein-coding
mm_53592.1	chr6	137782916	137782934	+	1	NA	intron (NM_172733, intron 4 of 8)	intron (NM_172733, intron 4 of 8)	28348	NM_172733	232449	Mm.29181	NM_172733	ENSMUSG00000030225	Dera	2010002D22Rik|2500002K03Rik|DEOC	deoxyribose-phosphate aldolase (putative)	protein-coding
mm_141349.1	chr17	28622067	28622081	-	1	NA	intron (NM_016795, intron 1 of 15)	CpG-6184	380	NM_016795	20815	Mm.15252	NM_016795	ENSMUSG00000004865	Srpk1	AU017960	serine/arginine-rich protein specific kinase 1	protein-coding
mm_101512.1	chr11	32278002	32278041	-	1	NA	TTS (NM_010405)	TTS (NM_010405)	1421	NM_010405	15126	Mm.141758	NM_010405	ENSMUSG00000055609	Hba-x	AI450015|Hbz	hemoglobin X, alpha-like embryonic chain in Hba complex	protein-coding
mm_97723.1	chr11	80383310	80383336	+	1	NA	promoter-TSS (NR_045038)	promoter-TSS (NR_045038)	44	NM_001130171	22680	Mm.401332	NM_011751	ENSMUSG00000017421	Zfp207	8430401D15Rik|BuGZ|Zep|Znf207	zinc finger protein 207	protein-coding
mm_164738.1	chr17	71787205	71787228	+	1	NA	intron (NM_030179, intron 1 of 15)	intron (NM_030179, intron 1 of 15)	5269	NM_030179	78785	Mm.196382	NM_030179	ENSMUSG00000024059	Clip4	1700024K14Rik|1700074B05Rik|4833417L20Rik|5830409B12Rik|Rsnl2	CAP-GLY domain containing linker protein family, member 4	protein-coding
mm_21039.1	chr2	152511732	152511748	-	1	NA	promoter-TSS (NM_001039120)	promoter-TSS (NM_001039120)	-4	NM_001039120	654457	Mm.389363	NM_001039120	ENSMUSG00000074680	Defb26	EG654457	defensin beta 26	protein-coding
mm_148816.1	chr19	6297987	6297995	+	1	NA	intron (NM_010119, intron 4 of 4)	intron (NM_010119, intron 4 of 4)	-8466	NM_001033342	240505	Mm.329622	NM_001033342	ENSMUSG00000024769	Cdc42bpg	BC046418|MRCKgamma	CDC42 binding protein kinase gamma (DMPK-like)	protein-coding
mm_29494.1	chr3	115888056	115888082	-	1	NA	promoter-TSS (NR_027895)	promoter-TSS (NR_027895)	-10	NR_027894	68161	Mm.392043	NR_015487	ENSMUSG00000054426	A930005H10Rik	-	RIKEN cDNA A930005H10 gene	ncRNA
mm_103661.1	chr11	78984967	78984972	-	1	NA	promoter-TSS (NM_010708)	promoter-TSS (NM_010708)	-45	NM_010708	16859	Mm.341434	NM_010708	ENSMUSG00000001123	Lgals9	AA407335|AI194909|AI265545|LGALS35|Lgals5|gal-9|galectin-9	lectin, galactose binding, soluble 9	protein-coding
mm_66496.1	chr7	45061652	45061691	-	1	NA	promoter-TSS (NM_025533)	promoter-TSS (NM_025533)	-19	NM_022999	65116	Mm.379098	NM_022999	ENSMUSG00000007837	Prrg2	1600014G02Rik|2510041M06Rik|N4WBP1	proline-rich Gla (G-carboxyglutamic acid) polypeptide 2	protein-coding
mm_159754.1	chr5	87885845	87885845	+	1	NA	intron (NM_027128, intron 1 of 9)	intron (NM_027128, intron 1 of 9)	150	NM_027128	69592	Mm.389652	NM_027128	ENSMUSG00000009580	Odam	2310011G06Rik|APIN	odontogenic, ameloblast asssociated	protein-coding
mm_12925.1	chr2	85037213	85037302	+	1	NA	promoter-TSS (NM_001136081)	promoter-TSS (NM_001136081)	137	NM_182990	20833	Mm.219793	NM_182990	ENSMUSG00000027067	Ssrp1	C81323|Hmg1-rs1|Hmgi-rs3|Hmgox|T160	structure specific recognition protein 1	protein-coding
mm_118612.1	chr14	21020682	21020698	+	1	NA	exon (NM_009502, exon 16 of 21)	exon (NM_009502, exon 16 of 21)	31752	NM_018829	55946	Mm.376269	NM_018829	ENSMUSG00000021824	Ap3m1	1200013D09Rik|C78982|R75378	adaptor-related protein complex 3, mu 1 subunit	protein-coding
mm_53340.1	chr6	129238422	129238429	+	1	NA	promoter-TSS (NR_040268)	promoter-TSS (NR_040268)	57	NR_040268	76432	Mm.261738	NR_040265	ENSMUSG00000097354	2310001H17Rik	AI646108	RIKEN cDNA 2310001H17 gene	ncRNA
mm_126951.1	chr15	92161322	92161339	+	1	NA	promoter-TSS (NM_001159647)	promoter-TSS (NM_001159647)	-27	NM_001159647	12805	Mm.4911	NM_007727	ENSMUSG00000055022	Cntn1	AW495098|CNTN|F3cam|usl	contactin 1	protein-coding
mm_15523.1	chr2	158381378	158381398	+	1	NA	3' UTR (NM_175692, exon 5 of 5)	3' UTR (NM_175692, exon 5 of 5)	5750	NM_175692	319317	Mm.294494	NM_175692	ENSMUSG00000044349	Snhg11	A930034L06Rik|AI854265|AL022637|AW319638|E130013N09Rik	small nucleolar RNA host gene 11	protein-coding
mm_93045.1	chr10	88479488	88479491	-	1	NA	intron (NR_027477, intron 5 of 8)	intron (NR_027477, intron 5 of 8)	19902	NM_011517	20962	Mm.297977	NM_011517	ENSMUSG00000020059	Sycp3	Cor1|Scp3	synaptonemal complex protein 3	protein-coding
mm_120485.1	chr14	65976901	65976924	+	1	NA	exon (NM_013492, exon 6 of 9)	exon (NM_013492, exon 6 of 9)	8429	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_145967.1	chr18	67800568	67800583	+	1	NA	promoter-TSS (NR_045376)	promoter-TSS (NR_045376)	468	NM_027556	70799	Mm.30857	NM_027556	ENSMUSG00000024542	Cep192	4631422C13Rik|D430014P18Rik	centrosomal protein 192	protein-coding
mm_77574.1	chr8	123432627	123432633	-	1	NA	Intergenic	MuLV-int|LTR|ERV1	-10326	NM_001253784	23854	Mm.275127	NM_054046	ENSMUSG00000001482	Def8	AI449518|D8Ertd713e|DEF-8	differentially expressed in FDCP 8	protein-coding
mm_884.1	chr1	52630693	52630757	+	1	NA	promoter-TSS (NM_001142647)	promoter-TSS (NM_001142647)	20	NM_001142647	227094	Mm.83541	NM_172654	ENSMUSG00000043015	Nemp2	5330401P04Rik|9830163O08|Tmem194b	nuclear envelope integral membrane protein 2	protein-coding
mm_114190.1	chr13	55727346	55727382	+	1	NA	promoter-TSS (NM_028281)	promoter-TSS (NM_028281)	-4	NM_028281	72562	Mm.28145	NM_028281	ENSMUSG00000021496	Pcbd2	2700061N24Rik|Dcoh2|Dcohm	pterin 4 alpha carbinolamine dehydratase/dimerization cofactor of hepatocyte nuclear factor 1 alpha (TCF1) 2	protein-coding
mm_126671.1	chr15	84412671	84412671	+	1	NA	intron (NM_001347543, intron 4 of 5)	intron (NM_001347543, intron 4 of 5)	33939	NM_001347543	72301	Mm.275387	NM_001163145	ENSMUSG00000062760	1810041L15Rik	Kiaa1644	RIKEN cDNA 1810041L15 gene	protein-coding
mm_88747.1	chr10	80292415	80292436	+	1	NA	promoter-TSS (NM_009091)	promoter-TSS (NM_009091)	-6	NM_009091	20054	Mm.643	NM_009091	ENSMUSG00000063457	Rps15	rig	ribosomal protein S15	protein-coding
mm_54343.1	chr6	30669499	30669501	-	1	NA	intron (NR_130781, intron 3 of 11)	intron (NR_130781, intron 3 of 11)	24249	NM_031998	83922	Mm.65389	NM_031998	ENSMUSG00000029790	Cep41	1700017E11Rik|2810431D15Rik|Tsga14	centrosomal protein 41	protein-coding
mm_77623.1	chr8	123953771	123953776	-	1	NA	3' UTR (NM_019552, exon 13 of 13)	3' UTR (NM_019552, exon 13 of 13)	-4508	NM_172288	234865	Mm.267812	NM_172288	ENSMUSG00000039509	Nup133	mermaid	nucleoporin 133	protein-coding
mm_29301.1	chr3	107931658	107931742	-	1	NA	promoter-TSS (NM_026672)	promoter-TSS (NM_026672)	45	NM_026672	68312	Mm.458189	NM_026672	ENSMUSG00000004035	Gstm7	0610005A07Rik|AI894236|Cd203c	glutathione S-transferase, mu 7	protein-coding
mm_1928.1	chr1	86110856	86110862	+	1	NA	exon (NM_008311, exon 2 of 4)	exon (NM_008311, exon 2 of 4)	1111	NM_008311	15559	Mm.439747	NM_008311	ENSMUSG00000026228	Htr2b	5-HT2B|AJ012488|AV377389	5-hydroxytryptamine (serotonin) receptor 2B	protein-coding
mm_93464.1	chr10	110898057	110898061	-	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	-1552	NR_045979	75630	Mm.392786	NR_045979	ENSMUSG00000101801	1700020G17Rik	4930480D05Rik	RIKEN cDNA 1700020G17 gene	ncRNA
mm_133794.1	chr16	95278509	95278523	+	1	NA	intron (NM_001271687, intron 3 of 4)	B4A|SINE|B4	20958	NM_001271690	16516	Mm.272239	NM_019664	ENSMUSG00000062609	Kcnj15	4930414N08Rik|AI182284|AI267127|IRKK|Kir4.2	potassium inwardly-rectifying channel, subfamily J, member 15	protein-coding
mm_12884.1	chr2	84738136	84738138	+	1	NA	TTS (NM_001005342)	TTS (NM_001005342)	3041	NR_029544	387149		NR_029544	ENSMUSG00000065484	Mir130a	Mirn130|Mirn130a|mir-130a	microRNA 130a	ncRNA
mm_54736.1	chr6	40940971	40940977	-	1	NA	promoter-TSS (NM_028550)	promoter-TSS (NM_028550)	-417	NM_028550	73481	Mm.333010	NM_028550	ENSMUSG00000029883	1700074P13Rik	AV047902|Tryx5	RIKEN cDNA 1700074P13 gene	protein-coding
mm_165408.1	chr2	143696656	143696659	+	1	NA	exon (NM_008792, exon 5 of 12)	exon (NM_008792, exon 5 of 12)	92529	NR_040625	378775	Mm.441313	NR_040625	ENSMUSG00000087115	Pcsk2os2	9430032N09Rik|Gm12360|OTTMUSG00000006467	proprotein convertase subtilisin/kexin type 2, opposite strand 2	ncRNA
mm_113418.1	chr13	34037592	34037605	+	1	NA	promoter-TSS (NM_026512)	promoter-TSS (NM_026512)	-43	NM_026512	68021	Mm.140243	NM_026512	ENSMUSG00000038286	Bphl	2010012D11Rik|5730533B08Rik|AI115341	biphenyl hydrolase-like (serine hydrolase, breast epithelial mucin-associated antigen)	protein-coding
mm_37320.1	chr4	119383806	119383810	-	1	NA	promoter-TSS (NM_028506)	promoter-TSS (NM_028506)	26	NM_028506	73332	Mm.425204	NM_028506	ENSMUSG00000028637	Ccdc30	1700001O02Rik|1700041C02Rik|1700111D19Rik|4930445I03Rik	coiled-coil domain containing 30	protein-coding
mm_142019.1	chr17	35201136	35201147	-	1	NA	intron (NM_001278601, intron 1 of 2)	intron (NM_001278601, intron 1 of 2)	866	NM_013693	21926	Mm.1293	NM_013693	ENSMUSG00000024401	Tnf	DIF|TNF-a|TNF-alpha|TNFSF2|TNFalpha|Tnfa|Tnfsf1a|Tnlg1f	tumor necrosis factor	protein-coding
mm_13975.1	chr2	121437608	121437646	+	1	NA	exon (NM_007952, exon 13 of 13)	exon (NM_007952, exon 13 of 13)	4974	NM_145973	269344	Mm.330522	NM_145973	ENSMUSG00000027246	Ell3	A930015D22Rik	elongation factor RNA polymerase II-like 3	protein-coding
mm_78979.1	chr9	45371707	45371731	+	1	NA	intron (NM_022004, intron 1 of 7)	intron (NM_022004, intron 1 of 7)	1534	NM_022004	59095	Mm.208287	NM_022004	ENSMUSG00000066705	Fxyd6	0610030I18Rik|Php	FXYD domain-containing ion transport regulator 6	protein-coding
mm_67975.1	chr7	100656894	100656914	-	1	NA	promoter-TSS (NM_001163187)	promoter-TSS (NM_001163187)	61	NM_001163187	27276	Mm.491216	NM_013746	ENSMUSG00000030701	Plekhb1	AI315628|PHR1|Phret1|evt-1	pleckstrin homology domain containing, family B (evectins) member 1	protein-coding
mm_169223.1	chr13	66802788	66802807	+	1	NA	Intergenic	Intergenic	102553	NM_026219	67530	Mm.379136	NM_026219	ENSMUSG00000021520	Uqcrb	2210415M14Rik|QP-C|QPC|UQBC|UQBP|UQPC	ubiquinol-cytochrome c reductase binding protein	protein-coding
mm_154356.1	chrM	6181	6197	+	1	NA	NA	Intergenic	NA	NA								
mm_422.1	chr1	34443869	34443886	+	1	NA	exon (NM_178601, exon 6 of 9)	exon (NM_178601, exon 6 of 9)	4048	NM_178601	27993	Mm.289667	NM_178601	ENSMUSG00000026127	Imp4	AA409888|AV031295|D1Wsu40e	IMP4, U3 small nucleolar ribonucleoprotein	protein-coding
mm_74330.1	chr8	126971234	126971240	+	1	NA	promoter-TSS (NM_172762)	promoter-TSS (NM_172762)	-158	NM_172762	52202	Mm.28199	NM_172762	ENSMUSG00000033931	Rbm34	4930547K05Rik|6330444B11|D8Ertd233e	RNA binding motif protein 34	protein-coding
mm_112617.1	chr13	15485449	15485452	+	1	NA	intron (NM_008130, intron 2 of 14)	AT_rich|Low_complexity|Low_complexity	21727	NM_008130	14634	Mm.5098	NM_008130	ENSMUSG00000021318	Gli3	AI854843|AU023367|Bph|GLI3-190|GLI3FL|Pdn|Xt|add	GLI-Kruppel family member GLI3	protein-coding
mm_121940.1	chr14	24004953	24004980	-	1	NA	promoter-TSS (NM_001253365)	promoter-TSS (NM_001253365)	-25	NR_131107	78019	Mm.243845	NR_131107		4930519K11Rik	-	RIKEN cDNA 4930519K11 gene	ncRNA
mm_141973.1	chr17	35158036	35158047	-	1	NA	exon (NM_020027, exon 14 of 31)	exon (NM_020027, exon 14 of 31)	6836	NM_001199044	53761	Mm.272462	NM_020027	ENSMUSG00000024393	Prrc2a	3110039B05Rik|Bat-2|Bat2|D17H6S51E|G2|Wbp12|mKIAA4178	proline-rich coiled-coil 2A	protein-coding
mm_31249.1	chr4	44967766	44967772	+	1	NA	Intergenic	Intergenic	-13625	NM_080289	76238	Mm.196574	NM_080289	ENSMUSG00000035637	Grhpr	1110059D05Rik|6430629L09Rik|Glxr	glyoxylate reductase/hydroxypyruvate reductase	protein-coding
mm_62846.1	chr7	114297535	114297541	+	1	NA	Intergenic	Intergenic	-21422	NM_011965	26440	Mm.121265	NM_011965	ENSMUSG00000030751	Psma1	C2|HC2|Pros-30|alpha-type	proteasome (prosome, macropain) subunit, alpha type 1	protein-coding
mm_121716.1	chr14	16249676	16249689	-	1	NA	5' UTR (NM_027695, exon 1 of 3)	5' UTR (NM_027695, exon 1 of 3)	126	NM_027695	71147	Mm.197960	NM_027695	ENSMUSG00000021786	Oxsm	4933425A18Rik|C80494	3-oxoacyl-ACP synthase, mitochondrial	protein-coding
mm_81097.1	chr9	106374426	106374429	+	1	NA	3' UTR (NM_153459, exon 3 of 3)	3' UTR (NM_153459, exon 3 of 3)	5795	NM_153459	235584	Mm.275584	NM_153459	ENSMUSG00000053716	Dusp7	AU015694|Mkpx|Pyst2	dual specificity phosphatase 7	protein-coding
mm_94914.1	chr11	29460944	29460986	+	1	NA	exon (NM_176841, exon 13 of 32)	exon (NM_176841, exon 13 of 32)	54068	NM_026465	67939	Mm.251087	NM_026465	ENSMUSG00000032673	Prorsd1	2010316F05Rik|Ncrna00117|Prdxdd1	prolyl-tRNA synthetase domain containing 1	protein-coding
mm_127584.1	chr15	102326401	102326429	+	1	NA	intron (NM_027044, intron 1 of 5)	intron (NM_027044, intron 1 of 5)	299	NM_027044	56612	Mm.158264	NM_020031	ENSMUSG00000001289	Pfdn5	1190001O17Rik|1700010A06Rik|D15Ertd697e|Eig1|MM-1	prefoldin 5	protein-coding
mm_128750.1	chr15	64383077	64383087	-	1	NA	promoter-TSS (NM_001276467)	promoter-TSS (NM_001276467)	-163	NM_010026	13196	Mm.277236	NM_010026	ENSMUSG00000022377	Asap1	AV239055|DEF-1|Ddef1|PAP|mKIAA1249|s19	ArfGAP with SH3 domain, ankyrin repeat and PH domain1	protein-coding
mm_87080.1	chr10	29313165	29313221	+	1	NA	promoter-TSS (NM_001110195)	promoter-TSS (NM_001110195)	27	NM_001110195	52665	Mm.28930	NM_025855	ENSMUSG00000019883	Echdc1	1700028A24Rik|AI314462|AI930038|D10Ertd667e|MMCD	enoyl Coenzyme A hydratase domain containing 1	protein-coding
mm_12055.1	chr2	59297409	59297411	+	1	NA	intron (NM_175464, intron 4 of 20)	intron (NM_175464, intron 4 of 20)	89272	NR_040510	76676	Mm.110038	NR_040510	ENSMUSG00000087455	5330411J11Rik	-	RIKEN cDNA 5330411J11 gene	ncRNA
mm_126410.1	chr15	80256338	80256349	+	1	NA	exon (NM_009716, exon 2 of 3)	exon (NM_009716, exon 2 of 3)	1159	NM_009716	11911	Mm.641	NM_009716	ENSMUSG00000042406	Atf4	Atf-4|C/ATF|CREB2|TAXREB67	activating transcription factor 4	protein-coding
mm_90118.1	chr10	117278077	117278091	+	1	NA	3' UTR (NM_017372, exon 4 of 4)	3' UTR (NM_017372, exon 4 of 4)	4188	NM_017372	17105	Mm.45436	NM_017372	ENSMUSG00000069516	Lyz2	AI326280|Lys|Lysm|Lyzf2|Lyzs|Lzm|Lzm-s1|Lzp	lysozyme 2	protein-coding
mm_16668.1	chr2	6721991	6722038	-	1	NA	promoter-TSS (NM_001310447)	promoter-TSS (NM_001310447)	-352	NM_001310447	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_149968.1	chr19	29047536	29047580	+	1	NA	promoter-TSS (NR_028360)	promoter-TSS (NR_028360)	75	NR_028360	67329	Mm.394933	NR_028360		1700018L02Rik	-	RIKEN cDNA 1700018L02 gene	ncRNA
mm_106376.1	chr11	118419019	118419046	-	1	NA	promoter-TSS (NM_029502)	promoter-TSS (NM_029502)	86	NM_001025617	76025	Mm.177551	NM_029502	ENSMUSG00000025575	Cant1	5830420C20Rik|Apy1h|D11Bwg0554e|Entpd8|SCAN-1|Shapy	calcium activated nucleotidase 1	protein-coding
mm_62759.1	chr7	112082462	112082494	+	1	NA	exon (NM_177249, exon 13 of 29)	exon (NM_177249, exon 13 of 29)	58972	NM_177249	74996	Mm.16974	NM_133758	ENSMUSG00000059263	Usp47	4930502N04Rik|A630020C16Rik	ubiquitin specific peptidase 47	protein-coding
mm_98331.1	chr11	90638418	90638445	+	1	NA	promoter-TSS (NM_011505)	promoter-TSS (NM_011505)	247	NM_199008	69802	Mm.151940	NM_199008	ENSMUSG00000020544	Cox11	2010004I09Rik	cytochrome c oxidase assembly protein 11	protein-coding
mm_85396.1	chr9	103305050	103305084	-	1	NA	promoter-TSS (NM_176979)	promoter-TSS (NM_176979)	-260	NM_176979	235559	Mm.259893	NM_176979	ENSMUSG00000032555	Topbp1	1110031N14Rik|2810429C13Rik|AI256758|D430026L04Rik|mKIAA0259	topoisomerase (DNA) II binding protein 1	protein-coding
mm_93146.1	chr10	92290592	92290603	-	1	NA	intron (NR_046027, intron 2 of 8)	intron (NR_046027, intron 2 of 8)	84776	NR_046027	627800	Mm.391417	NR_046027	ENSMUSG00000098040	Gm20757	-	predicted gene, 20757	ncRNA
mm_98321.1	chr11	90249581	90249589	+	1	NA	5' UTR (NM_026178, exon 1 of 7)	5' UTR (NM_026178, exon 1 of 7)	109	NM_026178	67468	Mm.277518	NM_026178	ENSMUSG00000003948	Mmd	1200017E07Rik|1810073C06Rik|AA690185	monocyte to macrophage differentiation-associated	protein-coding
mm_129808.1	chr15	82987877	82987890	-	1	NA	Intergenic	Intergenic	-28587	NR_037241	100526477		NR_037241	ENSMUSG00000092751	Mir3080	mmu-mir-3080	microRNA 3080	ncRNA
mm_140220.1	chr17	83856937	83856949	+	1	NA	Intergenic	Intergenic	-10153	NM_025325	107766	Mm.30100	NM_025325	ENSMUSG00000000673	Haao	0610007K21Rik|0610012J07Rik|3-HAO|3-HAOxase|3HAO	3-hydroxyanthranilate 3,4-dioxygenase	protein-coding
mm_92039.1	chr10	62494825	62494836	-	1	NA	3' UTR (NM_011157, exon 3 of 3)	3' UTR (NM_011157, exon 3 of 3)	-8025	NM_133672	30930	Mm.260703	NM_133672	ENSMUSG00000020078	Vps26a	AA407240|HB58|Vps26	VPS26 retromer complex component A	protein-coding
mm_101454.1	chr11	30243051	30243055	-	1	NA	Intergenic	Intergenic	-23281	NM_175836	20742	Mm.123110	NM_009260	ENSMUSG00000020315	Sptbn1	9930031C03Rik|AL033301|SPTB2|Spnb-2|Spnb2|elf1|elf3|mKIAA4049	spectrin beta, non-erythrocytic 1	protein-coding
mm_103776.1	chr11	82751495	82751536	-	1	NA	intron (NM_009839, intron 5 of 13)	PB1D10|SINE|Alu	12806	NM_009839	12467	Mm.4126	NM_009839	ENSMUSG00000020698	Cct6b	CCT-zeta-2|CCTzeta-2|Cctz-2|TCP-1-zeta-2	chaperonin containing Tcp1, subunit 6b (zeta)	protein-coding
mm_42702.1	chr5	119959211	119959245	+	1	NA	Intergenic	Intergenic	124565	NM_011537	21388	Mm.103636	NM_011537	ENSMUSG00000018263	Tbx5	-	T-box 5	protein-coding
mm_172568.1	chr8	111310244	111310244	-	1	NA	Intergenic	Intergenic	-10022	NM_146218	234736	Mm.334816	NM_146218	ENSMUSG00000033596	Rfwd3	BC027246	ring finger and WD repeat domain 3	protein-coding
mm_150785.1	chr19	44296840	44296860	+	1	NA	intron (NM_009128, intron 2 of 5)	intron (NM_009128, intron 2 of 5)	3174	NM_009128	20250	Mm.487021	NM_009128	ENSMUSG00000025203	Scd2	Mir5114|Scd-2|mir-5114|swty	stearoyl-Coenzyme A desaturase 2	protein-coding
mm_33389.1	chr4	129811184	129811207	+	1	NA	Intergenic	Intergenic	-9284	NM_008974	19244	Mm.193688	NM_008974	ENSMUSG00000028788	Ptp4a2	Prl-2	protein tyrosine phosphatase 4a2	protein-coding
mm_15961.1	chr2	166012934	166012946	+	1	NA	intron (NM_008679, intron 1 of 22)	intron (NM_008679, intron 1 of 22)	20303	NM_008679	17979	Mm.469663	NM_008679	ENSMUSG00000027678	Ncoa3	2010305B15Rik|AW321064|Actr|Aib1|KAT13B|Rac3|Src3|Tram-1|Tram1|bHLHe42|p/Cip|pCip	nuclear receptor coactivator 3	protein-coding
mm_127891.1	chr15	9155355	9155359	-	1	NA	promoter-TSS (NM_001285980)	promoter-TSS (NM_001285980)	68	NM_001285980	27401	Mm.35584	NM_013787	ENSMUSG00000054115	Skp2	4930500A04Rik|FBXL1|FWD1|p45	S-phase kinase-associated protein 2 (p45)	protein-coding
mm_140433.1	chr17	88191010	88191020	+	1	NA	Intergenic	Intergenic	65503	NM_001190356	225058	Mm.312053	NM_001190356		Gm4832	EG225058	predicted gene 4832	protein-coding
mm_38427.1	chr4	139291220	139291253	-	1	NA	3' UTR (NM_001271405, exon 9 of 9)	3' UTR (NM_001271405, exon 9 of 9)	19464	NM_145384	212555	Mm.45131	NM_145384	ENSMUSG00000028744	Pqlc2	BC019216	PQ loop repeat containing 2	protein-coding
mm_163278.1	chr11	116024059	116024082	-	1	NA	intron (NM_008211, intron 1 of 3)	CpG-2838	434	NM_008211	15081	Mm.18516	NM_008211	ENSMUSG00000016559	H3f3b	9430068D06Rik|H3.3B	H3 histone, family 3B	protein-coding
mm_149306.1	chr19	10735263	10735280	+	1	NA	intron (NM_007650, intron 1 of 10)	L2c|LINE|L2	3703	NM_007650	12507	Mm.779	NM_007650	ENSMUSG00000024669	Cd5	Ly-1|Ly-12|Ly-A|Lyt-1	CD5 antigen	protein-coding
mm_27733.1	chr3	69044986	69044999	-	1	NA	promoter-TSS (NM_025863)	promoter-TSS (NM_025863)	-250	NM_025863	66949	Mm.176695	NM_025863	ENSMUSG00000034317	Trim59	2310035M22Rik|2700022F13Rik|Mrf1|TSBF1	tripartite motif-containing 59	protein-coding
mm_83156.1	chr9	40465585	40465595	-	1	NA	Intergenic	Intergenic	-9826	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_99624.1	chr11	104685702	104685714	+	1	NA	Intergenic	CpG	77708	NM_016780	16416	Mm.87150	NM_016780	ENSMUSG00000020689	Itgb3	CD61|GP3A|INGRB3	integrin beta 3	protein-coding
mm_56435.1	chr6	97381107	97381117	-	1	NA	intron (NM_001346639, intron 5 of 22)	PB1D10|SINE|Alu	78174	NM_001346639	232288	Mm.27789	NM_145148	ENSMUSG00000030064	Frmd4b	6030440G05Rik|C87375|GOBLIN|GRSP1|R74720	FERM domain containing 4B	protein-coding
mm_60859.1	chr7	45872863	45872882	+	1	NA	promoter-TSS (NM_133950)	promoter-TSS (NM_133950)	32	NM_133950	68137	Mm.298433	NM_133950	ENSMUSG00000002778	Kdelr1	8030486F04Rik|AW215843|Erd2.1	KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 1	protein-coding
mm_132471.1	chr16	36708231	36708239	+	1	NA	intron (NM_001285791, intron 1 of 6)	intron (NM_001285791, intron 1 of 6)	14257	NM_001285791	106347	Mm.17807	NM_134109	ENSMUSG00000022900	Ildr1	AU041483|AU044638	immunoglobulin-like domain containing receptor 1	protein-coding
mm_65678.1	chr7	28318919	28318959	-	1	NA	intron (NM_013676, intron 19 of 29)	intron (NM_013676, intron 19 of 29)	-6893	NM_025616	66525	Mm.167913	NM_025616	ENSMUSG00000003438	Timm50	2810403L02Rik|AU015082|TIM50L	translocase of inner mitochondrial membrane 50	protein-coding
mm_73374.1	chr8	105623425	105623439	+	1	NA	Intergenic	Intergenic	7966	NR_035492	100316712		NR_035492	ENSMUSG00000089432	Mir1966	mir-1966|mmu-mir-1966	microRNA 1966	ncRNA
mm_141166.1	chr17	26532615	26532617	-	1	NA	Intergenic	Intergenic	-24144	NM_013642	19252	Mm.239041	NM_013642	ENSMUSG00000024190	Dusp1	3CH134|MKP1|Ptpn16|U19515|erp|mkp-1	dual specificity phosphatase 1	protein-coding
mm_49639.1	chr6	30805187	30805195	+	1	NA	intron (NM_017478, intron 20 of 23)	intron (NM_017478, intron 20 of 23)	63892	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_132531.1	chr16	37868120	37868170	+	1	NA	promoter-TSS (NM_177093)	promoter-TSS (NM_177093)	-255	NM_177093	320184	Mm.390882	NM_177093	ENSMUSG00000034158	Lrrc58	1810012N18Rik|C330018J07Rik	leucine rich repeat containing 58	protein-coding
mm_22674.1	chr3	14887389	14887416	+	1	NA	intron (NM_009801, intron 1 of 6)	intron (NM_009801, intron 1 of 6)	976	NM_009801	12349	Mm.1186	NM_009801	ENSMUSG00000027562	Car2	AI131712|CAII|Ca2|Car-2|Ltw-5|Lvtw-5	carbonic anhydrase 2	protein-coding
mm_106727.1	chr12	3873136	3873145	+	1	NA	intron (NM_007872, intron 5 of 22)	intron (NM_007872, intron 5 of 22)	-10896	NR_045884	100038522	Mm.417270	NR_045884	ENSMUSG00000073242	Dnmt3aos	ENSMUSG00000073242|Gm10485	DNA methyltransferase 3A, opposite strand	ncRNA
mm_74878.1	chr8	25067922	25067935	-	1	NA	intron (NM_031257, intron 3 of 11)	intron (NM_031257, intron 3 of 11)	-28966	NM_001081187	330723	Mm.334452	NM_001081187	ENSMUSG00000037406	Htra4	B430206E18Rik	HtrA serine peptidase 4	protein-coding
mm_53480.1	chr6	134948870	134948873	+	1	NA	intron (NR_037956, intron 1 of 1)	PB1D10|SINE|Alu	19779	NR_037955	381822	Mm.5935	NR_037955	ENSMUSG00000098318	Lockd	1190002F15Rik|AI120476|Droc	lncRNA downstream of Cdkn1b	ncRNA
mm_148281.1	chr18	82525859	82525895	-	1	NA	intron (NM_001025245, intron 3 of 3)	intron (NM_001025245, intron 3 of 3)	-28586	NM_001025256	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_81469.1	chr9	109931464	109931488	+	1	NA	promoter-TSS (NM_008633)	promoter-TSS (NM_008633)	-298	NM_001205331	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_120355.1	chr14	64072032	64072038	+	1	NA	Intergenic	RMER17C|LTR|ERVK	13354	NM_001081063	71037	Mm.19977	NM_001081063	ENSMUSG00000034623	Prss55	4933401F05Rik	protease, serine 55	protein-coding
mm_85805.1	chr9	110282654	110282678	-	1	NA	Intergenic	RLTR19|LTR|ERVK	1379	NR_105744	102465959		NR_105744	ENSMUSG00000098973	Mir6236	Gm27547|mmu-mir-6236	microRNA 6236	ncRNA
mm_113915.1	chr13	49504886	49504910	+	1	NA	promoter-TSS (NM_001012324)	promoter-TSS (NM_001012324)	88	NM_001012324	407800	Mm.386931	NM_001012324	ENSMUSG00000043631	Ecm2	9030618O22Rik|BC065151|tenonectin	extracellular matrix protein 2, female organ and adipocyte specific	protein-coding
mm_3516.1	chr1	150107454	150107464	+	1	NA	3' UTR (NM_011198, exon 10 of 10)	3' UTR (NM_011198, exon 10 of 10)	7428	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_163317.1	chr12	7351880	7351882	+	1	NA	Intergenic	RLTR14|LTR|ERV1	28449	NR_045045	73575	Mm.179463	NR_045045	ENSMUSG00000102096	1700101O22Rik	-	RIKEN cDNA 1700101O22 gene	ncRNA
mm_73912.1	chr8	119666244	119666252	+	1	NA	promoter-TSS (NM_023395)	promoter-TSS (NM_023395)	-117	NM_023395	67866	Mm.87599	NM_023395	ENSMUSG00000023336	Wfdc1	2310058A03Rik|ps20	WAP four-disulfide core domain 1	protein-coding
mm_78655.1	chr9	40455294	40455321	+	1	NA	exon (NM_172768, exon 1 of 20)	exon (NM_172768, exon 1 of 20)	457	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_7723.1	chr1	130661655	130661663	-	1	NA	promoter-TSS (NM_007576)	promoter-TSS (NM_007576)	-41	NM_007576	12269	Mm.306720	NM_007576	ENSMUSG00000026405	C4bp	AI195242|C4bpa	complement component 4 binding protein	protein-coding
mm_98335.1	chr11	90676025	90676044	+	1	NA	intron (NM_028011, intron 3 of 15)	intron (NM_028011, intron 3 of 15)	11567	NM_028011	71943	Mm.167868	NM_028011	ENSMUSG00000020541	Tom1l1	2310045L10Rik|C80573|Srcasm	target of myb1-like 1 (chicken)	protein-coding
mm_17404.1	chr2	27246723	27246733	-	1	NA	5' UTR (NM_138665, exon 1 of 21)	5' UTR (NM_138665, exon 1 of 21)	575	NM_138665	192166	Mm.278467	NM_138665	ENSMUSG00000009614	Sardh	-	sarcosine dehydrogenase	protein-coding
mm_88126.1	chr10	69248652	69248656	+	1	NA	intron (NM_001252637, intron 2 of 10)	intron (NM_001252637, intron 2 of 10)	35460	NM_001252638	69288	Mm.26659	NM_001081347	ENSMUSG00000019944	Rhobtb1	1700008H16Rik|3110048G13Rik|AI173445|AI573858|AV350930	Rho-related BTB domain containing 1	protein-coding
mm_8559.1	chr1	155244500	155244544	-	1	NA	Intergenic	CpG	85819	NM_021433	58244	Mm.66264	NM_021433	ENSMUSG00000026470	Stx6	2310039E05Rik|2410005I16Rik|AA437559|AI415714|AI845861	syntaxin 6	protein-coding
mm_140376.1	chr17	86993747	86993768	+	1	NA	intron (NM_145491, intron 2 of 4)	intron (NM_145491, intron 2 of 4)	30646	NM_145491	104215	Mm.826	NM_145491	ENSMUSG00000024143	Rhoq	Arhq|TC10A|Tc10	ras homolog family member Q	protein-coding
mm_72156.1	chr8	72161335	72161369	+	1	NA	5' UTR (NM_023126, exon 1 of 8)	5' UTR (NM_023126, exon 1 of 8)	152	NM_023126	17274	Mm.162811	NM_023126	ENSMUSG00000003037	Rab8a	AA409338|Mel	RAB8A, member RAS oncogene family	protein-coding
mm_57079.1	chr6	122581707	122581761	-	1	NA	exon (NM_031159, exon 6 of 8)	exon (NM_031159, exon 6 of 8)	20710	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_12712.1	chr2	76692420	76692424	+	1	NA	intron (NM_031256, intron 6 of 7)	B1_Mur3|SINE|Alu	17107	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_121065.1	chr14	95528967	95528967	+	1	NA	Intergenic	ORR1D1|LTR|ERVL-MaLR	-352299	NM_025733	66732	Mm.75060	NM_025733	ENSMUSG00000034689	4921530L21Rik	-	RIKEN cDNA 4921530L21 gene	protein-coding
mm_161953.1	chr19	5689088	5689088	+	1	NA	promoter-TSS (NM_022012)	promoter-TSS (NM_022012)	-43	NM_022012	26403	Mm.185026	NM_022012	ENSMUSG00000004054	Map3k11	2610017K16Rik|Mlk3|PTK1|SPRK	mitogen-activated protein kinase kinase kinase 11	protein-coding
mm_106848.1	chr12	8007961	8007987	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	30297	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_143732.1	chr17	81388327	81388341	-	1	NA	non-coding (NR_104580, exon 9 of 9)	non-coding (NR_104580, exon 9 of 9)	-323249	NM_028138	72167	Mm.273257	NM_028138	ENSMUSG00000024246	Thumpd2	2810025A12Rik	THUMP domain containing 2	protein-coding
mm_143928.1	chr17	85688964	85688967	-	1	NA	promoter-TSS (NM_011380)	promoter-TSS (NM_011380)	-711	NM_011380	20472	Mm.5039	NM_011380	ENSMUSG00000024134	Six2	-	sine oculis-related homeobox 2	protein-coding
mm_38082.1	chr4	134128708	134128770	-	1	NA	promoter-TSS (NM_080559)	promoter-TSS (NM_080559)	14	NM_080559	73723	Mm.22240	NM_080559	ENSMUSG00000028843	Sh3bgrl3	1110004L05Rik|AU022188	SH3 domain binding glutamic acid-rich protein-like 3	protein-coding
mm_43855.1	chr5	143403820	143403882	+	1	NA	promoter-TSS (NM_025841)	promoter-TSS (NM_025841)	31	NM_025841	66913	Mm.181880	NM_025841	ENSMUSG00000079111	Kdelr2	1110007A14Rik	KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 2	protein-coding
mm_156064.1	chrX	109160558	109160614	+	1	NA	3' UTR (NM_019989, exon 4 of 4)	3' UTR (NM_019989, exon 4 of 4)	-36170	NM_001037917	622976	Mm.482747	NM_001037917	ENSMUSG00000048621	Gm6377	EG622976	predicted gene 6377	protein-coding
mm_111335.1	chr12	86834568	86834610	-	1	NA	Intergenic	Intergenic	50225	NM_145836	238330	Mm.248358	NM_145836	ENSMUSG00000034168	Irf2bpl	6430527G18Rik|Eap1	interferon regulatory factor 2 binding protein-like	protein-coding
mm_138112.1	chr17	34135582	34135671	+	1	NA	5' UTR (NM_010386, exon 2 of 6)	5' UTR (NM_010386, exon 2 of 6)	-9790	NM_010388	15000	Mm.195060	NM_010388	ENSMUSG00000037548	H2-DMb2	H-2Mb2|H2-Mb2	histocompatibility 2, class II, locus Mb2	protein-coding
mm_82469.1	chr9	16252224	16252232	-	1	NA	intron (NM_001080814, intron 1 of 24)	intron (NM_001080814, intron 1 of 24)	126003	NM_001080814	270120	Mm.195010	NM_001080814	ENSMUSG00000074505	Fat3	9430076A06Rik|D430038H04Rik|Gm1132|Gm510|MFAT3F	FAT atypical cadherin 3	protein-coding
mm_147214.1	chr18	37969743	37969782	-	1	NA	promoter-TSS (NM_175684)	promoter-TSS (NM_175684)	-31	NM_175684	319262	Mm.285060	NM_175684	ENSMUSG00000038524	Fchsd1	A030002D08Rik	FCH and double SH3 domains 1	protein-coding
mm_96165.1	chr11	61488044	61488071	+	1	NA	TTS (NM_001291037)	TTS (NM_001291037)	2613	NM_029568	76293	Mm.272278	NM_029568	ENSMUSG00000042436	Mfap4	1110007F23Rik	microfibrillar-associated protein 4	protein-coding
mm_82093.1	chr9	123056431	123056436	+	1	NA	exon (NM_177911, exon 10 of 14)	exon (NM_177911, exon 10 of 14)	21692	NM_177911	331046	Mm.195309	NM_177911	ENSMUSG00000025787	Tgm4	9530008N10Rik|Eapa1|TGP	transglutaminase 4 (prostate)	protein-coding
mm_89050.1	chr10	82866649	82866674	+	1	NA	promoter-TSS (NM_025499)	promoter-TSS (NM_025499)	35	NM_025499	66341	Mm.443284	NM_025499	ENSMUSG00000109864	Eid3	1700027M21Rik|NS4EB	EP300 interacting inhibitor of differentiation 3	protein-coding
mm_117067.1	chr13	58912008	58912016	-	1	NA	intron (NM_001025074, intron 12 of 17)	ORR1C1|LTR|ERVL-MaLR	104315	NM_001025074	18212	Mm.130054	NM_008745	ENSMUSG00000055254	Ntrk2	GP145-TrkB/GP95-TrkB|Tkrb|trk-B|trkB	neurotrophic tyrosine kinase, receptor, type 2	protein-coding
mm_172658.1	chr8	40566899	40566915	+	1	NA	intron (NM_001040699, intron 7 of 13)	RLTRETN_Mm|LTR|ERVK	-51060	NM_001271542	18983	Mm.272551	NM_011135	ENSMUSG00000031601	Cnot7	AU022737|CAF-1|Caf1|Pop2	CCR4-NOT transcription complex, subunit 7	protein-coding
mm_170638.1	chr19	8966838	8966846	-	1	NA	promoter-TSS (NM_026007)	promoter-TSS (NM_026007)	-199	NM_026007	67160	Mm.247762	NM_026007	ENSMUSG00000071644	Eef1g	2610301D06Rik|AA407312|EF1G	eukaryotic translation elongation factor 1 gamma	protein-coding
mm_47929.1	chr5	135064052	135064060	-	1	NA	promoter-TSS (NM_025362)	promoter-TSS (NM_025362)	-150	NM_025362	66114	Mm.178012	NM_025362	ENSMUSG00000061118	Dnajc30	1300007M11Rik|Wbscr18	DnaJ heat shock protein family (Hsp40) member C30	protein-coding
mm_98727.1	chr11	96351899	96351908	+	1	NA	exon (NM_134032, exon 1 of 2)	exon (NM_134032, exon 1 of 2)	271	NM_134032	103889	Mm.281153	NM_134032	ENSMUSG00000075588	Hoxb2	AI894218|Hox-2.8|Hoxbes2	homeobox B2	protein-coding
mm_76338.1	chr8	84721672	84721697	-	1	NA	exon (NM_010906, exon 7 of 9)	exon (NM_010906, exon 7 of 9)	20227	NM_008535	17095	Mm.4925	NM_008535	ENSMUSG00000034041	Lyl1	Lyl-1|bHLHa18	lymphoblastomic leukemia 1	protein-coding
mm_7399.1	chr1	118459264	118459267	-	1	NA	promoter-TSS (NR_027901)	promoter-TSS (NR_027901)	0	NR_027901	68204	Mm.443536	NR_027901	ENSMUSG00000107722	2900060B14Rik	-	RIKEN cDNA 2900060B14 gene	ncRNA
mm_105295.1	chr11	102478506	102478546	-	1	NA	exon (NM_001159492, exon 8 of 8)	exon (NM_001159492, exon 8 of 8)	-8643	NM_010575	16399	Mm.26646	NM_010575	ENSMUSG00000034664	Itga2b	AI172977|CD41|CD41B|GpIIb|alphaIIb	integrin alpha 2b	protein-coding
mm_93802.1	chr10	120898990	120899011	-	1	NA	promoter-TSS (NM_177092)	promoter-TSS (NM_177092)	-29	NM_177092	320183	Mm.169755	NM_177092	ENSMUSG00000051236	Msrb3	D430026P16Rik|I-8-23|MsrB2	methionine sulfoxide reductase B3	protein-coding
mm_130104.1	chr15	89429633	89429680	-	1	NA	non-coding (NR_004843, exon 1 of 27)	non-coding (NR_004843, exon 1 of 27)	271	NR_037154	12651	Mm.485045	NM_007692	ENSMUSG00000022617	Chkb	Chetk|Chkl|Ck|Ck/Ek|Ck/Ek-beta|Ckb|Ckekb|Ek	choline kinase beta	protein-coding
mm_49406.1	chr6	28475102	28475121	+	1	NA	Intergenic	Intergenic	-5237	NM_019776	56463	Mm.439987	NM_019776	ENSMUSG00000001424	Snd1	AL033314|Tudor-SN	staphylococcal nuclease and tudor domain containing 1	protein-coding
mm_134799.1	chr16	24296201	24296211	-	1	NA	Intergenic	Intergenic	-97144	NM_178665	210126	Mm.209385	NM_178665	ENSMUSG00000033306	Lpp	9430020K16Rik|AA959454|AU024130|B130055L10Rik|C79715|D630048H16	LIM domain containing preferred translocation partner in lipoma	protein-coding
mm_33412.1	chr4	129906193	129906203	+	1	NA	promoter-TSS (NR_045190)	promoter-TSS (NR_045190)	-28	NR_045190	319894	Mm.59196	NR_045190	ENSMUSG00000086369	E330017L17Rik	-	RIKEN cDNA E330017L17 gene	ncRNA
mm_150475.1	chr19	38836678	38836692	+	1	NA	5' UTR (NM_145952, exon 1 of 13)	5' UTR (NM_145952, exon 1 of 13)	106	NM_145952	209478	Mm.391153	NM_145952	ENSMUSG00000048720	Tbc1d12	BC033574	TBC1D12: TBC1 domain family, member 12	protein-coding
mm_68535.1	chr7	113369300	113369310	-	1	NA	promoter-TSS (NM_133700)	promoter-TSS (NM_133700)	34	NM_133700	68815	Mm.238034	NM_133700	ENSMUSG00000038187	Btbd10	1110056N09Rik|Gmrp1	BTB (POZ) domain containing 10	protein-coding
mm_50519.1	chr6	49042767	49042801	+	1	NA	exon (NM_053110, exon 2 of 11)	exon (NM_053110, exon 2 of 11)	6266	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_135061.1	chr16	34081799	34081821	-	1	NA	intron (NM_177357, intron 34 of 59)	intron (NM_177357, intron 34 of 59)	-114807	NM_009471	22247	Mm.13145	NM_009471	ENSMUSG00000022814	Umps	1700095D23Rik|AA408257|AL033308|BB164745	uridine monophosphate synthetase	protein-coding
mm_128145.1	chr15	31531082	31531092	-	1	NA	promoter-TSS (NM_172606)	promoter-TSS (NM_172606)	-50	NM_172606	223455	Mm.272185	NM_172606	ENSMUSG00000039100	March6	3830408G03|F830029L24Rik|mKIAA0597	membrane-associated ring finger (C3HC4) 6	protein-coding
mm_156859.1	chrX	164402117	164402125	+	1	NA	exon (NM_010216, exon 7 of 7)	exon (NM_010216, exon 7 of 7)	-17666	NM_011081	18700	Mm.3781	NM_011081	ENSMUSG00000031381	Piga	AI194334|Pig-a	phosphatidylinositol glycan anchor biosynthesis, class A	protein-coding
mm_135294.1	chr16	38562715	38562753	-	1	NA	promoter-TSS (NM_026407)	promoter-TSS (NM_026407)	-80	NM_001205287	67846	Mm.310476	NM_026407	ENSMUSG00000002845	Tmem39a	2610033C09Rik	transmembrane protein 39a	protein-coding
mm_143593.1	chr17	74527911	74527932	-	1	NA	promoter-TSS (NM_007566)	promoter-TSS (NM_007566)	-374	NM_007566	12211	Mm.442564	NM_007566	ENSMUSG00000024073	Birc6	A430032G04Rik|A430040A19Rik|AA501170|Bruce|D630005A10Rik|mKIAA1289	baculoviral IAP repeat-containing 6	protein-coding
mm_146806.1	chr18	20745920	20745923	-	1	NA	5' UTR (NM_019737, exon 1 of 9)	5' UTR (NM_019737, exon 1 of 9)	483	NM_019737	56386	Mm.393827	NM_019737	ENSMUSG00000056124	B4galt6	AA536803|AU022389	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 6	protein-coding
mm_14006.1	chr2	122028587	122028598	+	1	NA	promoter-TSS (NM_001256055)	promoter-TSS (NM_001256055)	9	NM_001256055	100042807	Mm.329403	NM_001256055	ENSMUSG00000043424	Eif3j2	ENSMUSG00000043424|Eif3j-2|Gm9781|eIF3 p35|eIF3j-B	eukaryotic translation initiation factor 3, subunit J2	protein-coding
mm_23177.1	chr3	40792644	40792656	+	1	NA	Intergenic	Intergenic	-7301	NM_173169	20873	Mm.3794	NM_011495	ENSMUSG00000025758	Plk4	1700028H20|AI385771|Sak|Stk18	polo-like kinase 4	protein-coding
mm_103056.1	chr11	69818476	69818492	-	1	NA	promoter-TSS (NM_175368)	promoter-TSS (NM_175368)	-44	NM_175368	108803	Mm.73263	NM_175368	ENSMUSG00000044084	4933402P03Rik	-	RIKEN cDNA 4933402P03 gene	protein-coding
mm_146585.1	chr18	7869062	7869124	-	1	NA	promoter-TSS (NM_001146298)	promoter-TSS (NM_001146298)	-104	NM_001146298	225131	Mm.204524	NM_153085	ENSMUSG00000024283	Wac	1110067P07Rik|A230035H12Rik|AI256735|AI256776|Wwp4	WW domain containing adaptor with coiled-coil	protein-coding
mm_49488.1	chr6	29540978	29540983	+	1	NA	TTS (NM_001347079)	TTS (NM_001347079)	11698	NM_001252382	27056	Mm.6479	NM_012057	ENSMUSG00000029771	Irf5	AW491843|mirf5	interferon regulatory factor 5	protein-coding
mm_67672.1	chr7	88299533	88299559	-	1	NA	exon (NM_009982, exon 4 of 7)	exon (NM_009982, exon 4 of 7)	21461	NM_001311790	13032	Mm.89295	NM_009982	ENSMUSG00000030560	Ctsc	AI047818|CatC|DPP1|DPPI	cathepsin C	protein-coding
mm_151991.1	chr19	5850005	5850014	-	1	NA	TTS (NM_026169)	TTS (NM_026169)	-4529	NR_003513	66961	Mm.281895	NR_003513	ENSMUSG00000092274	Neat1	2310043N10Rik|VINC	nuclear paraspeckle assembly transcript 1 (non-protein coding)	ncRNA
mm_77358.1	chr8	119635512	119635536	-	1	NA	5' UTR (NM_025734, exon 1 of 3)	5' UTR (NM_025734, exon 1 of 3)	156	NM_025734	66733	Mm.358699	NM_025734	ENSMUSG00000045246	Kcng4	4921535I01Rik|AW049024|KV6.3|KV6.4	potassium voltage-gated channel, subfamily G, member 4	protein-coding
mm_83650.1	chr9	49505545	49505556	-	1	NA	exon (NM_001311065, exon 18 of 18)	exon (NM_001311065, exon 18 of 18)	-12738	NR_029465	100036537	Mm.437541	NR_029465	ENSMUSG00000079564	Gm11149	ENSMUSG00000060603|ENSMUSG00000079564	predicted gene 11149	ncRNA
mm_34195.1	chr4	140702217	140702238	+	1	NA	exon (NM_173867, exon 2 of 13)	exon (NM_173867, exon 2 of 13)	754	NM_173867	108911	Mm.253	NM_173867	ENSMUSG00000040945	Rcc2	2610510H01Rik|2610529N02Rik|AA536646|AA675016|Td60|mKIAA1470	regulator of chromosome condensation 2	protein-coding
mm_126674.1	chr15	84616071	84616071	+	1	NA	Intergenic	Intergenic	-47135	NM_001346662	109270	Mm.291372	NM_146061	ENSMUSG00000036106	Prr5	AU043908|Arhgap8|C030017C09Rik|C78947|Protor-1|Protor1	proline rich 5 (renal)	protein-coding
mm_124811.1	chr15	8967964	8967982	+	1	NA	promoter-TSS (NM_198024)	promoter-TSS (NM_198024)	24	NM_198024	223332	Mm.321371	NM_198024	ENSMUSG00000048424	Ranbp3l	C130037N17Rik	RAN binding protein 3-like	protein-coding
mm_158698.1	chrX	162018962	162018975	-	1	NA	intron (NM_001081052, intron 1 of 7)	L2a|LINE|L2	140473	NM_001081052	195727	Mm.336313	NM_001081052	ENSMUSG00000059493	Nhs	Gm389|Gm48|Nhs1|Xcat	Nance-Horan syndrome (human)	protein-coding
mm_32721.1	chr4	116303852	116303854	+	1	NA	TTS (NM_181585)	TTS (NM_181585)	81939	NM_181585	18710	Mm.253819	NM_181585	ENSMUSG00000028698	Pik3r3	AA414954|p55pik	phosphatidylinositol 3 kinase, regulatory subunit, polypeptide 3 (p55)	protein-coding
mm_162739.1	chr10	56388857	56388873	+	1	NA	3' UTR (NM_010288, exon 2 of 2)	3' UTR (NM_010288, exon 2 of 2)	11565	NM_010288	14609	Mm.378921	NM_010288	ENSMUSG00000050953	Gja1	AU042049|AW546267|Cnx43|Cx43|Cx43alpha1|Gja-1|Npm1|connexin43	gap junction protein, alpha 1	protein-coding
mm_31729.1	chr4	62966156	62966159	+	1	NA	intron (NM_028326, intron 1 of 14)	intron (NM_028326, intron 1 of 14)	583	NM_028326	72701	Mm.26479	NM_028326	ENSMUSG00000028358	Zfp618	2810031P15Rik|2810040O04Rik|AI415580|AI505139|D430033D05Rik|Nedd10|Znf618|bM257P7.1	zinc finger protein 618	protein-coding
mm_61558.1	chr7	79500082	79500095	+	1	NA	promoter-TSS (NR_040314)	promoter-TSS (NR_040314)	62	NR_040313	101694	Mm.41661	NR_040311	ENSMUSG00000097023	Mir9-3hg	AI854517	Mir9-3 host gene	ncRNA
mm_105936.1	chr11	115163130	115163135	-	1	NA	promoter-TSS (NM_012030)	promoter-TSS (NM_012030)	-209	NM_012030	26941	Mm.27842	NM_012030	ENSMUSG00000020733	Slc9a3r1	EBP-50|NHE-RF|NHERF-1|NHERF1	solute carrier family 9 (sodium/hydrogen exchanger), member 3 regulator 1	protein-coding
mm_125447.1	chr15	47539983	47539994	+	1	NA	Intergenic	Intergenic	916683	NR_045811	75281	Mm.159487	NR_045811	ENSMUSG00000051198	4930548G14Rik	-	RIKEN cDNA 4930548G14 gene	ncRNA
mm_12734.1	chr2	78869346	78869376	+	1	NA	5' UTR (NM_009454, exon 1 of 6)	5' UTR (NM_009454, exon 1 of 6)	314	NM_009454	22193	Mm.1485	NM_009454	ENSMUSG00000027011	Ube2e3	Ubce4|ubcM2	ubiquitin-conjugating enzyme E2E 3	protein-coding
mm_171914.1	chr5	55791772	55791787	-	1	NA	Intergenic	RLTR9E|LTR|ERVK	1441787	NR_038045	330086	Mm.254449	NM_177871	ENSMUSG00000105912	Gm10440	D130065D13|ENSMUSG00000072936	predicted gene 10440	ncRNA
mm_74723.1	chr8	17466839	17466842	-	1	NA	intron (NM_053171, intron 1 of 69)	intron (NM_053171, intron 1 of 69)	68545	NM_053171	94109	Mm.436988	NM_053171	ENSMUSG00000060924	Csmd1	B930082H09|mKIAA1890	CUB and Sushi multiple domains 1	protein-coding
mm_62511.1	chr7	102210429	102210445	+	1	NA	promoter-TSS (NM_001287167)	promoter-TSS (NM_001287167)	102	NM_001291358	233575	Mm.302013	NM_145583	ENSMUSG00000030990	Pgap2	1810006G21Rik|C76649|Frag1	post-GPI attachment to proteins 2	protein-coding
mm_113359.1	chr13	32861010	32861021	+	1	NA	Intergenic	Intergenic	-9830	NM_025429	66222	Mm.20144	NM_025429	ENSMUSG00000044734	Serpinb1a	1190005M04Rik|AI325983|EI|EIA|ELANH2|LEI|M/NEI|MNEI|PI2	serine (or cysteine) peptidase inhibitor, clade B, member 1a	protein-coding
mm_111605.1	chr12	102398320	102398338	-	1	NA	exon (NM_011175, exon 11 of 14)	exon (NM_011175, exon 11 of 14)	41484	NM_011175	19141	Mm.17185	NM_011175	ENSMUSG00000021190	Lgmn	AEP|AI746452|AU022324|Prsc1	legumain	protein-coding
mm_6327.1	chr1	71612558	71612605	-	1	NA	exon (NM_001276413, exon 25 of 44)	exon (NM_001276413, exon 25 of 44)	40653	NM_010233	14268	Mm.193099	NM_010233	ENSMUSG00000026193	Fn1	E330027I09|Fn|Fn-1	fibronectin 1	protein-coding
mm_61490.1	chr7	75710326	75710329	+	1	NA	intron (NM_029332, intron 17 of 36)	intron (NM_029332, intron 17 of 36)	-138011	NM_001122780	207952	Mm.206223	NM_029652	ENSMUSG00000055652	Klhl25	2810402K13Rik|BC027373|Enc-1	kelch-like 25	protein-coding
mm_134699.1	chr16	22657166	22657178	-	1	NA	promoter-TSS (NM_138650)	promoter-TSS (NM_138650)	59	NM_138650	110197	Mm.194986	NM_138650	ENSMUSG00000022861	Dgkg	2900055E17Rik|90kDa|AI854428|Dagk3|E430001K23Rik|mKIAA4131	diacylglycerol kinase, gamma	protein-coding
mm_56611.1	chr6	112490787	112490803	-	1	NA	promoter-TSS (NM_001081147)	promoter-TSS (NM_001081147)	-987	NM_001081147	18430	Mm.333310	NM_001081147	ENSMUSG00000049112	Oxtr	OTR	oxytocin receptor	protein-coding
mm_130947.1	chr15	103252815	103252829	-	1	NA	promoter-TSS (NM_001302339)	promoter-TSS (NM_001302339)	-12	NM_001302339	18022	Mm.457989	NM_008685	ENSMUSG00000058794	Nfe2	NF-E2|NF-E2/P45|p45|p45NFE2|p45nf-e2	nuclear factor, erythroid derived 2	protein-coding
mm_96531.1	chr11	68556310	68556319	+	1	NA	5' UTR (NM_146004, exon 1 of 1)	5' UTR (NM_146004, exon 1 of 1)	128	NM_146004	215723	Mm.131205	NM_146004	ENSMUSG00000048329	Mfsd6l	-	major facilitator superfamily domain containing 6-like	protein-coding
mm_161553.1	chr16	11313810	11313810	+	1	NA	promoter-TSS (NM_011608)	promoter-TSS (NM_011608)	1	NM_011608	21935	Mm.12935	NM_011608	ENSMUSG00000022496	Tnfrsf17	BCM|BCMA|Tnfrsf13|Tnfrsf13a	tumor necrosis factor receptor superfamily, member 17	protein-coding
mm_172918.1	chr9	65580022	65580023	-	1	NA	promoter-TSS (NM_153119)	promoter-TSS (NM_153119)	65	NM_153119	102595	Mm.247303	NM_153119	ENSMUSG00000050721	Plekho2	AI840980|Plekhq1	pleckstrin homology domain containing, family O member 2	protein-coding
mm_141485.1	chr17	31260509	31260512	-	1	NA	intron (NM_025290, intron 6 of 8)	intron (NM_025290, intron 6 of 8)	16846	NM_025290	22092	Mm.12743	NM_025290	ENSMUSG00000024033	Rsph1	MCA|Tsga2	radial spoke head 1 homolog (Chlamydomonas)	protein-coding
mm_124863.1	chr15	10177259	10177265	+	1	NA	promoter-TSS (NM_011169)	promoter-TSS (NM_011169)	24	NM_011169	19116	Mm.10516	NM_011169	ENSMUSG00000005268	Prlr	AI987712|Pr-1|Pr-3|Prlr-rs1	prolactin receptor	protein-coding
mm_164422.1	chr16	45030255	45030262	-	1	NA	Intergenic	Intergenic	-63795	NM_026439	67896	Mm.181074	NM_026439	ENSMUSG00000022665	Ccdc80	2610001E17Rik|DRO1|Ssg1|Urb	coiled-coil domain containing 80	protein-coding
mm_144601.1	chr18	32385560	32385572	+	1	NA	intron (NM_001083334, intron 1 of 14)	intron (NM_001083334, intron 1 of 14)	-7282	NR_045403	402767	Mm.385109	NR_045403	ENSMUSG00000097413	A830052D11Rik	-	RIKEN cDNA A830052D11 gene	ncRNA
mm_49940.1	chr6	39871434	39871460	+	1	NA	Intergenic	CpG	-60511	NM_001010930	14548	Mm.377071	NM_010270	ENSMUSG00000029918	Mrps33	AI841153|CGI-139|Gdap3|MRP-S33|PTD003	mitochondrial ribosomal protein S33	protein-coding
mm_84251.1	chr9	62453683	62453686	-	1	NA	intron (NM_175484, intron 3 of 11)	intron (NM_175484, intron 3 of 11)	83360	NM_175484	235431	Mm.335229	NM_175484	ENSMUSG00000041729	Coro2b	CLIPINC|E130012P22Rik	coronin, actin binding protein, 2B	protein-coding
mm_137416.1	chr17	26123515	26123554	+	1	NA	promoter-TSS (NM_024227)	promoter-TSS (NM_024227)	31	NM_024227	68611	Mm.273102	NM_024227	ENSMUSG00000024181	Mrpl28	1110015G04Rik|L28mt|MAAT1|MRP-L28|p15	mitochondrial ribosomal protein L28	protein-coding
mm_41611.1	chr5	96793388	96793404	+	1	NA	promoter-TSS (NM_013470)	promoter-TSS (NM_013470)	11	NM_013470	11745	Mm.7214	NM_013470	ENSMUSG00000029484	Anxa3	Anx3	annexin A3	protein-coding
mm_162685.1	chr10	14596545	14596548	+	1	NA	Intergenic	Intergenic	-51510	NM_001002268	215798	Mm.440142	NM_001002268	ENSMUSG00000039116	Adgrg6	1190004A11Rik|AI449247|AW045736|DREG|Gm222|Gpr126	adhesion G protein-coupled receptor G6	protein-coding
mm_155822.1	chrX	100656448	100656451	+	1	NA	intron (NM_008446, intron 6 of 29)	intron (NM_008446, intron 6 of 29)	30384	NM_008446	16571	Mm.383091	NM_008446	ENSMUSG00000034311	Kif4	AI323435|D330050K22Rik|Kns4	kinesin family member 4	protein-coding
mm_155368.1	chrX	71215069	71215079	+	1	NA	promoter-TSS (NM_001164192)	promoter-TSS (NM_001164192)	-8	NM_019926	17772	Mm.274981	NM_019926	ENSMUSG00000031337	Mtm1	AF073996|Mtm|mKIAA4176	X-linked myotubular myopathy gene 1	protein-coding
mm_133951.1	chr16	3976569	3976575	-	1	NA	promoter-TSS (NM_001081280)	promoter-TSS (NM_001081280)	60	NM_175547	268857	Mm.215994	NM_175547	ENSMUSG00000049871	Nlrc3	CLR16.2|D230007K08Rik|mFLJ00348	NLR family, CARD domain containing 3	protein-coding
mm_5054.1	chr1	194976343	194976391	+	1	NA	non-coding (NR_033564, exon 1 of 5)	non-coding (NR_033564, exon 1 of 5)	592	NR_033564	320400	Mm.417608	NR_033564	ENSMUSG00000097325	Gm16897	C030002c11rik	predicted gene, 16897	ncRNA
mm_35711.1	chr4	44169258	44169278	-	1	NA	promoter-TSS (NM_001038993)	promoter-TSS (NM_001038993)	-985	NM_001038993	73469	Mm.262859	NM_175201	ENSMUSG00000035696	Rnf38	1700065B19Rik|2610202O07Rik|AA673263|Oip1	ring finger protein 38	protein-coding
mm_20688.1	chr2	132698503	132698526	-	1	NA	intron (NM_028637, intron 2 of 2)	intron (NM_028637, intron 2 of 2)	8231	NM_028637	73747	Mm.284114	NM_028637	ENSMUSG00000044991	1110034G24Rik	-	RIKEN cDNA 1110034G24 gene	protein-coding
mm_114350.1	chr13	60939458	60939472	+	1	NA	3' UTR (NM_009411, exon 5 of 5)	3' UTR (NM_009411, exon 5 of 5)	2470	NM_009411	21984	Mm.2372	NM_009411	ENSMUSG00000033834	Tpbpa	AV033951|Tb-1|Tb1|Tpbp|b2b1247Clo	trophoblast specific protein alpha	protein-coding
mm_112124.1	chr12	112917627	112917638	-	1	NA	intron (NM_010588, intron 5 of 25)	intron (NM_010588, intron 5 of 25)	2909	NR_105906	102465567		NR_105906	ENSMUSG00000098338	Mir6941	Gm27923|mmu-mir-6941	microRNA 6941	ncRNA
mm_33953.1	chr4	137453321	137453335	+	1	NA	promoter-TSS (NM_027063)	promoter-TSS (NM_027063)	32	NM_027063	69380	Mm.272519	NM_027063	ENSMUSG00000041399	1700013G24Rik	AI507018	RIKEN cDNA 1700013G24 gene	protein-coding
mm_79356.1	chr9	54262341	54262341	+	1	NA	Intergenic	Intergenic	-24145	NM_177350	235379	Mm.123549	NM_177350	ENSMUSG00000046167	Gldn	CRG-L2|Clom|Colm|Crgl2|Crlg2	gliomedin	protein-coding
mm_62787.1	chr7	112679315	112679325	+	1	NA	promoter-TSS (NM_001166584)	promoter-TSS (NM_001166584)	0	NM_001166584	21676	Mm.24685	NM_009346	ENSMUSG00000055320	Tead1	2610024B07Rik|B230114H05Rik|Gtrgeo5|TEAD-1|TEF-1|Tcf13|mTEF-1	TEA domain family member 1	protein-coding
mm_100809.1	chr11	5098751	5098759	-	1	NA	promoter-TSS (NM_177370)	promoter-TSS (NM_177370)	333	NM_001283062	14030	Mm.142822	NM_007968	ENSMUSG00000009079	Ewsr1	Ews|Ewsh	Ewing sarcoma breakpoint region 1	protein-coding
mm_136445.1	chr16	94918323	94918334	-	1	NA	intron (NM_001025584, intron 2 of 4)	B4|SINE|B4	-61638	NM_001025590	16522	Mm.328720	NM_010606	ENSMUSG00000043301	Kcnj6	BIR1|GIRK2|KATP2|KCNJ7|Kir3.2|weaver|wv	potassium inwardly-rectifying channel, subfamily J, member 6	protein-coding
mm_138092.1	chr17	34039142	34039153	+	1	NA	promoter-TSS (NM_009926)	promoter-TSS (NM_009926)	9	NM_001317722	12815	Mm.20230	NM_009926	ENSMUSG00000024330	Col11a2	-	collagen, type XI, alpha 2	protein-coding
mm_49864.1	chr6	38551557	38551569	+	1	NA	5' UTR (NM_001170849, exon 1 of 8)	5' UTR (NM_001170849, exon 1 of 8)	229	NM_001170848	192196	Mm.276133	NM_138680	ENSMUSG00000029823	Luc7l2	4930471C18Rik|AA522013|AU015269|CGI59|Cgi74	LUC7-like 2 (S. cerevisiae)	protein-coding
mm_32268.1	chr4	102624952	102624969	+	1	NA	Intergenic	Intergenic	35117	NM_001177981	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_91871.1	chr10	59576431	59576435	-	1	NA	intron (NM_001033259, intron 1 of 7)	intron (NM_001033259, intron 1 of 7)	40259	NM_001033259	215999	Mm.296470	NM_001033259	ENSMUSG00000009647	Mcu	2010012O16Rik|AV064928|C10orf42|Ccdc109a|D130073L02Rik|Gm64	mitochondrial calcium uniporter	protein-coding
mm_72708.1	chr8	84986345	84986353	+	1	NA	Intergenic	Intergenic	-4246	NM_133255	170833	Mm.247775	NM_133255	ENSMUSG00000052566	Hook2	A630054I03Rik	hook microtubule tethering protein 2	protein-coding
mm_126567.1	chr15	82197520	82197530	+	1	NA	promoter-TSS (NR_029804)	promoter-TSS (NR_029804)	-597	NR_029804	723897		NR_029804	ENSMUSG00000065465	Mir33	Mirn33|mir-33|mmu-mir-33	microRNA 33	ncRNA
mm_139570.1	chr17	57032214	57032235	+	1	NA	promoter-TSS (NM_010613)	promoter-TSS (NM_010613)	-717	NM_010613	16549	Mm.34296	NM_010613	ENSMUSG00000007670	Khsrp	6330409F21Rik|Fbp2|Fubp2|Ksrp	KH-type splicing regulatory protein	protein-coding
mm_34786.1	chr4	154170771	154170806	+	1	NA	promoter-TSS (NM_001162977)	promoter-TSS (NM_001162977)	75	NM_001162977	230971	Mm.275216	NM_172273	ENSMUSG00000057751	Megf6	2600001P17Rik|Egfl3	multiple EGF-like-domains 6	protein-coding
mm_104209.1	chr11	88235245	88235250	-	1	NA	Intergenic	Intergenic	30859	NM_001291271	64656	Mm.168680	NM_024174	ENSMUSG00000023723	Mrps23	D11Bwg1153e|MRP-S23|Rpms23|S23mt	mitochondrial ribosomal protein S23	protein-coding
mm_140259.1	chr17	84576290	84576293	+	1	NA	intron (NM_177606, intron 14 of 29)	intron (NM_177606, intron 14 of 29)	-50208	NM_172256	213575	Mm.246119	NM_172256	ENSMUSG00000024253	Dync2li1	4933404O11Rik|CGI-60|D2lic|LIC3|mD2LIC	dynein cytoplasmic 2 light intermediate chain 1	protein-coding
mm_154781.1	chrX	13041800	13041836	+	1	NA	promoter-TSS (NR_038158)	promoter-TSS (NR_038158)	-197	NR_038158	70489	Mm.383563	NR_038158	ENSMUSG00000087424	5730405O15Rik	-	RIKEN cDNA 5730405O15 gene	ncRNA
mm_68094.1	chr7	101933781	101933806	-	1	NA	promoter-TSS (NM_027053)	promoter-TSS (NM_027053)	64	NM_027053	69358	Mm.214841	NM_027053	ENSMUSG00000064307	Lrrc51	1700008D07Rik|Lrtomt	leucine rich repeat containing 51	protein-coding
mm_15338.1	chr2	155979535	155979583	+	1	NA	intron (NM_001130000, intron 19 of 32)	intron (NM_001130000, intron 19 of 32)	23001	NM_177217	16328	Mm.288729	NM_008383	ENSMUSG00000038241	Cep250	AW490617|B230210E21Rik|Cep2|Inmp	centrosomal protein 250	protein-coding
mm_151617.1	chr19	3903657	3903673	-	1	NA	exon (NM_001136091, exon 4 of 20)	exon (NM_001136091, exon 4 of 20)	1565	NM_016921	27060	Mm.271689	NM_016921	ENSMUSG00000001750	Tcirg1	ATP6N1C|ATP6a3|Atp6i|OC-116|OPTB1|Stv1|TIRC7|Vph1|oc	T cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 protein A3	protein-coding
mm_165733.1	chr3	106775878	106775900	-	1	NA	intron (NM_007651, intron 1 of 7)	L1_Mur3|LINE|L1	14260	NM_007651	12508	Mm.316861	NM_007651	ENSMUSG00000040747	Cd53	AI323659|Ox-44|Tspan25	CD53 antigen	protein-coding
mm_115672.1	chr13	12616083	12616085	-	1	NA	intron (NR_003568, intron 6 of 6)	intron (NR_003568, intron 6 of 6)	34311	NR_003568	664862	Mm.415635	NR_003568		Gpr137b-ps	2310041G17Rik|ENSMUSG00000075118	G protein-coupled receptor 137B, pseudogene	pseudo
mm_141807.1	chr17	34549375	34549377	-	1	NA	Intergenic	Intergenic	-14919	NM_010929	18132	Mm.173813	NM_010929	ENSMUSG00000015468	Notch4	Int-3|Int3|N4	notch 4	protein-coding
mm_64226.1	chr7	141632517	141632518	+	1	NA	3' UTR (NM_007459, exon 22 of 22)	3' UTR (NM_007459, exon 22 of 22)	11816	NR_106030	102466798		NR_106030	ENSMUSG00000098759	Mir7063	Gm27654|mmu-mir-7063	microRNA 7063	ncRNA
mm_128924.1	chr15	73831009	73831024	-	1	NA	intron (NM_001033365, intron 1 of 10)	intron (NM_001033365, intron 1 of 10)	8655	NM_001033365	268816	Mm.440635	NM_001033365	ENSMUSG00000072487	Mroh5	Gm628	maestro heat-like repeat family member 5	protein-coding
mm_149697.1	chr19	21276439	21276457	+	1	NA	exon (NM_009551, exon 2 of 6)	exon (NM_009551, exon 2 of 6)	4170	NM_009551	22682	Mm.292405	NM_009551	ENSMUSG00000024750	Zfand5	2310057A04Rik|5830475F03Rik|AA415485|Za20d2|Zfp216	zinc finger, AN1-type domain 5	protein-coding
mm_55496.1	chr6	69701332	69701344	-	1	NA	Intergenic	Intergenic	-374164	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_136651.1	chr17	5926928	5926963	+	1	NA	intron (NM_025664, intron 15 of 17)	intron (NM_025664, intron 15 of 17)	-14335	NM_001113353	20975	Mm.236068	NM_011523	ENSMUSG00000023805	Synj2	AI481647|SJ2|mKIAA0348	synaptojanin 2	protein-coding
mm_25855.1	chr3	129624432	129624435	+	1	NA	intron (NM_130450, intron 3 of 4)	intron (NM_130450, intron 3 of 4)	92047	NM_130450	170439	Mm.314113	NM_130450	ENSMUSG00000041220	Elovl6	C77826|FAE|LCE	ELOVL family member 6, elongation of long chain fatty acids (yeast)	protein-coding
mm_25080.1	chr3	100162555	100162565	+	1	NA	promoter-TSS (NM_175552)	promoter-TSS (NM_175552)	97	NR_104341	14547	Mm.279228	NM_010269	ENSMUSG00000027865	Gdap2	C77050|D3Ertd801e	ganglioside-induced differentiation-associated-protein 2	protein-coding
mm_149555.1	chr19	12633330	12633352	+	1	NA	promoter-TSS (NM_145935)	promoter-TSS (NM_145935)	33	NM_145935	107146	Mm.39974	NM_145935	ENSMUSG00000063683	Glyat	A330009E03Rik|ACGNAT|AI195249|AI315345|CAT|GAT	glycine-N-acyltransferase	protein-coding
mm_4297.1	chr1	171778599	171778639	+	1	NA	intron (NM_013730, intron 3 of 6)	intron (NM_013730, intron 3 of 6)	11487	NM_013730	27218	Mm.103648	NM_013730	ENSMUSG00000015316	Slamf1	4933415F16|AA177906|CD150|CDw150|ESTM51|IPO-3|Slam	signaling lymphocytic activation molecule family member 1	protein-coding
mm_108362.1	chr12	80791432	80791443	+	1	NA	intron (NM_001242419, intron 1 of 6)	intron (NM_001242419, intron 1 of 6)	905	NM_001242419	217684	Mm.341776	NM_178682	ENSMUSG00000021133	Susd6	4933426M11Rik|mKIAA0247	sushi domain containing 6	protein-coding
mm_31136.1	chr4	43257862	43257875	+	1	NA	exon (NM_021468, exon 32 of 40)	exon (NM_021468, exon 32 of 40)	-9291	NM_177195	320571	Mm.74465	NM_177195	ENSMUSG00000028457	Atp8b5	4930417M19Rik|Feta	ATPase, class I, type 8B, member 5	protein-coding
mm_27136.1	chr3	32408978	32408984	-	1	NA	Intergenic	RMER15|LTR|ERVL	-27170	NM_008839	18706	Mm.260521	NM_008839	ENSMUSG00000027665	Pik3ca	6330412C24Rik|caPI3K|p110|p110alpha	phosphatidylinositol 3-kinase, catalytic, alpha polypeptide	protein-coding
mm_60342.1	chr7	44355916	44355929	+	1	NA	intron (NM_001034115, intron 24 of 24)	intron (NM_001034115, intron 24 of 24)	19108	NM_027049	69349	Mm.358922	NM_027049	ENSMUSG00000008028	1700008O03Rik	-	RIKEN cDNA 1700008O03 gene	protein-coding
mm_83089.1	chr9	40320915	40320949	-	1	NA	intron (NM_172768, intron 4 of 19)	intron (NM_172768, intron 4 of 19)	-12540	NR_040728	73558	Mm.398307	NR_040728		1700110K17Rik	-	RIKEN cDNA 1700110K17 gene	ncRNA
mm_114604.1	chr13	75771618	75771630	+	1	NA	3' UTR (NM_138953, exon 12 of 12)	3' UTR (NM_138953, exon 12 of 12)	64140	NM_138953	192657	Mm.21288	NM_138953	ENSMUSG00000001542	Ell2	-	elongation factor RNA polymerase II 2	protein-coding
mm_70046.1	chr7	142578041	142578041	-	1	NA	promoter-TSS (NR_030416)	promoter-TSS (NR_030416)	105	NR_130974	14955	Mm.14802	NR_001592	ENSMUSG00000000031	H19	AI747191	H19, imprinted maternally expressed transcript	ncRNA
mm_125605.1	chr15	60468056	60468064	+	1	NA	Intergenic	Intergenic	-354905	NR_030696	320469	Mm.230853	NM_177166		9930014A18Rik	-	RIKEN cDNA 9930014A18 gene	ncRNA
mm_148640.1	chr19	5476133	5476138	+	1	NA	exon (NM_021474, exon 4 of 11)	exon (NM_021474, exon 4 of 11)	1400	NM_001164352	58859	Mm.276367	NM_021474	ENSMUSG00000024909	Efemp2	0610011K11Rik|Fbln4|MBP1	epidermal growth factor-containing fibulin-like extracellular matrix protein 2	protein-coding
mm_1093.1	chr1	59698061	59698075	+	1	NA	intron (NM_018868, intron 4 of 14)	B1F|SINE|Alu	6110	NR_028554	100217459		NR_028554		Snord70	MBII-234|snoRNA234	small nucleolar RNA, C/D box 70	snoRNA
mm_87569.1	chr10	56380458	56380462	+	1	NA	intron (NM_010288, intron 1 of 1)	intron (NM_010288, intron 1 of 1)	3160	NM_010288	14609	Mm.378921	NM_010288	ENSMUSG00000050953	Gja1	AU042049|AW546267|Cnx43|Cx43|Cx43alpha1|Gja-1|Npm1|connexin43	gap junction protein, alpha 1	protein-coding
mm_95982.1	chr11	58977579	58977612	+	1	NA	promoter-TSS (NM_053168)	promoter-TSS (NM_053168)	-498	NM_001290988	94091	Mm.248049	NM_053168	ENSMUSG00000020455	Trim11	-	tripartite motif-containing 11	protein-coding
mm_108530.1	chr12	84202894	84202927	+	1	NA	intron (NM_001163501, intron 1 of 12)	intron (NM_001163501, intron 1 of 12)	-8895	NM_001163502	238317	Mm.31256	NM_001163501	ENSMUSG00000042507	Elmsan1	9430029N19Rik|C130039O16Rik|Gm260	ELM2 and Myb/SANT-like domain containing 1	protein-coding
mm_24765.1	chr3	95499793	95499811	+	1	NA	intron (NM_007802, intron 1 of 7)	intron (NM_007802, intron 1 of 7)	592	NM_007802	13038	Mm.272085	NM_007802	ENSMUSG00000028111	Ctsk	AI323530|MMS10-Q|Ms10q|catK	cathepsin K	protein-coding
mm_116189.1	chr13	31399737	31399745	-	1	NA	Intergenic	Intergenic	-158429	NM_008239	15220	Mm.44235	NM_008239	ENSMUSG00000038415	Foxq1	HFH-1|Hfh1|Hfh1l|sa	forkhead box Q1	protein-coding
mm_25577.1	chr3	116859594	116859605	+	1	NA	promoter-TSS (NM_001113478)	promoter-TSS (NM_001113478)	32	NM_001113478	20321	Mm.66293	NM_009146	ENSMUSG00000033386	Frrs1	AI131732|Sdfr2	ferric-chelate reductase 1	protein-coding
mm_163378.1	chr12	45468467	45468467	+	1	NA	Intergenic	Intergenic	-393984	NM_144552	217517	Mm.285400	NM_144552	ENSMUSG00000046314	Stxbp6	BC024598|C85317	syntaxin binding protein 6 (amisyn)	protein-coding
mm_36164.1	chr4	60739892	60739904	-	1	NA	intron (NM_001199995, intron 2 of 6)	intron (NM_001199995, intron 2 of 6)	1383	NM_001199995	100039054	Mm.482236	NM_001199995	ENSMUSG00000094793	Mup12	Gm2024	major urinary protein 12	protein-coding
mm_166111.1	chr4	148804331	148804341	+	1	NA	promoter-TSS (NM_001159344)	promoter-TSS (NM_001159344)	-56	NM_001159344	69743	Mm.233879	NM_027195	ENSMUSG00000028977	Casz1	2410019P08Rik|AV096627|BC040081|Cst|D4Ertd432e	castor zinc finger 1	protein-coding
mm_108822.1	chr12	95701113	95701119	+	1	NA	intron (NM_201518, intron 1 of 1)	intron (NM_201518, intron 1 of 1)	8890	NM_201518	399558	Mm.341948	NM_201518	ENSMUSG00000047414	Flrt2	-	fibronectin leucine rich transmembrane protein 2	protein-coding
mm_108653.1	chr12	86361113	86361131	+	1	NA	promoter-TSS (NM_001159500)	promoter-TSS (NM_001159500)	5	NM_001159500	26380	Mm.235550	NM_011934	ENSMUSG00000021255	Esrrb	Err2|Errb|Estrrb|Nr3b2	estrogen related receptor, beta	protein-coding
mm_168711.1	chr11	99932586	99932588	+	1	NA	Intergenic	CpG	-3704	NM_001025244	432602	Mm.246878	NM_001025244	ENSMUSG00000051481	Krtap31-2	OTTMUSG00000002177	keratin associated protein 31-2	protein-coding
mm_166742.1	chr6	124779667	124779680	-	1	NA	promoter-TSS (NM_001302555)	promoter-TSS (NM_001302555)	54	NM_001302555	16977	Mm.3207	NM_013588	ENSMUSG00000030125	Lrrc23	4921537K05Rik|B7|Lrpb7	leucine rich repeat containing 23	protein-coding
mm_150645.1	chr19	41911698	41911705	+	1	NA	promoter-TSS (NM_023418)	promoter-TSS (NM_023418)	-170	NM_023418	18648	Mm.16783	NM_023418	ENSMUSG00000011752	Pgam1	2310050F24Rik|Pgam-1	phosphoglycerate mutase 1	protein-coding
mm_39875.1	chr5	31077082	31077093	+	1	NA	intron (NM_023525, intron 39 of 43)	intron (NM_023525, intron 39 of 43)	16440	NM_011773	22784	Mm.1396	NM_011773	ENSMUSG00000029151	Slc30a3	Znt3	solute carrier family 30 (zinc transporter), member 3	protein-coding
mm_11642.1	chr2	34914322	34914338	+	1	NA	promoter-TSS (NM_028716)	promoter-TSS (NM_028716)	-354	NM_028716	74016	Mm.65691	NM_028716	ENSMUSG00000026873	Phf19	3110009G19Rik|3321402G02Rik	PHD finger protein 19	protein-coding
mm_57212.1	chr6	122856069	122856089	-	1	NA	promoter-TSS (NM_009779)	promoter-TSS (NM_009779)	78	NM_009779	12267	Mm.2408	NM_009779	ENSMUSG00000040552	C3ar1	AZ3B|C3AR|HNFAG09	complement component 3a receptor 1	protein-coding
mm_111258.1	chr12	85138703	85138732	-	1	NA	exon (NM_146244, exon 8 of 11)	exon (NM_146244, exon 8 of 11)	12547	NM_146244	238323	Mm.44829	NM_146244	ENSMUSG00000019235	Rps6kl1	A830084F09Rik|AW046440	ribosomal protein S6 kinase-like 1	protein-coding
mm_156597.1	chrX	152273889	152273892	+	1	NA	3' UTR (NM_013668, exon 26 of 26)	3' UTR (NM_013668, exon 26 of 26)	40663	NM_013668	20591	Mm.142655	NM_013668	ENSMUSG00000025332	Kdm5c	D930009K15Rik|Jarid1c|Smcx|mKIAA0234	lysine (K)-specific demethylase 5C	protein-coding
mm_97589.1	chr11	78945881	78945888	+	1	NA	exon (NM_010927, exon 15 of 27)	exon (NM_010927, exon 15 of 27)	20593	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_58289.1	chr6	145863672	145863782	-	1	NA	exon (NM_024469, exon 5 of 5)	exon (NM_024469, exon 5 of 5)	1693	NM_001271768	79362	Mm.154529	NM_024469	ENSMUSG00000030256	Bhlhe41	6430520M22Rik|Bhlhb2l|Bhlhb3|DEC2|Sharp1	basic helix-loop-helix family, member e41	protein-coding
mm_106552.1	chr11	120598515	120598518	-	1	NA	promoter-TSS (NM_011568)	promoter-TSS (NM_011568)	-16	NM_001038230	66156	Mm.21645	NM_025389	ENSMUSG00000025135	Anapc11	1110011I19Rik|R75218	anaphase promoting complex subunit 11	protein-coding
mm_103442.1	chr11	76015455	76015467	-	1	NA	Intergenic	Intergenic	12321	NM_029658	76566	Mm.34131	NM_029658	ENSMUSG00000020846	Rflnb	1500005K14Rik|Fam101b|RefilinB|cfm	refilin B	protein-coding
mm_135247.1	chr16	37539728	37539730	-	1	NA	promoter-TSS (NM_001042499)	promoter-TSS (NM_001042499)	40	NM_028812	74197	Mm.287795	NM_028812	ENSMUSG00000022828	Gtf2e1	2610024P03Rik|56kDa|AI303800|FE|TFIIE-A	general transcription factor II E, polypeptide 1 (alpha subunit)	protein-coding
mm_85345.1	chr9	103208985	103208993	-	1	NA	3' UTR (NM_133977, exon 17 of 17)	3' UTR (NM_133977, exon 17 of 17)	-6924	NM_009275	20818	Mm.273053	NM_009275	ENSMUSG00000032553	Srprb	AA409543	signal recognition particle receptor, B subunit	protein-coding
mm_26715.1	chr3	158006634	158006637	+	1	NA	3' UTR (NM_001013806, exon 13 of 13)	3' UTR (NM_001013806, exon 13 of 13)	25119	NM_001093753	69207	Mm.223946	NM_026989	ENSMUSG00000055436	Srsf11	0610009J05Rik|2610019N13Rik|BF642805|Sfrs11	serine/arginine-rich splicing factor 11	protein-coding
mm_51561.1	chr6	83523167	83523186	+	1	NA	exon (NM_009610, exon 4 of 9)	exon (NM_009610, exon 4 of 9)	13075	NM_009610	11468	Mm.292865	NM_009610	ENSMUSG00000059430	Actg2	ACTA3|Act-4|Act4|SMGA	actin, gamma 2, smooth muscle, enteric	protein-coding
mm_146202.1	chr18	76268439	76268455	+	1	NA	intron (NM_001311070, intron 1 of 8)	intron (NM_001311070, intron 1 of 8)	6002	NM_001311070	17126	Mm.152699	NM_010754	ENSMUSG00000024563	Smad2	7120426M23Rik|Madh2|Madr2|Smad-2|mMad2	SMAD family member 2	protein-coding
mm_154450.1	chrM	2025	2056	-	1	NA	NA	LSU-rRNA_Hsa|rRNA|rRNA	NA	NA								
mm_94640.1	chr11	16914241	16914250	+	1	NA	TTS (NM_207655)	TTS (NM_207655)	37037	NR_110421	72735	Mm.268598	NR_015469		Eldr	2810442I21Rik|4930500E12Rik|Fabl	Egfr long non-coding downstream RNA	ncRNA
mm_118656.1	chr14	21776767	21776799	+	1	NA	intron (NM_026283, intron 2 of 5)	intron (NM_026283, intron 2 of 5)	26252	NM_026283	67630	Mm.102765	NM_026283	ENSMUSG00000021770	Samd8	1110053F04Rik|1700010P07Rik|SMSr	sterile alpha motif domain containing 8	protein-coding
mm_64604.1	chr7	3228510	3228518	-	1	NA	exon (NM_001033431, exon 8 of 10)	exon (NM_001033431, exon 8 of 10)	7741	NR_029645	100049713		NR_029645	ENSMUSG00000077886	Mir295	Mirn295|mir-295|mmu-miR-295	microRNA 295	ncRNA
mm_133019.1	chr16	56477839	56477860	+	1	NA	promoter-TSS (NM_178790)	promoter-TSS (NM_178790)	3	NM_001014424	320712	Mm.209236	NM_178790	ENSMUSG00000035258	Abi3bp	5033411B22Rik|AI506287|BG172926|D930038M13Rik|TARSH|eratin	ABI gene family, member 3 (NESH) binding protein	protein-coding
mm_3855.1	chr1	160944714	160944729	+	1	NA	intron (NM_001024952, intron 6 of 19)	MT2B1|LTR|ERVL	-33885	NM_080844	11905	Mm.260770	NM_080844	ENSMUSG00000026715	Serpinc1	AI114908|ATIII|At-3|At3	serine (or cysteine) peptidase inhibitor, clade C (antithrombin), member 1	protein-coding
mm_72977.1	chr8	92901388	92901411	+	1	NA	promoter-TSS (NM_027112)	promoter-TSS (NM_027112)	4	NM_027112	69543	Mm.440514	NM_027112	ENSMUSG00000078144	Capns2	2310005G05Rik|30K-2	calpain, small subunit 2	protein-coding
mm_156828.1	chrX	164269500	164269522	+	1	NA	promoter-TSS (NM_027153)	promoter-TSS (NM_027153)	80	NM_027153	69656	Mm.293463	NM_027153	ENSMUSG00000031379	Pir	2310042L19Rik|Pirnl	pirin	protein-coding
mm_110471.1	chr12	51829737	51829803	-	1	NA	promoter-TSS (NM_144788)	promoter-TSS (NM_144788)	-234	NM_144788	207304	Mm.249391	NM_144788	ENSMUSG00000035247	Hectd1	A630086P08Rik|AI844876|b2b327Clo|opm	HECT domain containing 1	protein-coding
mm_152709.1	chr19	17372250	17372252	-	1	NA	intron (NM_010265, intron 1 of 2)	intron (NM_010265, intron 1 of 2)	593	NM_010265	14537	Mm.244825	NM_010265	ENSMUSG00000038843	Gcnt1	5630400D21Rik|B130048E03|C2 GlcNAcT|C2GNT|IGnT	glucosaminyl (N-acetyl) transferase 1, core 2	protein-coding
mm_57185.1	chr6	122848825	122848845	-	1	NA	3' UTR (NM_009779, exon 2 of 2)	3' UTR (NM_009779, exon 2 of 2)	7322	NM_009779	12267	Mm.2408	NM_009779	ENSMUSG00000040552	C3ar1	AZ3B|C3AR|HNFAG09	complement component 3a receptor 1	protein-coding
mm_156426.1	chrX	140956893	140956923	+	1	NA	promoter-TSS (NM_001164177)	promoter-TSS (NM_001164177)	-197	NM_001164177	53380	Mm.17640	NM_016883	ENSMUSG00000031429	Psmd10	AW554874	proteasome (prosome, macropain) 26S subunit, non-ATPase, 10	protein-coding
mm_123791.1	chr14	70443127	70443153	-	1	NA	promoter-TSS (NR_029802)	promoter-TSS (NR_029802)	87	NM_001164082	67065	Mm.20420	NM_025945	ENSMUSG00000000776	Polr3d	2810426M17Rik|44kDa|AI326118|AW489084|BN51T|RPC4|TSBN51	polymerase (RNA) III (DNA directed) polypeptide D	protein-coding
mm_129947.1	chr15	84960979	84960994	-	1	NA	intron (NM_001033273, intron 1 of 9)	intron (NM_001033273, intron 1 of 9)	-9363	NR_037206	100526461		NR_037206	ENSMUSG00000080441	Mir1249	mir-1249|mmu-mir-1249	microRNA 1249	ncRNA
mm_104765.1	chr11	98479517	98479519	-	1	NA	intron (NM_011771, intron 6 of 7)	intron (NM_011771, intron 6 of 7)	32684	NM_010346	14786	Mm.276702	NM_010346	ENSMUSG00000019312	Grb7	mKIAA4028	growth factor receptor bound protein 7	protein-coding
mm_58150.1	chr6	142323011	142323022	-	1	NA	promoter-TSS (NM_130861)	promoter-TSS (NM_130861)	-35	NM_130861	108096	Mm.206599	NM_130861	ENSMUSG00000063975	Slco1a5	Oatp-3|Oatp3|Slc21a7	solute carrier organic anion transporter family, member 1a5	protein-coding
mm_40353.1	chr5	46414255	46414255	+	1	NA	Intergenic	Intergenic	-481846	NR_110478	78106	Mm.243807	NR_110478	ENSMUSG00000106602	4930405L22Rik	-	RIKEN cDNA 4930405L22 gene	ncRNA
mm_129964.1	chr15	85581810	85581820	-	1	NA	promoter-TSS (NM_009528)	promoter-TSS (NM_009528)	6	NM_009528	22422	Mm.306946	NM_009528	ENSMUSG00000022382	Wnt7b	Wnt-7b	wingless-type MMTV integration site family, member 7B	protein-coding
mm_160823.1	chr11	32300140	32300140	+	1	NA	promoter-TSS (NM_175000)	promoter-TSS (NM_175000)	71	NM_175000	216635	Mm.338482	NM_175000	ENSMUSG00000020295	Hbq1a	A230090E05Rik|Gm876|Hbq1|Hbqt2	hemoglobin, theta 1A	protein-coding
mm_114281.1	chr13	58281214	58281218	+	1	NA	Intergenic	Intergenic	-7028	NM_019832	56278	Mm.296625	NM_019832	ENSMUSG00000021552	Gkap1	42kDa|4933400B15Rik|D13Ertd340e|Gkap42	G kinase anchoring protein 1	protein-coding
mm_9794.1	chr1	181841014	181841020	-	1	NA	intron (NM_133815, intron 1 of 13)	intron (NM_133815, intron 1 of 13)	1384	NM_133815	98386	Mm.4538	NM_133815	ENSMUSG00000004880	Lbr	AI505894|ic	lamin B receptor	protein-coding
mm_70961.1	chr8	26980113	26980127	+	1	NA	3' UTR (NM_001110508, exon 3 of 3)	3' UTR (NM_001110508, exon 3 of 3)	2784	NM_001110508	353310	Mm.212469	NM_001101502	ENSMUSG00000085795	Zfp703	1110032O19Rik|AI430822|AL022941|Csmn1|End2|Zeppo1|Znf703|Zpo1	zinc finger protein 703	protein-coding
mm_90375.1	chr10	127187779	127187790	+	1	NA	intron (NM_001166413, intron 2 of 15)	intron (NM_001166413, intron 2 of 15)	2039	NM_001166413	52666	Mm.272230	NM_028027	ENSMUSG00000019467	Arhgef25	2410008H17Rik|D10Ertd610e|GEFT	Rho guanine nucleotide exchange factor (GEF) 25	protein-coding
mm_153424.1	chr19	40730297	40730305	-	1	NA	intron (NM_001304721, intron 7 of 9)	intron (NM_001304721, intron 7 of 9)	70531	NM_009848	12495	Mm.2824	NM_009848	ENSMUSG00000048120	Entpd1	2610206B08Rik|AA408691|Cd39|NTPDase-1	ectonucleoside triphosphate diphosphohydrolase 1	protein-coding
mm_14883.1	chr2	148835198	148835227	+	1	NA	promoter-TSS (NM_009979)	promoter-TSS (NM_009979)	65	NM_009979	13013	Mm.21005	NM_009979	ENSMUSG00000027445	Cst9	M12|cresp|testatin	cystatin 9	protein-coding
mm_156917.1	chrX	169097806	169097816	+	1	NA	intron (NR_109847, intron 1 of 14)	intron (NR_109847, intron 1 of 14)	-15067	NM_001287530	11856	Mm.441810	NM_009707	ENSMUSG00000031355	Arhgap6	AI504284|RhoGAPX-1	Rho GTPase activating protein 6	protein-coding
mm_68325.1	chr7	106503960	106503971	-	1	NA	Intergenic	Intergenic	-62892	NR_003967	209380	Mm.461779	NM_001001318		Gm4759	EG209380	GTPase, very large interferon inducible 1 pseudogene	pseudo
mm_157994.1	chrX	94540244	94540260	-	1	NA	exon (NM_019791, exon 3 of 13)	exon (NM_019791, exon 3 of 13)	1822	NM_019791	94275	Mm.27578	NM_019791	ENSMUSG00000025151	Maged1	2810433C11Rik|5430405L04Rik|DXBwg1492e|Dlixin|Dlxin-1|Dlxin1|MAGE-D1|NRAGE|mFLJ00163	melanoma antigen, family D, 1	protein-coding
mm_56235.1	chr6	90662250	90662270	-	1	NA	3' UTR (NM_001134384, exon 14 of 14)	3' UTR (NM_001134384, exon 14 of 14)	43014	NM_001037493	71699	Mm.272633	NM_027868	ENSMUSG00000030089	Slc41a3	1010001P06Rik|AI480742|SLC41A1-L2	solute carrier family 41, member 3	protein-coding
mm_94778.1	chr11	21370734	21370737	+	1	NA	promoter-TSS (NM_139297)	promoter-TSS (NM_139297)	-106	NM_139297	216558	Mm.28877	NM_139297	ENSMUSG00000001891	Ugp2	UDPGP|UGPase	UDP-glucose pyrophosphorylase 2	protein-coding
mm_89634.1	chr10	96401096	96401104	+	1	NA	Intergenic	Intergenic	174893	NR_110448	74881	Mm.410819	NR_110448		4930459C07Rik	-	RIKEN cDNA 4930459C07 gene	ncRNA
mm_29064.1	chr3	103791538	103791563	-	1	NA	promoter-TSS (NR_125731)	promoter-TSS (NR_125731)	11	NR_125731	15257	Mm.20827	NM_010432	ENSMUSG00000008730	Hipk1	1110062K04Rik|Myak	homeodomain interacting protein kinase 1	protein-coding
mm_5611.1	chr1	39650855	39650887	-	1	NA	exon (NM_170597, exon 1 of 4)	exon (NM_170597, exon 1 of 4)	311	NM_170597	263764	Mm.122091	NM_170597	ENSMUSG00000050967	Creg2	A830098L22Rik	cellular repressor of E1A-stimulated genes 2	protein-coding
mm_150499.1	chr19	39018804	39018810	+	1	NA	intron (NM_028089, intron 4 of 8)	intron (NM_028089, intron 4 of 8)	11788	NM_028089	72082	Mm.142581	NM_028089	ENSMUSG00000025002	Cyp2c55	2010318C06Rik	cytochrome P450, family 2, subfamily c, polypeptide 55	protein-coding
mm_150580.1	chr19	40659456	40659462	+	1	NA	promoter-TSS (NM_009848)	promoter-TSS (NM_009848)	-311	NM_009848	12495	Mm.2824	NM_009848	ENSMUSG00000048120	Entpd1	2610206B08Rik|AA408691|Cd39|NTPDase-1	ectonucleoside triphosphate diphosphohydrolase 1	protein-coding
mm_32223.1	chr4	101717806	101717838	+	1	NA	5' UTR (NM_001122899, exon 1 of 19)	5' UTR (NM_001122899, exon 1 of 19)	415	NM_010704	16847	Mm.259282	NM_010704	ENSMUSG00000057722	Lepr	LEPROT|Leprb|Modb1|OB-RGRP|Obr|db|diabetes|obese-like|obl	leptin receptor	protein-coding
mm_121091.1	chr14	99301689	99301703	+	1	NA	exon (NM_009769, exon 2 of 4)	exon (NM_009769, exon 2 of 4)	3005	NM_009769	12224	Mm.30262	NM_009769	ENSMUSG00000005148	Klf5	4930520J07Rik|Bteb2|CKLF|IKLF	Kruppel-like factor 5	protein-coding
mm_145600.1	chr18	61045271	61045281	+	1	NA	5' UTR (NM_001146268, exon 1 of 23)	5' UTR (NM_001146268, exon 1 of 23)	126	NM_008809	18596	Mm.4146	NM_008809	ENSMUSG00000024620	Pdgfrb	AI528809|CD140b|PDGFR-1|Pdgfr	platelet derived growth factor receptor, beta polypeptide	protein-coding
mm_67009.1	chr7	65364203	65364206	-	1	NA	intron (NM_009386, intron 1 of 27)	intron (NM_009386, intron 1 of 27)	7040	NM_001163574	21872	Mm.4342	NM_009386	ENSMUSG00000030516	Tjp1	ZO1	tight junction protein 1	protein-coding
mm_128203.1	chr15	35938157	35938178	-	1	NA	promoter-TSS (NM_053071)	promoter-TSS (NM_053071)	79	NM_053071	12864	Mm.548	NM_053071	ENSMUSG00000014313	Cox6c	-	cytochrome c oxidase subunit VIc	protein-coding
mm_91068.1	chr10	19005681	19005691	-	1	NA	exon (NM_009397, exon 6 of 9)	exon (NM_009397, exon 6 of 9)	6277	NM_001166402	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_57018.1	chr6	121343277	121343303	-	1	NA	intron (NM_001347433, intron 1 of 14)	intron (NM_001347433, intron 1 of 14)	214	NM_001347433	14411	Mm.274506	NM_133661	ENSMUSG00000030109	Slc6a12	BGT1|GAT-2|GAT2|Gabt2	solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12	protein-coding
mm_149937.1	chr19	27217048	27217056	+	1	NA	promoter-TSS (NM_013703)	promoter-TSS (NM_013703)	32	NM_001161420	22359	Mm.4141	NM_013703	ENSMUSG00000024924	Vldlr	AA408956|AI451093|AW047288	very low density lipoprotein receptor	protein-coding
mm_31174.1	chr4	43482272	43482288	+	1	NA	3' UTR (NM_019436, exon 5 of 5)	3' UTR (NM_019436, exon 5 of 5)	1429	NM_019436	54390	Mm.31775	NM_019436	ENSMUSG00000028460	Sit1	Sit	suppression inducing transmembrane adaptor 1	protein-coding
mm_29493.1	chr3	115888038	115888054	-	1	NA	promoter-TSS (NR_027895)	promoter-TSS (NR_027895)	13	NR_027894	68161	Mm.392043	NR_015487	ENSMUSG00000054426	A930005H10Rik	-	RIKEN cDNA A930005H10 gene	ncRNA
mm_27164.1	chr3	33143200	33143220	-	1	NA	promoter-TSS (NM_001163516)	promoter-TSS (NM_001163516)	-19	NM_001163516	58869	Mm.151332	NM_021483	ENSMUSG00000027674	Pex5l	1700016J08Rik|PXR2|Pex2|TRIP8b|pex5Rp	peroxisomal biogenesis factor 5-like	protein-coding
mm_173330.1	chrY	90784183	90784190	+	1	NA	Intergenic	Intergenic	-1256	NR_137282	170942	Mm.76062	NM_133362	ENSMUSG00000096768	Erdr1	edr	erythroid differentiation regulator 1	protein-coding
mm_148125.1	chr18	75378252	75378256	-	1	NA	intron (NM_001042660, intron 3 of 3)	intron (NM_001042660, intron 3 of 3)	10889	NM_001042660	17131	Mm.34407	NM_008543	ENSMUSG00000025880	Smad7	Madh7	SMAD family member 7	protein-coding
mm_92025.1	chr10	62449680	62449733	-	1	NA	promoter-TSS (NM_181423)	promoter-TSS (NM_181423)	-13	NM_181423	338359	Mm.235898	NM_181423	ENSMUSG00000020079	Supv3l1	6330443E10Rik	suppressor of var1, 3-like 1 (S. cerevisiae)	protein-coding
mm_38652.1	chr4	143278899	143278915	-	1	NA	intron (NM_001290822, intron 1 of 4)	(A)n|Simple_repeat|Simple_repeat	20657	NM_010329	14726	Mm.2976	NM_010329	ENSMUSG00000028583	Pdpn	Gp38|OTS-8|RANDAM-2|T1-alpha|T1a|T1alpha	podoplanin	protein-coding
mm_124088.1	chr14	78732786	78732796	-	1	NA	Intergenic	CpG	-7702	NM_001081336	380921	Mm.89591	NM_001081336	ENSMUSG00000034731	Dgkh	5930402B05Rik|D130015C16|DGK	diacylglycerol kinase, eta	protein-coding
mm_160537.1	chr9	39950631	39950631	-	1	NA	exon (NM_146828, exon 1 of 1)	exon (NM_146828, exon 1 of 1)	138	NM_146828	258825	Mm.377710	NM_146828	ENSMUSG00000043331	Olfr975	MOR224-2	olfactory receptor 975	protein-coding
mm_77220.1	chr8	115695272	115695308	-	1	NA	Intergenic	Intergenic	11604	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_161858.1	chr18	25165768	25165768	-	1	NA	intron (NM_001004361, intron 1 of 6)	Lx7|LINE|L1	197	NM_001142697	66648	Mm.263189	NM_001004361	ENSMUSG00000024269	Tpgs2	5730437P09Rik|5730494M16Rik|AI666318|Pgs2	tubulin polyglutamylase complex subunit 2	protein-coding
mm_107574.1	chr12	44400831	44400834	+	1	NA	intron (NM_001146031, intron 2 of 27)	intron (NM_001146031, intron 2 of 27)	71947	NM_001146031	319504	Mm.208439	NM_176930	ENSMUSG00000020598	Nrcam	Bravo|C030017F07Rik|C130076O07Rik|mKIAA0343	neuronal cell adhesion molecule	protein-coding
mm_125723.1	chr15	73148143	73148185	+	1	NA	intron (NM_153178, intron 1 of 18)	intron (NM_153178, intron 1 of 18)	36783	NM_153178	239528	Mm.23095	NM_153178	ENSMUSG00000036698	Ago2	1110029L17Rik|2310051F07Rik|AI225898|AL022874|AW546247|ENSMUSG00000072493|Eif2c2|Gerp95|Gm10365|mKIAA4215	argonaute RISC catalytic subunit 2	protein-coding
mm_162507.1	chr1	150366965	150366965	+	1	NA	intron (NM_001077237, intron 11 of 12)	intron (NM_001077237, intron 11 of 12)	-20194	NR_040603	75584	Mm.47709	NR_040603	ENSMUSG00000099447	2310030A07Rik	-	RIKEN cDNA 2310030A07 gene	ncRNA
mm_141228.1	chr17	27426229	27426261	-	1	NA	3' UTR (NM_001291045, exon 10 of 10)	3' UTR (NM_001291045, exon 10 of 10)	68148	NR_106077	102466228		NR_106077	ENSMUSG00000106215	Mir7218	mmu-mir-7218	microRNA 7218	ncRNA
mm_131521.1	chr16	17619444	17619450	+	1	NA	promoter-TSS (NM_029945)	promoter-TSS (NM_029945)	93	NM_001164609	77626	Mm.34659	NM_029945	ENSMUSG00000005899	Smpd4	4122402O22Rik|mKIAA1418	sphingomyelin phosphodiesterase 4	protein-coding
mm_169462.1	chr1	46562815	46562818	+	1	NA	intron (NM_001310335, intron 19 of 64)	intron (NM_001310335, intron 19 of 64)	137298	NM_001310335	100101919	Mm.383402	NM_001310335	ENSMUSG00000101337	Dnah7c	Dnahc7c	dynein, axonemal, heavy chain 7C	protein-coding
mm_62345.1	chr7	100498341	100498361	+	1	NA	exon (NM_011671, exon 6 of 8)	exon (NM_011671, exon 6 of 8)	4993	NM_011671	22228	Mm.171378	NM_011671	ENSMUSG00000033685	Ucp2	Slc25a8	uncoupling protein 2 (mitochondrial, proton carrier)	protein-coding
mm_144516.1	chr18	24710372	24710374	+	1	NA	intron (NM_175276, intron 1 of 26)	intron (NM_175276, intron 1 of 26)	1750	NM_001289655	225288	Mm.329322	NM_175276	ENSMUSG00000034295	Fhod3	A930009H06Rik|FHOS2|mKIAA1695	formin homology 2 domain containing 3	protein-coding
mm_42935.1	chr5	122987581	122987612	+	1	NA	intron (NM_001003953, intron 2 of 22)	CpG	1503	NM_001003953	30841	Mm.86406	NM_013910	ENSMUSG00000029475	Kdm2b	Cxxc2|Fbl10|Fbxl10|Jhdm1b|PCCX2	lysine (K)-specific demethylase 2B	protein-coding
mm_42039.1	chr5	108404935	108404946	+	1	NA	intron (NM_008806, intron 3 of 21)	intron (NM_008806, intron 3 of 21)	16567	NM_008806	18587	Mm.1372	NM_008806	ENSMUSG00000029491	Pde6b	Pdeb|r|rd|rd-1|rd1|rd10	phosphodiesterase 6B, cGMP, rod receptor, beta polypeptide	protein-coding
mm_59779.1	chr7	28841607	28841625	+	1	NA	TTS (NM_010707)	TTS (NM_010707)	7446	NM_010707	16857	Mm.210336	NM_010707		Lgals6	galectin-6	lectin, galactose binding, soluble 6	protein-coding
mm_33931.1	chr4	136889965	136889988	+	1	NA	3' UTR (NM_007574, exon 3 of 3)	3' UTR (NM_007574, exon 3 of 3)	2938	NM_007574	12262	Mm.439732	NM_007574	ENSMUSG00000036896	C1qc	AI385742|C1qg|Ciqc	complement component 1, q subcomponent, C chain	protein-coding
mm_56854.1	chr6	118155334	118155352	-	1	NA	exon (NM_009050, exon 19 of 20)	exon (NM_009050, exon 19 of 20)	-16203	NM_030165	78752	Mm.300317	NM_030165	ENSMUSG00000042042	Csgalnact2	4632415D10Rik|Galnact2	chondroitin sulfate N-acetylgalactosaminyltransferase 2	protein-coding
mm_79975.1	chr9	66713720	66713736	+	1	NA	promoter-TSS (NM_178396)	promoter-TSS (NM_178396)	42	NM_001306148	76459	Mm.277921	NM_178396	ENSMUSG00000032373	Car12	2310047E01Rik|AI314958|CA-XII|Ca12	carbonic anhydrase 12	protein-coding
mm_30894.1	chr4	32291774	32291782	+	1	NA	Intergenic	Intergenic	-125657	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_61964.1	chr7	90387042	90387052	+	1	NA	promoter-TSS (NM_001040087)	promoter-TSS (NM_001040087)	66	NM_001040088	83671	Mm.26751	NM_031394	ENSMUSG00000030616	Sytl2	AI266830|Slp2|mKIAA1597	synaptotagmin-like 2	protein-coding
mm_137831.1	chr17	30747723	30747725	+	1	NA	intron (NM_013811, intron 51 of 92)	B4|SINE|B4	120788	NM_013811	13417	Mm.426017	NM_013811	ENSMUSG00000033826	Dnah8	ATPase|Dnahc8|Hst6.7b|P1-Loop	dynein, axonemal, heavy chain 8	protein-coding
mm_170159.1	chr17	47811924	47811925	-	1	NA	Intergenic	Intergenic	21367	NM_001276391	17240	Mm.329100	NM_010783	ENSMUSG00000032717	Mdfi	I-mf|I-mfa	MyoD family inhibitor	protein-coding
mm_68522.1	chr7	112024046	112024073	-	1	NA	intron (NM_133758, intron 1 of 27)	CpG	553	NM_177249	74996	Mm.16974	NM_133758	ENSMUSG00000059263	Usp47	4930502N04Rik|A630020C16Rik	ubiquitin specific peptidase 47	protein-coding
mm_5289.1	chr1	20820214	20820286	-	1	NA	promoter-TSS (NM_008563)	promoter-TSS (NM_008563)	-37	NM_008563	17215	Mm.4502	NM_008563	ENSMUSG00000041859	Mcm3	AL033361|C80350|Mcmd|P1|p1.m	minichromosome maintenance complex component 3	protein-coding
mm_24756.1	chr3	95434511	95434533	+	1	NA	5' UTR (NM_001037737, exon 1 of 22)	5' UTR (NM_001037737, exon 1 of 22)	132	NM_001037737	11863	Mm.250265	NM_009709	ENSMUSG00000015522	Arnt	D3Ertd557e|Drnt|ESTM42|Hif1b|W08714|bHLHe2|mKIAA4051	aryl hydrocarbon receptor nuclear translocator	protein-coding
mm_79539.1	chr9	57910507	57910530	+	1	NA	promoter-TSS (NM_027086)	promoter-TSS (NM_027086)	-468	NM_027086	69459	Mm.41735	NM_027086	ENSMUSG00000055720	Ubl7	2300004C15Rik	ubiquitin-like 7 (bone marrow stromal cell-derived)	protein-coding
mm_28729.1	chr3	95735873	95735885	-	1	NA	promoter-TSS (NR_105981)	promoter-TSS (NR_105981)	-906	NR_105981	102466787		NR_105981	ENSMUSG00000098737	Mir7014	Gm27837|mmu-mir-7014	microRNA 7014	ncRNA
mm_90472.1	chr10	127850004	127850021	+	1	NA	promoter-TSS (NM_147222)	promoter-TSS (NM_147222)	84	NM_147222	216453	Mm.222953	NM_147222	ENSMUSG00000054052	Rdh19	RDH-S|RDH-S2|Rdhs	retinol dehydrogenase 19	protein-coding
mm_76358.1	chr8	84772267	84772322	-	1	NA	exon (NM_010906, exon 2 of 9)	exon (NM_010906, exon 2 of 9)	2075	NM_001081981	18032	Mm.9394	NM_010906	ENSMUSG00000001911	Nfix	CTF|NF-I/X|NF1-X|NFI-X	nuclear factor I/X	protein-coding
mm_75995.1	chr8	72443704	72443760	-	1	NA	promoter-TSS (NM_028500)	promoter-TSS (NM_028500)	46	NM_028500	73316	Mm.196315	NM_028500	ENSMUSG00000019732	Calr3	1700031L01Rik|6330586I20Rik|Crt2|cspn	calreticulin 3	protein-coding
mm_105845.1	chr11	113684511	113684520	-	1	NA	promoter-TSS (NM_138598)	promoter-TSS (NM_138598)	103	NM_177777	276852	Mm.239566	NM_177777	ENSMUSG00000041623	D11Wsu47e	-	DNA segment, Chr 11, Wayne State University 47, expressed	protein-coding
mm_4442.1	chr1	172514122	172514147	+	1	NA	Intergenic	Intergenic	-6996	NM_027972	71870	Mm.78373	NM_027972	ENSMUSG00000026546	Cfap45	1700028D05Rik|Ccdc19|Nesg1	cilia and flagella associated protein 45	protein-coding
mm_56105.1	chr6	87491153	87491164	-	1	NA	intron (NM_001037727, intron 3 of 10)	intron (NM_001037727, intron 3 of 10)	5169	NR_104483	232201	Mm.119564	NM_175476	ENSMUSG00000030047	Arhgap25	A130039I20Rik	Rho GTPase activating protein 25	protein-coding
mm_113519.1	chr13	37803207	37803240	+	1	NA	Intergenic	L1MB3|LINE|L1	-22815	NM_026830	68750	Mm.491109	NM_026830	ENSMUSG00000039087	Rreb1	1110037N09Rik|AA414966|B930013M22Rik	ras responsive element binding protein 1	protein-coding
mm_111684.1	chr12	103425804	103425855	-	1	NA	promoter-TSS (NM_001159502)	promoter-TSS (NM_001159502)	38	NM_020494	27225	Mm.3935	NM_020494	ENSMUSG00000041645	Ddx24	1700055J08Rik|2510027P10Rik|AI649272	DEAD (Asp-Glu-Ala-Asp) box polypeptide 24	protein-coding
mm_14866.1	chr2	148798873	148798886	+	1	NA	promoter-TSS (NM_009978)	promoter-TSS (NM_009978)	40	NM_009978	13012	Mm.20435	NM_009978	ENSMUSG00000027442	Cst8	Cres|Cst-rs1	cystatin 8 (cystatin-related epididymal spermatogenic)	protein-coding
mm_97897.1	chr11	83404989	83404995	+	1	NA	TTS (NM_001035854)	TTS (NM_001035854)	-5080	NM_001013386	276952	Mm.66275	NM_001013386	ENSMUSG00000020684	Rasl10b	B230331P10Rik|Gm729|VTS58635	RAS-like, family 10, member B	protein-coding
mm_104948.1	chr11	100134497	100134552	-	1	NA	exon (NM_008469, exon 2 of 8)	exon (NM_008469, exon 2 of 8)	1425	NM_008469	16665	Mm.440010	NM_008469	ENSMUSG00000054146	Krt15	AI528832|K15|Krt1-15	keratin 15	protein-coding
mm_30333.1	chr3	151732232	151732236	-	1	NA	3' UTR (NM_133871, exon 8 of 8)	3' UTR (NM_133871, exon 8 of 8)	17725	NM_133871	99899	Mm.30756	NM_133871	ENSMUSG00000028037	Ifi44	A430056A10Rik|AW261460|MTAP44|p44	interferon-induced protein 44	protein-coding
mm_78475.1	chr9	32681459	32681461	+	1	NA	Intergenic	Intergenic	-14582	NM_011808	23871	Mm.292415	NM_011808	ENSMUSG00000032035	Ets1	AI196000|AI448617|D230050P06|Ets-1|Tpl1|vs	E26 avian leukemia oncogene 1, 5' domain	protein-coding
mm_80395.1	chr9	76014955	76015020	+	1	NA	promoter-TSS (NM_173731)	promoter-TSS (NM_173731)	10	NM_173731	208982	Mm.82306	NM_173731	ENSMUSG00000007908	Hmgcll1	BC037381	3-hydroxymethyl-3-methylglutaryl-Coenzyme A lyase-like 1	protein-coding
mm_72842.1	chr8	88300405	88300439	+	1	NA	intron (NM_001037723, intron 3 of 27)	intron (NM_001037723, intron 3 of 27)	6218	NM_001037724	11513	Mm.288206	NM_007406	ENSMUSG00000031659	Adcy7	AA407758	adenylate cyclase 7	protein-coding
mm_135563.1	chr16	50070856	50070870	-	1	NA	intron (NR_045935, intron 1 of 3)	intron (NR_045935, intron 1 of 3)	1989	NR_045935	224180	Mm.146439	NM_175010		Gm4827	B130050K08|EG224180	predicted gene 4827	ncRNA
mm_9583.1	chr1	174028453	174028462	-	1	NA	exon (NM_172648, exon 2 of 7)	exon (NM_172648, exon 2 of 7)	3298	NM_172648	226695	Mm.425061	NM_172648	ENSMUSG00000054203	Ifi205	D3|D3cDNA|Ifi205a	interferon activated gene 205	protein-coding
mm_115585.1	chr13	11825933	11825936	-	1	NA	intron (NM_023868, intron 15 of 104)	AT_rich|Low_complexity|Low_complexity	281011	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding
mm_80677.1	chr9	90245488	90245502	+	1	NA	intron (NM_194334, intron 2 of 12)	intron (NM_194334, intron 2 of 12)	25274	NM_194334	67016	Mm.335347	NM_194334	ENSMUSG00000037410	Tbc1d2b	1810061M12Rik|AI480956|AV021536|AV023399|AW491493|mKIAA1055	TBC1 domain family, member 2B	protein-coding
mm_132731.1	chr16	43664531	43664559	+	1	NA	promoter-TSS (NM_001146325)	promoter-TSS (NM_001146325)	-361	NM_001146325	100043314	Mm.390896	NM_001146325	ENSMUSG00000071552	Tigit	ENSMUSG00000071552|Vstm3	T cell immunoreceptor with Ig and ITIM domains	protein-coding
mm_60984.1	chr7	49018514	49018519	+	1	NA	intron (NM_001111016, intron 2 of 38)	intron (NM_001111016, intron 2 of 38)	59443	NM_001111016	78286	Mm.333881	NM_175272	ENSMUSG00000052512	Nav2	5330421F07Rik|AU067780|BQ960892|HELAD1|POMFIL2|RAINB1|RAINB2|Unc53H2|mKIAA3015	neuron navigator 2	protein-coding
mm_145481.1	chr18	60379240	60379278	+	1	NA	intron (NM_021792, intron 1 of 1)	L1Md_A|LINE|L1	3230	NM_001146275	60440	Mm.261140	NM_021792	ENSMUSG00000054072	Iigp1	2900074L10Rik|AI046432|AW111922|Ifgga1|Iigp|Irga6	interferon inducible GTPase 1	protein-coding
mm_20568.1	chr2	131083816	131083831	-	1	NA	exon (NM_011426, exon 4 of 21)	exon (NM_011426, exon 4 of 21)	2942	NM_011426	20612	Mm.1374	NM_011426	ENSMUSG00000027322	Siglec1	Cd169|Siglec-1|Sn	sialic acid binding Ig-like lectin 1, sialoadhesin	protein-coding
mm_18557.1	chr2	65237788	65237792	-	1	NA	intron (NM_027225, intron 1 of 12)	intron (NM_027225, intron 1 of 12)	836	NM_177025	319876	Mm.34159	NM_027225	ENSMUSG00000034903	Cobll1	1810047P18Rik|Coblr1|D430044D16Rik	Cobl-like 1	protein-coding
mm_148995.1	chr19	8618326	8618337	+	1	NA	exon (NM_008766, exon 1 of 10)	exon (NM_008766, exon 1 of 10)	335	NM_008766	18399	Mm.30090	NM_008766	ENSMUSG00000024650	Slc22a6	NKT|Oat1|Orctl1|mOat1	solute carrier family 22 (organic anion transporter), member 6	protein-coding
mm_29960.1	chr3	133310585	133310661	-	1	NA	intron (NM_146141, intron 1 of 11)	CpG	513	NM_146141	74776	Mm.210305	NM_146141	ENSMUSG00000028013	Ppa2	1110013G13Rik|Sid6306	pyrophosphatase (inorganic) 2	protein-coding
mm_104845.1	chr11	99230920	99230959	-	1	NA	promoter-TSS (NM_020618)	promoter-TSS (NM_020618)	78	NM_020618	57376	Mm.379086	NM_020618	ENSMUSG00000037935	Smarce1	2810417B20Rik|5830412H02Rik|9030408N19Rik|Baf27	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1	protein-coding
mm_49397.1	chr6	28424338	28424349	+	1	NA	exon (NM_007480, exon 2 of 6)	exon (NM_007480, exon 2 of 6)	703	NM_007480	11844	Mm.389075	NM_007480	ENSMUSG00000020440	Arf5	-	ADP-ribosylation factor 5	protein-coding
mm_76179.1	chr8	82401657	82401668	-	1	NA	intron (NM_001254747, intron 1 of 7)	intron (NM_001254747, intron 1 of 7)	924	NM_001254747	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_31610.1	chr4	58985592	58985613	+	1	NA	intron (NM_025968, intron 1 of 9)	intron (NM_025968, intron 1 of 9)	1476	NM_025968	67103	Mm.34497	NM_025968	ENSMUSG00000028378	Ptgr1	2510002C21Rik|Ltb4dh|Zadh3	prostaglandin reductase 1	protein-coding
mm_6588.1	chr1	75264135	75264194	-	1	NA	promoter-TSS (NM_008985)	promoter-TSS (NM_008985)	44	NM_008985	19275	Mm.2902	NM_008985	ENSMUSG00000026204	Ptprn	IA-2|mIA-A|mKIAA4064	protein tyrosine phosphatase, receptor type, N	protein-coding
mm_32070.1	chr4	97830236	97830240	+	1	NA	intron (NM_010905, intron 2 of 10)	intron (NM_010905, intron 2 of 10)	52612	NM_010905	18027	Mm.31274	NM_010905	ENSMUSG00000028565	Nfia	1110047K16Rik|9430022M17Rik|CTF|NF1-A|NF1A	nuclear factor I/A	protein-coding
mm_16291.1	chr2	174111200	174111208	+	1	NA	exon (NM_213733, exon 2 of 12)	exon (NM_213733, exon 2 of 12)	853	NM_213733	228961	Mm.295629	NM_213733	ENSMUSG00000039263	Npepl1	BC023239|C85514|mKIAA1974	aminopeptidase-like 1	protein-coding
mm_137336.1	chr17	25129573	25129601	+	1	NA	Intergenic	Intergenic	-3804	NM_011930	26373	Mm.270587	NM_011930	ENSMUSG00000036636	Clcn7	ClC-7|D17Wsu51e	chloride channel, voltage-sensitive 7	protein-coding
mm_21933.1	chr2	167056756	167056772	-	1	NA	exon (NM_001033196, exon 3 of 14)	exon (NM_001033196, exon 3 of 14)	-6170	NR_138563	68949	Mm.391959	NM_001081005		Zfas1	1500012F01Rik|Zfos1	zinc finger, NFX1-type containing 1, antisense RNA 1	ncRNA
mm_59605.1	chr7	28140196	28140216	+	1	NA	exon (NM_001164655, exon 5 of 20)	exon (NM_001164655, exon 5 of 20)	10740	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_972.1	chr1	58392864	58392879	+	1	NA	promoter-TSS (NM_025824)	promoter-TSS (NM_025824)	-265	NM_025824	66882	Mm.21848	NM_025824	ENSMUSG00000051223	Bzw1	1200015E15Rik|mKIAA0005	basic leucine zipper and W2 domains 1	protein-coding
mm_120.1	chr1	9798124	9798216	+	1	NA	promoter-TSS (NM_133220)	promoter-TSS (NM_133220)	40	NM_177547	170755	Mm.336410	NM_133220	ENSMUSG00000025915	Sgk3	2510015P22Rik|A330005P07Rik|Cisk|fy|fz	serum/glucocorticoid regulated kinase 3	protein-coding
mm_68304.1	chr7	105746535	105746587	-	1	NA	3' UTR (NM_009906, exon 13 of 13)	3' UTR (NM_009906, exon 13 of 13)	-2223	NM_020024	24075	Mm.274846	NM_020024	ENSMUSG00000043866	Taf10	30kDa|AU041226|TAFII30|Taf2h	TATA-box binding protein associated factor 10	protein-coding
mm_123555.1	chr14	66846520	66846535	-	1	NA	intron (NM_009955, intron 3 of 13)	intron (NM_009955, intron 3 of 13)	22073	NM_009955	12934	Mm.352648	NM_009955	ENSMUSG00000022048	Dpysl2	AI851130|Crmp2|DRP2|Musunc33|TOAD-64|Ulip2	dihydropyrimidinase-like 2	protein-coding
mm_139635.1	chr17	57375981	57375991	+	1	NA	intron (NM_010130, intron 2 of 21)	Lx4A|LINE|L1	17300	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_105036.1	chr11	100583091	100583097	-	1	NA	3' UTR (NM_019795, exon 14 of 14)	3' UTR (NM_019795, exon 14 of 14)	7203	NM_001146318	12799	Mm.15711	NM_009923	ENSMUSG00000006782	Cnp	CNPase|Cnp-1|Cnp1	2',3'-cyclic nucleotide 3' phosphodiesterase	protein-coding
mm_39119.1	chr4	154946444	154946446	-	1	NA	Intergenic	Intergenic	-14478	NM_010419	15208	Mm.137268	NM_010419	ENSMUSG00000048001	Hes5	bHLHb38	hairy and enhancer of split 5 (Drosophila)	protein-coding
mm_4919.1	chr1	190911866	190911873	+	1	NA	promoter-TSS (NM_178775)	promoter-TSS (NM_178775)	-99	NM_178775	320119	Mm.220912	NM_178775	ENSMUSG00000089872	Rps6kc1	AA682037|B130003F20Rik|C80612|Rpk118	ribosomal protein S6 kinase polypeptide 1	protein-coding
mm_45980.1	chr5	90474670	90474705	-	1	NA	exon (NM_009654, exon 13 of 15)	exon (NM_009654, exon 13 of 15)	13817	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_51062.1	chr6	65797508	65797528	+	1	NA	intron (NM_029549, intron 2 of 10)	RLTR11B|LTR|ERVK	18556	NM_029549	70779	Mm.263355	NM_027547	ENSMUSG00000029913	Prdm5	4432417F03Rik|6530401I24Rik|AI197291|E130112L17Rik|PFM2	PR domain containing 5	protein-coding
mm_110480.1	chr12	51865871	51865883	-	1	NA	Intergenic	Intergenic	-36341	NM_144788	207304	Mm.249391	NM_144788	ENSMUSG00000035247	Hectd1	A630086P08Rik|AI844876|b2b327Clo|opm	HECT domain containing 1	protein-coding
mm_87713.1	chr10	60062431	60062470	+	1	NA	intron (NM_026937, intron 7 of 10)	intron (NM_026937, intron 7 of 10)	-43807	NM_052994	94214	Mm.153429	NM_052994	ENSMUSG00000058297	Spock2	AA407235|Gcap26|mKIAA0275	sparc/osteonectin, cwcv and kazal-like domains proteoglycan 2	protein-coding
mm_73957.1	chr8	120372318	120372329	+	1	NA	Intergenic	Intergenic	-116543	NM_198671	382034	Mm.334856	NM_198671	ENSMUSG00000031822	Gse1	2210013I18Rik|mKIAA0182	genetic suppressor element 1, coiled-coil protein	protein-coding
mm_135882.1	chr16	64479235	64479240	-	1	NA	promoter-TSS (NM_173861)	promoter-TSS (NM_173861)	-103	NM_173861	224291	Mm.246580	NM_173861	ENSMUSG00000068167	Csnka2ip	Ckt2	casein kinase 2, alpha prime interacting protein	protein-coding
mm_42174.1	chr5	112261742	112261746	+	1	NA	intron (NM_023695, intron 3 of 5)	intron (NM_023695, intron 3 of 5)	5924	NM_001312893	12960	Mm.29488	NM_023695	ENSMUSG00000029343	Crybb1	3110006K12Rik|BB1CRY	crystallin, beta B1	protein-coding
mm_44040.1	chr5	147519698	147519720	+	1	NA	exon (NM_028291, exon 6 of 19)	exon (NM_028291, exon 6 of 19)	89129	NM_028291	72587	Mm.320469	NM_028291	ENSMUSG00000029647	Pan3	2700050F09Rik|A430027N15Rik|AU014670	PAN3 poly(A) specific ribonuclease subunit	protein-coding
mm_5753.1	chr1	46853610	46853630	-	1	NA	promoter-TSS (NM_172653)	promoter-TSS (NM_172653)	-111	NM_172653	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|mKIAA1265	solute carrier family 39 (zinc transporter), member 10	protein-coding
mm_65606.1	chr7	27396571	27396615	-	1	NA	promoter-TSS (NM_001199234)	promoter-TSS (NM_001199234)	-40	NM_001199236	80297	Mm.459123	NM_032610	ENSMUSG00000011751	Sptbn4	1700022P15Rik|5830426A08Rik|ROSA62|SpbIV|Spnb4|dyn|lnd|nmf261|nmf379|qv	spectrin beta, non-erythrocytic 4	protein-coding
mm_30761.1	chr4	15881256	15881272	+	1	NA	promoter-TSS (NM_009788)	promoter-TSS (NM_009788)	0	NM_009788	12307	Mm.277665	NM_009788	ENSMUSG00000028222	Calb1	Brain-2|CB|Calb|Calb-1	calbindin 1	protein-coding
mm_70811.1	chr8	23062452	23062453	+	1	NA	intron (NR_102385, intron 1 of 45)	intron (NR_102385, intron 1 of 45)	4193	NR_102385	11733	Mm.334444	NM_031158	ENSMUSG00000031543	Ank1	Ank-1|nb|pale	ankyrin 1, erythroid	protein-coding
mm_7299.1	chr1	97976956	97976991	-	1	NA	5' UTR (NM_013626, exon 2 of 26)	5' UTR (NM_013626, exon 2 of 26)	70820	NR_037993	78603	Mm.442597	NR_037993	ENSMUSG00000089706	B230216N24Rik	-	RIKEN cDNA B230216N24 gene	ncRNA
mm_102020.1	chr11	51644342	51644352	-	1	NA	exon (NM_145974, exon 4 of 5)	exon (NM_145974, exon 4 of 5)	-6607	NR_027958	97775	Mm.220299	NM_175289	ENSMUSG00000052563	D930048N14Rik	AI315703|R75254	RIKEN cDNA D930048N14 gene	ncRNA
mm_91183.1	chr10	20952161	20952190	-	1	NA	promoter-TSS (NM_026203)	promoter-TSS (NM_026203)	-372	NM_026203	52906	Mm.253280	NM_026203	ENSMUSG00000019986	Ahi1	1700015F03Rik|Ahi-1|D10Bwg0629e	Abelson helper integration site 1	protein-coding
mm_18243.1	chr2	52186082	52186092	-	1	NA	exon (NM_010889, exon 123 of 157)	exon (NM_010889, exon 123 of 157)	-104915	NR_040620	78049	Mm.243883	NR_040620		4930573O16Rik	-	RIKEN cDNA 4930573O16 gene	ncRNA
mm_129873.1	chr15	83423760	83423770	-	1	NA	intron (NM_001159509, intron 1 of 10)	intron (NM_001159509, intron 1 of 10)	9085	NM_011862	23970	Mm.23978	NM_011862	ENSMUSG00000016664	Pacsin2	AI197433	protein kinase C and casein kinase substrate in neurons 2	protein-coding
mm_71430.1	chr8	46492928	46492946	+	1	NA	exon (NM_007981, exon 2 of 21)	exon (NM_007981, exon 2 of 21)	1971	NM_001302163	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_71456.1	chr8	46521818	46521828	+	1	NA	intron (NM_001302163, intron 11 of 20)	Lx7|LINE|L1	-30246	NM_027973	71876	Mm.22108	NM_027973	ENSMUSG00000031629	Cenpu	1700029A22Rik|Mlf1ip	centromere protein U	protein-coding
mm_158824.1	chrX	167446572	167446587	-	1	NA	Intergenic	Intergenic	-63830	NM_001313758	110639	Mm.272955	NM_026662	ENSMUSG00000025742	Prps2	2610101M19Rik|AA589463|AI464149|Prps-2	phosphoribosyl pyrophosphate synthetase 2	protein-coding
mm_165832.1	chr3	152252871	152252913	+	1	NA	exon (NM_199465, exon 4 of 13)	exon (NM_199465, exon 4 of 13)	13428	NM_199465	68810	Mm.200188	NM_199465	ENSMUSG00000039103	Nexn	1110046H09Rik|AA553326|NELIN	nexilin	protein-coding
mm_44608.1	chr5	25330631	25330636	-	1	NA	intron (NM_001081383, intron 28 of 58)	intron (NM_001081383, intron 28 of 58)	107740	NM_144908	231050	Mm.21814	NM_144908	ENSMUSG00000038072	Galnt11	A430075I06Rik|AI648252|E430002F06Rik	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 11	protein-coding
mm_50483.1	chr6	48988505	48988507	+	1	NA	exon (NM_172888, exon 1 of 5)	exon (NM_172888, exon 1 of 5)	1645	NM_172888	243377	Mm.446302	NM_172888	ENSMUSG00000039215	Svs1	9530003A11	seminal vesicle secretory protein 1	protein-coding
mm_44079.1	chr5	149068453	149068466	+	1	NA	Intergenic	Intergenic	-15402	NM_010439	15289	Mm.207047	NM_010439	ENSMUSG00000066551	Hmgb1	HMG-1|Hmg1|SBP-1|p30	high mobility group box 1	protein-coding
mm_59809.1	chr7	29170205	29170224	+	1	NA	promoter-TSS (NM_182696)	promoter-TSS (NM_182696)	4	NM_182694	243897	Mm.389886	NM_182694	ENSMUSG00000031493	Ggn	AI593290	gametogenetin	protein-coding
mm_26782.1	chr3	9004761	9004771	-	1	NA	promoter-TSS (NM_009412)	promoter-TSS (NM_009412)	-251	NM_001025264	21985	Mm.371590	NM_009412	ENSMUSG00000027506	Tpd52	AI043038|mD52	tumor protein D52	protein-coding
mm_84765.1	chr9	75611105	75611182	-	1	NA	5' UTR (NM_016711, exon 1 of 10)	5' UTR (NM_016711, exon 1 of 10)	182	NM_016711	50876	Mm.291880	NM_016711	ENSMUSG00000032186	Tmod2	N-Tmod|NTMOD	tropomodulin 2	protein-coding
mm_9946.1	chr1	190911804	190911810	-	1	NA	promoter-TSS (NM_178775)	promoter-TSS (NM_178775)	-37	NM_178775	320119	Mm.220912	NM_178775	ENSMUSG00000089872	Rps6kc1	AA682037|B130003F20Rik|C80612|Rpk118	ribosomal protein S6 kinase polypeptide 1	protein-coding
mm_36981.1	chr4	109661261	109661275	-	1	NA	exon (NM_007671, exon 2 of 2)	exon (NM_007671, exon 2 of 2)	4104	NM_007671	12580	Mm.1912	NM_007671	ENSMUSG00000028551	Cdkn2c	C77269|INK4c|p18|p18-INK4c|p18-INK6|p18INK4c	cyclin-dependent kinase inhibitor 2C (p18, inhibits CDK4)	protein-coding
mm_91359.1	chr10	28985315	28985323	-	1	NA	intron (NM_026336, intron 1 of 5)	intron (NM_026336, intron 1 of 5)	987	NM_026336	67719	Mm.440480	NM_026336	ENSMUSG00000015519	2310057J18Rik	2210414P04Rik|Leg1	RIKEN cDNA 2310057J18 gene	protein-coding
mm_58322.1	chr6	146501995	146502033	-	1	NA	5' UTR (NM_019923, exon 1 of 57)	5' UTR (NM_019923, exon 1 of 57)	209	NM_010586	16439	Mm.7800	NM_010586	ENSMUSG00000030287	Itpr2	AI649341|InsP3R-2|InsP3R-5|Ip3r2|Itpr5|insP3R2	inositol 1,4,5-triphosphate receptor 2	protein-coding
mm_100387.1	chr11	119355552	119355612	+	1	NA	promoter-TSS (NM_018822)	promoter-TSS (NM_018822)	25	NM_178743	268512	Mm.31869	NM_178743	ENSMUSG00000039908	Slc26a11	F630021I08Rik	solute carrier family 26, member 11	protein-coding
mm_129085.1	chr15	75901496	75901513	-	1	NA	intron (NM_001285429, intron 1 of 7)	intron (NM_001285429, intron 1 of 7)	-7023	NM_172607	223646	Mm.288368	NM_172607	ENSMUSG00000022574	Naprt	9130210N20Rik|Naprt1	nicotinate phosphoribosyltransferase	protein-coding
mm_99330.1	chr11	101460125	101460140	+	1	NA	3' UTR (NM_012037, exon 6 of 6)	3' UTR (NM_012037, exon 6 of 6)	6067	NM_012037	26949	Mm.29210	NM_012037	ENSMUSG00000034993	Vat1	VAT-1	vesicle amine transport 1	protein-coding
mm_171156.1	chr3	22081226	22081234	-	1	NA	intron (NM_030732, intron 1 of 15)	intron (NM_030732, intron 1 of 15)	4578	NM_030732	81004	Mm.202966	NM_030732	ENSMUSG00000027630	Tbl1xr1	8030499H02Rik|A630076E03Rik|AW539987|C21|C230089I12Rik|DC42|Ira1|TBLR1	transducin (beta)-like 1X-linked receptor 1	protein-coding
mm_34224.1	chr4	140995557	140995583	+	1	NA	exon (NM_029097, exon 8 of 29)	exon (NM_029097, exon 8 of 29)	8697	NM_001164366	74772	Mm.205625	NM_029097	ENSMUSG00000036622	Atp13a2	1110012E06Rik|AA589443	ATPase type 13A2	protein-coding
mm_106420.1	chr11	119228462	119228504	-	1	NA	promoter-TSS (NM_172443)	promoter-TSS (NM_172443)	16	NM_001347625	207592	Mm.205263	NM_172443	ENSMUSG00000039976	Tbc1d16	B930087K01|BC026530|Tcd1d16	TBC1 domain family, member 16	protein-coding
mm_123836.1	chr14	70630196	70630206	-	1	NA	promoter-TSS (NM_013514)	promoter-TSS (NM_013514)	-47	NM_013514	13829	Mm.210863	NM_013514	ENSMUSG00000022099	Dmtn	AI325486|Epb4.9|Epb49|dematin	dematin actin binding protein	protein-coding
mm_131814.1	chr16	22920278	22920311	+	1	NA	promoter-TSS (NM_021564)	promoter-TSS (NM_021564)	72	NM_001083904	59083	Mm.28461	NM_021564	ENSMUSG00000022871	Fetub	2310011O17Rik|AI255764|D17980|Gugu	fetuin beta	protein-coding
mm_52072.1	chr6	97826937	97826969	+	1	NA	intron (NM_001113198, intron 1 of 9)	intron (NM_001113198, intron 1 of 9)	19895	NM_001113198	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_94304.1	chr11	4161095	4161119	+	1	NA	promoter-TSS (NM_177616)	promoter-TSS (NM_177616)	753	NM_026175	67465	Mm.156914	NM_026175	ENSMUSG00000002129	Sf3a1	1200014H24Rik|5930416L09Rik|AI159724	splicing factor 3a, subunit 1	protein-coding
mm_136152.1	chr16	87654292	87654298	-	1	NA	Intergenic	Intergenic	-44659	NM_007520	12013	Mm.26147	NM_007520	ENSMUSG00000025612	Bach1	6230421P05Rik|AI323795	BTB and CNC homology 1, basic leucine zipper transcription factor 1	protein-coding
mm_151119.1	chr19	47864709	47864717	+	1	NA	promoter-TSS (NM_030051)	promoter-TSS (NM_030051)	-832	NM_030051	68214	Mm.63791	NM_026619	ENSMUSG00000025069	Gsto2	1700020F09Rik|4930425C18Rik|GSTO 2-2	glutathione S-transferase omega 2	protein-coding
mm_46695.1	chr5	110097485	110097492	-	1	NA	Intergenic	Intergenic	-2481	NM_207279	403178	Mm.297057	NM_207279	ENSMUSG00000064247	Plcxd1	A330045H12Rik|Gm576	phosphatidylinositol-specific phospholipase C, X domain containing 1	protein-coding
mm_102771.1	chr11	68270954	68270961	-	1	NA	intron (NM_008744, intron 3 of 6)	intron (NM_008744, intron 3 of 6)	50065	NR_105833	102465219		NR_105833	ENSMUSG00000099174	Mir6406	Gm27981|mmu-mir-6406	microRNA 6406	ncRNA
mm_84085.1	chr9	58202748	58202772	-	1	NA	promoter-TSS (NM_177193)	promoter-TSS (NM_177193)	-137	NR_033522	665268	Mm.451475	NR_033522	ENSMUSG00000057818	1600029O15Rik	-	ribosomal protein L17 pseudogene	pseudo
mm_139074.1	chr17	46650643	46650661	+	1	NA	TTS (NM_001316742)	TTS (NM_001316742)	314	NM_025611	66515	Mm.329078	NM_025611	ENSMUSG00000038545	Cul7	2510004L20Rik|AA409809|C230011P08Rik|p185|p193	cullin 7	protein-coding
mm_3841.1	chr1	160044565	160044590	+	1	NA	non-coding (NR_028111, exon 1 of 3)	non-coding (NR_028111, exon 1 of 3)	197	NM_001162896	67647	Mm.171518	NM_001024470	ENSMUSG00000090394	4930523C07Rik	-	RIKEN cDNA 4930523C07 gene	protein-coding
mm_70062.1	chr7	142652254	142652265	-	1	NA	3' UTR (NM_010514, exon 4 of 4)	3' UTR (NM_010514, exon 4 of 4)	2737	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_26978.1	chr3	25431720	25431723	-	1	NA	TTS (NM_138666)	TTS (NM_138666)	-647715	NM_001326288	635702	Mm.448351	NM_001326288	ENSMUSG00000102758	Naaladl2	2810043G22Rik|EG635702|Gm1021	N-acetylated alpha-linked acidic dipeptidase-like 2	protein-coding
mm_112145.1	chr12	113215021	113215054	-	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	29134	NM_153776	69195	Mm.313244	NM_153776	ENSMUSG00000049036	Tmem121	2410008J05Rik|Hole	transmembrane protein 121	protein-coding
mm_88945.1	chr10	81328687	81328704	+	1	NA	promoter-TSS (NM_009325)	promoter-TSS (NM_009325)	-8	NM_009325	21390	Mm.4545	NM_009325	ENSMUSG00000034881	Tbxa2r	TP|TXA2-R	thromboxane A2 receptor	protein-coding
mm_64711.1	chr7	4628538	4628550	-	1	NA	exon (NM_023440, exon 3 of 3)	exon (NM_023440, exon 3 of 3)	1938	NM_023440	68255	Mm.389784	NM_023440	ENSMUSG00000045282	Tmem86b	C330014O21Rik	transmembrane protein 86B	protein-coding
mm_66970.1	chr7	63212543	63212570	-	1	NA	promoter-TSS (NM_007390)	promoter-TSS (NM_007390)	-30	NM_007390	11441	Mm.113464	NM_007390	ENSMUSG00000030525	Chrna7	Acra7|alpha7|nAchR	cholinergic receptor, nicotinic, alpha polypeptide 7	protein-coding
mm_42466.1	chr5	115453867	115453884	+	1	NA	3' UTR (NM_008629, exon 15 of 15)	3' UTR (NM_008629, exon 15 of 15)	-12391	NM_011107	18778	Mm.20190	NM_011107	ENSMUSG00000029522	Pla2g1b	Pla2a|sPLA2IB	phospholipase A2, group IB, pancreas	protein-coding
mm_166416.1	chr5	137151593	137151605	-	1	NA	Intergenic	Intergenic	-35392	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_22192.1	chr2	173276448	173276452	-	1	NA	promoter-TSS (NM_022995)	promoter-TSS (NM_022995)	83	NM_022995	65112	Mm.73682	NM_022995	ENSMUSG00000038400	Pmepa1	2210418I02Rik|AW455466|Erg1.2|N4wbp4|Stag1|Tmepai	prostate transmembrane protein, androgen induced 1	protein-coding
mm_2135.1	chr1	88070766	88070797	+	1	NA	promoter-TSS (NM_201644)	promoter-TSS (NM_201644)	2	NM_201644	394434	Mm.300095	NM_201644	ENSMUSG00000090175	Ugt1a9	UDPGT|UDPGT 1-9|UGT1-09|UGT1.9|UGTP4|Ugt1a12|mUGTBr/P	UDP glucuronosyltransferase 1 family, polypeptide A9	protein-coding
mm_149983.1	chr19	29151713	29151716	+	1	NA	Intergenic	Intergenic	16435	NR_029778	724062		NR_029778	ENSMUSG00000065556	Mir101b	Mirn101b|mir-101b	microRNA 101b	ncRNA
mm_101542.1	chr11	33529768	33529794	-	1	NA	Intergenic	Intergenic	-16035	NM_023146	66011	Mm.383775	NM_023146	ENSMUSG00000040594	Ranbp17	-	RAN binding protein 17	protein-coding
mm_157338.1	chrX	36807788	36807838	-	1	NA	Intergenic	CpG	9387	NR_131979	69591	Mm.482947	NR_131979	ENSMUSG00000097468	Mdrl	2310010G23Rik	mitochondrial dynamic related lncRNA	ncRNA
mm_49989.1	chr6	41047072	41047085	+	1	NA	Intergenic	Intergenic	-11569	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_156203.1	chrX	134427036	134427054	+	1	NA	intron (NM_010078, intron 2 of 22)	intron (NM_010078, intron 2 of 22)	22265	NM_010078	13497	Mm.121662	NM_010078	ENSMUSG00000000223	Drp2	AW495265|DRP-2	dystrophin related protein 2	protein-coding
mm_94265.1	chr11	3516830	3516876	+	1	NA	TTS (NM_001284429)	TTS (NM_001284429)	2169	NM_053267	114679	Mm.34046	NM_053267	ENSMUSG00000075702	Selenom	1500040L08Rik|A230103K18|Selm|Sepm	selenoprotein M	protein-coding
mm_170850.1	chr2	177840332	177840340	-	1	NA	promoter-TSS (NM_001024849)	promoter-TSS (NM_001024849)	0	NM_001024849	329575	Mm.425123	NM_001024849	ENSMUSG00000095362	Gm14325	OTTMUSG00000016325	predicted gene 14325	protein-coding
mm_84663.1	chr9	71896104	71896108	-	1	NA	promoter-TSS (NM_001253864)	promoter-TSS (NM_001253864)	-10	NM_001253863	21406	Mm.171615	NM_011544	ENSMUSG00000032228	Tcf12	A130037E08Rik|ALF1|HEB|HEBAlt|HTF-4|HTF4|ME1|REB|bHLHb20	transcription factor 12	protein-coding
mm_170116.1	chr17	39846273	39846282	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	3280	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_45329.1	chr5	65492926	65492970	-	1	NA	promoter-TSS (NM_133697)	promoter-TSS (NM_133697)	-113	NM_133697	68552	Mm.10709	NM_133697	ENSMUSG00000037822	Smim14	1110003E01Rik|1700127H04Rik|5430439C17Rik|MAd4	small integral membrane protein 14	protein-coding
mm_27554.1	chr3	58522394	58522429	-	1	NA	3' UTR (NM_030685, exon 3 of 3)	3' UTR (NM_030685, exon 3 of 3)	-3410	NM_001005509	229317	Mm.21617	NM_001005509	ENSMUSG00000027810	Eif2a	D030048D22|D3Ertd194e	eukaryotic translation initiation factor 2A	protein-coding
mm_156024.1	chrX	107149061	107149072	+	1	NA	promoter-TSS (NM_175442)	promoter-TSS (NM_175442)	139	NM_001122596	213438	Mm.265244	NM_175442	ENSMUSG00000054293	A630033H20Rik	AI662791|P2ry10	RIKEN cDNA A630033H20 gene	protein-coding
mm_36946.1	chr4	108834240	108834254	-	1	NA	promoter-TSS (NM_027453)	promoter-TSS (NM_027453)	-431	NM_025334	66073	Mm.159965	NM_025334	ENSMUSG00000028567	Txndc12	0610040B21Rik|ERp16|ERp19	thioredoxin domain containing 12 (endoplasmic reticulum)	protein-coding
mm_62760.1	chr7	112083117	112083141	+	1	NA	exon (NM_177249, exon 14 of 29)	exon (NM_177249, exon 14 of 29)	59623	NM_177249	74996	Mm.16974	NM_133758	ENSMUSG00000059263	Usp47	4930502N04Rik|A630020C16Rik	ubiquitin specific peptidase 47	protein-coding
mm_87635.1	chr10	58351893	58351943	+	1	NA	intron (NM_026148, intron 1 of 9)	intron (NM_026148, intron 1 of 9)	-19536	NM_201242	110829	Mm.57734	NM_026148	ENSMUSG00000019920	Lims1	2310016J22Rik|4921524A02Rik|AI507642|AU021743|AW551584|C430041B13Rik|Lims1l|PINCH|PINCH1	LIM and senescent cell antigen-like domains 1	protein-coding
mm_157036.1	chrX	7947820	7947832	-	1	NA	promoter-TSS (NM_010413)	promoter-TSS (NM_010413)	63	NM_001130416	15185	Mm.29854	NM_010413	ENSMUSG00000031161	Hdac6	Hd6|Hdac5|Sfc6|mHDA2	histone deacetylase 6	protein-coding
mm_112495.1	chr13	6604980	6605008	+	1	NA	exon (NM_001291071, exon 10 of 22)	exon (NM_001291071, exon 10 of 22)	43777	NM_019703	56421	Mm.273874	NM_019703	ENSMUSG00000021196	Pfkp	1200015H23Rik|9330125N24Rik|ATP-PFK|PFK-C|PFK-P	phosphofructokinase, platelet	protein-coding
mm_164324.1	chr16	5305324	5305327	+	1	NA	Intergenic	B4A|SINE|B4	-49369	NM_027446	70511	Mm.45780	NM_027446	ENSMUSG00000022544	Eef2kmt	5730409G15Rik|Fam86|Fam86a|eEF2-KMT	eukaryotic elongation factor 2 lysine methyltransferase	protein-coding
mm_58590.1	chr7	5015423	5015442	+	1	NA	promoter-TSS (NM_001110329)	promoter-TSS (NM_001110329)	-76	NM_025324	66056	Mm.19974	NM_025324	ENSMUSG00000051184	Zfp524	0610012F07Rik|2300009P13Rik|Znf524	zinc finger protein 524	protein-coding
mm_117734.1	chr13	95618663	95618669	-	1	NA	promoter-TSS (NM_010169)	promoter-TSS (NM_010169)	-233	NM_010169	14062	Mm.24816	NM_010169	ENSMUSG00000048376	F2r	AI482343|Cf2r|Par1|ThrR	coagulation factor II (thrombin) receptor	protein-coding
mm_83936.1	chr9	56636032	56636036	-	1	NA	promoter-TSS (NM_001311076)	promoter-TSS (NM_001311076)	-386	NM_001311076	235402	Mm.246605	NM_181074	ENSMUSG00000049556	Lingo1	4930471K13Rik|AV148400|LERN1|LINGO-1|Lrrn6a|UNQ201	leucine rich repeat and Ig domain containing 1	protein-coding
mm_93618.1	chr10	117277604	117277636	-	1	NA	TTS (NM_017372)	TTS (NM_017372)	4652	NM_017372	17105	Mm.45436	NM_017372	ENSMUSG00000069516	Lyz2	AI326280|Lys|Lysm|Lyzf2|Lyzs|Lzm|Lzm-s1|Lzp	lysozyme 2	protein-coding
mm_36736.1	chr4	99655086	99655116	-	1	NA	Intergenic	Intergenic	-1198	NM_010425	15221	Mm.4758	NM_010425	ENSMUSG00000067261	Foxd3	CWH3|Genesis|Hfh2	forkhead box D3	protein-coding
mm_34546.1	chr4	149545103	149545136	+	1	NA	promoter-TSS (NM_001141930)	promoter-TSS (NM_001141930)	2	NM_001141930	67087	Mm.299735	NM_023465	ENSMUSG00000028988	Ctnnbip1	1110008O09Rik|2310001I19Rik|AW457332|Catnbip1|Icat	catenin beta interacting protein 1	protein-coding
mm_3558.1	chr1	150423878	150423897	+	1	NA	exon (NM_133780, exon 27 of 52)	exon (NM_133780, exon 27 of 52)	-30832	NM_145511	226499	Mm.222093	NM_145511	ENSMUSG00000006010	BC003331	1810053E15Rik|Odr4|odr-4	cDNA sequence BC003331	protein-coding
mm_7018.1	chr1	86582501	86582565	-	1	NA	promoter-TSS (NM_008801)	promoter-TSS (NM_008801)	-32	NM_008801	18582	Mm.12925	NM_008801	ENSMUSG00000026239	Pde6d	AI841218|PrBP/delta	phosphodiesterase 6D, cGMP-specific, rod, delta	protein-coding
mm_163220.1	chr11	101593982	101593987	-	1	NA	Intergenic	Intergenic	11742	NM_144830	217203	Mm.280559	NM_144830	ENSMUSG00000034947	Tmem106a	0610008L10Rik|AI043106|BC022145	transmembrane protein 106A	protein-coding
mm_25925.1	chr3	131189272	131189276	+	1	NA	intron (NM_001276403, intron 4 of 11)	(T)n|Simple_repeat|Simple_repeat	76483	NM_001276403	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_156712.1	chrX	159627535	159627546	+	1	NA	5' UTR (NM_001135727, exon 1 of 18)	5' UTR (NM_001135727, exon 1 of 18)	268	NM_001135727	58194	Mm.286495	NM_021389	ENSMUSG00000040990	Sh3kbp1	1200007H22Rik|1700125L08Rik|5830464D22Rik|AI447724|Cin85|IN85|Ruk|Seta	SH3-domain kinase binding protein 1	protein-coding
mm_167153.1	chr7	131322397	131322407	-	1	NA	promoter-TSS (NM_008411)	promoter-TSS (NM_008411)	-110	NM_008411	16433	Mm.142717	NM_008411	ENSMUSG00000040205	Cuzd1	Erg-1|Itmap1|Uo-44|Usg|Utczp	CUB and zona pellucida-like domains 1	protein-coding
mm_32445.1	chr4	107314352	107314362	+	1	NA	promoter-TSS (NM_001205156)	promoter-TSS (NM_001205156)	-6	NM_145550	230584	Mm.29118	NM_145550	ENSMUSG00000057375	Yipf1	C030002N13Rik	Yip1 domain family, member 1	protein-coding
mm_28585.1	chr3	94377237	94377250	-	1	NA	promoter-TSS (NM_001293734)	promoter-TSS (NM_001293734)	-189	NM_001293734	19885	Mm.4372	NM_011281	ENSMUSG00000028150	Rorc	Nr1f3|RORgamma|TOR|Thor	RAR-related orphan receptor gamma	protein-coding
mm_51520.1	chr6	83156460	83156514	+	1	NA	promoter-TSS (NM_023790)	promoter-TSS (NM_023790)	83	NM_027948	71837	Mm.17621	NM_027948	ENSMUSG00000030030	1700003E16Rik	AU041756	RIKEN cDNA 1700003E16 gene	protein-coding
mm_91532.1	chr10	37321319	37321338	-	1	NA	Intergenic	Intergenic	-182402	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_149669.1	chr19	18840607	18840618	+	1	NA	intron (NM_153417, intron 25 of 38)	MTEa|LTR|ERVL-MaLR	90629	NM_153417	225997	Mm.215171	NM_153417	ENSMUSG00000024727	Trpm6	CHAK2|TRPM6/CHAK2	transient receptor potential cation channel, subfamily M, member 6	protein-coding
mm_95976.1	chr11	58963762	58963771	+	1	NA	promoter-TSS (NM_031172)	promoter-TSS (NM_031172)	-15	NM_031172	56631	Mm.179733	NM_031172	ENSMUSG00000036964	Trim17	Rnf16|terf	tripartite motif-containing 17	protein-coding
mm_523.1	chr1	37614410	37614420	+	1	NA	intron (NM_028096, intron 8 of 9)	intron (NM_028096, intron 8 of 9)	-73399	NM_173870	269181	Mm.25861	NM_173870	ENSMUSG00000026110	Mgat4a	9530018I07Rik|GnT-IVa|glcNAc-T-IVa	mannoside acetylglucosaminyltransferase 4, isoenzyme A	protein-coding
mm_33115.1	chr4	124741845	124741884	+	1	NA	promoter-TSS (NM_008385)	promoter-TSS (NM_008385)	14	NR_126474	16330	Mm.296202	NM_008385	ENSMUSG00000028894	Inpp5b	5PTase|AW260155|INPP5P	inositol polyphosphate-5-phosphatase B	protein-coding
mm_108137.1	chr12	76111359	76111361	+	1	NA	TTS (NM_001005510)	TTS (NM_001005510)	65899	NM_010157	13983	Mm.2561	NM_010157	ENSMUSG00000021055	Esr2	ER[b]|ERbeta|Estrb	estrogen receptor 2 (beta)	protein-coding
mm_118435.1	chr14	8016635	8016680	+	1	NA	intron (NM_001331064, intron 1 of 8)	intron (NM_001331064, intron 1 of 8)	13691	NM_001331064	66082	Mm.181473	NM_025341	ENSMUSG00000025277	Abhd6	0610041D24Rik|AA673485|AV065425	abhydrolase domain containing 6	protein-coding
mm_10463.1	chr2	14314281	14314300	+	1	NA	intron (NM_008625, intron 21 of 29)	intron (NM_008625, intron 21 of 29)	53287	NR_030609	100124488		NR_030609	ENSMUSG00000077897	Mir511	Mirn511|mir-511|mmu-mir-511	microRNA 511	ncRNA
mm_82103.1	chr9	123067119	123067124	+	1	NA	3' UTR (NM_177911, exon 14 of 14)	3' UTR (NM_177911, exon 14 of 14)	32380	NM_177911	331046	Mm.195309	NM_177911	ENSMUSG00000025787	Tgm4	9530008N10Rik|Eapa1|TGP	transglutaminase 4 (prostate)	protein-coding
mm_124545.1	chr14	122473536	122473558	-	1	NA	intron (NR_045046, intron 2 of 4)	intron (NR_045046, intron 2 of 4)	1652	NR_045046	69248	Mm.235369	NR_045046	ENSMUSG00000085555	2610035F20Rik	-	RIKEN cDNA 2610035F20 gene	ncRNA
mm_93482.1	chr10	111995892	111995902	-	1	NA	intron (NM_028608, intron 1 of 5)	L1M|LINE|L1	1367	NM_028608	73690	Mm.173790	NM_028608	ENSMUSG00000056888	Glipr1	2410114O14Rik|RTVP-1|RTVP1|mRTVP-1	GLI pathogenesis-related 1 (glioma)	protein-coding
mm_23797.1	chr3	79842760	79842785	+	1	NA	promoter-TSS (NM_027495)	promoter-TSS (NM_027495)	-110	NM_027495	70652	Mm.46635	NM_027495	ENSMUSG00000027956	Tmem144	1110057I03Rik|5730537D05Rik	transmembrane protein 144	protein-coding
mm_138485.1	chr17	35195972	35195978	+	1	NA	TTS (NR_105939)	TTS (NR_105939)	1003	NR_105939	102465588		NR_105939	ENSMUSG00000098291	Mir6973a	Gm27967|mmu-mir-6973a	microRNA 6973a	ncRNA
mm_156051.1	chrX	109095448	109095476	+	1	NA	promoter-TSS (NM_019989)	promoter-TSS (NM_019989)	55	NM_019989	56726	Mm.260760	NM_019989	ENSMUSG00000031246	Sh3bgrl	1190008F14Rik	SH3-binding domain glutamic acid-rich protein like	protein-coding
mm_42804.1	chr5	121738832	121738864	+	1	NA	intron (NM_009125, intron 1 of 24)	L1MC5|LINE|L1	27239	NM_009125	20239	Mm.260900	NM_009125	ENSMUSG00000042605	Atxn2	9630045M23Rik|ATX2|AW544490|Sca2	ataxin 2	protein-coding
mm_162005.1	chr19	40612531	40612531	+	1	NA	promoter-TSS (NM_026260)	promoter-TSS (NM_026260)	165	NM_001304721	12495	Mm.2824	NM_009848	ENSMUSG00000048120	Entpd1	2610206B08Rik|AA408691|Cd39|NTPDase-1	ectonucleoside triphosphate diphosphohydrolase 1	protein-coding
mm_41872.1	chr5	104508399	104508410	+	1	NA	promoter-TSS (NM_001166581)	promoter-TSS (NM_001166581)	52	NM_001166581	100042165	Mm.482189	NM_001166581	ENSMUSG00000079065	BC005561	-	cDNA sequence BC005561	protein-coding
mm_152327.1	chr19	9947988	9947996	-	1	NA	Intergenic	Intergenic	-32608	NR_073181	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
mm_145980.1	chr18	68059698	68059710	+	1	NA	intron (NM_172631, intron 1 of 5)	IMPB_01|Satellite|Satellite	126447	NM_172631	52662	Mm.440183	NM_172631	ENSMUSG00000024544	Ldlrad4	8230401C20Rik|A430083H02|A430108L08Rik|C18orf1|D18Ertd653e|D330030L18Rik	low density lipoprotein receptor class A domain containing 4	protein-coding
mm_47415.1	chr5	123139074	123139090	-	1	NA	Intergenic	CpG	-3111	NM_001040398	208043	Mm.250391	NM_177581	ENSMUSG00000038384	Setd1b	AA516740|BC035291|KMT2G|mKIAA1076	SET domain containing 1B	protein-coding
mm_146407.1	chr18	83996325	83996329	+	1	NA	Intergenic	Intergenic	90235	NM_001081300	110796	Mm.102136	NM_001081300	ENSMUSG00000046982	Tshz1	5730407I04Rik|D18Bwg1409e|Mtsh1|NY-CO-33|Sdccag33|Tsh1|mKIAA4206|teashirt1	teashirt zinc finger family member 1	protein-coding
mm_118543.1	chr14	16946648	16946650	+	1	NA	intron (NM_001289760, intron 1 of 9)	intron (NM_001289760, intron 1 of 9)	135682	NM_001289760	218772	Mm.259318	NM_011243	ENSMUSG00000017491	Rarb	A830025K23|Hap|Nr1b2	retinoic acid receptor, beta	protein-coding
mm_37103.1	chr4	116627922	116627956	-	1	NA	promoter-TSS (NM_016777)	promoter-TSS (NM_016777)	12	NM_016777	50927	Mm.257181	NM_016777	ENSMUSG00000028693	Nasp	5033430J04Rik|AI131596|AI317140|D4Ertd767e|Epcs32|Nasp-T	nuclear autoantigenic sperm protein (histone-binding)	protein-coding
mm_11013.1	chr2	26581123	26581135	+	1	NA	promoter-TSS (NM_178444)	promoter-TSS (NM_178444)	73	NM_178444	353156	Mm.268933	NM_178444	ENSMUSG00000026921	Egfl7	VE-statin|Zneu1	EGF-like domain 7	protein-coding
mm_8639.1	chr1	156428849	156428859	-	1	NA	3' UTR (NM_009230, exon 16 of 16)	3' UTR (NM_009230, exon 16 of 16)	-7939	NM_001346967	77352	Mm.428709	NM_001033180	ENSMUSG00000026601	Axdnd1	9430070O13Rik|Gm979	axonemal dynein light chain domain containing 1	protein-coding
mm_6884.1	chr1	84695753	84695766	-	1	NA	promoter-TSS (NR_039588)	promoter-TSS (NR_039588)	-80	NR_039588	100628595		NR_039588	ENSMUSG00000093254	Mir5126	mir-5126|mmu-mir-5126|mu-mir-5126	microRNA 5126	ncRNA
mm_4375.1	chr1	172136184	172136197	+	1	NA	3' UTR (NM_001159525, exon 6 of 6)	3' UTR (NM_001159525, exon 6 of 6)	9435	NM_023041	19298	Mm.247764	NM_023041	ENSMUSG00000003464	Pex19	Pxf	peroxisomal biogenesis factor 19	protein-coding
mm_90987.1	chr10	13868780	13868874	-	1	NA	5' UTR (NM_025446, exon 1 of 6)	5' UTR (NM_025446, exon 1 of 6)	130	NM_025446	66253	Mm.45755	NM_025446	ENSMUSG00000019806	Aig1	1500031O19Rik|AV064870|AW413422|CGI-103	androgen-induced 1	protein-coding
mm_124406.1	chr14	115477541	115477551	-	1	NA	intron (NM_175500, intron 5 of 7)	intron (NM_175500, intron 5 of 7)	-67994	NR_045761	75088	Mm.444706	NR_045761	ENSMUSG00000093551	4930505G20Rik	-	RIKEN cDNA 4930505G20 gene	ncRNA
mm_79682.1	chr9	59870951	59870956	+	1	NA	exon (NM_173018, exon 25 of 44)	exon (NM_173018, exon 25 of 44)	79126	NM_013708	23958	Mm.103641	NM_013708	ENSMUSG00000032292	Nr2e3	A930035N01Rik|PNR|RNR|rd7	nuclear receptor subfamily 2, group E, member 3	protein-coding
mm_62969.1	chr7	119895837	119895884	+	1	NA	promoter-TSS (NM_001285961)	promoter-TSS (NM_001285961)	-1	NM_001285961	73919	Mm.46381	NM_029610	ENSMUSG00000030922	Lyrm1	1110065L10Rik|2310004B22Rik|4930404J24Rik	LYR motif containing 1	protein-coding
mm_75909.1	chr8	71381994	71382004	-	1	NA	promoter-TSS (NM_010150)	promoter-TSS (NM_010150)	-47	NM_010150	13864	Mm.28989	NM_010150	ENSMUSG00000002393	Nr2f6	AV090102|COUP-TF3|EAR2|Erbal2	nuclear receptor subfamily 2, group F, member 6	protein-coding
mm_30140.1	chr3	142364277	142364281	-	1	NA	intron (NM_022554, intron 1 of 8)	Lx8|LINE|L1	27571	NM_022554	56376	Mm.117709	NM_019808	ENSMUSG00000028273	Pdlim5	1110001A05Rik|AI987914|C87059|Enh|Enh1|Enh2|Enh3|LIM	PDZ and LIM domain 5	protein-coding
mm_137585.1	chr17	28007696	28007704	+	1	NA	intron (NM_001286040, intron 11 of 24)	intron (NM_001286040, intron 11 of 24)	72884	NM_013687	21463	Mm.29758	NM_013687	ENSMUSG00000062859	Tcp11	D17Ken1|Tcp-11	t-complex protein 11	protein-coding
mm_150523.1	chr19	39042030	39042067	+	1	NA	exon (NM_028089, exon 9 of 9)	exon (NM_028089, exon 9 of 9)	-18958	NM_028191	72303	Mm.482578	NM_028191	ENSMUSG00000067231	Cyp2c65	2210009K14Rik	cytochrome P450, family 2, subfamily c, polypeptide 65	protein-coding
mm_18647.1	chr2	69564920	69564922	-	1	NA	intron (NM_001081088, intron 1 of 78)	B4A|SINE|B4	21146	NM_001081088	14725	Mm.23847	NM_001081088	ENSMUSG00000027070	Lrp2	AI315343|AW536255|D230004K18Rik|Gp330|Megalin|b2b1625.2Clo	low density lipoprotein receptor-related protein 2	protein-coding
mm_23897.1	chr3	83031718	83031730	+	1	NA	exon (NM_010196, exon 5 of 5)	exon (NM_010196, exon 5 of 5)	5571	NM_001111048	14161	Mm.88793	NM_010196	ENSMUSG00000028001	Fga	ENSMUSG00000059807|Fib	fibrinogen alpha chain	protein-coding
mm_32338.1	chr4	104464022	104464031	+	1	NA	intron (NM_010014, intron 1 of 6)	intron (NM_010014, intron 1 of 6)	96488	NM_177259	13131	Mm.289682	NM_010014	ENSMUSG00000028519	Dab1	AI956902|C630028C02Rik|scm|scr|scrambler|yot	disabled 1	protein-coding
mm_97136.1	chr11	75172554	75172569	+	1	NA	promoter-TSS (NR_029794)	promoter-TSS (NR_029794)	-827	NR_029794	387208		NR_029794	ENSMUSG00000065590	Mir212	Mirn212|mir-212|mmu-mir-212	microRNA 212	ncRNA
mm_85826.1	chr9	110422410	110422434	-	1	NA	3' UTR (NM_008694, exon 4 of 4)	3' UTR (NM_008694, exon 4 of 4)	2614	NM_008694	18054	Mm.236225	NM_008694	ENSMUSG00000032484	Ngp	bectenecin	neutrophilic granule protein	protein-coding
mm_72095.1	chr8	71586116	71586128	+	1	NA	3' UTR (NM_011977, exon 14 of 14)	3' UTR (NM_011977, exon 14 of 14)	-6062	NM_025396	66171	Mm.282284	NM_025396	ENSMUSG00000031807	Pgls	1110030K05Rik|AI447866|Plgs	6-phosphogluconolactonase	protein-coding
mm_102235.1	chr11	54956050	54956115	-	1	NA	5' UTR (NM_001199275, exon 2 of 19)	5' UTR (NM_001199275, exon 2 of 19)	6858	NM_021327	57783	Mm.259671	NM_021327	ENSMUSG00000020400	Tnip1	ABIN|ABIN-1|ABIN1|AU018810|Naf1|Nef|VAN	TNFAIP3 interacting protein 1	protein-coding
mm_68725.1	chr7	120201972	120202004	-	1	NA	promoter-TSS (NM_016669)	promoter-TSS (NM_016669)	0	NM_016669	12971	Mm.9114	NM_016669	ENSMUSG00000030905	Crym	-	crystallin, mu	protein-coding
mm_64820.1	chr7	7298762	7298790	-	1	NA	promoter-TSS (NM_001302387)	promoter-TSS (NM_001302387)	60	NM_001302387	12727	Mm.297883	NM_011334	ENSMUSG00000000605	Clcn4	Clc4-2|Clcn4-2	chloride channel, voltage-sensitive 4	protein-coding
mm_67104.1	chr7	70337828	70337877	-	1	NA	promoter-TSS (NR_131145)	promoter-TSS (NR_131145)	0	NR_131144	624549	Mm.116344	NR_131144	ENSMUSG00000109097	Gm29683	-	predicted gene, 29683	ncRNA
mm_3176.1	chr1	135740716	135740719	+	1	NA	intron (NM_007791, intron 2 of 5)	intron (NM_007791, intron 2 of 5)	11520	NM_007791	13007	Mm.196484	NM_007791	ENSMUSG00000026421	Csrp1	AA408841|AA959891|AW545626|CRP1|Csrp	cysteine and glycine-rich protein 1	protein-coding
mm_125421.1	chr15	41847997	41848000	+	1	NA	intron (NM_001130164, intron 1 of 5)	intron (NM_001130164, intron 1 of 5)	17040	NM_001130164	170719	Mm.254267	NM_130885	ENSMUSG00000022307	Oxr1	2210416C20Rik|C7|C7B	oxidation resistance 1	protein-coding
mm_131550.1	chr16	17898618	17898647	+	1	NA	promoter-TSS (NM_009436)	promoter-TSS (NM_009436)	-5	NM_009436	22115	Mm.310201	NM_009436	ENSMUSG00000045521	Tssk2	DGS-G|SPOGA2|Stk22b|Tsk2	testis-specific serine kinase 2	protein-coding
mm_134282.1	chr16	14204702	14204712	-	1	NA	exon (NM_013607, exon 35 of 42)	exon (NM_013607, exon 35 of 42)	41432	NM_001114085	67203	Mm.24105	NM_023317	ENSMUSG00000022678	Nde1	2810027M15Rik|AU042936|AW822251|Nude|mNudE	nudE neurodevelopment protein 1	protein-coding
mm_139077.1	chr17	46678801	46678827	+	1	NA	intron (NM_001163729, intron 1 of 10)	intron (NM_001163729, intron 1 of 10)	-1639	NM_001277310	17256	Mm.329083	NM_010787	ENSMUSG00000002768	Mea1	Mea-1	male enhanced antigen 1	protein-coding
mm_66994.1	chr7	64374027	64374069	-	1	NA	promoter-TSS (NM_177893)	promoter-TSS (NM_177893)	47	NM_177893	330554	Mm.236510	NM_177893	ENSMUSG00000033458	Fan1	6030441H18Rik|Mtmr15|mFAN1	FANCD2/FANCI-associated nuclease 1	protein-coding
mm_130415.1	chr15	98004635	98004652	-	1	NA	promoter-TSS (NM_001113515)	promoter-TSS (NM_001113515)	81	NM_031163	12824	Mm.2423	NM_031163	ENSMUSG00000022483	Col2a1	Col2|Col2a|Col2a-1|Del1|Dmm|Lpk|Rgsc856	collagen, type II, alpha 1	protein-coding
mm_103309.1	chr11	72796947	72796989	-	1	NA	intron (NM_001045536, intron 1 of 54)	intron (NM_001045536, intron 1 of 54)	742	NM_001045536	195018	Mm.272030	NM_001045536	ENSMUSG00000055670	Zzef1	8430405D05Rik|BC051585|C130099L13Rik|C85424|NSPA|mKIAA0399	zinc finger, ZZ-type with EF hand domain 1	protein-coding
mm_146846.1	chr18	23952254	23952268	-	1	NA	Intergenic	Intergenic	-2427	NM_027007	69256	Mm.218343	NM_027007	ENSMUSG00000024276	Zfp397	2810411K16Rik|6720480F11Rik|AI461664	zinc finger protein 397	protein-coding
mm_66820.1	chr7	48456332	48456345	-	1	NA	promoter-TSS (NM_205810)	promoter-TSS (NM_205810)	4	NM_205810	233231	Mm.297430	NM_205810	ENSMUSG00000070547	Mrgprb1	MrgB1	MAS-related GPR, member B1	protein-coding
mm_103565.1	chr11	77881188	77881193	-	1	NA	exon (NM_008952, exon 8 of 8)	exon (NM_008952, exon 8 of 8)	12682	NM_008952	19193	Mm.8543	NM_008952	ENSMUSG00000017453	Pipox	LPIPOX|Pso	pipecolic acid oxidase	protein-coding
mm_2682.1	chr1	127306606	127306616	+	1	NA	intron (NM_145128, intron 2 of 17)	intron (NM_145128, intron 2 of 17)	101625	NM_145128	107895	Mm.214682	NM_145128	ENSMUSG00000036155	Mgat5	4930471A21Rik|5330407H02Rik|AI480971|GlcNAc-TV	mannoside acetylglucosaminyltransferase 5	protein-coding
mm_125503.1	chr15	55307744	55307762	+	1	NA	promoter-TSS (NM_181277)	promoter-TSS (NM_181277)	3	NM_181277	12818	Mm.297859	NM_181277	ENSMUSG00000022371	Col14a1	5730412L22Rik|AW108078	collagen, type XIV, alpha 1	protein-coding
mm_90044.1	chr10	115817525	115817533	+	1	NA	5' UTR (NM_001168680, exon 2 of 9)	5' UTR (NM_001168680, exon 2 of 9)	245	NM_001168679	216350	Mm.22270	NM_146010	ENSMUSG00000034127	Tspan8	C76990|E330007O21Rik|Tm4sf3	tetraspanin 8	protein-coding
mm_64303.1	chr7	141861984	141861989	+	1	NA	exon (NM_028801, exon 31 of 49)	exon (NM_028801, exon 31 of 49)	22914	NM_028801	74180	Mm.200752	NM_028801	ENSMUSG00000066108	Muc5b	2300002I04Rik|A130042M24|AV085033|MUC5|MUC9|mucin 5b	mucin 5, subtype B, tracheobronchial	protein-coding
mm_147480.1	chr18	47248087	47248106	-	1	NA	3' UTR (NM_018744, exon 19 of 19)	3' UTR (NM_018744, exon 19 of 19)	120772	NM_018744	20358	Mm.40909	NM_018744	ENSMUSG00000019647	Sema6a	A730020P05Rik|AI851735|Sema6A-1|Semaq|VIa	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A	protein-coding
mm_113051.1	chr13	23652437	23652447	+	1	NA	Intergenic	RMER19B2|LTR|ERVK	-29884	NM_015787	50709	Mm.170587	NM_015787	ENSMUSG00000051627	Hist1h1e	H1-4|H1.4|H1e|H1f4|H1s-4|H1var2	histone cluster 1, H1e	protein-coding
mm_56721.1	chr6	115592531	115592537	-	1	NA	promoter-TSS (NM_001101431)	promoter-TSS (NM_001101431)	42	NM_001101431	70291	Mm.133694	NM_001101431	ENSMUSG00000068011	Mkrn2os	2510049J12Rik	makorin, ring finger protein 2, opposite strand	protein-coding
mm_161075.1	chr12	80518765	80518765	+	1	NA	promoter-TSS (NM_001081421)	promoter-TSS (NM_001081421)	-225	NM_001081421	108760	Mm.308296	NM_001081421	ENSMUSG00000021130	Galnt16	5730405L21Rik|AI415388|Galntl1|mpp-GalNAc-T16	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 16	protein-coding
mm_112753.1	chr13	19342082	19342142	+	1	NA	Intergenic	Intergenic	53701	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_17196.1	chr2	25468133	25468145	-	1	NA	exon (NM_008963, exon 4 of 7)	exon (NM_008963, exon 4 of 7)	1610	NM_008963	19215	Mm.1008	NM_008963	ENSMUSG00000015090	Ptgds	21kDa|L-PGDS|PGD2|PGDS|PGDS2|Ptgs3	prostaglandin D2 synthase (brain)	protein-coding
mm_43671.1	chr5	138775335	138775370	+	1	NA	intron (NM_030565, intron 3 of 9)	intron (NM_030565, intron 3 of 9)	20271	NM_030565	80752	Mm.320355	NM_030565	ENSMUSG00000025854	Fam20c	C76981|DMP-4|DMP4|GEF-CK|mKIAA4081	family with sequence similarity 20, member C	protein-coding
mm_18765.1	chr2	73462430	73462448	-	1	NA	intron (NM_153138, intron 1 of 7)	B1_Mus1|SINE|Alu	-8550	NM_001289722	215280	Mm.223504	NM_153138	ENSMUSG00000075284	Wipf1	AI115543|D2Ertd120e|WIP|Waspip	WAS/WASL interacting protein family, member 1	protein-coding
mm_147212.1	chr18	37954959	37955002	-	1	NA	promoter-TSS (NM_010411)	promoter-TSS (NM_010411)	8	NM_010411	15183	Mm.20521	NM_010411	ENSMUSG00000024454	Hdac3	AW537363	histone deacetylase 3	protein-coding
mm_93071.1	chr10	89345076	89345096	-	1	NA	Intergenic	CpG	-87296	NR_102339	320091	Mm.236464	NM_178773	ENSMUSG00000035189	Ano4	A330096O15Rik|Gm65|Tmem16d	anoctamin 4	protein-coding
mm_15339.1	chr2	155979600	155979616	+	1	NA	intron (NM_001130000, intron 19 of 32)	intron (NM_001130000, intron 19 of 32)	23050	NM_177217	16328	Mm.288729	NM_008383	ENSMUSG00000038241	Cep250	AW490617|B230210E21Rik|Cep2|Inmp	centrosomal protein 250	protein-coding
mm_123349.1	chr14	63142367	63142373	-	1	NA	3' UTR (NM_007798, exon 10 of 10)	3' UTR (NM_007798, exon 10 of 10)	19908	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_111112.1	chr12	80960526	80960536	-	1	NA	exon (NM_001177561, exon 2 of 5)	exon (NM_001177561, exon 2 of 5)	7548	NM_011387	20493	Mm.486361	NM_011387	ENSMUSG00000021135	Slc10a1	Ntcp	solute carrier family 10 (sodium/bile acid cotransporter family), member 1	protein-coding
mm_95369.1	chr11	49086808	49086838	+	1	NA	promoter-TSS (NM_008330)	promoter-TSS (NM_008330)	-194	NM_001271676	15953	Mm.24769	NM_008330	ENSMUSG00000078920	Ifi47	47kDa|IRG-47|Ifggc1|Igrd|Iigp4|Iipg4|Irgd	interferon gamma inducible protein 47	protein-coding
mm_158547.1	chrX	145480677	145480681	-	1	NA	intron (NM_001290274, intron 1 of 8)	intron (NM_001290274, intron 1 of 8)	6960	NM_001290274	27494	Mm.100068	NM_153319	ENSMUSG00000041688	Amot	CAG-2|D0Kist1|Sii6	angiomotin	protein-coding
mm_171775.1	chr5	109796295	109796303	-	1	NA	Intergenic	Intergenic	37843	NR_027964	667213	Mm.454429	NR_027964	ENSMUSG00000105044	Gm10416	EG667213|ENSMUSG00000072761	zinc finger protein pseudogene	pseudo
mm_124488.1	chr14	121738560	121738603	-	1	NA	5' UTR (NM_001128307, exon 1 of 56)	5' UTR (NM_001128307, exon 1 of 56)	348	NM_001128308	105445	Mm.378591	NM_134074	ENSMUSG00000025558	Dock9	AA959601|AW538057|B230309H04Rik|D14Wsu89e|Zizimin1|mKIAA1058	dedicator of cytokinesis 9	protein-coding
mm_162948.1	chr11	3332486	3332488	+	1	NA	intron (NM_178149, intron 3 of 5)	CpG-1656	1756	NM_178149	216505	Mm.390323	NM_178149	ENSMUSG00000034614	Pik3ip1	1500004A08Rik|5830455E04Rik|Crkd|Hgfl	phosphoinositide-3-kinase interacting protein 1	protein-coding
mm_99989.1	chr11	114720396	114720400	+	1	NA	3' UTR (NM_053273, exon 14 of 14)	3' UTR (NM_053273, exon 14 of 14)	-7014	NM_001034878	432611	Mm.212764	NM_001034878	ENSMUSG00000034706	Dnaic2	C030015H18Rik|Dnai2|Gm728	dynein, axonemal, intermediate chain 2	protein-coding
mm_81615.1	chr9	110769720	110769732	+	1	NA	TTS (NM_010859)	TTS (NM_010859)	6045	NM_010859	17897	Mm.7353	NM_010859	ENSMUSG00000059741	Myl3	MLC1s|MLC1v|Mylc|VLC1	myosin, light polypeptide 3	protein-coding
mm_20115.1	chr2	121160208	121160219	-	1	NA	3' UTR (NM_001290819, exon 5 of 5)	3' UTR (NM_001290819, exon 5 of 5)	10912	NM_001290819	99334	Mm.188422	NM_178889	ENSMUSG00000050619	Zscan29	AW125441|Zfp690	zinc finger SCAN domains 29	protein-coding
mm_97579.1	chr11	78944669	78944680	+	1	NA	exon (NM_010927, exon 12 of 27)	exon (NM_010927, exon 12 of 27)	19383	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_91571.1	chr10	40099431	40099441	-	1	NA	intron (NM_001114332, intron 1 of 5)	L1MC1|LINE|L1	42818	NM_028247	72472	Mm.186778	NM_028247	ENSMUSG00000019838	Slc16a10	2610103N14Rik|9830169E08|Mct10|PRO0813|TAT1	solute carrier family 16 (monocarboxylic acid transporters), member 10	protein-coding
mm_138640.1	chr17	35866153	35866203	+	1	NA	promoter-TSS (NM_001146710)	promoter-TSS (NM_001146710)	50	NM_001146710	76448	Mm.359982	NM_175242	ENSMUSG00000034595	Ppp1r18	2310014H01Rik|AA407849|AI450394	protein phosphatase 1, regulatory subunit 18	protein-coding
mm_107672.1	chr12	53838840	53838876	+	1	NA	intron (NM_013780, intron 5 of 11)	intron (NM_013780, intron 5 of 11)	365016	NM_028133	112407	Mm.133037	NM_028133	ENSMUSG00000035105	Egln3	2610021G09Rik|AI505553|AI648162|Hif-p4h-3|Phd3|SM-20	egl-9 family hypoxia-inducible factor 3	protein-coding
mm_137494.1	chr17	26952838	26952854	+	1	NA	intron (NM_001281491, intron 4 of 18)	intron (NM_001281491, intron 4 of 18)	-4727	NR_037244	100526534		NR_037244	ENSMUSG00000093118	Mir3083	mir-3083|mmu-mir-3083	microRNA 3083	ncRNA
mm_6269.1	chr1	69548942	69548944	-	1	NA	intron (NM_011770, intron 5 of 7)	intron (NM_011770, intron 5 of 7)	137017	NM_011770	22779	Mm.106343	NM_011770	ENSMUSG00000025997	Ikzf2	A730095J18Rik|Helios|Zfpn1a2|Znfn1a2	IKAROS family zinc finger 2	protein-coding
mm_172101.1	chr6	31142691	31142694	-	1	NA	intron (NR_110471, intron 2 of 3)	intron (NR_110471, intron 2 of 3)	75782	NR_110470	232685	Mm.443019	NM_144555	ENSMUSG00000044471	Lncpint	Lincpint|MNCb-1768|Pint|linc-Pint	long non-protein coding RNA, Trp53 induced transcript	ncRNA
mm_159390.1	chr3	92352293	92352293	+	1	NA	intron (NM_011471, intron 1 of 1)	intron (NM_011471, intron 1 of 1)	150	NM_011471	20759	Mm.261596	NM_011471	ENSMUSG00000055030	Sprr2e	-	small proline-rich protein 2E	protein-coding
mm_29321.1	chr3	108017656	108017662	-	1	NA	intron (NM_010358, intron 1 of 7)	intron (NM_010358, intron 1 of 7)	314	NM_010358	14862	Mm.37199	NM_010358	ENSMUSG00000058135	Gstm1	Gstb-1|Gstb1	glutathione S-transferase, mu 1	protein-coding
mm_58604.1	chr7	5051564	5051601	+	1	NA	promoter-TSS (NM_026900)	promoter-TSS (NM_026900)	50	NM_026900	68992	Mm.41484	NM_026900	ENSMUSG00000055633	Zfp580	1500015O20Rik|AI838225|Znf580	zinc finger protein 580	protein-coding
mm_161377.1	chr14	69609478	69609478	+	1	NA	promoter-TSS (NM_033325)	promoter-TSS (NM_033325)	2	NM_033325	94352	Mm.116714	NM_033325	ENSMUSG00000034205	Loxl2	1110004B06Rik|4930526G11Rik|9430067E15Rik	lysyl oxidase-like 2	protein-coding
mm_123298.1	chr14	61631889	61631893	-	1	NA	promoter-TSS (NR_029734)	promoter-TSS (NR_029734)	81	NR_029734	387134		NR_029734	ENSMUSG00000092995	Mir16-1	Mirn16|Mirn16-1|miR-16|mir-16-1	microRNA 16-1	ncRNA
mm_105015.1	chr11	100414858	100414872	-	1	NA	promoter-TSS (NM_010221)	promoter-TSS (NM_010221)	-46	NM_176830	66180	Mm.4940	NM_176830	ENSMUSG00000006931	P3h4	1110036O03Rik|AI413214|Leprel4|Sc65	prolyl 3-hydroxylase family member 4 (non-enzymatic)	protein-coding
mm_13311.1	chr2	102658819	102658834	+	1	NA	5' UTR (NM_001077514, exon 1 of 11)	5' UTR (NM_001077514, exon 1 of 11)	143	NM_001077514	20511	Mm.267547	NM_011393	ENSMUSG00000005089	Slc1a2	1700091C19Rik|2900019G14Rik|AI159670|Eaat2|GLT-1|GLT1|MGLT1	solute carrier family 1 (glial high affinity glutamate transporter), member 2	protein-coding
mm_111187.1	chr12	84172404	84172407	-	1	NA	intron (NM_001163502, intron 2 of 12)	intron (NM_001163502, intron 2 of 12)	21610	NM_001163502	238317	Mm.31256	NM_001163501	ENSMUSG00000042507	Elmsan1	9430029N19Rik|C130039O16Rik|Gm260	ELM2 and Myb/SANT-like domain containing 1	protein-coding
mm_136652.1	chr17	5941347	5941413	+	1	NA	promoter-TSS (NM_001113353)	promoter-TSS (NM_001113353)	100	NM_001113352	20975	Mm.236068	NM_011523	ENSMUSG00000023805	Synj2	AI481647|SJ2|mKIAA0348	synaptojanin 2	protein-coding
mm_166213.1	chr5	53469726	53469772	+	1	NA	Intergenic	Intergenic	-86030	NM_001080928	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_142103.1	chr17	35835572	35835617	-	1	NA	exon (NM_011655, exon 4 of 4)	exon (NM_011655, exon 4 of 4)	2707	NM_011655	22154	Mm.273538	NM_011655	ENSMUSG00000001525	Tubb5	AA408537|AI596182|B130022C14Rik|M(beta)5	tubulin, beta 5 class I	protein-coding
mm_148712.1	chr19	5802810	5802814	+	1	NA	promoter-TSS (NR_002847)	promoter-TSS (NR_002847)	-140	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_74005.1	chr8	121084335	121084341	+	1	NA	promoter-TSS (NM_010426)	promoter-TSS (NM_010426)	-48	NM_010426	15227	Mm.33897	NM_010426	ENSMUSG00000042812	Foxf1	AI450827|FREAC1|Foxf1a|Freac-1|HFH-8|Hfh8	forkhead box F1	protein-coding
mm_155726.1	chrX	96155546	96155588	+	1	NA	exon (NM_010833, exon 6 of 13)	exon (NM_010833, exon 6 of 13)	59522	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_77144.1	chr8	111537562	111537570	-	1	NA	promoter-TSS (NM_001168623)	promoter-TSS (NM_001168623)	-777	NM_001168623	170737	Mm.271578	NM_133206	ENSMUSG00000033545	Znrf1	B830022L21Rik|Rnf42|Zrfp1|nin283	zinc and ring finger 1	protein-coding
mm_70471.1	chr8	12323838	12323844	+	1	NA	Intergenic	Intergenic	-61930	NR_027975	434280	Mm.447484	NM_001013812	ENSMUSG00000047935	Gm5607	EG434280	predicted gene 5607	ncRNA
mm_18331.1	chr2	57292444	57292461	-	1	NA	intron (NM_001145820, intron 3 of 16)	tRNA-Ala-GCY_|tRNA|tRNA	54070	NM_010274	14571	Mm.3711	NM_010274	ENSMUSG00000026827	Gpd2	AA408484|AI448216|AU021455|AW494132|GPDH|Gdm1|Gpd-m|Gpdh-m|TISP38	glycerol phosphate dehydrogenase 2, mitochondrial	protein-coding
mm_94021.1	chr10	127666785	127666817	-	1	NA	promoter-TSS (NM_008668)	promoter-TSS (NM_008668)	-98	NM_008668	17937	Mm.336898	NM_008668	ENSMUSG00000025402	Nab2	AI451907	Ngfi-A binding protein 2	protein-coding
mm_142555.1	chr17	46630034	46630082	-	1	NA	promoter-TSS (NM_175168)	promoter-TSS (NM_175168)	-554	NM_175168	71461	Mm.181833	NM_175168	ENSMUSG00000023972	Ptk7	8430404F20Rik|chz|mPTK7/CCK4	PTK7 protein tyrosine kinase 7	protein-coding
mm_150253.1	chr19	34192241	34192266	+	1	NA	promoter-TSS (NM_029682)	promoter-TSS (NM_029682)	-17	NM_029682	76630	Mm.130952	NM_029682	ENSMUSG00000024776	Stambpl1	1700095N21Rik|8230401J17Rik|ALMalpha|AMSH-FP	STAM binding protein like 1	protein-coding
mm_160007.1	chr6	124756433	124756433	-	1	NA	promoter-TSS (NM_007881)	promoter-TSS (NM_007881)	54	NM_007881	13498	Mm.333380	NM_007881	ENSMUSG00000004263	Atn1	Atr1|Drpla|atrophin-1	atrophin 1	protein-coding
mm_29584.1	chr3	117360371	117360441	-	1	NA	5' UTR (NM_177664, exon 1 of 7)	5' UTR (NM_177664, exon 1 of 7)	470	NM_177664	229791	Mm.140138	NM_177664	ENSMUSG00000044667	Plppr4	A330086D10|D3Bwg0562e|Lppr4|PRG-1|mKIAA0455	phospholipid phosphatase related 4	protein-coding
mm_48260.1	chr5	137858035	137858054	-	1	NA	promoter-TSS (NM_133209)	promoter-TSS (NM_133209)	5	NM_133209	170741	Mm.347593	NM_133209	ENSMUSG00000066684	Pilrb1	FDFACT|Fdact|Pilrb	paired immunoglobin-like type 2 receptor beta 1	protein-coding
mm_26927.1	chr3	20251983	20252022	-	1	NA	exon (NM_029706, exon 10 of 11)	exon (NM_029706, exon 10 of 11)	-9821	NM_007753	12873	Mm.1135	NM_007753	ENSMUSG00000001865	Cpa3	MC-CPA	carboxypeptidase A3, mast cell	protein-coding
mm_153595.1	chr19	43740536	43740539	-	1	NA	intron (NM_144874, intron 6 of 8)	intron (NM_144874, intron 6 of 8)	12463	NM_144874	226139	Mm.248237	NM_144874	ENSMUSG00000040018	Cox15	2900026G05Rik	cytochrome c oxidase assembly protein 15	protein-coding
mm_85879.1	chr9	110990452	110990466	-	1	NA	promoter-TSS (NM_153100)	promoter-TSS (NM_153100)	-746	NM_153100	235636	Mm.441138	NM_153100	ENSMUSG00000066319	Rtp3	Tmem7	receptor transporter protein 3	protein-coding
mm_106327.1	chr11	118317480	118317505	-	1	NA	exon (NM_011594, exon 3 of 5)	exon (NM_011594, exon 3 of 5)	25042	NM_021440	58251	Mm.439815	NM_021440	ENSMUSG00000076433	BC100451	Cep295nl|Ddc8|FS39|Kiaa1731nl	cDNA sequence BC100451	protein-coding
mm_122791.1	chr14	54417782	54417810	-	1	NA	promoter-TSS (NM_011405)	promoter-TSS (NM_011405)	-94	NM_011405	20540	Mm.142455	NM_011405	ENSMUSG00000000958	Slc7a7	AI790233|my+lat1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 7	protein-coding
mm_168311.1	chr11	109011903	109011903	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	91554	NM_015732	12006	Mm.71710	NM_015732	ENSMUSG00000000142	Axin2	Axi1|Axil|Conductin	axin 2	protein-coding
mm_148499.1	chr19	4192130	4192217	+	1	NA	promoter-TSS (NM_031868)	promoter-TSS (NM_031868)	-1	NM_031868	19045	Mm.1970	NM_031868	ENSMUSG00000040385	Ppp1ca	Ppp1c|dism2	protein phosphatase 1, catalytic subunit, alpha isoform	protein-coding
mm_25369.1	chr3	107101701	107101712	+	1	NA	5' UTR (NM_008417, exon 1 of 3)	5' UTR (NM_008417, exon 1 of 3)	139	NM_008417	16490	Mm.39285	NM_008417	ENSMUSG00000040724	Kcna2	Akr6a4|ENSMUSG00000074335|Gm10672|Kca1-2|Kv1.2|Mk-2	potassium voltage-gated channel, shaker-related subfamily, member 2	protein-coding
mm_96570.1	chr11	69045641	69045713	+	1	NA	promoter-TSS (NM_011496)	promoter-TSS (NM_011496)	40	NM_011496	20877	Mm.3488	NM_011496	ENSMUSG00000020897	Aurkb	AIM-1|AIRK2|AL022959|Aik2|Aim1|Ark2|AurB|IPL1|STK-1|Stk12|Stk5	aurora kinase B	protein-coding
mm_122484.1	chr14	46387263	46387283	-	1	NA	5' UTR (NM_007554, exon 2 of 4)	5' UTR (NM_007554, exon 2 of 4)	3396	NM_001316360	12159	Mm.6813	NM_007554	ENSMUSG00000021835	Bmp4	Bmp-4|Bmp2b|Bmp2b-1|Bmp2b1	bone morphogenetic protein 4	protein-coding
mm_66927.1	chr7	61529885	61529895	-	1	NA	non-coding (NR_045727, exon 5 of 5)	non-coding (NR_045727, exon 5 of 5)	85437	NR_045727	319752	Mm.294476	NR_045727		B230209E15Rik	-	RIKEN cDNA B230209E15 gene	ncRNA
mm_108746.1	chr12	88794807	88794820	+	1	NA	5' UTR (NM_001198587, exon 1 of 20)	5' UTR (NM_001198587, exon 1 of 20)	309	NM_001198587	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding
mm_560.1	chr1	38022235	38022254	+	1	NA	exon (NM_198303, exon 6 of 24)	exon (NM_198303, exon 6 of 24)	24234	NM_198303	226982	Mm.260943	NM_198303	ENSMUSG00000026083	Eif5b	A030003E17Rik|BC018347|IF2	eukaryotic translation initiation factor 5B	protein-coding
mm_86352.1	chr9	123632546	123632548	-	1	NA	promoter-TSS (NM_011731)	promoter-TSS (NM_011731)	18	NM_011731	22599	Mm.41963	NM_011731	ENSMUSG00000025243	Slc6a20b	AA986306|Sit1|Slc6a20|XT3|Xtrp3	solute carrier family 6 (neurotransmitter transporter), member 20B	protein-coding
mm_43712.1	chr5	139389895	139389920	+	1	NA	promoter-TSS (NM_001038703)	promoter-TSS (NM_001038703)	3	NM_001038703	80290	Mm.270003	NM_030258	ENSMUSG00000044197	Gpr146	BC003323|PGR8	G protein-coupled receptor 146	protein-coding
mm_43913.1	chr5	144358725	144358727	+	1	NA	promoter-TSS (NM_025833)	promoter-TSS (NM_025833)	201	NR_102373	100579137		NR_102372	ENSMUSG00000104600	Dmrt1i	Dmr	Dmrt1 interacting ncRNA	ncRNA
mm_72401.1	chr8	81770070	81770088	+	1	NA	intron (NM_001024617, intron 6 of 24)	intron (NM_001024617, intron 6 of 24)	427517	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_58950.1	chr7	18718118	18718129	+	1	NA	promoter-TSS (NM_001004152)	promoter-TSS (NM_001004152)	33	NM_001004152	243862	Mm.389833	NM_001004152	ENSMUSG00000044903	Psg22	AA408604|cea9	pregnancy-specific glycoprotein 22	protein-coding
mm_165276.1	chr2	77335070	77335070	+	1	NA	Intergenic	Intergenic	-54478	NM_175465	228071	Mm.27120	NM_175465	ENSMUSG00000042272	Sestd1	1500031J16Rik|A930010O20|Solo/Trio8	SEC14 and spectrin domains 1	protein-coding
mm_163375.1	chr12	44254740	44254750	+	1	NA	Intergenic	Intergenic	-14409	NM_026164	67452	Mm.54126	NM_026164	ENSMUSG00000036257	Pnpla8	1200006O19Rik|AI467579|Ipla2(gamma)	patatin-like phospholipase domain containing 8	protein-coding
mm_145886.1	chr18	65580801	65580817	+	1	NA	intron (NM_207255, intron 1 of 5)	CpG	579	NM_207255	328977	Mm.286232	NM_207255	ENSMUSG00000042439	Zfp532	C530030I18Rik|Znf532|mKIAA1629	zinc finger protein 532	protein-coding
mm_9351.1	chr1	172082395	172082435	-	1	NA	promoter-TSS (NM_009938)	promoter-TSS (NM_009938)	-114	NM_009938	12847	Mm.30041	NM_009938	ENSMUSG00000026553	Copa	AU040324|xenin	coatomer protein complex subunit alpha	protein-coding
mm_45852.1	chr5	87781839	87781854	-	1	NA	exon (NM_001304768, exon 8 of 13)	exon (NM_001304768, exon 8 of 13)	7396	NM_007785	12993	Mm.4908	NM_007785	ENSMUSG00000061937	Csn1s2a	Csng|PP22	casein alpha s2-like A	protein-coding
mm_86346.1	chr9	123632361	123632370	-	1	NA	5' UTR (NM_011731, exon 1 of 11)	5' UTR (NM_011731, exon 1 of 11)	200	NM_011731	22599	Mm.41963	NM_011731	ENSMUSG00000025243	Slc6a20b	AA986306|Sit1|Slc6a20|XT3|Xtrp3	solute carrier family 6 (neurotransmitter transporter), member 20B	protein-coding
mm_172530.1	chr7	86119312	86119314	+	1	NA	Intergenic	L1Md_T|LINE|L1	52411	NM_001102578	546981	Mm.469835	NM_001102578	ENSMUSG00000090436	Vmn2r75	EG546981	vomeronasal 2, receptor 75	protein-coding
mm_43706.1	chr5	139354210	139354222	+	1	NA	intron (NM_001160265, intron 2 of 8)	intron (NM_001160265, intron 2 of 8)	1599	NM_001160265	545817	Mm.482474	NM_001160265	ENSMUSG00000029541	Cyp2w1	Gm455	cytochrome P450, family 2, subfamily w, polypeptide 1	protein-coding
mm_64145.1	chr7	141228819	141228834	+	1	NA	promoter-TSS (NM_001081118)	promoter-TSS (NM_001081118)	38	NM_001081118	101471	Mm.248656	NM_207211	ENSMUSG00000038611	Phrf1	AA673488	PHD and ring finger domains 1	protein-coding
mm_64325.1	chr7	141997482	141997491	+	1	NA	intron (NM_001009930, intron 16 of 19)	intron (NM_001009930, intron 16 of 19)	5307	NR_037291	100526509		NR_037291	ENSMUSG00000092652	Mir3104	mir-3104|mmu-mir-3104	microRNA 3104	ncRNA
mm_53239.1	chr6	127455314	127455316	+	1	NA	intron (NM_001346512, intron 1 of 5)	intron (NM_001346512, intron 1 of 5)	1592	NM_181402	101187	Mm.110818	NM_181402	ENSMUSG00000037997	Parp11	5330431N24Rik|AI851877|ARTD11|HIN1L|PARP-11	poly (ADP-ribose) polymerase family, member 11	protein-coding
mm_74491.1	chr8	4813462	4813462	-	1	NA	Intergenic	Intergenic	-33928	NM_011369	20419	Mm.37801	NM_011369	ENSMUSG00000022322	Shcbp1	mPAL	Shc SH2-domain binding protein 1	protein-coding
mm_12664.1	chr2	75659093	75659108	+	1	NA	promoter-TSS (NM_198090)	promoter-TSS (NM_198090)	-159	NM_146130	229279	Mm.316306	NM_053263	ENSMUSG00000059005	Hnrnpa3	2410013L13Rik|2610209F03Rik|2610510D13Rik|Hnrpa3	heterogeneous nuclear ribonucleoprotein A3	protein-coding
mm_14586.1	chr2	135987605	135987606	+	1	NA	intron (NM_013829, intron 29 of 36)	intron (NM_013829, intron 29 of 36)	-70322	NM_029530	76161	Mm.41638	NM_029530	ENSMUSG00000027270	Lamp5	3110035N03Rik|6330527O06Rik|BAD-LAMP|LAMP-5	lysosomal-associated membrane protein family, member 5	protein-coding
mm_15225.1	chr2	154536312	154536313	+	1	NA	3' UTR (NM_001285446, exon 11 of 11)	3' UTR (NM_001285446, exon 11 of 11)	-12592	NM_029305	75480	Mm.440434	NM_029305	ENSMUSG00000038523	1700003F12Rik	-	RIKEN cDNA 1700003F12 gene	protein-coding
mm_72793.1	chr8	86915073	86915093	+	1	NA	Intergenic	Intergenic	-29825	NM_030563	80750	Mm.25117	NM_030563	ENSMUSG00000031652	N4bp1	AI481586|C81621	NEDD4 binding protein 1	protein-coding
mm_18062.1	chr2	41988850	41988871	-	1	NA	intron (NM_053011, intron 2 of 90)	intron (NM_053011, intron 2 of 90)	458708	NR_105754	102465171		NR_105754	ENSMUSG00000098660	Mir6336	Gm27584|mmu-mir-6336	microRNA 6336	ncRNA
mm_112164.1	chr12	113360372	113360398	-	1	NA	Intergenic	Intergenic	-129180	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_120306.1	chr14	63141730	63141742	+	1	NA	exon (NM_007798, exon 9 of 10)	exon (NM_007798, exon 9 of 10)	19274	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_173273.1	chrX	98142289	98142289	-	1	NA	Intergenic	Lx9|LINE|L1	-6468	NM_013476	11835	Mm.39005	NM_013476	ENSMUSG00000046532	Ar	AW320017|Tfm	androgen receptor	protein-coding
mm_77208.1	chr8	113854949	113854955	-	1	NA	Intergenic	Intergenic	-6113	NM_172466	208936	Mm.167471	NM_172466	ENSMUSG00000053399	Adamts18	9630038L21|ADAMTS21|E130314N14Rik	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 18	protein-coding
mm_94858.1	chr11	24077148	24077163	+	1	NA	promoter-TSS (NM_001242934)	promoter-TSS (NM_001242934)	-901	NM_016707	14025	Mm.53687	NM_016707	ENSMUSG00000000861	Bcl11a	2810047E18Rik|BCL-11A|Ctip1|D930021L15Rik|Evi9|Evi9a|Evi9b|Evi9c|mKIAA1809	B cell CLL/lymphoma 11A (zinc finger protein)	protein-coding
mm_47257.1	chr5	121660478	121660519	-	1	NA	promoter-TSS (NM_001289543)	promoter-TSS (NM_001289543)	12	NM_028037	71985	Mm.45423	NM_028037	ENSMUSG00000029456	Acad10	2410021P16Rik	acyl-Coenzyme A dehydrogenase family, member 10	protein-coding
mm_89205.1	chr10	86691631	86691684	+	1	NA	exon (NM_011631, exon 17 of 18)	exon (NM_011631, exon 17 of 18)	6130	NR_015572	66263	Mm.392261	NR_015572		1810014B01Rik	-	RIKEN cDNA 1810014B01 gene	pseudo
mm_105893.1	chr11	114960464	114960474	-	1	NA	promoter-TSS (NM_199225)	promoter-TSS (NM_199225)	-52	NM_199225	387565	Mm.351450	NM_199225	ENSMUSG00000058728	Cd300c	Clm6	CD300C molecule	protein-coding
mm_1917.1	chr1	86022164	86022176	+	1	NA	exon (NM_001122732, exon 1 of 4)	exon (NM_001122732, exon 1 of 4)	228	NM_027029	70060	Mm.196313	NM_027029	ENSMUSG00000026226	Spata3	1700011N12Rik|1700029H01Rik|4930424D10Rik|Mtsarg1|Tsarg1	spermatogenesis associated 3	protein-coding
mm_29066.1	chr3	103791922	103791936	-	1	NA	promoter-TSS (NR_125731)	promoter-TSS (NR_125731)	-366	NM_001301304	15257	Mm.20827	NM_010432	ENSMUSG00000008730	Hipk1	1110062K04Rik|Myak	homeodomain interacting protein kinase 1	protein-coding
mm_121308.1	chr14	106023045	106023079	+	1	NA	Intergenic	Lx9|LINE|L1	-83136	NM_198601	212085	Mm.78128	NM_198601	ENSMUSG00000022113	Trim52	4921513B05Rik	tripartite motif-containing 52	protein-coding
mm_95018.1	chr11	32000497	32000507	+	1	NA	promoter-TSS (NM_008741)	promoter-TSS (NM_008741)	83	NM_008741	18197	Mm.3304	NM_008741	ENSMUSG00000020297	Nsg2	-	neuron specific gene family member 2	protein-coding
mm_139986.1	chr17	72838045	72838045	+	1	NA	intron (NM_027166, intron 1 of 2)	intron (NM_027166, intron 1 of 2)	1341	NM_027166	383295	Mm.277533	NM_027166	ENSMUSG00000039770	Ypel5	2310076K21Rik|CGI-127	yippee-like 5 (Drosophila)	protein-coding
mm_150096.1	chr19	29465966	29465970	+	1	NA	intron (NM_021396, intron 5 of 5)	RMER1A|Other|Other	55049	NM_021396	58205	Mm.116737	NM_021396	ENSMUSG00000016498	Pdcd1lg2	B7-DC|Btdc|F730015O22Rik|PD-L2	programmed cell death 1 ligand 2	protein-coding
mm_167577.1	chr9	44604710	44604714	+	1	NA	promoter-TSS (NM_001110826)	promoter-TSS (NM_001110826)	-180	NM_001110826	13209	Mm.267061	NM_007841	ENSMUSG00000032097	Ddx6	1110001P04Rik|E230023J21Rik|HLR2|mRCK/P54|p54|rck	DEAD (Asp-Glu-Ala-Asp) box polypeptide 6	protein-coding
mm_77214.1	chr8	114131598	114131604	-	1	NA	Intergenic	Intergenic	-1973	NM_024446	67528	Mm.27889	NM_024437	ENSMUSG00000031767	Nudt7	1300007B24Rik|2210404C19Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 7	protein-coding
mm_56822.1	chr6	116735389	116735399	-	1	NA	Intergenic	MER44B|DNA|TcMar-Tigger	-18636	NM_178768	319776	Mm.133120	NM_178768	ENSMUSG00000048108	Tmem72	C230095G01Rik	transmembrane protein 72	protein-coding
mm_27390.1	chr3	50683399	50683401	-	1	NA	Intergenic	MTE2b|LTR|ERVL-MaLR	-239787	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_80888.1	chr9	99451423	99451436	+	1	NA	Intergenic	Intergenic	-4814	NM_001165957	623534	Mm.484967	NM_001165957		Nme9	Txndc6	NME/NM23 family member 9	protein-coding
mm_21484.1	chr2	163054444	163054454	-	1	NA	promoter-TSS (NM_008652)	promoter-TSS (NM_008652)	-186	NM_008652	17865	Mm.4594	NM_008652	ENSMUSG00000017861	Mybl2	B-Myb|Bmyb	myeloblastosis oncogene-like 2	protein-coding
mm_108034.1	chr12	73765692	73765692	+	1	NA	intron (NM_001313977, intron 13 of 14)	intron (NM_001313977, intron 13 of 14)	-135632	NM_001313920	15251	Mm.3879	NM_010431	ENSMUSG00000021109	Hif1a	AA959795|HIF-1-alpha|HIF1-alpha|HIF1alpha|MOP1|bHLHe78	hypoxia inducible factor 1, alpha subunit	protein-coding
mm_16878.1	chr2	12419457	12419474	-	1	NA	promoter-TSS (NM_024185)	promoter-TSS (NM_024185)	-5	NM_024185	66960	Mm.34059	NM_024185	ENSMUSG00000026767	Fam188a	1810041E18Rik|2310047O13Rik|5830410F13Rik|AI447827|AW111958	family with sequence similarity 188, member A	protein-coding
mm_136232.1	chr16	90615960	90615960	-	1	NA	Intergenic	Intergenic	111411	NM_025642	66578	Mm.180363	NM_025642	ENSMUSG00000022978	Mis18a	2610039C10Rik|2810018N07Rik	MIS18 kinetochore protein A	protein-coding
mm_45659.1	chr5	77115084	77115094	-	1	NA	promoter-TSS (NM_175606)	promoter-TSS (NM_175606)	34	NM_175606	74318	Mm.181852	NM_175606	ENSMUSG00000059325	Hopx	1110018K11Rik|1200015P04Rik|2300002F06Rik|AI848177|AW490897|Cameo|Hdop|Hod|Hop|Ob1|Obl|Toto	HOP homeobox	protein-coding
mm_15919.1	chr2	165065702	165065719	+	1	NA	intron (NM_170703, intron 5 of 7)	intron (NM_170703, intron 5 of 7)	10074	NM_011611	21939	Mm.271833	NM_011611	ENSMUSG00000017652	Cd40	AI326936|Bp50|GP39|HIGM1|IGM|IMD3|T-BAM|TRAP|Tnfrsf5|p50	CD40 antigen	protein-coding
mm_166513.1	chr6	14748057	14748059	-	1	NA	intron (NM_080464, intron 1 of 3)	intron (NM_080464, intron 1 of 3)	7216	NM_080464	140491	Mm.209429	NM_080464	ENSMUSG00000042717	Ppp1r3a	GM|RG1|RGL	protein phosphatase 1, regulatory (inhibitor) subunit 3A	protein-coding
mm_13877.1	chr2	119903335	119903358	+	1	NA	exon (NM_013720, exon 2 of 24)	exon (NM_013720, exon 2 of 24)	6118	NM_013720	29808	Mm.87532	NM_013720	ENSMUSG00000033943	Mga	AV312082|C130042M01Rik|C80739|D030062C11Rik|Mad5	MAX gene associated	protein-coding
mm_158454.1	chrX	140589413	140589418	-	1	NA	intron (NM_001077364, intron 2 of 3)	intron (NM_001077364, intron 2 of 3)	11107	NM_001077364	14605	Mm.22216	NM_010286	ENSMUSG00000031431	Tsc22d3	DIP|Dsip1|Gilz|TSC-22R|Tilz3	TSC22 domain family, member 3	protein-coding
mm_133138.1	chr16	67648569	67648574	+	1	NA	Intergenic	Intergenic	-27663	NM_178721	239857	Mm.394300	NM_178721	ENSMUSG00000064115	Cadm2	2900078E11Rik|9330131D06|A830029E02Rik|Igdf4d|Igsf4d|NECL3|SynCAM 2|SynCAM2	cell adhesion molecule 2	protein-coding
mm_97496.1	chr11	78344534	78344536	+	1	NA	intron (NM_001313985, intron 1 of 4)	MIRb|SINE|MIR	1040	NM_011676	22248	Mm.284811	NM_011676	ENSMUSG00000002058	Unc119	D11Bhm52|HRG4|MRG4|Rg4|Rtg4|Unc119h	unc-119 lipid binding chaperone	protein-coding
mm_19973.1	chr2	118256928	118256928	-	1	NA	promoter-TSS (NM_027759)	promoter-TSS (NM_027759)	38	NM_027759	71313	Mm.85046	NM_027759	ENSMUSG00000027344	Fsip1	1700012M13Rik|4933432K11Rik	fibrous sheath-interacting protein 1	protein-coding
mm_44842.1	chr5	34187075	34187083	-	1	NA	intron (NM_010753, intron 2 of 5)	CpG	631	NM_010753	17122	Mm.259260	NM_010753	ENSMUSG00000037235	Mxd4	2810410A03Rik|Mad4|bHLHc12	Max dimerization protein 4	protein-coding
mm_75145.1	chr8	35588994	35589004	-	1	NA	promoter-TSS (NR_040376)	promoter-TSS (NR_040376)	21	NR_040376	100504714	Mm.381744	NR_040376	ENSMUSG00000097357	Gm16793	-	predicted gene, 16793	ncRNA
mm_144515.1	chr18	24709508	24709520	+	1	NA	5' UTR (NM_001289655, exon 1 of 26)	5' UTR (NM_001289655, exon 1 of 26)	891	NM_001289655	225288	Mm.329322	NM_175276	ENSMUSG00000034295	Fhod3	A930009H06Rik|FHOS2|mKIAA1695	formin homology 2 domain containing 3	protein-coding
mm_78651.1	chr9	40333471	40333473	+	1	NA	promoter-TSS (NR_040728)	promoter-TSS (NR_040728)	0	NR_040728	73558	Mm.398307	NR_040728		1700110K17Rik	-	RIKEN cDNA 1700110K17 gene	ncRNA
mm_96965.1	chr11	70647587	70647607	+	1	NA	promoter-TSS (NM_024211)	promoter-TSS (NM_024211)	310	NM_027445	70510	Mm.261818	NM_027445	ENSMUSG00000040746	Rnf167	0610010G05Rik|5730408C10Rik|AU019305|AV328608	ring finger protein 167	protein-coding
mm_126711.1	chr15	85242035	85242049	+	1	NA	exon (NM_010180, exon 13 of 17)	exon (NM_010180, exon 13 of 17)	36034	NM_010180	14114	Mm.297992	NM_010180	ENSMUSG00000006369	Fbln1	-	fibulin 1	protein-coding
mm_102152.1	chr11	53675982	53676010	-	1	NA	exon (NM_009012, exon 17 of 25)	exon (NM_009012, exon 17 of 25)	31323	NM_009012	19360	Mm.4888	NM_009012	ENSMUSG00000020380	Rad50	Mrell|Rad50l	RAD50 double strand break repair protein	protein-coding
mm_171505.1	chr4	146270364	146270364	+	1	NA	promoter-TSS (NM_001083918).2	promoter-TSS (NM_001083918).2	-21	NM_001083918	666532	Mm.392861	NM_001083918	ENSMUSG00000067916	Zfp991	Gm13139|OTTMUSG00000010657	zinc finger protein 991	protein-coding
mm_67679.1	chr7	89338590	89338600	-	1	NA	5' UTR (NM_028343, exon 1 of 15)	5' UTR (NM_028343, exon 1 of 15)	192	NM_028343	72759	Mm.208477	NM_028343	ENSMUSG00000039428	Tmem135	2810439K08Rik|AW319712|PMP52	transmembrane protein 135	protein-coding
mm_147903.1	chr18	65381897	65381919	-	1	NA	intron (NM_001037294, intron 1 of 12)	intron (NM_001037294, intron 1 of 12)	11980	NM_001037294	225638	Mm.296528	NM_001037294	ENSMUSG00000032845	Alpk2	Gm549|Hak	alpha-kinase 2	protein-coding
mm_24238.1	chr3	88984877	88984918	+	1	NA	exon (NM_138679, exon 2 of 27)	exon (NM_138679, exon 2 of 27)	19085	NM_138679	192195	Mm.130752	NM_138679	ENSMUSG00000028053	Ash1l	8030453L17Rik|Ash1|E430018P19Rik|Kmt2h	ash1 (absent, small, or homeotic)-like (Drosophila)	protein-coding
mm_97943.1	chr11	83663475	83663477	+	1	NA	exon (NM_013652, exon 2 of 3)	exon (NM_013652, exon 2 of 3)	892	NM_013652	20303	Mm.244263	NM_013652	ENSMUSG00000018930	Ccl4	AT744.1|Act-2|MIP-1B|Mip1b|Scya4	chemokine (C-C motif) ligand 4	protein-coding
mm_37060.1	chr4	116053457	116053500	-	1	NA	intron (NM_028142, intron 1 of 5)	intron (NM_028142, intron 1 of 5)	398	NM_028142	72181	Mm.282560	NM_028142	ENSMUSG00000028706	Nsun4	2310010O12Rik|2810405F18Rik|AI507900|Shtap	NOL1/NOP2/Sun domain family, member 4	protein-coding
mm_53951.1	chr6	5256282	5256288	-	1	NA	promoter-TSS (NM_173006)	promoter-TSS (NM_173006)	-52	NM_173006	269823	Mm.9122	NM_173006	ENSMUSG00000029759	Pon3	2810004E20|AI786302	paraoxonase 3	protein-coding
mm_19226.1	chr2	84670635	84670641	-	1	NA	promoter-TSS (NM_001033166)	promoter-TSS (NM_001033166)	70	NM_001033166	72657	Mm.259293	NM_001033166	ENSMUSG00000076437	Selenoh	2700094K13Rik|Selh	selenoprotein H	protein-coding
mm_89311.1	chr10	87921596	87921599	+	1	NA	intron (NM_001111274, intron 4 of 4)	intron (NM_001111274, intron 4 of 4)	-45074	NR_000040	22172	Mm.391420	NR_000040		Tyms-ps	-	thymidylate synthase, pseudogene	pseudo
mm_110017.1	chr12	16647008	16647019	-	1	NA	Intergenic	Intergenic	-6457	NM_008747	18217	Mm.281715	NM_008747	ENSMUSG00000020591	Ntsr2	NT2R|NTRL	neurotensin receptor 2	protein-coding
mm_52424.1	chr6	113472260	113472269	+	1	NA	exon (NM_178942, exon 3 of 18)	exon (NM_178942, exon 3 of 18)	809	NM_134159	171095	Mm.213397	NM_134159	ENSMUSG00000030281	Il17rc	1110025H02Rik|Gm19850|IL-17RC|IL17-RC|IL17-RL|Il17rl	interleukin 17 receptor C	protein-coding
mm_101808.1	chr11	46363823	46363868	-	1	NA	exon (NM_001281968, exon 4 of 17)	exon (NM_001281968, exon 4 of 17)	25670	NM_001281968	16428	Mm.339927	NM_010583	ENSMUSG00000020395	Itk	Emt|Tcsk|Tsk	IL2 inducible T cell kinase	protein-coding
mm_136472.1	chr16	95749271	95749280	-	1	NA	Intergenic	Intergenic	46868	NM_011809	23872	Mm.290207	NM_011809	ENSMUSG00000022895	Ets2	AU022856|Ets-2	E26 avian leukemia oncogene 2, 3' domain	protein-coding
mm_3867.1	chr1	160989473	160989482	+	1	NA	exon (NM_080844, exon 3 of 8)	exon (NM_080844, exon 3 of 8)	10871	NM_080844	11905	Mm.260770	NM_080844	ENSMUSG00000026715	Serpinc1	AI114908|ATIII|At-3|At3	serine (or cysteine) peptidase inhibitor, clade C (antithrombin), member 1	protein-coding
mm_104625.1	chr11	97310274	97310289	-	1	NA	Intergenic	Intergenic	-5435	NM_025927	67036	Mm.5381	NM_025927	ENSMUSG00000018882	Mrpl45	2600005P05Rik|AU043542|R75241	mitochondrial ribosomal protein L45	protein-coding
mm_75613.1	chr8	62123305	62123328	-	1	NA	promoter-TSS (NM_001136089)	promoter-TSS (NM_001136089)	-123	NM_011922	26359	Mm.42179	NM_011922	ENSMUSG00000031635	Anxa10	-	annexin A10	protein-coding
mm_62195.1	chr7	97735198	97735222	+	1	NA	intron (NM_175105, intron 1 of 2)	MER3|DNA|hAT-Charlie	3037	NM_175105	66333	Mm.29756	NM_175105	ENSMUSG00000042797	Aqp11	1700015P13Rik|AI648923|sjds	aquaporin 11	protein-coding
mm_8038.1	chr1	135257699	135257709	-	1	NA	exon (NM_001163131, exon 2 of 9)	exon (NM_001163131, exon 2 of 9)	768	NM_001163131	13710	Mm.441439	NM_007921	ENSMUSG00000003051	Elf3	ESE-1|ESX|jen	E74-like factor 3	protein-coding
mm_22266.1	chr2	178414406	178414446	-	1	NA	promoter-TSS (NM_001081289)	promoter-TSS (NM_001081289)	37	NM_001085501	228966	Mm.472736	NM_001085501	ENSMUSG00000049999	Ppp1r3d	2610024M03Rik|Gm359	protein phosphatase 1, regulatory subunit 3D	protein-coding
mm_42113.1	chr5	110630054	110630061	+	1	NA	Intergenic	MTC-int|LTR|ERVL-MaLR	23325	NM_153570	100608	Mm.29960	NM_153570	ENSMUSG00000033294	Noc4l	AI326906	NOC4 like	protein-coding
mm_55154.1	chr6	51469870	51469877	-	1	NA	promoter-TSS (NM_007624)	promoter-TSS (NM_007624)	21	NM_182650	53379	Mm.155896	NM_016806	ENSMUSG00000004980	Hnrnpa2b1	9130414A06Rik|Hnrpa2|Hnrpa2b1|hnrnp-A	heterogeneous nuclear ribonucleoprotein A2/B1	protein-coding
mm_120308.1	chr14	63141790	63141835	+	1	NA	exon (NM_007798, exon 9 of 10)	exon (NM_007798, exon 9 of 10)	19350	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_113869.1	chr13	48662526	48662539	+	1	NA	promoter-TSS (NM_007526)	promoter-TSS (NM_007526)	-504	NM_007526	12022	Mm.42241	NM_007526	ENSMUSG00000021381	Barx1	-	BarH-like homeobox 1	protein-coding
mm_83544.1	chr9	46235632	46235665	-	1	NA	promoter-TSS (NM_001289755)	promoter-TSS (NM_001289755)	-12	NM_001289756	11814	Mm.390161	NM_023114	ENSMUSG00000032081	Apoc3	apo-CIII|apoC-III	apolipoprotein C-III	protein-coding
mm_3316.1	chr1	137906806	137906825	+	1	NA	Intergenic	Intergenic	-59640	NR_029795	735252		NR_029795	ENSMUSG00000065565	Mir181a-1	Mirn181a-1|Mirn213|miR-213|mir-181a-1|mmu-mir-213	microRNA 181a-1	ncRNA
mm_164372.1	chr16	24452912	24452921	-	1	NA	intron (NM_001145952, intron 1 of 11)	intron (NM_001145952, intron 1 of 11)	4825	NM_001145952	210126	Mm.209385	NM_178665	ENSMUSG00000033306	Lpp	9430020K16Rik|AA959454|AU024130|B130055L10Rik|C79715|D630048H16	LIM domain containing preferred translocation partner in lipoma	protein-coding
mm_111461.1	chr12	98420088	98420096	-	1	NA	Intergenic	Intergenic	-103752	NR_136759	105245437	Mm.446375	NR_136759		Gm40893	-	predicted gene, 40893	ncRNA
mm_102085.1	chr11	52281834	52281866	-	1	NA	intron (NM_001313981, intron 3 of 10)	intron (NM_001313981, intron 3 of 10)	745	NM_009331	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_58904.1	chr7	17163709	17163720	+	1	NA	TTS (NM_054059)	TTS (NM_054059)	13314	NM_054059	384557	Mm.486145	NM_054059	ENSMUSG00000053228	Ceacam3	EG384557|Psg24|cea12	carcinoembryonic antigen-related cell adhesion molecule 3	protein-coding
mm_126196.1	chr15	78842633	78842652	+	1	NA	promoter-TSS (NM_027219)	promoter-TSS (NM_027219)	-5	NM_027219	104445	Mm.307488	NM_027219	ENSMUSG00000049521	Cdc42ep1	1810058K22Rik|AA980734|Borg5|CEP1|MSE55	CDC42 effector protein (Rho GTPase binding) 1	protein-coding
mm_139411.1	chr17	52602701	52602717	+	1	NA	promoter-TSS (NM_001031811)	promoter-TSS (NM_001031811)	0	NM_001031811	211468	Mm.399068	NM_001031811	ENSMUSG00000035580	Kcnh8	C130090D05Rik|ELK|ELK1|ELK3|Kv12.1	potassium voltage-gated channel, subfamily H (eag-related), member 8	protein-coding
mm_12166.1	chr2	62397944	62397948	+	1	NA	intron (NM_001159543, intron 2 of 24)	intron (NM_001159543, intron 2 of 24)	14285	NM_010074	13482	Mm.1151	NM_010074	ENSMUSG00000035000	Dpp4	Cd26|Dpp-4|THAM	dipeptidylpeptidase 4	protein-coding
mm_123097.1	chr14	55788811	55788828	-	1	NA	promoter-TSS (NM_019955)	promoter-TSS (NM_019955)	38	NM_001164107	56532	Mm.46612	NM_019955	ENSMUSG00000022221	Ripk3	2610528K09Rik|AW107945|Rip3	receptor-interacting serine-threonine kinase 3	protein-coding
mm_120676.1	chr14	70571123	70571130	+	1	NA	intron (NM_021877, intron 17 of 19)	intron (NM_021877, intron 17 of 19)	-6721	NM_153136	213484	Mm.34191	NM_153136	ENSMUSG00000045211	Nudt18	BC036718	nudix (nucleoside diphosphate linked moiety X)-type motif 18	protein-coding
mm_144820.1	chr18	36292625	36292628	+	1	NA	Intergenic	Intergenic	-7475	NM_001267796	109169	Mm.426423	NM_001267796	ENSMUSG00000110185	Igip	6330403M23Rik	IgA inducing protein	protein-coding
mm_39931.1	chr5	31614021	31614030	+	1	NA	promoter-TSS (NM_025796)	promoter-TSS (NM_025796)	74	NM_025796	66845	Mm.120763	NM_025796	ENSMUSG00000106918	Mrpl33	0610009M10Rik|L33mt|MRP-L33	mitochondrial ribosomal protein L33	protein-coding
mm_158946.1	chr1	85109831	85109831	-	1	NA	promoter-TSS (NM_213615)	promoter-TSS (NM_213615)	22	NM_213615	381287	Mm.487565	NM_213615	ENSMUSG00000089844	A530032D15Rik	Gm1888	RIKEN cDNA A530032D15Rik gene	protein-coding
mm_144922.1	chr18	37674304	37674365	+	1	NA	promoter-TSS (NM_033586)	promoter-TSS (NM_033586)	-1	NM_033586	93711	Mm.247203	NM_033586	ENSMUSG00000104346	Pcdhga3	-	protocadherin gamma subfamily A, 3	protein-coding
mm_50205.1	chr6	42245983	42246013	+	1	NA	promoter-TSS (NM_029555)	promoter-TSS (NM_029555)	63	NM_029555	76263	Mm.267014	NM_029555	ENSMUSG00000029864	Gstk1	0610025I19Rik|AW260476|DsbA-L	glutathione S-transferase kappa 1	protein-coding
mm_50264.1	chr6	44792928	44792929	+	1	NA	Intergenic	Intergenic	-267133	NM_001004357	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding
mm_67263.1	chr7	75776787	75776792	-	1	NA	Intergenic	B1_Mm|SINE|Alu	-71549	NM_001122780	207952	Mm.206223	NM_029652	ENSMUSG00000055652	Klhl25	2810402K13Rik|BC027373|Enc-1	kelch-like 25	protein-coding
mm_20623.1	chr2	131859827	131859827	-	1	NA	promoter-TSS (NM_001166206)	promoter-TSS (NM_001166206)	-80	NM_001166206	71995	Mm.22	NM_028045	ENSMUSG00000037482	Erv3	1600014E20Rik|AA389086|AI426069|AI448024|D19349	endogenous retroviral sequence 3	protein-coding
mm_86073.1	chr9	114778819	114778832	-	1	NA	intron (NM_001252479, intron 1 of 3)	intron (NM_001252479, intron 1 of 3)	3168	NM_133978	102545	Mm.35600	NM_133978	ENSMUSG00000032436	Cmtm7	AI481279|Cklfsf7|LNV	CKLF-like MARVEL transmembrane domain containing 7	protein-coding
mm_43433.1	chr5	136084023	136084038	+	1	NA	5' UTR (NM_133914, exon 1 of 21)	5' UTR (NM_133914, exon 1 of 21)	114	NM_001039103	54153	Mm.290655	NM_133914	ENSMUSG00000004952	Rasa4	AA793972|AW112107|BB079060|CAPRI|GAPL	RAS p21 protein activator 4	protein-coding
mm_120084.1	chr14	57798183	57798216	+	1	NA	promoter-TSS (NM_001142441)	promoter-TSS (NM_001142441)	10	NM_009119	20220	Mm.30173	NM_009119	ENSMUSG00000021963	Sap18	C530046K05Rik|D11Ertd539e|EMegR4|Sap18a|Sinbp1	Sin3-associated polypeptide 18	protein-coding
mm_15066.1	chr2	153051761	153051783	+	1	NA	intron (NM_001011732, intron 1 of 2)	intron (NM_001011732, intron 1 of 2)	-14183	NM_145536	228788	Mm.299979	NM_145536	ENSMUSG00000027474	Ccm2l	-	cerebral cavernous malformation 2-like	protein-coding
mm_56450.1	chr6	97617537	97617597	-	1	NA	promoter-TSS (NM_145148)	promoter-TSS (NM_145148)	90	NM_145148	232288	Mm.27789	NM_145148	ENSMUSG00000030064	Frmd4b	6030440G05Rik|C87375|GOBLIN|GRSP1|R74720	FERM domain containing 4B	protein-coding
mm_122698.1	chr14	52095802	52095805	-	1	NA	intron (NM_001170982, intron 1 of 7)	intron (NM_001170982, intron 1 of 7)	8225	NM_001170982	15381	Mm.427321	NM_016884	ENSMUSG00000060373	Hnrnpc	AL022939|D14Wsu171e|Hnrpc|Hnrpc1|Hnrpc2|hnRNPC1|hnRNPC2|hnrnp-C	heterogeneous nuclear ribonucleoprotein C	protein-coding
mm_17921.1	chr2	35442130	35442149	-	1	NA	intron (NM_001308300, intron 1 of 6)	intron (NM_001308300, intron 1 of 6)	19310	NM_001308299	14594	Mm.281124	NM_010283	ENSMUSG00000035778	Ggta1	AW108479|GALT|Gal|Ggta|Ggta-1|alpha Gal|alpha3GalT	glycoprotein galactosyltransferase alpha 1, 3	protein-coding
mm_119547.1	chr14	48446341	48446429	+	1	NA	promoter-TSS (NM_172600)	promoter-TSS (NM_172600)	33	NR_132324	218989	Mm.85211	NM_172600	ENSMUSG00000036339	Tmem260	5930435P15|6720456H20Rik	transmembrane protein 260	protein-coding
mm_82931.1	chr9	35176053	35176055	-	1	NA	promoter-TSS (NM_027030)	promoter-TSS (NM_027030)	-67	NM_027030	69305	Mm.229110	NM_027030	ENSMUSG00000032040	Dcps	1700001E16Rik|AA408441	decapping enzyme, scavenger	protein-coding
mm_129612.1	chr15	79958410	79958426	-	1	NA	Intergenic	Intergenic	-25772	NM_144811	52609	Mm.323442	NM_144811	ENSMUSG00000053411	Cbx7	1600014J01Rik|AI851678|D15Ertd417e	chromobox 7	protein-coding
mm_132950.1	chr16	49911986	49912008	+	1	NA	TTS (NM_010581)	TTS (NM_010581)	56343	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_24045.1	chr3	87847137	87847147	+	1	NA	intron (NM_001025571, intron 1 of 6)	intron (NM_001025571, intron 1 of 6)	387	NM_021309	27371	Mm.86361	NM_021309	ENSMUSG00000028071	Sh2d2a	Lad|Ribp|Tsad	SH2 domain containing 2A	protein-coding
mm_111222.1	chr12	84583146	84583153	-	1	NA	intron (NM_001301427, intron 3 of 4)	RMER17A|LTR|ERVK	13321	NM_001301427	12677	Mm.4405	NM_007701	ENSMUSG00000021239	Vsx2	Chx10|Hox-10|Hox10|or	visual system homeobox 2	protein-coding
mm_138302.1	chr17	34639790	34639800	+	1	NA	Intergenic	Intergenic	-5088	NM_019873	56299	Mm.10025	NM_019873	ENSMUSG00000033739	Fkbpl	DIR1|NG7|Ppiase-X|Wisp39	FK506 binding protein-like	protein-coding
mm_170161.1	chr17	51879845	51879850	-	1	NA	Intergenic	Intergenic	-2880	NR_045095	100504169	Mm.417731	NR_045095		Gm20098	-	predicted gene, 20098	ncRNA
mm_74932.1	chr8	25754353	25754424	-	1	NA	promoter-TSS (NM_028102)	promoter-TSS (NM_028102)	-108	NM_028102	72108	Mm.246875	NM_028102	ENSMUSG00000061313	Ddhd2	2010305K11Rik|SAMWD1|mKIAA0725	DDHD domain containing 2	protein-coding
mm_93266.1	chr10	95722347	95722353	-	1	NA	Intergenic	Intergenic	-158183	NM_027722	71207	Mm.24397	NM_027722	ENSMUSG00000020029	Nudt4	4933436C10Rik|DIPP2|DIPP2alpha|DIPP2beta|HDCMB47P	nudix (nucleoside diphosphate linked moiety X)-type motif 4	protein-coding
mm_1470.1	chr1	69917064	69917070	+	1	NA	intron (NM_029160, intron 10 of 16)	L1VL4|LINE|L1	-34548	NM_025728	66722	Mm.440554	NM_025728	ENSMUSG00000053153	Spag16	4921511D23Rik|4930524F24Rik|4930585K05Rik|AV261009|Pf20|Wdr29	sperm associated antigen 16	protein-coding
mm_66099.1	chr7	31037861	31037867	-	1	NA	exon (NM_001111073, exon 4 of 8)	exon (NM_001111073, exon 4 of 8)	2453	NR_106017	102465635		NR_106017	ENSMUSG00000098783	Mir7050	Gm27578|mmu-mir-7050	microRNA 7050	ncRNA
mm_1773.1	chr1	78309556	78309568	+	1	NA	promoter-TSS (NM_001004173)	promoter-TSS (NM_001004173)	-784	NM_001004173	433323	Mm.276248	NM_001004173	ENSMUSG00000032908	Sgpp2	SPPase2|Spp2	sphingosine-1-phosphate phosphotase 2	protein-coding
mm_96778.1	chr11	69940108	69940116	+	1	NA	exon (NM_016875, exon 5 of 9)	exon (NM_016875, exon 5 of 9)	3784	NM_001347634	53422	Mm.29286	NM_016875	ENSMUSG00000018554	Ybx2	Msy2	Y box protein 2	protein-coding
mm_83234.1	chr9	42399293	42399301	-	1	NA	intron (NM_009347, intron 1 of 23)	intron (NM_009347, intron 1 of 23)	632	NM_009347	21683	Mm.42209	NM_009347	ENSMUSG00000037705	Tecta	Tctna	tectorin alpha	protein-coding
mm_143420.1	chr17	70844799	70844828	-	1	NA	exon (NM_001164077, exon 2 of 2)	exon (NM_001164077, exon 2 of 2)	1964	NM_001164077	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_14253.1	chr2	128128718	128128735	+	1	NA	exon (NM_009754, exon 2 of 4)	exon (NM_009754, exon 2 of 4)	1151	NM_001284410	12125	Mm.141083	NM_009754	ENSMUSG00000027381	Bcl2l11	1500006F24Rik|Bim|Bod|bcl2-L-11	BCL2-like 11 (apoptosis facilitator)	protein-coding
mm_70801.1	chr8	22938188	22938215	+	1	NA	exon (NM_001081149, exon 18 of 18)	exon (NM_001081149, exon 18 of 18)	-36635	NM_001110783	11733	Mm.334444	NM_031158	ENSMUSG00000031543	Ank1	Ank-1|nb|pale	ankyrin 1, erythroid	protein-coding
mm_109089.1	chr12	104683467	104683485	+	1	NA	Intergenic	ORR1C1|LTR|ERVL-MaLR	68476	NM_148948	192119	Mm.21135	NM_148948	ENSMUSG00000041415	Dicer1	1110006F08Rik|D12Ertd7e|mKIAA0928	dicer 1, ribonuclease type III	protein-coding
mm_76707.1	chr8	94599707	94599714	-	1	NA	intron (NM_028221, intron 1 of 7)	PB1D11|SINE|Alu	2016	NM_028221	102122	Mm.250425	NM_028221	ENSMUSG00000031774	Fam192a	1700001O11Rik|2310065K24Rik|AI596259|Nip30	family with sequence similarity 192, member A	protein-coding
mm_57914.1	chr6	133849877	133849884	-	1	NA	TTS (NM_010594)	TTS (NM_010594)	3787	NM_010594	16483	Mm.13052	NM_010594	ENSMUSG00000032758	Kap	AW146435|FKSG22	kidney androgen regulated protein	protein-coding
mm_134983.1	chr16	32099670	32099696	-	1	NA	promoter-TSS (NM_025892)	promoter-TSS (NM_025892)	44	NM_001111025	72084	Mm.37613	NM_024464	ENSMUSG00000023791	Pigx	2010319C14Rik|PIG-X	phosphatidylinositol glycan anchor biosynthesis, class X	protein-coding
mm_31244.1	chr4	44880008	44880012	+	1	NA	intron (NM_138590, intron 2 of 8)	intron (NM_138590, intron 2 of 8)	-101384	NM_080289	76238	Mm.196574	NM_080289	ENSMUSG00000035637	Grhpr	1110059D05Rik|6430629L09Rik|Glxr	glyoxylate reductase/hydroxypyruvate reductase	protein-coding
mm_166525.1	chr6	24598085	24598091	+	1	NA	exon (NM_053098, exon 1 of 3)	exon (NM_053098, exon 1 of 3)	317	NM_053098	93677	Mm.332941	NM_053098	ENSMUSG00000029683	Lmod2	C-Lmod	leiomodin 2 (cardiac)	protein-coding
mm_25936.1	chr3	131466664	131466680	+	1	NA	Intergenic	Intergenic	-98096	NM_001289479	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_83571.1	chr9	46416165	46416172	-	1	NA	Intergenic	RMER17B|LTR|ERVK	-96182	NM_183104	74361	Mm.159169	NM_183104	ENSMUSG00000056617	4931429L15Rik	-	RIKEN cDNA 4931429L15 gene	protein-coding
mm_73667.1	chr8	111056542	111056600	+	1	NA	exon (NM_028274, exon 1 of 1)	exon (NM_028274, exon 1 of 1)	232	NM_028274	72544	Mm.24174	NM_028274	ENSMUSG00000109941	Exosc6	2610510N21Rik|C76919|Mtr3	exosome component 6	protein-coding
mm_15800.1	chr2	164461020	164461058	+	1	NA	promoter-TSS (NM_025575)	promoter-TSS (NM_025575)	68	NM_025575	66460	Mm.44218	NM_025575	ENSMUSG00000045503	Sys1	2610042O14Rik|AI266964|C87389	SYS1 Golgi-localized integral membrane protein homolog (S. cerevisiae)	protein-coding
mm_169995.1	chr1	71629472	71629484	-	1	NA	exon (NM_001276413, exon 15 of 44)	exon (NM_001276413, exon 15 of 44)	23756	NM_010233	14268	Mm.193099	NM_010233	ENSMUSG00000026193	Fn1	E330027I09|Fn|Fn-1	fibronectin 1	protein-coding
mm_101601.1	chr11	34771424	34771435	-	1	NA	intron (NM_033374, intron 1 of 51)	intron (NM_033374, intron 1 of 51)	12476	NM_033374	94176	Mm.380679	NM_033374	ENSMUSG00000020143	Dock2	AI662014|AW122239|CED-5|Hch|MBC	dedicator of cyto-kinesis 2	protein-coding
mm_149389.1	chr19	11386728	11386741	+	1	NA	intron (NM_001310331, intron 4 of 6)	intron (NM_001310331, intron 4 of 6)	11246	NM_001310331	666907		NM_001310331	ENSMUSG00000101389	Ms4a4a	EG666907	membrane-spanning 4-domains, subfamily A, member 4A	protein-coding
mm_8047.1	chr1	135372307	135372332	-	1	NA	exon (NM_175259, exon 4 of 5)	exon (NM_175259, exon 4 of 5)	2744	NM_175259	77552	Mm.41407	NM_175259	ENSMUSG00000041889	Shisa4	9330132O05Rik|Tmem58|mShisa4	shisa family member 4	protein-coding
mm_63226.1	chr7	126408450	126408452	+	1	NA	TTS (NM_009844)	TTS (NM_009844)	6419	NM_009844	12478	Mm.4360	NM_009844	ENSMUSG00000030724	Cd19	AW495831	CD19 antigen	protein-coding
mm_123716.1	chr14	70056971	70057015	-	1	NA	intron (NM_028560, intron 6 of 6)	intron (NM_028560, intron 6 of 6)	-20452	NM_018781	13655	Mm.103737	NM_018781	ENSMUSG00000033730	Egr3	Pilot	early growth response 3	protein-coding
mm_19902.1	chr2	114147067	114147080	-	1	NA	intron (NM_001290788, intron 12 of 33)	L1_Mur3|LINE|L1	3497	NR_105968	102465982		NR_105968	ENSMUSG00000098464	Mir7002	Gm27429|mmu-mir-7002	microRNA 7002	ncRNA
mm_58792.1	chr7	16130341	16130366	+	1	NA	5' UTR (NM_148946, exon 1 of 10)	5' UTR (NM_148946, exon 1 of 10)	527	NM_148946	110891	Mm.241147	NM_148946	ENSMUSG00000030376	Slc8a2	Ncx2	solute carrier family 8 (sodium/calcium exchanger), member 2	protein-coding
mm_8566.1	chr1	155417337	155417358	-	1	NA	promoter-TSS (NM_011273)	promoter-TSS (NM_011273)	97	NM_011273	19775	Mm.266215	NM_011273	ENSMUSG00000026469	Xpr1	Rmc-1|Rmc1|Sxv|Syg1|XR	xenotropic and polytropic retrovirus receptor 1	protein-coding
mm_3829.1	chr1	159523877	159523895	+	1	NA	5' UTR (NM_022312, exon 1 of 23)	5' UTR (NM_022312, exon 1 of 23)	117	NM_022312	21960	Mm.44701	NM_022312	ENSMUSG00000015829	Tnr	J1-tenascin|TN-R|janusin|restrictin	tenascin R	protein-coding
mm_169413.1	chr14	52769723	52769737	+	1	NA	Intergenic	Intergenic	-274035	NM_001170918	57269	Mm.88822	NM_020512	ENSMUSG00000059887	Olfr1507	MOR244-1|Mor28|Or28	olfactory receptor 1507	protein-coding
mm_142705.1	chr17	47878891	47878966	-	1	NA	intron (NM_001110824, intron 5 of 16)	intron (NM_001110824, intron 5 of 16)	-44237	NM_001109973	17240	Mm.329100	NM_010783	ENSMUSG00000032717	Mdfi	I-mf|I-mfa	MyoD family inhibitor	protein-coding
mm_25860.1	chr3	129836634	129836672	+	1	NA	promoter-TSS (NM_007686)	promoter-TSS (NM_007686)	-86	NM_001329552	12630	Mm.117180	NM_007686	ENSMUSG00000058952	Cfi	-	complement component factor i	protein-coding
mm_102351.1	chr11	58204912	58204937	-	1	NA	intron (NM_018738, intron 2 of 2)	B4|SINE|B4	5368	NM_018738	16145	Mm.33902	NM_018738	ENSMUSG00000078853	Igtp	AW558444|Irgm3	interferon gamma induced GTPase	protein-coding
mm_59596.1	chr7	28139723	28139746	+	1	NA	intron (NM_001164655, intron 4 of 19)	intron (NM_001164655, intron 4 of 19)	10268	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_166730.1	chr6	122570885	122570896	-	1	NA	Intergenic	Intergenic	17081	NM_009645	11628	Mm.391503	NM_009645	ENSMUSG00000040627	Aicda	Aid|Arp2	activation-induced cytidine deaminase	protein-coding
mm_125812.1	chr15	74931811	74931876	+	1	NA	Intergenic	Intergenic	-23208	NM_001164039	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_30770.1	chr4	17853285	17853325	+	1	NA	promoter-TSS (NM_019724)	promoter-TSS (NM_019724)	-153	NM_019724	17389	Mm.187315	NM_019724	ENSMUSG00000028226	Mmp16	MT-MMP 3|MT3-MMP|Mt3mmp	matrix metallopeptidase 16	protein-coding
mm_129018.1	chr15	74930501	74930518	-	1	NA	Intergenic	Intergenic	-24542	NM_001164039	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_164556.1	chr17	14398945	14398952	-	1	NA	promoter-TSS (NR_027986)	promoter-TSS (NR_027986)	-6	NR_027986	74917	Mm.32228	NM_183107		4930474M22Rik	-	RIKEN cDNA 4930474M22 gene	ncRNA
mm_133199.1	chr16	73045334	73045349	+	1	NA	3' UTR (NM_019413, exon 29 of 29)	3' UTR (NM_019413, exon 29 of 29)	382192	NM_019413	19876	Mm.310772	NM_019413	ENSMUSG00000022883	Robo1	AW494633|AW742721|DUTT1|Gm310	roundabout guidance receptor 1	protein-coding
mm_151945.1	chr19	5801038	5801048	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	1629	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_56134.1	chr6	87722742	87722755	-	1	NA	Intergenic	Intergenic	-8121	NM_001159697	58229	Mm.333229	NM_021418	ENSMUSG00000068263	Efcc1	Ccdc48	EF hand and coiled-coil domain containing 1	protein-coding
mm_128383.1	chr15	42680674	42680693	-	1	NA	Intergenic	Intergenic	-3706	NM_009640	11600	Mm.309336	NM_009640	ENSMUSG00000022309	Angpt1	1110046O21Rik|Ang-1|Ang1	angiopoietin 1	protein-coding
mm_124657.1	chr15	5495802	5495829	+	1	NA	promoter-TSS (NR_045274)	promoter-TSS (NR_045274)	-503	NR_045274	71432	Mm.291087	NR_045274		5430437J10Rik	-	RIKEN cDNA 5430437J10 gene	ncRNA
mm_121682.1	chr14	13170719	13170722	-	1	NA	intron (NR_121588, intron 2 of 3)	intron (NR_121588, intron 2 of 3)	113918	NR_121589	328354	Mm.252404	NM_177813	ENSMUSG00000051729	Gm5087	C630025C03|EG328354	predicted gene 5087	ncRNA
mm_115674.1	chr13	12650319	12650357	-	1	NA	promoter-TSS (NR_003568)	promoter-TSS (NR_003568)	57	NR_003568	664862	Mm.415635	NR_003568		Gpr137b-ps	2310041G17Rik|ENSMUSG00000075118	G protein-coupled receptor 137B, pseudogene	pseudo
mm_22690.1	chr3	17790121	17790134	+	1	NA	non-coding (NR_033490, exon 1 of 3)	non-coding (NR_033490, exon 1 of 3)	206	NR_033490	70441	Mm.458192	NR_033490	ENSMUSG00000100252	Mir124-2hg	100040120|2610100L16Rik|6430547I21Rik|A930005K07Rik|AW125202|Gm2612	Mir124-2 host gene (non-protein coding)	ncRNA
mm_172120.1	chr6	3201177	3201178	+	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	-87342	NR_036696	667335	Mm.380219	NR_036696	ENSMUSG00000106779	Gm8579	EG667335	spermatogenesis associated glutamate (E)-rich protein 4a pseudogene	pseudo
mm_54974.1	chr6	48738953	48738966	-	1	NA	promoter-TSS (NM_008376)	promoter-TSS (NM_008376)	-88	NM_175860	16205	Mm.252599	NM_008376	ENSMUSG00000090019	Gimap1	IAP38|Imap38|imap	GTPase, IMAP family member 1	protein-coding
mm_83004.1	chr9	36731061	36731065	-	1	NA	Intergenic	Intergenic	-4405	NM_007691	12649	Mm.16753	NM_007691	ENSMUSG00000032113	Chek1	C85740|Chk1|rad27	checkpoint kinase 1	protein-coding
mm_63503.1	chr7	127841701	127841743	+	1	NA	promoter-TSS (NM_009294)	promoter-TSS (NM_009294)	-86	NM_009294	20909	Mm.24867	NM_009294	ENSMUSG00000030805	Stx4a	Stx4|Syn-4|Syn4	syntaxin 4A (placental)	protein-coding
mm_84504.1	chr9	67022644	67022660	-	1	NA	TTS (NM_001164249)	TTS (NM_001164249)	21219	NM_001164252	22003	Mm.121878	NM_024427	ENSMUSG00000032366	Tpm1	AA986836|AI854628|TM2|Tm3|Tmpa|Tpm-1|alpha-TM	tropomyosin 1, alpha	protein-coding
mm_88587.1	chr10	79710802	79710868	+	1	NA	exon (NM_001077184, exon 5 of 7)	exon (NM_001077184, exon 5 of 7)	-5799	NM_008226	15166	Mm.12956	NM_008226	ENSMUSG00000020331	Hcn2	BCNG2|HAC1|trls	hyperpolarization-activated, cyclic nucleotide-gated K+ 2	protein-coding
mm_11258.1	chr2	29935414	29935499	+	1	NA	promoter-TSS (NM_028923)	promoter-TSS (NM_028923)	47	NM_028923	74412	Mm.275121	NM_028923	ENSMUSG00000019715	Gle1	4933405K21Rik|AA553313|Gle1l	GLE1 RNA export mediator (yeast)	protein-coding
mm_168501.1	chr11	53200652	53200669	+	1	NA	Intergenic	B2_Mm2|SINE|B2	-80604	NR_046047	790909	Mm.404626	NR_046047	ENSMUSG00000087668	Gm11186	OTTMUSG00000000039	predicted gene 11186	ncRNA
mm_135793.1	chr16	57191227	57191260	-	1	NA	intron (NM_026254, intron 10 of 17)	intron (NM_026254, intron 10 of 17)	-23911	NM_023175	52633	Mm.383203	NM_023175	ENSMUSG00000022751	Nit2	1190017B19Rik|D16Ertd502e	nitrilase family, member 2	protein-coding
mm_138255.1	chr17	34590504	34590539	+	1	NA	exon (NM_134116, exon 2 of 4)	exon (NM_134116, exon 2 of 4)	715	NM_134116	106512	Mm.26584	NM_134116	ENSMUSG00000034786	Gpsm3	AA960287|AGS4	G-protein signalling modulator 3 (AGS3-like, C. elegans)	protein-coding
mm_167938.1	chrX	112521783	112521784	+	1	NA	intron (NM_001168590, intron 4 of 6)	RMER17A-int|LTR|ERVK	26509	NM_001168590	67715	Mm.45323	NM_026333	ENSMUSG00000025528	2010106E10Rik	-	RIKEN cDNA 2010106E10 gene	protein-coding
mm_23844.1	chr3	82876697	82876707	+	1	NA	promoter-TSS (NM_001146328)	promoter-TSS (NM_001146328)	-3	NR_040382	78212	Mm.399202	NR_040381	ENSMUSG00000086273	Rbm46os	4930444E23Rik|4930564K09Rik|Lratos	RNA binding motif protein 46, opposite strand	ncRNA
mm_168796.1	chr12	19606627	19606638	+	1	NA	Intergenic	CpG	1092122	NM_001201330	236366	Mm.352227	NM_001033157	ENSMUSG00000073197	5730507C01Rik	-	RIKEN cDNA 5730507C01 gene	protein-coding
mm_153360.1	chr19	40180457	40180474	-	1	NA	exon (NM_145499, exon 3 of 9)	exon (NM_145499, exon 3 of 9)	6821	NM_145499	226105	Mm.29119	NM_145499	ENSMUSG00000060613	Cyp2c70	-	cytochrome P450, family 2, subfamily c, polypeptide 70	protein-coding
mm_46565.1	chr5	107130611	107130623	-	1	NA	intron (NM_011578, intron 13 of 16)	intron (NM_011578, intron 13 of 16)	158978	NM_011578	21814	Mm.200775	NM_011578	ENSMUSG00000029287	Tgfbr3	1110036H20Rik|AU015626|AW215636|TBRIII	transforming growth factor, beta receptor III	protein-coding
mm_105765.1	chr11	109611325	109611330	-	1	NA	promoter-TSS (NM_145940)	promoter-TSS (NM_145940)	62	NM_145940	52639	Mm.35817	NM_145940	ENSMUSG00000041895	Wipi1	4930533H01Rik|AW411817|D11Ertd498e	WD repeat domain, phosphoinositide interacting 1	protein-coding
mm_28983.1	chr3	101280287	101280307	-	1	NA	intron (NM_013486, intron 3 of 4)	intron (NM_013486, intron 3 of 4)	7642	NM_013486	12481	Mm.22842	NM_013486	ENSMUSG00000027863	Cd2	LFA-2|Ly-37|Ly37	CD2 antigen	protein-coding
mm_71072.1	chr8	34154663	34154686	+	1	NA	exon (NM_026432, exon 1 of 6)	exon (NM_026432, exon 1 of 6)	111	NM_026432	67887	Mm.290353	NM_026432	ENSMUSG00000031532	Saraf	1810045K07Rik|Tmem66	store-operated calcium entry-associated regulatory factor	protein-coding
mm_133117.1	chr16	65665078	65665104	+	1	NA	Intergenic	Intergenic	-102394	NM_026879	68942	Mm.432944	NM_026879	ENSMUSG00000004843	Chmp2b	1190006E07Rik	charged multivesicular body protein 2B	protein-coding
mm_30790.1	chr4	19584750	19584752	+	1	NA	intron (NM_025476, intron 2 of 9)	(TTTTTG)n|Simple_repeat|Simple_repeat	9685	NM_025476	66302	Mm.440686	NM_025476	ENSMUSG00000028229	Rmdn1	Fam82b|RMD-1	regulator of microtubule dynamics 1	protein-coding
mm_93274.1	chr10	95842887	95842893	-	1	NA	Intergenic	Intergenic	-97773	NM_001001932	216238	Mm.210035	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding
mm_25178.1	chr3	103279715	103279780	+	1	NA	5' UTR (NM_053170, exon 1 of 20)	5' UTR (NM_053170, exon 1 of 20)	454	NM_001079830	94093	Mm.195036	NM_053170	ENSMUSG00000033014	Trim33	8030451N04Rik|AI413936|Ecto|Tif1g	tripartite motif-containing 33	protein-coding
mm_15596.1	chr2	160645997	160646007	+	1	NA	5' UTR (NM_009408, exon 1 of 21)	5' UTR (NM_009408, exon 1 of 21)	105	NM_009408	21969	Mm.217233	NM_009408	ENSMUSG00000070544	Top1	AI467334|D130064I21Rik|Top-1	topoisomerase (DNA) I	protein-coding
mm_21353.1	chr2	157121970	157121977	-	1	NA	intron (NM_018851, intron 4 of 15)	intron (NM_018851, intron 4 of 15)	13249	NM_001139520	56045	Mm.248478	NM_018851	ENSMUSG00000027639	Samhd1	E330031J07Rik|Mg11	SAM domain and HD domain, 1	protein-coding
mm_140452.1	chr17	88626748	88626775	+	1	NA	5' UTR (NM_029858, exon 1 of 4)	5' UTR (NM_029858, exon 1 of 4)	206	NM_029858	77057	Mm.482203	NM_029858	ENSMUSG00000033855	Ston1	4921524J06Rik|C86231|Salf|Sblf	stonin 1	protein-coding
mm_117798.1	chr13	97207032	97207035	-	1	NA	Intergenic	MTE2b|LTR|ERVL-MaLR	-8676	NM_010422	15212	Mm.27816	NM_010422	ENSMUSG00000021665	Hexb	-	hexosaminidase B	protein-coding
mm_48358.1	chr5	139382895	139382908	-	1	NA	intron (NM_030258, intron 1 of 1)	intron (NM_030258, intron 1 of 1)	2234	NM_030258	80290	Mm.270003	NM_030258	ENSMUSG00000044197	Gpr146	BC003323|PGR8	G protein-coupled receptor 146	protein-coding
mm_94120.1	chr10	128642929	128642941	-	1	NA	intron (NM_011772, intron 2 of 7)	intron (NM_011772, intron 2 of 7)	3058	NM_011772	22781	Mm.358648	NM_011772	ENSMUSG00000002578	Ikzf4	A630026H08Rik|Eos|Zfpn1a4|Znfn1a4	IKAROS family zinc finger 4	protein-coding
mm_36341.1	chr4	72852623	72852648	-	1	NA	promoter-TSS (NM_001199270)	promoter-TSS (NM_001199270)	-1	NM_001199270	353204	Mm.317892	NM_001199270	ENSMUSG00000059343	Aldoart1	4921524E03Rik|Aldo1-ps|Aldo1-ps2|Aldoa-ps2	aldolase 1 A, retrogene 1	protein-coding
mm_34018.1	chr4	138014016	138014019	+	1	NA	intron (NM_172703, intron 2 of 34)	intron (NM_172703, intron 2 of 34)	20561	NM_172703	230861	Mm.268903	NM_172703	ENSMUSG00000028760	Eif4g3	1500002J22Rik|4930523M17Rik|G1-419-52|eIF4GII|repro8	eukaryotic translation initiation factor 4 gamma, 3	protein-coding
mm_113414.1	chr13	34010668	34010675	+	1	NA	exon (NM_009068, exon 3 of 11)	exon (NM_009068, exon 3 of 11)	7797	NM_009068	19766	Mm.374799	NM_009068	ENSMUSG00000021408	Ripk1	D330015H01Rik|RIP|Rinp|Rip1	receptor (TNFRSF)-interacting serine-threonine kinase 1	protein-coding
mm_116944.1	chr13	56128313	56128322	-	1	NA	exon (NM_001159515, exon 2 of 9)	exon (NM_001159515, exon 2 of 9)	7233	NM_012015	26914	Mm.283802	NM_012015	ENSMUSG00000015937	H2afy	H2AF12M|mH2a1|macroH2A1	H2A histone family, member Y	protein-coding
mm_67417.1	chr7	80232753	80232842	-	1	NA	promoter-TSS (NM_178752)	promoter-TSS (NM_178752)	8	NM_001291276	23991	Mm.30217	NM_011870	ENSMUSG00000030538	Cib1	Cibkip|Kip|Prkdcip	calcium and integrin binding 1 (calmyrin)	protein-coding
mm_59306.1	chr7	25268395	25268420	+	1	NA	intron (NM_001302811, intron 1 of 20)	CpG	708	NM_001302811	71722	Mm.28833	NM_027882	ENSMUSG00000005442	Cic	1200010B10Rik|mKIAA0306	capicua transcriptional repressor	protein-coding
mm_75848.1	chr8	70647127	70647133	-	1	NA	3' UTR (NM_023217, exon 5 of 5)	3' UTR (NM_023217, exon 5 of 5)	12608	NM_023217	66522	Mm.154906	NM_023217	ENSMUSG00000056204	Pgpep1	2810003H13Rik|Gm19458|PAP-I|PGP|PGP-I|PGPI|Pcp	pyroglutamyl-peptidase I	protein-coding
mm_116023.1	chr13	24937586	24937691	-	1	NA	promoter-TSS (NM_172532)	promoter-TSS (NM_172532)	23	NM_172532	214579	Mm.393311	NM_172532	ENSMUSG00000035936	Aldh5a1	6330403E24Rik|Ahd-1|Ahd1|D630032B01Rik|OTTMUSG00000000613|SSADH|Ssdh1	aldhehyde dehydrogenase family 5, subfamily A1	protein-coding
mm_102863.1	chr11	69405232	69405259	-	1	NA	exon (NM_001017426, exon 11 of 23)	exon (NM_001017426, exon 11 of 23)	-7011	NM_025915	67020	Mm.390406	NM_025915	ENSMUSG00000045377	Tmem88	2600017H02Rik	transmembrane protein 88	protein-coding
mm_145308.1	chr18	53862088	53862143	+	1	NA	promoter-TSS (NM_152809)	promoter-TSS (NM_152809)	2	NM_152809	70425	Mm.368668	NM_152809	ENSMUSG00000073563	Csnk1g3	3300002K07Rik|C330049O21Rik	casein kinase 1, gamma 3	protein-coding
mm_25193.1	chr3	103576134	103576147	+	1	NA	promoter-TSS (NM_001276680)	promoter-TSS (NM_001276680)	14	NM_001276681	54524	Mm.88818	NM_018800	ENSMUSG00000027849	Syt6	3110037A08Rik|AW048930|sytVI	synaptotagmin VI	protein-coding
mm_171495.1	chr4	146157234	146157250	+	1	NA	promoter-TSS (NM_001177545)	promoter-TSS (NM_001177545)	415	NM_001177546	667666	Mm.459230	NM_001177545	ENSMUSG00000066007	Zfp600	Gm13164|OTTMUSG00000010694	zinc finger protein 600	protein-coding
mm_29663.1	chr3	122590199	122590211	-	1	NA	exon (NM_001114665, exon 2 of 16)	exon (NM_001114665, exon 2 of 16)	29509	NM_001114665	214459	Mm.209491	NM_153118	ENSMUSG00000039735	Fnbp1l	2610318I01Rik|AW548221|TOCA1|toca-1	formin binding protein 1-like	protein-coding
mm_145794.1	chr18	65246153	65246179	+	1	NA	intron (NR_105742, intron 4 of 6)	intron (NR_105742, intron 4 of 6)	-2695	NR_029600	387231		NR_029600	ENSMUSG00000065402	Mir122	Mir122a|Mirn122a|mir-122|mmu-mir-122	microRNA 122	ncRNA
mm_61721.1	chr7	81843229	81843235	+	1	NA	Intergenic	ORR1C1|LTR|ERVL-MaLR	-13801	NM_146193	83962	Mm.439893	NM_146193	ENSMUSG00000025103	Btbd1	1190005H08Rik	BTB (POZ) domain containing 1	protein-coding
mm_86535.1	chr10	7858594	7858602	+	1	NA	intron (NM_172785, intron 3 of 5)	Lx7|LINE|L1	22217	NR_039563	100628581		NR_039563	ENSMUSG00000093060	Mir5104	mir-5104|mmu-mir-5104|mu-mir-5104	microRNA 5104	ncRNA
mm_29473.1	chr3	115682682	115682693	-	1	NA	Intergenic	Intergenic	32368	NM_007901	13609	Mm.982	NM_007901	ENSMUSG00000045092	S1pr1	AI849002|Edg1|Lpb1|S1p|S1p1	sphingosine-1-phosphate receptor 1	protein-coding
mm_52336.1	chr6	110645931	110645946	+	1	NA	exon (NM_177328, exon 1 of 10)	exon (NM_177328, exon 1 of 10)	340	NM_177328	108073	Mm.240881	NM_177328	ENSMUSG00000056755	Grm7	6330570A01Rik|BB176677|C030018L03|E130018M02Rik|Gpr1g|Gprc1g|SMN2|Tg(SMN2)89Ahmb|mGluR7	glutamate receptor, metabotropic 7	protein-coding
mm_164639.1	chr17	34804309	34804325	-	1	NA	exon (NM_009995, exon 1 of 10)	exon (NM_009995, exon 1 of 10)	109	NM_009995	13079	Mm.440407	NM_009995	ENSMUSG00000024365	Cyp21a1	21-OH|21OH|21OHA|21OHB|CYP21OH-A|Cyp21|Cyp21-ps1|Cyp21B|Cyp21a2-ps|Cyp21a2ps|Oh21-1|Oh21-2	cytochrome P450, family 21, subfamily a, polypeptide 1	protein-coding
mm_15512.1	chr2	158258261	158258276	+	1	NA	promoter-TSS (NM_177850)	promoter-TSS (NM_177850)	27	NM_177850	329547	Mm.260883	NM_177850	ENSMUSG00000052922	Bpi	9230105K17Rik|Bpifd1	bactericidal permeablility increasing protein	protein-coding
mm_73584.1	chr8	109868532	109868584	+	1	NA	promoter-TSS (NM_001122594)	promoter-TSS (NM_001122594)	-45	NM_001122594	244650	Mm.23494	NM_001122594	ENSMUSG00000031732	Phlpp2	AI481772|C130044A18Rik|Phlppl	PH domain and leucine rich repeat protein phosphatase 2	protein-coding
mm_140986.1	chr17	24724375	24724455	-	1	NA	promoter-TSS (NM_026684)	promoter-TSS (NM_026684)	-27	NM_026684	68342	Mm.1129	NM_026684	ENSMUSG00000040048	Ndufb10	0610011B04Rik|22kDa|PDSW	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 10	protein-coding
mm_11978.1	chr2	55292150	55292177	+	1	NA	Intergenic	Intergenic	-143807	NM_001304810	16519	Mm.5127	NM_008426	ENSMUSG00000026824	Kcnj3	GIRK-1|GIRK1|Kcnf3|Kir3.1	potassium inwardly-rectifying channel, subfamily J, member 3	protein-coding
mm_146166.1	chr18	75183889	75183897	+	1	NA	intron (NM_027727, intron 13 of 16)	intron (NM_027727, intron 13 of 16)	113424	NR_045394	100503117	Mm.250517	NR_045393	ENSMUSG00000102047	2010010A06Rik	5033420E22Rik	RIKEN cDNA 2010010A06 gene	ncRNA
mm_140150.1	chr17	80119223	80119238	+	1	NA	Intergenic	Intergenic	-8241	NM_176963	319625	Mm.29098	NM_176963	ENSMUSG00000035473	Galm	A530057M15Rik|AU015645|AU020959	galactose mutarotase	protein-coding
mm_156676.1	chrX	159303267	159303279	+	1	NA	intron (NM_001346675, intron 4 of 23)	intron (NM_001346675, intron 4 of 23)	47491	NM_001346675	110651	Mm.328476	NM_148945	ENSMUSG00000031309	Rps6ka3	MAPKAPK-1b|MPK-9|Rsk2|S6K-alpha3|p90RSK3|pp90RSK2	ribosomal protein S6 kinase polypeptide 3	protein-coding
mm_104569.1	chr11	96943774	96943784	-	1	NA	promoter-TSS (NR_003293)	promoter-TSS (NR_003293)	240	NM_134021	103711	Mm.254704	NM_134021	ENSMUSG00000018659	Pnpo	AI415282	pyridoxine 5'-phosphate oxidase	protein-coding
mm_45625.1	chr5	76182508	76182523	-	1	NA	Intergenic	Intergenic	-1365	NM_011626	21982	Mm.790	NM_011626	ENSMUSG00000029234	Tmem165	AV026557|Tpardl|Tparl|pFT27	transmembrane protein 165	protein-coding
mm_64151.1	chr7	141328123	141328139	+	1	NA	promoter-TSS (NM_001282076)	promoter-TSS (NM_001282076)	1	NM_027797	71448	Mm.248960	NM_027797	ENSMUSG00000025505	Tmem80	5530601I19Rik	transmembrane protein 80	protein-coding
mm_100739.1	chr11	4103798	4103801	-	1	NA	exon (NM_144520, exon 10 of 12)	exon (NM_144520, exon 10 of 12)	-8368	NM_026443	67900	Mm.41719	NM_026443	ENSMUSG00000004748	Mtfp1	1700020C11Rik|2610507A21Rik|AV005788|Mtp18	mitochondrial fission process 1	protein-coding
mm_136711.1	chr17	7928354	7928363	+	1	NA	intron (NM_145968, intron 4 of 9)	intron (NM_145968, intron 4 of 9)	2358	NM_145968	72536	Mm.119680	NM_145968	ENSMUSG00000033450	Tagap	2610315E15Rik	T cell activation Rho GTPase activating protein	protein-coding
mm_79186.1	chr9	48407722	48407760	+	1	NA	Intergenic	RMER15|LTR|ERVL	45700	NM_172921	244853	Mm.325522	NM_172921	ENSMUSG00000044229	Nxpe4	C130036J11|D930028F11Rik|Fam55d	neurexophilin and PC-esterase domain family, member 4	protein-coding
mm_122020.1	chr14	27508464	27508503	-	1	NA	promoter-TSS (NM_177111)	promoter-TSS (NM_177111)	-23	NM_177111	320234	Mm.247767	NM_177111	ENSMUSG00000046753	Ccdc66	E230015L20Rik	coiled-coil domain containing 66	protein-coding
mm_116708.1	chr13	51026411	51026454	-	1	NA	Intergenic	Intergenic	74295	NR_029463	77428	Mm.405630	NR_029463		9430083A17Rik	-	RIKEN cDNA 9430083A17 gene	ncRNA
mm_149130.1	chr19	9001776	9001806	+	1	NA	exon (NM_009643, exon 5 of 5)	exon (NM_009643, exon 5 of 5)	12507	NM_001286518	66395	Mm.203866	NM_009643	ENSMUSG00000069833	Ahnak	DY6	AHNAK nucleoprotein (desmoyokin)	protein-coding
mm_172865.1	chr9	40804186	40804201	+	1	NA	exon (NM_031165, exon 7 of 9)	exon (NM_031165, exon 7 of 9)	2920	NM_031165	15481	Mm.290774	NM_031165	ENSMUSG00000015656	Hspa8	2410008N15Rik|Hsc70|Hsc71|Hsc73|Hsp73|Hspa10	heat shock protein 8	protein-coding
mm_113546.1	chr13	37936994	37937001	+	1	NA	intron (NR_033218, intron 10 of 11)	RMER3D-int|LTR|ERVK	48126	NM_001177869	68750	Mm.491109	NM_026830	ENSMUSG00000039087	Rreb1	1110037N09Rik|AA414966|B930013M22Rik	ras responsive element binding protein 1	protein-coding
mm_28490.1	chr3	92484299	92484330	-	1	NA	exon (NM_009264, exon 2 of 2)	exon (NM_009264, exon 2 of 2)	1567	NM_009264	20753	Mm.331191	NM_009264	ENSMUSG00000050359	Sprr1a	AI528815|SPR1a|mSPRR1A	small proline-rich protein 1A	protein-coding
mm_15388.1	chr2	156721010	156721030	+	1	NA	promoter-TSS (NM_001042488)	promoter-TSS (NM_001042488)	55	NM_001042488	228836	Mm.22094	NM_146128	ENSMUSG00000061689	Dlgap4	AI225853|BC024558|DAP-4|DAP4|SAPAP-4|Sapap4|WBP16	discs, large homolog-associated protein 4 (Drosophila)	protein-coding
mm_83927.1	chr9	56635606	56635620	-	1	NA	promoter-TSS (NM_001311076)	promoter-TSS (NM_001311076)	35	NM_001311076	235402	Mm.246605	NM_181074	ENSMUSG00000049556	Lingo1	4930471K13Rik|AV148400|LERN1|LINGO-1|Lrrn6a|UNQ201	leucine rich repeat and Ig domain containing 1	protein-coding
mm_58174.1	chr6	142702566	142702586	-	1	NA	promoter-TSS (NM_011511)	promoter-TSS (NM_011511)	-302	NM_001310143	20928	Mm.35670	NM_011511	ENSMUSG00000030249	Abcc9	AI414027|AI449286|SUR2A|SUR2B|Sur2	ATP-binding cassette, sub-family C (CFTR/MRP), member 9	protein-coding
mm_125220.1	chr15	34083328	34083336	+	1	NA	exon (NM_026002, exon 1 of 12)	exon (NM_026002, exon 1 of 12)	613	NM_026002	67154	Mm.130883	NM_026002	ENSMUSG00000022255	Mtdh	2610103J23Rik|3D3|3D3/Lyric|AEG-1|AV353288|D8Bwg1112e|Lyric	metadherin	protein-coding
mm_80996.1	chr9	103423147	103423149	+	1	NA	promoter-TSS (NR_040466)	promoter-TSS (NR_040466)	-430	NR_040466	100529079	Mm.437003	NR_040466	ENSMUSG00000086236	5830418P13Rik	-	RIKEN cDNA 5830418P13 gene	ncRNA
mm_162536.1	chr1	167285216	167285230	-	1	NA	promoter-TSS (NM_030724)	promoter-TSS (NM_030724)	-96	NM_030724	80914	Mm.280895	NM_030724	ENSMUSG00000026558	Uck2	AA407809|AI481316|AU018180|AU020720|TSA903|UK|UMK|Umpk	uridine-cytidine kinase 2	protein-coding
mm_18923.1	chr2	76743769	76743780	-	1	NA	exon (NM_011652, exon 275 of 313)	exon (NM_011652, exon 275 of 313)	68459	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_62057.1	chr7	92447574	92447589	+	1	NA	3' UTR (NM_001243047, exon 11 of 11)	3' UTR (NM_001243047, exon 11 of 11)	-113568	NM_025515	66365	Mm.21173	NM_025515	ENSMUSG00000030613	Ccdc90b	2310015N07Rik|C86558	coiled-coil domain containing 90B	protein-coding
mm_8049.1	chr1	135373410	135373421	-	1	NA	intron (NM_175259, intron 2 of 4)	intron (NM_175259, intron 2 of 4)	1648	NM_175259	77552	Mm.41407	NM_175259	ENSMUSG00000041889	Shisa4	9330132O05Rik|Tmem58|mShisa4	shisa family member 4	protein-coding
mm_74883.1	chr8	25101600	25101608	-	1	NA	intron (NM_031257, intron 1 of 11)	intron (NM_031257, intron 1 of 11)	207	NM_031257	83436	Mm.261122	NM_031257	ENSMUSG00000031557	Plekha2	6430512N22Rik|AI851530|AU041791|TAPP2|W91773	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 2	protein-coding
mm_79598.1	chr9	58488117	58488132	+	1	NA	promoter-TSS (NM_176921)	promoter-TSS (NM_176921)	-479	NM_176921	319477	Mm.153674	NM_176921	ENSMUSG00000066607	6030419C18Rik	-	RIKEN cDNA 6030419C18 gene	protein-coding
mm_130526.1	chr15	98895412	98895432	-	1	NA	intron (NM_007857, intron 1 of 2)	intron (NM_007857, intron 1 of 2)	3118	NM_007857	13363	Mm.324688	NM_007857	ENSMUSG00000023000	Dhh	C78960	desert hedgehog	protein-coding
mm_121110.1	chr14	101654177	101654201	+	1	NA	intron (NM_016723, intron 1 of 8)	CpG	222	NM_016723	50933	Mm.275970	NM_016723	ENSMUSG00000022111	Uchl3	-	ubiquitin carboxyl-terminal esterase L3 (ubiquitin thiolesterase)	protein-coding
mm_74892.1	chr8	25104701	25104709	-	1	NA	Intergenic	Intergenic	-2894	NM_031257	83436	Mm.261122	NM_031257	ENSMUSG00000031557	Plekha2	6430512N22Rik|AI851530|AU041791|TAPP2|W91773	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 2	protein-coding
mm_150530.1	chr19	39290752	39290780	+	1	NA	exon (NM_007815, exon 2 of 9)	exon (NM_007815, exon 2 of 9)	3681	NM_007815	13095	Mm.20764	NM_007815	ENSMUSG00000003053	Cyp2c29	AHOH|AHOHase|AI159681|AI196010|Ah-2|Ahh-1|Cyp2c|P450-2C	cytochrome P450, family 2, subfamily c, polypeptide 29	protein-coding
mm_78245.1	chr9	21640946	21640961	+	1	NA	exon (NM_001174078, exon 9 of 34)	exon (NM_001174078, exon 9 of 34)	24784	NM_001174078	20586	Mm.286593	NM_011417	ENSMUSG00000032187	Smarca4	Brg1|HP1-BP72|SNF2beta|SW1/SNF|b2b508.1Clo|b2b692Clo	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	protein-coding
mm_91799.1	chr10	53629943	53629981	-	1	NA	exon (NM_027830, exon 2 of 14)	exon (NM_027830, exon 2 of 14)	477	NM_027830	71567	Mm.278221	NM_027830	ENSMUSG00000058298	Mcm9	9030408O17Rik|Gm235|Mcmdc1	minichromosome maintenance 9 homologous recombination repair factor	protein-coding
mm_113754.1	chr13	44731725	44731738	+	1	NA	5' UTR (NM_001205043, exon 1 of 18)	5' UTR (NM_001205043, exon 1 of 18)	460	NM_001205043	16468	Mm.25059	NM_021878	ENSMUSG00000038518	Jarid2	Jmj|jumonji	jumonji, AT rich interactive domain 2	protein-coding
mm_30087.1	chr3	138143689	138143713	-	1	NA	promoter-TSS (NM_001163457)	promoter-TSS (NM_001163457)	163	NM_175389	108943	Mm.471692	NM_175389	ENSMUSG00000004127	Trmt10a	3110023L08Rik|AA794508|Rg9mtd2|Rnmtd2	tRNA methyltransferase 10A	protein-coding
mm_65529.1	chr7	25788534	25788554	-	1	NA	5' UTR (NM_001190974, exon 1 of 19)	5' UTR (NM_001190974, exon 1 of 19)	189	NM_001190974	26362	Mm.4128	NM_009465	ENSMUSG00000002602	Axl	AI323647|Ark|Tyro7|Ufo	AXL receptor tyrosine kinase	protein-coding
mm_153766.1	chr19	45591973	45591975	-	1	NA	intron (NM_013907, intron 5 of 8)	intron (NM_013907, intron 5 of 8)	31359	NM_172639	226162	Mm.21978	NM_172639	ENSMUSG00000041035	Dpcd	5330431N19Rik|Ndac	deleted in primary ciliary dyskinesia	protein-coding
mm_71066.1	chr8	34142857	34142870	+	1	NA	intron (NM_026609, intron 1 of 3)	intron (NM_026609, intron 1 of 3)	3876	NM_026609	68192	Mm.34212	NM_026609	ENSMUSG00000031513	Leprotl1	1110067H13Rik|1520402O14Rik|AI854296	leptin receptor overlapping transcript-like 1	protein-coding
mm_124464.1	chr14	121286915	121286996	-	1	NA	3' UTR (NM_145465, exon 11 of 11)	3' UTR (NM_145465, exon 11 of 11)	92275	NM_145465	223255	Mm.390756	NM_145465	ENSMUSG00000063410	Stk24	1810013H02Rik|C76483|MST-3|Mst3|STE20	serine/threonine kinase 24	protein-coding
mm_23523.1	chr3	60617315	60617337	+	1	NA	intron (NM_001310514, intron 7 of 8)	intron (NM_001310514, intron 7 of 8)	116147	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_114502.1	chr13	70574432	70574472	+	1	NA	intron (NR_045934, intron 1 of 2)	intron (NR_045934, intron 1 of 2)	1211	NR_045934	73584	Mm.442491	NR_045934	ENSMUSG00000101051	1700100L14Rik	-	RIKEN cDNA 1700100L14 gene	ncRNA
mm_86019.1	chr9	112235512	112235536	-	1	NA	promoter-TSS (NM_001177619)	promoter-TSS (NM_001177619)	-683	NM_001177619	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_52512.1	chr6	115361291	115361299	+	1	NA	5' UTR (NM_001127330, exon 1 of 8)	5' UTR (NM_001127330, exon 1 of 8)	151	NM_001308352	19016	Mm.3020	NM_011146	ENSMUSG00000000440	Pparg	Nr1c3|PPAR-gamma|PPAR-gamma2|PPARgamma|PPARgamma2	peroxisome proliferator activated receptor gamma	protein-coding
mm_61146.1	chr7	57591148	57591191	+	1	NA	promoter-TSS (NM_008071)	promoter-TSS (NM_008071)	-4	NM_008071	14402	Mm.8004	NM_008071	ENSMUSG00000033676	Gabrb3	A230092K12Rik|AW049585|Cp1|Gabrb-3|beta3	gamma-aminobutyric acid (GABA) A receptor, subunit beta 3	protein-coding
mm_117441.1	chr13	74734243	74734245	-	1	NA	promoter-TSS (NM_001301181)	promoter-TSS (NM_001301181)	17	NM_001301158	12380	Mm.29163	NM_009817	ENSMUSG00000021585	Cast	-	calpastatin	protein-coding
mm_161682.1	chr17	18085105	18085105	+	1	NA	promoter-TSS (NM_001104540)	promoter-TSS (NM_001104540)	48	NM_001104540	665210	Mm.469864	NM_001104540	ENSMUSG00000091206	Vmn2r91	EG665210	vomeronasal 2, receptor 91	protein-coding
mm_55896.1	chr6	83536557	83536569	-	1	NA	promoter-TSS (NM_009610)	promoter-TSS (NM_009610)	-312	NM_009610	11468	Mm.292865	NM_009610	ENSMUSG00000059430	Actg2	ACTA3|Act-4|Act4|SMGA	actin, gamma 2, smooth muscle, enteric	protein-coding
mm_13834.1	chr2	119351223	119351233	+	1	NA	promoter-TSS (NM_026929)	promoter-TSS (NM_026929)	-14	NM_026929	69065	Mm.35083	NM_026929	ENSMUSG00000027313	Chac1	1810008K03Rik	ChaC, cation transport regulator 1	protein-coding
mm_51864.1	chr6	90540787	90540834	+	1	NA	Intergenic	Intergenic	-10038	NM_027406	107747	Mm.30035	NM_027406	ENSMUSG00000030088	Aldh1l1	1810048F20Rik|FDH|Fthfd|Neut2	aldehyde dehydrogenase 1 family, member L1	protein-coding
mm_169242.1	chr13	74729110	74729118	+	1	NA	intron (NM_001301153, intron 18 of 31)	ORR1A2|LTR|ERVL-MaLR	5147	NM_001301158	12380	Mm.29163	NM_009817	ENSMUSG00000021585	Cast	-	calpastatin	protein-coding
mm_173117.1	chrX	160659239	160659246	-	1	NA	intron (NM_011147, intron 6 of 15)	L1Md_T|LINE|L1	60730	NM_011147	237178	Mm.296779	NM_011147	ENSMUSG00000062168	Ppef1	PPEF-1	protein phosphatase with EF hand calcium-binding domain 1	protein-coding
mm_1736.1	chr1	75435938	75435992	+	1	NA	promoter-TSS (NM_133708)	promoter-TSS (NM_133708)	22	NM_133708	69080	Mm.23951	NM_133708	ENSMUSG00000033021	Gmppa	1810012N01Rik	GDP-mannose pyrophosphorylase A	protein-coding
mm_22875.1	chr3	29235928	29235931	+	1	NA	intron (NM_001167748, intron 4 of 12)	intron (NM_001167748, intron 4 of 12)	153352	NM_029412	75740	Mm.330948	NM_029412	ENSMUSG00000063600	Egfem1	6130401L20Rik|Efcab11	EGF-like and EMI domain containing 1	protein-coding
mm_157582.1	chrX	53053272	53053275	-	1	NA	promoter-TSS (NR_029776)	promoter-TSS (NR_029776)	80	NR_029776	723910		NR_029776	ENSMUSG00000065503	Mir351	Mirn351|mmu-mir-351	microRNA 351	ncRNA
mm_135111.1	chr16	35769548	35769563	-	1	NA	promoter-TSS (NM_153550)	promoter-TSS (NM_153550)	-199	NM_153550	224132	Mm.24094	NM_153550	ENSMUSG00000022848	Dirc2	RCC4	disrupted in renal carcinoma 2 (human)	protein-coding
mm_87781.1	chr10	60296480	60296482	+	1	NA	intron (NM_011179, intron 8 of 14)	intron (NM_011179, intron 8 of 14)	12020	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_135591.1	chr16	50721541	50721548	-	1	NA	Intergenic	Intergenic	-5588	NR_105782	102466634		NR_105782	ENSMUSG00000098482	Mir6363	Gm28026|mmu-mir-6363	microRNA 6363	ncRNA
mm_171149.1	chr3	15793847	15793848	-	1	NA	Intergenic	RLTR48B|LTR|ERV1	54640	NM_001173459	100038947	Mm.330924	NM_001173459	ENSMUSG00000074677	LOC100038947	-	signal-regulatory protein beta 1-like	protein-coding
mm_115007.1	chr13	98316434	98316441	+	1	NA	promoter-TSS (NR_137279)	promoter-TSS (NR_137279)	530	NM_145455	218490	Mm.371688	NM_145455	ENSMUSG00000021660	Btf3	1700054E11Rik	basic transcription factor 3	protein-coding
mm_81654.1	chr9	110960827	110960838	+	1	NA	exon (NM_028838, exon 3 of 9)	exon (NM_028838, exon 3 of 9)	9287	NM_028838	74249	Mm.307615	NM_028838	ENSMUSG00000032495	Lrrc2	2400002D05Rik|4933431K03Rik	leucine rich repeat containing 2	protein-coding
mm_17493.1	chr2	28620674	28620676	-	1	NA	intron (NM_008114, intron 1 of 6)	intron (NM_008114, intron 1 of 6)	1307	NM_008114	14582	Mm.373385	NM_008114	ENSMUSG00000026815	Gfi1b	Gfi-1B	growth factor independent 1B	protein-coding
mm_58029.1	chr6	136662130	136662140	-	1	NA	promoter-TSS (NM_025806)	promoter-TSS (NM_025806)	-242	NM_025806	66857	Mm.3311	NM_025806	ENSMUSG00000030214	Plbd1	1100001H23Rik	phospholipase B domain containing 1	protein-coding
mm_44682.1	chr5	30114646	30114652	-	1	NA	exon (NM_001167879, exon 4 of 6)	exon (NM_001167879, exon 4 of 6)	-8563	NM_001256263	433868	Mm.450696	NM_001256263	ENSMUSG00000086815	3110082J24Rik	ENSMUSG00000073106	RIKEN cDNA 3110082J24 gene	protein-coding
mm_163632.1	chr13	58730749	58730752	+	1	NA	Intergenic	Intergenic	31561	NR_045469	67585	Mm.84751	NR_045469		4930455J16Rik	-	RIKEN cDNA 4930455J16 gene	ncRNA
mm_165110.1	chr19	58143878	58143889	-	1	NA	Intergenic	Intergenic	92716	NR_049196	100885835		NR_049196	ENSMUSG00000093757	Mir5623	Gm26068|mir-5623|mmu-mir-5623	microRNA 5623	ncRNA
mm_165950.1	chr4	83527643	83527645	+	1	NA	intron (NM_001081012, intron 1 of 25)	U4|snRNA|snRNA	2099	NM_001081012	320226	Mm.180032	NM_029117	ENSMUSG00000052407	Ccdc171	4930418J05Rik|4930473A06Rik|A330015D16Rik	coiled-coil domain containing 171	protein-coding
mm_41334.1	chr5	90495975	90495986	+	1	NA	exon (NM_007423, exon 4 of 15)	exon (NM_007423, exon 4 of 15)	5266	NM_007423	11576	Mm.358570	NM_007423	ENSMUSG00000054932	Afp	-	alpha fetoprotein	protein-coding
mm_103241.1	chr11	70688061	70688070	-	1	NA	promoter-TSS (NM_001190378)	promoter-TSS (NM_001190378)	40	NM_001190376	216874	Mm.473726	NM_178116	ENSMUSG00000040712	Camta2	Kiaa0909-hp|mKIAA0909	calmodulin binding transcription activator 2	protein-coding
mm_145714.1	chr18	62977827	62977839	+	1	NA	promoter-TSS (NM_028017)	promoter-TSS (NM_028017)	-83	NM_028017	108123	Mm.292687	NM_028017	ENSMUSG00000024581	Napg	2400003O04Rik|SNARE	N-ethylmaleimide sensitive fusion protein attachment protein gamma	protein-coding
mm_18994.1	chr2	76868038	76868057	-	1	NA	exon (NM_011652, exon 105 of 313)	exon (NM_011652, exon 105 of 313)	114500	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_156772.1	chrX	160780604	160780607	+	1	NA	intron (NM_011302, intron 2 of 5)	ID_B1|SINE|B4	12592	NM_011302	20147	Mm.41982	NM_011302	ENSMUSG00000031293	Rs1	Rs1h|Xlrs1|tmgc1	retinoschisis (X-linked, juvenile) 1 (human)	protein-coding
mm_59638.1	chr7	28157665	28157677	+	1	NA	exon (NM_001164655, exon 16 of 20)	exon (NM_001164655, exon 16 of 20)	-12077	NM_007991	14113	Mm.4595	NM_007991	ENSMUSG00000046865	Fbl	AL022665|FIB|FLRN|RNU3IP1	fibrillarin	protein-coding
mm_82425.1	chr9	14903939	14903948	-	1	NA	promoter-TSS (NM_176807)	promoter-TSS (NM_176807)	8	NM_176807	64931	Mm.86738	NM_022888	ENSMUSG00000031933	Izumo1r	0910001L11Rik|C86255|Folbp3|Folr4|Juno	IZUMO1 receptor, JUNO	protein-coding
mm_119579.1	chr14	50870356	50870407	+	1	NA	intron (NM_009351, intron 1 of 54)	intron (NM_009351, intron 1 of 54)	173	NM_009351	21745	Mm.318736	NM_009351	ENSMUSG00000006281	Tep1	Tp1	telomerase associated protein 1	protein-coding
mm_101856.1	chr11	48871147	48871152	-	1	NA	5' UTR (NM_008326, exon 1 of 3)	5' UTR (NM_008326, exon 1 of 3)	197	NM_008326	15944	Mm.29938	NM_008326	ENSMUSG00000046879	Irgm1	Ifggd3|Ifi1|Iigp3|Iipg3|Irgm|LRG-47	immunity-related GTPase family M member 1	protein-coding
mm_76700.1	chr8	94375808	94375820	-	1	NA	Intergenic	MLT1I|LTR|ERVL-MaLR	-10686	NM_022331	64209	Mm.29151	NM_022331	ENSMUSG00000031770	Herpud1	Herp|Mifl|SUP	homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1	protein-coding
mm_96423.1	chr11	67256397	67256405	+	1	NA	exon (NM_010855, exon 34 of 40)	exon (NM_010855, exon 34 of 40)	18589	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_111375.1	chr12	87263900	87263910	-	1	NA	exon (NM_001142580, exon 2 of 20)	exon (NM_001142580, exon 2 of 20)	339	NM_134044	104799	Mm.208750	NM_134044	ENSMUSG00000021038	Vipas39	6720456H09Rik|9330175H22Rik|AI413782|SPE-39|Spe39|Vipar|hSPE-39	VPS33B interacting protein, apical-basolateral polarity regulator, spe-39 homolog	protein-coding
mm_13438.1	chr2	105126718	105126750	+	1	NA	promoter-TSS (NR_015462)	promoter-TSS (NR_015462)	205	NM_144783	22431	Mm.389339	NM_144783	ENSMUSG00000016458	Wt1	D630046I19Rik|Wt-1	Wilms tumor 1 homolog	protein-coding
mm_23720.1	chr3	69006033	69006072	+	1	NA	intron (NM_133786, intron 1 of 23)	CpG	1080	NM_133786	70099	Mm.206841	NM_133786	ENSMUSG00000034349	Smc4	2500002A22Rik|C79747|SMC-4|Smc4l1	structural maintenance of chromosomes 4	protein-coding
mm_96763.1	chr11	69916041	69916055	+	1	NA	TTS (NM_001166592)	TTS (NM_001166592)	1856	NM_019726	56310	Mm.477738	NM_019726	ENSMUSG00000023170	Gps2	AI505953	G protein pathway suppressor 2	protein-coding
mm_162754.1	chr10	60299879	60299907	+	1	NA	exon (NM_011179, exon 11 of 15)	exon (NM_011179, exon 11 of 15)	15432	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_77260.1	chr8	115707279	115707338	-	1	NA	promoter-TSS (NM_001025577)	promoter-TSS (NM_001025577)	-414	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_66632.1	chr7	45522028	45522063	-	1	NA	TTS (NM_008654)	TTS (NM_008654)	4223	NM_008654	17872	Mm.4048	NM_008654	ENSMUSG00000040435	Ppp1r15a	9630030H21|Gadd34|Myd116	protein phosphatase 1, regulatory (inhibitor) subunit 15A	protein-coding
mm_58542.1	chr7	4521671	4521676	+	1	NA	intron (NM_009406, intron 3 of 7)	intron (NM_009406, intron 3 of 7)	770	NM_009406	21954	Mm.27674	NM_009406	ENSMUSG00000035458	Tnni3	Tn1|cTnI	troponin I, cardiac 3	protein-coding
mm_5882.1	chr1	53914629	53914639	-	1	NA	intron (NM_001001883, intron 10 of 28)	intron (NM_001001883, intron 10 of 28)	65210	NR_106149	102465783		NR_106149	ENSMUSG00000098443	Mir7681	Gm27806|mmu-mir-7681	microRNA 7681	ncRNA
mm_52446.1	chr6	113660639	113660651	+	1	NA	intron (NM_001113553, intron 2 of 11)	ORR1D2|LTR|ERVL-MaLR	22178	NM_001113553	108960	Mm.152142	NM_172161	ENSMUSG00000060477	Irak2	6330415L08Rik|AI649099|IRAK-2	interleukin-1 receptor-associated kinase 2	protein-coding
mm_143025.1	chr17	56584310	56584323	-	1	NA	promoter-TSS (NM_001163300)	promoter-TSS (NM_001163300)	267	NM_001029979	224902	Mm.214973	NM_001029979	ENSMUSG00000042625	Safb2	AA389433|AI255170|mKIAA0138	scaffold attachment factor B2	protein-coding
mm_54024.1	chr6	8778456	8778501	-	1	NA	promoter-TSS (NM_010492)	promoter-TSS (NM_010492)	6	NM_010492	15893	Mm.275683	NM_010492	ENSMUSG00000062995	Ica1	69kDa|ICA69	islet cell autoantigen 1	protein-coding
mm_59302.1	chr7	25218915	25218924	+	1	NA	exon (NM_207677, exon 2 of 5)	exon (NM_207677, exon 2 of 5)	940	NM_207677	67379	Mm.280594	NM_026117	ENSMUSG00000054499	Dedd2	2410050E11Rik|FLAME-3	death effector domain-containing DNA binding protein 2	protein-coding
mm_60067.1	chr7	31291443	31291467	+	1	NA	exon (NM_020563, exon 2 of 3)	exon (NM_020563, exon 2 of 3)	361	NM_020563	57426	Mm.6205	NM_020563	ENSMUSG00000062556	Scgb1b2	Abpa2|Abph|Apbh|LGP|Mja1l|Scgb1b1	secretoglobin, family 1B, member 2	protein-coding
mm_144685.1	chr18	34777013	34777075	+	1	NA	promoter-TSS (NM_001081256)	promoter-TSS (NM_001081256)	36	NM_001081256	277250	Mm.277906	NM_029518	ENSMUSG00000038773	Kdm3b	5830462I21Rik|JHDM2B|Jmjd1b|mKIAA1082	KDM3B lysine (K)-specific demethylase 3B	protein-coding
mm_15205.1	chr2	154212999	154213009	+	1	NA	exon (NM_153418, exon 9 of 16)	exon (NM_153418, exon 9 of 16)	-10738	NM_144890	228802	Mm.167411	NM_144890	ENSMUSG00000038572	Bpifb5	Lplunc5	BPI fold containing family B, member 5	protein-coding
mm_168493.1	chr1	150426530	150426532	+	1	NA	intron (NM_133780, intron 29 of 51)	RLTR13C3|LTR|ERVK	-33476	NM_145511	226499	Mm.222093	NM_145511	ENSMUSG00000006010	BC003331	1810053E15Rik|Odr4|odr-4	cDNA sequence BC003331	protein-coding
mm_140490.1	chr17	3283245	3283267	-	1	NA	Intergenic	Intergenic	-43317	NM_001122998	24001	Mm.137134	NM_011878	ENSMUSG00000023800	Tiam2	3000002F19Rik|STEF|mKIAA2016	T cell lymphoma invasion and metastasis 2	protein-coding
mm_54549.1	chr6	36810137	36810147	-	1	NA	5' UTR (NM_008973, exon 1 of 5)	5' UTR (NM_008973, exon 1 of 5)	1219	NM_008973	19242	Mm.279690	NM_008973	ENSMUSG00000029838	Ptn	HARP|HB-GAM|HBBN|HBGF-8|HBNF|OSF|Osf-1|Osf1	pleiotrophin	protein-coding
mm_115558.1	chr13	9173085	9173089	-	1	NA	3' UTR (NM_172585, exon 18 of 18)	3' UTR (NM_172585, exon 18 of 18)	79206	NM_172585	217980	Mm.234944	NM_172585	ENSMUSG00000033499	Larp4b	A630096F19|AI256361|D13Wsu64e|Larp5	La ribonucleoprotein domain family, member 4B	protein-coding
mm_38814.1	chr4	148458873	148458883	-	1	NA	exon (NM_020009, exon 7 of 58)	exon (NM_020009, exon 7 of 58)	10296	NM_020009	56717	Mm.21158	NM_020009	ENSMUSG00000028991	Mtor	2610315D21Rik|AI327068|FRAP|FRAP2|Frap1|RAFT1|RAPT1|flat	mechanistic target of rapamycin (serine/threonine kinase)	protein-coding
mm_50202.1	chr6	42077929	42077929	+	1	NA	Intergenic	Intergenic	39535	NM_009299	20939	Mm.4119	NM_009299	ENSMUSG00000023289	Sva	-	seminal vesicle antigen	protein-coding
mm_94333.1	chr11	4435886	4435887	+	1	NA	intron (NM_029458, intron 1 of 10)	L1MB4|LINE|L1	5196	NM_029458	75828	Mm.159592	NM_029458	ENSMUSG00000020419	Hormad2	4930529M09Rik	HORMA domain containing 2	protein-coding
mm_162278.1	chr1	16665275	16665279	+	1	NA	promoter-TSS (NM_027415)	promoter-TSS (NM_027415)	86	NM_026392	70397	Mm.194225	NM_026392	ENSMUSG00000025940	Tmem70	1110020A09Rik|2210416J16Rik	transmembrane protein 70	protein-coding
mm_126013.1	chr15	76626214	76626226	+	1	NA	promoter-TSS (NM_025842)	promoter-TSS (NM_025842)	-136	NM_001305668	66914	Mm.30028	NM_025842	ENSMUSG00000059323	Vps28	1110014J03Rik|CIIA|D730005C08Rik	vacuolar protein sorting 28	protein-coding
mm_44222.1	chr5	4799093	4799097	-	1	NA	Intergenic	RMER19B|LTR|ERVK	-40879	NM_021457	14362	Mm.246003	NM_021457	ENSMUSG00000044674	Fzd1	AW227548|FZ-1|Fz1	frizzled class receptor 1	protein-coding
mm_159868.1	chr5	145469723	145469723	-	1	NA	promoter-TSS (NM_007820)	promoter-TSS (NM_007820)	0	NM_007820	13114	Mm.378905	NM_007820	ENSMUSG00000038656	Cyp3a16	-	cytochrome P450, family 3, subfamily a, polypeptide 16	protein-coding
mm_50666.1	chr6	51525513	51525516	+	1	NA	intron (NM_001127349, intron 1 of 6)	intron (NM_001127349, intron 1 of 6)	1611	NM_001127349	71982	Mm.294166	NM_028035	ENSMUSG00000038301	Snx10	2410004M09Rik	sorting nexin 10	protein-coding
mm_85057.1	chr9	90237617	90237617	-	1	NA	intron (NM_194334, intron 3 of 12)	MIR3|SINE|MIR	33152	NM_194334	67016	Mm.335347	NM_194334	ENSMUSG00000037410	Tbc1d2b	1810061M12Rik|AI480956|AV021536|AV023399|AW491493|mKIAA1055	TBC1 domain family, member 2B	protein-coding
mm_157560.1	chrX	52165270	52165280	-	1	NA	promoter-TSS (NM_008150)	promoter-TSS (NM_008150)	-352	NM_008150	14735	Mm.1528	NM_008150	ENSMUSG00000031119	Gpc4	9530073D23Rik|AF311610|AI385680|AI661372|K-glypican	glypican 4	protein-coding
mm_62015.1	chr7	91463868	91463894	+	1	NA	intron (NM_011807, intron 2 of 22)	(T)n|Simple_repeat|Simple_repeat	373095	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_97934.1	chr11	83648542	83648544	+	1	NA	intron (NM_011337, intron 2 of 2)	intron (NM_011337, intron 2 of 2)	835	NM_011337	20302	Mm.1282	NM_011337	ENSMUSG00000000982	Ccl3	AI323804|G0S19-1|LD78alpha|MIP-1alpha|MIP1-(a)|MIP1-alpha|Mip1a|Scya3	chemokine (C-C motif) ligand 3	protein-coding
mm_151050.1	chr19	47067722	47067768	+	1	NA	promoter-TSS (NM_177342)	promoter-TSS (NM_177342)	-3	NM_177342	226182	Mm.301522	NM_177342	ENSMUSG00000025049	Taf5	6330528C20Rik|AV117817	TATA-box binding protein associated factor 5	protein-coding
mm_92864.1	chr10	81600864	81600881	-	1	NA	promoter-TSS (NM_053254)	promoter-TSS (NM_053254)	28	NM_053254	114606	Mm.206764	NM_053254	ENSMUSG00000034758	Tle6	1810057E06Rik|Grg6	transducin-like enhancer of split 6	protein-coding
mm_58181.1	chr6	142883829	142883843	-	1	NA	intron (NM_011374, intron 2 of 4)	B3|SINE|B2	69605	NR_045707	665037	Mm.401493	NR_045707	ENSMUSG00000072683	Gm7457	EG665037|ENSMUSG00000072683	predicted gene 7457	ncRNA
mm_19535.1	chr2	94406648	94406696	-	1	NA	promoter-TSS (NR_027831)	promoter-TSS (NR_027831)	17	NM_183106	74569	Mm.248504	NM_183106	ENSMUSG00000027194	Ttc17	9130020K17Rik|D2Bwg1005e	tetratricopeptide repeat domain 17	protein-coding
mm_27343.1	chr3	50414786	50414824	-	1	NA	intron (NM_011990, intron 6 of 11)	intron (NM_011990, intron 6 of 11)	28808	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_107717.1	chr12	56253229	56253248	+	1	NA	promoter-TSS (NR_045048)	promoter-TSS (NR_045048)	-5	NR_045048	100503961	Mm.136732	NR_045048		Gm19990	-	predicted gene, 19990	ncRNA
mm_159954.1	chr6	86413903	86413903	+	1	NA	exon (NM_001164078, exon 2 of 12)	exon (NM_001164078, exon 2 of 12)	9684	NM_001164078	21841	Mm.333219	NM_011585	ENSMUSG00000071337	Tia1	2310050N03Rik|AI256674|TIA-1|mTIA-1	cytotoxic granule-associated RNA binding protein 1	protein-coding
mm_40451.1	chr5	53602403	53602438	+	1	NA	intron (NM_001277116, intron 3 of 12)	intron (NM_001277116, intron 3 of 12)	11934	NM_001080927	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_120652.1	chr14	70530997	70531003	+	1	NA	5' UTR (NM_145219, exon 1 of 8)	5' UTR (NM_145219, exon 1 of 8)	179	NM_145219	213469	Mm.41708	NM_145219	ENSMUSG00000033595	Lgi3	AI841179|AW049851	leucine-rich repeat LGI family, member 3	protein-coding
mm_88337.1	chr10	75589339	75589343	+	1	NA	promoter-TSS (NM_011820)	promoter-TSS (NM_011820)	-40	NM_011820	23887	Mm.257927	NM_011820	ENSMUSG00000006344	Ggt5	AI551243|GGL|GGT-REL|Ggtla1	gamma-glutamyltransferase 5	protein-coding
mm_8610.1	chr1	156036012	156036015	-	1	NA	promoter-TSS (NM_001160182)	promoter-TSS (NM_001160182)	-23	NM_001160182	240832	Mm.253335	NM_022329	ENSMUSG00000050565	Tor1aip2	1110020D10Rik|15kDa|A130072J07|AA103493|AW060462|AW610675|C77739|Ifrg15|Lull1	torsin A interacting protein 2	protein-coding
mm_123553.1	chr14	66845656	66845660	-	1	NA	intron (NM_009955, intron 3 of 13)	intron (NM_009955, intron 3 of 13)	22942	NM_009955	12934	Mm.352648	NM_009955	ENSMUSG00000022048	Dpysl2	AI851130|Crmp2|DRP2|Musunc33|TOAD-64|Ulip2	dihydropyrimidinase-like 2	protein-coding
mm_142892.1	chr17	51833206	51833246	-	1	NA	promoter-TSS (NM_001163632)	promoter-TSS (NM_001163632)	64	NM_001163632	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_63301.1	chr7	126823705	126823806	+	1	NA	promoter-TSS (NM_001146347)	promoter-TSS (NM_001146347)	452	NM_029978	68952	Mm.440393	NM_026884	ENSMUSG00000058966	Fam57b	1500016O10Rik|A330104J06Rik|AI413816|AW060769	family with sequence similarity 57, member B	protein-coding
mm_63480.1	chr7	127746255	127746321	+	1	NA	promoter-TSS (NM_172748)	promoter-TSS (NM_172748)	-487	NM_172748	233902	Mm.259353	NM_172748	ENSMUSG00000030811	Fbxl19	6030430O11|BC059812|Fbl19	F-box and leucine-rich repeat protein 19	protein-coding
mm_169856.1	chr16	3345878	3345884	+	1	NA	Intergenic	Intergenic	-246517	NM_146860	258859	Mm.377723	NM_146860	ENSMUSG00000051003	Olfr161	MOR131-1|OR912-47M6	olfactory receptor 161	protein-coding
mm_163867.1	chr14	19419054	19419062	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	183529	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_79550.1	chr9	57940105	57940120	+	1	NA	promoter-TSS (NM_011352)	promoter-TSS (NM_011352)	-23	NM_011352	20361	Mm.335187	NM_011352	ENSMUSG00000038264	Sema7a	2900057C09Rik|CDw108|H-Sema-L|M-Sema-L|Semal	sema domain, immunoglobulin domain (Ig), and GPI membrane anchor, (semaphorin) 7A	protein-coding
mm_51927.1	chr6	91272471	91272483	+	1	NA	TTS (NM_001081437)	TTS (NM_001081437)	59713	NM_007992	14115	Mm.249146	NM_007992	ENSMUSG00000064080	Fbln2	5730577E14Rik|FIBL-2	fibulin 2	protein-coding
mm_45033.1	chr5	39603522	39603536	-	1	NA	promoter-TSS (NR_045416)	promoter-TSS (NR_045416)	45	NR_045416	75095	Mm.332354	NR_045416	ENSMUSG00000106741	4930513D17Rik	-	RIKEN cDNA 4930513D17 gene	ncRNA
mm_95344.1	chr11	48800042	48800071	+	1	NA	promoter-TSS (NM_008143)	promoter-TSS (NM_008143)	-304	NM_008143	14694	Mm.5305	NM_008143	ENSMUSG00000020372	Rack1	AL033335|GB-like|Gnb2-rs1|Gnb2l1|p205	receptor for activated C kinase 1	protein-coding
mm_141744.1	chr17	34186984	34187011	-	1	NA	promoter-TSS (NM_001161730)	promoter-TSS (NM_001161730)	333	NM_013585	16912	Mm.390983	NM_013585	ENSMUSG00000096727	Psmb9	Lmp-2|Lmp2	proteasome (prosome, macropain) subunit, beta type 9 (large multifunctional peptidase 2)	protein-coding
mm_120927.1	chr14	76477106	76477140	+	1	NA	intron (NM_001310646, intron 3 of 4)	intron (NM_001310646, intron 3 of 4)	-11313	NM_001177751	21807	Mm.153272	NM_009366	ENSMUSG00000022010	Tsc22d1	AA589566|AW105905|Egr5|TSC-22|Tgfb1i4|Tsc|Tsc22	TSC22 domain family, member 1	protein-coding
mm_47858.1	chr5	134564071	134564087	-	1	NA	Intergenic	Intergenic	-3908	NM_001013751	214292	Mm.425290	NM_001013751	ENSMUSG00000085957	Syna	Gm453|Gm52|syncytin-A	syncytin a	protein-coding
mm_3863.1	chr1	160987483	160987518	+	1	NA	5' UTR (NM_080844, exon 2 of 8)	5' UTR (NM_080844, exon 2 of 8)	8894	NM_080844	11905	Mm.260770	NM_080844	ENSMUSG00000026715	Serpinc1	AI114908|ATIII|At-3|At3	serine (or cysteine) peptidase inhibitor, clade C (antithrombin), member 1	protein-coding
mm_160947.1	chr11	96343948	96343948	+	1	NA	5' UTR (NM_010458, exon 1 of 2)	5' UTR (NM_010458, exon 1 of 2)	179	NM_010458	15410	Mm.342481	NM_010458	ENSMUSG00000048763	Hoxb3	Hox-2.7	homeobox B3	protein-coding
mm_3882.1	chr1	161035849	161035852	+	1	NA	non-coding (NR_002840, exon 1 of 4)	non-coding (NR_002840, exon 1 of 4)	684	NR_002840	14455	Mm.270065	NR_002840	ENSMUSG00000053332	Gas5	Gas-5|Mir5117|Snhg2	growth arrest specific 5	ncRNA
mm_64588.1	chr7	3164511	3164520	-	1	NA	intron (NM_001004153, intron 1 of 11)	RMER6B|LTR|ERVK	4688	NM_001004153	245128	Mm.268551	NM_001004153	ENSMUSG00000054753	AU018091	-	expressed sequence AU018091	protein-coding
mm_97360.1	chr11	77503877	77503886	+	1	NA	intron (NM_001004144, intron 10 of 19)	intron (NM_001004144, intron 10 of 19)	9392	NM_001024920	216964	Mm.341211	NM_001024920	ENSMUSG00000044328	Trp53i13	2410019G02Rik|Tp53i13	transformation related protein 53 inducible protein 13	protein-coding
mm_66078.1	chr7	30946176	30946189	-	1	NA	3' UTR (NM_011680, exon 10 of 10)	3' UTR (NM_011680, exon 10 of 10)	-2153	NM_032541	84506	Mm.439939	NM_032541	ENSMUSG00000050440	Hamp	Hamp1|Hepc|Hepc1	hepcidin antimicrobial peptide	protein-coding
mm_3565.1	chr1	150432462	150432472	+	1	NA	exon (NM_133780, exon 35 of 52)	exon (NM_133780, exon 35 of 52)	33698	NM_021400	96875	Mm.174256	NM_021400	ENSMUSG00000006014	Prg4	CACP|DOL54|JCAP|MSF|SZP|lubricin	proteoglycan 4 (megakaryocyte stimulating factor, articular superficial zone protein)	protein-coding
mm_168224.1	chr10	79442476	79442479	+	1	NA	Intergenic	L1Md_A|LINE|L1	-26481	NM_001104537	625029	Mm.469865	NM_001104537	ENSMUSG00000091381	Vmn2r83	EG625029	vomeronasal 2, receptor 83	protein-coding
mm_38970.1	chr4	150902191	150902198	-	1	NA	intron (NM_020569, intron 5 of 6)	intron (NM_020569, intron 5 of 6)	7727	NM_020569	57320	Mm.277349	NM_020569	ENSMUSG00000028964	Park7	DJ-1|Dj1	Parkinson disease (autosomal recessive, early onset) 7	protein-coding
mm_16821.1	chr2	11473893	11473938	-	1	NA	3' UTR (NM_001177754, exon 16 of 16)	3' UTR (NM_001177754, exon 16 of 16)	28175	NM_001177754	170768	Mm.19669	NM_133232	ENSMUSG00000026773	Pfkfb3	E330010H22Rik|iPFK-2|uPFK-2	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	protein-coding
mm_3165.1	chr1	135324823	135324856	+	1	NA	promoter-TSS (NM_053106)	promoter-TSS (NM_053106)	26	NM_053106	93689	Mm.180124	NM_053106	ENSMUSG00000048096	Lmod1	9530015K06Rik|SM-Lmod	leiomodin 1 (smooth muscle)	protein-coding
mm_2475.1	chr1	105788071	105788076	+	1	NA	intron (NM_009399, intron 1 of 9)	intron (NM_009399, intron 1 of 9)	7350	NM_009399	21934	Mm.6251	NM_009399	ENSMUSG00000026321	Tnfrsf11a	Ly109|ODFR|OFE|Rank|TRANCE-R|mRANK	tumor necrosis factor receptor superfamily, member 11a, NFKB activator	protein-coding
mm_129214.1	chr15	76522576	76522591	-	1	NA	promoter-TSS (NM_130893)	promoter-TSS (NM_130893)	-454	NM_130893	170729	Mm.218747	NM_130893	ENSMUSG00000048385	Scrt1	-	scratch family zinc finger 1	protein-coding
mm_48103.1	chr5	137069421	137069444	-	1	NA	exon (NM_008871, exon 3 of 9)	exon (NM_008871, exon 3 of 9)	2840	NM_008871	18787	Mm.250422	NM_008871	ENSMUSG00000037411	Serpine1	PAI-1|PAI1|Planh1	serine (or cysteine) peptidase inhibitor, clade E, member 1	protein-coding
mm_4904.1	chr1	189879904	189879910	+	1	NA	TTS (NM_026796)	TTS (NM_026796)	42381	NM_026796	226830	Mm.156895	NM_026796	ENSMUSG00000026603	Smyd2	1110020E07Rik|4930402C15|KMT3C|Zmynd14	SET and MYND domain containing 2	protein-coding
mm_14475.1	chr2	131498629	131498635	+	1	NA	intron (NM_001177836, intron 1 of 7)	(T)n|Simple_repeat|Simple_repeat	6770	NM_001177838	228608	Mm.136586	NM_145533	ENSMUSG00000027333	Smox	B130066H01Rik|PAO|PAOh1|SMO	spermine oxidase	protein-coding
mm_171241.1	chr3	74242619	74242619	+	1	NA	Intergenic	Intergenic	-225342	NR_040450	100504692	Mm.394454	NR_040450	ENSMUSG00000104096	Gm20356	-	predicted gene, 20356	ncRNA
mm_40095.1	chr5	34559101	34559131	+	1	NA	exon (NM_001145859, exon 8 of 13)	exon (NM_001145859, exon 8 of 13)	9540	NM_001145859	24055	Mm.5012	NM_011893	ENSMUSG00000054520	Sh3bp2	3BP2	SH3-domain binding protein 2	protein-coding
mm_35807.1	chr4	46650086	46650100	-	1	NA	5' UTR (NM_198664, exon 1 of 13)	5' UTR (NM_198664, exon 1 of 13)	106	NM_198664	381605	Mm.331595	NM_198664	ENSMUSG00000039813	Tbc1d2	A630005A06Rik|BC022630|Gm1037|PARIS-1|PARIS1	TBC1 domain family, member 2	protein-coding
mm_11843.1	chr2	45133476	45133480	+	1	NA	Intergenic	RMER15|LTR|ERVL	-20199	NM_015753	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_79052.1	chr9	46229202	46229246	+	1	NA	exon (NM_009692, exon 3 of 4)	exon (NM_009692, exon 3 of 4)	594	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2|apo-AI|apoA-I	apolipoprotein A-I	protein-coding
mm_57849.1	chr6	129470816	129470821	-	1	NA	intron (NR_132130, intron 2 of 5)	MIR|SINE|MIR	1961	NM_001309637	56644	Mm.239516	NM_020008	ENSMUSG00000079293	Clec7a	BGR|Clecsf12|beta-GR	C-type lectin domain family 7, member a	protein-coding
mm_86644.1	chr10	14523064	14523065	+	1	NA	intron (NM_001002268, intron 2 of 24)	intron (NM_001002268, intron 2 of 24)	21972	NM_001002268	215798	Mm.440142	NM_001002268	ENSMUSG00000039116	Adgrg6	1190004A11Rik|AI449247|AW045736|DREG|Gm222|Gpr126	adhesion G protein-coupled receptor G6	protein-coding
mm_135445.1	chr16	45492963	45492993	-	1	NA	promoter-TSS (NM_001005854)	promoter-TSS (NM_001005854)	-9	NM_001005854	208166	Mm.451852	NM_001005854	ENSMUSG00000053182	Gm609	Gm1749|isec1	predicted gene 609	protein-coding
mm_95624.1	chr11	53583921	53583934	+	1	NA	exon (NM_008443, exon 7 of 18)	exon (NM_008443, exon 7 of 18)	16558	NM_001290806	16568	Mm.88694	NM_008443	ENSMUSG00000018395	Kif3a	Kif3|Kifl|Kns3	kinesin family member 3A	protein-coding
mm_75824.1	chr8	70487315	70487381	-	1	NA	promoter-TSS (NM_182991)	promoter-TSS (NM_182991)	10	NM_182991	67937	Mm.23002	NM_182991	ENSMUSG00000035964	Tmem59l	5330410G16Rik	transmembrane protein 59-like	protein-coding
mm_143067.1	chr17	57021688	57021700	-	1	NA	3' UTR (NM_010613, exon 18 of 18)	3' UTR (NM_010613, exon 18 of 18)	9813	NM_010613	16549	Mm.34296	NM_010613	ENSMUSG00000007670	Khsrp	6330409F21Rik|Fbp2|Fubp2|Ksrp	KH-type splicing regulatory protein	protein-coding
mm_10984.1	chr2	26154312	26154317	+	1	NA	Intergenic	Intergenic	-13808	NM_001256521	109299	Mm.389259	NM_001256521		C330006A16Rik	AI551216	RIKEN cDNA C330006A16 gene	protein-coding
mm_79797.1	chr9	64117156	64117191	+	1	NA	promoter-TSS (NM_145835)	promoter-TSS (NM_145835)	26	NM_145835	235435	Mm.436581	NM_145835	ENSMUSG00000032401	Lctl	E130104I05Rik|KLPH	lactase-like	protein-coding
mm_111547.1	chr12	100923591	100923595	-	1	NA	intron (NM_026681, intron 25 of 29)	intron (NM_026681, intron 25 of 29)	-15395	NM_001177673	238377	Mm.32160	NM_175493	ENSMUSG00000047415	Gpr68	BB131428|Ogr1	G protein-coupled receptor 68	protein-coding
mm_83337.1	chr9	44268157	44268167	-	1	NA	promoter-TSS (NM_001163743)	promoter-TSS (NM_001163743)	25	NM_001163743	270151	Mm.3957	NM_178420	ENSMUSG00000032109	Nlrx1	BC034204|NOD9	NLR family member X1	protein-coding
mm_63400.1	chr7	127297329	127297377	+	1	NA	intron (NM_001253874, intron 1 of 30)	intron (NM_001253874, intron 1 of 30)	1093	NM_001253874	16408	Mm.1618	NM_008400	ENSMUSG00000030830	Itgal	(p180)|Cd11a|LFA-1|LFA-1A|Ly-15|Ly-21	integrin alpha L	protein-coding
mm_62439.1	chr7	101373310	101373341	+	1	NA	exon (NM_001040111, exon 3 of 34)	exon (NM_001040111, exon 3 of 34)	-4797	NM_001040112	69710	Mm.277687	NM_027180	ENSMUSG00000032812	Arap1	2410002L19Rik|Centd2|mKIAA0782	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	protein-coding
mm_116936.1	chr13	55836107	55836155	-	1	NA	Intergenic	CpG	-4706	NM_011097	18740	Mm.135195	NM_011097	ENSMUSG00000021506	Pitx1	Bft|P-OTX|Potx|Ptx1	paired-like homeodomain transcription factor 1	protein-coding
mm_74753.1	chr8	19064913	19064932	-	1	NA	promoter-TSS (NM_183038)	promoter-TSS (NM_183038)	-112	NM_183038	360214	Mm.271559	NM_183038	ENSMUSG00000061847	Defb39	BD-39	defensin beta 39	protein-coding
mm_153698.1	chr19	44397518	44397530	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	10185	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_157131.1	chrX	9449658	9449739	-	1	NA	exon (NM_007807, exon 8 of 13)	exon (NM_007807, exon 8 of 13)	19626	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_56836.1	chr6	117179093	117179110	-	1	NA	3' UTR (NM_001012477, exon 4 of 4)	3' UTR (NM_001012477, exon 4 of 4)	10566	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_44458.1	chr5	22528711	22528715	-	1	NA	non-coding (NR_004442, exon 1 of 1)	non-coding (NR_004442, exon 1 of 1)	317	NR_004442	100042049	Mm.21724	NR_004442		Gm15421	OTTMUSG00000021442	ribosomal protein L22 like 1 pseudogene	pseudo
mm_44382.1	chr5	17828636	17828649	-	1	NA	intron (NM_007643, intron 3 of 14)	intron (NM_007643, intron 3 of 14)	7254	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_137347.1	chr17	25162442	25162456	+	1	NA	promoter-TSS (NM_001079929)	promoter-TSS (NM_001079929)	-12	NM_001079929	207209	Mm.207121	NM_001079929	ENSMUSG00000059562	Ccdc154	Ccdc157|Gm317	coiled-coil domain containing 154	protein-coding
mm_126074.1	chr15	77698905	77698910	+	1	NA	promoter-TSS (NM_001134802)	promoter-TSS (NM_001134802)	18	NM_001134802	666348	Mm.303207	NM_001134802	ENSMUSG00000071716	Apol7e	ENSMUSG00000071716	apolipoprotein L 7e	protein-coding
mm_25957.1	chr3	132154920	132154923	+	1	NA	intron (NM_020265, intron 1 of 3)	intron (NM_020265, intron 1 of 3)	69629	NM_020265	56811	Mm.103593	NM_020265	ENSMUSG00000028031	Dkk2	-	dickkopf WNT signaling pathway inhibitor 2	protein-coding
mm_56859.1	chr6	118197387	118197397	-	1	NA	5' UTR (NM_009050, exon 1 of 20)	5' UTR (NM_009050, exon 1 of 20)	352	NM_009050	19713	Mm.57199	NM_009050	ENSMUSG00000030110	Ret	PTC|RET51|RET9|c-Ret	ret proto-oncogene	protein-coding
mm_129184.1	chr15	76307232	76307296	-	1	NA	promoter-TSS (NM_153122)	promoter-TSS (NM_153122)	-19	NM_153122	75475	Mm.322738	NM_153122	ENSMUSG00000022562	Oplah	1700010G02Rik	5-oxoprolinase (ATP-hydrolysing)	protein-coding
mm_139097.1	chr17	46910470	46910487	+	1	NA	promoter-TSS (NM_008938)	promoter-TSS (NM_008938)	-7	NM_008938	19133	Mm.291370	NM_008938	ENSMUSG00000023978	Prph2	AOFMD|AVMD|Nmf193|PRPH|RP7|Rd-2|Rd2|Rds|Tspan22|rds	peripherin 2	protein-coding
mm_40810.1	chr5	71699919	71699949	+	1	NA	promoter-TSS (NM_008069)	promoter-TSS (NM_008069)	-82	NM_008069	14400	Mm.38567	NM_008069	ENSMUSG00000029212	Gabrb1	AW061132|B230208N19Rik|Gabrb-1	gamma-aminobutyric acid (GABA) A receptor, subunit beta 1	protein-coding
mm_108857.1	chr12	98747462	98747467	+	1	NA	intron (NM_001008506, intron 1 of 14)	intron (NM_001008506, intron 1 of 14)	496	NM_029334	75553	Mm.25549	NM_029334	ENSMUSG00000021012	Zc3h14	1010001P15Rik|1700016A15Rik|2700069A02Rik|AU014748	zinc finger CCCH type containing 14	protein-coding
mm_116994.1	chr13	56548475	56548487	-	1	NA	promoter-TSS (NM_010702)	promoter-TSS (NM_010702)	57	NM_010702	16841	Mm.16973	NM_010702	ENSMUSG00000021539	Lect2	-	leukocyte cell-derived chemotaxin 2	protein-coding
mm_11307.1	chr2	30266514	30266564	+	1	NA	promoter-TSS (NM_001281829)	promoter-TSS (NM_001281829)	-182	NM_001281829	227696	Mm.297949	NM_172267	ENSMUSG00000079484	Phyhd1	-	phytanoyl-CoA dioxygenase domain containing 1	protein-coding
mm_9643.1	chr1	177207416	177207421	-	1	NA	intron (NM_011785, intron 1 of 12)	L1M2|LINE|L1	41349	NM_011785	23797	Mm.235194	NM_011785	ENSMUSG00000019699	Akt3	AI851531|D930002M15Rik|Nmf350	thymoma viral proto-oncogene 3	protein-coding
mm_72582.1	chr8	84204289	84204304	+	1	NA	Intergenic	Intergenic	-4222	NR_029740	387216		NR_029740	ENSMUSG00000065611	Mir23a	Mirn23a|mir-23a|mmu-mir-23a	microRNA 23a	ncRNA
mm_8344.1	chr1	150165810	150165816	-	1	NA	promoter-TSS (NR_110420)	promoter-TSS (NR_110420)	-865	NR_110420	102639566	Mm.417208	NR_110420	ENSMUSG00000097754	Ptgs2os2	Gm26687|Linc-cox2|Lincrna-cox2	prostaglandin-endoperoxide synthase 2, opposite strand 2	ncRNA
mm_128719.1	chr15	64015525	64015540	-	1	NA	intron (NM_144846, intron 1 of 11)	intron (NM_144846, intron 1 of 11)	44916	NM_144846	223601	Mm.246108	NM_144846	ENSMUSG00000022378	Fam49b	0910001A06Rik|AW122079	family with sequence similarity 49, member B	protein-coding
mm_160489.1	chr8	126298470	126298470	+	1	NA	promoter-TSS (NM_175434)	promoter-TSS (NM_175434)	-109	NM_175434	210027	Mm.405238	NM_175434	ENSMUSG00000057060	Slc35f3	B230375D17Rik	solute carrier family 35, member F3	protein-coding
mm_4689.1	chr1	180726006	180726017	+	1	NA	promoter-TSS (NM_133225)	promoter-TSS (NM_133225)	-32	NM_133225	170760	Mm.272981	NM_133225	ENSMUSG00000026499	Acbd3	60kDa|8430407O11Rik|D1Ertd10e|GCP60|GOLPH1|Gocap1|Pap7	acyl-Coenzyme A binding domain containing 3	protein-coding
mm_26411.1	chr3	142608280	142608294	+	1	NA	exon (NM_010259, exon 8 of 11)	exon (NM_010259, exon 8 of 11)	-12376	NM_010260	14469	Mm.24038	NM_010260	ENSMUSG00000028270	Gbp2	-	guanylate binding protein 2	protein-coding
mm_68847.1	chr7	126368530	126368546	-	1	NA	promoter-TSS (NR_106025)	promoter-TSS (NR_106025)	-493	NR_106025	102466797		NR_106025	ENSMUSG00000099017	Mir7058	Gm27766|mmu-mir-7058	microRNA 7058	ncRNA
mm_1094.1	chr1	59705643	59705655	+	1	NA	TTS (NR_028521)	TTS (NR_028521)	841	NR_028521	100217421		NR_028521		Snord11	MBII-95	small nucleolar RNA, C/D box 11	snoRNA
mm_56916.1	chr6	119388672	119388739	-	1	NA	intron (NM_197985, intron 1 of 7)	CpG	28778	NM_197985	68465	Mm.291826	NM_197985	ENSMUSG00000030168	Adipor2	1110001I14Rik|ADCR2|AI115388|AW554121|D6Ucla1e|Paqr2	adiponectin receptor 2	protein-coding
mm_120244.1	chr14	62992365	62992373	+	1	NA	Intergenic	Intergenic	-5708	NM_001039125	654465	Mm.424929	NM_001039125	ENSMUSG00000075573	Defb47	Defb41|EG654465	defensin beta 47	protein-coding
mm_21817.1	chr2	165283712	165283725	-	1	NA	intron (NM_144893, intron 1 of 9)	intron (NM_144893, intron 1 of 9)	4069	NM_001252574	228875	Mm.21184	NM_144893	ENSMUSG00000017664	Slc35c2	C85957|CGI-15|D2Wsu58e|Ovcov1	solute carrier family 35, member C2	protein-coding
mm_122672.1	chr14	51988833	51988837	-	1	NA	promoter-TSS (NR_045728)	promoter-TSS (NR_045728)	-6	NR_045728	100502764	Mm.437219	NR_045728	ENSMUSG00000097633	Gm16617	-	predicted gene, 16617	ncRNA
mm_94448.1	chr11	6389086	6389106	+	1	NA	Intergenic	Intergenic	-6029	NM_001005867	52915	Mm.1144	NM_028601	ENSMUSG00000041164	Zmiz2	Zimp7	zinc finger, MIZ-type containing 2	protein-coding
mm_21354.1	chr2	157123332	157123348	-	1	NA	exon (NM_001139520, exon 4 of 17)	exon (NM_001139520, exon 4 of 17)	11882	NM_001139520	56045	Mm.248478	NM_018851	ENSMUSG00000027639	Samhd1	E330031J07Rik|Mg11	SAM domain and HD domain, 1	protein-coding
mm_4176.1	chr1	171123127	171123168	+	1	NA	5' UTR (NM_001081275, exon 2 of 6)	5' UTR (NM_001081275, exon 2 of 6)	1486	NM_001081275	75472	Mm.32760	NM_029301	ENSMUSG00000026649	Cfap126	1700009P17Rik|AV282292|Flattop|Fltp	cilia and flagella associated protein 126	protein-coding
mm_159431.1	chr3	113324029	113324029	-	1	NA	promoter-TSS (NM_001160152).2	promoter-TSS (NM_001160152).2	23	NM_001160151	100043686	Mm.275426	NM_001160151	ENSMUSG00000093931	Amy2a3	OTTMUSG00000022430|mAmy2-4	amylase 2a3	protein-coding
mm_155497.1	chrX	73765520	73765584	+	1	NA	intron (NM_019587, intron 15 of 34)	intron (NM_019587, intron 15 of 34)	8449	NM_019587	140571	Mm.275600	NM_019587	ENSMUSG00000031385	Plxnb3	AI451018|Plxn6	plexin B3	protein-coding
mm_49411.1	chr6	28624491	28624496	+	1	NA	intron (NM_019776, intron 10 of 23)	intron (NM_019776, intron 10 of 23)	144145	NM_019776	56463	Mm.439987	NM_019776	ENSMUSG00000001424	Snd1	AL033314|Tudor-SN	staphylococcal nuclease and tudor domain containing 1	protein-coding
mm_167501.1	chr9	13296965	13296979	+	1	NA	Intergenic	Intergenic	50016	NM_025534	66396	Mm.290620	NM_025534	ENSMUSG00000079084	Ccdc82	2310043N13Rik	coiled-coil domain containing 82	protein-coding
mm_29427.1	chr3	109021870	109021913	-	1	NA	intron (NM_001163567, intron 1 of 10)	intron (NM_001163567, intron 1 of 10)	5716	NM_001163567	329739	Mm.69013	NM_001163567	ENSMUSG00000040339	Fam102b	1600010D10Rik|B430201A12Rik	family with sequence similarity 102, member B	protein-coding
mm_89593.1	chr10	95940859	95940875	+	1	NA	5' UTR (NM_001001932, exon 1 of 29)	5' UTR (NM_001001932, exon 1 of 29)	204	NM_001001932	216238	Mm.210035	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding
mm_97451.1	chr11	78193380	78193424	+	1	NA	promoter-TSS (NM_001045516)	promoter-TSS (NM_001045516)	10	NM_001045516	216974	Mm.50974	NM_001045516	ENSMUSG00000044122	Proca1	4933404M19Rik	protein interacting with cyclin A1	protein-coding
mm_22983.1	chr3	32939307	32939327	+	1	NA	Intergenic	Intergenic	45762	NM_001163517	58869	Mm.151332	NM_021483	ENSMUSG00000027674	Pex5l	1700016J08Rik|PXR2|Pex2|TRIP8b|pex5Rp	peroxisomal biogenesis factor 5-like	protein-coding
mm_99828.1	chr11	108920844	108920856	+	1	NA	intron (NM_015732, intron 1 of 10)	CpG	501	NM_015732	12006	Mm.71710	NM_015732	ENSMUSG00000000142	Axin2	Axi1|Axil|Conductin	axin 2	protein-coding
mm_28837.1	chr3	96580138	96580148	-	1	NA	intron (NM_001293701, intron 4 of 6)	intron (NM_001293701, intron 4 of 6)	-13342	NR_040409	100038464	Mm.475126	NR_040409	ENSMUSG00000074398	Gm15441	ENSMUSG00000074398|OTTMUSG00000021867	predicted gene 15441	ncRNA
mm_136090.1	chr16	84977971	84977985	-	1	NA	intron (NR_045889, intron 3 of 3)	intron (NR_045889, intron 3 of 3)	5767	NR_045889	100038614	Mm.441351	NR_045889		Gm10791	ENSMUSG00000074933	predicted gene 10791	ncRNA
mm_25927.1	chr3	131200107	131200145	+	1	NA	intron (NM_001276403, intron 8 of 11)	intron (NM_001276403, intron 8 of 11)	71975	NM_008212	15107	Mm.260164	NM_008212	ENSMUSG00000027984	Hadh	AA409008|AU019341|AW742602|HCDH|Hadhsc|Schad	hydroxyacyl-Coenzyme A dehydrogenase	protein-coding
mm_1282.1	chr1	63730617	63730657	+	1	NA	promoter-TSS (NM_172422)	promoter-TSS (NM_172422)	12	NM_172422	75619	Mm.30965	NM_172422	ENSMUSG00000025962	Fastkd2	2810421I24Rik	FAST kinase domains 2	protein-coding
mm_135034.1	chr16	32868272	32868280	-	1	NA	promoter-TSS (NM_001200038)	promoter-TSS (NM_001200038)	90	NM_001200038	100502698	Mm.327319	NM_172615	ENSMUSG00000035629	Rubcn	1700021K19Rik|5330403K09|Kiaa0226|Rubicon|mKIAA0226	RUN domain and cysteine-rich domain containing, Beclin 1-interacting protein	protein-coding
mm_150844.1	chr19	44988367	44988376	+	1	NA	promoter-TSS (NM_011976)	promoter-TSS (NM_011976)	-973	NM_011976	26456	Mm.34404	NM_011976	ENSMUSG00000025207	Sema4g	AI507908|AW554132	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4G	protein-coding
mm_53604.1	chr6	138156297	138156308	+	1	NA	exon (NM_019946, exon 4 of 4)	exon (NM_019946, exon 4 of 4)	14708	NM_001347489	56615	Mm.14796	NM_019946	ENSMUSG00000008540	Mgst1	1500002K10Rik|Gst	microsomal glutathione S-transferase 1	protein-coding
mm_96108.1	chr11	60541371	60541374	+	1	NA	intron (NM_172943, intron 1 of 3)	intron (NM_172943, intron 1 of 3)	3689	NM_172943	268420	Mm.262056	NM_172943	ENSMUSG00000042650	Alkbh5	AW050020|AW215868|Abh5|E130207K11|Ofoxd	alkB homolog 5, RNA demethylase	protein-coding
mm_138116.1	chr17	34139400	34139403	+	1	NA	TTS (NM_010386)	TTS (NM_010386)	-6015	NM_010388	15000	Mm.195060	NM_010388	ENSMUSG00000037548	H2-DMb2	H-2Mb2|H2-Mb2	histocompatibility 2, class II, locus Mb2	protein-coding
mm_118895.1	chr14	26638037	26638047	+	1	NA	promoter-TSS (NM_007479)	promoter-TSS (NM_007479)	-155	NM_007479	11843	Mm.297768	NM_007479	ENSMUSG00000021877	Arf4	AA407803	ADP-ribosylation factor 4	protein-coding
mm_136230.1	chr16	90284383	90284393	-	1	NA	5' UTR (NM_001346799, exon 1 of 20)	5' UTR (NM_001346799, exon 1 of 20)	115	NM_178923	224432	Mm.439811	NM_178923	ENSMUSG00000022983	Scaf4	AA517739|Sfrs15|Sra4|Srsf15	SR-related CTD-associated factor 4	protein-coding
mm_667.1	chr1	40448671	40448680	+	1	NA	TTS (NM_010743)	TTS (NM_010743)	9046	NM_010743	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_100061.1	chr11	115307208	115307227	+	1	NA	promoter-TSS (NM_172801)	promoter-TSS (NM_172801)	54	NM_172801	237987	Mm.44542	NM_172801	ENSMUSG00000050201	Otop2	4732464P15	otopetrin 2	protein-coding
mm_63822.1	chr7	134670651	134670661	+	1	NA	promoter-TSS (NM_001033420)	promoter-TSS (NM_001033420)	-31	NM_001033420	330662	Mm.436572	NM_001033420	ENSMUSG00000058325	Dock1	9130006G06Rik|AI854900|D630004B07Rik	dedicator of cytokinesis 1	protein-coding
mm_25528.1	chr3	114904239	114904265	+	1	NA	promoter-TSS (NM_001286750)	promoter-TSS (NM_001286750)	174	NM_153458	229759	Mm.54183	NM_153157	ENSMUSG00000027965	Olfm3	B230206G02Rik	olfactomedin 3	protein-coding
mm_110184.1	chr12	27338244	27338250	-	1	NA	3' UTR (NM_009234, exon 1 of 1)	3' UTR (NM_009234, exon 1 of 1)	4471	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding
mm_90670.1	chr10	128861971	128861993	+	1	NA	intron (NM_025364, intron 9 of 10)	intron (NM_025364, intron 9 of 10)	29736	NM_010272	14561	Mm.299218	NM_010272	ENSMUSG00000025352	Gdf11	BMP-11|Bmp11	growth differentiation factor 11	protein-coding
mm_53508.1	chr6	135381963	135381975	+	1	NA	3' UTR (NM_001288627, exon 5 of 5)	3' UTR (NM_001288627, exon 5 of 5)	14476	NM_001288627	13730	Mm.182785	NM_010128	ENSMUSG00000030208	Emp1	I-8-09|TMP	epithelial membrane protein 1	protein-coding
mm_160639.1	chr9	108509306	108509306	+	1	NA	intron (NM_133794, intron 4 of 23)	intron (NM_133794, intron 4 of 23)	1301	NM_133794	97541	Mm.272427	NM_133794	ENSMUSG00000032604	Qars	1110018N24Rik|1200016L19Rik|C80286|GLNRS	glutaminyl-tRNA synthetase	protein-coding
mm_66950.1	chr7	62085257	62085283	-	1	NA	promoter-TSS (NR_049204)	promoter-TSS (NR_049204)	40	NR_049204	100885843		NR_049204	ENSMUSG00000095154	Mir344i	Gm26031|mir-344i|mmu-mir-344i	microRNA 344i	ncRNA
mm_91893.1	chr10	59951754	59951775	-	1	NA	promoter-TSS (NM_029083)	promoter-TSS (NM_029083)	6	NM_029083	74747	Mm.21697	NM_029083	ENSMUSG00000020108	Ddit4	5830413E08Rik|AA415483|REDD1|Rtp801|dig2	DNA-damage-inducible transcript 4	protein-coding
mm_134641.1	chr16	21762908	21762911	-	1	NA	exon (NM_023737, exon 7 of 7)	exon (NM_023737, exon 7 of 7)	24925	NM_023737	74147	Mm.28100	NM_023737	ENSMUSG00000022853	Ehhadh	1300002P22Rik|HD|L-PBE|LBFP|LBP|MFP|MFP1|PBFE	enoyl-Coenzyme A, hydratase/3-hydroxyacyl Coenzyme A dehydrogenase	protein-coding
mm_155718.1	chrX	96112083	96112098	+	1	NA	intron (NM_010833, intron 1 of 12)	intron (NM_010833, intron 1 of 12)	16045	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_134462.1	chr16	18426426	18426434	-	1	NA	promoter-TSS (NM_013711)	promoter-TSS (NM_013711)	13	NM_013711	26462	Mm.390906	NM_013711	ENSMUSG00000075704	Txnrd2	AA118373|ESTM573010|TGR|Tr3|Trxr2|Trxrd2	thioredoxin reductase 2	protein-coding
mm_114586.1	chr13	75749901	75749907	+	1	NA	intron (NM_138953, intron 3 of 11)	intron (NM_138953, intron 3 of 11)	42420	NM_138953	192657	Mm.21288	NM_138953	ENSMUSG00000001542	Ell2	-	elongation factor RNA polymerase II 2	protein-coding
mm_163499.1	chr12	111967029	111967034	-	1	NA	promoter-TSS (NM_027360)	promoter-TSS (NM_027360)	-54	NM_027360	70257	Mm.318	NM_027360	ENSMUSG00000021290	2010107E04Rik	9430003J03Rik|AU043134|AV124504|Mp68	RIKEN cDNA 2010107E04 gene	protein-coding
mm_41072.1	chr5	87668605	87668608	+	1	NA	intron (NM_001286015, intron 3 of 32)	RSINE1|SINE|B4	2398	NM_001286016	12990	Mm.427467	NM_007784	ENSMUSG00000070702	Csn1s1	AA959832|AW212882|Csna	casein alpha s1	protein-coding
mm_31622.1	chr4	59189640	59189646	+	1	NA	promoter-TSS (NM_011673)	promoter-TSS (NM_011673)	93	NM_011673	22234	Mm.198803	NM_011673	ENSMUSG00000028381	Ugcg	AU043821|C80537|Epcs21|GlcT-1|Ugcgl	UDP-glucose ceramide glucosyltransferase	protein-coding
mm_75492.1	chr8	50517648	50517665	-	1	NA	Intergenic	Lx8|LINE|L1	149544	NR_046067	100039954	Mm.400419	NR_046067	ENSMUSG00000110281	Gm2516	-	predicted gene 2516	ncRNA
mm_51818.1	chr6	88944566	88944574	+	1	NA	Intergenic	Intergenic	42319	NM_011906	24100	Mm.284480	NM_011906	ENSMUSG00000002871	Tpra1	40kDa|Gpr175|Tpra40	transmembrane protein, adipocyte asscociated 1	protein-coding
mm_86923.1	chr10	23851750	23851774	+	1	NA	exon (NM_011979, exon 1 of 7)	exon (NM_011979, exon 1 of 7)	300	NM_011979	26464	Mm.27334	NM_011979	ENSMUSG00000020010	Vnn3	-	vanin 3	protein-coding
mm_113072.1	chr13	23779263	23779271	+	1	NA	Intergenic	Intergenic	-3274	NM_001029935	214158	Mm.314151	NM_001029935	ENSMUSG00000064140	Trim38	Gm23	tripartite motif-containing 38	protein-coding
mm_42883.1	chr5	122371876	122371887	+	1	NA	promoter-TSS (NM_026883)	promoter-TSS (NM_026883)	82	NM_026883	68948	Mm.474469	NM_026883	ENSMUSG00000029463	Fam216a	1500011H22Rik	family with sequence similarity 216, member A	protein-coding
mm_25363.1	chr3	107101028	107101057	+	1	NA	promoter-TSS (NM_008417)	promoter-TSS (NM_008417)	-525	NM_008417	16490	Mm.39285	NM_008417	ENSMUSG00000040724	Kcna2	Akr6a4|ENSMUSG00000074335|Gm10672|Kca1-2|Kv1.2|Mk-2	potassium voltage-gated channel, shaker-related subfamily, member 2	protein-coding
mm_168259.1	chr10	8762498	8762498	-	1	NA	intron (NM_175155, intron 8 of 19)	intron (NM_175155, intron 8 of 19)	123572	NM_175155	70097	Mm.338275	NM_175155	ENSMUSG00000015305	Sash1	1100001C18Rik|2500002E12Rik|A330076K04Rik|mKIAA0790	SAM and SH3 domain containing 1	protein-coding
mm_162178.1	chrX	102707635	102707635	-	1	NA	promoter-TSS (NM_001039116)	promoter-TSS (NM_001039116)	35	NM_001177365	668339	Mm.394985	NM_001177365	ENSMUSG00000079479	Gm9112	EG668339	predicted gene 9112	protein-coding
mm_91387.1	chr10	30655725	30655729	-	1	NA	5' UTR (NM_001111267, exon 1 of 6)	5' UTR (NM_001111267, exon 1 of 6)	140	NM_001111267	211329	Mm.297903	NM_172495	ENSMUSG00000039697	Ncoa7	9030406N13Rik	nuclear receptor coactivator 7	protein-coding
mm_73779.1	chr8	116921755	116921763	+	1	NA	promoter-TSS (NM_028131)	promoter-TSS (NM_028131)	19	NM_028131	72155	Mm.23185	NM_028131	ENSMUSG00000031756	Cenpn	2610510J17Rik|AI426416|AW545024	centromere protein N	protein-coding
mm_106583.1	chr11	120729634	120729640	-	1	NA	3' UTR (NM_007621, exon 8 of 8)	3' UTR (NM_007621, exon 8 of 8)	-2353	NM_001347608	67880	Mm.231091	NM_026428	ENSMUSG00000039450	Dcxr	0610038K04Rik|1810027P18Rik|XR	dicarbonyl L-xylulose reductase	protein-coding
mm_70603.1	chr8	13351744	13351770	+	1	NA	intron (NM_001291766, intron 2 of 10)	intron (NM_001291766, intron 2 of 10)	12953	NM_009361	21781	Mm.925	NM_009361	ENSMUSG00000038482	Tfdp1	Dp1|Drtf1	transcription factor Dp 1	protein-coding
mm_30215.1	chr3	145009887	145009897	-	1	NA	exon (NM_017474, exon 10 of 14)	exon (NM_017474, exon 10 of 14)	22884	NM_017474	23844	Mm.33483	NM_017474	ENSMUSG00000028255	Clca1	Clca2|Clca3|gob-5|gob5	chloride channel accessory 1	protein-coding
mm_46026.1	chr5	91402845	91402851	-	1	NA	5' UTR (NM_007568, exon 1 of 6)	5' UTR (NM_007568, exon 1 of 6)	146	NM_007568	12223	Mm.2024	NM_007568	ENSMUSG00000082361	Btc	Bcn	betacellulin, epidermal growth factor family member	protein-coding
mm_58315.1	chr6	146401392	146401422	-	1	NA	intron (NM_010586, intron 9 of 55)	intron (NM_010586, intron 9 of 55)	100816	NM_010586	16439	Mm.7800	NM_010586	ENSMUSG00000030287	Itpr2	AI649341|InsP3R-2|InsP3R-5|Ip3r2|Itpr5|insP3R2	inositol 1,4,5-triphosphate receptor 2	protein-coding
mm_128530.1	chr15	54847382	54847396	-	1	NA	intron (NM_001136077, intron 22 of 25)	intron (NM_001136077, intron 22 of 25)	72757	NM_015744	18606	Mm.250256	NM_015744	ENSMUSG00000022425	Enpp2	ATX|E-NPP 2|Npps2|PD-Ialpha|Pdnp2|lysoPLD	ectonucleotide pyrophosphatase/phosphodiesterase 2	protein-coding
mm_55056.1	chr6	49047385	49047415	-	1	NA	exon (NM_053110, exon 5 of 11)	exon (NM_053110, exon 5 of 11)	10882	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_37762.1	chr4	129696580	129696602	-	1	NA	intron (NM_199305, intron 1 of 8)	CpG	247	NM_199305	230770	Mm.257157	NM_199305	ENSMUSG00000053730	Tmem39b	6330509E05Rik|BC037095	transmembrane protein 39b	protein-coding
mm_56013.1	chr6	86525293	86525303	-	1	NA	exon (NM_011865, exon 1 of 1)	exon (NM_011865, exon 1 of 1)	867	NM_011865	23983	Mm.274146	NM_011865	ENSMUSG00000051695	Pcbp1	WBP17|[a]CP-1|alphaCP-1|hnRNP E1	poly(rC) binding protein 1	protein-coding
mm_83727.1	chr9	50972740	50972743	-	1	NA	intron (NM_178710, intron 3 of 15)	B4A|SINE|B4	36332	NM_178710	235344	Mm.104932	NM_178710	ENSMUSG00000037112	Sik2	G630080D20Rik|Snf1lk2	salt inducible kinase 2	protein-coding
mm_46646.1	chr5	108582861	108582879	-	1	NA	exon (NM_153569, exon 21 of 28)	exon (NM_153569, exon 21 of 28)	-32843	NM_007756	12889	Mm.5195	NM_007756	ENSMUSG00000033615	Cplx1	921-S	complexin 1	protein-coding
mm_47931.1	chr5	135078225	135078260	-	1	NA	promoter-TSS (NM_177574)	promoter-TSS (NM_177574)	24	NM_177574	194309	Mm.44356	NM_177574	ENSMUSG00000043614	Vps37d	Wbscr24	vacuolar protein sorting 37D	protein-coding
mm_92336.1	chr10	75798577	75798587	-	1	NA	promoter-TSS (NM_008185)	promoter-TSS (NM_008185)	2	NM_008185	14871	Mm.2746	NM_008185	ENSMUSG00000001663	Gstt1	AI255817|Gstt1-1	glutathione S-transferase, theta 1	protein-coding
mm_27852.1	chr3	79157089	79157098	-	1	NA	Intergenic	L1_Mur3|LINE|L1	-11218	NM_001099624	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_59194.1	chr7	24500729	24500738	+	1	NA	exon (NM_153112, exon 6 of 9)	exon (NM_153112, exon 6 of 9)	-6354	NM_001290461	232969	Mm.181332	NM_146183	ENSMUSG00000064264	Zfp428	2410005H09Rik|AV271806|AW047854|Znf428	zinc finger protein 428	protein-coding
mm_2487.1	chr1	105990385	105990498	+	1	NA	promoter-TSS (NM_001122675)	promoter-TSS (NM_001122675)	35	NM_001122675	227449	Mm.210188	NM_001122675	ENSMUSG00000038866	Zcchc2	9930114B20Rik|AW212015	zinc finger, CCHC domain containing 2	protein-coding
mm_38042.1	chr4	133967195	133967227	-	1	NA	intron (NM_016957, intron 1 of 5)	CpG	780	NM_016957	15331	Mm.319660	NM_016957	ENSMUSG00000003038	Hmgn2	HMG-17|Hmg17	high mobility group nucleosomal binding domain 2	protein-coding
mm_57910.1	chr6	132627513	132627516	-	1	NA	promoter-TSS (NM_001142969)	promoter-TSS (NM_001142969)	-3	NM_001142969	381819	Mm.156682	NM_001142969	ENSMUSG00000067541	A630073D07Rik	Gm1688	RIKEN cDNA A630073D07 gene	protein-coding
mm_151181.1	chr19	53352888	53352893	+	1	NA	intron (NM_001008542, intron 3 of 5)	intron (NM_001008542, intron 3 of 5)	22444	NM_001008543	17859	Mm.2154	NM_010847	ENSMUSG00000025025	Mxi1	ENSMUSG00000067085|Gm10197|Mad2|bHLHc11	MAX interactor 1, dimerization protein	protein-coding
mm_117071.1	chr13	59229276	59229282	-	1	NA	Intergenic	Intergenic	315172	NM_001284221	67269	Mm.153008	NM_023328	ENSMUSG00000021557	Agtpbp1	1700020N17Rik|2310001G17Rik|2900054O13Rik|4930445M19Rik|5730402G09Rik|CCP1|Nna1|nmf243|pcd	ATP/GTP binding protein 1	protein-coding
mm_127788.1	chr15	3568704	3568705	-	1	NA	intron (NM_001048178, intron 1 of 8)	intron (NM_001048178, intron 1 of 8)	13138	NM_001286370	14600	Mm.3986	NM_010284	ENSMUSG00000055737	Ghr	GHBP|GHR/BP	growth hormone receptor	protein-coding
mm_146539.1	chr18	5593430	5593455	-	1	NA	intron (NM_011546, intron 1 of 7)	CpG-6713	-1005	NR_033552	791318	Mm.84339	NR_033552	ENSMUSG00000063087	Gm10125	ENSMUSG00000063087|Zeb1os	predicted gene 10125	ncRNA
mm_2074.1	chr1	87640700	87640748	+	1	NA	intron (NM_010566, intron 2 of 26)	intron (NM_010566, intron 2 of 26)	20412	NM_001110193	16331	Mm.15105	NM_010566	ENSMUSG00000026288	Inpp5d	SHIP|SHIP-1|SHIP1|SIP-145|p150Ship|s-SHIP	inositol polyphosphate-5-phosphatase D	protein-coding
mm_6738.1	chr1	83038433	83038459	-	1	NA	promoter-TSS (NM_030556)	promoter-TSS (NM_030556)	2	NM_030556	80721	Mm.261542	NM_030556	ENSMUSG00000038496	Slc19a3	A230084E24Rik|AI788884|ThTr2	solute carrier family 19, member 3	protein-coding
mm_9294.1	chr1	171637180	171637188	-	1	NA	intron (NM_001347184, intron 4 of 5)	intron (NM_001347184, intron 4 of 5)	4716	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_86153.1	chr9	117872546	117872602	-	1	NA	Intergenic	CpG	-167948	NM_001286508	27215	Mm.92705	NM_013727	ENSMUSG00000039285	Azi2	AA410145|AZ2	5-azacytidine induced gene 2	protein-coding
mm_517.1	chr1	37430336	37430348	+	1	NA	promoter-TSS (NM_198006)	promoter-TSS (NM_198006)	170	NM_026123	67387	Mm.27404	NM_026123	ENSMUSG00000026111	Unc50	1110002A21Rik|GMH1|UNCL|URP	unc-50 homolog (C. elegans)	protein-coding
mm_43513.1	chr5	137066969	137066994	+	1	NA	exon (NM_008871, exon 5 of 9)	exon (NM_008871, exon 5 of 9)	5291	NM_008871	18787	Mm.250422	NM_008871	ENSMUSG00000037411	Serpine1	PAI-1|PAI1|Planh1	serine (or cysteine) peptidase inhibitor, clade E, member 1	protein-coding
mm_68064.1	chr7	101866771	101866781	-	1	NA	intron (NM_001252552, intron 3 of 6)	intron (NM_001252552, intron 3 of 6)	4012	NM_001252554	14275	Mm.2135	NM_008034	ENSMUSG00000001827	Folr1	FBP1|Folbp-1|Folbp1	folate receptor 1 (adult)	protein-coding
mm_147501.1	chr18	49979233	49979254	-	1	NA	promoter-TSS (NM_001177760)	promoter-TSS (NM_001177760)	-184	NM_001177760	106869	Mm.27740	NM_134131	ENSMUSG00000062210	Tnfaip8	AA987150|E130304C20Rik|ENSMUSG00000073567|Gg2-1|Gm10539|Nded|Ssc-2|Tipe	tumor necrosis factor, alpha-induced protein 8	protein-coding
mm_69112.1	chr7	127025082	127025135	-	1	NA	intron (NM_010772, intron 2 of 4)	intron (NM_010772, intron 2 of 4)	1371	NM_010772	17188	Mm.378964	NM_010772	ENSMUSG00000030678	Maz	MAZI|PUR1|Pur-1|SAF-1|SAF-2	MYC-associated zinc finger protein (purine-binding transcription factor)	protein-coding
mm_141110.1	chr17	26058680	26058681	-	1	NA	intron (NM_001162869, intron 1 of 14)	PB1D9|SINE|Alu	10497	NM_001162868	215445	Mm.41191	NM_153140	ENSMUSG00000037098	Rab11fip3	Cart1|D030060O14Rik|Rab11-FIP3|mKIAA0665	RAB11 family interacting protein 3 (class II)	protein-coding
mm_92173.1	chr10	67596663	67596710	-	1	NA	Intergenic	Intergenic	-47731	NM_001005419	211488	Mm.297250	NM_001005419	ENSMUSG00000057134	Ado	Gm237	2-aminoethanethiol (cysteamine) dioxygenase	protein-coding
mm_146132.1	chr18	74625562	74625571	+	1	NA	exon (NM_201600, exon 6 of 39)	exon (NM_201600, exon 6 of 39)	-94442	NR_045368	73606	Mm.444734	NR_045368		1700120E14Rik	-	RIKEN cDNA 1700120E14 gene	ncRNA
mm_63730.1	chr7	130867509	130867514	+	1	NA	intron (NM_001346515, intron 1 of 12)	intron (NM_001346515, intron 1 of 12)	1601	NM_133942	101476	Mm.323554	NM_133942	ENSMUSG00000040268	Plekha1	AA960558|C920009D07Rik|TAPP1	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 1	protein-coding
mm_149164.1	chr19	9018582	9018584	+	1	NA	TTS (NR_105786)	TTS (NR_105786)	679	NR_105786	102465190		NR_105786	ENSMUSG00000099308	Mir6367	Gm27467|mmu-mir-6367	microRNA 6367	ncRNA
mm_89552.1	chr10	94725646	94725657	+	1	NA	exon (NM_029852, exon 4 of 16)	exon (NM_029852, exon 4 of 16)	36861	NM_029852	77048	Mm.296971	NM_029852	ENSMUSG00000020024	Cep83	2600001G24Rik|4921537D05Rik|5730513H21Rik|Ccdc41	centrosomal protein 83	protein-coding
mm_59168.1	chr7	24399960	24399975	+	1	NA	intron (NM_028047, intron 1 of 13)	CpG	339	NM_028047	71997	Mm.150977	NM_028047	ENSMUSG00000002210	Smg9	1500002O20Rik|AI429693|N28092	smg-9 homolog, nonsense mediated mRNA decay factor (C. elegans)	protein-coding
mm_105664.1	chr11	107413703	107413714	-	1	NA	intron (NM_145823, intron 1 of 9)	intron (NM_145823, intron 1 of 9)	57012	NM_145823	71795	Mm.397413	NM_145823	ENSMUSG00000040430	Pitpnc1	1110020B03Rik|5830436L09Rik|AI662802|AI851387|C330017I21Rik|Dnr411|RDGBB|RDGBB1|rdgB-beta	phosphatidylinositol transfer protein, cytoplasmic 1	protein-coding
mm_115244.1	chr13	110395042	110395057	+	1	NA	promoter-TSS (NM_152804)	promoter-TSS (NM_152804)	5	NM_152804	20620	Mm.380	NM_152804	ENSMUSG00000021701	Plk2	Snk	polo-like kinase 2	protein-coding
mm_61016.1	chr7	49372241	49372251	+	1	NA	intron (NM_175272, intron 2 of 37)	intron (NM_175272, intron 2 of 37)	126057	NM_175272	78286	Mm.333881	NM_175272	ENSMUSG00000052512	Nav2	5330421F07Rik|AU067780|BQ960892|HELAD1|POMFIL2|RAINB1|RAINB2|Unc53H2|mKIAA3015	neuron navigator 2	protein-coding
mm_103887.1	chr11	83574712	83574719	-	1	NA	3' UTR (NM_011338, exon 4 of 4)	3' UTR (NM_011338, exon 4 of 4)	3921	NM_011338	20308	Mm.416125	NM_011338	ENSMUSG00000019122	Ccl9	CCF18|MRP-2|Scya10|Scya9	chemokine (C-C motif) ligand 9	protein-coding
mm_115844.1	chr13	21287393	21287395	-	1	NA	exon (NM_010343, exon 5 of 5)	exon (NM_010343, exon 5 of 5)	5292	NM_010343	14780	Mm.1332	NM_010343	ENSMUSG00000004344	Gpx5	AV379049|Arep	glutathione peroxidase 5	protein-coding
mm_139724.1	chr17	57476323	57476358	+	1	NA	intron (NM_010130, intron 19 of 21)	MIRc|SINE|MIR	68974	NM_001104591	224916	Mm.469889	NM_001104591	ENSMUSG00000090655	Vmn2r120	EG224916	vomeronasal 2, receptor 120	protein-coding
mm_81271.1	chr9	108094658	108094696	+	1	NA	promoter-TSS (NM_146226)	promoter-TSS (NM_146226)	-197	NM_146226	235606	Mm.219639	NM_146226	ENSMUSG00000032590	Apeh	-	acylpeptide hydrolase	protein-coding
mm_76621.1	chr8	91713329	91713350	-	1	NA	Intergenic	Intergenic	88315	NM_001253822	16373	Mm.238044	NM_008393	ENSMUSG00000031734	Irx3	AI894186	Iroquois related homeobox 3	protein-coding
mm_122627.1	chr14	51145719	51145725	-	1	NA	exon (NM_011271, exon 2 of 2)	exon (NM_011271, exon 2 of 2)	1045	NM_011271	19752	Mm.235538	NM_011271	ENSMUSG00000035896	Rnase1	AI574248|Rib-1|Rib1	ribonuclease, RNase A family, 1 (pancreatic)	protein-coding
mm_138646.1	chr17	35866843	35866852	+	1	NA	5' UTR (NM_175242, exon 1 of 3)	5' UTR (NM_175242, exon 1 of 3)	232	NM_175242	76448	Mm.359982	NM_175242	ENSMUSG00000034595	Ppp1r18	2310014H01Rik|AA407849|AI450394	protein phosphatase 1, regulatory subunit 18	protein-coding
mm_79819.1	chr9	64340705	64340726	+	1	NA	promoter-TSS (NM_001177784)	promoter-TSS (NM_001177784)	58	NM_001177784	213550	Mm.268341	NM_172519	ENSMUSG00000032396	Dis3l	AV340375	DIS3 like exosome 3'-5' exoribonuclease	protein-coding
mm_109857.1	chr12	4769218	4769267	-	1	NA	promoter-TSS (NM_175431)	promoter-TSS (NM_175431)	25	NM_175431	207921	Mm.184898	NM_175431	ENSMUSG00000050545	Fam228b	A830093I24Rik	family with sequence similarity 228, member B	protein-coding
mm_30954.1	chr4	33310307	33310387	+	1	NA	promoter-TSS (NM_001305273)	promoter-TSS (NM_001305273)	36	NM_001305273	24018	Mm.240024	NM_011884	ENSMUSG00000028274	Rngtt	AU020997|HCE|MCE1	RNA guanylyltransferase and 5'-phosphatase	protein-coding
mm_119962.1	chr14	55478771	55478795	+	1	NA	promoter-TSS (NM_030686)	promoter-TSS (NM_030686)	25	NM_030686	28200	Mm.27427	NM_030686	ENSMUSG00000022210	Dhrs4	AI043103|AI790593|CR|D14Ucla2|NDRD|PHCR|PSCD|RRD|mouNRDR	dehydrogenase/reductase (SDR family) member 4	protein-coding
mm_41976.1	chr5	107437909	107437991	+	1	NA	promoter-TSS (NM_001255991)	promoter-TSS (NM_001255991)	-47	NM_001255991	100503185	Mm.366650	NM_001255991	ENSMUSG00000111375	Btbd8	EG627196|Gm16115|OTTMUSG00000030610	BTB (POZ) domain containing 8	protein-coding
mm_157105.1	chrX	9437849	9437853	-	1	NA	3' UTR (NM_007807, exon 13 of 13)	3' UTR (NM_007807, exon 13 of 13)	31473	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_24024.1	chr3	87527371	87527438	+	1	NA	intron (NM_001286844, intron 2 of 4)	intron (NM_001286844, intron 2 of 4)	1826	NM_012051	27049	Mm.219460	NM_012051	ENSMUSG00000003382	Etv3	AI414410|METS|Pe1	ets variant 3	protein-coding
mm_104816.1	chr11	98968779	98968795	-	1	NA	intron (NM_001176528, intron 3 of 7)	intron (NM_001176528, intron 3 of 7)	8316	NM_001176528	19401	Mm.439744	NM_009024	ENSMUSG00000037992	Rara	Nr1b1|RAR|RARalpha1	retinoic acid receptor, alpha	protein-coding
mm_40522.1	chr5	57918546	57918553	+	1	NA	intron (NM_001122758, intron 2 of 2)	intron (NM_001122758, intron 2 of 2)	200468	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_26649.1	chr3	154021340	154021346	+	1	NA	intron (NM_001081263, intron 1 of 21)	intron (NM_001081263, intron 1 of 21)	47907	NM_001081263	242259	Mm.239962	NM_001081263	ENSMUSG00000028360	Slc44a5	AA117069|Gm422	solute carrier family 44, member 5	protein-coding
mm_122177.1	chr14	31546035	31546037	-	1	NA	intron (NM_009937, intron 6 of 16)	B2_Mm2|SINE|B2	31347	NM_009937	382864	Mm.239821	NM_009937	ENSMUSG00000057606	Colq	A130034K24Rik	collagen-like tail subunit (single strand of homotrimer) of asymmetric acetylcholinesterase	protein-coding
mm_35321.1	chr4	25800240	25800266	-	1	NA	promoter-TSS (NM_010243)	promoter-TSS (NM_010243)	-250	NM_010243	14348	Mm.39101	NM_010243	ENSMUSG00000055373	Fut9	AI746471|AU067636|mFUT9|mFuc-TIX	fucosyltransferase 9	protein-coding
mm_3546.1	chr1	150407372	150407382	+	1	NA	exon (NM_133780, exon 9 of 52)	exon (NM_133780, exon 9 of 52)	-14322	NM_145511	226499	Mm.222093	NM_145511	ENSMUSG00000006010	BC003331	1810053E15Rik|Odr4|odr-4	cDNA sequence BC003331	protein-coding
mm_141938.1	chr17	35048434	35048452	-	1	NA	Intergenic	Intergenic	-1698	NM_001146215	17687	Mm.24192	NM_013600	ENSMUSG00000007035	Msh5	Mut5	mutS homolog 5	protein-coding
mm_162884.1	chr10	104941104	104941110	+	1	NA	Intergenic	Lx8|LINE|L1	633372	NM_177368	278279	Mm.25225	NM_177368	ENSMUSG00000036019	Tmtc2	8430438D04Rik|D330034A10Rik	transmembrane and tetratricopeptide repeat containing 2	protein-coding
mm_130381.1	chr15	97856096	97856104	-	1	NA	3' UTR (NM_009504, exon 10 of 10)	3' UTR (NM_009504, exon 10 of 10)	-11598	NM_001204278	56233	Mm.384027	NM_019572	ENSMUSG00000022475	Hdac7	5830434K02Rik|HD7|HD7a|Hdac7a|mFLJ00062	histone deacetylase 7	protein-coding
mm_101206.1	chr11	19056130	19056134	-	1	NA	Intergenic	Intergenic	-9143	NR_046037	74059	Mm.292321	NR_046037	ENSMUSG00000086025	4933406G16Rik	-	RIKEN cDNA 4933406G16 gene	ncRNA
mm_132175.1	chr16	32379937	32379941	+	1	NA	intron (NM_177633, intron 8 of 10)	RLTR19B|LTR|ERVK	-20567	NM_001160402	277203	Mm.484240	NM_001160402	ENSMUSG00000079625	Tm4sf19	EG277203	transmembrane 4 L six family member 19	protein-coding
mm_140284.1	chr17	85090621	85090645	+	1	NA	promoter-TSS (NM_001163624)	promoter-TSS (NM_001163624)	-67	NM_028576	73582	Mm.260753	NM_028576	ENSMUSG00000071037	Camkmt	1700106N22Rik|AI480743|AV099781|CLNMT|CaM KMT	calmodulin-lysine N-methyltransferase	protein-coding
mm_115934.1	chr13	23621091	23621115	-	1	NA	promoter-TSS (NM_178194)	promoter-TSS (NM_178194)	-9	NM_001177653	319179	Mm.440391	NM_178194	ENSMUSG00000047246	Hist1h2be	-	histone cluster 1, H2be	protein-coding
mm_129472.1	chr15	78673681	78673689	-	1	NA	exon (NM_183141, exon 2 of 2)	exon (NM_183141, exon 2 of 2)	44428	NM_183141	207393	Mm.323188	NM_183141	ENSMUSG00000043460	Elfn2	6330514E13|AW048948|BC094219|Lrrc62|Ppp1r29	leucine rich repeat and fibronectin type III, extracellular 2	protein-coding
mm_172560.1	chr8	106778651	106778651	-	1	NA	intron (NM_173037, intron 14 of 17)	intron (NM_173037, intron 14 of 17)	-91591	NM_008217	15118	Mm.56986	NM_008217	ENSMUSG00000031910	Has3	-	hyaluronan synthase 3	protein-coding
mm_143140.1	chr17	57220181	57220196	-	1	NA	exon (NM_009778, exon 18 of 41)	exon (NM_009778, exon 18 of 41)	-2960	NR_105944	102465591		NR_105944	ENSMUSG00000099066	Mir6978	Gm27858|mmu-mir-6978	microRNA 6978	ncRNA
mm_9200.1	chr1	171226313	171226323	-	1	NA	TTS (NM_013474)	TTS (NM_013474)	1264	NM_013474	11807	Mm.389209	NM_013474	ENSMUSG00000005681	Apoa2	Alp-2|Apo-AII|ApoA-II|ApoAII|Apoa-2|Hdl-1	apolipoprotein A-II	protein-coding
mm_110386.1	chr12	40248074	40248086	-	1	NA	Intergenic	Intergenic	24716	NR_045157	629820	Mm.435540	NR_045157	ENSMUSG00000035983	Gm7008	EG629820	predicted gene 7008	ncRNA
mm_161375.1	chr14	69567322	69567322	+	1	NA	intron (NM_026174, intron 2 of 12)	intron (NM_026174, intron 2 of 12)	11921	NM_026174	67464	Mm.489765	NM_026174	ENSMUSG00000095463	Entpd4	1200014F22Rik|4930513O14Rik|A430102M06Rik|AI414893|Lysal1|mKIAA0392	ectonucleoside triphosphate diphosphohydrolase 4	protein-coding
mm_130944.1	chr15	103251648	103251654	-	1	NA	promoter-TSS (NM_001302340)	promoter-TSS (NM_001302340)	25	NM_001302338	18022	Mm.457989	NM_008685	ENSMUSG00000058794	Nfe2	NF-E2|NF-E2/P45|p45|p45NFE2|p45nf-e2	nuclear factor, erythroid derived 2	protein-coding
mm_165699.1	chr3	95124438	95124449	+	1	NA	promoter-TSS (NM_016712)	promoter-TSS (NM_016712)	-71	NM_016712	50874	Mm.71935	NM_016712	ENSMUSG00000005628	Tmod4	MTMOD|Sk-Tmod	tropomodulin 4	protein-coding
mm_38114.1	chr4	134535316	134535330	-	1	NA	promoter-TSS (NM_001256112)	promoter-TSS (NM_001256112)	-55	NM_001256112	76824	Mm.30153	NM_029759	ENSMUSG00000046671	Mtfr1l	2410166I05Rik|AI480750|Fam54b	mitochondrial fission regulator 1-like	protein-coding
mm_34820.1	chr4	154961178	154961189	+	1	NA	exon (NM_010419, exon 2 of 3)	exon (NM_010419, exon 2 of 3)	260	NM_010419	15208	Mm.137268	NM_010419	ENSMUSG00000048001	Hes5	bHLHb38	hairy and enhancer of split 5 (Drosophila)	protein-coding
mm_77892.1	chr9	7347498	7347522	+	1	NA	exon (NM_008605, exon 1 of 10)	exon (NM_008605, exon 1 of 10)	136	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_99318.1	chr11	101442402	101442410	+	1	NA	5' UTR (NM_011289, exon 1 of 5)	5' UTR (NM_011289, exon 1 of 5)	161	NM_011289	19942	Mm.340658	NM_011289	ENSMUSG00000063316	Rpl27	-	ribosomal protein L27	protein-coding
mm_74343.1	chr8	127234162	127234246	+	1	NA	intron (NM_001309391, intron 2 of 24)	intron (NM_001309391, intron 2 of 24)	-65408	NM_001013581	93742	Mm.299254	NM_033620	ENSMUSG00000025812	Pard3	AA960621|AI256638|Asip|D8Ertd580e|Par-3|Par3|Pard-3|Pard3a|Phip	par-3 family cell polarity regulator	protein-coding
mm_147455.1	chr18	46574452	46574462	-	1	NA	promoter-TSS (NM_173394)	promoter-TSS (NM_173394)	76	NM_173394	225471	Mm.149280	NM_173394	ENSMUSG00000056130	Ticam2	B430113A10|TICAM-2|TRAM|Tirp|Trif	toll-like receptor adaptor molecule 2	protein-coding
mm_6809.1	chr1	84157287	84157305	-	1	NA	intron (NM_001003948, intron 2 of 2)	intron (NM_001003948, intron 2 of 2)	61665	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_152757.1	chr19	20373561	20373701	-	1	NA	3' UTR (NM_010730, exon 13 of 13)	3' UTR (NM_010730, exon 13 of 13)	17040	NM_010730	16952	Mm.248360	NM_010730	ENSMUSG00000024659	Anxa1	Anx-1|Anx-A1|C430014K04Rik|Lpc-1|Lpc1	annexin A1	protein-coding
mm_132222.1	chr16	32641509	32641515	+	1	NA	Intergenic	Intergenic	-3131	NM_001110147	51789	Mm.251115	NM_016788	ENSMUSG00000022791	Tnk2	Ack|Ack-1|Ack1|Cdgip|Pyk1	tyrosine kinase, non-receptor, 2	protein-coding
mm_31403.1	chr4	48047303	48047310	+	1	NA	intron (NM_015743, intron 1 of 7)	CpG	2001	NM_015743	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_118737.1	chr14	22310734	22310747	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	232058	NR_046307	74896	Mm.444661	NR_046307		4930405A10Rik	4930456G20Rik	RIKEN cDNA 4930405A10 gene	ncRNA
mm_69832.1	chr7	141273092	141273117	-	1	NA	exon (NM_028069, exon 8 of 14)	exon (NM_028069, exon 8 of 14)	3682	NM_028069	72040	Mm.29080	NM_028069	ENSMUSG00000025497	Cdhr5	1810074H01Rik|AI481143|Mucdhl|Mupcdh	cadherin-related family member 5	protein-coding
mm_165298.1	chr2	91877815	91877816	+	1	NA	intron (NM_172669, intron 12 of 17)	RSINE1|SINE|B4	-44374	NM_007699	12672	Mm.330405	NM_007699	ENSMUSG00000040495	Chrm4	Chrm-4|M4	cholinergic receptor, muscarinic 4	protein-coding
mm_124574.1	chr14	124527848	124527856	-	1	NA	intron (NM_207667, intron 1 of 4)	L1_Mus4|LINE|L1	149275	NM_207667	14169	Mm.206362	NM_010201	ENSMUSG00000025551	Fgf14	FHF-4|Fhf4|mFHF-4(1B)	fibroblast growth factor 14	protein-coding
mm_140077.1	chr17	75178719	75178731	+	1	NA	promoter-TSS (NM_001331237)	promoter-TSS (NM_001331237)	-56	NM_001331236	268977	Mm.269747	NM_019919	ENSMUSG00000001870	Ltbp1	9430031G15Rik|9830146M04|Ltbp-1|Ltbp1L|TGF-beta1-BP-1|Tgfb|b2b1000Clo	latent transforming growth factor beta binding protein 1	protein-coding
mm_41545.1	chr5	92897982	92898052	+	1	NA	promoter-TSS (NM_001077596)	promoter-TSS (NM_001077596)	24	NM_001077596	27428	Mm.46014	NM_015756	ENSMUSG00000029381	Shroom3	AL022960|D5Ertd287e|Shrm|Shrm3	shroom family member 3	protein-coding
mm_39089.1	chr4	154636832	154636853	-	1	NA	promoter-TSS (NM_027504)	promoter-TSS (NM_027504)	31	NM_001177995	70673	Mm.257785	NM_027504	ENSMUSG00000039410	Prdm16	5730557K01Rik|csp1|mel1	PR domain containing 16	protein-coding
mm_1775.1	chr1	78310378	78310386	+	1	NA	promoter-TSS (NM_001004173)	promoter-TSS (NM_001004173)	36	NM_001004173	433323	Mm.276248	NM_001004173	ENSMUSG00000032908	Sgpp2	SPPase2|Spp2	sphingosine-1-phosphate phosphotase 2	protein-coding
mm_68750.1	chr7	121064843	121064856	-	1	NA	3' UTR (NM_030691, exon 6 of 6)	3' UTR (NM_030691, exon 6 of 6)	9681	NM_030691	80719	Mm.160384	NM_030691	ENSMUSG00000035004	Igsf6	-	immunoglobulin superfamily, member 6	protein-coding
mm_2306.1	chr1	91540554	91540578	+	1	NA	promoter-TSS (NM_001039126)	promoter-TSS (NM_001039126)	1	NM_001039126	65247	Mm.234152	NM_023046	ENSMUSG00000026311	Asb1	1700029O08Rik|1700054C17Rik|AI426616|AI851378|mKIAA1146	ankyrin repeat and SOCS box-containing 1	protein-coding
mm_102809.1	chr11	68930061	68930071	-	1	NA	Intergenic	HAL1|LINE|L1	-2985	NM_145746	252868	Mm.76826	NM_145746	ENSMUSG00000032921	Odf4	Oppo1	outer dense fiber of sperm tails 4	protein-coding
mm_22572.1	chr3	10288046	10288085	+	1	NA	intron (NM_029310, intron 1 of 5)	RMER17D2|LTR|ERVK	13118	NM_029310	75497	Mm.47052	NM_029310	ENSMUSG00000027530	Fabp12	1700008G05Rik	fatty acid binding protein 12	protein-coding
mm_100152.1	chr11	116108919	116108928	+	1	NA	intron (NM_172570, intron 1 of 5)	intron (NM_172570, intron 1 of 5)	1312	NM_001205081	217333	Mm.347770	NM_172570	ENSMUSG00000020773	Trim47	2210023F24Rik	tripartite motif-containing 47	protein-coding
mm_17437.1	chr2	27578665	27578670	-	1	NA	Intergenic	RMER19B|LTR|ERVK	63520	NM_080848	140858	Mm.28265	NM_080848	ENSMUSG00000026917	Wdr5	2410008O07Rik|AA408785|AA960360|Big|Big-3	WD repeat domain 5	protein-coding
mm_81331.1	chr9	108517071	108517117	+	1	NA	promoter-TSS (NM_175143)	promoter-TSS (NM_175143)	7	NM_175143	69232	Mm.335449	NM_175143	ENSMUSG00000006673	Qrich1	2610028H07Rik	glutamine-rich 1	protein-coding
mm_53656.1	chr6	141275010	141275025	+	1	NA	intron (NM_018779, intron 1 of 15)	intron (NM_018779, intron 1 of 15)	25748	NM_018779	54611	Mm.103728	NM_018779	ENSMUSG00000041741	Pde3a	A930022O17Rik|C87899	phosphodiesterase 3A, cGMP inhibited	protein-coding
mm_66933.1	chr7	61563151	61563153	-	1	NA	intron (NR_045727, intron 2 of 4)	intron (NR_045727, intron 2 of 4)	52175	NR_045727	319752	Mm.294476	NR_045727		B230209E15Rik	-	RIKEN cDNA B230209E15 gene	ncRNA
mm_99543.1	chr11	103299338	103299346	+	1	NA	Intergenic	Intergenic	-31941	NM_016896	53859	Mm.158981	NM_016896	ENSMUSG00000020941	Map3k14	Nik|aly	mitogen-activated protein kinase kinase kinase 14	protein-coding
mm_99263.1	chr11	101246330	101246332	+	1	NA	promoter-TSS (NM_019444)	promoter-TSS (NM_019444)	-3	NM_019444	54409	Mm.260698	NM_019444	ENSMUSG00000001240	Ramp2	-	receptor (calcitonin) activity modifying protein 2	protein-coding
mm_166475.1	chr5	144026594	144026594	-	1	NA	intron (NM_033039, intron 1 of 4)	intron (NM_033039, intron 1 of 4)	-11741	NM_177682	231874	Mm.320432	NM_177682	ENSMUSG00000029617	Ccz1	AU022870	CCZ1 vacuolar protein trafficking and biogenesis associated	protein-coding
mm_65713.1	chr7	28378248	28378260	-	1	NA	exon (NM_011756, exon 2 of 2)	exon (NM_011756, exon 2 of 2)	974	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_161819.1	chr17	70851490	70851490	-	1	NA	promoter-TSS (NM_009372)	promoter-TSS (NM_009372)	244	NM_001164075	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_2818.1	chr1	131019800	131019816	+	1	NA	promoter-TSS (NM_010548)	promoter-TSS (NM_010548)	-37	NM_010548	16153	Mm.874	NM_010548	ENSMUSG00000016529	Il10	CSIF|Il-10	interleukin 10	protein-coding
mm_156277.1	chrX	136836858	136836866	+	1	NA	3' UTR (NM_011123, exon 7 of 7)	3' UTR (NM_011123, exon 7 of 7)	14116	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_84636.1	chr9	71163225	71163293	-	1	NA	promoter-TSS (NM_001271843)	promoter-TSS (NM_001271843)	30	NR_073483	64008	Mm.449427	NM_022026	ENSMUSG00000032204	Aqp9	1700020I22Rik|AI266899|AQP-9	aquaporin 9	protein-coding
mm_123727.1	chr14	70159434	70159483	-	1	NA	promoter-TSS (NM_001112735)	promoter-TSS (NM_001112735)	44	NM_001112735	268759	Mm.12148	NM_001004155	ENSMUSG00000044551	9930012K11Rik	-	RIKEN cDNA 9930012K11 gene	protein-coding
mm_36689.1	chr4	96591406	96591454	-	1	NA	promoter-TSS (NM_028979)	promoter-TSS (NM_028979)	55	NM_028979	74519	Mm.458387	NM_028979	ENSMUSG00000015224	Cyp2j9	8430417E17Rik	cytochrome P450, family 2, subfamily j, polypeptide 9	protein-coding
mm_76562.1	chr8	88521101	88521146	-	1	NA	promoter-TSS (NM_027280)	promoter-TSS (NM_027280)	-221	NM_027280	93960	Mm.30219	NM_027280	ENSMUSG00000031661	Nkd1	2810434J10Rik|9030215G15Rik|Nkd	naked cuticle 1 homolog (Drosophila)	protein-coding
mm_167521.1	chr9	20898572	20898575	-	1	NA	promoter-TSS (NM_016876)	promoter-TSS (NM_016876)	17	NM_016876	53356	Mm.427309	NM_016876	ENSMUSG00000070319	Eif3g	44kDa|D0Jmb4|Eif3s4|TU-189B2|eIF3-p44|p44	eukaryotic translation initiation factor 3, subunit G	protein-coding
mm_126488.1	chr15	81626335	81626358	+	1	NA	exon (NM_177821, exon 13 of 31)	exon (NM_177821, exon 13 of 31)	-37543	NM_001289712	214669	Mm.280768	NM_145993	ENSMUSG00000022394	L3mbtl2	4732493N06Rik|M4mbt	l(3)mbt-like 2 (Drosophila)	protein-coding
mm_132946.1	chr16	49908363	49908368	+	1	NA	intron (NM_010581, intron 9 of 9)	intron (NM_010581, intron 9 of 9)	52711	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_67109.1	chr7	70357924	70357963	-	1	NA	exon (NM_183261, exon 2 of 3)	exon (NM_183261, exon 2 of 3)	2650	NM_009697	11819	Mm.158143	NM_009697	ENSMUSG00000030551	Nr2f2	2700033K02Rik|9430015G03Rik|ARP-1|Aporp1|COUP-TF2|COUP-TFII|COUPTFB|EAR3|SVP40|Tcfcoup2	nuclear receptor subfamily 2, group F, member 2	protein-coding
mm_56410.1	chr6	97205589	97205593	-	1	NA	promoter-TSS (NM_011666)	promoter-TSS (NM_011666)	56	NM_001301858	22200	Mm.277626	NM_011666	ENSMUSG00000030061	Uba3	A830034N06Rik|AI256736|AI848246|AW546539|Ube1c	ubiquitin-like modifier activating enzyme 3	protein-coding
mm_114072.1	chr13	54382668	54382686	+	1	NA	3' UTR (NM_009946, exon 4 of 4)	3' UTR (NM_009946, exon 4 of 4)	11328	NM_009946	12890	Mm.268902	NM_009946	ENSMUSG00000025867	Cplx2	921-L|AI413745|AW492120	complexin 2	protein-coding
mm_111076.1	chr12	80167819	80167837	-	1	NA	3' UTR (NM_134156, exon 21 of 21)	3' UTR (NM_134156, exon 21 of 21)	-34984	NR_033514	69548	Mm.269712	NR_033514	ENSMUSG00000097729	2310015A10Rik	5330419I17Rik	RIKEN cDNA 2310015A10 gene	ncRNA
mm_91238.1	chr10	22303889	22303889	-	1	NA	intron (NM_009018, intron 5 of 5)	intron (NM_009018, intron 5 of 5)	-2831	NR_015465	606736	Mm.387042	NR_015465	ENSMUSG00000097352	C920009B18Rik	-	RIKEN cDNA C920009B18 gene	ncRNA
mm_85288.1	chr9	99858857	99858885	-	1	NA	Intergenic	Intergenic	17299	NM_011440	20669	Mm.261595	NM_011440	ENSMUSG00000053747	Sox14	-	SRY (sex determining region Y)-box 14	protein-coding
mm_107084.1	chr12	17348423	17348526	+	1	NA	promoter-TSS (NM_001008421)	promoter-TSS (NM_001008421)	-19	NM_001008421	217431	Mm.27536	NM_001008421	ENSMUSG00000061458	Nol10	Gm67	nucleolar protein 10	protein-coding
mm_46871.1	chr5	113832475	113832484	-	1	NA	Intergenic	Intergenic	-1978	NM_009151	20345	Mm.332590	NM_009151	ENSMUSG00000048163	Selplg	CD162|Psgl-1|Psgl1|Selp1|Selpl	selectin, platelet (p-selectin) ligand	protein-coding
mm_170355.1	chr1	85199631	85199632	+	1	NA	promoter-TSS (NM_001081746)	promoter-TSS (NM_001081746)	20	NM_001081746	665378	Mm.440912	NM_001081746		Gm7609	EG665378	predicted pseudogene 7609	protein-coding
mm_10128.1	chr2	3779923	3779938	+	1	NA	3' UTR (NM_025626, exon 4 of 4)	3' UTR (NM_025626, exon 4 of 4)	66472	NM_025626	66540	Mm.277864	NM_025626	ENSMUSG00000026655	Fam107b	3110001A13Rik|AA589595|AA959793|AI132312	family with sequence similarity 107, member B	protein-coding
mm_77653.1	chr8	124564449	124564482	-	1	NA	exon (NM_007428, exon 2 of 5)	exon (NM_007428, exon 2 of 5)	5242	NM_007428	11606	Mm.301626	NM_007428	ENSMUSG00000031980	Agt	AI265500|AngI|AngII|Aogen|Serpina8	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	protein-coding
mm_2024.1	chr1	87128374	87128388	+	1	NA	TTS (NM_007432)	TTS (NM_007432)	3373	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_3296.1	chr1	136690531	136690534	+	1	NA	intron (NR_045324, intron 2 of 2)	MTE2a|LTR|ERVL-MaLR	-5679	NR_037986	100503474	Mm.428276	NR_037986		Platr22	Gm16880	pluripotency associated transcript 22	ncRNA
mm_136072.1	chr16	84772586	84772614	-	1	NA	Intergenic	MLTR14|LTR|ERV1	-1523	NM_023844	67374	Mm.41758	NM_023844	ENSMUSG00000053062	Jam2	1110002N23Rik|2410030G21Rik|2410167M24Rik|JAM-2|JAM-B|Jcam2|VE-JAM	junction adhesion molecule 2	protein-coding
mm_53977.1	chr6	6578683	6578689	-	1	NA	promoter-TSS (NM_009169)	promoter-TSS (NM_009169)	-28	NM_009169	20422	Mm.2469	NM_009169	ENSMUSG00000042541	Shfm1	DSS1|Shfdg1|Shfg	split hand/foot malformation (ectrodactyly) type 1	protein-coding
mm_145243.1	chr18	50728467	50728493	+	1	NA	Intergenic	Intergenic	-159781	NM_026108	67365	Mm.158150	NM_026108	ENSMUSG00000048875	Hdhd1a	1700121L12Rik|GS1|Hdhd1|Pudp	haloacid dehalogenase-like hydrolase domain containing 1A	protein-coding
mm_155428.1	chrX	73492805	73492812	+	1	NA	exon (NM_007542, exon 5 of 8)	exon (NM_007542, exon 5 of 8)	9207	NM_007542	12111	Mm.2608	NM_007542	ENSMUSG00000031375	Bgn	BG|DSPG1|PG-S1|PGI|SLRR1A	biglycan	protein-coding
mm_101006.1	chr11	8479926	8479931	-	1	NA	intron (NM_001083587, intron 17 of 30)	intron (NM_001083587, intron 17 of 30)	184607	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_23315.1	chr3	53235208	53235210	+	1	NA	intron (NM_175386, intron 3 of 3)	intron (NM_175386, intron 3 of 3)	193662	NM_175386	108927	Mm.118617	NM_175386	ENSMUSG00000048332	Lhfp	2810489O06Rik|AI194968	lipoma HMGIC fusion partner	protein-coding
mm_43792.1	chr5	142694099	142694102	+	1	NA	Intergenic	ID_B1|SINE|B4	-8001	NM_146257	243328	Mm.125942	NM_146257	ENSMUSG00000050822	Slc29a4	ENT4|mPMAT	solute carrier family 29 (nucleoside transporters), member 4	protein-coding
mm_30510.1	chr3	158031706	158031774	-	1	NA	promoter-TSS (NM_001093753)	promoter-TSS (NM_001093753)	14	NM_001093753	69207	Mm.223946	NM_026989	ENSMUSG00000055436	Srsf11	0610009J05Rik|2610019N13Rik|BF642805|Sfrs11	serine/arginine-rich splicing factor 11	protein-coding
mm_160908.1	chr11	82764053	82764053	-	1	NA	promoter-TSS (NM_025884)	promoter-TSS (NM_025884)	268	NM_009839	12467	Mm.4126	NM_009839	ENSMUSG00000020698	Cct6b	CCT-zeta-2|CCTzeta-2|Cctz-2|TCP-1-zeta-2	chaperonin containing Tcp1, subunit 6b (zeta)	protein-coding
mm_86971.1	chr10	25383833	25383851	+	1	NA	intron (NM_001199265, intron 1 of 19)	intron (NM_001199265, intron 1 of 19)	24044	NM_001199265	13822	Mm.306026	NM_013511	ENSMUSG00000019978	Epb41l2	4.1G|AW555191|D10Ertd398e|Epb4.1l2|NBL2	erythrocyte membrane protein band 4.1 like 2	protein-coding
mm_122453.1	chr14	45318510	45318520	-	1	NA	promoter-TSS (NM_015774)	promoter-TSS (NM_015774)	57	NM_015774	50527	Mm.387108	NM_015774	ENSMUSG00000021831	Ero1l	ERO1-L|Ero1a	ERO1-like (S. cerevisiae)	protein-coding
mm_137692.1	chr17	28951966	28951978	+	1	NA	Intergenic	Intergenic	-1244	NM_025888	66989	Mm.435	NM_025888	ENSMUSG00000005936	Kctd20	2410004N11Rik|AI451943|AW541186|D17Ertd562e	potassium channel tetramerisation domain containing 20	protein-coding
mm_107767.1	chr12	59130017	59130028	+	1	NA	intron (NM_146034, intron 1 of 24)	(T)n|Simple_repeat|Simple_repeat	276	NM_001165254	338320	Mm.213215	NM_146034	ENSMUSG00000021000	Mia2	Ctage5|D12Bwg0579e|Mea6|Mgea|Mgea6	melanoma inhibitory activity 2	protein-coding
mm_23915.1	chr3	83046119	83046135	+	1	NA	exon (NM_181849, exon 3 of 8)	exon (NM_181849, exon 3 of 8)	3736	NM_181849	110135	Mm.30063	NM_181849	ENSMUSG00000033831	Fgb	2510049G14Rik	fibrinogen beta chain	protein-coding
mm_86885.1	chr10	22158522	22158537	+	1	NA	promoter-TSS (NM_009016)	promoter-TSS (NM_009016)	-80	NM_009016	19368	Mm.458004	NM_009016		Raet1a	RAE-1alpha|Rae1alpha|Raet1	retinoic acid early transcript 1, alpha	protein-coding
mm_111005.1	chr12	78906930	78906970	-	1	NA	promoter-TSS (NM_013738)	promoter-TSS (NM_013738)	-12	NM_013738	27260	Mm.103380	NM_013738	ENSMUSG00000021118	Plek2	-	pleckstrin 2	protein-coding
mm_143382.1	chr17	67955941	67955952	-	1	NA	intron (NM_172964, intron 1 of 17)	L1MA4|LINE|L1	-5006	NM_001347410	268970	Mm.9935	NM_172964	ENSMUSG00000024043	Arhgap28	AU044757|AW550892|E130310N06	Rho GTPase activating protein 28	protein-coding
mm_58135.1	chr6	141249815	141249895	-	1	NA	exon (NM_018779, exon 1 of 16)	exon (NM_018779, exon 1 of 16)	586	NM_018779	54611	Mm.103728	NM_018779	ENSMUSG00000041741	Pde3a	A930022O17Rik|C87899	phosphodiesterase 3A, cGMP inhibited	protein-coding
mm_95509.1	chr11	52000932	52000948	+	1	NA	promoter-TSS (NM_009458)	promoter-TSS (NM_009458)	-474	NM_009458	22210	Mm.384918	NM_009458	ENSMUSG00000020390	Ube2b	2610301N02Rik|E2-14k|HR6B|Rad6b|mHR6B	ubiquitin-conjugating enzyme E2B	protein-coding
mm_12615.1	chr2	74691942	74691963	+	1	NA	promoter-TSS (NM_013554)	promoter-TSS (NM_013554)	61	NM_013554	15430	Mm.24420	NM_013554	ENSMUSG00000050368	Hoxd10	AI385591|AI874987|Hox-4.5|Hox-5.3	homeobox D10	protein-coding
mm_99071.1	chr11	99168527	99168535	+	1	NA	Intergenic	Intergenic	-13454	NM_007719	12775	Mm.2932	NM_007719	ENSMUSG00000037944	Ccr7	CC-CKR-7|CCR-7|CD197|Cdw197|Cmkbr7|EBI1|Ebi1h	chemokine (C-C motif) receptor 7	protein-coding
mm_147786.1	chr18	61632682	61632691	-	1	NA	Intergenic	Intergenic	-6967	NR_045420	545261	Mm.426593	NR_045420	ENSMUSG00000098098	Bvht	Braveheart|Gm20748	braveheart long non-coding RNA	ncRNA
mm_17491.1	chr2	28613369	28613371	-	1	NA	intron (NM_008114, intron 4 of 6)	ID_B1|SINE|B4	8612	NM_008114	14582	Mm.373385	NM_008114	ENSMUSG00000026815	Gfi1b	Gfi-1B	growth factor independent 1B	protein-coding
mm_111391.1	chr12	88442221	88442257	-	1	NA	intron (NM_028105, intron 6 of 10)	intron (NM_028105, intron 6 of 10)	-64916	NR_045888	71818	Mm.490789	NR_045888		3200001D21Rik	-	RIKEN cDNA 3200001D21 gene	ncRNA
mm_107605.1	chr12	49384357	49384365	+	1	NA	5' UTR (NM_008241, exon 2 of 2)	5' UTR (NM_008241, exon 2 of 2)	1354	NM_008241	15228	Mm.4704	NM_008241	ENSMUSG00000020950	Foxg1	2900064B05Rik|BF-1|Bf1|Hfh9|Hfhbf1	forkhead box G1	protein-coding
mm_290.1	chr1	22534123	22534123	+	1	NA	exon (NM_001012625, exon 7 of 15)	exon (NM_001012625, exon 7 of 15)	-101280	NM_183018	116837	Mm.60061	NM_053270	ENSMUSG00000041670	Rims1	C030033M19Rik|RIM1|RIM1a|RIM1alpha|Rab3ip1|Rim|Serg1|mKIAA0340	regulating synaptic membrane exocytosis 1	protein-coding
mm_39088.1	chr4	154636810	154636822	-	1	NA	promoter-TSS (NM_027504)	promoter-TSS (NM_027504)	57	NM_001177995	70673	Mm.257785	NM_027504	ENSMUSG00000039410	Prdm16	5730557K01Rik|csp1|mel1	PR domain containing 16	protein-coding
mm_56226.1	chr6	90325215	90325227	-	1	NA	promoter-TSS (NM_027928)	promoter-TSS (NM_027928)	-36	NM_027928	71797	Mm.49071	NM_027928	ENSMUSG00000056643	Chst13	1110067M19Rik|C4ST-3	carbohydrate (chondroitin 4) sulfotransferase 13	protein-coding
mm_99559.1	chr11	103649641	103649649	+	1	NA	TTS (NR_131143)	TTS (NR_131143)	136	NM_001033212	104582	Mm.44618	NM_001033212	ENSMUSG00000046215	Rprml	AW049332	reprimo-like	protein-coding
mm_124847.1	chr15	9524315	9524318	+	1	NA	intron (NM_008372, intron 2 of 7)	intron (NM_008372, intron 2 of 7)	5560	NM_008372	16197	Mm.389	NM_008372	ENSMUSG00000003882	Il7r	CD127|IL-7Ralpha	interleukin 7 receptor	protein-coding
mm_3147.1	chr1	135146735	135146745	+	1	NA	promoter-TSS (NM_026823)	promoter-TSS (NM_026823)	-94	NM_026823	68724	Mm.174998	NM_026823	ENSMUSG00000026426	Arl8a	1110033P22Rik|Arl10b|gie2	ADP-ribosylation factor-like 8A	protein-coding
mm_45851.1	chr5	87780137	87780158	-	1	NA	exon (NM_001304767, exon 7 of 13)	exon (NM_001304767, exon 7 of 13)	5697	NM_007785	12993	Mm.4908	NM_007785	ENSMUSG00000061937	Csn1s2a	Csng|PP22	casein alpha s2-like A	protein-coding
mm_169320.1	chr14	113314655	113314655	+	1	NA	Intergenic	Intergenic	1293225	NR_030150	723922		NR_030150	ENSMUSG00000070099	Mir466	Mirn466|mmu-mir-466	microRNA 466	ncRNA
mm_38387.1	chr4	138809834	138809844	-	1	NA	intron (NM_011110, intron 1 of 4)	intron (NM_011110, intron 1 of 4)	9418	NM_011110	18784	Mm.486532	NM_011110	ENSMUSG00000041193	Pla2g5	PLA2|sPLA2	phospholipase A2, group V	protein-coding
mm_70730.1	chr8	18846469	18846489	+	1	NA	5' UTR (NM_026792, exon 1 of 8)	5' UTR (NM_026792, exon 1 of 8)	200	NM_026792	52123	Mm.24117	NM_026792	ENSMUSG00000031467	Agpat5	1110013A05Rik|D8Ertd319e	1-acylglycerol-3-phosphate O-acyltransferase 5 (lysophosphatidic acid acyltransferase, epsilon)	protein-coding
mm_94755.1	chr11	21136667	21136669	+	1	NA	intron (NM_023324, intron 2 of 6)	B2_Mm1t|SINE|B2	45344	NM_023324	67245	Mm.28957	NM_023324	ENSMUSG00000020134	Peli1	2810468L03Rik|A930031K15Rik|AA409794|AI586297|D11Ertd676e	pellino 1	protein-coding
mm_172026.1	chr6	12278348	12278366	+	1	NA	Intergenic	RLTR9E|LTR|ERVK	-168777	NR_003631	625347	Mm.389084	NM_001039041	ENSMUSG00000057223	Gm6578	EG625347	mitochondrial ribosomal protein L32 pseudogene	pseudo
mm_5840.1	chr1	52952835	52952854	-	1	NA	promoter-TSS (NM_144953)	promoter-TSS (NM_144953)	-4	NM_144953	67080	Mm.236287	NM_144953	ENSMUSG00000043629	1700019D03Rik	2410136C24Rik|AA410151|smAKAP	RIKEN cDNA 1700019D03 gene	protein-coding
mm_2636.1	chr1	121495410	121495420	+	1	NA	intron (NM_001025156, intron 21 of 23)	intron (NM_001025156, intron 21 of 23)	33050	NM_010483	15564	Mm.4833	NM_010483	ENSMUSG00000050534	Htr5b	5-Ht5b	5-hydroxytryptamine (serotonin) receptor 5B	protein-coding
mm_128041.1	chr15	25364981	25364987	-	1	NA	intron (NM_027395, intron 1 of 1)	intron (NM_027395, intron 1 of 1)	48780	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	brain abundant, membrane attached signal protein 1	protein-coding
mm_44231.1	chr5	5262110	5262132	-	1	NA	intron (NM_011074, intron 2 of 14)	intron (NM_011074, intron 2 of 14)	3947	NM_001310448	18647	Mm.389061	NM_011074	ENSMUSG00000028926	Cdk14	Pftk1|mKIAA0834	cyclin-dependent kinase 14	protein-coding
mm_27060.1	chr3	27691608	27691633	-	1	NA	intron (NM_173182, intron 1 of 25)	intron (NM_173182, intron 1 of 25)	18819	NM_173182	72007	Mm.38832	NM_173182	ENSMUSG00000039286	Fndc3b	1600019O04Rik|AW550168|Fad104|mKIAA4164	fibronectin type III domain containing 3B	protein-coding
mm_160140.1	chr7	33944984	33944984	-	1	NA	promoter-TSS (NM_178308)	promoter-TSS (NM_178308)	1	NM_178308	110187	Mm.155750	NM_178308	ENSMUSG00000066586	Scgb2b26	Abpbg26|Abpbg4|Abpg|C2d|Scgb2b4	secretoglobin, family 2B, member 26	protein-coding
mm_155967.1	chrX	106081240	106081246	+	1	NA	intron (NM_001109757, intron 2 of 22)	intron (NM_001109757, intron 2 of 22)	54019	NM_009726	11977	Mm.254297	NM_009726	ENSMUSG00000033792	Atp7a	MNK	ATPase, Cu++ transporting, alpha polypeptide	protein-coding
mm_63398.1	chr7	127296339	127296352	+	1	NA	promoter-TSS (NM_001253873)	promoter-TSS (NM_001253873)	85	NM_001253874	16408	Mm.1618	NM_008400	ENSMUSG00000030830	Itgal	(p180)|Cd11a|LFA-1|LFA-1A|Ly-15|Ly-21	integrin alpha L	protein-coding
mm_131246.1	chr16	10526465	10526468	+	1	NA	3' UTR (NM_001243761, exon 19 of 19)	3' UTR (NM_001243761, exon 19 of 19)	16588	NM_021428	58239	Mm.353006	NM_021428	ENSMUSG00000038055	Dexi	1810029J14Rik|AI836170|AW413143|D16Bwg0586e|Myle	dexamethasone-induced transcript	protein-coding
mm_71693.1	chr8	61395402	61395405	+	1	NA	3' UTR (NM_021506, exon 12 of 12)	3' UTR (NM_021506, exon 12 of 12)	-92331	NM_145595	234309	Mm.29059	NM_145595	ENSMUSG00000031641	Cbr4	A730083J17Rik|BC009118	carbonyl reductase 4	protein-coding
mm_9090.1	chr1	168675864	168675873	-	1	NA	Intergenic	Intergenic	185225	NR_105766	102465178		NR_105766	ENSMUSG00000098407	Mir6348	Gm27412|mmu-mir-6348	microRNA 6348	ncRNA
mm_102500.1	chr11	60537143	60537162	-	1	NA	promoter-TSS (NM_172943)	promoter-TSS (NM_172943)	-531	NM_172943	268420	Mm.262056	NM_172943	ENSMUSG00000042650	Alkbh5	AW050020|AW215868|Abh5|E130207K11|Ofoxd	alkB homolog 5, RNA demethylase	protein-coding
mm_170263.1	chr18	15988350	15988352	+	1	NA	Intergenic	Intergenic	-270305	NM_199055	71367	Mm.329304	NM_199055	ENSMUSG00000047161	Chst9	5430438D01Rik	carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 9	protein-coding
mm_13141.1	chr2	92184269	92184310	+	1	NA	5' UTR (NM_138755, exon 1 of 18)	5' UTR (NM_138755, exon 1 of 18)	107	NM_001346704	192285	Mm.330408	NM_138755	ENSMUSG00000058318	Phf21a	80kDa|Bhc|Bhc80|D030065N23Rik|PFTF1	PHD finger protein 21A	protein-coding
mm_158487.1	chrX	142320317	142320337	-	1	NA	3' UTR (NM_207625, exon 16 of 16)	3' UTR (NM_207625, exon 16 of 16)	-14129	NM_021487	66240	Mm.58507	NM_021487	ENSMUSG00000090122	Kcne1l	1500015C14Rik|Kcne5|Mink	potassium voltage-gated channel, Isk-related family, member 1-like, pseudogene	protein-coding
mm_169149.1	chr13	62602336	62602338	-	1	NA	TTS (NM_001324406)	TTS (NM_001324406)	21845	NM_001324406	211378	Mm.247448	NM_173381	ENSMUSG00000072066	6720489N17Rik	9330128I06	RIKEN cDNA 6720489N17 gene	protein-coding
mm_172638.1	chr8	22275672	22275672	-	1	NA	Intergenic	Intergenic	-7769	NM_199257	234129	Mm.450553	NM_181851	ENSMUSG00000031481	Tpte	Pten2	transmembrane phosphatase with tensin homology	protein-coding
mm_5390.1	chr1	31222628	31222643	-	1	NA	promoter-TSS (NM_029062)	promoter-TSS (NM_029062)	21	NR_033445	70988	Mm.161414	NM_027637	ENSMUSG00000086727	4931428L18Rik	4930563O14Rik	RIKEN cDNA 4931428L18 gene	ncRNA
mm_32202.1	chr4	101496677	101496722	+	1	NA	promoter-TSS (NM_198412)	promoter-TSS (NM_198412)	51	NM_198412	72685	Mm.76494	NM_198412	ENSMUSG00000028528	Dnajc6	2810027M23Rik|mKIAA0473	DnaJ heat shock protein family (Hsp40) member C6	protein-coding
mm_60017.1	chr7	30765407	30765450	+	1	NA	exon (NM_001166174, exon 5 of 18)	exon (NM_001166174, exon 5 of 18)	1672	NM_001166174	73712	Mm.30138	NM_028618	ENSMUSG00000060962	Dmkn	1110014F24Rik|AW561900|C130074A08|SK30|SK89|cI-36	dermokine	protein-coding
mm_84909.1	chr9	79977639	79977662	-	1	NA	5' UTR (NM_001081243, exon 1 of 6)	5' UTR (NM_001081243, exon 1 of 6)	232	NM_001081243	70598	Mm.23049	NM_001081243	ENSMUSG00000034898	Filip1	5730485H21Rik|AI843021	filamin A interacting protein 1	protein-coding
mm_119738.1	chr14	54121926	54121936	+	1	NA	Intergenic	Intergenic	131998	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_106199.1	chr11	116843125	116843134	-	1	NA	promoter-TSS (NM_028865)	promoter-TSS (NM_028865)	320	NM_033398	107817	Mm.481684	NM_033398	ENSMUSG00000056962	Jmjd6	5730436I23Rik|D11Ertd195e|PSR|PtdSerR|Ptdsr|mKIAA0585	jumonji domain containing 6	protein-coding
mm_46822.1	chr5	113163320	113163333	-	1	NA	promoter-TSS (NM_172884)	promoter-TSS (NM_172884)	-13	NM_172884	243219	Mm.160131	NM_172884	ENSMUSG00000051339	2900026A02Rik	8430408O14Rik|A530094D01|AW539426|Gm449|Kiaa1671|mKIAA1671	RIKEN cDNA 2900026A02 gene	protein-coding
mm_125294.1	chr15	36792727	36792769	+	1	NA	intron (NM_001253806, intron 1 of 5)	CpG	1790	NM_011740	22631	Mm.3360	NM_011740	ENSMUSG00000022285	Ywhaz	1110013I11Rik|14-3-3zeta|AI596267|AL022924|AU020854	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide	protein-coding
mm_97254.1	chr11	75756949	75756974	+	1	NA	exon (NM_009536, exon 4 of 6)	exon (NM_009536, exon 4 of 6)	24074	NM_009536	22627	Mm.234700	NM_009536	ENSMUSG00000020849	Ywhae	AU019196	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide	protein-coding
mm_139344.1	chr17	50239142	50239181	+	1	NA	promoter-TSS (NR_131975)	promoter-TSS (NR_131975)	-47	NR_131975	446210	Mm.378184	NM_001004437	ENSMUSG00000067103	AY702103	STDP2	cDNA sequence AY702103	ncRNA
mm_4860.1	chr1	187651512	187651534	+	1	NA	intron (NM_001243792, intron 1 of 7)	intron (NM_001243792, intron 1 of 7)	42517	NM_001243792	26381	Mm.89989	NM_011935	ENSMUSG00000026610	Esrrg	ERR3|Errg|NR3B3|mKIAA0832	estrogen-related receptor gamma	protein-coding
mm_91494.1	chr10	37135929	37135942	-	1	NA	3' UTR (NM_008538, exon 2 of 2)	3' UTR (NM_008538, exon 2 of 2)	2991	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_24983.1	chr3	96832183	96832191	+	1	NA	promoter-TSS (NM_001146001)	promoter-TSS (NM_001146001)	-117	NR_015596	67583	Mm.444284	NR_015596	ENSMUSG00000087223	4930442L01Rik	-	RIKEN cDNA 4930442L01 gene	ncRNA
mm_29197.1	chr3	106763239	106763287	-	1	NA	exon (NM_007651, exon 6 of 8)	exon (NM_007651, exon 6 of 8)	26886	NM_007651	12508	Mm.316861	NM_007651	ENSMUSG00000040747	Cd53	AI323659|Ox-44|Tspan25	CD53 antigen	protein-coding
mm_91603.1	chr10	41221398	41221402	-	1	NA	intron (NM_133999, intron 21 of 22)	intron (NM_133999, intron 21 of 22)	81841	NM_133999	103199	Mm.277242	NM_133999	ENSMUSG00000038417	Fig4	A530089I17Rik|AI326867|Sac3	FIG4 phosphoinositide 5-phosphatase	protein-coding
mm_60449.1	chr7	44477337	44477347	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	6995	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_26671.1	chr3	154718078	154718091	+	1	NA	intron (NM_175176, intron 2 of 6)	L1_Mur3|LINE|L1	6951	NM_175176	209601	Mm.331454	NM_175176	ENSMUSG00000078161	Erich3	1700013E18Rik|4922501L14Rik|5031409G23Rik|AI596448|Gm133	glutamate rich 3	protein-coding
mm_158256.1	chrX	108834273	108834283	-	1	NA	promoter-TSS (NM_001081477)	promoter-TSS (NM_001081477)	77	NM_001081477	382236	Mm.100112	NM_001081477	ENSMUSG00000063663	Brwd3	Brodl|D030064D06Rik|Gm596	bromodomain and WD repeat domain containing 3	protein-coding
mm_61920.1	chr7	90153519	90153535	+	1	NA	intron (NM_001252520, intron 1 of 20)	B1F1|SINE|Alu	23295	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_139634.1	chr17	57367669	57367740	+	1	NA	intron (NM_010130, intron 2 of 21)	intron (NM_010130, intron 2 of 21)	9018	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_39654.1	chr5	24709568	24709591	+	1	NA	3' UTR (NM_001305264, exon 15 of 15)	3' UTR (NM_001305264, exon 15 of 15)	21101	NM_001081441	269633	Mm.392539	NM_026621	ENSMUSG00000055235	Wdr86	2810046M22Rik|BC059069	WD repeat domain 86	protein-coding
mm_79638.1	chr9	59544829	59544835	+	1	NA	intron (NM_010421, intron 1 of 13)	intron (NM_010421, intron 1 of 13)	5292	NM_010421	15211	Mm.2284	NM_010421	ENSMUSG00000025232	Hexa	Hex-1	hexosaminidase A	protein-coding
mm_140537.1	chr17	6757445	6757446	-	1	NA	intron (NM_009510, intron 2 of 12)	intron (NM_009510, intron 2 of 12)	25335	NM_009510	22350	Mm.277812	NM_009510	ENSMUSG00000052397	Ezr	AW146364|R75297|Vil2|p81	ezrin	protein-coding
mm_105461.1	chr11	104637214	104637229	-	1	NA	intron (NM_016780, intron 5 of 14)	intron (NM_016780, intron 5 of 14)	29221	NM_016780	16416	Mm.87150	NM_016780	ENSMUSG00000020689	Itgb3	CD61|GP3A|INGRB3	integrin beta 3	protein-coding
mm_115770.1	chr13	19307369	19307376	-	1	NA	Intergenic	Intergenic	88441	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_166303.1	chr5	105131773	105131786	-	1	NA	intron (NM_008620, intron 3 of 10)	A-rich|Low_complexity|Low_complexity	7773	NM_008620	17472	Mm.440525	NM_008620	ENSMUSG00000079363	Gbp4	AW228052|Mag-2|Mpa-2|Mpa2	guanylate binding protein 4	protein-coding
mm_8183.1	chr1	138080900	138080936	-	1	NA	exon (NM_001268286, exon 20 of 29)	exon (NM_001268286, exon 20 of 29)	94208	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_807.1	chr1	45348965	45348996	+	1	NA	3' UTR (NM_009930, exon 51 of 51)	3' UTR (NM_009930, exon 51 of 51)	37442	NM_009930	12825	Mm.249555	NM_009930	ENSMUSG00000026043	Col3a1	AW550625|Col3a-1|Tsk-2|Tsk2	collagen, type III, alpha 1	protein-coding
mm_137044.1	chr17	17915915	17915947	+	1	NA	Intergenic	Intergenic	28107	NM_008039	14289	Mm.378918	NM_008039	ENSMUSG00000052270	Fpr2	E330010I07Rik|Fpr-rs2	formyl peptide receptor 2	protein-coding
mm_168248.1	chr10	82520288	82520293	+	1	NA	Intergenic	IAP1-MM_LTR|LTR|ERVK	-27672	NM_001255990	432480	Mm.280394	NM_001255990	ENSMUSG00000094186	Gm1553	Lcrn	predicted gene 1553	protein-coding
mm_9348.1	chr1	172067443	172067463	-	1	NA	exon (NM_021607, exon 16 of 17)	exon (NM_021607, exon 16 of 17)	-9857	NM_010916	18071	Mm.2474	NM_010916	ENSMUSG00000051251	Nhlh1	Hen1|Nscl|Tal2|bHLHa35	nescient helix loop helix 1	protein-coding
mm_29083.1	chr3	104220361	104220378	-	1	NA	promoter-TSS (NM_133853)	promoter-TSS (NM_133853)	37	NM_133853	99470	Mm.264849	NM_133853	ENSMUSG00000052539	Magi3	4732496O19Rik|6530407C02Rik|AA407180|AI120132|mKIAA1634	membrane associated guanylate kinase, WW and PDZ domain containing 3	protein-coding
mm_91056.1	chr10	18831901	18831913	-	1	NA	promoter-TSS (NR_102728)	promoter-TSS (NR_102728)	23	NR_038035	73968	Mm.55591	NR_038034		4930444F02Rik	1700010L24Rik|mpiR	RIKEN cDNA 4930444F02 gene	ncRNA
mm_119106.1	chr14	30951532	30951542	+	1	NA	5' UTR (NM_001308328, exon 1 of 14)	5' UTR (NM_001308328, exon 1 of 14)	160	NM_011849	23955	Mm.251494	NM_011849	ENSMUSG00000021918	Nek4	Stk2	NIMA (never in mitosis gene a)-related expressed kinase 4	protein-coding
mm_51261.1	chr6	72097562	72097630	+	1	NA	promoter-TSS (NM_011375)	promoter-TSS (NM_011375)	-12	NM_001035228	20454	Mm.38248	NM_011375	ENSMUSG00000056091	St3gal5	3S-T|Siat9|[a]2	ST3 beta-galactoside alpha-2,3-sialyltransferase 5	protein-coding
mm_118779.1	chr14	24069753	24069754	+	1	NA	Intergenic	Intergenic	-19124	NR_106069	102465697		NR_106069	ENSMUSG00000105723	Mir7210	mir-7210|mmu-mir-7210	microRNA 7210	ncRNA
mm_19361.1	chr2	91086408	91086437	-	1	NA	Intergenic	Intergenic	-10256	NM_011355	20375	Mm.1302	NM_011355	ENSMUSG00000002111	Spi1	Dis-1|Dis1|PU.1|Sfpi-1|Sfpi1|Spi-1|Tcfpu1|Tfpu.1	spleen focus forming virus (SFFV) proviral integration oncogene	protein-coding
mm_114439.1	chr13	66007545	66007554	+	1	NA	Intergenic	Intergenic	-105904	NM_001177832	628709	Mm.390595	NM_001177832	ENSMUSG00000095909	Gm10324	ENSMUSG00000071302	predicted gene 10324	protein-coding
mm_7325.1	chr1	101895863	101895909	-	1	NA	Intergenic	L1_Mus1|LINE|L1	740118	NR_037989	100504525	Mm.87065	NR_037989	ENSMUSG00000100684	Gm20268	-	predicted gene, 20268	ncRNA
mm_63532.1	chr7	127969741	127969755	+	1	NA	exon (NM_139149, exon 3 of 15)	exon (NM_139149, exon 3 of 15)	2269	NM_139149	233908	Mm.277680	NM_139149	ENSMUSG00000030795	Fus	D430004D17Rik|D930039C12Rik|Fus1|Tls	fused in sarcoma	protein-coding
mm_32467.1	chr4	107707031	107707048	+	1	NA	Intergenic	Intergenic	-22877	NM_019872	56296	Mm.141324	NM_019872	ENSMUSG00000028610	Dmrtb1	Dmrt6|Prp13	DMRT-like family B with proline-rich C-terminal, 1	protein-coding
mm_153760.1	chr19	45560509	45560532	-	1	NA	promoter-TSS (NM_172639)	promoter-TSS (NM_172639)	44	NM_001330506	56626	Mm.46509	NM_020032	ENSMUSG00000025218	Poll	1110003P06Rik|AV007317	polymerase (DNA directed), lambda	protein-coding
mm_155153.1	chrX	52912368	52912380	+	1	NA	5' UTR (NM_027642, exon 1 of 11)	5' UTR (NM_027642, exon 1 of 11)	160	NM_001290546	70998	Mm.26870	NM_027642	ENSMUSG00000025626	Phf6	2700007B13Rik|4931428F02Rik|mKIAA1823	PHD finger protein 6	protein-coding
mm_78063.1	chr9	15207109	15207109	+	1	NA	Intergenic	Intergenic	-31936	NM_026955	69137	Mm.41396	NM_026955	ENSMUSG00000031937	Vstm5	2200002K05Rik	V-set and transmembrane domain containing 5	protein-coding
mm_21826.1	chr2	165368724	165368747	-	1	NA	Intergenic	CpG	-6616	NM_001005425	381405	Mm.296323	NM_001005425	ENSMUSG00000056824	Zfp663	Gm1008	zinc finger protein 663	protein-coding
mm_95882.1	chr11	58102907	58102917	+	1	NA	Intergenic	Intergenic	-1241	NM_026949	69125	Mm.28910	NM_026949	ENSMUSG00000020515	Cnot8	1500015I04Rik|1810022F04Rik|AA536816|AU015770|AU043059	CCR4-NOT transcription complex, subunit 8	protein-coding
mm_117164.1	chr13	62858347	62858359	-	1	NA	promoter-TSS (NM_007994)	promoter-TSS (NM_007994)	17	NM_007994	14120	Mm.391871	NM_007994	ENSMUSG00000021456	Fbp2	Fbp-1|Fbp1|Rae-30	fructose bisphosphatase 2	protein-coding
mm_23115.1	chr3	37639906	37639912	+	1	NA	promoter-TSS (NM_011896)	promoter-TSS (NM_011896)	-38	NM_001305441	24063	Mm.330986	NM_011896	ENSMUSG00000037211	Spry1	sprouty1|spry-1	sprouty homolog 1 (Drosophila)	protein-coding
mm_91037.1	chr10	18235560	18235568	-	1	NA	promoter-TSS (NM_144820)	promoter-TSS (NM_144820)	-583	NM_144820	215814	Mm.296565	NM_144820	ENSMUSG00000059554	Ccdc28a	1700009P13Rik|AI480677	coiled-coil domain containing 28A	protein-coding
mm_78812.1	chr9	44069422	44069452	+	1	NA	promoter-TSS (NM_016808)	promoter-TSS (NM_016808)	8	NM_016808	53376	Mm.272770	NM_016808	ENSMUSG00000032010	Usp2	B930035K21Rik|Ubp41	ubiquitin specific peptidase 2	protein-coding
mm_129082.1	chr15	75894233	75894322	-	1	NA	TTS (NM_001285431)	TTS (NM_001285431)	204	NM_172607	223646	Mm.288368	NM_172607	ENSMUSG00000022574	Naprt	9130210N20Rik|Naprt1	nicotinate phosphoribosyltransferase	protein-coding
mm_74589.1	chr8	11476818	11476824	-	1	NA	intron (NM_011227, intron 1 of 1)	intron (NM_011227, intron 1 of 1)	-1108	NR_126558	102132	Mm.37632	NR_126558	ENSMUSG00000096957	E230013L22Rik	AI645545	RIKEN cDNA E230013L22 gene	ncRNA
mm_146621.1	chr18	10116842	10116871	-	1	NA	exon (NM_009071, exon 12 of 33)	exon (NM_009071, exon 12 of 33)	64936	NM_009071	19877	Mm.6710	NM_009071	ENSMUSG00000024290	Rock1	1110055K06Rik|Rock-I	Rho-associated coiled-coil containing protein kinase 1	protein-coding
mm_113730.1	chr13	43962246	43962281	+	1	NA	Intergenic	Intergenic	-158904	NR_045285	328235	Mm.188356	NR_045285	ENSMUSG00000089815	Gm5083	A730030A06	predicted gene 5083	ncRNA
mm_114729.1	chr13	83721330	83721344	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-6769	NR_015561	320203	Mm.245636	NM_177100	ENSMUSG00000050334	C130071C03Rik	2810449C10Rik	RIKEN cDNA C130071C03 gene	ncRNA
mm_50854.1	chr6	55037956	55037980	+	1	NA	promoter-TSS (NM_180678)	promoter-TSS (NM_180678)	-33	NM_180678	353172	Mm.250004	NM_180678	ENSMUSG00000029777	Gars	GENA202|Gena201|Nmf249|Sgrp23	glycyl-tRNA synthetase	protein-coding
mm_15781.1	chr2	164334277	164334283	+	1	NA	3' UTR (NM_009301, exon 3 of 3)	3' UTR (NM_009301, exon 3 of 3)	1515	NM_009301	20944	Mm.140154	NM_009301	ENSMUSG00000017004	Svs5	BB115186|Semg1|Svp-1|Svp1|Svp5	seminal vesicle secretory protein 5	protein-coding
mm_146082.1	chr18	70622626	70622645	+	1	NA	exon (NM_010773, exon 6 of 7)	exon (NM_010773, exon 6 of 7)	54343	NM_010773	17191	Mm.322	NM_010773	ENSMUSG00000024513	Mbd2	MBD2a	methyl-CpG binding domain protein 2	protein-coding
mm_24876.1	chr3	95985491	95985523	+	1	NA	promoter-TSS (NR_045872)	promoter-TSS (NR_045872)	-3	NR_045872	668224	Mm.357766	NR_045872		Gm9054	EG668224	predicted gene 9054	ncRNA
mm_22299.1	chr2	180334666	180334704	-	1	NA	promoter-TSS (NM_008093)	promoter-TSS (NM_008093)	-6	NM_008093	14464	Mm.388880	NM_008093	ENSMUSG00000015627	Gata5	-	GATA binding protein 5	protein-coding
mm_53180.1	chr6	125411308	125411335	+	1	NA	Intergenic	Intergenic	-30817	NM_198604	213522	Mm.333396	NM_198604	ENSMUSG00000038167	Plekhg6	BC026778|Gm155	pleckstrin homology domain containing, family G (with RhoGef domain) member 6	protein-coding
mm_144801.1	chr18	36109850	36109856	+	1	NA	non-coding (NR_015571, exon 2 of 2)	non-coding (NR_015571, exon 2 of 2)	3650	NR_015571	74966	Mm.379238	NM_030089		4930471G03Rik	1700007N01Rik	RIKEN cDNA 4930471G03 gene	ncRNA
mm_76221.1	chr8	83572431	83572471	-	1	NA	TTS (NM_025843)	TTS (NM_025843)	5693	NM_025843	66916	Mm.29683	NM_025843	ENSMUSG00000033938	Ndufb7	1110002H15Rik	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 7	protein-coding
mm_5752.1	chr1	46853584	46853605	-	1	NA	promoter-TSS (NM_172653)	promoter-TSS (NM_172653)	-85	NM_172653	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|mKIAA1265	solute carrier family 39 (zinc transporter), member 10	protein-coding
mm_103835.1	chr11	83020757	83020767	-	1	NA	promoter-TSS (NM_001167743)	promoter-TSS (NM_001167743)	-40	NM_001167743	276950	Mm.491599	NM_181545	ENSMUSG00000035208	Slfn8	-	schlafen 8	protein-coding
mm_8095.1	chr1	135845576	135845607	-	1	NA	exon (NM_001130176, exon 3 of 13)	exon (NM_001130176, exon 3 of 13)	4730	NM_001130176	21956	Mm.247470	NM_011619	ENSMUSG00000026414	Tnnt2	Tnt|cTnT	troponin T2, cardiac	protein-coding
mm_7884.1	chr1	133068395	133068398	-	1	NA	intron (NM_001099276, intron 2 of 32)	intron (NM_001099276, intron 2 of 32)	22384	NM_001099276	240752	Mm.387308	NM_001099276	ENSMUSG00000026447	Pik3c2b	C330011J12Rik|Gm199|PI3K-C2beta|PI3KC2beta	phosphoinositide-3-kinase, class 2, beta polypeptide	protein-coding
mm_18769.1	chr2	73485734	73485769	-	1	NA	promoter-TSS (NM_001289723)	promoter-TSS (NM_001289723)	2	NM_001289723	215280	Mm.223504	NM_153138	ENSMUSG00000075284	Wipf1	AI115543|D2Ertd120e|WIP|Waspip	WAS/WASL interacting protein family, member 1	protein-coding
mm_76616.1	chr8	91313224	91313279	-	1	NA	promoter-TSS (NM_173431)	promoter-TSS (NM_173431)	-29	NM_173431	244585	Mm.324592	NM_173431	ENSMUSG00000033282	Rpgrip1l	1700047E16Rik|4931437C01|Ftm|Nphp8	Rpgrip1-like	protein-coding
mm_31546.1	chr4	55534648	55534690	+	1	NA	Intergenic	Intergenic	-2194	NM_010637	16600	Mm.4325	NM_010637	ENSMUSG00000003032	Klf4	EZF|Gklf|Zie	Kruppel-like factor 4 (gut)	protein-coding
mm_148447.1	chr19	3972438	3972468	+	1	NA	5' UTR (NM_001177438, exon 1 of 10)	5' UTR (NM_001177438, exon 1 of 10)	125	NM_001177438	621603	Mm.34137	NM_001177438	ENSMUSG00000075296	Aldh3b2	AI848594|C130048D07Rik	aldehyde dehydrogenase 3 family, member B2	protein-coding
mm_17940.1	chr2	36091396	36091410	-	1	NA	exon (NM_008500, exon 7 of 10)	exon (NM_008500, exon 7 of 10)	12657	NM_001083126	16874	Mm.12881	NM_008500	ENSMUSG00000026890	Lhx6	Lhx6.1	LIM homeobox protein 6	protein-coding
mm_24337.1	chr3	89715017	89715084	+	1	NA	promoter-TSS (NM_001038587)	promoter-TSS (NM_001038587)	28	NM_001038587	56417	Mm.316628	NM_019655	ENSMUSG00000027951	Adar	AV242451|Adar1|Adar1p110|Adar1p150|mZaADAR	adenosine deaminase, RNA-specific	protein-coding
mm_68990.1	chr7	126601338	126601348	-	1	NA	Intergenic	RMER17B|LTR|ERVK	-6433	NM_145636	246779	Mm.222632	NM_145636	ENSMUSG00000044701	Il27	IL-27|IL-27p28|Il30|p28	interleukin 27	protein-coding
mm_112479.1	chr13	5868949	5868966	+	1	NA	3' UTR (NM_011803, exon 4 of 4)	3' UTR (NM_011803, exon 4 of 4)	7468	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_151841.1	chr19	5729358	5729416	-	1	NA	TTS (NM_020491)	TTS (NM_020491)	279	NM_181452	17826	Mm.391142	NM_023166	ENSMUSG00000024939	Fam89b	1110021A21Rik|MMTV|Mtvr2	family with sequence similarity 89, member B	protein-coding
mm_148962.1	chr19	7494246	7494264	+	1	NA	promoter-TSS (NM_146091)	promoter-TSS (NM_146091)	-183	NM_146091	109168	Mm.264016	NM_146091	ENSMUSG00000024759	Atl3	4633402C03Rik|5730596K20Rik|AI465397|AW228836	atlastin GTPase 3	protein-coding
mm_88895.1	chr10	81149254	81149297	+	1	NA	3' UTR (NM_010731, exon 3 of 3)	3' UTR (NM_010731, exon 3 of 3)	13004	NM_010731	16969	Mm.20920	NM_010731	ENSMUSG00000035011	Zbtb7a	9030619K07Rik|9130006G12Rik|AI452336|FBI-1|Lrf|Pokemon|Zbtb7	zinc finger and BTB domain containing 7a	protein-coding
mm_162848.1	chr10	87104859	87104860	+	1	NA	intron (NM_029685, intron 2 of 5)	intron (NM_029685, intron 2 of 5)	46813	NM_029685	76640	Mm.78423	NM_029685	ENSMUSG00000047129	1700113H08Rik	-	RIKEN cDNA 1700113H08 gene	protein-coding
mm_42801.1	chr5	121712468	121712475	+	1	NA	intron (NM_009125, intron 1 of 24)	CpG	862	NM_009125	20239	Mm.260900	NM_009125	ENSMUSG00000042605	Atxn2	9630045M23Rik|ATX2|AW544490|Sca2	ataxin 2	protein-coding
mm_110489.1	chr12	52006491	52006512	-	1	NA	promoter-TSS (NM_029545)	promoter-TSS (NM_029545)	6	NM_029545	328092	Mm.2821	NM_029545	ENSMUSG00000020956	Dtd2	4930578F06Rik|6530401N04Rik|B830049N13Rik	D-tyrosyl-tRNA deacylase 2	protein-coding
mm_127349.1	chr15	100619517	100619532	+	1	NA	3' UTR (NM_011873, exon 4 of 4)	3' UTR (NM_011873, exon 4 of 4)	3862	NM_011873	23994	Mm.486175	NM_011873	ENSMUSG00000000346	Dazap2	AI314727|Brbp|Gcap28|Prtb|gt6-12|mKIAA0058	DAZ associated protein 2	protein-coding
mm_109180.1	chr12	108450300	108450325	+	1	NA	intron (NM_001043335, intron 1 of 21)	Charlie1a|DNA|hAT-Charlie	27496	NM_001043335	68519	Mm.236645	NM_001043335	ENSMUSG00000058070	Eml1	1110008N23Rik|A930030P13Rik|AA171013|AI847476|AI853955|ELP79|EMAP|EMAPL|heco	echinoderm microtubule associated protein like 1	protein-coding
mm_36975.1	chr4	109476667	109476727	-	1	NA	promoter-TSS (NM_013876)	promoter-TSS (NM_013876)	-192	NM_013876	29864	Mm.392580	NM_013876	ENSMUSG00000028557	Rnf11	-	ring finger protein 11	protein-coding
mm_123691.1	chr14	69640186	69640203	-	1	NA	intron (NM_033325, intron 2 of 13)	B4A|SINE|B4	30718	NM_033325	94352	Mm.116714	NM_033325	ENSMUSG00000034205	Loxl2	1110004B06Rik|4930526G11Rik|9430067E15Rik	lysyl oxidase-like 2	protein-coding
mm_151627.1	chr19	3911802	3911846	-	1	NA	intron (NM_001271443, intron 1 of 6)	intron (NM_001271443, intron 1 of 6)	950	NM_144870	225887	Mm.44227	NM_144870	ENSMUSG00000059734	Ndufs8	BC021616|CI-23kD|TYKY	NADH dehydrogenase (ubiquinone) Fe-S protein 8	protein-coding
mm_53061.1	chr6	124830219	124830251	+	1	NA	promoter-TSS (NM_013538)	promoter-TSS (NM_013538)	59	NM_013538	14793	Mm.285723	NM_013538	ENSMUSG00000023505	Cdca3	2410005A12Rik|C8|Grcc8|Tome-1	cell division cycle associated 3	protein-coding
mm_88288.1	chr10	75212066	75212150	+	1	NA	promoter-TSS (NM_001145826)	promoter-TSS (NM_001145826)	35	NM_153406	74392	Mm.27716	NM_153406	ENSMUSG00000033444	Specc1l	4930470P14Rik|4932439K10Rik|9530057A13Rik|AI317249|Cytsa|mKIAA0376	sperm antigen with calponin homology and coiled-coil domains 1-like	protein-coding
mm_93615.1	chr10	117238866	117238897	-	1	NA	promoter-TSS (NM_029906)	promoter-TSS (NM_029906)	-200	NM_029906	77397	Mm.118350	NM_029906	ENSMUSG00000020177	9530003J23Rik	Lyzf1	RIKEN cDNA 9530003J23 gene	protein-coding
mm_125130.1	chr15	30303452	30303454	+	1	NA	intron (NM_008729, intron 1 of 22)	intron (NM_008729, intron 1 of 22)	130860	NM_008729	18163	Mm.321648	NM_008729	ENSMUSG00000022240	Ctnnd2	Catnd2|Nprap|neurojugin	catenin (cadherin associated protein), delta 2	protein-coding
mm_143104.1	chr17	57087615	57087636	-	1	NA	5' UTR (NM_009451, exon 1 of 4)	5' UTR (NM_009451, exon 1 of 4)	157	NM_009451	22153	Mm.7420	NM_009451	ENSMUSG00000062591	Tubb4a	AI325297|M(beta)4|Tubb|Tubb4	tubulin, beta 4A class IVA	protein-coding
mm_81235.1	chr9	107912569	107912574	+	1	NA	intron (NR_109782, intron 4 of 18)	intron (NR_109782, intron 4 of 18)	-2432	NM_001287261	19882	Mm.3901	NM_009074	ENSMUSG00000032584	Mst1r	CD136|CDw136|Fv-2|Fv2|PTK8|Ron|STK	macrophage stimulating 1 receptor (c-met-related tyrosine kinase)	protein-coding
mm_20212.1	chr2	125506420	125506445	-	1	NA	promoter-TSS (NM_007993)	promoter-TSS (NM_007993)	6	NM_007993	14118	Mm.271644	NM_007993	ENSMUSG00000027204	Fbn1	AI536462|B430209H23|Fib-1|Tsk	fibrillin 1	protein-coding
mm_53687.1	chr6	142402089	142402094	+	1	NA	3' UTR (NM_025872, exon 5 of 5)	3' UTR (NM_025872, exon 5 of 5)	-11340	NM_001242345	319552	Mm.39649	NM_001242345	ENSMUSG00000071112	Spx	B230216G23Rik|Npq	spexin hormone	protein-coding
mm_130899.1	chr15	102403836	102403873	-	1	NA	Intergenic	Intergenic	-2462	NM_013672	20683	Mm.4618	NM_013672	ENSMUSG00000001280	Sp1	1110003E12Rik|AA450830|AI845540|Sp1-1	trans-acting transcription factor 1	protein-coding
mm_150928.1	chr19	46304391	46304406	+	1	NA	promoter-TSS (NM_001177369)	promoter-TSS (NM_001177369)	-339	NM_001177369	18034	Mm.102365	NM_019408	ENSMUSG00000025225	Nfkb2	NF-kappaB2|lyt|p49|p49/p100|p50B|p52	nuclear factor of kappa light polypeptide gene enhancer in B cells 2, p49/p100	protein-coding
mm_159621.1	chr4	134532769	134532769	-	1	NA	intron (NM_029759, intron 1 of 6)	intron (NM_029759, intron 1 of 6)	2499	NM_001256112	76824	Mm.30153	NM_029759	ENSMUSG00000046671	Mtfr1l	2410166I05Rik|AI480750|Fam54b	mitochondrial fission regulator 1-like	protein-coding
mm_44628.1	chr5	26493284	26493294	-	1	NA	promoter-TSS (NR_029445)	promoter-TSS (NR_029445)	25	NR_029445	75942	Mm.50087	NR_029445	ENSMUSG00000029044	4930584F24Rik	1700001J09Rik|4930522C06Rik	RIKEN cDNA 4930584F24 gene	ncRNA
mm_59467.1	chr7	27258841	27258859	+	1	NA	promoter-TSS (NM_010950)	promoter-TSS (NM_010950)	89	NM_010950	18223	Mm.458153	NM_010950	ENSMUSG00000063160	Numbl	nbl	numb-like	protein-coding
mm_128992.1	chr15	74836965	74837010	-	1	NA	intron (NM_001033229, intron 5 of 8)	intron (NM_001033229, intron 5 of 8)	4656	NM_001033229	110115	Mm.322606	NM_001033229	ENSMUSG00000075604	Cyp11b1	AA389061|CPN1|Cyp11b|Cyp11b-1|FHI	cytochrome P450, family 11, subfamily b, polypeptide 1	protein-coding
mm_95842.1	chr11	57128904	57128920	+	1	NA	intron (NM_001252403, intron 2 of 15)	intron (NM_001252403, intron 2 of 15)	115866	NM_001252403	14799	Mm.4920	NM_008165	ENSMUSG00000020524	Gria1	2900051M01Rik|Glr-1|Glr1|GluA1|GluR-A|GluRA|Glur-1|Glur1|HIPA1|gluR-K1	glutamate receptor, ionotropic, AMPA1 (alpha 1)	protein-coding
mm_160298.1	chr7	132949811	132949811	+	1	NA	exon (NM_207302, exon 1 of 9)	exon (NM_207302, exon 1 of 9)	189	NM_207302	360216	Mm.389984	NM_207302	ENSMUSG00000030967	Zranb1	9330160G10Rik|D7Wsu87e|Gm1956|Trabid	zinc finger, RAN-binding domain containing 1	protein-coding
mm_12192.1	chr2	65620830	65620834	+	1	NA	promoter-TSS (NM_001346679)	promoter-TSS (NM_001346679)	63	NM_001346679	110876	Mm.220329	NM_001099298	ENSMUSG00000075318	Scn2a	6430408L10|A230052E19Rik|Nav1.2|Scn2a1	sodium channel, voltage-gated, type II, alpha	protein-coding
mm_78022.1	chr9	13749292	13749321	+	1	NA	non-coding (NR_024025, exon 1 of 16)	non-coding (NR_024025, exon 1 of 16)	125	NR_024025	77116	Mm.210405	NM_023858	ENSMUSG00000031918	Mtmr2	6030445P13Rik	myotubularin related protein 2	protein-coding
mm_109248.1	chr12	109453278	109453314	+	1	NA	promoter-TSS (NM_010052)	promoter-TSS (NM_010052)	-159	NM_001190704	13386	Mm.157069	NM_010052	ENSMUSG00000040856	Dlk1	AW742678|DLK-1|DlkI|FA1|Ly107|Peg9|SCP1|ZOG|pG2|pref-1	delta-like 1 homolog (Drosophila)	protein-coding
mm_77646.1	chr8	124559320	124559329	-	1	NA	exon (NM_007428, exon 3 of 5)	exon (NM_007428, exon 3 of 5)	10383	NM_007428	11606	Mm.301626	NM_007428	ENSMUSG00000031980	Agt	AI265500|AngI|AngII|Aogen|Serpina8	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	protein-coding
mm_130409.1	chr15	97977278	97977301	-	1	NA	exon (NM_001113515, exon 51 of 53)	exon (NM_001113515, exon 51 of 53)	13060	NM_001252153	380967	Mm.196630	NM_201359	ENSMUSG00000052369	Tmem106c	AI046681|BC046621|D15Ertd405e	transmembrane protein 106C	protein-coding
mm_30269.1	chr3	146771349	146771351	-	1	NA	promoter-TSS (NM_001164199)	promoter-TSS (NM_001164199)	-657	NM_001164199	18749	Mm.16766	NM_011100	ENSMUSG00000005034	Prkacb	CbPKA|Pkacb	protein kinase, cAMP dependent, catalytic, beta	protein-coding
mm_87780.1	chr10	60296422	60296433	+	1	NA	intron (NM_011179, intron 8 of 14)	intron (NM_011179, intron 8 of 14)	11966	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_105565.1	chr11	106568420	106568433	-	1	NA	exon (NM_198292, exon 2 of 12)	exon (NM_198292, exon 2 of 12)	44504	NM_198292	21763	Mm.102407	NM_198292	ENSMUSG00000040548	Tex2	4930568E07Rik|AI553404|Def-5|Taz4	testis expressed gene 2	protein-coding
mm_120206.1	chr14	61861677	61861684	+	1	NA	Intergenic	Intergenic	-179307	NR_028264	668253	Mm.32886	NR_028264	ENSMUSG00000097589	Dleu2	1810047A16Rik|4932411A06Rik|7730401J12Rik|AI197277|AI788824|Alt1|Gm9069|Leu2	deleted in lymphocytic leukemia, 2	ncRNA
mm_103379.1	chr11	75415046	75415056	-	1	NA	exon (NM_011340, exon 5 of 8)	exon (NM_011340, exon 5 of 8)	7572	NM_011340	20317	Mm.2044	NM_011340	ENSMUSG00000000753	Serpinf1	AI195227|EPC-1|Pedf|Pedfl|Sdf3	serine (or cysteine) peptidase inhibitor, clade F, member 1	protein-coding
mm_141693.1	chr17	33978455	33978480	-	1	NA	non-coding (NR_004446, exon 2 of 6)	non-coding (NR_004446, exon 2 of 6)	324	NR_004446	630499	Mm.440940	NM_001081015		H2-K2	EG630499|Gm7035|H-2K1|H-2K1K|H-2K2|H2-K1	histocompatibility 2, K region locus 2	pseudo
mm_106866.1	chr12	8009577	8009585	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	31904	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_33574.1	chr4	132310129	132310174	+	1	NA	promoter-TSS (NR_034046)	promoter-TSS (NR_034046)	-156	NR_034046	100217440		NR_034046		Snora61	MBI-164	small nucleolar RNA, H/ACA box 61	snoRNA
mm_120918.1	chr14	76415077	76415091	+	1	NA	promoter-TSS (NM_207652)	promoter-TSS (NM_207652)	123	NM_001310646	21807	Mm.153272	NM_009366	ENSMUSG00000022010	Tsc22d1	AA589566|AW105905|Egr5|TSC-22|Tgfb1i4|Tsc|Tsc22	TSC22 domain family, member 1	protein-coding
mm_81696.1	chr9	111185186	111185197	+	1	NA	intron (NM_001164838, intron 5 of 14)	intron (NM_001164838, intron 5 of 14)	67080	NM_001164838	71268	Mm.302287	NM_027742	ENSMUSG00000032497	Lrrfip2	5133400F20Rik|AI850587	leucine rich repeat (in FLII) interacting protein 2	protein-coding
mm_160502.1	chr9	15874702	15874702	-	1	NA	promoter-TSS (NM_145712)	promoter-TSS (NM_145712)	-146	NM_145712	244701	Mm.222631	NM_145712	ENSMUSG00000050901	Mtnr1b	Mel-1B-R|Mel1b|Mt2	melatonin receptor 1B	protein-coding
mm_10747.1	chr2	23156014	23156023	+	1	NA	promoter-TSS (NM_013771)	promoter-TSS (NM_013771)	6	NM_025979	67121	Mm.253721	NM_025979	ENSMUSG00000026779	Mastl	2700091H24Rik|C88295|GW|GWL|MAST-L|THC2	microtubule associated serine/threonine kinase-like	protein-coding
mm_40808.1	chr5	71658062	71658088	+	1	NA	5' UTR (NM_010251, exon 1 of 9)	5' UTR (NM_010251, exon 1 of 9)	233	NM_010251	14397	Mm.248731	NM_010251	ENSMUSG00000029211	Gabra4	Gabra-4	gamma-aminobutyric acid (GABA) A receptor, subunit alpha 4	protein-coding
mm_11601.1	chr2	33642597	33642604	+	1	NA	non-coding (NR_046275, exon 3 of 3)	non-coding (NR_046275, exon 3 of 3)	1407	NR_046275	100504399	Mm.72070	NM_177842		C130021I20Rik	-	Riken cDNA C130021I20 gene	ncRNA
mm_125146.1	chr15	30646515	30646572	+	1	NA	intron (NM_008729, intron 6 of 22)	CpG	-392583	NR_045186	73784	Mm.66947	NR_045186		4930430F21Rik	-	RIKEN cDNA 4930430F21 gene	ncRNA
mm_54041.1	chr6	13608012	13608050	-	1	NA	promoter-TSS (NM_001347059)	promoter-TSS (NM_001347059)	67	NM_001347059	101118	Mm.254845	NM_028990	ENSMUSG00000029569	Tmem168	5730526F17Rik|8430437G11Rik|AI462344|AI504145	transmembrane protein 168	protein-coding
mm_49676.1	chr6	31679333	31679339	+	1	NA	Intergenic	ORR1C2|LTR|ERVL-MaLR	-115399	NM_013723	27205	Mm.89918	NM_013723	ENSMUSG00000025608	Podxl	AW121214|Ly102|PC|PCLP-1|Pclp1	podocalyxin-like	protein-coding
mm_107342.1	chr12	32379906	32379940	+	1	NA	3' UTR (NM_001162903, exon 1 of 1)	3' UTR (NM_001162903, exon 1 of 1)	1134	NM_001162903	72123	Mm.341352	NM_028111	ENSMUSG00000090946	Ccdc71l	2010109K11Rik|AV375874	coiled-coil domain containing 71 like	protein-coding
mm_33683.1	chr4	133369766	133369780	+	1	NA	promoter-TSS (NM_016981)	promoter-TSS (NM_016981)	1	NM_016981	20544	Mm.4312	NM_016981	ENSMUSG00000028854	Slc9a1	AW554487|Apnh|Mir5122|Nhe1|mir-5122|swe	solute carrier family 9 (sodium/hydrogen exchanger), member 1	protein-coding
mm_34227.1	chr4	141012836	141012852	+	1	NA	5' UTR (NM_008546, exon 2 of 9)	5' UTR (NM_008546, exon 2 of 9)	2207	NM_008546	17150	Mm.7386	NM_008546	ENSMUSG00000060572	Mfap2	AI893631|Magp|Magp1	microfibrillar-associated protein 2	protein-coding
mm_40088.1	chr5	34543378	34543429	+	1	NA	promoter-TSS (NM_001145858)	promoter-TSS (NM_001145858)	38	NM_001145858	24055	Mm.5012	NM_011893	ENSMUSG00000054520	Sh3bp2	3BP2	SH3-domain binding protein 2	protein-coding
mm_73194.1	chr8	95534079	95534123	+	1	NA	promoter-TSS (NM_172914)	promoter-TSS (NM_172914)	1	NM_172914	244608	Mm.248902	NM_172914	ENSMUSG00000036598	Ccdc113	4933409I22|BC060957	coiled-coil domain containing 113	protein-coding
mm_101682.1	chr11	40692580	40692664	-	1	NA	promoter-TSS (NM_134017)	promoter-TSS (NM_134017)	60	NM_134017	108645	Mm.293771	NM_134017	ENSMUSG00000042032	Mat2b	1110064C04Rik|2410018D16Rik|AI182287|AU022853|MAT-II|MATIIbeta|TGR	methionine adenosyltransferase II, beta	protein-coding
mm_64406.1	chr7	142511338	142511352	+	1	NA	exon (NM_001163669, exon 11 of 17)	exon (NM_001163669, exon 11 of 17)	-4574	NR_033261	677289	Mm.350054	NR_033261	ENSMUSG00000043795	Prr33	ENSMUSG00000043795|Gm14492|OTTMUSG00000016823	proline rich 33	ncRNA
mm_111016.1	chr12	78989184	78989187	-	1	NA	intron (NM_178745, intron 1 of 2)	intron (NM_178745, intron 1 of 2)	-5707	NM_001170401	268567	Mm.341747	NM_178745	ENSMUSG00000046157	Tmem229b	6330442E10Rik|9830138K24|AU019070	transmembrane protein 229B	protein-coding
mm_163872.1	chr14	19419287	19419317	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	183285	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_145520.1	chr18	60556414	60556455	+	1	NA	exon (NM_026302, exon 13 of 13)	exon (NM_026302, exon 13 of 13)	-4352	NM_025776	66810	Mm.275106	NM_025776	ENSMUSG00000024604	Rbm22	8430430L24Rik	RNA binding motif protein 22	protein-coding
mm_22657.1	chr3	14871662	14871670	+	1	NA	3' UTR (NM_007606, exon 7 of 7)	3' UTR (NM_007606, exon 7 of 7)	8128	NM_007606	12350	Mm.300	NM_007606	ENSMUSG00000027559	Car3	BB219044|Ca3|Car-3	carbonic anhydrase 3	protein-coding
mm_155910.1	chrX	101794645	101794680	+	1	NA	Intergenic	CpG	-54723	NM_001163610	100042480	Mm.232	NM_001163610	ENSMUSG00000079481	Nhsl2	1110062M06Rik|6430511F03|AI225852|AW488865|EG621083|ENSMUSG00000073037|Gm10456	NHS-like 2	protein-coding
mm_69522.1	chr7	135645652	135645660	-	1	NA	intron (NM_001316680, intron 3 of 20)	intron (NM_001316680, intron 3 of 20)	-6243	NM_001316681	19267	Mm.945	NM_011212	ENSMUSG00000041836	Ptpre	PTPe|PTPepsilon|RPTPepsilon	protein tyrosine phosphatase, receptor type, E	protein-coding
mm_59588.1	chr7	28131542	28131556	+	1	NA	exon (NM_001164655, exon 3 of 20)	exon (NM_001164655, exon 3 of 20)	2083	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_51672.1	chr6	86404342	86404380	+	1	NA	5' UTR (NM_011585, exon 1 of 13)	5' UTR (NM_011585, exon 1 of 13)	142	NM_001164078	21841	Mm.333219	NM_011585	ENSMUSG00000071337	Tia1	2310050N03Rik|AI256674|TIA-1|mTIA-1	cytotoxic granule-associated RNA binding protein 1	protein-coding
mm_27695.1	chr3	66296808	66296822	-	1	NA	promoter-TSS (NM_145820)	promoter-TSS (NM_145820)	22	NM_145820	72789	Mm.443526	NM_028357	ENSMUSG00000027831	Veph1	2810471M23Rik|Veph	ventricular zone expressed PH domain-containing 1	protein-coding
mm_31917.1	chr4	85205519	85205522	+	1	NA	promoter-TSS (NM_019535)	promoter-TSS (NM_019535)	64	NM_019535	20404	Mm.143603	NM_019535	ENSMUSG00000028488	Sh3gl2	9530001L19Rik|AI120490|AW555077|B930049H17Rik|EEN-B1|SH3PA|Sh3d2a	SH3-domain GRB2-like 2	protein-coding
mm_46431.1	chr5	104441042	104441052	-	1	NA	TTS (NM_001204203)	TTS (NM_001204203)	4855	NM_001204233	20750	Mm.288474	NM_009263	ENSMUSG00000029304	Spp1	2AR|Apl-1|BNSP|BSPI|Bsp|ETA-1|Eta|OP|Opn|Opnl|Ric|Spp-1	secreted phosphoprotein 1	protein-coding
mm_148999.1	chr19	8664367	8664381	+	1	NA	5' UTR (NM_007698, exon 1 of 2)	5' UTR (NM_007698, exon 1 of 2)	369	NM_001112697	12669	Mm.240607	NM_007698	ENSMUSG00000032773	Chrm1	Chrm-1|M1|M1R	cholinergic receptor, muscarinic 1, CNS	protein-coding
mm_34646.1	chr4	150807776	150807784	+	1	NA	Intergenic	Intergenic	47169	NR_040649	73348	Mm.396218	NR_040649	ENSMUSG00000078492	1700045H11Rik	-	RIKEN cDNA 1700045H11 gene	ncRNA
mm_59569.1	chr7	28101296	28101307	+	1	NA	exon (NM_001122603, exon 11 of 20)	exon (NM_001122603, exon 11 of 20)	-28165	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_15693.1	chr2	163659135	163659167	+	1	NA	5' UTR (NM_001039390, exon 2 of 5)	5' UTR (NM_001039390, exon 2 of 5)	693	NM_001164053	18769	Mm.10091	NM_011106	ENSMUSG00000035268	Pkig	PKIgamma	protein kinase inhibitor, gamma	protein-coding
mm_90715.1	chr10	4409861	4409906	-	1	NA	intron (NM_025343, intron 10 of 12)	RSINE1|SINE|B4	19283	NR_002891	433224	Mm.153111	NR_002891		Gm5512	EG433224	required for meiotic nuclear division 1 pseudogene	pseudo
mm_90518.1	chr10	128058948	128058960	+	1	NA	promoter-TSS (NM_019766)	promoter-TSS (NM_019766)	-28	NM_019766	56351	Mm.305816	NM_019766	ENSMUSG00000071072	Ptges3	5730442A20Rik|Ptges|Tebp|cPGES|p23|sid3177	prostaglandin E synthase 3 (cytosolic)	protein-coding
mm_85161.1	chr9	96358508	96358536	-	1	NA	intron (NM_007502, intron 1 of 6)	RSINE1|SINE|B4	5777	NM_007502	11933	Mm.424	NM_007502	ENSMUSG00000032412	Atp1b3	AA409958|AI664000|AW212096	ATPase, Na+/K+ transporting, beta 3 polypeptide	protein-coding
mm_26045.1	chr3	135603029	135603068	+	1	NA	intron (NM_008689, intron 16 of 24)	intron (NM_008689, intron 16 of 24)	88499	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_108421.1	chr12	82169460	82169484	+	1	NA	promoter-TSS (NM_001167983)	promoter-TSS (NM_001167983)	-544	NM_001167983	217692	Mm.261333	NM_172579	ENSMUSG00000042700	Sipa1l1	4931426N11Rik|AW213287|Spar|mKIAA0440	signal-induced proliferation-associated 1 like 1	protein-coding
mm_88490.1	chr10	77720585	77720593	+	1	NA	promoter-TSS (NM_010670)	promoter-TSS (NM_010670)	3	NM_010670	16694	Mm.34372	NM_010670	ENSMUSG00000069583	Krtap12-1	D10Jhu14e	keratin associated protein 12-1	protein-coding
mm_9773.1	chr1	181017490	181017548	-	1	NA	promoter-TSS (NM_010145)	promoter-TSS (NM_010145)	50	NM_010145	13849	Mm.9075	NM_010145	ENSMUSG00000038776	Ephx1	EH|Eph-1|Eph1|Epxh1|mEH	epoxide hydrolase 1, microsomal	protein-coding
mm_157150.1	chrX	9462054	9462065	-	1	NA	intron (NM_007807, intron 3 of 12)	intron (NM_007807, intron 3 of 12)	7265	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_16683.1	chr2	6884477	6884498	-	1	NA	intron (NM_001110229, intron 2 of 14)	intron (NM_001110229, intron 2 of 14)	509	NM_010160	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_78653.1	chr9	40450297	40450342	+	1	NA	intron (NM_172768, intron 1 of 19)	intron (NM_172768, intron 1 of 19)	5445	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_63994.1	chr7	140115795	140115804	+	1	NA	intron (NM_053119, intron 1 of 7)	intron (NM_053119, intron 1 of 7)	624	NM_053119	93747	Mm.24452	NM_053119	ENSMUSG00000025465	Echs1	C80529	enoyl Coenzyme A hydratase, short chain, 1, mitochondrial	protein-coding
mm_139004.1	chr17	45568910	45568953	+	1	NA	exon (NM_008302, exon 9 of 11)	exon (NM_008302, exon 9 of 11)	4330	NM_008302	15516	Mm.2180	NM_008302	ENSMUSG00000023944	Hsp90ab1	90kDa|AL022974|C81438|Hsp84|Hsp84-1|Hsp90|Hspcb	heat shock protein 90 alpha (cytosolic), class B member 1	protein-coding
mm_112970.1	chr13	21286940	21286942	+	1	NA	3' UTR (NM_010343, exon 5 of 5)	3' UTR (NM_010343, exon 5 of 5)	5745	NM_010343	14780	Mm.1332	NM_010343	ENSMUSG00000004344	Gpx5	AV379049|Arep	glutathione peroxidase 5	protein-coding
mm_133541.1	chr16	91082939	91082943	+	1	NA	Intergenic	PB1D10|SINE|Alu	-13796	NM_028905	74387	Mm.236220	NM_028905	ENSMUSG00000039851	4932438H23Rik	4931406G06Rik|AI550392	RIKEN cDNA 4932438H23 gene	protein-coding
mm_73440.1	chr8	106168858	106168926	+	1	NA	promoter-TSS (NM_178798)	promoter-TSS (NM_178798)	17	NM_178798	330836	Mm.46749	NM_178798	ENSMUSG00000031904	Slc7a6	AI643885|LAT-2|LAT3	solute carrier family 7 (cationic amino acid transporter, y+ system), member 6	protein-coding
mm_117088.1	chr13	59746945	59746974	-	1	NA	Intergenic	Intergenic	13309	NR_045977	75223	Mm.444771	NR_045977	ENSMUSG00000097502	4930528D03Rik	-	RIKEN cDNA 4930528D03 gene	ncRNA
mm_93243.1	chr10	95416717	95416732	-	1	NA	promoter-TSS (NM_001168655)	promoter-TSS (NM_001168655)	133	NM_007706	216233	Mm.474283	NM_007706	ENSMUSG00000020027	Socs2	8030460M17|AI527257|AW108012|CIS2|Cish2|D130043N08Rik|JAB|SOCS-2|SSI-2|hg	suppressor of cytokine signaling 2	protein-coding
mm_165088.1	chr19	48769500	48769502	+	1	NA	intron (NM_025696, intron 19 of 26)	B4A|SINE|B4	563476	NM_025696	66673	Mm.70980	NM_025696	ENSMUSG00000063434	Sorcs3	6330404A12Rik|AW045579	sortilin-related VPS10 domain containing receptor 3	protein-coding
mm_40549.1	chr5	58109468	58109476	+	1	NA	intron (NM_001310608, intron 3 of 3)	intron (NM_001310608, intron 3 of 3)	343526	NR_046190	78163	Mm.243828	NR_046190	ENSMUSG00000105234	4930459L07Rik	-	RIKEN cDNA 4930459L07 gene	ncRNA
mm_45467.1	chr5	69341538	69341547	-	1	NA	5' UTR (NM_175519, exon 1 of 2)	5' UTR (NM_175519, exon 1 of 2)	167	NM_175519	243043	Mm.234821	NM_175519	ENSMUSG00000037653	Kctd8	A730087N02Rik	potassium channel tetramerisation domain containing 8	protein-coding
mm_91314.1	chr10	24926736	24926744	-	1	NA	intron (NM_007482, intron 1 of 7)	intron (NM_007482, intron 1 of 7)	730	NM_007482	11846	Mm.154144	NM_007482	ENSMUSG00000019987	Arg1	AI|AI256583|Arg-1|PGIF	arginase, liver	protein-coding
mm_58340.1	chr6	146954436	146954440	-	1	NA	promoter-TSS (NM_028509)	promoter-TSS (NM_028509)	-17	NM_028509	73344	Mm.391543	NM_028509	ENSMUSG00000040163	1700034J05Rik	-	RIKEN cDNA 1700034J05 gene	protein-coding
mm_115030.1	chr13	99247696	99247707	+	1	NA	TTS (NM_001004149)	TTS (NM_001004149)	62878	NM_001004149	238803	Mm.343207	NM_001004149	ENSMUSG00000050919	Zfp366	DC-SCRIPT|Znf366	zinc finger protein 366	protein-coding
mm_70516.1	chr8	12947966	12947976	+	1	NA	promoter-TSS (NR_128567)	promoter-TSS (NR_128567)	30	NR_128567	104797311		NR_128567	ENSMUSG00000105030	Gm38671	Mir9768|mmu-mir-9768	predicted gene, 38671	ncRNA
mm_135277.1	chr16	38433154	38433175	-	1	NA	promoter-TSS (NM_134102)	promoter-TSS (NM_134102)	-19	NM_134102	85031	Mm.279805	NM_134102	ENSMUSG00000002847	Pla1a	AA986889|Ps-pla1|Pspla1	phospholipase A1 member A	protein-coding
mm_71284.1	chr8	40920383	40920411	+	1	NA	3' UTR (NM_001044740, exon 12 of 12)	3' UTR (NM_001044740, exon 12 of 12)	-5836	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_75950.1	chr8	71665465	71665476	-	1	NA	intron (NM_001029873, intron 3 of 41)	intron (NM_001029873, intron 3 of 41)	6287	NM_001029873	382018	Mm.334606	NM_001029873	ENSMUSG00000034799	Unc13a	2410078G03Rik|Munc13-1	unc-13 homolog A (C. elegans)	protein-coding
mm_3823.1	chr1	159276203	159276220	+	1	NA	intron (NM_011931, intron 8 of 19)	intron (NM_011931, intron 8 of 19)	-17562	NR_144489	100846986		NR_144489		Pou5f1-rs1	Gm21053|Oct4P2|Otf-3rs|Otf3-rs1|Otf3a	POU domain, class 5, transcription factor 1, related sequence 1	pseudo
mm_141310.1	chr17	28356866	28356866	-	1	NA	intron (NM_021478, intron 11 of 14)	ID_B1|SINE|B4	-6061	NM_011566	21678	Mm.6655	NM_011566	ENSMUSG00000002249	Tead3	DTEF-1|ETFR-1|TEAD-3|TEF-5|Tcf13r2	TEA domain family member 3	protein-coding
mm_71287.1	chr8	40921820	40921832	+	1	NA	3' UTR (NM_001044740, exon 12 of 12)	3' UTR (NM_001044740, exon 12 of 12)	-4407	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_11748.1	chr2	38354795	38354804	+	1	NA	exon (NM_010710, exon 3 of 5)	exon (NM_010710, exon 3 of 5)	3491	NM_010710	16870	Mm.142856	NM_010710	ENSMUSG00000000247	Lhx2	LH2A|Lh-2|Lim2|ap|apterous	LIM homeobox protein 2	protein-coding
mm_17363.1	chr2	26668794	26668818	-	1	NA	intron (NM_010695, intron 4 of 6)	intron (NM_010695, intron 4 of 6)	2476	NM_010695	16821	Mm.123925	NM_010695	ENSMUSG00000026919	Lcn4	A630045M08Rik|Vnsp2	lipocalin 4	protein-coding
mm_87897.1	chr10	62071508	62071535	+	1	NA	Intergenic	Intergenic	39492	NM_027251	69894	Mm.294126	NM_027251	ENSMUSG00000020083	2010107G23Rik	AA545165	RIKEN cDNA 2010107G23 gene	protein-coding
mm_100284.1	chr11	117809654	117809685	+	1	NA	promoter-TSS (NM_009304)	promoter-TSS (NM_009304)	2	NM_009304	20973	Mm.468228	NM_009304	ENSMUSG00000048277	Syngr2	Clast2|cellugyrin	synaptogyrin 2	protein-coding
mm_32002.1	chr4	94614484	94614500	+	1	NA	promoter-TSS (NM_001290568)	promoter-TSS (NM_001290568)	1	NM_026319	67694	Mm.240619	NM_026319	ENSMUSG00000028576	Ift74	1700029H06Rik|Ccdc2|Cmg1|b2b796Clo	intraflagellar transport 74	protein-coding
mm_51974.1	chr6	91758641	91758648	+	1	NA	3' UTR (NM_009320, exon 15 of 15)	3' UTR (NM_009320, exon 15 of 15)	48749	NM_001159507	243547	Mm.333264	NM_001033353	ENSMUSG00000030098	Grip2	-	glutamate receptor interacting protein 2	protein-coding
mm_15575.1	chr2	158666744	158666752	+	1	NA	promoter-TSS (NM_001159662)	promoter-TSS (NM_001159662)	15	NM_153089	228852	Mm.150540	NM_153089	ENSMUSG00000037754	Ppp1r16b	ANKRD4|C130078N17Rik|TIMAP|Wdt4	protein phosphatase 1, regulatory (inhibitor) subunit 16B	protein-coding
mm_46645.1	chr5	108582142	108582164	-	1	NA	exon (NM_153569, exon 22 of 28)	exon (NM_153569, exon 22 of 28)	-32126	NM_007756	12889	Mm.5195	NM_007756	ENSMUSG00000033615	Cplx1	921-S	complexin 1	protein-coding
mm_49192.1	chr6	15185859	15185859	+	1	NA	intron (NM_212435, intron 1 of 16)	intron (NM_212435, intron 1 of 16)	353	NM_001286607	114142	Mm.332919	NM_053242	ENSMUSG00000029563	Foxp2	2810043D05Rik|AI449000|CAG-16|D0Kist7	forkhead box P2	protein-coding
mm_47005.1	chr5	115464612	115464616	-	1	NA	Intergenic	Intergenic	-1652	NM_011107	18778	Mm.20190	NM_011107	ENSMUSG00000029522	Pla2g1b	Pla2a|sPLA2IB	phospholipase A2, group IB, pancreas	protein-coding
mm_25383.1	chr3	107213374	107213399	+	1	NA	exon (NM_001111143, exon 7 of 9)	exon (NM_001111143, exon 7 of 9)	8346	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_152580.1	chr19	11603012	11603023	-	1	NA	intron (NM_026835, intron 2 of 6)	intron (NM_026835, intron 2 of 6)	1787	NM_026835	68774	Mm.290390	NM_026835	ENSMUSG00000024679	Ms4a6d	1110058E16Rik|AI447446|Ms4a11	membrane-spanning 4-domains, subfamily A, member 6D	protein-coding
mm_54629.1	chr6	38691877	38691899	-	1	NA	Intergenic	Intergenic	28819	NM_001101507	665180	Mm.349066	NM_001101507	ENSMUSG00000079598	Clec2l	AI414054|AW122724|Gm1064	C-type lectin domain family 2, member L	protein-coding
mm_105630.1	chr11	106920682	106920735	-	1	NA	promoter-TSS (NM_025481)	promoter-TSS (NM_025481)	7	NM_025481	66313	Mm.340955	NM_025481	ENSMUSG00000018363	Smurf2	2810411E22Rik|AI558114|AI649275	SMAD specific E3 ubiquitin protein ligase 2	protein-coding
mm_66869.1	chr7	57386973	57386991	-	1	NA	promoter-TSS (NM_008074)	promoter-TSS (NM_008074)	-111	NM_008074	14407	Mm.434343	NM_008074	ENSMUSG00000055026	Gabrg3	B230362M20Rik|Gabrg-3	gamma-aminobutyric acid (GABA) A receptor, subunit gamma 3	protein-coding
mm_123434.1	chr14	64441035	64441045	-	1	NA	promoter-TSS (NM_001253715)	promoter-TSS (NM_001253715)	0	NM_001253712	110265	Mm.26713	NM_026322	ENSMUSG00000054733	Msra	2310045J23Rik|6530413P12Rik|MSR-A	methionine sulfoxide reductase A	protein-coding
mm_128891.1	chr15	73185246	73185256	-	1	NA	promoter-TSS (NM_153178)	promoter-TSS (NM_153178)	-304	NM_153178	239528	Mm.23095	NM_153178	ENSMUSG00000036698	Ago2	1110029L17Rik|2310051F07Rik|AI225898|AL022874|AW546247|ENSMUSG00000072493|Eif2c2|Gerp95|Gm10365|mKIAA4215	argonaute RISC catalytic subunit 2	protein-coding
mm_139270.1	chr17	48089635	48089659	+	1	NA	promoter-TSS (NM_026625)	promoter-TSS (NM_026625)	15	NM_026625	68224	Mm.138490	NM_026625	ENSMUSG00000021545	1700067P10Rik	-	RIKEN cDNA 1700067P10 gene	protein-coding
mm_165166.1	chr2	25571372	25571384	-	1	NA	promoter-TSS (NM_001081199)	promoter-TSS (NM_001081199)	-62	NM_001081199	381352	Mm.289046	NM_001081199	ENSMUSG00000026941	Mamdc4	Gm995	MAM domain containing 4	protein-coding
mm_37491.1	chr4	123613776	123613799	-	1	NA	intron (NM_001199136, intron 1 of 97)	intron (NM_001199136, intron 1 of 97)	-2633	NR_105824	102465214		NR_105824	ENSMUSG00000099005	Mir6398	Gm27657|mmu-mir-6398	microRNA 6398	ncRNA
mm_72062.1	chr8	71464911	71465000	+	1	NA	promoter-TSS (NM_053162)	promoter-TSS (NM_053162)	29	NM_053162	94065	Mm.29489	NM_053162	ENSMUSG00000034880	Mrpl34	0610007O17Rik|D8Bwg1484e	mitochondrial ribosomal protein L34	protein-coding
mm_55877.1	chr6	83520756	83520768	-	1	NA	exon (NM_009610, exon 6 of 9)	exon (NM_009610, exon 6 of 9)	-13793	NM_001162521	27369	Mm.42234	NM_013764	ENSMUSG00000014554	Dguok	dGK|dGK1|dGK2|dGK3	deoxyguanosine kinase	protein-coding
mm_164340.1	chr16	14357623	14357642	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-3926	NM_008576	17250	Mm.196634	NM_008576	ENSMUSG00000023088	Abcc1	Abcc1a|Abcc1b|MRP|Mdrap|Mrp1	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	protein-coding
mm_18745.1	chr2	73214410	73214414	-	1	NA	promoter-TSS (NM_025942)	promoter-TSS (NM_025942)	35	NM_030091	67059	Mm.22661	NM_025942	ENSMUSG00000027108	Ola1	2510025G09Rik|2810405J23Rik|2810409H07Rik|Gtpbp9|PTD004	Obg-like ATPase 1	protein-coding
mm_117716.1	chr13	95368523	95368541	-	1	NA	exon (NM_025630, exon 5 of 14)	exon (NM_025630, exon 5 of 14)	6825	NM_025630	66549	Mm.36785	NM_025630	ENSMUSG00000021681	Aggf1	2010009L17Rik|2310029P06Rik|AW112072|Peg3|VG5Q	angiogenic factor with G patch and FHA domains 1	protein-coding
mm_37687.1	chr4	129228576	129228592	-	1	NA	promoter-TSS (NM_001285866)	promoter-TSS (NM_001285866)	-673	NM_001285866	97130	Mm.331907	NM_001033189	ENSMUSG00000050390	C77080	Kiaa1522|mKIAA1522	expressed sequence C77080	protein-coding
mm_43089.1	chr5	124450429	124450437	+	1	NA	intron (NM_001310725, intron 2 of 6)	intron (NM_001310725, intron 2 of 6)	3729	NM_001310727	67956	Mm.137966	NM_030241	ENSMUSG00000049327	Kmt5a	2410195B05Rik|AA617402|AW536475|PR-SET7|PR/SET07|Setd8	lysine methyltransferase 5A	protein-coding
mm_33064.1	chr4	123248352	123248354	+	1	NA	3' UTR (NM_013905, exon 5 of 5)	3' UTR (NM_013905, exon 5 of 5)	14797	NM_013905	56198	Mm.103615	NM_013905	ENSMUSG00000032744	Heyl	Hey3|Hrt3|bHLHb33|hesr3	hairy/enhancer-of-split related with YRPW motif-like	protein-coding
mm_105079.1	chr11	100822481	100822491	-	1	NA	promoter-TSS (NM_011489)	promoter-TSS (NM_011489)	84	NM_011489	20851	Mm.34064	NM_011489	ENSMUSG00000020919	Stat5b	-	signal transducer and activator of transcription 5B	protein-coding
mm_44107.1	chr5	149368445	149368461	+	1	NA	Intergenic	MLT1F2|LTR|ERVL-MaLR	-43353	NM_027519	70717	Mm.252139	NM_027519	ENSMUSG00000029659	Medag	6330406I15Rik|Awms3|MEDA-4|Meda4|mAWMS3	mesenteric estrogen dependent adipogenesis	protein-coding
mm_109749.1	chr12	117658051	117658064	+	1	NA	intron (NM_175930, intron 10 of 27)	intron (NM_175930, intron 10 of 27)	141578	NM_175930	217944	Mm.227642	NM_175930	ENSMUSG00000041992	Rapgef5	4932413M22|C86120|D030051B22Rik|GFR|Mrgef|mKIAA0277|mmr-gef	Rap guanine nucleotide exchange factor (GEF) 5	protein-coding
mm_165773.1	chr3	128258111	128258136	-	1	NA	Intergenic	(A)n|Simple_repeat|Simple_repeat	-26518	NR_045704	402774	Mm.209170	NR_045704	ENSMUSG00000105816	D030025E07Rik	-	RIKEN cDNA D030025E07 gene	ncRNA
mm_62590.1	chr7	105640784	105640809	+	1	NA	promoter-TSS (NM_029802)	promoter-TSS (NM_029802)	256	NM_019502	14356	Mm.220330	NM_019502	ENSMUSG00000089847	Timm10b	Fxc1|Tim10b|Tim9b	translocase of inner mitochondrial membrane 10B	protein-coding
mm_122574.1	chr14	50807759	50807776	-	1	NA	promoter-TSS (NR_002142)	promoter-TSS (NR_002142)	4	NR_002142	85029		NR_002142	ENSMUSG00000092837	Rpph1	Gm24821|H1RNA|Rmrp5|Rpr	ribonuclease P RNA component H1	ncRNA
mm_4826.1	chr1	185487289	185487299	+	1	NA	Intergenic	Intergenic	-10012	NR_033600	114668	Mm.379303	NR_033600	ENSMUSG00000102185	5033404E19Rik	-	NSA2 ribosome biogenesis homolog pseudogene	pseudo
mm_38202.1	chr4	135573533	135573552	-	1	NA	promoter-TSS (NM_001013756)	promoter-TSS (NM_001013756)	78	NM_001013756	230824	Mm.331972	NM_001013756	ENSMUSG00000037188	Grhl3	AI561912|Get1|Som|Tfcp2l4|ct	grainyhead-like 3 (Drosophila)	protein-coding
mm_63243.1	chr7	126585877	126585887	+	1	NA	promoter-TSS (NM_001146311)	promoter-TSS (NM_001146311)	-65	NM_001146311	12752	Mm.268930	NM_009907	ENSMUSG00000030720	Cln3	AI323623	ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease)	protein-coding
mm_1080.1	chr1	59482896	59482936	+	1	NA	5' UTR (NM_008057, exon 1 of 1)	5' UTR (NM_008057, exon 1 of 1)	769	NM_008057	14369	Mm.297906	NM_008057	ENSMUSG00000041075	Fzd7	Fz7	frizzled class receptor 7	protein-coding
mm_63077.1	chr7	122219649	122219649	+	1	NA	5' UTR (NM_027363, exon 1 of 7)	5' UTR (NM_027363, exon 1 of 7)	153	NM_027363	70261	Mm.96997	NM_027363	ENSMUSG00000030865	Chp2	2010110P09Rik|Cbhp2	calcineurin-like EF hand protein 2	protein-coding
mm_28314.1	chr3	89270482	89270488	-	1	NA	promoter-TSS (NM_009057)	promoter-TSS (NM_009057)	85	NM_009057	19729	Mm.17958	NM_009057	ENSMUSG00000027953	Slc50a1	MmSWEET1|Rag1ap1|Rga	solute carrier family 50 (sugar transporter), member 1	protein-coding
mm_26661.1	chr3	154664162	154664212	+	1	NA	Intergenic	Intergenic	-46946	NM_175176	209601	Mm.331454	NM_175176	ENSMUSG00000078161	Erich3	1700013E18Rik|4922501L14Rik|5031409G23Rik|AI596448|Gm133	glutamate rich 3	protein-coding
mm_15093.1	chr2	153278860	153278870	+	1	NA	Intergenic	Intergenic	-12551	NM_008444	16569	Mm.315560	NM_008444	ENSMUSG00000027475	Kif3b	AI854312|AW549267|mKIAA0359	kinesin family member 3B	protein-coding
mm_157042.1	chrX	7976589	7976607	-	1	NA	Intergenic	Intergenic	-8688	NM_008089	14460	Mm.335973	NM_008089	ENSMUSG00000031162	Gata1	Gata-1|Gf-1|eryf1	GATA binding protein 1	protein-coding
mm_11340.1	chr2	30718552	30718590	+	1	NA	Intergenic	Intergenic	-2639	NR_037272	100526499		NR_037272	ENSMUSG00000093091	Mir3089	mir-3089|mmu-mir-3089	microRNA 3089	ncRNA
mm_129836.1	chr15	83154326	83154378	-	1	NA	3' UTR (NM_029787, exon 9 of 9)	3' UTR (NM_029787, exon 9 of 9)	4707	NR_004432	104307	Mm.471434	NR_004432	ENSMUSG00000065176	Rnu12	-	RNA U12, small nuclear	snRNA
mm_52728.1	chr6	120189100	120189124	+	1	NA	intron (NM_016718, intron 1 of 3)	intron (NM_016718, intron 1 of 3)	-4711	NM_001347432	29862	Mm.103668	NM_016718	ENSMUSG00000041377	Ninj2	-	ninjurin 2	protein-coding
mm_13492.1	chr2	106693527	106693575	+	1	NA	promoter-TSS (NM_001143683)	promoter-TSS (NM_001143683)	92	NM_001143683	77015	Mm.45628	NM_029837	ENSMUSG00000016386	Mpped2	239Fb|2700082O15Rik|AV354767|AW060960	metallophosphoesterase domain containing 2	protein-coding
mm_74509.1	chr8	8657740	8657744	-	1	NA	intron (NM_010111, intron 1 of 4)	intron (NM_010111, intron 1 of 4)	3031	NM_010111	13642	Mm.209813	NM_010111	ENSMUSG00000001300	Efnb2	ELF-2|Epl5|Eplg5|Htk-L|LERK-5|Lerk5|NLERK-1	ephrin B2	protein-coding
mm_18516.1	chr2	62645607	62645638	-	1	NA	exon (NM_027835, exon 1 of 16)	exon (NM_027835, exon 1 of 16)	633	NM_027835	71586	Mm.136224	NM_027835	ENSMUSG00000026896	Ifih1	9130009C22Rik|Helicard|Hlcd|MDA5|RLR-2	interferon induced with helicase C domain 1	protein-coding
mm_19429.1	chr2	91940298	91940336	-	1	NA	exon (NM_138306, exon 10 of 31)	exon (NM_138306, exon 10 of 31)	4613	NR_105965	102465604		NR_105965	ENSMUSG00000098651	Mir6999	Gm27673|mmu-mir-6999	microRNA 6999	ncRNA
mm_133265.1	chr16	77351751	77351752	+	1	NA	intron (NR_015543, intron 1 of 4)	intron (NR_015543, intron 1 of 4)	22423	NR_015543	77994	Mm.394688	NR_015543	ENSMUSG00000090386	Mir99ahg	2810055G20Rik|D730043B02Rik	Mir99a and Mirlet7c-1 host gene (non-protein coding)	ncRNA
mm_153054.1	chr19	32108100	32108110	-	1	NA	Intergenic	Intergenic	-4965	NM_018830	54447	Mm.491229	NM_018830	ENSMUSG00000024887	Asah2	AI585898	N-acylsphingosine amidohydrolase 2	protein-coding
mm_121606.1	chr14	8258038	8258062	-	1	NA	intron (NM_053115, intron 1 of 14)	intron (NM_053115, intron 1 of 14)	789	NM_001161667	93732	Mm.28700	NM_053115	ENSMUSG00000021751	Acox2	THCCox	acyl-Coenzyme A oxidase 2, branched chain	protein-coding
mm_142411.1	chr17	45544378	45544381	-	1	NA	3' UTR (NM_001013749, exon 3 of 3)	3' UTR (NM_001013749, exon 3 of 3)	5298	NM_001013749	210573	Mm.329064	NM_001013749	ENSMUSG00000096847	Tmem151b	Gm323	transmembrane protein 151B	protein-coding
mm_38630.1	chr4	142192953	142192956	-	1	NA	intron (NM_144531, intron 1 of 13)	intron (NM_144531, intron 1 of 13)	17254	NM_144531	71529	Mm.255986	NM_144531	ENSMUSG00000040606	Kazn	2310007B04Rik|9030409G11Rik|AI256607|AI666764|AW061099|Kaz|Kazrin	kazrin, periplakin interacting protein	protein-coding
mm_37025.1	chr4	114925582	114925592	-	1	NA	exon (NM_015758, exon 1 of 1)	exon (NM_015758, exon 1 of 1)	426	NM_015758	30923	Mm.377122	NM_015758	ENSMUSG00000044518	Foxe3	FREAC8|dyl|rct	forkhead box E3	protein-coding
mm_93745.1	chr10	120159567	120159584	-	1	NA	intron (NM_028679, intron 8 of 11)	MLTR18_MM|LTR|ERVK	41962	NM_028679	73914	Mm.146194	NM_028679	ENSMUSG00000020227	Irak3	4833428C18Rik|AI563835|IRAK-M	interleukin-1 receptor-associated kinase 3	protein-coding
mm_131206.1	chr16	8638010	8638029	+	1	NA	promoter-TSS (NM_025708)	promoter-TSS (NM_025708)	312	NM_016881	54128	Mm.9699	NM_016881	ENSMUSG00000022711	Pmm2	AI585868|C86848	phosphomannomutase 2	protein-coding
mm_140421.1	chr17	87863420	87863424	+	1	NA	Intergenic	Intergenic	-65428	NM_199251	210741	Mm.312046	NM_199251	ENSMUSG00000050138	Kcnk12	mntk1	potassium channel, subfamily K, member 12	protein-coding
mm_120767.1	chr14	73385036	73385062	+	1	NA	exon (NM_008410, exon 1 of 6)	exon (NM_008410, exon 1 of 6)	222	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_16527.1	chr2	181540490	181540494	+	1	NA	intron (NM_001271584, intron 2 of 5)	intron (NM_001271584, intron 2 of 5)	20007	NM_001271584	13002	Mm.140761	NM_016775	ENSMUSG00000000826	Dnajc5	2610314I24Rik|AU018536|Csp	DnaJ heat shock protein family (Hsp40) member C5	protein-coding
mm_65334.1	chr7	24978434	24978436	-	1	NA	3' UTR (NM_001290469, exon 23 of 23)	3' UTR (NM_001290469, exon 23 of 23)	-5707	NM_010261	14470	Mm.22473	NM_010261	ENSMUSG00000003380	Rabac1	2310040I06Rik|Gbpap1|PRA1|prenylin	Rab acceptor 1 (prenylated)	protein-coding
mm_13358.1	chr2	103424089	103424111	+	1	NA	promoter-TSS (NM_010125)	promoter-TSS (NM_010125)	32	NM_010125	13711	Mm.20888	NM_010125	ENSMUSG00000027186	Elf5	ESE-2|ESE-5|ESE-5.	E74-like factor 5	protein-coding
mm_40163.1	chr5	35728409	35728412	+	1	NA	intron (NM_194344, intron 1 of 17)	intron (NM_194344, intron 1 of 17)	866	NM_194344	231147	Mm.290429	NM_194344	ENSMUSG00000036553	Sh3tc1	4631428G15|BC024909	SH3 domain and tetratricopeptide repeats 1	protein-coding
mm_63123.1	chr7	122969888	122969907	+	1	NA	promoter-TSS (NM_175023)	promoter-TSS (NM_175023)	562	NR_045614	73951	Mm.389936	NR_045614		4930413G21Rik	-	RIKEN cDNA 4930413G21 gene	ncRNA
mm_52255.1	chr6	107529797	107529807	+	1	NA	promoter-TSS (NM_008516)	promoter-TSS (NM_008516)	76	NM_008516	16979	Mm.428543	NM_008516	ENSMUSG00000034648	Lrrn1	2810047E21Rik|NLRR-1	leucine rich repeat protein 1, neuronal	protein-coding
mm_153993.1	chr19	50573175	50573178	-	1	NA	intron (NM_001290356, intron 1 of 24)	intron (NM_001290356, intron 1 of 24)	105470	NM_001252501	58178	Mm.313672	NM_021377	ENSMUSG00000043531	Sorcs1	Sorcs|mSorCS	sortilin-related VPS10 domain containing receptor 1	protein-coding
mm_125912.1	chr15	76032840	76032842	+	1	NA	Intergenic	Intergenic	-18505	NM_134087	105732	Mm.267178	NM_134087	ENSMUSG00000046761	Fam83h	AA409316	family with sequence similarity 83, member H	protein-coding
mm_128177.1	chr15	34443647	34443666	-	1	NA	promoter-TSS (NR_028101)	promoter-TSS (NR_028101)	-380	NM_001163485	19946	Mm.358632	NM_009083	ENSMUSG00000058600	Rpl30	-	ribosomal protein L30	protein-coding
mm_142005.1	chr17	35200104	35200115	-	1	NA	3' UTR (NM_013693, exon 4 of 4)	3' UTR (NM_013693, exon 4 of 4)	1898	NM_013693	21926	Mm.1293	NM_013693	ENSMUSG00000024401	Tnf	DIF|TNF-a|TNF-alpha|TNFSF2|TNFalpha|Tnfa|Tnfsf1a|Tnlg1f	tumor necrosis factor	protein-coding
mm_139034.1	chr17	46163203	46163225	+	1	NA	intron (NM_019581, intron 1 of 11)	intron (NM_019581, intron 1 of 11)	2182	NM_001145979	56055	Mm.22147	NM_019581	ENSMUSG00000023952	Gtpbp2	nmf205	GTP binding protein 2	protein-coding
mm_28105.1	chr3	86548319	86548328	-	1	NA	promoter-TSS (NM_011839)	promoter-TSS (NM_011839)	-40	NM_011839	23937	Mm.389466	NM_011839	ENSMUSG00000057777	Mab21l2	-	mab-21-like 2 (C. elegans)	protein-coding
mm_123959.1	chr14	74837806	74837813	-	1	NA	intron (NM_001252132, intron 2 of 18)	B2_Mm2|SINE|B2	105512	NM_016903	13885	Mm.38055	NM_016903	ENSMUSG00000021996	Esd	Es-10|Es10|FGH|sid478	esterase D/formylglutathione hydrolase	protein-coding
mm_11370.1	chr2	30995672	30995722	+	1	NA	intron (NM_028846, intron 1 of 24)	intron (NM_028846, intron 1 of 24)	13418	NM_028846	74270	Mm.346654	NM_028846	ENSMUSG00000026854	Usp20	1700055M05Rik|AI467231|Vdu2	ubiquitin specific peptidase 20	protein-coding
mm_11100.1	chr2	28076510	28076510	+	1	NA	TTS (NM_010190)	TTS (NM_010190)	8368	NM_010190	14134	Mm.182935	NM_010190	ENSMUSG00000026835	Fcnb	Fcn2	ficolin B	protein-coding
mm_158729.1	chrX	163958564	163958588	-	1	NA	promoter-TSS (NM_009453)	promoter-TSS (NM_009453)	90	NM_009453	22184	Mm.426178	NM_009453	ENSMUSG00000031370	Zrsr2	35kDa|5031411E02Rik|A230052C13Rik|C77286|U2af1-rs2|URP	zinc finger (CCCH type), RNA binding motif and serine/arginine rich 2	protein-coding
mm_17497.1	chr2	28699637	28699659	-	1	NA	promoter-TSS (NM_027283)	promoter-TSS (NM_027283)	3	NM_027283	69987	Mm.239376	NM_027283	ENSMUSG00000026809	Spaca9	1700026L06Rik|MAST	sperm acrosome associated 9	protein-coding
mm_47367.1	chr5	122949158	122949194	-	1	NA	intron (NM_001003953, intron 6 of 22)	intron (NM_001003953, intron 6 of 22)	39923	NM_001003953	30841	Mm.86406	NM_013910	ENSMUSG00000029475	Kdm2b	Cxxc2|Fbl10|Fbxl10|Jhdm1b|PCCX2	lysine (K)-specific demethylase 2B	protein-coding
mm_48120.1	chr5	137139109	137139117	-	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	-22906	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_107162.1	chr12	24651347	24651409	+	1	NA	promoter-TSS (NM_178357)	promoter-TSS (NM_178357)	7	NM_178357	194655	Mm.9616	NM_178357	ENSMUSG00000020653	Klf11	9830142A17|D12Ertd427e|Tieg2|Tieg2b|Tieg3	Kruppel-like factor 11	protein-coding
mm_73590.1	chr8	109992600	109992610	+	1	NA	exon (NM_146214, exon 4 of 12)	exon (NM_146214, exon 4 of 12)	2169	NM_146214	234724	Mm.28110	NM_146214	ENSMUSG00000001670	Tat	-	tyrosine aminotransferase	protein-coding
mm_6412.1	chr1	72874539	72874547	-	1	NA	5' UTR (NM_010518, exon 1 of 4)	5' UTR (NM_010518, exon 1 of 4)	322	NM_010518	16011	Mm.405761	NM_010518	ENSMUSG00000026185	Igfbp5	AI256729|AW208790|IGFBP-5|IGFBP-5P	insulin-like growth factor binding protein 5	protein-coding
mm_102619.1	chr11	62463332	62463341	-	1	NA	intron (NM_001039536, intron 1 of 6)	RSINE1|SINE|B4	4876	NM_001039536	327942	Mm.390358	NM_199026	ENSMUSG00000014245	Pigl	Gm737	phosphatidylinositol glycan anchor biosynthesis, class L	protein-coding
mm_114500.1	chr13	70292934	70292938	+	1	NA	Intergenic	Intergenic	60114	NR_036596	75086	Mm.390616	NR_036596		4930520P13Rik	-	RIKEN cDNA 4930520P13 gene	ncRNA
mm_85073.1	chr9	91361066	91361076	-	1	NA	3' UTR (NM_009573, exon 3 of 3)	3' UTR (NM_009573, exon 3 of 3)	4728	NM_009573	22771	Mm.335350	NM_009573	ENSMUSG00000032368	Zic1	ZIC|ZNF201	zinc finger protein of the cerebellum 1	protein-coding
mm_67478.1	chr7	80598893	80598934	-	1	NA	exon (NM_173863, exon 10 of 15)	exon (NM_173863, exon 10 of 15)	-37104	NR_040343	100504375	Mm.322881	NR_040343	ENSMUSG00000084821	Gm15880	OTTMUSG00000027171	predicted gene 15880	ncRNA
mm_20838.1	chr2	147362436	147362448	-	1	NA	non-coding (NR_040330, exon 1 of 2)	non-coding (NR_040330, exon 1 of 2)	351	NR_040330	99041	Mm.373081	NR_040330		AI646519	Aspax1|OTTMUSG00000015701	expressed sequence AI646519	ncRNA
mm_157425.1	chrX	38564891	38564895	-	1	NA	intron (NM_001110142, intron 3 of 22)	CpG	11303	NM_028288	72584	Mm.327675	NM_028288	ENSMUSG00000031095	Cul4b	2700050M05Rik|AA409770|CUL-4B|mKIAA0695	cullin 4B	protein-coding
mm_99737.1	chr11	106374821	106374832	+	1	NA	promoter-TSS (NM_029345)	promoter-TSS (NM_029345)	0	NM_029345	75573	Mm.159539	NM_029345	ENSMUSG00000009210	Prr29	2310007L24Rik	proline rich 29	protein-coding
mm_123069.1	chr14	55681777	55681818	-	1	NA	promoter-TSS (NM_145705)	promoter-TSS (NM_145705)	20	NM_145705	28113	Mm.29346	NM_145705	ENSMUSG00000007589	Tinf2	AW552114|D14Wsu146e|Tin2	Terf1 (TRF1)-interacting nuclear factor 2	protein-coding
mm_152550.1	chr19	11387764	11387779	-	1	NA	intron (NM_001310331, intron 4 of 6)	RMER19B2|LTR|ERVK	12283	NM_001310331	666907		NM_001310331	ENSMUSG00000101389	Ms4a4a	EG666907	membrane-spanning 4-domains, subfamily A, member 4A	protein-coding
mm_91476.1	chr10	34208252	34208276	-	1	NA	promoter-TSS (NM_172508)	promoter-TSS (NM_172508)	-713	NM_172508	212898	Mm.34557	NM_172508	ENSMUSG00000039497	Dse	6030499O08|AI480506|B130024B19Rik|DS-epi1|Sart2	dermatan sulfate epimerase	protein-coding
mm_165397.1	chr2	135309185	135309187	+	1	NA	intron (NM_019677, intron 10 of 32)	intron (NM_019677, intron 10 of 32)	-93570	NR_040517	78805	Mm.78702	NR_040517	ENSMUSG00000085247	4930545L23Rik	-	RIKEN cDNA 4930545L23 gene	ncRNA
mm_121168.1	chr14	103014486	103014495	+	1	NA	intron (NR_045657, intron 2 of 2)	RMER1B|Other|Other	19313	NR_045657	71264	Mm.399572	NR_045657		4933432I03Rik	-	RIKEN cDNA 4933432I03 gene	ncRNA
mm_24403.1	chr3	90359592	90359610	+	1	NA	Intergenic	Intergenic	17947	NM_139304	229542	Mm.270999	NM_139304	ENSMUSG00000042390	Gatad2b	AL118180|C430014D17Rik|P66beta|mKIAA1150	GATA zinc finger domain containing 2B	protein-coding
mm_74492.1	chr8	5085608	5085611	-	1	NA	3' UTR (NM_011388, exon 6 of 6)	3' UTR (NM_011388, exon 6 of 6)	19678	NM_011388	20494	Mm.3500	NM_011388	ENSMUSG00000023073	Slc10a2	9130221J18Rik|AI605518|ASBT|IBAT|ISBT	solute carrier family 10, member 2	protein-coding
mm_26202.1	chr3	138527245	138527289	+	1	NA	promoter-TSS (NM_001313980)	promoter-TSS (NM_001313980)	-1	NM_001313980	13684	Mm.3941	NM_007917	ENSMUSG00000028156	Eif4e	EG668879|Eif4e-ps|If4e|eIF-4E	eukaryotic translation initiation factor 4E	protein-coding
mm_31520.1	chr4	54946296	54946299	+	1	NA	Intergenic	Intergenic	-1648	NM_172867	242466	Mm.102904	NM_172867	ENSMUSG00000060206	Zfp462	6030417H05|9430078C22Rik|Gt4-2|Zfpip	zinc finger protein 462	protein-coding
mm_21743.1	chr2	164803628	164803631	-	1	NA	intron (NM_133240, intron 1 of 5)	intron (NM_133240, intron 1 of 5)	1252	NM_133240	170789	Mm.277878	NM_133240	ENSMUSG00000017307	Acot8	PTE-2|Pte1	acyl-CoA thioesterase 8	protein-coding
mm_155097.1	chrX	48274854	48274865	+	1	NA	exon (NM_028276, exon 11 of 15)	exon (NM_028276, exon 11 of 15)	10567	NR_045916	100500713	Mm.396609	NR_045916	ENSMUSG00000097197	9530027J09Rik	-	RIKEN cDNA 9530027J09 gene	ncRNA
mm_172200.1	chr6	51470693	51470694	+	1	NA	promoter-TSS (NM_007624)	promoter-TSS (NM_007624)	77	NM_007624	12417	Mm.280968	NM_007624	ENSMUSG00000029836	Cbx3	HP1g|M32	chromobox 3	protein-coding
mm_115339.1	chr13	112495239	112495260	+	1	NA	exon (NM_010560, exon 11 of 17)	exon (NM_010560, exon 11 of 17)	31179	NM_010560	16195	Mm.4364	NM_010560	ENSMUSG00000021756	Il6st	5133400A03Rik|AA389424|BB405851|CD130|D13Ertd699e|gp130	interleukin 6 signal transducer	protein-coding
mm_118218.1	chr13	110280887	110280906	-	1	NA	promoter-TSS (NM_023852)	promoter-TSS (NM_023852)	-690	NM_023852	67295	Mm.151600	NM_023852	ENSMUSG00000021700	Rab3c	2700062I01Rik|3110015B08Rik|3110037E15Rik|AI850886	RAB3C, member RAS oncogene family	protein-coding
mm_40724.1	chr5	65975851	65975866	+	1	NA	intron (NM_001081104, intron 4 of 4)	intron (NM_001081104, intron 4 of 4)	8734	NM_001081104	231252	Mm.140015	NM_001081104	ENSMUSG00000029205	Chrna9	2410015I05Rik|Acra9|EG666827|Gm8311	cholinergic receptor, nicotinic, alpha polypeptide 9	protein-coding
mm_128058.1	chr15	26402311	26402317	-	1	NA	intron (NM_177597, intron 3 of 3)	intron (NM_177597, intron 3 of 3)	93266	NM_001310774	211147	Mm.54257	NM_177597	ENSMUSG00000022269	March11	9630025C22	membrane-associated ring finger (C3HC4) 11	protein-coding
mm_45827.1	chr5	87694587	87694603	-	1	NA	exon (NM_001286023, exon 5 of 7)	exon (NM_001286023, exon 5 of 7)	4830	NM_001286020	12991	Mm.268737	NM_009972	ENSMUSG00000063157	Csn2	Csnb	casein beta	protein-coding
mm_71876.1	chr8	69791222	69791257	+	1	NA	promoter-TSS (NM_133224)	promoter-TSS (NM_133224)	76	NM_133224	170759	Mm.186066	NM_133224	ENSMUSG00000031862	Atp13a1	Atp13a|Cgi152|catp	ATPase type 13A1	protein-coding
mm_68262.1	chr7	105592385	105592428	-	1	NA	exon (NM_017371, exon 8 of 10)	exon (NM_017371, exon 8 of 10)	7710	NM_017371	15458	Mm.3485	NM_017371	ENSMUSG00000030895	Hpx	Hpxn|hx	hemopexin	protein-coding
mm_55806.1	chr6	82905193	82905206	-	1	NA	Intergenic	Intergenic	-23346	NR_040520	69652	Mm.96357	NR_040520	ENSMUSG00000100291	2310069B03Rik	-	RIKEN cDNA 2310069B03 gene	ncRNA
mm_133911.1	chr16	97554633	97554645	+	1	NA	intron (NR_003508, intron 10 of 13)	L1MB8|LINE|L1	18556	NM_013606	17858	Mm.14157	NM_013606	ENSMUSG00000023341	Mx2	AI528743|Mx-2	MX dynamin-like GTPase 2	protein-coding
mm_123216.1	chr14	59441104	59441108	-	1	NA	promoter-TSS (NM_001320721)	promoter-TSS (NM_001320721)	125	NM_026908	69008	Mm.179091	NM_026908	ENSMUSG00000021981	Cab39l	1500031K13Rik|2810425O13Rik|4930520C08Rik|AA589432|MO2L	calcium binding protein 39-like	protein-coding
mm_166160.1	chr5	16181275	16181281	+	1	NA	intron (NM_001110846, intron 4 of 37)	RLTR41|LTR|ERV1	246587	NM_001110844	12293	Mm.159842	NM_009784	ENSMUSG00000040118	Cacna2d1	Ca(v)alpha2delta1|Cacna2|Cchl2a	calcium channel, voltage-dependent, alpha2/delta subunit 1	protein-coding
mm_158379.1	chrX	135627683	135627693	-	1	NA	promoter-TSS (NM_029459)	promoter-TSS (NM_029459)	17	NM_029459	75829	Mm.159593	NM_029459	ENSMUSG00000031411	Prame	4930534P07Rik	preferentially expressed antigen in melanoma	protein-coding
mm_82065.1	chr9	122805525	122805580	+	1	NA	promoter-TSS (NM_001013405)	promoter-TSS (NM_001013405)	5	NM_001013405	382117	Mm.215892	NM_001013405	ENSMUSG00000046603	Tcaim	D9Ertd402e|Gm1129|TOAG-1	T cell activation inhibitor, mitochondrial	protein-coding
mm_72246.1	chr8	75058296	75058320	+	1	NA	intron (NM_001136259, intron 8 of 15)	intron (NM_001136259, intron 8 of 15)	24622	NM_011622	21968	Mm.1967	NM_011622	ENSMUSG00000042870	Tom1	-	target of myb1 trafficking protein	protein-coding
mm_109149.1	chr12	107225536	107225538	+	1	NA	Intergenic	Intergenic	-509213	NR_015512	71033	Mm.159404	NR_015512	ENSMUSG00000085820	4933406K04Rik	4930426M03Rik|4930485I22Rik|4933427G14Rik	RIKEN cDNA 4933406K04 gene	ncRNA
mm_84543.1	chr9	67318580	67318591	-	1	NA	intron (NM_001081242, intron 30 of 57)	intron (NM_001081242, intron 30 of 57)	-81859	NR_029576	387185		NR_029576	ENSMUSG00000076379	Mir190a	Mir190|Mirn190|mir-190|mir-190a|mmu-mir-190|mmu-mir-190a	microRNA 190a	ncRNA
mm_41903.1	chr5	105571269	105571272	+	1	NA	intron (NM_133897, intron 2 of 3)	intron (NM_133897, intron 2 of 3)	51799	NM_133897	100604	Mm.319847	NM_133897	ENSMUSG00000054720	Lrrc8c	AD158|AI326115|E430036I04Rik|fad158	leucine rich repeat containing 8 family, member C	protein-coding
mm_90198.1	chr10	120227110	120227148	+	1	NA	promoter-TSS (NM_025431)	promoter-TSS (NM_025431)	69	NM_025431	66225	Mm.291755	NM_025431	ENSMUSG00000020224	Llph	1190005P17Rik	LLP homolog, long-term synaptic facilitation (Aplysia)	protein-coding
mm_89664.1	chr10	97483477	97483479	+	1	NA	exon (NM_007833, exon 2 of 8)	exon (NM_007833, exon 2 of 8)	1147	NM_007833	13179	Mm.56769	NM_007833	ENSMUSG00000019929	Dcn	DC|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding
mm_49362.1	chr6	22926418	22926420	+	1	NA	intron (NM_001081306, intron 2 of 29)	intron (NM_001081306, intron 2 of 29)	50917	NM_001081306	19283	Mm.41639	NM_011219	ENSMUSG00000068748	Ptprz1	AI850339|DSD-1-PG|PTPbeta|PTPzeta|Ptprz|Ptpz|R-PTP-zeta|RPTPz|Rptpbeta	protein tyrosine phosphatase, receptor type Z, polypeptide 1	protein-coding
mm_99563.1	chr11	103774166	103774193	+	1	NA	promoter-TSS (NM_009521)	promoter-TSS (NM_009521)	4	NM_009521	22415	Mm.159091	NM_009521	ENSMUSG00000000125	Wnt3	Int-4|Wnt-3	wingless-type MMTV integration site family, member 3	protein-coding
mm_139865.1	chr17	70521966	70521972	+	1	NA	promoter-TSS (NM_001128180)	promoter-TSS (NM_001128180)	75	NM_001347413	224997	Mm.311840	NM_027712	ENSMUSG00000003279	Dlgap1	4933422O14Rik|9630002F18|AI845682|AI848168|BB075781|D17Bwg0511e|GKAP/SAPAP|GKPA/SAPAP|Gkap|Sapap1|mKIAA4162	discs, large (Drosophila) homolog-associated protein 1	protein-coding
mm_150045.1	chr19	29380277	29380287	+	1	NA	intron (NM_021893, intron 3 of 6)	intron (NM_021893, intron 3 of 6)	12844	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_23718.1	chr3	69005734	69005742	+	1	NA	intron (NM_133786, intron 1 of 23)	CpG	766	NM_133786	70099	Mm.206841	NM_133786	ENSMUSG00000034349	Smc4	2500002A22Rik|C79747|SMC-4|Smc4l1	structural maintenance of chromosomes 4	protein-coding
mm_51544.1	chr6	83207594	83207606	+	1	NA	Intergenic	Intergenic	21654	NM_001347310	13191	Mm.6919	NM_007835	ENSMUSG00000031865	Dctn1	AL022633|DAP-150|DP-150|Glued|p150|p150-glued|p150<glued>	dynactin 1	protein-coding
mm_74350.1	chr8	127579693	127579710	+	1	NA	intron (NM_001309391, intron 22 of 24)	ORR1D2|LTR|ERVL-MaLR	280049	NM_001013580	93742	Mm.299254	NM_033620	ENSMUSG00000025812	Pard3	AA960621|AI256638|Asip|D8Ertd580e|Par-3|Par3|Pard-3|Pard3a|Phip	par-3 family cell polarity regulator	protein-coding
mm_42030.1	chr5	108312785	108312823	+	1	NA	promoter-TSS (NM_001081234)	promoter-TSS (NM_001081234)	-121	NM_001081234	433931	Mm.319881	NM_001081234	ENSMUSG00000029263	Pigg	Gpi7	phosphatidylinositol glycan anchor biosynthesis, class G	protein-coding
mm_149345.1	chr19	10850497	10850507	+	1	NA	intron (NM_023044, intron 2 of 7)	(CA)n|Simple_repeat|Simple_repeat	7958	NM_023044	65221	Mm.27387	NM_023044	ENSMUSG00000024737	Slc15a3	Ci1|cI-1	solute carrier family 15, member 3	protein-coding
mm_123488.1	chr14	66077742	66077761	-	1	NA	promoter-TSS (NM_009618)	promoter-TSS (NM_009618)	18	NM_009618	11495	Mm.422850	NM_009618	ENSMUSG00000022039	Adam2	AI323749|Ftnb|Ph30-beta	a disintegrin and metallopeptidase domain 2	protein-coding
mm_100002.1	chr11	114851602	114851612	+	1	NA	promoter-TSS (NM_147217)	promoter-TSS (NM_147217)	67	NM_001110338	70355	Mm.242413	NM_147217	ENSMUSG00000051043	Gprc5c	1110028I06Rik|3200002M13Rik|Raig3	G protein-coupled receptor, family C, group 5, member C	protein-coding
mm_73749.1	chr8	114683939	114683943	+	1	NA	intron (NM_019573, intron 6 of 8)	intron (NM_019573, intron 6 of 8)	244289	NM_019573	80707	Mm.440420	NM_019573	ENSMUSG00000004637	Wwox	5330426P09Rik|9030416C10Rik|WOX1	WW domain-containing oxidoreductase	protein-coding
mm_134930.1	chr16	31039891	31039918	-	1	NA	intron (NM_198626, intron 2 of 3)	intron (NM_198626, intron 2 of 3)	41528	NM_198626	268880	Mm.286693	NM_198626	ENSMUSG00000047434	Xxylt1	AI480653	xyloside xylosyltransferase 1	protein-coding
mm_145774.1	chr18	65050918	65050954	+	1	NA	intron (NM_031881, intron 1 of 29)	intron (NM_031881, intron 1 of 29)	27409	NM_031881	83814	Mm.98668	NM_031881	ENSMUSG00000024589	Nedd4l	1300012C07Rik|Nedd4-2|Nedd4b	neural precursor cell expressed, developmentally down-regulated gene 4-like	protein-coding
mm_156633.1	chrX	155628066	155628071	+	1	NA	Intergenic	Intergenic	-4741	NM_001093750	211612	Mm.218811	NM_001093750	ENSMUSG00000041552	Ptchd1	9630036J22Rik|AI848149|Gm387	patched domain containing 1	protein-coding
mm_56461.1	chr6	98697668	98697680	-	1	NA	Intergenic	Intergenic	330624	NM_001197322	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_77533.1	chr8	123025433	123025434	-	1	NA	intron (NM_001081379, intron 1 of 12)	intron (NM_001081379, intron 1 of 12)	16851	NR_037865	77087	Mm.31567	NM_001081379	ENSMUSG00000035569	Ankrd11	2410104C19Rik|3010027A04Rik|6330578C09Rik|9530048I21Rik|AA930108|Gm176|Yod	ankyrin repeat domain 11	protein-coding
mm_55317.1	chr6	55132976	55132997	-	1	NA	promoter-TSS (NM_001288618)	promoter-TSS (NM_001288618)	30	NM_009953	12922	Mm.236081	NM_009953	ENSMUSG00000003476	Crhr2	CRF-R2|CRFR2alpha|CRFR2beta|Crfr2	corticotropin releasing hormone receptor 2	protein-coding
mm_35260.1	chr4	19881364	19881384	-	1	NA	exon (NM_175406, exon 6 of 8)	exon (NM_175406, exon 6 of 8)	41192	NM_175406	242341	Mm.19298	NM_175406	ENSMUSG00000028238	Atp6v0d2	1620401A02Rik|AI324824|V-ATPase	ATPase, H+ transporting, lysosomal V0 subunit D2	protein-coding
mm_167726.1	chr9	101074682	101074707	+	1	NA	promoter-TSS (NM_001100451)	promoter-TSS (NM_001100451)	-68	NM_001100451	77853	Mm.326206	NM_001100451	ENSMUSG00000066415	Msl2	E130103E02Rik|Msl2l1|Rnf184	male-specific lethal 2 homolog (Drosophila)	protein-coding
mm_123162.1	chr14	57133409	57133420	-	1	NA	5' UTR (NM_001271663, exon 1 of 3)	5' UTR (NM_001271663, exon 1 of 3)	197	NM_001271663	14623	Mm.25652	NM_008128	ENSMUSG00000040055	Gjb6	AA958971|Cx30|D14Bwg0506e	gap junction protein, beta 6	protein-coding
mm_56109.1	chr6	87502767	87502777	-	1	NA	intron (NM_001037727, intron 1 of 10)	MLT1A1|LTR|ERVL-MaLR	-6445	NM_175476	232201	Mm.119564	NM_175476	ENSMUSG00000030047	Arhgap25	A130039I20Rik	Rho GTPase activating protein 25	protein-coding
mm_111130.1	chr12	81485028	81485065	-	1	NA	promoter-TSS (NM_025461)	promoter-TSS (NM_025461)	91	NM_001309809	66272	Mm.439970	NM_025461	ENSMUSG00000091803	Cox16	1810020G14Rik|1810055I05Rik|BB388670	cytochrome c oxidase assembly protein 16	protein-coding
mm_164128.1	chr15	40655296	40655302	+	1	NA	5' UTR (NM_011766, exon 1 of 8)	5' UTR (NM_011766, exon 1 of 8)	257	NM_011766	22762	Mm.39496	NM_011766	ENSMUSG00000022306	Zfpm2	B330005D23Rik|FOG-2|FOG2	zinc finger protein, multitype 2	protein-coding
mm_138264.1	chr17	34597853	34597868	+	1	NA	promoter-TSS (NM_007425)	promoter-TSS (NM_007425)	10	NR_073173	11596	Mm.3383	NM_007425	ENSMUSG00000015452	Ager	RAGE	advanced glycosylation end product-specific receptor	protein-coding
mm_163044.1	chr11	54909642	54909644	-	1	NA	exon (NM_008161, exon 5 of 5)	exon (NM_008161, exon 5 of 5)	6789	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_126147.1	chr15	78349263	78349282	+	1	NA	TTS (NR_106138)	TTS (NR_106138)	673	NR_106138	102466845		NR_106138	ENSMUSG00000099059	Mir7676-2	Gm27790|mmu-mir-7676-2	microRNA 7676-2	ncRNA
mm_68671.1	chr7	118974619	118974631	-	1	NA	3' UTR (NM_022420, exon 4 of 4)	3' UTR (NM_022420, exon 4 of 4)	20586	NM_022420	64297	Mm.103439	NM_022420	ENSMUSG00000008734	Gprc5b	AW125761|Raig2	G protein-coupled receptor, family C, group 5, member B	protein-coding
mm_150848.1	chr19	44989320	44989330	+	1	NA	promoter-TSS (NM_011976)	promoter-TSS (NM_011976)	-19	NM_011976	26456	Mm.34404	NM_011976	ENSMUSG00000025207	Sema4g	AI507908|AW554132	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4G	protein-coding
mm_139885.1	chr17	70830191	70830219	+	1	NA	Intergenic	Intergenic	16572	NM_001164077	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_35452.1	chr4	40279390	40279434	-	1	NA	promoter-TSS (NM_001033305)	promoter-TSS (NM_001033305)	9	NM_001033305	230075	Mm.1103	NM_001033305	ENSMUSG00000071014	Ndufb6	CI-B17|Gm137	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 6	protein-coding
mm_28413.1	chr3	90389850	90389862	-	1	NA	promoter-TSS (NM_001316688)	promoter-TSS (NM_001316688)	82	NM_001316688	26568	Mm.45519	NM_011988	ENSMUSG00000027932	Slc27a3	Acsvl3|FATP-3|FATP3|Vlcs-3	solute carrier family 27 (fatty acid transporter), member 3	protein-coding
mm_80042.1	chr9	69165691	69165710	+	1	NA	intron (NM_013646, intron 1 of 10)	intron (NM_013646, intron 1 of 10)	-124141	NM_001289916	19883	Mm.378450	NM_013646	ENSMUSG00000032238	Rora	9530021D13Rik|Nr1f1|ROR1|ROR2|ROR3|nmf267|sg|staggerer|tmgc26	RAR-related orphan receptor alpha	protein-coding
mm_9369.1	chr1	172200558	172200589	-	1	NA	exon (NM_001329871, exon 2 of 4)	exon (NM_001329871, exon 2 of 4)	6231	NM_001329871	18611	Mm.544	NM_011063	ENSMUSG00000013698	Pea15a	Mat1|PEA-15|Pea15|Pkcs15	phosphoprotein enriched in astrocytes 15A	protein-coding
mm_20171.1	chr2	122306366	122306375	-	1	NA	intron (NM_001305262, intron 5 of 9)	intron (NM_001305262, intron 5 of 9)	7360	NM_001305262	213696	Mm.247121	NM_145395	ENSMUSG00000027224	Duoxa1	BC019755|Nip|Nip1	dual oxidase maturation factor 1	protein-coding
mm_1133.1	chr1	60409774	60409802	+	1	NA	5' UTR (NM_001198570, exon 1 of 12)	5' UTR (NM_001198570, exon 1 of 12)	169	NM_001198570	329165	Mm.212066	NM_198127	ENSMUSG00000026782	Abi2	8430425M24Rik|AI839867|C130078H13	abl-interactor 2	protein-coding
mm_119576.1	chr14	50807916	50807942	+	1	NA	promoter-TSS (NR_002142)	promoter-TSS (NR_002142)	-17	NM_009632	11546	Mm.281482	NM_009632	ENSMUSG00000036023	Parp2	ARTD2|Adprt2|Adprtl2|Aspartl2|C78626|PARP-2	poly (ADP-ribose) polymerase family, member 2	protein-coding
mm_20054.1	chr2	120314082	120314106	-	1	NA	promoter-TSS (NM_001024145)	promoter-TSS (NM_001024145)	71	NM_001024145	271844	Mm.24880	NM_001024145	ENSMUSG00000046971	Pla2g4f	4732472I07Rik|Gm647|Pla2zeta	phospholipase A2, group IVF	protein-coding
mm_2079.1	chr1	87662122	87662125	+	1	NA	intron (NM_010566, intron 2 of 26)	intron (NM_010566, intron 2 of 26)	41811	NM_001110193	16331	Mm.15105	NM_010566	ENSMUSG00000026288	Inpp5d	SHIP|SHIP-1|SHIP1|SIP-145|p150Ship|s-SHIP	inositol polyphosphate-5-phosphatase D	protein-coding
mm_97240.1	chr11	75679270	75679327	+	1	NA	promoter-TSS (NM_133656)	promoter-TSS (NM_133656)	39	NM_001277221	12928	Mm.280125	NM_133656	ENSMUSG00000017776	Crk	Crk-I|Crk-II|Crk-III|Crk3|CrkIII|Crko|c-Crk|p38	v-crk avian sarcoma virus CT10 oncogene homolog	protein-coding
mm_164415.1	chr16	38399621	38399628	-	1	NA	intron (NM_134102, intron 9 of 10)	intron (NM_134102, intron 9 of 10)	33521	NM_134102	85031	Mm.279805	NM_134102	ENSMUSG00000002847	Pla1a	AA986889|Ps-pla1|Pspla1	phospholipase A1 member A	protein-coding
mm_154674.1	chrX	7884322	7884339	+	1	NA	promoter-TSS (NM_001083937)	promoter-TSS (NM_001083937)	86	NM_078484	22232	Mm.214976	NM_078484	ENSMUSG00000031156	Slc35a2	AI327289|Had-1|Had1|Sfc8|UGT|Ugalt	solute carrier family 35 (UDP-galactose transporter), member A2	protein-coding
mm_100902.1	chr11	6199994	6200045	-	1	NA	exon (NM_173748, exon 1 of 6)	exon (NM_173748, exon 1 of 6)	432	NM_173748	209586	Mm.25321	NM_173748	ENSMUSG00000053838	Nudcd3	AI427847|BC024322|mKIAA1068	NudC domain containing 3	protein-coding
mm_153103.1	chr19	32739769	32739793	-	1	NA	Intergenic	Intergenic	-17796	NM_008960	19211	Mm.245395	NM_008960	ENSMUSG00000013663	Pten	2310035O07Rik|A130070J02Rik|AI463227|B430203M17Rik|MMAC1|TEP1	phosphatase and tensin homolog	protein-coding
mm_121972.1	chr14	25593962	25593981	-	1	NA	intron (NM_001310666, intron 6 of 23)	intron (NM_001310666, intron 6 of 23)	7167	NR_033492	77592	Mm.444871	NM_175264		4931406H21Rik	-	RIKEN cDNA 4931406H21 gene	ncRNA
mm_21393.1	chr2	157566295	157566305	-	1	NA	promoter-TSS (NM_016916)	promoter-TSS (NM_016916)	61	NM_016916	53619	Mm.480461	NM_016916	ENSMUSG00000067787	Blcap	AI462828|Bc10	bladder cancer associated protein	protein-coding
mm_18291.1	chr2	52676102	52676116	-	1	NA	promoter-TSS (NM_001285428)	promoter-TSS (NM_001285428)	34	NM_001285426	12298	Mm.330223	NM_146123	ENSMUSG00000017412	Cacnb4	3110038O15Rik|Cchb4|lh	calcium channel, voltage-dependent, beta 4 subunit	protein-coding
mm_110916.1	chr12	76246737	76246755	-	1	NA	promoter-TSS (NM_019784)	promoter-TSS (NM_019784)	0	NM_019784	80384	Mm.78551	NM_019784	ENSMUSG00000021056	Tex21	4931406F04Rik|4931412D23Rik|4931421K24Rik|tsec-2	testis expressed gene 21	protein-coding
mm_21504.1	chr2	163541716	163541728	-	1	NA	promoter-TSS (NR_027970)	promoter-TSS (NR_027970)	-1	NR_027970	68314	Mm.46190	NM_197983	ENSMUSG00000046840	Hnf4aos	0610008F07Rik	hepatic nuclear factor 4 alpha, opposite strand	ncRNA
mm_26149.1	chr3	138109065	138109092	+	1	NA	exon (NM_001163457, exon 13 of 20)	exon (NM_001163457, exon 13 of 20)	22299	NM_008642	17777	Mm.2941	NM_008642	ENSMUSG00000028158	Mttp	1810043K16Rik|MTP	microsomal triglyceride transfer protein	protein-coding
mm_60579.1	chr7	44482569	44482596	+	1	NA	Intergenic	Intergenic	-1935	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_14620.1	chr2	136770128	136770142	+	1	NA	exon (NM_011428, exon 5 of 8)	exon (NM_011428, exon 5 of 8)	56685	NM_001291056	20614	Mm.45953	NM_011428	ENSMUSG00000027273	Snap25	Bdr|GENA70|SNAP-25|SUP|sp	synaptosomal-associated protein 25	protein-coding
mm_129898.1	chr15	83595197	83595207	-	1	NA	promoter-TSS (NM_183017)	promoter-TSS (NM_183017)	-45	NM_183017	223723	Mm.46778	NM_183017	ENSMUSG00000016757	Ttll12	BC055368|D430005B17	tubulin tyrosine ligase-like family, member 12	protein-coding
mm_49992.1	chr6	41047426	41047458	+	1	NA	Intergenic	Intergenic	-11933	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_91650.1	chr10	42478489	42478503	-	1	NA	promoter-TSS (NM_145743)	promoter-TSS (NM_145743)	69	NM_145743	215951	Mm.89646	NM_145743	ENSMUSG00000038302	Lace1	CG8520	lactation elevated 1	protein-coding
mm_17881.1	chr2	34961790	34961796	-	1	NA	promoter-TSS (NM_001326601)	promoter-TSS (NM_001326601)	-21	NM_001326601	22029	Mm.239514	NM_009421	ENSMUSG00000026875	Traf1	4732496E14Rik	TNF receptor-associated factor 1	protein-coding
mm_63246.1	chr7	126586155	126586168	+	1	NA	promoter-TSS (NM_001146311)	promoter-TSS (NM_001146311)	-344	NM_001146311	12752	Mm.268930	NM_009907	ENSMUSG00000030720	Cln3	AI323623	ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease)	protein-coding
mm_49009.1	chr6	4758416	4758426	+	1	NA	3' UTR (NM_130877, exon 2 of 2)	3' UTR (NM_130877, exon 2 of 2)	11115	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_85551.1	chr9	106685763	106685790	-	1	NA	promoter-TSS (NM_011573)	promoter-TSS (NM_011573)	40	NM_011573	21767	Mm.22266	NM_011573	ENSMUSG00000040813	Tex264	TEG-264	testis expressed gene 264	protein-coding
mm_103758.1	chr11	80858291	80858304	-	1	NA	promoter-TSS (NM_029367)	promoter-TSS (NM_029367)	3	NR_110449	75043	Mm.410815	NR_110449	ENSMUSG00000086703	4930507D10Rik	-	RIKEN cDNA 4930507D10 gene	ncRNA
mm_22045.1	chr2	168230354	168230386	-	1	NA	promoter-TSS (NM_010072)	promoter-TSS (NM_010072)	9	NM_010072	13480	Mm.422657	NM_010072	ENSMUSG00000078919	Dpm1	AI118379|AI194292	dolichol-phosphate (beta-D) mannosyltransferase 1	protein-coding
mm_87406.1	chr10	45807534	45807540	+	1	NA	promoter-TSS (NR_040624)	promoter-TSS (NR_040624)	-167	NR_040624	320363	Mm.123343	NR_040624	ENSMUSG00000110874	D030045P18Rik	-	RIKEN cDNA D030045P18 gene	ncRNA
mm_29367.1	chr3	108704495	108704501	-	1	NA	intron (NM_029522, intron 2 of 14)	Lx8|LINE|L1	17801	NM_029522	76123	Mm.226941	NM_029522	ENSMUSG00000027883	Gpsm2	6230410J09Rik|LGN|Pins	G-protein signalling modulator 2 (AGS3-like, C. elegans)	protein-coding
mm_123211.1	chr14	59407758	59407762	-	1	NA	intron (NR_135463, intron 12 of 13)	L1MEg|LINE|L1	-14248	NM_001164289	628705	Mm.479244	NM_001164289	ENSMUSG00000091144	Phf11c	EG628705|Gm6907|Phf11	PHD finger protein 11C	protein-coding
mm_40836.1	chr5	73006923	73006937	+	1	NA	promoter-TSS (NM_173403)	promoter-TSS (NM_173403)	26	NM_173403	231290	Mm.491387	NM_173403	ENSMUSG00000029219	Slc10a4	E130304D01	solute carrier family 10 (sodium/bile acid cotransporter family), member 4	protein-coding
mm_106268.1	chr11	117969385	117969416	-	1	NA	promoter-TSS (NM_007707)	promoter-TSS (NM_007707)	-34	NM_007707	12702	Mm.3468	NM_007707	ENSMUSG00000053113	Socs3	Cis3|Cish3|EF-10|Ef10|SSI-3|Ssi3	suppressor of cytokine signaling 3	protein-coding
mm_115282.1	chr13	111807785	111807822	+	1	NA	intron (NM_011945, intron 1 of 19)	CpG	1180	NM_011945	26401	Mm.15918	NM_011945	ENSMUSG00000021754	Map3k1	MAPKKK1|MEKK1|Mekk	mitogen-activated protein kinase kinase kinase 1	protein-coding
mm_98055.1	chr11	85821910	85821949	+	1	NA	intron (NR_077059, intron 1 of 4)	intron (NR_077059, intron 1 of 4)	10459	NR_077059	69909	Mm.440214	NR_077059	ENSMUSG00000087013	2610027K06Rik	-	RIKEN cDNA 2610027K06 gene	ncRNA
mm_10790.1	chr2	24348571	24348574	+	1	NA	exon (NM_031167, exon 4 of 5)	exon (NM_031167, exon 4 of 5)	3201	NM_001039701	16181	Mm.882	NM_031167	ENSMUSG00000026981	Il1rn	F630041P17Rik|IL-1ra	interleukin 1 receptor antagonist	protein-coding
mm_159352.1	chr3	73057717	73057717	-	1	NA	promoter-TSS (NM_198864)	promoter-TSS (NM_198864)	-774	NM_198864	386750	Mm.331076	NM_198864	ENSMUSG00000048304	Slitrk3	-	SLIT and NTRK-like family, member 3	protein-coding
mm_93028.1	chr10	88135808	88135819	-	1	NA	intron (NM_029249, intron 3 of 10)	intron (NM_029249, intron 3 of 10)	11128	NM_029249	75317	Mm.179378	NM_029249	ENSMUSG00000035365	Parpbp	4930547N16Rik|AI503644|PARI	PARP1 binding protein	protein-coding
mm_10741.1	chr2	23069211	23069252	+	1	NA	5' UTR (NM_001102438, exon 1 of 13)	5' UTR (NM_001102438, exon 1 of 13)	159	NM_001102438	74159	Mm.181973	NM_028793	ENSMUSG00000026781	Acbd5	1300014E15Rik	acyl-Coenzyme A binding domain containing 5	protein-coding
mm_120264.1	chr14	63122451	63122459	+	1	NA	promoter-TSS (NM_007798)	promoter-TSS (NM_007798)	-7	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_39652.1	chr5	24697077	24697094	+	1	NA	exon (NM_001305264, exon 6 of 15)	exon (NM_001305264, exon 6 of 15)	11270	NM_001305264	53312	Mm.5856	NM_016736	ENSMUSG00000028954	Nub1	4931404D21Rik|6330412F12Rik|BS4|NY-REN-18	negative regulator of ubiquitin-like proteins 1	protein-coding
mm_135895.1	chr16	65515101	65515105	-	1	NA	Intergenic	Intergenic	-5526	NM_008849	18736	Mm.355440	NM_008849	ENSMUSG00000004842	Pou1f1	GHF-1|Hmp1|Pit-1|Pit1|Pit1-rs1|dw|dwarf	POU domain, class 1, transcription factor 1	protein-coding
mm_49037.1	chr6	4759967	4759977	+	1	NA	3' UTR (NM_130877, exon 2 of 2)	3' UTR (NM_130877, exon 2 of 2)	12666	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_133440.1	chr16	87719116	87719164	+	1	NA	exon (NM_007520, exon 3 of 5)	exon (NM_007520, exon 3 of 5)	20186	NM_007520	12013	Mm.26147	NM_007520	ENSMUSG00000025612	Bach1	6230421P05Rik|AI323795	BTB and CNC homology 1, basic leucine zipper transcription factor 1	protein-coding
mm_27661.1	chr3	65295908	65295918	-	1	NA	intron (NM_010597, intron 3 of 13)	intron (NM_010597, intron 3 of 13)	6772	NR_126080	102637797	Mm.446731	NR_126080	ENSMUSG00000104093	A330015K06Rik	-	RIKEN cDNA A330015K06 gene	ncRNA
mm_62907.1	chr7	117390032	117390066	+	1	NA	intron (NM_175645, intron 1 of 11)	intron (NM_175645, intron 1 of 11)	9070	NM_175645	233781	Mm.461427	NM_175645	ENSMUSG00000030657	Xylt1	8030490L12	xylosyltransferase 1	protein-coding
mm_168406.1	chr11	30159294	30159304	-	1	NA	exon (NM_009260, exon 2 of 31)	exon (NM_009260, exon 2 of 31)	38958	NM_009260	20742	Mm.123110	NM_009260	ENSMUSG00000020315	Sptbn1	9930031C03Rik|AL033301|SPTB2|Spnb-2|Spnb2|elf1|elf3|mKIAA4049	spectrin beta, non-erythrocytic 1	protein-coding
mm_99631.1	chr11	105164696	105164706	+	1	NA	Intergenic	RLTR31_Mur|LTR|ERVK	-14106	NM_001294331	24086	Mm.126976	NM_011903	ENSMUSG00000020694	Tlk2	4933403M19Rik|PKU-alpha|PKUalpha|Tlk	tousled-like kinase 2 (Arabidopsis)	protein-coding
mm_16488.1	chr2	180967625	180967637	+	1	NA	5' UTR (NM_001177706, exon 1 of 12)	5' UTR (NM_001177706, exon 1 of 12)	331	NM_001177706	228998	Mm.33765	NM_145760	ENSMUSG00000027575	Arfgap1	AI115377|Arf1gap	ADP-ribosylation factor GTPase activating protein 1	protein-coding
mm_150982.1	chr19	46514617	46514631	+	1	NA	exon (NM_053100, exon 5 of 6)	exon (NM_053100, exon 5 of 6)	12976	NM_053100	93679	Mm.392177	NM_053100	ENSMUSG00000025034	Trim8	AA408830|BB006755|GERP|Rnf27	tripartite motif-containing 8	protein-coding
mm_96075.1	chr11	59848277	59848328	+	1	NA	exon (NM_134029, exon 1 of 5)	exon (NM_134029, exon 1 of 5)	229	NM_134029	103850	Mm.41761	NM_134029	ENSMUSG00000032615	Nt5m	2010013E09Rik|AI846937|dNT-2	5',3'-nucleotidase, mitochondrial	protein-coding
mm_117748.1	chr13	95892280	95892286	-	1	NA	promoter-TSS (NM_027711)	promoter-TSS (NM_027711)	-361	NM_027711	544963	Mm.38878	NM_027711	ENSMUSG00000021676	Iqgap2	4933417J23Rik|A630053O10|AI788777	IQ motif containing GTPase activating protein 2	protein-coding
mm_72492.1	chr8	83715240	83715288	+	1	NA	promoter-TSS (NM_197982)	promoter-TSS (NM_197982)	87	NM_197982	68278	Mm.28222	NM_197982	ENSMUSG00000005481	Ddx39	2610307C23Rik|BAT1|DDXL|Ddx39a|URH49	DEAD (Asp-Glu-Ala-Asp) box polypeptide 39	protein-coding
mm_99691.1	chr11	106084546	106084559	+	1	NA	promoter-TSS (NM_011947)	promoter-TSS (NM_011947)	-350	NM_011947	26406	Mm.27041	NM_011947	ENSMUSG00000020700	Map3k3	AW548911|MAPKKK3|Mekk3|mKIAA4031	mitogen-activated protein kinase kinase kinase 3	protein-coding
mm_133084.1	chr16	60042350	60042351	+	1	NA	intron (NM_007938, intron 6 of 17)	intron (NM_007938, intron 6 of 17)	-402941	NM_001347244	56297	Mm.392505	NM_019665	ENSMUSG00000022722	Arl6	1110018H24Rik|2210411E14Rik|BBS3	ADP-ribosylation factor-like 6	protein-coding
mm_93570.1	chr10	116559327	116559339	-	1	NA	intron (NM_001037846, intron 1 of 15)	Charlie4a|DNA|hAT-Charlie	22178	NM_001037848	72068	Mm.351553	NM_028082	ENSMUSG00000020166	Cnot2	2600016M12Rik|2810470K03Rik|AA537049|AA959607|AW557563|C79650	CCR4-NOT transcription complex, subunit 2	protein-coding
mm_134218.1	chr16	11254097	11254107	-	1	NA	TTS (NR_035466)	TTS (NR_035466)	223	NM_001130008	14852	Mm.325827	NM_146066	ENSMUSG00000062203	Gspt1	AI314175|AI326449|AV307676|C79774|G1st|Gst-1	G1 to S phase transition 1	protein-coding
mm_83307.1	chr9	44041170	44041191	-	1	NA	Intergenic	Intergenic	-2204	NM_009382	21838	Mm.3951	NM_009382	ENSMUSG00000032011	Thy1	CD90|T25|Thy-1|Thy-1.2|Thy1.1|Thy1.2	thymus cell antigen 1, theta	protein-coding
mm_144794.1	chr18	35965089	35965110	+	1	NA	non-coding (NR_110349, exon 1 of 15)	non-coding (NR_110349, exon 1 of 15)	269	NR_110349	74002	Mm.196944	NM_028707	ENSMUSG00000024347	Psd2	6330404E20Rik|AW125584|EFA6C	pleckstrin and Sec7 domain containing 2	protein-coding
mm_120784.1	chr14	74683605	74683608	+	1	NA	intron (NM_172812, intron 2 of 2)	intron (NM_172812, intron 2 of 2)	42766	NM_172812	15558	Mm.214351	NM_172812	ENSMUSG00000034997	Htr2a	E030013E04|Htr-2|Htr2	5-hydroxytryptamine (serotonin) receptor 2A	protein-coding
mm_52949.1	chr6	122969440	122969457	+	1	NA	exon (NM_153197, exon 6 of 6)	exon (NM_153197, exon 6 of 6)	16804	NM_153197	73149	Mm.25684	NM_153197	ENSMUSG00000043832	Clec4a3	3110037K17Rik|Dcir3	C-type lectin domain family 4, member a3	protein-coding
mm_143186.1	chr17	58932527	58932539	-	1	NA	intron (NM_027001, intron 6 of 12)	intron (NM_027001, intron 6 of 12)	58842	NM_027001	69239	Mm.246732	NM_027001	ENSMUSG00000024227	Pdzph1	2610034M16Rik|AV114557	PDZ and pleckstrin homology domains 1	protein-coding
mm_159760.1	chr5	92082856	92082856	-	1	NA	promoter-TSS (NM_001080797)	promoter-TSS (NM_001080797)	61	NM_001080797	23881	Mm.290530	NM_011816	ENSMUSG00000029405	G3bp2	AA409541|E430034L04Rik|G3BP|mKIAA0660	GTPase activating protein (SH3 domain) binding protein 2	protein-coding
mm_39922.1	chr5	31562714	31562722	+	1	NA	Intergenic	Intergenic	8679	NR_102275	100740	Mm.23370	NR_102275		AI839979	-	expressed sequence AI839979	ncRNA
mm_123715.1	chr14	69827930	69827964	-	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-12460	NM_028560	73523	Mm.23509	NM_028526	ENSMUSG00000022085	Pebp4	PEBP-4	phosphatidylethanolamine binding protein 4	protein-coding
mm_135064.1	chr16	34175813	34175830	-	1	NA	exon (NM_177357, exon 31 of 60)	exon (NM_177357, exon 31 of 60)	-208818	NM_009471	22247	Mm.13145	NM_009471	ENSMUSG00000022814	Umps	1700095D23Rik|AA408257|AL033308|BB164745	uridine monophosphate synthetase	protein-coding
mm_55729.1	chr6	76902324	76902361	-	1	NA	exon (NM_009819, exon 18 of 19)	exon (NM_009819, exon 18 of 19)	-340375	NM_028880	74342	Mm.292568	NM_028880	ENSMUSG00000060780	Lrrtm1	4632401D06Rik|AW125451	leucine rich repeat transmembrane neuronal 1	protein-coding
mm_49745.1	chr6	34745992	34746004	+	1	NA	exon (NM_145575, exon 3 of 12)	exon (NM_145575, exon 3 of 12)	-34434	NM_001289657	76223	Mm.150047	NM_178630	ENSMUSG00000038836	Agbl3	2900053G10Rik|4930431N21Rik|6530406M24Rik|CCP3	ATP/GTP binding protein-like 3	protein-coding
mm_115894.1	chr13	22035590	22035606	-	1	NA	promoter-TSS (NM_175659)	promoter-TSS (NM_175659)	45	NM_175659	319168	Mm.250564	NM_175659	ENSMUSG00000069302	Hist1h2ah	-	histone cluster 1, H2ah	protein-coding
mm_9439.1	chr1	172558124	172558142	-	1	NA	intron (NM_177723, intron 1 of 6)	intron (NM_177723, intron 1 of 6)	-1773	NR_027644	240916	Mm.71940	NM_177723	ENSMUSG00000049598	Vsig8	A030011M19|EG240916	V-set and immunoglobulin domain containing 8	protein-coding
mm_148929.1	chr19	7017911	7017930	+	1	NA	intron (NM_153795, intron 2 of 14)	intron (NM_153795, intron 2 of 14)	1549	NM_153795	108101	Mm.157591	NM_153795	ENSMUSG00000024965	Fermt3	C79673|Kindlin3	fermitin family member 3	protein-coding
mm_81260.1	chr9	107998007	107998026	+	1	NA	Intergenic	Intergenic	-4632	NM_013785	27399	Mm.276155	NM_013785	ENSMUSG00000032594	Ip6k1	1200016D08Rik|AU022776|Ihpk1|InsP6|InsP6k1|Itpk6	inositol hexaphosphate kinase 1	protein-coding
mm_7497.1	chr1	121359864	121359876	-	1	NA	Intergenic	RSINE1|SINE|B4	-27281	NM_178082	72999	Mm.27136	NM_133748	ENSMUSG00000003721	Insig2	2900053I11Rik|C730043J18Rik|Insig-2	insulin induced gene 2	protein-coding
mm_114409.1	chr13	64204003	64204011	+	1	NA	intron (NM_172587, intron 13 of 13)	intron (NM_172587, intron 13 of 13)	42141	NM_019986	56541	Mm.40989	NM_019986	ENSMUSG00000021476	Habp4	4933413D03Rik|4933428J01Rik	hyaluronic acid binding protein 4	protein-coding
mm_164086.1	chr15	7173848	7173849	+	1	NA	intron (NM_001113386, intron 10 of 16)	intron (NM_001113386, intron 10 of 16)	33306	NM_013584	16880	Mm.149720	NM_013584	ENSMUSG00000054263	Lifr	A230075M04Rik|AW061234|LIF	leukemia inhibitory factor receptor	protein-coding
mm_147467.1	chr18	46713570	46713572	-	1	NA	3' UTR (NM_033037, exon 5 of 5)	3' UTR (NM_033037, exon 5 of 5)	14771	NM_033037	12583	Mm.241056	NM_033037	ENSMUSG00000033022	Cdo1	1300002L19Rik|Cdo|D18Ucla3	cysteine dioxygenase 1, cytosolic	protein-coding
mm_160994.1	chr11	109473266	109473266	+	1	NA	promoter-TSS (NM_028710)	promoter-TSS (NM_028710)	-37	NM_134038	104681	Mm.265874	NM_134038	ENSMUSG00000041920	Slc16a6	AW743111|ESTM12|MCT 6|MCT 7|MCT6	solute carrier family 16 (monocarboxylic acid transporters), member 6	protein-coding
mm_162109.1	chrX	50426379	50426379	-	1	NA	exon (NM_146292, exon 1 of 1)	exon (NM_146292, exon 1 of 1)	115	NM_146292	258289	Mm.451653	NM_146292	ENSMUSG00000048173	Olfr1324	MOR128-2	olfactory receptor 1324	protein-coding
mm_152567.1	chr19	11588692	11588739	-	1	NA	intron (NM_026835, intron 5 of 6)	intron (NM_026835, intron 5 of 6)	16089	NM_026835	68774	Mm.290390	NM_026835	ENSMUSG00000024679	Ms4a6d	1110058E16Rik|AI447446|Ms4a11	membrane-spanning 4-domains, subfamily A, member 6D	protein-coding
mm_34202.1	chr4	140906365	140906382	+	1	NA	promoter-TSS (NM_008812)	promoter-TSS (NM_008812)	13	NM_008812	18600	Mm.2296	NM_008812	ENSMUSG00000028927	Padi2	Pdi|Pdi2|mKIAA0994	peptidyl arginine deiminase, type II	protein-coding
mm_83077.1	chr9	39603552	39603603	-	1	NA	promoter-TSS (NM_001199556)	promoter-TSS (NM_001199556)	75	NM_001199556	244810	Mm.208855	NM_178737	ENSMUSG00000038112	AW551984	3222402N16	expressed sequence AW551984	protein-coding
mm_168743.1	chr12	115359590	115359590	-	1	NA	Intergenic	Intergenic	336204	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
mm_53000.1	chr6	123269311	123269323	+	1	NA	intron (NM_001163161, intron 4 of 5)	intron (NM_001163161, intron 4 of 5)	7210	NM_010819	17474	Mm.441101	NM_010819	ENSMUSG00000030144	Clec4d	Clecsf8|Mpcl|mcl	C-type lectin domain family 4, member d	protein-coding
mm_102380.1	chr11	58889299	58889301	-	1	NA	3' UTR (NM_011758, exon 5 of 5)	3' UTR (NM_011758, exon 5 of 5)	14925	NM_011758	22698	Mm.127646	NM_011758	ENSMUSG00000037001	Zfp39	CTfin33|Zfp-39	zinc finger protein 39	protein-coding
mm_114322.1	chr13	60601922	60602039	+	1	NA	promoter-TSS (NM_134062)	promoter-TSS (NM_134062)	33	NM_029653	69635	Mm.24103	NM_029653	ENSMUSG00000021559	Dapk1	D13Ucla1|DAP-Kinase	death associated protein kinase 1	protein-coding
mm_12331.1	chr2	69646838	69646849	+	1	NA	promoter-TSS (NM_028284)	promoter-TSS (NM_028284)	-412	NM_028284	72569	Mm.252136	NM_028284	ENSMUSG00000063145	Bbs5	1700049I01Rik|2700023J09Rik	Bardet-Biedl syndrome 5 (human)	protein-coding
mm_118105.1	chr13	103920509	103920572	-	1	NA	promoter-TSS (NM_001289475)	promoter-TSS (NM_001289475)	46	NM_001289473	59079	Mm.277354	NM_021563	ENSMUSG00000021709	Erbin	1700028E05Rik|Erbb2ip|mKIAA1225	Erbb2 interacting protein	protein-coding
mm_93186.1	chr10	93889705	93889727	-	1	NA	5' UTR (NM_019648, exon 2 of 12)	5' UTR (NM_019648, exon 2 of 12)	1486	NM_019648	56307	Mm.289329	NM_019648	ENSMUSG00000036112	Metap2	4930584B20Rik|A930035J23Rik|AI047573|AL024412|AU014659|Amp2|Mnpep|p67|p67eIF2	methionine aminopeptidase 2	protein-coding
mm_68648.1	chr7	118491735	118491767	-	1	NA	5' UTR (NM_001033380, exon 1 of 1)	5' UTR (NM_001033380, exon 1 of 1)	224	NM_001033380	319622	Mm.323386	NM_001033380	ENSMUSG00000095115	Itpripl2	C130081G24|E030018N11Rik	inositol 1,4,5-triphosphate receptor interacting protein-like 2	protein-coding
mm_124114.1	chr14	79481025	79481076	-	1	NA	promoter-TSS (NM_007920)	promoter-TSS (NM_007920)	-144	NM_007920	13709	Mm.20938	NM_007920	ENSMUSG00000036461	Elf1	Elf-1|Sts1|mElf-1|p70	E74-like factor 1	protein-coding
mm_39005.1	chr4	151996114	151996243	-	1	NA	promoter-TSS (NM_172705)	promoter-TSS (NM_172705)	1	NM_172705	230936	Mm.25582	NM_172705	ENSMUSG00000047777	Phf13	BC029632|Phf5|SPOC1	PHD finger protein 13	protein-coding
mm_84829.1	chr9	78205966	78205992	-	1	NA	exon (NM_010357, exon 5 of 7)	exon (NM_010357, exon 5 of 7)	14013	NM_010357	14860	Mm.2662	NM_010357	ENSMUSG00000032348	Gsta4	GST5.7|mGsta4	glutathione S-transferase, alpha 4	protein-coding
mm_165501.1	chr2	167588991	167589001	+	1	NA	Intergenic	RLTR13B2|LTR|ERVK	43009	NM_001311146	66589	Mm.278783	NM_023230	ENSMUSG00000078923	Ube2v1	0610011J09Rik|AI256840|CROC-1|CROC1|D7Bwg1382e|UEV-1	ubiquitin-conjugating enzyme E2 variant 1	protein-coding
mm_111311.1	chr12	85817875	85817892	-	1	NA	intron (NM_021446, intron 3 of 4)	intron (NM_021446, intron 3 of 4)	6662	NM_021446	58520	Mm.143795	NM_021446	ENSMUSG00000021252	0610007P14Rik	1190004E09Rik|AU019315|C77855|ORF11	RIKEN cDNA 0610007P14 gene	protein-coding
mm_56716.1	chr6	115484486	115484488	-	1	NA	intron (NM_001308352, intron 7 of 7)	intron (NM_001308352, intron 7 of 7)	-60217	NM_199033	381802	Mm.291208	NM_199033	ENSMUSG00000042389	Tsen2	AU067695	tRNA splicing endonuclease subunit 2	protein-coding
mm_119802.1	chr14	54218830	54218834	+	1	NA	Intergenic	Intergenic	35097	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_131970.1	chr16	24737449	24737460	+	1	NA	intron (NM_001145954, intron 2 of 7)	intron (NM_001145954, intron 2 of 7)	15599	NM_001145954	210126	Mm.209385	NM_178665	ENSMUSG00000033306	Lpp	9430020K16Rik|AA959454|AU024130|B130055L10Rik|C79715|D630048H16	LIM domain containing preferred translocation partner in lipoma	protein-coding
mm_87033.1	chr10	28668463	28668477	+	1	NA	non-coding (NR_131208, exon 1 of 4)	non-coding (NR_131208, exon 1 of 4)	110	NM_178666	210757	Mm.123021	NM_178666	ENSMUSG00000049109	Themis	E430004N04Rik|Gasp|Spot|Tsepa|thylex	thymocyte selection associated	protein-coding
mm_11278.1	chr2	30062091	30062098	+	1	NA	promoter-TSS (NM_023871)	promoter-TSS (NM_023871)	98	NM_023871	56086	Mm.326055	NM_023871	ENSMUSG00000054766	Set	2610030F17Rik|5730420M11Rik|AA407739|I-2PP2A|StF-IT-1|TAF-I	SET nuclear oncogene	protein-coding
mm_2320.1	chr1	92049131	92049156	+	1	NA	intron (NM_207225, intron 3 of 26)	intron (NM_207225, intron 3 of 26)	131198	NM_207225	208727	Mm.318567	NM_207225	ENSMUSG00000026313	Hdac4	4932408F19Rik|HD4	histone deacetylase 4	protein-coding
mm_133602.1	chr16	91485054	91485066	+	1	NA	promoter-TSS (NM_010508)	promoter-TSS (NM_010508)	-155	NM_010508	15975	Mm.502	NM_010508	ENSMUSG00000022967	Ifnar1	CD118|Ifar|Ifnar|Ifrc|Infar	interferon (alpha and beta) receptor 1	protein-coding
mm_172856.1	chr9	40423688	40423697	-	1	NA	intron (NM_172768, intron 1 of 19)	intron (NM_172768, intron 1 of 19)	32072	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_127787.1	chr15	3542616	3542632	-	1	NA	intron (NM_001048178, intron 1 of 8)	intron (NM_001048178, intron 1 of 8)	39218	NM_001286370	14600	Mm.3986	NM_010284	ENSMUSG00000055737	Ghr	GHBP|GHR/BP	growth hormone receptor	protein-coding
mm_136892.1	chr17	13012117	13012129	+	1	NA	intron (NM_013671, intron 3 of 4)	intron (NM_013671, intron 3 of 4)	4284	NM_013671	20656	Mm.290876	NM_013671	ENSMUSG00000006818	Sod2	MnSOD|Sod-2	superoxide dismutase 2, mitochondrial	protein-coding
mm_491.1	chr1	36771318	36771367	+	1	NA	intron (NM_009539, intron 2 of 12)	intron (NM_009539, intron 2 of 12)	4408	NM_001289765	22637	Mm.8038	NM_009539	ENSMUSG00000026117	Zap70	Srk|ZAP-70|mrtle|mur	zeta-chain (TCR) associated protein kinase	protein-coding
mm_61614.1	chr7	80082371	80082387	+	1	NA	exon (NM_175433, exon 2 of 5)	exon (NM_175433, exon 2 of 5)	-7122	NR_045695	100859962	Mm.392575	NR_045695	ENSMUSG00000108714	Gm21057	-	predicted gene, 21057	ncRNA
mm_131436.1	chr16	15892237	15892239	+	1	NA	intron (NM_146068, intron 19 of 19)	intron (NM_146068, intron 19 of 19)	4952	NM_007679	12609	Mm.347407	NM_007679	ENSMUSG00000071637	Cebpd	c/EBPdelta	CCAAT/enhancer binding protein (C/EBP), delta	protein-coding
mm_141644.1	chr17	33394663	33394673	-	1	NA	promoter-TSS (NM_009542)	promoter-TSS (NM_009542)	-31	NM_009542	22643	Mm.4417	NM_009542	ENSMUSG00000055240	Zfp101	AI316498|AI325003	zinc finger protein 101	protein-coding
mm_24816.1	chr3	95624972	95625021	+	1	NA	promoter-TSS (NM_019561)	promoter-TSS (NM_019561)	16	NM_001026212	56205	Mm.241365	NM_019561	ENSMUSG00000038619	Ensa	1700020C18Rik|2610007F17Rik|AI451924	endosulfine alpha	protein-coding
mm_142212.1	chr17	37023239	37023320	-	1	NA	5' UTR (NM_010814, exon 1 of 8)	5' UTR (NM_010814, exon 1 of 8)	119	NM_010814	17441	Mm.210857	NM_010814	ENSMUSG00000076439	Mog	B230317G11Rik	myelin oligodendrocyte glycoprotein	protein-coding
mm_159392.1	chr3	93442363	93442363	+	1	NA	promoter-TSS (NM_001163098)	promoter-TSS (NM_001163098)	33	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_109392.1	chr12	109748053	109748072	+	1	NA	TTS (NR_037233)	TTS (NR_037233)	184	NR_037233	100499517		NR_037233	ENSMUSG00000093351	Mir3072	mir-3072|mmu-mir-3072	microRNA 3072	ncRNA
mm_104350.1	chr11	94297124	94297138	-	1	NA	exon (NM_026313, exon 8 of 11)	exon (NM_026313, exon 8 of 11)	24780	NM_026313	67684	Mm.30927	NM_026313	ENSMUSG00000020863	Luc7l3	3300001P08Rik|Luc7a	LUC7-like 3 (S. cerevisiae)	protein-coding
mm_136408.1	chr16	93751943	93751950	-	1	NA	intron (NM_027293, intron 7 of 36)	intron (NM_027293, intron 7 of 36)	40039	NM_027293	70028	Mm.23230	NM_026700	ENSMUSG00000022946	Dopey2	0610038M01Rik|2610510B01Rik|AI503246|C21orf5|mKIAA0933	dopey family member 2	protein-coding
mm_62092.1	chr7	94042719	94042729	+	1	NA	Intergenic	Intergenic	962845	NM_021427	58238	Mm.113787	NM_021427	ENSMUSG00000051515	Fam181b	A830059I20Rik|AB041569	family with sequence similarity 181, member B	protein-coding
mm_171232.1	chr3	66994637	66994642	+	1	NA	exon (NM_025822, exon 2 of 10)	exon (NM_025822, exon 2 of 10)	8967	NM_025822	66880	Mm.316418	NM_025822	ENSMUSG00000034544	Rsrc1	1200013F24Rik|SRrp53	arginine/serine-rich coiled-coil 1	protein-coding
mm_126699.1	chr15	85042709	85042738	+	1	NA	intron (NM_133750, intron 1 of 8)	intron (NM_133750, intron 1 of 8)	5661	NM_133750	73225	Mm.247535	NM_133750	ENSMUSG00000022434	Fam118a	-	family with sequence similarity 118, member A	protein-coding
mm_54777.1	chr6	41541260	41541267	-	1	NA	Intergenic	A-rich|Low_complexity|Low_complexity	19487	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_56709.1	chr6	115251878	115251888	-	1	NA	promoter-TSS (NM_080639)	promoter-TSS (NM_080639)	-34	NM_080639	110595	Mm.255607	NM_080639	ENSMUSG00000030317	Timp4	TIMP-4	tissue inhibitor of metalloproteinase 4	protein-coding
mm_121732.1	chr14	18270954	18270991	-	1	NA	promoter-TSS (NM_025586)	promoter-TSS (NM_025586)	14	NM_025586	66480	Mm.2050	NM_025586	ENSMUSG00000012405	Rpl15	2510008H07Rik	ribosomal protein L15	protein-coding
mm_24351.1	chr3	89963429	89963462	+	1	NA	promoter-TSS (NM_001081182)	promoter-TSS (NM_001081182)	-113	NM_001081182	54667	Mm.30455	NM_001081182	ENSMUSG00000060671	Atp8b2	Id	ATPase, class I, type 8B, member 2	protein-coding
mm_57804.1	chr6	129385498	129385510	-	1	NA	promoter-TSS (NM_027709)	promoter-TSS (NM_027709)	-1	NM_027709	71183	Mm.79402	NM_027709	ENSMUSG00000030158	Clec12b	4933425B16Rik	C-type lectin domain family 12, member B	protein-coding
mm_132369.1	chr16	34807226	34807309	+	1	NA	intron (NM_139300, intron 1 of 31)	intron (NM_139300, intron 1 of 31)	22317	NM_139300	107589	Mm.33360	NM_139300	ENSMUSG00000022836	Mylk	9530072E15Rik|A930019C19Rik|AW489456|KRP|MLCK108|MLCK210|Mlck|nmMlck|smMLCK	myosin, light polypeptide kinase	protein-coding
mm_28295.1	chr3	89094857	89094860	-	1	NA	intron (NM_134469, intron 7 of 9)	intron (NM_134469, intron 7 of 9)	-1495	NM_028188	72296	Mm.27687	NM_028188	ENSMUSG00000041263	Rusc1	2210403N08Rik|AA408288|NESCA	RUN and SH3 domain containing 1	protein-coding
mm_114969.1	chr13	97199432	97199436	+	1	NA	Intergenic	MT2B2|LTR|ERVL	-1077	NM_010422	15212	Mm.27816	NM_010422	ENSMUSG00000021665	Hexb	-	hexosaminidase B	protein-coding
mm_83106.1	chr9	40346116	40346131	-	1	NA	intron (NM_172768, intron 2 of 19)	intron (NM_172768, intron 2 of 19)	12651	NR_040728	73558	Mm.398307	NR_040728		1700110K17Rik	-	RIKEN cDNA 1700110K17 gene	ncRNA
mm_88677.1	chr10	80047248	80047264	+	1	NA	promoter-TSS (NR_110342)	promoter-TSS (NR_110342)	90	NR_110342	625249	Mm.332810	NM_008162	ENSMUSG00000075706	Gpx4	GPx-4|GSHPx-4|PHGPx|mtPHGPx|snGPx	glutathione peroxidase 4	protein-coding
mm_57031.1	chr6	122323557	122323585	-	1	NA	exon (NM_001271579, exon 8 of 15)	exon (NM_001271579, exon 8 of 15)	14561	NM_010749	17113	Mm.249225	NM_010749	ENSMUSG00000007458	M6pr	CD-MPR|Mpr46	mannose-6-phosphate receptor, cation dependent	protein-coding
mm_51540.1	chr6	83196000	83196016	+	1	NA	exon (NM_001198867, exon 23 of 28)	exon (NM_001198867, exon 23 of 28)	10062	NM_001347310	13191	Mm.6919	NM_007835	ENSMUSG00000031865	Dctn1	AL022633|DAP-150|DP-150|Glued|p150|p150-glued|p150<glued>	dynactin 1	protein-coding
mm_142750.1	chr17	48451480	48451509	-	1	NA	promoter-TSS (NM_027292)	promoter-TSS (NM_027292)	7	NM_027292	70026	Mm.22613	NM_027292	ENSMUSG00000023995	Tspo2	2510027D20Rik|Bzrpl1	translocator protein 2	protein-coding
mm_36342.1	chr4	72903713	72903716	-	1	NA	Intergenic	ID_B1|SINE|B4	-51080	NM_001199270	353204	Mm.317892	NM_001199270	ENSMUSG00000059343	Aldoart1	4921524E03Rik|Aldo1-ps|Aldo1-ps2|Aldoa-ps2	aldolase 1 A, retrogene 1	protein-coding
mm_100506.1	chr11	120491930	120491949	+	1	NA	5' UTR (NM_013770, exon 1 of 11)	5' UTR (NM_013770, exon 1 of 11)	102	NM_013770	27376	Mm.3991	NM_013770	ENSMUSG00000025792	Slc25a10	Dic	solute carrier family 25 (mitochondrial carrier, dicarboxylate transporter), member 10	protein-coding
mm_143113.1	chr17	57205530	57205535	-	1	NA	intron (NM_009778, intron 37 of 40)	intron (NM_009778, intron 37 of 40)	-11351	NM_019418	50930	Mm.483369	NM_019418	ENSMUSG00000005824	Tnfsf14	HVEM-L|HVEML|LIGHT|LTg|Ly113|Tnlg1d	tumor necrosis factor (ligand) superfamily, member 14	protein-coding
mm_64561.1	chr7	144838054	144838079	+	1	NA	promoter-TSS (NM_008007)	promoter-TSS (NM_008007)	-546	NM_008007	14174	Mm.4947	NM_008007	ENSMUSG00000031074	Fgf3	Fgf-3|Int-2|Int-P	fibroblast growth factor 3	protein-coding
mm_149122.1	chr19	8989328	8989338	+	1	NA	promoter-TSS (NM_001286518)	promoter-TSS (NM_001286518)	49	NM_001286518	66395	Mm.203866	NM_009643	ENSMUSG00000069833	Ahnak	DY6	AHNAK nucleoprotein (desmoyokin)	protein-coding
mm_130720.1	chr15	101078370	101078380	-	1	NA	Intergenic	CpG	-23976	NM_001214911	668225	Mm.385011	NM_001214911	ENSMUSG00000095440	Fignl2	EG668225	fidgetin-like 2	protein-coding
mm_79279.1	chr9	50775376	50775380	+	1	NA	non-coding (NR_045601, exon 1 of 14)	non-coding (NR_045601, exon 1 of 14)	153	NR_045601	102580	Mm.160035	NM_133981	ENSMUSG00000032059	Alg9	8230402H15Rik|AI747665|B430313H07Rik|Dibd1	asparagine-linked glycosylation 9 (alpha 1,2 mannosyltransferase)	protein-coding
mm_67515.1	chr7	80815839	80815880	-	1	NA	Intergenic	tRNA-Ala-GCY_|tRNA|tRNA	-12528	NM_016721	29875	Mm.207619	NM_016721	ENSMUSG00000030536	Iqgap1	AA682088|D7Ertd237e|D7Ertd257e|mKIAA0051	IQ motif containing GTPase activating protein 1	protein-coding
mm_160074.1	chr7	6995588	6995588	+	1	NA	5' UTR (NM_020572, exon 1 of 7)	5' UTR (NM_020572, exon 1 of 7)	203	NM_001080965	20871	Mm.261572	NM_020572	ENSMUSG00000070837	Aurkc	AIE1|AIK3|ARK-3|IAK3|Stk13	aurora kinase C	protein-coding
mm_145149.1	chr18	46226027	46226034	+	1	NA	Intergenic	Intergenic	-13423	NM_178872	28105	Mm.277382	NM_178872	ENSMUSG00000033949	Trim36	D18Wsu100e|haprin	tripartite motif-containing 36	protein-coding
mm_169619.1	chr15	38243835	38243851	-	1	NA	Intergenic	(TCC)n|Simple_repeat|Simple_repeat	24640	NM_008757	18285	Mm.252830	NM_008757	ENSMUSG00000061923	Odf1	-	outer dense fiber of sperm tails 1	protein-coding
mm_49891.1	chr6	38918462	38918474	+	1	NA	promoter-TSS (NM_011539)	promoter-TSS (NM_011539)	-518	NM_011539	21391	Mm.4054	NM_011539	ENSMUSG00000029925	Tbxas1	CYP5|CYP5A1|THAS|TS|TXAS|TXS	thromboxane A synthase 1, platelet	protein-coding
mm_155330.1	chrX	65437483	65437483	+	1	NA	Intergenic	Lx4B|LINE|L1	389839	NM_027302	70062	Mm.45791	NM_027302	ENSMUSG00000031181	Ctag2	1700030B21Rik	cancer/testis antigen 2	protein-coding
mm_159373.1	chr3	88846416	88846416	+	1	NA	exon (NM_027389, exon 3 of 32)	exon (NM_027389, exon 3 of 32)	11185	NM_001242372	76022	Mm.126870	NM_027389	ENSMUSG00000054199	Gon4l	1500041I23Rik|2610100B20Rik|3632445O20Rik|5430404N14Rik|AA387005	gon-4-like (C.elegans)	protein-coding
mm_37893.1	chr4	132535408	132535456	-	1	NA	promoter-TSS (NM_172400)	promoter-TSS (NM_172400)	-18	NM_007512	11983	Mm.2171	NM_007512	ENSMUSG00000054428	Atpif1	Atpi|IF(1)|If1	ATPase inhibitory factor 1	protein-coding
mm_72150.1	chr8	72144645	72144661	+	1	NA	intron (NM_001001491, intron 3 of 7)	intron (NM_001001491, intron 3 of 7)	9361	NM_001001491	326618	Mm.295124	NM_001001491	ENSMUSG00000031799	Tpm4	2610528G24Rik|Tpm4.2|Tpm4.2cy	tropomyosin 4	protein-coding
mm_62265.1	chr7	99535144	99535184	+	1	NA	promoter-TSS (NM_178220)	promoter-TSS (NM_178220)	-322	NM_178220	109689	Mm.260193	NM_177231	ENSMUSG00000018909	Arrb1	1200006I17Rik|AW208571|G430100A01Rik	arrestin, beta 1	protein-coding
mm_141558.1	chr17	32214685	32214698	-	1	NA	exon (NM_001286630, exon 9 of 20)	exon (NM_001286630, exon 9 of 20)	-25142	NM_001347341	71932	Mm.176240	NM_001033163	ENSMUSG00000037577	Ephx3	2310063B19Rik|Abhd9	epoxide hydrolase 3	protein-coding
mm_121855.1	chr14	20664563	20664580	-	1	NA	promoter-TSS (NM_001310432)	promoter-TSS (NM_001310432)	3	NM_001310432	68760	Mm.35789	NM_175132	ENSMUSG00000039376	Synpo2l	1110054M18Rik|Chap	synaptopodin 2-like	protein-coding
mm_22865.1	chr3	28781306	28781344	+	1	NA	promoter-TSS (NM_177586)	promoter-TSS (NM_177586)	14	NM_177586	208691	Mm.193670	NM_177586	ENSMUSG00000050192	Eif5a2	9630038B20|eIF5AII	eukaryotic translation initiation factor 5A2	protein-coding
mm_52497.1	chr6	115134900	115134982	+	1	NA	promoter-TSS (NM_013681)	promoter-TSS (NM_013681)	39	NM_001111015	20965	Mm.441431	NM_013681	ENSMUSG00000009394	Syn2	2900074L19Rik|AI836018|AI841723	synapsin II	protein-coding
mm_93597.1	chr10	117148512	117148546	-	1	NA	promoter-TSS (NM_177798)	promoter-TSS (NM_177798)	-55	NM_177798	327826	Mm.135965	NM_177798	ENSMUSG00000020170	Frs2	4732458E18|C330018A15Rik|Frs2alpha|SNT1	fibroblast growth factor receptor substrate 2	protein-coding
mm_153324.1	chr19	38124051	38124059	-	1	NA	exon (NM_011255, exon 4 of 6)	exon (NM_011255, exon 4 of 6)	756	NM_011255	19662	Mm.2605	NM_011255	ENSMUSG00000024990	Rbp4	Rbp-4	retinol binding protein 4, plasma	protein-coding
mm_71527.1	chr8	46852767	46852782	+	1	NA	Intergenic	LTR67B|LTR|ERVL	113029	NM_008391	16363	Mm.1149	NM_008391	ENSMUSG00000031627	Irf2	9830146E22Rik|AI646973|Irf-2	interferon regulatory factor 2	protein-coding
mm_102378.1	chr11	58802194	58802221	-	1	NA	promoter-TSS (NM_001162878)	promoter-TSS (NM_001162878)	-247	NM_029283	75429	Mm.296819	NM_029283	ENSMUSG00000049154	Fam183b	3100002J23Rik|Theg6	family with sequence similarity 183, member B	protein-coding
mm_106930.1	chr12	8519697	8519733	+	1	NA	Intergenic	Intergenic	-19730	NM_007483	11852	Mm.687	NM_007483	ENSMUSG00000054364	Rhob	AA017882|Arh6|Arhb	ras homolog family member B	protein-coding
mm_142220.1	chr17	37185479	37185487	-	1	NA	Intergenic	Intergenic	-8409	NM_023137	24108	Mm.140210	NM_023137	ENSMUSG00000035186	Ubd	FAT10	ubiquitin D	protein-coding
mm_42749.1	chr5	120754032	120754106	+	1	NA	3' UTR (NM_145226, exon 16 of 16)	3' UTR (NM_145226, exon 16 of 16)	-4221	NM_001347448	246728	Mm.260926	NM_145227	ENSMUSG00000032690	Oas2	Oasl11	2'-5' oligoadenylate synthetase 2	protein-coding
mm_4272.1	chr1	171559187	171559205	+	1	NA	promoter-TSS (NM_018729)	promoter-TSS (NM_018729)	3	NM_018729	18106	Mm.2299	NM_018729	ENSMUSG00000004709	Cd244	2B4|C9.1|F730046O15Rik|Ly90|NAIL|NKR2B4|Nmrk|SLAMF4	CD244 natural killer cell receptor 2B4	protein-coding
mm_19638.1	chr2	102829387	102829407	-	1	NA	intron (NM_001039151, intron 5 of 8)	LSU-rRNA_Hsa|rRNA|rRNA	72268	NM_001177785	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_42557.1	chr5	117120186	117120196	+	1	NA	promoter-TSS (NM_001199685)	promoter-TSS (NM_001199685)	62	NM_001199685	330177	Mm.24343	NM_183306	ENSMUSG00000061288	Taok3	2900006A08Rik|A130052D22|A430105I05Rik	TAO kinase 3	protein-coding
mm_30618.1	chr4	8535819	8535851	+	1	NA	5' UTR (NM_021518, exon 1 of 8)	5' UTR (NM_021518, exon 1 of 8)	191	NM_021518	59021	Mm.397471	NM_021518	ENSMUSG00000047187	Rab2a	9330148M11Rik|C80220|Rab2	RAB2A, member RAS oncogene family	protein-coding
mm_171809.1	chr5	131050291	131050291	+	1	NA	intron (NM_145218, intron 5 of 10)	intron (NM_145218, intron 5 of 10)	257231	NM_145218	212996	Mm.299204	NM_145218	ENSMUSG00000034040	Wbscr17	AA388321|E330012B09Rik	Williams-Beuren syndrome chromosome region 17 homolog (human)	protein-coding
mm_154318.1	chrM	2167	2178	+	1	NA	NA	LSU-rRNA_Hsa|rRNA|rRNA	NA	NA								
mm_74516.1	chr8	8690494	8690538	-	1	NA	promoter-TSS (NR_106114)	promoter-TSS (NR_106114)	21	NM_176849	234023	Mm.251655	NM_176849	ENSMUSG00000040459	Arglu1	9430010O03Rik|C130008N12	arginine and glutamate rich 1	protein-coding
mm_37276.1	chr4	118636346	118636359	-	1	NA	Intergenic	Intergenic	9948	NR_029469	100041290	Mm.472885	NR_029469		D4Ertd617e	-	DNA segment, Chr 4, ERATO Doi 617, expressed	ncRNA
mm_130793.1	chr15	101690205	101690212	-	1	NA	3' UTR (NM_008476, exon 9 of 9)	3' UTR (NM_008476, exon 9 of 9)	4097	NM_008476	16687	Mm.302399	NM_008476	ENSMUSG00000058354	Krt6a	2310016L08Rik|Krt2-6a|Krt2-6c|MK6a|mK6[a]	keratin 6A	protein-coding
mm_101233.1	chr11	20464659	20464670	-	1	NA	Intergenic	Intergenic	-78589	NM_021372	58172	Mm.339676	NM_021372	ENSMUSG00000049800	Sertad2	AB041541|AU021878|Kiaa0127|MNCb-1504|SEI-2|Sei2|TRIP-Br2|mKIAA0127	SERTA domain containing 2	protein-coding
mm_114455.1	chr13	67128192	67128217	+	1	NA	promoter-TSS (NM_172392)	promoter-TSS (NM_172392)	-24	NM_172392	268670	Mm.56274	NM_172392	ENSMUSG00000057396	Zfp759	BC028265|Rslcan-8|Rslcan8	zinc finger protein 759	protein-coding
mm_99257.1	chr11	101180095	101180101	+	1	NA	intron (NM_016782, intron 7 of 23)	intron (NM_016782, intron 7 of 23)	3981	NM_016782	53321	Mm.474527	NM_016782	ENSMUSG00000017167	Cntnap1	AI841080|Caspr|NCP1|Nrxn4|p190|shm	contactin associated protein-like 1	protein-coding
mm_21840.1	chr2	165802544	165802557	-	1	NA	intron (NM_027230, intron 17 of 23)	intron (NM_027230, intron 17 of 23)	55623	NM_001252585	228880	Mm.227598	NM_027230	ENSMUSG00000039671	Zmynd8	1110013E22Rik|2010005I16Rik|3632413B07Rik|AI316811|AL024039|Prkcbp1|RACK7	zinc finger, MYND-type containing 8	protein-coding
mm_98295.1	chr11	89092300	89092316	+	1	NA	intron (NM_001033266, intron 3 of 3)	intron (NM_001033266, intron 3 of 3)	18467	NM_001033266	217071	Mm.342127	NM_001033266	ENSMUSG00000072553	Gm525	-	predicted gene 525	protein-coding
mm_169490.1	chr14	74783284	74783284	-	1	NA	intron (NM_001252132, intron 17 of 18)	L1Md_T|LINE|L1	50987	NM_016903	13885	Mm.38055	NM_016903	ENSMUSG00000021996	Esd	Es-10|Es10|FGH|sid478	esterase D/formylglutathione hydrolase	protein-coding
mm_133383.1	chr16	84773004	84773008	+	1	NA	Intergenic	Intergenic	-1117	NM_023844	67374	Mm.41758	NM_023844	ENSMUSG00000053062	Jam2	1110002N23Rik|2410030G21Rik|2410167M24Rik|JAM-2|JAM-B|Jcam2|VE-JAM	junction adhesion molecule 2	protein-coding
mm_17008.1	chr2	18867233	18867235	-	1	NA	intron (NM_008845, intron 5 of 9)	intron (NM_008845, intron 5 of 9)	-65416	NR_131254	66774	Mm.87075	NR_131254	ENSMUSG00000097638	Carlr	4933439G12Rik|Carl	cardiac and apoptosis-related long non-coding RNA	ncRNA
mm_110679.1	chr12	67059402	67059451	-	1	NA	intron (NM_001193266, intron 1 of 16)	GSAT_MM|Satellite|Satellite	163123	NM_001193266	320772	Mm.227680	NM_207010	ENSMUSG00000034912	Mdga2	6720489L24Rik|9330209L04Rik|Adp|Mamdc1	MAM domain containing glycosylphosphatidylinositol anchor 2	protein-coding
mm_94837.1	chr11	23665411	23665438	+	1	NA	promoter-TSS (NM_001033654)	promoter-TSS (NM_001033654)	-250	NM_028956	74467	Mm.29536	NM_028304	ENSMUSG00000020280	Pus10	2810013G11Rik|4933435A13Rik|AU014648|C77560|Ccdc139	pseudouridylate synthase 10	protein-coding
mm_22408.1	chr2	181313275	181313278	-	1	NA	intron (NM_009133, intron 1 of 4)	(A)n|Simple_repeat|Simple_repeat	1224	NM_009133	20262	Mm.2319	NM_009133	ENSMUSG00000027581	Stmn3	9330161A03Rik|AI604839|R75323|Sclip	stathmin-like 3	protein-coding
mm_29410.1	chr3	108911688	108911746	-	1	NA	promoter-TSS (NM_025845)	promoter-TSS (NM_025845)	-13	NM_025845	66921	Mm.51049	NM_025845	ENSMUSG00000027881	Prpf38b	1110021E09Rik|AU018955	PRP38 pre-mRNA processing factor 38 (yeast) domain containing B	protein-coding
mm_111271.1	chr12	85331500	85331502	-	1	NA	intron (NM_145138, intron 5 of 21)	PB1D7|SINE|Alu	7861	NM_145138	217718	Mm.29071	NM_145138	ENSMUSG00000034290	Nek9	C130021H08Rik	NIMA (never in mitosis gene a)-related expressed kinase 9	protein-coding
mm_140007.1	chr17	73126573	73126585	+	1	NA	intron (NM_001081071, intron 1 of 5)	intron (NM_001081071, intron 1 of 5)	18594	NM_001177967	225010	Mm.329194	NM_001081071	ENSMUSG00000054469	Lclat1	AI181996|Agpat8|Alcat1|Gm91|Lycat	lysocardiolipin acyltransferase 1	protein-coding
mm_44457.1	chr5	22344696	22344710	-	1	NA	promoter-TSS (NM_011261)	promoter-TSS (NM_011261)	2	NM_011261	19699	Mm.425236	NM_011261	ENSMUSG00000042453	Reln	reeler|rl	reelin	protein-coding
mm_131449.1	chr16	16306469	16306494	+	1	NA	exon (NM_198246, exon 3 of 5)	exon (NM_198246, exon 3 of 5)	3516	NM_198246	70120	Mm.37486	NM_198246	ENSMUSG00000022792	Yars2	2210023C10Rik|tyrRS	tyrosyl-tRNA synthetase 2 (mitochondrial)	protein-coding
mm_54678.1	chr6	39419572	39419582	-	1	NA	5' UTR (NM_001311109, exon 1 of 8)	5' UTR (NM_001311109, exon 1 of 8)	199	NM_001311109	54484	Mm.270484	NM_018810	ENSMUSG00000029922	Mkrn1	RFP	makorin, ring finger protein, 1	protein-coding
mm_60534.1	chr7	44480332	44480348	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-4177	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_118647.1	chr14	21560956	21560960	+	1	NA	intron (NM_017479, intron 2 of 16)	intron (NM_017479, intron 2 of 16)	61173	NM_017479	54169	Mm.248967	NM_017479	ENSMUSG00000021767	Kat6b	AI507552|B130044K16Rik|MYST-4|Morf|Myst4|mKIAA0383|qkf|querkopf	K(lysine) acetyltransferase 6B	protein-coding
mm_80792.1	chr9	96119423	96119437	+	1	NA	promoter-TSS (NM_177352)	promoter-TSS (NM_177352)	1	NM_177352	235533	Mm.213651	NM_177352	ENSMUSG00000041440	Gk5	AV095337|C330018K18Rik|G630067D24Rik	glycerol kinase 5 (putative)	protein-coding
mm_56387.1	chr6	94681685	94681694	-	1	NA	intron (NM_008377, intron 1 of 18)	intron (NM_008377, intron 1 of 18)	18456	NM_008377	16206	Mm.245210	NM_008377	ENSMUSG00000030029	Lrig1	D6Bwg0781e|Img|LIG-1	leucine-rich repeats and immunoglobulin-like domains 1	protein-coding
mm_17702.1	chr2	32381822	32381908	-	1	NA	promoter-TSS (NM_198001)	promoter-TSS (NM_198001)	50	NM_198001	73737	Mm.27608	NM_198001	ENSMUSG00000039195	1110008P14Rik	C79326	RIKEN cDNA 1110008P14 gene	protein-coding
mm_85372.1	chr9	103222183	103222191	-	1	NA	exon (NM_133977, exon 8 of 17)	exon (NM_133977, exon 8 of 17)	8099	NM_133977	22041	Mm.37214	NM_133977	ENSMUSG00000032554	Trf	AI266983|Cd176|HP|Tf|Tfn|hpx	transferrin	protein-coding
mm_150929.1	chr19	46304710	46304811	+	1	NA	promoter-TSS (NM_019408)	promoter-TSS (NM_019408)	23	NM_001177369	18034	Mm.102365	NM_019408	ENSMUSG00000025225	Nfkb2	NF-kappaB2|lyt|p49|p49/p100|p50B|p52	nuclear factor of kappa light polypeptide gene enhancer in B cells 2, p49/p100	protein-coding
mm_67177.1	chr7	73597331	73597360	-	1	NA	Intergenic	Intergenic	-38950	NR_037569	69170	Mm.34539	NR_037569	ENSMUSG00000101970	1810026B05Rik	-	RIKEN cDNA 1810026B05 gene	ncRNA
mm_20537.1	chr2	131054513	131054553	-	1	NA	exon (NM_001163529, exon 12 of 20)	exon (NM_001163529, exon 12 of 20)	9281	NR_136922	110751	Mm.108550	NM_033615	ENSMUSG00000027318	Adam33	Adaml	a disintegrin and metallopeptidase domain 33	protein-coding
mm_163152.1	chr11	83603703	83603732	+	1	NA	intron (NR_036453, intron 2 of 8)	MLT1G|LTR|ERVL-MaLR	-10630	NM_009139	20305	Mm.137	NM_009139	ENSMUSG00000018927	Ccl6	MRP-1|Scya6|c10	chemokine (C-C motif) ligand 6	protein-coding
mm_115464.1	chr13	119428889	119428960	+	1	NA	promoter-TSS (NM_145457)	promoter-TSS (NM_145457)	22	NM_145457	218693	Mm.490243	NM_145457	ENSMUSG00000025451	Paip1	PAIP-1	polyadenylate binding protein-interacting protein 1	protein-coding
mm_13224.1	chr2	97467540	97467559	+	1	NA	promoter-TSS (NM_178725)	promoter-TSS (NM_178725)	-108	NM_001289744	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_164571.1	chr17	23599485	23599490	-	1	NA	promoter-TSS (NM_011747)	promoter-TSS (NM_011747)	0	NM_011747	22654	Mm.40326	NM_011747	ENSMUSG00000062012	Zfp13	4933429B21|AI835008|Krox-8|Rhit|Zfp-13	zinc finger protein 13	protein-coding
mm_77205.1	chr8	113854886	113854894	-	1	NA	Intergenic	Intergenic	-6051	NM_172466	208936	Mm.167471	NM_172466	ENSMUSG00000053399	Adamts18	9630038L21|ADAMTS21|E130314N14Rik	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 18	protein-coding
mm_42798.1	chr5	121711909	121711915	+	1	NA	exon (NM_009125, exon 1 of 25)	exon (NM_009125, exon 1 of 25)	303	NM_009125	20239	Mm.260900	NM_009125	ENSMUSG00000042605	Atxn2	9630045M23Rik|ATX2|AW544490|Sca2	ataxin 2	protein-coding
mm_138081.1	chr17	33975481	33975497	+	1	NA	intron (NR_004446, intron 5 of 5)	intron (NR_004446, intron 5 of 5)	3302	NR_004446	630499	Mm.440940	NM_001081015		H2-K2	EG630499|Gm7035|H-2K1|H-2K1K|H-2K2|H2-K1	histocompatibility 2, K region locus 2	pseudo
mm_28008.1	chr3	83031584	83031610	-	1	NA	exon (NM_010196, exon 5 of 5)	exon (NM_010196, exon 5 of 5)	5444	NM_001111048	14161	Mm.88793	NM_010196	ENSMUSG00000028001	Fga	ENSMUSG00000059807|Fib	fibrinogen alpha chain	protein-coding
mm_158371.1	chrX	135036079	135036090	-	1	NA	non-coding (NR_040283, exon 1 of 3)	non-coding (NR_040283, exon 1 of 3)	518	NR_040281	320606	Mm.439072	NR_040281	ENSMUSG00000089759	3632454L22Rik	-	RIKEN cDNA 3632454L22 gene	ncRNA
mm_57213.1	chr6	122856098	122856110	-	1	NA	promoter-TSS (NM_009779)	promoter-TSS (NM_009779)	53	NM_009779	12267	Mm.2408	NM_009779	ENSMUSG00000040552	C3ar1	AZ3B|C3AR|HNFAG09	complement component 3a receptor 1	protein-coding
mm_159466.1	chr4	5772868	5772868	+	1	NA	intron (NM_173426, intron 2 of 2)	intron (NM_173426, intron 2 of 2)	128689	NM_173426	242297	Mm.331470	NM_173426	ENSMUSG00000049119	Fam110b	1700012H17Rik|5031405P22|AW049855	family with sequence similarity 110, member B	protein-coding
mm_9308.1	chr1	171641060	171641086	-	1	NA	TTS (NR_106151)	TTS (NR_106151)	827	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_134617.1	chr16	21063142	21063157	-	1	NA	Intergenic	Intergenic	90795	NM_025634	66561	Mm.422867	NM_025634	ENSMUSG00000090356	Teddm3	2310042E22Rik	transmembrane epididymal family member 3	protein-coding
mm_118600.1	chr14	20703043	20703077	+	1	NA	promoter-TSS (NR_029446)	promoter-TSS (NR_029446)	33	NM_025366	66121	Mm.246996	NM_025366	ENSMUSG00000063787	Chchd1	1110001O19Rik|2400010G13Rik|MRP-S37	coiled-coil-helix-coiled-coil-helix domain containing 1	protein-coding
mm_173113.1	chrX	158901670	158901677	+	1	NA	Intergenic	L1Md_T|LINE|L1	-354109	NM_148945	110651	Mm.328476	NM_148945	ENSMUSG00000031309	Rps6ka3	MAPKAPK-1b|MPK-9|Rsk2|S6K-alpha3|p90RSK3|pp90RSK2	ribosomal protein S6 kinase polypeptide 3	protein-coding
mm_163477.1	chr12	104988763	104988766	-	1	NA	intron (NM_172500, intron 1 of 16)	intron (NM_172500, intron 1 of 16)	9913	NM_001042699	212073	Mm.212688	NM_172500	ENSMUSG00000054150	Syne3	nesprin-3	spectrin repeat containing, nuclear envelope family member 3	protein-coding
mm_76248.1	chr8	83594441	83594481	-	1	NA	promoter-TSS (NM_027179)	promoter-TSS (NM_027179)	30	NM_027179	106529	Mm.352239	NM_027179	ENSMUSG00000031708	Tecr	2410016D23Rik|A230102P12Rik|AI173355|D17Ertd178e|Gpsn2|SC2	trans-2,3-enoyl-CoA reductase	protein-coding
mm_104960.1	chr11	100142187	100142208	-	1	NA	exon (NM_008471, exon 3 of 6)	exon (NM_008471, exon 3 of 6)	1502	NM_001313963	16669	Mm.439699	NM_008471	ENSMUSG00000020911	Krt19	AI663979|CK-19|EndoC|K19|Krt-1.19|Krt1-19	keratin 19	protein-coding
mm_149576.1	chr19	13054774	13054829	+	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	-8612	NM_146692	258687	Mm.271528	NM_146692	ENSMUSG00000094986	Olfr1454	MOR202-14	olfactory receptor 1454	protein-coding
mm_7610.1	chr1	126492864	126492874	-	1	NA	promoter-TSS (NM_172484)	promoter-TSS (NM_172484)	58	NM_172484	210356	Mm.377234	NM_172484	ENSMUSG00000049690	Nckap5	8430408F21|D130011D22Rik|E030049G20Rik|Erih1|Erih2|Gm1548|Nap5	NCK-associated protein 5	protein-coding
mm_157685.1	chrX	60147837	60147870	-	1	NA	promoter-TSS (NM_133197)	promoter-TSS (NM_133197)	-153	NM_001289730	109904	Mm.93796	NM_133197	ENSMUSG00000031139	Mcf2	B230117G22Rik|Dbl|Mcf-2	mcf.2 transforming sequence	protein-coding
mm_32568.1	chr4	109753605	109753608	+	1	NA	intron (NM_007983, intron 6 of 18)	intron (NM_007983, intron 6 of 18)	76979	NM_007983	14084	Mm.318259	NM_007983	ENSMUSG00000010517	Faf1	AA408698|Dffrx|Fam	Fas-associated factor 1	protein-coding
mm_29704.1	chr3	123236135	123236157	-	1	NA	promoter-TSS (NM_080451)	promoter-TSS (NM_080451)	3	NM_080451	118449	Mm.34359	NM_080451	ENSMUSG00000050315	Synpo2	1110069I04Rik|2310068J10Rik|9530006G20Rik|AI848603|Myo	synaptopodin 2	protein-coding
mm_165071.1	chr19	44407583	44407599	-	1	NA	5' UTR (NM_009127, exon 1 of 6)	5' UTR (NM_009127, exon 1 of 6)	118	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_62455.1	chr7	101451248	101451321	+	1	NA	promoter-TSS (NM_001143849)	promoter-TSS (NM_001143849)	32	NM_001243757	207728	Mm.247564	NM_001008548	ENSMUSG00000030653	Pde2a	CGS-PDE|cGSPDE	phosphodiesterase 2A, cGMP-stimulated	protein-coding
mm_101691.1	chr11	40737338	40737348	-	1	NA	intron (NM_001290697, intron 3 of 3)	B4A|SINE|B4	3682	NM_001290697	52653	Mm.276504	NM_026023	ENSMUSG00000020328	Nudcd2	-	NudC domain containing 2	protein-coding
mm_57615.1	chr6	128143526	128143594	-	1	NA	promoter-TSS (NM_175414)	promoter-TSS (NM_175414)	18	NM_175414	109246	Mm.21814	NM_175414	ENSMUSG00000030352	Tspan9	6720474K14Rik|9430079M16Rik|AU018597	tetraspanin 9	protein-coding
mm_112131.1	chr12	112951578	112951582	-	1	NA	Intergenic	Intergenic	-9438	NM_001316724	66174	Mm.7070	NM_025399	ENSMUSG00000002804	Nudt14	1110030M18Rik|UGPPase	nudix (nucleoside diphosphate linked moiety X)-type motif 14	protein-coding
mm_39476.1	chr5	20228172	20228222	+	1	NA	intron (NM_001170746, intron 5 of 22)	intron (NM_001170746, intron 5 of 22)	320679	NM_015823	50791	Mm.332231	NM_015823	ENSMUSG00000040003	Magi2	AIP-1|Acvri1|Acvrinp1|Acvrip1|Magi-2|S-SCAM|mKIAA0705	membrane associated guanylate kinase, WW and PDZ domain containing 2	protein-coding
mm_89078.1	chr10	83344114	83344154	+	1	NA	Intergenic	Intergenic	-6317	NM_177388	338365	Mm.67073	NM_177388	ENSMUSG00000034591	Slc41a2	A230035L05Rik|SLC41A1-L1	solute carrier family 41, member 2	protein-coding
mm_155138.1	chrX	50841390	50841421	+	1	NA	promoter-TSS (NM_133729)	promoter-TSS (NM_133729)	34	NM_001313744	70415	Mm.46254	NM_133729	ENSMUSG00000031112	Stk26	2610018G03Rik|Mst4	serine/threonine kinase 26	protein-coding
mm_122044.1	chr14	30019909	30019914	-	1	NA	intron (NM_001136240, intron 1 of 7)	intron (NM_001136240, intron 1 of 7)	-1392	NM_172264	218865	Mm.259916	NM_172264	ENSMUSG00000015970	Chdh	AU041472|D630034H06Rik	choline dehydrogenase	protein-coding
mm_13846.1	chr2	119547804	119547816	+	1	NA	promoter-TSS (NM_172857)	promoter-TSS (NM_172857)	103	NM_019769	56398	Mm.214765	NM_019769	ENSMUSG00000014077	Chp1	1500003O03Rik|AA960066|AI046351|Cahp|Chp|Sid470p|p24|vac	calcineurin-like EF hand protein 1	protein-coding
mm_140316.1	chr17	86338583	86338595	+	1	NA	intron (NM_011104, intron 1 of 14)	intron (NM_011104, intron 1 of 14)	-51411	NR_045435	72104	Mm.443401	NR_045435	ENSMUSG00000100738	2010106C02Rik	-	RIKEN cDNA 2010106C02 gene	ncRNA
mm_79906.1	chr9	65412918	65412934	+	1	NA	TTS (NM_001033158)	TTS (NM_001033158)	9847	NM_178933	330962	Mm.335247	NM_178933	ENSMUSG00000053862	Slc51b	Ostb	solute carrier family 51, beta subunit	protein-coding
mm_171870.1	chr5	28538490	28538496	+	1	NA	intron (NR_015562, intron 1 of 6)	L1Md_F|LINE|L1	-71392	NM_009170	20423	Mm.57202	NM_009170	ENSMUSG00000002633	Shh	9530036O11Rik|Dsh|Hhg1|Hx|Hxl3|M100081	sonic hedgehog	protein-coding
mm_23022.1	chr3	34638217	34638228	+	1	NA	promoter-TSS (NR_035433)	promoter-TSS (NR_035433)	-242	NR_035433	100316679		NR_035433	ENSMUSG00000104797	Mir1897	Mirn1897|mmu-mir-1897	microRNA 1897	ncRNA
mm_54954.1	chr6	48684455	48684469	-	1	NA	promoter-TSS (NM_001243199)	promoter-TSS (NM_001243199)	-116	NM_001243200	107526	Mm.333048	NM_174990	ENSMUSG00000054435	Gimap4	AU019574|E430007K16Rik|Ian-1|Ian1|Imap4	GTPase, IMAP family member 4	protein-coding
mm_68890.1	chr7	126448337	126448346	-	1	NA	exon (NM_007504, exon 16 of 23)	exon (NM_007504, exon 16 of 23)	14732	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_67438.1	chr7	80387365	80387381	-	1	NA	intron (NM_010194, intron 1 of 18)	intron (NM_010194, intron 1 of 18)	573	NM_010194	14159	Mm.48757	NM_010194	ENSMUSG00000053158	Fes	AI586313|BB137047|FPS|c-fes	feline sarcoma oncogene	protein-coding
mm_164839.1	chr18	42052456	42052466	+	1	NA	Intergenic	Intergenic	-1249	NM_172966	269016	Mm.45472	NM_172966	ENSMUSG00000057719	Sh3rf2	2310046K19|9130023G24Rik|AI452083|Ppp1r39|RNF158	SH3 domain containing ring finger 2	protein-coding
mm_67836.1	chr7	98361496	98361504	-	1	NA	promoter-TSS (NM_001168539)	promoter-TSS (NM_001168539)	-172	NM_001168539	244152	Mm.25317	NM_001024619	ENSMUSG00000049580	Tsku	9530051K01Rik|E2ig4|Lrrc54|Tsk	tsukushi, small leucine rich proteoglycan	protein-coding
mm_53553.1	chr6	136873165	136873187	+	1	NA	exon (NM_008597, exon 3 of 4)	exon (NM_008597, exon 3 of 4)	2647	NM_008597	17313	Mm.243085	NM_008597	ENSMUSG00000030218	Mgp	Mglap	matrix Gla protein	protein-coding
mm_44757.1	chr5	31526667	31526684	-	1	NA	promoter-TSS (NM_009206)	promoter-TSS (NM_009206)	87	NM_028150	72195	Mm.164187	NM_028150	ENSMUSG00000053134	Supt7l	2610524B01Rik|6030455L14Rik	suppressor of Ty 7-like	protein-coding
mm_127505.1	chr15	101447806	101447814	+	1	NA	promoter-TSS (NM_025487)	promoter-TSS (NM_025487)	65	NM_025487	66322	Mm.158111	NM_025487	ENSMUSG00000063971	Krt88	1700011A15Rik	keratin 88	protein-coding
mm_102358.1	chr11	58323140	58323161	-	1	NA	promoter-TSS (NM_001256518)	promoter-TSS (NM_001256518)	-37	NM_001256518	319475	Mm.72124	NM_178761	ENSMUSG00000049755	Zfp672	4930488P06Rik|4930511N19Rik|Znf672	zinc finger protein 672	protein-coding
mm_126687.1	chr15	84923384	84923422	+	1	NA	promoter-TSS (NM_016714)	promoter-TSS (NM_016714)	-25	NM_016714	18141	Mm.28379	NM_016714	ENSMUSG00000016619	Nup50	1700030K07Rik|AI413123|Npap60	nucleoporin 50	protein-coding
mm_39958.1	chr5	32136459	32136505	+	1	NA	promoter-TSS (NM_008037)	promoter-TSS (NM_008037)	10	NM_008037	14284	Mm.24684	NM_008037	ENSMUSG00000029135	Fosl2	Fra-2	fos-like antigen 2	protein-coding
mm_114832.1	chr13	92355240	92355248	+	1	NA	promoter-TSS (NM_010829)	promoter-TSS (NM_010829)	-241	NM_010829	17686	Mm.343101	NM_010829	ENSMUSG00000014850	Msh3	D13Em1|Rep-3|Rep3	mutS homolog 3	protein-coding
mm_164646.1	chr17	35267487	35267497	-	1	NA	TTS (NM_001267808)	TTS (NM_001267808)	4369	NM_001267808	14980	Mm.439675	NM_001267808		H2-L	H-2L	histocompatibility 2, D region locus L	protein-coding
mm_80951.1	chr9	102988747	102988752	+	1	NA	Intergenic	Intergenic	-19740	NM_033314	24059	Mm.207106	NM_033314	ENSMUSG00000032548	Slco2a1	2310021C19Rik|Pgt|Slc21a2|mPgt	solute carrier organic anion transporter family, member 2a1	protein-coding
mm_12653.1	chr2	74825865	74825879	+	1	NA	promoter-TSS (NM_016804)	promoter-TSS (NM_016804)	60	NM_016804	53375	Mm.292613	NM_016804	ENSMUSG00000027099	Mtx2	1500012G02Rik	metaxin 2	protein-coding
mm_127945.1	chr15	10714693	10714792	-	1	NA	promoter-TSS (NM_001166408)	promoter-TSS (NM_001166408)	-94	NR_045063	75259	Mm.33928	NR_045063	ENSMUSG00000097058	4930556M19Rik	1700009D01Rik|C130022M03Rik	RIKEN cDNA 4930556M19 gene	ncRNA
mm_9264.1	chr1	171632163	171632167	-	1	NA	TTS (NM_144539)	TTS (NM_144539)	9735	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_167148.1	chr7	129447374	129447374	+	1	NA	Intergenic	Intergenic	-144489	NM_172255	207425	Mm.229323	NM_172255	ENSMUSG00000042055	Wdr11	2900055P10Rik|AW489876|Brwd2|mKIAA1351	WD repeat domain 11	protein-coding
mm_171799.1	chr5	123628196	123628199	+	1	NA	intron (NM_001291229, intron 9 of 23)	intron (NM_001291229, intron 9 of 23)	-55182	NM_029929	77573	Mm.41372	NM_029929	ENSMUSG00000029434	Vps33a	3830421M04Rik|AI503300|AW048546|AW554476|bf	VPS33A CORVET/HOPS core subunit	protein-coding
mm_68381.1	chr7	109175314	109175356	-	1	NA	promoter-TSS (NM_001302205)	promoter-TSS (NM_001302205)	-128	NM_001302205	109594	Mm.360145	NM_057173	ENSMUSG00000036111	Lmo1	Rbtn-1|Rbtn1|Ttg1	LIM domain only 1	protein-coding
mm_108465.1	chr12	83526044	83526069	+	1	NA	promoter-TSS (NM_001165256)	promoter-TSS (NM_001165256)	7	NM_001165256	73828	Mm.38238	NM_030246	ENSMUSG00000021222	Dcaf4	1110018E21Rik|Wdr21	DDB1 and CUL4 associated factor 4	protein-coding
mm_22812.1	chr3	27183771	27183804	+	1	NA	intron (NM_178772, intron 1 of 4)	intron (NM_178772, intron 1 of 4)	783	NM_178772	320024	Mm.24576	NM_178772	ENSMUSG00000027698	Nceh1	Aadacl1|B230106I24Rik|CPO-BP|Nceh	neutral cholesterol ester hydrolase 1	protein-coding
mm_95223.1	chr11	44414101	44414112	+	1	NA	3' UTR (NM_001303244, exon 8 of 8)	3' UTR (NM_001303244, exon 8 of 8)	14043	NM_001303244	16160	Mm.239707	NM_008352	ENSMUSG00000004296	Il12b	Il-12b|Il-12p40|Il12p40|p40	interleukin 12b	protein-coding
mm_1942.1	chr1	86303438	86303446	+	1	NA	5' UTR (NM_145222, exon 1 of 2)	5' UTR (NM_145222, exon 1 of 2)	221	NM_145222	227327	Mm.86467	NM_145222	ENSMUSG00000079445	B3gnt7	C330001H22Rik|beta-3GnT7	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 7	protein-coding
mm_109406.1	chr12	110447152	110447188	+	1	NA	promoter-TSS (NM_001135001)	promoter-TSS (NM_001135001)	-9	NM_001135001	26931	Mm.240396	NM_012023	ENSMUSG00000017843	Ppp2r5c	2610043M05Rik|2700063L20Rik|AI060890|AW545884|C85228|D12Bwg0916e|mKIAA0044	protein phosphatase 2, regulatory subunit B', gamma	protein-coding
mm_115226.1	chr13	109837793	109837806	+	1	NA	intron (NM_011056, intron 7 of 16)	intron (NM_011056, intron 7 of 16)	-66010	NR_035442	100316683		NR_035442	ENSMUSG00000084651	Mir1904	Mirn1904|mmu-mir-1904	microRNA 1904	ncRNA
mm_31341.1	chr4	46472571	46472575	+	1	NA	TTS (NM_130889)	TTS (NM_130889)	-16756	NM_053179	94181	Mm.249349	NM_053179	ENSMUSG00000028334	Nans	4632418E04Rik|BB056474|Sas	N-acetylneuraminic acid synthase (sialic acid synthase)	protein-coding
mm_20290.1	chr2	126931902	126931906	-	1	NA	intron (NM_023220, intron 1 of 14)	intron (NM_023220, intron 1 of 14)	1331	NM_023220	66552	Mm.269928	NM_023220	ENSMUSG00000027366	Sppl2a	2010106G01Rik|C130089K23Rik	signal peptide peptidase like 2A	protein-coding
mm_80479.1	chr9	78204292	78204307	+	1	NA	exon (NM_010357, exon 4 of 7)	exon (NM_010357, exon 4 of 7)	12333	NM_010357	14860	Mm.2662	NM_010357	ENSMUSG00000032348	Gsta4	GST5.7|mGsta4	glutathione S-transferase, alpha 4	protein-coding
mm_86598.1	chr10	13304958	13304982	+	1	NA	intron (NM_001195065, intron 1 of 12)	intron (NM_001195065, intron 1 of 12)	19190	NM_001195096	215789	Mm.283359	NM_001033257	ENSMUSG00000062866	Phactr2	AV158170|BC012871	phosphatase and actin regulator 2	protein-coding
mm_105241.1	chr11	102319383	102319446	-	1	NA	promoter-TSS (NM_001302954)	promoter-TSS (NM_001302954)	-318	NM_011551	21429	Mm.2845	NM_011551	ENSMUSG00000020923	Ubtf	A930005G04Rik|NOR-90|Tcfubf|UBF|UBF-1|UBF1	upstream binding transcription factor, RNA polymerase I	protein-coding
mm_130649.1	chr15	100636704	100636735	-	1	NA	non-coding (NR_104338, exon 1 of 4)	non-coding (NR_104338, exon 1 of 4)	221	NR_104338	207818	Mm.26282	NM_174992	ENSMUSG00000053559	Smagp	-	small cell adhesion glycoprotein	protein-coding
mm_24263.1	chr3	89187820	89187830	+	1	NA	intron (NM_001014995, intron 9 of 11)	intron (NM_001014995, intron 9 of 11)	4600	NM_001014995	68521	Mm.274708	NM_001014995	ENSMUSG00000032657	Fam189b	1110013L07Rik	family with sequence similarity 189, member B	protein-coding
mm_33209.1	chr4	126556964	126556966	+	1	NA	promoter-TSS (NM_175554)	promoter-TSS (NM_175554)	-15	NM_175554	269582	Mm.243962	NM_175554	ENSMUSG00000042489	Clspn	B130025E01|C85083|E130314M08Rik	claspin	protein-coding
mm_154545.1	chrM	14770	14783	-	1	NA	NA	Intergenic	NA	NA								
mm_129172.1	chr15	76249506	76249539	-	1	NA	3' UTR (NM_023168, exon 7 of 7)	3' UTR (NM_023168, exon 7 of 7)	1331	NR_105918	102465575		NR_105918	ENSMUSG00000098625	Mir6953	Gm27738|mmu-mir-6953	microRNA 6953	ncRNA
mm_1805.1	chr1	80758147	80758157	+	1	NA	intron (NM_175291, intron 1 of 55)	CpG	401	NM_175291	210293	Mm.133473	NM_175291	ENSMUSG00000038608	Dock10	9330153B10Rik|A630054M16Rik|Jr4|Jr5|R75174|ZIZ3|Zizimin3|mKIAA0694	dedicator of cytokinesis 10	protein-coding
mm_86970.1	chr10	25377579	25377594	+	1	NA	intron (NM_001199265, intron 1 of 19)	ORR1A2|LTR|ERVL-MaLR	17788	NM_001199265	13822	Mm.306026	NM_013511	ENSMUSG00000019978	Epb41l2	4.1G|AW555191|D10Ertd398e|Epb4.1l2|NBL2	erythrocyte membrane protein band 4.1 like 2	protein-coding
mm_110551.1	chr12	55490437	55490458	-	1	NA	exon (NM_010907, exon 5 of 6)	exon (NM_010907, exon 5 of 6)	2200	NM_010907	18035	Mm.170515	NM_010907	ENSMUSG00000021025	Nfkbia	AI462015|Nfkbi	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, alpha	protein-coding
mm_124694.1	chr15	6438943	6438966	+	1	NA	3' UTR (NM_001102400, exon 13 of 13)	3' UTR (NM_001102400, exon 13 of 13)	-6379	NM_013485	12279	Mm.29095	NM_013485	ENSMUSG00000022149	C9	-	complement component 9	protein-coding
mm_90111.1	chr10	117277386	117277408	+	1	NA	TTS (NM_017372)	TTS (NM_017372)	4875	NM_017372	17105	Mm.45436	NM_017372	ENSMUSG00000069516	Lyz2	AI326280|Lys|Lysm|Lyzf2|Lyzs|Lzm|Lzm-s1|Lzp	lysozyme 2	protein-coding
mm_11968.1	chr2	53605145	53605152	+	1	NA	Intergenic	Intergenic	413064	NM_022989	65103	Mm.37623	NM_022989	ENSMUSG00000026960	Arl6ip6	2310057C01Rik|2610529A11Rik|Aip-6	ADP-ribosylation factor-like 6 interacting protein 6	protein-coding
mm_23482.1	chr3	60496212	60496259	+	1	NA	intron (NM_001253713, intron 2 of 9)	intron (NM_001253713, intron 2 of 9)	-4944	NM_001253711	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_38887.1	chr4	149738056	149738077	-	1	NA	promoter-TSS (NM_177672)	promoter-TSS (NM_177672)	2	NM_001284270	230917	Mm.266704	NM_177672	ENSMUSG00000044700	Tmem201	AV028368|D4Ertd429e|Net5|Samp1	transmembrane protein 201	protein-coding
mm_156557.1	chrX	151801164	151801203	+	1	NA	Intergenic	Intergenic	-2099	NM_021523	59026	Mm.27372	NM_021523	ENSMUSG00000025261	Huwe1	5430439H10Rik|AU041296|Arf-bp1|C430014N20Rik|C80292|Gm1718|Ib772|LASU1|Mule|Ureb1	HECT, UBA and WWE domain containing 1	protein-coding
mm_19017.1	chr2	76908047	76908066	-	1	NA	exon (NM_028004, exon 45 of 192)	exon (NM_028004, exon 45 of 192)	74491	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_151104.1	chr19	47860738	47860748	+	1	NA	intron (NM_010362, intron 4 of 5)	intron (NM_010362, intron 4 of 5)	-4802	NM_030051	68214	Mm.63791	NM_026619	ENSMUSG00000025069	Gsto2	1700020F09Rik|4930425C18Rik|GSTO 2-2	glutathione S-transferase omega 2	protein-coding
mm_48568.1	chr5	143315026	143315110	-	1	NA	exon (NM_172726, exon 1 of 6)	exon (NM_172726, exon 1 of 6)	292	NM_172726	231868	Mm.440105	NM_172726	ENSMUSG00000039244	E130309D02Rik	A630028N22	RIKEN cDNA E130309D02 gene	protein-coding
mm_12602.1	chr2	74679669	74679681	+	1	NA	non-coding (NR_073086, exon 1 of 2)	non-coding (NR_073086, exon 1 of 2)	117	NR_073086	15431	Mm.207763	NM_008273	ENSMUSG00000042499	Hoxd11	E230017H14Rik|Hox-4.6|Hox-5.4|Hox-5.5	homeobox D11	protein-coding
mm_12368.1	chr2	69821811	69821857	+	1	NA	promoter-TSS (NM_177784)	promoter-TSS (NM_177784)	-536	NM_177784	277396	Mm.138073	NM_177784	ENSMUSG00000042155	Klhl23	C130068N17Rik	kelch-like 23	protein-coding
mm_156059.1	chrX	109154340	109154363	+	1	NA	exon (NM_019989, exon 3 of 4)	exon (NM_019989, exon 3 of 4)	-42405	NM_001037917	622976	Mm.482747	NM_001037917	ENSMUSG00000048621	Gm6377	EG622976	predicted gene 6377	protein-coding
mm_9996.1	chr1	191397027	191397041	-	1	NA	promoter-TSS (NM_144880)	promoter-TSS (NM_144880)	7	NM_144880	226849	Mm.205569	NM_144880	ENSMUSG00000026626	Ppp2r5a	PR61alpha	protein phosphatase 2, regulatory subunit B', alpha	protein-coding
mm_9854.1	chr1	184735021	184735027	-	1	NA	Intergenic	Intergenic	-2531	NM_008250	15284	Mm.1347	NM_008250	ENSMUSG00000039377	Hlx	Hlx1	H2.0-like homeobox	protein-coding
mm_125355.1	chr15	39391854	39391898	+	1	NA	intron (NM_001256382, intron 3 of 26)	intron (NM_001256382, intron 3 of 26)	193590	NM_053271	116838	Mm.309296	NM_053271	ENSMUSG00000037386	Rims2	2810036I15Rik|AW048769|RIM2|Rab3ip2|Rim2(+40A)|Rim2(+44A)|Rim2(+4A)|Serg2|Syt3-rs|mKIAA0751	regulating synaptic membrane exocytosis 2	protein-coding
mm_97835.1	chr11	83064978	83064984	+	1	NA	promoter-TSS (NM_011408)	promoter-TSS (NM_011408)	-131	NM_011408	20556	Mm.278689	NM_011408	ENSMUSG00000072620	Slfn2	Shlf2	schlafen 2	protein-coding
mm_108170.1	chr12	76404386	76404396	+	1	NA	promoter-TSS (NM_008301)	promoter-TSS (NM_008301)	21	NM_008301	15512	Mm.296181	NM_008301	ENSMUSG00000059970	Hspa2	70kDa|HSP70.2|HSP70A2|Hsp70-2	heat shock protein 2	protein-coding
mm_158798.1	chrX	167244084	167244105	-	1	NA	exon (NM_001313760, exon 2 of 2)	exon (NM_001313760, exon 2 of 2)	20235	NM_001313761	170744	Mm.196676	NM_133212	ENSMUSG00000040522	Tlr8	-	toll-like receptor 8	protein-coding
mm_111581.1	chr12	101819082	101819106	-	1	NA	promoter-TSS (NM_011812)	promoter-TSS (NM_011812)	25	NM_011812	23876	Mm.288381	NM_011812	ENSMUSG00000021186	Fbln5	A55|DANCE|EVEC	fibulin 5	protein-coding
mm_165143.1	chr2	18672202	18672268	+	1	NA	promoter-TSS (NM_147778)	promoter-TSS (NM_147778)	-227	NM_147778	12238	Mm.249586	NM_147778	ENSMUSG00000051154	Commd3	AW550818|Bup|D2Ertd542e	COMM domain containing 3	protein-coding
mm_156336.1	chrX	139009651	139009661	+	1	NA	TTS (NM_013724)	TTS (NM_013724)	75580	NM_177920	331535	Mm.211704	NM_177920	ENSMUSG00000031271	Serpina7	C730040N12Rik|Tbg	serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 7	protein-coding
mm_125835.1	chr15	74958259	74958370	+	1	NA	exon (NM_001164036, exon 3 of 4)	exon (NM_001164036, exon 3 of 4)	3208	NM_001164040	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_89364.1	chr10	88459657	88459670	+	1	NA	promoter-TSS (NM_011517)	promoter-TSS (NM_011517)	76	NM_011517	20962	Mm.297977	NM_011517	ENSMUSG00000020059	Sycp3	Cor1|Scp3	synaptonemal complex protein 3	protein-coding
mm_35526.1	chr4	41275297	41275309	-	1	NA	promoter-TSS (NM_026872)	promoter-TSS (NM_026872)	-168	NM_026872	68926	Mm.41864	NM_026872	ENSMUSG00000028433	Ubap2	1190005K07Rik|AA408600|AU045235|UBAP-2|mKIAA1491	ubiquitin-associated protein 2	protein-coding
mm_68411.1	chr7	109637495	109637510	-	1	NA	Intergenic	Intergenic	-20355	NM_029811	76954	Mm.252009	NM_029811	ENSMUSG00000031024	St5	2010004M01Rik|2610305K15Rik	suppression of tumorigenicity 5	protein-coding
mm_107510.1	chr12	40108413	40108434	+	1	NA	intron (NM_009132, intron 3 of 13)	intron (NM_009132, intron 3 of 13)	25805	NM_009132	20259	Mm.2416	NM_009132	ENSMUSG00000002565	Scin	AW545522|adseverin	scinderin	protein-coding
mm_135730.1	chr16	55831225	55831244	-	1	NA	intron (NM_030612, intron 2 of 13)	B4|SINE|B4	7407	NM_030612	80859	Mm.247272	NM_030612	ENSMUSG00000035356	Nfkbiz	AA408868|INAP|Mail	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, zeta	protein-coding
mm_133413.1	chr16	85132408	85132453	+	1	NA	intron (NM_007471, intron 1 of 15)	intron (NM_007471, intron 1 of 15)	41277	NM_001198825	11820	Mm.277585	NM_007471	ENSMUSG00000022892	App	Abeta|Abpp|Adap|Ag|Cvap|E030013M08Rik|betaApp	amyloid beta (A4) precursor protein	protein-coding
mm_131855.1	chr16	23069281	23069291	+	1	NA	exon (NM_001102411, exon 5 of 10)	exon (NM_001102411, exon 5 of 10)	10986	NM_001102412	16644	Mm.2160	NM_023125	ENSMUSG00000022875	Kng1	Kng	kininogen 1	protein-coding
mm_126912.1	chr15	90883048	90883056	+	1	NA	Intergenic	Intergenic	15424	NR_033583	20738	Mm.431547	NR_033583		Spn-ps	Cd43-ps	sialophorin, pseudogene	pseudo
mm_26280.1	chr3	142505633	142505644	+	1	NA	exon (NM_153564, exon 7 of 11)	exon (NM_153564, exon 7 of 11)	8704	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_63072.1	chr7	122164068	122164086	+	1	NA	exon (NM_011121, exon 5 of 10)	exon (NM_011121, exon 5 of 10)	4642	NM_011121	18817	Mm.16525	NM_011121	ENSMUSG00000030867	Plk1	Plk|STPK13	polo-like kinase 1	protein-coding
mm_68231.1	chr7	104463631	104463676	-	1	NA	intron (NM_009099, intron 1 of 7)	RLTR20A4|LTR|ERVK	1540	NM_009099	20128	Mm.295578	NM_009099	ENSMUSG00000030921	Trim30a	Rpt-1|Rpt1|Trim30	tripartite motif-containing 30A	protein-coding
mm_156228.1	chrX	135801185	135801196	+	1	NA	exon (NM_026081, exon 11 of 11)	exon (NM_026081, exon 11 of 11)	-37844	NM_001163016	245607	Mm.489763	NM_001163015	ENSMUSG00000072966	Gprasp2	5330440H13Rik|GASP-2|GASP2|Prpl5	G protein-coupled receptor associated sorting protein 2	protein-coding
mm_61120.1	chr7	55132010	55132012	+	1	NA	intron (NM_178705, intron 5 of 11)	intron (NM_178705, intron 5 of 11)	296766	NM_178705	233271	Mm.387344	NM_178705	ENSMUSG00000063297	Luzp2	9330154K17Rik|D130073E01	leucine zipper protein 2	protein-coding
mm_51936.1	chr6	91690394	91690440	+	1	NA	intron (NM_009320, intron 1 of 14)	intron (NM_009320, intron 1 of 14)	6350	NM_009320	21366	Mm.395650	NM_009320	ENSMUSG00000030096	Slc6a6	AA589629|C80501|Taut	solute carrier family 6 (neurotransmitter transporter, taurine), member 6	protein-coding
mm_22099.1	chr2	169155702	169155728	-	1	NA	Intergenic	Intergenic	177446	NR_040326	75508	Mm.271256	NR_040326	ENSMUSG00000086348	1700017J07Rik	-	RIKEN cDNA 1700017J07 gene	ncRNA
mm_85647.1	chr9	107656622	107656639	-	1	NA	exon (NM_001199218, exon 8 of 16)	exon (NM_001199218, exon 8 of 16)	10769	NM_023805	76257	Mm.296560	NM_023805	ENSMUSG00000010064	Slc38a3	0610012J02Rik|D9Ucla2|Nat1|Slc38-3|Sn1|Snat3|mNAT	solute carrier family 38, member 3	protein-coding
mm_59275.1	chr7	24904340	24904351	+	1	NA	promoter-TSS (NM_001130152)	promoter-TSS (NM_001130152)	-1	NM_001130152	16801	Mm.3181	NM_008488	ENSMUSG00000040940	Arhgef1	Lbcl2|Lsc	Rho guanine nucleotide exchange factor (GEF) 1	protein-coding
mm_1125.1	chr1	60180566	60180618	+	1	NA	promoter-TSS (NM_173444)	promoter-TSS (NM_173444)	-7	NM_173444	269198	Mm.205224	NM_173444	ENSMUSG00000073664	Nbeal1	2310076G13Rik|A530050O19Rik|A530083I02Rik|AI662228|ALS2CR17	neurobeachin like 1	protein-coding
mm_99149.1	chr11	100554000	100554018	+	1	NA	exon (NM_028918, exon 7 of 12)	exon (NM_028918, exon 7 of 12)	8377	NM_028918	74407	Mm.31590	NM_028918	ENSMUSG00000006784	Ttc25	4933404O19Rik	tetratricopeptide repeat domain 25	protein-coding
mm_168155.1	chr10	42055414	42055415	-	1	NA	Intergenic	Intergenic	-37032	NM_001034858	213402	Mm.211320	NM_001034858	ENSMUSG00000071324	Armc2	2610018I05Rik	armadillo repeat containing 2	protein-coding
mm_79556.1	chr9	58014991	58015005	+	1	NA	promoter-TSS (NM_019779)	promoter-TSS (NM_019779)	46	NM_019779	13070	Mm.302865	NM_019779	ENSMUSG00000032323	Cyp11a1	Cyp11a|Cypxia1|D9Ertd411e|P450scc|Scc|cscc	cytochrome P450, family 11, subfamily a, polypeptide 1	protein-coding
mm_168576.1	chr1	171494495	171494504	+	1	NA	Intergenic	Intergenic	-8979	NM_019484	56009	Mm.389208	NM_019484	ENSMUSG00000060244	Alyref2	C130042O11Rik|REF2|Refbp2	Aly/REF export factor 2	protein-coding
mm_77262.1	chr8	115707569	115707609	-	1	NA	promoter-TSS (NM_001025577)	promoter-TSS (NM_001025577)	-695	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_94709.1	chr11	20453100	20453114	+	1	NA	Intergenic	Intergenic	-90146	NM_021372	58172	Mm.339676	NM_021372	ENSMUSG00000049800	Sertad2	AB041541|AU021878|Kiaa0127|MNCb-1504|SEI-2|Sei2|TRIP-Br2|mKIAA0127	SERTA domain containing 2	protein-coding
mm_24134.1	chr3	88218242	88218246	+	1	NA	Intergenic	PB1D7|SINE|Alu	2646	NR_029817	387133		NR_029817	ENSMUSG00000106493	Mir9-1	Mirn9|Mirn9-1|mir-9-1|mmu-mir-9-1	microRNA 9-1	ncRNA
mm_119815.1	chr14	54224034	54224047	+	1	NA	Intergenic	Intergenic	29889	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_7932.1	chr1	133911497	133911508	-	1	NA	3' UTR (NM_054077, exon 3 of 3)	3' UTR (NM_054077, exon 3 of 3)	-3503	NM_001160420	269120	Mm.59985	NM_054076	ENSMUSG00000010311	Optc	-	opticin	protein-coding
mm_2123.1	chr1	87901222	87901232	+	1	NA	intron (NM_177646, intron 3 of 29)	intron (NM_177646, intron 3 of 29)	-46928	NR_136921	100503175	Mm.426422	NR_136921	ENSMUSG00000101942	Gm19582	-	predicted gene, 19582	ncRNA
mm_137619.1	chr17	28280283	28280291	+	1	NA	intron (NM_011145, intron 2 of 7)	intron (NM_011145, intron 2 of 7)	-6665	NR_039557	100628577		NR_039557	ENSMUSG00000093061	Mir5098	mmu-mir-5098|mu-mir-5098	microRNA 5098	ncRNA
mm_46181.1	chr5	97111590	97111632	-	1	NA	promoter-TSS (NM_198422)	promoter-TSS (NM_198422)	-15	NM_198422	231474	Mm.332505	NM_198422	ENSMUSG00000055725	Paqr3	6330415A20Rik|AY424292|RKTG	progestin and adipoQ receptor family member III	protein-coding
mm_107947.1	chr12	72212284	72212296	+	1	NA	non-coding (NR_104446, exon 7 of 7)	non-coding (NR_104446, exon 7 of 7)	23456	NR_104446	104001	Mm.221275	NM_153457	ENSMUSG00000021087	Rtn1	Nsp	reticulon 1	protein-coding
mm_49921.1	chr6	39205513	39205526	+	1	NA	intron (NM_001033430, intron 1 of 19)	CpG	1254	NM_001033430	338523	Mm.293175	NM_001033430	ENSMUSG00000042599	Kdm7a	A630082K20Rik|BB041802|ENSMUSG00000073143|Jhdm1d|mKIAA1718	lysine (K)-specific demethylase 7A	protein-coding
mm_137697.1	chr17	29040992	29041002	+	1	NA	intron (NR_036613, intron 5 of 6)	B2_Mm2|SINE|B2	8337	NR_036613	20383	Mm.6787	NM_013663	ENSMUSG00000071172	Srsf3	AL024116|Sfrs3|X16	serine/arginine-rich splicing factor 3	protein-coding
mm_16628.1	chr2	5697882	5697899	-	1	NA	intron (NM_001290374, intron 1 of 9)	B4|SINE|B4	16872	NM_001290374	227541	Mm.191949	NM_177343	ENSMUSG00000039145	Camk1d	A630059D12Rik|CKLiK|CaMKIdelta|E030025C11Rik|mCKLiK	calcium/calmodulin-dependent protein kinase ID	protein-coding
mm_16763.1	chr2	9877987	9878016	-	1	NA	intron (NM_008091, intron 1 of 5)	intron (NM_008091, intron 1 of 5)	599	NM_008091	14462	Mm.313866	NM_008091	ENSMUSG00000015619	Gata3	Gata-3|jal	GATA binding protein 3	protein-coding
mm_60122.1	chr7	36696627	36696678	+	1	NA	Intergenic	CpG	-1466	NM_172298	243931	Mm.44141	NM_172298	ENSMUSG00000021217	Tshz3	A630038G13Rik|Tsh3|Zfp537|mKIAA1474|teashirt3	teashirt zinc finger family member 3	protein-coding
mm_107529.1	chr12	40504183	40504186	+	1	NA	intron (NM_172803, intron 1 of 52)	L1M2|LINE|L1	58131	NM_172803	238130	Mm.341423	NM_172803	ENSMUSG00000035954	Dock4	5330406C03|6330411N01Rik|AF263288|C030023J22|mKIAA0716	dedicator of cytokinesis 4	protein-coding
mm_103134.1	chr11	70237762	70237781	-	1	NA	TTS (NM_173742)	TTS (NM_173742)	143	NM_001177601	104457	Mm.30016	NM_026757	ENSMUSG00000020831	0610010K14Rik	1110020A23Rik|AL033328|AU045833|Bap18	RIKEN cDNA 0610010K14 gene	protein-coding
mm_145815.1	chr18	65430946	65430973	+	1	NA	promoter-TSS (NM_172833)	promoter-TSS (NM_172833)	-38	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_117893.1	chr13	99422913	99422927	-	1	NA	3' UTR (NM_008634, exon 7 of 7)	3' UTR (NM_008634, exon 7 of 7)	-10094	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_89033.1	chr10	82764263	82764277	+	1	NA	promoter-TSS (NM_010914)	promoter-TSS (NM_010914)	-129	NM_010914	18045	Mm.245998	NM_010914	ENSMUSG00000020248	Nfyb	AA985999|Cbf-A	nuclear transcription factor-Y beta	protein-coding
mm_78618.1	chr9	37555646	37555656	+	1	NA	Intergenic	Intergenic	-2906	NM_022029	64011	Mm.335065	NM_022029	ENSMUSG00000053310	Nrgn	0710001B06Rik|AI838505|NG|NG/RC3|Pss1|R75334|RC3	neurogranin	protein-coding
mm_24126.1	chr3	88206526	88206537	+	1	NA	Intergenic	Intergenic	-8640	NR_037276	100526540		NR_037276	ENSMUSG00000092988	Mir3093	mir-3093|mmu-mir-3093	microRNA 3093	ncRNA
mm_164138.1	chr15	53194158	53194158	+	1	NA	intron (NM_010162, intron 1 of 10)	intron (NM_010162, intron 1 of 10)	152025	NM_010162	14042	Mm.309395	NM_010162	ENSMUSG00000061731	Ext1	AA409028	exostoses (multiple) 1	protein-coding
mm_29422.1	chr3	108976694	108976702	-	1	NA	intron (NM_001163567, intron 10 of 10)	intron (NM_001163567, intron 10 of 10)	36141	NM_001078646	66715	Mm.158124	NM_025723	ENSMUSG00000045662	Henmt1	4921515J06Rik|Hen1|mHEN1	HEN1 methyltransferase homolog 1 (Arabidopsis)	protein-coding
mm_36701.1	chr4	96664209	96664219	-	1	NA	promoter-TSS (NM_010007)	promoter-TSS (NM_010007)	-95	NM_010007	13109	Mm.12838	NM_010007	ENSMUSG00000052520	Cyp2j5	-	cytochrome P450, family 2, subfamily j, polypeptide 5	protein-coding
mm_2387.1	chr1	93501569	93501581	+	1	NA	exon (NM_010891, exon 9 of 13)	exon (NM_010891, exon 9 of 13)	-10529	NM_145519	227377	Mm.243091	NM_145519	ENSMUSG00000034066	Farp2	AI465173|BC009153|D030026M03Rik|Fir|mKIAA0793	FERM, RhoGEF and pleckstrin domain protein 2	protein-coding
mm_129092.1	chr15	75921464	75921533	-	1	NA	promoter-TSS (NM_025412)	promoter-TSS (NM_025412)	62	NM_025412	66194	Mm.250599	NM_025412	ENSMUSG00000022571	Pycrl	1110058B13Rik|2700073G24Rik	pyrroline-5-carboxylate reductase-like	protein-coding
mm_116176.1	chr13	30820660	30820669	-	1	NA	intron (NM_025588, intron 25 of 27)	intron (NM_025588, intron 25 of 27)	71431	NM_013674	16364	Mm.4677	NM_013674	ENSMUSG00000021356	Irf4	AI385587|IRF-4|LSIRF|NF-EM5|Spip	interferon regulatory factor 4	protein-coding
mm_171774.1	chr5	109751732	109751738	-	1	NA	Intergenic	Intergenic	82407	NR_027964	667213	Mm.454429	NR_027964	ENSMUSG00000105044	Gm10416	EG667213|ENSMUSG00000072761	zinc finger protein pseudogene	pseudo
mm_169057.1	chr13	23324634	23324652	-	1	NA	intron (NR_131052, intron 2 of 3)	RLTRETN_Mm|LTR|ERVK	11118	NR_131052	75887	Mm.416957	NR_131052	ENSMUSG00000087097	4930586N03Rik	-	RIKEN cDNA 4930586N03 gene	ncRNA
mm_134618.1	chr16	21063160	21063204	-	1	NA	Intergenic	Intergenic	90762	NM_025634	66561	Mm.422867	NM_025634	ENSMUSG00000090356	Teddm3	2310042E22Rik	transmembrane epididymal family member 3	protein-coding
mm_149640.1	chr19	17399609	17399622	+	1	NA	3' UTR (NM_019437, exon 4 of 4)	3' UTR (NM_019437, exon 4 of 4)	5572	NM_019437	54391	Mm.7013	NM_019437	ENSMUSG00000024712	Rfk	0610038L10Rik|AF031381|KOI-4	riboflavin kinase	protein-coding
mm_170819.1	chr2	176520967	176520983	+	1	NA	promoter-TSS (NM_001177404).3	promoter-TSS (NM_001177404).3	-29	NM_001177405	667962	Mm.422667	NM_001177405	ENSMUSG00000089756	Zfp966	Gm8898|OTTMUSG00000016203	zinc finger protein 966	protein-coding
mm_57561.1	chr6	127109518	127109569	-	1	NA	promoter-TSS (NM_177003)	promoter-TSS (NM_177003)	9	NM_177003	319801	Mm.101836	NM_177003	ENSMUSG00000038028	Tigar	9630033F20Rik|AA793651|AI595337|C79710|C85509	Trp53 induced glycolysis repulatory phosphatase	protein-coding
mm_142597.1	chr17	46763692	46763708	-	1	NA	promoter-TSS (NM_011195)	promoter-TSS (NM_011195)	12	NM_011195	19208	Mm.215173	NM_011195	ENSMUSG00000036858	Ptcra	gp33|pT-alpha|pT-alpha-TCR|pT[a]|pTa|pTalpha	pre T cell antigen receptor alpha	protein-coding
mm_18636.1	chr2	69383035	69383046	-	1	NA	intron (NM_175512, intron 1 of 4)	intron (NM_175512, intron 1 of 4)	2578	NM_175512	241452	Mm.211655	NM_175512	ENSMUSG00000027068	Dhrs9	C730025I08Rik|Rdh15	dehydrogenase/reductase (SDR family) member 9	protein-coding
mm_106603.1	chr11	120748001	120748003	-	1	NA	Intergenic	RMER16_Mm|LTR|ERVK	-15981	NM_007621	12409	Mm.21454	NM_007621	ENSMUSG00000025150	Cbr2	MLCR	carbonyl reductase 2	protein-coding
mm_70480.1	chr8	12395671	12395682	+	1	NA	5' UTR (NM_009233, exon 1 of 1)	5' UTR (NM_009233, exon 1 of 1)	157	NM_009233	20664	Mm.39088	NM_009233	ENSMUSG00000096014	Sox1	BB176347|Sox-1	SRY (sex determining region Y)-box 1	protein-coding
mm_162667.1	chr10	7063131	7063141	-	1	NA	Intergenic	Intergenic	-39951	NM_001033391	320495	Mm.331674	NM_001033391	ENSMUSG00000064065	Ipcef1	A130090K04Rik	interaction protein for cytohesin exchange factors 1	protein-coding
mm_18266.1	chr2	52319240	52319247	-	1	NA	intron (NM_010889, intron 10 of 156)	intron (NM_010889, intron 10 of 156)	19555	NM_010889	17996	Mm.389247	NM_010889	ENSMUSG00000026950	Neb	AI595938	nebulin	protein-coding
mm_22235.1	chr2	174438941	174438959	-	1	NA	promoter-TSS (NM_022325)	promoter-TSS (NM_022325)	89	NM_022325	64138	Mm.156919	NM_022325	ENSMUSG00000016256	Ctsz	AI787083|AU019819|CTSX|D2Wsu143e	cathepsin Z	protein-coding
mm_84966.1	chr9	83806265	83806281	-	1	NA	promoter-TSS (NM_148941)	promoter-TSS (NM_148941)	32	NM_148941	83603	Mm.83949	NM_148941	ENSMUSG00000032262	Elovl4	-	elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 4	protein-coding
mm_156579.1	chrX	152026350	152026367	+	1	NA	exon (NM_019710, exon 4 of 25)	exon (NM_019710, exon 4 of 25)	9930	NM_019710	24061	Mm.482095	NM_019710	ENSMUSG00000041133	Smc1a	5830426I24Rik|SMC-1A|Sb1.8|Smc1|Smc1alpha|Smc1l1|Smcb|mKIAA0178	structural maintenance of chromosomes 1A	protein-coding
mm_119865.1	chr14	54476213	54476228	+	1	NA	5' UTR (NM_080726, exon 1 of 5)	5' UTR (NM_080726, exon 1 of 5)	120	NM_080726	140743	Mm.274727	NM_080726	ENSMUSG00000022176	Rem2	AW411893	rad and gem related GTP binding protein 2	protein-coding
mm_11753.1	chr2	38473125	38473136	+	1	NA	Intergenic	Intergenic	-38567	NM_021606	59126	Mm.143818	NM_021606	ENSMUSG00000026749	Nek6	1300007C09Rik	NIMA (never in mitosis gene a)-related expressed kinase 6	protein-coding
mm_81128.1	chr9	106484482	106484493	+	1	NA	exon (NM_145620, exon 13 of 15)	exon (NM_145620, exon 13 of 15)	7178	NM_145620	27966	Mm.239997	NM_145620	ENSMUSG00000041506	Rrp9	55kDa|D19435|D9Wsu10e|Rnu3ip2|U3-55k	RRP9, small subunit (SSU) processome component, homolog (yeast)	protein-coding
mm_1150.1	chr1	60771614	60771616	+	1	NA	3' UTR (NM_007642, exon 4 of 4)	3' UTR (NM_007642, exon 4 of 4)	25227	NM_007642	12487	Mm.255003	NM_007642	ENSMUSG00000026012	Cd28	-	CD28 antigen	protein-coding
mm_45047.1	chr5	41707970	41708014	-	1	NA	promoter-TSS (NM_001310592)	promoter-TSS (NM_001310592)	187	NR_132325	100972	Mm.41555	NM_027295	ENSMUSG00000029128	Rab28	2700023P08Rik|AW496496	RAB28, member RAS oncogene family	protein-coding
mm_158260.1	chrX	109013345	109013371	-	1	NA	promoter-TSS (NM_016710)	promoter-TSS (NM_016710)	22	NM_016710	50887	Mm.298443	NM_016710	ENSMUSG00000031245	Hmgn5	GARP45|NBP-45|Nsbp1	high-mobility group nucleosome binding domain 5	protein-coding
mm_110019.1	chr12	16740204	16740257	-	1	NA	5' UTR (NM_015764, exon 4 of 35)	5' UTR (NM_015764, exon 4 of 35)	17009	NM_001252071	268527	Mm.428062	NM_015764	ENSMUSG00000036523	Greb1	5730583K22Rik|9130004E13|AF180470|AU023194|mKIAA0575	gene regulated by estrogen in breast cancer protein	protein-coding
mm_29366.1	chr3	108704460	108704476	-	1	NA	intron (NM_029522, intron 2 of 14)	Lx8|LINE|L1	17831	NM_029522	76123	Mm.226941	NM_029522	ENSMUSG00000027883	Gpsm2	6230410J09Rik|LGN|Pins	G-protein signalling modulator 2 (AGS3-like, C. elegans)	protein-coding
mm_122054.1	chr14	30217006	30217009	-	1	NA	intron (NM_001302637, intron 3 of 48)	intron (NM_001302637, intron 3 of 48)	136479	NM_001302637	12289	Mm.9772	NM_028981	ENSMUSG00000015968	Cacna1d	8430418G19Rik|C79217|Cach3|Cacn4|Cacnl1a2|Cav1.3|Cchl1a|Cchl1a2|D-LTCC	calcium channel, voltage-dependent, L type, alpha 1D subunit	protein-coding
mm_8462.1	chr1	153262468	153262485	-	1	NA	exon (NM_010683, exon 2 of 28)	exon (NM_010683, exon 2 of 28)	70310	NM_010683	226519	Mm.1249	NM_010683	ENSMUSG00000026478	Lamc1	Lamb2	laminin, gamma 1	protein-coding
mm_165632.1	chr3	68824893	68824893	-	1	NA	Intergenic	Intergenic	-44693	NM_001167996	68725	Mm.45741	NM_001167996	ENSMUSG00000046999	1110032F04Rik	AI115547	RIKEN cDNA 1110032F04 gene	protein-coding
mm_25210.1	chr3	103832849	103832854	+	1	NA	exon (NM_001142960, exon 1 of 4)	exon (NM_001142960, exon 1 of 4)	155	NM_001142960	229672	Mm.297245	NM_001142959	ENSMUSG00000044165	Bcl2l15	Bfk|Gm566	BCLl2-like 15	protein-coding
mm_131721.1	chr16	21558640	21558645	+	1	NA	intron (NM_001285893, intron 36 of 46)	MTE2b|LTR|ERVL-MaLR	135524	NM_001285894	209018	Mm.235683	NM_145948	ENSMUSG00000033653	Vps8	AI315068|AU040738|mKIAA0804	VPS8 CORVET complex subunit	protein-coding
mm_17911.1	chr2	35337004	35337017	-	1	NA	promoter-TSS (NM_013515)	promoter-TSS (NM_013515)	-1	NM_013515	13830	Mm.295284	NM_013515	ENSMUSG00000026880	Stom	Epb7.2	stomatin	protein-coding
mm_49627.1	chr6	30804299	30804311	+	1	NA	intron (NM_017478, intron 20 of 23)	intron (NM_017478, intron 20 of 23)	63006	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_128647.1	chr15	59542201	59542203	-	1	NA	intron (NM_026746, intron 4 of 6)	intron (NM_026746, intron 4 of 6)	-106452	NM_144549	211770	Mm.40298	NM_144549	ENSMUSG00000032501	Trib1	A530090O15Rik|TRB-1|Trb1	tribbles pseudokinase 1	protein-coding
mm_54284.1	chr6	29216302	29216335	-	1	NA	promoter-TSS (NM_001302934)	promoter-TSS (NM_001302934)	46	NM_001302933	23917	Mm.260707	NM_011829	ENSMUSG00000003500	Impdh1	B930086D20Rik|IMPDH-I	inosine 5'-phosphate dehydrogenase 1	protein-coding
mm_31405.1	chr4	48047340	48047377	+	1	NA	intron (NM_015743, intron 1 of 7)	CpG	2053	NM_015743	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_109094.1	chr12	104857080	104857085	+	1	NA	intron (NM_001040682, intron 1 of 12)	intron (NM_001040682, intron 1 of 12)	7994	NR_104436	94040	Mm.244078	NM_053155	ENSMUSG00000021097	Clmn	9330188N17Rik|AI428889|AI788815|mKIAA1188	calmin	protein-coding
mm_116611.1	chr13	48870890	48870951	-	1	NA	promoter-TSS (NM_011078)	promoter-TSS (NM_011078)	-35	NM_011078	18676	Mm.486213	NM_011078	ENSMUSG00000038025	Phf2	GRC5	PHD finger protein 2	protein-coding
mm_48114.1	chr5	137116250	137116271	-	1	NA	promoter-TSS (NM_201373)	promoter-TSS (NM_201373)	-53	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_160571.1	chr9	57147856	57147856	-	1	NA	promoter-TSS (NM_028347)	promoter-TSS (NM_028347)	-822	NM_028347	72774	Mm.35749	NM_028347	ENSMUSG00000032298	Neil1	2810450N13Rik|Nei1	nei endonuclease VIII-like 1 (E. coli)	protein-coding
mm_78550.1	chr9	35421644	35421681	+	1	NA	Intergenic	CpG	-30414	NM_021339	57810	Mm.80509	NM_021339	ENSMUSG00000038119	Cdon	CDO|Cd0|Orcam	cell adhesion molecule-related/down-regulated by oncogenes	protein-coding
mm_164567.1	chr17	19988052	19988054	+	1	NA	Intergenic	Intergenic	60152	NM_001104566	22313	Mm.379039	NM_001104566	ENSMUSG00000090315	Vmn2r104	V2r7	vomeronasal 2, receptor 104	protein-coding
mm_12041.1	chr2	58770000	58770026	+	1	NA	intron (NM_029692, intron 2 of 6)	intron (NM_029692, intron 2 of 6)	14829	NM_029692	76654	Mm.200370	NM_029692	ENSMUSG00000026839	Upp2	1700124F02Rik|AI266885|UDRPASE2|UP2|UPASE2	uridine phosphorylase 2	protein-coding
mm_10954.1	chr2	25656652	25656653	+	1	NA	TTS (NM_033145)	TTS (NM_033145)	-1300	NM_007947	13863	Mm.12867	NM_007947	ENSMUSG00000026937	Lcn5	E-RABP|Erabp|MEP10	lipocalin 5	protein-coding
mm_118772.1	chr14	22742739	22742743	+	1	NA	intron (NM_028275, intron 5 of 6)	Lx9|LINE|L1	-199943	NR_046307	74896	Mm.444661	NR_046307		4930405A10Rik	4930456G20Rik	RIKEN cDNA 4930405A10 gene	ncRNA
mm_145512.1	chr18	60443050	60443061	+	1	NA	Intergenic	MER73|LTR|ERVL	58928	NM_134133	106878	Mm.273197	NM_134133	ENSMUSG00000038059	Smim3	2010002N04Rik|AI195350|AW561905|Nid67|cI-41	small integral membrane protein 3	protein-coding
mm_153988.1	chr19	48127391	48127393	-	1	NA	Intergenic	(A)n|Simple_repeat|Simple_repeat	-78633	NM_025696	66673	Mm.70980	NM_025696	ENSMUSG00000063434	Sorcs3	6330404A12Rik|AW045579	sortilin-related VPS10 domain containing receptor 3	protein-coding
mm_107005.1	chr12	11297177	11297191	+	1	NA	exon (NM_001324476, exon 17 of 26)	exon (NM_001324476, exon 17 of 26)	-2703	NR_106136	102465775		NR_106136	ENSMUSG00000098879	Mir7675	Gm27965|mmu-mir-7675	microRNA 7675	ncRNA
mm_85134.1	chr9	95753875	95753885	-	1	NA	3' UTR (NM_001033210, exon 16 of 16)	3' UTR (NM_001033210, exon 16 of 16)	-3522	NM_011643	22063	Mm.149633	NM_011643	ENSMUSG00000032839	Trpc1	Mtrp1|Trp1|Trrp1	transient receptor potential cation channel, subfamily C, member 1	protein-coding
mm_40589.1	chr5	64220910	64220916	+	1	NA	intron (NM_001310611, intron 2 of 21)	RLTR11B|LTR|ERVK	-9444	NM_001289514	57915	Mm.286353	NM_019636	ENSMUSG00000029174	Tbc1d1	1110062G02Rik|AI385682|AW555803|Nob1|Nobq1|Tbc1|mKIAA1108	TBC1 domain family, member 1	protein-coding
mm_46713.1	chr5	110387174	110387174	-	1	NA	promoter-TSS (NM_028596)	promoter-TSS (NM_028596)	-47	NM_028596	381668	Mm.348782	NM_028596	ENSMUSG00000043323	Fbrsl1	2410025L10Rik|AI467568|Gm1049|Gm29766|mKIAA1545	fibrosin-like 1	protein-coding
mm_97886.1	chr11	83291967	83291967	+	1	NA	non-coding (NR_028363, exon 2 of 3)	non-coding (NR_028363, exon 2 of 3)	268	NR_028363	613254	Mm.383758	NR_028363	ENSMUSG00000093483	AA465934	-	expressed sequence AA465934	ncRNA
mm_154597.1	chrX	7593226	7593236	+	1	NA	TTS (NM_138603)	TTS (NM_138603)	12189	NM_138603	54638	Mm.288192	NM_138603	ENSMUSG00000031143	Ccdc22	AI481216|DXImx40e|Ppp1r3f|Sfc22	coiled-coil domain containing 22	protein-coding
mm_38588.1	chr4	141821740	141821786	-	1	NA	exon (NM_007919, exon 4 of 8)	exon (NM_007919, exon 4 of 8)	4242	NM_007919	13706	Mm.45316	NM_007919	ENSMUSG00000058579	Cela2a	Ela-2|Ela2|Ela2a	chymotrypsin-like elastase family, member 2A	protein-coding
mm_98086.1	chr11	86587191	86587209	+	1	NA	intron (NM_029478, intron 10 of 11)	intron (NM_029478, intron 10 of 11)	-3042	NR_029738	387140		NR_029738	ENSMUSG00000065455	Mir21a	Mir21|Mirn21|mmu-mir-21|mmu-mir-21a	microRNA 21a	ncRNA
mm_106714.1	chr12	3834790	3834813	+	1	NA	intron (NM_001271753, intron 1 of 22)	intron (NM_001271753, intron 1 of 22)	27443	NR_045884	100038522	Mm.417270	NR_045884	ENSMUSG00000073242	Dnmt3aos	ENSMUSG00000073242|Gm10485	DNA methyltransferase 3A, opposite strand	ncRNA
mm_103336.1	chr11	74638085	74638099	-	1	NA	exon (NM_001013784, exon 4 of 4)	exon (NM_001013784, exon 4 of 4)	-11403	NM_001081158	74148	Mm.214574	NM_001081158	ENSMUSG00000020741	Cluh	1300001I01Rik|Kiaa0664|mKIAA0664	clustered mitochondria (cluA/CLU1) homolog	protein-coding
mm_131292.1	chr16	11397100	11397104	+	1	NA	intron (NM_028964, intron 5 of 20)	B4|SINE|B4	-8546	NM_001290148	74478	Mm.325831	NM_028964	ENSMUSG00000071669	Snx29	4933437K13Rik|ENSMUSG00000079738|Gm11170|Gm1737|Gm930|Rundc2a	sorting nexin 29	protein-coding
mm_49091.1	chr6	7555054	7555067	+	1	NA	promoter-TSS (NM_009311)	promoter-TSS (NM_009311)	-11	NM_009311	21333	Mm.1440	NM_009311	ENSMUSG00000061762	Tac1	4930528L02Rik|NK-1|NK1|Nkna|PPT-A|PPTA|SP	tachykinin 1	protein-coding
mm_86817.1	chr10	20907327	20907350	+	1	NA	Intergenic	Intergenic	-45209	NM_026203	52906	Mm.253280	NM_026203	ENSMUSG00000019986	Ahi1	1700015F03Rik|Ahi-1|D10Bwg0629e	Abelson helper integration site 1	protein-coding
mm_82383.1	chr9	14662907	14662920	-	1	NA	Intergenic	Intergenic	-47913	NM_001081395	75723	Mm.159552	NM_001081395	ENSMUSG00000013076	Amotl1	2310010G08Rik|2310067L22Rik|4932416D09Rik|JEAP|mFLJ00155	angiomotin-like 1	protein-coding
mm_67435.1	chr7	80385558	80385622	-	1	NA	intron (NM_010194, intron 3 of 18)	RSINE1|SINE|B4	2356	NM_010194	14159	Mm.48757	NM_010194	ENSMUSG00000053158	Fes	AI586313|BB137047|FPS|c-fes	feline sarcoma oncogene	protein-coding
mm_44360.1	chr5	17797072	17797195	-	1	NA	exon (NM_001159558, exon 11 of 16)	exon (NM_001159558, exon 11 of 16)	38763	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_112873.1	chr13	20853833	20853861	+	1	NA	intron (NM_012054, intron 4 of 20)	intron (NM_012054, intron 4 of 20)	59734	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_44723.1	chr5	30960327	30960339	-	1	NA	promoter-TSS (NM_001294302)	promoter-TSS (NM_001294302)	-6	NM_016703	50907	Mm.272414	NM_016703	ENSMUSG00000045302	Preb	C85705	prolactin regulatory element binding	protein-coding
mm_121470.1	chr14	120911178	120911198	+	1	NA	promoter-TSS (NM_023579)	promoter-TSS (NM_023579)	-6	NM_023579	70572	Mm.221452	NM_023579	ENSMUSG00000030662	Ipo5	1110011C18Rik|5730478E03Rik|AA409333|C76941|IMB3|Kpnb3|Ranbp5	importin 5	protein-coding
mm_124920.1	chr15	12117849	12117905	+	1	NA	promoter-TSS (NM_011767)	promoter-TSS (NM_011767)	26	NM_011767	22763	Mm.273496	NM_011767	ENSMUSG00000022201	Zfr	C920030H05Rik	zinc finger RNA binding protein	protein-coding
mm_76633.1	chr8	92158275	92158283	-	1	NA	Intergenic	Intergenic	197841	NR_110452	71296	Mm.86664	NR_033641	ENSMUSG00000031736	Crnde	4933436C20Rik	colorectal neoplasia differentially expressed (non-protein coding)	ncRNA
mm_115872.1	chr13	21716176	21716189	-	1	NA	promoter-TSS (NM_178199)	promoter-TSS (NM_178199)	-39	NM_178199	319185		NM_178199	ENSMUSG00000094338	Hist1h2bl	H2b-291a	histone cluster 1, H2bl	protein-coding
mm_60407.1	chr7	44476012	44476014	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	5666	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_148562.1	chr19	4756464	4756476	+	1	NA	promoter-TSS (NM_025717)	promoter-TSS (NM_025717)	-55	NM_025717	66704	Mm.396734	NM_025717	ENSMUSG00000033760	Rbm4b	4921506I22Rik|AI504630|AI506404|Lark2|Neosin	RNA binding motif protein 4B	protein-coding
mm_34079.1	chr4	138648545	138648580	+	1	NA	Intergenic	Intergenic	-24570	NM_029401	75718	Mm.251530	NM_029401	ENSMUSG00000028753	Vwa5b1	4931403E03Rik	von Willebrand factor A domain containing 5B1	protein-coding
mm_60583.1	chr7	44482690	44482698	+	1	NA	Intergenic	Intergenic	-1823	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_26308.1	chr3	142512187	142512200	+	1	NA	intron (NM_153564, intron 10 of 10)	intron (NM_153564, intron 10 of 10)	15259	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_34630.1	chr4	150573510	150573522	+	1	NA	intron (NM_001085492, intron 12 of 22)	B3|SINE|B2	78658	NM_173774	242773	Mm.29280	NM_173774	ENSMUSG00000039838	Slc45a1	C230078B22|Dnb5	solute carrier family 45, member 1	protein-coding
mm_17470.1	chr2	28559603	28559639	-	1	NA	exon (NM_009885, exon 6 of 11)	exon (NM_009885, exon 6 of 11)	3782	NM_009885	12613	Mm.236017	NM_009885	ENSMUSG00000026818	Cel	1810036E18Rik|BAL	carboxyl ester lipase	protein-coding
mm_85443.1	chr9	104213864	104213900	-	1	NA	exon (NM_001163026, exon 19 of 56)	exon (NM_001163026, exon 19 of 56)	49048	NM_001163026	235567	Mm.217256	NM_001163026	ENSMUSG00000032560	Dnajc13	D030002L11Rik|Gm1124|RME-8|Rme8|mKIAA0678	DnaJ heat shock protein family (Hsp40) member C13	protein-coding
mm_21747.1	chr2	164804877	164804894	-	1	NA	promoter-TSS (NM_178375)	promoter-TSS (NM_178375)	-4	NM_133240	170789	Mm.277878	NM_133240	ENSMUSG00000017307	Acot8	PTE-2|Pte1	acyl-CoA thioesterase 8	protein-coding
mm_162557.1	chr1	172082858	172082875	+	1	NA	promoter-TSS (NM_021607)	promoter-TSS (NM_021607)	-117	NM_021607	59287	Mm.218203	NM_021607	ENSMUSG00000003458	Ncstn	9430068N19Rik|AA727311|Aph2|D1Dau13e|Kiaa0253|Nct|mKIAA0253	nicastrin	protein-coding
mm_35434.1	chr4	36936312	36936315	-	1	NA	intron (NM_001165999, intron 1 of 7)	intron (NM_001165999, intron 1 of 7)	15431	NM_001165999	242384	Mm.132507	NM_175516	ENSMUSG00000045083	Lingo2	B230217C06Rik|Lern3|Lrrn6c	leucine rich repeat and Ig domain containing 2	protein-coding
mm_32353.1	chr4	105157340	105157354	+	1	NA	promoter-TSS (NM_080555)	promoter-TSS (NM_080555)	0	NM_080555	67916	Mm.348326	NM_080555	ENSMUSG00000028517	Plpp3	1110003O22Rik|2610002D05Rik|AV025606|D4Bwg0538e|D4Bwg1535e|Lpp3|Ppab2b|Ppap2b	phospholipid phosphatase 3	protein-coding
mm_84600.1	chr9	70038097	70038109	-	1	NA	promoter-TSS (NM_028087)	promoter-TSS (NM_028087)	-15	NM_028087	72077	Mm.195555	NM_028087	ENSMUSG00000032226	Gcnt3	2010013H22Rik|2210021I22Rik|2210401J11Rik	glucosaminyl (N-acetyl) transferase 3, mucin type	protein-coding
mm_107504.1	chr12	39941582	39941584	+	1	NA	Intergenic	Intergenic	95793	NM_007487	11861	Mm.12723	NM_007487	ENSMUSG00000047446	Arl4a	AI467555|Arl4	ADP-ribosylation factor-like 4A	protein-coding
mm_140480.1	chr17	3114513	3114534	-	1	NA	promoter-TSS (NM_134123)	promoter-TSS (NM_134123)	-449	NM_134123	106583	Mm.124373	NM_134123	ENSMUSG00000046201	Scaf8	A630086M08Rik|A930036P18Rik|AA408306|AI447644|AI448652|AU015035|Rbm16|mKIAA1116	SR-related CTD-associated factor 8	protein-coding
mm_87054.1	chr10	28827405	28827413	+	1	NA	intron (NM_001305663, intron 5 of 5)	intron (NM_001305663, intron 5 of 5)	96098	NR_033601	114676	Mm.390292	NR_033601		4930519F09Rik	-	pyruvate dehydrogenase E1 alpha 1 pseudogene	pseudo
mm_163304.1	chr11	121354614	121354626	+	1	NA	promoter-TSS (NM_025793)	promoter-TSS (NM_025793)	-173	NM_025793	66840	Mm.103986	NM_025793	ENSMUSG00000025173	Wdr45b	0610008N23Rik|AA408735|D16Bwg0193e|WIPI-3|Wdr45l	WD repeat domain 45B	protein-coding
mm_157710.1	chrX	64276938	64277002	-	1	NA	promoter-TSS (NM_178740)	promoter-TSS (NM_178740)	26	NM_178740	245446	Mm.101707	NM_178740	ENSMUSG00000046699	Slitrk4	6430513G13|D930039I09Rik	SLIT and NTRK-like family, member 4	protein-coding
mm_67880.1	chr7	99345488	99345519	-	1	NA	3' UTR (NM_009825, exon 5 of 5)	3' UTR (NM_009825, exon 5 of 5)	7736	NM_009825	12406	Mm.22708	NM_009825	ENSMUSG00000070436	Serpinh1	BERF-1|Cbp1|Cbp2|Hsp47|J6|Serpinh2|gp46	serine (or cysteine) peptidase inhibitor, clade H, member 1	protein-coding
mm_53285.1	chr6	128934374	128934387	+	1	NA	promoter-TSS (NM_027562)	promoter-TSS (NM_027562)	-1	NM_027562	70809	Mm.439891	NM_027562	ENSMUSG00000000248	Clec2g	4632413B12Rik|Clr-c|Clr-d|Clrc|Clrd|Clrx|Ddv10|Ocilrp1	C-type lectin domain family 2, member g	protein-coding
mm_139600.1	chr17	57279095	57279123	+	1	NA	promoter-TSS (NM_001163815)	promoter-TSS (NM_001163815)	9	NM_001163815	22324	Mm.248172	NM_011691	ENSMUSG00000034116	Vav1	Vav|vav-T	vav 1 oncogene	protein-coding
mm_135362.1	chr16	44016320	44016384	-	1	NA	promoter-TSS (NM_153528)	promoter-TSS (NM_153528)	84	NM_153528	207798	Mm.19316	NM_153528	ENSMUSG00000036292	Gramd1c	4921521N14Rik	GRAM domain containing 1C	protein-coding
mm_16999.1	chr2	18392695	18392699	-	1	NA	5' UTR (NM_001190817, exon 1 of 13)	5' UTR (NM_001190817, exon 1 of 13)	133	NM_001190817	13418	Mm.246674	NM_007869	ENSMUSG00000026740	Dnajc1	4733401K02Rik|AA960110|D230036H06Rik|Dnajl1|ERdj1|ERj1p|MTJ1	DnaJ heat shock protein family (Hsp40) member C1	protein-coding
mm_13112.1	chr2	91581148	91581166	+	1	NA	exon (NM_001165989, exon 23 of 43)	exon (NM_001165989, exon 23 of 43)	-14924	NR_028553	100217458		NR_028553	ENSMUSG00000077221	Snord67	MBII-166	small nucleolar RNA, C/D box 67	snoRNA
mm_94550.1	chr11	11462080	11462103	+	1	NA	exon (NM_015785, exon 1 of 8)	exon (NM_015785, exon 1 of 8)	328	NM_015785	53604	Mm.9500	NM_015785	ENSMUSG00000020193	Zpbp	4930486K01Rik|Iam38|Sp38	zona pellucida binding protein	protein-coding
mm_89208.1	chr10	86698328	86698369	+	1	NA	exon (NM_011631, exon 7 of 18)	exon (NM_011631, exon 7 of 18)	7096	NM_011631	22027	Mm.87773	NM_011631	ENSMUSG00000020048	Hsp90b1	ERp99|GRP94|TA-3|Targ2|Tra-1|Tra1|endoplasmin|gp96	heat shock protein 90, beta (Grp94), member 1	protein-coding
mm_111347.1	chr12	86896891	86896901	-	1	NA	Intergenic	Intergenic	-12082	NM_145836	238330	Mm.248358	NM_145836	ENSMUSG00000034168	Irf2bpl	6430527G18Rik|Eap1	interferon regulatory factor 2 binding protein-like	protein-coding
mm_13742.1	chr2	118118749	118118766	+	1	NA	exon (NM_011580, exon 10 of 22)	exon (NM_011580, exon 10 of 22)	6881	NM_001313914	21825	Mm.4159	NM_011580	ENSMUSG00000040152	Thbs1	TSP-1|TSP1|Thbs-1|tbsp1	thrombospondin 1	protein-coding
mm_62926.1	chr7	118600195	118600204	+	1	NA	5' UTR (NM_001105252, exon 2 of 22)	5' UTR (NM_001105252, exon 2 of 22)	2902	NM_001105252	74424	Mm.11068	NM_028930	ENSMUSG00000030650	Tmc5	4932443L08Rik|AU016085	transmembrane channel-like gene family 5	protein-coding
mm_133216.1	chr16	75907022	75907030	+	1	NA	intron (NM_023380, intron 1 of 7)	intron (NM_023380, intron 1 of 7)	2240	NM_023380	67742	Mm.131406	NM_023380	ENSMUSG00000022876	Samsn1	4930571B16Rik|930571B16Rik|Hacs1|SLy2	SAM domain, SH3 domain and nuclear localization signals, 1	protein-coding
mm_114933.1	chr13	95845240	95845253	+	1	NA	intron (NM_027711, intron 1 of 35)	PB1D10|SINE|Alu	46676	NM_027711	544963	Mm.38878	NM_027711	ENSMUSG00000021676	Iqgap2	4933417J23Rik|A630053O10|AI788777	IQ motif containing GTPase activating protein 2	protein-coding
mm_18360.1	chr2	58567158	58567288	-	1	NA	promoter-TSS (NM_001289660)	promoter-TSS (NM_001289660)	-111	NM_001289660	76654	Mm.200370	NM_029692	ENSMUSG00000026839	Upp2	1700124F02Rik|AI266885|UDRPASE2|UP2|UPASE2	uridine phosphorylase 2	protein-coding
mm_88056.1	chr10	67547940	67547959	+	1	NA	3' UTR (NM_001005419, exon 1 of 1)	3' UTR (NM_001005419, exon 1 of 1)	1006	NM_001005419	211488	Mm.297250	NM_001005419	ENSMUSG00000057134	Ado	Gm237	2-aminoethanethiol (cysteamine) dioxygenase	protein-coding
mm_158630.1	chrX	153037550	153037581	-	1	NA	promoter-TSS (NM_023788)	promoter-TSS (NM_023788)	-2	NM_023788	75625	Mm.6890	NM_023788	ENSMUSG00000047238	Mageh1	2010107K23Rik|APR-1|APR1	melanoma antigen, family H, 1	protein-coding
mm_152257.1	chr19	8774432	8774470	-	1	NA	promoter-TSS (NR_015538)	promoter-TSS (NR_015538)	16	NR_028419	67706	Mm.45155	NM_026325	ENSMUSG00000003680	Tmem179b	0610031L02Rik|1500003K22Rik|1810059G22Rik	transmembrane protein 179B	protein-coding
mm_77006.1	chr8	107439586	107439593	-	1	NA	intron (NM_025830, intron 1 of 23)	intron (NM_025830, intron 1 of 23)	3191	NM_025830	66894	Mm.390058	NM_025830	ENSMUSG00000031930	Wwp2	1300010O06Rik|AA690238|AIP2|AW554328	WW domain containing E3 ubiquitin protein ligase 2	protein-coding
mm_3693.1	chr1	153752784	153752802	+	1	NA	intron (NM_011882, intron 2 of 8)	intron (NM_011882, intron 2 of 8)	3367	NM_011882	24014	Mm.259254	NM_011882	ENSMUSG00000066800	Rnasel	E230029I04Rik	ribonuclease L (2', 5'-oligoisoadenylate synthetase-dependent)	protein-coding
mm_94643.1	chr11	16915226	16915300	+	1	NA	Intergenic	Intergenic	36019	NR_110421	72735	Mm.268598	NR_015469		Eldr	2810442I21Rik|4930500E12Rik|Fabl	Egfr long non-coding downstream RNA	ncRNA
mm_166823.1	chr7	18066011	18066018	+	1	NA	promoter-TSS (NM_001162524)	promoter-TSS (NM_001162524)	85	NM_001162523	67315	Mm.46089	NM_026087	ENSMUSG00000030366	Ceacam12	1600031J20Rik|Ceacam12-C1|Ceacam12-C3|Ceacam12C1|Ceacam12C3	carcinoembryonic antigen-related cell adhesion molecule 12	protein-coding
mm_53464.1	chr6	134920408	134920434	+	1	NA	promoter-TSS (NM_009875)	promoter-TSS (NM_009875)	20	NM_009875	12576	Mm.2958	NM_009875	ENSMUSG00000003031	Cdkn1b	AA408329|AI843786|Kip1|p27|p27Kip1	cyclin-dependent kinase inhibitor 1B	protein-coding
mm_160102.1	chr7	19077992	19077992	+	1	NA	intron (NM_010058, intron 1 of 4)	intron (NM_010058, intron 1 of 4)	1792	NM_010058	13401	Mm.2852	NM_010058	ENSMUSG00000030410	Dmwd	DMR-N9|Dm9	dystrophia myotonica-containing WD repeat motif	protein-coding
mm_112003.1	chr12	110840906	110840950	-	1	NA	promoter-TSS (NM_011973)	promoter-TSS (NM_011973)	11	NM_011973	26448	Mm.140948	NM_011973	ENSMUSG00000056458	Mok	RAGE1|Rage|Stk30	MOK protein kinase	protein-coding
mm_165453.1	chr2	157562442	157562457	-	1	NA	TTS (NM_010923)	TTS (NM_010923)	2371	NM_180960	18111	Mm.34330	NM_010923	ENSMUSG00000067786	Nnat	5730414I02Rik|AW107673|Peg5	neuronatin	protein-coding
mm_62303.1	chr7	100176684	100176690	+	1	NA	promoter-TSS (NM_001190869)	promoter-TSS (NM_001190869)	17	NM_001190869	57442	Mm.282386	NM_020574	ENSMUSG00000035165	Kcne3	2210017H05Rik|MiRP2	potassium voltage-gated channel, Isk-related subfamily, gene 3	protein-coding
mm_37190.1	chr4	117489940	117489958	-	1	NA	exon (NM_025739, exon 2 of 15)	exon (NM_025739, exon 2 of 15)	7103	NM_025739	66743	Mm.318331	NM_025739	ENSMUSG00000028677	Rnf220	4732477A13|4931406I20Rik|5730503K05Rik|AV302541	ring finger protein 220	protein-coding
mm_160429.1	chr8	88527388	88527388	+	1	NA	promoter-TSS (NM_001163660)	promoter-TSS (NM_001163660)	-245	NM_001163660	93960	Mm.30219	NM_027280	ENSMUSG00000031661	Nkd1	2810434J10Rik|9030215G15Rik|Nkd	naked cuticle 1 homolog (Drosophila)	protein-coding
mm_54590.1	chr6	38147442	38147447	-	1	NA	intron (NM_194061, intron 14 of 19)	intron (NM_194061, intron 14 of 19)	-22858	NM_080467	140494	Mm.462308	NM_080467	ENSMUSG00000038600	Atp6v0a4	Atp6n1b|a4	ATPase, H+ transporting, lysosomal V0 subunit A4	protein-coding
mm_126909.1	chr15	90224294	90224374	+	1	NA	promoter-TSS (NM_001033441)	promoter-TSS (NM_001033441)	23	NM_001033441	380959	Mm.17853	NM_001033441	ENSMUSG00000075470	Alg10b	AA469671|AU045404|AW123895|C85569|Deaf1|Gm917|nse5	asparagine-linked glycosylation 10B (alpha-1,2-glucosyltransferase)	protein-coding
mm_11912.1	chr2	52038143	52038155	+	1	NA	promoter-TSS (NM_009398)	promoter-TSS (NM_009398)	36	NM_009398	21930	Mm.3509	NM_009398	ENSMUSG00000053475	Tnfaip6	TSG-6|Tnfip6|Tsg6	tumor necrosis factor alpha induced protein 6	protein-coding
mm_66103.1	chr7	31039060	31039101	-	1	NA	exon (NM_001111073, exon 3 of 8)	exon (NM_001111073, exon 3 of 8)	1237	NR_106017	102465635		NR_106017	ENSMUSG00000098783	Mir7050	Gm27578|mmu-mir-7050	microRNA 7050	ncRNA
mm_162805.1	chr10	77788269	77788274	-	1	NA	intron (NM_001287074, intron 1 of 11)	intron (NM_001287074, intron 1 of 11)	10862	NM_001205034	100503388	Mm.482880	NM_001205034	ENSMUSG00000096380	Gm19668	-	predicted gene, 19668	protein-coding
mm_32651.1	chr4	115065108	115065110	+	1	NA	intron (NM_001287388, intron 4 of 4)	intron (NM_001287388, intron 4 of 4)	7298	NM_001287388	21349	Mm.239869	NM_011527	ENSMUSG00000028717	Tal1	Hpt|SCL/tal-1|Scl|bHLHa17|tal-1	T cell acute lymphocytic leukemia 1	protein-coding
mm_34532.1	chr4	149446138	149446175	+	1	NA	Intergenic	Intergenic	8812	NM_022020	63954	Mm.46023	NM_022020	ENSMUSG00000028996	Rbp7	1110002J23Rik|CRBP-III	retinol binding protein 7, cellular	protein-coding
mm_138954.1	chr17	44188565	44188594	+	1	NA	promoter-TSS (NM_172621)	promoter-TSS (NM_172621)	7	NM_172621	224796	Mm.37666	NM_172621	ENSMUSG00000023959	Clic5	5730531E12Rik|B330005L24|Gm322|jbg	chloride intracellular channel 5	protein-coding
mm_163522.1	chr12	115848334	115848371	-	1	NA	Intergenic	Intergenic	-152558	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
mm_140151.1	chr17	80127448	80127477	+	1	NA	promoter-TSS (NM_176963)	promoter-TSS (NM_176963)	-9	NM_176963	319625	Mm.29098	NM_176963	ENSMUSG00000035473	Galm	A530057M15Rik|AU015645|AU020959	galactose mutarotase	protein-coding
mm_108011.1	chr12	73585040	73585058	+	1	NA	5' UTR (NM_008856, exon 1 of 14)	5' UTR (NM_008856, exon 1 of 14)	253	NM_008856	18755	Mm.341677	NM_008856	ENSMUSG00000021108	Prkch	Pkch	protein kinase C, eta	protein-coding
mm_4108.1	chr1	167598451	167598476	+	1	NA	5' UTR (NM_009107, exon 1 of 10)	5' UTR (NM_009107, exon 1 of 10)	101	NM_009107	20183	Mm.3475	NM_009107	ENSMUSG00000015843	Rxrg	Nr2b3	retinoid X receptor gamma	protein-coding
mm_153132.1	chr19	34241690	34241700	-	1	NA	exon (NM_007392, exon 9 of 9)	exon (NM_007392, exon 9 of 9)	13678	NM_007392	11475	Mm.213025	NM_007392	ENSMUSG00000035783	Acta2	0610041G09Rik|Actvs|SMalphaA|a-SMA|alphaSMA	actin, alpha 2, smooth muscle, aorta	protein-coding
mm_14930.1	chr2	151542480	151542503	+	1	NA	promoter-TSS (NM_008019)	promoter-TSS (NM_008019)	8	NM_001302078	14225	Mm.278458	NM_008019	ENSMUSG00000032966	Fkbp1a	FKBP12|Fkbp|Fkbp1	FK506 binding protein 1a	protein-coding
mm_21786.1	chr2	164855736	164855746	-	1	NA	intron (NM_011125, intron 3 of 15)	B1_Mur1|SINE|Alu	1967	NM_011125	18830	Mm.6105	NM_011125	ENSMUSG00000017754	Pltp	Bpife|OD107	phospholipid transfer protein	protein-coding
mm_42648.1	chr5	118649592	118649601	+	1	NA	intron (NM_001347445, intron 2 of 30)	intron (NM_001347445, intron 2 of 30)	88877	NM_172424	76199	Mm.206238	NM_172424	ENSMUSG00000018076	Med13l	2210413I17Rik|6330591G05Rik|9030618F05Rik|Thrap2|Trap240L|mKIAA1025	mediator complex subunit 13-like	protein-coding
mm_37171.1	chr4	117182538	117182603	-	1	NA	promoter-TSS (NM_134471)	promoter-TSS (NM_134471)	54	NM_134471	73804	Mm.247651	NM_134471	ENSMUSG00000028678	Kif2c	4930402F02Rik|ESTM5|Knsl6|MCAK|X83316	kinesin family member 2C	protein-coding
mm_11233.1	chr2	29802834	29802855	+	1	NA	5' UTR (NM_011989, exon 1 of 13)	5' UTR (NM_011989, exon 1 of 13)	164	NM_011989	26569	Mm.330113	NM_011989	ENSMUSG00000059316	Slc27a4	BB144259|FATP4	solute carrier family 27 (fatty acid transporter), member 4	protein-coding
mm_23542.1	chr3	61364029	61364056	+	1	NA	promoter-TSS (NM_028712)	promoter-TSS (NM_028712)	-465	NM_028712	74012	Mm.422674	NM_028712	ENSMUSG00000036894	Rap2b	4021402C18Rik|AA408554	RAP2B, member of RAS oncogene family	protein-coding
mm_108884.1	chr12	99965793	99965817	+	1	NA	5' UTR (NM_001164426, exon 2 of 3)	5' UTR (NM_001164426, exon 2 of 3)	1306	NM_001164427	217826	Mm.312335	NM_146037	ENSMUSG00000045404	Kcnk13	BB085247|F730021E22Rik|Gm1570|Gm1685	potassium channel, subfamily K, member 13	protein-coding
mm_107756.1	chr12	59071469	59071490	+	1	NA	exon (NM_008891, exon 9 of 9)	exon (NM_008891, exon 9 of 9)	4560	NM_008891	18949	Mm.22347	NM_008891	ENSMUSG00000020994	Pnn	AU045199|D12Ertd512e	pinin	protein-coding
mm_81117.1	chr9	106460624	106460646	+	1	NA	intron (NM_021567, intron 4 of 12)	intron (NM_021567, intron 4 of 12)	5305	NM_001159652	436090	Mm.482905	NM_001159652	ENSMUSG00000091735	Gpr62	4933402E03Rik	G protein-coupled receptor 62	protein-coding
mm_59033.1	chr7	19307330	19307359	+	1	NA	exon (NM_008036, exon 2 of 4)	exon (NM_008036, exon 2 of 4)	2701	NM_008036	14282	Mm.248335	NM_008036	ENSMUSG00000003545	Fosb	-	FBJ osteosarcoma oncogene B	protein-coding
mm_113847.1	chr13	47201598	47201612	+	1	NA	intron (NM_001170643, intron 1 of 7)	intron (NM_001170643, intron 1 of 7)	7602	NM_001170643	218215	Mm.287609	NM_146042	ENSMUSG00000038068	Rnf144b	BC025007|E130105P19Rik|Ibrdc2|Pir2	ring finger protein 144B	protein-coding
mm_20259.1	chr2	126606173	126606183	-	1	NA	intron (NM_008230, intron 4 of 11)	intron (NM_008230, intron 4 of 11)	12500	NM_008230	15186	Mm.18603	NM_008230	ENSMUSG00000027360	Hdc	AW108189|Hdc-a|Hdc-c|Hdc-e|Hdc-s	histidine decarboxylase	protein-coding
mm_165623.1	chr3	63905328	63905334	+	1	NA	Intergenic	Intergenic	24054	NM_177856	329659	Mm.39342	NM_177856	ENSMUSG00000048581	E130311K13Rik	-	RIKEN cDNA E130311K13 gene	protein-coding
mm_37339.1	chr4	119657618	119657636	-	1	NA	exon (NM_008191, exon 2 of 3)	exon (NM_008191, exon 2 of 3)	1318	NM_008191	14916	Mm.278	NM_008191	ENSMUSG00000032978	Guca2b	AV066530|Gcap2|Ugn	guanylate cyclase activator 2b (retina)	protein-coding
mm_133178.1	chr16	72563385	72563395	+	1	NA	Intergenic	Intergenic	-99759	NM_019413	19876	Mm.310772	NM_019413	ENSMUSG00000022883	Robo1	AW494633|AW742721|DUTT1|Gm310	roundabout guidance receptor 1	protein-coding
mm_82180.1	chr9	123872295	123872332	+	1	NA	Intergenic	Intergenic	-10284	NM_011798	23832	Mm.390241	NM_011798	ENSMUSG00000060509	Xcr1	Ccxcr1|Gpr5|mXcr1	chemokine (C motif) receptor 1	protein-coding
mm_67087.1	chr7	68283840	68283868	-	1	NA	intron (NM_001013811, intron 1 of 8)	intron (NM_001013811, intron 1 of 8)	-7260	NR_040340	100504026	Mm.426764	NR_040340	ENSMUSG00000086628	Gm16157	OTTMUSG00000031023	predicted gene 16157	ncRNA
mm_21412.1	chr2	158120196	158120211	-	1	NA	exon (NM_009373, exon 11 of 13)	exon (NM_009373, exon 11 of 13)	26189	NM_009373	21817	Mm.330731	NM_009373	ENSMUSG00000037820	Tgm2	G[a]h|TG2|TGase2|tTG|tTGas	transglutaminase 2, C polypeptide	protein-coding
mm_114802.1	chr13	91098497	91098501	+	1	NA	intron (NM_025770, intron 3 of 7)	B4|SINE|B4	125488	NM_025770	66795	Mm.235385	NM_025770	ENSMUSG00000021619	Atg10	5330424L23Rik|5430428K15Rik|AI852123|APG10|Agp10|Apg10l|Apg10p|Atg10l	autophagy related 10	protein-coding
mm_146101.1	chr18	73949349	73949356	+	1	NA	intron (NM_172632, intron 2 of 5)	intron (NM_172632, intron 2 of 5)	-68555	NR_045390	77855	Mm.410760	NR_045390	ENSMUSG00000090263	D730045A05Rik	-	RIKEN cDNA D730045A05 gene	ncRNA
mm_119123.1	chr14	31131116	31131120	+	1	NA	Intergenic	CpG	-2188	NM_001308464	66487	Mm.379116	NM_001308091	ENSMUSG00000058351	Smim4	2010107H07Rik|Gm41122	small integral membrane protein 4	protein-coding
mm_153474.1	chr19	41273722	41273738	-	1	NA	TTS (NM_031376)	TTS (NM_031376)	-9726	NM_133352	107358	Mm.246440	NM_133352	ENSMUSG00000025016	Tm9sf3	1810073M23Rik|2810031D16Rik|AI115521|AI413748|AW146116|AW549777|Smbp|mKIAA4036	transmembrane 9 superfamily member 3	protein-coding
mm_14149.1	chr2	126553016	126553033	+	1	NA	promoter-TSS (NM_011978)	promoter-TSS (NM_011978)	0	NM_011978	26458	Mm.290044	NM_011978	ENSMUSG00000027359	Slc27a2	ACSVL1|FATP2|VLCS|Vlac|Vlacs	solute carrier family 27 (fatty acid transporter), member 2	protein-coding
mm_9384.1	chr1	172213143	172213162	-	1	NA	intron (NM_009813, intron 8 of 10)	intron (NM_009813, intron 8 of 10)	-6348	NM_011063	18611	Mm.544	NM_011063	ENSMUSG00000013698	Pea15a	Mat1|PEA-15|Pea15|Pkcs15	phosphoprotein enriched in astrocytes 15A	protein-coding
mm_168273.1	chr10	98551084	98551085	-	1	NA	Intergenic	Intergenic	-199217	NR_045179	667438	Mm.414522	NR_045179		Gm8633	EG667438	predicted gene 8633	ncRNA
mm_49901.1	chr6	38941374	38941386	+	1	NA	intron (NM_011539, intron 1 of 12)	intron (NM_011539, intron 1 of 12)	22394	NM_011539	21391	Mm.4054	NM_011539	ENSMUSG00000029925	Tbxas1	CYP5|CYP5A1|THAS|TS|TXAS|TXS	thromboxane A synthase 1, platelet	protein-coding
mm_71782.1	chr8	66511752	66511764	+	1	NA	promoter-TSS (NM_028927)	promoter-TSS (NM_028927)	18	NM_028927	74419	Mm.159193	NM_028927	ENSMUSG00000025519	Tktl2	4933401I19Rik	transketolase-like 2	protein-coding
mm_43861.1	chr5	143464660	143464670	+	1	NA	5' UTR (NM_144915, exon 1 of 15)	5' UTR (NM_144915, exon 1 of 15)	172	NM_144915	231871	Mm.469963	NM_144915	ENSMUSG00000039206	Daglb	E330036I19Rik	diacylglycerol lipase, beta	protein-coding
mm_744.1	chr1	43532226	43532235	+	1	NA	intron (NM_010879, intron 2 of 4)	intron (NM_010879, intron 2 of 4)	86479	NM_010879	17974	Mm.389903	NM_010879	ENSMUSG00000066877	Nck2	4833426I10Rik|Grb4|NCKbeta|Nck-2	non-catalytic region of tyrosine kinase adaptor protein 2	protein-coding
mm_96774.1	chr11	69935895	69935931	+	1	NA	promoter-TSS (NM_016875)	promoter-TSS (NM_016875)	14	NM_016875	53422	Mm.29286	NM_016875	ENSMUSG00000018554	Ybx2	Msy2	Y box protein 2	protein-coding
mm_136011.1	chr16	75909231	75909247	-	1	NA	promoter-TSS (NM_023380)	promoter-TSS (NM_023380)	27	NM_023380	67742	Mm.131406	NM_023380	ENSMUSG00000022876	Samsn1	4930571B16Rik|930571B16Rik|Hacs1|SLy2	SAM domain, SH3 domain and nuclear localization signals, 1	protein-coding
mm_33385.1	chr4	129600671	129600715	+	1	NA	promoter-TSS (NM_029748)	promoter-TSS (NM_029748)	-14	NM_029748	76799	Mm.293096	NM_029748	ENSMUSG00000028797	Tmem234	1500002D11Rik|2510006D16Rik|4933407D05Rik	transmembrane protein 234	protein-coding
mm_164498.1	chr16	91522654	91522665	-	1	NA	Intergenic	Intergenic	-24435	NM_008338	15980	Mm.249364	NM_008338	ENSMUSG00000022965	Ifngr2	Ifgr2|Ifgt	interferon gamma receptor 2	protein-coding
mm_74486.1	chr8	4678339	4678356	-	1	NA	Intergenic	CpG	65177	NM_145591	233987	Mm.102799	NM_145591	ENSMUSG00000058748	Zfp958	-	zinc finger protein 958	protein-coding
mm_74244.1	chr8	124793492	124793514	+	1	NA	5' UTR (NM_198632, exon 1 of 10)	5' UTR (NM_198632, exon 1 of 10)	484	NM_198632	330863	Mm.422769	NM_198632	ENSMUSG00000036913	Trim67	D130049O21Rik|TNL	tripartite motif-containing 67	protein-coding
mm_32660.1	chr4	115090169	115090169	+	1	NA	intron (NM_026018, intron 2 of 4)	intron (NM_026018, intron 2 of 4)	1461	NM_001164557	67182	Mm.30181	NM_026018	ENSMUSG00000028716	Pdzk1ip1	0610007F13Rik|2700030M23Rik|AU046042|Map17	PDZK1 interacting protein 1	protein-coding
mm_116607.1	chr13	48819702	48819713	-	1	NA	intron (NM_011078, intron 9 of 21)	intron (NM_011078, intron 9 of 21)	51178	NM_011078	18676	Mm.486213	NM_011078	ENSMUSG00000038025	Phf2	GRC5	PHD finger protein 2	protein-coding
mm_51468.1	chr6	82952738	82952743	+	1	NA	intron (NM_033079, intron 1 of 9)	intron (NM_033079, intron 1 of 9)	5818	NM_033079	110958	Mm.100652	NM_033079	ENSMUSG00000030041	M1ap	D6Mm5e	meiosis 1 associated protein	protein-coding
mm_55086.1	chr6	49215362	49215377	-	1	NA	promoter-TSS (NM_023670)	promoter-TSS (NM_023670)	-415	NM_023670	140488	Mm.281018	NM_023670	ENSMUSG00000029814	Igf2bp3	2610101N11Rik|AA522010|AL022933|AU045931|IMP-3|IMP3|Koc13|Neilsen|mimp3	insulin-like growth factor 2 mRNA binding protein 3	protein-coding
mm_30992.1	chr4	37970367	37970399	+	1	NA	Intergenic	Intergenic	-1018639	NM_001165999	242384	Mm.132507	NM_175516	ENSMUSG00000045083	Lingo2	B230217C06Rik|Lern3|Lrrn6c	leucine rich repeat and Ig domain containing 2	protein-coding
mm_55254.1	chr6	52909632	52909644	-	1	NA	promoter-TSS (NM_001168277)	promoter-TSS (NM_001168277)	-18	NM_001168277	231986	Mm.386865	NM_173406	ENSMUSG00000063568	Jazf1	AI591476|C820002C15|Jaz1|Tip27	JAZF zinc finger 1	protein-coding
mm_118644.1	chr14	21500928	21500934	+	1	NA	intron (NM_017479, intron 1 of 16)	CpG	1146	NM_017479	54169	Mm.248967	NM_017479	ENSMUSG00000021767	Kat6b	AI507552|B130044K16Rik|MYST-4|Morf|Myst4|mKIAA0383|qkf|querkopf	K(lysine) acetyltransferase 6B	protein-coding
mm_93324.1	chr10	99232603	99232620	-	1	NA	Intergenic	Intergenic	-30620	NM_026268	67603	Mm.1791	NM_026268	ENSMUSG00000019960	Dusp6	1300019I03Rik|MKP-3|MKP3|PYST1	dual specificity phosphatase 6	protein-coding
mm_96854.1	chr11	70054363	70054377	+	1	NA	promoter-TSS (NM_009714)	promoter-TSS (NM_009714)	15	NM_001291132	11889	Mm.6559	NM_009714	ENSMUSG00000020884	Asgr1	ASGPR1|Asgr|Asgr-1|HL-1	asialoglycoprotein receptor 1	protein-coding
mm_32525.1	chr4	108861600	108861629	+	1	NA	3' UTR (NM_025334, exon 7 of 7)	3' UTR (NM_025334, exon 7 of 7)	13757	NM_029571	100087	Mm.440007	NM_029571	ENSMUSG00000073775	Kti12	1110001A12Rik|AI326810|AU014758	KTI12 homolog, chromatin associated	protein-coding
mm_142173.1	chr17	36252488	36252503	-	1	NA	Intergenic	Intergenic	5351	NM_026308	67676	Mm.27131	NM_026308	ENSMUSG00000024446	Rpp21	0610037N01Rik	ribonuclease P 21 subunit	protein-coding
mm_96041.1	chr11	59556527	59556538	+	1	NA	intron (NM_145827, intron 6 of 9)	ID_B1|SINE|B4	13846	NM_145827	216799	Mm.54174	NM_145827	ENSMUSG00000032691	Nlrp3	AGTAVPRL|AII/AVP|Cias1|FCAS|FCU|MWS|Mmig1|NALP3|Pypaf1	NLR family, pyrin domain containing 3	protein-coding
mm_71492.1	chr8	46752644	46752664	+	1	NA	intron (NM_008391, intron 1 of 8)	intron (NM_008391, intron 1 of 8)	12909	NM_008391	16363	Mm.1149	NM_008391	ENSMUSG00000031627	Irf2	9830146E22Rik|AI646973|Irf-2	interferon regulatory factor 2	protein-coding
mm_169067.1	chr1	32702380	32702414	+	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	-155104	NM_001164286	408191	Mm.479439	NM_001164286	ENSMUSG00000091318	Gm5415	EG408191|Senp14	predicted gene 5415	protein-coding
mm_5029.1	chr1	193301954	193301960	+	1	NA	promoter-TSS (NM_001277928)	promoter-TSS (NM_001277928)	-37	NM_008484	16780	Mm.435441	NM_008484	ENSMUSG00000026639	Lamb3	-	laminin, beta 3	protein-coding
mm_129996.1	chr15	86185863	86185937	-	1	NA	5' UTR (NM_145475, exon 1 of 13)	5' UTR (NM_145475, exon 1 of 13)	241	NM_145475	223753	Mm.222685	NM_145475	ENSMUSG00000035891	Cerk	AI848610|D330016D08Rik|mKIAA1646	ceramide kinase	protein-coding
mm_55413.1	chr6	65022743	65022753	-	1	NA	Intergenic	Intergenic	-19919	NM_007958	13990	Mm.99113	NM_007958	ENSMUSG00000029920	Smarcad1	AV081750|AW226546|D6Pas1|Etl1|mKIAA1122	SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1	protein-coding
mm_105269.1	chr11	102403283	102403296	-	1	NA	TTS (NM_001252347)	TTS (NM_001252347)	1698	NR_105895	102465561		NR_105895	ENSMUSG00000098774	Mir6930	Gm27436|mmu-mir-6930	microRNA 6930	ncRNA
mm_157375.1	chrX	37878587	37878602	-	1	NA	intron (NM_001004193, intron 1 of 3)	intron (NM_001004193, intron 1 of 3)	350	NM_001004193	434768	Mm.336025	NM_001004193	ENSMUSG00000064137	Rhox8	Tox	reproductive homeobox 8	protein-coding
mm_21763.1	chr2	164840376	164840394	-	1	NA	3' UTR (NM_008906, exon 15 of 15)	3' UTR (NM_008906, exon 15 of 15)	6612	NM_008906	19025	Mm.359633	NM_008906	ENSMUSG00000017760	Ctsa	AU019505|PPCA|Ppgb	cathepsin A	protein-coding
mm_26725.1	chr3	159873076	159873096	+	1	NA	non-coding (NR_037590, exon 3 of 13)	non-coding (NR_037590, exon 3 of 13)	33391	NM_026582	68151	Mm.6766	NM_026582	ENSMUSG00000028173	Wls	5031439A09Rik|AI173978|AI987742|Gpr177	wntless homolog (Drosophila)	protein-coding
mm_37677.1	chr4	129189432	129189448	-	1	NA	promoter-TSS (NM_029036)	promoter-TSS (NM_029036)	42	NM_029036	74648	Mm.172064	NM_029036	ENSMUSG00000040928	S100pbp	4930429A08Rik|AI851343|S100pbpr	S100P binding protein	protein-coding
mm_71798.1	chr8	67956755	67956788	+	1	NA	intron (NM_177698, intron 3 of 14)	intron (NM_177698, intron 3 of 14)	17803	NM_177698	234353	Mm.32525	NM_027626	ENSMUSG00000030465	Psd3	4931420C21Rik|AI661273|BC003498|D430018P08|EFA6D	pleckstrin and Sec7 domain containing 3	protein-coding
mm_157667.1	chrX	58631307	58631308	-	1	NA	Intergenic	Intergenic	-280154	NM_023774	75352	Mm.60906	NM_023774	ENSMUSG00000046180	4930550L24Rik	mage-k1	RIKEN cDNA 4930550L24 gene	protein-coding
mm_131588.1	chr16	18548731	18548735	+	1	NA	intron (NM_001285494, intron 6 of 7)	intron (NM_001285494, intron 6 of 7)	38236	NM_011532	21380	Mm.295194	NM_011532	ENSMUSG00000009097	Tbx1	-	T-box 1	protein-coding
mm_88860.1	chr10	80930875	80930897	+	1	NA	intron (NM_008655, intron 2 of 3)	intron (NM_008655, intron 2 of 3)	795	NM_008655	17873	Mm.1360	NM_008655	ENSMUSG00000015312	Gadd45b	AI323528|Myd118	growth arrest and DNA-damage-inducible 45 beta	protein-coding
mm_102471.1	chr11	60031829	60031837	-	1	NA	intron (NM_001290012, intron 1 of 6)	intron (NM_001290012, intron 1 of 6)	5172	NM_008819	18618	Mm.2731	NM_008819	ENSMUSG00000000301	Pemt	PEAMT|PEMT2|PLMT|Pempt|Pempt2	phosphatidylethanolamine N-methyltransferase	protein-coding
mm_120962.1	chr14	77663272	77663276	+	1	NA	intron (NM_001253759, intron 15 of 19)	intron (NM_001253759, intron 15 of 19)	135694	NM_001033440	380920	Mm.297771	NM_001033440	ENSMUSG00000075512	Gm1587	-	predicted gene 1587	protein-coding
mm_161084.1	chr12	85106430	85106430	-	1	NA	promoter-TSS (NM_175198)	promoter-TSS (NM_175198)	1	NM_175198	73422	Mm.311944	NM_175198	ENSMUSG00000042320	Prox2	1700058C01Rik	prospero homeobox 2	protein-coding
mm_148667.1	chr19	5637476	5637486	+	1	NA	promoter-TSS (NM_009045)	promoter-TSS (NM_009045)	-9	NM_009045	19697	Mm.249966	NM_009045	ENSMUSG00000024927	Rela	p65	v-rel reticuloendotheliosis viral oncogene homolog A (avian)	protein-coding
mm_141254.1	chr17	27580609	27580620	-	1	NA	3' UTR (NM_001291046, exon 5 of 5)	3' UTR (NM_001291046, exon 5 of 5)	-14887	NM_001002895	106672	Mm.61488	NM_001002895	ENSMUSG00000062753	AI413582	AI854251	expressed sequence AI413582	protein-coding
mm_121398.1	chr14	119137872	119137915	+	1	NA	promoter-TSS (NM_015820)	promoter-TSS (NM_015820)	-372	NM_015820	50787	Mm.445777	NM_015820	ENSMUSG00000053465	Hs6st3	6OST3|HS6ST-3	heparan sulfate 6-O-sulfotransferase 3	protein-coding
mm_8389.1	chr1	151345094	151345111	-	1	NA	intron (NM_001039511, intron 1 of 7)	CpG	604	NM_001039511	117198	Mm.33764	NM_028582	ENSMUSG00000023150	Ivns1abp	1190004M08Rik|1700126I16Rik|AA960440|HSPC068|ND1|NS-1|NS1-BP|Nd1-L|Nd1-S|mKIAA0850	influenza virus NS1A binding protein	protein-coding
mm_24304.1	chr3	89392176	89392208	+	1	NA	non-coding (NR_040403, exon 1 of 2)	non-coding (NR_040403, exon 1 of 2)	328	NR_040403	545539	Mm.393389	NR_040403	ENSMUSG00000074466	Gm15417	ENSMUSG00000074466|OTTMUSG00000021274	predicted gene 15417	ncRNA
mm_25478.1	chr3	108940077	108940107	+	1	NA	promoter-TSS (NM_001078646)	promoter-TSS (NM_001078646)	8	NM_025723	66715	Mm.158124	NM_025723	ENSMUSG00000045662	Henmt1	4921515J06Rik|Hen1|mHEN1	HEN1 methyltransferase homolog 1 (Arabidopsis)	protein-coding
mm_57454.1	chr6	125165595	125165612	-	1	NA	5' UTR (NM_008084, exon 1 of 7)	5' UTR (NM_008084, exon 1 of 7)	170	NM_008084	14433	Mm.304088	NM_008084	ENSMUSG00000057666	Gapdh	Gapd	glyceraldehyde-3-phosphate dehydrogenase	protein-coding
mm_49779.1	chr6	34920972	34920973	+	1	NA	promoter-TSS (NM_009292)	promoter-TSS (NM_009292)	12	NM_009292	20899	Mm.5171	NM_009292	ENSMUSG00000029848	Stra8	-	stimulated by retinoic acid gene 8	protein-coding
mm_83859.1	chr9	54661667	54661716	-	1	NA	5' UTR (NM_053178, exon 1 of 14)	5' UTR (NM_053178, exon 1 of 14)	194	NM_053178	94180	Mm.20592	NM_053178	ENSMUSG00000032281	Acsbg1	BG1|Bgm|E230019G03Rik|GR-LACS|Lpd|R75185	acyl-CoA synthetase bubblegum family member 1	protein-coding
mm_74335.1	chr8	127064108	127064108	+	1	NA	promoter-TSS (NM_033620)	promoter-TSS (NM_033620)	52	NM_001309391	93742	Mm.299254	NM_033620	ENSMUSG00000025812	Pard3	AA960621|AI256638|Asip|D8Ertd580e|Par-3|Par3|Pard-3|Pard3a|Phip	par-3 family cell polarity regulator	protein-coding
mm_80453.1	chr9	77982681	77982687	+	1	NA	exon (NM_134255, exon 8 of 8)	exon (NM_134255, exon 8 of 8)	65319	NM_134255	68801	Mm.430736	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	ELOVL family member 5, elongation of long chain fatty acids (yeast)	protein-coding
mm_22162.1	chr2	172940396	172940406	-	1	NA	promoter-TSS (NM_007557)	promoter-TSS (NM_007557)	-80	NM_007557	12162	Mm.595	NM_007557	ENSMUSG00000008999	Bmp7	OP1	bone morphogenetic protein 7	protein-coding
mm_29250.1	chr3	107218748	107218752	-	1	NA	intron (NM_001111143, intron 2 of 8)	intron (NM_001111143, intron 2 of 8)	2982	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_4850.1	chr1	187215549	187215559	+	1	NA	promoter-TSS (NM_029067)	promoter-TSS (NM_029067)	43	NM_026367	67769	Mm.138321	NM_026367	ENSMUSG00000039210	Gpatch2	5830433G22Rik|5830436K05Rik|AI427714|AI447508|AW107440|AW491060|Gpatc2	G patch domain containing 2	protein-coding
mm_148990.1	chr19	8618006	8618044	+	1	NA	promoter-TSS (NM_008766)	promoter-TSS (NM_008766)	29	NM_008766	18399	Mm.30090	NM_008766	ENSMUSG00000024650	Slc22a6	NKT|Oat1|Orctl1|mOat1	solute carrier family 22 (organic anion transporter), member 6	protein-coding
mm_47636.1	chr5	125304477	125304485	-	1	NA	intron (NM_001205083, intron 1 of 10)	ORR1C2|LTR|ERVL-MaLR	36613	NM_016741	20778	Mm.282242	NM_016741	ENSMUSG00000037936	Scarb1	AI120173|CD36|Cd36l1|Chohd1|Cla-1|Cla1|D5Ertd460e|Hdlq1|Hlb398|SR-B1|SR-BI|SRBI|Srb1|mSR-BI	scavenger receptor class B, member 1	protein-coding
mm_51096.1	chr6	67270440	67270443	+	1	NA	intron (NM_001113564, intron 1 of 7)	intron (NM_001113564, intron 1 of 7)	3462	NM_025814	66870	Mm.240490	NM_025814	ENSMUSG00000036371	Serbp1	1200009K13Rik|9330147J08Rik|AL022786|Pairbp1	serpine1 mRNA binding protein 1	protein-coding
mm_56334.1	chr6	92673469	92673471	-	1	NA	intron (NM_001081146, intron 2 of 8)	PB1D9|SINE|Alu	32714	NM_001081146	243548	Mm.248820	NM_001081146	ENSMUSG00000030020	Prickle2	6230400G14Rik|6720451F06Rik|mpk2	prickle planar cell polarity protein 2	protein-coding
mm_161591.1	chr16	34784796	34784796	+	1	NA	promoter-TSS (NM_139300)	promoter-TSS (NM_139300)	-154	NM_139300	107589	Mm.33360	NM_139300	ENSMUSG00000022836	Mylk	9530072E15Rik|A930019C19Rik|AW489456|KRP|MLCK108|MLCK210|Mlck|nmMlck|smMLCK	myosin, light polypeptide kinase	protein-coding
mm_117949.1	chr13	99435449	99435459	-	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-22628	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_69919.1	chr7	141744711	141744721	-	1	NA	exon (NM_023566, exon 28 of 46)	exon (NM_023566, exon 28 of 46)	-44295	NM_010844	17833	Mm.334332	NM_010844	ENSMUSG00000037974	Muc5ac	2210005L13Rik|MGM	mucin 5, subtypes A and C, tracheobronchial/gastric	protein-coding
mm_60228.1	chr7	43607195	43607215	+	1	NA	promoter-TSS (NM_028913)	promoter-TSS (NM_028913)	36	NM_028913	74400	Mm.159188	NM_028913	ENSMUSG00000055102	Zfp819	4930427I11Rik|4933405K07Rik	zinc finger protein 819	protein-coding
mm_128292.1	chr15	37233162	37233182	-	1	NA	5' UTR (NM_026496, exon 1 of 16)	5' UTR (NM_026496, exon 1 of 16)	136	NM_026496	252973	Mm.244612	NM_026496	ENSMUSG00000022286	Grhl2	0610015A08Rik|BOM|Tcfcp2l3|clft3	grainyhead-like 2 (Drosophila)	protein-coding
mm_83831.1	chr9	54183304	54183310	-	1	NA	intron (NM_007810, intron 2 of 8)	intron (NM_007810, intron 2 of 8)	10135	NM_007810	13075	Mm.5199	NM_007810	ENSMUSG00000032274	Cyp19a1	Ar|ArKO|Cyp19|Int-5|Int5|p450arom	cytochrome P450, family 19, subfamily a, polypeptide 1	protein-coding
mm_67049.1	chr7	67316832	67316841	-	1	NA	exon (NM_001291195, exon 3 of 11)	exon (NM_001291195, exon 3 of 11)	56022	NM_001291192	17258	Mm.132788	NM_001033713	ENSMUSG00000030557	Mef2a	A430079H05Rik	myocyte enhancer factor 2A	protein-coding
mm_162669.1	chr10	7131958	7131959	+	1	NA	intron (NM_172546, intron 9 of 12)	intron (NM_172546, intron 9 of 12)	80279	NM_172546	215748	Mm.37984	NM_172546	ENSMUSG00000015202	Cnksr3	6820402C05|BC024086|Magi1	Cnksr family member 3	protein-coding
mm_32144.1	chr4	99656329	99656340	+	1	NA	promoter-TSS (NM_010425)	promoter-TSS (NM_010425)	35	NM_010425	15221	Mm.4758	NM_010425	ENSMUSG00000067261	Foxd3	CWH3|Genesis|Hfh2	forkhead box D3	protein-coding
mm_6044.1	chr1	59763305	59763317	-	1	NA	promoter-TSS (NM_007561)	promoter-TSS (NM_007561)	-968	NM_007561	12168	Mm.7106	NM_007561	ENSMUSG00000067336	Bmpr2	2610024H22Rik|AL117858|AW546137|BB189135|BMP-2|BMPR-2|BMPR-II|BMPRII|BRK-3|Gm20272	bone morphogenetic protein receptor, type II (serine/threonine kinase)	protein-coding
mm_96094.1	chr11	60417239	60417301	+	1	NA	promoter-TSS (NM_145427)	promoter-TSS (NM_145427)	125	NM_025757	66771	Mm.29950	NM_025757	ENSMUSG00000018415	Gid4	4933439F18Rik	GID complex subunit 4, VID24 homolog	protein-coding
mm_31666.1	chr4	59964273	59964283	+	1	NA	Intergenic	Intergenic	-3613	NM_008648	17843	Mm.457982	NM_008648	ENSMUSG00000041333	Mup4	Mup-4|Mup1	major urinary protein 4	protein-coding
mm_116244.1	chr13	33935701	33935724	-	1	NA	promoter-TSS (NR_040707)	promoter-TSS (NR_040707)	-320	NR_040707	68808	Mm.443347	NR_040707	ENSMUSG00000085457	1110046J04Rik	-	RIKEN cDNA 1110046J04 gene	ncRNA
mm_66531.1	chr7	45136180	45136184	-	1	NA	intron (NR_102725, intron 1 of 7)	intron (NR_102725, intron 1 of 7)	250	NM_013520	14256	Mm.1658	NM_013520	ENSMUSG00000110206	Flt3l	Flt3lg|Ly72L	FMS-like tyrosine kinase 3 ligand	protein-coding
mm_33892.1	chr4	136181144	136181164	+	1	NA	intron (NM_001305399, intron 1 of 4)	intron (NM_001305399, intron 1 of 4)	372	NM_001305399	242705	Mm.307932	NM_177733	ENSMUSG00000018983	E2f2	E2F-2	E2F transcription factor 2	protein-coding
mm_65103.1	chr7	19303624	19303641	-	1	NA	3' UTR (NM_008036, exon 4 of 4)	3' UTR (NM_008036, exon 4 of 4)	6413	NM_008036	14282	Mm.248335	NM_008036	ENSMUSG00000003545	Fosb	-	FBJ osteosarcoma oncogene B	protein-coding
mm_151809.1	chr19	5457505	5457573	-	1	NA	promoter-TSS (NM_198616)	promoter-TSS (NM_198616)	24	NM_198616	240514	Mm.329657	NM_198616	ENSMUSG00000095098	Ccdc85b	AI842788|BB115872	coiled-coil domain containing 85B	protein-coding
mm_29464.1	chr3	113574791	113574802	-	1	NA	promoter-TSS (NM_007446)	promoter-TSS (NM_007446)	-34	NM_007446	11722	Mm.439727	NM_007446	ENSMUSG00000074264	Amy1	Amy-1|Amy1a|C030014B17Rik	amylase 1, salivary	protein-coding
mm_8628.1	chr1	156280364	156280397	-	1	NA	intron (NM_001134741, intron 9 of 17)	B4|SINE|B4	22968	NM_001134741	214575	Mm.252800	NM_001134741	ENSMUSG00000060985	Tdrd5	Gm103	tudor domain containing 5	protein-coding
mm_4364.1	chr1	172082305	172082309	+	1	NA	promoter-TSS (NM_009938)	promoter-TSS (NM_009938)	-222	NM_009938	12847	Mm.30041	NM_009938	ENSMUSG00000026553	Copa	AU040324|xenin	coatomer protein complex subunit alpha	protein-coding
mm_90322.1	chr10	127067087	127067107	+	1	NA	TTS (NM_025982)	TTS (NM_025982)	3164	NM_025982	67125	Mm.35650	NM_025982	ENSMUSG00000006736	Tspan31	2700085A14Rik|AW742554|Sas	tetraspanin 31	protein-coding
mm_149120.1	chr19	8989022	8989064	+	1	NA	promoter-TSS (NM_001286518)	promoter-TSS (NM_001286518)	-241	NR_104460	66395	Mm.203866	NM_009643	ENSMUSG00000069833	Ahnak	DY6	AHNAK nucleoprotein (desmoyokin)	protein-coding
mm_81879.1	chr9	119339649	119339661	+	1	NA	exon (NM_010851, exon 1 of 6)	exon (NM_010851, exon 1 of 6)	385	NM_010851	17874	Mm.213003	NM_010851	ENSMUSG00000032508	Myd88	-	myeloid differentiation primary response gene 88	protein-coding
mm_128651.1	chr15	59648143	59648168	-	1	NA	promoter-TSS (NM_144549)	promoter-TSS (NM_144549)	-499	NM_144549	211770	Mm.40298	NM_144549	ENSMUSG00000032501	Trib1	A530090O15Rik|TRB-1|Trb1	tribbles pseudokinase 1	protein-coding
mm_69839.1	chr7	141327650	141327661	-	1	NA	promoter-TSS (NM_001282076)	promoter-TSS (NM_001282076)	70	NM_016874	54006	Mm.28392	NM_016874	ENSMUSG00000058886	Deaf1	AU042387|C230009B13Rik|NUDR	deformed epidermal autoregulatory factor 1 (Drosophila)	protein-coding
mm_94552.1	chr11	11464021	11464056	+	1	NA	5' UTR (NM_001347068, exon 1 of 9)	5' UTR (NM_001347068, exon 1 of 9)	294	NM_001347068	73862	Mm.159077	NM_028669	ENSMUSG00000020191	4930415F15Rik	-	RIKEN cDNA 4930415F15 gene	protein-coding
mm_52428.1	chr6	113483413	113483435	+	1	NA	promoter-TSS (NM_133930)	promoter-TSS (NM_133930)	-145	NM_133930	171508	Mm.41593	NM_133930	ENSMUSG00000030284	Creld1	AI843811	cysteine-rich with EGF-like domains 1	protein-coding
mm_114985.1	chr13	97482748	97482759	+	1	NA	promoter-TSS (NR_110431)	promoter-TSS (NR_110431)	52	NR_110431	100039691	Mm.219358	NR_110430	ENSMUSG00000078952	Lncenc1	ENSMUSG00000078952|Gm11019|Gm2373|Lincenc1|Platr18|linc-Enc1	long non-coding RNA, embryonic stem cells expressed 1	ncRNA
mm_67092.1	chr7	68749243	68749251	-	1	NA	promoter-TSS (NM_001042592)	promoter-TSS (NM_001042592)	-9	NM_025549	66412	Mm.251199	NM_025549	ENSMUSG00000042659	Arrdc4	2410003C09Rik|AV216361	arrestin domain containing 4	protein-coding
mm_57997.1	chr6	136173081	136173093	-	1	NA	5' UTR (NM_008171, exon 2 of 15)	5' UTR (NM_008171, exon 2 of 15)	424	NM_008171	14812	Mm.436649	NM_008171	ENSMUSG00000030209	Grin2b	AW490526|GluN2B|NR2B|Nmdar2b	glutamate receptor, ionotropic, NMDA2B (epsilon 2)	protein-coding
mm_19109.1	chr2	79455073	79455089	-	1	NA	intron (NM_010894, intron 1 of 1)	intron (NM_010894, intron 1 of 1)	1555	NM_010894	18012	Mm.4636	NM_010894	ENSMUSG00000034701	Neurod1	BETA2|BHF-1|Nd1|Neurod|bHLHa3	neurogenic differentiation 1	protein-coding
mm_22734.1	chr3	19692016	19692026	+	1	NA	TTS (NM_001081281)	TTS (NM_001081281)	3375	NM_205769	12918	Mm.290689	NM_205769	ENSMUSG00000049796	Crh	CRF|Gm1347	corticotropin releasing hormone	protein-coding
mm_67945.1	chr7	100467126	100467148	-	1	NA	intron (NM_001017985, intron 32 of 32)	intron (NM_001017985, intron 32 of 32)	-5854	NM_009464	22229	Mm.6254	NM_009464	ENSMUSG00000032942	Ucp3	AI645527|Slc25a9|UCP-3	uncoupling protein 3 (mitochondrial, proton carrier)	protein-coding
mm_164516.1	chr16	96280802	96280867	+	1	NA	promoter-TSS (NM_033149)	promoter-TSS (NM_033149)	-198	NM_033149	93961	Mm.154783	NM_033149	ENSMUSG00000074892	B3galt5	1190002B21Rik|AU045265|b3Galt-V	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 5	protein-coding
mm_171490.1	chr4	146148146	146148148	+	1	NA	Intergenic	RLTR27|LTR|ERVK	-8680	NM_001177546	667666	Mm.459230	NM_001177545	ENSMUSG00000066007	Zfp600	Gm13164|OTTMUSG00000010694	zinc finger protein 600	protein-coding
mm_167996.1	chrX	170017152	170017187	+	1	NA	Intergenic	Intergenic	-38252	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_122369.1	chr14	39471189	39471191	-	1	NA	intron (NM_001190187, intron 1 of 9)	intron (NM_001190187, intron 1 of 9)	-1239	NR_131973	432842	Mm.352566	NR_131973		LOC432842	-	uncharacterized LOC432842	ncRNA
mm_139282.1	chr17	48264271	48264312	+	1	NA	promoter-TSS (NM_001163796)	promoter-TSS (NM_001163796)	-4	NM_172623	224840	Mm.131234	NM_172623	ENSMUSG00000051682	Treml4	5031403H21Rik|BB137214|IDCP1|TLT-4|TLT4|Treml3	triggering receptor expressed on myeloid cells-like 4	protein-coding
mm_111376.1	chr12	87266209	87266219	-	1	NA	promoter-TSS (NM_001142580)	promoter-TSS (NM_001142580)	72	NM_001142580	104799	Mm.208750	NM_134044	ENSMUSG00000021038	Vipas39	6720456H09Rik|9330175H22Rik|AI413782|SPE-39|Spe39|Vipar|hSPE-39	VPS33B interacting protein, apical-basolateral polarity regulator, spe-39 homolog	protein-coding
mm_59541.1	chr7	27838561	27838612	+	1	NA	promoter-TSS (NM_011762)	promoter-TSS (NM_011762)	2	NM_011762	22717	Mm.379046	NM_011762	ENSMUSG00000078779	Zfp59	Mfg-2|Mfg2	zinc finger protein 59	protein-coding
mm_166580.1	chr6	52285030	52285034	+	1	NA	Intergenic	MIRb|SINE|MIR	22257	NR_110442	791364	Mm.97466	NR_110441	ENSMUSG00000055408	Hottip	ENSMUSG00000055408|Gm15053|OTTMUSG00000018874	Hoxa distal transcript antisense RNA	ncRNA
mm_35978.1	chr4	53632048	53632058	-	1	NA	intron (NM_001195284, intron 1 of 12)	intron (NM_001195284, intron 1 of 12)	582	NM_001195284	319636	Mm.103464	NM_176966	ENSMUSG00000054752	Fsd1l	A230072O16Rik|Ccdc10|Csdufd1|Fsd1nl|OTTMUSG00000007002	fibronectin type III and SPRY domain containing 1-like	protein-coding
mm_79277.1	chr9	50775280	50775327	+	1	NA	promoter-TSS (NM_133981)	promoter-TSS (NM_133981)	78	NR_045601	102580	Mm.160035	NM_133981	ENSMUSG00000032059	Alg9	8230402H15Rik|AI747665|B430313H07Rik|Dibd1	asparagine-linked glycosylation 9 (alpha 1,2 mannosyltransferase)	protein-coding
mm_14055.1	chr2	122572150	122572157	+	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	39124	NM_025961	67092	Mm.29975	NM_025961	ENSMUSG00000027199	Gatm	1810003P21Rik|AI314789|AT	glycine amidinotransferase (L-arginine:glycine amidinotransferase)	protein-coding
mm_139339.1	chr17	49454967	49454985	+	1	NA	3' UTR (NM_020042, exon 11 of 11)	3' UTR (NM_020042, exon 11 of 11)	26612	NM_020042	56738	Mm.22256	NM_020042	ENSMUSG00000064120	Mocs1	3110045D15Rik|AI043170|AW536397	molybdenum cofactor synthesis 1	protein-coding
mm_129685.1	chr15	81408282	81408301	-	1	NA	promoter-TSS (NM_021317)	promoter-TSS (NM_021317)	-18	NM_021317	57755	Mm.440590	NM_021317	ENSMUSG00000047108	Dnajb7	4933424H20Rik|Dj5|mDj5	DnaJ heat shock protein family (Hsp40) member B7	protein-coding
mm_128722.1	chr15	64059783	64059786	-	1	NA	intron (NM_144846, intron 1 of 11)	intron (NM_144846, intron 1 of 11)	664	NM_144846	223601	Mm.246108	NM_144846	ENSMUSG00000022378	Fam49b	0910001A06Rik|AW122079	family with sequence similarity 49, member B	protein-coding
mm_26468.1	chr3	144569983	144569989	+	1	NA	promoter-TSS (NM_053102)	promoter-TSS (NM_053102)	230	NM_011828	23908	Mm.12863	NM_011828	ENSMUSG00000040151	Hs2st1	AW214369|Hs2st|mKIAA0448	heparan sulfate 2-O-sulfotransferase 1	protein-coding
mm_544.1	chr1	38018068	38018084	+	1	NA	exon (NM_198303, exon 3 of 24)	exon (NM_198303, exon 3 of 24)	20066	NM_198303	226982	Mm.260943	NM_198303	ENSMUSG00000026083	Eif5b	A030003E17Rik|BC018347|IF2	eukaryotic translation initiation factor 5B	protein-coding
mm_171470.1	chr4	145781495	145781502	+	1	NA	promoter-TSS (NM_001083918)	promoter-TSS (NM_001083918)	-45	NM_001083918	666532	Mm.392861	NM_001083918	ENSMUSG00000067916	Zfp991	Gm13139|OTTMUSG00000010657	zinc finger protein 991	protein-coding
mm_73746.1	chr8	114439664	114439710	+	1	NA	promoter-TSS (NM_019573)	promoter-TSS (NM_019573)	35	NM_019573	80707	Mm.440420	NM_019573	ENSMUSG00000004637	Wwox	5330426P09Rik|9030416C10Rik|WOX1	WW domain-containing oxidoreductase	protein-coding
mm_100445.1	chr11	119491360	119491405	+	1	NA	promoter-TSS (NM_177394)	promoter-TSS (NM_177394)	35	NM_001164636	338371	Mm.271946	NM_177394	ENSMUSG00000039850	Endov	A730011L01Rik	endonuclease V	protein-coding
mm_128971.1	chr15	74832325	74832335	-	1	NA	Intergenic	Intergenic	9313	NM_001033229	110115	Mm.322606	NM_001033229	ENSMUSG00000075604	Cyp11b1	AA389061|CPN1|Cyp11b|Cyp11b-1|FHI	cytochrome P450, family 11, subfamily b, polypeptide 1	protein-coding
mm_12982.1	chr2	90783270	90783276	+	1	NA	intron (NM_178755, intron 1 of 17)	intron (NM_178755, intron 1 of 17)	529	NM_178755	271813	Mm.61146	NM_178755	ENSMUSG00000040812	Agbl2	4930524K04|A430081C19Rik|CCP2	ATP/GTP binding protein-like 2	protein-coding
mm_85212.1	chr9	96854568	96854570	-	1	NA	intron (NM_001289646, intron 3 of 6)	intron (NM_001289646, intron 3 of 6)	34905	NM_001289646	235534	Mm.233031	NM_153420	ENSMUSG00000043587	Pxylp1	9430094M07Rik|Acpl2|BB177120|C130099A20Rik	2-phosphoxylose phosphatase 1	protein-coding
mm_106548.1	chr11	120581197	120581237	-	1	NA	intron (NM_133796, intron 1 of 5)	CpG	403	NM_133796	192662	Mm.30016	NM_133796	ENSMUSG00000025132	Arhgdia	5330430M07Rik|Gdi-1|Rho-GDI|RhoDGI|RhoGDI-1	Rho GDP dissociation inhibitor (GDI) alpha	protein-coding
mm_88678.1	chr10	80053188	80053190	+	1	NA	promoter-TSS (NM_008162)	promoter-TSS (NM_008162)	-299	NM_008162	625249	Mm.332810	NM_008162	ENSMUSG00000075706	Gpx4	GPx-4|GSHPx-4|PHGPx|mtPHGPx|snGPx	glutathione peroxidase 4	protein-coding
mm_68760.1	chr7	121589824	121589850	-	1	NA	promoter-TSS (NR_131051)	promoter-TSS (NR_131051)	-1	NR_102286	75793	Mm.23397	NR_102286		4933432K03Rik	1700001C18Rik|4930433G11Rik|AI428127	RIKEN cDNA 4933432K03 gene	ncRNA
mm_95949.1	chr11	58390158	58390234	+	1	NA	exon (NM_001083884, exon 7 of 7)	exon (NM_001083884, exon 7 of 7)	9550	NM_001330197	70163	Mm.24119	NM_027339	ENSMUSG00000013643	Lypd8	2210415F13Rik	LY6/PLAUR domain containing 8	protein-coding
mm_151878.1	chr19	5798459	5798470	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	-2483	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_12299.1	chr2	69093074	69093093	+	1	NA	intron (NM_172856, intron 8 of 9)	B3|SINE|B2	-42717	NM_181547	329416	Mm.90047	NM_181547	ENSMUSG00000034738	Nostrin	Daip2|mDaIP2	nitric oxide synthase trafficker	protein-coding
mm_98762.1	chr11	96574872	96574872	+	1	NA	intron (NM_001033186, intron 4 of 12)	intron (NM_001033186, intron 4 of 12)	110281	NM_001177898	78473	Mm.395840	NM_001033186	ENSMUSG00000057058	Skap1	1700091G21Rik|Scap1|Skap-55	src family associated phosphoprotein 1	protein-coding
mm_121796.1	chr14	20083178	20083188	-	1	NA	promoter-TSS (NM_026209)	promoter-TSS (NM_026209)	-11	NM_026209	67509	Mm.292423	NM_026209	ENSMUSG00000045107	Saysd1	1810063B07Rik|4930488P03Rik	SAYSVFN motif domain containing 1	protein-coding
mm_25103.1	chr3	101286676	101286678	+	1	NA	intron (NM_013486, intron 2 of 4)	intron (NM_013486, intron 2 of 4)	1262	NM_013486	12481	Mm.22842	NM_013486	ENSMUSG00000027863	Cd2	LFA-2|Ly-37|Ly37	CD2 antigen	protein-coding
mm_7353.1	chr1	106608520	106608523	-	1	NA	intron (NM_009741, intron 1 of 1)	intron (NM_009741, intron 1 of 1)	-61890	NR_106164	102466254		NR_106164	ENSMUSG00000098344	Mir3473f	Gm27846|mmu-mir-3473f	microRNA 3473f	ncRNA
mm_100136.1	chr11	115974931	115974982	+	1	NA	5' UTR (NM_133663, exon 1 of 39)	5' UTR (NM_133663, exon 1 of 39)	231	NM_133663	192897	Mm.213873	NM_133663	ENSMUSG00000020758	Itgb4	AA407042|C230078O20|CD104	integrin beta 4	protein-coding
mm_14322.1	chr2	129365951	129365959	+	1	NA	intron (NM_008361, intron 6 of 6)	intron (NM_008361, intron 6 of 6)	-3947	NR_015474	329514	Mm.207315	NM_177848	ENSMUSG00000074805	Il1bos	9430083I22|Gm14047|OTTMUSG00000015529	interleukin 1 beta, opposite strand	ncRNA
mm_43087.1	chr5	124450373	124450384	+	1	NA	intron (NM_001310725, intron 2 of 6)	intron (NM_001310725, intron 2 of 6)	3674	NM_001310727	67956	Mm.137966	NM_030241	ENSMUSG00000049327	Kmt5a	2410195B05Rik|AA617402|AW536475|PR-SET7|PR/SET07|Setd8	lysine methyltransferase 5A	protein-coding
mm_38233.1	chr4	136053344	136053415	-	1	NA	promoter-TSS (NM_025919)	promoter-TSS (NM_025919)	-8	NM_025919	67025	Mm.276856	NM_025919	ENSMUSG00000059291	Rpl11	2010203J19Rik	ribosomal protein L11	protein-coding
mm_16362.1	chr2	174598696	174598726	+	1	NA	Intergenic	Intergenic	-44823	NM_001099328	100043757	Mm.48711	NM_001099328	ENSMUSG00000050600	Zfp831	ENSMUSG00000050600|OTTMUSG00000017459	zinc finger protein 831	protein-coding
mm_63636.1	chr7	128523730	128523734	+	1	NA	5' UTR (NM_013863, exon 1 of 4)	5' UTR (NM_013863, exon 1 of 4)	149	NM_013863	29810	Mm.84073	NM_013863	ENSMUSG00000030847	Bag3	AA407278|Bis|mg638	BCL2-associated athanogene 3	protein-coding
mm_154560.1	chrX	4899362	4899381	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-52764	NM_001243024	100042275	Mm.427352	NM_001243024	ENSMUSG00000094860	Btbd35f27	Gm3763	BTB domain containing 35, family member 27	protein-coding
mm_168938.1	chr12	69361474	69361488	-	1	NA	Intergenic	7SLRNA|srpRNA|srpRNA	-4305	NM_025441	66244	Mm.46705	NM_025441	ENSMUSG00000020982	Nemf	1500011I12Rik|4933405E14Rik|Sdccag1	nuclear export mediator factor	protein-coding
mm_58040.1	chr6	136826022	136826033	-	1	NA	exon (NM_021714, exon 2 of 12)	exon (NM_021714, exon 2 of 12)	2189	NM_021714	60321	Mm.141197	NM_021714	ENSMUSG00000030216	Wbp11	2510026P17Rik|D6Wsu113e|Npwbp|SIPP1	WW domain binding protein 11	protein-coding
mm_35529.1	chr4	41312927	41312930	-	1	NA	intron (NM_026893, intron 2 of 8)	intron (NM_026893, intron 2 of 8)	1973	NM_026893	68970	Mm.28891	NM_026893	ENSMUSG00000028436	Dcaf12	1500001L20Rik|5830424K06Rik|AA420338|AI851081|Wdr40a	DDB1 and CUL4 associated factor 12	protein-coding
mm_33827.1	chr4	135545231	135545242	+	1	NA	intron (NM_001013756, intron 15 of 15)	intron (NM_001013756, intron 15 of 15)	28384	NM_001013756	230824	Mm.331972	NM_001013756	ENSMUSG00000037188	Grhl3	AI561912|Get1|Som|Tfcp2l4|ct	grainyhead-like 3 (Drosophila)	protein-coding
mm_36976.1	chr4	109531199	109531212	-	1	NA	promoter-TSS (NM_026291)	promoter-TSS (NM_026291)	-1	NM_001199090	67646	Mm.45820	NM_026291	ENSMUSG00000060491	4930522H14Rik	1700007J23Rik	RIKEN cDNA 4930522H14 gene	protein-coding
mm_155181.1	chrX	53724895	53724897	+	1	NA	promoter-TSS (NM_029142)	promoter-TSS (NM_029142)	65	NM_029142	75013	Mm.336332	NM_029142	ENSMUSG00000055555	4930502E18Rik	Ct55	RIKEN cDNA 4930502E18 gene	protein-coding
mm_167852.1	chrX	9465737	9465750	+	1	NA	exon (NM_007807, exon 3 of 13)	exon (NM_007807, exon 3 of 13)	3581	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_140595.1	chr17	10282888	10282903	-	1	NA	exon (NM_001159517, exon 2 of 8)	exon (NM_001159517, exon 2 of 8)	36466	NM_021881	19317	Mm.130694	NM_021881	ENSMUSG00000062078	Qk	1110003F05Rik|1500005P18|QkI|l(17)-1Wis|l17Wis1	quaking	protein-coding
mm_80407.1	chr9	77636714	77636732	+	1	NA	promoter-TSS (NM_172925)	promoter-TSS (NM_172925)	-9	NM_172925	244923	Mm.138238	NM_172925	ENSMUSG00000044938	Klhl31	9830147P19Rik|D930047P17Rik|Kbtbd1	kelch-like 31	protein-coding
mm_78311.1	chr9	23222715	23222720	+	1	NA	promoter-TSS (NM_028472)	promoter-TSS (NM_028472)	-359	NM_028472	73230	Mm.335020	NM_028472	ENSMUSG00000031963	Bmper	3110056H04Rik|CV-2|Crim3|Cv2	BMP-binding endothelial regulator	protein-coding
mm_30752.1	chr4	14930620	14930701	+	1	NA	promoter-TSS (NM_001243100)	promoter-TSS (NM_001243100)	19	NM_001243100	100038514	Mm.331495	NM_001243100		Gm11837	OTTMUSG00000004551	predicted gene 11837	protein-coding
mm_70088.1	chr7	142655726	142655822	-	1	NA	promoter-TSS (NR_030251)	promoter-TSS (NR_030251)	-778	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_46733.1	chr5	110780570	110780626	-	1	NA	promoter-TSS (NM_019700)	promoter-TSS (NM_019700)	-2	NM_001025561	56361	Mm.23528	NM_019700	ENSMUSG00000029507	Pus1	A730013B20Rik|MPUS1|mPus1p	pseudouridine synthase 1	protein-coding
mm_74582.1	chr8	11279658	11279692	-	1	NA	intron (NR_133670, intron 1 of 52)	intron (NR_133670, intron 1 of 52)	-33130	NM_009932	12827	Mm.181021	NM_009932	ENSMUSG00000031503	Col4a2	Col4a-2	collagen, type IV, alpha 2	protein-coding
mm_38383.1	chr4	138770874	138770885	-	1	NA	Intergenic	Intergenic	-4856	NM_001347230	18782	Mm.71913	NM_011109	ENSMUSG00000041202	Pla2g2d	Splash|mGIID	phospholipase A2, group IID	protein-coding
mm_118735.1	chr14	22308224	22308225	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	234574	NR_046307	74896	Mm.444661	NR_046307		4930405A10Rik	4930456G20Rik	RIKEN cDNA 4930405A10 gene	ncRNA
mm_76132.1	chr8	80880481	80880499	-	1	NA	promoter-TSS (NM_001301298)	promoter-TSS (NM_001301298)	-11	NM_021356	14388	Mm.277409	NM_021356	ENSMUSG00000031714	Gab1	AA408973|AW107238	growth factor receptor bound protein 2-associated protein 1	protein-coding
mm_154317.1	chrM	2152	2162	+	1	NA	NA	LSU-rRNA_Hsa|rRNA|rRNA	NA	NA								
mm_119352.1	chr14	41114213	41114223	+	1	NA	exon (NM_133653, exon 5 of 10)	exon (NM_133653, exon 5 of 10)	9185	NM_133653	11720	Mm.14064	NM_133653	ENSMUSG00000037798	Mat1a	AI046368|AdoMet|Ams|MAT|MATA1|SAMS|SAMS1	methionine adenosyltransferase I, alpha	protein-coding
mm_148481.1	chr19	4126009	4126021	+	1	NA	promoter-TSS (NM_016666)	promoter-TSS (NM_016666)	55	NM_025889	66990	Mm.276255	NM_025889		Tmem134	2410001H17Rik|AI463452	transmembrane protein 134	protein-coding
mm_155815.1	chrX	100524259	100524288	+	1	NA	promoter-TSS (NM_001114084)	promoter-TSS (NM_001114084)	-565	NM_001114084	668257	Mm.95646	NM_001114084	ENSMUSG00000067597	Dgat2l6	9930021F22Rik	diacylglycerol O-acyltransferase 2-like 6	protein-coding
mm_49780.1	chr6	35133874	35133894	+	1	NA	promoter-TSS (NM_001164412)	promoter-TSS (NM_001164412)	-147	NM_016877	53621	Mm.214525	NM_016877	ENSMUSG00000038784	Cnot4	Not4|Not4h|Not4hp	CCR4-NOT transcription complex, subunit 4	protein-coding
mm_78606.1	chr9	37544954	37544958	+	1	NA	TTS (NM_020518)	TTS (NM_020518)	5701	NM_020518	57276	Mm.27478	NM_020518	ENSMUSG00000001943	Vsig2	1190004B15Rik|2210413P10Rik|AU040484|CTX|Ctm	V-set and immunoglobulin domain containing 2	protein-coding
mm_120969.1	chr14	77915161	77915165	+	1	NA	intron (NM_178825, intron 1 of 6)	intron (NM_178825, intron 1 of 6)	10924	NM_029495	108670	Mm.68134	NM_029495	ENSMUSG00000022014	Epsti1	2310046K10Rik|5033415K03Rik|BRESI1	epithelial stromal interaction 1 (breast)	protein-coding
mm_140879.1	chr17	23829001	23829012	-	1	NA	intron (NM_026305, intron 1 of 3)	CpG-6036	103	NM_026305	67673	Mm.153758	NM_026305	ENSMUSG00000055839	Elob	0610040H15Rik|Tceb2	elongin B	protein-coding
mm_167767.1	chr9	110763729	110763735	+	1	NA	promoter-TSS (NM_010859)	promoter-TSS (NM_010859)	51	NM_010859	17897	Mm.7353	NM_010859	ENSMUSG00000059741	Myl3	MLC1s|MLC1v|Mylc|VLC1	myosin, light polypeptide 3	protein-coding
mm_137950.1	chr17	32879127	32879133	+	1	NA	TTS (NM_207245)	TTS (NM_207245)	12473	NM_207245	240066	Mm.26636	NM_207245	ENSMUSG00000095325	Zfp870	AI173952	zinc finger protein 870	protein-coding
mm_69802.1	chr7	141183378	141183397	-	1	NA	Intergenic	L1MEf|LINE|L1	-10536	NM_001172100	107702	Mm.197493	NM_145135	ENSMUSG00000038650	Rnh1	AW546468|C80305|RNH	ribonuclease/angiogenin inhibitor 1	protein-coding
mm_119615.1	chr14	51114406	51114416	+	1	NA	Intergenic	Intergenic	-2142	NM_203508	219026	Mm.297297	NM_203508	ENSMUSG00000072575	Eddm3b	Fam12|Gm75	epididymal protein 3B	protein-coding
mm_57996.1	chr6	136172921	136172923	-	1	NA	5' UTR (NM_008171, exon 2 of 15)	5' UTR (NM_008171, exon 2 of 15)	589	NM_008171	14812	Mm.436649	NM_008171	ENSMUSG00000030209	Grin2b	AW490526|GluN2B|NR2B|Nmdar2b	glutamate receptor, ionotropic, NMDA2B (epsilon 2)	protein-coding
mm_23731.1	chr3	69028523	69028533	+	1	NA	exon (NM_133786, exon 16 of 24)	exon (NM_133786, exon 16 of 24)	16214	NM_025863	66949	Mm.176695	NM_025863	ENSMUSG00000034317	Trim59	2310035M22Rik|2700022F13Rik|Mrf1|TSBF1	tripartite motif-containing 59	protein-coding
mm_65368.1	chr7	25072492	25072533	-	1	NA	promoter-TSS (NM_008168)	promoter-TSS (NM_008168)	-143	NM_008168	14809	Mm.2879	NM_008168	ENSMUSG00000003378	Grik5	GluK5|GluRgamma2|KA2	glutamate receptor, ionotropic, kainate 5 (gamma 2)	protein-coding
mm_140666.1	chr17	12915636	12915656	-	1	NA	promoter-TSS (NM_013686)	promoter-TSS (NM_013686)	445	NM_026310	67681	Mm.290166	NM_026310	ENSMUSG00000057388	Mrpl18	1010001C05Rik|C79879|HSPC071|MRP-L18	mitochondrial ribosomal protein L18	protein-coding
mm_143302.1	chr17	65985858	65985872	-	1	NA	exon (NM_001025572, exon 9 of 13)	exon (NM_001025572, exon 9 of 13)	-34678	NM_023053	65960	Mm.10153	NM_023053	ENSMUSG00000024098	Twsg1	1810013J15Rik|9030422N06Rik|AW552143|D17Ertd403e|Tsg|Twg	twisted gastrulation BMP signaling modulator 1	protein-coding
mm_91671.1	chr10	43174590	43174615	-	1	NA	promoter-TSS (NR_102361)	promoter-TSS (NR_102361)	-72	NM_175407	109205	Mm.153750	NM_175407	ENSMUSG00000038248	Sobp	2900009C16Rik|5330439J01Rik|JXC1|jc	sine oculis-binding protein homolog (Drosophila)	protein-coding
mm_38052.1	chr4	134000858	134000904	-	1	NA	promoter-TSS (NM_026144)	promoter-TSS (NM_026144)	-17	NM_026144	67422	Mm.100290	NM_026144	ENSMUSG00000012117	Dhdds	3222401G21Rik|CIT|DS|HDS|W91638	dehydrodolichyl diphosphate synthase	protein-coding
mm_77919.1	chr9	7352376	7352386	+	1	NA	intron (NM_001320077, intron 5 of 10)	intron (NM_001320077, intron 5 of 10)	5007	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_95119.1	chr11	34078170	34078181	+	1	NA	intron (NM_010696, intron 10 of 20)	intron (NM_010696, intron 10 of 20)	30974	NM_010696	16822	Mm.265350	NM_010696	ENSMUSG00000002699	Lcp2	AI323664|BB161688|SLP-76|SLP76|m1Khoe|twm	lymphocyte cytosolic protein 2	protein-coding
mm_63068.1	chr7	122133053	122133090	+	1	NA	promoter-TSS (NM_001081238)	promoter-TSS (NM_001081238)	30	NM_021608	59288	Mm.478285	NM_021608	ENSMUSG00000030868	Dctn5	4930427E12Rik|C78178|b2b315Clo	dynactin 5	protein-coding
mm_55792.1	chr6	82726649	82726657	-	1	NA	3' UTR (NM_013820, exon 18 of 18)	3' UTR (NM_013820, exon 18 of 18)	47801	NM_013820	15277	Mm.255848	NM_013820	ENSMUSG00000000628	Hk2	AI642394|HKII	hexokinase 2	protein-coding
mm_103341.1	chr11	74723830	74723860	-	1	NA	promoter-TSS (NR_037610)	promoter-TSS (NR_037610)	13	NR_037610	18472	Mm.397111	NM_013625	ENSMUSG00000020745	Pafah1b1	LIS-1|Lis1|MMS10-U|Mdsh|Ms10u|Pafaha	platelet-activating factor acetylhydrolase, isoform 1b, subunit 1	protein-coding
mm_173082.1	chrX	142298284	142298287	+	1	NA	non-coding (NR_002883, exon 1 of 1)	non-coding (NR_002883, exon 1 of 1)	780	NR_002883	434858	Mm.391346	NR_002883		Gm5643	EG434858	heterogeneous nuclear ribonucleoprotein A1 pseudogene	pseudo
mm_145755.1	chr18	64887691	64887762	+	1	NA	promoter-TSS (NM_001114386)	promoter-TSS (NM_001114386)	-30	NM_001114386	83814	Mm.98668	NM_031881	ENSMUSG00000024589	Nedd4l	1300012C07Rik|Nedd4-2|Nedd4b	neural precursor cell expressed, developmentally down-regulated gene 4-like	protein-coding
mm_141008.1	chr17	24960662	24960693	-	1	NA	promoter-TSS (NM_198937)	promoter-TSS (NM_198937)	-54	NM_198937	52009	Mm.371601	NM_198937	ENSMUSG00000024165	Hn1l	2810430B18Rik|AL022629|C16orf34|D17Ertd441e	hematological and neurological expressed 1-like	protein-coding
mm_49868.1	chr6	38558949	38558962	+	1	NA	intron (NM_001331223, intron 1 of 12)	B2_Mm2|SINE|B2	3232	NM_001331223	192196	Mm.276133	NM_138680	ENSMUSG00000029823	Luc7l2	4930471C18Rik|AA522013|AU015269|CGI59|Cgi74	LUC7-like 2 (S. cerevisiae)	protein-coding
mm_136897.1	chr17	13015022	13015035	+	1	NA	exon (NM_013671, exon 5 of 5)	exon (NM_013671, exon 5 of 5)	7189	NM_013671	20656	Mm.290876	NM_013671	ENSMUSG00000006818	Sod2	MnSOD|Sod-2	superoxide dismutase 2, mitochondrial	protein-coding
mm_145691.1	chr18	61965609	61965610	+	1	NA	intron (NM_172628, intron 2 of 16)	intron (NM_172628, intron 2 of 16)	12534	NM_172628	225608	Mm.262320	NM_172628	ENSMUSG00000045629	Sh3tc2	D430044G18Rik	SH3 domain and tetratricopeptide repeats 2	protein-coding
mm_173340.1	chrY	90811859	90811859	+	1	NA	intron (NM_133362, intron 2 of 3)	(CAGA)n|Simple_repeat|Simple_repeat	26417	NM_133362	170942	Mm.76062	NM_133362	ENSMUSG00000096768	Erdr1	edr	erythroid differentiation regulator 1	protein-coding
mm_1597.1	chr1	74375259	74375269	+	1	NA	promoter-TSS (NM_013612)	promoter-TSS (NM_013612)	61	NM_013612	18173	Mm.2913	NM_013612	ENSMUSG00000026177	Slc11a1	Bcg|Ity|Ity1|Lsh|Nramp|Nramp1|ity	solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1	protein-coding
mm_54849.1	chr6	42590849	42590853	-	1	NA	intron (NM_203396, intron 5 of 6)	RLTR12B|LTR|ERVK	6521	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_58728.1	chr7	13029550	13029569	+	1	NA	exon (NM_011588, exon 12 of 17)	exon (NM_011588, exon 12 of 17)	5218	NM_026885	68953	Mm.295670	NM_026885	ENSMUSG00000033916	Chmp2a	1500016L11Rik	charged multivesicular body protein 2A	protein-coding
mm_139849.1	chr17	69417375	69417419	+	1	NA	non-coding (NR_026848, exon 1 of 1)	non-coding (NR_026848, exon 1 of 1)	950	NR_026848	77533	Mm.266592	NR_026848		C030034I22Rik	-	RIKEN cDNA C030034I22 gene	ncRNA
mm_108433.1	chr12	82246771	82246781	+	1	NA	intron (NM_001167983, intron 2 of 23)	intron (NM_001167983, intron 2 of 23)	-64573	NM_172579	217692	Mm.261333	NM_172579	ENSMUSG00000042700	Sipa1l1	4931426N11Rik|AW213287|Spar|mKIAA0440	signal-induced proliferation-associated 1 like 1	protein-coding
mm_14544.1	chr2	132846639	132846708	+	1	NA	promoter-TSS (NM_001024385)	promoter-TSS (NM_001024385)	7	NM_001024385	66586	Mm.357342	NM_025646	ENSMUSG00000027357	Crls1	0610009I22Rik|4930557M15Rik|5730490M08Rik	cardiolipin synthase 1	protein-coding
mm_120879.1	chr14	75284397	75284407	+	1	NA	promoter-TSS (NM_026083)	promoter-TSS (NM_026083)	29	NM_026083	67302	Mm.74704	NM_026083	ENSMUSG00000022000	Zc3h13	2600010B19Rik|3110050K21Rik|4930570G11Rik|C87618	zinc finger CCCH type containing 13	protein-coding
mm_99014.1	chr11	98863656	98863690	+	1	NA	promoter-TSS (NM_197940)	promoter-TSS (NM_197940)	75	NM_197940	68524	Mm.28661	NM_197940	ENSMUSG00000038013	Wipf2	1110014J05Rik|5730509C05Rik|AA407487|Gm1176|Wich|Wire	WAS/WASL interacting protein family, member 2	protein-coding
mm_123546.1	chr14	66831118	66831194	-	1	NA	intron (NM_009955, intron 4 of 13)	(TG)n|Simple_repeat|Simple_repeat	37444	NM_009955	12934	Mm.352648	NM_009955	ENSMUSG00000022048	Dpysl2	AI851130|Crmp2|DRP2|Musunc33|TOAD-64|Ulip2	dihydropyrimidinase-like 2	protein-coding
mm_66484.1	chr7	45017281	45017291	-	1	NA	promoter-TSS (NM_009101)	promoter-TSS (NM_009101)	-721	NM_009101	20130	Mm.389894	NM_009101	ENSMUSG00000038387	Rras	AI573426	related RAS viral (r-ras) oncogene	protein-coding
mm_164024.1	chr14	75185874	75185898	-	1	NA	intron (NM_008879, intron 2 of 16)	intron (NM_008879, intron 2 of 16)	49461	NM_008879	18826	Mm.153911	NM_008879	ENSMUSG00000021998	Lcp1	AW536232|D14Ertd310e|LCP-1|Pls2|pp65	lymphocyte cytosolic protein 1	protein-coding
mm_115359.1	chr13	112801156	112801183	+	1	NA	5' UTR (NM_008903, exon 1 of 6)	5' UTR (NM_008903, exon 1 of 6)	392	NM_008247	19012	Mm.291029	NM_008247	ENSMUSG00000021759	Plpp1	Hic53|Hpic53|LPP-1|LPP1|PAP-2a|PAP2-alpha|PAP2a|Ppap2a|mPAP	phospholipid phosphatase 1	protein-coding
mm_30173.1	chr3	144202580	144202615	-	1	NA	promoter-TSS (NM_001161769)	promoter-TSS (NM_001161769)	-201	NM_001161769	16911	Mm.29187	NM_010723	ENSMUSG00000028266	Lmo4	A730077C12Rik|Crp3|Etohi4	LIM domain only 4	protein-coding
mm_42323.1	chr5	114899758	114899772	+	1	NA	exon (NM_011854, exon 2 of 6)	exon (NM_011854, exon 2 of 6)	2831	NM_011854	23962	Mm.228363	NM_011854	ENSMUSG00000029561	Oasl2	M1204|Mmu-OASL|Oasl	2'-5' oligoadenylate synthetase-like 2	protein-coding
mm_62762.1	chr7	112225838	112225848	+	1	NA	promoter-TSS (NM_177282)	promoter-TSS (NM_177282)	7	NM_001193305	320878	Mm.52312	NM_177282	ENSMUSG00000038244	Mical2	5330438E18Rik|9530064J02|MICAL-2|mKIAA0750	microtubule associated monooxygenase, calponin and LIM domain containing 2	protein-coding
mm_67016.1	chr7	65635926	65635930	-	1	NA	Intergenic	Intergenic	-8970	NM_172310	272396	Mm.35127	NM_172310	ENSMUSG00000030515	Tarsl2	A530046H20Rik	threonyl-tRNA synthetase-like 2	protein-coding
mm_103710.1	chr11	79518672	79518702	-	1	NA	intron (NM_146023, intron 3 of 3)	intron (NM_146023, intron 3 of 3)	5075	NM_001077496	216984	Mm.439665	NM_001077496	ENSMUSG00000093938	Evi2b	Evi-2|Evi2	ecotropic viral integration site 2b	protein-coding
mm_105280.1	chr11	102430196	102430264	-	1	NA	promoter-TSS (NM_008175)	promoter-TSS (NM_008175)	-92	NM_008175	14824	Mm.1568	NM_008175	ENSMUSG00000034708	Grn	Pgrn|epithelin	granulin	protein-coding
mm_163945.1	chr14	51895347	51895347	-	1	NA	exon (NM_001039676, exon 4 of 4)	exon (NM_001039676, exon 4 of 4)	1737	NM_001039676	214922	Mm.281343	NM_001039676	ENSMUSG00000072572	Slc39a2	F730005G13Rik|Gm1789|Gm289|Zip2	solute carrier family 39 (zinc transporter), member 2	protein-coding
mm_124390.1	chr14	110755042	110755099	-	1	NA	promoter-TSS (NM_175499)	promoter-TSS (NM_175499)	79	NM_175499	239250	Mm.49728	NM_175499	ENSMUSG00000045871	Slitrk6	4832410J21Rik|Sltk6	SLIT and NTRK-like family, member 6	protein-coding
mm_50618.1	chr6	50110187	50110295	+	1	NA	promoter-TSS (NM_001164734)	promoter-TSS (NM_001164734)	0	NM_019939	56524	Mm.41288	NM_008016	ENSMUSG00000038388	Mpp6	P55t|Pals2	membrane protein, palmitoylated 6 (MAGUK p55 subfamily member 6)	protein-coding
mm_59759.1	chr7	28830008	28830028	+	1	NA	exon (NM_016772, exon 5 of 10)	exon (NM_016772, exon 5 of 10)	-3776	NM_010706	16855	Mm.210336	NM_010706	ENSMUSG00000053964	Lgals4	gal-4	lectin, galactose binding, soluble 4	protein-coding
mm_92819.1	chr10	81460759	81460773	-	1	NA	3' UTR (NM_176954, exon 12 of 12)	3' UTR (NM_176954, exon 12 of 12)	12365	NM_001311127	319586	Mm.152689	NM_176954	ENSMUSG00000034818	Celf5	4930565A21Rik|Brunol5	CUGBP, Elav-like family member 5	protein-coding
mm_28751.1	chr3	95818896	95818907	-	1	NA	promoter-TSS (NM_001081293)	promoter-TSS (NM_001081293)	52	NM_001081293	75137	Mm.196275	NM_028328	ENSMUSG00000028106	Rprd2	2810036A19Rik|4930535B03Rik|6720469I21Rik|AL022841|AL022940|AU021304|BB077382|mKIAA0460	regulation of nuclear pre-mRNA domain containing 2	protein-coding
mm_74597.1	chr8	11635642	11635645	-	1	NA	promoter-TSS (NR_106097)	promoter-TSS (NR_106097)	93	NR_106097	102465714		NR_106097	ENSMUSG00000104958	Mir7238	mmu-mir-7238	microRNA 7238	ncRNA
mm_61289.1	chr7	67647406	67647456	+	1	NA	promoter-TSS (NM_025905)	promoter-TSS (NM_025905)	21	NM_025905	67009	Mm.249356	NM_025905	ENSMUSG00000030555	Ttc23	1600012K10Rik	tetratricopeptide repeat domain 23	protein-coding
mm_164913.1	chr18	73754328	73754332	-	1	NA	intron (NM_053255, intron 1 of 3)	CpG	149	NM_053255	114615	Mm.50642	NM_053255	ENSMUSG00000036941	Elac1	2610018O07Rik|8430417G19Rik	elaC ribonuclease Z 1	protein-coding
mm_153923.1	chr19	47314765	47314788	-	1	NA	intron (NM_001164717, intron 7 of 13)	intron (NM_001164717, intron 7 of 13)	-41187	NR_105961	102466782		NR_105961	ENSMUSG00000098786	Mir6995	Gm27576|mmu-mir-6995	microRNA 6995	ncRNA
mm_49672.1	chr6	31398818	31398856	+	1	NA	promoter-TSS (NM_013791)	promoter-TSS (NM_013791)	9	NM_013791	27418	Mm.238038	NM_013791	ENSMUSG00000025609	Mkln1	A130067F06Rik|AU015903|BB154892	muskelin 1, intracellular mediator containing kelch motifs	protein-coding
mm_166530.1	chr6	29694252	29694254	+	1	NA	promoter-TSS (NM_001301407)	promoter-TSS (NM_001301407)	39	NM_146173	232670	Mm.225289	NM_146173	ENSMUSG00000001763	Tspan33	1300010A20Rik|Pen	tetraspanin 33	protein-coding
mm_58119.1	chr6	139501884	139501902	-	1	NA	promoter-TSS (NM_001128090)	promoter-TSS (NM_001128090)	16	NM_001128090	632971	Mm.475610	NM_001128090	ENSMUSG00000092164	Rergl	EG632971	RERG/RAS-like	protein-coding
mm_39575.1	chr5	23434092	23434130	+	1	NA	promoter-TSS (NM_026984)	promoter-TSS (NM_026984)	242	NR_040469	269630	Mm.425231	NR_040469	ENSMUSG00000073147	5031425E22Rik	-	RIKEN cDNA 5031425E22 gene	ncRNA
mm_12098.1	chr2	60972375	60972384	+	1	NA	intron (NR_045335, intron 1 of 3)	intron (NR_045335, intron 1 of 3)	2772	NR_045335	100038493	Mm.388076	NR_045335	ENSMUSG00000075325	Gm13582	ENSMUSG00000075325|OTTMUSG00000012844	predicted gene 13582	ncRNA
mm_94074.1	chr10	128409179	128409191	-	1	NA	intron (NM_027257, intron 2 of 6)	intron (NM_027257, intron 2 of 6)	611	NM_027257	69917	Mm.46614	NM_027257	ENSMUSG00000025374	Nabp2	2610036N15Rik|Obfc2b|SSB1	nucleic acid binding protein 2	protein-coding
mm_150247.1	chr19	34085624	34085640	+	1	NA	TTS (NM_027340)	TTS (NM_027340)	-15311	NM_023903	78753	Mm.195937	NM_023903	ENSMUSG00000056078	Lipm	4632427C23Rik|AW227514|Lipl3	lipase, family member M	protein-coding
mm_123079.1	chr14	55739603	55739613	-	1	NA	exon (NM_026819, exon 8 of 9)	exon (NM_026819, exon 8 of 9)	6076	NM_026819	52585	Mm.21623	NM_026819	ENSMUSG00000002332	Dhrs1	1110029G07Rik|AW112170|D14Ertd484e	dehydrogenase/reductase (SDR family) member 1	protein-coding
mm_44530.1	chr5	24445225	24445252	-	1	NA	promoter-TSS (NM_023229)	promoter-TSS (NM_023229)	-3	NM_023229	66587	Mm.28123	NM_023229	ENSMUSG00000028959	Fastk	0610011K02Rik|610011K02Rik	Fas-activated serine/threonine kinase	protein-coding
mm_555.1	chr1	38019449	38019482	+	1	NA	exon (NM_198303, exon 4 of 24)	exon (NM_198303, exon 4 of 24)	21455	NM_198303	226982	Mm.260943	NM_198303	ENSMUSG00000026083	Eif5b	A030003E17Rik|BC018347|IF2	eukaryotic translation initiation factor 5B	protein-coding
mm_20480.1	chr2	129630043	129630074	-	1	NA	exon (NM_001291022, exon 5 of 5)	exon (NM_001291022, exon 5 of 5)	36889	NM_001291022	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_155077.1	chrX	46328984	46328995	+	1	NA	promoter-TSS (NR_045440)	promoter-TSS (NR_045440)	-18	NM_028514	73360	Mm.60929	NM_028514	ENSMUSG00000046615	Actrt1	1700061J02Rik|Arp-T1	actin-related protein T1	protein-coding
mm_154269.1	chr19	60772735	60772760	-	1	NA	exon (NM_010123, exon 12 of 22)	exon (NM_010123, exon 12 of 22)	1638	NR_034047	100217439		NR_034047		Snora19	MBI-51	small nucleolar RNA, H/ACA box 19	snoRNA
mm_45343.1	chr5	65765033	65765050	-	1	NA	intron (NM_001024917, intron 1 of 19)	intron (NM_001024917, intron 1 of 19)	1520	NM_001024917	333789	Mm.332398	NM_001024917	ENSMUSG00000037795	N4bp2	B3bp|E430014I16|Gm1791|Gm868	NEDD4 binding protein 2	protein-coding
mm_73168.1	chr8	95020752	95020762	+	1	NA	intron (NM_173036, intron 1 of 11)	(CCCCCA)n|Simple_repeat|Simple_repeat	3065	NM_173036	54672	Mm.27995	NM_173036	ENSMUSG00000060470	Adgrg3	A030001G24Rik|AW214383|Gpr97|Pb1|Pb99	adhesion G protein-coupled receptor G3	protein-coding
mm_83955.1	chr9	56928296	56928314	-	1	NA	promoter-TSS (NM_175483)	promoter-TSS (NM_175483)	66	NM_175483	235406	Mm.191459	NM_175483	ENSMUSG00000032733	Snx33	E130307J07Rik|Sh3px3	sorting nexin 33	protein-coding
mm_110373.1	chr12	40199560	40199572	-	1	NA	promoter-TSS (NM_001033437)	promoter-TSS (NM_001033437)	-251	NM_001033437	380755	Mm.390463	NM_001033437	ENSMUSG00000071342	Lsmem1	Gm889	leucine-rich single-pass membrane protein 1	protein-coding
mm_113436.1	chr13	34875604	34875604	+	1	NA	5' UTR (NM_013830, exon 1 of 15)	5' UTR (NM_013830, exon 1 of 15)	110	NM_013830	19134	Mm.10027	NM_013830	ENSMUSG00000021413	Prpf4b	2610037H07|Prp4|Prp4k|Prpk|cbp143	pre-mRNA processing factor 4B	protein-coding
mm_18028.1	chr2	38623915	38623918	-	1	NA	intron (NM_011187, intron 5 of 7)	intron (NM_011187, intron 5 of 7)	19990	NM_011187	19177	Mm.389251	NM_011187	ENSMUSG00000026750	Psmb7	AU020723|MC14	proteasome (prosome, macropain) subunit, beta type 7	protein-coding
mm_109023.1	chr12	103640425	103640428	+	1	NA	Intergenic	RMER21A|LTR|ERV1	-8982	NM_144834	217847	Mm.29094	NM_144834	ENSMUSG00000061947	Serpina10	PZI|ZPI	serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 10	protein-coding
mm_29227.1	chr3	107213413	107213421	-	1	NA	exon (NM_001111143, exon 7 of 9)	exon (NM_001111143, exon 7 of 9)	8315	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_118716.1	chr14	22201927	22201937	+	1	NA	intron (NM_028275, intron 2 of 6)	Lx7|LINE|L1	182220	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_158856.1	chrX	169997907	169997963	-	1	NA	Intergenic	CpG	-19018	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_56298.1	chr6	91692727	91692727	-	1	NA	intron (NM_009320, intron 1 of 14)	intron (NM_009320, intron 1 of 14)	8660	NM_009320	21366	Mm.395650	NM_009320	ENSMUSG00000030096	Slc6a6	AA589629|C80501|Taut	solute carrier family 6 (neurotransmitter transporter, taurine), member 6	protein-coding
mm_91985.1	chr10	61784335	61784350	-	1	NA	promoter-TSS (NM_207000)	promoter-TSS (NM_207000)	-478	NM_207000	404634	Mm.272870	NM_207000	ENSMUSG00000020086	H2afy2	macroH2A2	H2A histone family, member Y2	protein-coding
mm_140024.1	chr17	73948408	73948418	+	1	NA	intron (NM_011723, intron 1 of 35)	intron (NM_011723, intron 1 of 35)	1783	NM_011723	22436	Mm.11223	NM_011723	ENSMUSG00000024066	Xdh	XO|Xor|Xox-1|Xox1	xanthine dehydrogenase	protein-coding
mm_31221.1	chr4	44012955	44012983	+	1	NA	exon (NM_001080385, exon 1 of 7)	exon (NM_001080385, exon 1 of 7)	319	NM_001290470	12757	Mm.298875	NM_016760	ENSMUSG00000028478	Clta	AV026556|Lca	clathrin, light polypeptide (Lca)	protein-coding
mm_124138.1	chr14	86857555	86857555	-	1	NA	intron (NM_019670, intron 21 of 27)	intron (NM_019670, intron 21 of 27)	283559	NM_019670	56419	Mm.440585	NM_019670	ENSMUSG00000022021	Diaph3	4930417P13Rik|Dia2|Diap3|Drf3|mDia2|mKIAA4117|p134MDia2	diaphanous related formin 3	protein-coding
mm_130631.1	chr15	100424170	100424173	-	1	NA	non-coding (NR_040351, exon 1 of 3)	non-coding (NR_040351, exon 1 of 3)	978	NR_040351	432982	Mm.234608	NM_001034883	ENSMUSG00000087444	Gm5475	EG432982	predicted gene 5475	ncRNA
mm_101423.1	chr11	29547872	29547878	-	1	NA	promoter-TSS (NM_028504)	promoter-TSS (NM_028504)	-75	NM_028504	73324	Mm.69388	NM_028504	ENSMUSG00000020461	Clhc1	1700034F02Rik	clathrin heavy chain linker domain containing 1	protein-coding
mm_126458.1	chr15	80937123	80937147	+	1	NA	3' UTR (NM_177124, exon 22 of 22)	3' UTR (NM_177124, exon 22 of 22)	-2904	NR_039573	100628612		NR_039573	ENSMUSG00000092868	Mir5113	mir-5113|mmu-mir-5113|mu-mir-5113	microRNA 5113	ncRNA
mm_133465.1	chr16	89183260	89183263	+	1	NA	Intergenic	Intergenic	-22600	NM_001163615	622935	Mm.459837	NM_001163615	ENSMUSG00000091039	Krtap20-2	1190004K03Rik|EG622935|Gm6371	keratin associated protein 20-2	protein-coding
mm_21959.1	chr2	167190125	167190173	-	1	NA	Intergenic	CpG	-1331	NM_008420	16500	Mm.205341	NM_008420	ENSMUSG00000050556	Kcnb1	Kcr1-1|Kv2.1|Shab	potassium voltage gated channel, Shab-related subfamily, member 1	protein-coding
mm_63700.1	chr7	130645674	130645692	+	1	NA	intron (NM_001004468, intron 3 of 21)	intron (NM_001004468, intron 3 of 21)	-46873	NM_001347637	57752	Mm.86322	NM_021314	ENSMUSG00000030852	Tacc2	mKIAA4180	transforming, acidic coiled-coil containing protein 2	protein-coding
mm_5419.1	chr1	33907827	33907837	-	1	NA	promoter-TSS (NM_001310484)	promoter-TSS (NM_001310484)	-65	NM_001310484	320705	Mm.336619	NM_177235	ENSMUSG00000042182	Bend6	B230209C24Rik	BEN domain containing 6	protein-coding
mm_156072.1	chrX	109161410	109161426	+	1	NA	3' UTR (NM_019989, exon 4 of 4)	3' UTR (NM_019989, exon 4 of 4)	-35338	NM_001037917	622976	Mm.482747	NM_001037917	ENSMUSG00000048621	Gm6377	EG622976	predicted gene 6377	protein-coding
mm_60887.1	chr7	46396662	46396669	+	1	NA	5' UTR (NM_001112739, exon 1 of 4)	5' UTR (NM_001112739, exon 1 of 4)	197	NM_001112739	16502	Mm.249386	NM_008421	ENSMUSG00000058975	Kcnc1	C230009H10Rik|KShIIIB|KV4|Kcr2-1|Kv3.1|NGK2|Shaw	potassium voltage gated channel, Shaw-related subfamily, member 1	protein-coding
mm_42411.1	chr5	115147703	115147723	+	1	NA	3' UTR (NM_175403, exon 5 of 5)	3' UTR (NM_175403, exon 5 of 5)	10463	NM_175403	109154	Mm.153963	NM_175403	ENSMUSG00000048578	Mlec	2410014A08Rik|AI850530|ESTM19|X83352|mKIAA0152	malectin	protein-coding
mm_64382.1	chr7	142472081	142472093	+	1	NA	5' UTR (NM_019391, exon 1 of 11)	5' UTR (NM_019391, exon 1 of 11)	244	NM_019391	16985	Mm.234003	NM_019391	ENSMUSG00000018819	Lsp1	Lsp-1|WP34|p50|pp52	lymphocyte specific 1	protein-coding
mm_95216.1	chr11	43697821	43697824	+	1	NA	intron (NM_027557, intron 1 of 1)	intron (NM_027557, intron 1 of 1)	15824	NM_001164231	70802	Mm.397449	NM_027557	ENSMUSG00000044950	Pwwp2a	4631424J17Rik|AI891583|AU024105|D930040F23Rik	PWWP domain containing 2A	protein-coding
mm_41129.1	chr5	87786676	87786680	+	1	NA	exon (NM_001304768, exon 11 of 13)	exon (NM_001304768, exon 11 of 13)	12228	NM_007785	12993	Mm.4908	NM_007785	ENSMUSG00000061937	Csn1s2a	Csng|PP22	casein alpha s2-like A	protein-coding
mm_130929.1	chr15	103102102	103102117	-	1	NA	Intergenic	Intergenic	44719	NR_045743	432989	Mm.383979	NR_045743	ENSMUSG00000097003	D930007P13Rik	-	Riken cDNA D930007P13 gene	ncRNA
mm_79911.1	chr9	65461322	65461351	+	1	NA	intron (NM_138584, intron 1 of 8)	CpG	399	NM_138584	27965	Mm.272475	NM_138584	ENSMUSG00000032388	Spg21	ACP33|BM-019|C78576|D9Wsu18e|GL010|MAST	spastic paraplegia 21 homolog (human)	protein-coding
mm_34233.1	chr4	141097082	141097092	+	1	NA	exon (NM_177867, exon 6 of 15)	exon (NM_177867, exon 6 of 15)	8742	NM_177867	329972	Mm.247201	NM_177867	ENSMUSG00000045004	Spata21	4933414G08	spermatogenesis associated 21	protein-coding
mm_47762.1	chr5	131476669	131476698	-	1	NA	exon (NM_177047, exon 7 of 19)	exon (NM_177047, exon 7 of 19)	-169161	NM_145218	212996	Mm.299204	NM_145218	ENSMUSG00000034040	Wbscr17	AA388321|E330012B09Rik	Williams-Beuren syndrome chromosome region 17 homolog (human)	protein-coding
mm_3502.1	chr1	150107018	150107024	+	1	NA	3' UTR (NM_011198, exon 10 of 10)	3' UTR (NM_011198, exon 10 of 10)	6990	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_130117.1	chr15	89477401	89477420	-	1	NA	promoter-TSS (NM_009713)	promoter-TSS (NM_009713)	14	NM_009713	11883	Mm.620	NM_009713	ENSMUSG00000022620	Arsa	AS-A|ASA|AW212749|As-2|As2|TISP73	arylsulfatase A	protein-coding
mm_109864.1	chr12	4907475	4907533	-	1	NA	promoter-TSS (NM_145441)	promoter-TSS (NM_145441)	16	NM_145441	217379	Mm.259170	NM_145441	ENSMUSG00000020634	Ubxn2a	6330407P03Rik|Ubxd4	UBX domain protein 2A	protein-coding
mm_140943.1	chr17	24477612	24477622	-	1	NA	intron (NM_001252463, intron 4 of 8)	intron (NM_001252463, intron 4 of 8)	1461	NM_001252464	56716	Mm.289516	NM_019988	ENSMUSG00000024142	Mlst8	0610033N12Rik|AA409454|AI505104|AI851821|Gbl	MTOR associated protein, LST8 homolog (S. cerevisiae)	protein-coding
mm_71854.1	chr8	68906189	68906197	+	1	NA	3' UTR (NM_008509, exon 10 of 10)	3' UTR (NM_008509, exon 10 of 10)	25638	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_127558.1	chr15	102151109	102151124	+	1	NA	exon (NM_146064, exon 2 of 15)	exon (NM_146064, exon 2 of 15)	541	NM_146064	223920	Mm.358862	NM_146064	ENSMUSG00000023045	Soat2	ACAT2|D15Wsu97e	sterol O-acyltransferase 2	protein-coding
mm_141493.1	chr17	31512218	31512233	-	1	NA	exon (NM_021322, exon 1 of 11)	exon (NM_021322, exon 1 of 11)	262	NM_021322	57773	Mm.143771	NM_021322	ENSMUSG00000024037	Wdr4	AI415180|AI448349|D530049K22Rik	WD repeat domain 4	protein-coding
mm_45415.1	chr5	66451652	66451664	-	1	NA	exon (NM_009686, exon 5 of 18)	exon (NM_009686, exon 5 of 18)	-113993	NM_001201416	11787	Mm.5159	NM_009686	ENSMUSG00000029207	Apbb2	2310007D03Rik|FE65L1|Rirl1|TR2L|Zfra	amyloid beta (A4) precursor protein-binding, family B, member 2	protein-coding
mm_60100.1	chr7	35186371	35186408	+	1	NA	promoter-TSS (NM_017394)	promoter-TSS (NM_017394)	4	NM_017394	53896	Mm.35567	NM_017394	ENSMUSG00000030495	Slc7a10	AL024237|Asc-1|D7Bwg0847e	solute carrier family 7 (cationic amino acid transporter, y+ system), member 10	protein-coding
mm_116960.1	chr13	56141502	56141550	-	1	NA	Intergenic	Intergenic	-5976	NM_001159513	26914	Mm.283802	NM_012015	ENSMUSG00000015937	H2afy	H2AF12M|mH2a1|macroH2A1	H2A histone family, member Y	protein-coding
mm_148171.1	chr18	78057436	78057446	-	1	NA	promoter-TSS (NM_001101038)	promoter-TSS (NM_001101038)	-173	NM_001101038	620235	Mm.35607	NM_001101038	ENSMUSG00000091055	Siglec15	Cd33l3|EG620235|SIGLEC-I	sialic acid binding Ig-like lectin 15	protein-coding
mm_150837.1	chr19	44918502	44918516	+	1	NA	Intergenic	Intergenic	-12610	NM_001081225	226151	Mm.212609	NM_172638	ENSMUSG00000036097	Fam178a	3632432H19|6030443O07Rik|AU014917|Slf2	family with sequence similarity 178, member A	protein-coding
mm_98751.1	chr11	96545427	96545433	+	1	NA	intron (NM_001033186, intron 4 of 12)	intron (NM_001033186, intron 4 of 12)	80839	NM_001177898	78473	Mm.395840	NM_001033186	ENSMUSG00000057058	Skap1	1700091G21Rik|Scap1|Skap-55	src family associated phosphoprotein 1	protein-coding
mm_11058.1	chr2	27496976	27496979	+	1	NA	Intergenic	MURVY-int|LTR|ERV1	-18170	NM_080848	140858	Mm.28265	NM_080848	ENSMUSG00000026917	Wdr5	2410008O07Rik|AA408785|AA960360|Big|Big-3	WD repeat domain 5	protein-coding
mm_53447.1	chr6	134414491	134414512	+	1	NA	intron (NM_025778, intron 2 of 6)	intron (NM_025778, intron 2 of 6)	18172	NM_025778	66813	Mm.474472	NM_025778	ENSMUSG00000030200	Bcl2l14	4930452K23Rik|4933405K19Rik|9030625M01Rik|AI429211|Bclg	BCL2-like 14 (apoptosis facilitator)	protein-coding
mm_116588.1	chr13	47992393	47992406	-	1	NA	intron (NR_038004, intron 2 of 7)	MER5A|DNA|hAT-Charlie	26209	NR_038004	70971	Mm.158514	NR_038004	ENSMUSG00000047324	4931429P17Rik	-	RIKEN cDNA 4931429P17 gene	ncRNA
mm_87860.1	chr10	61175655	61175671	+	1	NA	intron (NM_001017409, intron 1 of 3)	intron (NM_001017409, intron 1 of 3)	401	NM_023064	65971	Mm.30227	NM_023064	ENSMUSG00000020096	Tbata	1700021K02Rik|AI428928|Spatial|Titest	thymus, brain and testes associated	protein-coding
mm_27644.1	chr3	63891336	63891340	-	1	NA	Intergenic	ID4_|SINE|ID	38047	NM_177856	329659	Mm.39342	NM_177856	ENSMUSG00000048581	E130311K13Rik	-	RIKEN cDNA E130311K13 gene	protein-coding
mm_121268.1	chr14	103346575	103346596	+	1	NA	5' UTR (NM_207215, exon 1 of 85)	5' UTR (NM_207215, exon 1 of 85)	215	NM_207215	105689	Mm.6478	NM_207215	ENSMUSG00000033004	Mycbp2	AU023734|AW107953|AW546647|C130061D10Rik|Pam|Phr1|R75243	MYC binding protein 2	protein-coding
mm_137479.1	chr17	26917097	26917107	+	1	NA	promoter-TSS (NM_053173)	promoter-TSS (NM_053173)	11	NM_053173	16580	Mm.491138	NM_016761	ENSMUSG00000024301	Kifc5b	Hset|KNSL2|Kifc5a	kinesin family member C5B	protein-coding
mm_67620.1	chr7	84048147	84048152	-	1	NA	intron (NM_030728, intron 1 of 28)	L1MA4|LINE|L1	38356	NM_030728	80982	Mm.160389	NM_030728	ENSMUSG00000052353	Cemip	12H19.01.T7|6330404C01Rik|9930013L23Rik|AY007814|Kiaa1199	cell migration inducing protein, hyaluronan binding	protein-coding
mm_159950.1	chr6	85809875	85809875	-	1	NA	promoter-TSS (NM_001201389)	promoter-TSS (NM_001201389)	2	NM_001201389	100504710	Mm.486515	NM_001201389	ENSMUSG00000079495	Nat8f6	ENSMUSG00000079495|Gm11128	N-acetyltransferase 8 (GCN5-related) family member 6	protein-coding
mm_48874.1	chr5	150665316	150665377	-	1	NA	intron (NM_201369, intron 1 of 5)	CpG	266	NM_201369	381695	Mm.246934	NM_201369	ENSMUSG00000029655	N4bp2l2	2700092H06Rik|zag1	NEDD4 binding protein 2-like 2	protein-coding
mm_27180.1	chr3	34620379	34620381	-	1	NA	intron (NR_015580, intron 2 of 4)	intron (NR_015580, intron 2 of 4)	-18084	NR_035433	100316679		NR_035433	ENSMUSG00000104797	Mir1897	Mirn1897|mmu-mir-1897	microRNA 1897	ncRNA
mm_110323.1	chr12	34817493	34817501	-	1	NA	intron (NM_001271386, intron 3 of 27)	intron (NM_001271386, intron 3 of 27)	99598	NM_001271386	79221	Mm.310551	NM_024124	ENSMUSG00000004698	Hdac9	AV022454|D030072B18Rik|HD7B|HD9|HDRP|Hdac7b|Mitr|mKIAA0744	histone deacetylase 9	protein-coding
mm_137649.1	chr17	28558265	28558279	+	1	NA	TTS (NR_105935)	TTS (NR_105935)	229	NR_105935	102465585		NR_105935	ENSMUSG00000099152	Mir6969	Gm27305|mmu-mir-6969	microRNA 6969	ncRNA
mm_21582.1	chr2	164237266	164237274	-	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	1071	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_19845.1	chr2	113641092	113641100	-	1	NA	intron (NM_001285458, intron 13 of 16)	intron (NM_001285458, intron 13 of 16)	-43994	NM_001287818	14260	Mm.4938	NM_010230	ENSMUSG00000044042	Fmn1	Fmn|formin-1|ld	formin 1	protein-coding
mm_94184.1	chr10	128958806	128958816	-	1	NA	TTS (NM_008398)	TTS (NM_008398)	2177	NM_027853	71664	Mm.337232	NM_027853	ENSMUSG00000025347	Mettl7b	0610006F02Rik|AI266817	methyltransferase like 7B	protein-coding
mm_51844.1	chr6	90320768	90320771	+	1	NA	intron (NM_027928, intron 1 of 2)	intron (NM_027928, intron 1 of 2)	4416	NM_027928	71797	Mm.49071	NM_027928	ENSMUSG00000056643	Chst13	1110067M19Rik|C4ST-3	carbohydrate (chondroitin 4) sulfotransferase 13	protein-coding
mm_148583.1	chr19	5041338	5041416	+	1	NA	promoter-TSS (NM_134155)	promoter-TSS (NM_134155)	-27	NM_134155	107392	Mm.29628	NM_134155	ENSMUSG00000080268	Brms1	AV003220|AW554636	breast cancer metastasis-suppressor 1	protein-coding
mm_31770.1	chr4	63547864	63547867	+	1	NA	intron (NM_024173, intron 1 of 2)	intron (NM_024173, intron 1 of 2)	3100	NM_024173	66290	Mm.371615	NM_024173	ENSMUSG00000039105	Atp6v1g1	1810024D14Rik|AA960677|ATP6J|Atp6g1|VAG1|Vma10	ATPase, H+ transporting, lysosomal V1 subunit G1	protein-coding
mm_123846.1	chr14	70707995	70708011	-	1	NA	intron (NM_023045, intron 1 of 27)	intron (NM_023045, intron 1 of 27)	-54919	NM_181345	328440	Mm.347749	NM_181345	ENSMUSG00000047911	Npm2	-	nucleophosmin/nucleoplasmin 2	protein-coding
mm_79805.1	chr9	64175589	64175613	+	1	NA	TTS (NR_028548)	TTS (NR_028548)	169	NR_028548	100217453		NR_028548	ENSMUSG00000094411	Snord16a	MBII-98	small nucleolar RNA, C/D box 16A	snoRNA
mm_63277.1	chr7	126763771	126763796	+	1	NA	exon (NM_011952, exon 5 of 9)	exon (NM_011952, exon 5 of 9)	-2631	NM_024228	68616	Mm.246881	NM_024228	ENSMUSG00000030703	Gdpd3	1110015E22Rik	glycerophosphodiester phosphodiesterase domain containing 3	protein-coding
mm_107471.1	chr12	37569222	37569222	+	1	NA	intron (NM_178767, intron 12 of 12)	intron (NM_178767, intron 12 of 12)	-311483	NM_178681	217480	Mm.126525	NM_178681	ENSMUSG00000036095	Dgkb	6430574F24|90kda|C630029D13Rik|DAGK2|DGK|DGK-beta|mKIAA0718	diacylglycerol kinase, beta	protein-coding
mm_75179.1	chr8	36952208	36952218	-	1	NA	5' UTR (NM_001194940, exon 1 of 18)	5' UTR (NM_001194940, exon 1 of 18)	229	NM_001194940	50768	Mm.125155	NM_015802	ENSMUSG00000031523	Dlc1	A730069N07Rik|Arhgap7|HP|STARD12|dlc-1	deleted in liver cancer 1	protein-coding
mm_161200.1	chr13	58102311	58102311	-	1	NA	intron (NM_001195075, intron 1 of 16)	RLTR14|LTR|ERV1	117	NM_001195075	100503085	Mm.379256	NM_001195075	ENSMUSG00000014164	Klhl3	7530408C15Rik|AI430941|EG627648	kelch-like 3	protein-coding
mm_165764.1	chr3	121262928	121262942	-	1	NA	intron (NM_178936, intron 1 of 7)	CpG	381	NM_178936	99887	Mm.26088	NM_178936	ENSMUSG00000028132	Tmem56	4930577M16Rik|AU018104|AW109744|C730036B01Rik	transmembrane protein 56	protein-coding
mm_77200.1	chr8	113839889	113839892	-	1	NA	intron (NM_172466, intron 3 of 22)	RMER30|DNA|hAT-Charlie	8949	NM_172466	208936	Mm.167471	NM_172466	ENSMUSG00000053399	Adamts18	9630038L21|ADAMTS21|E130314N14Rik	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 18	protein-coding
mm_151691.1	chr19	4333841	4333972	-	1	NA	intron (NM_001001984, intron 12 of 20)	intron (NM_001001984, intron 12 of 20)	-27684	NM_001290818	110355	Mm.254144	NM_130863	ENSMUSG00000024858	Grk2	Adrbk-1|Adrbk1|Bark-1|beta ARK|betaARK1	G protein-coupled receptor kinase 2	protein-coding
mm_135717.1	chr16	55816527	55816540	-	1	NA	intron (NM_001159395, intron 7 of 12)	intron (NM_001159395, intron 7 of 12)	5605	NM_001159394	80859	Mm.247272	NM_030612	ENSMUSG00000035356	Nfkbiz	AA408868|INAP|Mail	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, zeta	protein-coding
mm_1010.1	chr1	58726197	58726222	+	1	NA	intron (NM_009805, intron 1 of 4)	intron (NM_009805, intron 1 of 4)	-4343	NM_001293805	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_92219.1	chr10	68276436	68276470	-	1	NA	intron (NM_023598, intron 2 of 9)	intron (NM_023598, intron 2 of 9)	2273	NM_023598	71371	Mm.440357	NM_023598	ENSMUSG00000019947	Arid5b	4930580B11|5430435G07Rik|AI467247|Desrt|Mrf2|Mrf2alpha|Mrf2beta	AT rich interactive domain 5B (MRF1-like)	protein-coding
mm_127466.1	chr15	101272757	101272763	+	1	NA	exon (NM_010444, exon 5 of 7)	exon (NM_010444, exon 5 of 7)	5914	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_95442.1	chr11	50232052	50232076	+	1	NA	promoter-TSS (NR_105884)	promoter-TSS (NR_105884)	-181	NR_105884	102466765		NR_105884	ENSMUSG00000098474	Mir6919	Gm27889|mmu-mir-6919	microRNA 6919	ncRNA
mm_50297.1	chr6	47480788	47480794	+	1	NA	intron (NM_012042, intron 1 of 21)	intron (NM_012042, intron 1 of 21)	26467	NM_012042	26965	Mm.87611	NM_012042	ENSMUSG00000029686	Cul1	-	cullin 1	protein-coding
mm_73803.1	chr8	117302467	117302481	+	1	NA	intron (NM_001163262, intron 1 of 20)	intron (NM_001163262, intron 1 of 20)	45455	NM_001163262	74440	Mm.233181	NM_028941	ENSMUSG00000034390	Cmip	4933407C03Rik|5830471E12Rik|AI314065|AI464126	c-Maf inducing protein	protein-coding
mm_52212.1	chr6	103510579	103510605	+	1	NA	promoter-TSS (NM_007697)	promoter-TSS (NM_007697)	-284	NM_007697	12661	Mm.251288	NM_007697	ENSMUSG00000030077	Chl1	A530023M13Rik|AI465420|CALL|LICAM2	cell adhesion molecule L1-like	protein-coding
mm_37009.1	chr4	112433980	112433993	-	1	NA	promoter-TSS (NM_177864)	promoter-TSS (NM_177864)	-1	NM_177864	329918	Mm.246783	NM_177864	ENSMUSG00000049972	Skint9	A030013N09Rik|Skint-9	selection and upkeep of intraepithelial T cells 9	protein-coding
mm_22792.1	chr3	22210635	22210652	+	1	NA	3' UTR (NM_030732, exon 16 of 16)	3' UTR (NM_030732, exon 16 of 16)	-40727	NR_004439	19784		NR_004439		Rprl2	RPRH3|Rmrp3	ribonuclease P RNA-like 2	ncRNA
mm_3915.1	chr1	162217658	162217671	+	1	NA	promoter-TSS (NR_029810)	promoter-TSS (NR_029810)	41	NR_002870	474332	Mm.479755	NR_002870	ENSMUSG00000078190	Dnm3os	6030416H16Rik|Hag2|Npn1|P/L01	dynamin 3, opposite strand	ncRNA
mm_13603.1	chr2	112943517	112943519	+	1	NA	intron (NM_177652, intron 10 of 103)	ID2|SINE|ID	86813	NM_177652	20192	Mm.436657	NM_177652	ENSMUSG00000057378	Ryr3	AI851294|C230090H21|RYR-3	ryanodine receptor 3	protein-coding
mm_59906.1	chr7	30332229	30332238	+	1	NA	Intergenic	MLT1K|LTR|ERVL-MaLR	-9858	NM_001033140	68332	Mm.6844	NM_001033140	ENSMUSG00000074211	Sdhaf1	0610010E21Rik|AI430885|AW490662|Lyrm8	succinate dehydrogenase complex assembly factor 1	protein-coding
mm_132535.1	chr16	37868489	37868497	+	1	NA	promoter-TSS (NM_177093)	promoter-TSS (NM_177093)	93	NM_177093	320184	Mm.390882	NM_177093	ENSMUSG00000034158	Lrrc58	1810012N18Rik|C330018J07Rik	leucine rich repeat containing 58	protein-coding
mm_26431.1	chr3	142618835	142618851	+	1	NA	3' UTR (NM_010259, exon 11 of 11)	3' UTR (NM_010259, exon 11 of 11)	-1820	NM_010260	14469	Mm.24038	NM_010260	ENSMUSG00000028270	Gbp2	-	guanylate binding protein 2	protein-coding
mm_162834.1	chr10	82578465	82578465	+	1	NA	Intergenic	Lx|LINE|L1	44763	NM_001135569	544717	Mm.334867	NM_001135567	ENSMUSG00000063320	1190007I07Rik	-	RIKEN cDNA 1190007I07 gene	protein-coding
mm_155268.1	chrX	58911504	58911513	+	1	NA	promoter-TSS (NM_023774)	promoter-TSS (NM_023774)	47	NM_023774	75352	Mm.60906	NM_023774	ENSMUSG00000046180	4930550L24Rik	mage-k1	RIKEN cDNA 4930550L24 gene	protein-coding
mm_165548.1	chr3	9853294	9853300	+	1	NA	Intergenic	Intergenic	-19618	NM_001195031	94212	Mm.23897	NM_053182	ENSMUSG00000027508	Pag1	Cbp|F730007C19Rik|Pag	phosphoprotein associated with glycosphingolipid microdomains 1	protein-coding
mm_41502.1	chr5	92331819	92331827	+	1	NA	promoter-TSS (NM_001310664)	promoter-TSS (NM_001310664)	-4	NM_001310664	109979	Mm.263514	NM_181728	ENSMUSG00000034842	Art3	4930569O04Rik|ARTC3	ADP-ribosyltransferase 3	protein-coding
mm_120941.1	chr14	76674295	76674308	+	1	NA	Intergenic	Intergenic	-3267	NR_015485	73272	Mm.116804	NR_015485	ENSMUSG00000101009	1700108F19Rik	1700020I02Rik|BB065030	RIKEN cDNA 1700108F19 gene	ncRNA
mm_56783.1	chr6	116636947	116636968	-	1	NA	3' UTR (NM_178045, exon 11 of 11)	3' UTR (NM_178045, exon 11 of 11)	-7958	NM_026057	67255	Mm.18810	NM_026057	ENSMUSG00000059878	Zfp422	2900028O21Rik|AU041373|KOX15|Krox-25-2|Krox-26|Krox25|Krox26|Znf22	zinc finger protein 422	protein-coding
mm_112213.1	chr12	113428609	113428624	-	1	NA	Intergenic	Intergenic	-60949	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_171784.1	chr5	110118701	110118717	-	1	NA	intron (NM_001163996, intron 2 of 4)	intron (NM_001163996, intron 2 of 4)	8617	NM_001163996	675812	Mm.442122	NM_001163996	ENSMUSG00000023284	Zfp605	A830023I12Rik	zinc finger protein 605	protein-coding
mm_56217.1	chr6	89364385	89364418	-	1	NA	Intergenic	Intergenic	-1788	NM_008881	18844	Mm.3789	NM_008881	ENSMUSG00000030084	Plxna1	2600013D04Rik|NOV|PlexA1|Plxn1|mKIAA4053	plexin A1	protein-coding
mm_103326.1	chr11	74522575	74522593	-	1	NA	intron (NM_001015046, intron 2 of 24)	CpG	67574	NM_001015046	380711	Mm.425690	NM_001015046	ENSMUSG00000038807	Rap1gap2	AU067654|Garnl4|Gm1561|mKIAA1039	RAP1 GTPase activating protein 2	protein-coding
mm_171659.1	chr4	44013191	44013203	+	1	NA	intron (NM_016760, intron 1 of 5)	CpG	547	NM_001290470	12757	Mm.298875	NM_016760	ENSMUSG00000028478	Clta	AV026556|Lca	clathrin, light polypeptide (Lca)	protein-coding
mm_45093.1	chr5	44169211	44169211	-	1	NA	Intergenic	Intergenic	57395	NM_173764	231225	Mm.30688	NM_173764	ENSMUSG00000046985	Tapt1	4932414K18Rik	transmembrane anterior posterior transformation 1	protein-coding
mm_118723.1	chr14	22214320	22214357	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	194626	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_169145.1	chr13	62182485	62182486	+	1	NA	Intergenic	Intergenic	52595	NM_001039239	630579	Mm.440905	NM_001039239	ENSMUSG00000074867	Zfp808	EG630579|Gm7036	zinc finger protein 80	protein-coding
mm_126851.1	chr15	89196138	89196164	+	1	NA	intron (NM_027081, intron 1 of 19)	CpG	323	NM_027081	69440	Mm.482128	NM_027081	ENSMUSG00000015377	Dennd6b	1700027J05Rik|AI414881|Fam116b	DENN/MADD domain containing 6B	protein-coding
mm_47812.1	chr5	134176721	134176784	-	1	NA	promoter-TSS (NM_033572)	promoter-TSS (NM_033572)	15	NM_033572	94254	Mm.29508	NM_033572	ENSMUSG00000061979	Rcc1l	5730496C04Rik|AU019812|Wbscr16	reculator of chromosome condensation 1 like	protein-coding
mm_15958.1	chr2	165997389	165997410	+	1	NA	intron (NM_008679, intron 1 of 22)	B2_Mm2|SINE|B2	4762	NM_008679	17979	Mm.469663	NM_008679	ENSMUSG00000027678	Ncoa3	2010305B15Rik|AW321064|Actr|Aib1|KAT13B|Rac3|Src3|Tram-1|Tram1|bHLHe42|p/Cip|pCip	nuclear receptor coactivator 3	protein-coding
mm_106389.1	chr11	118569963	118570000	-	1	NA	intron (NM_001285436, intron 3 of 13)	CpG	93021	NM_172573	217364	Mm.473963	NM_172573	ENSMUSG00000033857	Engase	C130099A03|D230014K01Rik	endo-beta-N-acetylglucosaminidase	protein-coding
mm_66905.1	chr7	59983428	59983441	-	1	NA	exon (NM_013670, exon 9 of 10)	exon (NM_013670, exon 9 of 10)	-4578	NR_028529	100217429		NR_028529		Snord64	MBII-13	small nucleolar RNA, C/D box 64	snoRNA
mm_34332.1	chr4	142238231	142238241	+	1	NA	intron (NM_001109685, intron 1 of 7)	intron (NM_001109685, intron 1 of 7)	1165	NM_001109685	71529	Mm.255986	NM_144531	ENSMUSG00000040606	Kazn	2310007B04Rik|9030409G11Rik|AI256607|AI666764|AW061099|Kaz|Kazrin	kazrin, periplakin interacting protein	protein-coding
mm_86766.1	chr10	19934071	19934105	+	1	NA	promoter-TSS (NM_008580)	promoter-TSS (NM_008580)	-438	NM_008580	26408	Mm.6595	NM_008580	ENSMUSG00000071369	Map3k5	7420452D20Rik|ASK|ASK1|MAPKKK5|Mekk5	mitogen-activated protein kinase kinase kinase 5	protein-coding
mm_72385.1	chr8	81667187	81667193	+	1	NA	intron (NM_001297591, intron 2 of 24)	intron (NM_001297591, intron 2 of 24)	324628	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_136850.1	chr17	12791094	12791097	+	1	NA	intron (NR_027784, intron 2 of 2)	intron (NR_027784, intron 2 of 2)	-21389	NM_010515	16004	Mm.26553	NM_010515	ENSMUSG00000023830	Igf2r	AI661837|CD222|CI-MPR|M6P/IGF2R|Mpr300	insulin-like growth factor 2 receptor	protein-coding
mm_75775.1	chr8	69996117	69996154	-	1	NA	5' UTR (NM_001286450, exon 1 of 13)	5' UTR (NM_001286450, exon 1 of 13)	249	NM_001286450	234366	Mm.270044	NM_145596	ENSMUSG00000036180	Gatad2a	1110066C11Rik|BC031407|C80248	GATA zinc finger domain containing 2A	protein-coding
mm_149570.1	chr19	12804877	12804887	+	1	NA	intron (NM_134152, intron 2 of 8)	intron (NM_134152, intron 2 of 8)	6273	NM_134152	107321	Mm.313136	NM_134152	ENSMUSG00000024696	Lpxn	4933402K05Rik|A530083L21Rik|AV278559|LDPL	leupaxin	protein-coding
mm_111607.1	chr12	102399941	102399972	-	1	NA	exon (NM_011175, exon 10 of 14)	exon (NM_011175, exon 10 of 14)	39857	NM_011175	19141	Mm.17185	NM_011175	ENSMUSG00000021190	Lgmn	AEP|AI746452|AU022324|Prsc1	legumain	protein-coding
mm_138742.1	chr17	37002528	37002569	+	1	NA	promoter-TSS (NM_001013745)	promoter-TSS (NM_001013745)	23	NM_001013745	22715	Mm.305561	NM_009559	ENSMUSG00000036036	Zfp57	G19|Zfp-57	zinc finger protein 57	protein-coding
mm_74943.1	chr8	25840756	25840794	-	1	NA	promoter-TSS (NM_001286207)	promoter-TSS (NM_001286207)	12	NM_011791	23808	Mm.27706	NM_011791	ENSMUSG00000031575	Ash2l	-	ash2 (absent, small, or homeotic)-like (Drosophila)	protein-coding
mm_95128.1	chr11	34299696	34299701	+	1	NA	intron (NM_033374, intron 30 of 51)	intron (NM_033374, intron 30 of 51)	-15124	NM_001025382	574403	Mm.444796	NM_001025382	ENSMUSG00000069911	Fam196b	EG574403|Gm6041	family with sequence similarity 196, member B	protein-coding
mm_144692.1	chr18	34856532	34856545	+	1	NA	Intergenic	Intergenic	-4669	NM_007913	13653	Mm.181959	NM_007913	ENSMUSG00000038418	Egr1	A530045N19Rik|ETR103|Egr-1|Krox-1|Krox-24|Krox24|NGF1-A|NGFI-A|NGFIA|TIS8|Zenk|Zfp-6|Zif268|egr	early growth response 1	protein-coding
mm_18719.1	chr2	72615165	72615169	-	1	NA	Intergenic	Intergenic	-88343	NR_040503	74541	Mm.410774	NR_040503	ENSMUSG00000085252	8430437L04Rik	-	RIKEN cDNA 8430437L04 gene	ncRNA
mm_34303.1	chr4	141750294	141750294	+	1	NA	intron (NM_001081408, intron 2 of 6)	intron (NM_001081408, intron 2 of 6)	3619	NM_001081408	75986	Mm.30032	NM_001081408	ENSMUSG00000040706	Agmat	5033405N08Rik	agmatine ureohydrolase (agmatinase)	protein-coding
mm_55440.1	chr6	67037208	67037220	-	1	NA	exon (NM_007836, exon 1 of 4)	exon (NM_007836, exon 1 of 4)	193	NM_007836	13197	Mm.72235	NM_007836	ENSMUSG00000036390	Gadd45a	AA545191|Ddit1|GADD45	growth arrest and DNA-damage-inducible 45 alpha	protein-coding
mm_106733.1	chr12	3894799	3894864	+	1	NA	intron (NM_153743, intron 1 of 17)	intron (NM_153743, intron 1 of 17)	3087	NM_153743	13435	Mm.5001	NM_007872	ENSMUSG00000020661	Dnmt3a	MmuIIIA	DNA methyltransferase 3A	protein-coding
mm_32065.1	chr4	97777867	97777867	+	1	NA	5' UTR (NM_001122953, exon 1 of 10)	5' UTR (NM_001122953, exon 1 of 10)	241	NM_010905	18027	Mm.31274	NM_010905	ENSMUSG00000028565	Nfia	1110047K16Rik|9430022M17Rik|CTF|NF1-A|NF1A	nuclear factor I/A	protein-coding
mm_63808.1	chr7	133637687	133637742	+	1	NA	promoter-TSS (NM_178115)	promoter-TSS (NM_178115)	39	NM_178115	214764	Mm.174044	NM_145995	ENSMUSG00000039990	Edrf1	2700050L05Rik|AU022667|AW558805	erythroid differentiation regulatory factor 1	protein-coding
mm_123890.1	chr14	72710575	72710638	-	1	NA	promoter-TSS (NM_207636)	promoter-TSS (NM_207636)	-603	NM_207636	319448	Mm.205421	NM_207636	ENSMUSG00000033487	Fndc3a	1700094E19Rik|D14Ertd453e|F730017H24Rik|Fndc3|sys	fibronectin type III domain containing 3A	protein-coding
mm_160161.1	chr7	44350809	44350809	+	1	NA	intron (NM_001034115, intron 22 of 24)	intron (NM_001034115, intron 22 of 24)	24221	NM_027049	69349	Mm.358922	NM_027049	ENSMUSG00000008028	1700008O03Rik	-	RIKEN cDNA 1700008O03 gene	protein-coding
mm_152060.1	chr19	6363341	6363429	-	1	NA	promoter-TSS (NR_122118)	promoter-TSS (NR_122118)	-305	NM_011750	22668	Mm.256422	NM_011750	ENSMUSG00000024949	Sf1	BBP|MZFM|WBP4|Zfp162	splicing factor 1	protein-coding
mm_159015.1	chr1	170232746	170232746	+	1	NA	promoter-TSS (NM_001033499)	promoter-TSS (NM_001033499)	-125	NM_001033499	545378	Mm.379942	NM_001033499	ENSMUSG00000073494	Sh2d1b2	EAT-2B|Eat2b|Ert|Sh2d1c	SH2 domain containing 1B2	protein-coding
mm_148845.1	chr19	6374772	6374791	+	1	NA	non-coding (NR_122118, exon 11 of 12)	non-coding (NR_122118, exon 11 of 12)	-9627	NM_011224	19309	Mm.27806	NM_011224	ENSMUSG00000032648	Pygm	AI115133|PG	muscle glycogen phosphorylase	protein-coding
mm_13055.1	chr2	91102512	91102524	+	1	NA	intron (NM_011355, intron 2 of 4)	intron (NM_011355, intron 2 of 4)	5840	NM_011355	20375	Mm.1302	NM_011355	ENSMUSG00000002111	Spi1	Dis-1|Dis1|PU.1|Sfpi-1|Sfpi1|Spi-1|Tcfpu1|Tfpu.1	spleen focus forming virus (SFFV) proviral integration oncogene	protein-coding
mm_44979.1	chr5	36830574	36830646	-	1	NA	promoter-TSS (NM_008550)	promoter-TSS (NM_008550)	39	NM_008550	17160	Mm.761	NM_008550	ENSMUSG00000029119	Man2b2	mKIAA0935	mannosidase 2, alpha B2	protein-coding
mm_52615.1	chr6	117173919	117173929	+	1	NA	3' UTR (NM_021704, exon 3 of 3)	3' UTR (NM_021704, exon 3 of 3)	5389	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_89039.1	chr10	82833927	82833945	+	1	NA	promoter-TSS (NM_001042523)	promoter-TSS (NM_001042523)	-15	NM_001042523	50493	Mm.210155	NM_015762	ENSMUSG00000020250	Txnrd1	TR|TR1|TrxR1	thioredoxin reductase 1	protein-coding
mm_110039.1	chr12	17176545	17176557	-	1	NA	5' UTR (NM_201531, exon 1 of 1)	5' UTR (NM_201531, exon 1 of 1)	337	NM_201531	382571	Mm.40173	NM_201531	ENSMUSG00000051726	Kcnf1	Gm1182|Kv5.1	potassium voltage-gated channel, subfamily F, member 1	protein-coding
mm_6093.1	chr1	63214276	63214286	-	1	NA	promoter-TSS (NM_146250)	promoter-TSS (NM_146250)	0	NM_146250	241070	Mm.103354	NM_146250	ENSMUSG00000046856	Gpr1	-	G protein-coupled receptor 1	protein-coding
mm_134906.1	chr16	30260028	30260036	-	1	NA	exon (NM_027904, exon 2 of 2)	exon (NM_027904, exon 2 of 2)	7500	NM_027904	71756	Mm.290614	NM_027904	ENSMUSG00000023176	Cpn2	1300018K11Rik	carboxypeptidase N, polypeptide 2	protein-coding
mm_18488.1	chr2	62602867	62602885	-	1	NA	intron (NM_001164477, intron 11 of 14)	intron (NM_001164477, intron 11 of 14)	-28855	NM_007986	14089	Mm.41816	NM_007986	ENSMUSG00000000392	Fap	SIMP	fibroblast activation protein	protein-coding
mm_109247.1	chr12	109453216	109453271	+	1	NA	promoter-TSS (NM_010052)	promoter-TSS (NM_010052)	-212	NM_001190704	13386	Mm.157069	NM_010052	ENSMUSG00000040856	Dlk1	AW742678|DLK-1|DlkI|FA1|Ly107|Peg9|SCP1|ZOG|pG2|pref-1	delta-like 1 homolog (Drosophila)	protein-coding
mm_66842.1	chr7	48883336	48883343	-	1	NA	Intergenic	Intergenic	-2298	NM_001013368	108961	Mm.240566	NM_001013368	ENSMUSG00000046179	E2f8	4432406C08Rik|AA410048	E2F transcription factor 8	protein-coding
mm_130751.1	chr15	101270300	101270310	-	1	NA	exon (NM_010444, exon 2 of 7)	exon (NM_010444, exon 2 of 7)	3459	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_13786.1	chr2	118814030	118814040	+	1	NA	promoter-TSS (NM_026412)	promoter-TSS (NM_026412)	32	NM_026412	51944	Mm.252695	NM_026412	ENSMUSG00000027331	Knstrn	1700025D04Rik|C15orf23|D2Ertd750e|SKAP|Traf4af1	kinetochore-localized astrin/SPAG5 binding	protein-coding
mm_82052.1	chr9	122569089	122569090	+	1	NA	Intergenic	CpG	-3412	NR_015610	319626	Mm.186748	NR_015610	ENSMUSG00000097736	9530059O14Rik	-	RIKEN cDNA 9530059O14 gene	ncRNA
mm_60140.1	chr7	38182789	38182822	+	1	NA	promoter-TSS (NM_028166)	promoter-TSS (NM_028166)	-412	NM_001085385	72244	Mm.187554	NM_028166		1600014C10Rik	AI428873	RIKEN cDNA 1600014C10 gene	protein-coding
mm_128979.1	chr15	74833512	74833524	-	1	NA	Intergenic	B3|SINE|B2	8125	NM_001033229	110115	Mm.322606	NM_001033229	ENSMUSG00000075604	Cyp11b1	AA389061|CPN1|Cyp11b|Cyp11b-1|FHI	cytochrome P450, family 11, subfamily b, polypeptide 1	protein-coding
mm_80568.1	chr9	83925119	83925175	+	1	NA	promoter-TSS (NM_001305935)	promoter-TSS (NM_001305935)	10	NM_001305935	12040	Mm.12819	NM_199195	ENSMUSG00000032263	Bckdhb	BCKDE1B|BCKDH E1-beta	branched chain ketoacid dehydrogenase E1, beta polypeptide	protein-coding
mm_52559.1	chr6	116173786	116173804	+	1	NA	intron (NM_177412, intron 1 of 5)	CpG	19579	NM_177412	330401	Mm.425352	NM_177412	ENSMUSG00000030126	Tmcc1	3632431M01Rik|mKIAA0779	transmembrane and coiled coil domains 1	protein-coding
mm_5911.1	chr1	55019327	55019344	-	1	NA	exon (NM_031179, exon 2 of 25)	exon (NM_031179, exon 2 of 25)	8143	NM_031179	81898	Mm.279736	NM_031179	ENSMUSG00000025982	Sf3b1	155kDa|2810001M05Rik|AA409119|Prp10|SAP155|SF3b155|TA-8|Targ4	splicing factor 3b, subunit 1	protein-coding
mm_120156.1	chr14	60709312	60709336	+	1	NA	intron (NM_001033272, intron 3 of 12)	intron (NM_001033272, intron 3 of 12)	-23580	NM_001310594	219140	Mm.149776	NM_001033272	ENSMUSG00000021990	Spata13	C79050|ESTM11|X83327|mFLJ00298	spermatogenesis associated 13	protein-coding
mm_13046.1	chr2	91096791	91096820	+	1	NA	5' UTR (NM_011355, exon 1 of 5)	5' UTR (NM_011355, exon 1 of 5)	127	NM_011355	20375	Mm.1302	NM_011355	ENSMUSG00000002111	Spi1	Dis-1|Dis1|PU.1|Sfpi-1|Sfpi1|Spi-1|Tcfpu1|Tfpu.1	spleen focus forming virus (SFFV) proviral integration oncogene	protein-coding
mm_162820.1	chr10	80330113	80330119	+	1	NA	promoter-TSS (NM_139292)	promoter-TSS (NM_139292)	-29	NM_001204931	70335	Mm.28147	NM_139292	ENSMUSG00000035504	Reep6	0610011M24Rik|Dp1l1	receptor accessory protein 6	protein-coding
mm_35837.1	chr4	48044894	48044904	-	1	NA	promoter-TSS (NM_015743)	promoter-TSS (NM_015743)	-406	NM_015743	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_88687.1	chr10	80115864	80115886	+	1	NA	promoter-TSS (NM_011492)	promoter-TSS (NM_011492)	72	NM_001301854	20869	Mm.44231	NM_011492	ENSMUSG00000003068	Stk11	AA408040|Lkb1|Par-4|R75140	serine/threonine kinase 11	protein-coding
mm_112632.1	chr13	15994177	15994182	+	1	NA	Intergenic	RMER5|LTR|ERV1	-17672	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_169905.1	chr16	53826256	53826256	+	1	NA	Intergenic	L1Md_T|LINE|L1	-1010512	NR_040495	73820	Mm.60493	NR_040495		4930404A05Rik	-	RIKEN cDNA 4930404A05 gene	ncRNA
mm_145217.1	chr18	50053015	50053024	+	1	NA	promoter-TSS (NM_134131)	promoter-TSS (NM_134131)	-263	NM_134131	106869	Mm.27740	NM_134131	ENSMUSG00000062210	Tnfaip8	AA987150|E130304C20Rik|ENSMUSG00000073567|Gg2-1|Gm10539|Nded|Ssc-2|Tipe	tumor necrosis factor, alpha-induced protein 8	protein-coding
mm_120902.1	chr14	75962391	75962401	+	1	NA	intron (NM_026214, intron 1 of 1)	intron (NM_026214, intron 1 of 1)	7393	NM_026214	67516	Mm.390712	NM_026214	ENSMUSG00000046523	Kctd4	2210017A09Rik|AU017169	potassium channel tetramerisation domain containing 4	protein-coding
mm_47567.1	chr5	124477466	124477491	-	1	NA	intron (NM_030259, intron 1 of 3)	B2_Mm2|SINE|B2	757	NM_030259	80291	Mm.425280	NM_030259	ENSMUSG00000029401	Rilpl2	-	Rab interacting lysosomal protein-like 2	protein-coding
mm_138889.1	chr17	43477082	43477089	+	1	NA	exon (NM_008585, exon 13 of 14)	exon (NM_008585, exon 13 of 14)	25688	NM_008585	17287	Mm.5346	NM_008585	ENSMUSG00000023914	Mep1a	AI098089|AW107200|Mep-1|Mep-1a|Mep1	meprin 1 alpha	protein-coding
mm_10366.1	chr2	11705824	11705832	+	1	NA	5' UTR (NM_001271500, exon 1 of 6)	5' UTR (NM_001271500, exon 1 of 6)	116	NM_001271500	16169	Mm.200196	NM_008358	ENSMUSG00000023206	Il15ra	AA690181|IL-15RA	interleukin 15 receptor, alpha chain	protein-coding
mm_84165.1	chr9	59664345	59664357	-	1	NA	intron (NM_001253883, intron 1 of 10)	B1F|SINE|Alu	7983	NM_001253883	18746	Mm.326167	NM_011099	ENSMUSG00000032294	Pkm	AA414905|AL024370|AL024424|Pk-2|Pk-3|Pk3|Pkm2	pyruvate kinase, muscle	protein-coding
mm_126195.1	chr15	78779556	78779583	+	1	NA	intron (NM_130859, intron 16 of 20)	intron (NM_130859, intron 16 of 20)	-6124	NM_008595	17305	Mm.149235	NM_008595	ENSMUSG00000018169	Mfng	AW546563	MFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	protein-coding
mm_152630.1	chr19	12501441	12501454	-	1	NA	5' UTR (NM_172442, exon 1 of 9)	5' UTR (NM_172442, exon 1 of 9)	549	NM_172442	207521	Mm.247695	NM_172442	ENSMUSG00000039982	Dtx4	AI449438|BC044798|D930042H13|RNF155	deltex 4, E3 ubiquitin ligase	protein-coding
mm_56423.1	chr6	97253156	97253172	-	1	NA	promoter-TSS (NM_001081157)	promoter-TSS (NM_001081157)	-384	NM_001081157	320502	Mm.68163	NM_001081157	ENSMUSG00000044086	Lmod3	5430424A14Rik	leiomodin 3 (fetal)	protein-coding
mm_125583.1	chr15	59525893	59525894	+	1	NA	intron (NM_026746, intron 4 of 6)	intron (NM_026746, intron 4 of 6)	-122761	NM_144549	211770	Mm.40298	NM_144549	ENSMUSG00000032501	Trib1	A530090O15Rik|TRB-1|Trb1	tribbles pseudokinase 1	protein-coding
mm_105093.1	chr11	100918106	100918107	-	1	NA	intron (NM_213660, intron 1 of 23)	ID_B1|SINE|B4	21434	NM_213660	20848	Mm.249934	NM_011486	ENSMUSG00000004040	Stat3	1110034C02Rik|AW109958|Aprf	signal transducer and activator of transcription 3	protein-coding
mm_142246.1	chr17	37483097	37483121	-	1	NA	exon (NM_008204, exon 2 of 4)	exon (NM_008204, exon 2 of 4)	420	NM_008204	14990	Mm.329041	NM_008204	ENSMUSG00000016283	H2-M2	H-2M2|Thy19.4	histocompatibility 2, M region locus 2	protein-coding
mm_148586.1	chr19	5068078	5068085	+	1	NA	promoter-TSS (NM_054042)	promoter-TSS (NM_054042)	3	NM_054042	70445	Mm.29597	NM_054042	ENSMUSG00000056481	Cd248	2610111G01Rik|AI842296|Cd164l1|Tem1	CD248 antigen, endosialin	protein-coding
mm_128061.1	chr15	26715355	26715367	-	1	NA	intron (NM_176959, intron 2 of 3)	intron (NM_176959, intron 2 of 3)	180203	NM_176959	448987	Mm.253378	NM_176959	ENSMUSG00000043556	Fbxl7	AL023057|D230018M15Rik|FBL7|Fbl6	F-box and leucine-rich repeat protein 7	protein-coding
mm_11506.1	chr2	32567800	32567811	+	1	NA	3' UTR (NM_153560, exon 11 of 11)	3' UTR (NM_153560, exon 11 of 11)	-3053	NM_010073	13481	Mm.22001	NM_010073	ENSMUSG00000026810	Dpm2	AW557993|R75484	dolichol-phosphate (beta-D) mannosyltransferase 2	protein-coding
mm_107253.1	chr12	28649653	28649670	+	1	NA	promoter-TSS (NM_001286865)	promoter-TSS (NM_001286865)	59	NM_001286865	19819	Mm.10152	NM_011275	ENSMUSG00000020630	Rnaseh1	-	ribonuclease H1	protein-coding
mm_15283.1	chr2	155276583	155276592	+	1	NA	non-coding (NR_046364, exon 1 of 3)	non-coding (NR_046364, exon 1 of 3)	223	NR_046364	66734	Mm.196239	NM_025735	ENSMUSG00000027602	Map1lc3a	1010001H21Rik|4922501H04Rik|LC3|LC3a	microtubule-associated protein 1 light chain 3 alpha	protein-coding
mm_38305.1	chr4	136898763	136898792	-	1	NA	promoter-TSS (NM_007572)	promoter-TSS (NM_007572)	67	NM_007572	12259	Mm.439957	NM_007572	ENSMUSG00000036887	C1qa	AI255395|C1q	complement component 1, q subcomponent, alpha polypeptide	protein-coding
mm_74297.1	chr8	126029252	126029263	+	1	NA	intron (NM_008430, intron 2 of 2)	intron (NM_008430, intron 2 of 2)	34155	NM_008430	16525	Mm.10800	NM_008430	ENSMUSG00000033998	Kcnk1	AI788889|TWIK-1	potassium channel, subfamily K, member 1	protein-coding
mm_19004.1	chr2	76881259	76881261	-	1	NA	exon (NM_011652, exon 87 of 313)	exon (NM_011652, exon 87 of 313)	101287	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_9844.1	chr1	184731937	184731949	-	1	NA	exon (NM_008250, exon 1 of 4)	exon (NM_008250, exon 1 of 4)	550	NM_008250	15284	Mm.1347	NM_008250	ENSMUSG00000039377	Hlx	Hlx1	H2.0-like homeobox	protein-coding
mm_63720.1	chr7	130820319	130820329	+	1	NA	intron (NM_001081038, intron 12 of 15)	intron (NM_001081038, intron 12 of 15)	-45400	NM_001346515	101476	Mm.323554	NM_133942	ENSMUSG00000040268	Plekha1	AA960558|C920009D07Rik|TAPP1	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 1	protein-coding
mm_64707.1	chr7	4604043	4604053	-	1	NA	promoter-TSS (NM_207270)	promoter-TSS (NM_207270)	-7	NM_207270	545902	Mm.188925	NM_207270	ENSMUSG00000035429	Ptprh	R-PTP-H|sap-1	protein tyrosine phosphatase, receptor type, H	protein-coding
mm_111670.1	chr12	103338224	103338230	-	1	NA	intron (NM_023049, intron 2 of 9)	intron (NM_023049, intron 2 of 9)	17774	NM_023049	65256	Mm.27159	NM_023049	ENSMUSG00000021200	Asb2	1110008E15Rik	ankyrin repeat and SOCS box-containing 2	protein-coding
mm_124175.1	chr14	93841073	93841077	-	1	NA	intron (NM_001346722, intron 2 of 4)	Lx5c|LINE|L1	47813	NM_001271800	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding
mm_43333.1	chr5	135009891	135009901	+	1	NA	non-coding (NR_033794, exon 1 of 5)	non-coding (NR_033794, exon 1 of 5)	440	NR_033794	68758	Mm.389700	NM_145215	ENSMUSG00000040532	Abhd11	1110054D16Rik|A630008N09Rik|Wbscr21	abhydrolase domain containing 11	protein-coding
mm_18147.1	chr2	45066775	45066796	-	1	NA	intron (NM_001289521, intron 1 of 8)	B1_Mur2|SINE|Alu	43492	NM_001289521	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_108817.1	chr12	95695351	95695365	+	1	NA	intron (NM_201518, intron 1 of 1)	CpG	3132	NM_201518	399558	Mm.341948	NM_201518	ENSMUSG00000047414	Flrt2	-	fibronectin leucine rich transmembrane protein 2	protein-coding
mm_25532.1	chr3	114913614	114913616	+	1	NA	intron (NM_001286750, intron 1 of 5)	intron (NM_001286750, intron 1 of 5)	8980	NM_001286750	229759	Mm.54183	NM_153157	ENSMUSG00000027965	Olfm3	B230206G02Rik	olfactomedin 3	protein-coding
mm_39117.1	chr4	154944126	154944135	-	1	NA	Intergenic	Intergenic	-16053	NM_178931	230979	Mm.215147	NM_178931	ENSMUSG00000042333	Tnfrsf14	Atar|HveA|Hvem|Tnfrs14	tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)	protein-coding
mm_160325.1	chr8	3602375	3602375	+	1	NA	exon (NM_027171, exon 8 of 17)	exon (NM_027171, exon 8 of 17)	14925	NM_001347111	69697	Mm.390010	NM_027171	ENSMUSG00000044433	Camsap3	2310057J16Rik|Kiaa1543|Nezha	calmodulin regulated spectrin-associated protein family, member 3	protein-coding
mm_33383.1	chr4	129573758	129573768	+	1	NA	promoter-TSS (NM_001162433)	promoter-TSS (NM_001162433)	-122	NM_001162433	16818	Mm.293753	NM_010693	ENSMUSG00000000409	Lck	Hck-3|Lsk|Lskt|p56<lck>|p56Lck	lymphocyte protein tyrosine kinase	protein-coding
mm_107945.1	chr12	72085848	72085864	+	1	NA	promoter-TSS (NM_024205)	promoter-TSS (NM_024205)	17	NM_024205	104771	Mm.258935	NM_024205	ENSMUSG00000005078	Jkamp	1200003C05Rik|2310047L11Rik|Jamp	JNK1/MAPK8-associated membrane protein	protein-coding
mm_104359.1	chr11	94305296	94305299	-	1	NA	intron (NM_026313, intron 3 of 10)	B1_Mur2|SINE|Alu	16614	NM_026313	67684	Mm.30927	NM_026313	ENSMUSG00000020863	Luc7l3	3300001P08Rik|Luc7a	LUC7-like 3 (S. cerevisiae)	protein-coding
mm_16776.1	chr2	9884338	9884345	-	1	NA	non-coding (NR_024257, exon 5 of 5)	non-coding (NR_024257, exon 5 of 5)	3095	NR_024257	381347	Mm.441450	NR_024257		4930412O13Rik	ENSMUSG00000075535|Gm10853	RIKEN cDNA 4930412O13 gene	ncRNA
mm_65859.1	chr7	29344845	29344860	-	1	NA	intron (NM_001081028, intron 16 of 22)	(TG)n|Simple_repeat|Simple_repeat	40847	NM_013874	29861	Mm.101885	NM_013874	ENSMUSG00000030584	Dpf1	Neud4	D4, zinc and double PHD fingers family 1	protein-coding
mm_87761.1	chr10	60291674	60291687	+	1	NA	exon (NM_011179, exon 2 of 15)	exon (NM_011179, exon 2 of 15)	7219	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_119446.1	chr14	46882932	46882936	+	1	NA	promoter-TSS (NM_028966)	promoter-TSS (NM_028966)	-31	NM_028966	74480	Mm.214454	NM_028966	ENSMUSG00000021838	Samd4	1700024G08Rik|1700111L17Rik|4933436G17Rik|Samd4a|Smaug|Smaug1|sunk	sterile alpha motif domain containing 4	protein-coding
mm_90441.1	chr10	127643175	127643185	+	1	NA	5' UTR (NM_009284, exon 1 of 22)	5' UTR (NM_009284, exon 1 of 22)	194	NM_009284	20852	Mm.121721	NM_009284	ENSMUSG00000002147	Stat6	-	signal transducer and activator of transcription 6	protein-coding
mm_142534.1	chr17	46520650	46520665	-	1	NA	intron (NM_001081335, intron 23 of 40)	intron (NM_001081335, intron 23 of 40)	23868	NM_207161	381101	Mm.35801	NM_207161	ENSMUSG00000040658	Dnph1	C76683|Rcl	2'-deoxynucleoside 5'-phosphate N-hydrolase 1	protein-coding
mm_103736.1	chr11	80063268	80063290	-	1	NA	intron (NM_001277106, intron 2 of 6)	intron (NM_001277106, intron 2 of 6)	17712	NM_001277106	54394	Mm.272093	NM_018776	ENSMUSG00000017561	Crlf3	BB164954|Creme9|Cytor4	cytokine receptor-like factor 3	protein-coding
mm_152399.1	chr19	10555809	10555814	-	1	NA	promoter-TSS (NM_001277861)	promoter-TSS (NM_001277861)	-48	NM_001277860	68642	Mm.31236	NM_026798	ENSMUSG00000024667	Tmem216	1110017C22Rik|2810441K11Rik|4921533J23Rik|A930021F15Rik|AI482550	transmembrane protein 216	protein-coding
mm_149545.1	chr19	12585865	12585868	+	1	NA	TTS (NR_015503)	TTS (NR_015503)	10700	NR_015503	74333	Mm.329744	NR_015503	ENSMUSG00000086213	A330040F15Rik	-	RIKEN cDNA A330040F15 gene	ncRNA
mm_101904.1	chr11	49203208	49203231	-	1	NA	promoter-TSS (NM_001024846)	promoter-TSS (NM_001024846)	-281	NM_001024846	22720	Mm.16650	NM_009562	ENSMUSG00000046311	Zfp62	-	zinc finger protein 62	protein-coding
mm_111135.1	chr12	81568193	81568204	-	1	NA	5' UTR (NM_020330, exon 1 of 2)	5' UTR (NM_020330, exon 1 of 2)	276	NM_020330	56622	Mm.117130	NM_020330	ENSMUSG00000008438	Adam21	Adam31	a disintegrin and metallopeptidase domain 21	protein-coding
mm_3273.1	chr1	136569909	136569917	+	1	NA	Intergenic	Intergenic	-54988	NM_177643	226442	Mm.62521	NM_177643	ENSMUSG00000041483	Zfp281	Znf281	zinc finger protein 281	protein-coding
mm_125750.1	chr15	73748366	73748384	+	1	NA	5' UTR (NM_008975, exon 1 of 6)	5' UTR (NM_008975, exon 1 of 6)	349	NM_008975	19245	Mm.390807	NM_008975	ENSMUSG00000059895	Ptp4a3	AV088979|Prl-3|pPtp4a3	protein tyrosine phosphatase 4a3	protein-coding
mm_83478.1	chr9	45900260	45900263	-	1	NA	intron (NM_001310839, intron 2 of 13)	intron (NM_001310839, intron 2 of 13)	-6308	NM_008794	18554	Mm.3255	NM_008794	ENSMUSG00000035382	Pcsk7	AA959856|PC7|SPC7	proprotein convertase subtilisin/kexin type 7	protein-coding
mm_163902.1	chr14	30148353	30148356	-	1	NA	intron (NM_001302637, intron 8 of 48)	intron (NM_001302637, intron 8 of 48)	125721	NM_175343	218865	Mm.259916	NM_172264	ENSMUSG00000015970	Chdh	AU041472|D630034H06Rik	choline dehydrogenase	protein-coding
mm_150602.1	chr19	40748796	40748826	+	1	NA	Intergenic	Intergenic	-82468	NM_172839	240665	Mm.309	NM_172839	ENSMUSG00000025010	Ccnj	D430039C20Rik	cyclin J	protein-coding
mm_19809.1	chr2	110314267	110314292	-	1	NA	Intergenic	Intergenic	-8554	NM_130452	170442	Mm.27335	NM_130452	ENSMUSG00000041660	Bbox1	AI874739	butyrobetaine (gamma), 2-oxoglutarate dioxygenase 1 (gamma-butyrobetaine hydroxylase)	protein-coding
mm_15201.1	chr2	154206520	154206525	+	1	NA	exon (NM_153418, exon 5 of 16)	exon (NM_153418, exon 5 of 16)	6142	NM_153418	228801	Mm.3783	NM_153418	ENSMUSG00000027485	Bpifb1	Lplunc1	BPI fold containing family B, member 1	protein-coding
mm_100717.1	chr11	3895086	3895104	-	1	NA	promoter-TSS (NM_026150)	promoter-TSS (NM_026150)	31	NM_026150	67430	Mm.347950	NM_026150	ENSMUSG00000020434	4921536K21Rik	AV043724	RIKEN cDNA 4921536K21 gene	protein-coding
mm_80506.1	chr9	78615805	78615809	+	1	NA	5' UTR (NM_153098, exon 1 of 33)	5' UTR (NM_153098, exon 1 of 33)	261	NM_153098	235505	Mm.32955	NM_153098	ENSMUSG00000046186	Cd109	9930012E15Rik|AI480638|GARP	CD109 antigen	protein-coding
mm_90951.1	chr10	13182412	13182444	-	1	NA	exon (NM_181470, exon 6 of 11)	exon (NM_181470, exon 6 of 11)	-4405	NM_029172	75122	Mm.159433	NM_029172	ENSMUSG00000019815	Zc2hc1b	4930519B02Rik|Fam164b	zinc finger, C2HC-type containing 1B	protein-coding
mm_87233.1	chr10	40630058	40630063	+	1	NA	promoter-TSS (NM_027442)	promoter-TSS (NM_027442)	49	NR_133568	70503	Mm.252862	NM_027442	ENSMUSG00000063428	Ddo	5330420D20Rik|5730402C02Rik|AI467244	D-aspartate oxidase	protein-coding
mm_79616.1	chr9	58652035	58652088	+	1	NA	TTS (NM_028598)	TTS (NM_028598)	69821	NM_009145	20320	Mm.15125	NM_009145	ENSMUSG00000032336	Nptn	AW554172|SDR-1|Sdfr1	neuroplastin	protein-coding
mm_87731.1	chr10	60131960	60131970	+	1	NA	3' UTR (NM_052994, exon 11 of 11)	3' UTR (NM_052994, exon 11 of 11)	5189	NR_105871	102465546		NR_105871	ENSMUSG00000105468	Mir6906	mmu-mir-6906	microRNA 6906	ncRNA
mm_155940.1	chrX	104200846	104200847	+	1	NA	5' UTR (NM_001077354, exon 1 of 5)	5' UTR (NM_001077354, exon 1 of 5)	271	NM_001077354	245555	Mm.381907	NM_001077354	ENSMUSG00000046449	C77370	A230051P11|C77386|KIDLIA|Kiaa2022|Xpn|mKIAA2022	expressed sequence C77370	protein-coding
mm_112860.1	chr13	20842320	20842331	+	1	NA	intron (NM_012054, intron 3 of 20)	intron (NM_012054, intron 3 of 20)	48212	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_10857.1	chr2	25054446	25054456	+	1	NA	promoter-TSS (NM_020276)	promoter-TSS (NM_020276)	72	NM_001177655	56876	Mm.42956	NM_020276	ENSMUSG00000006476	Nsmf	Jacob|Nelf	NMDA receptor synaptonuclear signaling and neuronal migration factor	protein-coding
mm_60004.1	chr7	30715873	30715893	+	1	NA	exon (NM_018731, exon 7 of 22)	exon (NM_018731, exon 7 of 22)	3674	NM_001290627	11944	Mm.12821	NM_018731	ENSMUSG00000005553	Atp4a	-	ATPase, H+/K+ exchanging, gastric, alpha polypeptide	protein-coding
mm_5234.1	chr1	14755952	14755962	-	1	NA	promoter-TSS (NM_010827)	promoter-TSS (NM_010827)	9	NM_010827	17681	Mm.5820	NM_010827	ENSMUSG00000025930	Msc	MyoR|bHLHa22	musculin	protein-coding
mm_1464.1	chr1	69681576	69681576	+	1	NA	intron (NM_011770, intron 3 of 7)	intron (NM_011770, intron 3 of 7)	4384	NM_011770	22779	Mm.106343	NM_011770	ENSMUSG00000025997	Ikzf2	A730095J18Rik|Helios|Zfpn1a2|Znfn1a2	IKAROS family zinc finger 2	protein-coding
mm_156509.1	chrX	150497505	150497519	+	1	NA	Intergenic	RLTR14-int|LTR|ERV1	-38362	NM_001164683	382245	Mm.277309	NM_001164683	ENSMUSG00000041353	Tmem29	2700081K05Rik|6330540D07Rik|CXorf44-like	transmembrane protein 29	protein-coding
mm_51247.1	chr6	71722828	71722829	+	1	NA	intron (NM_178608, intron 1 of 6)	intron (NM_178608, intron 1 of 6)	15147	NM_178608	52250	Mm.146332	NM_178608	ENSMUSG00000052852	Reep1	D6Ertd253e	receptor accessory protein 1	protein-coding
mm_143787.1	chr17	81731432	81731440	-	1	NA	intron (NR_104580, intron 1 of 8)	intron (NR_104580, intron 1 of 8)	6951	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_150371.1	chr19	34836992	34836992	+	1	NA	intron (NM_001114339, intron 2 of 6)	B1_Mus2|SINE|Alu	-16219	NR_029783	723826		NR_029783	ENSMUSG00000065594	Mir107	Mirn107|mir-107|mmu-mir-107	microRNA 107	ncRNA
mm_21948.1	chr2	167062733	167062745	-	1	NA	promoter-TSS (NR_138563)	promoter-TSS (NR_138563)	-195	NR_138563	68949	Mm.391959	NM_001081005		Zfas1	1500012F01Rik|Zfos1	zinc finger, NFX1-type containing 1, antisense RNA 1	ncRNA
mm_29905.1	chr3	131471005	131471015	-	1	NA	Intergenic	Intergenic	-93758	NM_001289479	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_43032.1	chr5	123973604	123973666	+	1	NA	promoter-TSS (NM_145070)	promoter-TSS (NM_145070)	7	NM_145070	29816	Mm.149954	NM_145070	ENSMUSG00000000915	Hip1r	AA410023|mKIAA0655	huntingtin interacting protein 1 related	protein-coding
mm_76593.1	chr8	89042844	89042869	-	1	NA	intron (NM_021390, intron 1 of 3)	CpG-14342	1306	NM_021390	58198	Mm.214361	NM_021390	ENSMUSG00000031665	Sall1	Msal-3	sal-like 1 (Drosophila)	protein-coding
mm_65003.1	chr7	17042566	17042587	-	1	NA	intron (NM_001162950, intron 11 of 14)	intron (NM_001162950, intron 11 of 14)	14103	NM_016868	53417	Mm.135110	NM_016868	ENSMUSG00000004328	Hif3a	Ipas|MOP7|NEPAS|bHLHe17	hypoxia inducible factor 3, alpha subunit	protein-coding
mm_97663.1	chr11	79653182	79653186	+	1	NA	intron (NM_175543, intron 3 of 14)	intron (NM_175543, intron 3 of 14)	21902	NR_045898	72218	Mm.443271	NR_045898	ENSMUSG00000086569	Rab11fip4os2	1700020F10Rik|4930542H20Rik|Rab11fib4os2	RAB11 family interacting protein 4 (class II), opposite strand 2	ncRNA
mm_106941.1	chr12	8712989	8712993	+	1	NA	intron (NM_001310519, intron 5 of 19)	intron (NM_001310519, intron 5 of 19)	38310	NM_030723	80913	Mm.341243	NM_030723	ENSMUSG00000020594	Pum2	5730503J23Rik|Pumm2	pumilio RNA-binding family member 2	protein-coding
mm_14120.1	chr2	125909126	125909130	+	1	NA	intron (NM_175154, intron 5 of 9)	intron (NM_175154, intron 5 of 9)	42905	NM_001291002	69976	Mm.20216	NM_175154	ENSMUSG00000027207	Galk2	2810017M24Rik|AI327030|Gk2	galactokinase 2	protein-coding
mm_136857.1	chr17	12805628	12805652	+	1	NA	intron (NR_027784, intron 2 of 2)	B1_Mur4|SINE|Alu	-35934	NM_010515	16004	Mm.26553	NM_010515	ENSMUSG00000023830	Igf2r	AI661837|CD222|CI-MPR|M6P/IGF2R|Mpr300	insulin-like growth factor 2 receptor	protein-coding
mm_152211.1	chr19	7802685	7802690	-	1	NA	promoter-TSS (NM_146232)	promoter-TSS (NM_146232)	-20	NM_146232	236149	Mm.207060	NM_146232	ENSMUSG00000053303	Slc22a26	-	solute carrier family 22 (organic cation transporter), member 26	protein-coding
mm_13487.1	chr2	106693166	106693174	+	1	NA	promoter-TSS (NM_001143683)	promoter-TSS (NM_001143683)	-289	NM_001143683	77015	Mm.45628	NM_029837	ENSMUSG00000016386	Mpped2	239Fb|2700082O15Rik|AV354767|AW060960	metallophosphoesterase domain containing 2	protein-coding
mm_102018.1	chr11	51635871	51635891	-	1	NA	promoter-TSS (NM_025346)	promoter-TSS (NM_025346)	15	NM_025346	66089	Mm.288183	NM_025346	ENSMUSG00000001054	Rmnd5b	0610039K22Rik|Gid2	required for meiotic nuclear division 5 homolog B	protein-coding
mm_64350.1	chr7	142383427	142383475	+	1	NA	exon (NM_009983, exon 3 of 9)	exon (NM_009983, exon 3 of 9)	4419	NM_009983	13033	Mm.231395	NM_009983	ENSMUSG00000007891	Ctsd	CD|CatD	cathepsin D	protein-coding
mm_164172.1	chr15	75116737	75116749	+	1	NA	Intergenic	RLTR14_RN|LTR|ERV1	-4794	NM_001099217	100041546	Mm.482110	NM_001099217	ENSMUSG00000022584	Ly6c2	Ly-6C.2|Ly-6C2	lymphocyte antigen 6 complex, locus C2	protein-coding
mm_35956.1	chr4	53130879	53130911	-	1	NA	intron (NM_013454, intron 3 of 49)	intron (NM_013454, intron 3 of 49)	29000	NM_013454	11303	Mm.277376	NM_013454	ENSMUSG00000015243	Abca1	ABC-1|Abc1	ATP-binding cassette, sub-family A (ABC1), member 1	protein-coding
mm_156972.1	chrX	170008342	170008363	+	1	NA	Intergenic	Intergenic	-29435	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_108623.1	chr12	85598708	85598735	+	1	NA	promoter-TSS (NM_030887)	promoter-TSS (NM_030887)	-384	NM_001205052	81703	Mm.103560	NM_030887	ENSMUSG00000034271	Jdp2	Jundm2|Jundp2|TIF	Jun dimerization protein 2	protein-coding
mm_166787.1	chr6	145049048	145049079	-	1	NA	promoter-TSS (NM_001024468)	promoter-TSS (NM_001024468)	-251	NM_001024468	12035	Mm.4606	NM_007532	ENSMUSG00000030268	Bcat1	BCATc|Eca39	branched chain aminotransferase 1, cytosolic	protein-coding
mm_97656.1	chr11	79528179	79528192	+	1	NA	5' UTR (NM_001033711, exon 2 of 2)	5' UTR (NM_001033711, exon 2 of 2)	2424	NM_146023	101488212	Mm.439665	NM_146023	ENSMUSG00000070354	Gm21975	Evi2a-evi2b	predicted gene 21975	protein-coding
mm_76759.1	chr8	95576263	95576286	-	1	NA	promoter-TSS (NM_001310539)	promoter-TSS (NM_001310539)	-667	NM_001310539	70993	Mm.486561	NM_027640	ENSMUSG00000048400	Prss54	4931432M23Rik|Klkbl4	protease, serine 54	protein-coding
mm_130931.1	chr15	103168030	103168046	-	1	NA	Intergenic	Intergenic	-4754	NM_027885	71726	Mm.254820	NM_027885	ENSMUSG00000036061	Smug1	1200013B09Rik|A930006H09Rik|C85220	single-strand selective monofunctional uracil DNA glycosylase	protein-coding
mm_18336.1	chr2	58052811	58052829	-	1	NA	promoter-TSS (NM_029972)	promoter-TSS (NM_029972)	-68	NM_029972	77767	Mm.91712	NM_029972	ENSMUSG00000026830	Ermn	A330104H05Rik|AI854460|ermin|mKIAA1189	ermin, ERM-like protein	protein-coding
mm_126565.1	chr15	82171189	82171204	+	1	NA	exon (NM_033218, exon 3 of 19)	exon (NM_033218, exon 3 of 19)	23927	NM_033218	20788	Mm.9002	NM_033218	ENSMUSG00000022463	Srebf2	AI608257|SREBP-2|SREBP2|SREBP2gc|bHLHd2|lop13|nuc	sterol regulatory element binding factor 2	protein-coding
mm_26518.1	chr3	145924281	145924297	+	1	NA	promoter-TSS (NM_009740)	promoter-TSS (NM_009740)	27	NM_009740	12042	Mm.239141	NM_009740	ENSMUSG00000028191	Bcl10	AI132454|BCL-10|C81403|CARMEN|CIPER|CLAP|ME10|cE10	B cell leukemia/lymphoma 10	protein-coding
mm_38711.1	chr4	145224387	145224497	-	1	NA	exon (NM_011610, exon 6 of 10)	exon (NM_011610, exon 6 of 10)	22428	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_82601.1	chr9	21321671	21321677	-	1	NA	intron (NM_001199186, intron 1 of 21)	intron (NM_001199186, intron 1 of 21)	955	NM_001199186	68682	Mm.148425	NM_152808	ENSMUSG00000057193	Slc44a2	1110028E10Rik|CTL2	solute carrier family 44, member 2	protein-coding
mm_66178.1	chr7	34013972	34013983	-	1	NA	promoter-TSS (NM_001276475)	promoter-TSS (NM_001276475)	-35	NM_001100464	233099	Mm.110829	NM_001100464	ENSMUSG00000066584	Scgb2b27	Abpbg27|Abpbg5|Scgb2b5	secretoglobin, family 2B, member 27	protein-coding
mm_59931.1	chr7	30423601	30423605	+	1	NA	intron (NM_172142, intron 1 of 10)	intron (NM_172142, intron 1 of 10)	299	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_81801.1	chr9	116175289	116175297	+	1	NA	promoter-TSS (NM_029575)	promoter-TSS (NM_029575)	70	NM_029575	21813	Mm.172346	NM_009371	ENSMUSG00000032440	Tgfbr2	1110020H15Rik|AU042018|DNIIR|RIIDN|TBR-II|TbetaR-II|TbetaRII	transforming growth factor, beta receptor II	protein-coding
mm_127300.1	chr15	100217198	100217201	+	1	NA	3' UTR (NM_172819, exon 33 of 33)	3' UTR (NM_172819, exon 33 of 33)	-10660	NM_007497	11908	Mm.676	NM_007497	ENSMUSG00000023027	Atf1	-	activating transcription factor 1	protein-coding
mm_26309.1	chr3	142519167	142519177	+	1	NA	intron (NM_153564, intron 10 of 10)	intron (NM_153564, intron 10 of 10)	-11164	NM_001083312	229900	Mm.45740	NM_145545	ENSMUSG00000040253	Gbp7	9830147J24Rik	guanylate binding protein 7	protein-coding
mm_32547.1	chr4	109385899	109385910	+	1	NA	3' UTR (NM_007943, exon 25 of 25)	3' UTR (NM_007943, exon 25 of 25)	20353	NR_131195	102635290	Mm.427859	NR_131195		Ttc39aos1	Gm12750|OTTMUSG00000008290|lincRNA-EPS	Ttc39a opposite strand RNA 1	ncRNA
mm_94380.1	chr11	5196006	5196012	+	1	NA	intron (NM_032396, intron 8 of 8)	intron (NM_032396, intron 8 of 8)	-43787	NM_080595	140703	Mm.840	NM_080595	ENSMUSG00000034164	Emid1	AW122071|CO-5|Emu1	EMI domain containing 1	protein-coding
mm_37948.1	chr4	133194515	133194528	-	1	NA	exon (NM_153423, exon 8 of 9)	exon (NM_153423, exon 8 of 9)	-1134	NR_105984	102466215		NR_105984	ENSMUSG00000099202	Mir7017	Gm27945|mmu-mir-7017	microRNA 7017	ncRNA
mm_77503.1	chr8	122678654	122678669	-	1	NA	promoter-TSS (NM_001109873)	promoter-TSS (NM_001109873)	-486	NM_177289	12398	Mm.194339	NM_009824	ENSMUSG00000006362	Cbfa2t3	A630044F12Rik|AI465270|AW229127|Cbfa2t3h|ETO-2|Eto2|MTGR2	core-binding factor, runt domain, alpha subunit 2, translocated to, 3 (human)	protein-coding
mm_126300.1	chr15	79358391	79358395	+	1	NA	3' UTR (NM_001304830, exon 3 of 3)	3' UTR (NM_001304830, exon 3 of 3)	9991	NM_001304832	17133	Mm.86646	NM_010755	ENSMUSG00000042622	Maff	-	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein F (avian)	protein-coding
mm_118800.1	chr14	24622133	24622143	+	1	NA	Intergenic	Intergenic	131457	NM_011297	20088	Mm.16775	NM_011297	ENSMUSG00000025290	Rps24	-	ribosomal protein S24	protein-coding
mm_41050.1	chr5	86173039	86173052	+	1	NA	promoter-TSS (NM_172712)	promoter-TSS (NM_172712)	-302	NM_172712	231380	Mm.34012	NM_172712	ENSMUSG00000035898	Uba6	4930542H01|5730469D23Rik|AU021846|AW124799|E1-L2|Ube1l2	ubiquitin-like modifier activating enzyme 6	protein-coding
mm_51704.1	chr6	86668802	86668806	+	1	NA	intron (NM_010751, intron 1 of 5)	CpG	355	NM_010751	17119	Mm.279580	NM_010751	ENSMUSG00000001156	Mxd1	AW122478|Mad|Mad1	MAX dimerization protein 1	protein-coding
mm_150995.1	chr19	46618648	46618653	+	1	NA	intron (NM_001177812, intron 2 of 4)	intron (NM_001177812, intron 2 of 4)	-4751	NM_001177813	226178	Mm.329895	NM_146099	ENSMUSG00000047731	Wbp1l	D19Wsu162e|Opal1	WW domain binding protein 1 like	protein-coding
mm_113995.1	chr13	52583302	52583312	+	1	NA	promoter-TSS (NM_001198977)	promoter-TSS (NM_001198977)	-130	NM_001198977	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_170410.1	chr1	86582950	86582951	+	1	NA	promoter-TSS (NM_008801)	promoter-TSS (NM_008801)	-449	NM_008801	18582	Mm.12925	NM_008801	ENSMUSG00000026239	Pde6d	AI841218|PrBP/delta	phosphodiesterase 6D, cGMP-specific, rod, delta	protein-coding
mm_96318.1	chr11	63989741	63989743	+	1	NA	intron (NM_178379, intron 5 of 6)	intron (NM_178379, intron 5 of 6)	25516	NR_131111	78883	Mm.410764	NR_131111	ENSMUSG00000086359	9630013K17Rik	-	RIKEN cDNA 9630013K17 gene	ncRNA
mm_47842.1	chr5	134314559	134314571	-	1	NA	5' UTR (NM_010365, exon 1 of 34)	5' UTR (NM_010365, exon 1 of 34)	195	NM_001080746	14886	Mm.261570	NM_010365	ENSMUSG00000060261	Gtf2i	6030441I21Rik|BAP-135|Diws1t|GtfII-I|Spin|TFII-I|WBSCR6	general transcription factor II I	protein-coding
mm_103873.1	chr11	83525995	83526021	-	1	NA	exon (NM_013653, exon 3 of 3)	exon (NM_013653, exon 3 of 3)	-3909	NM_001045543	629303	Mm.390417	NM_001045543	ENSMUSG00000018925	Heatr9	Gm11435|OTTMUSG00000000990	HEAT repeat containing 9	protein-coding
mm_119162.1	chr14	31929584	31929594	+	1	NA	Intergenic	Intergenic	-99174	NM_001024604	105522	Mm.37660	NM_001024604	ENSMUSG00000014496	Ankrd28	AI465466|AI604979|E430019N21Rik|mKIAA0379	ankyrin repeat domain 28	protein-coding
mm_166911.1	chr7	29281822	29281892	-	1	NA	5' UTR (NM_001082548, exon 1 of 6)	5' UTR (NM_001082548, exon 1 of 6)	120	NM_001082548	20733	Mm.295230	NM_011464	ENSMUSG00000074227	Spint2	AL024025|C76321|HAI-2	serine protease inhibitor, Kunitz type 2	protein-coding
mm_40209.1	chr5	37047110	37047125	+	1	NA	Intergenic	Intergenic	-3740	NM_178394	76071	Mm.85280	NM_178394	ENSMUSG00000063646	Jakmip1	5830437M04Rik|C330021K24Rik|Gababrbp|Marlin-1	janus kinase and microtubule interacting protein 1	protein-coding
mm_100333.1	chr11	118319057	118319069	+	1	NA	intron (NM_011594, intron 2 of 4)	intron (NM_011594, intron 2 of 4)	23471	NM_021440	58251	Mm.439815	NM_021440	ENSMUSG00000076433	BC100451	Cep295nl|Ddc8|FS39|Kiaa1731nl	cDNA sequence BC100451	protein-coding
mm_21918.1	chr2	166821384	166821385	-	1	NA	intron (NM_001085495, intron 1 of 38)	intron (NM_001085495, intron 1 of 38)	15803	NM_001085495	99371	Mm.297192	NM_001085495	ENSMUSG00000074582	Arfgef2	AI463430|AW493672|BIG2|E230011G24Rik	ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited)	protein-coding
mm_26125.1	chr3	137867808	137867834	+	1	NA	TTS (NM_016750)	TTS (NM_016750)	146	NM_001033155	70604	Mm.256488	NM_001033155	ENSMUSG00000074212	Dnajb14	5730496F10Rik	DnaJ heat shock protein family (Hsp40) member B14	protein-coding
mm_34196.1	chr4	140712781	140712782	+	1	NA	intron (NM_173867, intron 6 of 12)	intron (NM_173867, intron 6 of 12)	11308	NM_173867	108911	Mm.253	NM_173867	ENSMUSG00000040945	Rcc2	2610510H01Rik|2610529N02Rik|AA536646|AA675016|Td60|mKIAA1470	regulator of chromosome condensation 2	protein-coding
mm_21370.1	chr2	157204484	157204542	-	1	NA	promoter-TSS (NM_001139516)	promoter-TSS (NM_001139516)	21	NM_011249	19650	Mm.244671	NM_011249	ENSMUSG00000027641	Rbl1	AW547426|PRB1|p107	retinoblastoma-like 1 (p107)	protein-coding
mm_37123.1	chr4	116659553	116659560	-	1	NA	Intergenic	Intergenic	-7882	NM_021473	58810	Mm.30085	NM_021473	ENSMUSG00000028692	Akr1a1	2610201A18Rik|Akr1a4	aldo-keto reductase family 1, member A1 (aldehyde reductase)	protein-coding
mm_59662.1	chr7	28277718	28277770	+	1	NA	promoter-TSS (NM_001177427)	promoter-TSS (NM_001177427)	38	NM_001177427	434156	Mm.118535	NM_001177427	ENSMUSG00000070705	Eid2b	3010005C08Rik	EP300 interacting inhibitor of differentiation 2B	protein-coding
mm_166314.1	chr5	109558908	109558922	-	1	NA	promoter-TSS (NM_001164735)	promoter-TSS (NM_001164735)	78	NM_016715	57914	Mm.35771	NM_016715	ENSMUSG00000033467	Crlf2	CRLM2|Ly114|Tpte2|Tslpr	cytokine receptor-like factor 2	protein-coding
mm_52296.1	chr6	108783118	108783135	+	1	NA	promoter-TSS (NM_026011)	promoter-TSS (NM_026011)	67	NM_026011	67166	Mm.271178	NM_026011	ENSMUSG00000030105	Arl8b	2610313E07Rik|3100002J04Rik|Arl10c|gie1	ADP-ribosylation factor-like 8B	protein-coding
mm_779.1	chr1	44551749	44551758	+	1	NA	promoter-TSS (NM_028450)	promoter-TSS (NM_028450)	82	NM_028450	70676	Mm.133132	NM_027506	ENSMUSG00000056870	Gulp1	3110030A04Rik|5730529O06Rik|CED-6|Ced6|GULP|Gulp-2	GULP, engulfment adaptor PTB domain containing 1	protein-coding
mm_53603.1	chr6	138151125	138151155	+	1	NA	intron (NM_001347489, intron 3 of 3)	intron (NM_001347489, intron 3 of 3)	9546	NM_001347489	56615	Mm.14796	NM_019946	ENSMUSG00000008540	Mgst1	1500002K10Rik|Gst	microsomal glutathione S-transferase 1	protein-coding
mm_142807.1	chr17	50879815	50879853	-	1	NA	intron (NM_028162, intron 13 of 21)	Lx8|LINE|L1	181153	NM_001297747	12228	Mm.392910	NM_009770	ENSMUSG00000022863	Btg3	ANA|tob5	B cell translocation gene 3	protein-coding
mm_61696.1	chr7	81114800	81114808	+	1	NA	promoter-TSS (NM_001004184)	promoter-TSS (NM_001004184)	5	NM_001004184	434203	Mm.389909	NM_001004184	ENSMUSG00000025726	Slc28a1	Cnt1	solute carrier family 28 (sodium-coupled nucleoside transporter), member 1	protein-coding
mm_117579.1	chr13	88125752	88125752	-	1	NA	Intergenic	ORR1B2|LTR|ERVL-MaLR	-695720	NM_010103	13612	Mm.125580	NM_010103	ENSMUSG00000034488	Edil3	Del-1|Del1	EGF-like repeats and discoidin I-like domains 3	protein-coding
mm_50693.1	chr6	51590778	51590782	+	1	NA	TTS (NM_001127349)	TTS (NM_001127349)	46257	NM_001127348	71982	Mm.294166	NM_028035	ENSMUSG00000038301	Snx10	2410004M09Rik	sorting nexin 10	protein-coding
mm_118350.1	chr13	114932071	114932109	-	1	NA	promoter-TSS (NM_008396)	promoter-TSS (NM_008396)	-49	NM_008396	16398	Mm.5007	NM_008396	ENSMUSG00000015533	Itga2	CD49B|DX5	integrin alpha 2	protein-coding
mm_81090.1	chr9	106367944	106367976	+	1	NA	promoter-TSS (NM_153459)	promoter-TSS (NM_153459)	-672	NM_153459	235584	Mm.275584	NM_153459	ENSMUSG00000053716	Dusp7	AU015694|Mkpx|Pyst2	dual specificity phosphatase 7	protein-coding
mm_61946.1	chr7	90184398	90184430	+	1	NA	intron (NM_001252520, intron 13 of 20)	(TTTG)n|Simple_repeat|Simple_repeat	54182	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_55060.1	chr6	49047927	49047935	-	1	NA	exon (NM_053110, exon 6 of 11)	exon (NM_053110, exon 6 of 11)	11413	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_75632.1	chr8	64718671	64718691	-	1	NA	3' UTR (NM_025436, exon 6 of 6)	3' UTR (NM_025436, exon 6 of 6)	14897	NM_025436	66234	Mm.30119	NM_025436	ENSMUSG00000031604	Msmo1	1500001G16Rik|C78600|DESP4|ERG25|Sc4mol	methylsterol monoxygenase 1	protein-coding
mm_71203.1	chr8	40888017	40888033	+	1	NA	intron (NM_007514, intron 1 of 11)	intron (NM_007514, intron 1 of 11)	25658	NM_001044740	11988	Mm.4676	NM_007514	ENSMUSG00000031596	Slc7a2	20.5|AI158848|Atrc2|CAT-2|Cat2|Tea	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	protein-coding
mm_37284.1	chr4	119072959	119072967	-	1	NA	Intergenic	Intergenic	-3852	NR_131914	433751	Mm.224312	NR_131914	ENSMUSG00000066060	Gm12866	OTTMUSG00000008833	predicted gene 12866	ncRNA
mm_58051.1	chr6	136854403	136854408	-	1	NA	exon (NM_026639, exon 2 of 3)	exon (NM_026639, exon 2 of 3)	3195	NM_026639	109978	Mm.31840	NM_026639	ENSMUSG00000030217	Art4	4432404K01Rik|ARTC4|DO|DOK1	ADP-ribosyltransferase 4	protein-coding
mm_48947.1	chr6	4540007	4540016	+	1	NA	intron (NM_007743, intron 51 of 51)	intron (NM_007743, intron 51 of 51)	34393	NM_007743	12843	Mm.277792	NM_007743	ENSMUSG00000029661	Col1a2	AA960264|AI325291|Col1a-2|Cola-2|Cola2|oim	collagen, type I, alpha 2	protein-coding
mm_44629.1	chr5	26493309	26493318	-	1	NA	promoter-TSS (NR_029445)	promoter-TSS (NR_029445)	1	NR_029445	75942	Mm.50087	NR_029445	ENSMUSG00000029044	4930584F24Rik	1700001J09Rik|4930522C06Rik	RIKEN cDNA 4930584F24 gene	ncRNA
mm_73039.1	chr8	94227653	94227673	+	1	NA	5' UTR (NM_172410, exon 3 of 23)	5' UTR (NM_172410, exon 3 of 23)	13062	NM_172410	71805	Mm.458170	NM_172410	ENSMUSG00000032939	Nup93	2410008G02Rik	nucleoporin 93	protein-coding
mm_138657.1	chr17	35868462	35868492	+	1	NA	exon (NM_001146711, exon 2 of 4)	exon (NM_001146711, exon 2 of 4)	1862	NM_175242	76448	Mm.359982	NM_175242	ENSMUSG00000034595	Ppp1r18	2310014H01Rik|AA407849|AI450394	protein phosphatase 1, regulatory subunit 18	protein-coding
mm_53983.1	chr6	6862840	6862856	-	1	NA	promoter-TSS (NM_010057)	promoter-TSS (NM_010057)	-486	NM_010057	13396	Mm.439763	NM_010057	ENSMUSG00000029754	Dlx6	-	distal-less homeobox 6	protein-coding
mm_112430.1	chr13	4434338	4434388	+	1	NA	promoter-TSS (NM_030611)	promoter-TSS (NM_030611)	20	NM_030611	83702	Mm.196666	NM_030611	ENSMUSG00000021210	Akr1c6	3alpha-HSD|Akr1c1|Hsd17b5	aldo-keto reductase family 1, member C6	protein-coding
mm_153890.1	chr19	46962510	46962579	-	1	NA	promoter-TSS (NM_029810)	promoter-TSS (NM_029810)	-193	NR_028353	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_12603.1	chr2	74679686	74679701	+	1	NA	non-coding (NR_073086, exon 1 of 2)	non-coding (NR_073086, exon 1 of 2)	135	NR_073086	15431	Mm.207763	NM_008273	ENSMUSG00000042499	Hoxd11	E230017H14Rik|Hox-4.6|Hox-5.4|Hox-5.5	homeobox D11	protein-coding
mm_153995.1	chr19	50678578	50678586	-	1	NA	promoter-TSS (NM_021377)	promoter-TSS (NM_021377)	64	NM_001252501	58178	Mm.313672	NM_021377	ENSMUSG00000043531	Sorcs1	Sorcs|mSorCS	sortilin-related VPS10 domain containing receptor 1	protein-coding
mm_41687.1	chr5	100518413	100518474	+	1	NA	5' UTR (NM_012001, exon 1 of 10)	5' UTR (NM_012001, exon 1 of 10)	134	NM_012001	26891	Mm.957	NM_012001	ENSMUSG00000035297	Cops4	AW208976|D5Ertd774e	COP9 signalosome subunit 4	protein-coding
mm_104342.1	chr11	94242657	94242664	-	1	NA	promoter-TSS (NM_181819)	promoter-TSS (NM_181819)	-81	NM_181819	278507	Mm.342216	NM_181819	ENSMUSG00000044177	Wfikkn2	2610304F08Rik|AY100450|Gasp1|WFIKKNRP	WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 2	protein-coding
mm_72067.1	chr8	71487844	71487867	+	1	NA	promoter-TSS (NM_032544)	promoter-TSS (NM_032544)	-248	NM_032544	70359	Mm.142112	NM_032544	ENSMUSG00000007610	Gtpbp3	2410009F13Rik|AI607903	GTP binding protein 3	protein-coding
mm_110218.1	chr12	28623402	28623414	-	1	NA	promoter-TSS (NM_027866)	promoter-TSS (NM_027866)	-78	NM_027866	71693	Mm.30724	NM_027866	ENSMUSG00000036655	Colec11	CL-K1	collectin sub-family member 11	protein-coding
mm_136579.1	chr17	3557522	3557578	+	1	NA	promoter-TSS (NR_045303)	promoter-TSS (NR_045303)	163	NM_146074	224481	Mm.226554	NM_146074	ENSMUSG00000036983	Tfb1m	AI429207	transcription factor B1, mitochondrial	protein-coding
mm_149901.1	chr19	25505864	25505874	+	1	NA	exon (NM_015826, exon 1 of 5)	exon (NM_015826, exon 1 of 5)	163	NM_015826	50796	Mm.391208	NM_015826	ENSMUSG00000024837	Dmrt1	-	doublesex and mab-3 related transcription factor 1	protein-coding
mm_153148.1	chr19	34251777	34251821	-	1	NA	exon (NM_007392, exon 3 of 9)	exon (NM_007392, exon 3 of 9)	3574	NM_007392	11475	Mm.213025	NM_007392	ENSMUSG00000035783	Acta2	0610041G09Rik|Actvs|SMalphaA|a-SMA|alphaSMA	actin, alpha 2, smooth muscle, aorta	protein-coding
mm_86887.1	chr10	22283041	22283055	+	1	NA	intron (NM_001177775, intron 1 of 5)	intron (NM_001177775, intron 1 of 5)	9574	NM_001177775	667281	Mm.484254	NM_001177775	ENSMUSG00000075297	H60b	EG667281	histocompatibility 60b	protein-coding
mm_20112.1	chr2	121140650	121140690	-	1	NA	promoter-TSS (NM_177846)	promoter-TSS (NM_177846)	28	NM_177846	329504	Mm.219449	NM_177846	ENSMUSG00000074890	Lcmt2	D330024M17|Tyw4	leucine carboxyl methyltransferase 2	protein-coding
mm_100947.1	chr11	6560973	6560976	-	1	NA	intron (NM_001190344, intron 1 of 9)	intron (NM_001190344, intron 1 of 9)	791	NM_001190344	216527	Mm.221271	NM_146014	ENSMUSG00000000378	Ccm2	BC029157	cerebral cavernous malformation 2	protein-coding
mm_171224.1	chr3	60501212	60501213	+	1	NA	promoter-TSS (NM_001253711)	promoter-TSS (NM_001253711)	33	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_61453.1	chr7	75586308	75586333	+	1	NA	exon (NM_029332, exon 5 of 37)	exon (NM_029332, exon 5 of 37)	130786	NM_029332	75547	Mm.216107	NM_029332	ENSMUSG00000066406	Akap13	1700026G02Rik|5730522G15Rik|5830460E08Rik|AKAP-13|AKAP-Lbc|BRX|Ht31|LBC|PROTO-LB|PROTO-LBC	A kinase (PRKA) anchor protein 13	protein-coding
mm_148329.1	chr18	84086413	84086440	-	1	NA	5' UTR (NM_001081300, exon 1 of 2)	5' UTR (NM_001081300, exon 1 of 2)	136	NM_001081300	110796	Mm.102136	NM_001081300	ENSMUSG00000046982	Tshz1	5730407I04Rik|D18Bwg1409e|Mtsh1|NY-CO-33|Sdccag33|Tsh1|mKIAA4206|teashirt1	teashirt zinc finger family member 1	protein-coding
mm_69195.1	chr7	127345344	127345400	-	1	NA	promoter-TSS (NM_146202)	promoter-TSS (NM_146202)	-58	NM_146202	233890	Mm.23031	NM_146202	ENSMUSG00000047371	Zfp768	BC026432|Znf768	zinc finger protein 768	protein-coding
mm_134514.1	chr16	19200276	19200297	-	1	NA	Intergenic	Intergenic	86455	NM_146451	258443	Mm.377506	NM_146451	ENSMUSG00000050742	Olfr164	MOR279-2	olfactory receptor 164	protein-coding
mm_61954.1	chr7	90207822	90207837	+	1	NA	3' UTR (NM_001252521, exon 20 of 20)	3' UTR (NM_001252521, exon 20 of 20)	57603	NM_029256	75338	Mm.487222	NM_029256	ENSMUSG00000030617	Ccdc83	4930549K11Rik|4930554C01Rik|4932423M01Rik	coiled-coil domain containing 83	protein-coding
mm_46784.1	chr5	112577907	112577925	-	1	NA	promoter-TSS (NM_001253916)	promoter-TSS (NM_001253916)	-718	NM_001253916	56747	Mm.143742	NM_019982	ENSMUSG00000058153	Sez6l	AI843918|AIG1|AW539724|Acig1|BSRP-B|mKIAA0927	seizure related 6 homolog like	protein-coding
mm_58286.1	chr6	145863600	145863611	-	1	NA	exon (NM_024469, exon 5 of 5)	exon (NM_024469, exon 5 of 5)	1815	NM_001271768	79362	Mm.154529	NM_024469	ENSMUSG00000030256	Bhlhe41	6430520M22Rik|Bhlhb2l|Bhlhb3|DEC2|Sharp1	basic helix-loop-helix family, member e41	protein-coding
mm_161389.1	chr14	79301569	79301569	-	1	NA	promoter-TSS (NM_025427)	promoter-TSS (NM_025427)	66	NM_025427	66214	Mm.29811	NM_025427	ENSMUSG00000022018	Rgcc	1190002H23Rik|Rgc-32|Rgc32	regulator of cell cycle	protein-coding
mm_82075.1	chr9	122951052	122951106	+	1	NA	promoter-TSS (NM_025419)	promoter-TSS (NM_025419)	-2	NM_010620	209737	Mm.278920	NM_010620	ENSMUSG00000036768	Kif15	3110023M17Rik|3930402I10Rik|D330038N01|HKLP2|Knsl7|b2b1117.1Clo|b2b1117.1aClo	kinesin family member 15	protein-coding
mm_170777.1	chr2	168242439	168242439	-	1	NA	Intergenic	Intergenic	11817	NM_001160330	69372	Mm.482182	NM_001160330	ENSMUSG00000074576	Mocs3	1700020H17Rik|Uba4	molybdenum cofactor synthesis 3	protein-coding
mm_76665.1	chr8	93379764	93379770	-	1	NA	Intergenic	Intergenic	-42558	NM_021456	12623	Mm.22720	NM_021456	ENSMUSG00000057074	Ces1g	Ces-1|Ces1|Ses-1	carboxylesterase 1G	protein-coding
mm_49825.1	chr6	37732626	37732629	+	1	NA	Intergenic	Intergenic	-138184	NM_001272064	21848	Mm.41063	NM_145076	ENSMUSG00000029833	Trim24	A130082H20Rik|AI447469|D430004I05Rik|TIF1|TIF1-alpha|TIF1alpha|Tif1a	tripartite motif-containing 24	protein-coding
mm_168974.1	chr12	87583882	87583887	+	1	NA	Intergenic	L1Md_Gf|LINE|L1	-18781	NM_001270792	100039087	Mm.458830	NM_001270792	ENSMUSG00000096276	Gm2042	-	predicted gene 2042	protein-coding
mm_23103.1	chr3	37365452	37365452	+	1	NA	intron (NM_008006, intron 1 of 2)	MTE-int|LTR|ERVL-MaLR	16799	NM_008006	14173	Mm.473689	NM_008006	ENSMUSG00000037225	Fgf2	Fgf-2|Fgfb|bFGF	fibroblast growth factor 2	protein-coding
mm_13279.1	chr2	101621796	101621811	+	1	NA	intron (NM_026592, intron 1 of 6)	intron (NM_026592, intron 1 of 6)	-2945	NM_009020	19374	Mm.4988	NM_009020	ENSMUSG00000032864	Rag2	Rag-2	recombination activating gene 2	protein-coding
mm_58587.1	chr7	4943997	4944015	+	1	NA	exon (NM_173008, exon 14 of 14)	exon (NM_173008, exon 14 of 14)	18162	NM_173008	269855	Mm.44190	NM_173008	ENSMUSG00000035279	Ssc5d	A430110N23Rik|S5D-SRCRB	scavenger receptor cysteine rich family, 5 domains	protein-coding
mm_44396.1	chr5	17835715	17835741	-	1	NA	5' UTR (NM_001159555, exon 1 of 15)	5' UTR (NM_001159555, exon 1 of 15)	168	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_141528.1	chr17	31841163	31841165	-	1	NA	Intergenic	ID_B1|SINE|B4	14628	NM_010831	17691	Mm.290941	NM_010831	ENSMUSG00000024042	Sik1	Msk|Sik|Snf1lk	salt inducible kinase 1	protein-coding
mm_121438.1	chr14	120418952	120418963	+	1	NA	intron (NM_175341, intron 8 of 8)	intron (NM_175341, intron 8 of 8)	-59504	NM_029519	76108	Mm.261448	NM_029519	ENSMUSG00000051615	Rap2a	5830461H18Rik	RAS related protein 2a	protein-coding
mm_48149.1	chr5	137151047	137151051	-	1	NA	Intergenic	Intergenic	-34842	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_119838.1	chr14	54428578	54428615	+	1	NA	exon (NM_026851, exon 4 of 5)	exon (NM_026851, exon 4 of 5)	1687	NM_026851	68836	Mm.248163	NM_026851	ENSMUSG00000010406	Mrpl52	1110047B07Rik	mitochondrial ribosomal protein L52	protein-coding
mm_138263.1	chr17	34596078	34596097	+	1	NA	3' UTR (NM_017463, exon 9 of 9)	3' UTR (NM_017463, exon 9 of 9)	-1763	NM_001271424	11596	Mm.3383	NM_007425	ENSMUSG00000015452	Ager	RAGE	advanced glycosylation end product-specific receptor	protein-coding
mm_118253.1	chr13	112349222	112349246	-	1	NA	intron (NM_001168403, intron 7 of 11)	intron (NM_001168403, intron 7 of 11)	60716	NM_001168404	77318	Mm.159895	NM_029898	ENSMUSG00000049985	Ankrd55	C030011J08Rik	ankyrin repeat domain 55	protein-coding
mm_67936.1	chr7	100120524	100120549	-	1	NA	intron (NM_133692, intron 1 of 11)	intron (NM_133692, intron 1 of 11)	964	NM_133692	67967	Mm.37562	NM_133692	ENSMUSG00000030726	Pold3	2410142G14Rik|C85233|P66|P68	polymerase (DNA-directed), delta 3, accessory subunit	protein-coding
mm_163745.1	chr13	119755388	119755398	+	1	NA	intron (NM_175538, intron 1 of 3)	intron (NM_175538, intron 1 of 3)	489	NM_175538	245269	Mm.403943	NM_175538	ENSMUSG00000095930	Nim1k	E130304F04Rik|Nim1	NIM1 serine/threonine protein kinase	protein-coding
mm_120811.1	chr14	75052380	75052383	+	1	NA	3' UTR (NM_198642, exon 14 of 14)	3' UTR (NM_198642, exon 14 of 14)	36354	NM_198642	271221	Mm.320280	NM_198642	ENSMUSG00000034959	Rubcnl	5031414D18Rik|Gm744|Gm911|Kiaa0226l	RUN and cysteine rich domain containing beclin 1 interacting protein like	protein-coding
mm_167094.1	chr7	107801186	107801194	-	1	NA	promoter-TSS (NM_172908)	promoter-TSS (NM_172908)	-11	NM_172908	244199	Mm.99576	NM_172908	ENSMUSG00000048236	Ovch2	9230106D23Rik|Ovtn	ovochymase 2	protein-coding
mm_132653.1	chr16	41533303	41533325	+	1	NA	promoter-TSS (NM_175548)	promoter-TSS (NM_175548)	-28	NM_175548	268890	Mm.310524	NM_175548	ENSMUSG00000061080	Lsamp	5430428I19|AW046674|B130007O04Rik|D930023J12Rik|Lam|Lamp	limbic system-associated membrane protein	protein-coding
mm_21259.1	chr2	156392962	156392993	-	1	NA	promoter-TSS (NR_024329)	promoter-TSS (NR_024329)	2	NR_024329	347740	Mm.324242	NR_024329		2900097C17Rik	1810005K14Rik|4930563C06Rik	RIKEN cDNA 2900097C17 gene	ncRNA
mm_109804.1	chr12	3309900	3309910	-	1	NA	promoter-TSS (NM_016676)	promoter-TSS (NM_016676)	64	NM_016676	19325	Mm.378993	NM_016676	ENSMUSG00000020671	Rab10	AW107754	RAB10, member RAS oncogene family	protein-coding
mm_155556.1	chrX	75096040	75096109	+	1	NA	5' UTR (NM_001030307, exon 1 of 15)	5' UTR (NM_001030307, exon 1 of 15)	220	NM_001030307	245474	Mm.291062	NM_001030307	ENSMUSG00000031403	Dkc1	BC068171	dyskeratosis congenita 1, dyskerin	protein-coding
mm_106214.1	chr11	116852324	116852364	-	1	NA	intron (NM_011358, intron 1 of 2)	CpG	750	NM_011358	20382	Mm.21841	NM_011358	ENSMUSG00000034120	Srsf2	D11Wsu175e|MRF-1|Pr264|SC35|Sfrs10|Sfrs2	serine/arginine-rich splicing factor 2	protein-coding
mm_131211.1	chr16	8770601	8770610	+	1	NA	Intergenic	RMER17B|LTR|ERVK	-32263	NM_001003918	252870	Mm.295330	NM_001003918	ENSMUSG00000022710	Usp7	2210010O09Rik|AA409944|AA617399|AU019296|AW548146|C80752|Hausp	ubiquitin specific peptidase 7	protein-coding
mm_91970.1	chr10	61432769	61432821	-	1	NA	3' UTR (NM_010124, exon 3 of 3)	3' UTR (NM_010124, exon 3 of 3)	14823	NM_013611	18119	Mm.57195	NM_013611	ENSMUSG00000037171	Nodal	Tg.413d	nodal	protein-coding
mm_16792.1	chr2	10080155	10080166	-	1	NA	promoter-TSS (NM_025280)	promoter-TSS (NM_025280)	350	NM_020615	11949	Mm.12677	NM_020615	ENSMUSG00000025781	Atp5c1	1700094F02Rik	ATP synthase, H+ transporting, mitochondrial F1 complex, gamma polypeptide 1	protein-coding
mm_64182.1	chr7	141459518	141459529	+	1	NA	non-coding (NR_028142, exon 10 of 10)	non-coding (NR_028142, exon 10 of 10)	-1571	NM_001025103	213573	Mm.386851	NM_001025103	ENSMUSG00000048200	Cracr2b	6330520A15Rik|BC026645|Cracr2a|Efcab4|Efcab4a	calcium release activated channel regulator 2B	protein-coding
mm_149849.1	chr19	25057164	25057172	+	1	NA	intron (NM_028785, intron 2 of 47)	intron (NM_028785, intron 2 of 47)	57639	NM_028785	76088	Mm.102485	NM_028785	ENSMUSG00000052085	Dock8	1200017A24Rik|5830472H07Rik|A130095G14Rik|AI461977	dedicator of cytokinesis 8	protein-coding
mm_74494.1	chr8	5105241	5105254	-	1	NA	promoter-TSS (NM_011388)	promoter-TSS (NM_011388)	40	NM_011388	20494	Mm.3500	NM_011388	ENSMUSG00000023073	Slc10a2	9130221J18Rik|AI605518|ASBT|IBAT|ISBT	solute carrier family 10, member 2	protein-coding
mm_142824.1	chr17	51759809	51759814	-	1	NA	intron (NM_009122, intron 9 of 10)	intron (NM_009122, intron 9 of 10)	52243	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_58757.1	chr7	13450836	13450836	+	1	NA	promoter-TSS (NM_001301682)	promoter-TSS (NM_001301682)	-5	NM_001033418	330470	Mm.291102	NM_001033418	ENSMUSG00000074378	Bsph1	Gm767	binder of sperm protein homolog 1	protein-coding
mm_166383.1	chr5	131472372	131472388	-	1	NA	exon (NM_177047, exon 9 of 19)	exon (NM_177047, exon 9 of 19)	-164858	NM_145218	212996	Mm.299204	NM_145218	ENSMUSG00000034040	Wbscr17	AA388321|E330012B09Rik	Williams-Beuren syndrome chromosome region 17 homolog (human)	protein-coding
mm_16696.1	chr2	6885143	6885190	-	1	NA	promoter-TSS (NM_001110228)	promoter-TSS (NM_001110228)	-170	NM_001160293	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_139104.1	chr17	47207102	47207124	+	1	NA	intron (NM_001097623, intron 3 of 19)	intron (NM_001097623, intron 3 of 19)	-23117	NM_172622	224829	Mm.260989	NM_172622		Trerf1	9430096I18Rik|AI429294|B830015H24|RAPA|Trep-132|Trep132	transcriptional regulating factor 1	protein-coding
mm_167523.1	chr9	20953028	20953061	+	1	NA	promoter-TSS (NM_001199431)	promoter-TSS (NM_001199431)	-65	NM_001199431	13433	Mm.128580	NM_010066	ENSMUSG00000004099	Dnmt1	Cxxc9|Dnmt|Dnmt1o|MCMT|MTase|Met-1|Met1|MommeD2|m.MmuI	DNA methyltransferase (cytosine-5) 1	protein-coding
mm_126744.1	chr15	85735585	85735615	+	1	NA	promoter-TSS (NM_011144)	promoter-TSS (NM_011144)	36	NM_001113418	19013	Mm.212789	NM_011144	ENSMUSG00000022383	Ppara	4933429D07Rik|AW742785|Nr1c1|PPAR-alpha|PPARalpha|Ppar	peroxisome proliferator activated receptor alpha	protein-coding
mm_150717.1	chr19	43490104	43490107	+	1	NA	intron (NM_031396, intron 7 of 10)	B3|SINE|B2	34500	NM_010324	14718	Mm.19039	NM_010324	ENSMUSG00000025190	Got1	AI789014|Got-1|cAspAT|cCAT	glutamic-oxaloacetic transaminase 1, soluble	protein-coding
mm_26006.1	chr3	135298782	135298834	+	1	NA	intron (NM_001172055, intron 7 of 9)	intron (NM_001172055, intron 7 of 9)	-8892	NM_178877	97086	Mm.441764	NM_178877	ENSMUSG00000037994	Slc9b2	C80638|NHA2|NHE10|Nhedc2|nha-oc|nhaoc	solute carrier family 9, subfamily B (NHA2, cation proton antiporter 2), member 2	protein-coding
mm_119824.1	chr14	54253648	54253657	+	1	NA	promoter-TSS (NM_001205181)	promoter-TSS (NM_001205181)	277	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_45946.1	chr5	90263382	90263395	-	1	NA	exon (NM_030886, exon 22 of 34)	exon (NM_030886, exon 22 of 34)	-39392	NM_001163456	231430	Mm.319697	NM_001033310	ENSMUSG00000035505	Cox18	BC038311	cytochrome c oxidase assembly protein 18	protein-coding
mm_155420.1	chrX	73491315	73491365	+	1	NA	exon (NM_007542, exon 3 of 8)	exon (NM_007542, exon 3 of 8)	7739	NM_007542	12111	Mm.2608	NM_007542	ENSMUSG00000031375	Bgn	BG|DSPG1|PG-S1|PGI|SLRR1A	biglycan	protein-coding
mm_105318.1	chr11	102887941	102887949	-	1	NA	3' UTR (NM_010277, exon 9 of 9)	3' UTR (NM_010277, exon 9 of 9)	2776	NM_025766	66784	Mm.483216	NM_025766	ENSMUSG00000075510	Fam187a	4933439F11Rik	family with sequence similarity 187, member A	protein-coding
mm_1154.1	chr1	60812230	60812241	+	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	65847	NM_007642	12487	Mm.255003	NM_007642	ENSMUSG00000026012	Cd28	-	CD28 antigen	protein-coding
mm_9671.1	chr1	178318200	178318211	-	1	NA	promoter-TSS (NM_025511)	promoter-TSS (NM_025511)	-948	NM_025511	66359	Mm.489720	NM_025511	ENSMUSG00000026500	Cox20	2310005N03Rik|Fam36a	COX20 Cox2 chaperone	protein-coding
mm_161757.1	chr17	35263957	35263957	+	1	NA	exon (NM_001267808, exon 7 of 11)	exon (NM_001267808, exon 7 of 11)	834	NM_001267808	14980	Mm.439675	NM_001267808		H2-L	H-2L	histocompatibility 2, D region locus L	protein-coding
mm_56223.1	chr6	89867301	89867307	-	1	NA	Intergenic	LTRIS5|LTR|ERV1	3225	NM_053220	113847	Mm.431989	NM_053220	ENSMUSG00000068231	Vmn1r43	V1ra2|V1ra5	vomeronasal 1 receptor 43	protein-coding
mm_143056.1	chr17	57004811	57004828	-	1	NA	exon (NM_133801, exon 7 of 13)	exon (NM_133801, exon 7 of 13)	-4714	NM_008954	19197	Mm.86487	NM_008954	ENSMUSG00000002664	Pspn	PSP	persephin	protein-coding
mm_86510.1	chr10	7662796	7662800	+	1	NA	promoter-TSS (NR_030698)	promoter-TSS (NR_030698)	-573	NR_030698	320642	Mm.398806	NR_030698		A630066F11Rik	-	RIKEN cDNA A630066F11 gene	ncRNA
mm_72747.1	chr8	85091092	85091131	+	1	NA	exon (NM_010764, exon 9 of 24)	exon (NM_010764, exon 9 of 24)	7842	NM_010764	17159	Mm.4219	NM_010764	ENSMUSG00000005142	Man2b1	AW107687|LAMAN	mannosidase 2, alpha B1	protein-coding
mm_120872.1	chr14	75237658	75237685	+	1	NA	intron (NR_030568, intron 2 of 3)	intron (NR_030568, intron 2 of 3)	-4616	NM_019775	56373	Mm.24242	NM_019775	ENSMUSG00000021999	Cpb2	1110032P04Rik|4930405E17Rik|AI255929|CPR|Cpu|TAFI	carboxypeptidase B2 (plasma)	protein-coding
mm_11587.1	chr2	33216011	33216021	+	1	NA	promoter-TSS (NM_011923)	promoter-TSS (NM_011923)	55	NM_011923	26360	Mm.208919	NM_011923	ENSMUSG00000004105	Angptl2	AI593246|AW260363|Arp2	angiopoietin-like 2	protein-coding
mm_68800.1	chr7	125488743	125488753	-	1	NA	intron (NM_026330, intron 1 of 7)	intron (NM_026330, intron 1 of 7)	2794	NM_026330	67711	Mm.4467	NM_026330	ENSMUSG00000030750	Nsmce1	2510027N19Rik	NSE1 homolog, SMC5-SMC6 complex component	protein-coding
mm_146134.1	chr18	74714738	74714752	+	1	NA	intron (NM_201600, intron 23 of 38)	intron (NM_201600, intron 23 of 38)	63710	NR_028560	100217466		NR_028560		Scarna17	MBII-119	small Cajal body-specific RNA 17	ncRNA
mm_39823.1	chr5	30797529	30797540	+	1	NA	3' UTR (NM_023047, exon 13 of 13)	3' UTR (NM_023047, exon 13 of 13)	-17107	NM_133350	100732	Mm.332295	NM_133350	ENSMUSG00000029166	Mapre3	AI790651|EB2|EB3|EBF3|RP3	microtubule-associated protein, RP/EB family, member 3	protein-coding
mm_101590.1	chr11	34681908	34681955	-	1	NA	intron (NM_033374, intron 22 of 51)	RLTR44-int|LTR|ERVK	101974	NM_033374	94176	Mm.380679	NM_033374	ENSMUSG00000020143	Dock2	AI662014|AW122239|CED-5|Hch|MBC	dedicator of cyto-kinesis 2	protein-coding
mm_120376.1	chr14	64588099	64588108	+	1	NA	promoter-TSS (NR_040709)	promoter-TSS (NR_040709)	-12	NR_040709	268755	Mm.194050	NR_040709	ENSMUSG00000097545	Mir124a-1hg	A930011O12Rik|Rncr3|mir-124-1|mir-3078	Mir124-1 host gene (non-protein coding)	ncRNA
mm_158488.1	chrX	142323952	142323958	-	1	NA	intron (NM_019477, intron 15 of 15)	L1VL4|LINE|L1	-17757	NM_021487	66240	Mm.58507	NM_021487	ENSMUSG00000090122	Kcne1l	1500015C14Rik|Kcne5|Mink	potassium voltage-gated channel, Isk-related family, member 1-like, pseudogene	protein-coding
mm_118159.1	chr13	105291953	105291974	-	1	NA	intron (NM_027934, intron 1 of 7)	MMVL30-int|LTR|ERV1	1051	NM_027934	71816	Mm.317015	NM_027934	ENSMUSG00000021720	Rnf180	3110001E11Rik|Rines	ring finger protein 180	protein-coding
mm_104652.1	chr11	97575157	97575208	-	1	NA	promoter-TSS (NM_018873)	promoter-TSS (NM_018873)	-56	NM_018873	56013	Mm.342665	NM_018873	ENSMUSG00000038453	Srcin1	P140|SNIP|mKIAA1684|p140Cap	SRC kinase signaling inhibitor 1	protein-coding
mm_130968.1	chr15	103319724	103319726	-	1	NA	intron (NM_013866, intron 3 of 7)	B1_Mur2|SINE|Alu	-9287	NM_030720	80910	Mm.160369	NM_030720	ENSMUSG00000063234	Gpr84	EX33	G protein-coupled receptor 84	protein-coding
mm_74133.1	chr8	123212827	123212848	+	1	NA	promoter-TSS (NM_145606)	promoter-TSS (NM_145606)	-21	NM_177279	320869	Mm.258354	NM_177279	ENSMUSG00000048478	Spata33	4732415M23Rik|AI847264	spermatogenesis associated 33	protein-coding
mm_155488.1	chrX	73716713	73716750	+	1	NA	promoter-TSS (NM_012060)	promoter-TSS (NM_012060)	134	NM_007435	11666	Mm.365	NM_007435	ENSMUSG00000031378	Abcd1	ALDP|Ald|Aldgh	ATP-binding cassette, sub-family D (ALD), member 1	protein-coding
mm_102410.1	chr11	59187739	59187767	-	1	NA	promoter-TSS (NM_001159410)	promoter-TSS (NM_001159410)	-12	NM_001159410	14923	Mm.3624	NM_008193	ENSMUSG00000020444	Guk1	AA409738|AL033299|AL033300|AV026611|Gmk|Guk-1	guanylate kinase 1	protein-coding
mm_3762.1	chr1	156067469	156067473	+	1	NA	3' UTR (NM_172843, exon 7 of 7)	3' UTR (NM_172843, exon 7 of 7)	26610	NM_022329	240832	Mm.253335	NM_022329	ENSMUSG00000050565	Tor1aip2	1110020D10Rik|15kDa|A130072J07|AA103493|AW060462|AW610675|C77739|Ifrg15|Lull1	torsin A interacting protein 2	protein-coding
mm_146436.1	chr18	84934543	84934556	+	1	NA	promoter-TSS (NM_015798)	promoter-TSS (NM_015798)	-476	NM_015798	50764	Mm.28369	NM_015798	ENSMUSG00000034391	Fbxo15	AU019763|Fbx15|ecat3	F-box protein 15	protein-coding
mm_148140.1	chr18	76944064	76944080	-	1	NA	promoter-TSS (NM_001039201)	promoter-TSS (NM_001039201)	-43	NM_029826	76987	Mm.236127	NM_029826	ENSMUSG00000025421	Hdhd2	0610039H12Rik|3110052N05Rik	haloacid dehalogenase-like hydrolase domain containing 2	protein-coding
mm_65440.1	chr7	25388987	25389002	-	1	NA	intron (NM_010719, intron 1 of 9)	intron (NM_010719, intron 1 of 9)	1118	NM_001039507	16890	Mm.158548	NM_010719	ENSMUSG00000003123	Lipe	4933403G17Rik|HSL	lipase, hormone sensitive	protein-coding
mm_112547.1	chr13	12340486	12340488	+	1	NA	exon (NM_033268, exon 1 of 21)	exon (NM_033268, exon 1 of 21)	245	NM_033268	11472	Mm.37638	NM_033268	ENSMUSG00000052374	Actn2	1110008F24Rik	actinin alpha 2	protein-coding
mm_143802.1	chr17	83502814	83502819	-	1	NA	intron (NM_009187, intron 2 of 2)	intron (NM_009187, intron 2 of 2)	11517	NM_009187	20463	Mm.30072	NM_009187	ENSMUSG00000024248	Cox7a2l	COX7AR|COX7RP|EB1|SIG-81|SIG81|Silg81	cytochrome c oxidase subunit VIIa polypeptide 2-like	protein-coding
mm_100239.1	chr11	117241660	117241694	+	1	NA	intron (NM_001113486, intron 2 of 11)	RLTR20A4|LTR|ERVK	-24569	NM_001113487	53860	Mm.38450	NM_017380	ENSMUSG00000059248	Sept9	MSF1|Msf|PNUTL4|Sint1	septin 9	protein-coding
mm_51199.1	chr6	71284352	71284432	+	1	NA	exon (NM_145568, exon 4 of 4)	exon (NM_145568, exon 4 of 4)	12373	NM_145568	57896	Mm.250569	NM_145568	ENSMUSG00000053012	Krcc1	AA792894	lysine-rich coiled-coil 1	protein-coding
mm_132322.1	chr16	33794068	33794088	+	1	NA	promoter-TSS (NM_010739)	promoter-TSS (NM_010739)	41	NM_010739	17063	Mm.3177	NM_010739	ENSMUSG00000022824	Muc13	114/A10|14/A10|AI159736|Lrrp|Ly64|NJ-1	mucin 13, epithelial transmembrane	protein-coding
mm_156217.1	chrX	134717915	134717920	+	1	NA	promoter-TSS (NM_030066)	promoter-TSS (NM_030066)	-21	NM_001166380	78248	Mm.458522	NM_030066	ENSMUSG00000033460	Armcx1	3010033I09Rik|ALEX1	armadillo repeat containing, X-linked 1	protein-coding
mm_17254.1	chr2	25815863	25815871	-	1	NA	promoter-TSS (NM_001039095)	promoter-TSS (NM_001039095)	-31	NM_001039095	71103	Mm.236431	NM_001039095	ENSMUSG00000036401	Glt6d1	4933411C14Rik|GT6m7	glycosyltransferase 6 domain containing 1	protein-coding
mm_109557.1	chr12	111781754	111781770	+	1	NA	exon (NM_001025363, exon 8 of 14)	exon (NM_001025363, exon 8 of 14)	22894	NM_001025361	16593	Mm.278357	NM_008450	ENSMUSG00000021288	Klc1	AI874768|Kns2	kinesin light chain 1	protein-coding
mm_134806.1	chr16	24393699	24393716	-	1	NA	promoter-TSS (NR_037954)	promoter-TSS (NR_037954)	-52	NR_037954	68841	Mm.361995	NR_037954		Lppos	1110054M08Rik|AI481106	LIM domain containing preferred translocation partner in lipoma, opposite strand	ncRNA
mm_55375.1	chr6	58533614	58533640	-	1	NA	Intergenic	Intergenic	-60749	NM_001166729	626828	Mm.480268	NM_001166729	ENSMUSG00000093379	Vmn1r31	EG626828|Gm6709	vomeronasal 1 receptor 31	protein-coding
mm_6627.1	chr1	78196793	78196820	-	1	NA	5' UTR (NM_008781, exon 1 of 8)	5' UTR (NM_008781, exon 1 of 8)	330	NM_008781	18505	Mm.1371	NM_008781	ENSMUSG00000004872	Pax3	Pax-3|Sp|Splchl2|splotch	paired box 3	protein-coding
mm_163326.1	chr12	8345145	8345154	+	1	NA	Intergenic	Intergenic	31716	NM_021429	58240	Mm.309954	NM_021429	ENSMUSG00000020605	Hs1bp3	-	HCLS1 binding protein 3	protein-coding
mm_87313.1	chr10	42782531	42782546	+	1	NA	intron (NM_153055, intron 1 of 20)	intron (NM_153055, intron 1 of 20)	21042	NM_153055	140740	Mm.214344	NM_153055	ENSMUSG00000019802	Sec63	5730478J10Rik|AI649014|AW319215	SEC63-like (S. cerevisiae)	protein-coding
mm_108502.1	chr12	83950055	83950071	+	1	NA	promoter-TSS (NM_023633)	promoter-TSS (NM_023633)	-545	NM_023633	71952	Mm.251483	NM_023633	ENSMUSG00000046791	2410016O06Rik	MAPJD|NO66	RIKEN cDNA 2410016O06 gene	protein-coding
mm_110540.1	chr12	55302738	55302746	-	1	NA	5' UTR (NM_021529, exon 2 of 14)	5' UTR (NM_021529, exon 2 of 14)	105	NM_025373	66132	Mm.383213	NM_025373	ENSMUSG00000021023	1110008L16Rik	Kiaa0391|Mrpp3|mKIAA0391	RIKEN cDNA 1110008L16 gene	protein-coding
mm_85153.1	chr9	96333099	96333124	-	1	NA	3' UTR (NM_007502, exon 7 of 7)	3' UTR (NM_007502, exon 7 of 7)	31188	NM_007502	11933	Mm.424	NM_007502	ENSMUSG00000032412	Atp1b3	AA409958|AI664000|AW212096	ATPase, Na+/K+ transporting, beta 3 polypeptide	protein-coding
mm_45849.1	chr5	87699470	87699477	-	1	NA	promoter-TSS (NM_001286023)	promoter-TSS (NM_001286023)	-48	NM_001286021	12991	Mm.268737	NM_009972	ENSMUSG00000063157	Csn2	Csnb	casein beta	protein-coding
mm_114052.1	chr13	54336030	54336033	+	1	NA	Intergenic	Intergenic	-35318	NM_009946	12890	Mm.268902	NM_009946	ENSMUSG00000025867	Cplx2	921-L|AI413745|AW492120	complexin 2	protein-coding
mm_18518.1	chr2	62646147	62646234	-	1	NA	promoter-TSS (NM_027835)	promoter-TSS (NM_027835)	65	NM_027835	71586	Mm.136224	NM_027835	ENSMUSG00000026896	Ifih1	9130009C22Rik|Helicard|Hlcd|MDA5|RLR-2	interferon induced with helicase C domain 1	protein-coding
mm_28849.1	chr3	96814519	96814532	-	1	NA	promoter-TSS (NM_018767)	promoter-TSS (NM_018767)	-4	NM_018767	54215	Mm.34693	NM_018767	ENSMUSG00000038304	Cd160	AU045688|By55	CD160 antigen	protein-coding
mm_87028.1	chr10	28586731	28586771	+	1	NA	intron (NM_008983, intron 26 of 31)	intron (NM_008983, intron 26 of 31)	-81609	NM_001305663	210757	Mm.123021	NM_178666	ENSMUSG00000049109	Themis	E430004N04Rik|Gasp|Spot|Tsepa|thylex	thymocyte selection associated	protein-coding
mm_69652.1	chr7	139660180	139660180	-	1	NA	intron (NM_001302546, intron 13 of 58)	MLT1B|LTR|ERVL-MaLR	23635	NM_001302546	212124	Mm.425507	NM_177212	ENSMUSG00000049571	Cfap46	9330101J02Rik|E030019B06Rik|Gm170|Ttc40	cilia and flagella associated protein 46	protein-coding
mm_62809.1	chr7	112993897	112993908	+	1	NA	Intergenic	Intergenic	39940	NM_175279	78748	Mm.349943	NM_175279	ENSMUSG00000098132	Rassf10	4632411J06Rik	Ras association (RalGDS/AF-6) domain family (N-terminal) member 10	protein-coding
mm_32671.1	chr4	115737755	115737810	+	1	NA	promoter-TSS (NM_172698)	promoter-TSS (NM_172698)	-291	NM_172698	230648	Mm.283565	NM_172698	ENSMUSG00000034210	Efcab14	4732418C07Rik	EF-hand calcium binding domain 14	protein-coding
mm_96649.1	chr11	69360626	69360673	+	1	NA	exon (NM_146019, exon 9 of 40)	exon (NM_146019, exon 9 of 40)	8777	NM_146019	216848	Mm.178246	NM_146019	ENSMUSG00000018474	Chd3	2600010P09Rik|AF020312|Chd7|Prp7|Prp9-1	chromodomain helicase DNA binding protein 3	protein-coding
mm_49516.1	chr6	29876708	29876710	+	1	NA	intron (NM_001347084, intron 5 of 17)	intron (NM_001347084, intron 5 of 17)	17113	NM_001171001	74340	Mm.210899	NM_021414	ENSMUSG00000029772	Ahcyl2	4631427C17Rik|AI227036|Adohcyase3|mKIAA0828	S-adenosylhomocysteine hydrolase-like 2	protein-coding
mm_155576.1	chrX	77845044	77845048	+	1	NA	exon (NM_017471, exon 3 of 7)	exon (NM_017471, exon 3 of 7)	8454	NM_017471	54192	Mm.8034	NM_017471	ENSMUSG00000000003	Pbsn	PB|Prbs	probasin	protein-coding
mm_55861.1	chr6	83456428	83456444	-	1	NA	promoter-TSS (NM_001347313)	promoter-TSS (NM_001347313)	-44	NM_001347313	194388	Mm.211030	NM_183138	ENSMUSG00000034832	Tet3	B430006D22Rik|BC037432|D230004J03Rik	tet methylcytosine dioxygenase 3	protein-coding
mm_22827.1	chr3	27241578	27241615	+	1	NA	exon (NM_178772, exon 5 of 5)	exon (NM_178772, exon 5 of 5)	58592	NM_178772	320024	Mm.24576	NM_178772	ENSMUSG00000027698	Nceh1	Aadacl1|B230106I24Rik|CPO-BP|Nceh	neutral cholesterol ester hydrolase 1	protein-coding
mm_1522.1	chr1	72824567	72824577	+	1	NA	promoter-TSS (NM_008342)	promoter-TSS (NM_008342)	92	NM_008342	16008	Mm.141936	NM_008342	ENSMUSG00000039323	Igfbp2	AI255832|IBP-2|Igfbp-2|mIGFBP-2	insulin-like growth factor binding protein 2	protein-coding
mm_38277.1	chr4	136886190	136886200	-	1	NA	promoter-TSS (NM_009777)	promoter-TSS (NM_009777)	-18	NM_009777	12260	Mm.2570	NM_009777	ENSMUSG00000036905	C1qb	-	complement component 1, q subcomponent, beta polypeptide	protein-coding
mm_71010.1	chr8	31150308	31150346	+	1	NA	promoter-TSS (NM_144927)	promoter-TSS (NM_144927)	11	NR_103719	234138	Mm.349800	NM_144927	ENSMUSG00000031577	Tti2	-	TELO2 interacting protein 2	protein-coding
mm_113909.1	chr13	49341550	49341623	+	1	NA	promoter-TSS (NM_029791)	promoter-TSS (NM_029791)	37	NM_001039180	76895	Mm.197387	NM_029791	ENSMUSG00000037933	Bicd2	-	bicaudal D homolog 2 (Drosophila)	protein-coding
mm_161477.1	chr15	82070077	82070077	+	1	NA	promoter-TSS (NM_028897)	promoter-TSS (NM_028897)	-40	NM_028897	74369	Mm.289351	NM_028897	ENSMUSG00000068117	Mei1	4932408F18Rik|mei1	meiotic double-stranded break formation protein 1	protein-coding
mm_157406.1	chrX	38435472	38435486	-	1	NA	exon (NM_001017959, exon 4 of 9)	exon (NM_001017959, exon 4 of 9)	20981	NM_010685	16784	Mm.486	NM_010685	ENSMUSG00000016534	Lamp2	CD107b|LGP-B|Lamp II|Lamp-2|Lamp-2a|Lamp-2b|Lamp-2c|Mac3	lysosomal-associated membrane protein 2	protein-coding
mm_159179.1	chr2	111368786	111368786	+	1	NA	exon (NM_207236, exon 1 of 1)	exon (NM_207236, exon 1 of 1)	152	NM_207236	228443	Mm.377244	NM_207236	ENSMUSG00000109322	Olfr1283	GA_x6K02T2Q125-72420217-72421134|MOR248-19	olfactory receptor 1283	protein-coding
mm_80160.1	chr9	71069149	71069152	+	1	NA	Intergenic	Intergenic	93483	NM_001271843	64008	Mm.449427	NM_022026	ENSMUSG00000032204	Aqp9	1700020I22Rik|AI266899|AQP-9	aquaporin 9	protein-coding
mm_27392.1	chr3	50887010	50887022	-	1	NA	Intergenic	Intergenic	-337431	NM_009834	12457	Mm.86541	NM_009834	ENSMUSG00000023087	Noct	AU043840|Ccr4|Ccrn4l	nocturnin	protein-coding
mm_76893.1	chr8	105704713	105704742	-	1	NA	exon (NM_198299, exon 5 of 8)	exon (NM_198299, exon 5 of 8)	3080	NM_001286345	56513	Mm.472753	NM_019695	ENSMUSG00000005699	Pard6a	0710008C04Rik|2610010A15Rik|PAR-6A|PAR6alpha|Par-6|Par6|Par6c|TAX40|Tip-40	par-6 family cell polarity regulator alpha	protein-coding
mm_121298.1	chr14	105589533	105589546	+	1	NA	promoter-TSS (NR_102319)	promoter-TSS (NR_102319)	-10	NR_102319	380930	Mm.427836	NR_102319		9330188P03Rik	Gm1589|mgt-6	RIKEN cDNA 9330188P03 gene	ncRNA
mm_23017.1	chr3	34560627	34560646	+	1	NA	intron (NR_015580, intron 1 of 4)	intron (NR_015580, intron 1 of 4)	255	NR_015580	320478	Mm.444063	NR_015580	ENSMUSG00000105265	Sox2ot	B230215L15Rik	SOX2 overlapping transcript (non-protein coding)	ncRNA
mm_33291.1	chr4	128902207	128902211	+	1	NA	intron (NM_178110, intron 3 of 4)	intron (NM_178110, intron 3 of 4)	18069	NM_178110	67525	Mm.30653	NM_178110	ENSMUSG00000041000	Trim62	6330414G21Rik|AI450348|Dear1	tripartite motif-containing 62	protein-coding
mm_120305.1	chr14	63140853	63140885	+	1	NA	intron (NM_007798, intron 8 of 9)	PB1D10|SINE|Alu	18407	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_113954.1	chr13	51100811	51100933	+	1	NA	promoter-TSS (NM_001283028)	promoter-TSS (NM_001283028)	-8	NM_001283028	20729	Mm.188432	NM_011462	ENSMUSG00000021395	Spin1	Spin	spindlin 1	protein-coding
mm_106230.1	chr11	117327054	117327062	-	1	NA	intron (NM_001113487, intron 2 of 10)	intron (NM_001113487, intron 2 of 10)	-4657	NM_017380	53860	Mm.38450	NM_017380	ENSMUSG00000059248	Sept9	MSF1|Msf|PNUTL4|Sint1	septin 9	protein-coding
mm_37845.1	chr4	132183331	132183336	-	1	NA	Intergenic	Intergenic	28923	NM_145393	213541	Mm.23998	NM_145393	ENSMUSG00000040025	Ythdf2	9430020E02Rik|HGRG8|NY-REN-2	YTH domain family 2	protein-coding
mm_136398.1	chr16	93359537	93359550	-	1	NA	promoter-TSS (NR_040491)	promoter-TSS (NR_040491)	0	NR_040487	69857	Mm.81192	NR_040486	ENSMUSG00000100277	1810053B23Rik	1810008L18Rik|1810056K14Rik	RIKEN cDNA 1810053B23 gene	ncRNA
mm_87393.1	chr10	45289349	45289430	+	1	NA	promoter-TSS (NM_024286)	promoter-TSS (NM_024286)	84	NM_024286	78977	Mm.24748	NM_024286	ENSMUSG00000019848	Popdc3	AA682104|Pop3	popeye domain containing 3	protein-coding
mm_102320.1	chr11	57507103	57507106	-	1	NA	intron (NM_001168667, intron 6 of 13)	intron (NM_001168667, intron 6 of 13)	11540	NM_001168667	67726	Mm.25632	NM_026342	ENSMUSG00000020523	Fam114a2	1810073G14Rik|9030624B09Rik	family with sequence similarity 114, member A2	protein-coding
mm_99852.1	chr11	109362884	109362907	+	1	NA	5' UTR (NM_010303, exon 1 of 4)	5' UTR (NM_010303, exon 1 of 4)	101	NM_010303	14674	Mm.193925	NM_010303	ENSMUSG00000020611	Gna13	AU024132|AU043124|Galpha13	guanine nucleotide binding protein, alpha 13	protein-coding
mm_28434.1	chr3	90465859	90465874	-	1	NA	promoter-TSS (NM_008727)	promoter-TSS (NM_008727)	0	NM_008727	18160	Mm.4627	NM_008727	ENSMUSG00000027931	Npr1	AI893888|GC-A|NPR-A|NPRA|Pndr	natriuretic peptide receptor 1	protein-coding
mm_43959.1	chr5	145241313	145241325	+	1	NA	intron (NM_028298, intron 2 of 3)	B1F|SINE|Alu	9560	NM_028298	72611	Mm.206555	NM_028298	ENSMUSG00000007812	Zfp655	2700038I16Rik|9030409O18Rik|mKIAA4222	zinc finger protein 655	protein-coding
mm_91172.1	chr10	20724829	20724849	-	1	NA	5' UTR (NM_013875, exon 1 of 13)	5' UTR (NM_013875, exon 1 of 13)	239	NM_013875	29863	Mm.425617	NM_013875	ENSMUSG00000019990	Pde7b	-	phosphodiesterase 7B	protein-coding
mm_167398.1	chr8	95311597	95311627	+	1	NA	promoter-TSS (NM_028532)	promoter-TSS (NM_028532)	14	NM_199455	73407	Mm.472783	NM_028532	ENSMUSG00000090206	Tepp	1700055M20Rik	testis, prostate and placenta expressed	protein-coding
mm_118584.1	chr14	20306778	20306779	+	1	NA	intron (NM_026341, intron 4 of 8)	intron (NM_026341, intron 4 of 8)	12088	NM_026341	67725	Mm.317636	NM_026341	ENSMUSG00000021809	Nudt13	4933433B15Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 13	protein-coding
mm_17906.1	chr2	35315274	35315285	-	1	NA	3' UTR (NM_013515, exon 7 of 7)	3' UTR (NM_013515, exon 7 of 7)	21730	NM_013515	13830	Mm.295284	NM_013515	ENSMUSG00000026880	Stom	Epb7.2	stomatin	protein-coding
mm_108474.1	chr12	83653430	83653433	+	1	NA	intron (NM_027349, intron 6 of 18)	ID_B1|SINE|B4	21197	NM_027349	67039	Mm.46005	NM_027349	ENSMUSG00000010608	Rbm25	2600011C06Rik|2610015J01Rik|A130095G20Rik|AI159652|AL023075|AU043498|RNPC7	RNA binding motif protein 25	protein-coding
mm_134257.1	chr16	13730971	13730988	-	1	NA	promoter-TSS (NM_011987)	promoter-TSS (NM_011987)	-495	NM_011987	26565	Mm.4214	NM_011987	ENSMUSG00000022683	Pla2g10	GX sPLA2|PLA2GX|sPLA2-X	phospholipase A2, group X	protein-coding
mm_138095.1	chr17	34039463	34039481	+	1	NA	5' UTR (NM_009926, exon 1 of 64)	5' UTR (NM_009926, exon 1 of 64)	334	NM_001317722	12815	Mm.20230	NM_009926	ENSMUSG00000024330	Col11a2	-	collagen, type XI, alpha 2	protein-coding
mm_116519.1	chr13	45777492	45777526	-	1	NA	intron (NM_001199304, intron 4 of 6)	intron (NM_001199304, intron 4 of 6)	187482	NM_001199304	20238	Mm.342683	NM_009124	ENSMUSG00000046876	Atxn1	2900016G23Rik|Atx1|C85907|ENSMUSG00000074917|Gm10786|Sca1	ataxin 1	protein-coding
mm_50838.1	chr6	54816852	54816864	+	1	NA	promoter-TSS (NM_199143)	promoter-TSS (NM_199143)	-58	NM_199143	387524	Mm.286149	NM_199143	ENSMUSG00000058446	Znrf2	1190002C14Rik|AU044205|D6Ertd365e	zinc and ring finger 2	protein-coding
mm_15909.1	chr2	165058260	165058270	+	1	NA	intron (NM_170702, intron 1 of 7)	(GGAA)n|Simple_repeat|Simple_repeat	2629	NM_011611	21939	Mm.271833	NM_011611	ENSMUSG00000017652	Cd40	AI326936|Bp50|GP39|HIGM1|IGM|IMD3|T-BAM|TRAP|Tnfrsf5|p50	CD40 antigen	protein-coding
mm_165863.1	chr4	32652769	32652785	+	1	NA	3' UTR (NM_011997, exon 11 of 11)	3' UTR (NM_011997, exon 11 of 11)	-4342	NM_001081392	100019	Mm.24627	NM_133874	ENSMUSG00000058006	Mdn1	4833432B22Rik|A130070M06|AA958993|D4Abb1e|Gm135	midasin AAA ATPase 1	protein-coding
mm_97633.1	chr11	78959922	78959931	+	1	NA	3' UTR (NM_010927, exon 27 of 27)	3' UTR (NM_010927, exon 27 of 27)	24998	NM_001159301	16859	Mm.341434	NM_010708	ENSMUSG00000001123	Lgals9	AA407335|AI194909|AI265545|LGALS35|Lgals5|gal-9|galectin-9	lectin, galactose binding, soluble 9	protein-coding
mm_110970.1	chr12	76961446	76961467	-	1	NA	intron (NM_008558, intron 1 of 4)	intron (NM_008558, intron 1 of 4)	792	NM_008558	17187	Mm.268548	NM_008558	ENSMUSG00000059436	Max	AA960152|AI875693|bHLHd4|bHLHd5|bHLHd6|bHLHd7|bHLHd8	Max protein	protein-coding
mm_93952.1	chr10	127263064	127263101	-	1	NA	5' UTR (NM_001039000, exon 1 of 29)	5' UTR (NM_001039000, exon 1 of 29)	281	NM_008447	16572	Mm.30355	NM_008447	ENSMUSG00000074657	Kif5a	D10Bwg0738e|Khc|Kif5|Kns|mKIAA4086	kinesin family member 5A	protein-coding
mm_110771.1	chr12	70316320	70316326	-	1	NA	intron (NR_037248, intron 2 of 4)	intron (NR_037248, intron 2 of 4)	7818	NR_037248	100526482		NR_037248	ENSMUSG00000078026	Mir466o	Mir4660|mmu-mir-466o	microRNA 466o	ncRNA
mm_169512.1	chr14	85733336	85733342	-	1	NA	Intergenic	Intergenic	-512631	NR_040457	75155	Mm.399239	NR_040457		4930529K09Rik	4930507G21Rik	RIKEN cDNA 4930529K09 gene	ncRNA
mm_12447.1	chr2	71118105	71118113	+	1	NA	promoter-TSS (NM_028593)	promoter-TSS (NM_028593)	55	NM_028593	73649	Mm.45435	NM_028593	ENSMUSG00000027015	Cybrd1	2210407P13Rik|Dcytb	cytochrome b reductase 1	protein-coding
mm_119662.1	chr14	52197512	52197518	+	1	NA	promoter-TSS (NM_033618)	promoter-TSS (NM_033618)	-276	NM_033618	114741	Mm.21662	NM_033618	ENSMUSG00000035726	Supt16	Cdc68|Fact140|Spt16|Supt16h	suppressor of Ty 16	protein-coding
mm_54491.1	chr6	35510032	35510038	-	1	NA	3' UTR (NM_008098, exon 4 of 4)	3' UTR (NM_008098, exon 4 of 4)	29853	NM_008098	14489	Mm.182746	NM_008098	ENSMUSG00000029840	Mtpn	5033418D15Rik|Gcdp|V1	myotrophin	protein-coding
mm_167376.1	chr8	91801618	91801637	-	1	NA	promoter-TSS (NM_001253822)	promoter-TSS (NM_001253822)	27	NM_001253822	16373	Mm.238044	NM_008393	ENSMUSG00000031734	Irx3	AI894186	Iroquois related homeobox 3	protein-coding
mm_28024.1	chr3	83046676	83046683	-	1	NA	exon (NM_181849, exon 2 of 8)	exon (NM_181849, exon 2 of 8)	3184	NM_181849	110135	Mm.30063	NM_181849	ENSMUSG00000033831	Fgb	2510049G14Rik	fibrinogen beta chain	protein-coding
mm_56878.1	chr6	118987138	118987142	-	1	NA	intron (NM_001256002, intron 3 of 47)	PB1D10|SINE|Alu	106982	NR_046053	74363	Mm.399403	NR_046053		4931430N09Rik	-	RIKEN cDNA 4931430N09 gene	ncRNA
mm_124749.1	chr15	6630056	6630075	+	1	NA	intron (NM_011815, intron 2 of 17)	intron (NM_011815, intron 2 of 17)	50218	NM_011815	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_17333.1	chr2	26516730	26516741	-	1	NA	Intergenic	Intergenic	12808	NR_132655	102639736		NR_132655		Gm35978	-	predicted gene, 35978	ncRNA
mm_125645.1	chr15	62246525	62246528	+	1	NA	intron (NR_132746, intron 6 of 6)	intron (NR_132746, intron 6 of 6)	-27075	NR_003523	67552	Mm.484027	NM_026230		H2afy3	4933432H23Rik	H2A histone family, member Y3	pseudo
mm_132591.1	chr16	38445347	38445355	+	1	NA	TTS (NM_007414)	TTS (NM_007414)	7338	NM_007414	11544	Mm.20047	NM_007414	ENSMUSG00000002844	Adprh	Arh1	ADP-ribosylarginine hydrolase	protein-coding
mm_6069.1	chr1	60902535	60902538	-	1	NA	Intergenic	Intergenic	-6489	NM_009843	12477	Mm.390	NM_009843	ENSMUSG00000026011	Ctla4	Cd152|Ctla-4|Ly-56	cytotoxic T-lymphocyte-associated protein 4	protein-coding
mm_155660.1	chrX	86191767	86191782	+	1	NA	promoter-TSS (NM_007430)	promoter-TSS (NM_007430)	-1	NM_007430	11614	Mm.5180	NM_007430	ENSMUSG00000025056	Nr0b1	AHX|Ahc|Ahch|DAX-1|Dax1	nuclear receptor subfamily 0, group B, member 1	protein-coding
mm_32882.1	chr4	118961600	118961612	+	1	NA	promoter-TSS (NM_133892)	promoter-TSS (NM_133892)	-361	NM_133892	100470	Mm.26698	NM_133892	ENSMUSG00000024903	Lao1	AW990848	L-amino acid oxidase 1	protein-coding
mm_50988.1	chr6	63255972	63256036	+	1	NA	promoter-TSS (NM_008167)	promoter-TSS (NM_008167)	-853	NM_008167	14804	Mm.439651	NM_008167	ENSMUSG00000071424	Grid2	B230104L07Rik|GluD2|GluRdelta2|Lc|Lc<J>|MMS10-AC|Ms10ac|cpr|ho|nmf408|tpr	glutamate receptor, ionotropic, delta 2	protein-coding
mm_52907.1	chr6	122811505	122811521	+	1	NA	Intergenic	CpG	-8671	NM_021899	60611	Mm.87142	NM_021899	ENSMUSG00000003154	Foxj2	Fhx	forkhead box J2	protein-coding
mm_136905.1	chr17	13016410	13016428	+	1	NA	3' UTR (NM_013671, exon 5 of 5)	3' UTR (NM_013671, exon 5 of 5)	8580	NM_013671	20656	Mm.290876	NM_013671	ENSMUSG00000006818	Sod2	MnSOD|Sod-2	superoxide dismutase 2, mitochondrial	protein-coding
mm_144720.1	chr18	35119830	35119840	+	1	NA	intron (NM_009818, intron 1 of 17)	intron (NM_009818, intron 1 of 17)	923	NM_009818	12385	Mm.18962	NM_009818	ENSMUSG00000037815	Ctnna1	2010010M04Rik|AA517462|AI988031|Catna1	catenin (cadherin associated protein), alpha 1	protein-coding
mm_66976.1	chr7	63929351	63929354	-	1	NA	intron (NM_021366, intron 1 of 1)	intron (NM_021366, intron 1 of 1)	9563	NM_021366	50794	Mm.240473	NM_021366	ENSMUSG00000052040	Klf13	0610043C13Rik|9430029L20Rik|Bteb3|FKLF-2|FKLF2|NSLP1|RFLAT-1|RFLAT1	Kruppel-like factor 13	protein-coding
mm_36181.1	chr4	62208648	62208670	-	1	NA	promoter-TSS (NM_009554)	promoter-TSS (NM_009554)	-113	NM_001290350	22696	Mm.5011	NM_009554	ENSMUSG00000028389	Zfp37	Tzn|Zfp-37	zinc finger protein 37	protein-coding
mm_96546.1	chr11	68853374	68853388	+	1	NA	promoter-TSS (NM_023668)	promoter-TSS (NM_023668)	-250	NM_023668	83431	Mm.31979	NM_023668	ENSMUSG00000018736	Ndel1	2600006O07Rik|MITAP1|NUDEL|mNudel	nudE neurodevelopment protein 1 like 1	protein-coding
mm_68176.1	chr7	103843155	103843169	-	1	NA	promoter-TSS (NM_008219)	promoter-TSS (NM_008219)	0	NM_008219	15132	Mm.440281	NM_008219	ENSMUSG00000052217	Hbb-bh1	betaH1	hemoglobin Z, beta-like embryonic chain	protein-coding
mm_151005.1	chr19	46654930	46654959	+	1	NA	3' UTR (NM_001177813, exon 4 of 4)	3' UTR (NM_001177813, exon 4 of 4)	18056	NM_007809	13074	Mm.1262	NM_007809	ENSMUSG00000003555	Cyp17a1	Cyp17|p450c17	cytochrome P450, family 17, subfamily a, polypeptide 1	protein-coding
mm_60524.1	chr7	44480068	44480076	+	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	-4445	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_100771.1	chr11	4789735	4789760	-	1	NA	exon (NM_001252253, exon 12 of 15)	exon (NM_001252253, exon 12 of 15)	-42969	NM_138948	192650	Mm.207056	NM_138948	ENSMUSG00000009075	Cabp7	-	calcium binding protein 7	protein-coding
mm_144162.1	chr18	5688821	5688823	+	1	NA	intron (NM_011546, intron 1 of 7)	MTD|LTR|ERVL-MaLR	-96385	NR_033552	791318	Mm.84339	NR_033552	ENSMUSG00000063087	Gm10125	ENSMUSG00000063087|Zeb1os	predicted gene 10125	ncRNA
mm_145670.1	chr18	61448251	61448261	+	1	NA	Intergenic	Intergenic	36351	NR_045419	442846	Mm.417648	NR_045419		A530050N04Rik	-	RIKEN cDNA A530050N04 gene	ncRNA
mm_28950.1	chr3	100472599	100472617	-	1	NA	exon (NM_001142952, exon 2 of 2)	exon (NM_001142952, exon 2 of 2)	16584	NM_001142952	74645	Mm.226900	NM_001142952	ENSMUSG00000044468	Fam46c	4930431B09Rik|AI449797	family with sequence similarity 46, member C	protein-coding
mm_140221.1	chr17	83905649	83905656	+	1	NA	Intergenic	Intergenic	-58862	NM_025325	107766	Mm.30100	NM_025325	ENSMUSG00000000673	Haao	0610007K21Rik|0610012J07Rik|3-HAO|3-HAOxase|3HAO	3-hydroxyanthranilate 3,4-dioxygenase	protein-coding
mm_58480.1	chr7	3455535	3455538	+	1	NA	Intergenic	Lx8|LINE|L1	30874	NM_133183	54378	Mm.424047	NM_133183	ENSMUSG00000078815	Cacng6	2310033H20Rik	calcium channel, voltage-dependent, gamma subunit 6	protein-coding
mm_105182.1	chr11	101894356	101894372	-	1	NA	promoter-TSS (NM_010791)	promoter-TSS (NM_010791)	-10	NM_010791	17285	Mm.3404	NM_010791	ENSMUSG00000001493	Meox1	AI385561|D330041M02Rik|Mox-1|Mox1	mesenchyme homeobox 1	protein-coding
mm_18441.1	chr2	60883891	60883939	-	1	NA	intron (NM_020296, intron 1 of 13)	MLT1M|LTR|ERVL-MaLR	-2477	NM_001141931	56878	Mm.259667	NM_020296	ENSMUSG00000026970	Rbms1	2600014B10Rik|AI255215|MSSP-1|MSSP-2|MSSP-3|YC1	RNA binding motif, single stranded interacting protein 1	protein-coding
mm_17068.1	chr2	22744606	22744621	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-29714	NM_019456	54519	Mm.14255	NM_019456	ENSMUSG00000026786	Apbb1ip	9930118P07Rik|Prp48	amyloid beta (A4) precursor protein-binding, family B, member 1 interacting protein	protein-coding
mm_151295.1	chr19	55435374	55435380	+	1	NA	intron (NM_001293685, intron 6 of 8)	L1_Mus4|LINE|L1	119320	NM_001293686	53611	Mm.258637	NM_016862	ENSMUSG00000024983	Vti1a	1110014F16Rik|1110018K19Rik|4921537J05Rik|MVti1|MVti1a|Vti1|Vti1-rp2	vesicle transport through interaction with t-SNAREs 1A	protein-coding
mm_125874.1	chr15	75616676	75616729	+	1	NA	promoter-TSS (NM_011759)	promoter-TSS (NM_011759)	18	NM_011759	22701	Mm.87210	NM_011759	ENSMUSG00000047003	Zfp41	CTfin92|Zfp-41	zinc finger protein 41	protein-coding
mm_29770.1	chr3	127240662	127240678	-	1	NA	intron (NM_001327938, intron 1 of 47)	intron (NM_001327938, intron 1 of 47)	79365	NR_105029	100862268	Mm.444603	NR_105029	ENSMUSG00000097456	LOC100862268	-	uncharacterized LOC100862268	ncRNA
mm_85032.1	chr9	88480259	88480270	-	1	NA	intron (NM_001311113, intron 1 of 10)	intron (NM_001311113, intron 1 of 10)	2133	NM_019666	56403	Mm.260545	NM_019666	ENSMUSG00000032423	Syncrip	2610109K23Rik|4632417O19Rik|GRY-RBP|Nsap1|Nsap1l|hnRNP Q|pp68	synaptotagmin binding, cytoplasmic RNA interacting protein	protein-coding
mm_93444.1	chr10	109903853	109903871	-	1	NA	exon (NM_001081035, exon 2 of 39)	exon (NM_001081035, exon 2 of 39)	96357	NM_001081035	260315	Mm.225050	NM_177797	ENSMUSG00000020181	Nav3	4732483H20Rik|9630020C08Rik|POMFIL1|Pomfil1p|mKIAA0938|unc53H3	neuron navigator 3	protein-coding
mm_128062.1	chr15	26743507	26743519	-	1	NA	intron (NM_176959, intron 2 of 3)	intron (NM_176959, intron 2 of 3)	152051	NM_176959	448987	Mm.253378	NM_176959	ENSMUSG00000043556	Fbxl7	AL023057|D230018M15Rik|FBL7|Fbl6	F-box and leucine-rich repeat protein 7	protein-coding
mm_138273.1	chr17	34604930	34604951	+	1	NA	promoter-TSS (NM_001163379)	promoter-TSS (NM_001163379)	-921	NM_001163379	55979	Mm.8684	NM_018862	ENSMUSG00000034254	Agpat1	1-AGP|1-AGPAT|AW047140	1-acylglycerol-3-phosphate O-acyltransferase 1 (lysophosphatidic acid acyltransferase, alpha)	protein-coding
mm_92303.1	chr10	75053012	75053022	-	1	NA	3' UTR (NM_029781, exon 11 of 11)	3' UTR (NM_029781, exon 11 of 11)	-7879	NM_001081412	110279	Mm.333722	NM_001081412	ENSMUSG00000009681	Bcr	5133400C09Rik|AI561783|AI853148|mKIAA3017	breakpoint cluster region	protein-coding
mm_106568.1	chr11	120643698	120643762	-	1	NA	promoter-TSS (NM_144795)	promoter-TSS (NM_144795)	-60	NM_144795	209027	Mm.127731	NM_144795	ENSMUSG00000025140	Pycr1	-	pyrroline-5-carboxylate reductase 1	protein-coding
mm_75924.1	chr8	71498240	71498259	-	1	NA	3' UTR (NM_032398, exon 6 of 6)	3' UTR (NM_032398, exon 6 of 6)	10146	NM_032544	70359	Mm.142112	NM_032544	ENSMUSG00000007610	Gtpbp3	2410009F13Rik|AI607903	GTP binding protein 3	protein-coding
mm_34383.1	chr4	144919992	144920008	+	1	NA	exon (NM_001172424, exon 5 of 7)	exon (NM_001172424, exon 5 of 7)	26863	NM_011303	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding
mm_79250.1	chr9	50603908	50603952	+	1	NA	promoter-TSS (NM_013897)	promoter-TSS (NM_013897)	29	NM_013897	30057	Mm.335149	NM_013897	ENSMUSG00000039016	Timm8b	Tim8b	translocase of inner mitochondrial membrane 8B	protein-coding
mm_7811.1	chr1	131733533	131733548	-	1	NA	Intergenic	Intergenic	-10482	NM_177243	320718	Mm.482704	NM_177243	ENSMUSG00000042268	Slc26a9	E030002L01Rik	solute carrier family 26, member 9	protein-coding
mm_105199.1	chr11	102097527	102097529	-	1	NA	Intergenic	Intergenic	3772	NM_008918	19064	Mm.1269	NM_008918	ENSMUSG00000017316	Ppy	AV061413|IGSPP|PP	pancreatic polypeptide	protein-coding
mm_157182.1	chrX	10117598	10117677	-	1	NA	promoter-TSS (NM_016911)	promoter-TSS (NM_016911)	24	NM_016911	51795	Mm.1927	NM_016911	ENSMUSG00000090084	Srpx	drs|drs-1|drs-2|mDRS-1|mDRS-2	sushi-repeat-containing protein	protein-coding
mm_43033.1	chr5	123973676	123973697	+	1	NA	promoter-TSS (NM_145070)	promoter-TSS (NM_145070)	58	NM_145070	29816	Mm.149954	NM_145070	ENSMUSG00000000915	Hip1r	AA410023|mKIAA0655	huntingtin interacting protein 1 related	protein-coding
mm_106543.1	chr11	120579160	120579198	-	1	NA	3' UTR (NM_133796, exon 6 of 6)	3' UTR (NM_133796, exon 6 of 6)	2441	NM_133796	192662	Mm.30016	NM_133796	ENSMUSG00000025132	Arhgdia	5330430M07Rik|Gdi-1|Rho-GDI|RhoDGI|RhoGDI-1	Rho GDP dissociation inhibitor (GDI) alpha	protein-coding
mm_66917.1	chr7	60047952	60047968	-	1	NA	intron (NM_001082962, intron 2 of 10)	intron (NM_001082962, intron 2 of 10)	-42804	NM_033174	84704	Mm.274995	NM_033174	ENSMUSG00000000948	Snurf	2410045I01Rik|Snrpn	SNRPN upstream reading frame	protein-coding
mm_170690.1	chr2	132099824	132099824	+	1	NA	intron (NM_018824, intron 2 of 15)	intron (NM_018824, intron 2 of 15)	45284	NM_018824	54338	Mm.103581	NM_018824	ENSMUSG00000027340	Slc23a2	AI844736|NBTL1|SVCT2|Slc23a1|YSPL2|YSPL3|mKIAA0238	solute carrier family 23 (nucleobase transporters), member 2	protein-coding
mm_152169.1	chr19	7323085	7323087	-	1	NA	intron (NM_007928, intron 1 of 17)	intron (NM_007928, intron 1 of 17)	18774	NM_001080389	13728	Mm.258986	NM_007928	ENSMUSG00000024969	Mark2	EMK-1|Emk|Par-1|Par-1b	MAP/microtubule affinity regulating kinase 2	protein-coding
mm_31176.1	chr4	43493346	43493430	+	1	NA	promoter-TSS (NR_001460)	promoter-TSS (NR_001460)	23	NM_001037913	622404	Mm.289109	NM_001037913	ENSMUSG00000028461	Ccdc107	-	coiled-coil domain containing 107	protein-coding
mm_136080.1	chr16	84835296	84835311	-	1	NA	promoter-TSS (NM_001302216)	promoter-TSS (NM_001302216)	179	NM_008065	14390	Mm.18974	NM_008065	ENSMUSG00000008976	Gabpa	GABPalpha	GA repeat binding protein, alpha	protein-coding
mm_61060.1	chr7	49959936	49959944	+	1	NA	TTS (NM_001146013)	TTS (NM_001146013)	-15410	NM_001037906	338352	Mm.383528	NM_001037906	ENSMUSG00000055409	Nell1	B230343H07Rik|l7R6	NEL-like 1	protein-coding
mm_42242.1	chr5	113828374	113828386	+	1	NA	intron (NM_009151, intron 1 of 1)	intron (NM_009151, intron 1 of 1)	2121	NM_009151	20345	Mm.332590	NM_009151	ENSMUSG00000048163	Selplg	CD162|Psgl-1|Psgl1|Selp1|Selpl	selectin, platelet (p-selectin) ligand	protein-coding
mm_25737.1	chr3	122895370	122895384	+	1	NA	5' UTR (NM_007980, exon 1 of 4)	5' UTR (NM_007980, exon 1 of 4)	305	NM_007980	14079	Mm.28398	NM_007980	ENSMUSG00000023057	Fabp2	Fabpi|I-FABP	fatty acid binding protein 2, intestinal	protein-coding
mm_42827.1	chr5	122100945	122100958	+	1	NA	promoter-TSS (NM_010861)	promoter-TSS (NM_010861)	-29	NM_010861	17906	Mm.1529	NM_010861	ENSMUSG00000013936	Myl2	MLC-2|MLC-2s/v|MLC-2v|Mlc2v|Mylpc	myosin, light polypeptide 2, regulatory, cardiac, slow	protein-coding
mm_79125.1	chr9	46913591	46913614	+	1	NA	promoter-TSS (NR_015605)	promoter-TSS (NR_015605)	-1	NR_015605	73040	Mm.265384	NR_015605	ENSMUSG00000099696	2900052N01Rik	AU067665	RIKEN cDNA 2900052N01 gene	ncRNA
mm_37391.1	chr4	121078741	121078751	-	1	NA	intron (NM_172700, intron 6 of 9)	intron (NM_172700, intron 6 of 9)	19497	NM_172700	230709	Mm.34399	NM_172700	ENSMUSG00000043207	Zmpste24	A530043O15Rik|D030046F19|FACE1|Face-1|MADB|STE24|Ste24p	zinc metallopeptidase, STE24	protein-coding
mm_37996.1	chr4	133666672	133666678	-	1	NA	intron (NM_178698, intron 2 of 3)	intron (NM_178698, intron 2 of 3)	5972	NM_001145955	230801	Mm.217004	NM_178698	ENSMUSG00000043257	Pigv	B330013B03|D430024F16Rik	phosphatidylinositol glycan anchor biosynthesis, class V	protein-coding
mm_45242.1	chr5	54018630	54018632	-	1	NA	intron (NM_001081103, intron 1 of 11)	intron (NM_001081103, intron 1 of 11)	20108	NM_001081103	116873	Mm.265985	NM_054083	ENSMUSG00000039156	Stim2	-	stromal interaction molecule 2	protein-coding
mm_46832.1	chr5	113221259	113221299	-	1	NA	Intergenic	CpG	-5630	NM_001033428	333048	Mm.332586	NM_001033428	ENSMUSG00000066964	Tmem211	Gm854	transmembrane protein 211	protein-coding
mm_116549.1	chr13	46502788	46502794	-	1	NA	intron (NM_026056, intron 1 of 12)	intron (NM_026056, intron 1 of 12)	888	NM_026056	67252	Mm.44529	NM_026056	ENSMUSG00000021373	Cap2	2810452G09Rik|AV045235	CAP, adenylate cyclase-associated protein, 2 (yeast)	protein-coding
mm_47838.1	chr5	134314444	134314452	-	1	NA	5' UTR (NM_010365, exon 1 of 34)	5' UTR (NM_010365, exon 1 of 34)	312	NM_001080746	14886	Mm.261570	NM_010365	ENSMUSG00000060261	Gtf2i	6030441I21Rik|BAP-135|Diws1t|GtfII-I|Spin|TFII-I|WBSCR6	general transcription factor II I	protein-coding
mm_47072.1	chr5	116545851	116545880	-	1	NA	intron (NM_026886, intron 1 of 12)	intron (NM_026886, intron 1 of 12)	45952	NM_026886	68955	Mm.146779	NM_026886	ENSMUSG00000063919	Srrm4	1500001A10Rik|B230202K19Rik|bv|mKIAA1853|nSR100	serine/arginine repetitive matrix 4	protein-coding
mm_125647.1	chr15	62264415	62264418	+	1	NA	Intergenic	Intergenic	-44965	NR_003523	67552	Mm.484027	NM_026230		H2afy3	4933432H23Rik	H2A histone family, member Y3	pseudo
mm_27027.1	chr3	26119412	26119432	-	1	NA	intron (NM_138666, intron 3 of 7)	intron (NM_138666, intron 3 of 7)	33885	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_146409.1	chr18	84088078	84088178	+	1	NA	promoter-TSS (NM_146090)	promoter-TSS (NM_146090)	-30	NM_146090	225791	Mm.147052	NM_146090	ENSMUSG00000049090	Zadh2	C530046K17Rik|PTGR-3|Pthr3	zinc binding alcohol dehydrogenase, domain containing 2	protein-coding
mm_48452.1	chr5	140759939	140759964	-	1	NA	TTS (NM_010302)	TTS (NM_010302)	35824	NM_173405	231842	Mm.491298	NM_173405	ENSMUSG00000050022	Amz1	5330426I05|6530401C20Rik	archaelysin family metallopeptidase 1	protein-coding
mm_5388.1	chr1	31143785	31143789	-	1	NA	intron (NR_033445, intron 2 of 2)	RMER15|LTR|ERVL	-32648	NM_153601	266744	Mm.389093	NM_153601	ENSMUSG00000050217	Lgsn	Gluld1|Lgs|lengsin	lengsin, lens protein with glutamine synthetase domain	protein-coding
mm_58285.1	chr6	145863194	145863251	-	1	NA	exon (NM_024469, exon 5 of 5)	exon (NM_024469, exon 5 of 5)	2198	NM_001271768	79362	Mm.154529	NM_024469	ENSMUSG00000030256	Bhlhe41	6430520M22Rik|Bhlhb2l|Bhlhb3|DEC2|Sharp1	basic helix-loop-helix family, member e41	protein-coding
mm_91316.1	chr10	24927720	24927728	-	1	NA	promoter-TSS (NM_007482)	promoter-TSS (NM_007482)	-254	NM_007482	11846	Mm.154144	NM_007482	ENSMUSG00000019987	Arg1	AI|AI256583|Arg-1|PGIF	arginase, liver	protein-coding
mm_79299.1	chr9	51765419	51765425	+	1	NA	promoter-TSS (NM_175535)	promoter-TSS (NM_175535)	70	NM_175535	244867	Mm.400352	NM_175535	ENSMUSG00000053199	Arhgap20	6530403F17Rik|A530023E23Rik|RARhoGAP|mKIAA1391	Rho GTPase activating protein 20	protein-coding
mm_62721.1	chr7	110773406	110773423	+	1	NA	intron (NM_009667, intron 1 of 14)	intron (NM_009667, intron 1 of 14)	810	NM_009667	11717	Mm.3238	NM_009667	ENSMUSG00000005686	Ampd3	-	adenosine monophosphate deaminase 3	protein-coding
mm_12088.1	chr2	60223067	60223074	+	1	NA	intron (NM_020575, intron 1 of 9)	intron (NM_020575, intron 1 of 9)	13134	NM_020575	57438	Mm.260635	NM_020575	ENSMUSG00000026977	March7	Axo|Axot|Gtrgeo17	membrane-associated ring finger (C3HC4) 7	protein-coding
mm_46470.1	chr5	105124983	105125015	-	1	NA	intron (NM_008620, intron 5 of 10)	(CACCC)n|Simple_repeat|Simple_repeat	14553	NM_008620	17472	Mm.440525	NM_008620	ENSMUSG00000079363	Gbp4	AW228052|Mag-2|Mpa-2|Mpa2	guanylate binding protein 4	protein-coding
mm_124972.1	chr15	19632472	19632476	+	1	NA	Intergenic	RMER19C|LTR|ERVK	812145	NM_009865	320873	Mm.117794	NM_009865	ENSMUSG00000022321	Cdh10	A830016G23Rik|C030003B10Rik|C030011H18Rik	cadherin 10	protein-coding
mm_137069.1	chr17	20945334	20945355	+	1	NA	promoter-TSS (NM_016891)	promoter-TSS (NM_016891)	-110	NM_016891	51792	Mm.294138	NM_016891	ENSMUSG00000007564	Ppp2r1a	6330556D22Rik|PP2A|PR65	protein phosphatase 2, regulatory subunit A, alpha	protein-coding
mm_169401.1	chr14	49885124	49885124	-	1	NA	Intergenic	Intergenic	16817	NM_146494	258487	Mm.270514	NM_146494	ENSMUSG00000048933	Olfr722	MOR241-3	olfactory receptor 722	protein-coding
mm_111671.1	chr12	103338256	103338281	-	1	NA	intron (NM_023049, intron 2 of 9)	intron (NM_023049, intron 2 of 9)	17733	NM_023049	65256	Mm.27159	NM_023049	ENSMUSG00000021200	Asb2	1110008E15Rik	ankyrin repeat and SOCS box-containing 2	protein-coding
mm_50584.1	chr6	49056655	49056665	+	1	NA	3' UTR (NM_053110, exon 11 of 11)	3' UTR (NM_053110, exon 11 of 11)	-17135	NM_029353	75593	Mm.439947	NM_029353	ENSMUSG00000029815	Malsu1	2410003K15Rik|Matsu1	mitochondrial assembly of ribosomal large subunit 1	protein-coding
mm_72386.1	chr8	81731839	81731854	+	1	NA	intron (NM_001024617, intron 3 of 24)	intron (NM_001024617, intron 3 of 24)	389284	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_133641.1	chr16	91729437	91729474	+	1	NA	promoter-TSS (NM_001110276)	promoter-TSS (NM_001110276)	84	NM_010587	16443	Mm.40546	NM_010587	ENSMUSG00000022957	Itsn1	AA517634|AA545208|AI316805|AI839402|AI848451|Ehsh1|Ese1|Itsn|Sh3p17	intersectin 1 (SH3 domain protein 1A)	protein-coding
mm_148985.1	chr19	8593176	8593192	+	1	NA	promoter-TSS (NM_001164635)	promoter-TSS (NM_001164635)	2	NM_001164635	19879	Mm.285294	NM_031194	ENSMUSG00000063796	Slc22a8	Oat3|Roct	solute carrier family 22 (organic anion transporter), member 8	protein-coding
mm_153068.1	chr19	32223786	32223820	-	1	NA	intron (NM_001168525, intron 4 of 9)	intron (NM_001168525, intron 4 of 9)	-12790	NM_001168526	208449	Mm.329810	NM_144792	ENSMUSG00000040451	Sgms1	9530058O11Rik|AI841905|C80702|Mob|Sms1|Sor1|Tmem23	sphingomyelin synthase 1	protein-coding
mm_19601.1	chr2	102400992	102401109	-	1	NA	promoter-TSS (NM_020267)	promoter-TSS (NM_020267)	-150	NM_020267	80985	Mm.315002	NM_020267	ENSMUSG00000027189	Trim44	Dipb|Mc7	tripartite motif-containing 44	protein-coding
mm_138278.1	chr17	34605900	34605939	+	1	NA	promoter-TSS (NM_001163379)	promoter-TSS (NM_001163379)	58	NM_001163379	55979	Mm.8684	NM_018862	ENSMUSG00000034254	Agpat1	1-AGP|1-AGPAT|AW047140	1-acylglycerol-3-phosphate O-acyltransferase 1 (lysophosphatidic acid acyltransferase, alpha)	protein-coding
mm_159761.1	chr5	92253402	92253402	-	1	NA	promoter-TSS (NM_011148)	promoter-TSS (NM_011148)	-243	NM_011148	19023	Mm.87155	NM_011148	ENSMUSG00000029410	Ppef2	-	protein phosphatase, EF hand calcium-binding domain 2	protein-coding
mm_107669.1	chr12	53248424	53248474	+	1	NA	promoter-TSS (NM_013780)	promoter-TSS (NM_013780)	-228	NM_013780	27386	Mm.247044	NM_013780	ENSMUSG00000021010	Npas3	4930423H22Rik|bHLHe12	neuronal PAS domain protein 3	protein-coding
mm_60655.1	chr7	44896126	44896187	+	1	NA	promoter-TSS (NM_027376)	promoter-TSS (NM_027376)	77	NM_027376	70300	Mm.276298	NM_027376	ENSMUSG00000011658	Fuz	2600013E07Rik|b2b1273Clo	fuzzy planar cell polarity protein	protein-coding
mm_5722.1	chr1	44102378	44102398	-	1	NA	promoter-TSS (NM_029368)	promoter-TSS (NM_029368)	0	NM_029368	75623	Mm.348017	NM_029368	ENSMUSG00000026049	Tex30	1700029F09Rik|3110030D08Rik	testis expressed 30	protein-coding
mm_52979.1	chr6	123262190	123262200	+	1	NA	promoter-TSS (NM_010819)	promoter-TSS (NM_010819)	88	NM_010819	17474	Mm.441101	NM_010819	ENSMUSG00000030144	Clec4d	Clecsf8|Mpcl|mcl	C-type lectin domain family 4, member d	protein-coding
mm_89336.1	chr10	87933838	87933848	+	1	NA	3' UTR (NM_010512, exon 5 of 5)	3' UTR (NM_010512, exon 5 of 5)	-32828	NR_000040	22172	Mm.391420	NR_000040		Tyms-ps	-	thymidylate synthase, pseudogene	pseudo
mm_159979.1	chr6	113458647	113458647	+	1	NA	promoter-TSS (NM_001034029)	promoter-TSS (NM_001034029)	163	NM_145826	57890	Mm.131781	NM_145826	ENSMUSG00000043088	Il17re	AA589509|IL-17RE|Il25r	interleukin 17 receptor E	protein-coding
mm_49281.1	chr6	17637841	17637889	+	1	NA	intron (NM_007604, intron 1 of 9)	intron (NM_007604, intron 1 of 9)	767	NM_007604	12343	Mm.392504	NM_007604	ENSMUSG00000015733	Capza2	1110053K06Rik|AW208808|Cappa2	capping protein (actin filament) muscle Z-line, alpha 2	protein-coding
mm_169319.1	chr14	113293269	113293269	+	1	NA	Intergenic	IAPLTR1_Mm|LTR|ERVK	1271839	NR_030150	723922		NR_030150	ENSMUSG00000070099	Mir466	Mirn466|mmu-mir-466	microRNA 466	ncRNA
mm_36977.1	chr4	109531218	109531220	-	1	NA	promoter-TSS (NM_026291)	promoter-TSS (NM_026291)	-15	NM_001199090	67646	Mm.45820	NM_026291	ENSMUSG00000060491	4930522H14Rik	1700007J23Rik	RIKEN cDNA 4930522H14 gene	protein-coding
mm_87238.1	chr10	40883494	40883508	+	1	NA	promoter-TSS (NM_027879)	promoter-TSS (NM_027879)	-33	NM_031877	83767	Mm.41353	NM_031877	ENSMUSG00000019831	Wasf1	AI195380|AI838537|Scar|WAVE|WAVE-1	WAS protein family, member 1	protein-coding
mm_6193.1	chr1	65159388	65159397	-	1	NA	3' UTR (NM_010497, exon 9 of 9)	3' UTR (NM_010497, exon 9 of 9)	19750	NM_010497	15926	Mm.9925	NM_010497	ENSMUSG00000025950	Idh1	AI314845|AI788952|E030024J03Rik|Id-1|Idh-1|Idpc	isocitrate dehydrogenase 1 (NADP+), soluble	protein-coding
mm_103573.1	chr11	77923371	77923387	-	1	NA	intron (NR_033549, intron 1 of 2)	intron (NR_033549, intron 1 of 2)	5909	NR_033549	791423	Mm.483498	NR_033549	ENSMUSG00000055045	Gm11190	OTTMUSG00000000071	predicted gene 11190	ncRNA
mm_61234.1	chr7	64753278	64753293	+	1	NA	3' UTR (NM_001291167, exon 14 of 14)	3' UTR (NM_001291167, exon 14 of 14)	119755	NM_023239	66647	Mm.19944	NM_023239	ENSMUSG00000070520	Ndnl2	5730494G16Rik|AI642138|BB044375|HCA4|Mageg1|Nsmce3|mage-g1	necdin-like 2	protein-coding
mm_145345.1	chr18	56471041	56471045	+	1	NA	intron (NM_026240, intron 2 of 13)	intron (NM_026240, intron 2 of 13)	38911	NM_026240	107022	Mm.24356	NM_026240	ENSMUSG00000001700	Gramd3	9030613F08Rik|9130427A09Rik|AW061306|NS3TP2	GRAM domain containing 3	protein-coding
mm_59943.1	chr7	30425272	30425289	+	1	NA	exon (NM_172142, exon 4 of 11)	exon (NM_172142, exon 4 of 11)	1976	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_122119.1	chr14	31014357	31014360	-	1	NA	promoter-TSS (NR_028531)	promoter-TSS (NR_028531)	-7	NR_028531	100217431		NR_028531		Snord69	MBII-210	small nucleolar RNA, C/D box 69	snoRNA
mm_64485.1	chr7	143067366	143067388	+	1	NA	3' UTR (NM_133655, exon 8 of 8)	3' UTR (NM_133655, exon 8 of 8)	-1991	NM_020285	56844	Mm.139675	NM_020285	ENSMUSG00000045752	Tssc4	AA241958|ESTM671070	tumor-suppressing subchromosomal transferable fragment 4	protein-coding
mm_152192.1	chr19	7482337	7482341	-	1	NA	intron (NM_001003934, intron 1 of 8)	intron (NM_001003934, intron 1 of 8)	952	NM_001271486	20168	Mm.246990	NM_053076	ENSMUSG00000024758	Rtn3	RTN3-A1	reticulon 3	protein-coding
mm_66730.1	chr7	46349017	46349023	-	1	NA	Intergenic	CpG	-22383	NR_131190	105447647		NR_131190		Munc	DRReRNA	MyoD upstream noncoding	ncRNA
mm_34194.1	chr4	140702178	140702198	+	1	NA	exon (NM_173867, exon 2 of 13)	exon (NM_173867, exon 2 of 13)	715	NM_173867	108911	Mm.253	NM_173867	ENSMUSG00000040945	Rcc2	2610510H01Rik|2610529N02Rik|AA536646|AA675016|Td60|mKIAA1470	regulator of chromosome condensation 2	protein-coding
mm_118330.1	chr13	113663671	113663681	-	1	NA	promoter-TSS (NM_019960)	promoter-TSS (NM_019960)	0	NM_019960	56534	Mm.41410	NM_019960	ENSMUSG00000051456	Hspb3	2310035K17Rik|AI844863|Hsbp3|spb3	heat shock protein 3	protein-coding
mm_39590.1	chr5	23496400	23496417	+	1	NA	exon (NM_026984, exon 18 of 26)	exon (NM_026984, exon 18 of 26)	61979	NM_026984	69188	Mm.205190	NM_026984	ENSMUSG00000029004	Kmt2e	1810033J14Rik|9530077A04Rik|D230038D11Rik|Mll5|NKp44L	lysine (K)-specific methyltransferase 2E	protein-coding
mm_128521.1	chr15	54278421	54278433	-	1	NA	promoter-TSS (NM_008764)	promoter-TSS (NM_008764)	57	NM_008764	18383	Mm.15383	NM_008764	ENSMUSG00000063727	Tnfrsf11b	OCIF|Opg|TR1	tumor necrosis factor receptor superfamily, member 11b (osteoprotegerin)	protein-coding
mm_74304.1	chr8	126422562	126422575	+	1	NA	promoter-TSS (NM_174987)	promoter-TSS (NM_174987)	67	NM_174987	67892	Mm.31946	NM_174987	ENSMUSG00000051671	Coa6	1810063B05Rik|AI447995	cytochrome c oxidase assembly factor 6	protein-coding
mm_93214.1	chr10	94944924	94944939	-	1	NA	promoter-TSS (NM_018797)	promoter-TSS (NM_018797)	-353	NM_018797	54712	Mm.256712	NM_018797	ENSMUSG00000074785	Plxnc1	2510048K12Rik|AW742158|CD232|Vespr	plexin C1	protein-coding
mm_49730.1	chr6	34709518	34709542	+	1	NA	promoter-TSS (NM_145575)	promoter-TSS (NM_145575)	86	NM_145575	109624	Mm.308134	NM_145575	ENSMUSG00000029761	Cald1	4833423D12Rik|AI195384|AV071549|AW536160|C920027I18Rik	caldesmon 1	protein-coding
mm_164864.1	chr18	56075444	56075446	-	1	NA	Intergenic	Intergenic	-356687	NM_026240	107022	Mm.24356	NM_026240	ENSMUSG00000001700	Gramd3	9030613F08Rik|9130427A09Rik|AW061306|NS3TP2	GRAM domain containing 3	protein-coding
mm_131181.1	chr16	7149912	7149916	+	1	NA	intron (NM_183188, intron 1 of 12)	intron (NM_183188, intron 1 of 12)	80079	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_111686.1	chr12	103443654	103443673	-	1	NA	promoter-TSS (NM_029803)	promoter-TSS (NM_029803)	17	NM_029803	76933	Mm.271275	NM_029803	ENSMUSG00000079017	Ifi27l2a	2310061N23Rik|Ifi27|Isg12|Isg12(b1)	interferon, alpha-inducible protein 27 like 2A	protein-coding
mm_134344.1	chr16	16560372	16560382	-	1	NA	promoter-TSS (NM_139232)	promoter-TSS (NM_139232)	-158	NM_139232	224014	Mm.256131	NM_139232	ENSMUSG00000022788	Fgd4	9030023J02Rik|9330209B17Rik|Frabp|ZFYVE6	FYVE, RhoGEF and PH domain containing 4	protein-coding
mm_160370.1	chr8	33386409	33386409	+	1	NA	promoter-TSS (NM_001122822)	promoter-TSS (NM_001122822)	84	NM_001098233	75029	Mm.159402	NM_152821	ENSMUSG00000049184	Purg	4930486B15Rik	purine-rich element binding protein G	protein-coding
mm_34434.1	chr4	147234323	147234330	+	1	NA	intron (NM_001039209, intron 1 of 2)	intron (NM_001039209, intron 1 of 2)	58460	NM_001039209	195531	Mm.270762	NM_001039209	ENSMUSG00000078496	Zfp982	Gm13152|OTTMUSG00000010671	zinc finger protein 982	protein-coding
mm_171467.1	chr4	145774628	145774645	+	1	NA	Intergenic	CpG	-6907	NM_001083918	666532	Mm.392861	NM_001083918	ENSMUSG00000067916	Zfp991	Gm13139|OTTMUSG00000010657	zinc finger protein 991	protein-coding
mm_170428.1	chr18	75000504	75000504	+	1	NA	promoter-TSS (NR_028552)	promoter-TSS (NR_028552)	27	NM_001002239	319195	Mm.276337	NM_001002239	ENSMUSG00000062328	Rpl17	-	ribosomal protein L17	protein-coding
mm_37974.1	chr4	133545907	133546011	-	1	NA	promoter-TSS (NM_010948)	promoter-TSS (NM_010948)	68	NM_010948	18221	Mm.69	NM_010948	ENSMUSG00000028851	Nudc	SIG-92|Silg92	nudC nuclear distribution protein	protein-coding
mm_102134.1	chr11	53430780	53430838	-	1	NA	promoter-TSS (NM_025352)	promoter-TSS (NM_025352)	22	NM_025352	22272	Mm.251621	NM_025352	ENSMUSG00000044894	Uqcrq	1100001F06Rik|1500040F11Rik|5830407L17Rik|9.5kDa|AA959903|QP-C|Qpc|Uqcrb|c1502	ubiquinol-cytochrome c reductase, complex III subunit VII	protein-coding
mm_149193.1	chr19	9954684	9954718	+	1	NA	Intergenic	Intergenic	-25899	NR_073181	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
mm_127463.1	chr15	101272270	101272277	+	1	NA	exon (NM_010444, exon 4 of 7)	exon (NM_010444, exon 4 of 7)	5427	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_66162.1	chr7	31156235	31156244	-	1	NA	Intergenic	Intergenic	-5189	NM_027898	52857	Mm.27366	NM_027898	ENSMUSG00000001248	Gramd1a	1300003M23Rik|AI415002|AW547240|D7Bwg0611e	GRAM domain containing 1A	protein-coding
mm_52566.1	chr6	116264228	116264266	+	1	NA	promoter-TSS (NM_001290338)	promoter-TSS (NM_001290338)	28	NM_001290338	67492	Mm.272772	NM_001081317	ENSMUSG00000042213	Zfand4	Anubl1	zinc finger, AN1-type domain 4	protein-coding
mm_137191.1	chr17	23822452	23822465	+	1	NA	exon (NM_175229, exon 11 of 14)	exon (NM_175229, exon 11 of 14)	6651	NM_026305	67673	Mm.153758	NM_026305	ENSMUSG00000055839	Elob	0610040H15Rik|Tceb2	elongin B	protein-coding
mm_40815.1	chr5	72203297	72203364	+	1	NA	promoter-TSS (NR_003966)	promoter-TSS (NR_003966)	1	NR_003966	231287	Mm.32775	NM_153389	ENSMUSG00000046808	Atp10d	9830145H18Rik|ATPVD|D5Buc24e	ATPase, class V, type 10D	protein-coding
mm_169347.1	chr14	19861258	19861272	-	1	NA	Intergenic	BGLII|LTR|ERVK	22340	NR_105025	52512	Mm.483998	NR_105025		D14Ertd670e	-	DNA segment, Chr 14, ERATO Doi 670, expressed	ncRNA
mm_5815.1	chr1	52658278	52658296	-	1	NA	3' UTR (NM_133829, exon 7 of 7)	3' UTR (NM_133829, exon 7 of 7)	27582	NM_001142647	227094	Mm.83541	NM_172654	ENSMUSG00000043015	Nemp2	5330401P04Rik|9830163O08|Tmem194b	nuclear envelope integral membrane protein 2	protein-coding
mm_96828.1	chr11	69998368	69998388	+	1	NA	exon (NM_030064, exon 4 of 5)	exon (NM_030064, exon 4 of 5)	916	NM_001291127	78246	Mm.20805	NM_030064	ENSMUSG00000018572	Phf23	JUNE-1	PHD finger protein 23	protein-coding
mm_35796.1	chr4	46537591	46537593	-	1	NA	3' UTR (NM_001164804, exon 12 of 12)	3' UTR (NM_001164804, exon 12 of 12)	-1451	NM_029077	74735	Mm.240252	NM_029077	ENSMUSG00000039853	Trim14	5830400N10Rik|pub	tripartite motif-containing 14	protein-coding
mm_105007.1	chr11	100377105	100377158	-	1	NA	intron (NM_010593, intron 8 of 13)	intron (NM_010593, intron 8 of 13)	20659	NM_010593	16480	Mm.299774	NM_010593	ENSMUSG00000001552	Jup	Ctnng|D930025P04Rik|PG	junction plakoglobin	protein-coding
mm_86016.1	chr9	112234957	112234967	-	1	NA	promoter-TSS (NM_001177619)	promoter-TSS (NM_001177619)	-121	NM_001177619	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_132365.1	chr16	34784877	34784886	+	1	NA	promoter-TSS (NM_139300)	promoter-TSS (NM_139300)	-69	NM_139300	107589	Mm.33360	NM_139300	ENSMUSG00000022836	Mylk	9530072E15Rik|A930019C19Rik|AW489456|KRP|MLCK108|MLCK210|Mlck|nmMlck|smMLCK	myosin, light polypeptide kinase	protein-coding
mm_43816.1	chr5	142921000	142921011	+	1	NA	Intergenic	Intergenic	-14251	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_136567.1	chr17	3326678	3326684	+	1	NA	5' UTR (NM_001122998, exon 1 of 27)	5' UTR (NM_001122998, exon 1 of 27)	108	NM_001122998	24001	Mm.137134	NM_011878	ENSMUSG00000023800	Tiam2	3000002F19Rik|STEF|mKIAA2016	T cell lymphoma invasion and metastasis 2	protein-coding
mm_34221.1	chr4	140986882	140986936	+	1	NA	promoter-TSS (NM_029097)	promoter-TSS (NM_029097)	36	NM_001164366	74772	Mm.205625	NM_029097	ENSMUSG00000036622	Atp13a2	1110012E06Rik|AA589443	ATPase type 13A2	protein-coding
mm_160958.1	chr11	98478248	98478248	-	1	NA	intron (NM_011771, intron 6 of 7)	intron (NM_011771, intron 6 of 7)	31414	NM_010346	14786	Mm.276702	NM_010346	ENSMUSG00000019312	Grb7	mKIAA4028	growth factor receptor bound protein 7	protein-coding
mm_105684.1	chr11	107716545	107716557	-	1	NA	promoter-TSS (NM_007582)	promoter-TSS (NM_007582)	-75	NM_007582	12299	Mm.57093	NM_007582	ENSMUSG00000020722	Cacng1	-	calcium channel, voltage-dependent, gamma subunit 1	protein-coding
mm_2201.1	chr1	89580148	89580180	+	1	NA	intron (NM_001037136, intron 1 of 16)	GC_rich|Low_complexity|Low_complexity	103728	NR_015540	74403	Mm.444291	NR_015540		4933400F21Rik	1700091C04Rik|4930565K10Rik	RIKEN cDNA 4933400F21 gene	ncRNA
mm_94174.1	chr10	128882977	128882980	-	1	NA	3' UTR (NM_010272, exon 3 of 3)	3' UTR (NM_010272, exon 3 of 3)	8740	NM_010272	14561	Mm.299218	NM_010272	ENSMUSG00000025352	Gdf11	BMP-11|Bmp11	growth differentiation factor 11	protein-coding
mm_10509.1	chr2	16356275	16356291	+	1	NA	promoter-TSS (NM_026162)	promoter-TSS (NM_026162)	-21	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding
mm_11951.1	chr2	52967678	52967687	+	1	NA	intron (NM_172409, intron 1 of 26)	intron (NM_172409, intron 1 of 26)	109814	NM_172409	71409	Mm.394427	NM_172409	ENSMUSG00000036053	Fmnl2	5430425K04Rik|Man	formin-like 2	protein-coding
mm_23880.1	chr3	83031011	83031019	+	1	NA	exon (NM_010196, exon 5 of 5)	exon (NM_010196, exon 5 of 5)	4862	NM_001111048	14161	Mm.88793	NM_010196	ENSMUSG00000028001	Fga	ENSMUSG00000059807|Fib	fibrinogen alpha chain	protein-coding
mm_154771.1	chrX	12652239	12652241	+	1	NA	5' UTR (NM_001101484, exon 1 of 1)	5' UTR (NM_001101484, exon 1 of 1)	357	NM_001101484	245347	Mm.327568	NM_001101484		Gm4984	AI428901|EG245347	predicted pseudogene 4984	protein-coding
mm_230.1	chr1	17727410	17727424	+	1	NA	promoter-TSS (NM_031402)	promoter-TSS (NM_031402)	0	NM_031402	83691	Mm.289625	NM_031402	ENSMUSG00000025776	Crispld1	Cocoacrisp|Lcrisp1	cysteine-rich secretory protein LCCL domain containing 1	protein-coding
mm_107782.1	chr12	61524537	61524554	+	1	NA	5' UTR (NM_001310586, exon 1 of 6)	5' UTR (NM_001310586, exon 1 of 6)	1378	NM_001310586	238205	Mm.28802	NM_178714	ENSMUSG00000035653	Lrfn5	AI427653|AI604817|C130061B21|mKIAA4208	leucine rich repeat and fibronectin type III domain containing 5	protein-coding
mm_46289.1	chr5	100373507	100373527	-	1	NA	exon (NM_026969, exon 22 of 28)	exon (NM_026969, exon 22 of 28)	42717	NM_026969	69162	Mm.18634	NM_026969	ENSMUSG00000035325	Sec31a	1810024J13Rik|ABP125|ABP130|AU042160|HSPC275|Sec31l1	Sec31 homolog A (S. cerevisiae)	protein-coding
mm_118634.1	chr14	21313469	21313477	+	1	NA	intron (NM_001243041, intron 6 of 10)	(T)n|Simple_repeat|Simple_repeat	-186297	NM_001205241	54169	Mm.248967	NM_017479	ENSMUSG00000021767	Kat6b	AI507552|B130044K16Rik|MYST-4|Morf|Myst4|mKIAA0383|qkf|querkopf	K(lysine) acetyltransferase 6B	protein-coding
mm_71630.1	chr8	57456003	57456018	+	1	NA	promoter-TSS (NM_009136)	promoter-TSS (NM_009136)	87	NM_009136	20284	Mm.12886	NM_009136	ENSMUSG00000031610	Scrg1	AW124307	scrapie responsive gene 1	protein-coding
mm_169255.1	chr1	37847246	37847260	-	1	NA	intron (NM_001290721, intron 2 of 17)	U2|snRNA|snRNA	8120	NR_110976	211484	Mm.332756	NM_207228	ENSMUSG00000060771	Tsga10	4933432N21Rik|AI843383|Gm217|Mtsga10	testis specific 10	protein-coding
mm_14350.1	chr2	129601515	129601542	+	1	NA	intron (NM_001291022, intron 1 of 4)	intron (NM_001291022, intron 1 of 4)	8359	NM_001291022	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_119031.1	chr14	30479621	30479685	+	1	NA	promoter-TSS (NM_133761)	promoter-TSS (NM_133761)	88	NM_133761	75901	Mm.28733	NM_133761	ENSMUSG00000021962	Dcp1a	1110066A22Rik|4930568L04Rik|AU019772|D14Ertd817e|Mitc1|SMIF	decapping mRNA 1A	protein-coding
mm_101791.1	chr11	46087151	46087156	-	1	NA	intron (NM_001291890, intron 3 of 22)	intron (NM_001291890, intron 3 of 22)	-15117	NR_106177	102465996		NR_106177	ENSMUSG00000098942	Mir8100	Gm27638|mmu-mir-8100	microRNA 8100	ncRNA
mm_144439.1	chr18	21651451	21651466	+	1	NA	promoter-TSS (NM_001271580)	promoter-TSS (NM_001271580)	-107	NM_001271580	74644	Mm.329311	NM_001271580		4930426D05Rik	-	RIKEN cDNA 4930426D05 gene	protein-coding
mm_72258.1	chr8	75097006	75097018	+	1	NA	exon (NM_010442, exon 3 of 5)	exon (NM_010442, exon 3 of 5)	3394	NM_010442	15368	Mm.276389	NM_010442	ENSMUSG00000005413	Hmox1	D8Wsu38e|HO-1|HO1|Hemox|Hmox|Hsp32	heme oxygenase 1	protein-coding
mm_107183.1	chr12	25040096	25040102	+	1	NA	intron (NM_001081378, intron 24 of 31)	intron (NM_001081378, intron 24 of 31)	55993	NM_010496	15902	Mm.34871	NM_010496	ENSMUSG00000020644	Id2	AI255428|C78922|Idb2|bHLHb26	inhibitor of DNA binding 2	protein-coding
mm_135789.1	chr16	57163775	57163800	-	1	NA	intron (NM_023175, intron 3 of 9)	intron (NM_023175, intron 3 of 9)	3545	NM_023175	52633	Mm.383203	NM_023175	ENSMUSG00000022751	Nit2	1190017B19Rik|D16Ertd502e	nitrilase family, member 2	protein-coding
mm_103179.1	chr11	70459987	70460001	-	1	NA	promoter-TSS (NM_023158)	promoter-TSS (NM_023158)	-10	NM_023158	66102	Mm.425692	NM_023158	ENSMUSG00000018920	Cxcl16	0910001K24Rik|AV290116|BB024863|CXCL16v1|CXCL16v2|SR-PSOX|Zmynd15|b2b498Clo	chemokine (C-X-C motif) ligand 16	protein-coding
mm_31583.1	chr4	57782189	57782205	+	1	NA	intron (NM_001304544, intron 6 of 8)	CpG	-63051	NM_009649	11641	Mm.467752	NM_009649	ENSMUSG00000038729	Akap2	AA959716|AI649048|Akap-2|Akap-kl|B230340M18Rik|Prka2	A kinase (PRKA) anchor protein 2	protein-coding
mm_112835.1	chr13	20825833	20825848	+	1	NA	intron (NM_012054, intron 2 of 20)	L1MB8|LINE|L1	31727	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_122809.1	chr14	54577528	54577539	-	1	NA	5' UTR (NM_010590, exon 1 of 8)	5' UTR (NM_010590, exon 1 of 8)	128	NM_010590	16475	Mm.100253	NM_010590	ENSMUSG00000022178	Ajuba	Jub	ajuba LIM protein	protein-coding
mm_144043.1	chr17	90376026	90376031	-	1	NA	intron (NM_001346957, intron 14 of 18)	intron (NM_001346957, intron 14 of 18)	79852	NM_001346958	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_87750.1	chr10	60267243	60267258	+	1	NA	Intergenic	Intergenic	-10378	NM_001146123	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_52260.1	chr6	108213220	108213269	+	1	NA	5' UTR (NM_010585, exon 1 of 62)	5' UTR (NM_010585, exon 1 of 62)	148	NM_010585	16438	Mm.227912	NM_010585	ENSMUSG00000030102	Itpr1	D6Pas2|ENSMUSG00000072853|Gm10429|IP3R 1|IP3R1|InsP3R|Ip3r|Itpr-1|P400|Pcp-1|Pcp1|insP3R1|opt|wblo	inositol 1,4,5-trisphosphate receptor 1	protein-coding
mm_107265.1	chr12	29528383	29528468	+	1	NA	promoter-TSS (NM_008666)	promoter-TSS (NM_008666)	41	NM_008666	17933	Mm.253067	NM_008666	ENSMUSG00000061911	Myt1l	2900046C06Rik|2900093J19Rik|C630034G21Rik|Nztf1|Pmng1|Png-1|mKIAA1106	myelin transcription factor 1-like	protein-coding
mm_122342.1	chr14	37135275	37135308	-	1	NA	promoter-TSS (NM_001199122)	promoter-TSS (NM_001199122)	31	NM_078478	66092	Mm.182912	NM_078478	ENSMUSG00000041028	Ghitm	1010001P14Rik|C77840|MICS1|PTD010|Tmbim5	growth hormone inducible transmembrane protein	protein-coding
mm_3642.1	chr1	152824754	152824758	+	1	NA	intron (NM_010877, intron 6 of 15)	intron (NM_010877, intron 6 of 15)	24603	NM_010877	17970	Mm.270307	NM_010877	ENSMUSG00000026480	Ncf2	NOXA2|Ncf-2|p67phox	neutrophil cytosolic factor 2	protein-coding
mm_23592.1	chr3	64949291	64949295	+	1	NA	Intergenic	Intergenic	-104550	NR_003962	319210	Mm.246646	NM_175670	ENSMUSG00000097538	Vmn2r-ps11	4930518C23Rik	vomeronasal 2, receptor, pseudogene 11	pseudo
mm_90626.1	chr10	128459260	128459277	+	1	NA	promoter-TSS (NM_001114096)	promoter-TSS (NM_001114096)	32	NM_001114097	68094	Mm.417338	NM_198160	ENSMUSG00000025369	Smarcc2	5930405J04Rik	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2	protein-coding
mm_4626.1	chr1	179546435	179546520	+	1	NA	promoter-TSS (NM_146105)	promoter-TSS (NM_146105)	-52	NM_146105	226744	Mm.87662	NM_146105	ENSMUSG00000038949	Cnst	9630058J23Rik	consortin, connexin sorting protein	protein-coding
mm_3549.1	chr1	150407531	150407548	+	1	NA	exon (NM_133780, exon 10 of 52)	exon (NM_133780, exon 10 of 52)	-14484	NM_145511	226499	Mm.222093	NM_145511	ENSMUSG00000006010	BC003331	1810053E15Rik|Odr4|odr-4	cDNA sequence BC003331	protein-coding
mm_6397.1	chr1	72861029	72861039	-	1	NA	3' UTR (NM_010518, exon 4 of 4)	3' UTR (NM_010518, exon 4 of 4)	13831	NM_010518	16011	Mm.405761	NM_010518	ENSMUSG00000026185	Igfbp5	AI256729|AW208790|IGFBP-5|IGFBP-5P	insulin-like growth factor binding protein 5	protein-coding
mm_149905.1	chr19	25610257	25610261	+	1	NA	promoter-TSS (NM_177360)	promoter-TSS (NM_177360)	-278	NM_177360	240590	Mm.62785	NM_177360	ENSMUSG00000042372	Dmrt3	-	doublesex and mab-3 related transcription factor 3	protein-coding
mm_79724.1	chr9	61946980	61947023	+	1	NA	promoter-TSS (NM_024245)	promoter-TSS (NM_024245)	-202	NM_024245	71819	Mm.259374	NM_024245	ENSMUSG00000032254	Kif23	3110001D19Rik|C87313|CHO1|Knsl5|MKLP-1|MKLP1	kinesin family member 23	protein-coding
mm_166685.1	chr6	99775020	99775020	+	1	NA	Intergenic	Intergenic	-48628	NM_001170419	50501	Mm.87365	NM_015768	ENSMUSG00000030069	Prok2	Bv8|PK2|Prok1	prokineticin 2	protein-coding
mm_158031.1	chrX	97376495	97376508	-	1	NA	intron (NM_001161432, intron 1 of 7)	intron (NM_001161432, intron 1 of 7)	708	NM_001161432	245527	Mm.189270	NM_175540	ENSMUSG00000034457	Eda2r	9430060M22Rik|TNFRSF27|Xedar	ectodysplasin A2 receptor	protein-coding
mm_87855.1	chr10	61175185	61175200	+	1	NA	promoter-TSS (NM_001017407)	promoter-TSS (NM_001017407)	-70	NM_001017409	65971	Mm.30227	NM_023064	ENSMUSG00000020096	Tbata	1700021K02Rik|AI428928|Spatial|Titest	thymus, brain and testes associated	protein-coding
mm_150301.1	chr19	34563033	34563035	+	1	NA	intron (NM_008332, intron 1 of 2)	intron (NM_008332, intron 1 of 2)	12340	NM_008332	15958	Mm.2036	NM_008332	ENSMUSG00000045932	Ifit2	AV302338|Ifi54|P54	interferon-induced protein with tetratricopeptide repeats 2	protein-coding
mm_117632.1	chr13	92131850	92131866	-	1	NA	Intergenic	CpG	-143816	NM_009027	19418	Mm.248630	NM_009027	ENSMUSG00000021708	Rasgrf2	6330417G04Rik|AW048350|Grf2|Ras-GRF2	RAS protein-specific guanine nucleotide-releasing factor 2	protein-coding
mm_14162.1	chr2	126606431	126606442	+	1	NA	exon (NM_008230, exon 4 of 12)	exon (NM_008230, exon 4 of 12)	12242	NM_008230	15186	Mm.18603	NM_008230	ENSMUSG00000027360	Hdc	AW108189|Hdc-a|Hdc-c|Hdc-e|Hdc-s	histidine decarboxylase	protein-coding
mm_25009.1	chr3	97690830	97690839	+	1	NA	promoter-TSS (NR_106084)	promoter-TSS (NR_106084)	-272	NR_106084	102466229		NR_106084	ENSMUSG00000098381	Mir7225	Gm27499|mmu-mir-7225	microRNA 7225	ncRNA
mm_143438.1	chr17	70852276	70852284	-	1	NA	promoter-TSS (NM_001164075)	promoter-TSS (NM_001164075)	-546	NM_001164075	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_35026.1	chr4	4016525	4016539	-	1	NA	intron (NM_181989, intron 1 of 6)	intron (NM_181989, intron 1 of 6)	3131	NM_181989	242285	Mm.98096	NM_181989	ENSMUSG00000028236	Sdr16c5	Rdhe2|Scdr9	short chain dehydrogenase/reductase family 16C, member 5	protein-coding
mm_33946.1	chr4	137277588	137277589	+	1	NA	promoter-TSS (NM_009523)	promoter-TSS (NM_009523)	-47	NM_009523	22417	Mm.20355	NM_009523	ENSMUSG00000036856	Wnt4	Wnt-4	wingless-type MMTV integration site family, member 4	protein-coding
mm_88919.1	chr10	81183223	81183273	+	1	NA	promoter-TSS (NM_001190473)	promoter-TSS (NM_001190473)	-15	NM_001190473	13144	Mm.10294	NM_007828	ENSMUSG00000034974	Dapk3	ZIPK|dlk	death-associated protein kinase 3	protein-coding
mm_19262.1	chr2	84816109	84816147	-	1	NA	intron (NM_024230, intron 4 of 7)	intron (NM_024230, intron 4 of 7)	6524	NM_024230	68678	Mm.33452	NM_024230	ENSMUSG00000027077	Smtnl1	1110030K22Rik|CHASM	smoothelin-like 1	protein-coding
mm_105749.1	chr11	109472581	109472591	-	1	NA	promoter-TSS (NM_028710)	promoter-TSS (NM_028710)	643	NM_134038	104681	Mm.265874	NM_134038	ENSMUSG00000041920	Slc16a6	AW743111|ESTM12|MCT 6|MCT 7|MCT6	solute carrier family 16 (monocarboxylic acid transporters), member 6	protein-coding
mm_152613.1	chr19	11966146	11966154	-	1	NA	exon (NM_001033174, exon 1 of 14)	exon (NM_001033174, exon 1 of 14)	306	NM_001033174	76303	Mm.291279	NM_001033174	ENSMUSG00000024687	Osbp	1110018F06Rik|AW559088|mKIAA4220	oxysterol binding protein	protein-coding
mm_59362.1	chr7	25687482	25687540	+	1	NA	TTS (NM_172148)	TTS (NM_172148)	509	NM_011577	21803	Mm.248380	NM_011577	ENSMUSG00000002603	Tgfb1	TGF-beta1|TGFbeta1|Tgfb|Tgfb-1	transforming growth factor, beta 1	protein-coding
mm_37295.1	chr4	119189971	119189981	-	1	NA	promoter-TSS (NM_013848)	promoter-TSS (NM_013848)	35	NM_013848	27028	Mm.290753	NM_013848	ENSMUSG00000028644	Ermap	AA409279|AI666418	erythroblast membrane-associated protein	protein-coding
mm_137637.1	chr17	28334945	28334948	+	1	NA	exon (NM_001204156, exon 6 of 13)	exon (NM_001204156, exon 6 of 13)	6475	NM_011287	19896	Mm.336955	NM_011287	ENSMUSG00000037805	Rpl10a	CsA-19|Nedd6	ribosomal protein L10A	protein-coding
mm_103738.1	chr11	80080909	80080919	-	1	NA	promoter-TSS (NM_018776)	promoter-TSS (NM_018776)	77	NM_001277106	54394	Mm.272093	NM_018776	ENSMUSG00000017561	Crlf3	BB164954|Creme9|Cytor4	cytokine receptor-like factor 3	protein-coding
mm_90458.1	chr10	127739517	127739592	+	1	NA	promoter-TSS (NM_198035)	promoter-TSS (NM_198035)	16	NM_198035	320080	Mm.27258	NM_198035	ENSMUSG00000044617	Zbtb39	7030401O21Rik|mKIAA0352	zinc finger and BTB domain containing 39	protein-coding
mm_66139.1	chr7	31115228	31115308	-	1	NA	promoter-TSS (NM_008281)	promoter-TSS (NM_008281)	58	NM_008281	15451	Mm.19182	NM_008281	ENSMUSG00000001249	Hpn	Hlb320	hepsin	protein-coding
mm_104589.1	chr11	97041308	97041353	-	1	NA	promoter-TSS (NM_027026)	promoter-TSS (NM_027026)	39	NM_027026	69297	Mm.250465	NM_027026	ENSMUSG00000020878	Lrrc46	1700006D24Rik	leucine rich repeat containing 46	protein-coding
mm_67996.1	chr7	100928605	100928624	-	1	NA	exon (NM_001081116, exon 1 of 21)	exon (NM_001081116, exon 1 of 21)	3547	NM_001081116	207212	Mm.29954	NM_001081116	ENSMUSG00000032875	Arhgef17	8030463K16|AI428794|AW558066|BC035332|mKIAA0337	Rho guanine nucleotide exchange factor (GEF) 17	protein-coding
mm_123601.1	chr14	67933425	67933450	-	1	NA	5' UTR (NM_177780, exon 1 of 52)	5' UTR (NM_177780, exon 1 of 52)	135	NM_177780	68813	Mm.258155	NM_177780	ENSMUSG00000044447	Dock5	1110060D06Rik|AI666732|AI956923|BC016533|E130320D18|lr2|rlc	dedicator of cytokinesis 5	protein-coding
mm_79935.1	chr9	65890345	65890358	+	1	NA	promoter-TSS (NM_026515)	promoter-TSS (NM_026515)	28	NM_026515	68026	Mm.351273	NM_026515	ENSMUSG00000040204	Pclaf	2810417H13Rik|AA409629|Ns5apt9|Ns5atp9|PAF15|Paf|mKIAA0101|p15(PAF)	PCNA clamp associated factor	protein-coding
mm_465.1	chr1	36332693	36332699	+	1	NA	Intergenic	L1MDa|LINE|L1	16062	NR_105863	102465541		NR_105863	ENSMUSG00000098680	Mir6898	Gm27816|mmu-mir-6898	microRNA 6898	ncRNA
mm_130004.1	chr15	86214307	86214325	-	1	NA	promoter-TSS (NM_145476)	promoter-TSS (NM_145476)	-143	NM_145476	223754	Mm.28904	NM_145476	ENSMUSG00000051864	Tbc1d22a	BC023106|D15Ertd781e	TBC1 domain family, member 22a	protein-coding
mm_117519.1	chr13	81238894	81238907	-	1	NA	intron (NM_054053, intron 85 of 89)	intron (NM_054053, intron 85 of 89)	274826	NR_015587	319983	Mm.343027	NR_015587	ENSMUSG00000097098	9330111N05Rik	-	RIKEN cDNA 9330111N05 gene	ncRNA
mm_69931.1	chr7	142045814	142045815	-	1	NA	intron (NM_028308, intron 1 of 4)	ORR1A4-int|LTR|ERVL-MaLR	15039	NM_001347560	101513	Mm.53259	NM_028308	ENSMUSG00000025147	Mob2	1110017M21Rik|2700078K21Rik|AI256456|Mmh	MOB kinase activator 2	protein-coding
mm_99309.1	chr11	101377173	101377181	+	1	NA	3' UTR (NM_008061, exon 5 of 5)	3' UTR (NM_008061, exon 5 of 5)	9461	NM_008061	14377	Mm.18064	NM_008061	ENSMUSG00000078650	G6pc	AW107337|G6Pase|G6pt|Glc-6-Pase	glucose-6-phosphatase, catalytic	protein-coding
mm_140281.1	chr17	85027965	85027968	+	1	NA	promoter-TSS (NM_009205)	promoter-TSS (NM_009205)	-381	NM_009205	20532	Mm.227176	NM_009205	ENSMUSG00000024131	Slc3a1	D2H|NBAT|NTAA|RBAT	solute carrier family 3, member 1	protein-coding
mm_172139.1	chr6	36089170	36089172	-	1	NA	Intergenic	Intergenic	-298913	NM_203491	243764	Mm.448632	NM_203491	ENSMUSG00000045613	Chrm2	AChR-M2|Chrm-2|M2	cholinergic receptor, muscarinic 2, cardiac	protein-coding
mm_18281.1	chr2	52455700	52455723	-	1	NA	intron (NM_001285426, intron 9 of 13)	intron (NM_001285426, intron 9 of 13)	-30837	NM_182994	75423	Mm.314378	NM_182994	ENSMUSG00000036093	Arl5a	2410015N24Rik|2810410P22Rik|AA408731|AW610751|Arl5|T25534	ADP-ribosylation factor-like 5A	protein-coding
mm_69525.1	chr7	135651988	135651995	-	1	NA	promoter-TSS (NM_001316681)	promoter-TSS (NM_001316681)	92	NM_001316681	19267	Mm.945	NM_011212	ENSMUSG00000041836	Ptpre	PTPe|PTPepsilon|RPTPepsilon	protein tyrosine phosphatase, receptor type, E	protein-coding
mm_70406.1	chr8	11352047	11352061	+	1	NA	intron (NM_009932, intron 3 of 47)	intron (NM_009932, intron 3 of 47)	-39228	NM_009931	12826	Mm.738	NM_009931	ENSMUSG00000031502	Col4a1	Bru|Col4a-1|Raw|Svc	collagen, type IV, alpha 1	protein-coding
mm_82508.1	chr9	20492692	20492710	-	1	NA	promoter-TSS (NM_001110309)	promoter-TSS (NM_001110309)	45	NM_146221	235028	Mm.297660	NM_146221	ENSMUSG00000059475	Zfp426	2900057C04Rik|KRAB1|Zfo61|Zfp68-rs1|Znf426|mKIAA4237	zinc finger protein 426	protein-coding
mm_97480.1	chr11	78324288	78324301	+	1	NA	promoter-TSS (NM_009657)	promoter-TSS (NM_009657)	96	NM_009657	11676	Mm.7729	NM_009657	ENSMUSG00000017390	Aldoc	AI847350|AU040929|Aldo3|Scrg2	aldolase C, fructose-bisphosphate	protein-coding
mm_27254.1	chr3	37125944	37125969	-	1	NA	promoter-TSS (NM_008366)	promoter-TSS (NM_008366)	-2	NM_008366	16183	Mm.14190	NM_008366	ENSMUSG00000027720	Il2	Il-2	interleukin 2	protein-coding
mm_42380.1	chr5	114932810	114932820	+	1	NA	exon (NM_145209, exon 5 of 7)	exon (NM_145209, exon 5 of 7)	-9387	NM_028211	72357	Mm.292672	NM_028211	ENSMUSG00000029559	2210016L21Rik	-	RIKEN cDNA 2210016L21 gene	protein-coding
mm_56608.1	chr6	112488920	112488935	-	1	NA	exon (NM_001081147, exon 1 of 2)	exon (NM_001081147, exon 1 of 2)	881	NM_001081147	18430	Mm.333310	NM_001081147	ENSMUSG00000049112	Oxtr	OTR	oxytocin receptor	protein-coding
mm_88791.1	chr10	80622678	80622758	+	1	NA	promoter-TSS (NM_134002)	promoter-TSS (NM_134002)	-62	NM_134002	103236	Mm.29873	NM_134002	ENSMUSG00000003345	Csnk1g2	2810429I12Rik|AI463719	casein kinase 1, gamma 2	protein-coding
mm_115258.1	chr13	110400586	110400605	+	1	NA	3' UTR (NM_152804, exon 14 of 14)	3' UTR (NM_152804, exon 14 of 14)	5551	NM_152804	20620	Mm.380	NM_152804	ENSMUSG00000021701	Plk2	Snk	polo-like kinase 2	protein-coding
mm_74783.1	chr8	22039629	22039649	-	1	NA	intron (NM_007511, intron 1 of 20)	intron (NM_007511, intron 1 of 20)	20435	NM_007511	11979	Mm.87854	NM_007511	ENSMUSG00000006567	Atp7b	Atp7a|WND|tx	ATPase, Cu++ transporting, beta polypeptide	protein-coding
mm_113114.1	chr13	24434068	24434076	+	1	NA	intron (NM_007717, intron 6 of 15)	PB1D10|SINE|Alu	18950	NM_001284520	12763	Mm.8396	NM_007717	ENSMUSG00000016756	Cmah	-	cytidine monophospho-N-acetylneuraminic acid hydroxylase	protein-coding
mm_4319.1	chr1	171851853	171851867	+	1	NA	exon (NM_013489, exon 3 of 9)	exon (NM_013489, exon 3 of 9)	12163	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_92639.1	chr10	80348358	80348367	-	1	NA	promoter-TSS (NM_001285435)	promoter-TSS (NM_001285435)	86	NM_001285435	66548	Mm.71891	NM_025629	ENSMUSG00000043822	Adamtsl5	2010109H09Rik|Thsd6	ADAMTS-like 5	protein-coding
mm_133679.1	chr16	92301267	92301323	+	1	NA	promoter-TSS (NM_138743)	promoter-TSS (NM_138743)	-8	NM_138743	68936	Mm.21698	NM_138743	ENSMUSG00000051989	Smim11	1190017O12Rik|C21orf51|Fam165b|Smim11a	small integral membrane protein 11	protein-coding
mm_143035.1	chr17	56626873	56626893	-	1	NA	promoter-TSS (NM_028782)	promoter-TSS (NM_028782)	20	NM_028782	74142	Mm.329136	NM_028782	ENSMUSG00000041168	Lonp1	1200017E13Rik|LON|Prss15	lon peptidase 1, mitochondrial	protein-coding
mm_153837.1	chr19	46327053	46327057	-	1	NA	promoter-TSS (NM_001347454)	promoter-TSS (NM_001347454)	101	NM_028627	73728	Mm.268532	NM_028627	ENSMUSG00000037126	Psd	1110007H17Rik|A930015K15|Efa6|Efa6a|Psdl|mKIAA2011	pleckstrin and Sec7 domain containing	protein-coding
mm_148541.1	chr19	4618433	4618449	+	1	NA	exon (NM_001162946, exon 14 of 21)	exon (NM_001162946, exon 14 of 21)	-2774	NM_153388	225875	Mm.329675	NM_153388	ENSMUSG00000045045	Lrfn4	BC023156|Salm3	leucine rich repeat and fibronectin type III domain containing 4	protein-coding
mm_42329.1	chr5	114901947	114901972	+	1	NA	intron (NM_011854, intron 3 of 5)	Lx|LINE|L1	5025	NM_011854	23962	Mm.228363	NM_011854	ENSMUSG00000029561	Oasl2	M1204|Mmu-OASL|Oasl	2'-5' oligoadenylate synthetase-like 2	protein-coding
mm_111874.1	chr12	108003595	108003613	-	1	NA	promoter-TSS (NM_021399)	promoter-TSS (NM_021399)	-190	NM_021399	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_164309.1	chr15	103897479	103897496	-	1	NA	exon (NM_009267, exon 3 of 4)	exon (NM_009267, exon 3 of 4)	1813	NM_009268	20771	Mm.30276	NM_009268		Mucl1	Spt-2|Spt2	mucin-like 1	protein-coding
mm_95041.1	chr11	32277294	32277304	+	1	NA	intron (NM_010405, intron 1 of 2)	intron (NM_010405, intron 1 of 2)	699	NM_010405	15126	Mm.141758	NM_010405	ENSMUSG00000055609	Hba-x	AI450015|Hbz	hemoglobin X, alpha-like embryonic chain in Hba complex	protein-coding
mm_64494.1	chr7	143458700	143458728	+	1	NA	3' UTR (NM_001161624, exon 4 of 4)	3' UTR (NM_001161624, exon 4 of 4)	2336	NM_009876	12577	Mm.168789	NM_009876	ENSMUSG00000037664	Cdkn1c	AL024410|CDKI|Kip2|p57(kip2)|p57Kip2	cyclin-dependent kinase inhibitor 1C (P57)	protein-coding
mm_19658.1	chr2	102968545	102968549	-	1	NA	Intergenic	Intergenic	-66882	NM_001039150	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_134039.1	chr16	5089783	5089794	-	1	NA	exon (NM_008909, exon 22 of 22)	exon (NM_008909, exon 22 of 22)	39720	NM_026666	170644	Mm.66356	NM_026666	ENSMUSG00000039473	Ubn1	1110029L11Rik|2610108L02Rik|AA673476|AW124741	ubinuclein 1	protein-coding
mm_137576.1	chr17	27907856	27907867	+	1	NA	promoter-TSS (NM_026836)	promoter-TSS (NM_026836)	-137	NM_026836	68776	Mm.267998	NM_026836	ENSMUSG00000024218	Taf11	1110038O14Rik|28kDa|AI115401|AL024207|AW552398|PRO214|TAF2I|TAFII28	TATA-box binding protein associated factor 11	protein-coding
mm_144870.1	chr18	36735118	36735177	+	1	NA	promoter-TSS (NM_028036)	promoter-TSS (NM_028036)	77	NM_028036	71983	Mm.135188	NM_028036	ENSMUSG00000006850	Tmco6	2410015B03Rik	transmembrane and coiled-coil domains 6	protein-coding
mm_123784.1	chr14	70331515	70331523	-	1	NA	intron (NM_001135151, intron 1 of 9)	intron (NM_001135151, intron 1 of 9)	16914	NM_001135152	213053	Mm.270647	NM_144808	ENSMUSG00000022094	Slc39a14	FAD-123|ZIP-14|Zip14|fad123	solute carrier family 39 (zinc transporter), member 14	protein-coding
mm_32051.1	chr4	97581962	97581980	+	1	NA	promoter-TSS (NM_001122952)	promoter-TSS (NM_001122952)	28	NM_001122952	18027	Mm.31274	NM_010905	ENSMUSG00000028565	Nfia	1110047K16Rik|9430022M17Rik|CTF|NF1-A|NF1A	nuclear factor I/A	protein-coding
mm_162079.1	chrX	26051041	26051041	-	1	NA	promoter-TSS (NM_001025607)	promoter-TSS (NM_001025607)	0	NM_001025607	382275	Mm.370361	NM_001025607	ENSMUSG00000079655	Gm5168	EG382275	predicted gene 5168	protein-coding
mm_155817.1	chrX	100524871	100524881	+	1	NA	promoter-TSS (NM_001114084)	promoter-TSS (NM_001114084)	38	NM_001114084	668257	Mm.95646	NM_001114084	ENSMUSG00000067597	Dgat2l6	9930021F22Rik	diacylglycerol O-acyltransferase 2-like 6	protein-coding
mm_111941.1	chr12	108894117	108894170	-	1	NA	promoter-TSS (NM_177602)	promoter-TSS (NM_177602)	31	NM_001164314	22375	Mm.38433	NM_011710	ENSMUSG00000021266	Wars	TrpRS|WRS	tryptophanyl-tRNA synthetase	protein-coding
mm_112156.1	chr12	113307086	113307105	-	1	NA	Intergenic	Intergenic	121192	NM_153776	69195	Mm.313244	NM_153776	ENSMUSG00000049036	Tmem121	2410008J05Rik|Hole	transmembrane protein 121	protein-coding
mm_148179.1	chr18	78179164	78179176	-	1	NA	promoter-TSS (NM_001110273)	promoter-TSS (NM_001110273)	2	NM_001110273	27411	Mm.44158	NM_030683	ENSMUSG00000024552	Slc14a2	UT-A1|UT-A3	solute carrier family 14 (urea transporter), member 2	protein-coding
mm_62241.1	chr7	98703299	98703312	+	1	NA	promoter-TSS (NM_028410)	promoter-TSS (NM_028410)	-58	NM_028410	72981	Mm.4428	NM_028410	ENSMUSG00000030753	Thap12	2900052B10Rik|Dap4|Prkrir|Rpkrir	THAP domain containing 12	protein-coding
mm_170499.1	chr19	24290120	24290129	-	1	NA	Intergenic	(CCA)n|Simple_repeat|Simple_repeat	-9538	NM_008044	14297	Mm.7319	NM_008044	ENSMUSG00000059363	Fxn	FA|FARR|Frda|X25	frataxin	protein-coding
mm_149141.1	chr19	9003874	9003884	+	1	NA	exon (NM_009643, exon 5 of 5)	exon (NM_009643, exon 5 of 5)	-14025	NR_105786	102465190		NR_105786	ENSMUSG00000099308	Mir6367	Gm27467|mmu-mir-6367	microRNA 6367	ncRNA
mm_83244.1	chr9	42399883	42399895	-	1	NA	promoter-TSS (NM_001324548)	promoter-TSS (NM_001324548)	40	NM_009347	21683	Mm.42209	NM_009347	ENSMUSG00000037705	Tecta	Tctna	tectorin alpha	protein-coding
mm_111879.1	chr12	108004057	108004085	-	1	NA	promoter-TSS (NM_021399)	promoter-TSS (NM_021399)	-657	NM_021399	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_92925.1	chr10	84440652	84440658	-	1	NA	promoter-TSS (NM_001004363)	promoter-TSS (NM_001004363)	-184	NM_001004363	77976	Mm.25874	NM_001004363	ENSMUSG00000020032	Nuak1	AU014801|AW494241|B230104P22Rik|Omphk1	NUAK family, SNF1-like kinase, 1	protein-coding
mm_113560.1	chr13	38151722	38151754	+	1	NA	exon (NM_023842, exon 1 of 24)	exon (NM_023842, exon 1 of 24)	444	NM_023842	109620	Mm.355327	NM_023842	ENSMUSG00000054889	Dsp	2300002E22Rik|5730453H04Rik|AA407887|AA407888|AW109828|DP|rul	desmoplakin	protein-coding
mm_128816.1	chr15	67113910	67113946	-	1	NA	5' UTR (NM_009177, exon 4 of 9)	5' UTR (NM_009177, exon 4 of 9)	62954	NM_009177	20442	Mm.248334	NM_009177	ENSMUSG00000013846	St3gal1	5330418N22Rik|AI467004|ST3GalI|Siat4|Siat4a|St3gal-1	ST3 beta-galactoside alpha-2,3-sialyltransferase 1	protein-coding
mm_34349.1	chr4	144529262	144529268	+	1	NA	TTS (NM_198662)	TTS (NM_198662)	9443	NM_198662	381572	Mm.184290	NM_198662	ENSMUSG00000028593	9430007A20Rik	Aadacl4|Gm1034	RIKEN cDNA 9430007A20 gene	protein-coding
mm_23921.1	chr3	83055595	83055609	+	1	NA	promoter-TSS (NM_016784)	promoter-TSS (NM_016784)	64	NM_016784	53317	Mm.286349	NM_016784	ENSMUSG00000027998	Plrg1	AA958940|C80566|Tango4	pleiotropic regulator 1	protein-coding
mm_124785.1	chr15	7810042	7810056	+	1	NA	promoter-TSS (NM_010275)	promoter-TSS (NM_010275)	1	NM_001301332	14573	Mm.4679	NM_010275	ENSMUSG00000022144	Gdnf	AI385739|ATF	glial cell line derived neurotrophic factor	protein-coding
mm_85124.1	chr9	95489856	95489877	-	1	NA	exon (NM_001114977, exon 12 of 28)	exon (NM_001114977, exon 12 of 28)	22130	NM_026476	67958	Mm.292742	NM_026476	ENSMUSG00000032407	U2surp	2610101N10Rik|AU023006|Sr140	U2 snRNP-associated SURP domain containing	protein-coding
mm_142552.1	chr17	46629405	46629419	-	1	NA	promoter-TSS (NM_175168)	promoter-TSS (NM_175168)	92	NM_175168	71461	Mm.181833	NM_175168	ENSMUSG00000023972	Ptk7	8430404F20Rik|chz|mPTK7/CCK4	PTK7 protein tyrosine kinase 7	protein-coding
mm_13951.1	chr2	121300943	121300956	+	1	NA	exon (NM_001173506, exon 4 of 6)	exon (NM_001173506, exon 4 of 6)	5495	NM_001173506	17754	Mm.36501	NM_032393	ENSMUSG00000027254	Map1a	6330416M19Rik|AI853608|Mtap-1|Mtap1|Mtap1a|moth1	microtubule-associated protein 1 A	protein-coding
mm_133158.1	chr16	70401783	70401798	+	1	NA	exon (NM_028803, exon 3 of 16)	exon (NM_028803, exon 3 of 16)	87841	NM_028803	74185	Mm.396102	NM_028803	ENSMUSG00000022707	Gbe1	2310045H19Rik|2810426P10Rik|D16Ertd536e	glucan (1,4-alpha-), branching enzyme 1	protein-coding
mm_65968.1	chr7	30437018	30437062	-	1	NA	intron (NM_007467, intron 11 of 16)	intron (NM_007467, intron 11 of 16)	8542	NM_007467	11803	Mm.2381	NM_007467	ENSMUSG00000006651	Aplp1	-	amyloid beta (A4) precursor-like protein 1	protein-coding
mm_20989.1	chr2	152185704	152185714	-	1	NA	Intergenic	Intergenic	-41131	NM_007788	12995	Mm.23692	NM_007788	ENSMUSG00000074698	Csnk2a1	Csnk2a1-rs4	casein kinase 2, alpha 1 polypeptide	protein-coding
mm_147169.1	chr18	36726593	36726615	-	1	NA	5' UTR (NM_009841, exon 1 of 2)	5' UTR (NM_009841, exon 1 of 2)	211	NM_009841	12475	Mm.3460	NM_009841	ENSMUSG00000051439	Cd14	-	CD14 antigen	protein-coding
mm_105935.1	chr11	115133982	115133996	-	1	NA	promoter-TSS (NM_001169153)	promoter-TSS (NM_001169153)	3	NM_001347648	246746	Mm.277387	NM_145634	ENSMUSG00000047798	Cd300lf	CLIM1|CLM-1|CLM1|Digr2|F730004D16Rik|IREM1|IgSF13|LMIR3|Pigr3	CD300 molecule like family member F	protein-coding
mm_158885.1	chr1	10216563	10216563	-	1	NA	intron (NM_001102430, intron 1 of 37)	intron (NM_001102430, intron 1 of 37)	16107	NM_001102430	211673	Mm.229141	NM_001102430	ENSMUSG00000067851	Arfgef1	ARFGEP1|BIG1|D130059B05Rik|D730028O18Rik|P200	ADP-ribosylation factor guanine nucleotide-exchange factor 1(brefeldin A-inhibited)	protein-coding
mm_96310.1	chr11	63158758	63158783	+	1	NA	3' UTR (NM_008885, exon 5 of 5)	3' UTR (NM_008885, exon 5 of 5)	25967	NM_001302260	18858	Mm.1237	NM_008885	ENSMUSG00000018217	Pmp22	22kDa|Gas-3|HNPP|Tr|trembler	peripheral myelin protein 22	protein-coding
mm_98032.1	chr11	85311347	85311395	+	1	NA	5' UTR (NM_016910, exon 1 of 6)	5' UTR (NM_016910, exon 1 of 6)	117	NM_016910	53892	Mm.45609	NM_016910	ENSMUSG00000020525	Ppm1d	AV338790|Wip1	protein phosphatase 1D magnesium-dependent, delta isoform	protein-coding
mm_154999.1	chrX	38607319	38607321	+	1	NA	intron (NM_026902, intron 4 of 5)	PB1D9|SINE|Alu	6662	NM_026902	68995	Mm.262453	NM_026902	ENSMUSG00000000355	Mcts1	1500019M23Rik|MCT-1	malignant T cell amplified sequence 1	protein-coding
mm_1876.1	chr1	85608490	85608514	+	1	NA	intron (NM_001013817, intron 1 of 16)	intron (NM_001013817, intron 1 of 16)	-4611	NM_175397	109032	Mm.335802	NM_030194	ENSMUSG00000070034	Sp110	5031415C07Rik|52kDa|5830484A20Rik|ENSMUSG00000075603|Ifi75|Ipr1	Sp110 nuclear body protein	protein-coding
mm_123722.1	chr14	70153386	70153464	-	1	NA	TTS (NM_001112735)	TTS (NM_001112735)	366	NM_146055	219158	Mm.218284	NM_146055	ENSMUSG00000033712	Ccar2	2610301G19Rik|Dbc1|mKIAA1967	cell cycle activator and apoptosis regulator 2	protein-coding
mm_94179.1	chr10	128919249	128919253	-	1	NA	promoter-TSS (NM_134006)	promoter-TSS (NM_134006)	46	NM_134006	19682	Mm.439856	NM_134006	ENSMUSG00000025350	Rdh5	9-cis|AI987873|RDH4|cRDH	retinol dehydrogenase 5	protein-coding
mm_35200.1	chr4	19122512	19122524	-	1	NA	Intergenic	Intergenic	-158332	NM_013927	30952	Mm.445778	NM_013927	ENSMUSG00000056494	Cngb3	CCNC2|CNG6|Cngbeta2	cyclic nucleotide gated channel beta 3	protein-coding
mm_42386.1	chr5	114935976	114935986	+	1	NA	exon (NM_145209, exon 6 of 7)	exon (NM_145209, exon 6 of 7)	-6221	NM_028211	72357	Mm.292672	NM_028211	ENSMUSG00000029559	2210016L21Rik	-	RIKEN cDNA 2210016L21 gene	protein-coding
mm_116883.1	chr13	55182559	55182565	-	1	NA	Intergenic	Intergenic	-27220	NM_008739	18193	Mm.12964	NM_008739	ENSMUSG00000021488	Nsd1	AI528500|KMT3B	nuclear receptor-binding SET-domain protein 1	protein-coding
mm_7182.1	chr1	92717167	92717181	-	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-68333	NM_153114	260301	Mm.219545	NM_153114	ENSMUSG00000044055	Otos	OTOSP	otospiralin	protein-coding
mm_93962.1	chr10	127288434	127288460	-	1	NA	intron (NM_033072, intron 1 of 12)	intron (NM_033072, intron 1 of 12)	571	NM_001347171	110962	Mm.372826	NM_033072	ENSMUSG00000025409	Mbd6	D10Wsu93e	methyl-CpG binding domain protein 6	protein-coding
mm_70224.1	chr7	145208099	145208129	-	1	NA	promoter-TSS (NR_033626)	promoter-TSS (NR_033626)	5	NR_033626	100040049	Mm.102235	NR_033626	ENSMUSG00000109305	1810010D01Rik	Gm2572	RIKEN cDNA 1810010D01 gene	ncRNA
mm_149401.1	chr19	11390327	11390347	+	1	NA	exon (NM_001310331, exon 6 of 7)	exon (NM_001310331, exon 6 of 7)	14849	NM_001310331	666907		NM_001310331	ENSMUSG00000101389	Ms4a4a	EG666907	membrane-spanning 4-domains, subfamily A, member 4A	protein-coding
mm_131081.1	chr16	4741544	4741592	+	1	NA	promoter-TSS (NM_010443)	promoter-TSS (NM_010443)	-45	NM_010443	15369	Mm.272866	NM_010443	ENSMUSG00000004070	Hmox2	HO-2|HO2	heme oxygenase 2	protein-coding
mm_154665.1	chrX	7878299	7878314	+	1	NA	promoter-TSS (NM_138606)	promoter-TSS (NM_138606)	0	NM_138606	18715	Mm.347478	NM_138606	ENSMUSG00000031155	Pim2	DXCch3|Pim-2	proviral integration site 2	protein-coding
mm_76703.1	chr8	94532906	94532917	-	1	NA	promoter-TSS (NM_153507)	promoter-TSS (NM_153507)	-117	NM_153507	234577	Mm.291815	NM_153507	ENSMUSG00000034361	Cpne2	3322401K10Rik	copine II	protein-coding
mm_57116.1	chr6	122596569	122596593	-	1	NA	intron (NM_031159, intron 3 of 7)	intron (NM_031159, intron 3 of 7)	5863	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_31361.1	chr4	47242396	47242404	+	1	NA	intron (NM_009928, intron 2 of 39)	intron (NM_009928, intron 2 of 39)	34388	NM_009928	12819	Mm.233547	NM_009928	ENSMUSG00000028339	Col15a1	-	collagen, type XV, alpha 1	protein-coding
mm_28366.1	chr3	89891467	89891478	-	1	NA	intron (NM_001310676, intron 1 of 9)	intron (NM_001310676, intron 1 of 9)	21724	NM_001310676	16194	Mm.2856	NM_010559	ENSMUSG00000027947	Il6ra	CD126|IL-6R|IL-6R-alpha|IL-6RA|Il6r	interleukin 6 receptor, alpha	protein-coding
mm_22375.1	chr2	181156007	181156050	-	1	NA	intron (NM_007906, intron 1 of 7)	intron (NM_007906, intron 1 of 7)	987	NM_007906	13628	Mm.2645	NM_007906	ENSMUSG00000016349	Eef1a2	Eef1a|S1|wasted|wst	eukaryotic translation elongation factor 1 alpha 2	protein-coding
mm_39030.1	chr4	152178037	152178076	-	1	NA	promoter-TSS (NM_133348)	promoter-TSS (NM_133348)	-44	NM_133348	70025	Mm.296191	NM_133348	ENSMUSG00000028937	Acot7	2410041A17Rik|Ach1|Act|Bach|CTE-IIa|Cte-II|Lach1	acyl-CoA thioesterase 7	protein-coding
mm_158858.1	chrY	818647	818656	+	1	NA	promoter-TSS (NM_011667)	promoter-TSS (NM_011667)	-62	NM_011667	22202	Mm.422949	NM_011667	ENSMUSG00000069053	Uba1y	A1s9Y-1|Sby|Ube-2|Ube1ay|Ube1y|Ube1y-1|Ube1y1	ubiquitin-activating enzyme, Chr Y	protein-coding
mm_146446.1	chr18	85071834	85071859	+	1	NA	Intergenic	Intergenic	-120322	NM_025969	67105	Mm.250617	NM_025969	ENSMUSG00000024645	Timm21	1700034H14Rik|2700002I20Rik	tranlocase of inner mitochondrial membrane 21	protein-coding
mm_145290.1	chr18	53245663	53245673	+	1	NA	promoter-TSS (NM_029394)	promoter-TSS (NM_029394)	6	NM_029394	69226	Mm.32414	NM_029394	ENSMUSG00000024535	Snx24	2810011K15Rik|5730433I16Rik|AI451341	sorting nexing 24	protein-coding
mm_76667.1	chr8	93379818	93379825	-	1	NA	Intergenic	Intergenic	-42612	NM_021456	12623	Mm.22720	NM_021456	ENSMUSG00000057074	Ces1g	Ces-1|Ces1|Ses-1	carboxylesterase 1G	protein-coding
mm_96635.1	chr11	69325560	69325584	+	1	NA	promoter-TSS (NM_010599)	promoter-TSS (NM_010599)	-686	NM_010599	16499	Mm.232472	NM_010599	ENSMUSG00000018470	Kcnab3	C330022D06Rik|Kcnab4|mKv(beta)4	potassium voltage-gated channel, shaker-related subfamily, beta member 3	protein-coding
mm_84806.1	chr9	77261500	77261507	-	1	NA	intron (NM_027150, intron 1 of 7)	intron (NM_027150, intron 1 of 7)	86367	NM_027150	69642	Mm.35008	NM_027150	ENSMUSG00000032355	Mlip	2310046A06Rik|AI931782|CIP	muscular LMNA-interacting protein	protein-coding
mm_99856.1	chr11	109365031	109365061	+	1	NA	intron (NM_010303, intron 1 of 3)	intron (NM_010303, intron 1 of 3)	-1392	NR_038097	100036768	Mm.467767	NR_038097	ENSMUSG00000056687	Gm11696	OTTMUSG00000003456	predicted gene 11696	ncRNA
mm_47585.1	chr5	124861864	124861871	-	1	NA	promoter-TSS (NM_001081750)	promoter-TSS (NM_001081750)	354	NM_144819	215707	Mm.389693	NM_144819	ENSMUSG00000037979	Ccdc92	AW050178|D5Bwg0834e	coiled-coil domain containing 92	protein-coding
mm_49746.1	chr6	34746030	34746042	+	1	NA	intron (NM_001347100, intron 5 of 13)	intron (NM_001347100, intron 5 of 13)	-34396	NM_001289657	76223	Mm.150047	NM_178630	ENSMUSG00000038836	Agbl3	2900053G10Rik|4930431N21Rik|6530406M24Rik|CCP3	ATP/GTP binding protein-like 3	protein-coding
mm_25394.1	chr3	107219626	107219631	+	1	NA	exon (NM_001111143, exon 2 of 9)	exon (NM_001111143, exon 2 of 9)	2104	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_141760.1	chr17	34267466	34267475	-	1	NA	exon (NM_207105, exon 3 of 6)	exon (NM_207105, exon 3 of 6)	4243	NM_207105	14961	Mm.254067	NM_207105	ENSMUSG00000073421	H2-Ab1	AI845868|Abeta|H-2Ab|H2-Ab|I-Abeta|IAb|Ia-2|Ia2|Rmcs1	histocompatibility 2, class II antigen A, beta 1	protein-coding
mm_56233.1	chr6	90662100	90662119	-	1	NA	3' UTR (NM_001134384, exon 14 of 14)	3' UTR (NM_001134384, exon 14 of 14)	42863	NM_001037493	71699	Mm.272633	NM_027868	ENSMUSG00000030089	Slc41a3	1010001P06Rik|AI480742|SLC41A1-L2	solute carrier family 41, member 3	protein-coding
mm_92011.1	chr10	62340515	62340549	-	1	NA	promoter-TSS (NM_001146100)	promoter-TSS (NM_001146100)	-75	NR_038038	70162	Mm.441212	NR_038038		Hk1os	2210417K05Rik	hexokinase 1, opposite strand	ncRNA
mm_90167.1	chr10	119453539	119453608	+	1	NA	promoter-TSS (NM_001277293)	promoter-TSS (NM_001277293)	-461	NM_133442	74053	Mm.196692	NM_028736	ENSMUSG00000034813	Grip1	4931400F03Rik|GRIP|eb	glutamate receptor interacting protein 1	protein-coding
mm_64875.1	chr7	14438539	14438558	-	1	NA	promoter-TSS (NM_001199306)	promoter-TSS (NM_001199306)	3	NM_001199306	76971	Mm.290727	NM_175250	ENSMUSG00000030378	Sult2a8	2810007J24Rik	sulfotransferase family 2A, dehydroepiandrosterone (DHEA)-preferring, member 8	protein-coding
mm_21239.1	chr2	156152807	156152811	-	1	NA	intron (NM_133242, intron 13 of 16)	intron (NM_133242, intron 13 of 16)	8576	NM_025946	67067	Mm.371623	NM_025946	ENSMUSG00000067847	Romo1	2010100O12Rik|AI853864	reactive oxygen species modulator 1	protein-coding
mm_54475.1	chr6	34910870	34910887	-	1	NA	promoter-TSS (NM_001013366)	promoter-TSS (NM_001013366)	-47	NM_001013366	101240	Mm.152120	NM_001013366	ENSMUSG00000058486	Wdr91	9530020G05Rik|AI987683|AU018665	WD repeat domain 91	protein-coding
mm_113376.1	chr13	33004597	33004609	+	1	NA	promoter-TSS (NM_009256)	promoter-TSS (NM_009256)	62	NM_009256	20723	Mm.245041	NM_009256	ENSMUSG00000045827	Serpinb9	BB283241|CAP-3|CAP3|PI-9|PI9|Spi6|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 9	protein-coding
mm_136875.1	chr17	12991851	12991900	+	1	NA	intron (NM_175394, intron 1 of 5)	CpG	384	NM_001113533	60532	Mm.275521	NM_175394	ENSMUSG00000060475	Wtap	2810408K05Rik|9430038B09Rik	Wilms tumour 1-associating protein	protein-coding
mm_26802.1	chr3	9886726	9886732	-	1	NA	Intergenic	MIR|SINE|MIR	-53050	NM_001195031	94212	Mm.23897	NM_053182	ENSMUSG00000027508	Pag1	Cbp|F730007C19Rik|Pag	phosphoprotein associated with glycosphingolipid microdomains 1	protein-coding
mm_123471.1	chr14	65974862	65974894	-	1	NA	exon (NM_013492, exon 4 of 9)	exon (NM_013492, exon 4 of 9)	6395	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_131473.1	chr16	17070248	17070254	+	1	NA	5' UTR (NM_023249, exon 1 of 5)	5' UTR (NM_023249, exon 1 of 5)	112	NM_001291047	106369	Mm.237941	NM_023249	ENSMUSG00000022773	Ypel1	0610009L05Rik|1700016N17Rik|1700019O22Rik|4921520K19Rik|4930511F14Rik|AV118478|DGL-1|Dgl1|Ppil2|mdgl-1	yippee-like 1 (Drosophila)	protein-coding
mm_128637.1	chr15	59269790	59269794	-	1	NA	Intergenic	Intergenic	-37156	NR_045613	100416830	Mm.490788	NR_045613	ENSMUSG00000098528	Zfp572	4930472F24Rik	zinc finger protein 572	pseudo
mm_86977.1	chr10	25432477	25432517	+	1	NA	intron (NM_013511, intron 1 of 19)	intron (NM_013511, intron 1 of 19)	24129	NM_013511	13822	Mm.306026	NM_013511	ENSMUSG00000019978	Epb41l2	4.1G|AW555191|D10Ertd398e|Epb4.1l2|NBL2	erythrocyte membrane protein band 4.1 like 2	protein-coding
mm_58956.1	chr7	18840012	18840020	+	1	NA	promoter-TSS (NM_153761)	promoter-TSS (NM_153761)	50	NM_153760	243864	Mm.233503	NM_153760	ENSMUSG00000040987	Mill2	Micb	MHC I like leukocyte 2	protein-coding
mm_119828.1	chr14	54268721	54268724	+	1	NA	3' UTR (NM_001205181, exon 7 of 7)	3' UTR (NM_001205181, exon 7 of 7)	9490	NM_134076	105501	Mm.28771	NM_134076	ENSMUSG00000040997	Abhd4	1110035H23Rik|AI429574|Abh4	abhydrolase domain containing 4	protein-coding
mm_14710.1	chr2	143368737	143368738	+	1	NA	Intergenic	Lx2B2|LINE|L1	-177396	NM_008792	18549	Mm.294493	NM_008792	ENSMUSG00000027419	Pcsk2	6330411F23Rik|AI839700|Nec-2|Nec2|PC2|Phpp-2|SPC2	proprotein convertase subtilisin/kexin type 2	protein-coding
mm_157176.1	chrX	9655610	9655621	-	1	NA	3' UTR (NM_025975, exon 5 of 5)	3' UTR (NM_025975, exon 5 of 5)	7368	NM_025975	67117	Mm.29150	NM_025975	ENSMUSG00000031176	Dynlt3	2310075M16Rik|AU042796|Tcte1l	dynein light chain Tctex-type 3	protein-coding
mm_12090.1	chr2	60248209	60248227	+	1	NA	3' UTR (NM_020575, exon 10 of 10)	3' UTR (NM_020575, exon 10 of 10)	36266	NM_025422	66205	Mm.227281	NM_025422	ENSMUSG00000060703	Cd302	1110055L24Rik|AI159627	CD302 antigen	protein-coding
mm_40149.1	chr5	35388928	35388932	+	1	NA	promoter-TSS (NM_010445)	promoter-TSS (NM_010445)	-187	NM_010445	15371	Mm.358606	NM_010445	ENSMUSG00000067438	Hmx1	Nkx5-3	H6 homeobox 1	protein-coding
mm_40202.1	chr5	37028318	37028328	+	1	NA	Intergenic	CpG	-22534	NM_178394	76071	Mm.85280	NM_178394	ENSMUSG00000063646	Jakmip1	5830437M04Rik|C330021K24Rik|Gababrbp|Marlin-1	janus kinase and microtubule interacting protein 1	protein-coding
mm_68789.1	chr7	123358546	123358569	-	1	NA	intron (NM_001122641, intron 1 of 18)	intron (NM_001122641, intron 1 of 18)	11358	NM_001122643	70497	Mm.403318	NM_144529	ENSMUSG00000030766	Arhgap17	5730403H17Rik|Nadrin|Nadrin2|Rich1|Wbp15	Rho GTPase activating protein 17	protein-coding
mm_149492.1	chr19	11819037	11819042	+	1	NA	5' UTR (NM_001286543, exon 1 of 12)	5' UTR (NM_001286543, exon 1 of 12)	364	NM_001286543	20908	Mm.272264	NM_011502	ENSMUSG00000041488	Stx3	Syn-3	syntaxin 3	protein-coding
mm_18816.1	chr2	74578876	74578954	-	1	NA	promoter-TSS (NM_027133)	promoter-TSS (NM_027133)	33	NM_001110209	69605	Mm.156113	NM_027133	ENSMUSG00000009207	Lnpk	2310011O18Rik|4921514L11Rik|9530051D01Rik|AI666268|Lnp|Lnpk1|Ul|ulnaless	lunapark, ER junction formation factor	protein-coding
mm_87288.1	chr10	42502037	42502041	+	1	NA	promoter-TSS (NM_017472)	promoter-TSS (NM_017472)	-15	NM_017472	54198	Mm.277870	NM_017472	ENSMUSG00000019804	Snx3	SDP3	sorting nexin 3	protein-coding
mm_84490.1	chr9	66846361	66846383	-	1	NA	3' UTR (NM_173413, exon 8 of 8)	3' UTR (NM_173413, exon 8 of 8)	-11666	NM_026674	68318	Mm.284229	NM_026674	ENSMUSG00000053040	Aph1c	0610008A10Rik|APH-1b|Aph1b	aph1 homolog C, gamma secretase subunit	protein-coding
mm_41850.1	chr5	104439295	104439311	+	1	NA	exon (NM_001204203, exon 6 of 7)	exon (NM_001204203, exon 6 of 7)	3111	NM_001204233	20750	Mm.288474	NM_009263	ENSMUSG00000029304	Spp1	2AR|Apl-1|BNSP|BSPI|Bsp|ETA-1|Eta|OP|Opn|Opnl|Ric|Spp-1	secreted phosphoprotein 1	protein-coding
mm_83435.1	chr9	44999179	44999209	-	1	NA	3' UTR (NM_007648, exon 8 of 8)	3' UTR (NM_007648, exon 8 of 8)	10396	NM_007648	12501	Mm.210361	NM_007648	ENSMUSG00000032093	Cd3e	AI504783|CD3|CD3epsilon|T3e	CD3 antigen, epsilon polypeptide	protein-coding
mm_107333.1	chr12	32246294	32246303	+	1	NA	Intergenic	Intergenic	-37649	NM_001146200	30955	Mm.101369	NM_020272	ENSMUSG00000020573	Pik3cg	5830428L06Rik|PI3Kgamma|p110gamma	phosphoinositide-3-kinase, catalytic, gamma polypeptide	protein-coding
mm_79270.1	chr9	50754211	50754222	+	1	NA	intron (NM_009964, intron 1 of 2)	intron (NM_009964, intron 1 of 2)	1245	NM_009964	12955	Mm.178	NM_009964	ENSMUSG00000032060	Cryab	Crya-2|Crya2|HspB5|P23	crystallin, alpha B	protein-coding
mm_117934.1	chr13	99434465	99434475	-	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-21644	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_128331.1	chr15	38300661	38300671	-	1	NA	promoter-TSS (NM_013692)	promoter-TSS (NM_013692)	45	NM_013692	21847	Mm.4292	NM_013692	ENSMUSG00000037465	Klf10	AI115143|EGR[a]|Egral|Gdnfif|TIEG-1|Tieg|Tieg1|mGIF	Kruppel-like factor 10	protein-coding
mm_47380.1	chr5	122989284	122989338	-	1	NA	promoter-TSS (NM_001003953)	promoter-TSS (NM_001003953)	-43	NR_045820	109202	Mm.30769	NM_175405	ENSMUSG00000056735	A930024E05Rik	-	RIKEN cDNA A930024E05 gene	ncRNA
mm_135272.1	chr16	38400075	38400089	-	1	NA	intron (NM_134102, intron 9 of 10)	intron (NM_134102, intron 9 of 10)	33063	NM_134102	85031	Mm.279805	NM_134102	ENSMUSG00000002847	Pla1a	AA986889|Ps-pla1|Pspla1	phospholipase A1 member A	protein-coding
mm_23458.1	chr3	60472681	60472687	+	1	NA	promoter-TSS (NM_001253713)	promoter-TSS (NM_001253713)	-146	NM_001253713	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_81818.1	chr9	118040659	118040669	+	1	NA	5' UTR (NM_013727, exon 1 of 8)	5' UTR (NM_013727, exon 1 of 8)	142	NM_013727	27215	Mm.92705	NM_013727	ENSMUSG00000039285	Azi2	AA410145|AZ2	5-azacytidine induced gene 2	protein-coding
mm_60456.1	chr7	44477610	44477618	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-6903	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_22796.1	chr3	22251370	22251374	+	1	NA	promoter-TSS (NR_004439)	promoter-TSS (NR_004439)	2	NR_004439	19784		NR_004439		Rprl2	RPRH3|Rmrp3	ribonuclease P RNA-like 2	ncRNA
mm_24300.1	chr3	89367513	89367591	+	1	NA	Intergenic	Intergenic	-2299	NM_029974	77772	Mm.164013	NM_029974	ENSMUSG00000042672	Dcst1	A330106H01Rik	DC-STAMP domain containing 1	protein-coding
mm_142151.1	chr17	36020529	36020570	-	1	NA	promoter-TSS (NM_008207)	promoter-TSS (NM_008207)	11	NM_008207	15042	Mm.439654	NM_008207	ENSMUSG00000053835	H2-T24	H-2T24	histocompatibility 2, T region locus 24	protein-coding
mm_13171.1	chr2	92915052	92915066	+	1	NA	promoter-TSS (NM_030725)	promoter-TSS (NM_030725)	-42	NM_030725	80976	Mm.33490	NM_030725	ENSMUSG00000027220	Syt13	5730409J20Rik|AI549909|mKIAA1427	synaptotagmin XIII	protein-coding
mm_54523.1	chr6	35994653	35994655	-	1	NA	Intergenic	Intergenic	-393430	NM_203491	243764	Mm.448632	NM_203491	ENSMUSG00000045613	Chrm2	AChR-M2|Chrm-2|M2	cholinergic receptor, muscarinic 2, cardiac	protein-coding
mm_6922.1	chr1	84840466	84840479	-	1	NA	intron (NM_025386, intron 1 of 3)	intron (NM_025386, intron 1 of 3)	631	NM_025386	66153	Mm.381192	NM_025386	ENSMUSG00000073633	Fbxo36	0610008D19Rik|1110020F21Rik|2410002G19Rik|D1Ertd757e	F-box protein 36	protein-coding
mm_37703.1	chr4	129377827	129377838	-	1	NA	5' UTR (NM_028603, exon 1 of 5)	5' UTR (NM_028603, exon 1 of 5)	196	NM_028603	73680	Mm.32997	NM_028603	ENSMUSG00000028807	Zbtb8a	2410081M15Rik|AI480941	zinc finger and BTB domain containing 8a	protein-coding
mm_100927.1	chr11	6475451	6475470	-	1	NA	exon (NM_011221, exon 1 of 1)	exon (NM_011221, exon 1 of 1)	616	NM_011221	19291	Mm.296150	NM_011221	ENSMUSG00000094483	Purb	2310015K15Rik|AA114818|Cager-2|D11Bwg0414e	purine rich element binding protein B	protein-coding
mm_132840.1	chr16	45786980	45786988	+	1	NA	intron (NM_001252442, intron 6 of 18)	intron (NM_001252442, intron 6 of 18)	-44029	NM_172511	213012	Mm.247453	NM_172511	ENSMUSG00000033157	Abhd10	-	abhydrolase domain containing 10	protein-coding
mm_54336.1	chr6	30643025	30643057	-	1	NA	exon (NM_025350, exon 8 of 10)	exon (NM_025350, exon 8 of 10)	3823	NM_025350	109697	Mm.25377	NM_025350	ENSMUSG00000054446	Cpa1	0910001L12Rik|Cpa	carboxypeptidase A1, pancreatic	protein-coding
mm_63506.1	chr7	127841858	127841865	+	1	NA	promoter-TSS (NM_009294)	promoter-TSS (NM_009294)	53	NM_009294	20909	Mm.24867	NM_009294	ENSMUSG00000030805	Stx4a	Stx4|Syn-4|Syn4	syntaxin 4A (placental)	protein-coding
mm_23936.1	chr3	84180589	84180612	+	1	NA	intron (NM_001271725, intron 6 of 11)	RMER10B|LTR|ERVL	5962	NR_036654	624713	Mm.442604	NR_036654		Gm6525	EG624713	ribosomal protein L36a pseudogene	pseudo
mm_36575.1	chr4	88001711	88001732	-	1	NA	intron (NM_027326, intron 2 of 10)	intron (NM_027326, intron 2 of 10)	31686	NM_027326	70122	Mm.288898	NM_027326	ENSMUSG00000028496	Mllt3	2210011H10Rik|2610012I03Rik|3830408D16Rik|Af9|D4Ertd321e	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 3	protein-coding
mm_9282.1	chr1	171634567	171634589	-	1	NA	3' UTR (NM_144539, exon 8 of 8)	3' UTR (NM_144539, exon 8 of 8)	7322	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_60013.1	chr7	30737960	30737988	+	1	NA	exon (NM_001290631, exon 2 of 11)	exon (NM_001290631, exon 2 of 11)	1433	NM_008085	14447	Mm.436562	NM_008085	ENSMUSG00000061099	Gapdhs	Gapd-s|Gapds	glyceraldehyde-3-phosphate dehydrogenase, spermatogenic	protein-coding
mm_149447.1	chr19	11485889	11485904	+	1	NA	Intergenic	RMER19B2|LTR|ERVK	-6142	NM_001164202	666926	Mm.486382	NM_001164202	ENSMUSG00000058470	Gm8369	EG666926	predicted gene 8369	protein-coding
mm_131189.1	chr16	7224306	7224317	+	1	NA	exon (NM_183188, exon 2 of 13)	exon (NM_183188, exon 2 of 13)	154476	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_143940.1	chr17	86230417	86230423	-	1	NA	intron (NM_011104, intron 1 of 14)	intron (NM_011104, intron 1 of 14)	56758	NR_045435	72104	Mm.443401	NR_045435	ENSMUSG00000100738	2010106C02Rik	-	RIKEN cDNA 2010106C02 gene	ncRNA
mm_70254.1	chr8	3500531	3500548	+	1	NA	promoter-TSS (NM_053177)	promoter-TSS (NM_053177)	20	NM_053177	94178	Mm.8356	NM_053177	ENSMUSG00000004567	Mcoln1	2210015I05Rik|TRPML1|mucolipidin	mucolipin 1	protein-coding
mm_172458.1	chr7	40592087	40592088	+	1	NA	Intergenic	L1Md_F2|LINE|L1	-82650	NR_045504	71029	Mm.399496	NR_045504	ENSMUSG00000102004	4933402C06Rik	-	RIKEN cDNA 4933402C06 gene	ncRNA
mm_152737.1	chr19	19001100	19001119	-	1	NA	promoter-TSS (NM_001289921)	promoter-TSS (NM_001289921)	8	NM_146095	225998	Mm.234641	NM_146095	ENSMUSG00000036192	Rorb	Nr1f2|RZR-beta|RZRB|Rorbeta|hstp	RAR-related orphan receptor beta	protein-coding
mm_12754.1	chr2	79255344	79255399	+	1	NA	promoter-TSS (NM_010576)	promoter-TSS (NM_010576)	-55	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D|Itga4B	integrin alpha 4	protein-coding
mm_136533.1	chr16	97514813	97514828	-	1	NA	Intergenic	Intergenic	-9884	NM_020622	52793	Mm.327932	NM_020622	ENSMUSG00000022938	Fam3b	2-21|9030624C24Rik|D16Jhu19e|ORF9|Pander	family with sequence similarity 3, member B	protein-coding
mm_36982.1	chr4	109665250	109665278	-	1	NA	5' UTR (NM_007671, exon 1 of 2)	5' UTR (NM_007671, exon 1 of 2)	108	NM_007671	12580	Mm.1912	NM_007671	ENSMUSG00000028551	Cdkn2c	C77269|INK4c|p18|p18-INK4c|p18-INK6|p18INK4c	cyclin-dependent kinase inhibitor 2C (p18, inhibits CDK4)	protein-coding
mm_13298.1	chr2	102287383	102287390	+	1	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	-100926	NM_001290784	241576	Mm.489740	NM_178886	ENSMUSG00000048058	Ldlrad3	6430500P08|AI194318|Lrad3	low density lipoprotein receptor class A domain containing 3	protein-coding
mm_130753.1	chr15	101270498	101270506	-	1	NA	exon (NM_010444, exon 2 of 7)	exon (NM_010444, exon 2 of 7)	3656	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_50051.1	chr6	41177505	41177516	+	1	NA	Intergenic	Intergenic	-124762	NM_011646	22074	Mm.383263	NM_011646	ENSMUSG00000054106	Try4	0910001B19Rik|Td	trypsin 4	protein-coding
mm_59158.1	chr7	24370467	24370520	+	1	NA	exon (NM_001163510, exon 1 of 9)	exon (NM_001163510, exon 1 of 9)	230	NM_008433	16534	Mm.9911	NM_008433	ENSMUSG00000054342	Kcnn4	IK1|IKCA1|KCA4|KCa3.1|SK4|SKCas|mIKCa1	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4	protein-coding
mm_116366.1	chr13	40730868	40730879	-	1	NA	promoter-TSS (NM_001122948)	promoter-TSS (NM_001122948)	-416	NM_001122948	21418	Mm.85544	NM_011547	ENSMUSG00000021359	Tfap2a	AP-2|AP2alpha|Ap-2 (a)|Ap2|Ap2tf|Tcfap2a	transcription factor AP-2, alpha	protein-coding
mm_37250.1	chr4	118248918	118248942	-	1	NA	exon (NM_011213, exon 7 of 33)	exon (NM_011213, exon 7 of 33)	-38366	NR_106085	102466820		NR_106085	ENSMUSG00000098596	Mir7226	Gm27630|mmu-mir-7226	microRNA 7226	ncRNA
mm_150286.1	chr19	34313701	34313708	+	1	NA	intron (NM_007987, intron 2 of 8)	RMER1A|Other|Other	23045	NM_001146708	14102	Mm.1626	NM_007987	ENSMUSG00000024778	Fas	AI196731|APO1|APT1|CD95|TNFR6|Tnfrsf6|lpr	Fas (TNF receptor superfamily member 6)	protein-coding
mm_78277.1	chr9	22100270	22100284	+	1	NA	intron (NM_009922, intron 1 of 6)	intron (NM_009922, intron 1 of 6)	1024	NM_009922	12797	Mm.4356	NM_009922	ENSMUSG00000001349	Cnn1	CN|CnnI	calponin 1	protein-coding
mm_107259.1	chr12	28771498	28771503	+	1	NA	intron (NM_201357, intron 3 of 8)	intron (NM_201357, intron 3 of 8)	19672	NM_201357	380752	Mm.273724	NM_201357	ENSMUSG00000036613	Tssc1	D12Ertd604e|Eipr1	tumor suppressing subtransferable candidate 1	protein-coding
mm_18616.1	chr2	68471879	68471911	-	1	NA	promoter-TSS (NM_016866)	promoter-TSS (NM_016866)	86	NM_016866	53416	Mm.198414	NM_016866	ENSMUSG00000027030	Stk39	AW227544|AW556857|DCHT|RF005|Rnl5|SPAK	serine/threonine kinase 39	protein-coding
mm_37278.1	chr4	118791602	118791609	-	1	NA	Intergenic	Intergenic	-9019	NM_146309	258306	Mm.377426	NM_146309	ENSMUSG00000111159	Olfr1337	MOR259-10|Olfr219-ps1	olfactory receptor 1337	protein-coding
mm_70792.1	chr8	22564081	22564116	+	1	NA	exon (NM_011394, exon 9 of 11)	exon (NM_011394, exon 9 of 11)	29715	NM_001198998	22335	Mm.227704	NM_011696	ENSMUSG00000008892	Vdac3	-	voltage-dependent anion channel 3	protein-coding
mm_75533.1	chr8	57320387	57320399	-	1	NA	promoter-TSS (NM_010402)	promoter-TSS (NM_010402)	466	NR_110474	102636514		NR_110474	ENSMUSG00000100510	Uph	-	upperhand	ncRNA
mm_95051.1	chr11	32347801	32347865	+	1	NA	promoter-TSS (NM_177364)	promoter-TSS (NM_177364)	22	NM_177364	268396	Mm.227616	NM_177364	ENSMUSG00000040711	Sh3pxd2b	G431001E03Rik|TSK4|fad49	SH3 and PX domains 2B	protein-coding
mm_139719.1	chr17	57467301	57467316	+	1	NA	intron (NM_010130, intron 18 of 21)	Lx|LINE|L1	78006	NM_001104591	224916	Mm.469889	NM_001104591	ENSMUSG00000090655	Vmn2r120	EG224916	vomeronasal 2, receptor 120	protein-coding
mm_134292.1	chr16	14243914	14243924	-	1	NA	intron (NM_001161775, intron 8 of 40)	MER58B|DNA|hAT-Charlie	47489	NM_001161775	17880	Mm.250705	NM_013607	ENSMUSG00000018830	Myh11	AV071570|SM1|SM2|smMHC	myosin, heavy polypeptide 11, smooth muscle	protein-coding
mm_159687.1	chr5	14938477	14938477	-	1	NA	promoter-TSS (NM_001122661)	promoter-TSS (NM_001122661)	-2	NM_001122661	624245	Mm.368256	NM_001122661	ENSMUSG00000091255	Speer4e	-	spermatogenesis associated glutamate (E)-rich protein 4e	protein-coding
mm_52840.1	chr6	121644897	121644927	+	1	NA	exon (NM_175628, exon 9 of 36)	exon (NM_175628, exon 9 of 36)	8739	NM_175628	232345	Mm.30151	NM_175628	ENSMUSG00000030111	A2m	A2mp	alpha-2-macroglobulin	protein-coding
mm_93081.1	chr10	89533530	89533541	-	1	NA	promoter-TSS (NM_001163504)	promoter-TSS (NM_001163504)	87	NM_001163504	20186	Mm.3095	NM_009108	ENSMUSG00000047638	Nr1h4	AI957360|Fxr|HRR1|RIP14|Rxrip14	nuclear receptor subfamily 1, group H, member 4	protein-coding
mm_92905.1	chr10	83337846	83337880	-	1	NA	promoter-TSS (NM_177388)	promoter-TSS (NM_177388)	-46	NM_177388	338365	Mm.67073	NM_177388	ENSMUSG00000034591	Slc41a2	A230035L05Rik|SLC41A1-L1	solute carrier family 41, member 2	protein-coding
mm_17827.1	chr2	33887719	33887727	-	1	NA	5' UTR (NM_175184, exon 1 of 10)	5' UTR (NM_175184, exon 1 of 10)	223	NM_175184	72543	Mm.254914	NM_175184	ENSMUSG00000038740	Mvb12b	2610200O14Rik|2610528K11Rik|AI414895|Fam125b	multivesicular body subunit 12B	protein-coding
mm_23549.1	chr3	61366405	61366415	+	1	NA	3' UTR (NM_028712, exon 1 of 1)	3' UTR (NM_028712, exon 1 of 1)	1903	NM_028712	74012	Mm.422674	NM_028712	ENSMUSG00000036894	Rap2b	4021402C18Rik|AA408554	RAP2B, member of RAS oncogene family	protein-coding
mm_37573.1	chr4	126242293	126242330	-	1	NA	exon (NM_144941, exon 2 of 17)	exon (NM_144941, exon 2 of 17)	14008	NM_144941	245877	Mm.266716	NM_144941	ENSMUSG00000028849	Map7d1	AV028413|BC019977|Mtap7d1|Parcc1|Rprc1|mKIAA1187	MAP7 domain containing 1	protein-coding
mm_41318.1	chr5	90471999	90472052	+	1	NA	exon (NM_009654, exon 11 of 15)	exon (NM_009654, exon 11 of 15)	11155	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_112408.1	chr13	3563902	3563909	+	1	NA	intron (NM_008112, intron 8 of 10)	ID_B1|SINE|B4	25830	NM_008112	14569	Mm.153226	NM_008112	ENSMUSG00000021218	Gdi2	GDI-B|GDIB|Gdi3	guanosine diphosphate (GDP) dissociation inhibitor 2	protein-coding
mm_136027.1	chr16	76373840	76373852	-	1	NA	promoter-TSS (NM_173440)	promoter-TSS (NM_173440)	-797	NM_173440	268903	Mm.74711	NM_173440	ENSMUSG00000048490	Nrip1	6030458L20Rik|8430438I05Rik|9630050P12|AA959574|AW456757|RIP140	nuclear receptor interacting protein 1	protein-coding
mm_21558.1	chr2	164182593	164182612	-	1	NA	exon (NM_145369, exon 1 of 4)	exon (NM_145369, exon 1 of 4)	140	NM_145369	209232	Mm.218273	NM_145369	ENSMUSG00000040154	Wfdc5	BC019734|Prg5|Wap1	WAP four-disulfide core domain 5	protein-coding
mm_9590.1	chr1	174921697	174921707	-	1	NA	5' UTR (NM_011825, exon 1 of 2)	5' UTR (NM_011825, exon 1 of 2)	117	NM_011825	23893	Mm.25760	NM_011825	ENSMUSG00000050069	Grem2	Gremlin2|Prdc	gremlin 2, DAN family BMP antagonist	protein-coding
mm_106940.1	chr12	8700366	8700370	+	1	NA	intron (NR_027670, intron 4 of 21)	intron (NR_027670, intron 4 of 21)	25687	NM_030723	80913	Mm.341243	NM_030723	ENSMUSG00000020594	Pum2	5730503J23Rik|Pumm2	pumilio RNA-binding family member 2	protein-coding
mm_25300.1	chr3	105965078	105965105	+	1	NA	exon (NM_027432, exon 7 of 10)	exon (NM_027432, exon 7 of 10)	-4843	NM_009725	11950	Mm.251152	NM_009725	ENSMUSG00000000563	Atp5f1	C76477	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit B1	protein-coding
mm_58596.1	chr7	5020562	5020602	+	1	NA	5' UTR (NM_001290426, exon 1 of 3)	5' UTR (NM_001290426, exon 1 of 3)	206	NM_001033383	319748	Mm.86607	NM_001033383	ENSMUSG00000074405	Zfp865	6430526N21Rik|Znf865	zinc finger protein 865	protein-coding
mm_169881.1	chr16	3926542	3926558	+	1	NA	intron (NM_029738, intron 7 of 11)	intron (NM_029738, intron 7 of 11)	17541	NM_029738	76779	Mm.458921	NM_029738	ENSMUSG00000014232	Cluap1	2310030D15Rik|2610111M03Rik	clusterin associated protein 1	protein-coding
mm_58466.1	chr7	3367411	3367425	+	1	NA	TTS (NM_133189)	TTS (NM_133189)	-26624	NM_133190	81905	Mm.357990	NM_133190	ENSMUSG00000053395	Cacng8	-	calcium channel, voltage-dependent, gamma subunit 8	protein-coding
mm_78522.1	chr9	34488722	34488745	+	1	NA	promoter-TSS (NM_001190912)	promoter-TSS (NM_001190912)	2	NM_001190911	67703	Mm.220710	NM_026324	ENSMUSG00000032036	Kirrel3	1500010O20Rik|2900036G11Rik|NEPH2|SST4|mKIAA1867	kin of IRRE like 3 (Drosophila)	protein-coding
mm_117077.1	chr13	59557213	59557227	-	1	NA	promoter-TSS (NM_001284219)	promoter-TSS (NM_001284219)	127	NM_001284218	67269	Mm.153008	NM_023328	ENSMUSG00000021557	Agtpbp1	1700020N17Rik|2310001G17Rik|2900054O13Rik|4930445M19Rik|5730402G09Rik|CCP1|Nna1|nmf243|pcd	ATP/GTP binding protein 1	protein-coding
mm_27354.1	chr3	50417292	50417304	-	1	NA	intron (NM_011990, intron 6 of 11)	intron (NM_011990, intron 6 of 11)	26315	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_119668.1	chr14	52437079	52437087	+	1	NA	Intergenic	ORR1B2-int|LTR|ERVL-MaLR	-13310	NM_020514	57271	Mm.88824	NM_020514	ENSMUSG00000035626	Olfr1509	MOR244-3|Mor83|Or83	olfactory receptor 1509	protein-coding
mm_84524.1	chr9	67043954	67043960	-	1	NA	promoter-TSS (NM_001164256)	promoter-TSS (NM_001164256)	-86	NM_001164253	22003	Mm.121878	NM_024427	ENSMUSG00000032366	Tpm1	AA986836|AI854628|TM2|Tm3|Tmpa|Tpm-1|alpha-TM	tropomyosin 1, alpha	protein-coding
mm_56820.1	chr6	116735332	116735347	-	1	NA	Intergenic	MER44B|DNA|TcMar-Tigger	-18581	NM_178768	319776	Mm.133120	NM_178768	ENSMUSG00000048108	Tmem72	C230095G01Rik	transmembrane protein 72	protein-coding
mm_81498.1	chr9	110032197	110032208	+	1	NA	exon (NM_008633, exon 6 of 19)	exon (NM_008633, exon 6 of 19)	-19819	NM_001311163	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_69341.1	chr7	129657993	129658003	-	1	NA	Intergenic	Intergenic	66135	NM_172255	207425	Mm.229323	NM_172255	ENSMUSG00000042055	Wdr11	2900055P10Rik|AW489876|Brwd2|mKIAA1351	WD repeat domain 11	protein-coding
mm_59688.1	chr7	28443954	28443962	+	1	NA	intron (NM_001039192, intron 4 of 6)	B3|SINE|B2	3021	NM_001039192	63986	Mm.194536	NM_022024	ENSMUSG00000060791	Gmfg	0610039G16Rik|2310057N07Rik|AI324845	glia maturation factor, gamma	protein-coding
mm_122213.1	chr14	32146192	32146203	-	1	NA	intron (NM_020597, intron 1 of 3)	intron (NM_020597, intron 1 of 3)	4174	NM_020597	17695	Mm.2540	NM_020597	ENSMUSG00000021907	Msmb	PIP|PSP94|beta-MSP	beta-microseminoprotein	protein-coding
mm_21766.1	chr2	164844481	164844504	-	1	NA	exon (NM_011125, exon 12 of 16)	exon (NM_011125, exon 12 of 16)	10719	NM_008906	19025	Mm.359633	NM_008906	ENSMUSG00000017760	Ctsa	AU019505|PPCA|Ppgb	cathepsin A	protein-coding
mm_16873.1	chr2	12301989	12301991	-	1	NA	promoter-TSS (NM_001001309)	promoter-TSS (NM_001001309)	-46	NM_001001309	241226	Mm.329997	NM_001001309	ENSMUSG00000026768	Itga8	AI447669	integrin alpha 8	protein-coding
mm_67730.1	chr7	90129927	90129961	-	1	NA	promoter-TSS (NM_001252521)	promoter-TSS (NM_001252521)	-8	NR_046007	78329	Mm.389940	NR_046006	ENSMUSG00000097162	2310010J17Rik	-	RIKEN cDNA 2310010J17 gene	ncRNA
mm_115351.1	chr13	112752403	112752406	+	1	NA	Intergenic	Intergenic	-48373	NM_008903	19012	Mm.291029	NM_008247	ENSMUSG00000021759	Plpp1	Hic53|Hpic53|LPP-1|LPP1|PAP-2a|PAP2-alpha|PAP2a|Ppap2a|mPAP	phospholipid phosphatase 1	protein-coding
mm_77445.1	chr8	121792215	121792232	-	1	NA	Intergenic	Intergenic	37346	NM_145605	234825	Mm.209329	NM_145605	ENSMUSG00000040263	Klhdc4	AA408426|AV352552|BC012312|G430025P05Rik	kelch domain containing 4	protein-coding
mm_128549.1	chr15	55557344	55557354	-	1	NA	promoter-TSS (NM_026759)	promoter-TSS (NM_026759)	-37	NM_026759	68537	Mm.236795	NM_026759	ENSMUSG00000022370	Mrpl13	1110002D09Rik	mitochondrial ribosomal protein L13	protein-coding
mm_49153.1	chr6	12041375	12041395	+	1	NA	intron (NM_001168382, intron 16 of 17)	B1F2|SINE|Alu	68195	NR_003631	625347	Mm.389084	NM_001039041	ENSMUSG00000057223	Gm6578	EG625347	mitochondrial ribosomal protein L32 pseudogene	pseudo
mm_102400.1	chr11	59002422	59002449	-	1	NA	intron (NM_001171512, intron 89 of 103)	intron (NM_001171512, intron 89 of 103)	24342	NM_053168	94091	Mm.248049	NM_053168	ENSMUSG00000020455	Trim11	-	tripartite motif-containing 11	protein-coding
mm_14960.1	chr2	152080966	152080975	+	1	NA	promoter-TSS (NM_001160410)	promoter-TSS (NM_001160410)	-559	NM_001160410	545474	Mm.214317	NM_001160410	ENSMUSG00000060257	Scrt2	AW060659	scratch family zinc finger 2	protein-coding
mm_78533.1	chr9	35127866	35127876	+	1	NA	intron (NM_027030, intron 4 of 5)	intron (NM_027030, intron 4 of 5)	-11061	NM_009178	20443	Mm.275973	NM_009178	ENSMUSG00000032038	St3gal4	Siat4c	ST3 beta-galactoside alpha-2,3-sialyltransferase 4	protein-coding
mm_113782.1	chr13	45507439	45507515	+	1	NA	promoter-TSS (NM_025508)	promoter-TSS (NM_025508)	33	NM_025508	66355	Mm.290802	NM_025508	ENSMUSG00000000253	Gmpr	2310004P21Rik|AV028449|GMPR 1	guanosine monophosphate reductase	protein-coding
mm_118136.1	chr13	104863884	104863894	-	1	NA	promoter-TSS (NM_029984)	promoter-TSS (NM_029984)	4	NM_029984	77803	Mm.159995	NM_029984	ENSMUSG00000042655	Fam159b	A930021C24Rik	family with sequence similarity 159, member B	protein-coding
mm_47289.1	chr5	122234622	122234634	-	1	NA	intron (NM_028752, intron 3 of 6)	B4A|SINE|B4	24341	NM_028752	74096	Mm.28804	NM_028752	ENSMUSG00000064267	Hvcn1	0610039P13Rik|AI450555|BTS|HV1|Vsop.|mVSOP	hydrogen voltage-gated channel 1	protein-coding
mm_53111.1	chr6	125083422	125083441	+	1	NA	TTS (NM_001163269)	TTS (NM_001163269)	12154	NM_001163268	381810	Mm.333386	NM_001163268	ENSMUSG00000067714	Lpar5	GPR93|Gm1072|Gpr92|LPA5	lysophosphatidic acid receptor 5	protein-coding
mm_47573.1	chr5	124496971	124497007	-	1	NA	intron (NM_021430, intron 6 of 6)	intron (NM_021430, intron 6 of 6)	13834	NM_029532	76167	Mm.156035	NM_029532	ENSMUSG00000029402	Snrnp35	6330548G22Rik	small nuclear ribonucleoprotein 35 (U11/U12)	protein-coding
mm_164901.1	chr18	67252343	67252346	+	1	NA	Intergenic	Lx8|LINE|L1	-6514	NM_172630	225651	Mm.235792	NM_172630	ENSMUSG00000062526	Mppe1	A530095G11	metallophosphoesterase 1	protein-coding
mm_128859.1	chr15	72806426	72806446	-	1	NA	non-coding (NR_002864, exon 1 of 1)	non-coding (NR_002864, exon 1 of 1)	3888	NR_002864	353342	Mm.440245	NR_002864	ENSMUSG00000106847	Peg13	-	paternally expressed 13	ncRNA
mm_59173.1	chr7	24407236	24407260	+	1	NA	intron (NM_028047, intron 5 of 13)	intron (NM_028047, intron 5 of 13)	7620	NM_028047	71997	Mm.150977	NM_028047	ENSMUSG00000002210	Smg9	1500002O20Rik|AI429693|N28092	smg-9 homolog, nonsense mediated mRNA decay factor (C. elegans)	protein-coding
mm_80714.1	chr9	92275705	92275740	+	1	NA	5' UTR (NM_001195084, exon 1 of 8)	5' UTR (NM_001195084, exon 1 of 8)	120	NM_001195084	18828	Mm.10306	NM_008880	ENSMUSG00000032372	Plscr2	-	phospholipid scramblase 2	protein-coding
mm_65032.1	chr7	18532395	18532413	-	1	NA	promoter-TSS (NM_054060)	promoter-TSS (NM_054060)	-177	NM_054060	114868	Mm.389809	NM_054060	ENSMUSG00000070798	Psg25	cea13	pregnancy-specific glycoprotein 25	protein-coding
mm_3668.1	chr1	153652944	153652954	+	1	NA	promoter-TSS (NM_026380)	promoter-TSS (NM_026380)	-88	NM_026380	67792	Mm.379143	NM_026380	ENSMUSG00000042671	Rgs8	6530413N01Rik	regulator of G-protein signaling 8	protein-coding
mm_8474.1	chr1	153414228	153414233	-	1	NA	promoter-TSS (NR_033736)	promoter-TSS (NR_033736)	3	NR_033736	626058	Mm.31556	NM_001177359		E330020D12Rik	EG626058|F430003O07Rik|Gm6648	Riken cDNA E330020D12 gene	ncRNA
mm_32609.1	chr4	112072677	112072685	+	1	NA	intron (NM_001347180, intron 1 of 11)	intron (NM_001347180, intron 1 of 11)	665	NM_001347180	320640	Mm.253775	NM_178786	ENSMUSG00000055960	Skint4	9530098N22Rik	selection and upkeep of intraepithelial T cells 4	protein-coding
mm_156913.1	chrX	169082523	169082538	+	1	NA	intron (NR_109847, intron 1 of 14)	intron (NR_109847, intron 1 of 14)	-30348	NM_001287530	11856	Mm.441810	NM_009707	ENSMUSG00000031355	Arhgap6	AI504284|RhoGAPX-1	Rho GTPase activating protein 6	protein-coding
mm_51875.1	chr6	90553008	90553050	+	1	NA	intron (NM_027406, intron 1 of 22)	L1M5|LINE|L1	2181	NM_027406	107747	Mm.30035	NM_027406	ENSMUSG00000030088	Aldh1l1	1810048F20Rik|FDH|Fthfd|Neut2	aldehyde dehydrogenase 1 family, member L1	protein-coding
mm_163491.1	chr12	109460083	109460105	+	1	NA	exon (NM_010052, exon 5 of 5)	exon (NM_010052, exon 5 of 5)	6639	NM_010052	13386	Mm.157069	NM_010052	ENSMUSG00000040856	Dlk1	AW742678|DLK-1|DlkI|FA1|Ly107|Peg9|SCP1|ZOG|pG2|pref-1	delta-like 1 homolog (Drosophila)	protein-coding
mm_119305.1	chr14	34819812	34819834	+	1	NA	promoter-TSS (NM_008166)	promoter-TSS (NM_008166)	-313	NM_008166	14803	Mm.121569	NM_008166	ENSMUSG00000041078	Grid1	GluD1|GluRdelta1	glutamate receptor, ionotropic, delta 1	protein-coding
mm_62419.1	chr7	101321139	101321149	+	1	NA	promoter-TSS (NM_019990)	promoter-TSS (NM_019990)	-175	NM_019990	56018	Mm.28896	NM_019990	ENSMUSG00000030688	Stard10	AV048538|CGI-52|NY-C0-28|PC-TP2|PCTP2|Pctpl|Sdccag28|SdccagG28|TISP-81	START domain containing 10	protein-coding
mm_24749.1	chr3	95319969	95319977	+	1	NA	intron (NM_001320492, intron 1 of 10)	intron (NM_001320492, intron 1 of 10)	1143	NM_001320492	76893	Mm.181009	NM_029789	ENSMUSG00000015714	Cers2	0610013I17Rik|AI225939|Lass2|TRH3	ceramide synthase 2	protein-coding
mm_165327.1	chr2	110721560	110721581	+	1	NA	promoter-TSS (NM_001290786)	promoter-TSS (NM_001290786)	76	NM_172979	269328	Mm.32566	NM_172979	ENSMUSG00000050808	Muc15	4732460E09|D730046L02Rik|MUC-15	mucin 15	protein-coding
mm_46512.1	chr5	105235426	105235430	-	1	NA	intron (NM_001039646, intron 2 of 10)	B3|SINE|B2	4105	NM_001039646	626578	Mm.275893	NM_001039646	ENSMUSG00000105096	Gbp10	-	guanylate-binding protein 10	protein-coding
mm_154779.1	chrX	12936918	12936942	+	1	NA	promoter-TSS (NM_001272033)	promoter-TSS (NM_001272033)	57	NM_001272033	245350	Mm.302695	NM_001272033		AA414768	OTTMUSG00000017000	expressed sequence AA414768	protein-coding
mm_49336.1	chr6	21312146	21312165	+	1	NA	intron (NM_019697, intron 1 of 5)	B3A|SINE|B2	96046	NM_019697	16508	Mm.425316	NM_019697	ENSMUSG00000060882	Kcnd2	AI839615|AW555701|Kv4.2|R75121|mKIAA1044	potassium voltage-gated channel, Shal-related family, member 2	protein-coding
mm_162978.1	chr11	19924097	19924107	+	1	NA	promoter-TSS (NM_033523)	promoter-TSS (NM_033523)	-340	NM_033523	114716	Mm.266627	NM_033523	ENSMUSG00000045671	Spred2	C79158	sprouty-related, EVH1 domain containing 2	protein-coding
mm_121038.1	chr14	80006219	80006250	+	1	NA	exon (NM_001030294, exon 2 of 7)	exon (NM_001030294, exon 2 of 7)	5932	NM_001030294	380924	Mm.26456	NM_001030294	ENSMUSG00000022026	Olfm4	GC1|GW112|Gm296|Gm913|OlfD|pPD4	olfactomedin 4	protein-coding
mm_78477.1	chr9	32695693	32695705	+	1	NA	promoter-TSS (NM_001038642)	promoter-TSS (NM_001038642)	-343	NM_011808	23871	Mm.292415	NM_011808	ENSMUSG00000032035	Ets1	AI196000|AI448617|D230050P06|Ets-1|Tpl1|vs	E26 avian leukemia oncogene 1, 5' domain	protein-coding
mm_141583.1	chr17	32391865	32391866	-	1	NA	intron (NM_001347343, intron 17 of 18)	intron (NM_001347343, intron 17 of 18)	-2426	NR_033525	22404	Mm.274948	NM_011717	ENSMUSG00000024050	Wiz	-	widely-interspaced zinc finger motifs	protein-coding
mm_169249.1	chr13	75645235	75645239	-	1	NA	TTS (NR_030451)	TTS (NR_030451)	191	NR_030451	751556		NR_030451	ENSMUSG00000076236	Mir682	Mirn682|mir-682|mmu-mir-682	microRNA 682	ncRNA
mm_138900.1	chr17	43568642	43568676	+	1	NA	5' UTR (NM_013737, exon 1 of 12)	5' UTR (NM_013737, exon 1 of 12)	208	NM_013737	27226	Mm.9277	NM_013737	ENSMUSG00000023913	Pla2g7	PAF-AH|R75400	phospholipase A2, group VII (platelet-activating factor acetylhydrolase, plasma)	protein-coding
mm_71947.1	chr8	70376803	70376826	+	1	NA	intron (NM_016685, intron 9 of 18)	intron (NM_016685, intron 9 of 18)	3266	NM_016685	12845	Mm.45071	NM_016685	ENSMUSG00000031849	Comp	TSP5	cartilage oligomeric matrix protein	protein-coding
mm_34464.1	chr4	148140772	148140774	+	1	NA	5' UTR (NM_027985, exon 1 of 8)	5' UTR (NM_027985, exon 1 of 8)	283	NM_027985	71890	Mm.9648	NM_027985	ENSMUSG00000029003	Mad2l2	2310033C13Rik|G1-453-4|MAD2B|REV7|repro22	MAD2 mitotic arrest deficient-like 2	protein-coding
mm_141823.1	chr17	34616048	34616056	-	1	NA	promoter-TSS (NM_152922)	promoter-TSS (NM_152922)	-81	NM_152922	81701	Mm.231343	NM_152922	ENSMUSG00000015467	Egfl8	Ng3	EGF-like domain 8	protein-coding
mm_13773.1	chr2	118663723	118663762	+	1	NA	5' UTR (NM_001033254, exon 1 of 11)	5' UTR (NM_001033254, exon 1 of 11)	165	NM_001033254	214230	Mm.241857	NM_001033254	ENSMUSG00000074923	Pak6	4732456M09	p21 protein (Cdc42/Rac)-activated kinase 6	protein-coding
mm_75732.1	chr8	69395565	69395575	-	1	NA	promoter-TSS (NR_038043)	promoter-TSS (NR_038043)	-26	NR_038043	378466	Mm.37846	NM_194351	ENSMUSG00000110444	Gm10033	9330175B10Rik|ENSMUSG00000057924|Gm10311	predicted gene 10033	ncRNA
mm_160731.1	chr10	77771394	77771394	-	1	NA	promoter-TSS (NM_001101630)	promoter-TSS (NM_001101630)	-69	NM_001101630	100041261	Mm.477434	NM_001101630	ENSMUSG00000095817	Gm3238	-	predicted gene 3238	protein-coding
mm_16097.1	chr2	168978295	168978302	+	1	NA	promoter-TSS (NR_040326)	promoter-TSS (NR_040326)	29	NR_040326	75508	Mm.271256	NR_040326	ENSMUSG00000086348	1700017J07Rik	-	RIKEN cDNA 1700017J07 gene	ncRNA
mm_89523.1	chr10	94357060	94357077	+	1	NA	Intergenic	Intergenic	-58365	NR_033209	215472	Mm.255656	NM_174999	ENSMUSG00000053420	Gm4792	E130012K09|EG215472	predicted gene 4792	ncRNA
mm_79311.1	chr9	52049436	52049442	+	1	NA	promoter-TSS (NR_023357)	promoter-TSS (NR_023357)	-734	NR_023357	629557	Mm.422775	NR_023357		Gm6981	EG629557	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_137597.1	chr17	28147541	28147544	+	1	NA	intron (NM_001004366, intron 1 of 21)	intron (NM_001004366, intron 1 of 21)	5016	NM_001004366	268935	Mm.258491	NM_001004366	ENSMUSG00000038677	Scube3	CEGF3|D030038I21Rik	signal peptide, CUB domain, EGF-like 3	protein-coding
mm_124959.1	chr15	12924093	12924105	+	1	NA	exon (NM_026799, exon 30 of 35)	exon (NM_026799, exon 30 of 35)	99284	NM_001130149	14000	Mm.293142	NM_026799	ENSMUSG00000022191	Drosha	1110013A17Rik|AI874853|Etohi2|Rn3|Rnasen	drosha, ribonuclease type III	protein-coding
mm_88007.1	chr10	67097000	67097025	+	1	NA	promoter-TSS (NM_001204915)	promoter-TSS (NM_001204915)	-24	NM_178606	28193	Mm.41272	NM_178606	ENSMUSG00000019873	Reep3	D10Ucla1	receptor accessory protein 3	protein-coding
mm_78358.1	chr9	25562677	25562705	+	1	NA	intron (NM_026189, intron 3 of 7)	intron (NM_026189, intron 3 of 7)	81094	NM_026189	67484	Mm.112977	NM_026189	ENSMUSG00000036611	Eepd1	2310005P05Rik|AI481005	endonuclease/exonuclease/phosphatase family domain containing 1	protein-coding
mm_10992.1	chr2	26315514	26315602	+	1	NA	promoter-TSS (NM_001199146)	promoter-TSS (NM_001199146)	25	NM_153410	67839	Mm.266611	NM_153410	ENSMUSG00000026930	Gpsm1	1810037C22Rik|AW107933|Ags3	G-protein signalling modulator 1 (AGS3-like, C. elegans)	protein-coding
mm_45036.1	chr5	39641868	39641894	-	1	NA	intron (NM_010474, intron 1 of 1)	intron (NM_010474, intron 1 of 1)	2750	NM_010474	15476	Mm.12559	NM_010474	ENSMUSG00000051022	Hs3st1	3-Ost|D5Wsu110e|Hsg3ost	heparan sulfate (glucosamine) 3-O-sulfotransferase 1	protein-coding
mm_45272.1	chr5	64680346	64680356	-	1	NA	Intergenic	Intergenic	-69652	NR_045078	100042198	Mm.25191	NR_045078	ENSMUSG00000105402	Gm3716	Gm1683	predicted gene 3716	ncRNA
mm_56355.1	chr6	93717615	93717622	-	1	NA	intron (NM_001083321, intron 11 of 21)	intron (NM_001083321, intron 11 of 21)	195345	NR_104594	14924	Mm.217216	NM_010367	ENSMUSG00000045095	Magi1	AIP3|BAP1|Baiap1|Gukmi1|MAGI1c|Magi-1|TNRC19|WWP3|mKIAA4129	membrane associated guanylate kinase, WW and PDZ domain containing 1	protein-coding
mm_129205.1	chr15	76512269	76512277	-	1	NA	promoter-TSS (NM_010046)	promoter-TSS (NM_010046)	-455	NM_010046	13350	Mm.22633	NM_010046	ENSMUSG00000022555	Dgat1	ARAT|C75990|D15Ertd23e|Dgat	diacylglycerol O-acyltransferase 1	protein-coding
mm_56396.1	chr6	96115915	96115918	-	1	NA	intron (NM_182808, intron 2 of 4)	intron (NM_182808, intron 2 of 4)	2762	NM_182808	320265	Mm.489890	NM_182808	ENSMUSG00000059187	Fam19a1	C630007B19Rik|FAM19A1 TAFA-1|TAFA1|Tafa-1	family with sequence similarity 19, member A1	protein-coding
mm_136461.1	chr16	95349770	95349782	-	1	NA	Intergenic	Intergenic	92218	NM_001271690	16516	Mm.272239	NM_019664	ENSMUSG00000062609	Kcnj15	4930414N08Rik|AI182284|AI267127|IRKK|Kir4.2	potassium inwardly-rectifying channel, subfamily J, member 15	protein-coding
mm_145725.1	chr18	63988518	63988532	+	1	NA	3' UTR (NM_001014981, exon 28 of 28)	3' UTR (NM_001014981, exon 28 of 28)	-265834	NM_009182	20451	Mm.252110	NM_009182	ENSMUSG00000056812	St8sia3	AI847333|ST8SiaIII|Siat8c	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3	protein-coding
mm_118369.1	chr13	116309640	116309699	-	1	NA	promoter-TSS (NM_021459)	promoter-TSS (NM_021459)	19	NM_021459	16392	Mm.42242	NM_021459	ENSMUSG00000042258	Isl1	-	ISL1 transcription factor, LIM/homeodomain	protein-coding
mm_165415.1	chr2	147275630	147275633	+	1	NA	intron (NR_030769, intron 1 of 5)	intron (NR_030769, intron 1 of 5)	87162	NR_040330	99041	Mm.373081	NR_040330		AI646519	Aspax1|OTTMUSG00000015701	expressed sequence AI646519	ncRNA
mm_96321.1	chr11	63989875	63989883	+	1	NA	intron (NM_178379, intron 5 of 6)	PB1D11|SINE|Alu	25653	NR_131111	78883	Mm.410764	NR_131111	ENSMUSG00000086359	9630013K17Rik	-	RIKEN cDNA 9630013K17 gene	ncRNA
mm_98208.1	chr11	87797485	87797493	+	1	NA	exon (NM_010824, exon 8 of 14)	exon (NM_010824, exon 8 of 14)	3705	NM_010824	17523	Mm.4668	NM_010824	ENSMUSG00000009350	Mpo	mKIAA4033	myeloperoxidase	protein-coding
mm_20348.1	chr2	127744514	127744560	-	1	NA	intron (NM_001291012, intron 18 of 19)	intron (NM_001291012, intron 18 of 19)	-14640	NM_145532	228576	Mm.133036	NM_145532	ENSMUSG00000027377	Mall	BC012256|BENE	mal, T cell differentiation protein-like	protein-coding
mm_113064.1	chr13	23742302	23742317	+	1	NA	Intergenic	B1_Mur2|SINE|Alu	3212	NM_175653	319148	Mm.262517	NM_175653	ENSMUSG00000069310	Hist1h3c	H3-143	histone cluster 1, H3c	protein-coding
mm_83577.1	chr9	48339723	48339754	-	1	NA	intron (NM_030069, intron 1 of 5)	intron (NM_030069, intron 1 of 5)	1160	NM_030069	78252	Mm.31626	NM_030069	ENSMUSG00000032028	Nxpe2	4432416J03Rik|AI323362|Fam55b	neurexophilin and PC-esterase domain family, member 2	protein-coding
mm_22637.1	chr3	14863452	14863467	+	1	NA	promoter-TSS (NM_007606)	promoter-TSS (NM_007606)	-79	NM_007606	12350	Mm.300	NM_007606	ENSMUSG00000027559	Car3	BB219044|Ca3|Car-3	carbonic anhydrase 3	protein-coding
mm_55248.1	chr6	52713628	52713639	-	1	NA	promoter-TSS (NM_025816)	promoter-TSS (NM_025816)	-96	NM_025816	52440	Mm.389757	NM_025816	ENSMUSG00000004535	Tax1bp1	1200003J11Rik|1700069J21Rik|AA930106|D6Ertd404e|D6Ertd772e|T6bp|TXBP151	Tax1 (human T cell leukemia virus type I) binding protein 1	protein-coding
mm_123556.1	chr14	66847293	66847306	-	1	NA	intron (NM_009955, intron 3 of 13)	intron (NM_009955, intron 3 of 13)	21301	NM_009955	12934	Mm.352648	NM_009955	ENSMUSG00000022048	Dpysl2	AI851130|Crmp2|DRP2|Musunc33|TOAD-64|Ulip2	dihydropyrimidinase-like 2	protein-coding
mm_129380.1	chr15	78173957	78173988	-	1	NA	5' UTR (NM_025931, exon 1 of 7)	5' UTR (NM_025931, exon 1 of 7)	136	NM_025931	67042	Mm.30191	NM_025931	ENSMUSG00000016637	Ift27	2600013G09Rik|Rabl4	intraflagellar transport 27	protein-coding
mm_132810.1	chr16	45159088	45159110	+	1	NA	promoter-TSS (NM_028756)	promoter-TSS (NM_028756)	270	NM_026402	67841	Mm.41775	NM_026402	ENSMUSG00000022663	Atg3	2610016C12Rik|APG3|Apg3l|Atg3l|PC3-96	autophagy related 3	protein-coding
mm_101075.1	chr11	11675215	11675221	-	1	NA	Intergenic	Intergenic	-10707	NM_009578	22778	Mm.103545	NM_009578	ENSMUSG00000018654	Ikzf1	5832432G11Rik|Ikaros|LyF-1|Zfpn1a1|Znfn1a1|hlk-1|mKIAA4227	IKAROS family zinc finger 1	protein-coding
mm_107113.1	chr12	18135906	18135922	+	1	NA	Intergenic	CpG	-378596	NM_001033157	236366	Mm.352227	NM_001033157	ENSMUSG00000073197	5730507C01Rik	-	RIKEN cDNA 5730507C01 gene	protein-coding
mm_144054.1	chr17	90606899	90606916	-	1	NA	intron (NM_001346957, intron 9 of 18)	intron (NM_001346957, intron 9 of 18)	-151027	NM_001346959	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_139951.1	chr17	71214797	71214838	+	1	NA	intron (NM_001164885, intron 1 of 19)	intron (NM_001164885, intron 1 of 19)	10163	NM_001164885	64898	Mm.227924	NM_022882	ENSMUSG00000024052	Lpin2	2610511G02Rik|AI481352|AW742896	lipin 2	protein-coding
mm_100342.1	chr11	118393937	118393962	+	1	NA	exon (NM_011150, exon 6 of 6)	exon (NM_011150, exon 6 of 6)	7982	NM_011150	19039	Mm.3152	NM_011150	ENSMUSG00000033880	Lgals3bp	90K|CyCAP|MAC-2BP|Ppicap|Tango10b	lectin, galactoside-binding, soluble, 3 binding protein	protein-coding
mm_131597.1	chr16	18877248	18877275	+	1	NA	promoter-TSS (NM_010922)	promoter-TSS (NM_010922)	511	NM_010435	15260	Mm.15694	NM_010435	ENSMUSG00000022702	Hira	AA138857|D16Ertd95e|Gm15797|N28177|OTTMUSG00000026264|Tuple1	histone cell cycle regulator	protein-coding
mm_138297.1	chr17	34630890	34630939	+	1	NA	exon (NM_030890, exon 2 of 4)	exon (NM_030890, exon 2 of 4)	1228	NM_030890	260297	Mm.390965	NM_030890	ENSMUSG00000015476	Prrt1	Bat-4|Bat4|D17H6S54E|DSPD1|G5b|NG5|ORF31	proline-rich transmembrane protein 1	protein-coding
mm_59749.1	chr7	28820653	28820713	+	1	NA	exon (NM_177301, exon 10 of 13)	exon (NM_177301, exon 10 of 13)	-4655	NM_016772	51798	Mm.291776	NM_016772	ENSMUSG00000053898	Ech1	AA617331	enoyl coenzyme A hydratase 1, peroxisomal	protein-coding
mm_138892.1	chr17	43568097	43568137	+	1	NA	promoter-TSS (NM_013737)	promoter-TSS (NM_013737)	-334	NM_013737	27226	Mm.9277	NM_013737	ENSMUSG00000023913	Pla2g7	PAF-AH|R75400	phospholipase A2, group VII (platelet-activating factor acetylhydrolase, plasma)	protein-coding
mm_121701.1	chr14	14764555	14764563	-	1	NA	intron (NM_001033270, intron 12 of 24)	intron (NM_001033270, intron 12 of 24)	-56256	NM_001195229	674895	Mm.317563	NM_001034865	ENSMUSG00000042567	Nek10	Gm282	NIMA (never in mitosis gene a)- related kinase 10	protein-coding
mm_115100.1	chr13	102733326	102733345	+	1	NA	3' UTR (NM_175171, exon 29 of 29)	3' UTR (NM_175171, exon 29 of 29)	-26920	NR_130318	76624	Mm.426384	NR_130171	ENSMUSG00000091906	1700099I09Rik	-	RIKEN cDNA 1700099I09 gene	ncRNA
mm_145846.1	chr18	65449067	65449108	+	1	NA	intron (NM_172833, intron 6 of 15)	intron (NM_172833, intron 6 of 15)	18090	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_23790.1	chr3	79542838	79542855	+	1	NA	intron (NM_001162999, intron 1 of 16)	intron (NM_001162999, intron 1 of 16)	24833	NM_001162999	329679	Mm.244005	NM_001162999	ENSMUSG00000061175	Fnip2	D630023B12Rik|mKIAA1450	folliculin interacting protein 2	protein-coding
mm_79582.1	chr9	58139551	58139554	+	1	NA	intron (NM_001162475, intron 4 of 18)	intron (NM_001162475, intron 4 of 18)	4887	NM_001162479	20897	Mm.10801	NM_009291	ENSMUSG00000032327	Stra6	AI891933	stimulated by retinoic acid gene 6	protein-coding
mm_41282.1	chr5	90460893	90460908	+	1	NA	promoter-TSS (NM_009654)	promoter-TSS (NM_009654)	30	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_163015.1	chr11	45852605	45852607	-	1	NA	intron (NM_001346760, intron 1 of 11)	intron (NM_001346760, intron 1 of 11)	642	NM_001045520	216705	Mm.169673	NM_001045520	ENSMUSG00000006169	Clint1	AI642036|AW537616|C530049I24Rik|Enth|Epn4|F630206G17Rik|mKIAA0171	clathrin interactor 1	protein-coding
mm_161563.1	chr16	17980398	17980398	+	1	NA	promoter-TSS (NM_016983)	promoter-TSS (NM_016983)	-167	NM_016983	22363	Mm.377118	NM_016983	ENSMUSG00000059280	Vpreb2	CD179b|VpreB1|Vpreb-2	pre-B lymphocyte gene 2	protein-coding
mm_48264.1	chr5	137893624	137893641	-	1	NA	3' UTR (NM_007819, exon 13 of 13)	3' UTR (NM_007819, exon 13 of 13)	-21874	NM_001024932	545812	Mm.332769	NM_001024932	ENSMUSG00000066682	Pilrb2	EG545812	paired immunoglobin-like type 2 receptor beta 2	protein-coding
mm_108755.1	chr12	89013156	89013168	+	1	NA	intron (NM_172544, intron 2 of 19)	RMER1A|Other|Other	59772	NM_172544	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding
mm_5462.1	chr1	36369174	36369186	-	1	NA	promoter-TSS (NM_172652)	promoter-TSS (NM_172652)	1	NM_172652	226976	Mm.24734	NM_172652	ENSMUSG00000010453	Kansl3	4632411B12Rik|4932435K23|AI431067|AI647574|C85723|Kiaa1310|mKIAA1310	KAT8 regulatory NSL complex subunit 3	protein-coding
mm_94638.1	chr11	16905342	16905349	+	1	NA	intron (NM_207655, intron 21 of 27)	intron (NM_207655, intron 21 of 27)	45937	NR_110421	72735	Mm.268598	NR_015469		Eldr	2810442I21Rik|4930500E12Rik|Fabl	Egfr long non-coding downstream RNA	ncRNA
mm_42957.1	chr5	123066208	123066234	+	1	NA	Intergenic	Intergenic	-10054	NM_001039723	330189	Mm.391872	NM_001039723	ENSMUSG00000054434	Tmem120b	-	transmembrane protein 120B	protein-coding
mm_156867.1	chrX	164438113	164438126	+	1	NA	5' UTR (NM_026853, exon 2 of 8)	5' UTR (NM_026853, exon 2 of 8)	1125	NM_001313737	68854	Mm.33225	NM_026853	ENSMUSG00000031382	Asb11	1110067L12Rik|1600009D24Rik	ankyrin repeat and SOCS box-containing 11	protein-coding
mm_49432.1	chr6	29272685	29272730	+	1	NA	promoter-TSS (NM_023516)	promoter-TSS (NM_023516)	81	NM_023516	69573	Mm.45161	NM_023516	ENSMUSG00000043421	Hilpda	2310016C08Rik|AW049004|Hig2	hypoxia inducible lipid droplet associated	protein-coding
mm_96509.1	chr11	68458385	68458412	+	1	NA	intron (NM_177320, intron 1 of 18)	intron (NM_177320, intron 1 of 18)	26273	NM_177320	320207	Mm.244960	NM_177320	ENSMUSG00000020901	Pik3r5	AV230647|F730038I15Rik	phosphoinositide-3-kinase, regulatory subunit 5, p101	protein-coding
mm_36691.1	chr4	96591556	96591594	-	1	NA	promoter-TSS (NM_028979)	promoter-TSS (NM_028979)	-90	NM_028979	74519	Mm.458387	NM_028979	ENSMUSG00000015224	Cyp2j9	8430417E17Rik	cytochrome P450, family 2, subfamily j, polypeptide 9	protein-coding
mm_121473.1	chr14	121035157	121035186	+	1	NA	promoter-TSS (NM_134082)	promoter-TSS (NM_134082)	-403	NM_134082	223254	Mm.223980	NM_134082	ENSMUSG00000025555	Farp1	AW228844|BC030329|Cdep	FERM, RhoGEF (Arhgef) and pleckstrin domain protein 1 (chondrocyte-derived)	protein-coding
mm_55148.1	chr6	51466832	51466835	-	1	NA	intron (NR_104468, intron 3 of 10)	intron (NR_104468, intron 3 of 10)	3061	NM_182650	53379	Mm.155896	NM_016806	ENSMUSG00000004980	Hnrnpa2b1	9130414A06Rik|Hnrpa2|Hnrpa2b1|hnrnp-A	heterogeneous nuclear ribonucleoprotein A2/B1	protein-coding
mm_143938.1	chr17	86230376	86230379	-	1	NA	intron (NM_011104, intron 1 of 14)	intron (NM_011104, intron 1 of 14)	56801	NR_045435	72104	Mm.443401	NR_045435	ENSMUSG00000100738	2010106C02Rik	-	RIKEN cDNA 2010106C02 gene	ncRNA
mm_98415.1	chr11	94564870	94564886	+	1	NA	promoter-TSS (NM_007689)	promoter-TSS (NM_007689)	-196	NM_007689	12643	Mm.440523	NM_007689	ENSMUSG00000039084	Chad	SLRR4A	chondroadherin	protein-coding
mm_114555.1	chr13	74121436	74121446	+	1	NA	promoter-TSS (NM_001081060)	promoter-TSS (NM_001081060)	-74	NM_001081060	105243	Mm.261564	NM_001081060	ENSMUSG00000036123	Slc9a3	9030624O13Rik|AI930210|NHE-3|NHE3	solute carrier family 9 (sodium/hydrogen exchanger), member 3	protein-coding
mm_163892.1	chr14	27237919	27237937	-	1	NA	promoter-TSS (NM_027871)	promoter-TSS (NM_027871)	-82	NM_027871	71704	Mm.248606	NM_027871	ENSMUSG00000021895	Arhgef3	1200004I24Rik|9830169H03Rik|C76747|Xpln	Rho guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_128087.1	chr15	27763053	27763059	-	1	NA	intron (NM_001081302, intron 40 of 56)	MTE-int|LTR|ERVL-MaLR	-81514	NM_001242423	223433	Mm.266485	NM_198301	ENSMUSG00000056069	Fam105a	9830126M18	family with sequence similarity 105, member A	protein-coding
mm_95727.1	chr11	54596197	54596230	+	1	NA	promoter-TSS (NM_001252498)	promoter-TSS (NM_001252498)	67	NM_001252497	192786	Mm.254404	NM_175258	ENSMUSG00000037533	Rapgef6	A530068K01|AI844632|BB085664|C030018K18Rik|PDZ-GEF2|Pdzgef2|RA-GEF-2|Ragef2|mKIAA4052	Rap guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_3457.1	chr1	150103907	150103955	+	1	NA	exon (NM_011198, exon 7 of 10)	exon (NM_011198, exon 7 of 10)	3900	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_62391.1	chr7	100950818	100950828	+	1	NA	intron (NM_183168, intron 1 of 2)	intron (NM_183168, intron 1 of 2)	13543	NM_183168	233571	Mm.235193	NM_183168	ENSMUSG00000048779	P2ry6	2010204J23Rik|P2Y6	pyrimidinergic receptor P2Y, G-protein coupled, 6	protein-coding
mm_18822.1	chr2	74606163	74606171	-	1	NA	Intergenic	B1_Mus2|SINE|Alu	-27219	NM_027133	69605	Mm.156113	NM_027133	ENSMUSG00000009207	Lnpk	2310011O18Rik|4921514L11Rik|9530051D01Rik|AI666268|Lnp|Lnpk1|Ul|ulnaless	lunapark, ER junction formation factor	protein-coding
mm_119299.1	chr14	34695002	34695013	+	1	NA	exon (NM_001301330, exon 4 of 19)	exon (NM_001301330, exon 4 of 19)	21079	NM_001301330	218914	Mm.27957	NM_001004436	ENSMUSG00000041408	Wapl	A530089A20Rik|BC037674|DIF-2|FOE|Wapal	WAPL cohesin release factor	protein-coding
mm_145071.1	chr18	42053676	42053689	+	1	NA	promoter-TSS (NM_001146299)	promoter-TSS (NM_001146299)	-28	NM_172966	269016	Mm.45472	NM_172966	ENSMUSG00000057719	Sh3rf2	2310046K19|9130023G24Rik|AI452083|Ppp1r39|RNF158	SH3 domain containing ring finger 2	protein-coding
mm_32195.1	chr4	101419302	101419332	+	1	NA	promoter-TSS (NM_009647)	promoter-TSS (NM_009647)	-4	NM_001177604	11639	Mm.42040	NM_009647	ENSMUSG00000028527	Ak4	AK 4|Ak-3|Ak-4|Ak3|Ak3l1|D4Ertd274e	adenylate kinase 4	protein-coding
mm_148861.1	chr19	6400612	6400622	+	1	NA	promoter-TSS (NM_011242)	promoter-TSS (NM_011242)	34	NM_011242	19395	Mm.77017	NM_011242	ENSMUSG00000032946	Rasgrp2	CDC25L|Caldaggef1	RAS, guanyl releasing protein 2	protein-coding
mm_21207.1	chr2	155640743	155640756	-	1	NA	intron (NM_019828, intron 12 of 18)	intron (NM_019828, intron 12 of 18)	17869	NR_030757	735275		NR_030757	ENSMUSG00000076312	Mir499	Mirn499|mir-499|mmu-mir-499	microRNA 499	ncRNA
mm_140263.1	chr17	84626517	84626529	+	1	NA	promoter-TSS (NM_172256)	promoter-TSS (NM_172256)	24	NM_172256	213575	Mm.246119	NM_172256	ENSMUSG00000024253	Dync2li1	4933404O11Rik|CGI-60|D2lic|LIC3|mD2LIC	dynein cytoplasmic 2 light intermediate chain 1	protein-coding
mm_86029.1	chr9	113662501	113662520	-	1	NA	exon (NM_001164677, exon 13 of 18)	exon (NM_001164677, exon 13 of 18)	45749	NM_001164678	18571	Mm.29816	NM_011052	ENSMUSG00000032504	Pdcd6ip	AI480591|AW544830|Aip1|Alix|C76364|Eig2|mKIAA1375	programmed cell death 6 interacting protein	protein-coding
mm_17070.1	chr2	22744903	22744932	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-29410	NM_019456	54519	Mm.14255	NM_019456	ENSMUSG00000026786	Apbb1ip	9930118P07Rik|Prp48	amyloid beta (A4) precursor protein-binding, family B, member 1 interacting protein	protein-coding
mm_21895.1	chr2	166155696	166155706	-	1	NA	promoter-TSS (NM_028072)	promoter-TSS (NM_028072)	-18	NM_028072	72043	Mm.1011	NM_028072	ENSMUSG00000006800	Sulf2	2010004N24Rik|AU020235|MSulf-2|mKIAA1247	sulfatase 2	protein-coding
mm_62734.1	chr7	110951034	110951080	+	1	NA	intron (NM_194464, intron 1 of 20)	intron (NM_194464, intron 1 of 20)	-4870	NM_010826	17540	Mm.250023	NM_010826	ENSMUSG00000005611	Mrvi1	BB115629|Irag|Ris1	MRV integration site 1	protein-coding
mm_163065.1	chr11	67090361	67090370	+	1	NA	exon (NM_001099635, exon 19 of 41)	exon (NM_001099635, exon 19 of 41)	-9439	NR_105888	102466766		NR_105888	ENSMUSG00000098855	Mir6923	Gm27312|mmu-mir-6923	microRNA 6923	ncRNA
mm_111046.1	chr12	79663617	79663619	-	1	NA	intron (NM_009014, intron 8 of 10)	intron (NM_009014, intron 8 of 10)	261115	NR_131075	77290	Mm.395042	NR_131073		9430078K24Rik	-	RIKEN cDNA 9430078K24 gene	ncRNA
mm_82709.1	chr9	24503128	24503197	-	1	NA	promoter-TSS (NM_172920)	promoter-TSS (NM_172920)	-22	NM_172920	244745	Mm.38526	NM_172920	ENSMUSG00000043067	Dpy19l1	1100001I19Rik|6030402K12|AI225861|AW558481	dpy-19-like 1 (C. elegans)	protein-coding
mm_127053.1	chr15	96709957	96709971	+	1	NA	Intergenic	CpG	-10266	NM_175121	67760	Mm.46754	NM_175121	ENSMUSG00000022462	Slc38a2	5033402L14Rik|AI316867|ATA2|SAT2|mKIAA1382	solute carrier family 38, member 2	protein-coding
mm_127158.1	chr15	98632346	98632390	+	1	NA	promoter-TSS (NM_001044741)	promoter-TSS (NM_001044741)	40	NM_001044741	12297	Mm.3544	NM_007581	ENSMUSG00000003352	Cacnb3	Beta3|CAB3|Ca(v)beta3|Cchb3	calcium channel, voltage-dependent, beta 3 subunit	protein-coding
mm_68127.1	chr7	102209827	102209910	-	1	NA	promoter-TSS (NM_001291358)	promoter-TSS (NM_001291358)	-1	NM_001287167	269966	Mm.439800	NM_022979	ENSMUSG00000063550	Nup98	4732457F17|AI849286|Nup96	nucleoporin 98	protein-coding
mm_129156.1	chr15	76233802	76233816	-	1	NA	exon (NM_001163575, exon 10 of 11)	exon (NM_001163575, exon 10 of 11)	-2431	NM_011117	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
mm_150679.1	chr19	42052951	42052957	+	1	NA	exon (NM_025752, exon 1 of 1)	exon (NM_025752, exon 1 of 1)	726	NM_025752	66765	Mm.440412	NM_025752	ENSMUSG00000090369	4933411K16Rik	-	RIKEN cDNA 4933411K16 gene	protein-coding
mm_76795.1	chr8	102785766	102785776	-	1	NA	promoter-TSS (NM_009866)	promoter-TSS (NM_009866)	-660	NM_009866	12552	Mm.1571	NM_009866	ENSMUSG00000031673	Cdh11	Cad11|OSF-4	cadherin 11	protein-coding
mm_107420.1	chr12	34990611	34990615	+	1	NA	Intergenic	RLTR19|LTR|ERVK	5852	NM_029294	75456	Mm.79179	NM_029294	ENSMUSG00000092305	Prps1l1	1700011K15Rik	phosphoribosyl pyrophosphate synthetase 1-like 1	protein-coding
mm_148899.1	chr19	6910120	6910146	+	1	NA	promoter-TSS (NM_012021)	promoter-TSS (NM_012021)	435	NM_026306	67674	Mm.318804	NM_026306	ENSMUSG00000038812	Trmt112	0610038D11Rik|Trm112p	tRNA methyltransferase 11-2	protein-coding
mm_159731.1	chr5	52775317	52775317	+	1	NA	promoter-TSS (NM_001309445)	promoter-TSS (NM_001309445)	-92	NM_001309445	78796	Mm.266886	NM_030185	ENSMUSG00000029179	Zcchc4	4930449I23Rik	zinc finger, CCHC domain containing 4	protein-coding
mm_88473.1	chr10	77606245	77606255	+	1	NA	promoter-TSS (NM_001301671)	promoter-TSS (NM_001301671)	153	NM_019929	20610	Mm.24433	NM_019929	ENSMUSG00000020265	Sumo3	2810014B19Rik|D10Ertd345e|SMT3A|SUMO-3|Smt3h1	small ubiquitin-like modifier 3	protein-coding
mm_13544.1	chr2	110731717	110731724	+	1	NA	exon (NM_001290786, exon 2 of 4)	exon (NM_001290786, exon 2 of 4)	10226	NM_172979	269328	Mm.32566	NM_172979	ENSMUSG00000050808	Muc15	4732460E09|D730046L02Rik|MUC-15	mucin 15	protein-coding
mm_15852.1	chr2	164777558	164777583	+	1	NA	exon (NM_009394, exon 5 of 6)	exon (NM_009394, exon 5 of 6)	2164	NM_009394	21925	Mm.1716	NM_009394	ENSMUSG00000017300	Tnnc2	Tncs	troponin C2, fast	protein-coding
mm_94324.1	chr11	4257582	4257592	+	1	NA	promoter-TSS (NM_008501)	promoter-TSS (NM_008501)	19	NM_008501	16878	Mm.4964	NM_008501	ENSMUSG00000034394	Lif	-	leukemia inhibitory factor	protein-coding
mm_100884.1	chr11	6008820	6008851	-	1	NA	intron (NM_007595, intron 3 of 20)	RLTR4_MM-int|LTR|ERV1	53077	NM_019661	56418	Mm.294821	NM_019661	ENSMUSG00000002741	Ykt6	0610042I15Rik|1810013M05Rik|AW105923	YKT6 v-SNARE homolog (S. cerevisiae)	protein-coding
mm_135749.1	chr16	55934809	55934840	-	1	NA	promoter-TSS (NM_001159365)	promoter-TSS (NM_001159365)	24	NM_001159364	74201	Mm.178427	NM_028815	ENSMUSG00000022604	Cep97	2810403B08Rik|4932439K18Rik|AA437768|E130116N02Rik|Lrriq2	centrosomal protein 97	protein-coding
mm_78946.1	chr9	45138551	45138561	+	1	NA	promoter-TSS (NM_001013390)	promoter-TSS (NM_001013390)	-486	NM_001013390	399548	Mm.335112	NM_001013390	ENSMUSG00000046480	Scn4b	Gm1471	sodium channel, type IV, beta	protein-coding
mm_16352.1	chr2	174346603	174346638	+	1	NA	non-coding (NR_003258, exon 13 of 13)	non-coding (NR_003258, exon 13 of 13)	16531	NM_001077510	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_53190.1	chr6	125483654	125483699	+	1	NA	intron (NM_007657, intron 1 of 7)	intron (NM_007657, intron 1 of 7)	11079	NM_007657	12527	Mm.210676	NM_007657	ENSMUSG00000030342	Cd9	Tspan29	CD9 antigen	protein-coding
mm_133230.1	chr16	76824771	76824772	+	1	NA	Intergenic	Intergenic	186110	NR_040573	76601	Mm.396217	NR_040573	ENSMUSG00000100857	1700041M19Rik	-	RIKEN cDNA 1700041M19 gene	ncRNA
mm_172368.1	chr7	123211872	123211877	+	1	NA	Intergenic	RLTR11B|LTR|ERVK	-2992	NM_146198	233836	Mm.211838	NM_146198	ENSMUSG00000030769	Slc5a11	2010013B02Rik|Kst1|RKST2|SMIT2|Slc5a10	solute carrier family 5 (sodium/glucose cotransporter), member 11	protein-coding
mm_165722.1	chr3	101606941	101606943	+	1	NA	Intergenic	Intergenic	-2235	NM_144900	11928	Mm.193670	NM_144900	ENSMUSG00000033161	Atp1a1	Atpa-1|BC010319	ATPase, Na+/K+ transporting, alpha 1 polypeptide	protein-coding
mm_162352.1	chr1	55335892	55335895	-	1	NA	intron (NM_001113367, intron 6 of 9)	intron (NM_001113367, intron 6 of 9)	26814	NM_001113367	75388	Mm.483408	NM_029267	ENSMUSG00000025977	Boll	4930554P13Rik|4930597B14Rik	bol, boule-like (Drosophila)	protein-coding
mm_169727.1	chr15	80920325	80920325	-	1	NA	intron (NM_144812, intron 21 of 24)	ORR1A2-int|LTR|ERVL-MaLR	-19714	NR_039573	100628612		NR_039573	ENSMUSG00000092868	Mir5113	mir-5113|mmu-mir-5113|mu-mir-5113	microRNA 5113	ncRNA
mm_37469.1	chr4	123564608	123564622	-	1	NA	intron (NM_001199136, intron 1 of 97)	intron (NM_001199136, intron 1 of 97)	-51805	NR_105824	102465214		NR_105824	ENSMUSG00000099005	Mir6398	Gm27657|mmu-mir-6398	microRNA 6398	ncRNA
mm_85688.1	chr9	108057294	108057308	-	1	NA	intron (NM_001311152, intron 31 of 38)	intron (NM_001311152, intron 31 of 38)	4142	NM_177275	320844	Mm.449806	NM_177275	ENSMUSG00000032593	Amigo3	E430002N15Rik|ali3|mKIAA1851	adhesion molecule with Ig like domain 3	protein-coding
mm_112081.1	chr12	112671567	112671577	-	1	NA	5' UTR (NM_001165894, exon 2 of 14)	5' UTR (NM_001165894, exon 2 of 14)	2704	NM_001165894	11651	Mm.6645	NM_009652	ENSMUSG00000001729	Akt1	Akt|LTR-akt|PKB|PKB/Akt|PKBalpha|Rac	thymoma viral proto-oncogene 1	protein-coding
mm_138252.1	chr17	34590163	34590205	+	1	NA	5' UTR (NM_134116, exon 1 of 4)	5' UTR (NM_134116, exon 1 of 4)	378	NM_134116	106512	Mm.26584	NM_134116	ENSMUSG00000034786	Gpsm3	AA960287|AGS4	G-protein signalling modulator 3 (AGS3-like, C. elegans)	protein-coding
mm_20597.1	chr2	131328983	131328989	-	1	NA	intron (NM_178607, intron 1 of 5)	MTD|LTR|ERVL-MaLR	23906	NM_178607	51902	Mm.477523	NM_178607	ENSMUSG00000048911	Rnf24	2810473M14Rik|4930505A13Rik|AI317164|C86507|D2Ertd504e	ring finger protein 24	protein-coding
mm_52481.1	chr6	114315681	114315689	+	1	NA	3' UTR (NM_178703, exon 16 of 16)	3' UTR (NM_178703, exon 16 of 16)	33050	NM_178703	232333	Mm.5260	NM_178703	ENSMUSG00000030310	Slc6a1	A730043E01|GABATHG|GABATR|GAT-1|Gabt|Gabt1|Gat1|XT-1|Xtrp1	solute carrier family 6 (neurotransmitter transporter, GABA), member 1	protein-coding
mm_74768.1	chr8	20922093	20922098	-	1	NA	promoter-TSS (NM_001025353)	promoter-TSS (NM_001025353)	-24	NM_001025353	100503992	Mm.490240	NM_001025353	ENSMUSG00000071165	Gm6040	Defb51|EG574083	predicted gene 6040	protein-coding
mm_131406.1	chr16	14403154	14403156	+	1	NA	intron (NM_008576, intron 5 of 30)	MIR|SINE|MIR	41597	NM_008576	17250	Mm.196634	NM_008576	ENSMUSG00000023088	Abcc1	Abcc1a|Abcc1b|MRP|Mdrap|Mrp1	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	protein-coding
mm_72627.1	chr8	84660199	84660205	+	1	NA	Intergenic	Intergenic	2650	NM_010499	15936	Mm.399	NM_010499	ENSMUSG00000053560	Ier2	AI317238|Ch1|Pip92	immediate early response 2	protein-coding
mm_69922.1	chr7	141875202	141875205	-	1	NA	Intergenic	Intergenic	27203	NM_023764	54473	Mm.103551	NM_023764	ENSMUSG00000025139	Tollip	4930403G24Rik|4931428G15Rik	toll interacting protein	protein-coding
mm_35361.1	chr4	32375159	32375166	-	1	NA	Intergenic	Intergenic	-42273	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_144890.1	chr18	36939179	36939212	+	1	NA	promoter-TSS (NM_198117)	promoter-TSS (NM_198117)	-10	NM_198117	353234	Mm.308500	NM_198117	ENSMUSG00000104148	Pcdha2	-	protocadherin alpha 2	protein-coding
mm_71472.1	chr8	46535163	46535173	+	1	NA	3' UTR (NM_007981, exon 21 of 21)	3' UTR (NM_007981, exon 21 of 21)	-16901	NM_027973	71876	Mm.22108	NM_027973	ENSMUSG00000031629	Cenpu	1700029A22Rik|Mlf1ip	centromere protein U	protein-coding
mm_160482.1	chr8	123982907	123982907	-	1	NA	5' UTR (NM_019552, exon 1 of 13)	5' UTR (NM_019552, exon 1 of 13)	215	NM_019552	56199	Mm.274243	NM_019552	ENSMUSG00000031974	Abcb10	Abc-me|Abcb12	ATP-binding cassette, sub-family B (MDR/TAP), member 10	protein-coding
mm_69695.1	chr7	140036257	140036318	-	1	NA	promoter-TSS (NM_001286011)	promoter-TSS (NM_001286011)	63	NM_133755	74237	Mm.40888	NM_133755	ENSMUSG00000025474	Tubgcp2	1700022B05Rik	tubulin, gamma complex associated protein 2	protein-coding
mm_131764.1	chr16	22892551	22892581	+	1	NA	intron (NR_075099, intron 1 of 5)	intron (NR_075099, intron 1 of 5)	551	NM_001276449	11625	Mm.197554	NM_013465	ENSMUSG00000022868	Ahsg	-	alpha-2-HS-glycoprotein	protein-coding
mm_105604.1	chr11	106779484	106779559	-	1	NA	promoter-TSS (NR_027785)	promoter-TSS (NR_027785)	-6	NR_027785	50776	Mm.859	NM_015810	ENSMUSG00000020718	Polg2	-	polymerase (DNA directed), gamma 2, accessory subunit	protein-coding
mm_26958.1	chr3	21958629	21958642	-	1	NA	Intergenic	MIR|SINE|MIR	-118017	NM_030732	81004	Mm.202966	NM_030732	ENSMUSG00000027630	Tbl1xr1	8030499H02Rik|A630076E03Rik|AW539987|C21|C230089I12Rik|DC42|Ira1|TBLR1	transducin (beta)-like 1X-linked receptor 1	protein-coding
mm_24591.1	chr3	93445081	93445092	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	2756	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_151754.1	chr19	5098461	5098559	-	1	NA	promoter-TSS (NM_009920)	promoter-TSS (NM_009920)	11	NM_001302333	12794	Mm.299737	NM_009920	ENSMUSG00000024873	Cnih2	CNIH-2|Cnil	cornichon family AMPA receptor auxiliary protein 2	protein-coding
mm_15006.1	chr2	152477078	152477085	+	1	NA	promoter-TSS (NM_176950)	promoter-TSS (NM_176950)	18	NM_176950	319579	Mm.190454	NM_176950	ENSMUSG00000049560	Defb20	9230107O10Rik|BD-20|mBD-20	defensin beta 20	protein-coding
mm_133952.1	chr16	3976627	3976636	-	1	NA	promoter-TSS (NM_001081280)	promoter-TSS (NM_001081280)	1	NM_175547	268857	Mm.215994	NM_175547	ENSMUSG00000049871	Nlrc3	CLR16.2|D230007K08Rik|mFLJ00348	NLR family, CARD domain containing 3	protein-coding
mm_40418.1	chr5	53378919	53378933	+	1	NA	Intergenic	Intergenic	111820	NM_001145433	66278	Mm.27900	NM_001145433	ENSMUSG00000061461	Smim20	1110067B18Rik|1810013D10Rik|N28078	small integral membrane protein 20	protein-coding
mm_64533.1	chr7	144175453	144175486	+	1	NA	promoter-TSS (NM_001113373)	promoter-TSS (NM_001113373)	-51	NM_001113373	210274	Mm.483624	NM_001081370	ENSMUSG00000037541	Shank2	ProSAP1|mKIAA1022	SH3/ankyrin domain gene 2	protein-coding
mm_121410.1	chr14	119445623	119445631	+	1	NA	intron (NM_015820, intron 1 of 1)	intron (NM_015820, intron 1 of 1)	-303600	NR_045621	75432	Mm.443277	NR_045621	ENSMUSG00000100274	1700006F04Rik	-	RIKEN cDNA 1700006F04 gene	ncRNA
mm_41097.1	chr5	87694765	87694765	+	1	NA	exon (NM_001286023, exon 5 of 7)	exon (NM_001286023, exon 5 of 7)	4660	NM_001286020	12991	Mm.268737	NM_009972	ENSMUSG00000063157	Csn2	Csnb	casein beta	protein-coding
mm_146757.1	chr18	16808551	16808561	-	1	NA	5' UTR (NM_007664, exon 1 of 16)	5' UTR (NM_007664, exon 1 of 16)	690	NM_007664	12558	Mm.257437	NM_007664	ENSMUSG00000024304	Cdh2	CDHN|N-CAD|Ncad	cadherin 2	protein-coding
mm_106052.1	chr11	116086930	116086979	-	1	NA	promoter-TSS (NM_016852)	promoter-TSS (NM_016852)	10	NM_016852	22378	Mm.284792	NM_016852	ENSMUSG00000034341	Wbp2	-	WW domain binding protein 2	protein-coding
mm_122080.1	chr14	30607809	30607821	-	1	NA	intron (NM_011103, intron 3 of 17)	intron (NM_011103, intron 3 of 17)	2495	NM_001310682	18753	Mm.2314	NM_011103	ENSMUSG00000021948	Prkcd	AI385711|D14Ertd420e|PKC[d]|PKCdelta|Pkcd	protein kinase C, delta	protein-coding
mm_37308.1	chr4	119294448	119294470	-	1	NA	promoter-TSS (NM_011732)	promoter-TSS (NM_011732)	54	NM_011732	22608	Mm.258204	NM_011732	ENSMUSG00000028639	Ybx1	1700102N10Rik|C79409|EF1A|MSY1|Nsep1|YB-1|dbpB|mYB-1a	Y box protein 1	protein-coding
mm_55308.1	chr6	54972561	54972583	-	1	NA	promoter-TSS (NM_172729)	promoter-TSS (NM_172729)	40	NM_172729	107607	Mm.28498	NM_172729	ENSMUSG00000038058	Nod1	C230079P11|Card4|F830007N14Rik|Nlrc1	nucleotide-binding oligomerization domain containing 1	protein-coding
mm_9642.1	chr1	177203905	177203913	-	1	NA	intron (NM_011785, intron 1 of 12)	intron (NM_011785, intron 1 of 12)	44858	NM_011785	23797	Mm.235194	NM_011785	ENSMUSG00000019699	Akt3	AI851531|D930002M15Rik|Nmf350	thymoma viral proto-oncogene 3	protein-coding
mm_39414.1	chr5	15619088	15619110	+	1	NA	promoter-TSS (NM_025759)	promoter-TSS (NM_025759)	0	NM_025759	360220	Mm.425235	NM_025759	ENSMUSG00000070933	Speer4d	4933431D05Rik|SPEER-4D	spermatogenesis associated glutamate (E)-rich protein 4D	protein-coding
mm_54164.1	chr6	23122401	23122408	-	1	NA	intron (NM_013930, intron 2 of 23)	intron (NM_013930, intron 2 of 23)	10582	NM_013930	30956	Mm.18651	NM_013930	ENSMUSG00000029695	Aass	LKR|LKR/SDH|LOR|LOR/SDH|Lorsdh|SDH	aminoadipate-semialdehyde synthase	protein-coding
mm_143600.1	chr17	75551839	75551901	-	1	NA	promoter-TSS (NM_133747)	promoter-TSS (NM_133747)	76	NM_133747	72722	Mm.24641	NM_133747	ENSMUSG00000002017	Fam98a	2810405J04Rik|AL024114	family with sequence similarity 98, member A	protein-coding
mm_121251.1	chr14	103057521	103057529	+	1	NA	TTS (NM_008392)	TTS (NM_008392)	10513	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_132615.1	chr16	38712452	38712454	+	1	NA	intron (NM_020260, intron 1 of 11)	intron (NM_020260, intron 1 of 11)	582	NM_020260	12549	Mm.370848	NM_020260	ENSMUSG00000022799	Arhgap31	5830477L08Rik|AU041750|Cdgap|D330026I07Rik	Rho GTPase activating protein 31	protein-coding
mm_12834.1	chr2	80638799	80638834	+	1	NA	promoter-TSS (NM_027091)	promoter-TSS (NM_027091)	4	NM_027091	69482	Mm.29200	NM_027091	ENSMUSG00000026999	Nup35	2310006I24Rik|35kDa|5330402E05Rik|MP44|NO44	nucleoporin 35	protein-coding
mm_159692.1	chr5	24030078	24030078	-	1	NA	5' UTR (NM_001310471, exon 1 of 11)	5' UTR (NM_001310471, exon 1 of 11)	234	NM_001310471	84652	Mm.304976	NM_053090	ENSMUSG00000028995	Fam126a	AB030242|Drctnnb1a	family with sequence similarity 126, member A	protein-coding
mm_68501.1	chr7	111080290	111080313	-	1	NA	exon (NM_013507, exon 4 of 22)	exon (NM_013507, exon 4 of 22)	2729	NM_001040131	13690	Mm.185453	NM_013507	ENSMUSG00000005610	Eif4g2	DAP-5|E130105L11Rik|Nat1|Natm1|p97	eukaryotic translation initiation factor 4, gamma 2	protein-coding
mm_108645.1	chr12	85956438	85956452	+	1	NA	intron (NM_001347395, intron 28 of 32)	intron (NM_001347395, intron 28 of 32)	122596	NM_009368	21809	Mm.3992	NM_009368	ENSMUSG00000021253	Tgfb3	TGF-beta-3|Tgfb-3	transforming growth factor, beta 3	protein-coding
mm_82741.1	chr9	26791926	26791928	-	1	NA	intron (NM_001310768, intron 4 of 18)	intron (NM_001310768, intron 4 of 18)	14490	NM_153803	244757	Mm.293696	NM_153803	ENSMUSG00000036395	Glb1l2	-	galactosidase, beta 1-like 2	protein-coding
mm_153660.1	chr19	44395324	44395333	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	12381	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_48686.1	chr5	146732926	146732952	-	1	NA	Intergenic	PB1D11|SINE|Alu	62017	NM_011669	22217	Mm.167971	NM_011669	ENSMUSG00000029640	Usp12	Ubh1	ubiquitin specific peptidase 12	protein-coding
mm_36249.1	chr4	63403278	63403286	-	1	NA	5' UTR (NM_001045514, exon 1 of 22)	5' UTR (NM_001045514, exon 1 of 22)	163	NM_001045514	100182	Mm.387725	NM_001045514	ENSMUSG00000039158	Akna	AI597013	AT-hook transcription factor	protein-coding
mm_169599.1	chr15	34367907	34367911	-	1	NA	intron (NM_016762, intron 4 of 18)	RLTR11C_MM|LTR|ERVK	-10037	NM_001256161	77358	Mm.402759	NM_001256161	ENSMUSG00000094447	9430069I07Rik	-	RIKEN cDNA 9430069I07 gene	protein-coding
mm_105531.1	chr11	106300897	106300929	-	1	NA	exon (NM_008117, exon 4 of 5)	exon (NM_008117, exon 4 of 5)	983	NM_008117	14599	Mm.343934	NM_008117	ENSMUSG00000020713	Gh	Gh1|Ghb1	growth hormone	protein-coding
mm_50348.1	chr6	48589547	48589555	+	1	NA	5' UTR (NM_183309, exon 1 of 2)	5' UTR (NM_183309, exon 1 of 2)	106	NM_183309	330305	Mm.123868	NM_183309	ENSMUSG00000052730	Gm5111	A630038D02|EG330305	predicted gene 5111	protein-coding
mm_690.1	chr1	40542995	40543008	+	1	NA	exon (NM_010553, exon 11 of 13)	exon (NM_010553, exon 11 of 13)	27639	NM_010553	16174	Mm.20466	NM_010553	ENSMUSG00000026068	Il18rap	AcPL|IL-18R-beta|IL-18RAcP|IL-18Rbeta|IL-1RAcPL	interleukin 18 receptor accessory protein	protein-coding
mm_77675.1	chr8	124949151	124949161	-	1	NA	promoter-TSS (NM_053207)	promoter-TSS (NM_053207)	98	NM_053207	112405	Mm.140619	NM_053207	ENSMUSG00000031987	Egln1	AI503754|C1orf12|HIF-PH2|HPH-2|Hif-p4h-2|ORF13|Phd2|SM-20	egl-9 family hypoxia-inducible factor 1	protein-coding
mm_32889.1	chr4	118964178	118964181	+	1	NA	intron (NM_133892, intron 2 of 6)	intron (NM_133892, intron 2 of 6)	2212	NM_133892	100470	Mm.26698	NM_133892	ENSMUSG00000024903	Lao1	AW990848	L-amino acid oxidase 1	protein-coding
mm_82005.1	chr9	121710347	121710361	+	1	NA	promoter-TSS (NM_026794)	promoter-TSS (NM_026794)	-35	NM_026794	26901	Mm.24848	NM_026794	ENSMUSG00000032526	Ss18l2	1110020I04Rik|AI463209|Deb1	SS18, nBAF chromatin remodeling complex subunit like 2	protein-coding
mm_159423.1	chr3	108210915	108210915	-	1	NA	promoter-TSS (NM_001289545)	promoter-TSS (NM_001289545)	-388	NM_175183	72522	Mm.187326	NM_175183	ENSMUSG00000048997	Atxn7l2	2610528J18Rik	ataxin 7-like 2	protein-coding
mm_115499.1	chr13	3894296	3894300	-	1	NA	promoter-TSS (NM_001047159)	promoter-TSS (NM_001047159)	-717	NM_001047159	56349	Mm.22261	NM_019671	ENSMUSG00000021215	Net1	Net1a|mNET1	neuroepithelial cell transforming gene 1	protein-coding
mm_90561.1	chr10	128194677	128194687	+	1	NA	promoter-TSS (NM_001285779)	promoter-TSS (NM_001285779)	47	NM_001285779	216456	Mm.30102	NM_001033264	ENSMUSG00000044005	Gls2	A330074B06Rik|AI195532|GA|GLS|Lga	glutaminase 2 (liver, mitochondrial)	protein-coding
mm_93702.1	chr10	118097964	118097967	-	1	NA	Intergenic	Intergenic	-43822	NM_001162904	17245	Mm.101191	NM_010785	ENSMUSG00000020212	Mdm1	Arrd2|Mdm-1	transformed mouse 3T3 cell double minute 1	protein-coding
mm_142932.1	chr17	55712635	55712655	-	1	NA	promoter-TSS (NM_028370)	promoter-TSS (NM_028370)	-17	NM_028370	72836	Mm.177073	NM_028370	ENSMUSG00000024174	Pot1b	2810458H16Rik	protection of telomeres 1B	protein-coding
mm_152741.1	chr19	19035517	19035517	-	1	NA	intron (NM_001043354, intron 1 of 9)	MTD|LTR|ERVL-MaLR	-34400	NM_001289921	225998	Mm.234641	NM_146095	ENSMUSG00000036192	Rorb	Nr1f2|RZR-beta|RZRB|Rorbeta|hstp	RAR-related orphan receptor beta	protein-coding
mm_149790.1	chr19	23141065	23141077	+	1	NA	promoter-TSS (NM_010638)	promoter-TSS (NM_010638)	-155	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_172866.1	chr9	40804245	40804250	+	1	NA	exon (NM_031165, exon 7 of 9)	exon (NM_031165, exon 7 of 9)	2974	NM_031165	15481	Mm.290774	NM_031165	ENSMUSG00000015656	Hspa8	2410008N15Rik|Hsc70|Hsc71|Hsc73|Hsp73|Hspa10	heat shock protein 8	protein-coding
mm_72374.1	chr8	81342525	81342545	+	1	NA	promoter-TSS (NM_001297596)	promoter-TSS (NM_001297596)	-27	NM_001024617	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_152571.1	chr19	11590043	11590133	-	1	NA	exon (NM_026835, exon 5 of 7)	exon (NM_026835, exon 5 of 7)	14716	NM_026835	68774	Mm.290390	NM_026835	ENSMUSG00000024679	Ms4a6d	1110058E16Rik|AI447446|Ms4a11	membrane-spanning 4-domains, subfamily A, member 6D	protein-coding
mm_43114.1	chr5	124579135	124579184	+	1	NA	promoter-TSS (NM_145371)	promoter-TSS (NM_145371)	11	NM_181410	209357	Mm.185467	NM_181410	ENSMUSG00000029387	Gtf2h3	34kDa|5033417D07Rik|BTF2|BTF2 p34|C730029A10|D5Ertd679e|TFIIH	general transcription factor IIH, polypeptide 3	protein-coding
mm_85370.1	chr9	103221560	103221566	-	1	NA	intron (NM_133977, intron 8 of 16)	intron (NM_133977, intron 8 of 16)	8723	NM_133977	22041	Mm.37214	NM_133977	ENSMUSG00000032554	Trf	AI266983|Cd176|HP|Tf|Tfn|hpx	transferrin	protein-coding
mm_91565.1	chr10	40025292	40025302	-	1	NA	promoter-TSS (NM_144821)	promoter-TSS (NM_144821)	-29	NM_144821	215929	Mm.55513	NM_144821	ENSMUSG00000038522	Mfsd4b1	AI317395|AI482555|Naglt1a	major facilitator superfamily domain containing 4B1	protein-coding
mm_110157.1	chr12	26456424	26456440	-	1	NA	promoter-TSS (NM_021384)	promoter-TSS (NM_021384)	20	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_147744.1	chr18	61130835	61130847	-	1	NA	TTS (NM_178277)	TTS (NM_178277)	13373	NR_105949	102466212		NR_105949	ENSMUSG00000098389	Mir6983	Gm27496|mmu-mir-6983	microRNA 6983	ncRNA
mm_37281.1	chr4	118967994	118967998	-	1	NA	exon (NM_133892, exon 7 of 7)	exon (NM_133892, exon 7 of 7)	6029	NM_133892	100470	Mm.26698	NM_133892	ENSMUSG00000024903	Lao1	AW990848	L-amino acid oxidase 1	protein-coding
mm_22536.1	chr3	8560327	8560357	+	1	NA	3' UTR (NM_025285, exon 5 of 5)	3' UTR (NM_025285, exon 5 of 5)	50815	NM_025285	20257	Mm.29580	NM_025285	ENSMUSG00000027500	Stmn2	AI159727|SCG10|Scgn10|Stmb2	stathmin-like 2	protein-coding
mm_74336.1	chr8	127069096	127069115	+	1	NA	intron (NM_001309391, intron 1 of 24)	(GGGA)n|Simple_repeat|Simple_repeat	5049	NM_001309391	93742	Mm.299254	NM_033620	ENSMUSG00000025812	Pard3	AA960621|AI256638|Asip|D8Ertd580e|Par-3|Par3|Pard-3|Pard3a|Phip	par-3 family cell polarity regulator	protein-coding
mm_16404.1	chr2	180034611	180034617	+	1	NA	3' UTR (NM_177727, exon 9 of 9)	3' UTR (NM_177727, exon 9 of 9)	7850	NM_001289476	26444	Mm.21728	NM_011969	ENSMUSG00000027566	Psma7	C6-I	proteasome (prosome, macropain) subunit, alpha type 7	protein-coding
mm_28520.1	chr3	92586844	92586852	-	1	NA	intron (NM_008574, intron 1 of 1)	intron (NM_008574, intron 1 of 1)	2176	NM_008574	17235	Mm.331192	NM_008574		Smcp	Mcs|Mcsp	sperm mitochondria-associated cysteine-rich protein	protein-coding
mm_40500.1	chr5	57721866	57721875	+	1	NA	exon (NM_001310606, exon 1 of 3)	exon (NM_001310606, exon 1 of 3)	3789	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_116660.1	chr13	49195970	49195988	-	1	NA	3' UTR (NM_013610, exon 4 of 4)	3' UTR (NM_013610, exon 4 of 4)	8432	NM_013610	18081	Mm.18503	NM_013610	ENSMUSG00000037966	Ninj1	AU024536	ninjurin 1	protein-coding
mm_105912.1	chr11	114983899	114983935	-	1	NA	3' UTR (NM_145437, exon 4 of 4)	3' UTR (NM_145437, exon 4 of 4)	5969	NM_145437	217305	Mm.275986	NM_145437	ENSMUSG00000034641	Cd300ld	4732429D16Rik|CLM5|Cd300ld1|LMIR4|MAIR-IV|clm-5	CD300 molecule like family member d	protein-coding
mm_49717.1	chr6	34486623	34486642	+	1	NA	intron (NM_007563, intron 1 of 2)	intron (NM_007563, intron 1 of 2)	10276	NM_007563	12183	Mm.282863	NM_007563	ENSMUSG00000038871	Bpgm	AI323730|AL022789|C86192	2,3-bisphosphoglycerate mutase	protein-coding
mm_113906.1	chr13	49307915	49307937	+	1	NA	intron (NM_015759, intron 1 of 17)	B4|SINE|B4	1282	NM_015759	30938	Mm.291089	NM_015759	ENSMUSG00000037946	Fgd3	5830461L01Rik|ZFYVE5	FYVE, RhoGEF and PH domain containing 3	protein-coding
mm_114630.1	chr13	76189074	76189079	+	1	NA	Intergenic	Intergenic	90342	NM_001081352	218343	Mm.277964	NM_001081352	ENSMUSG00000033991	Ttc37	mKIAA0372	tetratricopeptide repeat domain 37	protein-coding
mm_94091.1	chr10	128520737	128520748	-	1	NA	exon (NM_011843, exon 9 of 31)	exon (NM_011843, exon 9 of 31)	5117	NM_011843	23943	Mm.66056	NM_011843	ENSMUSG00000025366	Esyt1	Fam62a|Mbc2|vp115	extended synaptotagmin-like protein 1	protein-coding
mm_164650.1	chr17	35567436	35567447	+	1	NA	promoter-TSS (NM_175148)	promoter-TSS (NM_175148)	-44	NM_175148	69542	Mm.265291	NM_175148	ENSMUSG00000039269	2300002M23Rik	Stg|emprin	RIKEN cDNA 2300002M23 gene	protein-coding
mm_146949.1	chr18	32555426	32555430	-	1	NA	intron (NM_001048207, intron 1 of 2)	intron (NM_001048207, intron 1 of 2)	4606	NM_001347610	71683	Mm.292145	NM_027863	ENSMUSG00000090523	Gypc	0610037F22Rik|Cd236r	glycophorin C	protein-coding
mm_23497.1	chr3	60517150	60517152	+	1	NA	intron (NM_001253710, intron 1 of 7)	intron (NM_001253710, intron 1 of 7)	15972	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_49529.1	chr6	30048063	30048078	+	1	NA	promoter-TSS (NM_001164227)	promoter-TSS (NM_001164227)	82	NM_001164226	18181	Mm.259258	NM_010938	ENSMUSG00000058440	Nrf1	C87038|D6Ertd415e	nuclear respiratory factor 1	protein-coding
mm_127903.1	chr15	9508758	9508786	-	1	NA	exon (NM_008372, exon 7 of 8)	exon (NM_008372, exon 7 of 8)	21104	NM_008372	16197	Mm.389	NM_008372	ENSMUSG00000003882	Il7r	CD127|IL-7Ralpha	interleukin 7 receptor	protein-coding
mm_73890.1	chr8	119417379	119417394	+	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	-19776	NM_027950	71839	Mm.272357	NM_027950	ENSMUSG00000074063	Osgin1	1700012B18Rik|Okl38	oxidative stress induced growth inhibitor 1	protein-coding
mm_59500.1	chr7	27541655	27541704	+	1	NA	intron (NM_001317355, intron 6 of 13)	intron (NM_001317355, intron 6 of 13)	11539	NM_011116	18807	Mm.6483	NM_011116	ENSMUSG00000003363	Pld3	Sam-9	phospholipase D family, member 3	protein-coding
mm_148635.1	chr19	5474618	5474644	+	1	NA	promoter-TSS (NM_021474)	promoter-TSS (NM_021474)	-59	NM_021474	58859	Mm.276367	NM_021474	ENSMUSG00000024909	Efemp2	0610011K11Rik|Fbln4|MBP1	epidermal growth factor-containing fibulin-like extracellular matrix protein 2	protein-coding
mm_155300.1	chrX	61185701	61185734	+	1	NA	promoter-TSS (NM_001166658)	promoter-TSS (NM_001166658)	-159	NM_001166658	631990	Mm.401324	NM_001166658	ENSMUSG00000090546	Cdr1	100039759|Cdr|Cdr34|EG631990|Gm2409|Gm7077	cerebellar degeneration related antigen 1	protein-coding
mm_4833.1	chr1	186587363	186587372	+	1	NA	Intergenic	MIR|SINE|MIR	-28686	NR_131158	320449	Mm.404477	NR_131124	ENSMUSG00000103690	A730004F24Rik	-	RIKEN cDNA A730004F24 gene	ncRNA
mm_125338.1	chr15	39006092	39006106	+	1	NA	promoter-TSS (NM_008056)	promoter-TSS (NM_008056)	-181	NM_001162494	14368	Mm.4769	NM_008056	ENSMUSG00000022297	Fzd6	Fz6	frizzled class receptor 6	protein-coding
mm_124080.1	chr14	78644444	78644456	-	1	NA	promoter-TSS (NR_104044)	promoter-TSS (NR_104044)	1	NR_104044	380921	Mm.89591	NM_001081336	ENSMUSG00000034731	Dgkh	5930402B05Rik|D130015C16|DGK	diacylglycerol kinase, eta	protein-coding
mm_154612.1	chrX	7652816	7652829	+	1	NA	3' UTR (NM_009305, exon 7 of 7)	3' UTR (NM_009305, exon 7 of 7)	-4557	NM_001290624	54630	Mm.232232	NM_175097	ENSMUSG00000031145	Prickle3	Lmo6|Sfc16	prickle planar cell polarity protein 3	protein-coding
mm_24574.1	chr3	93444654	93444665	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	2329	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_135998.1	chr16	75307976	75307979	-	1	NA	Intergenic	Intergenic	278084	NM_001252513	320355	Mm.99517	NM_177142	ENSMUSG00000032948	Lipi	D930038D03Rik|lpd1	lipase, member I	protein-coding
mm_158004.1	chrX	95196451	95196519	-	1	NA	Intergenic	CpG	-29946	NM_001033329	236915	Mm.44841	NM_001033329	ENSMUSG00000025656	Arhgef9	9630036L12Rik	CDC42 guanine nucleotide exchange factor (GEF) 9	protein-coding
mm_40556.1	chr5	59685079	59685080	+	1	NA	Intergenic	Lx8|LINE|L1	300923	NR_040683	71057	Mm.50817	NR_040682	ENSMUSG00000106013	4933402J10Rik	-	RIKEN cDNA 4933402J10 gene	ncRNA
mm_144366.1	chr18	20473245	20473245	+	1	NA	Intergenic	Intergenic	-37029	NM_030596	13512	Mm.106811	NM_030596	ENSMUSG00000056632	Dsg3	bal	desmoglein 3	protein-coding
mm_90477.1	chr10	127866499	127866507	+	1	NA	promoter-TSS (NM_145424)	promoter-TSS (NM_145424)	27	NM_145424	216454	Mm.214923	NM_145424	ENSMUSG00000074639	BC089597	CRAD-L	cDNA sequence BC089597	protein-coding
mm_40879.1	chr5	74402993	74402998	+	1	NA	intron (NM_001286437, intron 4 of 7)	MTD|LTR|ERVL-MaLR	128747	NM_178672	212986	Mm.134147	NM_178672	ENSMUSG00000062110	Scfd2	E430013M20Rik|STXBP1L1	Sec1 family domain containing 2	protein-coding
mm_77561.1	chr8	123427646	123427659	-	1	NA	Intergenic	MuLV-int|LTR|ERV1	-15304	NM_001253784	23854	Mm.275127	NM_054046	ENSMUSG00000001482	Def8	AI449518|D8Ertd713e|DEF-8	differentially expressed in FDCP 8	protein-coding
mm_154407.1	chrM	14637	14662	+	1	NA	NA	Intergenic	NA	NA								
mm_93517.1	chr10	115287992	115288001	-	1	NA	Intergenic	Intergenic	27595	NM_024454	216344	Mm.21936	NM_024454	ENSMUSG00000020132	Rab21	9630024B22	RAB21, member RAS oncogene family	protein-coding
mm_26268.1	chr3	142503029	142503081	+	1	NA	exon (NM_153564, exon 4 of 11)	exon (NM_153564, exon 4 of 11)	6121	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_61121.1	chr7	55768174	55768187	+	1	NA	promoter-TSS (NM_001310740)	promoter-TSS (NM_001310740)	-4	NM_001310740	233274	Mm.44425	NM_178706	ENSMUSG00000051504	Siglech	6430529G09Rik|Siglec-H	sialic acid binding Ig-like lectin H	protein-coding
mm_168670.1	chr11	92155597	92155601	-	1	NA	Intergenic	B1_Mus2|SINE|Alu	-578044	NM_028547	73470	Mm.67677	NM_028547	ENSMUSG00000046755	Kif2b	1700063D03Rik	kinesin family member 2B	protein-coding
mm_67513.1	chr7	80803254	80803312	-	1	NA	promoter-TSS (NM_016721)	promoter-TSS (NM_016721)	48	NM_016721	29875	Mm.207619	NM_016721	ENSMUSG00000030536	Iqgap1	AA682088|D7Ertd237e|D7Ertd257e|mKIAA0051	IQ motif containing GTPase activating protein 1	protein-coding
mm_46463.1	chr5	105120954	105120983	-	1	NA	exon (NM_001256005, exon 8 of 11)	exon (NM_001256005, exon 8 of 11)	-10676	NM_172777	236573	Mm.425261	NM_172777	ENSMUSG00000029298	Gbp9	-	guanylate-binding protein 9	protein-coding
mm_115197.1	chr13	108956150	108956157	+	1	NA	intron (NM_011056, intron 2 of 16)	L1_Mur3|LINE|L1	301976	NM_011056	238871	Mm.434429	NM_011056	ENSMUSG00000021699	Pde4d	9630011N22Rik|Dpde3	phosphodiesterase 4D, cAMP specific	protein-coding
mm_83439.1	chr9	44999352	44999362	-	1	NA	3' UTR (NM_007648, exon 8 of 8)	3' UTR (NM_007648, exon 8 of 8)	10233	NM_007648	12501	Mm.210361	NM_007648	ENSMUSG00000032093	Cd3e	AI504783|CD3|CD3epsilon|T3e	CD3 antigen, epsilon polypeptide	protein-coding
mm_6366.1	chr1	72228993	72229016	-	1	NA	Intergenic	Intergenic	-16697	NM_001005423	381269	Mm.422636	NM_001005423	ENSMUSG00000039395	Mreg	Gm974|Wdt2|dsu	melanoregulin	protein-coding
mm_166031.1	chr4	126495848	126495849	+	1	NA	intron (NM_153177, intron 17 of 17)	L2c|LINE|L2	-27265	NM_153403	236511	Mm.30800	NM_153403	ENSMUSG00000041530	Ago1	Eif2c1	argonaute RISC catalytic subunit 1	protein-coding
mm_39258.1	chr5	3543863	3543884	+	1	NA	promoter-TSS (NM_001042501)	promoter-TSS (NM_001042501)	40	NM_001042501	68152	Mm.240265	NM_026583	ENSMUSG00000058503	Fam133b	2900022K02Rik|5830415L20Rik	family with sequence similarity 133, member B	protein-coding
mm_98519.1	chr11	94952704	94952718	+	1	NA	3' UTR (NM_007742, exon 51 of 51)	3' UTR (NM_007742, exon 51 of 51)	-14882	NM_018792	54388	Mm.30482	NM_018792	ENSMUSG00000038994	Hils1	H1.9|TISP64	histone H1-like protein in spermatids 1	protein-coding
mm_146462.1	chr18	86711060	86711063	+	1	NA	promoter-TSS (NM_001302356)	promoter-TSS (NM_001302356)	-49	NM_001302356	12405	Mm.70775	NM_172633	ENSMUSG00000024647	Cbln2	6330593N19Rik|A730004O05	cerebellin 2 precursor protein	protein-coding
mm_107667.1	chr12	53248218	53248240	+	1	NA	promoter-TSS (NM_013780)	promoter-TSS (NM_013780)	-448	NM_013780	27386	Mm.247044	NM_013780	ENSMUSG00000021010	Npas3	4930423H22Rik|bHLHe12	neuronal PAS domain protein 3	protein-coding
mm_167162.1	chr7	135698960	135698998	-	1	NA	exon (NM_001081117, exon 12 of 14)	exon (NM_001081117, exon 12 of 14)	17400	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_21265.1	chr2	156781578	156781593	-	1	NA	TTS (NM_172118)	TTS (NM_172118)	6121	NM_172118	98932	Mm.271770	NM_172118	ENSMUSG00000067818	Myl9	AI327049|MLC20|Mylc2c|RLC-C	myosin, light polypeptide 9, regulatory	protein-coding
mm_109617.1	chr12	112761631	112761644	+	1	NA	intron (NM_178911, intron 1 of 10)	intron (NM_178911, intron 1 of 10)	982	NM_178911	104759	Mm.203915	NM_178911	ENSMUSG00000052160	Pld4	AI132321|thss	phospholipase D family, member 4	protein-coding
mm_40982.1	chr5	77205354	77205368	+	1	NA	3' UTR (NM_001289764, exon 4 of 4)	3' UTR (NM_001289764, exon 4 of 4)	5844	NM_001289767	69982	Mm.46106	NM_183284	ENSMUSG00000053030	Spink2	1700007F22Rik|AV038945|HUSI-II	serine peptidase inhibitor, Kazal type 2	protein-coding
mm_70975.1	chr8	27143170	27143181	+	1	NA	non-coding (NR_045840, exon 1 of 4)	non-coding (NR_045840, exon 1 of 4)	265	NR_045840	71082	Mm.395259	NR_045840		4933416M07Rik	-	RIKEN cDNA 4933416M07 gene	ncRNA
mm_166888.1	chr7	28107320	28107328	+	1	NA	exon (NM_001122603, exon 16 of 20)	exon (NM_001122603, exon 16 of 20)	-22142	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_54661.1	chr6	39165031	39165036	-	1	NA	intron (NM_001033430, intron 9 of 19)	intron (NM_001033430, intron 9 of 19)	41740	NM_001033430	338523	Mm.293175	NM_001033430	ENSMUSG00000042599	Kdm7a	A630082K20Rik|BB041802|ENSMUSG00000073143|Jhdm1d|mKIAA1718	lysine (K)-specific demethylase 7A	protein-coding
mm_122331.1	chr14	37110066	37110077	-	1	NA	promoter-TSS (NM_001206684)	promoter-TSS (NM_001206684)	30	NM_001206684	70045	Mm.271619	NM_001206684	ENSMUSG00000096001	2610528A11Rik	AW494830	RIKEN cDNA 2610528A11 gene	protein-coding
mm_136247.1	chr16	90937202	90937220	-	1	NA	3' UTR (NM_001045515, exon 33 of 33)	3' UTR (NM_001045515, exon 33 of 33)	-2362	NM_026502	68001	Mm.45374	NM_026502	ENSMUSG00000022972	1110004E09Rik	-	RIKEN cDNA 1110004E09 gene	protein-coding
mm_150300.1	chr19	34560760	34560769	+	1	NA	intron (NM_008332, intron 1 of 2)	RMER17C2|LTR|ERVK	10070	NM_008332	15958	Mm.2036	NM_008332	ENSMUSG00000045932	Ifit2	AV302338|Ifi54|P54	interferon-induced protein with tetratricopeptide repeats 2	protein-coding
mm_19121.1	chr2	80039003	80039017	-	1	NA	intron (NM_001159582, intron 2 of 15)	intron (NM_001159582, intron 2 of 15)	89961	NM_016744	18573	Mm.40678	NM_016744	ENSMUSG00000059173	Pde1a	AI987702|AW125737	phosphodiesterase 1A, calmodulin-dependent	protein-coding
mm_92378.1	chr10	76416861	76416876	-	1	NA	intron (NM_008787, intron 13 of 41)	intron (NM_008787, intron 13 of 41)	26044	NM_008787	18541	Mm.251794	NM_008787	ENSMUSG00000001151	Pcnt	AW476095|C86676|KEN|Pcnt2|kendrin|m239Asp|m275Asp	pericentrin (kendrin)	protein-coding
mm_148711.1	chr19	5802409	5802433	+	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	251	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_134049.1	chr16	5255924	5255965	-	1	NA	promoter-TSS (NM_027446)	promoter-TSS (NM_027446)	12	NM_027446	70511	Mm.45780	NM_027446	ENSMUSG00000022544	Eef2kmt	5730409G15Rik|Fam86|Fam86a|eEF2-KMT	eukaryotic elongation factor 2 lysine methyltransferase	protein-coding
mm_135890.1	chr16	64852549	64852562	-	1	NA	promoter-TSS (NM_001347245)	promoter-TSS (NM_001347245)	470	NM_178647	106143	Mm.10160	NM_178647	ENSMUSG00000054604	Cggbp1	AA960172|AL023996|AW045841	CGG triplet repeat binding protein 1	protein-coding
mm_54684.1	chr6	39420244	39420270	-	1	NA	promoter-TSS (NM_001311109)	promoter-TSS (NM_001311109)	112	NM_018810	54484	Mm.270484	NM_018810	ENSMUSG00000029922	Mkrn1	RFP	makorin, ring finger protein, 1	protein-coding
mm_158934.1	chr1	73937270	73937270	-	1	NA	exon (NM_001289895, exon 22 of 33)	exon (NM_001289895, exon 22 of 33)	-72804	NR_045311	109198	Mm.359721	NR_045311	ENSMUSG00000100301	6030407O03Rik	-	RIKEN cDNA 6030407O03 gene	ncRNA
mm_604.1	chr1	39901740	39901742	+	1	NA	intron (NM_001252200, intron 2 of 31)	intron (NM_001252200, intron 2 of 31)	828	NM_008696	26921	Mm.491139	NM_008696	ENSMUSG00000026074	Map4k4	9430080K19Rik|AU043147|AU045934|AW046177|HGK|Nik	mitogen-activated protein kinase kinase kinase kinase 4	protein-coding
mm_149839.1	chr19	24999570	24999580	+	1	NA	promoter-TSS (NM_028785)	promoter-TSS (NM_028785)	46	NM_028785	76088	Mm.102485	NM_028785	ENSMUSG00000052085	Dock8	1200017A24Rik|5830472H07Rik|A130095G14Rik|AI461977	dedicator of cytokinesis 8	protein-coding
mm_133687.1	chr16	92498609	92498618	+	1	NA	exon (NM_172469, exon 1 of 6)	exon (NM_172469, exon 1 of 6)	466	NM_172469	209195	Mm.44747	NM_172469	ENSMUSG00000022949	Clic6	5730466J16Rik|AL022908|AW045520|CLIC1L	chloride intracellular channel 6	protein-coding
mm_144355.1	chr18	15832773	15832774	+	1	NA	Intergenic	Intergenic	-114727	NM_199055	71367	Mm.329304	NM_199055	ENSMUSG00000047161	Chst9	5430438D01Rik	carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 9	protein-coding
mm_94165.1	chr10	128747721	128747744	-	1	NA	promoter-TSS (NM_001170869)	promoter-TSS (NM_001170869)	-147	NM_030100	78428	Mm.27358	NM_030100	ENSMUSG00000064030	Pym1	A030010B05Rik|Pym|Wibg	PYM homolog 1, exon junction complex associated factor	protein-coding
mm_63384.1	chr7	127214207	127214244	+	1	NA	TTS (NM_017461)	TTS (NM_017461)	2617	NM_016754	17907	Mm.14526	NM_016754	ENSMUSG00000030672	Mylpf	2410014J02Rik|MLC-2|Mlc2	myosin light chain, phosphorylatable, fast skeletal muscle	protein-coding
mm_8505.1	chr1	154117631	154117642	-	1	NA	Intergenic	Intergenic	-83551	NM_001204908	100503355	Mm.484410	NM_001204908	ENSMUSG00000066797	Zfp648	ENSMUSG00000066797|Gm10178|Gm203	zinc finger protein 648	protein-coding
mm_98586.1	chr11	95751361	95751364	+	1	NA	intron (NM_201609, intron 1 of 4)	intron (NM_201609, intron 1 of 4)	2295	NM_201609	268469	Mm.389038	NM_201609	ENSMUSG00000075595	Zfp652	9530033F24Rik|ZNF652	zinc finger protein 652	protein-coding
mm_132420.1	chr16	35156507	35156548	+	1	NA	exon (NM_001012765, exon 1 of 21)	exon (NM_001012765, exon 1 of 21)	891	NM_001012765	224129	Mm.41137	NM_001012765	ENSMUSG00000022840	Adcy5	AW121902|Ac5	adenylate cyclase 5	protein-coding
mm_30650.1	chr4	8840484	8840493	+	1	NA	exon (NM_001277149, exon 18 of 38)	exon (NM_001277149, exon 18 of 38)	150082	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_111256.1	chr12	84970815	84970884	-	1	NA	promoter-TSS (NM_028632)	promoter-TSS (NM_028632)	37	NM_178065	68497	Mm.24446	NM_178065	ENSMUSG00000042350	Arel1	1110018G07Rik|AI649076|AW610792|Kiaa0317|mKIAA0317	apoptosis resistant E3 ubiquitin protein ligase 1	protein-coding
mm_61130.1	chr7	55885975	55885998	+	1	NA	intron (NM_011370, intron 9 of 30)	intron (NM_011370, intron 9 of 30)	43915	NM_001164661	20430	Mm.37249	NM_011370	ENSMUSG00000030447	Cyfip1	E030028J09Rik|P140SRA-1|P140sra1|Shyc|Sra-1|Sra1|l(7)1Rl|l71Rl|l7Rl1|mKIAA0068|pl-1	cytoplasmic FMR1 interacting protein 1	protein-coding
mm_169863.1	chr16	3383290	3383294	+	1	NA	Intergenic	IAPLTR4|LTR|ERVK	-209106	NM_146860	258859	Mm.377723	NM_146860	ENSMUSG00000051003	Olfr161	MOR131-1|OR912-47M6	olfactory receptor 161	protein-coding
mm_162495.1	chr1	136685229	136685252	-	1	NA	intron (NR_045325, intron 1 of 2)	intron (NR_045325, intron 1 of 2)	1611	NR_045325	100503460	Mm.30630	NR_045324	ENSMUSG00000097113	Gm19705	-	predicted gene, 19705	ncRNA
mm_105427.1	chr11	103810073	103810083	-	1	NA	intron (NM_009521, intron 2 of 4)	CpG	35903	NM_009521	22415	Mm.159091	NM_009521	ENSMUSG00000000125	Wnt3	Int-4|Wnt-3	wingless-type MMTV integration site family, member 3	protein-coding
mm_11581.1	chr2	32966945	32966976	+	1	NA	Intergenic	CpG	3659	NR_002898	104367	Mm.250030	NR_002898	ENSMUSG00000065124	Snora65	MBII-351|Rnu65	small nucleolar RNA, H/ACA box 65	snoRNA
mm_16025.1	chr2	167538193	167538210	+	1	NA	promoter-TSS (NM_011427)	promoter-TSS (NM_011427)	6	NM_011427	20613	Mm.2093	NM_011427	ENSMUSG00000042821	Snai1	Sna|Sna1|Snail|Snail1	snail family zinc finger 1	protein-coding
mm_129638.1	chr15	80255007	80255018	-	1	NA	promoter-TSS (NM_009716)	promoter-TSS (NM_009716)	-172	NM_001287180	11911	Mm.641	NM_009716	ENSMUSG00000042406	Atf4	Atf-4|C/ATF|CREB2|TAXREB67	activating transcription factor 4	protein-coding
mm_136450.1	chr16	94995143	94995153	-	1	NA	intron (NM_001025584, intron 1 of 4)	intron (NM_001025584, intron 1 of 4)	2548	NM_001025584	16522	Mm.328720	NM_010606	ENSMUSG00000043301	Kcnj6	BIR1|GIRK2|KATP2|KCNJ7|Kir3.2|weaver|wv	potassium inwardly-rectifying channel, subfamily J, member 6	protein-coding
mm_78383.1	chr9	28185440	28185464	+	1	NA	intron (NM_177906, intron 1 of 7)	intron (NM_177906, intron 1 of 7)	394183	NM_177906	330908	Mm.379474	NM_177906	ENSMUSG00000062257	Opcml	2900075O15Rik|3732419F12|AI844366|B930023M13Rik|C230027C17|Gm181|Obcam	opioid binding protein/cell adhesion molecule-like	protein-coding
mm_151462.1	chr19	58606362	58606370	+	1	NA	promoter-TSS (NR_038136)	promoter-TSS (NR_038136)	37	NR_038136	69055	Mm.396318	NR_038136	ENSMUSG00000100001	1810007D17Rik	-	RIKEN cDNA 1810007D17 gene	ncRNA
mm_4337.1	chr1	171856079	171856089	+	1	NA	TTS (NM_001252472)	TTS (NM_001252472)	16387	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_114111.1	chr13	54913230	54913240	+	1	NA	Intergenic	Intergenic	-36176	NM_001311128	107448	Mm.23573	NM_153131	ENSMUSG00000025876	Unc5a	Unc5h1|mKIAA1976	unc-5 netrin receptor A	protein-coding
mm_34676.1	chr4	150935743	150935755	+	1	NA	intron (NM_011612, intron 7 of 7)	intron (NM_011612, intron 7 of 7)	7750	NM_001077509	21942	Mm.244187	NM_011612	ENSMUSG00000028965	Tnfrsf9	4-1BB|A930040I11Rik|AA408498|AI325004|CDw137|Cd137|ILA|Ly63	tumor necrosis factor receptor superfamily, member 9	protein-coding
mm_146155.1	chr18	75001882	75001883	+	1	NA	TTS (NR_028552)	TTS (NR_028552)	814	NR_028552	100217457		NR_028552	ENSMUSG00000064871	Snord58b	MBII-199	small nucleolar RNA, C/D box 58B	snoRNA
mm_30759.1	chr4	15269609	15269633	+	1	NA	intron (NM_181401, intron 1 of 2)	intron (NM_181401, intron 1 of 2)	3801	NM_181401	100201	Mm.394111	NM_181401	ENSMUSG00000043252	Tmem64	9630015D15Rik|AI790744|AV300874	transmembrane protein 64	protein-coding
mm_14277.1	chr2	128769219	128769224	+	1	NA	intron (NM_008587, intron 8 of 18)	RLTR11B|LTR|ERVK	-49082	NM_028248	72477	Mm.259688	NM_028248	ENSMUSG00000014353	Tmem87b	2610301K12Rik|2810431I02Rik|AU014804	transmembrane protein 87B	protein-coding
mm_160762.1	chr10	93208180	93208180	+	1	NA	5' UTR (NM_146239, exon 2 of 17)	5' UTR (NM_146239, exon 2 of 17)	45395	NR_035452	100316689		NR_035452	ENSMUSG00000089214	Mir1931	mir-1931|mmu-mir-1931	microRNA 1931	ncRNA
mm_74261.1	chr8	124897878	124897901	+	1	NA	promoter-TSS (NM_198103)	promoter-TSS (NM_198103)	3	NM_001111141	244666	Mm.482915	NM_001111141	ENSMUSG00000031986	Sprtn	Gm505	SprT-like N-terminal domain	protein-coding
mm_159370.1	chr3	88653183	88653183	-	1	NA	promoter-TSS (NM_181817)	promoter-TSS (NM_181817)	-41	NM_181817	242093	Mm.269130	NM_181817	ENSMUSG00000049741	Rxfp4	GPCR142|Gpr100|Rln3r2|SALPR	relaxin family peptide receptor 4	protein-coding
mm_2702.1	chr1	127978334	127978352	+	1	NA	intron (NM_027678, intron 12 of 20)	intron (NM_027678, intron 12 of 20)	109570	NM_178690	226407	Mm.489713	NM_178690	ENSMUSG00000036104	Rab3gap1	1700003B17Rik|4732493F09Rik|AL117896|Rab3gap|p130	RAB3 GTPase activating protein subunit 1	protein-coding
mm_124835.1	chr15	9203659	9203660	+	1	NA	Intergenic	Intergenic	-48234	NM_001285980	27401	Mm.35584	NM_013787	ENSMUSG00000054115	Skp2	4930500A04Rik|FBXL1|FWD1|p45	S-phase kinase-associated protein 2 (p45)	protein-coding
mm_21029.1	chr2	152414819	152414834	-	1	NA	promoter-TSS (NM_177656)	promoter-TSS (NM_177656)	218	NM_175126	67917	Mm.391810	NM_175126	ENSMUSG00000074682	Zcchc3	2810406K24Rik	zinc finger, CCHC domain containing 3	protein-coding
mm_159928.1	chr6	61180419	61180419	+	1	NA	promoter-TSS (NM_183310)	promoter-TSS (NM_183310)	94	NM_183310	232035	Mm.150324	NM_183310	ENSMUSG00000039578	Ccser1	6230405M12Rik|C130092O11Rik|Fam190a	coiled-coil serine rich 1	protein-coding
mm_117913.1	chr13	99431225	99431245	-	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-18409	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_83352.1	chr9	44344160	44344203	-	1	NA	promoter-TSS (NM_013551)	promoter-TSS (NM_013551)	47	NM_013551	15288	Mm.247676	NM_013551	ENSMUSG00000032126	Hmbs	PBGD|T25658|Ups|Uros1	hydroxymethylbilane synthase	protein-coding
mm_93854.1	chr10	122047766	122047852	-	1	NA	promoter-TSS (NM_001081037)	promoter-TSS (NM_001081037)	-494	NM_001081037	117600	Mm.288698	NM_001081037	ENSMUSG00000020121	Srgap1	4930572H05Rik|Arhgap13	SLIT-ROBO Rho GTPase activating protein 1	protein-coding
mm_171744.1	chr4	9725112	9725115	+	1	NA	Intergenic	RLTR9D|LTR|ERVK	-45472	NR_030693	320152	Mm.159946	NR_030693		4930412C18Rik	5730591J02Rik	RIKEN cDNA 4930412C18 gene	ncRNA
mm_134577.1	chr16	20405490	20405502	-	1	NA	exon (NM_013790, exon 4 of 30)	exon (NM_013790, exon 4 of 30)	20898	NM_013790	27416	Mm.20845	NM_013790	ENSMUSG00000022822	Abcc5	2900011L11Rik|AI132311|Abcc5a|Abcc5b|Mrp5	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	protein-coding
mm_63311.1	chr7	126862588	126862611	+	1	NA	intron (NM_172746, intron 1 of 6)	CpG	627	NM_172746	233876	Mm.363427	NM_172746	ENSMUSG00000042606	Hirip3	B130036O03|C86302	HIRA interacting protein 3	protein-coding
mm_10918.1	chr2	25403045	25403115	+	1	NA	promoter-TSS (NM_008721)	promoter-TSS (NM_008721)	30	NM_008721	18146	Mm.1131	NM_008721	ENSMUSG00000015094	Npdc1	AI314472|NPDC-1	neural proliferation, differentiation and control 1	protein-coding
mm_3538.1	chr1	150393440	150393500	+	1	NA	promoter-TSS (NM_145511)	promoter-TSS (NM_145511)	-415	NM_145511	226499	Mm.222093	NM_145511	ENSMUSG00000006010	BC003331	1810053E15Rik|Odr4|odr-4	cDNA sequence BC003331	protein-coding
mm_164703.1	chr17	51755164	51755200	-	1	NA	intron (NM_009122, intron 9 of 10)	Charlie4a|DNA|hAT-Charlie	56872	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_66194.1	chr7	34221664	34221688	-	1	NA	intron (NM_008155, intron 4 of 17)	intron (NM_008155, intron 4 of 17)	8660	NM_008155	14751	Mm.589	NM_008155	ENSMUSG00000036427	Gpi1	Amf|Gpi|Gpi-1|Gpi-1r|Gpi-1s|Gpi-1t|Gpi1-r|Gpi1-s|Gpi1-t|Gpi1s|MF|NK|NK/GPI|Nlk|Org|Pgi|Phi	glucose phosphate isomerase 1	protein-coding
mm_111962.1	chr12	109600329	109600348	-	1	NA	Intergenic	Intergenic	-3607	NR_028261	75745	Mm.293263	NR_028261		Rian	5530401N18Rik|C130089L09Rik|Meg8	RNA imprinted and accumulated in nucleus	ncRNA
mm_163191.1	chr11	94991172	94991172	-	1	NA	promoter-TSS (NM_172261)	promoter-TSS (NM_172261)	-40	NM_172261	217124	Mm.229087	NM_172261	ENSMUSG00000038976	Ppp1r9b	SPL|Spn	protein phosphatase 1, regulatory subunit 9B	protein-coding
mm_128150.1	chr15	31735420	31735427	-	1	NA	Intergenic	Intergenic	133307	NM_026546	68073	Mm.119185	NM_026546	ENSMUSG00000039065	Fam173b	A930016P21Rik|AA987072	family with sequence similarity 173, member B	protein-coding
mm_10579.1	chr2	18129805	18129834	+	1	NA	intron (NR_045539, intron 10 of 24)	B1_Mus1|SINE|Alu	65234	NM_001252561	17354	Mm.209175	NM_010804	ENSMUSG00000026743	Mllt10	Af10|B130021D15Rik|D630001B22Rik|mKIAA4140	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 10	protein-coding
mm_160144.1	chr7	36698121	36698121	+	1	NA	promoter-TSS (NM_172298)	promoter-TSS (NM_172298)	3	NM_172298	243931	Mm.44141	NM_172298	ENSMUSG00000021217	Tshz3	A630038G13Rik|Tsh3|Zfp537|mKIAA1474|teashirt3	teashirt zinc finger family member 3	protein-coding
mm_15526.1	chr2	158382609	158382624	+	1	NA	3' UTR (NM_175692, exon 5 of 5)	3' UTR (NM_175692, exon 5 of 5)	6978	NM_175692	319317	Mm.294494	NM_175692	ENSMUSG00000044349	Snhg11	A930034L06Rik|AI854265|AL022637|AW319638|E130013N09Rik	small nucleolar RNA host gene 11	protein-coding
mm_1456.1	chr1	67230811	67230823	+	1	NA	3' UTR (NM_001080809, exon 38 of 38)	3' UTR (NM_001080809, exon 38 of 38)	107790	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_52010.1	chr6	93241983	93241987	+	1	NA	Intergenic	Intergenic	301403	NR_015530	330385	Mm.483472	NR_015530	ENSMUSG00000097462	9530026P05Rik	B430306B02	RIKEN cDNA 9530026P05 gene	ncRNA
mm_98622.1	chr11	95858882	95858901	+	1	NA	promoter-TSS (NR_045187)	promoter-TSS (NR_045187)	74	NR_045187	73906	Mm.399894	NR_045187	ENSMUSG00000086015	4833417C18Rik	-	RIKEN cDNA 4833417C18 gene	ncRNA
mm_48705.1	chr5	147076483	147076565	-	1	NA	promoter-TSS (NM_080795)	promoter-TSS (NM_080795)	48	NM_080795	140887	Mm.272203	NM_080795	ENSMUSG00000016520	Lnx2	9630046H24|AW209022	ligand of numb-protein X 2	protein-coding
mm_111346.1	chr12	86892541	86892569	-	1	NA	Intergenic	Intergenic	-7741	NM_145836	238330	Mm.248358	NM_145836	ENSMUSG00000034168	Irf2bpl	6430527G18Rik|Eap1	interferon regulatory factor 2 binding protein-like	protein-coding
mm_67127.1	chr7	70366426	70366466	-	1	NA	5' UTR (NM_183261, exon 1 of 3)	5' UTR (NM_183261, exon 1 of 3)	300	NM_183261	11819	Mm.158143	NM_009697	ENSMUSG00000030551	Nr2f2	2700033K02Rik|9430015G03Rik|ARP-1|Aporp1|COUP-TF2|COUP-TFII|COUPTFB|EAR3|SVP40|Tcfcoup2	nuclear receptor subfamily 2, group F, member 2	protein-coding
mm_102729.1	chr11	67243458	67243466	-	1	NA	exon (NM_010855, exon 11 of 40)	exon (NM_010855, exon 11 of 40)	5650	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_164480.1	chr16	73794141	73794141	-	1	NA	Intergenic	Intergenic	547926	NR_030464	751561		NR_030464	ENSMUSG00000104758	Mir691	Mirn691|mir-691|mmu-mir-691	microRNA 691	ncRNA
mm_81354.1	chr9	108649815	108649818	+	1	NA	promoter-TSS (NM_011790)	promoter-TSS (NM_011790)	-436	NM_011790	23807	Mm.290447	NM_011790	ENSMUSG00000064145	Arih2	AI843547|ARI2|TRIAD1|UIP48	ariadne RBR E3 ubiquitin protein ligase 2	protein-coding
mm_106107.1	chr11	116306676	116306691	-	1	NA	promoter-TSS (NM_001162872)	promoter-TSS (NM_001162872)	55	NM_016857	53413	Mm.22530	NM_016857	ENSMUSG00000020792	Exoc7	Exo70|sec70	exocyst complex component 7	protein-coding
mm_54652.1	chr6	39049051	39049064	-	1	NA	intron (NM_011539, intron 9 of 12)	intron (NM_011539, intron 9 of 12)	18529	NR_040523	69986	Mm.490941	NR_040523	ENSMUSG00000100121	1700025N23Rik	-	RIKEN cDNA 1700025N23 gene	ncRNA
mm_131679.1	chr16	20674255	20674274	+	1	NA	exon (NM_145941, exon 3 of 33)	exon (NM_145941, exon 3 of 33)	1537	NM_001304432	208643	Mm.260256	NM_145941	ENSMUSG00000045983	Eif4g1	E030015G23Rik|eIF-4-gamma 1|eIF-4G 1|eIF-4G1|eIF4GI	eukaryotic translation initiation factor 4, gamma 1	protein-coding
mm_14313.1	chr2	129205207	129205210	+	1	NA	TTS (NM_001159593)	TTS (NM_001159593)	6435	NM_001159593	20515	Mm.272675	NM_015747	ENSMUSG00000027397	Slc20a1	AI607883|Glvr-1|Glvr1	solute carrier family 20, member 1	protein-coding
mm_28913.1	chr3	98852944	98852962	-	1	NA	exon (NM_001304800, exon 4 of 4)	exon (NM_001304800, exon 4 of 4)	6841	NM_001304800	15492	Mm.140811	NM_008293	ENSMUSG00000027871	Hsd3b1	3-beta-HSD I|D3Ertd383e	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1	protein-coding
mm_26348.1	chr3	142547763	142547769	+	1	NA	3' UTR (NM_001083312, exon 11 of 11)	3' UTR (NM_001083312, exon 11 of 11)	-12286	NM_018734	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_114708.1	chr13	83572339	83572357	+	1	NA	intron (NM_001347566, intron 1 of 10)	intron (NM_001347566, intron 1 of 10)	-1259	NM_001347577	17260	Mm.24001	NM_025282	ENSMUSG00000005583	Mef2c	5430401D19Rik|9930028G15Rik|AV011172|Mef2	myocyte enhancer factor 2C	protein-coding
mm_49216.1	chr6	15755683	15755686	+	1	NA	intron (NM_175088, intron 3 of 4)	intron (NM_175088, intron 3 of 4)	35023	NM_175088	16543	Mm.1314	NM_175088	ENSMUSG00000041390	Mdfic	Kdt1|Mdfid	MyoD family inhibitor domain containing	protein-coding
mm_78264.1	chr9	21937076	21937098	+	1	NA	promoter-TSS (NM_001290299)	promoter-TSS (NM_001290299)	77	NM_001290299	235044	Mm.277521	NM_144935	ENSMUSG00000040563	Plppr2	Lppr2|PRG-4	phospholipid phosphatase related 2	protein-coding
mm_18507.1	chr2	62615665	62615714	-	1	NA	intron (NM_001164477, intron 4 of 14)	intron (NM_001164477, intron 4 of 14)	30566	NM_027835	71586	Mm.136224	NM_027835	ENSMUSG00000026896	Ifih1	9130009C22Rik|Helicard|Hlcd|MDA5|RLR-2	interferon induced with helicase C domain 1	protein-coding
mm_1704.1	chr1	75192144	75192230	+	1	NA	promoter-TSS (NM_001288613)	promoter-TSS (NM_001288613)	27	NR_051999	52231	Mm.259326	NM_026187	ENSMUSG00000026199	Ankzf1	1300008P06Rik|2810025E10Rik|D1Ertd161e	ankyrin repeat and zinc finger domain containing 1	protein-coding
mm_78088.1	chr9	18195054	18195057	+	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	-97212	NM_025844	66917	Mm.103534	NM_025844	ENSMUSG00000001774	Chordc1	1110001O09Rik|AA409036|Chp-1|morgana	cysteine and histidine-rich domain (CHORD)-containing, zinc-binding protein 1	protein-coding
mm_130008.1	chr15	86475092	86475108	-	1	NA	intron (NM_145476, intron 12 of 12)	intron (NM_145476, intron 12 of 12)	260641	NM_145476	223754	Mm.28904	NM_145476	ENSMUSG00000051864	Tbc1d22a	BC023106|D15Ertd781e	TBC1 domain family, member 22a	protein-coding
mm_149267.1	chr19	10577482	10577492	+	1	NA	promoter-TSS (NM_028411)	promoter-TSS (NM_028411)	-101	NR_126092	72982	Mm.391194	NM_028411	ENSMUSG00000024666	Tmem138	1700113I01Rik|2900055D14Rik	transmembrane protein 138	protein-coding
mm_36320.1	chr4	70307306	70307316	-	1	NA	intron (NM_145990, intron 14 of 36)	intron (NM_145990, intron 14 of 36)	103124	NM_001313762	214444	Mm.370777	NM_145990	ENSMUSG00000039298	Cdk5rap2	2900018K03Rik|an|mKIAA1633	CDK5 regulatory subunit associated protein 2	protein-coding
mm_7484.1	chr1	121307948	121307973	-	1	NA	intron (NM_001271532, intron 2 of 4)	intron (NM_001271532, intron 2 of 4)	19718	NM_001271531	72999	Mm.27136	NM_133748	ENSMUSG00000003721	Insig2	2900053I11Rik|C730043J18Rik|Insig-2	insulin induced gene 2	protein-coding
mm_85764.1	chr9	108854561	108854571	-	1	NA	5' UTR (NM_134420, exon 1 of 18)	5' UTR (NM_134420, exon 1 of 18)	523	NM_134420	171429	Mm.45201	NM_134420	ENSMUSG00000023259	Slc26a6	B930010B04Rik|CFEX|Pat-1|Pat1	solute carrier family 26, member 6	protein-coding
mm_111646.1	chr12	102704897	102704980	-	1	NA	promoter-TSS (NM_172584)	promoter-TSS (NM_172584)	-69	NM_172584	217837	Mm.482192	NM_172584	ENSMUSG00000057963	Itpk1	BC031182	inositol 1,3,4-triphosphate 5/6 kinase	protein-coding
mm_76021.1	chr8	75039817	75039824	-	1	NA	intron (NM_001136259, intron 1 of 15)	B4A|SINE|B4	6134	NM_011622	21968	Mm.1967	NM_011622	ENSMUSG00000042870	Tom1	-	target of myb1 trafficking protein	protein-coding
mm_113617.1	chr13	41569297	41569305	+	1	NA	Intergenic	Intergenic	-36915	NM_001163572	621976	Mm.259830	NM_001163572	ENSMUSG00000087370	Tmem170b	EG621976	transmembrane protein 170B	protein-coding
mm_38065.1	chr4	134093576	134093585	-	1	NA	TTS (NM_013706)	TTS (NM_013706)	1493	NM_013706	23833	Mm.24130	NM_013706	ENSMUSG00000000682	Cd52	AI463198|B7|B7-Ag|CAMPATH-1|CLS1|MB7	CD52 antigen	protein-coding
mm_45763.1	chr5	86906939	86906955	-	1	NA	promoter-TSS (NM_153598)	promoter-TSS (NM_153598)	-10	NM_153598	100727	Mm.281844	NM_153598	ENSMUSG00000029260	Ugt2b34	AI788959	UDP glucuronosyltransferase 2 family, polypeptide B34	protein-coding
mm_42850.1	chr5	122209849	122209914	+	1	NA	promoter-TSS (NM_028752)	promoter-TSS (NM_028752)	152	NM_001042489	74096	Mm.28804	NM_028752	ENSMUSG00000064267	Hvcn1	0610039P13Rik|AI450555|BTS|HV1|Vsop.|mVSOP	hydrogen voltage-gated channel 1	protein-coding
mm_96412.1	chr11	67254778	67254787	+	1	NA	exon (NM_010855, exon 30 of 40)	exon (NM_010855, exon 30 of 40)	16970	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_59650.1	chr7	28169691	28169743	+	1	NA	promoter-TSS (NM_007991)	promoter-TSS (NM_007991)	-31	NM_007991	14113	Mm.4595	NM_007991	ENSMUSG00000046865	Fbl	AL022665|FIB|FLRN|RNU3IP1	fibrillarin	protein-coding
mm_20254.1	chr2	126598015	126598020	-	1	NA	intron (NM_008230, intron 9 of 11)	intron (NM_008230, intron 9 of 11)	20661	NM_008230	15186	Mm.18603	NM_008230	ENSMUSG00000027360	Hdc	AW108189|Hdc-a|Hdc-c|Hdc-e|Hdc-s	histidine decarboxylase	protein-coding
mm_26670.1	chr3	154711391	154711402	+	1	NA	intron (NM_175176, intron 1 of 6)	intron (NM_175176, intron 1 of 6)	263	NM_175176	209601	Mm.331454	NM_175176	ENSMUSG00000078161	Erich3	1700013E18Rik|4922501L14Rik|5031409G23Rik|AI596448|Gm133	glutamate rich 3	protein-coding
mm_91515.1	chr10	37138574	37138574	-	1	NA	5' UTR (NM_008538, exon 1 of 2)	5' UTR (NM_008538, exon 1 of 2)	352	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_160285.1	chr7	125672798	125672798	-	1	NA	exon (NM_207239, exon 12 of 37)	exon (NM_207239, exon 12 of 37)	34890	NM_207239	233863	Mm.294173	NM_207239	ENSMUSG00000032777	Gtf3c1	-	general transcription factor III C 1	protein-coding
mm_168566.1	chr11	69670172	69670173	-	1	NA	exon (NM_144958, exon 4 of 11)	exon (NM_144958, exon 4 of 11)	2251	NM_144958	13681	Mm.26680	NM_144958	ENSMUSG00000059796	Eif4a1	BM-010|Ddx2a|Eif4	eukaryotic translation initiation factor 4A1	protein-coding
mm_94890.1	chr11	28730473	28730482	+	1	NA	Intergenic	Intergenic	-15714	NR_030419	735308		NR_030419	ENSMUSG00000076318	Mir216b	Mirn216b|mir-216b	microRNA 216b	ncRNA
mm_111953.1	chr12	109545810	109545818	-	1	NA	non-coding (NR_003633, exon 1 of 5)	non-coding (NR_003633, exon 1 of 5)	416	NR_003633	17263	Mm.289645	NM_144513	ENSMUSG00000021268	Meg3	2900016C05Rik|3110050O07Rik|6330408G06Rik|AI425946|AW108224|D12Bwg1266e|Gtl2|R74756|R75394	maternally expressed 3	ncRNA
mm_79008.1	chr9	45431358	45431366	+	1	NA	promoter-TSS (NR_040732)	promoter-TSS (NR_040732)	-130	NR_040732	74602	Mm.394117	NR_040732	ENSMUSG00000097074	4833428L15Rik	-	RIKEN cDNA 4833428L15 gene	ncRNA
mm_142949.1	chr17	56109757	56109767	-	1	NA	promoter-TSS (NM_020568)	promoter-TSS (NM_020568)	40	NM_020568	57435	Mm.12966	NM_020568	ENSMUSG00000002831	Plin4	S3-12|mKIAA1881	perilipin 4	protein-coding
mm_77556.1	chr8	123318542	123318550	-	1	NA	promoter-TSS (NM_016925)	promoter-TSS (NM_016925)	30	NM_016925	14087	Mm.6536	NM_016925	ENSMUSG00000032815	Fanca	AW208693|FACA	Fanconi anemia, complementation group A	protein-coding
mm_136777.1	chr17	10319895	10319932	+	1	NA	promoter-TSS (NM_001159517)	promoter-TSS (NM_001159517)	-6	NR_037588	100526796	Mm.384135	NR_037588		Cahm	B930003M22Rik	colon adenocarcinoma hypermethylated RNA	ncRNA
mm_30828.1	chr4	21874531	21874541	+	1	NA	exon (NM_025669, exon 11 of 12)	exon (NM_025669, exon 11 of 12)	-5139	NM_172687	230027	Mm.5662	NM_172687	ENSMUSG00000028247	Coq3	4732433J24|C77934	coenzyme Q3 methyltransferase	protein-coding
mm_170075.1	chr1	7335741	7335745	-	1	NA	Intergenic	MYSERV6-int|LTR|ERVK	246823	NM_183028	319263	Mm.21539	NM_183028	ENSMUSG00000051285	Pcmtd1	8430411F12Rik|A030012M09Rik	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding
mm_15553.1	chr2	158437025	158437041	+	1	NA	exon (NM_001291138, exon 8 of 30)	exon (NM_001291138, exon 8 of 30)	27180	NM_001291138	228850	Mm.398185	NM_177227	ENSMUSG00000027652	Ralgapb	AI507211|B230339M05Rik|p170	Ral GTPase activating protein, beta subunit (non-catalytic)	protein-coding
mm_38149.1	chr4	134914941	134914973	-	1	NA	promoter-TSS (NM_027935)	promoter-TSS (NM_027935)	-41	NM_027935	71817	Mm.88349	NM_027935	ENSMUSG00000028822	Tmem50a	3200001F09Rik|CAM|Smp1	transmembrane protein 50A	protein-coding
mm_36918.1	chr4	108118471	108118498	-	1	NA	promoter-TSS (NM_011327)	promoter-TSS (NM_011327)	63	NM_011327	20280	Mm.379011	NM_011327	ENSMUSG00000028603	Scp2	AA409774|AA409893|C76618|C79031|NSL-TP|SCP-2|SCP-X|SCPX|ns-LTP	sterol carrier protein 2, liver	protein-coding
mm_156392.1	chrX	139800982	139800992	+	1	NA	5' UTR (NM_016675, exon 1 of 2)	5' UTR (NM_016675, exon 1 of 2)	179	NM_016675	12738	Mm.117068	NM_016675	ENSMUSG00000047230	Cldn2	AL022813	claudin 2	protein-coding
mm_40336.1	chr5	43913147	43913151	+	1	NA	TTS (NM_007646)	TTS (NM_007646)	44340	NM_007646	12494	Mm.249873	NM_007646	ENSMUSG00000029084	Cd38	ADPRC 1|Cd38-rs1|I-19	CD38 antigen	protein-coding
mm_53975.1	chr6	6578563	6578573	-	1	NA	promoter-TSS (NM_009169)	promoter-TSS (NM_009169)	90	NM_009169	20422	Mm.2469	NM_009169	ENSMUSG00000042541	Shfm1	DSS1|Shfdg1|Shfg	split hand/foot malformation (ectrodactyly) type 1	protein-coding
mm_86085.1	chr9	114844091	114844171	-	1	NA	promoter-TSS (NM_027294)	promoter-TSS (NM_027294)	21	NM_027294	70031	Mm.150064	NM_027294	ENSMUSG00000041012	Cmtm8	2700018N07Rik|AA408515|Cklfsf8	CKLF-like MARVEL transmembrane domain containing 8	protein-coding
mm_43445.1	chr5	136110541	136110563	+	1	NA	intron (NM_001039103, intron 18 of 19)	B1_Mur3|SINE|Alu	5030	NR_106002	102465626		NR_106002	ENSMUSG00000099003	Mir7035	Gm27661|mmu-mir-7035	microRNA 7035	ncRNA
mm_3521.1	chr1	150107616	150107624	+	1	NA	3' UTR (NM_011198, exon 10 of 10)	3' UTR (NM_011198, exon 10 of 10)	7589	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_95360.1	chr11	48872559	48872560	+	1	NA	Intergenic	Intergenic	-1213	NM_008326	15944	Mm.29938	NM_008326	ENSMUSG00000046879	Irgm1	Ifggd3|Ifi1|Iigp3|Iipg3|Irgm|LRG-47	immunity-related GTPase family M member 1	protein-coding
mm_142614.1	chr17	46857723	46857741	-	1	NA	Intergenic	RLTR20A4|LTR|ERVK	-26319	NM_001100452	210982	Mm.37642	NM_001100452	ENSMUSG00000036568	Gltscr1l	mKIAA0240	GLTSCR1-like	protein-coding
mm_73107.1	chr8	94666701	94666711	+	1	NA	promoter-TSS (NM_024269)	promoter-TSS (NM_024269)	106	NM_024191	107566	Mm.393247	NM_024191	ENSMUSG00000031776	Arl2bp	1700010P10Rik|1700027H16Rik|6330544B05Rik|AI482273|AI849834|BART|Bart1	ADP-ribosylation factor-like 2 binding protein	protein-coding
mm_171933.1	chr5	64159973	64159990	+	1	NA	promoter-TSS (NM_019636)	promoter-TSS (NM_019636)	-279	NM_019636	57915	Mm.286353	NM_019636	ENSMUSG00000029174	Tbc1d1	1110062G02Rik|AI385682|AW555803|Nob1|Nobq1|Tbc1|mKIAA1108	TBC1 domain family, member 1	protein-coding
mm_102399.1	chr11	59002392	59002401	-	1	NA	intron (NM_001171512, intron 89 of 103)	intron (NM_001171512, intron 89 of 103)	24303	NM_053168	94091	Mm.248049	NM_053168	ENSMUSG00000020455	Trim11	-	tripartite motif-containing 11	protein-coding
mm_9057.1	chr1	167350361	167350370	-	1	NA	exon (NM_019993, exon 1 of 11)	exon (NM_019993, exon 1 of 11)	374	NM_019993	56752	Mm.292539	NM_019993	ENSMUSG00000026687	Aldh9a1	AA139417|Abaldh|ESTM40|TMABA-DH|Tmabadh	aldehyde dehydrogenase 9, subfamily A1	protein-coding
mm_170438.1	chr18	80022515	80022522	+	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	-24377	NM_053117	93737	Mm.24678	NM_053117	ENSMUSG00000056214	Pard6g	2410049N21Rik|Par6a	par-6 family cell polarity regulator gamma	protein-coding
mm_50163.1	chr6	41547783	41547794	+	1	NA	Intergenic	Intergenic	26012	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_85108.1	chr9	95404543	95404561	-	1	NA	3' UTR (NM_018763, exon 2 of 2)	3' UTR (NM_018763, exon 2 of 2)	2718	NM_018763	54371	Mm.212446	NM_018763	ENSMUSG00000033350	Chst2	AI428561|AW121776|C130041E03Rik|Chts2|GST-2|GlcNAc6ST|Gn6st	carbohydrate sulfotransferase 2	protein-coding
mm_46558.1	chr5	106696789	106696816	-	1	NA	promoter-TSS (NM_026856)	promoter-TSS (NM_026856)	28	NM_026856	52397	Mm.249474	NM_026856	ENSMUSG00000049606	Zfp644	1110068L01Rik|AA408882|BM-005|D5Ertd689e|Zep-2	zinc finger protein 644	protein-coding
mm_70055.1	chr7	142651340	142651345	-	1	NA	3' UTR (NM_010514, exon 4 of 4)	3' UTR (NM_010514, exon 4 of 4)	3654	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_88359.1	chr10	75936306	75936322	+	1	NA	exon (NM_175329, exon 2 of 4)	exon (NM_175329, exon 2 of 4)	741	NM_175329	103172	Mm.333849	NM_175329	ENSMUSG00000049422	Chchd10	1620401E04Rik|AI267078|Ndg2	coiled-coil-helix-coiled-coil-helix domain containing 10	protein-coding
mm_115250.1	chr13	110396934	110396959	+	1	NA	exon (NM_152804, exon 5 of 14)	exon (NM_152804, exon 5 of 14)	1902	NM_152804	20620	Mm.380	NM_152804	ENSMUSG00000021701	Plk2	Snk	polo-like kinase 2	protein-coding
mm_18564.1	chr2	65239093	65239125	-	1	NA	promoter-TSS (NM_177025)	promoter-TSS (NM_177025)	-483	NM_027225	319876	Mm.34159	NM_027225	ENSMUSG00000034903	Cobll1	1810047P18Rik|Coblr1|D430044D16Rik	Cobl-like 1	protein-coding
mm_11099.1	chr2	28032771	28032793	+	1	NA	exon (NM_015734, exon 65 of 66)	exon (NM_015734, exon 65 of 66)	52096	NM_010190	14134	Mm.182935	NM_010190	ENSMUSG00000026835	Fcnb	Fcn2	ficolin B	protein-coding
mm_167772.1	chr9	111090616	111090627	+	1	NA	Intergenic	Intergenic	-27490	NM_027742	71268	Mm.302287	NM_027742	ENSMUSG00000032497	Lrrfip2	5133400F20Rik|AI850587	leucine rich repeat (in FLII) interacting protein 2	protein-coding
mm_128810.1	chr15	66978408	66978408	-	1	NA	Intergenic	ID_B1|SINE|B4	-8767	NM_008681	17988	Mm.30837	NM_008681	ENSMUSG00000005125	Ndrg1	CAP43|CMT4D|DRG1|HMSNL|NMSL|Ndr1|Ndrl|PROXY1|RTP|TDD5	N-myc downstream regulated gene 1	protein-coding
mm_26305.1	chr3	142511550	142511592	+	1	NA	intron (NM_153564, intron 10 of 10)	MERV1_I-int|LTR|ERV1	14637	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_60824.1	chr7	45705519	45705532	+	1	NA	TTS (NM_009800)	TTS (NM_009800)	278	NM_016974	13170	Mm.24222	NM_016974	ENSMUSG00000059824	Dbp	-	D site albumin promoter binding protein	protein-coding
mm_86359.1	chr9	123717577	123717632	-	1	NA	promoter-TSS (NM_033322)	promoter-TSS (NM_033322)	-47	NM_033322	93730	Mm.378263	NM_033322	ENSMUSG00000025245	Lztfl1	5530402H04Rik|6130400H19Rik|AI414725|AW048545	leucine zipper transcription factor-like 1	protein-coding
mm_43719.1	chr5	139423192	139423202	+	1	NA	promoter-TSS (NM_029771)	promoter-TSS (NM_029771)	18	NM_029771	76854	Mm.389706	NM_029771	ENSMUSG00000053647	Gper1	6330420K13Rik|CMKRL2|Ceprl|FEG-1|GPCR-Br|Gper|Gpr30	G protein-coupled estrogen receptor 1	protein-coding
mm_139304.1	chr17	48347829	48347873	+	1	NA	intron (NM_001272078, intron 1 of 4)	B4|SINE|B4	1450	NM_001272078	83433	Mm.261623	NM_031254	ENSMUSG00000023992	Trem2	TREM-2|Trem2a|Trem2b|Trem2c	triggering receptor expressed on myeloid cells 2	protein-coding
mm_97080.1	chr11	73009801	73009820	+	1	NA	intron (NM_008771, intron 6 of 11)	intron (NM_008771, intron 6 of 11)	-9198	NM_018883	55984	Mm.9998	NM_018883	ENSMUSG00000020785	Camkk1	AI846603|CaMKKalpha|Camkk	calcium/calmodulin-dependent protein kinase kinase 1, alpha	protein-coding
mm_127743.1	chr15	103335780	103335781	+	1	NA	intron (NM_013866, intron 1 of 7)	intron (NM_013866, intron 1 of 7)	4306	NM_013866	29813	Mm.14099	NM_013866	ENSMUSG00000000552	Zfp385a	Hzf|Zfp385|Znf385a	zinc finger protein 385A	protein-coding
mm_161618.1	chr16	56024375	56024375	-	1	NA	exon (NM_001024622, exon 2 of 5)	exon (NM_001024622, exon 2 of 5)	5342	NM_001024622	76302	Mm.310642	NM_001024622	ENSMUSG00000071533	Pcnp	1110018D06Rik|AI647035	PEST proteolytic signal containing nuclear protein	protein-coding
mm_67390.1	chr7	79843276	79843283	-	1	NA	promoter-TSS (NM_008486)	promoter-TSS (NM_008486)	-927	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_53578.1	chr6	137410846	137410852	+	1	NA	intron (NM_001164402, intron 1 of 15)	intron (NM_001164402, intron 1 of 15)	128	NM_001164403	19277	Mm.186361	NM_011216	ENSMUSG00000030223	Ptpro	D28|GLEPP1|PTPBK|PTPROt|PTPU2|PTPoc|PTPphi|Ptpn15|R-PTP-O	protein tyrosine phosphatase, receptor type, O	protein-coding
mm_125766.1	chr15	74516733	74516760	+	1	NA	5' UTR (NM_174991, exon 1 of 31)	5' UTR (NM_174991, exon 1 of 31)	550	NM_174991	107831	Mm.43133	NM_174991	ENSMUSG00000034730	Adgrb1	B830018M07Rik|Bai1|R75078|mKIAA4089	adhesion G protein-coupled receptor B1	protein-coding
mm_20750.1	chr2	140170529	140170569	-	1	NA	promoter-TSS (NM_001081090)	promoter-TSS (NM_001081090)	9	NM_001081090	66580	Mm.21228	NM_001081090	ENSMUSG00000045624	Esf1	2610101J03Rik|ABTAP|AW545818|C79684	ESF1 nucleolar pre-rRNA processing protein homolog	protein-coding
mm_132497.1	chr16	36948029	36948031	+	1	NA	intron (NM_008225, intron 4 of 13)	B4A|SINE|B4	13047	NM_008225	15163	Mm.4091	NM_008225	ENSMUSG00000022831	Hcls1	AW213261|HS1	hematopoietic cell specific Lyn substrate 1	protein-coding
mm_18235.1	chr2	51973083	51973123	-	1	NA	5' UTR (NM_001141948, exon 1 of 8)	5' UTR (NM_001141948, exon 1 of 8)	105	NM_001141949	64685	Mm.7491	NM_019401	ENSMUSG00000026946	Nmi	-	N-myc (and STAT) interactor	protein-coding
mm_23100.1	chr3	37312515	37312575	+	1	NA	promoter-TSS (NM_001255992)	promoter-TSS (NM_001255992)	-9	NM_001008502	241950	Mm.32171	NM_001008502	ENSMUSG00000051444	Bbs12	Gm1805|Gm407|Gm721	Bardet-Biedl syndrome 12 (human)	protein-coding
mm_133101.1	chr16	64911197	64911198	+	1	NA	Intergenic	MTB|LTR|ERVL-MaLR	59112	NM_178647	106143	Mm.10160	NM_178647	ENSMUSG00000054604	Cggbp1	AA960172|AL023996|AW045841	CGG triplet repeat binding protein 1	protein-coding
mm_79016.1	chr9	45839943	45839954	+	1	NA	intron (NM_011792, intron 1 of 8)	intron (NM_011792, intron 1 of 8)	1403	NM_011792	23821	Mm.24044	NM_011792	ENSMUSG00000032086	Bace1	ASP2|Bace|C76936	beta-site APP cleaving enzyme 1	protein-coding
mm_142368.1	chr17	44607501	44607520	-	1	NA	non-coding (NR_073392, exon 8 of 8)	non-coding (NR_073392, exon 8 of 8)	128666	NR_073425	12393	Mm.391013	NM_009820	ENSMUSG00000039153	Runx2	AML3|Cbf|Cbfa-1|Cbfa1|LS3|Osf2|PEBP2aA|Pebp2a1|Pebpa2a	runt related transcription factor 2	protein-coding
mm_44201.1	chr5	3648046	3648074	-	1	NA	promoter-TSS (NM_026033)	promoter-TSS (NM_026033)	-124	NM_026033	67210	Mm.178424	NM_026033	ENSMUSG00000007415	Gatad1	2310031E19Rik|2810047M21Rik|8430439A17Rik|9130430G15Rik|B330017N08Rik|ENSMUSG00000073241|Odag	GATA zinc finger domain containing 1	protein-coding
mm_8812.1	chr1	161897332	161897341	-	1	NA	Intergenic	Intergenic	-20675	NM_172645	226551	Mm.170002	NM_172645	ENSMUSG00000040297	Suco	4732491B11|AI848100|AU016931|Opt	SUN domain containing ossification factor	protein-coding
mm_93125.1	chr10	91181436	91181450	-	1	NA	Intergenic	tRNA-Trp-TGG|tRNA|tRNA	-9824	NM_001080130	21917	Mm.159684	NM_011605	ENSMUSG00000019961	Tmpo	5630400D24Rik|AI195756|AI606875|AW214352|AW547477|LAP2|TP	thymopoietin	protein-coding
mm_51282.1	chr6	72181298	72181298	+	1	NA	Intergenic	Intergenic	54279	NM_153778	71093	Mm.87449	NM_153778	ENSMUSG00000037621	Atoh8	4933425C05Rik|Hath6|Math6|bHLHa21|okadin	atonal bHLH transcription factor 8	protein-coding
mm_58294.1	chr6	145865372	145865383	-	1	NA	promoter-TSS (NM_001271768)	promoter-TSS (NM_001271768)	43	NM_001271768	79362	Mm.154529	NM_024469	ENSMUSG00000030256	Bhlhe41	6430520M22Rik|Bhlhb2l|Bhlhb3|DEC2|Sharp1	basic helix-loop-helix family, member e41	protein-coding
mm_92047.1	chr10	62497271	62497274	-	1	NA	intron (NM_011157, intron 2 of 2)	intron (NM_011157, intron 2 of 2)	-10467	NM_133672	30930	Mm.260703	NM_133672	ENSMUSG00000020078	Vps26a	AA407240|HB58|Vps26	VPS26 retromer complex component A	protein-coding
mm_162102.1	chrX	37901730	37901730	-	1	NA	promoter-TSS (NM_023894)	promoter-TSS (NM_023894)	40	NM_023894	104384	Mm.156958	NM_023894	ENSMUSG00000068048	Rhox9	1600026O01Rik|Gpbox|Psx2	reproductive homeobox 9	protein-coding
mm_118046.1	chr13	101701876	101701935	-	1	NA	exon (NM_001077495, exon 6 of 16)	exon (NM_001077495, exon 6 of 16)	-9275	NM_001024955	18708	Mm.259333	NM_001024955	ENSMUSG00000041417	Pik3r1	PI3K|p50alpha|p55alpha|p85alpha	phosphatidylinositol 3-kinase, regulatory subunit, polypeptide 1 (p85 alpha)	protein-coding
mm_132053.1	chr16	29579332	29579342	+	1	NA	promoter-TSS (NM_133752)	promoter-TSS (NM_133752)	3	NM_001199177	74143	Mm.274285	NM_133752	ENSMUSG00000038084	Opa1	1200011N24Rik|AI225888|AI847218|lilr3|mKIAA0567	OPA1, mitochondrial dynamin like GTPase	protein-coding
mm_82803.1	chr9	29820951	29820952	-	1	NA	intron (NM_172290, intron 1 of 7)	intron (NM_172290, intron 1 of 7)	142178	NM_172290	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding
mm_67751.1	chr7	92637080	92637147	-	1	NA	promoter-TSS (NM_028665)	promoter-TSS (NM_028665)	29	NM_028665	73845	Mm.73248	NM_028665	ENSMUSG00000041343	Ankrd42	4931426M20|4933417L02Rik|Ikbn	ankyrin repeat domain 42	protein-coding
mm_44400.1	chr5	17836007	17836040	-	1	NA	promoter-TSS (NM_001159555)	promoter-TSS (NM_001159555)	-127	NM_007643	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_72716.1	chr8	85021976	85021994	+	1	NA	intron (NM_019652, intron 2 of 6)	B3|SINE|B2	3293	NM_019652	56495	Mm.41475	NM_019652	ENSMUSG00000052456	Asna1	1810048H22Rik|ArsA	arsA arsenite transporter, ATP-binding, homolog 1 (bacterial)	protein-coding
mm_154161.1	chr19	58455948	58455962	-	1	NA	promoter-TSS (NM_010279)	promoter-TSS (NM_010279)	-557	NM_010279	14585	Mm.88367	NM_010279	ENSMUSG00000025089	Gfra1	AU042498	glial cell line derived neurotrophic factor family receptor alpha 1	protein-coding
mm_74736.1	chr8	18741504	18741525	-	1	NA	promoter-TSS (NM_007426)	promoter-TSS (NM_007426)	48	NM_007426	11601	Mm.439874	NM_007426	ENSMUSG00000031465	Angpt2	Agpt2|Ang-2|Ang2	angiopoietin 2	protein-coding
mm_100069.1	chr11	115419317	115419348	+	1	NA	promoter-TSS (NM_183285)	promoter-TSS (NM_183285)	587	NM_027862	71679	Mm.371641	NM_027862	ENSMUSG00000034566	Atp5h	0610009D10Rik	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit D	protein-coding
mm_54660.1	chr6	39118212	39118252	-	1	NA	promoter-TSS (NR_045813)	promoter-TSS (NR_045813)	117	NM_172893	243771	Mm.268462	NM_172893	ENSMUSG00000038507	Parp12	9930021O16|AA409132|AA536654|ARTD12|PARP-12|Zc3hdc1	poly (ADP-ribose) polymerase family, member 12	protein-coding
mm_96139.1	chr11	60935620	60935631	+	1	NA	intron (NM_008928, intron 1 of 11)	intron (NM_008928, intron 1 of 11)	3568	NM_008928	26397	Mm.18494	NM_008928	ENSMUSG00000018932	Map2k3	AW212142|MEK3|MKK3|Prkmk3|mMKK3b	mitogen-activated protein kinase kinase 3	protein-coding
mm_41795.1	chr5	103753662	103753668	+	1	NA	promoter-TSS (NM_133919)	promoter-TSS (NM_133919)	-497	NM_133919	17355	Mm.6949	NM_133919	ENSMUSG00000029313	Aff1	9630032B01Rik|AW319193|Af4|Mllt2h|Rob	AF4/FMR2 family, member 1	protein-coding
mm_39887.1	chr5	31116682	31116690	+	1	NA	promoter-TSS (NM_021447)	promoter-TSS (NM_021447)	74	NM_021447	58522	Mm.143796	NM_021447	ENSMUSG00000062077	Trim54	4930486E09Rik|4930566I02Rik|MURF|MURF-3|MuRF3|Rnf30	tripartite motif-containing 54	protein-coding
mm_86792.1	chr10	20205357	20205366	+	1	NA	intron (NM_001198635, intron 1 of 17)	intron (NM_001198635, intron 1 of 17)	-3078	NM_001101561	621697	Mm.440587	NM_001101561		Rpl32l	EG621697|Gm6251	ribosomal protein L32-like	protein-coding
mm_94805.1	chr11	23008421	23008500	+	1	NA	Intergenic	CpG	-4927	NM_028672	73873	Mm.252406	NM_028672	ENSMUSG00000049811	Fam161a	4930430E16Rik	family with sequence similarity 161, member A	protein-coding
mm_169593.1	chr15	30447647	30447651	-	1	NA	intron (NM_008729, intron 2 of 22)	L1Md_T|LINE|L1	275056	NM_008729	18163	Mm.321648	NM_008729	ENSMUSG00000022240	Ctnnd2	Catnd2|Nprap|neurojugin	catenin (cadherin associated protein), delta 2	protein-coding
mm_33614.1	chr4	132611589	132611608	+	1	NA	Intergenic	Intergenic	-27448	NM_210071	14050	Mm.227733	NM_010166	ENSMUSG00000028886	Eya3	AI844637	EYA transcriptional coactivator and phosphatase 3	protein-coding
mm_38419.1	chr4	139186571	139186574	-	1	NA	Intergenic	B4A|SINE|B4	-5917	NR_033543	100038595	Mm.385206	NR_033543	ENSMUSG00000073739	Gm16287	ENSMUSG00000073739|OTTMUSG00000009902|OTTMUSG00000033208	predicted gene 16287	ncRNA
mm_5914.1	chr1	55027378	55027406	-	1	NA	promoter-TSS (NM_031179)	promoter-TSS (NM_031179)	86	NM_031179	81898	Mm.279736	NM_031179	ENSMUSG00000025982	Sf3b1	155kDa|2810001M05Rik|AA409119|Prp10|SAP155|SF3b155|TA-8|Targ4	splicing factor 3b, subunit 1	protein-coding
mm_142686.1	chr17	47734315	47734328	-	1	NA	exon (NM_025973, exon 9 of 9)	exon (NM_025973, exon 9 of 9)	-2716	NM_001161722	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_2019.1	chr1	87128049	87128051	+	1	NA	TTS (NM_007432)	TTS (NM_007432)	3042	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_90417.1	chr10	127471810	127471819	+	1	NA	exon (NM_001168293, exon 12 of 24)	exon (NM_001168293, exon 12 of 24)	-29903	NM_177707	237611	Mm.32087	NM_177707	ENSMUSG00000040287	Stac3	9830125E18	SH3 and cysteine rich domain 3	protein-coding
mm_95596.1	chr11	53332530	53332541	+	1	NA	exon (NM_026479, exon 4 of 4)	exon (NM_026479, exon 4 of 4)	7846	NM_026479	67966	Mm.288072	NM_026479	ENSMUSG00000018239	Zcchc10	2410141K03Rik|AA675321|D11Ertd416e	zinc finger, CCHC domain containing 10	protein-coding
mm_31732.1	chr4	63018344	63018347	+	1	NA	intron (NM_028326, intron 1 of 14)	L1MCa|LINE|L1	52771	NM_028326	72701	Mm.26479	NM_028326	ENSMUSG00000028358	Zfp618	2810031P15Rik|2810040O04Rik|AI415580|AI505139|D430033D05Rik|Nedd10|Znf618|bM257P7.1	zinc finger protein 618	protein-coding
mm_23835.1	chr3	82358057	82358075	+	1	NA	promoter-TSS (NM_001081230)	promoter-TSS (NM_001081230)	-6	NM_001081230	213582	Mm.271269	NM_001081230	ENSMUSG00000033900	Map9	5033421J10Rik|5330427D05Rik|ASAP|Mtap9	microtubule-associated protein 9	protein-coding
mm_24690.1	chr3	95004957	95005002	+	1	NA	TTS (NR_105980)	TTS (NR_105980)	811	NR_105980	102465613		NR_105980	ENSMUSG00000099033	Mir7013	Gm27488|mmu-mir-7013	microRNA 7013	ncRNA
mm_109472.1	chr12	111421448	111421456	+	1	NA	intron (NM_001289487, intron 2 of 13)	intron (NM_001289487, intron 2 of 13)	4007	NM_001289488	74190	Mm.248640	NM_028807	ENSMUSG00000021280	Exoc3l4	1200009I06Rik|1600013K19Rik	exocyst complex component 3-like 4	protein-coding
mm_13503.1	chr2	107956024	107956043	+	1	NA	Intergenic	RLTR45|LTR|ERVK	665444	NM_021275	16492	Mm.142718	NM_021275	ENSMUSG00000042604	Kcna4	Kv1.4	potassium voltage-gated channel, shaker-related subfamily, member 4	protein-coding
mm_158830.1	chrX	168123312	168123334	-	1	NA	promoter-TSS (NM_001290427)	promoter-TSS (NM_001290427)	-326	NM_001290427	333605	Mm.426168	NM_001033330	ENSMUSG00000049176	Frmpd4	Gm196|PKAP1|Pdzd10|Pdzk10|Preso1|preso	FERM and PDZ domain containing 4	protein-coding
mm_74919.1	chr8	25556135	25556152	-	1	NA	promoter-TSS (NR_110510)	promoter-TSS (NR_110510)	-60	NR_110510	102633315	Mm.437828	NR_110510	ENSMUSG00000086134	Gm16159	OTTMUSG00000031030	predicted gene 16159	ncRNA
mm_59841.1	chr7	29534408	29534414	+	1	NA	Intergenic	Intergenic	-28951	NM_001081028	74206	Mm.447042	NM_001081028	ENSMUSG00000030583	Sipa1l3	2610511M17Rik	signal-induced proliferation-associated 1 like 3	protein-coding
mm_3733.1	chr1	155098285	155098296	+	1	NA	3' UTR (NM_010500, exon 1 of 1)	3' UTR (NM_010500, exon 1 of 1)	1346	NM_010500	15939	Mm.12246	NM_010500	ENSMUSG00000056708	Ier5	-	immediate early response 5	protein-coding
mm_8327.1	chr1	149946362	149946364	-	1	NA	intron (NM_008869, intron 1 of 17)	PB1D9|SINE|Alu	14927	NM_008869	18783	Mm.4186	NM_008869	ENSMUSG00000056220	Pla2g4a	Pla2g4|cPLA2|cPLA2-alpha|cPLA2alpha	phospholipase A2, group IVA (cytosolic, calcium-dependent)	protein-coding
mm_49277.1	chr6	17637060	17637120	+	1	NA	promoter-TSS (NM_007604)	promoter-TSS (NM_007604)	-8	NM_007604	12343	Mm.392504	NM_007604	ENSMUSG00000015733	Capza2	1110053K06Rik|AW208808|Cappa2	capping protein (actin filament) muscle Z-line, alpha 2	protein-coding
mm_137744.1	chr17	29370602	29370622	+	1	NA	intron (NM_001159538, intron 9 of 15)	B1F1|SINE|Alu	9698	NM_001159538	26382	Mm.279187	NM_013710	ENSMUSG00000024013	Fgd2	Tcd-2|Tcd2|ZFYVE4|tcs-2|tcs2	FYVE, RhoGEF and PH domain containing 2	protein-coding
mm_155366.1	chrX	71118942	71118950	+	1	NA	exon (NM_001256048, exon 3 of 6)	exon (NM_001256048, exon 3 of 6)	68690	NM_001081354	333639	Mm.371730	NM_001081354	ENSMUSG00000059401	Mamld1	G630014P10Rik	mastermind-like domain containing 1	protein-coding
mm_114286.1	chr13	58402709	58402727	+	1	NA	promoter-TSS (NM_025279)	promoter-TSS (NM_025279)	121	NM_001168248	74386	Mm.85289	NM_028904	ENSMUSG00000035367	Rmi1	4932432N11Rik|C79893	RecQ mediated genome instability 1	protein-coding
mm_68979.1	chr7	126589257	126589273	-	1	NA	TTS (NM_138310)	TTS (NM_138310)	-3448	NM_001146311	12752	Mm.268930	NM_009907	ENSMUSG00000030720	Cln3	AI323623	ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease)	protein-coding
mm_167506.1	chr9	13310791	13310830	+	1	NA	Intergenic	Intergenic	63854	NM_025534	66396	Mm.290620	NM_025534	ENSMUSG00000079084	Ccdc82	2310043N13Rik	coiled-coil domain containing 82	protein-coding
mm_64910.1	chr7	16204127	16204133	-	1	NA	intron (NM_001285931, intron 9 of 16)	intron (NM_001285931, intron 9 of 16)	17863	NM_001285931	71723	Mm.75259	NM_027883	ENSMUSG00000006019	Dhx34	1200013B07Rik|1810012L18Rik|Ddx34|mKIAA0134	DEAH (Asp-Glu-Ala-His) box polypeptide 34	protein-coding
mm_125637.1	chr15	62060778	62060782	+	1	NA	intron (NR_132746, intron 1 of 6)	intron (NR_132746, intron 1 of 6)	21523	NR_132746	19296	Mm.4608	NM_011222	ENSMUSG00000097039	Pvt1	Ayu21-84Imeg|Gt(pU21)84Imeg|Mis-1|Mlvi-1|Pvt-1	plasmacytoma variant translocation 1	ncRNA
mm_134752.1	chr16	23157254	23157262	-	1	NA	exon (NM_009605, exon 3 of 3)	exon (NM_009605, exon 3 of 3)	10722	NM_009605	11450	Mm.3969	NM_009605	ENSMUSG00000022878	Adipoq	30kDa|APN|Acdc|Acrp30|Ad|GBP28|adipo|apM1	adiponectin, C1Q and collagen domain containing	protein-coding
mm_27881.1	chr3	79173189	79173246	-	1	NA	Intergenic	Intergenic	-27342	NM_001099624	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_156869.1	chrX	164442179	164442192	+	1	NA	intron (NM_026853, intron 2 of 7)	intron (NM_026853, intron 2 of 7)	5191	NM_001313737	68854	Mm.33225	NM_026853	ENSMUSG00000031382	Asb11	1110067L12Rik|1600009D24Rik	ankyrin repeat and SOCS box-containing 11	protein-coding
mm_94092.1	chr10	128522466	128522480	-	1	NA	exon (NM_011843, exon 3 of 31)	exon (NM_011843, exon 3 of 31)	3386	NM_011843	23943	Mm.66056	NM_011843	ENSMUSG00000025366	Esyt1	Fam62a|Mbc2|vp115	extended synaptotagmin-like protein 1	protein-coding
mm_145526.1	chr18	60636170	60636174	+	1	NA	Intergenic	Intergenic	-11867	NM_177340	104027	Mm.252321	NM_177340	ENSMUSG00000043079	Synpo	9030217H17Rik|9130229N11|9330140I15Rik|AW046661	synaptopodin	protein-coding
mm_153397.1	chr19	40487542	40487566	-	1	NA	intron (NM_178362, intron 1 of 28)	intron (NM_178362, intron 1 of 28)	26182	NM_178362	20411	Mm.210815	NM_009166	ENSMUSG00000025006	Sorbs1	2310065E01Rik|9530001P15Rik|CAP|SH3P12|Sh3d5|mKIAA1296	sorbin and SH3 domain containing 1	protein-coding
mm_160596.1	chr9	72925571	72925571	+	1	NA	promoter-TSS (NM_028116)	promoter-TSS (NM_028116)	-79	NM_028116	72135	Mm.273605	NM_028116	ENSMUSG00000034910	Pygo1	2600014C22Rik	pygopus 1	protein-coding
mm_118794.1	chr14	24293453	24293463	+	1	NA	promoter-TSS (NM_001033214)	promoter-TSS (NM_001033214)	94	NM_001033214	105418	Mm.2077	NM_001033214	ENSMUSG00000038925	E330034G19Rik	AA415275|Zpac	RIKEN cDNA E330034G19 gene	protein-coding
mm_135636.1	chr16	52346738	52346760	-	1	NA	intron (NM_009655, intron 1 of 15)	intron (NM_009655, intron 1 of 15)	106332	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_166548.1	chr6	39653800	39653804	+	1	NA	intron (NM_139294, intron 8 of 21)	intron (NM_139294, intron 8 of 21)	61219	NM_026612	68198	Mm.29415	NM_026612	ENSMUSG00000002416	Ndufb2	1810011O01Rik|8kDa|AGGG|AI325567|CI-AGGG	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 2	protein-coding
mm_31823.1	chr4	67930853	67930854	+	1	NA	Intergenic	Intergenic	1023544	NM_019967	56710	Mm.248788	NM_019967	ENSMUSG00000028351	Brinp1	BRINP|Dbc1|Dbccr1|Fam5a	bone morphogenic protein/retinoic acid inducible neural specific 1	protein-coding
mm_20383.1	chr2	128943961	128943976	-	1	NA	promoter-TSS (NM_020594)	promoter-TSS (NM_020594)	52	NM_020594	57432	Mm.11675	NM_020594	ENSMUSG00000027387	Zc3h8	AU020882|E130108N08Rik|Fliz1|Zc3hdc8	zinc finger CCCH type containing 8	protein-coding
mm_84725.1	chr9	74528653	74528668	-	1	NA	Intergenic	Intergenic	-319777	NR_045284	100503019	Mm.482658	NR_045284	ENSMUSG00000066477	Gm16551	-	predicted gene 16551	ncRNA
mm_52143.1	chr6	97977863	97977878	+	1	NA	intron (NM_001113198, intron 2 of 9)	B4A|SINE|B4	-13913	NM_008601	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_29544.1	chr3	116712645	116712655	-	1	NA	promoter-TSS (NM_144902)	promoter-TSS (NM_144902)	-370	NM_144902	229782	Mm.190758	NM_144902	ENSMUSG00000027957	Slc35a3	2310050P13Rik	solute carrier family 35 (UDP-N-acetylglucosamine (UDP-GlcNAc) transporter), member 3	protein-coding
mm_173134.1	chrX	19442223	19442228	-	1	NA	Intergenic	Intergenic	-295254	NR_029807	723828		NR_029807	ENSMUSG00000065471	Mir222	Mirn222|mir-222|mmu-mir-222	microRNA 222	ncRNA
mm_69617.1	chr7	137311002	137311006	-	1	NA	intron (NM_001113415, intron 4 of 15)	intron (NM_001113415, intron 4 of 15)	3441	NM_001113415	13593	Mm.258708	NM_010096	ENSMUSG00000010476	Ebf3	3110018A08Rik|O/E-2|mKIAA4201	early B cell factor 3	protein-coding
mm_29518.1	chr3	116428723	116428750	-	1	NA	Intergenic	Intergenic	-4704	NM_001173553	229776	Mm.17647	NM_001080818	ENSMUSG00000033502	Cdc14a	A830059A17Rik|CDC14A2|CDC14a1|Cdc14	CDC14 cell division cycle 14A	protein-coding
mm_90304.1	chr10	126978691	126978749	+	1	NA	promoter-TSS (NM_001113470)	promoter-TSS (NM_001113470)	3	NM_001113470	52468	Mm.29490	NM_146012	ENSMUSG00000078429	Ctdsp2	AI586070|D10Ertd73e|OS-4|OS4|SCP2	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 2	protein-coding
mm_113367.1	chr13	32996970	32996989	+	1	NA	Intergenic	Intergenic	-7562	NM_009256	20723	Mm.245041	NM_009256	ENSMUSG00000045827	Serpinb9	BB283241|CAP-3|CAP3|PI-9|PI9|Spi6|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 9	protein-coding
mm_7085.1	chr1	88554845	88554851	-	1	NA	intron (NR_037971, intron 1 of 5)	RMER17C2|LTR|ERVK	3331	NR_037971	100503197	Mm.99352	NR_037971	ENSMUSG00000100798	Gm19589	-	predicted gene, 19589	ncRNA
mm_120125.1	chr14	60087530	60087546	+	1	NA	promoter-TSS (NM_015803)	promoter-TSS (NM_015803)	-704	NM_015803	50769	Mm.319599	NM_015803	ENSMUSG00000021983	Atp8a2	AI415030|Atpc1b|agil|wl	ATPase, aminophospholipid transporter-like, class I, type 8A, member 2	protein-coding
mm_135334.1	chr16	38828781	38828783	-	1	NA	promoter-TSS (NM_029042)	promoter-TSS (NM_029042)	-33	NM_029042	74663	Mm.50263	NM_029042	ENSMUSG00000022798	4930435E12Rik	TSCPA	RIKEN cDNA 4930435E12 gene	protein-coding
mm_153493.1	chr19	41329993	41330014	-	1	NA	intron (NM_031376, intron 3 of 16)	Lx8b|LINE|L1	55067	NM_031376	83490	Mm.222266	NM_031376	ENSMUSG00000025017	Pik3ap1	1810044J04Rik|BCAP	phosphoinositide-3-kinase adaptor protein 1	protein-coding
mm_120805.1	chr14	74922141	74922148	+	1	NA	intron (NM_001252132, intron 1 of 18)	intron (NM_001252132, intron 1 of 18)	25733	NM_001252132	380916	Mm.288868	NM_001033439	ENSMUSG00000068015	Lrch1	4832412D13Rik|AI552548|AW215503|Chdc1|mKIAA1016	leucine-rich repeats and calponin homology (CH) domain containing 1	protein-coding
mm_88883.1	chr10	81134465	81134495	+	1	NA	Intergenic	Intergenic	-1791	NM_010731	16969	Mm.20920	NM_010731	ENSMUSG00000035011	Zbtb7a	9030619K07Rik|9130006G12Rik|AI452336|FBI-1|Lrf|Pokemon|Zbtb7	zinc finger and BTB domain containing 7a	protein-coding
mm_87202.1	chr10	39613136	39613154	+	1	NA	5' UTR (NM_134000, exon 1 of 9)	5' UTR (NM_134000, exon 1 of 9)	211	NM_134000	103213	Mm.436686	NM_134000	ENSMUSG00000019842	Traf3ip2	AI429613|Act1|CIKS	TRAF3 interacting protein 2	protein-coding
mm_142549.1	chr17	46590487	46590510	-	1	NA	intron (NM_175168, intron 3 of 19)	intron (NM_175168, intron 3 of 19)	-34336	NM_020493	20807	Mm.45044	NM_020493	ENSMUSG00000015605	Srf	AW049942|AW240594	serum response factor	protein-coding
mm_87953.1	chr10	63061587	63061602	+	1	NA	promoter-TSS (NM_026701)	promoter-TSS (NM_026701)	-23	NM_026701	68371	Mm.261389	NM_026701	ENSMUSG00000020072	Pbld1	0610038K03Rik|Mawbp|Pbld	phenazine biosynthesis-like protein domain containing 1	protein-coding
mm_66660.1	chr7	45717032	45717034	-	1	NA	5' UTR (NM_203280, exon 2 of 7)	5' UTR (NM_203280, exon 2 of 7)	969	NM_203280	56632	Mm.24222	NM_020011	ENSMUSG00000057342	Sphk2	C76851	sphingosine kinase 2	protein-coding
mm_168325.1	chr11	116023413	116023421	-	1	NA	exon (NM_008211, exon 4 of 4)	exon (NM_008211, exon 4 of 4)	1087	NM_008211	15081	Mm.18516	NM_008211	ENSMUSG00000016559	H3f3b	9430068D06Rik|H3.3B	H3 histone, family 3B	protein-coding
mm_160891.1	chr11	70606564	70606564	+	1	NA	intron (NM_016713, intron 13 of 30)	intron (NM_016713, intron 13 of 30)	-9330	NM_001145537	668433	Mm.425687	NM_001145537	ENSMUSG00000087279	4930544D05Rik	-	RIKEN cDNA 4930544D05 gene	protein-coding
mm_160983.1	chr11	103339767	103339767	-	1	NA	intron (NM_133715, intron 2 of 15)	intron (NM_133715, intron 2 of 15)	4935	NM_133715	544817	Mm.259113	NM_133715	ENSMUSG00000034255	Arhgap27	2310069I04Rik|5730442P18Rik|Gm21552|Sh3d20	Rho GTPase activating protein 27	protein-coding
mm_116715.1	chr13	51569172	51569192	-	1	NA	Intergenic	Intergenic	-2098	NM_009167	20418	Mm.131870	NM_009167	ENSMUSG00000021448	Shc3	N-Shc|Rai|ShcC	src homology 2 domain-containing transforming protein C3	protein-coding
mm_49650.1	chr6	30806494	30806516	+	1	NA	intron (NM_017478, intron 20 of 23)	intron (NM_017478, intron 20 of 23)	65206	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_46237.1	chr5	99218431	99218441	-	1	NA	3' UTR (NM_181318, exon 14 of 14)	3' UTR (NM_181318, exon 14 of 14)	34491	NM_181318	320292	Mm.259074	NM_145839	ENSMUSG00000089809	Rasgef1b	4732452O09Rik|GPIgamma4|Gpig4	RasGEF domain family, member 1B	protein-coding
mm_59974.1	chr7	30458281	30458293	+	1	NA	promoter-TSS (NM_172898)	promoter-TSS (NM_172898)	-772	NM_172898	243911	Mm.113908	NM_172898	ENSMUSG00000036915	Kirrel2	C330019F22Rik|NEPH3|NLG1	kin of IRRE like 2 (Drosophila)	protein-coding
mm_108904.1	chr12	100203609	100203622	+	1	NA	exon (NM_009790, exon 3 of 6)	exon (NM_009790, exon 3 of 6)	3471	NM_001313934	12313	Mm.285993	NM_009790	ENSMUSG00000001175	Calm1	AI256814|AI327027|AI461935|AL024000|CaM|Calm	calmodulin 1	protein-coding
mm_69708.1	chr7	140102327	140102357	-	1	NA	promoter-TSS (NR_104415)	promoter-TSS (NR_104415)	99	NM_001286217	69064	Mm.41915	NM_026928	ENSMUSG00000025466	Fuom	Fucu|Le51	fucose mutarotase	protein-coding
mm_64511.1	chr7	143628240	143628286	+	1	NA	promoter-TSS (NM_175649)	promoter-TSS (NM_175649)	-418	NM_175649	244237	Mm.247498	NM_175649	ENSMUSG00000045362	Tnfrsf26	Tnfrh3|Tnfrsf24	tumor necrosis factor receptor superfamily, member 26	protein-coding
mm_87143.1	chr10	34483518	34483533	+	1	NA	5' UTR (NM_001159544, exon 1 of 8)	5' UTR (NM_001159544, exon 1 of 8)	125	NM_010237	14302	Mm.332432	NM_010237	ENSMUSG00000019779	Frk	BSK|BSK/IYK|C85044|GTK|RAK	fyn-related kinase	protein-coding
mm_9845.1	chr1	184732108	184732118	-	1	NA	exon (NM_008250, exon 1 of 4)	exon (NM_008250, exon 1 of 4)	380	NM_008250	15284	Mm.1347	NM_008250	ENSMUSG00000039377	Hlx	Hlx1	H2.0-like homeobox	protein-coding
mm_69486.1	chr7	133917665	133917667	-	1	NA	intron (NM_007400, intron 16 of 22)	B4|SINE|B4	-134881	NM_001286031	101437	Mm.199223	NM_133941	ENSMUSG00000030986	Dhx32	3110079L04Rik|4732469F02Rik|AA408140|Ddx32	DEAH (Asp-Glu-Ala-His) box polypeptide 32	protein-coding
mm_48454.1	chr5	140760445	140760462	-	1	NA	3' UTR (NM_010302, exon 4 of 4)	3' UTR (NM_010302, exon 4 of 4)	36326	NM_173405	231842	Mm.491298	NM_173405	ENSMUSG00000050022	Amz1	5330426I05|6530401C20Rik	archaelysin family metallopeptidase 1	protein-coding
mm_71843.1	chr8	68904882	68904902	+	1	NA	3' UTR (NM_008509, exon 10 of 10)	3' UTR (NM_008509, exon 10 of 10)	24337	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_22554.1	chr3	9658353	9658359	+	1	NA	Intergenic	RMER17A|LTR|ERVK	-48271	NM_133218	170753	Mm.212908	NM_133218	ENSMUSG00000040209	Zfp704	C030026M03|C030034L19Rik|Gig1|Znf704	zinc finger protein 704	protein-coding
mm_3117.1	chr1	134632130	134632133	+	1	NA	3' UTR (NM_152895, exon 27 of 27)	3' UTR (NM_152895, exon 27 of 27)	-14550	NM_009307	20980	Mm.5102	NM_009307	ENSMUSG00000026452	Syt2	IP4BP|R74640|mKIAA4194	synaptotagmin II	protein-coding
mm_153371.1	chr19	40299706	40299710	-	1	NA	intron (NM_001034963, intron 20 of 22)	intron (NM_001034963, intron 20 of 22)	-28092	NM_016861	54132	Mm.5567	NM_016861	ENSMUSG00000055044	Pdlim1	CLP36|Clim1|mClim1	PDZ and LIM domain 1 (elfin)	protein-coding
mm_109921.1	chr12	8500002	8500017	-	1	NA	promoter-TSS (NM_007483)	promoter-TSS (NM_007483)	-24	NM_007483	11852	Mm.687	NM_007483	ENSMUSG00000054364	Rhob	AA017882|Arh6|Arhb	ras homolog family member B	protein-coding
mm_64639.1	chr7	3993720	3993722	-	1	NA	Intergenic	Intergenic	69483	NM_001302677	52855	Mm.290880	NM_178611	ENSMUSG00000055541	Lair1	5133400O11Rik|BB115266|D7Bwg0421e|Lair-1	leukocyte-associated Ig-like receptor 1	protein-coding
mm_11134.1	chr2	28468057	28468094	+	1	NA	promoter-TSS (NM_001166031)	promoter-TSS (NM_001166031)	9	NM_001166031	118451	Mm.294951	NM_080452	ENSMUSG00000035772	Mrps2	1500019M10Rik	mitochondrial ribosomal protein S2	protein-coding
mm_128135.1	chr15	31453565	31453694	-	1	NA	promoter-TSS (NM_145852)	promoter-TSS (NM_145852)	60	NM_145852	252967	Mm.436668	NM_145852	ENSMUSG00000022236	Ropn1l	ASP|AV047578|Akapasp	ropporin 1-like	protein-coding
mm_7649.1	chr1	128319099	128319114	-	1	NA	exon (NM_001081078, exon 2 of 17)	exon (NM_001081078, exon 2 of 17)	9212	NM_001081078	226413	Mm.26930	NM_001081078	ENSMUSG00000026354	Lct	Gm100|LAC|LPH|Lphl	lactase	protein-coding
mm_6849.1	chr1	84245237	84245256	-	1	NA	intron (NM_001003948, intron 1 of 2)	L1_Mus1|LINE|L1	-26285	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_100105.1	chr11	115766802	115766821	+	1	NA	intron (NM_028014, intron 1 of 31)	intron (NM_028014, intron 1 of 31)	1378	NM_028014	71947	Mm.23168	NM_028014	ENSMUSG00000020747	Tmem94	2310067B10Rik|Kiaa0195|mKIAA0195	transmembrane protein 94	protein-coding
mm_162680.1	chr10	12869443	12869487	-	1	NA	Intergenic	CpG	-7730	NM_011682	22288	Mm.331784	NM_011682	ENSMUSG00000019820	Utrn	AA589569|DRP|Dmdl	utrophin	protein-coding
mm_65874.1	chr7	29518537	29518541	-	1	NA	Intergenic	CpG	-13079	NM_001081028	74206	Mm.447042	NM_001081028	ENSMUSG00000030583	Sipa1l3	2610511M17Rik	signal-induced proliferation-associated 1 like 3	protein-coding
mm_78931.1	chr9	45102875	45102884	+	1	NA	intron (NM_001005421, intron 8 of 10)	intron (NM_001005421, intron 8 of 10)	-14997	NM_001014761	72821	Mm.229373	NM_001014761	ENSMUSG00000070304	Scn2b	2810451E09Rik|AI840361|Gm183	sodium channel, voltage-gated, type II, beta	protein-coding
mm_166688.1	chr6	104493133	104493156	+	1	NA	promoter-TSS (NM_017383)	promoter-TSS (NM_017383)	100	NM_017383	53870	Mm.321671	NM_017383	ENSMUSG00000030092	Cntn6	NB-3	contactin 6	protein-coding
mm_128730.1	chr15	64133248	64133264	-	1	NA	intron (NM_010026, intron 16 of 30)	B3A|SINE|B2	-72808	NM_144846	223601	Mm.246108	NM_144846	ENSMUSG00000022378	Fam49b	0910001A06Rik|AW122079	family with sequence similarity 49, member B	protein-coding
mm_124554.1	chr14	122913109	122913190	-	1	NA	promoter-TSS (NM_145466)	promoter-TSS (NM_145466)	16	NM_145466	223267	Mm.379358	NM_145466	ENSMUSG00000041625	Ggact	A2ld1	gamma-glutamylamine cyclotransferase	protein-coding
mm_42367.1	chr5	114923235	114923246	+	1	NA	promoter-TSS (NM_145209)	promoter-TSS (NM_145209)	0	NM_145209	231655	Mm.95479	NM_145209	ENSMUSG00000041827	Oasl1	7530414C13Rik|oasl9	2'-5' oligoadenylate synthetase-like 1	protein-coding
mm_114711.1	chr13	83573578	83573603	+	1	NA	promoter-TSS (NM_001347569)	promoter-TSS (NM_001347569)	-17	NM_001347577	17260	Mm.24001	NM_025282	ENSMUSG00000005583	Mef2c	5430401D19Rik|9930028G15Rik|AV011172|Mef2	myocyte enhancer factor 2C	protein-coding
mm_51532.1	chr6	83188992	83189002	+	1	NA	intron (NM_001347310, intron 2 of 26)	C-rich|Low_complexity|Low_complexity	3051	NM_001347310	13191	Mm.6919	NM_007835	ENSMUSG00000031865	Dctn1	AL022633|DAP-150|DP-150|Glued|p150|p150-glued|p150<glued>	dynactin 1	protein-coding
mm_110451.1	chr12	51634920	51634922	-	1	NA	intron (NM_052973, intron 8 of 17)	intron (NM_052973, intron 8 of 17)	41580	NM_001198835	12810	Mm.21325	NM_007728	ENSMUSG00000020953	Coch	AW122937|Coch-5B2|D12H14S564E	cochlin	protein-coding
mm_9767.1	chr1	180994026	180994035	-	1	NA	exon (NM_010145, exon 6 of 9)	exon (NM_010145, exon 6 of 9)	23539	NM_010145	13849	Mm.9075	NM_010145	ENSMUSG00000038776	Ephx1	EH|Eph-1|Eph1|Epxh1|mEH	epoxide hydrolase 1, microsomal	protein-coding
mm_2158.1	chr1	88211957	88211985	+	1	NA	promoter-TSS (NM_201645)	promoter-TSS (NM_201645)	12	NM_201645	394436	Mm.300095	NM_201645	ENSMUSG00000089960	Ugt1a1	Gnt1|UDPGT 1-1|UGT1A01|Udpgt-1a|UgtBr1	UDP glucuronosyltransferase 1 family, polypeptide A1	protein-coding
mm_35519.1	chr4	41203584	41203593	-	1	NA	intron (NM_026872, intron 16 of 28)	intron (NM_026872, intron 16 of 28)	67567	NM_026275	67615	Mm.389540	NM_026275	ENSMUSG00000036241	Ube2r2	1200003M11Rik|Cdc34b|Ubc3b	ubiquitin-conjugating enzyme E2R 2	protein-coding
mm_120018.1	chr14	55757867	55757893	+	1	NA	exon (NM_009894, exon 2 of 5)	exon (NM_009894, exon 2 of 5)	544	NM_009894	12684	Mm.466766	NM_009894	ENSMUSG00000022219	Cideb	1110030C18Rik|AI790179|CIDE-B	cell death-inducing DNA fragmentation factor, alpha subunit-like effector B	protein-coding
mm_82990.1	chr9	36534007	36534015	-	1	NA	3' UTR (NM_001033783, exon 3 of 3)	3' UTR (NM_001033783, exon 3 of 3)	7952	NM_001033783	434396	Mm.118836	NM_001033783	ENSMUSG00000074448	Gm5615	EG434396|Pate-H|Pate9	predicted gene 5615	protein-coding
mm_8472.1	chr1	153406521	153406543	-	1	NA	non-coding (NR_033736, exon 4 of 4)	non-coding (NR_033736, exon 4 of 4)	7701	NR_033736	626058	Mm.31556	NM_001177359		E330020D12Rik	EG626058|F430003O07Rik|Gm6648	Riken cDNA E330020D12 gene	ncRNA
mm_124432.1	chr14	118237039	118237047	-	1	NA	promoter-TSS (NM_177753)	promoter-TSS (NM_177753)	-13	NM_177753	223227	Mm.70950	NM_177753	ENSMUSG00000061517	Sox21	Sox25	SRY (sex determining region Y)-box 21	protein-coding
mm_65487.1	chr7	25679062	25679108	-	1	NA	Intergenic	Intergenic	-2073	NM_172148	232987	Mm.22849	NM_172148	ENSMUSG00000063439	B9d2	stumpy	B9 protein domain 2	protein-coding
mm_51681.1	chr6	86472767	86472809	+	1	NA	intron (NR_131126, intron 2 of 2)	intron (NR_131126, intron 2 of 2)	8042	NR_131125	320486	Mm.391625	NR_131125	ENSMUSG00000085589	A430078I02Rik	T25621	RIKEN cDNA A430078I02 gene	ncRNA
mm_132735.1	chr16	43889812	43889820	+	1	NA	promoter-TSS (NM_029128)	promoter-TSS (NM_029128)	-86	NM_027801	212153	Mm.209835	NM_027801	ENSMUSG00000022701	Ccdc191	2610015P09Rik|8430422M09Rik|AU040712	coiled-coil domain containing 191	protein-coding
mm_148714.1	chr19	5808575	5808583	+	1	NA	Intergenic	Intergenic	-5907	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_42892.1	chr5	122396748	122396753	+	1	NA	intron (NM_019824, intron 1 of 6)	intron (NM_019824, intron 1 of 6)	4872	NM_019824	56378	Mm.275942	NM_019824	ENSMUSG00000029465	Arpc3	1110006A04Rik|p21-ARC|p21-Ar|p21Arc	actin related protein 2/3 complex, subunit 3	protein-coding
mm_137750.1	chr17	29395714	29395729	+	1	NA	Intergenic	Intergenic	34807	NM_001159538	26382	Mm.279187	NM_013710	ENSMUSG00000024013	Fgd2	Tcd-2|Tcd2|ZFYVE4|tcs-2|tcs2	FYVE, RhoGEF and PH domain containing 2	protein-coding
mm_47116.1	chr5	119628708	119628754	-	1	NA	intron (NR_046178, intron 1 of 3)	intron (NR_046178, intron 1 of 3)	2789	NR_046178	330183	Mm.413133	NR_046178	ENSMUSG00000085708	Gm16063	G630008E18|OTTMUSG00000029664	predicted gene 16063	ncRNA
mm_128818.1	chr15	67115177	67115193	-	1	NA	intron (NM_009177, intron 3 of 8)	intron (NM_009177, intron 3 of 8)	61697	NM_009177	20442	Mm.248334	NM_009177	ENSMUSG00000013846	St3gal1	5330418N22Rik|AI467004|ST3GalI|Siat4|Siat4a|St3gal-1	ST3 beta-galactoside alpha-2,3-sialyltransferase 1	protein-coding
mm_88229.1	chr10	70599815	70599836	+	1	NA	promoter-TSS (NM_178621)	promoter-TSS (NM_178621)	-534	NM_178621	70911	Mm.19825	NM_178621	ENSMUSG00000037747	Phyhipl	4921522K17Rik|AI267048	phytanoyl-CoA hydroxylase interacting protein-like	protein-coding
mm_77099.1	chr8	111027671	111027721	-	1	NA	promoter-TSS (NM_001190800)	promoter-TSS (NM_001190800)	74	NM_172284	234733	Mm.482176	NM_172284	ENSMUSG00000033658	Ddx19b	2810457M08Rik|4921519L13Rik|AW260119	DEAD (Asp-Glu-Ala-Asp) box polypeptide 19b	protein-coding
mm_133254.1	chr16	77329247	77329353	+	1	NA	promoter-TSS (NR_015543)	promoter-TSS (NR_015543)	-28	NR_015543	77994	Mm.394688	NR_015543	ENSMUSG00000090386	Mir99ahg	2810055G20Rik|D730043B02Rik	Mir99a and Mirlet7c-1 host gene (non-protein coding)	ncRNA
mm_115230.1	chr13	109902857	109902867	+	1	NA	promoter-TSS (NR_035442)	promoter-TSS (NR_035442)	-947	NR_035442	100316683		NR_035442	ENSMUSG00000084651	Mir1904	Mirn1904|mmu-mir-1904	microRNA 1904	ncRNA
mm_23576.1	chr3	63345207	63345227	+	1	NA	exon (NM_008604, exon 13 of 23)	exon (NM_008604, exon 13 of 23)	49122	NM_001289463	17380	Mm.296022	NM_008604	ENSMUSG00000027820	Mme	6030454K05Rik|C85356|CALLA|CD10|NEP|SFE	membrane metallo endopeptidase	protein-coding
mm_1065.1	chr1	59150890	59150905	+	1	NA	intron (NM_001164682, intron 5 of 22)	intron (NM_001164682, intron 5 of 22)	10739	NM_145143	227157	Mm.474049	NM_145143	ENSMUSG00000079550	Mpp4	Dlg6	membrane protein, palmitoylated 4 (MAGUK p55 subfamily member 4)	protein-coding
mm_120122.1	chr14	59625561	59625586	+	1	NA	5' UTR (NM_145463, exon 1 of 2)	5' UTR (NM_145463, exon 1 of 2)	292	NM_145463	219134	Mm.275409	NM_145463	ENSMUSG00000044461	Shisa2	9430059P22Rik|MAd2|Tmem46|mShisa|shisa	shisa family member 2	protein-coding
mm_166174.1	chr5	30155116	30155126	-	1	NA	promoter-TSS (NM_001289798)	promoter-TSS (NM_001289798)	-132	NM_145558	231086	Mm.291463	NM_145558	ENSMUSG00000059447	Hadhb	4930479F15Rik|Mtpb|TP-beta	hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), beta subunit	protein-coding
mm_59748.1	chr7	28820630	28820646	+	1	NA	exon (NM_177301, exon 10 of 13)	exon (NM_177301, exon 10 of 13)	-4700	NM_016772	51798	Mm.291776	NM_016772	ENSMUSG00000053898	Ech1	AA617331	enoyl coenzyme A hydratase 1, peroxisomal	protein-coding
mm_109021.1	chr12	103550360	103550363	+	1	NA	intron (NM_028980, intron 2 of 24)	intron (NM_028980, intron 2 of 24)	17796	NM_028980	74521	Mm.248619	NM_028980	ENSMUSG00000021209	Ppp4r4	8430415E04Rik|mKIAA1622	protein phosphatase 4, regulatory subunit 4	protein-coding
mm_148510.1	chr19	4215833	4215847	+	1	NA	intron (NM_001310038, intron 2 of 3)	intron (NM_001310038, intron 2 of 3)	1451	NM_001310039	56708	Mm.347919	NM_019952	ENSMUSG00000040663	Clcf1	BSF-3|Bsf3|CLC|NNT-1	cardiotrophin-like cytokine factor 1	protein-coding
mm_120893.1	chr14	75845280	75845286	+	1	NA	promoter-TSS (NM_009429)	promoter-TSS (NM_009429)	27	NM_009429	22070	Mm.297482	NM_009429	ENSMUSG00000060126	Tpt1	TCTP|Trt|p21|p23	tumor protein, translationally-controlled 1	protein-coding
mm_122090.1	chr14	30625319	30625339	-	1	NA	intron (NM_011103, intron 1 of 17)	intron (NM_011103, intron 1 of 17)	879	NM_011103	18753	Mm.2314	NM_011103	ENSMUSG00000021948	Prkcd	AI385711|D14Ertd420e|PKC[d]|PKCdelta|Pkcd	protein kinase C, delta	protein-coding
mm_118488.1	chr14	12284199	12284239	+	1	NA	promoter-TSS (NM_146051)	promoter-TSS (NM_146051)	16	NM_001284386	218734	Mm.44068	NM_146051	ENSMUSG00000033111	3830406C13Rik	-	RIKEN cDNA 3830406C13 gene	protein-coding
mm_15027.1	chr2	152687164	152687177	+	1	NA	promoter-TSS (NM_025543)	promoter-TSS (NM_025543)	22	NM_025543	66405	Mm.440291	NM_025543	ENSMUSG00000042814	Mcts2	2400002F11Rik|MCT-2	malignant T cell amplified sequence 2	protein-coding
mm_121791.1	chr14	20082676	20082702	-	1	NA	intron (NM_026209, intron 1 of 1)	intron (NM_026209, intron 1 of 1)	483	NM_026209	67509	Mm.292423	NM_026209	ENSMUSG00000045107	Saysd1	1810063B07Rik|4930488P03Rik	SAYSVFN motif domain containing 1	protein-coding
mm_25107.1	chr3	101376991	101377023	+	1	NA	promoter-TSS (NM_207205)	promoter-TSS (NM_207205)	-118	NM_207205	78908	Mm.257997	NM_207205	ENSMUSG00000042035	Igsf3	1700016K10Rik|2810035F16Rik|4833439O17Rik|mKIAA0466	immunoglobulin superfamily, member 3	protein-coding
mm_97276.1	chr11	75999981	75999994	+	1	NA	promoter-TSS (NM_198637)	promoter-TSS (NM_198637)	75	NM_198637	74230	Mm.271247	NM_198637	ENSMUSG00000053783	1700016K19Rik	Liat1	RIKEN cDNA 1700016K19 gene	protein-coding
mm_138210.1	chr17	34305890	34305909	+	1	NA	promoter-TSS (NM_010382)	promoter-TSS (NM_010382)	32	NM_010382	14969	Mm.22564	NM_010382	ENSMUSG00000060586	H2-Eb1	Eb|H-2Eb|H2Eb|Ia-4|Ia4	histocompatibility 2, class II antigen E beta	protein-coding
mm_71047.1	chr8	33680776	33680805	+	1	NA	intron (NM_010344, intron 6 of 12)	intron (NM_010344, intron 6 of 12)	27552	NM_010344	14782	Mm.283573	NM_010344	ENSMUSG00000031584	Gsr	AI325518|D8Ertd238e|Gr-1|Gr1	glutathione reductase	protein-coding
mm_63491.1	chr7	127769810	127769854	+	1	NA	promoter-TSS (NM_198424)	promoter-TSS (NM_198424)	17	NM_198424	269999	Mm.36852	NM_198424	ENSMUSG00000043964	Orai3	9930124N15|BC061259|Tmem142c	ORAI calcium release-activated calcium modulator 3	protein-coding
mm_22319.1	chr2	180541419	180541423	-	1	NA	intron (NM_018766, intron 2 of 3)	intron (NM_018766, intron 2 of 3)	-39883	NM_028479	73247	Mm.426558	NM_028479	ENSMUSG00000027569	Mrgbp	1600027N09Rik|AW060503|C80444	MRG/MORF4L binding protein	protein-coding
mm_129992.1	chr15	86168246	86168269	-	1	NA	intron (NM_145475, intron 1 of 12)	intron (NM_145475, intron 1 of 12)	17884	NM_145475	223753	Mm.222685	NM_145475	ENSMUSG00000035891	Cerk	AI848610|D330016D08Rik|mKIAA1646	ceramide kinase	protein-coding
mm_71312.1	chr8	43180530	43180546	+	1	NA	Intergenic	Intergenic	-2584	NM_001160412	622117	Mm.390031	NM_001160412	ENSMUSG00000091490	Triml2	EG622117|Tu4	tripartite motif family-like 2	protein-coding
mm_62678.1	chr7	109610264	109610302	+	1	NA	intron (NM_001001326, intron 1 of 19)	intron (NM_001001326, intron 1 of 19)	6285	NR_037617	76954	Mm.252009	NM_029811	ENSMUSG00000031024	St5	2010004M01Rik|2610305K15Rik	suppression of tumorigenicity 5	protein-coding
mm_146695.1	chr18	12941664	12941678	-	1	NA	5' UTR (NM_207530, exon 1 of 28)	5' UTR (NM_207530, exon 1 of 28)	170	NM_207530	64291	Mm.259470	NM_020573	ENSMUSG00000044252	Osbpl1a	G430090F17Rik|Gm753|ORP-1|Osbpl1b	oxysterol binding protein-like 1A	protein-coding
mm_61264.1	chr7	66109451	66109473	+	1	NA	promoter-TSS (NM_001081163)	promoter-TSS (NM_001081163)	-53	NM_001081163	269941	Mm.333916	NM_001081163	ENSMUSG00000032640	Chsy1	mKIAA0990	chondroitin sulfate synthase 1	protein-coding
mm_141400.1	chr17	29263929	29263982	-	1	NA	promoter-TSS (NM_026845)	promoter-TSS (NM_026845)	16	NM_026845	68816	Mm.328928	NM_026845	ENSMUSG00000024007	Ppil1	1110060O10Rik|AI327391|Cypl1	peptidylprolyl isomerase (cyclophilin)-like 1	protein-coding
mm_88564.1	chr10	79664588	79664603	+	1	NA	promoter-TSS (NM_013591)	promoter-TSS (NM_013591)	21	NM_013591	17123	Mm.391556	NM_013591	ENSMUSG00000020310	Madcam1	AV211525	mucosal vascular addressin cell adhesion molecule 1	protein-coding
mm_72676.1	chr8	84913321	84913353	+	1	NA	promoter-TSS (NR_103491)	promoter-TSS (NR_103491)	2	NR_103491	100503676	Mm.437155	NR_103491	ENSMUSG00000003812	Gm38426	-	predicted gene, 38426	ncRNA
mm_118761.1	chr14	22428747	22428756	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	114047	NR_046307	74896	Mm.444661	NR_046307		4930405A10Rik	4930456G20Rik	RIKEN cDNA 4930405A10 gene	ncRNA
mm_125226.1	chr15	34131154	34131187	+	1	NA	exon (NM_026002, exon 8 of 12)	exon (NM_026002, exon 8 of 12)	48451	NM_026002	67154	Mm.130883	NM_026002	ENSMUSG00000022255	Mtdh	2610103J23Rik|3D3|3D3/Lyric|AEG-1|AV353288|D8Bwg1112e|Lyric	metadherin	protein-coding
mm_83750.1	chr9	51165655	51165664	-	1	NA	Intergenic	Intergenic	-48031	NM_011136	18985	Mm.897	NM_011136	ENSMUSG00000032053	Pou2af1	BOB.1|Bob-1|Bob1|OBF-1|OBF.1|OCA-B|OCAB	POU domain, class 2, associating factor 1	protein-coding
mm_83049.1	chr9	37544967	37545018	-	1	NA	TTS (NM_020518)	TTS (NM_020518)	5737	NM_020518	57276	Mm.27478	NM_020518	ENSMUSG00000001943	Vsig2	1190004B15Rik|2210413P10Rik|AU040484|CTX|Ctm	V-set and immunoglobulin domain containing 2	protein-coding
mm_52765.1	chr6	120932855	120932865	+	1	NA	3' UTR (NM_001270475, exon 32 of 32)	3' UTR (NM_001270475, exon 32 of 32)	-16040	NM_007544	12122	Mm.235081	NM_007544	ENSMUSG00000004446	Bid	2700049M22Rik|AI875481|AU022477	BH3 interacting domain death agonist	protein-coding
mm_149392.1	chr19	11386866	11386876	+	1	NA	intron (NM_001310331, intron 4 of 6)	intron (NM_001310331, intron 4 of 6)	11383	NM_001310331	666907		NM_001310331	ENSMUSG00000101389	Ms4a4a	EG666907	membrane-spanning 4-domains, subfamily A, member 4A	protein-coding
mm_39701.1	chr5	27261982	27262003	+	1	NA	promoter-TSS (NM_001136060)	promoter-TSS (NM_001136060)	57	NM_001136060	13483	Mm.42078	NM_010075	ENSMUSG00000061576	Dpp6	B930011P16Rik|D5Buc3|D5Buc4|D5Buc5|DPP VI|Dpp-6|Gm1377|In(5)6H-p|Peplb|Rw	dipeptidylpeptidase 6	protein-coding
mm_155528.1	chrX	74282723	74282770	+	1	NA	promoter-TSS (NM_001242616)	promoter-TSS (NM_001242616)	28	NM_001242615	66826	Mm.268483	NM_181516	ENSMUSG00000009995	Taz	5031411C02Rik|9130012G04Rik|AW107266|AW552613|G4.5	tafazzin	protein-coding
mm_90091.1	chr10	116950554	116950625	+	1	NA	promoter-TSS (NR_038026)	promoter-TSS (NR_038026)	27	NR_038026	71086	Mm.214134	NR_038025		4933412E12Rik	-	RIKEN cDNA 4933412E12 gene	ncRNA
mm_44745.1	chr5	31202231	31202329	-	1	NA	promoter-TSS (NM_001177901)	promoter-TSS (NM_001177901)	23	NM_175311	101023	Mm.45033	NM_175311	ENSMUSG00000043059	Zfp513	AW990386|D430028M17Rik|Znf513	zinc finger protein 513	protein-coding
mm_81281.1	chr9	108296875	108296937	+	1	NA	promoter-TSS (NM_001013814)	promoter-TSS (NM_001013814)	-16	NM_001013814	434437	Mm.390225	NM_001013814	ENSMUSG00000032607	Amt	EG434437	aminomethyltransferase	protein-coding
mm_9605.1	chr1	175625619	175625628	-	1	NA	promoter-TSS (NM_010209)	promoter-TSS (NM_010209)	12	NM_010209	14194	Mm.41502	NM_010209	ENSMUSG00000026526	Fh1	Fh|Fh-1	fumarate hydratase 1	protein-coding
mm_127632.1	chr15	102470700	102470716	+	1	NA	promoter-TSS (NM_001174073)	promoter-TSS (NM_001174073)	76	NM_001174073	18521	Mm.236513	NM_011042	ENSMUSG00000056851	Pcbp2	AW412548|Hnrpx|alphaCP-2	poly(rC) binding protein 2	protein-coding
mm_11373.1	chr2	31081711	31081736	+	1	NA	intron (NM_001038700, intron 6 of 14)	intron (NM_001038700, intron 6 of 14)	14777	NM_001177650	14269	Mm.52297	NM_019406	ENSMUSG00000075415	Fnbp1	1110057E06Rik|2210010H06Rik|FBP1|Fbp17	formin binding protein 1	protein-coding
mm_169261.1	chr13	82694700	82694703	-	1	NA	Intergenic	Lx3_Mus|LINE|L1	3632	NR_039537	100628621		NR_039537	ENSMUSG00000106655	Mir3961	mmu-mir-3961	microRNA 3961	ncRNA
mm_55233.1	chr6	52240842	52240854	-	1	NA	promoter-TSS (NM_001122950)	promoter-TSS (NM_001122950)	6	NM_001122950	15395	Mm.5	NM_008263	ENSMUSG00000000938	Hoxa10	Hox-1.8|Hoxa-10	homeobox A10	protein-coding
mm_157977.1	chrX	93923008	93923012	-	1	NA	Intergenic	CpG	-45646	NR_028320	385493	Mm.328014	NM_001033480	ENSMUSG00000081044	AU015836	-	expressed sequence AU015836	ncRNA
mm_100899.1	chr11	6066397	6066411	-	1	NA	promoter-TSS (NM_001174054)	promoter-TSS (NM_001174054)	-656	NM_007595	12323	Mm.439733	NM_007595	ENSMUSG00000057897	Camk2b	CaMKII	calcium/calmodulin-dependent protein kinase II, beta	protein-coding
mm_35985.1	chr4	55475380	55475401	-	1	NA	Intergenic	Intergenic	-56548	NR_040674	100415914	Mm.261765	NR_040674	ENSMUSG00000087070	Gm12505	OTTMUSG00000007226	predicted gene 12505	ncRNA
mm_103589.1	chr11	78233582	78233599	-	1	NA	exon (NM_009297, exon 2 of 37)	exon (NM_009297, exon 2 of 37)	12113	NM_009297	20926	Mm.20755	NM_009297	ENSMUSG00000002052	Supt6	5131400N11Rik|AI132449|SPT6|Supt6h|mKIAA0162	suppressor of Ty 6	protein-coding
mm_107645.1	chr12	52504247	52504285	+	1	NA	Intergenic	CpG	-11811	NM_009706	11855	Mm.35059	NM_009706	ENSMUSG00000035133	Arhgap5	p190-B|p190B	Rho GTPase activating protein 5	protein-coding
mm_160916.1	chr11	83409959	83409959	+	1	NA	promoter-TSS (NM_001013386)	promoter-TSS (NM_001013386)	-113	NM_001013386	276952	Mm.66275	NM_001013386	ENSMUSG00000020684	Rasl10b	B230331P10Rik|Gm729|VTS58635	RAS-like, family 10, member B	protein-coding
mm_134116.1	chr16	10294453	10294462	-	1	NA	intron (NM_007929, intron 1 of 4)	(CAGAGA)n|Simple_repeat|Simple_repeat	19511	NM_007929	13731	Mm.246009	NM_007929	ENSMUSG00000022505	Emp2	XMP	epithelial membrane protein 2	protein-coding
mm_23865.1	chr3	83014134	83014153	+	1	NA	exon (NM_133862, exon 9 of 10)	exon (NM_133862, exon 9 of 10)	6419	NM_001317105	99571	Mm.16422	NM_133862	ENSMUSG00000033860	Fgg	3010002H13Rik|AI256424	fibrinogen gamma chain	protein-coding
mm_154448.1	chrM	1879	1945	-	1	NA	NA	Intergenic	NA	NA								
mm_76107.1	chr8	80395201	80395205	-	1	NA	Intergenic	Intergenic	-98842	NM_010369	14934	Mm.13123	NM_010369	ENSMUSG00000051839	Gypa	AI853584|CD235a|GPA	glycophorin A	protein-coding
mm_163321.1	chr12	7977768	7977792	+	1	NA	exon (NM_009693, exon 1 of 29)	exon (NM_009693, exon 1 of 29)	103	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_61826.1	chr7	87861720	87861737	+	1	NA	intron (NM_001143834, intron 4 of 10)	Lx3B|LINE|L1	277560	NM_001143834	108071	Mm.235018	NM_001033224	ENSMUSG00000049583	Grm5	6430542K11Rik|AI850523|Glu5R|Gprc1e|mGluR5|mGluR5b	glutamate receptor, metabotropic 5	protein-coding
mm_61151.1	chr7	58458532	58458536	+	1	NA	Intergenic	RLTR10D|LTR|ERVK	-199668	NM_009728	11982	Mm.135129	NM_009728	ENSMUSG00000025324	Atp10a	Atp10c|pfatp	ATPase, class V, type 10A	protein-coding
mm_56020.1	chr6	86569419	86569441	-	1	NA	Intergenic	Intergenic	42029	NR_037961	72012	Mm.349174	NR_037960	ENSMUSG00000097048	1600020E01Rik	-	RIKEN cDNA 1600020E01 gene	ncRNA
mm_144789.1	chr18	35889676	35889697	+	1	NA	Intergenic	CpG	59868	NM_133687	67393	Mm.94560	NM_133687	ENSMUSG00000046668	Cxxc5	4930415K17Rik	CXXC finger 5	protein-coding
mm_54301.1	chr6	29507947	29507974	-	1	NA	promoter-TSS (NM_001029985)	promoter-TSS (NM_001029985)	-8	NM_001029985	333088	Mm.332961	NM_001029985	ENSMUSG00000059022	Kcp	AW060220|CRIM-2|Crim2|Gm793|KCP-1	kielin/chordin-like protein	protein-coding
mm_84941.1	chr9	82975380	82975396	-	1	NA	5' UTR (NM_001081216, exon 1 of 40)	5' UTR (NM_001081216, exon 1 of 40)	101	NM_001081216	83946	Mm.221688	NM_031879	ENSMUSG00000032253	Phip	2810004D21Rik|4632404O06Rik|Ndrp|Wdr11	pleckstrin homology domain interacting protein	protein-coding
mm_80293.1	chr9	73094845	73094854	+	1	NA	intron (NM_001301230, intron 6 of 6)	MLT1L|LTR|ERVL-MaLR	-7549	NM_025890	66991	Mm.471745	NM_025890	ENSMUSG00000092622	Khdc3	2410004A20Rik|AI467128|FILIA|OEEP48	KH domain containing 3, subcortical maternal complex member	protein-coding
mm_61012.1	chr7	49364953	49364972	+	1	NA	intron (NM_175272, intron 2 of 37)	intron (NM_175272, intron 2 of 37)	118773	NM_175272	78286	Mm.333881	NM_175272	ENSMUSG00000052512	Nav2	5330421F07Rik|AU067780|BQ960892|HELAD1|POMFIL2|RAINB1|RAINB2|Unc53H2|mKIAA3015	neuron navigator 2	protein-coding
mm_60671.1	chr7	45018011	45018021	+	1	NA	promoter-TSS (NM_009101)	promoter-TSS (NM_009101)	9	NM_009101	20130	Mm.389894	NM_009101	ENSMUSG00000038387	Rras	AI573426	related RAS viral (r-ras) oncogene	protein-coding
mm_132370.1	chr16	34807322	34807344	+	1	NA	intron (NM_139300, intron 1 of 31)	intron (NM_139300, intron 1 of 31)	22383	NM_139300	107589	Mm.33360	NM_139300	ENSMUSG00000022836	Mylk	9530072E15Rik|A930019C19Rik|AW489456|KRP|MLCK108|MLCK210|Mlck|nmMlck|smMLCK	myosin, light polypeptide kinase	protein-coding
mm_85374.1	chr9	103222996	103223120	-	1	NA	exon (NM_133977, exon 7 of 17)	exon (NM_133977, exon 7 of 17)	7228	NM_133977	22041	Mm.37214	NM_133977	ENSMUSG00000032554	Trf	AI266983|Cd176|HP|Tf|Tfn|hpx	transferrin	protein-coding
mm_51760.1	chr6	87839092	87839101	+	1	NA	promoter-TSS (NM_133934)	promoter-TSS (NM_133934)	-337	NM_133934	57905	Mm.241546	NM_133934	ENSMUSG00000030056	Isy1	5830446M03Rik|AI181014|AU020769	ISY1 splicing factor homolog	protein-coding
mm_157428.1	chrX	38564992	38565024	-	1	NA	exon (NM_028288, exon 3 of 23)	exon (NM_028288, exon 3 of 23)	11188	NM_028288	72584	Mm.327675	NM_028288	ENSMUSG00000031095	Cul4b	2700050M05Rik|AA409770|CUL-4B|mKIAA0695	cullin 4B	protein-coding
mm_170248.1	chr1	79381159	79381176	+	1	NA	Intergenic	L1Md_T|LINE|L1	58923	NM_009129	20254	Mm.5038	NM_009129	ENSMUSG00000050711	Scg2	Chgc|SgII	secretogranin II	protein-coding
mm_118742.1	chr14	22318672	22318682	+	1	NA	intron (NM_028275, intron 2 of 6)	B3|SINE|B2	224121	NR_046307	74896	Mm.444661	NR_046307		4930405A10Rik	4930456G20Rik	RIKEN cDNA 4930405A10 gene	ncRNA
mm_14323.1	chr2	129365964	129365996	+	1	NA	exon (NM_008361, exon 6 of 7)	exon (NM_008361, exon 6 of 7)	-3922	NR_015474	329514	Mm.207315	NM_177848	ENSMUSG00000074805	Il1bos	9430083I22|Gm14047|OTTMUSG00000015529	interleukin 1 beta, opposite strand	ncRNA
mm_69590.1	chr7	135705765	135705779	-	1	NA	exon (NM_001081117, exon 7 of 14)	exon (NM_001081117, exon 7 of 14)	10607	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_96254.1	chr11	62602868	62602886	+	1	NA	promoter-TSS (NR_028526)	promoter-TSS (NR_028526)	0	NR_030738	69221	Mm.270874	NR_030738	ENSMUSG00000086841	2410006H16Rik	-	RIKEN cDNA 2410006H16 gene	ncRNA
mm_60956.1	chr7	47053973	47053984	+	1	NA	3' UTR (NM_026436, exon 3 of 3)	3' UTR (NM_026436, exon 3 of 3)	3338	NM_026436	67893	Mm.27338	NM_026436	ENSMUSG00000010307	Tmem86a	1810054O13Rik|AI414959|AW742698	transmembrane protein 86A	protein-coding
mm_56569.1	chr6	102564380	102564427	-	1	NA	Intergenic	CpG	-99736	NM_008779	18488	Mm.435479	NM_008779	ENSMUSG00000030075	Cntn3	Pang	contactin 3	protein-coding
mm_102691.1	chr11	65728021	65728024	-	1	NA	intron (NM_001316369, intron 2 of 9)	intron (NM_001316369, intron 2 of 9)	6810	NR_030417	791070		NR_030417	ENSMUSG00000076460	Mir744	Mirn744|mir-744|mmu-mir-744	microRNA 744	ncRNA
mm_91694.1	chr10	43997428	43997442	-	1	NA	exon (NM_172393, exon 2 of 20)	exon (NM_172393, exon 2 of 20)	7411	NM_172393	11630	Mm.292082	NM_172393	ENSMUSG00000019866	Aim1	AI462491|AI463325	absent in melanoma 1	protein-coding
mm_48105.1	chr5	137071233	137071249	-	1	NA	exon (NM_008871, exon 2 of 9)	exon (NM_008871, exon 2 of 9)	1031	NM_008871	18787	Mm.250422	NM_008871	ENSMUSG00000037411	Serpine1	PAI-1|PAI1|Planh1	serine (or cysteine) peptidase inhibitor, clade E, member 1	protein-coding
mm_70420.1	chr8	11463970	11463982	+	1	NA	intron (NM_011227, intron 1 of 1)	MLT1B|LTR|ERVL-MaLR	-13953	NR_126558	102132	Mm.37632	NR_126558	ENSMUSG00000096957	E230013L22Rik	AI645545	RIKEN cDNA E230013L22 gene	ncRNA
mm_112935.1	chr13	20985136	20985146	+	1	NA	intron (NM_012054, intron 13 of 20)	intron (NM_012054, intron 13 of 20)	88158	NM_146535	258528	Mm.377554	NM_146535	ENSMUSG00000042869	Olfr1370	MOR256-14	olfactory receptor 1370	protein-coding
mm_166081.1	chr4	137681725	137681735	+	1	NA	exon (NM_001081155, exon 1 of 25)	exon (NM_001081155, exon 1 of 25)	103	NM_001256218	110351	Mm.180763	NM_029563	ENSMUSG00000041351	Rap1gap	1300019I11Rik|2310004O14Rik|AI427470|ARPP-90|Gap|Rap1GAP1|Rap1ga1	Rap1 GTPase-activating protein	protein-coding
mm_52463.1	chr6	113697317	113697343	+	1	NA	5' UTR (NM_001347356, exon 1 of 8)	5' UTR (NM_001347356, exon 1 of 8)	280	NM_001033463	381801	Mm.333322	NM_001033463	ENSMUSG00000056952	Tatdn2	AI646012|mKIAA0218	TatD DNase domain containing 2	protein-coding
mm_142696.1	chr17	47834484	47834513	-	1	NA	5' UTR (NM_001109973, exon 1 of 5)	5' UTR (NM_001109973, exon 1 of 5)	193	NM_001109973	17240	Mm.329100	NM_010783	ENSMUSG00000032717	Mdfi	I-mf|I-mfa	MyoD family inhibitor	protein-coding
mm_62192.1	chr7	97637689	97637691	+	1	NA	intron (NM_001081267, intron 3 of 15)	intron (NM_001081267, intron 3 of 15)	7422	NR_126461	75448	Mm.439818	NR_126461	ENSMUSG00000086433	Rsf1os1	1700006D18Rik	remodeling and spacing factor 1, opposite strand 1	ncRNA
mm_31320.1	chr4	46166054	46166064	+	1	NA	intron (NM_001033201, intron 16 of 22)	intron (NM_001033201, intron 16 of 22)	27548	NM_001033201	433702	Mm.389536	NM_001033201	ENSMUSG00000028330	Ncbp1	AU014645|AW538051|CBP80	nuclear cap binding protein subunit 1	protein-coding
mm_120094.1	chr14	57999306	57999338	+	1	NA	promoter-TSS (NM_028643)	promoter-TSS (NM_028643)	-60	NM_028643	68514	Mm.26834	NM_028643	ENSMUSG00000021973	Micu2	1110008L20Rik|4833427E09Rik|AU041871|Efha1|Smhs2	mitochondrial calcium uptake 2	protein-coding
mm_120129.1	chr14	60197256	60197268	+	1	NA	Intergenic	Intergenic	31653	NR_030458	751526		NR_030458	ENSMUSG00000076270	Mir719	Mirn719|mmu-mir-719	microRNA 719	ncRNA
mm_136867.1	chr17	12909964	12910012	+	1	NA	promoter-TSS (NM_001034866)	promoter-TSS (NM_001034866)	12	NM_001034866	240023	Mm.242315	NM_001034866	ENSMUSG00000073460	Pnldc1	Gm313	poly(A)-specific ribonuclease (PARN)-like domain containing 1	protein-coding
mm_139655.1	chr17	57402563	57402618	+	1	NA	exon (NM_010130, exon 4 of 22)	exon (NM_010130, exon 4 of 22)	43904	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_38329.1	chr4	137388372	137388430	-	1	NA	Intergenic	CpG	21390	NM_001126318	242711	Mm.475541	NM_001126318	ENSMUSG00000078520	Cela3a	Gm13011|OTTMUSG00000009877	chymotrypsin-like elastase family, member 3A	protein-coding
mm_157181.1	chrX	9662951	9662970	-	1	NA	promoter-TSS (NM_025975)	promoter-TSS (NM_025975)	23	NM_025975	67117	Mm.29150	NM_025975	ENSMUSG00000031176	Dynlt3	2310075M16Rik|AU042796|Tcte1l	dynein light chain Tctex-type 3	protein-coding
mm_153436.1	chr19	40959751	40959762	-	1	NA	exon (NM_008528, exon 6 of 17)	exon (NM_008528, exon 6 of 17)	34779	NM_008528	17060	Mm.9749	NM_008528	ENSMUSG00000061132	Blnk	BASH|Bca|Ly-57|Ly57|Lyw-57|SLP-65	B cell linker	protein-coding
mm_126901.1	chr15	89548475	89548498	+	1	NA	exon (NM_021423, exon 21 of 22)	exon (NM_021423, exon 21 of 22)	-19840	NM_013455	11434	Mm.57	NM_013455	ENSMUSG00000022622	Acr	-	acrosin prepropeptide	protein-coding
mm_149561.1	chr19	12794962	12795000	+	1	NA	intron (NR_024093, intron 1 of 12)	CpG	1142	NR_024093	664779	Mm.290924	NM_001039718	ENSMUSG00000024695	Gm44505	Zfp91-Cntf|Zfp91Cntf	predicted readthrough transcript (NMD candidate), 44505	ncRNA
mm_5400.1	chr1	33720080	33720097	-	1	NA	promoter-TSS (NM_001159729)	promoter-TSS (NM_001159729)	192	NM_008999	19335	Mm.86744	NM_008999	ENSMUSG00000004768	Rab23	AW545388|opb|opb2	RAB23, member RAS oncogene family	protein-coding
mm_135249.1	chr16	37539753	37539780	-	1	NA	promoter-TSS (NM_001042499)	promoter-TSS (NM_001042499)	3	NM_028812	74197	Mm.287795	NM_028812	ENSMUSG00000022828	Gtf2e1	2610024P03Rik|56kDa|AI303800|FE|TFIIE-A	general transcription factor II E, polypeptide 1 (alpha subunit)	protein-coding
mm_55884.1	chr6	83527453	83527500	-	1	NA	5' UTR (NM_009610, exon 2 of 9)	5' UTR (NM_009610, exon 2 of 9)	8775	NM_009610	11468	Mm.292865	NM_009610	ENSMUSG00000059430	Actg2	ACTA3|Act-4|Act4|SMGA	actin, gamma 2, smooth muscle, enteric	protein-coding
mm_39098.1	chr4	154919074	154919088	-	1	NA	Intergenic	Intergenic	8996	NM_178931	230979	Mm.215147	NM_178931	ENSMUSG00000042333	Tnfrsf14	Atar|HveA|Hvem|Tnfrs14	tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)	protein-coding
mm_79077.1	chr9	46242188	46242196	+	1	NA	intron (NM_007468, intron 2 of 2)	intron (NM_007468, intron 2 of 2)	1348	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_92343.1	chr10	75837314	75837332	-	1	NA	Intergenic	CpG	-2442	NM_010361	14872	Mm.24118	NM_010361	ENSMUSG00000033318	Gstt2	AI266894|Yrs|mGSTT2	glutathione S-transferase, theta 2	protein-coding
mm_60809.1	chr7	45641740	45641787	+	1	NA	intron (NM_172418, intron 2 of 9)	intron (NM_172418, intron 2 of 9)	1786	NM_172418	74490	Mm.107442	NM_172418	ENSMUSG00000042918	Mamstr	2810022D01Rik|5430432N15Rik|AW743872|Mastr	MEF2 activating motif and SAP domain containing transcriptional regulator	protein-coding
mm_2189.1	chr1	89070407	89070421	+	1	NA	promoter-TSS (NM_133816)	promoter-TSS (NM_133816)	-48	NM_133816	98402	Mm.170983	NM_133816	ENSMUSG00000036206	Sh3bp4	AI594717|AW227605|BOG25	SH3-domain binding protein 4	protein-coding
mm_109242.1	chr12	109452764	109452770	+	1	NA	promoter-TSS (NM_010052)	promoter-TSS (NM_010052)	-56	NR_033813	13386	Mm.157069	NM_010052	ENSMUSG00000040856	Dlk1	AW742678|DLK-1|DlkI|FA1|Ly107|Peg9|SCP1|ZOG|pG2|pref-1	delta-like 1 homolog (Drosophila)	protein-coding
mm_40275.1	chr5	41342097	41342098	+	1	NA	Intergenic	Intergenic	365594	NM_001310592	100972	Mm.41555	NM_027295	ENSMUSG00000029128	Rab28	2700023P08Rik|AW496496	RAB28, member RAS oncogene family	protein-coding
mm_50258.1	chr6	43067288	43067314	+	1	NA	Intergenic	Intergenic	-48443	NM_146655	258649	Mm.271494	NM_146655	ENSMUSG00000094669	Olfr441	MOR261-3	olfactory receptor 441	protein-coding
mm_133920.1	chr16	97715183	97715186	+	1	NA	Intergenic	Intergenic	48571	NM_023663	72388	Mm.35290	NM_023663	ENSMUSG00000005251	Ripk4	2310069J12Rik|AI552420|ANKK2|Ankrd3|DIk|PKK|RIP4	receptor-interacting serine-threonine kinase 4	protein-coding
mm_12274.1	chr2	68999875	68999886	+	1	NA	intron (NM_172856, intron 3 of 9)	intron (NM_172856, intron 3 of 9)	-135920	NM_181547	329416	Mm.90047	NM_181547	ENSMUSG00000034738	Nostrin	Daip2|mDaIP2	nitric oxide synthase trafficker	protein-coding
mm_33004.1	chr4	120588729	120588739	+	1	NA	promoter-TSS (NM_001101603)	promoter-TSS (NM_001101603)	-11	NM_001101603	667063	Mm.90231	NM_001101603	ENSMUSG00000091297	Gm8439	EG667063|Gm1664	predicted gene 8439	protein-coding
mm_83958.1	chr9	57071851	57071862	-	1	NA	promoter-TSS (NM_001110351)	promoter-TSS (NM_001110351)	110	NR_045886	100038566	Mm.361900	NR_045886		Gm10658	ENSMUSG00000074284	predicted gene 10658	ncRNA
mm_2785.1	chr1	130846370	130846401	+	1	NA	exon (NM_011082, exon 5 of 11)	exon (NM_011082, exon 5 of 11)	-19392	NM_026976	69169	Mm.46042	NM_026976	ENSMUSG00000042474	Fcmr	1810037B05Rik|Faim3|FcmuR|Toso	Fc fragment of IgM receptor	protein-coding
mm_104313.1	chr11	93885661	93885719	-	1	NA	promoter-TSS (NM_134012)	promoter-TSS (NM_134012)	76	NM_001013375	217109	Mm.379350	NM_001013375	ENSMUSG00000054079	Utp18	6230425C22Rik|6430513M13|Wdr50	UTP18 small subunit processome component	protein-coding
mm_1112.1	chr1	59867346	59867391	+	1	NA	exon (NM_007561, exon 12 of 13)	exon (NM_007561, exon 12 of 13)	-45638	NM_001037725	72750	Mm.258250	NM_001037725	ENSMUSG00000041040	Fam117b	2810425F24Rik|6330416D14Rik|Als2cr13	family with sequence similarity 117, member B	protein-coding
mm_52775.1	chr6	121210792	121210813	+	1	NA	promoter-TSS (NM_017379)	promoter-TSS (NM_017379)	68	NM_017379	53857	Mm.32884	NM_017379	ENSMUSG00000030137	Tuba8	-	tubulin, alpha 8	protein-coding
mm_130621.1	chr15	100403335	100403344	-	1	NA	exon (NM_001146161, exon 10 of 16)	exon (NM_001146161, exon 10 of 16)	19716	NM_001146161	18174	Mm.234608	NM_008732	ENSMUSG00000023030	Slc11a2	DCT1|DMT1|Nramp2|mk|van	solute carrier family 11 (proton-coupled divalent metal ion transporters), member 2	protein-coding
mm_53067.1	chr6	124914396	124914434	+	1	NA	exon (NM_026988, exon 4 of 5)	exon (NM_026988, exon 4 of 5)	-2710	NM_008479	16768	Mm.4528	NM_008479	ENSMUSG00000030124	Lag3	CD223|LAG-3|Ly66	lymphocyte-activation gene 3	protein-coding
mm_23288.1	chr3	52047357	52047378	+	1	NA	intron (NM_001004176, intron 1 of 4)	intron (NM_001004176, intron 1 of 4)	57639	NM_001004176	433586	Mm.234972	NM_001004176	ENSMUSG00000061143	Maml3	AV234550|BC049812|Mam-2|mKIAA1816	mastermind like 3 (Drosophila)	protein-coding
mm_101514.1	chr11	32349403	32349419	-	1	NA	intron (NM_177364, intron 1 of 12)	intron (NM_177364, intron 1 of 12)	1600	NM_177364	268396	Mm.227616	NM_177364	ENSMUSG00000040711	Sh3pxd2b	G431001E03Rik|TSK4|fad49	SH3 and PX domains 2B	protein-coding
mm_110305.1	chr12	32953773	32953846	-	1	NA	promoter-TSS (NM_198710)	promoter-TSS (NM_198710)	-20	NR_044986	74076	Mm.50114	NR_044986	ENSMUSG00000097494	4933406C10Rik	-	RIKEN cDNA 4933406C10 gene	ncRNA
mm_126137.1	chr15	78345477	78345495	+	1	NA	exon (NM_007780, exon 10 of 14)	exon (NM_007780, exon 10 of 14)	-3113	NR_106137	102465776		NR_106137	ENSMUSG00000098996	Mir7676-1	Gm27600|mmu-mir-7676-1	microRNA 7676-1	ncRNA
mm_17666.1	chr2	32084651	32084731	-	1	NA	promoter-TSS (NM_175511)	promoter-TSS (NM_175511)	-986	NM_175511	241303	Mm.250441	NM_175511	ENSMUSG00000050592	Fam78a	A130092J06Rik	family with sequence similarity 78, member A	protein-coding
mm_79736.1	chr9	62344874	62344910	+	1	NA	intron (NM_009672, intron 1 of 6)	intron (NM_009672, intron 1 of 6)	3549	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	protein-coding
mm_33410.1	chr4	129849167	129849187	+	1	NA	3' UTR (NM_001164745, exon 6 of 6)	3' UTR (NM_001164745, exon 6 of 6)	28469	NM_001164745	19244	Mm.193688	NM_008974	ENSMUSG00000028788	Ptp4a2	Prl-2	protein tyrosine phosphatase 4a2	protein-coding
mm_120609.1	chr14	70203395	70203407	+	1	NA	exon (NM_011366, exon 2 of 21)	exon (NM_011366, exon 2 of 21)	1222	NM_001271408	20410	Mm.5068	NM_011366	ENSMUSG00000022091	Sorbs3	SCAM-1|SH3P3|Sh3d4|vinexin-g	sorbin and SH3 domain containing 3	protein-coding
mm_155166.1	chrX	53016359	53016404	+	1	NA	exon (NM_013556, exon 6 of 9)	exon (NM_013556, exon 6 of 9)	28303	NM_013556	15452	Mm.299381	NM_013556	ENSMUSG00000025630	Hprt	C81579|HPGRT|Hprt1	hypoxanthine guanine phosphoribosyl transferase	protein-coding
mm_108334.1	chr12	80115132	80115178	+	1	NA	Intergenic	Intergenic	-2142	NM_007564	12192	Mm.235132	NM_007564	ENSMUSG00000021127	Zfp36l1	AW742437|AW743212|Berg36|Brf1|D530020L18Rik|ERF1|TIS11b|cMG1	zinc finger protein 36, C3H type-like 1	protein-coding
mm_108447.1	chr12	82451191	82451202	+	1	NA	3' UTR (NM_001167983, exon 24 of 24)	3' UTR (NM_001167983, exon 24 of 24)	139847	NM_172579	217692	Mm.261333	NM_172579	ENSMUSG00000042700	Sipa1l1	4931426N11Rik|AW213287|Spar|mKIAA0440	signal-induced proliferation-associated 1 like 1	protein-coding
mm_25106.1	chr3	101310452	101310466	+	1	NA	Intergenic	Intergenic	-22520	NM_013486	12481	Mm.22842	NM_013486	ENSMUSG00000027863	Cd2	LFA-2|Ly-37|Ly37	CD2 antigen	protein-coding
mm_6452.1	chr1	74016570	74016576	-	1	NA	intron (NM_027884, intron 3 of 34)	intron (NM_027884, intron 3 of 34)	107874	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_159115.1	chr2	58566809	58566809	-	1	NA	promoter-TSS (NM_001289660)	promoter-TSS (NM_001289660)	19	NM_001110205	11477	Mm.689	NM_007394	ENSMUSG00000026836	Acvr1	ALK2|ActR-I|ActRIA|Acvr|Acvrlk2|Alk-2|Alk8|D330013D15Rik|SKR1|Tsk7L	activin A receptor, type 1	protein-coding
mm_132495.1	chr16	36941405	36941445	+	1	NA	intron (NM_008225, intron 3 of 13)	intron (NM_008225, intron 3 of 13)	6442	NM_008225	15163	Mm.4091	NM_008225	ENSMUSG00000022831	Hcls1	AW213261|HS1	hematopoietic cell specific Lyn substrate 1	protein-coding
mm_33620.1	chr4	132690657	132690664	+	1	NA	intron (NM_211357, intron 5 of 14)	B1_Mur2|SINE|Alu	41886	NM_201368	381560	Mm.44558	NM_201368	ENSMUSG00000037752	Xkr8	4931440N07Rik|AI597014|Gm1031|XRG8|mXkr8	X-linked Kx blood group related 8	protein-coding
mm_158966.1	chr1	93082394	93082394	-	1	NA	promoter-TSS (NM_001294150)	promoter-TSS (NM_001294150)	86	NM_001294150	16560	Mm.276408	NM_008440	ENSMUSG00000014602	Kif1a	ATSV|C630002N23Rik|Gm1626|Kns1	kinesin family member 1A	protein-coding
mm_41144.1	chr5	87925595	87925621	+	1	NA	promoter-TSS (NM_007786)	promoter-TSS (NM_007786)	-25	NM_007786	12994	Mm.296303	NM_007786	ENSMUSG00000001622	Csn3	AW208918|CSN10|Csnk	casein kappa	protein-coding
mm_172603.1	chr8	15519967	15519967	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	462314	NM_008664	17930	Mm.272115	NM_008664	ENSMUSG00000031461	Myom2	AW146149	myomesin 2	protein-coding
mm_51059.1	chr6	65671757	65671770	+	1	NA	5' UTR (NM_172399, exon 1 of 4)	5' UTR (NM_172399, exon 1 of 4)	152	NM_172399	68169	Mm.52392	NM_172399	ENSMUSG00000049001	Ndnf	A930038C07Rik|epidermacan	neuron-derived neurotrophic factor	protein-coding
mm_153671.1	chr19	44396120	44396131	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	11584	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_34072.1	chr4	138457369	138457380	+	1	NA	3' UTR (NM_025451, exon 2 of 2)	3' UTR (NM_025451, exon 2 of 2)	2226	NM_025451	66259	Mm.41603	NM_025451	ENSMUSG00000046447	Camk2n1	1810006K23Rik|AI848599|AI891706	calcium/calmodulin-dependent protein kinase II inhibitor 1	protein-coding
mm_135797.1	chr16	57199088	57199097	-	1	NA	intron (NM_026254, intron 5 of 17)	intron (NM_026254, intron 5 of 17)	-31760	NM_023175	52633	Mm.383203	NM_023175	ENSMUSG00000022751	Nit2	1190017B19Rik|D16Ertd502e	nitrilase family, member 2	protein-coding
mm_68982.1	chr7	126589409	126589415	-	1	NA	TTS (NM_138310)	TTS (NM_138310)	-3595	NM_001146311	12752	Mm.268930	NM_009907	ENSMUSG00000030720	Cln3	AI323623	ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease)	protein-coding
mm_24421.1	chr3	90527143	90527176	+	1	NA	5' UTR (NM_001163525, exon 2 of 4)	5' UTR (NM_001163525, exon 2 of 4)	310	NM_001163526	66166	Mm.24006	NM_025393	ENSMUSG00000042306	S100a14	1110013O05Rik|S100a15|S114	S100 calcium binding protein A14	protein-coding
mm_5670.1	chr1	42711340	42711342	-	1	NA	intron (NR_110495, intron 2 of 3)	intron (NR_110495, intron 2 of 3)	2113	NR_110495	66620	Mm.383631	NR_110495	ENSMUSG00000097063	Pantr2	2610207O16Rik|Pou3f3os2|linc-Brn1b	POU domain, class 3, transcription factor 3 adjacent noncoding transcript 2	ncRNA
mm_76285.1	chr8	84198352	84198364	-	1	NA	Intergenic	Intergenic	-10160	NR_029740	387216		NR_029740	ENSMUSG00000065611	Mir23a	Mirn23a|mir-23a|mmu-mir-23a	microRNA 23a	ncRNA
mm_148040.1	chr18	70244686	70244696	-	1	NA	promoter-TSS (NM_029346)	promoter-TSS (NM_029346)	-107	NM_029346	75577	Mm.58214	NM_029346	ENSMUSG00000024512	Dynap	2310002L13Rik	dynactin associated protein	protein-coding
mm_96052.1	chr11	59565976	59565986	+	1	NA	exon (NM_145827, exon 9 of 10)	exon (NM_145827, exon 9 of 10)	5757	NM_001011789	257962	Mm.377316	NM_001011789	ENSMUSG00000059610	Olfr222	MOR256-45P	olfactory receptor 222	protein-coding
mm_170097.1	chr17	39843133	39843135	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	137	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_66145.1	chr7	31126994	31127042	-	1	NA	promoter-TSS (NM_011322)	promoter-TSS (NM_011322)	5	NM_011322	20266	Mm.1418	NM_011322	ENSMUSG00000019194	Scn1b	-	sodium channel, voltage-gated, type I, beta	protein-coding
mm_38560.1	chr4	141652456	141652479	-	1	NA	intron (NM_001347237, intron 1 of 18)	intron (NM_001347237, intron 1 of 18)	11648	NM_001347237	69582	Mm.33220	NM_001033150	ENSMUSG00000028917	Plekhm2	2310034J19Rik|AI854247|mKIAA0842	pleckstrin homology domain containing, family M (with RUN domain) member 2	protein-coding
mm_74130.1	chr8	123194001	123194012	+	1	NA	intron (NM_007876, intron 1 of 10)	intron (NM_007876, intron 1 of 10)	7771	NM_007876	13479	Mm.20388	NM_007876	ENSMUSG00000019278	Dpep1	AI327012|MBD	dipeptidase 1 (renal)	protein-coding
mm_154986.1	chrX	38189781	38189826	+	1	NA	promoter-TSS (NM_020256)	promoter-TSS (NM_020256)	10	NM_001079513	56805	Mm.391248	NM_020256	ENSMUSG00000048047	Zbtb33	AW260253|E130014G12Rik|Kaiso|Znf-kaiso	zinc finger and BTB domain containing 33	protein-coding
mm_103117.1	chr11	70015347	70015435	-	1	NA	promoter-TSS (NM_017366)	promoter-TSS (NM_017366)	37	NM_017366	11370	Mm.18630	NM_017366	ENSMUSG00000018574	Acadvl	vlcad	acyl-Coenzyme A dehydrogenase, very long chain	protein-coding
mm_65375.1	chr7	25076862	25076932	-	1	NA	promoter-TSS (NM_001168506)	promoter-TSS (NM_001168506)	-308	NM_001168506	232976	Mm.41568	NM_175477	ENSMUSG00000045252	Zfp574	A630056B21Rik|Znf574	zinc finger protein 574	protein-coding
mm_32517.1	chr4	108633121	108633131	+	1	NA	intron (NM_177045, intron 23 of 24)	intron (NM_177045, intron 23 of 24)	13170	NM_177045	319965	Mm.151129	NM_177045	ENSMUSG00000028582	Cc2d1b	A830039B04Rik|Freud2	coiled-coil and C2 domain containing 1B	protein-coding
mm_166554.1	chr6	41547521	41547521	+	1	NA	Intergenic	Intergenic	25745	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_15185.1	chr2	154200324	154200334	+	1	NA	promoter-TSS (NM_153418)	promoter-TSS (NM_153418)	-51	NM_153418	228801	Mm.3783	NM_153418	ENSMUSG00000027485	Bpifb1	Lplunc1	BPI fold containing family B, member 1	protein-coding
mm_7043.1	chr1	87102237	87102252	-	1	NA	promoter-TSS (NM_001081082)	promoter-TSS (NM_001081082)	-638	NM_001081082	76768	Mm.58068	NM_001081082	ENSMUSG00000079440	Alpi	2010001C14Rik|Akp6|gIAP	alkaline phosphatase, intestinal	protein-coding
mm_94906.1	chr11	29373619	29373723	+	1	NA	promoter-TSS (NM_176841)	promoter-TSS (NM_176841)	-501	NM_176841	108686	Mm.338284	NM_176841	ENSMUSG00000032740	Ccdc88a	A430106J12Rik|AI848406|Ape|C130096N06Rik|C330012F17Rik|D130005J21Rik|Girdin|Giv|Grdn|Hkrp1	coiled coil domain containing 88A	protein-coding
mm_12678.1	chr2	75832238	75832284	+	1	NA	promoter-TSS (NM_172666)	promoter-TSS (NM_172666)	84	NM_172666	228061	Mm.31227	NM_172666	ENSMUSG00000042410	Agps	5832437L22|9930035G10Rik|AW123847|Adaps|Adas|Adhaps|Adps|Aldhpsy|bs2	alkylglycerone phosphate synthase	protein-coding
mm_170350.1	chr1	85109464	85109464	-	1	NA	5' UTR (NM_213615, exon 1 of 7)	5' UTR (NM_213615, exon 1 of 7)	389	NM_213615	381287	Mm.487565	NM_213615	ENSMUSG00000089844	A530032D15Rik	Gm1888	RIKEN cDNA A530032D15Rik gene	protein-coding
mm_172284.1	chr6	93376144	93376144	+	1	NA	Intergenic	Intergenic	435562	NR_015530	330385	Mm.483472	NR_015530	ENSMUSG00000097462	9530026P05Rik	B430306B02	RIKEN cDNA 9530026P05 gene	ncRNA
mm_23058.1	chr3	35783023	35783060	+	1	NA	intron (NM_029570, intron 3 of 29)	PB1D11|SINE|Alu	28903	NM_029570	76295	Mm.239416	NM_029570	ENSMUSG00000037400	Atp11b	1110019I14Rik|ATPIF|ATPIR|mKIAA0956	ATPase, class VI, type 11B	protein-coding
mm_166708.1	chr6	116459405	116459411	+	1	NA	intron (NM_009662, intron 1 of 13)	intron (NM_009662, intron 1 of 13)	1770	NM_009662	11689	Mm.41072	NM_009662	ENSMUSG00000025701	Alox5	5-LO|5-LOX|5LO|5LX|AI850497|F730011J02	arachidonate 5-lipoxygenase	protein-coding
mm_157369.1	chrX	37218270	37218281	-	1	NA	intron (NM_001025084, intron 1 of 4)	intron (NM_001025084, intron 1 of 4)	3983	NM_001025084	385343	Mm.379566	NM_001025084	ENSMUSG00000071773	Rhox1	-	reproductive homeobox 1	protein-coding
mm_101364.1	chr11	23745582	23745590	-	1	NA	exon (NM_009044, exon 7 of 10)	exon (NM_009044, exon 7 of 10)	25384	NM_009044	19696	Mm.4869	NM_009044	ENSMUSG00000020275	Rel	c-Rel	reticuloendotheliosis oncogene	protein-coding
mm_154160.1	chr19	58455904	58455914	-	1	NA	promoter-TSS (NM_010279)	promoter-TSS (NM_010279)	-511	NM_010279	14585	Mm.88367	NM_010279	ENSMUSG00000025089	Gfra1	AU042498	glial cell line derived neurotrophic factor family receptor alpha 1	protein-coding
mm_53991.1	chr6	6877953	6877955	-	1	NA	3' UTR (NM_010056, exon 3 of 3)	3' UTR (NM_010056, exon 3 of 3)	4114	NM_198854	13395	Mm.4873	NM_010056	ENSMUSG00000029755	Dlx5	AI385752	distal-less homeobox 5	protein-coding
mm_12738.1	chr2	78918408	78918410	+	1	NA	intron (NM_009454, intron 4 of 5)	intron (NM_009454, intron 4 of 5)	49362	NM_009454	22193	Mm.1485	NM_009454	ENSMUSG00000027011	Ube2e3	Ubce4|ubcM2	ubiquitin-conjugating enzyme E2E 3	protein-coding
mm_113173.1	chr13	24813668	24813713	+	1	NA	TTS (NM_024473)	TTS (NM_024473)	12033	NM_024473	79555	Mm.266668	NM_024473	ENSMUSG00000019132	BC005537	8030460C05Rik|C78201	cDNA sequence BC005537	protein-coding
mm_168098.1	chr10	128909938	128909938	+	1	NA	promoter-TSS (NM_007653)	promoter-TSS (NM_007653)	72	NM_007653	12512	Mm.371552	NM_007653	ENSMUSG00000025351	Cd63	C75951|ME491|Tspan30	CD63 antigen	protein-coding
mm_38772.1	chr4	147936714	147936733	-	1	NA	promoter-TSS (NM_011122)	promoter-TSS (NM_011122)	53	NM_011122	18822	Mm.23951	NM_011122	ENSMUSG00000019055	Plod1	2410042F05Rik|AI854890|AV007929|Lh1|Plod	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1	protein-coding
mm_46154.1	chr5	96093090	96093093	-	1	NA	intron (NM_144910, intron 7 of 11)	B1F1|SINE|Alu	68456	NM_001285511	231464	Mm.28374	NM_144910	ENSMUSG00000034724	Cnot6l	4932442K20Rik	CCR4-NOT transcription complex, subunit 6-like	protein-coding
mm_67015.1	chr7	65527735	65527838	-	1	NA	Intergenic	(CCGCG)n|Simple_repeat|Simple_repeat	-54245	NR_131060	407810	Mm.249337	NR_131060	ENSMUSG00000086662	BC046251	-	cDNA sequence BC046251	ncRNA
mm_149356.1	chr19	10945263	10945268	+	1	NA	intron (NM_023731, intron 2 of 3)	intron (NM_023731, intron 2 of 3)	4001	NM_023731	108673	Mm.294908	NM_023731	ENSMUSG00000024732	Ccdc86	4933411H20Rik|6720480F16Rik|D19Ertd678e	coiled-coil domain containing 86	protein-coding
mm_167080.1	chr7	101012129	101012168	+	1	NA	promoter-TSS (NM_001302347)	promoter-TSS (NM_001302347)	-95	NM_001302346	18442	Mm.3000	NM_008773	ENSMUSG00000032860	P2ry2	P2U1|P2Y2	purinergic receptor P2Y, G-protein coupled 2	protein-coding
mm_85166.1	chr9	96394943	96394951	-	1	NA	Intergenic	Intergenic	-30648	NM_007502	11933	Mm.424	NM_007502	ENSMUSG00000032412	Atp1b3	AA409958|AI664000|AW212096	ATPase, Na+/K+ transporting, beta 3 polypeptide	protein-coding
mm_104271.1	chr11	89077696	89077702	-	1	NA	intron (NM_001033266, intron 2 of 3)	intron (NM_001033266, intron 2 of 3)	3858	NM_001033266	217071	Mm.342127	NM_001033266	ENSMUSG00000072553	Gm525	-	predicted gene 525	protein-coding
mm_84137.1	chr9	59284153	59284163	-	1	NA	Intergenic	Intergenic	-7414	NM_028121	72141	Mm.22456	NM_028121	ENSMUSG00000025236	Adpgk	2610017G09Rik|Adp-gk|C77577	ADP-dependent glucokinase	protein-coding
mm_69421.1	chr7	132748759	132748760	-	1	NA	intron (NM_001347630, intron 3 of 3)	intron (NM_001347630, intron 3 of 3)	28157	NM_001347630	77938	Mm.225649	NM_175268	ENSMUSG00000030956	Fam53b	A930008G19Rik|mKIAA0140	family with sequence similarity 53, member B	protein-coding
mm_933.1	chr1	55450300	55450389	+	1	NA	intron (NM_001114663, intron 1 of 5)	intron (NM_001114663, intron 1 of 5)	44398	NM_001114663	227120	Mm.194183	NM_001114663	ENSMUSG00000038349	Plcl1	C230017K02Rik|PLC-L|PLC-L1|PLCE|PLCL|PLDL1|PRIP|PRIP-1	phospholipase C-like 1	protein-coding
mm_148720.1	chr19	5845280	5845362	+	1	NA	non-coding (NR_003513, exon 1 of 1)	non-coding (NR_003513, exon 1 of 1)	157	NR_131212	66961	Mm.281895	NR_003513	ENSMUSG00000092274	Neat1	2310043N10Rik|VINC	nuclear paraspeckle assembly transcript 1 (non-protein coding)	ncRNA
mm_2402.1	chr1	93754934	93754946	+	1	NA	promoter-TSS (NM_025920)	promoter-TSS (NM_025920)	-93	NM_174874	66615	Mm.29087	NM_174874	ENSMUSG00000026280	Atg4b	2510009N07Rik|AW048066|Apg4b|Atg4bl|Autl1	autophagy related 4B, cysteine peptidase	protein-coding
mm_142436.1	chr17	45571038	45571064	-	1	NA	exon (NM_008302, exon 4 of 11)	exon (NM_008302, exon 4 of 11)	2210	NM_008302	15516	Mm.2180	NM_008302	ENSMUSG00000023944	Hsp90ab1	90kDa|AL022974|C81438|Hsp84|Hsp84-1|Hsp90|Hspcb	heat shock protein 90 alpha (cytosolic), class B member 1	protein-coding
mm_112820.1	chr13	20800039	20800064	+	1	NA	intron (NM_012054, intron 1 of 20)	intron (NM_012054, intron 1 of 20)	5938	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_113776.1	chr13	44961548	44961550	+	1	NA	intron (NM_025772, intron 6 of 9)	intron (NM_025772, intron 6 of 9)	40547	NM_025772	94245	Mm.352311	NM_025772	ENSMUSG00000057531	Dtnbp1	5430437B18Rik|AW048963|Bloc1s8|dysbindin|sdy	dystrobrevin binding protein 1	protein-coding
mm_38400.1	chr4	138938616	138938631	-	1	NA	Intergenic	Intergenic	-24676	NM_028453	73162	Mm.238081	NM_028453	ENSMUSG00000041161	Otud3	3110030K17Rik	OTU domain containing 3	protein-coding
mm_24802.1	chr3	95554473	95554482	+	1	NA	intron (NM_001267695, intron 7 of 7)	ID_B1|SINE|B4	-5200	NM_026489	67981	Mm.179050	NM_026489	ENSMUSG00000028109	Hormad1	4921522K05Rik|Nohma	HORMA domain containing 1	protein-coding
mm_33519.1	chr4	130929498	130929514	+	1	NA	exon (NM_010686, exon 5 of 8)	exon (NM_010686, exon 5 of 8)	-14879	NM_010769	17180	Mm.271796	NM_010769	ENSMUSG00000040533	Matn1	CMP|Crtm|Mat1|matrilin-1	matrilin 1, cartilage matrix protein	protein-coding
mm_135680.1	chr16	52420125	52420135	-	1	NA	intron (NM_009655, intron 1 of 15)	PB1D10|SINE|Alu	32951	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_161645.1	chr17	3178402	3178402	+	1	NA	intron (NM_134123, intron 12 of 19)	intron (NM_134123, intron 12 of 19)	63430	NM_134123	106583	Mm.124373	NM_134123	ENSMUSG00000046201	Scaf8	A630086M08Rik|A930036P18Rik|AA408306|AI447644|AI448652|AU015035|Rbm16|mKIAA1116	SR-related CTD-associated factor 8	protein-coding
mm_7332.1	chr1	105356481	105356516	-	1	NA	5' UTR (NM_001160368, exon 1 of 2)	5' UTR (NM_001160368, exon 1 of 2)	212	NM_178779	320311	Mm.389162	NM_178779	ENSMUSG00000047496	Rnf152	A930029B02Rik	ring finger protein 152	protein-coding
mm_99975.1	chr11	114091405	114091413	+	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-25458	NM_172800	237979	Mm.130504	NM_172800	ENSMUSG00000041592	Sdk2	4632412F08Rik|5330435L01Rik|Sdk-2|mKIAA1514	sidekick cell adhesion molecule 2	protein-coding
mm_63096.1	chr7	122377310	122377338	+	1	NA	intron (NM_001316672, intron 2 of 16)	intron (NM_001316672, intron 2 of 16)	88199	NM_008855	18751	Mm.207496	NM_008855	ENSMUSG00000052889	Prkcb	PKC-B|PKC-Beta|Pkcb|Prkcb1|Prkcb2	protein kinase C, beta	protein-coding
mm_33145.1	chr4	125146226	125146237	+	1	NA	Intergenic	Intergenic	-18350	NM_153159	230738	Mm.402	NM_153159	ENSMUSG00000042677	Zc3h12a	BC036563|MCPIP|MCPIP-1|Mcpip1|Reg1	zinc finger CCCH type containing 12A	protein-coding
mm_126543.1	chr15	82028055	82028075	+	1	NA	intron (NM_010247, intron 7 of 12)	intron (NM_010247, intron 7 of 12)	11696	NM_010247	14375	Mm.288809	NM_010247	ENSMUSG00000022471	Xrcc6	70kDa|G22p1|Ku70	X-ray repair complementing defective repair in Chinese hamster cells 6	protein-coding
mm_44075.1	chr5	148959792	148959810	+	1	NA	Intergenic	Intergenic	9551	NR_040686	71473	Mm.90306	NR_040686	ENSMUSG00000079069	8430423G03Rik	-	RIKEN cDNA 8430423G03 gene	ncRNA
mm_138132.1	chr17	34187790	34187828	+	1	NA	promoter-TSS (NM_013585)	promoter-TSS (NM_013585)	253	NM_013683	21354	Mm.482076	NM_013683	ENSMUSG00000037321	Tap1	ABC17|APT1|Abcb2|Ham-1|Ham1|MTP1|PSF1|RING4|TAP|Tap-1|Y3	transporter 1, ATP-binding cassette, sub-family B (MDR/TAP)	protein-coding
mm_170106.1	chr17	39844742	39844742	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	1745	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_125562.1	chr15	58899567	58899584	+	1	NA	exon (NM_175226, exon 2 of 2)	exon (NM_175226, exon 2 of 2)	10346	NM_175226	75841	Mm.4537	NM_175226	ENSMUSG00000037075	Rnf139	4930555P18Rik	ring finger protein 139	protein-coding
mm_26762.1	chr3	8667278	8667296	-	1	NA	promoter-TSS (NM_010423)	promoter-TSS (NM_010423)	-249	NM_010423	15213	Mm.29581	NM_010423	ENSMUSG00000040289	Hey1	AI316788|AI414254|CHF2|HRT1|Herp2|Hesr1|bHLHb31|hesr-1	hairy/enhancer-of-split related with YRPW motif 1	protein-coding
mm_120064.1	chr14	56908550	56908554	+	1	NA	intron (NM_029498, intron 2 of 23)	intron (NM_029498, intron 2 of 23)	20757	NM_029498	76007	Mm.31417	NM_029498	ENSMUSG00000021945	Zmym2	5830413P05Rik|FIM|MYM|RAMP|SCLL|Zfp198|Znf198	zinc finger, MYM-type 2	protein-coding
mm_5151.1	chr1	9942156	9942167	-	1	NA	TTS (NR_004410)	TTS (NR_004410)	382	NR_004410	266793		NR_004410	ENSMUSG00000093178	Snord87	MBII-276|Rnu87|U87	small nucleolar RNA, C/D box 87	snoRNA
mm_135978.1	chr16	75047829	75047834	-	1	NA	Intergenic	Lx2|LINE|L1	538230	NM_001252513	320355	Mm.99517	NM_177142	ENSMUSG00000032948	Lipi	D930038D03Rik|lpd1	lipase, member I	protein-coding
mm_148352.1	chr18	84682046	84682056	-	1	NA	promoter-TSS (NM_001289531)	promoter-TSS (NM_001289531)	8	NM_001289531	66054	Mm.29646	NM_023149	ENSMUSG00000024644	Cndp2	0610010E05Rik|C76600|Cn2|Dip-2|Pep-1|Pep1	CNDP dipeptidase 2 (metallopeptidase M20 family)	protein-coding
mm_70347.1	chr8	4678662	4678675	+	1	NA	Intergenic	Intergenic	65498	NM_145591	233987	Mm.102799	NM_145591	ENSMUSG00000058748	Zfp958	-	zinc finger protein 958	protein-coding
mm_91109.1	chr10	19185844	19185848	-	1	NA	intron (NR_038022, intron 1 of 1)	intron (NR_038022, intron 1 of 1)	18608	NR_038022	100504265	Mm.383417	NR_038021		Gm20139	-	predicted gene, 20139	ncRNA
mm_75171.1	chr8	36732137	36732147	-	1	NA	intron (NM_001194940, intron 5 of 17)	intron (NM_001194940, intron 5 of 17)	912	NM_001194941	50768	Mm.125155	NM_015802	ENSMUSG00000031523	Dlc1	A730069N07Rik|Arhgap7|HP|STARD12|dlc-1	deleted in liver cancer 1	protein-coding
mm_101749.1	chr11	43379452	43379467	-	1	NA	Intergenic	Intergenic	-4998	NR_029558	387164		NR_029558	ENSMUSG00000065601	Mir146	Mirn146|miR-146a|mmu-mir-146	microRNA 146	ncRNA
mm_154283.1	chr19	60860657	60860659	-	1	NA	intron (NM_053198, intron 1 of 13)	Charlie5|DNA|hAT-Charlie	772	NM_053198	94281	Mm.48179	NM_053198	ENSMUSG00000063698	Sfxn4	-	sideroflexin 4	protein-coding
mm_96682.1	chr11	69580283	69580303	+	1	NA	promoter-TSS (NM_144824)	promoter-TSS (NM_144824)	-66	NM_011640	22059	Mm.222	NM_011640	ENSMUSG00000059552	Trp53	Tp53|bbl|bfy|bhy|p44|p53	transformation related protein 53	protein-coding
mm_87986.1	chr10	64017769	64017772	+	1	NA	intron (NM_178678, intron 2 of 2)	Lx8|LINE|L1	72485	NM_178678	216028	Mm.431318	NM_178678	ENSMUSG00000042846	Lrrtm3	9630044H04Rik	leucine rich repeat transmembrane neuronal 3	protein-coding
mm_126873.1	chr15	89377719	89377726	+	1	NA	promoter-TSS (NM_138302)	promoter-TSS (NM_138302)	-685	NM_138302	72962	Mm.287977	NM_138302	ENSMUSG00000022615	Tymp	2900072D10Rik|Ecgf1|PD-ECGF|PDECGF|Pdgfec	thymidine phosphorylase	protein-coding
mm_22327.1	chr2	180642682	180642757	-	1	NA	promoter-TSS (NM_178254)	promoter-TSS (NM_178254)	-28	NM_178254	277353	Mm.473700	NM_178254	ENSMUSG00000038932	Tcfl5	AV260129|Figlb|Sosf1	transcription factor-like 5 (basic helix-loop-helix)	protein-coding
mm_108824.1	chr12	95709703	95709706	+	1	NA	intron (NM_201518, intron 1 of 1)	B1_Mus1|SINE|Alu	17478	NM_201518	399558	Mm.341948	NM_201518	ENSMUSG00000047414	Flrt2	-	fibronectin leucine rich transmembrane protein 2	protein-coding
mm_116282.1	chr13	34993197	34993219	-	1	NA	exon (NM_001110331, exon 2 of 10)	exon (NM_001110331, exon 2 of 10)	936	NM_011868	23986	Mm.491141	NM_011868	ENSMUSG00000021417	Eci2	Acbd2|Drs1|Hca88|Peci	enoyl-Coenzyme A delta isomerase 2	protein-coding
mm_7758.1	chr1	131136422	131136425	-	1	NA	intron (NM_145508, intron 1 of 2)	intron (NM_145508, intron 1 of 2)	1811	NM_145508	226419	Mm.39299	NM_145508	ENSMUSG00000016526	Dyrk3	BC006704	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 3	protein-coding
mm_122223.1	chr14	32464765	32464777	-	1	NA	promoter-TSS (NM_021712)	promoter-TSS (NM_021712)	79	NM_021712	20508	Mm.190503	NM_021712	ENSMUSG00000100241	Slc18a3	VAChT|VAT	solute carrier family 18 (vesicular monoamine), member 3	protein-coding
mm_51327.1	chr6	72355426	72355487	+	1	NA	promoter-TSS (NM_144916)	promoter-TSS (NM_144916)	-27	NM_144916	232086	Mm.491165	NM_144916	ENSMUSG00000055912	Tmem150a	BC014685|Tmem150	transmembrane protein 150A	protein-coding
mm_18795.1	chr2	73892158	73892167	-	1	NA	intron (NM_001284374, intron 1 of 11)	CpG	477	NM_001284371	11909	Mm.209903	NM_009715	ENSMUSG00000027104	Atf2	Atf-2|CRE-BP|Creb2|D130078H02Rik|D18875|Tg(Gzma-Klra1)7Wum|mXBP	activating transcription factor 2	protein-coding
mm_71577.1	chr8	54550424	54550439	+	1	NA	promoter-TSS (NM_029569)	promoter-TSS (NM_029569)	100	NM_029569	76294	Mm.33171	NM_029569	ENSMUSG00000031519	Asb5	1110018D09Rik	ankyrin repeat and SOCs box-containing 5	protein-coding
mm_99109.1	chr11	100133761	100133771	+	1	NA	exon (NM_008469, exon 4 of 8)	exon (NM_008469, exon 4 of 8)	2183	NM_008469	16665	Mm.440010	NM_008469	ENSMUSG00000054146	Krt15	AI528832|K15|Krt1-15	keratin 15	protein-coding
mm_61035.1	chr7	49608728	49608732	+	1	NA	3' UTR (NM_001111016, exon 39 of 39)	3' UTR (NM_001111016, exon 39 of 39)	28105	NM_001005232	13172	Mm.307176	NM_001005232	ENSMUSG00000030507	Dbx1	AI426026|Dbx	developing brain homeobox 1	protein-coding
mm_25892.1	chr3	131110406	131110412	+	1	NA	5' UTR (NM_001276402, exon 1 of 10)	5' UTR (NM_001276402, exon 1 of 10)	112	NM_001276402	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_107899.1	chr12	70825493	70825514	+	1	NA	promoter-TSS (NM_028127)	promoter-TSS (NM_028127)	-11	NM_028127	319710	Mm.2962	NM_028127	ENSMUSG00000048285	Frmd6	2610019M19Rik|4930488L10Rik|AW212977|Willin	FERM domain containing 6	protein-coding
mm_73952.1	chr8	120265800	120265830	+	1	NA	Intergenic	Intergenic	-37585	NR_110496	434353	Mm.411793	NR_110496	ENSMUSG00000097960	A330074K22Rik	-	RIKEN cDNA A330074K22 gene	ncRNA
mm_58327.1	chr6	146577400	146577427	-	1	NA	promoter-TSS (NM_026218)	promoter-TSS (NM_026218)	422	NM_138757	71177	Mm.271774	NM_138757	ENSMUSG00000040250	Asun	4933424B01Rik|Spata30	asunder, spermatogenesis regulator	protein-coding
mm_168672.1	chr1	193632877	193632895	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-125356	NR_029592	387201		NR_029592	ENSMUSG00000065533	Mir205	Mirn205|mir-205|mmu-mir-205	microRNA 205	ncRNA
mm_92544.1	chr10	79711662	79711674	-	1	NA	3' UTR (NM_001077184, exon 7 of 7)	3' UTR (NM_001077184, exon 7 of 7)	-4966	NM_008226	15166	Mm.12956	NM_008226	ENSMUSG00000020331	Hcn2	BCNG2|HAC1|trls	hyperpolarization-activated, cyclic nucleotide-gated K+ 2	protein-coding
mm_8019.1	chr1	134955909	134955955	-	1	NA	promoter-TSS (NM_001081307)	promoter-TSS (NM_001081307)	8	NM_001081307	329251	Mm.188709	NM_001081307	ENSMUSG00000073557	Ppp1r12b	1810037O03Rik|9530009M10Rik|AI132431|Mypt2	protein phosphatase 1, regulatory (inhibitor) subunit 12B	protein-coding
mm_114185.1	chr13	55652925	55652949	+	1	NA	exon (NM_001282055, exon 8 of 23)	exon (NM_001282055, exon 8 of 23)	17938	NM_001282055	212880	Mm.202725	NM_145975	ENSMUSG00000021500	Ddx46	2200005K02Rik|8430438J23Rik|AI325430|AI957095|mKIAA0801	DEAD (Asp-Glu-Ala-Asp) box polypeptide 46	protein-coding
mm_154704.1	chrX	8272245	8272264	+	1	NA	intron (NM_172479, intron 3 of 15)	intron (NM_172479, intron 3 of 15)	873	NM_172479	209837	Mm.6055	NM_172479	ENSMUSG00000031170	Slc38a5	C81234|E330031E14|JM24|SN2	solute carrier family 38, member 5	protein-coding
mm_139560.1	chr17	56883974	56884019	+	1	NA	intron (NM_030141, intron 10 of 13)	intron (NM_030141, intron 10 of 13)	8363	NM_030141	78625	Mm.160106	NM_030141	ENSMUSG00000024209	1700061G19Rik	1700026H02|AI507598	RIKEN cDNA 1700061G19 gene	protein-coding
mm_78692.1	chr9	40804740	40804751	+	1	NA	intron (NM_031165, intron 8 of 8)	intron (NM_031165, intron 8 of 8)	3472	NM_031165	15481	Mm.290774	NM_031165	ENSMUSG00000015656	Hspa8	2410008N15Rik|Hsc70|Hsc71|Hsc73|Hsp73|Hspa10	heat shock protein 8	protein-coding
mm_145385.1	chr18	57133066	57133079	+	1	NA	promoter-TSS (NM_001001979)	promoter-TSS (NM_001001979)	-18	NM_001001979	70417	Mm.297863	NM_001001979	ENSMUSG00000024593	Megf10	3000002B06Rik|Gm331	multiple EGF-like-domains 10	protein-coding
mm_21730.1	chr2	164743133	164743147	-	1	NA	5' UTR (NM_027961, exon 1 of 4)	5' UTR (NM_027961, exon 1 of 4)	127	NM_027961	71856	Mm.330770	NM_027961	ENSMUSG00000076434	Wfdc3	1700015L13Rik|1700127F16Rik	WAP four-disulfide core domain 3	protein-coding
mm_10453.1	chr2	14279577	14279585	+	1	NA	intron (NM_008625, intron 10 of 29)	RMER15|LTR|ERVL	18578	NR_030609	100124488		NR_030609	ENSMUSG00000077897	Mir511	Mirn511|mir-511|mmu-mir-511	microRNA 511	ncRNA
mm_34845.1	chr4	155414923	155414951	+	1	NA	intron (NR_102283, intron 1 of 4)	RSINE1|SINE|B4	5747	NM_001166029	544678	Mm.472798	NM_177674	ENSMUSG00000078490	Cfap74	2010015L04Rik|A530045M11	cilia and flagella associated protein 74	protein-coding
mm_63516.1	chr7	127876899	127876919	+	1	NA	promoter-TSS (NM_146259)	promoter-TSS (NM_146259)	-86	NM_146259	244219	Mm.207872	NM_146259	ENSMUSG00000049728	Zfp668	BC030314|E130018B19Rik|Znf668	zinc finger protein 668	protein-coding
mm_101408.1	chr11	27507956	27507970	-	1	NA	Intergenic	Intergenic	722855	NR_002890	654472	Mm.347777	NR_002890		Gm12070	OTTMUSG00000005300	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_99039.1	chr11	98960734	98960758	+	1	NA	5' UTR (NM_001176528, exon 1 of 8)	5' UTR (NM_001176528, exon 1 of 8)	275	NM_001176528	19401	Mm.439744	NM_009024	ENSMUSG00000037992	Rara	Nr1b1|RAR|RARalpha1	retinoic acid receptor, alpha	protein-coding
mm_96368.1	chr11	67201744	67201754	+	1	NA	intron (NM_030679, intron 2 of 39)	intron (NM_030679, intron 2 of 39)	1635	NM_030679	17879	Mm.477065	NM_030679	ENSMUSG00000056328	Myh1	A530084A17Rik|IId|IId/x|MHC-2X/D|MHC2X/D|MYHC-IIX|MdMs|MyHC-IId/x|MyHC-IIx/d|Myhs-f|Myhs-f2|Myhsf2	myosin, heavy polypeptide 1, skeletal muscle, adult	protein-coding
mm_66208.1	chr7	34305519	34305543	-	1	NA	Intergenic	Intergenic	-19922	NM_172741	233103	Mm.491097	NM_172741	ENSMUSG00000066571	4931406P16Rik	AA553327|mKIAA0355	RIKEN cDNA 4931406P16 gene	protein-coding
mm_43082.1	chr5	124447163	124447177	+	1	NA	intron (NM_001310727, intron 1 of 6)	intron (NM_001310727, intron 1 of 6)	466	NM_001310727	67956	Mm.137966	NM_030241	ENSMUSG00000049327	Kmt5a	2410195B05Rik|AA617402|AW536475|PR-SET7|PR/SET07|Setd8	lysine methyltransferase 5A	protein-coding
mm_111195.1	chr12	84193946	84193965	-	1	NA	promoter-TSS (NM_001163502)	promoter-TSS (NM_001163502)	60	NM_001163502	238317	Mm.31256	NM_001163501	ENSMUSG00000042507	Elmsan1	9430029N19Rik|C130039O16Rik|Gm260	ELM2 and Myb/SANT-like domain containing 1	protein-coding
mm_30121.1	chr3	141211836	141211838	-	1	NA	5' UTR (NM_008811, exon 1 of 1)	5' UTR (NM_008811, exon 1 of 1)	518	NM_008811	18598	Mm.4223	NM_008811	ENSMUSG00000047674	Pdha2	Pdhal	pyruvate dehydrogenase E1 alpha 2	protein-coding
mm_80220.1	chr9	72551123	72551126	+	1	NA	intron (NM_001033536, intron 1 of 8)	L1MB7|LINE|L1	18884	NM_001033536	319758	Mm.32081	NM_001033536	ENSMUSG00000037674	Rfx7	2510005N23Rik|9930116O05Rik|D130086K05Rik|Rfxdc2	regulatory factor X, 7	protein-coding
mm_3570.1	chr1	150449148	150449178	+	1	NA	TTS (NM_021400)	TTS (NM_021400)	17002	NM_021400	96875	Mm.174256	NM_021400	ENSMUSG00000006014	Prg4	CACP|DOL54|JCAP|MSF|SZP|lubricin	proteoglycan 4 (megakaryocyte stimulating factor, articular superficial zone protein)	protein-coding
mm_159287.1	chr2	170131116	170131116	-	1	NA	5' UTR (NM_001033299, exon 1 of 6)	5' UTR (NM_001033299, exon 1 of 6)	104	NM_001033299	228913	Mm.22858	NM_001033299	ENSMUSG00000052056	Zfp217	4933431C08Rik|AW987152|Gm562|ZABC1|Znf217	zinc finger protein 217	protein-coding
mm_119605.1	chr14	51095264	51095268	+	1	NA	promoter-TSS (NM_201239)	promoter-TSS (NM_201239)	-734	NM_007447	11727	Mm.202665	NM_007447	ENSMUSG00000072115	Ang	AI385586|Ang1|Rnase5|Rnase5a	angiogenin, ribonuclease, RNase A family, 5	protein-coding
mm_147165.1	chr18	36726201	36726226	-	1	NA	exon (NM_009841, exon 2 of 2)	exon (NM_009841, exon 2 of 2)	602	NM_009841	12475	Mm.3460	NM_009841	ENSMUSG00000051439	Cd14	-	CD14 antigen	protein-coding
mm_88252.1	chr10	73171317	73171345	+	1	NA	Intergenic	Intergenic	-84626	NR_040646	327768	Mm.417745	NR_040646		A330049N07Rik	-	RIKEN cDNA A330049N07 gene	ncRNA
mm_19792.1	chr2	109224858	109224861	-	1	NA	intron (NM_029790, intron 2 of 5)	intron (NM_029790, intron 2 of 5)	53431	NM_029790	76894	Mm.330451	NM_029790	ENSMUSG00000057234	Mettl15	0610027B03Rik|AI303697|AW049952|Mett5d1	methyltransferase like 15	protein-coding
mm_116955.1	chr13	56135949	56135956	-	1	NA	promoter-TSS (NM_001159515)	promoter-TSS (NM_001159515)	-402	NM_001159513	26914	Mm.283802	NM_012015	ENSMUSG00000015937	H2afy	H2AF12M|mH2a1|macroH2A1	H2A histone family, member Y	protein-coding
mm_12396.1	chr2	70091927	70091931	+	1	NA	intron (NM_177376, intron 2 of 34)	RLTR14|LTR|ERV1	52803	NM_177376	329421	Mm.99648	NM_177376	ENSMUSG00000042064	Myo3b	A430065P19Rik	myosin IIIB	protein-coding
mm_88259.1	chr10	73821899	73821914	+	1	NA	promoter-TSS (NM_001142743)	promoter-TSS (NM_001142743)	39	NM_001142735	11994	Mm.338933	NM_023115	ENSMUSG00000052613	Pcdh15	BB078305|ENSMUSG00000046980|Gm9815|Ush1f|av|nmf19|roda	protocadherin 15	protein-coding
mm_135172.1	chr16	35932768	35932778	-	1	NA	exon (NM_001013371, exon 3 of 5)	exon (NM_001013371, exon 3 of 5)	-5697	NM_030253	80285	Mm.49074	NM_030253	ENSMUSG00000022906	Parp9	ARTD9|AW214463|BC003281|Bagl|Bal|PARP-9	poly (ADP-ribose) polymerase family, member 9	protein-coding
mm_16946.1	chr2	15055060	15055079	-	1	NA	promoter-TSS (NM_001165941)	promoter-TSS (NM_001165941)	-197	NM_001165943	74455	Mm.478923	NM_028950	ENSMUSG00000026707	Nsun6	4933403D21Rik|4933414E04Rik|NOPD1	NOL1/NOP2/Sun domain family member 6	protein-coding
mm_154956.1	chrX	36795595	36795610	+	1	NA	promoter-TSS (NM_007451)	promoter-TSS (NM_007451)	5	NM_007451	11740	Mm.371544	NM_007451	ENSMUSG00000016319	Slc25a5	Ant2	solute carrier family 25 (mitochondrial carrier, adenine nucleotide translocator), member 5	protein-coding
mm_4795.1	chr1	184732785	184732804	+	1	NA	promoter-TSS (NM_008250)	promoter-TSS (NM_008250)	-301	NM_008250	15284	Mm.1347	NM_008250	ENSMUSG00000039377	Hlx	Hlx1	H2.0-like homeobox	protein-coding
mm_147789.1	chr18	61646317	61646321	-	1	NA	non-coding (NR_045402, exon 5 of 5)	non-coding (NR_045402, exon 5 of 5)	1575	NR_029557	387163		NR_029557	ENSMUSG00000065592	Mir145a	Mir145|Mirn145|mir-145a|mmu-mir-145|mmu-mir-145a	microRNA 145a	ncRNA
mm_100820.1	chr11	5253713	5253722	-	1	NA	promoter-TSS (NR_037240)	promoter-TSS (NR_037240)	-881	NR_037240	100526548		NR_037240	ENSMUSG00000093169	Mir3079	mmu-mir-3079	microRNA 3079	ncRNA
mm_155824.1	chrX	100729819	100729823	+	1	NA	promoter-TSS (NM_023608)	promoter-TSS (NM_023608)	-26	NM_023608	71584	Mm.283495	NM_023608	ENSMUSG00000019359	Gdpd2	9130017L10Rik|Gde3|Obdpf	glycerophosphodiester phosphodiesterase domain containing 2	protein-coding
mm_92360.1	chr10	75938389	75938393	-	1	NA	TTS (NM_175329)	TTS (NM_175329)	2281	NM_001277132	333670	Mm.291320	NM_001037714	ENSMUSG00000050157	Gm867	Gm736	predicted gene 867	protein-coding
mm_67067.1	chr7	67757622	67757626	-	1	NA	intron (NM_183312, intron 1 of 3)	intron (NM_183312, intron 1 of 3)	2118	NM_183312	233335	Mm.60526	NM_183312	ENSMUSG00000030554	Synm	4930412K21Rik|AI852401|Dmn|E130104F11|Syn|Synemin	synemin, intermediate filament protein	protein-coding
mm_10811.1	chr2	24350118	24350128	+	1	NA	3' UTR (NM_031167, exon 5 of 5)	3' UTR (NM_031167, exon 5 of 5)	4752	NM_001039701	16181	Mm.882	NM_031167	ENSMUSG00000026981	Il1rn	F630041P17Rik|IL-1ra	interleukin 1 receptor antagonist	protein-coding
mm_37406.1	chr4	122455302	122455350	-	1	NA	Intergenic	Intergenic	-233933	NM_023865	77432	Mm.491436	NM_023865	ENSMUSG00000023263	9530002B09Rik	Aump|Vpp1|Vppl	RIKEN cDNA 9530002B09 gene	protein-coding
mm_69214.1	chr7	127512334	127512387	-	1	NA	non-coding (NR_024331, exon 1 of 1)	non-coding (NR_024331, exon 1 of 1)	377	NM_001304266	100043597	Mm.428042	NM_175144	ENSMUSG00000053877	Srcap	B930091H02Rik|D030022P06Rik|F630004O05Rik	Snf2-related CREBBP activator protein	protein-coding
mm_91267.1	chr10	23787196	23787206	-	1	NA	promoter-TSS (NM_011295)	promoter-TSS (NM_011295)	8	NM_011295	20042	Mm.371846	NM_011295	ENSMUSG00000061983	Rps12	-	ribosomal protein S12	protein-coding
mm_126626.1	chr15	83389618	83389618	+	1	NA	intron (NM_011862, intron 4 of 10)	intron (NM_011862, intron 4 of 10)	-22321	NR_027980	69291	Mm.66794	NM_001033147		1700001L05Rik	-	RIKEN cDNA 1700001L05 gene	ncRNA
mm_155772.1	chrX	96255604	96255694	+	1	NA	intron (NM_177789, intron 4 of 6)	MTEa|LTR|ERVL-MaLR	12832	NR_029801	723814		NR_029801	ENSMUSG00000076066	Mir223	Mirn223|miR-223|mmu-mir-223	microRNA 223	ncRNA
mm_125335.1	chr15	38951117	38951123	+	1	NA	3' UTR (NM_080640, exon 2 of 2)	3' UTR (NM_080640, exon 2 of 2)	17211	NM_080640	118452	Mm.233837	NM_080640		Baalc	2810457D07Rik	brain and acute leukemia, cytoplasmic	protein-coding
mm_21768.1	chr2	164844672	164844689	-	1	NA	exon (NM_011125, exon 11 of 16)	exon (NM_011125, exon 11 of 16)	10907	NM_008906	19025	Mm.359633	NM_008906	ENSMUSG00000017760	Ctsa	AU019505|PPCA|Ppgb	cathepsin A	protein-coding
mm_91864.1	chr10	59441841	59441851	-	1	NA	promoter-TSS (NM_010959)	promoter-TSS (NM_010959)	-67	NM_010959	18302	Mm.123013	NM_010959	ENSMUSG00000009654	Oit3	EF-9|LZP	oncoprotein induced transcript 3	protein-coding
mm_51105.1	chr6	67277813	67277833	+	1	NA	exon (NM_025814, exon 6 of 8)	exon (NM_025814, exon 6 of 8)	10844	NM_025814	66870	Mm.240490	NM_025814	ENSMUSG00000036371	Serbp1	1200009K13Rik|9330147J08Rik|AL022786|Pairbp1	serpine1 mRNA binding protein 1	protein-coding
mm_168004.1	chrY	1286497	1286501	-	1	NA	exon (NM_012008, exon 1 of 17)	exon (NM_012008, exon 1 of 17)	114	NM_012008	26900	Mm.302938	NM_012008	ENSMUSG00000069045	Ddx3y	8030469F12Rik|D1Pas1-rs1|Dby	DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, Y-linked	protein-coding
mm_125428.1	chr15	43524058	43524061	+	1	NA	intron (NM_025736, intron 10 of 10)	intron (NM_025736, intron 10 of 10)	46830	NM_025736	66736	Mm.244512	NM_025736	ENSMUSG00000022337	Emc2	4921531G14Rik|AV060620|AW209495|Ttc35	ER membrane protein complex subunit 2	protein-coding
mm_21732.1	chr2	164743183	164743211	-	1	NA	promoter-TSS (NM_027961)	promoter-TSS (NM_027961)	70	NM_027961	71856	Mm.330770	NM_027961	ENSMUSG00000076434	Wfdc3	1700015L13Rik|1700127F16Rik	WAP four-disulfide core domain 3	protein-coding
mm_66568.1	chr7	45298207	45298216	-	1	NA	Intergenic	Intergenic	15338	NM_001033176	76713	Mm.425445	NM_001033176	ENSMUSG00000070568	Slc6a21	1700039E15Rik|Gm19188	solute carrier family 6 member 21	protein-coding
mm_155534.1	chrX	74303845	74303888	+	1	NA	exon (NM_018794, exon 10 of 10)	exon (NM_018794, exon 10 of 10)	-1146	NM_010273	14567	Mm.205830	NM_010273	ENSMUSG00000015291	Gdi1	GDIA|GDIalpha	guanosine diphosphate (GDP) dissociation inhibitor 1	protein-coding
mm_72734.1	chr8	85083444	85083447	+	1	NA	exon (NM_010764, exon 1 of 24)	exon (NM_010764, exon 1 of 24)	176	NM_010764	17159	Mm.4219	NM_010764	ENSMUSG00000005142	Man2b1	AW107687|LAMAN	mannosidase 2, alpha B1	protein-coding
mm_18151.1	chr2	45068406	45068422	-	1	NA	intron (NM_001289521, intron 1 of 8)	intron (NM_001289521, intron 1 of 8)	41863	NM_001289521	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_147164.1	chr18	36726173	36726186	-	1	NA	exon (NM_009841, exon 2 of 2)	exon (NM_009841, exon 2 of 2)	636	NM_009841	12475	Mm.3460	NM_009841	ENSMUSG00000051439	Cd14	-	CD14 antigen	protein-coding
mm_91016.1	chr10	16425118	16425127	-	1	NA	Intergenic	Intergenic	633345	NR_131087	77538	Mm.128235	NR_131087		C330004P14Rik	-	RIKEN cDNA C330004P14 gene	ncRNA
mm_88494.1	chr10	77836292	77836306	+	1	NA	exon (NM_001024709, exon 1 of 1)	exon (NM_001024709, exon 1 of 1)	352	NM_001024709	544710	Mm.441890	NM_001024709		Krtap10-10	EG544710	keratin associated protein 10-10	protein-coding
mm_29874.1	chr3	130901483	130901521	-	1	NA	Intergenic	Intergenic	-171104	NM_001005859	68436	Mm.140568	NM_026724	ENSMUSG00000062006	Rpl34	1100001I22Rik	ribosomal protein L34	protein-coding
mm_20773.1	chr2	143081689	143081712	-	1	NA	TTS (NM_020595)	TTS (NM_020595)	3208	NM_020595	57329	Mm.157751	NM_020595	ENSMUSG00000027416	Otor	CDRAP|Fdp|MIA|MIAL	otoraplin	protein-coding
mm_140973.1	chr17	24696148	24696166	-	1	NA	promoter-TSS (NM_027988)	promoter-TSS (NM_027988)	-1	NM_023040	11692	Mm.28124	NM_023040	ENSMUSG00000040888	Gfer	Alr|ERV1	growth factor, erv1 (S. cerevisiae)-like (augmenter of liver regeneration)	protein-coding
mm_53566.1	chr6	137252393	137252423	+	1	NA	5' UTR (NM_011216, exon 1 of 27)	5' UTR (NM_011216, exon 1 of 27)	109	NM_011216	19277	Mm.186361	NM_011216	ENSMUSG00000030223	Ptpro	D28|GLEPP1|PTPBK|PTPROt|PTPU2|PTPoc|PTPphi|Ptpn15|R-PTP-O	protein tyrosine phosphatase, receptor type, O	protein-coding
mm_62751.1	chr7	111325979	111325983	+	1	NA	Intergenic	Intergenic	-203306	NR_015573	75479	Mm.381620	NR_015573	ENSMUSG00000110424	1700012D14Rik	-	RIKEN cDNA 1700012D14 gene	ncRNA
mm_112903.1	chr13	20899639	20899663	+	1	NA	intron (NM_012054, intron 4 of 20)	intron (NM_012054, intron 4 of 20)	105538	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_93318.1	chr10	99108030	99108085	-	1	NA	promoter-TSS (NM_015737)	promoter-TSS (NM_015737)	-78	NM_015737	14426	Mm.314	NM_015737	ENSMUSG00000090035	Galnt4	AV011803	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 4	protein-coding
mm_1894.1	chr1	85708064	85708097	+	1	NA	exon (NM_013673, exon 19 of 20)	exon (NM_013673, exon 19 of 20)	28526	NM_177055	319997	Mm.116691	NM_177055	ENSMUSG00000052760	A630001G21Rik	-	RIKEN cDNA A630001G21 gene	protein-coding
mm_102167.1	chr11	53859188	53859241	-	1	NA	promoter-TSS (NR_033332)	promoter-TSS (NR_033332)	42	NR_033332	622459	Mm.479656	NR_033332	ENSMUSG00000081769	Gm12216	602-19-115|OTTMUSG00000005650	predicted gene 12216	ncRNA
mm_124899.1	chr15	10486095	10486105	+	1	NA	promoter-TSS (NM_011232)	promoter-TSS (NM_011232)	62	NM_001289447	19355	Mm.38376	NM_011232	ENSMUSG00000022248	Rad1	mRAD1	RAD1 checkpoint DNA exonuclease	protein-coding
mm_47546.1	chr5	124350913	124350924	-	1	NA	intron (NM_013812, intron 1 of 3)	intron (NM_013812, intron 1 of 3)	3710	NM_013812	13445	Mm.391838	NM_013812	ENSMUSG00000029394	Cdk2ap1	Apc10|Cdkap1|DORC1|Doc1|ST19|doc-1|p12	CDK2 (cyclin-dependent kinase 2)-associated protein 1	protein-coding
mm_75302.1	chr8	41112798	41112804	-	1	NA	intron (NM_001005863, intron 1 of 13)	MT2B1|LTR|ERVL	1866	NM_001286413	102103	Mm.149438	NM_001005863	ENSMUSG00000045636	Mtus1	AI481402|ATBP135|Atip1|B430010I23Rik|B430305I03Rik|C85752|Cctsg1-440|MD44|MTSG1|mKIAA1288	mitochondrial tumor suppressor 1	protein-coding
mm_166056.1	chr4	132796396	132796417	-	1	NA	promoter-TSS (NM_001033308)	promoter-TSS (NM_001033308)	-42	NM_001033308	230787	Mm.290912	NM_001033308	ENSMUSG00000037731	Themis2	ICB-1	thymocyte selection associated family member 2	protein-coding
mm_79469.1	chr9	56865019	56865047	+	1	NA	promoter-TSS (NM_139001)	promoter-TSS (NM_139001)	-71	NM_139001	121021	Mm.41329	NM_139001	ENSMUSG00000032911	Cspg4	4732461B14Rik|AN2|NG2	chondroitin sulfate proteoglycan 4	protein-coding
mm_60448.1	chr7	44477278	44477333	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	6958	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_45427.1	chr5	67094872	67094879	-	1	NA	3' UTR (NM_008888, exon 3 of 3)	3' UTR (NM_008888, exon 3 of 3)	4251	NM_008888	18935	Mm.62505	NM_008888	ENSMUSG00000012520	Phox2b	Dilp1|NBPhox|Pmx2b|Px2b	paired-like homeobox 2b	protein-coding
mm_61395.1	chr7	73255966	73255997	+	1	NA	Intergenic	Intergenic	-54399	NR_105062	100505025	Mm.445959	NR_105062	ENSMUSG00000108530	LOC100505025	-	uncharacterized LOC100505025	ncRNA
mm_164341.1	chr16	14705620	14705635	+	1	NA	promoter-TSS (NM_011415)	promoter-TSS (NM_011415)	-232	NM_011415	20583	Mm.4272	NM_011415	ENSMUSG00000022676	Snai2	Slug|Slugh|Snail2	snail family zinc finger 2	protein-coding
mm_12710.1	chr2	76675963	76675967	+	1	NA	intron (NM_031256, intron 1 of 7)	intron (NM_031256, intron 1 of 7)	650	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_108864.1	chr12	98920645	98920662	+	1	NA	promoter-TSS (NM_198311)	promoter-TSS (NM_198311)	41	NM_198311	76260	Mm.282660	NM_029553	ENSMUSG00000021013	Ttc8	0610012F22Rik|AV001447|BBS8	tetratricopeptide repeat domain 8	protein-coding
mm_87823.1	chr10	60349319	60349325	+	1	NA	intron (NM_028732, intron 1 of 6)	intron (NM_028732, intron 1 of 6)	2471	NM_028732	74048	Mm.273584	NM_028732	ENSMUSG00000020101	Vsir	4632428N05Rik|Dies1|PD-1H|VISTA	V-set immunoregulatory receptor	protein-coding
mm_98898.1	chr11	97999530	97999547	+	1	NA	Intergenic	Intergenic	-3365	NM_207231	217151	Mm.277896	NM_207231	ENSMUSG00000038352	Arl5c	Arl12|BC065791	ADP-ribosylation factor-like 5C	protein-coding
mm_49058.1	chr6	5163674	5163684	+	1	NA	3' UTR (NM_181595, exon 16 of 16)	3' UTR (NM_181595, exon 16 of 16)	30267	NM_011134	18979	Mm.237657	NM_011134	ENSMUSG00000002588	Pon1	Pon	paraoxonase 1	protein-coding
mm_96183.1	chr11	61661047	61661050	+	1	NA	intron (NM_027817, intron 2 of 4)	intron (NM_027817, intron 2 of 4)	7727	NM_027817	71520	Mm.202760	NM_027817	ENSMUSG00000004837	Grap	8430435N19Rik|BB233594	GRB2-related adaptor protein	protein-coding
mm_168752.1	chr12	115920762	115920762	-	1	NA	Intergenic	Intergenic	-126962	NM_001004066	56220	Mm.254997	NM_019565	ENSMUSG00000042063	Zfp386	Kzf1|mKIAA4205	zinc finger protein 386 (Kruppel-like)	protein-coding
mm_44442.1	chr5	21645542	21645610	-	1	NA	promoter-TSS (NM_026034)	promoter-TSS (NM_026034)	29	NM_001199632	320118	Mm.442295	NM_177076	ENSMUSG00000048520	Fbxl13	4921539K22Rik	F-box and leucine-rich repeat protein 13	protein-coding
mm_74374.1	chr8	128504467	128504478	+	1	NA	3' UTR (NM_008737, exon 17 of 17)	3' UTR (NM_008737, exon 17 of 17)	145231	NR_035436	100316680		NR_035436	ENSMUSG00000084523	Mir1903	Mirn1903|mmu-mir-1903	microRNA 1903	ncRNA
mm_162545.1	chr1	170689998	170690025	+	1	NA	Intergenic	Intergenic	45479	NM_177068	320078	Mm.287131	NM_177068	ENSMUSG00000038463	Olfml2b	1110018N05Rik|4832415H08Rik|AI467542	olfactomedin-like 2B	protein-coding
mm_158167.1	chrX	103605596	103605635	-	1	NA	non-coding (NR_028380, exon 8 of 11)	non-coding (NR_028380, exon 8 of 11)	18139	NR_028381	78878	Mm.259724	NR_028380	ENSMUSG00000086370	Ftx	B230206F22Rik|BB219131|NCRNA00182|Thcytx	Ftx transcript, Xist regulator (non-protein coding)	ncRNA
mm_71908.1	chr8	70083454	70083468	+	1	NA	promoter-TSS (NM_177900)	promoter-TSS (NM_177900)	-68	NM_177900	330790	Mm.152048	NM_177900	ENSMUSG00000007594	Hapln4	9330174O11|Bral2|Lpr4	hyaluronan and proteoglycan link protein 4	protein-coding
mm_150932.1	chr19	46305746	46305787	+	1	NA	promoter-TSS (NM_001177370)	promoter-TSS (NM_001177370)	71	NM_019408	18034	Mm.102365	NM_019408	ENSMUSG00000025225	Nfkb2	NF-kappaB2|lyt|p49|p49/p100|p50B|p52	nuclear factor of kappa light polypeptide gene enhancer in B cells 2, p49/p100	protein-coding
mm_27063.1	chr3	27710414	27710467	-	1	NA	promoter-TSS (NM_173182)	promoter-TSS (NM_173182)	-1	NM_173182	72007	Mm.38832	NM_173182	ENSMUSG00000039286	Fndc3b	1600019O04Rik|AW550168|Fad104|mKIAA4164	fibronectin type III domain containing 3B	protein-coding
mm_171855.1	chr5	20127325	20127327	-	1	NA	intron (NM_001170746, intron 3 of 22)	L1Md_T|LINE|L1	219808	NM_015823	50791	Mm.332231	NM_015823	ENSMUSG00000040003	Magi2	AIP-1|Acvri1|Acvrinp1|Acvrip1|Magi-2|S-SCAM|mKIAA0705	membrane associated guanylate kinase, WW and PDZ domain containing 2	protein-coding
mm_84869.1	chr9	79599155	79599157	-	1	NA	3' UTR (NM_001290308, exon 66 of 66)	3' UTR (NM_001290308, exon 66 of 66)	-79854	NR_045336	100038575	Mm.367838	NR_045336	ENSMUSG00000111765	Gm10635	ENSMUSG00000074174	predicted gene 10635	ncRNA
mm_36888.1	chr4	107307129	107307161	-	1	NA	promoter-TSS (NM_007860)	promoter-TSS (NM_007860)	23	NM_007860	13370	Mm.148342	NM_007860	ENSMUSG00000034785	Dio1	5DI|D1|ITDI1|TXDI1	deiodinase, iodothyronine, type I	protein-coding
mm_45081.1	chr5	43981783	43981794	-	1	NA	promoter-TSS (NM_008009)	promoter-TSS (NM_008009)	11	NM_008009	14181	Mm.46053	NM_008009	ENSMUSG00000048373	Fgfbp1	FGF-BP|FGF-BP1|FGFBP-1	fibroblast growth factor binding protein 1	protein-coding
mm_23043.1	chr3	34764884	34764892	+	1	NA	Intergenic	Intergenic	-7187	NR_110488	102638436	Mm.261793	NR_110488	ENSMUSG00000106519	Gm38509	Peril	predicted gene, 38509	ncRNA
mm_78225.1	chr9	21588492	21588516	+	1	NA	TTS (NM_138303)	TTS (NM_138303)	-4218	NM_178619	69773	Mm.39704	NM_178619	ENSMUSG00000048429	Timm29	1810026J23Rik	translocase of inner mitochondrial membrane 29	protein-coding
mm_64559.1	chr7	144837480	144837509	+	1	NA	Intergenic	Intergenic	-1118	NM_008007	14174	Mm.4947	NM_008007	ENSMUSG00000031074	Fgf3	Fgf-3|Int-2|Int-P	fibroblast growth factor 3	protein-coding
mm_111196.1	chr12	84193988	84193998	-	1	NA	promoter-TSS (NM_001163502)	promoter-TSS (NM_001163502)	22	NM_001163502	238317	Mm.31256	NM_001163501	ENSMUSG00000042507	Elmsan1	9430029N19Rik|C130039O16Rik|Gm260	ELM2 and Myb/SANT-like domain containing 1	protein-coding
mm_110625.1	chr12	57197196	57197260	-	1	NA	5' UTR (NM_172577, exon 1 of 10)	5' UTR (NM_172577, exon 1 of 10)	244	NM_172577	217593	Mm.32835	NM_172577	ENSMUSG00000035472	Slc25a21	9930033G19Rik|A630030I10|BB158148	solute carrier family 25 (mitochondrial oxodicarboxylate carrier), member 21	protein-coding
mm_34400.1	chr4	145213930	145213970	+	1	NA	3' UTR (NM_011610, exon 10 of 10)	3' UTR (NM_011610, exon 10 of 10)	-18945	NM_001276465	230895	Mm.240310	NM_001033190	ENSMUSG00000020220	Vps13d	-	vacuolar protein sorting 13D	protein-coding
mm_43361.1	chr5	135218029	135218046	+	1	NA	exon (NM_011714, exon 7 of 19)	exon (NM_011714, exon 7 of 19)	30714	NM_011714	22385	Mm.40331	NM_011714	ENSMUSG00000002748	Baz1b	C87820|WSTF|Wbscr9	bromodomain adjacent to zinc finger domain, 1B	protein-coding
mm_15383.1	chr2	156547571	156547614	+	1	NA	promoter-TSS (NM_001164818)	promoter-TSS (NM_001164818)	16	NM_001164818	68295	Mm.253648	NM_026661	ENSMUSG00000027628	Aar2	0610011L14Rik	AAR2 splicing factor homolog	protein-coding
mm_119899.1	chr14	54938623	54938637	+	1	NA	exon (NM_026066, exon 3 of 5)	exon (NM_026066, exon 3 of 5)	2133	NM_029390	67272	Mm.41614	NM_026066	ENSMUSG00000040759	Cmtm5	1500005P16Rik|2900052H21Rik|Cklfsf5	CKLF-like MARVEL transmembrane domain containing 5	protein-coding
mm_2425.1	chr1	95314151	95314161	+	1	NA	exon (NM_026321, exon 1 of 3)	exon (NM_026321, exon 1 of 3)	528	NM_026321	67698	Mm.272705	NM_026321	ENSMUSG00000051185	Fam174a	2310044D20Rik|Fam174|Naa6|Tmem157	family with sequence similarity 174, member A	protein-coding
mm_139037.1	chr17	46202741	46202854	+	1	NA	promoter-TSS (NM_028198)	promoter-TSS (NM_028198)	-58	NM_028198	72322	Mm.275039	NM_028198	ENSMUSG00000067150	Xpo5	2410004H11Rik|2700038C24Rik|AI648907|AW549301|Exp5|RanBp21|mKIAA1291	exportin 5	protein-coding
mm_21222.1	chr2	155826607	155826618	-	1	NA	5' UTR (NM_010579, exon 1 of 6)	5' UTR (NM_010579, exon 1 of 6)	313	NM_010579	16418	Mm.271674	NM_010579	ENSMUSG00000027613	Eif6	1110004P11|AA408895|CAB|Itgb4bp|eIF-6|imc-415|p27(BBP)|p27BBP	eukaryotic translation initiation factor 6	protein-coding
mm_58649.1	chr7	6285612	6285636	+	1	NA	promoter-TSS (NM_001024928)	promoter-TSS (NM_001024928)	-956	NM_001024928	384763	Mm.276279	NM_001024928	ENSMUSG00000054893	Zfp667	A830025F02Rik|Mip1|ZNF667	zinc finger protein 667	protein-coding
mm_58578.1	chr7	4915177	4915199	+	1	NA	promoter-TSS (NM_170759)	promoter-TSS (NM_170759)	-29	NM_170759	232816	Mm.27442	NM_170759	ENSMUSG00000074406	Zfp628	Zec|Znf628	zinc finger protein 628	protein-coding
mm_36376.1	chr4	76748229	76748244	-	1	NA	intron (NM_011211, intron 9 of 39)	L1Md_A|LINE|L1	1463659	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding
mm_42302.1	chr5	114707778	114707866	+	1	NA	promoter-TSS (NM_029992)	promoter-TSS (NM_029992)	43	NM_029992	77832	Mm.239698	NM_029992	ENSMUSG00000002486	Tchp	A930031F18Rik|AV279199	trichoplein, keratin filament binding	protein-coding
mm_47499.1	chr5	124034550	124034559	-	1	NA	Intergenic	Intergenic	-2294	NM_177876	330192	Mm.4079	NM_177876	ENSMUSG00000066278	Vps37b	2300007F24Rik|AI415429|BC026744	vacuolar protein sorting 37B	protein-coding
mm_117470.1	chr13	76098570	76098605	-	1	NA	promoter-TSS (NM_001081352)	promoter-TSS (NM_001081352)	73	NM_029847	77041	Mm.196399	NM_029847	ENSMUSG00000021592	Arsk	2810429K17Rik|4833414G15Rik	arylsulfatase K	protein-coding
mm_140650.1	chr17	12692019	12692021	-	1	NA	exon (NM_010515, exon 40 of 48)	exon (NM_010515, exon 40 of 48)	-16182	NM_009202	20517	Mm.594	NM_009202	ENSMUSG00000023829	Slc22a1	Lx1|Oct1|Orct|Orct1	solute carrier family 22 (organic cation transporter), member 1	protein-coding
mm_26508.1	chr3	145810474	145810494	+	1	NA	intron (NM_026993, intron 1 of 5)	intron (NM_026993, intron 1 of 5)	51792	NM_026993	69219	Mm.234247	NM_026993	ENSMUSG00000028194	Ddah1	2410006N07Rik|2510015N06Rik|AI987801|AW050362	dimethylarginine dimethylaminohydrolase 1	protein-coding
mm_46458.1	chr5	105118089	105118095	-	1	NA	3' UTR (NM_001256005, exon 11 of 11)	3' UTR (NM_001256005, exon 11 of 11)	-7800	NM_172777	236573	Mm.425261	NM_172777	ENSMUSG00000029298	Gbp9	-	guanylate-binding protein 9	protein-coding
mm_85844.1	chr9	110624362	110624439	-	1	NA	promoter-TSS (NM_026012)	promoter-TSS (NM_026012)	-7	NM_026012	67169	Mm.46680	NM_026012	ENSMUSG00000032491	Nradd	2610311B09Rik|BB104149|NRDD|NRH2|PLAIDD	neurotrophin receptor associated death domain	protein-coding
mm_152035.1	chr19	6118216	6118233	-	1	NA	exon (NM_133678, exon 1 of 2)	exon (NM_133678, exon 1 of 2)	362	NM_133678	66406	Mm.303924	NM_133678	ENSMUSG00000024790	Sac3d1	2410004C24Rik|AU015683|shd1	SAC3 domain containing 1	protein-coding
mm_74824.1	chr8	23095653	23095681	-	1	NA	intron (NR_102385, intron 11 of 45)	GSAT_MM|Satellite|Satellite	37408	NR_102385	11733	Mm.334444	NM_031158	ENSMUSG00000031543	Ank1	Ank-1|nb|pale	ankyrin 1, erythroid	protein-coding
mm_48942.1	chr6	4539517	4539528	+	1	NA	exon (NM_007743, exon 51 of 52)	exon (NM_007743, exon 51 of 52)	33904	NM_007743	12843	Mm.277792	NM_007743	ENSMUSG00000029661	Col1a2	AA960264|AI325291|Col1a-2|Cola-2|Cola2|oim	collagen, type I, alpha 2	protein-coding
mm_78216.1	chr9	21526223	21526233	+	1	NA	promoter-TSS (NM_206536)	promoter-TSS (NM_206536)	51	NM_001198794	382062	Mm.325205	NM_206536	ENSMUSG00000057191	AB124611	Gm1706	cDNA sequence AB124611	protein-coding
mm_18543.1	chr2	64975660	64975674	-	1	NA	intron (NM_016719, intron 2 of 13)	intron (NM_016719, intron 2 of 13)	47099	NM_016719	50915	Mm.214554	NM_016719	ENSMUSG00000026888	Grb14	AI505286	growth factor receptor bound protein 14	protein-coding
mm_40862.1	chr5	73651332	73651344	+	1	NA	promoter-TSS (NM_178387)	promoter-TSS (NM_178387)	-42	NM_178387	73472	Mm.87067	NM_178387	ENSMUSG00000029155	Spata18	1700067I02Rik	spermatogenesis associated 18	protein-coding
mm_51112.1	chr6	67555631	67555635	+	1	NA	Intergenic	Intergenic	10066	NR_003100	75070	Mm.463364	NR_003100		4930515G16Rik	-	myc induced nuclear antigen pseudogene	pseudo
mm_6523.1	chr1	74544276	74544307	-	1	NA	promoter-TSS (NM_148937)	promoter-TSS (NM_148937)	-5	NM_176972	319651	Mm.66568	NM_176972	ENSMUSG00000033364	Usp37	4932415L06Rik|C330008N13Rik	ubiquitin specific peptidase 37	protein-coding
mm_81591.1	chr9	110477068	110477073	+	1	NA	promoter-TSS (NM_001163569)	promoter-TSS (NM_001163569)	76	NM_001163569	16578	Mm.42170	NM_010628	ENSMUSG00000032489	Kif9	-	kinesin family member 9	protein-coding
mm_92210.1	chr10	68212196	68212207	-	1	NA	intron (NM_023598, intron 3 of 9)	intron (NM_023598, intron 3 of 9)	66525	NM_023598	71371	Mm.440357	NM_023598	ENSMUSG00000019947	Arid5b	4930580B11|5430435G07Rik|AI467247|Desrt|Mrf2|Mrf2alpha|Mrf2beta	AT rich interactive domain 5B (MRF1-like)	protein-coding
mm_77299.1	chr8	117157786	117157803	-	1	NA	promoter-TSS (NM_001081151)	promoter-TSS (NM_001081151)	-341	NM_001081151	209239	Mm.132992	NM_001081151	ENSMUSG00000052557	Gan	A330045G18|gigaxonin	giant axonal neuropathy	protein-coding
mm_61467.1	chr7	75611793	75611802	+	1	NA	intron (NM_029332, intron 7 of 36)	intron (NM_029332, intron 7 of 36)	156263	NM_029332	75547	Mm.216107	NM_029332	ENSMUSG00000066406	Akap13	1700026G02Rik|5730522G15Rik|5830460E08Rik|AKAP-13|AKAP-Lbc|BRX|Ht31|LBC|PROTO-LB|PROTO-LBC	A kinase (PRKA) anchor protein 13	protein-coding
mm_63888.1	chr7	137437940	137437956	+	1	NA	intron (NR_033611, intron 1 of 10)	CpG	274	NR_033611	620016	Mm.388932	NR_033611	ENSMUSG00000100863	Gm12669	OTTMUSG00000007920	glutaredoxin 3 pseudogene	pseudo
mm_27128.1	chr3	32341206	32341236	-	1	NA	3' UTR (NM_009517, exon 6 of 6)	3' UTR (NM_009517, exon 6 of 6)	-24268	NR_027966	67576	Mm.435324	NR_027966		4930429B21Rik	-	RIKEN cDNA 4930429B21 gene	ncRNA
mm_31188.1	chr4	43562614	43562670	+	1	NA	promoter-TSS (NM_013497)	promoter-TSS (NM_013497)	8	NM_013497	12913	Mm.12407	NM_013497	ENSMUSG00000028466	Creb3	AU044960|AW538053|C80076|LZIP|LZIP-1|LZIP-2|Luman	cAMP responsive element binding protein 3	protein-coding
mm_2266.1	chr1	91180026	91180055	+	1	NA	5' UTR (NM_001168392, exon 1 of 4)	5' UTR (NM_001168392, exon 1 of 4)	218	NM_001168392	51801	Mm.3272	NM_016894	ENSMUSG00000034353	Ramp1	9130218E19Rik	receptor (calcitonin) activity modifying protein 1	protein-coding
mm_47322.1	chr5	122469485	122469542	-	1	NA	exon (NM_009722, exon 8 of 21)	exon (NM_009722, exon 8 of 21)	32712	NM_001110140	11938	Mm.227583	NM_009722	ENSMUSG00000029467	Atp2a2	9530097L16Rik|D5Wsu150e|SERCA2|SERCA2B|Serca2a|mKIAA4195	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	protein-coding
mm_74537.1	chr8	9762474	9762493	-	1	NA	intron (NM_001347127, intron 1 of 3)	(TG)n|Simple_repeat|Simple_repeat	8540	NM_173446	270028	Mm.268163	NM_173446	ENSMUSG00000079157	Fam155a	6430500D16|AW121567|Tmem28	family with sequence similarity 155, member A	protein-coding
mm_69496.1	chr7	134225155	134225170	-	1	NA	promoter-TSS (NM_007400)	promoter-TSS (NM_007400)	-65	NM_007400	11489	Mm.439714	NM_007400	ENSMUSG00000054555	Adam12	Mltna	a disintegrin and metallopeptidase domain 12 (meltrin alpha)	protein-coding
mm_17991.1	chr2	38036837	38036848	-	1	NA	intron (NM_146122, intron 8 of 21)	HAL1|LINE|L1	250542	NM_146122	227801	Mm.314245	NM_146122	ENSMUSG00000035392	Dennd1a	6030446I19Rik|connecdenn	DENN/MADD domain containing 1A	protein-coding
mm_151125.1	chr19	47915558	47915564	+	1	NA	intron (NM_001001738, intron 1 of 1)	intron (NM_001001738, intron 1 of 1)	3738	NM_001001738	414801	Mm.29457	NM_001001738	ENSMUSG00000044948	Itprip	4833424O12Rik|DANGER|mKIAA1754	inositol 1,4,5-triphosphate receptor interacting protein	protein-coding
mm_35763.1	chr4	46138357	46138375	-	1	NA	promoter-TSS (NM_001033201)	promoter-TSS (NM_001033201)	109	NM_173033	272027	Mm.331588	NM_173033	ENSMUSG00000035495	Tstd2	3010020C06	thiosulfate sulfurtransferase (rhodanese)-like domain containing 2	protein-coding
mm_96507.1	chr11	68451637	68451654	+	1	NA	intron (NM_177320, intron 1 of 18)	intron (NM_177320, intron 1 of 18)	19520	NM_177320	320207	Mm.244960	NM_177320	ENSMUSG00000020901	Pik3r5	AV230647|F730038I15Rik	phosphoinositide-3-kinase, regulatory subunit 5, p101	protein-coding
mm_120150.1	chr14	60506557	60506568	+	1	NA	Intergenic	Intergenic	-128143	NM_001033272	219140	Mm.149776	NM_001033272	ENSMUSG00000021990	Spata13	C79050|ESTM11|X83327|mFLJ00298	spermatogenesis associated 13	protein-coding
mm_130231.1	chr15	96460744	96460834	-	1	NA	promoter-TSS (NM_028148)	promoter-TSS (NM_028148)	54	NM_028148	72193	Mm.324474	NM_028148	ENSMUSG00000033228	Scaf11	1110061H03Rik|2610510E10Rik|AI462454|CASP11|SIP1|SRRP129|Sfrs2ip|Srsf2ip|mKIAA3013	SR-related CTD-associated factor 11	protein-coding
mm_56918.1	chr6	119388965	119388968	-	1	NA	intron (NM_197985, intron 1 of 7)	CpG	28517	NM_197985	68465	Mm.291826	NM_197985	ENSMUSG00000030168	Adipor2	1110001I14Rik|ADCR2|AI115388|AW554121|D6Ucla1e|Paqr2	adiponectin receptor 2	protein-coding
mm_97516.1	chr11	78499789	78499805	+	1	NA	exon (NM_011707, exon 3 of 8)	exon (NM_011707, exon 3 of 8)	677	NM_011707	22370	Mm.3667	NM_011707	ENSMUSG00000017344	Vtn	AI256434|Vn	vitronectin	protein-coding
mm_79826.1	chr9	64546896	64546901	+	1	NA	intron (NM_001134399, intron 5 of 24)	intron (NM_001134399, intron 5 of 24)	161272	NM_001134399	214058	Mm.127721	NM_172522	ENSMUSG00000036466	Megf11	2410080H04Rik|D130061K05	multiple EGF-like-domains 11	protein-coding
mm_121736.1	chr14	18331738	18331751	-	1	NA	promoter-TSS (NM_009455)	promoter-TSS (NM_009455)	100	NM_009455	22194	Mm.4429	NM_009455	ENSMUSG00000021774	Ube2e1	UbcM3|Ubce5|ubcM2	ubiquitin-conjugating enzyme E2E 1	protein-coding
mm_51785.1	chr6	88199722	88199733	+	1	NA	exon (NM_008090, exon 2 of 6)	exon (NM_008090, exon 2 of 6)	1063	NM_008090	14461	Mm.491156	NM_008090	ENSMUSG00000015053	Gata2	Gata-2	GATA binding protein 2	protein-coding
mm_11808.1	chr2	43917527	43917568	+	1	NA	intron (NM_001301832, intron 7 of 14)	B1_Mur3|SINE|Alu	147777	NR_040622	320872	Mm.445023	NR_040622	ENSMUSG00000085089	Arhgap15os	A430092G05Rik	Rho GTPase activating protein 15, opposite strand	ncRNA
mm_32188.1	chr4	101185573	101185576	+	1	NA	intron (NM_146145, intron 4 of 24)	intron (NM_146145, intron 4 of 24)	79708	NM_146145	16451	Mm.289657	NM_146145	ENSMUSG00000028530	Jak1	AA960307|BAP004|C130039L05Rik	Janus kinase 1	protein-coding
mm_103643.1	chr11	78965734	78965754	-	1	NA	exon (NM_010708, exon 10 of 11)	exon (NM_010708, exon 10 of 11)	19180	NM_001159301	16859	Mm.341434	NM_010708	ENSMUSG00000001123	Lgals9	AA407335|AI194909|AI265545|LGALS35|Lgals5|gal-9|galectin-9	lectin, galactose binding, soluble 9	protein-coding
mm_77705.1	chr8	126591635	126591645	-	1	NA	exon (NM_001164598, exon 2 of 2)	exon (NM_001164598, exon 2 of 2)	1796	NM_001164598	270110	Mm.334918	NM_001164598	ENSMUSG00000051495	Irf2bp2	E130305N23Rik|IRF-2BP2	interferon regulatory factor 2 binding protein 2	protein-coding
mm_104894.1	chr11	99591376	99591380	-	1	NA	promoter-TSS (NM_001085526)	promoter-TSS (NM_001085526)	-1	NM_001085526	435273		NM_001085526	ENSMUSG00000078131	Krtap1-3	-	keratin associated protein 1-3	protein-coding
mm_21921.1	chr2	166905852	166905874	-	1	NA	promoter-TSS (NM_023565)	promoter-TSS (NM_023565)	-233	NM_023565	110750	Mm.22417	NM_023565	ENSMUSG00000002718	Cse1l	2610100P18Rik|AA407533|Capts|Cas|Xpo2	chromosome segregation 1-like (S. cerevisiae)	protein-coding
mm_114205.1	chr13	56104319	56104335	+	1	NA	exon (NM_001159515, exon 4 of 9)	exon (NM_001159515, exon 4 of 9)	31223	NM_012015	26914	Mm.283802	NM_012015	ENSMUSG00000015937	H2afy	H2AF12M|mH2a1|macroH2A1	H2A histone family, member Y	protein-coding
mm_133373.1	chr16	84709906	84709910	+	1	NA	Intergenic	Intergenic	-3115	NR_132106	100653389	Mm.261808	NR_132106	ENSMUSG00000097418	Mir155hg	Bic|Gm26667	Mir155 host gene (non-protein coding)	ncRNA
mm_140044.1	chr17	74489596	74489606	+	1	NA	5' UTR (NM_026417, exon 1 of 6)	5' UTR (NM_026417, exon 1 of 6)	108	NM_026417	67864	Mm.41891	NM_026417	ENSMUSG00000024072	Yipf4	2310034L04Rik	Yip1 domain family, member 4	protein-coding
mm_29230.1	chr3	107213467	107213471	-	1	NA	exon (NM_001111143, exon 7 of 9)	exon (NM_001111143, exon 7 of 9)	8263	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_52376.1	chr6	113077632	113077642	+	1	NA	promoter-TSS (NR_027008)	promoter-TSS (NR_027008)	-2	NM_028385	72895	Mm.367159	NM_028385	ENSMUSG00000034269	Setd5	2900045N06Rik|C330007C20|C85544|mKIAA1757	SET domain containing 5	protein-coding
mm_138270.1	chr17	34604796	34604809	+	1	NA	Intergenic	Intergenic	-1059	NM_001163379	55979	Mm.8684	NM_018862	ENSMUSG00000034254	Agpat1	1-AGP|1-AGPAT|AW047140	1-acylglycerol-3-phosphate O-acyltransferase 1 (lysophosphatidic acid acyltransferase, alpha)	protein-coding
mm_95995.1	chr11	59208330	59208355	+	1	NA	promoter-TSS (NM_024210)	promoter-TSS (NM_024210)	-19	NM_024210	67862	Mm.358708	NM_024210	ENSMUSG00000020441	2310033P09Rik	Mmtag2	RIKEN cDNA 2310033P09 gene	protein-coding
mm_166659.1	chr6	88060867	88060873	+	1	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	-15600	NM_009005	19349	Mm.333233	NM_009005	ENSMUSG00000079477	Rab7	Rab7a	RAB7, member RAS oncogene family	protein-coding
mm_109385.1	chr12	109736736	109736739	+	1	NA	intron (NR_028265, intron 1 of 7)	intron (NR_028265, intron 1 of 7)	1118	NR_030559	100124484		NR_030559	ENSMUSG00000077925	Mir453	Mirn453|mmu-mir-453	microRNA 453	ncRNA
mm_126275.1	chr15	79166035	79166063	+	1	NA	promoter-TSS (NR_029470)	promoter-TSS (NR_029470)	-17	NR_029470	100041655	Mm.483310	NR_029470	ENSMUSG00000075555	Gm10863	ENSMUSG00000075555	predicted gene 10863	ncRNA
mm_41241.1	chr5	88765193	88765199	+	1	NA	5' UTR (NM_007832, exon 1 of 7)	5' UTR (NM_007832, exon 1 of 7)	183	NM_007832	13178	Mm.298892	NM_007832	ENSMUSG00000029366	Dck	-	deoxycytidine kinase	protein-coding
mm_28727.1	chr3	95710697	95710699	-	1	NA	Intergenic	RMER20B|LTR|ERVK	-22781	NM_001301705	229595	Mm.490574	NM_144899	ENSMUSG00000015850	Adamtsl4	ADAMTSL-4|Tsrc1	ADAMTS-like 4	protein-coding
mm_43268.1	chr5	130369523	130369525	+	1	NA	promoter-TSS (NM_181045)	promoter-TSS (NM_181045)	66	NM_181045	140904	Mm.40875	NM_021371	ENSMUSG00000060371	Caln1	9630012C17Rik|Cabp8|MNCb-0849	calneuron 1	protein-coding
mm_55431.1	chr6	65779715	65779723	-	1	NA	intron (NM_029549, intron 1 of 10)	intron (NM_029549, intron 1 of 10)	757	NM_029549	70779	Mm.263355	NM_027547	ENSMUSG00000029913	Prdm5	4432417F03Rik|6530401I24Rik|AI197291|E130112L17Rik|PFM2	PR domain containing 5	protein-coding
mm_1455.1	chr1	67230763	67230787	+	1	NA	3' UTR (NM_001080809, exon 38 of 38)	3' UTR (NM_001080809, exon 38 of 38)	107748	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_99713.1	chr11	106256125	106256135	+	1	NA	promoter-TSS (NM_025310)	promoter-TSS (NM_025310)	-55	NM_008950	19184	Mm.272361	NM_008950	ENSMUSG00000020708	Psmc5	mSUG1	protease (prosome, macropain) 26S subunit, ATPase 5	protein-coding
mm_8953.1	chr1	164458346	164458363	-	1	NA	promoter-TSS (NM_009721)	promoter-TSS (NM_009721)	1	NM_009721	11931	Mm.4550	NM_009721	ENSMUSG00000026576	Atp1b1	Atp4b|Atpb|Atpb-1|NKbeta1	ATPase, Na+/K+ transporting, beta 1 polypeptide	protein-coding
mm_113383.1	chr13	33027409	33027419	+	1	NA	promoter-TSS (NM_011452)	promoter-TSS (NM_011452)	0	NM_011452	20706	Mm.45371	NM_011452	ENSMUSG00000021403	Serpinb9b	1600019A21Rik|R86|SPI-CI|Spi10|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 9b	protein-coding
mm_92261.1	chr10	71058521	71058524	-	1	NA	intron (NM_031397, intron 2 of 20)	intron (NM_031397, intron 2 of 20)	101168	NM_031397	83675	Mm.286834	NM_031397	ENSMUSG00000014329	Bicc1	Bic-C|bpk|jcpk	BicC family RNA binding protein 1	protein-coding
mm_99485.1	chr11	102665535	102665560	+	1	NA	promoter-TSS (NM_001127576)	promoter-TSS (NM_001127576)	-38	NM_001127576	268491	Mm.447643	NM_001127576	ENSMUSG00000051455	Meioc	Gm1564|Gm663	meiosis specific with coiled-coil domain	protein-coding
mm_10616.1	chr2	19344318	19344326	+	1	NA	promoter-TSS (NR_126563)	promoter-TSS (NR_126563)	5	NR_126563	108871	Mm.107666	NR_126563		4930447M23Rik	-	RIKEN cDNA 4930447M23 gene	ncRNA
mm_1628.1	chr1	74423926	74423934	+	1	NA	exon (NM_009509, exon 12 of 20)	exon (NM_009509, exon 12 of 20)	14546	NM_009509	22349	Mm.471601	NM_009509	ENSMUSG00000026175	Vil1	Vil	villin 1	protein-coding
mm_97846.1	chr11	83066414	83066434	+	1	NA	intron (NM_011408, intron 1 of 1)	G-rich|Low_complexity|Low_complexity	1312	NM_011408	20556	Mm.278689	NM_011408	ENSMUSG00000072620	Slfn2	Shlf2	schlafen 2	protein-coding
mm_109486.1	chr12	111442424	111442435	+	1	NA	promoter-TSS (NM_009396)	promoter-TSS (NM_009396)	-232	NM_009396	21928	Mm.255332	NM_009396	ENSMUSG00000021281	Tnfaip2	B94|Exoc3l3|M-sec|Tnfip2|tnfb94	tumor necrosis factor, alpha-induced protein 2	protein-coding
mm_141502.1	chr17	31633155	31633176	-	1	NA	intron (NM_178224, intron 1 of 15)	L1M4|LINE|L1	4040	NM_144855	12411	Mm.206417	NM_144855	ENSMUSG00000024039	Cbs	AI047524|AI303044|HIP4	cystathionine beta-synthase	protein-coding
mm_26835.1	chr3	11214203	11214211	-	1	NA	Intergenic	RLTR9E|LTR|ERVK	630152	NR_040751	100038545	Mm.388494	NR_040751	ENSMUSG00000104015	Gm10745	ENSMUSG00000074696	predicted gene 10745	ncRNA
mm_166055.1	chr4	132794286	132794296	+	1	NA	intron (NM_001033308, intron 1 of 5)	intron (NM_001033308, intron 1 of 5)	2073	NM_001033308	230787	Mm.290912	NM_001033308	ENSMUSG00000037731	Themis2	ICB-1	thymocyte selection associated family member 2	protein-coding
mm_13394.1	chr2	103970093	103970103	+	1	NA	promoter-TSS (NM_008505)	promoter-TSS (NM_008505)	-189	NM_008505	16909	Mm.29266	NM_008505	ENSMUSG00000032698	Lmo2	Rbtn-2|Rbtn2|Rhom-2|Ttg2	LIM domain only 2	protein-coding
mm_84655.1	chr9	71631102	71631115	-	1	NA	intron (NM_001304362, intron 16 of 18)	intron (NM_001304362, intron 16 of 18)	-38748	NM_001033208	102371	Mm.27585	NM_001033208	ENSMUSG00000041361	Myzap	AA407270|AV006038|Gcom1|Gm640|Grinl1a7|Myozap	myocardial zonula adherens protein	protein-coding
mm_61955.1	chr7	90207906	90207916	+	1	NA	3' UTR (NM_001252521, exon 20 of 20)	3' UTR (NM_001252521, exon 20 of 20)	57521	NM_029256	75338	Mm.487222	NM_029256	ENSMUSG00000030617	Ccdc83	4930549K11Rik|4930554C01Rik|4932423M01Rik	coiled-coil domain containing 83	protein-coding
mm_59258.1	chr7	24870132	24870141	+	1	NA	promoter-TSS (NM_027732)	promoter-TSS (NM_027732)	79	NM_027732	71241	Mm.66855	NM_027732	ENSMUSG00000011349	Dmrtc2	4933432E21Rik|Dmrt7	doublesex and mab-3 related transcription factor like family C2	protein-coding
mm_65325.1	chr7	24972581	24972616	-	1	NA	5' UTR (NM_010261, exon 1 of 5)	5' UTR (NM_010261, exon 1 of 5)	130	NM_010261	14470	Mm.22473	NM_010261	ENSMUSG00000003380	Rabac1	2310040I06Rik|Gbpap1|PRA1|prenylin	Rab acceptor 1 (prenylated)	protein-coding
mm_152103.1	chr19	6925312	6925321	-	1	NA	promoter-TSS (NM_001039494)	promoter-TSS (NM_001039494)	64	NM_001039494	67077	Mm.251306	NM_001039494	ENSMUSG00000050623	Tex40	1700019N12Rik|A430107B04Rik|MLZ-622	testis expressed 40	protein-coding
mm_33540.1	chr4	130934509	130934532	+	1	NA	exon (NM_010686, exon 8 of 8)	exon (NM_010686, exon 8 of 8)	-9865	NM_010769	17180	Mm.271796	NM_010769	ENSMUSG00000040533	Matn1	CMP|Crtm|Mat1|matrilin-1	matrilin 1, cartilage matrix protein	protein-coding
mm_127210.1	chr15	99233891	99233904	+	1	NA	exon (NM_010601, exon 10 of 15)	exon (NM_010601, exon 10 of 15)	8921	NM_010601	16512	Mm.374793	NM_010601	ENSMUSG00000037579	Kcnh3	AU019351|C030044P22Rik|Elk2|Kv12.2|Melk2	potassium voltage-gated channel, subfamily H (eag-related), member 3	protein-coding
mm_101586.1	chr11	34544846	34544903	-	1	NA	intron (NM_033374, intron 22 of 51)	RLTR44-int|LTR|ERVK	230052	NM_001025382	574403	Mm.444796	NM_001025382	ENSMUSG00000069911	Fam196b	EG574403|Gm6041	family with sequence similarity 196, member B	protein-coding
mm_134688.1	chr16	22439732	22439733	-	1	NA	promoter-TSS (NM_023794)	promoter-TSS (NM_023794)	-162	NM_023794	104156	Mm.155708	NM_023794	ENSMUSG00000013089	Etv5	1110005E01Rik|8430401F14Rik|ERM	ets variant 5	protein-coding
mm_138821.1	chr17	39847682	39847695	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	4691	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_165044.1	chr19	39510827	39510833	+	1	NA	promoter-TSS (NM_010003)	promoter-TSS (NM_010003)	8	NM_010003	13098	Mm.42101	NM_010003	ENSMUSG00000025003	Cyp2c39	CYPIIC39	cytochrome P450, family 2, subfamily c, polypeptide 39	protein-coding
mm_146570.1	chr18	6516068	6516083	-	1	NA	promoter-TSS (NM_007935)	promoter-TSS (NM_007935)	33	NM_007935	13831	Mm.312133	NM_007935	ENSMUSG00000024240	Epc1	2400007E14Rik|5730566F07Rik|A930032N02Rik|mir-1893	enhancer of polycomb homolog 1 (Drosophila)	protein-coding
mm_164981.1	chr19	8839454	8839458	-	1	NA	promoter-TSS (NM_010316)	promoter-TSS (NM_010316)	128	NM_008144	14705	Mm.345134	NM_008144	ENSMUSG00000071657	Bscl2	2900097C17Rik|AI046355|Gng3lg	Berardinelli-Seip congenital lipodystrophy 2 (seipin)	protein-coding
mm_49941.1	chr6	39871462	39871506	+	1	NA	Intergenic	CpG	-60548	NM_001010930	14548	Mm.377071	NM_010270	ENSMUSG00000029918	Mrps33	AI841153|CGI-139|Gdap3|MRP-S33|PTD003	mitochondrial ribosomal protein S33	protein-coding
mm_138960.1	chr17	44192720	44192722	+	1	NA	intron (NM_172621, intron 1 of 5)	intron (NM_172621, intron 1 of 5)	4149	NM_172621	224796	Mm.37666	NM_172621	ENSMUSG00000023959	Clic5	5730531E12Rik|B330005L24|Gm322|jbg	chloride intracellular channel 5	protein-coding
mm_48069.1	chr5	136581684	136581688	-	1	NA	Intergenic	Intergenic	-14196	NM_001291238	13047	Mm.320317	NM_009986	ENSMUSG00000029705	Cux1	CDP|Cutl1|Cux|Cux-1	cut-like homeobox 1	protein-coding
mm_164276.1	chr15	101858034	101858040	+	1	NA	Intergenic	Intergenic	-7251	NM_008473	16678	Mm.183137	NM_008473	ENSMUSG00000046834	Krt1	Krt-2.1|Krt2-1|Krt86	keratin 1	protein-coding
mm_40731.1	chr5	66150786	66150810	+	1	NA	5' UTR (NM_001291226, exon 1 of 6)	5' UTR (NM_001291226, exon 1 of 6)	180	NM_001291226	245945	Mm.36863	NM_139065	ENSMUSG00000070780	Rbm47	9530077J19Rik	RNA binding motif protein 47	protein-coding
mm_118685.1	chr14	22120435	22120445	+	1	NA	intron (NM_028275, intron 2 of 6)	B3|SINE|B2	100728	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_172582.1	chr8	122589697	122589712	+	1	NA	intron (NM_001193645, intron 9 of 11)	MTC|LTR|ERVL-MaLR	-12797	NM_009698	11821	Mm.1786	NM_009698	ENSMUSG00000006589	Aprt	C85684	adenine phosphoribosyl transferase	protein-coding
mm_35626.1	chr4	43454914	43454928	-	1	NA	promoter-TSS (NM_001110320)	promoter-TSS (NM_001110320)	-295	NM_007654	12517	Mm.188157	NM_007654	ENSMUSG00000028459	Cd72	CD72c|Ly-19|Ly-32|Ly-m19|Lyb-2	CD72 antigen	protein-coding
mm_115074.1	chr13	101664254	101664263	+	1	NA	Intergenic	Intergenic	28372	NM_001024955	18708	Mm.259333	NM_001024955	ENSMUSG00000041417	Pik3r1	PI3K|p50alpha|p55alpha|p85alpha	phosphatidylinositol 3-kinase, regulatory subunit, polypeptide 1 (p85 alpha)	protein-coding
mm_120190.1	chr14	61598243	61598252	+	1	NA	promoter-TSS (NM_001164220)	promoter-TSS (NM_001164220)	21	NM_001164220	66597	Mm.491258	NM_023233	ENSMUSG00000035235	Trim13	3110001L12Rik|CAR|LEU5|RNF77|Rfp2	tripartite motif-containing 13	protein-coding
mm_88378.1	chr10	76388838	76388847	+	1	NA	promoter-TSS (NR_040580)	promoter-TSS (NR_040580)	-173	NR_040580	67523	Mm.437833	NR_040580	ENSMUSG00000101695	1700094J05Rik	-	RIKEN cDNA 1700094J05 gene	ncRNA
mm_108014.1	chr12	73593627	73593637	+	1	NA	intron (NM_008856, intron 1 of 13)	intron (NM_008856, intron 1 of 13)	8836	NM_008856	18755	Mm.341677	NM_008856	ENSMUSG00000021108	Prkch	Pkch	protein kinase C, eta	protein-coding
mm_137164.1	chr17	23807069	23807122	+	1	NA	intron (NM_175229, intron 1 of 13)	CpG	3908	NM_175229	75956	Mm.5222	NM_175229	ENSMUSG00000039218	Srrm2	5033413A03Rik|AA410130|SRm300|mKIAA0324	serine/arginine repetitive matrix 2	protein-coding
mm_87103.1	chr10	33158245	33158250	+	1	NA	exon (NM_029726, exon 4 of 38)	exon (NM_029726, exon 4 of 38)	74764	NM_029726	76757	Mm.338508	NM_029726	ENSMUSG00000019787	Trdn	2310045H21Rik|EG432451|TDN	triadin	protein-coding
mm_158438.1	chrX	140062585	140062605	-	1	NA	promoter-TSS (NM_001081668)	promoter-TSS (NM_001081668)	-27	NM_001081668	279706	Mm.102590	NM_001081668	ENSMUSG00000072944	Nup62cl	Gm719	nucleoporin 62 C-terminal like	protein-coding
mm_52746.1	chr6	120489079	120489113	+	1	NA	3' UTR (NM_033567, exon 1 of 1)	3' UTR (NM_033567, exon 1 of 1)	4711	NM_033567	94047	Mm.23088	NM_033567	ENSMUSG00000094626	Cecr6	AW048664	cat eye syndrome chromosome region, candidate 6	protein-coding
mm_165937.1	chr4	74043434	74043435	-	1	NA	intron (NM_172869, intron 1 of 13)	intron (NM_172869, intron 1 of 13)	29831	NM_172869	242506	Mm.221597	NM_172869	ENSMUSG00000049122	Frmd3	4.1O|9430066I12Rik|EPB41L4O|P410	FERM domain containing 3	protein-coding
mm_106171.1	chr11	116679222	116679226	-	1	NA	intron (NM_009180, intron 7 of 8)	intron (NM_009180, intron 7 of 8)	4627	NR_028570	100216538		NR_028570	ENSMUSG00000065094	Snord1a	snR38	small nucleolar RNA, C/D box 1A	snoRNA
mm_21940.1	chr2	167060418	167060430	-	1	NA	intron (NM_001033196, intron 1 of 13)	intron (NM_001033196, intron 1 of 13)	-2510	NR_138563	68949	Mm.391959	NM_001081005		Zfas1	1500012F01Rik|Zfos1	zinc finger, NFX1-type containing 1, antisense RNA 1	ncRNA
mm_99312.1	chr11	101377222	101377231	+	1	NA	3' UTR (NM_008061, exon 5 of 5)	3' UTR (NM_008061, exon 5 of 5)	9510	NM_008061	14377	Mm.18064	NM_008061	ENSMUSG00000078650	G6pc	AW107337|G6Pase|G6pt|Glc-6-Pase	glucose-6-phosphatase, catalytic	protein-coding
mm_73241.1	chr8	104170539	104170612	+	1	NA	promoter-TSS (NM_001141925)	promoter-TSS (NM_001141925)	62	NM_001141925	65115	Mm.41849	NM_001141922	ENSMUSG00000031872	Bean1	Bean	brain expressed, associated with Nedd4, 1	protein-coding
mm_116927.1	chr13	55571119	55571123	-	1	NA	promoter-TSS (NM_145382)	promoter-TSS (NM_145382)	-1	NM_145382	212483	Mm.35661	NM_145382	ENSMUSG00000021495	Fam193b	IRIZIO|Kiaa1931	family with sequence similarity 193, member B	protein-coding
mm_161474.1	chr15	79765129	79765129	-	1	NA	intron (NM_017470, intron 1 of 3)	intron (NM_017470, intron 1 of 3)	9338	NM_017470	54152	Mm.288159	NM_017470	ENSMUSG00000022420	Dnal4	D15Ertd424e|Dnalc4	dynein, axonemal, light chain 4	protein-coding
mm_49937.1	chr6	39573895	39573940	+	1	NA	promoter-TSS (NM_178873)	promoter-TSS (NM_178873)	41	NM_178873	57869	Mm.247957	NM_178873	ENSMUSG00000046947	Adck2	AA408112|BB006057	aarF domain containing kinase 2	protein-coding
mm_169655.1	chr15	56886125	56886138	+	1	NA	Intergenic	L1Md_T|LINE|L1	-191585	NM_008216	15117	Mm.5148	NM_008216	ENSMUSG00000022367	Has2	-	hyaluronan synthase 2	protein-coding
mm_50261.1	chr6	43382467	43382552	+	1	NA	intron (NM_001311111, intron 7 of 7)	ORR1D1|LTR|ERVL-MaLR	-59920	NR_045988	319812	Mm.446393	NR_045988		9430018G01Rik	-	RIKEN cDNA 9430018G01 gene	ncRNA
mm_38403.1	chr4	138972806	138972834	-	1	NA	promoter-TSS (NM_029857)	promoter-TSS (NM_029857)	-85	NM_029857	77056	Mm.122336	NM_029857	ENSMUSG00000041143	Tmco4	4632413C14Rik|AI430825	transmembrane and coiled-coil domains 4	protein-coding
mm_55876.1	chr6	83512935	83512974	-	1	NA	TTS (NM_009610)	TTS (NM_009610)	-5985	NM_001162521	27369	Mm.42234	NM_013764	ENSMUSG00000014554	Dguok	dGK|dGK1|dGK2|dGK3	deoxyguanosine kinase	protein-coding
mm_122684.1	chr14	52014977	52015003	-	1	NA	promoter-TSS (NM_001253695)	promoter-TSS (NM_001253695)	-432	NM_001253695	69890	Mm.475652	NM_027248	ENSMUSG00000049295	Zfp219	2010302A17Rik	zinc finger protein 219	protein-coding
mm_18754.1	chr2	73437215	73437236	-	1	NA	exon (NM_153138, exon 5 of 8)	exon (NM_153138, exon 5 of 8)	16664	NM_001289722	215280	Mm.223504	NM_153138	ENSMUSG00000075284	Wipf1	AI115543|D2Ertd120e|WIP|Waspip	WAS/WASL interacting protein family, member 1	protein-coding
mm_58068.1	chr6	136922201	136922220	-	1	NA	promoter-TSS (NM_026983)	promoter-TSS (NM_026983)	-30	NM_026983	69187	Mm.33692	NM_026983	ENSMUSG00000030219	Erp27	1810033M07Rik|1810047B09Rik	endoplasmic reticulum protein 27	protein-coding
mm_121097.1	chr14	99314277	99314285	+	1	NA	TTS (NM_009769)	TTS (NM_009769)	15590	NM_009769	12224	Mm.30262	NM_009769	ENSMUSG00000005148	Klf5	4930520J07Rik|Bteb2|CKLF|IKLF	Kruppel-like factor 5	protein-coding
mm_131930.1	chr16	23610001	23610032	+	1	NA	promoter-TSS (NM_023386)	promoter-TSS (NM_023386)	97	NM_023386	67775	Mm.475107	NM_023386	ENSMUSG00000033355	Rtp4	5830458K16Rik|Ifrg28	receptor transporter protein 4	protein-coding
mm_27701.1	chr3	66981742	66981788	-	1	NA	promoter-TSS (NM_013665)	promoter-TSS (NM_013665)	6	NM_013665	20429	Mm.39093	NM_013665	ENSMUSG00000027833	Shox2	6330543G17Rik|OG12|Og12x|Prx3|SHOT	short stature homeobox 2	protein-coding
mm_92966.1	chr10	86057636	86057648	-	1	NA	exon (NM_013722, exon 13 of 14)	exon (NM_013722, exon 13 of 14)	35488	NM_001347151	69754	Mm.44236	NM_153195	ENSMUSG00000001786	Fbxo7	2410015K21Rik|A230052G17Rik|AI117679|AW260462|C85118	F-box protein 7	protein-coding
mm_97234.1	chr11	75655912	75655918	+	1	NA	promoter-TSS (NM_001080775)	promoter-TSS (NM_001080775)	-100	NM_001080775	17913	Mm.234502	NM_008659	ENSMUSG00000017774	Myo1c	C80397|MMIb|MYO1E|NMI|mm1beta|myr2	myosin IC	protein-coding
mm_15252.1	chr2	154805254	154805269	+	1	NA	intron (NM_001139511, intron 1 of 7)	intron (NM_001139511, intron 1 of 7)	14151	NM_001139511	19383	Mm.221440	NM_023130	ENSMUSG00000027593	Raly	AI663842|Merc	hnRNP-associated with lethal yellow	protein-coding
mm_86447.1	chr10	4266354	4266374	+	1	NA	promoter-TSS (NM_031185)	promoter-TSS (NM_031185)	35	NM_031185	83397	Mm.27481	NM_031185	ENSMUSG00000038587	Akap12	AI317366|SSeCKS|Srcs5|Tsga12	A kinase (PRKA) anchor protein (gravin) 12	protein-coding
mm_84940.1	chr9	82975115	82975153	-	1	NA	exon (NM_001081216, exon 2 of 40)	exon (NM_001081216, exon 2 of 40)	355	NM_001081216	83946	Mm.221688	NM_031879	ENSMUSG00000032253	Phip	2810004D21Rik|4632404O06Rik|Ndrp|Wdr11	pleckstrin homology domain interacting protein	protein-coding
mm_156567.1	chrX	151906305	151906318	+	1	NA	exon (NM_021523, exon 52 of 83)	exon (NM_021523, exon 52 of 83)	-6035	NR_029732	387253		NR_029732	ENSMUSG00000065602	Mirlet7f-2	Mirlet7f2|Mirnlet7f2|let-7f-2	microRNA let7f-2	ncRNA
mm_63153.1	chr7	123418207	123418228	+	1	NA	intron (NM_025304, intron 6 of 10)	intron (NM_025304, intron 6 of 10)	40235	NM_025304	30949	Mm.260527	NM_025304	ENSMUSG00000030763	Lcmt1	AL033290|LCMT-1|Lcmt	leucine carboxyl methyltransferase 1	protein-coding
mm_47406.1	chr5	123132384	123132403	-	1	NA	5' UTR (NM_175092, exon 1 of 5)	5' UTR (NM_175092, exon 1 of 5)	236	NM_175092	23912	Mm.253876	NM_175092	ENSMUSG00000029449	Rhof	AI845056|AV026554|Arhf|Ifld1|Rif	ras homolog family member F (in filopodia)	protein-coding
mm_150969.1	chr19	46500827	46500837	+	1	NA	promoter-TSS (NM_053100)	promoter-TSS (NM_053100)	-816	NM_053100	93679	Mm.392177	NM_053100	ENSMUSG00000025034	Trim8	AA408830|BB006755|GERP|Rnf27	tripartite motif-containing 8	protein-coding
mm_159746.1	chr5	75152936	75152936	+	1	NA	promoter-TSS (NM_001347719)	promoter-TSS (NM_001347719)	0	NM_001347719	18595	Mm.221403	NM_011058	ENSMUSG00000029231	Pdgfra	AI115593|CD140a|Pdgfr-2	platelet derived growth factor receptor, alpha polypeptide	protein-coding
mm_30301.1	chr3	149077237	149077266	-	1	NA	Intergenic	Intergenic	-122616	NM_001081298	99633	Mm.9776	NM_001081298	ENSMUSG00000028184	Adgrl2	AI450192|CIRL-2|Gm619|Lec1|Lphh1|Lphn2|mKIAA0786	adhesion G protein-coupled receptor L2	protein-coding
mm_154419.1	chrM	16099	16107	+	1	NA	NA	Intergenic	NA	NA								
mm_85634.1	chr9	107651664	107651684	-	1	NA	3' UTR (NM_001199218, exon 16 of 16)	3' UTR (NM_001199218, exon 16 of 16)	15725	NM_023805	76257	Mm.296560	NM_023805	ENSMUSG00000010064	Slc38a3	0610012J02Rik|D9Ucla2|Nat1|Slc38-3|Sn1|Snat3|mNAT	solute carrier family 38, member 3	protein-coding
mm_140563.1	chr17	8283616	8283634	-	1	NA	promoter-TSS (NM_018819)	promoter-TSS (NM_018819)	-188	NM_018819	55951	Mm.288510	NM_018819	ENSMUSG00000023861	Mpc1	0610006G08Rik|3830411I18Rik|Brp44l	mitochondrial pyruvate carrier 1	protein-coding
mm_105736.1	chr11	109298091	109298118	-	1	NA	promoter-TSS (NM_011268)	promoter-TSS (NM_011268)	77	NM_001165934	19739	Mm.38548	NM_011268	ENSMUSG00000020599	Rgs9	RGS9-1|Rgs9-2	regulator of G-protein signaling 9	protein-coding
mm_116674.1	chr13	49215979	49216052	-	1	NA	promoter-TSS (NM_026738)	promoter-TSS (NM_026738)	11	NM_026738	68480	Mm.3336	NM_026738	ENSMUSG00000037960	Card19	1110007C09Rik|AI851695|Bincard	caspase recruitment domain family, member 19	protein-coding
mm_21317.1	chr2	157099140	157099153	-	1	NA	3' UTR (NM_001139520, exon 17 of 17)	3' UTR (NM_001139520, exon 17 of 17)	12091	NM_001177439	383766	Mm.480305	NM_001177439	ENSMUSG00000074628	Tldc2	Gm1332	TBC/LysM associated domain containing 2	protein-coding
mm_132433.1	chr16	35871458	35871482	+	1	NA	promoter-TSS (NM_001039530)	promoter-TSS (NM_001039530)	-88	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_83959.1	chr9	57071880	57071905	-	1	NA	promoter-TSS (NM_001110351)	promoter-TSS (NM_001110351)	74	NR_045886	100038566	Mm.361900	NR_045886		Gm10658	ENSMUSG00000074284	predicted gene 10658	ncRNA
mm_25902.1	chr3	131111518	131111531	+	1	NA	exon (NM_001276402, exon 1 of 10)	exon (NM_001276402, exon 1 of 10)	1227	NM_001276402	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_166145.1	chr5	3571561	3571564	+	1	NA	promoter-TSS (NM_029843)	promoter-TSS (NM_029843)	-154	NM_029843	77036	Mm.389069	NM_029843	ENSMUSG00000008307	1700109H08Rik	-	RIKEN cDNA 1700109H08 gene	protein-coding
mm_124250.1	chr14	101640671	101640700	-	1	NA	promoter-TSS (NM_001168592)	promoter-TSS (NM_001168592)	-214	NM_001168592	66200	Mm.250474	NM_001033132	ENSMUSG00000075486	Commd6	1110059J08Rik|1700063H17Rik	COMM domain containing 6	protein-coding
mm_170013.1	chr17	17294415	17294432	+	1	NA	promoter-TSS (NM_001324550)	promoter-TSS (NM_001324550)	-20	NM_001324550	100862203	Mm.484235	NM_001324550		Gm6712	EG626854	predicted gene 6712	protein-coding
mm_23180.1	chr3	40800779	40800786	+	1	NA	intron (NM_173169, intron 1 of 15)	intron (NM_173169, intron 1 of 15)	831	NR_045576	20873	Mm.3794	NM_011495	ENSMUSG00000025758	Plk4	1700028H20|AI385771|Sak|Stk18	polo-like kinase 4	protein-coding
mm_36026.1	chr4	57077221	57077260	-	1	NA	exon (NM_019427, exon 8 of 16)	exon (NM_019427, exon 8 of 16)	65916	NM_019427	54357	Mm.28217	NM_019427	ENSMUSG00000028434	Epb41l4b	6430543G08Rik|AA589614|AU021054|BB007528|D4Ertd346e|Ehm2|Epb4.1l4b|Lulu2	erythrocyte membrane protein band 4.1 like 4b	protein-coding
mm_47885.1	chr5	134703389	134703406	-	1	NA	3' UTR (NM_007925, exon 37 of 37)	3' UTR (NM_007925, exon 37 of 37)	-14807	NM_010717	16885	Mm.15409	NM_010717	ENSMUSG00000029674	Limk1	KIZ-1|LIMK-1|Limk	LIM-domain containing, protein kinase	protein-coding
mm_81299.1	chr9	108339244	108339247	+	1	NA	5' UTR (NM_008160, exon 1 of 2)	5' UTR (NM_008160, exon 1 of 2)	165	NM_001329528	14775	Mm.1090	NM_008160	ENSMUSG00000063856	Gpx1	AI195024|AL033363|CGPx|GPx-1|GSHPx-1|Gpx	glutathione peroxidase 1	protein-coding
mm_147240.1	chr18	38338935	38338985	-	1	NA	promoter-TSS (NM_011937)	promoter-TSS (NM_011937)	33	NM_011937	26384	Mm.22374	NM_011937	ENSMUSG00000052102	Gnpda1	GNPDA|Gnp1|Gnpi|oscillin	glucosamine-6-phosphate deaminase 1	protein-coding
mm_93030.1	chr10	88135837	88135862	-	1	NA	intron (NM_029249, intron 3 of 10)	intron (NM_029249, intron 3 of 10)	11092	NM_029249	75317	Mm.179378	NM_029249	ENSMUSG00000035365	Parpbp	4930547N16Rik|AI503644|PARI	PARP1 binding protein	protein-coding
mm_108993.1	chr12	102948844	102948874	+	1	NA	promoter-TSS (NM_001081017)	promoter-TSS (NM_001081017)	0	NM_001081017	217843	Mm.387073	NM_177621	ENSMUSG00000021198	Unc79	9030205A07Rik|Mlca3	unc-79 homolog (C. elegans)	protein-coding
mm_57051.1	chr6	122393461	122393474	-	1	NA	Intergenic	Intergenic	-53240	NM_001271579	13619	Mm.6822	NM_007905	ENSMUSG00000040669	Phc1	AW557034|Edr|Edr1|Mph1|Rae-28|rae28	polyhomeotic-like 1 (Drosophila)	protein-coding
mm_132696.1	chr16	43302394	43302406	+	1	NA	intron (NM_181058, intron 1 of 6)	intron (NM_181058, intron 1 of 6)	55116	NM_019778	56490	Mm.136238	NM_019778	ENSMUSG00000022708	Zbtb20	1300017A20Rik|7330412A13Rik|A930017C21Rik|D16Wsu73e|DPZF|HOF|ODA-8S|Oda8|Zfp288	zinc finger and BTB domain containing 20	protein-coding
mm_137396.1	chr17	25823643	25823706	+	1	NA	promoter-TSS (NM_173741)	promoter-TSS (NM_173741)	47	NM_173741	268933	Mm.95512	NM_173741	ENSMUSG00000025737	Wdr24	BC037651	WD repeat domain 24	protein-coding
mm_71517.1	chr8	46846617	46846627	+	1	NA	3' UTR (NM_008391, exon 9 of 9)	3' UTR (NM_008391, exon 9 of 9)	106877	NM_008391	16363	Mm.1149	NM_008391	ENSMUSG00000031627	Irf2	9830146E22Rik|AI646973|Irf-2	interferon regulatory factor 2	protein-coding
mm_127613.1	chr15	102460114	102460122	+	1	NA	5' UTR (NM_025385, exon 3 of 5)	5' UTR (NM_025385, exon 3 of 5)	948	NM_025385	66151	Mm.393955	NM_025385	ENSMUSG00000023048	Prr13	1110020C13Rik|2010324E22Rik	proline rich 13	protein-coding
mm_52468.1	chr6	114131380	114131438	+	1	NA	exon (NM_172890, exon 1 of 14)	exon (NM_172890, exon 1 of 14)	168	NM_172890	243616	Mm.44683	NM_172890	ENSMUSG00000030307	Slc6a11	D930045G19Rik|E130202I16Rik|GAT4|Gabt4|Gat3	solute carrier family 6 (neurotransmitter transporter, GABA), member 11	protein-coding
mm_105965.1	chr11	115474066	115474084	-	1	NA	3' UTR (NM_001080934, exon 4 of 4)	3' UTR (NM_001080934, exon 4 of 4)	-1602	NM_177778	276905	Mm.38019	NM_177778	ENSMUSG00000057219	Armc7	A630084C13|BC023126	armadillo repeat containing 7	protein-coding
mm_139192.1	chr17	47611558	47611568	+	1	NA	promoter-TSS (NM_020048)	promoter-TSS (NM_020048)	-33	NM_020048	56771	Mm.59393	NM_020048	ENSMUSG00000092558	Med20	1110011O05Rik|2410115I17Rik|AU018348|Trfp	mediator complex subunit 20	protein-coding
mm_84434.1	chr9	66069703	66069741	-	1	NA	promoter-TSS (NM_001025612)	promoter-TSS (NM_001025612)	9	NM_001025612	382083	Mm.477103	NM_001025612	ENSMUSG00000039452	Snx22	Gm1120	sorting nexin 22	protein-coding
mm_68166.1	chr7	103812639	103812649	-	1	NA	3' UTR (NM_016956, exon 3 of 3)	3' UTR (NM_016956, exon 3 of 3)	1279	NM_016956	15130	Mm.288567	NM_016956		Hbb-b2	AI036344|Hbb2|Hbbt2|beta2	hemoglobin, beta adult minor chain	protein-coding
mm_42236.1	chr5	113717378	113717414	+	1	NA	intron (NR_033216, intron 2 of 2)	RMER17C|LTR|ERVK	7376	NR_033216	381707	Mm.159016	NR_033216	ENSMUSG00000042184	1700069L16Rik	1700096P12Rik	RIKEN cDNA 1700069L16 gene	ncRNA
mm_123200.1	chr14	59260204	59260228	-	1	NA	promoter-TSS (NM_001164329)	promoter-TSS (NM_001164329)	0	NM_001164329	628693	Mm.479519	NM_001164329	ENSMUSG00000090881	Gm6904	EG628693	predicted gene 6904	protein-coding
mm_49927.1	chr6	39381348	39381366	+	1	NA	promoter-TSS (NM_011226)	promoter-TSS (NM_011226)	-71	NM_011226	19331	Mm.123866	NM_011226	ENSMUSG00000029923	Rab19	-	RAB19, member RAS oncogene family	protein-coding
mm_98630.1	chr11	96081070	96081090	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-5386	NM_007506	11951	Mm.258	NM_007506	ENSMUSG00000006057	Atp5g1	-	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit C1 (subunit 9)	protein-coding
mm_96922.1	chr11	70505315	70505332	+	1	NA	promoter-TSS (NM_029360)	promoter-TSS (NM_029360)	49	NM_029360	75604	Mm.24400	NM_029360	ENSMUSG00000018919	Tm4sf5	2010003F10Rik|AI323987	transmembrane 4 superfamily member 5	protein-coding
mm_85197.1	chr9	96732175	96732201	-	1	NA	promoter-TSS (NM_175537)	promoter-TSS (NM_175537)	-513	NM_175537	245007	Mm.485954	NM_175537	ENSMUSG00000040433	Zbtb38	A930014K01Rik|CIBZ	zinc finger and BTB domain containing 38	protein-coding
mm_36443.1	chr4	82374112	82374149	-	1	NA	intron (NM_001113210, intron 3 of 11)	B4A|SINE|B4	131649	NM_001286127	18028	Mm.317947	NM_008687	ENSMUSG00000008575	Nfib	6720429L07Rik|CTF|E030026I10Rik|NF-I/B|NF1-B|NFI-B	nuclear factor I/B	protein-coding
mm_88870.1	chr10	81010283	81010284	+	1	NA	intron (NM_010319, intron 1 of 3)	B4A|SINE|B4	4642	NM_010319	14708	Mm.222496	NM_010319	ENSMUSG00000048240	Gng7	AI840417	guanine nucleotide binding protein (G protein), gamma 7	protein-coding
mm_118588.1	chr14	20640995	20641021	+	1	NA	Intergenic	CpG	15532	NM_021508	59011	Mm.439911	NM_021508	ENSMUSG00000068697	Myoz1	2310001N11Rik|AV090278|FATZ|Myoz	myozenin 1	protein-coding
mm_82934.1	chr9	35199878	35199920	-	1	NA	promoter-TSS (NM_001177847)	promoter-TSS (NM_001177847)	6	NM_001177847	117149	Mm.23987	NM_054096	ENSMUSG00000032041	Tirap	AA407980|C130027E04Rik|Mal|Tlr4ap|Wyatt	toll-interleukin 1 receptor (TIR) domain-containing adaptor protein	protein-coding
mm_72068.1	chr8	71488716	71488743	+	1	NA	5' UTR (NM_032544, exon 1 of 9)	5' UTR (NM_032544, exon 1 of 9)	626	NM_032544	70359	Mm.142112	NM_032544	ENSMUSG00000007610	Gtpbp3	2410009F13Rik|AI607903	GTP binding protein 3	protein-coding
mm_59729.1	chr7	28795973	28796001	+	1	NA	exon (NM_177158, exon 8 of 12)	exon (NM_177158, exon 8 of 12)	7018	NM_177158	320435	Mm.74632	NM_177158	ENSMUSG00000051735	Rinl	5830482F20Rik|9930116N10Rik	Ras and Rab interactor-like	protein-coding
mm_22535.1	chr3	8554895	8554906	+	1	NA	exon (NM_025285, exon 4 of 5)	exon (NM_025285, exon 4 of 5)	45373	NM_025285	20257	Mm.29580	NM_025285	ENSMUSG00000027500	Stmn2	AI159727|SCG10|Scgn10|Stmb2	stathmin-like 2	protein-coding
mm_93584.1	chr10	116950367	116950432	-	1	NA	promoter-TSS (NR_038026)	promoter-TSS (NR_038026)	-19	NM_001003950	216363	Mm.336394	NM_001003950	ENSMUSG00000064181	Rab3ip	B230311A06|Gtpat12|Rabin3	RAB3A interacting protein	protein-coding
mm_132284.1	chr16	33057042	33057068	+	1	NA	promoter-TSS (NM_178378)	promoter-TSS (NM_178378)	541	NM_021338	57808	Mm.19355	NM_021338	ENSMUSG00000060636	Rpl35a	2810431L15Rik|Rpl35	ribosomal protein L35A	protein-coding
mm_137826.1	chr17	30635504	30635548	+	1	NA	exon (NM_013811, exon 2 of 93)	exon (NM_013811, exon 2 of 93)	8590	NM_013811	13417	Mm.426017	NM_013811	ENSMUSG00000033826	Dnah8	ATPase|Dnahc8|Hst6.7b|P1-Loop	dynein, axonemal, heavy chain 8	protein-coding
mm_81626.1	chr9	110844523	110844531	+	1	NA	promoter-TSS (NM_183103)	promoter-TSS (NM_183103)	21	NM_183103	74306	Mm.87419	NM_183103	ENSMUSG00000049719	Prss46	1700112C13Rik|79H19B|Tessp6	protease, serine 46	protein-coding
mm_62225.1	chr7	98491971	98491998	+	1	NA	Intergenic	Intergenic	-2238	NM_001113379	434215	Mm.323057	NM_001113379	ENSMUSG00000090958	Lrrc32	AI426318|D11S833Eh|D7H11S833E|EG434215|Garp	leucine rich repeat containing 32	protein-coding
mm_149294.1	chr19	10688919	10688959	+	1	NA	5' UTR (NM_181403, exon 1 of 5)	5' UTR (NM_181403, exon 1 of 5)	124	NM_181403	107305	Mm.19091	NM_181403	ENSMUSG00000048832	Vps37c	5730409F24Rik|AU042646	vacuolar protein sorting 37C	protein-coding
mm_119315.1	chr14	36970006	36970016	+	1	NA	Intergenic	Intergenic	-1247	NM_027045	72972	Mm.27621	NM_027045	ENSMUSG00000058690	Ccser2	1700012P13Rik|2900054P12Rik|AI035535|AW108503|Fam190b|Gcap14	coiled-coil serine rich 2	protein-coding
mm_112598.1	chr13	14097457	14097467	+	1	NA	intron (NM_198122, intron 2 of 22)	B1_Mus1|SINE|Alu	33678	NM_198122	94246	Mm.439784	NM_194262	ENSMUSG00000039219	Arid4b	BCAA|BRCAA1|RBBP1L1|Rbp1l1|SAP180	AT rich interactive domain 4B (RBP1-like)	protein-coding
mm_97665.1	chr11	79660573	79660618	+	1	NA	intron (NM_175543, intron 3 of 14)	CpG	14491	NR_045898	72218	Mm.443271	NR_045898	ENSMUSG00000086569	Rab11fip4os2	1700020F10Rik|4930542H20Rik|Rab11fib4os2	RAB11 family interacting protein 4 (class II), opposite strand 2	ncRNA
mm_128670.1	chr15	60187269	60187283	-	1	NA	Intergenic	Intergenic	-170658	NM_027668	71088	Mm.425950	NM_027668	ENSMUSG00000071749	4933412E24Rik	-	RIKEN cDNA 4933412E24 gene	protein-coding
mm_136718.1	chr17	7945993	7946041	+	1	NA	exon (NM_025789, exon 1 of 8)	exon (NM_025789, exon 1 of 8)	403	NM_025789	66832	Mm.29830	NM_025789	ENSMUSG00000073471	Rsph3a	1700012G05Rik|4930524H12Rik|R74860|Rshl2|Rshl2a	radial spoke 3A homolog (Chlamydomonas)	protein-coding
mm_20301.1	chr2	127140965	127141004	-	1	NA	exon (NM_001163528, exon 2 of 2)	exon (NM_001163528, exon 2 of 2)	1606	NM_001163528	73338	Mm.57559	NM_001163527	ENSMUSG00000074825	Itpripl1	1700041B20Rik	inositol 1,4,5-triphosphate receptor interacting protein-like 1	protein-coding
mm_103946.1	chr11	84067758	84067770	-	1	NA	intron (NM_019819, intron 1 of 2)	intron (NM_019819, intron 1 of 2)	593	NM_019819	56405	Mm.240885	NM_019819	ENSMUSG00000018648	Dusp14	1110014C10Rik|2310042C07Rik|D11Ertd395e|MKP-L|Mkp6	dual specificity phosphatase 14	protein-coding
mm_156404.1	chrX	140062905	140062928	+	1	NA	promoter-TSS (NM_001081668)	promoter-TSS (NM_001081668)	37	NM_177921	331537	Mm.328336	NM_177921	ENSMUSG00000042433	Pih1h3b	E230019M04Rik	PIH1 domain containing 3B	protein-coding
mm_17075.1	chr2	22761318	22761334	-	1	NA	Intergenic	Intergenic	-13001	NM_019456	54519	Mm.14255	NM_019456	ENSMUSG00000026786	Apbb1ip	9930118P07Rik|Prp48	amyloid beta (A4) precursor protein-binding, family B, member 1 interacting protein	protein-coding
mm_18406.1	chr2	60383236	60383290	-	1	NA	promoter-TSS (NM_013825)	promoter-TSS (NM_013825)	-32	NM_013825	17076	Mm.2074	NM_013825	ENSMUSG00000026980	Ly75	CD205|DEC-205|DEC205	lymphocyte antigen 75	protein-coding
mm_62500.1	chr7	101976874	101976880	+	1	NA	intron (NM_133947, intron 1 of 24)	B2_Mm2|SINE|B2	7034	NM_133947	101706	Mm.27259	NM_133947	ENSMUSG00000066306	Numa1	6720401E04Rik|AA764025|AL022610|AU014979|NuMA	nuclear mitotic apparatus protein 1	protein-coding
mm_77135.1	chr8	111393787	111393799	-	1	NA	promoter-TSS (NM_178086)	promoter-TSS (NM_178086)	28	NM_178086	338521	Mm.41083	NM_178086	ENSMUSG00000033579	Fa2h	FAAH|Faxdc1|G630055L08Rik	fatty acid 2-hydroxylase	protein-coding
mm_13241.1	chr2	98662675	98662700	+	1	NA	Intergenic	SYNREP_MM|Satellite|Satellite	1195030	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_27328.1	chr3	50368669	50368716	-	1	NA	3' UTR (NM_011990, exon 12 of 12)	3' UTR (NM_011990, exon 12 of 12)	74921	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_135713.1	chr16	55787944	55787964	-	1	NA	Intergenic	Intergenic	34184	NM_001159394	80859	Mm.247272	NM_030612	ENSMUSG00000035356	Nfkbiz	AA408868|INAP|Mail	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, zeta	protein-coding
mm_132842.1	chr16	45945585	45945641	+	1	NA	Intergenic	Intergenic	64800	NM_001134480	433022	Mm.380993	NM_001134480	ENSMUSG00000087141	Plcxd2	AW494639|EG433022	phosphatidylinositol-specific phospholipase C, X domain containing 2	protein-coding
mm_42424.1	chr5	115327645	115327677	+	1	NA	intron (NR_036616, intron 1 of 4)	CpG	484	NR_036616	108014	Mm.287826	NM_025573	ENSMUSG00000029538	Srsf9	25kDa|2610029M16Rik|SRp30c|Sfrs9	serine/arginine-rich splicing factor 9	protein-coding
mm_52634.1	chr6	117174417	117174426	+	1	NA	3' UTR (NM_021704, exon 3 of 3)	3' UTR (NM_021704, exon 3 of 3)	5886	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_136928.1	chr17	13874523	13874537	+	1	NA	intron (NM_010806, intron 22 of 32)	intron (NM_010806, intron 22 of 32)	-73843	NM_001122977	635895	Mm.388844	NM_001122977	ENSMUSG00000067941	Gm7168	EG635895	predicted gene 7168	protein-coding
mm_105283.1	chr11	102435388	102435435	-	1	NA	exon (NM_008175, exon 10 of 13)	exon (NM_008175, exon 10 of 13)	5089	NM_008175	14824	Mm.1568	NM_008175	ENSMUSG00000034708	Grn	Pgrn|epithelin	granulin	protein-coding
mm_14115.1	chr2	125866284	125866305	+	1	NA	promoter-TSS (NM_001291002)	promoter-TSS (NM_001291002)	71	NM_001291002	69976	Mm.20216	NM_175154	ENSMUSG00000027207	Galk2	2810017M24Rik|AI327030|Gk2	galactokinase 2	protein-coding
mm_106721.1	chr12	3860981	3860998	+	1	NA	intron (NR_045884, intron 3 of 3)	ID_B1|SINE|B4	1255	NR_045884	100038522	Mm.417270	NR_045884	ENSMUSG00000073242	Dnmt3aos	ENSMUSG00000073242|Gm10485	DNA methyltransferase 3A, opposite strand	ncRNA
mm_138219.1	chr17	34315087	34315097	+	1	NA	exon (NM_010382, exon 4 of 6)	exon (NM_010382, exon 4 of 6)	9225	NM_010382	14969	Mm.22564	NM_010382	ENSMUSG00000060586	H2-Eb1	Eb|H-2Eb|H2Eb|Ia-4|Ia4	histocompatibility 2, class II antigen E beta	protein-coding
mm_77409.1	chr8	120589060	120589068	-	1	NA	promoter-TSS (NM_178856)	promoter-TSS (NM_178856)	11	NM_178856	272551	Mm.275910	NM_178856	ENSMUSG00000031821	Gins2	2210013I18Rik|4833427B12Rik|AI323585|Pfs2	GINS complex subunit 2 (Psf2 homolog)	protein-coding
mm_92767.1	chr10	81129451	81129461	-	1	NA	Intergenic	Intergenic	-6815	NM_010731	16969	Mm.20920	NM_010731	ENSMUSG00000035011	Zbtb7a	9030619K07Rik|9130006G12Rik|AI452336|FBI-1|Lrf|Pokemon|Zbtb7	zinc finger and BTB domain containing 7a	protein-coding
mm_117109.1	chr13	60177167	60177202	-	1	NA	5' UTR (NM_008086, exon 1 of 1)	5' UTR (NM_008086, exon 1 of 1)	351	NM_008086	14451	Mm.22701	NM_008086	ENSMUSG00000052957	Gas1	AW554192|Gas-1	growth arrest specific 1	protein-coding
mm_110200.1	chr12	27340737	27340746	-	1	NA	3' UTR (NM_009234, exon 1 of 1)	3' UTR (NM_009234, exon 1 of 1)	1977	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding
mm_85679.1	chr9	107818065	107818080	-	1	NA	intron (NM_011251, intron 6 of 20)	MTC|LTR|ERVL-MaLR	-47070	NM_148930	83486	Mm.259197	NM_148930	ENSMUSG00000032580	Rbm5	D030069N10Rik	RNA binding motif protein 5	protein-coding
mm_93228.1	chr10	95319997	95320014	-	1	NA	intron (NM_009950, intron 2 of 2)	ORR1D1|LTR|ERVL-MaLR	3704	NM_001330138	12905	Mm.473739	NM_009950	ENSMUSG00000045867	Cradd	RAIDD	CASP2 and RIPK1 domain containing adaptor with death domain	protein-coding
mm_159209.1	chr2	121787342	121787342	-	1	NA	intron (NM_172673, intron 1 of 14)	intron (NM_172673, intron 1 of 14)	19715	NM_172673	228564	Mm.121514	NM_172673	ENSMUSG00000027238	Frmd5	1500032A09Rik|5830442F04|A930004K21Rik|R75430	FERM domain containing 5	protein-coding
mm_36352.1	chr4	73950835	73950853	-	1	NA	promoter-TSS (NM_027104)	promoter-TSS (NM_027104)	2	NM_027981	71886	Mm.158769	NM_027104	ENSMUSG00000028396	2310002L09Rik	2310003M01Rik|AV083437	RIKEN cDNA 2310002L09 gene	protein-coding
mm_13293.1	chr2	101991964	101991984	+	1	NA	intron (NM_001290784, intron 4 of 5)	ORR1E|LTR|ERVL-MaLR	105712	NM_029635	76501	Mm.330424	NM_029635	ENSMUSG00000027163	Commd9	1810029F08Rik|AA409293	COMM domain containing 9	protein-coding
mm_91422.1	chr10	32889675	32889727	-	1	NA	5' UTR (NM_001025286, exon 1 of 4)	5' UTR (NM_001025286, exon 1 of 4)	214	NM_001013411	432450	Mm.49665	NM_001013411	ENSMUSG00000069670	Nkain2	6330571D19Rik|AW455467|Tcba1	Na+/K+ transporting ATPase interacting 2	protein-coding
mm_82558.1	chr9	21028301	21028311	-	1	NA	3' UTR (NM_010493, exon 7 of 7)	3' UTR (NM_010493, exon 7 of 7)	-1067	NM_023892	78369	Mm.30220	NM_023892	ENSMUSG00000001014	Icam4	1810015M19Rik|Cd242|ICAM-4	intercellular adhesion molecule 4, Landsteiner-Wiener blood group	protein-coding
mm_26589.1	chr3	151383669	151383674	+	1	NA	Intergenic	Intergenic	-54211	NM_133222	170757	Mm.317261	NM_133222	ENSMUSG00000039167	Adgrl4	1110033N21Rik|ETL1|Eltd1|Etl	adhesion G protein-coupled receptor L4	protein-coding
mm_171175.1	chr3	34036046	34036054	+	1	NA	intron (NM_001113189, intron 1 of 16)	PB1D9|SINE|Alu	15971	NM_001113188	14359	Mm.259021	NM_008053	ENSMUSG00000027680	Fxr1	1110050J02Rik|9530073J07Rik|AI851072|Fxr1h|Fxr1p	fragile X mental retardation gene 1, autosomal homolog	protein-coding
mm_70569.1	chr8	13159209	13159215	+	1	NA	promoter-TSS (NM_010684)	promoter-TSS (NM_010684)	51	NM_010684	16783	Mm.16716	NM_010684	ENSMUSG00000031447	Lamp1	CD107a|LGP-120|LGP-A|Lamp-1|P2B	lysosomal-associated membrane protein 1	protein-coding
mm_16150.1	chr2	172345580	172345590	+	1	NA	promoter-TSS (NM_025912)	promoter-TSS (NM_025912)	8	NM_025912	67017	Mm.30013	NM_025912	ENSMUSG00000027495	Fam210b	2010011I20Rik|AI430961|AV108736	family with sequence similarity 210, member B	protein-coding
mm_112077.1	chr12	112654730	112654750	-	1	NA	exon (NM_009652, exon 14 of 14)	exon (NM_009652, exon 14 of 14)	4611	NR_105904	102465566		NR_105904	ENSMUSG00000098380	Mir6939	Gm27498|mmu-mir-6939	microRNA 6939	ncRNA
mm_74987.1	chr8	27154723	27154745	-	1	NA	exon (NM_001080813, exon 3 of 6)	exon (NM_001080813, exon 3 of 6)	11824	NR_045840	71082	Mm.395259	NR_045840		4933416M07Rik	-	RIKEN cDNA 4933416M07 gene	ncRNA
mm_67728.1	chr7	90129848	90129852	-	1	NA	promoter-TSS (NM_001252521)	promoter-TSS (NM_001252521)	86	NR_046007	78329	Mm.389940	NR_046006	ENSMUSG00000097162	2310010J17Rik	-	RIKEN cDNA 2310010J17 gene	ncRNA
mm_138994.1	chr17	45555694	45555714	+	1	NA	promoter-TSS (NM_008690)	promoter-TSS (NM_008690)	4	NM_001304956	18037	Mm.57043	NM_008690	ENSMUSG00000023947	Nfkbie	I-kappa-B-epsilon|IKBE|IkB-E|NF-kappa-BIE|ikB-epsilon	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, epsilon	protein-coding
mm_3664.1	chr1	153425182	153425219	+	1	NA	promoter-TSS (NM_001033162)	promoter-TSS (NM_001033162)	-9	NM_001033162	71836	Mm.49460	NM_001033162	ENSMUSG00000042708	Shcbp1l	1700012A16Rik	Shc SH2-domain binding protein 1-like	protein-coding
mm_136071.1	chr16	84745895	84745926	-	1	NA	Intergenic	ERVL-B4-int|LTR|ERVL	-10608	NM_017404	27393	Mm.103655	NM_017404	ENSMUSG00000022889	Mrpl39	C21orf8|MRP-L5|ORF22|Rpml5	mitochondrial ribosomal protein L39	protein-coding
mm_52218.1	chr6	103510875	103510898	+	1	NA	promoter-TSS (NM_007697)	promoter-TSS (NM_007697)	10	NM_007697	12661	Mm.251288	NM_007697	ENSMUSG00000030077	Chl1	A530023M13Rik|AI465420|CALL|LICAM2	cell adhesion molecule L1-like	protein-coding
mm_26444.1	chr3	142635322	142635332	+	1	NA	intron (NM_010260, intron 9 of 10)	intron (NM_010260, intron 9 of 10)	-11381	NR_105802	102465200		NR_105802	ENSMUSG00000098871	Mir6381	Gm27963|mmu-mir-6381	microRNA 6381	ncRNA
mm_172944.1	chr9	81677683	81677694	+	1	NA	Intergenic	Intergenic	-45136	NM_010482	15551	Mm.445308	NM_010482	ENSMUSG00000049511	Htr1b	-	5-hydroxytryptamine (serotonin) receptor 1B	protein-coding
mm_7464.1	chr1	120477390	120477437	-	1	NA	intron (NM_010766, intron 14 of 16)	intron (NM_010766, intron 14 of 16)	27671	NM_010766	17167	Mm.1856	NM_010766	ENSMUSG00000026390	Marco	AI323439|Ly112|Scara2	macrophage receptor with collagenous structure	protein-coding
mm_74139.1	chr8	123235065	123235072	+	1	NA	promoter-TSS (NR_045849)	promoter-TSS (NR_045849)	-23	NR_045849	71186	Mm.449984	NR_045849	ENSMUSG00000097637	4933417D19Rik	-	RIKEN cDNA 4933417D19 gene	ncRNA
mm_162737.1	chr10	56387679	56387698	+	1	NA	exon (NM_010288, exon 2 of 2)	exon (NM_010288, exon 2 of 2)	10388	NM_010288	14609	Mm.378921	NM_010288	ENSMUSG00000050953	Gja1	AU042049|AW546267|Cnx43|Cx43|Cx43alpha1|Gja-1|Npm1|connexin43	gap junction protein, alpha 1	protein-coding
mm_32581.1	chr4	110589415	110589417	+	1	NA	intron (NM_001048189, intron 3 of 12)	intron (NM_001048189, intron 3 of 12)	191718	NM_030231	78933	Mm.435620	NM_030231	ENSMUSG00000061298	Agbl4	4930578N11Rik|4931433A01Rik	ATP/GTP binding protein-like 4	protein-coding
mm_75545.1	chr8	57487802	57487871	-	1	NA	promoter-TSS (NM_021788)	promoter-TSS (NM_021788)	24	NM_021788	60406	Mm.118	NM_021788	ENSMUSG00000031609	Sap30	30kDa	sin3 associated polypeptide	protein-coding
mm_111296.1	chr12	85477266	85477273	-	1	NA	TTS (NM_010234)	TTS (NM_010234)	3368	NM_010234	14281	Mm.246513	NM_010234	ENSMUSG00000021250	Fos	D12Rfj1|c-fos|cFos	FBJ osteosarcoma oncogene	protein-coding
mm_87983.1	chr10	63906908	63906918	+	1	NA	intron (NM_177612, intron 7 of 17)	L1MA7|LINE|L1	85858	NM_001164519	216033	Mm.444692	NM_177612	ENSMUSG00000060843	Ctnna3	4930429L08Rik|4933408A16|Catna3|Vr22	catenin (cadherin associated protein), alpha 3	protein-coding
mm_42397.1	chr5	114937912	114937926	+	1	NA	TTS (NM_145209)	TTS (NM_145209)	-4283	NM_028211	72357	Mm.292672	NM_028211	ENSMUSG00000029559	2210016L21Rik	-	RIKEN cDNA 2210016L21 gene	protein-coding
mm_119319.1	chr14	37054819	37054853	+	1	NA	promoter-TSS (NM_146245)	promoter-TSS (NM_146245)	6	NM_146245	239037	Mm.37907	NM_146245	ENSMUSG00000041044	Lrit1	BC032270|Lrrc21	leucine-rich repeat, immunoglobulin-like and transmembrane domains 1	protein-coding
mm_154251.1	chr19	60766699	60766729	-	1	NA	exon (NM_010123, exon 19 of 22)	exon (NM_010123, exon 19 of 22)	7671	NR_034047	100217439		NR_034047		Snora19	MBI-51	small nucleolar RNA, H/ACA box 19	snoRNA
mm_95249.1	chr11	44618209	44618223	+	1	NA	exon (NM_001290710, exon 1 of 15)	exon (NM_001290710, exon 1 of 15)	116	NM_001290710	13591	Mm.439662	NM_007897	ENSMUSG00000057098	Ebf1	Ebf|O/E-1|OE-1|Olf-1|Olf1	early B cell factor 1	protein-coding
mm_122220.1	chr14	32388356	32388396	-	1	NA	promoter-TSS (NM_001034037)	promoter-TSS (NM_001034037)	-3	NM_001034037	67085	Mm.109099	NM_001034037	ENSMUSG00000072473	1700024G13Rik	C10orf53	RIKEN cDNA 1700024G13 gene	protein-coding
mm_49065.1	chr6	5390704	5390716	+	1	NA	exon (NM_023048, exon 2 of 6)	exon (NM_023048, exon 2 of 6)	7324	NM_023048	65255	Mm.51340	NM_023048	ENSMUSG00000042607	Asb4	8430401O13Rik|AV117194|AW060255	ankyrin repeat and SOCS box-containing 4	protein-coding
mm_12938.1	chr2	85136356	85136371	+	1	NA	promoter-TSS (NM_011784)	promoter-TSS (NM_011784)	3	NM_011784	23796	Mm.29368	NM_011784	ENSMUSG00000044338	Aplnr	APJ|Agtrl1|msr/apj	apelin receptor	protein-coding
mm_118188.1	chr13	107565340	107565350	-	1	NA	Intergenic	RMER19A|LTR|ERVK	95523	NR_045084	105120	Mm.417700	NR_045083		AI197445	-	expressed sequence AI197445	ncRNA
mm_148668.1	chr19	5637490	5637500	+	1	NA	promoter-TSS (NM_009045)	promoter-TSS (NM_009045)	5	NM_009045	19697	Mm.249966	NM_009045	ENSMUSG00000024927	Rela	p65	v-rel reticuloendotheliosis viral oncogene homolog A (avian)	protein-coding
mm_63973.1	chr7	139950435	139950446	+	1	NA	Intergenic	Intergenic	6584	NM_009482	22286	Mm.10205	NM_009482	ENSMUSG00000047751	Utf1	AI505934	undifferentiated embryonic cell transcription factor 1	protein-coding
mm_22184.1	chr2	173218857	173218876	-	1	NA	promoter-TSS (NM_021394)	promoter-TSS (NM_021394)	56	NM_021394	58203	Mm.116687	NM_021394	ENSMUSG00000027514	Zbp1	2010010H03Rik|Dai|Dlm1|mZaDLM	Z-DNA binding protein 1	protein-coding
mm_167609.1	chr9	54949350	54949358	+	1	NA	TTS (NM_145229)	TTS (NM_145229)	-1505	NM_011966	26441	Mm.30270	NM_011966	ENSMUSG00000032301	Psma4	C9	proteasome (prosome, macropain) subunit, alpha type 4	protein-coding
mm_52083.1	chr6	97829261	97829303	+	1	NA	intron (NM_001113198, intron 1 of 9)	intron (NM_001113198, intron 1 of 9)	22224	NM_001113198	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_147820.1	chr18	61826998	61827037	-	1	NA	intron (NM_198649, intron 7 of 22)	intron (NM_198649, intron 7 of 22)	-40355	NM_178928	106877	Mm.26632	NM_178928	ENSMUSG00000033032	Afap1l1	AI173486	actin filament associated protein 1-like 1	protein-coding
mm_76819.1	chr8	104534631	104534646	-	1	NA	promoter-TSS (NM_144931)	promoter-TSS (NM_144931)	-1	NM_144931	234664	Mm.237670	NM_144931	ENSMUSG00000031878	Nae1	59kDa|Appbp1	NEDD8 activating enzyme E1 subunit 1	protein-coding
mm_132612.1	chr16	38661711	38661715	+	1	NA	intron (NM_020260, intron 1 of 11)	intron (NM_020260, intron 1 of 11)	51322	NM_020260	12549	Mm.370848	NM_020260	ENSMUSG00000022799	Arhgap31	5830477L08Rik|AU041750|Cdgap|D330026I07Rik	Rho GTPase activating protein 31	protein-coding
mm_15049.1	chr2	152869453	152869461	+	1	NA	intron (NM_001141977, intron 3 of 17)	intron (NM_001141977, intron 3 of 17)	4390	NR_049195	100885834		NR_049195	ENSMUSG00000093746	Mir5622	Gm24421|mmu-mir-5622	microRNA 5622	ncRNA
mm_32463.1	chr4	107434620	107434654	+	1	NA	promoter-TSS (NM_147221)	promoter-TSS (NM_147221)	-82	NM_147221	230587	Mm.331757	NM_147221	ENSMUSG00000034762	Glis1	Gli5|Gli6|GliH1	GLIS family zinc finger 1	protein-coding
mm_34008.1	chr4	137964475	137964540	+	1	NA	3' UTR (NM_199307, exon 20 of 20)	3' UTR (NM_199307, exon 20 of 20)	-28949	NM_001256198	230861	Mm.268903	NM_172703	ENSMUSG00000028760	Eif4g3	1500002J22Rik|4930523M17Rik|G1-419-52|eIF4GII|repro8	eukaryotic translation initiation factor 4 gamma, 3	protein-coding
mm_54645.1	chr6	38875924	38875937	-	1	NA	5' UTR (NM_010433, exon 1 of 15)	5' UTR (NM_010433, exon 1 of 15)	260	NM_010433	15258	Mm.23790	NM_010433	ENSMUSG00000061436	Hipk2	1110014O20Rik|B230339E18Rik|Stank	homeodomain interacting protein kinase 2	protein-coding
mm_132790.1	chr16	45038449	45038458	+	1	NA	Intergenic	MLT2B2|LTR|ERVL	-55600	NM_026439	67896	Mm.181074	NM_026439	ENSMUSG00000022665	Ccdc80	2610001E17Rik|DRO1|Ssg1|Urb	coiled-coil domain containing 80	protein-coding
mm_112063.1	chr12	111966955	111967017	-	1	NA	promoter-TSS (NM_027360)	promoter-TSS (NM_027360)	-9	NM_027360	70257	Mm.318	NM_027360	ENSMUSG00000021290	2010107E04Rik	9430003J03Rik|AU043134|AV124504|Mp68	RIKEN cDNA 2010107E04 gene	protein-coding
mm_91159.1	chr10	20553529	20553532	-	1	NA	intron (NM_013875, intron 2 of 12)	intron (NM_013875, intron 2 of 12)	-5202	NM_001347366	29863	Mm.425617	NM_013875	ENSMUSG00000019990	Pde7b	-	phosphodiesterase 7B	protein-coding
mm_105447.1	chr11	104442310	104442327	-	1	NA	promoter-TSS (NM_001081045)	promoter-TSS (NM_001081045)	-27	NM_001081045	76719	Mm.136418	NM_001081045	ENSMUSG00000018412	Kansl1	1700081L11Rik|9430041J06Rik|mKIAA1267	KAT8 regulatory NSL complex subunit 1	protein-coding
mm_71469.1	chr8	46534741	46534751	+	1	NA	3' UTR (NM_007981, exon 21 of 21)	3' UTR (NM_007981, exon 21 of 21)	-17323	NM_027973	71876	Mm.22108	NM_027973	ENSMUSG00000031629	Cenpu	1700029A22Rik|Mlf1ip	centromere protein U	protein-coding
mm_58662.1	chr7	6730688	6730716	+	1	NA	promoter-TSS (NM_008817)	promoter-TSS (NM_008817)	119	NM_001290994	57775	Mm.40752	NM_021323	ENSMUSG00000051527	Usp29	Ocat	ubiquitin specific peptidase 29	protein-coding
mm_121236.1	chr14	103056126	103056136	+	1	NA	3' UTR (NM_008392, exon 5 of 5)	3' UTR (NM_008392, exon 5 of 5)	9119	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_157746.1	chrX	73401712	73401723	-	1	NA	Intergenic	Intergenic	-9379	NM_009566	22754	Mm.5060	NM_009566	ENSMUSG00000031374	Zfp92	-	zinc finger protein 92	protein-coding
mm_132074.1	chr16	30066414	30066432	+	1	NA	intron (NM_008235, intron 3 of 3)	CpG	1066	NM_008235	15205	Mm.390859	NM_008235	ENSMUSG00000022528	Hes1	Hry|bHLHb39	hairy and enhancer of split 1 (Drosophila)	protein-coding
mm_158965.1	chr1	92978764	92978764	+	1	NA	promoter-TSS (NM_022320)	promoter-TSS (NM_022320)	-139	NM_022320	64095	Mm.152780	NM_022320	ENSMUSG00000026271	Gpr35	KPG_007	G protein-coupled receptor 35	protein-coding
mm_99389.1	chr11	102097514	102097518	+	1	NA	Intergenic	Intergenic	3784	NM_008918	19064	Mm.1269	NM_008918	ENSMUSG00000017316	Ppy	AV061413|IGSPP|PP	pancreatic polypeptide	protein-coding
mm_119440.1	chr14	46760527	46760557	+	1	NA	promoter-TSS (NM_028222)	promoter-TSS (NM_028222)	1	NM_028222	72391	Mm.272394	NM_028222	ENSMUSG00000037628	Cdkn3	2410006H10Rik|KAP	cyclin-dependent kinase inhibitor 3	protein-coding
mm_87467.1	chr10	51491140	51491153	+	1	NA	intron (NM_001291894, intron 1 of 8)	intron (NM_001291894, intron 1 of 8)	248	NM_013532	14728	Mm.34408	NM_013532	ENSMUSG00000062593	Lilrb4a	CD85K|Gp49b|HM18|ILT3|LIR-5|Lilrb4|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4A	protein-coding
mm_11487.1	chr2	32423751	32423773	+	1	NA	intron (NM_146118, intron 1 of 10)	intron (NM_146118, intron 1 of 10)	304	NM_001290558	227731	Mm.37395	NM_146118	ENSMUSG00000026819	Slc25a25	1110030N17Rik|MCSC|mKIAA1896	solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 25	protein-coding
mm_167017.1	chr7	63896503	63896514	+	1	NA	intron (NM_021366, intron 1 of 1)	intron (NM_021366, intron 1 of 1)	-20349	NM_001256311	381994	Mm.425466	NM_001256311	ENSMUSG00000095061	E030018B13Rik	Gm1697	RIKEN cDNA E030018B13 gene	protein-coding
mm_145525.1	chr18	60566453	60566467	+	1	NA	exon (NM_025776, exon 6 of 11)	exon (NM_025776, exon 6 of 11)	5674	NM_025776	66810	Mm.275106	NM_025776	ENSMUSG00000024604	Rbm22	8430430L24Rik	RNA binding motif protein 22	protein-coding
mm_81307.1	chr9	108347933	108347947	+	1	NA	exon (NM_011678, exon 1 of 22)	exon (NM_011678, exon 1 of 22)	109	NM_011678	22258	Mm.3974	NM_011678	ENSMUSG00000032612	Usp4	F730026I20Rik|Unp|mKIAA4155	ubiquitin specific peptidase 4 (proto-oncogene)	protein-coding
mm_139003.1	chr17	45568357	45568382	+	1	NA	TTS (NM_028662)	TTS (NM_028662)	4217	NM_028662	73836	Mm.289716	NM_028662	ENSMUSG00000037089	Slc35b2	1110003M08Rik|AA407792|AI842275|PAPST1|Slc35b1	solute carrier family 35, member B2	protein-coding
mm_29744.1	chr3	126936665	126936678	-	1	NA	exon (NM_178655, exon 19 of 25)	exon (NM_178655, exon 19 of 25)	6715	NM_001034168	109676	Mm.220242	NM_178655	ENSMUSG00000032826	Ank2	100043364|AI835472|AW491075|Ank-2|Gm4392	ankyrin 2, brain	protein-coding
mm_115220.1	chr13	109685467	109685486	+	1	NA	intron (NM_011056, intron 3 of 16)	intron (NM_011056, intron 3 of 16)	-218333	NR_035442	100316683		NR_035442	ENSMUSG00000084651	Mir1904	Mirn1904|mmu-mir-1904	microRNA 1904	ncRNA
mm_45407.1	chr5	66299401	66299419	-	1	NA	3' UTR (NM_009686, exon 18 of 18)	3' UTR (NM_009686, exon 18 of 18)	38255	NM_001201416	11787	Mm.5159	NM_009686	ENSMUSG00000029207	Apbb2	2310007D03Rik|FE65L1|Rirl1|TR2L|Zfra	amyloid beta (A4) precursor protein-binding, family B, member 2	protein-coding
mm_109120.1	chr12	105685385	105685430	+	1	NA	promoter-TSS (NM_178613)	promoter-TSS (NM_178613)	55	NM_178613	66787	Mm.248019	NM_178613	ENSMUSG00000044715	Gskip	4933433P14Rik	GSK3B interacting protein	protein-coding
mm_73757.1	chr8	115110187	115110188	+	1	NA	intron (NM_019573, intron 8 of 8)	B1_Mur4|SINE|Alu	596707	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_17380.1	chr2	27020047	27020061	-	1	NA	3' UTR (NM_029862, exon 6 of 6)	3' UTR (NM_029862, exon 6 of 6)	7944	NM_172659	227659	Mm.41203	NM_172659	ENSMUSG00000036067	Slc2a6	A330096C23|F630103L12Rik|Glut6|Glut9	solute carrier family 2 (facilitated glucose transporter), member 6	protein-coding
mm_65013.1	chr7	17090592	17090604	-	1	NA	exon (NM_007676, exon 2 of 5)	exon (NM_007676, exon 2 of 5)	16558	NM_007676	26436	Mm.143686	NM_007676	ENSMUSG00000066760	Psg16	Cea11|PSG|bCEA	pregnancy specific glycoprotein 16	protein-coding
mm_134626.1	chr16	21650156	21650163	-	1	NA	3' UTR (NM_001001881, exon 2 of 2)	3' UTR (NM_001001881, exon 2 of 2)	44506	NM_001001881	72190	Mm.131606	NM_001001881	ENSMUSG00000043391	2510009E07Rik	AI194952	RIKEN cDNA 2510009E07 gene	protein-coding
mm_20661.1	chr2	132114598	132114611	-	1	NA	intron (NM_018824, intron 1 of 15)	intron (NM_018824, intron 1 of 15)	30504	NM_018824	54338	Mm.103581	NM_018824	ENSMUSG00000027340	Slc23a2	AI844736|NBTL1|SVCT2|Slc23a1|YSPL2|YSPL3|mKIAA0238	solute carrier family 23 (nucleobase transporters), member 2	protein-coding
mm_12711.1	chr2	76688082	76688098	+	1	NA	intron (NM_031256, intron 5 of 7)	MIRb|SINE|MIR	12775	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_75421.1	chr8	46773618	46773624	-	1	NA	intron (NM_008391, intron 1 of 8)	intron (NM_008391, intron 1 of 8)	33876	NM_008391	16363	Mm.1149	NM_008391	ENSMUSG00000031627	Irf2	9830146E22Rik|AI646973|Irf-2	interferon regulatory factor 2	protein-coding
mm_143586.1	chr17	74436203	74436236	-	1	NA	intron (NM_001033367, intron 6 of 8)	intron (NM_001033367, intron 6 of 8)	22889	NM_001033367	268973	Mm.311884	NM_001033367	ENSMUSG00000039193	Nlrc4	9530011P19Rik|CLAN|CLAN1|CLANA|CLANB|CLANC|CLAND|Card12|IPAF	NLR family, CARD domain containing 4	protein-coding
mm_108504.1	chr12	83950635	83950705	+	1	NA	promoter-TSS (NM_023633)	promoter-TSS (NM_023633)	62	NM_023633	71952	Mm.251483	NM_023633	ENSMUSG00000046791	2410016O06Rik	MAPJD|NO66	RIKEN cDNA 2410016O06 gene	protein-coding
mm_21225.1	chr2	155930039	155930066	-	1	NA	non-coding (NR_024487, exon 1 of 10)	non-coding (NR_024487, exon 1 of 10)	258	NM_018888	56046	Mm.158827	NM_018888	ENSMUSG00000005882	Uqcc1	2310079L17Rik|2410003P15Rik|3110038N19Rik|Bfzb|Bfzp|Cbp3|Uqcc	ubiquinol-cytochrome c reductase complex assembly factor 1	protein-coding
mm_171981.1	chr5	89690321	89690329	-	1	NA	intron (NM_001081401, intron 18 of 21)	intron (NM_001081401, intron 18 of 21)	73889	NR_037571	631105	Mm.7732	NR_037571		Gm7056	Gm149	predicted gene 7056	ncRNA
mm_97397.1	chr11	77838048	77838075	+	1	NA	intron (NM_001291214, intron 19 of 38)	intron (NM_001291214, intron 19 of 38)	36763	NM_001291215	360013	Mm.341248	NM_011586	ENSMUSG00000000631	Myo18a	MAJN|MyoPDZ|MysPDZ|SP-R210	myosin XVIIIA	protein-coding
mm_65348.1	chr7	24994247	24994266	-	1	NA	exon (NM_001290469, exon 11 of 23)	exon (NM_001290469, exon 11 of 23)	-6589	NR_106014	102465634		NR_106014	ENSMUSG00000099258	Mir7047	Gm27270|mmu-mir-7047	microRNA 7047	ncRNA
mm_99707.1	chr11	106216519	106216532	+	1	NA	promoter-TSS (NM_026009)	promoter-TSS (NM_026009)	-158	NM_026009	67163	Mm.22109	NM_026009	ENSMUSG00000078622	Ccdc47	2610204L23Rik|C88307|asp4|calumin	coiled-coil domain containing 47	protein-coding
mm_121131.1	chr14	101869370	101869405	+	1	NA	intron (NM_001347628, intron 1 of 26)	intron (NM_001347628, intron 1 of 26)	28764	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_10511.1	chr2	16356324	16356357	+	1	NA	promoter-TSS (NM_026162)	promoter-TSS (NM_026162)	36	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding
mm_128149.1	chr15	31735402	31735410	-	1	NA	Intergenic	Intergenic	133290	NM_026546	68073	Mm.119185	NM_026546	ENSMUSG00000039065	Fam173b	A930016P21Rik|AA987072	family with sequence similarity 173, member B	protein-coding
mm_122694.1	chr14	52078031	52078035	-	1	NA	intron (NM_016884, intron 5 of 8)	intron (NM_016884, intron 5 of 8)	8718	NR_028552	100217457		NR_028552	ENSMUSG00000064871	Snord58b	MBII-199	small nucleolar RNA, C/D box 58B	snoRNA
mm_67617.1	chr7	83937772	83937815	-	1	NA	intron (NM_030728, intron 27 of 28)	intron (NM_030728, intron 27 of 28)	45793	NM_023403	67943	Mm.117365	NM_023403	ENSMUSG00000038503	Mesdc2	2210015O11Rik|AW537813|mKIAA0081|mesd|msd	mesoderm development candidate 2	protein-coding
mm_146693.1	chr18	12879985	12879991	-	1	NA	promoter-TSS (NM_001252489)	promoter-TSS (NM_001252489)	-9	NM_001252489	64291	Mm.259470	NM_020573	ENSMUSG00000044252	Osbpl1a	G430090F17Rik|Gm753|ORP-1|Osbpl1b	oxysterol binding protein-like 1A	protein-coding
mm_140906.1	chr17	24163619	24163629	-	1	NA	TTS (NM_009729)	TTS (NM_009729)	109	NM_172935	245847	Mm.87319	NM_172935	ENSMUSG00000036820	Amdhd2	5730457F11Rik	amidohydrolase domain containing 2	protein-coding
mm_148691.1	chr19	5740886	5740904	+	1	NA	promoter-TSS (NM_008520)	promoter-TSS (NM_008520)	-9	NM_008520	16998	Mm.182396	NM_008520	ENSMUSG00000024940	Ltbp3	Ltbp2|mFLJ00070	latent transforming growth factor beta binding protein 3	protein-coding
mm_21101.1	chr2	153241344	153241354	-	1	NA	promoter-TSS (NM_080463)	promoter-TSS (NM_080463)	9	NM_018807	54711	Mm.103199	NM_018807	ENSMUSG00000051413	Plagl2	AU018672|AW552839|mKIAA0198	pleiomorphic adenoma gene-like 2	protein-coding
mm_60391.1	chr7	44474679	44474694	+	1	NA	Intergenic	Intergenic	4339	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_82930.1	chr9	35176040	35176051	-	1	NA	promoter-TSS (NM_027030)	promoter-TSS (NM_027030)	-58	NM_027030	69305	Mm.229110	NM_027030	ENSMUSG00000032040	Dcps	1700001E16Rik|AA408441	decapping enzyme, scavenger	protein-coding
mm_151846.1	chr19	5771271	5771301	-	1	NA	exon (NM_023912, exon 1 of 17)	exon (NM_023912, exon 1 of 17)	115	NM_023912	78891	Mm.276063	NM_023912	ENSMUSG00000024941	Scyl1	2810011O19Rik|C85140|Ntkl|mdf|mfd|p105	SCY1-like 1 (S. cerevisiae)	protein-coding
mm_54179.1	chr6	23839244	23839267	-	1	NA	5' UTR (NM_153163, exon 1 of 30)	5' UTR (NM_153163, exon 1 of 30)	166	NM_001252106	320405	Mm.259632	NM_153163	ENSMUSG00000017978	Cadps2	A230044C21Rik|Caps-2|Caps2|Cpd2	Ca2+-dependent activator protein for secretion 2	protein-coding
mm_123498.1	chr14	66213560	66213570	-	1	NA	promoter-TSS (NM_001162366)	promoter-TSS (NM_001162366)	-13	NM_001162366	19229	Mm.21613	NM_172498	ENSMUSG00000059456	Ptk2b	CADTK|CAKB|CAKbeta|E430023O05Rik|FADK2|FAK2|PYK2|Raftk	PTK2 protein tyrosine kinase 2 beta	protein-coding
mm_50485.1	chr6	48988547	48988547	+	1	NA	exon (NM_172888, exon 1 of 5)	exon (NM_172888, exon 1 of 5)	1686	NM_172888	243377	Mm.446302	NM_172888	ENSMUSG00000039215	Svs1	9530003A11	seminal vesicle secretory protein 1	protein-coding
mm_163257.1	chr11	109674866	109674870	+	1	NA	intron (NM_153782, intron 9 of 10)	intron (NM_153782, intron 9 of 10)	23947	NM_001313976	19084	Mm.30039	NM_021880	ENSMUSG00000020612	Prkar1a	1300018C22Rik|RIalpha|Tse-1|Tse1	protein kinase, cAMP dependent regulatory, type I, alpha	protein-coding
mm_65574.1	chr7	27195701	27195711	-	1	NA	promoter-TSS (NM_001046637)	promoter-TSS (NM_001046637)	54	NM_001046637	53607	Mm.386890	NM_015782	ENSMUSG00000061479	Snrpa	C430021M15Rik|Rnu1a-1|Rnu1a1|U1-A|U1A	small nuclear ribonucleoprotein polypeptide A	protein-coding
mm_687.1	chr1	40534526	40534534	+	1	NA	intron (NM_010553, intron 7 of 12)	intron (NM_010553, intron 7 of 12)	19168	NM_010553	16174	Mm.20466	NM_010553	ENSMUSG00000026068	Il18rap	AcPL|IL-18R-beta|IL-18RAcP|IL-18Rbeta|IL-1RAcPL	interleukin 18 receptor accessory protein	protein-coding
mm_125142.1	chr15	30632983	30632985	+	1	NA	intron (NM_008729, intron 5 of 22)	intron (NM_008729, intron 5 of 22)	-406142	NR_045186	73784	Mm.66947	NR_045186		4930430F21Rik	-	RIKEN cDNA 4930430F21 gene	ncRNA
mm_49748.1	chr6	34746217	34746227	+	1	NA	intron (NM_001347100, intron 5 of 13)	intron (NM_001347100, intron 5 of 13)	-34210	NM_001289657	76223	Mm.150047	NM_178630	ENSMUSG00000038836	Agbl3	2900053G10Rik|4930431N21Rik|6530406M24Rik|CCP3	ATP/GTP binding protein-like 3	protein-coding
mm_79399.1	chr9	54950809	54950820	+	1	NA	promoter-TSS (NM_011966)	promoter-TSS (NM_011966)	-45	NM_011966	26441	Mm.30270	NM_011966	ENSMUSG00000032301	Psma4	C9	proteasome (prosome, macropain) subunit, alpha type 4	protein-coding
mm_59521.1	chr7	27605848	27605860	+	1	NA	promoter-TSS (NM_007434)	promoter-TSS (NM_007434)	57	NM_007434	11652	Mm.177194	NM_007434	ENSMUSG00000004056	Akt2	2410016A19Rik|AW554154|PKB|PKBbeta	thymoma viral proto-oncogene 2	protein-coding
mm_163978.1	chr14	55885032	55885042	+	1	NA	promoter-TSS (NM_019820)	promoter-TSS (NM_019820)	95	NR_138134	219094	Mm.37592	NM_027143	ENSMUSG00000047153	Khnyn	6330555F21|9130227C08Rik|AI605259|Kiaa0323|mKIAA0323	KH and NYN domain containing	protein-coding
mm_58529.1	chr7	4151395	4151408	+	1	NA	exon (NM_021454, exon 3 of 3)	exon (NM_021454, exon 3 of 3)	-1529	NM_175529	243813	Mm.347643	NM_175529	ENSMUSG00000043432	Leng9	9530024C23Rik|F630035L11Rik	leukocyte receptor cluster (LRC) member 9	protein-coding
mm_168201.1	chr10	69325221	69325238	+	1	NA	Intergenic	Intergenic	27683	NM_007659	12534	Mm.281367	NM_007659	ENSMUSG00000019942	Cdk1	Cdc2|Cdc2a|p34<CDC2>	cyclin-dependent kinase 1	protein-coding
mm_136694.1	chr17	7138439	7138451	+	1	NA	Intergenic	Intergenic	-31670	NM_011299	20112	Mm.268383	NM_011299	ENSMUSG00000023809	Rps6ka2	90kDa|D17Wsu134e|Rps6ka-rs1|Rsk3|p90rsk|pp90rsk	ribosomal protein S6 kinase, polypeptide 2	protein-coding
mm_138495.1	chr17	35200720	35200727	+	1	NA	intron (NM_001278601, intron 2 of 2)	intron (NM_001278601, intron 2 of 2)	1284	NM_013693	21926	Mm.1293	NM_013693	ENSMUSG00000024401	Tnf	DIF|TNF-a|TNF-alpha|TNFSF2|TNFalpha|Tnfa|Tnfsf1a|Tnlg1f	tumor necrosis factor	protein-coding
mm_78786.1	chr9	44032189	44032195	+	1	NA	Intergenic	Intergenic	-11192	NM_009382	21838	Mm.3951	NM_009382	ENSMUSG00000032011	Thy1	CD90|T25|Thy-1|Thy-1.2|Thy1.1|Thy1.2	thymus cell antigen 1, theta	protein-coding
mm_151269.1	chr19	55180717	55180733	+	1	NA	promoter-TSS (NM_009348)	promoter-TSS (NM_009348)	-160	NM_009348	21684	Mm.42139	NM_009348	ENSMUSG00000024979	Tectb	Tctnb	tectorin beta	protein-coding
mm_116664.1	chr13	49200720	49200736	-	1	NA	Intergenic	Intergenic	13181	NM_013610	18081	Mm.18503	NM_013610	ENSMUSG00000037966	Ninj1	AU024536	ninjurin 1	protein-coding
mm_162925.1	chr10	121310823	121310823	+	1	NA	5' UTR (NM_029057, exon 1 of 12)	5' UTR (NM_029057, exon 1 of 12)	366	NM_029057	74694	Mm.233833	NM_029057	ENSMUSG00000052302	Tbc1d30	4930505D03Rik	TBC1 domain family, member 30	protein-coding
mm_129330.1	chr15	77775927	77775943	-	1	NA	intron (NM_022410, intron 20 of 40)	intron (NM_022410, intron 20 of 40)	-20706	NM_001081970	239552	Mm.125650	NM_001081970	ENSMUSG00000056656	Apol8	9830006J20Rik|APOL-II|Apol2	apolipoprotein L 8	protein-coding
mm_91351.1	chr10	27616816	27616825	-	1	NA	5' UTR (NM_008481, exon 1 of 64)	5' UTR (NM_008481, exon 1 of 64)	122	NM_008481	16773	Mm.256087	NM_008481	ENSMUSG00000019899	Lama2	5830440B04|dy|mKIAA4087|mer|merosin	laminin, alpha 2	protein-coding
mm_50548.1	chr6	49046743	49046753	+	1	NA	intron (NM_053110, intron 4 of 10)	intron (NM_053110, intron 4 of 10)	10230	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_57835.1	chr6	129465183	129465195	-	1	NA	intron (NR_132130, intron 5 of 5)	intron (NR_132130, intron 5 of 5)	7590	NM_001309637	56644	Mm.239516	NM_020008	ENSMUSG00000079293	Clec7a	BGR|Clecsf12|beta-GR	C-type lectin domain family 7, member a	protein-coding
mm_124586.1	chr15	3270972	3271006	+	1	NA	promoter-TSS (NM_009155)	promoter-TSS (NM_009155)	12	NM_009155	20363	Mm.392203	NM_009155	ENSMUSG00000064373	Selenop	AU018766|D15Ucla1|Se-P|Sepp1|selp	selenoprotein P	protein-coding
mm_145027.1	chr18	39072540	39072542	+	1	NA	intron (NM_175164, intron 1 of 22)	intron (NM_175164, intron 1 of 22)	79396	NM_175164	71302	Mm.329396	NM_175164	ENSMUSG00000036452	Arhgap26	1810044B20Rik|2610010G17Rik|4933432P15Rik|AI853435|mKIAA0621	Rho GTPase activating protein 26	protein-coding
mm_16920.1	chr2	13574967	13575029	-	1	NA	intron (NM_011701, intron 1 of 8)	CpG	687	NM_011701	22352	Mm.268000	NM_011701	ENSMUSG00000026728	Vim	-	vimentin	protein-coding
mm_111324.1	chr12	86469991	86470007	-	1	NA	intron (NM_011934, intron 1 of 6)	intron (NM_011934, intron 1 of 6)	48355	NM_011934	26380	Mm.235550	NM_011934	ENSMUSG00000021255	Esrrb	Err2|Errb|Estrrb|Nr3b2	estrogen related receptor, beta	protein-coding
mm_135315.1	chr16	38713355	38713363	-	1	NA	promoter-TSS (NM_020260)	promoter-TSS (NM_020260)	-324	NM_020260	12549	Mm.370848	NM_020260	ENSMUSG00000022799	Arhgap31	5830477L08Rik|AU041750|Cdgap|D330026I07Rik	Rho GTPase activating protein 31	protein-coding
mm_166163.1	chr5	18156126	18156126	+	1	NA	Intergenic	ERVL-E-int|LTR|ERVL	193556	NM_001081143	242851	Mm.332230	NM_001081143	ENSMUSG00000028777	Gnat3	Ggust|Gtn	guanine nucleotide binding protein, alpha transducing 3	protein-coding
mm_120282.1	chr14	63132524	63132563	+	1	NA	intron (NM_007798, intron 1 of 9)	intron (NM_007798, intron 1 of 9)	10081	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_55.1	chr1	6528277	6528310	+	1	NA	intron (NM_001244693, intron 2 of 22)	intron (NM_001244693, intron 2 of 22)	41062	NM_001244692	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding
mm_157580.1	chrX	52772764	52772774	-	1	NA	Intergenic	CpG	-18431	NM_001034059	434778	Mm.23411	NM_001034059	ENSMUSG00000073207	Ccdc160	6330534C20Rik	coiled-coil domain containing 160	protein-coding
mm_85483.1	chr9	106080315	106080321	-	1	NA	exon (NM_026763, exon 3 of 38)	exon (NM_026763, exon 3 of 38)	16373	NM_026763	68553	Mm.28854	NM_026763	ENSMUSG00000032572	Col6a4	1110001D15Rik|AI413310|AU023415|Dvwa|EG235580|Vwa6	collagen, type VI, alpha 4	protein-coding
mm_95009.1	chr11	31931783	31931804	+	1	NA	3' UTR (NM_026252, exon 10 of 10)	3' UTR (NM_026252, exon 10 of 10)	-33840	NM_026262	67592	Mm.78654	NM_026262	ENSMUSG00000020299	4930524B15Rik	-	RIKEN cDNA 4930524B15 gene	protein-coding
mm_150376.1	chr19	35975049	35975049	+	1	NA	intron (NM_001347442, intron 1 of 3)	intron (NM_001347442, intron 1 of 3)	82311	NM_001347442	15566	Mm.254266	NM_008315	ENSMUSG00000024798	Htr7	5-HT7	5-hydroxytryptamine (serotonin) receptor 7	protein-coding
mm_59977.1	chr7	30459753	30459763	+	1	NA	promoter-TSS (NM_019459)	promoter-TSS (NM_019459)	-300	NM_019459	54631	Mm.437830	NM_019459	ENSMUSG00000006649	Nphs1	NephrinB|nephrin	nephrosis 1, nephrin	protein-coding
mm_104560.1	chr11	96829466	96829476	-	1	NA	promoter-TSS (NM_001130450)	promoter-TSS (NM_001130450)	31	NM_001130450	18023	Mm.6743	NM_008686	ENSMUSG00000038615	Nfe2l1	AA408798|AW212678|LCR-F1|Lcrf1|NRF1|TCF-11|TCF11	nuclear factor, erythroid derived 2,-like 1	protein-coding
mm_134104.1	chr16	9995349	9995372	-	1	NA	Intergenic	CpG	-2827	NM_008170	14811	Mm.2953	NM_008170	ENSMUSG00000059003	Grin2a	GluN2A|NMDAR2A|NR2A	glutamate receptor, ionotropic, NMDA2A (epsilon 1)	protein-coding
mm_35759.1	chr4	45826853	45826863	-	1	NA	promoter-TSS (NM_018741)	promoter-TSS (NM_018741)	-31	NM_018741	75426	Mm.3919	NM_018741	ENSMUSG00000035551	Igfbpl1	2810011G06Rik|2810453O06Rik|IGFBPL	insulin-like growth factor binding protein-like 1	protein-coding
mm_64513.1	chr7	143823116	143823128	+	1	NA	promoter-TSS (NM_007856)	promoter-TSS (NM_007856)	-45	NM_007856	13360	Mm.249342	NM_007856	ENSMUSG00000058454	Dhcr7	AA409147	7-dehydrocholesterol reductase	protein-coding
mm_152597.1	chr19	11640804	11640808	-	1	NA	promoter-TSS (NM_133246)	promoter-TSS (NM_133246)	45	NM_133246	170813	Mm.240438	NM_133246	ENSMUSG00000024681	Ms4a3	HTm4	membrane-spanning 4-domains, subfamily A, member 3	protein-coding
mm_5182.1	chr1	12992651	12992666	-	1	NA	Intergenic	CpG	-1523	NM_172841	240726	Mm.24481	NM_172841	ENSMUSG00000025938	Slco5a1	4732454B15|A630033C23Rik|AA407151	solute carrier organic anion transporter family, member 5A1	protein-coding
mm_1290.1	chr1	64301784	64301800	+	1	NA	Intergenic	Intergenic	-180403	NM_033563	93691	Mm.29466	NM_033563	ENSMUSG00000025959	Klf7	9830124P08Rik	Kruppel-like factor 7 (ubiquitous)	protein-coding
mm_160545.1	chr9	44407705	44407705	+	1	NA	promoter-TSS (NM_021789)	promoter-TSS (NM_021789)	-9	NM_024266	75617	Mm.292027	NM_024266	ENSMUSG00000009927	Rps25	2810009D21Rik	ribosomal protein S25	protein-coding
mm_17731.1	chr2	32493416	32493438	-	1	NA	Intergenic	Intergenic	-41932	NM_153560	98952	Mm.4065	NM_153560	ENSMUSG00000039157	Fam102a	AI426465|C230093N12Rik|Eeig1	family with sequence similarity 102, member A	protein-coding
mm_91106.1	chr10	19122219	19122262	-	1	NA	Intergenic	Intergenic	-19509	NR_038021	100504265	Mm.383417	NR_038021		Gm20139	-	predicted gene, 20139	ncRNA
mm_913.1	chr1	55026350	55026376	+	1	NA	intron (NM_031179, intron 1 of 24)	intron (NM_031179, intron 1 of 24)	1115	NM_031179	81898	Mm.279736	NM_031179	ENSMUSG00000025982	Sf3b1	155kDa|2810001M05Rik|AA409119|Prp10|SAP155|SF3b155|TA-8|Targ4	splicing factor 3b, subunit 1	protein-coding
mm_95612.1	chr11	53478852	53478858	+	1	NA	exon (NM_183173, exon 1 of 1)	exon (NM_183173, exon 1 of 1)	1340	NM_183173	237761	Mm.145208	NM_183173	ENSMUSG00000044352	Sowaha	A830006N08Rik|Ankrd43	sosondowah ankyrin repeat domain family member A	protein-coding
mm_86371.1	chr9	123797980	123797990	-	1	NA	intron (NM_148925, intron 16 of 18)	intron (NM_148925, intron 16 of 18)	-8492	NM_030712	80901	Mm.124289	NM_030712	ENSMUSG00000048521	Cxcr6	BB217514|BONZO|STRL33	chemokine (C-X-C motif) receptor 6	protein-coding
mm_43731.1	chr5	139736798	139736803	+	1	NA	promoter-TSS (NM_174850)	promoter-TSS (NM_174850)	-467	NM_174850	231830	Mm.240510	NM_174850	ENSMUSG00000036718	Micall2	A930021H16Rik|JRAB|MICAL-L2|mFLJ00139	MICAL-like 2	protein-coding
mm_3638.1	chr1	152811612	152811631	+	1	NA	intron (NM_010877, intron 3 of 15)	intron (NM_010877, intron 3 of 15)	11468	NM_010877	17970	Mm.270307	NM_010877	ENSMUSG00000026480	Ncf2	NOXA2|Ncf-2|p67phox	neutrophil cytosolic factor 2	protein-coding
mm_160532.1	chr9	38975877	38975877	+	1	NA	exon (NM_146441, exon 1 of 1)	exon (NM_146441, exon 1 of 1)	199	NM_146441	258433	Mm.271361	NM_146441	ENSMUSG00000058515	Olfr933	MOR171-22	olfactory receptor 933	protein-coding
mm_79028.1	chr9	46012811	46012821	+	1	NA	promoter-TSS (NM_027498)	promoter-TSS (NM_027498)	-4	NM_027498	70661	Mm.219459	NM_027498	ENSMUSG00000034135	Sik3	5730525O22Rik|9030204A07Rik|AI447252|AI846254|AI849445|Qsk|SIK-3|mKIAA0999	SIK family kinase 3	protein-coding
mm_32659.1	chr4	115090161	115090165	+	1	NA	intron (NM_026018, intron 2 of 4)	intron (NM_026018, intron 2 of 4)	1455	NM_001164557	67182	Mm.30181	NM_026018	ENSMUSG00000028716	Pdzk1ip1	0610007F13Rik|2700030M23Rik|AU046042|Map17	PDZK1 interacting protein 1	protein-coding
mm_94716.1	chr11	20543131	20543183	+	1	NA	promoter-TSS (NM_021372)	promoter-TSS (NM_021372)	-96	NM_021372	58172	Mm.339676	NM_021372	ENSMUSG00000049800	Sertad2	AB041541|AU021878|Kiaa0127|MNCb-1504|SEI-2|Sei2|TRIP-Br2|mKIAA0127	SERTA domain containing 2	protein-coding
mm_97797.1	chr11	82951367	82951393	+	1	NA	promoter-TSS (NM_183201)	promoter-TSS (NM_183201)	-722	NM_183201	327978	Mm.42147	NM_183201	ENSMUSG00000054404	Slfn5	AI956840	schlafen 5	protein-coding
mm_29742.1	chr3	126922958	126922968	-	1	NA	3' UTR (NM_178655, exon 25 of 25)	3' UTR (NM_178655, exon 25 of 25)	20423	NM_001034168	109676	Mm.220242	NM_178655	ENSMUSG00000032826	Ank2	100043364|AI835472|AW491075|Ank-2|Gm4392	ankyrin 2, brain	protein-coding
mm_5825.1	chr1	52799486	52799518	-	1	NA	5' UTR (NM_008384, exon 2 of 6)	5' UTR (NM_008384, exon 2 of 6)	18186	NM_008384	16329	Mm.917	NM_008384	ENSMUSG00000026102	Inpp1	2300002C06Rik|AV137389	inositol polyphosphate-1-phosphatase	protein-coding
mm_122392.1	chr14	40966853	40966869	-	1	NA	promoter-TSS (NM_145928)	promoter-TSS (NM_145928)	35	NM_145928	52588	Mm.28876	NM_145928	ENSMUSG00000037824	Tspan14	AA958793|D14Ertd226e|Tm4sf14|tspan-14	tetraspanin 14	protein-coding
mm_141553.1	chr17	32189458	32189476	-	1	NA	promoter-TSS (NM_001033163)	promoter-TSS (NM_001033163)	-4	NM_001033163	71932	Mm.176240	NM_001033163	ENSMUSG00000037577	Ephx3	2310063B19Rik|Abhd9	epoxide hydrolase 3	protein-coding
mm_127806.1	chr15	4988351	4988367	-	1	NA	TTS (NM_001243837)	TTS (NM_001243837)	75414	NM_001243837	109828	Mm.208034	NM_001243837	ENSMUSG00000079105	C7	A530026G17|Gm1238	complement component 7	protein-coding
mm_89722.1	chr10	98915118	98915172	+	1	NA	promoter-TSS (NM_026482)	promoter-TSS (NM_026482)	-7	NM_026482	67972	Mm.166944	NM_026482	ENSMUSG00000019943	Atp2b1	2810442I22Rik|E130111D10Rik|Pmca1	ATPase, Ca++ transporting, plasma membrane 1	protein-coding
mm_16913.1	chr2	13493675	13493690	-	1	NA	Intergenic	Intergenic	-1806	NM_001081084	65969	Mm.313915	NM_001081084	ENSMUSG00000026726	Cubn	AA408369|AL022750|D2Wsu88e	cubilin (intrinsic factor-cobalamin receptor)	protein-coding
mm_75724.1	chr8	69089201	69089215	-	1	NA	promoter-TSS (NM_153054)	promoter-TSS (NM_153054)	14	NM_153054	110877	Mm.19301	NM_153054	ENSMUSG00000036330	Slc18a1	4832416I10Rik|Vat1|Vmat1	solute carrier family 18 (vesicular monoamine), member 1	protein-coding
mm_63087.1	chr7	122295752	122295755	+	1	NA	intron (NM_001316672, intron 2 of 16)	intron (NM_001316672, intron 2 of 16)	6628	NM_008855	18751	Mm.207496	NM_008855	ENSMUSG00000052889	Prkcb	PKC-B|PKC-Beta|Pkcb|Prkcb1|Prkcb2	protein kinase C, beta	protein-coding
mm_66767.1	chr7	46729163	46729169	-	1	NA	3' UTR (NM_011316, exon 4 of 4)	3' UTR (NM_011316, exon 4 of 4)	3437	NM_011316	20211	Mm.3489	NM_011316	ENSMUSG00000040017	Saa4	Saa-4|Saa-5	serum amyloid A 4	protein-coding
mm_142154.1	chr17	36032564	36032575	-	1	NA	intron (NM_010398, intron 1 of 6)	intron (NM_010398, intron 1 of 6)	132	NM_010398	15040	Mm.439648	NM_010398	ENSMUSG00000067212	H2-T23	37b|37c|H-2T23|H2-Qa1|Qa-1|Qa-1(b)|Qa1|Qed-1|T18c|T18c(37)|T23b|T23d	histocompatibility 2, T region locus 23	protein-coding
mm_169872.1	chr16	36072115	36072116	+	1	NA	promoter-TSS (NM_027342)	promoter-TSS (NM_027342)	455	NM_001159421	381045	Mm.310434	NM_198645	ENSMUSG00000075229	Ccdc58	A930007B11Rik|AI413631	coiled-coil domain containing 58	protein-coding
mm_15654.1	chr2	163203173	163203179	+	1	NA	Intergenic	CpG	-22278	NM_001098799	269389	Mm.207709	NM_001098799	ENSMUSG00000074607	Tox2	AI851523|AV026525|BI987407|Gcx1|RxHMG1	TOX high mobility group box family member 2	protein-coding
mm_170481.1	chr19	12503090	12503093	+	1	NA	Intergenic	Intergenic	-1095	NM_172442	207521	Mm.247695	NM_172442	ENSMUSG00000039982	Dtx4	AI449438|BC044798|D930042H13|RNF155	deltex 4, E3 ubiquitin ligase	protein-coding
mm_129580.1	chr15	79741302	79741315	-	1	NA	intron (NM_001205346, intron 1 of 17)	intron (NM_001205346, intron 1 of 17)	1228	NM_194342	223697	Mm.202715	NM_194342	ENSMUSG00000042524	Sun2	B230369L08Rik|C030011B15|Unc84b	Sad1 and UNC84 domain containing 2	protein-coding
mm_78256.1	chr9	21835490	21835504	+	1	NA	promoter-TSS (NM_001080940)	promoter-TSS (NM_001080940)	-13	NM_001080940	624219	Mm.440264	NM_001080940	ENSMUSG00000047822	Angptl8	EG624219|Gm6484|Rifl	angiopoietin-like 8	protein-coding
mm_87268.1	chr10	41685915	41685963	+	1	NA	Intergenic	Intergenic	-79344	NM_001303469	75973	Mm.228517	NM_029493	ENSMUSG00000075225	Ccdc162	5033413D22Rik|Ccdc162p|Gm29096|Gm61|Gm6976	coiled-coil domain containing 162	protein-coding
mm_170396.1	chr1	86358199	86358210	-	1	NA	exon (NM_010880, exon 2 of 14)	exon (NM_010880, exon 2 of 14)	1251	NM_010880	17975	Mm.154378	NM_010880	ENSMUSG00000026234	Ncl	B530004O11Rik|C23|D0Nds28|D1Nds28|Nucl	nucleolin	protein-coding
mm_125540.1	chr15	58141398	58141417	+	1	NA	promoter-TSS (NM_001326602)	promoter-TSS (NM_001326602)	41	NM_001326599	76773	Mm.26771	NM_029734	ENSMUSG00000022359	Wdyhv1	2410187C16Rik|AU014961|AW550036|Ntaq1	WDYHV motif containing 1	protein-coding
mm_44734.1	chr5	31138876	31138887	-	1	NA	promoter-TSS (NM_021290)	promoter-TSS (NM_021290)	14	NM_021290	22226	Mm.377116	NM_021290	ENSMUSG00000038676	Ucn	Mpv17|Ucn1	urocortin	protein-coding
mm_58575.1	chr7	4877048	4877111	+	1	NA	promoter-TSS (NM_001101598)	promoter-TSS (NM_001101598)	26	NM_001101598	664994	Mm.302624	NM_001101598	ENSMUSG00000086784	Isoc2a	Isoc2	isochorismatase domain containing 2a	protein-coding
mm_115059.1	chr13	100676141	100676150	+	1	NA	intron (NM_183115, intron 1 of 11)	intron (NM_183115, intron 1 of 11)	6664	NM_001168386	76041	Mm.23977	NM_183115	ENSMUSG00000048924	Ccdc125	5830436D01Rik|AL023012	coiled-coil domain containing 125	protein-coding
mm_128622.1	chr15	58956582	58956585	-	1	NA	exon (NM_144800, exon 8 of 15)	exon (NM_144800, exon 8 of 15)	22773	NM_023172	66218	Mm.322294	NM_023172	ENSMUSG00000022354	Ndufb9	1190008J14Rik	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 9	protein-coding
mm_11430.1	chr2	31962063	31962072	+	1	NA	intron (NM_145144, intron 2 of 5)	intron (NM_145144, intron 2 of 5)	11764	NM_145144	108897	Mm.24838	NM_145144	ENSMUSG00000001864	Aif1l	2810003C17Rik|AI043124|C87647|Iba2	allograft inflammatory factor 1-like	protein-coding
mm_1180.1	chr1	61638994	61639013	+	1	NA	5' UTR (NM_001081050, exon 1 of 23)	5' UTR (NM_001081050, exon 1 of 23)	179	NM_001081050	72823	Mm.35153	NM_001081050	ENSMUSG00000052062	Pard3b	1810008K04Rik|2010002N16Rik|2810455B10Rik|Als2cr19|PAR3B|PAR3L|PAR3beta	par-3 family cell polarity regulator beta	protein-coding
mm_33617.1	chr4	132624324	132624330	+	1	NA	Intergenic	RMER19B|LTR|ERVK	-14719	NM_210071	14050	Mm.227733	NM_010166	ENSMUSG00000028886	Eya3	AI844637	EYA transcriptional coactivator and phosphatase 3	protein-coding
mm_7877.1	chr1	133019389	133019407	-	1	NA	5' UTR (NM_008575, exon 2 of 12)	5' UTR (NM_008575, exon 2 of 12)	6018	NR_126506	17248	Mm.426531	NM_008575	ENSMUSG00000054387	Mdm4	4933417N07Rik|AA414968|AL023055|AU018793|AU021806|C85810|Mdmx	transformed mouse 3T3 cell double minute 4	protein-coding
mm_138029.1	chr17	33919471	33919477	+	1	NA	promoter-TSS (NM_009318)	promoter-TSS (NM_009318)	-4	NM_001025313	21356	Mm.154457	NM_009318	ENSMUSG00000024308	Tapbp	D17Wsu91e|TPN	TAP binding protein	protein-coding
mm_25796.1	chr3	127632799	127632810	+	1	NA	promoter-TSS (NM_009718)	promoter-TSS (NM_009718)	-341	NM_009718	11924	Mm.42017	NM_009718	ENSMUSG00000027967	Neurog2	Atoh4|Math4A|bHLHa8|ngn-2|ngn2	neurogenin 2	protein-coding
mm_101614.1	chr11	35834493	35834509	-	1	NA	promoter-TSS (NM_025936)	promoter-TSS (NM_025936)	27	NM_025936	104458	Mm.284906	NM_025936	ENSMUSG00000018848	Rars	2610011N19Rik|2610037E21Rik|AL033339|AW985894	arginyl-tRNA synthetase	protein-coding
mm_144068.1	chr17	90992561	90992566	-	1	NA	intron (NM_001346957, intron 2 of 18)	intron (NM_001346957, intron 2 of 18)	97042	NM_001346957	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_106441.1	chr11	119834348	119834360	-	1	NA	promoter-TSS (NR_045313)	promoter-TSS (NR_045313)	11	NR_045313	319454	Mm.442144	NR_045312	ENSMUSG00000085081	Rptoros	A430071A18Rik	regulatory associated protein of MTOR, complex 1, opposite strand	ncRNA
mm_117346.1	chr13	69611350	69611362	-	1	NA	promoter-TSS (NM_145354)	promoter-TSS (NM_145354)	107	NM_175283	78925	Mm.451912	NM_175283	ENSMUSG00000021594	Srd5a1	0610031P22Rik|4930435F02Rik|S5AR 1|Srd5a-1	steroid 5 alpha-reductase 1	protein-coding
mm_123619.1	chr14	68120947	68120960	-	1	NA	exon (NM_008691, exon 3 of 3)	exon (NM_008691, exon 3 of 3)	-2799	NR_045897	100043072	Mm.242832	NR_045897		A230070E04Rik	Gm4210	RIKEN cDNA A230070E04 gene	ncRNA
mm_30058.1	chr3	137336128	137336130	-	1	NA	Intergenic	Intergenic	-4949	NM_001163522	59308	Mm.27343	NM_016885	ENSMUSG00000054690	Emcn	0610012K22Rik|AI315669|Muc14	endomucin	protein-coding
mm_25916.1	chr3	131156287	131156300	+	1	NA	intron (NM_001276403, intron 3 of 11)	intron (NM_001276403, intron 3 of 11)	43502	NM_001276403	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_119086.1	chr14	30890162	30890169	+	1	NA	exon (NM_001289633, exon 5 of 22)	exon (NM_001289633, exon 5 of 22)	3689	NM_001289632	16427	Mm.34819	NM_018746	ENSMUSG00000021922	Itih4	ITI-HC4|Itih-4|PK-120	inter alpha-trypsin inhibitor, heavy chain 4	protein-coding
mm_58347.1	chr6	147263934	147263940	-	1	NA	promoter-TSS (NM_008970)	promoter-TSS (NM_008970)	76	NM_008970	19227	Mm.28440	NM_008970	ENSMUSG00000048776	Pthlh	PLP|PTH-like|Pthrp	parathyroid hormone-like peptide	protein-coding
mm_69250.1	chr7	127841474	127841481	-	1	NA	promoter-TSS (NM_009294)	promoter-TSS (NM_009294)	-331	NM_009294	20909	Mm.24867	NM_009294	ENSMUSG00000030805	Stx4a	Stx4|Syn-4|Syn4	syntaxin 4A (placental)	protein-coding
mm_86721.1	chr10	19044177	19044189	+	1	NA	Intergenic	Intergenic	-28773	NM_009397	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_170411.1	chr18	66200420	66200435	+	1	NA	intron (NM_178793, intron 2 of 10)	MTA_Mm|LTR|ERVL-MaLR	18906	NR_030467	751558		NR_030467	ENSMUSG00000076147	Mir694	Mirn694|mir-694|mmu-mir-694	microRNA 694	ncRNA
mm_133366.1	chr16	84705645	84705648	+	1	NA	Intergenic	Intergenic	-7377	NR_132106	100653389	Mm.261808	NR_132106	ENSMUSG00000097418	Mir155hg	Bic|Gm26667	Mir155 host gene (non-protein coding)	ncRNA
mm_115608.1	chr13	11991869	11991884	-	1	NA	intron (NM_023868, intron 1 of 104)	(TC)n|Simple_repeat|Simple_repeat	115069	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding
mm_96951.1	chr11	70562981	70563031	+	1	NA	5' UTR (NM_001045964, exon 1 of 33)	5' UTR (NM_001045964, exon 1 of 33)	125	NM_016713	50932	Mm.42967	NM_016713	ENSMUSG00000020827	Mink1	B55|MINK|Map4k6|Ysk2	misshapen-like kinase 1 (zebrafish)	protein-coding
mm_67845.1	chr7	98562983	98563004	-	1	NA	Intergenic	Intergenic	68771	NM_001113379	434215	Mm.323057	NM_001113379	ENSMUSG00000090958	Lrrc32	AI426318|D11S833Eh|D7H11S833E|EG434215|Garp	leucine rich repeat containing 32	protein-coding
mm_171903.1	chr5	43204982	43204987	+	1	NA	intron (NR_028417, intron 1 of 7)	MT2_Mm|LTR|ERVL	-28479	NM_175937	231207	Mm.7233	NM_175937	ENSMUSG00000039782	Cpeb2	A630055H10Rik|Cpe-bp2	cytoplasmic polyadenylation element binding protein 2	protein-coding
mm_66874.1	chr7	57509412	57509425	-	1	NA	intron (NM_176942, intron 1 of 9)	CpG	591	NM_176942	110886	Mm.273114	NM_176942	ENSMUSG00000055078	Gabra5	A230018I05Rik	gamma-aminobutyric acid (GABA) A receptor, subunit alpha 5	protein-coding
mm_161083.1	chr12	84642531	84642531	+	1	NA	promoter-TSS (NM_001033776)	promoter-TSS (NM_001033776)	-24	NM_001168588	432677	Mm.311913	NM_001033776	ENSMUSG00000071235	Vrtn	7420416P09Rik	vertebrae development associated	protein-coding
mm_38517.1	chr4	141416003	141416016	-	1	NA	promoter-TSS (NM_019701)	promoter-TSS (NM_019701)	-21	NM_019701	56365	Mm.24882	NM_019701	ENSMUSG00000006216	Clcnkb	CLCKB|Clc-Ka|Clck2|Clcnk1l	chloride channel, voltage-sensitive Kb	protein-coding
mm_140265.1	chr17	84683085	84683089	+	1	NA	promoter-TSS (NM_031884)	promoter-TSS (NM_031884)	-34	NM_001347418	67470	Mm.26581	NM_026180	ENSMUSG00000024254	Abcg8	1300003C16Rik|AI114946|sterolin-2	ATP-binding cassette, sub-family G (WHITE), member 8	protein-coding
mm_95973.1	chr11	58954719	58954729	+	1	NA	promoter-TSS (NM_178218)	promoter-TSS (NM_178218)	39	NM_178218	319162	Mm.212549	NM_178218	ENSMUSG00000078851	Hist3h2a	-	histone cluster 3, H2a	protein-coding
mm_19791.1	chr2	109167531	109167531	-	1	NA	intron (NM_029790, intron 3 of 5)	Lx9|LINE|L1	110759	NM_029790	76894	Mm.330451	NM_029790	ENSMUSG00000057234	Mettl15	0610027B03Rik|AI303697|AW049952|Mett5d1	methyltransferase like 15	protein-coding
mm_83381.1	chr9	44567764	44567775	-	1	NA	Intergenic	B4A|SINE|B4	-37123	NM_001110826	13209	Mm.267061	NM_007841	ENSMUSG00000032097	Ddx6	1110001P04Rik|E230023J21Rik|HLR2|mRCK/P54|p54|rck	DEAD (Asp-Glu-Ala-Asp) box polypeptide 6	protein-coding
mm_109346.1	chr12	109603039	109603067	+	1	NA	promoter-TSS (NR_028261)	promoter-TSS (NR_028261)	-892	NR_028261	75745	Mm.293263	NR_028261		Rian	5530401N18Rik|C130089L09Rik|Meg8	RNA imprinted and accumulated in nucleus	ncRNA
mm_100106.1	chr11	115776237	115776277	+	1	NA	intron (NM_028014, intron 1 of 31)	intron (NM_028014, intron 1 of 31)	10824	NM_028014	71947	Mm.23168	NM_028014	ENSMUSG00000020747	Tmem94	2310067B10Rik|Kiaa0195|mKIAA0195	transmembrane protein 94	protein-coding
mm_134343.1	chr16	16560202	16560223	-	1	NA	promoter-TSS (NM_139232)	promoter-TSS (NM_139232)	7	NM_139232	224014	Mm.256131	NM_139232	ENSMUSG00000022788	Fgd4	9030023J02Rik|9330209B17Rik|Frabp|ZFYVE6	FYVE, RhoGEF and PH domain containing 4	protein-coding
mm_143218.1	chr17	62882984	62883036	-	1	NA	Intergenic	CpG-6536	-1693	NM_010109	13640	Mm.7978	NM_010109	ENSMUSG00000048915	Efna5	AL-1|AV158822|EFL-5|Ephrin-A5|Epl7|LERK-7|RAGS	ephrin A5	protein-coding
mm_159300.1	chr2	176708334	176708334	+	1	NA	promoter-TSS (NM_001099327)	promoter-TSS (NM_001099327)	-19	NM_001099327	100043387	Mm.444048	NM_001099327	ENSMUSG00000078878	Gm14305	OTTMUSG00000016251	predicted gene 14305	protein-coding
mm_3645.1	chr1	152903804	152903814	+	1	NA	Intergenic	CpG-603	-1163	NM_001005507	226517	Mm.270775	NM_001005507	ENSMUSG00000042772	Smg7	9430023P16Rik|mKIAA0250	Smg-7 homolog, nonsense mediated mRNA decay factor (C. elegans)	protein-coding
mm_132682.1	chr16	42955556	42955565	+	1	NA	promoter-TSS (NR_002445)	promoter-TSS (NR_002445)	-20	NR_002445	170658	Mm.375824	NR_002445		BC002163	-	NADH dehydrogenase Fe-S protein 5 pseudogene	pseudo
mm_137541.1	chr17	27556762	27556779	+	1	NA	5' UTR (NM_016660, exon 1 of 5)	intron (NM_001025427, intron 1 of 4)	117	NM_001166477	111241	Mm.426212	NM_001166476	ENSMUSG00000078249	Hmga1-rs1	ENSMUSG00000041059|Hmgi-rs1	high mobility group AT-hook I, related sequence 1	protein-coding
mm_106216.1	chr11	116853084	116853099	-	1	NA	promoter-TSS (NM_178620)	promoter-TSS (NM_178620)	3	NM_011358	20382	Mm.21841	NM_011358	ENSMUSG00000034120	Srsf2	D11Wsu175e|MRF-1|Pr264|SC35|Sfrs10|Sfrs2	serine/arginine-rich splicing factor 2	protein-coding
mm_54208.1	chr6	25689316	25689339	-	1	NA	5' UTR (NM_010338, exon 1 of 2)	5' UTR (NM_010338, exon 1 of 2)	653	NM_010338	14763	Mm.409670	NM_010338	ENSMUSG00000039904	Gpr37	AI848630|Pael-R	G protein-coupled receptor 37	protein-coding
mm_162997.1	chr11	30139442	30139452	-	1	NA	exon (NM_009260, exon 13 of 31)	exon (NM_009260, exon 13 of 31)	58810	NM_009260	20742	Mm.123110	NM_009260	ENSMUSG00000020315	Sptbn1	9930031C03Rik|AL033301|SPTB2|Spnb-2|Spnb2|elf1|elf3|mKIAA4049	spectrin beta, non-erythrocytic 1	protein-coding
mm_101492.1	chr11	31779460	31779503	-	1	NA	Intergenic	Intergenic	45066	NR_102310	414116	Mm.150222	NR_102310	ENSMUSG00000085772	D630024D03Rik	-	RIKEN cDNA D630024D03 gene	ncRNA
mm_109984.1	chr12	13249199	13249224	-	1	NA	promoter-TSS (NM_134040)	promoter-TSS (NM_134040)	-37	NM_134040	104721	Mm.251255	NM_134040	ENSMUSG00000037149	Ddx1	AA409185|DBP-RB	DEAD (Asp-Glu-Ala-Asp) box polypeptide 1	protein-coding
mm_120100.1	chr14	58072281	58072305	+	1	NA	promoter-TSS (NM_013518)	promoter-TSS (NM_013518)	-393	NM_013518	14180	Mm.8846	NM_013518	ENSMUSG00000021974	Fgf9	Eks	fibroblast growth factor 9	protein-coding
mm_55990.1	chr6	85961962	85961974	-	1	NA	promoter-TSS (NM_028099)	promoter-TSS (NM_028099)	-301	NM_028099	72102	Mm.24007	NM_028099	ENSMUSG00000030002	Dusp11	2010300F21Rik|AI481497	dual specificity phosphatase 11 (RNA/RNP complex 1-interacting)	protein-coding
mm_129435.1	chr15	78495213	78495223	-	1	NA	promoter-TSS (NM_008368)	promoter-TSS (NM_008368)	-152	NM_008368	16185	Mm.35287	NM_008368	ENSMUSG00000068227	Il2rb	CD122|IL-15Rbeta|IL15Rbeta|Il-2/15Rbeta|Il-2Rbeta|p70	interleukin 2 receptor, beta chain	protein-coding
mm_35989.1	chr4	55530939	55530956	-	1	NA	exon (NM_010637, exon 3 of 5)	exon (NM_010637, exon 3 of 5)	1528	NM_010637	16600	Mm.4325	NM_010637	ENSMUSG00000003032	Klf4	EZF|Gklf|Zie	Kruppel-like factor 4 (gut)	protein-coding
mm_45806.1	chr5	87591568	87591578	-	1	NA	promoter-TSS (NM_023135)	promoter-TSS (NM_023135)	38	NM_023135	20860	Mm.89655	NM_023135	ENSMUSG00000029272	Sult1e1	EST|ST1E1|Ste	sulfotransferase family 1E, member 1	protein-coding
mm_106108.1	chr11	116306697	116306750	-	1	NA	promoter-TSS (NM_001162872)	promoter-TSS (NM_001162872)	15	NM_016857	53413	Mm.22530	NM_016857	ENSMUSG00000020792	Exoc7	Exo70|sec70	exocyst complex component 7	protein-coding
mm_133376.1	chr16	84710485	84710495	+	1	NA	Intergenic	Intergenic	-2533	NR_132106	100653389	Mm.261808	NR_132106	ENSMUSG00000097418	Mir155hg	Bic|Gm26667	Mir155 host gene (non-protein coding)	ncRNA
mm_104027.1	chr11	86201145	86201200	-	1	NA	promoter-TSS (NM_178309)	promoter-TSS (NM_178309)	21	NM_178309	237911	Mm.186143	NM_178309	ENSMUSG00000034329	Brip1	3110009N10Rik|8030460J03Rik|Bach1|FACJ|Fancj|OF	BRCA1 interacting protein C-terminal helicase 1	protein-coding
mm_152842.1	chr19	23448357	23448378	-	1	NA	promoter-TSS (NM_174857)	promoter-TSS (NM_174857)	-45	NM_174857	71738	Mm.50841	NM_174857	ENSMUSG00000033207	Mamdc2	1200015L10Rik|AI591564|mamcan	MAM domain containing 2	protein-coding
mm_84952.1	chr9	83250126	83250132	-	1	NA	Intergenic	Intergenic	-103522	NM_026122	94353	Mm.244426	NM_026122	ENSMUSG00000066456	Hmgn3	1110002A15Rik|6330514M13Rik|BB071015|TRIP7	high mobility group nucleosomal binding domain 3	protein-coding
mm_149588.1	chr19	16132813	16132910	+	1	NA	promoter-TSS (NM_008139)	promoter-TSS (NM_008139)	30	NM_008139	14682	Mm.439701	NM_008139	ENSMUSG00000024639	Gnaq	1110005L02Rik|6230401I02Rik|AA408290|AW060788|Dsk1|Dsk10|Galphaq|Gq|GqI	guanine nucleotide binding protein, alpha q polypeptide	protein-coding
mm_88709.1	chr10	80150953	80150979	+	1	NA	intron (NM_001347117, intron 2 of 7)	CpG-1261	1284	NM_001305799	59090	Mm.143813	NM_021565	ENSMUSG00000035621	Midn	3000003C15Rik	midnolin	protein-coding
mm_83667.1	chr9	49715961	49715987	-	1	NA	intron (NM_001081445, intron 1 of 17)	intron (NM_001081445, intron 1 of 17)	83095	NM_001081445	17967	Mm.4974	NM_010875	ENSMUSG00000039542	Ncam1	CD56|E-NCAM|NCAM-1|Ncam	neural cell adhesion molecule 1	protein-coding
mm_142296.1	chr17	40880526	40880579	-	1	NA	promoter-TSS (NM_027834)	promoter-TSS (NM_027834)	6	NM_027834	71583	Mm.158733	NM_027834	ENSMUSG00000054951	9130008F23Rik	-	RIKEN cDNA 9130008F23 gene	protein-coding
mm_163483.1	chr12	108760828	108760863	+	1	NA	Intergenic	MMAR1|DNA|TcMar-Mariner	-32466	NM_009537	22632	Mm.3868	NM_009537	ENSMUSG00000021264	Yy1	AW488674|NF-E1	YY1 transcription factor	protein-coding
mm_115260.1	chr13	110400687	110400690	+	1	NA	3' UTR (NM_152804, exon 14 of 14)	3' UTR (NM_152804, exon 14 of 14)	5644	NM_152804	20620	Mm.380	NM_152804	ENSMUSG00000021701	Plk2	Snk	polo-like kinase 2	protein-coding
mm_39446.1	chr5	17574424	17574439	+	1	NA	promoter-TSS (NM_013657)	promoter-TSS (NM_013657)	-385	NM_013657	20348	Mm.5071	NM_013657	ENSMUSG00000028780	Sema3c	1110036B02Rik|SemE|Semae	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	protein-coding
mm_160585.1	chr9	64235270	64235270	+	1	NA	promoter-TSS (NM_033607)	promoter-TSS (NM_033607)	69	NM_033607	93841	Mm.390180	NM_033607	ENSMUSG00000035337	Uchl4	-	ubiquitin carboxyl-terminal esterase L4	protein-coding
mm_93875.1	chr10	123264685	123264712	-	1	NA	non-coding (NR_045514, exon 1 of 6)	non-coding (NR_045514, exon 1 of 6)	622	NM_001252387	268354	Mm.51939	NM_182807	ENSMUSG00000044071	Fam19a2	6330575M02|FAM19A2 TAFA-2|TAFA2|Tafa-2	family with sequence similarity 19, member A2	protein-coding
mm_91534.1	chr10	39122278	39122279	-	1	NA	5' UTR (NM_183254, exon 3 of 5)	5' UTR (NM_183254, exon 3 of 5)	11617	NM_183254	66337	Mm.45187	NM_183254	ENSMUSG00000051736	Fam229b	1700025K23Rik	family with sequence similarity 229, member B	protein-coding
mm_16503.1	chr2	181240600	181240635	+	1	NA	exon (NM_183162, exon 2 of 19)	exon (NM_183162, exon 2 of 19)	1410	NM_183162	229003	Mm.315872	NM_183162	ENSMUSG00000027580	Helz2	PDIP1|Pric285|mKIAA1769|mPDIP1	helicase with zinc finger 2, transcriptional coactivator	protein-coding
mm_51655.1	chr6	86078071	86078089	+	1	NA	promoter-TSS (NM_001271861)	promoter-TSS (NM_001271861)	32	NM_001271859	11519	Mm.104155	NM_013458	ENSMUSG00000030000	Add2	2900072M03Rik|add97	adducin 2 (beta)	protein-coding
mm_59.1	chr1	6574170	6574193	+	1	NA	intron (NM_001244693, intron 2 of 22)	intron (NM_001244693, intron 2 of 22)	86950	NM_001244692	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding
mm_95391.1	chr11	49250543	49250572	+	1	NA	promoter-TSS (NM_001110150)	promoter-TSS (NM_001110150)	5	NM_001110150	17308	Mm.196933	NM_010794	ENSMUSG00000020346	Mgat1	Mgat-1	mannoside acetylglucosaminyltransferase 1	protein-coding
mm_80350.1	chr9	75184177	75184196	+	1	NA	intron (NM_010864, intron 25 of 40)	intron (NM_010864, intron 25 of 40)	-47828	NM_001081322	208943	Mm.41339	NM_001081322	ENSMUSG00000033590	Myo5c	9130003O20Rik|BB085560|C330029I24	myosin VC	protein-coding
mm_124316.1	chr14	103219159	103219180	-	1	NA	intron (NM_207215, intron 33 of 84)	Lx4B|LINE|L1	-119603	NM_001347600	50789	Mm.214746	NM_015822	ENSMUSG00000022124	Fbxl3	AU041772|AW212966|FBK|Fbl3a|Fbxl3a|Ovtm|Play68	F-box and leucine-rich repeat protein 3	protein-coding
mm_115338.1	chr13	112489976	112489983	+	1	NA	intron (NM_010560, intron 7 of 16)	intron (NM_010560, intron 7 of 16)	25909	NM_010560	16195	Mm.4364	NM_010560	ENSMUSG00000021756	Il6st	5133400A03Rik|AA389424|BB405851|CD130|D13Ertd699e|gp130	interleukin 6 signal transducer	protein-coding
mm_127628.1	chr15	102462520	102462536	+	1	NA	3' UTR (NM_025385, exon 5 of 5)	3' UTR (NM_025385, exon 5 of 5)	3358	NM_025385	66151	Mm.393955	NM_025385	ENSMUSG00000023048	Prr13	1110020C13Rik|2010324E22Rik	proline rich 13	protein-coding
mm_83116.1	chr9	40390395	40390401	-	1	NA	intron (NM_172768, intron 2 of 19)	intron (NM_172768, intron 2 of 19)	56926	NR_040728	73558	Mm.398307	NR_040728		1700110K17Rik	-	RIKEN cDNA 1700110K17 gene	ncRNA
mm_35829.1	chr4	47474284	47474349	-	1	NA	promoter-TSS (NM_024171)	promoter-TSS (NM_024171)	51	NM_019998	56737	Mm.22218	NM_019998	ENSMUSG00000039740	Alg2	1110018A23Rik|1300013N08Rik|ALPG2|CDGIi|MNCb-5081	asparagine-linked glycosylation 2 (alpha-1,3-mannosyltransferase)	protein-coding
mm_83280.1	chr9	43105776	43105793	-	1	NA	promoter-TSS (NM_027144)	promoter-TSS (NM_027144)	-66	NM_027144	69632	Mm.275266	NM_027144	ENSMUSG00000059495	Arhgef12	2310014B11Rik|AU019857|Larg|mKIAA0382	Rho guanine nucleotide exchange factor (GEF) 12	protein-coding
mm_106242.1	chr11	117780631	117780688	-	1	NA	promoter-TSS (NM_181321)	promoter-TSS (NM_181321)	24	NM_145439	217353	Mm.286963	NM_145439	ENSMUSG00000025572	Tmc6	D11Ertd204e|EVER1	transmembrane channel-like gene family 6	protein-coding
mm_144184.1	chr18	7868474	7868494	+	1	NA	promoter-TSS (NM_001146298)	promoter-TSS (NM_001146298)	-348	NM_001282093	225131	Mm.204524	NM_153085	ENSMUSG00000024283	Wac	1110067P07Rik|A230035H12Rik|AI256735|AI256776|Wwp4	WW domain containing adaptor with coiled-coil	protein-coding
mm_74275.1	chr8	125109187	125109190	+	1	NA	intron (NM_174853, intron 3 of 11)	intron (NM_174853, intron 3 of 11)	54993	NM_174854	244667	Mm.233504	NM_170596	ENSMUSG00000043051	Disc1	-	disrupted in schizophrenia 1	protein-coding
mm_104819.1	chr11	98999228	98999240	-	1	NA	exon (NM_011623, exon 28 of 36)	exon (NM_011623, exon 28 of 36)	-16218	NM_178596	353155	Mm.453253	NM_178596	ENSMUSG00000047197	Gjd3	Gja11|Gjc1|cx30.2	gap junction protein, delta 3	protein-coding
mm_7982.1	chr1	134099255	134099294	-	1	NA	Intergenic	Intergenic	-11968	NM_001284524	71884	Mm.328268	NM_027979	ENSMUSG00000026450	Chit1	2300002L19Rik	chitinase 1 (chitotriosidase)	protein-coding
mm_142609.1	chr17	46830100	46830148	-	1	NA	intron (NM_001100452, intron 1 of 10)	intron (NM_001100452, intron 1 of 10)	1289	NM_001100452	210982	Mm.37642	NM_001100452	ENSMUSG00000036568	Gltscr1l	mKIAA0240	GLTSCR1-like	protein-coding
mm_81823.1	chr9	118049763	118049773	+	1	NA	intron (NM_001286507, intron 3 of 6)	intron (NM_001286507, intron 3 of 6)	9246	NM_013727	27215	Mm.92705	NM_013727	ENSMUSG00000039285	Azi2	AA410145|AZ2	5-azacytidine induced gene 2	protein-coding
mm_68680.1	chr7	118995092	118995105	-	1	NA	5' UTR (NM_001195774, exon 1 of 4)	5' UTR (NM_001195774, exon 1 of 4)	113	NM_022420	64297	Mm.103439	NM_022420	ENSMUSG00000008734	Gprc5b	AW125761|Raig2	G protein-coupled receptor, family C, group 5, member B	protein-coding
mm_136233.1	chr16	90726764	90726777	-	1	NA	intron (NM_025642, intron 1 of 4)	MIR|SINE|MIR	601	NM_025642	66578	Mm.180363	NM_025642	ENSMUSG00000022978	Mis18a	2610039C10Rik|2810018N07Rik	MIS18 kinetochore protein A	protein-coding
mm_76073.1	chr8	78813190	78813200	-	1	NA	intron (NM_030145, intron 1 of 3)	intron (NM_030145, intron 1 of 3)	7957	NM_001191004	78651	Mm.28694	NM_030145	ENSMUSG00000031683	Lsm6	1500031N17Rik|2410088K19Rik|AI747288	LSM6 homolog, U6 small nuclear RNA and mRNA degradation associated	protein-coding
mm_28922.1	chr3	98858124	98858139	-	1	NA	intron (NM_001304800, intron 1 of 3)	intron (NM_001304800, intron 1 of 3)	1663	NM_001304800	15492	Mm.140811	NM_008293	ENSMUSG00000027871	Hsd3b1	3-beta-HSD I|D3Ertd383e	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1	protein-coding
mm_143134.1	chr17	57217889	57217899	-	1	NA	promoter-TSS (NR_105944)	promoter-TSS (NR_105944)	-666	NR_105944	102465591		NR_105944	ENSMUSG00000099066	Mir6978	Gm27858|mmu-mir-6978	microRNA 6978	ncRNA
mm_48107.1	chr5	137108915	137108943	-	1	NA	Intergenic	ID_B1|SINE|B4	7278	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_128798.1	chr15	66813198	66813226	-	1	NA	intron (NM_009192, intron 1 of 8)	intron (NM_009192, intron 1 of 8)	18617	NM_001029841	20491	Mm.7601	NM_009192	ENSMUSG00000022372	Sla	Slap|Slap-1	src-like adaptor	protein-coding
mm_93355.1	chr10	103028604	103028657	-	1	NA	5' UTR (NM_172553, exon 1 of 4)	5' UTR (NM_172553, exon 1 of 4)	147	NM_172553	216285	Mm.19287	NM_172553	ENSMUSG00000036602	Alx1	AI314867|C130005I02|Cart1	ALX homeobox 1	protein-coding
mm_28514.1	chr3	92584398	92584405	-	1	NA	exon (NM_008574, exon 2 of 2)	exon (NM_008574, exon 2 of 2)	4623	NM_008574	17235	Mm.331192	NM_008574		Smcp	Mcs|Mcsp	sperm mitochondria-associated cysteine-rich protein	protein-coding
mm_83884.1	chr9	55411252	55411278	-	1	NA	intron (NM_172923, intron 5 of 10)	intron (NM_172923, intron 5 of 10)	84316	NM_172923	244886	Mm.24361	NM_172923	ENSMUSG00000032313	Tmem266	9630029F15|AI118078|HVRP1	transmembrane protein 266	protein-coding
mm_23158.1	chr3	40531609	40531626	+	1	NA	Intergenic	CpG	-8705	NR_040445	100040882	Mm.272869	NR_040445	ENSMUSG00000037884	1700017G19Rik	-	RIKEN cDNA 1700017G19 gene	ncRNA
mm_5392.1	chr1	33480514	33480530	-	1	NA	exon (NM_008922, exon 12 of 14)	exon (NM_008922, exon 12 of 14)	189272	NM_008922	19076	Mm.27705	NM_008922	ENSMUSG00000026134	Prim2	AI323589	DNA primase, p58 subunit	protein-coding
mm_164060.1	chr14	113574528	113574530	+	1	NA	Intergenic	MLT1D-int|LTR|ERVL-MaLR	-1257436	NR_045661	75822	Mm.410813	NR_045661		4930524C18Rik	-	RIKEN cDNA 4930524C18 gene	ncRNA
mm_84366.1	chr9	64811036	64811049	-	1	NA	promoter-TSS (NM_001162917)	promoter-TSS (NM_001162917)	31	NM_001162917	102442	Mm.222473	NM_176935	ENSMUSG00000053641	Dennd4a	AI115600|AI851943|F730015K02Rik	DENN/MADD domain containing 4A	protein-coding
mm_41726.1	chr5	102481603	102481628	+	1	NA	5' UTR (NM_029270, exon 1 of 10)	5' UTR (NM_029270, exon 1 of 10)	224	NM_029270	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding
mm_154354.1	chrM	6038	6048	+	1	NA	NA	Intergenic	NA	NA								
mm_105617.1	chr11	106788846	106788882	-	1	NA	promoter-TSS (NM_177088)	promoter-TSS (NM_177088)	-370	NM_007840	13207	Mm.491096	NM_007840	ENSMUSG00000020719	Ddx5	2600009A06Rik|G17P1|HUMP68|Hlr1|p68	DEAD (Asp-Glu-Ala-Asp) box polypeptide 5	protein-coding
mm_54835.1	chr6	42586201	42586212	-	1	NA	Intergenic	B4A|SINE|B4	11166	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_144662.1	chr18	34315759	34315770	+	1	NA	exon (NM_007462, exon 16 of 16)	exon (NM_007462, exon 16 of 16)	-15381	NM_025527	66384	Mm.29452	NM_025527	ENSMUSG00000014504	Srp19	2310020D23Rik	signal recognition particle 19	protein-coding
mm_164747.1	chr17	74016917	74016924	-	1	NA	TTS (NM_053188)	TTS (NM_053188)	30996	NM_053188	94224	Mm.38933	NM_053188	ENSMUSG00000038541	Srd5a2	5ART2|S5AR 2	steroid 5 alpha-reductase 2	protein-coding
mm_116329.1	chr13	38036891	38036913	-	1	NA	promoter-TSS (NM_027724)	promoter-TSS (NM_027724)	35	NM_027724	71213	Mm.314688	NM_027724	ENSMUSG00000044566	Cage1	4933427I01Rik|Ctag3	cancer antigen 1	protein-coding
mm_145926.1	chr18	67133098	67133109	+	1	NA	promoter-TSS (NM_010307)	promoter-TSS (NM_010307)	-457	NM_010307	14680	Mm.440746	NM_010307	ENSMUSG00000024524	Gnal	2610011C15Rik|9630020G10Rik|Galphaolf|Gna10|Golf	guanine nucleotide binding protein, alpha stimulating, olfactory type	protein-coding
mm_12666.1	chr2	75683200	75683211	+	1	NA	intron (NM_010902, intron 1 of 4)	intron (NM_010902, intron 1 of 4)	21458	NR_132727	18024	Mm.1025	NM_010902	ENSMUSG00000015839	Nfe2l2	Nrf2	nuclear factor, erythroid derived 2, like 2	protein-coding
mm_58449.1	chr7	3303702	3303708	+	1	NA	5' UTR (NM_011102, exon 1 of 18)	5' UTR (NM_011102, exon 1 of 18)	173	NM_011102	18752	Mm.7980	NM_011102	ENSMUSG00000078816	Prkcg	PKCgamma|Pkcc|Prkcc	protein kinase C, gamma	protein-coding
mm_84914.1	chr9	80004060	80004077	-	1	NA	Intergenic	Intergenic	-26186	NM_001081243	70598	Mm.23049	NM_001081243	ENSMUSG00000034898	Filip1	5730485H21Rik|AI843021	filamin A interacting protein 1	protein-coding
mm_59677.1	chr7	28392917	28393013	+	1	NA	promoter-TSS (NM_019458)	promoter-TSS (NM_019458)	-31	NM_019458	54624	Mm.7916	NM_019458	ENSMUSG00000003437	Paf1	5730511K23Rik|AA675045	Paf1, RNA polymerase II complex component	protein-coding
mm_168469.1	chr1	14865017	14865041	+	1	NA	Intergenic	Intergenic	53833	NM_177781	277328	Mm.186329	NM_177781	ENSMUSG00000032769	Trpa1	Anktm1|TRPA1b	transient receptor potential cation channel, subfamily A, member 1	protein-coding
mm_80820.1	chr9	96719465	96719518	+	1	NA	intron (NM_175537, intron 1 of 2)	intron (NM_175537, intron 1 of 2)	12184	NM_175537	245007	Mm.485954	NM_175537	ENSMUSG00000040433	Zbtb38	A930014K01Rik|CIBZ	zinc finger and BTB domain containing 38	protein-coding
mm_101603.1	chr11	34783851	34783900	-	1	NA	promoter-TSS (NM_033374)	promoter-TSS (NM_033374)	30	NM_033374	94176	Mm.380679	NM_033374	ENSMUSG00000020143	Dock2	AI662014|AW122239|CED-5|Hch|MBC	dedicator of cyto-kinesis 2	protein-coding
mm_141065.1	chr17	25792384	25792401	-	1	NA	promoter-TSS (NM_001285984)	promoter-TSS (NM_001285984)	2	NM_145410	214917	Mm.26783	NM_145410	ENSMUSG00000057411	Fam173a	-	family with sequence similarity 173, member A	protein-coding
mm_77535.1	chr8	123032381	123032384	-	1	NA	intron (NM_001081379, intron 1 of 12)	B1_Mur2|SINE|Alu	9902	NR_037865	77087	Mm.31567	NM_001081379	ENSMUSG00000035569	Ankrd11	2410104C19Rik|3010027A04Rik|6330578C09Rik|9530048I21Rik|AA930108|Gm176|Yod	ankyrin repeat domain 11	protein-coding
mm_12990.1	chr2	90885504	90885523	+	1	NA	promoter-TSS (NM_026161)	promoter-TSS (NM_026161)	-273	NM_026161	67445	Mm.258993	NM_026161	ENSMUSG00000040794	C1qtnf4	0710001E10Rik|9430004J15Rik|CTRP4	C1q and tumor necrosis factor related protein 4	protein-coding
mm_40712.1	chr5	65885734	65885737	+	1	NA	intron (NM_001081105, intron 1 of 2)	ID4|SINE|ID	22166	NM_001081105	74734	Mm.20323	NM_001081105	ENSMUSG00000029204	Rhoh	5830400A04Rik|AU019774|Arhh	ras homolog family member H	protein-coding
mm_91413.1	chr10	31609639	31609705	-	1	NA	promoter-TSS (NM_001146349)	promoter-TSS (NM_001146349)	53	NM_001146349	268291	Mm.295212	NM_001146349	ENSMUSG00000063760	Rnf217	AU016819|Ibrdc1	ring finger protein 217	protein-coding
mm_104100.1	chr11	86695354	86695366	-	1	NA	3' UTR (NM_001003908, exon 32 of 32)	3' UTR (NM_001003908, exon 32 of 32)	11279	NM_001098810	217057	Mm.24868	NM_175004	ENSMUSG00000072582	Ptrh2	A230072I16Rik|Bit1|CGI-147	peptidyl-tRNA hydrolase 2	protein-coding
mm_95668.1	chr11	53805006	53805008	+	1	NA	intron (NR_033332, intron 3 of 3)	intron (NR_033332, intron 3 of 3)	34534	NM_001159396	16362	Mm.105218	NM_008390	ENSMUSG00000018899	Irf1	AU020929|Irf-1	interferon regulatory factor 1	protein-coding
mm_53496.1	chr6	135279655	135279670	+	1	NA	Intergenic	Intergenic	-25326	NM_001080553	14840	Mm.272306	NM_010352	ENSMUSG00000030206	Gsg1	-	germ cell associated 1	protein-coding
mm_127807.1	chr15	4988506	4988518	-	1	NA	TTS (NM_001243837)	TTS (NM_001243837)	75261	NM_001243837	109828	Mm.208034	NM_001243837	ENSMUSG00000079105	C7	A530026G17|Gm1238	complement component 7	protein-coding
mm_112257.1	chr12	113859683	113859700	-	1	NA	Intergenic	Intergenic	315783	NM_174885	238406	Mm.188683	NM_174885	ENSMUSG00000043945	Adam6a	Adam6|tMDCIV	a disintegrin and metallopeptidase domain 6A	protein-coding
mm_157992.1	chrX	94539083	94539094	-	1	NA	exon (NM_019791, exon 4 of 13)	exon (NM_019791, exon 4 of 13)	2986	NM_019791	94275	Mm.27578	NM_019791	ENSMUSG00000025151	Maged1	2810433C11Rik|5430405L04Rik|DXBwg1492e|Dlixin|Dlxin-1|Dlxin1|MAGE-D1|NRAGE|mFLJ00163	melanoma antigen, family D, 1	protein-coding
mm_158006.1	chrX	95211789	95211802	-	1	NA	Intergenic	Intergenic	-45256	NM_001033329	236915	Mm.44841	NM_001033329	ENSMUSG00000025656	Arhgef9	9630036L12Rik	CDC42 guanine nucleotide exchange factor (GEF) 9	protein-coding
mm_45281.1	chr5	64932912	64932952	-	1	NA	promoter-TSS (NM_030682)	promoter-TSS (NM_030682)	-233	NM_030682	21897	Mm.273024	NM_030682	ENSMUSG00000044827	Tlr1	-	toll-like receptor 1	protein-coding
mm_32992.1	chr4	120405289	120405404	+	1	NA	promoter-TSS (NM_013883)	promoter-TSS (NM_013883)	65	NM_013883	29871	Mm.427014	NM_013883	ENSMUSG00000000085	Scmh1	AI315320|AI851618|Scml1|Scml3	sex comb on midleg homolog 1	protein-coding
mm_128129.1	chr15	31356938	31356954	-	1	NA	intron (NM_027496, intron 1 of 3)	intron (NM_027496, intron 1 of 3)	10813	NM_001164441	67434	Mm.102470	NM_026153	ENSMUSG00000022237	Ankrd33b	0610012A05Rik|3021401C12Rik|5730557B15Rik	ankyrin repeat domain 33B	protein-coding
mm_141045.1	chr17	25433264	25433307	-	1	NA	intron (NM_001163691, intron 1 of 34)	CpG-6090	498	NM_021415	58226	Mm.268378	NM_021415	ENSMUSG00000024112	Cacna1h	Cav3.2|MNCb-1209|alpha13.2	calcium channel, voltage-dependent, T type, alpha 1H subunit	protein-coding
mm_56521.1	chr6	99518638	99518640	-	1	NA	intron (NM_001347345, intron 1 of 19)	intron (NM_001347345, intron 1 of 19)	2354	NM_001347345	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_108340.1	chr12	80210189	80210197	+	1	NA	intron (NM_001346669, intron 1 of 20)	intron (NM_001346669, intron 1 of 20)	50178	NM_134156	109711	Mm.253564	NM_134156	ENSMUSG00000015143	Actn1	3110023F10Rik|Actn1a	actinin, alpha 1	protein-coding
mm_120795.1	chr14	74734839	74734850	+	1	NA	intron (NM_001285423, intron 1 of 8)	intron (NM_001285423, intron 1 of 8)	2547	NM_016903	13885	Mm.38055	NM_016903	ENSMUSG00000021996	Esd	Es-10|Es10|FGH|sid478	esterase D/formylglutathione hydrolase	protein-coding
mm_3982.1	chr1	164275560	164275660	+	1	NA	promoter-TSS (NM_029115)	promoter-TSS (NM_029115)	12	NM_029115	74895	Mm.167258	NM_029115	ENSMUSG00000026578	Ccdc181	4930455F23Rik|AI427889	coiled-coil domain containing 181	protein-coding
mm_118360.1	chr13	115101718	115101744	-	1	NA	5' UTR (NM_001033228, exon 1 of 29)	5' UTR (NM_001033228, exon 1 of 29)	233	NM_001033228	109700	Mm.317280	NM_001033228	ENSMUSG00000042284	Itga1	CD49A|E130012M19Rik|Vla1	integrin alpha 1	protein-coding
mm_73008.1	chr8	93811084	93811094	+	1	NA	TTS (NR_026888)	TTS (NR_026888)	251	NM_001113384	14681	Mm.251445	NM_010308	ENSMUSG00000031748	Gnao1	AW050213|Galphao|Gnao|alphaO	guanine nucleotide binding protein, alpha O	protein-coding
mm_66658.1	chr7	45714699	45714729	-	1	NA	5' UTR (NM_020011, exon 1 of 6)	5' UTR (NM_020011, exon 1 of 6)	493	NM_020011	56632	Mm.24222	NM_020011	ENSMUSG00000057342	Sphk2	C76851	sphingosine kinase 2	protein-coding
mm_31101.1	chr4	41760492	41760520	+	1	NA	promoter-TSS (NM_001172054)	promoter-TSS (NM_001172054)	63	NM_001172054	16157	Mm.193451	NM_010549	ENSMUSG00000073889	Il11ra1	AI314697|GP130|Il-11ra|Il11ra|Il11ra2|NR1	interleukin 11 receptor, alpha chain 1	protein-coding
mm_111163.1	chr12	83562466	83562466	-	1	NA	intron (NM_183154, intron 4 of 11)	intron (NM_183154, intron 4 of 11)	34681	NM_183154	217695	Mm.59257	NM_183154	ENSMUSG00000042628	Zfyve1	DFCP1|G630053K23|TAFF1|ZNFN2A1|mKIAA1589	zinc finger, FYVE domain containing 1	protein-coding
mm_141427.1	chr17	29443847	29443861	-	1	NA	Intergenic	MIRc|SINE|MIR	-47191	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_22603.1	chr3	14506184	14506192	+	1	NA	TTS (NM_080852)	TTS (NM_080852)	25489	NM_080852	140918	Mm.215250	NM_080852	ENSMUSG00000039710	Slc7a12	Asc-2|XAT1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 12	protein-coding
mm_134979.1	chr16	32079171	32079183	-	1	NA	5' UTR (NM_177326, exon 1 of 15)	5' UTR (NM_177326, exon 1 of 15)	165	NM_177326	224105	Mm.234204	NM_177326	ENSMUSG00000022781	Pak2	5330420P17Rik|A130002K10Rik|AI836325|D16Ertd269e|PAK-2|mKIAA4182	p21 protein (Cdc42/Rac)-activated kinase 2	protein-coding
mm_9473.1	chr1	173335320	173335348	-	1	NA	3' UTR (NM_053199, exon 9 of 9)	3' UTR (NM_053199, exon 9 of 9)	-1831	NM_010045	13349	Mm.6393	NM_010045	ENSMUSG00000037872	Ackr1	AA162249|CCBP1|CD234|Darc|Dfy|ESTM35|FY|GPD	atypical chemokine receptor 1 (Duffy blood group)	protein-coding
mm_161016.1	chr11	120348492	120348492	-	1	NA	promoter-TSS (NM_009609)	promoter-TSS (NM_009609)	3	NM_001313923	11465	Mm.196173	NM_009609	ENSMUSG00000062825	Actg1	AL023024|Actg|Actl|E51	actin, gamma, cytoplasmic 1	protein-coding
mm_150548.1	chr19	39319524	39319544	+	1	NA	intron (NM_007815, intron 5 of 8)	intron (NM_007815, intron 5 of 8)	32449	NM_007815	13095	Mm.20764	NM_007815	ENSMUSG00000003053	Cyp2c29	AHOH|AHOHase|AI159681|AI196010|Ah-2|Ahh-1|Cyp2c|P450-2C	cytochrome P450, family 2, subfamily c, polypeptide 29	protein-coding
mm_135956.1	chr16	74672470	74672480	-	1	NA	Intergenic	Intergenic	-261563	NM_175549	268902	Mm.171736	NM_175549	ENSMUSG00000052516	Robo2	2600013A04Rik|9430089E08Rik|BB097918|D230004I22Rik|mKIAA1568	roundabout guidance receptor 2	protein-coding
mm_32236.1	chr4	102255100	102255121	+	1	NA	5' UTR (NM_001177983, exon 1 of 6)	5' UTR (NM_001177983, exon 1 of 6)	171	NM_019840	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_14973.1	chr2	152104803	152104818	+	1	NA	promoter-TSS (NM_029688)	promoter-TSS (NM_029688)	-714	NM_029688	76650	Mm.218639	NM_029688	ENSMUSG00000032802	Srxn1	1700127B04Rik|AI854065|AW488194|Npn3|Srx|Srx1|TX01	sulfiredoxin 1 homolog (S. cerevisiae)	protein-coding
mm_94594.1	chr11	11809075	11809088	+	1	NA	promoter-TSS (NM_021891)	promoter-TSS (NM_021891)	-119	NM_001163360	60530	Mm.236114	NM_021891	ENSMUSG00000035455	Fignl1	-	fidgetin-like 1	protein-coding
mm_126555.1	chr15	82147337	82147359	+	1	NA	promoter-TSS (NM_033218)	promoter-TSS (NM_033218)	79	NM_033218	20788	Mm.9002	NM_033218	ENSMUSG00000022463	Srebf2	AI608257|SREBP-2|SREBP2|SREBP2gc|bHLHd2|lop13|nuc	sterol regulatory element binding factor 2	protein-coding
mm_27648.1	chr3	63899438	63899477	-	1	NA	Intergenic	Intergenic	29928	NM_177856	329659	Mm.39342	NM_177856	ENSMUSG00000048581	E130311K13Rik	-	RIKEN cDNA E130311K13 gene	protein-coding
mm_168056.1	chrY	90813558	90813572	+	1	NA	intron (NM_133362, intron 2 of 3)	IMPB_01|Satellite|Satellite	25841	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_163574.1	chr13	30948935	30948950	+	1	NA	intron (NM_025588, intron 1 of 27)	intron (NM_025588, intron 1 of 27)	-1181	NM_153072	210554	Mm.450571	NM_153072	ENSMUSG00000076430	Hus1b	-	HUS1 checkpoint clamp component B	protein-coding
mm_38204.1	chr4	135615512	135615548	-	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	-11125	NR_015613	73937	Mm.292326	NM_028688	ENSMUSG00000086788	1700029M20Rik	4930406E24Rik	RIKEN cDNA 1700029M20 gene	ncRNA
mm_157893.1	chrX	76602897	76602945	-	1	NA	promoter-TSS (NM_001201395)	promoter-TSS (NM_001201395)	3	NM_001201395	74987	Mm.107996	NM_001201395	ENSMUSG00000079525	Cldn34d	4930468A15Rik	claudin 34D	protein-coding
mm_164051.1	chr14	102828150	102828163	-	1	NA	Intergenic	Intergenic	154476	NR_039592	100628599		NR_039592	ENSMUSG00000092901	Mir5130	mir-5130|mmu-mir-5130|mu-mir-5130	microRNA 5130	ncRNA
mm_156809.1	chrX	163927722	163927733	+	1	NA	3' UTR (NM_026887, exon 5 of 5)	3' UTR (NM_026887, exon 5 of 5)	18710	NM_001290379	108012	Mm.426783	NM_026887	ENSMUSG00000031367	Ap1s2	1500012A13Rik|AI853648|EST1	adaptor-related protein complex 1, sigma 2 subunit	protein-coding
mm_2252.1	chr1	91073701	91073705	+	1	NA	intron (NM_001310732, intron 3 of 24)	intron (NM_001310732, intron 3 of 24)	20259	NM_008515	16978	Mm.45039	NM_008515	ENSMUSG00000026305	Lrrfip1	AU024550|Fliiap1	leucine rich repeat (in FLII) interacting protein 1	protein-coding
mm_130655.1	chr15	100637085	100637107	-	1	NA	promoter-TSS (NM_174992)	promoter-TSS (NM_174992)	-156	NM_001033872	207818	Mm.26282	NM_174992	ENSMUSG00000053559	Smagp	-	small cell adhesion glycoprotein	protein-coding
mm_147167.1	chr18	36726336	36726349	-	1	NA	exon (NM_009841, exon 2 of 2)	exon (NM_009841, exon 2 of 2)	473	NM_009841	12475	Mm.3460	NM_009841	ENSMUSG00000051439	Cd14	-	CD14 antigen	protein-coding
mm_30613.1	chr4	7455514	7455532	+	1	NA	Intergenic	Intergenic	-105165	NR_040645	71510	Mm.410775	NR_040645	ENSMUSG00000086070	8430436N08Rik	-	RIKEN cDNA 8430436N08 gene	ncRNA
mm_143729.1	chr17	81380646	81380676	-	1	NA	non-coding (NR_104580, exon 9 of 9)	non-coding (NR_104580, exon 9 of 9)	-315576	NM_028138	72167	Mm.273257	NM_028138	ENSMUSG00000024246	Thumpd2	2810025A12Rik	THUMP domain containing 2	protein-coding
mm_26784.1	chr3	9610034	9610040	-	1	NA	promoter-TSS (NM_133218)	promoter-TSS (NM_133218)	48	NM_133218	170753	Mm.212908	NM_133218	ENSMUSG00000040209	Zfp704	C030026M03|C030034L19Rik|Gig1|Znf704	zinc finger protein 704	protein-coding
mm_15667.1	chr2	163323427	163323437	+	1	NA	TTS (NM_001098799)	TTS (NM_001098799)	74541	NM_021566	59091	Mm.34459	NM_021566	ENSMUSG00000017817	Jph2	1110002E14Rik|JP-2|Jp2	junctophilin 2	protein-coding
mm_30167.1	chr3	144199387	144199390	-	1	NA	intron (NM_001161770, intron 1 of 3)	intron (NM_001161770, intron 1 of 3)	2944	NM_001161770	16911	Mm.29187	NM_010723	ENSMUSG00000028266	Lmo4	A730077C12Rik|Crp3|Etohi4	LIM domain only 4	protein-coding
mm_140578.1	chr17	10209423	10209433	-	1	NA	TTS (NM_001159516)	TTS (NM_001159516)	109933	NM_021881	19317	Mm.130694	NM_021881	ENSMUSG00000062078	Qk	1110003F05Rik|1500005P18|QkI|l(17)-1Wis|l17Wis1	quaking	protein-coding
mm_156580.1	chrX	152026527	152026544	+	1	NA	exon (NM_019710, exon 5 of 25)	exon (NM_019710, exon 5 of 25)	10107	NM_019710	24061	Mm.482095	NM_019710	ENSMUSG00000041133	Smc1a	5830426I24Rik|SMC-1A|Sb1.8|Smc1|Smc1alpha|Smc1l1|Smcb|mKIAA0178	structural maintenance of chromosomes 1A	protein-coding
mm_172199.1	chr6	51469697	51469708	-	1	NA	promoter-TSS (NM_007624)	promoter-TSS (NM_007624)	192	NM_182650	53379	Mm.155896	NM_016806	ENSMUSG00000004980	Hnrnpa2b1	9130414A06Rik|Hnrpa2|Hnrpa2b1|hnrnp-A	heterogeneous nuclear ribonucleoprotein A2/B1	protein-coding
mm_155197.1	chrX	56474209	56474212	+	1	NA	intron (NM_172779, intron 2 of 16)	intron (NM_172779, intron 2 of 16)	19371	NM_172779	236790	Mm.474772	NM_172779	ENSMUSG00000035967	Ints6l	4930535D10Rik|6330505F04Rik|D130066O12|Ddx26b	integrator complex subunit 6 like	protein-coding
mm_76525.1	chr8	87472577	87472597	-	1	NA	promoter-TSS (NM_019626)	promoter-TSS (NM_019626)	5	NM_019626	12404	Mm.4880	NM_019626	ENSMUSG00000031654	Cbln1	AI323299	cerebellin 1 precursor protein	protein-coding
mm_130900.1	chr15	102405505	102405521	-	1	NA	promoter-TSS (NM_013672)	promoter-TSS (NM_013672)	-803	NM_013672	20683	Mm.4618	NM_013672	ENSMUSG00000001280	Sp1	1110003E12Rik|AA450830|AI845540|Sp1-1	trans-acting transcription factor 1	protein-coding
mm_161458.1	chr15	76389998	76389998	+	1	NA	promoter-TSS (NM_001162489)	promoter-TSS (NM_001162489)	-33	NM_001162489	223658	Mm.123240	NM_175457	ENSMUSG00000022558	Mroh1	D330001F17Rik|Heatr7a	maestro heat-like repeat family member 1	protein-coding
mm_112225.1	chr12	113430394	113430441	-	1	NA	Intergenic	Intergenic	-59148	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_80534.1	chr9	80286332	80286348	+	1	NA	exon (NM_001039546, exon 25 of 33)	exon (NM_001039546, exon 25 of 33)	121306	NM_001039546	17920	Mm.4040	NM_008662	ENSMUSG00000033577	Myo6	BC029719|Tlc|sv	myosin VI	protein-coding
mm_56879.1	chr6	118997384	118997395	-	1	NA	intron (NM_001256002, intron 3 of 47)	intron (NM_001256002, intron 3 of 47)	111106	NM_001159534	12288	Mm.41628	NM_009781	ENSMUSG00000051331	Cacna1c	Cav1.2|Cchl1a1|D930026N18Rik|MBC|MELC-CC	calcium channel, voltage-dependent, L type, alpha 1C subunit	protein-coding
mm_96794.1	chr11	69980769	69980779	+	1	NA	promoter-TSS (NM_026017)	promoter-TSS (NM_026017)	-394	NM_026017	67181	Mm.41678	NM_026017	ENSMUSG00000018559	Ctdnep1	2610507E10Rik|Dullard	CTD nuclear envelope phosphatase 1	protein-coding
mm_128879.1	chr15	73061005	73061096	-	1	NA	5' UTR (NM_001164643, exon 1 of 9)	5' UTR (NM_001164643, exon 1 of 9)	154	NM_001164641	76510	Mm.158902	NM_029640	ENSMUSG00000047921	Trappc9	1810044A24Rik|2900005P22Rik|4632408O18Rik|Ibp|Nibp|TRS130|mKIAA1882	trafficking protein particle complex 9	protein-coding
mm_110195.1	chr12	27340370	27340374	-	1	NA	3' UTR (NM_009234, exon 1 of 1)	3' UTR (NM_009234, exon 1 of 1)	2346	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding
mm_31264.1	chr4	45203922	45203931	+	1	NA	intron (NM_001081172, intron 1 of 15)	intron (NM_001081172, intron 1 of 15)	19020	NM_001081172	666060	Mm.24783	NM_001081172	ENSMUSG00000035615	Frmpd1	BC031840|mKIAA0967	FERM and PDZ domain containing 1	protein-coding
mm_116850.1	chr13	54759375	54759403	-	1	NA	3' UTR (NM_033610, exon 6 of 6)	3' UTR (NM_033610, exon 6 of 6)	7051	NM_033610	104069	Mm.200843	NM_033610	ENSMUSG00000034891	Sncb	AI838531|betaSYN	synuclein, beta	protein-coding
mm_34390.1	chr4	144927414	144927448	+	1	NA	3' UTR (NM_001172424, exon 7 of 7)	3' UTR (NM_001172424, exon 7 of 7)	34294	NM_011303	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding
mm_2366.1	chr1	93135333	93135339	+	1	NA	promoter-TSS (NM_016702)	promoter-TSS (NM_016702)	96	NM_001276710	11611	Mm.7457	NM_016702	ENSMUSG00000026272	Agxt	AGT|Agt1|Agxt1|SPT	alanine-glyoxylate aminotransferase	protein-coding
mm_110817.1	chr12	72408327	72408338	-	1	NA	exon (NM_001286448, exon 1 of 7)	exon (NM_001286448, exon 1 of 7)	722	NM_001286448	104001	Mm.221275	NM_153457	ENSMUSG00000021087	Rtn1	Nsp	reticulon 1	protein-coding
mm_124395.1	chr14	111778209	111778213	-	1	NA	Intergenic	Lx6|LINE|L1	103096	NM_198865	75409	Mm.235097	NM_029273	ENSMUSG00000033214	Slitrk5	2610019D03Rik	SLIT and NTRK-like family, member 5	protein-coding
mm_14811.1	chr2	146047199	146047242	+	1	NA	Intergenic	Intergenic	112436	NM_175280	78774	Mm.136347	NM_175280	ENSMUSG00000037143	Cfap61	4930529M08Rik|BB178539|BC024760	cilia and flagella associated protein 61	protein-coding
mm_153092.1	chr19	32485851	32485868	-	1	NA	promoter-TSS (NM_010799)	promoter-TSS (NM_010799)	90	NM_010799	17330	Mm.255116	NM_010799	ENSMUSG00000024896	Minpp1	AA408516	multiple inositol polyphosphate histidine phosphatase 1	protein-coding
mm_158051.1	chrX	100412592	100412606	-	1	NA	promoter-TSS (NM_177746)	promoter-TSS (NM_177746)	-12	NM_177746	245532	Mm.118171	NM_177746	ENSMUSG00000031220	Awat2	9430062J17Rik|ARAT|Dgat2l4|WS	acyl-CoA wax alcohol acyltransferase 2	protein-coding
mm_57676.1	chr6	128494816	128494832	-	1	NA	exon (NM_007376, exon 21 of 36)	exon (NM_007376, exon 21 of 36)	31896	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_36368.1	chr4	76449769	76449785	-	1	NA	intron (NM_011211, intron 10 of 39)	CpG	-1171491	NM_025849	66928	Mm.24332	NM_025849	ENSMUSG00000028398	Tmem261	1700027K24Rik|3110001D03Rik	transmembrane protein 261	protein-coding
mm_16966.1	chr2	17690131	17690144	-	1	NA	intron (NM_028757, intron 2 of 6)	intron (NM_028757, intron 2 of 6)	40931	NM_028757	74103	Mm.120298	NM_028757	ENSMUSG00000053702	Nebl	1200007O21Rik|A630080F05Rik|BB140644|D830029A09Rik|Lnebl	nebulette	protein-coding
mm_91021.1	chr10	17799436	17799446	-	1	NA	exon (NM_138628, exon 2 of 10)	exon (NM_138628, exon 2 of 10)	3222	NM_138628	378431	Mm.283493	NM_138628	ENSMUSG00000039891	Txlnb	2310001N14Rik|Mdp77	taxilin beta	protein-coding
mm_11411.1	chr2	31572702	31572724	+	1	NA	promoter-TSS (NM_001290548)	promoter-TSS (NM_001290548)	62	NM_001290548	320267	Mm.207261	NM_001033389	ENSMUSG00000026843	Fubp3	A330051M14Rik|AV006371|FBP3|Marta2	far upstream element (FUSE) binding protein 3	protein-coding
mm_162324.1	chr1	39614645	39614651	+	1	NA	Intergenic	Intergenic	36534	NM_170597	263764	Mm.122091	NM_170597	ENSMUSG00000050967	Creg2	A830098L22Rik	cellular repressor of E1A-stimulated genes 2	protein-coding
mm_109578.1	chr12	112489534	112489538	+	1	NA	promoter-TSS (NM_177039)	promoter-TSS (NM_177039)	88	NM_177039	319942	Mm.185209	NM_177039	ENSMUSG00000043122	A530016L24Rik	Nrac	RIKEN cDNA A530016L24 gene	protein-coding
mm_37936.1	chr4	132922606	132922613	-	1	NA	promoter-TSS (NM_145553)	promoter-TSS (NM_145553)	-58	NM_001163792	230789	Mm.11473	NM_145553	ENSMUSG00000028878	Fam76a	-	family with sequence similarity 76, member A	protein-coding
mm_100691.1	chr11	3527917	3527959	-	1	NA	intron (NM_001159284, intron 12 of 21)	intron (NM_001159284, intron 12 of 21)	11354	NM_013870	29856	Mm.188516	NM_013870	ENSMUSG00000020439	Smtn	smsmo	smoothelin	protein-coding
mm_140838.1	chr17	23670891	23670913	-	1	NA	exon (NM_001008425, exon 2 of 13)	exon (NM_001008425, exon 2 of 13)	-2706	NM_181821	353502	Mm.359030	NM_181821	ENSMUSG00000023904	Hcfc1r1	HPIP	host cell factor C1 regulator 1 (XPO1-dependent)	protein-coding
mm_152696.1	chr19	17125522	17125542	-	1	NA	exon (NM_181348, exon 9 of 20)	exon (NM_181348, exon 9 of 20)	169414	NM_181348	353211	Mm.257354	NM_181348	ENSMUSG00000039126	Prune2	6330414G02Rik|A230083H22Rik|A330102H22Rik|Bmcc1|mKIAA0367	prune homolog 2	protein-coding
mm_53187.1	chr6	125481926	125481949	+	1	NA	intron (NM_007657, intron 1 of 7)	intron (NM_007657, intron 1 of 7)	12818	NM_007657	12527	Mm.210676	NM_007657	ENSMUSG00000030342	Cd9	Tspan29	CD9 antigen	protein-coding
mm_103009.1	chr11	69696038	69696055	-	1	NA	promoter-TSS (NM_001159503)	promoter-TSS (NM_001159503)	52	NM_011614	21944	Mm.8983	NM_011614	ENSMUSG00000097328	Tnfsf12	Apo3l|Dr3l|Dr3lg|Tweak	tumor necrosis factor (ligand) superfamily, member 12	protein-coding
mm_86034.1	chr9	113708210	113708258	-	1	NA	promoter-TSS (NM_001164677)	promoter-TSS (NM_001164677)	25	NM_001164678	18571	Mm.29816	NM_011052	ENSMUSG00000032504	Pdcd6ip	AI480591|AW544830|Aip1|Alix|C76364|Eig2|mKIAA1375	programmed cell death 6 interacting protein	protein-coding
mm_61618.1	chr7	80153246	80153250	+	1	NA	Intergenic	MTEb|LTR|ERVL-MaLR	-33593	NM_013659	20352	Mm.275909	NM_013659	ENSMUSG00000030539	Sema4b	SemC|Semac|mKIAA1745	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B	protein-coding
mm_34243.1	chr4	141222720	141222724	+	1	NA	Intergenic	MurERV4_19-int|LTR|ERVK	8766	NM_001081174	76166	Mm.271064	NM_001081174	ENSMUSG00000073733	Rsg1	6330545A04Rik|Gm723	REM2 and RAB-like small GTPase 1	protein-coding
mm_93527.1	chr10	115315547	115315615	-	1	NA	promoter-TSS (NM_024454)	promoter-TSS (NM_024454)	10	NM_024454	216344	Mm.21936	NM_024454	ENSMUSG00000020132	Rab21	9630024B22	RAB21, member RAS oncogene family	protein-coding
mm_111310.1	chr12	85817823	85817837	-	1	NA	intron (NM_021446, intron 3 of 4)	intron (NM_021446, intron 3 of 4)	6715	NM_021446	58520	Mm.143795	NM_021446	ENSMUSG00000021252	0610007P14Rik	1190004E09Rik|AU019315|C77855|ORF11	RIKEN cDNA 0610007P14 gene	protein-coding
mm_13397.1	chr2	103970222	103970243	+	1	NA	promoter-TSS (NM_008505)	promoter-TSS (NM_008505)	-55	NM_008505	16909	Mm.29266	NM_008505	ENSMUSG00000032698	Lmo2	Rbtn-2|Rbtn2|Rhom-2|Ttg2	LIM domain only 2	protein-coding
mm_79813.1	chr9	64179272	64179282	+	1	NA	promoter-TSS (NM_183316)	promoter-TSS (NM_183316)	-20	NM_183316	330959	Mm.24082	NM_183316	ENSMUSG00000032398	Snapc5	2010103A03Rik	small nuclear RNA activating complex, polypeptide 5	protein-coding
mm_66565.1	chr7	45239339	45239350	-	1	NA	promoter-TSS (NM_007645)	promoter-TSS (NM_007645)	-229	NM_001290804	12493	Mm.3689	NM_007645	ENSMUSG00000030798	Cd37	Tspan26	CD37 antigen	protein-coding
mm_3748.1	chr1	155972501	155972549	+	1	NA	intron (NM_001039184, intron 1 of 37)	intron (NM_001039184, intron 1 of 37)	730	NM_001039184	74081	Mm.260247	NM_001039184	ENSMUSG00000033671	Cep350	4933409L06Rik|6430546F08Rik	centrosomal protein 350	protein-coding
mm_100664.1	chr11	3291643	3291662	-	1	NA	exon (NM_001253691, exon 1 of 5)	exon (NM_001253691, exon 1 of 5)	1195	NM_019574	56218	Mm.275563	NM_019574	ENSMUSG00000020453	Patz1	8430401L15Rik|AI447519|Mazr|Patz|Zfp278	POZ (BTB) and AT hook containing zinc finger 1	protein-coding
mm_101768.1	chr11	43836452	43836460	-	1	NA	promoter-TSS (NM_007416)	promoter-TSS (NM_007416)	33	NM_007416	11548	Mm.39086	NM_007416	ENSMUSG00000050541	Adra1b	[a]1b	adrenergic receptor, alpha 1b	protein-coding
mm_169474.1	chr14	69337166	69337167	+	1	NA	promoter-TSS (NM_026174).2	promoter-TSS (NM_026174).2	15	NM_026174	67464	Mm.489765	NM_026174	ENSMUSG00000095463	Entpd4	1200014F22Rik|4930513O14Rik|A430102M06Rik|AI414893|Lysal1|mKIAA0392	ectonucleoside triphosphate diphosphohydrolase 4	protein-coding
mm_3279.1	chr1	136579667	136579673	+	1	NA	Intergenic	Intergenic	-45231	NM_177643	226442	Mm.62521	NM_177643	ENSMUSG00000041483	Zfp281	Znf281	zinc finger protein 281	protein-coding
mm_9086.1	chr1	168432143	168432186	-	1	NA	promoter-TSS (NM_001291509)	promoter-TSS (NM_001291509)	5	NM_001291508	18514	Mm.43358	NM_008783	ENSMUSG00000052534	Pbx1	2310056B04Rik|D230003C07Rik|Pbx-1	pre B cell leukemia homeobox 1	protein-coding
mm_37342.1	chr4	119658115	119658128	-	1	NA	intron (NM_008191, intron 1 of 2)	intron (NM_008191, intron 1 of 2)	824	NM_008191	14916	Mm.278	NM_008191	ENSMUSG00000032978	Guca2b	AV066530|Gcap2|Ugn	guanylate cyclase activator 2b (retina)	protein-coding
mm_82894.1	chr9	32549508	32549529	-	1	NA	Intergenic	Intergenic	-8066	NM_008026	14247	Mm.258908	NM_008026	ENSMUSG00000016087	Fli1	EWSR2|Fli-1|SIC-1|Sic1	Friend leukemia integration 1	protein-coding
mm_106209.1	chr11	116851280	116851315	-	1	NA	intron (NM_011358, intron 2 of 2)	intron (NM_011358, intron 2 of 2)	1797	NM_011358	20382	Mm.21841	NM_011358	ENSMUSG00000034120	Srsf2	D11Wsu175e|MRF-1|Pr264|SC35|Sfrs10|Sfrs2	serine/arginine-rich splicing factor 2	protein-coding
mm_139050.1	chr17	46297407	46297447	+	1	NA	promoter-TSS (NM_001286013)	promoter-TSS (NM_001286013)	-56	NM_001286028	106565	Mm.23633	NM_134120	ENSMUSG00000047428	Dlk2	AI413481|DLK-2|Egfl9	delta-like 2 homolog (Drosophila)	protein-coding
mm_50351.1	chr6	48589641	48589658	+	1	NA	5' UTR (NM_183309, exon 1 of 2)	5' UTR (NM_183309, exon 1 of 2)	204	NM_183309	330305	Mm.123868	NM_183309	ENSMUSG00000052730	Gm5111	A630038D02|EG330305	predicted gene 5111	protein-coding
mm_127669.1	chr15	102657467	102657477	+	1	NA	Intergenic	Intergenic	13575	NM_026468	67942	Mm.10314	NM_026468	ENSMUSG00000062683	Atp5g2	1810041M08Rik	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit C2 (subunit 9)	protein-coding
mm_81420.1	chr9	109056015	109056063	+	1	NA	exon (NM_026381, exon 2 of 4)	exon (NM_026381, exon 2 of 4)	1173	NM_026381	66940	Mm.196533	NM_025858	ENSMUSG00000025647	Shisa5	2310008D10Rik|6430628I05Rik|Scotin|mShisa5	shisa family member 5	protein-coding
mm_122632.1	chr14	51145860	51145868	-	1	NA	exon (NM_011271, exon 2 of 2)	exon (NM_011271, exon 2 of 2)	903	NM_011271	19752	Mm.235538	NM_011271	ENSMUSG00000035896	Rnase1	AI574248|Rib-1|Rib1	ribonuclease, RNase A family, 1 (pancreatic)	protein-coding
mm_132861.1	chr16	48431331	48431339	+	1	NA	promoter-TSS (NM_010816)	promoter-TSS (NM_010816)	98	NM_010816	17450	Mm.250060	NM_010816	ENSMUSG00000022652	Morc1	Morc	microrchidia 1	protein-coding
mm_52276.1	chr6	108658804	108658813	+	1	NA	intron (NR_104577, intron 1 of 6)	intron (NR_104577, intron 1 of 6)	-1821	NM_011498	20893	Mm.2436	NM_011498	ENSMUSG00000030103	Bhlhe40	Bhlhb2|C130042M06Rik|CR8|Clast5|Dec1|Sharp2|Stra13|Stra14	basic helix-loop-helix family, member e40	protein-coding
mm_106686.1	chr12	3350188	3350196	+	1	NA	Intergenic	MIRc|SINE|MIR	-14940	NM_008445	16570	Mm.7688	NM_008445	ENSMUSG00000020668	Kif3c	mKIAA4058	kinesin family member 3C	protein-coding
mm_57858.1	chr6	129507157	129507171	-	1	NA	promoter-TSS (NM_138648)	promoter-TSS (NM_138648)	1	NM_001301094	108078	Mm.293626	NM_138648	ENSMUSG00000030162	Olr1	LOX-1|SR-EI|Scare1	oxidized low density lipoprotein (lectin-like) receptor 1	protein-coding
mm_69237.1	chr7	127708887	127708918	-	1	NA	promoter-TSS (NM_009746)	promoter-TSS (NM_009746)	-136	NM_001347652	12055	Mm.89667	NM_009746	ENSMUSG00000030814	Bcl7c	C230096E12Rik	B cell CLL/lymphoma 7C	protein-coding
mm_11692.1	chr2	35680568	35680572	+	1	NA	intron (NM_001290637, intron 3 of 16)	intron (NM_001290637, intron 3 of 16)	-11424	NM_001001602	69601	Mm.29629	NM_001001602	ENSMUSG00000026883	Dab2ip	2310011D08Rik|AI480459|Aip1|mKIAA1743	disabled 2 interacting protein	protein-coding
mm_158696.1	chrX	161832117	161832127	-	1	NA	Intergenic	Intergenic	114569	NM_198409	24004	Mm.328503	NM_198409	ENSMUSG00000043518	Rai2	3f8	retinoic acid induced 2	protein-coding
mm_90805.1	chr10	7664088	7664095	-	1	NA	promoter-TSS (NM_008786)	promoter-TSS (NM_008786)	-483	NM_001347228	18537	Mm.258431	NM_008786	ENSMUSG00000019795	Pcmt1	C79501|PIMT	protein-L-isoaspartate (D-aspartate) O-methyltransferase 1	protein-coding
mm_31378.1	chr4	47474653	47474707	+	1	NA	promoter-TSS (NM_024171)	promoter-TSS (NM_024171)	19	NM_024171	66212	Mm.20188	NM_024171	ENSMUSG00000053317	Sec61b	1190006C12Rik|AI326121|AW122942	Sec61 beta subunit	protein-coding
mm_43157.1	chr5	125850013	125850031	+	1	NA	Intergenic	Intergenic	317604	NM_001190352	208151	Mm.40397	NM_001190352	ENSMUSG00000070498	Tmem132b	AK220418|mKIAA1786	transmembrane protein 132B	protein-coding
mm_128362.1	chr15	41448529	41448538	-	1	NA	intron (NM_001130166, intron 1 of 16)	intron (NM_001130166, intron 1 of 16)	1051	NM_001130166	170719	Mm.254267	NM_130885	ENSMUSG00000022307	Oxr1	2210416C20Rik|C7|C7B	oxidation resistance 1	protein-coding
mm_1441.1	chr1	67220513	67220533	+	1	NA	exon (NM_001080809, exon 34 of 38)	exon (NM_001080809, exon 34 of 38)	97496	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_80019.1	chr9	67903602	67903608	+	1	NA	exon (NM_177184, exon 27 of 85)	exon (NM_177184, exon 27 of 85)	63209	NM_177184	320528	Mm.241454	NM_177184	ENSMUSG00000035284	Vps13c	AI552542|AV026040|C230055H22Rik|W51662|chorein	vacuolar protein sorting 13C	protein-coding
mm_54482.1	chr6	35133689	35133730	-	1	NA	promoter-TSS (NM_001164412)	promoter-TSS (NM_001164412)	28	NM_001164412	53621	Mm.214525	NM_016877	ENSMUSG00000038784	Cnot4	Not4|Not4h|Not4hp	CCR4-NOT transcription complex, subunit 4	protein-coding
mm_14020.1	chr2	122150958	122150966	+	1	NA	exon (NM_009735, exon 2 of 4)	exon (NM_009735, exon 2 of 4)	3275	NM_009735	12010	Mm.163	NM_009735	ENSMUSG00000060802	B2m	Ly-m11|beta2-m|beta2m	beta-2 microglobulin	protein-coding
mm_166329.1	chr5	113364904	113364908	+	1	NA	Intergenic	Intergenic	7612	NM_001012726	503692	Mm.348794	NM_001012726	ENSMUSG00000053873	Aym1	-	activator of yeast meiotic promoters 1	protein-coding
mm_159541.1	chr4	88805936	88805936	+	1	NA	promoter-TSS (NM_001161609)	promoter-TSS (NM_001161609)	-90	NM_001243165	545647	Mm.380019	NM_001243165	ENSMUSG00000096582	Gm13289	OTTMUSG00000011290	predicted gene 13289	protein-coding
mm_45655.1	chr5	77095226	77095275	-	1	NA	promoter-TSS (NM_001159901)	promoter-TSS (NM_001159901)	17	NM_001159901	74318	Mm.181852	NM_175606	ENSMUSG00000059325	Hopx	1110018K11Rik|1200015P04Rik|2300002F06Rik|AI848177|AW490897|Cameo|Hdop|Hod|Hop|Ob1|Obl|Toto	HOP homeobox	protein-coding
mm_159853.1	chr5	137739786	137739786	-	1	NA	5' UTR (NM_175521, exon 1 of 6)	5' UTR (NM_175521, exon 1 of 6)	212	NM_175521	243300	Mm.74750	NM_175521	ENSMUSG00000045348	Nyap1	6430598A04Rik	neuronal tyrosine-phosphorylated phosphoinositide 3-kinase adaptor 1	protein-coding
mm_156307.1	chrX	136838044	136838050	+	1	NA	3' UTR (NM_011123, exon 7 of 7)	3' UTR (NM_011123, exon 7 of 7)	15301	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_35658.1	chr4	43558162	43558182	-	1	NA	intron (NM_011602, intron 1 of 56)	intron (NM_011602, intron 1 of 56)	4411	NM_011602	21894	Mm.208601	NM_011602	ENSMUSG00000028465	Tln1	Tln	talin 1	protein-coding
mm_53863.1	chr6	149325393	149325446	+	1	NA	5' UTR (NM_001289662, exon 3 of 5)	5' UTR (NM_001289662, exon 3 of 5)	16005	NM_001289662	67246	Mm.333515	NM_026054	ENSMUSG00000032712	2810474O19Rik	6720435I21Rik|AA536804|AU020969|GET|Kiaa1551	RIKEN cDNA 2810474O19 gene	protein-coding
mm_21199.1	chr2	155495583	155495584	-	1	NA	intron (NM_144786, intron 12 of 14)	intron (NM_144786, intron 12 of 14)	19263	NM_144786	207182	Mm.41757	NM_144786	ENSMUSG00000027603	Ggt7	1110017C11Rik|6330563L03Rik|Ggtl3	gamma-glutamyltransferase 7	protein-coding
mm_55608.1	chr6	71888783	71888783	-	1	NA	intron (NM_027275, intron 16 of 23)	intron (NM_027275, intron 16 of 23)	19979	NM_027275	69956	Mm.30256	NM_027275	ENSMUSG00000063884	Ptcd3	2610034F17Rik|2810422B04Rik|AA589622|AU045708|MRP-S39	pentatricopeptide repeat domain 3	protein-coding
mm_114779.1	chr13	88821917	88821942	+	1	NA	5' UTR (NM_001037987, exon 1 of 11)	5' UTR (NM_001037987, exon 1 of 11)	457	NM_001037987	13612	Mm.125580	NM_010103	ENSMUSG00000034488	Edil3	Del-1|Del1	EGF-like repeats and discoidin I-like domains 3	protein-coding
mm_125002.1	chr15	24255564	24255566	+	1	NA	Intergenic	Intergenic	1158199	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	brain abundant, membrane attached signal protein 1	protein-coding
mm_57201.1	chr6	122850683	122850735	-	1	NA	exon (NM_009779, exon 2 of 2)	exon (NM_009779, exon 2 of 2)	5448	NM_009779	12267	Mm.2408	NM_009779	ENSMUSG00000040552	C3ar1	AZ3B|C3AR|HNFAG09	complement component 3a receptor 1	protein-coding
mm_97545.1	chr11	78925175	78925197	+	1	NA	promoter-TSS (NM_001313922)	promoter-TSS (NM_001313922)	-105	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_143775.1	chr17	81704875	81704899	-	1	NA	intron (NR_104580, intron 1 of 8)	intron (NR_104580, intron 1 of 8)	33500	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_151036.1	chr19	47023388	47023400	+	1	NA	exon (NM_146100, exon 3 of 3)	exon (NM_146100, exon 3 of 3)	-8205	NM_001164363	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_65744.1	chr7	28544039	28544062	-	1	NA	3' UTR (NM_001081115, exon 6 of 6)	3' UTR (NM_001081115, exon 6 of 6)	3165	NM_026716	68416	Mm.25210	NM_026716	ENSMUSG00000084174	Sycn	0910001K16Rik|1810038B08Rik|SYL	syncollin	protein-coding
mm_151734.1	chr19	4906599	4906632	-	1	NA	promoter-TSS (NM_001033128)	promoter-TSS (NM_001033128)	12	NM_001033128	52028	Mm.23636	NM_001033128	ENSMUSG00000006464	Bbs1	AI451249|D19Ertd609e	Bardet-Biedl syndrome 1 (human)	protein-coding
mm_41303.1	chr5	90467341	90467353	+	1	NA	exon (NM_009654, exon 7 of 15)	exon (NM_009654, exon 7 of 15)	6477	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_101184.1	chr11	17044335	17044337	-	1	NA	Intergenic	RMER19B2|LTR|ERVK	-7598	NM_029861	380686	Mm.425666	NM_029861	ENSMUSG00000044629	Cnrip1	1500041B16Rik|3110054C06Rik|5330437A18Rik|AI854501|C2orf32	cannabinoid receptor interacting protein 1	protein-coding
mm_151960.1	chr19	5801533	5801559	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	1126	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_86702.1	chr10	18526618	18526626	+	1	NA	exon (NM_001163592, exon 6 of 8)	exon (NM_001163592, exon 6 of 8)	19454	NM_019487	56016	Mm.35551	NM_019487	ENSMUSG00000019853	Hebp2	SOUL	heme binding protein 2	protein-coding
mm_2604.1	chr1	120120826	120120869	+	1	NA	promoter-TSS (NM_001172074)	promoter-TSS (NM_001172074)	72	NM_001037999	13167	Mm.2785	NM_007830	ENSMUSG00000026385	Dbi	ACBD1|Acbp|EP|endozepine	diazepam binding inhibitor	protein-coding
mm_140998.1	chr17	24886305	24886353	-	1	NA	promoter-TSS (NM_001163750)	promoter-TSS (NM_001163750)	21	NM_011956	26426	Mm.36718	NM_011956	ENSMUSG00000039183	Nubp2	D17Wsu11e	nucleotide binding protein 2	protein-coding
mm_1225.1	chr1	62750373	62750378	+	1	NA	intron (NM_001077405, intron 7 of 15)	intron (NM_001077405, intron 7 of 15)	44357	NR_040601	74992	Mm.401979	NR_040601		4930487H11Rik	-	RIKEN cDNA 4930487H11 gene	ncRNA
mm_89643.1	chr10	96642093	96642096	+	1	NA	Intergenic	Intergenic	25093	NM_007569	12226	Mm.23811	NM_007569	ENSMUSG00000036478	Btg1	AI426953|AW546738	B cell translocation gene 1, anti-proliferative	protein-coding
mm_133472.1	chr16	89278409	89278410	+	1	NA	Intergenic	Intergenic	72548	NM_001163615	622935	Mm.459837	NM_001163615	ENSMUSG00000091039	Krtap20-2	1190004K03Rik|EG622935|Gm6371	keratin associated protein 20-2	protein-coding
mm_148094.1	chr18	73815756	73815794	-	1	NA	promoter-TSS (NM_145494)	promoter-TSS (NM_145494)	-383	NM_145494	107029	Mm.36817	NM_145494	ENSMUSG00000024556	Me2	AW120568|D030040L20Rik|NAD-ME	malic enzyme 2, NAD(+)-dependent, mitochondrial	protein-coding
mm_89203.1	chr10	86498285	86498292	+	1	NA	intron (NM_001164495, intron 1 of 6)	intron (NM_001164495, intron 1 of 6)	608	NM_001164495	27204	Mm.394931	NM_013722	ENSMUSG00000059602	Syn3	-	synapsin III	protein-coding
mm_95521.1	chr11	52122264	52122279	+	1	NA	3' UTR (NM_019411, exon 7 of 7)	3' UTR (NM_019411, exon 7 of 7)	-4475	NR_037221	100526467		NR_037221	ENSMUSG00000092870	Mir3061	mir-3061|mmu-mir-3061	microRNA 3061	ncRNA
mm_99676.1	chr11	105985738	105985751	+	1	NA	promoter-TSS (NR_104047)	promoter-TSS (NR_104047)	-50	NR_104047	100379610	Mm.754	NR_104047	ENSMUSG00000085297	Gm11651	OTTMUSG00000003114	predicted gene 11651	ncRNA
mm_109618.1	chr12	112763449	112763480	+	1	NA	exon (NM_178911, exon 3 of 11)	exon (NM_178911, exon 3 of 11)	2809	NM_178911	104759	Mm.203915	NM_178911	ENSMUSG00000052160	Pld4	AI132321|thss	phospholipase D family, member 4	protein-coding
mm_89765.1	chr10	100096520	100096523	+	1	NA	3' UTR (NM_013598, exon 10 of 10)	3' UTR (NM_013598, exon 10 of 10)	80700	NM_013598	17311	Mm.45124	NM_013598	ENSMUSG00000019966	Kitl	Clo|Con|Gb|Kitlg|Mgf|SCF|SF|SLF|Sl|blz|contrasted	kit ligand	protein-coding
mm_116160.1	chr13	30629954	30629988	-	1	NA	Intergenic	Intergenic	14928	NR_045975	75090	Mm.292232	NR_045975	ENSMUSG00000086263	4930519D14Rik	-	RIKEN cDNA 4930519D14 gene	ncRNA
mm_143684.1	chr17	80062305	80062329	-	1	NA	promoter-TSS (NM_144802)	promoter-TSS (NM_144802)	-49	NM_144802	72692	Mm.64579	NM_144802	ENSMUSG00000024095	Hnrnpll	2510028H02Rik|2810036L13Rik|AI256697|AI852082|Hnrpll	heterogeneous nuclear ribonucleoprotein L-like	protein-coding
mm_95788.1	chr11	54958661	54958664	+	1	NA	intron (NM_001199275, intron 1 of 18)	intron (NM_001199275, intron 1 of 18)	4278	NM_021327	57783	Mm.259671	NM_021327	ENSMUSG00000020400	Tnip1	ABIN|ABIN-1|ABIN1|AU018810|Naf1|Nef|VAN	TNFAIP3 interacting protein 1	protein-coding
mm_42864.1	chr5	122227129	122227140	+	1	NA	intron (NM_028752, intron 2 of 6)	B1F|SINE|Alu	16847	NM_028752	74096	Mm.28804	NM_028752	ENSMUSG00000064267	Hvcn1	0610039P13Rik|AI450555|BTS|HV1|Vsop.|mVSOP	hydrogen voltage-gated channel 1	protein-coding
mm_9474.1	chr1	173336040	173336048	-	1	NA	3' UTR (NM_053199, exon 9 of 9)	3' UTR (NM_053199, exon 9 of 9)	-2541	NM_010045	13349	Mm.6393	NM_010045	ENSMUSG00000037872	Ackr1	AA162249|CCBP1|CD234|Darc|Dfy|ESTM35|FY|GPD	atypical chemokine receptor 1 (Duffy blood group)	protein-coding
mm_57490.1	chr6	125286016	125286050	-	1	NA	promoter-TSS (NM_009446)	promoter-TSS (NM_009446)	9	NM_009446	22144	Mm.287784	NM_009446	ENSMUSG00000067702	Tuba3a	AI528779|M[a]3|Tuba3	tubulin, alpha 3A	protein-coding
mm_123820.1	chr14	70599814	70599831	-	1	NA	promoter-TSS (NM_194345)	promoter-TSS (NM_194345)	13	NM_194345	239170	Mm.247582	NM_194345	ENSMUSG00000022095	Fam160b2	G430067P06Rik|Rai16	family with sequence similarity 160, member B2	protein-coding
mm_29110.1	chr3	104863869	104863871	-	1	NA	promoter-TSS (NM_001253703)	promoter-TSS (NM_001253703)	635	NM_009797	12340	Mm.19142	NM_009797	ENSMUSG00000070372	Capza1	CAPZ|CAZ1|Cappa1	capping protein (actin filament) muscle Z-line, alpha 1	protein-coding
mm_141409.1	chr17	29395522	29395528	-	1	NA	Intergenic	Intergenic	34611	NM_001159538	26382	Mm.279187	NM_013710	ENSMUSG00000024013	Fgd2	Tcd-2|Tcd2|ZFYVE4|tcs-2|tcs2	FYVE, RhoGEF and PH domain containing 2	protein-coding
mm_157003.1	chrX	7574245	7574312	-	1	NA	promoter-TSS (NM_001290574)	promoter-TSS (NM_001290574)	3	NM_001290574	54646	Mm.148163	NM_138605	ENSMUSG00000039556	Ppp1r3f	DXImx48e|R3F|RF3|Sfc15	protein phosphatase 1, regulatory (inhibitor) subunit 3F	protein-coding
mm_82185.1	chr9	123936922	123936932	+	1	NA	Intergenic	Intergenic	31765	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_64662.1	chr7	4164721	4164741	-	1	NA	promoter-TSS (NM_021454)	promoter-TSS (NM_021454)	-32	NM_021454	58804	Mm.34268	NM_021454	ENSMUSG00000063838	Cdc42ep5	1700027J19Rik|2010007O02Rik|Borg3|C85526|CEP5	CDC42 effector protein (Rho GTPase binding) 5	protein-coding
mm_22106.1	chr2	169963170	169963201	-	1	NA	promoter-TSS (NR_131974)	promoter-TSS (NR_131974)	2	NR_131974	446211	Mm.266854	NR_131974	ENSMUSG00000103935	AY702102	STDP1	cDNA sequence AY702102	ncRNA
mm_56441.1	chr6	97459280	97459303	-	1	NA	promoter-TSS (NM_001346639)	promoter-TSS (NM_001346639)	-5	NM_001346639	232288	Mm.27789	NM_145148	ENSMUSG00000030064	Frmd4b	6030440G05Rik|C87375|GOBLIN|GRSP1|R74720	FERM domain containing 4B	protein-coding
mm_165388.1	chr2	131430647	131430676	+	1	NA	intron (NR_037281, intron 1 of 2)	intron (NR_037281, intron 1 of 2)	-61201	NM_001177834	228608	Mm.136586	NM_145533	ENSMUSG00000027333	Smox	B130066H01Rik|PAO|PAOh1|SMO	spermine oxidase	protein-coding
mm_65844.1	chr7	29247945	29247972	-	1	NA	TTS (NM_001110201)	TTS (NM_001110201)	509	NM_028179	72275	Mm.441142	NM_028179	ENSMUSG00000030587	2200002D01Rik	2010005J02Rik|H2RSP|IMUP|IMUP-1|IMUP-2	RIKEN cDNA 2200002D01 gene	protein-coding
mm_126495.1	chr15	81663975	81663985	+	1	NA	promoter-TSS (NM_145993)	promoter-TSS (NM_145993)	91	NR_110362	214669	Mm.280768	NM_145993	ENSMUSG00000022394	L3mbtl2	4732493N06Rik|M4mbt	l(3)mbt-like 2 (Drosophila)	protein-coding
mm_86142.1	chr9	117046531	117046543	-	1	NA	intron (NM_001172122, intron 3 of 13)	B3A|SINE|B2	205946	NM_001172123	207181	Mm.326411	NM_178660	ENSMUSG00000039607	Rbms3	6720477E09Rik|8430436O14Rik	RNA binding motif, single stranded interacting protein	protein-coding
mm_95779.1	chr11	54909831	54909831	+	1	NA	TTS (NM_021327)	TTS (NM_021327)	6977	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_43502.1	chr5	136987358	136987383	+	1	NA	promoter-TSS (NM_001310748)	promoter-TSS (NM_001310748)	351	NM_011962	26433	Mm.251003	NM_011962	ENSMUSG00000004846	Plod3	AI414586|LH3	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3	protein-coding
mm_85580.1	chr9	107295606	107295642	-	1	NA	Intergenic	Intergenic	-1035	NM_001317354	12700	Mm.4592	NM_009895	ENSMUSG00000032578	Cish	CIS-1|CIS1|Cis|F17|F23|SOCS	cytokine inducible SH2-containing protein	protein-coding
mm_35567.1	chr4	41640297	41640312	-	1	NA	promoter-TSS (NM_027147)	promoter-TSS (NM_027147)	-2	NM_027147	69638	Mm.372459	NM_027147	ENSMUSG00000028445	Enho	1110065P19Rik|2310040A07Rik	energy homeostasis associated	protein-coding
mm_161048.1	chr12	41024552	41024552	+	1	NA	intron (NM_053122, intron 1 of 6)	intron (NM_053122, intron 1 of 6)	462	NM_053122	93757	Mm.363813	NM_053122	ENSMUSG00000056899	Immp2l	AI853880|IMP2	IMP2 inner mitochondrial membrane peptidase-like (S. cerevisiae)	protein-coding
mm_83985.1	chr9	57426091	57426114	-	1	NA	intron (NM_176831, intron 3 of 6)	PB1D10|SINE|Alu	14012	NM_176831	66812	Mm.250508	NM_176831	ENSMUSG00000063849	Ppcdc	1810057I13Rik|8430432M10Rik	phosphopantothenoylcysteine decarboxylase	protein-coding
mm_8877.1	chr1	162860098	162860108	-	1	NA	promoter-TSS (NM_001330291)	promoter-TSS (NM_001330291)	-103	NM_001330318	14261	Mm.976	NM_010231	ENSMUSG00000040181	Fmo1	-	flavin containing monooxygenase 1	protein-coding
mm_153605.1	chr19	43921411	43921419	-	1	NA	intron (NM_028029, intron 1 of 15)	intron (NM_028029, intron 1 of 15)	18783	NM_028029	71972	Mm.159024	NM_028029	ENSMUSG00000025195	Dnmbp	2410003L07Rik|2410003M15Rik|TUBA	dynamin binding protein	protein-coding
mm_49016.1	chr6	4758670	4758682	+	1	NA	3' UTR (NM_130877, exon 2 of 2)	3' UTR (NM_130877, exon 2 of 2)	11370	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_136841.1	chr17	12756019	12756032	+	1	NA	intron (NM_010515, intron 1 of 47)	intron (NM_010515, intron 1 of 47)	13681	NM_010515	16004	Mm.26553	NM_010515	ENSMUSG00000023830	Igf2r	AI661837|CD222|CI-MPR|M6P/IGF2R|Mpr300	insulin-like growth factor 2 receptor	protein-coding
mm_33985.1	chr4	137719245	137719253	+	1	NA	intron (NM_001256218, intron 14 of 24)	intron (NM_001256218, intron 14 of 24)	-5212	NR_138592	110351	Mm.180763	NM_029563	ENSMUSG00000041351	Rap1gap	1300019I11Rik|2310004O14Rik|AI427470|ARPP-90|Gap|Rap1GAP1|Rap1ga1	Rap1 GTPase-activating protein	protein-coding
mm_34760.1	chr4	152341549	152341551	+	1	NA	intron (NM_029216, intron 1 of 40)	MIRb|SINE|MIR	2899	NM_001081376	269610	Mm.40192	NM_029216	ENSMUSG00000005045	Chd5	4930532L22Rik|AW060752|B230399N07Rik|CHD-5	chromodomain helicase DNA binding protein 5	protein-coding
mm_102597.1	chr11	62281343	62281419	-	1	NA	promoter-TSS (NM_028360)	promoter-TSS (NM_028360)	14	NM_027198	69747	Mm.141150	NM_027198	ENSMUSG00000014243	Zswim7	2410012H22Rik	zinc finger SWIM-type containing 7	protein-coding
mm_48949.1	chr6	4540544	4540573	+	1	NA	exon (NM_007743, exon 52 of 52)	exon (NM_007743, exon 52 of 52)	34940	NM_007743	12843	Mm.277792	NM_007743	ENSMUSG00000029661	Col1a2	AA960264|AI325291|Col1a-2|Cola-2|Cola2|oim	collagen, type I, alpha 2	protein-coding
mm_97952.1	chr11	83695265	83695268	+	1	NA	Intergenic	Intergenic	-8790	NM_001081957	100034251	Mm.24097	NM_001081957	ENSMUSG00000069792	Wfdc17	Amwap|Gm11428|OTTMUSG00000000971	WAP four-disulfide core domain 17	protein-coding
mm_40741.1	chr5	66677004	66677031	+	1	NA	promoter-TSS (NR_102714)	promoter-TSS (NR_102714)	-520	NR_102714	101202684	Mm.381468	NR_102714	ENSMUSG00000087601	Uchl1os	Gm16832|Uchl1as	ubiquitin carboxy-terminal hydrolase L1, opposite strand	ncRNA
mm_5920.1	chr1	55088157	55088180	-	1	NA	promoter-TSS (NM_010477)	promoter-TSS (NM_010477)	20	NM_008303	15528	Mm.215667	NM_008303	ENSMUSG00000073676	Hspe1	10kDa|Hsp10|mt-cpn10	heat shock protein 1 (chaperonin 10)	protein-coding
mm_171628.1	chr4	17409366	17409381	+	1	NA	Intergenic	L1Md_T|LINE|L1	-443520	NR_135158	17389	Mm.187315	NM_019724	ENSMUSG00000028226	Mmp16	MT-MMP 3|MT3-MMP|Mt3mmp	matrix metallopeptidase 16	protein-coding
mm_80707.1	chr9	92250084	92250098	+	1	NA	promoter-TSS (NM_011636)	promoter-TSS (NM_011636)	-103	NM_011636	22038	Mm.421956	NM_011636	ENSMUSG00000032369	Plscr1	MmTRA1a|MmTRA1b|Nor1|Tra1|Tra1a|Tra1b|Tras1|Tras2	phospholipid scramblase 1	protein-coding
mm_96333.1	chr11	65272236	65272244	+	1	NA	Intergenic	Intergenic	-2251	NM_146386	214384	Mm.32257	NM_145136	ENSMUSG00000020542	Myocd	BSAC2A|Srfcp	myocardin	protein-coding
mm_119147.1	chr14	31336796	31336806	+	1	NA	promoter-TSS (NM_009796)	promoter-TSS (NM_009796)	77	NM_009796	12339	Mm.201535	NM_009796	ENSMUSG00000021893	Capn7	AU022319|PalBH	calpain 7	protein-coding
mm_115511.1	chr13	4609123	4609189	-	1	NA	promoter-TSS (NM_018859)	promoter-TSS (NM_018859)	8	NM_018859	56043	Mm.251908	NM_018859	ENSMUSG00000045410	Akr1e1	1810061I10Rik|Akr1e2	aldo-keto reductase family 1, member E1	protein-coding
mm_104250.1	chr11	88864510	88864527	-	1	NA	promoter-TSS (NM_001042541)	promoter-TSS (NM_001042541)	68	NM_001042541	11640	Mm.2969	NM_009648	ENSMUSG00000018428	Akap1	AKAP121|AKAP84|Akap|C76494|C81186|DAKAP1|S-AKAP84	A kinase (PRKA) anchor protein 1	protein-coding
mm_125404.1	chr15	41603316	41603328	+	1	NA	intron (NM_001130166, intron 2 of 16)	intron (NM_001130166, intron 2 of 16)	155840	NM_001130166	170719	Mm.254267	NM_130885	ENSMUSG00000022307	Oxr1	2210416C20Rik|C7|C7B	oxidation resistance 1	protein-coding
mm_68963.1	chr7	126583328	126583371	-	1	NA	promoter-TSS (NM_009907)	promoter-TSS (NM_009907)	-113	NM_009907	12752	Mm.268930	NM_009907	ENSMUSG00000030720	Cln3	AI323623	ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease)	protein-coding
mm_60143.1	chr7	38183648	38183668	+	1	NA	promoter-TSS (NM_028166)	promoter-TSS (NM_028166)	-129	NM_028166	72244	Mm.187554	NM_028166		1600014C10Rik	AI428873	RIKEN cDNA 1600014C10 gene	protein-coding
mm_122805.1	chr14	54568215	54568257	-	1	NA	3' UTR (NM_010590, exon 8 of 8)	3' UTR (NM_010590, exon 8 of 8)	9425	NM_010590	16475	Mm.100253	NM_010590	ENSMUSG00000022178	Ajuba	Jub	ajuba LIM protein	protein-coding
mm_68931.1	chr7	126494321	126494341	-	1	NA	intron (NM_001347658, intron 17 of 21)	intron (NM_001347658, intron 17 of 21)	6976	NM_001163713	233870	Mm.197829	NM_172745	ENSMUSG00000073838	Tufm	2300002G02Rik|C76308|C76389|EF-TuMT|EFTU	Tu translation elongation factor, mitochondrial	protein-coding
mm_105072.1	chr11	100759742	100759754	-	1	NA	promoter-TSS (NM_001081194)	promoter-TSS (NM_001081194)	30	NM_001081194	380728	Mm.297539	NM_001081194	ENSMUSG00000035355	Kcnh4	BEC2	potassium voltage-gated channel, subfamily H (eag-related), member 4	protein-coding
mm_161928.1	chr18	78184623	78184623	-	1	NA	exon (NM_207651, exon 10 of 22)	exon (NM_207651, exon 10 of 22)	-5451	NM_001110273	27411	Mm.44158	NM_030683	ENSMUSG00000024552	Slc14a2	UT-A1|UT-A3	solute carrier family 14 (urea transporter), member 2	protein-coding
mm_91384.1	chr10	30628500	30628505	-	1	NA	Intergenic	LTRIS2|LTR|ERV1	-10136	NM_025798	66847	Mm.46218	NM_025798	ENSMUSG00000019791	Hint3	0610010I17Rik|AV009015|HINT-3|HINT-4|HINT4	histidine triad nucleotide binding protein 3	protein-coding
mm_151377.1	chr19	55976676	55976696	+	1	NA	Intergenic	Intergenic	81365	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_27121.1	chr3	31310247	31310265	-	1	NA	promoter-TSS (NM_172861)	promoter-TSS (NM_172861)	63	NM_172861	241919	Mm.285366	NM_172861	ENSMUSG00000069072	Slc7a14	A930013N06|BC061928	solute carrier family 7 (cationic amino acid transporter, y+ system), member 14	protein-coding
mm_151187.1	chr19	53421375	53421386	+	1	NA	Intergenic	Intergenic	-30807	NM_172429	76479	Mm.313687	NM_172429	ENSMUSG00000025024	Smndc1	2410004J23Rik|4933440I19Rik	survival motor neuron domain containing 1	protein-coding
mm_158401.1	chrX	136832084	136832106	-	1	NA	exon (NM_011123, exon 3 of 7)	exon (NM_011123, exon 3 of 7)	9349	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_106502.1	chr11	120404912	120404918	-	1	NA	intron (NM_199469, intron 11 of 15)	ID_B1|SINE|B4	-26169	NM_027980	71885	Mm.274890	NM_027980	ENSMUSG00000025384	Faap100	2310003H01Rik	Fanconi anemia core complex associated protein 100	protein-coding
mm_50187.1	chr6	41684364	41684368	+	1	NA	promoter-TSS (NM_029671)	promoter-TSS (NM_029671)	-65	NM_029671	76606	Mm.272520	NM_029671	ENSMUSG00000029867	1700034O15Rik	-	RIKEN cDNA 1700034O15 gene	protein-coding
mm_73132.1	chr8	94973568	94973569	+	1	NA	Intergenic	Intergenic	-3541	NM_001198894	14766	Mm.290834	NM_018882	ENSMUSG00000031785	Adgrg1	Cyt28|Gpr56|TM7LN4|TM7XN1	adhesion G protein-coupled receptor G1	protein-coding
mm_7571.1	chr1	124845895	124845949	-	1	NA	Intergenic	Intergenic	589805	NM_023735	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding
mm_136351.1	chr16	92695219	92695231	-	1	NA	intron (NM_001111023, intron 1 of 5)	intron (NM_001111023, intron 1 of 5)	2104	NM_001111023	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_120817.1	chr14	75132022	75132038	+	1	NA	intron (NM_001247984, intron 1 of 15)	intron (NM_001247984, intron 1 of 15)	907	NM_001247984	18826	Mm.153911	NM_008879	ENSMUSG00000021998	Lcp1	AW536232|D14Ertd310e|LCP-1|Pls2|pp65	lymphocyte cytosolic protein 1	protein-coding
mm_141495.1	chr17	31519917	31519980	-	1	NA	promoter-TSS (NM_001083891)	promoter-TSS (NM_001083891)	-167	NM_030087	78330	Mm.28349	NM_030087	ENSMUSG00000024038	Ndufv3	1500032D16Rik	NADH dehydrogenase (ubiquinone) flavoprotein 3	protein-coding
mm_144750.1	chr18	35607932	35607935	+	1	NA	intron (NM_026420, intron 1 of 3)	PB1D9|SINE|Alu	9266	NM_026420	67869	Mm.126534	NM_026420	ENSMUSG00000037058	Paip2	2310050K10Rik|AU045972	polyadenylate-binding protein-interacting protein 2	protein-coding
mm_21387.1	chr2	157555582	157555582	-	1	NA	TTS (NM_016916)	TTS (NM_016916)	-4496	NM_001291129	18111	Mm.34330	NM_010923	ENSMUSG00000067786	Nnat	5730414I02Rik|AW107673|Peg5	neuronatin	protein-coding
mm_34478.1	chr4	148418441	148418446	+	1	NA	Intergenic	Intergenic	26308	NM_027873	71707	Mm.292503	NM_027873	ENSMUSG00000047719	Ubiad1	1200002M06Rik|AI426463|AW320947|Tere1	UbiA prenyltransferase domain containing 1	protein-coding
mm_98230.1	chr11	88068317	88068332	+	1	NA	promoter-TSS (NM_016686)	promoter-TSS (NM_016686)	45	NM_016686	22344	Mm.46628	NM_016686	ENSMUSG00000018377	Vezf1	AI848691|AW046909|db1	vascular endothelial zinc finger 1	protein-coding
mm_64853.1	chr7	13034704	13034714	-	1	NA	promoter-TSS (NM_026885)	promoter-TSS (NM_026885)	68	NM_026885	68953	Mm.295670	NM_026885	ENSMUSG00000033916	Chmp2a	1500016L11Rik	charged multivesicular body protein 2A	protein-coding
mm_44336.1	chr5	15883807	15883810	-	1	NA	promoter-TSS (NR_045974)	promoter-TSS (NR_045974)	-42	NR_045974	75058	Mm.183467	NR_045974	ENSMUSG00000105185	4930519H02Rik	-	RIKEN cDNA 4930519H02 gene	ncRNA
mm_62710.1	chr7	110768107	110768127	+	1	NA	promoter-TSS (NM_001276301)	promoter-TSS (NM_001276301)	-89	NM_001276301	11717	Mm.3238	NM_009667	ENSMUSG00000005686	Ampd3	-	adenosine monophosphate deaminase 3	protein-coding
mm_104073.1	chr11	86586590	86586598	-	1	NA	exon (NM_029478, exon 11 of 12)	exon (NM_029478, exon 11 of 12)	-2436	NR_029738	387140		NR_029738	ENSMUSG00000065455	Mir21a	Mir21|Mirn21|mmu-mir-21|mmu-mir-21a	microRNA 21a	ncRNA
mm_125681.1	chr15	66670750	66670754	+	1	NA	promoter-TSS (NM_009375)	promoter-TSS (NM_009375)	-18	NM_009375	21819	Mm.441333	NM_009375	ENSMUSG00000053469	Tg	Tgn|cog	thyroglobulin	protein-coding
mm_83519.1	chr9	46229935	46229975	-	1	NA	exon (NM_009692, exon 4 of 4)	exon (NM_009692, exon 4 of 4)	1325	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2|apo-AI|apoA-I	apolipoprotein A-I	protein-coding
mm_131585.1	chr16	18498785	18498816	+	1	NA	promoter-TSS (NM_001081682)	promoter-TSS (NM_001081682)	-71	NM_001285494	13972	Mm.236139	NM_023120	ENSMUSG00000000884	Gnb1l	ESTM55|Gm16314|Me49f07|OTTMUSG00000033458|Wdr14|Wdvcf	guanine nucleotide binding protein (G protein), beta polypeptide 1-like	protein-coding
mm_57566.1	chr6	127128755	127128766	-	1	NA	3' UTR (NM_009829, exon 5 of 5)	3' UTR (NM_009829, exon 5 of 5)	-19208	NM_177003	319801	Mm.101836	NM_177003	ENSMUSG00000038028	Tigar	9630033F20Rik|AA793651|AI595337|C79710|C85509	Trp53 induced glycolysis repulatory phosphatase	protein-coding
mm_123931.1	chr14	73366420	73366431	-	1	NA	exon (NM_008410, exon 3 of 6)	exon (NM_008410, exon 3 of 6)	18846	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_112289.1	chr12	114487616	114487622	-	1	NA	Intergenic	Intergenic	-18153	NR_106062	102465663		NR_106062	ENSMUSG00000105438	Mir7094-1	mmu-mir-7094-1	microRNA 7094-1	ncRNA
mm_34989.1	chr4	156027483	156027496	+	1	NA	intron (NM_021985, intron 2 of 3)	intron (NM_021985, intron 2 of 3)	1147	NM_021985	21936	Mm.3180	NM_009400	ENSMUSG00000041954	Tnfrsf18	AITR|Gitr	tumor necrosis factor receptor superfamily, member 18	protein-coding
mm_135160.1	chr16	35860478	35860505	-	1	NA	exon (NM_001039530, exon 5 of 17)	exon (NM_001039530, exon 5 of 17)	10891	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_143163.1	chr17	57224881	57224952	-	1	NA	exon (NM_009778, exon 7 of 41)	exon (NM_009778, exon 7 of 41)	3220	NM_009778	12266	Mm.19131	NM_009778	ENSMUSG00000024164	C3	AI255234|ASP|HSE-MSF|Plp	complement component 3	protein-coding
mm_80857.1	chr9	98425489	98425513	+	1	NA	exon (NM_011254, exon 2 of 4)	exon (NM_011254, exon 2 of 4)	2540	NM_011254	19659	Mm.279741	NM_011254	ENSMUSG00000046402	Rbp1	CRBPI|Crbp|Rbp-1	retinol binding protein 1, cellular	protein-coding
mm_36891.1	chr4	107680742	107680770	-	1	NA	exon (NM_019872, exon 2 of 4)	exon (NM_019872, exon 2 of 4)	3406	NM_019872	56296	Mm.141324	NM_019872	ENSMUSG00000028610	Dmrtb1	Dmrt6|Prp13	DMRT-like family B with proline-rich C-terminal, 1	protein-coding
mm_60114.1	chr7	35586233	35586290	+	1	NA	promoter-TSS (NM_178263)	promoter-TSS (NM_178263)	14	NM_178263	245886	Mm.272620	NM_145633	ENSMUSG00000034867	Ankrd27	AA408090|BC016493|D330003H11Rik|Varp	ankyrin repeat domain 27 (VPS9 domain)	protein-coding
mm_58253.1	chr6	145075961	145076018	-	1	NA	5' UTR (NM_007532, exon 1 of 11)	5' UTR (NM_007532, exon 1 of 11)	168	NM_007532	12035	Mm.4606	NM_007532	ENSMUSG00000030268	Bcat1	BCATc|Eca39	branched chain aminotransferase 1, cytosolic	protein-coding
mm_90270.1	chr10	122680097	122680100	+	1	NA	TTS (NR_106182)	TTS (NR_106182)	783	NR_106182	102466884		NR_106182	ENSMUSG00000099225	Mir8104	Gm27380|mmu-mir-8104	microRNA 8104	ncRNA
mm_62453.1	chr7	101406594	101406618	+	1	NA	intron (NM_001040112, intron 26 of 30)	intron (NM_001040112, intron 26 of 30)	12218	NM_198096	69710	Mm.277687	NM_027180	ENSMUSG00000032812	Arap1	2410002L19Rik|Centd2|mKIAA0782	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	protein-coding
mm_40805.1	chr5	69919094	69919099	+	1	NA	Intergenic	U2|snRNA|snRNA	-326792	NM_001347363	67980	Mm.33830	NM_027681	ENSMUSG00000029209	Gnpda2	4921523I18Rik|4933412A11Rik|BB189630|GNPDA|Gnp2|Sb52|mKIAA4008	glucosamine-6-phosphate deaminase 2	protein-coding
mm_156865.1	chrX	164436988	164437036	+	1	NA	promoter-TSS (NM_026853)	promoter-TSS (NM_026853)	18	NM_001313737	68854	Mm.33225	NM_026853	ENSMUSG00000031382	Asb11	1110067L12Rik|1600009D24Rik	ankyrin repeat and SOCS box-containing 11	protein-coding
mm_85422.1	chr9	103489302	103489310	-	1	NA	exon (NM_178638, exon 5 of 6)	exon (NM_178638, exon 5 of 6)	-8978	NM_001002896	107993	Mm.335403	NM_001002896	ENSMUSG00000032556	Bfsp2	AI448593|CP49	beaded filament structural protein 2, phakinin	protein-coding
mm_91423.1	chr10	32889904	32889919	-	1	NA	promoter-TSS (NM_001025286)	promoter-TSS (NM_001025286)	4	NM_001013411	432450	Mm.49665	NM_001013411	ENSMUSG00000069670	Nkain2	6330571D19Rik|AW455467|Tcba1	Na+/K+ transporting ATPase interacting 2	protein-coding
mm_128470.1	chr15	50850384	50850387	-	1	NA	intron (NM_032000, intron 1 of 5)	intron (NM_032000, intron 1 of 5)	38664	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_54923.1	chr6	47813378	47813409	-	1	NA	5' UTR (NM_009787, exon 1 of 10)	5' UTR (NM_009787, exon 1 of 10)	119	NM_009787	12304	Mm.2442	NM_009787	ENSMUSG00000025823	Pdia4	AI987846|Cai|ERp-72|Erp72	protein disulfide isomerase associated 4	protein-coding
mm_134824.1	chr16	26073921	26073935	-	1	NA	intron (NM_173379, intron 1 of 14)	RSINE1|SINE|B4	31856	NM_173379	210530	Mm.326869	NM_173379	ENSMUSG00000038168	P3h2	4832416N06|AW553532|Leprel1|Mlat4	prolyl 3-hydroxylase 2	protein-coding
mm_62321.1	chr7	100372052	100372084	+	1	NA	promoter-TSS (NM_001017985)	promoter-TSS (NM_001017985)	-165	NM_001017985	277939	Mm.276374	NM_001017985	ENSMUSG00000047248	C2cd3	AU020772	C2 calcium-dependent domain containing 3	protein-coding
mm_156694.1	chrX	159472841	159472854	+	1	NA	exon (NM_001081124, exon 8 of 17)	exon (NM_001081124, exon 8 of 17)	13722	NM_001313753	78283	Mm.160079	NM_001081124	ENSMUSG00000041020	Map7d2	1600028E09Rik|2900002G04Rik|5330432J06Rik|C030036K04Rik|Mtap7d2	MAP7 domain containing 2	protein-coding
mm_160096.1	chr7	18355167	18355167	-	1	NA	promoter-TSS (NM_011963)	promoter-TSS (NM_011963)	-160	NM_011963	26438	Mm.89991	NM_011963	ENSMUSG00000003505	Psg18	Cea-3|Cea3|mmCGM6	pregnancy specific glycoprotein 18	protein-coding
mm_155155.1	chrX	52926950	52926963	+	1	NA	intron (NM_027642, intron 3 of 10)	intron (NM_027642, intron 3 of 10)	14742	NM_001290546	70998	Mm.26870	NM_027642	ENSMUSG00000025626	Phf6	2700007B13Rik|4931428F02Rik|mKIAA1823	PHD finger protein 6	protein-coding
mm_18427.1	chr2	60761292	60761309	-	1	NA	intron (NM_001141932, intron 9 of 14)	intron (NM_001141932, intron 9 of 14)	-38697	NM_001159564	16420	Mm.98193	NM_021359	ENSMUSG00000026971	Itgb6	2210409C20Rik|4831415H04Rik	integrin beta 6	protein-coding
mm_19753.1	chr2	104850043	104850089	-	1	NA	promoter-TSS (NM_178695)	promoter-TSS (NM_178695)	-216	NM_178695	228413	Mm.259609	NM_178695	ENSMUSG00000027171	Prrg4	9930111I18Rik|TMG4	proline rich Gla (G-carboxyglutamic acid) 4 (transmembrane)	protein-coding
mm_43497.1	chr5	136967897	136967907	+	1	NA	promoter-TSS (NM_021719)	promoter-TSS (NM_021719)	33	NM_021719	60363	Mm.87202	NM_021719	ENSMUSG00000001739	Cldn15	2210009B08Rik|BB107105	claudin 15	protein-coding
mm_9520.1	chr1	173755934	173755953	-	1	NA	exon (NM_008329, exon 5 of 9)	exon (NM_008329, exon 5 of 9)	10976	NM_008329	15951	Mm.261270	NM_008329	ENSMUSG00000073489	Ifi204	Ifi16|p204	interferon activated gene 204	protein-coding
mm_95472.1	chr11	50793713	50793729	+	1	NA	intron (NM_175643, intron 19 of 21)	intron (NM_175643, intron 19 of 21)	34010	NM_013922	30944	Mm.103674	NM_013922	ENSMUSG00000044807	Zfp354c	5330421P20Rik|AJ18|AW743325|Kid3|Tcf17l2|Znf354c|mKIAA4218	zinc finger protein 354C	protein-coding
mm_73381.1	chr8	105664168	105664179	+	1	NA	exon (NM_181322, exon 3 of 12)	exon (NM_181322, exon 3 of 12)	-26733	NM_001033320	234695	Mm.471640	NM_001033320	ENSMUSG00000050357	Carmil2	CG1399-PB|D130029J02Rik|Gm585|Rltpr	capping protein regulator and myosin 1 linker 2	protein-coding
mm_52851.1	chr6	121861120	121861137	+	1	NA	exon (NM_008645, exon 12 of 36)	exon (NM_008645, exon 12 of 36)	22587	NM_008645	17836	Mm.1311	NM_008645	ENSMUSG00000059908	Mug1	-	murinoglobulin 1	protein-coding
mm_4198.1	chr1	171226274	171226297	+	1	NA	TTS (NM_013474)	TTS (NM_013474)	1231	NM_013474	11807	Mm.389209	NM_013474	ENSMUSG00000005681	Apoa2	Alp-2|Apo-AII|ApoA-II|ApoAII|Apoa-2|Hdl-1	apolipoprotein A-II	protein-coding
mm_90703.1	chr10	130363677	130363689	+	1	NA	Intergenic	B2_Mm2|SINE|B2	30558	NM_001081448	625068	Mm.359168	NM_001081448	ENSMUSG00000070601	Vmn2r84	EG625068	vomeronasal 2, receptor 84	protein-coding
mm_131779.1	chr16	22895294	22895301	+	1	NA	promoter-TSS (NR_110508)	promoter-TSS (NR_110508)	-911	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_135644.1	chr16	52366875	52366881	-	1	NA	intron (NM_009655, intron 1 of 15)	intron (NM_009655, intron 1 of 15)	86203	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_13735.1	chr2	118112365	118112390	+	1	NA	intron (NM_001313914, intron 1 of 21)	intron (NM_001313914, intron 1 of 21)	501	NM_001313914	21825	Mm.4159	NM_011580	ENSMUSG00000040152	Thbs1	TSP-1|TSP1|Thbs-1|tbsp1	thrombospondin 1	protein-coding
mm_58517.1	chr7	4137033	4137066	+	1	NA	promoter-TSS (NM_172736)	promoter-TSS (NM_172736)	-7	NM_172736	232798	Mm.22831	NM_172736	ENSMUSG00000035545	Leng8	AW049671	leukocyte receptor cluster (LRC) member 8	protein-coding
mm_29667.1	chr3	122619684	122619698	-	1	NA	promoter-TSS (NM_001114665)	promoter-TSS (NM_001114665)	23	NM_001114665	214459	Mm.209491	NM_153118	ENSMUSG00000039735	Fnbp1l	2610318I01Rik|AW548221|TOCA1|toca-1	formin binding protein 1-like	protein-coding
mm_27519.1	chr3	57294881	57294899	-	1	NA	5' UTR (NM_008536, exon 3 of 7)	5' UTR (NM_008536, exon 3 of 7)	7029	NM_008536	17112	Mm.856	NM_008536	ENSMUSG00000027800	Tm4sf1	L6|M3s1	transmembrane 4 superfamily member 1	protein-coding
mm_27979.1	chr3	80913543	80913666	-	1	NA	promoter-TSS (NM_001281969)	promoter-TSS (NM_001281969)	56	NM_001345956	14658	Mm.275639	NM_010298	ENSMUSG00000028020	Glrb	AI853901|Glyrb|spa|spastic	glycine receptor, beta subunit	protein-coding
mm_155362.1	chrX	71050127	71050144	+	1	NA	promoter-TSS (NM_001256048)	promoter-TSS (NM_001256048)	-121	NM_001256048	333639	Mm.371730	NM_001081354	ENSMUSG00000059401	Mamld1	G630014P10Rik	mastermind-like domain containing 1	protein-coding
mm_147225.1	chr18	38203834	38203836	-	1	NA	intron (NM_029357, intron 1 of 2)	intron (NM_029357, intron 1 of 2)	5927	NM_029357	75599	Mm.36560	NM_029357	ENSMUSG00000051375	Pcdh1	2010005A06Rik|AI585920	protocadherin 1	protein-coding
mm_110629.1	chr12	57542268	57542277	-	1	NA	exon (NM_008259, exon 2 of 2)	exon (NM_008259, exon 2 of 2)	3849	NM_008259	15375	Mm.4578	NM_008259	ENSMUSG00000035451	Foxa1	Hnf-3a|Hnf3a|Tcf-3a|Tcf3a	forkhead box A1	protein-coding
mm_92237.1	chr10	69328153	69328161	-	1	NA	Intergenic	Intergenic	24755	NM_007659	12534	Mm.281367	NM_007659	ENSMUSG00000019942	Cdk1	Cdc2|Cdc2a|p34<CDC2>	cyclin-dependent kinase 1	protein-coding
mm_149104.1	chr19	8943118	8943120	+	1	NA	intron (NM_011842, intron 1 of 17)	T-rich|Low_complexity|Low_complexity	1199	NM_011842	23942	Mm.25339	NM_011842	ENSMUSG00000071646	Mta2	AW550797|Mata1l1|Mta1l1|mmta2	metastasis-associated gene family, member 2	protein-coding
mm_35952.1	chr4	53118824	53118867	-	1	NA	intron (NM_013454, intron 5 of 49)	MIR|SINE|MIR	41050	NM_013454	11303	Mm.277376	NM_013454	ENSMUSG00000015243	Abca1	ABC-1|Abc1	ATP-binding cassette, sub-family A (ABC1), member 1	protein-coding
mm_164363.1	chr16	23050345	23050367	+	1	NA	Intergenic	Intergenic	-7944	NM_023125	16644	Mm.2160	NM_023125	ENSMUSG00000022875	Kng1	Kng	kininogen 1	protein-coding
mm_155911.1	chrX	101849344	101849367	+	1	NA	promoter-TSS (NM_001163610)	promoter-TSS (NM_001163610)	-30	NM_001163610	100042480	Mm.232	NM_001163610	ENSMUSG00000079481	Nhsl2	1110062M06Rik|6430511F03|AI225852|AW488865|EG621083|ENSMUSG00000073037|Gm10456	NHS-like 2	protein-coding
mm_86408.1	chr9	124066868	124066871	-	1	NA	Intergenic	L1_Mur2|LINE|L1	-35314	NM_009915	12772	Mm.6272	NM_009915	ENSMUSG00000049103	Ccr2	Cc-ckr-2|Ccr2a|Ccr2b|Ckr2|Ckr2a|Ckr2b|Cmkbr2|mJe-r	chemokine (C-C motif) receptor 2	protein-coding
mm_46407.1	chr5	104093199	104093209	-	1	NA	exon (NM_010097, exon 4 of 11)	exon (NM_010097, exon 4 of 11)	-15596	NM_001163772	100271704	Mm.366664	NM_001163772	ENSMUSG00000091034	Gm17660	Scpppq1	predicted gene, 17660	protein-coding
mm_100252.1	chr11	117326487	117326517	+	1	NA	intron (NM_001113487, intron 2 of 10)	intron (NM_001113487, intron 2 of 10)	-5213	NM_017380	53860	Mm.38450	NM_017380	ENSMUSG00000059248	Sept9	MSF1|Msf|PNUTL4|Sint1	septin 9	protein-coding
mm_49890.1	chr6	38892437	38892452	+	1	NA	Intergenic	Intergenic	-16254	NM_001294143	15258	Mm.23790	NM_010433	ENSMUSG00000061436	Hipk2	1110014O20Rik|B230339E18Rik|Stank	homeodomain interacting protein kinase 2	protein-coding
mm_44369.1	chr5	17813095	17813118	-	1	NA	intron (NM_007643, intron 6 of 14)	intron (NM_007643, intron 6 of 14)	22790	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_82622.1	chr9	21798695	21798755	-	1	NA	promoter-TSS (NM_145611)	promoter-TSS (NM_145611)	-179	NM_145611	235041	Mm.257371	NM_145611	ENSMUSG00000032194	Kank2	AI504612|Ankrd25|BC010245	KN motif and ankyrin repeat domains 2	protein-coding
mm_9449.1	chr1	172590668	172590679	-	1	NA	promoter-TSS (NM_029084)	promoter-TSS (NM_029084)	-105	NM_029084	74748	Mm.179812	NM_029084	ENSMUSG00000053318	Slamf8	5830408F06Rik|Blame|SBBI42	SLAM family member 8	protein-coding
mm_172341.1	chr7	11069715	11069727	-	1	NA	Intergenic	Intergenic	63976	NM_001013765	245109	Mm.131747	NM_001013765	ENSMUSG00000054272	Zscan4c	Gm397|XM_142517|Zscan4d	zinc finger and SCAN domain containing 4C	protein-coding
mm_67433.1	chr7	80371482	80371494	-	1	NA	promoter-TSS (NM_172903)	promoter-TSS (NM_172903)	-113	NM_172903	140481	Mm.269245	NM_172903	ENSMUSG00000038886	Man2a2	1700052O22Rik|4931438M07Rik|AI480988|MX|Man IIx	mannosidase 2, alpha 2	protein-coding
mm_33355.1	chr4	129461662	129461689	+	1	NA	promoter-TSS (NM_133889)	promoter-TSS (NM_133889)	-4	NM_133889	100383	Mm.17918	NM_133889	ENSMUSG00000040859	Bsdc1	1110063F24Rik|AW011758	BSD domain containing 1	protein-coding
mm_65990.1	chr7	30535007	30535047	-	1	NA	promoter-TSS (NM_001289670)	promoter-TSS (NM_001289670)	33	NM_001289670	233071	Mm.190704	NM_178252	ENSMUSG00000036882	Arhgap33	AW324378|NOMA-GAP|Snx26|TCGAP	Rho GTPase activating protein 33	protein-coding
mm_14856.1	chr2	148681200	148681218	+	1	NA	promoter-TSS (NM_028986)	promoter-TSS (NM_028986)	89	NM_028986	74533	Mm.136913	NM_028986	ENSMUSG00000027439	Gzf1	8430437G08Rik|Zfp336|mGZF1	GDNF-inducible zinc finger protein 1	protein-coding
mm_22650.1	chr3	14870029	14870037	+	1	NA	intron (NM_007606, intron 5 of 6)	intron (NM_007606, intron 5 of 6)	6495	NM_007606	12350	Mm.300	NM_007606	ENSMUSG00000027559	Car3	BB219044|Ca3|Car-3	carbonic anhydrase 3	protein-coding
mm_172946.1	chr9	81678077	81678077	+	1	NA	Intergenic	Intergenic	-45525	NM_010482	15551	Mm.445308	NM_010482	ENSMUSG00000049511	Htr1b	-	5-hydroxytryptamine (serotonin) receptor 1B	protein-coding
mm_68881.1	chr7	126447681	126447693	-	1	NA	exon (NM_007504, exon 18 of 23)	exon (NM_007504, exon 18 of 23)	15386	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_69039.1	chr7	126799551	126799588	-	1	NA	promoter-TSS (NM_001177307)	promoter-TSS (NM_001177307)	-315	NM_007438	11674	Mm.275831	NM_007438	ENSMUSG00000030695	Aldoa	Aldo-1|Aldo1	aldolase A, fructose-bisphosphate	protein-coding
mm_57532.1	chr6	126535425	126535452	-	1	NA	5' UTR (NM_145983, exon 1 of 1)	5' UTR (NM_145983, exon 1 of 1)	117	NM_145983	16493	Mm.222831	NM_145983	ENSMUSG00000045534	Kcna5	Kv1.5	potassium voltage-gated channel, shaker-related subfamily, member 5	protein-coding
mm_130083.1	chr15	89378933	89378943	-	1	NA	intron (NM_001013022, intron 1 of 4)	CpG-5245	316	NM_001013022	70113	Mm.247273	NM_001013022	ENSMUSG00000047394	Odf3b	2010001J22Rik	outer dense fiber of sperm tails 3B	protein-coding
mm_59257.1	chr7	24870081	24870124	+	1	NA	promoter-TSS (NM_027732)	promoter-TSS (NM_027732)	45	NM_027732	71241	Mm.66855	NM_027732	ENSMUSG00000011349	Dmrtc2	4933432E21Rik|Dmrt7	doublesex and mab-3 related transcription factor like family C2	protein-coding
mm_1090.1	chr1	59670824	59670857	+	1	NA	promoter-TSS (NM_009460)	promoter-TSS (NM_009460)	-6	NM_009460	22218	Mm.362118	NM_009460	ENSMUSG00000026021	Sumo1	GMP1|PIC1|SENTRIN|SMT3|SMT3H3|SMTP3|SUMO-1|Smt3C|Ubl1	small ubiquitin-like modifier 1	protein-coding
mm_98166.1	chr11	87749733	87749751	+	1	NA	Intergenic	Intergenic	-7122	NR_029555	387160		NR_029555	ENSMUSG00000105196	Mir142	Mirn142|miR-142|mir-142a|mmu-mir-142|mmu-mir-142a	microRNA 142	ncRNA
mm_172923.1	chr9	68653790	68653794	+	1	NA	promoter-TSS (NM_001289917)	promoter-TSS (NM_001289917)	6	NM_013646	19883	Mm.378450	NM_013646	ENSMUSG00000032238	Rora	9530021D13Rik|Nr1f1|ROR1|ROR2|ROR3|nmf267|sg|staggerer|tmgc26	RAR-related orphan receptor alpha	protein-coding
mm_131910.1	chr16	23280191	23280194	+	1	NA	intron (NM_001252505, intron 2 of 7)	intron (NM_001252505, intron 2 of 7)	-10278	NM_001252506	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_64189.1	chr7	141461076	141461101	+	1	NA	promoter-TSS (NM_001025103)	promoter-TSS (NM_001025103)	-6	NM_001025103	213573	Mm.386851	NM_001025103	ENSMUSG00000048200	Cracr2b	6330520A15Rik|BC026645|Cracr2a|Efcab4|Efcab4a	calcium release activated channel regulator 2B	protein-coding
mm_55633.1	chr6	72315007	72315021	-	1	NA	TTS (NM_001282071)	TTS (NM_001282071)	10404	NM_147779	20388	Mm.46033	NM_147779	ENSMUSG00000056370	Sftpb	AI562151|SF-B|SP-B|Sftp-3|Sftp3	surfactant associated protein B	protein-coding
mm_27961.1	chr3	80688117	80688130	-	1	NA	3' UTR (NM_013540, exon 16 of 16)	3' UTR (NM_013540, exon 16 of 16)	114668	NM_013540	14800	Mm.220224	NM_013540	ENSMUSG00000033981	Gria2	GluA2|GluR-B|Glur-2|Glur2	glutamate receptor, ionotropic, AMPA2 (alpha 2)	protein-coding
mm_126684.1	chr15	84906631	84906635	+	1	NA	Intergenic	LFSINE_Vert|SINE|tRNA	-16795	NM_016714	18141	Mm.28379	NM_016714	ENSMUSG00000016619	Nup50	1700030K07Rik|AI413123|Npap60	nucleoporin 50	protein-coding
mm_8352.1	chr1	150269465	150269465	-	1	NA	Intergenic	Intergenic	-49952	NM_024458	20028	Mm.440883	NM_024458	ENSMUSG00000006007	Pdc	Rpr-1|Rpr1	phosducin	protein-coding
mm_44829.1	chr5	33936302	33936353	-	1	NA	promoter-TSS (NM_011914)	promoter-TSS (NM_011914)	-69	NM_011914	24116	Mm.332320	NM_011914	ENSMUSG00000029111	Nelfa	Whsc2|Whsc2h	negative elongation factor complex member A, Whsc2	protein-coding
mm_153410.1	chr19	40565043	40565058	-	1	NA	exon (NM_153554, exon 13 of 19)	exon (NM_153554, exon 13 of 19)	23413	NM_019698	56454	Mm.233117	NM_019698	ENSMUSG00000025007	Aldh18a1	2810433K04Rik|AI429789|Pycs	aldehyde dehydrogenase 18 family, member A1	protein-coding
mm_49330.1	chr6	21215415	21215435	+	1	NA	promoter-TSS (NM_019697)	promoter-TSS (NM_019697)	-684	NM_019697	16508	Mm.425316	NM_019697	ENSMUSG00000060882	Kcnd2	AI839615|AW555701|Kv4.2|R75121|mKIAA1044	potassium voltage-gated channel, Shal-related family, member 2	protein-coding
mm_90343.1	chr10	127129641	127129652	+	1	NA	Intergenic	B3|SINE|B2	-8486	NM_001171026	216440	Mm.295246	NM_177614	ENSMUSG00000040462	Os9	4632413K17Rik|AU022351	amplified in osteosarcoma	protein-coding
mm_98824.1	chr11	97362373	97362385	+	1	NA	promoter-TSS (NM_138657)	promoter-TSS (NM_138657)	-172	NM_138657	192157	Mm.34339	NM_138657	ENSMUSG00000038485	Socs7	2310063P06Rik|C85125|Nap4	suppressor of cytokine signaling 7	protein-coding
mm_93997.1	chr10	127563814	127563821	-	1	NA	intron (NM_008512, intron 41 of 88)	intron (NM_008512, intron 41 of 88)	-29258	NM_183297	104080	Mm.437200	NM_183297	ENSMUSG00000040258	Nxph4	1110036M10Rik|AI851051	neurexophilin 4	protein-coding
mm_96934.1	chr11	70525362	70525394	+	1	NA	promoter-TSS (NM_008946)	promoter-TSS (NM_008946)	21	NM_008946	19175	Mm.98	NM_008946	ENSMUSG00000018286	Psmb6	Lmp19|Mpnd	proteasome (prosome, macropain) subunit, beta type 6	protein-coding
mm_37441.1	chr4	123286885	123286911	-	1	NA	intron (NM_148917, intron 2 of 13)	intron (NM_148917, intron 2 of 13)	3613	NM_148917	230721	Mm.277091	NM_130881	ENSMUSG00000011257	Pabpc4	-	poly(A) binding protein, cytoplasmic 4	protein-coding
mm_45113.1	chr5	45639255	45639274	-	1	NA	promoter-TSS (NR_102378)	promoter-TSS (NR_102378)	-11	NR_102378	319251	Mm.402857	NR_102378	ENSMUSG00000097825	9630001P10Rik	-	RIKEN cDNA 9630001P10 gene	ncRNA
mm_145013.1	chr18	38631668	38631716	+	1	NA	Intergenic	Intergenic	-30424	NM_011898	24066	Mm.42038	NM_011898	ENSMUSG00000024427	Spry4	A030006O18Rik|sprouty4	sprouty homolog 4 (Drosophila)	protein-coding
mm_17327.1	chr2	26503665	26503669	-	1	NA	promoter-TSS (NR_132655)	promoter-TSS (NR_132655)	155	NM_008714	18128	Mm.290610	NM_008714	ENSMUSG00000026923	Notch1	9930111A19Rik|Mis6|N1|Tan1|lin-12	notch 1	protein-coding
mm_67144.1	chr7	73455529	73455532	-	1	NA	exon (NM_001081345, exon 30 of 39)	exon (NM_001081345, exon 30 of 39)	-79756	NR_040324	319783	Mm.349813	NR_040324	ENSMUSG00000097756	A730056A06Rik	C76391	RIKEN cDNA A730056A06 gene	ncRNA
mm_20504.1	chr2	130424743	130424790	-	1	NA	promoter-TSS (NM_178762)	promoter-TSS (NM_178762)	-125	NM_001114541	319513	Mm.482539	NM_178762	ENSMUSG00000037773	Pced1a	A930025D01Rik|AI480484|Fam113a	PC-esterase domain containing 1A	protein-coding
mm_51971.1	chr6	91758529	91758541	+	1	NA	3' UTR (NM_009320, exon 15 of 15)	3' UTR (NM_009320, exon 15 of 15)	48858	NM_001159507	243547	Mm.333264	NM_001033353	ENSMUSG00000030098	Grip2	-	glutamate receptor interacting protein 2	protein-coding
mm_147531.1	chr18	53033614	53033645	-	1	NA	Intergenic	Intergenic	-130982	NR_035420	100316749		NR_035420	ENSMUSG00000080573	Mir467f	Mirn467f|mmu-mir-467f	microRNA 467f	ncRNA
mm_166993.1	chr7	46715071	46715076	-	1	NA	exon (NM_011315, exon 2 of 4)	exon (NM_011315, exon 2 of 4)	603	NM_011315	20210	Mm.14277	NM_011315	ENSMUSG00000040026	Saa3	AV098916|Saa-3|l7R3	serum amyloid A 3	protein-coding
mm_148314.1	chr18	83768105	83768109	-	1	NA	Intergenic	Intergenic	318455	NM_001081300	110796	Mm.102136	NM_001081300	ENSMUSG00000046982	Tshz1	5730407I04Rik|D18Bwg1409e|Mtsh1|NY-CO-33|Sdccag33|Tsh1|mKIAA4206|teashirt1	teashirt zinc finger family member 1	protein-coding
mm_105373.1	chr11	103218451	103218461	-	1	NA	promoter-TSS (NM_177801)	promoter-TSS (NM_177801)	-24	NM_177801	328019	Mm.189646	NM_177801	ENSMUSG00000044787	Spata32	4933400C05Rik|VAD1.2	spermatogenesis associated 32	protein-coding
mm_64204.1	chr7	141475225	141475231	+	1	NA	promoter-TSS (NM_025593)	promoter-TSS (NM_025593)	-8	NM_053082	64540	Mm.489619	NM_053082	ENSMUSG00000025511	Tspan4	AI325509|AI746565|D130042I01Rik|NAG-2|Tm4sf7|Tspan-4	tetraspanin 4	protein-coding
mm_76722.1	chr8	94838855	94838864	-	1	NA	promoter-TSS (NM_134141)	promoter-TSS (NM_134141)	442	NM_026452	67914	Mm.169234	NM_026452	ENSMUSG00000031782	Coq9	2310005O14Rik|C78387	coenzyme Q9	protein-coding
mm_126265.1	chr15	79109095	79109106	+	1	NA	5' UTR (NM_177461, exon 1 of 16)	5' UTR (NM_177461, exon 1 of 16)	117	NM_177461	27008	Mm.196480	NM_177461	ENSMUSG00000033039	Micall1	AI448246|D15Mit260|D15N2e|EST573322|EST820961|MIRab13|mKIAA1668	microtubule associated monooxygenase, calponin and LIM domain containing -like 1	protein-coding
mm_16141.1	chr2	170731970	170731988	+	1	NA	5' UTR (NM_029761, exon 1 of 8)	5' UTR (NM_029761, exon 1 of 8)	172	NM_001163686	76829	Mm.41633	NM_029761	ENSMUSG00000027560	Dok5	2700055C10Rik	docking protein 5	protein-coding
mm_93711.1	chr10	118868778	118868792	-	1	NA	5' UTR (NM_001014390, exon 1 of 3)	5' UTR (NM_001014390, exon 1 of 3)	118	NM_001014390	69181	Mm.45565	NM_001014390	ENSMUSG00000028630	Dyrk2	1810038L18Rik	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 2	protein-coding
mm_162662.1	chr10	5367836	5367868	-	1	NA	intron (NM_001347732, intron 14 of 145)	intron (NM_001347732, intron 14 of 145)	120462	NM_001347711	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_16872.1	chr2	12301935	12301987	-	1	NA	promoter-TSS (NM_001001309)	promoter-TSS (NM_001001309)	-17	NM_001001309	241226	Mm.329997	NM_001001309	ENSMUSG00000026768	Itga8	AI447669	integrin alpha 8	protein-coding
mm_44824.1	chr5	33747494	33747498	-	1	NA	exon (NM_019694, exon 10 of 14)	exon (NM_019694, exon 10 of 14)	25190	NM_001163216	14184	Mm.6904	NM_008010	ENSMUSG00000054252	Fgfr3	CD333|FR3|Fgfr-3|Flg-2|HBGFR|Mfr3|sam3	fibroblast growth factor receptor 3	protein-coding
mm_42971.1	chr5	123141430	123141436	+	1	NA	promoter-TSS (NM_001040398)	promoter-TSS (NM_001040398)	-760	NM_001040398	208043	Mm.250391	NM_177581	ENSMUSG00000038384	Setd1b	AA516740|BC035291|KMT2G|mKIAA1076	SET domain containing 1B	protein-coding
mm_122129.1	chr14	31160308	31160339	-	1	NA	exon (NM_138672, exon 13 of 69)	exon (NM_138672, exon 13 of 69)	8318	NM_138672	192187	Mm.220821	NM_138672	ENSMUSG00000042286	Stab1	FEEL-1|FELE-1|MFEEL-1|MS-1|STAB-1|mKIAA0246	stabilin 1	protein-coding
mm_125644.1	chr15	62220511	62220517	+	1	NA	intron (NR_132746, intron 3 of 6)	intron (NR_132746, intron 3 of 6)	-1063	NR_003523	67552	Mm.484027	NM_026230		H2afy3	4933432H23Rik	H2A histone family, member Y3	pseudo
mm_57670.1	chr6	128488106	128488117	-	1	NA	intron (NM_007376, intron 29 of 35)	intron (NM_007376, intron 29 of 35)	38609	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_7174.1	chr1	92180272	92180324	-	1	NA	promoter-TSS (NM_207225)	promoter-TSS (NM_207225)	43	NM_207225	208727	Mm.318567	NM_207225	ENSMUSG00000026313	Hdac4	4932408F19Rik|HD4	histone deacetylase 4	protein-coding
mm_95652.1	chr11	53724619	53724639	+	1	NA	3' UTR (NM_010558, exon 4 of 4)	3' UTR (NM_010558, exon 4 of 4)	3835	NM_010558	16191	Mm.4461	NM_010558	ENSMUSG00000036117	Il5	Il-5	interleukin 5	protein-coding
mm_139038.1	chr17	46202862	46202878	+	1	NA	promoter-TSS (NM_028198)	promoter-TSS (NM_028198)	15	NM_028198	72322	Mm.275039	NM_028198	ENSMUSG00000067150	Xpo5	2410004H11Rik|2700038C24Rik|AI648907|AW549301|Exp5|RanBp21|mKIAA1291	exportin 5	protein-coding
mm_64679.1	chr7	4509889	4509900	-	1	NA	intron (NM_011618, intron 8 of 13)	intron (NM_011618, intron 8 of 13)	6081	NM_001277903	21955	Mm.358643	NM_011618	ENSMUSG00000064179	Tnnt1	AW146156|Tnt|sTnT|ssTnT	troponin T1, skeletal, slow	protein-coding
mm_49481.1	chr6	29531259	29531270	+	1	NA	exon (NM_001252382, exon 2 of 9)	exon (NM_001252382, exon 2 of 9)	1982	NM_001252382	27056	Mm.6479	NM_012057	ENSMUSG00000029771	Irf5	AW491843|mirf5	interferon regulatory factor 5	protein-coding
mm_23242.1	chr3	51221204	51221211	+	1	NA	Intergenic	Intergenic	-3240	NM_009834	12457	Mm.86541	NM_009834	ENSMUSG00000023087	Noct	AU043840|Ccr4|Ccrn4l	nocturnin	protein-coding
mm_32060.1	chr4	97777607	97777632	+	1	NA	promoter-TSS (NM_001122953)	promoter-TSS (NM_001122953)	-7	NM_001122953	18027	Mm.31274	NM_010905	ENSMUSG00000028565	Nfia	1110047K16Rik|9430022M17Rik|CTF|NF1-A|NF1A	nuclear factor I/A	protein-coding
mm_123195.1	chr14	58183217	58183222	-	1	NA	Intergenic	Intergenic	110533	NM_013518	14180	Mm.8846	NM_013518	ENSMUSG00000021974	Fgf9	Eks	fibroblast growth factor 9	protein-coding
mm_18255.1	chr2	52263660	52263668	-	1	NA	exon (NM_010889, exon 54 of 157)	exon (NM_010889, exon 54 of 157)	-27338	NR_040620	78049	Mm.243883	NR_040620		4930573O16Rik	-	RIKEN cDNA 4930573O16 gene	ncRNA
mm_172929.1	chr9	73113463	73113463	+	1	NA	promoter-TSS (NM_198609)	promoter-TSS (NM_198609)	-6	NM_198609	225215	Mm.379366	NM_198609	ENSMUSG00000032215	Rsl24d1	2410159K22Rik	ribosomal L24 domain containing 1	protein-coding
mm_55679.1	chr6	72610437	72610449	-	1	NA	TTS (NM_009444)	TTS (NM_009444)	6305	NM_009444	22135	Mm.246563	NM_009444		Tgoln2	TGN38B|TGN41|TGN46|Ttgn2	trans-golgi network protein 2	protein-coding
mm_129717.1	chr15	81920002	81920006	-	1	NA	intron (NM_030229, intron 2 of 5)	intron (NM_030229, intron 2 of 5)	6209	NM_030229	78929	Mm.215115	NM_030229	ENSMUSG00000022476	Polr3h	5031409G22Rik|RPC8	polymerase (RNA) III (DNA directed) polypeptide H	protein-coding
mm_138688.1	chr17	35969886	35969966	+	1	NA	promoter-TSS (NM_013854)	promoter-TSS (NM_013854)	-176	NM_013854	224742	Mm.329022	NM_013854	ENSMUSG00000038762	Abcf1	AU041969|Abc50|D17Wsu166e|GCN20	ATP-binding cassette, sub-family F (GCN20), member 1	protein-coding
mm_122970.1	chr14	54974348	54974353	-	1	NA	TTS (NR_033497)	TTS (NR_033497)	1426	NR_030607	100124433		NR_030607	ENSMUSG00000077928	Mir208b	Mirn208b|mir-208b	microRNA 208b	ncRNA
mm_81912.1	chr9	120092107	120092121	+	1	NA	promoter-TSS (NM_007720)	promoter-TSS (NM_007720)	-19	NM_007720	12776	Mm.442098	NM_007720	ENSMUSG00000042262	Ccr8	C-C|C-C CKR-8|CC-CKR-8|CCR-8|CKR-8|Cmkbr8|mCCR8	chemokine (C-C motif) receptor 8	protein-coding
mm_53379.1	chr6	129512580	129512644	+	1	NA	promoter-TSS (NM_001081186)	promoter-TSS (NM_001081186)	55	NM_001081186	330428	Mm.44237	NM_001081186	ENSMUSG00000030160	Tmem52b	D630042F21Rik	transmembrane protein 52B	protein-coding
mm_53144.1	chr6	125235945	125235954	+	1	NA	intron (NM_001033126, intron 2 of 5)	RSINE1|SINE|B4	1078	NM_001033126	21940	Mm.367714	NM_001033126	ENSMUSG00000030336	Cd27	S152|Tnfrsf7|Tp55	CD27 antigen	protein-coding
mm_36997.1	chr4	110290885	110290913	-	1	NA	intron (NM_001163397, intron 1 of 5)	intron (NM_001163397, intron 1 of 5)	-3372	NM_001347178	15572	Mm.3970	NM_010488	ENSMUSG00000028546	Elavl4	Elav|Hud|PNEM	ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4 (Hu antigen D)	protein-coding
mm_27702.1	chr3	66981936	66981951	-	1	NA	promoter-TSS (NM_013665)	promoter-TSS (NM_013665)	-172	NM_001302357	20429	Mm.39093	NM_013665	ENSMUSG00000027833	Shox2	6330543G17Rik|OG12|Og12x|Prx3|SHOT	short stature homeobox 2	protein-coding
mm_158048.1	chrX	99135947	99135950	-	1	NA	promoter-TSS (NM_010110)	promoter-TSS (NM_010110)	-113	NM_010110	13641	Mm.3374	NM_010110	ENSMUSG00000031217	Efnb1	Cek5-L|EFL-3|Elk-L|Epl2|Eplg2|LERK-2|Lerk2|Stra1	ephrin B1	protein-coding
mm_137842.1	chr17	31039861	31039865	+	1	NA	Intergenic	Intergenic	-17831	NM_009593	11307	Mm.15691	NM_009593	ENSMUSG00000024030	Abcg1	AW413978|Abc8|White	ATP-binding cassette, sub-family G (WHITE), member 1	protein-coding
mm_114343.1	chr13	60762548	60762587	+	1	NA	3' UTR (NM_134062, exon 27 of 27)	3' UTR (NM_134062, exon 27 of 27)	23797	NM_199148	218275	Mm.222427	NM_199148	ENSMUSG00000042243	BC051665	-	cDNA sequence BC051665	protein-coding
mm_128534.1	chr15	54853408	54853424	-	1	NA	intron (NM_001285994, intron 19 of 25)	intron (NM_001285994, intron 19 of 25)	66730	NM_015744	18606	Mm.250256	NM_015744	ENSMUSG00000022425	Enpp2	ATX|E-NPP 2|Npps2|PD-Ialpha|Pdnp2|lysoPLD	ectonucleotide pyrophosphatase/phosphodiesterase 2	protein-coding
mm_3445.1	chr1	150102813	150102827	+	1	NA	intron (NM_011198, intron 5 of 9)	intron (NM_011198, intron 5 of 9)	2789	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_109860.1	chr12	4841584	4841611	-	1	NA	promoter-TSS (NM_016863)	promoter-TSS (NM_016863)	-2	NM_016863	14226	Mm.20453	NM_016863	ENSMUSG00000020635	Fkbp1b	12.6kDa|AW494148|FKBP12.6|calstabin2	FK506 binding protein 1b	protein-coding
mm_35930.1	chr4	53032345	53032395	-	1	NA	3' UTR (NM_013454, exon 50 of 50)	3' UTR (NM_013454, exon 50 of 50)	20490	NM_025623	66536	Mm.38244	NM_025623	ENSMUSG00000015247	Nipsnap3b	2700063N13Rik|Nipsnap3a	nipsnap homolog 3B (C. elegans)	protein-coding
mm_19424.1	chr2	91931729	91931772	-	1	NA	promoter-TSS (NM_001291481)	promoter-TSS (NM_001291481)	-48	NM_001012335	17242	Mm.906	NM_010784	ENSMUSG00000027239	Mdk	MK|Mek	midkine	protein-coding
mm_82766.1	chr9	26920876	26920880	-	1	NA	intron (NM_001281475, intron 2 of 20)	intron (NM_001281475, intron 2 of 20)	2203	NM_001281475	382064	Mm.335028	NM_001177509	ENSMUSG00000079644	Gm1110	-	predicted gene 1110	protein-coding
mm_10290.1	chr2	10371266	10371288	+	1	NA	intron (NM_001198808, intron 1 of 22)	intron (NM_001198808, intron 1 of 22)	826	NM_001198808	353282	Mm.329991	NM_177386	ENSMUSG00000061186	Sfmbt2	D2Wsu23e|D330030P06Rik	Scm-like with four mbt domains 2	protein-coding
mm_41064.1	chr5	86997090	86997099	+	1	NA	Intergenic	Intergenic	-3766	NM_172881	243085	Mm.312095	NM_172881	ENSMUSG00000035811	Ugt2b35	C730031G17	UDP glucuronosyltransferase 2 family, polypeptide B35	protein-coding
mm_21699.1	chr2	164549321	164549335	-	1	NA	Intergenic	Intergenic	-13388	NM_026323	67701	Mm.27289	NM_026323	ENSMUSG00000017723	Wfdc2	1600023A02Rik|HE4|WAP5	WAP four-disulfide core domain 2	protein-coding
mm_5105.1	chr1	5070337	5070338	-	1	NA	promoter-TSS (NM_001177795)	promoter-TSS (NM_001177795)	-52	NM_001177795	58175	Mm.103771	NM_021374	ENSMUSG00000002459	Rgs20	2900073E09Rik|Rgsz1	regulator of G-protein signaling 20	protein-coding
mm_152158.1	chr19	7265911	7265921	-	1	NA	Intergenic	Intergenic	-1478	NM_054048	104383	Mm.283859	NM_054048	ENSMUSG00000024968	Rcor2	1A13|AW122124|CoREST|Rcor|Rcor1	REST corepressor 2	protein-coding
mm_109079.1	chr12	104408886	104408912	+	1	NA	exon (NM_009252, exon 2 of 5)	exon (NM_009252, exon 2 of 5)	2191	NM_009252	20716	Mm.482074	NM_009252	ENSMUSG00000021091	Serpina3n	Spi2-2|Spi2.2|Spi2/eb.4	serine (or cysteine) peptidase inhibitor, clade A, member 3N	protein-coding
mm_144392.1	chr18	20671549	20671564	+	1	NA	intron (NM_013697, intron 3 of 3)	intron (NM_013697, intron 3 of 3)	6306	NM_013697	22139	Mm.2108	NM_013697	ENSMUSG00000061808	Ttr	AA408768|AI787086|D17860|prealbumin	transthyretin	protein-coding
mm_24663.1	chr3	94486305	94486305	+	1	NA	intron (NR_110353, intron 4 of 11)	L1MEc|LINE|L1	3583	NR_110353	78784	Mm.44292	NM_172434	ENSMUSG00000028137	Celf3	4930415M08Rik|BRUNOL1|CAGH4|ERDA4|Tnrc4	CUGBP, Elav-like family member 3	protein-coding
mm_36547.1	chr4	86670031	86670043	-	1	NA	promoter-TSS (NM_007408)	promoter-TSS (NM_007408)	22	NM_007408	11520	Mm.381	NM_007408	ENSMUSG00000028494	Plin2	AA407157|ADPH|Adfp|Adrp	perilipin 2	protein-coding
mm_88608.1	chr10	79821007	79821029	+	1	NA	promoter-TSS (NM_030218)	promoter-TSS (NM_030218)	-3	NM_030218	78906	Mm.33087	NM_030218	ENSMUSG00000035852	Misp	9130017N09Rik	mitotic spindle positioning	protein-coding
mm_50387.1	chr6	48691355	48691382	+	1	NA	exon (NM_001243201, exon 4 of 4)	exon (NM_001243201, exon 4 of 4)	6790	NM_174990	107526	Mm.333048	NM_174990	ENSMUSG00000054435	Gimap4	AU019574|E430007K16Rik|Ian-1|Ian1|Imap4	GTPase, IMAP family member 4	protein-coding
mm_137445.1	chr17	26531809	26531839	+	1	NA	Intergenic	Tigger5|DNA|TcMar-Tigger	-23352	NM_013642	19252	Mm.239041	NM_013642	ENSMUSG00000024190	Dusp1	3CH134|MKP1|Ptpn16|U19515|erp|mkp-1	dual specificity phosphatase 1	protein-coding
mm_42621.1	chr5	118038021	118038028	+	1	NA	intron (NM_021344, intron 1 of 7)	intron (NM_021344, intron 1 of 7)	10200	NM_021344	57816	Mm.273285	NM_021344	ENSMUSG00000029359	Tesc	1010001A17Rik|2410011K10Rik|TE-1	tescalcin	protein-coding
mm_68658.1	chr7	118705709	118705786	-	1	NA	promoter-TSS (NM_019580)	promoter-TSS (NM_019580)	-9	NM_019580	56209	Mm.273142	NM_019580	ENSMUSG00000033917	Gde1	1200003M13Rik|Mir16|RGS16	glycerophosphodiester phosphodiesterase 1	protein-coding
mm_164730.1	chr17	64100436	64100463	+	1	NA	intron (NM_008000, intron 11 of 13)	intron (NM_008000, intron 11 of 13)	-49777	NR_130982	68771	Mm.443351	NR_130982		1110058D11Rik	-	RIKEN cDNA 1110058D11 gene	ncRNA
mm_119683.1	chr14	53370014	53370025	+	1	NA	Intergenic	Intergenic	-874324	NM_001170918	57269	Mm.88822	NM_020512	ENSMUSG00000059887	Olfr1507	MOR244-1|Mor28|Or28	olfactory receptor 1507	protein-coding
mm_69956.1	chr7	142375993	142375999	-	1	NA	TTS (NM_009983)	TTS (NM_009983)	-2250	NM_001347541	320802	Mm.154486	NM_177265	ENSMUSG00000045777	Ifitm10	6330512M04Rik|AI848576|DSPA3	interferon induced transmembrane protein 10	protein-coding
mm_172500.1	chr7	67083145	67083160	+	1	NA	intron (NM_001033877, intron 19 of 22)	intron (NM_001033877, intron 19 of 22)	139306	NR_131044	76628	Mm.384589	NR_131043	ENSMUSG00000097527	1700112J16Rik	-	RIKEN cDNA 1700112J16 gene	ncRNA
mm_146327.1	chr18	80708289	80708301	+	1	NA	promoter-TSS (NM_016791)	promoter-TSS (NM_016791)	-122	NM_001164112	18018	Mm.329560	NM_016791	ENSMUSG00000033016	Nfatc1	2210017P03Rik|AI449492|AV076380|NF-ATc|NFAT2|NFATc|Nfatcb	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 1	protein-coding
mm_79084.1	chr9	46242495	46242522	+	1	NA	exon (NM_007468, exon 3 of 3)	exon (NM_007468, exon 3 of 3)	1664	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_57521.1	chr6	125540303	125540322	-	1	NA	Intergenic	Intergenic	-12636	NM_011708	22371	Mm.22339	NM_011708	ENSMUSG00000001930	Vwf	6820430P06Rik|AI551257|B130011O06Rik|C630030D09|F8VWF|VWD	Von Willebrand factor	protein-coding
mm_116865.1	chr13	54930258	54930265	-	1	NA	Intergenic	Intergenic	-19150	NM_001311128	107448	Mm.23573	NM_153131	ENSMUSG00000025876	Unc5a	Unc5h1|mKIAA1976	unc-5 netrin receptor A	protein-coding
mm_91567.1	chr10	40033967	40033991	-	1	NA	3' UTR (NM_001114332, exon 6 of 6)	3' UTR (NM_001114332, exon 6 of 6)	-8711	NM_144821	215929	Mm.55513	NM_144821	ENSMUSG00000038522	Mfsd4b1	AI317395|AI482555|Naglt1a	major facilitator superfamily domain containing 4B1	protein-coding
mm_24890.1	chr3	96108589	96108612	+	1	NA	intron (NM_001025614, intron 1 of 11)	intron (NM_001025614, intron 1 of 11)	4073	NM_001025614	229603	Mm.272336	NM_001025613	ENSMUSG00000038495	Otud7b	2900060B22Rik|4930463P07Rik|AI462125|CEZANNE|Trabid2|Za20d1	OTU domain containing 7B	protein-coding
mm_127321.1	chr15	100304156	100304175	+	1	NA	promoter-TSS (NM_027334)	promoter-TSS (NM_027334)	-652	NM_027334	70152	Mm.488086	NM_027334	ENSMUSG00000054619	Mettl7a1	2210414H16Rik|3300001H21Rik|Aam-B|Mettl7a|UbiE1	methyltransferase like 7A1	protein-coding
mm_74996.1	chr8	27223785	27223798	-	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	5797	NM_013462	11556	Mm.278475	NM_013462	ENSMUSG00000031489	Adrb3	Adrb-3	adrenergic receptor, beta 3	protein-coding
mm_23258.1	chr3	51340843	51340884	+	1	NA	promoter-TSS (NM_001291059)	promoter-TSS (NM_001291059)	-219	NM_023502	69257	Mm.131038	NM_023502	ENSMUSG00000037174	Elf2	2610036A20Rik|A230104O07Rik|AW111824|BB183398|EU32|NERF|NERF-1A|NERF-1B|NERF-2	E74-like factor 2	protein-coding
mm_25746.1	chr3	123264777	123264787	+	1	NA	Intergenic	(CATTC)n|Simple_repeat|Simple_repeat	-2714	NM_027135	69608	Mm.29293	NM_027135	ENSMUSG00000039234	Sec24d	2310020L09Rik|Gm1349	Sec24 related gene family, member D (S. cerevisiae)	protein-coding
mm_168295.1	chr11	104655375	104655378	-	1	NA	intron (NM_016780, intron 10 of 14)	L1Md_A|LINE|L1	47376	NM_016780	16416	Mm.87150	NM_016780	ENSMUSG00000020689	Itgb3	CD61|GP3A|INGRB3	integrin beta 3	protein-coding
mm_97731.1	chr11	80394276	80394413	+	1	NA	non-coding (NR_045038, exon 9 of 17)	non-coding (NR_045038, exon 9 of 17)	11065	NM_001130171	22680	Mm.401332	NM_011751	ENSMUSG00000017421	Zfp207	8430401D15Rik|BuGZ|Zep|Znf207	zinc finger protein 207	protein-coding
mm_60403.1	chr7	44475911	44475932	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	5574	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_110396.1	chr12	44207078	44207084	-	1	NA	exon (NM_013760, exon 3 of 3)	exon (NM_013760, exon 3 of 3)	2987	NM_013760	27362	Mm.27432	NM_013760	ENSMUSG00000014905	Dnajb9	AA408011|AA673251|AA673481|AW556981|ERdj4|Mdg1|mDj7	DnaJ heat shock protein family (Hsp40) member B9	protein-coding
mm_162611.1	chr1	183297308	183297323	+	1	NA	promoter-TSS (NM_027861)	promoter-TSS (NM_027861)	255	NM_181732	108909	Mm.290502	NM_145626	ENSMUSG00000042901	Aida	2610208M17Rik|BC004835	axin interactor, dorsalization associated	protein-coding
mm_3828.1	chr1	159523769	159523873	+	1	NA	promoter-TSS (NM_022312)	promoter-TSS (NM_022312)	52	NM_022312	21960	Mm.44701	NM_022312	ENSMUSG00000015829	Tnr	J1-tenascin|TN-R|janusin|restrictin	tenascin R	protein-coding
mm_13944.1	chr2	121289700	121289710	+	1	NA	exon (NM_032393, exon 1 of 7)	exon (NM_032393, exon 1 of 7)	103	NM_032393	17754	Mm.36501	NM_032393	ENSMUSG00000027254	Map1a	6330416M19Rik|AI853608|Mtap-1|Mtap1|Mtap1a|moth1	microtubule-associated protein 1 A	protein-coding
mm_41471.1	chr5	91517679	91517694	+	1	NA	promoter-TSS (NM_145562)	promoter-TSS (NM_145562)	-14	NM_145562	231440	Mm.5002	NM_145562	ENSMUSG00000034981	Parm1	2210012L08Rik|9130213B05Rik|W91666	prostate androgen-regulated mucin-like protein 1	protein-coding
mm_80424.1	chr9	77917398	77917453	+	1	NA	promoter-TSS (NM_134255)	promoter-TSS (NM_134255)	60	NM_134255	68801	Mm.430736	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	ELOVL family member 5, elongation of long chain fatty acids (yeast)	protein-coding
mm_109852.1	chr12	4738350	4738356	-	1	NA	promoter-TSS (NM_029107)	promoter-TSS (NM_029107)	30	NM_029107	74855	Mm.269534	NM_029107	ENSMUSG00000079177	Fam228a	4930417G10Rik	family with sequence similarity 228, member A	protein-coding
mm_44177.1	chr5	150987462	150987469	+	1	NA	intron (NM_013823, intron 3 of 4)	intron (NM_013823, intron 3 of 4)	34858	NM_013823	16591	Mm.6500	NM_013823	ENSMUSG00000058488	Kl	alpha-kl	klotho	protein-coding
mm_97322.1	chr11	76916871	76916874	+	1	NA	TTS (NM_025655)	TTS (NM_025655)	12327	NM_025655	66601	Mm.25138	NM_025655	ENSMUSG00000020839	Tmigd1	2010002A20Rik|Tmigd	transmembrane and immunoglobulin domain containing 1	protein-coding
mm_68905.1	chr7	126456770	126456778	-	1	NA	exon (NM_007504, exon 8 of 23)	exon (NM_007504, exon 8 of 23)	6299	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_17889.1	chr2	35030377	35030381	-	1	NA	exon (NM_010406, exon 15 of 41)	exon (NM_010406, exon 15 of 41)	31062	NM_010406	15139	Mm.2168	NM_010406	ENSMUSG00000026874	Hc	C5|C5a|He	hemolytic complement	protein-coding
mm_31573.1	chr4	57604700	57604745	+	1	NA	intron (NM_001304544, intron 1 of 8)	intron (NM_001304544, intron 1 of 8)	36474	NM_172868	242481	Mm.331630	NM_172868	ENSMUSG00000090053	Palm2	53-H12|B130066I24|R75368|pEN70	paralemmin 2	protein-coding
mm_134318.1	chr16	15957741	15957743	-	1	NA	intron (NM_146068, intron 10 of 19)	intron (NM_146068, intron 10 of 19)	70456	NM_007679	12609	Mm.347407	NM_007679	ENSMUSG00000071637	Cebpd	c/EBPdelta	CCAAT/enhancer binding protein (C/EBP), delta	protein-coding
mm_146196.1	chr18	76241333	76241362	+	1	NA	promoter-TSS (NM_010754)	promoter-TSS (NM_010754)	-354	NM_010754	17126	Mm.152699	NM_010754	ENSMUSG00000024563	Smad2	7120426M23Rik|Madh2|Madr2|Smad-2|mMad2	SMAD family member 2	protein-coding
mm_16381.1	chr2	178327543	178327567	+	1	NA	intron (NM_001177790, intron 8 of 12)	intron (NM_001177790, intron 8 of 12)	80103	NM_177191	320558	Mm.70781	NM_177191	ENSMUSG00000060445	Sycp2	3830402K23Rik|4930518F03Rik	synaptonemal complex protein 2	protein-coding
mm_63202.1	chr7	125753729	125753738	+	1	NA	intron (NM_001081022, intron 3 of 27)	intron (NM_001081022, intron 3 of 27)	45857	NM_001081022	233865	Mm.274389	NM_001081022	ENSMUSG00000032743	D430042O09Rik	Kiaa0556	RIKEN cDNA D430042O09 gene	protein-coding
mm_16023.1	chr2	167504158	167504168	+	1	NA	intron (NM_030743, intron 3 of 7)	CpG-8879	-11289	NM_170756	263876	Mm.34342	NM_170756	ENSMUSG00000047030	Spata2	AI504642|mKIAA0757	spermatogenesis associated 2	protein-coding
mm_119839.1	chr14	54431462	54431471	+	1	NA	promoter-TSS (NM_008608)	promoter-TSS (NM_008608)	-132	NM_008608	17387	Mm.280175	NM_008608	ENSMUSG00000000957	Mmp14	AI325305|MMP-X1|MT-MMP-1|MT1-MMP|sabe	matrix metallopeptidase 14 (membrane-inserted)	protein-coding
mm_116215.1	chr13	32784026	32784042	-	1	NA	Intergenic	Intergenic	-2255	NM_001166030	238564	Mm.60041	NM_001166030	ENSMUSG00000044951	Mylk4	EG238564	myosin light chain kinase family, member 4	protein-coding
mm_98688.1	chr11	96298806	96298821	+	1	NA	promoter-TSS (NM_008269)	promoter-TSS (NM_008269)	-358	NM_008269	15414	Mm.215	NM_008269	ENSMUSG00000000690	Hoxb6	Hox-2.2	homeobox B6	protein-coding
mm_150460.1	chr19	38264762	38264831	+	1	NA	promoter-TSS (NM_020278)	promoter-TSS (NM_020278)	14	NM_020278	56839	Mm.298251	NM_020278	ENSMUSG00000067242	Lgi1	BB130740	leucine-rich repeat LGI family, member 1	protein-coding
mm_162401.1	chr1	85326709	85326716	+	1	NA	Intergenic	Intergenic	-56146	NM_001037909	620078	Mm.386456	NM_175219	ENSMUSG00000052477	C130026I21Rik	4930565N07Rik|OTTMUSG00000029174	RIKEN cDNA C130026I21 gene	protein-coding
mm_168145.1	chr10	34233524	34233526	-	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	-25974	NM_172508	212898	Mm.34557	NM_172508	ENSMUSG00000039497	Dse	6030499O08|AI480506|B130024B19Rik|DS-epi1|Sart2	dermatan sulfate epimerase	protein-coding
mm_133321.1	chr16	77838144	77838147	+	1	NA	Intergenic	Intergenic	191872	NR_029540	723952		NR_029540	ENSMUSG00000065472	Mir125b-2	Mirn125b-2|mir-125b-2	microRNA 125b-2	ncRNA
mm_146718.1	chr18	15064078	15064114	-	1	NA	promoter-TSS (NM_001142731)	promoter-TSS (NM_001142731)	-514	NM_001142731	106931	Mm.329299	NM_134112	ENSMUSG00000036225	Kctd1	4933402K10Rik|AI661543|AW553000	potassium channel tetramerisation domain containing 1	protein-coding
mm_84588.1	chr9	70035557	70035574	-	1	NA	intron (NM_028087, intron 2 of 2)	intron (NM_028087, intron 2 of 2)	2523	NM_028087	72077	Mm.195555	NM_028087	ENSMUSG00000032226	Gcnt3	2010013H22Rik|2210021I22Rik|2210401J11Rik	glucosaminyl (N-acetyl) transferase 3, mucin type	protein-coding
mm_41948.1	chr5	105732218	105732259	+	1	NA	5' UTR (NM_178701, exon 2 of 3)	5' UTR (NM_178701, exon 2 of 3)	31428	NM_178701	231549	Mm.23837	NM_178701	ENSMUSG00000046079	Lrrc8d	2810473G09Rik|4930525N13Rik|A930019F03|Lrrc5	leucine rich repeat containing 8D	protein-coding
mm_73324.1	chr8	105276384	105276426	+	1	NA	promoter-TSS (NM_030152)	promoter-TSS (NM_030152)	-42	NM_030152	78688	Mm.475715	NM_030152	ENSMUSG00000014776	Nol3	ARC|B430311C09Rik|MYC|NOP|Nop30	nucleolar protein 3 (apoptosis repressor with CARD domain)	protein-coding
mm_116122.1	chr13	28950763	28950786	-	1	NA	TTS (NM_009238)	TTS (NM_009238)	2908	NM_009238	20677	Mm.240627	NM_009238	ENSMUSG00000076431	Sox4	AA682046|Sox-4	SRY (sex determining region Y)-box 4	protein-coding
mm_39489.1	chr5	20950931	20950950	+	1	NA	promoter-TSS (NR_030699)	promoter-TSS (NR_030699)	-49	NR_030699	320770	Mm.491217	NR_030699	ENSMUSG00000101013	A630072M18Rik	Aptr	RIKEN cDNA A630072M18 gene	ncRNA
mm_47527.1	chr5	124172569	124172570	-	1	NA	intron (NM_011256, intron 2 of 24)	intron (NM_011256, intron 2 of 24)	14613	NM_001289472	19679	Mm.44261	NM_011256	ENSMUSG00000029406	Pitpnm2	NIR3|RDGBA2|Rdgb2|mKIAA1457	phosphatidylinositol transfer protein, membrane-associated 2	protein-coding
mm_155558.1	chrX	75382385	75382395	+	1	NA	promoter-TSS (NM_026126)	promoter-TSS (NM_026126)	-9	NM_026126	67391	Mm.126404	NM_026126	ENSMUSG00000031198	Fundc2	4833415N24Rik|DC44|HCBP6	FUN14 domain containing 2	protein-coding
mm_63030.1	chr7	121065117	121065136	+	1	NA	3' UTR (NM_030691, exon 6 of 6)	3' UTR (NM_030691, exon 6 of 6)	9404	NM_030691	80719	Mm.160384	NM_030691	ENSMUSG00000035004	Igsf6	-	immunoglobulin superfamily, member 6	protein-coding
mm_12544.1	chr2	72390402	72390405	+	1	NA	TTS (NM_178084)	TTS (NM_178084)	-85816	NM_025866	66953	Mm.270676	NM_025866	ENSMUSG00000055612	Cdca7	2310021G01Rik|AU044109|JPO1	cell division cycle associated 7	protein-coding
mm_57620.1	chr6	128200639	128200650	-	1	NA	Intergenic	CpG	-16841	NR_077223	330427	Mm.426356	NR_077223	ENSMUSG00000107879	9330102E08Rik	-	RIKEN cDNA 9330102E08 gene	ncRNA
mm_124462.1	chr14	121145893	121145904	-	1	NA	intron (NM_134082, intron 2 of 26)	intron (NM_134082, intron 2 of 26)	110324	NM_134082	223254	Mm.223980	NM_134082	ENSMUSG00000025555	Farp1	AW228844|BC030329|Cdep	FERM, RhoGEF (Arhgef) and pleckstrin domain protein 1 (chondrocyte-derived)	protein-coding
mm_104127.1	chr11	86757484	86757572	-	1	NA	promoter-TSS (NM_001003908)	promoter-TSS (NM_001003908)	-36	NM_001003908	67300	Mm.254588	NM_001003908	ENSMUSG00000047126	Cltc	3110065L21Rik|CHC|R74732	clathrin, heavy polypeptide (Hc)	protein-coding
mm_12959.1	chr2	90459635	90459656	+	1	NA	exon (NM_008982, exon 9 of 24)	exon (NM_008982, exon 9 of 24)	19529	NM_001135657	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_31394.1	chr4	48045145	48045160	+	1	NA	promoter-TSS (NM_015743)	promoter-TSS (NM_015743)	-153	NM_015743	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_130143.1	chr15	90915970	90915975	-	1	NA	Intergenic	MTB_Mm|LTR|ERVL-MaLR	-17496	NR_033583	20738	Mm.431547	NR_033583		Spn-ps	Cd43-ps	sialophorin, pseudogene	pseudo
mm_26941.1	chr3	20266259	20266280	-	1	NA	exon (NM_029706, exon 5 of 11)	exon (NM_029706, exon 5 of 11)	9464	NM_029706	76703	Mm.34692	NM_029706	ENSMUSG00000011463	Cpb1	0910001A18Rik|1810063F02Rik|2210008M23Rik|AI504870	carboxypeptidase B1 (tissue)	protein-coding
mm_21537.1	chr2	163690826	163690835	-	1	NA	intron (NM_001039390, intron 2 of 4)	intron (NM_001039390, intron 2 of 4)	-3207	NM_011106	18769	Mm.10091	NM_011106	ENSMUSG00000035268	Pkig	PKIgamma	protein kinase inhibitor, gamma	protein-coding
mm_116772.1	chr13	52929641	52929678	-	1	NA	promoter-TSS (NM_016709)	promoter-TSS (NM_016709)	18	NM_016709	11992	Mm.252034	NM_016709	ENSMUSG00000021460	Auh	C77140|W91705	AU RNA binding protein/enoyl-coenzyme A hydratase	protein-coding
mm_171934.1	chr5	64159997	64159997	+	1	NA	promoter-TSS (NM_019636)	promoter-TSS (NM_019636)	-263	NM_019636	57915	Mm.286353	NM_019636	ENSMUSG00000029174	Tbc1d1	1110062G02Rik|AI385682|AW555803|Nob1|Nobq1|Tbc1|mKIAA1108	TBC1 domain family, member 1	protein-coding
mm_27287.1	chr3	41555537	41555551	-	1	NA	promoter-TSS (NM_001130184)	promoter-TSS (NM_001130184)	-190	NM_001130184	269424	Mm.286285	NM_172303	ENSMUSG00000025764	Jade1	AU041499|D530048A03Rik|Phf17|mKIAA1807	jade family PHD finger 1	protein-coding
mm_82116.1	chr9	123461994	123462000	+	1	NA	3' UTR (NM_153168, exon 21 of 21)	3' UTR (NM_153168, exon 21 of 21)	-16704	NM_013860	29806	Mm.10987	NM_013860	ENSMUSG00000025239	Limd1	AW822033|D9Ertd192e	LIM domains containing 1	protein-coding
mm_99344.1	chr11	101552392	101552426	+	1	NA	promoter-TSS (NM_001252222)	promoter-TSS (NM_001252222)	-245	NM_001252222	17966	Mm.784	NM_008676	ENSMUSG00000017119	Nbr1	mKIAA0049	neighbor of Brca1 gene 1	protein-coding
mm_49845.1	chr6	38354707	38354719	+	1	NA	promoter-TSS (NM_028421)	promoter-TSS (NM_028421)	-110	NM_028421	78781	Mm.25243	NM_028421	ENSMUSG00000029826	Zc3hav1	1200014N16Rik|2900058M19Rik|9130009D18Rik|9830115L13Rik|ARTD13|D6Bwg1452e|ZAP	zinc finger CCCH type, antiviral 1	protein-coding
mm_83262.1	chr9	42461378	42461388	-	1	NA	intron (NM_173038, intron 1 of 7)	intron (NM_173038, intron 1 of 7)	10843	NM_173038	272589	Mm.34483	NM_173038	ENSMUSG00000037287	Tbcel	D330014K23|E130107N23Rik|Lrrc35	tubulin folding cofactor E-like	protein-coding
mm_44729.1	chr5	31048015	31048038	-	1	NA	promoter-TSS (NM_177870)	promoter-TSS (NM_177870)	53	NM_177870	330064	Mm.205463	NM_177870	ENSMUSG00000006641	Slc5a6	E430023I20	solute carrier family 5 (sodium-dependent vitamin transporter), member 6	protein-coding
mm_31421.1	chr4	48051431	48051444	+	1	NA	exon (NM_015743, exon 3 of 8)	exon (NM_015743, exon 3 of 8)	191	NM_001307989	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_9513.1	chr1	173741759	173741786	-	1	NA	promoter-TSS (NM_001204910)	promoter-TSS (NM_001204910)	37	NM_001204910	226691	Mm.440876	NM_001204910	ENSMUSG00000073490	Ifi207	AI607873|Pyhin-A	interferon activated gene 207	protein-coding
mm_107659.1	chr12	52790984	52791020	+	1	NA	intron (NM_198111, intron 1 of 13)	intron (NM_198111, intron 1 of 13)	91619	NM_198111	238161	Mm.310822	NM_198111	ENSMUSG00000061603	Akap6	AI482140|Akapalpha|Akapbeta|PRKA	A kinase (PRKA) anchor protein 6	protein-coding
mm_108608.1	chr12	85474718	85474739	+	1	NA	intron (NM_010234, intron 1 of 3)	CpG	827	NM_010234	14281	Mm.246513	NM_010234	ENSMUSG00000021250	Fos	D12Rfj1|c-fos|cFos	FBJ osteosarcoma oncogene	protein-coding
mm_127465.1	chr15	101272739	101272743	+	1	NA	exon (NM_010444, exon 5 of 7)	exon (NM_010444, exon 5 of 7)	5895	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_10231.1	chr2	6386284	6386306	+	1	NA	intron (NM_181399, intron 1 of 13)	intron (NM_181399, intron 1 of 13)	33559	NM_181399	98910	Mm.40673	NM_181399	ENSMUSG00000039046	Usp6nl	AI316785|RNTRE|TRE2NL|mKIAA0019	USP6 N-terminal like	protein-coding
mm_34071.1	chr4	138457004	138457060	+	1	NA	3' UTR (NM_025451, exon 2 of 2)	3' UTR (NM_025451, exon 2 of 2)	1884	NM_025451	66259	Mm.41603	NM_025451	ENSMUSG00000046447	Camk2n1	1810006K23Rik|AI848599|AI891706	calcium/calmodulin-dependent protein kinase II inhibitor 1	protein-coding
mm_126423.1	chr15	80572470	80572480	+	1	NA	promoter-TSS (NM_001289442)	promoter-TSS (NM_001289442)	-122	NM_001289442	17444	Mm.12947	NM_010815	ENSMUSG00000042351	Grap2	GRAP-2|GRB2L|GRBLG|GRID|Gads|GrbX|Grf40|GrpL|Mona|P38	GRB2-related adaptor protein 2	protein-coding
mm_77896.1	chr9	7348605	7348618	+	1	NA	exon (NM_008605, exon 2 of 10)	exon (NM_008605, exon 2 of 10)	1237	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_163701.1	chr13	104178145	104178156	-	1	NA	promoter-TSS (NM_030731)	promoter-TSS (NM_030731)	316	NM_025879	66975	Mm.272541	NM_025879	ENSMUSG00000021711	Trappc13	2410002O22Rik|2610524F24Rik|AI451892|AU017229	trafficking protein particle complex 13	protein-coding
mm_3537.1	chr1	150393271	150393411	+	1	NA	promoter-TSS (NM_145511)	promoter-TSS (NM_145511)	-286	NM_145511	226499	Mm.222093	NM_145511	ENSMUSG00000006010	BC003331	1810053E15Rik|Odr4|odr-4	cDNA sequence BC003331	protein-coding
mm_152485.1	chr19	11049930	11049932	-	1	NA	intron (NR_102366, intron 1 of 2)	intron (NR_102366, intron 1 of 2)	635	NR_102366	107350	Mm.6381	NM_001177351	ENSMUSG00000075010	AW112010	-	expressed sequence AW112010	ncRNA
mm_58078.1	chr6	136941495	136941505	-	1	NA	promoter-TSS (NM_001301305)	promoter-TSS (NM_001301305)	3	NM_001301305	11857	Mm.2241	NM_007486	ENSMUSG00000030220	Arhgdib	D4|Gdid4|Ly-GDI	Rho, GDP dissociation inhibitor (GDI) beta	protein-coding
mm_102368.1	chr11	58390259	58390289	-	1	NA	exon (NM_001083884, exon 7 of 7)	exon (NM_001083884, exon 7 of 7)	9628	NM_001330197	70163	Mm.24119	NM_027339	ENSMUSG00000013643	Lypd8	2210415F13Rik	LY6/PLAUR domain containing 8	protein-coding
mm_71645.1	chr8	57652648	57652681	+	1	NA	intron (NR_040698, intron 1 of 3)	CpG	391	NM_001167981	108150	Mm.62886	NM_144731	ENSMUSG00000031608	Galnt7	AI225872	UDP-N-acetyl-alpha-D-galactosamine: polypeptide N-acetylgalactosaminyltransferase 7	protein-coding
mm_96418.1	chr11	67255677	67255688	+	1	NA	exon (NM_010855, exon 32 of 40)	exon (NM_010855, exon 32 of 40)	17870	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_170267.1	chr18	20682982	20682982	-	1	NA	Intergenic	Intergenic	17732	NM_013697	22139	Mm.2108	NM_013697	ENSMUSG00000061808	Ttr	AA408768|AI787086|D17860|prealbumin	transthyretin	protein-coding
mm_149698.1	chr19	21276460	21276476	+	1	NA	exon (NM_009551, exon 2 of 6)	exon (NM_009551, exon 2 of 6)	4190	NM_009551	22682	Mm.292405	NM_009551	ENSMUSG00000024750	Zfand5	2310057A04Rik|5830475F03Rik|AA415485|Za20d2|Zfp216	zinc finger, AN1-type domain 5	protein-coding
mm_144998.1	chr18	38297487	38297507	+	1	NA	intron (NM_001164621, intron 1 of 9)	intron (NM_001164621, intron 1 of 9)	692	NM_001164621	56736	Mm.228903	NM_020012	ENSMUSG00000060450	Rnf14	2310075C09Rik|2610005D23Rik|AA986456|AU041447|D18Ertd188e|D7Bwg0165e|Triad2	ring finger protein 14	protein-coding
mm_10457.1	chr2	14293504	14293514	+	1	NA	exon (NM_008625, exon 14 of 30)	exon (NM_008625, exon 14 of 30)	32506	NR_030609	100124488		NR_030609	ENSMUSG00000077897	Mir511	Mirn511|mir-511|mmu-mir-511	microRNA 511	ncRNA
mm_42701.1	chr5	119947682	119947686	+	1	NA	Intergenic	Intergenic	113021	NM_011537	21388	Mm.103636	NM_011537	ENSMUSG00000018263	Tbx5	-	T-box 5	protein-coding
mm_19185.1	chr2	84407788	84407790	-	1	NA	intron (NM_018782, intron 1 of 15)	intron (NM_018782, intron 1 of 15)	17477	NM_018782	54598	Mm.75467	NM_018782	ENSMUSG00000059588	Calcrl	AV071593|CRLR	calcitonin receptor-like	protein-coding
mm_102806.1	chr11	68871860	68871874	-	1	NA	Intergenic	Intergenic	-16686	NM_177060	320040	Mm.305696	NM_177060	ENSMUSG00000046490	Rnf222	9930039A11Rik	ring finger protein 222	protein-coding
mm_126823.1	chr15	88839477	88839484	+	1	NA	Intergenic	Intergenic	19834	NM_029720	76737	Mm.292567	NM_029720	ENSMUSG00000023272	Creld2	5730592L21Rik|C85758	cysteine-rich with EGF-like domains 2	protein-coding
mm_54050.1	chr6	13838575	13838618	-	1	NA	5' UTR (NM_001330667, exon 2 of 3)	5' UTR (NM_001330667, exon 2 of 3)	1346	NM_001330666	64450	Mm.167625	NM_145066	ENSMUSG00000048216	Gpr85	2900026B03Rik	G protein-coupled receptor 85	protein-coding
mm_3356.1	chr1	138172298	138172300	+	1	NA	intron (NM_001111316, intron 1 of 31)	intron (NM_001111316, intron 1 of 31)	2827	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_134841.1	chr16	26371829	26371846	-	1	NA	promoter-TSS (NM_016674)	promoter-TSS (NM_016674)	2	NM_016674	12737	Mm.289441	NM_016674	ENSMUSG00000022512	Cldn1	AI596271	claudin 1	protein-coding
mm_50328.1	chr6	48395838	48395872	+	1	NA	5' UTR (NM_133922, exon 1 of 18)	5' UTR (NM_133922, exon 1 of 18)	269	NM_001347153	77827	Mm.107646	NM_133922	ENSMUSG00000042810	Krba1	A930040G15Rik|AI448780	KRAB-A domain containing 1	protein-coding
mm_51534.1	chr6	83189937	83189950	+	1	NA	exon (NM_001198867, exon 7 of 28)	exon (NM_001198867, exon 7 of 28)	3997	NM_001347310	13191	Mm.6919	NM_007835	ENSMUSG00000031865	Dctn1	AL022633|DAP-150|DP-150|Glued|p150|p150-glued|p150<glued>	dynactin 1	protein-coding
mm_136401.1	chr16	93586562	93586594	-	1	NA	intron (NM_145482, intron 9 of 11)	MTC|LTR|ERVL-MaLR	17237	NM_145482	224440	Mm.10628	NM_145482	ENSMUSG00000022948	Setd4	AY037804|C21orf18|ORF21	SET domain containing 4	protein-coding
mm_60646.1	chr7	44850394	44850414	+	1	NA	TTS (NR_030488)	TTS (NR_030488)	397	NM_001253920	67605	Mm.148007	NM_026270	ENSMUSG00000011096	Akt1s1	1110012J22Rik|AI227026|Lobe|Lobel|PRAS40	AKT1 substrate 1 (proline-rich)	protein-coding
mm_113979.1	chr13	52096713	52096718	+	1	NA	promoter-TSS (NR_045061)	promoter-TSS (NR_045061)	-26	NR_045061	74050	Mm.84860	NR_045061		4921525O09Rik	-	RIKEN cDNA 4921525O09 gene	ncRNA
mm_78009.1	chr9	13414343	13414388	+	1	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	-16996	NR_028271	18689	Mm.41972	NM_008835	ENSMUSG00000031802	Phxr4	Sp5	per-hexamer repeat gene 4	ncRNA
mm_124572.1	chr14	124367895	124367917	-	1	NA	intron (NM_207667, intron 1 of 4)	intron (NM_207667, intron 1 of 4)	-175360	NM_010201	14169	Mm.206362	NM_010201	ENSMUSG00000025551	Fgf14	FHF-4|Fhf4|mFHF-4(1B)	fibroblast growth factor 14	protein-coding
mm_14800.1	chr2	145886403	145886420	+	1	NA	3' UTR (NM_028724, exon 13 of 13)	3' UTR (NM_028724, exon 13 of 13)	-16830	NM_026425	67877	Mm.151168	NM_026425	ENSMUSG00000002728	Naa20	1500004D14Rik|2900026I01Rik|AU041458|D2Ertd186e|Nat5	N(alpha)-acetyltransferase 20, NatB catalytic subunit	protein-coding
mm_13341.1	chr2	102787632	102787645	+	1	NA	3' UTR (NM_001077514, exon 11 of 11)	3' UTR (NM_001077514, exon 11 of 11)	81200	NM_001077515	20511	Mm.267547	NM_011393	ENSMUSG00000005089	Slc1a2	1700091C19Rik|2900019G14Rik|AI159670|Eaat2|GLT-1|GLT1|MGLT1	solute carrier family 1 (glial high affinity glutamate transporter), member 2	protein-coding
mm_76640.1	chr8	92357583	92357605	-	1	NA	promoter-TSS (NM_018826)	promoter-TSS (NM_018826)	-202	NM_018826	54352	Mm.101153	NM_018826	ENSMUSG00000031737	Irx5	-	Iroquois related homeobox 5 (Drosophila)	protein-coding
mm_26042.1	chr3	135553161	135553168	+	1	NA	intron (NM_027288, intron 12 of 16)	intron (NM_027288, intron 12 of 16)	67553	NM_027288	110173	Mm.280536	NM_027288	ENSMUSG00000028164	Manba	2410030O07Rik|B930014J03Rik|Bmn	mannosidase, beta A, lysosomal	protein-coding
mm_168087.1	chr10	127620941	127620941	-	1	NA	5' UTR (NM_008512, exon 1 of 89)	5' UTR (NM_008512, exon 1 of 89)	207	NM_008512	16971	Mm.271854	NM_008512	ENSMUSG00000040249	Lrp1	A2mr|AI316852|CD91|Lrp|b2b1554Clo	low density lipoprotein receptor-related protein 1	protein-coding
mm_94760.1	chr11	21149203	21149213	+	1	NA	3' UTR (NM_023324, exon 7 of 7)	3' UTR (NM_023324, exon 7 of 7)	57884	NM_023324	67245	Mm.28957	NM_023324	ENSMUSG00000020134	Peli1	2810468L03Rik|A930031K15Rik|AA409794|AI586297|D11Ertd676e	pellino 1	protein-coding
mm_120124.1	chr14	60087503	60087514	+	1	NA	promoter-TSS (NM_015803)	promoter-TSS (NM_015803)	-674	NM_015803	50769	Mm.319599	NM_015803	ENSMUSG00000021983	Atp8a2	AI415030|Atpc1b|agil|wl	ATPase, aminophospholipid transporter-like, class I, type 8A, member 2	protein-coding
mm_10678.1	chr2	21367822	21367870	+	1	NA	5' UTR (NM_001004761, exon 1 of 11)	5' UTR (NM_001004761, exon 1 of 11)	279	NM_001004761	241263	Mm.166647	NM_175706	ENSMUSG00000045967	Gpr158	5330427M13Rik|mKIAA1136	G protein-coupled receptor 158	protein-coding
mm_166232.1	chr5	66962680	66962705	+	1	NA	intron (NM_001001980, intron 6 of 25)	RSINE1|SINE|B4	-5724	NM_001256122	77569	Mm.374778	NM_001001980	ENSMUSG00000037736	Limch1	3732412D22Rik|mKIAA1102	LIM and calponin homology domains 1	protein-coding
mm_162154.1	chrX	81458122	81458122	-	1	NA	promoter-TSS (NM_173435)	promoter-TSS (NM_173435)	0	NM_173435	245492	Mm.109633	NM_173435	ENSMUSG00000060673	4930595M18Rik	-	RIKEN cDNA 4930595M18 gene	protein-coding
mm_107376.1	chr12	32953915	32953936	+	1	NA	promoter-TSS (NM_198710)	promoter-TSS (NM_198710)	-20	NM_013635	19027	Mm.246304	NM_013635	ENSMUSG00000020570	Sypl	AI314763|AI604763|D12Ertd446e|PanI|Pphn|Sypl1	synaptophysin-like protein	protein-coding
mm_164427.1	chr16	45382728	45382738	-	1	NA	3' UTR (NM_010818, exon 6 of 6)	3' UTR (NM_010818, exon 6 of 6)	26320	NM_010818	17470	Mm.245851	NM_010818	ENSMUSG00000022661	Cd200	Mox2|OX2	CD200 antigen	protein-coding
mm_25152.1	chr3	102995800	102995810	+	1	NA	promoter-TSS (NM_025679)	promoter-TSS (NM_025679)	65	NM_025679	66641	Mm.33937	NM_025679	ENSMUSG00000027854	Sike1	2810005O12Rik|5730470L24Rik|AI450236|AI839862|Sike|Sikeb	suppressor of IKBKE 1	protein-coding
mm_123816.1	chr14	70524069	70524084	-	1	NA	promoter-TSS (NM_011359)	promoter-TSS (NM_011359)	5	NM_011359	20389	Mm.24040	NM_011359	ENSMUSG00000022097	Sftpc	Bricd6|SP-C|SP5|SPC|Sftp-2|Sftp2|pro-SpC	surfactant associated protein C	protein-coding
mm_120439.1	chr14	65837402	65837412	+	1	NA	5' UTR (NM_145944, exon 1 of 9)	5' UTR (NM_145944, exon 1 of 9)	105	NM_145944	67179	Mm.214576	NM_145944	ENSMUSG00000022035	Ccdc25	2610528H13Rik|NSrp70	coiled-coil domain containing 25	protein-coding
mm_121688.1	chr14	13914494	13914509	-	1	NA	Intergenic	Intergenic	46812	NM_001285780	66231	Mm.295875	NM_025435	ENSMUSG00000053453	Thoc7	Nif3l1bp1	THO complex 7	protein-coding
mm_129701.1	chr15	81697312	81697324	-	1	NA	promoter-TSS (NM_001164320)	promoter-TSS (NM_001164320)	-31	NM_001164320	214685	Mm.393287	NM_001164320	ENSMUSG00000063765	Chadl	AY100452|D930017K21Rik	chondroadherin-like	protein-coding
mm_95741.1	chr11	54691542	54691552	+	1	NA	exon (NM_001252494, exon 27 of 29)	exon (NM_001252494, exon 27 of 29)	95401	NM_001252497	192786	Mm.254404	NM_175258	ENSMUSG00000037533	Rapgef6	A530068K01|AI844632|BB085664|C030018K18Rik|PDZ-GEF2|Pdzgef2|RA-GEF-2|Ragef2|mKIAA4052	Rap guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_169680.1	chr15	69486692	69486698	+	1	NA	Intergenic	RMER16_Mm|LTR|ERVK	216162	NR_130983	75076		NR_130983		4930504C09Rik	-	RIKEN cDNA 4930504C09 gene	ncRNA
mm_24900.1	chr3	96181157	96181167	+	1	NA	promoter-TSS (NM_022030)	promoter-TSS (NM_022030)	-65	NM_022030	64051	Mm.491135	NM_022030	ENSMUSG00000038486	Sv2a	AI746429|mKIAA0736	synaptic vesicle glycoprotein 2 a	protein-coding
mm_74384.1	chr8	128713238	128713266	+	1	NA	exon (NM_010578, exon 5 of 16)	exon (NM_010578, exon 5 of 16)	27598	NM_010578	16412	Mm.263396	NM_010578	ENSMUSG00000025809	Itgb1	4633401G24Rik|AA409975|AA960159|CD29|ENSMUSG00000051907|Fnrb|Gm9863|gpIIa	integrin beta 1 (fibronectin receptor beta)	protein-coding
mm_94838.1	chr11	23665616	23665623	+	1	NA	promoter-TSS (NM_001033654)	promoter-TSS (NM_001033654)	-55	NM_028956	74467	Mm.29536	NM_028304	ENSMUSG00000020280	Pus10	2810013G11Rik|4933435A13Rik|AU014648|C77560|Ccdc139	pseudouridylate synthase 10	protein-coding
mm_47002.1	chr5	115348954	115348959	-	1	NA	promoter-TSS (NM_007748)	promoter-TSS (NM_007748)	-1	NM_007748	12861	Mm.43415	NM_007748	ENSMUSG00000041697	Cox6a1	VIaL	cytochrome c oxidase subunit VIa polypeptide 1	protein-coding
mm_109550.1	chr12	111712974	111712985	+	1	NA	promoter-TSS (NM_026511)	promoter-TSS (NM_026511)	-26	NM_001324482	70369	Mm.44239	NM_027404	ENSMUSG00000049792	Bag5	1600025G07Rik|4930405J06Rik|Bag-5	BCL2-associated athanogene 5	protein-coding
mm_96937.1	chr11	70525982	70526034	+	1	NA	intron (NM_008946, intron 2 of 5)	intron (NM_008946, intron 2 of 5)	651	NM_008946	19175	Mm.98	NM_008946	ENSMUSG00000018286	Psmb6	Lmp19|Mpnd	proteasome (prosome, macropain) subunit, beta type 6	protein-coding
mm_138862.1	chr17	42876950	42876953	+	1	NA	promoter-TSS (NM_009847)	promoter-TSS (NM_009847)	-527	NM_009847	12488	Mm.218637	NM_009847	ENSMUSG00000061665	Cd2ap	AL024079|C78928|METS-1|Mets1	CD2-associated protein	protein-coding
mm_145793.1	chr18	65245994	65246005	+	1	NA	intron (NR_105742, intron 4 of 6)	intron (NR_105742, intron 4 of 6)	-2862	NR_029600	387231		NR_029600	ENSMUSG00000065402	Mir122	Mir122a|Mirn122a|mir-122|mmu-mir-122	microRNA 122	ncRNA
mm_24927.1	chr3	96557986	96557989	+	1	NA	promoter-TSS (NM_023719)	promoter-TSS (NM_023719)	30	NM_023719	56338	Mm.410189	NM_023719	ENSMUSG00000038393	Txnip	1200008J08Rik|AA682105|Hyplip1|THIF|Tbp-2|VDUP1	thioredoxin interacting protein	protein-coding
mm_120327.1	chr14	63248044	63248063	+	1	NA	Intergenic	Intergenic	-2782	NM_001310610	14463	Mm.247669	NM_008092	ENSMUSG00000021944	Gata4	Gata-4	GATA binding protein 4	protein-coding
mm_61937.1	chr7	90176311	90176332	+	1	NA	exon (NM_001252521, exon 10 of 20)	exon (NM_001252521, exon 10 of 20)	46089	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_21644.1	chr2	164333475	164333486	-	1	NA	exon (NM_009301, exon 2 of 3)	exon (NM_009301, exon 2 of 3)	715	NM_009301	20944	Mm.140154	NM_009301	ENSMUSG00000017004	Svs5	BB115186|Semg1|Svp-1|Svp1|Svp5	seminal vesicle secretory protein 5	protein-coding
mm_50578.1	chr6	49053002	49053037	+	1	NA	intron (NM_053110, intron 9 of 10)	B4|SINE|B4	16501	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_67911.1	chr7	99706735	99706737	-	1	NA	5' UTR (NM_001252530, exon 1 of 14)	5' UTR (NM_001252530, exon 1 of 14)	106	NM_001252530	101488	Mm.11249	NM_175316	ENSMUSG00000030737	Slco2b1	AI060904|AI852653|OATP-B|Slc21a9	solute carrier organic anion transporter family, member 2b1	protein-coding
mm_91672.1	chr10	43221312	43221333	-	1	NA	promoter-TSS (NM_001168289)	promoter-TSS (NM_001168289)	-164	NM_027772	71365	Mm.490430	NM_027772	ENSMUSG00000038240	Pdss2	5430420P03Rik|Gm60|Plmp|kd|mDLP1	prenyl (solanesyl) diphosphate synthase, subunit 2	protein-coding
mm_123250.1	chr14	61023900	61023902	-	1	NA	intron (NM_001164155, intron 3 of 9)	intron (NM_001164155, intron 3 of 9)	14086	NM_001164155	29820	Mm.281356	NM_013869	ENSMUSG00000060548	Tnfrsf19	AL023044|AW123854|TAJ|TAJ-ALPHA|TRADE|Troy	tumor necrosis factor receptor superfamily, member 19	protein-coding
mm_121524.1	chr14	122107120	122107172	+	1	NA	promoter-TSS (NM_080556)	promoter-TSS (NM_080556)	64	NM_080556	68059	Mm.275191	NM_080556	ENSMUSG00000025544	Tm9sf2	1500001N15Rik|AA536814|D14Ertd64e|P76	transmembrane 9 superfamily member 2	protein-coding
mm_85587.1	chr9	107313060	107313077	-	1	NA	Intergenic	Intergenic	16409	NM_009895	12700	Mm.4592	NM_009895	ENSMUSG00000032578	Cish	CIS-1|CIS1|Cis|F17|F23|SOCS	cytokine inducible SH2-containing protein	protein-coding
mm_89652.1	chr10	97479626	97479650	+	1	NA	5' UTR (NM_001190451, exon 1 of 8)	5' UTR (NM_001190451, exon 1 of 8)	138	NM_001190451	13179	Mm.56769	NM_007833	ENSMUSG00000019929	Dcn	DC|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding
mm_49515.1	chr6	29870559	29870602	+	1	NA	exon (NM_021414, exon 3 of 17)	exon (NM_021414, exon 3 of 17)	10984	NM_001171001	74340	Mm.210899	NM_021414	ENSMUSG00000029772	Ahcyl2	4631427C17Rik|AI227036|Adohcyase3|mKIAA0828	S-adenosylhomocysteine hydrolase-like 2	protein-coding
mm_162061.1	chrX	9033478	9033478	+	1	NA	promoter-TSS (NM_031261)	promoter-TSS (NM_031261)	-8	NM_031261	83457	Mm.388703	NM_031261	ENSMUSG00000071815	Fthl17e	Fthl17	ferritin, heavy polypeptide-like 17, member E	protein-coding
mm_112108.1	chr12	112786212	112786237	-	1	NA	Intergenic	Intergenic	-22751	NM_145450	217887	Mm.186678	NM_145450	ENSMUSG00000037594	BC022687	AW050009|C130001I08Rik|Flj20080	cDNA sequence BC022687	protein-coding
mm_46742.1	chr5	110839740	110839756	-	1	NA	promoter-TSS (NM_016681)	promoter-TSS (NM_016681)	29	NM_153571	100900	Mm.200231	NM_153571	ENSMUSG00000043510	Hscb	AI325508|AW049829|Hsc20	HscB iron-sulfur cluster co-chaperone	protein-coding
mm_55800.1	chr6	82774428	82774444	-	1	NA	promoter-TSS (NM_013820)	promoter-TSS (NM_013820)	18	NM_013820	15277	Mm.255848	NM_013820	ENSMUSG00000000628	Hk2	AI642394|HKII	hexokinase 2	protein-coding
mm_21201.1	chr2	155514797	155514860	-	1	NA	promoter-TSS (NM_144786)	promoter-TSS (NM_144786)	18	NM_144786	207182	Mm.41757	NM_144786	ENSMUSG00000027603	Ggt7	1110017C11Rik|6330563L03Rik|Ggtl3	gamma-glutamyltransferase 7	protein-coding
mm_173080.1	chrX	141980732	141980745	+	1	NA	Intergenic	Intergenic	216198	NM_001007576	245650	Mm.208511	NM_001007576	ENSMUSG00000042282	Gucy2f	A930002I06|GC-F|GC2	guanylate cyclase 2f	protein-coding
mm_90493.1	chr10	128033600	128033608	+	1	NA	Intergenic	Intergenic	-1742	NM_013608	17938	Mm.3746	NM_013608	ENSMUSG00000061315	Naca	AL022831|AL024382|Gm1878|mKIAA0363|skNAC	nascent polypeptide-associated complex alpha polypeptide	protein-coding
mm_83045.1	chr9	37433247	37433250	-	1	NA	promoter-TSS (NM_001164767)	promoter-TSS (NM_001164767)	-73	NM_001164767	19649	Mm.212826	NM_011248	ENSMUSG00000032128	Robo3	Rbig1|Rig-1|Rig1|Robo3a|Robo3b	roundabout guidance receptor 3	protein-coding
mm_162458.1	chr1	128570053	128570061	-	1	NA	Intergenic	B3|SINE|B2	22242	NM_009911	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding
mm_3673.1	chr1	153665628	153665653	+	1	NA	promoter-TSS (NM_001347115)	promoter-TSS (NM_001347115)	-33	NM_001347115	67792	Mm.379143	NM_026380	ENSMUSG00000042671	Rgs8	6530413N01Rik	regulator of G-protein signaling 8	protein-coding
mm_56484.1	chr6	99096956	99096961	-	1	NA	intron (NM_001347345, intron 5 of 19)	intron (NM_001347345, intron 5 of 19)	-68660	NM_001197322	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_98723.1	chr11	96332818	96332840	+	1	NA	intron (NM_001079869, intron 1 of 3)	CpG	9703	NM_001079869	15410	Mm.342481	NM_010458	ENSMUSG00000048763	Hoxb3	Hox-2.7	homeobox B3	protein-coding
mm_59204.1	chr7	24507292	24507310	+	1	NA	non-coding (NR_110958, exon 1 of 3)	non-coding (NR_110958, exon 1 of 3)	214	NR_110958	232969	Mm.181332	NM_146183	ENSMUSG00000064264	Zfp428	2410005H09Rik|AV271806|AW047854|Znf428	zinc finger protein 428	protein-coding
mm_93433.1	chr10	109010736	109010746	-	1	NA	5' UTR (NM_001252342, exon 1 of 11)	5' UTR (NM_001252342, exon 1 of 11)	234	NM_009306	20979	Mm.289702	NM_009306	ENSMUSG00000035864	Syt1	AW124717|G630098F17Rik|SytI	synaptotagmin I	protein-coding
mm_62196.1	chr7	97749798	97749806	+	1	NA	Intergenic	Intergenic	-11555	NM_175105	66333	Mm.29756	NM_175105	ENSMUSG00000042797	Aqp11	1700015P13Rik|AI648923|sjds	aquaporin 11	protein-coding
mm_61983.1	chr7	90972387	90972403	+	1	NA	Intergenic	Intergenic	-118391	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_103487.1	chr11	76509339	76509352	-	1	NA	promoter-TSS (NM_198018)	promoter-TSS (NM_198018)	74	NM_198018	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_8101.1	chr1	135848859	135848897	-	1	NA	exon (NM_001130176, exon 8 of 13)	exon (NM_001130176, exon 8 of 13)	8017	NM_001130176	21956	Mm.247470	NM_011619	ENSMUSG00000026414	Tnnt2	Tnt|cTnT	troponin T2, cardiac	protein-coding
mm_67877.1	chr7	99223589	99223595	-	1	NA	exon (NM_177448, exon 3 of 6)	exon (NM_177448, exon 3 of 6)	15019	NM_177448	233549	Mm.208030	NM_177448	ENSMUSG00000052396	Mogat2	DGAT2L5|MGAT2|Mgat1l	monoacylglycerol O-acyltransferase 2	protein-coding
mm_104324.1	chr11	93965933	93965956	-	1	NA	intron (NM_008704, intron 1 of 4)	intron (NM_008704, intron 1 of 4)	2577	NM_008704	18102	Mm.439702	NM_008704	ENSMUSG00000037601	Nme1	AL024257|NDPK-A|NM23-M1|NM23A	NME/NM23 nucleoside diphosphate kinase 1	protein-coding
mm_170591.1	chr19	5802136	5802136	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	536	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_26666.1	chr3	154711109	154711121	+	1	NA	promoter-TSS (NM_175176)	promoter-TSS (NM_175176)	-18	NM_175176	209601	Mm.331454	NM_175176	ENSMUSG00000078161	Erich3	1700013E18Rik|4922501L14Rik|5031409G23Rik|AI596448|Gm133	glutamate rich 3	protein-coding
mm_12910.1	chr2	84840613	84840640	+	1	NA	promoter-TSS (NM_001083809)	promoter-TSS (NM_001083809)	0	NM_001083809	72401	Mm.22716	NM_024497	ENSMUSG00000027075	Slc43a1	2610016F07Rik|AA986141|Lat3|PB39|Pov1|R00504	solute carrier family 43, member 1	protein-coding
mm_46969.1	chr5	115158170	115158180	-	1	NA	promoter-TSS (NM_175403)	promoter-TSS (NM_175403)	1	NM_175403	109154	Mm.153963	NM_175403	ENSMUSG00000048578	Mlec	2410014A08Rik|AI850530|ESTM19|X83352|mKIAA0152	malectin	protein-coding
mm_35075.1	chr4	6990460	6990534	-	1	NA	5' UTR (NM_145711, exon 1 of 9)	5' UTR (NM_145711, exon 1 of 9)	226	NM_145711	252838	Mm.435828	NM_145711	ENSMUSG00000041272	Tox	1700007F02Rik	thymocyte selection-associated high mobility group box	protein-coding
mm_151083.1	chr19	47622629	47622646	+	1	NA	exon (NM_001164639, exon 11 of 18)	exon (NM_001164639, exon 11 of 18)	42618	NM_001164639	20874	Mm.281011	NM_009289	ENSMUSG00000025060	Slk	9A2|AV021402|AW411554|Etk4|SMAK|Stk2|mKIAA0204|mSLK	STE20-like kinase	protein-coding
mm_38916.1	chr4	150001232	150001245	-	1	NA	intron (NM_173371, intron 1 of 4)	intron (NM_173371, intron 1 of 4)	1998	NM_001291004	100198	Mm.22183	NM_173371	ENSMUSG00000028980	H6pd	AI785303|G6pd1|Gpd-1|Gpd1	hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase)	protein-coding
mm_77530.1	chr8	123013287	123013300	-	1	NA	intron (NM_001081379, intron 1 of 12)	B3A|SINE|B2	28991	NR_037865	77087	Mm.31567	NM_001081379	ENSMUSG00000035569	Ankrd11	2410104C19Rik|3010027A04Rik|6330578C09Rik|9530048I21Rik|AA930108|Gm176|Yod	ankyrin repeat domain 11	protein-coding
mm_173025.1	chrX	103980650	103980655	-	1	NA	intron (NM_011276, intron 1 of 4)	intron (NM_011276, intron 1 of 4)	632	NM_011276	19820	Mm.427762	NM_011276	ENSMUSG00000056537	Rlim	AL022832|AW743871|Ha1r|Rlim1|Rnf12	ring finger protein, LIM domain interacting	protein-coding
mm_59555.1	chr7	28075296	28075302	+	1	NA	exon (NM_001122603, exon 3 of 20)	exon (NM_001122603, exon 3 of 20)	4063	NM_001122603	215384	Mm.292276	NM_175444	ENSMUSG00000047730	Fcgbp	A430096B05Rik	Fc fragment of IgG binding protein	protein-coding
mm_155675.1	chrX	91155163	91155173	+	1	NA	promoter-TSS (NR_126535)	promoter-TSS (NR_126535)	0	NR_126535	101055749	Mm.300769	NR_126535	ENSMUSG00000059972	LOC101055749	-	Gm5941 pseudogene	pseudo
mm_71657.1	chr8	60522685	60522709	+	1	NA	intron (NM_011834, intron 4 of 12)	L1VL4|LINE|L1	16573	NM_011834	23923	Mm.35020	NM_011834	ENSMUSG00000057228	Aadat	AI875679|Aadt|KATII|Kat2|Kyat2|mKat-2	aminoadipate aminotransferase	protein-coding
mm_58130.1	chr6	140620588	140620607	-	1	NA	Intergenic	Intergenic	-2066	NM_178803	11569	Mm.86453	NM_009637	ENSMUSG00000030232	Aebp2	AU023766|B230313N05Rik	AE binding protein 2	protein-coding
mm_107202.1	chr12	25381960	25381972	+	1	NA	Intergenic	Intergenic	252792	NR_045844	432641	Mm.112955	NR_045844		Gm17746	-	predicted gene, 17746	ncRNA
mm_42855.1	chr5	122210306	122210316	+	1	NA	promoter-TSS (NM_028752)	promoter-TSS (NM_028752)	24	NM_028752	74096	Mm.28804	NM_028752	ENSMUSG00000064267	Hvcn1	0610039P13Rik|AI450555|BTS|HV1|Vsop.|mVSOP	hydrogen voltage-gated channel 1	protein-coding
mm_135146.1	chr16	35857325	35857342	-	1	NA	exon (NM_001039530, exon 6 of 17)	exon (NM_001039530, exon 6 of 17)	14049	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_24007.1	chr3	87376382	87376393	+	1	NA	promoter-TSS (NM_178165)	promoter-TSS (NM_178165)	0	NM_001310545	229499	Mm.255203	NM_153090	ENSMUSG00000059994	Fcrl1	A230020G22Rik|Bxmas1|Bxmh1|Bxmh1b|Fcrh1|Fcrh1l|Fcrh1s|Ifgp1	Fc receptor-like 1	protein-coding
mm_119685.1	chr14	53428709	53428721	+	1	NA	Intergenic	Intergenic	825214	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_20437.1	chr2	129306664	129306678	-	1	NA	exon (NM_010554, exon 4 of 7)	exon (NM_010554, exon 4 of 7)	3301	NM_010554	16175	Mm.15534	NM_010554	ENSMUSG00000027399	Il1a	Il-1a	interleukin 1 alpha	protein-coding
mm_18602.1	chr2	67516496	67516509	-	1	NA	exon (NM_001083919, exon 7 of 9)	exon (NM_001083919, exon 7 of 9)	70500	NM_001024618	241431	Mm.261043	NM_001024618	ENSMUSG00000027022	Xirp2	2310003D02Rik|2310008C07Rik|A530024P18Rik|AI452089|Cmya3|Gm352|Xin2	xin actin-binding repeat containing 2	protein-coding
mm_41198.1	chr5	88328207	88328222	+	1	NA	exon (NM_008644, exon 3 of 3)	exon (NM_008644, exon 3 of 3)	10902	NM_008644	17830	Mm.200411	NM_008644	ENSMUSG00000064156	Prol1	Muc10	proline rich, lacrimal 1	protein-coding
mm_58061.1	chr6	136857797	136857827	-	1	NA	promoter-TSS (NM_026639)	promoter-TSS (NM_026639)	-212	NM_026639	109978	Mm.31840	NM_026639	ENSMUSG00000030217	Art4	4432404K01Rik|ARTC4|DO|DOK1	ADP-ribosyltransferase 4	protein-coding
mm_43168.1	chr5	127257165	127257166	+	1	NA	non-coding (NR_038129, exon 4 of 4)	non-coding (NR_038129, exon 4 of 4)	15339	NM_175432	208213	Mm.444235	NM_175432	ENSMUSG00000034324	Tmem132c	2810482M11Rik|3230401P16|4632425D07Rik	transmembrane protein 132C	protein-coding
mm_83814.1	chr9	53610330	53610367	-	1	NA	promoter-TSS (NM_144784)	promoter-TSS (NM_144784)	2	NM_144784	110446	Mm.293233	NM_144784	ENSMUSG00000032047	Acat1	6330585C21Rik|Acat	acetyl-Coenzyme A acetyltransferase 1	protein-coding
mm_58711.1	chr7	12978278	12978285	+	1	NA	intron (NM_001168561, intron 1 of 4)	CpG	433	NM_001168561	269870	Mm.62083	NM_175558	ENSMUSG00000033961	Zfp446	A630035I11Rik|A930031C22|AA120513|AV306632	zinc finger protein 446	protein-coding
mm_161851.1	chr18	13971501	13971501	-	1	NA	intron (NM_145492, intron 1 of 7)	CpG-6755	1232	NM_145492	225207	Mm.40325	NM_145492	ENSMUSG00000024420	Zfp521	B930086A16Rik|Evi3|Znf521	zinc finger protein 521	protein-coding
mm_68266.1	chr7	105595541	105595547	-	1	NA	exon (NM_017371, exon 6 of 10)	exon (NM_017371, exon 6 of 10)	4572	NM_017371	15458	Mm.3485	NM_017371	ENSMUSG00000030895	Hpx	Hpxn|hx	hemopexin	protein-coding
mm_98629.1	chr11	96076099	96076130	+	1	NA	promoter-TSS (NM_001161419)	promoter-TSS (NM_001161419)	-420	NM_007506	11951	Mm.258	NM_007506	ENSMUSG00000006057	Atp5g1	-	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit C1 (subunit 9)	protein-coding
mm_15159.1	chr2	154009754	154009758	+	1	NA	intron (NM_008953, intron 2 of 8)	intron (NM_008953, intron 2 of 8)	1480	NM_008953	19194	Mm.29197	NM_008953	ENSMUSG00000042459	Bpifa2	Bpifa2e|Psp	BPI fold containing family A, member 2	protein-coding
mm_130330.1	chr15	97719733	97719743	-	1	NA	intron (NM_001168693, intron 4 of 9)	intron (NM_001168693, intron 4 of 9)	1412	NM_008902	19011	Mm.1001	NM_008902	ENSMUSG00000022468	Endou	Pp11r|Tcl-30	endonuclease, polyU-specific	protein-coding
mm_148401.1	chr19	3851824	3851840	+	1	NA	promoter-TSS (NM_001271496)	promoter-TSS (NM_001271496)	59	NR_073190	12660	Mm.225505	NM_013490	ENSMUSG00000024843	Chka	CK|CK/EK-alpha|Chetk-alpha|Chk|ChoK|EK|EtnK-alpha	choline kinase alpha	protein-coding
mm_123985.1	chr14	75593120	75593158	-	1	NA	promoter-TSS (NM_001164139)	promoter-TSS (NM_001164139)	-23	NM_001164139	67926	Mm.23361	NM_026457	ENSMUSG00000034913	Spert	1700086N05Rik|AI596460|Nurit	spermatid associated	protein-coding
mm_9978.1	chr1	191225260	191225265	-	1	NA	Intergenic	Intergenic	-41929	NM_007498	11910	Mm.2706	NM_007498	ENSMUSG00000026628	Atf3	LRG-21	activating transcription factor 3	protein-coding
mm_132054.1	chr16	29579348	29579417	+	1	NA	promoter-TSS (NM_133752)	promoter-TSS (NM_133752)	48	NM_001199177	74143	Mm.274285	NM_133752	ENSMUSG00000038084	Opa1	1200011N24Rik|AI225888|AI847218|lilr3|mKIAA0567	OPA1, mitochondrial dynamin like GTPase	protein-coding
mm_35705.1	chr4	44167906	44167976	-	1	NA	promoter-TSS (NM_175201)	promoter-TSS (NM_175201)	342	NM_001038993	73469	Mm.262859	NM_175201	ENSMUSG00000035696	Rnf38	1700065B19Rik|2610202O07Rik|AA673263|Oip1	ring finger protein 38	protein-coding
mm_108229.1	chr12	77238839	77238870	+	1	NA	non-coding (NR_045554, exon 1 of 12)	non-coding (NR_045554, exon 1 of 12)	115	NR_045554	53618	Mm.35628	NM_016893	ENSMUSG00000021065	Fut8	-	fucosyltransferase 8	protein-coding
mm_152431.1	chr19	10678028	10678038	-	1	NA	promoter-TSS (NM_021453)	promoter-TSS (NM_021453)	38	NM_021453	58803	Mm.34037	NM_021453	ENSMUSG00000024738	Pga5	1110035E17Rik|Pepf	pepsinogen 5, group I	protein-coding
mm_134404.1	chr16	17576662	17576698	-	1	NA	promoter-TSS (NM_144852)	promoter-TSS (NM_144852)	-9	NM_144852	224022	Mm.298878	NM_144852	ENSMUSG00000022756	Slc7a4	AI853530	solute carrier family 7 (cationic amino acid transporter, y+ system), member 4	protein-coding
mm_88559.1	chr10	79506900	79506929	+	1	NA	Intergenic	Intergenic	24176	NR_105874	102465548		NR_105874	ENSMUSG00000098414	Mir6909	Gm27727|mmu-mir-6909	microRNA 6909	ncRNA
mm_15175.1	chr2	154142881	154142885	+	1	NA	promoter-TSS (NM_011126)	promoter-TSS (NM_011126)	3	NM_011126	18843	Mm.268852	NM_011126	ENSMUSG00000027483	Bpifa1	LUNX|NASG|Plunc|SPLUNC1|SPURT	BPI fold containing family A, member 1	protein-coding
mm_160700.1	chr10	42568640	42568640	-	1	NA	intron (NM_152229, intron 5 of 8)	intron (NM_152229, intron 5 of 8)	14948	NM_152229	21907	Mm.287100	NM_152229	ENSMUSG00000019803	Nr2e1	Mtl1|Mtll|TLL|Tlx|XTLL|fierce|frc|tailless	nuclear receptor subfamily 2, group E, member 1	protein-coding
mm_103727.1	chr11	79530606	79530614	-	1	NA	promoter-TSS (NM_010161)	promoter-TSS (NM_010161)	-1	NM_010161	14017	Mm.439665	NM_010161	ENSMUSG00000078771	Evi2a	AW491894|Evi-2|Evi2	ecotropic viral integration site 2a	protein-coding
mm_83392.1	chr9	44648838	44648886	-	1	NA	Intergenic	Intergenic	-24371	NM_001277851	58866	Mm.45380	NM_021481	ENSMUSG00000032098	Treh	2210412M19Rik	trehalase (brush-border membrane glycoprotein)	protein-coding
mm_66075.1	chr7	30915017	30915049	-	1	NA	promoter-TSS (NM_001346089)	promoter-TSS (NM_001346089)	-111	NM_010758	17136	Mm.241355	NM_010758	ENSMUSG00000036634	Mag	Gma|siglec-4a	myelin-associated glycoprotein	protein-coding
mm_104864.1	chr11	99386583	99386699	-	1	NA	exon (NM_010660, exon 6 of 8)	exon (NM_010660, exon 6 of 8)	2723	NM_010660	16661	Mm.22662	NM_010660	ENSMUSG00000019761	Krt10	D130054E02Rik|K10|K1C1|Krt-1.10|Krt1-10	keratin 10	protein-coding
mm_147643.1	chr18	60269787	60269798	-	1	NA	exon (NM_001034859, exon 2 of 2)	exon (NM_001034859, exon 2 of 2)	3475	NM_001034859	225594	Mm.329460	NM_001034859	ENSMUSG00000068606	Gm4841	EG225594|Ifgga3	predicted gene 4841	protein-coding
mm_65981.1	chr7	30445509	30445591	-	1	NA	promoter-TSS (NM_007467)	promoter-TSS (NM_007467)	32	NM_007467	11803	Mm.2381	NM_007467	ENSMUSG00000006651	Aplp1	-	amyloid beta (A4) precursor-like protein 1	protein-coding
mm_98435.1	chr11	94937953	94938055	+	1	NA	exon (NM_007742, exon 2 of 51)	exon (NM_007742, exon 2 of 51)	1780	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_45367.1	chr5	66019006	66019009	-	1	NA	3' UTR (NM_139065, exon 7 of 7)	3' UTR (NM_139065, exon 7 of 7)	-14722	NR_027961	231253	Mm.436542	NM_177679	ENSMUSG00000054598	9130230L23Rik	-	RIKEN cDNA 9130230L23 gene	ncRNA
mm_40829.1	chr5	72914265	72914303	+	1	NA	promoter-TSS (NM_001113423)	promoter-TSS (NM_001113423)	-78	NM_001113423	75991	Mm.121285	NM_153567	ENSMUSG00000036087	Slain2	5033405K12Rik|8030444K12Rik|AI596370	SLAIN motif family, member 2	protein-coding
mm_97046.1	chr11	72435512	72435529	+	1	NA	promoter-TSS (NM_027819)	promoter-TSS (NM_027819)	-6	NM_027819	71522	Mm.23336	NM_027819	ENSMUSG00000040471	Ggt6	9030405D14Rik|AI427679|AW490214	gamma-glutamyltransferase 6	protein-coding
mm_78044.1	chr9	14500661	14500737	+	1	NA	promoter-TSS (NM_023153)	promoter-TSS (NM_023153)	80	NM_023153	66070	Mm.245938	NM_023153	ENSMUSG00000004096	Cwc15	0610040D20Rik|2900052N06Rik|Ed1|c11orf5|mED1	CWC15 spliceosome-associated protein	protein-coding
mm_13466.1	chr2	105675687	105675695	+	1	NA	promoter-TSS (NM_013627)	promoter-TSS (NM_013627)	-53	NM_001244200	18508	Mm.3608	NM_013627	ENSMUSG00000027168	Pax6	1500038E17Rik|AEY11|Dey|Gsfaey11|Pax-6|Sey	paired box 6	protein-coding
mm_33440.1	chr4	130308605	130308653	+	1	NA	promoter-TSS (NM_010174)	promoter-TSS (NM_010174)	-149	NM_010174	14077	Mm.388886	NM_010174	ENSMUSG00000028773	Fabp3	Fabph-1|Fabph-4|Fabph1|Fabph4|H-FABP|Mdgi	fatty acid binding protein 3, muscle and heart	protein-coding
mm_31853.1	chr4	76450885	76450911	+	1	NA	intron (NM_011211, intron 10 of 39)	intron (NM_011211, intron 10 of 39)	-1172612	NM_025849	66928	Mm.24332	NM_025849	ENSMUSG00000028398	Tmem261	1700027K24Rik|3110001D03Rik	transmembrane protein 261	protein-coding
mm_38626.1	chr4	142084222	142084262	-	1	NA	promoter-TSS (NM_145402)	promoter-TSS (NM_145402)	-56	NR_027137	100038693	Mm.402714	NR_027137	ENSMUSG00000073728	Tmem51os1	ENSMUSG00000073728|Gm10565|Tmem51as1	Tmem51 opposite strand 1	ncRNA
mm_164440.1	chr16	49792598	49792615	-	1	NA	Intergenic	Intergenic	-63048	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_61668.1	chr7	80779738	80779748	+	1	NA	intron (NM_016721, intron 2 of 37)	intron (NM_016721, intron 2 of 37)	23588	NM_016721	29875	Mm.207619	NM_016721	ENSMUSG00000030536	Iqgap1	AA682088|D7Ertd237e|D7Ertd257e|mKIAA0051	IQ motif containing GTPase activating protein 1	protein-coding
mm_98899.1	chr11	97999551	97999563	+	1	NA	Intergenic	Intergenic	-3384	NM_207231	217151	Mm.277896	NM_207231	ENSMUSG00000038352	Arl5c	Arl12|BC065791	ADP-ribosylation factor-like 5C	protein-coding
mm_96703.1	chr11	69655000	69655013	+	1	NA	promoter-TSS (NM_009235)	promoter-TSS (NM_009235)	-31	NM_009235	20670	Mm.347499	NM_009235	ENSMUSG00000041287	Sox15	-	SRY (sex determining region Y)-box 15	protein-coding
mm_171858.1	chr5	21646065	21646065	+	1	NA	promoter-TSS (NM_026034)	promoter-TSS (NM_026034)	81	NM_026034	67211	Mm.260782	NM_026034	ENSMUSG00000038525	Armc10	2810037C14Rik|Svh	armadillo repeat containing 10	protein-coding
mm_123659.1	chr14	69244071	69244097	-	1	NA	3' UTR (NM_026331, exon 4 of 4)	3' UTR (NM_026331, exon 4 of 4)	41019	NM_026331	67712	Mm.293635	NM_026331	ENSMUSG00000034248	Slc25a37	1700020E22Rik|4930513O14Rik|4930526G11Rik|AI848481|C330015G08Rik|Mfrn|Mfrn1|Mscp|frascati|mitoferrin	solute carrier family 25, member 37	protein-coding
mm_100339.1	chr11	118393364	118393410	+	1	NA	exon (NM_011150, exon 6 of 6)	exon (NM_011150, exon 6 of 6)	8544	NM_011150	19039	Mm.3152	NM_011150	ENSMUSG00000033880	Lgals3bp	90K|CyCAP|MAC-2BP|Ppicap|Tango10b	lectin, galactoside-binding, soluble, 3 binding protein	protein-coding
mm_90344.1	chr10	127141171	127141182	+	1	NA	Intergenic	Intergenic	-20016	NM_001171026	216440	Mm.295246	NM_177614	ENSMUSG00000040462	Os9	4632413K17Rik|AU022351	amplified in osteosarcoma	protein-coding
mm_97582.1	chr11	78944809	78944824	+	1	NA	exon (NM_010927, exon 12 of 27)	exon (NM_010927, exon 12 of 27)	19525	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_61906.1	chr7	90131190	90131193	+	1	NA	intron (NM_001252520, intron 1 of 20)	intron (NM_001252520, intron 1 of 20)	959	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_8887.1	chr1	162886470	162886491	-	1	NA	intron (NM_018881, intron 4 of 8)	intron (NM_018881, intron 4 of 8)	12232	NM_018881	55990	Mm.10929	NM_018881	ENSMUSG00000040170	Fmo2	2310008D08Rik|2310042I22Rik|AW107733	flavin containing monooxygenase 2	protein-coding
mm_11450.1	chr2	32083868	32083897	+	1	NA	promoter-TSS (NM_175511)	promoter-TSS (NM_175511)	-177	NM_175511	241303	Mm.250441	NM_175511	ENSMUSG00000050592	Fam78a	A130092J06Rik	family with sequence similarity 78, member A	protein-coding
mm_82742.1	chr9	26791941	26791943	-	1	NA	intron (NM_001310768, intron 4 of 18)	intron (NM_001310768, intron 4 of 18)	14475	NM_153803	244757	Mm.293696	NM_153803	ENSMUSG00000036395	Glb1l2	-	galactosidase, beta 1-like 2	protein-coding
mm_97527.1	chr11	78502174	78502194	+	1	NA	exon (NM_011707, exon 8 of 8)	exon (NM_011707, exon 8 of 8)	-1329	NM_008759	18292	Mm.134360	NM_008759	ENSMUSG00000001103	Sebox	OG9|Og9x	SEBOX homeobox	protein-coding
mm_120065.1	chr14	56919750	56919753	+	1	NA	intron (NM_029498, intron 6 of 23)	intron (NM_029498, intron 6 of 23)	31956	NM_029498	76007	Mm.31417	NM_029498	ENSMUSG00000021945	Zmym2	5830413P05Rik|FIM|MYM|RAMP|SCLL|Zfp198|Znf198	zinc finger, MYM-type 2	protein-coding
mm_121346.1	chr14	116529381	116529385	+	1	NA	Intergenic	Intergenic	-395914	NM_001079844	23888	Mm.440025	NM_011821	ENSMUSG00000058571	Gpc6	-	glypican 6	protein-coding
mm_100744.1	chr11	4118779	4118790	-	1	NA	promoter-TSS (NM_144520)	promoter-TSS (NM_144520)	-55	NM_144520	67815	Mm.253922	NM_144520	ENSMUSG00000003585	Sec14l2	1300013M05Rik|Spf|TAP	SEC14-like lipid binding 2	protein-coding
mm_96619.1	chr11	69103648	69103691	+	1	NA	exon (NM_001159367, exon 13 of 23)	exon (NM_001159367, exon 13 of 23)	3511	NM_001159367	18626	Mm.7373	NM_011065	ENSMUSG00000020893	Per1	Hftm|Per|m-rigui|mPer1	period circadian clock 1	protein-coding
mm_134727.1	chr16	22898932	22898952	-	1	NA	exon (NM_001276450, exon 7 of 7)	exon (NM_001276450, exon 7 of 7)	-4556	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_141758.1	chr17	34264830	34264872	-	1	NA	exon (NM_207105, exon 2 of 6)	exon (NM_207105, exon 2 of 6)	1624	NM_207105	14961	Mm.254067	NM_207105	ENSMUSG00000073421	H2-Ab1	AI845868|Abeta|H-2Ab|H2-Ab|I-Abeta|IAb|Ia-2|Ia2|Rmcs1	histocompatibility 2, class II antigen A, beta 1	protein-coding
mm_127468.1	chr15	101272778	101272785	+	1	NA	exon (NM_010444, exon 5 of 7)	exon (NM_010444, exon 5 of 7)	5935	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_16096.1	chr2	168978263	168978281	+	1	NA	promoter-TSS (NR_040326)	promoter-TSS (NR_040326)	3	NR_040326	75508	Mm.271256	NR_040326	ENSMUSG00000086348	1700017J07Rik	-	RIKEN cDNA 1700017J07 gene	ncRNA
mm_152877.1	chr19	24518462	24518506	-	1	NA	intron (NM_008846, intron 1 of 14)	(TG)n|Simple_repeat|Simple_repeat	37343	NM_008846	18719	Mm.217214	NM_008846	ENSMUSG00000024867	Pip5k1b	PI4P5K-I[b]|PIP5K1-beta|PIP5KIbeta|Pipk5b|STM7	phosphatidylinositol-4-phosphate 5-kinase, type 1 beta	protein-coding
mm_12625.1	chr2	74698015	74698026	+	1	NA	5' UTR (NM_013555, exon 1 of 2)	5' UTR (NM_013555, exon 1 of 2)	257	NM_013555	15438	Mm.26544	NM_013555	ENSMUSG00000043342	Hoxd9	Hox-4.4|Hox-5.2	homeobox D9	protein-coding
mm_163428.1	chr12	82307717	82307725	+	1	NA	intron (NM_001167983, intron 3 of 23)	intron (NM_001167983, intron 3 of 23)	-3628	NM_172579	217692	Mm.261333	NM_172579	ENSMUSG00000042700	Sipa1l1	4931426N11Rik|AW213287|Spar|mKIAA0440	signal-induced proliferation-associated 1 like 1	protein-coding
mm_97521.1	chr11	78500472	78500485	+	1	NA	exon (NM_011707, exon 5 of 8)	exon (NM_011707, exon 5 of 8)	1358	NM_011707	22370	Mm.3667	NM_011707	ENSMUSG00000017344	Vtn	AI256434|Vn	vitronectin	protein-coding
mm_97654.1	chr11	79520213	79520226	+	1	NA	intron (NM_146023, intron 3 of 3)	intron (NM_146023, intron 3 of 3)	3543	NM_001077496	216984	Mm.439665	NM_001077496	ENSMUSG00000093938	Evi2b	Evi-2|Evi2	ecotropic viral integration site 2b	protein-coding
mm_10912.1	chr2	25372715	25372719	+	1	NA	exon (NM_001290407, exon 1 of 6)	exon (NM_001290407, exon 1 of 6)	682	NM_001081085	72080	Mm.250293	NM_001081085	ENSMUSG00000026955	Sapcd2	2010317E24Rik|6030458L21Rik|AL033337|ang	suppressor APC domain containing 2	protein-coding
mm_23946.1	chr3	84814584	84814658	+	1	NA	promoter-TSS (NM_001177773)	promoter-TSS (NM_001177773)	-956	NM_001177773	50754	Mm.196475	NM_080428	ENSMUSG00000028086	Fbxw7	1110001A17Rik|AGO|Cdc4|Fbw7|Fbwd6|Fbx30|Fbxo30|Fbxw6|SEL-10	F-box and WD-40 domain protein 7	protein-coding
mm_52193.1	chr6	99877608	99877621	+	1	NA	Intergenic	Intergenic	-151222	NM_001170419	50501	Mm.87365	NM_015768	ENSMUSG00000030069	Prok2	Bv8|PK2|Prok1	prokineticin 2	protein-coding
mm_7691.1	chr1	128712848	128712865	-	1	NA	Intergenic	Intergenic	-120557	NM_009911	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding
mm_115697.1	chr13	14063378	14063384	-	1	NA	promoter-TSS (NM_194262)	promoter-TSS (NM_194262)	107	NM_001331119	14593	Mm.148039	NM_010282	ENSMUSG00000021302	Ggps1	1810026C22Rik|9530089B04Rik|AI843169|C79210	geranylgeranyl diphosphate synthase 1	protein-coding
mm_56512.1	chr6	99402048	99402050	-	1	NA	intron (NM_001347345, intron 2 of 19)	B4A|SINE|B4	33296	NM_053202	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_111762.1	chr12	103989951	103989972	-	1	NA	promoter-TSS (NM_001166350)	promoter-TSS (NM_001166350)	-4	NM_001166350	380780	Mm.201338	NM_199314	ENSMUSG00000063232	Serpina11	Gm895	serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 11	protein-coding
mm_68833.1	chr7	126200475	126200500	-	1	NA	promoter-TSS (NM_028816)	promoter-TSS (NM_028816)	12	NM_001311143	74204	Mm.235663	NM_028816	ENSMUSG00000000131	Xpo6	2610005L19Rik|AL022631|C230091E20Rik|R75304|Ranbp20|mKIAA0370	exportin 6	protein-coding
mm_26326.1	chr3	142539111	142539133	+	1	NA	intron (NM_145545, intron 5 of 10)	intron (NM_145545, intron 5 of 10)	8786	NM_145545	229900	Mm.45740	NM_145545	ENSMUSG00000040253	Gbp7	9830147J24Rik	guanylate binding protein 7	protein-coding
mm_152789.1	chr19	21465190	21465191	-	1	NA	intron (NM_010266, intron 1 of 13)	intron (NM_010266, intron 1 of 13)	7471	NM_010266	14544	Mm.45054	NM_010266	ENSMUSG00000058624	Gda	AU015411|AW047581|GAH	guanine deaminase	protein-coding
mm_143357.1	chr17	67243075	67243077	-	1	NA	intron (NM_008984, intron 1 of 30)	intron (NM_008984, intron 1 of 30)	111383	NM_008984	19274	Mm.311809	NM_008984	ENSMUSG00000033278	Ptprm	RPTPmu|mKIAA4044	protein tyrosine phosphatase, receptor type, M	protein-coding
mm_119018.1	chr14	30009019	30009030	+	1	NA	promoter-TSS (NM_001136240)	promoter-TSS (NM_001136240)	24	NM_001136240	218865	Mm.259916	NM_172264	ENSMUSG00000015970	Chdh	AU041472|D630034H06Rik	choline dehydrogenase	protein-coding
mm_136790.1	chr17	11329295	11329336	+	1	NA	intron (NM_001317726, intron 4 of 6)	intron (NM_001317726, intron 4 of 6)	488956	NM_016694	50873	Mm.311110	NM_016694	ENSMUSG00000023826	Park2	PRKN	Parkinson disease (autosomal recessive, juvenile) 2, parkin	protein-coding
mm_121643.1	chr14	8666204	8666235	-	1	NA	promoter-TSS (NM_028934)	promoter-TSS (NM_028934)	71	NM_028934	74430	Mm.271901	NM_028934	ENSMUSG00000021747	4930452B06Rik	4933406L09Rik|AI854000	RIKEN cDNA 4930452B06 gene	protein-coding
mm_112491.1	chr13	6555395	6555434	+	1	NA	exon (NM_145131, exon 5 of 27)	exon (NM_145131, exon 5 of 27)	7257	NM_145131	69617	Mm.41933	NM_145131	ENSMUSG00000021193	Pitrm1	2310012C15Rik|AA410010|MP-1|MP1|Ntup1|PreP|mKIAA1104	pitrilysin metallepetidase 1	protein-coding
mm_125102.1	chr15	27741195	27741198	+	1	NA	intron (NM_001081302, intron 51 of 56)	intron (NM_001081302, intron 51 of 56)	-59654	NM_001242423	223433	Mm.266485	NM_198301	ENSMUSG00000056069	Fam105a	9830126M18	family with sequence similarity 105, member A	protein-coding
mm_127038.1	chr15	96638576	96638582	+	1	NA	intron (NM_001166458, intron 1 of 15)	intron (NM_001166458, intron 1 of 15)	3383	NM_134086	105727	Mm.103568	NM_134086	ENSMUSG00000023169	Slc38a1	AA408026|AA409865|AL022800|AU015942|NAT2	solute carrier family 38, member 1	protein-coding
mm_35412.1	chr4	34806928	34806975	-	1	NA	exon (NM_013889, exon 8 of 8)	exon (NM_013889, exon 8 of 8)	-28585	NM_025471	66291	Mm.28071	NM_025471	ENSMUSG00000028295	Smim8	1810030N24Rik|2810406B13Rik	small integral membrane protein 8	protein-coding
mm_58100.1	chr6	137570747	137570760	-	1	NA	exon (NM_001271587, exon 1 of 21)	exon (NM_001271587, exon 1 of 21)	256	NM_001271595	13860	Mm.235346	NM_007945	ENSMUSG00000015766	Eps8	AW261790	epidermal growth factor receptor pathway substrate 8	protein-coding
mm_168054.1	chrY	90812660	90812695	+	1	NA	intron (NM_133362, intron 2 of 3)	IMPB_01|Satellite|Satellite	26729	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_37355.1	chr4	120287697	120287754	-	1	NA	promoter-TSS (NM_194060)	promoter-TSS (NM_194060)	-464	NM_194060	329934	Mm.277090	NM_194060	ENSMUSG00000052135	Foxo6	-	forkhead box O6	protein-coding
mm_49454.1	chr6	29396577	29396658	+	1	NA	promoter-TSS (NM_001347073)	promoter-TSS (NM_001347073)	33	NM_001347073	232664	Mm.251303	NM_145574	ENSMUSG00000029769	Ccdc136	4921511K06Rik|BC006583	coiled-coil domain containing 136	protein-coding
mm_87732.1	chr10	60132894	60132915	+	1	NA	3' UTR (NM_052994, exon 11 of 11)	3' UTR (NM_052994, exon 11 of 11)	6128	NR_105871	102465546		NR_105871	ENSMUSG00000105468	Mir6906	mmu-mir-6906	microRNA 6906	ncRNA
mm_118580.1	chr14	19779585	19779621	+	1	NA	exon (NM_008695, exon 7 of 21)	exon (NM_008695, exon 7 of 21)	28346	NM_008695	18074	Mm.20348	NM_008695	ENSMUSG00000021806	Nid2	AW547149|Ly111|NID-2|entactin-2|nidogen-2	nidogen 2	protein-coding
mm_136068.1	chr16	84735756	84735795	-	1	NA	promoter-TSS (NM_017404)	promoter-TSS (NM_017404)	-473	NM_017404	27393	Mm.103655	NM_017404	ENSMUSG00000022889	Mrpl39	C21orf8|MRP-L5|ORF22|Rpml5	mitochondrial ribosomal protein L39	protein-coding
mm_141590.1	chr17	32420918	32420948	-	1	NA	promoter-TSS (NM_021319)	promoter-TSS (NM_021319)	42	NM_021319	57757	Mm.86752	NM_021319	ENSMUSG00000079563	Pglyrp2	C730002N09Rik|PGRP-L|Pglyrpl|tagL	peptidoglycan recognition protein 2	protein-coding
mm_148155.1	chr18	77565286	77565302	-	1	NA	promoter-TSS (NM_001164504)	promoter-TSS (NM_001164504)	-158	NM_001164504	225743	Mm.23293	NM_001164504	ENSMUSG00000025427	Rnf165	2900024M11Rik|AI427432|Akd2|Ark2c|G630064H08Rik|Gm96	ring finger protein 165	protein-coding
mm_165217.1	chr2	38500005	38500006	+	1	NA	Intergenic	Intergenic	-11692	NM_021606	59126	Mm.143818	NM_021606	ENSMUSG00000026749	Nek6	1300007C09Rik	NIMA (never in mitosis gene a)-related expressed kinase 6	protein-coding
mm_67990.1	chr7	100863354	100863368	-	1	NA	promoter-TSS (NM_177073)	promoter-TSS (NM_177073)	52	NM_177073	320100	Mm.40336	NM_177073	ENSMUSG00000008318	Relt	E430021K24Rik|Tnfrsf19l	RELT tumor necrosis factor receptor	protein-coding
mm_148702.1	chr19	5800994	5801121	+	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	1615	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_160052.1	chr7	3676731	3676731	-	1	NA	exon (NM_181820, exon 2 of 15)	exon (NM_181820, exon 2 of 15)	822	NM_181820	353499	Mm.360398	NM_181820	ENSMUSG00000019734	Tmc4	-	transmembrane channel-like gene family 4	protein-coding
mm_72915.1	chr8	91070140	91070151	+	1	NA	promoter-TSS (NM_001282001)	promoter-TSS (NM_001282001)	88	NM_001282000	19651	Mm.235580	NM_011250	ENSMUSG00000031666	Rbl2	PRB2|RBR-2|Rb2|p130	retinoblastoma-like 2	protein-coding
mm_103601.1	chr11	78404575	78404583	-	1	NA	non-coding (NR_003282, exon 5 of 5)	non-coding (NR_003282, exon 5 of 5)	10094	NR_003282	790911	Mm.457257	NR_003282	ENSMUSG00000085747	Slc13a2os	Gm11194|OTTMUSG00000000132	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 2, opposite strand	ncRNA
mm_118694.1	chr14	22140171	22140183	+	1	NA	intron (NM_028275, intron 2 of 6)	ORR1C1|LTR|ERVL-MaLR	120465	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_29896.1	chr3	131343490	131343508	-	1	NA	intron (NM_028943, intron 1 of 5)	intron (NM_028943, intron 1 of 5)	1424	NM_028943	74442	Mm.273360	NM_028943	ENSMUSG00000050931	Sgms2	4933405A16Rik|5133401H06Rik|AI854299	sphingomyelin synthase 2	protein-coding
mm_93646.1	chr10	117360962	117360972	-	1	NA	exon (NM_001013391, exon 6 of 10)	exon (NM_001013391, exon 6 of 10)	16006	NM_001013391	432508	Mm.478881	NM_001013391	ENSMUSG00000055531	Cpsf6	4733401N12Rik|AI256641|CFIM|CFIM68|HPBRII-4|HPBRII-7	cleavage and polyadenylation specific factor 6	protein-coding
mm_21729.1	chr2	164743114	164743124	-	1	NA	5' UTR (NM_027961, exon 1 of 4)	5' UTR (NM_027961, exon 1 of 4)	148	NM_027961	71856	Mm.330770	NM_027961	ENSMUSG00000076434	Wfdc3	1700015L13Rik|1700127F16Rik	WAP four-disulfide core domain 3	protein-coding
mm_47871.1	chr5	134657534	134657582	-	1	NA	exon (NM_010717, exon 15 of 16)	exon (NM_010717, exon 15 of 16)	-18149	NM_033561	22384	Mm.27955	NM_033561	ENSMUSG00000040731	Eif4h	AU018978|D5Ertd355e|E430026L18Rik|Ef4h|Wbscr1|Wscr1|eIF-4H	eukaryotic translation initiation factor 4H	protein-coding
mm_48558.1	chr5	143154696	143154704	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	11051	NR_040426	100042605	Mm.332809	NR_040424	ENSMUSG00000104529	Rbakdn	Gm3925	RB-associated KRAB zinc finger downstream neighbor (non-protein coding)	ncRNA
mm_100480.1	chr11	120232903	120232918	+	1	NA	promoter-TSS (NM_198423)	promoter-TSS (NM_198423)	-37	NM_001347621	268515	Mm.309498	NM_198423	ENSMUSG00000039741	Bahcc1	B930044J06|BC060615	BAH domain and coiled-coil containing 1	protein-coding
mm_171847.1	chr5	16904042	16904044	+	1	NA	Intergenic	L1Md_T|LINE|L1	350142	NM_001289461	15234	Mm.267078	NM_010427	ENSMUSG00000028864	Hgf	C230052L06Rik|HGF/SF|NK1|NK2|SF|SF/HGF	hepatocyte growth factor	protein-coding
mm_18931.1	chr2	76748763	76748772	-	1	NA	exon (NM_011652, exon 275 of 313)	exon (NM_011652, exon 275 of 313)	73452	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_83994.1	chr9	57443560	57443570	-	1	NA	3' UTR (NM_020270, exon 7 of 7)	3' UTR (NM_020270, exon 7 of 7)	-3451	NM_176831	66812	Mm.250508	NM_176831	ENSMUSG00000063849	Ppcdc	1810057I13Rik|8430432M10Rik	phosphopantothenoylcysteine decarboxylase	protein-coding
mm_85012.1	chr9	87731137	87731157	-	1	NA	5' UTR (NM_023814, exon 1 of 8)	5' UTR (NM_023814, exon 1 of 8)	113	NM_023814	76365	Mm.158789	NM_023814	ENSMUSG00000032419	Tbx18	2810012F10Rik|2810404D13Rik	T-box18	protein-coding
mm_60741.1	chr7	45447887	45447894	+	1	NA	intron (NM_030678, intron 10 of 15)	intron (NM_030678, intron 10 of 15)	11996	NM_010240	14325	Mm.30357	NM_010240	ENSMUSG00000050708	Ftl1	Ftl|Ftl-1|L-ferritin	ferritin light polypeptide 1	protein-coding
mm_94731.1	chr11	20742300	20742309	+	1	NA	promoter-TSS (NM_001252503)	promoter-TSS (NM_001252503)	-748	NM_181411	216549	Mm.356580	NM_181411	ENSMUSG00000049659	Aftph	-	aftiphilin	protein-coding
mm_168635.1	chr1	183205848	183205849	-	1	NA	intron (NM_026866, intron 1 of 9)	intron (NM_026866, intron 1 of 9)	15681	NM_001278218	68897	Mm.327216	NM_026866	ENSMUSG00000030768	Disp1	1190008H24Rik|DispA	dispatched RND transporter family member 1	protein-coding
mm_133194.1	chr16	72788401	72788401	+	1	NA	intron (NM_019413, intron 2 of 28)	intron (NM_019413, intron 2 of 28)	125252	NM_019413	19876	Mm.310772	NM_019413	ENSMUSG00000022883	Robo1	AW494633|AW742721|DUTT1|Gm310	roundabout guidance receptor 1	protein-coding
mm_162022.1	chr19	46036149	46036149	-	1	NA	exon (NM_010697, exon 3 of 11)	exon (NM_010697, exon 3 of 11)	3472	NM_010697	16825	Mm.327442	NM_010697	ENSMUSG00000025223	Ldb1	CLIM2|NLI	LIM domain binding 1	protein-coding
mm_106966.1	chr12	8934931	8934942	+	1	NA	exon (NM_008640, exon 4 of 7)	exon (NM_008640, exon 4 of 7)	-12993	NM_010770	17182	Mm.42226	NM_010770	ENSMUSG00000020583	Matn3	AV009181	matrilin 3	protein-coding
mm_116342.1	chr13	38503581	38503586	-	1	NA	intron (NM_001289598, intron 8 of 9)	intron (NM_001289598, intron 8 of 9)	24331	NM_001289599	105245	Mm.28622	NM_145367	ENSMUSG00000038991	Txndc5	AL022641|ERp46|PC-TRP	thioredoxin domain containing 5	protein-coding
mm_97367.1	chr11	77518567	77518576	+	1	NA	exon (NM_026185, exon 2 of 2)	exon (NM_026185, exon 2 of 2)	3454	NM_026185	67477	Mm.432526	NM_026185	ENSMUSG00000000686	Abhd15	1300007F04Rik	abhydrolase domain containing 15	protein-coding
mm_17208.1	chr2	25470418	25470456	-	1	NA	promoter-TSS (NM_008963)	promoter-TSS (NM_008963)	-688	NM_008963	19215	Mm.1008	NM_008963	ENSMUSG00000015090	Ptgds	21kDa|L-PGDS|PGD2|PGDS|PGDS2|Ptgs3	prostaglandin D2 synthase (brain)	protein-coding
mm_71309.1	chr8	43180455	43180461	+	1	NA	Intergenic	Intergenic	-2664	NM_001160412	622117	Mm.390031	NM_001160412	ENSMUSG00000091490	Triml2	EG622117|Tu4	tripartite motif family-like 2	protein-coding
mm_162736.1	chr10	54160705	54160708	-	1	NA	Intergenic	Lx8|LINE|L1	84784	NR_038016	100502920	Mm.403982	NR_038016	ENSMUSG00000097069	Gm16998	-	predicted gene, 16998	ncRNA
mm_2807.1	chr1	130865771	130865785	+	1	NA	promoter-TSS (NM_026976)	promoter-TSS (NM_026976)	1	NM_026976	69169	Mm.46042	NM_026976	ENSMUSG00000042474	Fcmr	1810037B05Rik|Faim3|FcmuR|Toso	Fc fragment of IgM receptor	protein-coding
mm_6219.1	chr1	66863296	66863297	-	1	NA	promoter-TSS (NM_007381)	promoter-TSS (NM_007381)	13	NM_007381	11363	Mm.2445	NM_007381	ENSMUSG00000026003	Acadl	AA960361|AU018452|C79855|LCAD	acyl-Coenzyme A dehydrogenase, long-chain	protein-coding
mm_41188.1	chr5	88327864	88327878	+	1	NA	exon (NM_008644, exon 3 of 3)	exon (NM_008644, exon 3 of 3)	10559	NM_008644	17830	Mm.200411	NM_008644	ENSMUSG00000064156	Prol1	Muc10	proline rich, lacrimal 1	protein-coding
mm_62941.1	chr7	119476944	119476945	+	1	NA	exon (NM_001278605, exon 3 of 11)	exon (NM_001278605, exon 3 of 11)	2318	NM_009470	22242	Mm.10826	NM_009470	ENSMUSG00000030963	Umod	THP|Urehd1|urehr4	uromodulin	protein-coding
mm_16514.1	chr2	181365560	181365570	+	1	NA	promoter-TSS (NM_001165995)	promoter-TSS (NM_001165995)	142	NM_001048148	229007	Mm.87720	NM_144894	ENSMUSG00000027582	Zgpat	1500006I01Rik|BC021513	zinc finger, CCCH-type with G patch domain	protein-coding
mm_16561.1	chr2	3332424	3332441	-	1	NA	intron (NM_001013376, intron 1 of 1)	CpG	196	NM_001013376	227522	Mm.293948	NM_001013376	ENSMUSG00000049950	Rpp38	C330006A15Rik	ribonuclease P/MRP 38 subunit	protein-coding
mm_68494.1	chr7	111076179	111076194	-	1	NA	intron (NM_001040131, intron 13 of 20)	intron (NM_001040131, intron 13 of 20)	6844	NM_001040131	13690	Mm.185453	NM_013507	ENSMUSG00000005610	Eif4g2	DAP-5|E130105L11Rik|Nat1|Natm1|p97	eukaryotic translation initiation factor 4, gamma 2	protein-coding
mm_115572.1	chr13	11545401	11545401	-	1	NA	Intergenic	Intergenic	23349	NR_027813	664793	Mm.410565	NR_027813		Zp4-ps	EG664793|Zp4|Zpb	zona pellucida glycoprotein 4, pseudogene	pseudo
mm_117142.1	chr13	60941945	60941945	-	1	NA	promoter-TSS (NM_009411)	promoter-TSS (NM_009411)	-10	NM_009411	21984	Mm.2372	NM_009411	ENSMUSG00000033834	Tpbpa	AV033951|Tb-1|Tb1|Tpbp|b2b1247Clo	trophoblast specific protein alpha	protein-coding
mm_106208.1	chr11	116851259	116851271	-	1	NA	intron (NM_011358, intron 2 of 2)	intron (NM_011358, intron 2 of 2)	1829	NM_011358	20382	Mm.21841	NM_011358	ENSMUSG00000034120	Srsf2	D11Wsu175e|MRF-1|Pr264|SC35|Sfrs10|Sfrs2	serine/arginine-rich splicing factor 2	protein-coding
mm_5959.1	chr1	56971751	56971760	-	1	NA	promoter-TSS (NM_139146)	promoter-TSS (NM_139146)	286	NR_024325	329160	Mm.419039	NR_024325	ENSMUSG00000087022	9130024F11Rik	B530002L08|EG329160	RIKEN cDNA 9130024F11 gene	ncRNA
mm_122016.1	chr14	27379423	27379438	-	1	NA	intron (NM_001289686, intron 5 of 12)	intron (NM_001289686, intron 5 of 12)	18041	NM_001289688	71704	Mm.248606	NM_027871	ENSMUSG00000021895	Arhgef3	1200004I24Rik|9830169H03Rik|C76747|Xpln	Rho guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_147535.1	chr18	53418005	53418044	-	1	NA	promoter-TSS (NM_008908)	promoter-TSS (NM_008908)	-17	NM_008908	19038	Mm.4587	NM_008908	ENSMUSG00000024538	Ppic	CyP-20c	peptidylprolyl isomerase C	protein-coding
mm_93913.1	chr10	127060259	127060306	-	1	NA	promoter-TSS (NM_001033262)	promoter-TSS (NM_001033262)	-98	NM_001033262	216438	Mm.37892	NM_001033262	ENSMUSG00000040502	March9	AI608492|BC019560	membrane-associated ring finger (C3HC4) 9	protein-coding
mm_131949.1	chr16	24393548	24393554	+	1	NA	non-coding (NR_037954, exon 1 of 2)	non-coding (NR_037954, exon 1 of 2)	104	NR_037954	68841	Mm.361995	NR_037954		Lppos	1110054M08Rik|AI481106	LIM domain containing preferred translocation partner in lipoma, opposite strand	ncRNA
mm_101216.1	chr11	20089639	20089647	-	1	NA	intron (NM_146243, intron 4 of 8)	MTC|LTR|ERVL-MaLR	23308	NM_146243	66713	Mm.259045	NM_146243	ENSMUSG00000020152	Actr2	4921510D23Rik|AA409782|Arp2|D6Ertd746e	ARP2 actin-related protein 2	protein-coding
mm_36792.1	chr4	103114306	103114314	-	1	NA	promoter-TSS (NM_027696)	promoter-TSS (NM_027696)	-11	NM_146254	242584	Mm.374877	NM_146254	ENSMUSG00000035126	Wdr78	BC028975	WD repeat domain 78	protein-coding
mm_102909.1	chr11	69560187	69560213	-	1	NA	promoter-TSS (NM_007911)	promoter-TSS (NM_007911)	37	NM_007911	13643	Mm.249637	NM_007911	ENSMUSG00000003934	Efnb3	EFL-6|ELF-3|Elk-L3|Epl8|LERK-8|NLERK-2	ephrin B3	protein-coding
mm_134761.1	chr16	23237910	23237912	-	1	NA	intron (NM_001252505, intron 1 of 7)	RMER10A|LTR|ERVL	11890	NM_001252505	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_80528.1	chr9	80165003	80165010	+	1	NA	promoter-TSS (NM_001039546)	promoter-TSS (NM_001039546)	-28	NM_001039546	17920	Mm.4040	NM_008662	ENSMUSG00000033577	Myo6	BC029719|Tlc|sv	myosin VI	protein-coding
mm_124014.1	chr14	76237571	76237575	-	1	NA	Intergenic	Intergenic	126682	NM_013745	27275	Mm.21138	NM_013745	ENSMUSG00000022009	Nufip1	Nufip	nuclear fragile X mental retardation protein interacting protein 1	protein-coding
mm_33616.1	chr4	132620005	132620045	+	1	NA	Intergenic	MTC|LTR|ERVL-MaLR	-19021	NM_210071	14050	Mm.227733	NM_010166	ENSMUSG00000028886	Eya3	AI844637	EYA transcriptional coactivator and phosphatase 3	protein-coding
mm_132477.1	chr16	36717725	36717756	+	1	NA	intron (NM_001285791, intron 5 of 6)	intron (NM_001285791, intron 5 of 6)	23762	NM_001285791	106347	Mm.17807	NM_134109	ENSMUSG00000022900	Ildr1	AU041483|AU044638	immunoglobulin-like domain containing receptor 1	protein-coding
mm_14011.1	chr2	122147681	122147696	+	1	NA	promoter-TSS (NM_009735)	promoter-TSS (NM_009735)	1	NM_009735	12010	Mm.163	NM_009735	ENSMUSG00000060802	B2m	Ly-m11|beta2-m|beta2m	beta-2 microglobulin	protein-coding
mm_129057.1	chr15	75566898	75566909	-	1	NA	promoter-TSS (NM_001135689)	promoter-TSS (NM_001135689)	-47	NM_001135688	23934	Mm.22154	NM_011837	ENSMUSG00000022577	Ly6h	-	lymphocyte antigen 6 complex, locus H	protein-coding
mm_169722.1	chr15	79075180	79075183	+	1	NA	promoter-TSS (NM_145139)	promoter-TSS (NM_145139)	-42	NM_145139	223691	Mm.206404	NM_145139	ENSMUSG00000033047	Eif3l	0610011H21Rik|D15N1e|Eif3eip|Eif3ip|Eif3s6ip|HSP-66Y|PAF67	eukaryotic translation initiation factor 3, subunit L	protein-coding
mm_154206.1	chr19	59075531	59075537	-	1	NA	5' UTR (NM_001114312, exon 1 of 17)	5' UTR (NM_001114312, exon 1 of 17)	535	NM_175172	71653	Mm.37338	NM_175172	ENSMUSG00000041362	Shtn1	4930506M07Rik|Kiaa1598|Shootin1|mKIAA1598	shootin 1	protein-coding
mm_46834.1	chr5	113280573	113280606	-	1	NA	promoter-TSS (NM_001309528)	promoter-TSS (NM_001309528)	12	NM_001309528	52850	Mm.200203	NM_172718	ENSMUSG00000042216	Sgsm1	2410098H20Rik|AA408781|D5Bwg1524e|E130107M15|NuIP|Rutbc2	small G protein signaling modulator 1	protein-coding
mm_23330.1	chr3	54156153	54156178	+	1	NA	non-coding (NR_046161, exon 1 of 11)	non-coding (NR_046161, exon 1 of 11)	108	NM_001253682	22066	Mm.10100	NM_016984	ENSMUSG00000027748	Trpc4	CCE1|STRPC4|Trp4|Trrp4	transient receptor potential cation channel, subfamily C, member 4	protein-coding
mm_156877.1	chrX	166238785	166238795	+	1	NA	promoter-TSS (NM_001177961)	promoter-TSS (NM_001177961)	-153	NM_001177961	14758	Mm.222320	NM_023122	ENSMUSG00000031342	Gpm6b	AI593561|Gpm6|M6B	glycoprotein m6b	protein-coding
mm_55914.1	chr6	83775611	83775615	-	1	NA	intron (NM_009357, intron 1 of 5)	CpG	199	NM_009357	21766	Mm.28371	NM_009357	ENSMUSG00000014748	Tex261	3110001O07Rik|AA409339|AI480706|AL033351|TEG-261	testis expressed gene 261	protein-coding
mm_32677.1	chr4	115781192	115781203	+	1	NA	promoter-TSS (NM_029196)	promoter-TSS (NM_029196)	-163	NM_029196	75173	Mm.331798	NM_029196	ENSMUSG00000044556	Tex38	4930544O15Rik|Theg4	testis expressed 38	protein-coding
mm_79872.1	chr9	65141176	65141198	+	1	NA	promoter-TSS (NM_008988)	promoter-TSS (NM_008988)	-2	NM_008988	19289	Mm.41529	NM_008988	ENSMUSG00000032394	Igdcc3	2810401C09Rik|AI851425|Punc|WI-14920	immunoglobulin superfamily, DCC subclass, member 3	protein-coding
mm_123214.1	chr14	59440780	59440887	-	1	NA	promoter-TSS (NM_026908)	promoter-TSS (NM_026908)	47	NM_001320725	107303348		NM_001320725		Setdb2-phf11c	-	Setdb2-Phf11c readthrough	protein-coding
mm_138404.1	chr17	35059239	35059247	+	1	NA	TTS (NM_033444)	TTS (NM_033444)	208	NM_016765	51793	Mm.1457	NM_016765	ENSMUSG00000007039	Ddah2	1110003M04Rik|AU019324|AW413173|DDAH-2|DDAHII|Ddah|G6a|NG30	dimethylarginine dimethylaminohydrolase 2	protein-coding
mm_53494.1	chr6	135214319	135214330	+	1	NA	intron (NM_028982, intron 3 of 12)	intron (NM_028982, intron 3 of 12)	16337	NM_028982	74525	Mm.34182	NM_028982	ENSMUSG00000030207	Fam234b	8430419L09Rik|Kiaa1467|mKIAA1467	family with sequence similarity 234, member B	protein-coding
mm_22528.1	chr3	7660278	7660306	+	1	NA	Intergenic	MT2A|LTR|ERVL	-46532	NM_001313888	16196	Mm.3825	NM_008371	ENSMUSG00000040329	Il7	A630026I06Rik|Il-7|hlb368	interleukin 7	protein-coding
mm_55144.1	chr6	51464496	51464515	-	1	NA	exon (NM_016806, exon 8 of 11)	exon (NM_016806, exon 8 of 11)	5389	NM_182650	53379	Mm.155896	NM_016806	ENSMUSG00000004980	Hnrnpa2b1	9130414A06Rik|Hnrpa2|Hnrpa2b1|hnrnp-A	heterogeneous nuclear ribonucleoprotein A2/B1	protein-coding
mm_147572.1	chr18	55767866	55767878	-	1	NA	Intergenic	Intergenic	-664260	NM_026240	107022	Mm.24356	NM_026240	ENSMUSG00000001700	Gramd3	9030613F08Rik|9130427A09Rik|AW061306|NS3TP2	GRAM domain containing 3	protein-coding
mm_117197.1	chr13	63815116	63815165	-	1	NA	promoter-TSS (NM_023507)	promoter-TSS (NM_023507)	-180	NM_001013608	76251	Mm.186610	NM_023507	ENSMUSG00000021470	Ercc6l2	0610007P08Rik|1700019D06Rik|9330134C04Rik|Rad26l|Sr278	excision repair cross-complementing rodent repair deficiency, complementation group 6 like 2	protein-coding
mm_27157.1	chr3	33110787	33110796	-	1	NA	intron (NM_001163516, intron 1 of 12)	intron (NM_001163516, intron 1 of 12)	-27731	NM_001289505	58869	Mm.151332	NM_021483	ENSMUSG00000027674	Pex5l	1700016J08Rik|PXR2|Pex2|TRIP8b|pex5Rp	peroxisomal biogenesis factor 5-like	protein-coding
mm_66628.1	chr7	45493715	45493726	-	1	NA	3' UTR (NM_008749, exon 13 of 13)	3' UTR (NM_008749, exon 13 of 13)	-4924	NM_027903	71755	Mm.34208	NM_027903	ENSMUSG00000011382	Dhdh	1300018L09Rik|AA591799|Xld-1|Xld1	dihydrodiol dehydrogenase (dimeric)	protein-coding
mm_72871.1	chr8	88678995	88679000	+	1	NA	intron (NM_145857, intron 9 of 12)	RMER15-int|LTR|ERVL	-18031	NM_001128170	74256	Mm.490395	NM_173369	ENSMUSG00000036712	Cyld	2010013M14Rik|2900009M21Rik|C130039D01Rik|CDMT|CYLD1|EAC|mKIAA0849	CYLD lysine 63 deubiquitinase	protein-coding
mm_71598.1	chr8	54955247	54955280	+	1	NA	5' UTR (NM_153581, exon 1 of 7)	5' UTR (NM_153581, exon 1 of 7)	535	NM_001253756	234267	Mm.241700	NM_153581	ENSMUSG00000031517	Gpm6a	Gpm6|M6A	glycoprotein m6a	protein-coding
mm_93555.1	chr10	116297892	116297923	-	1	NA	Intergenic	Intergenic	-3467	NM_029928	19263	Mm.37213	NM_029928	ENSMUSG00000020154	Ptprb	3230402H02Rik|C130094E24|Ptpz|Rptpb|VE-PTP|Veptp	protein tyrosine phosphatase, receptor type, B	protein-coding
mm_117058.1	chr13	58402477	58402524	-	1	NA	promoter-TSS (NM_025279)	promoter-TSS (NM_025279)	12	NM_001301345	15387	Mm.142872	NM_025279	ENSMUSG00000021546	Hnrnpk	Hnrpk|KBBP|NOVA	heterogeneous nuclear ribonucleoprotein K	protein-coding
mm_129729.1	chr15	82027850	82027860	-	1	NA	intron (NM_010247, intron 7 of 12)	intron (NM_010247, intron 7 of 12)	11486	NM_010247	14375	Mm.288809	NM_010247	ENSMUSG00000022471	Xrcc6	70kDa|G22p1|Ku70	X-ray repair complementing defective repair in Chinese hamster cells 6	protein-coding
mm_143890.1	chr17	84466174	84466184	-	1	NA	promoter-TSS (NM_183021)	promoter-TSS (NM_183021)	29	NM_183021	240174	Mm.246767	NM_177826	ENSMUSG00000024251	Thada	6530405K19|A930021O22|AU019899|BC052885|GITA	thyroid adenoma associated	protein-coding
mm_36550.1	chr4	86691441	86691450	-	1	NA	Intergenic	Intergenic	-21386	NM_007408	11520	Mm.381	NM_007408	ENSMUSG00000028494	Plin2	AA407157|ADPH|Adfp|Adrp	perilipin 2	protein-coding
mm_9390.1	chr1	172216827	172216839	-	1	NA	exon (NM_009813, exon 3 of 11)	exon (NM_009813, exon 3 of 11)	3062	NM_009813	12372	Mm.12829	NM_009813	ENSMUSG00000007122	Casq1	CSQ|CSQ-1|CSQ1|sCSQ	calsequestrin 1	protein-coding
mm_133992.1	chr16	4679661	4679699	-	1	NA	promoter-TSS (NM_030205)	promoter-TSS (NM_030205)	40	NM_030205	78885	Mm.325512	NM_030205	ENSMUSG00000039637	Coro7	0610011B16Rik|AW048373|AW556392	coronin 7	protein-coding
mm_87747.1	chr10	60267087	60267089	+	1	NA	Intergenic	Intergenic	-10540	NM_001146123	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_74933.1	chr8	25769584	25769593	-	1	NA	intron (NM_026121, intron 3 of 4)	intron (NM_026121, intron 3 of 4)	-15308	NM_028102	72108	Mm.246875	NM_028102	ENSMUSG00000061313	Ddhd2	2010305K11Rik|SAMWD1|mKIAA0725	DDHD domain containing 2	protein-coding
mm_46304.1	chr5	100562762	100562769	-	1	NA	intron (NM_139198, intron 1 of 4)	intron (NM_139198, intron 1 of 4)	9440	NM_139198	231507	Mm.34609	NM_139198	ENSMUSG00000029322	Plac8	C15|D5Wsu111e	placenta-specific 8	protein-coding
mm_62231.1	chr7	98563163	98563170	+	1	NA	Intergenic	Intergenic	68944	NM_001113379	434215	Mm.323057	NM_001113379	ENSMUSG00000090958	Lrrc32	AI426318|D11S833Eh|D7H11S833E|EG434215|Garp	leucine rich repeat containing 32	protein-coding
mm_38986.1	chr4	151057896	151057906	-	1	NA	promoter-TSS (NM_009498)	promoter-TSS (NM_009498)	52	NM_009498	22319	Mm.273930	NM_009498	ENSMUSG00000028955	Vamp3	D130027G05Rik|VAMP-3|ceb	vesicle-associated membrane protein 3	protein-coding
mm_135541.1	chr16	49772771	49772785	-	1	NA	Intergenic	Intergenic	73484	NM_028680	73916	Mm.241276	NM_028680	ENSMUSG00000032965	Ift57	4833420A15Rik|Esrrbl1|Hippi|MHS4R2	intraflagellar transport 57	protein-coding
mm_162999.1	chr11	32024681	32024691	+	1	NA	intron (NM_001290680, intron 3 of 4)	intron (NM_001290680, intron 3 of 4)	23409	NM_001290681	18197	Mm.3304	NM_008741	ENSMUSG00000020297	Nsg2	-	neuron specific gene family member 2	protein-coding
mm_107762.1	chr12	59080989	59080993	+	1	NA	Intergenic	Intergenic	14072	NM_008891	18949	Mm.22347	NM_008891	ENSMUSG00000020994	Pnn	AU045199|D12Ertd512e	pinin	protein-coding
mm_26791.1	chr3	9778794	9778804	-	1	NA	intron (NM_053182, intron 1 of 7)	Lx7|LINE|L1	54880	NM_053182	94212	Mm.23897	NM_053182	ENSMUSG00000027508	Pag1	Cbp|F730007C19Rik|Pag	phosphoprotein associated with glycosphingolipid microdomains 1	protein-coding
mm_74676.1	chr8	13974924	13974946	-	1	NA	promoter-TSS (NM_173744)	promoter-TSS (NM_173744)	-158	NM_173744	72148	Mm.5727	NM_173744	ENSMUSG00000050052	Tdrp	2610019F03Rik	testis development related protein	protein-coding
mm_55227.1	chr6	52234882	52234894	-	1	NA	promoter-TSS (NM_008263)	promoter-TSS (NM_008263)	51	NM_008263	15395	Mm.5	NM_008263	ENSMUSG00000000938	Hoxa10	Hox-1.8|Hoxa-10	homeobox A10	protein-coding
mm_105383.1	chr11	103344652	103344719	-	1	NA	promoter-TSS (NM_133715)	promoter-TSS (NM_133715)	17	NM_133715	544817	Mm.259113	NM_133715	ENSMUSG00000034255	Arhgap27	2310069I04Rik|5730442P18Rik|Gm21552|Sh3d20	Rho GTPase activating protein 27	protein-coding
mm_12582.1	chr2	73312674	73312688	+	1	NA	promoter-TSS (NM_025854)	promoter-TSS (NM_025854)	29	NM_029022	74616	Mm.247457	NM_029022	ENSMUSG00000008226	Scrn3	4833415E20Rik|AI427019|AV002033|Ses3	secernin 3	protein-coding
mm_58673.1	chr7	10636802	10636804	+	1	NA	Intergenic	Intergenic	3216	NM_134228	171262	Mm.222634	NM_134228	ENSMUSG00000045340	Vmn1r70	V1rd2|V1rl1	vomeronasal 1 receptor 70	protein-coding
mm_168215.1	chr10	75932503	75932504	-	1	NA	promoter-TSS (NM_008606)	promoter-TSS (NM_008606)	-1	NM_008606	17385	Mm.4561	NM_008606	ENSMUSG00000000901	Mmp11	MMP-11|SL-3|ST3|Stmy3	matrix metallopeptidase 11	protein-coding
mm_164021.1	chr14	75179734	75179779	-	1	NA	intron (NM_008879, intron 2 of 16)	intron (NM_008879, intron 2 of 16)	43331	NM_008879	18826	Mm.153911	NM_008879	ENSMUSG00000021998	Lcp1	AW536232|D14Ertd310e|LCP-1|Pls2|pp65	lymphocyte cytosolic protein 1	protein-coding
mm_132508.1	chr16	36962142	36962154	+	1	NA	exon (NM_008225, exon 12 of 14)	exon (NM_008225, exon 12 of 14)	16988	NM_001037321	207215	Mm.211899	NM_001037321	ENSMUSG00000047746	Fbxo40	9830003A13Rik|mKIAA1195	F-box protein 40	protein-coding
mm_132628.1	chr16	38902373	38902437	+	1	NA	promoter-TSS (NM_170599)	promoter-TSS (NM_170599)	60	NM_170599	207683	Mm.245564	NM_170599	ENSMUSG00000022790	Igsf11	1700025L02Rik|BT-IgSF|Igsf13	immunoglobulin superfamily, member 11	protein-coding
mm_143839.1	chr17	84121585	84121608	-	1	NA	Intergenic	MLT1G1|LTR|ERVL-MaLR	42936	NR_045458	74473	Mm.399575	NR_045458		4933433H22Rik	-	RIKEN cDNA 4933433H22 gene	ncRNA
mm_89788.1	chr10	102159001	102159018	+	1	NA	promoter-TSS (NM_001162369)	promoter-TSS (NM_001162369)	-70	NM_001162369	67569	Mm.25252	NM_026243	ENSMUSG00000019888	Mgat4c	9130411I17Rik|GntIVh	MGAT4 family, member C	protein-coding
mm_127055.1	chr15	96710372	96710376	+	1	NA	Intergenic	Intergenic	-10676	NM_175121	67760	Mm.46754	NM_175121	ENSMUSG00000022462	Slc38a2	5033402L14Rik|AI316867|ATA2|SAT2|mKIAA1382	solute carrier family 38, member 2	protein-coding
mm_143758.1	chr17	81606123	81606126	-	1	NA	intron (NR_104580, intron 2 of 8)	intron (NR_104580, intron 2 of 8)	132263	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_61780.1	chr7	83658824	83658838	+	1	NA	intron (NM_010551, intron 12 of 18)	intron (NM_010551, intron 12 of 18)	26814	NM_023377	170460	Mm.357953	NM_023377	ENSMUSG00000046027	Stard5	2310058G22Rik|AI607880|D7Ertd152e	StAR-related lipid transfer (START) domain containing 5	protein-coding
mm_52555.1	chr6	115995390	115995432	+	1	NA	promoter-TSS (NM_026376)	promoter-TSS (NM_026376)	-406	NM_026376	67784	Mm.3085	NM_026376	ENSMUSG00000030123	Plxnd1	6230425C21Rik|b2b1863Clo|b2b553Clo	plexin D1	protein-coding
mm_60740.1	chr7	45447867	45447878	+	1	NA	intron (NM_030678, intron 10 of 15)	intron (NM_030678, intron 10 of 15)	12014	NM_010240	14325	Mm.30357	NM_010240	ENSMUSG00000050708	Ftl1	Ftl|Ftl-1|L-ferritin	ferritin light polypeptide 1	protein-coding
mm_78504.1	chr9	32745384	32745416	+	1	NA	intron (NM_011808, intron 6 of 7)	intron (NM_011808, intron 6 of 7)	49358	NM_001038642	23871	Mm.292415	NM_011808	ENSMUSG00000032035	Ets1	AI196000|AI448617|D230050P06|Ets-1|Tpl1|vs	E26 avian leukemia oncogene 1, 5' domain	protein-coding
mm_104648.1	chr11	97574012	97574022	-	1	NA	intron (NM_018873, intron 1 of 19)	intron (NM_018873, intron 1 of 19)	1109	NM_018873	56013	Mm.342665	NM_018873	ENSMUSG00000038453	Srcin1	P140|SNIP|mKIAA1684|p140Cap	SRC kinase signaling inhibitor 1	protein-coding
mm_18404.1	chr2	60312250	60312254	-	1	NA	intron (NM_013825, intron 28 of 34)	B1_Mur2|SINE|Alu	-27768	NM_001290660	66205	Mm.227281	NM_025422	ENSMUSG00000060703	Cd302	1110055L24Rik|AI159627	CD302 antigen	protein-coding
mm_91847.1	chr10	58536448	58536458	-	1	NA	intron (NM_001162956, intron 10 of 15)	RLTR9E|LTR|ERVK	38516	NM_001162956	76138	Mm.211744	NM_001162956	ENSMUSG00000038010	Ccdc138	6230424H07Rik|BC042726	coiled-coil domain containing 138	protein-coding
mm_40908.1	chr5	75576095	75576101	+	1	NA	intron (NM_021099, intron 1 of 20)	intron (NM_021099, intron 1 of 20)	1107	NM_021099	16590	Mm.247073	NM_021099	ENSMUSG00000005672	Kit	Bs|CD117|Fdc|Gsfsco1|Gsfsco5|Gsfsow3|SCO1|SCO5|SOW3|Ssm|Tr-kit|W|c-KIT	KIT proto-oncogene receptor tyrosine kinase	protein-coding
mm_92764.1	chr10	81092654	81092664	-	1	NA	intron (NM_145365, intron 2 of 11)	intron (NM_145365, intron 2 of 11)	6213	NM_145365	208677	Mm.294693	NM_145365	ENSMUSG00000035041	Creb3l3	BC010786|CREB-H|D10Bur1e	cAMP responsive element binding protein 3-like 3	protein-coding
mm_35244.1	chr4	19877542	19877552	-	1	NA	3' UTR (NM_175406, exon 8 of 8)	3' UTR (NM_175406, exon 8 of 8)	45019	NM_175406	242341	Mm.19298	NM_175406	ENSMUSG00000028238	Atp6v0d2	1620401A02Rik|AI324824|V-ATPase	ATPase, H+ transporting, lysosomal V0 subunit D2	protein-coding
mm_141335.1	chr17	28507537	28507557	-	1	NA	Intergenic	Intergenic	-21398	NM_010220	14229	Mm.276405	NM_010220	ENSMUSG00000024222	Fkbp5	D17Ertd592e|Dit1|FKBP-5|FKBP51	FK506 binding protein 5	protein-coding
mm_61480.1	chr7	75669683	75669687	+	1	NA	intron (NM_029332, intron 10 of 36)	intron (NM_029332, intron 10 of 36)	-178653	NM_001122780	207952	Mm.206223	NM_029652	ENSMUSG00000055652	Klhl25	2810402K13Rik|BC027373|Enc-1	kelch-like 25	protein-coding
mm_23945.1	chr3	84666305	84666354	+	1	NA	5' UTR (NM_177260, exon 1 of 7)	5' UTR (NM_177260, exon 1 of 7)	137	NM_177260	320782	Mm.107370	NM_177260	ENSMUSG00000056498	Tmem154	9930117H01Rik	transmembrane protein 154	protein-coding
mm_9894.1	chr1	186705317	186705325	-	1	NA	5' UTR (NM_009367, exon 1 of 7)	5' UTR (NM_009367, exon 1 of 7)	668	NM_009367	21808	Mm.18213	NM_009367	ENSMUSG00000039239	Tgfb2	BB105277|Tgf-beta2|Tgfb-2	transforming growth factor, beta 2	protein-coding
mm_93437.1	chr10	109638850	109638853	-	1	NA	Intergenic	MTC|LTR|ERVL-MaLR	361368	NM_001081035	260315	Mm.225050	NM_177797	ENSMUSG00000020181	Nav3	4732483H20Rik|9630020C08Rik|POMFIL1|Pomfil1p|mKIAA0938|unc53H3	neuron navigator 3	protein-coding
mm_100382.1	chr11	119307765	119307769	+	1	NA	Intergenic	Intergenic	-7020	NM_130886	170720	Mm.130832	NM_130886	ENSMUSG00000013483	Card14	Bimp2|CARMA2	caspase recruitment domain family, member 14	protein-coding
mm_32820.1	chr4	117445984	117445987	+	1	NA	intron (NM_025739, intron 2 of 14)	intron (NM_025739, intron 2 of 14)	51067	NM_025739	66743	Mm.318331	NM_025739	ENSMUSG00000028677	Rnf220	4732477A13|4931406I20Rik|5730503K05Rik|AV302541	ring finger protein 220	protein-coding
mm_46223.1	chr5	98943878	98943891	-	1	NA	intron (NM_008926, intron 15 of 18)	intron (NM_008926, intron 15 of 18)	89469	NM_001310677	110075	Mm.136461	NM_173404	ENSMUSG00000029335	Bmp3	9530029I04Rik	bone morphogenetic protein 3	protein-coding
mm_71686.1	chr8	61224259	61224275	+	1	NA	promoter-TSS (NM_021506)	promoter-TSS (NM_021506)	96	NM_021506	59009	Mm.27949	NM_021506	ENSMUSG00000031642	Sh3rf1	2200003J05Rik|Posh|R75531|Sh3md2	SH3 domain containing ring finger 1	protein-coding
mm_53142.1	chr6	125231256	125231285	+	1	NA	promoter-TSS (NR_015604)	promoter-TSS (NR_015604)	-6	NR_015604	78668	Mm.10626	NR_015604	ENSMUSG00000030337	E130112N10Rik	5830448L21Rik|9530059J11Rik	RIKEN cDNA E130112N10 gene	ncRNA
mm_2910.1	chr1	132007641	132007673	+	1	NA	promoter-TSS (NM_007923)	promoter-TSS (NM_007923)	52	NM_007923	13714	Mm.254233	NM_007923	ENSMUSG00000026436	Elk4	2310011G17Rik|A130026I01Rik|BB162516|SAP-1|Sap1	ELK4, member of ETS oncogene family	protein-coding
mm_49618.1	chr6	30751908	30751918	+	1	NA	intron (NM_017478, intron 20 of 23)	intron (NM_017478, intron 20 of 23)	10614	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_12448.1	chr2	71129776	71129801	+	1	NA	exon (NM_028593, exon 2 of 4)	exon (NM_028593, exon 2 of 4)	11734	NM_028593	73649	Mm.45435	NM_028593	ENSMUSG00000027015	Cybrd1	2210407P13Rik|Dcytb	cytochrome b reductase 1	protein-coding
mm_161759.1	chr17	35517209	35517209	+	1	NA	promoter-TSS (NM_001163763)	promoter-TSS (NM_001163763)	93	NM_146248	240084	Mm.49544	NM_146248	ENSMUSG00000040312	Cchcr1	Hcr	coiled-coil alpha-helical rod protein 1	protein-coding
mm_164979.1	chr19	8839278	8839294	-	1	NA	promoter-TSS (NM_008144)	promoter-TSS (NM_008144)	-40	NM_010316	14704	Mm.329700	NM_010316	ENSMUSG00000071658	Gng3	-	guanine nucleotide binding protein (G protein), gamma 3	protein-coding
mm_152677.1	chr19	15924561	15924569	-	1	NA	promoter-TSS (NM_001205339)	promoter-TSS (NM_001205339)	57	NM_001205339	107272	Mm.289936	NM_177420	ENSMUSG00000024640	Psat1	D8Ertd814e|EPIP|PSA|Psat	phosphoserine aminotransferase 1	protein-coding
mm_101260.1	chr11	20898727	20898743	-	1	NA	Intergenic	Intergenic	-67627	NM_173752	216551	Mm.76694	NM_173752	ENSMUSG00000042363	Lgalsl	1110067D22Rik|A530071M23|Grpa|Hspc159|Lgalsla	lectin, galactoside binding-like	protein-coding
mm_144341.1	chr18	14848007	14848007	+	1	NA	intron (NM_001100449, intron 13 of 14)	B1_Mur2|SINE|Alu	64762	NM_001100449	72504	Mm.312233	NM_001100449	ENSMUSG00000054321	Taf4b	105kDa|2610524B04Rik|4932409F03Rik|AW987595|TAFII-105|TAFII105|Taf2c2	TATA-box binding protein associated factor 4b	protein-coding
mm_101067.1	chr11	11451201	11451204	-	1	NA	intron (NM_001185153, intron 2 of 7)	intron (NM_001185153, intron 2 of 7)	11217	NM_015785	53604	Mm.9500	NM_015785	ENSMUSG00000020193	Zpbp	4930486K01Rik|Iam38|Sp38	zona pellucida binding protein	protein-coding
mm_94775.1	chr11	21264995	21265005	+	1	NA	intron (NM_139061, intron 3 of 22)	intron (NM_139061, intron 3 of 22)	25968	NM_001290628	245944	Mm.170103	NM_139061	ENSMUSG00000020128	Vps54	Hcc8|Vps54l|mSLP8|wr	VPS54 GARP complex subunit	protein-coding
mm_169142.1	chr13	62125686	62125703	+	1	NA	Intergenic	Intergenic	-4196	NM_001039239	630579	Mm.440905	NM_001039239	ENSMUSG00000074867	Zfp808	EG630579|Gm7036	zinc finger protein 80	protein-coding
mm_19899.1	chr2	114053516	114053562	-	1	NA	promoter-TSS (NM_009608)	promoter-TSS (NM_009608)	-664	NM_009608	11464	Mm.686	NM_009608	ENSMUSG00000068614	Actc1	Actc-1	actin, alpha, cardiac muscle 1	protein-coding
mm_110734.1	chr12	69790275	69790276	-	1	NA	promoter-TSS (NR_033573)	promoter-TSS (NR_033573)	-69	NR_033573	74724	Mm.399254	NR_033573		4930512B01Rik	4930472D12Rik	RIKEN cDNA 4930512B01 gene	ncRNA
mm_53616.1	chr6	140041550	140041562	+	1	NA	promoter-TSS (NM_054066)	promoter-TSS (NM_054066)	31	NM_007605	12344	Mm.12817	NM_007605	ENSMUSG00000041791	Capza3	510-4|Cappa3|Gsg3|Tex8|repro32	capping protein (actin filament) muscle Z-line, alpha 3	protein-coding
mm_101007.1	chr11	8492407	8492411	-	1	NA	exon (NM_001083587, exon 17 of 31)	exon (NM_001083587, exon 17 of 31)	172126	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_40085.1	chr5	34530649	34530651	+	1	NA	intron (NM_011893, intron 1 of 12)	U1|snRNA|snRNA	4866	NM_011893	24055	Mm.5012	NM_011893	ENSMUSG00000054520	Sh3bp2	3BP2	SH3-domain binding protein 2	protein-coding
mm_86325.1	chr9	123056671	123056677	-	1	NA	exon (NM_177911, exon 10 of 14)	exon (NM_177911, exon 10 of 14)	21933	NM_177911	331046	Mm.195309	NM_177911	ENSMUSG00000025787	Tgm4	9530008N10Rik|Eapa1|TGP	transglutaminase 4 (prostate)	protein-coding
mm_51641.1	chr6	86017218	86017229	+	1	NA	promoter-TSS (NM_012013)	promoter-TSS (NM_012013)	32	NM_012013	26910	Mm.8024	NM_012013	ENSMUSG00000030001	Figla	FIGalpha|bHLHc8	folliculogenesis specific basic helix-loop-helix	protein-coding
mm_77337.1	chr8	119558719	119558766	-	1	NA	promoter-TSS (NM_001167910)	promoter-TSS (NM_001167910)	19	NM_001167910	56453	Mm.206934	NM_019709	ENSMUSG00000031835	Mbtps1	0610038M03Rik|AV003995|S1P|SKI-1|Ski1|mKIAA0091	membrane-bound transcription factor peptidase, site 1	protein-coding
mm_26656.1	chr3	154597200	154597202	+	1	NA	promoter-TSS (NM_172474)	promoter-TSS (NM_172474)	-103	NM_172474	209584	Mm.347513	NM_172474	ENSMUSG00000047583	Tyw3	5230400J09Rik	tRNA-yW synthesizing protein 3 homolog (S. cerevisiae)	protein-coding
mm_74673.1	chr8	13890234	13890300	-	1	NA	promoter-TSS (NM_025556)	promoter-TSS (NM_025556)	4	NM_025556	66423	Mm.29063	NM_025556	ENSMUSG00000031458	Coprs	1700029I03Rik|2410022L05Rik|AA409325|AI256813|C85432|Copr5	coordinator of PRMT5, differentiation stimulator	protein-coding
mm_103886.1	chr11	83574590	83574600	-	1	NA	3' UTR (NM_011338, exon 4 of 4)	3' UTR (NM_011338, exon 4 of 4)	4041	NM_011338	20308	Mm.416125	NM_011338	ENSMUSG00000019122	Ccl9	CCF18|MRP-2|Scya10|Scya9	chemokine (C-C motif) ligand 9	protein-coding
mm_10513.1	chr2	16356451	16356486	+	1	NA	5' UTR (NM_026162, exon 1 of 14)	5' UTR (NM_026162, exon 1 of 14)	164	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding
mm_155291.1	chrX	61183806	61183817	+	1	NA	3' UTR (NM_001166658, exon 1 of 1)	3' UTR (NM_001166658, exon 1 of 1)	1747	NM_001166658	631990	Mm.401324	NM_001166658	ENSMUSG00000090546	Cdr1	100039759|Cdr|Cdr34|EG631990|Gm2409|Gm7077	cerebellar degeneration related antigen 1	protein-coding
mm_106692.1	chr12	3365386	3365405	+	1	NA	5' UTR (NM_008445, exon 1 of 8)	5' UTR (NM_008445, exon 1 of 8)	263	NM_008445	16570	Mm.7688	NM_008445	ENSMUSG00000020668	Kif3c	mKIAA4058	kinesin family member 3C	protein-coding
mm_67212.1	chr7	74399888	74399898	-	1	NA	intron (NM_001038643, intron 2 of 10)	intron (NM_001038643, intron 2 of 10)	154887	NM_023908	108116	Mm.425467	NM_023908	ENSMUSG00000025790	Slco3a1	5830414C08Rik|Anr1|MJAM|OATP-D|R75096|Slc21a11	solute carrier organic anion transporter family, member 3a1	protein-coding
mm_112104.1	chr12	112785562	112785580	-	1	NA	Intergenic	Intergenic	-23404	NM_145450	217887	Mm.186678	NM_145450	ENSMUSG00000037594	BC022687	AW050009|C130001I08Rik|Flj20080	cDNA sequence BC022687	protein-coding
mm_160570.1	chr9	57081081	57081081	+	1	NA	intron (NM_001110350, intron 1 of 20)	L1MB3|LINE|L1	4705	NM_011378	20466	Mm.15755	NM_011378	ENSMUSG00000042557	Sin3a	AW553200|Sin3|mKIAA4126|mSin3A	transcriptional regulator, SIN3A (yeast)	protein-coding
mm_57977.1	chr6	135724743	135724749	-	1	NA	Intergenic	Intergenic	65833	NR_126088	75024	Mm.399147	NR_126088	ENSMUSG00000107396	4930425L21Rik	4930473P14Rik	RIKEN cDNA 4930425L21 gene	ncRNA
mm_164181.1	chr15	76269993	76270002	+	1	NA	promoter-TSS (NR_045747)	promoter-TSS (NR_045747)	-158	NR_045747	100038659	Mm.448549	NR_045747		Mirt2	ENSMUSG00000075583|Gm10872|Gm24562	myocardial infraction associated transcript 2	ncRNA
mm_16422.1	chr2	180257374	180257396	+	1	NA	promoter-TSS (NM_025587)	promoter-TSS (NM_025587)	6	NM_025587	66481	Mm.289669	NM_025587	ENSMUSG00000039001	Rps21	1810049N11Rik|2410030A14Rik	ribosomal protein S21	protein-coding
mm_95962.1	chr11	58884043	58884074	+	1	NA	3' UTR (NM_172403, exon 5 of 5)	3' UTR (NM_172403, exon 5 of 5)	16818	NM_172403	69944	Mm.32118	NM_172403	ENSMUSG00000020491	2810021J22Rik	AI449137	RIKEN cDNA 2810021J22 gene	protein-coding
mm_126678.1	chr15	84672863	84672866	+	1	NA	intron (NM_001346662, intron 1 of 8)	intron (NM_001346662, intron 1 of 8)	-8134	NM_146061	109270	Mm.291372	NM_146061	ENSMUSG00000036106	Prr5	AU043908|Arhgap8|C030017C09Rik|C78947|Protor-1|Protor1	proline rich 5 (renal)	protein-coding
mm_12831.1	chr2	80635244	80635250	+	1	NA	Intergenic	Intergenic	-3565	NM_027091	69482	Mm.29200	NM_027091	ENSMUSG00000026999	Nup35	2310006I24Rik|35kDa|5330402E05Rik|MP44|NO44	nucleoporin 35	protein-coding
mm_32667.1	chr4	115532607	115532638	+	1	NA	exon (NM_010011, exon 12 of 13)	exon (NM_010011, exon 12 of 13)	14335	NM_010011	13117	Mm.10742	NM_010011	ENSMUSG00000066072	Cyp4a10	AI647584|Cyp4a|D4Rp1|Msp-3|RP1	cytochrome P450, family 4, subfamily a, polypeptide 10	protein-coding
mm_97345.1	chr11	77462568	77462596	+	1	NA	Intergenic	CpG	-1331	NM_139129	216961	Mm.33477	NM_139128	ENSMUSG00000020836	Coro6	-	coronin 6	protein-coding
mm_148706.1	chr19	5801888	5801923	+	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	767	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_122477.1	chr14	45657971	45658016	-	1	NA	promoter-TSS (NR_039593)	promoter-TSS (NR_039593)	60	NR_039593	100628600		NR_039593	ENSMUSG00000093167	Mir5131	mmu-mir-5131|mu-mir-5131	microRNA 5131	ncRNA
mm_12111.1	chr2	61593113	61593123	+	1	NA	promoter-TSS (NM_001164072)	promoter-TSS (NM_001164072)	21	NM_001164071	21353	Mm.244393	NM_011529	ENSMUSG00000064289	Tank	C86182|E430026L09Rik|I-TRAF	TRAF family member-associated Nf-kappa B activator	protein-coding
mm_171540.1	chr4	146971969	146971987	+	1	NA	Intergenic	Intergenic	-49872	NM_001177767	100043034	Mm.422606	NM_001177767	ENSMUSG00000067919	Rex2	Gm13138|OTTMUSG00000010655	reduced expression 2	protein-coding
mm_125201.1	chr15	32944360	32944363	+	1	NA	intron (NM_008304, intron 1 of 4)	intron (NM_008304, intron 1 of 4)	23638	NM_008304	15529	Mm.234266	NM_008304	ENSMUSG00000022261	Sdc2	4833414L08Rik|AA960457|Hspg1|Synd2|syndecan-2	syndecan 2	protein-coding
mm_29264.1	chr3	107333013	107333023	-	1	NA	exon (NM_001045807, exon 1 of 2)	exon (NM_001045807, exon 1 of 2)	271	NM_001045807	229700	Mm.27966	NM_001045807	ENSMUSG00000048109	Rbm15	C230088J01Rik|mKIAA1438	RNA binding motif protein 15	protein-coding
mm_50127.1	chr6	41539242	41539253	+	1	NA	Intergenic	Intergenic	17471	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_57769.1	chr6	129237026	129237042	-	1	NA	intron (NR_040265, intron 1 of 2)	MTE2a|LTR|ERVL-MaLR	1011	NR_040265	76432	Mm.261738	NR_040265	ENSMUSG00000097354	2310001H17Rik	AI646108	RIKEN cDNA 2310001H17 gene	ncRNA
mm_169579.1	chr15	22714244	22714248	-	1	NA	exon (NM_001165971, exon 1 of 1)	exon (NM_001165971, exon 1 of 1)	738	NM_001165971	545091	Mm.475598	NM_001165971		Gm5803	EG545091	predicted gene 5803	protein-coding
mm_86077.1	chr9	114781361	114781381	-	1	NA	intron (NM_001252479, intron 1 of 3)	CpG	622	NM_133978	102545	Mm.35600	NM_133978	ENSMUSG00000032436	Cmtm7	AI481279|Cklfsf7|LNV	CKLF-like MARVEL transmembrane domain containing 7	protein-coding
mm_43437.1	chr5	136089949	136089964	+	1	NA	intron (NM_001039103, intron 2 of 19)	intron (NM_001039103, intron 2 of 19)	6040	NM_001039103	54153	Mm.290655	NM_133914	ENSMUSG00000004952	Rasa4	AA793972|AW112107|BB079060|CAPRI|GAPL	RAS p21 protein activator 4	protein-coding
mm_9626.1	chr1	176797316	176797320	-	1	NA	intron (NM_001099637, intron 1 of 19)	intron (NM_001099637, intron 1 of 19)	9806	NM_001099637	545389	Mm.269991	NM_001024722	ENSMUSG00000057335	Cep170	4933426L22Rik|A330004A13Rik|AI195353	centrosomal protein 170	protein-coding
mm_161746.1	chr17	33890576	33890576	-	1	NA	promoter-TSS (NM_001195298)	promoter-TSS (NM_001195298)	57	NM_001195298	100502766	Mm.335713	NM_001195298	ENSMUSG00000079553	Kifc1	100042970|Gm4137|HSET|KNSL2|Kifc5a|Knsl2a|Tctex-7|Tctex-7A|Tctex7|Tctex7a	kinesin family member C1	protein-coding
mm_15903.1	chr2	164968220	164968255	+	1	NA	5' UTR (NM_020333, exon 1 of 26)	5' UTR (NM_020333, exon 1 of 26)	249	NM_020333	57138	Mm.252987	NM_020333	ENSMUSG00000017740	Slc12a5	KCC2|mKIAA1176	solute carrier family 12, member 5	protein-coding
mm_19431.1	chr2	91947478	91947492	-	1	NA	intron (NM_001166597, intron 1 of 31)	intron (NM_001166597, intron 1 of 31)	-2555	NR_105965	102465604		NR_105965	ENSMUSG00000098651	Mir6999	Gm27673|mmu-mir-6999	microRNA 6999	ncRNA
mm_38487.1	chr4	140810647	140810649	-	1	NA	promoter-TSS (NM_011060)	promoter-TSS (NM_011060)	0	NM_011060	18601	Mm.20851	NM_011060	ENSMUSG00000025328	Padi3	AI507004|Pad3|Pdi3|mKIAA4171	peptidyl arginine deiminase, type III	protein-coding
mm_83285.1	chr9	43106181	43106196	-	1	NA	promoter-TSS (NM_027144)	promoter-TSS (NM_027144)	-470	NM_027144	69632	Mm.275266	NM_027144	ENSMUSG00000059495	Arhgef12	2310014B11Rik|AU019857|Larg|mKIAA0382	Rho guanine nucleotide exchange factor (GEF) 12	protein-coding
mm_46244.1	chr5	99240818	99240824	-	1	NA	intron (NM_145839, intron 4 of 13)	intron (NM_145839, intron 4 of 13)	12106	NM_181318	320292	Mm.259074	NM_145839	ENSMUSG00000089809	Rasgef1b	4732452O09Rik|GPIgamma4|Gpig4	RasGEF domain family, member 1B	protein-coding
mm_99836.1	chr11	109011870	109011906	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	91539	NM_015732	12006	Mm.71710	NM_015732	ENSMUSG00000000142	Axin2	Axi1|Axil|Conductin	axin 2	protein-coding
mm_85330.1	chr9	102354627	102354633	-	1	NA	promoter-TSS (NM_173447)	promoter-TSS (NM_173447)	63	NM_001168296	270190	Mm.22897	NM_173447	ENSMUSG00000032537	Ephb1	9330129L11|AW488255|C130099E04Rik|Cek6|ENSMUSG00000074119|Elk|Elkh|Hek6|Net	Eph receptor B1	protein-coding
mm_92530.1	chr10	79533751	79533797	-	1	NA	promoter-TSS (NM_015817)	promoter-TSS (NM_015817)	13	NM_001302442	50784	Mm.28873	NM_015817	ENSMUSG00000052151	Plpp2	Lpp2|PAP2-G|PAP2-gamma|PAP2c|Ppap2c	phospholipid phosphatase 2	protein-coding
mm_162040.1	chr19	56874314	56874314	+	1	NA	promoter-TSS (NM_172840)	promoter-TSS (NM_172840)	-102	NM_172840	240675	Mm.129534	NM_172840	ENSMUSG00000025082	Vwa2	Amaco	von Willebrand factor A domain containing 2	protein-coding
mm_33462.1	chr4	130792740	130792769	+	1	NA	exon (NM_011520, exon 1 of 5)	exon (NM_011520, exon 1 of 5)	217	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_65395.1	chr7	25121521	25121530	-	1	NA	intron (NM_001163554, intron 1 of 14)	intron (NM_001163554, intron 1 of 14)	10935	NM_011138	18987	Mm.76683	NM_011138	ENSMUSG00000008496	Pou2f2	Oct-2|Oct2a|Oct2b|Oct2c|Oct2d|Otf-2|Otf2	POU domain, class 2, transcription factor 2	protein-coding
mm_127871.1	chr15	8444219	8444246	-	1	NA	5' UTR (NM_027707, exon 1 of 47)	5' UTR (NM_027707, exon 1 of 47)	231	NM_027707	71175	Mm.240329	NM_027707	ENSMUSG00000022141	Nipbl	Idn3	Nipped-B homolog (Drosophila)	protein-coding
mm_95093.1	chr11	33963207	33963243	+	1	NA	5' UTR (NM_031169, exon 1 of 4)	5' UTR (NM_031169, exon 1 of 4)	212	NM_031169	16533	Mm.6206	NM_031169	ENSMUSG00000020155	Kcnmb1	BKbeta1	potassium large conductance calcium-activated channel, subfamily M, beta member 1	protein-coding
mm_82538.1	chr9	20814994	20814998	-	1	NA	promoter-TSS (NM_001317388)	promoter-TSS (NM_001317388)	71	NM_001317388	53867	Mm.334994	NM_016919	ENSMUSG00000004098	Col5a3	-	collagen, type V, alpha 3	protein-coding
mm_82519.1	chr9	20642484	20642506	-	1	NA	promoter-TSS (NM_025401)	promoter-TSS (NM_025401)	311	NM_013911	30843	Mm.24608	NM_013911	ENSMUSG00000066892	Fbxl12	3110048D16Rik|Fbl12	F-box and leucine-rich repeat protein 12	protein-coding
mm_130908.1	chr15	102513487	102513490	-	1	NA	intron (NM_001163643, intron 1 of 15)	B2_Mm2|SINE|B2	3516	NM_001163643	26404	Mm.172897	NM_009582	ENSMUSG00000023050	Map3k12	DLK|MUK|Zpk	mitogen-activated protein kinase kinase kinase 12	protein-coding
mm_27944.1	chr3	79628885	79628885	-	1	NA	promoter-TSS (NM_025794)	promoter-TSS (NM_025794)	-118	NM_025794	66841	Mm.28336	NM_025794	ENSMUSG00000027809	Etfdh	0610010I20Rik|AV001013	electron transferring flavoprotein, dehydrogenase	protein-coding
mm_63196.1	chr7	125607627	125607669	+	1	NA	intron (NM_021887, intron 1 of 8)	L2b|LINE|L2	4219	NM_021887	60504	Mm.155643	NM_021887	ENSMUSG00000030745	Il21r	NILR	interleukin 21 receptor	protein-coding
mm_68515.1	chr7	111735949	111735976	-	1	NA	intron (NM_173739, intron 1 of 10)	intron (NM_173739, intron 1 of 10)	44015	NM_173739	233733	Mm.323322	NM_173739	ENSMUSG00000038296	Galnt18	2900011G21Rik|BC024988|Galntl4	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 18	protein-coding
mm_45842.1	chr5	87697166	87697170	-	1	NA	intron (NM_001286022, intron 2 of 7)	intron (NM_001286022, intron 2 of 7)	2257	NM_001286020	12991	Mm.268737	NM_009972	ENSMUSG00000063157	Csn2	Csnb	casein beta	protein-coding
mm_88660.1	chr10	79997464	79997501	+	1	NA	promoter-TSS (NM_013850)	promoter-TSS (NM_013850)	-126	NM_001347081	27403	Mm.103351	NM_013850	ENSMUSG00000035722	Abca7	ABCX|Abc51	ATP-binding cassette, sub-family A (ABC1), member 7	protein-coding
mm_88550.1	chr10	78592036	78592037	+	1	NA	promoter-TSS (NM_027875)	promoter-TSS (NM_027875)	-72	NM_027875	71709	Mm.86439	NM_027875	ENSMUSG00000032714	Syde1	1200008N06Rik|BB043000|mSYD1A	synapse defective 1, Rho GTPase, homolog 1 (C. elegans)	protein-coding
mm_138376.1	chr17	35016519	35016546	+	1	NA	promoter-TSS (NM_138582)	promoter-TSS (NM_138582)	-47	NM_138582	27762	Mm.56895	NM_138582	ENSMUSG00000007030	Vwa7	C6orf27|D17H6S56E-3|G7c|NG37	von Willebrand factor A domain containing 7	protein-coding
mm_7760.1	chr1	131138140	131138160	-	1	NA	promoter-TSS (NM_145508)	promoter-TSS (NM_145508)	84	NM_145508	226419	Mm.39299	NM_145508	ENSMUSG00000016526	Dyrk3	BC006704	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 3	protein-coding
mm_169317.1	chr14	112432630	112432634	+	1	NA	Intergenic	L1Md_T|LINE|L1	411202	NR_030150	723922		NR_030150	ENSMUSG00000070099	Mir466	Mirn466|mmu-mir-466	microRNA 466	ncRNA
mm_91445.1	chr10	33933395	33933406	-	1	NA	intron (NM_028287, intron 6 of 9)	intron (NM_028287, intron 6 of 9)	17812	NM_028287	72580	Mm.248081	NM_028287	ENSMUSG00000039531	Zufsp	2700019D07Rik	zinc finger with UFM1-specific peptidase domain	protein-coding
mm_172764.1	chr8	92717002	92717002	-	1	NA	Intergenic	Intergenic	42713	NM_001301137	64379	Mm.137247	NM_022428	ENSMUSG00000031738	Irx6	-	Iroquois related homeobox 6 (Drosophila)	protein-coding
mm_61359.1	chr7	68618434	68618446	+	1	NA	promoter-TSS (NR_003648)	promoter-TSS (NR_003648)	-16	NR_003648	384639	Mm.261760	NM_001013781		Gm5334	EG384639	tetraspanin 7 pseudogene	pseudo
mm_13696.1	chr2	117121389	117121399	+	1	NA	5' UTR (NM_001277256, exon 1 of 5)	5' UTR (NM_001277256, exon 1 of 5)	323	NM_033524	114715	Mm.245890	NM_033524	ENSMUSG00000027351	Spred1	5730461F13Rik|AL024345|AW047647	sprouty protein with EVH-1 domain 1, related sequence	protein-coding
mm_167600.1	chr9	50617005	50617020	-	1	NA	promoter-TSS (NM_028300)	promoter-TSS (NM_028300)	-309	NM_028300	72614	Mm.147232	NM_028300	ENSMUSG00000000167	Pih1d2	2700059L22Rik	PIH1 domain containing 2	protein-coding
mm_135191.1	chr16	36367535	36367551	-	1	NA	promoter-TSS (NM_001082546)	promoter-TSS (NM_001082546)	27	NM_001082546	100034684	Mm.383561	NM_001082546	ENSMUSG00000071561	BC100530	-	cDNA sequence BC100530	protein-coding
mm_56523.1	chr6	99521051	99521072	-	1	NA	promoter-TSS (NM_001347345)	promoter-TSS (NM_001347345)	-68	NM_001347345	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_32989.1	chr4	120338397	120338398	+	1	NA	Intergenic	MLT1A1|LTR|ERVL-MaLR	-51136	NM_194060	329934	Mm.277090	NM_194060	ENSMUSG00000052135	Foxo6	-	forkhead box O6	protein-coding
mm_65390.1	chr7	25092549	25092562	-	1	NA	3' UTR (NM_001163556, exon 14 of 14)	3' UTR (NM_001163556, exon 14 of 14)	4620	NR_105855	102465968		NR_105855	ENSMUSG00000098441	Mir6537	Gm27808|mmu-mir-6537	microRNA 6537	ncRNA
mm_119152.1	chr14	31496418	31496423	+	1	NA	intron (NM_028932, intron 1 of 5)	intron (NM_028932, intron 1 of 5)	1341	NM_028932	74427	Mm.491208	NM_028932	ENSMUSG00000021890	Eaf1	4933403C17Rik|AI666536	ELL associated factor 1	protein-coding
mm_119409.1	chr14	44988654	44988672	+	1	NA	5' UTR (NM_008964, exon 1 of 2)	5' UTR (NM_008964, exon 1 of 2)	552	NM_008964	19217	Mm.4630	NM_008964	ENSMUSG00000037759	Ptger2	EP2|Ptgerep2	prostaglandin E receptor 2 (subtype EP2)	protein-coding
mm_119488.1	chr14	47375339	47375375	+	1	NA	intron (NM_001145953, intron 1 of 5)	intron (NM_001145953, intron 1 of 5)	1497	NM_001145953	16854	Mm.248615	NM_010705	ENSMUSG00000050335	Lgals3	GBP|L-34|Mac-2|gal3	lectin, galactose binding, soluble 3	protein-coding
mm_160467.1	chr8	111094632	111094632	+	1	NA	promoter-TSS (NM_198308)	promoter-TSS (NM_198308)	-113	NM_198308	319518	Mm.28350	NM_198308	ENSMUSG00000033624	Pdpr	4930402E16Rik|AU018056|mKIAA1990	pyruvate dehydrogenase phosphatase regulatory subunit	protein-coding
mm_159237.1	chr2	145822625	145822625	+	1	NA	5' UTR (NM_028724, exon 4 of 13)	5' UTR (NM_028724, exon 4 of 13)	36509	NM_028724	74030	Mm.228799	NM_028724	ENSMUSG00000001768	Rin2	2010003K16Rik|4632403N06Rik|AW821980|RASSF4	Ras and Rab interactor 2	protein-coding
mm_35466.1	chr4	40781874	40781895	-	1	NA	Intergenic	Intergenic	-23999	NM_021535	74255	Mm.289929	NM_021535	ENSMUSG00000028409	Smu1	2600001O03Rik|2610203K23Rik|AB044414|AI845086|AW556129|Bwd	smu-1 suppressor of mec-8 and unc-52 homolog (C. elegans)	protein-coding
mm_101112.1	chr11	11945541	11945559	-	1	NA	exon (NM_010345, exon 9 of 17)	exon (NM_010345, exon 9 of 17)	-47406	NM_001190448	13195	Mm.12906	NM_016672	ENSMUSG00000020182	Ddc	Aadc	dopa decarboxylase	protein-coding
mm_139687.1	chr17	57420558	57420571	+	1	NA	intron (NM_010130, intron 12 of 21)	intron (NM_010130, intron 12 of 21)	61878	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_68899.1	chr7	126450179	126450190	-	1	NA	exon (NM_007504, exon 14 of 23)	exon (NM_007504, exon 14 of 23)	12889	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_27880.1	chr3	79173172	79173183	-	1	NA	Intergenic	Intergenic	-27302	NM_001099624	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_138353.1	chr17	34972709	34972729	+	1	NA	promoter-TSS (NM_013558)	promoter-TSS (NM_013558)	16	NM_013558	15482	Mm.14287	NM_013558	ENSMUSG00000007033	Hspa1l	Hsc70t|Msh5	heat shock protein 1-like	protein-coding
mm_137434.1	chr17	26442154	26442156	+	1	NA	3' UTR (NM_001081656, exon 5 of 5)	3' UTR (NM_001081656, exon 5 of 5)	27190	NM_001081656	240055	Mm.133211	NM_001081656	ENSMUSG00000034413	Neurl1b	C230078M08Rik|EG240055	neuralized E3 ubiquitin protein ligase 1B	protein-coding
mm_98271.1	chr11	89008117	89008129	+	1	NA	intron (NM_009546, intron 2 of 8)	B1_Mur4|SINE|Alu	8720	NM_009546	217069	Mm.248445	NM_009546	ENSMUSG00000000275	Trim25	AA960166|AL022677|EFP|Zfp147	tripartite motif-containing 25	protein-coding
mm_123460.1	chr14	65833852	65833866	-	1	NA	5' UTR (NM_028039, exon 1 of 11)	5' UTR (NM_028039, exon 1 of 11)	110	NM_028039	71988	Mm.249280	NM_028039	ENSMUSG00000022034	Esco2	2410004I17Rik|D030072L07Rik	establishment of sister chromatid cohesion N-acetyltransferase 2	protein-coding
mm_40282.1	chr5	43233218	43233237	+	1	NA	promoter-TSS (NM_001177379)	promoter-TSS (NM_001177379)	-236	NM_175937	231207	Mm.7233	NM_175937	ENSMUSG00000039782	Cpeb2	A630055H10Rik|Cpe-bp2	cytoplasmic polyadenylation element binding protein 2	protein-coding
mm_126789.1	chr15	86325230	86325250	+	1	NA	intron (NM_145476, intron 8 of 12)	intron (NM_145476, intron 8 of 12)	110781	NM_145476	223754	Mm.28904	NM_145476	ENSMUSG00000051864	Tbc1d22a	BC023106|D15Ertd781e	TBC1 domain family, member 22a	protein-coding
mm_21566.1	chr2	164200077	164200150	-	1	NA	promoter-TSS (NM_183271)	promoter-TSS (NM_183271)	4	NM_183271	68221	Mm.142735	NM_183271	ENSMUSG00000051769	Wfdc15a	1700049M11Rik|Wfdcl1	WAP four-disulfide core domain 15A	protein-coding
mm_84847.1	chr9	78443077	78443117	-	1	NA	non-coding (NR_125721, exon 1 of 5)	non-coding (NR_125721, exon 1 of 5)	140	NR_125721	214763	Mm.101559	NM_173386	ENSMUSG00000032344	Mb21d1	E330016A19Rik|cGAS	Mab-21 domain containing 1	protein-coding
mm_65105.1	chr7	19304505	19304526	-	1	NA	3' UTR (NM_008036, exon 4 of 4)	3' UTR (NM_008036, exon 4 of 4)	5530	NM_008036	14282	Mm.248335	NM_008036	ENSMUSG00000003545	Fosb	-	FBJ osteosarcoma oncogene B	protein-coding
mm_154837.1	chrX	19167457	19167468	+	1	NA	Intergenic	Intergenic	-20491	NR_029807	723828		NR_029807	ENSMUSG00000065471	Mir222	Mirn222|mir-222|mmu-mir-222	microRNA 222	ncRNA
mm_162180.1	chrX	102802963	102802963	+	1	NA	promoter-TSS (NM_001142691)	promoter-TSS (NM_001142691)	0	NM_001142691	71083	Mm.50914	NM_001142691	ENSMUSG00000067562	Dmrtc1c1	4933424F23Rik|Dmrt8.3|Dmrtc1c	DMRT-like family C1c1	protein-coding
mm_64317.1	chr7	141866772	141866777	+	1	NA	exon (NM_028801, exon 34 of 49)	exon (NM_028801, exon 34 of 49)	27702	NM_028801	74180	Mm.200752	NM_028801	ENSMUSG00000066108	Muc5b	2300002I04Rik|A130042M24|AV085033|MUC5|MUC9|mucin 5b	mucin 5, subtype B, tracheobronchial	protein-coding
mm_133905.1	chr16	97548736	97548764	+	1	NA	intron (NM_013606, intron 7 of 13)	L1_Mur3|LINE|L1	12667	NM_013606	17858	Mm.14157	NM_013606	ENSMUSG00000023341	Mx2	AI528743|Mx-2	MX dynamin-like GTPase 2	protein-coding
mm_32759.1	chr4	116687438	116687474	+	1	NA	exon (NM_011034, exon 2 of 6)	exon (NM_011034, exon 2 of 6)	-1434	NR_040442	100502959	Mm.395400	NR_040442		AV051173	-	expressed sequence AV051173	ncRNA
mm_91224.1	chr10	22058649	22058659	-	1	NA	Intergenic	CpG	9425	NM_053264	114671	Mm.288194	NM_053264	ENSMUSG00000069712	4930444G20Rik	-	RIKEN cDNA 4930444G20 gene	protein-coding
mm_104457.1	chr11	95060932	95060962	-	1	NA	intron (NM_001306071, intron 6 of 24)	MIR|SINE|MIR	8251	NM_001306071	16400	Mm.57035	NM_013565	ENSMUSG00000001507	Itga3	AA407068|CD49C|GAPB3	integrin alpha 3	protein-coding
mm_76373.1	chr8	84800413	84800417	-	1	NA	promoter-TSS (NM_010906)	promoter-TSS (NM_010906)	-77	NM_001081982	18032	Mm.9394	NM_010906	ENSMUSG00000001911	Nfix	CTF|NF-I/X|NF1-X|NFI-X	nuclear factor I/X	protein-coding
mm_60119.1	chr7	35981153	35981153	+	1	NA	Intergenic	Intergenic	-178164	NM_177739	668501	Mm.286296	NM_177739	ENSMUSG00000044452	Zfp507	1810022O10Rik|A230056M16Rik|AL024009|AU021817|BB105092|Gm480|Znf507|mKIAA1084	zinc finger protein 507	protein-coding
mm_93635.1	chr10	117282323	117282327	-	1	NA	promoter-TSS (NM_017372)	promoter-TSS (NM_017372)	-53	NM_017372	17105	Mm.45436	NM_017372	ENSMUSG00000069516	Lyz2	AI326280|Lys|Lysm|Lyzf2|Lyzs|Lzm|Lzm-s1|Lzp	lysozyme 2	protein-coding
mm_133456.1	chr16	89084022	89084025	+	1	NA	Intergenic	Intergenic	-20021	NM_001276278	68637	Mm.384089	NM_001276278	ENSMUSG00000068073	1110025L11Rik	-	RIKEN cDNA 1110025L11 gene	protein-coding
mm_130260.1	chr15	96642801	96642819	-	1	NA	promoter-TSS (NM_001166456)	promoter-TSS (NM_001166456)	103	NM_001166458	105727	Mm.103568	NM_134086	ENSMUSG00000023169	Slc38a1	AA408026|AA409865|AL022800|AU015942|NAT2	solute carrier family 38, member 1	protein-coding
mm_57791.1	chr6	129274410	129274417	-	1	NA	intron (NM_001033122, intron 1 of 4)	intron (NM_001033122, intron 1 of 4)	956	NM_001033122	12515	Mm.74745	NM_001033122	ENSMUSG00000030156	Cd69	5830438K24Rik|AI452015|AIM|VEA	CD69 antigen	protein-coding
mm_98780.1	chr11	96807793	96807802	+	1	NA	intron (NM_007622, intron 5 of 5)	(T)n|Simple_repeat|Simple_repeat	-9641	NR_033523	629750	Mm.390396	NR_033523		Gm11517	OTTMUSG00000001634	ubiquitin A-52 residue ribosomal protein fusion product 1 pseudogene	pseudo
mm_62592.1	chr7	105641053	105641070	+	1	NA	promoter-TSS (NM_029802)	promoter-TSS (NM_029802)	521	NM_019502	14356	Mm.220330	NM_019502	ENSMUSG00000089847	Timm10b	Fxc1|Tim10b|Tim9b	translocase of inner mitochondrial membrane 10B	protein-coding
mm_101685.1	chr11	40694868	40694923	-	1	NA	5' UTR (NM_001199274, exon 1 of 7)	5' UTR (NM_001199274, exon 1 of 7)	308	NM_001199274	108645	Mm.293771	NM_134017	ENSMUSG00000042032	Mat2b	1110064C04Rik|2410018D16Rik|AI182287|AU022853|MAT-II|MATIIbeta|TGR	methionine adenosyltransferase II, beta	protein-coding
mm_31187.1	chr4	43555910	43555937	+	1	NA	exon (NM_011602, exon 4 of 57)	exon (NM_011602, exon 4 of 57)	6660	NM_011602	21894	Mm.208601	NM_011602	ENSMUSG00000028465	Tln1	Tln	talin 1	protein-coding
mm_15074.1	chr2	153117609	153117630	+	1	NA	intron (NM_001172117, intron 1 of 12)	intron (NM_001172117, intron 1 of 12)	9151	NM_010407	15162	Mm.715	NM_010407	ENSMUSG00000003283	Hck	AI849071|Bmk	hemopoietic cell kinase	protein-coding
mm_152822.1	chr19	23136366	23136383	-	1	NA	Intergenic	CpG	-4852	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_130181.1	chr15	93398620	93398630	-	1	NA	promoter-TSS (NM_026025)	promoter-TSS (NM_026025)	161	NM_001285863	223828	Mm.74208	NM_146062	ENSMUSG00000036167	Pphln1	CR|HSPC206|HSPC232	periphilin 1	protein-coding
mm_158792.1	chrX	167229097	167229108	-	1	NA	Intergenic	Intergenic	-19884	NM_021278	19241	Mm.142729	NM_021278	ENSMUSG00000049775	Tmsb4x	Ptmb4|Tb4	thymosin, beta 4, X chromosome	protein-coding
mm_105888.1	chr11	114933738	114933752	-	1	NA	intron (NM_199221, intron 1 of 3)	intron (NM_199221, intron 1 of 3)	641	NM_001347651	217304	Mm.185355	NM_199221	ENSMUSG00000063193	Cd300lb	CLM-7|Clm7|Gm253|LMIR5	CD300 molecule like family member B	protein-coding
mm_118987.1	chr14	28504737	28504762	+	1	NA	promoter-TSS (NM_009524)	promoter-TSS (NM_009524)	-724	NM_009524	22418	Mm.287544	NM_009524	ENSMUSG00000021994	Wnt5a	8030457G12Rik|Wnt-5a	wingless-type MMTV integration site family, member 5A	protein-coding
mm_23840.1	chr3	82358206	82358213	+	1	NA	5' UTR (NM_001081230, exon 1 of 14)	5' UTR (NM_001081230, exon 1 of 14)	137	NM_001081230	213582	Mm.271269	NM_001081230	ENSMUSG00000033900	Map9	5033421J10Rik|5330427D05Rik|ASAP|Mtap9	microtubule-associated protein 9	protein-coding
mm_35644.1	chr4	43522728	43522750	-	1	NA	exon (NM_009416, exon 2 of 9)	exon (NM_009416, exon 2 of 9)	815	NM_009416	22004	Mm.646	NM_009416	ENSMUSG00000028464	Tpm2	Tpm-2|Trop-2	tropomyosin 2, beta	protein-coding
mm_55760.1	chr6	78466321	78466339	-	1	NA	TTS (NM_011260)	TTS (NM_011260)	2544	NM_011260	19695	Mm.252385	NM_011260	ENSMUSG00000030017	Reg3g	AI449515|REG-3-gamma|reg III-gamma	regenerating islet-derived 3 gamma	protein-coding
mm_59722.1	chr7	28785366	28785384	+	1	NA	intron (NM_001122765, intron 8 of 14)	intron (NM_001122765, intron 8 of 14)	-3594	NM_177158	320435	Mm.74632	NM_177158	ENSMUSG00000051735	Rinl	5830482F20Rik|9930116N10Rik	Ras and Rab interactor-like	protein-coding
mm_131036.1	chr16	3872369	3872385	+	1	NA	promoter-TSS (NM_001033159)	promoter-TSS (NM_001033159)	-3	NM_001033159	71063	Mm.379190	NM_001033159	ENSMUSG00000039789	Zfp597	4933407K12Rik|AI462383|AI666357	zinc finger protein 597	protein-coding
mm_171178.1	chr3	35754150	35754150	+	1	NA	promoter-TSS (NM_029570)	promoter-TSS (NM_029570)	12	NM_029570	76295	Mm.239416	NM_029570	ENSMUSG00000037400	Atp11b	1110019I14Rik|ATPIF|ATPIR|mKIAA0956	ATPase, class VI, type 11B	protein-coding
mm_79691.1	chr9	60527242	60527250	+	1	NA	intron (NR_040464, intron 2 of 3)	intron (NR_040464, intron 2 of 3)	-16211	NM_001040426	207596	Mm.28791	NM_172444	ENSMUSG00000032289	Thsd4	ADAMTSL-6|ADAMTSL6|AI585901|Adamtsl4|B230114P05Rik	thrombospondin, type I, domain containing 4	protein-coding
mm_22080.1	chr2	168765305	168765315	-	1	NA	intron (NM_201395, intron 1 of 3)	intron (NM_201395, intron 1 of 3)	1891	NM_201395	99377	Mm.434054	NM_175303	ENSMUSG00000027547	Sall4	5730441M18Rik|AA407717|AL022809|AW536104|C330011P20Rik|C78083|C78563|Tex20	sal-like 4 (Drosophila)	protein-coding
mm_99993.1	chr11	114765364	114765438	+	1	NA	promoter-TSS (NM_001102615)	promoter-TSS (NM_001102615)	12	NM_001102615	286942	Mm.308713	NM_001102615	ENSMUSG00000010021	Kif19a	Kif19	kinesin family member 19A	protein-coding
mm_130500.1	chr15	98831317	98831358	-	1	NA	TTS (NM_001033276)	TTS (NM_001033276)	171	NM_016781	19082	Mm.6670	NM_016781	ENSMUSG00000067713	Prkag1	AA571379|BB036179|Prkaac	protein kinase, AMP-activated, gamma 1 non-catalytic subunit	protein-coding
mm_153004.1	chr19	30175380	30175394	-	1	NA	promoter-TSS (NM_138595)	promoter-TSS (NM_138595)	54	NM_138595	104174	Mm.274852	NM_138595	ENSMUSG00000024827	Gldc	D030049L12Rik|D19Wsu57e	glycine decarboxylase	protein-coding
mm_126433.1	chr15	80597721	80597765	+	1	NA	intron (NM_001289442, intron 1 of 7)	intron (NM_001289442, intron 1 of 7)	25146	NM_001289442	17444	Mm.12947	NM_010815	ENSMUSG00000042351	Grap2	GRAP-2|GRB2L|GRBLG|GRID|Gads|GrbX|Grf40|GrpL|Mona|P38	GRB2-related adaptor protein 2	protein-coding
mm_26413.1	chr3	142608593	142608621	+	1	NA	intron (NM_010259, intron 8 of 10)	intron (NM_010259, intron 8 of 10)	-12056	NM_010260	14469	Mm.24038	NM_010260	ENSMUSG00000028270	Gbp2	-	guanylate binding protein 2	protein-coding
mm_87615.1	chr10	57794371	57794390	+	1	NA	promoter-TSS (NM_020561)	promoter-TSS (NM_020561)	-164	NM_020561	57319	Mm.2379	NM_020561	ENSMUSG00000019872	Smpdl3a	0610010C24Rik|AI529588|ASM3A|ASML3|ASML3A	sphingomyelin phosphodiesterase, acid-like 3A	protein-coding
mm_66409.1	chr7	44480180	44480188	-	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-4333	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_76892.1	chr8	105701078	105701118	-	1	NA	promoter-TSS (NM_019695)	promoter-TSS (NM_019695)	-3	NM_001012638	497652	Mm.12964	NM_001012638	ENSMUSG00000038000	Acd	-	adrenocortical dysplasia	protein-coding
mm_42018.1	chr5	108268930	108268980	+	1	NA	promoter-TSS (NM_026106)	promoter-TSS (NM_026106)	58	NM_026106	13486	Mm.303534	NM_026106	ENSMUSG00000029265	Dr1	1700121L09Rik|Dr1l|NC2|NC2beta	down-regulator of transcription 1	protein-coding
mm_127666.1	chr15	102625585	102625602	+	1	NA	promoter-TSS (NM_001310070)	promoter-TSS (NM_001310070)	-129	NM_001310066	223922	Mm.208714	NM_146065	ENSMUSG00000052414	Atf7	1110012F10Rik|9430065F09Rik|AI549878|C130020M04Rik	activating transcription factor 7	protein-coding
mm_59712.1	chr7	28756139	28756157	+	1	NA	promoter-TSS (NM_001195091)	promoter-TSS (NM_001195091)	-26	NM_001195091	100504112	Mm.379654	NM_001195091	ENSMUSG00000096257	Ccer2	EG624918|Gm6537	coiled-coil glutamate-rich protein 2	protein-coding
mm_55910.1	chr6	83762504	83762511	-	1	NA	promoter-TSS (NR_105027)	promoter-TSS (NR_105027)	1	NR_105027	67934	Mm.126190	NR_105027	ENSMUSG00000099354	1700124L16Rik	-	RIKEN cDNA 1700124L16 gene	ncRNA
mm_109123.1	chr12	105706108	105706158	+	1	NA	5' UTR (NM_030187, exon 1 of 18)	5' UTR (NM_030187, exon 1 of 18)	151	NM_030187	78801	Mm.36006	NM_030187	ENSMUSG00000041323	Ak7	4930502N02Rik|AK 7	adenylate kinase 7	protein-coding
mm_105039.1	chr11	100584716	100584727	-	1	NA	intron (NM_019795, intron 10 of 13)	intron (NM_019795, intron 10 of 13)	8830	NM_001146318	12799	Mm.15711	NM_009923	ENSMUSG00000006782	Cnp	CNPase|Cnp-1|Cnp1	2',3'-cyclic nucleotide 3' phosphodiesterase	protein-coding
mm_25937.1	chr3	131466704	131466710	+	1	NA	Intergenic	Intergenic	-98061	NM_001289479	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_52339.1	chr6	110663424	110663427	+	1	NA	intron (NM_001346640, intron 1 of 10)	intron (NM_001346640, intron 1 of 10)	17827	NM_177328	108073	Mm.240881	NM_177328	ENSMUSG00000056755	Grm7	6330570A01Rik|BB176677|C030018L03|E130018M02Rik|Gpr1g|Gprc1g|SMN2|Tg(SMN2)89Ahmb|mGluR7	glutamate receptor, metabotropic 7	protein-coding
mm_102510.1	chr11	60777227	60777239	-	1	NA	promoter-TSS (NM_001085440)	promoter-TSS (NM_001085440)	132	NM_009410	21975	Mm.10708	NM_009410	ENSMUSG00000002814	Top3a	-	topoisomerase (DNA) III alpha	protein-coding
mm_131924.1	chr16	23320864	23320876	+	1	NA	intron (NM_001252505, intron 3 of 7)	intron (NM_001252505, intron 3 of 7)	30400	NM_001252506	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_37809.1	chr4	130914129	130914144	-	1	NA	intron (NM_010686, intron 1 of 7)	L3b|LINE|CR1	802	NM_010686	16792	Mm.271868	NM_010686	ENSMUSG00000028581	Laptm5	E3	lysosomal-associated protein transmembrane 5	protein-coding
mm_81633.1	chr9	110880158	110880187	+	1	NA	promoter-TSS (NM_001146059)	promoter-TSS (NM_001146059)	-2	NM_146228	235633	Mm.86338	NM_146228	ENSMUSG00000044037	Als2cl	79H19D|79H19E|BC022645|D930044G19Rik|mRn.49018	ALS2 C-terminal like	protein-coding
mm_110473.1	chr12	51830090	51830105	-	1	NA	promoter-TSS (NM_144788)	promoter-TSS (NM_144788)	-561	NM_144788	207304	Mm.249391	NM_144788	ENSMUSG00000035247	Hectd1	A630086P08Rik|AI844876|b2b327Clo|opm	HECT domain containing 1	protein-coding
mm_150458.1	chr19	38264630	38264647	+	1	NA	promoter-TSS (NM_020278)	promoter-TSS (NM_020278)	-144	NM_020278	56839	Mm.298251	NM_020278	ENSMUSG00000067242	Lgi1	BB130740	leucine-rich repeat LGI family, member 1	protein-coding
mm_106516.1	chr11	120549696	120549728	-	1	NA	promoter-TSS (NM_001033231)	promoter-TSS (NM_001033231)	15	NM_001033231	192173	Mm.262300	NM_001033231	ENSMUSG00000061111	Fam195b	Mcrip1	family with sequence similarity 195, member B	protein-coding
mm_138802.1	chr17	38639444	38639453	+	1	NA	promoter-TSS (NM_001177586)	promoter-TSS (NM_001177586)	1	NM_001177586	100126768	Mm.471528	NM_001177586	ENSMUSG00000092342	Esp31	Gm20516	exocrine gland secreted peptide 31	protein-coding
mm_112710.1	chr13	18957933	18957942	+	1	NA	intron (NM_175007, intron 1 of 20)	intron (NM_175007, intron 1 of 20)	9586	NM_001289546	218038	Mm.101650	NM_175007	ENSMUSG00000021314	Amph	-	amphiphysin	protein-coding
mm_55029.1	chr6	48940181	48940183	-	1	NA	Intergenic	Intergenic	10286	NM_001081273	69761	Mm.333053	NM_001081273	ENSMUSG00000029813	1600015I10Rik	AI429442|Doxl1	RIKEN cDNA 1600015I10 gene	protein-coding
mm_109329.1	chr12	109565928	109565939	+	1	NA	non-coding (NR_003633, exon 5 of 5)	non-coding (NR_003633, exon 5 of 5)	2241	NR_030427	791079		NR_030427	ENSMUSG00000076451	Mir770	Mirn770|mir-770|mmu-mir-770	microRNA 770	ncRNA
mm_62058.1	chr7	92447608	92447608	+	1	NA	3' UTR (NM_001243047, exon 11 of 11)	3' UTR (NM_001243047, exon 11 of 11)	-113541	NM_025515	66365	Mm.21173	NM_025515	ENSMUSG00000030613	Ccdc90b	2310015N07Rik|C86558	coiled-coil domain containing 90B	protein-coding
mm_134715.1	chr16	22895277	22895284	-	1	NA	promoter-TSS (NR_110508)	promoter-TSS (NR_110508)	-894	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_170325.1	chr18	42200653	42200657	+	1	NA	Intergenic	Intergenic	-3946	NM_027072	69401	Mm.34841	NM_027072	ENSMUSG00000059455	Plac8l1	1700009N18Rik|1700015M15Rik	PLAC8-like 1	protein-coding
mm_47892.1	chr5	134721557	134721568	-	1	NA	intron (NM_007925, intron 16 of 36)	intron (NM_007925, intron 16 of 36)	25761	NM_007925	13717	Mm.275320	NM_007925	ENSMUSG00000029675	Eln	AI385707|AI480567|E030024M20Rik	elastin	protein-coding
mm_102858.1	chr11	69399321	69399338	-	1	NA	3' UTR (NM_001017426, exon 23 of 23)	3' UTR (NM_001017426, exon 23 of 23)	-1095	NM_025915	67020	Mm.390406	NM_025915	ENSMUSG00000045377	Tmem88	2600017H02Rik	transmembrane protein 88	protein-coding
mm_135929.1	chr16	72823666	72823666	-	1	NA	intron (NM_019413, intron 2 of 28)	intron (NM_019413, intron 2 of 28)	160517	NM_019413	19876	Mm.310772	NM_019413	ENSMUSG00000022883	Robo1	AW494633|AW742721|DUTT1|Gm310	roundabout guidance receptor 1	protein-coding
mm_76854.1	chr8	105349224	105349234	-	1	NA	5' UTR (NM_001081332, exon 1 of 16)	5' UTR (NM_001081332, exon 1 of 16)	971	NM_001081332	277973	Mm.334766	NM_001081332	ENSMUSG00000014786	Slc9a5	Gm696	solute carrier family 9 (sodium/hydrogen exchanger), member 5	protein-coding
mm_106986.1	chr12	10369968	10369984	+	1	NA	promoter-TSS (NM_001310582)	promoter-TSS (NM_001310582)	5	NM_001310582	70881	Mm.272843	NM_027588	ENSMUSG00000020622	Nt5c1b	4921514H13Rik|AIRP|CN-IB|cN1B	5'-nucleotidase, cytosolic IB	protein-coding
mm_125920.1	chr15	76190475	76190482	+	1	NA	exon (NM_201393, exon 11 of 32)	exon (NM_201393, exon 11 of 32)	5232	NM_201394	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
mm_126350.1	chr15	79911082	79911086	+	1	NA	Intergenic	Intergenic	16061	NM_001347041	80287	Mm.284059	NM_030255	ENSMUSG00000009585	Apobec3	Apobec|Arp3|BC003314|Cem15|Rfv3	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 3	protein-coding
mm_81161.1	chr9	107296844	107296900	+	1	NA	5' UTR (NM_009895, exon 1 of 3)	5' UTR (NM_009895, exon 1 of 3)	213	NM_009895	12700	Mm.4592	NM_009895	ENSMUSG00000032578	Cish	CIS-1|CIS1|Cis|F17|F23|SOCS	cytokine inducible SH2-containing protein	protein-coding
mm_62741.1	chr7	111029008	111029018	+	1	NA	promoter-TSS (NM_009431)	promoter-TSS (NM_009431)	62	NM_009431	22083	Mm.255858	NM_009431	ENSMUSG00000005609	Ctr9	AA409336|Sh2bp1|Tsbp|Tsp|mKIAA0155	CTR9 homolog, Paf1/RNA polymerase II complex component	protein-coding
mm_22469.1	chr3	4797338	4797364	+	1	NA	Intergenic	Intergenic	-1357	NR_045272	100503859	Mm.75172	NR_045272	ENSMUSG00000098659	1110015O18Rik	-	RIKEN cDNA 1110015O18 gene	ncRNA
mm_89882.1	chr10	108333257	108333292	+	1	NA	exon (NM_054056, exon 2 of 7)	exon (NM_054056, exon 2 of 7)	1085	NM_054056	114774	Mm.391419	NM_054056	ENSMUSG00000035873	Pawr	2310001G03Rik|PAR4|Par-4	PRKC, apoptosis, WT1, regulator	protein-coding
mm_127418.1	chr15	101260694	101260709	+	1	NA	Intergenic	Intergenic	-6145	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_140915.1	chr17	24169649	24169713	-	1	NA	promoter-TSS (NM_009729)	promoter-TSS (NM_009729)	-252	NM_009729	11984	Mm.30155	NM_009729	ENSMUSG00000024121	Atp6v0c	Atp6c|Atp6c2|Atp6l|Atpl|Atpl-rs1|PL16|VATL|Vma3	ATPase, H+ transporting, lysosomal V0 subunit C	protein-coding
mm_63022.1	chr7	121034582	121034718	+	1	NA	5' UTR (NM_021554, exon 1 of 5)	5' UTR (NM_021554, exon 1 of 5)	205	NM_021554	59052	Mm.29122	NM_021554	ENSMUSG00000030876	Mettl9	0610012D09Rik|AA517660|Drev|MNCb-5680	methyltransferase like 9	protein-coding
mm_154463.1	chrM	3308	3337	-	1	NA	NA	Intergenic	NA	NA								
mm_90145.1	chr10	118141532	118141533	+	1	NA	promoter-TSS (NM_010785)	promoter-TSS (NM_010785)	-255	NM_001162904	17245	Mm.101191	NM_010785	ENSMUSG00000020212	Mdm1	Arrd2|Mdm-1	transformed mouse 3T3 cell double minute 1	protein-coding
mm_60570.1	chr7	44481525	44481541	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-2984	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_19579.1	chr2	101649418	101649422	-	1	NA	intron (NM_009019, intron 1 of 1)	intron (NM_009019, intron 1 of 1)	112	NM_009019	19373	Mm.828	NM_009019	ENSMUSG00000061311	Rag1	Rag-1	recombination activating gene 1	protein-coding
mm_125907.1	chr15	75996763	75996778	+	1	NA	intron (NM_177922, intron 7 of 13)	intron (NM_177922, intron 7 of 13)	3001	NM_177922	332110	Mm.40843	NM_177922	ENSMUSG00000063704	Mapk15	BC048082	mitogen-activated protein kinase 15	protein-coding
mm_68198.1	chr7	104380099	104380100	-	1	NA	Intergenic	Intergenic	-21453	NM_175648	244183	Mm.347647	NM_175648	ENSMUSG00000052749	Trim30b	A530023O14Rik|Trim30-1	tripartite motif-containing 30B	protein-coding
mm_68148.1	chr7	102249543	102249559	-	1	NA	intron (NM_019566, intron 1 of 1)	intron (NM_019566, intron 1 of 1)	567	NM_019566	56212	Mm.259795	NM_019566	ENSMUSG00000073982	Rhog	2810426G09Rik|Arhg|Sid10750	ras homolog family member G	protein-coding
mm_7448.1	chr1	120258846	120258866	-	1	NA	intron (NM_001085409, intron 2 of 5)	intron (NM_001085409, intron 2 of 5)	6424	NM_133186	68428	Mm.181033	NM_133186	ENSMUSG00000026389	Steap3	1010001D01Rik|Tsap6|pHyde	STEAP family member 3	protein-coding
mm_166388.1	chr5	134139566	134139566	-	1	NA	3' UTR (NM_030719, exon 9 of 9)	3' UTR (NM_030719, exon 9 of 9)	37201	NM_033572	94254	Mm.29508	NM_033572	ENSMUSG00000061979	Rcc1l	5730496C04Rik|AU019812|Wbscr16	reculator of chromosome condensation 1 like	protein-coding
mm_116952.1	chr13	56135785	56135810	-	1	NA	promoter-TSS (NM_001159515)	promoter-TSS (NM_001159515)	-247	NM_001159513	26914	Mm.283802	NM_012015	ENSMUSG00000015937	H2afy	H2AF12M|mH2a1|macroH2A1	H2A histone family, member Y	protein-coding
mm_72465.1	chr8	83332612	83332647	+	1	NA	promoter-TSS (NM_178736)	promoter-TSS (NM_178736)	-143	NM_178736	244548	Mm.38762	NM_178736	ENSMUSG00000035151	Elmod2	9830169G11Rik	ELMO/CED-12 domain containing 2	protein-coding
mm_1444.1	chr1	67228238	67228248	+	1	NA	exon (NM_001080809, exon 36 of 38)	exon (NM_001080809, exon 36 of 38)	105216	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_19545.1	chr2	98662906	98662920	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	1195256	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_71724.1	chr8	61976380	61976394	+	1	NA	intron (NM_001293783, intron 17 of 37)	RLTR31_Mur|LTR|ERVK	48300	NM_001293783	234311	Mm.275233	NM_144928	ENSMUSG00000037921	Ddx60	9830118M07	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	protein-coding
mm_109308.1	chr12	109560769	109560791	+	1	NA	non-coding (NR_003633, exon 5 of 5)	non-coding (NR_003633, exon 5 of 5)	-2912	NR_030427	791079		NR_030427	ENSMUSG00000076451	Mir770	Mirn770|mir-770|mmu-mir-770	microRNA 770	ncRNA
mm_89010.1	chr10	81633695	81633710	+	1	NA	intron (NM_027480, intron 2 of 19)	intron (NM_027480, intron 2 of 19)	5162	NM_027480	70615	Mm.304382	NM_027480	ENSMUSG00000054708	Ankrd24	4631433D01Rik|5730519E19Rik|D10Bur2e	ankyrin repeat domain 24	protein-coding
mm_31431.1	chr4	48124904	48124938	+	1	NA	promoter-TSS (NM_026343)	promoter-TSS (NM_026343)	2	NM_026343	67727	Mm.171334	NM_026343	ENSMUSG00000061455	Stx17	4833418L03Rik|6330411F21Rik|9030425C21Rik|AW048351	syntaxin 17	protein-coding
mm_83797.1	chr9	52679678	52679686	-	1	NA	promoter-TSS (NM_178906)	promoter-TSS (NM_178906)	98	NM_001286641	330941	Mm.335160	NM_177907	ENSMUSG00000078307	AI593442	E130102D23	expressed sequence AI593442	protein-coding
mm_72428.1	chr8	82863399	82863409	+	1	NA	promoter-TSS (NM_177378)	promoter-TSS (NM_177378)	48	NM_177378	330812	Mm.491438	NM_177378	ENSMUSG00000047747	Rnf150	A630007N06Rik|C030044C12Rik|Greul5|mKIAA1214	ring finger protein 150	protein-coding
mm_67697.1	chr7	89518222	89518232	-	1	NA	promoter-TSS (NM_029614)	promoter-TSS (NM_029614)	-641	NM_029614	76453	Mm.250438	NM_029614	ENSMUSG00000039405	Prss23	2310046G15Rik|4930479H08Rik|AI790574|Spuve	protease, serine 23	protein-coding
mm_106128.1	chr11	116433793	116433822	-	1	NA	promoter-TSS (NR_003376)	promoter-TSS (NR_003376)	-287	NM_176902	319370	Mm.258466	NM_176902	ENSMUSG00000050628	Ubald2	1110014K08Rik|D030012E24Rik|Fam100b	UBA-like domain containing 2	protein-coding
mm_44814.1	chr5	33629536	33629544	-	1	NA	promoter-TSS (NM_178390)	promoter-TSS (NM_178390)	95	NM_178390	74504	Mm.294695	NM_178390	ENSMUSG00000037339	Fam53a	2410018C17Rik|5430419M09Rik|Dntnp	family with sequence similarity 53, member A	protein-coding
mm_60086.1	chr7	34389748	34389803	+	1	NA	promoter-TSS (NM_025948)	promoter-TSS (NM_025948)	-235	NM_025948	67070	Mm.276503	NM_025948	ENSMUSG00000066568	Lsm14a	2700023B17Rik|AA407828|AU017544|Tral	LSM14A mRNA processing body assembly factor	protein-coding
mm_140830.1	chr17	23645067	23645073	-	1	NA	5' UTR (NM_001033339, exon 1 of 10)	5' UTR (NM_001033339, exon 1 of 10)	199	NM_001033339	240047	Mm.235343	NM_001033339	ENSMUSG00000023903	Mmp25	F730048C11Rik|Leukolysin|MMP20|MT6-MMP	matrix metallopeptidase 25	protein-coding
mm_143291.1	chr17	65884761	65884778	-	1	NA	5' UTR (NM_001198949, exon 1 of 10)	5' UTR (NM_001198949, exon 1 of 10)	154	NM_001198949	19765	Mm.17009	NM_009067	ENSMUSG00000024096	Ralbp1	RLIP76|Rip1	ralA binding protein 1	protein-coding
mm_151374.1	chr19	55932743	55932746	+	1	NA	non-coding (NR_138565, exon 16 of 16)	non-coding (NR_138565, exon 16 of 16)	37423	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_157392.1	chrX	38406706	38406727	-	1	NA	intron (NM_001017959, intron 8 of 8)	L1M3|LINE|L1	49744	NM_010685	16784	Mm.486	NM_010685	ENSMUSG00000016534	Lamp2	CD107b|LGP-B|Lamp II|Lamp-2|Lamp-2a|Lamp-2b|Lamp-2c|Mac3	lysosomal-associated membrane protein 2	protein-coding
mm_122918.1	chr14	54959836	54959866	-	1	NA	exon (NM_010856, exon 14 of 39)	exon (NM_010856, exon 14 of 39)	6756	NM_001164171	17888	Mm.290003	NM_010856	ENSMUSG00000040752	Myh6	A830009F23Rik|AA517445|Myhc-a|Myhca|alpha-MHC	myosin, heavy polypeptide 6, cardiac muscle, alpha	protein-coding
mm_55036.1	chr6	48987445	48987448	-	1	NA	exon (NM_172888, exon 1 of 5)	exon (NM_172888, exon 1 of 5)	585	NM_172888	243377	Mm.446302	NM_172888	ENSMUSG00000039215	Svs1	9530003A11	seminal vesicle secretory protein 1	protein-coding
mm_107145.1	chr12	21543276	21543281	+	1	NA	Intergenic	CpG	-125842	NM_011739	22630	Mm.289630	NM_011739	ENSMUSG00000076432	Ywhaq	2700028P07Rik|AA409740|AU021156|R74690	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide	protein-coding
mm_1317.1	chr1	65080527	65080543	+	1	NA	exon (NM_144761, exon 3 of 3)	exon (NM_144761, exon 3 of 3)	1755	NM_144761	12965	Mm.440053	NM_144761	ENSMUSG00000073658	Crygb	Cryg-3|DGcry-3|Nop	crystallin, gamma B	protein-coding
mm_96385.1	chr11	67245432	67245468	+	1	NA	exon (NM_010855, exon 13 of 40)	exon (NM_010855, exon 13 of 40)	7638	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_167858.1	chrX	12826329	12826330	+	1	NA	Intergenic	Intergenic	64051	NR_045852	552913	Mm.216846	NR_045852	ENSMUSG00000085891	Gm14634	OTTMUSG00000017535	predicted gene 14634	ncRNA
mm_159201.1	chr2	120609632	120609632	-	1	NA	promoter-TSS (NM_025657)	promoter-TSS (NM_025657)	37	NM_001290807	66296	Mm.221900	NM_025475	ENSMUSG00000027285	Haus2	1700101G24Rik|2410007P03Rik|AU020217|Cep27	HAUS augmin-like complex, subunit 2	protein-coding
mm_34929.1	chr4	155831631	155831698	+	1	NA	5' UTR (NM_025338, exon 1 of 4)	5' UTR (NM_025338, exon 1 of 4)	395	NM_025338	66077	Mm.28999	NM_025338	ENSMUSG00000065990	Aurkaip1	0610033H09Rik|Aip|Akip|MRP-S38	aurora kinase A interacting protein 1	protein-coding
mm_13635.1	chr2	114047285	114047297	+	1	NA	TTS (NM_009608)	TTS (NM_009608)	5584	NM_009608	11464	Mm.686	NM_009608	ENSMUSG00000068614	Actc1	Actc-1	actin, alpha, cardiac muscle 1	protein-coding
mm_49612.1	chr6	30747337	30747361	+	1	NA	TTS (NM_017478)	TTS (NM_017478)	6050	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_75380.1	chr8	45382132	45382142	-	1	NA	5' UTR (NM_153535, exon 1 of 14)	5' UTR (NM_153535, exon 1 of 14)	154	NM_153535	212326	Mm.51259	NM_153535	ENSMUSG00000070044	Fam149a	AW213256|mKIAA4166	family with sequence similarity 149, member A	protein-coding
mm_65742.1	chr7	28528079	28528087	-	1	NA	Intergenic	Intergenic	5247	NM_177396	338374	Mm.246799	NM_177396	ENSMUSG00000060747	Ifnl3	IFL-1|IL-28B|INF-alpha|INF-lambda|Il28|Il28b	interferon lambda 3	protein-coding
mm_1501.1	chr1	72236500	72236524	+	1	NA	Intergenic	CpG	-24205	NM_001005423	381269	Mm.422636	NM_001005423	ENSMUSG00000039395	Mreg	Gm974|Wdt2|dsu	melanoregulin	protein-coding
mm_145614.1	chr18	61105617	61105635	+	1	NA	promoter-TSS (NM_001037859)	promoter-TSS (NM_001037859)	54	NM_001037859	12978	Mm.22574	NM_007779	ENSMUSG00000024621	Csf1r	AI323359|CD115|CSF-1R|Csfmr|Fim-2|Fim2|Fms|M-CSF-R|M-CSFR	colony stimulating factor 1 receptor	protein-coding
mm_8277.1	chr1	139923101	139923102	-	1	NA	Intergenic	Intergenic	-64402	NM_001025575	545366	Mm.439660	NM_001025575	ENSMUSG00000033898	Cfhr2	Cfhrb_4/2	complement factor H-related 2	protein-coding
mm_95937.1	chr11	58382334	58382348	+	1	NA	exon (NM_001083884, exon 3 of 7)	exon (NM_001083884, exon 3 of 7)	1695	NM_001330197	70163	Mm.24119	NM_027339	ENSMUSG00000013643	Lypd8	2210415F13Rik	LY6/PLAUR domain containing 8	protein-coding
mm_71832.1	chr8	68896795	68896804	+	1	NA	exon (NM_008509, exon 6 of 10)	exon (NM_008509, exon 6 of 10)	16244	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_62347.1	chr7	100498390	100498408	+	1	NA	exon (NM_011671, exon 6 of 8)	exon (NM_011671, exon 6 of 8)	5041	NM_011671	22228	Mm.171378	NM_011671	ENSMUSG00000033685	Ucp2	Slc25a8	uncoupling protein 2 (mitochondrial, proton carrier)	protein-coding
mm_88912.1	chr10	81179874	81179907	+	1	NA	TTS (NR_028549)	TTS (NR_028549)	929	NR_028549	100217454		NR_028549	ENSMUSG00000064441	Snord37	MBII-376	small nucleolar RNA, C/D box 37	snoRNA
mm_149377.1	chr19	11375582	11375592	+	1	NA	promoter-TSS (NM_001310331)	promoter-TSS (NM_001310331)	99	NM_001310331	666907		NM_001310331	ENSMUSG00000101389	Ms4a4a	EG666907	membrane-spanning 4-domains, subfamily A, member 4A	protein-coding
mm_27758.1	chr3	69598961	69599003	-	1	NA	promoter-TSS (NM_020026)	promoter-TSS (NM_020026)	-22	NM_020026	26879	Mm.153710	NM_020026	ENSMUSG00000043300	B3galnt1	B3galt3|b3GT3	UDP-GalNAc:betaGlcNAc beta 1,3-galactosaminyltransferase, polypeptide 1	protein-coding
mm_121413.1	chr14	119544499	119544502	+	1	NA	intron (NM_015820, intron 1 of 1)	intron (NM_015820, intron 1 of 1)	-204727	NR_045621	75432	Mm.443277	NR_045621	ENSMUSG00000100274	1700006F04Rik	-	RIKEN cDNA 1700006F04 gene	ncRNA
mm_32469.1	chr4	107707067	107707072	+	1	NA	Intergenic	Intergenic	-22907	NM_019872	56296	Mm.141324	NM_019872	ENSMUSG00000028610	Dmrtb1	Dmrt6|Prp13	DMRT-like family B with proline-rich C-terminal, 1	protein-coding
mm_39347.1	chr5	8893924	8893932	+	1	NA	intron (NM_008830, intron 1 of 27)	CpG	207	NM_008830	18670	Mm.297825	NM_008830	ENSMUSG00000042476	Abcb4	Mdr2|Pgy-2|Pgy2|mdr-2	ATP-binding cassette, sub-family B (MDR/TAP), member 4	protein-coding
mm_24230.1	chr3	88950351	88950395	+	1	NA	promoter-TSS (NM_022994)	promoter-TSS (NM_022994)	-91	NM_001164533	65111	Mm.29028	NM_022994	ENSMUSG00000068921	Dap3	4921514D13Rik|DAP-3|MRP-S29|S29mt	death associated protein 3	protein-coding
mm_159190.1	chr2	118388966	118388966	+	1	NA	promoter-TSS (NM_001177806)	promoter-TSS (NM_001177806)	-146	NM_001177806	27103	Mm.217616	NM_013719	ENSMUSG00000005102	Eif2ak4	2610011M03|GCN2|MGCN2	eukaryotic translation initiation factor 2 alpha kinase 4	protein-coding
mm_71807.1	chr8	68880549	68880564	+	1	NA	promoter-TSS (NM_008509)	promoter-TSS (NM_008509)	1	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_739.1	chr1	43457249	43457282	+	1	NA	intron (NM_010879, intron 1 of 4)	intron (NM_010879, intron 1 of 4)	11514	NM_010879	17974	Mm.389903	NM_010879	ENSMUSG00000066877	Nck2	4833426I10Rik|Grb4|NCKbeta|Nck-2	non-catalytic region of tyrosine kinase adaptor protein 2	protein-coding
mm_71446.1	chr8	46521342	46521353	+	1	NA	intron (NM_001302163, intron 11 of 20)	intron (NM_001302163, intron 11 of 20)	30381	NM_001302163	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_116124.1	chr13	28951668	28951687	-	1	NA	3' UTR (NM_009238, exon 1 of 1)	3' UTR (NM_009238, exon 1 of 1)	2005	NM_009238	20677	Mm.240627	NM_009238	ENSMUSG00000076431	Sox4	AA682046|Sox-4	SRY (sex determining region Y)-box 4	protein-coding
mm_48603.1	chr5	144255111	144255122	-	1	NA	promoter-TSS (NM_018772)	promoter-TSS (NM_018772)	-109	NM_018772	55950	Mm.38011	NM_018772	ENSMUSG00000047843	Bri3	I3	brain protein I3	protein-coding
mm_23725.1	chr3	69016675	69016686	+	1	NA	exon (NM_133786, exon 7 of 24)	exon (NM_133786, exon 7 of 24)	6778	NR_029735	723949		NR_029735	ENSMUSG00000065606	Mir16-2	Mirn16-2|mir-16-2	microRNA 16-2	ncRNA
mm_25914.1	chr3	131134454	131134459	+	1	NA	intron (NM_001276403, intron 3 of 11)	L3b|LINE|CR1	21665	NM_001276403	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_49015.1	chr6	4758592	4758598	+	1	NA	3' UTR (NM_130877, exon 2 of 2)	3' UTR (NM_130877, exon 2 of 2)	11289	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_100513.1	chr11	120530538	120530559	+	1	NA	promoter-TSS (NM_008101)	promoter-TSS (NM_008101)	-179	NM_008101	14527	Mm.22329	NM_008101	ENSMUSG00000025127	Gcgr	GR	glucagon receptor	protein-coding
mm_19790.1	chr2	108686025	108686025	-	1	NA	Intergenic	Intergenic	592265	NM_029790	76894	Mm.330451	NM_029790	ENSMUSG00000057234	Mettl15	0610027B03Rik|AI303697|AW049952|Mett5d1	methyltransferase like 15	protein-coding
mm_38941.1	chr4	150198178	150198199	-	1	NA	exon (NM_009802, exon 2 of 8)	exon (NM_009802, exon 2 of 8)	2947	NM_009802	12353	Mm.232523	NM_009802	ENSMUSG00000028972	Car6	Ca6|DOC1	carbonic anhydrase 6	protein-coding
mm_66902.1	chr7	59977726	59977738	-	1	NA	Intergenic	Intergenic	1124	NR_028529	100217429		NR_028529		Snord64	MBII-13	small nucleolar RNA, C/D box 64	snoRNA
mm_4316.1	chr1	171848069	171848092	+	1	NA	intron (NM_001289470, intron 2 of 8)	MLT1J|LTR|ERVL-MaLR	8383	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_15485.1	chr2	157562030	157562032	+	1	NA	3' UTR (NM_010923, exon 3 of 3)	3' UTR (NM_010923, exon 3 of 3)	1953	NM_180960	18111	Mm.34330	NM_010923	ENSMUSG00000067786	Nnat	5730414I02Rik|AW107673|Peg5	neuronatin	protein-coding
mm_109742.1	chr12	117516490	117516534	+	1	NA	promoter-TSS (NM_175930)	promoter-TSS (NM_175930)	33	NM_175930	217944	Mm.227642	NM_175930	ENSMUSG00000041992	Rapgef5	4932413M22|C86120|D030051B22Rik|GFR|Mrgef|mKIAA0277|mmr-gef	Rap guanine nucleotide exchange factor (GEF) 5	protein-coding
mm_27182.1	chr3	34648953	34648963	-	1	NA	intron (NR_015580, intron 3 of 4)	CpG	-1037	NM_011443	20674	Mm.65396	NM_011443	ENSMUSG00000074637	Sox2	Sox-2|lcc|ysb	SRY (sex determining region Y)-box 2	protein-coding
mm_50715.1	chr6	52190445	52190448	+	1	NA	exon (NM_008265, exon 2 of 2)	exon (NM_008265, exon 2 of 2)	1257	NM_008265	15401	Mm.439647	NM_008265	ENSMUSG00000000942	Hoxa4	AV206827|Hox-1.4	homeobox A4	protein-coding
mm_59728.1	chr7	28788956	28788986	+	1	NA	promoter-TSS (NM_177158)	promoter-TSS (NM_177158)	2	NM_177158	320435	Mm.74632	NM_177158	ENSMUSG00000051735	Rinl	5830482F20Rik|9930116N10Rik	Ras and Rab interactor-like	protein-coding
mm_123802.1	chr14	70520627	70520640	-	1	NA	promoter-TSS (NM_009755)	promoter-TSS (NM_009755)	-373	NR_033241	12153	Mm.27757	NM_009755	ENSMUSG00000022098	Bmp1	Pcp|Tld	bone morphogenetic protein 1	protein-coding
mm_173049.1	chrX	12047716	12047724	-	1	NA	exon (NM_029510, exon 9 of 15)	exon (NM_029510, exon 9 of 15)	32833	NM_175045	71458	Mm.196328	NM_029510	ENSMUSG00000040363	Bcor	2900008C10Rik|5830466J11Rik|8430401K06Rik|BcorR|D930024N20Rik|mKIAA1575	BCL6 interacting corepressor	protein-coding
mm_56757.1	chr6	116101812	116101825	-	1	NA	intron (NM_177412, intron 3 of 5)	intron (NM_177412, intron 3 of 5)	91556	NM_177412	330401	Mm.425352	NM_177412	ENSMUSG00000030126	Tmcc1	3632431M01Rik|mKIAA0779	transmembrane and coiled coil domains 1	protein-coding
mm_49844.1	chr6	38354688	38354702	+	1	NA	promoter-TSS (NM_028421)	promoter-TSS (NM_028421)	-92	NM_028421	78781	Mm.25243	NM_028421	ENSMUSG00000029826	Zc3hav1	1200014N16Rik|2900058M19Rik|9130009D18Rik|9830115L13Rik|ARTD13|D6Bwg1452e|ZAP	zinc finger CCCH type, antiviral 1	protein-coding
mm_82144.1	chr9	123773313	123773344	+	1	NA	intron (NM_001166625, intron 2 of 3)	B4|SINE|B4	6117	NM_001166625	12769	Mm.440604	NM_009913	ENSMUSG00000029530	Ccr9	A130091K22Rik|Cmkbr10|GPR-9-6	chemokine (C-C motif) receptor 9	protein-coding
mm_59280.1	chr7	24907334	24907344	+	1	NA	intron (NM_001130152, intron 1 of 28)	intron (NM_001130152, intron 1 of 28)	2993	NM_001130152	16801	Mm.3181	NM_008488	ENSMUSG00000040940	Arhgef1	Lbcl2|Lsc	Rho guanine nucleotide exchange factor (GEF) 1	protein-coding
mm_55053.1	chr6	49045439	49045475	-	1	NA	exon (NM_053110, exon 4 of 11)	exon (NM_053110, exon 4 of 11)	8939	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_75053.1	chr8	33330575	33330604	-	1	NA	intron (NM_011721, intron 7 of 33)	L2a|LINE|L2	54938	NM_001122822	22427	Mm.228805	NM_011721	ENSMUSG00000031583	Wrn	AI846146	Werner syndrome homolog (human)	protein-coding
mm_61753.1	chr7	82771276	82771282	+	1	NA	intron (NM_175317, intron 18 of 19)	intron (NM_175317, intron 18 of 19)	-15635	NR_046004	77800	Mm.444811	NR_046004	ENSMUSG00000086690	4933406J10Rik	A930009F24Rik	RIKEN cDNA 4933406J10 gene	ncRNA
mm_53215.1	chr6	126821594	126821614	+	1	NA	TTS (NM_025358)	TTS (NM_025358)	27540	NM_025358	66108	Mm.29939	NM_025358	ENSMUSG00000000399	Ndufa9	1010001N11Rik	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 9	protein-coding
mm_63643.1	chr7	128638584	128638587	+	1	NA	intron (NM_178641, intron 2 of 19)	B4A|SINE|B4	27220	NM_178641	101490	Mm.490344	NM_178641	ENSMUSG00000042105	Inpp5f	5830435P03Rik|AI115354|AW561896|SAC2|cI-27|hSAC2|mKIAA0966	inositol polyphosphate-5-phosphatase F	protein-coding
mm_124714.1	chr15	6578708	6578716	+	1	NA	Intergenic	ID_B1|SINE|B4	-1135	NM_001278269	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_12203.1	chr2	65930194	65930216	+	1	NA	intron (NM_178634, intron 2 of 5)	intron (NM_178634, intron 2 of 5)	-1660	NM_001290665	77771	Mm.102025	NM_153409	ENSMUSG00000044647	Csrnp3	A330102K23Rik|CSRNP-3|Csnrp3|Mbu1|taip-2	cysteine-serine-rich nuclear protein 3	protein-coding
mm_60519.1	chr7	44479924	44479929	+	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	-4591	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_142521.1	chr17	46282649	46282676	-	1	NA	intron (NM_001252474, intron 1 of 9)	intron (NM_001252474, intron 1 of 9)	364	NM_001252475	74094	Mm.284594	NM_028751	ENSMUSG00000012296	Tjap1	0610041D19Rik|AI415281|AW121008|Pilt|Tjp4	tight junction associated protein 1	protein-coding
mm_90741.1	chr10	5368274	5368287	-	1	NA	exon (NM_153399, exon 14 of 32)	exon (NM_153399, exon 14 of 32)	120034	NM_001347711	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_129282.1	chr15	77153773	77153817	-	1	NA	promoter-TSS (NM_001110830)	promoter-TSS (NM_001110830)	17	NM_001110830	93686	Mm.202774	NM_053104	ENSMUSG00000033565	Rbfox2	Fbm2|Fxh|Hrnbp2|Rbm9	RNA binding protein, fox-1 homolog (C. elegans) 2	protein-coding
mm_33423.1	chr4	130047361	130047389	+	1	NA	promoter-TSS (NM_028266)	promoter-TSS (NM_028266)	-465	NM_028266	107581	Mm.41860	NM_028266	ENSMUSG00000040690	Col16a1	2700007F12Rik|A530052M23Rik|AI838662|CA1F	collagen, type XVI, alpha 1	protein-coding
mm_50611.1	chr6	49586962	49586982	+	1	NA	Intergenic	Intergenic	191368	NM_029916	77485	Mm.128054	NM_029916	ENSMUSG00000023403	Stk31	C330007K24Rik	serine threonine kinase 31	protein-coding
mm_71513.1	chr8	46846459	46846470	+	1	NA	3' UTR (NM_008391, exon 9 of 9)	3' UTR (NM_008391, exon 9 of 9)	106719	NM_008391	16363	Mm.1149	NM_008391	ENSMUSG00000031627	Irf2	9830146E22Rik|AI646973|Irf-2	interferon regulatory factor 2	protein-coding
mm_41794.1	chr5	103753625	103753651	+	1	NA	promoter-TSS (NM_133919)	promoter-TSS (NM_133919)	-524	NM_133919	17355	Mm.6949	NM_133919	ENSMUSG00000029313	Aff1	9630032B01Rik|AW319193|Af4|Mllt2h|Rob	AF4/FMR2 family, member 1	protein-coding
mm_61670.1	chr7	80781585	80781592	+	1	NA	intron (NM_016721, intron 2 of 37)	intron (NM_016721, intron 2 of 37)	21743	NM_016721	29875	Mm.207619	NM_016721	ENSMUSG00000030536	Iqgap1	AA682088|D7Ertd237e|D7Ertd257e|mKIAA0051	IQ motif containing GTPase activating protein 1	protein-coding
mm_115145.1	chr13	104849626	104849637	+	1	NA	intron (NM_029984, intron 2 of 2)	MTD|LTR|ERVL-MaLR	14262	NM_029984	77803	Mm.159995	NM_029984	ENSMUSG00000042655	Fam159b	A930021C24Rik	family with sequence similarity 159, member B	protein-coding
mm_132677.1	chr16	42921847	42921856	+	1	NA	intron (NM_001285805, intron 1 of 10)	intron (NM_001285805, intron 1 of 10)	-9781	NR_040402	100503040	Mm.490721	NR_040402		Gm19522	-	predicted gene, 19522	ncRNA
mm_172461.1	chr7	42107277	42107292	-	1	NA	Intergenic	Intergenic	-9187	NM_001105057	637898	Mm.469900	NM_001105057	ENSMUSG00000090619	Vmn2r60	Casr-rs3|EG637898|Gprc2a-rs3	vomeronasal 2, receptor 60	protein-coding
mm_78847.1	chr9	44329056	44329068	+	1	NA	exon (NM_007875, exon 4 of 9)	exon (NM_007875, exon 4 of 9)	2217	NM_007875	13478	Mm.18353	NM_007875	ENSMUSG00000032123	Dpagt1	AU021132|Dpagt2|GPT|Gnpta	dolichyl-phosphate (UDP-N-acetylglucosamine) acetylglucosaminephosphotransferase 1 (GlcNAc-1-P transferase)	protein-coding
mm_6634.1	chr1	78658274	78658282	-	1	NA	promoter-TSS (NM_001136226)	promoter-TSS (NM_001136226)	-162	NM_001136226	195434	Mm.276016	NM_001001981	ENSMUSG00000079470	Utp14b	4932411L21Rik|jsd	UTP14B small subunit processome component	protein-coding
mm_52511.1	chr6	115361253	115361280	+	1	NA	5' UTR (NM_001127330, exon 1 of 8)	5' UTR (NM_001127330, exon 1 of 8)	122	NM_001308352	19016	Mm.3020	NM_011146	ENSMUSG00000000440	Pparg	Nr1c3|PPAR-gamma|PPAR-gamma2|PPARgamma|PPARgamma2	peroxisome proliferator activated receptor gamma	protein-coding
mm_84173.1	chr9	59948566	59948576	-	1	NA	intron (NM_013708, intron 4 of 7)	intron (NM_013708, intron 4 of 7)	1508	NM_013708	23958	Mm.103641	NM_013708	ENSMUSG00000032292	Nr2e3	A930035N01Rik|PNR|RNR|rd7	nuclear receptor subfamily 2, group E, member 3	protein-coding
mm_67744.1	chr7	90457143	90457153	-	1	NA	promoter-TSS (NM_025460)	promoter-TSS (NM_025460)	60	NM_025460	66271	Mm.28963	NM_025460	ENSMUSG00000030615	Tmem126a	1810020E01Rik	transmembrane protein 126A	protein-coding
mm_150302.1	chr19	34570257	34570274	+	1	NA	5' UTR (NM_008332, exon 2 of 3)	5' UTR (NM_008332, exon 2 of 3)	-13264	NM_010501	15959	Mm.426079	NM_010501	ENSMUSG00000074896	Ifit3	Ifi49|P49	interferon-induced protein with tetratricopeptide repeats 3	protein-coding
mm_17173.1	chr2	25319110	25319170	-	1	NA	promoter-TSS (NM_001177657)	promoter-TSS (NM_001177657)	47	NM_008169	14810	Mm.278672	NM_008169	ENSMUSG00000026959	Grin1	GluN1|GluRdelta1|GluRzeta1|M100174|NMD-R1|NMDAR1|NR1|Nmdar|Rgsc174	glutamate receptor, ionotropic, NMDA1 (zeta 1)	protein-coding
mm_159659.1	chr4	150198436	150198436	-	1	NA	intron (NM_009802, intron 1 of 7)	intron (NM_009802, intron 1 of 7)	2699	NM_009802	12353	Mm.232523	NM_009802	ENSMUSG00000028972	Car6	Ca6|DOC1	carbonic anhydrase 6	protein-coding
mm_86528.1	chr10	7832316	7832325	+	1	NA	promoter-TSS (NM_172785)	promoter-TSS (NM_172785)	-150	NM_172785	237256	Mm.140055	NM_172785	ENSMUSG00000039981	Zc3h12d	D730019B10Rik|TFL	zinc finger CCCH type containing 12D	protein-coding
mm_80828.1	chr9	96897015	96897027	+	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-7547	NM_001289645	235534	Mm.233031	NM_153420	ENSMUSG00000043587	Pxylp1	9430094M07Rik|Acpl2|BB177120|C130099A20Rik	2-phosphoxylose phosphatase 1	protein-coding
mm_102061.1	chr11	52253860	52253890	-	1	NA	3' UTR (NM_009331, exon 10 of 10)	3' UTR (NM_009331, exon 10 of 10)	21880	NM_011543	21402	Mm.42944	NM_011543	ENSMUSG00000036309	Skp1a	15kDa|2610043E24Rik|2610206H23Rik|EMC19|OCP-II|OCP2|SKP1|Tceb1l|p19A|p19Skp1	S-phase kinase-associated protein 1A	protein-coding
mm_160858.1	chr11	59183203	59183203	-	1	NA	promoter-TSS (NM_080454)	promoter-TSS (NM_080454)	10	NM_080454	118454	Mm.40016	NM_080454	ENSMUSG00000043448	Gjc2	B230382L12Rik|Cx47|Gja12	gap junction protein, gamma 2	protein-coding
mm_145797.1	chr18	65248239	65248260	+	1	NA	promoter-TSS (NR_029600)	promoter-TSS (NR_029600)	-612	NR_029600	387231		NR_029600	ENSMUSG00000065402	Mir122	Mir122a|Mirn122a|mir-122|mmu-mir-122	microRNA 122	ncRNA
mm_143395.1	chr17	70687498	70687499	-	1	NA	intron (NM_001347412, intron 8 of 13)	intron (NM_001347412, intron 8 of 13)	125751	NM_001128181	224997	Mm.311840	NM_027712	ENSMUSG00000003279	Dlgap1	4933422O14Rik|9630002F18|AI845682|AI848168|BB075781|D17Bwg0511e|GKAP/SAPAP|GKPA/SAPAP|Gkap|Sapap1|mKIAA4162	discs, large (Drosophila) homolog-associated protein 1	protein-coding
mm_33243.1	chr4	127029847	127029899	+	1	NA	exon (NM_023603, exon 10 of 10)	exon (NM_023603, exon 10 of 10)	8572	NM_023603	71514	Mm.257276	NM_023603	ENSMUSG00000028820	Sfpq	1110004P21Rik|2810416M14Rik|5730453G22Rik|9030402K04Rik|AU021830|D4Ertd314e|Gm12940|OTTMUSG00000009329|PSF|REP1	splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)	protein-coding
mm_113820.1	chr13	46810327	46810363	+	1	NA	intron (NM_010617, intron 14 of 37)	ORR1E|LTR|ERVL-MaLR	-82496	NM_175749	218210	Mm.255398	NM_175749	ENSMUSG00000021374	Nup153	B130015D15Rik|C88147	nucleoporin 153	protein-coding
mm_172041.1	chr6	127146041	127146041	-	1	NA	exon (NM_009829, exon 3 of 5)	exon (NM_009829, exon 3 of 5)	-3348	NR_040274	77558	Mm.358918	NR_040273	ENSMUSG00000097166	9330179D12Rik	-	RIKEN cDNA 9330179D12 gene	ncRNA
mm_69519.1	chr7	135528601	135528632	-	1	NA	promoter-TSS (NM_178669)	promoter-TSS (NM_178669)	38	NM_178669	212070	Mm.39721	NM_178669	ENSMUSG00000050866	Clrn3	AI649392|Tmem12	clarin 3	protein-coding
mm_65628.1	chr7	27542330	27542352	-	1	NA	intron (NM_001317355, intron 3 of 13)	intron (NM_001317355, intron 3 of 13)	10877	NM_011116	18807	Mm.6483	NM_011116	ENSMUSG00000003363	Pld3	Sam-9	phospholipase D family, member 3	protein-coding
mm_157130.1	chrX	9446924	9446932	-	1	NA	exon (NM_007807, exon 9 of 13)	exon (NM_007807, exon 9 of 13)	22396	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_59114.1	chr7	19822929	19822943	+	1	NA	promoter-TSS (NM_033601)	promoter-TSS (NM_033601)	-181	NM_033601	12051	Mm.439658	NM_033601	ENSMUSG00000053175	Bcl3	AI528691|Bcl-3	B cell leukemia/lymphoma 3	protein-coding
mm_93929.1	chr10	127166257	127166272	-	1	NA	intron (NR_045166, intron 2 of 9)	intron (NR_045166, intron 2 of 9)	433	NM_001244618	14421	Mm.386762	NM_008080	ENSMUSG00000006731	B4galnt1	4933429D13Rik|Gal-NAc-T|GalNAc-T|GalNAcT|Galgt1|Ggm-2|Ggm2	beta-1,4-N-acetyl-galactosaminyl transferase 1	protein-coding
mm_4254.1	chr1	171409616	171409625	+	1	NA	3' UTR (NM_001005508, exon 12 of 12)	3' UTR (NM_001005508, exon 12 of 12)	-1693	NM_001305678	22278	Mm.8	NM_009480	ENSMUSG00000026641	Usf1	bHLHb11	upstream transcription factor 1	protein-coding
mm_91587.1	chr10	40247118	40247135	-	1	NA	promoter-TSS (NM_023323)	promoter-TSS (NM_023323)	-87	NM_023323	67239	Mm.11480	NM_023323	ENSMUSG00000038510	Rpf2	2810470K21Rik|AU040229|AU043242|Bxdc1	ribosome production factor 2 homolog	protein-coding
mm_128783.1	chr15	66801675	66801693	-	1	NA	intron (NM_001029841, intron 1 of 7)	intron (NM_001029841, intron 1 of 7)	30145	NM_001029841	20491	Mm.7601	NM_009192	ENSMUSG00000022372	Sla	Slap|Slap-1	src-like adaptor	protein-coding
mm_118328.1	chr13	113663637	113663649	-	1	NA	promoter-TSS (NM_019960)	promoter-TSS (NM_019960)	33	NM_019960	56534	Mm.41410	NM_019960	ENSMUSG00000051456	Hspb3	2310035K17Rik|AI844863|Hsbp3|spb3	heat shock protein 3	protein-coding
mm_27539.1	chr3	57576448	57576452	-	1	NA	promoter-TSS (NM_133784)	promoter-TSS (NM_133784)	-540	NM_001168281	97064	Mm.405029	NM_133784	ENSMUSG00000027803	Wwtr1	2310058J06Rik|2610021I22Rik|C78399|Taz	WW domain containing transcription regulator 1	protein-coding
mm_81847.1	chr9	118558437	118558439	+	1	NA	exon (NM_018748, exon 15 of 24)	exon (NM_018748, exon 15 of 24)	-48271	NM_133721	104099	Mm.335520	NM_133721	ENSMUSG00000039115	Itga9	(alpha)9|2610002H11Rik|6720458D17Rik|AI461869|D130073C02|D9Ertd428e	integrin alpha 9	protein-coding
mm_81655.1	chr9	110960844	110960874	+	1	NA	exon (NM_028838, exon 3 of 9)	exon (NM_028838, exon 3 of 9)	9314	NM_028838	74249	Mm.307615	NM_028838	ENSMUSG00000032495	Lrrc2	2400002D05Rik|4933431K03Rik	leucine rich repeat containing 2	protein-coding
mm_99730.1	chr11	106301170	106301187	+	1	NA	exon (NM_008117, exon 3 of 5)	exon (NM_008117, exon 3 of 5)	718	NM_008117	14599	Mm.343934	NM_008117	ENSMUSG00000020713	Gh	Gh1|Ghb1	growth hormone	protein-coding
mm_126422.1	chr15	80572456	80572460	+	1	NA	promoter-TSS (NM_001289442)	promoter-TSS (NM_001289442)	-139	NM_001289442	17444	Mm.12947	NM_010815	ENSMUSG00000042351	Grap2	GRAP-2|GRB2L|GRBLG|GRID|Gads|GrbX|Grf40|GrpL|Mona|P38	GRB2-related adaptor protein 2	protein-coding
mm_37534.1	chr4	124936834	124936844	-	1	NA	promoter-TSS (NM_177573)	promoter-TSS (NM_177573)	78	NM_026560	52276	Mm.28038	NM_026560	ENSMUSG00000028873	Cdca8	4831429J16Rik|AU044747|BOR|Borealin|D4Ertd421e|DasraB|MESRGP	cell division cycle associated 8	protein-coding
mm_162141.1	chrX	74282552	74282552	-	1	NA	promoter-TSS (NM_001242616)	promoter-TSS (NM_001242616)	-166	NM_001173547	66826	Mm.268483	NM_181516	ENSMUSG00000009995	Taz	5031411C02Rik|9130012G04Rik|AW107266|AW552613|G4.5	tafazzin	protein-coding
mm_80466.1	chr9	78113276	78113346	+	1	NA	promoter-TSS (NM_019987)	promoter-TSS (NM_019987)	73	NM_019987	56542	Mm.288719	NM_019987	ENSMUSG00000009828	Ick	2210420N10Rik|AI848300|Mrk	intestinal cell kinase	protein-coding
mm_54592.1	chr6	38195381	38195427	-	1	NA	exon (NM_194061, exon 2 of 20)	exon (NM_194061, exon 2 of 20)	58605	NM_194061	330286	Mm.277163	NM_194061	ENSMUSG00000063455	D630045J12Rik	Kiaa1549|mKIAA1549	RIKEN cDNA D630045J12 gene	protein-coding
mm_114679.1	chr13	80886222	80886251	+	1	NA	intron (NM_001042591, intron 1 of 7)	CpG	2814	NM_001042591	105171	Mm.423137	NM_001042591	ENSMUSG00000074794	Arrdc3	AI450344|mKIAA1376	arrestin domain containing 3	protein-coding
mm_81830.1	chr9	118059449	118059466	+	1	NA	3' UTR (NM_001048146, exon 7 of 7)	3' UTR (NM_001048146, exon 7 of 7)	18935	NM_013727	27215	Mm.92705	NM_013727	ENSMUSG00000039285	Azi2	AA410145|AZ2	5-azacytidine induced gene 2	protein-coding
mm_81388.1	chr9	108982976	108982996	+	1	NA	intron (NM_007738, intron 113 of 117)	intron (NM_007738, intron 113 of 117)	-3177	NM_145077	171530	Mm.388865	NM_145077	ENSMUSG00000049699	Ucn2	Ucn II|Ucn-2|ucn-II	urocortin 2	protein-coding
mm_16273.1	chr2	173719468	173719502	+	1	NA	promoter-TSS (NM_029308)	promoter-TSS (NM_029308)	70	NM_029308	75485	Mm.308031	NM_029308	ENSMUSG00000057047	1700010B08Rik	-	RIKEN cDNA 1700010B08 gene	protein-coding
mm_43814.1	chr5	142905405	142905440	+	1	NA	exon (NM_007393, exon 3 of 6)	exon (NM_007393, exon 3 of 6)	1332	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_91905.1	chr10	60219299	60219345	-	1	NA	promoter-TSS (NM_016803)	promoter-TSS (NM_016803)	-62	NM_016803	53374	Mm.12866	NM_016803	ENSMUSG00000057337	Chst3	C6ST|C6ST-1|GST-0	carbohydrate (chondroitin 6/keratan) sulfotransferase 3	protein-coding
mm_114157.1	chr13	55405082	55405086	+	1	NA	intron (NM_011392, intron 8 of 12)	intron (NM_011392, intron 8 of 12)	5436	NM_011392	20505	Mm.276355	NM_011392	ENSMUSG00000021490	Slc34a1	NaPi-IIa|Npt2|Npt2a|Slc17a2	solute carrier family 34 (sodium phosphate), member 1	protein-coding
mm_151837.1	chr19	5720696	5720725	-	1	NA	exon (NM_001114597, exon 8 of 19)	exon (NM_001114597, exon 8 of 19)	5607	NM_001114595	114601	Mm.210447	NM_053252	ENSMUSG00000024937	Ehbp1l1	G430002G23Rik	EH domain binding protein 1-like 1	protein-coding
mm_149088.1	chr19	8922058	8922074	+	1	NA	intron (NM_024256, intron 2 of 4)	intron (NM_024256, intron 2 of 4)	1673	NM_024256	72727	Mm.259	NM_024256	ENSMUSG00000071649	B3gat3	2810405M13Rik	beta-1,3-glucuronyltransferase 3 (glucuronosyltransferase I)	protein-coding
mm_84201.1	chr9	60649794	60649805	-	1	NA	intron (NM_001311095, intron 7 of 15)	intron (NM_001311095, intron 7 of 15)	37735	NM_001311095	102747	Mm.269413	NM_145616	ENSMUSG00000047766	Lrrc49	AI430817|AW050057|D430025H09Rik|PGs4|p79	leucine rich repeat containing 49	protein-coding
mm_107085.1	chr12	17354839	17354845	+	1	NA	promoter-TSS (NR_037226)	promoter-TSS (NR_037226)	-550	NR_037226	100526470		NR_037226	ENSMUSG00000093037	Mir3066	mir-3066|mmu-mir-3066	microRNA 3066	ncRNA
mm_148762.1	chr19	6061439	6061449	+	1	NA	exon (NM_013859, exon 1 of 1)	exon (NM_013859, exon 1 of 1)	237	NM_013859	29805	Mm.2310	NM_013859	ENSMUSG00000075227	Znhit2	C11orf5|Fon|ORF6|Znhit2-ps	zinc finger, HIT domain containing 2	protein-coding
mm_79414.1	chr9	55209006	55209020	+	1	NA	promoter-TSS (NM_028049)	promoter-TSS (NM_028049)	78	NM_028049	71999	Mm.276429	NM_028049	ENSMUSG00000032309	Fbxo22	0610033L19Rik|1600016C16Rik	F-box protein 22	protein-coding
mm_173182.1	chrX	57657794	57657794	-	1	NA	Intergenic	(TC)n|Simple_repeat|Simple_repeat	-154037	NM_001033360	245424	Mm.336070	NM_001033360	ENSMUSG00000036357	Gpr101	GPCR6|Gm365	G protein-coupled receptor 101	protein-coding
mm_87169.1	chr10	37139526	37139540	+	1	NA	promoter-TSS (NM_008538)	promoter-TSS (NM_008538)	-607	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_48734.1	chr5	147566745	147566757	-	1	NA	intron (NM_010228, intron 28 of 29)	B4A|SINE|B4	136171	NM_028291	72587	Mm.320469	NM_028291	ENSMUSG00000029647	Pan3	2700050F09Rik|A430027N15Rik|AU014670	PAN3 poly(A) specific ribonuclease subunit	protein-coding
mm_142238.1	chr17	37481230	37481248	-	1	NA	exon (NM_001347387, exon 5 of 5)	exon (NM_001347387, exon 5 of 5)	2290	NM_008204	14990	Mm.329041	NM_008204	ENSMUSG00000016283	H2-M2	H-2M2|Thy19.4	histocompatibility 2, M region locus 2	protein-coding
mm_118012.1	chr13	100730840	100730962	-	1	NA	promoter-TSS (NM_009874)	promoter-TSS (NM_009874)	41	NM_009874	12572	Mm.259718	NM_009874	ENSMUSG00000069089	Cdk7	AI323415|AI528512|C230069N13|Cdkn7|Crk4	cyclin-dependent kinase 7	protein-coding
mm_99618.1	chr11	104608041	104608063	+	1	NA	promoter-TSS (NM_016780)	promoter-TSS (NM_016780)	52	NM_016780	16416	Mm.87150	NM_016780	ENSMUSG00000020689	Itgb3	CD61|GP3A|INGRB3	integrin beta 3	protein-coding
mm_118300.1	chr13	113087328	113087351	-	1	NA	intron (NM_001281487, intron 11 of 11)	Lx8|LINE|L1	13642	NM_010370	14938	Mm.15510	NM_010370	ENSMUSG00000023132	Gzma	AW494114|Ctla-3|Ctla3|Hf|Hf1|SE1|TSP-1|TSP1	granzyme A	protein-coding
mm_99765.1	chr11	106789236	106789335	+	1	NA	promoter-TSS (NM_177088)	promoter-TSS (NM_177088)	33	NM_001166685	320162	Mm.30524	NM_177088	ENSMUSG00000018372	Cep95	4732496G21Rik|AI118346|AI448335|Ccdc45|D330027A14Rik|F630025I20Rik	centrosomal protein 95	protein-coding
mm_166102.1	chr4	146431033	146431044	+	1	NA	intron (NM_001083918, intron 3 of 6).2	intron (NM_001083918, intron 3 of 6).2	-17992	NM_001085522	433791	Mm.276881	NM_001085522	ENSMUSG00000070605	Zfp992	Gm13251|OTTMUSG00000011097	zinc finger protein 992	protein-coding
mm_139166.1	chr17	47557788	47557826	+	1	NA	intron (NM_001081635, intron 1 of 6)	intron (NM_001081635, intron 1 of 6)	-35660	NM_007632	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_139744.1	chr17	63422126	63422135	+	1	NA	intron (NM_015794, intron 4 of 8)	intron (NM_015794, intron 4 of 8)	78450	NM_015794	50758	Mm.136366	NM_015794	ENSMUSG00000023965	Fbxl17	6330576B01Rik|AI452053|BB073797|C130023C01Rik|Fbx13|Fbxo13	F-box and leucine-rich repeat protein 17	protein-coding
mm_130446.1	chr15	98523766	98523793	-	1	NA	intron (NM_001289437, intron 8 of 9)	L1MC5|LINE|L1	2680	NR_034052	100217416	Mm.296240	NR_034052	ENSMUSG00000065939	Snora2b	MBI-137	small nucleolar RNA, H/ACA box 2B	snoRNA
mm_30270.1	chr3	146781214	146781251	-	1	NA	exon (NM_001164200, exon 1 of 10)	exon (NM_001164200, exon 1 of 10)	184	NM_001164200	18749	Mm.16766	NM_011100	ENSMUSG00000005034	Prkacb	CbPKA|Pkacb	protein kinase, cAMP dependent, catalytic, beta	protein-coding
mm_54479.1	chr6	35090687	35090690	-	1	NA	intron (NM_016877, intron 1 of 10)	B1_Mus2|SINE|Alu	43049	NM_001164412	53621	Mm.214525	NM_016877	ENSMUSG00000038784	Cnot4	Not4|Not4h|Not4hp	CCR4-NOT transcription complex, subunit 4	protein-coding
mm_54844.1	chr6	42586872	42586885	-	1	NA	TTS (NM_203396)	TTS (NM_203396)	10494	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_32275.1	chr4	102760165	102760184	+	1	NA	promoter-TSS (NM_144906)	promoter-TSS (NM_144906)	39	NM_001285859	73094	Mm.54201	NM_144906	ENSMUSG00000028524	Sgip1	3110007P09Rik|SGIP1alpha|gag	SH3-domain GRB2-like (endophilin) interacting protein 1	protein-coding
mm_2626.1	chr1	120644682	120644690	+	1	NA	Intergenic	Intergenic	42199	NM_010133	13798	Mm.2657	NM_010133	ENSMUSG00000058665	En1	En-1|Mo-en.1|engrailed-1	engrailed 1	protein-coding
mm_153496.1	chr19	41332321	41332353	-	1	NA	exon (NM_031376, exon 3 of 17)	exon (NM_031376, exon 3 of 17)	52733	NM_031376	83490	Mm.222266	NM_031376	ENSMUSG00000025017	Pik3ap1	1810044J04Rik|BCAP	phosphoinositide-3-kinase adaptor protein 1	protein-coding
mm_32415.1	chr4	107047432	107047437	+	1	NA	exon (NM_198438, exon 16 of 17)	exon (NM_198438, exon 16 of 17)	19432	NM_025500	56280	Mm.29517	NM_025500	ENSMUSG00000028622	Mrpl37	2300004O14Rik|AI132596|MRP-L2|Rpml2	mitochondrial ribosomal protein L37	protein-coding
mm_170894.1	chr2	28477115	28477117	+	1	NA	Intergenic	Intergenic	9050	NM_001166031	118451	Mm.294951	NM_080452	ENSMUSG00000035772	Mrps2	1500019M10Rik	mitochondrial ribosomal protein S2	protein-coding
mm_65581.1	chr7	27228606	27228636	-	1	NA	promoter-TSS (NM_181593)	promoter-TSS (NM_181593)	-24	NM_181593	233011	Mm.30963	NM_181593	ENSMUSG00000003752	Itpkc	9130023N17Rik	inositol 1,4,5-trisphosphate 3-kinase C	protein-coding
mm_117812.1	chr13	97747400	97747414	-	1	NA	Intergenic	Intergenic	187407	NR_046157	328314	Mm.138047	NR_046157	ENSMUSG00000110235	Gm5086	B230311A21|EG328314	predicted gene 5086	ncRNA
mm_138628.1	chr17	35841824	35841834	+	1	NA	intron (NM_001010833, intron 1 of 15)	intron (NM_001010833, intron 1 of 15)	331	NM_001010833	240087	Mm.218511	NM_001010833	ENSMUSG00000061607	Mdc1	6820401C03|AA413496|Nfbd1|mKIAA0170	mediator of DNA damage checkpoint 1	protein-coding
mm_63851.1	chr7	135662210	135662228	+	1	NA	intron (NM_001316681, intron 4 of 17)	intron (NM_001316681, intron 4 of 17)	-9905	NR_015548	67765	Mm.445272	NR_015548	ENSMUSG00000097471	5830432E09Rik	-	RIKEN cDNA 5830432E09 gene	ncRNA
mm_69047.1	chr7	126831666	126831681	-	1	NA	promoter-TSS (NM_183131)	promoter-TSS (NM_183131)	-177	NM_183131	78118	Mm.107753	NM_183131	ENSMUSG00000045989	4930451I11Rik	-	RIKEN cDNA 4930451I11 gene	protein-coding
mm_5510.1	chr1	37496090	37496106	-	1	NA	intron (NM_001290801, intron 2 of 14)	intron (NM_001290801, intron 2 of 14)	-7493	NR_024017	77633	Mm.483177	NR_024017	ENSMUSG00000103948	4930594C11Rik	-	G1 to S phase transition pseudogene	pseudo
mm_151518.1	chr19	58738304	58738312	+	1	NA	intron (NM_018874, intron 10 of 12)	intron (NM_018874, intron 10 of 12)	9421	NM_018874	18946	Mm.10753	NM_018874	ENSMUSG00000042179	Pnliprp1	Plrp1	pancreatic lipase related protein 1	protein-coding
mm_52833.1	chr6	121365847	121365863	+	1	NA	TTS (NM_133661)	TTS (NM_133661)	19158	NM_133661	14411	Mm.274506	NM_133661	ENSMUSG00000030109	Slc6a12	BGT1|GAT-2|GAT2|Gabt2	solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12	protein-coding
mm_68023.1	chr7	100964442	100964452	-	1	NA	promoter-TSS (NM_183168)	promoter-TSS (NM_183168)	-81	NM_183168	233571	Mm.235193	NM_183168	ENSMUSG00000048779	P2ry6	2010204J23Rik|P2Y6	pyrimidinergic receptor P2Y, G-protein coupled, 6	protein-coding
mm_115418.1	chr13	117048726	117048768	+	1	NA	Intergenic	MLT1N2|LTR|ERVL-MaLR	-23231	NM_001081009	52552	Mm.274466	NM_027272	ENSMUSG00000021725	Parp8	2810430O08Rik|ARTD16|D13Ertd275e	poly (ADP-ribose) polymerase family, member 8	protein-coding
mm_170836.1	chr2	177080231	177080241	+	1	NA	Intergenic	Intergenic	-152423	NM_001305133	102639598	Mm.379980	NM_029813	ENSMUSG00000074527	Gm14296	-	predicted gene 14296	protein-coding
mm_100987.1	chr11	7213916	7213929	-	1	NA	promoter-TSS (NM_008343)	promoter-TSS (NM_008343)	1	NM_008343	16009	Mm.29254	NM_008343	ENSMUSG00000020427	Igfbp3	AI649005|IGFBP-3|IGgfbp3	insulin-like growth factor binding protein 3	protein-coding
mm_64661.1	chr7	4164685	4164715	-	1	NA	promoter-TSS (NM_021454)	promoter-TSS (NM_021454)	-1	NM_021454	58804	Mm.34268	NM_021454	ENSMUSG00000063838	Cdc42ep5	1700027J19Rik|2010007O02Rik|Borg3|C85526|CEP5	CDC42 effector protein (Rho GTPase binding) 5	protein-coding
mm_59006.1	chr7	19181408	19181457	+	1	NA	promoter-TSS (NR_029763)	promoter-TSS (NR_029763)	-33	NR_029763	724063		NR_029763	ENSMUSG00000065543	Mir330	Mirn330|mir-330|mmu-mir-330	microRNA 330	ncRNA
mm_96330.1	chr11	64979122	64979136	+	1	NA	promoter-TSS (NM_023479)	promoter-TSS (NM_023479)	94	NM_023479	68626	Mm.157711	NM_023479	ENSMUSG00000020549	Elac2	1110017O07Rik|D11Wsu80e|Hpc2	elaC ribonuclease Z 2	protein-coding
mm_71591.1	chr8	54954995	54955010	+	1	NA	5' UTR (NM_153581, exon 1 of 7)	5' UTR (NM_153581, exon 1 of 7)	274	NM_001253756	234267	Mm.241700	NM_153581	ENSMUSG00000031517	Gpm6a	Gpm6|M6A	glycoprotein m6a	protein-coding
mm_127391.1	chr15	101115774	101115786	+	1	NA	promoter-TSS (NM_144790)	promoter-TSS (NM_144790)	25	NM_144790	208258	Mm.152952	NM_144790	ENSMUSG00000047034	Ankrd33	A930021G21Rik|Panky|Panky-a	ankyrin repeat domain 33	protein-coding
mm_135208.1	chr16	36610852	36610875	-	1	NA	intron (NM_019388, intron 5 of 7)	intron (NM_019388, intron 5 of 7)	-48729	NM_013803	12374	Mm.103619	NM_013803	ENSMUSG00000051980	Casr	CaR|Gprc2a	calcium-sensing receptor	protein-coding
mm_64259.1	chr7	141745466	141745494	+	1	NA	exon (NM_023566, exon 29 of 46)	exon (NM_023566, exon 29 of 46)	-43531	NM_010844	17833	Mm.334332	NM_010844	ENSMUSG00000037974	Muc5ac	2210005L13Rik|MGM	mucin 5, subtypes A and C, tracheobronchial/gastric	protein-coding
mm_130729.1	chr15	101225136	101225158	-	1	NA	promoter-TSS (NR_045328)	promoter-TSS (NR_045328)	39	NR_045328	380977	Mm.399924	NR_045326	ENSMUSG00000097915	A330009N23Rik	-	RIKEN cDNA A330009N23 gene	ncRNA
mm_143368.1	chr17	67354543	67354553	-	1	NA	promoter-TSS (NM_008984)	promoter-TSS (NM_008984)	-89	NM_008984	19274	Mm.311809	NM_008984	ENSMUSG00000033278	Ptprm	RPTPmu|mKIAA4044	protein tyrosine phosphatase, receptor type, M	protein-coding
mm_21167.1	chr2	154632643	154632662	-	1	NA	intron (NM_199304, intron 8 of 14)	MIR3|SINE|MIR	19284	NM_199304	228807	Mm.103555	NM_199304	ENSMUSG00000059842	Zfp341	Znf341	zinc finger protein 341	protein-coding
mm_8840.1	chr1	162688173	162688187	-	1	NA	exon (NM_001081290, exon 24 of 35)	exon (NM_001081290, exon 24 of 35)	-29961	NM_001177581	100038657	Mm.416999	NM_001177581	ENSMUSG00000091060	7420461P10Rik	ENSMUSG00000073516	RIKEN cDNA 7420461P10 gene	protein-coding
mm_33403.1	chr4	129827298	129827301	+	1	NA	intron (NM_001164745, intron 1 of 5)	intron (NM_001164745, intron 1 of 5)	6591	NM_001164745	19244	Mm.193688	NM_008974	ENSMUSG00000028788	Ptp4a2	Prl-2	protein tyrosine phosphatase 4a2	protein-coding
mm_84416.1	chr9	65573008	65573054	-	1	NA	exon (NM_153119, exon 2 of 6)	exon (NM_153119, exon 2 of 6)	7056	NM_153119	102595	Mm.247303	NM_153119	ENSMUSG00000050721	Plekho2	AI840980|Plekhq1	pleckstrin homology domain containing, family O member 2	protein-coding
mm_7121.1	chr1	90775773	90775777	-	1	NA	exon (NM_001243009, exon 37 of 41)	exon (NM_001243009, exon 37 of 41)	68196	NM_001243009	12835	Mm.7562	NM_009935	ENSMUSG00000048126	Col6a3	AI507288|Col6a-3	collagen, type VI, alpha 3	protein-coding
mm_159829.1	chr5	125042784	125042784	-	1	NA	exon (NM_001253904, exon 22 of 48)	exon (NM_001253904, exon 22 of 48)	39309	NM_028443	73121	Mm.296138	NM_028443	ENSMUSG00000037962	Rflna	3110032G18Rik|Fam101a|cfm|cfm2	refilin A	protein-coding
mm_142492.1	chr17	46017754	46017770	-	1	NA	3' UTR (NM_001025250, exon 8 of 8)	3' UTR (NM_001025250, exon 8 of 8)	7401	NM_001110267	22339	Mm.282184	NM_009505	ENSMUSG00000023951	Vegfa	Vegf|Vpf	vascular endothelial growth factor A	protein-coding
mm_96217.1	chr11	62458583	62458600	+	1	NA	exon (NM_001039536, exon 1 of 7)	exon (NM_001039536, exon 1 of 7)	131	NM_001039536	327942	Mm.390358	NM_199026	ENSMUSG00000014245	Pigl	Gm737	phosphatidylinositol glycan anchor biosynthesis, class L	protein-coding
mm_44152.1	chr5	150418420	150418434	+	1	NA	intron (NM_172887, intron 34 of 60)	intron (NM_172887, intron 34 of 60)	83792	NR_024513	194292	Mm.300184	NR_024513		Gm5	Gm1812	predicted gene 5	ncRNA
mm_122841.1	chr14	54724180	54724191	-	1	NA	exon (NM_016972, exon 11 of 11)	exon (NM_016972, exon 11 of 11)	-12011	NM_207131	110794	Mm.236223	NM_207131	ENSMUSG00000052435	Cebpe	C/EBPe|CRP1|Gm294	CCAAT/enhancer binding protein (C/EBP), epsilon	protein-coding
mm_4349.1	chr1	171868810	171868833	+	1	NA	intron (NM_001289470, intron 3 of 8)	Lx6|LINE|L1	29124	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_74019.1	chr8	121570635	121570648	+	1	NA	intron (NM_133765, intron 1 of 8)	intron (NM_133765, intron 1 of 8)	8165	NM_133765	76454	Mm.24829	NM_133765	ENSMUSG00000052934	Fbxo31	1110003O08Rik|2310046N15Rik|Fbx14|Fbxo14	F-box protein 31	protein-coding
mm_117818.1	chr13	98014994	98015023	-	1	NA	intron (NM_012026, intron 9 of 35)	intron (NM_012026, intron 9 of 35)	191157	NM_012026	110596	Mm.252718	NM_012026	ENSMUSG00000021662	Arhgef28	9230110L08Rik|AI323540|D13Bwg1089e|RIP2|Rgnef|RhoGEF|Rhoip2|p190RhoGEF	Rho guanine nucleotide exchange factor (GEF) 28	protein-coding
mm_90256.1	chr10	122406390	122406390	+	1	NA	Intergenic	Intergenic	-42109	NM_016847	54140	Mm.4351	NM_016847	ENSMUSG00000020123	Avpr1a	AVPR|Avpr1|V1a|V1aR	arginine vasopressin receptor 1A	protein-coding
mm_85991.1	chr9	112199907	112199915	-	1	NA	intron (NM_001177619, intron 1 of 10)	intron (NM_001177619, intron 1 of 10)	-11982	NM_028755	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_117103.1	chr13	60175025	60175038	-	1	NA	3' UTR (NM_008086, exon 1 of 1)	3' UTR (NM_008086, exon 1 of 1)	2504	NM_008086	14451	Mm.22701	NM_008086	ENSMUSG00000052957	Gas1	AW554192|Gas-1	growth arrest specific 1	protein-coding
mm_58766.1	chr7	15881691	15881693	+	1	NA	promoter-TSS (NR_038092)	promoter-TSS (NR_038092)	-925	NR_038092	546024	Mm.259041	NM_001033638	ENSMUSG00000074365	Crxos	AA606869|AY590891|Crxos1|Egam1	cone-rod homeobox, opposite strand	protein-coding
mm_127720.1	chr15	103135798	103135808	+	1	NA	intron (NR_045743, intron 3 of 6)	intron (NR_045743, intron 3 of 6)	11025	NR_045743	432989	Mm.383979	NR_045743	ENSMUSG00000097003	D930007P13Rik	-	Riken cDNA D930007P13 gene	ncRNA
mm_101964.1	chr11	50307568	50307624	-	1	NA	exon (NM_001110500, exon 7 of 15)	exon (NM_001110500, exon 7 of 15)	-15260	NM_175334	103806	Mm.51116	NM_175334	ENSMUSG00000050567	Maml1	AI644666|AW743257|D930008C07Rik|Mam-1|Mam1|mKIAA0200	mastermind like 1 (Drosophila)	protein-coding
mm_103766.1	chr11	81858724	81858728	-	1	NA	intron (NM_001034013, intron 1 of 9)	intron (NM_001034013, intron 1 of 9)	-1951	NR_038010	71388	Mm.158687	NR_038010	ENSMUSG00000020703	5530401A14Rik	-	RIKEN cDNA 5530401A14 gene	ncRNA
mm_38201.1	chr4	135507611	135507622	-	1	NA	intron (NM_030189, intron 2 of 8)	intron (NM_030189, intron 2 of 8)	11629	NM_030189	78806	Mm.374844	NM_030189	ENSMUSG00000028801	Stpg1	4930403G18Rik|4930555I21Rik|Mapo2	sperm tail PG rich repeat containing 1	protein-coding
mm_144137.1	chr18	4993796	4993819	+	1	NA	Intergenic	Intergenic	-52782	NM_153153	225115	Mm.136791	NM_153153	ENSMUSG00000024236	Svil	AU024053|B430302E16Rik	supervillin	protein-coding
mm_13591.1	chr2	112498169	112498171	+	1	NA	intron (NM_028844, intron 1 of 5)	RLTR41A2|LTR|ERV1	5206	NM_028844	74268	Mm.315125	NM_028844	ENSMUSG00000003604	Aven	1700013A01Rik|1700056A21Rik|mAven-L|mAven-S	apoptosis, caspase activation inhibitor	protein-coding
mm_22880.1	chr3	29467900	29467904	+	1	NA	intron (NM_029412, intron 5 of 14)	intron (NM_029412, intron 5 of 14)	51079	NR_030422	791072		NR_030422	ENSMUSG00000076120	Mir551b	Mirn551b|mir-551b	microRNA 551b	ncRNA
mm_82496.1	chr9	18674825	18674878	-	1	NA	Intergenic	Intergenic	80782	NM_146606	18322	Mm.246530	NM_146606	ENSMUSG00000054141	Olfr24	MOR132-1|MTPCR51	olfactory receptor 24	protein-coding
mm_71613.1	chr8	56617486	56617497	+	1	NA	Intergenic	Intergenic	66357	NM_015791	50753	Mm.251174	NM_015791	ENSMUSG00000038206	Fbxo8	Fbx8	F-box protein 8	protein-coding
mm_7086.1	chr1	88559307	88559325	-	1	NA	intron (NR_037971, intron 4 of 5)	intron (NR_037971, intron 4 of 5)	7799	NR_037971	100503197	Mm.99352	NR_037971	ENSMUSG00000100798	Gm19589	-	predicted gene, 19589	ncRNA
mm_119350.1	chr14	41109519	41109521	+	1	NA	intron (NM_133653, intron 3 of 9)	intron (NM_133653, intron 3 of 9)	4487	NM_133653	11720	Mm.14064	NM_133653	ENSMUSG00000037798	Mat1a	AI046368|AdoMet|Ams|MAT|MATA1|SAMS|SAMS1	methionine adenosyltransferase I, alpha	protein-coding
mm_72217.1	chr8	72688387	72688397	+	1	NA	intron (NM_176940, intron 11 of 18)	B3A|SINE|B2	-34878	NM_001113248	20467	Mm.2137	NM_009188	ENSMUSG00000031622	Sin3b	2810430C10Rik	transcriptional regulator, SIN3B (yeast)	protein-coding
mm_133079.1	chr16	59457606	59457627	+	1	NA	intron (NM_001081190, intron 8 of 8)	intron (NM_001081190, intron 8 of 8)	11622	NR_040568	75636	Mm.490522	NR_040568	ENSMUSG00000099983	1700022E09Rik	-	RIKEN cDNA 1700022E09 gene	ncRNA
mm_171859.1	chr5	21689320	21689334	+	1	NA	intron (NM_178728, intron 1 of 4)	intron (NM_178728, intron 1 of 4)	12018	NM_178728	242864	Mm.153292	NM_178728	ENSMUSG00000044968	Napepld	A530089G06|Mbldc1|NAPE-PLD	N-acyl phosphatidylethanolamine phospholipase D	protein-coding
mm_89048.1	chr10	82866603	82866614	+	1	NA	promoter-TSS (NM_025499)	promoter-TSS (NM_025499)	-18	NM_025499	66341	Mm.443284	NM_025499	ENSMUSG00000109864	Eid3	1700027M21Rik|NS4EB	EP300 interacting inhibitor of differentiation 3	protein-coding
mm_109508.1	chr12	111452338	111452353	+	1	NA	intron (NM_009396, intron 11 of 11)	(TCCA)n|Simple_repeat|Simple_repeat	9684	NM_009396	21928	Mm.255332	NM_009396	ENSMUSG00000021281	Tnfaip2	B94|Exoc3l3|M-sec|Tnfip2|tnfb94	tumor necrosis factor, alpha-induced protein 2	protein-coding
mm_92873.1	chr10	82354143	82354158	-	1	NA	Intergenic	Intergenic	-112875	NM_001105557	237411		NM_172789	ENSMUSG00000062931	Zfp938	B230315N10Rik	zinc finger protein 938	protein-coding
mm_124821.1	chr15	9071625	9071635	+	1	NA	exon (NM_001085410, exon 1 of 14)	exon (NM_001085410, exon 1 of 14)	370	NM_001040395	68646	Mm.244226	NM_001040395	ENSMUSG00000022253	Nadk2	MNADK|Nadkd1	NAD kinase 2, mitochondrial	protein-coding
mm_93055.1	chr10	88675760	88675768	-	1	NA	exon (NM_011461, exon 6 of 6)	exon (NM_011461, exon 6 of 6)	7259	NM_011461	20728	Mm.21642	NM_011461	ENSMUSG00000004359	Spic	AU019198|C76795|Prf|Spi-C	Spi-C transcription factor (Spi-1/PU.1 related)	protein-coding
mm_74186.1	chr8	123649741	123649777	+	1	NA	Intergenic	Intergenic	-4170	NM_133955	69581	Mm.168257	NM_133955	ENSMUSG00000039960	Rhou	2310026M05Rik|AI182090|Arhu|CDC42L1|G28K|WRCH-1|WRCH1|mG28K	ras homolog family member U	protein-coding
mm_124871.1	chr15	10177768	10177773	+	1	NA	5' UTR (NM_011169, exon 1 of 10)	5' UTR (NM_011169, exon 1 of 10)	532	NM_011169	19116	Mm.10516	NM_011169	ENSMUSG00000005268	Prlr	AI987712|Pr-1|Pr-3|Prlr-rs1	prolactin receptor	protein-coding
mm_17056.1	chr2	21205343	21205371	-	1	NA	promoter-TSS (NM_027728)	promoter-TSS (NM_027728)	8	NM_027728	71233	Mm.27658	NM_027728	ENSMUSG00000026679	Enkur	4933434I06Rik|AU016229	enkurin, TRPC channel interacting protein	protein-coding
mm_58498.1	chr7	3704679	3704691	+	1	NA	exon (NM_029767, exon 3 of 5)	exon (NM_029767, exon 3 of 5)	644	NM_029767	76846	Mm.13944	NM_029767	ENSMUSG00000006333	Rps9	3010033P07Rik|AL022771|AL022885	ribosomal protein S9	protein-coding
mm_4782.1	chr1	184033673	184033685	+	1	NA	promoter-TSS (NM_022019)	promoter-TSS (NM_022019)	319	NM_028516	73363	Mm.50115	NM_028516	ENSMUSG00000044854	1700056E22Rik	-	RIKEN cDNA 1700056E22 gene	protein-coding
mm_11815.1	chr2	44029651	44029655	+	1	NA	intron (NM_001301832, intron 7 of 14)	intron (NM_001301832, intron 7 of 14)	35671	NR_040622	320872	Mm.445023	NR_040622	ENSMUSG00000085089	Arhgap15os	A430092G05Rik	Rho GTPase activating protein 15, opposite strand	ncRNA
mm_114921.1	chr13	95325170	95325189	+	1	NA	5' UTR (NM_028106, exon 1 of 2)	5' UTR (NM_028106, exon 1 of 2)	354	NM_028106	72114	Mm.3774	NM_028106	ENSMUSG00000041995	Zbed3	0610037K01Rik|2610005H11Rik|AU018975|AU024588	zinc finger, BED type containing 3	protein-coding
mm_49413.1	chr6	28754729	28754750	+	1	NA	intron (NM_019776, intron 15 of 23)	intron (NM_019776, intron 15 of 23)	77008	NM_138682	192198	Mm.443660	NM_138682	ENSMUSG00000049939	Lrrc4	MBAG1|NGL-2|NGL2|NLG-2|Nag14	leucine rich repeat containing 4	protein-coding
mm_6890.1	chr1	84696028	84696038	-	1	NA	TTS (NR_039588)	TTS (NR_039588)	188	NM_152915	227325	Mm.292560	NM_152915	ENSMUSG00000036766	Dner	A930026D19Rik|BET|Bret	delta/notch-like EGF repeat containing	protein-coding
mm_126255.1	chr15	79075210	79075245	+	1	NA	promoter-TSS (NM_145139)	promoter-TSS (NM_145139)	4	NM_145139	223691	Mm.206404	NM_145139	ENSMUSG00000033047	Eif3l	0610011H21Rik|D15N1e|Eif3eip|Eif3ip|Eif3s6ip|HSP-66Y|PAF67	eukaryotic translation initiation factor 3, subunit L	protein-coding
mm_164504.1	chr16	92831275	92831290	-	1	NA	Intergenic	Intergenic	-5208	NM_001111022	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_70003.1	chr7	142387854	142387885	-	1	NA	promoter-TSS (NM_009983)	promoter-TSS (NM_009983)	1	NM_009983	13033	Mm.231395	NM_009983	ENSMUSG00000007891	Ctsd	CD|CatD	cathepsin D	protein-coding
mm_66992.1	chr7	64345395	64345428	-	1	NA	Intergenic	PB1D7|SINE|Alu	28684	NM_177893	330554	Mm.236510	NM_177893	ENSMUSG00000033458	Fan1	6030441H18Rik|Mtmr15|mFAN1	FANCD2/FANCI-associated nuclease 1	protein-coding
mm_53999.1	chr6	7692464	7692469	-	1	NA	intron (NM_012055, intron 1 of 11)	(A)n|Simple_repeat|Simple_repeat	716	NM_012055	27053	Mm.2942	NM_012055	ENSMUSG00000029752	Asns	-	asparagine synthetase	protein-coding
mm_88932.1	chr10	81258149	81258167	+	1	NA	intron (NM_001285853, intron 1 of 12)	intron (NM_001285853, intron 1 of 12)	859	NM_001285853	17179	Mm.2918	NM_010768	ENSMUSG00000004933	Matk	CHK|HYL|Ntk|p56ntk	megakaryocyte-associated tyrosine kinase	protein-coding
mm_161321.1	chr14	46884075	46884075	+	1	NA	intron (NM_001037221, intron 1 of 12)	CpG	1110	NM_001037221	74480	Mm.214454	NM_028966	ENSMUSG00000021838	Samd4	1700024G08Rik|1700111L17Rik|4933436G17Rik|Samd4a|Smaug|Smaug1|sunk	sterile alpha motif domain containing 4	protein-coding
mm_165645.1	chr3	82308416	82308442	+	1	NA	Intergenic	Intergenic	-49643	NM_001081230	213582	Mm.271269	NM_001081230	ENSMUSG00000033900	Map9	5033421J10Rik|5330427D05Rik|ASAP|Mtap9	microtubule-associated protein 9	protein-coding
mm_143622.1	chr17	78856611	78856626	-	1	NA	exon (NM_011163, exon 14 of 16)	exon (NM_011163, exon 14 of 16)	-4074	NR_003363	625054	Mm.311918	NR_003363		Gm6548	EG625054	eukaryotic translation elongation factor 1 alpha 1 pseudogene	pseudo
mm_47687.1	chr5	129008547	129008596	-	1	NA	promoter-TSS (NM_007941)	promoter-TSS (NM_007941)	1	NM_001286034	13852	Mm.260716	NM_007941	ENSMUSG00000029428	Stx2	AW538950|Epim|G1-536-1|Syn-2|repro34	syntaxin 2	protein-coding
mm_64358.1	chr7	142390279	142390293	+	1	NA	Intergenic	Intergenic	-2416	NM_009983	13033	Mm.231395	NM_009983	ENSMUSG00000007891	Ctsd	CD|CatD	cathepsin D	protein-coding
mm_94104.1	chr10	128568666	128568688	-	1	NA	TTS (NM_010153)	TTS (NM_010153)	-2743	NM_011119	18813	Mm.4742	NM_011119	ENSMUSG00000025364	Pa2g4	38kDa|AA672939|Ebp1|Plfap	proliferation-associated 2G4	protein-coding
mm_93696.1	chr10	117845960	117846009	-	1	NA	promoter-TSS (NM_024457)	promoter-TSS (NM_024457)	-10	NM_024457	215449	Mm.233009	NM_024457	ENSMUSG00000052681	Rap1b	2810443E11Rik	RAS related protein 1b	protein-coding
mm_89624.1	chr10	96227811	96227826	+	1	NA	intron (NR_110448, intron 1 of 2)	intron (NR_110448, intron 1 of 2)	1611	NR_110448	74881	Mm.410819	NR_110448		4930459C07Rik	-	RIKEN cDNA 4930459C07 gene	ncRNA
mm_56075.1	chr6	87180767	87180768	-	1	NA	intron (NM_054041, intron 16 of 17)	intron (NM_054041, intron 16 of 17)	76021	NM_001167937	52372	Mm.282851	NM_001167937	ENSMUSG00000090891	D6Ertd527e	AU043841	DNA segment, Chr 6, ERATO Doi 527, expressed	protein-coding
mm_124663.1	chr15	6299858	6299868	+	1	NA	promoter-TSS (NM_001008702)	promoter-TSS (NM_001008702)	74	NM_001008702	13132	Mm.240830	NM_023118	ENSMUSG00000022150	Dab2	5730435J12Rik|AA960054|AI957090|D15Wsu122e|D630005B22Rik|Doc-2|Doc2|p96	disabled 2, mitogen-responsive phosphoprotein	protein-coding
mm_152464.1	chr19	10948298	10948342	-	1	NA	exon (NM_023731, exon 1 of 4)	exon (NM_023731, exon 1 of 4)	946	NM_023731	108673	Mm.294908	NM_023731	ENSMUSG00000024732	Ccdc86	4933411H20Rik|6720480F16Rik|D19Ertd678e	coiled-coil domain containing 86	protein-coding
mm_55717.1	chr6	73221666	73221676	-	1	NA	promoter-TSS (NM_001164669)	promoter-TSS (NM_001164669)	-40	NM_001164669	330355	Mm.333166	NM_001164669	ENSMUSG00000052861	Dnah6	9830168K20|A730004I20Rik|Dnahc6|mKIAA1697|mdhc6	dynein, axonemal, heavy chain 6	protein-coding
mm_34921.1	chr4	155761336	155761339	+	1	NA	promoter-TSS (NM_179203)	promoter-TSS (NM_179203)	145	NR_027972	70448	Mm.70636	NM_175157	ENSMUSG00000054514	Atad3aos	2610204G22Rik	ATPase family, AAA domain containing 3A, opposite strand	ncRNA
mm_85363.1	chr9	103219247	103219260	-	1	NA	exon (NM_133977, exon 11 of 17)	exon (NM_133977, exon 11 of 17)	11033	NM_133977	22041	Mm.37214	NM_133977	ENSMUSG00000032554	Trf	AI266983|Cd176|HP|Tf|Tfn|hpx	transferrin	protein-coding
mm_41789.1	chr5	103738464	103738466	+	1	NA	Intergenic	Intergenic	-15697	NM_133919	17355	Mm.6949	NM_133919	ENSMUSG00000029313	Aff1	9630032B01Rik|AW319193|Af4|Mllt2h|Rob	AF4/FMR2 family, member 1	protein-coding
mm_169440.1	chr14	56694039	56694052	-	1	NA	intron (NM_023773, intron 11 of 13)	LSU-rRNA_Hsa|rRNA|rRNA	6955	NR_046209	100503823	Mm.474486	NR_046209		Gm16973	-	predicted gene, 16973	ncRNA
mm_55388.1	chr6	59024454	59024465	-	1	NA	promoter-TSS (NM_153574)	promoter-TSS (NM_153574)	43	NM_153574	58909	Mm.28813	NM_153574	ENSMUSG00000037709	Fam13a	AI462012|D430015B01Rik|FAM13A1|Precm1	family with sequence similarity 13, member A	protein-coding
mm_154952.1	chrX	36604820	36604873	+	1	NA	exon (NM_016783, exon 3 of 3)	exon (NM_016783, exon 3 of 3)	6653	NM_016783	53328	Mm.9052	NM_016783	ENSMUSG00000006373	Pgrmc1	AA415812|HPR6.6|PPMR|Vema	progesterone receptor membrane component 1	protein-coding
mm_53257.1	chr6	127887583	127887639	+	1	NA	promoter-TSS (NM_026743)	promoter-TSS (NM_026743)	-11	NM_026743	68498	Mm.174368	NM_026743	ENSMUSG00000030351	Tspan11	1110014F12Rik|AU067806	tetraspanin 11	protein-coding
mm_30859.1	chr4	28965102	28965143	+	1	NA	3' UTR (NM_010141, exon 17 of 17)	3' UTR (NM_010141, exon 17 of 17)	151977	NM_001122889	13841	Mm.257266	NM_010141	ENSMUSG00000028289	Epha7	Cek11|Ebk|Ehk3|Hek11|Mdk1	Eph receptor A7	protein-coding
mm_159157.1	chr2	89753003	89753003	-	1	NA	promoter-TSS (NM_146373)	promoter-TSS (NM_146373)	-177	NM_146373	258370	Mm.480193	NM_146373	ENSMUSG00000075075	Olfr1253	MOR231-18|MOR231-19P|Olfr1253-ps1|Olfr1559-ps1	olfactory receptor 1253	protein-coding
mm_6388.1	chr1	72849287	72849299	-	1	NA	exon (NM_008342, exon 2 of 4)	exon (NM_008342, exon 2 of 4)	23906	NM_001310659	16008	Mm.141936	NM_008342	ENSMUSG00000039323	Igfbp2	AI255832|IBP-2|Igfbp-2|mIGFBP-2	insulin-like growth factor binding protein 2	protein-coding
mm_66813.1	chr7	48124220	48124222	-	1	NA	Intergenic	IAPEY4_LTR|LTR|ERVK	44764	NM_207538	404239	Mm.377927	NM_207538	ENSMUSG00000070551	Mrgprb5	Mgrg11|MrgB5	MAS-related GPR, member B5	protein-coding
mm_141284.1	chr17	27909647	27909658	-	1	NA	intron (NM_001286040, intron 1 of 24)	CpG	346	NM_181413	224650	Mm.32556	NM_181413	ENSMUSG00000024219	Anks1	Anks1a|mKIAA0229	ankyrin repeat and SAM domain containing 1	protein-coding
mm_53051.1	chr6	124805817	124805854	+	1	NA	Intergenic	CpG	-2826	NM_001306051	14794	Mm.261906	NM_013539	ENSMUSG00000038451	Spsb2	AI461677|C9|Grcc9|SSB2	splA/ryanodine receptor domain and SOCS box containing 2	protein-coding
mm_162406.1	chr1	86357022	86357031	+	1	NA	promoter-TSS (NR_002851)	promoter-TSS (NR_002851)	-699	NR_002851	80828		NR_002851	ENSMUSG00000064823	Snord82	Rnu82|U82|Z25	small nucleolar RNA, C/D box 82	snoRNA
mm_147807.1	chr18	61665526	61665532	-	1	NA	promoter-TSS (NR_045402)	promoter-TSS (NR_045402)	9	NR_045402	328968	Mm.392305	NR_045402		Carmn	Carmen|E330013P06|Gm16908|Mir143hg	cardiac mesoderm enhancer-associated non-coding RNA	ncRNA
mm_36184.1	chr4	62208724	62208737	-	1	NA	promoter-TSS (NM_009554)	promoter-TSS (NM_009554)	-184	NM_001290350	22696	Mm.5011	NM_009554	ENSMUSG00000028389	Zfp37	Tzn|Zfp-37	zinc finger protein 37	protein-coding
mm_50746.1	chr6	52745696	52745698	+	1	NA	intron (NM_025816, intron 11 of 17)	intron (NM_025816, intron 11 of 17)	31968	NM_025816	52440	Mm.389757	NM_025816	ENSMUSG00000004535	Tax1bp1	1200003J11Rik|1700069J21Rik|AA930106|D6Ertd404e|D6Ertd772e|T6bp|TXBP151	Tax1 (human T cell leukemia virus type I) binding protein 1	protein-coding
mm_78053.1	chr9	14784719	14784758	+	1	NA	promoter-TSS (NM_018736)	promoter-TSS (NM_018736)	84	NM_018736	17535	Mm.149071	NM_018736	ENSMUSG00000031928	Mre11a	Mre11|Mre11b	MRE11A homolog A, double strand break repair nuclease	protein-coding
mm_161895.1	chr18	43963140	43963140	+	1	NA	promoter-TSS (NM_001081180)	promoter-TSS (NM_001081180)	-101	NM_001081180	72432	Mm.35369	NM_001081180	ENSMUSG00000055561	Spink5	2310065D10Rik|AV238912|LEKT1|LETK1|VAKT1	serine peptidase inhibitor, Kazal type 5	protein-coding
mm_98117.1	chr11	87127043	87127051	+	1	NA	promoter-TSS (NM_197987)	promoter-TSS (NM_197987)	-28	NM_197987	68729	Mm.17436	NM_197987	ENSMUSG00000018548	Trim37	1110032A10Rik|2810004E07Rik|AI848587|AU043018|MUL|TEF3|mKIAA0898	tripartite motif-containing 37	protein-coding
mm_109665.1	chr12	113023371	113023389	+	1	NA	intron (NM_001291444, intron 1 of 23)	L1MEg|LINE|L1	8872	NM_001291444	217893	Mm.35754	NM_198165	ENSMUSG00000021143	Pacs2	6720425G15Rik|AW208651|AW489976|E230011J22|Pacs1l|mKIAA0602	phosphofurin acidic cluster sorting protein 2	protein-coding
mm_74938.1	chr8	25808249	25808250	-	1	NA	promoter-TSS (NM_011485)	promoter-TSS (NM_011485)	-225	NM_011485	20845	Mm.293314	NM_011485	ENSMUSG00000031574	Star	AV363654|D8Ertd419e|stARD1	steroidogenic acute regulatory protein	protein-coding
mm_128312.1	chr15	37899694	37899707	-	1	NA	Intergenic	Intergenic	61355	NM_199476	382985	Mm.24738	NM_199476	ENSMUSG00000022292	Rrm2b	p53R2	ribonucleotide reductase M2 B (TP53 inducible)	protein-coding
mm_65528.1	chr7	25788515	25788525	-	1	NA	5' UTR (NM_001190974, exon 1 of 19)	5' UTR (NM_001190974, exon 1 of 19)	213	NM_001190974	26362	Mm.4128	NM_009465	ENSMUSG00000002602	Axl	AI323647|Ark|Tyro7|Ufo	AXL receptor tyrosine kinase	protein-coding
mm_69129.1	chr7	127026722	127026780	-	1	NA	promoter-TSS (NM_010772)	promoter-TSS (NM_010772)	-272	NM_010772	17188	Mm.378964	NM_010772	ENSMUSG00000030678	Maz	MAZI|PUR1|Pur-1|SAF-1|SAF-2	MYC-associated zinc finger protein (purine-binding transcription factor)	protein-coding
mm_66889.1	chr7	59280052	59280057	-	1	NA	intron (NM_173010, intron 4 of 8)	intron (NM_173010, intron 4 of 8)	44095	NR_015479	330544	Mm.9002	NR_015479	ENSMUSG00000100826	C230091D08Rik	-	RIKEN cDNA C230091D08 gene	ncRNA
mm_53148.1	chr6	125241954	125241976	+	1	NA	Intergenic	Intergenic	-4938	NM_001286753	21940	Mm.367714	NM_001033126	ENSMUSG00000030336	Cd27	S152|Tnfrsf7|Tp55	CD27 antigen	protein-coding
mm_2539.1	chr1	107422682	107422695	+	1	NA	promoter-TSS (NM_027548)	promoter-TSS (NM_027548)	-1	NM_027548	116872	Mm.66015	NM_027548	ENSMUSG00000067001	Serpinb7	4631416M05Rik|megsin|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 7	protein-coding
mm_85271.1	chr9	99436614	99436622	-	1	NA	promoter-TSS (NM_008624)	promoter-TSS (NM_008624)	94	NM_008624	17532	Mm.2045	NM_008624	ENSMUSG00000032470	Mras	2900078C09Rik|AI326250	muscle and microspikes RAS	protein-coding
mm_153418.1	chr19	40638730	40638738	-	1	NA	intron (NM_001304721, intron 1 of 9)	intron (NM_001304721, intron 1 of 9)	-21036	NM_009848	12495	Mm.2824	NM_009848	ENSMUSG00000048120	Entpd1	2610206B08Rik|AA408691|Cd39|NTPDase-1	ectonucleoside triphosphate diphosphohydrolase 1	protein-coding
mm_127170.1	chr15	98790001	98790017	+	1	NA	5' UTR (NM_021279, exon 1 of 4)	5' UTR (NM_021279, exon 1 of 4)	152	NM_021279	22408	Mm.1123	NM_021279	ENSMUSG00000022997	Wnt1	Int-1|Wnt-1|sw|swaying	wingless-type MMTV integration site family, member 1	protein-coding
mm_143406.1	chr17	70819783	70819786	-	1	NA	3' UTR (NM_177639, exon 12 of 12)	3' UTR (NM_177639, exon 12 of 12)	26993	NM_001164077	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_87230.1	chr10	40570372	40570390	+	1	NA	promoter-TSS (NM_027572)	promoter-TSS (NM_027572)	19	NM_027572	70840	Mm.332570	NM_027572	ENSMUSG00000019834	Slc22a16	4921504E14Rik|CT2|FLIPT2|OCT6|OKB1	solute carrier family 22 (organic cation transporter), member 16	protein-coding
mm_147007.1	chr18	34506665	34506684	-	1	NA	5' UTR (NM_146084, exon 1 of 21)	5' UTR (NM_146084, exon 1 of 21)	149	NM_146084	225358	Mm.226899	NM_146084	ENSMUSG00000036501	Fam13b	2610024E20Rik|AW060714|AW546153	family with sequence similarity 13, member B	protein-coding
mm_75518.1	chr8	54724475	54724494	-	1	NA	promoter-TSS (NM_001172152)	promoter-TSS (NM_001172152)	-116	NM_001172152	244484	Mm.95281	NM_028220	ENSMUSG00000039375	Wdr17	3010002I12Rik|B230207L18Rik	WD repeat domain 17	protein-coding
mm_38725.1	chr4	145234972	145234981	-	1	NA	intron (NM_011610, intron 1 of 9)	intron (NM_011610, intron 1 of 9)	11894	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_4398.1	chr1	172370865	172370881	+	1	NA	3' UTR (NM_001039484, exon 2 of 2)	3' UTR (NM_001039484, exon 2 of 2)	-5658	NM_026234	67556	Mm.26612	NM_026234	ENSMUSG00000050229	Pigm	4933437L05Rik|AI644422|AV302080|C920011G20Rik	phosphatidylinositol glycan anchor biosynthesis, class M	protein-coding
mm_65319.1	chr7	24904131	24904141	-	1	NA	promoter-TSS (NM_001130152)	promoter-TSS (NM_001130152)	-210	NM_001130152	16801	Mm.3181	NM_008488	ENSMUSG00000040940	Arhgef1	Lbcl2|Lsc	Rho guanine nucleotide exchange factor (GEF) 1	protein-coding
mm_110739.1	chr12	69791295	69791295	-	1	NA	promoter-TSS (NM_183294)	promoter-TSS (NM_183294)	-588	NM_183294	71091	Mm.132325	NM_183294	ENSMUSG00000020990	Cdkl1	4933411O17Rik	cyclin-dependent kinase-like 1 (CDC2-related kinase)	protein-coding
mm_78853.1	chr9	44336293	44336296	+	1	NA	TTS (NM_001110251)	TTS (NM_001110251)	1579	NM_010436	15270	Mm.245931	NM_010436	ENSMUSG00000049932	H2afx	AW228881|H2A.X|H2ax|Hist5-2ax|gammaH2ax	H2A histone family, member X	protein-coding
mm_129228.1	chr15	76614218	76614251	-	1	NA	intron (NM_028064, intron 5 of 11)	intron (NM_028064, intron 5 of 11)	2618	NM_028064	72027	Mm.276829	NM_028064	ENSMUSG00000063354	Slc39a4	1600025H15Rik|AU041686|AWMS2|ZIP4	solute carrier family 39 (zinc transporter), member 4	protein-coding
mm_45976.1	chr5	90472025	90472103	-	1	NA	exon (NM_009654, exon 11 of 15)	exon (NM_009654, exon 11 of 15)	11194	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_151383.1	chr19	56319686	56319695	+	1	NA	TTS (NM_198059)	TTS (NM_198059)	31778	NM_146101	226243	Mm.25791	NM_146101	ENSMUSG00000025075	Habp2	AI035669|FSAP|HABP|HGFAL|PHBP	hyaluronic acid binding protein 2	protein-coding
mm_62182.1	chr7	97453236	97453303	+	1	NA	promoter-TSS (NM_001012434)	promoter-TSS (NM_001012434)	65	NM_001012434	233529	Mm.334033	NM_001010826	ENSMUSG00000051727	Kctd14	AI449310|D7Ertd760e	potassium channel tetramerisation domain containing 14	protein-coding
mm_116879.1	chr13	55022772	55022783	-	1	NA	Intergenic	Intergenic	-1392	NM_001033245	212032	Mm.267479	NM_001033245	ENSMUSG00000025877	Hk3	HK III|HK-III	hexokinase 3	protein-coding
mm_30360.1	chr3	151835931	151835944	-	1	NA	5' UTR (NM_008966, exon 2 of 3)	5' UTR (NM_008966, exon 2 of 3)	1591	NM_008966	19220	Mm.331442	NM_008966	ENSMUSG00000028036	Ptgfr	AI957154|PGF|fp	prostaglandin F receptor	protein-coding
mm_85549.1	chr9	106685703	106685728	-	1	NA	5' UTR (NM_011573, exon 1 of 6)	5' UTR (NM_011573, exon 1 of 6)	101	NM_011573	21767	Mm.22266	NM_011573	ENSMUSG00000040813	Tex264	TEG-264	testis expressed gene 264	protein-coding
mm_87193.1	chr10	39465462	39465485	+	1	NA	intron (NM_001122893, intron 3 of 13)	intron (NM_001122893, intron 3 of 13)	95674	NM_001122893	14360	Mm.4848	NM_008054	ENSMUSG00000019843	Fyn	AI448320|AW552119	Fyn proto-oncogene	protein-coding
mm_104240.1	chr11	88718166	88718196	-	1	NA	promoter-TSS (NM_054043)	promoter-TSS (NM_054043)	48	NM_054043	76626	Mm.400451	NM_054043	ENSMUSG00000069769	Msi2	1700105C15Rik|AI451722|AI563628|AW489193|Msi2h	musashi RNA-binding protein 2	protein-coding
mm_140361.1	chr17	86855691	86855695	+	1	NA	Intergenic	RMER4B|LTR|ERVK	-61655	NM_001277980	78469	Mm.67234	NM_030104	ENSMUSG00000037689	Tmem247	1700090G07Rik	transmembrane protein 247	protein-coding
mm_3865.1	chr1	160989373	160989388	+	1	NA	exon (NM_080844, exon 3 of 8)	exon (NM_080844, exon 3 of 8)	10774	NM_080844	11905	Mm.260770	NM_080844	ENSMUSG00000026715	Serpinc1	AI114908|ATIII|At-3|At3	serine (or cysteine) peptidase inhibitor, clade C (antithrombin), member 1	protein-coding
mm_150348.1	chr19	34643325	34643330	+	1	NA	intron (NM_008331, intron 1 of 1)	intron (NM_008331, intron 1 of 1)	2438	NM_008331	15957	Mm.439751	NM_008331	ENSMUSG00000034459	Ifit1	ISG56|Ifi56|P56	interferon-induced protein with tetratricopeptide repeats 1	protein-coding
mm_173055.1	chrX	124549353	124549354	+	1	NA	Intergenic	Intergenic	-413443	NM_001100616	100038941	Mm.388852	NM_001100616	ENSMUSG00000072049	Vmn2r121	EG625699	vomeronasal 2, receptor 121	protein-coding
mm_53347.1	chr6	129350223	129350231	+	1	NA	promoter-TSS (NM_177686)	promoter-TSS (NM_177686)	-17	NM_177686	232413	Mm.90241	NM_177686	ENSMUSG00000053063	Clec12a	CLL-1|D230024O04|KLRL1|Micl	C-type lectin domain family 12, member a	protein-coding
mm_19822.1	chr2	110840117	110840154	-	1	NA	intron (NM_001128103, intron 4 of 26)	intron (NM_001128103, intron 4 of 26)	110109	NM_001128103	228432	Mm.483325	NM_001081556	ENSMUSG00000074968	Ano3	AI838058|B230324K02Rik|Tmem16c	anoctamin 3	protein-coding
mm_124912.1	chr15	11064802	11064823	+	1	NA	promoter-TSS (NM_175501)	promoter-TSS (NM_175501)	39	NM_175501	239337	Mm.224825	NM_175501	ENSMUSG00000047497	Adamts12	ADAMTS-12|AI605170	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 12	protein-coding
mm_55756.1	chr6	78378895	78378917	-	1	NA	promoter-TSS (NM_001161741)	promoter-TSS (NM_001161741)	-41	NM_013893	30053	Mm.33691	NM_013893	ENSMUSG00000068341	Reg3d	INGAP|Ingaprp	regenerating islet-derived 3 delta	protein-coding
mm_139421.1	chr17	53479460	53479470	+	1	NA	5' UTR (NM_025887, exon 1 of 6)	5' UTR (NM_025887, exon 1 of 6)	231	NM_025887	271457	Mm.329123	NM_025887	ENSMUSG00000017831	Rab5a	2410015H04Rik|AI663973|AU021172|nnyRab5a	RAB5A, member RAS oncogene family	protein-coding
mm_159994.1	chr6	116506271	116506271	+	1	NA	promoter-TSS (NM_001011800)	promoter-TSS (NM_001011800)	-245	NM_001011800	258019	Mm.67253	NM_001011800	ENSMUSG00000053251	Olfr212	4931403F16Rik|MOR119-4	olfactory receptor 212	protein-coding
mm_10010.1	chr1	191872181	191872193	-	1	NA	Intergenic	Intergenic	-34594	NM_009579	22782	Mm.9024	NM_009579	ENSMUSG00000037434	Slc30a1	AI839647|C130040I11Rik|Znt1	solute carrier family 30 (zinc transporter), member 1	protein-coding
mm_129850.1	chr15	83170499	83170515	-	1	NA	intron (NM_029787, intron 1 of 8)	intron (NM_029787, intron 1 of 8)	1701	NM_029787	109754	Mm.22560	NM_029787	ENSMUSG00000018042	Cyb5r3	0610016L08Rik|2500002N19Rik|C85115|Dia-1|Dia1|WU:AL591952.1-001|WU:AL591952.1-002|WU:AL591952.1-003|WU:Cyb5r3	cytochrome b5 reductase 3	protein-coding
mm_52968.1	chr6	123138433	123138444	+	1	NA	intron (NM_011999, intron 3 of 5)	intron (NM_011999, intron 3 of 5)	15122	NM_001170333	26888	Mm.47384	NM_011999	ENSMUSG00000030148	Clec4a2	Clec4a|Clecsf6|DCIR|Dcir1	C-type lectin domain family 4, member a2	protein-coding
mm_16985.1	chr2	18048348	18048351	-	1	NA	promoter-TSS (NM_028317)	promoter-TSS (NM_028317)	100	NM_028317	72668	Mm.102183	NM_028317	ENSMUSG00000054074	Skida1	2810030E01Rik|5730507N06Rik|BB088113	SKI/DACH domain containing 1	protein-coding
mm_23561.1	chr3	62444874	62444877	+	1	NA	intron (NM_001081295, intron 10 of 13)	intron (NM_001081295, intron 10 of 13)	62113	NM_028136	72162	Mm.224233	NM_028136	ENSMUSG00000027770	Dhx36	2810407E23Rik|AI452301|AU022184|Ddx36|mKIAA1488	DEAH (Asp-Glu-Ala-His) box polypeptide 36	protein-coding
mm_140744.1	chr17	15830805	15830816	-	1	NA	Intergenic	CpG	-4224	NM_178615	68799	Mm.293466	NM_178615	ENSMUSG00000048027	Rgmb	1110059F19Rik|DRAGON	repulsive guidance molecule family member B	protein-coding
mm_141943.1	chr17	35055297	35055329	-	1	NA	exon (NM_033444, exon 5 of 6)	exon (NM_033444, exon 5 of 6)	-3722	NM_001190449	51793	Mm.1457	NM_016765	ENSMUSG00000007039	Ddah2	1110003M04Rik|AU019324|AW413173|DDAH-2|DDAHII|Ddah|G6a|NG30	dimethylarginine dimethylaminohydrolase 2	protein-coding
mm_29217.1	chr3	107091785	107091820	-	1	NA	Intergenic	Intergenic	-9765	NM_008417	16490	Mm.39285	NM_008417	ENSMUSG00000040724	Kcna2	Akr6a4|ENSMUSG00000074335|Gm10672|Kca1-2|Kv1.2|Mk-2	potassium voltage-gated channel, shaker-related subfamily, member 2	protein-coding
mm_107877.1	chr12	69985825	69985839	+	1	NA	intron (NM_022028, intron 1 of 4)	intron (NM_022028, intron 1 of 4)	1170	NM_022028	64010	Mm.390480	NM_022028	ENSMUSG00000021067	Sav1	1700040G09Rik|Salv|Sav|WW45|Wwp3|Wwp4	salvador family WW domain containing 1	protein-coding
mm_142888.1	chr17	51832667	51832678	-	1	NA	promoter-TSS (NM_009122)	promoter-TSS (NM_009122)	-25	NM_009122	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_145445.1	chr18	59240023	59240025	+	1	NA	intron (NM_001081328, intron 2 of 2)	intron (NM_001081328, intron 2 of 2)	64684	NM_001081328	78923	Mm.84007	NM_001081328	ENSMUSG00000058152	Chsy3	4833446K15Rik|AI662215	chondroitin sulfate synthase 3	protein-coding
mm_76871.1	chr8	105529377	105529415	-	1	NA	intron (NM_013477, intron 3 of 7)	intron (NM_013477, intron 3 of 7)	10650	NM_008289	15484	Mm.5079	NM_008289	ENSMUSG00000031891	Hsd11b2	11HSD2	hydroxysteroid 11-beta dehydrogenase 2	protein-coding
mm_144454.1	chr18	23352589	23352614	+	1	NA	intron (NM_001285813, intron 1 of 21)	intron (NM_001285813, intron 1 of 21)	42581	NM_001285813	13527	Mm.94371	NM_010087	ENSMUSG00000024302	Dtna	2210407P21Rik|DTN-A|Dtn|Gm19389|a-DB-1|adbn	dystrobrevin alpha	protein-coding
mm_170403.1	chr18	64081512	64081516	-	1	NA	Intergenic	Intergenic	-172845	NM_009182	20451	Mm.252110	NM_009182	ENSMUSG00000056812	St8sia3	AI847333|ST8SiaIII|Siat8c	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3	protein-coding
mm_127302.1	chr15	100227814	100227824	+	1	NA	promoter-TSS (NM_007497)	promoter-TSS (NM_007497)	-40	NM_007497	11908	Mm.676	NM_007497	ENSMUSG00000023027	Atf1	-	activating transcription factor 1	protein-coding
mm_118394.1	chr13	118715687	118715735	-	1	NA	exon (NM_008002, exon 1 of 3)	exon (NM_008002, exon 1 of 3)	1012	NM_008002	14165	Mm.317323	NM_008002	ENSMUSG00000021732	Fgf10	AEY17|BB213776|Fgf-10|Gsfaey17	fibroblast growth factor 10	protein-coding
mm_62985.1	chr7	120204001	120204013	+	1	NA	promoter-TSS (NM_026458)	promoter-TSS (NM_026458)	43	NM_026458	67928	Mm.158178	NM_026458	ENSMUSG00000062017	Abca14	1700110B15Rik|4930539G24Rik	ATP-binding cassette, sub-family A (ABC1), member 14	protein-coding
mm_144541.1	chr18	27336852	27336854	+	1	NA	Intergenic	Lx5b|LINE|L1	-1223311	NR_045398	320624	Mm.50107	NR_045398		4930474G06Rik	-	RIKEN cDNA 4930474G06 gene	ncRNA
mm_102029.1	chr11	51688615	51688669	-	1	NA	promoter-TSS (NM_025319)	promoter-TSS (NM_025319)	-8	NM_025319	66050	Mm.35693	NM_025319	ENSMUSG00000007777	0610009B22Rik	-	RIKEN cDNA 0610009B22 gene	protein-coding
mm_133612.1	chr16	91545712	91545722	+	1	NA	Intergenic	Intergenic	-1377	NM_008338	15980	Mm.249364	NM_008338	ENSMUSG00000022965	Ifngr2	Ifgr2|Ifgt	interferon gamma receptor 2	protein-coding
mm_145168.1	chr18	46850035	46850059	+	1	NA	promoter-TSS (NM_029008)	promoter-TSS (NM_029008)	8	NM_029008	74574	Mm.26379	NM_029008	ENSMUSG00000024481	Lvrn	4833403I15Rik|APQ|Aqpep	laeverin	protein-coding
mm_11520.1	chr2	32608986	32609033	+	1	NA	intron (NM_001289549, intron 2 of 6)	intron (NM_001289549, intron 2 of 6)	2024	NR_110347	50935	Mm.88831	NM_016973	ENSMUSG00000026811	St6galnac6	ST6GalNAcVI|Siat7f	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 6	protein-coding
mm_105514.1	chr11	106267606	106267619	-	1	NA	promoter-TSS (NM_031878)	promoter-TSS (NM_031878)	20	NM_031878	83796	Mm.21772	NM_031878	ENSMUSG00000078619	Smarcd2	AW322457|Baf60b	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2	protein-coding
mm_69422.1	chr7	132762521	132762524	-	1	NA	intron (NM_001347630, intron 2 of 3)	L1MEd|LINE|L1	14394	NM_001347630	77938	Mm.225649	NM_175268	ENSMUSG00000030956	Fam53b	A930008G19Rik|mKIAA0140	family with sequence similarity 53, member B	protein-coding
mm_93874.1	chr10	123196977	123196987	-	1	NA	promoter-TSS (NM_027604)	promoter-TSS (NM_027604)	37	NM_027604	14479	Mm.244209	NM_027604	ENSMUSG00000020124	Usp15	4921514G19Rik|AI327321|E430033I05Rik|Gcap18	ubiquitin specific peptidase 15	protein-coding
mm_164767.1	chr17	86505219	86505225	-	1	NA	intron (NM_011104, intron 10 of 14)	intron (NM_011104, intron 10 of 14)	-218044	NR_045435	72104	Mm.443401	NR_045435	ENSMUSG00000100738	2010106C02Rik	-	RIKEN cDNA 2010106C02 gene	ncRNA
mm_50498.1	chr6	49033123	49033142	+	1	NA	Intergenic	Intergenic	-3386	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_2292.1	chr1	91456776	91456789	+	1	NA	intron (NM_011066, intron 1 of 22)	intron (NM_011066, intron 1 of 22)	2546	NM_011066	18627	Mm.482463	NM_011066	ENSMUSG00000055866	Per2	mKIAA0347|mPer2	period circadian clock 2	protein-coding
mm_104954.1	chr11	100141012	100141158	-	1	NA	exon (NM_008471, exon 6 of 6)	exon (NM_008471, exon 6 of 6)	2614	NM_001313963	16669	Mm.439699	NM_008471	ENSMUSG00000020911	Krt19	AI663979|CK-19|EndoC|K19|Krt-1.19|Krt1-19	keratin 19	protein-coding
mm_84709.1	chr9	72985345	72985397	-	1	NA	promoter-TSS (NM_001286546)	promoter-TSS (NM_001286546)	5	NM_001198789	546143	Mm.260946	NM_001198789	ENSMUSG00000086158	Ccpg1os	EG546143|Gm5918	cell cycle progression 1, opposite strand	protein-coding
mm_169940.1	chr16	64950031	64950041	-	1	NA	intron (NM_008310, intron 2 of 2)	IAP1-MM_LTR|LTR|ERVK	97951	NM_178647	106143	Mm.10160	NM_178647	ENSMUSG00000054604	Cggbp1	AA960172|AL023996|AW045841	CGG triplet repeat binding protein 1	protein-coding
mm_78218.1	chr9	21545079	21545100	+	1	NA	3' UTR (NM_206536, exon 6 of 6)	3' UTR (NM_206536, exon 6 of 6)	-1805	NM_021531	59035	Mm.178115	NM_021531	ENSMUSG00000032185	Carm1	Prmt4	coactivator-associated arginine methyltransferase 1	protein-coding
mm_16884.1	chr2	13011075	13011107	-	1	NA	promoter-TSS (NM_153155)	promoter-TSS (NM_153155)	-227	NM_153155	227580	Mm.229322	NM_153155	ENSMUSG00000049630	C1ql3	1110065A22Rik|AI661623|C1ql|C1qtnf13|CTRP13|K100	C1q-like 3	protein-coding
mm_137225.1	chr17	24252585	24252589	+	1	NA	Intergenic	Intergenic	-1178	NM_007634	12449	Mm.77695	NM_007634	ENSMUSG00000072082	Ccnf	CycF|Fbxo1	cyclin F	protein-coding
mm_27783.1	chr3	74126381	74126390	-	1	NA	Intergenic	RMER17B|LTR|ERVK	-109108	NR_040450	100504692	Mm.394454	NR_040450	ENSMUSG00000104096	Gm20356	-	predicted gene, 20356	ncRNA
mm_66617.1	chr7	45474277	45474299	-	1	NA	3' UTR (NM_027903, exon 7 of 7)	3' UTR (NM_027903, exon 7 of 7)	-7390	NM_007527	12028	Mm.19904	NM_007527	ENSMUSG00000003873	Bax	-	BCL2-associated X protein	protein-coding
mm_7189.1	chr1	92902884	92902921	-	1	NA	promoter-TSS (NM_172850)	promoter-TSS (NM_172850)	4	NM_172850	241158	Mm.108280	NM_172850	ENSMUSG00000034212	Ankmy1	4930483I10Rik|ZMYND13	ankyrin repeat and MYND domain containing 1	protein-coding
mm_47468.1	chr5	123671151	123671172	-	1	NA	intron (NM_001347468, intron 1 of 24)	intron (NM_001347468, intron 1 of 24)	13200	NM_019765	56430	Mm.241109	NM_019765	ENSMUSG00000049550	Clip1	1110007I12Rik|4631429H07Rik|AV017631|C81039|CLIP-170|CLIP170|CYLN1|Clip50|Rsn|mKIAA4046|restin	CAP-GLY domain containing linker protein 1	protein-coding
mm_85101.1	chr9	94538076	94538089	-	1	NA	promoter-TSS (NM_001033145)	promoter-TSS (NM_001033145)	-1	NM_001033145	68861	Mm.258746	NM_001033145	ENSMUSG00000045414	1190002N15Rik	GoPro49|HASF	RIKEN cDNA 1190002N15 gene	protein-coding
mm_6225.1	chr1	66930238	66930261	-	1	NA	exon (NM_001113387, exon 3 of 7)	exon (NM_001113387, exon 3 of 7)	5117	NM_001113387	17901	Mm.1000	NM_021285	ENSMUSG00000061816	Myl1	AI325107|MLC1f|MLC3f|Mylf	myosin, light polypeptide 1	protein-coding
mm_117044.1	chr13	58358815	58358823	-	1	NA	Intergenic	CpG	-3957	NM_175214	75050	Mm.446094	NM_175214	ENSMUSG00000060176	Kif27	4930517I18Rik	kinesin family member 27	protein-coding
mm_44247.1	chr5	5367131	5367154	-	1	NA	intron (NM_011074, intron 2 of 14)	intron (NM_011074, intron 2 of 14)	13109	NM_011074	18647	Mm.389061	NM_011074	ENSMUSG00000028926	Cdk14	Pftk1|mKIAA0834	cyclin-dependent kinase 14	protein-coding
mm_116598.1	chr13	48546494	48546524	-	1	NA	Intergenic	CpG	-8237	NR_029725	387244		NR_029725	ENSMUSG00000065421	Mirlet7a-1	Let-7a|Mirnlet7a|Mirnlet7a-1|let-7a-1	microRNA let7a-1	ncRNA
mm_86706.1	chr10	18845013	18845023	+	1	NA	promoter-TSS (NM_022032)	promoter-TSS (NM_022032)	-53	NM_022032	64058	Mm.28209	NM_022032	ENSMUSG00000019851	Perp	1110017A08Rik|KCP1|KRTCAP1|PIGPC1|THW	PERP, TP53 apoptosis effector	protein-coding
mm_130316.1	chr15	97247307	97247315	-	1	NA	promoter-TSS (NM_001164602)	promoter-TSS (NM_001164602)	-24	NM_001164602	105827	Mm.24005	NM_178114	ENSMUSG00000048218	Amigo2	AI415330|AMIGO-2|AW208913|Ali1	adhesion molecule with Ig like domain 2	protein-coding
mm_146647.1	chr18	11050689	11050702	-	1	NA	non-coding (NR_105023, exon 3 of 6)	non-coding (NR_105023, exon 3 of 6)	-1815	NM_010258	14465	Mm.329287	NM_010258	ENSMUSG00000005836	Gata6	AA410133|GATA-6	GATA binding protein 6	protein-coding
mm_169391.1	chr14	43312482	43312482	+	1	NA	Intergenic	BGLII|LTR|ERVK	35329	NM_027940	71826	Mm.335855	NM_027940	ENSMUSG00000095384	1700001F09Rik	Gm10377	RIKEN cDNA 1700001F09 gene	protein-coding
mm_75119.1	chr8	34759057	34759060	-	1	NA	Intergenic	Intergenic	-48552	NM_176933	319520	Mm.170276	NM_176933	ENSMUSG00000031530	Dusp4	2700078F24Rik|AI844617|BB104621|E130306H24Rik|MKP2	dual specificity phosphatase 4	protein-coding
mm_39666.1	chr5	25246776	25246802	+	1	NA	intron (NM_144908, intron 1 of 11)	intron (NM_144908, intron 1 of 11)	23896	NM_144908	231050	Mm.21814	NM_144908	ENSMUSG00000038072	Galnt11	A430075I06Rik|AI648252|E430002F06Rik	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 11	protein-coding
mm_131633.1	chr16	20188792	20188802	+	1	NA	intron (NM_001033237, intron 10 of 29)	RLTR40|LTR|ERVK	-12563	NR_030454	735274		NR_030454	ENSMUSG00000106252	Mir684-1	Mirn684-1	microRNA 684-1	ncRNA
mm_23707.1	chr3	68868806	68868813	+	1	NA	promoter-TSS (NM_001167996)	promoter-TSS (NM_001167996)	-777	NM_001167996	68725	Mm.45741	NM_001167996	ENSMUSG00000046999	1110032F04Rik	AI115547	RIKEN cDNA 1110032F04 gene	protein-coding
mm_51854.1	chr6	90462589	90462607	+	1	NA	promoter-TSS (NM_023184)	promoter-TSS (NM_023184)	-28	NM_023184	66277	Mm.38343	NM_023184	ENSMUSG00000030087	Klf15	1810013I09Rik|AV048136|AW494632|CKLF|KKLF	Kruppel-like factor 15	protein-coding
mm_167391.1	chr8	94984030	94984041	+	1	NA	promoter-TSS (NM_018882)	promoter-TSS (NM_018882)	-364	NM_018882	14766	Mm.290834	NM_018882	ENSMUSG00000031785	Adgrg1	Cyt28|Gpr56|TM7LN4|TM7XN1	adhesion G protein-coupled receptor G1	protein-coding
mm_92119.1	chr10	63338974	63338992	-	1	NA	promoter-TSS (NM_001159589)	promoter-TSS (NM_001159589)	52	NM_019812	93759	Mm.351459	NM_019812	ENSMUSG00000020063	Sirt1	AA673258|SIR2L1|Sir2|Sir2a|Sir2alpha	sirtuin 1	protein-coding
mm_141871.1	chr17	34836649	34836692	-	1	NA	promoter-TSS (NM_001163770)	promoter-TSS (NM_001163770)	233	NM_019442	54402	Mm.440064	NM_019442	ENSMUSG00000061207	Stk19	G11|RP1	serine/threonine kinase 19	protein-coding
mm_148334.1	chr18	84243259	84243262	-	1	NA	intron (NM_001033341, intron 8 of 8)	intron (NM_001033341, intron 8 of 8)	155102	NM_146090	225791	Mm.147052	NM_146090	ENSMUSG00000049090	Zadh2	C530046K17Rik|PTGR-3|Pthr3	zinc binding alcohol dehydrogenase, domain containing 2	protein-coding
mm_82327.1	chr9	8693289	8693308	-	1	NA	intron (NR_110513, intron 3 of 4)	intron (NR_110513, intron 3 of 4)	47690	NR_110513	102634431	Mm.387913	NR_110513	ENSMUSG00000111602	Gm32014	-	predicted gene, 32014	ncRNA
mm_135069.1	chr16	34239165	34239172	-	1	NA	intron (NM_001164268, intron 14 of 33)	ID4|SINE|ID	-272165	NM_009471	22247	Mm.13145	NM_009471	ENSMUSG00000022814	Umps	1700095D23Rik|AA408257|AL033308|BB164745	uridine monophosphate synthetase	protein-coding
mm_68629.1	chr7	118139192	118139218	-	1	NA	intron (NM_001031814, intron 60 of 62)	intron (NM_001031814, intron 60 of 62)	-9580	NM_019419	54208	Mm.29924	NM_019419	ENSMUSG00000030654	Arl6ip1	AIP-6|AL022945|ARMER|AU042858|Aip-1|Arl6ip|C85138|mKIAA0069	ADP-ribosylation factor-like 6 interacting protein 1	protein-coding
mm_91993.1	chr10	62071897	62071916	-	1	NA	Intergenic	Intergenic	39107	NM_027251	69894	Mm.294126	NM_027251	ENSMUSG00000020083	2010107G23Rik	AA545165	RIKEN cDNA 2010107G23 gene	protein-coding
mm_20990.1	chr2	152226722	152226753	-	1	NA	promoter-TSS (NM_007788)	promoter-TSS (NM_007788)	-103	NM_007788	12995	Mm.23692	NM_007788	ENSMUSG00000074698	Csnk2a1	Csnk2a1-rs4	casein kinase 2, alpha 1 polypeptide	protein-coding
mm_154224.1	chr19	59914061	59914083	-	1	NA	intron (NM_001033172, intron 3 of 5)	intron (NM_001033172, intron 3 of 5)	29292	NM_001033172	74998	Mm.24167	NM_001033172	ENSMUSG00000040022	Rab11fip2	4930470G04Rik|A830046J09Rik|AW558126|Nrip11	RAB11 family interacting protein 2 (class I)	protein-coding
mm_154032.1	chr19	53460249	53460262	-	1	NA	intron (NR_028427, intron 2 of 9)	intron (NR_028427, intron 2 of 9)	4541	NR_028427	381232	Mm.248624	NR_028427	ENSMUSG00000097636	Mirt1	4833407H14Rik|5430437C04Rik|5830416P10Rik|ENSMUSG00000074788|Gm10758	myocardial infarction associated transcript 1	ncRNA
mm_32241.1	chr4	102430073	102430079	+	1	NA	intron (NM_019840, intron 1 of 14)	intron (NM_019840, intron 1 of 14)	-139984	NM_001177980	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_46341.1	chr5	101922580	101922629	-	1	NA	exon (NM_172882, exon 21 of 67)	exon (NM_172882, exon 21 of 67)	147317	NM_172882	72145	Mm.332522	NM_172882	ENSMUSG00000043940	Wdfy3	2610509D04Rik|ALFY|AW319683|B930017C24|BWF1|Bchs|D5Ertd66e|Ggtb3|ZFYVE25|mKIAA0993	WD repeat and FYVE domain containing 3	protein-coding
mm_32114.1	chr4	98978710	98978734	+	1	NA	intron (NM_001290636, intron 29 of 48)	B4A|SINE|B4	-52232	NM_013913	30924	Mm.28341	NM_013913	ENSMUSG00000028553	Angptl3	hypl	angiopoietin-like 3	protein-coding
mm_108579.1	chr12	85013022	85013061	+	1	NA	exon (NM_001347421, exon 2 of 20)	exon (NM_001347421, exon 2 of 20)	16720	NM_178363	56531	Mm.153183	NM_178363	ENSMUSG00000021244	Ylpm1	A930013E17Rik|ZAP|Zap3	YLP motif containing 1	protein-coding
mm_132286.1	chr16	33174948	33174950	+	1	NA	Intergenic	Intergenic	-10122	NM_176840	106326	Mm.486405	NM_176840	ENSMUSG00000022807	Osbpl11	9430097N02Rik|AI132306|AU019795|ORP-11	oxysterol binding protein-like 11	protein-coding
mm_92815.1	chr10	81430805	81430845	-	1	NA	Intergenic	CpG	-3652	NM_026756	18029	Mm.426936	NM_008688	ENSMUSG00000055053	Nfic	1110019L22Rik|1500041O16Rik|AA589446|AI746521|NF1-C	nuclear factor I/C	protein-coding
mm_124775.1	chr15	7192895	7192922	+	1	NA	3' UTR (NM_013584, exon 20 of 20)	3' UTR (NM_013584, exon 20 of 20)	52366	NM_013584	16880	Mm.149720	NM_013584	ENSMUSG00000054263	Lifr	A230075M04Rik|AW061234|LIF	leukemia inhibitory factor receptor	protein-coding
mm_133826.1	chr16	95900383	95900416	+	1	NA	intron (NR_040484, intron 1 of 3)	intron (NR_040484, intron 1 of 3)	-1686	NR_040485	69776	Mm.120470	NR_040484	ENSMUSG00000086899	1600002D24Rik	-	RIKEN cDNA 1600002D24 gene	ncRNA
mm_126809.1	chr15	87654937	87654945	+	1	NA	intron (NM_134096, intron 1 of 3)	intron (NM_134096, intron 1 of 3)	29711	NM_134096	106014	Mm.244319	NM_134096	ENSMUSG00000054863	Fam19a5	TAFA5|Tafa-5|Tara-5	family with sequence similarity 19, member A5	protein-coding
mm_34302.1	chr4	141746793	141746814	+	1	NA	5' UTR (NM_001081408, exon 1 of 7)	5' UTR (NM_001081408, exon 1 of 7)	128	NM_001081408	75986	Mm.30032	NM_001081408	ENSMUSG00000040706	Agmat	5033405N08Rik	agmatine ureohydrolase (agmatinase)	protein-coding
mm_40875.1	chr5	74093133	74093139	+	1	NA	promoter-TSS (NR_145131)	promoter-TSS (NR_145131)	76	NR_145131	70036	Mm.46547	NR_015531	ENSMUSG00000053656	Dancr	2700023E23Rik	differentiation antagonizing non-protein coding RNA	ncRNA
mm_153593.1	chr19	43717636	43717641	-	1	NA	intron (NM_053103, intron 8 of 12)	intron (NM_053103, intron 8 of 12)	27949	NM_053103	93685	Mm.248237	NM_053103	ENSMUSG00000025192	Entpd7	1810012B13Rik|1810020C02Rik|2810003F23Rik|LALP1|Lysal2	ectonucleoside triphosphate diphosphohydrolase 7	protein-coding
mm_39428.1	chr5	16553489	16553502	+	1	NA	promoter-TSS (NM_010427)	promoter-TSS (NM_010427)	0	NM_001289460	15234	Mm.267078	NM_010427	ENSMUSG00000028864	Hgf	C230052L06Rik|HGF/SF|NK1|NK2|SF|SF/HGF	hepatocyte growth factor	protein-coding
mm_69786.1	chr7	141094962	141094983	-	1	NA	5' UTR (NM_023059, exon 2 of 10)	5' UTR (NM_023059, exon 2 of 10)	5574	NM_023059	24058	Mm.38017	NM_023059	ENSMUSG00000025494	Sigirr	AI256711|TIR8	single immunoglobulin and toll-interleukin 1 receptor (TIR) domain	protein-coding
mm_65891.1	chr7	30051362	30051411	-	1	NA	promoter-TSS (NM_178733)	promoter-TSS (NM_178733)	10	NM_011748	243906	Mm.347644	NM_011748	ENSMUSG00000053985	Zfp14	4732429I09Rik|Krox-9|Zfp-14|mKIAA1559	zinc finger protein 14	protein-coding
mm_49663.1	chr6	31216953	31216963	+	1	NA	intron (NR_110469, intron 1 of 3)	CpG	1516	NR_110470	232685	Mm.443019	NM_144555	ENSMUSG00000044471	Lncpint	Lincpint|MNCb-1768|Pint|linc-Pint	long non-protein coding RNA, Trp53 induced transcript	ncRNA
mm_120873.1	chr14	75242309	75242354	+	1	NA	promoter-TSS (NM_019775)	promoter-TSS (NM_019775)	44	NM_019775	56373	Mm.24242	NM_019775	ENSMUSG00000021999	Cpb2	1110032P04Rik|4930405E17Rik|AI255929|CPR|Cpu|TAFI	carboxypeptidase B2 (plasma)	protein-coding
mm_4749.1	chr1	182255310	182255341	+	1	NA	Intergenic	Intergenic	27434	NM_007853	13244	Mm.29648	NM_007853	ENSMUSG00000038633	Degs1	AA536663|Degs|Des1|Mdes	delta(4)-desaturase, sphingolipid 1	protein-coding
mm_121190.1	chr14	103049866	103049876	+	1	NA	intron (NM_008392, intron 3 of 4)	intron (NM_008392, intron 3 of 4)	2859	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_134896.1	chr16	29849630	29849645	-	1	NA	Intergenic	Lx8|LINE|L1	129487	NR_037689	328657	Mm.425982	NM_001033403		Gm1968	-	predicted gene 1968	ncRNA
mm_163400.1	chr12	72939892	72939900	+	1	NA	promoter-TSS (NM_011384)	promoter-TSS (NM_011384)	14	NM_011384	20476	Mm.57138	NM_011384	ENSMUSG00000021099	Six6	Optx2|Six9	sine oculis-related homeobox 6	protein-coding
mm_137977.1	chr17	33578136	33578144	+	1	NA	exon (NM_053214, exon 5 of 28)	exon (NM_053214, exon 5 of 28)	22433	NM_053214	17916	Mm.42019	NM_053214	ENSMUSG00000024300	Myo1f	C330006B10Rik	myosin IF	protein-coding
mm_80161.1	chr9	71157344	71157373	+	1	NA	intron (NR_073483, intron 1 of 6)	intron (NR_073483, intron 1 of 6)	5275	NM_001271843	64008	Mm.449427	NM_022026	ENSMUSG00000032204	Aqp9	1700020I22Rik|AI266899|AQP-9	aquaporin 9	protein-coding
mm_139852.1	chr17	69969047	69969058	+	1	NA	promoter-TSS (NM_001347412)	promoter-TSS (NM_001347412)	-21	NM_001347412	224997	Mm.311840	NM_027712	ENSMUSG00000003279	Dlgap1	4933422O14Rik|9630002F18|AI845682|AI848168|BB075781|D17Bwg0511e|GKAP/SAPAP|GKPA/SAPAP|Gkap|Sapap1|mKIAA4162	discs, large (Drosophila) homolog-associated protein 1	protein-coding
mm_132809.1	chr16	45159057	45159079	+	1	NA	promoter-TSS (NM_028756)	promoter-TSS (NM_028756)	239	NM_026402	67841	Mm.41775	NM_026402	ENSMUSG00000022663	Atg3	2610016C12Rik|APG3|Apg3l|Atg3l|PC3-96	autophagy related 3	protein-coding
mm_79563.1	chr9	58129322	58129338	+	1	NA	promoter-TSS (NM_009291)	promoter-TSS (NM_009291)	-19	NM_009291	20897	Mm.10801	NM_009291	ENSMUSG00000032327	Stra6	AI891933	stimulated by retinoic acid gene 6	protein-coding
mm_161584.1	chr16	32271846	32271846	+	1	NA	intron (NM_183283, intron 1 of 2)	ID4_|SINE|ID	237	NM_183283	69576	Mm.432545	NM_183283	ENSMUSG00000046345	Smco1	2310010M20Rik	single-pass membrane protein with coiled-coil domains 1	protein-coding
mm_153309.1	chr19	38025818	38025830	-	1	NA	intron (NM_001302140, intron 1 of 53)	intron (NM_001302140, intron 1 of 53)	17753	NM_001099634	226101	Mm.34674	NM_177035	ENSMUSG00000048612	Myof	2310004N10Rik|2310051D19Rik|E030042N20Rik|Fer1l3	myoferlin	protein-coding
mm_135949.1	chr16	74411802	74411806	-	1	NA	promoter-TSS (NM_175549)	promoter-TSS (NM_175549)	-892	NM_175549	268902	Mm.171736	NM_175549	ENSMUSG00000052516	Robo2	2600013A04Rik|9430089E08Rik|BB097918|D230004I22Rik|mKIAA1568	roundabout guidance receptor 2	protein-coding
mm_149632.1	chr19	17222652	17222654	+	1	NA	3' UTR (NM_181348, exon 20 of 20)	3' UTR (NM_181348, exon 20 of 20)	116852	NM_001136484	14537	Mm.244825	NM_010265	ENSMUSG00000038843	Gcnt1	5630400D21Rik|B130048E03|C2 GlcNAcT|C2GNT|IGnT	glucosaminyl (N-acetyl) transferase 1, core 2	protein-coding
mm_149859.1	chr19	25097806	25097815	+	1	NA	intron (NM_028785, intron 12 of 47)	RMER12B|LTR|ERVK	98281	NM_028785	76088	Mm.102485	NM_028785	ENSMUSG00000052085	Dock8	1200017A24Rik|5830472H07Rik|A130095G14Rik|AI461977	dedicator of cytokinesis 8	protein-coding
mm_106775.1	chr12	4624895	4624916	+	1	NA	exon (NM_001198969, exon 3 of 17)	exon (NM_001198969, exon 3 of 17)	31897	NM_001198968	20403	Mm.341204	NM_011365	ENSMUSG00000020640	Itsn2	AI327390|Ese2|Sh3d1B|Sh3p18|mKIAA1256	intersectin 2	protein-coding
mm_18115.1	chr2	44996508	44996517	-	1	NA	exon (NM_015753, exon 8 of 10)	exon (NM_015753, exon 8 of 10)	26665	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_40037.1	chr5	33759334	33759336	+	1	NA	intron (NM_019694, intron 6 of 13)	intron (NM_019694, intron 6 of 13)	23369	NM_019694	56384	Mm.260538	NM_019694	ENSMUSG00000005299	Letm1	-	leucine zipper-EF-hand containing transmembrane protein 1	protein-coding
mm_110720.1	chr12	69596820	69596822	-	1	NA	intron (NM_001135559, intron 17 of 22)	intron (NM_001135559, intron 17 of 22)	-13793	NM_001033236	207965	Mm.102487	NM_001033236	ENSMUSG00000049882	Vcpkmt	Gm71|Mettl21d|Mettl221d|VCP-KMT	valosin containing protein lysine (K) methyltransferase	protein-coding
mm_48642.1	chr5	145231560	145231570	-	1	NA	promoter-TSS (NM_028298)	promoter-TSS (NM_028298)	-150	NM_001083958	72611	Mm.206555	NM_028298	ENSMUSG00000007812	Zfp655	2700038I16Rik|9030409O18Rik|mKIAA4222	zinc finger protein 655	protein-coding
mm_55215.1	chr6	52225823	52225864	-	1	NA	exon (NM_010456, exon 1 of 2)	exon (NM_010456, exon 1 of 2)	1527	NM_010456	15405	Mm.4694	NM_010456	ENSMUSG00000038227	Hoxa9	D6a9|Hox-1.7	homeobox A9	protein-coding
mm_17883.1	chr2	34961821	34961838	-	1	NA	promoter-TSS (NM_001326601)	promoter-TSS (NM_001326601)	-57	NM_001326601	22029	Mm.239514	NM_009421	ENSMUSG00000026875	Traf1	4732496E14Rik	TNF receptor-associated factor 1	protein-coding
mm_138604.1	chr17	35567528	35567544	+	1	NA	promoter-TSS (NM_175148)	promoter-TSS (NM_175148)	51	NM_175148	69542	Mm.265291	NM_175148	ENSMUSG00000039269	2300002M23Rik	Stg|emprin	RIKEN cDNA 2300002M23 gene	protein-coding
mm_70799.1	chr8	22922283	22922285	+	1	NA	intron (NM_001081149, intron 10 of 17)	PB1D9|SINE|Alu	-52552	NM_001110783	11733	Mm.334444	NM_031158	ENSMUSG00000031543	Ank1	Ank-1|nb|pale	ankyrin 1, erythroid	protein-coding
mm_47077.1	chr5	116633016	116633019	-	1	NA	Intergenic	Intergenic	-41200	NM_026886	68955	Mm.146779	NM_026886	ENSMUSG00000063919	Srrm4	1500001A10Rik|B230202K19Rik|bv|mKIAA1853|nSR100	serine/arginine repetitive matrix 4	protein-coding
mm_75151.1	chr8	36176032	36176039	-	1	NA	Intergenic	Intergenic	73481	NM_001081150	244421	Mm.324032	NM_001081150	ENSMUSG00000039633	Lonrf1	-	LON peptidase N-terminal domain and ring finger 1	protein-coding
mm_87787.1	chr10	60297361	60297392	+	1	NA	intron (NM_011179, intron 8 of 14)	intron (NM_011179, intron 8 of 14)	12915	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_16417.1	chr2	180170356	180170403	+	1	NA	Intergenic	RSINE1|SINE|B4	-1209	NM_019822	56436	Mm.316654	NM_019822	ENSMUSG00000039041	Adrm1	1110063P18Rik|2510006J17Rik|AA408205|ARM-1|AU043535|Arm1|Gp110|Rpn13	adhesion regulating molecule 1	protein-coding
mm_155402.1	chrX	73064235	73064256	+	1	NA	promoter-TSS (NM_153169)	promoter-TSS (NM_153169)	-542	NM_153169	245468	Mm.256249	NM_153169	ENSMUSG00000046287	Pnma3	-	paraneoplastic antigen MA3	protein-coding
mm_157238.1	chrX	17571564	17571595	-	1	NA	intron (NM_001313745, intron 1 of 3)	intron (NM_001313745, intron 1 of 3)	428	NM_001313746	72018	Mm.41558	NM_028058	ENSMUSG00000025040	Fundc1	1500005J14Rik|1810033P05Rik	FUN14 domain containing 1	protein-coding
mm_79339.1	chr9	53367680	53367692	+	1	NA	intron (NM_176846, intron 5 of 5)	intron (NM_176846, intron 5 of 5)	-16337	NM_212445	68304	Mm.427519	NM_212445	ENSMUSG00000034487	Kdelc2	2010004J24Rik|4833410J10Rik|AW549401	KDEL (Lys-Asp-Glu-Leu) containing 2	protein-coding
mm_147894.1	chr18	65222687	65222691	-	1	NA	intron (NR_105742, intron 4 of 6)	L2|LINE|L2	-26172	NR_029600	387231		NR_029600	ENSMUSG00000065402	Mir122	Mir122a|Mirn122a|mir-122|mmu-mir-122	microRNA 122	ncRNA
mm_136848.1	chr17	12788312	12788326	+	1	NA	intron (NR_027784, intron 2 of 2)	RMER6C|LTR|ERVK	-18613	NM_010515	16004	Mm.26553	NM_010515	ENSMUSG00000023830	Igf2r	AI661837|CD222|CI-MPR|M6P/IGF2R|Mpr300	insulin-like growth factor 2 receptor	protein-coding
mm_35257.1	chr4	19878301	19878307	-	1	NA	exon (NM_175406, exon 8 of 8)	exon (NM_175406, exon 8 of 8)	44262	NM_175406	242341	Mm.19298	NM_175406	ENSMUSG00000028238	Atp6v0d2	1620401A02Rik|AI324824|V-ATPase	ATPase, H+ transporting, lysosomal V0 subunit D2	protein-coding
mm_155046.1	chrX	42150778	42150781	+	1	NA	promoter-TSS (NM_021465)	promoter-TSS (NM_021465)	78	NM_021465	20843	Mm.290422	NM_021465	ENSMUSG00000025862	Stag2	9230105L23Rik|B230112I07Rik|SA-2|SAP2	stromal antigen 2	protein-coding
mm_166474.1	chr5	143562158	143562164	+	1	NA	intron (NM_026050, intron 2 of 2)	intron (NM_026050, intron 2 of 2)	13455	NM_026050	67238	Mm.383219	NM_026050	ENSMUSG00000083012	Fam220a	1500026F15Rik|2810453I06Rik|AW047776|Acpin1|Sipar	family with sequence similarity 220, member A	protein-coding
mm_80465.1	chr9	78113252	78113261	+	1	NA	promoter-TSS (NM_019987)	promoter-TSS (NM_019987)	18	NM_019987	56542	Mm.288719	NM_019987	ENSMUSG00000009828	Ick	2210420N10Rik|AI848300|Mrk	intestinal cell kinase	protein-coding
mm_105561.1	chr11	106503300	106503303	-	1	NA	3' UTR (NM_198292, exon 12 of 12)	3' UTR (NM_198292, exon 12 of 12)	2310	NR_030703	100216537		NR_030703	ENSMUSG00000065126	Snord104	-	small nucleolar RNA, C/D box 104	snoRNA
mm_16313.1	chr2	174302263	174302267	+	1	NA	intron (NM_001310085, intron 2 of 12)	intron (NM_001310085, intron 2 of 12)	4406	NM_001310085	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_104154.1	chr11	87108767	87108783	-	1	NA	promoter-TSS (NM_175563)	promoter-TSS (NM_175563)	-61	NM_175563	270906	Mm.132381	NM_175563	ENSMUSG00000020493	Prr11	B930067F20Rik	proline rich 11	protein-coding
mm_19035.1	chr2	76969926	76969937	-	1	NA	exon (NM_011652, exon 7 of 313)	exon (NM_011652, exon 7 of 313)	12616	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_56547.1	chr6	99896830	99896858	-	1	NA	Intergenic	RLTR35B_MM|LTR|ERVL	-170452	NM_001170419	50501	Mm.87365	NM_015768	ENSMUSG00000030069	Prok2	Bv8|PK2|Prok1	prokineticin 2	protein-coding
mm_95462.1	chr11	50382794	50382816	+	1	NA	exon (NM_021510, exon 7 of 14)	exon (NM_021510, exon 7 of 14)	5086	NM_001347487	59013	Mm.21740	NM_021510	ENSMUSG00000007850	Hnrnph1	AI642080|E430005G16Rik|Hnrnph|Hnrph1	heterogeneous nuclear ribonucleoprotein H1	protein-coding
mm_59528.1	chr7	27653882	27653900	+	1	NA	promoter-TSS (NM_028417)	promoter-TSS (NM_028417)	-33	NM_028417	73032	Mm.44095	NM_028417	ENSMUSG00000007944	Ttc9b	2900074C18Rik	tetratricopeptide repeat domain 9B	protein-coding
mm_57738.1	chr6	128975020	128975048	-	1	NA	promoter-TSS (NR_045009)	promoter-TSS (NR_045009)	-5	NR_045009	100504591	Mm.441029	NR_045009		Gm15987	OTTMUSG00000028624	predicted gene 15987	ncRNA
mm_15270.1	chr2	155195279	155195325	+	1	NA	intron (NM_008395, intron 13 of 24)	intron (NM_008395, intron 13 of 24)	-41231	NR_111891	67068	Mm.23693	NM_025947	ENSMUSG00000047459	Dynlrb1	2010012N15Rik|2010320M17Rik|9430076K19Rik|AV124457|DNLC2A|Dncl2a|km23-1	dynein light chain roadblock-type 1	protein-coding
mm_118912.1	chr14	26691612	26691636	+	1	NA	Intergenic	Intergenic	-21778	NM_178668	211948	Mm.290758	NM_178668	ENSMUSG00000043702	Pde12	2'-PDE|E430028B21Rik	phosphodiesterase 12	protein-coding
mm_123160.1	chr14	57133269	57133314	-	1	NA	5' UTR (NM_001271663, exon 1 of 3)	5' UTR (NM_001271663, exon 1 of 3)	320	NM_001271663	14623	Mm.25652	NM_008128	ENSMUSG00000040055	Gjb6	AA958971|Cx30|D14Bwg0506e	gap junction protein, beta 6	protein-coding
mm_25164.1	chr3	103058710	103058742	+	1	NA	TTS (NM_001310693)	TTS (NM_001310693)	441	NM_010937	18176	Mm.400954	NM_010937	ENSMUSG00000027852	Nras	AV095280|N-ras	neuroblastoma ras oncogene	protein-coding
mm_48537.1	chr5	142904699	142904712	-	1	NA	exon (NM_007393, exon 4 of 6)	exon (NM_007393, exon 4 of 6)	2049	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_52317.1	chr6	108836305	108836314	+	1	NA	intron (NM_138677, intron 1 of 11)	intron (NM_138677, intron 1 of 11)	7668	NM_138677	192193	Mm.21596	NM_138677	ENSMUSG00000030104	Edem1	A130059K23Rik|EDEM|mKIAA0212	ER degradation enhancer, mannosidase alpha-like 1	protein-coding
mm_84371.1	chr9	64951548	64951557	-	1	NA	promoter-TSS (NM_144813)	promoter-TSS (NM_144813)	55	NM_144813	214111	Mm.156124	NM_144813	ENSMUSG00000034452	Slc24a1	-	solute carrier family 24 (sodium/potassium/calcium exchanger), member 1	protein-coding
mm_6841.1	chr1	84233487	84233522	-	1	NA	intron (NM_001003948, intron 1 of 2)	intron (NM_001003948, intron 1 of 2)	-14543	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_41731.1	chr5	102481781	102481800	+	1	NA	5' UTR (NM_029270, exon 1 of 10)	5' UTR (NM_029270, exon 1 of 10)	399	NM_029270	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding
mm_84246.1	chr9	62374687	62374728	-	1	NA	exon (NM_009672, exon 5 of 7)	exon (NM_009672, exon 5 of 7)	33364	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	protein-coding
mm_61551.1	chr7	79392306	79392346	+	1	NA	promoter-TSS (NM_145946)	promoter-TSS (NM_145946)	-12	NM_145946	208836	Mm.349493	NM_145946	ENSMUSG00000039187	Fanci	-	Fanconi anemia, complementation group I	protein-coding
mm_121740.1	chr14	18545318	18545330	-	1	NA	Intergenic	Intergenic	-213480	NM_009455	22194	Mm.4429	NM_009455	ENSMUSG00000021774	Ube2e1	UbcM3|Ubce5|ubcM2	ubiquitin-conjugating enzyme E2E 1	protein-coding
mm_41606.1	chr5	96374426	96374448	+	1	NA	5' UTR (NM_175473, exon 1 of 74)	5' UTR (NM_175473, exon 1 of 74)	482	NM_175473	231470	Mm.291120	NM_175473	ENSMUSG00000034687	Fras1	E130113P14Rik|bl|mKIAA1500	Fraser extracellular matrix complex subunit 1	protein-coding
mm_51425.1	chr6	78427398	78427433	+	1	NA	exon (NM_009042, exon 4 of 6)	exon (NM_009042, exon 4 of 6)	1432	NM_009042	19692	Mm.142731	NM_009042	ENSMUSG00000059654	Reg1	-	regenerating islet-derived 1	protein-coding
mm_32830.1	chr4	117585301	117585311	+	1	NA	intron (NM_001285901, intron 3 of 7)	B1F|SINE|Alu	34941	NM_080469	140546	Mm.235891	NM_080469	ENSMUSG00000033423	Eri3	PINT1|Prnpip1	exoribonuclease 3	protein-coding
mm_172694.1	chr8	61364478	61364497	-	1	NA	intron (NM_021506, intron 8 of 11)	intron (NM_021506, intron 8 of 11)	-75615	NR_045475	69279	Mm.417857	NR_045475	ENSMUSG00000099419	1700001D01Rik	-	RIKEN cDNA 1700001D01 gene	ncRNA
mm_54238.1	chr6	28243770	28243789	-	1	NA	exon (NM_001081678, exon 5 of 6)	exon (NM_001081678, exon 5 of 6)	17822	NM_001081678	627049	Mm.84441	NM_001081678	ENSMUSG00000039841	Zfp800	AA407452|Znf800	zinc finger protein 800	protein-coding
mm_10710.1	chr2	22774433	22774472	+	1	NA	5' UTR (NM_019456, exon 1 of 14)	5' UTR (NM_019456, exon 1 of 14)	125	NM_019456	54519	Mm.14255	NM_019456	ENSMUSG00000026786	Apbb1ip	9930118P07Rik|Prp48	amyloid beta (A4) precursor protein-binding, family B, member 1 interacting protein	protein-coding
mm_26602.1	chr3	152209900	152209928	+	1	NA	promoter-TSS (NM_057172)	promoter-TSS (NM_057172)	169	NM_027287	67035	Mm.46746	NM_025926	ENSMUSG00000028035	Dnajb4	1700029A20Rik|2010306G19Rik|5730460G06Rik	DnaJ heat shock protein family (Hsp40) member B4	protein-coding
mm_57415.1	chr6	124905094	124905108	-	1	NA	intron (NM_008479, intron 6 of 7)	MIR3|SINE|MIR	6604	NM_008479	16768	Mm.4528	NM_008479	ENSMUSG00000030124	Lag3	CD223|LAG-3|Ly66	lymphocyte-activation gene 3	protein-coding
mm_157041.1	chrX	7976545	7976562	-	1	NA	Intergenic	ID_B1|SINE|B4	-8643	NM_008089	14460	Mm.335973	NM_008089	ENSMUSG00000031162	Gata1	Gata-1|Gf-1|eryf1	GATA binding protein 1	protein-coding
mm_64504.1	chr7	143476164	143476192	+	1	NA	5' UTR (NM_008767, exon 2 of 11)	5' UTR (NM_008767, exon 2 of 11)	1062	NM_001042760	18400	Mm.271740	NM_008767	ENSMUSG00000000154	Slc22a18	AW260131|BWR1A|BWSCR1A|HET|ITM|Impt1|Orctl2|Slc22a1l|TSSC5|p45-BWR1A	solute carrier family 22 (organic cation transporter), member 18	protein-coding
mm_144473.1	chr18	23883533	23883553	+	1	NA	exon (NM_001162942, exon 7 of 8)	exon (NM_001162942, exon 7 of 8)	-71145	NM_027007	69256	Mm.218343	NM_027007	ENSMUSG00000024276	Zfp397	2810411K16Rik|6720480F11Rik|AI461664	zinc finger protein 397	protein-coding
mm_170360.1	chr1	85270169	85270169	-	1	NA	5' UTR (NM_001037909, exon 1 of 7)	5' UTR (NM_001037909, exon 1 of 7)	397	NM_175219	620078	Mm.386456	NM_175219	ENSMUSG00000052477	C130026I21Rik	4930565N07Rik|OTTMUSG00000029174	RIKEN cDNA C130026I21 gene	protein-coding
mm_27035.1	chr3	26331038	26331054	-	1	NA	5' UTR (NM_138666, exon 1 of 8)	5' UTR (NM_138666, exon 1 of 8)	863	NM_138666	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_78029.1	chr9	13806025	13806027	+	1	NA	non-coding (NR_024025, exon 16 of 16)	non-coding (NR_024025, exon 16 of 16)	21027	NR_037622	74360	Mm.157212	NM_026665	ENSMUSG00000031922	Cep57	3110002L15Rik|4921510P06Rik|4931428M20Rik|AI467480|Tsp57|mKIAA0092	centrosomal protein 57	protein-coding
mm_48163.1	chr5	137152837	137152847	-	1	NA	Intergenic	Intergenic	-36635	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_170402.1	chr18	63880782	63880783	-	1	NA	intron (NM_001014981, intron 21 of 27)	RLTRETN_Mm|LTR|ERVK	172087	NM_001014981	104082	Mm.30850	NM_001014981	ENSMUSG00000040560	Wdr7	AI462727|TRAG|mKIAA0541	WD repeat domain 7	protein-coding
mm_159909.1	chr6	47595394	47595394	-	1	NA	promoter-TSS (NM_001146689)	promoter-TSS (NM_001146689)	-364	NM_001146689	14056	Mm.246688	NM_007971	ENSMUSG00000029687	Ezh2	Enx-1|Enx1h|KMT6|mKIAA4065	enhancer of zeste 2 polycomb repressive complex 2 subunit	protein-coding
mm_168009.1	chrY	11858266	11858291	+	1	NA	Intergenic	(TTC)n|Simple_repeat|Simple_repeat	-523711	NM_001199332	100041550	Mm.485768	NM_001199332	ENSMUSG00000095520	Gm20877	-	predicted gene, 20877	protein-coding
mm_156881.1	chrX	166239027	166239054	+	1	NA	promoter-TSS (NM_001177961)	promoter-TSS (NM_001177961)	97	NM_001177962	14758	Mm.222320	NM_023122	ENSMUSG00000031342	Gpm6b	AI593561|Gpm6|M6B	glycoprotein m6b	protein-coding
mm_146700.1	chr18	13122480	13122493	-	1	NA	Intergenic	Intergenic	115496	NM_153087	225192	Mm.207073	NM_153087	ENSMUSG00000037346	Hrh4	AXOR35|BG26|GPCR105|GPRv53|H4|H4R|HH4R	histamine receptor H4	protein-coding
mm_38513.1	chr4	141398232	141398241	-	1	NA	promoter-TSS (NM_001146307)	promoter-TSS (NM_001146307)	-137	NM_001146307	12733	Mm.167900	NM_024412	ENSMUSG00000033770	Clcnka	C75963|CLC-K1|Clcnk1	chloride channel, voltage-sensitive Ka	protein-coding
mm_57083.1	chr6	122582546	122582580	-	1	NA	intron (NM_001134391, intron 5 of 7)	B1F2|SINE|Alu	19881	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_15676.1	chr2	163547134	163547146	+	1	NA	promoter-TSS (NM_008261)	promoter-TSS (NM_008261)	-15	NM_008261	15378	Mm.202383	NM_008261	ENSMUSG00000017950	Hnf4a	HNF-4|Hnf4|Hnf4alpha|MODY1|Nr2a1|TCF-14|Tcf14	hepatic nuclear factor 4, alpha	protein-coding
mm_107585.1	chr12	44930506	44930508	+	1	NA	intron (NM_144552, intron 2 of 5)	ORR1A2|LTR|ERVL-MaLR	143976	NM_144552	217517	Mm.285400	NM_144552	ENSMUSG00000046314	Stxbp6	BC024598|C85317	syntaxin binding protein 6 (amisyn)	protein-coding
mm_162937.1	chr10	127705282	127705291	+	1	NA	promoter-TSS (NM_001081219)	promoter-TSS (NM_001081219)	30	NM_001081219	432516	Mm.90450	NM_001081219	ENSMUSG00000025401	Myo1a	BBM-I|Myhl	myosin IA	protein-coding
mm_14952.1	chr2	151996506	151996556	+	1	NA	promoter-TSS (NM_027172)	promoter-TSS (NM_027172)	20	NM_027172	69698	Mm.258262	NM_027172	ENSMUSG00000027463	Slc52a3	2310046K01Rik|RFT2	solute carrier protein family 52, member 3	protein-coding
mm_136810.1	chr17	12390288	12390305	+	1	NA	exon (NM_008877, exon 5 of 19)	exon (NM_008877, exon 5 of 19)	11687	NM_008877	18815	Mm.971	NM_008877	ENSMUSG00000059481	Plg	AI649309|Pg	plasminogen	protein-coding
mm_126729.1	chr15	85634866	85634891	+	1	NA	Intergenic	CpG	-53057	NM_009528	22422	Mm.306946	NM_009528	ENSMUSG00000022382	Wnt7b	Wnt-7b	wingless-type MMTV integration site family, member 7B	protein-coding
mm_110236.1	chr12	30373321	30373337	-	1	NA	promoter-TSS (NM_172951)	promoter-TSS (NM_172951)	46	NM_172951	268534	Mm.279765	NM_172951	ENSMUSG00000020672	Sntg2	2210008K22Rik|9530013L23|BB121248|G2syn|Syn5	syntrophin, gamma 2	protein-coding
mm_84430.1	chr9	65885107	65885117	-	1	NA	promoter-TSS (NM_001170907)	promoter-TSS (NM_001170907)	61	NM_001170907	56404	Mm.208379	NM_019797	ENSMUSG00000032386	Trip4	4930558E03Rik|ASC-1|Asc1|BB191711	thyroid hormone receptor interactor 4	protein-coding
mm_147646.1	chr18	60443629	60443648	-	1	NA	Intergenic	MER73|LTR|ERVL	58345	NM_134133	106878	Mm.273197	NM_134133	ENSMUSG00000038059	Smim3	2010002N04Rik|AI195350|AW561905|Nid67|cI-41	small integral membrane protein 3	protein-coding
mm_100058.1	chr11	115277422	115277429	+	1	NA	promoter-TSS (NM_007997)	promoter-TSS (NM_007997)	-456	NM_007997	14149	Mm.4719	NM_007997	ENSMUSG00000018861	Fdxr	-	ferredoxin reductase	protein-coding
mm_170790.1	chr2	175110104	175110117	-	1	NA	Intergenic	Intergenic	-42341	NM_001085546	664987		NM_001085546	ENSMUSG00000078905	Gm14393	OTTMUSG00000016546	predicted gene 14393	protein-coding
mm_100975.1	chr11	6896128	6896128	-	1	NA	Intergenic	Intergenic	-167361	NM_009622	432530	Mm.259733	NM_009622	ENSMUSG00000020431	Adcy1	AC1|D11Bwg1392e|I-AC|brl|mKIAA4070	adenylate cyclase 1	protein-coding
mm_81088.1	chr9	106327717	106327730	+	1	NA	intron (NM_027354, intron 9 of 10)	intron (NM_027354, intron 9 of 10)	-40909	NM_153459	235584	Mm.275584	NM_153459	ENSMUSG00000053716	Dusp7	AU015694|Mkpx|Pyst2	dual specificity phosphatase 7	protein-coding
mm_145130.1	chr18	44634149	44634181	+	1	NA	intron (NM_001085373, intron 3 of 18)	intron (NM_001085373, intron 3 of 18)	-27500	NR_026853	626275	Mm.427116	NR_026853	ENSMUSG00000097610	A930012L18Rik	-	RIKEN cDNA A930012L18 gene	ncRNA
mm_149329.1	chr19	10843016	10843020	+	1	NA	5' UTR (NM_023044, exon 1 of 8)	5' UTR (NM_023044, exon 1 of 8)	474	NM_023044	65221	Mm.27387	NM_023044	ENSMUSG00000024737	Slc15a3	Ci1|cI-1	solute carrier family 15, member 3	protein-coding
mm_39765.1	chr5	30013334	30013373	+	1	NA	intron (NM_001314054, intron 1 of 4)	intron (NM_001314054, intron 1 of 4)	239	NM_031168	16193	Mm.1019	NM_031168	ENSMUSG00000025746	Il6	Il-6	interleukin 6	protein-coding
mm_124235.1	chr14	101463210	101463230	-	1	NA	intron (NM_001081278, intron 11 of 18)	intron (NM_001081278, intron 11 of 18)	145971	NM_001081278	210789	Mm.320639	NM_173380	ENSMUSG00000033083	Tbc1d4	5930406J04Rik|A930035N22|AV295684|As160	TBC1 domain family, member 4	protein-coding
mm_13903.1	chr2	120481950	120481975	+	1	NA	intron (NM_001109761, intron 2 of 20)	intron (NM_001109761, intron 2 of 20)	5053	NM_001109761	12335	Mm.458021	NM_007601	ENSMUSG00000079110	Capn3	AI323605|Capa-3|Capa3|Lp82|p94	calpain 3	protein-coding
mm_45019.1	chr5	38561156	38561171	-	1	NA	exon (NM_011715, exon 2 of 15)	exon (NM_011715, exon 2 of 15)	432	NM_011715	22388	Mm.2654	NM_011715	ENSMUSG00000005103	Wdr1	Aip1|D5Wsu185e|rede	WD repeat domain 1	protein-coding
mm_56000.1	chr6	86472183	86472228	-	1	NA	non-coding (NR_131125, exon 5 of 5)	non-coding (NR_131125, exon 5 of 5)	8625	NR_131125	320486	Mm.391625	NR_131125	ENSMUSG00000085589	A430078I02Rik	T25621	RIKEN cDNA A430078I02 gene	ncRNA
mm_59854.1	chr7	29943990	29944001	+	1	NA	intron (NM_178384, intron 1 of 4)	RLTR20C2_MM|LTR|ERVK	7898	NM_178384	72723	Mm.371648	NM_178384	ENSMUSG00000059975	Zfp74	2810054M15Rik|KRAB8|Zfp66|Znf569|mszf21|mszf77	zinc finger protein 74	protein-coding
mm_25485.1	chr3	109123280	109123290	+	1	NA	exon (NM_172685, exon 1 of 10)	exon (NM_172685, exon 1 of 10)	136	NM_172685	229731	Mm.33574	NM_172685	ENSMUSG00000040322	Slc25a24	2610016M12Rik	solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 24	protein-coding
mm_114771.1	chr13	88821595	88821603	+	1	NA	5' UTR (NM_001037987, exon 1 of 11)	5' UTR (NM_001037987, exon 1 of 11)	127	NM_001037987	13612	Mm.125580	NM_010103	ENSMUSG00000034488	Edil3	Del-1|Del1	EGF-like repeats and discoidin I-like domains 3	protein-coding
mm_121147.1	chr14	101899383	101899385	+	1	NA	intron (NM_001347628, intron 10 of 26)	intron (NM_001347628, intron 10 of 26)	58761	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_125182.1	chr15	32244802	32244836	+	1	NA	promoter-TSS (NM_009154)	promoter-TSS (NM_009154)	6	NM_009154	20356	Mm.260374	NM_009154	ENSMUSG00000022231	Sema5a	5930434A13|9130201M22Rik|AI464145|Semaf|semF	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A	protein-coding
mm_65057.1	chr7	18792248	18792264	-	1	NA	intron (NM_011964, intron 4 of 4)	intron (NM_011964, intron 4 of 4)	5954	NR_024208	20958	Mm.423480	NR_024208	ENSMUSG00000109116	Sycp1-ps1	Sycp1-rs	synaptonemal complex protein 1, pseudogene 1	pseudo
mm_7169.1	chr1	92114616	92114619	-	1	NA	intron (NM_207225, intron 2 of 26)	intron (NM_207225, intron 2 of 26)	65724	NM_207225	208727	Mm.318567	NM_207225	ENSMUSG00000026313	Hdac4	4932408F19Rik|HD4	histone deacetylase 4	protein-coding
mm_69037.1	chr7	126799135	126799155	-	1	NA	promoter-TSS (NM_001177307)	promoter-TSS (NM_001177307)	33	NM_001177307	11674	Mm.275831	NM_007438	ENSMUSG00000030695	Aldoa	Aldo-1|Aldo1	aldolase A, fructose-bisphosphate	protein-coding
mm_145903.1	chr18	65698328	65698336	+	1	NA	promoter-TSS (NM_177028)	promoter-TSS (NM_177028)	64	NM_177028	319888	Mm.183576	NM_177028	ENSMUSG00000046610	Oacyl	5330437I02Rik|Acyl3	O-acyltransferase like	protein-coding
mm_109754.1	chr12	117742762	117742771	+	1	NA	intron (NM_175930, intron 23 of 27)	intron (NM_175930, intron 23 of 27)	-101095	NM_146040	217946	Mm.281149	NM_146040	ENSMUSG00000021175	Cdca7l	BC006933|JPO2	cell division cycle associated 7 like	protein-coding
mm_137677.1	chr17	28801772	28801822	+	1	NA	intron (NM_001081315, intron 1 of 12)	CpG	671	NM_001081315	268936	Mm.291877	NM_199061	ENSMUSG00000063952	Brpf3	AI413466|AW493400|mKIAA1286	bromodomain and PHD finger containing, 3	protein-coding
mm_51382.1	chr6	76005319	76005319	+	1	NA	Intergenic	Intergenic	-1237398	NM_028880	74342	Mm.292568	NM_028880	ENSMUSG00000060780	Lrrtm1	4632401D06Rik|AW125451	leucine rich repeat transmembrane neuronal 1	protein-coding
mm_110299.1	chr12	32770854	32770866	-	1	NA	Intergenic	Intergenic	-49475	NM_021524	59027	Mm.202727	NM_021524	ENSMUSG00000020572	Nampt	1110035O14Rik|AI314458|AI480535|NAmPRTase|Pbef|Pbef1|Visfatin	nicotinamide phosphoribosyltransferase	protein-coding
mm_20485.1	chr2	129801479	129801495	-	1	NA	promoter-TSS (NR_029452)	promoter-TSS (NR_029452)	-28	NR_029452	654409	Mm.305555	NR_029452		4932416H05Rik	-	RIKEN cDNA 4932416H05 gene	ncRNA
mm_141384.1	chr17	29080823	29080856	-	1	NA	Intergenic	Intergenic	-1713	NR_036469	100504267	Mm.438550	NR_036469	ENSMUSG00000085912	Trp53cor1	Gm16197|OTTMUSG00000031656|linc-p21|lincRNA-p21	tumor protein p53 pathway corepressor 1	ncRNA
mm_63071.1	chr7	122162406	122162447	+	1	NA	exon (NM_011121, exon 4 of 10)	exon (NM_011121, exon 4 of 10)	2991	NM_011121	18817	Mm.16525	NM_011121	ENSMUSG00000030867	Plk1	Plk|STPK13	polo-like kinase 1	protein-coding
mm_166562.1	chr6	47584176	47584182	-	1	NA	intron (NM_007971, intron 1 of 19)	B2_Mm1a|SINE|B2	10851	NM_007971	14056	Mm.246688	NM_007971	ENSMUSG00000029687	Ezh2	Enx-1|Enx1h|KMT6|mKIAA4065	enhancer of zeste 2 polycomb repressive complex 2 subunit	protein-coding
mm_146666.1	chr18	12195121	12195165	-	1	NA	exon (NM_008720, exon 21 of 25)	exon (NM_008720, exon 21 of 25)	26413	NM_029623	76482	Mm.196596	NM_029623	ENSMUSG00000024410	3110002H16Rik	2400010D15Rik|Mic-1|Mic1	RIKEN cDNA 3110002H16 gene	protein-coding
mm_149140.1	chr19	9003815	9003829	+	1	NA	exon (NM_009643, exon 5 of 5)	exon (NM_009643, exon 5 of 5)	-14082	NR_105786	102465190		NR_105786	ENSMUSG00000099308	Mir6367	Gm27467|mmu-mir-6367	microRNA 6367	ncRNA
mm_44434.1	chr5	21055881	21055961	-	1	NA	promoter-TSS (NM_011203)	promoter-TSS (NM_011203)	-124	NM_011203	19248	Mm.319117	NM_011203	ENSMUSG00000028771	Ptpn12	P19-PTP|PTP-P19|PTP-PEST|PTPG1	protein tyrosine phosphatase, non-receptor type 12	protein-coding
mm_106280.1	chr11	118145779	118145803	-	1	NA	Intergenic	Intergenic	-16572	NM_001167746	69926	Mm.473893	NM_001167746	ENSMUSG00000033987	Dnah17	2810003K23Rik|Dnahc17|Dnahcl1|Gm1178|mKIAA3028	dynein, axonemal, heavy chain 17	protein-coding
mm_25854.1	chr3	129619113	129619119	+	1	NA	intron (NM_130450, intron 3 of 4)	intron (NM_130450, intron 3 of 4)	86730	NM_130450	170439	Mm.314113	NM_130450	ENSMUSG00000041220	Elovl6	C77826|FAE|LCE	ELOVL family member 6, elongation of long chain fatty acids (yeast)	protein-coding
mm_145432.1	chr18	58836185	58836209	+	1	NA	promoter-TSS (NM_175506)	promoter-TSS (NM_175506)	-166	NM_175506	240322	Mm.71963	NM_175506	ENSMUSG00000053441	Adamts19	4831407I23Rik|AU015154|D230034E10Rik	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 19	protein-coding
mm_17465.1	chr2	28558058	28558072	-	1	NA	exon (NM_009885, exon 8 of 11)	exon (NM_009885, exon 8 of 11)	5338	NM_009885	12613	Mm.236017	NM_009885	ENSMUSG00000026818	Cel	1810036E18Rik|BAL	carboxyl ester lipase	protein-coding
mm_156779.1	chrX	161297794	161297806	+	1	NA	Intergenic	Intergenic	135050	NM_001290651	107815	Mm.159173	NM_133194	ENSMUSG00000000037	Scml2	4932420G07Rik	sex comb on midleg-like 2 (Drosophila)	protein-coding
mm_111997.1	chr12	110696333	110696418	-	1	NA	promoter-TSS (NM_010480)	promoter-TSS (NM_010480)	20	NM_010480	15519	Mm.1843	NM_010480	ENSMUSG00000021270	Hsp90aa1	86kDa|89kDa|AL024080|AL024147|Hsp86-1|Hsp89|Hsp90|Hspca|hsp4	heat shock protein 90, alpha (cytosolic), class A member 1	protein-coding
mm_132432.1	chr16	35857143	35857220	+	1	NA	exon (NM_001039530, exon 6 of 17)	exon (NM_001039530, exon 6 of 17)	14201	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_18720.1	chr2	72630397	72630409	-	1	NA	Intergenic	Intergenic	-73107	NR_040503	74541	Mm.410774	NR_040503	ENSMUSG00000085252	8430437L04Rik	-	RIKEN cDNA 8430437L04 gene	ncRNA
mm_164053.1	chr14	103033722	103033750	+	1	NA	promoter-TSS (NR_045657)	promoter-TSS (NR_045657)	67	NR_045657	71264	Mm.399572	NR_045657		4933432I03Rik	-	RIKEN cDNA 4933432I03 gene	ncRNA
mm_39973.1	chr5	32241170	32241184	+	1	NA	intron (NM_001081407, intron 1 of 58)	intron (NM_001081407, intron 1 of 58)	2093	NM_001081407	665270	Mm.160067	NM_030072	ENSMUSG00000029134	Plb1	4632413E21Rik|4930433E17Rik|4930539A06Rik|BC033606	phospholipase B1	protein-coding
mm_81894.1	chr9	119444953	119444982	+	1	NA	promoter-TSS (NM_001172136)	promoter-TSS (NM_001172136)	44	NM_172456	208194	Mm.101578	NM_172456	ENSMUSG00000042787	Exog	AW557704|ENGL-B|ENGL-a|Endogl1|Endogl2|Engl|Engla|Englb	endo/exonuclease (5'-3'), endonuclease G-like	protein-coding
mm_75638.1	chr8	64849848	64849861	-	1	NA	promoter-TSS (NM_178633)	promoter-TSS (NM_178633)	70	NM_178633	77113	Mm.350347	NM_178633	ENSMUSG00000031605	Klhl2	6030411N21Rik|ABP-KELCH|AU020744|Mav	kelch-like 2, Mayven	protein-coding
mm_57113.1	chr6	122595924	122595942	-	1	NA	intron (NM_031159, intron 3 of 7)	intron (NM_031159, intron 3 of 7)	6511	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_135703.1	chr16	52468528	52468557	-	1	NA	Intergenic	Intergenic	-15461	NM_001331110	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_155690.1	chrX	94123202	94123242	+	1	NA	5' UTR (NM_011768, exon 1 of 8)	5' UTR (NM_011768, exon 1 of 8)	185	NM_011768	22764	Mm.919	NM_011768	ENSMUSG00000079509	Zfx	Zfx5|Zfx5,6|Zfx6	zinc finger protein X-linked	protein-coding
mm_67606.1	chr7	83794821	83794841	-	1	NA	promoter-TSS (NM_029335)	promoter-TSS (NM_029335)	8	NM_029335	75556	Mm.17649	NM_029335	ENSMUSG00000011154	Cfap161	1700026D08Rik|AW047638|AW551802	cilia and flagella associated protein 161	protein-coding
mm_115163.1	chr13	107687406	107687412	+	1	NA	promoter-TSS (NR_045900)	promoter-TSS (NR_045900)	12	NR_045900	72257	Mm.234155	NR_045900	ENSMUSG00000102000	1700006H21Rik	-	RIKEN cDNA 1700006H21 gene	ncRNA
mm_99143.1	chr11	100415723	100415763	+	1	NA	promoter-TSS (NM_010221)	promoter-TSS (NM_010221)	49	NM_001163481	14230	Mm.3894	NM_010221	ENSMUSG00000001555	Fkbp10	AI325255|FKBP-10|FKBP-65|FKBP65|Fkbp-rs1|Fkbp1-rs|Fkbp6|Fkbprp	FK506 binding protein 10	protein-coding
mm_99410.1	chr11	102268770	102268778	+	1	NA	promoter-TSS (NM_148953)	promoter-TSS (NM_148953)	-49	NM_148953	217217	Mm.216432	NM_148953	ENSMUSG00000034768	Asb16	-	ankyrin repeat and SOCS box-containing 16	protein-coding
mm_124916.1	chr15	11971309	11971311	+	1	NA	Intergenic	B1F|SINE|Alu	4248	NR_040447	73339	Mm.231975	NR_040447	ENSMUSG00000099349	1700047G03Rik	-	RIKEN cDNA 1700047G03 gene	ncRNA
mm_54924.1	chr6	47813515	47813528	-	1	NA	promoter-TSS (NM_009787)	promoter-TSS (NM_009787)	-9	NM_009787	12304	Mm.2442	NM_009787	ENSMUSG00000025823	Pdia4	AI987846|Cai|ERp-72|Erp72	protein disulfide isomerase associated 4	protein-coding
mm_165740.1	chr3	107216043	107216051	+	1	NA	exon (NM_001111143, exon 5 of 9)	exon (NM_001111143, exon 5 of 9)	5685	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_122428.1	chr14	44989851	44989870	-	1	NA	intron (NM_008964, intron 1 of 1)	intron (NM_008964, intron 1 of 1)	1749	NM_008964	19217	Mm.4630	NM_008964	ENSMUSG00000037759	Ptger2	EP2|Ptgerep2	prostaglandin E receptor 2 (subtype EP2)	protein-coding
mm_132603.1	chr16	38562807	38562819	+	1	NA	promoter-TSS (NM_026407)	promoter-TSS (NM_026407)	-1	NM_001205287	67846	Mm.310476	NM_026407	ENSMUSG00000002845	Tmem39a	2610033C09Rik	transmembrane protein 39a	protein-coding
mm_30233.1	chr3	146107990	146108003	-	1	NA	promoter-TSS (NM_172864)	promoter-TSS (NM_172864)	40	NM_172864	242253	Mm.235040	NM_172864	ENSMUSG00000043020	Wdr63	4931433A13Rik	WD repeat domain 63	protein-coding
mm_31509.1	chr4	53631507	53631520	+	1	NA	promoter-TSS (NM_176966)	promoter-TSS (NM_176966)	42	NM_001195284	319636	Mm.103464	NM_176966	ENSMUSG00000054752	Fsd1l	A230072O16Rik|Ccdc10|Csdufd1|Fsd1nl|OTTMUSG00000007002	fibronectin type III and SPRY domain containing 1-like	protein-coding
mm_149060.1	chr19	8839509	8839558	+	1	NA	promoter-TSS (NM_010316)	promoter-TSS (NM_010316)	205	NM_008144	14705	Mm.345134	NM_008144	ENSMUSG00000071657	Bscl2	2900097C17Rik|AI046355|Gng3lg	Berardinelli-Seip congenital lipodystrophy 2 (seipin)	protein-coding
mm_24307.1	chr3	89394269	89394321	+	1	NA	promoter-TSS (NR_040404)	promoter-TSS (NR_040404)	5	NR_040404	545539	Mm.393389	NR_040403	ENSMUSG00000074466	Gm15417	ENSMUSG00000074466|OTTMUSG00000021274	predicted gene 15417	ncRNA
mm_52832.1	chr6	121365199	121365227	+	1	NA	intron (NM_001347433, intron 14 of 14)	intron (NM_001347433, intron 14 of 14)	18516	NM_133661	14411	Mm.274506	NM_133661	ENSMUSG00000030109	Slc6a12	BGT1|GAT-2|GAT2|Gabt2	solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12	protein-coding
mm_107904.1	chr12	70937866	70937939	+	1	NA	promoter-TSS (NM_019785)	promoter-TSS (NM_019785)	45	NM_019785	56444	Mm.29317	NM_019785	ENSMUSG00000021076	Actr10	Actr11|Arp11	ARP10 actin-related protein 10	protein-coding
mm_76824.1	chr8	104624189	104624203	-	1	NA	5' UTR (NM_001252627, exon 1 of 17)	5' UTR (NM_001252627, exon 1 of 17)	200	NM_007663	12556	Mm.19423	NM_007663	ENSMUSG00000031881	Cdh16	-	cadherin 16	protein-coding
mm_95402.1	chr11	49794158	49794184	+	1	NA	promoter-TSS (NM_013529)	promoter-TSS (NM_013529)	16	NM_013529	14584	Mm.24402	NM_013529	ENSMUSG00000020363	Gfpt2	AI480523|GFAT2	glutamine fructose-6-phosphate transaminase 2	protein-coding
mm_112892.1	chr13	20885143	20885152	+	1	NA	intron (NM_012054, intron 4 of 20)	B4|SINE|B4	91034	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_118560.1	chr14	17981814	17981820	+	1	NA	5' UTR (NM_009380, exon 1 of 7)	5' UTR (NM_009380, exon 1 of 7)	173	NM_009380	21834	Mm.32563	NM_009380	ENSMUSG00000021779	Thrb	Nr1a2|T3R[b]|T3Rbeta|Thrb1|Thrb2|c-erbAbeta	thyroid hormone receptor beta	protein-coding
mm_155992.1	chrX	106149661	106149668	+	1	NA	intron (NM_205820, intron 2 of 2)	intron (NM_205820, intron 2 of 2)	6389	NM_205820	279572	Mm.336203	NM_205820	ENSMUSG00000033777	Tlr13	AI666735|Gm713	toll-like receptor 13	protein-coding
mm_172162.1	chr6	44792986	44792988	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-267074	NM_001004357	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding
mm_71395.1	chr8	46163734	46163750	+	1	NA	Intergenic	CpG	-5814	NM_025747	66756	Mm.133623	NM_025747	ENSMUSG00000031631	Cfap97	1110068E21Rik|4933411K20Rik|AW049273|Kiaa1430|mKIAA1430	cilia and flagella associated protein 97	protein-coding
mm_107962.1	chr12	72735861	72735865	+	1	NA	Intergenic	MT2B|LTR|ERVL	-25348	NM_008910	19042	Mm.261045	NM_008910	ENSMUSG00000021096	Ppm1a	2310003C21Rik|2900017D14Rik|AI427932|AU017636|MMPa-2|MPPa-1	protein phosphatase 1A, magnesium dependent, alpha isoform	protein-coding
mm_12338.1	chr2	69722798	69722840	+	1	NA	promoter-TSS (NM_001081086)	promoter-TSS (NM_001081086)	-269	NM_001081086	228005	Mm.11815	NM_001081086	ENSMUSG00000042133	Ppig	AU019516|AU022200|B230312B02Rik|CYP|SRCyp	peptidyl-prolyl isomerase G (cyclophilin G)	protein-coding
mm_56627.1	chr6	112802154	112802154	-	1	NA	intron (NM_080448, intron 3 of 21)	L1MEg|LINE|L1	-105484	NM_001167730	58186	Mm.103812	NM_021385	ENSMUSG00000030254	Rad18	2810024C04Rik|Rad18sc	RAD18 E3 ubiquitin protein ligase	protein-coding
mm_145585.1	chr18	60985671	60985682	+	1	NA	3' UTR (NM_001286809, exon 6 of 6)	3' UTR (NM_001286809, exon 6 of 6)	22122	NM_001286809	12322	Mm.131530	NM_009792	ENSMUSG00000024617	Camk2a	CaMKII|R74975|mKIAA0968	calcium/calmodulin-dependent protein kinase II alpha	protein-coding
mm_169902.1	chr16	52083861	52083866	+	1	NA	intron (NM_001033238, intron 3 of 17)	(AGGTG)n|Simple_repeat|Simple_repeat	52314	NM_001033238	208650	Mm.328206	NM_001033238	ENSMUSG00000022637	Cblb	AI429560|AI851073|Cbl-b	Casitas B-lineage lymphoma b	protein-coding
mm_82847.1	chr9	31170544	31170559	-	1	NA	exon (NM_009691, exon 5 of 16)	exon (NM_009691, exon 5 of 16)	-38752	NM_011176	19143	Mm.243926	NM_011176	ENSMUSG00000031995	St14	Epithin|MT-SP1|Prss14|Tmprss14|mCAP3|matriptase	suppression of tumorigenicity 14 (colon carcinoma)	protein-coding
mm_69393.1	chr7	132154619	132154627	-	1	NA	5' UTR (NM_018867, exon 1 of 14)	5' UTR (NM_018867, exon 1 of 14)	118	NM_018867	55987	Mm.471654	NM_018867	ENSMUSG00000030862	Cpxm2	4632435C11Rik|CPX-2|Cpx2	carboxypeptidase X 2 (M14 family)	protein-coding
mm_136315.1	chr16	91728768	91728776	-	1	NA	promoter-TSS (NM_001110276)	promoter-TSS (NM_001110276)	30	NM_026994	66609	Mm.109823	NM_026994	ENSMUSG00000058240	Cryzl1	2210407J23Rik|2410006O11Rik|QOH-1	crystallin, zeta (quinone reductase)-like 1	protein-coding
mm_98007.1	chr11	84179853	84179863	+	1	NA	Intergenic	CpG	-12382	NM_001037932	628813	Mm.390389	NM_001037932	ENSMUSG00000051452	Gm11437	AI463690|OTTMUSG00000000997	predicted gene 11437	protein-coding
mm_87850.1	chr10	61031269	61031307	+	1	NA	promoter-TSS (NR_040638)	promoter-TSS (NR_040638)	-15	NR_040638	327760	Mm.23529	NR_040638	ENSMUSG00000093568	Gm20611	4930565A17	predicted gene 20611	ncRNA
mm_76081.1	chr8	79356462	79356493	-	1	NA	intron (NM_008539, intron 2 of 6)	intron (NM_008539, intron 2 of 6)	42991	NM_008539	17125	Mm.223717	NM_008539	ENSMUSG00000031681	Smad1	AI528653|Madh1|Madr1|Mlp1|MusMLP	SMAD family member 1	protein-coding
mm_118830.1	chr14	25607408	25607441	+	1	NA	intron (NM_001310666, intron 6 of 23)	CpG	3911	NM_001309430	100188919	Mm.473810	NM_001309430		Israa	-	immune system released activating agent	protein-coding
mm_34217.1	chr4	140971890	140971904	+	1	NA	intron (NM_023374, intron 3 of 7)	intron (NM_023374, intron 3 of 7)	10626	NM_023374	67680	Mm.246965	NM_023374	ENSMUSG00000009863	Sdhb	0710008N11Rik	succinate dehydrogenase complex, subunit B, iron sulfur (Ip)	protein-coding
mm_65147.1	chr7	19586450	19586462	-	1	NA	non-coding (NR_125836, exon 11 of 18)	non-coding (NR_125836, exon 11 of 18)	9169	NM_022409	63872	Mm.23310	NM_022409	ENSMUSG00000011267	Zfp296	2210018A16Rik|Znf296	zinc finger protein 296	protein-coding
mm_143795.1	chr17	82410898	82410900	-	1	NA	Intergenic	Lx2A|LINE|L1	667326	NR_045094	100503434	Mm.187281	NR_045094		Gm19689	-	predicted gene, 19689	ncRNA
mm_79396.1	chr9	54917299	54917328	+	1	NA	promoter-TSS (NM_177351)	promoter-TSS (NM_177351)	23	NM_177351	235386	Mm.259334	NM_177351	ENSMUSG00000035878	Hykk	Agphd1|C630028N24Rik	hydroxylysine kinase 1	protein-coding
mm_98920.1	chr11	98348429	98348434	+	1	NA	promoter-TSS (NM_144828)	promoter-TSS (NM_144828)	25	NM_144828	19049	Mm.45372	NM_144828	ENSMUSG00000061718	Ppp1r1b	AU040756|DARPP-32|Darpp32	protein phosphatase 1, regulatory (inhibitor) subunit 1B	protein-coding
mm_109979.1	chr12	12940601	12940612	-	1	NA	intron (NM_008709, intron 1 of 2)	intron (NM_008709, intron 1 of 2)	1230	NM_008709	18109	Mm.16469	NM_008709	ENSMUSG00000037169	Mycn	N-myc|Nmyc|Nmyc-1|Nmyc1|bHLHe37|c-nmyc	v-myc avian myelocytomatosis viral related oncogene, neuroblastoma derived	protein-coding
mm_73539.1	chr8	108703944	108703956	+	1	NA	Intergenic	Intergenic	-10694	NM_007496	11906	Mm.416972	NM_007496	ENSMUSG00000038872	Zfhx3	A230102L03Rik|Atbf1|Sci|WBP9|mKIAA4228	zinc finger homeobox 3	protein-coding
mm_94886.1	chr11	27322305	27322310	+	1	NA	Intergenic	Intergenic	537199	NR_002890	654472	Mm.347777	NR_002890		Gm12070	OTTMUSG00000005300	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_149554.1	chr19	12633304	12633325	+	1	NA	promoter-TSS (NM_145935)	promoter-TSS (NM_145935)	6	NM_145935	107146	Mm.39974	NM_145935	ENSMUSG00000063683	Glyat	A330009E03Rik|ACGNAT|AI195249|AI315345|CAT|GAT	glycine-N-acyltransferase	protein-coding
mm_42758.1	chr5	120952760	120952761	+	1	NA	intron (NM_001302345, intron 12 of 20)	intron (NM_001302345, intron 12 of 20)	37942	NM_133893	100535	Mm.247620	NM_133893	ENSMUSG00000032623	Oas1d	AA536864|C85127|oasl8	2'-5' oligoadenylate synthetase 1D	protein-coding
mm_10116.1	chr2	3723753	3723798	+	1	NA	intron (NM_025626, intron 1 of 3)	intron (NM_025626, intron 1 of 3)	10317	NM_025626	66540	Mm.277864	NM_025626	ENSMUSG00000026655	Fam107b	3110001A13Rik|AA589595|AA959793|AI132312	family with sequence similarity 107, member B	protein-coding
mm_113390.1	chr13	33040057	33040074	+	1	NA	3' UTR (NM_011452, exon 7 of 7)	3' UTR (NM_011452, exon 7 of 7)	12651	NM_011452	20706	Mm.45371	NM_011452	ENSMUSG00000021403	Serpinb9b	1600019A21Rik|R86|SPI-CI|Spi10|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 9b	protein-coding
mm_118407.1	chr13	119488335	119488389	-	1	NA	promoter-TSS (NR_027974)	promoter-TSS (NR_027974)	22	NR_027974	67304	Mm.474382	NM_026084	ENSMUSG00000074635	3110070M22Rik	-	RIKEN cDNA 3110070M22 gene	ncRNA
mm_146593.1	chr18	9414746	9414749	-	1	NA	intron (NM_026484, intron 1 of 9)	intron (NM_026484, intron 1 of 9)	35403	NM_026484	67974	Mm.86523	NM_026484	ENSMUSG00000024286	Ccny	1700025H17Rik|3110050L10Rik|4631402G10Rik|5730405I09Rik	cyclin Y	protein-coding
mm_42046.1	chr5	108461415	108461425	+	1	NA	promoter-TSS (NM_172716)	promoter-TSS (NM_172716)	88	NM_172716	69587	Mm.261218	NM_172716	ENSMUSG00000033623	Pcgf3	2310035N15Rik|AI662857|D630042K08Rik|DONG1|E430039C14|RNF3A|Rnf3	polycomb group ring finger 3	protein-coding
mm_63176.1	chr7	125418701	125418726	+	1	NA	Intergenic	ORR1D2|LTR|ERVL-MaLR	-25907	NM_029842	77035	Mm.307239	NM_029842	ENSMUSG00000030752	Kdm8	3110005O21Rik|Jmjd5	lysine (K)-specific demethylase 8	protein-coding
mm_53763.1	chr6	145807197	145807232	+	1	NA	Intergenic	Intergenic	-1169	NM_027760	71323	Mm.158669	NM_027760	ENSMUSG00000030259	Rassf8	5133400D11Rik|AA815821|AW123240|Hoj1|mHoj-1	Ras association (RalGDS/AF-6) domain family (N-terminal) member 8	protein-coding
mm_69361.1	chr7	130519966	130520004	-	1	NA	promoter-TSS (NM_001136054)	promoter-TSS (NM_001136054)	384	NM_001029895	11907	Mm.216321	NM_013799	ENSMUSG00000030850	Ate1	AI225793|AW547406	arginyltransferase 1	protein-coding
mm_8611.1	chr1	156036026	156036074	-	1	NA	promoter-TSS (NM_001160182)	promoter-TSS (NM_001160182)	14	NM_001160182	240832	Mm.253335	NM_022329	ENSMUSG00000050565	Tor1aip2	1110020D10Rik|15kDa|A130072J07|AA103493|AW060462|AW610675|C77739|Ifrg15|Lull1	torsin A interacting protein 2	protein-coding
mm_158591.1	chrX	150954857	150954868	-	1	NA	Intergenic	MLT1M|LTR|ERVL-MaLR	62431	NM_001168600	237107	Mm.45987	NM_198110	ENSMUSG00000025266	Gnl3l	BC020354	guanine nucleotide binding protein-like 3 (nucleolar)-like	protein-coding
mm_82225.1	chr9	3026672	3026720	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	12047	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_89177.1	chr10	86344554	86344562	+	1	NA	exon (NM_011595, exon 4 of 5)	exon (NM_011595, exon 4 of 5)	44146	NM_011595	21859	Mm.4871	NM_011595	ENSMUSG00000020044	Timp3	Timp-3	tissue inhibitor of metalloproteinase 3	protein-coding
mm_129500.1	chr15	78855518	78855536	-	1	NA	promoter-TSS (NM_025622)	promoter-TSS (NM_025622)	2	NM_025622	107753	Mm.390793	NM_025622	ENSMUSG00000043501	Lgals2	2200008F12Rik|AI324147	lectin, galactose-binding, soluble 2	protein-coding
mm_63080.1	chr7	122219698	122219704	+	1	NA	5' UTR (NM_027363, exon 1 of 7)	5' UTR (NM_027363, exon 1 of 7)	205	NM_027363	70261	Mm.96997	NM_027363	ENSMUSG00000030865	Chp2	2010110P09Rik|Cbhp2	calcineurin-like EF hand protein 2	protein-coding
mm_51072.1	chr6	66896411	66896421	+	1	NA	promoter-TSS (NM_001177559)	promoter-TSS (NM_001177559)	19	NM_001177556	14701	Mm.234342	NM_025278	ENSMUSG00000036402	Gng12	2010305F15Rik|AA536815|AI115529|AI314170|AI842738	guanine nucleotide binding protein (G protein), gamma 12	protein-coding
mm_57433.1	chr6	124914677	124914694	-	1	NA	exon (NM_026988, exon 3 of 5)	exon (NM_026988, exon 3 of 5)	-2980	NM_008479	16768	Mm.4528	NM_008479	ENSMUSG00000030124	Lag3	CD223|LAG-3|Ly66	lymphocyte-activation gene 3	protein-coding
mm_99028.1	chr11	98942388	98942396	+	1	NA	intron (NM_001177303, intron 1 of 8)	intron (NM_001177303, intron 1 of 8)	2681	NM_001177303	19401	Mm.439744	NM_009024	ENSMUSG00000037992	Rara	Nr1b1|RAR|RARalpha1	retinoic acid receptor, alpha	protein-coding
mm_164594.1	chr17	27444942	27444975	-	1	NA	intron (NM_001013385, intron 5 of 8)	B4|SINE|B4	58575	NM_001013385	268934	Mm.358940	NM_001013385	ENSMUSG00000063239	Grm4	Gprc1d|mGluR4	glutamate receptor, metabotropic 4	protein-coding
mm_163291.1	chr11	118248587	118248587	-	1	NA	promoter-TSS (NM_011180)	promoter-TSS (NM_011180)	5	NM_001112699	19157	Mm.86413	NM_011180	ENSMUSG00000017132	Cyth1	CLM1|CTH-1|CYTIP|Pscd1	cytohesin 1	protein-coding
mm_115183.1	chr13	108449737	108449748	+	1	NA	Intergenic	Intergenic	133405	NM_178683	218581	Mm.32318	NM_178683	ENSMUSG00000021697	Depdc1b	9830132O03|AW260467|XTP1	DEP domain containing 1B	protein-coding
mm_119290.1	chr14	34673889	34673930	+	1	NA	promoter-TSS (NM_001301330)	promoter-TSS (NM_001301330)	-19	NM_001004436	218914	Mm.27957	NM_001004436	ENSMUSG00000041408	Wapl	A530089A20Rik|BC037674|DIF-2|FOE|Wapal	WAPL cohesin release factor	protein-coding
mm_25660.1	chr3	121723557	121723561	+	1	NA	promoter-TSS (NM_010171)	promoter-TSS (NM_010171)	22	NM_010171	14066	Mm.273188	NM_010171	ENSMUSG00000028128	F3	AA409063|CD142|Cf-3|Cf3|TF	coagulation factor III	protein-coding
mm_138652.1	chr17	35867746	35867775	+	1	NA	exon (NM_001146711, exon 2 of 4)	exon (NM_001146711, exon 2 of 4)	1145	NM_175242	76448	Mm.359982	NM_175242	ENSMUSG00000034595	Ppp1r18	2310014H01Rik|AA407849|AI450394	protein phosphatase 1, regulatory subunit 18	protein-coding
mm_69160.1	chr7	127195926	127196006	-	1	NA	5' UTR (NM_027353, exon 1 of 7)	5' UTR (NM_027353, exon 1 of 7)	111	NM_001285907	70233	Mm.28050	NM_027353	ENSMUSG00000042502	Cd2bp2	1500011B02Rik|2410024K20Rik|AW048183	CD2 antigen (cytoplasmic tail) binding protein 2	protein-coding
mm_133949.1	chr16	3976520	3976535	-	1	NA	5' UTR (NM_001081280, exon 1 of 18)	5' UTR (NM_001081280, exon 1 of 18)	105	NM_175547	268857	Mm.215994	NM_175547	ENSMUSG00000049871	Nlrc3	CLR16.2|D230007K08Rik|mFLJ00348	NLR family, CARD domain containing 3	protein-coding
mm_150882.1	chr19	45076900	45076939	+	1	NA	exon (NM_178929, exon 2 of 5)	exon (NM_178929, exon 2 of 5)	780	NM_178929	107250	Mm.24417	NM_178929	ENSMUSG00000025213	Kazald1	AI842353|Bono1|IGFBP-rP10	Kazal-type serine peptidase inhibitor domain 1	protein-coding
mm_87593.1	chr10	57512485	57512489	+	1	NA	3' UTR (NM_008297, exon 12 of 12)	3' UTR (NM_008297, exon 12 of 12)	20042	NM_019760	56442	Mm.29344	NM_019760	ENSMUSG00000019877	Serinc1	1500011D18Rik|AI315070|AIGP-2|TMS-2|Tde1l|Tde2|Tms2|mKIAA1253	serine incorporator 1	protein-coding
mm_62000.1	chr7	91176780	91176788	+	1	NA	intron (NM_011807, intron 1 of 22)	intron (NM_011807, intron 1 of 22)	85998	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_44504.1	chr5	23922661	23922694	-	1	NA	intron (NM_001310471, intron 10 of 10)	MTC|LTR|ERVL-MaLR	70444	NR_028536	100217436		NR_028536		Snord93	Gm22397|MBII-336	small nucleolar RNA, C/D box 93	snoRNA
mm_86986.1	chr10	25476249	25476253	+	1	NA	intron (NM_001199265, intron 8 of 19)	intron (NM_001199265, intron 8 of 19)	60021	NM_001195596	100504474	Mm.46323	NM_001195596	ENSMUSG00000096546	Smlr1	2010003K15Rik	small leucine-rich protein 1	protein-coding
mm_163668.1	chr13	80883380	80883386	+	1	NA	promoter-TSS (NM_001042591)	promoter-TSS (NM_001042591)	-39	NM_001042591	105171	Mm.423137	NM_001042591	ENSMUSG00000074794	Arrdc3	AI450344|mKIAA1376	arrestin domain containing 3	protein-coding
mm_23205.1	chr3	41555724	41555745	+	1	NA	promoter-TSS (NM_001130184)	promoter-TSS (NM_001130184)	0	NM_001130184	269424	Mm.286285	NM_172303	ENSMUSG00000025764	Jade1	AU041499|D530048A03Rik|Phf17|mKIAA1807	jade family PHD finger 1	protein-coding
mm_103319.1	chr11	73196753	73196767	-	1	NA	intron (NM_031251, intron 1 of 10)	intron (NM_031251, intron 1 of 10)	2259	NM_031251	83429	Mm.259852	NM_031251	ENSMUSG00000005949	Ctns	AI195360|AW049661	cystinosis, nephropathic	protein-coding
mm_70835.1	chr8	23167778	23167824	+	1	NA	Intergenic	Intergenic	14530	NM_029002	74561	Mm.290028	NM_029002	ENSMUSG00000063672	Nkx6-3	9130417I07Rik|Nkx6.3	NK6 homeobox 3	protein-coding
mm_116106.1	chr13	28949152	28949172	-	1	NA	Intergenic	(A)n|Simple_repeat|Simple_repeat	4520	NM_009238	20677	Mm.240627	NM_009238	ENSMUSG00000076431	Sox4	AA682046|Sox-4	SRY (sex determining region Y)-box 4	protein-coding
mm_78073.1	chr9	15493526	15493607	+	1	NA	Intergenic	CpG	-11929	NM_133214	170748	Mm.86572	NM_133214	ENSMUSG00000058173	Smco4	Fn5	single-pass membrane protein with coiled-coil domains 4	protein-coding
mm_37980.1	chr4	133601872	133601889	-	1	NA	5' UTR (NM_018754, exon 1 of 1)	5' UTR (NM_018754, exon 1 of 1)	288	NM_018754	55948	Mm.44482	NM_018754	ENSMUSG00000047281	Sfn	Er|Mme1|Ywhas	stratifin	protein-coding
mm_23638.1	chr3	66985948	66985986	+	1	NA	intron (NM_025822, intron 1 of 9)	CpG	295	NM_025822	66880	Mm.316418	NM_025822	ENSMUSG00000034544	Rsrc1	1200013F24Rik|SRrp53	arginine/serine-rich coiled-coil 1	protein-coding
mm_127478.1	chr15	101274083	101274087	+	1	NA	exon (NM_010444, exon 7 of 7)	exon (NM_010444, exon 7 of 7)	7239	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_25761.1	chr3	124321032	124321113	+	1	NA	promoter-TSS (NM_146140)	promoter-TSS (NM_146140)	35	NM_146140	229801	Mm.165810	NM_146140	ENSMUSG00000044528	Tram1l1	A830091N21Rik	translocation associated membrane protein 1-like 1	protein-coding
mm_113654.1	chr13	42307274	42307281	+	1	NA	3' UTR (NM_010104, exon 5 of 5)	3' UTR (NM_010104, exon 5 of 5)	5801	NM_010104	13614	Mm.14543	NM_010104	ENSMUSG00000021367	Edn1	ET-1|PPET1|preproET	endothelin 1	protein-coding
mm_36955.1	chr4	109133067	109133079	-	1	NA	intron (NM_001346502, intron 4 of 23)	PB1D7|SINE|Alu	-15037	NM_001134791	100273	Mm.366315	NM_133885	ENSMUSG00000028559	Osbpl9	2600011I06Rik|AU015843|Orp-9	oxysterol binding protein-like 9	protein-coding
mm_160538.1	chr9	40101238	40101238	-	1	NA	exon (NM_146608, exon 1 of 1)	exon (NM_146608, exon 1 of 1)	250	NM_146608	258601	Mm.377587	NM_146608	ENSMUSG00000045812	Olfr984	MOR239-6	olfactory receptor 984	protein-coding
mm_118162.1	chr13	105294304	105294340	-	1	NA	Intergenic	CpG	-1308	NM_027934	71816	Mm.317015	NM_027934	ENSMUSG00000021720	Rnf180	3110001E11Rik|Rines	ring finger protein 180	protein-coding
mm_112828.1	chr13	20817786	20817821	+	1	NA	intron (NM_012054, intron 2 of 20)	intron (NM_012054, intron 2 of 20)	23690	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_8368.1	chr1	150653881	150653886	-	1	NA	intron (NM_001024720, intron 63 of 106)	intron (NM_001024720, intron 63 of 106)	-187718	NM_001110146	96875	Mm.174256	NM_021400	ENSMUSG00000006014	Prg4	CACP|DOL54|JCAP|MSF|SZP|lubricin	proteoglycan 4 (megakaryocyte stimulating factor, articular superficial zone protein)	protein-coding
mm_170435.1	chr18	78862405	78862419	+	1	NA	intron (NM_053099, intron 3 of 5)	L1Md_T|LINE|L1	246979	NM_053099	240427	Mm.312871	NM_053099	ENSMUSG00000024548	Setbp1	C130092E12|Seb|mKIAA0437	SET binding protein 1	protein-coding
mm_27980.1	chr3	81958612	81958620	-	1	NA	3' UTR (NM_019911, exon 12 of 12)	3' UTR (NM_019911, exon 12 of 12)	17112	NM_019911	56720	Mm.258622	NM_019911	ENSMUSG00000028011	Tdo2	AA407491|TDO|TO|chky	tryptophan 2,3-dioxygenase	protein-coding
mm_130101.1	chr15	89429215	89429223	-	1	NA	intron (NR_037153, intron 1 of 9)	intron (NR_037153, intron 1 of 9)	708	NR_037154	12651	Mm.485045	NM_007692	ENSMUSG00000022617	Chkb	Chetk|Chkl|Ck|Ck/Ek|Ck/Ek-beta|Ckb|Ckekb|Ek	choline kinase beta	protein-coding
mm_147521.1	chr18	52529596	52529618	-	1	NA	5' UTR (NM_010728, exon 1 of 7)	5' UTR (NM_010728, exon 1 of 7)	114	NM_001286181	16948	Mm.172	NM_010728	ENSMUSG00000024529	Lox	AI893619|TSC-160|rrg	lysyl oxidase	protein-coding
mm_146656.1	chr18	11052860	11052892	-	1	NA	promoter-TSS (NR_105023)	promoter-TSS (NR_105023)	-309	NR_105023	68434	Mm.57626	NR_105022	ENSMUSG00000097222	1010001N08Rik	Gata6as	RIKEN cDNA 1010001N08 gene	ncRNA
mm_110102.1	chr12	26187554	26187582	-	1	NA	intron (NR_131149, intron 2 of 4)	intron (NR_131149, intron 2 of 4)	22937	NR_131149	629481	Mm.390460	NR_131149		Gm29687	-	predicted gene, 29687	ncRNA
mm_32063.1	chr4	97777781	97777823	+	1	NA	5' UTR (NM_001122953, exon 1 of 10)	5' UTR (NM_001122953, exon 1 of 10)	176	NM_010905	18027	Mm.31274	NM_010905	ENSMUSG00000028565	Nfia	1110047K16Rik|9430022M17Rik|CTF|NF1-A|NF1A	nuclear factor I/A	protein-coding
mm_97330.1	chr11	77078477	77078505	+	1	NA	promoter-TSS (NR_030756)	promoter-TSS (NR_030756)	-54	NM_001012309	237859	Mm.156195	NM_001012309	ENSMUSG00000037958	Nsrp1	8030451K07|AI851076|AL022898|Ccdc55|NSpr70|NSrp70	nuclear speckle regulatory protein 1	protein-coding
mm_108178.1	chr12	76417517	76417543	+	1	NA	promoter-TSS (NM_001163103)	promoter-TSS (NM_001163103)	-69	NM_001163103	210762	Mm.292354	NM_001163103	ENSMUSG00000052221	Ppp1r36	Gm70	protein phosphatase 1, regulatory subunit 36	protein-coding
mm_119249.1	chr14	33923484	33923499	+	1	NA	promoter-TSS (NM_145741)	promoter-TSS (NM_145741)	-96	NM_145741	14560	Mm.432071	NM_145741	ENSMUSG00000021943	Gdf10	Bmp3b	growth differentiation factor 10	protein-coding
mm_165373.1	chr2	128306974	128306982	+	1	NA	intron (NR_028589, intron 2 of 2)	intron (NR_028589, intron 2 of 2)	122373	NR_028591	100043424	Mm.297222	NR_028589		Gm14005	OTTMUSG00000015351	predicted gene 14005	ncRNA
mm_170898.1	chr2	29980175	29980176	+	1	NA	exon (NM_001177668, exon 3 of 56)	exon (NM_001177668, exon 3 of 56)	14615	NM_001309460	20740	Mm.204969	NM_001076554	ENSMUSG00000057738	Sptan1	2610027H02Rik|Spna-2|Spna2	spectrin alpha, non-erythrocytic 1	protein-coding
mm_141365.1	chr17	28942225	28942254	-	1	NA	promoter-TSS (NM_153390)	promoter-TSS (NM_153390)	23	NM_153390	69307	Mm.107605	NM_153390	ENSMUSG00000045378	Pxt1	1700001G18Rik|Stepp	peroxisomal, testis specific 1	protein-coding
mm_54649.1	chr6	38876503	38876515	-	1	NA	promoter-TSS (NM_010433)	promoter-TSS (NM_010433)	-319	NM_001294143	15258	Mm.23790	NM_010433	ENSMUSG00000061436	Hipk2	1110014O20Rik|B230339E18Rik|Stank	homeodomain interacting protein kinase 2	protein-coding
mm_25526.1	chr3	114904063	114904142	+	1	NA	promoter-TSS (NM_153458)	promoter-TSS (NM_153458)	24	NM_153458	229759	Mm.54183	NM_153157	ENSMUSG00000027965	Olfm3	B230206G02Rik	olfactomedin 3	protein-coding
mm_87486.1	chr10	51494582	51494592	+	1	NA	intron (NM_001291894, intron 6 of 8)	intron (NM_001291894, intron 6 of 8)	3689	NM_013532	14728	Mm.34408	NM_013532	ENSMUSG00000062593	Lilrb4a	CD85K|Gp49b|HM18|ILT3|LIR-5|Lilrb4|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4A	protein-coding
mm_67148.1	chr7	73502629	73502632	-	1	NA	intron (NM_001081345, intron 8 of 38)	intron (NM_001081345, intron 8 of 38)	39116	NM_001081345	244059	Mm.34539	NM_001081345	ENSMUSG00000078671	Chd2	2810013C04Rik|2810040A01Rik|5630401D06Rik|AI851092|BC029703|CHD-2	chromodomain helicase DNA binding protein 2	protein-coding
mm_140531.1	chr17	6746888	6746892	-	1	NA	intron (NM_009510, intron 7 of 12)	intron (NM_009510, intron 7 of 12)	35890	NM_009510	22350	Mm.277812	NM_009510	ENSMUSG00000052397	Ezr	AW146364|R75297|Vil2|p81	ezrin	protein-coding
mm_165150.1	chr2	19423189	19423195	-	1	NA	Intergenic	Intergenic	-22471	NM_018809	19213	Mm.69647	NM_018809	ENSMUSG00000026735	Ptf1a	PTF1-p48|PTF1p48|bHLHa29	pancreas specific transcription factor, 1a	protein-coding
mm_20508.1	chr2	130629973	130629990	-	1	NA	promoter-TSS (NM_001255994)	promoter-TSS (NM_001255994)	46	NM_198176	380601	Mm.27090	NM_198176	ENSMUSG00000079043	Fastkd5	C78212|mKIAA1792	FAST kinase domains 5	protein-coding
mm_3130.1	chr1	134962632	134962642	+	1	NA	promoter-TSS (NM_026024)	promoter-TSS (NM_026024)	72	NM_001278115	67196	Mm.284587	NM_026024	ENSMUSG00000026429	Ube2t	2700084L22Rik|C80607	ubiquitin-conjugating enzyme E2T	protein-coding
mm_14287.1	chr2	128818105	128818135	+	1	NA	promoter-TSS (NM_028248)	promoter-TSS (NM_028248)	-183	NM_028248	72477	Mm.259688	NM_028248	ENSMUSG00000014353	Tmem87b	2610301K12Rik|2810431I02Rik|AU014804	transmembrane protein 87B	protein-coding
mm_133627.1	chr16	91611492	91611537	+	1	NA	Intergenic	Intergenic	7485	NM_001099738	246738	Mm.101927	NM_138664	ENSMUSG00000039763	Dnajc28	BC020175|ORF28	DnaJ heat shock protein family (Hsp40) member C28	protein-coding
mm_37835.1	chr4	132049029	132049044	-	1	NA	promoter-TSS (NM_001128606)	promoter-TSS (NM_001128606)	42	NM_001128606	269587	Mm.30038	NM_183428	ENSMUSG00000028906	Epb41	4.1R|AI415518|D4Ertd442e|Elp-1|Elp1|Epb4.1|mKIAA4056	erythrocyte membrane protein band 4.1	protein-coding
mm_89859.1	chr10	108162081	108162112	+	1	NA	promoter-TSS (NM_027892)	promoter-TSS (NM_027892)	-304	NM_027892	17931	Mm.422959	NM_027892	ENSMUSG00000019907	Ppp1r12a	1200015F06Rik|5730577I22Rik|AA792106|AV099298|D10Ertd625e|Mypt1	protein phosphatase 1, regulatory (inhibitor) subunit 12A	protein-coding
mm_110188.1	chr12	27339407	27339414	-	1	NA	3' UTR (NM_009234, exon 1 of 1)	3' UTR (NM_009234, exon 1 of 1)	3308	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding
mm_123255.1	chr14	61046463	61046487	-	1	NA	5' UTR (NM_013869, exon 1 of 10)	5' UTR (NM_013869, exon 1 of 10)	380	NM_013869	29820	Mm.281356	NM_013869	ENSMUSG00000060548	Tnfrsf19	AL023044|AW123854|TAJ|TAJ-ALPHA|TRADE|Troy	tumor necrosis factor receptor superfamily, member 19	protein-coding
mm_145341.1	chr18	56469240	56469278	+	1	NA	intron (NM_026240, intron 1 of 13)	intron (NM_026240, intron 1 of 13)	37127	NM_026240	107022	Mm.24356	NM_026240	ENSMUSG00000001700	Gramd3	9030613F08Rik|9130427A09Rik|AW061306|NS3TP2	GRAM domain containing 3	protein-coding
mm_115384.1	chr13	113139270	113139293	+	1	NA	intron (NR_131045, intron 2 of 2)	RMER17C|LTR|ERVK	3205	NR_131045	76720	Mm.54263	NR_131045		1700084D21Rik	-	RIKEN cDNA 1700084D21 gene	ncRNA
mm_67470.1	chr7	80419418	80419429	-	1	NA	Intergenic	Intergenic	-13987	NM_001081454	18550	Mm.5241	NM_011046	ENSMUSG00000030530	Furin	9130404I01Rik|Fur|PACE|Pcsk3|SPC1	furin (paired basic amino acid cleaving enzyme)	protein-coding
mm_20830.1	chr2	147013318	147013335	-	1	NA	intron (NM_011917, intron 1 of 29)	CpG	266	NM_011917	24128	Mm.3065	NM_011917	ENSMUSG00000027433	Xrn2	-	5'-3' exoribonuclease 2	protein-coding
mm_168753.1	chr12	115920763	115920770	-	1	NA	Intergenic	Intergenic	-126958	NM_001004066	56220	Mm.254997	NM_019565	ENSMUSG00000042063	Zfp386	Kzf1|mKIAA4205	zinc finger protein 386 (Kruppel-like)	protein-coding
mm_52602.1	chr6	117173509	117173519	+	1	NA	exon (NM_021704, exon 3 of 3)	exon (NM_021704, exon 3 of 3)	4979	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_41017.1	chr5	81140147	81140150	+	1	NA	intron (NM_001347369, intron 2 of 25)	intron (NM_001347369, intron 2 of 25)	118555	NM_198702	319387	Mm.273631	NM_198702	ENSMUSG00000037605	Adgrl3	5430402I23Rik|CIRL-3|D130075K09Rik|Gm1379|LEC3|Lphn3|mKIAA0768	adhesion G protein-coupled receptor L3	protein-coding
mm_111131.1	chr12	81485076	81485140	-	1	NA	promoter-TSS (NM_025461)	promoter-TSS (NM_025461)	29	NM_001309809	66272	Mm.439970	NM_025461	ENSMUSG00000091803	Cox16	1810020G14Rik|1810055I05Rik|BB388670	cytochrome c oxidase assembly protein 16	protein-coding
mm_109185.1	chr12	108485300	108485329	+	1	NA	intron (NM_001043335, intron 3 of 21)	intron (NM_001043335, intron 3 of 21)	62498	NM_001043335	68519	Mm.236645	NM_001043335	ENSMUSG00000058070	Eml1	1110008N23Rik|A930030P13Rik|AA171013|AI847476|AI853955|ELP79|EMAP|EMAPL|heco	echinoderm microtubule associated protein like 1	protein-coding
mm_136476.1	chr16	95869530	95869562	-	1	NA	intron (NR_040484, intron 1 of 3)	intron (NR_040484, intron 1 of 3)	29167	NR_040485	69776	Mm.120470	NR_040484	ENSMUSG00000086899	1600002D24Rik	-	RIKEN cDNA 1600002D24 gene	ncRNA
mm_142621.1	chr17	47010575	47010592	-	1	NA	promoter-TSS (NM_001177374)	promoter-TSS (NM_001177374)	-51	NM_001177374	224826	Mm.28234	NM_146078	ENSMUSG00000023977	Ubr2	9930021A08Rik|AI462103|AW540746|E130209G04Rik|ENSMUSG00000043296|mKIAA0349	ubiquitin protein ligase E3 component n-recognin 2	protein-coding
mm_135807.1	chr16	57353133	57353163	-	1	NA	promoter-TSS (NM_001040397)	promoter-TSS (NM_001040397)	-129	NM_001040397	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding
mm_47903.1	chr5	134915513	134915542	-	1	NA	promoter-TSS (NM_020504)	promoter-TSS (NM_020504)	3	NM_020504	57255	Mm.86652	NM_020504	ENSMUSG00000008843	Cldn13	2500004B14Rik	claudin 13	protein-coding
mm_56303.1	chr6	91758817	91758841	-	1	NA	3' UTR (NM_009320, exon 15 of 15)	3' UTR (NM_009320, exon 15 of 15)	48564	NM_001159507	243547	Mm.333264	NM_001033353	ENSMUSG00000030098	Grip2	-	glutamate receptor interacting protein 2	protein-coding
mm_136866.1	chr17	12878666	12878668	+	1	NA	TTS (NM_030726)	TTS (NM_030726)	2633	NM_030726	80978	Mm.160368	NM_030726	ENSMUSG00000059408	Mrgprh	Gpr90|Mgrb|MrgH	MAS-related GPR, member H	protein-coding
mm_154997.1	chrX	38600859	38600888	+	1	NA	intron (NM_026902, intron 1 of 5)	intron (NM_026902, intron 1 of 5)	215	NM_026902	68995	Mm.262453	NM_026902	ENSMUSG00000000355	Mcts1	1500019M23Rik|MCT-1	malignant T cell amplified sequence 1	protein-coding
mm_156766.1	chrX	160530050	160530061	+	1	NA	intron (NM_172783, intron 5 of 32)	Lx9|LINE|L1	27621	NM_001177878	110094	Mm.350712	NM_172783	ENSMUSG00000031295	Phka2	6330505C01Rik|D330034O08|Phk	phosphorylase kinase alpha 2	protein-coding
mm_73447.1	chr8	106243301	106243311	+	1	NA	exon (NM_145404, exon 11 of 18)	exon (NM_145404, exon 11 of 18)	32252	NM_145404	214572	Mm.251804	NM_145404	ENSMUSG00000060098	Prmt7	4933402B05Rik|BC006705	protein arginine N-methyltransferase 7	protein-coding
mm_15129.1	chr2	153875066	153875077	+	1	NA	promoter-TSS (NM_025631)	promoter-TSS (NM_025631)	26	NM_025631	66557	Mm.46448	NM_025631	ENSMUSG00000027481	Bpifb2	2310034L21Rik|2310069A01Rik|AV089125|Bpil1|LPLUNC2|RYSR	BPI fold containing family B, member 2	protein-coding
mm_161658.1	chr17	7385418	7385418	-	1	NA	promoter-TSS (NM_001142539)	promoter-TSS (NM_001142539)	-113	NM_001142539	667055	Mm.327371	NM_001142539	ENSMUSG00000056133	Gm9992	ENSMUSG00000056133	predicted gene 9992	protein-coding
mm_66182.1	chr7	34168500	34168510	-	1	NA	promoter-TSS (NM_016682)	promoter-TSS (NM_016682)	24	NM_016682	50995	Mm.27560	NM_016682	ENSMUSG00000052997	Uba2	AA986091|Arx|Sae2|UBA1|Ubl1a2|Uble1b	ubiquitin-like modifier activating enzyme 2	protein-coding
mm_64916.1	chr7	16239885	16239925	-	1	NA	intron (NM_176912, intron 1 of 1)	intron (NM_176912, intron 1 of 1)	2426	NM_001146005	319430	Mm.239570	NM_176912	ENSMUSG00000074361	C5ar2	C5L2|E030029A11Rik|Gpr77	complement component 5a receptor 2	protein-coding
mm_23679.1	chr3	68584337	68584343	+	1	NA	intron (NM_013928, intron 1 of 6)	intron (NM_013928, intron 1 of 6)	11972	NM_013928	30953	Mm.331064	NM_013928	ENSMUSG00000027777	Schip1	Nf2ip|Schip-1	schwannomin interacting protein 1	protein-coding
mm_53872.1	chr6	149408880	149408890	+	1	NA	promoter-TSS (NM_001112796)	promoter-TSS (NM_001112796)	-99	NM_001112796	12121	Mm.177181	NM_009753	ENSMUSG00000003452	Bicd1	B830009D06Rik|bic-D 1	bicaudal D homolog 1 (Drosophila)	protein-coding
mm_64754.1	chr7	4812544	4812562	-	1	NA	promoter-TSS (NM_133777)	promoter-TSS (NM_133777)	-213	NM_133777	77891	Mm.389787	NM_133777	ENSMUSG00000060860	Ube2s	0910001J09Rik|6720465F12Rik|AA409170|E2-EPF	ubiquitin-conjugating enzyme E2S	protein-coding
mm_99207.1	chr11	101022980	101022986	+	1	NA	intron (NM_001243050, intron 5 of 20)	intron (NM_001243050, intron 5 of 20)	-7357	NR_105893	102466767		NR_105893	ENSMUSG00000098415	Mir6928	Gm27728|mmu-mir-6928	microRNA 6928	ncRNA
mm_135521.1	chr16	48872467	48872491	-	1	NA	promoter-TSS (NM_181596)	promoter-TSS (NM_181596)	-129	NM_181596	245195	Mm.231288	NM_181596	ENSMUSG00000022651	Retnlg	Fizz3|Relmg|Xcp1	resistin like gamma	protein-coding
mm_56810.1	chr6	116668368	116668391	-	1	NA	intron (NM_178045, intron 1 of 10)	intron (NM_178045, intron 1 of 10)	5457	NM_178045	213391	Mm.257931	NM_178045	ENSMUSG00000042129	Rassf4	3830411C14Rik|AD037|AI586137	Ras association (RalGDS/AF-6) domain family member 4	protein-coding
mm_162985.1	chr11	22859722	22859732	-	1	NA	promoter-TSS (NM_016888)	promoter-TSS (NM_016888)	8	NM_016888	53625	Mm.395495	NM_016888	ENSMUSG00000051650	B3gnt2	AA408337|AA409404|AW260308|B3Galt6|B3gnt1|BGnT-1|BGnT-2|BGnT1|BGnT2|Beta3gnt	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 2	protein-coding
mm_110042.1	chr12	17324723	17324736	-	1	NA	promoter-TSS (NM_133699)	promoter-TSS (NM_133699)	1	NM_133699	68775	Mm.178798	NM_133699	ENSMUSG00000020566	Atp6v1c2	1110038G14Rik	ATPase, H+ transporting, lysosomal V1 subunit C2	protein-coding
mm_60213.1	chr7	43463146	43463185	+	1	NA	promoter-TSS (NM_001290316)	promoter-TSS (NM_001290316)	-68	NM_001290316	75690	Mm.30200	NM_001290316	ENSMUSG00000070604	Vsig10l	-	V-set and immunoglobulin domain containing 10 like	protein-coding
mm_6934.1	chr1	85591660	85591686	-	1	NA	exon (NM_030194, exon 4 of 12)	exon (NM_030194, exon 4 of 12)	7137	NM_030194	109032	Mm.335802	NM_030194	ENSMUSG00000070034	Sp110	5031415C07Rik|52kDa|5830484A20Rik|ENSMUSG00000075603|Ifi75|Ipr1	Sp110 nuclear body protein	protein-coding
mm_100738.1	chr11	4095345	4095440	-	1	NA	promoter-TSS (NM_026443)	promoter-TSS (NM_026443)	39	NM_026443	67900	Mm.41719	NM_026443	ENSMUSG00000004748	Mtfp1	1700020C11Rik|2610507A21Rik|AV005788|Mtp18	mitochondrial fission process 1	protein-coding
mm_95680.1	chr11	54141798	54141804	+	1	NA	Intergenic	Intergenic	40877	NM_011031	18452	Mm.3705	NM_011031	ENSMUSG00000018906	P4ha2	AA407196|C76437|P4hl	procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha II polypeptide	protein-coding
mm_111915.1	chr12	108871611	108871617	-	1	NA	intron (NM_011710, intron 6 of 10)	intron (NM_011710, intron 6 of 10)	20485	NM_001012310	104910	Mm.202653	NM_001012310	ENSMUSG00000048856	Slc25a47	AI132487|AI876593|HDMCP	solute carrier family 25, member 47	protein-coding
mm_127598.1	chr15	102399836	102399852	+	1	NA	Intergenic	Intergenic	-6472	NM_013672	20683	Mm.4618	NM_013672	ENSMUSG00000001280	Sp1	1110003E12Rik|AA450830|AI845540|Sp1-1	trans-acting transcription factor 1	protein-coding
mm_38351.1	chr4	137770056	137770066	-	1	NA	intron (NM_007431, intron 1 of 11)	intron (NM_007431, intron 1 of 11)	-3586	NM_001287172	11647	Mm.288186	NM_007431	ENSMUSG00000028766	Alpl	ALP|APTNAP|Akp-2|Akp2|TNAP|TNSALP	alkaline phosphatase, liver/bone/kidney	protein-coding
mm_11399.1	chr2	31476861	31476868	+	1	NA	intron (NR_002687, intron 2 of 15)	intron (NR_002687, intron 2 of 15)	6556	NR_002687	432466	Mm.333323	NR_002687	ENSMUSG00000046687	Gm5424	EG432466	argininosuccinate synthase pseudogene	pseudo
mm_57269.1	chr6	123288880	123288898	-	1	NA	intron (NM_019948, intron 2 of 5)	intron (NM_019948, intron 2 of 5)	982	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_152801.1	chr19	21652780	21652819	-	1	NA	promoter-TSS (NM_025423)	promoter-TSS (NM_025423)	-8	NM_025423	66206	Mm.272430	NM_025423	ENSMUSG00000035171	1110059E24Rik	-	RIKEN cDNA 1110059E24 gene	protein-coding
mm_170194.1	chr17	66414001	66414012	-	1	NA	intron (NM_001114098, intron 3 of 14)	intron (NM_001114098, intron 3 of 14)	35744	NM_172963	68617	Mm.33421	NM_172963	ENSMUSG00000052105	Mtcl1	1110012J17Rik|Ccdc165|D130071O13|Kiaa0802|Soga2|mKIAA0802|t8219b25	microtubule crosslinking factor 1	protein-coding
mm_167507.1	chr9	13310877	13310889	+	1	NA	Intergenic	IMPB_01|Satellite|Satellite	63927	NM_025534	66396	Mm.290620	NM_025534	ENSMUSG00000079084	Ccdc82	2310043N13Rik	coiled-coil domain containing 82	protein-coding
mm_165917.1	chr4	58289130	58289138	+	1	NA	intron (NM_001037130, intron 1 of 12)	intron (NM_001037130, intron 1 of 12)	3172	NM_010944	18198	Mm.16148	NM_010944	ENSMUSG00000057280	Musk	Mdk4|Mlk|Nsk1|Nsk2|Nsk3	muscle, skeletal, receptor tyrosine kinase	protein-coding
mm_65942.1	chr7	30413420	30413451	-	1	NA	promoter-TSS (NM_011662)	promoter-TSS (NM_011662)	-353	NM_011662	22177	Mm.46301	NM_011662	ENSMUSG00000030579	Tyrobp	DAP12|KARAP|Ly83	TYRO protein tyrosine kinase binding protein	protein-coding
mm_124036.1	chr14	77033334	77033347	-	1	NA	exon (NM_172488, exon 5 of 8)	exon (NM_172488, exon 5 of 8)	3277	NM_172488	210808	Mm.89278	NM_172488	ENSMUSG00000044350	Lacc1	9030625A04Rik	laccase (multicopper oxidoreductase) domain containing 1	protein-coding
mm_54262.1	chr6	28398055	28398065	-	1	NA	Intergenic	Intergenic	23664	NM_028900	74375	Mm.332950	NM_028900	ENSMUSG00000029708	Gcc1	4932417P04Rik	golgi coiled coil 1	protein-coding
mm_123926.1	chr14	73365729	73365742	-	1	NA	intron (NM_008410, intron 4 of 5)	intron (NM_008410, intron 4 of 5)	19536	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_3907.1	chr1	161896347	161896358	+	1	NA	Intergenic	Intergenic	-19691	NM_172645	226551	Mm.170002	NM_172645	ENSMUSG00000040297	Suco	4732491B11|AI848100|AU016931|Opt	SUN domain containing ossification factor	protein-coding
mm_109499.1	chr12	111451856	111451877	+	1	NA	intron (NM_009396, intron 11 of 11)	intron (NM_009396, intron 11 of 11)	9205	NM_009396	21928	Mm.255332	NM_009396	ENSMUSG00000021281	Tnfaip2	B94|Exoc3l3|M-sec|Tnfip2|tnfb94	tumor necrosis factor, alpha-induced protein 2	protein-coding
mm_34327.1	chr4	142017980	142017990	+	1	NA	promoter-TSS (NR_131014)	promoter-TSS (NR_131014)	87	NR_131014	78917	Mm.139995	NR_131014	ENSMUSG00000085761	4930455G09Rik	-	RIKEN cDNA 4930455G09 gene	ncRNA
mm_44287.1	chr5	8368111	8368115	-	1	NA	promoter-TSS (NM_001007221)	promoter-TSS (NM_001007221)	47	NM_001007221	11496	Mm.275895	NM_001007220	ENSMUSG00000040537	Adam22	2900022I03Rik|AI854032|MDC2	a disintegrin and metallopeptidase domain 22	protein-coding
mm_155841.1	chrX	101242736	101242738	+	1	NA	Intergenic	Intergenic	-11791	NM_018789	54601	Mm.240299	NM_018789	ENSMUSG00000042903	Foxo4	Afxh|Mllt7|afx	forkhead box O4	protein-coding
mm_52857.1	chr6	122136629	122136638	+	1	NA	promoter-TSS (NR_003624)	promoter-TSS (NR_003624)	5	NR_003624	381806	Mm.482418	NM_001013775	ENSMUSG00000071204	Gm10319	EG381806|ENSMUSG00000071204	murinoglobulin pseudogene	pseudo
mm_12861.1	chr2	83771710	83771713	+	1	NA	intron (NM_008402, intron 12 of 29)	AT_rich|Low_complexity|Low_complexity	-41017	NM_175514	241520	Mm.330351	NM_175514	ENSMUSG00000048388	Fam171b	D430039N05Rik	family with sequence similarity 171, member B	protein-coding
mm_155856.1	chrX	101320042	101320060	+	1	NA	exon (NM_172932, exon 7 of 7)	exon (NM_172932, exon 7 of 7)	20872	NM_172932	245537	Mm.121508	NM_172932	ENSMUSG00000031302	Nlgn3	A230085M13Rik|HNL3|NL3	neuroligin 3	protein-coding
mm_24559.1	chr3	93443631	93443642	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	1306	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_81226.1	chr9	107652138	107652156	+	1	NA	exon (NM_001199218, exon 15 of 16)	exon (NM_001199218, exon 15 of 16)	15252	NM_023805	76257	Mm.296560	NM_023805	ENSMUSG00000010064	Slc38a3	0610012J02Rik|D9Ucla2|Nat1|Slc38-3|Sn1|Snat3|mNAT	solute carrier family 38, member 3	protein-coding
mm_3775.1	chr1	156524075	156524107	+	1	NA	Intergenic	Intergenic	-34696	NM_009595	11352	Mm.329515	NM_009595	ENSMUSG00000026596	Abl2	AA536808|Abll|Arg	v-abl Abelson murine leukemia viral oncogene 2 (arg, Abelson-related gene)	protein-coding
mm_118691.1	chr14	22123778	22123791	+	1	NA	intron (NM_028275, intron 2 of 6)	B4A|SINE|B4	104072	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_14573.1	chr2	135473794	135473802	+	1	NA	3' UTR (NM_001145830, exon 32 of 32)	3' UTR (NM_001145830, exon 32 of 32)	67968	NR_039540	100628568		NR_039540	ENSMUSG00000092830	Mir3963	mmu-mir-3963|mu-mir-3963	microRNA 3963	ncRNA
mm_135823.1	chr16	58499383	58499402	-	1	NA	intron (NM_018784, intron 2 of 10)	intron (NM_018784, intron 2 of 10)	23920	NM_018784	54613	Mm.212742	NM_018784	ENSMUSG00000022747	St3gal6	1700023B24Rik|AI930218|AW552396|Siat10|St3galVI	ST3 beta-galactoside alpha-2,3-sialyltransferase 6	protein-coding
mm_113646.1	chr13	42301510	42301518	+	1	NA	promoter-TSS (NM_010104)	promoter-TSS (NM_010104)	38	NM_010104	13614	Mm.14543	NM_010104	ENSMUSG00000021367	Edn1	ET-1|PPET1|preproET	endothelin 1	protein-coding
mm_133686.1	chr16	92498211	92498219	+	1	NA	promoter-TSS (NM_172469)	promoter-TSS (NM_172469)	68	NM_172469	209195	Mm.44747	NM_172469	ENSMUSG00000022949	Clic6	5730466J16Rik|AL022908|AW045520|CLIC1L	chloride intracellular channel 6	protein-coding
mm_149355.1	chr19	10937752	10937759	+	1	NA	intron (NM_009962, intron 1 of 2)	intron (NM_009962, intron 1 of 2)	595	NM_009962	14764	Mm.470721	NM_009962	ENSMUSG00000034117	Ptgdr2	Crth2|Gpr44|Grp45	prostaglandin D2 receptor 2	protein-coding
mm_78271.1	chr9	22003042	22003046	+	1	NA	promoter-TSS (NM_029939)	promoter-TSS (NM_029939)	56	NM_008925	19089	Mm.214593	NM_008925	ENSMUSG00000003402	Prkcsh	80K-H|PKCSH	protein kinase C substrate 80K-H	protein-coding
mm_95248.1	chr11	44618186	44618204	+	1	NA	promoter-TSS (NM_001290711)	promoter-TSS (NM_001290711)	95	NM_001290710	13591	Mm.439662	NM_007897	ENSMUSG00000057098	Ebf1	Ebf|O/E-1|OE-1|Olf-1|Olf1	early B cell factor 1	protein-coding
mm_111909.1	chr12	108792671	108792683	-	1	NA	promoter-TSS (NM_009537)	promoter-TSS (NM_009537)	-634	NM_009537	22632	Mm.3868	NM_009537	ENSMUSG00000021264	Yy1	AW488674|NF-E1	YY1 transcription factor	protein-coding
mm_64687.1	chr7	4514610	4514632	-	1	NA	intron (NM_011618, intron 1 of 13)	intron (NM_011618, intron 1 of 13)	1354	NM_001277903	21955	Mm.358643	NM_011618	ENSMUSG00000064179	Tnnt1	AW146156|Tnt|sTnT|ssTnT	troponin T1, skeletal, slow	protein-coding
mm_156320.1	chrX	137358695	137358705	+	1	NA	Intergenic	Intergenic	-212054	NM_030688	60367	Mm.328321	NM_030688	ENSMUSG00000059203	Il1rapl2	-	interleukin 1 receptor accessory protein-like 2	protein-coding
mm_149624.1	chr19	16956165	16956171	+	1	NA	promoter-TSS (NM_181348)	promoter-TSS (NM_181348)	50	NM_181348	353211	Mm.257354	NM_181348	ENSMUSG00000039126	Prune2	6330414G02Rik|A230083H22Rik|A330102H22Rik|Bmcc1|mKIAA0367	prune homolog 2	protein-coding
mm_131870.1	chr16	23175254	23175313	+	1	NA	Intergenic	Intergenic	28747	NM_009605	11450	Mm.3969	NM_009605	ENSMUSG00000022878	Adipoq	30kDa|APN|Acdc|Acrp30|Ad|GBP28|adipo|apM1	adiponectin, C1Q and collagen domain containing	protein-coding
mm_31297.1	chr4	45972767	45972787	+	1	NA	intron (NM_146142, intron 1 of 16)	CpG	480	NM_146142	100121	Mm.275413	NM_146142	ENSMUSG00000035517	Tdrd7	5730495N10Rik|AI447470|PCTAIRE2BP	tudor domain containing 7	protein-coding
mm_8836.1	chr1	162672150	162672152	-	1	NA	3' UTR (NM_001081290, exon 35 of 35)	3' UTR (NM_001081290, exon 35 of 35)	-13932	NM_001177581	100038657	Mm.416999	NM_001177581	ENSMUSG00000091060	7420461P10Rik	ENSMUSG00000073516	RIKEN cDNA 7420461P10 gene	protein-coding
mm_104089.1	chr11	86631063	86631064	-	1	NA	intron (NM_029478, intron 7 of 11)	intron (NM_029478, intron 7 of 11)	-25008	NR_106195	102465902		NR_106195	ENSMUSG00000099324	Mir8115	Gm28012|mmu-mir-8115	microRNA 8115	ncRNA
mm_87841.1	chr10	60399850	60399876	+	1	NA	5' UTR (NM_001164374, exon 1 of 2)	5' UTR (NM_001164374, exon 1 of 2)	137	NM_001164374	100302688	Mm.444135	NM_001164374	ENSMUSG00000090439	Gm17455	-	predicted gene, 17455	protein-coding
mm_164322.1	chr16	4964013	4964017	-	1	NA	promoter-TSS (NM_001271586)	promoter-TSS (NM_001271586)	222	NM_028301	72615	Mm.290628	NM_028301	ENSMUSG00000022515	Anks3	2700067D09Rik|C81345|mKIAA1977	ankyrin repeat and sterile alpha motif domain containing 3	protein-coding
mm_53381.1	chr6	129512734	129512745	+	1	NA	5' UTR (NM_001081186, exon 1 of 5)	5' UTR (NM_001081186, exon 1 of 5)	182	NM_001081186	330428	Mm.44237	NM_001081186	ENSMUSG00000030160	Tmem52b	D630042F21Rik	transmembrane protein 52B	protein-coding
mm_133353.1	chr16	84605557	84605574	+	1	NA	Intergenic	MT2B2|LTR|ERVL	-74224	NR_040537	78023	Mm.243853	NR_040537		4930529L06Rik	-	RIKEN cDNA 4930529L06 gene	ncRNA
mm_3883.1	chr1	161036054	161036066	+	1	NA	non-coding (NR_002840, exon 1 of 4)	non-coding (NR_002840, exon 1 of 4)	894	NR_002840	14455	Mm.270065	NR_002840	ENSMUSG00000053332	Gas5	Gas-5|Mir5117|Snhg2	growth arrest specific 5	ncRNA
mm_915.1	chr1	55034091	55034095	+	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-6615	NM_031179	81898	Mm.279736	NM_031179	ENSMUSG00000025982	Sf3b1	155kDa|2810001M05Rik|AA409119|Prp10|SAP155|SF3b155|TA-8|Targ4	splicing factor 3b, subunit 1	protein-coding
mm_43385.1	chr5	135730294	135730310	+	1	NA	exon (NM_008898, exon 5 of 16)	exon (NM_008898, exon 5 of 16)	5587	NR_106001	102466791		NR_106001	ENSMUSG00000099197	Mir7034	Gm27372|mmu-mir-7034	microRNA 7034	ncRNA
mm_45088.1	chr5	44099221	44099237	-	1	NA	intron (NM_001163577, intron 1 of 27)	intron (NM_001163577, intron 1 of 27)	2507	NM_008935	19126	Mm.6250	NM_008935	ENSMUSG00000029086	Prom1	4932416E19Rik|AC133|CD133|Prom|Prom-1|Proml1	prominin 1	protein-coding
mm_87397.1	chr10	45335906	45335927	+	1	NA	intron (NM_024285, intron 1 of 7)	CpG	154	NM_024285	23828	Mm.332793	NM_024285	ENSMUSG00000071317	Bves	Pop1|Popdc1|mBVES	blood vessel epicardial substance	protein-coding
mm_66395.1	chr7	44241272	44241281	-	1	NA	Intergenic	Intergenic	-5154	NR_029436	70004	Mm.158317	NR_029436	ENSMUSG00000038782	1700028J19Rik	-	RIKEN cDNA 1700028J19 gene	ncRNA
mm_137070.1	chr17	20945408	20945508	+	1	NA	promoter-TSS (NM_016891)	promoter-TSS (NM_016891)	4	NM_016891	51792	Mm.294138	NM_016891	ENSMUSG00000007564	Ppp2r1a	6330556D22Rik|PP2A|PR65	protein phosphatase 2, regulatory subunit A, alpha	protein-coding
mm_48154.1	chr5	137152131	137152147	-	1	NA	Intergenic	Intergenic	-35932	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_70610.1	chr8	13414267	13414279	+	1	NA	intron (NM_011881, intron 5 of 6)	intron (NM_011881, intron 5 of 6)	9192	NM_011881	24013	Mm.257501	NM_011881	ENSMUSG00000031450	Grk1	Gprk1|Rhok|Rk	G protein-coupled receptor kinase 1	protein-coding
mm_23352.1	chr3	55055238	55055269	+	1	NA	promoter-TSS (NM_007628)	promoter-TSS (NM_007628)	11	NR_040593	70970	Mm.251485	NR_040593	ENSMUSG00000106589	4931419H13Rik	-	RIKEN cDNA 4931419H13 gene	ncRNA
mm_51737.1	chr6	87104745	87104752	+	1	NA	promoter-TSS (NM_001167937)	promoter-TSS (NM_001167937)	2	NM_001167937	52372	Mm.282851	NM_001167937	ENSMUSG00000090891	D6Ertd527e	AU043841	DNA segment, Chr 6, ERATO Doi 527, expressed	protein-coding
mm_52322.1	chr6	108836612	108836633	+	1	NA	intron (NM_138677, intron 1 of 11)	intron (NM_138677, intron 1 of 11)	7981	NM_138677	192193	Mm.21596	NM_138677	ENSMUSG00000030104	Edem1	A130059K23Rik|EDEM|mKIAA0212	ER degradation enhancer, mannosidase alpha-like 1	protein-coding
mm_129076.1	chr15	75810517	75810527	-	1	NA	intron (NM_172121, intron 3 of 11)	intron (NM_172121, intron 3 of 11)	31386	NM_172121	223642	Mm.209800	NM_172121	ENSMUSG00000075600	Zc3h3	BC049953|Kiaa0150|Smicl|Zc3hdc3	zinc finger CCCH type containing 3	protein-coding
mm_82924.1	chr9	35116805	35116891	-	1	NA	promoter-TSS (NM_009178)	promoter-TSS (NM_009178)	-38	NM_009178	20443	Mm.275973	NM_009178	ENSMUSG00000032038	St3gal4	Siat4c	ST3 beta-galactoside alpha-2,3-sialyltransferase 4	protein-coding
mm_18003.1	chr2	38224489	38224507	-	1	NA	intron (NM_146122, intron 2 of 21)	intron (NM_146122, intron 2 of 21)	62886	NM_146122	227801	Mm.314245	NM_146122	ENSMUSG00000035392	Dennd1a	6030446I19Rik|connecdenn	DENN/MADD domain containing 1A	protein-coding
mm_167765.1	chr9	110532694	110532728	+	1	NA	exon (NM_001081340, exon 1 of 21)	exon (NM_001081340, exon 1 of 21)	114	NM_001081340	235626	Mm.288949	NM_001081340	ENSMUSG00000044791	Setd2	4921524K10Rik|BC031601|KMT3A	SET domain containing 2	protein-coding
mm_28675.1	chr3	95307187	95307202	-	1	NA	promoter-TSS (NM_023628)	promoter-TSS (NM_023628)	-18	NM_023628	71790	Mm.218844	NM_023628	ENSMUSG00000015702	Anxa9	1110003P15Rik|2310069F17Rik	annexin A9	protein-coding
mm_34207.1	chr4	140946275	140946283	+	1	NA	intron (NM_008812, intron 13 of 15)	intron (NM_008812, intron 13 of 15)	11623	NR_045911	100126227	Mm.404073	NR_045911	ENSMUSG00000087698	Gm13031	OTTMUSG00000010081	predicted gene 13031	ncRNA
mm_108588.1	chr12	85289633	85289660	+	1	NA	exon (NM_172414, exon 2 of 3)	exon (NM_172414, exon 2 of 3)	1055	NM_172414	72350	Mm.158810	NM_172414	ENSMUSG00000045064	Zc2hc1c	2810002I04Rik|AV046379|Fam164c	zinc finger, C2HC-type containing 1C	protein-coding
mm_30176.1	chr3	144204957	144204981	-	1	NA	5' UTR (NM_010723, exon 1 of 5)	5' UTR (NM_010723, exon 1 of 5)	286	NM_010723	16911	Mm.29187	NM_010723	ENSMUSG00000028266	Lmo4	A730077C12Rik|Crp3|Etohi4	LIM domain only 4	protein-coding
mm_153033.1	chr19	31765239	31765283	-	1	NA	promoter-TSS (NM_001013833)	promoter-TSS (NM_001013833)	-228	NM_001013833	19091	Mm.381170	NM_011160	ENSMUSG00000052920	Prkg1	AW125416|CGKI|Gm19690|Prkg1b|Prkgr1b	protein kinase, cGMP-dependent, type I	protein-coding
mm_32831.1	chr4	117609745	117609757	+	1	NA	intron (NM_001285901, intron 5 of 7)	intron (NM_001285901, intron 5 of 7)	59386	NM_080469	140546	Mm.235891	NM_080469	ENSMUSG00000033423	Eri3	PINT1|Prnpip1	exoribonuclease 3	protein-coding
mm_20245.1	chr2	126499682	126499712	-	1	NA	Intergenic	Intergenic	-8144	NM_001080944	241633	Mm.222235	NM_001080944	ENSMUSG00000060131	Atp8b4	A530043E15|Im	ATPase, class I, type 8B, member 4	protein-coding
mm_78598.1	chr9	37488771	37488782	+	1	NA	promoter-TSS (NM_146222)	promoter-TSS (NM_146222)	-545	NM_146222	235184	Mm.127892	NM_146222	ENSMUSG00000042138	Msantd2	2810450G17Rik|9530092B10Rik	Myb/SANT-like DNA-binding domain containing 2	protein-coding
mm_51391.1	chr6	78370653	78370670	+	1	NA	promoter-TSS (NM_011036)	promoter-TSS (NM_011036)	-224	NM_011036	18489	Mm.2553	NM_011036	ENSMUSG00000071356	Reg3b	HIP|PAP1|Pap|REG-III	regenerating islet-derived 3 beta	protein-coding
mm_166340.1	chr5	114884220	114884249	-	1	NA	TTS (NM_026263)	TTS (NM_026263)	-12700	NM_011854	23962	Mm.228363	NM_011854	ENSMUSG00000029561	Oasl2	M1204|Mmu-OASL|Oasl	2'-5' oligoadenylate synthetase-like 2	protein-coding
mm_24508.1	chr3	92584131	92584133	+	1	NA	exon (NM_008574, exon 2 of 2)	exon (NM_008574, exon 2 of 2)	4892	NM_008574	17235	Mm.331192	NM_008574		Smcp	Mcs|Mcsp	sperm mitochondria-associated cysteine-rich protein	protein-coding
mm_86155.1	chr9	118040376	118040391	-	1	NA	promoter-TSS (NM_013727)	promoter-TSS (NM_013727)	-139	NM_001286508	27215	Mm.92705	NM_013727	ENSMUSG00000039285	Azi2	AA410145|AZ2	5-azacytidine induced gene 2	protein-coding
mm_93131.1	chr10	92089187	92089231	-	1	NA	intron (NR_028262, intron 11 of 12)	PB1D10|SINE|Alu	-17024	NR_029812	723955		NR_029812	ENSMUSG00000065524	Mir135a-2	Mirn135a-2|mir-135a-2	microRNA 135a-2	ncRNA
mm_43515.1	chr5	137149779	137149801	+	1	NA	Intergenic	Intergenic	-33583	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_160820.1	chr11	29764192	29764192	-	1	NA	intron (NM_146016, intron 28 of 41)	intron (NM_146016, intron 28 of 41)	45629	NM_024226	68585	Mm.192580	NM_024226	ENSMUSG00000020458	Rtn4	1110020G17Rik|AA407876|AA409940|AA960376|ASY|C130026I10Rik|NOGO|NSP-CL|NgA|Nogo-A|Nogo-B|Nogo-C|mKIAA0886|mKIAA4153	reticulon 4	protein-coding
mm_21509.1	chr2	163624973	163625017	-	1	NA	3' UTR (NM_012032, exon 10 of 10)	3' UTR (NM_012032, exon 10 of 10)	17783	NM_001305803	76080	Mm.89828	NM_029512	ENSMUSG00000017679	Ttpal	3110080A02Rik|5830472M02Rik	tocopherol (alpha) transfer protein-like	protein-coding
mm_92704.1	chr10	80723387	80723391	-	1	NA	intron (NM_007460, intron 8 of 30)	PB1D10|SINE|Alu	18822	NM_007460	11776	Mm.27082	NM_007460	ENSMUSG00000020198	Ap3d1	AA407035|Ap3d|Bolvr|mBLVR1|mh|mocha	adaptor-related protein complex 3, delta 1 subunit	protein-coding
mm_113746.1	chr13	44730727	44730816	+	1	NA	promoter-TSS (NM_001205043)	promoter-TSS (NM_001205043)	-3	NM_021878	16468	Mm.25059	NM_021878	ENSMUSG00000038518	Jarid2	Jmj|jumonji	jumonji, AT rich interactive domain 2	protein-coding
mm_169755.1	chr15	90882511	90882523	+	1	NA	Intergenic	Intergenic	15959	NR_033583	20738	Mm.431547	NR_033583		Spn-ps	Cd43-ps	sialophorin, pseudogene	pseudo
mm_162001.1	chr19	40073827	40073827	-	1	NA	promoter-TSS (NM_206537)	promoter-TSS (NM_206537)	-14	NM_206537	404195	Mm.379575	NM_206537	ENSMUSG00000067225	Cyp2c54	EG404195	cytochrome P450, family 2, subfamily c, polypeptide 54	protein-coding
mm_18744.1	chr2	73214347	73214387	-	1	NA	promoter-TSS (NM_025942)	promoter-TSS (NM_025942)	80	NM_030091	67059	Mm.22661	NM_025942	ENSMUSG00000027108	Ola1	2510025G09Rik|2810405J23Rik|2810409H07Rik|Gtpbp9|PTD004	Obg-like ATPase 1	protein-coding
mm_76870.1	chr8	105525381	105525394	-	1	NA	exon (NM_013477, exon 6 of 8)	exon (NM_013477, exon 6 of 8)	6641	NM_008289	15484	Mm.5079	NM_008289	ENSMUSG00000031891	Hsd11b2	11HSD2	hydroxysteroid 11-beta dehydrogenase 2	protein-coding
mm_69375.1	chr7	131146292	131146299	-	1	NA	promoter-TSS (NM_173409)	promoter-TSS (NM_173409)	-12	NM_173409	233918	Mm.78341	NM_173409	ENSMUSG00000013668	4933402N03Rik	4930412O05	RIKEN cDNA 4933402N03 gene	protein-coding
mm_100942.1	chr11	6528442	6528462	-	1	NA	intron (NR_045893, intron 1 of 3)	intron (NR_045893, intron 1 of 3)	308	NR_045893	100041286	Mm.459507	NR_045893	ENSMUSG00000085156	Snhg15	Gm11974|OTTMUSG00000005115	small nucleolar RNA host gene 15	ncRNA
mm_157752.1	chrX	73492082	73492127	-	1	NA	exon (NM_007542, exon 4 of 8)	exon (NM_007542, exon 4 of 8)	8503	NM_007542	12111	Mm.2608	NM_007542	ENSMUSG00000031375	Bgn	BG|DSPG1|PG-S1|PGI|SLRR1A	biglycan	protein-coding
mm_14182.1	chr2	127070647	127070709	+	1	NA	promoter-TSS (NM_026678)	promoter-TSS (NM_026678)	21	NM_026678	109778	Mm.22028	NM_026678	ENSMUSG00000001999	Blvra	0610006A11Rik|2500001N03Rik|Blvr	biliverdin reductase A	protein-coding
mm_24554.1	chr3	93443491	93443493	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	1162	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_121213.1	chr14	103054570	103054582	+	1	NA	exon (NM_008392, exon 5 of 5)	exon (NM_008392, exon 5 of 5)	7564	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_117786.1	chr13	97034368	97034382	-	1	NA	promoter-TSS (NM_001284205)	promoter-TSS (NM_001284205)	-13	NM_001080777	66479	Mm.390629	NM_025585	ENSMUSG00000052075	1700029F12Rik	-	RIKEN cDNA 1700029F12 gene	protein-coding
mm_129843.1	chr15	83158859	83158894	-	1	NA	exon (NM_029787, exon 8 of 9)	exon (NM_029787, exon 8 of 9)	9231	NR_004432	104307	Mm.471434	NR_004432	ENSMUSG00000065176	Rnu12	-	RNA U12, small nuclear	snRNA
mm_64476.1	chr7	143053475	143053483	+	1	NA	non-coding (NR_015529, exon 1 of 4)	non-coding (NR_015529, exon 1 of 4)	207	NR_110355	97423	Mm.5250	NM_133790	ENSMUSG00000059277	R74862	-	expressed sequence R74862	ncRNA
mm_76048.1	chr8	77610743	77610757	-	1	NA	promoter-TSS (NM_145599)	promoter-TSS (NM_145599)	-97	NM_145599	234463	Mm.273578	NM_145599	ENSMUSG00000031617	Tmem184c	8430433H16Rik|AI645453|AL033298|BC004056|Tmem34	transmembrane protein 184C	protein-coding
mm_159945.1	chr6	84088031	84088031	+	1	NA	intron (NM_001077694, intron 17 of 54)	intron (NM_001077694, intron 17 of 54)	68645	NM_021469	26903	Mm.220982	NM_021469	ENSMUSG00000033788	Dysf	2310004N10Rik|AI604795|D6Pas3	dysferlin	protein-coding
mm_16143.1	chr2	171253273	171253295	+	1	NA	Intergenic	Intergenic	521477	NM_001163686	76829	Mm.41633	NM_029761	ENSMUSG00000027560	Dok5	2700055C10Rik	docking protein 5	protein-coding
mm_167118.1	chr7	119479367	119479402	-	1	NA	promoter-TSS (NM_001278605)	promoter-TSS (NM_001278605)	-122	NM_001278605	22242	Mm.10826	NM_009470	ENSMUSG00000030963	Umod	THP|Urehd1|urehr4	uromodulin	protein-coding
mm_112880.1	chr13	20855829	20855837	+	1	NA	intron (NM_012054, intron 4 of 20)	intron (NM_012054, intron 4 of 20)	61720	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_42393.1	chr5	114937305	114937315	+	1	NA	exon (NM_145209, exon 7 of 7)	exon (NM_145209, exon 7 of 7)	-4892	NM_028211	72357	Mm.292672	NM_028211	ENSMUSG00000029559	2210016L21Rik	-	RIKEN cDNA 2210016L21 gene	protein-coding
mm_117425.1	chr13	74363994	74364010	-	1	NA	promoter-TSS (NM_001033042)	promoter-TSS (NM_001033042)	-2	NM_001033042	432779	Mm.324679	NM_001033042	ENSMUSG00000021579	Lrrc14b	AI595366	leucine rich repeat containing 14B	protein-coding
mm_117943.1	chr13	99434893	99434902	-	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-22071	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_138690.1	chr17	35979555	35979563	+	1	NA	promoter-TSS (NM_001282024)	promoter-TSS (NM_001282024)	-92	NM_001165892	75210	Mm.40036	NM_145487	ENSMUSG00000038500	Prr3	4930540G07Rik|Cat56	proline-rich polypeptide 3	protein-coding
mm_7318.1	chr1	99791091	99791102	-	1	NA	intron (NM_172851, intron 1 of 23)	intron (NM_172851, intron 1 of 23)	18331	NM_172851	241175	Mm.251301	NM_172851	ENSMUSG00000067028	Cntnap5b	C230078M14Rik|Caspr5-2	contactin associated protein-like 5B	protein-coding
mm_154878.1	chrX	20694128	20694146	+	1	NA	exon (NM_011049, exon 3 of 16)	exon (NM_011049, exon 3 of 16)	5711	NM_011049	18555	Mm.102574	NM_011049	ENSMUSG00000031065	Cdk16	Crk5|Pctaire1|Pctk1	cyclin-dependent kinase 16	protein-coding
mm_81776.1	chr9	114688783	114688813	+	1	NA	promoter-TSS (NM_146229)	promoter-TSS (NM_146229)	-33	NM_146229	235661	Mm.128627	NM_146229	ENSMUSG00000032435	Dync1li1	1110053F02Rik|Dnclic1|LIC-1	dynein cytoplasmic 1 light intermediate chain 1	protein-coding
mm_42553.1	chr5	116802692	116802699	+	1	NA	Intergenic	Intergenic	-210878	NM_026886	68955	Mm.146779	NM_026886	ENSMUSG00000063919	Srrm4	1500001A10Rik|B230202K19Rik|bv|mKIAA1853|nSR100	serine/arginine repetitive matrix 4	protein-coding
mm_122865.1	chr14	54912444	54912458	-	1	NA	5' UTR (NM_021551, exon 2 of 9)	5' UTR (NM_021551, exon 2 of 9)	681	NM_021551	59049	Mm.27435	NM_021551	ENSMUSG00000022199	Slc22a17	1700094C23Rik|24p3R|AU041908|AW555662|BOIT|Boct	solute carrier family 22 (organic cation transporter), member 17	protein-coding
mm_60214.1	chr7	43463188	43463215	+	1	NA	promoter-TSS (NM_001290316)	promoter-TSS (NM_001290316)	-32	NM_001290316	75690	Mm.30200	NM_001290316	ENSMUSG00000070604	Vsig10l	-	V-set and immunoglobulin domain containing 10 like	protein-coding
mm_6011.1	chr1	59003536	59003540	-	1	NA	Intergenic	Intergenic	29967	NM_172656	227154	Mm.286006	NM_172656	ENSMUSG00000026027	Stradb	AA792893|Als2cr2|B830008M19|D1Ucla2|ILPIP|ILPIPA|PRO1038|Papk|Syradb	STE20-related kinase adaptor beta	protein-coding
mm_111829.1	chr12	107131919	107131926	-	1	NA	Intergenic	Intergenic	-415598	NR_015512	71033	Mm.159404	NR_015512	ENSMUSG00000085820	4933406K04Rik	4930426M03Rik|4930485I22Rik|4933427G14Rik	RIKEN cDNA 4933406K04 gene	ncRNA
mm_169809.1	chr16	18533315	18533330	-	1	NA	intron (NR_104347, intron 2 of 8)	SSU-rRNA_Hsa|rRNA|rRNA	34451	NR_104347	13972	Mm.236139	NM_023120	ENSMUSG00000000884	Gnb1l	ESTM55|Gm16314|Me49f07|OTTMUSG00000033458|Wdr14|Wdvcf	guanine nucleotide binding protein (G protein), beta polypeptide 1-like	protein-coding
mm_172258.1	chr6	72375780	72375780	-	1	NA	intron (NM_016872, intron 1 of 2)	B1_Mus1|SINE|Alu	4688	NM_016872	53620	Mm.440321	NM_016872	ENSMUSG00000073002	Vamp5	AF119384|Camp	vesicle-associated membrane protein 5	protein-coding
mm_55827.1	chr6	83121386	83121470	-	1	NA	promoter-TSS (NM_001083922)	promoter-TSS (NM_001083922)	33	NM_001083923	22377	Mm.1109	NM_016757	ENSMUSG00000030035	Wbp1	AI255152	WW domain binding protein 1	protein-coding
mm_111527.1	chr12	100206487	100206501	-	1	NA	3' UTR (NM_009790, exon 6 of 6)	3' UTR (NM_009790, exon 6 of 6)	6350	NM_001313934	12313	Mm.285993	NM_009790	ENSMUSG00000001175	Calm1	AI256814|AI327027|AI461935|AL024000|CaM|Calm	calmodulin 1	protein-coding
mm_118206.1	chr13	109837655	109837665	-	1	NA	intron (NM_011056, intron 7 of 16)	intron (NM_011056, intron 7 of 16)	-66149	NR_035442	100316683		NR_035442	ENSMUSG00000084651	Mir1904	Mirn1904|mmu-mir-1904	microRNA 1904	ncRNA
mm_49634.1	chr6	30804971	30804980	+	1	NA	intron (NM_017478, intron 20 of 23)	intron (NM_017478, intron 20 of 23)	63676	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_167550.1	chr9	32620947	32620949	+	1	NA	Intergenic	BC1_Mm|scRNA|scRNA	-75094	NM_011808	23871	Mm.292415	NM_011808	ENSMUSG00000032035	Ets1	AI196000|AI448617|D230050P06|Ets-1|Tpl1|vs	E26 avian leukemia oncogene 1, 5' domain	protein-coding
mm_70780.1	chr8	22405245	22405245	+	1	NA	Intergenic	B3|SINE|B2	-6095	NM_020560	57312	Mm.289402	NM_020560	ENSMUSG00000031533	Mrps31	1500002D03Rik|AA960481|Imogen38|Imogen44	mitochondrial ribosomal protein S31	protein-coding
mm_128942.1	chr15	74734315	74734335	-	1	NA	promoter-TSS (NM_026671)	promoter-TSS (NM_026671)	-12	NM_026671	68311	Mm.306880	NM_026671	ENSMUSG00000022595	Lypd2	0610005K03Rik|Lypdc2|VLL	Ly6/Plaur domain containing 2	protein-coding
mm_25841.1	chr3	129215516	129215530	+	1	NA	intron (NM_001042502, intron 1 of 2)	intron (NM_001042502, intron 1 of 2)	1591	NM_001287048	18741	Mm.246804	NM_011098	ENSMUSG00000028023	Pitx2	9430085M16Rik|Brx1|Brx1b|Munc30|Otlx2|Ptx2|Rieg	paired-like homeodomain transcription factor 2	protein-coding
mm_59437.1	chr7	27131269	27131314	+	1	NA	exon (NM_007817, exon 8 of 10)	exon (NM_007817, exon 8 of 10)	11336	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_62188.1	chr7	97536215	97536227	+	1	NA	intron (NM_027256, intron 21 of 22)	RMER6A|LTR|ERVK	43276	NM_001177945	66273	Mm.41583	NM_183251	ENSMUSG00000035642	Aamdc	1810020D17Rik|1810037D19Rik|LI2	adipogenesis associated Mth938 domain containing	protein-coding
mm_31942.1	chr4	86657259	86657317	+	1	NA	exon (NM_007408, exon 8 of 8)	exon (NM_007408, exon 8 of 8)	12771	NM_007408	11520	Mm.381	NM_007408	ENSMUSG00000028494	Plin2	AA407157|ADPH|Adfp|Adrp	perilipin 2	protein-coding
mm_135870.1	chr16	61389934	61389936	-	1	NA	Intergenic	Lx3C|LINE|L1	-784404	NM_007938	13840	Mm.455790	NM_007938	ENSMUSG00000055540	Epha6	Ehk2|Hek12|m-ehk2	Eph receptor A6	protein-coding
mm_10136.1	chr2	4058105	4058134	+	1	NA	intron (NM_001347086, intron 2 of 24)	B4|SINE|B4	40436	NM_001347086	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding
mm_30962.1	chr4	33924992	33925012	+	1	NA	5' UTR (NM_007726, exon 1 of 2)	5' UTR (NM_007726, exon 1 of 2)	370	NM_007726	12801	Mm.7992	NM_007726	ENSMUSG00000044288	Cnr1	CB-R|CB1|CB1R	cannabinoid receptor 1 (brain)	protein-coding
mm_49772.1	chr6	34873355	34873365	+	1	NA	3' UTR (NM_197986, exon 2 of 2)	3' UTR (NM_197986, exon 2 of 2)	4705	NM_199145	78412	Mm.248440	NM_199145	ENSMUSG00000046806	3110062M04Rik	AL023049|Mri	RIKEN cDNA 3110062M04 gene	protein-coding
mm_147811.1	chr18	61719348	61719360	-	1	NA	intron (NM_021296, intron 2 of 3)	L3|LINE|CR1	6977	NM_021296	17714	Mm.269657	NM_021296	ENSMUSG00000024580	Grpel2	mt-GrpE#2|mt-Grpel2	GrpE-like 2, mitochondrial	protein-coding
mm_139541.1	chr17	56710943	56710954	+	1	NA	non-coding (NR_045519, exon 17 of 17)	non-coding (NR_045519, exon 17 of 17)	5973	NM_178926	106639	Mm.37290	NM_178926	ENSMUSG00000054723	Vmac	AI662250	vimentin-type intermediate filament associated coiled-coil protein	protein-coding
mm_106979.1	chr12	9574479	9574497	+	1	NA	promoter-TSS (NM_011859)	promoter-TSS (NM_011859)	46	NM_011859	23967	Mm.45055	NM_011859	ENSMUSG00000048387	Osr1	Odd1|Osr	odd-skipped related 1 (Drosophila)	protein-coding
mm_6175.1	chr1	65100454	65100470	-	1	NA	TTS (NM_007774)	TTS (NM_007774)	2901	NM_007774	12964	Mm.26904	NM_007774	ENSMUSG00000044429	Cryga	Cryg-4|DGcry-4	crystallin, gamma A	protein-coding
mm_100092.1	chr11	115603921	115603969	+	1	NA	promoter-TSS (NM_173048)	promoter-TSS (NM_173048)	-29	NM_173048	260302	Mm.119479	NM_173048	ENSMUSG00000020740	Gga3	C230037M19Rik|mKIAA0154	golgi associated, gamma adaptin ear containing, ARF binding protein 3	protein-coding
mm_7442.1	chr1	120116419	120116445	-	1	NA	exon (NM_007830, exon 3 of 4)	exon (NM_007830, exon 3 of 4)	4487	NM_001037999	13167	Mm.2785	NM_007830	ENSMUSG00000026385	Dbi	ACBD1|Acbp|EP|endozepine	diazepam binding inhibitor	protein-coding
mm_28227.1	chr3	88453474	88453479	-	1	NA	intron (NM_001163491, intron 2 of 14)	intron (NM_001163491, intron 2 of 14)	2285	NM_013658	20351	Mm.439752	NM_013658	ENSMUSG00000028064	Sema4a	AI132332|SemB|Semab	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A	protein-coding
mm_34244.1	chr4	141239570	141239633	+	1	NA	Intergenic	Intergenic	-3283	NM_172520	213649	Mm.134460	NM_172520	ENSMUSG00000028919	Arhgef19	6030432F23|6430573B13Rik|WGEF	Rho guanine nucleotide exchange factor (GEF) 19	protein-coding
mm_5417.1	chr1	33907700	33907710	-	1	NA	promoter-TSS (NM_001310484)	promoter-TSS (NM_001310484)	62	NM_001310484	320705	Mm.336619	NM_177235	ENSMUSG00000042182	Bend6	B230209C24Rik	BEN domain containing 6	protein-coding
mm_35221.1	chr4	19659610	19659635	-	1	NA	exon (NM_177327, exon 8 of 25)	exon (NM_177327, exon 8 of 25)	49382	NM_177327	107568	Mm.78312	NM_177327	ENSMUSG00000041058	Wwp1	8030445B08Rik|AIP5|SDRP1|Tiul1	WW domain containing E3 ubiquitin protein ligase 1	protein-coding
mm_951.1	chr1	57576697	57576697	+	1	NA	Intergenic	ORR1A3|LTR|ERVL-MaLR	-170023	NM_001302963	68736	Mm.288490	NM_001037742	ENSMUSG00000048495	Tyw5	1110034B05Rik	tRNA-yW synthesizing protein 5	protein-coding
mm_124571.1	chr14	124309784	124309785	-	1	NA	intron (NM_207667, intron 1 of 4)	intron (NM_207667, intron 1 of 4)	-117238	NM_010201	14169	Mm.206362	NM_010201	ENSMUSG00000025551	Fgf14	FHF-4|Fhf4|mFHF-4(1B)	fibroblast growth factor 14	protein-coding
mm_138167.1	chr17	34264398	34264410	+	1	NA	intron (NM_207105, intron 1 of 5)	Lx8b|LINE|L1	1177	NM_207105	14961	Mm.254067	NM_207105	ENSMUSG00000073421	H2-Ab1	AI845868|Abeta|H-2Ab|H2-Ab|I-Abeta|IAb|Ia-2|Ia2|Rmcs1	histocompatibility 2, class II antigen A, beta 1	protein-coding
mm_43347.1	chr5	135149658	135149739	+	1	NA	promoter-TSS (NM_013763)	promoter-TSS (NM_013763)	-13	NM_013763	27368	Mm.36746	NM_013763	ENSMUSG00000005374	Tbl2	C76179|WS-bTRP	transducin (beta)-like 2	protein-coding
mm_32555.1	chr4	109415658	109415668	+	1	NA	promoter-TSS (NM_001145948)	promoter-TSS (NM_001145948)	16	NM_001145948	230603	Mm.33091	NM_153392	ENSMUSG00000028555	Ttc39a	4922503N01Rik	tetratricopeptide repeat domain 39A	protein-coding
mm_99855.1	chr11	109363783	109363786	+	1	NA	promoter-TSS (NR_038097)	promoter-TSS (NR_038097)	-130	NR_038097	100036768	Mm.467767	NR_038097	ENSMUSG00000056687	Gm11696	OTTMUSG00000003456	predicted gene 11696	ncRNA
mm_1855.1	chr1	84710355	84710383	+	1	NA	Intergenic	Intergenic	-14148	NM_152915	227325	Mm.292560	NM_152915	ENSMUSG00000036766	Dner	A930026D19Rik|BET|Bret	delta/notch-like EGF repeat containing	protein-coding
mm_105135.1	chr11	101459247	101459277	-	1	NA	TTS (NM_027320)	TTS (NM_027320)	6937	NM_012037	26949	Mm.29210	NM_012037	ENSMUSG00000034993	Vat1	VAT-1	vesicle amine transport 1	protein-coding
mm_47474.1	chr5	123720963	123720973	-	1	NA	promoter-TSS (NM_027494)	promoter-TSS (NM_027494)	76	NM_027494	70650	Mm.279427	NM_027494	ENSMUSG00000029427	Zcchc8	5730565F05Rik	zinc finger, CCHC domain containing 8	protein-coding
mm_105661.1	chr11	107348153	107348179	-	1	NA	intron (NM_145823, intron 1 of 9)	intron (NM_145823, intron 1 of 9)	122554	NM_145823	71795	Mm.397413	NM_145823	ENSMUSG00000040430	Pitpnc1	1110020B03Rik|5830436L09Rik|AI662802|AI851387|C330017I21Rik|Dnr411|RDGBB|RDGBB1|rdgB-beta	phosphatidylinositol transfer protein, cytoplasmic 1	protein-coding
mm_165301.1	chr2	92568025	92568030	+	1	NA	Intergenic	(TGAA)n|Simple_repeat|Simple_repeat	-24179	NR_106080	102466819		NR_106080	ENSMUSG00000099223	Mir7221	Gm27378|mmu-mir-7221	microRNA 7221	ncRNA
mm_93753.1	chr10	120171351	120171357	-	1	NA	intron (NM_028679, intron 5 of 11)	intron (NM_028679, intron 5 of 11)	30183	NM_028679	73914	Mm.146194	NM_028679	ENSMUSG00000020227	Irak3	4833428C18Rik|AI563835|IRAK-M	interleukin-1 receptor-associated kinase 3	protein-coding
mm_3641.1	chr1	152817442	152817445	+	1	NA	intron (NM_010877, intron 4 of 15)	intron (NM_010877, intron 4 of 15)	17290	NM_010877	17970	Mm.270307	NM_010877	ENSMUSG00000026480	Ncf2	NOXA2|Ncf-2|p67phox	neutrophil cytosolic factor 2	protein-coding
mm_99938.1	chr11	111027021	111027031	+	1	NA	3' UTR (NM_001252208, exon 2 of 2)	3' UTR (NM_001252208, exon 2 of 2)	3166	NM_001252208	16517	Mm.30176	NM_010604	ENSMUSG00000051497	Kcnj16	6430410F18Rik|AI132396|Kir5.1	potassium inwardly-rectifying channel, subfamily J, member 16	protein-coding
mm_110204.1	chr12	27341605	27341615	-	1	NA	exon (NM_009234, exon 1 of 1)	exon (NM_009234, exon 1 of 1)	1108	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding
mm_83890.1	chr9	55938094	55938143	-	1	NA	promoter-TSS (NM_001081341)	promoter-TSS (NM_001081341)	-3	NM_001081341	244891	Mm.86588	NM_175536	ENSMUSG00000034007	Scaper	C430017I08|D530014O03Rik|Zfp291	S phase cyclin A-associated protein in the ER	protein-coding
mm_142323.1	chr17	43477744	43477754	-	1	NA	intron (NM_008585, intron 12 of 13)	L1MA6|LINE|L1	25024	NM_008585	17287	Mm.5346	NM_008585	ENSMUSG00000023914	Mep1a	AI098089|AW107200|Mep-1|Mep-1a|Mep1	meprin 1 alpha	protein-coding
mm_129803.1	chr15	82963749	82963765	-	1	NA	Intergenic	Intergenic	-4461	NR_037241	100526477		NR_037241	ENSMUSG00000092751	Mir3080	mmu-mir-3080	microRNA 3080	ncRNA
mm_23829.1	chr3	81037380	81037391	+	1	NA	5' UTR (NM_019971, exon 1 of 6)	5' UTR (NM_019971, exon 1 of 6)	969	NM_019971	54635	Mm.331089	NM_019971	ENSMUSG00000028019	Pdgfc	1110064L01Rik|AI647969|PDGF-C	platelet-derived growth factor, C polypeptide	protein-coding
mm_162138.1	chrX	73892233	73892233	+	1	NA	5' UTR (NM_001276299, exon 1 of 3)	5' UTR (NM_001276299, exon 1 of 3)	131	NM_019404	12000	Mm.383171	NM_019404	ENSMUSG00000031390	Avpr2	ADHR|DI1|DIR|ND1|V2R|VPV2R	arginine vasopressin receptor 2	protein-coding
mm_97906.1	chr11	83437710	83437718	+	1	NA	promoter-TSS (NM_025492)	promoter-TSS (NM_025492)	20	NM_025492	66330	Mm.44800	NM_025492	ENSMUSG00000035085	1700020L24Rik	-	RIKEN cDNA 1700020L24 gene	protein-coding
mm_115494.1	chr13	3803286	3803291	-	1	NA	3' UTR (NM_027416, exon 1 of 1)	3' UTR (NM_027416, exon 1 of 1)	1030	NM_027416	70405	Mm.20079	NM_027416	ENSMUSG00000063130	Calml3	2310068O22Rik|AI326174	calmodulin-like 3	protein-coding
mm_14300.1	chr2	129065935	129065994	+	1	NA	promoter-TSS (NM_027192)	promoter-TSS (NM_027192)	17	NM_027192	69737	Mm.33909	NM_027192	ENSMUSG00000027394	Ttl	2410003M22Rik|2700049H19Rik|AI848570	tubulin tyrosine ligase	protein-coding
mm_3451.1	chr1	150103070	150103101	+	1	NA	intron (NM_011198, intron 5 of 9)	intron (NM_011198, intron 5 of 9)	3054	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_130846.1	chr15	101924726	101924742	-	1	NA	promoter-TSS (NM_008475)	promoter-TSS (NM_008475)	1	NM_008475	16682	Mm.46425	NM_008475	ENSMUSG00000059668	Krt4	AW108092|K4|Krt-2.4|Krt2-4	keratin 4	protein-coding
mm_148396.1	chr19	3767954	3767970	+	1	NA	intron (NM_144871, intron 1 of 11)	CpG	541	NM_001167885	225888	Mm.278578	NM_144871	ENSMUSG00000045098	Kmt5b	AA117471|C630029K18Rik|Suv4-20h1|Suv420h1	lysine methyltransferase 5B	protein-coding
mm_41146.1	chr5	87927032	87927049	+	1	NA	intron (NM_007786, intron 1 of 4)	intron (NM_007786, intron 1 of 4)	1407	NM_007786	12994	Mm.296303	NM_007786	ENSMUSG00000001622	Csn3	AW208918|CSN10|Csnk	casein kappa	protein-coding
mm_3960.1	chr1	164115351	164115369	+	1	NA	promoter-TSS (NM_011347)	promoter-TSS (NM_011347)	96	NM_011347	20344	Mm.3337	NM_011347	ENSMUSG00000026580	Selp	CD62P|GMP-140|Grmp|LECAM3|PADGEM	selectin, platelet	protein-coding
mm_8908.1	chr1	163312708	163312732	-	1	NA	5' UTR (NM_175686, exon 1 of 5)	5' UTR (NM_175686, exon 1 of 5)	930	NM_011127	18933	Mm.288642	NM_011127	ENSMUSG00000026586	Prrx1	A230024N07Rik|AA755424|AI385634|AI843499|K-2|Pmx|Pmx1|Prx1|mHox	paired related homeobox 1	protein-coding
mm_135960.1	chr16	74754646	74754649	-	1	NA	Intergenic	AT_rich|Low_complexity|Low_complexity	-343735	NM_175549	268902	Mm.171736	NM_175549	ENSMUSG00000052516	Robo2	2600013A04Rik|9430089E08Rik|BB097918|D230004I22Rik|mKIAA1568	roundabout guidance receptor 2	protein-coding
mm_146059.1	chr18	69683074	69683090	+	1	NA	3' UTR (NM_001083967, exon 20 of 20)	3' UTR (NM_001083967, exon 20 of 20)	-242477	NM_201362	381175	Mm.266831	NM_201362	ENSMUSG00000038903	Ccdc68	BC046343	coiled-coil domain containing 68	protein-coding
mm_82817.1	chr9	31018736	31018736	-	1	NA	Intergenic	B1_Mus1|SINE|Alu	-11908	NM_001115130	235132	Mm.239355	NM_172765	ENSMUSG00000047412	Zbtb44	6030404E16Rik|Btbd15|E230011F09	zinc finger and BTB domain containing 44	protein-coding
mm_60972.1	chr7	48877956	48877974	+	1	NA	exon (NM_001013368, exon 4 of 13)	exon (NM_001013368, exon 4 of 13)	3076	NM_001013368	108961	Mm.240566	NM_001013368	ENSMUSG00000046179	E2f8	4432406C08Rik|AA410048	E2F transcription factor 8	protein-coding
mm_50331.1	chr6	48412157	48412170	+	1	NA	intron (NM_001347153, intron 12 of 17)	intron (NM_001347153, intron 12 of 17)	16577	NM_001347153	77827	Mm.107646	NM_133922	ENSMUSG00000042810	Krba1	A930040G15Rik|AI448780	KRAB-A domain containing 1	protein-coding
mm_79512.1	chr9	57520530	57520560	+	1	NA	promoter-TSS (NM_007747)	promoter-TSS (NM_007747)	-687	NM_007747	12858	Mm.273403	NM_007747	ENSMUSG00000000088	Cox5a	AA959768|CcOX	cytochrome c oxidase subunit Va	protein-coding
mm_108819.1	chr12	95695427	95695446	+	1	NA	intron (NM_201518, intron 1 of 1)	CpG	3210	NM_201518	399558	Mm.341948	NM_201518	ENSMUSG00000047414	Flrt2	-	fibronectin leucine rich transmembrane protein 2	protein-coding
mm_45782.1	chr5	87336553	87336563	-	1	NA	exon (NM_028094, exon 1 of 6)	exon (NM_028094, exon 1 of 6)	637	NM_028094	72094	Mm.482739	NM_028094	ENSMUSG00000035780	Ugt2a3	2010321J07Rik	UDP glucuronosyltransferase 2 family, polypeptide A3	protein-coding
mm_65053.1	chr7	18656721	18656728	-	1	NA	promoter-TSS (NM_027403)	promoter-TSS (NM_027403)	1	NM_027403	72242	Mm.326858	NM_027403	ENSMUSG00000070796	Psg21	1600019C01Rik|1600025N01Rik|1600026N13Rik|cea8	pregnancy-specific glycoprotein 21	protein-coding
mm_82236.1	chr9	3038184	3038194	-	1	NA	TTS (NR_039546)	TTS (NR_039546)	554	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_158589.1	chrX	150954765	150954801	-	1	NA	Intergenic	MLT1M|LTR|ERVL-MaLR	62510	NM_001168600	237107	Mm.45987	NM_198110	ENSMUSG00000025266	Gnl3l	BC020354	guanine nucleotide binding protein-like 3 (nucleolar)-like	protein-coding
mm_3288.1	chr1	136676414	136676443	+	1	NA	Intergenic	Intergenic	-6968	NR_045324	100503460	Mm.30630	NR_045324	ENSMUSG00000097113	Gm19705	-	predicted gene, 19705	ncRNA
mm_52678.1	chr6	117917282	117917349	+	1	NA	promoter-TSS (NM_001166427)	promoter-TSS (NM_001166427)	21	NM_001166427	98758	Mm.422979	NM_133834	ENSMUSG00000042079	Hnrnpf	4833420I20Rik|AA407306|Hnrpf	heterogeneous nuclear ribonucleoprotein F	protein-coding
mm_121291.1	chr14	105258822	105258834	+	1	NA	exon (NM_029561, exon 1 of 8)	exon (NM_029561, exon 1 of 8)	155	NM_001190989	76273	Mm.290669	NM_029561	ENSMUSG00000053253	Ndfip2	0710001O20Rik|2810436B12Rik|9130207N19Rik|N4wbp5a|mKIAA1165	Nedd4 family interacting protein 2	protein-coding
mm_135357.1	chr16	43889643	43889668	-	1	NA	promoter-TSS (NM_029128)	promoter-TSS (NM_029128)	21	NM_029128	106248	Mm.275354	NM_029128	ENSMUSG00000022704	Qtrtd1	3110012M05Rik|4930470H18Rik|AI648807|Qtrt2	queuine tRNA-ribosyltransferase domain containing 1	protein-coding
mm_63901.1	chr7	139096324	139096327	+	1	NA	intron (NM_011993, intron 9 of 13)	intron (NM_011993, intron 9 of 13)	10324	NM_011993	26757	Mm.250414	NM_011993	ENSMUSG00000025478	Dpysl4	AI173505|CRMP-3|Crmp3|DPY4|Drp-4|Ulip4	dihydropyrimidinase-like 4	protein-coding
mm_110627.1	chr12	57197292	57197305	-	1	NA	5' UTR (NM_172577, exon 1 of 10)	5' UTR (NM_172577, exon 1 of 10)	174	NM_172577	217593	Mm.32835	NM_172577	ENSMUSG00000035472	Slc25a21	9930033G19Rik|A630030I10|BB158148	solute carrier family 25 (mitochondrial oxodicarboxylate carrier), member 21	protein-coding
mm_25127.1	chr3	102086472	102086524	+	1	NA	promoter-TSS (NM_009814)	promoter-TSS (NM_009814)	43	NM_009814	12373	Mm.15343	NM_009814	ENSMUSG00000027861	Casq2	AA033488|AW146219|Csq2|ESTM52|cCSQ	calsequestrin 2	protein-coding
mm_121374.1	chr14	118212340	118212350	+	1	NA	Intergenic	Intergenic	-23887	NR_131969	105245869	Mm.460408	NR_131969	ENSMUSG00000090534	LOC105245869	-	uncharacterized LOC105245869	ncRNA
mm_48374.1	chr5	139484421	139484473	-	1	NA	promoter-TSS (NM_001159908)	promoter-TSS (NM_001159908)	44	NM_133349	100494	Mm.24521	NM_133349	ENSMUSG00000053581	Zfand2a	AA407930|AU016206|Airap	zinc finger, AN1-type domain 2A	protein-coding
mm_99277.1	chr11	101268780	101268785	+	1	NA	exon (NM_175638, exon 8 of 19)	exon (NM_175638, exon 8 of 19)	8215	NM_175638	69847	Mm.23656	NM_175638	ENSMUSG00000035112	Wnk4	2010002J11Rik|Pha2b|Prkwnk4	WNK lysine deficient protein kinase 4	protein-coding
mm_85439.1	chr9	104102429	104102447	-	1	NA	5' UTR (NM_145700, exon 2 of 3)	5' UTR (NM_145700, exon 2 of 3)	24205	NM_145700	252837	Mm.269254	NM_145700	ENSMUSG00000079355	Ackr4	A630091E18Rik|CCBP2|CCR11|CCX-CKR|CCX-CKR1|Ccrl1|Cmkbrl1|PPR1|VSHK1	atypical chemokine receptor 4	protein-coding
mm_128478.1	chr15	50889694	50889714	-	1	NA	promoter-TSS (NR_035444)	promoter-TSS (NR_035444)	337	NM_032000	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_37035.1	chr4	115487068	115487117	-	1	NA	3' UTR (NM_007822, exon 12 of 12)	3' UTR (NM_007822, exon 12 of 12)	9049	NM_007822	13119	Mm.250901	NM_007822	ENSMUSG00000028715	Cyp4a14	AI314743	cytochrome P450, family 4, subfamily a, polypeptide 14	protein-coding
mm_32254.1	chr4	102570556	102570568	+	1	NA	5' UTR (NM_001177980, exon 1 of 10)	5' UTR (NM_001177980, exon 1 of 10)	502	NM_001177980	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_10105.1	chr2	3513093	3513127	+	1	NA	promoter-TSS (NR_103465)	promoter-TSS (NR_103465)	45	NM_177647	227526	Mm.211455	NM_177647	ENSMUSG00000039496	Cdnf	9330140G23|Armetl1	cerebral dopamine neurotrophic factor	protein-coding
mm_145053.1	chr18	40265808	40265814	+	1	NA	intron (NM_026135, intron 1 of 1)	intron (NM_026135, intron 1 of 1)	7450	NM_026135	383348	Mm.76366	NM_026135	ENSMUSG00000051401	Kctd16	4930434H12Rik|Gm1267	potassium channel tetramerisation domain containing 16	protein-coding
mm_147892.1	chr18	65152927	65152928	-	1	NA	intron (NM_001114386, intron 6 of 30)	intron (NM_001114386, intron 6 of 30)	-95934	NR_029600	387231		NR_029600	ENSMUSG00000065402	Mir122	Mir122a|Mirn122a|mir-122|mmu-mir-122	microRNA 122	ncRNA
mm_107280.1	chr12	29566750	29566760	+	1	NA	5' UTR (NM_001093776, exon 2 of 25)	5' UTR (NM_001093776, exon 2 of 25)	31850	NM_001093776	17933	Mm.253067	NM_008666	ENSMUSG00000061911	Myt1l	2900046C06Rik|2900093J19Rik|C630034G21Rik|Nztf1|Pmng1|Png-1|mKIAA1106	myelin transcription factor 1-like	protein-coding
mm_121055.1	chr14	87416008	87416022	+	1	NA	promoter-TSS (NM_001253755)	promoter-TSS (NM_001253755)	-568	NM_172605	219249	Mm.35168	NM_172605	ENSMUSG00000022019	Tdrd3	4732418C03Rik|6720468N18	tudor domain containing 3	protein-coding
mm_111098.1	chr12	80760533	80760546	-	1	NA	5' UTR (NM_001008423, exon 1 of 2)	5' UTR (NM_001008423, exon 1 of 2)	176	NM_001008423	380768	Mm.29367	NM_001008423	ENSMUSG00000062961	Ccdc177	Gm1568	coiled-coil domain containing 177	protein-coding
mm_66561.1	chr7	45239109	45239133	-	1	NA	promoter-TSS (NM_007645)	promoter-TSS (NM_007645)	-6	NM_001290804	12493	Mm.3689	NM_007645	ENSMUSG00000030798	Cd37	Tspan26	CD37 antigen	protein-coding
mm_71273.1	chr8	40919561	40919571	+	1	NA	3' UTR (NM_001044740, exon 12 of 12)	3' UTR (NM_001044740, exon 12 of 12)	-6667	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_15496.1	chr2	157797350	157797352	+	1	NA	intron (NM_025680, intron 4 of 15)	intron (NM_025680, intron 4 of 15)	59950	NM_025680	66642	Mm.45193	NM_025680	ENSMUSG00000027649	Ctnnbl1	5730471K09Rik|NAP|NYD-SP19|P14L	catenin, beta like 1	protein-coding
mm_38873.1	chr4	149676067	149676124	-	1	NA	promoter-TSS (NM_001164051)	promoter-TSS (NM_001164051)	-6	NM_001164051	18707	Mm.229108	NM_008840	ENSMUSG00000039936	Pik3cd	2410099E07Rik|2610208K16Rik|AW545373|p110delta	phosphatidylinositol 3-kinase catalytic delta polypeptide	protein-coding
mm_147421.1	chr18	46198839	46198863	-	1	NA	promoter-TSS (NM_001170855)	promoter-TSS (NM_001170855)	-33	NM_001170855	28105	Mm.277382	NM_178872	ENSMUSG00000033949	Trim36	D18Wsu100e|haprin	tripartite motif-containing 36	protein-coding
mm_97976.1	chr11	83862875	83862885	+	1	NA	intron (NM_001291269, intron 3 of 8)	RLTR20A4|LTR|ERVK	9920	NM_001291269	21410	Mm.7226	NM_009330	ENSMUSG00000020679	Hnf1b	HNF-1-beta|HNF-1B|HNF-1Beta|Hnf1beta|LFB3|Tcf-2|Tcf2|vHNF1	HNF1 homeobox B	protein-coding
mm_20886.1	chr2	148851166	148851170	-	1	NA	promoter-TSS (NM_029960)	promoter-TSS (NM_029960)	-234	NM_029960	77705	Mm.159975	NM_029960	ENSMUSG00000027446	9230104L09Rik	mCST E2	RIKEN cDNA 9230104L09 gene	protein-coding
mm_56347.1	chr6	92943486	92943507	-	1	NA	intron (NR_015530, intron 1 of 2)	CpG	2914	NR_015530	330385	Mm.483472	NR_015530	ENSMUSG00000097462	9530026P05Rik	B430306B02	RIKEN cDNA 9530026P05 gene	ncRNA
mm_81406.1	chr9	109051356	109051392	+	1	NA	exon (NM_001284332, exon 3 of 6)	exon (NM_001284332, exon 3 of 6)	-3492	NM_026381	66940	Mm.196533	NM_025858	ENSMUSG00000025647	Shisa5	2310008D10Rik|6430628I05Rik|Scotin|mShisa5	shisa family member 5	protein-coding
mm_105648.1	chr11	107132174	107132201	-	1	NA	promoter-TSS (NM_176850)	promoter-TSS (NM_176850)	-265	NM_176850	207165	Mm.343986	NM_176850	ENSMUSG00000040481	Bptf	9430093H17Rik|Falz	bromodomain PHD finger transcription factor	protein-coding
mm_133716.1	chr16	93628026	93628043	+	1	NA	Intergenic	Intergenic	20197	NM_007620	12408	Mm.26940	NM_007620	ENSMUSG00000051483	Cbr1	AW261796|CR|Cbr	carbonyl reductase 1	protein-coding
mm_152387.1	chr19	10461435	10461437	-	1	NA	Intergenic	Intergenic	-3989	NM_001111140	278795	Mm.490638	NM_001111140	ENSMUSG00000090291	Lrrc10b	Gm705|SerdinR	leucine rich repeat containing 10B	protein-coding
mm_1427.1	chr1	67174667	67174675	+	1	NA	intron (NM_001080809, intron 19 of 37)	intron (NM_001080809, intron 19 of 37)	51644	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_57394.1	chr6	124857688	124857705	-	1	NA	promoter-TSS (NM_013534)	promoter-TSS (NM_013534)	-9	NM_013534	14789	Mm.9002	NM_013534	ENSMUSG00000023191	P3h3	BC016431|Grcb|Leprel2	prolyl 3-hydroxylase 3	protein-coding
mm_164992.1	chr19	12502065	12502079	-	1	NA	promoter-TSS (NM_172442)	promoter-TSS (NM_172442)	-76	NM_172442	207521	Mm.247695	NM_172442	ENSMUSG00000039982	Dtx4	AI449438|BC044798|D930042H13|RNF155	deltex 4, E3 ubiquitin ligase	protein-coding
mm_39665.1	chr5	25222863	25222951	+	1	NA	promoter-TSS (NM_144908)	promoter-TSS (NM_144908)	14	NM_144908	231050	Mm.21814	NM_144908	ENSMUSG00000038072	Galnt11	A430075I06Rik|AI648252|E430002F06Rik	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 11	protein-coding
mm_121363.1	chr14	117324724	117324724	+	1	NA	intron (NM_001079844, intron 2 of 9)	intron (NM_001079844, intron 2 of 9)	399427	NM_011821	23888	Mm.440025	NM_011821	ENSMUSG00000058571	Gpc6	-	glypican 6	protein-coding
mm_50657.1	chr6	51470548	51470561	+	1	NA	promoter-TSS (NM_007624)	promoter-TSS (NM_007624)	-62	NM_007624	12417	Mm.280968	NM_007624	ENSMUSG00000029836	Cbx3	HP1g|M32	chromobox 3	protein-coding
mm_108379.1	chr12	80864932	80864940	+	1	NA	intron (NM_001242419, intron 3 of 6)	PB1D10|SINE|Alu	59511	NR_033786	67340	Mm.386790	NR_033786	ENSMUSG00000101912	1700052I22Rik	-	RIKEN cDNA 1700052I22 gene	ncRNA
mm_40057.1	chr5	33996586	33996594	+	1	NA	5' UTR (NM_001001985, exon 1 of 3)	5' UTR (NM_001001985, exon 1 of 3)	606	NM_001001985	269642	Mm.274610	NM_001001985	ENSMUSG00000048142	Nat8l	1110038O08Rik|Shati	N-acetyltransferase 8-like	protein-coding
mm_171448.1	chr4	145410245	145410248	+	1	NA	Intergenic	Intergenic	-53964	NR_002888	545700	Mm.389595	NR_002888	ENSMUSG00000052912	Smarca5-ps	9230115A19Rik|OTTMUSG00000011029	SWI/SNF related, matrix associated, actin depenent ragulator of chromatin, subfamily a, member 5, pseudogene	pseudo
mm_107589.1	chr12	47833930	47833957	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	467519	NR_039586	100628593		NR_039586	ENSMUSG00000092981	Mir5125	mmu-mir-5125|mu-mir-5125	microRNA 5125	ncRNA
mm_147127.1	chr18	35938206	35938209	-	1	NA	Intergenic	Intergenic	-26623	NM_028707	74002	Mm.196944	NM_028707	ENSMUSG00000024347	Psd2	6330404E20Rik|AW125584|EFA6C	pleckstrin and Sec7 domain containing 2	protein-coding
mm_39709.1	chr5	27598884	27598885	+	1	NA	exon (NM_001198886, exon 8 of 26)	exon (NM_001198886, exon 8 of 26)	-97492	NM_028561	73526	Mm.389608	NM_028561	ENSMUSG00000048703	Speer4b	1700081O22Rik|SPEER-4B	spermatogenesis associated glutamate (E)-rich protein 4B	protein-coding
mm_42637.1	chr5	118560282	118560307	+	1	NA	promoter-TSS (NM_172424)	promoter-TSS (NM_172424)	-425	NM_001347445	76199	Mm.206238	NM_172424	ENSMUSG00000018076	Med13l	2210413I17Rik|6330591G05Rik|9030618F05Rik|Thrap2|Trap240L|mKIAA1025	mediator complex subunit 13-like	protein-coding
mm_20129.1	chr2	121313742	121313745	-	1	NA	intron (NM_178795, intron 29 of 29)	intron (NM_178795, intron 29 of 29)	18289	NM_001173506	17754	Mm.36501	NM_032393	ENSMUSG00000027254	Map1a	6330416M19Rik|AI853608|Mtap-1|Mtap1|Mtap1a|moth1	microtubule-associated protein 1 A	protein-coding
mm_58997.1	chr7	19176447	19176474	+	1	NA	promoter-TSS (NM_001347582)	promoter-TSS (NM_001347582)	39	NM_001347582	72205	Mm.154121	NM_028153	ENSMUSG00000040811	Eml2	1600029N02Rik|EMAP-2	echinoderm microtubule associated protein like 2	protein-coding
mm_88152.1	chr10	69534210	69534218	+	1	NA	5' UTR (NM_170688, exon 1 of 43)	5' UTR (NM_170688, exon 1 of 43)	506	NM_146005	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_131919.1	chr16	23317572	23317582	+	1	NA	5' UTR (NM_001252506, exon 2 of 7)	5' UTR (NM_001252506, exon 2 of 7)	27107	NM_001252506	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_58127.1	chr6	140398119	140398139	-	1	NA	Intergenic	Intergenic	-25970	NM_144920	109135	Mm.247670	NM_144920	ENSMUSG00000030231	Plekha5	2810431N21Rik|AI428202|AK129423|AMH-Cre|Ayu21-9|Gt(pU21)9Imeg|Pepp2|Tg(AMH-cre)1Flor	pleckstrin homology domain containing, family A member 5	protein-coding
mm_1073.1	chr1	59448852	59448856	+	1	NA	Intergenic	Intergenic	-33293	NM_008057	14369	Mm.297906	NM_008057	ENSMUSG00000041075	Fzd7	Fz7	frizzled class receptor 7	protein-coding
mm_70376.1	chr8	10006657	10006702	+	1	NA	promoter-TSS (NM_033622)	promoter-TSS (NM_033622)	46	NM_033622	24099	Mm.28835	NM_033622	ENSMUSG00000031497	Tnfsf13b	BAFF|BLyS|D8Ertd387e|TALL-1|TALL1|THANK|TNFSF20|Tnlg7a|zTNF4	tumor necrosis factor (ligand) superfamily, member 13b	protein-coding
mm_135499.1	chr16	46496286	46496311	-	1	NA	intron (NM_021496, intron 1 of 8)	intron (NM_021496, intron 1 of 8)	669	NM_021496	58998	Mm.40477	NM_021495	ENSMUSG00000022656	Nectin3	2610301B19Rik|3000002N23Rik|4921513D19Rik|AA407785|AU016832|AW538082|CD113|Pvrl3	nectin cell adhesion molecule 3	protein-coding
mm_139899.1	chr17	70853001	70853011	+	1	NA	intron (NM_001164074, intron 1 of 2)	CpG	526	NM_001164074	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_143877.1	chr17	84187828	84187899	-	1	NA	promoter-TSS (NM_001001806)	promoter-TSS (NM_001001806)	84	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_37818.1	chr4	131838238	131838291	-	1	NA	promoter-TSS (NM_011214)	promoter-TSS (NM_011214)	14	NM_011214	19273	Mm.4860	NM_011214	ENSMUSG00000028909	Ptpru	Ftp-1|PCP-2|PTP|PTP-lambda|PTPlambda|Pcp2|Ptpf|Ptprl|R-PTP-U|R-PTP-psi|RPTPlambda	protein tyrosine phosphatase, receptor type, U	protein-coding
mm_171772.1	chr5	108880667	108880668	+	1	NA	Intergenic	L1Md_Gf|LINE|L1	-28157	NM_001104621	435864	Mm.387745	NM_001104621	ENSMUSG00000091624	Vmn2r9	EG435864	vomeronasal 2, receptor 9	protein-coding
mm_35318.1	chr4	25799790	25799863	-	1	NA	5' UTR (NM_010243, exon 1 of 3)	5' UTR (NM_010243, exon 1 of 3)	177	NM_010243	14348	Mm.39101	NM_010243	ENSMUSG00000055373	Fut9	AI746471|AU067636|mFUT9|mFuc-TIX	fucosyltransferase 9	protein-coding
mm_34872.1	chr4	155559773	155559808	+	1	NA	TTS (NM_008142)	TTS (NM_008142)	-2602	NM_138671	192185	Mm.28347	NM_138671	ENSMUSG00000029063	Nadk	4432404C02Rik|BC004012	NAD kinase	protein-coding
mm_95251.1	chr11	44621151	44621181	+	1	NA	intron (NM_007897, intron 2 of 15)	intron (NM_007897, intron 2 of 15)	3066	NM_001290710	13591	Mm.439662	NM_007897	ENSMUSG00000057098	Ebf1	Ebf|O/E-1|OE-1|Olf-1|Olf1	early B cell factor 1	protein-coding
mm_148506.1	chr19	4214352	4214363	+	1	NA	promoter-TSS (NM_001310039)	promoter-TSS (NM_001310039)	-32	NM_001310039	56708	Mm.347919	NM_019952	ENSMUSG00000040663	Clcf1	BSF-3|Bsf3|CLC|NNT-1	cardiotrophin-like cytokine factor 1	protein-coding
mm_168909.1	chr12	55230404	55230404	+	1	NA	promoter-TSS (NM_001100110)	promoter-TSS (NM_001100110)	-74	NM_001100110	100101806	Mm.471968	NM_001100110	ENSMUSG00000079108	Srp54c	E330029E12Rik	signal recognition particle 54C	protein-coding
mm_127551.1	chr15	102150362	102150376	+	1	NA	promoter-TSS (NM_146064)	promoter-TSS (NM_146064)	-206	NM_146064	223920	Mm.358862	NM_146064	ENSMUSG00000023045	Soat2	ACAT2|D15Wsu97e	sterol O-acyltransferase 2	protein-coding
mm_16502.1	chr2	181219999	181220055	+	1	NA	promoter-TSS (NM_199312)	promoter-TSS (NM_199312)	11	NM_199312	332713	Mm.23349	NM_199312	ENSMUSG00000047841	BC051628	1700026M20Rik|Fndc11	cDNA sequence BC051628	protein-coding
mm_73280.1	chr8	104755711	104755713	+	1	NA	Intergenic	Intergenic	21709	NM_133960	102022	Mm.212983	NM_133960	ENSMUSG00000055730	Ces2a	9130231C15Rik|AI266984|Ces6	carboxylesterase 2A	protein-coding
mm_114769.1	chr13	88821544	88821580	+	1	NA	promoter-TSS (NM_001037987)	promoter-TSS (NM_001037987)	90	NM_001037987	13612	Mm.125580	NM_010103	ENSMUSG00000034488	Edil3	Del-1|Del1	EGF-like repeats and discoidin I-like domains 3	protein-coding
mm_20043.1	chr2	120137604	120137609	-	1	NA	intron (NM_133838, intron 1 of 5)	intron (NM_133838, intron 1 of 5)	16969	NM_133838	98878	Mm.132226	NM_133838	ENSMUSG00000027293	Ehd4	2210022F10Rik|AI197390|AI846352|AV006278|Past2	EH-domain containing 4	protein-coding
mm_99305.1	chr11	101376475	101376488	+	1	NA	exon (NM_008061, exon 5 of 5)	exon (NM_008061, exon 5 of 5)	8765	NM_008061	14377	Mm.18064	NM_008061	ENSMUSG00000078650	G6pc	AW107337|G6Pase|G6pt|Glc-6-Pase	glucose-6-phosphatase, catalytic	protein-coding
mm_112397.1	chr12	119238795	119238863	-	1	NA	promoter-TSS (NM_177290)	promoter-TSS (NM_177290)	-553	NM_177290	320910	Mm.217000	NM_177290	ENSMUSG00000025321	Itgb8	4832412O06Rik	integrin beta 8	protein-coding
mm_144443.1	chr18	22171442	22171456	+	1	NA	promoter-TSS (NM_027616)	promoter-TSS (NM_027616)	-53	NM_027616	70950	Mm.235716	NM_027616	ENSMUSG00000024306	Ccdc178	4921528I01Rik	coiled coil domain containing 178	protein-coding
mm_81832.1	chr9	118284383	118284393	+	1	NA	Intergenic	Lx9|LINE|L1	-134192	NM_026442	67899	Mm.9953	NM_026442	ENSMUSG00000039163	Cmc1	2010110K16Rik|2010312P05Rik|AI596001	COX assembly mitochondrial protein 1	protein-coding
mm_125986.1	chr15	76344381	76344395	+	1	NA	exon (NM_025567, exon 2 of 7)	exon (NM_025567, exon 2 of 7)	865	NM_025567	66445	Mm.29196	NM_025567	ENSMUSG00000022551	Cyc1	2610002H19Rik|AA408921|Cyct1	cytochrome c-1	protein-coding
mm_91523.1	chr10	37138820	37138830	-	1	NA	5' UTR (NM_008538, exon 1 of 2)	5' UTR (NM_008538, exon 1 of 2)	101	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_40140.1	chr5	35166296	35166313	+	1	NA	Intergenic	Intergenic	-60607	NM_013587	16976	Mm.277661	NM_013587	ENSMUSG00000029103	Lrpap1	AA617339|AI790446|AU042172|C77774|HBP44|RAP	low density lipoprotein receptor-related protein associated protein 1	protein-coding
mm_45476.1	chr5	69590784	69590803	-	1	NA	intron (NM_001347363, intron 1 of 6)	intron (NM_001347363, intron 1 of 6)	1492	NM_001038015	67980	Mm.33830	NM_027681	ENSMUSG00000029209	Gnpda2	4921523I18Rik|4933412A11Rik|BB189630|GNPDA|Gnp2|Sb52|mKIAA4008	glucosamine-6-phosphate deaminase 2	protein-coding
mm_84174.1	chr9	59949282	59949294	-	1	NA	exon (NM_013708, exon 2 of 8)	exon (NM_013708, exon 2 of 8)	791	NM_013708	23958	Mm.103641	NM_013708	ENSMUSG00000032292	Nr2e3	A930035N01Rik|PNR|RNR|rd7	nuclear receptor subfamily 2, group E, member 3	protein-coding
mm_70774.1	chr8	22192789	22192797	+	1	NA	promoter-TSS (NM_027338)	promoter-TSS (NM_027338)	-67	NM_027338	70160	Mm.41453	NM_027338	ENSMUSG00000031479	Vps36	1700010A24Rik|2210415M20Rik|2810408E15Rik|Eap45	vacuolar protein sorting 36	protein-coding
mm_76005.1	chr8	72492593	72492662	-	1	NA	promoter-TSS (NM_177766)	promoter-TSS (NM_177766)	-13	NM_177766	270066	Mm.291461	NM_177766	ENSMUSG00000019731	Slc35e1	6030458H05|AA408278	solute carrier family 35, member E1	protein-coding
mm_141541.1	chr17	31858081	31858089	-	1	NA	Intergenic	Intergenic	-2293	NM_010831	17691	Mm.290941	NM_010831	ENSMUSG00000024042	Sik1	Msk|Sik|Snf1lk	salt inducible kinase 1	protein-coding
mm_34433.1	chr4	146101615	146101638	+	1	NA	intron (NM_001037926, intron 1 of 3)	intron (NM_001037926, intron 1 of 3)	4314	NM_001037926	626316	Mm.270762	NM_001037926	ENSMUSG00000066009	Zfp987	Gm13051|OTTMUSG00000010104|OTTMUSG00000010173	zinc finger protein 987	protein-coding
mm_20460.1	chr2	129366108	129366118	-	1	NA	intron (NM_008361, intron 5 of 6)	intron (NM_008361, intron 5 of 6)	-3789	NR_015474	329514	Mm.207315	NM_177848	ENSMUSG00000074805	Il1bos	9430083I22|Gm14047|OTTMUSG00000015529	interleukin 1 beta, opposite strand	ncRNA
mm_96225.1	chr11	62511941	62511951	+	1	NA	intron (NM_001039536, intron 5 of 6)	intron (NM_001039536, intron 5 of 6)	27315	NM_028448	73139	Mm.390409	NM_028448	ENSMUSG00000018509	Cenpv	3110013H01Rik|AA671303|Prr6	centromere protein V	protein-coding
mm_153958.1	chr19	47692043	47692053	-	1	NA	promoter-TSS (NM_007732)	promoter-TSS (NM_007732)	-6	NM_001290825	12821	Mm.1225	NM_007732	ENSMUSG00000025064	Col17a1	BP180|Bpag|Bpag2	collagen, type XVII, alpha 1	protein-coding
mm_11915.1	chr2	52071555	52071566	+	1	NA	Intergenic	PB1D7|SINE|Alu	-1277	NM_175238	51869	Mm.254530	NM_175238	ENSMUSG00000036202	Rif1	5730435J01Rik|6530403D07Rik|AU016181|AW549474|D2Ertd145e	replication timing regulatory factor 1	protein-coding
mm_63219.1	chr7	126293408	126293413	+	1	NA	3' UTR (NM_145587, exon 4 of 4)	3' UTR (NM_145587, exon 4 of 4)	20791	NM_145587	104175	Mm.29660	NM_145587	ENSMUSG00000042978	Sbk1	Sbk	SH3-binding kinase 1	protein-coding
mm_100636.1	chr11	121718538	121718560	+	1	NA	Intergenic	Intergenic	16122	NM_144797	210029	Mm.153566	NM_144797	ENSMUSG00000039208	Metrnl	9430048M07Rik|BC019776	meteorin, glial cell differentiation regulator-like	protein-coding
mm_155870.1	chrX	101384631	101384643	+	1	NA	exon (NM_008124, exon 2 of 2)	exon (NM_008124, exon 2 of 2)	905	NM_001302497	14618	Mm.21198	NM_008124	ENSMUSG00000047797	Gjb1	Cnx32|Cx32|connexin-32	gap junction protein, beta 1	protein-coding
mm_137253.1	chr17	24548705	24548713	+	1	NA	Intergenic	Intergenic	-1241	NM_013630	18763	Mm.30435	NM_013630	ENSMUSG00000032855	Pkd1	PC1|mFLJ00285	polycystic kidney disease 1 homolog	protein-coding
mm_51725.1	chr6	86949539	86949563	+	1	NA	exon (NM_177762, exon 8 of 20)	exon (NM_177762, exon 8 of 20)	-60285	NM_001170591	56748	Mm.23809	NM_020045	ENSMUSG00000029993	Nfu1	0610006G17Rik|CGI-33|Hirip5	NFU1 iron-sulfur cluster scaffold	protein-coding
mm_87708.1	chr10	60002817	60002851	+	1	NA	promoter-TSS (NM_001199187)	promoter-TSS (NM_001199187)	29	NM_026937	69090	Mm.155839	NM_026937	ENSMUSG00000044475	Ascc1	1810015P09Rik|AI550520|ASC1p50|CGI-18	activating signal cointegrator 1 complex subunit 1	protein-coding
mm_57383.1	chr6	124818012	124818021	-	1	NA	exon (NM_001326594, exon 16 of 20)	exon (NM_001326594, exon 16 of 20)	-3720	NM_009415	21991	Mm.4222	NM_009415	ENSMUSG00000023456	Tpi1	AI255506|Tpi|Tpi-1	triosephosphate isomerase 1	protein-coding
mm_96062.1	chr11	59634195	59634196	+	1	NA	Intergenic	Intergenic	21229	NM_001011740	257886	Mm.457883	NM_001011740	ENSMUSG00000044061	Olfr225	MOR256-51	olfactory receptor 225	protein-coding
mm_98296.1	chr11	89715356	89715363	+	1	NA	Intergenic	MLT1A0|LTR|ERVL-MaLR	-18423	NM_001327810	382543	Mm.60997	NM_172534	ENSMUSG00000047773	Ankfn1	4932411E22Rik|Gm1175|nmf9	ankyrin-repeat and fibronectin type III domain containing 1	protein-coding
mm_25889.1	chr3	131110283	131110334	+	1	NA	promoter-TSS (NM_001276402)	promoter-TSS (NM_001276402)	11	NM_001276402	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_125910.1	chr15	76009900	76009921	+	1	NA	promoter-TSS (NM_001168253)	promoter-TSS (NM_001168253)	-412	NM_001168253	105732	Mm.267178	NM_134087	ENSMUSG00000046761	Fam83h	AA409316	family with sequence similarity 83, member H	protein-coding
mm_168683.1	chr11	95842182	95842182	-	1	NA	promoter-TSS (NM_001284393)	promoter-TSS (NM_001284393)	-113	NM_023121	14710	Mm.46299	NM_023121	ENSMUSG00000038811	Gngt2	AV096488	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 2	protein-coding
mm_86219.1	chr9	120091126	120091153	-	1	NA	promoter-TSS (NM_007720)	promoter-TSS (NM_007720)	-994	NM_007720	12776	Mm.442098	NM_007720	ENSMUSG00000042262	Ccr8	C-C|C-C CKR-8|CC-CKR-8|CCR-8|CKR-8|Cmkbr8|mCCR8	chemokine (C-C motif) receptor 8	protein-coding
mm_131322.1	chr16	12261265	12261266	+	1	NA	intron (NM_028277, intron 4 of 4)	intron (NM_028277, intron 4 of 4)	277152	NM_001174086	72555	Mm.310139	NM_028277	ENSMUSG00000022494	Shisa9	2700045P11Rik|Ckamp44	shisa family member 9	protein-coding
mm_62205.1	chr7	97830980	97831005	+	1	NA	Intergenic	Intergenic	-11947	NM_011035	18479	Mm.260227	NM_011035	ENSMUSG00000030774	Pak1	AW045634|PAK-1|Paka	p21 protein (Cdc42/Rac)-activated kinase 1	protein-coding
mm_92695.1	chr10	80668702	80668724	-	1	NA	exon (NM_021462, exon 11 of 14)	exon (NM_021462, exon 11 of 14)	7580	NM_021462	17347	Mm.42126	NM_021462	ENSMUSG00000020190	Mknk2	2010016G11Rik|Gprk7|Mnk2	MAP kinase-interacting serine/threonine kinase 2	protein-coding
mm_90320.1	chr10	127064287	127064310	+	1	NA	exon (NM_009870, exon 2 of 8)	exon (NM_009870, exon 2 of 8)	695	NM_009870	12567	Mm.6839	NM_009870	ENSMUSG00000006728	Cdk4	Crk3	cyclin-dependent kinase 4	protein-coding
mm_35776.1	chr4	46404069	46404094	-	1	NA	5' UTR (NM_053149, exon 1 of 4)	5' UTR (NM_053149, exon 1 of 4)	102	NM_053149	93966	Mm.25793	NM_053149	ENSMUSG00000028332	Hemgn	4921524M03Rik|AI317176|EDAG|Hgn|mNDR	hemogen	protein-coding
mm_87796.1	chr10	60299917	60299939	+	1	NA	exon (NM_011179, exon 11 of 15)	exon (NM_011179, exon 11 of 15)	15467	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_96969.1	chr11	70647907	70647918	+	1	NA	promoter-TSS (NM_024211)	promoter-TSS (NM_024211)	625	NM_027445	70510	Mm.261818	NM_027445	ENSMUSG00000040746	Rnf167	0610010G05Rik|5730408C10Rik|AU019305|AV328608	ring finger protein 167	protein-coding
mm_106596.1	chr11	120730852	120730867	-	1	NA	exon (NM_007621, exon 3 of 8)	exon (NM_007621, exon 3 of 8)	1162	NM_007621	12409	Mm.21454	NM_007621	ENSMUSG00000025150	Cbr2	MLCR	carbonyl reductase 2	protein-coding
mm_108102.1	chr12	75220340	75220341	+	1	NA	Intergenic	Intergenic	-43008	NM_172805	238271	Mm.44465	NM_172805	ENSMUSG00000034402	Kcnh5	Eag2	potassium voltage-gated channel, subfamily H (eag-related), member 5	protein-coding
mm_168109.1	chr10	14746288	14746295	-	1	NA	intron (NR_045824, intron 3 of 5)	intron (NR_045824, intron 3 of 5)	-13998	NM_008703	18101	Mm.487342	NM_008703	ENSMUSG00000019865	Nmbr	BB182387	neuromedin B receptor	protein-coding
mm_33838.1	chr4	135728117	135728190	+	1	NA	promoter-TSS (NM_178257)	promoter-TSS (NM_178257)	-6	NM_178257	230828	Mm.261647	NM_178257	ENSMUSG00000037157	Il22ra1	9130219A07Rik|ENSMUSG00000073746|IL-22R|Il22r	interleukin 22 receptor, alpha 1	protein-coding
mm_95290.1	chr11	45980310	45980337	+	1	NA	promoter-TSS (NM_173384)	promoter-TSS (NM_173384)	13	NM_173384	214105	Mm.66708	NM_173384	ENSMUSG00000040489	Sox30	-	SRY (sex determining region Y)-box 30	protein-coding
mm_116976.1	chr13	56179046	56179056	-	1	NA	promoter-TSS (NM_001168615)	promoter-TSS (NM_001168615)	-166	NM_001168615	212937	Mm.116697	NM_145976	ENSMUSG00000049625	Tifab	-	TRAF-interacting protein with forkhead-associated domain, family member B	protein-coding
mm_126503.1	chr15	81776273	81776279	+	1	NA	intron (NM_001081016, intron 8 of 22)	intron (NM_001081016, intron 8 of 22)	-26397	NM_153484	21685	Mm.270278	NM_017376	ENSMUSG00000022389	Tef	2310028D20Rik	thyrotroph embryonic factor	protein-coding
mm_69385.1	chr7	131329494	131329504	-	1	NA	promoter-TSS (NM_027037)	promoter-TSS (NM_027037)	0	NM_027037	69318	Mm.233840	NM_027037	ENSMUSG00000030858	1700007K09Rik	-	RIKEN cDNA 1700007K09 gene	protein-coding
mm_148692.1	chr19	5741301	5741325	+	1	NA	intron (NM_008520, intron 1 of 27)	intron (NM_008520, intron 1 of 27)	409	NM_008520	16998	Mm.182396	NM_008520	ENSMUSG00000024940	Ltbp3	Ltbp2|mFLJ00070	latent transforming growth factor beta binding protein 3	protein-coding
mm_46546.1	chr5	106458456	106458470	-	1	NA	promoter-TSS (NM_001005477)	promoter-TSS (NM_001005477)	-297	NM_001005477	104382	Mm.271593	NM_001005477	ENSMUSG00000034384	Barhl2	E130309B19Rik|MBH1	BarH-like 2 (Drosophila)	protein-coding
mm_24402.1	chr3	90359493	90359508	+	1	NA	Intergenic	Intergenic	17846	NM_139304	229542	Mm.270999	NM_139304	ENSMUSG00000042390	Gatad2b	AL118180|C430014D17Rik|P66beta|mKIAA1150	GATA zinc finger domain containing 2B	protein-coding
mm_28836.1	chr3	96579945	96579968	-	1	NA	intron (NM_001293701, intron 5 of 6)	intron (NM_001293701, intron 5 of 6)	-13155	NR_040409	100038464	Mm.475126	NR_040409	ENSMUSG00000074398	Gm15441	ENSMUSG00000074398|OTTMUSG00000021867	predicted gene 15441	ncRNA
mm_119356.1	chr14	41114863	41114883	+	1	NA	intron (NM_133653, intron 6 of 9)	intron (NM_133653, intron 6 of 9)	9840	NM_133653	11720	Mm.14064	NM_133653	ENSMUSG00000037798	Mat1a	AI046368|AdoMet|Ams|MAT|MATA1|SAMS|SAMS1	methionine adenosyltransferase I, alpha	protein-coding
mm_73724.1	chr8	112570022	112570039	+	1	NA	promoter-TSS (NM_130457)	promoter-TSS (NM_130457)	-13	NM_130457	170571	Mm.209232	NM_130457	ENSMUSG00000031772	Cntnap4	Caspr4|E130114F09Rik	contactin associated protein-like 4	protein-coding
mm_9986.1	chr1	191270173	191270190	-	1	NA	Intergenic	Intergenic	47937	NM_025424	66208	Mm.46444	NM_025424	ENSMUSG00000037499	Nenf	1110060M21Rik|SCIRP10|Spuf	neuron derived neurotrophic factor	protein-coding
mm_48398.1	chr5	140118061	140118069	-	1	NA	intron (NM_010752, intron 13 of 17)	intron (NM_010752, intron 13 of 17)	203487	NM_010752	17120	Mm.27250	NM_010752	ENSMUSG00000029554	Mad1l1	AI173502|AW550425|Mad1	MAD1 mitotic arrest deficient 1-like 1	protein-coding
mm_82445.1	chr9	15301677	15301683	-	1	NA	promoter-TSS (NM_133732)	promoter-TSS (NM_133732)	-73	NM_133732	70984	Mm.261842	NM_133732	ENSMUSG00000031938	4931406C07Rik	-	RIKEN cDNA 4931406C07 gene	protein-coding
mm_90869.1	chr10	8886526	8886543	-	1	NA	promoter-TSS (NM_175155)	promoter-TSS (NM_175155)	-464	NM_175155	70097	Mm.338275	NM_175155	ENSMUSG00000015305	Sash1	1100001C18Rik|2500002E12Rik|A330076K04Rik|mKIAA0790	SAM and SH3 domain containing 1	protein-coding
mm_34384.1	chr4	144920788	144920809	+	1	NA	intron (NM_011303, intron 4 of 5)	RSINE1|SINE|B4	27661	NM_011303	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding
mm_5764.1	chr1	46925786	46925804	-	1	NA	Intergenic	Intergenic	-72286	NM_172653	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|mKIAA1265	solute carrier family 39 (zinc transporter), member 10	protein-coding
mm_33066.1	chr4	123282752	123282762	+	1	NA	promoter-TSS (NM_130881)	promoter-TSS (NM_130881)	-154	NM_130881	230721	Mm.277091	NM_130881	ENSMUSG00000011257	Pabpc4	-	poly(A) binding protein, cytoplasmic 4	protein-coding
mm_82231.1	chr9	3035913	3035922	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	2826	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_162152.1	chrX	79517057	79517057	-	1	NA	intron (NM_001099307, intron 1 of 15)	intron (NM_001099307, intron 1 of 15)	228	NM_001099307	636104	Mm.459420	NM_001099307	ENSMUSG00000073077	Gm7173	EG636104	predicted gene 7173	protein-coding
mm_34290.1	chr4	141572262	141572272	+	1	NA	Intergenic	Intergenic	26105	NR_030695	320456	Mm.32859	NM_177163		B330016D10Rik	-	RIKEN cDNA B330016D10 gene	ncRNA
mm_77636.1	chr8	124152915	124152939	-	1	NA	Intergenic	MLT1A|LTR|ERVL-MaLR	-78467	NM_139272	108148	Mm.33808	NM_139272	ENSMUSG00000089704	Galnt2	AI480629	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2	protein-coding
mm_169115.1	chr13	49544460	49544461	+	1	NA	promoter-TSS (NM_025711)	promoter-TSS (NM_025711)	17	NM_025711	66695	Mm.383216	NM_025711	ENSMUSG00000021388	Aspn	4631401G09Rik|AA986886|Plap1|Slrr1c	asporin	protein-coding
mm_1642.1	chr1	74544346	74544367	+	1	NA	promoter-TSS (NM_148937)	promoter-TSS (NM_148937)	-4	NM_148937	18802	Mm.290731	NM_148937	ENSMUSG00000026173	Plcd4	4921507K24Rik	phospholipase C, delta 4	protein-coding
mm_120424.1	chr14	65396635	65396650	+	1	NA	3' UTR (NM_199029, exon 10 of 10)	3' UTR (NM_199029, exon 10 of 10)	28830	NM_001205075	18155	Mm.16347	NM_010932	ENSMUSG00000045731	Pnoc	N/OFQ|Npnc1|OFQ/N	prepronociceptin	protein-coding
mm_160201.1	chr7	81092244	81092244	+	1	NA	exon (NM_054085, exon 6 of 14)	exon (NM_054085, exon 6 of 14)	-22555	NM_001004184	434203	Mm.389909	NM_001004184	ENSMUSG00000025726	Slc28a1	Cnt1	solute carrier family 28 (sodium-coupled nucleoside transporter), member 1	protein-coding
mm_105240.1	chr11	102319343	102319349	-	1	NA	promoter-TSS (NM_001302954)	promoter-TSS (NM_001302954)	-250	NM_011551	21429	Mm.2845	NM_011551	ENSMUSG00000020923	Ubtf	A930005G04Rik|NOR-90|Tcfubf|UBF|UBF-1|UBF1	upstream binding transcription factor, RNA polymerase I	protein-coding
mm_124.1	chr1	9848271	9848285	+	1	NA	promoter-TSS (NM_001037759)	promoter-TSS (NM_001037759)	-3	NM_001037759	170755	Mm.336410	NM_133220	ENSMUSG00000025915	Sgk3	2510015P22Rik|A330005P07Rik|Cisk|fy|fz	serum/glucocorticoid regulated kinase 3	protein-coding
mm_105017.1	chr11	100440973	100440990	-	1	NA	promoter-TSS (NM_025727)	promoter-TSS (NM_025727)	108	NM_026561	68106	Mm.28738	NM_026561	ENSMUSG00000017176	Nt5c3b	2610037D24Rik|AI841843|C330027I04Rik|Nt5c3l	5'-nucleotidase, cytosolic IIIB	protein-coding
mm_140370.1	chr17	86963331	86963346	+	1	NA	5' UTR (NM_145491, exon 1 of 5)	5' UTR (NM_145491, exon 1 of 5)	227	NM_145491	104215	Mm.826	NM_145491	ENSMUSG00000024143	Rhoq	Arhq|TC10A|Tc10	ras homolog family member Q	protein-coding
mm_156903.1	chrX	168997527	168997531	+	1	NA	intron (NM_009707, intron 1 of 12)	intron (NM_009707, intron 1 of 12)	-39082	NM_178754	11856	Mm.441810	NM_009707	ENSMUSG00000031355	Arhgap6	AI504284|RhoGAPX-1	Rho GTPase activating protein 6	protein-coding
mm_140517.1	chr17	6008728	6008765	-	1	NA	intron (NM_001113352, intron 8 of 25)	intron (NM_001113352, intron 8 of 25)	1166	NM_001290698	20975	Mm.236068	NM_011523	ENSMUSG00000023805	Synj2	AI481647|SJ2|mKIAA0348	synaptojanin 2	protein-coding
mm_168262.1	chr10	90248943	90248954	+	1	NA	intron (NM_001128086, intron 9 of 24)	intron (NM_001128086, intron 9 of 24)	-326779	NM_001177397	77531	Mm.440605	NM_181398	ENSMUSG00000058589	Anks1b	AIDA-1b|C030032C09Rik|E530015N03Rik|ENSMUSG00000078431|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding
mm_152851.1	chr19	24125810	24125846	-	1	NA	intron (NM_001198985, intron 5 of 22)	intron (NM_001198985, intron 5 of 22)	48312	NM_001198985	21873	Mm.104744	NM_011597	ENSMUSG00000024812	Tjp2	ZO-2	tight junction protein 2	protein-coding
mm_150942.1	chr19	46306244	46306255	+	1	NA	intron (NM_001177369, intron 2 of 22)	intron (NM_001177369, intron 2 of 22)	319	NM_001177370	18034	Mm.102365	NM_019408	ENSMUSG00000025225	Nfkb2	NF-kappaB2|lyt|p49|p49/p100|p50B|p52	nuclear factor of kappa light polypeptide gene enhancer in B cells 2, p49/p100	protein-coding
mm_90904.1	chr10	11081093	11081132	-	1	NA	intron (NM_016976, intron 1 of 8)	intron (NM_016976, intron 1 of 8)	1219	NM_001114333	14816	Mm.391904	NM_016976	ENSMUSG00000019828	Grm1	4930455H15Rik|ENSMUSG00000075319|Gm10828|Gprc1a|mGluR1|nmf373|rcw|wobl	glutamate receptor, metabotropic 1	protein-coding
mm_33181.1	chr4	126096667	126096708	+	1	NA	promoter-TSS (NM_001163266)	promoter-TSS (NM_001163266)	34	NM_138721	116748	Mm.41865	NM_138721	ENSMUSG00000050188	Lsm10	-	U7 snRNP-specific Sm-like protein LSM10	protein-coding
mm_34805.1	chr4	154869565	154869566	+	1	NA	promoter-TSS (NM_013783)	promoter-TSS (NM_013783)	-20	NM_013783	27390	Mm.116944	NM_013783	ENSMUSG00000058183	Mmel1	Mell1|NEP2|NEPII|Nl1|SEP	membrane metallo-endopeptidase-like 1	protein-coding
mm_123396.1	chr14	63418448	63418474	-	1	NA	Intergenic	Intergenic	-1274	NM_007549	12143	Mm.3962	NM_007549	ENSMUSG00000014453	Blk	-	B lymphoid kinase	protein-coding
mm_23494.1	chr3	60513532	60513537	+	1	NA	intron (NM_001253710, intron 1 of 7)	intron (NM_001253710, intron 1 of 7)	12355	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_136903.1	chr17	13015518	13015533	+	1	NA	3' UTR (NM_013671, exon 5 of 5)	3' UTR (NM_013671, exon 5 of 5)	7686	NM_013671	20656	Mm.290876	NM_013671	ENSMUSG00000006818	Sod2	MnSOD|Sod-2	superoxide dismutase 2, mitochondrial	protein-coding
mm_36930.1	chr4	108406677	108406745	-	1	NA	promoter-TSS (NM_024198)	promoter-TSS (NM_024198)	2	NM_024198	67305	Mm.20164	NM_024198	ENSMUSG00000028597	Gpx7	3110050F08Rik|AI327032|GPX6	glutathione peroxidase 7	protein-coding
mm_80804.1	chr9	96278870	96278873	+	1	NA	intron (NM_001184711, intron 2 of 10)	intron (NM_001184711, intron 2 of 10)	19623	NM_001184710	211586	Mm.17977	NM_178667	ENSMUSG00000032411	Tfdp2	1110029I05Rik|A330080J22Rik|DP-3|DP3	transcription factor Dp 2	protein-coding
mm_169409.1	chr14	52055800	52055819	-	1	NA	Intergenic	(CCCTAA)n|Simple_repeat|Simple_repeat	-13506	NR_028552	100217457		NR_028552	ENSMUSG00000064871	Snord58b	MBII-199	small nucleolar RNA, C/D box 58B	snoRNA
mm_169008.1	chr13	106338755	106338757	+	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	598159	NM_029665	76582	Mm.132208	NM_029665	ENSMUSG00000042590	Ipo11	1700081H05Rik|2510001A17Rik|AI314624|AW555235|E330021B14Rik|Ranbp11	importin 11	protein-coding
mm_163783.1	chr13	120263066	120263069	+	1	NA	promoter-TSS (NM_199060)	promoter-TSS (NM_199060)	-28	NM_001310627	236546	Mm.247428	NM_199060	ENSMUSG00000095071	AF067061	-	cDNA sequence AF067061	protein-coding
mm_169553.1	chr15	103243636	103243642	+	1	NA	exon (NM_010447, exon 8 of 10)	exon (NM_010447, exon 8 of 10)	3185	NR_002883	434858	Mm.391346	NR_002883		Gm5643	EG434858	heterogeneous nuclear ribonucleoprotein A1 pseudogene	pseudo
mm_155508.1	chrX	73891816	73891833	+	1	NA	promoter-TSS (NM_001276299)	promoter-TSS (NM_001276299)	-278	NM_001276299	12000	Mm.383171	NM_019404	ENSMUSG00000031390	Avpr2	ADHR|DI1|DIR|ND1|V2R|VPV2R	arginine vasopressin receptor 2	protein-coding
mm_81129.1	chr9	106499937	106499939	+	1	NA	promoter-TSS (NM_001146701)	promoter-TSS (NM_001146701)	-29	NM_028843	74267	Mm.116682	NM_028843	ENSMUSG00000066383	Iqcf1	1700055J15Rik	IQ motif containing F1	protein-coding
mm_110763.1	chr12	70227431	70227454	-	1	NA	promoter-TSS (NR_045174)	promoter-TSS (NR_045174)	241	NM_133198	110095	Mm.256926	NM_133198	ENSMUSG00000021069	Pygl	-	liver glycogen phosphorylase	protein-coding
mm_34706.1	chr4	152113828	152113853	+	1	NA	exon (NM_001285999, exon 20 of 21)	exon (NM_001285999, exon 20 of 21)	-2094	NM_001291010	85030	Mm.101198	NM_033042	ENSMUSG00000024793	Tnfrsf25	APO-3|DDR3|DR3|LARD|TR3|TRAMP|Tnfrsf12|WSL-1|WSL-LR|Wsl	tumor necrosis factor receptor superfamily, member 25	protein-coding
mm_101148.1	chr11	16592895	16592897	-	1	NA	Intergenic	RMER17C|LTR|ERVK	-84412	NM_001109971	20335	Mm.325350	NM_011343	ENSMUSG00000078974	Sec61g	-	SEC61, gamma subunit	protein-coding
mm_121128.1	chr14	101840842	101840857	+	1	NA	5' UTR (NM_001347628, exon 1 of 27)	5' UTR (NM_001347628, exon 1 of 27)	226	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_58495.1	chr7	3704200	3704248	+	1	NA	intron (NM_029767, intron 1 of 4)	CpG	183	NM_029767	76846	Mm.13944	NM_029767	ENSMUSG00000006333	Rps9	3010033P07Rik|AL022771|AL022885	ribosomal protein S9	protein-coding
mm_152716.1	chr19	17511396	17511411	-	1	NA	exon (NM_001190483, exon 23 of 38)	exon (NM_001190483, exon 23 of 38)	117360	NM_019437	54391	Mm.7013	NM_019437	ENSMUSG00000024712	Rfk	0610038L10Rik|AF031381|KOI-4	riboflavin kinase	protein-coding
mm_119856.1	chr14	54463899	54463912	+	1	NA	promoter-TSS (NM_022993)	promoter-TSS (NM_022993)	-242	NM_022993	65107	Mm.472719	NM_022993	ENSMUSG00000022175	Lrp10	Lrp9	low-density lipoprotein receptor-related protein 10	protein-coding
mm_24214.1	chr3	88629500	88629510	+	1	NA	intron (NM_001198912, intron 1 of 21)	intron (NM_001198912, intron 1 of 21)	8111	NM_001198912	16800	Mm.239329	NM_008487	ENSMUSG00000028059	Arhgef2	AA408978|GEF|GEF-H1|GEFH1|LFP40|Lbcl1|Lfc|P40|mKIAA0651	rho/rac guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_42922.1	chr5	122720362	122720394	+	1	NA	intron (NM_001310720, intron 5 of 10)	intron (NM_001310720, intron 5 of 10)	12834	NM_001310718	18438	Mm.290884	NM_011026	ENSMUSG00000029470	P2rx4	AI504491|AW555605|D5Ertd444e|P2X4	purinergic receptor P2X, ligand-gated ion channel 4	protein-coding
mm_93246.1	chr10	95417041	95417077	-	1	NA	promoter-TSS (NM_007706)	promoter-TSS (NM_007706)	-202	NM_007706	216233	Mm.474283	NM_007706	ENSMUSG00000020027	Socs2	8030460M17|AI527257|AW108012|CIS2|Cish2|D130043N08Rik|JAB|SOCS-2|SSI-2|hg	suppressor of cytokine signaling 2	protein-coding
mm_34673.1	chr4	150929696	150929708	+	1	NA	intron (NM_001077509, intron 1 of 7)	ID_B1|SINE|B4	1703	NM_001077509	21942	Mm.244187	NM_011612	ENSMUSG00000028965	Tnfrsf9	4-1BB|A930040I11Rik|AA408498|AI325004|CDw137|Cd137|ILA|Ly63	tumor necrosis factor receptor superfamily, member 9	protein-coding
mm_110462.1	chr12	51773463	51773487	-	1	NA	intron (NM_144788, intron 22 of 42)	RLTR20A4|LTR|ERVK	56061	NM_144788	207304	Mm.249391	NM_144788	ENSMUSG00000035247	Hectd1	A630086P08Rik|AI844876|b2b327Clo|opm	HECT domain containing 1	protein-coding
mm_134669.1	chr16	22265534	22265535	-	1	NA	intron (NM_001330555, intron 1 of 9)	CpG	471	NM_001330554	20462	Mm.210352	NM_009186	ENSMUSG00000022858	Tra2b	5730405G21Rik|D16Ertd266e|SIG-41|Sfrs10|Silg41|TRA2beta	transformer 2 beta homolog (Drosophila)	protein-coding
mm_116929.1	chr13	55773364	55773364	-	1	NA	intron (NM_028281, intron 2 of 3)	intron (NM_028281, intron 2 of 3)	-11215	NM_029772	76856	Mm.159795	NM_029772	ENSMUSG00000021499	Catsper3	4921522D01Rik|CACRC	cation channel, sperm associated 3	protein-coding
mm_138194.1	chr17	34286192	34286199	+	1	NA	intron (NM_010378, intron 1 of 4)	intron (NM_010378, intron 1 of 4)	1576	NM_010378	14960	Mm.235338	NM_010378	ENSMUSG00000036594	H2-Aa	Aalpha|H-2Aa|H2Aa|I-Aalpha|IAalpha|Ia-1|Ia1	histocompatibility 2, class II antigen A, alpha	protein-coding
mm_153123.1	chr19	33788544	33788583	-	1	NA	Intergenic	Intergenic	-1111	NM_001323065	329055	Mm.353851	NM_001323065	ENSMUSG00000079342	Lipo1	EG329055|Gm5097	lipase, member O1	protein-coding
mm_50876.1	chr6	55467441	55467441	+	1	NA	intron (NM_007407, intron 3 of 16)	intron (NM_007407, intron 3 of 16)	15463	NM_007407	11517	Mm.44245	NM_007407	ENSMUSG00000029778	Adcyap1r1	2900024I10Rik|AI846590|PAC1|PAC1R|PACAP1-R	adenylate cyclase activating polypeptide 1 receptor 1	protein-coding
mm_131365.1	chr16	13813295	13813332	+	1	NA	3' UTR (NM_001039521, exon 18 of 18)	3' UTR (NM_001039521, exon 18 of 18)	-5938	NM_010946	18203	Mm.380410	NM_010946	ENSMUSG00000022681	Ntan1	PNAA|PNAD	N-terminal Asn amidase	protein-coding
mm_30294.1	chr3	148990101	148990123	-	1	NA	Intergenic	CpG	-35477	NM_001081298	99633	Mm.9776	NM_001081298	ENSMUSG00000028184	Adgrl2	AI450192|CIRL-2|Gm619|Lec1|Lphh1|Lphn2|mKIAA0786	adhesion G protein-coupled receptor L2	protein-coding
mm_56744.1	chr6	115853300	115853343	-	1	NA	promoter-TSS (NM_031177)	promoter-TSS (NM_031177)	20	NM_010774	17193	Mm.259308	NM_010774	ENSMUSG00000030322	Mbd4	Med1	methyl-CpG binding domain protein 4	protein-coding
mm_7028.1	chr1	87099136	87099144	-	1	NA	exon (NM_001081082, exon 10 of 11)	exon (NM_001081082, exon 10 of 11)	2466	NM_001081082	76768	Mm.58068	NM_001081082	ENSMUSG00000079440	Alpi	2010001C14Rik|Akp6|gIAP	alkaline phosphatase, intestinal	protein-coding
mm_87934.1	chr10	62672311	62672332	+	1	NA	intron (NM_001033260, intron 1 of 3)	intron (NM_001033260, intron 1 of 3)	-10187	NR_106074	102465987		NR_106074	ENSMUSG00000105329	Mir7215	mmu-mir-7215	microRNA 7215	ncRNA
mm_163140.1	chr11	80177468	80177491	+	1	NA	intron (NM_172133, intron 10 of 10)	intron (NM_172133, intron 10 of 10)	-6393	NM_028019	71956	Mm.22985	NM_028019	ENSMUSG00000020707	Rnf135	0610037N03Rik|2410006N06Rik	ring finger protein 135	protein-coding
mm_152933.1	chr19	28561018	28561025	-	1	NA	intron (NM_175459, intron 2 of 10)	intron (NM_175459, intron 2 of 10)	-117203	NR_045330	320176	Mm.406716	NR_045330	ENSMUSG00000097735	D930032P07Rik	-	RIKEN cDNA D930032P07 gene	ncRNA
mm_156927.1	chrX	169303517	169303521	+	1	NA	non-coding (NR_109847, exon 15 of 15)	non-coding (NR_109847, exon 15 of 15)	16853	NM_001331050	15159	Mm.284033	NM_008222	ENSMUSG00000031352	Hccs	-	holocytochrome c synthetase	protein-coding
mm_76823.1	chr8	104623902	104623913	-	1	NA	intron (NM_001252628, intron 1 of 17)	intron (NM_001252628, intron 1 of 17)	489	NM_007663	12556	Mm.19423	NM_007663	ENSMUSG00000031881	Cdh16	-	cadherin 16	protein-coding
mm_83707.1	chr9	50728118	50728129	-	1	NA	promoter-TSS (NM_178118)	promoter-TSS (NM_178118)	-139	NM_178118	330938	Mm.82598	NM_178118	ENSMUSG00000032064	Dixdc1	4930563F16Rik|BC048182|Ccd1|Ccd1Aalpha1L|Ccd1Abeta1L|Ccd1BalphaL|Ccd1BbetaL|Ccd1CL|mKIAA1735	DIX domain containing 1	protein-coding
mm_155221.1	chrX	57053850	57053868	+	1	NA	promoter-TSS (NM_029371)	promoter-TSS (NM_029371)	25	NM_029371	72459	Mm.2152	NM_028242	ENSMUSG00000067873	Htatsf1	1600023H17Rik|2600017A12Rik|2700077B20Rik|TAT-SF1	HIV TAT specific factor 1	protein-coding
mm_77805.1	chr9	3035878	3035903	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	2853	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_127799.1	chr15	3984847	3984859	-	1	NA	3' UTR (NM_145930, exon 6 of 6)	3' UTR (NM_145930, exon 6 of 6)	-5280	NM_134099	106052	Mm.234191	NM_134099	ENSMUSG00000022184	Fbxo4	1700096C12Rik|AI851261|AW494535|Fbx4	F-box protein 4	protein-coding
mm_56670.1	chr6	113654206	113654215	-	1	NA	intron (NM_001113553, intron 2 of 11)	intron (NM_001113553, intron 2 of 11)	15743	NM_001113553	108960	Mm.152142	NM_172161	ENSMUSG00000060477	Irak2	6330415L08Rik|AI649099|IRAK-2	interleukin-1 receptor-associated kinase 2	protein-coding
mm_73100.1	chr8	94568422	94568435	+	1	NA	intron (NM_153507, intron 14 of 15)	MIRc|SINE|MIR	33298	NM_028221	102122	Mm.250425	NM_028221	ENSMUSG00000031774	Fam192a	1700001O11Rik|2310065K24Rik|AI596259|Nip30	family with sequence similarity 192, member A	protein-coding
mm_48143.1	chr5	137150517	137150526	-	1	NA	Intergenic	Intergenic	-34314	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_135622.1	chr16	52273438	52273451	-	1	NA	intron (NM_009655, intron 11 of 15)	intron (NM_009655, intron 11 of 15)	179637	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_71495.1	chr8	46788349	46788362	+	1	NA	intron (NM_008391, intron 1 of 8)	intron (NM_008391, intron 1 of 8)	48610	NM_008391	16363	Mm.1149	NM_008391	ENSMUSG00000031627	Irf2	9830146E22Rik|AI646973|Irf-2	interferon regulatory factor 2	protein-coding
mm_162622.1	chr1	183418509	183418511	+	1	NA	promoter-TSS (NM_030175)	promoter-TSS (NM_030175)	40	NM_030175	78772	Mm.29003	NM_030175	ENSMUSG00000053461	Hhipl2	4930507C10Rik|AW208802|Hhip3	hedgehog interacting protein-like 2	protein-coding
mm_128791.1	chr15	66812059	66812103	-	1	NA	intron (NM_001029841, intron 1 of 7)	intron (NM_001029841, intron 1 of 7)	19748	NM_001029841	20491	Mm.7601	NM_009192	ENSMUSG00000022372	Sla	Slap|Slap-1	src-like adaptor	protein-coding
mm_63340.1	chr7	126961747	126961764	+	1	NA	exon (NM_001252566, exon 9 of 17)	exon (NM_001252566, exon 9 of 17)	11220	NM_001252566	233878	Mm.283926	NM_144926	ENSMUSG00000030683	Sez6l2	AI835913|AW121566|BSRP-A|Psk1	seizure related 6 homolog like 2	protein-coding
mm_53688.1	chr6	142405080	142405080	+	1	NA	Intergenic	Intergenic	-8351	NM_001242345	319552	Mm.39649	NM_001242345	ENSMUSG00000071112	Spx	B230216G23Rik|Npq	spexin hormone	protein-coding
mm_55689.1	chr6	72771061	72771061	-	1	NA	intron (NM_001079822, intron 3 of 12)	B4|SINE|B4	17984	NM_001079822	21415	Mm.440067	NM_009332	ENSMUSG00000055799	Tcf7l1	Tcf-3|Tcf3|bHLHb21	transcription factor 7 like 1 (T cell specific, HMG box)	protein-coding
mm_48353.1	chr5	139345113	139345148	-	1	NA	promoter-TSS (NM_197980)	promoter-TSS (NM_197980)	36	NM_197980	68033	Mm.261064	NM_197980	ENSMUSG00000045438	Cox19	1810074D02Rik|2810437L13Rik	cytochrome c oxidase assembly protein 19	protein-coding
mm_93942.1	chr10	127195199	127195222	-	1	NA	promoter-TSS (NR_045716)	promoter-TSS (NR_045716)	-39	NR_045715	100038591	Mm.441071	NR_045715	ENSMUSG00000097331	F420014N23Rik	ENSMUSG00000074658	RIKEN cDNA F420014N23 gene	ncRNA
mm_34468.1	chr4	148149219	148149219	+	1	NA	intron (NM_015797, intron 2 of 5)	intron (NM_015797, intron 2 of 5)	-2223	NR_105989	102465619		NR_105989	ENSMUSG00000099043	Mir7022	Gm27291|mmu-mir-7022	microRNA 7022	ncRNA
mm_83026.1	chr9	37238799	37238801	-	1	NA	intron (NM_020258, intron 6 of 17)	MER20|DNA|hAT-Charlie	16938	NM_020258	56857	Mm.440037	NM_020258	ENSMUSG00000032122	Slc37a2	G3PP|Slc37a1|cI-2|ci2	solute carrier family 37 (glycerol-3-phosphate transporter), member 2	protein-coding
mm_36208.1	chr4	62434685	62434696	-	1	NA	promoter-TSS (NM_153504)	promoter-TSS (NM_153504)	36	NM_153504	76072	Mm.169565	NM_153504	ENSMUSG00000063851	Rnf183	5830442J12Rik	ring finger protein 183	protein-coding
mm_83869.1	chr9	55026510	55026523	-	1	NA	promoter-TSS (NM_145129)	promoter-TSS (NM_145129)	43	NM_145129	110834	Mm.63569	NM_145129	ENSMUSG00000032303	Chrna3	(a)3|A730007P14Rik|Acra-3|Acra3	cholinergic receptor, nicotinic, alpha polypeptide 3	protein-coding
mm_99137.1	chr11	100320539	100320594	+	1	NA	intron (NM_011508, intron 1 of 3)	intron (NM_011508, intron 1 of 3)	617	NM_011508	20918	Mm.13886	NM_011508	ENSMUSG00000035530	Eif1	Sui1-rs1	eukaryotic translation initiation factor 1	protein-coding
mm_78167.1	chr9	21029444	21029455	+	1	NA	promoter-TSS (NM_023892)	promoter-TSS (NM_023892)	76	NM_023892	78369	Mm.30220	NM_023892	ENSMUSG00000001014	Icam4	1810015M19Rik|Cd242|ICAM-4	intercellular adhesion molecule 4, Landsteiner-Wiener blood group	protein-coding
mm_86252.1	chr9	121490012	121490037	-	1	NA	3' UTR (NM_001284508, exon 4 of 4)	3' UTR (NM_001284508, exon 4 of 4)	5670	NM_001284508	12424	Mm.2619	NM_031161	ENSMUSG00000032532	Cck	-	cholecystokinin	protein-coding
mm_43612.1	chr5	137989798	137989806	+	1	NA	exon (NM_013478, exon 4 of 4)	exon (NM_013478, exon 4 of 4)	8281	NM_013478	12007	Mm.30061	NM_013478	ENSMUSG00000037053	Azgp1	Zag	alpha-2-glycoprotein 1, zinc	protein-coding
mm_64258.1	chr7	141745441	141745458	+	1	NA	exon (NM_023566, exon 29 of 46)	exon (NM_023566, exon 29 of 46)	-43562	NM_010844	17833	Mm.334332	NM_010844	ENSMUSG00000037974	Muc5ac	2210005L13Rik|MGM	mucin 5, subtypes A and C, tracheobronchial/gastric	protein-coding
mm_95929.1	chr11	58377542	58377546	+	1	NA	Intergenic	Intergenic	-1488	NM_027339	70163	Mm.24119	NM_027339	ENSMUSG00000013643	Lypd8	2210415F13Rik	LY6/PLAUR domain containing 8	protein-coding
mm_98870.1	chr11	97799587	97799597	+	1	NA	promoter-TSS (NM_010688)	promoter-TSS (NM_010688)	-80	NM_010688	16796	Mm.271967	NM_010688	ENSMUSG00000038366	Lasp1	AA408629|Def-4|SH3P6|Tg(Col1a1-lacZ)1Ngma	LIM and SH3 protein 1	protein-coding
mm_164145.1	chr15	59650271	59650277	-	1	NA	intron (NM_144549, intron 1 of 2)	intron (NM_144549, intron 1 of 2)	1620	NM_144549	211770	Mm.40298	NM_144549	ENSMUSG00000032501	Trib1	A530090O15Rik|TRB-1|Trb1	tribbles pseudokinase 1	protein-coding
mm_34208.1	chr4	140950063	140950079	+	1	NA	3' UTR (NM_008812, exon 16 of 16)	3' UTR (NM_008812, exon 16 of 16)	7831	NR_045911	100126227	Mm.404073	NR_045911	ENSMUSG00000087698	Gm13031	OTTMUSG00000010081	predicted gene 13031	ncRNA
mm_163123.1	chr11	76904467	76904469	+	1	NA	promoter-TSS (NM_025655)	promoter-TSS (NM_025655)	-77	NM_025655	66601	Mm.25138	NM_025655	ENSMUSG00000020839	Tmigd1	2010002A20Rik|Tmigd	transmembrane and immunoglobulin domain containing 1	protein-coding
mm_42599.1	chr5	117417689	117417709	+	1	NA	intron (NM_001312914, intron 1 of 19)	intron (NM_001312914, intron 1 of 19)	3697	NM_001312914	333050	Mm.437947	NM_001034873	ENSMUSG00000061578	Ksr2	-	kinase suppressor of ras 2	protein-coding
mm_139559.1	chr17	56878638	56878640	+	1	NA	intron (NM_030141, intron 3 of 13)	intron (NM_030141, intron 3 of 13)	3006	NM_030141	78625	Mm.160106	NM_030141	ENSMUSG00000024209	1700061G19Rik	1700026H02|AI507598	RIKEN cDNA 1700061G19 gene	protein-coding
mm_72395.1	chr8	81767915	81767996	+	1	NA	intron (NM_001297593, intron 4 of 23)	intron (NM_001297593, intron 4 of 23)	425393	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_56021.1	chr6	86570832	86570845	-	1	NA	Intergenic	Intergenic	43437	NR_037961	72012	Mm.349174	NR_037960	ENSMUSG00000097048	1600020E01Rik	-	RIKEN cDNA 1600020E01 gene	ncRNA
mm_59228.1	chr7	24640200	24640217	+	1	NA	exon (NM_133743, exon 5 of 5)	exon (NM_133743, exon 5 of 5)	3638	NM_133743	72434	Mm.281093	NM_133743	ENSMUSG00000057454	Lypd3	2310061G07Rik|C4.4a	Ly6/Plaur domain containing 3	protein-coding
mm_55597.1	chr6	71632898	71632947	-	1	NA	promoter-TSS (NM_173001)	promoter-TSS (NM_173001)	-5	NM_001038695	104263	Mm.260479	NM_173001	ENSMUSG00000053470	Kdm3a	1700105C21Rik|C230043E16Rik|JHDM2a|Jmjd1|Jmjd1a|KDM2A|TGSA|Tsga	lysine (K)-specific demethylase 3A	protein-coding
mm_102915.1	chr11	69580231	69580256	-	1	NA	promoter-TSS (NM_144824)	promoter-TSS (NM_144824)	-116	NM_011640	22059	Mm.222	NM_011640	ENSMUSG00000059552	Trp53	Tp53|bbl|bfy|bhy|p44|p53	transformation related protein 53	protein-coding
mm_68435.1	chr7	109927338	109927340	-	1	NA	intron (NM_001311139, intron 3 of 21)	intron (NM_001311139, intron 3 of 21)	33083	NM_021494	19347	Mm.21904	NM_021494	ENSMUSG00000035901	Dennd5a	1500012B19Rik|AJ245569|AW496491|ORF37|Rab6ip1|mKIAA1091	DENN/MADD domain containing 5A	protein-coding
mm_161251.1	chr13	103769459	103769459	-	1	NA	Intergenic	Intergenic	-4877	NM_172592	218543	Mm.458176	NM_172592	ENSMUSG00000032621	Srek1	8430401B01|AI450757|AI462342|SRrp508|SRrp86|Sfrs12|Srsf12	splicing regulatory glutamine/lysine-rich protein 1	protein-coding
mm_134639.1	chr16	21762607	21762613	-	1	NA	exon (NM_023737, exon 7 of 7)	exon (NM_023737, exon 7 of 7)	25224	NM_023737	74147	Mm.28100	NM_023737	ENSMUSG00000022853	Ehhadh	1300002P22Rik|HD|L-PBE|LBFP|LBP|MFP|MFP1|PBFE	enoyl-Coenzyme A, hydratase/3-hydroxyacyl Coenzyme A dehydrogenase	protein-coding
mm_164664.1	chr17	43630629	43630651	-	1	NA	promoter-TSS (NM_198418)	promoter-TSS (NM_198418)	-341	NM_001161367	210510	Mm.329058	NM_198418	ENSMUSG00000040140	Tdrd6	AB097085|Tdr2	tudor domain containing 6	protein-coding
mm_7660.1	chr1	128417222	128417230	-	1	NA	5' UTR (NM_145507, exon 1 of 4)	5' UTR (NM_145507, exon 1 of 4)	190	NM_177445	226414	Mm.28693	NM_145507	ENSMUSG00000026356	Dars	5730439G15Rik	aspartyl-tRNA synthetase	protein-coding
mm_45623.1	chr5	75979216	75979221	-	1	NA	promoter-TSS (NM_010612)	promoter-TSS (NM_010612)	-790	NM_010612	16542	Mm.285	NM_010612	ENSMUSG00000062960	Kdr	6130401C07|Flk-1|Flk1|Krd-1|Ly73|VEGFR-2|VEGFR2|sVEGFR-2	kinase insert domain protein receptor	protein-coding
mm_14837.1	chr2	147373849	147373863	+	1	NA	3' UTR (NM_008780, exon 5 of 5)	3' UTR (NM_008780, exon 5 of 5)	8862	NM_008780	18503	Mm.315502	NM_008780	ENSMUSG00000037034	Pax1	Pax-1|hbs|hunchback|un|undulated|wt	paired box 1	protein-coding
mm_24005.1	chr3	87357904	87357942	+	1	NA	promoter-TSS (NM_009690)	promoter-TSS (NM_009690)	42	NM_009690	11801	Mm.6676	NM_009690	ENSMUSG00000015854	Cd5l	1/6|AAC-11|AI047839|Api6|CT2|Pdp|Sp-alpha|mAIM	CD5 antigen-like	protein-coding
mm_100733.1	chr11	3983309	3983318	-	1	NA	promoter-TSS (NM_001177703)	promoter-TSS (NM_001177703)	-323	NM_001177703	53897	Mm.103414	NM_016922	ENSMUSG00000049721	Gal3st1	Cst|Gcst	galactose-3-O-sulfotransferase 1	protein-coding
mm_47256.1	chr5	121660411	121660419	-	1	NA	promoter-TSS (NM_001289543)	promoter-TSS (NM_001289543)	95	NM_028037	71985	Mm.45423	NM_028037	ENSMUSG00000029456	Acad10	2410021P16Rik	acyl-Coenzyme A dehydrogenase family, member 10	protein-coding
mm_78382.1	chr9	28148282	28148284	+	1	NA	intron (NM_177906, intron 1 of 7)	intron (NM_177906, intron 1 of 7)	357014	NM_177906	330908	Mm.379474	NM_177906	ENSMUSG00000062257	Opcml	2900075O15Rik|3732419F12|AI844366|B930023M13Rik|C230027C17|Gm181|Obcam	opioid binding protein/cell adhesion molecule-like	protein-coding
mm_6925.1	chr1	84850001	84850014	-	1	NA	intron (NM_025386, intron 1 of 3)	ORR1D1|LTR|ERVL-MaLR	10166	NM_025386	66153	Mm.381192	NM_025386	ENSMUSG00000073633	Fbxo36	0610008D19Rik|1110020F21Rik|2410002G19Rik|D1Ertd757e	F-box protein 36	protein-coding
mm_4300.1	chr1	171800457	171800467	+	1	NA	3' UTR (NM_013730, exon 7 of 7)	3' UTR (NM_013730, exon 7 of 7)	33330	NM_013730	27218	Mm.103648	NM_013730	ENSMUSG00000015316	Slamf1	4933415F16|AA177906|CD150|CDw150|ESTM51|IPO-3|Slam	signaling lymphocytic activation molecule family member 1	protein-coding
mm_103908.1	chr11	83578587	83578595	-	1	NA	promoter-TSS (NM_011338)	promoter-TSS (NM_011338)	45	NM_011338	20308	Mm.416125	NM_011338	ENSMUSG00000019122	Ccl9	CCF18|MRP-2|Scya10|Scya9	chemokine (C-C motif) ligand 9	protein-coding
mm_104581.1	chr11	96968656	96968673	-	1	NA	intron (NM_030220, intron 1 of 6)	intron (NM_030220, intron 1 of 6)	9024	NM_030220	78912	Mm.491183	NM_030220	ENSMUSG00000018678	Sp2	4930480I16Rik|mKIAA0048	Sp2 transcription factor	protein-coding
mm_109085.1	chr12	104413823	104413862	+	1	NA	3' UTR (NM_009252, exon 5 of 5)	3' UTR (NM_009252, exon 5 of 5)	7134	NM_009252	20716	Mm.482074	NM_009252	ENSMUSG00000021091	Serpina3n	Spi2-2|Spi2.2|Spi2/eb.4	serine (or cysteine) peptidase inhibitor, clade A, member 3N	protein-coding
mm_67159.1	chr7	73541720	73541737	-	1	NA	promoter-TSS (NM_001081345)	promoter-TSS (NM_001081345)	18	NM_001081345	244059	Mm.34539	NM_001081345	ENSMUSG00000078671	Chd2	2810013C04Rik|2810040A01Rik|5630401D06Rik|AI851092|BC029703|CHD-2	chromodomain helicase DNA binding protein 2	protein-coding
mm_20519.1	chr2	130714295	130714298	-	1	NA	intron (NM_029432, intron 31 of 36)	B1_Mur4|SINE|Alu	-16777	NM_001081162	269356	Mm.441391	NM_001081162	ENSMUSG00000074796	Slc4a11	AI503023|BTR1|NaBC1	solute carrier family 4, sodium bicarbonate transporter-like, member 11	protein-coding
mm_114418.1	chr13	64367967	64367982	+	1	NA	exon (NM_009984, exon 4 of 8)	exon (NM_009984, exon 4 of 8)	2546	NM_009984	13039	Mm.930	NM_009984	ENSMUSG00000021477	Ctsl	1190035F06Rik|CatL|Ctsl1|MEP|fs|nkt	cathepsin L	protein-coding
mm_28986.1	chr3	101287547	101287554	-	1	NA	exon (NM_013486, exon 2 of 5)	exon (NM_013486, exon 2 of 5)	389	NM_013486	12481	Mm.22842	NM_013486	ENSMUSG00000027863	Cd2	LFA-2|Ly-37|Ly37	CD2 antigen	protein-coding
mm_157212.1	chrX	12762121	12762125	-	1	NA	promoter-TSS (NM_001048208)	promoter-TSS (NM_001048208)	-150	NM_001048208	26896	Mm.17616	NM_012005	ENSMUSG00000064127	Med14	9930001L01Rik|AU041628|Crsp2|ENSMUSG00000073278|Gm641|ORF1|Trap170	mediator complex subunit 14	protein-coding
mm_12796.1	chr2	79635655	79635671	+	1	NA	exon (NM_080558, exon 1 of 18)	exon (NM_080558, exon 1 of 18)	238	NM_080558	70599	Mm.272881	NM_080558	ENSMUSG00000027007	Ssfa2	5730488C15Rik|CS-1|CS1|KRAP|SPAG13|mKIAA1927	sperm specific antigen 2	protein-coding
mm_141726.1	chr17	34116229	34116243	-	1	NA	exon (NM_001204973, exon 4 of 13)	exon (NM_001204973, exon 4 of 13)	3664	NR_037970	14312	Mm.3444	NM_010238	ENSMUSG00000024335	Brd2	AW228947|D17H6S113E|Frg-1|Fsrg-1|Fsrg1|Nat|Ring3|Rnf3|mKIAA4005	bromodomain containing 2	protein-coding
mm_49334.1	chr6	21283422	21283425	+	1	NA	intron (NM_019697, intron 1 of 5)	intron (NM_019697, intron 1 of 5)	67314	NM_019697	16508	Mm.425316	NM_019697	ENSMUSG00000060882	Kcnd2	AI839615|AW555701|Kv4.2|R75121|mKIAA1044	potassium voltage-gated channel, Shal-related family, member 2	protein-coding
mm_24911.1	chr3	96245531	96245546	+	1	NA	promoter-TSS (NM_178212).2	promoter-TSS (NM_178212).2	41	NM_013549	15267	Mm.5220	NM_013549	ENSMUSG00000064220	Hist2h2aa1	AI448581|H2a-614|H2a-615|Hist2	histone cluster 2, H2aa1	protein-coding
mm_77903.1	chr9	7348903	7348917	+	1	NA	intron (NM_001320077, intron 3 of 10)	intron (NM_001320077, intron 3 of 10)	1536	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_171252.1	chr3	79591550	79591550	+	1	NA	exon (NM_026352, exon 1 of 10)	exon (NM_026352, exon 1 of 10)	161	NM_026352	67738	Mm.295252	NM_026352	ENSMUSG00000027804	Ppid	4930564J03Rik|CYP-40|Ppidl|Ppif	peptidylprolyl isomerase D (cyclophilin D)	protein-coding
mm_171732.1	chr4	93693222	93693224	+	1	NA	Intergenic	Intergenic	-357712	NM_026954	69136	Mm.171558	NM_026954	ENSMUSG00000054000	Tusc1	2200001D17Rik|TSG-9	tumor suppressor candidate 1	protein-coding
mm_45328.1	chr5	65492901	65492921	-	1	NA	promoter-TSS (NM_133697)	promoter-TSS (NM_133697)	-76	NM_133697	68552	Mm.10709	NM_133697	ENSMUSG00000037822	Smim14	1110003E01Rik|1700127H04Rik|5430439C17Rik|MAd4	small integral membrane protein 14	protein-coding
mm_25780.1	chr3	126597300	126597413	+	1	NA	5' UTR (NM_001293663, exon 1 of 20)	5' UTR (NM_001293663, exon 1 of 20)	405	NM_023813	108058	Mm.255822	NM_023813	ENSMUSG00000053819	Camk2d	2810011D23Rik|8030469K03Rik|CaMK II|[d]-CaMKII	calcium/calmodulin-dependent protein kinase II, delta	protein-coding
mm_16784.1	chr2	9890027	9890035	-	1	NA	promoter-TSS (NR_040511)	promoter-TSS (NR_040511)	-491	NR_040511	77682	Mm.488621	NR_040511	ENSMUSG00000079602	9230102O04Rik	-	RIKEN cDNA 9230102O04 gene	ncRNA
mm_22350.1	chr2	180920926	180920964	-	1	NA	promoter-TSS (NM_173761)	promoter-TSS (NM_173761)	-9	NM_173761	228994	Mm.30205	NM_173761	ENSMUSG00000038848	Ythdf1	2210410K23Rik|8030473O16	YTH domain family 1	protein-coding
mm_36095.1	chr4	58499413	58499427	-	1	NA	promoter-TSS (NM_001290486)	promoter-TSS (NM_001290486)	-17	NM_001290486	14745	Mm.4772	NM_010336	ENSMUSG00000038668	Lpar1	AI326300|Edg2|Gpcr26|Kdt2|lpA1|vzg-1	lysophosphatidic acid receptor 1	protein-coding
mm_9175.1	chr1	171053980	171054011	-	1	NA	exon (NM_010188, exon 4 of 5)	exon (NM_010188, exon 4 of 5)	5408	NM_010188	14131	Mm.22119	NM_010188	ENSMUSG00000059498	Fcgr3	CD16	Fc receptor, IgG, low affinity III	protein-coding
mm_150397.1	chr19	36464038	36464053	+	1	NA	Intergenic	Intergenic	84978	NM_029508	76073	Mm.259180	NM_029508	ENSMUSG00000024805	Pcgf5	0610009F02Rik|1110054A01Rik|5830406C17Rik|5830443C21Rik|9530023M17Rik|AI324127	polycomb group ring finger 5	protein-coding
mm_4342.1	chr1	171856749	171856759	+	1	NA	intron (NM_001289470, intron 3 of 8)	L1_Mur3|LINE|L1	17057	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_8606.1	chr1	156035882	156035890	-	1	NA	promoter-TSS (NM_001160182)	promoter-TSS (NM_001160182)	-150	NM_001160182	240832	Mm.253335	NM_022329	ENSMUSG00000050565	Tor1aip2	1110020D10Rik|15kDa|A130072J07|AA103493|AW060462|AW610675|C77739|Ifrg15|Lull1	torsin A interacting protein 2	protein-coding
mm_85778.1	chr9	109058237	109058271	-	1	NA	TTS (NM_026381)	TTS (NM_026381)	997	NM_001012236	22040	Mm.439964	NM_011637	ENSMUSG00000049734	Trex1	AU041952	three prime repair exonuclease 1	protein-coding
mm_70042.1	chr7	142577889	142577897	-	1	NA	promoter-TSS (NR_030416)	promoter-TSS (NR_030416)	253	NR_130974	14955	Mm.14802	NR_001592	ENSMUSG00000000031	H19	AI747191	H19, imprinted maternally expressed transcript	ncRNA
mm_3548.1	chr1	150407507	150407529	+	1	NA	exon (NM_133780, exon 10 of 52)	exon (NM_133780, exon 10 of 52)	-14463	NM_145511	226499	Mm.222093	NM_145511	ENSMUSG00000006010	BC003331	1810053E15Rik|Odr4|odr-4	cDNA sequence BC003331	protein-coding
mm_24127.1	chr3	88206787	88206824	+	1	NA	Intergenic	Intergenic	-8366	NR_037276	100526540		NR_037276	ENSMUSG00000092988	Mir3093	mir-3093|mmu-mir-3093	microRNA 3093	ncRNA
mm_128743.1	chr15	64312637	64312692	-	1	NA	promoter-TSS (NM_001276463)	promoter-TSS (NM_001276463)	9	NM_001276462	13196	Mm.277236	NM_010026	ENSMUSG00000022377	Asap1	AV239055|DEF-1|Ddef1|PAP|mKIAA1249|s19	ArfGAP with SH3 domain, ankyrin repeat and PH domain1	protein-coding
mm_63539.1	chr7	128003912	128004002	+	1	NA	promoter-TSS (NM_001079932)	promoter-TSS (NM_001079932)	-421	NM_001079932	434246	Mm.389924	NM_001079932	ENSMUSG00000042828	Trim72	BC067209|MG53	tripartite motif-containing 72	protein-coding
mm_15323.1	chr2	155751111	155751120	+	1	NA	promoter-TSS (NM_011171)	promoter-TSS (NM_011171)	-102	NM_011171	19124	Mm.3243	NM_011171	ENSMUSG00000027611	Procr	AI325044|Ccca|Ccd41|Epcr	protein C receptor, endothelial	protein-coding
mm_97758.1	chr11	80821233	80821243	+	1	NA	exon (NM_029537, exon 7 of 7)	exon (NM_029537, exon 7 of 7)	10823	NM_029537	103743	Mm.27682	NM_029537	ENSMUSG00000035413	Tmem98	6530411B15Rik|AI463522	transmembrane protein 98	protein-coding
mm_134709.1	chr16	22892321	22892333	-	1	NA	exon (NM_001276450, exon 1 of 7)	exon (NM_001276450, exon 1 of 7)	312	NM_001276449	11625	Mm.197554	NM_013465	ENSMUSG00000022868	Ahsg	-	alpha-2-HS-glycoprotein	protein-coding
mm_164592.1	chr17	26535830	26535836	+	1	NA	Intergenic	Intergenic	-25679	NM_026170	67458	Mm.30496	NM_026170	ENSMUSG00000001576	Ergic1	1200007D18Rik|maa-136	endoplasmic reticulum-golgi intermediate compartment (ERGIC) 1	protein-coding
mm_172554.1	chr8	105225228	105225247	+	1	NA	promoter-TSS (NM_145604)	promoter-TSS (NM_145604)	49	NM_145604	234678	Mm.27186	NM_145604	ENSMUSG00000031889	D230025D16Rik	BC006874|Lin10	RIKEN cDNA D230025D16 gene	protein-coding
mm_4380.1	chr1	172157533	172157534	+	1	NA	intron (NM_153555, intron 2 of 13)	Lx9|LINE|L1	9518	NM_153555	98193	Mm.159915	NM_153555	ENSMUSG00000026554	Dcaf8	AA408877|AA433120|AA792214|AU018973|C76055|D1Dau35e|D1Ucla4|H326|Wdr42a	DDB1 and CUL4 associated factor 8	protein-coding
mm_146828.1	chr18	21652078	21652089	-	1	NA	exon (NM_001081403, exon 1 of 8)	exon (NM_001081403, exon 1 of 8)	285	NM_001081403	225266	Mm.436836	NM_001081403	ENSMUSG00000042514	Klhl14	6330403N15Rik|AI785250|printor	kelch-like 14	protein-coding
mm_110382.1	chr12	40222106	40222107	-	1	NA	TTS (NR_035459)	TTS (NR_035459)	705	NR_035459	100316693		NR_035459	ENSMUSG00000089371	Mir1938	mir-1938|mmu-mir-1938	microRNA 1938	ncRNA
mm_146208.1	chr18	76856312	76856327	+	1	NA	promoter-TSS (NM_001109743)	promoter-TSS (NM_001109743)	-86	NM_001109743	664805	Mm.329543	NM_001109743	ENSMUSG00000091519	Skor2	Corl2|EG664805|Fussel18|Gm7348	SKI family transcriptional corepressor 2	protein-coding
mm_47137.1	chr5	120543943	120543975	-	1	NA	intron (NM_145853, intron 18 of 27)	intron (NM_145853, intron 18 of 27)	32767	NM_001177594	170756	Mm.291070	NM_133221	ENSMUSG00000032754	Slc8b1	AF261233|NCKX6|NCLX|Slc24a6	solute carrier family 8 (sodium/lithium/calcium exchanger), member B1	protein-coding
mm_32849.1	chr4	117975028	117975040	+	1	NA	intron (NM_009176, intron 5 of 11)	intron (NM_009176, intron 5 of 11)	-45271	NM_001284192	11876	Mm.56897	NM_009711	ENSMUSG00000028539	Artn	neublastin	artemin	protein-coding
mm_145111.1	chr18	44200846	44200849	+	1	NA	Intergenic	Intergenic	-4670	NM_001048217	433181	Mm.117440	NM_001048217	ENSMUSG00000073573	Spink11	9230112K01Rik	serine peptidase inhibitor, Kazal type 11	protein-coding
mm_78381.1	chr9	27791277	27791336	+	1	NA	promoter-TSS (NM_177906)	promoter-TSS (NM_177906)	37	NM_177906	330908	Mm.379474	NM_177906	ENSMUSG00000062257	Opcml	2900075O15Rik|3732419F12|AI844366|B930023M13Rik|C230027C17|Gm181|Obcam	opioid binding protein/cell adhesion molecule-like	protein-coding
mm_147195.1	chr18	37644216	37644226	-	1	NA	promoter-TSS (NM_175770)	promoter-TSS (NM_175770)	-17	NM_175770	24074	Mm.236009	NM_175770	ENSMUSG00000051316	Taf7	55kDa|AI607308|BB007175|TAFII55|Taf2f	TATA-box binding protein associated factor 7	protein-coding
mm_97257.1	chr11	75758879	75758889	+	1	NA	intron (NM_009536, intron 4 of 5)	intron (NM_009536, intron 4 of 5)	25997	NM_009536	22627	Mm.234700	NM_009536	ENSMUSG00000020849	Ywhae	AU019196	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide	protein-coding
mm_105055.1	chr11	100704066	100704077	-	1	NA	TTS (NM_020004)	TTS (NM_020004)	200	NM_030150	80861	Mm.271830	NM_030150	ENSMUSG00000017830	Dhx58	B430001I08Rik|D11Lgp2e|LPG2|Lgp2|RLR-3	DEXH (Asp-Glu-X-His) box polypeptide 58	protein-coding
mm_122571.1	chr14	50807709	50807720	-	1	NA	promoter-TSS (NR_002142)	promoter-TSS (NR_002142)	57	NR_002142	85029		NR_002142	ENSMUSG00000092837	Rpph1	Gm24821|H1RNA|Rmrp5|Rpr	ribonuclease P RNA component H1	ncRNA
mm_150553.1	chr19	39325006	39325038	+	1	NA	exon (NM_007815, exon 7 of 9)	exon (NM_007815, exon 7 of 9)	37937	NM_007815	13095	Mm.20764	NM_007815	ENSMUSG00000003053	Cyp2c29	AHOH|AHOHase|AI159681|AI196010|Ah-2|Ahh-1|Cyp2c|P450-2C	cytochrome P450, family 2, subfamily c, polypeptide 29	protein-coding
mm_26986.1	chr3	25698016	25698036	-	1	NA	intron (NM_001163387, intron 3 of 5)	intron (NM_001163387, intron 3 of 5)	455281	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_156898.1	chrX	167207442	167207474	+	1	NA	3' UTR (NM_021278, exon 3 of 3)	3' UTR (NM_021278, exon 3 of 3)	1760	NM_021278	19241	Mm.142729	NM_021278	ENSMUSG00000049775	Tmsb4x	Ptmb4|Tb4	thymosin, beta 4, X chromosome	protein-coding
mm_122856.1	chr14	54875037	54875071	-	1	NA	TTS (NM_001167908)	TTS (NM_001167908)	2484	NM_001167908	105651	Mm.297365	NM_001167908	ENSMUSG00000072494	Ppp1r3e	A630071A11Rik|AW049239|Gm1211	protein phosphatase 1, regulatory (inhibitor) subunit 3E	protein-coding
mm_101769.1	chr11	43836470	43836517	-	1	NA	promoter-TSS (NM_007416)	promoter-TSS (NM_007416)	-4	NM_007416	11548	Mm.39086	NM_007416	ENSMUSG00000050541	Adra1b	[a]1b	adrenergic receptor, alpha 1b	protein-coding
mm_35256.1	chr4	19878156	19878169	-	1	NA	3' UTR (NM_175406, exon 8 of 8)	3' UTR (NM_175406, exon 8 of 8)	44404	NM_175406	242341	Mm.19298	NM_175406	ENSMUSG00000028238	Atp6v0d2	1620401A02Rik|AI324824|V-ATPase	ATPase, H+ transporting, lysosomal V0 subunit D2	protein-coding
mm_135077.1	chr16	34263027	34263038	-	1	NA	intron (NM_001164268, intron 10 of 33)	intron (NM_001164268, intron 10 of 33)	250995	NM_001164268	545156	Mm.82274	NM_177357	ENSMUSG00000061751	Kalrn	2210407G14Rik|AV235988|DUET|E530005C20Rik|Gm539|Hapip|TRAD	kalirin, RhoGEF kinase	protein-coding
mm_84540.1	chr9	67290289	67290292	-	1	NA	intron (NM_001081242, intron 39 of 57)	intron (NM_001081242, intron 39 of 57)	-53564	NR_029576	387185		NR_029576	ENSMUSG00000076379	Mir190a	Mir190|Mirn190|mir-190|mir-190a|mmu-mir-190|mmu-mir-190a	microRNA 190a	ncRNA
mm_41900.1	chr5	105531619	105531638	+	1	NA	intron (NM_133897, intron 1 of 3)	L1MEf|LINE|L1	12157	NM_133897	100604	Mm.319847	NM_133897	ENSMUSG00000054720	Lrrc8c	AD158|AI326115|E430036I04Rik|fad158	leucine rich repeat containing 8 family, member C	protein-coding
mm_33910.1	chr4	136332538	136332583	+	1	NA	exon (NM_001277123, exon 7 of 10)	exon (NM_001277123, exon 7 of 10)	21618	NM_001277123	74326	Mm.31051	NM_028871	ENSMUSG00000066037	Hnrnpr	2610003J05Rik|2610528B01Rik|Hnrpr	heterogeneous nuclear ribonucleoprotein R	protein-coding
mm_40732.1	chr5	66195578	66195585	+	1	NA	Intergenic	Intergenic	-4246	NR_040695	73639	Mm.48851	NR_040695	ENSMUSG00000107014	1700126H18Rik	-	RIKEN cDNA 1700126H18 gene	ncRNA
mm_148257.1	chr18	80860915	80860922	-	1	NA	intron (NM_001201569, intron 7 of 29)	intron (NM_001201569, intron 7 of 29)	73140	NM_001201569	50771	Mm.247138	NM_015805	ENSMUSG00000024566	Atp9b	AA934181|Atpc2b|IIb|MMR	ATPase, class II, type 9B	protein-coding
mm_98829.1	chr11	97415528	97415538	+	1	NA	Intergenic	CpG	-34627	NM_021493	58996	Mm.394118	NM_021493	ENSMUSG00000049807	Arhgap23	A330041B18Rik	Rho GTPase activating protein 23	protein-coding
mm_169418.1	chr14	53091202	53091219	+	1	NA	Intergenic	Intergenic	-595515	NM_001170918	57269	Mm.88822	NM_020512	ENSMUSG00000059887	Olfr1507	MOR244-1|Mor28|Or28	olfactory receptor 1507	protein-coding
mm_167258.1	chr8	25754253	25754275	-	1	NA	promoter-TSS (NM_028102)	promoter-TSS (NM_028102)	16	NM_028102	72108	Mm.246875	NM_028102	ENSMUSG00000061313	Ddhd2	2010305K11Rik|SAMWD1|mKIAA0725	DDHD domain containing 2	protein-coding
mm_127150.1	chr15	98567962	98567980	+	1	NA	promoter-TSS (NM_009833)	promoter-TSS (NM_009833)	-335	NM_009833	12455	Mm.29941	NM_009833	ENSMUSG00000011960	Ccnt1	2810478G24Rik|AI115585|CycT1	cyclin T1	protein-coding
mm_57854.1	chr6	129486963	129486976	-	1	NA	3' UTR (NM_138648, exon 8 of 8)	3' UTR (NM_138648, exon 8 of 8)	-14190	NR_132130	56644	Mm.239516	NM_020008	ENSMUSG00000079293	Clec7a	BGR|Clecsf12|beta-GR	C-type lectin domain family 7, member a	protein-coding
mm_24049.1	chr3	87906334	87906356	+	1	NA	promoter-TSS (NM_008231)	promoter-TSS (NM_008231)	24	NM_008231	15191	Mm.292208	NM_008231	ENSMUSG00000004897	Hdgf	AI118077|D3Ertd299e	hepatoma-derived growth factor	protein-coding
mm_126068.1	chr15	77357098	77357100	+	1	NA	Intergenic	Intergenic	42011	NM_029419	75761	Mm.232636	NM_029419	ENSMUSG00000010601	Apol7a	9130022K13Rik|Apol3	apolipoprotein L 7a	protein-coding
mm_121870.1	chr14	20793984	20793994	-	1	NA	promoter-TSS (NM_178597)	promoter-TSS (NM_178597)	99	NM_001039138	12325	Mm.235182	NM_178597	ENSMUSG00000021820	Camk2g	Camkg	calcium/calmodulin-dependent protein kinase II gamma	protein-coding
mm_22425.1	chr2	181597582	181597609	-	1	NA	exon (NM_172676, exon 2 of 5)	exon (NM_172676, exon 2 of 5)	1552	NM_172676	229011	Mm.205422	NM_172676	ENSMUSG00000038605	Samd10	D930033N23Rik|E130318E08	sterile alpha motif domain containing 10	protein-coding
mm_29734.1	chr3	126831464	126831477	-	1	NA	intron (NM_001346636, intron 16 of 20)	intron (NM_001346636, intron 16 of 20)	111916	NM_001034168	109676	Mm.220242	NM_178655	ENSMUSG00000032826	Ank2	100043364|AI835472|AW491075|Ank-2|Gm4392	ankyrin 2, brain	protein-coding
mm_81427.1	chr9	109057249	109057260	+	1	NA	TTS (NM_011637)	TTS (NM_011637)	1997	NM_001012236	22040	Mm.439964	NM_011637	ENSMUSG00000049734	Trex1	AU041952	three prime repair exonuclease 1	protein-coding
mm_86578.1	chr10	12974806	12974819	+	1	NA	Intergenic	Intergenic	-10553	NM_001163591	74732	Mm.248648	NM_029075	ENSMUSG00000039232	Stx11	5830405C08Rik	syntaxin 11	protein-coding
mm_85028.1	chr9	88462991	88463002	-	1	NA	exon (NM_001284328, exon 8 of 12)	exon (NM_001284328, exon 8 of 12)	19401	NM_019666	56403	Mm.260545	NM_019666	ENSMUSG00000032423	Syncrip	2610109K23Rik|4632417O19Rik|GRY-RBP|Nsap1|Nsap1l|hnRNP Q|pp68	synaptotagmin binding, cytoplasmic RNA interacting protein	protein-coding
mm_23401.1	chr3	58031515	58031516	+	1	NA	Intergenic	RMER1C|Other|Other	132292	NR_040538	67850	Mm.416968	NR_040538	ENSMUSG00000100666	1700007F19Rik	-	RIKEN cDNA 1700007F19 gene	ncRNA
mm_146250.1	chr18	77778756	77778797	+	1	NA	exon (NM_007505, exon 5 of 12)	exon (NM_007505, exon 5 of 12)	5008	NM_007505	11946	Mm.276137	NM_007505	ENSMUSG00000025428	Atp5a1	AI035633|AL022851|AL023067|Atpm|D18Ertd206e|Mom2	ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1	protein-coding
mm_59133.1	chr7	23385889	23385895	+	1	NA	promoter-TSS (NM_001039143)	promoter-TSS (NM_001039143)	3	NM_011860	23968	Mm.333653	NM_011860	ENSMUSG00000015721	Nlrp5	Mater|Nalp5|Op1|PAN11	NLR family, pyrin domain containing 5	protein-coding
mm_62355.1	chr7	100499229	100499245	+	1	NA	exon (NM_011671, exon 8 of 8)	exon (NM_011671, exon 8 of 8)	5879	NM_011671	22228	Mm.171378	NM_011671	ENSMUSG00000033685	Ucp2	Slc25a8	uncoupling protein 2 (mitochondrial, proton carrier)	protein-coding
mm_99625.1	chr11	104685738	104685746	+	1	NA	Intergenic	CpG	77742	NM_016780	16416	Mm.87150	NM_016780	ENSMUSG00000020689	Itgb3	CD61|GP3A|INGRB3	integrin beta 3	protein-coding
mm_23862.1	chr3	83012834	83012857	+	1	NA	exon (NM_133862, exon 8 of 10)	exon (NM_133862, exon 8 of 10)	5121	NM_001317105	99571	Mm.16422	NM_133862	ENSMUSG00000033860	Fgg	3010002H13Rik|AI256424	fibrinogen gamma chain	protein-coding
mm_158868.1	chrY	1245656	1245676	-	1	NA	promoter-TSS (NM_001326682)	promoter-TSS (NM_001326682)	93	NM_001326683	22290	Mm.20477	NM_009484	ENSMUSG00000068457	Uty	Hydb|mKIAA4057	ubiquitously transcribed tetratricopeptide repeat gene, Y chromosome	protein-coding
mm_112724.1	chr13	19192257	19192263	+	1	NA	Intergenic	Intergenic	203553	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_96850.1	chr11	70044602	70044603	+	1	NA	exon (NM_007864, exon 20 of 20)	exon (NM_007864, exon 20 of 20)	-9522	NM_001291131	11889	Mm.6559	NM_009714	ENSMUSG00000020884	Asgr1	ASGPR1|Asgr|Asgr-1|HL-1	asialoglycoprotein receptor 1	protein-coding
mm_9688.1	chr1	178336146	178336164	-	1	NA	exon (NM_016805, exon 2 of 14)	exon (NM_016805, exon 2 of 14)	1629	NM_016805	51810	Mm.86589	NM_016805	ENSMUSG00000039630	Hnrnpu	AA408410|AI256620|AL024194|AL024437|AW557595|C86794|Hnrpu|SAFA|Sp120|hnRNP U	heterogeneous nuclear ribonucleoprotein U	protein-coding
mm_160869.1	chr11	66526061	66526061	-	1	NA	promoter-TSS (NM_001034874)	promoter-TSS (NM_001034874)	65	NM_001034874	380702	Mm.351764	NM_001034874	ENSMUSG00000053930	Shisa6	Gm879|ckamp52	shisa family member 6	protein-coding
mm_134025.1	chr16	4997783	4997831	-	1	NA	promoter-TSS (NM_029374)	promoter-TSS (NM_029374)	45	NM_027669	71089	Mm.87382	NM_027669	ENSMUSG00000022542	Sept12	1700028G04Rik|4933413B09Rik|Septin12	septin 12	protein-coding
mm_106429.1	chr11	119347947	119347962	-	1	NA	intron (NM_018822, intron 6 of 7)	intron (NM_018822, intron 6 of 7)	7556	NM_018822	27029	Mm.103788	NM_018822	ENSMUSG00000005043	Sgsh	4632406A19Rik	N-sulfoglucosamine sulfohydrolase (sulfamidase)	protein-coding
mm_123829.1	chr14	70627082	70627086	-	1	NA	promoter-TSS (NM_001252663)	promoter-TSS (NM_001252663)	-19	NM_001252663	13829	Mm.210863	NM_013514	ENSMUSG00000022099	Dmtn	AI325486|Epb4.9|Epb49|dematin	dematin actin binding protein	protein-coding
mm_44542.1	chr5	24540977	24541008	-	1	NA	promoter-TSS (NM_080444)	promoter-TSS (NM_080444)	-14	NM_001310476	117590	Mm.207071	NM_080444	ENSMUSG00000038204	Asb10	Asb-10|BB137407	ankyrin repeat and SOCS box-containing 10	protein-coding
mm_14129.1	chr2	126034667	126034679	+	1	NA	promoter-TSS (NM_008008)	promoter-TSS (NM_008008)	15	NM_008008	14178	Mm.330557	NM_008008	ENSMUSG00000027208	Fgf7	Kgf	fibroblast growth factor 7	protein-coding
mm_39809.1	chr5	30647922	30647932	+	1	NA	promoter-TSS (NM_175675)	promoter-TSS (NM_175675)	-9	NR_049199	100885838		NR_049199	ENSMUSG00000093710	Mir5625	Gm23930|mmu-mir-5625	microRNA 5625	ncRNA
mm_130197.1	chr15	94588056	94588060	-	1	NA	intron (NM_008971, intron 2 of 8)	intron (NM_008971, intron 2 of 8)	1766	NM_008971	19230	Mm.490250	NM_008971	ENSMUSG00000022451	Twf1	A6|Ptk9|twinfilin	twinfilin actin binding protein 1	protein-coding
mm_94499.1	chr11	7160051	7160063	+	1	NA	intron (NM_009622, intron 14 of 19)	intron (NM_009622, intron 14 of 19)	28512	NR_045101	100041347	Mm.300962	NR_045101	ENSMUSG00000087512	Gm11985	OTTMUSG00000005133	predicted gene 11985	ncRNA
mm_50904.1	chr6	57581623	57581636	+	1	NA	intron (NM_025992, intron 1 of 22)	intron (NM_025992, intron 1 of 22)	637	NM_025992	67138	Mm.297393	NM_025992	ENSMUSG00000029798	Herc6	1700121D12Rik|2510038N07Rik|4930427L17Rik|AI451296|CEB1|Herc5	hect domain and RLD 6	protein-coding
mm_151881.1	chr19	5798525	5798529	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	-2546	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_80461.1	chr9	77983783	77983800	+	1	NA	3' UTR (NM_134255, exon 8 of 8)	3' UTR (NM_134255, exon 8 of 8)	66426	NM_134255	68801	Mm.430736	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	ELOVL family member 5, elongation of long chain fatty acids (yeast)	protein-coding
mm_76733.1	chr8	95037121	95037131	-	1	NA	intron (NM_173036, intron 8 of 11)	intron (NM_173036, intron 8 of 11)	-17977	NM_001042715	330830	Mm.277112	NM_001042715	ENSMUSG00000031786	Drc7	Ccdc135|Gm770|SRG-L|SRG-S	dynein regulatory complex subunit 7	protein-coding
mm_157673.1	chrX	59134707	59134717	-	1	NA	promoter-TSS (NM_010200)	promoter-TSS (NM_010200)	-276	NM_010200	14168	Mm.7995	NM_010200	ENSMUSG00000031137	Fgf13	Fhf2	fibroblast growth factor 13	protein-coding
mm_144869.1	chr18	36735033	36735058	+	1	NA	promoter-TSS (NM_028036)	promoter-TSS (NM_028036)	-25	NM_028036	71983	Mm.135188	NM_028036	ENSMUSG00000006850	Tmco6	2410015B03Rik	transmembrane and coiled-coil domains 6	protein-coding
mm_30029.1	chr3	135689256	135689268	-	1	NA	intron (NM_008689, intron 1 of 24)	intron (NM_008689, intron 1 of 24)	2285	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_58392.1	chr7	3206965	3206971	+	1	NA	Intergenic	B1F2|SINE|Alu	-11658	NR_029640	100049710		NR_029640	ENSMUSG00000077815	Mir290a	Mir290|Mirn290|mir-290a|mmu-miR-290|mmu-mir-290a	microRNA 290a	ncRNA
mm_86659.1	chr10	17772735	17772741	+	1	NA	Intergenic	Intergenic	-23481	NM_138628	378431	Mm.283493	NM_138628	ENSMUSG00000039891	Txlnb	2310001N14Rik|Mdp77	taxilin beta	protein-coding
mm_64794.1	chr7	6678247	6678250	-	1	NA	exon (NM_011769, exon 8 of 8)	exon (NM_011769, exon 8 of 8)	-15880	NR_131759	76637	Mm.159751	NR_131759	ENSMUSG00000108113	Zim2	1700116N21Rik	zinc finger, imprinted 2	ncRNA
mm_115914.1	chr13	23465873	23465879	-	1	NA	promoter-TSS (NM_013483)	promoter-TSS (NM_013483)	25	NM_013483	12231	Mm.1420	NM_013483	ENSMUSG00000000706	Btn1a1	Btn	butyrophilin, subfamily 1, member A1	protein-coding
mm_15897.1	chr2	164951151	164951161	+	1	NA	exon (NM_013599, exon 8 of 13)	exon (NM_013599, exon 8 of 13)	2937	NM_013599	17395	Mm.4406	NM_013599	ENSMUSG00000017737	Mmp9	AW743869|B/MMP9|Clg4b|Gel B|MMP-9|pro-MMP-9	matrix metallopeptidase 9	protein-coding
mm_72880.1	chr8	88950252	88950278	+	1	NA	Intergenic	Intergenic	-74470	NR_106190	102465899		NR_106190	ENSMUSG00000099078	Mir8110	Gm27571|mmu-mir-8110	microRNA 8110	ncRNA
mm_139518.1	chr17	56593948	56593961	+	1	NA	exon (NM_001163300, exon 4 of 21)	exon (NM_001163300, exon 4 of 21)	8972	NM_001163300	224903	Mm.255066	NM_001163300	ENSMUSG00000071054	Safb	3110021E02Rik|5330423C17Rik|AU018122|D18386|E130307D12|HAP|HET|SAF-B1|SAFB1	scaffold attachment factor B	protein-coding
mm_13235.1	chr2	98662250	98662269	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	1194602	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_117273.1	chr13	65052817	65052823	-	1	NA	Intergenic	Intergenic	19762	NM_001083890	238683	Mm.295543	NM_001083890	ENSMUSG00000074849	Spata31d1c	4932441B19Rik|Fam75d1c	spermatogenesis associated 31 subfamily D, member 1C	protein-coding
mm_136791.1	chr17	11329608	11329623	+	1	NA	intron (NM_001317726, intron 4 of 6)	B4|SINE|B4	489256	NM_016694	50873	Mm.311110	NM_016694	ENSMUSG00000023826	Park2	PRKN	Parkinson disease (autosomal recessive, juvenile) 2, parkin	protein-coding
mm_159351.1	chr3	73057148	73057148	-	1	NA	promoter-TSS (NM_198864)	promoter-TSS (NM_198864)	-205	NM_198864	386750	Mm.331076	NM_198864	ENSMUSG00000048304	Slitrk3	-	SLIT and NTRK-like family, member 3	protein-coding
mm_36643.1	chr4	94331593	94331602	-	1	NA	Intergenic	Intergenic	225199	NM_026368	67770	Mm.35170	NM_026368	ENSMUSG00000028578	Caap1	5830433M19Rik|AI536248|CAAP	caspase activity and apoptosis inhibitor 1	protein-coding
mm_60969.1	chr7	47772854	47772880	+	1	NA	Intergenic	Intergenic	-171495	NM_153067	233222	Mm.240142	NM_153067	ENSMUSG00000078698	Mrgpra3	Mrga3	MAS-related GPR, member A3	protein-coding
mm_79331.1	chr9	53341061	53341080	+	1	NA	intron (NM_176846, intron 3 of 5)	intron (NM_176846, intron 3 of 5)	39400	NM_176846	320051	Mm.277540	NM_176846	ENSMUSG00000034584	Exph5	AC079869.22gm5|B130009M24Rik|E030050P12|Kiaa0624|Slac2b|slac2-b	exophilin 5	protein-coding
mm_166840.1	chr7	19310483	19310487	+	1	NA	promoter-TSS (NM_008036)	promoter-TSS (NM_008036)	-440	NM_001347586	14282	Mm.248335	NM_008036	ENSMUSG00000003545	Fosb	-	FBJ osteosarcoma oncogene B	protein-coding
mm_53161.1	chr6	125321334	125321360	+	1	NA	promoter-TSS (NM_011324)	promoter-TSS (NM_011324)	7	NM_011324	20276	Mm.144114	NM_011324	ENSMUSG00000030340	Scnn1a	ENaC|SCNEA|Scnn1|mENaC	sodium channel, nonvoltage-gated 1 alpha	protein-coding
mm_89417.1	chr10	90837821	90837823	+	1	NA	intron (NM_001347053, intron 1 of 8)	HAL1b|LINE|L1	7979	NM_001347053	77531	Mm.440605	NM_181398	ENSMUSG00000058589	Anks1b	AIDA-1b|C030032C09Rik|E530015N03Rik|ENSMUSG00000078431|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding
mm_22992.1	chr3	34019902	34019916	+	1	NA	promoter-TSS (NM_001113188)	promoter-TSS (NM_001113188)	-170	NM_001113189	14359	Mm.259021	NM_008053	ENSMUSG00000027680	Fxr1	1110050J02Rik|9530073J07Rik|AI851072|Fxr1h|Fxr1p	fragile X mental retardation gene 1, autosomal homolog	protein-coding
mm_85597.1	chr9	107517336	107517338	-	1	NA	intron (NM_001174047, intron 19 of 38)	intron (NM_001174047, intron 19 of 38)	-16608	NM_019704	56395	Mm.260153	NM_019704	ENSMUSG00000010045	Tmem115	C78915|Pl6|Pp6	transmembrane protein 115	protein-coding
mm_55027.1	chr6	48902987	48903006	-	1	NA	intron (NM_029638, intron 1 of 4)	ERVB7_2-LTR_MM|LTR|ERVK	-1990	NM_001161622	76507	Mm.213898	NM_029638	ENSMUSG00000029811	Aoc1	1600012D06Rik|Abp1|DAO	amine oxidase, copper-containing 1	protein-coding
mm_87021.1	chr10	28074917	28074927	+	1	NA	5' UTR (NM_008983, exon 1 of 32)	5' UTR (NM_008983, exon 1 of 32)	102	NM_008983	19272	Mm.332303	NM_008983	ENSMUSG00000019889	Ptprk	AI853699|PTPk|RPTPkappa	protein tyrosine phosphatase, receptor type, K	protein-coding
mm_106249.1	chr11	117813724	117813770	-	1	NA	3' UTR (NM_009304, exon 4 of 4)	3' UTR (NM_009304, exon 4 of 4)	4080	NM_009304	20973	Mm.468228	NM_009304	ENSMUSG00000048277	Syngr2	Clast2|cellugyrin	synaptogyrin 2	protein-coding
mm_166882.1	chr7	25801232	25801233	+	1	NA	Intergenic	ID_B1|SINE|B4	-12499	NM_001190975	26362	Mm.4128	NM_009465	ENSMUSG00000002602	Axl	AI323647|Ark|Tyro7|Ufo	AXL receptor tyrosine kinase	protein-coding
mm_91673.1	chr10	43221357	43221369	-	1	NA	promoter-TSS (NM_001168289)	promoter-TSS (NM_001168289)	-123	NM_027772	71365	Mm.490430	NM_027772	ENSMUSG00000038240	Pdss2	5430420P03Rik|Gm60|Plmp|kd|mDLP1	prenyl (solanesyl) diphosphate synthase, subunit 2	protein-coding
mm_14568.1	chr2	135193445	135193447	+	1	NA	intron (NR_040517, intron 2 of 5)	intron (NR_040517, intron 2 of 5)	22170	NR_040517	78805	Mm.78702	NR_040517	ENSMUSG00000085247	4930545L23Rik	-	RIKEN cDNA 4930545L23 gene	ncRNA
mm_71427.1	chr8	46492362	46492387	+	1	NA	intron (NM_001302163, intron 1 of 20)	intron (NM_001302163, intron 1 of 20)	1408	NM_001302163	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_61933.1	chr7	90166175	90166187	+	1	NA	intron (NM_001252520, intron 4 of 20)	intron (NM_001252520, intron 4 of 20)	35949	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_89644.1	chr10	96690592	96690595	+	1	NA	Intergenic	Intergenic	73592	NM_007569	12226	Mm.23811	NM_007569	ENSMUSG00000036478	Btg1	AI426953|AW546738	B cell translocation gene 1, anti-proliferative	protein-coding
mm_133024.1	chr16	57121767	57121782	+	1	NA	promoter-TSS (NM_138599)	promoter-TSS (NM_138599)	60	NM_138599	28185	Mm.196933	NM_138599	ENSMUSG00000022752	Tomm70a	2610044B22Rik|D16Ium22|D16Ium22e|D16Wsu109e|Tom70|Tomm70|mKIAA0719	translocase of outer mitochondrial membrane 70 homolog A (yeast)	protein-coding
mm_19992.1	chr2	118715468	118715478	-	1	NA	exon (NM_177568, exon 18 of 32)	exon (NM_177568, exon 18 of 32)	-11510	NM_001081971	383787	Mm.35758	NM_001081971	ENSMUSG00000078137	Ankrd63	Gm1337	ankyrin repeat domain 63	protein-coding
mm_161287.1	chr14	26067364	26067364	-	1	NA	promoter-TSS (NM_001270495)	promoter-TSS (NM_001270495)	45	NM_001270495	100039257	Mm.33344	NM_001270495	ENSMUSG00000021867	Tmem254b	ENSMUSG00000021867|Gm9746	transmembrane protein 254b	protein-coding
mm_168236.1	chr10	81704784	81704791	+	1	NA	promoter-TSS (NM_001243067)	promoter-TSS (NM_001243067)	-38	NM_001243067	73610	Mm.490466	NM_001243067	ENSMUSG00000096795	Zfp433	1700123A16Rik	zinc finger protein 433	protein-coding
mm_139654.1	chr17	57402535	57402546	+	1	NA	exon (NM_010130, exon 4 of 22)	exon (NM_010130, exon 4 of 22)	43854	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_140236.1	chr17	84119436	84119450	+	1	NA	Intergenic	Intergenic	40783	NR_045458	74473	Mm.399575	NR_045458		4933433H22Rik	-	RIKEN cDNA 4933433H22 gene	ncRNA
mm_118510.1	chr14	14013530	14013574	+	1	NA	intron (NM_139227, intron 2 of 11)	intron (NM_139227, intron 2 of 11)	1061	NM_139227	246103	Mm.133625	NM_139227	ENSMUSG00000021738	Atxn7	A430107N12Rik|AI627028|Sca7|ataxin-7	ataxin 7	protein-coding
mm_41697.1	chr5	100845875	100845882	+	1	NA	promoter-TSS (NM_172715)	promoter-TSS (NM_172715)	-351	NM_172715	231510	Mm.271911	NM_172715	ENSMUSG00000029314	Agpat9	1-AGPAT|1-AGPAT 9|4933407I02Rik|4933408F15|A230097K15Rik|GPAT-3|Gpat3|mGPAT3	1-acylglycerol-3-phosphate O-acyltransferase 9	protein-coding
mm_9911.1	chr1	188978405	188978427	-	1	NA	intron (NM_172650, intron 14 of 17)	intron (NM_172650, intron 14 of 17)	29424	NM_172650	226823	Mm.209880	NM_172650	ENSMUSG00000026608	Kctd3	4930438A20Rik|9330185B06|E330032J19Rik|NY-REN-45	potassium channel tetramerisation domain containing 3	protein-coding
mm_45569.1	chr5	73284151	73284184	-	1	NA	promoter-TSS (NR_040689)	promoter-TSS (NR_040689)	17	NR_040689	72276	Mm.271215	NR_040687	ENSMUSG00000100175	1700025M24Rik	-	RIKEN cDNA 1700025M24 gene	ncRNA
mm_148988.1	chr19	8594148	8594154	+	1	NA	exon (NM_001164634, exon 2 of 11)	exon (NM_001164634, exon 2 of 11)	969	NM_001164635	19879	Mm.285294	NM_031194	ENSMUSG00000063796	Slc22a8	Oat3|Roct	solute carrier family 22 (organic anion transporter), member 8	protein-coding
mm_131816.1	chr16	22920340	22920357	+	1	NA	5' UTR (NM_021564, exon 1 of 8)	5' UTR (NM_021564, exon 1 of 8)	126	NM_001083904	59083	Mm.28461	NM_021564	ENSMUSG00000022871	Fetub	2310011O17Rik|AI255764|D17980|Gugu	fetuin beta	protein-coding
mm_170449.1	chr18	83707666	83707666	+	1	NA	Intergenic	IAPLTR1_Mm|LTR|ERVK	378896	NM_001081300	110796	Mm.102136	NM_001081300	ENSMUSG00000046982	Tshz1	5730407I04Rik|D18Bwg1409e|Mtsh1|NY-CO-33|Sdccag33|Tsh1|mKIAA4206|teashirt1	teashirt zinc finger family member 1	protein-coding
mm_17822.1	chr2	33887368	33887381	-	1	NA	exon (NM_175184, exon 1 of 10)	exon (NM_175184, exon 1 of 10)	572	NM_175184	72543	Mm.254914	NM_175184	ENSMUSG00000038740	Mvb12b	2610200O14Rik|2610528K11Rik|AI414895|Fam125b	multivesicular body subunit 12B	protein-coding
mm_35019.1	chr4	3875203	3875270	-	1	NA	Intergenic	CpG	-3131	NM_020021	17451	Mm.459300	NM_020021	ENSMUSG00000078365	Mos	c-mos	Moloney sarcoma oncogene	protein-coding
mm_157382.1	chrX	37945655	37945675	-	1	NA	Intergenic	Intergenic	-43895	NM_023894	104384	Mm.156958	NM_023894	ENSMUSG00000068048	Rhox9	1600026O01Rik|Gpbox|Psx2	reproductive homeobox 9	protein-coding
mm_169555.1	chr15	103411895	103411900	+	1	NA	intron (NM_028797, intron 6 of 8)	L1Md_T|LINE|L1	18530	NM_028797	74174	Mm.325325	NM_028797	ENSMUSG00000022487	Gtsf1	1700006H03Rik|Cue110	gametocyte specific factor 1	protein-coding
mm_152269.1	chr19	8818672	8818712	-	1	NA	promoter-TSS (NM_001081196)	promoter-TSS (NM_001081196)	602	NM_027412	70387	Mm.261082	NM_027412	ENSMUSG00000071660	Ttc9c	2210019E14Rik|6330408J23Rik	tetratricopeptide repeat domain 9C	protein-coding
mm_38830.1	chr4	149137600	149137625	-	1	NA	promoter-TSS (NM_027263)	promoter-TSS (NM_027263)	-12	NM_027263	69928	Mm.260893	NM_027263	ENSMUSG00000073705	Apitd1	2610040C18Rik|2810407L01Rik|CENP-S	apoptosis-inducing, TAF9-like domain 1	protein-coding
mm_58055.1	chr6	136857548	136857562	-	1	NA	promoter-TSS (NM_026639)	promoter-TSS (NM_026639)	45	NM_026639	109978	Mm.31840	NM_026639	ENSMUSG00000030217	Art4	4432404K01Rik|ARTC4|DO|DOK1	ADP-ribosyltransferase 4	protein-coding
mm_20986.1	chr2	152105368	152105387	-	1	NA	promoter-TSS (NM_029688)	promoter-TSS (NM_029688)	-147	NM_029688	76650	Mm.218639	NM_029688	ENSMUSG00000032802	Srxn1	1700127B04Rik|AI854065|AW488194|Npn3|Srx|Srx1|TX01	sulfiredoxin 1 homolog (S. cerevisiae)	protein-coding
mm_154263.1	chr19	60770013	60770023	-	1	NA	exon (NM_010123, exon 16 of 22)	exon (NM_010123, exon 16 of 22)	4367	NR_034047	100217439		NR_034047		Snora19	MBI-51	small nucleolar RNA, H/ACA box 19	snoRNA
mm_115966.1	chr13	23934211	23934225	-	1	NA	promoter-TSS (NM_175663)	promoter-TSS (NM_175663)	-62	NM_175663	319177	Mm.377879	NM_175663	ENSMUSG00000050799	Hist1h2ba	Th2b	histone cluster 1, H2ba	protein-coding
mm_113649.1	chr13	42301824	42301834	+	1	NA	5' UTR (NM_010104, exon 1 of 5)	5' UTR (NM_010104, exon 1 of 5)	353	NM_010104	13614	Mm.14543	NM_010104	ENSMUSG00000021367	Edn1	ET-1|PPET1|preproET	endothelin 1	protein-coding
mm_154261.1	chr19	60769940	60769954	-	1	NA	exon (NM_010123, exon 16 of 22)	exon (NM_010123, exon 16 of 22)	4438	NR_034047	100217439		NR_034047		Snora19	MBI-51	small nucleolar RNA, H/ACA box 19	snoRNA
mm_146252.1	chr18	77780071	77780120	+	1	NA	exon (NM_007505, exon 8 of 12)	exon (NM_007505, exon 8 of 12)	6327	NM_007505	11946	Mm.276137	NM_007505	ENSMUSG00000025428	Atp5a1	AI035633|AL022851|AL023067|Atpm|D18Ertd206e|Mom2	ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1	protein-coding
mm_43917.1	chr5	144767933	144767990	+	1	NA	promoter-TSS (NM_001081362)	promoter-TSS (NM_001081362)	-831	NM_001081362	100683	Mm.273570	NM_001081362	ENSMUSG00000045482	Trrap	AI481500	transformation/transcription domain-associated protein	protein-coding
mm_23471.1	chr3	60480536	60480557	+	1	NA	intron (NM_001253713, intron 2 of 9)	intron (NM_001253713, intron 2 of 9)	7716	NM_001253713	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_7547.1	chr1	124507716	124507724	-	1	NA	Intergenic	Lx4A|LINE|L1	-462161	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_111967.1	chr12	109675921	109675945	-	1	NA	Intergenic	L1MA6|LINE|L1	-6264	NR_030540	100124461		NR_030540	ENSMUSG00000077881	Mir882	Mirn882|mmu-mir-882	microRNA 882	ncRNA
mm_44068.1	chr5	148552378	148552393	+	1	NA	5' UTR (NM_011908, exon 1 of 5)	5' UTR (NM_011908, exon 1 of 5)	403	NM_011908	24109	Mm.21846	NM_011908	ENSMUSG00000001687	Ubl3	AW108023|HCG	ubiquitin-like 3	protein-coding
mm_158462.1	chrX	140600498	140600525	-	1	NA	promoter-TSS (NM_001077364)	promoter-TSS (NM_001077364)	11	NM_001077364	14605	Mm.22216	NM_010286	ENSMUSG00000031431	Tsc22d3	DIP|Dsip1|Gilz|TSC-22R|Tilz3	TSC22 domain family, member 3	protein-coding
mm_67566.1	chr7	81933815	81933872	-	1	NA	intron (NM_013886, intron 1 of 5)	CpG	616	NM_013886	29877	Mm.392934	NM_013886	ENSMUSG00000025104	Hdgfrp3	2700022B06Rik|HRP-3	hepatoma-derived growth factor, related protein 3	protein-coding
mm_20926.1	chr2	150855707	150855720	-	1	NA	intron (NM_024465, intron 2 of 12)	(TG)n|Simple_repeat|Simple_repeat	49018	NM_024465	76192	Mm.112632	NM_024465	ENSMUSG00000032046	Abhd12	1500011G07Rik|6330583M11Rik|AI431047|AW547313	abhydrolase domain containing 12	protein-coding
mm_79173.1	chr9	47852622	47852637	+	1	NA	3' UTR (NM_018770, exon 10 of 10)	3' UTR (NM_018770, exon 10 of 10)	-34421	NR_046048	100038460	Mm.447649	NR_046048		Gm10677	ENSMUSG00000074363	predicted gene 10677	ncRNA
mm_29256.1	chr3	107219770	107219775	-	1	NA	exon (NM_001111143, exon 2 of 9)	exon (NM_001111143, exon 2 of 9)	1960	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_102912.1	chr11	69579213	69579289	-	1	NA	promoter-TSS (NM_144824)	promoter-TSS (NM_144824)	73	NM_144824	216853	Mm.31586	NM_144824	ENSMUSG00000041346	Wrap53	BC021790|Wdr79	WD repeat containing, antisense to Trp53	protein-coding
mm_84123.1	chr9	58582074	58582090	-	1	NA	promoter-TSS (NM_009145)	promoter-TSS (NM_009145)	-158	NM_001293673	20320	Mm.15125	NM_009145	ENSMUSG00000032336	Nptn	AW554172|SDR-1|Sdfr1	neuroplastin	protein-coding
mm_80274.1	chr9	72985528	72985567	+	1	NA	promoter-TSS (NM_001286546)	promoter-TSS (NM_001286546)	43	NM_028181	72278	Mm.268475	NM_028181	ENSMUSG00000034563	Ccpg1	1700030B06Rik|1810073J13Rik|9430028F23Rik|AI426686|AI875170|CPR8|D9Ertd392e	cell cycle progression 1	protein-coding
mm_163170.1	chr11	87662717	87662727	+	1	NA	promoter-TSS (NM_172448)	promoter-TSS (NM_172448)	-365	NM_172448	207742	Mm.440230	NM_172448	ENSMUSG00000034177	Rnf43	4732452J19Rik	ring finger protein 43	protein-coding
mm_121461.1	chr14	120506246	120506258	+	1	NA	3' UTR (NM_029519, exon 2 of 2)	3' UTR (NM_029519, exon 2 of 2)	27791	NM_029519	76108	Mm.261448	NM_029519	ENSMUSG00000051615	Rap2a	5830461H18Rik	RAS related protein 2a	protein-coding
mm_136214.1	chr16	89948500	89948508	-	1	NA	intron (NM_009384, intron 2 of 27)	intron (NM_009384, intron 2 of 27)	12323	NM_009384	21844	Mm.310902	NM_009384	ENSMUSG00000002489	Tiam1	AI847750|D16Ium10|D16Ium10e	T cell lymphoma invasion and metastasis 1	protein-coding
mm_24697.1	chr3	95124452	95124465	+	1	NA	promoter-TSS (NM_016712)	promoter-TSS (NM_016712)	-56	NM_016712	50874	Mm.71935	NM_016712	ENSMUSG00000005628	Tmod4	MTMOD|Sk-Tmod	tropomodulin 4	protein-coding
mm_80893.1	chr9	99629532	99629592	+	1	NA	promoter-TSS (NM_028258)	promoter-TSS (NM_028258)	-16	NM_001311142	72507	Mm.221455	NM_028258	ENSMUSG00000037784	Dzip1l	2610524A10Rik|AI663976	DAZ interacting protein 1-like	protein-coding
mm_102356.1	chr11	58239682	58239731	-	1	NA	Intergenic	CpG	24729	NM_019440	54396	Mm.458517	NM_019440	ENSMUSG00000069874	Irgm2	AI481100|GTPI|Ifggd2|Iigp2	immunity-related GTPase family M member 2	protein-coding
mm_103754.1	chr11	80779990	80780033	-	1	NA	promoter-TSS (NM_177390)	promoter-TSS (NM_177390)	14	NM_177390	338367	Mm.151948	NM_177390	ENSMUSG00000035441	Myo1d	9930104H07Rik|AW544947|D11Ertd9e|myosin-1d	myosin ID	protein-coding
mm_92811.1	chr10	81404969	81405004	-	1	NA	exon (NM_008688, exon 8 of 10)	exon (NM_008688, exon 8 of 10)	11311	NR_106141	102465778		NR_106141	ENSMUSG00000105379	Mir1191b	mmu-mir-1191b	microRNA 1191b	ncRNA
mm_136012.1	chr16	75909250	75909254	-	1	NA	promoter-TSS (NM_023380)	promoter-TSS (NM_023380)	14	NM_023380	67742	Mm.131406	NM_023380	ENSMUSG00000022876	Samsn1	4930571B16Rik|930571B16Rik|Hacs1|SLy2	SAM domain, SH3 domain and nuclear localization signals, 1	protein-coding
mm_56268.1	chr6	90988682	90988692	-	1	NA	Intergenic	CpG	128139	NM_018815	54563	Mm.28162	NM_018815	ENSMUSG00000030091	Nup210	9830001L10|AI836801|Pom210|gp190|gp210	nucleoporin 210	protein-coding
mm_92634.1	chr10	80329427	80329482	-	1	NA	promoter-TSS (NM_139292)	promoter-TSS (NM_139292)	19	NM_008793	18551	Mm.299916	NM_008793	ENSMUSG00000020131	Pcsk4	AI647044|L21221|NEC 3|NEC3|PC4|SPC5	proprotein convertase subtilisin/kexin type 4	protein-coding
mm_97966.1	chr11	83753690	83753722	+	1	NA	promoter-TSS (NM_145432)	promoter-TSS (NM_145432)	69	NM_145432	217026	Mm.117874	NM_145432	ENSMUSG00000000976	Heatr6	2700008B19Rik|BB135312|BB249351	HEAT repeat containing 6	protein-coding
mm_95046.1	chr11	32286947	32286980	+	1	NA	promoter-TSS (NM_001033981)	promoter-TSS (NM_001033981)	-1	NM_001033981	544763	Mm.450958	NM_001033981	ENSMUSG00000073063	Hbq1b	F830116E18Rik|Hbqt1	hemoglobin, theta 1B	protein-coding
mm_159841.1	chr5	135009170	135009170	+	1	NA	promoter-TSS (NM_001190437)	promoter-TSS (NM_001190437)	18	NM_001190437	68758	Mm.389700	NM_145215	ENSMUSG00000040532	Abhd11	1110054D16Rik|A630008N09Rik|Wbscr21	abhydrolase domain containing 11	protein-coding
mm_116705.1	chr13	50991328	50991337	-	1	NA	Intergenic	Intergenic	109395	NR_029463	77428	Mm.405630	NR_029463		9430083A17Rik	-	RIKEN cDNA 9430083A17 gene	ncRNA
mm_64818.1	chr7	7298387	7298456	-	1	NA	promoter-TSS (NR_049193)	promoter-TSS (NR_049193)	415	NM_001302387	12727	Mm.297883	NM_011334	ENSMUSG00000000605	Clcn4	Clc4-2|Clcn4-2	chloride channel, voltage-sensitive 4	protein-coding
mm_135536.1	chr16	49770806	49770817	-	1	NA	Intergenic	Intergenic	71517	NM_028680	73916	Mm.241276	NM_028680	ENSMUSG00000032965	Ift57	4833420A15Rik|Esrrbl1|Hippi|MHS4R2	intraflagellar transport 57	protein-coding
mm_75718.1	chr8	69019842	69019852	-	1	NA	Intergenic	RMER20B|LTR|ERVK	-68889	NM_007509	11966	Mm.249096	NM_007509	ENSMUSG00000006273	Atp6v1b2	AI194269|AI790362|Atp6b2|HO57|R74844	ATPase, H+ transporting, lysosomal V1 subunit B2	protein-coding
mm_172706.1	chr8	65710831	65710831	-	1	NA	intron (NM_175188, intron 1 of 7)	L1Md_T|LINE|L1	92306	NM_175188	72925	Mm.380457	NM_175188	ENSMUSG00000036469	March1	2900024D24Rik|BB085186	membrane-associated ring finger (C3HC4) 1	protein-coding
mm_13730.1	chr2	117966090	117966098	+	1	NA	intron (NR_126479, intron 8 of 9)	intron (NR_126479, intron 8 of 9)	144166	NR_040631	73938	Mm.399107	NR_040631	ENSMUSG00000086221	4930412B13Rik	-	RIKEN cDNA 4930412B13 gene	ncRNA
mm_125764.1	chr15	74516392	74516434	+	1	NA	5' UTR (NM_174991, exon 1 of 31)	5' UTR (NM_174991, exon 1 of 31)	217	NM_174991	107831	Mm.43133	NM_174991	ENSMUSG00000034730	Adgrb1	B830018M07Rik|Bai1|R75078|mKIAA4089	adhesion G protein-coupled receptor B1	protein-coding
mm_118880.1	chr14	25869623	25869629	+	1	NA	intron (NM_013469, intron 2 of 14)	intron (NM_013469, intron 2 of 14)	27471	NM_013469	11744	Mm.294083	NM_013469	ENSMUSG00000021866	Anxa11	A830099O17Rik|Anx11	annexin A11	protein-coding
mm_133214.1	chr16	75855713	75855729	+	1	NA	Intergenic	Intergenic	53545	NM_023380	67742	Mm.131406	NM_023380	ENSMUSG00000022876	Samsn1	4930571B16Rik|930571B16Rik|Hacs1|SLy2	SAM domain, SH3 domain and nuclear localization signals, 1	protein-coding
mm_155842.1	chrX	101254154	101254171	+	1	NA	promoter-TSS (NM_018789)	promoter-TSS (NM_018789)	-366	NM_018789	54601	Mm.240299	NM_018789	ENSMUSG00000042903	Foxo4	Afxh|Mllt7|afx	forkhead box O4	protein-coding
mm_114629.1	chr13	76130269	76130295	+	1	NA	exon (NM_001081352, exon 19 of 44)	exon (NM_001081352, exon 19 of 44)	31548	NM_001081352	218343	Mm.277964	NM_001081352	ENSMUSG00000033991	Ttc37	mKIAA0372	tetratricopeptide repeat domain 37	protein-coding
mm_3079.1	chr1	134325545	134325551	+	1	NA	intron (NM_001144855, intron 8 of 28)	RLTRETN_Mm|LTR|ERVK	7380	NM_001144855	68507	Mm.295105	NM_001144855	ENSMUSG00000026458	Ppfia4	100042382|1110008G13Rik|AI448359|AI852265|C81506|Gm3812	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 4	protein-coding
mm_65657.1	chr7	28137519	28137539	-	1	NA	exon (NM_001164655, exon 4 of 20)	exon (NM_001164655, exon 4 of 20)	8063	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_115321.1	chr13	112427747	112427755	+	1	NA	Intergenic	Intergenic	-36319	NM_010560	16195	Mm.4364	NM_010560	ENSMUSG00000021756	Il6st	5133400A03Rik|AA389424|BB405851|CD130|D13Ertd699e|gp130	interleukin 6 signal transducer	protein-coding
mm_151453.1	chr19	57804672	57804677	+	1	NA	intron (NM_181415, intron 26 of 28)	(T)n|Simple_repeat|Simple_repeat	193640	NM_181415	226255	Mm.245340	NM_181415	ENSMUSG00000054843	Atrnl1	AI504415|AW555641|Alp|Atrnl|Atrnlp	attractin like 1	protein-coding
mm_33918.1	chr4	136495598	136495601	+	1	NA	intron (NM_024452, intron 1 of 4)	PB1D9|SINE|Alu	25838	NM_024452	269593	Mm.485824	NM_024452	ENSMUSG00000001089	Luzp1	2700072H04Rik|AI266952|Luzp|mFLJ00226	leucine zipper protein 1	protein-coding
mm_46815.1	chr5	113138154	113138177	-	1	NA	5' UTR (NM_001347397, exon 1 of 8)	5' UTR (NM_001347397, exon 1 of 8)	420	NM_001347397	243219	Mm.160131	NM_172884	ENSMUSG00000051339	2900026A02Rik	8430408O14Rik|A530094D01|AW539426|Gm449|Kiaa1671|mKIAA1671	RIKEN cDNA 2900026A02 gene	protein-coding
mm_21937.1	chr2	167060055	167060069	-	1	NA	exon (NM_001033196, exon 2 of 14)	exon (NM_001033196, exon 2 of 14)	-2872	NR_138563	68949	Mm.391959	NM_001081005		Zfas1	1500012F01Rik|Zfos1	zinc finger, NFX1-type containing 1, antisense RNA 1	ncRNA
mm_126880.1	chr15	89453699	89453761	+	1	NA	promoter-TSS (NM_021921)	promoter-TSS (NM_021921)	-181	NM_021921	60597	Mm.173337	NM_021921	ENSMUSG00000022619	Mapk8ip2	3230402N03Rik|AI847694|AW049958|IB2|Jip2|R75148	mitogen-activated protein kinase 8 interacting protein 2	protein-coding
mm_73512.1	chr8	107368778	107368791	+	1	NA	exon (NM_018823, exon 13 of 15)	exon (NM_018823, exon 13 of 15)	34421	NM_008706	18104	Mm.252	NM_008706	ENSMUSG00000003849	Nqo1	AV001255|Dia4|Dtd|Nmo-1|Nmo1|Nmor1|Ox-1|Ox1|Qr1	NAD(P)H dehydrogenase, quinone 1	protein-coding
mm_100831.1	chr11	5444780	5444823	-	1	NA	promoter-TSS (NM_001080924)	promoter-TSS (NM_001080924)	46	NM_001080924	407821	Mm.216313	NM_001080924	ENSMUSG00000041961	Znrf3	Gm1167	zinc and ring finger 3	protein-coding
mm_97268.1	chr11	75765289	75765299	+	1	NA	3' UTR (NM_009536, exon 6 of 6)	3' UTR (NM_009536, exon 6 of 6)	-30515	NR_136933	102641247	Mm.411386	NR_136932		Gm12339	OTTMUSG00000006218	predicted gene 12339	ncRNA
mm_111565.1	chr12	101718408	101718423	-	1	NA	5' UTR (NM_001082976, exon 1 of 12)	5' UTR (NM_001082976, exon 1 of 12)	108	NM_001082976	74413	Mm.275939	NM_028924	ENSMUSG00000021187	Tc2n	4933406D09Rik|Mtac2d1|Tac2-N	tandem C2 domains, nuclear	protein-coding
mm_29011.1	chr3	101604656	101604689	-	1	NA	promoter-TSS (NM_144900)	promoter-TSS (NM_144900)	35	NM_144900	11928	Mm.193670	NM_144900	ENSMUSG00000033161	Atp1a1	Atpa-1|BC010319	ATPase, Na+/K+ transporting, alpha 1 polypeptide	protein-coding
mm_119890.1	chr14	54936481	54936534	+	1	NA	promoter-TSS (NM_026066)	promoter-TSS (NM_026066)	10	NM_029390	67272	Mm.41614	NM_026066	ENSMUSG00000040759	Cmtm5	1500005P16Rik|2900052H21Rik|Cklfsf5	CKLF-like MARVEL transmembrane domain containing 5	protein-coding
mm_32558.1	chr4	109475831	109475850	+	1	NA	intron (NM_013876, intron 1 of 2)	intron (NM_013876, intron 1 of 2)	665	NM_013876	29864	Mm.392580	NM_013876	ENSMUSG00000028557	Rnf11	-	ring finger protein 11	protein-coding
mm_40391.1	chr5	52783059	52783091	+	1	NA	promoter-TSS (NM_030185)	promoter-TSS (NM_030185)	20	NM_030185	78796	Mm.266886	NM_030185	ENSMUSG00000029179	Zcchc4	4930449I23Rik	zinc finger, CCHC domain containing 4	protein-coding
mm_153959.1	chr19	47692090	47692096	-	1	NA	promoter-TSS (NM_007732)	promoter-TSS (NM_007732)	-51	NM_001290825	12821	Mm.1225	NM_007732	ENSMUSG00000025064	Col17a1	BP180|Bpag|Bpag2	collagen, type XVII, alpha 1	protein-coding
mm_9715.1	chr1	179803194	179803214	-	1	NA	intron (NM_026375, intron 1 of 35)	CpG	811	NM_026375	226747	Mm.128165	NM_026375	ENSMUSG00000026491	Ahctf1	6230412P20Rik|AV011447|Elys	AT hook containing transcription factor 1	protein-coding
mm_137043.1	chr17	17909468	17909468	+	1	NA	Intergenic	Intergenic	21644	NM_008039	14289	Mm.378918	NM_008039	ENSMUSG00000052270	Fpr2	E330010I07Rik|Fpr-rs2	formyl peptide receptor 2	protein-coding
mm_116035.1	chr13	26770096	26770104	-	1	NA	promoter-TSS (NM_008232)	promoter-TSS (NM_008232)	65	NM_008232	15192	Mm.7411	NM_008232	ENSMUSG00000045835	Hdgfl1	4921520N01Rik|HRP-1|Hdgfrp1|Pwwp1	hepatoma derived growth factor-like 1	protein-coding
mm_165032.1	chr19	34248687	34248702	-	1	NA	intron (NM_007392, intron 3 of 8)	intron (NM_007392, intron 3 of 8)	6679	NM_007392	11475	Mm.213025	NM_007392	ENSMUSG00000035783	Acta2	0610041G09Rik|Actvs|SMalphaA|a-SMA|alphaSMA	actin, alpha 2, smooth muscle, aorta	protein-coding
mm_113738.1	chr13	44592699	44592709	+	1	NA	Intergenic	Intergenic	-138070	NM_021878	16468	Mm.25059	NM_021878	ENSMUSG00000038518	Jarid2	Jmj|jumonji	jumonji, AT rich interactive domain 2	protein-coding
mm_83937.1	chr9	56636365	56636377	-	1	NA	promoter-TSS (NM_001311076)	promoter-TSS (NM_001311076)	-723	NM_001311076	235402	Mm.246605	NM_181074	ENSMUSG00000049556	Lingo1	4930471K13Rik|AV148400|LERN1|LINGO-1|Lrrn6a|UNQ201	leucine rich repeat and Ig domain containing 1	protein-coding
mm_44929.1	chr5	36152929	36152958	-	1	NA	intron (NM_030889, intron 3 of 26)	intron (NM_030889, intron 3 of 26)	-51078	NM_175249	76943	Mm.44242	NM_175249	ENSMUSG00000043430	Psapl1	2310020A21Rik	prosaposin-like 1	protein-coding
mm_104135.1	chr11	86867646	86867660	-	1	NA	intron (NR_106195, intron 4 of 8)	intron (NR_106195, intron 4 of 8)	-59993	NM_026191	67487	Mm.260627	NM_026191	ENSMUSG00000018425	Dhx40	2410016C14Rik|ARG147|DDX40|PAD	DEAH (Asp-Glu-Ala-His) box polypeptide 40	protein-coding
mm_57798.1	chr6	129284477	129284488	-	1	NA	Intergenic	Intergenic	-9113	NM_001033122	12515	Mm.74745	NM_001033122	ENSMUSG00000030156	Cd69	5830438K24Rik|AI452015|AIM|VEA	CD69 antigen	protein-coding
mm_2753.1	chr1	128787550	128787581	+	1	NA	Intergenic	Intergenic	-195266	NM_009911	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding
mm_167093.1	chr7	107665365	107665381	+	1	NA	intron (NM_001163557, intron 3 of 25)	intron (NM_001163557, intron 3 of 25)	58529	NM_001163557	19024	Mm.2817	NM_008905	ENSMUSG00000036528	Ppfibp2	Cclp1	PTPRF interacting protein, binding protein 2 (liprin beta 2)	protein-coding
mm_11455.1	chr2	32162379	32162410	+	1	NA	intron (NM_172661, intron 1 of 29)	RSINE1|SINE|B4	11246	NM_001159634	227723	Mm.25504	NM_172661	ENSMUSG00000039262	Prrc2b	5830434P21Rik|AI173903|Bat2l|Bat2l1|D430039P21|mKIAA0515	proline-rich coiled-coil 2B	protein-coding
mm_122943.1	chr14	54965436	54965461	-	1	NA	exon (NM_010856, exon 3 of 39)	exon (NM_010856, exon 3 of 39)	1159	NM_001164171	17888	Mm.290003	NM_010856	ENSMUSG00000040752	Myh6	A830009F23Rik|AA517445|Myhc-a|Myhca|alpha-MHC	myosin, heavy polypeptide 6, cardiac muscle, alpha	protein-coding
mm_19873.1	chr2	114048181	114048214	-	1	NA	exon (NM_009608, exon 6 of 7)	exon (NM_009608, exon 6 of 7)	4678	NM_009608	11464	Mm.686	NM_009608	ENSMUSG00000068614	Actc1	Actc-1	actin, alpha, cardiac muscle 1	protein-coding
mm_166976.1	chr7	45103230	45103236	-	1	NA	5' UTR (NM_010189, exon 2 of 7)	5' UTR (NM_010189, exon 2 of 7)	589	NM_010189	14132	Mm.3303	NM_010189	ENSMUSG00000003420	Fcgrt	FcRn	Fc receptor, IgG, alpha chain transporter	protein-coding
mm_71814.1	chr8	68884435	68884451	+	1	NA	intron (NM_008509, intron 1 of 9)	intron (NM_008509, intron 1 of 9)	3888	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_79496.1	chr9	57096747	57096772	+	1	NA	exon (NM_011378, exon 7 of 22)	exon (NM_011378, exon 7 of 22)	20383	NM_011378	20466	Mm.15755	NM_011378	ENSMUSG00000042557	Sin3a	AW553200|Sin3|mKIAA4126|mSin3A	transcriptional regulator, SIN3A (yeast)	protein-coding
mm_121947.1	chr14	24176689	24176699	-	1	NA	exon (NM_027726, exon 6 of 31)	exon (NM_027726, exon 6 of 31)	69226	NM_001163513	71228	Mm.68971	NM_027726	ENSMUSG00000021782	Dlg5	4933429D20Rik|T25557|mKIAA0583	discs, large homolog 5 (Drosophila)	protein-coding
mm_171390.1	chr4	122141697	122141697	+	1	NA	Intergenic	RLTR10C|LTR|ERVK	-519572	NM_001099309	666927	Mm.465133	NM_001099309	ENSMUSG00000078575	Gm12887	OTTMUSG00000008910	predicted gene 12887	protein-coding
mm_122628.1	chr14	51145728	51145738	-	1	NA	exon (NM_011271, exon 2 of 2)	exon (NM_011271, exon 2 of 2)	1034	NM_011271	19752	Mm.235538	NM_011271	ENSMUSG00000035896	Rnase1	AI574248|Rib-1|Rib1	ribonuclease, RNase A family, 1 (pancreatic)	protein-coding
mm_136590.1	chr17	4995903	4995959	+	1	NA	exon (NM_001085355, exon 1 of 20)	exon (NM_001085355, exon 1 of 20)	857	NM_001085355	239985	Mm.133401	NM_001085355	ENSMUSG00000069729	Arid1b	8030481M12|9330189K18Rik|AI836955|Ardi1b|B230217J03Rik|mKIAA1235	AT rich interactive domain 1B (SWI-like)	protein-coding
mm_19234.1	chr2	84712023	84712023	-	1	NA	intron (NM_144887, intron 1 of 11)	intron (NM_144887, intron 1 of 11)	3141	NM_144887	228136	Mm.288508	NM_144887	ENSMUSG00000034075	Zdhhc5	1110032A17Rik|AI451382|Zisp	zinc finger, DHHC domain containing 5	protein-coding
mm_42944.1	chr5	122990759	122990769	+	1	NA	intron (NR_045820, intron 1 of 2)	intron (NR_045820, intron 1 of 2)	1410	NR_045820	109202	Mm.30769	NM_175405	ENSMUSG00000056735	A930024E05Rik	-	RIKEN cDNA A930024E05 gene	ncRNA
mm_154754.1	chrX	10717440	10717450	+	1	NA	promoter-TSS (NM_001166635)	promoter-TSS (NM_001166635)	80	NM_001166635	68041	Mm.29429	NM_026524	ENSMUSG00000008035	Mid1ip1	3110038L01Rik|Mig12|S14R	Mid1 interacting protein 1 (gastrulation specific G12-like (zebrafish))	protein-coding
mm_57708.1	chr6	128583868	128583868	-	1	NA	Intergenic	GA-rich|Low_complexity|Low_complexity	-2262	NM_001001179	232400	Mm.259234	NM_001001179	ENSMUSG00000047228	BC048546	Ovos	cDNA sequence BC048546	protein-coding
mm_153247.1	chr19	36264179	36264185	-	1	NA	Intergenic	Intergenic	-114885	NM_029508	76073	Mm.259180	NM_029508	ENSMUSG00000024805	Pcgf5	0610009F02Rik|1110054A01Rik|5830406C17Rik|5830443C21Rik|9530023M17Rik|AI324127	polycomb group ring finger 5	protein-coding
mm_99171.1	chr11	100846270	100846277	+	1	NA	intron (NM_001113563, intron 1 of 18)	intron (NM_001113563, intron 1 of 18)	4312	NM_001113563	20851	Mm.34064	NM_011489	ENSMUSG00000020919	Stat5b	-	signal transducer and activator of transcription 5B	protein-coding
mm_82610.1	chr9	21615863	21615879	-	1	NA	promoter-TSS (NM_001174078)	promoter-TSS (NM_001174078)	-298	NM_011417	20586	Mm.286593	NM_011417	ENSMUSG00000032187	Smarca4	Brg1|HP1-BP72|SNF2beta|SW1/SNF|b2b508.1Clo|b2b692Clo	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	protein-coding
mm_39040.1	chr4	152332410	152332434	-	1	NA	exon (NM_001277113, exon 4 of 4)	exon (NM_001277113, exon 4 of 4)	-6229	NM_029216	269610	Mm.40192	NM_029216	ENSMUSG00000005045	Chd5	4930532L22Rik|AW060752|B230399N07Rik|CHD-5	chromodomain helicase DNA binding protein 5	protein-coding
mm_5272.1	chr1	18223571	18223582	-	1	NA	promoter-TSS (NR_002879)	promoter-TSS (NR_002879)	-12	NR_002879	654454	Mm.383637	NR_002879	ENSMUSG00000070977	Defb44-ps	Defb44|Defb49|Defb49-ps|EG574082	defensin beta 44, pseudogene	pseudo
mm_110454.1	chr12	51673602	51673609	-	1	NA	intron (NM_052973, intron 1 of 17)	RMER19B|LTR|ERVK	-17361	NM_001329699	11782	Mm.386749	NM_021710	ENSMUSG00000020955	Ap4s1	AI314282	adaptor-related protein complex AP-4, sigma 1	protein-coding
mm_147626.1	chr18	58168356	58168360	-	1	NA	intron (NM_010181, intron 5 of 64)	intron (NM_010181, intron 5 of 64)	41568	NM_010181	14119	Mm.20271	NM_010181	ENSMUSG00000024598	Fbn2	BC063774|Fib-2|mKIAA4226|sne|sy	fibrillin 2	protein-coding
mm_15426.1	chr2	157086999	157087041	+	1	NA	promoter-TSS (NM_001177439)	promoter-TSS (NM_001177439)	-35	NM_001177439	383766	Mm.480305	NM_001177439	ENSMUSG00000074628	Tldc2	Gm1332	TBC/LysM associated domain containing 2	protein-coding
mm_72898.1	chr8	90876357	90876365	+	1	NA	intron (NM_177224, intron 2 of 39)	intron (NM_177224, intron 2 of 39)	47526	NM_177224	109151	Mm.100615	NM_177224	ENSMUSG00000056608	Chd9	1810014J18Rik|9030205D12Rik|A330063D19Rik|AD013|PRIC320|mKIAA0308	chromodomain helicase DNA binding protein 9	protein-coding
mm_23450.1	chr3	60031755	60031771	+	1	NA	promoter-TSS (NM_023383)	promoter-TSS (NM_023383)	-25	NM_023383	67758	Mm.24547	NM_023383	ENSMUSG00000027761	Aadac	5033417E09Rik|AI265437|Aada	arylacetamide deacetylase (esterase)	protein-coding
mm_59882.1	chr7	30292002	30292012	+	1	NA	intron (NM_001081114, intron 1 of 13)	intron (NM_001081114, intron 1 of 13)	254	NM_001081114	76686	Mm.159258	NM_001081114	ENSMUSG00000013921	Clip3	1500005P14Rik|AI844915|Clipr-59	CAP-GLY domain containing linker protein 3	protein-coding
mm_92132.1	chr10	65908228	65908258	-	1	NA	Intergenic	RLTR13D5|LTR|ERVK	215821	NR_038039	69433	Mm.23366	NR_038039	ENSMUSG00000100000	1700023F02Rik	AV205046	RIKEN cDNA 1700023F02 gene	ncRNA
mm_34216.1	chr4	140971872	140971888	+	1	NA	intron (NM_023374, intron 3 of 7)	intron (NM_023374, intron 3 of 7)	10609	NM_023374	67680	Mm.246965	NM_023374	ENSMUSG00000009863	Sdhb	0710008N11Rik	succinate dehydrogenase complex, subunit B, iron sulfur (Ip)	protein-coding
mm_133526.1	chr16	90924830	90924850	+	1	NA	TTS (NM_026502)	TTS (NM_026502)	10009	NM_026502	68001	Mm.45374	NM_026502	ENSMUSG00000022972	1110004E09Rik	-	RIKEN cDNA 1110004E09 gene	protein-coding
mm_10062.1	chr1	193370261	193370287	-	1	NA	promoter-TSS (NM_144817)	promoter-TSS (NM_144817)	8	NM_144817	215303	Mm.40329	NM_144817	ENSMUSG00000016179	Camk1g	CLICK-III|CaMKIgamma	calcium/calmodulin-dependent protein kinase I gamma	protein-coding
mm_106658.1	chr11	121229039	121229103	-	1	NA	promoter-TSS (NM_001254735)	promoter-TSS (NM_001254735)	-131	NM_001254735	217370	Mm.27182	NM_144832	ENSMUSG00000039294	BC017643	-	cDNA sequence BC017643	protein-coding
mm_150269.1	chr19	34232630	34232662	+	1	NA	intron (NM_029682, intron 5 of 10)	RLTR11C_MM|LTR|ERVK	22727	NM_007392	11475	Mm.213025	NM_007392	ENSMUSG00000035783	Acta2	0610041G09Rik|Actvs|SMalphaA|a-SMA|alphaSMA	actin, alpha 2, smooth muscle, aorta	protein-coding
mm_146227.1	chr18	77070737	77070744	+	1	NA	intron (NM_001164170, intron 1 of 12)	intron (NM_001164170, intron 1 of 12)	5060	NM_001164168	17344	Mm.6370	NM_008602	ENSMUSG00000025423	Pias2	6330408K17Rik|AI462206|ARIP3|AU018068|Dib|Miz1|PIASxalpha|PIASxb|PIASxbeta|SIZ2	protein inhibitor of activated STAT 2	protein-coding
mm_167828.1	chr9	124423582	124423643	-	1	NA	promoter-TSS (NR_015516)	promoter-TSS (NR_015516)	-175	NR_102721	75135	Mm.476814	NR_015516		4930526I15Rik	1600027J15Rik	RIKEN cDNA 4930526I15 gene	ncRNA
mm_155431.1	chrX	73493195	73493214	+	1	NA	exon (NM_007542, exon 7 of 8)	exon (NM_007542, exon 7 of 8)	9603	NM_007542	12111	Mm.2608	NM_007542	ENSMUSG00000031375	Bgn	BG|DSPG1|PG-S1|PGI|SLRR1A	biglycan	protein-coding
mm_93123.1	chr10	91171526	91171610	-	1	NA	promoter-TSS (NM_001080132)	promoter-TSS (NM_001080132)	51	NM_001080132	21917	Mm.159684	NM_011605	ENSMUSG00000019961	Tmpo	5630400D24Rik|AI195756|AI606875|AW214352|AW547477|LAP2|TP	thymopoietin	protein-coding
mm_119886.1	chr14	54924824	54924839	+	1	NA	intron (NM_010112, intron 1 of 5)	intron (NM_010112, intron 1 of 5)	1957	NM_010112	13644	Mm.236438	NM_010112	ENSMUSG00000022203	Efs	-	embryonal Fyn-associated substrate	protein-coding
mm_33136.1	chr4	125052750	125052778	+	1	NA	exon (NM_145552, exon 13 of 16)	exon (NM_145552, exon 13 of 16)	12893	NM_175223	75563	Mm.50304	NM_175223	ENSMUSG00000042707	Dnali1	1700023A09Rik|AW049135	dynein, axonemal, light intermediate polypeptide 1	protein-coding
mm_100729.1	chr11	3931589	3931599	-	1	NA	intron (NM_001130458, intron 1 of 9)	intron (NM_001130458, intron 1 of 9)	367	NM_001130459	21452	Mm.20948	NM_015749	ENSMUSG00000020432	Tcn2	AW208754|Tcn-2	transcobalamin 2	protein-coding
mm_100441.1	chr11	119486403	119486478	+	1	NA	Intergenic	Intergenic	-4907	NM_001164636	338371	Mm.271946	NM_177394	ENSMUSG00000039850	Endov	A730011L01Rik	endonuclease V	protein-coding
mm_137636.1	chr17	28330494	28330497	+	1	NA	intron (NM_011287, intron 4 of 5)	intron (NM_011287, intron 4 of 5)	2024	NM_011287	19896	Mm.336955	NM_011287	ENSMUSG00000037805	Rpl10a	CsA-19|Nedd6	ribosomal protein L10A	protein-coding
mm_134507.1	chr16	19063591	19063599	-	1	NA	Intergenic	Intergenic	186845	NM_010435	15260	Mm.15694	NM_010435	ENSMUSG00000022702	Hira	AA138857|D16Ertd95e|Gm15797|N28177|OTTMUSG00000026264|Tuple1	histone cell cycle regulator	protein-coding
mm_83680.1	chr9	50447900	50447921	-	1	NA	Intergenic	Charlie2b|DNA|hAT-Charlie	-46615	NM_029639	76509	Mm.29959	NM_029639	ENSMUSG00000032068	Plet1	0610037B23Rik|1600029D21Rik|AA407923|AU043048	placenta expressed transcript 1	protein-coding
mm_130380.1	chr15	97844913	97844935	-	1	NA	promoter-TSS (NM_001204278)	promoter-TSS (NM_001204278)	-422	NM_001204278	56233	Mm.384027	NM_019572	ENSMUSG00000022475	Hdac7	5830434K02Rik|HD7|HD7a|Hdac7a|mFLJ00062	histone deacetylase 7	protein-coding
mm_158893.1	chr1	21349643	21349643	+	1	NA	promoter-TSS (NM_183322)	promoter-TSS (NM_183322)	-34	NM_183322	368204	Mm.26006	NM_183322	ENSMUSG00000067750	Khdc1a	AU014713|C88118|Ndg1	KH domain containing 1A	protein-coding
mm_154176.1	chr19	58734940	58734954	-	1	NA	exon (NM_018874, exon 8 of 13)	exon (NM_018874, exon 8 of 13)	6060	NM_018874	18946	Mm.10753	NM_018874	ENSMUSG00000042179	Pnliprp1	Plrp1	pancreatic lipase related protein 1	protein-coding
mm_120854.1	chr14	75224137	75224150	+	1	NA	exon (NM_001247984, exon 14 of 16)	exon (NM_001247984, exon 14 of 16)	-18144	NM_019775	56373	Mm.24242	NM_019775	ENSMUSG00000021999	Cpb2	1110032P04Rik|4930405E17Rik|AI255929|CPR|Cpu|TAFI	carboxypeptidase B2 (plasma)	protein-coding
mm_10807.1	chr2	24349880	24349886	+	1	NA	3' UTR (NM_031167, exon 5 of 5)	3' UTR (NM_031167, exon 5 of 5)	4512	NM_001039701	16181	Mm.882	NM_031167	ENSMUSG00000026981	Il1rn	F630041P17Rik|IL-1ra	interleukin 1 receptor antagonist	protein-coding
mm_95561.1	chr11	52339764	52339772	+	1	NA	Intergenic	Intergenic	-21094	NM_011694	22333	Mm.3555	NM_011694	ENSMUSG00000020402	Vdac1	AL033343|Vdac5|mVDAC1|mVDAC5	voltage-dependent anion channel 1	protein-coding
mm_148567.1	chr19	4811837	4811864	+	1	NA	promoter-TSS (NM_019869)	promoter-TSS (NM_019869)	-216	NM_019869	56275	Mm.276338	NM_019869	ENSMUSG00000006456	Rbm14	1300007E16Rik|PSP2|Sytip|p16|p16K	RNA binding motif protein 14	protein-coding
mm_154023.1	chr19	53390551	53390555	-	1	NA	promoter-TSS (NM_172429)	promoter-TSS (NM_172429)	20	NM_172429	76479	Mm.313687	NM_172429	ENSMUSG00000025024	Smndc1	2410004J23Rik|4933440I19Rik	survival motor neuron domain containing 1	protein-coding
mm_157220.1	chrX	13218621	13218656	-	1	NA	Intergenic	Intergenic	17645	NR_045430	72122	Mm.75434	NR_045429	ENSMUSG00000100714	2010308F09Rik	-	RIKEN cDNA 2010308F09 gene	ncRNA
mm_95474.1	chr11	50810590	50810592	+	1	NA	TTS (NM_013922)	TTS (NM_013922)	17140	NM_013922	30944	Mm.103674	NM_013922	ENSMUSG00000044807	Zfp354c	5330421P20Rik|AJ18|AW743325|Kid3|Tcf17l2|Znf354c|mKIAA4218	zinc finger protein 354C	protein-coding
mm_57873.1	chr6	129876660	129876677	-	1	NA	promoter-TSS (NM_133203)	promoter-TSS (NM_133203)	4	NM_133203	170733	Mm.155514	NM_133203	ENSMUSG00000014543	Klra17	Ly49q|Ly49q1	killer cell lectin-like receptor, subfamily A, member 17	protein-coding
mm_125688.1	chr15	66804158	66804205	+	1	NA	intron (NM_001029841, intron 1 of 7)	intron (NM_001029841, intron 1 of 7)	27648	NM_001029841	20491	Mm.7601	NM_009192	ENSMUSG00000022372	Sla	Slap|Slap-1	src-like adaptor	protein-coding
mm_106900.1	chr12	8012824	8012832	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	35151	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_116625.1	chr13	48922200	48922218	-	1	NA	exon (NM_001033268, exon 6 of 18)	exon (NM_001033268, exon 6 of 18)	45619	NM_001033268	218236	Mm.426571	NM_001033268	ENSMUSG00000038014	Fam120a	C9orf10|Ossa	family with sequence similarity 120, member A	protein-coding
mm_73159.1	chr8	94995705	94995748	+	1	NA	intron (NM_018882, intron 1 of 13)	intron (NM_018882, intron 1 of 13)	11327	NM_018882	14766	Mm.290834	NM_018882	ENSMUSG00000031785	Adgrg1	Cyt28|Gpr56|TM7LN4|TM7XN1	adhesion G protein-coupled receptor G1	protein-coding
mm_67052.1	chr7	67338535	67338538	-	1	NA	intron (NM_001033713, intron 2 of 11)	intron (NM_001033713, intron 2 of 11)	34322	NM_001291192	17258	Mm.132788	NM_001033713	ENSMUSG00000030557	Mef2a	A430079H05Rik	myocyte enhancer factor 2A	protein-coding
mm_124485.1	chr14	121698457	121698465	-	1	NA	promoter-TSS (NM_001081039)	promoter-TSS (NM_001081039)	-44	NM_001081039	105445	Mm.378591	NM_134074	ENSMUSG00000025558	Dock9	AA959601|AW538057|B230309H04Rik|D14Wsu89e|Zizimin1|mKIAA1058	dedicator of cytokinesis 9	protein-coding
mm_58718.1	chr7	13023355	13023367	+	1	NA	promoter-TSS (NM_011588)	promoter-TSS (NM_011588)	-791	NM_011588	21849	Mm.15701	NM_011588	ENSMUSG00000005566	Trim28	AA408787|KAP-1|KRIP-1|MommeD9|Tif1b|Tif1beta	tripartite motif-containing 28	protein-coding
mm_149468.1	chr19	11592080	11592083	+	1	NA	intron (NM_026835, intron 4 of 6)	RMER6C|LTR|ERVK	12723	NM_026835	68774	Mm.290390	NM_026835	ENSMUSG00000024679	Ms4a6d	1110058E16Rik|AI447446|Ms4a11	membrane-spanning 4-domains, subfamily A, member 6D	protein-coding
mm_51245.1	chr6	71707862	71707878	+	1	NA	5' UTR (NM_178608, exon 1 of 7)	5' UTR (NM_178608, exon 1 of 7)	189	NM_178608	52250	Mm.146332	NM_178608	ENSMUSG00000052852	Reep1	D6Ertd253e	receptor accessory protein 1	protein-coding
mm_19536.1	chr2	94438062	94438075	-	1	NA	5' UTR (NM_001305258, exon 1 of 14)	5' UTR (NM_001305258, exon 1 of 14)	118	NM_007466	11800	Mm.181824	NM_007466	ENSMUSG00000027193	Api5	AAC-11|AI196452|API-5	apoptosis inhibitor 5	protein-coding
mm_14028.1	chr2	122152752	122152762	+	1	NA	3' UTR (NM_009735, exon 4 of 4)	3' UTR (NM_009735, exon 4 of 4)	5070	NM_009735	12010	Mm.163	NM_009735	ENSMUSG00000060802	B2m	Ly-m11|beta2-m|beta2m	beta-2 microglobulin	protein-coding
mm_160567.1	chr9	56685429	56685429	-	1	NA	promoter-TSS (NM_181074)	promoter-TSS (NM_181074)	-176	NM_181074	235402	Mm.246605	NM_181074	ENSMUSG00000049556	Lingo1	4930471K13Rik|AV148400|LERN1|LINGO-1|Lrrn6a|UNQ201	leucine rich repeat and Ig domain containing 1	protein-coding
mm_58318.1	chr6	146445602	146445614	-	1	NA	intron (NM_010586, intron 2 of 55)	intron (NM_010586, intron 2 of 55)	56615	NM_010586	16439	Mm.7800	NM_010586	ENSMUSG00000030287	Itpr2	AI649341|InsP3R-2|InsP3R-5|Ip3r2|Itpr5|insP3R2	inositol 1,4,5-triphosphate receptor 2	protein-coding
mm_2793.1	chr1	130851434	130851444	+	1	NA	3' UTR (NM_011082, exon 11 of 11)	3' UTR (NM_011082, exon 11 of 11)	-14338	NM_026976	69169	Mm.46042	NM_026976	ENSMUSG00000042474	Fcmr	1810037B05Rik|Faim3|FcmuR|Toso	Fc fragment of IgM receptor	protein-coding
mm_141464.1	chr17	30576442	30576506	-	1	NA	promoter-TSS (NM_027060)	promoter-TSS (NM_027060)	-187	NM_027060	224671	Mm.41220	NM_027060	ENSMUSG00000062202	Btbd9	1700023F20Rik|4930402L05|AI464421	BTB (POZ) domain containing 9	protein-coding
mm_21778.1	chr2	164847858	164847872	-	1	NA	intron (NM_011125, intron 8 of 15)	B1F|SINE|Alu	9843	NM_011125	18830	Mm.6105	NM_011125	ENSMUSG00000017754	Pltp	Bpife|OD107	phospholipid transfer protein	protein-coding
mm_163656.1	chr13	73699511	73699512	+	1	NA	promoter-TSS (NM_027780)	promoter-TSS (NM_027780)	-315	NM_027780	71390	Mm.105251	NM_027780		Slc6a19os	5430425J12Rik	solute carrier family 6 (neurotransmitter transporter), member 19, opposite strand	protein-coding
mm_124509.1	chr14	121915808	121915863	-	1	NA	promoter-TSS (NM_182806)	promoter-TSS (NM_182806)	-61	NM_182806	110168	Mm.37405	NM_182806	ENSMUSG00000050350	Gpr18	-	G protein-coupled receptor 18	protein-coding
mm_75347.1	chr8	43320552	43320560	-	1	NA	Intergenic	B1_Mur3|SINE|Alu	-13547	NM_009556	22702	Mm.285848	NM_009556	ENSMUSG00000051176	Zfp42	Rex-1|Rex1|Zfp-42	zinc finger protein 42	protein-coding
mm_46112.1	chr5	92361305	92361314	-	1	NA	exon (NM_019494, exon 2 of 4)	exon (NM_019494, exon 2 of 4)	1968	NM_019494	56066	Mm.131723	NM_019494	ENSMUSG00000060183	Cxcl11	Cxc11|H174|I-tac|Ip9|Itac|Scyb11|Scyb9b|b-R1|betaR1	chemokine (C-X-C motif) ligand 11	protein-coding
mm_58835.1	chr7	16816300	16816361	+	1	NA	5' UTR (NM_001039878, exon 1 of 18)	5' UTR (NM_001039878, exon 1 of 18)	402	NM_173430	243853	Mm.39703	NM_173430	ENSMUSG00000048920	Fkrp	A830029B19Rik|AI842067|AI847300|LGMD1I|MDC1C	fukutin related protein	protein-coding
mm_109198.1	chr12	108636237	108636255	+	1	NA	intron (NM_001163396, intron 1 of 14)	intron (NM_001163396, intron 1 of 14)	493	NM_001163396	14026	Mm.238841	NM_007965	ENSMUSG00000021262	Evl	AI528774	Ena-vasodilator stimulated phosphoprotein	protein-coding
mm_16731.1	chr2	9175768	9175774	-	1	NA	Intergenic	Intergenic	-13744	NR_038180	73438	Mm.23558	NR_038180	ENSMUSG00000085580	1700061F12Rik	-	RIKEN cDNA 1700061F12 gene	ncRNA
mm_166075.1	chr4	136140764	136140767	+	1	NA	Intergenic	Intergenic	-3057	NM_008321	15903	Mm.110	NM_008321	ENSMUSG00000007872	Id3	Hlh462|Idb3|bHLHb25	inhibitor of DNA binding 3	protein-coding
mm_101898.1	chr11	49187053	49187076	-	1	NA	promoter-TSS (NM_172793)	promoter-TSS (NM_172793)	25	NM_172793	237754	Mm.130787	NM_172793	ENSMUSG00000040283	Btnl9	B430208I01|Btn3|D330012D11Rik	butyrophilin-like 9	protein-coding
mm_132372.1	chr16	34883433	34883441	+	1	NA	intron (NM_139300, intron 9 of 31)	L1MB7|LINE|L1	55892	NR_040536	76649	Mm.420532	NR_040536	ENSMUSG00000100593	1700119H24Rik	-	RIKEN cDNA 1700119H24 gene	ncRNA
mm_13676.1	chr2	116878673	116878682	+	1	NA	promoter-TSS (NM_026104)	promoter-TSS (NM_026104)	-14	NM_026104	67356	Mm.131623	NM_026104	ENSMUSG00000027355	Tmco5	1700095F04Rik|Tmco5a	transmembrane and coiled-coil domains 5	protein-coding
mm_99108.1	chr11	100133679	100133699	+	1	NA	exon (NM_008469, exon 4 of 8)	exon (NM_008469, exon 4 of 8)	2260	NM_008469	16665	Mm.440010	NM_008469	ENSMUSG00000054146	Krt15	AI528832|K15|Krt1-15	keratin 15	protein-coding
mm_34615.1	chr4	150372144	150372186	+	1	NA	intron (NM_001085492, intron 1 of 22)	CpG	90249	NM_001085492	68703	Mm.291274	NM_001085492	ENSMUSG00000039852	Rere	1110033A15Rik|AI414665|ARG|ARP|ATN1L|AW742570|Atr2|DNB1|eye<m03Jus>|eyes3|mKIAA0458	arginine glutamic acid dipeptide (RE) repeats	protein-coding
mm_151988.1	chr19	5846751	5846783	-	1	NA	Intergenic	Intergenic	-1287	NR_003513	66961	Mm.281895	NR_003513	ENSMUSG00000092274	Neat1	2310043N10Rik|VINC	nuclear paraspeckle assembly transcript 1 (non-protein coding)	ncRNA
mm_23420.1	chr3	58576725	58576736	+	1	NA	promoter-TSS (NM_001040396)	promoter-TSS (NM_001040396)	72	NM_001040396	69227	Mm.270950	NM_001040396	ENSMUSG00000075700	Selenot	2810407C02Rik|5730408P04Rik|Selt	selenoprotein T	protein-coding
mm_85741.1	chr9	108567278	108567302	-	1	NA	promoter-TSS (NM_023247)	promoter-TSS (NM_023247)	52	NM_023247	66706	Mm.29471	NM_023247	ENSMUSG00000070283	Ndufaf3	4733401H18Rik	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, assembly factor 3	protein-coding
mm_123251.1	chr14	61037938	61037998	-	1	NA	promoter-TSS (NM_001164155)	promoter-TSS (NM_001164155)	19	NM_001164155	29820	Mm.281356	NM_013869	ENSMUSG00000060548	Tnfrsf19	AL023044|AW123854|TAJ|TAJ-ALPHA|TRADE|Troy	tumor necrosis factor receptor superfamily, member 19	protein-coding
mm_71795.1	chr8	67685468	67685483	+	1	NA	Intergenic	RMER17A|LTR|ERVK	132820	NM_027626	234353	Mm.32525	NM_027626	ENSMUSG00000030465	Psd3	4931420C21Rik|AI661273|BC003498|D430018P08|EFA6D	pleckstrin and Sec7 domain containing 3	protein-coding
mm_102859.1	chr11	69399422	69399445	-	1	NA	3' UTR (NM_001017426, exon 23 of 23)	3' UTR (NM_001017426, exon 23 of 23)	-1199	NM_025915	67020	Mm.390406	NM_025915	ENSMUSG00000045377	Tmem88	2600017H02Rik	transmembrane protein 88	protein-coding
mm_114527.1	chr13	73498426	73498448	+	1	NA	intron (NM_145376, intron 5 of 13)	intron (NM_145376, intron 5 of 13)	31054	NM_145376	210992	Mm.284649	NM_145376	ENSMUSG00000021608	Lpcat1	2900035H07Rik|Aytl2|BB137372|BC005662|C87117|LPCAT|rd11	lysophosphatidylcholine acyltransferase 1	protein-coding
mm_157430.1	chrX	38566589	38566599	-	1	NA	intron (NM_001110142, intron 2 of 22)	intron (NM_001110142, intron 2 of 22)	9602	NM_028288	72584	Mm.327675	NM_028288	ENSMUSG00000031095	Cul4b	2700050M05Rik|AA409770|CUL-4B|mKIAA0695	cullin 4B	protein-coding
mm_47798.1	chr5	132499855	132499858	-	1	NA	intron (NM_177047, intron 1 of 18)	intron (NM_177047, intron 1 of 18)	42487	NM_177047	319974	Mm.409595	NM_177047	ENSMUSG00000029673	Auts2	2700063G02Rik|A730011F23Rik|D830032G16Rik	autism susceptibility candidate 2	protein-coding
mm_99091.1	chr11	99785192	99785198	+	1	NA	promoter-TSS (NM_001085548)	promoter-TSS (NM_001085548)	-5	NM_001085548	665998	Mm.425699	NM_001085548	ENSMUSG00000078262	Krtap4-9	OTTMUSG00000002198	keratin associated protein 4-9	protein-coding
mm_62740.1	chr7	111028980	111029005	+	1	NA	promoter-TSS (NM_009431)	promoter-TSS (NM_009431)	41	NM_009431	22083	Mm.255858	NM_009431	ENSMUSG00000005609	Ctr9	AA409336|Sh2bp1|Tsbp|Tsp|mKIAA0155	CTR9 homolog, Paf1/RNA polymerase II complex component	protein-coding
mm_30947.1	chr4	33077426	33077434	+	1	NA	intron (NM_008076, intron 2 of 8)	intron (NM_008076, intron 2 of 8)	14318	NM_008076	14409	Mm.6227	NM_008076	ENSMUSG00000023267	Gabrr2	-	gamma-aminobutyric acid (GABA) C receptor, subunit rho 2	protein-coding
mm_31450.1	chr4	48610489	48610507	+	1	NA	exon (NM_021436, exon 3 of 10)	exon (NM_021436, exon 3 of 10)	25305	NM_021436	230157	Mm.422686	NM_021436	ENSMUSG00000028347	Tmeff1	A830033E11|M7365|Tr1	transmembrane protein with EGF-like and two follistatin-like domains 1	protein-coding
mm_120382.1	chr14	64589690	64589753	+	1	NA	promoter-TSS (NR_029813)	promoter-TSS (NR_029813)	-936	NR_029813	387233		NR_029813	ENSMUSG00000065597	Mir124a-1	Mirn124a|Mirn124a-1	microRNA 124a-1	ncRNA
mm_116048.1	chr13	27342919	27342930	-	1	NA	Intergenic	Intergenic	-2749	NM_010088	13529	Mm.291450	NM_010088	ENSMUSG00000018259	Prl8a2	D/tPRP|DPRP|Dtprp|Ghd11|mdPRP	prolactin family 8, subfamily a, member 2	protein-coding
mm_147552.1	chr18	54956714	54956725	-	1	NA	intron (NM_175751, intron 2 of 9)	intron (NM_175751, intron 2 of 9)	33461	NM_175751	269023	Mm.192984	NM_175751	ENSMUSG00000052713	Zfp608	4932417D18Rik|D430007A19Rik|Znf608	zinc finger protein 608	protein-coding
mm_160035.1	chr6	132701048	132701048	-	1	NA	promoter-TSS (NM_207024)	promoter-TSS (NM_207024)	-41	NM_207024	387349	Mm.377911	NM_207024	ENSMUSG00000071150	Tas2r121	T2R21|Tas2r13|Tas2r21|mGR21|mT2r48	taste receptor, type 2, member 121	protein-coding
mm_3772.1	chr1	156455284	156455295	+	1	NA	intron (NM_009230, intron 3 of 15)	ORR1B1|LTR|ERVL-MaLR	19039	NM_009230	20652	Mm.28099	NM_009230	ENSMUSG00000026600	Soat1	8430426K15Rik|ACAT-1|AW550831|Acact|ald|hid	sterol O-acyltransferase 1	protein-coding
mm_58819.1	chr7	16452928	16452968	+	1	NA	5' UTR (NM_026938, exon 1 of 3)	5' UTR (NM_026938, exon 1 of 3)	169	NM_026938	69094	Mm.29633	NM_026938	ENSMUSG00000019158	Tmem160	1810008O21Rik	transmembrane protein 160	protein-coding
mm_163276.1	chr11	115730696	115730697	+	1	NA	Intergenic	Intergenic	-22099	NM_008163	14784	Mm.439649	NM_008163	ENSMUSG00000059923	Grb2	AA408164|Ash	growth factor receptor bound protein 2	protein-coding
mm_2921.1	chr1	132065763	132065764	+	1	NA	intron (NM_172510, intron 1 of 10)	intron (NM_172510, intron 1 of 10)	2299	NM_172510	213006	Mm.208445	NM_172510	ENSMUSG00000059149	Mfsd4a	A230072B04|A930031D07Rik|AI850289|Mfsd4	major facilitator superfamily domain containing 4A	protein-coding
mm_128581.1	chr15	58034277	58034287	-	1	NA	promoter-TSS (NM_029418)	promoter-TSS (NM_029418)	12	NM_029418	75758	Mm.455792	NM_029418	ENSMUSG00000101892	9130401M01Rik	AI849328	RIKEN cDNA 9130401M01 gene	protein-coding
mm_144332.1	chr18	13452000	13452004	+	1	NA	Intergenic	Intergenic	445012	NM_153087	225192	Mm.207073	NM_153087	ENSMUSG00000037346	Hrh4	AXOR35|BG26|GPCR105|GPRv53|H4|H4R|HH4R	histamine receptor H4	protein-coding
mm_114200.1	chr13	55929325	55929338	+	1	NA	Intergenic	Intergenic	-97906	NM_011097	18740	Mm.135195	NM_011097	ENSMUSG00000021506	Pitx1	Bft|P-OTX|Potx|Ptx1	paired-like homeodomain transcription factor 1	protein-coding
mm_94823.1	chr11	23269614	23269620	+	1	NA	intron (NM_001035226, intron 4 of 25)	intron (NM_001035226, intron 4 of 25)	13576	NM_134014	103573	Mm.217547	NM_134014	ENSMUSG00000020290	Xpo1	AA420417|Crm1|Exp1	exportin 1	protein-coding
mm_10617.1	chr2	19344821	19344858	+	1	NA	non-coding (NR_126563, exon 1 of 4)	non-coding (NR_126563, exon 1 of 4)	522	NR_126563	108871	Mm.107666	NR_126563		4930447M23Rik	-	RIKEN cDNA 4930447M23 gene	ncRNA
mm_64564.1	chr7	144861379	144861395	+	1	NA	promoter-TSS (NM_010202)	promoter-TSS (NM_010202)	1	NM_010202	14175	Mm.4956	NM_010202	ENSMUSG00000050917	Fgf4	Fgf-4|Fgfk|HBGF-4|Hst1|Hstf-1|KS3|hst|hst-1|kFGF	fibroblast growth factor 4	protein-coding
mm_102693.1	chr11	65745853	65745880	-	1	NA	intron (NM_009157, intron 2 of 10)	L3|LINE|CR1	-11034	NR_030417	791070		NR_030417	ENSMUSG00000076460	Mir744	Mirn744|mir-744|mmu-mir-744	microRNA 744	ncRNA
mm_92744.1	chr10	80998122	80998132	-	1	NA	intron (NM_010319, intron 1 of 3)	intron (NM_010319, intron 1 of 3)	3238	NM_001038655	14708	Mm.222496	NM_010319	ENSMUSG00000048240	Gng7	AI840417	guanine nucleotide binding protein (G protein), gamma 7	protein-coding
mm_34029.1	chr4	138075170	138075183	+	1	NA	intron (NM_001256195, intron 4 of 34)	L1M3|LINE|L1	63342	NR_126429	73563	Mm.444294	NR_126429	ENSMUSG00000084804	1700095J12Rik	-	RIKEN cDNA 1700095J12 gene	ncRNA
mm_25900.1	chr3	131111272	131111289	+	1	NA	5' UTR (NM_001276402, exon 1 of 10)	5' UTR (NM_001276402, exon 1 of 10)	983	NM_001276402	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_40466.1	chr5	53651476	53651490	+	1	NA	intron (NM_001080928, intron 8 of 10)	intron (NM_001080928, intron 8 of 10)	47105	NR_024201	19866		NR_024201	ENSMUSG00000089083	Rnu7	-	U7 small nuclear RNA	snRNA
mm_62797.1	chr7	112755686	112755690	+	1	NA	intron (NM_009346, intron 1 of 12)	intron (NM_009346, intron 1 of 12)	-3696	NM_001166585	21676	Mm.24685	NM_009346	ENSMUSG00000055320	Tead1	2610024B07Rik|B230114H05Rik|Gtrgeo5|TEAD-1|TEF-1|Tcf13|mTEF-1	TEA domain family member 1	protein-coding
mm_105042.1	chr11	100610070	100610072	-	1	NA	intron (NM_019795, intron 1 of 13)	intron (NM_019795, intron 1 of 13)	10097	NM_019795	56354	Mm.402409	NM_019795	ENSMUSG00000014195	Dnajc7	2010003F24Rik|2010004G07Rik|CCRP|Ttc2|mDj11|mTpr2	DnaJ heat shock protein family (Hsp40) member C7	protein-coding
mm_17932.1	chr2	35504334	35504337	-	1	NA	Intergenic	Intergenic	-42886	NM_001145821	14594	Mm.281124	NM_010283	ENSMUSG00000035778	Ggta1	AW108479|GALT|Gal|Ggta|Ggta-1|alpha Gal|alpha3GalT	glycoprotein galactosyltransferase alpha 1, 3	protein-coding
mm_115154.1	chr13	106283145	106283156	+	1	NA	Intergenic	Intergenic	653765	NM_029665	76582	Mm.132208	NM_029665	ENSMUSG00000042590	Ipo11	1700081H05Rik|2510001A17Rik|AI314624|AW555235|E330021B14Rik|Ranbp11	importin 11	protein-coding
mm_166124.1	chr4	153082055	153082055	+	1	NA	Intergenic	Intergenic	384515	NR_033138	330004	Mm.291863	NM_001033414		Gm833	-	predicted gene 833	ncRNA
mm_54074.1	chr6	14755137	14755146	-	1	NA	exon (NM_080464, exon 1 of 4)	exon (NM_080464, exon 1 of 4)	133	NM_080464	140491	Mm.209429	NM_080464	ENSMUSG00000042717	Ppp1r3a	GM|RG1|RGL	protein phosphatase 1, regulatory (inhibitor) subunit 3A	protein-coding
mm_91270.1	chr10	24294651	24294675	-	1	NA	intron (NM_021509, intron 10 of 11)	RMER19B|LTR|ERVK	71146	NM_021509	59012	Mm.285934	NM_021509	ENSMUSG00000020000	Moxd1	3230402N08Rik|MNCb-5203	monooxygenase, DBH-like 1	protein-coding
mm_26382.1	chr3	142568508	142568519	+	1	NA	intron (NM_001289493, intron 7 of 10)	intron (NM_001289493, intron 7 of 10)	8017	NM_001289493	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_114379.1	chr13	63240014	63240051	+	1	NA	promoter-TSS (NR_110521)	promoter-TSS (NR_110521)	3	NR_110521	72061	Mm.188105	NM_028079	ENSMUSG00000021458	2010111I01Rik	2300006M17Rik|AP-O|AW742919|Aopep|ApO|mir-23b|mir-24-1|mir-27b	RIKEN cDNA 2010111I01 gene	protein-coding
mm_97464.1	chr11	78262777	78262800	+	1	NA	exon (NM_001002004, exon 2 of 39)	exon (NM_001002004, exon 2 of 39)	1034	NM_001002004	72503	Mm.237103	NM_001002004	ENSMUSG00000010277	2610507B11Rik	AU022687|D11Bhm178e|D11Bhm179e|E1|Kiaa0100|mKIAA0100	RIKEN cDNA 2610507B11 gene	protein-coding
mm_127339.1	chr15	100598968	100599015	+	1	NA	intron (NM_001304965, intron 1 of 10)	intron (NM_001304965, intron 1 of 10)	993	NM_001304965	19009	Mm.28825	NM_010127	ENSMUSG00000009739	Pou6f1	2310038G18Rik|C79593|Emb|cns-1	POU domain, class 6, transcription factor 1	protein-coding
mm_48350.1	chr5	139325758	139325768	-	1	NA	promoter-TSS (NM_172723)	promoter-TSS (NM_172723)	-299	NM_172723	231821	Mm.297819	NM_172723	ENSMUSG00000056413	Adap1	4930431P11Rik|Centa1|GC1L|p42IP4	ArfGAP with dual PH domains 1	protein-coding
mm_113788.1	chr13	45730428	45730438	+	1	NA	intron (NM_001199305, intron 5 of 7)	intron (NM_001199305, intron 5 of 7)	222989	NM_025508	66355	Mm.290802	NM_025508	ENSMUSG00000000253	Gmpr	2310004P21Rik|AV028449|GMPR 1	guanosine monophosphate reductase	protein-coding
mm_74918.1	chr8	25548077	25548088	-	1	NA	TTS (NR_110510)	TTS (NR_110510)	8001	NR_110510	102633315	Mm.437828	NR_110510	ENSMUSG00000086134	Gm16159	OTTMUSG00000031030	predicted gene 16159	ncRNA
mm_46673.1	chr5	109016923	109016941	-	1	NA	Intergenic	Intergenic	-10496	NM_009491	22307	Mm.261598	NM_009491	ENSMUSG00000067010	Vmn2r10	V2r16|VR16	vomeronasal 2, receptor 10	protein-coding
mm_119423.1	chr14	45351053	45351084	+	1	NA	promoter-TSS (NM_019637)	promoter-TSS (NM_019637)	-118	NM_019637	56291	Mm.202561	NM_019637	ENSMUSG00000053205	Styx	0610039A20Rik|hStyxb	serine/threonine/tyrosine interaction protein	protein-coding
mm_42671.1	chr5	119671653	119671662	+	1	NA	5' UTR (NM_011535, exon 1 of 8)	5' UTR (NM_011535, exon 1 of 8)	424	NM_011535	21386	Mm.219139	NM_011535	ENSMUSG00000018604	Tbx3	D5Ertd189e	T-box 3	protein-coding
mm_167995.1	chrX	170011431	170011442	+	1	NA	Intergenic	B2_Mm1t|SINE|B2	-32519	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_128117.1	chr15	28066666	28066674	-	1	NA	Intergenic	Intergenic	-40822	NM_001081302	223435	Mm.485422	NM_001081302	ENSMUSG00000022263	Trio	6720464I07Rik|AA408740|Solo	triple functional domain (PTPRF interacting)	protein-coding
mm_157548.1	chrX	51681252	51681263	-	1	NA	promoter-TSS (NM_015819)	promoter-TSS (NM_015819)	345	NM_001077202	50786	Mm.252561	NM_015819	ENSMUSG00000062184	Hs6st2	6OST2	heparan sulfate 6-O-sulfotransferase 2	protein-coding
mm_146498.1	chr18	3281577	3281582	-	1	NA	promoter-TSS (NM_001311067)	promoter-TSS (NM_001311067)	168	NM_001110854	12916	Mm.5244	NM_013498	ENSMUSG00000063889	Crem	ICER|ICERI	cAMP responsive element modulator	protein-coding
mm_12221.1	chr2	67653991	67653995	+	1	NA	Intergenic	MLTR11A|LTR|ERVK	-21464	NR_106083	102465706		NR_106083	ENSMUSG00000098299	Mir7224	Gm27971|mmu-mir-7224	microRNA 7224	ncRNA
mm_138409.1	chr17	35067318	35067332	+	1	NA	promoter-TSS (NM_023463)	promoter-TSS (NM_023463)	0	NM_023463	68468	Mm.215096	NM_023463	ENSMUSG00000092586	Ly6g6c	1110003M04Rik|AU016360|G6c|NG24	lymphocyte antigen 6 complex, locus G6C	protein-coding
mm_5358.1	chr1	25759734	25759737	-	1	NA	intron (NM_175642, intron 2 of 30)	intron (NM_175642, intron 2 of 30)	69972	NM_175642	210933	Mm.336569	NM_175642	ENSMUSG00000033569	Adgrb3	A830096D10Rik|Bai3	adhesion G protein-coupled receptor B3	protein-coding
mm_120286.1	chr14	63133385	63133440	+	1	NA	exon (NM_007798, exon 2 of 10)	exon (NM_007798, exon 2 of 10)	10950	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_127255.1	chr15	99702279	99702312	+	1	NA	promoter-TSS (NM_031842)	promoter-TSS (NM_031842)	8	NM_031842	83797	Mm.273756	NM_031842	ENSMUSG00000023018	Smarcd1	AA407987|Baf60a|D15Kz1	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1	protein-coding
mm_132955.1	chr16	49955856	49955856	+	1	NA	Intergenic	Intergenic	-24604	NR_045001	628951	Mm.428032	NR_045001		Gm6936	-	predicted gene 6936	ncRNA
mm_162523.1	chr1	157398234	157398241	-	1	NA	intron (NM_177644, intron 1 of 17)	Lx7|LINE|L1	-14115	NR_027984	69953	Mm.286863	NM_027274	ENSMUSG00000049881	2810025M15Rik	AI429618	RIKEN cDNA 2810025M15 gene	ncRNA
mm_92960.1	chr10	85917163	85917191	-	1	NA	promoter-TSS (NM_181650)	promoter-TSS (NM_181650)	-191	NM_001302886	72843	Mm.25307	NM_181650	ENSMUSG00000035529	Prdm4	1700031E19Rik|2810470D21Rik|AW552272|SC-1|SC1	PR domain containing 4	protein-coding
mm_149520.1	chr19	12442782	12442793	+	1	NA	Intergenic	RMER1C|Other|Other	14882	NM_019540	56093	Mm.285849	NM_019540	ENSMUSG00000040065	Pfpl	Epcs5|Epcs50	pore forming protein-like	protein-coding
mm_35277.1	chr4	19922600	19922614	-	1	NA	promoter-TSS (NM_175406)	promoter-TSS (NM_175406)	-41	NM_175406	242341	Mm.19298	NM_175406	ENSMUSG00000028238	Atp6v0d2	1620401A02Rik|AI324824|V-ATPase	ATPase, H+ transporting, lysosomal V0 subunit D2	protein-coding
mm_46628.1	chr5	108448883	108448912	-	1	NA	promoter-TSS (NM_172883)	promoter-TSS (NM_172883)	-6	NM_172883	243197	Mm.106818	NM_172883	ENSMUSG00000029490	Mfsd7a	4732482E20Rik|Mfsd7	major facilitator superfamily domain containing 7A	protein-coding
mm_135578.1	chr16	50432175	50432191	-	1	NA	intron (NM_001347240, intron 1 of 16)	CpG	206	NM_027444	70508	Mm.28940	NM_027444	ENSMUSG00000022641	Bbx	5530401J07Rik|5730403O13Rik	bobby sox HMG box containing	protein-coding
mm_28289.1	chr3	89089855	89089870	-	1	NA	intron (NM_001083807, intron 2 of 9)	intron (NM_001083807, intron 2 of 9)	169	NM_001083808	72296	Mm.27687	NM_028188	ENSMUSG00000041263	Rusc1	2210403N08Rik|AA408288|NESCA	RUN and SH3 domain containing 1	protein-coding
mm_64668.1	chr7	4445569	4445575	-	1	NA	promoter-TSS (NM_001290411)	promoter-TSS (NM_001290411)	85	NM_175372	108841	Mm.413106	NM_175372	ENSMUSG00000008435	Rdh13	8430425D21Rik	retinol dehydrogenase 13 (all-trans and 9-cis)	protein-coding
mm_57129.1	chr6	122602314	122602344	-	1	NA	5' UTR (NM_031159, exon 1 of 8)	5' UTR (NM_031159, exon 1 of 8)	115	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_79266.1	chr9	50753258	50753263	+	1	NA	promoter-TSS (NM_024441)	promoter-TSS (NM_024441)	289	NM_009964	12955	Mm.178	NM_009964	ENSMUSG00000032060	Cryab	Crya-2|Crya2|HspB5|P23	crystallin, alpha B	protein-coding
mm_149590.1	chr19	16133302	16133328	+	1	NA	5' UTR (NM_008139, exon 1 of 7)	5' UTR (NM_008139, exon 1 of 7)	484	NM_008139	14682	Mm.439701	NM_008139	ENSMUSG00000024639	Gnaq	1110005L02Rik|6230401I02Rik|AA408290|AW060788|Dsk1|Dsk10|Galphaq|Gq|GqI	guanine nucleotide binding protein, alpha q polypeptide	protein-coding
mm_35426.1	chr4	35225200	35225207	-	1	NA	intron (NM_001081343, intron 1 of 10)	intron (NM_001081343, intron 1 of 10)	677	NM_001081343	73205	Mm.331544	NM_001081343	ENSMUSG00000028300	3110043O21Rik	AI840585	RIKEN cDNA 3110043O21 gene	protein-coding
mm_98256.1	chr11	88718443	88718504	+	1	NA	promoter-TSS (NM_054043)	promoter-TSS (NM_054043)	-170	NR_038058	193280	Mm.396842	NR_038058		C030037D09Rik	9330160M04	RIKEN cDNA C030037D09 gene	ncRNA
mm_43048.1	chr5	124076114	124076136	+	1	NA	exon (NM_019875, exon 9 of 12)	exon (NM_019875, exon 9 of 12)	19673	NM_019875	56325	Mm.254839	NM_019875	ENSMUSG00000029408	Abcb9	TAPL|mKIAA1520	ATP-binding cassette, sub-family B (MDR/TAP), member 9	protein-coding
mm_5404.1	chr1	33757712	33757780	-	1	NA	promoter-TSS (NM_145392)	promoter-TSS (NM_145392)	4	NM_145392	213539	Mm.247037	NM_145392	ENSMUSG00000042215	Bag2	2610042A13Rik|BC016230	BCL2-associated athanogene 2	protein-coding
mm_10892.1	chr2	25263373	25263381	+	1	NA	exon (NM_175286, exon 1 of 4)	exon (NM_175286, exon 1 of 4)	779	NM_175286	97031	Mm.308539	NM_175286	ENSMUSG00000048707	Tprn	C430004E15Rik|C87750	taperin	protein-coding
mm_162886.1	chr10	106723612	106723613	+	1	NA	intron (NM_001205341, intron 3 of 31)	MIRc|SINE|MIR	-121132	NR_131026	75833	Mm.159596	NR_131026		4930532I03Rik	-	RIKEN cDNA 4930532I03 gene	ncRNA
mm_15900.1	chr2	164960810	164960833	+	1	NA	Intergenic	CpG	-7167	NM_020333	57138	Mm.252987	NM_020333	ENSMUSG00000017740	Slc12a5	KCC2|mKIAA1176	solute carrier family 12, member 5	protein-coding
mm_15860.1	chr2	164823002	164823040	+	1	NA	TTS (NM_178375)	TTS (NM_178375)	335	NM_028028	71971	Mm.161149	NM_028028	ENSMUSG00000017764	Zswim1	2410003H12Rik|AI850991|BB046916	zinc finger SWIM-type containing 1	protein-coding
mm_151655.1	chr19	4124559	4124570	-	1	NA	intron (NM_016666, intron 1 of 6)	intron (NM_016666, intron 1 of 6)	1294	NM_016666	11632	Mm.10433	NM_016666	ENSMUSG00000024847	Aip	AA408703|AW476050|Ara9|D19Bwg1412e|Fkbp16|Xap2	aryl-hydrocarbon receptor-interacting protein	protein-coding
mm_70370.1	chr8	9977734	9977763	+	1	NA	promoter-TSS (NM_026868)	promoter-TSS (NM_026868)	31	NM_026868	68904	Mm.142570	NM_026868	ENSMUSG00000040396	Abhd13	1110065L07Rik|AI463703|AI788994	abhydrolase domain containing 13	protein-coding
mm_118079.1	chr13	103300950	103300953	-	1	NA	intron (NM_175171, intron 1 of 28)	intron (NM_175171, intron 1 of 28)	33541	NM_175171	328329	Mm.202606	NM_175171	ENSMUSG00000034751	Mast4	4930420O11Rik|AI642422|mKIAA0303	microtubule associated serine/threonine kinase family member 4	protein-coding
mm_78426.1	chr9	31280526	31280566	+	1	NA	Intergenic	Intergenic	9145	NM_001101597	638580	Mm.373655	NM_001101597		Gm7244	EG638580	predicted gene 7244	protein-coding
mm_8850.1	chr1	162709589	162709604	-	1	NA	exon (NM_001081290, exon 13 of 35)	exon (NM_001081290, exon 13 of 35)	30960	NM_001081290	226562	Mm.245446	NM_001081290	ENSMUSG00000040225	Prrc2c	1810043M20Rik|9630039I18Rik|A630006J20|Bat2d|Bat2d1|Bat2l2|E130112L15Rik|Prrc3|mKIAA1096	proline-rich coiled-coil 2C	protein-coding
mm_163621.1	chr13	55402937	55402946	+	1	NA	exon (NM_011392, exon 7 of 13)	exon (NM_011392, exon 7 of 13)	3293	NM_011392	20505	Mm.276355	NM_011392	ENSMUSG00000021490	Slc34a1	NaPi-IIa|Npt2|Npt2a|Slc17a2	solute carrier family 34 (sodium phosphate), member 1	protein-coding
mm_6410.1	chr1	72874390	72874408	-	1	NA	5' UTR (NM_010518, exon 1 of 4)	5' UTR (NM_010518, exon 1 of 4)	466	NM_010518	16011	Mm.405761	NM_010518	ENSMUSG00000026185	Igfbp5	AI256729|AW208790|IGFBP-5|IGFBP-5P	insulin-like growth factor binding protein 5	protein-coding
mm_146469.1	chr18	87757694	87757697	+	1	NA	Intergenic	Intergenic	1045630	NM_172633	12405	Mm.70775	NM_172633	ENSMUSG00000024647	Cbln2	6330593N19Rik|A730004O05	cerebellin 2 precursor protein	protein-coding
mm_144123.1	chr18	4743054	4743061	+	1	NA	Intergenic	Intergenic	-69429	NR_045881	100038439	Mm.387569	NR_045881	ENSMUSG00000097043	Gm10556	ENSMUSG00000073646	predicted gene 10556	ncRNA
mm_80782.1	chr9	95815523	95815528	+	1	NA	intron (NM_001033210, intron 1 of 15)	intron (NM_001033210, intron 1 of 15)	29754	NM_001033210	102502	Mm.11869	NM_001033210	ENSMUSG00000049493	Pls1	AI427122	plastin 1 (I-isoform)	protein-coding
mm_134.1	chr1	10059261	10059266	+	1	NA	intron (NM_026493, intron 4 of 29)	intron (NM_026493, intron 4 of 29)	21045	NM_026493	211660	Mm.244046	NM_026493	ENSMUSG00000056763	Cspp1	2310020J12Rik|4930413O22Rik|AA387550|BC055915|Cspp2|Cspp3	centrosome and spindle pole associated protein 1	protein-coding
mm_42991.1	chr5	123343957	123343970	+	1	NA	promoter-TSS (NM_029850)	promoter-TSS (NM_029850)	-485	NM_029850	77045	Mm.151960	NM_029850	ENSMUSG00000029438	Bcl7a	4432415N06Rik|AI448316	B cell CLL/lymphoma 7A	protein-coding
mm_99502.1	chr11	103027845	103027862	+	1	NA	promoter-TSS (NM_008707)	promoter-TSS (NM_008707)	-709	NM_008707	18107	Mm.10265	NM_008707	ENSMUSG00000020936	Nmt1	AW536594	N-myristoyltransferase 1	protein-coding
mm_149367.1	chr19	11362274	11362288	+	1	NA	Intergenic	Intergenic	-13207	NM_001310331	666907		NM_001310331	ENSMUSG00000101389	Ms4a4a	EG666907	membrane-spanning 4-domains, subfamily A, member 4A	protein-coding
mm_60135.1	chr7	37479889	37479893	+	1	NA	exon (NM_172385, exon 6 of 6)	exon (NM_172385, exon 6 of 6)	289861	NM_172385	243937	Mm.322505	NM_172385	ENSMUSG00000043456	Zfp536	9630010P11Rik|Znf536|mKIAA0390	zinc finger protein 536	protein-coding
mm_30235.1	chr3	146108048	146108091	-	1	NA	promoter-TSS (NM_172864)	promoter-TSS (NM_172864)	-33	NM_172864	242253	Mm.235040	NM_172864	ENSMUSG00000043020	Wdr63	4931433A13Rik	WD repeat domain 63	protein-coding
mm_7996.1	chr1	134326965	134326992	-	1	NA	intron (NM_001144855, intron 6 of 28)	intron (NM_001144855, intron 6 of 28)	5950	NM_001144855	68507	Mm.295105	NM_001144855	ENSMUSG00000026458	Ppfia4	100042382|1110008G13Rik|AI448359|AI852265|C81506|Gm3812	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 4	protein-coding
mm_120825.1	chr14	75151422	75151446	+	1	NA	intron (NM_008879, intron 1 of 16)	intron (NM_008879, intron 1 of 16)	15009	NM_008879	18826	Mm.153911	NM_008879	ENSMUSG00000021998	Lcp1	AW536232|D14Ertd310e|LCP-1|Pls2|pp65	lymphocyte cytosolic protein 1	protein-coding
mm_86813.1	chr10	20353243	20353248	+	1	NA	intron (NM_027930, intron 3 of 6)	(T)n|Simple_repeat|Simple_repeat	5426	NM_027930	71804	Mm.262151	NM_027930	ENSMUSG00000019992	Mtfr2	2610016C23Rik|4933412C16Rik|Dufd1|Fam54a	mitochondrial fission regulator 2	protein-coding
mm_132460.1	chr16	36160944	36160945	+	1	NA	intron (NM_173869, intron 2 of 2)	B3|SINE|B2	4133	NM_173869	268885	Mm.187847	NM_173869	ENSMUSG00000059657	Stfa2l1	-	stefin A2 like 1	protein-coding
mm_85490.1	chr9	106133578	106133587	-	1	NA	Intergenic	RMER15|LTR|ERVL	-20542	NR_029549	387153		NR_029549	ENSMUSG00000065407	Mir135a-1	Mir135a01|Mirn135|Mirn135a-1|mir-135a-1	microRNA 135a-1	ncRNA
mm_98627.1	chr11	96024541	96024558	+	1	NA	promoter-TSS (NM_008119)	promoter-TSS (NM_008119)	4	NM_008119	14607	Mm.248452	NM_008119	ENSMUSG00000014351	Gip	-	gastric inhibitory polypeptide	protein-coding
mm_149875.1	chr19	25182398	25182410	+	1	NA	intron (NM_028785, intron 40 of 47)	intron (NM_028785, intron 40 of 47)	-54798	NM_181404	107351	Mm.260722	NM_181404	ENSMUSG00000032702	Kank1	A930031B09Rik|AU015049|AW121052|Ankrd15|D330024H06Rik|mKIAA0172	KN motif and ankyrin repeat domains 1	protein-coding
mm_142413.1	chr17	45549656	45549668	-	1	NA	promoter-TSS (NM_001013749)	promoter-TSS (NM_001013749)	15	NM_001013749	210573	Mm.329064	NM_001013749	ENSMUSG00000096847	Tmem151b	Gm323	transmembrane protein 151B	protein-coding
mm_151041.1	chr19	47023810	47023820	+	1	NA	3' UTR (NM_146100, exon 3 of 3)	3' UTR (NM_146100, exon 3 of 3)	-8626	NM_001164363	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_43982.1	chr5	146261334	146261344	+	1	NA	intron (NM_153599, intron 2 of 12)	LSU-rRNA_Hsa|rRNA|rRNA	29664	NM_153599	264064	Mm.260576	NM_153599	ENSMUSG00000029635	Cdk8	-	cyclin-dependent kinase 8	protein-coding
mm_52364.1	chr6	112696714	112696753	+	1	NA	promoter-TSS (NM_021385)	promoter-TSS (NM_021385)	-63	NM_001167730	58186	Mm.103812	NM_021385	ENSMUSG00000030254	Rad18	2810024C04Rik|Rad18sc	RAD18 E3 ubiquitin protein ligase	protein-coding
mm_56428.1	chr6	97312045	97312055	-	1	NA	intron (NM_001346639, intron 11 of 22)	intron (NM_001346639, intron 11 of 22)	-59270	NM_001081157	320502	Mm.68163	NM_001081157	ENSMUSG00000044086	Lmod3	5430424A14Rik	leiomodin 3 (fetal)	protein-coding
mm_162608.1	chr1	183296945	183297015	-	1	NA	promoter-TSS (NM_027861)	promoter-TSS (NM_027861)	28	NM_027861	71678	Mm.392270	NM_027861	ENSMUSG00000046836	Brox	0610010K06Rik	BRO1 domain and CAAX motif containing	protein-coding
mm_158767.1	chrX	166585615	166585625	-	1	NA	promoter-TSS (NM_019397)	promoter-TSS (NM_019397)	96	NM_019397	54156	Mm.37707	NM_019397	ENSMUSG00000000402	Egfl6	Maeg	EGF-like-domain, multiple 6	protein-coding
mm_143971.1	chr17	87332024	87332041	-	1	NA	intron (NM_028639, intron 10 of 19)	intron (NM_028639, intron 10 of 19)	49146	NM_028639	225049	Mm.77396	NM_028639	ENSMUSG00000036918	Ttc7	1110035E02Rik|1700007L07Rik|Ttc7a|fsn|hea	tetratricopeptide repeat domain 7	protein-coding
mm_23439.1	chr3	59431377	59431406	+	1	NA	Intergenic	Intergenic	-87135	NM_001162884	242050	Mm.228086	NM_001162884	ENSMUSG00000036334	Igsf10	6530405F15Rik|9030224D03|AA409708|AA536958|AI414626|Adlican2|CMF608	immunoglobulin superfamily, member 10	protein-coding
mm_62876.1	chr7	114753699	114753713	+	1	NA	intron (NM_173767, intron 1 of 12)	intron (NM_173767, intron 1 of 12)	7940	NM_173767	233752	Mm.83037	NM_173767	ENSMUSG00000048782	Insc	3830422K02Rik|C730020D23	inscuteable homolog (Drosophila)	protein-coding
mm_5111.1	chr1	6214540	6214572	-	1	NA	promoter-TSS (NM_009826)	promoter-TSS (NM_009826)	-106	NM_009826	12421	Mm.293811	NM_009826	ENSMUSG00000025907	Rb1cc1	2900055E04Rik|5930404L04Rik|Cc1|FIP200|LaXp180	RB1-inducible coiled-coil 1	protein-coding
mm_10188.1	chr2	4882272	4882293	+	1	NA	intron (NM_175400, intron 1 of 8)	CpG	718	NM_175400	109079	Mm.34329	NM_175400	ENSMUSG00000026662	Sephs1	1110046B24Rik|AA589574|AI505014|AW111620|SELD|SPS|SPS1	selenophosphate synthetase 1	protein-coding
mm_33078.1	chr4	123904976	123904984	+	1	NA	promoter-TSS (NM_019660)	promoter-TSS (NM_019660)	-33	NM_019660	56309	Mm.446553	NM_019660	ENSMUSG00000028647	Mycbp	5730488M09Rik|AW552132|AW742590|Amy-1	MYC binding protein	protein-coding
mm_49354.1	chr6	21986971	21986996	+	1	NA	exon (NM_001081351, exon 1 of 22)	exon (NM_001081351, exon 1 of 22)	1073	NM_001081351	214642	Mm.221404	NM_001081351	ENSMUSG00000062980	Cped1	6720481P07|A430107O13Rik|AI552584	cadherin-like and PC-esterase domain containing 1	protein-coding
mm_21096.1	chr2	153231140	153231156	-	1	NA	3' UTR (NM_018807, exon 3 of 3)	3' UTR (NM_018807, exon 3 of 3)	-5707	NM_198617	241732	Mm.277243	NM_198617	ENSMUSG00000074671	Tspyl3	AW212607|Gm36	TSPY-like 3	protein-coding
mm_21213.1	chr2	155692356	155692364	-	1	NA	promoter-TSS (NM_001163452)	promoter-TSS (NM_001163452)	24	NM_019828	56407	Mm.234944	NM_019828	ENSMUSG00000038324	Trpc4ap	4833429F06Rik|D2Ertd113e|Trrp4ap|mFLJ00177|truss	transient receptor potential cation channel, subfamily C, member 4 associated protein	protein-coding
mm_87408.1	chr10	45807760	45807778	+	1	NA	promoter-TSS (NR_040624)	promoter-TSS (NR_040624)	65	NR_040624	320363	Mm.123343	NR_040624	ENSMUSG00000110874	D030045P18Rik	-	RIKEN cDNA D030045P18 gene	ncRNA
mm_43011.1	chr5	123809641	123809643	+	1	NA	intron (NM_001042421, intron 53 of 63)	PB1D7|SINE|Alu	55874	NM_030701	80885	Mm.440567	NM_030701	ENSMUSG00000045502	Hcar2	Gpr109a|Gpr109b|HM74|Niacr1|PUMA-G|Pumag|mHM74b	hydroxycarboxylic acid receptor 2	protein-coding
mm_81848.1	chr9	118560355	118560372	+	1	NA	exon (NM_018748, exon 16 of 24)	exon (NM_018748, exon 16 of 24)	-46346	NM_133721	104099	Mm.335520	NM_133721	ENSMUSG00000039115	Itga9	(alpha)9|2610002H11Rik|6720458D17Rik|AI461869|D130073C02|D9Ertd428e	integrin alpha 9	protein-coding
mm_21523.1	chr2	163634498	163634518	-	1	NA	exon (NM_012032, exon 4 of 10)	exon (NM_012032, exon 4 of 10)	-10342	NR_028113	68386	Mm.410649	NR_028113	ENSMUSG00000058812	0610039K10Rik	-	RIKEN cDNA 0610039K10 gene	ncRNA
mm_151830.1	chr19	5663675	5663694	-	1	NA	promoter-TSS (NM_001164482)	promoter-TSS (NM_001164482)	23	NM_001164482	20469	Mm.3072	NM_011379	ENSMUSG00000056917	Sipa1	Spa1	signal-induced proliferation associated gene 1	protein-coding
mm_109390.1	chr12	109743788	109743789	+	1	NA	promoter-TSS (NR_029914)	promoter-TSS (NR_029914)	73	NR_029914	723863		NR_029914	ENSMUSG00000065497	Mir410	Mirn410|mmu-mir-410	microRNA 410	ncRNA
mm_147235.1	chr18	38250559	38250607	-	1	NA	promoter-TSS (NR_015475)	promoter-TSS (NR_015475)	-18	NR_027904	73516	Mm.48776	NR_015475	ENSMUSG00000097080	1700086O06Rik	-	RIKEN cDNA 1700086O06 gene	ncRNA
mm_45166.1	chr5	51457746	51457757	-	1	NA	non-coding (NR_027710, exon 13 of 13)	non-coding (NR_027710, exon 13 of 13)	96170	NR_027710	19017	Mm.259072	NM_008904	ENSMUSG00000029167	Ppargc1a	A830037N07Rik|ENSMUSG00000079510|Gm11133|PGC-1|PPARGC-1-alpha|Pgc-1alpha|Pgc1|Pgco1|Ppargc1	peroxisome proliferative activated receptor, gamma, coactivator 1 alpha	protein-coding
mm_156266.1	chrX	136832062	136832077	+	1	NA	exon (NM_011123, exon 3 of 7)	exon (NM_011123, exon 3 of 7)	9323	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_122255.1	chr14	34152474	34152486	-	1	NA	promoter-TSS (NM_008919)	promoter-TSS (NM_008919)	-61	NM_008919	19065	Mm.57059	NM_008919	ENSMUSG00000048337	Npy4r	NYYR-D|Ppyr1|Y4	neuropeptide Y receptor Y4	protein-coding
mm_148698.1	chr19	5742020	5742036	+	1	NA	5' UTR (NM_008520, exon 2 of 28)	5' UTR (NM_008520, exon 2 of 28)	1124	NM_008520	16998	Mm.182396	NM_008520	ENSMUSG00000024940	Ltbp3	Ltbp2|mFLJ00070	latent transforming growth factor beta binding protein 3	protein-coding
mm_118203.1	chr13	108164084	108164087	-	1	NA	intron (NM_028042, intron 2 of 11)	intron (NM_028042, intron 2 of 11)	5347	NM_028042	71991	Mm.212208	NM_028042	ENSMUSG00000021694	Ercc8	2410022P04Rik|2810431L23Rik|4631412O06Rik|B130065P18Rik|Ckn1|Csa	excision repaiross-complementing rodent repair deficiency, complementation group 8	protein-coding
mm_10780.1	chr2	24336847	24336867	+	1	NA	promoter-TSS (NM_031167)	promoter-TSS (NM_031167)	-3	NM_031167	16181	Mm.882	NM_031167	ENSMUSG00000026981	Il1rn	F630041P17Rik|IL-1ra	interleukin 1 receptor antagonist	protein-coding
mm_20872.1	chr2	148443625	148443626	-	1	NA	promoter-TSS (NM_010740)	promoter-TSS (NM_010740)	-90	NM_010740	17064	Mm.681	NM_010740	ENSMUSG00000027435	Cd93	6030404G09Rik|AA145088|AA4.1|AW555904|C1qr1|C1qrp|Ly68	CD93 antigen	protein-coding
mm_157834.1	chrX	74274916	74274947	-	1	NA	promoter-TSS (NR_106059)	promoter-TSS (NR_106059)	-826	NR_106059	102466804		NR_106059	ENSMUSG00000099226	Mir7091	Gm27381|mmu-mir-7091	microRNA 7091	ncRNA
mm_76626.1	chr8	91801548	91801560	-	1	NA	promoter-TSS (NM_001253822)	promoter-TSS (NM_001253822)	100	NM_001253822	16373	Mm.238044	NM_008393	ENSMUSG00000031734	Irx3	AI894186	Iroquois related homeobox 3	protein-coding
mm_140767.1	chr17	17624638	17624652	-	1	NA	promoter-TSS (NM_172827)	promoter-TSS (NM_172827)	-156	NM_172827	240028	Mm.328807	NM_172827	ENSMUSG00000023845	Lnpep	2010309L07Rik|4732490P18Rik|CAP|IRAP|PLAP|gp160|vp165	leucyl/cystinyl aminopeptidase	protein-coding
mm_147213.1	chr18	37955010	37955025	-	1	NA	promoter-TSS (NM_010411)	promoter-TSS (NM_010411)	-29	NM_010411	15183	Mm.20521	NM_010411	ENSMUSG00000024454	Hdac3	AW537363	histone deacetylase 3	protein-coding
mm_4105.1	chr1	167598361	167598374	+	1	NA	promoter-TSS (NM_009107)	promoter-TSS (NM_009107)	5	NM_009107	20183	Mm.3475	NM_009107	ENSMUSG00000015843	Rxrg	Nr2b3	retinoid X receptor gamma	protein-coding
mm_146577.1	chr18	7346011	7346014	-	1	NA	Intergenic	U2|snRNA|snRNA	-48111	NM_001081393	74934	Mm.107918	NM_001081393	ENSMUSG00000061802	Armc4	4930463I21Rik|b2b227.1Clo|b2b643Clo	armadillo repeat containing 4	protein-coding
mm_16699.1	chr2	6895636	6895642	-	1	NA	intron (NM_001110229, intron 2 of 14)	intron (NM_001110229, intron 2 of 14)	-10643	NM_001160293	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_20371.1	chr2	128429158	128429166	-	1	NA	non-coding (NR_028591, exon 1 of 2)	non-coding (NR_028591, exon 1 of 2)	189	NR_028591	100043424	Mm.297222	NR_028589		Gm14005	OTTMUSG00000015351	predicted gene 14005	ncRNA
mm_65546.1	chr7	27130419	27130437	-	1	NA	exon (NM_007817, exon 7 of 10)	exon (NM_007817, exon 7 of 10)	10473	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_53877.1	chr6	149566134	149566150	+	1	NA	Intergenic	Intergenic	157158	NM_009753	12121	Mm.177181	NM_009753	ENSMUSG00000003452	Bicd1	B830009D06Rik|bic-D 1	bicaudal D homolog 1 (Drosophila)	protein-coding
mm_131079.1	chr16	4734973	4734976	+	1	NA	intron (NM_001136066, intron 1 of 5)	intron (NM_001136066, intron 1 of 5)	-6639	NM_010443	15369	Mm.272866	NM_010443	ENSMUSG00000004070	Hmox2	HO-2|HO2	heme oxygenase 2	protein-coding
mm_141659.1	chr17	33760316	33760348	-	1	NA	5' UTR (NM_008997, exon 1 of 5)	5' UTR (NM_008997, exon 1 of 5)	154	NM_008997	19326	Mm.387587	NM_008997	ENSMUSG00000077450	Rab11b	A730055L17Rik	RAB11B, member RAS oncogene family	protein-coding
mm_79904.1	chr9	65400898	65400912	+	1	NA	intron (NM_001033158, intron 1 of 4)	intron (NM_001033158, intron 1 of 4)	2417	NM_001033158	70784	Mm.35827	NM_001033158	ENSMUSG00000041696	Rasl12	4631404I11Rik	RAS-like, family 12	protein-coding
mm_73124.1	chr8	94780827	94780840	+	1	NA	3' UTR (NM_009142, exon 3 of 3)	3' UTR (NM_009142, exon 3 of 3)	8653	NM_009142	20312	Mm.103711	NM_009142	ENSMUSG00000031778	Cx3cl1	AB030188|ABCD-3|AI848747|CX3C|Cxc3|D8Bwg0439e|Scyd1	chemokine (C-X3-C motif) ligand 1	protein-coding
mm_139957.1	chr17	71552032	71552079	+	1	NA	promoter-TSS (NM_029254)	promoter-TSS (NM_029254)	-6	NM_001142631	70891	Mm.477599	NM_029254	ENSMUSG00000052525	Spdya	4921517J08Rik|4930548B21Rik|GS4|MLZ-465|Spdy1	speedy/RINGO cell cycle regulator family, member A	protein-coding
mm_40967.1	chr5	76995872	76995884	+	1	NA	exon (NM_025691, exon 16 of 19)	exon (NM_025691, exon 16 of 19)	-8177	NM_206935	384185	Mm.451858	NM_206935	ENSMUSG00000063820	Arl9	1700110A09Rik	ADP-ribosylation factor-like 9	protein-coding
mm_46397.1	chr5	104092466	104092486	-	1	NA	exon (NM_010097, exon 4 of 11)	exon (NM_010097, exon 4 of 11)	-14868	NM_001163772	100271704	Mm.366664	NM_001163772	ENSMUSG00000091034	Gm17660	Scpppq1	predicted gene, 17660	protein-coding
mm_9941.1	chr1	190170822	190170832	-	1	NA	promoter-TSS (NM_008937)	promoter-TSS (NM_008937)	-147	NM_008937	19130	Mm.132579	NM_008937	ENSMUSG00000010175	Prox1	A230003G05Rik	prospero homeobox 1	protein-coding
mm_135734.1	chr16	55831486	55831497	-	1	NA	intron (NM_030612, intron 2 of 13)	MLT1B|LTR|ERVL-MaLR	7150	NM_030612	80859	Mm.247272	NM_030612	ENSMUSG00000035356	Nfkbiz	AA408868|INAP|Mail	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, zeta	protein-coding
mm_37591.1	chr4	126533274	126533321	-	1	NA	5' UTR (NM_153177, exon 1 of 18)	5' UTR (NM_153177, exon 1 of 18)	161	NM_153177	76850	Mm.86705	NM_153177	ENSMUSG00000042500	Ago4	5730550L01Rik|AI481660|Eif2c4	argonaute RISC catalytic subunit 4	protein-coding
mm_122364.1	chr14	39361157	39361170	-	1	NA	intron (NM_001190187, intron 1 of 9)	intron (NM_001190187, intron 1 of 9)	-111266	NR_131973	432842	Mm.352566	NR_131973		LOC432842	-	uncharacterized LOC432842	ncRNA
mm_94409.1	chr11	5799285	5799305	+	1	NA	exon (NM_001146309, exon 12 of 13)	exon (NM_001146309, exon 12 of 13)	4501	NM_018870	56012	Mm.219627	NM_018870	ENSMUSG00000020475	Pgam2	-	phosphoglycerate mutase 2	protein-coding
mm_42420.1	chr5	115327060	115327070	+	1	NA	promoter-TSS (NM_025573)	promoter-TSS (NM_025573)	-112	NM_025573	108014	Mm.287826	NM_025573	ENSMUSG00000029538	Srsf9	25kDa|2610029M16Rik|SRp30c|Sfrs9	serine/arginine-rich splicing factor 9	protein-coding
mm_57962.1	chr6	135254276	135254289	-	1	NA	promoter-TSS (NM_010352)	promoter-TSS (NM_010352)	54	NM_010352	14840	Mm.272306	NM_010352	ENSMUSG00000030206	Gsg1	-	germ cell associated 1	protein-coding
mm_59445.1	chr7	27133317	27133336	+	1	NA	exon (NM_007817, exon 10 of 10)	exon (NM_007817, exon 10 of 10)	13371	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_21200.1	chr2	155499121	155499128	-	1	NA	exon (NM_144786, exon 9 of 15)	exon (NM_144786, exon 9 of 15)	15722	NM_144786	207182	Mm.41757	NM_144786	ENSMUSG00000027603	Ggt7	1110017C11Rik|6330563L03Rik|Ggtl3	gamma-glutamyltransferase 7	protein-coding
mm_73980.1	chr8	120537448	120537471	+	1	NA	promoter-TSS (NM_001145896)	promoter-TSS (NM_001145896)	50	NM_001145896	382034	Mm.334856	NM_198671	ENSMUSG00000031822	Gse1	2210013I18Rik|mKIAA0182	genetic suppressor element 1, coiled-coil protein	protein-coding
mm_11452.1	chr2	32095519	32095595	+	1	NA	promoter-TSS (NM_145521)	promoter-TSS (NM_145521)	-94	NM_145521	227721	Mm.257236	NM_145521	ENSMUSG00000051373	Plpp7	D830019K17Rik|NET39|Ppapdc3	phospholipid phosphatase 7 (inactive)	protein-coding
mm_159467.1	chr4	8691082	8691082	+	1	NA	intron (NM_001277149, intron 1 of 37)	CpG	676	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_99114.1	chr11	100140896	100140917	+	1	NA	TTS (NM_008471)	TTS (NM_008471)	2793	NM_001313963	16669	Mm.439699	NM_008471	ENSMUSG00000020911	Krt19	AI663979|CK-19|EndoC|K19|Krt-1.19|Krt1-19	keratin 19	protein-coding
mm_131821.1	chr16	22929126	22929170	+	1	NA	exon (NM_021564, exon 2 of 8)	exon (NM_021564, exon 2 of 8)	8926	NM_001083904	59083	Mm.28461	NM_021564	ENSMUSG00000022871	Fetub	2310011O17Rik|AI255764|D17980|Gugu	fetuin beta	protein-coding
mm_126532.1	chr15	82017076	82017087	+	1	NA	promoter-TSS (NM_134095)	promoter-TSS (NM_134095)	712	NM_010247	14375	Mm.288809	NM_010247	ENSMUSG00000022471	Xrcc6	70kDa|G22p1|Ku70	X-ray repair complementing defective repair in Chinese hamster cells 6	protein-coding
mm_156701.1	chrX	159532675	159532748	+	1	NA	promoter-TSS (NM_001033472)	promoter-TSS (NM_001033472)	43	NM_001033472	382252	Mm.296254	NM_001033472	ENSMUSG00000044150	A830080D01Rik	2310067E24Rik|Gm1146	RIKEN cDNA A830080D01 gene	protein-coding
mm_17473.1	chr2	28559880	28559892	-	1	NA	exon (NM_009885, exon 5 of 11)	exon (NM_009885, exon 5 of 11)	3517	NM_009885	12613	Mm.236017	NM_009885	ENSMUSG00000026818	Cel	1810036E18Rik|BAL	carboxyl ester lipase	protein-coding
mm_168757.1	chr1	21166521	21166523	+	1	NA	Intergenic	Intergenic	-52053	NM_001290679	75712	Mm.304763	NM_029398	ENSMUSG00000025933	Tmem14a	5730496E24Rik|C85783|PTD011	transmembrane protein 14A	protein-coding
mm_109815.1	chr12	3427712	3427722	-	1	NA	promoter-TSS (NR_030694)	promoter-TSS (NR_030694)	860	NM_172421	75302	Mm.120475	NM_172421	ENSMUSG00000037486	Asxl2	4930556B16Rik|mKIAA1685	additional sex combs like 2 (Drosophila)	protein-coding
mm_128678.1	chr15	60819841	60819857	-	1	NA	3' UTR (NM_001162926, exon 2 of 2)	3' UTR (NM_001162926, exon 2 of 2)	-3116	NR_030696	320469	Mm.230853	NM_177166		9930014A18Rik	-	RIKEN cDNA 9930014A18 gene	ncRNA
mm_84029.1	chr9	57764684	57764693	-	1	NA	intron (NM_007713, intron 1 of 12)	CpG	1172	NM_007713	102414	Mm.25720	NM_007713	ENSMUSG00000032316	Clk3	AI256811	CDC-like kinase 3	protein-coding
mm_1702.1	chr1	75168661	75168683	+	1	NA	promoter-TSS (NM_001159905)	promoter-TSS (NM_001159905)	26	NM_001159906	68818	Mm.32646	NM_026846	ENSMUSG00000026197	Zfand2b	1110060O18Rik|C81256	zinc finger, AN1 type domain 2B	protein-coding
mm_95576.1	chr11	52407172	52407185	+	1	NA	3' UTR (NM_153117, exon 3 of 3)	3' UTR (NM_153117, exon 3 of 3)	10750	NM_153117	213673	Mm.291979	NM_153117	ENSMUSG00000036275	9530068E07Rik	C85061|Kct2	RIKEN cDNA 9530068E07 gene	protein-coding
mm_9762.1	chr1	180885552	180885601	-	1	NA	Intergenic	GA-rich|Low_complexity|Low_complexity	-7532	NM_177099	320202	Mm.87078	NM_177099	ENSMUSG00000066652	Lefty2	6030463A22Rik|Ebaf|Lefta|Leftb|lefty-2|lefty-B	left-right determination factor 2	protein-coding
mm_59400.1	chr7	26771769	26771801	+	1	NA	3' UTR (NM_007814, exon 9 of 9)	3' UTR (NM_007814, exon 9 of 9)	14643	NM_007814	13090	Mm.14098	NM_007814	ENSMUSG00000066704	Cyp2b19	CYPIIB19	cytochrome P450, family 2, subfamily b, polypeptide 19	protein-coding
mm_771.1	chr1	44147938	44147952	+	1	NA	5' UTR (NM_011729, exon 1 of 15)	5' UTR (NM_011729, exon 1 of 15)	201	NM_011729	22592	Mm.2213	NM_011729	ENSMUSG00000026048	Ercc5	Xpg	excision repair cross-complementing rodent repair deficiency, complementation group 5	protein-coding
mm_150195.1	chr19	32712381	32712417	+	1	NA	promoter-TSS (NM_026487)	promoter-TSS (NM_026487)	-101	NM_026487	67979	Mm.27123	NM_026487	ENSMUSG00000013662	Atad1	4921525H23Rik|AW107648|Thorase	ATPase family, AAA domain containing 1	protein-coding
mm_101806.1	chr11	46326866	46326897	-	1	NA	3' UTR (NM_001281968, exon 17 of 17)	3' UTR (NM_001281968, exon 17 of 17)	-14022	NM_001252459	76884	Mm.154358	NM_133769	ENSMUSG00000020340	Cyfip2	1500004I01Rik|6430511D02Rik|AA930218|AU022376|Pir121|mKIAA1168	cytoplasmic FMR1 interacting protein 2	protein-coding
mm_70601.1	chr8	13339657	13339661	+	1	NA	intron (NM_001291766, intron 1 of 10)	L1MEg|LINE|L1	855	NM_009361	21781	Mm.925	NM_009361	ENSMUSG00000038482	Tfdp1	Dp1|Drtf1	transcription factor Dp 1	protein-coding
mm_89143.1	chr10	85871905	85871919	+	1	NA	promoter-TSS (NM_133993)	promoter-TSS (NM_133993)	81	NM_133993	103136	Mm.18834	NM_133993	ENSMUSG00000001785	Pwp1	2310058A11Rik|2610205J09Rik|AI098170|AL022879|AV083409|AW550690	PWP1 homolog, endonuclein	protein-coding
mm_169333.1	chr14	119278296	119278312	+	1	NA	intron (NM_015820, intron 1 of 1)	intron (NM_015820, intron 1 of 1)	140039	NM_015820	50787	Mm.445777	NM_015820	ENSMUSG00000053465	Hs6st3	6OST3|HS6ST-3	heparan sulfate 6-O-sulfotransferase 3	protein-coding
mm_45528.1	chr5	72647668	72647683	-	1	NA	promoter-TSS (NM_001081205)	promoter-TSS (NM_001081205)	-121	NM_001081205	70701	Mm.38884	NM_001081205	ENSMUSG00000067219	Nipal1	3830408G10Rik|Npal1	NIPA-like domain containing 1	protein-coding
mm_157786.1	chrX	73824550	73824598	-	1	NA	5' UTR (NM_001290540, exon 1 of 6)	5' UTR (NM_001290540, exon 1 of 6)	395	NM_001029868	245469	Mm.103782	NM_001029868	ENSMUSG00000002006	Pdzd4	B230341P03|D130075J17Rik|Kiaa1444-hp|LU1|PDZRN4L|Pdzk4|Pdzrnk4l|Xlu	PDZ domain containing 4	protein-coding
mm_76301.1	chr8	84249667	84249681	-	1	NA	promoter-TSS (NM_001007571)	promoter-TSS (NM_001007571)	87	NM_001007571	101966	Mm.200723	NM_001007571	ENSMUSG00000019362	D8Ertd738e	AA589584	DNA segment, Chr 8, ERATO Doi 738, expressed	protein-coding
mm_97628.1	chr11	78959653	78959663	+	1	NA	exon (NM_010927, exon 27 of 27)	exon (NM_010927, exon 27 of 27)	25266	NM_001159301	16859	Mm.341434	NM_010708	ENSMUSG00000001123	Lgals9	AA407335|AI194909|AI265545|LGALS35|Lgals5|gal-9|galectin-9	lectin, galactose binding, soluble 9	protein-coding
mm_12930.1	chr2	85048022	85048093	+	1	NA	TTS (NM_001136081)	TTS (NM_001136081)	-2403	NM_001081260	228140	Mm.23606	NM_001081260	ENSMUSG00000033955	Tnks1bp1	Tab182|mKIAA1741	tankyrase 1 binding protein 1	protein-coding
mm_3598.1	chr1	151571134	151571185	+	1	NA	promoter-TSS (NM_022018)	promoter-TSS (NM_022018)	-214	NM_022018	63913	Mm.157700	NM_022018	ENSMUSG00000026483	Fam129a	AI256368|AU019833|Niban	family with sequence similarity 129, member A	protein-coding
mm_73748.1	chr8	114652076	114652085	+	1	NA	intron (NM_019573, intron 5 of 8)	intron (NM_019573, intron 5 of 8)	212428	NM_019573	80707	Mm.440420	NM_019573	ENSMUSG00000004637	Wwox	5330426P09Rik|9030416C10Rik|WOX1	WW domain-containing oxidoreductase	protein-coding
mm_102899.1	chr11	69423972	69423977	-	1	NA	exon (NM_001081330, exon 78 of 86)	exon (NM_001081330, exon 78 of 86)	-10299	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_132859.1	chr16	48310428	48310466	+	1	NA	5' UTR (NM_028615, exon 1 of 7)	5' UTR (NM_028615, exon 1 of 7)	173	NM_028615	73703	Mm.27857	NM_028615	ENSMUSG00000072419	Dppa2	2410088E07Rik|C80932|D19Mgi18|ECAT15-2	developmental pluripotency associated 2	protein-coding
mm_31721.1	chr4	62668865	62668915	+	1	NA	intron (NM_134257, intron 10 of 15)	intron (NM_134257, intron 10 of 15)	-5084	NM_001310706	50780	Mm.286753	NM_019492	ENSMUSG00000059810	Rgs3	4930506N09Rik|C2PA-RGS3|C2pa|PDZ-RGS3|RGS3S	regulator of G-protein signaling 3	protein-coding
mm_144012.1	chr17	88441821	88441850	-	1	NA	intron (NM_180974, intron 1 of 5)	intron (NM_180974, intron 1 of 5)	1123	NM_180974	14236	Mm.112824	NM_180974	ENSMUSG00000034998	Foxn2	3230402J05Rik|6030465J18Rik|Fkh19|Foxn1|HTLF	forkhead box N2	protein-coding
mm_127509.1	chr15	101676533	101676543	+	1	NA	exon (NM_010669, exon 9 of 9)	exon (NM_010669, exon 9 of 9)	3751	NM_010669	16688	Mm.441891	NM_010669	ENSMUSG00000023041	Krt6b	BB144589|Krt2-6b|mK6[b]	keratin 6B	protein-coding
mm_145756.1	chr18	64887772	64887795	+	1	NA	promoter-TSS (NM_001114386)	promoter-TSS (NM_001114386)	27	NM_001114386	83814	Mm.98668	NM_031881	ENSMUSG00000024589	Nedd4l	1300012C07Rik|Nedd4-2|Nedd4b	neural precursor cell expressed, developmentally down-regulated gene 4-like	protein-coding
mm_18770.1	chr2	73486406	73486418	-	1	NA	promoter-TSS (NM_001289723)	promoter-TSS (NM_001289723)	-659	NM_001289723	215280	Mm.223504	NM_153138	ENSMUSG00000075284	Wipf1	AI115543|D2Ertd120e|WIP|Waspip	WAS/WASL interacting protein family, member 1	protein-coding
mm_42588.1	chr5	117356844	117356876	+	1	NA	promoter-TSS (NM_021539)	promoter-TSS (NM_021539)	-445	NM_021539	59043	Mm.28489	NM_021539	ENSMUSG00000029364	Wsb2	AA673511|Swip2|WSB-2	WD repeat and SOCS box-containing 2	protein-coding
mm_19079.1	chr2	77817669	77817682	-	1	NA	promoter-TSS (NM_178723)	promoter-TSS (NM_178723)	-859	NM_178723	241494	Mm.490320	NM_178723	ENSMUSG00000027016	Zfp385b	B830010L13Rik|C130013B13Rik|Zfp533|Znf385b	zinc finger protein 385B	protein-coding
mm_128322.1	chr15	38022240	38022244	-	1	NA	intron (NM_001112721, intron 15 of 58)	intron (NM_001112721, intron 15 of 58)	56612	NM_001112721	70790	Mm.476840	NM_027553	ENSMUSG00000037487	Ubr5	Edd|Edd1	ubiquitin protein ligase E3 component n-recognin 5	protein-coding
mm_116406.1	chr13	41425157	41425194	-	1	NA	intron (NM_001111324, intron 2 of 7)	(TG)n|Simple_repeat|Simple_repeat	62185	NM_001111324	18003	Mm.288980	NM_017464	ENSMUSG00000021365	Nedd9	Cas-L|CasL|HEF1|MEF1|Nedd-9|p105	neural precursor cell expressed, developmentally down-regulated gene 9	protein-coding
mm_23876.1	chr3	83030287	83030296	+	1	NA	exon (NM_010196, exon 4 of 5)	exon (NM_010196, exon 4 of 5)	4138	NM_001111048	14161	Mm.88793	NM_010196	ENSMUSG00000028001	Fga	ENSMUSG00000059807|Fib	fibrinogen alpha chain	protein-coding
mm_140291.1	chr17	85613433	85613485	+	1	NA	non-coding (NR_038082, exon 4 of 4)	non-coding (NR_038082, exon 4 of 4)	4937	NR_038084	100043902	Mm.150838	NR_015385	ENSMUSG00000093460	Six3os1	D17Mgi26|E130112H22Rik|Rncr1|Six3os	SIX homeobox 3, opposite strand 1	ncRNA
mm_152020.1	chr19	6015770	6015830	-	1	NA	promoter-TSS (NM_007600)	promoter-TSS (NM_007600)	25	NM_001110504	12333	Mm.6221	NM_007600	ENSMUSG00000024942	Capn1	Capa-1|Capa1|mu-calpin	calpain 1	protein-coding
mm_141962.1	chr17	35121060	35121078	-	1	NA	promoter-TSS (NM_001128597)	promoter-TSS (NM_001128597)	223	NM_001303476	13001	Mm.378901	NM_009975	ENSMUSG00000024387	Csnk2b	CK II beta	casein kinase 2, beta polypeptide	protein-coding
mm_49892.1	chr6	38918954	38918960	+	1	NA	promoter-TSS (NM_011539)	promoter-TSS (NM_011539)	-29	NM_011539	21391	Mm.4054	NM_011539	ENSMUSG00000029925	Tbxas1	CYP5|CYP5A1|THAS|TS|TXAS|TXS	thromboxane A synthase 1, platelet	protein-coding
mm_5808.1	chr1	52233212	52233229	-	1	NA	promoter-TSS (NM_001113383)	promoter-TSS (NM_001113383)	12	NM_001081081	14660	Mm.398608	NM_001081081	ENSMUSG00000026103	Gls	6330442B14|AI314027|B230365M23Rik	glutaminase	protein-coding
mm_41887.1	chr5	105495456	105495475	+	1	NA	Intergenic	Intergenic	-24006	NM_133897	100604	Mm.319847	NM_133897	ENSMUSG00000054720	Lrrc8c	AD158|AI326115|E430036I04Rik|fad158	leucine rich repeat containing 8 family, member C	protein-coding
mm_101062.1	chr11	9048494	9048511	-	1	NA	promoter-TSS (NM_001037928)	promoter-TSS (NM_001037928)	-90	NM_001037928	626870	Mm.369429	NM_001037928	ENSMUSG00000040978	Gm11992	OTTMUSG00000005148	predicted gene 11992	protein-coding
mm_14554.1	chr2	133552276	133552278	+	1	NA	5' UTR (NM_007553, exon 1 of 3)	5' UTR (NM_007553, exon 1 of 3)	118	NM_007553	12156	Mm.103205	NM_007553	ENSMUSG00000027358	Bmp2	AI467020|Bmp2a	bone morphogenetic protein 2	protein-coding
mm_85878.1	chr9	110990331	110990344	-	1	NA	promoter-TSS (NM_153100)	promoter-TSS (NM_153100)	-624	NM_153100	235636	Mm.441138	NM_153100	ENSMUSG00000066319	Rtp3	Tmem7	receptor transporter protein 3	protein-coding
mm_18368.1	chr2	59882542	59882555	-	1	NA	promoter-TSS (NM_028118)	promoter-TSS (NM_028118)	58	NM_001159636	72137	Mm.288734	NM_028118	ENSMUSG00000026988	Wdsub1	1700048E19Rik|2610014F08Rik	WD repeat, SAM and U-box domain containing 1	protein-coding
mm_100281.1	chr11	117797708	117797723	+	1	NA	promoter-TSS (NM_029964)	promoter-TSS (NM_029964)	55	NM_029964	77727	Mm.159981	NM_029964	ENSMUSG00000025573	6030468B19Rik	-	RIKEN cDNA 6030468B19 gene	protein-coding
mm_97471.1	chr11	78301611	78301634	+	1	NA	promoter-TSS (NM_017407)	promoter-TSS (NM_017407)	31	NM_017407	54141	Mm.24250	NM_017407	ENSMUSG00000002055	Spag5	AI874642|D11Bhm180e|Deepest|MAP126|Mastrin|S17	sperm associated antigen 5	protein-coding
mm_127965.1	chr15	11995999	11996014	-	1	NA	promoter-TSS (NM_011294)	promoter-TSS (NM_011294)	1	NM_011294	20024	Mm.41746	NM_011294	ENSMUSG00000022205	Sub1	AI842364|P15|P9|Pc4|Rpo2tc1	SUB1 homolog (S. cerevisiae)	protein-coding
mm_39324.1	chr5	8567094	8567110	+	1	NA	intron (NM_001347311, intron 4 of 10)	intron (NM_001347311, intron 4 of 10)	55850	NM_001347311	242819	Mm.332192	NM_198620	ENSMUSG00000040570	Rundc3b	Gm440	RUN domain containing 3B	protein-coding
mm_118221.1	chr13	110394860	110394866	-	1	NA	promoter-TSS (NM_152804)	promoter-TSS (NM_152804)	-181	NM_152804	20620	Mm.380	NM_152804	ENSMUSG00000021701	Plk2	Snk	polo-like kinase 2	protein-coding
mm_163929.1	chr14	47307918	47307929	+	1	NA	intron (NM_178684, intron 1 of 3)	intron (NM_178684, intron 1 of 3)	9609	NM_178684	218975	Mm.212297	NM_178684	ENSMUSG00000021840	Mapk1ip1l	9130202B12|C130032J12Rik	mitogen-activated protein kinase 1 interacting protein 1-like	protein-coding
mm_93341.1	chr10	99759619	99759629	-	1	NA	promoter-TSS (NM_027945)	promoter-TSS (NM_027945)	34	NM_027945	71832	Mm.483162	NM_027945	ENSMUSG00000046934	Csl	1700007H16Rik	citrate synthase like	protein-coding
mm_33472.1	chr4	130818614	130818628	+	1	NA	exon (NM_011520, exon 3 of 5)	exon (NM_011520, exon 3 of 5)	26084	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_102967.1	chr11	69666066	69666076	-	1	NA	promoter-TSS (NR_110993)	promoter-TSS (NR_110993)	99	NM_001291058	12514	Mm.15819	NM_009853	ENSMUSG00000018774	Cd68	Lamp4|Scard1|gp110	CD68 antigen	protein-coding
mm_67404.1	chr7	80014957	80014992	-	1	NA	Intergenic	B1_Mus2|SINE|Alu	-9840	NM_001145999	209225	Mm.290925	NM_175433	ENSMUSG00000048897	Zfp710	5430400N05Rik|9830165K13|AI324798|Znf710	zinc finger protein 710	protein-coding
mm_75474.1	chr8	48554879	48554900	-	1	NA	intron (NM_011857, intron 2 of 28)	intron (NM_011857, intron 2 of 28)	119801	NM_001145937	23965	Mm.42191	NM_011857	ENSMUSG00000031561	Tenm3	2610100B16Rik|Odz1|Odz3|Ten-m3|mKIAA1455	teneurin transmembrane protein 3	protein-coding
mm_506.1	chr1	37153859	37153870	+	1	NA	Intergenic	Intergenic	-64414	NM_001282010	12790	Mm.214224	NM_009918	ENSMUSG00000026114	Cnga3	CNG3	cyclic nucleotide gated channel alpha 3	protein-coding
mm_13186.1	chr2	93187560	93187570	+	1	NA	promoter-TSS (NM_001025246)	promoter-TSS (NM_001025246)	-19	NM_001025246	277414	Mm.41033	NM_001025246	ENSMUSG00000068735	Trp53i11	Tp53i11	transformation related protein 53 inducible protein 11	protein-coding
mm_21054.1	chr2	152627331	152627339	-	1	NA	intron (NM_009047, intron 1 of 4)	CpG	327	NM_009047	19700	Mm.8752	NM_009047	ENSMUSG00000000359	Rem1	E030011C07Rik|Ras|Rem	rad and gem related GTP binding protein 1	protein-coding
mm_82079.1	chr9	122999451	122999456	+	1	NA	intron (NM_010620, intron 21 of 34)	intron (NM_010620, intron 21 of 34)	-21873	NM_025339	66079	Mm.482265	NM_025339	ENSMUSG00000066233	Tmem42	0610027O18Rik|4933429E06Rik|AV003444|D9Ertd662e	transmembrane protein 42	protein-coding
mm_71443.1	chr8	46513346	46513364	+	1	NA	exon (NM_007981, exon 6 of 21)	exon (NM_007981, exon 6 of 21)	22389	NM_001302163	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_83150.1	chr9	40456196	40456224	-	1	NA	promoter-TSS (NM_172768)	promoter-TSS (NM_172768)	-446	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_15857.1	chr2	164805083	164805109	+	1	NA	promoter-TSS (NM_178375)	promoter-TSS (NM_178375)	-18	NM_178375	67538	Mm.33184	NM_178375	ENSMUSG00000045822	Zswim3	4921517A06Rik|C86566	zinc finger SWIM-type containing 3	protein-coding
mm_93590.1	chr10	117063765	117063802	-	1	NA	promoter-TSS (NM_007636)	promoter-TSS (NM_007636)	31	NM_007636	12461	Mm.247788	NM_007636	ENSMUSG00000034024	Cct2	Cctb	chaperonin containing Tcp1, subunit 2 (beta)	protein-coding
mm_11041.1	chr2	27025793	27025840	+	1	NA	intron (NM_001177627, intron 3 of 8)	intron (NM_001177627, intron 3 of 8)	2182	NM_172659	227659	Mm.41203	NM_172659	ENSMUSG00000036067	Slc2a6	A330096C23|F630103L12Rik|Glut6|Glut9	solute carrier family 2 (facilitated glucose transporter), member 6	protein-coding
mm_49233.1	chr6	17206031	17206031	+	1	NA	TTS (NR_102304)	TTS (NR_102304)	7924	NR_102304	319682	Mm.136046	NR_102304	ENSMUSG00000085171	D830026I12Rik	-	RIKEN cDNA D830026I12 gene	ncRNA
mm_64884.1	chr7	15917338	15917433	-	1	NA	3' UTR (NM_009156, exon 6 of 6)	3' UTR (NM_009156, exon 6 of 6)	4986	NM_009156	20364	Mm.42829	NM_009156	ENSMUSG00000041571	Selenow	Sepw1|selW	selenoprotein W	protein-coding
mm_2485.1	chr1	105989786	105989798	+	1	NA	promoter-TSS (NM_001122675)	promoter-TSS (NM_001122675)	-614	NM_001122676	227449	Mm.210188	NM_001122675	ENSMUSG00000038866	Zcchc2	9930114B20Rik|AW212015	zinc finger, CCHC domain containing 2	protein-coding
mm_145287.1	chr18	53245579	53245607	+	1	NA	promoter-TSS (NM_029394)	promoter-TSS (NM_029394)	-69	NM_029394	69226	Mm.32414	NM_029394	ENSMUSG00000024535	Snx24	2810011K15Rik|5730433I16Rik|AI451341	sorting nexing 24	protein-coding
mm_55347.1	chr6	56796722	56796751	-	1	NA	intron (NM_145958, intron 1 of 3)	intron (NM_145958, intron 1 of 3)	1077	NM_145958	210973	Mm.57295	NM_145958	ENSMUSG00000059486	Kbtbd2	BC022962|Bklhd1|mKIAA1489	kelch repeat and BTB (POZ) domain containing 2	protein-coding
mm_114075.1	chr13	54382794	54382866	+	1	NA	3' UTR (NM_009946, exon 4 of 4)	3' UTR (NM_009946, exon 4 of 4)	11481	NM_009946	12890	Mm.268902	NM_009946	ENSMUSG00000025867	Cplx2	921-L|AI413745|AW492120	complexin 2	protein-coding
mm_45412.1	chr5	66337626	66337646	-	1	NA	promoter-TSS (NM_001201416)	promoter-TSS (NM_001201416)	29	NM_001201416	11787	Mm.5159	NM_009686	ENSMUSG00000029207	Apbb2	2310007D03Rik|FE65L1|Rirl1|TR2L|Zfra	amyloid beta (A4) precursor protein-binding, family B, member 2	protein-coding
mm_50353.1	chr6	48593931	48593952	+	1	NA	promoter-TSS (NM_001079905)	promoter-TSS (NM_001079905)	58	NM_001079904	58887	Mm.219183	NM_175099	ENSMUSG00000052751	Repin1	AI425994|Ap4|E430037F08Rik|Zfp-464|Zfp464	replication initiator 1	protein-coding
mm_111307.1	chr12	85759453	85759461	-	1	NA	intron (NM_145447, intron 1 of 9)	MER21C|LTR|ERVL	12918	NM_145447	217721	Mm.301076	NM_145447	ENSMUSG00000034258	Mfsd7c	CCT|Flvcr2	major facilitator superfamily domain containing 7C	protein-coding
mm_68017.1	chr7	100958415	100958418	-	1	NA	intron (NM_183168, intron 1 of 2)	B1_Mus1|SINE|Alu	5950	NM_183168	233571	Mm.235193	NM_183168	ENSMUSG00000048779	P2ry6	2010204J23Rik|P2Y6	pyrimidinergic receptor P2Y, G-protein coupled, 6	protein-coding
mm_37811.1	chr4	130934544	130934573	-	1	NA	3' UTR (NM_010686, exon 8 of 8)	3' UTR (NM_010686, exon 8 of 8)	-9827	NM_010769	17180	Mm.271796	NM_010769	ENSMUSG00000040533	Matn1	CMP|Crtm|Mat1|matrilin-1	matrilin 1, cartilage matrix protein	protein-coding
mm_38122.1	chr4	134552123	134552200	-	1	NA	promoter-TSS (NM_029100)	promoter-TSS (NM_029100)	5	NM_029100	74777	Mm.29773	NM_029100	ENSMUSG00000050989	Selenon	1110019I12Rik|AI414492|SelN|Sepn1	selenoprotein N	protein-coding
mm_46297.1	chr5	100429492	100429502	-	1	NA	promoter-TSS (NR_034038)	promoter-TSS (NR_034038)	38	NR_034038	100503199	Mm.392282	NR_034038	ENSMUSG00000097772	5430416N02Rik	100041797|Adapt33|Gm3514	RIKEN cDNA 5430416N02 gene	ncRNA
mm_39268.1	chr5	3596307	3596393	+	1	NA	5' UTR (NM_172991, exon 1 of 5)	5' UTR (NM_172991, exon 1 of 5)	197	NM_172991	269623	Mm.38014	NM_172991	ENSMUSG00000040302	Rbm48	AW548102|C030048B08Rik	RNA binding motif protein 48	protein-coding
mm_103298.1	chr11	72502410	72502427	-	1	NA	intron (NM_029932, intron 9 of 11)	intron (NM_029932, intron 9 of 11)	-12498	NM_153060	216892	Mm.212812	NM_153060	ENSMUSG00000040447	Spns2	-	spinster homolog 2	protein-coding
mm_133728.1	chr16	93780946	93780980	+	1	NA	intron (NM_027293, intron 24 of 36)	intron (NM_027293, intron 24 of 36)	-51158	NM_001045529	338467	Mm.287329	NM_001045529	ENSMUSG00000039456	Morc3	1110051N18Rik|AI452146|BF318192|D16Jhu32e|NXP2|Zcwcc3	microrchidia 3	protein-coding
mm_79505.1	chr9	57428132	57428146	+	1	NA	intron (NM_176831, intron 3 of 6)	intron (NM_176831, intron 3 of 6)	11975	NM_176831	66812	Mm.250508	NM_176831	ENSMUSG00000063849	Ppcdc	1810057I13Rik|8430432M10Rik	phosphopantothenoylcysteine decarboxylase	protein-coding
mm_118907.1	chr14	26656104	26656116	+	1	NA	3' UTR (NM_007479, exon 6 of 6)	3' UTR (NM_007479, exon 6 of 6)	13498	NR_106132	102465773		NR_106132	ENSMUSG00000098751	Mir7672	Gm27314|mmu-mir-7672	microRNA 7672	ncRNA
mm_150710.1	chr19	42591524	42591529	+	1	NA	TTS (NM_053083)	TTS (NM_053083)	21280	NM_001164311	67573	Mm.178767	NM_053083	ENSMUSG00000025185	Loxl4	4833426I20Rik|Loxc	lysyl oxidase-like 4	protein-coding
mm_154928.1	chrX	32305111	32305112	+	1	NA	Intergenic	L1_Mur2|LINE|L1	26717	NM_001168334	100040482	Mm.479861	NM_001168334	ENSMUSG00000096194	Btbd35f2	Gm2799	BTB domain containing 35, family member 2	protein-coding
mm_107524.1	chr12	40465650	40465672	+	1	NA	intron (NM_172803, intron 1 of 52)	Lx7|LINE|L1	19608	NM_172803	238130	Mm.341423	NM_172803	ENSMUSG00000035954	Dock4	5330406C03|6330411N01Rik|AF263288|C030023J22|mKIAA0716	dedicator of cytokinesis 4	protein-coding
mm_17554.1	chr2	30124460	30124470	-	1	NA	5' UTR (NM_178694, exon 1 of 16)	5' UTR (NM_178694, exon 1 of 16)	146	NM_178694	227693	Mm.44526	NM_178694	ENSMUSG00000039686	Zer1	C230075L19Rik|Zyg11bl	zyg-11 related, cell cycle regulator	protein-coding
mm_29932.1	chr3	131504903	131504909	-	1	NA	Intergenic	Intergenic	-59862	NM_001289479	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_120130.1	chr14	60197285	60197294	+	1	NA	Intergenic	Intergenic	31626	NR_030458	751526		NR_030458	ENSMUSG00000076270	Mir719	Mirn719|mmu-mir-719	microRNA 719	ncRNA
mm_63401.1	chr7	127297388	127297399	+	1	NA	intron (NM_001253874, intron 1 of 30)	intron (NM_001253874, intron 1 of 30)	1133	NM_001253874	16408	Mm.1618	NM_008400	ENSMUSG00000030830	Itgal	(p180)|Cd11a|LFA-1|LFA-1A|Ly-15|Ly-21	integrin alpha L	protein-coding
mm_149204.1	chr19	9980577	9980606	+	1	NA	promoter-TSS (NR_073181)	promoter-TSS (NR_073181)	-9	NR_073181	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
mm_33284.1	chr4	128752055	128752091	+	1	NA	3' UTR (NM_018774, exon 15 of 15)	3' UTR (NM_018774, exon 15 of 15)	-7185	NM_001009819	215493	Mm.300900	NM_001009819	ENSMUSG00000028794	A3galt2	Gm433|iGb3|iGb3S	alpha 1,3-galactosyltransferase 2 (isoglobotriaosylceramide synthase)	protein-coding
mm_1071.1	chr1	59315274	59315288	+	1	NA	intron (NM_001033373, intron 10 of 13)	intron (NM_001033373, intron 10 of 13)	58374	NM_001033373	271697	Mm.297713	NM_001033373	ENSMUSG00000026023	Cdk15	Als2cr7|Pftk2	cyclin-dependent kinase 15	protein-coding
mm_93985.1	chr10	127370551	127370561	-	1	NA	promoter-TSS (NM_010565)	promoter-TSS (NM_010565)	-8	NM_010565	16325	Mm.2594	NM_010565	ENSMUSG00000025405	Inhbc	-	inhibin beta-C	protein-coding
mm_70619.1	chr8	13507185	13507193	+	1	NA	Intergenic	Intergenic	-12654	NM_019521	14456	Mm.3982	NM_019521	ENSMUSG00000031451	Gas6	Gas-6	growth arrest specific 6	protein-coding
mm_94370.1	chr11	5098916	5098926	+	1	NA	promoter-TSS (NM_177370)	promoter-TSS (NM_177370)	167	NM_001283062	14030	Mm.142822	NM_007968	ENSMUSG00000009079	Ewsr1	Ews|Ewsh	Ewing sarcoma breakpoint region 1	protein-coding
mm_172976.1	chr9	94538711	94538711	+	1	NA	promoter-TSS (NM_001033145)	promoter-TSS (NM_001033145)	-630	NM_001033145	68861	Mm.258746	NM_001033145	ENSMUSG00000045414	1190002N15Rik	GoPro49|HASF	RIKEN cDNA 1190002N15 gene	protein-coding
mm_68383.1	chr7	109438787	109438837	-	1	NA	intron (NM_054103, intron 1 of 13)	CpG	241	NM_054103	117229	Mm.389950	NM_054103	ENSMUSG00000031027	Stk33	4921505G21Rik|AW061264	serine/threonine kinase 33	protein-coding
mm_132210.1	chr16	32611776	32611779	+	1	NA	intron (NM_011638, intron 1 of 18)	intron (NM_011638, intron 1 of 18)	2881	NM_011638	22042	Mm.28683	NM_011638	ENSMUSG00000022797	Tfrc	2610028K12Rik|CD71|E430033M20Rik|Mtvr1|TFR|TFR1|TR|Trfr|p90	transferrin receptor	protein-coding
mm_143408.1	chr17	70827719	70827740	-	1	NA	Intergenic	Intergenic	19048	NM_001164077	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_36724.1	chr4	98999976	98999981	-	1	NA	intron (NM_001290636, intron 22 of 48)	intron (NM_001290636, intron 22 of 48)	-30976	NM_013913	30924	Mm.28341	NM_013913	ENSMUSG00000028553	Angptl3	hypl	angiopoietin-like 3	protein-coding
mm_52619.1	chr6	117173997	117174014	+	1	NA	3' UTR (NM_021704, exon 3 of 3)	3' UTR (NM_021704, exon 3 of 3)	5470	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_153790.1	chr19	45878158	45878165	-	1	NA	intron (NM_198296, intron 23 of 25)	intron (NM_198296, intron 23 of 25)	-62098	NM_145703	80906	Mm.213204	NM_030716	ENSMUSG00000025221	Kcnip2	KChIP2	Kv channel-interacting protein 2	protein-coding
mm_164063.1	chr14	117527620	117527637	+	1	NA	intron (NM_001079844, intron 3 of 9)	intron (NM_001079844, intron 3 of 9)	426219	NR_105747	102465148		NR_105747	ENSMUSG00000098648	Mir6239	Gm28025|mmu-mir-6239	microRNA 6239	ncRNA
mm_125998.1	chr15	76457447	76457464	+	1	NA	promoter-TSS (NM_198885)	promoter-TSS (NM_198885)	17	NM_198885	20289	Mm.322821	NM_198885	ENSMUSG00000034161	Scx	BB114693|Bhlha41|Scl	scleraxis	protein-coding
mm_15318.1	chr2	155679821	155679823	+	1	NA	intron (NM_019828, intron 1 of 18)	intron (NM_019828, intron 1 of 18)	12562	NM_019828	56407	Mm.234944	NM_019828	ENSMUSG00000038324	Trpc4ap	4833429F06Rik|D2Ertd113e|Trrp4ap|mFLJ00177|truss	transient receptor potential cation channel, subfamily C, member 4 associated protein	protein-coding
mm_49046.1	chr6	4902914	4903014	+	1	NA	promoter-TSS (NM_181595)	promoter-TSS (NM_181595)	-356	NM_181595	243725	Mm.332901	NM_181595	ENSMUSG00000032827	Ppp1r9a	2810430P21Rik|4930518N04Rik|5330407E15|A230094E16Rik|BB181831|NRB|mKIAA1222|neurabin-I	protein phosphatase 1, regulatory (inhibitor) subunit 9A	protein-coding
mm_84218.1	chr9	61920413	61920435	-	1	NA	intron (NM_024245, intron 19 of 22)	intron (NM_024245, intron 19 of 22)	-5914	NM_018853	56040	Mm.3158	NM_018853	ENSMUSG00000007892	Rplp1	2410042H16Rik|Arpp1|C430017H15Rik	ribosomal protein, large, P1	protein-coding
mm_94350.1	chr11	4895329	4895354	+	1	NA	promoter-TSS (NM_172438)	promoter-TSS (NM_172438)	-2	NM_172438	107829	Mm.28969	NM_172438	ENSMUSG00000034274	Thoc5	1700060C24Rik|A430085L24Rik|Fmip|PK1.3|Sgk2	THO complex 5	protein-coding
mm_99525.1	chr11	103170758	103170830	+	1	NA	promoter-TSS (NM_001077698)	promoter-TSS (NM_001077698)	-344	NM_001077698	57778	Mm.138913	NM_019679	ENSMUSG00000055805	Fmnl1	8030453N10Rik|AI553564|Fmnl|Fnrl|Frls	formin-like 1	protein-coding
mm_59191.1	chr7	24481981	24481987	+	1	NA	promoter-TSS (NM_153112)	promoter-TSS (NM_153112)	-39	NM_153112	260299	Mm.178322	NM_153112	ENSMUSG00000054793	Cadm4	Igdf4c|Igsf4c|Tsll2	cell adhesion molecule 4	protein-coding
mm_132620.1	chr16	38784219	38784243	+	1	NA	exon (NM_178924, exon 5 of 8)	exon (NM_178924, exon 5 of 8)	15972	NM_178924	22268	Mm.130793	NM_178924	ENSMUSG00000049436	Upk1b	AI413235|Tspan20|UPIb|Upk1	uroplakin 1B	protein-coding
mm_152771.1	chr19	21053678	21053713	-	1	NA	Intergenic	Intergenic	-51015	NR_126458	75354	Mm.243873	NR_126458		4930554I06Rik	-	RIKEN cDNA 4930554I06 gene	ncRNA
mm_66502.1	chr7	45083668	45083709	-	1	NA	exon (NM_026555, exon 6 of 7)	exon (NM_026555, exon 6 of 7)	8525	NM_026555	52377	Mm.29997	NM_026555	ENSMUSG00000019539	Rcn3	6030455P07Rik|D530026G20Rik|D7Ertd671e|RLP49	reticulocalbin 3, EF-hand calcium binding domain	protein-coding
mm_83996.1	chr9	57449167	57449202	-	1	NA	intron (NM_001301634, intron 3 of 6)	RSINE1|SINE|B4	-9070	NM_176831	66812	Mm.250508	NM_176831	ENSMUSG00000063849	Ppcdc	1810057I13Rik|8430432M10Rik	phosphopantothenoylcysteine decarboxylase	protein-coding
mm_50972.1	chr6	61180314	61180400	+	1	NA	promoter-TSS (NM_183310)	promoter-TSS (NM_183310)	32	NM_183310	232035	Mm.150324	NM_183310	ENSMUSG00000039578	Ccser1	6230405M12Rik|C130092O11Rik|Fam190a	coiled-coil serine rich 1	protein-coding
mm_4120.1	chr1	169655494	169655508	+	1	NA	promoter-TSS (NM_009063)	promoter-TSS (NM_009063)	0	NM_001313705	19737	Mm.20954	NM_009063	ENSMUSG00000026678	Rgs5	1110070A02Rik	regulator of G-protein signaling 5	protein-coding
mm_63154.1	chr7	123418235	123418250	+	1	NA	exon (NM_025304, exon 7 of 11)	exon (NM_025304, exon 7 of 11)	40260	NM_025304	30949	Mm.260527	NM_025304	ENSMUSG00000030763	Lcmt1	AL033290|LCMT-1|Lcmt	leucine carboxyl methyltransferase 1	protein-coding
mm_92611.1	chr10	80137152	80137184	-	1	NA	exon (NM_001195268, exon 2 of 9)	exon (NM_001195268, exon 2 of 9)	219	NM_001195268	100503659	Mm.485395	NM_015761	ENSMUSG00000035640	Cbarp	9630008F14|Dos|R29144/1	calcium channel, voltage-dependent, beta subunit associated regulatory protein	protein-coding
mm_43893.1	chr5	144100388	144100396	+	1	NA	promoter-TSS (NM_001081109)	promoter-TSS (NM_001081109)	-44	NM_001081109	231876	Mm.288726	NM_001081109	ENSMUSG00000038970	Lmtk2	2900041G10Rik|A330101P12Rik|BREK|KPI-2|KPI2|aatyk2|cprk	lemur tyrosine kinase 2	protein-coding
mm_34226.1	chr4	141010674	141010696	+	1	NA	promoter-TSS (NM_008546)	promoter-TSS (NM_008546)	48	NM_008546	17150	Mm.7386	NM_008546	ENSMUSG00000060572	Mfap2	AI893631|Magp|Magp1	microfibrillar-associated protein 2	protein-coding
mm_71003.1	chr8	31106612	31106618	+	1	NA	Intergenic	Intergenic	-5231	NM_175136	68867	Mm.29532	NM_175136	ENSMUSG00000039328	Rnf122	1110063C11Rik	ring finger protein 122	protein-coding
mm_21264.1	chr2	156781184	156781194	-	1	NA	3' UTR (NM_172118, exon 4 of 4)	3' UTR (NM_172118, exon 4 of 4)	5725	NM_172118	98932	Mm.271770	NM_172118	ENSMUSG00000067818	Myl9	AI327049|MLC20|Mylc2c|RLC-C	myosin, light polypeptide 9, regulatory	protein-coding
mm_122237.1	chr14	33247832	33247842	-	1	NA	intron (NM_153800, intron 2 of 10)	intron (NM_153800, intron 2 of 10)	31014	NM_153800	239027	Mm.318350	NM_153800	ENSMUSG00000063506	Arhgap22	B230341L19Rik|RHOGAP2|p68RacGAP	Rho GTPase activating protein 22	protein-coding
mm_30584.1	chr4	5644085	5644129	+	1	NA	promoter-TSS (NM_173426)	promoter-TSS (NM_173426)	-72	NM_173426	242297	Mm.331470	NM_173426	ENSMUSG00000049119	Fam110b	1700012H17Rik|5031405P22|AW049855	family with sequence similarity 110, member B	protein-coding
mm_105471.1	chr11	105936295	105936301	-	1	NA	intron (NM_007805, intron 3 of 5)	intron (NM_007805, intron 3 of 5)	7849	NM_007805	13056	Mm.149403	NM_007805	ENSMUSG00000019590	Cyb561	-	cytochrome b-561	protein-coding
mm_20494.1	chr2	130279476	130279492	-	1	NA	TTS (NM_024193)	TTS (NM_024193)	1458	NR_028528	100217428		NR_028528	ENSMUSG00000065272	Snord57	MBII-434	small nucleolar RNA, C/D box 57	snoRNA
mm_105228.1	chr11	102296982	102296998	-	1	NA	promoter-TSS (NM_001098836)	promoter-TSS (NM_001098836)	-361	NM_001098837	217218	Mm.390381	NM_001098836	ENSMUSG00000059995	Atxn7l3	E030022H21Rik	ataxin 7-like 3	protein-coding
mm_140235.1	chr17	84116864	84116879	+	1	NA	Intergenic	Intergenic	38211	NR_045458	74473	Mm.399575	NR_045458		4933433H22Rik	-	RIKEN cDNA 4933433H22 gene	ncRNA
mm_63438.1	chr7	127479853	127479865	+	1	NA	Intergenic	Intergenic	-5362	NM_010183	14123	Mm.323505	NM_010183	ENSMUSG00000042423	Fbrs	Fbs|Fbs1	fibrosin	protein-coding
mm_115529.1	chr13	5867845	5867851	-	1	NA	3' UTR (NM_011803, exon 4 of 4)	3' UTR (NM_011803, exon 4 of 4)	6359	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_157759.1	chrX	73495154	73495171	-	1	NA	3' UTR (NM_007542, exon 8 of 8)	3' UTR (NM_007542, exon 8 of 8)	-7924	NM_001310537	320707	Mm.210095	NM_177236	ENSMUSG00000031376	Atp2b3	6430519O13Rik|Pmca3	ATPase, Ca++ transporting, plasma membrane 3	protein-coding
mm_165913.1	chr4	57887580	57887590	+	1	NA	intron (NM_001035533, intron 3 of 3)	RMER12|LTR|ERVK	28679	NM_178727	242484	Mm.23214	NM_178727	ENSMUSG00000052117	D630039A03Rik	-	RIKEN cDNA D630039A03 gene	protein-coding
mm_146138.1	chr18	74733712	74733720	+	1	NA	intron (NM_201600, intron 30 of 38)	intron (NM_201600, intron 30 of 38)	44739	NR_028560	100217466		NR_028560		Scarna17	MBII-119	small Cajal body-specific RNA 17	ncRNA
mm_110314.1	chr12	33936292	33936307	-	1	NA	Intergenic	RLTR10B|LTR|ERVK	7874	NM_033522	114712	Mm.204643	NM_033522	ENSMUSG00000046518	Ferd3l	Mnato3|N-twist|Nato|Nato3|Ntwist|Ptfb|bHLHa31|fer3	Fer3-like (Drosophila)	protein-coding
mm_22724.1	chr3	19644453	19644466	+	1	NA	promoter-TSS (NM_001081281)	promoter-TSS (NM_001081281)	-1	NM_001081281	381485	Mm.35419	NM_001081281	ENSMUSG00000060913	Trim55	D830041C10Rik|Murf2|Rnf29	tripartite motif-containing 55	protein-coding
mm_101352.1	chr11	23739822	23739838	-	1	NA	Intergenic	Intergenic	31140	NM_009044	19696	Mm.4869	NM_009044	ENSMUSG00000020275	Rel	c-Rel	reticuloendotheliosis oncogene	protein-coding
mm_41994.1	chr5	107830155	107830170	+	1	NA	promoter-TSS (NM_001276397)	promoter-TSS (NM_001276397)	0	NM_001276397	73318	Mm.441500	NM_028502	ENSMUSG00000063447	Ube2d2b	1700013N18Rik	ubiquitin-conjugating enzyme E2D 2B	protein-coding
mm_5922.1	chr1	55131624	55131654	-	1	NA	intron (NM_001310585, intron 1 of 6)	CpG	394	NM_025283	19070	Mm.291037	NM_025283	ENSMUSG00000025979	Mob4	2610109B12Rik|Mobkl3|Phocn|Prei3	MOB family member 4, phocein	protein-coding
mm_59276.1	chr7	24904357	24904377	+	1	NA	promoter-TSS (NM_001130152)	promoter-TSS (NM_001130152)	21	NM_001130152	16801	Mm.3181	NM_008488	ENSMUSG00000040940	Arhgef1	Lbcl2|Lsc	Rho guanine nucleotide exchange factor (GEF) 1	protein-coding
mm_4483.1	chr1	173630814	173630834	+	1	NA	promoter-TSS (NM_175026)	promoter-TSS (NM_175026)	-35	NM_175026	236312	Mm.447	NM_175026	ENSMUSG00000043263	Ifi209	4930422C14|AI447904|Ifix|Pyhin-1|Pyhin1	interferon activated gene 209	protein-coding
mm_122476.1	chr14	45648282	45648284	-	1	NA	intron (NM_001039106, intron 1 of 11)	intron (NM_001039106, intron 1 of 11)	9770	NR_039593	100628600		NR_039593	ENSMUSG00000093167	Mir5131	mmu-mir-5131|mu-mir-5131	microRNA 5131	ncRNA
mm_134857.1	chr16	28445365	28445395	-	1	NA	5' UTR (NM_183064, exon 1 of 5)	5' UTR (NM_183064, exon 1 of 5)	695	NM_183064	14167	Mm.7996	NM_010199	ENSMUSG00000022523	Fgf12	AV114868|B230343J05Rik|FGF-12|FHF-1|Fhf1	fibroblast growth factor 12	protein-coding
mm_35255.1	chr4	19878017	19878027	-	1	NA	3' UTR (NM_175406, exon 8 of 8)	3' UTR (NM_175406, exon 8 of 8)	44544	NM_175406	242341	Mm.19298	NM_175406	ENSMUSG00000028238	Atp6v0d2	1620401A02Rik|AI324824|V-ATPase	ATPase, H+ transporting, lysosomal V0 subunit D2	protein-coding
mm_78781.1	chr9	43804680	43804693	+	1	NA	3' UTR (NM_021424, exon 6 of 6)	3' UTR (NM_021424, exon 6 of 6)	60110	NM_021424	58235	Mm.335096	NM_021424	ENSMUSG00000032012	Nectin1	AI835281|AW549174|Cd111|HIgR|HveC|PRR|PRR1|Pvrl1|nectin-1	nectin cell adhesion molecule 1	protein-coding
mm_103923.1	chr11	83604720	83604760	-	1	NA	intron (NR_036453, intron 2 of 8)	LTR16E2|LTR|ERVL	-11653	NM_009139	20305	Mm.137	NM_009139	ENSMUSG00000018927	Ccl6	MRP-1|Scya6|c10	chemokine (C-C motif) ligand 6	protein-coding
mm_99088.1	chr11	99580568	99580592	+	1	NA	3' UTR (NM_027157, exon 1 of 1)	3' UTR (NM_027157, exon 1 of 1)	436	NM_027157	69664	Mm.38303	NM_027157	ENSMUSG00000047253	Krtap1-5	2310043L02Rik|AI592983	keratin associated protein 1-5	protein-coding
mm_94308.1	chr11	4186867	4186877	+	1	NA	promoter-TSS (NM_134023)	promoter-TSS (NM_134023)	39	NM_134023	103724	Mm.28140	NM_134023	ENSMUSG00000034412	Tbc1d10a	AI447804|EPI64|Tbc1d10|mFLJ00288	TBC1 domain family, member 10a	protein-coding
mm_16855.1	chr2	11637185	11637205	-	1	NA	Intergenic	Intergenic	-5597	NM_008367	16184	Mm.915	NM_008367	ENSMUSG00000026770	Il2ra	CD25|Il2r|Ly-43	interleukin 2 receptor, alpha chain	protein-coding
mm_161232.1	chr13	92426421	92426421	+	1	NA	intron (NM_175455, intron 1 of 4)	CpG	452	NM_175455	218440	Mm.213623	NM_175455	ENSMUSG00000045034	Ankrd34b	6430502M16Rik|DP58	ankyrin repeat domain 34B	protein-coding
mm_153256.1	chr19	36797085	36797094	-	1	NA	Intergenic	Intergenic	-37143	NM_001163635	74493	Mm.249310	NM_001163635	ENSMUSG00000024811	Tnks2	5430432P15Rik|AA517131|AI662480|ARTD6|TNKS-2|Tank2	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase 2	protein-coding
mm_165796.1	chr3	141211761	141211762	-	1	NA	5' UTR (NM_008811, exon 1 of 1)	5' UTR (NM_008811, exon 1 of 1)	594	NM_008811	18598	Mm.4223	NM_008811	ENSMUSG00000047674	Pdha2	Pdhal	pyruvate dehydrogenase E1 alpha 2	protein-coding
mm_33714.1	chr4	133944020	133944027	+	1	NA	Intergenic	RMER19B|LTR|ERVK	23968	NM_016957	15331	Mm.319660	NM_016957	ENSMUSG00000003038	Hmgn2	HMG-17|Hmg17	high mobility group nucleosomal binding domain 2	protein-coding
mm_39879.1	chr5	31077473	31077482	+	1	NA	exon (NM_001289522, exon 40 of 43)	exon (NM_001289522, exon 40 of 43)	16050	NM_011773	22784	Mm.1396	NM_011773	ENSMUSG00000029151	Slc30a3	Znt3	solute carrier family 30 (zinc transporter), member 3	protein-coding
mm_66540.1	chr7	45188701	45188713	-	1	NA	intron (NM_201374, intron 13 of 19)	intron (NM_201374, intron 13 of 19)	7712	NM_053256	114640	Mm.207078	NM_053256	ENSMUSG00000038300	Pth2	Tifp39|Tip39	parathyroid hormone 2	protein-coding
mm_25560.1	chr3	116549173	116549184	+	1	NA	3' UTR (NM_010022, exon 11 of 11)	3' UTR (NM_010022, exon 11 of 11)	-13795	NM_027321	109245	Mm.216027	NM_027321	ENSMUSG00000027961	Lrrc39	2010005E21Rik|9430028I06Rik|Myomasp	leucine rich repeat containing 39	protein-coding
mm_80808.1	chr9	96392232	96392247	+	1	NA	Intergenic	Intergenic	-27940	NM_007502	11933	Mm.424	NM_007502	ENSMUSG00000032412	Atp1b3	AA409958|AI664000|AW212096	ATPase, Na+/K+ transporting, beta 3 polypeptide	protein-coding
mm_7735.1	chr1	130820707	130820729	-	1	NA	Intergenic	Intergenic	-5966	NM_011082	18703	Mm.276414	NM_011082	ENSMUSG00000026417	Pigr	-	polymeric immunoglobulin receptor	protein-coding
mm_80129.1	chr9	70581321	70581337	+	1	NA	exon (NM_025690, exon 14 of 21)	exon (NM_025690, exon 14 of 21)	38459	NM_025690	66660	Mm.22379	NM_025690	ENSMUSG00000032212	Sltm	5730455C01Rik|5730555F13Rik|9130215G10Rik|Met	SAFB-like, transcription modulator	protein-coding
mm_91597.1	chr10	40883074	40883130	-	1	NA	promoter-TSS (NM_027879)	promoter-TSS (NM_027879)	41	NM_027879	71713	Mm.46063	NM_027879	ENSMUSG00000038446	Cdc40	1200003H23Rik|EHB3|PRP17	cell division cycle 40	protein-coding
mm_88953.1	chr10	81364416	81364426	+	1	NA	TTS (NM_028657)	TTS (NM_028657)	1399	NM_001014836	432479	Mm.440450	NM_001014836	ENSMUSG00000020234	4930404N11Rik	2210409H10Rik|5730551K18Rik|AI854616	RIKEN cDNA 4930404N11 gene	protein-coding
mm_161943.1	chr19	4154616	4154616	+	1	NA	promoter-TSS (NM_016933)	promoter-TSS (NM_016933)	-30	NM_016933	19265	Mm.271937	NM_016933	ENSMUSG00000045826	Ptprcap	AI605264|CD-45-AP|LPAP|LSM-1	protein tyrosine phosphatase, receptor type, C polypeptide-associated protein	protein-coding
mm_5859.1	chr1	53760774	53760777	-	1	NA	intron (NM_133810, intron 7 of 7)	intron (NM_133810, intron 7 of 7)	24440	NM_133810	98267	Mm.25559	NM_133810	ENSMUSG00000026094	Stk17b	3110009A03Rik|AI120141|Drak2	serine/threonine kinase 17b (apoptosis-inducing)	protein-coding
mm_1772.1	chr1	78201213	78201246	+	1	NA	Intergenic	Intergenic	-4093	NM_001159520	18505	Mm.1371	NM_008781	ENSMUSG00000004872	Pax3	Pax-3|Sp|Splchl2|splotch	paired box 3	protein-coding
mm_107073.1	chr12	16910470	16910474	+	1	NA	intron (NM_009072, intron 1 of 32)	intron (NM_009072, intron 1 of 32)	15494	NM_009072	19878	Mm.276024	NM_009072	ENSMUSG00000020580	Rock2	B230113H15Rik|ROKalpha|Rho-kinase|Rock-II|Rock2m|mKIAA0619	Rho-associated coiled-coil containing protein kinase 2	protein-coding
mm_114993.1	chr13	97560023	97560034	+	1	NA	promoter-TSS (NR_046157)	promoter-TSS (NR_046157)	28	NR_046157	328314	Mm.138047	NR_046157	ENSMUSG00000110235	Gm5086	B230311A21|EG328314	predicted gene 5086	ncRNA
mm_155504.1	chrX	73787127	73787131	+	1	NA	promoter-TSS (NM_008323)	promoter-TSS (NM_008323)	-14	NM_009279	20832	Mm.831	NM_009279	ENSMUSG00000002014	Ssr4	AW743063|C78062|Trap	signal sequence receptor, delta	protein-coding
mm_169678.1	chr1	56782350	56782368	-	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	-144908	NM_027661	71066	Mm.152656	NM_027661	ENSMUSG00000045336	Hsfy2	4933413G11Rik|Hspy2l	heat shock transcription factor, Y-linked 2	protein-coding
mm_93846.1	chr10	121740312	121740324	-	1	NA	intron (NM_173022, intron 1 of 2)	intron (NM_173022, intron 1 of 2)	381	NM_173022	270802	Mm.209172	NM_173022	ENSMUSG00000053684	BC048403	E030027L10	cDNA sequence BC048403	protein-coding
mm_121723.1	chr14	16575365	16575412	-	1	NA	promoter-TSS (NM_001289762)	promoter-TSS (NM_001289762)	88	NM_011243	218772	Mm.259318	NM_011243	ENSMUSG00000017491	Rarb	A830025K23|Hap|Nr1b2	retinoic acid receptor, beta	protein-coding
mm_162153.1	chrX	79671378	79671378	-	1	NA	promoter-TSS (NM_028025)	promoter-TSS (NM_028025)	57	NM_028025	71967	Mm.379207	NM_028025	ENSMUSG00000046942	Mageb16	2410003J06Rik	melanoma antigen family B, 16	protein-coding
mm_37302.1	chr4	119233717	119233732	-	1	NA	promoter-TSS (NM_001042411)	promoter-TSS (NM_001042411)	-105	NM_001042411	56401	Mm.27961	NM_019782	ENSMUSG00000028641	P3h1	2410024C15Rik|Gros1|Lepre1	prolyl 3-hydroxylase 1	protein-coding
mm_74738.1	chr8	18741571	18741587	-	1	NA	promoter-TSS (NM_007426)	promoter-TSS (NM_007426)	-17	NM_007426	11601	Mm.439874	NM_007426	ENSMUSG00000031465	Angpt2	Agpt2|Ang-2|Ang2	angiopoietin 2	protein-coding
mm_44251.1	chr5	5380186	5380229	-	1	NA	promoter-TSS (NM_011074)	promoter-TSS (NM_011074)	44	NM_011074	18647	Mm.389061	NM_011074	ENSMUSG00000028926	Cdk14	Pftk1|mKIAA0834	cyclin-dependent kinase 14	protein-coding
mm_104392.1	chr11	94486243	94486264	-	1	NA	promoter-TSS (NM_144827)	promoter-TSS (NM_144827)	-943	NM_144827	217116	Mm.156123	NM_144827	ENSMUSG00000020867	Spata20	Tisp78	spermatogenesis associated 20	protein-coding
mm_97900.1	chr11	83409721	83409727	+	1	NA	promoter-TSS (NM_001013386)	promoter-TSS (NM_001013386)	-348	NM_001013386	276952	Mm.66275	NM_001013386	ENSMUSG00000020684	Rasl10b	B230331P10Rik|Gm729|VTS58635	RAS-like, family 10, member B	protein-coding
mm_170679.1	chr2	122219904	122219922	+	1	NA	Intergenic	Intergenic	-14926	NM_146126	20322	Mm.371580	NM_146126	ENSMUSG00000027227	Sord	Sdh-1|Sdh1|Sodh-1	sorbitol dehydrogenase	protein-coding
mm_146423.1	chr18	84838665	84838688	+	1	NA	Intergenic	Intergenic	-12738	NM_025797	109672	Mm.31018	NM_025797	ENSMUSG00000024646	Cyb5a	0610009N12Rik|Cyb5	cytochrome b5 type A (microsomal)	protein-coding
mm_87329.1	chr10	42901621	42901637	+	1	NA	intron (NM_172938, intron 1 of 8)	intron (NM_172938, intron 1 of 8)	41117	NM_172938	268297	Mm.98731	NM_172938	ENSMUSG00000044770	Scml4	9330161D17|mFLJ00197	sex comb on midleg-like 4 (Drosophila)	protein-coding
mm_35747.1	chr4	45482764	45482777	-	1	NA	intron (NM_001033306, intron 2 of 5)	intron (NM_001033306, intron 2 of 5)	48058	NM_001033306	230126	Mm.251716	NM_001033306	ENSMUSG00000044813	Shb	BC028832	src homology 2 domain-containing transforming protein B	protein-coding
mm_74381.1	chr8	128685875	128685911	+	1	NA	5' UTR (NM_010578, exon 1 of 16)	5' UTR (NM_010578, exon 1 of 16)	239	NM_010578	16412	Mm.263396	NM_010578	ENSMUSG00000025809	Itgb1	4633401G24Rik|AA409975|AA960159|CD29|ENSMUSG00000051907|Fnrb|Gm9863|gpIIa	integrin beta 1 (fibronectin receptor beta)	protein-coding
mm_71623.1	chr8	57436374	57436388	+	1	NA	Intergenic	Intergenic	-19542	NM_009136	20284	Mm.12886	NM_009136	ENSMUSG00000031610	Scrg1	AW124307	scrapie responsive gene 1	protein-coding
mm_55623.1	chr6	72235403	72235419	-	1	NA	5' UTR (NM_153778, exon 1 of 3)	5' UTR (NM_153778, exon 1 of 3)	166	NM_153778	71093	Mm.87449	NM_153778	ENSMUSG00000037621	Atoh8	4933425C05Rik|Hath6|Math6|bHLHa21|okadin	atonal bHLH transcription factor 8	protein-coding
mm_8516.1	chr1	154726747	154726772	-	1	NA	promoter-TSS (NM_009782)	promoter-TSS (NM_009782)	-839	NM_009782	12290	Mm.267517	NM_009782	ENSMUSG00000004110	Cacna1e	A430040I15|BII|Cach6|Cacnl1a6|Cav2.3|Cchra1|alpha1E	calcium channel, voltage-dependent, R type, alpha 1E subunit	protein-coding
mm_121351.1	chr14	116925506	116925513	+	1	NA	5' UTR (NM_011821, exon 1 of 9)	5' UTR (NM_011821, exon 1 of 9)	212	NM_011821	23888	Mm.440025	NM_011821	ENSMUSG00000058571	Gpc6	-	glypican 6	protein-coding
mm_35617.1	chr4	43452458	43452489	-	1	NA	exon (NM_001110320, exon 5 of 9)	exon (NM_001110320, exon 5 of 9)	2153	NM_001110320	12517	Mm.188157	NM_007654	ENSMUSG00000028459	Cd72	CD72c|Ly-19|Ly-32|Ly-m19|Lyb-2	CD72 antigen	protein-coding
mm_73684.1	chr8	111553101	111553107	+	1	NA	intron (NM_001168623, intron 1 of 4)	B3|SINE|B2	14761	NM_001168623	170737	Mm.271578	NM_133206	ENSMUSG00000033545	Znrf1	B830022L21Rik|Rnf42|Zrfp1|nin283	zinc and ring finger 1	protein-coding
mm_53900.1	chr6	3494487	3494526	-	1	NA	promoter-TSS (NM_178899)	promoter-TSS (NM_178899)	-8	NM_178899	101202	Mm.206911	NM_178899	ENSMUSG00000044156	Hepacam2	AI987662	HEPACAM family member 2	protein-coding
mm_95220.1	chr11	44215624	44215653	+	1	NA	Intergenic	Tigger7|DNA|TcMar-Tigger	-184425	NM_001303244	16160	Mm.239707	NM_008352	ENSMUSG00000004296	Il12b	Il-12b|Il-12p40|Il12p40|p40	interleukin 12b	protein-coding
mm_60194.1	chr7	43408275	43408285	+	1	NA	promoter-TSS (NM_172900)	promoter-TSS (NM_172900)	0	NM_172900	243958	Mm.24444	NM_172900	ENSMUSG00000030468	Siglecg	9830164H23|A630096C01Rik|Siglec-G|Siglec10|mSiglec-G	sialic acid binding Ig-like lectin G	protein-coding
mm_131078.1	chr16	4731216	4731217	+	1	NA	intron (NM_001136066, intron 1 of 5)	intron (NM_001136066, intron 1 of 5)	4855	NM_001136066	15369	Mm.272866	NM_010443	ENSMUSG00000004070	Hmox2	HO-2|HO2	heme oxygenase 2	protein-coding
mm_11442.1	chr2	32045725	32045749	+	1	NA	intron (NM_172268, intron 32 of 35)	intron (NM_172268, intron 32 of 35)	-5209	NR_106135	102466844		NR_106135	ENSMUSG00000099075	Mir7674	Gm27563|mmu-mir-7674	microRNA 7674	ncRNA
mm_57156.1	chr6	122732439	122732459	-	1	NA	exon (NM_011401, exon 8 of 10)	exon (NM_011401, exon 8 of 10)	10296	NM_011401	20527	Mm.395108	NM_011401	ENSMUSG00000003153	Slc2a3	AA408729|AL023014|AL024341|AU040424|C78366|Glut-3|Glut3	solute carrier family 2 (facilitated glucose transporter), member 3	protein-coding
mm_111642.1	chr12	102657863	102657871	-	1	NA	intron (NM_172584, intron 2 of 9)	intron (NM_172584, intron 2 of 9)	27153	NR_035457	100316812		NR_035457	ENSMUSG00000089324	Mir1936	mir-1936|mmu-mir-1936	microRNA 1936	ncRNA
mm_163340.1	chr12	13566128	13566152	+	1	NA	exon (NM_027706, exon 51 of 52)	exon (NM_027706, exon 51 of 52)	61506	NR_136761	102639399	Mm.122052	NR_136761		Gm35725	-	predicted gene, 35725	ncRNA
mm_55332.1	chr6	56361857	56361870	-	1	NA	5' UTR (NM_001159953, exon 1 of 19)	5' UTR (NM_001159953, exon 1 of 19)	529	NM_001159952	18575	Mm.5145	NM_011054	ENSMUSG00000004347	Pde1c	-	phosphodiesterase 1C	protein-coding
mm_23612.1	chr3	65528435	65528454	+	1	NA	promoter-TSS (NM_178892)	promoter-TSS (NM_178892)	-3	NM_178892	99929	Mm.246398	NM_178892	ENSMUSG00000034640	Tiparp	ARTD14|AW558171|PARP7	TCDD-inducible poly(ADP-ribose) polymerase	protein-coding
mm_110986.1	chr12	77113631	77113655	-	1	NA	Intergenic	Intergenic	-124461	NM_001252614	53618	Mm.35628	NM_016893	ENSMUSG00000021065	Fut8	-	fucosyltransferase 8	protein-coding
mm_8708.1	chr1	158958170	158958180	-	1	NA	promoter-TSS (NM_001085376)	promoter-TSS (NM_001085376)	-737	NM_001085376	23850	Mm.458621	NM_001085376	ENSMUSG00000073530	Pappa2	PAPP-A2|PLAC3|Pappe	pappalysin 2	protein-coding
mm_23428.1	chr3	59005814	59005865	+	1	NA	Intergenic	CpG	-1139	NM_177855	329650	Mm.240059	NM_177855	ENSMUSG00000056476	Med12l	A130035F20|A630079M02|AU044581|TRALPUSH	mediator complex subunit 12-like	protein-coding
mm_23989.1	chr3	86224666	86224717	+	1	NA	promoter-TSS (NM_030695)	promoter-TSS (NM_030695)	1	NM_001077687	80877	Mm.439825	NM_030695	ENSMUSG00000028080	Lrba	C80285|D3Ertd775e|Lab300|Lba	LPS-responsive beige-like anchor	protein-coding
mm_35309.1	chr4	25242834	25242873	-	1	NA	promoter-TSS (NM_021318)	promoter-TSS (NM_021318)	23	NM_021318	57756	Mm.87325	NM_021318	ENSMUSG00000028259	Fhl5	1700027G07Rik|Act	four and a half LIM domains 5	protein-coding
mm_141035.1	chr17	25273507	25273526	-	1	NA	promoter-TSS (NR_027452)	promoter-TSS (NR_027452)	-85	NM_001177610	22196	Mm.240044	NM_011665	ENSMUSG00000015120	Ube2i	5830467E05Rik|F830028O17Rik|UBC9|Ubce2i|Ubce9	ubiquitin-conjugating enzyme E2I	protein-coding
mm_142625.1	chr17	47395381	47395391	-	1	NA	intron (NM_008189, intron 2 of 3)	intron (NM_008189, intron 2 of 3)	5220	NM_008189	14913	Mm.16224	NM_008189	ENSMUSG00000023982	Guca1a	GC-A|Gcap1|Guca1|mGCAP1	guanylate cyclase activator 1a (retina)	protein-coding
mm_94300.1	chr11	4135168	4135222	+	1	NA	promoter-TSS (NM_027859)	promoter-TSS (NM_027859)	35	NM_027859	71673	Mm.240586	NM_027859	ENSMUSG00000003581	Rnf215	0610009J22Rik|AW557025|C77903	ring finger protein 215	protein-coding
mm_129783.1	chr15	82794290	82794300	-	1	NA	promoter-TSS (NM_029562)	promoter-TSS (NM_029562)	-50	NM_029562	76279	Mm.439931	NM_029562	ENSMUSG00000022445	Cyp2d26	1300006E06Rik	cytochrome P450, family 2, subfamily d, polypeptide 26	protein-coding
mm_153888.1	chr19	46962302	46962317	-	1	NA	promoter-TSS (NM_029810)	promoter-TSS (NM_029810)	42	NM_029810	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_155085.1	chrX	48106851	48106864	+	1	NA	Intergenic	Intergenic	-1868	NM_001289729	170745	Mm.129279	NM_133213	ENSMUSG00000037005	Xpnpep2	9030008G12Rik|mAPP	X-prolyl aminopeptidase (aminopeptidase P) 2, membrane-bound	protein-coding
mm_70795.1	chr8	22706627	22706632	+	1	NA	promoter-TSS (NM_010546)	promoter-TSS (NM_010546)	-46	NM_001159774	16150	Mm.277886	NM_010546	ENSMUSG00000031537	Ikbkb	AI132552|IKK-2|IKK-beta|IKK2|IKK[b]|IKKbeta	inhibitor of kappaB kinase beta	protein-coding
mm_87206.1	chr10	39732100	39732140	+	1	NA	promoter-TSS (NM_011264)	promoter-TSS (NM_011264)	-40	NM_011264	19714	Mm.439723	NM_011264	ENSMUSG00000019841	Rev3l	Rev|Rev3|Sez4	REV3 like, DNA directed polymerase zeta catalytic subunit	protein-coding
mm_70283.1	chr8	3621601	3621609	+	1	NA	promoter-TSS (NM_026156)	promoter-TSS (NM_026156)	54	NM_001195244	100503890	Mm.254898	NM_001195244	ENSMUSG00000087687	Pet100	2900053A13Rik	PET100 homolog	protein-coding
mm_56024.1	chr6	86594713	86594719	-	1	NA	Intergenic	MTEa|LTR|ERVL-MaLR	-33458	NM_026414	67855	Mm.183043	NM_026414	ENSMUSG00000033508	Asprv1	2300003P22Rik|AA986851|SASP|SASPase|Taps	aspartic peptidase, retroviral-like 1	protein-coding
mm_87237.1	chr10	40883470	40883483	+	1	NA	promoter-TSS (NM_027879)	promoter-TSS (NM_027879)	-58	NM_031877	83767	Mm.41353	NM_031877	ENSMUSG00000019831	Wasf1	AI195380|AI838537|Scar|WAVE|WAVE-1	WAS protein family, member 1	protein-coding
mm_11971.1	chr2	54436433	54436441	+	1	NA	promoter-TSS (NM_173030)	promoter-TSS (NM_173030)	50	NM_173030	271786	Mm.330227	NM_173030	ENSMUSG00000060988	Galnt13	A230002A12|A230020F20|BB182356	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13	protein-coding
mm_9987.1	chr1	191277616	191277628	-	1	NA	Intergenic	Intergenic	40496	NM_025424	66208	Mm.46444	NM_025424	ENSMUSG00000037499	Nenf	1110060M21Rik|SCIRP10|Spuf	neuron derived neurotrophic factor	protein-coding
mm_59632.1	chr7	28157526	28157535	+	1	NA	intron (NM_001164655, intron 15 of 19)	intron (NM_001164655, intron 15 of 19)	-12218	NM_007991	14113	Mm.4595	NM_007991	ENSMUSG00000046865	Fbl	AL022665|FIB|FLRN|RNU3IP1	fibrillarin	protein-coding
mm_115985.1	chr13	24281293	24281325	-	1	NA	promoter-TSS (NM_026825)	promoter-TSS (NM_026825)	-519	NM_026825	68732	Mm.211047	NM_026825	ENSMUSG00000021338	Carmil1	1110037D04Rik|AI425970|CARMIL|CARML1|D130057M20|Lrrc16|Lrrc16a	capping protein regulator and myosin 1 linker 1	protein-coding
mm_17247.1	chr2	25627914	25627926	-	1	NA	promoter-TSS (NM_007995)	promoter-TSS (NM_007995)	54	NM_007995	14133	Mm.10510	NM_007995	ENSMUSG00000026938	Fcna	Fcn1	ficolin A	protein-coding
mm_50505.1	chr6	49036570	49036580	+	1	NA	promoter-TSS (NM_053110)	promoter-TSS (NM_053110)	57	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_67041.1	chr7	67239375	67239405	-	1	NA	intron (NM_001291191, intron 9 of 10)	B1_Mus1|SINE|Alu	16774	NM_001191051	75099	Mm.121691	NM_175215	ENSMUSG00000043831	Lysmd4	4930506D23Rik	LysM, putative peptidoglycan-binding, domain containing 4	protein-coding
mm_110967.1	chr12	76910463	76910499	-	1	NA	intron (NM_145927, intron 9 of 11)	intron (NM_145927, intron 9 of 11)	51767	NM_008558	17187	Mm.268548	NM_008558	ENSMUSG00000059436	Max	AA960152|AI875693|bHLHd4|bHLHd5|bHLHd6|bHLHd7|bHLHd8	Max protein	protein-coding
mm_129079.1	chr15	75841908	75841932	-	1	NA	promoter-TSS (NM_172121)	promoter-TSS (NM_172121)	-12	NM_172121	223642	Mm.209800	NM_172121	ENSMUSG00000075600	Zc3h3	BC049953|Kiaa0150|Smicl|Zc3hdc3	zinc finger CCCH type containing 3	protein-coding
mm_128568.1	chr15	57265127	57265150	-	1	NA	intron (NM_172378, intron 2 of 11)	intron (NM_172378, intron 2 of 11)	212487	NM_172378	210463	Mm.26555	NM_172378	ENSMUSG00000022366	Slc22a22	oat-pg	solute carrier family 22 (organic cation transporter), member 22	protein-coding
mm_152324.1	chr19	9938835	9938849	-	1	NA	Intergenic	Intergenic	-39309	NM_016692	16319	Mm.29755	NM_016692	ENSMUSG00000024660	Incenp	2700067E22Rik|AU019509|C130081E20|C77457	inner centromere protein	protein-coding
mm_102882.1	chr11	69410653	69410667	-	1	NA	intron (NM_001017426, intron 1 of 22)	CpG	3015	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_25819.1	chr3	127798232	127798249	+	1	NA	3' UTR (NM_145133, exon 3 of 3)	3' UTR (NM_145133, exon 3 of 3)	8327	NM_145133	211550	Mm.31852	NM_145133	ENSMUSG00000046688	Tifa	T2bp	TRAF-interacting protein with forkhead-associated domain	protein-coding
mm_62828.1	chr7	113514112	113514139	+	1	NA	intron (NM_001285831, intron 1 of 12)	L1M4b|LINE|L1	291	NM_027379	67420	Mm.206919	NM_026143	ENSMUSG00000030759	Far1	2600011M19Rik|2900034E22Rik|3732409C05Rik|AI850429|Mlstd2	fatty acyl CoA reductase 1	protein-coding
mm_66015.1	chr7	30598832	30598855	-	1	NA	Intergenic	Intergenic	-5901	NM_021397	58206	Mm.116789	NM_021397	ENSMUSG00000006310	Zbtb32	4930524C15Rik|FAXF|FAZF|PLZP|Rog|Tzfp	zinc finger and BTB domain containing 32	protein-coding
mm_44660.1	chr5	28458897	28458910	-	1	NA	intron (NM_009170, intron 2 of 2)	CpG	-8081	NR_015562	654796	Mm.57202	NR_015562	ENSMUSG00000097726	9530036O11Rik	-	RIKEN cDNA 9530036O11Rik	ncRNA
mm_86469.1	chr10	4611621	4611633	+	1	NA	promoter-TSS (NR_126357)	promoter-TSS (NR_126357)	-362	NM_001302532	13982	Mm.9213	NM_007956	ENSMUSG00000019768	Esr1	ER|ER-alpha|ERa|ERalpha|ESR|Estr|Estra|Nr3a1	estrogen receptor 1 (alpha)	protein-coding
mm_122711.1	chr14	52237771	52237792	-	1	NA	promoter-TSS (NM_201637)	promoter-TSS (NM_201637)	-209	NM_201637	67772	Mm.289934	NM_201637	ENSMUSG00000053754	Chd8	5830451P18Rik|AU015341|Duplin|HELSNF1|mKIAA1564	chromodomain helicase DNA binding protein 8	protein-coding
mm_62296.1	chr7	100006035	100006064	+	1	NA	promoter-TSS (NM_133709)	promoter-TSS (NM_133709)	-355	NM_133709	69121	Mm.285295	NM_133709	ENSMUSG00000030732	Chrdl2	1810022C01Rik|Chl2	chordin-like 2	protein-coding
mm_50350.1	chr6	48589607	48589636	+	1	NA	5' UTR (NM_183309, exon 1 of 2)	5' UTR (NM_183309, exon 1 of 2)	176	NM_183309	330305	Mm.123868	NM_183309	ENSMUSG00000052730	Gm5111	A630038D02|EG330305	predicted gene 5111	protein-coding
mm_31637.1	chr4	59440139	59440155	+	1	NA	Intergenic	Intergenic	-1514	NM_001163288	634731	Mm.483589	NM_001163288	ENSMUSG00000038578	Susd1	A530080P10|Gm12528|OTTMUSG00000007332	sushi domain containing 1	protein-coding
mm_48330.1	chr5	138997636	138997646	-	1	NA	Intergenic	CpG	-2688	NM_008808	18590	Mm.2675	NM_008808	ENSMUSG00000025856	Pdgfa	-	platelet derived growth factor, alpha	protein-coding
mm_113760.1	chr13	44749069	44749073	+	1	NA	intron (NM_001205044, intron 2 of 18)	intron (NM_001205044, intron 2 of 18)	17800	NM_001205043	16468	Mm.25059	NM_021878	ENSMUSG00000038518	Jarid2	Jmj|jumonji	jumonji, AT rich interactive domain 2	protein-coding
mm_113937.1	chr13	49654401	49654418	+	1	NA	exon (NM_001271397, exon 2 of 17)	exon (NM_001271397, exon 2 of 17)	1331	NR_073167	70930	Mm.258915	NM_001081350	ENSMUSG00000021392	Nol8	4921532D18Rik|5730412B09Rik	nucleolar protein 8	protein-coding
mm_85213.1	chr9	96862975	96862985	-	1	NA	intron (NM_001289645, intron 1 of 6)	intron (NM_001289645, intron 1 of 6)	26494	NM_001289646	235534	Mm.233031	NM_153420	ENSMUSG00000043587	Pxylp1	9430094M07Rik|Acpl2|BB177120|C130099A20Rik	2-phosphoxylose phosphatase 1	protein-coding
mm_148948.1	chr19	7268236	7268294	+	1	NA	promoter-TSS (NM_001320554)	promoter-TSS (NM_001320554)	-14	NM_001320554	104383	Mm.283859	NM_054048	ENSMUSG00000024968	Rcor2	1A13|AW122124|CoREST|Rcor|Rcor1	REST corepressor 2	protein-coding
mm_29160.1	chr3	106149775	106149792	-	1	NA	exon (NM_009892, exon 8 of 11)	exon (NM_009892, exon 8 of 11)	17781	NM_009892	12655	Mm.387173	NM_009892	ENSMUSG00000040809	Chil3	AI505981|Chi3l3|ECF-L|Ym1	chitinase-like 3	protein-coding
mm_41166.1	chr5	87963274	87963276	+	1	NA	intron (NR_045924, intron 1 of 4)	intron (NR_045924, intron 1 of 4)	16076	NR_045924	73471	Mm.396240	NR_045924	ENSMUSG00000099605	1700066N21Rik	-	RIKEN cDNA 1700066N21 gene	ncRNA
mm_93723.1	chr10	119239816	119239826	-	1	NA	5' UTR (NM_027994, exon 1 of 15)	5' UTR (NM_027994, exon 1 of 15)	234	NM_027994	71902	Mm.203965	NM_027994	ENSMUSG00000020114	Cand1	2310038O07Rik|6330512O03Rik|AI195005|AI846556|D10Ertd516e|Tp120a|mKIAA0829	cullin associated and neddylation disassociated 1	protein-coding
mm_106813.1	chr12	7977641	7977654	+	1	NA	promoter-TSS (NM_009693)	promoter-TSS (NM_009693)	-30	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_14565.1	chr2	135022250	135022254	+	1	NA	intron (NM_019677, intron 3 of 32)	intron (NM_019677, intron 3 of 32)	193364	NR_040517	78805	Mm.78702	NR_040517	ENSMUSG00000085247	4930545L23Rik	-	RIKEN cDNA 4930545L23 gene	ncRNA
mm_8860.1	chr1	162724790	162724813	-	1	NA	exon (NM_001081290, exon 2 of 35)	exon (NM_001081290, exon 2 of 35)	15755	NM_001081290	226562	Mm.245446	NM_001081290	ENSMUSG00000040225	Prrc2c	1810043M20Rik|9630039I18Rik|A630006J20|Bat2d|Bat2d1|Bat2l2|E130112L15Rik|Prrc3|mKIAA1096	proline-rich coiled-coil 2C	protein-coding
mm_106036.1	chr11	116077955	116077979	-	1	NA	promoter-TSS (NM_001009573)	promoter-TSS (NM_001009573)	-6	NM_001009573	70450	Mm.259460	NM_001009573	ENSMUSG00000057948	Unc13d	2610108D09Rik|Jinx|Munc13-4|mFLJ00067	unc-13 homolog D (C. elegans)	protein-coding
mm_124060.1	chr14	78088995	78089031	-	1	NA	promoter-TSS (NM_177629)	promoter-TSS (NM_177629)	-6	NM_177629	219170	Mm.320428	NM_177629	ENSMUSG00000045655	Fam216b	9330158N17|AU021034	family with sequence similarity 216, member B	protein-coding
mm_173171.1	chrX	46977953	46977967	+	1	NA	Intergenic	L1Md_T|LINE|L1	648953	NM_028514	73360	Mm.60929	NM_028514	ENSMUSG00000046615	Actrt1	1700061J02Rik|Arp-T1	actin-related protein T1	protein-coding
mm_125893.1	chr15	75886990	75887003	+	1	NA	intron (NM_001282443, intron 4 of 13)	intron (NM_001282443, intron 4 of 13)	1727	NM_001282443	223645		NM_001282443	ENSMUSG00000098678	Mroh6	Gm19570	maestro heat-like repeat family member 6	protein-coding
mm_35287.1	chr4	21767116	21767142	-	1	NA	promoter-TSS (NM_029840)	promoter-TSS (NM_029840)	82	NM_029840	77032	Mm.87238	NM_029840	ENSMUSG00000028251	Tstd3	2610029I01Rik	thiosulfate sulfurtransferase (rhodanese)-like domain containing 3	protein-coding
mm_87705.1	chr10	59932800	59932819	+	1	NA	Intergenic	Intergenic	18961	NM_029083	74747	Mm.21697	NM_029083	ENSMUSG00000020108	Ddit4	5830413E08Rik|AA415483|REDD1|Rtp801|dig2	DNA-damage-inducible transcript 4	protein-coding
mm_92571.1	chr10	79908892	79908936	-	1	NA	promoter-TSS (NM_001163276)	promoter-TSS (NM_001163276)	24	NM_001163276	216154	Mm.260089	NM_198107	ENSMUSG00000013833	Med16	95kDa|A630083L04|Thrap5|Trap95	mediator complex subunit 16	protein-coding
mm_14298.1	chr2	128967384	128967443	+	1	NA	promoter-TSS (NM_178404)	promoter-TSS (NM_178404)	11	NM_178404	78751	Mm.26377	NM_178404	ENSMUSG00000042851	Zc3h6	4631426G04Rik|4833425H18Rik|AU024389|AW060453|Zc3hdc6|mKIAA2035	zinc finger CCCH type containing 6	protein-coding
mm_15874.1	chr2	164835630	164835651	+	1	NA	exon (NM_008906, exon 7 of 15)	exon (NM_008906, exon 7 of 15)	1867	NM_008906	19025	Mm.359633	NM_008906	ENSMUSG00000017760	Ctsa	AU019505|PPCA|Ppgb	cathepsin A	protein-coding
mm_67287.1	chr7	78736103	78736106	-	1	NA	Intergenic	L1MD2|LINE|L1	-17884	NR_015542	414121	Mm.482537	NR_015542	ENSMUSG00000059146	E430016F16Rik	-	RIKEN cDNA E430016F16 gene	ncRNA
mm_20647.1	chr2	132029825	132029844	-	1	NA	5' UTR (NM_175445, exon 1 of 11)	5' UTR (NM_175445, exon 1 of 11)	154	NM_175445	215653	Mm.204737	NM_175445	ENSMUSG00000027339	Rassf2	3830431H01Rik|9030412M04Rik|AI852669|AW495050	Ras association (RalGDS/AF-6) domain family member 2	protein-coding
mm_169340.1	chr14	13230511	13230517	+	1	NA	intron (NR_121588, intron 2 of 3)	RLTR9F|LTR|ERVK	54124	NR_121589	328354	Mm.252404	NM_177813	ENSMUSG00000051729	Gm5087	C630025C03|EG328354	predicted gene 5087	ncRNA
mm_143089.1	chr17	57080458	57080508	-	1	NA	3' UTR (NM_009451, exon 4 of 4)	3' UTR (NM_009451, exon 4 of 4)	-1973	NM_153551	70785	Mm.284447	NM_153551	ENSMUSG00000002668	Dennd1c	4432409M07Rik	DENN/MADD domain containing 1C	protein-coding
mm_30316.1	chr3	151731528	151731550	-	1	NA	3' UTR (NM_133871, exon 8 of 8)	3' UTR (NM_133871, exon 8 of 8)	18420	NM_133871	99899	Mm.30756	NM_133871	ENSMUSG00000028037	Ifi44	A430056A10Rik|AW261460|MTAP44|p44	interferon-induced protein 44	protein-coding
mm_60532.1	chr7	44480302	44480310	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-4211	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_142491.1	chr17	46017636	46017646	-	1	NA	3' UTR (NM_001025250, exon 8 of 8)	3' UTR (NM_001025250, exon 8 of 8)	7522	NM_001110267	22339	Mm.282184	NM_009505	ENSMUSG00000023951	Vegfa	Vegf|Vpf	vascular endothelial growth factor A	protein-coding
mm_16866.1	chr2	12013905	12013911	-	1	NA	Intergenic	RMER19B2|LTR|ERVK	236155	NM_177268	320816	Mm.260201	NM_177268	ENSMUSG00000047909	Ankrd16	2810455F06Rik|AI646698|D430029B21Rik	ankyrin repeat domain 16	protein-coding
mm_109078.1	chr12	104406734	104406754	+	1	NA	promoter-TSS (NM_009252)	promoter-TSS (NM_009252)	36	NM_009252	20716	Mm.482074	NM_009252	ENSMUSG00000021091	Serpina3n	Spi2-2|Spi2.2|Spi2/eb.4	serine (or cysteine) peptidase inhibitor, clade A, member 3N	protein-coding
mm_74155.1	chr8	123383376	123383400	+	1	NA	exon (NM_001037877, exon 4 of 18)	exon (NM_001037877, exon 4 of 18)	9677	NM_001286363	66855	Mm.178818	NM_025804	ENSMUSG00000001472	Tcf25	1100001J13Rik|1810041K11Rik|D8Ertd325e|Nulp1|mKIAA1049	transcription factor 25 (basic helix-loop-helix)	protein-coding
mm_67528.1	chr7	81213202	81213213	-	1	NA	promoter-TSS (NM_008803)	promoter-TSS (NM_008803)	-597	NM_008803	18584	Mm.371577	NM_008803	ENSMUSG00000025584	Pde8a	AI551852|Pde8	phosphodiesterase 8A	protein-coding
mm_132762.1	chr16	44724272	44724325	+	1	NA	promoter-TSS (NM_145972)	promoter-TSS (NM_145972)	-3	NM_145972	212547	Mm.310573	NM_145972	ENSMUSG00000036208	Nepro	-	nucleolus and neural progenitor protein	protein-coding
mm_137176.1	chr17	23816085	23816101	+	1	NA	exon (NM_175229, exon 10 of 14)	exon (NM_175229, exon 10 of 14)	12906	NM_175229	75956	Mm.5222	NM_175229	ENSMUSG00000039218	Srrm2	5033413A03Rik|AA410130|SRm300|mKIAA0324	serine/arginine repetitive matrix 2	protein-coding
mm_156462.1	chrX	143483007	143483015	+	1	NA	Intergenic	SYNREP_MM|Satellite|Satellite	-35580	NM_001195048	18481	Mm.40035	NM_008778	ENSMUSG00000031284	Pak3	PAK-3|Pak65alpha|Pak65beta|Stk4	p21 protein (Cdc42/Rac)-activated kinase 3	protein-coding
mm_82146.1	chr9	123774597	123774601	+	1	NA	intron (NM_009913, intron 2 of 2)	intron (NM_009913, intron 2 of 2)	7388	NM_001166625	12769	Mm.440604	NM_009913	ENSMUSG00000029530	Ccr9	A130091K22Rik|Cmkbr10|GPR-9-6	chemokine (C-C motif) receptor 9	protein-coding
mm_83713.1	chr9	50752052	50752063	-	1	NA	promoter-TSS (NM_001289784)	promoter-TSS (NM_001289784)	297	NM_001164708	69253	Mm.1980	NM_024441	ENSMUSG00000038086	Hspb2	27kDa|2810021G24Rik|HSP27|MKBP	heat shock protein 2	protein-coding
mm_111848.1	chr12	107938831	107938839	-	1	NA	intron (NM_001286343, intron 1 of 1)	RLTR20C1_MM|LTR|ERVK	64579	NM_001079883	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_165559.1	chr3	14886419	14886427	+	1	NA	promoter-TSS (NM_009801)	promoter-TSS (NM_009801)	-3	NM_009801	12349	Mm.1186	NM_009801	ENSMUSG00000027562	Car2	AI131712|CAII|Ca2|Car-2|Ltw-5|Lvtw-5	carbonic anhydrase 2	protein-coding
mm_105863.1	chr11	114066175	114066188	-	1	NA	promoter-TSS (NM_172800)	promoter-TSS (NM_172800)	-230	NM_172800	237979	Mm.130504	NM_172800	ENSMUSG00000041592	Sdk2	4632412F08Rik|5330435L01Rik|Sdk-2|mKIAA1514	sidekick cell adhesion molecule 2	protein-coding
mm_112501.1	chr13	8243745	8243747	+	1	NA	intron (NR_110345, intron 1 of 10)	intron (NR_110345, intron 1 of 10)	40880	NM_052977	94191	Mm.425794	NM_052977	ENSMUSG00000052551	Adarb2	Adar3|RED2	adenosine deaminase, RNA-specific, B2	protein-coding
mm_82786.1	chr9	28996207	28996223	-	1	NA	3' UTR (NM_172290, exon 8 of 8)	3' UTR (NM_172290, exon 8 of 8)	966914	NM_172290	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding
mm_87798.1	chr10	60299982	60300021	+	1	NA	exon (NM_011179, exon 11 of 15)	exon (NM_011179, exon 11 of 15)	15540	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_81041.1	chr9	105395349	105395411	+	1	NA	promoter-TSS (NM_025651)	promoter-TSS (NM_025651)	-12	NM_025651	66595	Mm.84941	NM_025651	ENSMUSG00000032567	Aste1	1100001A21Rik|AV006403	asteroid homolog 1 (Drosophila)	protein-coding
mm_131386.1	chr16	14207647	14207653	+	1	NA	exon (NM_013607, exon 31 of 42)	exon (NM_013607, exon 31 of 42)	44375	NM_001114085	67203	Mm.24105	NM_023317	ENSMUSG00000022678	Nde1	2810027M15Rik|AU042936|AW822251|Nude|mNudE	nudE neurodevelopment protein 1	protein-coding
mm_168741.1	chr12	115208577	115208582	-	1	NA	Intergenic	Intergenic	487215	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
mm_117510.1	chr13	78203431	78203452	-	1	NA	intron (NR_045195, intron 1 of 2)	CpG	-4568	NM_010151	13865	Mm.439653	NM_010151	ENSMUSG00000069171	Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR-3|EAR3|Erbal3|SVP44|Tcfcoup1	nuclear receptor subfamily 2, group F, member 1	protein-coding
mm_42112.1	chr5	110603497	110603528	+	1	NA	promoter-TSS (NR_104449)	promoter-TSS (NR_104449)	7	NR_104449	231605	Mm.275748	NM_198306	ENSMUSG00000033316	Galnt9	GalNAc-T9	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 9	protein-coding
mm_154297.1	chr19	61224610	61224630	-	1	NA	3' UTR (NM_009970, exon 12 of 12)	3' UTR (NM_009970, exon 12 of 12)	3798	NM_009970	12982	Mm.287228	NM_009970	ENSMUSG00000059326	Csf2ra	CD116|Csfgmra|GM-CSF-Ra|GM-CSFR	colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)	protein-coding
mm_146005.1	chr18	69344470	69344501	+	1	NA	promoter-TSS (NM_013685)	promoter-TSS (NM_013685)	-7	NM_013685	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding
mm_17914.1	chr2	35397175	35397208	-	1	NA	promoter-TSS (NM_001272040)	promoter-TSS (NM_001272040)	-17	NM_001272040	74854	Mm.159338	NM_001080709	ENSMUSG00000079421	4930402F06Rik	-	RIKEN cDNA 4930402F06 gene	protein-coding
mm_35042.1	chr4	4138962	4138968	-	1	NA	promoter-TSS (NM_001002927)	promoter-TSS (NM_001002927)	-520	NM_001002927	18619	Mm.475097	NM_001002927	ENSMUSG00000045573	Penk	AI326464|ENK|PPA|Penk1	preproenkephalin	protein-coding
mm_69243.1	chr7	127807018	127807034	-	1	NA	3' UTR (NM_024414, exon 10 of 10)	3' UTR (NM_024414, exon 10 of 10)	6417	NM_001040684	101502	Mm.157103	NM_133943	ENSMUSG00000042289	Hsd3b7	AI195443|BB098564	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 7	protein-coding
mm_90027.1	chr10	115411387	115411392	+	1	NA	intron (NM_001033261, intron 14 of 34)	intron (NM_001033261, intron 14 of 34)	26430	NM_001033261	216345	Mm.207621	NM_001033261	ENSMUSG00000034163	Zfc3h1	BC033596|Ccdc131|Psrc2	zinc finger, C3H1-type containing	protein-coding
mm_166910.1	chr7	29281770	29281784	-	1	NA	5' UTR (NM_001082548, exon 1 of 6)	5' UTR (NM_001082548, exon 1 of 6)	200	NM_001082548	20733	Mm.295230	NM_011464	ENSMUSG00000074227	Spint2	AL024025|C76321|HAI-2	serine protease inhibitor, Kunitz type 2	protein-coding
mm_26714.1	chr3	157993719	157993731	+	1	NA	intron (NM_001013806, intron 8 of 12)	intron (NM_001013806, intron 8 of 12)	38029	NM_001093753	69207	Mm.223946	NM_026989	ENSMUSG00000055436	Srsf11	0610009J05Rik|2610019N13Rik|BF642805|Sfrs11	serine/arginine-rich splicing factor 11	protein-coding
mm_9417.1	chr1	172326229	172326238	-	1	NA	exon (NM_008429, exon 3 of 4)	exon (NM_008429, exon 3 of 4)	3030	NM_008429	16524	Mm.261168	NM_008429	ENSMUSG00000038026	Kcnj9	1700085N21Rik|Girk3|Kir3.3|mbGIRK3	potassium inwardly-rectifying channel, subfamily J, member 9	protein-coding
mm_139455.1	chr17	55952729	55952739	+	1	NA	5' UTR (NM_015766, exon 1 of 5)	5' UTR (NM_015766, exon 1 of 5)	111	NM_015766	50498	Mm.256798	NM_015766	ENSMUSG00000003206	Ebi3	EBI-3|IL-27	Epstein-Barr virus induced gene 3	protein-coding
mm_19932.1	chr2	116065646	116065656	-	1	NA	promoter-TSS (NM_010825)	promoter-TSS (NM_010825)	-593	NM_010825	17536	Mm.247566	NM_010825	ENSMUSG00000027210	Meis2	A430109D20Rik|Mrg1|Stra10	Meis homeobox 2	protein-coding
mm_10908.1	chr2	25356448	25356476	+	1	NA	promoter-TSS (NM_031843)	promoter-TSS (NM_031843)	-130	NM_031843	83768	Mm.21440	NM_031843	ENSMUSG00000026958	Dpp7	DPPII|Dpp2|QPP	dipeptidylpeptidase 7	protein-coding
mm_81122.1	chr9	106463258	106463272	+	1	NA	TTS (NM_001159652)	TTS (NM_001159652)	2675	NM_001159652	436090	Mm.482905	NM_001159652	ENSMUSG00000091735	Gpr62	4933402E03Rik	G protein-coupled receptor 62	protein-coding
mm_126172.1	chr15	78561913	78561952	+	1	NA	exon (NM_009008, exon 6 of 7)	exon (NM_009008, exon 6 of 7)	10851	NM_009008	19354	Mm.1972	NM_009008	ENSMUSG00000033220	Rac2	AI323801|AI452260	RAS-related C3 botulinum substrate 2	protein-coding
mm_77029.1	chr8	109251420	109251436	-	1	NA	non-coding (NR_126329, exon 10 of 10)	non-coding (NR_126329, exon 10 of 10)	89480	NR_002928	384864	Mm.390083	NR_002928		Gm1943	-	WD repeat domain 70 pseudogene	pseudo
mm_93348.1	chr10	100487317	100487357	-	1	NA	promoter-TSS (NM_001110013)	promoter-TSS (NM_001110013)	10	NM_001033332	237500	Mm.296805	NM_001033332	ENSMUSG00000036676	Tmtc3	9130014E20Rik|B130008E12Rik|mSmile	transmembrane and tetratricopeptide repeat containing 3	protein-coding
mm_96382.1	chr11	67243424	67243444	+	1	NA	exon (NM_010855, exon 11 of 40)	exon (NM_010855, exon 11 of 40)	5622	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_61022.1	chr7	49484747	49484757	+	1	NA	intron (NM_175272, intron 10 of 37)	intron (NM_175272, intron 10 of 37)	152083	NM_001005232	13172	Mm.307176	NM_001005232	ENSMUSG00000030507	Dbx1	AI426026|Dbx	developing brain homeobox 1	protein-coding
mm_87550.1	chr10	54074021	54074027	+	1	NA	intron (NM_008548, intron 2 of 12)	intron (NM_008548, intron 2 of 12)	1772	NM_008548	17155	Mm.117294	NM_008548	ENSMUSG00000003746	Man1a	Man1a1|PCR1	mannosidase 1, alpha	protein-coding
mm_14933.1	chr2	151542660	151542670	+	1	NA	non-coding (NR_126058, exon 1 of 4)	non-coding (NR_126058, exon 1 of 4)	182	NM_001302078	14225	Mm.278458	NM_008019	ENSMUSG00000032966	Fkbp1a	FKBP12|Fkbp|Fkbp1	FK506 binding protein 1a	protein-coding
mm_130701.1	chr15	100687151	100687212	-	1	NA	exon (NM_033612, exon 2 of 8)	exon (NM_033612, exon 2 of 8)	739	NM_033612	109901	Mm.2131	NM_033612	ENSMUSG00000023031	Cela1	1810009A17Rik|1810062B19Rik|Ela-1|Ela1|PC-TsF	chymotrypsin-like elastase family, member 1	protein-coding
mm_102370.1	chr11	58570560	58570573	-	1	NA	Intergenic	Intergenic	-3223	NM_207695	258198	Mm.480307	NM_207695	ENSMUSG00000059279	Olfr224	MOR275-3|Olfr224-ps1|Olfr327-ps1	olfactory receptor 224	protein-coding
mm_160882.1	chr11	69413857	69413857	-	1	NA	promoter-TSS (NM_001017426)	promoter-TSS (NM_001017426)	-182	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_1136.1	chr1	60609202	60609218	+	1	NA	Intergenic	Intergenic	-42445	NM_001045513	77300	Mm.440325	NM_001045513	ENSMUSG00000026014	Raph1	9430025M21Rik|C730009O10Rik|Lpd	Ras association (RalGDS/AF-6) and pleckstrin homology domains 1	protein-coding
mm_157435.1	chrX	38635021	38635035	-	1	NA	5' UTR (NM_021550, exon 1 of 2)	5' UTR (NM_021550, exon 1 of 2)	115	NM_021550	59048	Mm.441410	NM_021550	ENSMUSG00000048970	C1galt1c1	1500002I11Rik|AB030184|C1GalT2|C81205|Cosmc	C1GALT1-specific chaperone 1	protein-coding
mm_164261.1	chr15	100313914	100313926	+	1	NA	3' UTR (NM_027334, exon 2 of 2)	3' UTR (NM_027334, exon 2 of 2)	9103	NM_027334	70152	Mm.488086	NM_027334	ENSMUSG00000054619	Mettl7a1	2210414H16Rik|3300001H21Rik|Aam-B|Mettl7a|UbiE1	methyltransferase like 7A1	protein-coding
mm_31598.1	chr4	57893064	57893104	+	1	NA	3' UTR (NM_001035533, exon 4 of 4)	3' UTR (NM_001035533, exon 4 of 4)	23180	NM_178727	242484	Mm.23214	NM_178727	ENSMUSG00000052117	D630039A03Rik	-	RIKEN cDNA D630039A03 gene	protein-coding
mm_116844.1	chr13	54749614	54749625	-	1	NA	5' UTR (NM_001316710, exon 1 of 2)	5' UTR (NM_001316710, exon 1 of 2)	255	NM_001316710	26913	Mm.41812	NM_012014	ENSMUSG00000069227	Gprin1	GRIN1|Z16	G protein-regulated inducer of neurite outgrowth 1	protein-coding
mm_141887.1	chr17	34861089	34861127	-	1	NA	exon (NM_008198, exon 3 of 18)	exon (NM_008198, exon 3 of 18)	1406	NM_001142706	14962	Mm.653	NM_008198	ENSMUSG00000090231	Cfb	AI195813|AI255840|B|Bf|C2|Fb|H2-Bf	complement factor B	protein-coding
mm_166726.1	chr6	122309044	122309045	+	1	NA	promoter-TSS (NM_010749)	promoter-TSS (NM_010749)	34	NM_010749	17113	Mm.249225	NM_010749	ENSMUSG00000007458	M6pr	CD-MPR|Mpr46	mannose-6-phosphate receptor, cation dependent	protein-coding
mm_110830.1	chr12	72628957	72628965	-	1	NA	Intergenic	Intergenic	35867	NM_025522	66375	Mm.289653	NM_025522	ENSMUSG00000021094	Dhrs7	2310016E22Rik|5730564L20Rik|AW061210|Retdsr4|Retsdr4	dehydrogenase/reductase (SDR family) member 7	protein-coding
mm_76452.1	chr8	85112111	85112120	-	1	NA	intron (NM_001037745, intron 4 of 4)	intron (NM_001037745, intron 4 of 4)	10980	NM_001037745	244556	Mm.334682	NM_001037745	ENSMUSG00000074194	Zfp791	EG244556	zinc finger protein 791	protein-coding
mm_128708.1	chr15	63808748	63808752	-	1	NA	promoter-TSS (NM_031378)	promoter-TSS (NM_031378)	-11	NM_031378	83492	Mm.335619	NM_031378	ENSMUSG00000079025	Gsdmc	Gsdmc1|Mlze	gasdermin C	protein-coding
mm_13654.1	chr2	114055136	114055144	+	1	NA	non-coding (NR_028422, exon 1 of 3)	non-coding (NR_028422, exon 1 of 3)	744	NR_028422	100303644	Mm.330469	NR_028422	ENSMUSG00000092397	C130080G10Rik	-	RIKEN cDNA C130080G10 gene	ncRNA
mm_121887.1	chr14	21741450	21741456	-	1	NA	intron (NM_001007268, intron 5 of 7)	intron (NM_001007268, intron 5 of 7)	1426	NM_013849	27389	Mm.390674	NM_013849	ENSMUSG00000021768	Dusp13	DUSP13A|DUSP13B|Gm1203|LMW-DSP6|MDSP|TMDP|TS-DSP6	dual specificity phosphatase 13	protein-coding
mm_44486.1	chr5	23586621	23586627	-	1	NA	intron (NM_009274, intron 1 of 14)	Lx8|LINE|L1	29947	NM_009274	20817	Mm.288728	NM_009274	ENSMUSG00000062604	Srpk2	AW226533|AW492537|AW547358|Wbp6|mSRPK2	serine/arginine-rich protein specific kinase 2	protein-coding
mm_126076.1	chr15	77729153	77729172	+	1	NA	promoter-TSS (NM_173743)	promoter-TSS (NM_173743)	41	NM_001168660	71898	Mm.422856	NM_173743	ENSMUSG00000068246	Apol9b	2310016F22Rik	apolipoprotein L 9b	protein-coding
mm_160270.1	chr7	116189648	116189648	-	1	NA	promoter-TSS (NM_001305190)	promoter-TSS (NM_001305190)	-44	NM_001305190	233765	Mm.3741	NM_172743	ENSMUSG00000045659	Plekha7	A430081P20Rik|AI414265	pleckstrin homology domain containing, family A member 7	protein-coding
mm_165129.1	chr2	7395935	7395937	-	1	NA	promoter-TSS (NM_001110232)	promoter-TSS (NM_001110232)	64	NM_001110232	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_20991.1	chr2	152227232	152227264	-	1	NA	intron (NM_007788, intron 1 of 12)	CpG	408	NM_007788	12995	Mm.23692	NM_007788	ENSMUSG00000074698	Csnk2a1	Csnk2a1-rs4	casein kinase 2, alpha 1 polypeptide	protein-coding
mm_65211.1	chr7	19697992	19697998	-	1	NA	intron (NM_001305843, intron 3 of 4)	RSINE1|SINE|B4	403	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_77711.1	chr8	126592052	126592075	-	1	NA	intron (NM_001164598, intron 1 of 1)	intron (NM_001164598, intron 1 of 1)	1373	NM_001164598	270110	Mm.334918	NM_001164598	ENSMUSG00000051495	Irf2bp2	E130305N23Rik|IRF-2BP2	interferon regulatory factor 2 binding protein 2	protein-coding
mm_63865.1	chr7	135684275	135684305	+	1	NA	3' UTR (NM_011212, exon 21 of 21)	3' UTR (NM_011212, exon 21 of 21)	-31976	NR_015548	67765	Mm.445272	NR_015548	ENSMUSG00000097471	5830432E09Rik	-	RIKEN cDNA 5830432E09 gene	ncRNA
mm_81726.1	chr9	112505006	112505012	+	1	NA	Intergenic	RLTR20C|LTR|ERVK	248435	NR_033433	620760	Mm.259863	NR_015468	ENSMUSG00000087038	2900079G21Rik	C130083B14|Gm6179	RIKEN cDNA 2900079G21 gene	ncRNA
mm_170440.1	chr18	80029061	80029070	+	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	-17830	NM_053117	93737	Mm.24678	NM_053117	ENSMUSG00000056214	Pard6g	2410049N21Rik|Par6a	par-6 family cell polarity regulator gamma	protein-coding
mm_23823.1	chr3	81036361	81036371	+	1	NA	promoter-TSS (NM_019971)	promoter-TSS (NM_019971)	-50	NM_019971	54635	Mm.331089	NM_019971	ENSMUSG00000028019	Pdgfc	1110064L01Rik|AI647969|PDGF-C	platelet-derived growth factor, C polypeptide	protein-coding
mm_120369.1	chr14	64587174	64587191	+	1	NA	promoter-TSS (NR_040709)	promoter-TSS (NR_040709)	-933	NR_040709	268755	Mm.194050	NR_040709	ENSMUSG00000097545	Mir124a-1hg	A930011O12Rik|Rncr3|mir-124-1|mir-3078	Mir124-1 host gene (non-protein coding)	ncRNA
mm_137116.1	chr17	22497379	22497385	+	1	NA	Intergenic	MLT1K|LTR|ERVL-MaLR	73180	NM_001331198	74149	Mm.30767	NM_198003	ENSMUSG00000071266	Zfp946	1300003B13Rik	zinc finger protein 946	protein-coding
mm_166985.1	chr7	45714879	45714890	+	1	NA	5' UTR (NM_020011, exon 1 of 6)	5' UTR (NM_020011, exon 1 of 6)	323	NM_020011	56632	Mm.24222	NM_020011	ENSMUSG00000057342	Sphk2	C76851	sphingosine kinase 2	protein-coding
mm_148032.1	chr18	70053433	70053443	-	1	NA	5' UTR (NM_030554, exon 1 of 6)	5' UTR (NM_030554, exon 1 of 6)	150	NM_001302798	80718	Mm.246753	NM_030554	ENSMUSG00000024511	Rab27b	2310021G14Rik|B130064M09Rik	RAB27B, member RAS oncogene family	protein-coding
mm_62002.1	chr7	91226519	91226522	+	1	NA	intron (NM_011807, intron 1 of 22)	intron (NM_011807, intron 1 of 22)	135734	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_71344.1	chr8	45627947	45627975	+	1	NA	5' UTR (NM_001310707, exon 1 of 24)	5' UTR (NM_001310707, exon 1 of 24)	210	NM_001310707	234214	Mm.211096	NM_172752	ENSMUSG00000031626	Sorbs2	2010203O03Rik|9430041O17Rik|A530071H08|Argbp2|mKIAA0777|nArgBP2	sorbin and SH3 domain containing 2	protein-coding
mm_147754.1	chr18	61211573	61211607	-	1	NA	promoter-TSS (NM_007885)	promoter-TSS (NM_007885)	6	NM_007885	13521	Mm.24803	NM_007885	ENSMUSG00000034320	Slc26a2	Dtd|ST-OB	solute carrier family 26 (sulfate transporter), member 2	protein-coding
mm_7175.1	chr1	92318257	92318259	-	1	NA	Intergenic	Intergenic	-137917	NM_207225	208727	Mm.318567	NM_207225	ENSMUSG00000026313	Hdac4	4932408F19Rik|HD4	histone deacetylase 4	protein-coding
mm_30798.1	chr4	20007973	20008006	+	1	NA	promoter-TSS (NM_015767)	promoter-TSS (NM_015767)	-254	NM_001317723	50500	Mm.24375	NM_015767	ENSMUSG00000073988	Ttpa	alpha-TTP	tocopherol (alpha) transfer protein	protein-coding
mm_46997.1	chr5	115341143	115341191	-	1	NA	promoter-TSS (NM_026933)	promoter-TSS (NM_026933)	-6	NM_029645	384281	Mm.229308	NM_029645	ENSMUSG00000029536	Gatc	2010003O18Rik	glutamyl-tRNA(Gln) amidotransferase, subunit C	protein-coding
mm_162605.1	chr1	183221466	183221510	-	1	NA	promoter-TSS (NM_001278219)	promoter-TSS (NM_001278219)	41	NM_001278218	68897	Mm.327216	NM_026866	ENSMUSG00000030768	Disp1	1190008H24Rik|DispA	dispatched RND transporter family member 1	protein-coding
mm_17933.1	chr2	35874678	35874689	-	1	NA	intron (NM_029774, intron 6 of 9)	MTE2a|LTR|ERVL-MaLR	55493	NR_040618	77665	Mm.400558	NR_040618	ENSMUSG00000086449	9030204H09Rik	-	RIKEN cDNA 9030204H09 gene	ncRNA
mm_13619.1	chr2	113440854	113440891	+	1	NA	promoter-TSS (NM_001285459)	promoter-TSS (NM_001285459)	-192	NM_001285459	14260	Mm.4938	NM_010230	ENSMUSG00000044042	Fmn1	Fmn|formin-1|ld	formin 1	protein-coding
mm_82856.1	chr9	31459288	31459289	-	1	NA	intron (NM_144936, intron 1 of 5)	L1M2|LINE|L1	4950	NM_144936	235135	Mm.390134	NM_144936	ENSMUSG00000041737	Tmem45b	BC018222	transmembrane protein 45b	protein-coding
mm_151970.1	chr19	5806501	5806513	-	1	NA	Intergenic	Intergenic	-3835	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_40468.1	chr5	53677122	53677125	+	1	NA	Intergenic	Intergenic	21465	NR_024201	19866		NR_024201	ENSMUSG00000089083	Rnu7	-	U7 small nuclear RNA	snRNA
mm_66680.1	chr7	45812914	45812916	-	1	NA	intron (NM_011181, intron 2 of 11)	intron (NM_011181, intron 2 of 11)	1401	NM_011181	19158	Mm.272130	NM_011181	ENSMUSG00000003269	Cyth2	ARNO|CLM2|Pscd2	cytohesin 2	protein-coding
mm_38232.1	chr4	136028848	136028897	-	1	NA	Intergenic	Intergenic	-7223	NM_013736	27224	Mm.27663	NM_013736	ENSMUSG00000028668	Eloa	110kDa|AA408125|Tceb3|Tceb3a	elongin A	protein-coding
mm_149062.1	chr19	8839587	8839597	+	1	NA	promoter-TSS (NM_010316)	promoter-TSS (NM_010316)	264	NM_008144	14705	Mm.345134	NM_008144	ENSMUSG00000071657	Bscl2	2900097C17Rik|AI046355|Gng3lg	Berardinelli-Seip congenital lipodystrophy 2 (seipin)	protein-coding
mm_62897.1	chr7	116443570	116443593	+	1	NA	promoter-TSS (NM_011083)	promoter-TSS (NM_011083)	-123	NM_011083	18704	Mm.3810	NM_011083	ENSMUSG00000030660	Pik3c2a	Cpk-m|PI3KC2	phosphatidylinositol 3-kinase, C2 domain containing, alpha polypeptide	protein-coding
mm_100846.1	chr11	5788263	5788276	-	1	NA	promoter-TSS (NM_001146309)	promoter-TSS (NM_001146309)	-214	NM_001146309	13169	Mm.256925	NM_013810	ENSMUSG00000020476	Dbnl	Abp1|SH3P7|mAbp1	drebrin-like	protein-coding
mm_3722.1	chr1	154204880	154204890	+	1	NA	exon (NM_001204908, exon 2 of 2)	exon (NM_001204908, exon 2 of 2)	3698	NM_001204908	100503355	Mm.484410	NM_001204908	ENSMUSG00000066797	Zfp648	ENSMUSG00000066797|Gm10178|Gm203	zinc finger protein 648	protein-coding
mm_39378.1	chr5	12466875	12466879	+	1	NA	intron (NM_028882, intron 3 of 17)	B4A|SINE|B4	83711	NM_028882	108151	Mm.89313	NM_028882	ENSMUSG00000040254	Sema3d	4631426B19Rik	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D	protein-coding
mm_103675.1	chr11	79242492	79242501	-	1	NA	5' UTR (NM_001042565, exon 1 of 4)	5' UTR (NM_001042565, exon 1 of 4)	528	NM_001042565	78889	Mm.307022	NM_019653	ENSMUSG00000017677	Wsb1	1110056B13Rik|2700038M07Rik	WD repeat and SOCS box-containing 1	protein-coding
mm_132270.1	chr16	32878102	32878121	+	1	NA	intron (NM_027226, intron 1 of 8)	CpG	327	NM_001159349	69823	Mm.12831	NM_027226	ENSMUSG00000022800	Fyttd1	2010005M05Rik|3830411L18Rik|3830421F13Rik|4933423A17Rik|AI098218|AW539567|C85190	forty-two-three domain containing 1	protein-coding
mm_153476.1	chr19	41273783	41273798	-	1	NA	TTS (NM_031376)	TTS (NM_031376)	-9786	NM_133352	107358	Mm.246440	NM_133352	ENSMUSG00000025016	Tm9sf3	1810073M23Rik|2810031D16Rik|AI115521|AI413748|AW146116|AW549777|Smbp|mKIAA4036	transmembrane 9 superfamily member 3	protein-coding
mm_103764.1	chr11	81573517	81573542	-	1	NA	promoter-TSS (NM_001033765)	promoter-TSS (NM_001033765)	10	NM_001033765	237880	Mm.435528	NM_001033765		1700071K01Rik	-	RIKEN cDNA 1700071K01 gene	protein-coding
mm_101954.1	chr11	50296001	50296073	-	1	NA	3' UTR (NM_001110500, exon 15 of 15)	3' UTR (NM_001110500, exon 15 of 15)	-3701	NM_175334	103806	Mm.51116	NM_175334	ENSMUSG00000050567	Maml1	AI644666|AW743257|D930008C07Rik|Mam-1|Mam1|mKIAA0200	mastermind like 1 (Drosophila)	protein-coding
mm_155789.1	chrX	96713548	96713554	+	1	NA	promoter-TSS (NM_029536)	promoter-TSS (NM_029536)	83	NM_029536	76206	Mm.256065	NM_029536	ENSMUSG00000031210	Gpr165	6530406P05Rik	G protein-coupled receptor 165	protein-coding
mm_58643.1	chr7	6191225	6191228	+	1	NA	3' UTR (NM_001146024, exon 5 of 5)	3' UTR (NM_001146024, exon 5 of 5)	-5864	NM_178028	232836	Mm.246599	NM_178028	ENSMUSG00000034660	Galp	-	galanin-like peptide	protein-coding
mm_110449.1	chr12	51611605	51611606	-	1	NA	intron (NM_052973, intron 16 of 17)	Lx4B|LINE|L1	18264	NM_001198835	12810	Mm.21325	NM_007728	ENSMUSG00000020953	Coch	AW122937|Coch-5B2|D12H14S564E	cochlin	protein-coding
mm_106455.1	chr11	120020128	120020140	-	1	NA	intron (NM_001198787, intron 2 of 13)	intron (NM_001198787, intron 2 of 13)	-5272	NR_029767	723844		NR_029767	ENSMUSG00000065600	Mir338	Mirn338|mir-338|mmu-mir-338	microRNA 338	ncRNA
mm_39861.1	chr5	30968638	30968646	+	1	NA	promoter-TSS (NM_053085)	promoter-TSS (NM_053085)	-35	NM_053085	69852	Mm.57874	NM_053085	ENSMUSG00000006642	Tcf23	2010002O16Rik|Out|bHLHa24	transcription factor 23	protein-coding
mm_138296.1	chr17	34630689	34630706	+	1	NA	exon (NM_030890, exon 2 of 4)	exon (NM_030890, exon 2 of 4)	1011	NM_030890	260297	Mm.390965	NM_030890	ENSMUSG00000015476	Prrt1	Bat-4|Bat4|D17H6S54E|DSPD1|G5b|NG5|ORF31	proline-rich transmembrane protein 1	protein-coding
mm_143232.1	chr17	63494371	63494374	-	1	NA	intron (NM_015794, intron 1 of 8)	intron (NM_015794, intron 1 of 8)	6208	NM_015794	50758	Mm.136366	NM_015794	ENSMUSG00000023965	Fbxl17	6330576B01Rik|AI452053|BB073797|C130023C01Rik|Fbx13|Fbxo13	F-box and leucine-rich repeat protein 17	protein-coding
mm_54498.1	chr6	35510334	35510344	-	1	NA	3' UTR (NM_008098, exon 4 of 4)	3' UTR (NM_008098, exon 4 of 4)	29549	NM_008098	14489	Mm.182746	NM_008098	ENSMUSG00000029840	Mtpn	5033418D15Rik|Gcdp|V1	myotrophin	protein-coding
mm_5079.1	chr1	4360257	4360312	-	1	NA	promoter-TSS (NM_011283)	promoter-TSS (NM_011283)	30	NM_011283	19888	Mm.294263	NM_011283	ENSMUSG00000025900	Rp1	Dcdc3|Orp1|Rp1h|mG145	retinitis pigmentosa 1 (human)	protein-coding
mm_102661.1	chr11	64060233	64060247	-	1	NA	intron (NM_178379, intron 3 of 6)	intron (NM_178379, intron 3 of 6)	19232	NM_178379	70383	Mm.340211	NM_178379	ENSMUSG00000042148	Cox10	2410004F01Rik|AU042636	cytochrome c oxidase assembly protein 10	protein-coding
mm_126041.1	chr15	76904368	76904410	+	1	NA	exon (NM_012053, exon 2 of 6)	exon (NM_012053, exon 2 of 6)	318	NM_012053	26961	Mm.30066	NM_012053	ENSMUSG00000003970	Rpl8	-	ribosomal protein L8	protein-coding
mm_66225.1	chr7	35029301	35029308	-	1	NA	intron (NM_008820, intron 11 of 14)	intron (NM_008820, intron 11 of 14)	27262	NM_009884	12611	Mm.273090	NM_009884	ENSMUSG00000056216	Cebpg	C/EBP[g]|C/EBPgamma|GPE1-BP|Gpe1bp|Ig/EBP	CCAAT/enhancer binding protein (C/EBP), gamma	protein-coding
mm_124010.1	chr14	76110721	76110731	-	1	NA	promoter-TSS (NM_013745)	promoter-TSS (NM_013745)	89	NM_026177	67467	Mm.260767	NM_026177	ENSMUSG00000022008	Gpalpp1	1200011I18Rik|Kiaa1704	GPALPP motifs containing 1	protein-coding
mm_949.1	chr1	57377594	57377689	+	1	NA	promoter-TSS (NM_028546)	promoter-TSS (NM_028546)	21	NM_028546	73467	Mm.263673	NM_028546	ENSMUSG00000038323	1700066M21Rik	AI428479	RIKEN cDNA 1700066M21 gene	protein-coding
mm_116622.1	chr13	48880307	48880328	-	1	NA	3' UTR (NM_001033268, exon 18 of 18)	3' UTR (NM_001033268, exon 18 of 18)	-9432	NM_011078	18676	Mm.486213	NM_011078	ENSMUSG00000038025	Phf2	GRC5	PHD finger protein 2	protein-coding
mm_153653.1	chr19	44394760	44394768	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	12945	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_3192.1	chr1	135801700	135801710	+	1	NA	intron (NM_001112702, intron 2 of 8)	intron (NM_001112702, intron 2 of 8)	2194	NM_001112702	21952	Mm.44379	NM_021467	ENSMUSG00000026418	Tnni1	2700018B22Rik|AI747285|ssTnI	troponin I, skeletal, slow 1	protein-coding
mm_130485.1	chr15	98755068	98755106	-	1	NA	intron (NM_007478, intron 1 of 4)	intron (NM_007478, intron 1 of 4)	8031	NM_007478	11842	Mm.221298	NM_007478	ENSMUSG00000051853	Arf3	5430400P17Rik|AI854770	ADP-ribosylation factor 3	protein-coding
mm_106822.1	chr12	7985343	7985373	+	1	NA	exon (NM_009693, exon 7 of 29)	exon (NM_009693, exon 7 of 29)	7681	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_116977.1	chr13	56183768	56183780	-	1	NA	Intergenic	Intergenic	-4889	NM_001168615	212937	Mm.116697	NM_145976	ENSMUSG00000049625	Tifab	-	TRAF-interacting protein with forkhead-associated domain, family member B	protein-coding
mm_144986.1	chr18	38250295	38250305	+	1	NA	promoter-TSS (NM_024179)	promoter-TSS (NM_024179)	51	NM_024179	66839	Mm.281086	NM_024179	ENSMUSG00000024442	0610009O20Rik	2700004E22Rik|Dele|Kiaa0141	RIKEN cDNA 0610009O20 gene	protein-coding
mm_100758.1	chr11	4464294	4464302	-	1	NA	Intergenic	ORR1B2|LTR|ERVL-MaLR	-23216	NM_029458	75828	Mm.159592	NM_029458	ENSMUSG00000020419	Hormad2	4930529M09Rik	HORMA domain containing 2	protein-coding
mm_22962.1	chr3	32529453	32529527	+	1	NA	promoter-TSS (NM_024200)	promoter-TSS (NM_024200)	8	NM_024200	67414	Mm.290414	NM_024200	ENSMUSG00000027668	Mfn1	2310002F04Rik|6330416C07Rik|D3Ertd265e|HR2|mKIAA4032	mitofusin 1	protein-coding
mm_58080.1	chr6	136941695	136941726	-	1	NA	promoter-TSS (NM_007486)	promoter-TSS (NM_007486)	46	NM_001301308	11857	Mm.2241	NM_007486	ENSMUSG00000030220	Arhgdib	D4|Gdid4|Ly-GDI	Rho, GDP dissociation inhibitor (GDI) beta	protein-coding
mm_126810.1	chr15	87654973	87654981	+	1	NA	intron (NM_134096, intron 1 of 3)	intron (NM_134096, intron 1 of 3)	29747	NM_134096	106014	Mm.244319	NM_134096	ENSMUSG00000054863	Fam19a5	TAFA5|Tafa-5|Tara-5	family with sequence similarity 19, member A5	protein-coding
mm_49595.1	chr6	30670141	30670158	+	1	NA	intron (NR_130781, intron 3 of 11)	intron (NR_130781, intron 3 of 11)	23600	NM_031998	83922	Mm.65389	NM_031998	ENSMUSG00000029790	Cep41	1700017E11Rik|2810431D15Rik|Tsga14	centrosomal protein 41	protein-coding
mm_161059.1	chr12	69892937	69892937	+	1	NA	promoter-TSS (NM_178628)	promoter-TSS (NM_178628)	-168	NM_178628	73991	Mm.474462	NM_178628	ENSMUSG00000021066	Atl1	4930435M24Rik|Adfsp|Fsp1|Spg3|Spg3a	atlastin GTPase 1	protein-coding
mm_24766.1	chr3	95499857	95499868	+	1	NA	intron (NM_007802, intron 1 of 7)	intron (NM_007802, intron 1 of 7)	652	NM_007802	13038	Mm.272085	NM_007802	ENSMUSG00000028111	Ctsk	AI323530|MMS10-Q|Ms10q|catK	cathepsin K	protein-coding
mm_50373.1	chr6	48680629	48680631	+	1	NA	Intergenic	Intergenic	-3948	NM_001243200	107526	Mm.333048	NM_174990	ENSMUSG00000054435	Gimap4	AU019574|E430007K16Rik|Ian-1|Ian1|Imap4	GTPase, IMAP family member 4	protein-coding
mm_128340.1	chr15	38633433	38633439	-	1	NA	Intergenic	RLTR23|LTR|ERV1	-28468	NM_025494	66335	Mm.276618	NM_025494	ENSMUSG00000022295	Atp6v1c1	1700025B18Rik|U13839	ATPase, H+ transporting, lysosomal V1 subunit C1	protein-coding
mm_15097.1	chr2	153345810	153345889	+	1	NA	promoter-TSS (NM_001039939)	promoter-TSS (NM_001039939)	-39	NR_040318	72326	Mm.400102	NR_040318	ENSMUSG00000073236	2500004C02Rik	-	RIKEN cDNA 2500004C02 gene	ncRNA
mm_90281.1	chr10	122860368	122860408	+	1	NA	intron (NM_176919, intron 5 of 8)	MLT1A0|LTR|ERVL-MaLR	125336	NR_029527	387251		NR_029527	ENSMUSG00000065406	Mirlet7i	Mirnlet7i|let-7i|mmu-let-7i	microRNA let7i	ncRNA
mm_32698.1	chr4	116067224	116067232	+	1	NA	intron (NM_025641, intron 3 of 3)	intron (NM_025641, intron 3 of 3)	7842	NM_025641	66576	Mm.181721	NM_025641	ENSMUSG00000063882	Uqcrh	2210416J04Rik|2310021J10Rik|2610041P16Rik	ubiquinol-cytochrome c reductase hinge protein	protein-coding
mm_73258.1	chr8	104340648	104340658	+	1	NA	promoter-TSS (NM_024217)	promoter-TSS (NM_024217)	59	NM_024217	68119	Mm.390108	NM_024217	ENSMUSG00000031875	Cmtm3	9430096L06Rik|AI413895|BNAS2|Cklfsf3	CKLF-like MARVEL transmembrane domain containing 3	protein-coding
mm_106330.1	chr11	118340615	118340642	-	1	NA	intron (NM_021440, intron 2 of 2)	intron (NM_021440, intron 2 of 2)	1906	NM_021440	58251	Mm.439815	NM_021440	ENSMUSG00000076433	BC100451	Cep295nl|Ddc8|FS39|Kiaa1731nl	cDNA sequence BC100451	protein-coding
mm_165759.1	chr3	115774233	115774237	+	1	NA	Intergenic	Intergenic	-59180	NM_007901	13609	Mm.982	NM_007901	ENSMUSG00000045092	S1pr1	AI849002|Edg1|Lpb1|S1p|S1p1	sphingosine-1-phosphate receptor 1	protein-coding
mm_63291.1	chr7	126799572	126799600	+	1	NA	promoter-TSS (NM_001177307)	promoter-TSS (NM_001177307)	-332	NM_007438	11674	Mm.275831	NM_007438	ENSMUSG00000030695	Aldoa	Aldo-1|Aldo1	aldolase A, fructose-bisphosphate	protein-coding
mm_75557.1	chr8	57796534	57796562	-	1	NA	intron (NM_175032, intron 10 of 11)	intron (NM_175032, intron 10 of 11)	-143493	NM_144731	108150	Mm.62886	NM_144731	ENSMUSG00000031608	Galnt7	AI225872	UDP-N-acetyl-alpha-D-galactosamine: polypeptide N-acetylgalactosaminyltransferase 7	protein-coding
mm_93662.1	chr10	117693159	117693177	-	1	NA	intron (NM_001288586, intron 8 of 10)	intron (NM_001288586, intron 8 of 10)	17590	NM_010786	17246	Mm.22670	NM_010786	ENSMUSG00000020184	Mdm2	1700007J15Rik|AA415488|Mdm-2	transformed mouse 3T3 cell double minute 2	protein-coding
mm_119541.1	chr14	48120842	48120865	+	1	NA	promoter-TSS (NM_033602)	promoter-TSS (NM_033602)	-16	NM_033602	93834	Mm.296457	NM_033602	ENSMUSG00000021846	Peli2	AW047589|BB129927	pellino 2	protein-coding
mm_28796.1	chr3	96058447	96058459	-	1	NA	promoter-TSS (NM_013841)	promoter-TSS (NM_013841)	2	NM_013841	22365	Mm.263185	NM_013841	ENSMUSG00000015747	Vps45	AI462172|AW554165|mVps45	vacuolar protein sorting 45	protein-coding
mm_31558.1	chr4	57434404	57434408	+	1	NA	Intergenic	CpG	-70114	NR_038178	73349	Mm.393774	NR_038178		1700042G15Rik	-	RIKEN cDNA 1700042G15 gene	ncRNA
mm_102755.1	chr11	67299323	67299360	-	1	NA	exon (NM_177369, exon 28 of 40)	exon (NM_177369, exon 28 of 40)	22217	NM_177369	17885	Mm.340163	NM_177369	ENSMUSG00000055775	Myh8	4832426G23Rik|AI327267|MHCp|MyHC-pn|Myhs-p|Myhsp	myosin, heavy polypeptide 8, skeletal muscle, perinatal	protein-coding
mm_164551.1	chr17	13590982	13590991	+	1	NA	Intergenic	Intergenic	-36892	NR_045437	72578	Mm.46549	NR_045436	ENSMUSG00000038347	2700054A10Rik	-	RIKEN cDNA 2700054A10 gene	ncRNA
mm_10948.1	chr2	25607854	25607880	+	1	NA	TTS (NM_029859)	TTS (NM_029859)	579	NM_001024616	227624	Mm.29600	NM_001024616	ENSMUSG00000015087	Rabl6	B230208H17Rik|Rbel1|Rbel1a|Rbel1b|parf	RAB, member RAS oncogene family-like 6	protein-coding
mm_52081.1	chr6	97828318	97828332	+	1	NA	intron (NM_001113198, intron 1 of 9)	intron (NM_001113198, intron 1 of 9)	21267	NM_001113198	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_95338.1	chr11	46817538	46817564	+	1	NA	exon (NM_178759, exon 3 of 9)	exon (NM_178759, exon 3 of 9)	6752	NM_178759	276891	Mm.69002	NM_178759	ENSMUSG00000055546	Timd4	B430010N18Rik|TIM-4|Tim4	T cell immunoglobulin and mucin domain containing 4	protein-coding
mm_155898.1	chrX	101653470	101653558	+	1	NA	intron (NM_139144, intron 4 of 21)	intron (NM_139144, intron 4 of 21)	13296	NM_001290535	108155	Mm.487332	NM_139144	ENSMUSG00000034160	Ogt	1110038P24Rik|4831420N21Rik|AI115525|Ogtl	O-linked N-acetylglucosamine (GlcNAc) transferase (UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase)	protein-coding
mm_22357.1	chr2	181020429	181020449	-	1	NA	Intergenic	B4A|SINE|B4	18738	NM_015730	11438	Mm.252369	NM_015730	ENSMUSG00000027577	Chrna4	Acra-4|Acra4|EBN1|ENFL1	cholinergic receptor, nicotinic, alpha polypeptide 4	protein-coding
mm_146944.1	chr18	32448433	32448446	-	1	NA	Intergenic	Intergenic	-70155	NR_045403	402767	Mm.385109	NR_045403	ENSMUSG00000097413	A830052D11Rik	-	RIKEN cDNA A830052D11 gene	ncRNA
mm_168749.1	chr12	115758462	115758470	-	1	NA	Intergenic	Intergenic	-62672	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
mm_158919.1	chr1	57406548	57406548	+	1	NA	promoter-TSS (NM_001081181)	promoter-TSS (NM_001081181)	0	NM_001081181	68115	Mm.275428	NM_001081181	ENSMUSG00000025971	Maip1	9430016H08Rik|AA409999|C78988	matrix AAA peptidase interacting protein 1	protein-coding
mm_34866.1	chr4	155557941	155557968	+	1	NA	3' UTR (NM_008142, exon 12 of 12)	3' UTR (NM_008142, exon 12 of 12)	-4438	NM_138671	192185	Mm.28347	NM_138671	ENSMUSG00000029063	Nadk	4432404C02Rik|BC004012	NAD kinase	protein-coding
mm_53349.1	chr6	129350260	129350270	+	1	NA	promoter-TSS (NM_177686)	promoter-TSS (NM_177686)	21	NM_177686	232413	Mm.90241	NM_177686	ENSMUSG00000053063	Clec12a	CLL-1|D230024O04|KLRL1|Micl	C-type lectin domain family 12, member a	protein-coding
mm_116262.1	chr13	34246948	34246954	-	1	NA	intron (NM_001033167, intron 3 of 10)	intron (NM_001033167, intron 3 of 10)	83987	NM_001110515	69666	Mm.24788	NM_001101430	ENSMUSG00000071451	Psmg4	PAC-4|mPAC4	proteasome (prosome, macropain) assembly chaperone 4	protein-coding
mm_10500.1	chr2	15055383	15055402	+	1	NA	promoter-TSS (NM_001165941)	promoter-TSS (NM_001165941)	30	NM_029466	75869	Mm.174068	NM_029466	ENSMUSG00000017418	Arl5b	4930587A11Rik|AW146430|Arl8	ADP-ribosylation factor-like 5B	protein-coding
mm_13162.1	chr2	92608308	92608316	+	1	NA	intron (NM_023850, intron 1 of 2)	intron (NM_023850, intron 1 of 2)	8605	NM_023850	76969	Mm.38021	NM_023850	ENSMUSG00000027221	Chst1	2610008E20Rik|AW125896|C6ST|GST-1|Gst1|KSGAL6ST	carbohydrate (keratan sulfate Gal-6) sulfotransferase 1	protein-coding
mm_105048.1	chr11	100619599	100619657	-	1	NA	5' UTR (NM_019795, exon 1 of 14)	5' UTR (NM_019795, exon 1 of 14)	540	NM_019795	56354	Mm.402409	NM_019795	ENSMUSG00000014195	Dnajc7	2010003F24Rik|2010004G07Rik|CCRP|Ttc2|mDj11|mTpr2	DnaJ heat shock protein family (Hsp40) member C7	protein-coding
mm_15908.1	chr2	165055669	165055690	+	1	NA	promoter-TSS (NR_027852)	promoter-TSS (NR_027852)	43	NM_011611	21939	Mm.271833	NM_011611	ENSMUSG00000017652	Cd40	AI326936|Bp50|GP39|HIGM1|IGM|IMD3|T-BAM|TRAP|Tnfrsf5|p50	CD40 antigen	protein-coding
mm_132364.1	chr16	34784780	34784793	+	1	NA	promoter-TSS (NM_139300)	promoter-TSS (NM_139300)	-164	NM_139300	107589	Mm.33360	NM_139300	ENSMUSG00000022836	Mylk	9530072E15Rik|A930019C19Rik|AW489456|KRP|MLCK108|MLCK210|Mlck|nmMlck|smMLCK	myosin, light polypeptide kinase	protein-coding
mm_116544.1	chr13	45946238	45946271	-	1	NA	intron (NM_001199304, intron 2 of 6)	intron (NM_001199304, intron 2 of 6)	18737	NM_001199304	20238	Mm.342683	NM_009124	ENSMUSG00000046876	Atxn1	2900016G23Rik|Atx1|C85907|ENSMUSG00000074917|Gm10786|Sca1	ataxin 1	protein-coding
mm_63823.1	chr7	134670668	134670715	+	1	NA	promoter-TSS (NM_001033420)	promoter-TSS (NM_001033420)	4	NM_001033420	330662	Mm.436572	NM_001033420	ENSMUSG00000058325	Dock1	9130006G06Rik|AI854900|D630004B07Rik	dedicator of cytokinesis 1	protein-coding
mm_92779.1	chr10	81230759	81230769	-	1	NA	promoter-TSS (NM_178662)	promoter-TSS (NM_178662)	15	NM_178662	16467	Mm.127681	NM_178662	ENSMUSG00000034958	Atcay	3322401A10Rik|BB077577|BNIP-H|CLAC|hes|ji	ataxia, cerebellar, Cayman type	protein-coding
mm_49496.1	chr6	29735668	29735680	+	1	NA	5' UTR (NM_176996, exon 1 of 12)	5' UTR (NM_176996, exon 1 of 12)	177	NM_176996	319757	Mm.29279	NM_176996	ENSMUSG00000001761	Smo	E130215L21Rik|Smoh|bnb|smoothened	smoothened, frizzled class receptor	protein-coding
mm_66594.1	chr7	45434453	45434478	-	1	NA	promoter-TSS (NM_030678)	promoter-TSS (NM_030678)	-1	NM_011304	20174	Mm.34410	NM_011304	ENSMUSG00000003868	Ruvbl2	mp47|p47	RuvB-like protein 2	protein-coding
mm_59214.1	chr7	24547480	24547490	+	1	NA	intron (NM_009532, intron 1 of 16)	intron (NM_009532, intron 1 of 16)	335	NM_009532	22594	Mm.4347	NM_009532	ENSMUSG00000051768	Xrcc1	Xrcc-1	X-ray repair complementing defective repair in Chinese hamster cells 1	protein-coding
mm_96677.1	chr11	69418254	69418266	+	1	NA	Intergenic	CpG	-4585	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_100233.1	chr11	117204846	117204861	+	1	NA	intron (NM_001113486, intron 1 of 11)	intron (NM_001113486, intron 1 of 11)	5192	NM_001113486	53860	Mm.38450	NM_017380	ENSMUSG00000059248	Sept9	MSF1|Msf|PNUTL4|Sint1	septin 9	protein-coding
mm_25124.1	chr3	102012498	102012507	+	1	NA	intron (NM_178777, intron 2 of 2)	CpG	2357	NM_178777	18072	Mm.137286	NM_178777	ENSMUSG00000048540	Nhlh2	6230401I09Rik|Hen2|NSCL2|Nscl-2|bHLHa34	nescient helix loop helix 2	protein-coding
mm_64064.1	chr7	140856737	140856767	+	1	NA	promoter-TSS (NM_053194)	promoter-TSS (NM_053194)	-369	NM_018742	54399	Mm.155696	NM_018742	ENSMUSG00000025484	Bet1l	2610021K23Rik|Gs15	Bet1 golgi vesicular membrane trafficking protein like	protein-coding
mm_6998.1	chr1	86359952	86359966	-	1	NA	promoter-TSS (NM_010880)	promoter-TSS (NM_010880)	385	NR_015507	319336	Mm.389155	NR_015507	ENSMUSG00000073627	C130036L24Rik	ENSMUSG00000073627	RIKEN cDNA C130036L24 gene	ncRNA
mm_11092.1	chr2	27895292	27895302	+	1	NA	intron (NM_015734, intron 1 of 65)	MIR|SINE|MIR	8872	NM_015734	12831	Mm.7281	NM_015734	ENSMUSG00000026837	Col5a1	AI413331	collagen, type V, alpha 1	protein-coding
mm_114727.1	chr13	83721283	83721285	+	1	NA	Intergenic	Intergenic	-6822	NR_015561	320203	Mm.245636	NM_177100	ENSMUSG00000050334	C130071C03Rik	2810449C10Rik	RIKEN cDNA C130071C03 gene	ncRNA
mm_170312.1	chr18	36255485	36255494	+	1	NA	Intergenic	RMER20C_Mm|LTR|ERVK	-25673	NM_008989	19290	Mm.231802	NM_008989	ENSMUSG00000043991	Pura	CAGER-1|Pur-alpha|ssCRE-BP	purine rich element binding protein A	protein-coding
mm_23514.1	chr3	60560199	60560202	+	1	NA	intron (NM_001310514, intron 2 of 8)	intron (NM_001310514, intron 2 of 8)	59021	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_58020.1	chr6	136661728	136661736	-	1	NA	5' UTR (NM_025806, exon 1 of 11)	5' UTR (NM_025806, exon 1 of 11)	161	NM_025806	66857	Mm.3311	NM_025806	ENSMUSG00000030214	Plbd1	1100001H23Rik	phospholipase B domain containing 1	protein-coding
mm_44545.1	chr5	24577310	24577320	-	1	NA	intron (NM_013853, intron 1 of 13)	CpG	152	NM_013853	27407	Mm.21629	NM_013853	ENSMUSG00000028953	Abcf2	0710005O05Rik|Drr3|E430001O06	ATP-binding cassette, sub-family F (GCN20), member 2	protein-coding
mm_155593.1	chrX	81094553	81094565	+	1	NA	exon (NM_138751, exon 3 of 3)	exon (NM_138751, exon 3 of 3)	23915	NM_138751	192216	Mm.490421	NM_138751	ENSMUSG00000025666	Tmem47	3010015F07Rik|AI115536|BCMP1|Tm4sf10	transmembrane protein 47	protein-coding
mm_8777.1	chr1	161131429	161131486	-	1	NA	promoter-TSS (NM_001039482)	promoter-TSS (NM_001039482)	22	NM_001039482	226541	Mm.255165	NM_144876	ENSMUSG00000026705	Klhl20	AI504637|D930050H05Rik|Kleip|mKIAA4210	kelch-like 20	protein-coding
mm_104853.1	chr11	99337931	99337967	-	1	NA	promoter-TSS (NM_001033397)	promoter-TSS (NM_001033397)	16	NM_001033397	320864	Mm.440509	NM_001033397	ENSMUSG00000075570	Krt26	4732407F15Rik|Krt25b	keratin 26	protein-coding
mm_136578.1	chr17	3557453	3557462	+	1	NA	promoter-TSS (NR_045303)	promoter-TSS (NR_045303)	256	NM_146074	224481	Mm.226554	NM_146074	ENSMUSG00000036983	Tfb1m	AI429207	transcription factor B1, mitochondrial	protein-coding
mm_157331.1	chrX	23365045	23365090	-	1	NA	promoter-TSS (NM_026167)	promoter-TSS (NM_026167)	15	NM_026167	67455	Mm.224306	NM_026167	ENSMUSG00000036782	Klhl13	1200009K10Rik|AI451128|Bklhd2|D130072F20Rik	kelch-like 13	protein-coding
mm_136115.1	chr16	85550425	85550432	-	1	NA	promoter-TSS (NM_144853)	promoter-TSS (NM_144853)	-55	NM_144853	224405	Mm.213203	NM_144853	ENSMUSG00000041134	Cyyr1	-	cysteine and tyrosine-rich protein 1	protein-coding
mm_14327.1	chr2	129367302	129367325	+	1	NA	exon (NM_008361, exon 5 of 7)	exon (NM_008361, exon 5 of 7)	-2589	NR_015474	329514	Mm.207315	NM_177848	ENSMUSG00000074805	Il1bos	9430083I22|Gm14047|OTTMUSG00000015529	interleukin 1 beta, opposite strand	ncRNA
mm_144309.1	chr18	12569261	12569272	+	1	NA	intron (NM_010680, intron 68 of 74)	intron (NM_010680, intron 68 of 74)	65067	NM_001347461	16774	Mm.42012	NM_010680	ENSMUSG00000024421	Lama3	Lama3B|[a]3B	laminin, alpha 3	protein-coding
mm_85753.1	chr9	108648764	108648771	-	1	NA	intron (NM_011790, intron 1 of 15)	CpG	613	NM_011790	23807	Mm.290447	NM_011790	ENSMUSG00000064145	Arih2	AI843547|ARI2|TRIAD1|UIP48	ariadne RBR E3 ubiquitin protein ligase 2	protein-coding
mm_56511.1	chr6	99376045	99376065	-	1	NA	intron (NM_001347345, intron 2 of 19)	intron (NM_001347345, intron 2 of 19)	59290	NM_053202	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_104076.1	chr11	86586886	86586939	-	1	NA	intron (NM_029478, intron 10 of 11)	intron (NM_029478, intron 10 of 11)	-2754	NR_029738	387140		NR_029738	ENSMUSG00000065455	Mir21a	Mir21|Mirn21|mmu-mir-21|mmu-mir-21a	microRNA 21a	ncRNA
mm_42604.1	chr5	117769613	117769614	+	1	NA	Intergenic	Intergenic	-97226	NM_008712	18125	Mm.44249	NM_008712	ENSMUSG00000029361	Nos1	2310005C01Rik|N-NOS|NC-NOS|NO|NOS|NOS-I|Nos-1|bNOS|nNOS	nitric oxide synthase 1, neuronal	protein-coding
mm_32947.1	chr4	119540490	119540499	+	1	NA	intron (NM_172699, intron 1 of 12)	intron (NM_172699, intron 1 of 12)	833	NM_172699	230700	Mm.259227	NM_172699	ENSMUSG00000032998	Foxj3	C330039G02Rik|Fhd6	forkhead box J3	protein-coding
mm_158894.1	chr1	21368277	21368277	+	1	NA	promoter-TSS (NM_001033904)	promoter-TSS (NM_001033904)	-54	NM_001033904	433278	Mm.26006	NM_001033904	ENSMUSG00000041722	Khdc1c	Khdc1b	KH domain containing 1C	protein-coding
mm_165969.1	chr4	97579497	97579503	+	1	NA	intron (NR_015513, intron 1 of 2)	intron (NR_015513, intron 1 of 2)	-2443	NM_001122952	18027	Mm.31274	NM_010905	ENSMUSG00000028565	Nfia	1110047K16Rik|9430022M17Rik|CTF|NF1-A|NF1A	nuclear factor I/A	protein-coding
mm_48735.1	chr5	147566771	147566777	-	1	NA	intron (NM_010228, intron 28 of 29)	B4A|SINE|B4	136194	NM_028291	72587	Mm.320469	NM_028291	ENSMUSG00000029647	Pan3	2700050F09Rik|A430027N15Rik|AU014670	PAN3 poly(A) specific ribonuclease subunit	protein-coding
mm_76995.1	chr8	107085407	107085417	-	1	NA	intron (NM_001083118, intron 3 of 6)	intron (NM_001083118, intron 3 of 6)	10694	NR_106043	102465652		NR_106043	ENSMUSG00000098671	Mir7075	Gm27821|mmu-mir-7075	microRNA 7075	ncRNA
mm_146482.1	chr18	89206603	89206613	+	1	NA	exon (NM_178687, exon 2 of 7)	exon (NM_178687, exon 2 of 7)	9181	NM_001039149	225825	Mm.139293	NM_178687	ENSMUSG00000034028	Cd226	BC051526|DNAM-1|DNAM1|Pta1|TLiSA1	CD226 antigen	protein-coding
mm_25126.1	chr3	102086437	102086447	+	1	NA	promoter-TSS (NM_009814)	promoter-TSS (NM_009814)	-13	NM_009814	12373	Mm.15343	NM_009814	ENSMUSG00000027861	Casq2	AA033488|AW146219|Csq2|ESTM52|cCSQ	calsequestrin 2	protein-coding
mm_108257.1	chr12	78351036	78351072	+	1	NA	intron (NM_145965, intron 2 of 22)	LSU-rRNA_Hsa|rRNA|rRNA	124399	NM_145965	268566	Mm.341742	NM_145965	ENSMUSG00000047454	Gphn	5730552E08Rik|AI662856|BC027112|C230040D23|GPH|GPHRYN|geph	gephyrin	protein-coding
mm_98110.1	chr11	87025654	87025667	+	1	NA	intron (NR_106195, intron 4 of 8)	intron (NR_106195, intron 4 of 8)	-31898	NM_001005341	77864	Mm.191894	NM_001005341	ENSMUSG00000018427	Ypel2	6430570G24|E130113K08Rik	yippee-like 2 (Drosophila)	protein-coding
mm_98039.1	chr11	85352776	85352797	+	1	NA	promoter-TSS (NM_001166643)	promoter-TSS (NM_001166643)	-378	NM_001166642	192197	Mm.209989	NM_138681	ENSMUSG00000059439	Bcas3	1500019F07Rik|2610028P08Rik|AU021018|BC028339|K20D4|rudhira	breast carcinoma amplified sequence 3	protein-coding
mm_168139.1	chr10	30945976	30945981	+	1	NA	Intergenic	BGLII|LTR|ERVK	-103195	NM_013904	15214	Mm.103573	NM_013904	ENSMUSG00000019789	Hey2	CHF1|Herp1|Hrt2|bHLHb32|hesr2	hairy/enhancer-of-split related with YRPW motif 2	protein-coding
mm_150239.1	chr19	34067526	34067534	+	1	NA	5' UTR (NM_027340, exon 1 of 10)	5' UTR (NM_027340, exon 1 of 10)	172	NM_027340	70166	Mm.75602	NM_027340	ENSMUSG00000024770	Lipn	2210418G03Rik|Lipl4	lipase, family member N	protein-coding
mm_37963.1	chr4	133353477	133353505	-	1	NA	Intergenic	B1F1|SINE|Alu	-14176	NM_199306	230796	Mm.226576	NM_199306	ENSMUSG00000037622	Wdtc1	Gm695|adipose|adp	WD and tetratricopeptide repeats 1	protein-coding
mm_53358.1	chr6	129352712	129352728	+	1	NA	intron (NM_177686, intron 1 of 5)	intron (NM_177686, intron 1 of 5)	2476	NM_177686	232413	Mm.90241	NM_177686	ENSMUSG00000053063	Clec12a	CLL-1|D230024O04|KLRL1|Micl	C-type lectin domain family 12, member a	protein-coding
mm_115377.1	chr13	113093825	113093827	+	1	NA	TTS (NM_010370)	TTS (NM_010370)	7155	NM_010370	14938	Mm.15510	NM_010370	ENSMUSG00000023132	Gzma	AW494114|Ctla-3|Ctla3|Hf|Hf1|SE1|TSP-1|TSP1	granzyme A	protein-coding
mm_79768.1	chr9	62826086	62826099	+	1	NA	Intergenic	ORR1D2|LTR|ERVL-MaLR	-12695	NM_001033175	76524	Mm.283636	NM_001033175	ENSMUSG00000032245	Cln6	1810065L06Rik|AW743417|D9Bwg1455e|nclf	ceroid-lipofuscinosis, neuronal 6	protein-coding
mm_61775.1	chr7	83631988	83632022	+	1	NA	promoter-TSS (NM_023377)	promoter-TSS (NM_023377)	-12	NM_023377	170460	Mm.357953	NM_023377	ENSMUSG00000046027	Stard5	2310058G22Rik|AI607880|D7Ertd152e	StAR-related lipid transfer (START) domain containing 5	protein-coding
mm_61798.1	chr7	84152140	84152182	+	1	NA	promoter-TSS (NM_133722)	promoter-TSS (NM_133722)	-268	NM_133722	70178	Mm.23914	NM_133722	ENSMUSG00000038459	Abhd17c	2210412D01Rik|AL023007|Fam108c|Fam108c1	abhydrolase domain containing 17C	protein-coding
mm_16080.1	chr2	168532357	168532372	+	1	NA	intron (NR_111898, intron 4 of 5)	intron (NR_111898, intron 4 of 5)	58001	NM_001291178	18019	Mm.116802	NM_010899	ENSMUSG00000027544	Nfatc2	AI607462|NF-ATc2|NF-ATp|NFAT1|NFAT1-D|Nfatp	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 2	protein-coding
mm_157302.1	chrX	20929668	20929696	-	1	NA	exon (NM_008823, exon 3 of 9)	exon (NM_008823, exon 3 of 9)	1873	NM_008823	18636	Mm.3064	NM_008823	ENSMUSG00000001128	Cfp	BCFG|Pfc	complement factor properdin	protein-coding
mm_1194.1	chr1	62703917	62703934	+	1	NA	5' UTR (NM_001077407, exon 1 of 16)	5' UTR (NM_001077407, exon 1 of 16)	608	NM_001077405	18187	Mm.266341	NM_010939	ENSMUSG00000025969	Nrp2	1110048P06Rik|Np-2|Np2|Npn-2|Npn2	neuropilin 2	protein-coding
mm_167085.1	chr7	102017389	102017398	+	1	NA	intron (NM_010531, intron 2 of 6)	intron (NM_010531, intron 2 of 6)	762	NM_010531	16068	Mm.422756	NM_010531	ENSMUSG00000070427	Il18bp	IL-18BP|Igifbp|MC54L	interleukin 18 binding protein	protein-coding
mm_35932.1	chr4	53032447	53032464	-	1	NA	3' UTR (NM_013454, exon 50 of 50)	3' UTR (NM_013454, exon 50 of 50)	20575	NM_025623	66536	Mm.38244	NM_025623	ENSMUSG00000015247	Nipsnap3b	2700063N13Rik|Nipsnap3a	nipsnap homolog 3B (C. elegans)	protein-coding
mm_10568.1	chr2	18064320	18064330	+	1	NA	promoter-TSS (NM_001252561)	promoter-TSS (NM_001252561)	-260	NM_001252560	17354	Mm.209175	NM_010804	ENSMUSG00000026743	Mllt10	Af10|B130021D15Rik|D630001B22Rik|mKIAA4140	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 10	protein-coding
mm_106704.1	chr12	3780535	3780549	+	1	NA	intron (NR_027869, intron 20 of 20)	intron (NR_027869, intron 20 of 20)	-26438	NM_007872	13435	Mm.5001	NM_007872	ENSMUSG00000020661	Dnmt3a	MmuIIIA	DNA methyltransferase 3A	protein-coding
mm_59058.1	chr7	19414932	19414949	+	1	NA	exon (NM_007710, exon 3 of 8)	exon (NM_007710, exon 3 of 8)	3846	NM_007710	12715	Mm.2375	NM_007710	ENSMUSG00000030399	Ckm	Ckmm|M-CK|MCK	creatine kinase, muscle	protein-coding
mm_80651.1	chr9	89960983	89960997	+	1	NA	intron (NM_011245, intron 5 of 26)	(TAGA)n|Simple_repeat|Simple_repeat	51215	NM_001039655	19417	Mm.44561	NM_011245	ENSMUSG00000032356	Rasgrf1	AI844718|CDC25|CDC25Mm|Gnrp|Grf1|Grfbeta|P190-A|Ras-GRF1|p190|p190RhoGEF	RAS protein-specific guanine nucleotide-releasing factor 1	protein-coding
mm_58600.1	chr7	5051468	5051476	+	1	NA	promoter-TSS (NM_026900)	promoter-TSS (NM_026900)	-60	NM_026900	68992	Mm.41484	NM_026900	ENSMUSG00000055633	Zfp580	1500015O20Rik|AI838225|Znf580	zinc finger protein 580	protein-coding
mm_158883.1	chr1	9848444	9848444	+	1	NA	intron (NM_001037759, intron 1 of 16)	CpG	163	NM_001037759	170755	Mm.336410	NM_133220	ENSMUSG00000025915	Sgk3	2510015P22Rik|A330005P07Rik|Cisk|fy|fz	serum/glucocorticoid regulated kinase 3	protein-coding
mm_113304.1	chr13	30749957	30749982	+	1	NA	intron (NM_001347508, intron 1 of 8)	intron (NM_001347508, intron 1 of 8)	736	NM_013674	16364	Mm.4677	NM_013674	ENSMUSG00000021356	Irf4	AI385587|IRF-4|LSIRF|NF-EM5|Spip	interferon regulatory factor 4	protein-coding
mm_35053.1	chr4	6355364	6355374	-	1	NA	Intergenic	Intergenic	-10311	NM_016807	53378	Mm.247473	NM_016807	ENSMUSG00000028249	Sdcbp	MDA-9|Sycl|syntenin-1	syndecan binding protein	protein-coding
mm_128332.1	chr15	38300694	38300715	-	1	NA	promoter-TSS (NM_013692)	promoter-TSS (NM_013692)	7	NM_013692	21847	Mm.4292	NM_013692	ENSMUSG00000037465	Klf10	AI115143|EGR[a]|Egral|Gdnfif|TIEG-1|Tieg|Tieg1|mGIF	Kruppel-like factor 10	protein-coding
mm_152583.1	chr19	11603298	11603330	-	1	NA	intron (NM_026835, intron 1 of 6)	intron (NM_026835, intron 1 of 6)	1490	NM_026835	68774	Mm.290390	NM_026835	ENSMUSG00000024679	Ms4a6d	1110058E16Rik|AI447446|Ms4a11	membrane-spanning 4-domains, subfamily A, member 6D	protein-coding
mm_79695.1	chr9	60813671	60813705	+	1	NA	intron (NM_028283, intron 1 of 18)	intron (NM_028283, intron 1 of 18)	19140	NM_028283	72565	Mm.68819	NM_028283	ENSMUSG00000034485	Uaca	2700059D02Rik|nucling	uveal autoantigen with coiled-coil domains and ankyrin repeats	protein-coding
mm_116506.1	chr13	45002141	45002151	-	1	NA	promoter-TSS (NM_025772)	promoter-TSS (NM_025772)	-50	NM_025772	94245	Mm.352311	NM_025772	ENSMUSG00000057531	Dtnbp1	5430437B18Rik|AW048963|Bloc1s8|dysbindin|sdy	dystrobrevin binding protein 1	protein-coding
mm_90591.1	chr10	128277640	128277658	+	1	NA	exon (NM_019963, exon 5 of 24)	exon (NM_019963, exon 5 of 24)	7073	NM_019963	20847	Mm.293120	NM_019963	ENSMUSG00000040033	Stat2	1600010G07Rik|AW496480	signal transducer and activator of transcription 2	protein-coding
mm_62378.1	chr7	100706799	100706809	+	1	NA	5' UTR (NM_178764, exon 1 of 9)	5' UTR (NM_178764, exon 1 of 9)	102	NM_178764	319604	Mm.260362	NM_178764	ENSMUSG00000029461	Fam168a	2610030B18Rik|B930006L02Rik|mKIAA0280	family with sequence similarity 168, member A	protein-coding
mm_39136.1	chr4	155200758	155200771	-	1	NA	intron (NM_011385, intron 1 of 6)	intron (NM_011385, intron 1 of 6)	21771	NM_011385	20481	Mm.28520	NM_011385	ENSMUSG00000029050	Ski	2310012I02Rik|2610001A11Rik|AA062172|AA589460|BC004088	ski sarcoma viral oncogene homolog (avian)	protein-coding
mm_98557.1	chr11	95145095	95145114	+	1	NA	promoter-TSS (NR_040279)	promoter-TSS (NR_040279)	51	NR_040279	320453	Mm.442212	NR_040279	ENSMUSG00000086552	Dlx4os	A730090H04Rik|Dlx4as	distal-less homeobox 4, opposite strand	ncRNA
mm_23392.1	chr3	57441286	57441288	+	1	NA	3' UTR (NM_145539, exon 5 of 5)	3' UTR (NM_145539, exon 5 of 5)	15877	NM_145539	229302	Mm.26618	NM_145539	ENSMUSG00000027801	Tm4sf4	Iltmp	transmembrane 4 superfamily member 4	protein-coding
mm_141809.1	chr17	34603478	34603488	-	1	NA	promoter-TSS (NM_019403)	promoter-TSS (NM_019403)	78	NM_019403	54197	Mm.274542	NM_019403	ENSMUSG00000015478	Rnf5	2410131O05Rik|AA407576|NG2	ring finger protein 5	protein-coding
mm_18249.1	chr2	52206219	52206226	-	1	NA	exon (NM_010889, exon 100 of 157)	exon (NM_010889, exon 100 of 157)	-84780	NR_040620	78049	Mm.243883	NR_040620		4930573O16Rik	-	RIKEN cDNA 4930573O16 gene	ncRNA
mm_12560.1	chr2	72476226	72476259	+	1	NA	promoter-TSS (NM_025866)	promoter-TSS (NM_025866)	23	NM_025866	66953	Mm.270676	NM_025866	ENSMUSG00000055612	Cdca7	2310021G01Rik|AU044109|JPO1	cell division cycle associated 7	protein-coding
mm_72642.1	chr8	84701804	84701827	+	1	NA	5' UTR (NM_008535, exon 1 of 4)	5' UTR (NM_008535, exon 1 of 4)	358	NM_008535	17095	Mm.4925	NM_008535	ENSMUSG00000034041	Lyl1	Lyl-1|bHLHa18	lymphoblastomic leukemia 1	protein-coding
mm_134278.1	chr16	14159233	14159286	-	1	NA	promoter-TSS (NR_030252)	promoter-TSS (NR_030252)	15	NM_001081154	223989	Mm.85442	NM_001081154	ENSMUSG00000060657	Marf1	4921513D23Rik|BC031575|C87306|E030019O05|Lkap|mKIAA0430	meiosis arrest female 1	protein-coding
mm_131336.1	chr16	13358376	13358439	+	1	NA	promoter-TSS (NM_153588)	promoter-TSS (NM_153588)	-14	NM_153588	239719	Mm.270643	NM_153588	ENSMUSG00000009569	Mkl2	ENSMUSG00000075401|Gt4-1|MRTF-B|Mrtfb|mKIAA1243	MKL/myocardin-like 2	protein-coding
mm_96409.1	chr11	67254058	67254070	+	1	NA	exon (NM_010855, exon 28 of 40)	exon (NM_010855, exon 28 of 40)	16252	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_42499.1	chr5	115489457	115489458	+	1	NA	Intergenic	Intergenic	-4973	NM_133760	75387	Mm.332616	NM_133760	ENSMUSG00000029524	Sirt4	4930596O17Rik	sirtuin 4	protein-coding
mm_69906.1	chr7	141639974	141639984	-	1	NA	intron (NM_001330001, intron 31 of 33)	intron (NM_001330001, intron 31 of 33)	15340	NM_001330001	353328	Mm.246621	NM_181729	ENSMUSG00000048191	Muc6	-	mucin 6, gastric	protein-coding
mm_99606.1	chr11	104577004	104577022	+	1	NA	intron (NM_010858, intron 2 of 8)	intron (NM_010858, intron 2 of 8)	-14815	NR_130177	100415912	Mm.446786	NR_130177		Gm11665	Gm11664|OTTMUSG00000003182|OTTMUSG00000003183	predicted gene 11665	ncRNA
mm_32704.1	chr4	116075524	116075534	+	1	NA	promoter-TSS (NM_025641)	promoter-TSS (NM_025641)	260	NM_153521	230654	Mm.3655	NM_153521	ENSMUSG00000028703	Lrrc41	AA409966|AW555107|D630045E04Rik|D730026A16Rik|MUF1	leucine rich repeat containing 41	protein-coding
mm_33166.1	chr4	126023484	126023494	+	1	NA	Intergenic	MT2A|LTR|ERVL	-1170	NR_045561	12986	Mm.271701	NM_007782	ENSMUSG00000028859	Csf3r	Cd114|Csfgr|G-CSF-R|G-CSFR	colony stimulating factor 3 receptor (granulocyte)	protein-coding
mm_55467.1	chr6	67954709	67954716	-	1	NA	Intergenic	Intergenic	-389013	NR_003100	75070	Mm.463364	NR_003100		4930515G16Rik	-	myc induced nuclear antigen pseudogene	pseudo
mm_110247.1	chr12	31351434	31351444	-	1	NA	promoter-TSS (NM_007861)	promoter-TSS (NM_007861)	32	NM_007861	13382	Mm.3131	NM_007861	ENSMUSG00000020664	Dld	-	dihydrolipoamide dehydrogenase	protein-coding
mm_50496.1	chr6	49022963	49022992	+	1	NA	Intergenic	Intergenic	-13541	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_100277.1	chr11	117782359	117782381	+	1	NA	promoter-TSS (NM_181856)	promoter-TSS (NM_181856)	73	NM_001195089	217356	Mm.116675	NM_181856	ENSMUSG00000050106	Tmc8	EVIN2|Ever2|mFLJ00400	transmembrane channel-like gene family 8	protein-coding
mm_40300.1	chr5	43665450	43665463	+	1	NA	intron (NM_172274, intron 1 of 39)	intron (NM_172274, intron 1 of 39)	3077	NM_172274	231214	Mm.44434	NM_172274	ENSMUSG00000039765	Cc2d2a	5730509K17Rik|b2b1035Clo	coiled-coil and C2 domain containing 2A	protein-coding
mm_119895.1	chr14	54938471	54938479	+	1	NA	intron (NM_026066, intron 2 of 4)	intron (NM_026066, intron 2 of 4)	1978	NM_029390	67272	Mm.41614	NM_026066	ENSMUSG00000040759	Cmtm5	1500005P16Rik|2900052H21Rik|Cklfsf5	CKLF-like MARVEL transmembrane domain containing 5	protein-coding
mm_135679.1	chr16	52420047	52420072	-	1	NA	intron (NM_009655, intron 1 of 15)	intron (NM_009655, intron 1 of 15)	33022	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_64484.1	chr7	143066731	143066739	+	1	NA	exon (NM_133655, exon 6 of 8)	exon (NM_133655, exon 6 of 8)	-2633	NM_020285	56844	Mm.139675	NM_020285	ENSMUSG00000045752	Tssc4	AA241958|ESTM671070	tumor-suppressing subchromosomal transferable fragment 4	protein-coding
mm_57560.1	chr6	127109497	127109507	-	1	NA	promoter-TSS (NM_177003)	promoter-TSS (NM_177003)	50	NM_177003	319801	Mm.101836	NM_177003	ENSMUSG00000038028	Tigar	9630033F20Rik|AA793651|AI595337|C79710|C85509	Trp53 induced glycolysis repulatory phosphatase	protein-coding
mm_34333.1	chr4	142307709	142307742	+	1	NA	Intergenic	Intergenic	-68324	NM_001109685	71529	Mm.255986	NM_144531	ENSMUSG00000040606	Kazn	2310007B04Rik|9030409G11Rik|AI256607|AI666764|AW061099|Kaz|Kazrin	kazrin, periplakin interacting protein	protein-coding
mm_41289.1	chr5	90463705	90463713	+	1	NA	intron (NM_009654, intron 3 of 14)	intron (NM_009654, intron 3 of 14)	2839	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_86003.1	chr9	112232450	112232460	-	1	NA	promoter-TSS (NM_001177616)	promoter-TSS (NM_001177616)	46	NM_001177616	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_84905.1	chr9	79962046	79962088	-	1	NA	intron (NM_001081243, intron 1 of 5)	intron (NM_001081243, intron 1 of 5)	15815	NM_001081243	70598	Mm.23049	NM_001081243	ENSMUSG00000034898	Filip1	5730485H21Rik|AI843021	filamin A interacting protein 1	protein-coding
mm_134650.1	chr16	21995390	21995392	-	1	NA	5' UTR (NM_153404, exon 1 of 9)	5' UTR (NM_153404, exon 1 of 9)	151	NM_001289582	239759	Mm.33192	NM_153404	ENSMUSG00000044626	Liph	C130037N08Rik|D16Wsu119e|H06|Lpdlr|P3|PLA1B|lpd1|lpd2|mPA-PLA1	lipase, member H	protein-coding
mm_31747.1	chr4	63344549	63344593	+	1	NA	promoter-TSS (NM_008768)	promoter-TSS (NM_008768)	15	NM_008768	18405	Mm.4777	NM_008768	ENSMUSG00000039196	Orm1	Agp-1|Agp-2|Orm-1	orosomucoid 1	protein-coding
mm_52300.1	chr6	108805678	108805684	+	1	NA	intron (NM_026011, intron 1 of 6)	(T)n|Simple_repeat|Simple_repeat	22622	NM_026011	67166	Mm.271178	NM_026011	ENSMUSG00000030105	Arl8b	2610313E07Rik|3100002J04Rik|Arl10c|gie1	ADP-ribosylation factor-like 8B	protein-coding
mm_166249.1	chr5	77351305	77351339	-	1	NA	exon (NM_008048, exon 4 of 5)	exon (NM_008048, exon 4 of 5)	40838	NM_153798	231329	Mm.273217	NM_153798	ENSMUSG00000029250	Polr2b	Pol2rb|Rpb140|Rpb2	polymerase (RNA) II (DNA directed) polypeptide B	protein-coding
mm_98839.1	chr11	97440220	97440238	+	1	NA	Intergenic	CpG	-9931	NM_021493	58996	Mm.394118	NM_021493	ENSMUSG00000049807	Arhgap23	A330041B18Rik	Rho GTPase activating protein 23	protein-coding
mm_65913.1	chr7	30195033	30195043	-	1	NA	promoter-TSS (NM_009795)	promoter-TSS (NM_009795)	10	NM_009795	12336	Mm.439782	NM_009795	ENSMUSG00000001794	Capns1	Capa-4|Capa4|Capn4|D7Ertd146e	calpain, small subunit 1	protein-coding
mm_153537.1	chr19	41917025	41917030	-	1	NA	intron (NM_023418, intron 3 of 3)	PB1D9|SINE|Alu	5156	NM_023418	18648	Mm.16783	NM_023418	ENSMUSG00000011752	Pgam1	2310050F24Rik|Pgam-1	phosphoglycerate mutase 1	protein-coding
mm_61323.1	chr7	68190033	68190065	+	1	NA	exon (NM_010513, exon 10 of 21)	exon (NM_010513, exon 10 of 21)	74184	NM_030101	78444	Mm.425468	NM_030101	ENSMUSG00000030553	Pgpep1l	C330024D12Rik	pyroglutamyl-peptidase I-like	protein-coding
mm_138912.1	chr17	43600328	43600329	+	1	NA	intron (NM_013737, intron 6 of 11)	intron (NM_013737, intron 6 of 11)	-8819	NR_045444	73504	Mm.9277	NR_045444	ENSMUSG00000090307	1700071M16Rik	-	RIKEN cDNA 1700071M16 gene	ncRNA
mm_165834.1	chr3	154711411	154711416	+	1	NA	intron (NM_175176, intron 1 of 6)	intron (NM_175176, intron 1 of 6)	280	NM_175176	209601	Mm.331454	NM_175176	ENSMUSG00000078161	Erich3	1700013E18Rik|4922501L14Rik|5031409G23Rik|AI596448|Gm133	glutamate rich 3	protein-coding
mm_98386.1	chr11	94210405	94210436	+	1	NA	Intergenic	CpG	-1034	NM_009427	22057	Mm.259673	NM_009427	ENSMUSG00000037573	Tob1	Tob|Trob	transducer of ErbB-2.1	protein-coding
mm_153435.1	chr19	40959726	40959742	-	1	NA	exon (NM_008528, exon 6 of 17)	exon (NM_008528, exon 6 of 17)	34801	NM_008528	17060	Mm.9749	NM_008528	ENSMUSG00000061132	Blnk	BASH|Bca|Ly-57|Ly57|Lyw-57|SLP-65	B cell linker	protein-coding
mm_81802.1	chr9	116189175	116189185	+	1	NA	Intergenic	Intergenic	-13817	NM_009371	21813	Mm.172346	NM_009371	ENSMUSG00000032440	Tgfbr2	1110020H15Rik|AU042018|DNIIR|RIIDN|TBR-II|TbetaR-II|TbetaRII	transforming growth factor, beta receptor II	protein-coding
mm_154995.1	chrX	38600591	38600597	+	1	NA	promoter-TSS (NM_026902)	promoter-TSS (NM_026902)	-64	NM_026902	68995	Mm.262453	NM_026902	ENSMUSG00000000355	Mcts1	1500019M23Rik|MCT-1	malignant T cell amplified sequence 1	protein-coding
mm_75906.1	chr8	71381446	71381482	-	1	NA	5' UTR (NM_010150, exon 1 of 4)	5' UTR (NM_010150, exon 1 of 4)	488	NM_010150	13864	Mm.28989	NM_010150	ENSMUSG00000002393	Nr2f6	AV090102|COUP-TF3|EAR2|Erbal2	nuclear receptor subfamily 2, group F, member 6	protein-coding
mm_91241.1	chr10	22306424	22306431	-	1	NA	promoter-TSS (NR_015465)	promoter-TSS (NR_015465)	-293	NR_015465	606736	Mm.387042	NR_015465	ENSMUSG00000097352	C920009B18Rik	-	RIKEN cDNA C920009B18 gene	ncRNA
mm_25697.1	chr3	122274372	122274415	+	1	NA	promoter-TSS (NM_153806)	promoter-TSS (NM_153806)	-21	NM_153806	99480	Mm.398647	NM_153806	ENSMUSG00000039756	Dnttip2	4930588M11Rik|AA408582|AU014960|HSU15552	deoxynucleotidyltransferase, terminal, interacting protein 2	protein-coding
mm_11676.1	chr2	35426546	35426549	+	1	NA	intron (NM_001308300, intron 2 of 6)	intron (NM_001308300, intron 2 of 6)	-29373	NM_001272040	74854	Mm.159338	NM_001080709	ENSMUSG00000079421	4930402F06Rik	-	RIKEN cDNA 4930402F06 gene	protein-coding
mm_170889.1	chr2	24178502	24178519	+	1	NA	Intergenic	Intergenic	-7966	NM_153511	215257	Mm.249379	NM_153511	ENSMUSG00000044103	Il1f9	Il36g	interleukin 1 family, member 9	protein-coding
mm_119702.1	chr14	53763138	53763185	+	1	NA	Intergenic	Intergenic	490768	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_170888.1	chr2	23068208	23068209	+	1	NA	promoter-TSS (NM_001102438)	promoter-TSS (NM_001102438)	7	NM_001102436	74159	Mm.181973	NM_028793	ENSMUSG00000026781	Acbd5	1300014E15Rik	acyl-Coenzyme A binding domain containing 5	protein-coding
mm_6281.1	chr1	69683377	69683385	-	1	NA	intron (NM_011770, intron 2 of 7)	intron (NM_011770, intron 2 of 7)	2579	NM_011770	22779	Mm.106343	NM_011770	ENSMUSG00000025997	Ikzf2	A730095J18Rik|Helios|Zfpn1a2|Znfn1a2	IKAROS family zinc finger 2	protein-coding
mm_65605.1	chr7	27396543	27396566	-	1	NA	promoter-TSS (NM_001199234)	promoter-TSS (NM_001199234)	-1	NM_001199236	80297	Mm.459123	NM_032610	ENSMUSG00000011751	Sptbn4	1700022P15Rik|5830426A08Rik|ROSA62|SpbIV|Spnb4|dyn|lnd|nmf261|nmf379|qv	spectrin beta, non-erythrocytic 4	protein-coding
mm_98632.1	chr11	96096968	96096971	+	1	NA	Intergenic	Intergenic	14993	NM_001271018	76815	Mm.296049	NM_029755	ENSMUSG00000006056	Calcoco2	2410154J16Rik|C77254|Ndp52|Ndp52l1	calcium binding and coiled-coil domain 2	protein-coding
mm_84005.1	chr9	57620761	57620778	-	1	NA	promoter-TSS (NM_199222)	promoter-TSS (NM_199222)	5	NM_199222	235416	Mm.295630	NM_199222	ENSMUSG00000056271	Lman1l	BC020188|slamp	lectin, mannose-binding 1 like	protein-coding
mm_125677.1	chr15	66604081	66604091	+	1	NA	exon (NM_001081409, exon 7 of 21)	exon (NM_001081409, exon 7 of 21)	26514	NM_001081409	239510	Mm.267473	NM_178718	ENSMUSG00000072501	Phf20l1	CGI-72|E130113K22Rik	PHD finger protein 20-like 1	protein-coding
mm_143688.1	chr17	80207300	80207308	-	1	NA	promoter-TSS (NM_001195487)	promoter-TSS (NM_001195487)	1	NM_001195486	225027	Mm.292016	NM_146083	ENSMUSG00000024097	Srsf7	35kDa|9430065L19Rik|9G8|NX-96|Sfrs7	serine/arginine-rich splicing factor 7	protein-coding
mm_80967.1	chr9	103111938	103111990	+	1	NA	promoter-TSS (NM_173781)	promoter-TSS (NM_173781)	-110	NM_173781	270192	Mm.490252	NM_173781	ENSMUSG00000032549	Rab6b	9630015C03|AI844641|C330006L04Rik|D9Bwg0185e	RAB6B, member RAS oncogene family	protein-coding
mm_26755.1	chr3	8022829	8022857	-	1	NA	Intergenic	RLTR44B|LTR|ERVK	-67956	NR_040587	75476	Mm.491752	NR_040587	ENSMUSG00000100010	1700010I02Rik	-	RIKEN cDNA 1700010I02 gene	ncRNA
mm_22092.1	chr2	168932566	168932568	-	1	NA	intron (NM_009564, intron 5 of 5)	intron (NM_009564, intron 5 of 5)	23020	NM_009564	22722	Mm.2095	NM_009564	ENSMUSG00000027551	Zfp64	-	zinc finger protein 64	protein-coding
mm_144735.1	chr18	35562263	35562273	+	1	NA	5' UTR (NM_010771, exon 1 of 15)	5' UTR (NM_010771, exon 1 of 15)	110	NM_010771	17184	Mm.215034	NM_010771	ENSMUSG00000037236	Matr3	1110061A14Rik|2810017I02Rik|AI841759|AW555618|D030046F20Rik|mKIAA0723	matrin 3	protein-coding
mm_119308.1	chr14	35057178	35057180	+	1	NA	intron (NM_008166, intron 4 of 15)	RMER3D-int|LTR|ERVK	162570	NR_029774	723847		NR_029774	ENSMUSG00000065481	Mir346	Mirn346|mir-346|mmu-mir-346	microRNA 346	ncRNA
mm_63372.1	chr7	127196184	127196196	+	1	NA	promoter-TSS (NM_027353)	promoter-TSS (NM_027353)	-113	NM_027353	70233	Mm.28050	NM_027353	ENSMUSG00000042502	Cd2bp2	1500011B02Rik|2410024K20Rik|AW048183	CD2 antigen (cytoplasmic tail) binding protein 2	protein-coding
mm_45195.1	chr5	52192185	52192205	-	1	NA	intron (NR_015537, intron 1 of 3)	intron (NR_015537, intron 1 of 3)	1514	NR_015537	414108	Mm.383512	NR_015537	ENSMUSG00000097145	9230114K14Rik	-	RIKEN cDNA 9230114K14 gene	ncRNA
mm_154818.1	chrX	15926091	15926095	+	1	NA	Intergenic	Intergenic	-596776	NM_001310461	66742	Mm.45302	NM_025738	ENSMUSG00000023257	Cypt1	4931420D14Rik|Ckt1r3|Cypt5|Cypt6|TISP55	cysteine-rich perinuclear theca 1	protein-coding
mm_168160.1	chr10	4353462	4353463	+	1	NA	exon (NM_031185, exon 3 of 4)	exon (NM_031185, exon 3 of 4)	34646	NM_001033466	381990	Mm.262466	NM_001033466	ENSMUSG00000075327	Zbtb2	Gm1103	zinc finger and BTB domain containing 2	protein-coding
mm_5138.1	chr1	9721456	9721503	-	1	NA	3' UTR (NM_173443, exon 3 of 3)	3' UTR (NM_173443, exon 3 of 3)	-21270	NM_008651	17864	Mm.479	NM_008651	ENSMUSG00000025912	Mybl1	A-myb|G1-419-6|repro9	myeloblastosis oncogene-like 1	protein-coding
mm_95987.1	chr11	58999360	58999370	+	1	NA	exon (NM_001171512, exon 93 of 104)	exon (NM_001171512, exon 93 of 104)	21272	NM_053168	94091	Mm.248049	NM_053168	ENSMUSG00000020455	Trim11	-	tripartite motif-containing 11	protein-coding
mm_90197.1	chr10	120227031	120227081	+	1	NA	promoter-TSS (NM_025431)	promoter-TSS (NM_025431)	-4	NM_025431	66225	Mm.291755	NM_025431	ENSMUSG00000020224	Llph	1190005P17Rik	LLP homolog, long-term synaptic facilitation (Aplysia)	protein-coding
mm_163084.1	chr11	69368851	69368874	+	1	NA	intron (NM_146019, intron 1 of 39)	CpG	564	NM_146019	216848	Mm.178246	NM_146019	ENSMUSG00000018474	Chd3	2600010P09Rik|AF020312|Chd7|Prp7|Prp9-1	chromodomain helicase DNA binding protein 3	protein-coding
mm_131128.1	chr16	5885271	5885311	+	1	NA	5' UTR (NM_021477, exon 1 of 17)	5' UTR (NM_021477, exon 1 of 17)	498	NM_021477	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_138795.1	chr17	37525847	37525873	+	1	NA	Intergenic	Intergenic	-4097	NM_001005485	545205	Mm.383371	NM_001005485	ENSMUSG00000090675	Olfr111	-	olfactory receptor 111	protein-coding
mm_17482.1	chr2	28562412	28562422	-	1	NA	intron (NM_009885, intron 1 of 10)	intron (NM_009885, intron 1 of 10)	986	NM_009885	12613	Mm.236017	NM_009885	ENSMUSG00000026818	Cel	1810036E18Rik|BAL	carboxyl ester lipase	protein-coding
mm_21573.1	chr2	164237112	164237127	-	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	1222	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_58284.1	chr6	145863139	145863184	-	1	NA	exon (NM_024469, exon 5 of 5)	exon (NM_024469, exon 5 of 5)	2259	NM_001271768	79362	Mm.154529	NM_024469	ENSMUSG00000030256	Bhlhe41	6430520M22Rik|Bhlhb2l|Bhlhb3|DEC2|Sharp1	basic helix-loop-helix family, member e41	protein-coding
mm_56763.1	chr6	116131850	116131884	-	1	NA	intron (NM_177412, intron 3 of 5)	B1_Mur1|SINE|Alu	61507	NM_177412	330401	Mm.425352	NM_177412	ENSMUSG00000030126	Tmcc1	3632431M01Rik|mKIAA0779	transmembrane and coiled coil domains 1	protein-coding
mm_5452.1	chr1	36267989	36268009	-	1	NA	intron (NM_153408, intron 3 of 3)	B4A|SINE|B4	5426	NM_153408	214854	Mm.389110	NM_153408	ENSMUSG00000047180	Neurl3	2010300P06Rik|Lincr	neuralized E3 ubiquitin protein ligase 3	protein-coding
mm_144891.1	chr18	36946082	36946096	+	1	NA	promoter-TSS (NM_138662)	promoter-TSS (NM_138662)	-118	NM_138662	192163	Mm.308500	NM_138662	ENSMUSG00000102312	Pcdha3	mKIAA0345	protocadherin alpha 3	protein-coding
mm_95417.1	chr11	50071207	50071219	+	1	NA	exon (NM_021540, exon 3 of 9)	exon (NM_021540, exon 3 of 9)	1511	NR_029769	723845		NR_029769	ENSMUSG00000065417	Mir340	Mirn340|mir-340|mmu-mir-340	microRNA 340	ncRNA
mm_2558.1	chr1	112785546	112785547	+	1	NA	Intergenic	Intergenic	-920628	NM_001081316	319901	Mm.103468	NM_001081316	ENSMUSG00000038702	Dsel	9330132E09Rik|DS-epi2	dermatan sulfate epimerase-like	protein-coding
mm_101451.1	chr11	30198233	30198261	-	1	NA	promoter-TSS (NM_009260)	promoter-TSS (NM_009260)	10	NM_009260	20742	Mm.123110	NM_009260	ENSMUSG00000020315	Sptbn1	9930031C03Rik|AL033301|SPTB2|Spnb-2|Spnb2|elf1|elf3|mKIAA4049	spectrin beta, non-erythrocytic 1	protein-coding
mm_70176.1	chr7	143685864	143685880	-	1	NA	promoter-TSS (NM_024290)	promoter-TSS (NM_024290)	3	NM_001308111	79201	Mm.290780	NM_024290	ENSMUSG00000037613	Tnfrsf23	SOB|TNFRSFH23|Tnfrh1|Tnfrsf1al1|mDcTRAILR1|mSOB	tumor necrosis factor receptor superfamily, member 23	protein-coding
mm_8155.1	chr1	136942304	136942305	-	1	NA	intron (NM_030676, intron 5 of 8)	intron (NM_030676, intron 5 of 8)	11326	NM_001159769	26424	Mm.16794	NM_030676	ENSMUSG00000026398	Nr5a2	AU020803|D1Ertd308e|Ftf|LRH-1|UF2-H3B	nuclear receptor subfamily 5, group A, member 2	protein-coding
mm_21853.1	chr2	165879514	165879534	-	1	NA	intron (NM_027230, intron 1 of 23)	intron (NM_027230, intron 1 of 23)	-1087	NM_001291158	228880	Mm.227598	NM_027230	ENSMUSG00000039671	Zmynd8	1110013E22Rik|2010005I16Rik|3632413B07Rik|AI316811|AL024039|Prkcbp1|RACK7	zinc finger, MYND-type containing 8	protein-coding
mm_63850.1	chr7	135653971	135653980	+	1	NA	exon (NM_011212, exon 6 of 21)	exon (NM_011212, exon 6 of 21)	-1661	NR_015548	67765	Mm.445272	NR_015548	ENSMUSG00000097471	5830432E09Rik	-	RIKEN cDNA 5830432E09 gene	ncRNA
mm_6959.1	chr1	86110750	86110761	-	1	NA	exon (NM_008311, exon 2 of 4)	exon (NM_008311, exon 2 of 4)	1215	NM_008311	15559	Mm.439747	NM_008311	ENSMUSG00000026228	Htr2b	5-HT2B|AJ012488|AV377389	5-hydroxytryptamine (serotonin) receptor 2B	protein-coding
mm_132704.1	chr16	43363991	43364017	+	1	NA	intron (NM_181058, intron 2 of 6)	intron (NM_181058, intron 2 of 6)	56192	NR_046026	626693	Mm.447083	NR_046026	ENSMUSG00000085499	Gm15713	OTTMUSG00000025617	predicted gene 15713	ncRNA
mm_84008.1	chr9	57645126	57645136	-	1	NA	5' UTR (NM_007783, exon 1 of 13)	5' UTR (NM_007783, exon 1 of 13)	522	NM_007783	12988	Mm.21974	NM_007783	ENSMUSG00000032312	Csk	AW212630|p50CSK	c-src tyrosine kinase	protein-coding
mm_113167.1	chr13	24813399	24813451	+	1	NA	TTS (NM_024473)	TTS (NM_024473)	11768	NM_024473	79555	Mm.266668	NM_024473	ENSMUSG00000019132	BC005537	8030460C05Rik|C78201	cDNA sequence BC005537	protein-coding
mm_46429.1	chr5	104440460	104440576	-	1	NA	exon (NM_001204203, exon 7 of 7)	exon (NM_001204203, exon 7 of 7)	4326	NM_001204233	20750	Mm.288474	NM_009263	ENSMUSG00000029304	Spp1	2AR|Apl-1|BNSP|BSPI|Bsp|ETA-1|Eta|OP|Opn|Opnl|Ric|Spp-1	secreted phosphoprotein 1	protein-coding
mm_51414.1	chr6	78381840	78381841	+	1	NA	intron (NM_011259, intron 2 of 5)	intron (NM_011259, intron 2 of 5)	1131	NM_011259	19694	Mm.2552	NM_011259	ENSMUSG00000079516	Reg3a	AV063448	regenerating islet-derived 3 alpha	protein-coding
mm_108664.1	chr12	86470132	86470150	+	1	NA	intron (NM_011934, intron 1 of 6)	CpG	48497	NM_011934	26380	Mm.235550	NM_011934	ENSMUSG00000021255	Esrrb	Err2|Errb|Estrrb|Nr3b2	estrogen related receptor, beta	protein-coding
mm_170250.1	chr1	80588052	80588058	-	1	NA	intron (NM_175291, intron 11 of 55)	CT-rich|Low_complexity|Low_complexity	77297	NM_001285927	210293	Mm.133473	NM_175291	ENSMUSG00000038608	Dock10	9330153B10Rik|A630054M16Rik|Jr4|Jr5|R75174|ZIZ3|Zizimin3|mKIAA0694	dedicator of cytokinesis 10	protein-coding
mm_128426.1	chr15	48792156	48792174	-	1	NA	promoter-TSS (NM_001081391)	promoter-TSS (NM_001081391)	-176	NM_001081391	239420	Mm.309363	NM_001081391	ENSMUSG00000022311	Csmd3	4930500N14Rik|mKIAA1894	CUB and Sushi multiple domains 3	protein-coding
mm_129407.1	chr15	78297010	78297020	-	1	NA	exon (NM_007781, exon 3 of 14)	exon (NM_007781, exon 3 of 14)	8706	NM_007781	12984	Mm.1940	NM_007781	ENSMUSG00000071714	Csf2rb2	AIC2A|BetaIl3|Bil3|Csfgmrb|Il3r|Il3rb|Il3rb2	colony stimulating factor 2 receptor, beta 2, low-affinity (granulocyte-macrophage)	protein-coding
mm_15218.1	chr2	154427036	154427046	+	1	NA	Intergenic	Intergenic	-9443	NM_172860	12396	Mm.29914	NM_009823	ENSMUSG00000038533	Cbfa2t2	A430091M07|C330013D05Rik|Cbfa2t2h|MTGR1	core-binding factor, runt domain, alpha subunit 2, translocated to, 2 (human)	protein-coding
mm_18058.1	chr2	39226420	39226426	-	1	NA	promoter-TSS (NM_024209)	promoter-TSS (NM_024209)	-85	NM_024209	67857	Mm.389242	NM_024209	ENSMUSG00000026753	Ppp6c	2310003C10Rik	protein phosphatase 6, catalytic subunit	protein-coding
mm_155621.1	chrX	83588484	83588498	+	1	NA	intron (NM_007868, intron 7 of 78)	(CAGA)n|Simple_repeat|Simple_repeat	-100567	NM_021898	100502723	Mm.383210	NM_021898	ENSMUSG00000035522	Tsga8	Halap-X|Halapx	testis specific gene A8	protein-coding
mm_59246.1	chr7	24784600	24784605	+	1	NA	TTS (NM_007675)	TTS (NM_007675)	7398	NM_007675	26366	Mm.30300	NM_007675	ENSMUSG00000054169	Ceacam10	Bgp3|Cea10	carcinoembryonic antigen-related cell adhesion molecule 10	protein-coding
mm_154414.1	chrM	15521	15532	+	1	NA	NA	Intergenic	NA	NA								
mm_48481.1	chr5	141230297	141230300	-	1	NA	Intergenic	B4A|SINE|B4	-11236	NM_177879	330222	Mm.151931	NM_177879	ENSMUSG00000039683	Sdk1	5330440E10|6720466O15Rik	sidekick cell adhesion molecule 1	protein-coding
mm_14764.1	chr2	145186410	145186414	+	1	NA	Intergenic	Intergenic	-56199	NM_053195	94249	Mm.217171	NM_053195	ENSMUSG00000063873	Slc24a3	NCKX3	solute carrier family 24 (sodium/potassium/calcium exchanger), member 3	protein-coding
mm_156439.1	chrX	142227924	142227951	+	1	NA	promoter-TSS (NM_001161430)	promoter-TSS (NM_001161430)	0	NM_001161430	237082	Mm.41899	NM_172782	ENSMUSG00000042271	Nxt2	6330587F24Rik|AI787442|P15-2	nuclear transport factor 2-like export factor 2	protein-coding
mm_33768.1	chr4	134401660	134401674	+	1	NA	intron (NM_001285872, intron 1 of 10)	intron (NM_001285872, intron 1 of 10)	-1245	NM_001285874	100163	Mm.22116	NM_133880	ENSMUSG00000037366	Pafah2	2310074E22Rik|AI507170	platelet-activating factor acetylhydrolase 2	protein-coding
mm_15087.1	chr2	153240930	153240943	+	1	NA	promoter-TSS (NM_080463)	promoter-TSS (NM_080463)	422	NM_018807	54711	Mm.103199	NM_018807	ENSMUSG00000051413	Plagl2	AU018672|AW552839|mKIAA0198	pleiomorphic adenoma gene-like 2	protein-coding
mm_62803.1	chr7	112856632	112856636	+	1	NA	intron (NM_009346, intron 5 of 12)	intron (NM_009346, intron 5 of 12)	97250	NM_001166585	21676	Mm.24685	NM_009346	ENSMUSG00000055320	Tead1	2610024B07Rik|B230114H05Rik|Gtrgeo5|TEAD-1|TEF-1|Tcf13|mTEF-1	TEA domain family member 1	protein-coding
mm_95049.1	chr11	32297128	32297159	+	1	NA	exon (NM_008218, exon 3 of 3).2	exon (NM_008218, exon 3 of 3).2	651	NM_001083955	110257	Mm.196110	NM_001083955	ENSMUSG00000069917	Hba-a2	-	hemoglobin alpha, adult chain 2	protein-coding
mm_154982.1	chrX	38121175	38121189	+	1	NA	5' UTR (NM_001185002, exon 1 of 3)	5' UTR (NM_001185002, exon 1 of 3)	342	NM_001185002	73614	Mm.50505	NM_001185002	ENSMUSG00000050197	Rhox13	1700123J19Rik	reproductive homeobox 13	protein-coding
mm_68920.1	chr7	126463101	126463115	-	1	NA	promoter-TSS (NM_007504)	promoter-TSS (NM_007504)	-35	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_117093.1	chr13	59822570	59822580	-	1	NA	intron (NM_153538, intron 1 of 27)	CpG	572	NM_153538	214290	Mm.233082	NM_153538	ENSMUSG00000035248	Zcchc6	6030448M23Rik|AA420405	zinc finger, CCHC domain containing 6	protein-coding
mm_31851.1	chr4	75278349	75278360	+	1	NA	promoter-TSS (NM_025849)	promoter-TSS (NM_025849)	-68	NM_025849	66928	Mm.24332	NM_025849	ENSMUSG00000028398	Tmem261	1700027K24Rik|3110001D03Rik	transmembrane protein 261	protein-coding
mm_39.1	chr1	6475234	6475244	+	1	NA	Intergenic	Intergenic	-11992	NM_001244693	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding
mm_69340.1	chr7	129657954	129657976	-	1	NA	Intergenic	Intergenic	66102	NM_172255	207425	Mm.229323	NM_172255	ENSMUSG00000042055	Wdr11	2900055P10Rik|AW489876|Brwd2|mKIAA1351	WD repeat domain 11	protein-coding
mm_142848.1	chr17	51797599	51797610	-	1	NA	intron (NM_009122, intron 5 of 10)	intron (NM_009122, intron 5 of 10)	14450	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_60796.1	chr7	45617576	45617611	+	1	NA	promoter-TSS (NM_008051)	promoter-TSS (NM_008051)	-13	NM_001271981	14343	Mm.56933	NM_008051	ENSMUSG00000008461	Fut1	-	fucosyltransferase 1	protein-coding
mm_25304.1	chr3	105985084	105985098	+	1	NA	exon (NM_007696, exon 10 of 11)	exon (NM_007696, exon 10 of 11)	11289	NM_007696	12659	Mm.431947	NM_007696	ENSMUSG00000074340	Ovgp1	120kDa|AU016433|AU019448|Chit5|MOGP|OGP|muc9	oviductal glycoprotein 1	protein-coding
mm_67490.1	chr7	80726760	80726780	-	1	NA	exon (NM_016721, exon 31 of 38)	exon (NM_016721, exon 31 of 38)	-37893	NM_173863	70461	Mm.392175	NM_173863	ENSMUSG00000030527	Crtc3	2610312F20Rik|6332415K15Rik|AI429792|BC011210|TORC3	CREB regulated transcription coactivator 3	protein-coding
mm_20850.1	chr2	148047055	148047085	-	1	NA	promoter-TSS (NM_010446)	promoter-TSS (NM_010446)	-101	NM_010446	15376	Mm.938	NM_010446	ENSMUSG00000037025	Foxa2	HNF3-beta|HNF3beta|Hnf-3b|Hnf3b|Tcf-3b|Tcf3b	forkhead box A2	protein-coding
mm_83861.1	chr9	54661885	54661912	-	1	NA	promoter-TSS (NM_053178)	promoter-TSS (NM_053178)	-13	NM_053178	94180	Mm.20592	NM_053178	ENSMUSG00000032281	Acsbg1	BG1|Bgm|E230019G03Rik|GR-LACS|Lpd|R75185	acyl-CoA synthetase bubblegum family member 1	protein-coding
mm_60994.1	chr7	49276071	49276077	+	1	NA	intron (NM_175272, intron 1 of 37)	intron (NM_175272, intron 1 of 37)	29885	NM_175272	78286	Mm.333881	NM_175272	ENSMUSG00000052512	Nav2	5330421F07Rik|AU067780|BQ960892|HELAD1|POMFIL2|RAINB1|RAINB2|Unc53H2|mKIAA3015	neuron navigator 2	protein-coding
mm_61581.1	chr7	79842558	79842585	+	1	NA	promoter-TSS (NM_008486)	promoter-TSS (NM_008486)	-219	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_85940.1	chr9	112099279	112099289	-	1	NA	intron (NM_001177618, intron 17 of 18)	B4|SINE|B4	19427	NR_029823	723815		NR_029823	ENSMUSG00000065441	Mir128-2	Mirn128-2|Mirn128b|mir-128-2|mir-128b	microRNA 128-2	ncRNA
mm_123981.1	chr14	75328033	75328079	-	1	NA	exon (NM_026083, exon 12 of 19)	exon (NM_026083, exon 12 of 19)	43683	NM_026083	67302	Mm.74704	NM_026083	ENSMUSG00000022000	Zc3h13	2600010B19Rik|3110050K21Rik|4930570G11Rik|C87618	zinc finger CCCH type containing 13	protein-coding
mm_125071.1	chr15	25971908	25971912	+	1	NA	exon (NM_001277316, exon 7 of 7)	exon (NM_001277316, exon 7 of 7)	-12456	NM_144523	52521	Mm.29145	NM_144523	ENSMUSG00000052253	Zfp622	1110033B05Rik|D15Ertd806e|ZPR9|Znf622	zinc finger protein 622	protein-coding
mm_51743.1	chr6	87375751	87375768	+	1	NA	exon (NM_025467, exon 3 of 6)	exon (NM_025467, exon 3 of 6)	2394	NM_025467	66284	Mm.46446	NM_025467	ENSMUSG00000030049	Gkn2	1810036H07Rik|Bricd1b	gastrokine 2	protein-coding
mm_166915.1	chr7	30394827	30394828	+	1	NA	Intergenic	Intergenic	-18961	NM_011662	22177	Mm.46301	NM_011662	ENSMUSG00000030579	Tyrobp	DAP12|KARAP|Ly83	TYRO protein tyrosine kinase binding protein	protein-coding
mm_3767.1	chr1	156303504	156303510	+	1	NA	promoter-TSS (NM_001277730)	promoter-TSS (NM_001277730)	99	NM_001277730	214575	Mm.252800	NM_001134741	ENSMUSG00000060985	Tdrd5	Gm103	tudor domain containing 5	protein-coding
mm_102503.1	chr11	60722652	60722678	-	1	NA	exon (NM_022009, exon 6 of 30)	exon (NM_022009, exon 6 of 30)	4598	NM_022009	14248	Mm.339755	NM_022009	ENSMUSG00000002812	Flii	3632430F08Rik|Fliih	flightless I actin binding protein	protein-coding
mm_69706.1	chr7	140082560	140082570	-	1	NA	promoter-TSS (NM_026769)	promoter-TSS (NM_026769)	-17	NM_026769	68566	Mm.44241	NM_026769	ENSMUSG00000025468	Caly	0710001P07Rik|1110004A22Rik|Calcyon|Drd1ip	calcyon neuron-specific vesicular protein	protein-coding
mm_62153.1	chr7	97133836	97133845	+	1	NA	intron (NM_001162477, intron 1 of 9)	L1_Mur1|LINE|L1	52089	NM_010248	14389	Mm.42033	NM_010248	ENSMUSG00000004508	Gab2	AI463667|D130058I17Rik|p97	growth factor receptor bound protein 2-associated protein 2	protein-coding
mm_86554.1	chr10	10751074	10751112	+	1	NA	promoter-TSS (NR_046010)	promoter-TSS (NR_046010)	47	NR_046010	78056	Mm.271285	NR_046010		4930567K20Rik	1700038H22Rik	RIKEN cDNA 4930567K20 gene	ncRNA
mm_50077.1	chr6	41354171	41354185	+	1	NA	promoter-TSS (NM_001038996)	promoter-TSS (NM_001038996)	73	NM_001038996	436522	Mm.443385	NM_001038996	ENSMUSG00000071521	Try10	-	trypsin 10	protein-coding
mm_13854.1	chr2	119692154	119692186	+	1	NA	exon (NM_030112, exon 2 of 18)	exon (NM_030112, exon 2 of 18)	17102	NM_030112	76246	Mm.33437	NM_030112	ENSMUSG00000027304	Rtf1	2900005O08Rik|6530416A09Rik|AI853581|AU043144|AW553985|Gtl7|cbp82	RTF1, Paf1/RNA polymerase II complex component	protein-coding
mm_64345.1	chr7	142380851	142380865	+	1	NA	exon (NM_009983, exon 5 of 9)	exon (NM_009983, exon 5 of 9)	7012	NM_009983	13033	Mm.231395	NM_009983	ENSMUSG00000007891	Ctsd	CD|CatD	cathepsin D	protein-coding
mm_136059.1	chr16	80384005	80384006	-	1	NA	Intergenic	Lx8|LINE|L1	-816692	NM_001113208	17968	Mm.433941	NM_010954	ENSMUSG00000022762	Ncam2	Ncam-2|Ocam|RNCAM	neural cell adhesion molecule 2	protein-coding
mm_28103.1	chr3	86548053	86548081	-	1	NA	5' UTR (NM_011839, exon 1 of 1)	5' UTR (NM_011839, exon 1 of 1)	216	NM_011839	23937	Mm.389466	NM_011839	ENSMUSG00000057777	Mab21l2	-	mab-21-like 2 (C. elegans)	protein-coding
mm_15229.1	chr2	154549022	154549039	+	1	NA	exon (NM_029305, exon 1 of 3)	exon (NM_029305, exon 1 of 3)	126	NM_029305	75480	Mm.440434	NM_029305	ENSMUSG00000038523	1700003F12Rik	-	RIKEN cDNA 1700003F12 gene	protein-coding
mm_115479.1	chr13	3140152	3140164	-	1	NA	Intergenic	Intergenic	-9317	NR_001581	73266	Mm.335891	NR_001581		Speer6-ps1	1700039A02Rik|SPEER-6	spermatogenesis associated glutamate (E)-rich protein 6, pseudogene 1	pseudo
mm_143725.1	chr17	81378919	81378936	-	1	NA	non-coding (NR_104580, exon 9 of 9)	non-coding (NR_104580, exon 9 of 9)	-313842	NM_028138	72167	Mm.273257	NM_028138	ENSMUSG00000024246	Thumpd2	2810025A12Rik	THUMP domain containing 2	protein-coding
mm_155802.1	chrX	99042621	99042661	+	1	NA	promoter-TSS (NM_199018)	promoter-TSS (NM_199018)	60	NM_199018	236920	Mm.236928	NM_199018	ENSMUSG00000031216	Stard8	Dlc3|mKIAA0189	START domain containing 8	protein-coding
mm_145632.1	chr18	61111255	61111270	+	1	NA	intron (NM_001037859, intron 4 of 21)	ID4|SINE|ID	5690	NM_001037859	12978	Mm.22574	NM_007779	ENSMUSG00000024621	Csf1r	AI323359|CD115|CSF-1R|Csfmr|Fim-2|Fim2|Fms|M-CSF-R|M-CSFR	colony stimulating factor 1 receptor	protein-coding
mm_24975.1	chr3	96795922	96795934	+	1	NA	Intergenic	B1_Mus2|SINE|Alu	18593	NM_018767	54215	Mm.34693	NM_018767	ENSMUSG00000038304	Cd160	AU045688|By55	CD160 antigen	protein-coding
mm_50516.1	chr6	49040367	49040374	+	1	NA	intron (NM_053110, intron 1 of 10)	intron (NM_053110, intron 1 of 10)	3852	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_143515.1	chr17	72976445	72976449	-	1	NA	Intergenic	Intergenic	58142	NM_029999	77889	Mm.154109	NM_029999	ENSMUSG00000024063	Lbh	1810009F10Rik|6720416L16Rik	limb-bud and heart	protein-coding
mm_86088.1	chr9	114933587	114933646	-	1	NA	intron (NM_175380, intron 1 of 7)	CpG	371	NM_175380	333433	Mm.38198	NM_175380	ENSMUSG00000050627	Gpd1l	2210409H23Rik|D9Ertd660e	glycerol-3-phosphate dehydrogenase 1-like	protein-coding
mm_34643.1	chr4	150705206	150705216	+	1	NA	Intergenic	Intergenic	-53037	NM_173774	242773	Mm.29280	NM_173774	ENSMUSG00000039838	Slc45a1	C230078B22|Dnb5	solute carrier family 45, member 1	protein-coding
mm_43448.1	chr5	136116679	136116740	+	1	NA	promoter-TSS (NM_011293)	promoter-TSS (NM_011293)	18	NM_011293	20022	Mm.4896	NM_011293	ENSMUSG00000039771	Polr2j	14.5kDa|Polr2i|Rpb11a|Rpo2-4	polymerase (RNA) II (DNA directed) polypeptide J	protein-coding
mm_67522.1	chr7	80947500	80947579	-	1	NA	promoter-TSS (NM_019951)	promoter-TSS (NM_019951)	11	NM_019951	56529	Mm.43760	NM_019951	ENSMUSG00000025724	Sec11a	1810012E07Rik|18kDa|Sec11l1|Sid2895p|Spc18|sid2895	SEC11 homolog A, signal peptidase complex subunit	protein-coding
mm_28843.1	chr3	96629789	96629828	-	1	NA	promoter-TSS (NR_003619)	promoter-TSS (NR_003619)	11	NR_003619	229613	Mm.445135	NM_175469	ENSMUSG00000045327	6330549D23Rik	-	RIKEN cDNA 6330549D23 gene	pseudo
mm_3134.1	chr1	135131241	135131258	+	1	NA	intron (NM_007955, intron 1 of 37)	intron (NM_007955, intron 1 of 37)	1326	NM_007955	13924	Mm.4450	NM_007955		Ptprv	Esp|OST|OST-PTP|mOST-PTP	protein tyrosine phosphatase, receptor type, V	protein-coding
mm_119198.1	chr14	32685690	32685698	+	1	NA	promoter-TSS (NM_001195097)	promoter-TSS (NM_001195097)	-422	NM_001195097	100504518	Mm.318319	NM_001195097	ENSMUSG00000071540	3425401B19Rik	-	RIKEN cDNA 3425401B19 gene	protein-coding
mm_80920.1	chr9	101034878	101034879	+	1	NA	promoter-TSS (NM_001311149)	promoter-TSS (NM_001311149)	6	NM_001311149	66904	Mm.335385	NM_025835	ENSMUSG00000032527	Pccb	1300012P06Rik|AI314687|R74805	propionyl Coenzyme A carboxylase, beta polypeptide	protein-coding
mm_117016.1	chr13	58127044	58127065	-	1	NA	3' UTR (NM_029872, exon 1 of 1)	3' UTR (NM_029872, exon 1 of 1)	1502	NM_029872	77134	Mm.490274	NM_029872	ENSMUSG00000007836	Hnrnpa0	1110055B05Rik|3010025E17Rik|Hnrpa0|hnRNP A0	heterogeneous nuclear ribonucleoprotein A0	protein-coding
mm_90257.1	chr10	122448532	122448550	+	1	NA	promoter-TSS (NM_016847)	promoter-TSS (NM_016847)	42	NM_016847	54140	Mm.4351	NM_016847	ENSMUSG00000020123	Avpr1a	AVPR|Avpr1|V1a|V1aR	arginine vasopressin receptor 1A	protein-coding
mm_169135.1	chr13	59477877	59477889	-	1	NA	intron (NM_023328, intron 18 of 25)	intron (NM_023328, intron 18 of 25)	66568	NM_001284221	67269	Mm.153008	NM_023328	ENSMUSG00000021557	Agtpbp1	1700020N17Rik|2310001G17Rik|2900054O13Rik|4930445M19Rik|5730402G09Rik|CCP1|Nna1|nmf243|pcd	ATP/GTP binding protein 1	protein-coding
mm_84347.1	chr9	64253569	64253614	-	1	NA	promoter-TSS (NM_008927)	promoter-TSS (NM_008927)	14	NM_008927	26395	Mm.248907	NM_008927	ENSMUSG00000004936	Map2k1	MAPKK1|MEKK1|Mek1|Prkmk1	mitogen-activated protein kinase kinase 1	protein-coding
mm_110202.1	chr12	27341121	27341132	-	1	NA	3' UTR (NM_009234, exon 1 of 1)	3' UTR (NM_009234, exon 1 of 1)	1592	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding
mm_41707.1	chr5	101765121	101765145	+	1	NA	promoter-TSS (NM_173370)	promoter-TSS (NM_173370)	3	NM_173370	74596	Mm.46764	NM_173370	ENSMUSG00000029330	Cds1	4833409J18Rik|AI314024|AW125888	CDP-diacylglycerol synthase 1	protein-coding
mm_129731.1	chr15	82047546	82047563	-	1	NA	promoter-TSS (NM_011482)	promoter-TSS (NM_011482)	44	NM_011482	20826	Mm.299312	NM_011482	ENSMUSG00000063480	Nhp2l1	FA-1|Fta1|Snu13|Ssfa1	NHP2 non-histone chromosome protein 2-like 1 (S. cerevisiae)	protein-coding
mm_84187.1	chr9	60193691	60193702	-	1	NA	intron (NM_001040426, intron 7 of 17)	ID4_|SINE|ID	-52476	NM_172444	207596	Mm.28791	NM_172444	ENSMUSG00000032289	Thsd4	ADAMTSL-6|ADAMTSL6|AI585901|Adamtsl4|B230114P05Rik	thrombospondin, type I, domain containing 4	protein-coding
mm_128410.1	chr15	44748362	44748377	-	1	NA	exon (NM_176998, exon 2 of 8)	exon (NM_176998, exon 2 of 8)	303	NM_001285840	319613	Mm.207715	NM_176998	ENSMUSG00000022340	Sybu	Golsyn	syntabulin (syntaxin-interacting)	protein-coding
mm_36159.1	chr4	59914951	59914961	-	1	NA	promoter-TSS (NM_021053)	promoter-TSS (NM_021053)	100	NM_021053	30936	Mm.284433	NM_021053	ENSMUSG00000028386	Slc46a2	5430429N04Rik|Ly110|TSO-1C12|Tscot	solute carrier family 46, member 2	protein-coding
mm_65343.1	chr7	24988033	24988120	-	1	NA	promoter-TSS (NR_106014)	promoter-TSS (NR_106014)	-409	NR_106014	102465634		NR_106014	ENSMUSG00000099258	Mir7047	Gm27270|mmu-mir-7047	microRNA 7047	ncRNA
mm_117283.1	chr13	65557691	65557709	-	1	NA	Intergenic	Intergenic	278846	NM_178364	170936	Mm.151546	NM_178364	ENSMUSG00000021514	Zfp369	B930030B22Rik|D230020H11Rik|NRIF2	zinc finger protein 369	protein-coding
mm_69897.1	chr7	141638017	141638025	-	1	NA	intron (NM_001330001, intron 31 of 33)	intron (NM_001330001, intron 31 of 33)	17298	NM_001330001	353328	Mm.246621	NM_181729	ENSMUSG00000048191	Muc6	-	mucin 6, gastric	protein-coding
mm_55539.1	chr6	70791998	70792017	-	1	NA	exon (NM_009075, exon 1 of 9)	exon (NM_009075, exon 1 of 9)	168	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_8345.1	chr1	150197161	150197174	-	1	NA	Intergenic	Lx|LINE|L1	-32219	NR_110420	102639566	Mm.417208	NR_110420	ENSMUSG00000097754	Ptgs2os2	Gm26687|Linc-cox2|Lincrna-cox2	prostaglandin-endoperoxide synthase 2, opposite strand 2	ncRNA
mm_99633.1	chr11	105178766	105178771	+	1	NA	promoter-TSS (NM_001294331)	promoter-TSS (NM_001294331)	-39	NM_001294331	24086	Mm.126976	NM_011903	ENSMUSG00000020694	Tlk2	4933403M19Rik|PKU-alpha|PKUalpha|Tlk	tousled-like kinase 2 (Arabidopsis)	protein-coding
mm_75.1	chr1	6707862	6707878	+	1	NA	intron (NM_001244693, intron 2 of 22)	L1_Mur3|LINE|L1	-22181	NR_045189	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding
mm_17073.1	chr2	22745116	22745139	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-29200	NM_019456	54519	Mm.14255	NM_019456	ENSMUSG00000026786	Apbb1ip	9930118P07Rik|Prp48	amyloid beta (A4) precursor protein-binding, family B, member 1 interacting protein	protein-coding
mm_135143.1	chr16	35856213	35856238	-	1	NA	intron (NM_001039530, intron 6 of 16)	B2_Mm1a|SINE|B2	15157	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_26298.1	chr3	142507954	142507971	+	1	NA	exon (NM_153564, exon 10 of 11)	exon (NM_153564, exon 10 of 11)	11028	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_75860.1	chr8	70700448	70700461	-	1	NA	3' UTR (NM_001286944, exon 1 of 1)	3' UTR (NM_001286944, exon 1 of 1)	2715	NM_001286944	16478	Mm.419851	NM_010592	ENSMUSG00000071076	Jund	Jund1	jun D proto-oncogene	protein-coding
mm_61893.1	chr7	90023411	90023413	+	1	NA	Intergenic	Intergenic	-5747	NR_110365	319711	Mm.31753	NR_015614	ENSMUSG00000097585	E230029C05Rik	AI452102|B230337J15	RIKEN cDNA E230029C05 gene	ncRNA
mm_145158.1	chr18	46597699	46597765	+	1	NA	promoter-TSS (NM_025698)	promoter-TSS (NM_025698)	28	NM_010120	13664	Mm.262037	NM_010120	ENSMUSG00000057561	Eif1a	C76390|Ef1a|Eftu|Eif4c|eIF-1A|eIF-4C	eukaryotic translation initiation factor 1A	protein-coding
mm_58566.1	chr7	4788931	4788953	+	1	NA	intron (NM_029384, intron 1 of 1)	intron (NM_029384, intron 1 of 1)	618	NM_029384	664968	Mm.292837	NM_029384	ENSMUSG00000030431	Tmem238	2210411K11Rik	transmembrane protein 238	protein-coding
mm_139896.1	chr17	70852732	70852742	+	1	NA	intron (NM_001164074, intron 1 of 2)	intron (NM_001164074, intron 1 of 2)	795	NM_001164074	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_153467.1	chr19	41264314	41264323	-	1	NA	promoter-TSS (NM_133352)	promoter-TSS (NM_133352)	-314	NM_133352	107358	Mm.246440	NM_133352	ENSMUSG00000025016	Tm9sf3	1810073M23Rik|2810031D16Rik|AI115521|AI413748|AW146116|AW549777|Smbp|mKIAA4036	transmembrane 9 superfamily member 3	protein-coding
mm_49530.1	chr6	30065520	30065522	+	1	NA	intron (NM_010938, intron 1 of 11)	B1_Mur1|SINE|Alu	-10800	NM_001164229	18181	Mm.259258	NM_010938	ENSMUSG00000058440	Nrf1	C87038|D6Ertd415e	nuclear respiratory factor 1	protein-coding
mm_120112.1	chr14	59478865	59478923	+	1	NA	intron (NM_026908, intron 3 of 10)	intron (NM_026908, intron 3 of 10)	37913	NM_026908	69008	Mm.179091	NM_026908	ENSMUSG00000021981	Cab39l	1500031K13Rik|2810425O13Rik|4930520C08Rik|AA589432|MO2L	calcium binding protein 39-like	protein-coding
mm_19063.1	chr2	77519537	77519549	-	1	NA	5' UTR (NM_001113400, exon 1 of 8)	5' UTR (NM_001113400, exon 1 of 8)	123	NM_001113400	241494	Mm.490320	NM_178723	ENSMUSG00000027016	Zfp385b	B830010L13Rik|C130013B13Rik|Zfp533|Znf385b	zinc finger protein 385B	protein-coding
mm_112967.1	chr13	21242596	21242608	+	1	NA	Intergenic	tRNA-Ala-GCY_|tRNA|tRNA	50084	NM_010343	14780	Mm.1332	NM_010343	ENSMUSG00000004344	Gpx5	AV379049|Arep	glutathione peroxidase 5	protein-coding
mm_75697.1	chr8	68212121	68212136	-	1	NA	Intergenic	Intergenic	-64400	NM_028182	72281	Mm.40974	NM_028182	ENSMUSG00000053886	Sh2d4a	2210402M20Rik|SH2A	SH2 domain containing 4A	protein-coding
mm_164185.1	chr15	76671714	76671731	+	1	NA	promoter-TSS (NM_033371)	promoter-TSS (NM_033371)	42	NM_033371	73062	Mm.322901	NM_033371	ENSMUSG00000033819	Ppp1r16a	2900084E10Rik|Mypt3|R75527	protein phosphatase 1, regulatory (inhibitor) subunit 16A	protein-coding
mm_102879.1	chr11	69410397	69410432	-	1	NA	intron (NM_001017426, intron 1 of 22)	CpG	3261	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_17973.1	chr2	37647200	37647229	-	1	NA	promoter-TSS (NM_009261)	promoter-TSS (NM_009261)	71	NM_009261	20744	Mm.237095	NM_009261	ENSMUSG00000026915	Strbp	6430510M02Rik|AI852513|C230082I21Rik|C86322|Spnr	spermatid perinuclear RNA binding protein	protein-coding
mm_167447.1	chr8	121805499	121805511	+	1	NA	intron (NM_145605, intron 6 of 11)	intron (NM_145605, intron 6 of 11)	24064	NM_145605	234825	Mm.209329	NM_145605	ENSMUSG00000040263	Klhdc4	AA408426|AV352552|BC012312|G430025P05Rik	kelch domain containing 4	protein-coding
mm_41053.1	chr5	86804215	86804276	+	1	NA	promoter-TSS (NM_177680)	promoter-TSS (NM_177680)	-21	NM_001347375	231386	Mm.196325	NM_177680	ENSMUSG00000035851	Ythdc1	A730098D12Rik|C80342|mKIAA1966	YTH domain containing 1	protein-coding
mm_170956.1	chr2	5379369	5379373	-	1	NA	promoter-TSS (NR_030601)	promoter-TSS (NR_030601)	-19	NR_030601	100124465		NR_030601	ENSMUSG00000078031	Mir466d	Mirn466d	microRNA 466d	ncRNA
mm_24598.1	chr3	93445342	93445348	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	3015	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_157563.1	chrX	52272673	52272694	-	1	NA	3' UTR (NM_016697, exon 8 of 8)	3' UTR (NM_016697, exon 8 of 8)	105498	NR_105805	102465202		NR_105805	ENSMUSG00000105738	Mir6384	mmu-mir-6384	microRNA 6384	ncRNA
mm_82916.1	chr9	35055659	35055669	-	1	NA	intron (NM_009178, intron 1 of 10)	intron (NM_009178, intron 1 of 10)	-61064	NR_029475	78934	Mm.391688	NR_029475	ENSMUSG00000070315	4930581F22Rik	-	RIKEN cDNA 4930581F22 gene	ncRNA
mm_85358.1	chr9	103215839	103215936	-	1	NA	exon (NM_133977, exon 13 of 17)	exon (NM_133977, exon 13 of 17)	-13822	NM_009275	20818	Mm.273053	NM_009275	ENSMUSG00000032553	Srprb	AA409543	signal recognition particle receptor, B subunit	protein-coding
mm_161068.1	chr12	76369651	76369651	-	1	NA	promoter-TSS (NM_001172104)	promoter-TSS (NM_001172104)	-91	NM_028356	109929	Mm.41880	NM_028356	ENSMUSG00000056459	Zbtb25	2810462M08Rik|2900064P18Rik|AI842128|Kup|Zfp-50|Zfp50	zinc finger and BTB domain containing 25	protein-coding
mm_59250.1	chr7	24818790	24818795	+	1	NA	promoter-TSS (NR_045096)	promoter-TSS (NR_045096)	-3	NR_045096	545936	Mm.376228	NR_045096	ENSMUSG00000011350	Gm5893	EG545936|Gm477	predicted gene 5893	pseudo
mm_54379.1	chr6	31211056	31211063	-	1	NA	intron (NR_110469, intron 1 of 3)	intron (NR_110469, intron 1 of 3)	7415	NR_110470	232685	Mm.443019	NM_144555	ENSMUSG00000044471	Lncpint	Lincpint|MNCb-1768|Pint|linc-Pint	long non-protein coding RNA, Trp53 induced transcript	ncRNA
mm_61968.1	chr7	90442775	90442865	+	1	NA	promoter-TSS (NR_073438)	promoter-TSS (NR_073438)	39	NR_073438	233490	Mm.29496	NM_145151	ENSMUSG00000051451	Crebzf	1110034C16Rik|6330417B10Rik|LAZip|LAZipII|SMILE|Zf	CREB/ATF bZIP transcription factor	protein-coding
mm_112366.1	chr12	119160841	119160854	-	1	NA	Intergenic	Intergenic	77429	NM_177290	320910	Mm.217000	NM_177290	ENSMUSG00000025321	Itgb8	4832412O06Rik	integrin beta 8	protein-coding
mm_138659.1	chr17	35868580	35868590	+	1	NA	exon (NM_001146711, exon 2 of 4)	exon (NM_001146711, exon 2 of 4)	1970	NM_175242	76448	Mm.359982	NM_175242	ENSMUSG00000034595	Ppp1r18	2310014H01Rik|AA407849|AI450394	protein phosphatase 1, regulatory subunit 18	protein-coding
mm_146910.1	chr18	31317280	31317307	-	1	NA	promoter-TSS (NM_009065)	promoter-TSS (NM_009065)	-165	NM_009065	19762	Mm.5163	NM_009065	ENSMUSG00000057455	Rit2	RIBA|Rin|Roc2	Ras-like without CAAX 2	protein-coding
mm_74162.1	chr8	123403540	123403576	+	1	NA	3' UTR (NM_001037877, exon 18 of 18)	3' UTR (NM_001037877, exon 18 of 18)	-3524	NM_008559	17199	Mm.324942	NM_008559	ENSMUSG00000074037	Mc1r	Mcr1|Mshra|Tob|e	melanocortin 1 receptor	protein-coding
mm_60298.1	chr7	44016134	44016159	+	1	NA	exon (NM_010644, exon 3 of 5)	exon (NM_010644, exon 3 of 5)	3449	NM_010115	13647	Mm.439663	NM_010115		Egfbp2	Egfbp-2|Klk1b26|mGk-13	epidermal growth factor binding protein type B	protein-coding
mm_62850.1	chr7	114415206	114415267	+	1	NA	promoter-TSS (NM_011055)	promoter-TSS (NM_011055)	-18	NM_011055	18576	Mm.430730	NM_011055	ENSMUSG00000030671	Pde3b	9830102A01Rik|AI847709	phosphodiesterase 3B, cGMP-inhibited	protein-coding
mm_75884.1	chr8	70804980	70804999	-	1	NA	Intergenic	CpG	-3460	NM_008353	16161	Mm.731	NM_008353	ENSMUSG00000000791	Il12rb1	CD212|IL-12R[b]	interleukin 12 receptor, beta 1	protein-coding
mm_7423.1	chr1	119648904	119648981	-	1	NA	promoter-TSS (NM_001113416)	promoter-TSS (NM_001113416)	58	NM_001113416	226352	Mm.253156	NM_145506	ENSMUSG00000026383	Epb41l5	1700030C16Rik|AL022914|BE37|E230025E14Rik|Epb4.1l5|Lulu1|NBL5	erythrocyte membrane protein band 4.1 like 5	protein-coding
mm_31565.1	chr4	57568122	57568136	+	1	NA	promoter-TSS (NM_172868)	promoter-TSS (NM_172868)	-119	NM_001304544	677884	Mm.331630	NM_001304544	ENSMUSG00000089945	Pakap	AF064781|Gm20459|Palm2-Akap2|Palm2Akap2|Palm2akap2	paralemmin A kinase anchor protein	protein-coding
mm_113977.1	chr13	51837808	51837814	+	1	NA	Intergenic	L1MA4|LINE|L1	-8864	NM_011817	23882	Mm.281298	NM_011817	ENSMUSG00000021453	Gadd45g	AI327420|C86281|CR6|DDIT2|OIG37	growth arrest and DNA-damage-inducible 45 gamma	protein-coding
mm_145805.1	chr18	65382691	65382712	+	1	NA	intron (NM_001037294, intron 1 of 12)	intron (NM_001037294, intron 1 of 12)	11187	NM_001037294	225638	Mm.296528	NM_001037294	ENSMUSG00000032845	Alpk2	Gm549|Hak	alpha-kinase 2	protein-coding
mm_48819.1	chr5	149050595	149050605	-	1	NA	exon (NM_001313894, exon 2 of 5)	exon (NM_001313894, exon 2 of 5)	1016	NM_001313894	15289	Mm.207047	NM_010439	ENSMUSG00000066551	Hmgb1	HMG-1|Hmg1|SBP-1|p30	high mobility group box 1	protein-coding
mm_83900.1	chr9	56155863	56155864	-	1	NA	intron (NM_019793, intron 1 of 6)	intron (NM_019793, intron 1 of 6)	5207	NM_019793	56434	Mm.28484	NM_019793	ENSMUSG00000032324	Tspan3	1700055K04Rik|TM4-A|Tm4sf8	tetraspanin 3	protein-coding
mm_97736.1	chr11	80429733	80429743	+	1	NA	intron (NM_178616, intron 1 of 13)	B1_Mus2|SINE|Alu	1123	NM_178616	69077	Mm.260539	NM_178616	ENSMUSG00000017428	Psmd11	1700089D09Rik|1810019E17Rik|2610024G20Rik|2810055C24Rik|C78232|P44.5|S9	proteasome (prosome, macropain) 26S subunit, non-ATPase, 11	protein-coding
mm_5161.1	chr1	10037884	10037894	-	1	NA	promoter-TSS (NM_026493)	promoter-TSS (NM_026493)	270	NR_102282	26754	Mm.402384	NM_013715	ENSMUSG00000025917	Cops5	AI303502|CSN5|Jab1|Mov34|Sgn5	COP9 signalosome subunit 5	protein-coding
mm_60355.1	chr7	44384720	44384750	+	1	NA	intron (NM_001114116, intron 1 of 10)	intron (NM_001114116, intron 1 of 10)	609	NM_016663	20981	Mm.4824	NM_016663	ENSMUSG00000030731	Syt3	AI385753|sytIII	synaptotagmin III	protein-coding
mm_48677.1	chr5	146209643	146209685	-	1	NA	3' UTR (NM_001256087, exon 5 of 5)	3' UTR (NM_001256087, exon 5 of 5)	11237	NM_001256087	74132	Mm.26696	NM_028774	ENSMUSG00000029634	Rnf6	1200013I08Rik|5730419H05Rik|AA537053	ring finger protein (C3H2C3 type) 6	protein-coding
mm_106306.1	chr11	118290220	118290236	-	1	NA	promoter-TSS (NM_001033528)	promoter-TSS (NM_001033528)	16	NM_001033528	72344	Mm.232293	NM_001033528	ENSMUSG00000033909	Usp36	2700002L06Rik|mKIAA1453	ubiquitin specific peptidase 36	protein-coding
mm_86137.1	chr9	116673286	116673289	-	1	NA	intron (NM_001172121, intron 10 of 14)	intron (NM_001172121, intron 10 of 14)	-497924	NM_009371	21813	Mm.172346	NM_009371	ENSMUSG00000032440	Tgfbr2	1110020H15Rik|AU042018|DNIIR|RIIDN|TBR-II|TbetaR-II|TbetaRII	transforming growth factor, beta receptor II	protein-coding
mm_70208.1	chr7	144778933	144778936	-	1	NA	Intergenic	Intergenic	-40342	NM_001242349	101772	Mm.26700	NM_178642	ENSMUSG00000031075	Ano1	Tmem16a	anoctamin 1, calcium activated chloride channel	protein-coding
mm_154220.1	chr19	59458252	59458267	-	1	NA	promoter-TSS (NM_010132)	promoter-TSS (NM_010132)	376	NR_002863	329078	Mm.80382	NR_002863	ENSMUSG00000087095	Emx2os	-	Emx2 opposite strand/antisense transcript (non-protein coding)	ncRNA
mm_82964.1	chr9	35648170	35648180	-	1	NA	promoter-TSS (NM_001167592)	promoter-TSS (NM_001167592)	27	NM_001167592	100312956	Mm.475850	NM_001167592	ENSMUSG00000094995	Pate3	Gm17365|Pate-dj	prostate and testis expressed 3	protein-coding
mm_60513.1	chr7	44479698	44479741	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-4798	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_119522.1	chr14	47494209	47494215	+	1	NA	intron (NM_030236, intron 1 of 1)	ORR1A2|LTR|ERVL-MaLR	21651	NM_001146085	78938	Mm.11935	NM_030236	ENSMUSG00000037536	Fbxo34	2900057B08Rik|5830426G16Rik	F-box protein 34	protein-coding
mm_126259.1	chr15	79089593	79089644	+	1	NA	exon (NM_145139, exon 11 of 13)	exon (NM_145139, exon 11 of 13)	14395	NM_145139	223691	Mm.206404	NM_145139	ENSMUSG00000033047	Eif3l	0610011H21Rik|D15N1e|Eif3eip|Eif3ip|Eif3s6ip|HSP-66Y|PAF67	eukaryotic translation initiation factor 3, subunit L	protein-coding
mm_1788.1	chr1	78657875	78657889	+	1	NA	promoter-TSS (NM_001136222)	promoter-TSS (NM_001136222)	57	NM_001001981	195434	Mm.276016	NM_001001981	ENSMUSG00000079470	Utp14b	4932411L21Rik|jsd	UTP14B small subunit processome component	protein-coding
mm_164002.1	chr14	65980981	65980984	+	1	NA	exon (NM_013492, exon 8 of 9)	exon (NM_013492, exon 8 of 9)	12499	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_77687.1	chr8	126537354	126537387	-	1	NA	Intergenic	Intergenic	56066	NM_001164598	270110	Mm.334918	NM_001164598	ENSMUSG00000051495	Irf2bp2	E130305N23Rik|IRF-2BP2	interferon regulatory factor 2 binding protein 2	protein-coding
mm_13534.1	chr2	110600701	110600717	+	1	NA	intron (NM_001177624, intron 1 of 14)	MLT1H|LTR|ERVL-MaLR	3410	NM_001177624	241612	Mm.277148	NM_001003915	ENSMUSG00000041644	Slc5a12	AI315119|D630015G19|SMCT2	solute carrier family 5 (sodium/glucose cotransporter), member 12	protein-coding
mm_21506.1	chr2	163623272	163623273	-	1	NA	TTS (NM_012032)	TTS (NM_012032)	16060	NM_001305803	76080	Mm.89828	NM_029512	ENSMUSG00000017679	Ttpal	3110080A02Rik|5830472M02Rik	tocopherol (alpha) transfer protein-like	protein-coding
mm_54118.1	chr6	18030436	18030460	-	1	NA	promoter-TSS (NM_023653)	promoter-TSS (NM_023653)	-3	NM_023653	22413	Mm.33653	NM_023653	ENSMUSG00000010797	Wnt2	2610510E18Rik|Int1l1|Irp|Mirp|Wnt-2|Wnt2a	wingless-type MMTV integration site family, member 2	protein-coding
mm_8783.1	chr1	161250885	161250909	-	1	NA	intron (NM_001303408, intron 1 of 5)	CpG	313	NR_130150	11758	Mm.186185	NM_007453	ENSMUSG00000026701	Prdx6	1-Cys Prx|1-cysPrx|9430088D19Rik|AA690119|Aop2|Brp-12|CP-3|GPx|Ltw-4|Ltw4|Lvtw-4|NSGPx|ORF06|Prdx5|aiPLA2	peroxiredoxin 6	protein-coding
mm_27690.1	chr3	66088258	66088259	-	1	NA	intron (NM_145820, intron 11 of 13)	U1|snRNA|snRNA	-130033	NM_019937	56706	Mm.175612	NM_019937	ENSMUSG00000027829	Ccnl1	2610030E23Rik|AU018493|Ccnl|ania-6a	cyclin L1	protein-coding
mm_143594.1	chr17	74528063	74528106	-	1	NA	promoter-TSS (NM_007566)	promoter-TSS (NM_007566)	-211	NM_007566	12211	Mm.442564	NM_007566	ENSMUSG00000024073	Birc6	A430032G04Rik|A430040A19Rik|AA501170|Bruce|D630005A10Rik|mKIAA1289	baculoviral IAP repeat-containing 6	protein-coding
mm_19392.1	chr2	91444630	91444726	-	1	NA	promoter-TSS (NM_175123)	promoter-TSS (NM_175123)	-36	NM_175123	228356	Mm.386861	NM_175123	ENSMUSG00000040591	1110051M20Rik	AI586322	RIKEN cDNA 1110051M20 gene	protein-coding
mm_8369.1	chr1	150724745	150724750	-	1	NA	intron (NM_001024720, intron 30 of 106)	Cheshire|DNA|hAT-Charlie	-258582	NM_001110146	96875	Mm.174256	NM_021400	ENSMUSG00000006014	Prg4	CACP|DOL54|JCAP|MSF|SZP|lubricin	proteoglycan 4 (megakaryocyte stimulating factor, articular superficial zone protein)	protein-coding
mm_58220.1	chr6	144209441	144209447	-	1	NA	5' UTR (NM_011444, exon 1 of 15)	5' UTR (NM_011444, exon 1 of 15)	124	NM_001113559	20678	Mm.1752	NM_011444	ENSMUSG00000041540	Sox5	A730017D01Rik|AI528773	SRY (sex determining region Y)-box 5	protein-coding
mm_87197.1	chr10	39532988	39533014	+	1	NA	intron (NM_001122892, intron 9 of 12)	intron (NM_001122892, intron 9 of 12)	-79933	NM_134000	103213	Mm.436686	NM_134000	ENSMUSG00000019842	Traf3ip2	AI429613|Act1|CIKS	TRAF3 interacting protein 2	protein-coding
mm_150692.1	chr19	42147433	42147454	+	1	NA	promoter-TSS (NM_183195)	promoter-TSS (NM_183195)	54	NM_183195	277010	Mm.206250	NM_183195	ENSMUSG00000044345	Marveld1	AI504298|Mrvldc1	MARVEL (membrane-associating) domain containing 1	protein-coding
mm_167414.1	chr8	107373218	107373231	+	1	NA	3' UTR (NM_018823, exon 15 of 15)	3' UTR (NM_018823, exon 15 of 15)	29981	NM_008706	18104	Mm.252	NM_008706	ENSMUSG00000003849	Nqo1	AV001255|Dia4|Dtd|Nmo-1|Nmo1|Nmor1|Ox-1|Ox1|Qr1	NAD(P)H dehydrogenase, quinone 1	protein-coding
mm_78528.1	chr9	34686795	34686799	+	1	NA	intron (NM_001190912, intron 1 of 15)	L1MC3|LINE|L1	198066	NM_001190911	67703	Mm.220710	NM_026324	ENSMUSG00000032036	Kirrel3	1500010O20Rik|2900036G11Rik|NEPH2|SST4|mKIAA1867	kin of IRRE like 3 (Drosophila)	protein-coding
mm_7882.1	chr1	133025331	133025391	-	1	NA	promoter-TSS (NR_126506)	promoter-TSS (NR_126506)	55	NR_126506	17248	Mm.426531	NM_008575	ENSMUSG00000054387	Mdm4	4933417N07Rik|AA414968|AL023055|AU018793|AU021806|C85810|Mdmx	transformed mouse 3T3 cell double minute 4	protein-coding
mm_170782.1	chr2	172558008	172558008	-	1	NA	3' UTR (NM_001159696, exon 7 of 7)	3' UTR (NM_001159696, exon 7 of 7)	7017	NM_001159696	21420	Mm.3629	NM_009335	ENSMUSG00000028640	Tfap2c	AA409384|AP2gamma|Ap-2.2|Stra2|Tcfap2c	transcription factor AP-2, gamma	protein-coding
mm_32297.1	chr4	103119405	103119416	+	1	NA	promoter-TSS (NM_001039081)	promoter-TSS (NM_001039081)	20	NM_001039081	71148	Mm.288721	NM_027696	ENSMUSG00000028522	Mier1	4933425I22Rik|5830411K19Rik|er1	MEIR1 treanscription regulator	protein-coding
mm_3041.1	chr1	134040326	134040331	+	1	NA	exon (NM_021355, exon 2 of 3)	exon (NM_021355, exon 2 of 3)	2813	NM_021355	14264	Mm.287146	NM_021355	ENSMUSG00000041559	Fmod	AI131919|AU041740|SLRR2E	fibromodulin	protein-coding
mm_14347.1	chr2	129593423	129593436	+	1	NA	5' UTR (NM_001291022, exon 1 of 5)	5' UTR (NM_001291022, exon 1 of 5)	260	NM_001291022	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_134946.1	chr16	31275415	31275425	-	1	NA	promoter-TSS (NM_025800)	promoter-TSS (NM_025800)	-143	NM_025800	66849	Mm.291593	NM_025800	ENSMUSG00000047714	Ppp1r2	0610025N14Rik|2310007G06Rik|4930440J04Rik|5430408E15Rik|D16Ertd248e|IPP-2	protein phosphatase 1, regulatory (inhibitor) subunit 2	protein-coding
mm_10660.1	chr2	20737282	20737301	+	1	NA	intron (NM_029895, intron 6 of 18)	intron (NM_029895, intron 6 of 18)	217778	NM_001177631	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding
mm_98864.1	chr11	97766827	97766860	+	1	NA	promoter-TSS (NM_026186)	promoter-TSS (NM_026186)	-230	NM_026186	67480	Mm.33206	NM_026186	ENSMUSG00000018541	Cwc25	1300013D05Rik|AA473636|Ccdc49|R75228	CWC25 spliceosome-associated protein	protein-coding
mm_51842.1	chr6	90302528	90302535	+	1	NA	intron (NM_177738, intron 2 of 4)	intron (NM_177738, intron 2 of 4)	1261	NM_177738	243535	Mm.233854	NM_177738	ENSMUSG00000049694	BC048671	-	cDNA sequence BC048671	protein-coding
mm_94910.1	chr11	29374379	29374385	+	1	NA	exon (NM_176841, exon 1 of 32)	exon (NM_176841, exon 1 of 32)	210	NM_176841	108686	Mm.338284	NM_176841	ENSMUSG00000032740	Ccdc88a	A430106J12Rik|AI848406|Ape|C130096N06Rik|C330012F17Rik|D130005J21Rik|Girdin|Giv|Grdn|Hkrp1	coiled coil domain containing 88A	protein-coding
mm_121765.1	chr14	19823808	19823832	-	1	NA	promoter-TSS (NM_026528)	promoter-TSS (NM_026528)	3	NM_026528	68045	Mm.21932	NM_026528	ENSMUSG00000021807	2700060E02Rik	-	RIKEN cDNA 2700060E02 gene	protein-coding
mm_152181.1	chr19	7426520	7426559	-	1	NA	TTS (NM_175381)	TTS (NM_175381)	3966	NR_105957	102466781		NR_105957	ENSMUSG00000098293	Mir6991	Gm27966|mmu-mir-6991	microRNA 6991	ncRNA
mm_165375.1	chr2	128319212	128319243	+	1	NA	intron (NR_028590, intron 2 of 2)	intron (NR_028590, intron 2 of 2)	110124	NR_028591	100043424	Mm.297222	NR_028589		Gm14005	OTTMUSG00000015351	predicted gene 14005	ncRNA
mm_83073.1	chr9	37657190	37657273	-	1	NA	promoter-TSS (NM_025289)	promoter-TSS (NM_025289)	81	NM_025289	21376	Mm.28689	NM_025289	ENSMUSG00000011114	Tbrg1	AA408552|AA409675|Niam|Tb-5|mFLJ00213	transforming growth factor beta regulated gene 1	protein-coding
mm_90941.1	chr10	12963866	12963873	-	1	NA	intron (NM_029075, intron 1 of 2)	intron (NM_029075, intron 1 of 2)	390	NM_029075	74732	Mm.248648	NM_029075	ENSMUSG00000039232	Stx11	5830405C08Rik	syntaxin 11	protein-coding
mm_144287.1	chr18	12128743	12128807	+	1	NA	promoter-TSS (NM_024182)	promoter-TSS (NM_024182)	-75	NM_024182	66878	Mm.28551	NM_024182	ENSMUSG00000024404	Riok3	1200013N13Rik|D18Ertd331e|E130306C24Rik|Sudd	RIO kinase 3	protein-coding
mm_21488.1	chr2	163089595	163089617	-	1	NA	promoter-TSS (NM_026630)	promoter-TSS (NM_026630)	-5	NM_026630	68236	Mm.33648	NM_026630	ENSMUSG00000070708	Gtsf1l	2410116G06Rik	gametocyte specific factor 1-like	protein-coding
mm_92388.1	chr10	76596157	76596181	-	1	NA	3' UTR (NM_146007, exon 28 of 28)	3' UTR (NM_146007, exon 28 of 28)	20521	NM_080845	14317	Mm.36278	NM_080845	ENSMUSG00000001155	Ftcd	-	formiminotransferase cyclodeaminase	protein-coding
mm_34726.1	chr4	152178106	152178112	+	1	NA	promoter-TSS (NM_133348)	promoter-TSS (NM_133348)	9	NM_133348	70025	Mm.296191	NM_133348	ENSMUSG00000028937	Acot7	2410041A17Rik|Ach1|Act|Bach|CTE-IIa|Cte-II|Lach1	acyl-CoA thioesterase 7	protein-coding
mm_81673.1	chr9	111035738	111035750	+	1	NA	intron (NM_008522, intron 13 of 16)	intron (NM_008522, intron 13 of 16)	16452	NM_008522	17002	Mm.282359	NM_008522	ENSMUSG00000032496	Ltf	Csp82|Lf|MMS10R|Ms10r	lactotransferrin	protein-coding
mm_113932.1	chr13	49622967	49622979	+	1	NA	exon (NM_008760, exon 7 of 7)	exon (NM_008760, exon 7 of 7)	14902	NM_008760	18295	Mm.4258	NM_008760	ENSMUSG00000021390	Ogn	3110079A16Rik|OG|OIF|SLRR3A|mimecan|mimican	osteoglycin	protein-coding
mm_141933.1	chr17	35046449	35046459	-	1	NA	non-coding (NR_130641, exon 1 of 24)	non-coding (NR_130641, exon 1 of 24)	168	NM_013600	17687	Mm.24192	NM_013600	ENSMUSG00000007035	Msh5	Mut5	mutS homolog 5	protein-coding
mm_130044.1	chr15	89123112	89123173	-	1	NA	promoter-TSS (NM_001163319)	promoter-TSS (NM_001163319)	8	NM_001163319	328580	Mm.380934	NM_001163319	ENSMUSG00000051786	Tubgcp6	AI843275|D430023H11|GCP-6|mKIAA1669	tubulin, gamma complex associated protein 6	protein-coding
mm_134532.1	chr16	19241808	19241814	-	1	NA	Intergenic	Intergenic	44930	NM_146451	258443	Mm.377506	NM_146451	ENSMUSG00000050742	Olfr164	MOR279-2	olfactory receptor 164	protein-coding
mm_82783.1	chr9	28996055	28996064	-	1	NA	TTS (NM_172290)	TTS (NM_172290)	967070	NM_172290	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding
mm_9722.1	chr1	180027450	180027451	-	1	NA	intron (NM_001346805, intron 2 of 34)	intron (NM_001346805, intron 2 of 34)	66361	NM_001033285	226751	Mm.259655	NM_001033285	ENSMUSG00000026490	Cdc42bpa	A930014J19Rik|DMPK-like	CDC42 binding protein kinase alpha	protein-coding
mm_134350.1	chr16	16571524	16571535	-	1	NA	intron (NM_001301817, intron 1 of 16)	intron (NM_001301817, intron 1 of 16)	-11310	NM_139232	224014	Mm.256131	NM_139232	ENSMUSG00000022788	Fgd4	9030023J02Rik|9330209B17Rik|Frabp|ZFYVE6	FYVE, RhoGEF and PH domain containing 4	protein-coding
mm_4110.1	chr1	167598693	167598729	+	1	NA	5' UTR (NM_009107, exon 1 of 10)	5' UTR (NM_009107, exon 1 of 10)	349	NM_009107	20183	Mm.3475	NM_009107	ENSMUSG00000015843	Rxrg	Nr2b3	retinoid X receptor gamma	protein-coding
mm_6304.1	chr1	71414882	71414915	-	1	NA	promoter-TSS (NM_175210)	promoter-TSS (NM_175210)	12	NM_175210	74591	Mm.159251	NM_175210	ENSMUSG00000050296	Abca12	4832428G11Rik|4833417A11Rik	ATP-binding cassette, sub-family A (ABC1), member 12	protein-coding
mm_85233.1	chr9	98033191	98033207	-	1	NA	promoter-TSS (NM_022319)	promoter-TSS (NM_022319)	-32	NM_022319	64085	Mm.440903	NM_022319	ENSMUSG00000032452	Clstn2	2900042C18Rik|AI448973|CSTN2|Cs2|Cst-2|mKIAA4134	calsyntenin 2	protein-coding
mm_6507.1	chr1	74304314	74304343	-	1	NA	promoter-TSS (NM_027154)	promoter-TSS (NM_027154)	8	NM_027154	69660	Mm.261182	NM_027154	ENSMUSG00000006301	Tmbim1	2310061B02Rik|AA960455|AU024746|C78899|RECS1|Tmbib1|mKIAA4161	transmembrane BAX inhibitor motif containing 1	protein-coding
mm_116093.1	chr13	28757877	28757887	-	1	NA	intron (NR_045053, intron 3 of 8)	intron (NR_045053, intron 3 of 8)	-47009	NR_105787	102466635		NR_105787	ENSMUSG00000099158	Mir6368	Gm27800|mmu-mir-6368	microRNA 6368	ncRNA
mm_101415.1	chr11	29246396	29246398	-	1	NA	intron (NM_025740, intron 1 of 9)	intron (NM_025740, intron 1 of 9)	875	NM_025740	216618	Mm.128663	NM_025740	ENSMUSG00000020462	Cfap36	2300003H10|4931428D14Rik|Ccdc104	cilia and flagella associated protein 36	protein-coding
mm_38859.1	chr4	149426374	149426393	-	1	NA	5' UTR (NM_022022, exon 1 of 27)	5' UTR (NM_022022, exon 1 of 27)	248	NM_022022	63958	Mm.415260	NM_022022	ENSMUSG00000028960	Ube4b	4930551I19Rik|4933406G05Rik|AU014668|D4Bwg0973e|UFD2|UFD2a|Ufd2p|mKIAA0684	ubiquitination factor E4B	protein-coding
mm_74064.1	chr8	122421801	122421803	+	1	NA	promoter-TSS (NM_145834)	promoter-TSS (NM_145834)	-283	NM_145834	234836	Mm.222808	NM_145834	ENSMUSG00000046108	Il17c	IL-17C	interleukin 17C	protein-coding
mm_24145.1	chr3	88325079	88325080	+	1	NA	promoter-TSS (NM_020003)	promoter-TSS (NM_020003)	56	NM_020003	56700	Mm.439922	NM_020003	ENSMUSG00000001418	Glmp	0610031J06Rik|AB027141|NCU-G1	glycosylated lysosomal membrane protein	protein-coding
mm_102717.1	chr11	67114883	67114889	-	1	NA	non-coding (NR_038055, exon 4 of 5)	non-coding (NR_038055, exon 4 of 5)	5194	NR_038055	74184	Mm.162554	NR_038055	ENSMUSG00000087410	2310065F04Rik	linc-Myh	RIKEN cDNA 2310065F04 gene	ncRNA
mm_100891.1	chr11	6065698	6065728	-	1	NA	promoter-TSS (NM_001174054)	promoter-TSS (NM_001174054)	35	NM_001174054	12323	Mm.439733	NM_007595	ENSMUSG00000057897	Camk2b	CaMKII	calcium/calmodulin-dependent protein kinase II, beta	protein-coding
mm_99374.1	chr11	101984292	101984303	+	1	NA	intron (NM_028207, intron 1 of 2)	intron (NM_028207, intron 1 of 2)	494	NM_028207	72349	Mm.196295	NM_028207	ENSMUSG00000003518	Dusp3	2210015O03Rik|5031436O03Rik|T-DSP11|VHR	dual specificity phosphatase 3 (vaccinia virus phosphatase VH1-related)	protein-coding
mm_167648.1	chr9	65460913	65460917	+	1	NA	promoter-TSS (NM_138584)	promoter-TSS (NM_138584)	-22	NM_138584	27965	Mm.272475	NM_138584	ENSMUSG00000032388	Spg21	ACP33|BM-019|C78576|D9Wsu18e|GL010|MAST	spastic paraplegia 21 homolog (human)	protein-coding
mm_15506.1	chr2	158068877	158068881	+	1	NA	intron (NM_001291134, intron 6 of 6)	B1_Mus2|SINE|Alu	22918	NR_040609	72340	Mm.443395	NR_040609	ENSMUSG00000100860	2010009K17Rik	-	RIKEN cDNA 2010009K17 gene	ncRNA
mm_96673.1	chr11	69411320	69411342	+	1	NA	intron (NM_001017426, intron 1 of 22)	CpG	2344	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_158257.1	chrX	108834304	108834381	-	1	NA	promoter-TSS (NM_001081477)	promoter-TSS (NM_001081477)	13	NM_001081477	382236	Mm.100112	NM_001081477	ENSMUSG00000063663	Brwd3	Brodl|D030064D06Rik|Gm596	bromodomain and WD repeat domain containing 3	protein-coding
mm_85000.1	chr9	86880366	86880372	-	1	NA	promoter-TSS (NM_001277986)	promoter-TSS (NM_001277986)	28	NM_001277982	20616	Mm.281651	NM_013669	ENSMUSG00000033419	Snap91	91kDa|AP180|F1-20|mKIAA0656	synaptosomal-associated protein 91	protein-coding
mm_77984.1	chr9	7873125	7873141	+	1	NA	promoter-TSS (NM_007464)	promoter-TSS (NM_007464)	37	NM_007464	11796	Mm.2026	NM_007464	ENSMUSG00000032000	Birc3	AW107670|Api1|Api2|Birc2|C-IAP2|HIAP2|IAP1|IAP2|MIAP1|MIAP2|MIHB|MIHC|RNF49|cIAP-1|cIAP-2|cIAP1|cIAP2	baculoviral IAP repeat-containing 3	protein-coding
mm_17146.1	chr2	25196709	25196715	-	1	NA	5' UTR (NM_146115, exon 1 of 2)	5' UTR (NM_146115, exon 1 of 2)	101	NM_146115	227612	Mm.119747	NM_146115	ENSMUSG00000059555	Tor4a	A830007P12Rik	torsin family 4, member A	protein-coding
mm_68873.1	chr7	126446998	126447001	-	1	NA	intron (NM_007504, intron 20 of 22)	intron (NM_007504, intron 20 of 22)	16074	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_97929.1	chr11	83648158	83648162	+	1	NA	3' UTR (NM_011337, exon 3 of 3)	3' UTR (NM_011337, exon 3 of 3)	1218	NM_011337	20302	Mm.1282	NM_011337	ENSMUSG00000000982	Ccl3	AI323804|G0S19-1|LD78alpha|MIP-1alpha|MIP1-(a)|MIP1-alpha|Mip1a|Scya3	chemokine (C-C motif) ligand 3	protein-coding
mm_37163.1	chr4	117156076	117156085	-	1	NA	promoter-TSS (NR_030704)	promoter-TSS (NR_030704)	52	NM_009098	20116	Mm.260904	NM_009098	ENSMUSG00000047675	Rps8	-	ribosomal protein S8	protein-coding
mm_90917.1	chr10	12548887	12548914	-	1	NA	intron (NM_011682, intron 50 of 73)	intron (NM_011682, intron 50 of 73)	312835	NM_011682	22288	Mm.331784	NM_011682	ENSMUSG00000019820	Utrn	AA589569|DRP|Dmdl	utrophin	protein-coding
mm_77442.1	chr8	121652896	121652913	-	1	NA	promoter-TSS (NM_080855)	promoter-TSS (NM_080855)	-971	NM_080855	142682	Mm.103202	NM_080855	ENSMUSG00000061410	Zcchc14	AA792890|BDG29	zinc finger, CCHC domain containing 14	protein-coding
mm_153551.1	chr19	42091365	42091366	-	1	NA	intron (NM_145501, intron 1 of 8)	intron (NM_145501, intron 1 of 8)	930	NM_145501	84095	Mm.117037	NM_145501	ENSMUSG00000025178	Pi4k2a	Pi4k2	phosphatidylinositol 4-kinase type 2 alpha	protein-coding
mm_35935.1	chr4	53032814	53032830	-	1	NA	3' UTR (NM_013454, exon 50 of 50)	3' UTR (NM_013454, exon 50 of 50)	20942	NM_025623	66536	Mm.38244	NM_025623	ENSMUSG00000015247	Nipsnap3b	2700063N13Rik|Nipsnap3a	nipsnap homolog 3B (C. elegans)	protein-coding
mm_163997.1	chr14	64441021	64441029	-	1	NA	promoter-TSS (NM_001253715)	promoter-TSS (NM_001253715)	1	NM_001253715	110265	Mm.26713	NM_026322	ENSMUSG00000054733	Msra	2310045J23Rik|6530413P12Rik|MSR-A	methionine sulfoxide reductase A	protein-coding
mm_5269.1	chr1	17429575	17429575	-	1	NA	Intergenic	Intergenic	-172326	NM_053191	94227	Mm.442452	NM_053191	ENSMUSG00000067780	Pi15	P24TI|P25TI|PI-15|SugarCrisp	peptidase inhibitor 15	protein-coding
mm_152954.1	chr19	29176544	29176555	-	1	NA	Intergenic	Intergenic	41270	NR_029778	724062		NR_029778	ENSMUSG00000065556	Mir101b	Mirn101b|mir-101b	microRNA 101b	ncRNA
mm_52591.1	chr6	116671546	116671551	+	1	NA	intron (NM_178045, intron 1 of 10)	LTR16D1|LTR|ERVL	2288	NM_178045	213391	Mm.257931	NM_178045	ENSMUSG00000042129	Rassf4	3830411C14Rik|AD037|AI586137	Ras association (RalGDS/AF-6) domain family member 4	protein-coding
mm_105685.1	chr11	107716572	107716582	-	1	NA	promoter-TSS (NM_007582)	promoter-TSS (NM_007582)	-101	NM_007582	12299	Mm.57093	NM_007582	ENSMUSG00000020722	Cacng1	-	calcium channel, voltage-dependent, gamma subunit 1	protein-coding
mm_20286.1	chr2	126913104	126913122	-	1	NA	intron (NM_023220, intron 11 of 14)	intron (NM_023220, intron 11 of 14)	-10728	NR_106202	102466258		NR_106202	ENSMUSG00000098896	Mir3473g	Gm27751|mmu-mir-3473g	microRNA 3473g	ncRNA
mm_48849.1	chr5	149619078	149619088	-	1	NA	intron (NM_001347534, intron 13 of 16)	intron (NM_001347534, intron 13 of 16)	17232	NM_013559	15505	Mm.270681	NM_013559	ENSMUSG00000029657	Hsph1	105kDa|AI790491|Hsp105|Hsp110|hsp-E7I|hsp110/105	heat shock 105kDa/110kDa protein 1	protein-coding
mm_133767.1	chr16	94569807	94569831	+	1	NA	promoter-TSS (NM_007890)	promoter-TSS (NM_007890)	-387	NM_007890	13548	Mm.310973	NM_007890	ENSMUSG00000022897	Dyrk1a	2310043O08Rik|D16Ertd272e|D16Ertd493e|Dyrk|ENSMUSG00000074897|Gm10783|Mnbh|Mp86|mmb	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1a	protein-coding
mm_152025.1	chr19	6057737	6057769	-	1	NA	promoter-TSS (NM_001190436)	promoter-TSS (NM_001190436)	-2	NM_026246	18120	Mm.181290	NM_026246	ENSMUSG00000007338	Mrpl49	4833419D18Rik|Nof1	mitochondrial ribosomal protein L49	protein-coding
mm_95308.1	chr11	46227139	46227145	+	1	NA	intron (NM_133769, intron 23 of 30)	ORR1A2|LTR|ERVL-MaLR	-4993	NR_105955	102465598		NR_105955	ENSMUSG00000099230	Mir6989	Gm27885|mmu-mir-6989	microRNA 6989	ncRNA
mm_130005.1	chr15	86214336	86214395	-	1	NA	promoter-TSS (NM_145476)	promoter-TSS (NM_145476)	-94	NM_145476	223754	Mm.28904	NM_145476	ENSMUSG00000051864	Tbc1d22a	BC023106|D15Ertd781e	TBC1 domain family, member 22a	protein-coding
mm_6681.1	chr1	80599036	80599039	-	1	NA	intron (NM_175291, intron 7 of 55)	intron (NM_175291, intron 7 of 55)	66315	NM_001285927	210293	Mm.133473	NM_175291	ENSMUSG00000038608	Dock10	9330153B10Rik|A630054M16Rik|Jr4|Jr5|R75174|ZIZ3|Zizimin3|mKIAA0694	dedicator of cytokinesis 10	protein-coding
mm_129145.1	chr15	76202262	76202274	-	1	NA	intron (NM_011117, intron 1 of 31)	G-rich|Low_complexity|Low_complexity	-1661	NM_201390	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
mm_167898.1	chrX	73494698	73494721	-	1	NA	exon (NM_007542, exon 8 of 8)	exon (NM_007542, exon 8 of 8)	-8377	NM_001310537	320707	Mm.210095	NM_177236	ENSMUSG00000031376	Atp2b3	6430519O13Rik|Pmca3	ATPase, Ca++ transporting, plasma membrane 3	protein-coding
mm_28550.1	chr3	93279630	93279694	-	1	NA	Intergenic	Intergenic	-40087	NM_133698	68723	Mm.208047	NM_133698	ENSMUSG00000041991	Hrnr	1110033K19Rik|A530063N20Rik|S100a18	hornerin	protein-coding
mm_46218.1	chr5	98931710	98931713	-	1	NA	3' UTR (NM_008926, exon 19 of 19)	3' UTR (NM_008926, exon 19 of 19)	77296	NM_001310677	110075	Mm.136461	NM_173404	ENSMUSG00000029335	Bmp3	9530029I04Rik	bone morphogenetic protein 3	protein-coding
mm_118123.1	chr13	104178400	104178480	-	1	NA	promoter-TSS (NR_003546)	promoter-TSS (NR_003546)	26	NM_025879	66975	Mm.272541	NM_025879	ENSMUSG00000021711	Trappc13	2410002O22Rik|2610524F24Rik|AI451892|AU017229	trafficking protein particle complex 13	protein-coding
mm_4781.1	chr1	183631440	183631450	+	1	NA	Intergenic	PB1D7|SINE|Alu	212197	NM_001308052	78772	Mm.29003	NM_030175	ENSMUSG00000053461	Hhipl2	4930507C10Rik|AW208802|Hhip3	hedgehog interacting protein-like 2	protein-coding
mm_98255.1	chr11	88625004	88625017	+	1	NA	intron (NM_054043, intron 5 of 13)	intron (NM_054043, intron 5 of 13)	5759	NR_131025	68397	Mm.426889	NR_131025		0610039H22Rik	-	RIKEN cDNA 0610039H22 gene	ncRNA
mm_14660.1	chr2	137855851	137855856	+	1	NA	Intergenic	U3|snRNA|snRNA	-400731	NM_001025431	228662	Mm.153405	NM_145534	ENSMUSG00000062098	Btbd3	mKIAA0952	BTB (POZ) domain containing 3	protein-coding
mm_21333.1	chr2	157101711	157101723	-	1	NA	intron (NM_001139520, intron 15 of 16)	intron (NM_001139520, intron 15 of 16)	14662	NM_001177439	383766	Mm.480305	NM_001177439	ENSMUSG00000074628	Tldc2	Gm1332	TBC/LysM associated domain containing 2	protein-coding
mm_52005.1	chr6	92940573	92940592	+	1	NA	promoter-TSS (NR_015530)	promoter-TSS (NR_015530)	0	NR_015530	330385	Mm.483472	NR_015530	ENSMUSG00000097462	9530026P05Rik	B430306B02	RIKEN cDNA 9530026P05 gene	ncRNA
mm_111631.1	chr12	102439811	102439821	-	1	NA	promoter-TSS (NM_011175)	promoter-TSS (NM_011175)	-3	NM_011175	19141	Mm.17185	NM_011175	ENSMUSG00000021190	Lgmn	AEP|AI746452|AU022324|Prsc1	legumain	protein-coding
mm_74229.1	chr8	124231360	124231450	+	1	NA	promoter-TSS (NM_139272)	promoter-TSS (NM_139272)	11	NM_139272	108148	Mm.33808	NM_139272	ENSMUSG00000089704	Galnt2	AI480629	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2	protein-coding
mm_91895.1	chr10	60002974	60002984	-	1	NA	promoter-TSS (NM_001199187)	promoter-TSS (NM_001199187)	156	NM_001347451	52717	Mm.21793	NM_025514	ENSMUSG00000020107	Anapc16	2310005G07Rik|APC16|D10Ertd641e	anaphase promoting complex subunit 16	protein-coding
mm_89279.1	chr10	87864029	87864069	+	1	NA	intron (NM_001111274, intron 1 of 4)	intron (NM_001111274, intron 1 of 4)	2938	NM_001111276	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_146544.1	chr18	6135228	6135230	-	1	NA	intron (NM_029277, intron 1 of 17)	intron (NM_029277, intron 1 of 17)	869	NM_029277	75415	Mm.239675	NM_029277	ENSMUSG00000041225	Arhgap12	2810011M08Rik	Rho GTPase activating protein 12	protein-coding
mm_89481.1	chr10	93595961	93596003	+	1	NA	non-coding (NR_045810, exon 2 of 4)	non-coding (NR_045810, exon 2 of 4)	-6324	NM_027246	69878	Mm.259642	NM_027246	ENSMUSG00000020018	Snrpf	2010013O18Rik|SMF|sm-F|snRNP-F	small nuclear ribonucleoprotein polypeptide F	protein-coding
mm_68167.1	chr7	103812655	103812674	-	1	NA	exon (NM_016956, exon 3 of 3)	exon (NM_016956, exon 3 of 3)	1259	NM_016956	15130	Mm.288567	NM_016956		Hbb-b2	AI036344|Hbb2|Hbbt2|beta2	hemoglobin, beta adult minor chain	protein-coding
mm_42000.1	chr5	107900751	107900792	+	1	NA	intron (NM_016980, intron 1 of 7)	CpG	243	NM_016980	100503670	Mm.277897	NM_016980	ENSMUSG00000058558	Rpl5	U21RNA	ribosomal protein L5	protein-coding
mm_78676.1	chr9	40782278	40782322	+	1	NA	intron (NM_133733, intron 6 of 6)	intron (NM_133733, intron 6 of 6)	-18973	NM_031165	15481	Mm.290774	NM_031165	ENSMUSG00000015656	Hspa8	2410008N15Rik|Hsc70|Hsc71|Hsc73|Hsp73|Hspa10	heat shock protein 8	protein-coding
mm_123186.1	chr14	57847149	57847155	-	1	NA	intron (NM_029492, intron 7 of 12)	intron (NM_029492, intron 7 of 12)	20913	NM_026401	67840	Mm.319530	NM_026401	ENSMUSG00000021967	Mrpl57	2610025P17Rik|AV005697|Mrp63	mitochondrial ribosomal protein L57	protein-coding
mm_140760.1	chr17	17600355	17600387	-	1	NA	intron (NM_172827, intron 1 of 17)	intron (NM_172827, intron 1 of 17)	24118	NM_172827	240028	Mm.328807	NM_172827	ENSMUSG00000023845	Lnpep	2010309L07Rik|4732490P18Rik|CAP|IRAP|PLAP|gp160|vp165	leucyl/cystinyl aminopeptidase	protein-coding
mm_141939.1	chr17	35048469	35048483	-	1	NA	Intergenic	Intergenic	-1731	NM_001146215	17687	Mm.24192	NM_013600	ENSMUSG00000007035	Msh5	Mut5	mutS homolog 5	protein-coding
mm_47044.1	chr5	116024442	116024450	-	1	NA	promoter-TSS (NM_031869)	promoter-TSS (NM_031869)	-18	NM_031869	19079	Mm.458152	NM_031869	ENSMUSG00000029513	Prkab1	1300015D22Rik|AU021155|E430008F22	protein kinase, AMP-activated, beta 1 non-catalytic subunit	protein-coding
mm_170990.1	chr2	7509485	7509485	-	1	NA	Intergenic	RLTR27|LTR|ERVK	-113287	NM_001110231	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_118050.1	chr13	101709683	101709703	-	1	NA	exon (NM_001077495, exon 3 of 16)	exon (NM_001077495, exon 3 of 16)	-17063	NM_001024955	18708	Mm.259333	NM_001024955	ENSMUSG00000041417	Pik3r1	PI3K|p50alpha|p55alpha|p85alpha	phosphatidylinositol 3-kinase, regulatory subunit, polypeptide 1 (p85 alpha)	protein-coding
mm_64928.1	chr7	16285427	16285440	-	1	NA	promoter-TSS (NM_172297)	promoter-TSS (NM_172297)	-774	NM_172297	243846	Mm.482401	NM_172297	ENSMUSG00000041375	Ccdc9	2600011L02Rik	coiled-coil domain containing 9	protein-coding
mm_31360.1	chr4	47208299	47208316	+	1	NA	5' UTR (NM_009928, exon 1 of 40)	5' UTR (NM_009928, exon 1 of 40)	295	NM_009928	12819	Mm.233547	NM_009928	ENSMUSG00000028339	Col15a1	-	collagen, type XV, alpha 1	protein-coding
mm_77610.1	chr8	123893460	123893475	-	1	NA	exon (NM_009606, exon 3 of 7)	exon (NM_009606, exon 3 of 7)	1308	NM_001272041	11459	Mm.214950	NM_009606	ENSMUSG00000031972	Acta1	AA959943|Acta-2|Acts|Actsk-1	actin, alpha 1, skeletal muscle	protein-coding
mm_131163.1	chr16	6996643	6996655	+	1	NA	intron (NM_021477, intron 5 of 16)	intron (NM_021477, intron 5 of 16)	-73186	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_64693.1	chr7	4522817	4522829	-	1	NA	promoter-TSS (NM_009406)	promoter-TSS (NM_009406)	-380	NM_009406	21954	Mm.27674	NM_009406	ENSMUSG00000035458	Tnni3	Tn1|cTnI	troponin I, cardiac 3	protein-coding
mm_68672.1	chr7	118974959	118974979	-	1	NA	3' UTR (NM_022420, exon 4 of 4)	3' UTR (NM_022420, exon 4 of 4)	20242	NM_022420	64297	Mm.103439	NM_022420	ENSMUSG00000008734	Gprc5b	AW125761|Raig2	G protein-coupled receptor, family C, group 5, member B	protein-coding
mm_36205.1	chr4	62408619	62408643	-	1	NA	promoter-TSS (NM_027297)	promoter-TSS (NM_027297)	-8	NM_139291	66440	Mm.109930	NM_139291	ENSMUSG00000066149	Cdc26	2010012C09Rik	cell division cycle 26	protein-coding
mm_153871.1	chr19	46761202	46761215	-	1	NA	promoter-TSS (NM_001102471)	promoter-TSS (NM_001102471)	-401	NM_033569	94219	Mm.306903	NM_033569	ENSMUSG00000064105	Cnnm2	AU015877|AW048635|Acdp2|Clp2	cyclin M2	protein-coding
mm_62407.1	chr7	101201169	101201173	+	1	NA	intron (NM_199012, intron 8 of 20)	intron (NM_199012, intron 8 of 20)	92396	NM_199012	207278	Mm.263041	NM_199012	ENSMUSG00000030691	Fchsd2	BC034086|R74866|Sh3md3|mKIAA0769	FCH and double SH3 domains 2	protein-coding
mm_87984.1	chr10	63951594	63951595	+	1	NA	intron (NM_178678, intron 2 of 2)	intron (NM_178678, intron 2 of 2)	130539	NM_001164519	216033	Mm.444692	NM_177612	ENSMUSG00000060843	Ctnna3	4930429L08Rik|4933408A16|Catna3|Vr22	catenin (cadherin associated protein), alpha 3	protein-coding
mm_318.1	chr1	24678434	24678460	+	1	NA	promoter-TSS (NM_026719)	promoter-TSS (NM_026719)	-97	NM_026719	68421	Mm.336563	NM_026719	ENSMUSG00000073725	Lmbrd1	0910001K20Rik|AV347960	LMBR1 domain containing 1	protein-coding
mm_145020.1	chr18	38993094	38993107	+	1	NA	promoter-TSS (NM_175164)	promoter-TSS (NM_175164)	-45	NM_175164	71302	Mm.329396	NM_175164	ENSMUSG00000036452	Arhgap26	1810044B20Rik|2610010G17Rik|4933432P15Rik|AI853435|mKIAA0621	Rho GTPase activating protein 26	protein-coding
mm_25762.1	chr3	124321143	124321153	+	1	NA	5' UTR (NM_146140, exon 1 of 1)	5' UTR (NM_146140, exon 1 of 1)	111	NM_146140	229801	Mm.165810	NM_146140	ENSMUSG00000044528	Tram1l1	A830091N21Rik	translocation associated membrane protein 1-like 1	protein-coding
mm_40917.1	chr5	75648579	75648585	+	1	NA	intron (NM_021099, intron 16 of 20)	intron (NM_021099, intron 16 of 20)	73591	NM_021099	16590	Mm.247073	NM_021099	ENSMUSG00000005672	Kit	Bs|CD117|Fdc|Gsfsco1|Gsfsco5|Gsfsow3|SCO1|SCO5|SOW3|Ssm|Tr-kit|W|c-KIT	KIT proto-oncogene receptor tyrosine kinase	protein-coding
mm_132504.1	chr16	36955268	36955317	+	1	NA	exon (NM_008225, exon 7 of 14)	exon (NM_008225, exon 7 of 14)	20309	NM_008225	15163	Mm.4091	NM_008225	ENSMUSG00000022831	Hcls1	AW213261|HS1	hematopoietic cell specific Lyn substrate 1	protein-coding
mm_111225.1	chr12	84755530	84755558	-	1	NA	3' UTR (NM_023409, exon 4 of 4)	3' UTR (NM_023409, exon 4 of 4)	17568	NM_023409	67963	Mm.282556	NM_023409	ENSMUSG00000021242	Npc2	2700012J19Rik|AA408070|AU045843|HE1	Niemann-Pick type C2	protein-coding
mm_68885.1	chr7	126447977	126447986	-	1	NA	exon (NM_007504, exon 17 of 23)	exon (NM_007504, exon 17 of 23)	15092	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_89178.1	chr10	86344598	86344617	+	1	NA	exon (NM_011595, exon 4 of 5)	exon (NM_011595, exon 4 of 5)	44195	NM_011595	21859	Mm.4871	NM_011595	ENSMUSG00000020044	Timp3	Timp-3	tissue inhibitor of metalloproteinase 3	protein-coding
mm_66166.1	chr7	31362096	31362100	-	1	NA	promoter-TSS (NM_001270541)	promoter-TSS (NM_001270541)	-26	NM_001270541	100043326	Mm.479858	NM_001270541	ENSMUSG00000078754	Scgb2b3	Abpbg3|Gm4362	secretoglobin, family 2B, member 3	protein-coding
mm_5676.1	chr1	43145562	43145569	-	1	NA	intron (NM_010212, intron 2 of 5)	intron (NM_010212, intron 2 of 5)	18396	NM_010212	14200	Mm.6799	NM_010212	ENSMUSG00000008136	Fhl2	FHL-2|SLIM-3|SLIM3	four and a half LIM domains 2	protein-coding
mm_95010.1	chr11	31933345	31933358	+	1	NA	3' UTR (NM_026252, exon 10 of 10)	3' UTR (NM_026252, exon 10 of 10)	-32282	NM_026262	67592	Mm.78654	NM_026262	ENSMUSG00000020299	4930524B15Rik	-	RIKEN cDNA 4930524B15 gene	protein-coding
mm_89833.1	chr10	106632399	106632442	+	1	NA	intron (NM_001205341, intron 3 of 31)	intron (NM_001205341, intron 3 of 31)	-29940	NR_131026	75833	Mm.159596	NR_131026		4930532I03Rik	-	RIKEN cDNA 4930532I03 gene	ncRNA
mm_159888.1	chr6	28428360	28428360	-	1	NA	intron (NM_019569, intron 1 of 6)	intron (NM_019569, intron 1 of 6)	459	NM_019569	56223	Mm.31708	NM_019569	ENSMUSG00000029707	Fscn3	-	fascin actin-bundling protein 3	protein-coding
mm_71298.1	chr8	41239719	41239767	+	1	NA	promoter-TSS (NM_023662)	promoter-TSS (NM_023662)	-16	NM_023662	18536	Mm.117896	NM_023662	ENSMUSG00000031592	Pcm1	2600002H09Rik|9430077F19Rik|C030044G17Rik	pericentriolar material 1	protein-coding
mm_93557.1	chr10	116473419	116473514	-	1	NA	promoter-TSS (NM_021452)	promoter-TSS (NM_021452)	57	NM_021452	58802	Mm.440652	NM_021452	ENSMUSG00000054934	Kcnmb4	1700058G18Rik|2900045G12Rik	potassium large conductance calcium-activated channel, subfamily M, beta member 4	protein-coding
mm_64067.1	chr7	140881961	140881983	+	1	NA	promoter-TSS (NM_001127351)	promoter-TSS (NM_001127351)	-103	NM_001177804	64384	Mm.29760	NM_022433	ENSMUSG00000025486	Sirt3	2310003L23Rik|AI848213|Sir2l3	sirtuin 3	protein-coding
mm_119743.1	chr14	54122191	54122228	+	1	NA	Intergenic	Intergenic	131720	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_64680.1	chr7	4509917	4509940	-	1	NA	intron (NM_011618, intron 8 of 13)	intron (NM_011618, intron 8 of 13)	6047	NM_001277903	21955	Mm.358643	NM_011618	ENSMUSG00000064179	Tnnt1	AW146156|Tnt|sTnT|ssTnT	troponin T1, skeletal, slow	protein-coding
mm_19289.1	chr2	90451253	90451273	-	1	NA	intron (NM_001135657, intron 14 of 25)	intron (NM_001135657, intron 14 of 25)	27911	NM_001135657	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_107236.1	chr12	26478340	26478367	+	1	NA	3' UTR (NM_020557, exon 5 of 5)	3' UTR (NM_020557, exon 5 of 5)	9138	NM_020557	22169	Mm.271839	NM_020557	ENSMUSG00000020638	Cmpk2	1200004E04Rik|TDKI|Tyki	cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial	protein-coding
mm_136870.1	chr17	12916458	12916475	+	1	NA	promoter-TSS (NM_026310)	promoter-TSS (NM_026310)	137	NM_013686	21454	Mm.229342	NM_013686	ENSMUSG00000068039	Tcp1	AI528772|CCT|Cct1|Ccta|TRic|Tcp-1|Tp63|c-cpn|p63	t-complex protein 1	protein-coding
mm_168159.1	chr10	4266223	4266226	+	1	NA	promoter-TSS (NM_031185)	promoter-TSS (NM_031185)	-105	NM_031185	83397	Mm.27481	NM_031185	ENSMUSG00000038587	Akap12	AI317366|SSeCKS|Srcs5|Tsga12	A kinase (PRKA) anchor protein (gravin) 12	protein-coding
mm_92927.1	chr10	84440686	84440705	-	1	NA	promoter-TSS (NM_001004363)	promoter-TSS (NM_001004363)	-224	NM_001004363	77976	Mm.25874	NM_001004363	ENSMUSG00000020032	Nuak1	AU014801|AW494241|B230104P22Rik|Omphk1	NUAK family, SNF1-like kinase, 1	protein-coding
mm_142766.1	chr17	49509939	49509943	-	1	NA	intron (NM_001008231, intron 1 of 25)	intron (NM_001008231, intron 1 of 25)	54396	NM_001008231	76441	Mm.211275	NM_001008231	ENSMUSG00000040260	Daam2	2310016D11Rik|AI843643|AW557870	dishevelled associated activator of morphogenesis 2	protein-coding
mm_64380.1	chr7	142471759	142471777	+	1	NA	promoter-TSS (NM_019391)	promoter-TSS (NM_019391)	-75	NM_001271508	16985	Mm.234003	NM_019391	ENSMUSG00000018819	Lsp1	Lsp-1|WP34|p50|pp52	lymphocyte specific 1	protein-coding
mm_136002.1	chr16	75447187	75447214	-	1	NA	Intergenic	Intergenic	138861	NM_001252513	320355	Mm.99517	NM_177142	ENSMUSG00000032948	Lipi	D930038D03Rik|lpd1	lipase, member I	protein-coding
mm_102663.1	chr11	64209042	64209052	-	1	NA	Intergenic	A-rich|Low_complexity|Low_complexity	129563	NR_033780	66456	Mm.124828	NR_033780	ENSMUSG00000087497	2810001G20Rik	AW045514	RIKEN cDNA 2810001G20 gene	ncRNA
mm_100828.1	chr11	5394430	5394433	-	1	NA	intron (NM_001080924, intron 1 of 8)	intron (NM_001080924, intron 1 of 8)	-12691	NM_001290501	407821	Mm.216313	NM_001080924	ENSMUSG00000041961	Znrf3	Gm1167	zinc and ring finger 3	protein-coding
mm_114271.1	chr13	58148554	58148566	+	1	NA	intron (NR_126543, intron 1 of 1)	intron (NR_126543, intron 1 of 1)	1611	NR_126543	67339	Mm.121929	NR_126543		1700066J03Rik	-	RIKEN cDNA 1700066J03 gene	ncRNA
mm_158328.1	chrX	133961675	133961677	-	1	NA	intron (NM_001290719, intron 3 of 12)	intron (NM_001290719, intron 3 of 12)	20136	NM_001290718	27359	Mm.38674	NM_013757	ENSMUSG00000031255	Sytl4	Gph|Slp4	synaptotagmin-like 4	protein-coding
mm_83055.1	chr9	37545141	37545162	-	1	NA	TTS (NM_020518)	TTS (NM_020518)	5896	NM_020518	57276	Mm.27478	NM_020518	ENSMUSG00000001943	Vsig2	1190004B15Rik|2210413P10Rik|AU040484|CTX|Ctm	V-set and immunoglobulin domain containing 2	protein-coding
mm_106955.1	chr12	8792428	8792446	+	1	NA	3' UTR (NM_011519, exon 5 of 5)	3' UTR (NM_011519, exon 5 of 5)	21041	NM_011519	20969	Mm.2580	NM_011519	ENSMUSG00000020592	Sdc1	AA408134|AA409076|CD138|Sstn|Synd|Synd1|syn-1	syndecan 1	protein-coding
mm_109949.1	chr12	11332058	11332071	-	1	NA	exon (NM_012038, exon 3 of 4)	exon (NM_012038, exon 3 of 4)	32177	NR_106136	102465775		NR_106136	ENSMUSG00000098879	Mir7675	Gm27965|mmu-mir-7675	microRNA 7675	ncRNA
mm_144760.1	chr18	35771575	35771599	+	1	NA	promoter-TSS (NM_019912)	promoter-TSS (NM_019912)	28	NM_019912	56550	Mm.180052	NM_019912	ENSMUSG00000091896	Ube2d2a	1500034D03Rik|Ubc2e|Ube2d2|ubc4	ubiquitin-conjugating enzyme E2D 2A	protein-coding
mm_137461.1	chr17	26602268	26602274	+	1	NA	intron (NM_026170, intron 1 of 9)	intron (NM_026170, intron 1 of 9)	40759	NM_026170	67458	Mm.30496	NM_026170	ENSMUSG00000001576	Ergic1	1200007D18Rik|maa-136	endoplasmic reticulum-golgi intermediate compartment (ERGIC) 1	protein-coding
mm_27069.1	chr3	28157163	28157165	-	1	NA	Intergenic	RMER19C|LTR|ERVK	-106050	NM_001163007	665113	Mm.126193	NM_026910	ENSMUSG00000027692	Tnik	1500031A17Rik|4831440I19Rik|AI451411|C530008O15Rik|C630040K21Rik	TRAF2 and NCK interacting kinase	protein-coding
mm_122104.1	chr14	30919407	30919419	-	1	NA	exon (NM_008407, exon 7 of 21)	exon (NM_008407, exon 7 of 21)	4174	NM_008407	16426	Mm.4517	NM_008407	ENSMUSG00000006522	Itih3	AW108094|ITI-HC3|Intin3|Itih-3	inter-alpha trypsin inhibitor, heavy chain 3	protein-coding
mm_75298.1	chr8	41056573	41056583	-	1	NA	intron (NM_001005863, intron 3 of 13)	intron (NM_001005863, intron 3 of 13)	-1782	NM_001005864	102103	Mm.149438	NM_001005863	ENSMUSG00000045636	Mtus1	AI481402|ATBP135|Atip1|B430010I23Rik|B430305I03Rik|C85752|Cctsg1-440|MD44|MTSG1|mKIAA1288	mitochondrial tumor suppressor 1	protein-coding
mm_92077.1	chr10	62665370	62665392	-	1	NA	exon (NM_001033260, exon 3 of 4)	exon (NM_001033260, exon 3 of 4)	-14183	NM_053183	94213	Mm.114116	NM_053183	ENSMUSG00000020076	Ddx50	4933429B04Rik|8430408E17Rik|GU2|RH-II	DEAD (Asp-Glu-Ala-Asp) box polypeptide 50	protein-coding
mm_160078.1	chr7	12422441	12422441	-	1	NA	promoter-TSS (NM_001033820)	promoter-TSS (NM_001033820)	50	NM_001033820	619331	Mm.361832	NM_001033820	ENSMUSG00000034071	Zfp551	9630004E07Rik|Znf551	zinc fingr protein 551	protein-coding
mm_23151.1	chr3	40459844	40459844	+	1	NA	Intergenic	U2|snRNA|snRNA	63068	NR_040445	100040882	Mm.272869	NR_040445	ENSMUSG00000037884	1700017G19Rik	-	RIKEN cDNA 1700017G19 gene	ncRNA
mm_53063.1	chr6	124913677	124913696	+	1	NA	TTS (NM_026988)	TTS (NM_026988)	-1981	NM_008479	16768	Mm.4528	NM_008479	ENSMUSG00000030124	Lag3	CD223|LAG-3|Ly66	lymphocyte-activation gene 3	protein-coding
mm_149807.1	chr19	23758985	23758998	+	1	NA	5' UTR (NM_177034, exon 1 of 13)	5' UTR (NM_177034, exon 1 of 13)	115	NM_177034	319924	Mm.22879	NM_177034	ENSMUSG00000024897	Apba1	6430513E09Rik|Lin-10|Mint|Mint1|Urop11|X11|X11alpha	amyloid beta (A4) precursor protein binding, family A, member 1	protein-coding
mm_165414.1	chr2	147237390	147237391	+	1	NA	intron (NR_030769, intron 1 of 5)	intron (NR_030769, intron 1 of 5)	49966	NR_108091	78068	Mm.261511	NR_108091	ENSMUSG00000053545	6430503K07Rik	-	RIKEN cDNA 6430503K07 gene	ncRNA
mm_69804.1	chr7	141193935	141194012	-	1	NA	promoter-TSS (NM_001172065)	promoter-TSS (NM_001172065)	31	NM_001130444	15461	Mm.334313	NM_008284	ENSMUSG00000025499	Hras	H-ras|Ha-ras|Harvey-ras|Hras-1|Hras1|Kras2|c-H-ras|c-Ha-ras|c-rasHa|ras	Harvey rat sarcoma virus oncogene	protein-coding
mm_36459.1	chr4	82505680	82505690	-	1	NA	promoter-TSS (NM_001113209)	promoter-TSS (NM_001113209)	94	NM_001286127	18028	Mm.317947	NM_008687	ENSMUSG00000008575	Nfib	6720429L07Rik|CTF|E030026I10Rik|NF-I/B|NF1-B|NFI-B	nuclear factor I/B	protein-coding
mm_141388.1	chr17	29099526	29099586	-	1	NA	3' UTR (NM_007669, exon 3 of 3)	3' UTR (NM_007669, exon 3 of 3)	5787	NM_007669	12575	Mm.195663	NM_007669	ENSMUSG00000023067	Cdkn1a	CAP20|CDKI|CIP1|Cdkn1|P21|SDI1|Waf1|mda6|p21Cip1|p21WAF	cyclin-dependent kinase inhibitor 1A (P21)	protein-coding
mm_131059.1	chr16	4276532	4276549	+	1	NA	Intergenic	Intergenic	47311	NR_003628	436332	Mm.478141	NM_001013830	ENSMUSG00000089645	Gm5766	EG436332	ribosomal protein L7a pseudogene	pseudo
mm_79204.1	chr9	48985359	48985451	+	1	NA	promoter-TSS (NM_175482)	promoter-TSS (NM_175482)	20	NM_175482	235323	Mm.21630	NM_175482	ENSMUSG00000032267	Usp28	9830148O20Rik|AU022237|mKIAA1515	ubiquitin specific peptidase 28	protein-coding
mm_140.1	chr1	10993366	10993375	+	1	NA	promoter-TSS (NM_029525)	promoter-TSS (NM_029525)	-95	NM_029525	109294	Mm.123247	NM_029525	ENSMUSG00000048960	Prex2	6230420N16Rik|AI316880|AI553603|C030045D06Rik|D430013K02|Depdc2|P-Rex2	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	protein-coding
mm_151379.1	chr19	56066128	56066140	+	1	NA	Intergenic	Intergenic	170813	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_43860.1	chr5	143464575	143464652	+	1	NA	5' UTR (NM_144915, exon 1 of 15)	5' UTR (NM_144915, exon 1 of 15)	120	NM_144915	231871	Mm.469963	NM_144915	ENSMUSG00000039206	Daglb	E330036I19Rik	diacylglycerol lipase, beta	protein-coding
mm_167373.1	chr8	91117655	91117659	-	1	NA	intron (NM_011250, intron 21 of 21)	intron (NM_011250, intron 21 of 21)	16370	NM_001302337	14339	Mm.324588	NM_010241	ENSMUSG00000031667	Aktip	AL023020|Fif|Ft|Ft1|Fts	thymoma viral proto-oncogene 1 interacting protein	protein-coding
mm_8690.1	chr1	157256628	157256650	-	1	NA	intron (NM_177644, intron 3 of 17)	intron (NM_177644, intron 3 of 17)	-147959	NM_001305063	73435	Mm.116705	NM_028540	ENSMUSG00000026592	Tex35	1700057K13Rik	testis expressed 35	protein-coding
mm_92474.1	chr10	78092751	78092758	-	1	NA	Intergenic	Intergenic	23386	NM_015790	50723	Mm.17819	NM_015790	ENSMUSG00000000732	Icosl	AU044799|B7-H2|B7RP-1|B7h|BG071784|GI50|GL50|GL50-B|ICOS-L|Icoslg|LICOS|Ly115l|mKIAA0653	icos ligand	protein-coding
mm_103238.1	chr11	70686900	70686958	-	1	NA	intron (NM_178116, intron 1 of 22)	intron (NM_178116, intron 1 of 22)	1176	NM_001190376	216874	Mm.473726	NM_178116	ENSMUSG00000040712	Camta2	Kiaa0909-hp|mKIAA0909	calmodulin binding transcription activator 2	protein-coding
mm_118596.1	chr14	20688477	20688494	+	1	NA	exon (NM_172596, exon 9 of 23)	exon (NM_172596, exon 9 of 23)	-2150	NR_105911	102465571		NR_105911	ENSMUSG00000098602	Mir6946	Gm27799|mmu-mir-6946	microRNA 6946	ncRNA
mm_29423.1	chr3	109009080	109009081	-	1	NA	intron (NM_001163567, intron 1 of 10)	intron (NM_001163567, intron 1 of 10)	18527	NM_001163567	329739	Mm.69013	NM_001163567	ENSMUSG00000040339	Fam102b	1600010D10Rik|B430201A12Rik	family with sequence similarity 102, member B	protein-coding
mm_93532.1	chr10	115362178	115362184	-	1	NA	promoter-TSS (NM_133683)	promoter-TSS (NM_133683)	81	NM_133683	67226	Mm.29647	NM_133683	ENSMUSG00000069520	Tmem19	2810428F02Rik|AW125171	transmembrane protein 19	protein-coding
mm_74799.1	chr8	22463218	22463229	-	1	NA	3' UTR (NM_001146117, exon 4 of 4)	3' UTR (NM_001146117, exon 4 of 4)	-13477	NM_011394	20516	Mm.323901	NM_011394	ENSMUSG00000037656	Slc20a2	MolPit2|Pit-2|Pit2|Ram-1|Ram1	solute carrier family 20, member 2	protein-coding
mm_91435.1	chr10	33624588	33624611	-	1	NA	promoter-TSS (NM_175448)	promoter-TSS (NM_175448)	1	NM_175448	215890	Mm.94461	NM_175448	ENSMUSG00000019785	Clvs2	A330019N05Rik|Rlbp1l2	clavesin 2	protein-coding
mm_91762.1	chr10	51494470	51494511	-	1	NA	intron (NM_001291894, intron 6 of 8)	intron (NM_001291894, intron 6 of 8)	3592	NM_013532	14728	Mm.34408	NM_013532	ENSMUSG00000062593	Lilrb4a	CD85K|Gp49b|HM18|ILT3|LIR-5|Lilrb4|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4A	protein-coding
mm_70020.1	chr7	142575617	142575629	-	1	NA	TTS (NR_130974)	TTS (NR_130974)	1524	NR_030416	735280		NR_030416	ENSMUSG00000076275	Mir675	Mirn675|mir-675|mmu-mir-675	microRNA 675	ncRNA
mm_153805.1	chr19	46045133	46045151	-	1	NA	promoter-TSS (NM_001113408)	promoter-TSS (NM_001113408)	69	NM_001113408	16825	Mm.327442	NM_010697	ENSMUSG00000025223	Ldb1	CLIM2|NLI	LIM domain binding 1	protein-coding
mm_96751.1	chr11	69901129	69901143	+	1	NA	promoter-TSS (NM_001291119)	promoter-TSS (NM_001291119)	-150	NM_027419	70419	Mm.272859	NM_027419	ENSMUSG00000018570	2810408A11Rik	1700019L01Rik|4930470J18Rik	RIKEN cDNA 2810408A11 gene	protein-coding
mm_89876.1	chr10	108295039	108295049	+	1	NA	Intergenic	ORR1B2|LTR|ERVL-MaLR	-37145	NM_054056	114774	Mm.391419	NM_054056	ENSMUSG00000035873	Pawr	2310001G03Rik|PAR4|Par-4	PRKC, apoptosis, WT1, regulator	protein-coding
mm_135600.1	chr16	51686760	51686767	-	1	NA	Intergenic	L2a|LINE|L2	-344786	NM_001033238	208650	Mm.328206	NM_001033238	ENSMUSG00000022637	Cblb	AI429560|AI851073|Cbl-b	Casitas B-lineage lymphoma b	protein-coding
mm_5949.1	chr1	56871688	56871691	-	1	NA	exon (NM_139146, exon 7 of 11)	exon (NM_139146, exon 7 of 11)	99645	NM_139146	212712	Mm.145599	NM_139146	ENSMUSG00000038331	Satb2	mKIAA1034	special AT-rich sequence binding protein 2	protein-coding
mm_78883.1	chr9	44581654	44581678	+	1	NA	Intergenic	Intergenic	-23226	NM_001110826	13209	Mm.267061	NM_007841	ENSMUSG00000032097	Ddx6	1110001P04Rik|E230023J21Rik|HLR2|mRCK/P54|p54|rck	DEAD (Asp-Glu-Ala-Asp) box polypeptide 6	protein-coding
mm_125379.1	chr15	40655021	40655054	+	1	NA	promoter-TSS (NM_011766)	promoter-TSS (NM_011766)	-5	NM_011766	22762	Mm.39496	NM_011766	ENSMUSG00000022306	Zfpm2	B330005D23Rik|FOG-2|FOG2	zinc finger protein, multitype 2	protein-coding
mm_53961.1	chr6	5495920	5495932	-	1	NA	intron (NM_013743, intron 1 of 10)	intron (NM_013743, intron 1 of 10)	352	NM_013743	27273	Mm.235547	NM_013743	ENSMUSG00000019577	Pdk4	AV005916	pyruvate dehydrogenase kinase, isoenzyme 4	protein-coding
mm_60046.1	chr7	31059674	31059699	+	1	NA	promoter-TSS (NM_144556)	promoter-TSS (NM_144556)	-249	NM_144556	243914	Mm.389870	NM_144556	ENSMUSG00000036560	Lgi4	Lgil3|clp	leucine-rich repeat LGI family, member 4	protein-coding
mm_85817.1	chr9	110408161	110408204	-	1	NA	promoter-TSS (NM_001081043)	promoter-TSS (NM_001081043)	28	NM_001081043	104831	Mm.335477	NM_001081043	ENSMUSG00000036057	Ptpn23	AI462446|PTP-TD14	protein tyrosine phosphatase, non-receptor type 23	protein-coding
mm_143081.1	chr17	57059796	57059857	-	1	NA	promoter-TSS (NM_025877)	promoter-TSS (NM_025877)	37	NM_025877	66972	Mm.23720	NM_025877	ENSMUSG00000046329	Slc25a23	2310067G05Rik|SCaMC-3	solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 23	protein-coding
mm_112379.1	chr12	119237948	119238001	-	1	NA	5' UTR (NM_177290, exon 1 of 14)	5' UTR (NM_177290, exon 1 of 14)	302	NM_177290	320910	Mm.217000	NM_177290	ENSMUSG00000025321	Itgb8	4832412O06Rik	integrin beta 8	protein-coding
mm_158996.1	chr1	138967699	138967699	+	1	NA	promoter-TSS (NM_181347)	promoter-TSS (NM_181347)	-22	NM_181347	329260	Mm.337604	NM_181347	ENSMUSG00000056268	Dennd1b	4632404N19Rik|4930467M19Rik|6820401H01Rik|F730008N07Rik	DENN/MADD domain containing 1B	protein-coding
mm_112746.1	chr13	19341766	19341771	+	1	NA	Intergenic	Intergenic	54045	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_124031.1	chr14	77024936	77024950	-	1	NA	3' UTR (NM_172488, exon 8 of 8)	3' UTR (NM_172488, exon 8 of 8)	11674	NM_172488	210808	Mm.89278	NM_172488	ENSMUSG00000044350	Lacc1	9030625A04Rik	laccase (multicopper oxidoreductase) domain containing 1	protein-coding
mm_30668.1	chr4	11123951	11123980	+	1	NA	Intergenic	Intergenic	-10132	NR_030455	735261		NR_030455	ENSMUSG00000105333	Mir684-2	Mirn684-2	microRNA 684-2	ncRNA
mm_67453.1	chr7	80401491	80401507	-	1	NA	intron (NM_001081454, intron 1 of 15)	intron (NM_001081454, intron 1 of 15)	1313	NM_011046	18550	Mm.5241	NM_011046	ENSMUSG00000030530	Furin	9130404I01Rik|Fur|PACE|Pcsk3|SPC1	furin (paired basic amino acid cleaving enzyme)	protein-coding
mm_20813.1	chr2	144527342	144527424	-	1	NA	promoter-TSS (NM_029763)	promoter-TSS (NM_029763)	15	NM_172859	241688	Mm.442156	NM_172859	ENSMUSG00000037259	Dzank1	2810039F03Rik|6330439K17Rik|6430408C01|AI851115|Ankrd64	double zinc ribbon and ankyrin repeat domains 1	protein-coding
mm_119134.1	chr14	31166518	31166530	+	1	NA	intron (NM_138672, intron 1 of 68)	intron (NM_138672, intron 1 of 68)	2117	NM_138672	192187	Mm.220821	NM_138672	ENSMUSG00000042286	Stab1	FEEL-1|FELE-1|MFEEL-1|MS-1|STAB-1|mKIAA0246	stabilin 1	protein-coding
mm_146601.1	chr18	9485345	9485349	-	1	NA	Intergenic	Intergenic	-35197	NM_026484	67974	Mm.86523	NM_026484	ENSMUSG00000024286	Ccny	1700025H17Rik|3110050L10Rik|4631402G10Rik|5730405I09Rik	cyclin Y	protein-coding
mm_134793.1	chr16	24193031	24193035	-	1	NA	Intergenic	L2|LINE|L2	-200317	NM_178665	210126	Mm.209385	NM_178665	ENSMUSG00000033306	Lpp	9430020K16Rik|AA959454|AU024130|B130055L10Rik|C79715|D630048H16	LIM domain containing preferred translocation partner in lipoma	protein-coding
mm_57883.1	chr6	131348367	131348377	-	1	NA	Intergenic	Intergenic	-34545	NM_172891	243659	Mm.20114	NM_172891	ENSMUSG00000032899	Styk1	9130025L13|AI326477|Nok	serine/threonine/tyrosine kinase 1	protein-coding
mm_97722.1	chr11	80383300	80383304	+	1	NA	promoter-TSS (NR_045038)	promoter-TSS (NR_045038)	23	NM_001130171	22680	Mm.401332	NM_011751	ENSMUSG00000017421	Zfp207	8430401D15Rik|BuGZ|Zep|Znf207	zinc finger protein 207	protein-coding
mm_112548.1	chr13	12395348	12395358	+	1	NA	promoter-TSS (NM_144835)	promoter-TSS (NM_144835)	-22	NM_144835	217995	Mm.171186	NM_144835	ENSMUSG00000050244	Heatr1	AA517551|B130016L12Rik|BC019693	HEAT repeat containing 1	protein-coding
mm_37586.1	chr4	126429422	126429474	-	1	NA	promoter-TSS (NM_153402)	promoter-TSS (NM_153402)	94	NM_153402	214150	Mm.440915	NM_153402	ENSMUSG00000028842	Ago3	AW048688|C130014L07Rik|Eif2c3	argonaute RISC catalytic subunit 3	protein-coding
mm_1743.1	chr1	75450714	75450731	+	1	NA	5' UTR (NM_183022, exon 1 of 10)	5' UTR (NM_183022, exon 1 of 10)	212	NM_183022	241118	Mm.110790	NM_183022	ENSMUSG00000033007	Asic4	Accn4|BNAC4	acid-sensing (proton-gated) ion channel family member 4	protein-coding
mm_161601.1	chr16	37654367	37654367	-	1	NA	promoter-TSS (NM_026610)	promoter-TSS (NM_026610)	1	NM_026610	68194	Mm.379154	NM_026610	ENSMUSG00000022820	Ndufb4	0610006N12Rik|1300010H20Rik	NADH dehydrogenase (ubiquinone) 1 beta subcomplex 4	protein-coding
mm_45902.1	chr5	88676227	88676237	-	1	NA	promoter-TSS (NM_178700)	promoter-TSS (NM_178700)	-61	NM_178700	231413	Mm.332474	NM_178700	ENSMUSG00000044221	Grsf1	BB232551|C80280|D5Wsu31e	G-rich RNA sequence binding factor 1	protein-coding
mm_162013.1	chr19	44293456	44293456	+	1	NA	promoter-TSS (NM_009128)	promoter-TSS (NM_009128)	-220	NM_009128	20250	Mm.487021	NM_009128	ENSMUSG00000025203	Scd2	Mir5114|Scd-2|mir-5114|swty	stearoyl-Coenzyme A desaturase 2	protein-coding
mm_54083.1	chr6	15731959	15731988	-	1	NA	intron (NM_175088, intron 2 of 4)	intron (NM_175088, intron 2 of 4)	11312	NM_175088	16543	Mm.1314	NM_175088	ENSMUSG00000041390	Mdfic	Kdt1|Mdfid	MyoD family inhibitor domain containing	protein-coding
mm_87583.1	chr10	56556088	56556091	+	1	NA	Intergenic	B1F|SINE|Alu	178789	NM_010288	14609	Mm.378921	NM_010288	ENSMUSG00000050953	Gja1	AU042049|AW546267|Cnx43|Cx43|Cx43alpha1|Gja-1|Npm1|connexin43	gap junction protein, alpha 1	protein-coding
mm_89809.1	chr10	103347096	103347106	+	1	NA	Intergenic	RMER17C|LTR|ERVK	-20707	NM_001252330	103098	Mm.458408	NM_175328	ENSMUSG00000019894	Slc6a15	AA536730|AI326450|AI326451|v7-3	solute carrier family 6 (neurotransmitter transporter), member 15	protein-coding
mm_40564.1	chr5	62766326	62766341	+	1	NA	promoter-TSS (NM_178407)	promoter-TSS (NM_178407)	-156	NM_178407	212285	Mm.244403	NM_178407	ENSMUSG00000037999	Arap2	Centd1|Gm148|mKIAA0580	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2	protein-coding
mm_47845.1	chr5	134344230	134344242	-	1	NA	Intergenic	B1_Mur1|SINE|Alu	-29476	NM_010365	14886	Mm.261570	NM_010365	ENSMUSG00000060261	Gtf2i	6030441I21Rik|BAP-135|Diws1t|GtfII-I|Spin|TFII-I|WBSCR6	general transcription factor II I	protein-coding
mm_155350.1	chrX	68683942	68683954	+	1	NA	intron (NM_001290424, intron 1 of 16)	(T)n|Simple_repeat|Simple_repeat	5407	NM_001290424	14265	Mm.3451	NM_008031	ENSMUSG00000000838	Fmr1	FMRP|Fmr-1	fragile X mental retardation syndrome 1	protein-coding
mm_71575.1	chr8	54550325	54550339	+	1	NA	promoter-TSS (NM_029569)	promoter-TSS (NM_029569)	1	NM_029569	76294	Mm.33171	NM_029569	ENSMUSG00000031519	Asb5	1110018D09Rik	ankyrin repeat and SOCs box-containing 5	protein-coding
mm_11402.1	chr2	31492316	31492338	+	1	NA	exon (NM_007494, exon 8 of 16)	exon (NM_007494, exon 8 of 16)	22019	NR_002687	432466	Mm.333323	NR_002687	ENSMUSG00000046687	Gm5424	EG432466	argininosuccinate synthase pseudogene	pseudo
mm_151063.1	chr19	47240325	47240349	+	1	NA	intron (NM_001163480, intron 2 of 5)	intron (NM_001163480, intron 2 of 5)	11494	NM_001163480	18011	Mm.313651	NM_021360	ENSMUSG00000006435	Neurl1a	2410129E16Rik|AI450910|AI481072|Neu1|Neur1|Neurl|Neurl1|Nlz|Rnf67	neuralized E3 ubiquitin protein ligase 1A	protein-coding
mm_49396.1	chr6	28423540	28423640	+	1	NA	promoter-TSS (NM_007480)	promoter-TSS (NM_007480)	-50	NM_007480	11844	Mm.389075	NM_007480	ENSMUSG00000020440	Arf5	-	ADP-ribosylation factor 5	protein-coding
mm_120675.1	chr14	70563474	70563507	+	1	NA	intron (NM_021877, intron 8 of 19)	intron (NM_021877, intron 8 of 19)	9434	NM_021877	15460	Mm.7598	NM_021877	ENSMUSG00000022096	Hr	ALUNC|AU|N|ba|bldy|hr|rh|rh-bmh|rhino	hairless	protein-coding
mm_32797.1	chr4	117019441	117019452	+	1	NA	promoter-TSS (NM_001111277)	promoter-TSS (NM_001111277)	38	NM_001111277	108067	Mm.34612	NM_175135	ENSMUSG00000028683	Eif2b3	1190002P15Rik	eukaryotic translation initiation factor 2B, subunit 3	protein-coding
mm_79337.1	chr9	53341807	53341812	+	1	NA	intron (NM_176846, intron 3 of 5)	intron (NM_176846, intron 3 of 5)	40139	NM_176846	320051	Mm.277540	NM_176846	ENSMUSG00000034584	Exph5	AC079869.22gm5|B130009M24Rik|E030050P12|Kiaa0624|Slac2b|slac2-b	exophilin 5	protein-coding
mm_114017.1	chr13	52617397	52617403	+	1	NA	intron (NM_001198977, intron 3 of 13)	intron (NM_001198977, intron 3 of 13)	20518	NM_011518	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_108084.1	chr12	73997737	73997744	+	1	NA	promoter-TSS (NM_172804)	promoter-TSS (NM_172804)	-21	NM_172804	238266	Mm.311393	NM_172804	ENSMUSG00000044912	Syt16	6430703N11|Strep14|Syt14l|syt14r	synaptotagmin XVI	protein-coding
mm_171354.1	chr4	110670094	110670107	+	1	NA	intron (NM_001048189, intron 3 of 12)	(CAG)n|Simple_repeat|Simple_repeat	272402	NM_030231	78933	Mm.435620	NM_030231	ENSMUSG00000061298	Agbl4	4930578N11Rik|4931433A01Rik	ATP/GTP binding protein-like 4	protein-coding
mm_40448.1	chr5	53594997	53595007	+	1	NA	intron (NM_001080927, intron 1 of 10)	intron (NM_001080927, intron 1 of 10)	4516	NM_001080927	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_133328.1	chr16	78309541	78309551	+	1	NA	intron (NM_001276263, intron 1 of 2)	intron (NM_001276263, intron 1 of 2)	7875	NM_001276263	13052	Mm.66222	NM_009988	ENSMUSG00000022865	Cxadr	2610206D03Rik|AU016810|AW553441|CAR|MCAR|MCVADR	coxsackie virus and adenovirus receptor	protein-coding
mm_142242.1	chr17	37482501	37482509	-	1	NA	exon (NM_008204, exon 3 of 4)	exon (NM_008204, exon 3 of 4)	1024	NM_008204	14990	Mm.329041	NM_008204	ENSMUSG00000016283	H2-M2	H-2M2|Thy19.4	histocompatibility 2, M region locus 2	protein-coding
mm_46267.1	chr5	99964792	99964807	-	1	NA	exon (NM_007516, exon 5 of 8)	exon (NM_007516, exon 5 of 8)	14139	NM_001077266	11991	Mm.150231	NM_007516	ENSMUSG00000000568	Hnrnpd	Auf1|Hnrpd	heterogeneous nuclear ribonucleoprotein D	protein-coding
mm_164752.1	chr17	81375484	81375498	-	1	NA	non-coding (NR_104580, exon 9 of 9)	non-coding (NR_104580, exon 9 of 9)	-310406	NM_028138	72167	Mm.273257	NM_028138	ENSMUSG00000024246	Thumpd2	2810025A12Rik	THUMP domain containing 2	protein-coding
mm_67893.1	chr7	99480009	99480029	-	1	NA	promoter-TSS (NR_002173)	promoter-TSS (NR_002173)	-312	NR_002173	449631	Mm.236868	NR_002173	ENSMUSG00000064966	Snord15b	Gm5775|Rnu15-b|Rnu15b|U15B	small nucleolar RNA, C/D box 14B	snoRNA
mm_58580.1	chr7	4915234	4915256	+	1	NA	promoter-TSS (NM_170759)	promoter-TSS (NM_170759)	28	NM_170759	232816	Mm.27442	NM_170759	ENSMUSG00000074406	Zfp628	Zec|Znf628	zinc finger protein 628	protein-coding
mm_36595.1	chr4	88720027	88720031	-	1	NA	3' UTR (NM_172871, exon 1 of 1)	3' UTR (NM_172871, exon 1 of 1)	2479	NM_172871	242521	Mm.260601	NM_172871	ENSMUSG00000070923	Klhl9	8030469P05|C530050O22Rik|ENSMUSG00000070923|mKIAA1354	kelch-like 9	protein-coding
mm_7409.1	chr1	119422152	119422164	-	1	NA	promoter-TSS (NM_008381)	promoter-TSS (NM_008381)	90	NM_008381	16324	Mm.3092	NM_008381	ENSMUSG00000037035	Inhbb	-	inhibin beta-B	protein-coding
mm_108806.1	chr12	92782527	92782530	+	1	NA	Intergenic	Intergenic	662295	NR_126436	75295	Mm.243878	NR_126436		4930559C10Rik	-	RIKEN cDNA 4930559C10 gene	ncRNA
mm_134742.1	chr16	23029372	23029376	-	1	NA	promoter-TSS (NM_201375)	promoter-TSS (NM_201375)	-273	NM_001102410	385643	Mm.440414	NM_201375	ENSMUSG00000060459	Kng2	-	kininogen 2	protein-coding
mm_41354.1	chr5	90504951	90504965	+	1	NA	exon (NM_007423, exon 11 of 15)	exon (NM_007423, exon 11 of 15)	-13991	NM_145146	280662	Mm.348786	NM_145146	ENSMUSG00000029369	Afm	Alf|alpha-Alb	afamin	protein-coding
mm_95039.1	chr11	32267706	32267748	+	1	NA	promoter-TSS (NM_001284360)	promoter-TSS (NM_001284360)	-20	NM_001284359	17168	Mm.263161	NM_181569	ENSMUSG00000020289	Nprl3	Aag|CGTHBA|HS-26|HS-40|Mare|Phg|Prox1|m(alpha)RE	nitrogen permease regulator-like 3	protein-coding
mm_54909.1	chr6	47778337	47778339	-	1	NA	Intergenic	4.5SRNA|scRNA|scRNA	25314	NR_030485	735289		NR_030485	ENSMUSG00000076060	Mir704	Mirn704|mir-704|mmu-mir-704	microRNA 704	ncRNA
mm_21423.1	chr2	158146386	158146396	-	1	NA	promoter-TSS (NM_009373)	promoter-TSS (NM_009373)	1	NM_009373	21817	Mm.330731	NM_009373	ENSMUSG00000037820	Tgm2	G[a]h|TG2|TGase2|tTG|tTGas	transglutaminase 2, C polypeptide	protein-coding
mm_104616.1	chr11	97280455	97280465	-	1	NA	5' UTR (NM_008942, exon 1 of 23)	5' UTR (NM_008942, exon 1 of 23)	116	NM_008942	19155	Mm.29824	NM_008942	ENSMUSG00000001441	Npepps	AAP-S|MP100|Psa|R74825|goku	aminopeptidase puromycin sensitive	protein-coding
mm_92409.1	chr10	76721457	76721473	-	1	NA	exon (NM_009933, exon 5 of 35)	exon (NM_009933, exon 5 of 35)	4579	NM_009933	12833	Mm.2509	NM_009933	ENSMUSG00000001119	Col6a1	AI747156|Col6a-1	collagen, type VI, alpha 1	protein-coding
mm_122365.1	chr14	39385207	39385211	-	1	NA	intron (NM_001190187, intron 1 of 9)	L1M5|LINE|L1	-87220	NR_131973	432842	Mm.352566	NR_131973		LOC432842	-	uncharacterized LOC432842	ncRNA
mm_31266.1	chr4	45320374	45320383	+	1	NA	exon (NM_025513, exon 1 of 4)	exon (NM_025513, exon 1 of 4)	225	NM_025513	66362	Mm.275788	NM_025513	ENSMUSG00000028322	Exosc3	2310005D06Rik|AI593501|Rrp40	exosome component 3	protein-coding
mm_23967.1	chr3	84977567	84977595	+	1	NA	3' UTR (NM_080428, exon 11 of 11)	3' UTR (NM_080428, exon 11 of 11)	25370	NM_080428	50754	Mm.196475	NM_080428	ENSMUSG00000028086	Fbxw7	1110001A17Rik|AGO|Cdc4|Fbw7|Fbwd6|Fbx30|Fbxo30|Fbxw6|SEL-10	F-box and WD-40 domain protein 7	protein-coding
mm_76409.1	chr8	84893278	84893333	-	1	NA	intron (NM_008097, intron 2 of 10)	intron (NM_008097, intron 2 of 10)	616	NM_001044744	270076	Mm.2475	NM_008097	ENSMUSG00000003809	Gcdh	9030411L18|AI266902|D17825|GCD	glutaryl-Coenzyme A dehydrogenase	protein-coding
mm_4425.1	chr1	172505264	172505300	+	1	NA	exon (NM_178598, exon 2 of 5)	exon (NM_178598, exon 2 of 5)	5036	NM_178598	21346	Mm.271711	NM_178598	ENSMUSG00000026547	Tagln2	2700094C18Rik|SM22beta|Sm22B|Sm22a	transgelin 2	protein-coding
mm_110854.1	chr12	73286699	73286752	-	1	NA	promoter-TSS (NM_029580)	promoter-TSS (NM_029580)	-14	NM_029580	76357	Mm.311344	NM_029580	ENSMUSG00000034442	Trmt5	2610027O18Rik|mKIAA1393	TRM5 tRNA methyltransferase 5	protein-coding
mm_128519.1	chr15	53902473	53902515	-	1	NA	promoter-TSS (NM_177225)	promoter-TSS (NM_177225)	-58	NM_177225	320679	Mm.442455	NM_177225	ENSMUSG00000058656	Samd12	A830094I09Rik	sterile alpha motif domain containing 12	protein-coding
mm_59761.1	chr7	28830108	28830137	+	1	NA	intron (NM_016772, intron 5 of 9)	intron (NM_016772, intron 5 of 9)	-3672	NM_010706	16855	Mm.210336	NM_010706	ENSMUSG00000053964	Lgals4	gal-4	lectin, galactose binding, soluble 4	protein-coding
mm_72161.1	chr8	72219721	72219723	+	1	NA	promoter-TSS (NM_026455)	promoter-TSS (NM_026455)	-8	NM_026455	67922	Mm.28327	NM_026455	ENSMUSG00000003039	Fam32a	2510049I19Rik|AW822030|OTAG-12|Otag12	family with sequence similarity 32, member A	protein-coding
mm_112920.1	chr13	20924762	20924771	+	1	NA	intron (NM_012054, intron 11 of 20)	Lx8b|LINE|L1	130653	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_2476.1	chr1	105845044	105845062	+	1	NA	3' UTR (NM_009399, exon 10 of 10)	3' UTR (NM_009399, exon 10 of 10)	64330	NM_009399	21934	Mm.6251	NM_009399	ENSMUSG00000026321	Tnfrsf11a	Ly109|ODFR|OFE|Rank|TRANCE-R|mRANK	tumor necrosis factor receptor superfamily, member 11a, NFKB activator	protein-coding
mm_134315.1	chr16	15895725	15895732	-	1	NA	intron (NM_146068, intron 17 of 19)	intron (NM_146068, intron 17 of 19)	8442	NM_007679	12609	Mm.347407	NM_007679	ENSMUSG00000071637	Cebpd	c/EBPdelta	CCAAT/enhancer binding protein (C/EBP), delta	protein-coding
mm_61770.1	chr7	83148391	83148401	+	1	NA	promoter-TSS (NM_177895)	promoter-TSS (NM_177895)	-74	NM_177895	330578	Mm.5796	NM_177895	ENSMUSG00000053528	A530021J07Rik	-	Riken cDNA A530021J07 gene	protein-coding
mm_97692.1	chr11	80154104	80154137	+	1	NA	promoter-TSS (NM_172133)	promoter-TSS (NM_172133)	-42	NM_172133	216991	Mm.341520	NM_172133	ENSMUSG00000020709	Adap2	Centa2	ArfGAP with dual PH domains 2	protein-coding
mm_145680.1	chr18	61587570	61587620	+	1	NA	3' UTR (NM_146087, exon 10 of 10)	3' UTR (NM_146087, exon 10 of 10)	32013	NM_146087	93687	Mm.26908	NM_146087	ENSMUSG00000024576	Csnk1a1	2610208K14Rik|4632404G05Rik|5430427P18Rik|CK1a|Csnk1a	casein kinase 1, alpha 1	protein-coding
mm_54223.1	chr6	26766903	26766908	-	1	NA	Intergenic	Intergenic	835479	NR_040771	626904	Mm.126787	NR_040771	ENSMUSG00000106799	Gm20756	-	predicted gene, 20756	ncRNA
mm_165084.1	chr19	47023372	47023382	+	1	NA	exon (NM_146100, exon 3 of 3)	exon (NM_146100, exon 3 of 3)	-8188	NM_001164363	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_82664.1	chr9	22117096	22117120	-	1	NA	intron (NR_030448, intron 3 of 4)	CpG	-2939	NM_170777	66126	Mm.29801	NM_170777	ENSMUSG00000013822	Elof1	1110011K10Rik	ELF1 homolog, elongation factor 1	protein-coding
mm_171.1	chr1	13372917	13372918	+	1	NA	promoter-TSS (NM_001302702)	promoter-TSS (NM_001302702)	-488	NM_001302702	17978	Mm.2537	NM_008678	ENSMUSG00000005886	Ncoa2	D1Ertd433e|GRIP-1|Grip1|KAT13C|NCoA-2|SRC-2|TIF2|bHLHe75	nuclear receptor coactivator 2	protein-coding
mm_148427.1	chr19	3941624	3941646	+	1	NA	exon (NM_019449, exon 4 of 11)	exon (NM_019449, exon 4 of 11)	6449	NM_001161428	54445	Mm.262094	NM_019449	ENSMUSG00000036908	Unc93b1	Unc-93B1|Unc93b	unc-93 homolog B1 (C. elegans)	protein-coding
mm_159614.1	chr4	133176450	133176450	+	1	NA	5' UTR (NM_153423, exon 2 of 9)	5' UTR (NM_153423, exon 2 of 9)	-19205	NR_105984	102466215		NR_105984	ENSMUSG00000099202	Mir7017	Gm27945|mmu-mir-7017	microRNA 7017	ncRNA
mm_120541.1	chr14	67234846	67234865	+	1	NA	5' UTR (NM_001276387, exon 2 of 17)	5' UTR (NM_001276387, exon 2 of 17)	1563	NM_001276387	13592	Mm.319947	NM_010095	ENSMUSG00000022053	Ebf2	D14Ggc1e|EBF-2|Mmot1|O/E-3|OE-3	early B cell factor 2	protein-coding
mm_105890.1	chr11	114934254	114934255	-	1	NA	exon (NM_199221, exon 1 of 4)	exon (NM_199221, exon 1 of 4)	132	NM_001347651	217304	Mm.185355	NM_199221	ENSMUSG00000063193	Cd300lb	CLM-7|Clm7|Gm253|LMIR5	CD300 molecule like family member B	protein-coding
mm_95494.1	chr11	51650902	51650995	+	1	NA	promoter-TSS (NR_027958)	promoter-TSS (NR_027958)	-6	NR_027958	97775	Mm.220299	NM_175289	ENSMUSG00000052563	D930048N14Rik	AI315703|R75254	RIKEN cDNA D930048N14 gene	ncRNA
mm_75243.1	chr8	39642637	39642647	-	1	NA	promoter-TSS (NM_031195)	promoter-TSS (NM_031195)	36	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_81736.1	chr9	113792736	113792752	+	1	NA	promoter-TSS (NM_001286603)	promoter-TSS (NM_001286603)	-586	NM_001286603	76499	Mm.222272	NM_029633	ENSMUSG00000033392	Clasp2	1500004F14Rik|8030404L10Rik|C77448|CLASP2beta|mKIAA0627	CLIP associating protein 2	protein-coding
mm_32997.1	chr4	120516775	120516788	+	1	NA	intron (NM_001159630, intron 12 of 17)	intron (NM_001159630, intron 12 of 17)	-15450	NM_177570	194219	Mm.29788	NM_177570	ENSMUSG00000047518	Slfnl1	4933406A14Rik	schlafen like 1	protein-coding
mm_144142.1	chr18	4994671	4994706	+	1	NA	Intergenic	Intergenic	-51901	NM_153153	225115	Mm.136791	NM_153153	ENSMUSG00000024236	Svil	AU024053|B430302E16Rik	supervillin	protein-coding
mm_146184.1	chr18	75767065	75767072	+	1	NA	Intergenic	Intergenic	-53110	NM_145356	207259	Mm.159332	NM_145356	ENSMUSG00000044646	Zbtb7c	B230208J24Rik|Kr-pok|Zbtb36	zinc finger and BTB domain containing 7C	protein-coding
mm_166004.1	chr4	116685657	116685674	+	1	NA	promoter-TSS (NM_011034)	promoter-TSS (NM_011034)	66	NM_011034	18477	Mm.30929	NM_011034	ENSMUSG00000028691	Prdx1	MSP23|NkefA|OSF-3|OSF3|PAG|Paga|PrdxI|PrxI|TDX2|TPxA|Tdpx2|prx1	peroxiredoxin 1	protein-coding
mm_149293.1	chr19	10688745	10688818	+	1	NA	promoter-TSS (NM_181403)	promoter-TSS (NM_181403)	-34	NM_181403	107305	Mm.19091	NM_181403	ENSMUSG00000048832	Vps37c	5730409F24Rik|AU042646	vacuolar protein sorting 37C	protein-coding
mm_131975.1	chr16	24982700	24982713	+	1	NA	3' UTR (NM_178665, exon 13 of 13)	3' UTR (NM_178665, exon 13 of 13)	-76933	NR_040374	319487	Mm.137341	NR_040374	ENSMUSG00000096960	A230028O05Rik	-	RIKEN cDNA A230028O05 gene	ncRNA
mm_137185.1	chr17	23818946	23818956	+	1	NA	exon (NM_175229, exon 10 of 14)	exon (NM_175229, exon 10 of 14)	10158	NM_026305	67673	Mm.153758	NM_026305	ENSMUSG00000055839	Elob	0610040H15Rik|Tceb2	elongin B	protein-coding
mm_31864.1	chr4	80002823	80002843	+	1	NA	Intergenic	Intergenic	-831380	NM_031202	22178	Mm.30438	NM_031202	ENSMUSG00000005994	Tyrp1	Oca3|TRP-1|TRP1|Tyrp|b|brown|isa	tyrosinase-related protein 1	protein-coding
mm_160266.1	chr7	112759438	112759438	+	1	NA	promoter-TSS (NM_001166585)	promoter-TSS (NM_001166585)	54	NM_001166585	21676	Mm.24685	NM_009346	ENSMUSG00000055320	Tead1	2610024B07Rik|B230114H05Rik|Gtrgeo5|TEAD-1|TEF-1|Tcf13|mTEF-1	TEA domain family member 1	protein-coding
mm_96025.1	chr11	59548637	59548647	+	1	NA	exon (NM_145827, exon 4 of 10)	exon (NM_145827, exon 4 of 10)	5956	NM_145827	216799	Mm.54174	NM_145827	ENSMUSG00000032691	Nlrp3	AGTAVPRL|AII/AVP|Cias1|FCAS|FCU|MWS|Mmig1|NALP3|Pypaf1	NLR family, pyrin domain containing 3	protein-coding
mm_87163.1	chr10	36974722	36974751	+	1	NA	5' UTR (NM_008229, exon 1 of 14)	5' UTR (NM_008229, exon 1 of 14)	192	NM_008229	15182	Mm.19806	NM_008229	ENSMUSG00000019777	Hdac2	D10Wsu179e|YAF1|Yy1bp|mRPD3	histone deacetylase 2	protein-coding
mm_23318.1	chr3	53261200	53261205	+	1	NA	3' UTR (NM_175386, exon 4 of 4)	3' UTR (NM_175386, exon 4 of 4)	202056	NM_172501	212114	Mm.85744	NM_172501	ENSMUSG00000042997	Nhlrc3	4833441N19|8030451K01Rik|mKIAA4083	NHL repeat containing 3	protein-coding
mm_164446.1	chr16	49913166	49913167	+	1	NA	Intergenic	Intergenic	57512	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_69555.1	chr7	135698865	135698897	-	1	NA	exon (NM_001081117, exon 12 of 14)	exon (NM_001081117, exon 12 of 14)	17498	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_29781.1	chr3	127409045	127409064	-	1	NA	promoter-TSS (NM_001327939)	promoter-TSS (NM_001327939)	4	NM_001327939	109676	Mm.220242	NM_178655	ENSMUSG00000032826	Ank2	100043364|AI835472|AW491075|Ank-2|Gm4392	ankyrin 2, brain	protein-coding
mm_60334.1	chr7	44319810	44319835	+	1	NA	intron (NM_001034115, intron 8 of 24)	intron (NM_001034115, intron 8 of 24)	9558	NM_001034115	243961	Mm.360368	NM_001034115	ENSMUSG00000038738	Shank1	-	SH3/ankyrin domain gene 1	protein-coding
mm_34020.1	chr4	138017347	138017354	+	1	NA	intron (NM_172703, intron 2 of 34)	intron (NM_172703, intron 2 of 34)	23894	NM_172703	230861	Mm.268903	NM_172703	ENSMUSG00000028760	Eif4g3	1500002J22Rik|4930523M17Rik|G1-419-52|eIF4GII|repro8	eukaryotic translation initiation factor 4 gamma, 3	protein-coding
mm_111496.1	chr12	99376128	99376132	-	1	NA	intron (NM_183186, intron 2 of 5)	intron (NM_183186, intron 2 of 5)	73944	NM_183186	71375	Mm.341972	NM_183186	ENSMUSG00000033713	Foxn3	5430426H20Rik|AA589593|AW556347|Ches1|Ches1l|HTLFL1	forkhead box N3	protein-coding
mm_159974.1	chr6	112489770	112489770	-	1	NA	promoter-TSS (NM_001081147)	promoter-TSS (NM_001081147)	38	NM_001081147	18430	Mm.333310	NM_001081147	ENSMUSG00000049112	Oxtr	OTR	oxytocin receptor	protein-coding
mm_98354.1	chr11	93600487	93600517	+	1	NA	3' UTR (NM_028296, exon 9 of 9)	3' UTR (NM_028296, exon 9 of 9)	285264	NM_001013375	217109	Mm.379350	NM_001013375	ENSMUSG00000054079	Utp18	6230425C22Rik|6430513M13|Wdr50	UTP18 small subunit processome component	protein-coding
mm_125659.1	chr15	64055374	64055386	+	1	NA	intron (NM_144846, intron 1 of 11)	intron (NM_144846, intron 1 of 11)	5068	NM_144846	223601	Mm.246108	NM_144846	ENSMUSG00000022378	Fam49b	0910001A06Rik|AW122079	family with sequence similarity 49, member B	protein-coding
mm_14178.1	chr2	126758697	126758732	+	1	NA	3' UTR (NM_001252580, exon 19 of 19)	3' UTR (NM_001252580, exon 19 of 19)	24746	NM_029163	75083	Mm.389373	NM_029163	ENSMUSG00000027364	Usp50	1700086G18Rik|4930511O11Rik	ubiquitin specific peptidase 50	protein-coding
mm_9372.1	chr1	172206776	172206786	-	1	NA	promoter-TSS (NM_001329871)	promoter-TSS (NM_001329871)	23	NM_001329871	18611	Mm.544	NM_011063	ENSMUSG00000013698	Pea15a	Mat1|PEA-15|Pea15|Pkcs15	phosphoprotein enriched in astrocytes 15A	protein-coding
mm_149196.1	chr19	9954873	9954888	+	1	NA	Intergenic	Intergenic	-25720	NR_073181	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
mm_92909.1	chr10	83534131	83534141	-	1	NA	promoter-TSS (NM_153543)	promoter-TSS (NM_153543)	4	NM_153543	216188	Mm.263138	NM_153543	ENSMUSG00000020256	Aldh1l2	D330038I09Rik|mtFDH	aldehyde dehydrogenase 1 family, member L2	protein-coding
mm_42127.1	chr5	110906574	110906588	+	1	NA	intron (NM_001267622, intron 2 of 22)	intron (NM_001267622, intron 2 of 22)	26778	NM_001267622	209683	Mm.295660	NM_024477	ENSMUSG00000033209	Ttc28	2310015L07Rik|6030435N04|AI428795|AI851761|BC002262|TPRBK	tetratricopeptide repeat domain 28	protein-coding
mm_152215.1	chr19	8218833	8218849	-	1	NA	promoter-TSS (NM_172776)	promoter-TSS (NM_172776)	-2	NM_172776	236293	Mm.440581	NM_172776	ENSMUSG00000075044	Slc22a29	D630002G06Rik	solute carrier family 22. member 29	protein-coding
mm_109363.1	chr12	109636316	109636378	+	1	NA	TTS (NR_046302)	TTS (NR_046302)	335	NR_046302	449562		NR_046302	ENSMUSG00000088294	AF357425	MBII-48	snoRNA AF357425	snoRNA
mm_694.1	chr1	40580341	40580349	+	1	NA	5' UTR (NM_177084, exon 1 of 12)	5' UTR (NM_177084, exon 1 of 12)	118	NM_177084	110895	Mm.108602	NM_177084	ENSMUSG00000026065	Slc9a4	AW990558|D730009J23Rik|NHE4	solute carrier family 9 (sodium/hydrogen exchanger), member 4	protein-coding
mm_147502.1	chr18	49980327	49980336	-	1	NA	intron (NM_001177759, intron 1 of 1)	intron (NM_001177759, intron 1 of 1)	904	NM_001177759	106869	Mm.27740	NM_134131	ENSMUSG00000062210	Tnfaip8	AA987150|E130304C20Rik|ENSMUSG00000073567|Gg2-1|Gm10539|Nded|Ssc-2|Tipe	tumor necrosis factor, alpha-induced protein 8	protein-coding
mm_50283.1	chr6	47244439	47244449	+	1	NA	promoter-TSS (NM_025771)	promoter-TSS (NM_025771)	48	NM_025771	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding
mm_90811.1	chr10	7792796	7792833	-	1	NA	promoter-TSS (NM_026141)	promoter-TSS (NM_026141)	-80	NM_026141	67418	Mm.38927	NM_026141	ENSMUSG00000015757	Ppil4	3732410E19Rik|3830425H19Rik|AI788954|AW146233|PPIase	peptidylprolyl isomerase (cyclophilin)-like 4	protein-coding
mm_146803.1	chr18	20745579	20745623	-	1	NA	5' UTR (NM_019737, exon 1 of 9)	5' UTR (NM_019737, exon 1 of 9)	803	NM_019737	56386	Mm.393827	NM_019737	ENSMUSG00000056124	B4galt6	AA536803|AU022389	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 6	protein-coding
mm_148992.1	chr19	8618134	8618153	+	1	NA	5' UTR (NM_008766, exon 1 of 10)	5' UTR (NM_008766, exon 1 of 10)	147	NM_008766	18399	Mm.30090	NM_008766	ENSMUSG00000024650	Slc22a6	NKT|Oat1|Orctl1|mOat1	solute carrier family 22 (organic anion transporter), member 6	protein-coding
mm_92323.1	chr10	75668033	75668046	-	1	NA	intron (NM_172549, intron 29 of 36)	CpG	-24031	NM_027890	71733	Mm.247956	NM_027890	ENSMUSG00000006342	Susd2	1200011D11Rik	sushi domain containing 2	protein-coding
mm_146108.1	chr18	74220506	74220535	+	1	NA	exon (NM_028868, exon 13 of 15)	exon (NM_028868, exon 13 of 15)	4308	NM_028868	74322	Mm.17537	NM_028868	ENSMUSG00000024560	Cxxc1	2410002I16Rik|5830420C16Rik|AI426635|Cfp1|Cgbp|PHF18	CXXC finger 1 (PHD domain)	protein-coding
mm_148247.1	chr18	80708085	80708091	-	1	NA	promoter-TSS (NM_016791)	promoter-TSS (NM_016791)	85	NM_001164111	18018	Mm.329560	NM_016791	ENSMUSG00000033016	Nfatc1	2210017P03Rik|AI449492|AV076380|NF-ATc|NFAT2|NFATc|Nfatcb	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 1	protein-coding
mm_113596.1	chr13	41001252	41001298	+	1	NA	5' UTR (NM_026550, exon 1 of 10)	5' UTR (NM_026550, exon 1 of 10)	265	NM_026550	68083	Mm.24789	NM_026550	ENSMUSG00000038683	Pak1ip1	5830431I15Rik|5930415H02Rik|AA419825|AI314040|AW556169|Gdpd1|PIP1	PAK1 interacting protein 1	protein-coding
mm_144073.1	chr17	91065199	91065201	-	1	NA	intron (NM_001346957, intron 1 of 18)	intron (NM_001346957, intron 1 of 18)	24405	NM_001346957	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_147816.1	chr18	61735672	61735682	-	1	NA	exon (NM_178928, exon 17 of 19)	exon (NM_178928, exon 17 of 19)	9287	NR_029432	68982	Mm.441992	NR_029432	ENSMUSG00000098702	1500015A07Rik	-	RIKEN cDNA 1500015A07 gene	ncRNA
mm_154027.1	chr19	53424229	53424236	-	1	NA	Intergenic	Intergenic	-33659	NM_172429	76479	Mm.313687	NM_172429	ENSMUSG00000025024	Smndc1	2410004J23Rik|4933440I19Rik	survival motor neuron domain containing 1	protein-coding
mm_13118.1	chr2	91663955	91663973	+	1	NA	intron (NR_027371, intron 5 of 13)	intron (NR_027371, intron 5 of 13)	10756	NM_146124	228359	Mm.22413	NM_146124	ENSMUSG00000027247	Arhgap1	B230365D05Rik|C76222|Cdc42GAP|p50rhoGAP	Rho GTPase activating protein 1	protein-coding
mm_71819.1	chr8	68892590	68892726	+	1	NA	exon (NM_008509, exon 3 of 10)	exon (NM_008509, exon 3 of 10)	12103	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_88413.1	chr10	77033261	77033284	+	1	NA	promoter-TSS (NM_031196)	promoter-TSS (NM_031196)	60	NM_031196	20509	Mm.265060	NM_031196	ENSMUSG00000001436	Slc19a1	AI323572|RFC|RFC-1|RFC1	solute carrier family 19 (folate transporter), member 1	protein-coding
mm_139198.1	chr17	47655808	47655809	+	1	NA	intron (NM_198421, intron 2 of 6)	intron (NM_198421, intron 2 of 6)	25118	NM_198421	224836	Mm.59393	NM_198421	ENSMUSG00000090115	Usp49	C330046L10Rik|Gm545	ubiquitin specific peptidase 49	protein-coding
mm_62818.1	chr7	113295516	113295526	+	1	NA	exon (NM_007489, exon 12 of 20)	exon (NM_007489, exon 12 of 20)	73818	NM_133700	68815	Mm.238034	NM_133700	ENSMUSG00000038187	Btbd10	1110056N09Rik|Gmrp1	BTB (POZ) domain containing 10	protein-coding
mm_94666.1	chr11	17211913	17211964	+	1	NA	promoter-TSS (NM_178909)	promoter-TSS (NM_178909)	45	NM_178909	103784	Mm.298132	NM_178909	ENSMUSG00000078970	Wdr92	AI553587|HZGJ	WD repeat domain 92	protein-coding
mm_157229.1	chrX	15111457	15111471	-	1	NA	promoter-TSS (NR_033171)	promoter-TSS (NR_033171)	25	NR_033171	67395	Mm.50369	NM_026128	ENSMUSG00000045217	Ppp1r2-ps9	4930403L05Rik	protein phosphatase 1, regulatory (inhibitor) subunit 2, pseudogene 9	pseudo
mm_46247.1	chr5	99248554	99248569	-	1	NA	intron (NM_145839, intron 1 of 13)	intron (NM_145839, intron 1 of 13)	4366	NM_181318	320292	Mm.259074	NM_145839	ENSMUSG00000089809	Rasgef1b	4732452O09Rik|GPIgamma4|Gpig4	RasGEF domain family, member 1B	protein-coding
mm_106393.1	chr11	118796740	118796753	-	1	NA	intron (NM_001039168, intron 2 of 14)	intron (NM_001039168, intron 2 of 14)	-35705	NM_001285438	52897	Mm.341103	NM_001024931	ENSMUSG00000025576	Rbfox3	Fox-3|Hrnbp3|NeuN|Neuna60	RNA binding protein, fox-1 homolog (C. elegans) 3	protein-coding
mm_70248.1	chr8	3470814	3470823	+	1	NA	promoter-TSS (NM_029598)	promoter-TSS (NM_029598)	-44	NM_029598	76406	Mm.74996	NM_029598	ENSMUSG00000040340	1700019B03Rik	-	RIKEN cDNA 1700019B03 gene	protein-coding
mm_5719.1	chr1	44101662	44101673	-	1	NA	intron (NM_029368, intron 2 of 7)	intron (NM_029368, intron 2 of 7)	721	NM_029368	75623	Mm.348017	NM_029368	ENSMUSG00000026049	Tex30	1700029F09Rik|3110030D08Rik	testis expressed 30	protein-coding
mm_129130.1	chr15	76195667	76195677	-	1	NA	promoter-TSS (NM_201394)	promoter-TSS (NM_201394)	38	NM_201394	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
mm_164495.1	chr16	91056426	91056432	-	1	NA	intron (NM_001163695, intron 1 of 1)	intron (NM_001163695, intron 1 of 1)	-12050	NM_026110	67367	Mm.347	NM_026110	ENSMUSG00000022974	Paxbp1	1810007M14Rik|C21orf66|Gcfc|Gcfc1|Pax3/7bp	PAX3 and PAX7 binding protein 1	protein-coding
mm_139762.1	chr17	64600787	64600793	+	1	NA	promoter-TSS (NM_008549)	promoter-TSS (NM_008549)	-859	NM_008549	17158	Mm.2433	NM_008549	ENSMUSG00000024085	Man2a1	Mana-2|Mana2|Map-2	mannosidase 2, alpha 1	protein-coding
mm_113362.1	chr13	32965273	32965283	+	1	NA	promoter-TSS (NM_011454)	promoter-TSS (NM_011454)	-235	NM_011454	20708	Mm.36526	NM_011454	ENSMUSG00000042842	Serpinb6b	NK13|Spi12|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 6b	protein-coding
mm_67934.1	chr7	100101434	100101460	-	1	NA	intron (NM_133692, intron 5 of 11)	intron (NM_133692, intron 5 of 11)	20053	NM_133692	67967	Mm.37562	NM_133692	ENSMUSG00000030726	Pold3	2410142G14Rik|C85233|P66|P68	polymerase (DNA-directed), delta 3, accessory subunit	protein-coding
mm_84894.1	chr9	79793509	79793519	-	1	NA	promoter-TSS (NR_040734)	promoter-TSS (NR_040734)	-84	NM_133718	69981	Mm.486324	NM_133718	ENSMUSG00000032328	Tmem30a	2010200I23Rik|AW540225|Cdc50a|D9Wsu20e	transmembrane protein 30A	protein-coding
mm_64653.1	chr7	4149482	4149517	-	1	NA	exon (NM_175529, exon 1 of 1)	exon (NM_175529, exon 1 of 1)	373	NM_175529	243813	Mm.347643	NM_175529	ENSMUSG00000043432	Leng9	9530024C23Rik|F630035L11Rik	leukocyte receptor cluster (LRC) member 9	protein-coding
mm_24541.1	chr3	93293080	93293098	+	1	NA	Intergenic	Intergenic	-26660	NM_133698	68723	Mm.208047	NM_133698	ENSMUSG00000041991	Hrnr	1110033K19Rik|A530063N20Rik|S100a18	hornerin	protein-coding
mm_157654.1	chrX	57326756	57326779	-	1	NA	intron (NM_152801, intron 2 of 21)	intron (NM_152801, intron 2 of 21)	11962	NM_152801	73341	Mm.261443	NM_152801	ENSMUSG00000031133	Arhgef6	1600028C08Rik|1700038J06Rik|4930592P22Rik|alpha-PIX	Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_18544.1	chr2	64975684	64975691	-	1	NA	intron (NM_016719, intron 2 of 13)	intron (NM_016719, intron 2 of 13)	47079	NM_016719	50915	Mm.214554	NM_016719	ENSMUSG00000026888	Grb14	AI505286	growth factor receptor bound protein 14	protein-coding
mm_40880.1	chr5	74535467	74535524	+	1	NA	promoter-TSS (NM_001159573)	promoter-TSS (NM_001159573)	13	NM_001159574	66899	Mm.272468	NM_024183	ENSMUSG00000029227	Fip1l1	1300019H17Rik|Rje	FIP1 like 1 (S. cerevisiae)	protein-coding
mm_113587.1	chr13	40887236	40887252	+	1	NA	5' UTR (NM_008105, exon 1 of 3)	5' UTR (NM_008105, exon 1 of 3)	486	NM_008105	14538	Mm.314757	NM_008105	ENSMUSG00000021360	Gcnt2	5330430K10Rik|IGnT|IGnTA|IGnTB|IGnTC	glucosaminyl (N-acetyl) transferase 2, I-branching enzyme	protein-coding
mm_1436.1	chr1	67209584	67209595	+	1	NA	intron (NM_001080809, intron 28 of 37)	intron (NM_001080809, intron 28 of 37)	86562	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_121655.1	chr14	11162009	11162041	-	1	NA	promoter-TSS (NM_001308285)	promoter-TSS (NM_001308285)	10	NM_010210	14198	Mm.397619	NM_010210	ENSMUSG00000060579	Fhit	AW045638|Fra14A2	fragile histidine triad gene	protein-coding
mm_26683.1	chr3	156561951	156561993	+	1	NA	promoter-TSS (NR_040400)	promoter-TSS (NR_040400)	178	NM_001039094	320840	Mm.317293	NM_177274	ENSMUSG00000040037	Negr1	5330422G01Rik|KILON|Ntra	neuronal growth regulator 1	protein-coding
mm_72005.1	chr8	70698527	70698545	+	1	NA	5' UTR (NM_001286944, exon 1 of 1)	5' UTR (NM_001286944, exon 1 of 1)	797	NM_001286944	16478	Mm.419851	NM_010592	ENSMUSG00000071076	Jund	Jund1	jun D proto-oncogene	protein-coding
mm_142608.1	chr17	46812357	46812369	-	1	NA	intron (NM_001100452, intron 5 of 10)	intron (NM_001100452, intron 5 of 10)	19050	NM_001100452	210982	Mm.37642	NM_001100452	ENSMUSG00000036568	Gltscr1l	mKIAA0240	GLTSCR1-like	protein-coding
mm_7669.1	chr1	128588701	128588732	-	1	NA	3' UTR (NM_009911, exon 2 of 2)	3' UTR (NM_009911, exon 2 of 2)	3583	NM_009911	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding
mm_144363.1	chr18	20376840	20376846	+	1	NA	5' UTR (NM_181682, exon 1 of 15)	5' UTR (NM_181682, exon 1 of 15)	114	NM_181682	225256	Mm.269128	NM_181682	ENSMUSG00000061928	Dsg1b	Dsg5|dsg1-beta	desmoglein 1 beta	protein-coding
mm_11504.1	chr2	32565748	32565775	+	1	NA	exon (NM_153560, exon 8 of 11)	exon (NM_153560, exon 8 of 11)	-5097	NM_010073	13481	Mm.22001	NM_010073	ENSMUSG00000026810	Dpm2	AW557993|R75484	dolichol-phosphate (beta-D) mannosyltransferase 2	protein-coding
mm_169828.1	chr16	24529344	24529345	+	1	NA	promoter-TSS (NR_038091)	promoter-TSS (NR_038091)	30	NR_038091	624582	Mm.439775	NR_038091		Morf4l1-ps1	A730098P11Rik	mortality factor 4 like 1, pseudogene 1	pseudo
mm_40230.1	chr5	37286472	37286490	+	1	NA	exon (NM_001136058, exon 12 of 14)	exon (NM_001136058, exon 12 of 14)	40717	NM_007765	12933	Mm.290995	NM_007765	ENSMUSG00000029121	Crmp1	CRMP-1|DRP-1|Dpysl1|ULIP-3|Ulip3	collapsin response mediator protein 1	protein-coding
mm_48337.1	chr5	139130017	139130042	-	1	NA	promoter-TSS (NM_008923)	promoter-TSS (NM_008923)	-277	NM_008923	19085	Mm.306163	NM_008923	ENSMUSG00000025855	Prkar1b	AI385716|RIbeta	protein kinase, cAMP dependent regulatory, type I beta	protein-coding
mm_39939.1	chr5	31730482	31730494	+	1	NA	exon (NM_181280, exon 3 of 13)	exon (NM_181280, exon 3 of 13)	32438	NM_144541	107976	Mm.482126	NM_144541	ENSMUSG00000052139	Bre	6030405P19Rik|AI429776|B830038C02Rik	brain and reproductive organ-expressed protein	protein-coding
mm_38303.1	chr4	136896416	136896429	-	1	NA	exon (NM_007572, exon 3 of 3)	exon (NM_007572, exon 3 of 3)	2422	NM_007572	12259	Mm.439957	NM_007572	ENSMUSG00000036887	C1qa	AI255395|C1q	complement component 1, q subcomponent, alpha polypeptide	protein-coding
mm_117749.1	chr13	95892503	95892519	-	1	NA	promoter-TSS (NM_027711)	promoter-TSS (NM_027711)	-589	NM_027711	544963	Mm.38878	NM_027711	ENSMUSG00000021676	Iqgap2	4933417J23Rik|A630053O10|AI788777	IQ motif containing GTPase activating protein 2	protein-coding
mm_19641.1	chr2	102835837	102835871	-	1	NA	intron (NM_001177786, intron 5 of 11)	intron (NM_001177786, intron 5 of 11)	65811	NM_001177785	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_169673.1	chr15	65928980	65928984	-	1	NA	intron (NM_001145096, intron 15 of 16)	intron (NM_001145096, intron 15 of 16)	-16695	NM_010953	18256	Mm.41776	NM_010953	ENSMUSG00000015001	Oc90	Ocn-95|PLA2L|Pla2ll|oc95	otoconin 90	protein-coding
mm_129432.1	chr15	78494373	78494381	-	1	NA	intron (NM_008368, intron 1 of 9)	intron (NM_008368, intron 1 of 9)	689	NM_008368	16185	Mm.35287	NM_008368	ENSMUSG00000068227	Il2rb	CD122|IL-15Rbeta|IL15Rbeta|Il-2/15Rbeta|Il-2Rbeta|p70	interleukin 2 receptor, beta chain	protein-coding
mm_79713.1	chr9	61372466	61372478	+	1	NA	5' UTR (NM_009389, exon 1 of 20)	5' UTR (NM_009389, exon 1 of 20)	106	NM_001083927	21887	Mm.24255	NM_009389	ENSMUSG00000032280	Tle3	2610103N05Rik|ESG|Grg3a|Grg3b|mKIAA1547	transducin-like enhancer of split 3	protein-coding
mm_99294.1	chr11	101330864	101330874	+	1	NA	5' UTR (NM_009675, exon 1 of 4)	5' UTR (NM_009675, exon 1 of 4)	263	NM_009675	11754	Mm.67281	NM_009675	ENSMUSG00000019326	Aoc3	SSAO|VAP1	amine oxidase, copper containing 3	protein-coding
mm_145337.1	chr18	56432117	56432163	+	1	NA	promoter-TSS (NM_026240)	promoter-TSS (NM_026240)	8	NM_026240	107022	Mm.24356	NM_026240	ENSMUSG00000001700	Gramd3	9030613F08Rik|9130427A09Rik|AW061306|NS3TP2	GRAM domain containing 3	protein-coding
mm_159643.1	chr4	143950807	143950807	-	1	NA	exon (NM_001126315, exon 1 of 3)	exon (NM_001126315, exon 1 of 3)	209	NM_001126315	329984		NM_001126315	ENSMUSG00000078511	Pramef25	Gm13109|OTTMUSG00000010441	PRAME family member 25	protein-coding
mm_37014.1	chr4	113245312	113245314	-	1	NA	intron (NM_001103199, intron 2 of 48)	MYSERV6-int|LTR|ERVK	41660	NM_001103199	230622	Mm.291107	NM_001103199	ENSMUSG00000087194	Skint6	OTTMUSG00000008519	selection and upkeep of intraepithelial T cells 6	protein-coding
mm_122829.1	chr14	54712121	54712134	-	1	NA	promoter-TSS (NM_207131)	promoter-TSS (NM_207131)	47	NM_207131	110794	Mm.236223	NM_207131	ENSMUSG00000052435	Cebpe	C/EBPe|CRP1|Gm294	CCAAT/enhancer binding protein (C/EBP), epsilon	protein-coding
mm_73189.1	chr8	95352259	95352329	+	1	NA	promoter-TSS (NM_008609)	promoter-TSS (NM_008609)	-2	NM_008609	17388	Mm.217116	NM_008609	ENSMUSG00000031790	Mmp15	AI503551|MT-MMP 2|MT2-MMP	matrix metallopeptidase 15	protein-coding
mm_24251.1	chr3	89177464	89177543	+	1	NA	TTS (NM_007712)	TTS (NM_007712)	112	NM_001309909	24045	Mm.257052	NM_011886	ENSMUSG00000028049	Scamp3	Sc3	secretory carrier membrane protein 3	protein-coding
mm_94658.1	chr11	17159275	17159357	+	1	NA	promoter-TSS (NM_024459)	promoter-TSS (NM_024459)	18	NM_024459	19058	Mm.41840	NM_024459	ENSMUSG00000033953	Ppp3r1	CaNB1|Cnb1|MCIP1	protein phosphatase 3, regulatory subunit B, alpha isoform (calcineurin B, type I)	protein-coding
mm_29212.1	chr3	106790144	106790154	-	1	NA	promoter-TSS (NM_007651)	promoter-TSS (NM_007651)	0	NM_007651	12508	Mm.316861	NM_007651	ENSMUSG00000040747	Cd53	AI323659|Ox-44|Tspan25	CD53 antigen	protein-coding
mm_90117.1	chr10	117277982	117278020	+	1	NA	3' UTR (NM_017372, exon 4 of 4)	3' UTR (NM_017372, exon 4 of 4)	4271	NM_017372	17105	Mm.45436	NM_017372	ENSMUSG00000069516	Lyz2	AI326280|Lys|Lysm|Lyzf2|Lyzs|Lzm|Lzm-s1|Lzp	lysozyme 2	protein-coding
mm_21901.1	chr2	166156285	166156317	-	1	NA	promoter-TSS (NM_028072)	promoter-TSS (NM_028072)	-618	NM_028072	72043	Mm.1011	NM_028072	ENSMUSG00000006800	Sulf2	2010004N24Rik|AU020235|MSulf-2|mKIAA1247	sulfatase 2	protein-coding
mm_6632.1	chr1	78488850	78488866	-	1	NA	promoter-TSS (NM_011811)	promoter-TSS (NM_011811)	39	NR_102758	23874	Mm.17898	NM_011811	ENSMUSG00000026245	Farsb	C76708|Farsa|Farsl|Farslb|Frsb	phenylalanyl-tRNA synthetase, beta subunit	protein-coding
mm_22424.1	chr2	181592734	181592790	-	1	NA	promoter-TSS (NM_001164597)	promoter-TSS (NM_001164597)	-301	NM_001164597	269401	Mm.386888	NM_001164597	ENSMUSG00000000823	Zfp512b	Gm632|Znf512b	zinc finger protein 512B	protein-coding
mm_52278.1	chr6	108660435	108660446	+	1	NA	promoter-TSS (NM_011498)	promoter-TSS (NM_011498)	-189	NM_011498	20893	Mm.2436	NM_011498	ENSMUSG00000030103	Bhlhe40	Bhlhb2|C130042M06Rik|CR8|Clast5|Dec1|Sharp2|Stra13|Stra14	basic helix-loop-helix family, member e40	protein-coding
mm_92633.1	chr10	80329405	80329421	-	1	NA	promoter-TSS (NM_139292)	promoter-TSS (NM_139292)	60	NM_008793	18551	Mm.299916	NM_008793	ENSMUSG00000020131	Pcsk4	AI647044|L21221|NEC 3|NEC3|PC4|SPC5	proprotein convertase subtilisin/kexin type 4	protein-coding
mm_27990.1	chr3	82145739	82145754	-	1	NA	5' UTR (NM_021896, exon 1 of 9)	5' UTR (NM_021896, exon 1 of 9)	131	NM_021896	60596	Mm.143831	NM_021896	ENSMUSG00000033910	Gucy1a3	1200016O07Rik|sGC-alpha1	guanylate cyclase 1, soluble, alpha 3	protein-coding
mm_141178.1	chr17	26841520	26841524	-	1	NA	promoter-TSS (NM_008700)	promoter-TSS (NM_008700)	43	NM_008700	18091	Mm.41974	NM_008700	ENSMUSG00000015579	Nkx2-5	Csx|Nkx-2.5|Nkx2.5|tinman	NK2 homeobox 5	protein-coding
mm_133271.1	chr16	77374706	77374730	+	1	NA	intron (NR_015543, intron 2 of 4)	B1_Mm|SINE|Alu	45390	NR_015543	77994	Mm.394688	NR_015543	ENSMUSG00000090386	Mir99ahg	2810055G20Rik|D730043B02Rik	Mir99a and Mirlet7c-1 host gene (non-protein coding)	ncRNA
mm_46525.1	chr5	105400104	105400114	-	1	NA	Intergenic	ORR1D1|LTR|ERVL-MaLR	-15666	NM_001033550	433926	Mm.439781	NM_001033550	ENSMUSG00000070639	Lrrc8b	R75581|Ta-lrrp|mKIAA0231	leucine rich repeat containing 8 family, member B	protein-coding
mm_37132.1	chr4	116708541	116708555	-	1	NA	promoter-TSS (NM_026714)	promoter-TSS (NM_026714)	-163	NM_025962	67096	Mm.252785	NM_025962	ENSMUSG00000028690	Mmachc	1810037K07Rik|CblC	methylmalonic aciduria cblC type, with homocystinuria	protein-coding
mm_81540.1	chr9	110245110	110245190	+	1	NA	5' UTR (NM_013884, exon 1 of 5)	5' UTR (NM_013884, exon 1 of 5)	1367	NM_001166273	29873	Mm.38496	NM_013884	ENSMUSG00000032482	Cspg5	Caleb|Ngc	chondroitin sulfate proteoglycan 5	protein-coding
mm_144577.1	chr18	31910763	31910848	+	1	NA	exon (NM_026006, exon 1 of 1)	exon (NM_026006, exon 1 of 1)	1098	NM_026006	67158	Mm.31537	NM_026006	ENSMUSG00000044982	Sft2d3	2610206C24Rik|AI847965|AW046173	SFT2 domain containing 3	protein-coding
mm_47040.1	chr5	116024230	116024279	-	1	NA	5' UTR (NM_031869, exon 1 of 7)	5' UTR (NM_031869, exon 1 of 7)	174	NM_031869	19079	Mm.458152	NM_031869	ENSMUSG00000029513	Prkab1	1300015D22Rik|AU021155|E430008F22	protein kinase, AMP-activated, beta 1 non-catalytic subunit	protein-coding
mm_42505.1	chr5	115499749	115499751	+	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	-6926	NM_011223	19303	Mm.18714	NM_011223	ENSMUSG00000029528	Pxn	AW108311|AW123232|Pax	paxillin	protein-coding
mm_51323.1	chr6	72347302	72347379	+	1	NA	promoter-TSS (NM_026696)	promoter-TSS (NM_026696)	23	NM_026696	68364	Mm.52711	NM_026696	ENSMUSG00000058706	0610030E20Rik	1500031N04Rik|2810411C16Rik|AI461894	RIKEN cDNA 0610030E20 gene	protein-coding
mm_89796.1	chr10	102512084	102512105	+	1	NA	promoter-TSS (NM_146240)	promoter-TSS (NM_146240)	-128	NM_146240	237504	Mm.282672	NM_146240	ENSMUSG00000044921	Rassf9	AW322107|Pamci	Ras association (RalGDS/AF-6) domain family (N-terminal) member 9	protein-coding
mm_133262.1	chr16	77340572	77340604	+	1	NA	intron (NR_015543, intron 1 of 4)	L1_Mur3|LINE|L1	11260	NR_015543	77994	Mm.394688	NR_015543	ENSMUSG00000090386	Mir99ahg	2810055G20Rik|D730043B02Rik	Mir99a and Mirlet7c-1 host gene (non-protein coding)	ncRNA
mm_116190.1	chr13	31431055	31431068	-	1	NA	Intergenic	Intergenic	-127109	NM_008239	15220	Mm.44235	NM_008239	ENSMUSG00000038415	Foxq1	HFH-1|Hfh1|Hfh1l|sa	forkhead box Q1	protein-coding
mm_132404.1	chr16	35001668	35001731	+	1	NA	3' UTR (NM_139300, exon 32 of 32)	3' UTR (NM_139300, exon 32 of 32)	-20722	NM_023587	70757	Mm.27286	NM_023587	ENSMUSG00000035376	Hacd2	6330408J20Rik|AI255777|AI481689|Hcad2|Ptplb	3-hydroxyacyl-CoA dehydratase 2	protein-coding
mm_141104.1	chr17	26021796	26021807	-	1	NA	promoter-TSS (NM_153140)	promoter-TSS (NM_153140)	59	NM_153140	215445	Mm.41191	NM_153140	ENSMUSG00000037098	Rab11fip3	Cart1|D030060O14Rik|Rab11-FIP3|mKIAA0665	RAB11 family interacting protein 3 (class II)	protein-coding
mm_32607.1	chr4	112072641	112072656	+	1	NA	intron (NM_001347180, intron 1 of 11)	intron (NM_001347180, intron 1 of 11)	632	NM_001347180	320640	Mm.253775	NM_178786	ENSMUSG00000055960	Skint4	9530098N22Rik	selection and upkeep of intraepithelial T cells 4	protein-coding
mm_155367.1	chrX	71215022	71215063	+	1	NA	promoter-TSS (NM_001164192)	promoter-TSS (NM_001164192)	36	NM_001164193	17772	Mm.274981	NM_019926	ENSMUSG00000031337	Mtm1	AF073996|Mtm|mKIAA4176	X-linked myotubular myopathy gene 1	protein-coding
mm_77756.1	chr8	128680638	128680681	-	1	NA	Intergenic	Intergenic	-4995	NM_010578	16412	Mm.263396	NM_010578	ENSMUSG00000025809	Itgb1	4633401G24Rik|AA409975|AA960159|CD29|ENSMUSG00000051907|Fnrb|Gm9863|gpIIa	integrin beta 1 (fibronectin receptor beta)	protein-coding
mm_110491.1	chr12	52602312	52602348	-	1	NA	promoter-TSS (NR_045910)	promoter-TSS (NR_045910)	-8	NR_045910	73278	Mm.396209	NR_045910	ENSMUSG00000100315	1700031P21Rik	-	RIKEN cDNA 1700031P21 gene	ncRNA
mm_19692.1	chr2	103485139	103485158	-	1	NA	promoter-TSS (NM_009804)	promoter-TSS (NM_009804)	5	NM_009804	12359	Mm.4215	NM_009804	ENSMUSG00000027187	Cat	2210418N07|Cas-1|Cas1|Cs-1	catalase	protein-coding
mm_169162.1	chr13	65415363	65415382	+	1	NA	Intergenic	Intergenic	136518	NM_178364	170936	Mm.151546	NM_178364	ENSMUSG00000021514	Zfp369	B930030B22Rik|D230020H11Rik|NRIF2	zinc finger protein 369	protein-coding
mm_83119.1	chr9	40403682	40403692	-	1	NA	intron (NM_172768, intron 2 of 19)	intron (NM_172768, intron 2 of 19)	52077	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_119369.1	chr14	41122557	41122573	+	1	NA	exon (NM_133653, exon 10 of 10)	exon (NM_133653, exon 10 of 10)	-9223	NM_023134	20387	Mm.46062	NM_023134	ENSMUSG00000021789	Sftpa1	SP-A|Sftp-1|Sftp1	surfactant associated protein A1	protein-coding
mm_139736.1	chr17	58996244	58996278	+	1	NA	promoter-TSS (NM_001331155)	promoter-TSS (NM_001331155)	10	NM_001331155	75039	Mm.444693	NM_001331155		Nudt12os	4930505H01Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 12, opposite strand	protein-coding
mm_102460.1	chr11	59839804	59839818	-	1	NA	promoter-TSS (NM_011991)	promoter-TSS (NM_011991)	-44	NM_011991	26572	Mm.40	NM_011991	ENSMUSG00000019373	Cops3	Csn3|Sgn3	COP9 signalosome subunit 3	protein-coding
mm_41422.1	chr5	90891832	90891842	+	1	NA	intron (NM_008176, intron 3 of 3)	intron (NM_008176, intron 3 of 3)	592	NM_008176	14825	Mm.21013	NM_008176	ENSMUSG00000029380	Cxcl1	Fsp|Gro1|KC|Mgsa|N51|Scyb1|gro	chemokine (C-X-C motif) ligand 1	protein-coding
mm_81682.1	chr9	111059593	111059609	+	1	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	-2083	NM_001302376	54199	Mm.7336	NM_017466	ENSMUSG00000043953	Ccrl2	1810047I05Rik|Ackr5|CCR11|Cmkbr1l2|E01|L-CCR	chemokine (C-C motif) receptor-like 2	protein-coding
mm_80483.1	chr9	78230666	78230675	+	1	NA	promoter-TSS (NM_008181)	promoter-TSS (NM_008181)	1	NM_008181	14857	Mm.467426	NM_008181	ENSMUSG00000074183	Gsta1	Gst2-1|OTTMUSG00000031890	glutathione S-transferase, alpha 1 (Ya)	protein-coding
mm_77094.1	chr8	110805864	110805952	-	1	NA	promoter-TSS (NM_001135100)	promoter-TSS (NM_001135100)	16	NM_029646	76527	Mm.77697	NM_029646	ENSMUSG00000031750	Il34	2010004A03Rik|AI593503	interleukin 34	protein-coding
mm_747.1	chr1	43542509	43542549	+	1	NA	intron (NM_010879, intron 3 of 4)	intron (NM_010879, intron 3 of 4)	96778	NM_010879	17974	Mm.389903	NM_010879	ENSMUSG00000066877	Nck2	4833426I10Rik|Grb4|NCKbeta|Nck-2	non-catalytic region of tyrosine kinase adaptor protein 2	protein-coding
mm_67448.1	chr7	80391563	80391576	-	1	NA	exon (NM_001081454, exon 15 of 16)	exon (NM_001081454, exon 15 of 16)	-3623	NM_010194	14159	Mm.48757	NM_010194	ENSMUSG00000053158	Fes	AI586313|BB137047|FPS|c-fes	feline sarcoma oncogene	protein-coding
mm_111542.1	chr12	100888074	100888081	-	1	NA	intron (NM_001177673, intron 1 of 2)	intron (NM_001177673, intron 1 of 2)	11447	NM_001177674	238377	Mm.32160	NM_175493	ENSMUSG00000047415	Gpr68	BB131428|Ogr1	G protein-coupled receptor 68	protein-coding
mm_112958.1	chr13	21179984	21179992	+	1	NA	promoter-TSS (NM_009054)	promoter-TSS (NM_009054)	57	NM_009054	19720	Mm.314056	NM_009054	ENSMUSG00000021326	Trim27	AW538890|Gm19403|Rfp	tripartite motif-containing 27	protein-coding
mm_20808.1	chr2	144331372	144331392	-	1	NA	promoter-TSS (NM_152947)	promoter-TSS (NM_152947)	-20	NM_152947	107586	Mm.252750	NM_026924	ENSMUSG00000037279	Ovol2	1700108N11Rik|1810007D21Rik|M-OVO|M-OVO-A|M-OVO-B|MOVO|Ovo2|Zfp339|movo2	ovo like zinc finger 2	protein-coding
mm_89987.1	chr10	111996141	111996145	+	1	NA	intron (NM_028608, intron 1 of 5)	L1MA7|LINE|L1	1121	NM_028608	73690	Mm.173790	NM_028608	ENSMUSG00000056888	Glipr1	2410114O14Rik|RTVP-1|RTVP1|mRTVP-1	GLI pathogenesis-related 1 (glioma)	protein-coding
mm_34218.1	chr4	140971981	140971996	+	1	NA	intron (NM_023374, intron 3 of 7)	intron (NM_023374, intron 3 of 7)	10717	NM_023374	67680	Mm.246965	NM_023374	ENSMUSG00000009863	Sdhb	0710008N11Rik	succinate dehydrogenase complex, subunit B, iron sulfur (Ip)	protein-coding
mm_100243.1	chr11	117266275	117266298	+	1	NA	promoter-TSS (NM_001113487)	promoter-TSS (NM_001113487)	40	NM_001113487	53860	Mm.38450	NM_017380	ENSMUSG00000059248	Sept9	MSF1|Msf|PNUTL4|Sint1	septin 9	protein-coding
mm_118712.1	chr14	22185126	22185133	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	165417	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_36018.1	chr4	56960312	56960325	-	1	NA	3' UTR (NM_001142965, exon 5 of 5)	3' UTR (NM_001142965, exon 5 of 5)	-12889	NM_175518	242474	Mm.296632	NM_175518	ENSMUSG00000055296	Tmem245	A630051L19Rik|AI957324|D730040F13Rik	transmembrane protein 245	protein-coding
mm_80044.1	chr9	69239124	69239126	+	1	NA	intron (NM_013646, intron 2 of 10)	intron (NM_013646, intron 2 of 10)	-50716	NM_001289916	19883	Mm.378450	NM_013646	ENSMUSG00000032238	Rora	9530021D13Rik|Nr1f1|ROR1|ROR2|ROR3|nmf267|sg|staggerer|tmgc26	RAR-related orphan receptor alpha	protein-coding
mm_879.1	chr1	52177377	52177378	+	1	NA	intron (NM_001081081, intron 14 of 17)	intron (NM_001081081, intron 14 of 17)	55855	NM_001081081	14660	Mm.398608	NM_001081081	ENSMUSG00000026103	Gls	6330442B14|AI314027|B230365M23Rik	glutaminase	protein-coding
mm_40007.1	chr5	33018770	33018770	+	1	NA	promoter-TSS (NM_011738)	promoter-TSS (NM_011738)	-46	NM_011738	22629	Mm.332314	NM_011738	ENSMUSG00000018965	Ywhah	-	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta polypeptide	protein-coding
mm_73697.1	chr8	111643457	111643490	+	1	NA	promoter-TSS (NM_011742)	promoter-TSS (NM_011742)	30	NM_011742	22640	Mm.4184	NM_011742	ENSMUSG00000055835	Zfp1	Fnp-1|Zfp-1|mkr-1	zinc finger protein 1	protein-coding
mm_126234.1	chr15	78967333	78967335	+	1	NA	exon (NM_001039155, exon 8 of 8)	exon (NM_001039155, exon 8 of 8)	-15722	NM_001024716	110253	Mm.123714	NM_138579	ENSMUSG00000033088	Triobp	AI428493|EST478828|Tara|mKIAA1662	TRIO and F-actin binding protein	protein-coding
mm_145958.1	chr18	67774880	67774882	+	1	NA	promoter-TSS (NM_001039088)	promoter-TSS (NM_001039088)	5	NM_001039088	72124	Mm.307315	NM_028112	ENSMUSG00000079614	Seh1l	2610007A16Rik|AW540070|SEC13L|SEH1A|SEH1B|Seh1	SEH1-like (S. cerevisiae	protein-coding
mm_59243.1	chr7	24780946	24780954	+	1	NA	exon (NM_007675, exon 3 of 4)	exon (NM_007675, exon 3 of 4)	3746	NM_007675	26366	Mm.30300	NM_007675	ENSMUSG00000054169	Ceacam10	Bgp3|Cea10	carcinoembryonic antigen-related cell adhesion molecule 10	protein-coding
mm_146669.1	chr18	12232720	12232731	-	1	NA	intron (NM_008720, intron 1 of 24)	RMER1C|Other|Other	3661	NM_008720	18145	Mm.3484	NM_008720	ENSMUSG00000024413	Npc1	A430089E03Rik|C85354|D18Ertd139e|D18Ertd723e|lcsd|nmf164|spm	Niemann-Pick type C1	protein-coding
mm_74092.1	chr8	122568022	122568060	+	1	NA	promoter-TSS (NM_026014)	promoter-TSS (NM_026014)	26	NM_026014	67177	Mm.21873	NM_026014	ENSMUSG00000006585	Cdt1	2610318F11Rik|AW545653|C76791|Ris2	chromatin licensing and DNA replication factor 1	protein-coding
mm_160116.1	chr7	27233404	27233404	+	1	NA	intron (NM_133770, intron 1 of 14)	intron (NM_133770, intron 1 of 14)	391	NM_133770	76889	Mm.124728	NM_133770	ENSMUSG00000003762	Coq8b	0610012P18Rik|Adck4	coenzyme Q8B	protein-coding
mm_10.1	chr1	4828576	4828616	+	1	NA	exon (NM_008866, exon 3 of 9)	exon (NM_008866, exon 3 of 9)	20703	NM_008866	18777	Mm.299955	NM_008866	ENSMUSG00000025903	Lypla1	Pla1a	lysophospholipase 1	protein-coding
mm_45962.1	chr5	90464881	90464914	-	1	NA	exon (NM_009654, exon 5 of 15)	exon (NM_009654, exon 5 of 15)	4027	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_43794.1	chr5	142812159	142812173	+	1	NA	intron (NM_178242, intron 2 of 15)	intron (NM_178242, intron 2 of 15)	5221	NM_178242	231861	Mm.354649	NM_178242	ENSMUSG00000039477	Tnrc18	BC025631|EG381742|Zfp469	trinucleotide repeat containing 18	protein-coding
mm_65217.1	chr7	19698384	19698405	-	1	NA	promoter-TSS (NM_001305819)	promoter-TSS (NM_001305819)	4	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_89544.1	chr10	94575306	94575325	+	1	NA	promoter-TSS (NM_177026)	promoter-TSS (NM_177026)	58	NM_001168684	319880	Mm.23047	NM_172051	ENSMUSG00000020023	Tmcc3	AW488095|C630016B22Rik|C88213|Tmcc1	transmembrane and coiled coil domains 3	protein-coding
mm_25207.1	chr3	103832563	103832567	+	1	NA	promoter-TSS (NM_001142960)	promoter-TSS (NM_001142960)	-131	NM_001142959	229672	Mm.297245	NM_001142959	ENSMUSG00000044165	Bcl2l15	Bfk|Gm566	BCLl2-like 15	protein-coding
mm_114120.1	chr13	55152802	55152833	+	1	NA	promoter-TSS (NM_008011)	promoter-TSS (NM_008011)	-1	NM_008011	14186	Mm.276715	NM_008011	ENSMUSG00000005320	Fgfr4	Fgfr-4	fibroblast growth factor receptor 4	protein-coding
mm_28379.1	chr3	89963305	89963355	-	1	NA	promoter-TSS (NM_001081182)	promoter-TSS (NM_001081182)	2	NM_001081182	54667	Mm.30455	NM_001081182	ENSMUSG00000060671	Atp8b2	Id	ATPase, class I, type 8B, member 2	protein-coding
mm_154051.1	chr19	55103031	55103064	-	1	NA	Intergenic	Intergenic	-3600	NM_008149	14732	Mm.210196	NM_008149	ENSMUSG00000024978	Gpam	GPAT|GPAT1	glycerol-3-phosphate acyltransferase, mitochondrial	protein-coding
mm_53708.1	chr6	143171443	143171455	+	1	NA	intron (NM_029250, intron 1 of 7)	intron (NM_029250, intron 1 of 7)	4219	NM_029250	75320	Mm.272548	NM_029250	ENSMUSG00000030275	Etnk1	1110061E11Rik|4930555L11Rik|AI195356|AI841245|C80956|D6Ertd3e|EKI1	ethanolamine kinase 1	protein-coding
mm_58117.1	chr6	138427077	138427100	-	1	NA	intron (NR_126072, intron 2 of 3)	intron (NR_126072, intron 2 of 3)	3983	NR_126072	319702	Mm.403785	NR_126072	ENSMUSG00000089957	A830011K09Rik	-	RIKEN cDNA A830011K09 gene	ncRNA
mm_35843.1	chr4	48279503	48279515	-	1	NA	promoter-TSS (NM_029572)	promoter-TSS (NM_029572)	80	NM_029572	76299	Mm.317701	NM_029572	ENSMUSG00000028343	Erp44	1110001E24Rik|AI849526|AL033348|Txndc4	endoplasmic reticulum protein 44	protein-coding
mm_1659.1	chr1	74713271	74713298	+	1	NA	promoter-TSS (NM_024264)	promoter-TSS (NM_024264)	-251	NM_024264	104086	Mm.85083	NM_024264	ENSMUSG00000026170	Cyp27a1	1300013A03Rik|Cyp27	cytochrome P450, family 27, subfamily a, polypeptide 1	protein-coding
mm_68250.1	chr7	105568647	105568675	-	1	NA	exon (NM_001310600, exon 1 of 13)	exon (NM_001310600, exon 1 of 13)	116	NM_001310600	11785	Mm.38469	NM_009685	ENSMUSG00000037032	Apbb1	Fe65|Rir	amyloid beta (A4) precursor protein-binding, family B, member 1	protein-coding
mm_125852.1	chr15	74989223	74989255	+	1	NA	Intergenic	Intergenic	-5809	NM_020498	57248	Mm.358339	NM_020498	ENSMUSG00000022586	Ly6i	AI789751|Ly-6I|Ly-6M	lymphocyte antigen 6 complex, locus I	protein-coding
mm_151827.1	chr19	5658247	5658251	-	1	NA	intron (NM_001164568, intron 4 of 15)	intron (NM_001164568, intron 4 of 15)	5458	NM_001164482	20469	Mm.3072	NM_011379	ENSMUSG00000056917	Sipa1	Spa1	signal-induced proliferation associated gene 1	protein-coding
mm_13379.1	chr2	103795971	103796015	+	1	NA	intron (NM_001111289, intron 1 of 17)	intron (NM_001111289, intron 1 of 17)	1085	NM_001111290	53872	Mm.427589	NM_016739	ENSMUSG00000027184	Caprin1	AL022980|Caprin-1|Gpiap|Gpiap1|Mmgpip137|P137|rng105	cell cycle associated protein 1	protein-coding
mm_105515.1	chr11	106267623	106267641	-	1	NA	promoter-TSS (NM_031878)	promoter-TSS (NM_031878)	0	NM_031878	83796	Mm.21772	NM_031878	ENSMUSG00000078619	Smarcd2	AW322457|Baf60b	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2	protein-coding
mm_125713.1	chr15	68928415	68928421	+	1	NA	promoter-TSS (NM_010158)	promoter-TSS (NM_010158)	-2	NM_010158	13992	Mm.17964	NM_010158	ENSMUSG00000022332	Khdrbs3	Etle|SLM-2|Salp|Slm2|T-STAR	KH domain containing, RNA binding, signal transduction associated 3	protein-coding
mm_146223.1	chr18	77065478	77065545	+	1	NA	promoter-TSS (NM_001164168)	promoter-TSS (NM_001164168)	-169	NM_001164170	17344	Mm.6370	NM_008602	ENSMUSG00000025423	Pias2	6330408K17Rik|AI462206|ARIP3|AU018068|Dib|Miz1|PIASxalpha|PIASxb|PIASxbeta|SIZ2	protein inhibitor of activated STAT 2	protein-coding
mm_77244.1	chr8	115705349	115705361	-	1	NA	3' UTR (NM_001025577, exon 1 of 1)	3' UTR (NM_001025577, exon 1 of 1)	1539	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_58326.1	chr6	146515905	146515911	-	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	-13685	NM_019923	16439	Mm.7800	NM_010586	ENSMUSG00000030287	Itpr2	AI649341|InsP3R-2|InsP3R-5|Ip3r2|Itpr5|insP3R2	inositol 1,4,5-triphosphate receptor 2	protein-coding
mm_98907.1	chr11	98026984	98026992	+	1	NA	promoter-TSS (NM_009078)	promoter-TSS (NM_009078)	64	NM_009078	19921	Mm.10247	NM_009078	ENSMUSG00000017404	Rpl19	-	ribosomal protein L19	protein-coding
mm_149950.1	chr19	27428839	27428846	+	1	NA	intron (NR_131940, intron 1 of 17)	intron (NR_131940, intron 1 of 17)	1066	NM_177474	52874	Mm.261027	NM_177474	ENSMUSG00000041360	Pum3	1110069H02Rik|AA675048|D19Bwg1357e|Kiaa0020	pumilio RNA-binding family member 3	protein-coding
mm_83784.1	chr9	52164739	52164769	-	1	NA	intron (NM_001162921, intron 1 of 5)	intron (NM_001162921, intron 1 of 5)	3357	NM_001162921	244871	Mm.295686	NM_001162921	ENSMUSG00000035164	Zc3h12c	A230108E06|C230027N18Rik|mKIAA1726	zinc finger CCCH type containing 12C	protein-coding
mm_35939.1	chr4	53043283	53043302	-	1	NA	intron (NM_013454, intron 40 of 49)	intron (NM_013454, intron 40 of 49)	31412	NM_025623	66536	Mm.38244	NM_025623	ENSMUSG00000015247	Nipsnap3b	2700063N13Rik|Nipsnap3a	nipsnap homolog 3B (C. elegans)	protein-coding
mm_146790.1	chr18	20114794	20114813	-	1	NA	promoter-TSS (NM_001291804)	promoter-TSS (NM_001291804)	-30	NM_013504	13505	Mm.33740	NM_013504	ENSMUSG00000044322	Dsc1	1110020A10Rik|AI507491	desmocollin 1	protein-coding
mm_125734.1	chr15	73423282	73423326	+	1	NA	promoter-TSS (NM_007982)	promoter-TSS (NM_007982)	-113	NM_001130409	14083	Mm.254494	NM_007982	ENSMUSG00000022607	Ptk2	FAK|FRNK|Fadk|mKIAA4203|p125FAK	PTK2 protein tyrosine kinase 2	protein-coding
mm_38250.1	chr4	136687991	136687999	-	1	NA	intron (NM_001290753, intron 5 of 15)	intron (NM_001290753, intron 5 of 15)	65374	NM_001243262	242707	Mm.448979	NM_001243262	ENSMUSG00000070683	Lactbl1	-	lactamase, beta-like 1	protein-coding
mm_44960.1	chr5	36711983	36712029	-	1	NA	Intergenic	Intergenic	-15985	NM_001081232	320661	Mm.26480	NM_177221	ENSMUSG00000029190	D5Ertd579e	9030221A05Rik|A930018H20Rik|Kiaa0232	DNA segment, Chr 5, ERATO Doi 579, expressed	protein-coding
mm_36312.1	chr4	69758529	69758549	-	1	NA	Intergenic	Intergenic	651896	NM_001313762	214444	Mm.370777	NM_145990	ENSMUSG00000039298	Cdk5rap2	2900018K03Rik|an|mKIAA1633	CDK5 regulatory subunit associated protein 2	protein-coding
mm_54538.1	chr6	36741392	36741415	-	1	NA	exon (NM_008973, exon 4 of 5)	exon (NM_008973, exon 4 of 5)	69958	NM_008973	19242	Mm.279690	NM_008973	ENSMUSG00000029838	Ptn	HARP|HB-GAM|HBBN|HBGF-8|HBNF|OSF|Osf-1|Osf1	pleiotrophin	protein-coding
mm_91787.1	chr10	53348510	53348517	-	1	NA	exon (NM_001204983, exon 3 of 13)	exon (NM_001204983, exon 3 of 13)	10827	NM_001141927	18821	Mm.34145	NM_023129	ENSMUSG00000038583	Pln	Plb	phospholamban	protein-coding
mm_171282.1	chr3	89246941	89246955	-	1	NA	intron (NM_001310625, intron 2 of 4)	intron (NM_001310625, intron 2 of 4)	475	NM_001310625	66059	Mm.177991	NM_025327	ENSMUSG00000042747	Krtcap2	0610010I12Rik|Kcp2	keratinocyte associated protein 2	protein-coding
mm_35440.1	chr4	40063793	40063811	-	1	NA	Intergenic	Intergenic	-79463	NM_007386	11428	Mm.331547	NM_007386	ENSMUSG00000028405	Aco1	Aco-1|Irebp|Irp1	aconitase 1	protein-coding
mm_172903.1	chr9	58582905	58582908	+	1	NA	intron (NM_001293673, intron 1 of 7)	intron (NM_001293673, intron 1 of 7)	666	NM_009145	20320	Mm.15125	NM_009145	ENSMUSG00000032336	Nptn	AW554172|SDR-1|Sdfr1	neuroplastin	protein-coding
mm_143657.1	chr17	79713682	79713700	-	1	NA	exon (NM_009994, exon 2 of 3)	exon (NM_009994, exon 2 of 3)	1350	NM_009994	13078	Mm.214016	NM_009994	ENSMUSG00000024087	Cyp1b1	CP1B|P4501b1	cytochrome P450, family 1, subfamily b, polypeptide 1	protein-coding
mm_138942.1	chr17	44038867	44038880	+	1	NA	3' UTR (NM_207649, exon 5 of 5)	3' UTR (NM_207649, exon 5 of 5)	-39929	NM_001168620	83965	Mm.30145	NM_032003	ENSMUSG00000023960	Enpp5	AW061004|D17Abb1e|E-NPP 5	ectonucleotide pyrophosphatase/phosphodiesterase 5	protein-coding
mm_169119.1	chr13	51123113	51123123	+	1	NA	5' UTR (NM_001283028, exon 2 of 6)	5' UTR (NM_001283028, exon 2 of 6)	-11200	NM_011462	20729	Mm.188432	NM_011462	ENSMUSG00000021395	Spin1	Spin	spindlin 1	protein-coding
mm_164158.1	chr15	70514991	70514998	-	1	NA	Intergenic	Intergenic	590761	NR_045071	100503580	Mm.404646	NR_045071		Gm19782	-	predicted gene, 19782	ncRNA
mm_131545.1	chr16	17832682	17832690	+	1	NA	promoter-TSS (NR_027959)	promoter-TSS (NR_027959)	-433	NR_027959	433004	Mm.310200	NM_001002790		B830017H08Rik	-	RIKEN cDNA B830017H08 gene	ncRNA
mm_22105.1	chr2	169963076	169963082	-	1	NA	non-coding (NR_131974, exon 1 of 1)	non-coding (NR_131974, exon 1 of 1)	108	NR_131974	446211	Mm.266854	NR_131974	ENSMUSG00000103935	AY702102	STDP1	cDNA sequence AY702102	ncRNA
mm_153736.1	chr19	44545810	44545832	-	1	NA	promoter-TSS (NM_001033343)	promoter-TSS (NM_001033343)	27	NM_001033343	240667	Mm.329873	NM_001033343	ENSMUSG00000051984	Sec31b	Gm341|Sec31l2	Sec31 homolog B (S. cerevisiae)	protein-coding
mm_63707.1	chr7	130663003	130663010	+	1	NA	intron (NM_001004468, intron 3 of 21)	(T)n|Simple_repeat|Simple_repeat	-29550	NM_001347637	57752	Mm.86322	NM_021314	ENSMUSG00000030852	Tacc2	mKIAA4180	transforming, acidic coiled-coil containing protein 2	protein-coding
mm_40064.1	chr5	34169733	34169764	+	1	NA	promoter-TSS (NM_001289804)	promoter-TSS (NM_001289804)	-222	NM_001289803	272158	Mm.319286	NM_181857	ENSMUSG00000045102	Poln	POL4P	DNA polymerase N	protein-coding
mm_145479.1	chr18	60376608	60376622	+	1	NA	intron (NM_021792, intron 1 of 1)	RMER17A|LTR|ERVK	586	NM_001146275	60440	Mm.261140	NM_021792	ENSMUSG00000054072	Iigp1	2900074L10Rik|AI046432|AW111922|Ifgga1|Iigp|Irga6	interferon inducible GTPase 1	protein-coding
mm_161539.1	chr15	102977264	102977264	+	1	NA	intron (NM_008272, intron 1 of 2)	intron (NM_008272, intron 1 of 2)	232	NM_008272	15427	Mm.4765	NM_008272	ENSMUSG00000036139	Hoxc9	Hox-3.2	homeobox C9	protein-coding
mm_43836.1	chr5	142972685	142972726	+	1	NA	3' UTR (NM_007984, exon 5 of 5)	3' UTR (NM_007984, exon 5 of 5)	12350	NM_007984	14086	Mm.289707	NM_007984	ENSMUSG00000029581	Fscn1	AI663989|Fan1|fascin-1	fascin actin-bundling protein 1	protein-coding
mm_82716.1	chr9	24696259	24696308	-	1	NA	promoter-TSS (NM_001166207)	promoter-TSS (NM_001166207)	10	NM_001166207	320752	Mm.46158	NM_001166207	ENSMUSG00000085576	Dpy19l2	4932443J21Rik|Gm18376	dpy-19-like 2 (C. elegans)	protein-coding
mm_5737.1	chr1	45339918	45339957	-	1	NA	exon (NM_009930, exon 36 of 51)	exon (NM_009930, exon 36 of 51)	28399	NM_009930	12825	Mm.249555	NM_009930	ENSMUSG00000026043	Col3a1	AW550625|Col3a-1|Tsk-2|Tsk2	collagen, type III, alpha 1	protein-coding
mm_31151.1	chr4	43406267	43406277	+	1	NA	promoter-TSS (NM_199057)	promoter-TSS (NM_199057)	-230	NM_199057	100213	Mm.235730	NM_199057	ENSMUSG00000035969	Rusc2	AI840675|mKIAA0375	RUN and SH3 domain containing 2	protein-coding
mm_66875.1	chr7	57509440	57509453	-	1	NA	intron (NM_176942, intron 1 of 9)	CpG	563	NM_176942	110886	Mm.273114	NM_176942	ENSMUSG00000055078	Gabra5	A230018I05Rik	gamma-aminobutyric acid (GABA) A receptor, subunit alpha 5	protein-coding
mm_146203.1	chr18	76268465	76268479	+	1	NA	intron (NM_001311070, intron 1 of 8)	intron (NM_001311070, intron 1 of 8)	6027	NM_001311070	17126	Mm.152699	NM_010754	ENSMUSG00000024563	Smad2	7120426M23Rik|Madh2|Madr2|Smad-2|mMad2	SMAD family member 2	protein-coding
mm_143760.1	chr17	81622463	81622465	-	1	NA	intron (NR_104580, intron 2 of 8)	intron (NR_104580, intron 2 of 8)	115923	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_40919.1	chr5	75734841	75734856	+	1	NA	Intergenic	Intergenic	159857	NM_021099	16590	Mm.247073	NM_021099	ENSMUSG00000005672	Kit	Bs|CD117|Fdc|Gsfsco1|Gsfsco5|Gsfsow3|SCO1|SCO5|SOW3|Ssm|Tr-kit|W|c-KIT	KIT proto-oncogene receptor tyrosine kinase	protein-coding
mm_96692.1	chr11	69591491	69591508	+	1	NA	3' UTR (NM_011640, exon 11 of 11)	3' UTR (NM_011640, exon 11 of 11)	11140	NM_001127233	22059	Mm.222	NM_011640	ENSMUSG00000059552	Trp53	Tp53|bbl|bfy|bhy|p44|p53	transformation related protein 53	protein-coding
mm_146843.1	chr18	23041642	23041671	-	1	NA	promoter-TSS (NM_199024)	promoter-TSS (NM_199024)	-3	NM_199024	319211	Mm.209896	NM_199024	ENSMUSG00000041923	Nol4	1700013J13Rik|4930568N03Rik|Gm1262	nucleolar protein 4	protein-coding
mm_64123.1	chr7	141131342	141131378	+	1	NA	promoter-TSS (NM_013782)	promoter-TSS (NM_013782)	74	NM_013782	27388	Mm.293591	NM_013782	ENSMUSG00000025495	Ptdss2	AI481134|AI988017|PSS2	phosphatidylserine synthase 2	protein-coding
mm_52621.1	chr6	117174045	117174054	+	1	NA	3' UTR (NM_021704, exon 3 of 3)	3' UTR (NM_021704, exon 3 of 3)	5514	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_67345.1	chr7	79825336	79825347	-	1	NA	exon (NM_008486, exon 19 of 20)	exon (NM_008486, exon 19 of 20)	14614	NM_008589	17293	Mm.31472	NM_008589	ENSMUSG00000030543	Mesp2	bHLHc6	mesoderm posterior 2	protein-coding
mm_20705.1	chr2	132945925	132945934	-	1	NA	5' UTR (NM_198029, exon 1 of 15)	5' UTR (NM_198029, exon 1 of 15)	107	NM_198029	241639	Mm.209784	NM_198029	ENSMUSG00000027356	Fermt1	5830467P10Rik|Kindlin-1	fermitin family member 1	protein-coding
mm_80658.1	chr9	90054530	90054545	+	1	NA	5' UTR (NM_007801, exon 1 of 12)	5' UTR (NM_007801, exon 1 of 12)	270	NM_001312649	13036	Mm.2277	NM_007801	ENSMUSG00000032359	Ctsh	AL022844	cathepsin H	protein-coding
mm_79681.1	chr9	59751251	59751268	+	1	NA	promoter-TSS (NM_001172071)	promoter-TSS (NM_001172071)	85	NM_173018	270163	Mm.249545	NM_173018	ENSMUSG00000039585	Myo9a	4732465J09Rik|C130068I12Rik|C230003M11	myosin IXa	protein-coding
mm_142190.1	chr17	36894029	36894035	-	1	NA	Intergenic	Intergenic	-3907	NM_001172168	195359	Mm.32606	NM_001033235	ENSMUSG00000073399	Trim40	Gm319|Gm35|Gm865	tripartite motif-containing 40	protein-coding
mm_157024.1	chrX	7898639	7898654	-	1	NA	promoter-TSS (NM_011591)	promoter-TSS (NM_011591)	354	NM_001252528	54633	Mm.14616	NM_019478	ENSMUSG00000031157	Pqbp1	PQBP-1|Sfc2|npw38	polyglutamine binding protein 1	protein-coding
mm_111205.1	chr12	84361803	84361838	-	1	NA	promoter-TSS (NM_172581)	promoter-TSS (NM_172581)	1	NM_172581	217705	Mm.259468	NM_172581	ENSMUSG00000021234	Fam161b	9330169D17|9830169C18Rik	family with sequence similarity 161, member B	protein-coding
mm_112291.1	chr12	114513808	114513822	-	1	NA	promoter-TSS (NR_106063)	promoter-TSS (NR_106063)	-121	NR_106063	102465664		NR_106063	ENSMUSG00000098357	Mir7094-2	Gm27508|mmu-mir-7094-2	microRNA 7094-2	ncRNA
mm_28095.1	chr3	85894910	85894917	-	1	NA	Intergenic	RMER19C|LTR|ERVK	-7395	NM_177130	320302	Mm.482978	NM_177130	ENSMUSG00000031286	Glt28d2	4732486J07Rik|Glt28d1l	glycosyltransferase 28 domain containing 2	protein-coding
mm_125351.1	chr15	39391557	39391585	+	1	NA	intron (NM_001256382, intron 3 of 26)	intron (NM_001256382, intron 3 of 26)	193285	NM_053271	116838	Mm.309296	NM_053271	ENSMUSG00000037386	Rims2	2810036I15Rik|AW048769|RIM2|Rab3ip2|Rim2(+40A)|Rim2(+44A)|Rim2(+4A)|Serg2|Syt3-rs|mKIAA0751	regulating synaptic membrane exocytosis 2	protein-coding
mm_78008.1	chr9	12865362	12865364	+	1	NA	Intergenic	Intergenic	240492	NR_040755	78219	Mm.414868	NR_040755	ENSMUSG00000111830	4930568E12Rik	-	RIKEN cDNA 4930568E12 gene	ncRNA
mm_73903.1	chr8	119446842	119446852	+	1	NA	TTS (NM_027950)	TTS (NM_027950)	128	NM_054095	117148	Mm.356184	NM_054095	ENSMUSG00000031837	Necab2	Efcbp2	N-terminal EF-hand calcium binding protein 2	protein-coding
mm_70727.1	chr8	18595527	18595583	+	1	NA	5' UTR (NM_173189, exon 1 of 14)	5' UTR (NM_173189, exon 1 of 14)	382	NM_173189	244329	Mm.235296	NM_173189	ENSMUSG00000039842	Mcph1	5430437K10Rik|BRIT1|D030046N04Rik|MCT	microcephaly, primary autosomal recessive 1	protein-coding
mm_70382.1	chr8	10249335	10249366	+	1	NA	intron (NM_001319151, intron 1 of 34)	intron (NM_001319151, intron 1 of 34)	95439	NM_001319151	244281	Mm.422761	NM_001081397	ENSMUSG00000039057	Myo16	BM140241|C230040D10Rik|Gm1105|NYAP3|mKIAA0865	myosin XVI	protein-coding
mm_105923.1	chr11	115062110	115062121	-	1	NA	promoter-TSS (NM_172050)	promoter-TSS (NM_172050)	-76	NM_172050	217306	Mm.222667	NM_172050	ENSMUSG00000048498	Cd300e	BC034097|CLM2|Cd300le|TREM5	CD300E molecule	protein-coding
mm_25700.1	chr3	122419740	122419754	+	1	NA	promoter-TSS (NM_013867)	promoter-TSS (NM_013867)	-33	NM_013867	29815	Mm.45815	NM_013867	ENSMUSG00000028121	Bcar3	AI131758|AND-34	breast cancer anti-estrogen resistance 3	protein-coding
mm_170380.1	chr1	85600737	85600744	+	1	NA	promoter-TSS (NM_001013817)	promoter-TSS (NM_001013817)	37	NM_001013817	434484	Mm.445821	NM_001013817	ENSMUSG00000070031	Sp140	-	Sp140 nuclear body protein	protein-coding
mm_74454.1	chr8	4214344	4214357	-	1	NA	exon (NM_207203, exon 6 of 7)	exon (NM_207203, exon 6 of 7)	2962	NM_207203	73072	Mm.477379	NM_207203	ENSMUSG00000064125	Prr36	-	proline rich 36	protein-coding
mm_162981.1	chr11	21286494	21286506	+	1	NA	intron (NM_139061, intron 7 of 22)	Tigger2b|DNA|TcMar-Tigger	47468	NM_001290628	245944	Mm.170103	NM_139061	ENSMUSG00000020128	Vps54	Hcc8|Vps54l|mSLP8|wr	VPS54 GARP complex subunit	protein-coding
mm_99941.1	chr11	111065926	111065945	+	1	NA	promoter-TSS (NM_008425)	promoter-TSS (NM_008425)	-229	NM_008425	16518	Mm.4951	NM_008425	ENSMUSG00000041695	Kcnj2	IRK1|Kcnf1|Kir2.1	potassium inwardly-rectifying channel, subfamily J, member 2	protein-coding
mm_4934.1	chr1	191098407	191098436	+	1	NA	promoter-TSS (NM_030060)	promoter-TSS (NM_030060)	7	NM_030060	381319	Mm.6922	NM_030060	ENSMUSG00000026630	Batf3	9130211I03Rik|Snft	basic leucine zipper transcription factor, ATF-like 3	protein-coding
mm_44995.1	chr5	38159500	38159517	-	1	NA	promoter-TSS (NM_010942)	promoter-TSS (NM_010942)	-41	NM_010942	18196	Mm.7414	NM_010942	ENSMUSG00000029126	Nsg1	Neep21|m234|p21	neuron specific gene family member 1	protein-coding
mm_59122.1	chr7	19887342	19887350	+	1	NA	intron (NM_177036, intron 1 of 6)	B1F|SINE|Alu	619	NM_177036	319930	Mm.215839	NM_177036	ENSMUSG00000049848	Ceacam19	C130022P09Rik|CEAL1	carcinoembryonic antigen-related cell adhesion molecule 19	protein-coding
mm_150476.1	chr19	38836700	38836707	+	1	NA	5' UTR (NM_145952, exon 1 of 13)	5' UTR (NM_145952, exon 1 of 13)	124	NM_145952	209478	Mm.391153	NM_145952	ENSMUSG00000048720	Tbc1d12	BC033574	TBC1D12: TBC1 domain family, member 12	protein-coding
mm_107576.1	chr12	44439079	44439089	+	1	NA	intron (NM_001146031, intron 2 of 27)	intron (NM_001146031, intron 2 of 27)	110199	NM_001146031	319504	Mm.208439	NM_176930	ENSMUSG00000020598	Nrcam	Bravo|C030017F07Rik|C130076O07Rik|mKIAA0343	neuronal cell adhesion molecule	protein-coding
mm_128937.1	chr15	74709264	74709305	-	1	NA	promoter-TSS (NM_008415)	promoter-TSS (NM_008415)	38	NM_008415	16469	Mm.87052	NM_008415	ENSMUSG00000046380	Jrk	-	jerky	protein-coding
mm_141819.1	chr17	34615777	34615793	-	1	NA	TTS (NM_019441)	TTS (NM_019441)	186	NM_152922	81701	Mm.231343	NM_152922	ENSMUSG00000015467	Egfl8	Ng3	EGF-like domain 8	protein-coding
mm_128289.1	chr15	37232907	37232925	-	1	NA	promoter-TSS (NM_026496)	promoter-TSS (NM_026496)	-120	NM_026496	252973	Mm.244612	NM_026496	ENSMUSG00000022286	Grhl2	0610015A08Rik|BOM|Tcfcp2l3|clft3	grainyhead-like 2 (Drosophila)	protein-coding
mm_110895.1	chr12	75596196	75596261	-	1	NA	promoter-TSS (NM_012024)	promoter-TSS (NM_012024)	-28	NM_012024	26932	Mm.259626	NM_012024	ENSMUSG00000021051	Ppp2r5e	4633401M22Rik|AI449017|B56beta	protein phosphatase 2, regulatory subunit B', epsilon	protein-coding
mm_10785.1	chr2	24345283	24345295	+	1	NA	promoter-TSS (NM_001039701)	promoter-TSS (NM_001039701)	-2	NM_001159562	16181	Mm.882	NM_031167	ENSMUSG00000026981	Il1rn	F630041P17Rik|IL-1ra	interleukin 1 receptor antagonist	protein-coding
mm_165352.1	chr2	120501261	120501270	+	1	NA	exon (NM_007601, exon 16 of 24)	exon (NM_007601, exon 16 of 24)	24356	NM_001109761	12335	Mm.458021	NM_007601	ENSMUSG00000079110	Capn3	AI323605|Capa-3|Capa3|Lp82|p94	calpain 3	protein-coding
mm_166110.1	chr4	148130834	148130863	+	1	NA	promoter-TSS (NM_027426)	promoter-TSS (NM_027426)	-72	NM_001305420	71890	Mm.9648	NM_027985	ENSMUSG00000029003	Mad2l2	2310033C13Rik|G1-453-4|MAD2B|REV7|repro22	MAD2 mitotic arrest deficient-like 2	protein-coding
mm_44780.1	chr5	32133013	32133022	-	1	NA	Intergenic	CpG	-3455	NM_008037	14284	Mm.24684	NM_008037	ENSMUSG00000029135	Fosl2	Fra-2	fos-like antigen 2	protein-coding
mm_131151.1	chr16	6816117	6816132	+	1	NA	intron (NM_021477, intron 5 of 16)	intron (NM_021477, intron 5 of 16)	-253711	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_104781.1	chr11	98546656	98546666	-	1	NA	promoter-TSS (NM_011771)	promoter-TSS (NM_011771)	-630	NM_011771	22780	Mm.133367	NM_011771	ENSMUSG00000018168	Ikzf3	5830411O07Rik|Aiolos|Zfpn1a3|Znfn1a3	IKAROS family zinc finger 3	protein-coding
mm_25646.1	chr3	121387795	121387800	+	1	NA	Intergenic	Intergenic	-38744	NM_028044	71994	Mm.275555	NM_028044	ENSMUSG00000053931	Cnn3	1600014M03Rik|C85854|Calpo3	calponin 3, acidic	protein-coding
mm_12216.1	chr2	67565681	67565773	+	1	NA	Intergenic	CpG	-109730	NR_106083	102465706		NR_106083	ENSMUSG00000098299	Mir7224	Gm27971|mmu-mir-7224	microRNA 7224	ncRNA
mm_5967.1	chr1	56978535	56978544	-	1	NA	Intergenic	Intergenic	7070	NR_024325	329160	Mm.419039	NR_024325	ENSMUSG00000087022	9130024F11Rik	B530002L08|EG329160	RIKEN cDNA 9130024F11 gene	ncRNA
mm_169778.1	chr16	11143917	11143918	+	1	NA	intron (NR_027502, intron 19 of 22)	LSU-rRNA_Hsa|rRNA|rRNA	-9385	NM_029582	106200	Mm.291015	NM_029582	ENSMUSG00000022498	Txndc11	2810408E11Rik|AI427833|EFP1|Txdc11	thioredoxin domain containing 11	protein-coding
mm_64601.1	chr7	3212588	3212597	-	1	NA	Intergenic	B1F|SINE|Alu	-6034	NR_029640	100049710		NR_029640	ENSMUSG00000077815	Mir290a	Mir290|Mirn290|mir-290a|mmu-miR-290|mmu-mir-290a	microRNA 290a	ncRNA
mm_40213.1	chr5	37050855	37050865	+	1	NA	promoter-TSS (NM_178394)	promoter-TSS (NM_178394)	3	NM_178394	76071	Mm.85280	NM_178394	ENSMUSG00000063646	Jakmip1	5830437M04Rik|C330021K24Rik|Gababrbp|Marlin-1	janus kinase and microtubule interacting protein 1	protein-coding
mm_59042.1	chr7	19345136	19345147	+	1	NA	promoter-TSS (NM_007948)	promoter-TSS (NM_007948)	70	NM_007948	13870	Mm.280913	NM_007948	ENSMUSG00000003549	Ercc1	Ercc-1	excision repair cross-complementing rodent repair deficiency, complementation group 1	protein-coding
mm_1088.1	chr1	59606759	59606781	+	1	NA	intron (NM_001013771, intron 12 of 19)	intron (NM_001013771, intron 12 of 19)	64064	NM_009460	22218	Mm.362118	NM_009460	ENSMUSG00000026021	Sumo1	GMP1|PIC1|SENTRIN|SMT3|SMT3H3|SMTP3|SUMO-1|Smt3C|Ubl1	small ubiquitin-like modifier 1	protein-coding
mm_168492.1	chr11	50405659	50405676	-	1	NA	intron (NM_172557, intron 10 of 17)	B1_Mus1|SINE|Alu	25444	NM_172557	216724	Mm.390400	NM_172557	ENSMUSG00000020375	Rufy1	3000002E04Rik|Rabip4|ZFYVE12	RUN and FYVE domain containing 1	protein-coding
mm_99589.1	chr11	104309696	104309710	+	1	NA	intron (NM_001038609, intron 7 of 11)	intron (NM_001038609, intron 7 of 11)	78267	NM_001285454	17762	Mm.1287	NM_010838	ENSMUSG00000018411	Mapt	AI413597|AW045860|Mtapt|Tau	microtubule-associated protein tau	protein-coding
mm_156174.1	chrX	130330076	130330090	+	1	NA	intron (NM_172493, intron 26 of 26)	intron (NM_172493, intron 26 of 26)	580341	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diaph2	Dia3|Diap2|Drf2|E430022I22Rik	diaphanous related formin 2	protein-coding
mm_145937.1	chr18	67289236	67289258	+	1	NA	promoter-TSS (NM_053261)	promoter-TSS (NM_053261)	24	NM_053261	114663	Mm.34079	NM_053261	ENSMUSG00000024525	Impa2	2210415D20Rik|AI326924|AW259601	inositol (myo)-1(or 4)-monophosphatase 2	protein-coding
mm_166128.1	chr4	154900307	154900309	+	1	NA	Intergenic	Intergenic	-1265	NM_025582	66469	Mm.41868	NM_025582	ENSMUSG00000029059	Fam213b	2810405K02Rik|AI836168|PM/PGFS	family with sequence similarity 213, member B	protein-coding
mm_105850.1	chr11	113710054	113710061	-	1	NA	promoter-TSS (NM_001164532)	promoter-TSS (NM_001164532)	-40	NM_029794	52670	Mm.229207	NM_026682	ENSMUSG00000018727	Cpsf4l	0610010C04Rik|1500000C01Rik|D11Ertd636e	cleavage and polyadenylation specific factor 4-like	protein-coding
mm_31830.1	chr4	70378176	70378216	+	1	NA	intron (NM_145990, intron 4 of 36)	GSAT_MM|Satellite|Satellite	32239	NM_001313762	214444	Mm.370777	NM_145990	ENSMUSG00000039298	Cdk5rap2	2900018K03Rik|an|mKIAA1633	CDK5 regulatory subunit associated protein 2	protein-coding
mm_168588.1	chr1	173535948	173535961	-	1	NA	promoter-TSS (NM_001024721)	promoter-TSS (NM_001024721)	3	NM_001024721	545384	Mm.371698	NM_001024721	ENSMUSG00000070501	Ifi214	Pyhin-B|p214	interferon activated gene 214	protein-coding
mm_90413.1	chr10	127421181	127421203	+	1	NA	5' UTR (NM_001168293, exon 1 of 24)	5' UTR (NM_001168293, exon 1 of 24)	325	NM_001168293	71750	Mm.29342	NM_027900	ENSMUSG00000025404	R3hdm2	1300003K24Rik|AU041262|mKIAA1002	R3H domain containing 2	protein-coding
mm_88592.1	chr10	79755104	79755126	+	1	NA	promoter-TSS (NM_023304)	promoter-TSS (NM_023304)	-4	NM_023304	67112	Mm.154211	NM_023304	ENSMUSG00000020327	Fgf22	2210414E06Rik|FGF-22	fibroblast growth factor 22	protein-coding
mm_1495.1	chr1	71888475	71888491	+	1	NA	non-coding (NR_027658, exon 1 of 3)	non-coding (NR_027658, exon 1 of 3)	371	NR_027659	667931	Mm.214128	NR_027658	ENSMUSG00000099707	Gm8883	EG667931|Gm554	predicted gene 8883	ncRNA
mm_40008.1	chr5	33018835	33018865	+	1	NA	promoter-TSS (NM_011738)	promoter-TSS (NM_011738)	34	NM_011738	22629	Mm.332314	NM_011738	ENSMUSG00000018965	Ywhah	-	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta polypeptide	protein-coding
mm_19342.1	chr2	90745271	90745288	-	1	NA	promoter-TSS (NM_018828)	promoter-TSS (NM_018828)	-91	NM_018828	55935	Mm.489638	NM_018828	ENSMUSG00000008200	Fnbp4	FBP30|Fnbp30|mKIAA1014	formin binding protein 4	protein-coding
mm_117902.1	chr13	99429892	99429901	-	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-17070	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_130668.1	chr15	100674571	100674588	-	1	NA	3' UTR (NM_033612, exon 8 of 8)	3' UTR (NM_033612, exon 8 of 8)	-5079	NM_001270537	668218	Mm.451225	NM_001270537	ENSMUSG00000098112	Bin2	-	bridging integrator 2	protein-coding
mm_156945.1	chrX	169979129	169979135	+	1	NA	promoter-TSS (NR_029457)	promoter-TSS (NR_029457)	-215	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_141039.1	chr17	25273862	25273886	-	1	NA	promoter-TSS (NR_027452)	promoter-TSS (NR_027452)	40	NM_001177609	22196	Mm.240044	NM_011665	ENSMUSG00000015120	Ube2i	5830467E05Rik|F830028O17Rik|UBC9|Ubce2i|Ubce9	ubiquitin-conjugating enzyme E2I	protein-coding
mm_139917.1	chr17	70963824	70963837	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	26686	NM_023402	67938	Mm.261329	NM_023402	ENSMUSG00000034868	Myl12b	1500001M02Rik|C77744|Mylc2b|RLC-B	myosin, light chain 12B, regulatory	protein-coding
mm_150992.1	chr19	46599082	46599150	+	1	NA	promoter-TSS (NM_001177812)	promoter-TSS (NM_001177812)	10	NM_146099	226178	Mm.329895	NM_146099	ENSMUSG00000047731	Wbp1l	D19Wsu162e|Opal1	WW domain binding protein 1 like	protein-coding
mm_15813.1	chr2	164502578	164502596	+	1	NA	exon (NM_133779, exon 9 of 12)	exon (NM_133779, exon 9 of 12)	5062	NM_133779	78928	Mm.28228	NM_133779	ENSMUSG00000017721	Pigt	2510012P17Rik|4930534E15Rik|CGI-06|NDAP|Ndap7	phosphatidylinositol glycan anchor biosynthesis, class T	protein-coding
mm_77248.1	chr8	115705644	115705654	-	1	NA	3' UTR (NM_001025577, exon 1 of 1)	3' UTR (NM_001025577, exon 1 of 1)	1245	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_9307.1	chr1	171641021	171641036	-	1	NA	TTS (NR_106151)	TTS (NR_106151)	872	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_120152.1	chr14	60634780	60634790	+	1	NA	promoter-TSS (NM_001033272)	promoter-TSS (NM_001033272)	80	NM_001033272	219140	Mm.149776	NM_001033272	ENSMUSG00000021990	Spata13	C79050|ESTM11|X83327|mFLJ00298	spermatogenesis associated 13	protein-coding
mm_162456.1	chr1	128373505	128373515	+	1	NA	intron (NM_177445, intron 10 of 15)	intron (NM_177445, intron 10 of 15)	-13805	NM_001313695	17219	Mm.4933	NM_008567	ENSMUSG00000026355	Mcm6	ASP-l1|D1Wsu22e|Mcmd6	minichromosome maintenance complex component 6	protein-coding
mm_136065.1	chr16	84734508	84734529	-	1	NA	exon (NM_017404, exon 2 of 10)	exon (NM_017404, exon 2 of 10)	784	NM_017404	27393	Mm.103655	NM_017404	ENSMUSG00000022889	Mrpl39	C21orf8|MRP-L5|ORF22|Rpml5	mitochondrial ribosomal protein L39	protein-coding
mm_34125.1	chr4	139257104	139257123	+	1	NA	intron (NM_001037761, intron 2 of 9)	intron (NM_001037761, intron 2 of 9)	53587	NM_145384	212555	Mm.45131	NM_145384	ENSMUSG00000028744	Pqlc2	BC019216	PQ loop repeat containing 2	protein-coding
mm_75377.1	chr8	45358738	45358819	-	1	NA	intron (NM_153535, intron 1 of 13)	intron (NM_153535, intron 1 of 13)	23513	NM_153535	212326	Mm.51259	NM_153535	ENSMUSG00000070044	Fam149a	AW213256|mKIAA4166	family with sequence similarity 149, member A	protein-coding
mm_77660.1	chr8	124663144	124663230	-	1	NA	5' UTR (NM_175149, exon 1 of 4)	5' UTR (NM_175149, exon 1 of 4)	182	NM_175149	69551	Mm.261920	NM_175149	ENSMUSG00000031983	2310022B05Rik	-	RIKEN cDNA 2310022B05 gene	protein-coding
mm_8096.1	chr1	135847757	135847775	-	1	NA	exon (NM_001130176, exon 6 of 13)	exon (NM_001130176, exon 6 of 13)	6905	NM_001130176	21956	Mm.247470	NM_011619	ENSMUSG00000026414	Tnnt2	Tnt|cTnT	troponin T2, cardiac	protein-coding
mm_19355.1	chr2	91070303	91070346	-	1	NA	promoter-TSS (NR_110981)	promoter-TSS (NR_110981)	-9	NM_001290765	68427	Mm.192375	NM_026721	ENSMUSG00000002105	Slc39a13	1100001L14Rik|AA387663|ZIP-13|ZIP13	solute carrier family 39 (metal ion transporter), member 13	protein-coding
mm_3228.1	chr1	135849344	135849356	+	1	NA	exon (NM_001130176, exon 9 of 13)	exon (NM_001130176, exon 9 of 13)	8489	NM_001130176	21956	Mm.247470	NM_011619	ENSMUSG00000026414	Tnnt2	Tnt|cTnT	troponin T2, cardiac	protein-coding
mm_15420.1	chr2	156840992	156841017	+	1	NA	intron (NM_173396, intron 1 of 2)	CpG	997	NM_173396	228839	Mm.315625	NM_173396	ENSMUSG00000062175	Tgif2	4921501K24|5730599O09Rik|C80753|C81206	TGFB-induced factor homeobox 2	protein-coding
mm_167973.1	chrX	155712220	155712224	-	1	NA	Intergenic	Lx9|LINE|L1	-88895	NM_001093750	211612	Mm.218811	NM_001093750	ENSMUSG00000041552	Ptchd1	9630036J22Rik|AI848149|Gm387	patched domain containing 1	protein-coding
mm_3648.1	chr1	153073695	153073729	+	1	NA	intron (NM_175460, intron 1 of 10)	intron (NM_175460, intron 1 of 10)	112735	NM_008485	16782	Mm.329272	NM_008485	ENSMUSG00000026479	Lamc2	AA589349	laminin, gamma 2	protein-coding
mm_140778.1	chr17	17877106	17877125	-	1	NA	exon (NM_013521, exon 2 of 2)	exon (NM_013521, exon 2 of 2)	6824	NM_013521	14293	Mm.56951	NM_013521	ENSMUSG00000045551	Fpr1	FPR|LXA4R|fMLF-R	formyl peptide receptor 1	protein-coding
mm_68369.1	chr7	107757994	107758010	-	1	NA	promoter-TSS (NM_001205227)	promoter-TSS (NM_001205227)	30	NM_001205227	320635	Mm.132828	NM_177216	ENSMUSG00000048065	Cyb5r2	D630003K02Rik|b5R.2	cytochrome b5 reductase 2	protein-coding
mm_38850.1	chr4	149313970	149313993	-	1	NA	Intergenic	Intergenic	-6248	NM_001290995	16561	Mm.402393	NM_008441	ENSMUSG00000063077	Kif1b	A530096N05Rik|AI448212|AI506502|D4Mil1e|KIF1Bp130|KIF1Bp204	kinesin family member 1B	protein-coding
mm_83703.1	chr9	50693781	50693793	-	1	NA	intron (NM_178118, intron 6 of 19)	intron (NM_178118, intron 6 of 19)	-34007	NM_145614	235339	Mm.285076	NM_145614	ENSMUSG00000000168	Dlat	6332404G05Rik|DLTA|PDC-E2	dihydrolipoamide S-acetyltransferase (E2 component of pyruvate dehydrogenase complex)	protein-coding
mm_6804.1	chr1	84155350	84155352	-	1	NA	intron (NM_001003948, intron 2 of 2)	intron (NM_001003948, intron 2 of 2)	63610	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_70583.1	chr8	13167881	13167893	+	1	NA	exon (NM_010684, exon 4 of 9)	exon (NM_010684, exon 4 of 9)	8726	NM_010684	16783	Mm.16716	NM_010684	ENSMUSG00000031447	Lamp1	CD107a|LGP-120|LGP-A|Lamp-1|P2B	lysosomal-associated membrane protein 1	protein-coding
mm_92603.1	chr10	80105587	80105617	-	1	NA	intron (NR_038088, intron 1 of 4)	intron (NR_038088, intron 1 of 4)	-2900	NM_183426	216161	Mm.262102	NM_183426	ENSMUSG00000035673	Sbno2	BC019206|F730040C21|Sno|Stno	strawberry notch homolog 2 (Drosophila)	protein-coding
mm_28230.1	chr3	88455143	88455166	-	1	NA	intron (NM_001163489, intron 1 of 14)	intron (NM_001163489, intron 1 of 14)	607	NM_013658	20351	Mm.439752	NM_013658	ENSMUSG00000028064	Sema4a	AI132332|SemB|Semab	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A	protein-coding
mm_2755.1	chr1	129273472	129273482	+	1	NA	5' UTR (NM_172485, exon 1 of 28)	5' UTR (NM_172485, exon 1 of 28)	173	NM_172485	210417	Mm.380518	NM_172485	ENSMUSG00000042581	Thsd7b	1700074E13Rik|B930082A18|D130067I03Rik	thrombospondin, type I, domain containing 7B	protein-coding
mm_90223.1	chr10	121034200	121034218	+	1	NA	5' UTR (NM_011915, exon 1 of 10)	5' UTR (NM_011915, exon 1 of 10)	205	NM_011915	24117	Mm.32831	NM_011915	ENSMUSG00000020218	Wif1	AW107799|WIF-1	Wnt inhibitory factor 1	protein-coding
mm_147999.1	chr18	67680875	67680906	-	1	NA	exon (NM_001127177, exon 6 of 9)	exon (NM_001127177, exon 6 of 9)	39291	NM_134138	107047	Mm.150701	NM_134138	ENSMUSG00000024537	Psmg2	1700017I17Rik|AW545363|Clast3|Tnfsf5ip1	proteasome (prosome, macropain) assembly chaperone 2	protein-coding
mm_160394.1	chr8	60655125	60655125	+	1	NA	promoter-TSS (NM_001177882)	promoter-TSS (NM_001177882)	21	NM_001177881	71306	Mm.23242	NM_027756	ENSMUSG00000031647	Mfap3l	4933428A15Rik|5430405D20Rik|AI461995|AW125052|NYD-sp9|mKIAA0626	microfibrillar-associated protein 3-like	protein-coding
mm_32293.1	chr4	103114917	103114983	+	1	NA	promoter-TSS (NM_146254)	promoter-TSS (NM_146254)	560	NM_001286222	71148	Mm.288721	NM_027696	ENSMUSG00000028522	Mier1	4933425I22Rik|5830411K19Rik|er1	MEIR1 treanscription regulator	protein-coding
mm_143422.1	chr17	70845166	70845178	-	1	NA	exon (NM_001164077, exon 2 of 2)	exon (NM_001164077, exon 2 of 2)	1605	NM_001164077	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_144713.1	chr18	35046652	35046680	+	1	NA	Intergenic	Intergenic	-72246	NM_009818	12385	Mm.18962	NM_009818	ENSMUSG00000037815	Ctnna1	2010010M04Rik|AA517462|AI988031|Catna1	catenin (cadherin associated protein), alpha 1	protein-coding
mm_117631.1	chr13	92131819	92131837	-	1	NA	Intergenic	CpG	-143786	NM_009027	19418	Mm.248630	NM_009027	ENSMUSG00000021708	Rasgrf2	6330417G04Rik|AW048350|Grf2|Ras-GRF2	RAS protein-specific guanine nucleotide-releasing factor 2	protein-coding
mm_138041.1	chr17	33920491	33920514	+	1	NA	exon (NM_009318, exon 3 of 8)	exon (NM_009318, exon 3 of 8)	1024	NM_009318	21356	Mm.154457	NM_009318	ENSMUSG00000024308	Tapbp	D17Wsu91e|TPN	TAP binding protein	protein-coding
mm_172599.1	chr8	15519846	15519846	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	462193	NM_008664	17930	Mm.272115	NM_008664	ENSMUSG00000031461	Myom2	AW146149	myomesin 2	protein-coding
mm_31945.1	chr4	86689599	86689605	+	1	NA	Intergenic	Intergenic	-19543	NM_007408	11520	Mm.381	NM_007408	ENSMUSG00000028494	Plin2	AA407157|ADPH|Adfp|Adrp	perilipin 2	protein-coding
mm_109580.1	chr12	112588754	112588842	+	1	NA	promoter-TSS (NM_198411)	promoter-TSS (NM_198411)	14	NM_198411	70435	Mm.250193	NM_198411	ENSMUSG00000037679	Inf2	2610204M08Rik|AA589465|AW125550|EG629699	inverted formin, FH2 and WH2 domain containing	protein-coding
mm_146836.1	chr18	22850739	22850759	-	1	NA	intron (NM_001347510, intron 5 of 9)	intron (NM_001347510, intron 5 of 9)	187914	NM_001161483	319211	Mm.209896	NM_199024	ENSMUSG00000041923	Nol4	1700013J13Rik|4930568N03Rik|Gm1262	nucleolar protein 4	protein-coding
mm_61547.1	chr7	79363621	79363644	+	1	NA	Intergenic	Intergenic	23395	NM_020599	19771	Mm.41653	NM_020599	ENSMUSG00000039194	Rlbp1	3110056M11Rik|CRALBP	retinaldehyde binding protein 1	protein-coding
mm_63203.1	chr7	125829530	125829548	+	1	NA	intron (NM_001081022, intron 13 of 27)	intron (NM_001081022, intron 13 of 27)	121663	NM_001081022	233865	Mm.274389	NM_001081022	ENSMUSG00000032743	D430042O09Rik	Kiaa0556	RIKEN cDNA D430042O09 gene	protein-coding
mm_156812.1	chrX	164090189	164090201	+	1	NA	promoter-TSS (NM_020626)	promoter-TSS (NM_020626)	8	NM_020626	57394	Mm.143766	NM_020626	ENSMUSG00000015401	Tmem27	0610008J07Rik|NX-17|NX17	transmembrane protein 27	protein-coding
mm_155252.1	chrX	57223975	57223985	+	1	NA	TTS (NM_011616)	TTS (NM_011616)	11837	NM_011616	21947	Mm.4861	NM_011616	ENSMUSG00000031132	Cd40lg	CD154|CD40-L|Cd40l|HIGM1|IGM|IMD3|Ly-62|Ly62|T-BAM|TRAP|Tnfsf5|Tnlg8b|gp39	CD40 ligand	protein-coding
mm_144326.1	chr18	12955822	12955851	+	1	NA	Intergenic	Intergenic	-13995	NM_207530	64291	Mm.259470	NM_020573	ENSMUSG00000044252	Osbpl1a	G430090F17Rik|Gm753|ORP-1|Osbpl1b	oxysterol binding protein-like 1A	protein-coding
mm_143664.1	chr17	79857344	79857346	-	1	NA	intron (NM_001286647, intron 6 of 12)	intron (NM_001286647, intron 6 of 12)	38778	NM_178050	56298	Mm.175403	NM_019717	ENSMUSG00000059811	Atl2	2010110I21Rik|AA407293|AV334690|Aip-2|Arl6ip2	atlastin GTPase 2	protein-coding
mm_115421.1	chr13	117218389	117218395	+	1	NA	Intergenic	RMER17C|LTR|ERVK	-2181	NM_010330	13723	Mm.274926	NM_010330	ENSMUSG00000021728	Emb	AL022799|Gp70	embigin	protein-coding
mm_21702.1	chr2	164568493	164568512	-	1	NA	TTS (NM_026323)	TTS (NM_026323)	4954	NM_001177401	629747	Mm.234248	NM_001177401	ENSMUSG00000074596	Spint3	Gm14315|OTTMUSG00000016288	serine peptidase inhibitor, Kunitz type, 3	protein-coding
mm_53272.1	chr6	128485594	128485605	+	1	NA	exon (NM_007376, exon 34 of 36)	exon (NM_007376, exon 34 of 36)	41121	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_165592.1	chr3	35937387	35937390	-	1	NA	Intergenic	Intergenic	-4422	NM_001205361	114893	Mm.374810	NM_033623	ENSMUSG00000027708	Dcun1d1	Rp42|SCCRO|Tes3|pTes3	DCN1, defective in cullin neddylation 1, domain containing 1 (S. cerevisiae)	protein-coding
mm_124826.1	chr15	9092206	9092213	+	1	NA	intron (NM_001040395, intron 5 of 12)	intron (NM_001040395, intron 5 of 12)	20949	NM_001040395	68646	Mm.244226	NM_001040395	ENSMUSG00000022253	Nadk2	MNADK|Nadkd1	NAD kinase 2, mitochondrial	protein-coding
mm_23096.1	chr3	37063699	37063700	+	1	NA	promoter-TSS (NM_009350)	promoter-TSS (NM_009350)	43	NM_009350	21744	Mm.8122	NM_009350	ENSMUSG00000027719	Adad1	Tenr	adenosine deaminase domain containing 1 (testis specific)	protein-coding
mm_120486.1	chr14	65976931	65976953	+	1	NA	exon (NM_013492, exon 6 of 9)	exon (NM_013492, exon 6 of 9)	8459	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_10429.1	chr2	14073608	14073625	+	1	NA	promoter-TSS (NM_011484)	promoter-TSS (NM_011484)	318	NR_038162	70957	Mm.399049	NR_038162	ENSMUSG00000086657	Stamos	4921530L18Rik	signal transducing adaptor molecule (SH3 domain and ITAM motif) 1, opposite strand	ncRNA
mm_128943.1	chr15	74734359	74734367	-	1	NA	promoter-TSS (NM_026671)	promoter-TSS (NM_026671)	-50	NM_026671	68311	Mm.306880	NM_026671	ENSMUSG00000022595	Lypd2	0610005K03Rik|Lypdc2|VLL	Ly6/Plaur domain containing 2	protein-coding
mm_80429.1	chr9	77921523	77921527	+	1	NA	intron (NM_134255, intron 1 of 7)	intron (NM_134255, intron 1 of 7)	4160	NM_134255	68801	Mm.430736	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	ELOVL family member 5, elongation of long chain fatty acids (yeast)	protein-coding
mm_120580.1	chr14	69695425	69695430	+	1	NA	3' UTR (NM_033325, exon 14 of 14)	3' UTR (NM_033325, exon 14 of 14)	3179	NR_105915	102465573		NR_105915	ENSMUSG00000098666	Mir6950	Gm27586|mmu-mir-6950	microRNA 6950	ncRNA
mm_22434.1	chr2	181689154	181689192	-	1	NA	exon (NM_026446, exon 6 of 6)	exon (NM_026446, exon 6 of 6)	2644	NM_001291205	56470	Mm.274366	NM_026446	ENSMUSG00000002458	Rgs19	2610042F04Rik|AI324841|AW547781|GAIP	regulator of G-protein signaling 19	protein-coding
mm_49148.1	chr6	11926129	11926195	+	1	NA	5' UTR (NM_001168382, exon 1 of 18)	5' UTR (NM_001168382, exon 1 of 18)	281	NM_001168382	75725	Mm.212411	NM_029404	ENSMUSG00000029629	Phf14	1110001C23Rik|4932409F11Rik|5730446A07Rik|AA623952|AV297001|mKIAA0783	PHD finger protein 14	protein-coding
mm_152754.1	chr19	20123891	20123908	-	1	NA	Intergenic	Intergenic	266772	NM_010730	16952	Mm.248360	NM_010730	ENSMUSG00000024659	Anxa1	Anx-1|Anx-A1|C430014K04Rik|Lpc-1|Lpc1	annexin A1	protein-coding
mm_199.1	chr1	16105331	16105359	+	1	NA	promoter-TSS (NM_133832)	promoter-TSS (NM_133832)	-537	NM_133832	98711	Mm.274376	NM_133832	ENSMUSG00000025921	Rdh10	3110069K09Rik|4921506A21Rik|AI875664|AW549993|D1Ertd762e|m366Asp	retinol dehydrogenase 10 (all-trans)	protein-coding
mm_135877.1	chr16	63600556	63600556	-	1	NA	intron (NM_010140, intron 9 of 16)	intron (NM_010140, intron 9 of 16)	263601	NM_010140	13837	Mm.1977	NM_010140	ENSMUSG00000052504	Epha3	AW492086|Cek4|ETK1|End3|Hek|Hek4|Mek4|Tyro4	Eph receptor A3	protein-coding
mm_15978.1	chr2	166548658	166548698	+	1	NA	Intergenic	ORR1D1|LTR|ERVL-MaLR	101227	NR_015558	319684	Mm.399746	NR_015558		5031425F14Rik	-	RIKEN cDNA 5031425F14 gene	ncRNA
mm_66485.1	chr7	45019274	45019290	-	1	NA	intron (NM_009101, intron 1 of 5)	intron (NM_009101, intron 1 of 5)	1275	NM_009101	20130	Mm.389894	NM_009101	ENSMUSG00000038387	Rras	AI573426	related RAS viral (r-ras) oncogene	protein-coding
mm_55106.1	chr6	50261792	50261813	-	1	NA	promoter-TSS (NM_018769)	promoter-TSS (NM_018769)	-33	NM_018769	54722	Mm.248361	NM_018769	ENSMUSG00000029821	Dfna5	2310037D07Rik|4932441K13Rik|Dfna5h|EG14210|Fin15	deafness, autosomal dominant 5 (human)	protein-coding
mm_104605.1	chr11	97187816	97187835	-	1	NA	promoter-TSS (NM_008379)	promoter-TSS (NM_008379)	67	NM_008379	16211	Mm.251013	NM_008379	ENSMUSG00000001440	Kpnb1	AA409963|IPOB|Impnb	karyopherin (importin) beta 1	protein-coding
mm_144591.1	chr18	32162973	32162982	+	1	NA	promoter-TSS (NM_011946)	promoter-TSS (NM_011946)	-112	NM_011946	26405	Mm.211762	NM_011946	ENSMUSG00000024383	Map3k2	9630061B06Rik|AI585793|Mekk2|Mekk2b	mitogen-activated protein kinase kinase kinase 2	protein-coding
mm_60862.1	chr7	45897047	45897089	+	1	NA	promoter-TSS (NM_144801)	promoter-TSS (NM_144801)	-1	NM_144801	70209	Mm.163766	NM_144801	ENSMUSG00000002781	Tmem143	2310076O21Rik|AI481604	transmembrane protein 143	protein-coding
mm_93089.1	chr10	89621280	89621290	-	1	NA	promoter-TSS (NM_182959)	promoter-TSS (NM_182959)	-36	NM_182959	216227	Mm.233921	NM_182959	ENSMUSG00000019935	Slc17a8	BC042593|Vglut3	solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 8	protein-coding
mm_108881.1	chr12	99964671	99964697	+	1	NA	5' UTR (NM_001164426, exon 1 of 3)	5' UTR (NM_001164426, exon 1 of 3)	185	NM_001164427	217826	Mm.312335	NM_146037	ENSMUSG00000045404	Kcnk13	BB085247|F730021E22Rik|Gm1570|Gm1685	potassium channel, subfamily K, member 13	protein-coding
mm_137375.1	chr17	25717189	25717213	+	1	NA	promoter-TSS (NM_022422)	promoter-TSS (NM_022422)	29	NM_022422	64337	Mm.171123	NM_022422	ENSMUSG00000025739	Gng13	1500031D04Rik|AB030194|Ggamma13	guanine nucleotide binding protein (G protein), gamma 13	protein-coding
mm_13495.1	chr2	106987217	106987217	+	1	NA	Intergenic	Intergenic	-12820	NM_001025102	212772	Mm.381231	NM_173750	ENSMUSG00000027122	Arl14ep	2700007P21Rik|4930448O08Rik|ARF7EP	ADP-ribosylation factor-like 14 effector protein	protein-coding
mm_55921.1	chr6	83845118	83845127	-	1	NA	Intergenic	Intergenic	-13381	NM_146169	232164	Mm.404420	NM_146169	ENSMUSG00000045896	Paip2b	-	poly(A) binding protein interacting protein 2B	protein-coding
mm_166643.1	chr6	83775929	83775941	+	1	NA	promoter-TSS (NM_009357)	promoter-TSS (NM_009357)	-123	NM_009357	21766	Mm.28371	NM_009357	ENSMUSG00000014748	Tex261	3110001O07Rik|AA409339|AI480706|AL033351|TEG-261	testis expressed gene 261	protein-coding
mm_105803.1	chr11	110241659	110241665	-	1	NA	exon (NM_147218, exon 7 of 39)	exon (NM_147218, exon 7 of 39)	10114	NM_147218	76184	Mm.159704	NM_147218	ENSMUSG00000044749	Abca6	6330565N06Rik	ATP-binding cassette, sub-family A (ABC1), member 6	protein-coding
mm_47716.1	chr5	130000925	130000955	-	1	NA	exon (NM_010368, exon 2 of 12)	exon (NM_010368, exon 2 of 12)	1888	NM_010368	110006	Mm.3317	NM_010368	ENSMUSG00000025534	Gusb	AI747421|Gur|Gus|Gus-r|Gus-s|Gus-t|Gus-u|Gut|asd|g	glucuronidase, beta	protein-coding
mm_17397.1	chr2	27142503	27142513	-	1	NA	promoter-TSS (NM_175427)	promoter-TSS (NM_175427)	-31	NM_175427	109349	Mm.314080	NM_175427	ENSMUSG00000009216	Fam163b	C630035N08Rik	family with sequence similarity 163, member B	protein-coding
mm_167644.1	chr9	64830121	64830130	-	1	NA	intron (NM_001162917, intron 2 of 34)	intron (NM_001162917, intron 2 of 34)	19114	NM_001162917	102442	Mm.222473	NM_176935	ENSMUSG00000053641	Dennd4a	AI115600|AI851943|F730015K02Rik	DENN/MADD domain containing 4A	protein-coding
mm_87529.1	chr10	53344084	53344097	+	1	NA	3' UTR (NM_001141927, exon 3 of 3)	3' UTR (NM_001141927, exon 3 of 3)	6404	NM_001141927	18821	Mm.34145	NM_023129	ENSMUSG00000038583	Pln	Plb	phospholamban	protein-coding
mm_139550.1	chr17	56831354	56831367	+	1	NA	promoter-TSS (NM_009056)	promoter-TSS (NM_009056)	-352	NM_027787	19725	Mm.102	NM_009056	ENSMUSG00000024206	Rfx2	5430432H19Rik	regulatory factor X, 2 (influences HLA class II expression)	protein-coding
mm_53334.1	chr6	129235090	129235101	+	1	NA	intron (NR_040265, intron 1 of 2)	RMER17C|LTR|ERVK	2950	NR_040265	76432	Mm.261738	NR_040265	ENSMUSG00000097354	2310001H17Rik	AI646108	RIKEN cDNA 2310001H17 gene	ncRNA
mm_120780.1	chr14	74641378	74641395	+	1	NA	5' UTR (NM_172812, exon 1 of 3)	5' UTR (NM_172812, exon 1 of 3)	546	NM_172812	15558	Mm.214351	NM_172812	ENSMUSG00000034997	Htr2a	E030013E04|Htr-2|Htr2	5-hydroxytryptamine (serotonin) receptor 2A	protein-coding
mm_149270.1	chr19	10582271	10582280	+	1	NA	intron (NM_001282067, intron 4 of 8)	intron (NM_001282067, intron 4 of 8)	-4889	NR_126092	72982	Mm.391194	NM_028411	ENSMUSG00000024666	Tmem138	1700113I01Rik|2900055D14Rik	transmembrane protein 138	protein-coding
mm_23758.1	chr3	70007669	70007679	+	1	NA	promoter-TSS (NM_001018031)	promoter-TSS (NM_001018031)	61	NM_001018031	229389	Mm.331071	NM_001018031	ENSMUSG00000027788	Otol1	Gm414	otolin 1	protein-coding
mm_84243.1	chr9	62343567	62343599	-	1	NA	intron (NM_009672, intron 1 of 6)	CpG	2240	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	protein-coding
mm_114807.1	chr13	91461146	91461188	+	1	NA	promoter-TSS (NM_024186)	promoter-TSS (NM_024186)	70	NM_024186	66970	Mm.343095	NM_024186	ENSMUSG00000003992	Ssbp2	1500004K09Rik|2310079I02Rik|9330163K02Rik|A830008M03Rik|AU067692|AW558684|Hspc116|SSDP2	single-stranded DNA binding protein 2	protein-coding
mm_41603.1	chr5	96210129	96210161	+	1	NA	promoter-TSS (NM_053158)	promoter-TSS (NM_053158)	30	NM_053158	94061	Mm.295499	NM_053158	ENSMUSG00000029486	Mrpl1	2410002L03Rik|5830418D04Rik|AI462572|L1mt	mitochondrial ribosomal protein L1	protein-coding
mm_29542.1	chr3	116712242	116712269	-	1	NA	promoter-TSS (NM_144902)	promoter-TSS (NM_144902)	25	NM_144902	229782	Mm.190758	NM_144902	ENSMUSG00000027957	Slc35a3	2310050P13Rik	solute carrier family 35 (UDP-N-acetylglucosamine (UDP-GlcNAc) transporter), member 3	protein-coding
mm_102318.1	chr11	57481784	57481787	-	1	NA	Intergenic	B1_Mur1|SINE|Alu	36859	NM_001168667	67726	Mm.25632	NM_026342	ENSMUSG00000020523	Fam114a2	1810073G14Rik|9030624B09Rik	family with sequence similarity 114, member A2	protein-coding
mm_122660.1	chr14	51912328	51912346	-	1	NA	intron (NM_013864, intron 1 of 15)	intron (NM_013864, intron 1 of 15)	1151	NM_001145959	29811	Mm.26722	NM_013864	ENSMUSG00000004558	Ndrg2	AI182517|AU040374|Ndr2|SYLD	N-myc downstream regulated gene 2	protein-coding
mm_46922.1	chr5	114669756	114669759	-	1	NA	3' UTR (NM_019821, exon 5 of 5)	3' UTR (NM_019821, exon 5 of 5)	-11336	NM_022017	63873	Mm.266450	NM_022017	ENSMUSG00000014158	Trpv4	0610033B08Rik|OTRPC4|Trp12|VR-OAC|VRL-2|VROAC	transient receptor potential cation channel, subfamily V, member 4	protein-coding
mm_52269.1	chr6	108473085	108473101	+	1	NA	intron (NM_010585, intron 45 of 61)	MIRc|SINE|MIR	-16650	NR_106121	102465766		NR_106121	ENSMUSG00000105697	Mir7661	mmu-mir-7661	microRNA 7661	ncRNA
mm_99011.1	chr11	98836868	98836878	+	1	NA	promoter-TSS (NM_001080925)	promoter-TSS (NM_001080925)	88	NM_001080925	268480	Mm.340766	NM_001080925	ENSMUSG00000038020	Rapgefl1	B230105J10	Rap guanine nucleotide exchange factor (GEF)-like 1	protein-coding
mm_10081.1	chr1	195176638	195176646	-	1	NA	promoter-TSS (NM_007758)	promoter-TSS (NM_007758)	73	NM_007758	12902	Mm.235387	NM_007758	ENSMUSG00000026616	Cr2	C3DR|CD21|CD35|Cr-1|Cr-2|Cr1	complement receptor 2	protein-coding
mm_31596.1	chr4	57892951	57892968	+	1	NA	exon (NM_001035533, exon 4 of 4)	exon (NM_001035533, exon 4 of 4)	23305	NM_178727	242484	Mm.23214	NM_178727	ENSMUSG00000052117	D630039A03Rik	-	RIKEN cDNA D630039A03 gene	protein-coding
mm_51346.1	chr6	72549733	72549763	+	1	NA	5' UTR (NM_001271395, exon 1 of 10)	5' UTR (NM_001271395, exon 1 of 10)	101	NM_001271395	12332	Mm.18626	NM_007599	ENSMUSG00000056737	Capg	gCap39|mbh1	capping protein (actin filament), gelsolin-like	protein-coding
mm_99483.1	chr11	102606245	102606254	+	1	NA	exon (NM_020510, exon 1 of 1)	exon (NM_020510, exon 1 of 1)	1818	NM_020510	57265	Mm.36416	NM_020510	ENSMUSG00000050288	Fzd2	AL033370|AW456835|Fz10|Fzd10|Mfz10|Mfz10a	frizzled class receptor 2	protein-coding
mm_145529.1	chr18	60774615	60774625	+	1	NA	promoter-TSS (NM_020600)	promoter-TSS (NM_020600)	24	NM_020600	20044	Mm.43778	NM_020600	ENSMUSG00000024608	Rps14	2600014J02Rik|AL023078	ribosomal protein S14	protein-coding
mm_28069.1	chr3	84270743	84270775	-	1	NA	promoter-TSS (NM_001271725)	promoter-TSS (NM_001271725)	24	NM_001271725	80890	Mm.44876	NM_030706	ENSMUSG00000027993	Trim2	mKIAA0517|narf	tripartite motif-containing 2	protein-coding
mm_37167.1	chr4	117156200	117156227	-	1	NA	promoter-TSS (NR_030704)	promoter-TSS (NR_030704)	-81	NM_009098	20116	Mm.260904	NM_009098	ENSMUSG00000047675	Rps8	-	ribosomal protein S8	protein-coding
mm_110428.1	chr12	46819044	46819058	-	1	NA	promoter-TSS (NM_021361)	promoter-TSS (NM_021361)	-276	NM_021361	664883	Mm.247195	NM_021361	ENSMUSG00000021047	Nova1	9430099M15Rik|G630039L02|Nova-1	neuro-oncological ventral antigen 1	protein-coding
mm_22075.1	chr2	168749485	168749512	-	1	NA	3' UTR (NM_201396, exon 3 of 3)	3' UTR (NM_201396, exon 3 of 3)	-7362	NM_001289446	11981	Mm.330819	NM_015731	ENSMUSG00000027546	Atp9a	IIa	ATPase, class II, type 9A	protein-coding
mm_55604.1	chr6	71830698	71830701	-	1	NA	promoter-TSS (NM_029673)	promoter-TSS (NM_029673)	-621	NM_001253681	76614	Mm.235123	NM_029673	ENSMUSG00000052337	Immt	1700082C19Rik|D830041H16Rik|HMP|P87|P87/89|P89	inner membrane protein, mitochondrial	protein-coding
mm_37739.1	chr4	129578522	129578532	-	1	NA	promoter-TSS (NM_182783)	promoter-TSS (NM_182783)	53	NM_182783	230766	Mm.20377	NM_182783	ENSMUSG00000050493	Fam167b	SEC	family with sequence similarity 167, member B	protein-coding
mm_39604.1	chr5	23850591	23850607	+	1	NA	promoter-TSS (NR_045042)	promoter-TSS (NR_045042)	2	NR_045040	67194	Mm.423733	NR_045040	ENSMUSG00000097180	2700038G22Rik	-	RIKEN cDNA 2700038G22 gene	ncRNA
mm_128060.1	chr15	26705751	26705754	-	1	NA	intron (NM_176959, intron 2 of 3)	intron (NM_176959, intron 2 of 3)	189812	NM_176959	448987	Mm.253378	NM_176959	ENSMUSG00000043556	Fbxl7	AL023057|D230018M15Rik|FBL7|Fbl6	F-box and leucine-rich repeat protein 7	protein-coding
mm_139024.1	chr17	46159213	46159223	+	1	NA	Intergenic	Intergenic	-1814	NM_019581	56055	Mm.22147	NM_019581	ENSMUSG00000023952	Gtpbp2	nmf205	GTP binding protein 2	protein-coding
mm_71345.1	chr8	45627977	45628001	+	1	NA	5' UTR (NM_001310707, exon 1 of 24)	5' UTR (NM_001310707, exon 1 of 24)	238	NM_001310707	234214	Mm.211096	NM_172752	ENSMUSG00000031626	Sorbs2	2010203O03Rik|9430041O17Rik|A530071H08|Argbp2|mKIAA0777|nArgBP2	sorbin and SH3 domain containing 2	protein-coding
mm_10693.1	chr2	22622447	22622461	+	1	NA	5' UTR (NM_008078, exon 1 of 16)	5' UTR (NM_008078, exon 1 of 16)	127	NM_008078	14417	Mm.4784	NM_008078	ENSMUSG00000026787	Gad2	6330404F12Rik|GAD(65)|GAD65|Gad-2	glutamic acid decarboxylase 2	protein-coding
mm_79765.1	chr9	62772928	62772941	+	1	NA	intron (NM_176922, intron 23 of 29)	intron (NM_176922, intron 23 of 29)	38714	NM_010193	14155	Mm.24069	NM_010193	ENSMUSG00000032244	Fem1b	mKIAA0396	feminization 1 homolog b (C. elegans)	protein-coding
mm_45289.1	chr5	65019118	65019120	-	1	NA	intron (NM_026667, intron 7 of 13)	intron (NM_026667, intron 7 of 13)	48801	NR_030577	100124451		NR_030577	ENSMUSG00000077042	Mir574	Mirn574|mir-574|mmu-mir-574	microRNA 574	ncRNA
mm_14567.1	chr2	135146732	135146735	+	1	NA	intron (NM_019677, intron 3 of 32)	intron (NM_019677, intron 3 of 32)	68883	NR_040517	78805	Mm.78702	NR_040517	ENSMUSG00000085247	4930545L23Rik	-	RIKEN cDNA 4930545L23 gene	ncRNA
mm_130363.1	chr15	97786957	97786963	-	1	NA	intron (NM_026353, intron 1 of 2)	intron (NM_026353, intron 1 of 2)	2595	NM_026353	67739	Mm.28955	NM_026353	ENSMUSG00000081534	Slc48a1	4930570C03Rik	solute carrier family 48 (heme transporter), member 1	protein-coding
mm_1586.1	chr1	74295999	74296001	+	1	NA	intron (NM_027154, intron 1 of 11)	intron (NM_027154, intron 1 of 11)	8336	NM_027154	69660	Mm.261182	NM_027154	ENSMUSG00000006301	Tmbim1	2310061B02Rik|AA960455|AU024746|C78899|RECS1|Tmbib1|mKIAA4161	transmembrane BAX inhibitor motif containing 1	protein-coding
mm_90279.1	chr10	122817971	122817987	+	1	NA	intron (NM_176919, intron 4 of 8)	MER5A|DNA|hAT-Charlie	138664	NR_106182	102466884		NR_106182	ENSMUSG00000099225	Mir8104	Gm27380|mmu-mir-8104	microRNA 8104	ncRNA
mm_111381.1	chr12	87388249	87388289	-	1	NA	promoter-TSS (NM_011479)	promoter-TSS (NM_011479)	86	NM_011479	20773	Mm.565	NM_011479	ENSMUSG00000021036	Sptlc2	LCB2|LCB2a|Spt2	serine palmitoyltransferase, long chain base subunit 2	protein-coding
mm_138719.1	chr17	36869533	36869541	+	1	NA	promoter-TSS (NM_011280)	promoter-TSS (NM_011280)	-37	NM_011280	19824	Mm.299155	NM_011280	ENSMUSG00000073400	Trim10	AI324236|BB139825|Herf1|Rnf9	tripartite motif-containing 10	protein-coding
mm_2521.1	chr1	106407311	106407316	+	1	NA	Intergenic	Intergenic	139318	NR_106164	102466254		NR_106164	ENSMUSG00000098344	Mir3473f	Gm27846|mmu-mir-3473f	microRNA 3473f	ncRNA
mm_85537.1	chr9	106570984	106571005	-	1	NA	promoter-TSS (NM_026090)	promoter-TSS (NM_026090)	-27	NM_026090	67320	Mm.335431	NM_026090	ENSMUSG00000041009	Iqcf4	1700042N06Rik|mtIQ1	IQ motif containing F4	protein-coding
mm_81300.1	chr9	108339268	108339284	+	1	NA	5' UTR (NM_008160, exon 1 of 2)	5' UTR (NM_008160, exon 1 of 2)	196	NM_001329528	14775	Mm.1090	NM_008160	ENSMUSG00000063856	Gpx1	AI195024|AL033363|CGPx|GPx-1|GSHPx-1|Gpx	glutathione peroxidase 1	protein-coding
mm_72429.1	chr8	82863454	82863474	+	1	NA	5' UTR (NM_177378, exon 1 of 7)	5' UTR (NM_177378, exon 1 of 7)	108	NM_177378	330812	Mm.491438	NM_177378	ENSMUSG00000047747	Rnf150	A630007N06Rik|C030044C12Rik|Greul5|mKIAA1214	ring finger protein 150	protein-coding
mm_61921.1	chr7	90153554	90153569	+	1	NA	intron (NM_001252520, intron 1 of 20)	B1F1|SINE|Alu	23329	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_82797.1	chr9	29412378	29412393	-	1	NA	intron (NM_172290, intron 1 of 7)	CpG	550744	NM_172290	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding
mm_97646.1	chr11	79339850	79339913	+	1	NA	promoter-TSS (NM_010897)	promoter-TSS (NM_010897)	-11	NM_010897	18015	Mm.255596	NM_010897	ENSMUSG00000020716	Nf1	AW494271|Dsk9|E030030H24Rik|Mhdadsk9|Nf-1	neurofibromin 1	protein-coding
mm_92467.1	chr10	78009738	78009757	-	1	NA	promoter-TSS (NM_008826)	promoter-TSS (NM_008826)	49	NM_008826	18641	Mm.269649	NM_008826	ENSMUSG00000020277	Pfkl	AA407869|ATP-PFK|PFK-L	phosphofructokinase, liver, B-type	protein-coding
mm_69044.1	chr7	126800607	126800655	-	1	NA	promoter-TSS (NM_001177308)	promoter-TSS (NM_001177308)	-184	NM_001177308	11674	Mm.275831	NM_007438	ENSMUSG00000030695	Aldoa	Aldo-1|Aldo1	aldolase A, fructose-bisphosphate	protein-coding
mm_75809.1	chr8	70302447	70302478	-	1	NA	promoter-TSS (NM_021538)	promoter-TSS (NM_021538)	-10	NM_001024922	234374	Mm.388127	NM_001024922	ENSMUSG00000057788	Ddx49	R27090_2	DEAD (Asp-Glu-Ala-Asp) box polypeptide 49	protein-coding
mm_128436.1	chr15	50688064	50688081	-	1	NA	intron (NM_001310481, intron 4 of 5)	intron (NM_001310481, intron 4 of 5)	200977	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_161722.1	chr17	27705901	27705901	+	1	NA	intron (NM_011861, intron 5 of 9)	intron (NM_011861, intron 5 of 9)	20662	NM_178365	23969	Mm.4926	NM_011861	ENSMUSG00000040276	Pacsin1	A830061D09Rik|H74|mKIAA1379|syndapin	protein kinase C and casein kinase substrate in neurons 1	protein-coding
mm_20273.1	chr2	126810239	126810241	-	1	NA	intron (NM_021450, intron 26 of 38)	intron (NM_021450, intron 26 of 38)	-26780	NM_029163	75083	Mm.389373	NM_029163	ENSMUSG00000027364	Usp50	1700086G18Rik|4930511O11Rik	ubiquitin specific peptidase 50	protein-coding
mm_65123.1	chr7	19421327	19421351	-	1	NA	promoter-TSS (NR_073015)	promoter-TSS (NR_073015)	78	NR_073014	100503495	Mm.410762	NR_073014	ENSMUSG00000040705	A930016O22Rik	-	RIKEN cDNA A930016O22 gene	ncRNA
mm_113107.1	chr13	24415105	24415123	+	1	NA	promoter-TSS (NM_001284520)	promoter-TSS (NM_001284520)	-8	NM_007717	12763	Mm.8396	NM_007717	ENSMUSG00000016756	Cmah	-	cytidine monophospho-N-acetylneuraminic acid hydroxylase	protein-coding
mm_38318.1	chr4	137321103	137321155	-	1	NA	TTS (NM_001243769)	TTS (NM_001243769)	36630	NM_009861	12540	Mm.1022	NM_009861	ENSMUSG00000006699	Cdc42	AI747189|AU018915	cell division cycle 42	protein-coding
mm_45150.1	chr5	49285654	49285699	-	1	NA	promoter-TSS (NM_001199244)	promoter-TSS (NM_001199244)	-17	NM_001199244	80334	Mm.160172	NM_030265	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding
mm_93969.1	chr10	127289057	127289067	-	1	NA	promoter-TSS (NM_001347171)	promoter-TSS (NM_001347171)	-44	NM_033072	110962	Mm.372826	NM_033072	ENSMUSG00000025409	Mbd6	D10Wsu93e	methyl-CpG binding domain protein 6	protein-coding
mm_98585.1	chr11	95748643	95748687	+	1	NA	promoter-TSS (NM_201609)	promoter-TSS (NM_201609)	-402	NM_201609	268469	Mm.389038	NM_201609	ENSMUSG00000075595	Zfp652	9530033F24Rik|ZNF652	zinc finger protein 652	protein-coding
mm_165712.1	chr3	98858302	98858305	-	1	NA	5' UTR (NM_008293, exon 2 of 5)	5' UTR (NM_008293, exon 2 of 5)	1491	NM_001304800	15492	Mm.140811	NM_008293	ENSMUSG00000027871	Hsd3b1	3-beta-HSD I|D3Ertd383e	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1	protein-coding
mm_44171.1	chr5	150925044	150925049	+	1	NA	Intergenic	Intergenic	-27561	NM_013823	16591	Mm.6500	NM_013823	ENSMUSG00000058488	Kl	alpha-kl	klotho	protein-coding
mm_76719.1	chr8	94838208	94838246	-	1	NA	promoter-TSS (NM_026452)	promoter-TSS (NM_026452)	113	NM_134141	109006	Mm.27582	NM_134141	ENSMUSG00000031781	Ciapin1	2810413N20Rik|AA617265|AU021794|anamorsin	cytokine induced apoptosis inhibitor 1	protein-coding
mm_6105.1	chr1	64030362	64030381	-	1	NA	Intergenic	Intergenic	12130	NR_105864	102466760		NR_105864	ENSMUSG00000098487	Mir6899	Gm27384|mmu-mir-6899	microRNA 6899	ncRNA
mm_33775.1	chr4	134496997	134497013	+	1	NA	promoter-TSS (NM_001285849)	promoter-TSS (NM_001285849)	-36	NM_001285849	71904	Mm.142343	NM_027995	ENSMUSG00000037348	Paqr7	2310021M12Rik|AV001994|BB007237|Mpra|PGLP|mPR	progestin and adipoQ receptor family member VII	protein-coding
mm_6515.1	chr1	74394698	74394709	-	1	NA	TTS (NR_029743)	TTS (NR_029743)	393	NR_029743	387219		NR_029743	ENSMUSG00000065468	Mir26b	Mirn26b|mir-26b|mmu-mir-26b	microRNA 26b	ncRNA
mm_131418.1	chr16	14705869	14705885	+	1	NA	promoter-TSS (NM_011415)	promoter-TSS (NM_011415)	18	NM_011415	20583	Mm.4272	NM_011415	ENSMUSG00000022676	Snai2	Slug|Slugh|Snail2	snail family zinc finger 2	protein-coding
mm_60902.1	chr7	46712069	46712085	+	1	NA	TTS (NM_011315)	TTS (NM_011315)	-1426	NM_030233	78935	Mm.289866	NM_030233	ENSMUSG00000006763	Saal1	5031425D22Rik|SPACIA1	serum amyloid A-like 1	protein-coding
mm_150338.1	chr19	34575796	34575809	+	1	NA	3' UTR (NM_008332, exon 3 of 3)	3' UTR (NM_008332, exon 3 of 3)	-7727	NM_010501	15959	Mm.426079	NM_010501	ENSMUSG00000074896	Ifit3	Ifi49|P49	interferon-induced protein with tetratricopeptide repeats 3	protein-coding
mm_59150.1	chr7	24370021	24370030	+	1	NA	promoter-TSS (NM_001163510)	promoter-TSS (NM_001163510)	-238	NM_001163510	16534	Mm.9911	NM_008433	ENSMUSG00000054342	Kcnn4	IK1|IKCA1|KCA4|KCa3.1|SK4|SKCas|mIKCa1	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4	protein-coding
mm_44477.1	chr5	23433914	23433931	-	1	NA	promoter-TSS (NM_026984)	promoter-TSS (NM_026984)	431	NR_040469	269630	Mm.425231	NR_040469	ENSMUSG00000073147	5031425E22Rik	-	RIKEN cDNA 5031425E22 gene	ncRNA
mm_6155.1	chr1	64994634	64994640	-	1	NA	Intergenic	Intergenic	-37813	NM_001039493	241075	Mm.239534	NM_175509	ENSMUSG00000051344	Plekhm3	9430067K14Rik|A230102O09Rik|AI449570|DAPR|Plekhm1l	pleckstrin homology domain containing, family M, member 3	protein-coding
mm_60209.1	chr7	43440822	43440840	+	1	NA	promoter-TSS (NM_028849)	promoter-TSS (NM_028849)	15	NM_028849	74276	Mm.159153	NM_028849	ENSMUSG00000038973	Cldnd2	1700071E18Rik	claudin domain containing 2	protein-coding
mm_166761.1	chr6	129350480	129350491	+	1	NA	exon (NM_177686, exon 1 of 6)	exon (NM_177686, exon 1 of 6)	241	NM_177686	232413	Mm.90241	NM_177686	ENSMUSG00000053063	Clec12a	CLL-1|D230024O04|KLRL1|Micl	C-type lectin domain family 12, member a	protein-coding
mm_1207.1	chr1	62726398	62726408	+	1	NA	intron (NM_001077405, intron 2 of 15)	MIRb|SINE|MIR	23086	NM_001077405	18187	Mm.266341	NM_010939	ENSMUSG00000025969	Nrp2	1110048P06Rik|Np-2|Np2|Npn-2|Npn2	neuropilin 2	protein-coding
mm_30135.1	chr3	142169312	142169329	-	1	NA	promoter-TSS (NM_001277217)	promoter-TSS (NM_001277217)	-92	NM_001277216	12167	Mm.39089	NM_007560	ENSMUSG00000052430	Bmpr1b	AI385617|ALK-6|AV355320|Acvrlk6|Alk6|BMPR-1B|BMPR-IB|CFK-43a|SKR6	bone morphogenetic protein receptor, type 1B	protein-coding
mm_134447.1	chr16	18289200	18289260	-	1	NA	promoter-TSS (NM_033324)	promoter-TSS (NM_033324)	-62	NM_033324	94223	Mm.447352	NM_033324	ENSMUSG00000022718	Dgcr8	D16H22S1742E|D16H22S788E|D16Wis2|Gy1|N41|Vo59c07|mir-1306	DiGeorge syndrome critical region gene 8	protein-coding
mm_162487.1	chr1	135766071	135766079	+	1	NA	promoter-TSS (NM_013750)	promoter-TSS (NM_013750)	-10	NM_013750	27280	Mm.34346	NM_013750	ENSMUSG00000041801	Phlda3	Tih1	pleckstrin homology like domain, family A, member 3	protein-coding
mm_77441.1	chr8	121652853	121652888	-	1	NA	promoter-TSS (NM_080855)	promoter-TSS (NM_080855)	-937	NM_080855	142682	Mm.103202	NM_080855	ENSMUSG00000061410	Zcchc14	AA792890|BDG29	zinc finger, CCHC domain containing 14	protein-coding
mm_118291.1	chr13	113046344	113046354	-	1	NA	promoter-TSS (NM_027127)	promoter-TSS (NM_027127)	39	NM_027127	69590	Mm.12715	NM_027127	ENSMUSG00000021760	Gpx8	2310016C16Rik|AU017063	glutathione peroxidase 8 (putative)	protein-coding
mm_108700.1	chr12	86949723	86949742	+	1	NA	intron (NM_001289432, intron 1 of 4)	intron (NM_001289432, intron 1 of 4)	2389	NM_001289432	217732	Mm.22337	NM_173735	ENSMUSG00000034157	Cipc	2310044G17Rik|AI842544|AI853744|Kiaa1737|mKIAA1737	CLOCK interacting protein, circadian	protein-coding
mm_2016.1	chr1	87127929	87127953	+	1	NA	TTS (NM_007432)	TTS (NM_007432)	2933	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_169457.1	chr14	63498041	63498045	+	1	NA	intron (NM_021480, intron 2 of 8)	B1_Mus2|SINE|Alu	11049	NM_021480	58865	Mm.354229	NM_021480	ENSMUSG00000021953	Tdh	-	L-threonine dehydrogenase	protein-coding
mm_38643.1	chr4	143212692	143212728	-	1	NA	promoter-TSS (NM_001081355)	promoter-TSS (NM_001081355)	-1	NM_001256380	110593	Mm.332020	NM_001081355	ENSMUSG00000057637	Prdm2	4833427P12Rik|E330024L24Rik|Gm1033|Gm19732|KMT8|Riz|Riz1|Znfpr1c1	PR domain containing 2, with ZNF domain	protein-coding
mm_73317.1	chr8	105225198	105225222	+	1	NA	promoter-TSS (NM_145604)	promoter-TSS (NM_145604)	22	NM_145604	234678	Mm.27186	NM_145604	ENSMUSG00000031889	D230025D16Rik	BC006874|Lin10	RIKEN cDNA D230025D16 gene	protein-coding
mm_6872.1	chr1	84284527	84284537	-	1	NA	5' UTR (NM_001003948, exon 1 of 3)	5' UTR (NM_001003948, exon 1 of 3)	113	NM_001003948	98496	Mm.187470	NM_001003948	ENSMUSG00000045658	Pid1	5033414K04Rik|NYGGF4	phosphotyrosine interaction domain containing 1	protein-coding
mm_147131.1	chr18	36126344	36126345	-	1	NA	intron (NM_001167891, intron 1 of 9)	intron (NM_001167891, intron 1 of 9)	20141	NR_015571	74966	Mm.379238	NM_030089		4930471G03Rik	1700007N01Rik	RIKEN cDNA 4930471G03 gene	ncRNA
mm_128793.1	chr15	66812188	66812214	-	1	NA	intron (NM_001029841, intron 1 of 7)	MIRb|SINE|MIR	19628	NM_001029841	20491	Mm.7601	NM_009192	ENSMUSG00000022372	Sla	Slap|Slap-1	src-like adaptor	protein-coding
mm_59656.1	chr7	28180175	28180219	+	1	NA	promoter-TSS (NM_001271370)	promoter-TSS (NM_001271370)	-119	NM_001271370	13549	Mm.57249	NM_010092	ENSMUSG00000002409	Dyrk1b	Mirk	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1b	protein-coding
mm_52404.1	chr6	113333305	113333332	+	1	NA	TTS (NM_133926)	TTS (NM_133926)	6342	NM_010957	18294	Mm.43612	NM_010957	ENSMUSG00000030271	Ogg1	Mmh	8-oxoguanine DNA-glycosylase 1	protein-coding
mm_111430.1	chr12	91746021	91746089	-	1	NA	intron (NM_175367, intron 1 of 6)	intron (NM_175367, intron 1 of 6)	40381	NM_175367	108800	Mm.23125	NM_175367	ENSMUSG00000020961	Ston2	4933401N24Rik|AI425999|AW544599	stonin 2	protein-coding
mm_20154.1	chr2	121806989	121807018	-	1	NA	promoter-TSS (NM_172673)	promoter-TSS (NM_172673)	54	NM_172673	228564	Mm.121514	NM_172673	ENSMUSG00000027238	Frmd5	1500032A09Rik|5830442F04|A930004K21Rik|R75430	FERM domain containing 5	protein-coding
mm_18225.1	chr2	51149101	51149115	-	1	NA	promoter-TSS (NM_028810)	promoter-TSS (NM_028810)	3	NM_028810	74194	Mm.46497	NM_028810	ENSMUSG00000017144	Rnd3	2610017M01Rik|AI661404|Arhe|Rhoe	Rho family GTPase 3	protein-coding
mm_97949.1	chr11	83664566	83664577	+	1	NA	3' UTR (NM_013652, exon 3 of 3)	3' UTR (NM_013652, exon 3 of 3)	1987	NM_013652	20303	Mm.244263	NM_013652	ENSMUSG00000018930	Ccl4	AT744.1|Act-2|MIP-1B|Mip1b|Scya4	chemokine (C-C motif) ligand 4	protein-coding
mm_151398.1	chr19	56461618	56461628	+	1	NA	promoter-TSS (NM_001164263)	promoter-TSS (NM_001164263)	-14	NM_001164263	226245	Mm.156742	NM_172641	ENSMUSG00000035818	Plekhs1	9930023K05Rik	pleckstrin homology domain containing, family S member 1	protein-coding
mm_48343.1	chr5	139306262	139306305	-	1	NA	intron (NM_172723, intron 2 of 10)	intron (NM_172723, intron 2 of 10)	19181	NM_172723	231821	Mm.297819	NM_172723	ENSMUSG00000056413	Adap1	4930431P11Rik|Centa1|GC1L|p42IP4	ArfGAP with dual PH domains 1	protein-coding
mm_126467.1	chr15	81235601	81235628	+	1	NA	5' UTR (NM_145132, exon 1 of 2)	5' UTR (NM_145132, exon 1 of 2)	115	NM_145132	207911	Mm.323523	NM_145132	ENSMUSG00000050164	Mchr1	AW049955|Gpr24|Mch1r	melanin-concentrating hormone receptor 1	protein-coding
mm_142442.1	chr17	45572878	45572898	-	1	NA	intron (NM_008302, intron 1 of 10)	CpG	373	NM_008302	15516	Mm.2180	NM_008302	ENSMUSG00000023944	Hsp90ab1	90kDa|AL022974|C81438|Hsp84|Hsp84-1|Hsp90|Hspcb	heat shock protein 90 alpha (cytosolic), class B member 1	protein-coding
mm_146830.1	chr18	21652197	21652207	-	1	NA	exon (NM_001081403, exon 1 of 8)	exon (NM_001081403, exon 1 of 8)	166	NM_001081403	225266	Mm.436836	NM_001081403	ENSMUSG00000042514	Klhl14	6330403N15Rik|AI785250|printor	kelch-like 14	protein-coding
mm_9893.1	chr1	186705265	186705295	-	1	NA	5' UTR (NM_009367, exon 1 of 7)	5' UTR (NM_009367, exon 1 of 7)	709	NM_009367	21808	Mm.18213	NM_009367	ENSMUSG00000039239	Tgfb2	BB105277|Tgf-beta2|Tgfb-2	transforming growth factor, beta 2	protein-coding
mm_124860.1	chr15	9556204	9556218	+	1	NA	Intergenic	Intergenic	-26335	NM_008372	16197	Mm.389	NM_008372	ENSMUSG00000003882	Il7r	CD127|IL-7Ralpha	interleukin 7 receptor	protein-coding
mm_146851.1	chr18	24112043	24112076	-	1	NA	intron (NM_172625, intron 3 of 4)	intron (NM_172625, intron 3 of 4)	9760	NM_172625	225280	Mm.258973	NM_172625	ENSMUSG00000047989	Ino80c	D030070L09Rik	INO80 complex subunit C	protein-coding
mm_101157.1	chr11	16972755	16972827	-	1	NA	3' UTR (NM_019549, exon 10 of 10)	3' UTR (NM_019549, exon 10 of 10)	21381	NM_176982	319701	Mm.120672	NM_176982	ENSMUSG00000044966	Fbxo48	A630050E13Rik	F-box protein 48	protein-coding
mm_31436.1	chr4	48540119	48540138	+	1	NA	promoter-TSS (NM_028137)	promoter-TSS (NM_028137)	47	NM_001145924	66665	Mm.140749	NM_028137	ENSMUSG00000039693	Msantd3	2410046L14Rik|2810429P03Rik|5730528L13Rik|Mysantd3	Myb/SANT-like DNA-binding domain containing 3	protein-coding
mm_59089.1	chr7	19696403	19696413	+	1	NA	exon (NM_009696, exon 4 of 4)	exon (NM_009696, exon 4 of 4)	1990	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_89211.1	chr10	86704282	86704300	+	1	NA	intron (NM_011631, intron 2 of 17)	intron (NM_011631, intron 2 of 17)	1153	NM_011631	22027	Mm.87773	NM_011631	ENSMUSG00000020048	Hsp90b1	ERp99|GRP94|TA-3|Targ2|Tra-1|Tra1|endoplasmin|gp96	heat shock protein 90, beta (Grp94), member 1	protein-coding
mm_149033.1	chr19	8802780	8802791	+	1	NA	intron (NM_001098237, intron 1 of 1)	intron (NM_001098237, intron 1 of 1)	255	NM_001098237	75291	Mm.23423	NM_133759	ENSMUSG00000071661	Zbtb3	4930563M09Rik	zinc finger and BTB domain containing 3	protein-coding
mm_26077.1	chr3	136670521	136670527	+	1	NA	5' UTR (NM_001293622, exon 1 of 13)	5' UTR (NM_001293622, exon 1 of 13)	458	NM_001293622	19055	Mm.331389	NM_008913	ENSMUSG00000028161	Ppp3ca	2900074D19Rik|CN|Caln|Calna|CnA	protein phosphatase 3, catalytic subunit, alpha isoform	protein-coding
mm_91087.1	chr10	19015279	19015300	-	1	NA	5' UTR (NM_009397, exon 1 of 9)	5' UTR (NM_009397, exon 1 of 9)	121	NM_009397	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_10487.1	chr2	14824015	14824027	+	1	NA	promoter-TSS (NM_001252533)	promoter-TSS (NM_001252533)	-71	NM_001252533	12296	Mm.313930	NM_023116	ENSMUSG00000057914	Cacnb2	AW060387|CAB2|Cavbeta2|Cchb2	calcium channel, voltage-dependent, beta 2 subunit	protein-coding
mm_126888.1	chr15	89497920	89497934	+	1	NA	Intergenic	Intergenic	-1930	NM_021423	58234	Mm.146855	NM_021423	ENSMUSG00000022623	Shank3	AI841104|SHANK3c-3|SHANK3c-4|Shank3b	SH3/ankyrin domain gene 3	protein-coding
mm_155604.1	chrX	82950535	82950538	+	1	NA	intron (NM_007868, intron 1 of 78)	intron (NM_007868, intron 1 of 78)	1666	NM_007868	13405	Mm.275608	NM_007868	ENSMUSG00000045103	Dmd	DXSmh7|DXSmh9|Dp427|Dp71|dys|mdx|pke	dystrophin, muscular dystrophy	protein-coding
mm_50433.1	chr6	48845199	48845242	+	1	NA	3' UTR (NM_025326, exon 7 of 7)	3' UTR (NM_025326, exon 7 of 7)	3564	NM_001098271	66058	Mm.27061	NM_025326	ENSMUSG00000023367	Tmem176a	0610011I04Rik|AU040201|AU041743|Keg2	transmembrane protein 176A	protein-coding
mm_130607.1	chr15	99820073	99820154	-	1	NA	promoter-TSS (NM_023063)	promoter-TSS (NM_023063)	36	NM_023063	65970	Mm.33207	NM_023063	ENSMUSG00000023022	Lima1	Eplin	LIM domain and actin binding 1	protein-coding
mm_135656.1	chr16	52400591	52400613	-	1	NA	intron (NM_009655, intron 1 of 15)	intron (NM_009655, intron 1 of 15)	52479	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_55848.1	chr6	83367802	83367804	-	1	NA	3' UTR (NM_183138, exon 11 of 11)	3' UTR (NM_183138, exon 11 of 11)	18319	NM_175277	78653	Mm.391470	NM_175277	ENSMUSG00000045160	Bola3	1810056O20Rik	bolA-like 3 (E. coli)	protein-coding
mm_165206.1	chr2	34913531	34913537	+	1	NA	intron (NM_028716, intron 1 of 14)	intron (NM_028716, intron 1 of 14)	442	NM_028716	74016	Mm.65691	NM_028716	ENSMUSG00000026873	Phf19	3110009G19Rik|3321402G02Rik	PHD finger protein 19	protein-coding
mm_28269.1	chr3	88755965	88755966	-	1	NA	intron (NM_018804, intron 2 of 3)	intron (NM_018804, intron 2 of 3)	16634	NM_018804	229521	Mm.379376	NM_018804	ENSMUSG00000068923	Syt11	1500004A13Rik|3632445O20Rik|5430404N14Rik|6530420C11Rik|AI851970	synaptotagmin XI	protein-coding
mm_20292.1	chr2	126933123	126933133	-	1	NA	5' UTR (NM_023220, exon 1 of 15)	5' UTR (NM_023220, exon 1 of 15)	107	NM_023220	66552	Mm.269928	NM_023220	ENSMUSG00000027366	Sppl2a	2010106G01Rik|C130089K23Rik	signal peptide peptidase like 2A	protein-coding
mm_63644.1	chr7	128687537	128687579	+	1	NA	intron (NM_178641, intron 15 of 19)	intron (NM_178641, intron 15 of 19)	-1312	NM_001346517	101490	Mm.490344	NM_178641	ENSMUSG00000042105	Inpp5f	5830435P03Rik|AI115354|AW561896|SAC2|cI-27|hSAC2|mKIAA0966	inositol polyphosphate-5-phosphatase F	protein-coding
mm_56337.1	chr6	92706238	92706296	-	1	NA	promoter-TSS (NM_001081146)	promoter-TSS (NM_001081146)	-83	NM_001081146	243548	Mm.248820	NM_001081146	ENSMUSG00000030020	Prickle2	6230400G14Rik|6720451F06Rik|mpk2	prickle planar cell polarity protein 2	protein-coding
mm_59098.1	chr7	19696977	19696990	+	1	NA	exon (NM_009696, exon 4 of 4)	exon (NM_009696, exon 4 of 4)	1415	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_120751.1	chr14	73239396	73239439	+	1	NA	exon (NM_175116, exon 1 of 1)	exon (NM_175116, exon 1 of 1)	1526	NM_175116	67168	Mm.390681	NM_175116	ENSMUSG00000033446	Lpar6	2610302I02Rik|P2ry5|P2y5	lysophosphatidic acid receptor 6	protein-coding
mm_169955.1	chr16	85813950	85813956	-	1	NA	Intergenic	RLTR9D|LTR|ERVK	-5258	NR_040506	75310	Mm.108627	NR_040506		4930556C24Rik	-	RIKEN cDNA 4930556C24 gene	ncRNA
mm_71496.1	chr8	46791880	46791883	+	1	NA	intron (NM_008391, intron 1 of 8)	intron (NM_008391, intron 1 of 8)	52136	NM_008391	16363	Mm.1149	NM_008391	ENSMUSG00000031627	Irf2	9830146E22Rik|AI646973|Irf-2	interferon regulatory factor 2	protein-coding
mm_7338.1	chr1	105663666	105663680	-	1	NA	promoter-TSS (NM_013784)	promoter-TSS (NM_013784)	3	NM_013784	27392	Mm.268911	NM_013784	ENSMUSG00000056536	Pign	Gm20308|PIG-N	phosphatidylinositol glycan anchor biosynthesis, class N	protein-coding
mm_91623.1	chr10	41746634	41746650	-	1	NA	intron (NM_001243074, intron 2 of 10)	intron (NM_001243074, intron 2 of 10)	63021	NM_001243075	103268	Mm.338605	NM_026643	ENSMUSG00000019813	Cep57l1	2410017P07Rik|4930484D11Rik|AI607327|cep57R	centrosomal protein 57-like 1	protein-coding
mm_168075.1	chr10	111493363	111493374	+	1	NA	exon (NM_015781, exon 10 of 16)	exon (NM_015781, exon 10 of 16)	-7420	NR_033603	382421	Mm.245643	NR_033603		Gm5176	EG382421	high mobility group box 2 pseudogene	pseudo
mm_2244.1	chr1	91056590	91056597	+	1	NA	intron (NM_001310732, intron 1 of 24)	intron (NM_001310732, intron 1 of 24)	3149	NM_008515	16978	Mm.45039	NM_008515	ENSMUSG00000026305	Lrrfip1	AU024550|Fliiap1	leucine rich repeat (in FLII) interacting protein 1	protein-coding
mm_155031.1	chrX	42068367	42068388	+	1	NA	promoter-TSS (NR_125870)	promoter-TSS (NR_125870)	-21	NM_001301639	11798	Mm.259879	NM_009688	ENSMUSG00000025860	Xiap	1110015C02Rik|Aipa|Api3|Birc4|IAP3|ILP-1|MIHA	X-linked inhibitor of apoptosis	protein-coding
mm_161653.1	chr17	6655741	6655741	-	1	NA	promoter-TSS (NM_001166630).2	promoter-TSS (NM_001166630).2	90	NM_001166630	100040563	Mm.457381	NM_001166630	ENSMUSG00000000579	Dynlt1c	100040603|Dynlt1d	dynein light chain Tctex-type 1C	protein-coding
mm_154372.1	chrM	10093	10103	+	1	NA	NA	Intergenic	NA	NA								
mm_56071.1	chr6	86793591	86793601	-	1	NA	promoter-TSS (NM_013471)	promoter-TSS (NM_013471)	-12	NM_013471	11746	Mm.259702	NM_013471	ENSMUSG00000029994	Anxa4	AI265406|AIV|AW106930|Anx4|Xanx-4	annexin A4	protein-coding
mm_153811.1	chr19	46045363	46045386	-	1	NA	promoter-TSS (NM_001113408)	promoter-TSS (NM_001113408)	-163	NM_001113408	16825	Mm.327442	NM_010697	ENSMUSG00000025223	Ldb1	CLIM2|NLI	LIM domain binding 1	protein-coding
mm_27235.1	chr3	36474527	36474530	-	1	NA	TTS (NR_105976)	TTS (NR_105976)	996	NR_105976	102466786		NR_105976	ENSMUSG00000098808	Mir7009	Gm27472|mmu-mir-7009	microRNA 7009	ncRNA
mm_166437.1	chr5	137207698	137207707	-	1	NA	Intergenic	Intergenic	-80552	NM_009599	11423	Mm.255464	NM_009599	ENSMUSG00000023328	Ache	-	acetylcholinesterase	protein-coding
mm_53366.1	chr6	129397479	129397498	+	1	NA	5' UTR (NM_019985, exon 1 of 6)	5' UTR (NM_019985, exon 1 of 6)	191	NM_001204239	56760	Mm.30700	NM_019985	ENSMUSG00000030159	Clec1b	1810061I13Rik|Clec-2|Clec2	C-type lectin domain family 1, member b	protein-coding
mm_7722.1	chr1	130661614	130661637	-	1	NA	promoter-TSS (NM_007576)	promoter-TSS (NM_007576)	-7	NM_007576	12269	Mm.306720	NM_007576	ENSMUSG00000026405	C4bp	AI195242|C4bpa	complement component 4 binding protein	protein-coding
mm_133112.1	chr16	65523572	65523583	+	1	NA	exon (NM_008849, exon 2 of 6)	exon (NM_008849, exon 2 of 6)	2948	NM_008849	18736	Mm.355440	NM_008849	ENSMUSG00000004842	Pou1f1	GHF-1|Hmp1|Pit-1|Pit1|Pit1-rs1|dw|dwarf	POU domain, class 1, transcription factor 1	protein-coding
mm_16639.1	chr2	5942720	5942729	-	1	NA	promoter-TSS (NM_001081131)	promoter-TSS (NM_001081131)	68	NM_001081131	209692	Mm.222517	NM_001081131	ENSMUSG00000025815	Dhtkd1	C330018I04Rik	dehydrogenase E1 and transketolase domain containing 1	protein-coding
mm_27461.1	chr3	52179966	52179976	-	1	NA	Intergenic	Intergenic	-74965	NM_001004176	433586	Mm.234972	NM_001004176	ENSMUSG00000061143	Maml3	AV234550|BC049812|Mam-2|mKIAA1816	mastermind like 3 (Drosophila)	protein-coding
mm_150430.1	chr19	37495516	37495519	+	1	NA	Intergenic	Intergenic	30263	NR_131009	78640	Mm.234265	NR_131008		1700122C19Rik	-	RIKEN cDNA 1700122C19 gene	ncRNA
mm_25838.1	chr3	129213951	129213972	+	1	NA	promoter-TSS (NM_001287048)	promoter-TSS (NM_001287048)	29	NM_001287048	18741	Mm.246804	NM_011098	ENSMUSG00000028023	Pitx2	9430085M16Rik|Brx1|Brx1b|Munc30|Otlx2|Ptx2|Rieg	paired-like homeodomain transcription factor 2	protein-coding
mm_165970.1	chr4	98546615	98546624	+	1	NA	promoter-TSS (NM_007704)	promoter-TSS (NM_007704)	-15	NM_007704	12695	Mm.90218	NM_007704	ENSMUSG00000061859	Patj	Cipp|Inadl	PATJ, crumbs cell polarity complex component	protein-coding
mm_78392.1	chr9	28674996	28675001	+	1	NA	intron (NM_177906, intron 2 of 7)	CT-rich|Low_complexity|Low_complexity	883729	NM_177906	330908	Mm.379474	NM_177906	ENSMUSG00000062257	Opcml	2900075O15Rik|3732419F12|AI844366|B930023M13Rik|C230027C17|Gm181|Obcam	opioid binding protein/cell adhesion molecule-like	protein-coding
mm_169164.1	chr13	65484810	65484828	-	1	NA	Intergenic	Intergenic	205965	NM_178364	170936	Mm.151546	NM_178364	ENSMUSG00000021514	Zfp369	B930030B22Rik|D230020H11Rik|NRIF2	zinc finger protein 369	protein-coding
mm_17801.1	chr2	33336903	33336909	-	1	NA	intron (NM_001290572, intron 2 of 17)	ORR1A1|LTR|ERVL-MaLR	34588	NM_001290570	241308	Mm.274249	NM_175211	ENSMUSG00000038831	Ralgps1	5830418G11Rik|AI853783|AI854138|RALGEF2|RALGPS1A|RalGEF 2|mKIAA0351	Ral GEF with PH domain and SH3 binding motif 1	protein-coding
mm_52947.1	chr6	122952795	122952809	+	1	NA	5' UTR (NM_153197, exon 1 of 6)	5' UTR (NM_153197, exon 1 of 6)	158	NM_153197	73149	Mm.25684	NM_153197	ENSMUSG00000043832	Clec4a3	3110037K17Rik|Dcir3	C-type lectin domain family 4, member a3	protein-coding
mm_30844.1	chr4	24585465	24585478	+	1	NA	intron (NM_199467, intron 17 of 23)	intron (NM_199467, intron 17 of 23)	89009	NM_199467	212377	Mm.120919	NM_199467	ENSMUSG00000045751	Mms22l	F730047E07Rik|Gm134	MMS22-like, DNA repair protein	protein-coding
mm_58098.1	chr6	137537783	137537795	-	1	NA	intron (NM_001271595, intron 2 of 20)	intron (NM_001271595, intron 2 of 20)	-17894	NM_001271589	13860	Mm.235346	NM_007945	ENSMUSG00000015766	Eps8	AW261790	epidermal growth factor receptor pathway substrate 8	protein-coding
mm_77164.1	chr8	111688577	111688732	-	1	NA	TTS (NR_106044)	TTS (NR_106044)	1020	NR_106044	102466993		NR_106044	ENSMUSG00000099129	Mir7076	Gm27318|mmu-mir-7076	microRNA 7076	ncRNA
mm_16245.1	chr2	173158410	173158431	+	1	NA	exon (NM_011044, exon 10 of 10)	exon (NM_011044, exon 10 of 10)	5347	NM_011044	18534	Mm.266867	NM_011044	ENSMUSG00000027513	Pck1	AI265463|PEPCK|Pck-1	phosphoenolpyruvate carboxykinase 1, cytosolic	protein-coding
mm_59831.1	chr7	29303939	29303947	+	1	NA	promoter-TSS (NM_013874)	promoter-TSS (NM_013874)	-62	NM_013874	29861	Mm.101885	NM_013874	ENSMUSG00000030584	Dpf1	Neud4	D4, zinc and double PHD fingers family 1	protein-coding
mm_126050.1	chr15	76948491	76948539	+	1	NA	promoter-TSS (NM_054099)	promoter-TSS (NM_054099)	-29	NM_054099	117171	Mm.322968	NM_054099	ENSMUSG00000063236	1110038F14Rik	-	RIKEN cDNA 1110038F14 gene	protein-coding
mm_48973.1	chr6	4754194	4754201	+	1	NA	5' UTR (NM_130877, exon 2 of 2)	5' UTR (NM_130877, exon 2 of 2)	6891	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_86032.1	chr9	113707678	113707701	-	1	NA	intron (NM_011052, intron 1 of 17)	intron (NM_011052, intron 1 of 17)	570	NM_001164678	18571	Mm.29816	NM_011052	ENSMUSG00000032504	Pdcd6ip	AI480591|AW544830|Aip1|Alix|C76364|Eig2|mKIAA1375	programmed cell death 6 interacting protein	protein-coding
mm_20265.1	chr2	126675449	126675460	-	1	NA	non-coding (NR_073183, exon 1 of 6)	non-coding (NR_073183, exon 1 of 6)	138	NM_001271469	14391	Mm.293266	NM_010249	ENSMUSG00000027361	Gabpb1	BABPB2|E4TF1|E4TF1-47|E4TF1-53|E4Tf1B|GABPB|GABPB-1|GABPB-2|GABPB1-1|GABPB1-2|NRF2B1|NRF2B2	GA repeat binding protein, beta 1	protein-coding
mm_58906.1	chr7	17203449	17203457	+	1	NA	promoter-TSS (NM_054064)	promoter-TSS (NM_054064)	-24	NM_054064	114872	Mm.322280	NM_054064	ENSMUSG00000023159	Psg29	AA102956|AA409969|cea17	pregnancy-specific glycoprotein 29	protein-coding
mm_144808.1	chr18	36281512	36281518	+	1	NA	5' UTR (NM_008989, exon 1 of 2)	5' UTR (NM_008989, exon 1 of 2)	353	NM_008989	19290	Mm.231802	NM_008989	ENSMUSG00000043991	Pura	CAGER-1|Pur-alpha|ssCRE-BP	purine rich element binding protein A	protein-coding
mm_54407.1	chr6	31563889	31563910	-	1	NA	promoter-TSS (NM_013723)	promoter-TSS (NM_013723)	38	NM_013723	27205	Mm.89918	NM_013723	ENSMUSG00000025608	Podxl	AW121214|Ly102|PC|PCLP-1|Pclp1	podocalyxin-like	protein-coding
mm_99216.1	chr11	101030404	101030430	+	1	NA	promoter-TSS (NR_105893)	promoter-TSS (NR_105893)	77	NR_105893	102466767		NR_105893	ENSMUSG00000098415	Mir6928	Gm27728|mmu-mir-6928	microRNA 6928	ncRNA
mm_1759.1	chr1	75524989	75524999	+	1	NA	intron (NM_027886, intron 3 of 24)	intron (NM_027886, intron 3 of 24)	3465	NM_027886	71728	Mm.312650	NM_027886	ENSMUSG00000026213	Stk11ip	1200014D22Rik|BB131189|LIP1|LKB1IP	serine/threonine kinase 11 interacting protein	protein-coding
mm_64143.1	chr7	141216647	141216660	+	1	NA	intron (NM_025886, intron 1 of 5)	intron (NM_025886, intron 1 of 5)	793	NM_025886	66985	Mm.21202	NM_025886	ENSMUSG00000038618	Rassf7	2400009B11Rik|AW210608	Ras association (RalGDS/AF-6) domain family (N-terminal) member 7	protein-coding
mm_17222.1	chr2	25500665	25500692	-	1	NA	promoter-TSS (NM_027062)	promoter-TSS (NM_027062)	-100	NM_013908	30839	Mm.29170	NM_013908	ENSMUSG00000015095	Fbxw5	AI159739|Fbw5	F-box and WD-40 domain protein 5	protein-coding
mm_5429.1	chr1	34560917	34560930	-	1	NA	promoter-TSS (NM_009356)	promoter-TSS (NM_009356)	20	NM_009356	21756	Mm.14418	NM_009356	ENSMUSG00000037529	Prss40	Tesp2	protease, serine 40	protein-coding
mm_153506.1	chr19	41363636	41363653	-	1	NA	intron (NM_031376, intron 2 of 16)	intron (NM_031376, intron 2 of 16)	21426	NM_031376	83490	Mm.222266	NM_031376	ENSMUSG00000025017	Pik3ap1	1810044J04Rik|BCAP	phosphoinositide-3-kinase adaptor protein 1	protein-coding
mm_94007.1	chr10	127620669	127620717	-	1	NA	5' UTR (NM_008512, exon 1 of 89)	5' UTR (NM_008512, exon 1 of 89)	455	NM_008512	16971	Mm.271854	NM_008512	ENSMUSG00000040249	Lrp1	A2mr|AI316852|CD91|Lrp|b2b1554Clo	low density lipoprotein receptor-related protein 1	protein-coding
mm_164054.1	chr14	103049080	103049095	+	1	NA	intron (NM_008392, intron 1 of 4)	intron (NM_008392, intron 1 of 4)	2075	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_35138.1	chr4	11386689	11386702	-	1	NA	promoter-TSS (NM_001290383)	promoter-TSS (NM_001290383)	83	NM_001347052	207920	Mm.387719	NM_194055	ENSMUSG00000040728	Esrp1	2210008M09Rik|A630065D16|BC031468|Rbm35a	epithelial splicing regulatory protein 1	protein-coding
mm_156442.1	chrX	142228700	142228714	+	1	NA	promoter-TSS (NM_001290533)	promoter-TSS (NM_001290533)	4	NM_001290533	237082	Mm.41899	NM_172782	ENSMUSG00000042271	Nxt2	6330587F24Rik|AI787442|P15-2	nuclear transport factor 2-like export factor 2	protein-coding
mm_115097.1	chr13	102723250	102723253	+	1	NA	Intergenic	Lx2|LINE|L1	29693	NM_008533	17079	Mm.373974	NM_008533	ENSMUSG00000021624	Cd180	F630107B15|Ly78|RP105	CD180 antigen	protein-coding
mm_11690.1	chr2	35661486	35661518	+	1	NA	exon (NM_001114125, exon 3 of 17)	exon (NM_001114125, exon 3 of 17)	-30492	NM_001001602	69601	Mm.29629	NM_001001602	ENSMUSG00000026883	Dab2ip	2310011D08Rik|AI480459|Aip1|mKIAA1743	disabled 2 interacting protein	protein-coding
mm_8441.1	chr1	152809925	152809929	-	1	NA	intron (NM_010877, intron 2 of 15)	intron (NM_010877, intron 2 of 15)	9774	NM_010877	17970	Mm.270307	NM_010877	ENSMUSG00000026480	Ncf2	NOXA2|Ncf-2|p67phox	neutrophil cytosolic factor 2	protein-coding
mm_149116.1	chr19	8967110	8967171	+	1	NA	promoter-TSS (NM_026007)	promoter-TSS (NM_026007)	99	NM_026007	67160	Mm.247762	NM_026007	ENSMUSG00000071644	Eef1g	2610301D06Rik|AA407312|EF1G	eukaryotic translation elongation factor 1 gamma	protein-coding
mm_141031.1	chr17	25273255	25273265	-	1	NA	promoter-TSS (NR_027452)	promoter-TSS (NR_027452)	171	NM_001177610	22196	Mm.240044	NM_011665	ENSMUSG00000015120	Ube2i	5830467E05Rik|F830028O17Rik|UBC9|Ubce2i|Ubce9	ubiquitin-conjugating enzyme E2I	protein-coding
mm_46331.1	chr5	101239648	101239658	-	1	NA	Intergenic	Intergenic	393424	NM_172715	231510	Mm.271911	NM_172715	ENSMUSG00000029314	Agpat9	1-AGPAT|1-AGPAT 9|4933407I02Rik|4933408F15|A230097K15Rik|GPAT-3|Gpat3|mGPAT3	1-acylglycerol-3-phosphate O-acyltransferase 9	protein-coding
mm_89152.1	chr10	86032820	86032829	+	1	NA	intron (NM_001347151, intron 4 of 8)	intron (NM_001347151, intron 4 of 8)	10670	NM_001347151	69754	Mm.44236	NM_153195	ENSMUSG00000001786	Fbxo7	2410015K21Rik|A230052G17Rik|AI117679|AW260462|C85118	F-box protein 7	protein-coding
mm_67662.1	chr7	86775793	86775806	-	1	NA	promoter-TSS (NM_001159706)	promoter-TSS (NM_001159706)	65	NM_016770	53320	Mm.269137	NM_016770	ENSMUSG00000001773	Folh1	GCP2|mopsm	folate hydrolase 1	protein-coding
mm_65512.1	chr7	25754753	25754771	-	1	NA	promoter-TSS (NM_178089)	promoter-TSS (NM_178089)	-42	NM_144922	232989	Mm.254223	NM_144922	ENSMUSG00000040725	Hnrnpul1	E130317O14Rik|E1B-AP5|E1BAP5|Hnrnpul|Hnrpul1	heterogeneous nuclear ribonucleoprotein U-like 1	protein-coding
mm_9900.1	chr1	186749285	186749293	-	1	NA	promoter-TSS (NM_026041)	promoter-TSS (NM_026041)	69	NM_026041	67223	Mm.289841	NM_026041	ENSMUSG00000001305	Rrp15	2810430M08Rik|5430437H21Rik	ribosomal RNA processing 15 homolog (S. cerevisiae)	protein-coding
mm_105094.1	chr11	100931450	100931453	-	1	NA	intron (NM_213660, intron 1 of 23)	intron (NM_213660, intron 1 of 23)	8089	NM_213660	20848	Mm.249934	NM_011486	ENSMUSG00000004040	Stat3	1110034C02Rik|AW109958|Aprf	signal transducer and activator of transcription 3	protein-coding
mm_107946.1	chr12	72086094	72086147	+	1	NA	promoter-TSS (NM_026038)	promoter-TSS (NM_026038)	281	NM_024205	104771	Mm.258935	NM_024205	ENSMUSG00000005078	Jkamp	1200003C05Rik|2310047L11Rik|Jamp	JNK1/MAPK8-associated membrane protein	protein-coding
mm_33601.1	chr4	132568661	132568694	+	1	NA	intron (NM_001081211, intron 1 of 1)	B4|SINE|B4	4610	NM_001081211	19204	Mm.89389	NM_001081211	ENSMUSG00000056529	Ptafr	PAFR	platelet-activating factor receptor	protein-coding
mm_167839.1	chr9	124440825	124440842	+	1	NA	Intergenic	Intergenic	17046	NR_015516	75135	Mm.476814	NR_015516		4930526I15Rik	1600027J15Rik	RIKEN cDNA 4930526I15 gene	ncRNA
mm_47518.1	chr5	124095735	124095745	-	1	NA	promoter-TSS (NM_019875)	promoter-TSS (NM_019875)	58	NM_019875	56325	Mm.254839	NM_019875	ENSMUSG00000029408	Abcb9	TAPL|mKIAA1520	ATP-binding cassette, sub-family B (MDR/TAP), member 9	protein-coding
mm_76572.1	chr8	88664292	88664314	-	1	NA	exon (NM_145857, exon 4 of 13)	exon (NM_145857, exon 4 of 13)	16956	NM_145857	257632	Mm.222633	NM_145857	ENSMUSG00000055994	Nod2	ACUG|BLAU|CD|Card15|F830032C23Rik|IBD1|Nlrc2	nucleotide-binding oligomerization domain containing 2	protein-coding
mm_129185.1	chr15	76309767	76309783	-	1	NA	Intergenic	Intergenic	-2530	NM_153122	75475	Mm.322738	NM_153122	ENSMUSG00000022562	Oplah	1700010G02Rik	5-oxoprolinase (ATP-hydrolysing)	protein-coding
mm_153063.1	chr19	32196394	32196411	-	1	NA	intron (NM_001168525, intron 5 of 9)	intron (NM_001168525, intron 5 of 9)	14611	NM_001168526	208449	Mm.329810	NM_144792	ENSMUSG00000040451	Sgms1	9530058O11Rik|AI841905|C80702|Mob|Sms1|Sor1|Tmem23	sphingomyelin synthase 1	protein-coding
mm_27800.1	chr3	75891963	75891978	-	1	NA	exon (NM_175193, exon 10 of 15)	exon (NM_175193, exon 10 of 15)	64979	NM_175193	73124	Mm.249232	NM_175193	ENSMUSG00000034109	Golim4	3110027H23Rik|GIMPC|GPP130|Golph4|P138	golgi integral membrane protein 4	protein-coding
mm_26623.1	chr3	152702666	152702706	+	1	NA	Intergenic	RLTR20C1_MM|LTR|ERVK	-11414	NM_178016	329777	Mm.331447	NM_025662	ENSMUSG00000039047	Pigk	3000001O05Rik	phosphatidylinositol glycan anchor biosynthesis, class K	protein-coding
mm_24236.1	chr3	88950860	88950872	+	1	NA	promoter-TSS (NM_022994)	promoter-TSS (NM_022994)	-584	NM_001164533	65111	Mm.29028	NM_022994	ENSMUSG00000068921	Dap3	4921514D13Rik|DAP-3|MRP-S29|S29mt	death associated protein 3	protein-coding
mm_122964.1	chr14	54973791	54973818	-	1	NA	exon (NM_080728, exon 35 of 41)	exon (NM_080728, exon 35 of 41)	1972	NR_030607	100124433		NR_030607	ENSMUSG00000077928	Mir208b	Mirn208b|mir-208b	microRNA 208b	ncRNA
mm_114518.1	chr13	73260557	73260569	+	1	NA	promoter-TSS (NM_018885)	promoter-TSS (NM_018885)	66	NM_018885	50916	Mm.103784	NM_018885	ENSMUSG00000021604	Irx4	-	Iroquois related homeobox 4 (Drosophila)	protein-coding
mm_163906.1	chr14	31001940	31001950	+	1	NA	promoter-TSS (NM_026911)	promoter-TSS (NM_026911)	-279	NM_026911	69019	Mm.28852	NM_026911	ENSMUSG00000021917	Spcs1	1810004F21Rik	signal peptidase complex subunit 1 homolog (S. cerevisiae)	protein-coding
mm_102247.1	chr11	55109667	55109691	-	1	NA	3' UTR (NM_010299, exon 4 of 4)	3' UTR (NM_010299, exon 4 of 4)	11694	NM_010299	14667	Mm.287807	NM_010299	ENSMUSG00000000594	Gm2a	AA408702|AW215435|GM2-AP|SAP-3	GM2 ganglioside activator protein	protein-coding
mm_18324.1	chr2	57116604	57116614	-	1	NA	intron (NM_001139509, intron 1 of 7)	CpG	-1571	NM_013613	18227	Mm.3507	NM_013613	ENSMUSG00000026826	Nr4a2	HZF-3|NOT|Nurr1|RNR-1|TINOR|TINUR	nuclear receptor subfamily 4, group A, member 2	protein-coding
mm_68772.1	chr7	121993398	121993400	-	1	NA	intron (NM_028758, intron 14 of 16)	intron (NM_028758, intron 14 of 16)	-11706	NM_001033318	233824	Mm.442015	NM_001033318	ENSMUSG00000034951	Cog7	5630400E24Rik|Gm167	component of oligomeric golgi complex 7	protein-coding
mm_103424.1	chr11	75594794	75594804	-	1	NA	intron (NM_008850, intron 2 of 11)	intron (NM_008850, intron 2 of 11)	5432	NR_110477	654359	Mm.439961	NR_110477		Gm12338	OTTMUSG00000006216	cytochrome c oxidase, subunit VIIc pseudogene	pseudo
mm_100033.1	chr11	114982361	114982409	+	1	NA	TTS (NM_145437)	TTS (NM_145437)	7501	NM_145437	217305	Mm.275986	NM_145437	ENSMUSG00000034641	Cd300ld	4732429D16Rik|CLM5|Cd300ld1|LMIR4|MAIR-IV|clm-5	CD300 molecule like family member d	protein-coding
mm_15347.1	chr2	156144024	156144035	+	1	NA	promoter-TSS (NM_025946)	promoter-TSS (NM_025946)	-124	NM_001164216	67067	Mm.371623	NM_025946	ENSMUSG00000067847	Romo1	2010100O12Rik|AI853864	reactive oxygen species modulator 1	protein-coding
mm_148881.1	chr19	6532231	6532240	+	1	NA	3' UTR (NM_020253, exon 23 of 23)	3' UTR (NM_020253, exon 23 of 23)	10835	NM_009203	20521	Mm.391146	NM_009203	ENSMUSG00000061742	Slc22a12	AI987855|OAT4L|Rst|Slc22al2|URAT1	solute carrier family 22 (organic anion/cation transporter), member 12	protein-coding
mm_154911.1	chrX	21484533	21484547	+	1	NA	promoter-TSS (NM_007429)	promoter-TSS (NM_007429)	-84	NM_007429	11609	Mm.2679	NM_007429	ENSMUSG00000068122	Agtr2	AI316812|AW107640	angiotensin II receptor, type 2	protein-coding
mm_145790.1	chr18	65244275	65244280	+	1	NA	intron (NR_105742, intron 4 of 6)	intron (NR_105742, intron 4 of 6)	-4584	NR_029600	387231		NR_029600	ENSMUSG00000065402	Mir122	Mir122a|Mirn122a|mir-122|mmu-mir-122	microRNA 122	ncRNA
mm_111552.1	chr12	101029060	101029087	-	1	NA	promoter-TSS (NM_026681)	promoter-TSS (NM_026681)	-90	NM_026681	68339	Mm.156217	NM_026681	ENSMUSG00000021182	Ccdc88c	0610010D24Rik|AV000935|AW324073|Daple|mKIAA1509	coiled-coil domain containing 88C	protein-coding
mm_96803.1	chr11	69981476	69981480	+	1	NA	promoter-TSS (NM_018740)	promoter-TSS (NM_018740)	-243	NM_018740	54351	Mm.13430	NM_018740	ENSMUSG00000018565	Elp5	Derp6|Rai12	elongator acetyltransferase complex subunit 5	protein-coding
mm_141133.1	chr17	26206445	26206453	-	1	NA	intron (NM_001081069, intron 9 of 16)	intron (NM_001081069, intron 9 of 16)	3487	NM_001081069	50782	Mm.109840	NM_001081069	ENSMUSG00000024186	Rgs11	C78048	regulator of G-protein signaling 11	protein-coding
mm_112513.1	chr13	9093815	9093828	+	1	NA	promoter-TSS (NM_172585)	promoter-TSS (NM_172585)	-60	NM_001311117	217980	Mm.234944	NM_172585	ENSMUSG00000033499	Larp4b	A630096F19|AI256361|D13Wsu64e|Larp5	La ribonucleoprotein domain family, member 4B	protein-coding
mm_37118.1	chr4	116651542	116651549	-	1	NA	5' UTR (NM_021473, exon 1 of 9)	5' UTR (NM_021473, exon 1 of 9)	129	NM_021473	58810	Mm.30085	NM_021473	ENSMUSG00000028692	Akr1a1	2610201A18Rik|Akr1a4	aldo-keto reductase family 1, member A1 (aldehyde reductase)	protein-coding
mm_28407.1	chr3	90254079	90254092	-	1	NA	promoter-TSS (NM_028881)	promoter-TSS (NM_028881)	-196	NM_028881	74343	Mm.35627	NM_028881	ENSMUSG00000027936	Crtc2	4632407F12Rik|Torc2|mTORC2	CREB regulated transcription coactivator 2	protein-coding
mm_135927.1	chr16	70517586	70517587	-	1	NA	intron (NM_028803, intron 12 of 15)	intron (NM_028803, intron 12 of 15)	-98839	NR_040474	52645	Mm.188475	NR_040474		D16Ertd519e	-	DNA segment, Chr 16, ERATO Doi 519, expressed	ncRNA
mm_109393.1	chr12	109748093	109748115	+	1	NA	TTS (NR_037233)	TTS (NR_037233)	226	NR_037233	100499517		NR_037233	ENSMUSG00000093351	Mir3072	mir-3072|mmu-mir-3072	microRNA 3072	ncRNA
mm_71800.1	chr8	68276692	68276705	+	1	NA	5' UTR (NM_028182, exon 1 of 9)	5' UTR (NM_028182, exon 1 of 9)	170	NM_028182	72281	Mm.40974	NM_028182	ENSMUSG00000053886	Sh2d4a	2210402M20Rik|SH2A	SH2 domain containing 4A	protein-coding
mm_20321.1	chr2	127334041	127334055	-	1	NA	Intergenic	Intergenic	-2111	NM_010090	13537	Mm.4729	NM_010090	ENSMUSG00000027368	Dusp2	PAC1	dual specificity phosphatase 2	protein-coding
mm_56953.1	chr6	120002240	120002251	-	1	NA	exon (NM_001185020, exon 2 of 26)	exon (NM_001185020, exon 2 of 26)	32066	NR_030487	735290		NR_030487	ENSMUSG00000076217	Mir706	Mirn706|mir-706|mmu-mir-706	microRNA 706	ncRNA
mm_105169.1	chr11	101784323	101784350	-	1	NA	intron (NM_008815, intron 2 of 12)	intron (NM_008815, intron 2 of 12)	974	NM_008815	18612	Mm.5025	NM_008815	ENSMUSG00000017724	Etv4	AW414408|Pea-3|Pea3	ets variant 4	protein-coding
mm_45416.1	chr5	66492092	66492103	-	1	NA	5' UTR (NM_009686, exon 3 of 18)	5' UTR (NM_009686, exon 3 of 18)	126720	NM_009686	11787	Mm.5159	NM_009686	ENSMUSG00000029207	Apbb2	2310007D03Rik|FE65L1|Rirl1|TR2L|Zfra	amyloid beta (A4) precursor protein-binding, family B, member 2	protein-coding
mm_112238.1	chr12	113482410	113482416	-	1	NA	Intergenic	Intergenic	-7152	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_22658.1	chr3	14871683	14871692	+	1	NA	3' UTR (NM_007606, exon 7 of 7)	3' UTR (NM_007606, exon 7 of 7)	8149	NM_007606	12350	Mm.300	NM_007606	ENSMUSG00000027559	Car3	BB219044|Ca3|Car-3	carbonic anhydrase 3	protein-coding
mm_88389.1	chr10	76481033	76481042	+	1	NA	exon (NM_019434, exon 7 of 29)	exon (NM_019434, exon 7 of 29)	-11923	NM_172550	216119	Mm.344778	NM_172550	ENSMUSG00000033126	Ybey	1110068N23Rik|A130042E20Rik|C21orf57|ORF57|ORF66	ybeY metallopeptidase	protein-coding
mm_58881.1	chr7	17056274	17056306	+	1	NA	exon (NM_016868, exon 2 of 15)	exon (NM_016868, exon 2 of 15)	389	NM_016868	53417	Mm.135110	NM_016868	ENSMUSG00000004328	Hif3a	Ipas|MOP7|NEPAS|bHLHe17	hypoxia inducible factor 3, alpha subunit	protein-coding
mm_109669.1	chr12	113050546	113050556	+	1	NA	exon (NM_001291445, exon 5 of 23)	exon (NM_001291445, exon 5 of 23)	-23951	NM_029381	75671	Mm.23377	NM_029381	ENSMUSG00000012211	Tex22	1700028O09Rik|AV210422|Tep22	testis expressed gene 22	protein-coding
mm_140126.1	chr17	79615059	79615071	+	1	NA	intron (NM_201361, intron 1 of 10)	CpG	165	NM_201361	381110	Mm.209801	NM_201361	ENSMUSG00000036368	Rmdn2	AW061290|Fam82a1|RMD-2|mRMD-2	regulator of microtubule dynamics 2	protein-coding
mm_114372.1	chr13	63109003	63109016	+	1	NA	intron (NM_001289926, intron 5 of 15)	intron (NM_001289926, intron 5 of 15)	-131020	NR_110520	72061	Mm.188105	NM_028079	ENSMUSG00000021458	2010111I01Rik	2300006M17Rik|AP-O|AW742919|Aopep|ApO|mir-23b|mir-24-1|mir-27b	RIKEN cDNA 2010111I01 gene	protein-coding
mm_16619.1	chr2	5670287	5670307	-	1	NA	intron (NM_001290374, intron 1 of 9)	RMER2|LTR|ERV1	5749	NM_001290376	227541	Mm.191949	NM_177343	ENSMUSG00000039145	Camk1d	A630059D12Rik|CKLiK|CaMKIdelta|E030025C11Rik|mCKLiK	calcium/calmodulin-dependent protein kinase ID	protein-coding
mm_161298.1	chr14	30607936	30607936	-	1	NA	intron (NM_011103, intron 3 of 17)	intron (NM_011103, intron 3 of 17)	2374	NM_001310682	18753	Mm.2314	NM_011103	ENSMUSG00000021948	Prkcd	AI385711|D14Ertd420e|PKC[d]|PKCdelta|Pkcd	protein kinase C, delta	protein-coding
mm_51895.1	chr6	90619170	90619186	+	1	NA	promoter-TSS (NM_001037493)	promoter-TSS (NM_001037493)	-68	NM_001037493	71699	Mm.272633	NM_027868	ENSMUSG00000030089	Slc41a3	1010001P06Rik|AI480742|SLC41A1-L2	solute carrier family 41, member 3	protein-coding
mm_107647.1	chr12	52507272	52507274	+	1	NA	Intergenic	Intergenic	-8804	NM_009706	11855	Mm.35059	NM_009706	ENSMUSG00000035133	Arhgap5	p190-B|p190B	Rho GTPase activating protein 5	protein-coding
mm_168713.1	chr12	102412547	102412570	-	1	NA	intron (NM_011175, intron 3 of 13)	L1Md_T|LINE|L1	27255	NM_011175	19141	Mm.17185	NM_011175	ENSMUSG00000021190	Lgmn	AEP|AI746452|AU022324|Prsc1	legumain	protein-coding
mm_30169.1	chr3	144201916	144201953	-	1	NA	exon (NM_010723, exon 2 of 5)	exon (NM_010723, exon 2 of 5)	398	NM_001161770	16911	Mm.29187	NM_010723	ENSMUSG00000028266	Lmo4	A730077C12Rik|Crp3|Etohi4	LIM domain only 4	protein-coding
mm_149796.1	chr19	23605838	23605843	+	1	NA	intron (NM_026188, intron 2 of 5)	intron (NM_026188, intron 2 of 5)	46972	NM_026188	67483	Mm.443287	NM_026188	ENSMUSG00000033053	1700028P14Rik	AV209940	RIKEN cDNA 1700028P14 gene	protein-coding
mm_3034.1	chr1	133977480	133977490	+	1	NA	Intergenic	LTR85c|LTR|Gypsy?	-56084	NM_054077	116847	Mm.214514	NM_054077	ENSMUSG00000041577	Prelp	7330409J17Rik|SLRR2A	proline arginine-rich end leucine-rich repeat	protein-coding
mm_75152.1	chr8	36176042	36176051	-	1	NA	Intergenic	Intergenic	73470	NM_001081150	244421	Mm.324032	NM_001081150	ENSMUSG00000039633	Lonrf1	-	LON peptidase N-terminal domain and ring finger 1	protein-coding
mm_155634.1	chrX	84772813	84772830	+	1	NA	intron (NM_007868, intron 55 of 78)	intron (NM_007868, intron 55 of 78)	-275474	NM_001314038	13405	Mm.275608	NM_007868	ENSMUSG00000045103	Dmd	DXSmh7|DXSmh9|Dp427|Dp71|dys|mdx|pke	dystrophin, muscular dystrophy	protein-coding
mm_27284.1	chr3	41497027	41497047	-	1	NA	Intergenic	MER31-int|LTR|ERV1	-3838	NR_040385	78706	Mm.366094	NR_040385	ENSMUSG00000097639	Platr4	C430002E04Rik	pluripotency associated transcript 4	ncRNA
mm_26652.1	chr3	154314091	154314094	+	1	NA	intron (NM_010713, intron 7 of 8)	intron (NM_010713, intron 7 of 8)	16468	NM_010713	16875	Mm.15530	NM_010713	ENSMUSG00000096225	Lhx8	L3|Lhx7	LIM homeobox protein 8	protein-coding
mm_132595.1	chr16	38458798	38458825	+	1	NA	promoter-TSS (NM_009855)	promoter-TSS (NM_009855)	-122	NM_009855	12519	Mm.89474	NM_009855	ENSMUSG00000075122	Cd80	B71|Cd28l|Ly-53|Ly53|MIC17|TSA1	CD80 antigen	protein-coding
mm_110528.1	chr12	54986329	54986342	-	1	NA	promoter-TSS (NM_013815)	promoter-TSS (NM_013815)	1	NM_013815	217578	Mm.479583	NM_013815	ENSMUSG00000035021	Baz1a	Acf1|B930060C03|BC065123|Gtl5|Wcrf180|cbp146	bromodomain adjacent to zinc finger domain 1A	protein-coding
mm_111778.1	chr12	104153847	104153891	-	1	NA	promoter-TSS (NM_008458)	promoter-TSS (NM_008458)	3	NM_008458	16625	Mm.422814	NM_008458	ENSMUSG00000066361	Serpina3c	1A1|Kalbp|Klkbp|spi2	serine (or cysteine) peptidase inhibitor, clade A, member 3C	protein-coding
mm_70200.1	chr7	144582393	144582454	-	1	NA	promoter-TSS (NM_010175)	promoter-TSS (NM_010175)	13	NM_010175	14082	Mm.5126	NM_010175	ENSMUSG00000031077	Fadd	Mort1/FADD	Fas (TNFRSF6)-associated via death domain	protein-coding
mm_19891.1	chr2	114050956	114050966	-	1	NA	intron (NM_009608, intron 2 of 6)	intron (NM_009608, intron 2 of 6)	1914	NM_009608	11464	Mm.686	NM_009608	ENSMUSG00000068614	Actc1	Actc-1	actin, alpha, cardiac muscle 1	protein-coding
mm_170463.1	chr1	8936481	8936487	+	1	NA	intron (NM_027671, intron 3 of 20)	RLTR9E|LTR|ERVK	363393	NM_001290390	71096	Mm.336395	NM_027671	ENSMUSG00000025909	Sntg1	4933426D16Rik|G1SYN|SYN4	syntrophin, gamma 1	protein-coding
mm_166969.1	chr7	44553883	44553891	-	1	NA	promoter-TSS (NM_009473)	promoter-TSS (NM_009473)	78	NM_009473	22260	Mm.968	NM_009473	ENSMUSG00000060601	Nr1h2	AI194859|LXR|LXRB|LXRBSV|LXRbeta|NER1|OR-1|RIP15|UR|Unr|Unr2	nuclear receptor subfamily 1, group H, member 2	protein-coding
mm_129640.1	chr15	80257534	80257541	-	1	NA	TTS (NM_009716)	TTS (NM_009716)	2353	NM_009716	11911	Mm.641	NM_009716	ENSMUSG00000042406	Atf4	Atf-4|C/ATF|CREB2|TAXREB67	activating transcription factor 4	protein-coding
mm_71808.1	chr8	68880632	68880642	+	1	NA	promoter-TSS (NM_008509)	promoter-TSS (NM_008509)	82	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_113252.1	chr13	27801639	27801654	+	1	NA	promoter-TSS (NM_019991)	promoter-TSS (NM_019991)	-9	NM_019991	56635	Mm.23585	NM_019991	ENSMUSG00000022886	Prl2a1	Ghd21|PLP-M|Prlpm	prolactin family 2, subfamily a, member 1	protein-coding
mm_64747.1	chr7	4778142	4778144	-	1	NA	promoter-TSS (NM_008350)	promoter-TSS (NM_008350)	-2	NM_008350	16156	Mm.35814	NM_008350	ENSMUSG00000004371	Il11	IL-11	interleukin 11	protein-coding
mm_162296.1	chr1	33738924	33738959	+	1	NA	intron (NM_001159729, intron 7 of 7)	intron (NM_001159729, intron 7 of 7)	18522	NM_001159729	19335	Mm.86744	NM_008999	ENSMUSG00000004768	Rab23	AW545388|opb|opb2	RAB23, member RAS oncogene family	protein-coding
mm_172130.1	chr6	3344212	3344224	+	1	NA	Intergenic	RLTR9D|LTR|ERVK	55353	NM_010156	209086	Mm.196013	NM_010156	ENSMUSG00000047735	Samd9l	AA175286|ESTM25|mKIAA2005	sterile alpha motif domain containing 9-like	protein-coding
mm_41159.1	chr5	87929910	87929916	+	1	NA	exon (NM_007786, exon 4 of 5)	exon (NM_007786, exon 4 of 5)	4280	NM_007786	12994	Mm.296303	NM_007786	ENSMUSG00000001622	Csn3	AW208918|CSN10|Csnk	casein kappa	protein-coding
mm_51987.1	chr6	92091496	92091506	+	1	NA	promoter-TSS (NM_011630)	promoter-TSS (NM_011630)	83	NM_011630	22026	Mm.87062	NM_011630	ENSMUSG00000005893	Nr2c2	TAK1|Tr4|mKIAA4145	nuclear receptor subfamily 2, group C, member 2	protein-coding
mm_58954.1	chr7	18812573	18812587	+	1	NA	Intergenic	RLTR48B|LTR|ERV1	9011	NM_007677	26437	Mm.302844	NM_007677	ENSMUSG00000004540	Psg17	Cea-2|Cea2|mmCGM5	pregnancy specific glycoprotein 17	protein-coding
mm_95918.1	chr11	58220732	58220755	+	1	NA	3' UTR (NM_019440, exon 2 of 2)	3' UTR (NM_019440, exon 2 of 2)	5766	NM_019440	54396	Mm.458517	NM_019440	ENSMUSG00000069874	Irgm2	AI481100|GTPI|Ifggd2|Iigp2	immunity-related GTPase family M member 2	protein-coding
mm_112887.1	chr13	20860613	20860621	+	1	NA	intron (NM_012054, intron 4 of 20)	MIR3|SINE|MIR	66504	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_127140.1	chr15	98172045	98172051	+	1	NA	Intergenic	Intergenic	4242	NM_177716	239650	Mm.54140	NM_177716	ENSMUSG00000029875	Ccdc184	5630400A08|AI836003	coiled-coil domain containing 184	protein-coding
mm_30678.1	chr4	11171899	11171964	+	1	NA	3' UTR (NM_001199105, exon 5 of 5)	3' UTR (NM_001199105, exon 5 of 5)	15490	NM_021897	60599	Mm.393018	NM_021897	ENSMUSG00000028211	Trp53inp1	2700057G22Rik|SIP|SIP18|SIP27|Stinp|Teap	transformation related protein 53 inducible nuclear protein 1	protein-coding
mm_8658.1	chr1	156474250	156474281	-	1	NA	promoter-TSS (NM_009230)	promoter-TSS (NM_009230)	63	NM_009230	20652	Mm.28099	NM_009230	ENSMUSG00000026600	Soat1	8430426K15Rik|ACAT-1|AW550831|Acact|ald|hid	sterol O-acyltransferase 1	protein-coding
mm_99256.1	chr11	101155969	101156040	+	1	NA	5' UTR (NM_134028, exon 1 of 11)	5' UTR (NM_134028, exon 1 of 11)	120	NM_134028	103768	Mm.142348	NM_134028	ENSMUSG00000045007	Tubg2	AI504772|Tubgl	tubulin, gamma 2	protein-coding
mm_119346.1	chr14	41105205	41105219	+	1	NA	5' UTR (NM_133653, exon 1 of 10)	5' UTR (NM_133653, exon 1 of 10)	179	NM_133653	11720	Mm.14064	NM_133653	ENSMUSG00000037798	Mat1a	AI046368|AdoMet|Ams|MAT|MATA1|SAMS|SAMS1	methionine adenosyltransferase I, alpha	protein-coding
mm_26201.1	chr3	138526621	138526631	+	1	NA	promoter-TSS (NM_001313980)	promoter-TSS (NM_001313980)	205	NR_035481	100316706		NR_035481	ENSMUSG00000088373	Mir1956	mir-1956|mmu-mir-1956	microRNA 1956	ncRNA
mm_79781.1	chr9	62868641	62868649	+	1	NA	intron (NM_001102468, intron 2 of 3)	intron (NM_001102468, intron 2 of 3)	-6621	NR_003965	677044	Mm.422004	NR_003965	ENSMUSG00000074250	Gm10653	ENSMUSG00000074250	ribsomal protein S2 pseudogene	pseudo
mm_2761.1	chr1	130462559	130462609	+	1	NA	exon (NM_010016, exon 1 of 10)	exon (NM_010016, exon 1 of 10)	160	NM_010016	13136	Mm.101591	NM_010016	ENSMUSG00000026399	Cd55	Daf|Daf-GPI|Daf1|GPI-DAF	CD55 molecule, decay accelerating factor for complement	protein-coding
mm_115105.1	chr13	103332601	103332608	+	1	NA	intron (NM_175171, intron 1 of 28)	intron (NM_175171, intron 1 of 28)	1888	NM_175171	328329	Mm.202606	NM_175171	ENSMUSG00000034751	Mast4	4930420O11Rik|AI642422|mKIAA0303	microtubule associated serine/threonine kinase family member 4	protein-coding
mm_5710.1	chr1	43826553	43826583	-	1	NA	intron (NM_026430, intron 1 of 14)	(CTG)n|Simple_repeat|Simple_repeat	1140	NM_026430	67883	Mm.387202	NM_026430	ENSMUSG00000057363	Uxs1	1600025I13Rik|AI451869|AI649125|AW550562	UDP-glucuronate decarboxylase 1	protein-coding
mm_140951.1	chr17	24533710	24533732	-	1	NA	promoter-TSS (NM_177375)	promoter-TSS (NM_177375)	26	NM_177375	328778	Mm.266033	NM_177375	ENSMUSG00000079657	Rab26	A830020M03Rik	RAB26, member RAS oncogene family	protein-coding
mm_90610.1	chr10	128337834	128337844	+	1	NA	5' UTR (NM_026444, exon 1 of 11)	5' UTR (NM_026444, exon 1 of 11)	112	NM_026444	12974	Mm.58836	NM_026444	ENSMUSG00000005683	Cs	2610511A05Rik|9030605P22Rik|Ahl4|BB234005|Cis	citrate synthase	protein-coding
mm_46804.1	chr5	113076987	113077005	-	1	NA	intron (NM_001159650, intron 5 of 5)	intron (NM_001159650, intron 5 of 5)	4588	NM_001159650	12962	Mm.378899	NM_021352	ENSMUSG00000029352	Crybb3	AI852419	crystallin, beta B3	protein-coding
mm_143984.1	chr17	87613425	87613433	-	1	NA	Intergenic	Intergenic	-22550	NM_008532	17075	Mm.4259	NM_008532	ENSMUSG00000045394	Epcam	CD326|EGP|EGP-2|Egp314|Ep-CAM|EpCAM1|GA733-2|Ly74|TROP1|Tacsd1|Tacstd1|gp40	epithelial cell adhesion molecule	protein-coding
mm_107171.1	chr12	24708985	24709004	+	1	NA	exon (NM_009104, exon 3 of 10)	exon (NM_009104, exon 3 of 10)	740	NM_009104	20135	Mm.99	NM_009104	ENSMUSG00000020649	Rrm2	AA407299|R2	ribonucleotide reductase M2	protein-coding
mm_144219.1	chr18	9769969	9770017	+	1	NA	intron (NM_130449, intron 2 of 9)	PB1D9|SINE|Alu	62345	NM_130449	140792	Mm.218571	NM_130449	ENSMUSG00000036103	Colec12	CL-P1|SRCL|Scara4	collectin sub-family member 12	protein-coding
mm_138291.1	chr17	34629349	34629406	+	1	NA	promoter-TSS (NM_030890)	promoter-TSS (NM_030890)	-309	NM_030890	260297	Mm.390965	NM_030890	ENSMUSG00000015476	Prrt1	Bat-4|Bat4|D17H6S54E|DSPD1|G5b|NG5|ORF31	proline-rich transmembrane protein 1	protein-coding
mm_168537.1	chr1	161877943	161877947	+	1	NA	Intergenic	RMER10A|LTR|ERVL	-1284	NM_172645	226551	Mm.170002	NM_172645	ENSMUSG00000040297	Suco	4732491B11|AI848100|AU016931|Opt	SUN domain containing ossification factor	protein-coding
mm_144797.1	chr18	36106165	36106173	+	1	NA	promoter-TSS (NR_015571)	promoter-TSS (NR_015571)	-34	NR_015571	74966	Mm.379238	NM_030089		4930471G03Rik	1700007N01Rik	RIKEN cDNA 4930471G03 gene	ncRNA
mm_37173.1	chr4	117182950	117182951	-	1	NA	promoter-TSS (NM_134471)	promoter-TSS (NM_134471)	-326	NM_134471	73804	Mm.247651	NM_134471	ENSMUSG00000028678	Kif2c	4930402F02Rik|ESTM5|Knsl6|MCAK|X83316	kinesin family member 2C	protein-coding
mm_132611.1	chr16	38651330	38651332	+	1	NA	intron (NM_020260, intron 1 of 11)	intron (NM_020260, intron 1 of 11)	61704	NM_020260	12549	Mm.370848	NM_020260	ENSMUSG00000022799	Arhgap31	5830477L08Rik|AU041750|Cdgap|D330026I07Rik	Rho GTPase activating protein 31	protein-coding
mm_103666.1	chr11	79059844	79059853	-	1	NA	intron (NM_013571, intron 2 of 17)	intron (NM_013571, intron 2 of 17)	36251	NR_045873	790910	Mm.440410	NR_045873		Gm11201	ENSMUSG00000072637|OTTMUSG00000000169	predicted gene 11201	ncRNA
mm_3542.1	chr1	150403643	150403657	+	1	NA	exon (NM_133780, exon 6 of 52)	exon (NM_133780, exon 6 of 52)	-10595	NM_145511	226499	Mm.222093	NM_145511	ENSMUSG00000006010	BC003331	1810053E15Rik|Odr4|odr-4	cDNA sequence BC003331	protein-coding
mm_74808.1	chr8	22633268	22633285	-	1	NA	intron (NM_011130, intron 11 of 13)	intron (NM_011130, intron 11 of 13)	3533	NR_027886	68074	Mm.463136	NR_027886		A930013F10Rik	-	RIKEN cDNA A930013F10 gene	ncRNA
mm_25476.1	chr3	108911829	108911856	+	1	NA	promoter-TSS (NM_025845)	promoter-TSS (NM_025845)	-138	NM_025845	66921	Mm.51049	NM_025845	ENSMUSG00000027881	Prpf38b	1110021E09Rik|AU018955	PRP38 pre-mRNA processing factor 38 (yeast) domain containing B	protein-coding
mm_88830.1	chr10	80805234	80805249	+	1	NA	promoter-TSS (NM_007445)	promoter-TSS (NM_007445)	-7	NM_007445	11705	Mm.376094	NM_007445	ENSMUSG00000035262	Amh	MIS	anti-Mullerian hormone	protein-coding
mm_154481.1	chrM	4459	4469	-	1	NA	NA	Intergenic	NA	NA								
mm_60472.1	chr7	44478137	44478147	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-6375	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_129053.1	chr15	75566553	75566567	-	1	NA	promoter-TSS (NM_001135689)	promoter-TSS (NM_001135689)	88	NM_001135689	23934	Mm.22154	NM_011837	ENSMUSG00000022577	Ly6h	-	lymphocyte antigen 6 complex, locus H	protein-coding
mm_134298.1	chr16	15114101	15114132	-	1	NA	Intergenic	Intergenic	207470	NM_025769	66793	Mm.100270	NM_025769	ENSMUSG00000068617	Efcab1	4930449A16Rik|5430404L10Rik	EF hand calcium binding domain 1	protein-coding
mm_22569.1	chr3	10088107	10088126	+	1	NA	promoter-TSS (NR_045710)	promoter-TSS (NR_045710)	-161	NR_045710	100041480	Mm.455632	NR_045710	ENSMUSG00000049230	Gm9833	ENSMUSG00000049230	myelin basic protein expression factor 2, repressor pseudogene	pseudo
mm_159086.1	chr2	30078725	30078725	+	1	NA	promoter-TSS (NM_153805)	promoter-TSS (NM_153805)	-41	NM_153805	263803	Mm.233843	NM_153805	ENSMUSG00000026785	Pkn3	AW209115|BC034126	protein kinase N3	protein-coding
mm_149965.1	chr19	29046484	29046513	+	1	NA	promoter-TSS (NR_028360)	promoter-TSS (NR_028360)	-985	NR_028360	67329	Mm.394933	NR_028360		1700018L02Rik	-	RIKEN cDNA 1700018L02 gene	ncRNA
mm_89793.1	chr10	102374430	102374445	+	1	NA	promoter-TSS (NM_026243)	promoter-TSS (NM_026243)	0	NM_026243	67569	Mm.25252	NM_026243	ENSMUSG00000019888	Mgat4c	9130411I17Rik|GntIVh	MGAT4 family, member C	protein-coding
mm_105499.1	chr11	106160441	106160483	-	1	NA	promoter-TSS (NM_172397)	promoter-TSS (NM_172397)	-320	NM_172397	67803	Mm.21687	NM_172397	ENSMUSG00000040699	Limd2	0610025L06Rik|AI413966	LIM domain containing 2	protein-coding
mm_148779.1	chr19	6108681	6108697	+	1	NA	exon (NM_001009546, exon 5 of 18)	exon (NM_001009546, exon 5 of 18)	2891	NM_001009546	381204	Mm.359041	NM_001009546	ENSMUSG00000054999	Naaladl1	Gm964|Naaladasel	N-acetylated alpha-linked acidic dipeptidase-like 1	protein-coding
mm_40496.1	chr5	57717746	57717771	+	1	NA	promoter-TSS (NM_001310606)	promoter-TSS (NM_001310606)	161	NR_015588	319216	Mm.332387	NR_015588	ENSMUSG00000097216	4932441J04Rik	-	RIKEN cDNA 4932441J04 gene	ncRNA
mm_146026.1	chr18	69519840	69519846	+	1	NA	intron (NM_013685, intron 5 of 19)	intron (NM_013685, intron 5 of 19)	174122	NM_001083967	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding
mm_25832.1	chr3	129199907	129199913	+	1	NA	promoter-TSS (NM_001042504)	promoter-TSS (NM_001042504)	32	NM_001042504	18741	Mm.246804	NM_011098	ENSMUSG00000028023	Pitx2	9430085M16Rik|Brx1|Brx1b|Munc30|Otlx2|Ptx2|Rieg	paired-like homeodomain transcription factor 2	protein-coding
mm_165843.1	chr3	159839766	159839791	+	1	NA	promoter-TSS (NR_037590)	promoter-TSS (NR_037590)	83	NM_026582	68151	Mm.6766	NM_026582	ENSMUSG00000028173	Wls	5031439A09Rik|AI173978|AI987742|Gpr177	wntless homolog (Drosophila)	protein-coding
mm_93457.1	chr10	110337102	110337104	-	1	NA	Intergenic	Intergenic	-263547	NR_028438	109335	Mm.367727	NR_028438		9230102K24Rik	-	RIKEN cDNA 9230102K24 gene	ncRNA
mm_147886.1	chr18	64700050	64700056	-	1	NA	Intergenic	Intergenic	-39053	NM_001001488	54670	Mm.270043	NM_001001488	ENSMUSG00000039529	Atp8b1	AI451886|FIC1|Ic	ATPase, class I, type 8B, member 1	protein-coding
mm_33022.1	chr4	121053031	121053043	+	1	NA	intron (NM_007741, intron 27 of 31)	intron (NM_007741, intron 27 of 31)	13471	NM_007741	12840	Mm.269384	NM_007741	ENSMUSG00000028626	Col9a2	AI427499|Col9a-2	collagen, type IX, alpha 2	protein-coding
mm_119905.1	chr14	54949918	54949939	+	1	NA	promoter-TSS (NR_029724)	promoter-TSS (NR_029724)	-786	NR_029724	387204		NR_029724	ENSMUSG00000065432	Mir208a	Mirn208|Mirn208a|mir-208|mir-208a|mmu-mir-208	microRNA 208a	ncRNA
mm_40837.1	chr5	73230470	73230470	+	1	NA	intron (NM_028194, intron 1 of 62)	intron (NM_028194, intron 1 of 62)	26148	NM_028194	72313	Mm.260594	NM_028194	ENSMUSG00000070733	Fryl	2010313D22Rik|2310004H21Rik|2510002A14Rik|9030227G01Rik|mKIAA0826	FRY like transcription coactivator	protein-coding
mm_29028.1	chr3	102166388	102166408	-	1	NA	intron (NM_177545, intron 5 of 7)	intron (NM_177545, intron 5 of 7)	38295	NM_177545	229658	Mm.118004	NM_177545	ENSMUSG00000027860	Vangl1	Kitenin|Lpp2|Stb2|Stbm	vang-like 1 (van gogh, Drosophila)	protein-coding
mm_35883.1	chr4	49539758	49539779	-	1	NA	exon (NM_144903, exon 6 of 9)	exon (NM_144903, exon 6 of 9)	9778	NM_144903	230163	Mm.482116	NM_144903	ENSMUSG00000028307	Aldob	Aldo-2|Aldo2|BC016435	aldolase B, fructose-bisphosphate	protein-coding
mm_13790.1	chr2	118861987	118862008	+	1	NA	promoter-TSS (NM_019826)	promoter-TSS (NM_019826)	-3	NM_019826	56357	Mm.6635	NM_019826	ENSMUSG00000027332	Ivd	1300016K07Rik|6720455E18Rik|AI463340	isovaleryl coenzyme A dehydrogenase	protein-coding
mm_160070.1	chr7	6222197	6222197	+	1	NA	promoter-TSS (NM_133204)	promoter-TSS (NM_133204)	-81	NM_133204	170734	Mm.155595	NM_133204	ENSMUSG00000058028	Zscan5b	Zfg1|Zfp371	zinc finger and SCAN domain containing 5B	protein-coding
mm_130598.1	chr15	99772597	99772608	-	1	NA	promoter-TSS (NM_028015)	promoter-TSS (NM_028015)	-87	NM_028015	71949	Mm.390821	NM_028015	ENSMUSG00000023021	Cers5	2310081H14Rik|AU045339|AW544927|Lass5|Trh4	ceramide synthase 5	protein-coding
mm_131823.1	chr16	22929639	22929652	+	1	NA	exon (NM_021564, exon 3 of 8)	exon (NM_021564, exon 3 of 8)	9423	NM_001083904	59083	Mm.28461	NM_021564	ENSMUSG00000022871	Fetub	2310011O17Rik|AI255764|D17980|Gugu	fetuin beta	protein-coding
mm_158558.1	chrX	150367161	150367164	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-53798	NM_001101501	333588	Mm.159296	NM_001101501		Gm15104	OTTMUSG00000018998	predicted gene 15104	protein-coding
mm_53442.1	chr6	134396317	134396319	+	1	NA	promoter-TSS (NM_025778)	promoter-TSS (NM_025778)	-11	NM_025778	66813	Mm.474472	NM_025778	ENSMUSG00000030200	Bcl2l14	4930452K23Rik|4933405K19Rik|9030625M01Rik|AI429211|Bclg	BCL2-like 14 (apoptosis facilitator)	protein-coding
mm_122195.1	chr14	31780999	31781014	-	1	NA	intron (NM_001024604, intron 1 of 27)	intron (NM_001024604, intron 1 of 27)	49409	NM_001024604	105522	Mm.37660	NM_001024604	ENSMUSG00000014496	Ankrd28	AI465466|AI604979|E430019N21Rik|mKIAA0379	ankyrin repeat domain 28	protein-coding
mm_110538.1	chr12	55302621	55302623	-	1	NA	promoter-TSS (NM_025373)	promoter-TSS (NM_025373)	-15	NM_025373	66132	Mm.383213	NM_025373	ENSMUSG00000021023	1110008L16Rik	Kiaa0391|Mrpp3|mKIAA0391	RIKEN cDNA 1110008L16 gene	protein-coding
mm_30861.1	chr4	30664605	30664614	+	1	NA	promoter-TSS (NR_040655)	promoter-TSS (NR_040655)	13	NR_040655	75332	Mm.108636	NR_040655		4930556G01Rik	-	RIKEN cDNA 4930556G01 gene	ncRNA
mm_52864.1	chr6	122308815	122308839	+	1	NA	promoter-TSS (NM_010749)	promoter-TSS (NM_010749)	-183	NM_010749	17113	Mm.249225	NM_010749	ENSMUSG00000007458	M6pr	CD-MPR|Mpr46	mannose-6-phosphate receptor, cation dependent	protein-coding
mm_52527.1	chr6	115675984	115676004	+	1	NA	intron (NM_029780, intron 1 of 16)	intron (NM_029780, intron 1 of 16)	641	NM_029780	110157	Mm.184163	NM_029780	ENSMUSG00000000441	Raf1	6430402F14Rik|AA990557|BB129353|Craf1|D830050J10Rik|Raf-1|c-Raf|v-Raf	v-raf-leukemia viral oncogene 1	protein-coding
mm_3198.1	chr1	135818687	135818711	+	1	NA	5' UTR (NM_133664, exon 1 of 10)	5' UTR (NM_133664, exon 1 of 10)	101	NM_133664	16763	Mm.36726	NM_133664	ENSMUSG00000041782	Lad1	-	ladinin	protein-coding
mm_149409.1	chr19	11407653	11407700	+	1	NA	promoter-TSS (NM_029499)	promoter-TSS (NM_029499)	15	NM_029499	64380	Mm.440715	NM_029499	ENSMUSG00000024675	Ms4a4c	5830413L19Rik|AI449185|Ms4a9	membrane-spanning 4-domains, subfamily A, member 4C	protein-coding
mm_69606.1	chr7	137194610	137194666	-	1	NA	3' UTR (NM_001113414, exon 16 of 16)	3' UTR (NM_001113414, exon 16 of 16)	-40045	NR_045885	100038555	Mm.444788	NR_045885	ENSMUSG00000109722	Gm10578	ENSMUSG00000073800	predicted gene 10578	ncRNA
mm_2796.1	chr1	130851550	130851556	+	1	NA	3' UTR (NM_011082, exon 11 of 11)	3' UTR (NM_011082, exon 11 of 11)	-14224	NM_026976	69169	Mm.46042	NM_026976	ENSMUSG00000042474	Fcmr	1810037B05Rik|Faim3|FcmuR|Toso	Fc fragment of IgM receptor	protein-coding
mm_165270.1	chr2	75704429	75704441	-	1	NA	non-coding (NR_132727, exon 1 of 2)	non-coding (NR_132727, exon 1 of 2)	228	NR_132727	18024	Mm.1025	NM_010902	ENSMUSG00000015839	Nfe2l2	Nrf2	nuclear factor, erythroid derived 2, like 2	protein-coding
mm_57123.1	chr6	122599447	122599465	-	1	NA	intron (NM_001134391, intron 2 of 7)	intron (NM_001134391, intron 2 of 7)	2988	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_83070.1	chr9	37613579	37613626	-	1	NA	promoter-TSS (NM_011734)	promoter-TSS (NM_011734)	118	NM_011449	20686	Mm.8637	NM_011449	ENSMUSG00000001948	Spa17	Sp17	sperm autoantigenic protein 17	protein-coding
mm_17131.1	chr2	24927726	24927729	-	1	NA	intron (NR_027876, intron 2 of 6)	intron (NR_027876, intron 2 of 6)	7554	NR_027876	215705	Mm.45275	NM_178408	ENSMUSG00000026972	Arrdc1	AI957342|BC004091	arrestin domain containing 1	protein-coding
mm_124837.1	chr15	9279873	9279881	+	1	NA	promoter-TSS (NM_207216)	promoter-TSS (NM_207216)	48	NM_207216	105887	Mm.482274	NM_207216	ENSMUSG00000072664	Ugt3a1	AI746432	UDP glycosyltransferases 3 family, polypeptide A1	protein-coding
mm_41765.1	chr5	103425234	103425259	+	1	NA	promoter-TSS (NM_011204)	promoter-TSS (NM_011204)	54	NM_011204	19249	Mm.3414	NM_011204	ENSMUSG00000034573	Ptpn13	AI324989|PTP-BL|PTPL1|Ptpri|RIP	protein tyrosine phosphatase, non-receptor type 13	protein-coding
mm_51270.1	chr6	72115205	72115215	+	1	NA	intron (NM_011375, intron 1 of 6)	intron (NM_011375, intron 1 of 6)	7730	NR_045163	71265	Mm.442035	NR_045163	ENSMUSG00000108709	4933431G14Rik	4930565C19Rik	RIKEN cDNA 4933431G14 gene	ncRNA
mm_93859.1	chr10	122679414	122679443	-	1	NA	TTS (NR_106182)	TTS (NR_106182)	113	NR_106182	102466884		NR_106182	ENSMUSG00000099225	Mir8104	Gm27380|mmu-mir-8104	microRNA 8104	ncRNA
mm_101102.1	chr11	11931723	11931735	-	1	NA	3' UTR (NM_010345, exon 17 of 17)	3' UTR (NM_010345, exon 17 of 17)	-33585	NM_001190448	13195	Mm.12906	NM_016672	ENSMUSG00000020182	Ddc	Aadc	dopa decarboxylase	protein-coding
mm_126670.1	chr15	84327124	84327133	+	1	NA	intron (NM_022321, intron 2 of 12)	intron (NM_022321, intron 2 of 12)	1009	NM_001162500	64099	Mm.251356	NM_022321	ENSMUSG00000022439	Parvg	AI413459	parvin, gamma	protein-coding
mm_136612.1	chr17	5334838	5334850	+	1	NA	intron (NM_001085355, intron 16 of 19)	intron (NM_001085355, intron 16 of 19)	83923	NM_175349	106557	Mm.432764	NM_175349	ENSMUSG00000101959	Ldhal6b	4933402O15Rik|AI326310|LDHL|Ldhal	lactate dehydrogenase A-like 6B	protein-coding
mm_87898.1	chr10	62071590	62071608	+	1	NA	Intergenic	Intergenic	39414	NM_027251	69894	Mm.294126	NM_027251	ENSMUSG00000020083	2010107G23Rik	AA545165	RIKEN cDNA 2010107G23 gene	protein-coding
mm_40902.1	chr5	75180111	75180126	+	1	NA	intron (NM_001347718, intron 12 of 15)	intron (NM_001347718, intron 12 of 15)	3287	NR_105992	102465620		NR_105992	ENSMUSG00000099060	Mir7025	Gm27860|mmu-mir-7025	microRNA 7025	ncRNA
mm_136889.1	chr17	13010516	13010530	+	1	NA	exon (NM_013671, exon 3 of 5)	exon (NM_013671, exon 3 of 5)	2684	NM_013671	20656	Mm.290876	NM_013671	ENSMUSG00000006818	Sod2	MnSOD|Sod-2	superoxide dismutase 2, mitochondrial	protein-coding
mm_26604.1	chr3	152210470	152210534	+	1	NA	promoter-TSS (NM_027287)	promoter-TSS (NM_027287)	44	NM_057172	51886	Mm.278922	NM_057172	ENSMUSG00000028034	Fubp1	9530027K12Rik|D3Ertd330e|FBP|Fubp|Fubp4	far upstream element (FUSE) binding protein 1	protein-coding
mm_114733.1	chr13	83729458	83729468	+	1	NA	intron (NR_015561, intron 1 of 3)	intron (NR_015561, intron 1 of 3)	1357	NR_015561	320203	Mm.245636	NM_177100	ENSMUSG00000050334	C130071C03Rik	2810449C10Rik	RIKEN cDNA C130071C03 gene	ncRNA
mm_33622.1	chr4	132716253	132716254	+	1	NA	intron (NM_211357, intron 13 of 14)	intron (NM_211357, intron 13 of 14)	16293	NM_201368	381560	Mm.44558	NM_201368	ENSMUSG00000037752	Xkr8	4931440N07Rik|AI597014|Gm1031|XRG8|mXkr8	X-linked Kx blood group related 8	protein-coding
mm_90161.1	chr10	119107829	119107832	+	1	NA	Intergenic	Intergenic	14925	NR_045348	73400	Mm.416864	NR_045348	ENSMUSG00000100681	1700064J06Rik	-	RIKEN cDNA 1700064J06 gene	ncRNA
mm_125041.1	chr15	25776384	25776397	+	1	NA	exon (NM_019472, exon 21 of 41)	exon (NM_019472, exon 21 of 41)	-66908	NM_001034851	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_89887.1	chr10	108691022	108691032	+	1	NA	exon (NM_001252342, exon 4 of 11)	exon (NM_001252342, exon 4 of 11)	9133	NM_203660	368203	Mm.452758	NM_203660		Gm5136	C6.1AL|EG368203	predicted gene 5136	protein-coding
mm_118432.1	chr14	8006591	8006602	+	1	NA	intron (NM_001331064, intron 1 of 8)	intron (NM_001331064, intron 1 of 8)	3630	NM_001331064	66082	Mm.181473	NM_025341	ENSMUSG00000025277	Abhd6	0610041D24Rik|AA673485|AV065425	abhydrolase domain containing 6	protein-coding
mm_8580.1	chr1	155813044	155813056	-	1	NA	promoter-TSS (NM_023268)	promoter-TSS (NM_023268)	-151	NM_001024945	104009	Mm.27035	NM_023268	ENSMUSG00000033684	Qsox1	1300003H02Rik|QSOX|Qscn6|SOx	quiescin Q6 sulfhydryl oxidase 1	protein-coding
mm_42639.1	chr5	118560625	118560690	+	1	NA	promoter-TSS (NM_172424)	promoter-TSS (NM_172424)	-62	NM_001347445	76199	Mm.206238	NM_172424	ENSMUSG00000018076	Med13l	2210413I17Rik|6330591G05Rik|9030618F05Rik|Thrap2|Trap240L|mKIAA1025	mediator complex subunit 13-like	protein-coding
mm_66455.1	chr7	44869794	44869817	-	1	NA	promoter-TSS (NM_133949)	promoter-TSS (NM_133949)	-17	NM_133949	84113	Mm.42855	NM_133949	ENSMUSG00000038502	Ptov1	1110030G05Rik|AU041779|Gcap3	prostate tumor over expressed gene 1	protein-coding
mm_68526.1	chr7	112159035	112159095	-	1	NA	promoter-TSS (NM_015814)	promoter-TSS (NM_015814)	-8	NM_015814	50781	Mm.55143	NM_015814	ENSMUSG00000030772	Dkk3	AW061014|C87148	dickkopf WNT signaling pathway inhibitor 3	protein-coding
mm_123074.1	chr14	55721861	55721894	-	1	NA	5' UTR (NM_019519, exon 1 of 16)	5' UTR (NM_019519, exon 1 of 16)	299	NM_019519	56187	Mm.87216	NM_019519	ENSMUSG00000040472	Rabggta	gm	Rab geranylgeranyl transferase, a subunit	protein-coding
mm_47286.1	chr5	122131959	122131973	-	1	NA	intron (NM_001289809, intron 1 of 11)	intron (NM_001289809, intron 1 of 11)	2927	NM_001289811	330188	Mm.386907	NM_183307	ENSMUSG00000043036	Ccdc63	4921511C16Rik	coiled-coil domain containing 63	protein-coding
mm_29723.1	chr3	125938498	125938517	-	1	NA	promoter-TSS (NM_011674)	promoter-TSS (NM_011674)	43	NM_011674	22239	Mm.306021	NM_011674	ENSMUSG00000032854	Ugt8a	AI850488|AW455908|Cgt|Ugt8|mCerGT	UDP galactosyltransferase 8A	protein-coding
mm_155010.1	chrX	41401390	41401427	+	1	NA	promoter-TSS (NM_001290451)	promoter-TSS (NM_001290451)	107	NR_104053	53623	Mm.327681	NM_016886	ENSMUSG00000001986	Gria3	2900064I19Rik|GluA3|GluR-C|GluR-K3|Glur-3|Glur3|Gluralpha3	glutamate receptor, ionotropic, AMPA3 (alpha 3)	protein-coding
mm_5178.1	chr1	12693372	12693396	-	1	NA	intron (NM_001198566, intron 1 of 20)	intron (NM_001198566, intron 1 of 20)	954	NM_001198566	240725	Mm.45563	NM_172294	ENSMUSG00000016918	Sulf1	AI467640|AW121680|mKIAA1077	sulfatase 1	protein-coding
mm_23108.1	chr3	37420399	37420407	+	1	NA	promoter-TSS (NM_001291044)	promoter-TSS (NM_001291044)	453	NM_021343	57815	Mm.172679	NM_021343	ENSMUSG00000027722	Spata5	2510048F20Rik|C78064|Spaf	spermatogenesis associated 5	protein-coding
mm_157254.1	chrX	19150875	19150887	-	1	NA	Intergenic	Intergenic	-3910	NR_029807	723828		NR_029807	ENSMUSG00000065471	Mir222	Mirn222|mir-222|mmu-mir-222	microRNA 222	ncRNA
mm_71761.1	chr8	66392144	66392193	+	1	NA	intron (NM_175188, intron 5 of 7)	intron (NM_175188, intron 5 of 7)	5867	NM_001166375	72925	Mm.380457	NM_175188	ENSMUSG00000036469	March1	2900024D24Rik|BB085186	membrane-associated ring finger (C3HC4) 1	protein-coding
mm_68640.1	chr7	118443528	118443545	-	1	NA	promoter-TSS (NM_138649)	promoter-TSS (NM_138649)	16	NM_138649	110058	Mm.156558	NM_138649	ENSMUSG00000058420	Syt17	Bk	synaptotagmin XVII	protein-coding
mm_56490.1	chr6	99193039	99193041	-	1	NA	intron (NM_001347345, intron 4 of 19)	intron (NM_001347345, intron 4 of 19)	73475	NM_001197321	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_129271.1	chr15	77017645	77017655	-	1	NA	exon (NM_013593, exon 3 of 4)	exon (NM_013593, exon 3 of 4)	5077	NM_001164048	17189	Mm.404074	NM_013593	ENSMUSG00000018893	Mb	AI325109	myoglobin	protein-coding
mm_122587.1	chr14	50870558	50870571	-	1	NA	promoter-TSS (NM_009351)	promoter-TSS (NM_009351)	-10	NM_009351	21745	Mm.318736	NM_009351	ENSMUSG00000006281	Tep1	Tp1	telomerase associated protein 1	protein-coding
mm_3312.1	chr1	137906031	137906059	+	1	NA	Intergenic	Intergenic	-60410	NR_029795	735252		NR_029795	ENSMUSG00000065565	Mir181a-1	Mirn181a-1|Mirn213|miR-213|mir-181a-1|mmu-mir-213	microRNA 181a-1	ncRNA
mm_167734.1	chr9	106127089	106127094	-	1	NA	Intergenic	Intergenic	-27033	NR_029549	387153		NR_029549	ENSMUSG00000065407	Mir135a-1	Mir135a01|Mirn135|Mirn135a-1|mir-135a-1	microRNA 135a-1	ncRNA
mm_93130.1	chr10	92078062	92078066	-	1	NA	Intergenic	Intergenic	-5879	NR_029812	723955		NR_029812	ENSMUSG00000065524	Mir135a-2	Mirn135a-2|mir-135a-2	microRNA 135a-2	ncRNA
mm_115733.1	chr13	17776494	17776496	-	1	NA	intron (NM_027118, intron 1 of 13)	B1_Mur1|SINE|Alu	28602	NM_001081058	69562	Mm.193924	NM_027118	ENSMUSG00000041297	Cdk13	2310015O17Rik|Cdc2l5	cyclin-dependent kinase 13	protein-coding
mm_23054.1	chr3	35754090	35754114	+	1	NA	promoter-TSS (NM_029570)	promoter-TSS (NM_029570)	-36	NM_029570	76295	Mm.239416	NM_029570	ENSMUSG00000037400	Atp11b	1110019I14Rik|ATPIF|ATPIR|mKIAA0956	ATPase, class VI, type 11B	protein-coding
mm_65530.1	chr7	25788636	25788710	-	1	NA	promoter-TSS (NM_001190974)	promoter-TSS (NM_001190974)	60	NM_001190974	26362	Mm.4128	NM_009465	ENSMUSG00000002602	Axl	AI323647|Ark|Tyro7|Ufo	AXL receptor tyrosine kinase	protein-coding
mm_105866.1	chr11	114186745	114186756	-	1	NA	Intergenic	Intergenic	-11508	NR_045930	73536	Mm.54275	NR_045930	ENSMUSG00000078600	1700092K14Rik	-	RIKEN cDNA 1700092K14 gene	ncRNA
mm_48657.1	chr5	145875197	145875245	-	1	NA	intron (NM_007818, intron 3 of 12)	intron (NM_007818, intron 3 of 12)	4633	NM_007818	13112	Mm.332844	NM_007818	ENSMUSG00000056035	Cyp3a11	AI256190|Cyp3a|IIIAm1|Pcn	cytochrome P450, family 3, subfamily a, polypeptide 11	protein-coding
mm_84219.1	chr9	61925059	61925069	-	1	NA	exon (NM_024245, exon 16 of 23)	exon (NM_024245, exon 16 of 23)	-10554	NM_018853	56040	Mm.3158	NM_018853	ENSMUSG00000007892	Rplp1	2410042H16Rik|Arpp1|C430017H15Rik	ribosomal protein, large, P1	protein-coding
mm_63538.1	chr7	128003890	128003896	+	1	NA	promoter-TSS (NM_001079932)	promoter-TSS (NM_001079932)	-485	NM_001079932	434246	Mm.389924	NM_001079932	ENSMUSG00000042828	Trim72	BC067209|MG53	tripartite motif-containing 72	protein-coding
mm_117742.1	chr13	95884056	95884060	-	1	NA	intron (NM_027711, intron 1 of 35)	ORR1D2|LTR|ERVL-MaLR	7864	NM_027711	544963	Mm.38878	NM_027711	ENSMUSG00000021676	Iqgap2	4933417J23Rik|A630053O10|AI788777	IQ motif containing GTPase activating protein 2	protein-coding
mm_39657.1	chr5	24919588	24919592	+	1	NA	intron (NM_001310480, intron 2 of 13)	MLT1L|LTR|ERVL-MaLR	-11081	NM_001170555	108099	Mm.33649	NM_145401	ENSMUSG00000028944	Prkag2	2410051C13Rik|AAKG|AAKG2|AI854673|H91620p|WPWS	protein kinase, AMP-activated, gamma 2 non-catalytic subunit	protein-coding
mm_29042.1	chr3	102964125	102964137	-	1	NA	promoter-TSS (NM_201622)	promoter-TSS (NM_201622)	2	NM_201622	381463	Mm.331269	NM_198658	ENSMUSG00000048938	Nr1h5	Fxrb	nuclear receptor subfamily 1, group H, member 5	protein-coding
mm_79463.1	chr9	56418868	56418874	+	1	NA	promoter-TSS (NM_025812)	promoter-TSS (NM_025812)	25	NM_025812	66867	Mm.150856	NM_025812	ENSMUSG00000032329	Hmg20a	1200004E06Rik|5730490E10Rik|Hmgxb1|Ibraf	high mobility group 20A	protein-coding
mm_38178.1	chr4	135271164	135271168	-	1	NA	intron (NM_013885, intron 1 of 5)	intron (NM_013885, intron 1 of 5)	1594	NM_013885	29876	Mm.257765	NM_013885	ENSMUSG00000037242	Clic4	D0Jmb3|TU-74|mc3s5|mtCLIC	chloride intracellular channel 4 (mitochondrial)	protein-coding
mm_150228.1	chr19	33970771	33970778	+	1	NA	exon (NM_026334, exon 7 of 10)	exon (NM_026334, exon 7 of 10)	9526	NM_026334	67717	Mm.329816	NM_026334	ENSMUSG00000024768	Lipf	2310051B21Rik|AV082900	lipase, gastric	protein-coding
mm_67603.1	chr7	83744834	83744853	-	1	NA	Intergenic	MIR|SINE|MIR	-9353	NM_010551	16170	Mm.10137	NM_010551	ENSMUSG00000001741	Il16	mKIAA4048	interleukin 16	protein-coding
mm_11770.1	chr2	38823230	38823272	+	1	NA	intron (NM_010264, intron 3 of 10)	intron (NM_010264, intron 3 of 10)	-29484	NR_029568	387176		NR_029568	ENSMUSG00000065423	Mir181a-2	Mirn181|Mirn181a|Mirn181a-2|miR-181|mir-181a|mir-181a-2	microRNA 181a-2	ncRNA
mm_64329.1	chr7	142222159	142222163	+	1	NA	Intergenic	Intergenic	7810	NM_001037822	114666	Mm.444495	NM_001037822	ENSMUSG00000073785	Krtap5-5	A030001H12Rik|AI586182|BB149782	keratin associated protein 5-5	protein-coding
mm_168428.1	chr11	33754802	33754812	-	1	NA	intron (NM_001190885, intron 1 of 8)	LSU-rRNA_Hsa|rRNA|rRNA	88778	NM_027398	70357	Mm.252514	NM_027398	ENSMUSG00000053519	Kcnip1	KCHIP1|Kchip1.2	Kv channel-interacting protein 1	protein-coding
mm_123469.1	chr14	65973414	65973427	-	1	NA	exon (NM_013492, exon 3 of 9)	exon (NM_013492, exon 3 of 9)	4937	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_122509.1	chr14	47167748	47167766	-	1	NA	intron (NM_008102, intron 2 of 5)	(TAGA)n|Simple_repeat|Simple_repeat	21645	NM_008102	14528	Mm.10651	NM_008102	ENSMUSG00000037580	Gch1	GTP-CH|GTPCH|Gch	GTP cyclohydrolase 1	protein-coding
mm_38198.1	chr4	135494460	135494494	-	1	NA	promoter-TSS (NM_028995)	promoter-TSS (NM_028995)	27	NM_028995	74552	Mm.26548	NM_028995	ENSMUSG00000028803	Nipal3	9130020G22Rik|AI480660|Npal3	NIPA-like domain containing 3	protein-coding
mm_54075.1	chr6	14755170	14755193	-	1	NA	promoter-TSS (NM_080464)	promoter-TSS (NM_080464)	93	NM_080464	140491	Mm.209429	NM_080464	ENSMUSG00000042717	Ppp1r3a	GM|RG1|RGL	protein phosphatase 1, regulatory (inhibitor) subunit 3A	protein-coding
mm_108198.1	chr12	76837470	76837480	+	1	NA	promoter-TSS (NM_145927)	promoter-TSS (NM_145927)	8	NM_145927	110606	Mm.151174	NM_145927	ENSMUSG00000033373	Fntb	2010013E13Rik|AA409500	farnesyltransferase, CAAX box, beta	protein-coding
mm_207.1	chr1	16619469	16619498	+	1	NA	promoter-TSS (NM_001271017)	promoter-TSS (NM_001271017)	-145	NM_001271017	66799	Mm.122430	NM_025773	ENSMUSG00000025939	Ube2w	6130401J04Rik	ubiquitin-conjugating enzyme E2W (putative)	protein-coding
mm_73468.1	chr8	106668755	106668791	+	1	NA	3' UTR (NM_009864, exon 16 of 16)	3' UTR (NM_009864, exon 16 of 16)	-14295	NM_173037	272538	Mm.87151	NM_173037	ENSMUSG00000041949	Tango6	AW413431|E330010G16|Tmco7	transport and golgi organization 6	protein-coding
mm_68146.1	chr7	102249413	102249421	-	1	NA	intron (NM_019566, intron 1 of 1)	intron (NM_019566, intron 1 of 1)	701	NM_019566	56212	Mm.259795	NM_019566	ENSMUSG00000073982	Rhog	2810426G09Rik|Arhg|Sid10750	ras homolog family member G	protein-coding
mm_170189.1	chr17	6477131	6477149	-	1	NA	Intergenic	CpG	-26146	NR_033520	547127	Mm.297552	NM_001045538		Tmem181b-ps	Tmem181b	transmembrane protein 181B, pseudogene	pseudo
mm_29725.1	chr3	125938538	125938605	-	1	NA	promoter-TSS (NM_011674)	promoter-TSS (NM_011674)	-21	NM_011674	22239	Mm.306021	NM_011674	ENSMUSG00000032854	Ugt8a	AI850488|AW455908|Cgt|Ugt8|mCerGT	UDP galactosyltransferase 8A	protein-coding
mm_134239.1	chr16	12690872	12690874	-	1	NA	Intergenic	Intergenic	-120517	NR_040507	75493	Mm.396146	NR_040507	ENSMUSG00000101565	1700003L19Rik	-	RIKEN cDNA 1700003L19 gene	ncRNA
mm_51266.1	chr6	72097824	72097834	+	1	NA	5' UTR (NM_011375, exon 1 of 7)	5' UTR (NM_011375, exon 1 of 7)	221	NM_011375	20454	Mm.38248	NM_011375	ENSMUSG00000056091	St3gal5	3S-T|Siat9|[a]2	ST3 beta-galactoside alpha-2,3-sialyltransferase 5	protein-coding
mm_149865.1	chr19	25132067	25132098	+	1	NA	exon (NM_028785, exon 22 of 48)	exon (NM_028785, exon 22 of 48)	-105120	NM_181404	107351	Mm.260722	NM_181404	ENSMUSG00000032702	Kank1	A930031B09Rik|AU015049|AW121052|Ankrd15|D330024H06Rik|mKIAA0172	KN motif and ankyrin repeat domains 1	protein-coding
mm_70321.1	chr8	4250434	4250444	+	1	NA	intron (NM_001195258, intron 4 of 6)	intron (NM_001195258, intron 4 of 6)	2225	NM_001195258	100044509	Mm.439193	NM_001195258	ENSMUSG00000089736	Tgfbr3l	Gm14378|OTTMUSG00000016477	transforming growth factor, beta receptor III-like	protein-coding
mm_117055.1	chr13	58401521	58401590	-	1	NA	promoter-TSS (NR_031761)	promoter-TSS (NR_031761)	614	NM_001301343	15387	Mm.142872	NM_025279	ENSMUSG00000021546	Hnrnpk	Hnrpk|KBBP|NOVA	heterogeneous nuclear ribonucleoprotein K	protein-coding
mm_138169.1	chr17	34264759	34264768	+	1	NA	exon (NM_207105, exon 2 of 6)	exon (NM_207105, exon 2 of 6)	1536	NM_207105	14961	Mm.254067	NM_207105	ENSMUSG00000073421	H2-Ab1	AI845868|Abeta|H-2Ab|H2-Ab|I-Abeta|IAb|Ia-2|Ia2|Rmcs1	histocompatibility 2, class II antigen A, beta 1	protein-coding
mm_147682.1	chr18	60718684	60718687	-	1	NA	Intergenic	Intergenic	-5296	NM_008306	15531	Mm.181862	NM_008306	ENSMUSG00000054008	Ndst1	1200015G06Rik|HSNST|HSNST 1|Hsst|N-HSST|N-HSST 1|NDST-1|b2b2230Clo	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 1	protein-coding
mm_121380.1	chr14	118854956	118854976	+	1	NA	promoter-TSS (NM_001160099)	promoter-TSS (NM_001160099)	16	NM_001160099	58187	Mm.390755	NM_021386	ENSMUSG00000022132	Cldn10	6720456I16Rik|Cldn10a|Cldn10b|D14Ertd728e	claudin 10	protein-coding
mm_141363.1	chr17	28909383	28909407	-	1	NA	exon (NM_172450, exon 2 of 12)	exon (NM_172450, exon 2 of 12)	4130	NR_045457	74179	Mm.248931	NR_045457	ENSMUSG00000085333	1700030A11Rik	-	RIKEN cDNA 1700030A11 gene	ncRNA
mm_64508.1	chr7	143628049	143628063	+	1	NA	promoter-TSS (NM_175649)	promoter-TSS (NM_175649)	-211	NM_175649	244237	Mm.247498	NM_175649	ENSMUSG00000045362	Tnfrsf26	Tnfrh3|Tnfrsf24	tumor necrosis factor receptor superfamily, member 26	protein-coding
mm_150080.1	chr19	29386996	29387006	+	1	NA	3' UTR (NM_021893, exon 7 of 7)	3' UTR (NM_021893, exon 7 of 7)	19563	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_45990.1	chr5	90501520	90501533	-	1	NA	exon (NM_007423, exon 8 of 15)	exon (NM_007423, exon 8 of 15)	10812	NM_007423	11576	Mm.358570	NM_007423	ENSMUSG00000054932	Afp	-	alpha fetoprotein	protein-coding
mm_49373.1	chr6	24528212	24528218	+	1	NA	promoter-TSS (NM_001311068)	promoter-TSS (NM_001311068)	71	NM_080847	78910	Mm.160150	NM_080847	ENSMUSG00000029685	Asb15	4930400E23Rik|Asb-15	ankyrin repeat and SOCS box-containing 15	protein-coding
mm_42181.1	chr5	112262028	112262046	+	1	NA	intron (NM_023695, intron 3 of 5)	(TCCA)n|Simple_repeat|Simple_repeat	6217	NM_001312893	12960	Mm.29488	NM_023695	ENSMUSG00000029343	Crybb1	3110006K12Rik|BB1CRY	crystallin, beta B1	protein-coding
mm_118884.1	chr14	26357508	26357529	+	1	NA	promoter-TSS (NR_038005)	promoter-TSS (NR_038005)	-29	NR_038005	71106	Mm.158564	NR_038005	ENSMUSG00000021874	4933413J09Rik	GCSE	RIKEN cDNA 4933413J09 gene	ncRNA
mm_28492.1	chr3	92484361	92484371	-	1	NA	exon (NM_009264, exon 2 of 2)	exon (NM_009264, exon 2 of 2)	1515	NM_009264	20753	Mm.331191	NM_009264	ENSMUSG00000050359	Sprr1a	AI528815|SPR1a|mSPRR1A	small proline-rich protein 1A	protein-coding
mm_144082.1	chr17	92949397	92949397	-	1	NA	Intergenic	Intergenic	-249620	NM_001315503	11516	Mm.3407	NM_009625	ENSMUSG00000024256	Adcyap1	PACAP	adenylate cyclase activating polypeptide 1	protein-coding
mm_90018.1	chr10	115362575	115362592	+	1	NA	promoter-TSS (NM_133683)	promoter-TSS (NM_133683)	-321	NM_133683	67226	Mm.29647	NM_133683	ENSMUSG00000069520	Tmem19	2810428F02Rik|AW125171	transmembrane protein 19	protein-coding
mm_44551.1	chr5	24598920	24598929	-	1	NA	intron (NM_025891, intron 1 of 12)	CpG-10886	3078	NM_025891	66993	Mm.436539	NM_025891	ENSMUSG00000028949	Smarcd3	1500001J14Rik|2210409C08Rik|BAF60C	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3	protein-coding
mm_25896.1	chr3	131110819	131110834	+	1	NA	5' UTR (NM_001276402, exon 1 of 10)	5' UTR (NM_001276402, exon 1 of 10)	529	NM_001276402	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_77937.1	chr9	7355319	7355358	+	1	NA	exon (NM_008605, exon 8 of 10)	exon (NM_008605, exon 8 of 10)	7964	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_37645.1	chr4	128618610	128618625	-	1	NA	promoter-TSS (NM_205823)	promoter-TSS (NM_205823)	2	NM_205823	384059	Mm.331901	NM_205823	ENSMUSG00000062545	Tlr12	Gm1365|Tlr11	toll-like receptor 12	protein-coding
mm_45895.1	chr5	88675191	88675227	-	1	NA	intron (NM_178700, intron 1 of 9)	CpG	371	NM_001098476	231413	Mm.332474	NM_178700	ENSMUSG00000044221	Grsf1	BB232551|C80280|D5Wsu31e	G-rich RNA sequence binding factor 1	protein-coding
mm_79278.1	chr9	50775348	50775369	+	1	NA	non-coding (NR_045601, exon 1 of 14)	non-coding (NR_045601, exon 1 of 14)	133	NR_045601	102580	Mm.160035	NM_133981	ENSMUSG00000032059	Alg9	8230402H15Rik|AI747665|B430313H07Rik|Dibd1	asparagine-linked glycosylation 9 (alpha 1,2 mannosyltransferase)	protein-coding
mm_141876.1	chr17	34850163	34850205	-	1	NA	promoter-TSS (NM_021337)	promoter-TSS (NM_021337)	20	NM_021337	108077	Mm.18845	NM_021337	ENSMUSG00000040356	Skiv2l	4930534J06Rik|AW214248|Ddx13|SKI|Ski2w	superkiller viralicidic activity 2-like (S. cerevisiae)	protein-coding
mm_150358.1	chr19	34649129	34649139	+	1	NA	3' UTR (NM_008331, exon 2 of 2)	3' UTR (NM_008331, exon 2 of 2)	8245	NM_008331	15957	Mm.439751	NM_008331	ENSMUSG00000034459	Ifit1	ISG56|Ifi56|P56	interferon-induced protein with tetratricopeptide repeats 1	protein-coding
mm_30413.1	chr3	152265040	152265054	-	1	NA	intron (NM_199465, intron 1 of 12)	intron (NM_199465, intron 1 of 12)	1273	NM_199465	68810	Mm.200188	NM_199465	ENSMUSG00000039103	Nexn	1110046H09Rik|AA553326|NELIN	nexilin	protein-coding
mm_36500.1	chr4	83389984	83390020	-	1	NA	intron (NR_045450, intron 1 of 2)	MER57C2|LTR|ERV1	666	NR_045450	790913	Mm.406752	NR_045450	ENSMUSG00000086321	Gm11413	OTTMUSG00000000829	predicted gene 11413	ncRNA
mm_138772.1	chr17	37193890	37193897	+	1	NA	promoter-TSS (NM_023137)	promoter-TSS (NM_023137)	1	NM_023137	24108	Mm.140210	NM_023137	ENSMUSG00000035186	Ubd	FAT10	ubiquitin D	protein-coding
mm_36762.1	chr4	101356508	101356518	-	1	NA	promoter-TSS (NR_040708)	promoter-TSS (NR_040708)	-265	NR_040708	77866	Mm.137053	NR_040708	ENSMUSG00000086782	E130102H24Rik	-	RIKEN cDNA E130102H24 gene	ncRNA
mm_321.1	chr1	24678631	24678637	+	1	NA	promoter-TSS (NM_026719)	promoter-TSS (NM_026719)	90	NM_026719	68421	Mm.336563	NM_026719	ENSMUSG00000073725	Lmbrd1	0910001K20Rik|AV347960	LMBR1 domain containing 1	protein-coding
mm_82524.1	chr9	20643198	20643215	-	1	NA	promoter-TSS (NM_013911)	promoter-TSS (NM_013911)	-112	NM_025401	66177	Mm.390165	NM_025401	ENSMUSG00000084786	Ubl5	1110030M22Rik|beacon	ubiquitin-like 5	protein-coding
mm_101293.1	chr11	22058469	22058471	-	1	NA	intron (NM_001252515, intron 18 of 24)	intron (NM_001252515, intron 18 of 24)	-56819	NM_011023	18423	Mm.129663	NM_011023	ENSMUSG00000005917	Otx1	A730044F23Rik|jv	orthodenticle homeobox 1	protein-coding
mm_27192.1	chr3	34757942	34757948	-	1	NA	Intergenic	Intergenic	-14130	NR_110488	102638436	Mm.261793	NR_110488	ENSMUSG00000106519	Gm38509	Peril	predicted gene, 38509	ncRNA
mm_160401.1	chr8	70856997	70856997	-	1	NA	promoter-TSS (NM_032397)	promoter-TSS (NM_032397)	11	NM_032397	84036	Mm.32074	NM_032397	ENSMUSG00000002908	Kcnn1	AI854248|KCa2.1|SK1	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 1	protein-coding
mm_115293.1	chr13	111978104	111978112	+	1	NA	Intergenic	CpG	110172	NR_130345	102636620	Mm.402328	NR_130345	ENSMUSG00000086111	Gm15326	OTTMUSG00000020187	predicted gene 15326	ncRNA
mm_76361.1	chr8	84772534	84772590	-	1	NA	intron (NM_001081982, intron 1 of 9)	intron (NM_001081982, intron 1 of 9)	1807	NM_001081981	18032	Mm.9394	NM_010906	ENSMUSG00000001911	Nfix	CTF|NF-I/X|NF1-X|NFI-X	nuclear factor I/X	protein-coding
mm_121922.1	chr14	23524782	23524784	-	1	NA	intron (NM_001253366, intron 9 of 29)	intron (NM_001253366, intron 9 of 29)	-430212	NR_033550	791307	Mm.364384	NR_033550	ENSMUSG00000068680	Gm10248	ENSMUSG00000068680	predicted gene 10248	ncRNA
mm_119217.1	chr14	33216570	33216611	+	1	NA	promoter-TSS (NM_153800)	promoter-TSS (NM_153800)	-233	NM_153800	239027	Mm.318350	NM_153800	ENSMUSG00000063506	Arhgap22	B230341L19Rik|RHOGAP2|p68RacGAP	Rho GTPase activating protein 22	protein-coding
mm_37093.1	chr4	116597605	116597644	-	1	NA	promoter-TSS (NR_029450)	promoter-TSS (NR_029450)	6	NR_029450	654318	Mm.255685	NR_029450	ENSMUSG00000085408	C530005A16Rik	D930044c15rik	RIKEN cDNA C530005A16 gene	ncRNA
mm_135898.1	chr16	65562687	65562769	-	1	NA	promoter-TSS (NM_026879)	promoter-TSS (NM_026879)	-31	NM_026879	68942	Mm.432944	NM_026879	ENSMUSG00000004843	Chmp2b	1190006E07Rik	charged multivesicular body protein 2B	protein-coding
mm_110286.1	chr12	32123664	32123678	-	1	NA	Intergenic	Intergenic	-62392	NM_011158	19088	Mm.25594	NM_011158	ENSMUSG00000002997	Prkar2b	AI451071|AW061005|PKARIIbeta|Pkarb2|RII(beta)	protein kinase, cAMP dependent regulatory, type II beta	protein-coding
mm_132346.1	chr16	33885333	33885336	+	1	NA	intron (NM_010580, intron 5 of 14)	intron (NM_010580, intron 5 of 14)	55669	NM_001145884	16419	Mm.6424	NM_010580	ENSMUSG00000022817	Itgb5	AA475909|AI874634|ESTM23|[b]-5|[b]5|[b]5A|[b]5B|beta-5|beta5	integrin beta 5	protein-coding
mm_140907.1	chr17	24163646	24163656	-	1	NA	promoter-TSS (NM_172935)	promoter-TSS (NM_172935)	82	NM_172935	245847	Mm.87319	NM_172935	ENSMUSG00000036820	Amdhd2	5730457F11Rik	amidohydrolase domain containing 2	protein-coding
mm_153040.1	chr19	32061367	32061381	-	1	NA	5' UTR (NM_018830, exon 3 of 24)	5' UTR (NM_018830, exon 3 of 24)	41766	NM_018830	54447	Mm.491229	NM_018830	ENSMUSG00000024887	Asah2	AI585898	N-acylsphingosine amidohydrolase 2	protein-coding
mm_70967.1	chr8	27038155	27038167	+	1	NA	3' UTR (NM_153592, exon 12 of 12)	3' UTR (NM_153592, exon 12 of 12)	-4394	NM_001039078	114863	Mm.277501	NM_054057	ENSMUSG00000031485	Prosc	1700024N20Rik|2200002F22Rik	proline synthetase co-transcribed	protein-coding
mm_23560.1	chr3	62435658	62435664	+	1	NA	intron (NM_001081295, intron 10 of 13)	(T)n|Simple_repeat|Simple_repeat	71327	NM_028136	72162	Mm.224233	NM_028136	ENSMUSG00000027770	Dhx36	2810407E23Rik|AI452301|AU022184|Ddx36|mKIAA1488	DEAH (Asp-Glu-Ala-His) box polypeptide 36	protein-coding
mm_36530.1	chr4	86611963	86611973	-	1	NA	promoter-TSS (NM_173400)	promoter-TSS (NM_173400)	54	NM_173400	230376	Mm.74730	NM_173400	ENSMUSG00000038047	Haus6	6230416J20Rik|9830144E06|D4Ertd27e|mKIAA1574	HAUS augmin-like complex, subunit 6	protein-coding
mm_111210.1	chr12	84399759	84399768	-	1	NA	intron (NM_001026214, intron 2 of 15)	intron (NM_001026214, intron 2 of 15)	1171	NM_001286058	12499	Mm.10211	NM_007647	ENSMUSG00000021236	Entpd5	AI196558|AI987697|Cd39l4|ER-UDPase|NTPDase-5|NTPDase5|Pcph|mNTPase	ectonucleoside triphosphate diphosphohydrolase 5	protein-coding
mm_64426.1	chr7	142577506	142577557	+	1	NA	promoter-TSS (NR_030416)	promoter-TSS (NR_030416)	-384	NR_030416	735280		NR_030416	ENSMUSG00000076275	Mir675	Mirn675|mir-675|mmu-mir-675	microRNA 675	ncRNA
mm_117336.1	chr13	69534142	69534156	-	1	NA	promoter-TSS (NM_198600)	promoter-TSS (NM_198600)	-285	NM_001169131	210106	Mm.315959	NM_198600	ENSMUSG00000034575	Papd7	LAK-1|POLK|Pols|TRF4|TRF4-1	PAP associated domain containing 7	protein-coding
mm_89228.1	chr10	87521921	87521937	+	1	NA	5' UTR (NM_008777, exon 1 of 13)	5' UTR (NM_008777, exon 1 of 13)	134	NM_008777	18478	Mm.263539	NM_008777	ENSMUSG00000020051	Pah	AW106920	phenylalanine hydroxylase	protein-coding
mm_119929.1	chr14	54969296	54969302	+	1	NA	intron (NR_033497, intron 1 of 4)	intron (NR_033497, intron 1 of 4)	512	NR_033497	791403	Mm.319176	NR_033497	ENSMUSG00000097652	Mhrt	D830015G02Rik|ENSMUSG00000053118|Myheart	myosin heavy chain associated RNA transcript	ncRNA
mm_124544.1	chr14	122473505	122473517	-	1	NA	intron (NR_045046, intron 2 of 4)	intron (NR_045046, intron 2 of 4)	1688	NR_045046	69248	Mm.235369	NR_045046	ENSMUSG00000085555	2610035F20Rik	-	RIKEN cDNA 2610035F20 gene	ncRNA
mm_137152.1	chr17	23681039	23681058	+	1	NA	5' UTR (NM_018777, exon 3 of 3)	5' UTR (NM_018777, exon 3 of 3)	1683	NM_018777	54419	Mm.86421	NM_018777	ENSMUSG00000023906	Cldn6	AL024037	claudin 6	protein-coding
mm_138106.1	chr17	34119550	34119594	+	1	NA	non-coding (NR_037970, exon 1 of 13)	non-coding (NR_037970, exon 1 of 13)	328	NR_037970	14312	Mm.3444	NM_010238	ENSMUSG00000024335	Brd2	AW228947|D17H6S113E|Frg-1|Fsrg-1|Fsrg1|Nat|Ring3|Rnf3|mKIAA4005	bromodomain containing 2	protein-coding
mm_22951.1	chr3	32365337	32365353	+	1	NA	promoter-TSS (NR_027966)	promoter-TSS (NR_027966)	-144	NR_027966	67576	Mm.435324	NR_027966		4930429B21Rik	-	RIKEN cDNA 4930429B21 gene	ncRNA
mm_120069.1	chr14	57056669	57056675	+	1	NA	intron (NM_016975, intron 1 of 1)	intron (NM_016975, intron 1 of 1)	1051	NM_001271623	14611	Mm.57207	NM_016975	ENSMUSG00000048582	Gja3	Cnx46|Cx43|Cx46|Gja-3	gap junction protein, alpha 3	protein-coding
mm_89318.1	chr10	87930730	87930808	+	1	NA	3' UTR (NM_010512, exon 5 of 5)	3' UTR (NM_010512, exon 5 of 5)	-35902	NR_000040	22172	Mm.391420	NR_000040		Tyms-ps	-	thymidylate synthase, pseudogene	pseudo
mm_93714.1	chr10	118869794	118869805	-	1	NA	promoter-TSS (NM_001014390)	promoter-TSS (NM_001014390)	-896	NM_001014390	69181	Mm.45565	NM_001014390	ENSMUSG00000028630	Dyrk2	1810038L18Rik	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 2	protein-coding
mm_27038.1	chr3	26331831	26331849	-	1	NA	promoter-TSS (NM_138666)	promoter-TSS (NM_138666)	69	NM_138666	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_59598.1	chr7	28139776	28139795	+	1	NA	exon (NM_001164655, exon 5 of 20)	exon (NM_001164655, exon 5 of 20)	10319	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_164555.1	chr17	14202526	14202529	+	1	NA	intron (NM_172826, intron 1 of 3)	intron (NM_172826, intron 1 of 3)	1304	NM_172826	240025	Mm.79993	NM_172826	ENSMUSG00000048826	Dact2	2900084M21Rik|A630024E20|Dpr2|Frd2|dapper2	dishevelled-binding antagonist of beta-catenin 2	protein-coding
mm_133064.1	chr16	58622618	58622632	+	1	NA	Intergenic	RLTR19-int|LTR|ERVK	-5647	NM_001033404	328695	Mm.293308	NM_001033404	ENSMUSG00000075002	Gm813	Gm1781	predicted gene 813	protein-coding
mm_101780.1	chr11	45753610	45753614	-	1	NA	Intergenic	RMER2|LTR|ERV1	-54471	NR_045876	100009664	Mm.415439	NR_045876		F630206G17Rik	-	RIKEN cDNA F630206G17 gene	ncRNA
mm_60683.1	chr7	45154362	45154368	+	1	NA	promoter-TSS (NM_029406)	promoter-TSS (NM_029406)	62	NM_001278207	68845	Mm.181689	NM_029406	ENSMUSG00000003423	Pih1d1	1110061L23Rik|4933413A04Rik|Nop17	PIH1 domain containing 1	protein-coding
mm_10327.1	chr2	11339506	11339526	+	1	NA	promoter-TSS (NR_040369)	promoter-TSS (NR_040369)	27	NR_040369	100503147	Mm.91961	NR_040369	ENSMUSG00000086006	Gm13293	OTTMUSG00000011311	predicted gene 13293	ncRNA
mm_44920.1	chr5	35729089	35729095	-	1	NA	5' UTR (NM_194344, exon 1 of 18)	5' UTR (NM_194344, exon 1 of 18)	184	NM_194344	231147	Mm.290429	NM_194344	ENSMUSG00000036553	Sh3tc1	4631428G15|BC024909	SH3 domain and tetratricopeptide repeats 1	protein-coding
mm_120252.1	chr14	63011683	63011692	+	1	NA	promoter-TSS (NM_001039121)	promoter-TSS (NM_001039121)	-84	NM_001039121	654458	Mm.390737	NM_001039121	ENSMUSG00000075572	Defb43	BD-43|EG654458|mBD-43	defensin beta 43	protein-coding
mm_133154.1	chr16	70321173	70321183	+	1	NA	intron (NM_028803, intron 1 of 15)	intron (NM_028803, intron 1 of 15)	7229	NM_028803	74185	Mm.396102	NM_028803	ENSMUSG00000022707	Gbe1	2310045H19Rik|2810426P10Rik|D16Ertd536e	glucan (1,4-alpha-), branching enzyme 1	protein-coding
mm_105440.1	chr11	104377378	104377380	-	1	NA	intron (NM_001081045, intron 3 of 13)	intron (NM_001081045, intron 3 of 13)	64912	NM_001081045	76719	Mm.136418	NM_001081045	ENSMUSG00000018412	Kansl1	1700081L11Rik|9430041J06Rik|mKIAA1267	KAT8 regulatory NSL complex subunit 1	protein-coding
mm_47564.1	chr5	124439540	124439593	-	1	NA	promoter-TSS (NM_030241)	promoter-TSS (NM_030241)	-364	NM_030241	67956	Mm.137966	NM_030241	ENSMUSG00000049327	Kmt5a	2410195B05Rik|AA617402|AW536475|PR-SET7|PR/SET07|Setd8	lysine methyltransferase 5A	protein-coding
mm_51058.1	chr6	65671604	65671618	+	1	NA	promoter-TSS (NM_172399)	promoter-TSS (NM_172399)	0	NM_172399	68169	Mm.52392	NM_172399	ENSMUSG00000049001	Ndnf	A930038C07Rik|epidermacan	neuron-derived neurotrophic factor	protein-coding
mm_50956.1	chr6	58833690	58833734	+	1	NA	promoter-TSS (NM_028705)	promoter-TSS (NM_028705)	12	NM_028705	73998	Mm.191892	NM_028705	ENSMUSG00000029804	Herc3	5730409F18Rik|AI646603|mKIAA0032	hect domain and RLD 3	protein-coding
mm_77602.1	chr8	123892957	123893003	-	1	NA	exon (NM_009606, exon 4 of 7)	exon (NM_009606, exon 4 of 7)	1795	NM_001272041	11459	Mm.214950	NM_009606	ENSMUSG00000031972	Acta1	AA959943|Acta-2|Acts|Actsk-1	actin, alpha 1, skeletal muscle	protein-coding
mm_103748.1	chr11	80383151	80383182	-	1	NA	promoter-TSS (NR_045038)	promoter-TSS (NR_045038)	-113	NM_001130169	22680	Mm.401332	NM_011751	ENSMUSG00000017421	Zfp207	8430401D15Rik|BuGZ|Zep|Znf207	zinc finger protein 207	protein-coding
mm_147381.1	chr18	43737187	43737214	-	1	NA	promoter-TSS (NM_009258)	promoter-TSS (NM_009258)	37	NM_009258	20730	Mm.272	NM_009258	ENSMUSG00000024503	Spink1	Spink3|p12	serine peptidase inhibitor, Kazal type 1	protein-coding
mm_72014.1	chr8	70704048	70704064	+	1	NA	Intergenic	Intergenic	6317	NM_001286944	16478	Mm.419851	NM_010592	ENSMUSG00000071076	Jund	Jund1	jun D proto-oncogene	protein-coding
mm_164295.1	chr15	103895987	103896022	-	1	NA	3' UTR (NM_009267, exon 4 of 4)	3' UTR (NM_009267, exon 4 of 4)	3296	NM_009268	20771	Mm.30276	NM_009268		Mucl1	Spt-2|Spt2	mucin-like 1	protein-coding
mm_42202.1	chr5	112326353	112326426	+	1	NA	promoter-TSS (NM_018783)	promoter-TSS (NM_018783)	20	NM_018783	54723	Mm.172947	NM_018783	ENSMUSG00000029345	Tfip11	2810002G02Rik|AF097181|AW046167|Srr1|TIP33|Tip39	tuftelin interacting protein 11	protein-coding
mm_3639.1	chr1	152812474	152812492	+	1	NA	intron (NM_010877, intron 3 of 15)	B2_Mm2|SINE|B2	12330	NM_010877	17970	Mm.270307	NM_010877	ENSMUSG00000026480	Ncf2	NOXA2|Ncf-2|p67phox	neutrophil cytosolic factor 2	protein-coding
mm_81501.1	chr9	110034548	110034565	+	1	NA	exon (NM_008633, exon 7 of 19)	exon (NM_008633, exon 7 of 19)	-17465	NM_001311163	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_120287.1	chr14	63133967	63134032	+	1	NA	exon (NM_007798, exon 3 of 10)	exon (NM_007798, exon 3 of 10)	11537	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_96583.1	chr11	69088483	69088493	+	1	NA	promoter-TSS (NM_009497)	promoter-TSS (NM_009497)	-40	NM_009497	22318	Mm.28643	NM_009497	ENSMUSG00000020894	Vamp2	Syb-2|Syb2|sybII	vesicle-associated membrane protein 2	protein-coding
mm_120520.1	chr14	66784508	66784513	+	1	NA	Intergenic	Intergenic	84090	NM_009955	12934	Mm.352648	NM_009955	ENSMUSG00000022048	Dpysl2	AI851130|Crmp2|DRP2|Musunc33|TOAD-64|Ulip2	dihydropyrimidinase-like 2	protein-coding
mm_149635.1	chr19	17370063	17370103	+	1	NA	intron (NM_010265, intron 1 of 2)	RLTR14|LTR|ERV1	2761	NM_010265	14537	Mm.244825	NM_010265	ENSMUSG00000038843	Gcnt1	5630400D21Rik|B130048E03|C2 GlcNAcT|C2GNT|IGnT	glucosaminyl (N-acetyl) transferase 1, core 2	protein-coding
mm_125176.1	chr15	31568852	31568925	+	1	NA	promoter-TSS (NM_181588)	promoter-TSS (NM_181588)	-24	NM_181588	69574	Mm.28108	NM_181588	ENSMUSG00000022235	Cmbl	2310016A09Rik	carboxymethylenebutenolidase-like (Pseudomonas)	protein-coding
mm_126427.1	chr15	80572607	80572617	+	1	NA	promoter-TSS (NM_001289442)	promoter-TSS (NM_001289442)	15	NM_001289442	17444	Mm.12947	NM_010815	ENSMUSG00000042351	Grap2	GRAP-2|GRB2L|GRBLG|GRID|Gads|GrbX|Grf40|GrpL|Mona|P38	GRB2-related adaptor protein 2	protein-coding
mm_143334.1	chr17	66483835	66483840	-	1	NA	Intergenic	Intergenic	-34087	NM_001114098	68617	Mm.33421	NM_172963	ENSMUSG00000052105	Mtcl1	1110012J17Rik|Ccdc165|D130071O13|Kiaa0802|Soga2|mKIAA0802|t8219b25	microtubule crosslinking factor 1	protein-coding
mm_7752.1	chr1	131097800	131097812	-	1	NA	promoter-TSS (NM_008551)	promoter-TSS (NM_008551)	37	NM_008551	17164	Mm.221235	NM_008551	ENSMUSG00000016528	Mapkapk2	AA960234|MAPKAP-K2|MK-2|MK2|Rps6kc1	MAP kinase-activated protein kinase 2	protein-coding
mm_167089.1	chr7	104513647	104513649	+	1	NA	Intergenic	RLTR6C_Mm|LTR|ERV1	-5799	NM_001167828	209387	Mm.277377	NM_199146	ENSMUSG00000057596	Trim30d	AI451617|TRIM30-3|Trim79	tripartite motif-containing 30D	protein-coding
mm_170289.1	chr18	3000094	3000094	+	1	NA	Intergenic	Intergenic	123318	NM_001167539	100312476	Mm.480293	NM_001167539	ENSMUSG00000091539	Vmn1r238	-	vomeronasal 1 receptor, 238	protein-coding
mm_3143.1	chr1	135144576	135144593	+	1	NA	3' UTR (NM_177081, exon 10 of 10)	3' UTR (NM_177081, exon 10 of 10)	-2250	NM_026823	68724	Mm.174998	NM_026823	ENSMUSG00000026426	Arl8a	1110033P22Rik|Arl10b|gie2	ADP-ribosylation factor-like 8A	protein-coding
mm_69565.1	chr7	135700564	135700573	-	1	NA	exon (NM_001081117, exon 12 of 14)	exon (NM_001081117, exon 12 of 14)	15811	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_13189.1	chr2	93191112	93191117	+	1	NA	intron (NM_001025246, intron 1 of 7)	intron (NM_001025246, intron 1 of 7)	3530	NM_001025246	277414	Mm.41033	NM_001025246	ENSMUSG00000068735	Trp53i11	Tp53i11	transformation related protein 53 inducible protein 11	protein-coding
mm_50524.1	chr6	49044061	49044113	+	1	NA	exon (NM_053110, exon 3 of 11)	exon (NM_053110, exon 3 of 11)	7569	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_143166.1	chr17	57226018	57226034	-	1	NA	exon (NM_009778, exon 4 of 41)	exon (NM_009778, exon 4 of 41)	2110	NM_009778	12266	Mm.19131	NM_009778	ENSMUSG00000024164	C3	AI255234|ASP|HSE-MSF|Plp	complement component 3	protein-coding
mm_171565.1	chr4	147305601	147305616	+	1	NA	intron (NM_001039209, intron 1 of 2)	intron (NM_001039209, intron 1 of 2)	129742	NM_001039209	195531	Mm.270762	NM_001039209	ENSMUSG00000078496	Zfp982	Gm13152|OTTMUSG00000010671	zinc finger protein 982	protein-coding
mm_70381.1	chr8	10249190	10249200	+	1	NA	intron (NM_001319151, intron 1 of 34)	intron (NM_001319151, intron 1 of 34)	95284	NM_001319151	244281	Mm.422761	NM_001081397	ENSMUSG00000039057	Myo16	BM140241|C230040D10Rik|Gm1105|NYAP3|mKIAA0865	myosin XVI	protein-coding
mm_52203.1	chr6	100800904	100800941	+	1	NA	intron (NM_198612, intron 6 of 6)	intron (NM_198612, intron 6 of 6)	-32716	NM_182939	232314	Mm.27223	NM_182939	ENSMUSG00000052144	Ppp4r2	BE691708|C230060M08Rik	protein phosphatase 4, regulatory subunit 2	protein-coding
mm_171909.1	chr5	49544818	49544825	-	1	NA	Intergenic	L1Md_T|LINE|L1	-259162	NM_001199244	80334	Mm.160172	NM_030265	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding
mm_166298.1	chr5	104113950	104113964	-	1	NA	5' UTR (NM_010097, exon 1 of 11)	5' UTR (NM_010097, exon 1 of 11)	131	NM_010097	13602	Mm.29027	NM_010097	ENSMUSG00000029309	Sparcl1	Ecm2|Sc1|hevin|mast9	SPARC-like 1	protein-coding
mm_13113.1	chr2	91586127	91586137	+	1	NA	intron (NM_029437, intron 24 of 42)	intron (NM_029437, intron 24 of 42)	-9949	NR_028553	100217458		NR_028553	ENSMUSG00000077221	Snord67	MBII-166	small nucleolar RNA, C/D box 67	snoRNA
mm_127544.1	chr15	102119075	102119093	+	1	NA	intron (NM_001033277, intron 7 of 10)	intron (NM_001033277, intron 7 of 10)	16096	NM_153533	209039	Mm.29389	NM_153533	ENSMUSG00000037003	Tns2	C1-ten|Tenc1|nep|nph	tensin 2	protein-coding
mm_11378.1	chr2	31171950	31171963	+	1	NA	exon (NM_178760, exon 5 of 18)	exon (NM_178760, exon 5 of 18)	19640	NM_178760	277463	Mm.236074	NM_178760	ENSMUSG00000000194	Gpr107	9930033D15Rik|AI790205|C530034M11|mKIAA1624	G protein-coupled receptor 107	protein-coding
mm_109541.1	chr12	111583641	111583654	+	1	NA	intron (NM_022801, intron 1 of 15)	intron (NM_022801, intron 1 of 15)	9137	NM_022801	17169	Mm.260504	NM_021516	ENSMUSG00000007411	Mark3	1600015G02Rik|A430080F22Rik|C-TAK1|ETK-1|ETK1|Emk2|MPK10	MAP/microtubule affinity regulating kinase 3	protein-coding
mm_106723.1	chr12	3865113	3865119	+	1	NA	intron (NM_007872, intron 3 of 22)	B2_Mm2|SINE|B2	-2872	NR_045884	100038522	Mm.417270	NR_045884	ENSMUSG00000073242	Dnmt3aos	ENSMUSG00000073242|Gm10485	DNA methyltransferase 3A, opposite strand	ncRNA
mm_123889.1	chr14	72710053	72710060	-	1	NA	promoter-TSS (NM_207636)	promoter-TSS (NM_207636)	-53	NM_207636	319448	Mm.205421	NM_207636	ENSMUSG00000033487	Fndc3a	1700094E19Rik|D14Ertd453e|F730017H24Rik|Fndc3|sys	fibronectin type III domain containing 3A	protein-coding
mm_62725.1	chr7	110773867	110773934	+	1	NA	intron (NM_009667, intron 1 of 14)	intron (NM_009667, intron 1 of 14)	1296	NM_009667	11717	Mm.3238	NM_009667	ENSMUSG00000005686	Ampd3	-	adenosine monophosphate deaminase 3	protein-coding
mm_57504.1	chr6	125460606	125460615	-	1	NA	3' UTR (NM_007657, exon 8 of 8)	3' UTR (NM_007657, exon 8 of 8)	34145	NM_007657	12527	Mm.210676	NM_007657	ENSMUSG00000030342	Cd9	Tspan29	CD9 antigen	protein-coding
mm_18767.1	chr2	73485683	73485704	-	1	NA	promoter-TSS (NM_001289723)	promoter-TSS (NM_001289723)	60	NM_001289723	215280	Mm.223504	NM_153138	ENSMUSG00000075284	Wipf1	AI115543|D2Ertd120e|WIP|Waspip	WAS/WASL interacting protein family, member 1	protein-coding
mm_146339.1	chr18	82475181	82475196	+	1	NA	promoter-TSS (NM_010777)	promoter-TSS (NM_010777)	65	NM_001025245	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_102341.1	chr11	58010629	58010637	-	1	NA	intron (NM_028451, intron 1 of 18)	intron (NM_028451, intron 1 of 18)	1569	NM_028451	73158	Mm.248843	NM_028451	ENSMUSG00000037331	Larp1	1810024J12Rik|3110040D16Rik|Larp|mKIAA0731	La ribonucleoprotein domain family, member 1	protein-coding
mm_42256.1	chr5	114005951	114005954	+	1	NA	intron (NM_001286396, intron 1 of 10)	intron (NM_001286396, intron 1 of 10)	1144	NM_001286396	13142	Mm.20115	NM_010018	ENSMUSG00000042096	Dao	AI987963|DAAO|DAMOX|Dao-1|Dao1	D-amino acid oxidase	protein-coding
mm_112365.1	chr12	119160795	119160804	-	1	NA	Intergenic	Intergenic	77477	NM_177290	320910	Mm.217000	NM_177290	ENSMUSG00000025321	Itgb8	4832412O06Rik	integrin beta 8	protein-coding
mm_69404.1	chr7	132317259	132317279	-	1	NA	promoter-TSS (NM_029935)	promoter-TSS (NM_029935)	-114	NM_029935	77590	Mm.213582	NM_029935	ENSMUSG00000030930	Chst15	4631426J05Rik|BRAG|GalNAcS-6ST|MAd5|mKIAA0598	carbohydrate (N-acetylgalactosamine 4-sulfate 6-O) sulfotransferase 15	protein-coding
mm_113219.1	chr13	27057572	27057584	+	1	NA	promoter-TSS (NM_011164)	promoter-TSS (NM_011164)	8	NM_011164	19109	Mm.1270	NM_011164	ENSMUSG00000021342	Prl	AV290867|Gha1|Prl1a1	prolactin	protein-coding
mm_149558.1	chr19	12654963	12654967	+	1	NA	Intergenic	Intergenic	-19214	NM_146697	258692	Mm.223127	NM_146697	ENSMUSG00000044441	Olfr1442	MOR202-9	olfactory receptor 1442	protein-coding
mm_150070.1	chr19	29386610	29386649	+	1	NA	3' UTR (NM_021893, exon 7 of 7)	3' UTR (NM_021893, exon 7 of 7)	19191	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_106256.1	chr11	117871882	117871893	-	1	NA	intron (NM_027919, intron 1 of 6)	intron (NM_027919, intron 1 of 6)	1639	NM_027919	71776	Mm.3200	NM_027919	ENSMUSG00000017713	Tha1	1300017K07Rik|GLY1	threonine aldolase 1	protein-coding
mm_30362.1	chr3	151837429	151837441	-	1	NA	promoter-TSS (NM_008966)	promoter-TSS (NM_008966)	93	NM_008966	19220	Mm.331442	NM_008966	ENSMUSG00000028036	Ptgfr	AI957154|PGF|fp	prostaglandin F receptor	protein-coding
mm_9180.1	chr1	171058606	171058637	-	1	NA	intron (NM_010188, intron 1 of 4)	intron (NM_010188, intron 1 of 4)	782	NM_010188	14131	Mm.22119	NM_010188	ENSMUSG00000059498	Fcgr3	CD16	Fc receptor, IgG, low affinity III	protein-coding
mm_44770.1	chr5	31766904	31766906	-	1	NA	intron (NM_144541, intron 3 of 11)	intron (NM_144541, intron 3 of 11)	68855	NM_144541	107976	Mm.482126	NM_144541	ENSMUSG00000052139	Bre	6030405P19Rik|AI429776|B830038C02Rik	brain and reproductive organ-expressed protein	protein-coding
mm_2809.1	chr1	130866057	130866072	+	1	NA	intron (NM_026976, intron 1 of 7)	intron (NM_026976, intron 1 of 7)	287	NM_026976	69169	Mm.46042	NM_026976	ENSMUSG00000042474	Fcmr	1810037B05Rik|Faim3|FcmuR|Toso	Fc fragment of IgM receptor	protein-coding
mm_87185.1	chr10	39369729	39369739	+	1	NA	promoter-TSS (NM_008054)	promoter-TSS (NM_008054)	-65	NM_001122892	14360	Mm.4848	NM_008054	ENSMUSG00000019843	Fyn	AI448320|AW552119	Fyn proto-oncogene	protein-coding
mm_98152.1	chr11	87595665	87595719	+	1	NA	intron (NM_133215, intron 2 of 18)	CpG	3475	NM_133215	170749	Mm.399376	NM_133215	ENSMUSG00000018401	Mtmr4	AA596759|ESTM44|FYVE-DSP2|ZFYVE11|mKIAA0647	myotubularin related protein 4	protein-coding
mm_138121.1	chr17	34145232	34145265	+	1	NA	promoter-TSS (NM_010388)	promoter-TSS (NM_010388)	-168	NM_010388	15000	Mm.195060	NM_010388	ENSMUSG00000037548	H2-DMb2	H-2Mb2|H2-Mb2	histocompatibility 2, class II, locus Mb2	protein-coding
mm_41042.1	chr5	86090953	86090966	+	1	NA	exon (NM_019992, exon 6 of 9)	exon (NM_019992, exon 6 of 9)	19213	NM_001310639	56792	Mm.131237	NM_019992	ENSMUSG00000029254	Stap1	AI586015|Brdg1|STAP-1	signal transducing adaptor family member 1	protein-coding
mm_147218.1	chr18	37997544	37997569	-	1	NA	promoter-TSS (NM_139206)	promoter-TSS (NM_139206)	18	NM_139206	106952	Mm.247642	NM_139206	ENSMUSG00000024451	Arap3	Centd3|Drag1|E030006K04Rik|cnt-d3	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3	protein-coding
mm_5314.1	chr1	22512573	22512579	-	1	NA	intron (NM_001012623, intron 8 of 14).2	intron (NM_001012623, intron 8 of 14).2	-79733	NM_183018	116837	Mm.60061	NM_053270	ENSMUSG00000041670	Rims1	C030033M19Rik|RIM1|RIM1a|RIM1alpha|Rab3ip1|Rim|Serg1|mKIAA0340	regulating synaptic membrane exocytosis 1	protein-coding
mm_146562.1	chr18	6241487	6241550	-	1	NA	promoter-TSS (NM_008448)	promoter-TSS (NM_008448)	6	NM_008448	16573	Mm.223744	NM_008448	ENSMUSG00000006740	Kif5b	AL022807|Khc|Khcs|Kns1|Ukhc	kinesin family member 5B	protein-coding
mm_61305.1	chr7	67952083	67952092	+	1	NA	promoter-TSS (NM_010513)	promoter-TSS (NM_010513)	-170	NM_010513	16001	Mm.275742	NM_010513	ENSMUSG00000005533	Igf1r	A330103N21Rik|CD221|D930020L01|IGF-1R|hyft	insulin-like growth factor I receptor	protein-coding
mm_109595.1	chr12	112644863	112644881	+	1	NA	promoter-TSS (NM_001161737)	promoter-TSS (NM_001161737)	44	NM_013929	30954	Mm.289812	NM_013929	ENSMUSG00000064326	Siva1	CD27bp|Siva	SIVA1, apoptosis-inducing factor	protein-coding
mm_43218.1	chr5	129747018	129747037	+	1	NA	intron (NM_008095, intron 6 of 9)	Lx4A|LINE|L1	21952	NM_008095	14467	Mm.12468	NM_008095	ENSMUSG00000029432	Gbas	AV006093|Nipsnap2	glioblastoma amplified sequence	protein-coding
mm_18226.1	chr2	51437878	51437913	-	1	NA	promoter-TSS (NR_130155)	promoter-TSS (NR_130155)	5	NR_130155	73375	Mm.396227	NR_130155	ENSMUSG00000086007	1700057H21Rik	-	RIKEN cDNA 1700057H21 gene	ncRNA
mm_159587.1	chr4	123116287	123116287	+	1	NA	promoter-TSS (NM_181859)	promoter-TSS (NM_181859)	39	NM_181859	353371	Mm.189660	NM_181859	ENSMUSG00000076438	Oxct2b	Scot-t2	3-oxoacid CoA transferase 2B	protein-coding
mm_5539.1	chr1	38129720	38129801	-	1	NA	promoter-TSS (NM_019570)	promoter-TSS (NM_019570)	-98	NM_019570	56210	Mm.389103	NM_019570	ENSMUSG00000026082	Rev1	1110027I23Rik|AU022044|Rev1l	REV1, DNA directed polymerase	protein-coding
mm_85663.1	chr9	107675291	107675297	-	1	NA	3' UTR (NM_008140, exon 9 of 9)	3' UTR (NM_008140, exon 9 of 9)	4298	NM_008140	14685	Mm.284853	NM_008140	ENSMUSG00000034837	Gnat1	Gnat-1|Ird1|Ird2|Tralpha|irdc|irdr|transducin	guanine nucleotide binding protein, alpha transducing 1	protein-coding
mm_136295.1	chr16	91466643	91466677	-	1	NA	intron (NR_077219, intron 1 of 1)	intron (NR_077219, intron 1 of 1)	1556	NR_077219	100503120	Mm.387130	NR_077219	ENSMUSG00000084866	A930006K02Rik	-	RIKEN cDNA A930006K02 gene	ncRNA
mm_1476.1	chr1	70725922	70725927	+	1	NA	TTS (NM_025728)	TTS (NM_025728)	209	NM_001310658	320460	Mm.360649	NM_177164	ENSMUSG00000045648	Vwc2l	A830006F12Rik|Brl	von Willebrand factor C domain-containing protein 2-like	protein-coding
mm_84996.1	chr9	86695898	86695958	-	1	NA	promoter-TSS (NM_008615)	promoter-TSS (NM_008615)	-14	NM_008615	17436	Mm.148155	NM_008615	ENSMUSG00000032418	Me1	D9Ertd267e|Mdh-1|Mod-1|Mod1	malic enzyme 1, NADP(+)-dependent, cytosolic	protein-coding
mm_64993.1	chr7	16917681	16917699	-	1	NA	exon (NM_007590, exon 3 of 6)	exon (NM_007590, exon 3 of 6)	6342	NM_007590	12315	Mm.288630	NM_007590	ENSMUSG00000019370	Calm3	CaMA|R75142	calmodulin 3	protein-coding
mm_161730.1	chr17	29887771	29887771	-	1	NA	5' UTR (NM_001081160, exon 1 of 16)	5' UTR (NM_001081160, exon 1 of 16)	111	NM_001081160	74762	Mm.40901	NM_001081160	ENSMUSG00000043557	Mdga1	1200011I03Rik|GPIM|Mamdc3	MAM domain containing glycosylphosphatidylinositol anchor 1	protein-coding
mm_15572.1	chr2	158666598	158666646	+	1	NA	promoter-TSS (NM_001159662)	promoter-TSS (NM_001159662)	-111	NM_153089	228852	Mm.150540	NM_153089	ENSMUSG00000037754	Ppp1r16b	ANKRD4|C130078N17Rik|TIMAP|Wdt4	protein phosphatase 1, regulatory (inhibitor) subunit 16B	protein-coding
mm_16082.1	chr2	168579356	168579398	+	1	NA	intron (NM_001291168, intron 1 of 9)	intron (NM_001291168, intron 1 of 9)	10988	NM_001291178	18019	Mm.116802	NM_010899	ENSMUSG00000027544	Nfatc2	AI607462|NF-ATc2|NF-ATp|NFAT1|NFAT1-D|Nfatp	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 2	protein-coding
mm_71997.1	chr8	70619184	70619193	+	1	NA	intron (NM_153074, intron 2 of 2)	intron (NM_153074, intron 2 of 2)	2344	NM_153074	211228	Mm.132939	NM_153074	ENSMUSG00000049988	Lrrc25	Mapa	leucine rich repeat containing 25	protein-coding
mm_133578.1	chr16	91407030	91407041	+	1	NA	intron (NM_008349, intron 1 of 6)	intron (NM_008349, intron 1 of 6)	800	NM_008349	16155	Mm.4154	NM_008349	ENSMUSG00000022969	Il10rb	6620401D04Rik|AI528744|CRF2-4|Crfb4|D16H21S58|D21S58h|IL-10R2|Il10r2	interleukin 10 receptor, beta	protein-coding
mm_121080.1	chr14	99099469	99099476	+	1	NA	promoter-TSS (NM_029320)	promoter-TSS (NM_029320)	48	NM_029320	52023	Mm.22835	NM_029320	ENSMUSG00000022064	Pibf1	-	progesterone immunomodulatory binding factor 1	protein-coding
mm_34686.1	chr4	151862649	151862671	+	1	NA	promoter-TSS (NM_001195565)	promoter-TSS (NM_001195565)	-892	NM_001195565	100072	Mm.318846	NM_001081557	ENSMUSG00000014592	Camta1	1810059M14Rik|2310058O09Rik|AI316882|AW987475|mKIAA0833	calmodulin binding transcription activator 1	protein-coding
mm_15208.1	chr2	154214008	154214018	+	1	NA	exon (NM_153418, exon 11 of 16)	exon (NM_153418, exon 11 of 16)	-9729	NM_144890	228802	Mm.167411	NM_144890	ENSMUSG00000038572	Bpifb5	Lplunc5	BPI fold containing family B, member 5	protein-coding
mm_152229.1	chr19	8708019	8708038	-	1	NA	exon (NM_008577, exon 9 of 9)	exon (NM_008577, exon 9 of 9)	5869	NM_008577	17254	Mm.4114	NM_008577	ENSMUSG00000010095	Slc3a2	4F2|4F2HC|AI314110|Cd98|Ly-10|Ly-m10|Ly10|Mdu1|Mgp-2hc|NACAE	solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2	protein-coding
mm_151177.1	chr19	53311376	53311391	+	1	NA	intron (NM_001008542, intron 1 of 5)	T-rich|Low_complexity|Low_complexity	877	NM_001008542	17859	Mm.2154	NM_010847	ENSMUSG00000025025	Mxi1	ENSMUSG00000067085|Gm10197|Mad2|bHLHc11	MAX interactor 1, dimerization protein	protein-coding
mm_24895.1	chr3	96172328	96172338	+	1	NA	promoter-TSS (NM_153053)	promoter-TSS (NM_153053)	-173	NM_153053	107701	Mm.219671	NM_153053	ENSMUSG00000068856	Sf3b4	SF3b49|SF3b50|Sap49	splicing factor 3b, subunit 4	protein-coding
mm_172906.1	chr9	59375773	59375779	-	1	NA	Intergenic	RLTR10D2|LTR|ERVK	-22268	NM_175325	102774	Mm.200714	NM_175325	ENSMUSG00000025235	Bbs4	AW537059|AW742241|D9Ertd464e	Bardet-Biedl syndrome 4 (human)	protein-coding
mm_173056.1	chrX	125104305	125104316	+	1	NA	Intergenic	MMVL30-int|LTR|ERV1	-968400	NM_001100616	100038941	Mm.388852	NM_001100616	ENSMUSG00000072049	Vmn2r121	EG625699	vomeronasal 2, receptor 121	protein-coding
mm_112481.1	chr13	5869119	5869129	+	1	NA	3' UTR (NM_011803, exon 4 of 4)	3' UTR (NM_011803, exon 4 of 4)	7635	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_130705.1	chr15	100720181	100720194	-	1	NA	5' UTR (NM_172451, exon 2 of 12)	5' UTR (NM_172451, exon 2 of 12)	290	NM_001161768	207839	Mm.22969	NM_172451	ENSMUSG00000037280	Galnt6	4632410F13|AW047994|GalNAc-T6	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 6	protein-coding
mm_61489.1	chr7	75703285	75703294	+	1	NA	intron (NM_029332, intron 16 of 36)	intron (NM_029332, intron 16 of 36)	-145049	NM_001122780	207952	Mm.206223	NM_029652	ENSMUSG00000055652	Klhl25	2810402K13Rik|BC027373|Enc-1	kelch-like 25	protein-coding
mm_113438.1	chr13	34883588	34883600	+	1	NA	exon (NM_013830, exon 2 of 15)	exon (NM_013830, exon 2 of 15)	8100	NM_013830	19134	Mm.10027	NM_013830	ENSMUSG00000021413	Prpf4b	2610037H07|Prp4|Prp4k|Prpk|cbp143	pre-mRNA processing factor 4B	protein-coding
mm_120488.1	chr14	65979712	65979723	+	1	NA	exon (NM_013492, exon 7 of 9)	exon (NM_013492, exon 7 of 9)	11234	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_133153.1	chr16	70315749	70315761	+	1	NA	intron (NM_028803, intron 1 of 15)	intron (NM_028803, intron 1 of 15)	1806	NM_028803	74185	Mm.396102	NM_028803	ENSMUSG00000022707	Gbe1	2310045H19Rik|2810426P10Rik|D16Ertd536e	glucan (1,4-alpha-), branching enzyme 1	protein-coding
mm_85661.1	chr9	107674932	107674937	-	1	NA	3' UTR (NM_008140, exon 9 of 9)	3' UTR (NM_008140, exon 9 of 9)	4658	NM_008140	14685	Mm.284853	NM_008140	ENSMUSG00000034837	Gnat1	Gnat-1|Ird1|Ird2|Tralpha|irdc|irdr|transducin	guanine nucleotide binding protein, alpha transducing 1	protein-coding
mm_62966.1	chr7	119794103	119794157	+	1	NA	promoter-TSS (NM_028129)	promoter-TSS (NM_028129)	0	NM_028129	434234	Mm.38237	NM_028129	ENSMUSG00000030924	2610020H08Rik	-	RIKEN cDNA 2610020H08 gene	protein-coding
mm_130805.1	chr15	101709717	101709753	-	1	NA	intron (NM_027011, intron 6 of 8)	intron (NM_027011, intron 6 of 8)	3156	NM_027011	110308	Mm.451847	NM_027011	ENSMUSG00000061527	Krt5	3300001P10Rik|AW146334|CK5|K5|Krt2-5|Tfip8	keratin 5	protein-coding
mm_115668.1	chr13	12502000	12502001	-	1	NA	intron (NM_133643, intron 3 of 5)	BC1_Mm|scRNA|scRNA	18450	NM_133643	171211	Mm.159671	NM_133643	ENSMUSG00000095105	Edaradd	1810032E07Rik|5830469M23Rik|A630043P06|cr	EDAR (ectodysplasin-A receptor)-associated death domain	protein-coding
mm_71963.1	chr8	70529379	70529384	+	1	NA	intron (NM_001199631, intron 1 of 8)	intron (NM_001199631, intron 1 of 8)	1535	NM_001199631	14232	Mm.141864	NM_010223	ENSMUSG00000019428	Fkbp8	38kDa|FKBP-38|FKBP-8|Fkbp38	FK506 binding protein 8	protein-coding
mm_159147.1	chr2	87693930	87693930	-	1	NA	promoter-TSS (NM_146659)	promoter-TSS (NM_146659)	17	NM_146659	258653	Mm.377616	NM_146659	ENSMUSG00000075151	Olfr1136	MOR177-3	olfactory receptor 1136	protein-coding
mm_24320.1	chr3	89430582	89430597	+	1	NA	promoter-TSS (NM_026869)	promoter-TSS (NM_026869)	-151	NM_001293767	68911	Mm.22521	NM_026869	ENSMUSG00000047824	Pygo2	1190004M21Rik	pygopus 2	protein-coding
mm_156139.1	chrX	128261750	128261764	+	1	NA	Intergenic	Intergenic	-525203	NM_001281537	73934	Mm.159093	NM_001281537	ENSMUSG00000043569	Cldn34c4	4930412D23Rik	claudin 34C4	protein-coding
mm_132423.1	chr16	35541276	35541339	+	1	NA	promoter-TSS (NM_013661)	promoter-TSS (NM_013661)	-55	NM_013661	20357	Mm.42015	NM_013661	ENSMUSG00000052133	Sema5b	AI893641|SemG|Semag|mKIAA1445	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B	protein-coding
mm_95340.1	chr11	46821462	46821466	+	1	NA	intron (NM_178759, intron 5 of 8)	B3A|SINE|B2	10665	NM_178759	276891	Mm.69002	NM_178759	ENSMUSG00000055546	Timd4	B430010N18Rik|TIM-4|Tim4	T cell immunoglobulin and mucin domain containing 4	protein-coding
mm_43576.1	chr5	137746184	137746194	+	1	NA	5' UTR (NM_023910, exon 1 of 5)	5' UTR (NM_023910, exon 1 of 5)	220	NM_029805	78829	Mm.286399	NM_023910	ENSMUSG00000029723	Tsc22d4	0610009M14Rik|1700023B23Rik|AI415410|Thg-1pit|Tilz2	TSC22 domain family, member 4	protein-coding
mm_59777.1	chr7	28836643	28836646	+	1	NA	intron (NM_010706, intron 3 of 9)	PB1D7|SINE|Alu	2474	NM_010707	16857	Mm.210336	NM_010707		Lgals6	galectin-6	lectin, galactose binding, soluble 6	protein-coding
mm_84720.1	chr9	73969032	73969045	-	1	NA	Intergenic	Intergenic	-35471	NM_001081153	208898	Mm.41035	NM_001081153	ENSMUSG00000062151	Unc13c	1500037O19Rik|AU019458|D9Ertd414e|Munc13-3|Unc13h3	unc-13 homolog C (C. elegans)	protein-coding
mm_119694.1	chr14	53598826	53598855	+	1	NA	Intergenic	Intergenic	655089	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_101027.1	chr11	8579463	8579504	-	1	NA	intron (NM_001083587, intron 3 of 30)	intron (NM_001083587, intron 3 of 30)	85052	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_90454.1	chr10	127714034	127714044	+	1	NA	exon (NM_001081219, exon 15 of 27)	exon (NM_001081219, exon 15 of 27)	8783	NM_001081219	432516	Mm.90450	NM_001081219	ENSMUSG00000025401	Myo1a	BBM-I|Myhl	myosin IA	protein-coding
mm_116621.1	chr13	48880143	48880147	-	1	NA	3' UTR (NM_001033268, exon 18 of 18)	3' UTR (NM_001033268, exon 18 of 18)	-9260	NM_011078	18676	Mm.486213	NM_011078	ENSMUSG00000038025	Phf2	GRC5	PHD finger protein 2	protein-coding
mm_138467.1	chr17	35186863	35186912	+	1	NA	intron (NM_010734, intron 2 of 3)	intron (NM_010734, intron 2 of 3)	1553	NM_010734	16988	Mm.19379	NM_010734	ENSMUSG00000073412	Lst1	B144	leukocyte specific transcript 1	protein-coding
mm_40897.1	chr5	75155872	75155886	+	1	NA	promoter-TSS (NM_001083316)	promoter-TSS (NM_001083316)	-287	NM_001083316	18595	Mm.221403	NM_011058	ENSMUSG00000029231	Pdgfra	AI115593|CD140a|Pdgfr-2	platelet derived growth factor receptor, alpha polypeptide	protein-coding
mm_47015.1	chr5	115488945	115488949	-	1	NA	Intergenic	Intergenic	-4463	NM_133760	75387	Mm.332616	NM_133760	ENSMUSG00000029524	Sirt4	4930596O17Rik	sirtuin 4	protein-coding
mm_48873.1	chr5	150665213	150665226	-	1	NA	intron (NM_201369, intron 1 of 5)	CpG	393	NM_201369	381695	Mm.246934	NM_201369	ENSMUSG00000029655	N4bp2l2	2700092H06Rik|zag1	NEDD4 binding protein 2-like 2	protein-coding
mm_18372.1	chr2	59948156	59948192	-	1	NA	exon (NM_001001182, exon 13 of 36)	exon (NM_001001182, exon 13 of 36)	-65568	NM_028118	72137	Mm.288734	NM_028118	ENSMUSG00000026988	Wdsub1	1700048E19Rik|2610014F08Rik	WD repeat, SAM and U-box domain containing 1	protein-coding
mm_165833.1	chr3	154664004	154664026	+	1	NA	Intergenic	Intergenic	-47118	NM_175176	209601	Mm.331454	NM_175176	ENSMUSG00000078161	Erich3	1700013E18Rik|4922501L14Rik|5031409G23Rik|AI596448|Gm133	glutamate rich 3	protein-coding
mm_112905.1	chr13	20902917	20902944	+	1	NA	intron (NM_012054, intron 5 of 20)	intron (NM_012054, intron 5 of 20)	108817	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_132626.1	chr16	38902306	38902316	+	1	NA	promoter-TSS (NM_170599)	promoter-TSS (NM_170599)	-34	NM_170599	207683	Mm.245564	NM_170599	ENSMUSG00000022790	Igsf11	1700025L02Rik|BT-IgSF|Igsf13	immunoglobulin superfamily, member 11	protein-coding
mm_108189.1	chr12	76676297	76676301	+	1	NA	intron (NM_013675, intron 1 of 35)	intron (NM_013675, intron 1 of 35)	34248	NM_013675	20741	Mm.32881	NM_013675	ENSMUSG00000021061	Sptb	AI842465|D330027P03Rik|Gm1301|Spnb-1|Spnb1|ja|jaundiced|mKIAA4219	spectrin beta, erythrocytic	protein-coding
mm_148118.1	chr18	75187341	75187369	-	1	NA	intron (NM_027727, intron 13 of 16)	intron (NM_027727, intron 13 of 16)	109962	NR_045394	100503117	Mm.250517	NR_045393	ENSMUSG00000102047	2010010A06Rik	5033420E22Rik	RIKEN cDNA 2010010A06 gene	ncRNA
mm_111951.1	chr12	109460355	109460386	-	1	NA	non-coding (NR_033813, exon 6 of 6)	non-coding (NR_033813, exon 6 of 6)	6915	NM_010052	13386	Mm.157069	NM_010052	ENSMUSG00000040856	Dlk1	AW742678|DLK-1|DlkI|FA1|Ly107|Peg9|SCP1|ZOG|pG2|pref-1	delta-like 1 homolog (Drosophila)	protein-coding
mm_24501.1	chr3	92418121	92418133	+	1	NA	promoter-TSS (NR_003185)	promoter-TSS (NR_003185)	40	NR_003185	20764	Mm.57084	NR_003185	ENSMUSG00000027925	Sprr2j-ps	Sprr2j	small proline-rich protein 2J, pseudogene	pseudo
mm_122440.1	chr14	45220742	45220761	-	1	NA	intron (NM_027518, intron 1 of 6)	intron (NM_027518, intron 1 of 6)	1034	NM_027518	70713	Mm.343793	NM_027518	ENSMUSG00000049092	Gpr137c	6330416L11Rik|Gm908|TM7SF1L2	G protein-coupled receptor 137C	protein-coding
mm_149820.1	chr19	24224038	24224052	+	1	NA	intron (NM_011597, intron 1 of 22)	intron (NM_011597, intron 1 of 22)	981	NM_011597	21873	Mm.104744	NM_011597	ENSMUSG00000024812	Tjp2	ZO-2	tight junction protein 2	protein-coding
mm_53428.1	chr6	134042266	134042274	+	1	NA	intron (NM_007961, intron 1 of 7)	intron (NM_007961, intron 1 of 7)	6570	NM_007961	14011	Mm.269995	NM_007961	ENSMUSG00000030199	Etv6	AW123102|AW557856|Tel	ets variant 6	protein-coding
mm_86126.1	chr9	116175267	116175305	-	1	NA	promoter-TSS (NM_029575)	promoter-TSS (NM_029575)	77	NM_029575	21813	Mm.172346	NM_009371	ENSMUSG00000032440	Tgfbr2	1110020H15Rik|AU042018|DNIIR|RIIDN|TBR-II|TbetaR-II|TbetaRII	transforming growth factor, beta receptor II	protein-coding
mm_73171.1	chr8	95020875	95020891	+	1	NA	intron (NM_173036, intron 1 of 11)	intron (NM_173036, intron 1 of 11)	3191	NM_173036	54672	Mm.27995	NM_173036	ENSMUSG00000060470	Adgrg3	A030001G24Rik|AW214383|Gpr97|Pb1|Pb99	adhesion G protein-coupled receptor G3	protein-coding
mm_171400.1	chr4	123513969	123513982	-	1	NA	exon (NM_001199137, exon 6 of 93)	exon (NM_001199137, exon 6 of 93)	-102064	NM_001167918	442834	Mm.483803	NM_001167918		D830031N03Rik	Kiaa0754|mKIAA0754	RIKEN cDNA D830031N03 gene	protein-coding
mm_79392.1	chr9	54863743	54863801	+	1	NA	promoter-TSS (NM_022655)	promoter-TSS (NM_022655)	17	NM_022655	64602	Mm.208991	NM_022655	ENSMUSG00000032293	Ireb2	D9Ertd85e|Irp2	iron responsive element binding protein 2	protein-coding
mm_78089.1	chr9	18292236	18292246	+	1	NA	promoter-TSS (NM_025844)	promoter-TSS (NM_025844)	-26	NM_025844	66917	Mm.103534	NM_025844	ENSMUSG00000001774	Chordc1	1110001O09Rik|AA409036|Chp-1|morgana	cysteine and histidine-rich domain (CHORD)-containing, zinc-binding protein 1	protein-coding
mm_119157.1	chr14	31619004	31619011	+	1	NA	exon (NM_019975, exon 12 of 17)	exon (NM_019975, exon 12 of 17)	21958	NM_019975	56794	Mm.38887	NM_019975	ENSMUSG00000021884	Hacl1	1600020H07Rik|Hpcl|Phyh2	2-hydroxyacyl-CoA lyase 1	protein-coding
mm_119163.1	chr14	31929618	31929640	+	1	NA	Intergenic	Intergenic	-99214	NM_001024604	105522	Mm.37660	NM_001024604	ENSMUSG00000014496	Ankrd28	AI465466|AI604979|E430019N21Rik|mKIAA0379	ankyrin repeat domain 28	protein-coding
mm_38016.1	chr4	133754223	133754237	-	1	NA	promoter-TSS (NM_001080819)	promoter-TSS (NM_001080819)	-619	NM_001080819	93760	Mm.22478	NM_001080819	ENSMUSG00000007880	Arid1a	1110030E03Rik|BAF250a|Osa1|Smarcf1	AT rich interactive domain 1A (SWI-like)	protein-coding
mm_58704.1	chr7	12949765	12949776	+	1	NA	Intergenic	Intergenic	-16094	NM_178732	243834	Mm.133086	NM_178732	ENSMUSG00000004500	Zfp324	A930002M05|D430030K24Rik|ZF5128	zinc finger protein 324	protein-coding
mm_40921.1	chr5	75830456	75830471	+	1	NA	Intergenic	L2a|LINE|L2	147965	NM_010612	16542	Mm.285	NM_010612	ENSMUSG00000062960	Kdr	6130401C07|Flk-1|Flk1|Krd-1|Ly73|VEGFR-2|VEGFR2|sVEGFR-2	kinase insert domain protein receptor	protein-coding
mm_60637.1	chr7	44828478	44828492	+	1	NA	intron (NM_001171024, intron 1 of 8)	intron (NM_001171024, intron 1 of 8)	-7803	NM_010215	14204	Mm.2565	NM_010215	ENSMUSG00000074141	Il4i1	Fig1|Fig1-ps|LAAO|LAO	interleukin 4 induced 1	protein-coding
mm_127756.1	chr15	103503164	103503217	+	1	NA	5' UTR (NM_008800, exon 1 of 16)	5' UTR (NM_008800, exon 1 of 16)	156	NM_008800	18574	Mm.390792	NM_008800	ENSMUSG00000022489	Pde1b	Pde1b1	phosphodiesterase 1B, Ca2+-calmodulin dependent	protein-coding
mm_61267.1	chr7	66172902	66172917	+	1	NA	3' UTR (NM_001081163, exon 3 of 3)	3' UTR (NM_001081163, exon 3 of 3)	63394	NM_001081163	269941	Mm.333916	NM_001081163	ENSMUSG00000032640	Chsy1	mKIAA0990	chondroitin sulfate synthase 1	protein-coding
mm_68560.1	chr7	114634141	114634158	-	1	NA	intron (NM_001305616, intron 3 of 3)	intron (NM_001305616, intron 3 of 3)	2208	NM_001289444	12310	Mm.4361	NM_007587	ENSMUSG00000030669	Calca	CA|CGRP-1|CGRP1|Calc|Calc1|Cgrp|Ct|Ctn	calcitonin/calcitonin-related polypeptide, alpha	protein-coding
mm_17722.1	chr2	32393141	32393174	-	1	NA	Intergenic	MLT1-int|LTR|ERVL-MaLR	-2733	NM_133783	96979	Mm.28048	NM_133783	ENSMUSG00000026820	Ptges2	0610038H10Rik|C79137|Gbf1|Mpges2|Pges2	prostaglandin E synthase 2	protein-coding
mm_147963.1	chr18	67134118	67134126	-	1	NA	intron (NM_010307, intron 1 of 11)	CpG	562	NM_010307	14680	Mm.440746	NM_010307	ENSMUSG00000024524	Gnal	2610011C15Rik|9630020G10Rik|Galphaolf|Gna10|Golf	guanine nucleotide binding protein, alpha stimulating, olfactory type	protein-coding
mm_1761.1	chr1	75546259	75546312	+	1	NA	promoter-TSS (NM_009208)	promoter-TSS (NM_009208)	19	NM_009208	20536	Mm.5053	NM_009208	ENSMUSG00000006576	Slc4a3	A930038D23Rik|Ae3	solute carrier family 4 (anion exchanger), member 3	protein-coding
mm_2214.1	chr1	89767728	89767746	+	1	NA	intron (NM_178119, intron 12 of 17)	intron (NM_178119, intron 12 of 17)	-83845	NR_015540	74403	Mm.444291	NR_015540		4933400F21Rik	1700091C04Rik|4930565K10Rik	RIKEN cDNA 4933400F21 gene	ncRNA
mm_108217.1	chr12	77060223	77060271	+	1	NA	Intergenic	Intergenic	-97999	NM_001146176	17187	Mm.268548	NM_008558	ENSMUSG00000059436	Max	AA960152|AI875693|bHLHd4|bHLHd5|bHLHd6|bHLHd7|bHLHd8	Max protein	protein-coding
mm_107384.1	chr12	33147756	33147770	+	1	NA	promoter-TSS (NM_028139)	promoter-TSS (NM_028139)	77	NM_028139	380753	Mm.41540	NM_028139	ENSMUSG00000020564	Atxn7l1	2810423G08Rik|Atxn7l4	ataxin 7-like 1	protein-coding
mm_152533.1	chr19	11326914	11326928	-	1	NA	intron (NM_027836, intron 3 of 6)	intron (NM_027836, intron 3 of 6)	7774	NM_001276398	109225	Mm.491251	NM_027836	ENSMUSG00000024672	Ms4a7	9130422I10Rik|A430103C15Rik|CD20l4|CFFMA	membrane-spanning 4-domains, subfamily A, member 7	protein-coding
mm_91367.1	chr10	29361347	29361351	-	1	NA	intron (NM_001110198, intron 1 of 3)	intron (NM_001110198, intron 1 of 3)	1093	NM_026518	68031	Mm.28930	NM_026518	ENSMUSG00000038876	Rnf146	2610509H23Rik|Iduna	ring finger protein 146	protein-coding
mm_99899.1	chr11	109650926	109651003	+	1	NA	promoter-TSS (NM_021880)	promoter-TSS (NM_021880)	43	NM_001313976	19084	Mm.30039	NM_021880	ENSMUSG00000020612	Prkar1a	1300018C22Rik|RIalpha|Tse-1|Tse1	protein kinase, cAMP dependent regulatory, type I, alpha	protein-coding
mm_142570.1	chr17	46678561	46678582	-	1	NA	intron (NM_001163729, intron 1 of 10)	intron (NM_001163729, intron 1 of 10)	-1882	NM_001277310	17256	Mm.329083	NM_010787	ENSMUSG00000002768	Mea1	Mea-1	male enhanced antigen 1	protein-coding
mm_117711.1	chr13	95223082	95223104	-	1	NA	promoter-TSS (NM_001170669)	promoter-TSS (NM_001170669)	-43	NM_001170669	218461	Mm.100167	NM_172263	ENSMUSG00000021684	Pde8b	B230331L10Rik|C030047E14Rik	phosphodiesterase 8B	protein-coding
mm_26701.1	chr3	157566917	157566921	+	1	NA	promoter-TSS (NM_011196)	promoter-TSS (NM_011196)	27	NM_011196	19218	Mm.30424	NM_011196	ENSMUSG00000040016	Ptger3	EP3|Pgerep3|Ptgerep3	prostaglandin E receptor 3 (subtype EP3)	protein-coding
mm_7986.1	chr1	134234836	134234880	-	1	NA	promoter-TSS (NM_001291928)	promoter-TSS (NM_001291928)	-2	NM_001291928	11539	Mm.298908	NM_009629	ENSMUSG00000042429	Adora1	A1-AR|A1AR|A1R|AA1R|AI848715|BB176431|Ri	adenosine A1 receptor	protein-coding
mm_166307.1	chr5	105800608	105800632	+	1	NA	intron (NM_001122768, intron 2 of 2)	intron (NM_001122768, intron 2 of 2)	-75948	NR_030777	54367	Mm.248876	NM_018759	ENSMUSG00000029290	Zfp326	5730470H14Rik|ZAN75|Znf326	zinc finger protein 326	protein-coding
mm_89140.1	chr10	85829424	85829446	+	1	NA	Intergenic	CpG	-42396	NM_133993	103136	Mm.18834	NM_133993	ENSMUSG00000001785	Pwp1	2310058A11Rik|2610205J09Rik|AI098170|AL022879|AV083409|AW550690	PWP1 homolog, endonuclein	protein-coding
mm_9552.1	chr1	173929062	173929079	-	1	NA	exon (NM_001302649, exon 7 of 10)	exon (NM_001302649, exon 7 of 10)	13422	NM_001302649	15950	Mm.463437	NM_008328	ENSMUSG00000039997	Ifi203	Mndal	interferon activated gene 203	protein-coding
mm_128543.1	chr15	55023150	55023153	-	1	NA	intron (NM_001081288, intron 24 of 25)	intron (NM_001081288, intron 24 of 25)	49001	NM_001081288	319944	Mm.380957	NM_001081288	ENSMUSG00000037343	Taf2	150kDa|4732460C16Rik|AI425886|CIF150|TAF2B|TAFII-150|TAFII150	TATA-box binding protein associated factor 2	protein-coding
mm_14790.1	chr2	145860703	145860725	+	1	NA	exon (NM_028724, exon 9 of 13)	exon (NM_028724, exon 9 of 13)	-42527	NM_026425	67877	Mm.151168	NM_026425	ENSMUSG00000002728	Naa20	1500004D14Rik|2900026I01Rik|AU041458|D2Ertd186e|Nat5	N(alpha)-acetyltransferase 20, NatB catalytic subunit	protein-coding
mm_34645.1	chr4	150748348	150748353	+	1	NA	Intergenic	Intergenic	-96176	NM_173774	242773	Mm.29280	NM_173774	ENSMUSG00000039838	Slc45a1	C230078B22|Dnb5	solute carrier family 45, member 1	protein-coding
mm_29965.1	chr3	133464983	133465026	-	1	NA	3' UTR (NM_001346736, exon 12 of 12)	3' UTR (NM_001346736, exon 12 of 12)	79386	NM_001346736	214133	Mm.347816	NM_145989	ENSMUSG00000040943	Tet2	Ayu17-449|E130014J05Rik|mKIAA1546	tet methylcytosine dioxygenase 2	protein-coding
mm_157204.1	chrX	12673541	12673583	-	1	NA	promoter-TSS (NM_175141)	promoter-TSS (NM_175141)	77	NM_175141	69155	Mm.15974	NM_175141	ENSMUSG00000044148	1810030O07Rik	-	RIKEN cDNA 1810030O07 gene	protein-coding
mm_158023.1	chrX	96165431	96165473	-	1	NA	exon (NM_010833, exon 11 of 13)	exon (NM_010833, exon 11 of 13)	69407	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_17825.1	chr2	33887436	33887515	-	1	NA	5' UTR (NM_175184, exon 1 of 10)	5' UTR (NM_175184, exon 1 of 10)	471	NM_175184	72543	Mm.254914	NM_175184	ENSMUSG00000038740	Mvb12b	2610200O14Rik|2610528K11Rik|AI414895|Fam125b	multivesicular body subunit 12B	protein-coding
mm_5158.1	chr1	9991937	9991949	-	1	NA	intron (NR_110971, intron 5 of 6)	intron (NR_110971, intron 5 of 6)	17193	NR_110971	69312	Mm.386795	NM_027033	ENSMUSG00000025916	Ppp1r42	1700011J18Rik|4930418G15Rik|Lrrc67|TLRR	protein phosphatase 1, regulatory subunit 42	protein-coding
mm_116147.1	chr13	29947042	29947048	-	1	NA	intron (NM_010093, intron 1 of 6)	intron (NM_010093, intron 1 of 6)	37346	NM_001289920	13557	Mm.268356	NM_010093	ENSMUSG00000016477	E2f3	E2F3b|E2f3a	E2F transcription factor 3	protein-coding
mm_144421.1	chr18	20971653	20971662	+	1	NA	intron (NM_026301, intron 1 of 5)	ID_B1|SINE|B4	27032	NM_026301	67664	Mm.45980	NM_026301	ENSMUSG00000033107	Rnf125	4930553F04Rik	ring finger protein 125	protein-coding
mm_12282.1	chr2	69008421	69008435	+	1	NA	intron (NM_172856, intron 4 of 9)	intron (NM_172856, intron 4 of 9)	-127372	NM_181547	329416	Mm.90047	NM_181547	ENSMUSG00000034738	Nostrin	Daip2|mDaIP2	nitric oxide synthase trafficker	protein-coding
mm_34283.1	chr4	141424694	141424705	+	1	NA	3' UTR (NM_013868, exon 3 of 3)	3' UTR (NM_013868, exon 3 of 3)	3920	NM_013868	29818	Mm.46181	NM_013868	ENSMUSG00000006221	Hspb7	27kDa|Hsp25-2|cvHsp	heat shock protein family, member 7 (cardiovascular)	protein-coding
mm_40512.1	chr5	57788998	57789015	+	1	NA	intron (NM_001310608, intron 1 of 3)	intron (NM_001310608, intron 1 of 3)	70925	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_115871.1	chr13	21531085	21531103	-	1	NA	promoter-TSS (NM_001251834)	promoter-TSS (NM_001251834)	20	NM_139141	93681	Mm.290601	NM_139141	ENSMUSG00000063894	Zkscan8	2510038J07Rik|D430019P06Rik|LD5-1|Zfp192	zinc finger with KRAB and SCAN domains 8	protein-coding
mm_59837.1	chr7	29317288	29317296	+	1	NA	3' UTR (NM_013874, exon 12 of 12)	3' UTR (NM_013874, exon 12 of 12)	13287	NM_013874	29861	Mm.101885	NM_013874	ENSMUSG00000030584	Dpf1	Neud4	D4, zinc and double PHD fingers family 1	protein-coding
mm_126377.1	chr15	80171896	80171912	+	1	NA	Intergenic	Intergenic	-1817	NM_010795	17309	Mm.299693	NM_010795	ENSMUSG00000042428	Mgat3	1110038J12Rik|AI848272|GnT-III	mannoside acetylglucosaminyltransferase 3	protein-coding
mm_125830.1	chr15	74957573	74957576	+	1	NA	intron (NM_001164039, intron 2 of 4)	intron (NM_001164039, intron 2 of 4)	2468	NM_001164040	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_165450.1	chr2	156755348	156755350	+	1	NA	intron (NM_001042487, intron 4 of 6)	Lx|LINE|L1	-20115	NM_172118	98932	Mm.271770	NM_172118	ENSMUSG00000067818	Myl9	AI327049|MLC20|Mylc2c|RLC-C	myosin, light polypeptide 9, regulatory	protein-coding
mm_75810.1	chr8	70302488	70302488	-	1	NA	promoter-TSS (NM_021538)	promoter-TSS (NM_021538)	-36	NM_001024922	234374	Mm.388127	NM_001024922	ENSMUSG00000057788	Ddx49	R27090_2	DEAD (Asp-Glu-Ala-Asp) box polypeptide 49	protein-coding
mm_7713.1	chr1	130629564	130629574	-	1	NA	promoter-TSS (NM_009581)	promoter-TSS (NM_009581)	37	NM_009581	22789	Mm.4644	NM_009581	ENSMUSG00000042554	Zp3r	AV264399|SP56	zona pellucida 3 receptor	protein-coding
mm_87172.1	chr10	38965193	38965201	+	1	NA	promoter-TSS (NM_010681)	promoter-TSS (NM_010681)	-318	NM_010681	16775	Mm.258065	NM_010681	ENSMUSG00000019846	Lama4	-	laminin, alpha 4	protein-coding
mm_123744.1	chr14	70191565	70191584	-	1	NA	exon (NM_001271407, exon 13 of 21)	exon (NM_001271407, exon 13 of 21)	672	NM_001271409	20410	Mm.5068	NM_011366	ENSMUSG00000022091	Sorbs3	SCAM-1|SH3P3|Sh3d4|vinexin-g	sorbin and SH3 domain containing 3	protein-coding
mm_143325.1	chr17	66378894	66378908	-	1	NA	intron (NM_001114098, intron 5 of 14)	L1MEc|LINE|L1	70849	NM_172963	68617	Mm.33421	NM_172963	ENSMUSG00000052105	Mtcl1	1110012J17Rik|Ccdc165|D130071O13|Kiaa0802|Soga2|mKIAA0802|t8219b25	microtubule crosslinking factor 1	protein-coding
mm_164735.1	chr17	68314573	68314577	+	1	NA	5' UTR (NM_177278, exon 2 of 21)	5' UTR (NM_177278, exon 2 of 21)	40778	NM_177278	320858	Mm.137356	NM_177278	ENSMUSG00000041565	L3mbtl4	A730037L19Rik|D930040M24Rik	l(3)mbt-like 4 (Drosophila)	protein-coding
mm_115988.1	chr13	24329125	24329147	-	1	NA	intron (NM_001111110, intron 1 of 16)	MuLV-int|LTR|ERV1	1732	NM_001111110	12763	Mm.8396	NM_007717	ENSMUSG00000016756	Cmah	-	cytidine monophospho-N-acetylneuraminic acid hydroxylase	protein-coding
mm_169656.1	chr15	56908166	56908170	-	1	NA	Intergenic	L1Md_T|LINE|L1	-213622	NM_008216	15117	Mm.5148	NM_008216	ENSMUSG00000022367	Has2	-	hyaluronan synthase 2	protein-coding
mm_2650.1	chr1	125676849	125676855	+	1	NA	promoter-TSS (NM_027677)	promoter-TSS (NM_027677)	-144	NM_027677	71111	Mm.32727	NM_027677	ENSMUSG00000026343	Gpr39	4933415E13Rik	G protein-coupled receptor 39	protein-coding
mm_54132.1	chr6	21013160	21013195	-	1	NA	Intergenic	Intergenic	-202932	NM_019697	16508	Mm.425316	NM_019697	ENSMUSG00000060882	Kcnd2	AI839615|AW555701|Kv4.2|R75121|mKIAA1044	potassium voltage-gated channel, Shal-related family, member 2	protein-coding
mm_49854.1	chr6	38433914	38433965	+	1	NA	promoter-TSS (NM_177185)	promoter-TSS (NM_177185)	14	NM_177185	320538	Mm.302831	NM_177185	ENSMUSG00000038538	Ubn2	2900060J04Rik|6030408G03Rik|BC060116|D130059P03Rik|mKIAA2030	ubinuclein 2	protein-coding
mm_17064.1	chr2	22590260	22590275	-	1	NA	Intergenic	Intergenic	-32060	NM_008078	14417	Mm.4784	NM_008078	ENSMUSG00000026787	Gad2	6330404F12Rik|GAD(65)|GAD65|Gad-2	glutamic acid decarboxylase 2	protein-coding
mm_132936.1	chr16	49855746	49855756	+	1	NA	promoter-TSS (NM_010581)	promoter-TSS (NM_010581)	97	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_59353.1	chr7	25659451	25659461	+	1	NA	promoter-TSS (NM_007533)	promoter-TSS (NM_007533)	303	NR_104358	27998	Mm.27853	NM_138586	ENSMUSG00000061286	Exosc5	D7Wsu180e	exosome component 5	protein-coding
mm_150852.1	chr19	44992432	44992456	+	1	NA	5' UTR (NM_011976, exon 2 of 15)	5' UTR (NM_011976, exon 2 of 15)	3100	NM_011976	26456	Mm.34404	NM_011976	ENSMUSG00000025207	Sema4g	AI507908|AW554132	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4G	protein-coding
mm_69399.1	chr7	132311612	132311626	-	1	NA	intron (NM_029935, intron 1 of 7)	intron (NM_029935, intron 1 of 7)	-4045	NR_028578	100043682	Mm.482794	NR_028578	ENSMUSG00000109270	Gm10584	ENSMUSG00000073814	predicted gene 10584	ncRNA
mm_150025.1	chr19	29373592	29373603	+	1	NA	exon (NM_021893, exon 3 of 7)	exon (NM_021893, exon 3 of 7)	6159	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_100293.1	chr11	117825886	117825926	+	1	NA	promoter-TSS (NM_027827)	promoter-TSS (NM_027827)	-13	NM_027827	71562	Mm.273958	NM_027827	ENSMUSG00000017718	Afmid	9030621K19Rik|Ammd|FKF|KFA|Kf|formylase	arylformamidase	protein-coding
mm_93579.1	chr10	116913873	116913901	-	1	NA	intron (NM_001003950, intron 7 of 9)	intron (NM_001003950, intron 7 of 9)	-17008	NM_001033333	237558	Mm.336386	NM_001033333	ENSMUSG00000034057	Myrfl	Gm239	myelin regulatory factor-like	protein-coding
mm_37877.1	chr4	132398202	132398220	-	1	NA	intron (NM_001161797, intron 2 of 12)	intron (NM_001161797, intron 2 of 12)	24235	NM_001161797	100169	Mm.158361	NM_175306	ENSMUSG00000066043	Phactr4	3110001B12Rik|AI527228|AW495572|C330013F19Rik|N28169|mKIAA4120	phosphatase and actin regulator 4	protein-coding
mm_50339.1	chr6	48537561	48537622	+	1	NA	promoter-TSS (NM_133764)	promoter-TSS (NM_133764)	22	NM_133764	76252	Mm.30214	NM_133764	ENSMUSG00000039347	Atp6v0e2	0610006O14Rik|NM9.2	ATPase, H+ transporting, lysosomal V0 subunit E2	protein-coding
mm_65403.1	chr7	25219824	25219880	-	1	NA	promoter-TSS (NM_207677)	promoter-TSS (NM_207677)	7	NM_207677	67379	Mm.280594	NM_026117	ENSMUSG00000054499	Dedd2	2410050E11Rik|FLAME-3	death effector domain-containing DNA binding protein 2	protein-coding
mm_21227.1	chr2	155945250	155945259	-	1	NA	5' UTR (NM_008109, exon 1 of 2)	5' UTR (NM_008109, exon 1 of 2)	113	NM_008109	14563	Mm.4744	NM_008109	ENSMUSG00000038259	Gdf5	BMP-14|Cdmp-1|bp|brp	growth differentiation factor 5	protein-coding
mm_63841.1	chr7	135650385	135650406	+	1	NA	intron (NR_015548, intron 2 of 2)	intron (NR_015548, intron 2 of 2)	-1504	NM_001316681	19267	Mm.945	NM_011212	ENSMUSG00000041836	Ptpre	PTPe|PTPepsilon|RPTPepsilon	protein tyrosine phosphatase, receptor type, E	protein-coding
mm_69114.1	chr7	127025547	127025564	-	1	NA	exon (NM_010772, exon 2 of 5)	exon (NM_010772, exon 2 of 5)	924	NM_010772	17188	Mm.378964	NM_010772	ENSMUSG00000030678	Maz	MAZI|PUR1|Pur-1|SAF-1|SAF-2	MYC-associated zinc finger protein (purine-binding transcription factor)	protein-coding
mm_159004.1	chr1	156399990	156399990	-	1	NA	promoter-TSS (NM_001198597)	promoter-TSS (NM_001198597)	0	NM_001198597	77352	Mm.428709	NM_001033180	ENSMUSG00000026601	Axdnd1	9430070O13Rik|Gm979	axonemal dynein light chain domain containing 1	protein-coding
mm_153297.1	chr19	37697699	37697714	-	1	NA	promoter-TSS (NM_007811)	promoter-TSS (NM_007811)	-102	NM_007811	13082	Mm.42230	NM_007811	ENSMUSG00000024987	Cyp26a1	Cyp26|P450RA|P450RAI|RAH	cytochrome P450, family 26, subfamily a, polypeptide 1	protein-coding
mm_39529.1	chr5	21279624	21279626	+	1	NA	intron (NM_175437, intron 24 of 30)	intron (NM_175437, intron 24 of 30)	-93048	NM_008013	14190	Mm.292100	NM_008013	ENSMUSG00000039899	Fgl2	AI385601|musfiblp	fibrinogen-like protein 2	protein-coding
mm_34867.1	chr4	155558022	155558043	+	1	NA	3' UTR (NM_008142, exon 12 of 12)	3' UTR (NM_008142, exon 12 of 12)	-4360	NM_138671	192185	Mm.28347	NM_138671	ENSMUSG00000029063	Nadk	4432404C02Rik|BC004012	NAD kinase	protein-coding
mm_66242.1	chr7	35555194	35555223	-	1	NA	exon (NM_033080, exon 1 of 3)	exon (NM_033080, exon 1 of 3)	720	NM_033080	110959	Mm.410206	NM_033080	ENSMUSG00000034875	Nudt19	D7Rp2|D7Rp2-r|D7Rp2-s|D7Rp2e|RP2-r|RP2-s	nudix (nucleoside diphosphate linked moiety X)-type motif 19	protein-coding
mm_4821.1	chr1	185454776	185454800	+	1	NA	promoter-TSS (NM_001033286)	promoter-TSS (NM_001033286)	-60	NM_001033286	226781	Mm.227117	NM_001033286	ENSMUSG00000026614	Slc30a10	E130106K10Rik|Gm212	solute carrier family 30, member 10	protein-coding
mm_69073.1	chr7	126975845	126975847	-	1	NA	promoter-TSS (NM_026638)	promoter-TSS (NM_026638)	-68	NM_026638	52858	Mm.28219	NM_026638	ENSMUSG00000030682	Cdipt	9530042F15Rik|D7Bwg0575e|Pis|Pis1	CDP-diacylglycerol--inositol 3-phosphatidyltransferase (phosphatidylinositol synthase)	protein-coding
mm_160657.1	chr9	118711683	118711683	+	1	NA	promoter-TSS (NM_001113514)	promoter-TSS (NM_001113514)	-9	NM_001113514	104099	Mm.335520	NM_133721	ENSMUSG00000039115	Itga9	(alpha)9|2610002H11Rik|6720458D17Rik|AI461869|D130073C02|D9Ertd428e	integrin alpha 9	protein-coding
mm_57192.1	chr6	122849911	122849927	-	1	NA	exon (NM_009779, exon 2 of 2)	exon (NM_009779, exon 2 of 2)	6238	NM_009779	12267	Mm.2408	NM_009779	ENSMUSG00000040552	C3ar1	AZ3B|C3AR|HNFAG09	complement component 3a receptor 1	protein-coding
mm_109677.1	chr12	113098200	113098267	+	1	NA	promoter-TSS (NM_054081)	promoter-TSS (NM_054081)	-45	NM_001346696	116870	Mm.212577	NM_054081	ENSMUSG00000021144	Mta1	-	metastasis associated 1	protein-coding
mm_166764.1	chr6	133105820	133105832	+	1	NA	3' UTR (NM_001163445, exon 1 of 1)	3' UTR (NM_001163445, exon 1 of 1)	587	NR_073368	381820	Mm.291762	NM_001163445	ENSMUSG00000072704	Smim10l1	2700089E24Rik|AI662692	small integral membrane protein 10 like 1	protein-coding
mm_162433.1	chr1	98349894	98349894	+	1	NA	Intergenic	Intergenic	-71230	NM_001164233	70866	Mm.389164	NM_027584	ENSMUSG00000026336	Slco6d1	4921511I05Rik	solute carrier organic anion transporter family, member 6d1	protein-coding
mm_126028.1	chr15	76701527	76701574	+	1	NA	promoter-TSS (NM_027122)	promoter-TSS (NM_027122)	8	NM_027122	69572	Mm.34920	NM_027122	ENSMUSG00000019080	Mfsd3	2310010G13Rik	major facilitator superfamily domain containing 3	protein-coding
mm_1604.1	chr1	74381728	74381736	+	1	NA	intron (NM_013612, intron 8 of 14)	intron (NM_013612, intron 8 of 14)	6529	NM_013612	18173	Mm.2913	NM_013612	ENSMUSG00000026177	Slc11a1	Bcg|Ity|Ity1|Lsh|Nramp|Nramp1|ity	solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1	protein-coding
mm_78650.1	chr9	40333453	40333463	+	1	NA	promoter-TSS (NR_040728)	promoter-TSS (NR_040728)	-14	NR_040728	73558	Mm.398307	NR_040728		1700110K17Rik	-	RIKEN cDNA 1700110K17 gene	ncRNA
mm_168196.1	chr10	65389464	65389467	-	1	NA	Intergenic	L1Md_T|LINE|L1	734599	NR_038039	69433	Mm.23366	NR_038039	ENSMUSG00000100000	1700023F02Rik	AV205046	RIKEN cDNA 1700023F02 gene	ncRNA
mm_170937.1	chr2	47669554	47669556	-	1	NA	Intergenic	L1Md_T|LINE|L1	-1144554	NM_007396	11480	Mm.314338	NM_007396	ENSMUSG00000052155	Acvr2a	ActrIIa|Acvr2|TactrII	activin receptor IIA	protein-coding
mm_131962.1	chr16	24594777	24594788	+	1	NA	intron (NM_001145952, intron 3 of 11)	intron (NM_001145952, intron 3 of 11)	65468	NR_038091	624582	Mm.439775	NR_038091		Morf4l1-ps1	A730098P11Rik	mortality factor 4 like 1, pseudogene 1	pseudo
mm_141071.1	chr17	25833366	25833402	-	1	NA	promoter-TSS (NM_019719)	promoter-TSS (NM_019719)	-23	NM_019719	56424	Mm.277599	NM_019719	ENSMUSG00000039615	Stub1	0610033N24Rik|2210017D18Rik|2310040B03Rik|AW046544|Chip	STIP1 homology and U-Box containing protein 1	protein-coding
mm_78102.1	chr9	19622276	19622285	+	1	NA	5' UTR (NM_172918, exon 1 of 9)	5' UTR (NM_172918, exon 1 of 9)	189	NM_172918	244713	Mm.67366	NM_172918	ENSMUSG00000057551	Zfp317	4932416G03|D230022C05Rik|KRAB9|Zfp67|Zfp75|mszf40	zinc finger protein 317	protein-coding
mm_78441.1	chr9	32116007	32116032	+	1	NA	promoter-TSS (NM_001195632)	promoter-TSS (NM_001195632)	-117	NM_001195632	330914	Mm.46683	NM_177379	ENSMUSG00000041444	Arhgap32	3426406O18Rik|Gc-gap|Grit|Px-rics|Rics|mKIAA0712|p200Rhogap|p250Gap	Rho GTPase activating protein 32	protein-coding
mm_127792.1	chr15	3582625	3582677	-	1	NA	promoter-TSS (NM_001286370)	promoter-TSS (NM_001286370)	701	NM_001048178	14600	Mm.3986	NM_010284	ENSMUSG00000055737	Ghr	GHBP|GHR/BP	growth hormone receptor	protein-coding
mm_81120.1	chr9	106461885	106461895	+	1	NA	exon (NM_021567, exon 8 of 13)	exon (NM_021567, exon 8 of 13)	4050	NM_001159652	436090	Mm.482905	NM_001159652	ENSMUSG00000091735	Gpr62	4933402E03Rik	G protein-coupled receptor 62	protein-coding
mm_32468.1	chr4	107707057	107707062	+	1	NA	Intergenic	Intergenic	-22897	NM_019872	56296	Mm.141324	NM_019872	ENSMUSG00000028610	Dmrtb1	Dmrt6|Prp13	DMRT-like family B with proline-rich C-terminal, 1	protein-coding
mm_126164.1	chr15	78493852	78493860	+	1	NA	intron (NM_008368, intron 1 of 9)	intron (NM_008368, intron 1 of 9)	1210	NM_008368	16185	Mm.35287	NM_008368	ENSMUSG00000068227	Il2rb	CD122|IL-15Rbeta|IL15Rbeta|Il-2/15Rbeta|Il-2Rbeta|p70	interleukin 2 receptor, beta chain	protein-coding
mm_105146.1	chr11	101460484	101460544	-	1	NA	exon (NM_012037, exon 5 of 6)	exon (NM_012037, exon 5 of 6)	5685	NM_012037	26949	Mm.29210	NM_012037	ENSMUSG00000034993	Vat1	VAT-1	vesicle amine transport 1	protein-coding
mm_64971.1	chr7	16657497	16657500	-	1	NA	promoter-TSS (NR_003247)	promoter-TSS (NR_003247)	-20	NR_003247	100038912	Mm.389813	NR_003247	ENSMUSG00000108307	Ceacam-ps1	Gm1978	carcinoembryonic antigen-related cell adhesion molecule pseudogene 1	pseudo
mm_165545.1	chr3	5860697	5860726	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-284463	NM_001163305	19302	Mm.132336	NM_008994	ENSMUSG00000040374	Pex2	D3Ertd138e|PAF-1|PMP35|Pxmp3	peroxisomal biogenesis factor 2	protein-coding
mm_106743.1	chr12	3907747	3907766	+	1	NA	3' UTR (NM_153743, exon 18 of 18)	3' UTR (NM_153743, exon 18 of 18)	16012	NM_153743	13435	Mm.5001	NM_007872	ENSMUSG00000020661	Dnmt3a	MmuIIIA	DNA methyltransferase 3A	protein-coding
mm_113021.1	chr13	22006590	22006602	+	1	NA	intron (NM_019429, intron 7 of 11)	intron (NM_019429, intron 7 of 11)	3145	NM_019429	54373	Mm.32043	NM_019429	ENSMUSG00000006179	Prss16	AI448615|TSSP	protease, serine 16 (thymus)	protein-coding
mm_89712.1	chr10	98668002	98668004	+	1	NA	Intergenic	Intergenic	-247149	NM_026482	67972	Mm.166944	NM_026482	ENSMUSG00000019943	Atp2b1	2810442I22Rik|E130111D10Rik|Pmca1	ATPase, Ca++ transporting, plasma membrane 1	protein-coding
mm_162377.1	chr1	70543194	70543195	+	1	NA	intron (NM_029160, intron 16 of 16)	ORR1C1|LTR|ERVL-MaLR	-182521	NM_177164	320460	Mm.360649	NM_177164	ENSMUSG00000045648	Vwc2l	A830006F12Rik|Brl	von Willebrand factor C domain-containing protein 2-like	protein-coding
mm_104220.1	chr11	88394669	88394679	-	1	NA	exon (NM_054043, exon 9 of 14)	exon (NM_054043, exon 9 of 14)	41901	NR_039545	100628571		NR_039545	ENSMUSG00000092985	Mir378b	mir-378b|mmu-mir-378b	microRNA 378b	ncRNA
mm_88606.1	chr10	79814587	79814623	+	1	NA	intron (NM_023128, intron 6 of 8)	intron (NM_023128, intron 6 of 8)	-6416	NM_030218	78906	Mm.33087	NM_030218	ENSMUSG00000035852	Misp	9130017N09Rik	mitotic spindle positioning	protein-coding
mm_101243.1	chr11	20712257	20712329	-	1	NA	exon (NM_001252503, exon 3 of 8)	exon (NM_001252503, exon 3 of 8)	29263	NM_001290545	216549	Mm.356580	NM_181411	ENSMUSG00000049659	Aftph	-	aftiphilin	protein-coding
mm_23545.1	chr3	61364793	61364807	+	1	NA	5' UTR (NM_028712, exon 1 of 1)	5' UTR (NM_028712, exon 1 of 1)	293	NM_028712	74012	Mm.422674	NM_028712	ENSMUSG00000036894	Rap2b	4021402C18Rik|AA408554	RAP2B, member of RAS oncogene family	protein-coding
mm_86928.1	chr10	24149528	24149577	+	1	NA	5' UTR (NM_016797, exon 1 of 10)	5' UTR (NM_016797, exon 1 of 10)	235	NM_016797	53331	Mm.248042	NM_016797	ENSMUSG00000019998	Stx7	AI315064|AI317144|AW107239|Syn7	syntaxin 7	protein-coding
mm_14025.1	chr2	122151093	122151104	+	1	NA	exon (NM_009735, exon 2 of 4)	exon (NM_009735, exon 2 of 4)	3411	NM_009735	12010	Mm.163	NM_009735	ENSMUSG00000060802	B2m	Ly-m11|beta2-m|beta2m	beta-2 microglobulin	protein-coding
mm_145754.1	chr18	64852133	64852178	+	1	NA	Intergenic	Lx8|LINE|L1	-35601	NM_001114386	83814	Mm.98668	NM_031881	ENSMUSG00000024589	Nedd4l	1300012C07Rik|Nedd4-2|Nedd4b	neural precursor cell expressed, developmentally down-regulated gene 4-like	protein-coding
mm_14594.1	chr2	136058168	136058176	+	1	NA	5' UTR (NM_029530, exon 1 of 6)	5' UTR (NM_029530, exon 1 of 6)	245	NM_029530	76161	Mm.41638	NM_029530	ENSMUSG00000027270	Lamp5	3110035N03Rik|6330527O06Rik|BAD-LAMP|LAMP-5	lysosomal-associated membrane protein family, member 5	protein-coding
mm_83678.1	chr9	50430283	50430294	-	1	NA	Intergenic	B1_Mus1|SINE|Alu	-64237	NM_029639	76509	Mm.29959	NM_029639	ENSMUSG00000032068	Plet1	0610037B23Rik|1600029D21Rik|AA407923|AU043048	placenta expressed transcript 1	protein-coding
mm_73401.1	chr8	105860637	105860661	+	1	NA	promoter-TSS (NM_026532)	promoter-TSS (NM_026532)	-11	NR_033574	100043462	Mm.269188	NR_033574	ENSMUSG00000071497	Nutf2-ps1	ENSMUSG00000071497|Gm10333|Ntf2|Nutf2	nuclear transport factor 2, pseudogene 1	pseudo
mm_34715.1	chr4	152125079	152125089	+	1	NA	intron (NM_207688, intron 8 of 10)	CT-rich|Low_complexity|Low_complexity	3841	NM_019585	56226	Mm.264215	NM_019585	ENSMUSG00000028943	Espn	je	espin	protein-coding
mm_122897.1	chr14	54950163	54950181	-	1	NA	exon (NM_010856, exon 27 of 39)	exon (NM_010856, exon 27 of 39)	-1030	NR_029724	387204		NR_029724	ENSMUSG00000065432	Mir208a	Mirn208|Mirn208a|mir-208|mir-208a|mmu-mir-208	microRNA 208a	ncRNA
mm_93199.1	chr10	94479580	94479597	-	1	NA	Intergenic	Intergenic	-35269	NM_172051	319880	Mm.23047	NM_172051	ENSMUSG00000020023	Tmcc3	AW488095|C630016B22Rik|C88213|Tmcc1	transmembrane and coiled coil domains 3	protein-coding
mm_130836.1	chr15	101849074	101849114	-	1	NA	exon (NM_008473, exon 2 of 9)	exon (NM_008473, exon 2 of 9)	1692	NM_008473	16678	Mm.183137	NM_008473	ENSMUSG00000046834	Krt1	Krt-2.1|Krt2-1|Krt86	keratin 1	protein-coding
mm_155561.1	chrX	75416670	75416722	+	1	NA	promoter-TSS (NM_001166459)	promoter-TSS (NM_001166459)	68	NM_001166459	210766	Mm.226957	NM_145956	ENSMUSG00000031201	Brcc3	C6.1A	BRCA1/BRCA2-containing complex, subunit 3	protein-coding
mm_105906.1	chr11	114983145	114983153	-	1	NA	3' UTR (NM_145437, exon 4 of 4)	3' UTR (NM_145437, exon 4 of 4)	6737	NM_145437	217305	Mm.275986	NM_145437	ENSMUSG00000034641	Cd300ld	4732429D16Rik|CLM5|Cd300ld1|LMIR4|MAIR-IV|clm-5	CD300 molecule like family member d	protein-coding
mm_1053.1	chr1	58831586	58831632	+	1	NA	exon (NM_001277926, exon 7 of 10)	exon (NM_001277926, exon 7 of 10)	29107	NM_001080126	12370	Mm.336851	NM_009812	ENSMUSG00000026029	Casp8	CASP-8|FLICE|MACH|Mch5	caspase 8	protein-coding
mm_36658.1	chr4	94945965	94945972	-	1	NA	3' UTR (NM_177239, exon 20 of 20)	3' UTR (NM_177239, exon 20 of 20)	-17125	NM_001290623	67753	Mm.25097	NM_027089	ENSMUSG00000028575	Eqtn	1700028B15Rik|4930579C15Rik|Afaf|C81058|Eqtl|Eqts	equatorin, sperm acrosome associated	protein-coding
mm_164996.1	chr19	18063877	18063877	+	1	NA	Intergenic	Intergenic	-226245	NM_001190483	18552	Mm.3401	NM_001163144	ENSMUSG00000024713	Pcsk5	PC5|PC6|SPC6|b2b1549Clo|b2b585Clo	proprotein convertase subtilisin/kexin type 5	protein-coding
mm_165451.1	chr2	157201669	157201703	-	1	NA	intron (NM_011249, intron 1 of 21)	intron (NM_011249, intron 1 of 21)	2848	NM_011249	19650	Mm.244671	NM_011249	ENSMUSG00000027641	Rbl1	AW547426|PRB1|p107	retinoblastoma-like 1 (p107)	protein-coding
mm_57117.1	chr6	122596609	122596619	-	1	NA	intron (NM_031159, intron 3 of 7)	intron (NM_031159, intron 3 of 7)	5830	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_117304.1	chr13	67360555	67360595	-	1	NA	promoter-TSS (NM_001038651)	promoter-TSS (NM_001038651)	-3	NM_001038651	629016	Mm.440800	NM_001038651	ENSMUSG00000098905	Zfp953	E130120F12Rik	zinc finger protein 953	protein-coding
mm_123524.1	chr14	66750024	66750046	-	1	NA	intron (NM_001271761, intron 2 of 2)	intron (NM_001271761, intron 2 of 2)	114784	NM_001271760	11549	Mm.57064	NM_013461	ENSMUSG00000045875	Adra1a	Adra1c	adrenergic receptor, alpha 1a	protein-coding
mm_91379.1	chr10	30618341	30618395	-	1	NA	promoter-TSS (NM_025798)	promoter-TSS (NM_025798)	-2	NM_025798	66847	Mm.46218	NM_025798	ENSMUSG00000019791	Hint3	0610010I17Rik|AV009015|HINT-3|HINT-4|HINT4	histidine triad nucleotide binding protein 3	protein-coding
mm_81000.1	chr9	103426544	103426558	+	1	NA	intron (NM_001002896, intron 6 of 6)	intron (NM_001002896, intron 6 of 6)	2973	NR_040466	100529079	Mm.437003	NR_040466	ENSMUSG00000086236	5830418P13Rik	-	RIKEN cDNA 5830418P13 gene	ncRNA
mm_4563.1	chr1	177447354	177447375	+	1	NA	exon (NM_013915, exon 1 of 1)	exon (NM_013915, exon 1 of 1)	1543	NM_013915	30928	Mm.330700	NM_013915	ENSMUSG00000063659	Zbtb18	RP58|Zfp238|Znf238	zinc finger and BTB domain containing 18	protein-coding
mm_62085.1	chr7	92982087	92982120	+	1	NA	Intergenic	RLTR26C_MM|LTR|ERVK	-97776	NM_021427	58238	Mm.113787	NM_021427	ENSMUSG00000051515	Fam181b	A830059I20Rik|AB041569	family with sequence similarity 181, member B	protein-coding
mm_66857.1	chr7	52918724	52918730	-	1	NA	Intergenic	Intergenic	-903011	NM_001195601	100503036	Mm.279725	NM_001195601	ENSMUSG00000094445	1700015G11Rik	Ccdc179	RIKEN cDNA 1700015G11 gene	protein-coding
mm_14714.1	chr2	143912528	143912531	+	1	NA	Intergenic	Intergenic	-2802	NM_019771	56431	Mm.28919	NM_019771	ENSMUSG00000015932	Dstn	2610043P17Rik|ADF|AU042046|Dsn|corn1|sid23p	destrin	protein-coding
mm_40705.1	chr5	65861359	65861368	+	1	NA	Intergenic	Intergenic	-2206	NM_001081105	74734	Mm.20323	NM_001081105	ENSMUSG00000029204	Rhoh	5830400A04Rik|AU019774|Arhh	ras homolog family member H	protein-coding
mm_95804.1	chr11	55109808	55109826	+	1	NA	3' UTR (NM_010299, exon 4 of 4)	3' UTR (NM_010299, exon 4 of 4)	11832	NM_010299	14667	Mm.287807	NM_010299	ENSMUSG00000000594	Gm2a	AA408702|AW215435|GM2-AP|SAP-3	GM2 ganglioside activator protein	protein-coding
mm_85862.1	chr9	110750102	110750120	-	1	NA	Intergenic	Intergenic	-2966	NM_011199	19228	Mm.3542	NM_011199	ENSMUSG00000032492	Pth1r	PPR|Pthr|Pthr1	parathyroid hormone 1 receptor	protein-coding
mm_158222.1	chrX	106011767	106011818	-	1	NA	exon (NM_001190409, exon 1 of 10)	exon (NM_001190409, exon 1 of 10)	107	NM_001190409	67075	Mm.275943	NM_025952	ENSMUSG00000031232	Magt1	2410001C15Rik|2610529C04Rik|2810482I07Rik|IAG2|IAP	magnesium transporter 1	protein-coding
mm_155030.1	chrX	42068325	42068361	+	1	NA	promoter-TSS (NR_125870)	promoter-TSS (NR_125870)	-55	NM_001301639	11798	Mm.259879	NM_009688	ENSMUSG00000025860	Xiap	1110015C02Rik|Aipa|Api3|Birc4|IAP3|ILP-1|MIHA	X-linked inhibitor of apoptosis	protein-coding
mm_86495.1	chr10	5639211	5639225	+	1	NA	promoter-TSS (NM_011702)	promoter-TSS (NM_011702)	0	NM_011702	22353	Mm.98916	NM_011702	ENSMUSG00000019772	Vip	-	vasoactive intestinal polypeptide	protein-coding
mm_145224.1	chr18	50057241	50057254	+	1	NA	intron (NM_134131, intron 1 of 1)	RSINE1|SINE|B4	3965	NM_134131	106869	Mm.27740	NM_134131	ENSMUSG00000062210	Tnfaip8	AA987150|E130304C20Rik|ENSMUSG00000073567|Gg2-1|Gm10539|Nded|Ssc-2|Tipe	tumor necrosis factor, alpha-induced protein 8	protein-coding
mm_134114.1	chr16	10280239	10280240	-	1	NA	Intergenic	MMERGLN-int|LTR|ERV1	33729	NM_007929	13731	Mm.246009	NM_007929	ENSMUSG00000022505	Emp2	XMP	epithelial membrane protein 2	protein-coding
mm_94701.1	chr11	20225000	20225017	+	1	NA	3' UTR (NM_008996, exon 6 of 6)	3' UTR (NM_008996, exon 6 of 6)	23406	NM_008996	19324	Mm.271944	NM_008996	ENSMUSG00000020149	Rab1a	Gtbp|Rab-1|Rab1|Ypt1|mKIAA3012	RAB1A, member RAS oncogene family	protein-coding
mm_103674.1	chr11	79239898	79239914	-	1	NA	3' UTR (NM_001042565, exon 4 of 4)	3' UTR (NM_001042565, exon 4 of 4)	3118	NM_001042565	78889	Mm.307022	NM_019653	ENSMUSG00000017677	Wsb1	1110056B13Rik|2700038M07Rik	WD repeat and SOCS box-containing 1	protein-coding
mm_42306.1	chr5	114785748	114785761	+	1	NA	intron (NM_026718, intron 1 of 14)	PB1D10|SINE|Alu	10614	NM_026718	68420	Mm.275554	NM_026718	ENSMUSG00000041870	Ankrd13a	1100001D10Rik|ANKRD13|AU046136	ankyrin repeat domain 13a	protein-coding
mm_152888.1	chr19	24749719	24749722	-	1	NA	intron (NM_175013, intron 7 of 10)	B1F|SINE|Alu	75712	NM_183160	226040	Mm.391170	NM_183160	ENSMUSG00000048572	Tmem252	E030010A14Rik	transmembrane protein 252	protein-coding
mm_45474.1	chr5	69542623	69542636	-	1	NA	promoter-TSS (NM_023784)	promoter-TSS (NM_023784)	18	NM_023784	75581	Mm.154776	NM_023784	ENSMUSG00000029158	Yipf7	2310016N21Rik|Yip1b	Yip1 domain family, member 7	protein-coding
mm_119327.1	chr14	38380450	38380471	+	1	NA	intron (NM_001190188, intron 7 of 8)	intron (NM_001190188, intron 7 of 8)	-517842	NR_045713	75170	Mm.372967	NR_045713	ENSMUSG00000093528	Nrg3os	4930529F24Rik	neuregulin 3, opposite strand	ncRNA
mm_137379.1	chr17	25727727	25727797	+	1	NA	promoter-TSS (NM_145409)	promoter-TSS (NM_145409)	11	NM_028009	106707	Mm.24603	NM_028009	ENSMUSG00000041199	Rpusd1	2310051D06Rik|AU019540|Rlucl	RNA pseudouridylate synthase domain containing 1	protein-coding
mm_74445.1	chr8	4087381	4087437	-	1	NA	Intergenic	CpG	18355	NM_026956	69142	Mm.171061	NM_026956	ENSMUSG00000051906	Cd209f	1810029C22Rik|AI647041|SIGNR8	CD209f antigen	protein-coding
mm_155141.1	chrX	51792099	51792104	+	1	NA	intron (NM_031388, intron 7 of 8)	intron (NM_031388, intron 7 of 8)	9132	NM_031388	83563	Mm.242827	NM_031388	ENSMUSG00000055780	Usp26	-	ubiquitin specific peptidase 26	protein-coding
mm_80422.1	chr9	77917249	77917257	+	1	NA	promoter-TSS (NM_134255)	promoter-TSS (NM_134255)	-112	NM_134255	68801	Mm.430736	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	ELOVL family member 5, elongation of long chain fatty acids (yeast)	protein-coding
mm_39548.1	chr5	21646034	21646057	+	1	NA	promoter-TSS (NM_026034)	promoter-TSS (NM_026034)	61	NM_026034	67211	Mm.260782	NM_026034	ENSMUSG00000038525	Armc10	2810037C14Rik|Svh	armadillo repeat containing 10	protein-coding
mm_114990.1	chr13	97511152	97511180	+	1	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	28465	NR_110431	100039691	Mm.219358	NR_110430	ENSMUSG00000078952	Lncenc1	ENSMUSG00000078952|Gm11019|Gm2373|Lincenc1|Platr18|linc-Enc1	long non-coding RNA, embryonic stem cells expressed 1	ncRNA
mm_16605.1	chr2	5064053	5064075	-	1	NA	promoter-TSS (NM_181848)	promoter-TSS (NM_181848)	-126	NM_181848	71648	Mm.116942	NM_181848	ENSMUSG00000026672	Optn	4930441O07Rik|FIP2|HYPL|NRP	optineurin	protein-coding
mm_70997.1	chr8	28593524	28593538	+	1	NA	Intergenic	Intergenic	-508678	NR_033590	666422	Mm.484413	NR_033590	ENSMUSG00000110372	Gm8096	EG666422	3-phosphoglycerate dehydrogenase pseudogene	pseudo
mm_122800.1	chr14	54554269	54554279	-	1	NA	promoter-TSS (NM_145462)	promoter-TSS (NM_145462)	87	NM_145462	219072	Mm.202152	NM_145462	ENSMUSG00000022177	Haus4	9430093H08Rik|AU016300|D14Ertd500e	HAUS augmin-like complex, subunit 4	protein-coding
mm_58714.1	chr7	12999122	12999130	+	1	NA	promoter-TSS (NM_009512)	promoter-TSS (NM_009512)	-934	NM_009512	26459	Mm.10984	NM_009512	ENSMUSG00000030382	Slc27a5	FACVL3|FATP5|VLCS-H2|VLCSH2|Vlacsr	solute carrier family 27 (fatty acid transporter), member 5	protein-coding
mm_156674.1	chrX	159255920	159255926	+	1	NA	5' UTR (NM_148945, exon 1 of 22)	5' UTR (NM_148945, exon 1 of 22)	141	NM_001346675	110651	Mm.328476	NM_148945	ENSMUSG00000031309	Rps6ka3	MAPKAPK-1b|MPK-9|Rsk2|S6K-alpha3|p90RSK3|pp90RSK2	ribosomal protein S6 kinase polypeptide 3	protein-coding
mm_69612.1	chr7	137199237	137199250	-	1	NA	exon (NM_001113414, exon 14 of 16)	exon (NM_001113414, exon 14 of 16)	-35440	NR_045885	100038555	Mm.444788	NR_045885	ENSMUSG00000109722	Gm10578	ENSMUSG00000073800	predicted gene 10578	ncRNA
mm_111314.1	chr12	85824507	85824555	-	1	NA	promoter-TSS (NM_001081423)	promoter-TSS (NM_001081423)	14	NM_021446	58520	Mm.143795	NM_021446	ENSMUSG00000021252	0610007P14Rik	1190004E09Rik|AU019315|C77855|ORF11	RIKEN cDNA 0610007P14 gene	protein-coding
mm_149728.1	chr19	21793253	21793256	+	1	NA	intron (NM_001033759, intron 2 of 23)	intron (NM_001033759, intron 2 of 23)	14914	NM_031997	83921	Mm.329776	NM_031997	ENSMUSG00000024754	Tmem2	-	transmembrane protein 2	protein-coding
mm_153913.1	chr19	47171200	47171203	-	1	NA	Intergenic	RMER16-int|LTR|ERVK	-7619	NM_021360	18011	Mm.313651	NM_021360	ENSMUSG00000006435	Neurl1a	2410129E16Rik|AI450910|AI481072|Neu1|Neur1|Neurl|Neurl1|Nlz|Rnf67	neuralized E3 ubiquitin protein ligase 1A	protein-coding
mm_76104.1	chr8	80395130	80395134	-	1	NA	Intergenic	Intergenic	-98913	NM_010369	14934	Mm.13123	NM_010369	ENSMUSG00000051839	Gypa	AI853584|CD235a|GPA	glycophorin A	protein-coding
mm_1020.1	chr1	58745145	58745152	+	1	NA	intron (NM_001293805, intron 6 of 7)	intron (NM_001293805, intron 6 of 7)	14596	NM_001293805	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_42930.1	chr5	122850168	122850178	+	1	NA	promoter-TSS (NM_030564)	promoter-TSS (NM_030564)	-15	NM_030564	80751	Mm.388529	NM_030564	ENSMUSG00000029474	Rnf34	AW061037|AW536122|BC004042|C88279|RIFF	ring finger protein 34	protein-coding
mm_30831.1	chr4	21931292	21931366	+	1	NA	promoter-TSS (NM_175234)	promoter-TSS (NM_175234)	3	NM_175234	76132	Mm.159689	NM_175234	ENSMUSG00000028246	Faxc	6230409E13Rik|AW742931	failed axon connections homolog	protein-coding
mm_13649.1	chr2	114054363	114054385	+	1	NA	promoter-TSS (NR_028422)	promoter-TSS (NR_028422)	-22	NR_028422	100303644	Mm.330469	NR_028422	ENSMUSG00000092397	C130080G10Rik	-	RIKEN cDNA C130080G10 gene	ncRNA
mm_138024.1	chr17	33911985	33911999	+	1	NA	exon (NM_001199733, exon 3 of 8)	exon (NM_001199733, exon 3 of 8)	2391	NM_001199733	13163	Mm.271809	NM_007829	ENSMUSG00000002307	Daxx	-	Fas death domain-associated protein	protein-coding
mm_110993.1	chr12	77453215	77453229	-	1	NA	intron (NR_045554, intron 10 of 11)	intron (NR_045554, intron 10 of 11)	43081	NM_001252616	53618	Mm.35628	NM_016893	ENSMUSG00000021065	Fut8	-	fucosyltransferase 8	protein-coding
mm_137304.1	chr17	24850720	24850726	+	1	NA	promoter-TSS (NM_023480)	promoter-TSS (NM_023480)	56	NM_001159626	14651	Mm.43784	NM_024284	ENSMUSG00000024158	Hagh	BC019817|Glo-2|Glo2|Rsp29	hydroxyacyl glutathione hydrolase	protein-coding
mm_67967.1	chr7	100607659	100607692	-	1	NA	promoter-TSS (NM_024287)	promoter-TSS (NM_024287)	89	NM_001163663	19346	Mm.28650	NM_024287	ENSMUSG00000030704	Rab6a	2610028L11Rik|AA419671|Rab6	RAB6A, member RAS oncogene family	protein-coding
mm_50358.1	chr6	48647225	48647298	+	1	NA	promoter-TSS (NM_001286629)	promoter-TSS (NM_001286629)	27	NM_001077410	243374	Mm.86514	NM_212486	ENSMUSG00000064262	Gimap8	Gm457|IAN9|IMAP8	GTPase, IMAP family member 8	protein-coding
mm_106155.1	chr11	116624210	116624227	-	1	NA	promoter-TSS (NM_001167680)	promoter-TSS (NM_001167680)	34	NM_001167680	217344	Mm.89695	NM_172572	ENSMUSG00000020806	Rhbdf2	4732465I17Rik|Rhbdl6|cub	rhomboid 5 homolog 2	protein-coding
mm_6364.1	chr1	72212311	72212318	-	1	NA	promoter-TSS (NM_001005423)	promoter-TSS (NM_001005423)	-7	NM_001005423	381269	Mm.422636	NM_001005423	ENSMUSG00000039395	Mreg	Gm974|Wdt2|dsu	melanoregulin	protein-coding
mm_10398.1	chr2	13575165	13575177	+	1	NA	intron (NM_011701, intron 1 of 8)	intron (NM_011701, intron 1 of 8)	860	NM_011701	22352	Mm.268000	NM_011701	ENSMUSG00000026728	Vim	-	vimentin	protein-coding
mm_84035.1	chr9	57765610	57765632	-	1	NA	5' UTR (NM_007713, exon 1 of 13)	5' UTR (NM_007713, exon 1 of 13)	239	NM_007713	102414	Mm.25720	NM_007713	ENSMUSG00000032316	Clk3	AI256811	CDC-like kinase 3	protein-coding
mm_102005.1	chr11	51601797	51601816	-	1	NA	exon (NM_001048061, exon 7 of 8)	exon (NM_001048061, exon 7 of 8)	5075	NM_001048061	15384	Mm.256875	NM_010448	ENSMUSG00000020358	Hnrnpab	3010025C11Rik|CBF-A|Cgbfa|Hnrpab	heterogeneous nuclear ribonucleoprotein A/B	protein-coding
mm_169292.1	chr13	98977665	98977675	+	1	NA	Intergenic	ORR1A3|LTR|ERVL-MaLR	6895	NM_027064	69382	Mm.45466	NM_027064	ENSMUSG00000045022	1700024P04Rik	H2bl1|Subh2bv	RIKEN cDNA 1700024P04 gene	protein-coding
mm_133581.1	chr16	91407136	91407149	+	1	NA	intron (NM_008349, intron 1 of 6)	intron (NM_008349, intron 1 of 6)	907	NM_008349	16155	Mm.4154	NM_008349	ENSMUSG00000022969	Il10rb	6620401D04Rik|AI528744|CRF2-4|Crfb4|D16H21S58|D21S58h|IL-10R2|Il10r2	interleukin 10 receptor, beta	protein-coding
mm_71039.1	chr8	33657986	33658000	+	1	NA	intron (NM_010344, intron 1 of 12)	intron (NM_010344, intron 1 of 12)	4755	NM_010344	14782	Mm.283573	NM_010344	ENSMUSG00000031584	Gsr	AI325518|D8Ertd238e|Gr-1|Gr1	glutathione reductase	protein-coding
mm_61595.1	chr7	80025994	80026028	+	1	NA	promoter-TSS (NM_175433)	promoter-TSS (NM_175433)	-217	NM_175433	209225	Mm.290925	NM_175433	ENSMUSG00000048897	Zfp710	5430400N05Rik|9830165K13|AI324798|Znf710	zinc finger protein 710	protein-coding
mm_25733.1	chr3	122834782	122834798	+	1	NA	intron (NM_153422, intron 14 of 20)	intron (NM_153422, intron 14 of 20)	-32810	NR_045168	71647	Mm.449992	NR_045168	ENSMUSG00000106583	4930447N08Rik	-	RIKEN cDNA 4930447N08 gene	ncRNA
mm_173019.1	chrX	101429721	101429722	+	1	NA	promoter-TSS (NM_001252518)	promoter-TSS (NM_001252518)	70	NM_001252518	53610	Mm.280069	NM_023144	ENSMUSG00000031311	Nono	AA407051|AV149256|NRB54|P54NRB|nonA	non-POU-domain-containing, octamer binding protein	protein-coding
mm_167460.1	chr8	123427474	123427480	-	1	NA	Intergenic	MuLV-int|LTR|ERV1	-15479	NM_001253784	23854	Mm.275127	NM_054046	ENSMUSG00000001482	Def8	AI449518|D8Ertd713e|DEF-8	differentially expressed in FDCP 8	protein-coding
mm_5619.1	chr1	39847323	39847334	-	1	NA	promoter-TSS (NR_040465)	promoter-TSS (NR_040465)	2	NR_040465	73426	Mm.396239	NR_040465	ENSMUSG00000101634	1700066B17Rik	-	RIKEN cDNA 1700066B17 gene	ncRNA
mm_148868.1	chr19	6497453	6497487	+	1	NA	intron (NM_001205234, intron 17 of 22)	CpG	45600	NM_009203	20521	Mm.391146	NM_009203	ENSMUSG00000061742	Slc22a12	AI987855|OAT4L|Rst|Slc22al2|URAT1	solute carrier family 22 (organic anion/cation transporter), member 12	protein-coding
mm_36969.1	chr4	109476266	109476289	-	1	NA	5' UTR (NM_013876, exon 1 of 3)	5' UTR (NM_013876, exon 1 of 3)	228	NM_013876	29864	Mm.392580	NM_013876	ENSMUSG00000028557	Rnf11	-	ring finger protein 11	protein-coding
mm_66011.1	chr7	30588831	30588855	-	1	NA	promoter-TSS (NR_106134)	promoter-TSS (NR_106134)	-117	NM_029274	75410	Mm.168688	NM_029274	ENSMUSG00000006307	Kmt2b	2610014H22Rik|Mll2|Wbp7|mKIAA0304	lysine (K)-specific methyltransferase 2B	protein-coding
mm_23483.1	chr3	60497891	60497929	+	1	NA	intron (NM_001253713, intron 2 of 9)	intron (NM_001253713, intron 2 of 9)	-3269	NM_001253711	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_3437.1	chr1	150102130	150102146	+	1	NA	intron (NM_011198, intron 4 of 9)	intron (NM_011198, intron 4 of 9)	2107	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_93851.1	chr10	122047266	122047289	-	1	NA	promoter-TSS (NM_001081037)	promoter-TSS (NM_001081037)	38	NM_001242411	117600	Mm.288698	NM_001081037	ENSMUSG00000020121	Srgap1	4930572H05Rik|Arhgap13	SLIT-ROBO Rho GTPase activating protein 1	protein-coding
mm_107020.1	chr12	12766029	12766031	+	1	NA	Intergenic	Intergenic	-96113	NR_136889	102637952	Mm.421393	NR_136889		Gm34637	-	predicted gene, 34637	ncRNA
mm_59402.1	chr7	26808881	26808909	+	1	NA	promoter-TSS (NM_013809)	promoter-TSS (NM_013809)	-32	NM_013809	13108	Mm.102312	NM_013809	ENSMUSG00000049685	Cyp2g1	-	cytochrome P450, family 2, subfamily g, polypeptide 1	protein-coding
mm_85626.1	chr9	107615799	107615829	-	1	NA	exon (NM_008138, exon 8 of 9)	exon (NM_008138, exon 8 of 9)	-6573	NM_001291539	20347	Mm.4083	NM_009153	ENSMUSG00000057969	Sema3b	SemA|Semaa|sema5|semaV	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B	protein-coding
mm_113322.1	chr13	30786369	30786380	+	1	NA	Intergenic	Intergenic	37141	NM_013674	16364	Mm.4677	NM_013674	ENSMUSG00000021356	Irf4	AI385587|IRF-4|LSIRF|NF-EM5|Spip	interferon regulatory factor 4	protein-coding
mm_152404.1	chr19	10592524	10592552	-	1	NA	3' UTR (NM_145496, exon 17 of 17)	3' UTR (NM_145496, exon 17 of 17)	11720	NM_145496	225913	Mm.374868	NM_145496	ENSMUSG00000034371	Tkfc	BC021917|Dak	triokinase, FMN cyclase	protein-coding
mm_81862.1	chr9	118877133	118877145	+	1	NA	exon (NM_133721, exon 26 of 28)	exon (NM_133721, exon 26 of 28)	-49397	NM_133710	69274	Mm.439928	NM_133710	ENSMUSG00000047409	Ctdspl	2810418J22Rik|AI426263|HYA22|SCP3	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase-like	protein-coding
mm_41109.1	chr5	87777212	87777227	+	1	NA	intron (NM_007785, intron 2 of 13)	(TG)n|Simple_repeat|Simple_repeat	2769	NM_007785	12993	Mm.4908	NM_007785	ENSMUSG00000061937	Csn1s2a	Csng|PP22	casein alpha s2-like A	protein-coding
mm_53764.1	chr6	145808190	145808224	+	1	NA	promoter-TSS (NM_027760)	promoter-TSS (NM_027760)	-176	NM_027760	71323	Mm.158669	NM_027760	ENSMUSG00000030259	Rassf8	5133400D11Rik|AA815821|AW123240|Hoj1|mHoj-1	Ras association (RalGDS/AF-6) domain family (N-terminal) member 8	protein-coding
mm_2637.1	chr1	121495866	121495895	+	1	NA	intron (NM_001025156, intron 21 of 23)	RMER6BA|LTR|ERVK	32585	NM_010483	15564	Mm.4833	NM_010483	ENSMUSG00000050534	Htr5b	5-Ht5b	5-hydroxytryptamine (serotonin) receptor 5B	protein-coding
mm_130244.1	chr15	96639728	96639744	-	1	NA	intron (NM_001166458, intron 1 of 15)	intron (NM_001166458, intron 1 of 15)	2226	NM_134086	105727	Mm.103568	NM_134086	ENSMUSG00000023169	Slc38a1	AA408026|AA409865|AL022800|AU015942|NAT2	solute carrier family 38, member 1	protein-coding
mm_134925.1	chr16	30550561	30550594	-	1	NA	promoter-TSS (NM_172614)	promoter-TSS (NM_172614)	1	NM_172614	224090	Mm.241459	NM_172614	ENSMUSG00000022537	Tmem44	1700007N03Rik|9330161C17Rik|B230220N21	transmembrane protein 44	protein-coding
mm_25515.1	chr3	113629834	113629869	+	1	NA	intron (NM_001287015, intron 1 of 14)	CpG	298	NM_026043	67225	Mm.316928	NM_026043	ENSMUSG00000027981	Rnpc3	2810441O16Rik|AI447568|C030014B17Rik	RNA-binding region (RNP1, RRM) containing 3	protein-coding
mm_15872.1	chr2	164835175	164835199	+	1	NA	exon (NM_008906, exon 6 of 15)	exon (NM_008906, exon 6 of 15)	1414	NM_008906	19025	Mm.359633	NM_008906	ENSMUSG00000017760	Ctsa	AU019505|PPCA|Ppgb	cathepsin A	protein-coding
mm_95953.1	chr11	58393925	58393934	+	1	NA	Intergenic	IMPB_01|Satellite|Satellite	13283	NM_001330197	70163	Mm.24119	NM_027339	ENSMUSG00000013643	Lypd8	2210415F13Rik	LY6/PLAUR domain containing 8	protein-coding
mm_169364.1	chr14	32201854	32201856	-	1	NA	promoter-TSS (NM_011960)	promoter-TSS (NM_011960)	36	NM_016897	53600	Mm.303703	NM_016897	ENSMUSG00000013701	Timm23	Tim23	translocase of inner mitochondrial membrane 23	protein-coding
mm_41798.1	chr5	103753723	103753733	+	1	NA	promoter-TSS (NM_133919)	promoter-TSS (NM_133919)	-434	NM_133919	17355	Mm.6949	NM_133919	ENSMUSG00000029313	Aff1	9630032B01Rik|AW319193|Af4|Mllt2h|Rob	AF4/FMR2 family, member 1	protein-coding
mm_28263.1	chr3	88622729	88622733	-	1	NA	intron (NM_001198912, intron 1 of 21)	intron (NM_001198912, intron 1 of 21)	1337	NM_001198912	16800	Mm.239329	NM_008487	ENSMUSG00000028059	Arhgef2	AA408978|GEF|GEF-H1|GEFH1|LFP40|Lbcl1|Lfc|P40|mKIAA0651	rho/rac guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_77924.1	chr9	7352932	7352952	+	1	NA	exon (NM_008605, exon 5 of 10)	exon (NM_008605, exon 5 of 10)	5568	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_86629.1	chr10	13975842	13975842	+	1	NA	intron (NM_010437, intron 1 of 8)	intron (NM_010437, intron 1 of 8)	9463	NM_010437	15273	Mm.42157	NM_010437	ENSMUSG00000015501	Hivep2	Gm20114|MIBP1|Schnurri-2|Shn-2	human immunodeficiency virus type I enhancer binding protein 2	protein-coding
mm_161167.1	chr13	35738294	35738294	+	1	NA	intron (NM_009881, intron 3 of 9)	intron (NM_009881, intron 3 of 9)	-3108	NM_001123386	12593	Mm.29002	NM_009881	ENSMUSG00000059288	Cdyl	AI325931	chromodomain protein, Y chromosome-like	protein-coding
mm_42818.1	chr5	121981633	121981634	+	1	NA	intron (NM_001312908, intron 2 of 22)	intron (NM_001312908, intron 2 of 22)	66192	NM_007804	13048	Mm.156172	NM_007804	ENSMUSG00000042589	Cux2	1700051K22Rik|Cutl2|Cux-2|ENSMUSG00000072641	cut-like homeobox 2	protein-coding
mm_170279.1	chr18	27599066	27599082	+	1	NA	Intergenic	Intergenic	-961090	NR_045398	320624	Mm.50107	NR_045398		4930474G06Rik	-	RIKEN cDNA 4930474G06 gene	ncRNA
mm_47507.1	chr5	124035808	124035815	-	1	NA	Intergenic	Intergenic	-3551	NM_177876	330192	Mm.4079	NM_177876	ENSMUSG00000066278	Vps37b	2300007F24Rik|AI415429|BC026744	vacuolar protein sorting 37B	protein-coding
mm_122466.1	chr14	45529991	45530019	-	1	NA	promoter-TSS (NM_146054)	promoter-TSS (NM_146054)	60	NM_146054	218952	Mm.210018	NM_146054	ENSMUSG00000037712	Fermt2	AA960555|Kindlin-2|Mig2|Plekhc1	fermitin family member 2	protein-coding
mm_148256.1	chr18	80743050	80743061	-	1	NA	intron (NM_001201569, intron 26 of 29)	intron (NM_001201569, intron 26 of 29)	-29984	NM_001164109	18018	Mm.329560	NM_016791	ENSMUSG00000033016	Nfatc1	2210017P03Rik|AI449492|AV076380|NF-ATc|NFAT2|NFATc|Nfatcb	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 1	protein-coding
mm_50474.1	chr6	48987970	48987976	+	1	NA	exon (NM_172888, exon 1 of 5)	exon (NM_172888, exon 1 of 5)	1112	NM_172888	243377	Mm.446302	NM_172888	ENSMUSG00000039215	Svs1	9530003A11	seminal vesicle secretory protein 1	protein-coding
mm_128267.1	chr15	36792406	36792430	-	1	NA	intron (NM_001253806, intron 1 of 5)	CpG	-1486	NM_001253807	22631	Mm.3360	NM_011740	ENSMUSG00000022285	Ywhaz	1110013I11Rik|14-3-3zeta|AI596267|AL022924|AU020854	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide	protein-coding
mm_12148.1	chr2	61804977	61804996	+	1	NA	exon (NM_009322, exon 1 of 6)	exon (NM_009322, exon 1 of 6)	533	NM_009322	21375	Mm.308525	NM_009322	ENSMUSG00000035033	Tbr1	-	T-box brain gene 1	protein-coding
mm_171696.1	chr4	67941220	67941235	-	1	NA	Intergenic	L1Md_Gf|LINE|L1	1013170	NM_019967	56710	Mm.248788	NM_019967	ENSMUSG00000028351	Brinp1	BRINP|Dbc1|Dbccr1|Fam5a	bone morphogenic protein/retinoic acid inducible neural specific 1	protein-coding
mm_139482.1	chr17	56040351	56040420	+	1	NA	promoter-TSS (NM_013733)	promoter-TSS (NM_013733)	-31	NM_013733	27221	Mm.391010	NM_013733	ENSMUSG00000002835	Chaf1a	AL023013|AL024058|CAF-1|Cac1p	chromatin assembly factor 1, subunit A (p150)	protein-coding
mm_50772.1	chr6	53629784	53629796	+	1	NA	intron (NM_001327821, intron 7 of 10)	intron (NM_001327821, intron 7 of 10)	56416	NM_172728	231991	Mm.227444	NM_172728	ENSMUSG00000053007	Creb5	9430076C15Rik|CRE-BPa|Crebpa|D430026C09Rik	cAMP responsive element binding protein 5	protein-coding
mm_51085.1	chr6	67020298	67020334	+	1	NA	3' UTR (NM_001177559, exon 5 of 5)	3' UTR (NM_001177559, exon 5 of 5)	-16283	NR_040278	320172	Mm.449039	NR_040278	ENSMUSG00000087231	E230016M11Rik	-	RIKEN cDNA E230016M11 gene	ncRNA
mm_172419.1	chr7	25569847	25569862	+	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	-29850	NM_001113369	26367	Mm.439731	NM_007543	ENSMUSG00000054385	Ceacam2	AI267129|Bgp2|Ceacam2-L	carcinoembryonic antigen-related cell adhesion molecule 2	protein-coding
mm_60759.1	chr7	45525514	45525549	+	1	NA	promoter-TSS (NM_148927)	promoter-TSS (NM_148927)	737	NM_008654	17872	Mm.4048	NM_008654	ENSMUSG00000040435	Ppp1r15a	9630030H21|Gadd34|Myd116	protein phosphatase 1, regulatory (inhibitor) subunit 15A	protein-coding
mm_51591.1	chr6	83867133	83867143	+	1	NA	Intergenic	CpG	-35397	NM_146169	232164	Mm.404420	NM_146169	ENSMUSG00000045896	Paip2b	-	poly(A) binding protein interacting protein 2B	protein-coding
mm_168419.1	chr11	33160103	33160113	-	1	NA	intron (NM_008722, intron 5 of 10)	B1_Mus2|SINE|Alu	3098	NM_001252261	18148	Mm.485384	NM_008722	ENSMUSG00000057113	Npm1	B23|NO38|Npm	nucleophosmin 1	protein-coding
mm_3141.1	chr1	135142669	135142671	+	1	NA	intron (NM_177081, intron 9 of 9)	B1_Mur4|SINE|Alu	-4164	NM_026823	68724	Mm.174998	NM_026823	ENSMUSG00000026426	Arl8a	1110033P22Rik|Arl10b|gie2	ADP-ribosylation factor-like 8A	protein-coding
mm_1361.1	chr1	66364624	66364663	+	1	NA	intron (NM_001310634, intron 3 of 14)	intron (NM_001310634, intron 3 of 14)	42919	NM_001310634	17756	Mm.256966	NM_008632	ENSMUSG00000015222	Map2	G1-397-34|MAP-2|Mtap-2|Mtap2|repro4	microtubule-associated protein 2	protein-coding
mm_34766.1	chr4	153031038	153031041	+	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	333499	NR_033138	330004	Mm.291863	NM_001033414		Gm833	-	predicted gene 833	ncRNA
mm_71621.1	chr8	57332426	57332455	+	1	NA	promoter-TSS (NR_131041)	promoter-TSS (NR_131041)	5	NR_131041	75996	Mm.399754	NR_131041	ENSMUSG00000097910	5033428I22Rik	-	RIKEN cDNA 5033428I22 gene	ncRNA
mm_90131.1	chr10	117717901	117717949	+	1	NA	Intergenic	Intergenic	-7167	NM_001288586	17246	Mm.22670	NM_010786	ENSMUSG00000020184	Mdm2	1700007J15Rik|AA415488|Mdm-2	transformed mouse 3T3 cell double minute 2	protein-coding
mm_102491.1	chr11	60239726	60239742	-	1	NA	TTS (NM_001039093)	TTS (NM_001039093)	-19107	NM_001313979	20787	Mm.278701	NM_011480	ENSMUSG00000020538	Srebf1	ADD1|SREBP-1a|SREBP1|SREBP1c|bHLHd1	sterol regulatory element binding transcription factor 1	protein-coding
mm_29564.1	chr3	116861811	116861821	-	1	NA	intron (NM_009146, intron 1 of 16)	intron (NM_009146, intron 1 of 16)	136	NM_009146	20321	Mm.66293	NM_009146	ENSMUSG00000033386	Frrs1	AI131732|Sdfr2	ferric-chelate reductase 1	protein-coding
mm_141108.1	chr17	26021917	26021935	-	1	NA	promoter-TSS (NM_153140)	promoter-TSS (NM_153140)	-66	NM_153140	215445	Mm.41191	NM_153140	ENSMUSG00000037098	Rab11fip3	Cart1|D030060O14Rik|Rab11-FIP3|mKIAA0665	RAB11 family interacting protein 3 (class II)	protein-coding
mm_165952.1	chr4	86558395	86558398	+	1	NA	promoter-TSS (NM_001081096)	promoter-TSS (NM_001081096)	-48	NR_131920	74888		NR_131920	ENSMUSG00000085108	Saxo1os	4930457A20Rik|Fam154aos	stabilizer of axonemal microtubules 1, opposite strand	ncRNA
mm_50661.1	chr6	51482993	51483001	+	1	NA	3' UTR (NM_007624, exon 6 of 6)	3' UTR (NM_007624, exon 6 of 6)	12381	NM_007624	12417	Mm.280968	NM_007624	ENSMUSG00000029836	Cbx3	HP1g|M32	chromobox 3	protein-coding
mm_71549.1	chr8	48062111	48062129	+	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	-36972	NM_001161516	320685	Mm.121549	NM_178788	ENSMUSG00000031562	Dctd	6030466N05Rik	dCMP deaminase	protein-coding
mm_128746.1	chr15	64382909	64382936	-	1	NA	promoter-TSS (NM_001276467)	promoter-TSS (NM_001276467)	-3	NM_010026	13196	Mm.277236	NM_010026	ENSMUSG00000022377	Asap1	AV239055|DEF-1|Ddef1|PAP|mKIAA1249|s19	ArfGAP with SH3 domain, ankyrin repeat and PH domain1	protein-coding
mm_14723.1	chr2	144033063	144033067	+	1	NA	promoter-TSS (NM_207275)	promoter-TSS (NM_207275)	-37	NM_001044750	403171	Mm.389362	NM_207275	ENSMUSG00000037307	Banf2	4930517K23Rik|Baf-L|Baf-like|Gm115	barrier to autointegration factor 2	protein-coding
mm_85072.1	chr9	91360999	91361015	-	1	NA	3' UTR (NM_009573, exon 3 of 3)	3' UTR (NM_009573, exon 3 of 3)	4792	NM_009573	22771	Mm.335350	NM_009573	ENSMUSG00000032368	Zic1	ZIC|ZNF201	zinc finger protein of the cerebellum 1	protein-coding
mm_160692.1	chr10	26229736	26229736	+	1	NA	promoter-TSS (NM_001013766)	promoter-TSS (NM_001013766)	29	NM_001115154	268288	Mm.213322	NM_001013766	ENSMUSG00000051354	Samd3	Gm623	sterile alpha motif domain containing 3	protein-coding
mm_69412.1	chr7	132576319	132576319	-	1	NA	promoter-TSS (NM_016978)	promoter-TSS (NM_016978)	79	NM_016978	18242	Mm.13694	NM_016978	ENSMUSG00000030934	Oat	AI194874|rhg	ornithine aminotransferase	protein-coding
mm_29624.1	chr3	121532241	121532269	-	1	NA	promoter-TSS (NM_145394)	promoter-TSS (NM_145394)	89	NM_145394	213603	Mm.33062	NM_145394	ENSMUSG00000039865	Slc44a3	BC010552	solute carrier family 44, member 3	protein-coding
mm_34470.1	chr4	148160614	148160630	+	1	NA	promoter-TSS (NM_001161852)	promoter-TSS (NM_001161852)	-46	NM_176848	230904	Mm.262287	NM_176848	ENSMUSG00000041556	Fbxo2	FBG1|FBX2|Fbs1|Fbs2|NFB42|Prpl4	F-box protein 2	protein-coding
mm_90355.1	chr10	127165341	127165363	+	1	NA	promoter-TSS (NM_027739)	promoter-TSS (NM_027739)	196	NM_001244617	14421	Mm.386762	NM_008080	ENSMUSG00000006731	B4galnt1	4933429D13Rik|Gal-NAc-T|GalNAc-T|GalNAcT|Galgt1|Ggm-2|Ggm2	beta-1,4-N-acetyl-galactosaminyl transferase 1	protein-coding
mm_88214.1	chr10	70245084	70245140	+	1	NA	promoter-TSS (NM_025807)	promoter-TSS (NM_025807)	-164	NM_025807	66859	Mm.19325	NM_025807	ENSMUSG00000037762	Slc16a9	1200003C15Rik|4930425B13Rik|AI552636	solute carrier family 16 (monocarboxylic acid transporters), member 9	protein-coding
mm_106085.1	chr11	116178170	116178181	-	1	NA	exon (NM_015729, exon 9 of 14)	exon (NM_015729, exon 9 of 14)	-9997	NM_172571	217335	Mm.35241	NM_172571	ENSMUSG00000020776	Fbf1	1110033G01Rik|5930413D20|mKIAA1863	Fas (TNFRSF6) binding factor 1	protein-coding
mm_24620.1	chr3	93511298	93511320	+	1	NA	Intergenic	Intergenic	-9187	NM_016740	20195	Mm.280038	NM_016740	ENSMUSG00000027907	S100a11	EMAPI|Emap1|S100a14|S100c|cal	S100 calcium binding protein A11	protein-coding
mm_86316.1	chr9	122866009	122866015	-	1	NA	promoter-TSS (NM_173364)	promoter-TSS (NM_173364)	-6	NM_173364	235682	Mm.326477	NM_173364	ENSMUSG00000047036	Zfp445	AW610627|ZNF168|Znf445|mszf29|mszf50	zinc finger protein 445	protein-coding
mm_124850.1	chr15	9525111	9525154	+	1	NA	exon (NM_008372, exon 2 of 8)	exon (NM_008372, exon 2 of 8)	4744	NM_008372	16197	Mm.389	NM_008372	ENSMUSG00000003882	Il7r	CD127|IL-7Ralpha	interleukin 7 receptor	protein-coding
mm_137513.1	chr17	27057364	27057372	+	1	NA	promoter-TSS (NM_080553)	promoter-TSS (NM_080553)	64	NM_080553	16440	Mm.458106	NM_080553	ENSMUSG00000042644	Itpr3	IP3R 3|Ip3r3|Itpr-3|tf	inositol 1,4,5-triphosphate receptor 3	protein-coding
mm_167667.1	chr9	72985299	72985315	-	1	NA	promoter-TSS (NM_001286546)	promoter-TSS (NM_001286546)	69	NM_001198789	546143	Mm.260946	NM_001198789	ENSMUSG00000086158	Ccpg1os	EG546143|Gm5918	cell cycle progression 1, opposite strand	protein-coding
mm_1863.1	chr1	85012079	85012085	+	1	NA	Intergenic	B2_Mm2|SINE|B2	-76999	NM_027921	71781	Mm.158754	NM_027921	ENSMUSG00000026220	Slc16a14	1110004H10Rik	solute carrier family 16 (monocarboxylic acid transporters), member 14	protein-coding
mm_100487.1	chr11	120361157	120361202	+	1	NA	promoter-TSS (NM_172802)	promoter-TSS (NM_172802)	-355	NM_172802	238021	Mm.481403	NM_172802	ENSMUSG00000025380	Fscn2	A930022G03|Ahl8|C630046B20Rik	fascin actin-bundling protein 2	protein-coding
mm_25102.1	chr3	101286641	101286646	+	1	NA	intron (NM_013486, intron 2 of 4)	intron (NM_013486, intron 2 of 4)	1296	NM_013486	12481	Mm.22842	NM_013486	ENSMUSG00000027863	Cd2	LFA-2|Ly-37|Ly37	CD2 antigen	protein-coding
mm_138638.1	chr17	35866072	35866085	+	1	NA	promoter-TSS (NM_001146710)	promoter-TSS (NM_001146710)	-50	NM_001146710	76448	Mm.359982	NM_175242	ENSMUSG00000034595	Ppp1r18	2310014H01Rik|AA407849|AI450394	protein phosphatase 1, regulatory subunit 18	protein-coding
mm_112932.1	chr13	20964548	20964551	+	1	NA	intron (NM_012054, intron 12 of 20)	L1_Rod|LINE|L1	108750	NM_146535	258528	Mm.377554	NM_146535	ENSMUSG00000042869	Olfr1370	MOR256-14	olfactory receptor 1370	protein-coding
mm_75666.1	chr8	66971950	66971950	-	1	NA	Intergenic	Intergenic	111733	NM_001163564	234344	Mm.334561	NM_001163564	ENSMUSG00000014907	Naf1	Gm174	nuclear assembly factor 1 ribonucleoprotein	protein-coding
mm_15313.1	chr2	155568106	155568126	+	1	NA	intron (NM_008180, intron 9 of 12)	B1_Mur1|SINE|Alu	-11186	NR_040613	74945	Mm.401956	NR_040613	ENSMUSG00000086529	Acss2os	4930471I20Rik	acyl-CoA synthetase short-chain family member 2, opposite strand	ncRNA
mm_18130.1	chr2	45004985	45005050	-	1	NA	intron (NM_001289521, intron 3 of 8)	intron (NM_001289521, intron 3 of 8)	18160	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_116553.1	chr13	46727564	46727588	-	1	NA	5' UTR (NM_175749, exon 1 of 22)	5' UTR (NM_175749, exon 1 of 22)	273	NM_175749	218210	Mm.255398	NM_175749	ENSMUSG00000021374	Nup153	B130015D15Rik|C88147	nucleoporin 153	protein-coding
mm_106426.1	chr11	119300071	119300088	-	1	NA	promoter-TSS (NM_138669)	promoter-TSS (NM_138669)	-36	NM_138669	192170	Mm.197555	NM_138669	ENSMUSG00000025580	Eif4a3	2400003O03Rik|Ddx48|eIF4A-III|mKIAA0111	eukaryotic translation initiation factor 4A3	protein-coding
mm_28411.1	chr3	90292866	90292876	-	1	NA	Intergenic	CpG	22722	NR_105979	102465612		NR_105979	ENSMUSG00000099199	Mir7012	Gm27370|mmu-mir-7012	microRNA 7012	ncRNA
mm_66312.1	chr7	39797766	39797768	-	1	NA	Intergenic	MTEa-int|LTR|ERVL-MaLR	280001	NM_001004139	70227	Mm.333800	NM_001004139	ENSMUSG00000068959	Zfp619	3000002G13Rik	zinc finger protein 619	protein-coding
mm_132722.1	chr16	43610689	43610708	+	1	NA	exon (NM_019778, exon 8 of 9)	exon (NM_019778, exon 8 of 9)	-29957	NR_030576	100124467		NR_030576	ENSMUSG00000076372	Mir568	Mirn568|mmu-mir-568	microRNA 568	ncRNA
mm_165191.1	chr2	31965683	31965685	+	1	NA	intron (NM_145144, intron 4 of 5)	PB1D9|SINE|Alu	-8766	NM_172268	227720	Mm.289686	NM_172268	ENSMUSG00000001855	Nup214	BC039282|CAN|D2H9S46E	nucleoporin 214	protein-coding
mm_28442.1	chr3	90508060	90508063	-	1	NA	intron (NM_001293777, intron 1 of 5)	intron (NM_001293777, intron 1 of 5)	1437	NM_001293776	66511	Mm.154136	NM_023215	ENSMUSG00000001017	Chtop	2500003M10Rik|Fop|Srag	chromatin target of PRMT1	protein-coding
mm_160385.1	chr8	46169543	46169543	+	1	NA	promoter-TSS (NM_025747)	promoter-TSS (NM_025747)	-13	NM_025747	66756	Mm.133623	NM_025747	ENSMUSG00000031631	Cfap97	1110068E21Rik|4933411K20Rik|AW049273|Kiaa1430|mKIAA1430	cilia and flagella associated protein 97	protein-coding
mm_3808.1	chr1	158362419	158362428	+	1	NA	5' UTR (NM_001205204, exon 1 of 23)	5' UTR (NM_001205204, exon 1 of 23)	119	NM_001205204	11899	Mm.329586	NM_007495	ENSMUSG00000026587	Astn1	Astn|GC14|mKIAA0289	astrotactin 1	protein-coding
mm_102616.1	chr11	62458353	62458390	-	1	NA	promoter-TSS (NM_001039536)	promoter-TSS (NM_001039536)	-89	NM_001039536	327942	Mm.390358	NM_199026	ENSMUSG00000014245	Pigl	Gm737	phosphatidylinositol glycan anchor biosynthesis, class L	protein-coding
mm_106071.1	chr11	116168296	116168306	-	1	NA	promoter-TSS (NM_172571)	promoter-TSS (NM_172571)	-123	NM_172571	217335	Mm.35241	NM_172571	ENSMUSG00000020776	Fbf1	1110033G01Rik|5930413D20|mKIAA1863	Fas (TNFRSF6) binding factor 1	protein-coding
mm_138340.1	chr17	34903342	34903354	+	1	NA	exon (NM_001286575, exon 7 of 28)	exon (NM_001286575, exon 7 of 28)	4374	NM_145830	110147	Mm.35345	NM_145830	ENSMUSG00000013787	Ehmt2	Bat8|D17Ertd710e|G9a|KMT1C|NG36	euchromatic histone lysine N-methyltransferase 2	protein-coding
mm_76650.1	chr8	93154449	93154452	-	1	NA	Intergenic	Intergenic	-23167	NM_007954	13884	Mm.88078	NM_007954	ENSMUSG00000057400	Ces1c	Ces-N|Ee-1|Ee1|Es-4|Es-N|Es1|Es4|EsN|PESN	carboxylesterase 1C	protein-coding
mm_143735.1	chr17	81471283	81471294	-	1	NA	intron (NR_104580, intron 2 of 8)	intron (NR_104580, intron 2 of 8)	267099	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_73348.1	chr8	105427588	105427619	+	1	NA	promoter-TSS (NM_001170789)	promoter-TSS (NM_001170789)	-37	NM_001033371	270091	Mm.212709	NM_001033371	ENSMUSG00000054320	Lrrc36	BC036564	leucine rich repeat containing 36	protein-coding
mm_132049.1	chr16	29210110	29210153	+	1	NA	intron (NM_013751, intron 1 of 3)	CpG	436	NM_013751	27281	Mm.103650	NM_013751	ENSMUSG00000022525	Hrasls	2810012B06Rik|A-C1|HRSL1|Hrasrs	HRAS-like suppressor	protein-coding
mm_48601.1	chr5	144223517	144223618	-	1	NA	promoter-TSS (NM_027410)	promoter-TSS (NM_027410)	11	NM_027410	70381	Mm.239412	NM_027410	ENSMUSG00000066621	Tecpr1	2210010N04Rik|mKIAA1358	tectonin beta-propeller repeat containing 1	protein-coding
mm_147305.1	chr18	39519602	39519614	-	1	NA	Intergenic	Intergenic	-32363	NM_008173	14815	Mm.129481	NM_008173	ENSMUSG00000024431	Nr3c1	GR|Grl-1|Grl1	nuclear receptor subfamily 3, group C, member 1	protein-coding
mm_12064.1	chr2	59484646	59484663	+	1	NA	promoter-TSS (NM_029723)	promoter-TSS (NM_029723)	1	NM_029723	76747	Mm.275769	NM_029723	ENSMUSG00000026989	Dapl1	2310032F03Rik|EEDA	death associated protein-like 1	protein-coding
mm_5747.1	chr1	45928000	45928009	-	1	NA	Intergenic	Intergenic	-2410	NM_016917	53945	Mm.28756	NM_016917	ENSMUSG00000025993	Slc40a1	Dusg|Fpn1|IREG1|MTP|MTP1|Ol5|Pcm|Slc11a3|Slc39a1	solute carrier family 40 (iron-regulated transporter), member 1	protein-coding
mm_28279.1	chr3	88950193	88950221	-	1	NA	promoter-TSS (NM_022994)	promoter-TSS (NM_022994)	75	NM_022994	65111	Mm.29028	NM_022994	ENSMUSG00000068921	Dap3	4921514D13Rik|DAP-3|MRP-S29|S29mt	death associated protein 3	protein-coding
mm_18963.1	chr2	76807366	76807384	-	1	NA	intron (NM_028004, intron 67 of 191)	intron (NM_028004, intron 67 of 191)	132060	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_36860.1	chr4	106865951	106865956	-	1	NA	Intergenic	Intergenic	-45517	NM_198438	72475	Mm.195635	NM_023672	ENSMUSG00000061887	Ssbp3	2610021L12Rik|2610200M23Rik|5730488C10Rik|AI854733|AW551939|LAST|SSDP1	single-stranded DNA binding protein 3	protein-coding
mm_125946.1	chr15	76248516	76248563	+	1	NA	TTS (NR_105918)	TTS (NR_105918)	348	NR_105918	102465575		NR_105918	ENSMUSG00000098625	Mir6953	Gm27738|mmu-mir-6953	microRNA 6953	ncRNA
mm_136531.1	chr16	97504926	97504943	-	1	NA	promoter-TSS (NM_020622)	promoter-TSS (NM_020622)	2	NM_020622	52793	Mm.327932	NM_020622	ENSMUSG00000022938	Fam3b	2-21|9030624C24Rik|D16Jhu19e|ORF9|Pander	family with sequence similarity 3, member B	protein-coding
mm_16910.1	chr2	13492035	13492046	-	1	NA	promoter-TSS (NM_001081084)	promoter-TSS (NM_001081084)	-164	NM_001081084	65969	Mm.313915	NM_001081084	ENSMUSG00000026726	Cubn	AA408369|AL022750|D2Wsu88e	cubilin (intrinsic factor-cobalamin receptor)	protein-coding
mm_39991.1	chr5	32491974	32491982	+	1	NA	3' UTR (NM_172707, exon 8 of 8)	3' UTR (NM_172707, exon 8 of 8)	33008	NM_172707	19046	Mm.241931	NM_172707	ENSMUSG00000014956	Ppp1cb	1200010B19	protein phosphatase 1, catalytic subunit, beta isoform	protein-coding
mm_84247.1	chr9	62377328	62377355	-	1	NA	exon (NM_009672, exon 6 of 7)	exon (NM_009672, exon 6 of 7)	35998	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	protein-coding
mm_101894.1	chr11	49087307	49087323	-	1	NA	intron (NM_010999, intron 2 of 5)	intron (NM_010999, intron 2 of 5)	298	NM_008330	15953	Mm.24769	NM_008330	ENSMUSG00000078920	Ifi47	47kDa|IRG-47|Ifggc1|Igrd|Iigp4|Iipg4|Irgd	interferon gamma inducible protein 47	protein-coding
mm_143958.1	chr17	86987154	86987158	-	1	NA	intron (NM_145491, intron 2 of 4)	intron (NM_145491, intron 2 of 4)	24045	NM_145491	104215	Mm.826	NM_145491	ENSMUSG00000024143	Rhoq	Arhq|TC10A|Tc10	ras homolog family member Q	protein-coding
mm_17405.1	chr2	27246742	27246750	-	1	NA	5' UTR (NM_138665, exon 1 of 21)	5' UTR (NM_138665, exon 1 of 21)	557	NM_138665	192166	Mm.278467	NM_138665	ENSMUSG00000009614	Sardh	-	sarcosine dehydrogenase	protein-coding
mm_41607.1	chr5	96374521	96374531	+	1	NA	5' UTR (NM_175473, exon 1 of 74)	5' UTR (NM_175473, exon 1 of 74)	571	NM_175473	231470	Mm.291120	NM_175473	ENSMUSG00000034687	Fras1	E130113P14Rik|bl|mKIAA1500	Fraser extracellular matrix complex subunit 1	protein-coding
mm_124201.1	chr14	98169604	98169618	-	1	NA	5' UTR (NM_001038610, exon 1 of 11)	5' UTR (NM_001038610, exon 1 of 11)	154	NM_001038610	13134	Mm.320593	NM_007826	ENSMUSG00000055639	Dach1	Dac|Dach	dachshund 1 (Drosophila)	protein-coding
mm_22869.1	chr3	28893724	28893727	+	1	NA	intron (NM_001033479, intron 1 of 14)	intron (NM_001033479, intron 1 of 14)	1108	NM_001033479	385263	Mm.60893	NM_001033479	ENSMUSG00000074655	Gm1527	Gm1136	predicted gene 1527	protein-coding
mm_80663.1	chr9	90067752	90067787	+	1	NA	intron (NM_001312649, intron 7 of 10)	intron (NM_001312649, intron 7 of 10)	13502	NM_001312649	13036	Mm.2277	NM_007801	ENSMUSG00000032359	Ctsh	AL022844	cathepsin H	protein-coding
mm_68289.1	chr7	105640318	105640370	-	1	NA	promoter-TSS (NM_019502)	promoter-TSS (NM_019502)	72	NM_029802	76932	Mm.41637	NM_029802	ENSMUSG00000030881	Arfip2	2310002N04Rik|POR|Por1	ADP-ribosylation factor interacting protein 2	protein-coding
mm_40208.1	chr5	37047080	37047100	+	1	NA	Intergenic	Intergenic	-3767	NM_178394	76071	Mm.85280	NM_178394	ENSMUSG00000063646	Jakmip1	5830437M04Rik|C330021K24Rik|Gababrbp|Marlin-1	janus kinase and microtubule interacting protein 1	protein-coding
mm_106660.1	chr11	121229294	121229314	-	1	NA	promoter-TSS (NM_001254735)	promoter-TSS (NM_001254735)	5	NM_144832	217370	Mm.27182	NM_144832	ENSMUSG00000039294	BC017643	-	cDNA sequence BC017643	protein-coding
mm_82002.1	chr9	121705104	121705120	+	1	NA	promoter-TSS (NM_178677)	promoter-TSS (NM_178677)	-83	NM_178677	215474	Mm.31421	NM_178677	ENSMUSG00000061536	Sec22c	4932412K21|5930407I15Rik|C530046H07|Sec22l3	SEC22 homolog C, vesicle trafficking protein	protein-coding
mm_5659.1	chr1	42665077	42665086	-	1	NA	intron (NR_027826, intron 2 of 3)	L1_Mus1|LINE|L1	29744	NR_027826	66297	Mm.45203	NM_183252	ENSMUSG00000060424	Pantr1	2610017I09Rik|Pou3f3os|linc-Brn1a	POU domain, class 3, transcription factor 3 adjacent noncoding transcript 1	ncRNA
mm_119692.1	chr14	53554044	53554046	+	1	NA	Intergenic	Intergenic	699884	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_143631.1	chr17	78934190	78934194	-	1	NA	intron (NM_001024806, intron 2 of 15)	intron (NM_001024806, intron 2 of 15)	2878	NM_001024806	12607	Mm.24169	NM_009882	ENSMUSG00000024081	Cebpz	AI848081|CBF2|Cbf|Cebpa-rs1	CCAAT/enhancer binding protein zeta	protein-coding
mm_86380.1	chr9	123851805	123851815	-	1	NA	promoter-TSS (NM_001110253)	promoter-TSS (NM_001110253)	89	NM_001110253	17281	Mm.252941	NM_148925	ENSMUSG00000025241	Fyco1	2810409M01Rik|Mem2|RUFY3|ZFYVE7	FYVE and coiled-coil domain containing 1	protein-coding
mm_43740.1	chr5	139908413	139908424	+	1	NA	intron (NM_175522, intron 1 of 1)	CpG	475	NM_175522	243312	Mm.237102	NM_175522	ENSMUSG00000048988	Elfn1	A930017N06Rik|AI197272|Ppp1r28	leucine rich repeat and fibronectin type III, extracellular 1	protein-coding
mm_64191.1	chr7	141461729	141461757	+	1	NA	TTS (NR_028142)	TTS (NR_028142)	649	NM_001025103	213573	Mm.386851	NM_001025103	ENSMUSG00000048200	Cracr2b	6330520A15Rik|BC026645|Cracr2a|Efcab4|Efcab4a	calcium release activated channel regulator 2B	protein-coding
mm_3784.1	chr1	156735728	156735736	+	1	NA	Intergenic	Intergenic	-16822	NM_145413	215015	Mm.229107	NM_145413	ENSMUSG00000033557	Fam20b	C530043G21Rik|mKIAA0475	family with sequence similarity 20, member B	protein-coding
mm_47544.1	chr5	124327884	124327894	-	1	NA	promoter-TSS (NM_001134717)	promoter-TSS (NM_001134717)	83	NM_001081323	269702	Mm.60224	NM_001081323	ENSMUSG00000038126	Mphosph9	4930548D04Rik|9630025B04Rik|AW413446|AW547060|B930097C17Rik|C87456|MPP-9|MPP9	M-phase phosphoprotein 9	protein-coding
mm_71369.1	chr8	45749286	45749299	+	1	NA	intron (NM_172752, intron 6 of 22)	intron (NM_172752, intron 6 of 22)	70005	NR_045739	319940	Mm.441720	NR_045739	ENSMUSG00000085440	Sorbs2os	D330022K07Rik	sorbin and SH3 domain containing 2, opposite strand	ncRNA
mm_78500.1	chr9	32737726	32737730	+	1	NA	intron (NM_001038642, intron 5 of 6)	intron (NM_001038642, intron 5 of 6)	41686	NM_001038642	23871	Mm.292415	NM_011808	ENSMUSG00000032035	Ets1	AI196000|AI448617|D230050P06|Ets-1|Tpl1|vs	E26 avian leukemia oncogene 1, 5' domain	protein-coding
mm_162614.1	chr1	183345401	183345423	-	1	NA	intron (NM_177389, intron 6 of 26)	CpG	24153	NM_177389	338366	Mm.41152	NM_177389		Mia3	9130229H14Rik|A930039G15Rik|AU022327|B230399H06Rik|C80126|Gm1525|TANGO1|Tango	melanoma inhibitory activity 3	protein-coding
mm_152610.1	chr19	11912072	11912080	-	1	NA	promoter-TSS (NM_172635)	promoter-TSS (NM_172635)	-323	NM_172635	225929	Mm.42711	NM_172635	ENSMUSG00000046139	Patl1	AV312086|Pat1b	protein associated with topoisomerase II homolog 1 (yeast)	protein-coding
mm_26650.1	chr3	154132321	154132328	+	1	NA	intron (NM_001081263, intron 1 of 21)	intron (NM_001081263, intron 1 of 21)	158888	NM_001081263	242259	Mm.239962	NM_001081263	ENSMUSG00000028360	Slc44a5	AA117069|Gm422	solute carrier family 44, member 5	protein-coding
mm_37768.1	chr4	129742234	129742268	-	1	NA	promoter-TSS (NR_045036)	promoter-TSS (NR_045036)	52	NM_011317	20218	Mm.8256	NM_011317	ENSMUSG00000028790	Khdrbs1	Sam68|p62|p68	KH domain containing, RNA binding, signal transduction associated 1	protein-coding
mm_772.1	chr1	44173333	44173378	+	1	NA	exon (NM_011729, exon 9 of 15)	exon (NM_011729, exon 9 of 15)	25611	NM_011729	22592	Mm.2213	NM_011729	ENSMUSG00000026048	Ercc5	Xpg	excision repair cross-complementing rodent repair deficiency, complementation group 5	protein-coding
mm_144210.1	chr18	9722532	9722536	+	1	NA	intron (NM_130449, intron 2 of 9)	intron (NM_130449, intron 2 of 9)	14886	NM_130449	140792	Mm.218571	NM_130449	ENSMUSG00000036103	Colec12	CL-P1|SRCL|Scara4	collectin sub-family member 12	protein-coding
mm_86738.1	chr10	19141741	19141764	+	1	NA	promoter-TSS (NR_038021)	promoter-TSS (NR_038021)	3	NR_038021	100504265	Mm.383417	NR_038021		Gm20139	-	predicted gene, 20139	ncRNA
mm_52163.1	chr6	98275463	98275473	+	1	NA	intron (NM_001128092, intron 2 of 3)	intron (NM_001128092, intron 2 of 3)	67286	NM_001128092	330390	Mm.484161	NM_001128092	ENSMUSG00000090667	Gm765	-	predicted gene 765	protein-coding
mm_112115.1	chr12	112802647	112802665	-	1	NA	Intergenic	CpG	-6319	NM_145450	217887	Mm.186678	NM_145450	ENSMUSG00000037594	BC022687	AW050009|C130001I08Rik|Flj20080	cDNA sequence BC022687	protein-coding
mm_21968.1	chr2	167301479	167301487	-	1	NA	exon (NM_019835, exon 9 of 9)	exon (NM_019835, exon 9 of 9)	47695	NM_019835	56336	Mm.200886	NM_019835	ENSMUSG00000017929	B4galt5	9430078I07Rik|AW049941|AW539721	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 5	protein-coding
mm_77784.1	chr9	3025473	3025490	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	13262	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_104820.1	chr11	99001054	99001070	-	1	NA	exon (NM_011623, exon 26 of 36)	exon (NM_011623, exon 26 of 36)	-18046	NM_178596	353155	Mm.453253	NM_178596	ENSMUSG00000047197	Gjd3	Gja11|Gjc1|cx30.2	gap junction protein, delta 3	protein-coding
mm_44386.1	chr5	17828898	17828944	-	1	NA	5' UTR (NM_001159558, exon 4 of 16)	5' UTR (NM_001159558, exon 4 of 16)	6975	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_2209.1	chr1	89603225	89603260	+	1	NA	intron (NM_001037136, intron 1 of 16)	intron (NM_001037136, intron 1 of 16)	80650	NR_015540	74403	Mm.444291	NR_015540		4933400F21Rik	1700091C04Rik|4930565K10Rik	RIKEN cDNA 4933400F21 gene	ncRNA
mm_77772.1	chr9	3015270	3015302	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	23457	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_61160.1	chr7	58755380	58755391	+	1	NA	intron (NM_009728, intron 2 of 20)	intron (NM_009728, intron 2 of 20)	97183	NM_009728	11982	Mm.135129	NM_009728	ENSMUSG00000025324	Atp10a	Atp10c|pfatp	ATPase, class V, type 10A	protein-coding
mm_64412.1	chr7	142533044	142533054	+	1	NA	promoter-TSS (NM_011288)	promoter-TSS (NM_011288)	-68	NM_011288	19935	Mm.12144	NM_011288	ENSMUSG00000037772	Mrpl23	L23mrp|Rpl23|Rpl23l	mitochondrial ribosomal protein L23	protein-coding
mm_124500.1	chr14	121879496	121879523	-	1	NA	promoter-TSS (NR_130999)	promoter-TSS (NR_130999)	-101	NR_130999	78312	Mm.188743	NR_130999	ENSMUSG00000102112	1810041H14Rik	-	RIKEN cDNA 1810041H14 gene	ncRNA
mm_158725.1	chrX	163761294	163761315	-	1	NA	promoter-TSS (NM_028842)	promoter-TSS (NM_028842)	28	NM_028842	74264	Mm.39304	NM_028842	ENSMUSG00000083695	Rnf138rt1	-	ring finger protein 138, retrogene 1	protein-coding
mm_34926.1	chr4	155813115	155813124	+	1	NA	intron (NM_207678, intron 1 of 10)	intron (NM_207678, intron 1 of 10)	630	NM_207678	56036	Mm.23492	NM_018856	ENSMUSG00000029068	Ccnl2	1700010A01Rik|1810019L15Rik|2010319M22Rik|AA409936|AW261738|Ania-6b|HCLA-150|Pcee|SB138	cyclin L2	protein-coding
mm_167161.1	chr7	135357765	135357766	+	1	NA	Intergenic	Intergenic	-52602	NM_183193	270004	Mm.132547	NM_183193	ENSMUSG00000048377	Foxi2	B130055A05Rik	forkhead box I2	protein-coding
mm_170081.1	chr17	34546457	34546462	+	1	NA	Intergenic	IAP1-MM_LTR|LTR|ERVK	-17836	NM_010929	18132	Mm.173813	NM_010929	ENSMUSG00000015468	Notch4	Int-3|Int3|N4	notch 4	protein-coding
mm_12540.1	chr2	72297864	72297874	+	1	NA	intron (NM_023057, intron 1 of 19)	intron (NM_023057, intron 1 of 19)	12168	NM_178084	65964	Mm.304143	NM_023057	ENSMUSG00000004085	Map3k20	AV006891|B230120H23Rik|MLTK|MLTKalpha|MLTKbeta|Zak	mitogen-activated protein kinase kinase kinase 20	protein-coding
mm_160736.1	chr10	79550424	79550424	-	1	NA	intron (NM_001316699, intron 1 of 13)	intron (NM_001316699, intron 1 of 13)	4704	NM_001316699	70427	Mm.334193	NM_027422	ENSMUSG00000042570	Mier2	2700087H15Rik|mKIAA1193	MIER family member 2	protein-coding
mm_144824.1	chr18	36344577	36344589	+	1	NA	Intergenic	Intergenic	-4041	NM_001081365	66060	Mm.272527	NM_001081365	ENSMUSG00000046727	Cystm1	0610010O12Rik	cysteine-rich transmembrane module containing 1	protein-coding
mm_83663.1	chr9	49570825	49570850	-	1	NA	intron (NM_001081445, intron 1 of 17)	intron (NM_001081445, intron 1 of 17)	52549	NR_029465	100036537	Mm.437541	NR_029465	ENSMUSG00000079564	Gm11149	ENSMUSG00000060603|ENSMUSG00000079564	predicted gene 11149	ncRNA
mm_64909.1	chr7	16052808	16052827	-	1	NA	Intergenic	CpG	-19028	NM_001347559	666528	Mm.290718	NM_001099277	ENSMUSG00000078796	Zfp541	EG666528|Znf541	zinc finger protein 541	protein-coding
mm_112376.1	chr12	119227808	119227817	-	1	NA	intron (NM_177290, intron 1 of 13)	intron (NM_177290, intron 1 of 13)	10464	NM_177290	320910	Mm.217000	NM_177290	ENSMUSG00000025321	Itgb8	4832412O06Rik	integrin beta 8	protein-coding
mm_16616.1	chr2	5538682	5538716	-	1	NA	intron (NM_177343, intron 2 of 10)	intron (NM_177343, intron 2 of 10)	137347	NM_001290376	227541	Mm.191949	NM_177343	ENSMUSG00000039145	Camk1d	A630059D12Rik|CKLiK|CaMKIdelta|E030025C11Rik|mCKLiK	calcium/calmodulin-dependent protein kinase ID	protein-coding
mm_123507.1	chr14	66235564	66235584	-	1	NA	intron (NM_001162365, intron 1 of 30)	intron (NM_001162365, intron 1 of 30)	-22022	NM_001162366	19229	Mm.21613	NM_172498	ENSMUSG00000059456	Ptk2b	CADTK|CAKB|CAKbeta|E430023O05Rik|FADK2|FAK2|PYK2|Raftk	PTK2 protein tyrosine kinase 2 beta	protein-coding
mm_34888.1	chr4	155601374	155601413	+	1	NA	promoter-TSS (NM_177186)	promoter-TSS (NM_177186)	-23	NM_177186	320541	Mm.306018	NM_177186	ENSMUSG00000042202	Slc35e2	A530082C11Rik|AI957035	solute carrier family 35, member E2	protein-coding
mm_42973.1	chr5	123142188	123142229	+	1	NA	promoter-TSS (NM_001040398)	promoter-TSS (NM_001040398)	15	NM_001040398	208043	Mm.250391	NM_177581	ENSMUSG00000038384	Setd1b	AA516740|BC035291|KMT2G|mKIAA1076	SET domain containing 1B	protein-coding
mm_81865.1	chr9	118947328	118947330	+	1	NA	intron (NM_133710, intron 1 of 7)	intron (NM_133710, intron 1 of 7)	20793	NM_133710	69274	Mm.439928	NM_133710	ENSMUSG00000047409	Ctdspl	2810418J22Rik|AI426263|HYA22|SCP3	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase-like	protein-coding
mm_26023.1	chr3	135438723	135438780	+	1	NA	promoter-TSS (NM_025356)	promoter-TSS (NM_025356)	-8	NM_025356	66105	Mm.49884	NM_025356	ENSMUSG00000078578	Ube2d3	1100001F19Rik|9430029A22Rik|AA414951	ubiquitin-conjugating enzyme E2D 3	protein-coding
mm_95364.1	chr11	48910579	48910580	+	1	NA	intron (NM_001045540, intron 2 of 2)	L1VL2|LINE|L1	-8427	NM_001024230	432555	Mm.338931	NM_001024230	ENSMUSG00000058163	Gm5431	EG432555|Irgb9b8	predicted gene 5431	protein-coding
mm_127894.1	chr15	9155406	9155408	-	1	NA	promoter-TSS (NM_001285980)	promoter-TSS (NM_001285980)	18	NM_001285980	27401	Mm.35584	NM_013787	ENSMUSG00000054115	Skp2	4930500A04Rik|FBXL1|FWD1|p45	S-phase kinase-associated protein 2 (p45)	protein-coding
mm_128717.1	chr15	63998175	63998185	-	1	NA	intron (NM_144846, intron 1 of 11)	CpG	62268	NM_144846	223601	Mm.246108	NM_144846	ENSMUSG00000022378	Fam49b	0910001A06Rik|AW122079	family with sequence similarity 49, member B	protein-coding
mm_127816.1	chr15	5108382	5108405	-	1	NA	intron (NM_001163138, intron 1 of 3)	intron (NM_001163138, intron 1 of 3)	140	NM_001163138	239319	Mm.31252	NM_001163138	ENSMUSG00000041849	Card6	D730008L15	caspase recruitment domain family, member 6	protein-coding
mm_93138.1	chr10	92164671	92164679	-	1	NA	non-coding (NR_028262, exon 2 of 13)	non-coding (NR_028262, exon 2 of 13)	503	NR_028262	110333	Mm.429764	NR_028262		Rmst	100041799|AI853140|C230053E11Rik|D930049J19Rik|Dmt2|Gm3515|M2|Ncrms	rhabdomyosarcoma 2 associated transcript (non-coding RNA)	ncRNA
mm_33991.1	chr4	137862271	137862321	+	1	NA	promoter-TSS (NM_199307)	promoter-TSS (NM_199307)	59	NM_199307	230857	Mm.401062	NM_199307	ENSMUSG00000057530	Ece1	AW322500|ECE-1|ECE-1a|ECE-1b|ECE-1d	endothelin converting enzyme 1	protein-coding
mm_164761.1	chr17	85618354	85618354	-	1	NA	promoter-TSS (NR_015387)	promoter-TSS (NR_015387)	42	NR_038084	100043902	Mm.150838	NR_015385	ENSMUSG00000093460	Six3os1	D17Mgi26|E130112H22Rik|Rncr1|Six3os	SIX homeobox 3, opposite strand 1	ncRNA
mm_12185.1	chr2	65238785	65238804	+	1	NA	promoter-TSS (NM_177025)	promoter-TSS (NM_177025)	-168	NM_027225	319876	Mm.34159	NM_027225	ENSMUSG00000034903	Cobll1	1810047P18Rik|Coblr1|D430044D16Rik	Cobl-like 1	protein-coding
mm_135520.1	chr16	48871899	48871909	-	1	NA	promoter-TSS (NM_181596)	promoter-TSS (NM_181596)	-704	NM_181596	245195	Mm.231288	NM_181596	ENSMUSG00000022651	Retnlg	Fizz3|Relmg|Xcp1	resistin like gamma	protein-coding
mm_125203.1	chr15	33083111	33083147	+	1	NA	promoter-TSS (NM_018755)	promoter-TSS (NM_018755)	0	NM_018755	54381	Mm.158251	NM_018755	ENSMUSG00000039007	Cpq	1190003P12Rik|2610034C17Rik|Hls2|Lal-1|Pgcp	carboxypeptidase Q	protein-coding
mm_140640.1	chr17	12675699	12675714	-	1	NA	5' UTR (NM_009202, exon 1 of 11)	5' UTR (NM_009202, exon 1 of 11)	132	NM_009202	20517	Mm.594	NM_009202	ENSMUSG00000023829	Slc22a1	Lx1|Oct1|Orct|Orct1	solute carrier family 22 (organic cation transporter), member 1	protein-coding
mm_11625.1	chr2	34774681	34774746	+	1	NA	exon (NM_001163434, exon 7 of 9)	exon (NM_001163434, exon 7 of 9)	2623	NM_022310	14828	Mm.330160	NM_022310	ENSMUSG00000026864	Hspa5	AL022860|AU019543|Bip|D2Wsu141e|D2Wsu17e|Grp78|Hsce70|SEZ-7|Sez7|baffled|mBiP	heat shock protein 5	protein-coding
mm_127683.1	chr15	102966740	102966751	+	1	NA	promoter-TSS (NM_010462)	promoter-TSS (NM_010462)	-51	NM_010462	209448	Mm.31665	NM_010462	ENSMUSG00000022484	Hoxc10	AI506621|Hox-3.6	homeobox C10	protein-coding
mm_119302.1	chr14	34714926	34714935	+	1	NA	intron (NM_001004436, intron 4 of 18)	L1MC5|LINE|L1	41002	NM_001301330	218914	Mm.27957	NM_001004436	ENSMUSG00000041408	Wapl	A530089A20Rik|BC037674|DIF-2|FOE|Wapal	WAPL cohesin release factor	protein-coding
mm_152261.1	chr19	8786432	8786440	-	1	NA	promoter-TSS (NM_001177798)	promoter-TSS (NM_001177798)	-19	NM_001177798	225895	Mm.220886	NM_146092	ENSMUSG00000003680	Taf6l	2810417N14Rik|BB223262|C530024J06Rik|Paf65a	TATA-box binding protein associated factor 6 like	protein-coding
mm_36137.1	chr4	59350010	59350022	-	1	NA	intron (NM_001163288, intron 11 of 16)	intron (NM_001163288, intron 11 of 16)	88617	NM_001163288	634731	Mm.483589	NM_001163288	ENSMUSG00000038578	Susd1	A530080P10|Gm12528|OTTMUSG00000007332	sushi domain containing 1	protein-coding
mm_123191.1	chr14	57925393	57925422	-	1	NA	intron (NM_028643, intron 8 of 11)	B4A|SINE|B4	-35145	NM_029492	75965	Mm.29044	NM_029492	ENSMUSG00000021969	Zdhhc20	4930542A17Rik|5033406L14Rik|AI448102|B230110O18Rik|ENSMUSG00000055956|HK11	zinc finger, DHHC domain containing 20	protein-coding
mm_1486.1	chr1	71651576	71651604	+	1	NA	exon (NM_001276413, exon 2 of 44)	exon (NM_001276413, exon 2 of 44)	1644	NM_010233	14268	Mm.193099	NM_010233	ENSMUSG00000026193	Fn1	E330027I09|Fn|Fn-1	fibronectin 1	protein-coding
mm_80684.1	chr9	91368812	91368828	+	1	NA	promoter-TSS (NM_009576)	promoter-TSS (NM_009576)	-152	NM_009576	22774	Mm.8062	NM_009576	ENSMUSG00000036972	Zic4	-	zinc finger protein of the cerebellum 4	protein-coding
mm_99716.1	chr11	106262217	106262238	+	1	NA	TTS (NM_031878)	TTS (NM_031878)	5405	NM_031878	83796	Mm.21772	NM_031878	ENSMUSG00000078619	Smarcd2	AW322457|Baf60b	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2	protein-coding
mm_25709.1	chr3	122511273	122511284	+	1	NA	exon (NM_013867, exon 6 of 12)	exon (NM_013867, exon 6 of 12)	30403	NR_106117	102465764		NR_106117	ENSMUSG00000104773	Mir7657	mmu-mir-7657	microRNA 7657	ncRNA
mm_161594.1	chr16	36131244	36131244	-	1	NA	promoter-TSS (NM_001033239)	promoter-TSS (NM_001033239)	-55	NM_001033239	209294	Mm.300592	NM_001033239	ENSMUSG00000034362	Csta1	Csta	cystatin A1	protein-coding
mm_34609.1	chr4	150281574	150281633	+	1	NA	promoter-TSS (NM_001085492)	promoter-TSS (NM_001085492)	-313	NM_001085492	68703	Mm.291274	NM_001085492	ENSMUSG00000039852	Rere	1110033A15Rik|AI414665|ARG|ARP|ATN1L|AW742570|Atr2|DNB1|eye<m03Jus>|eyes3|mKIAA0458	arginine glutamic acid dipeptide (RE) repeats	protein-coding
mm_171899.1	chr5	41832809	41832826	-	1	NA	exon (NM_001081422, exon 4 of 27)	exon (NM_001081422, exon 4 of 27)	11498	NM_001310601	665775	Mm.158726	NM_001081422	ENSMUSG00000061755	Bod1l	A230054D04Rik|AI853319|FAM44A|mKIAA1327	biorientation of chromosomes in cell division 1-like	protein-coding
mm_56290.1	chr6	91493138	91493162	-	1	NA	exon (NM_009531, exon 12 of 16)	exon (NM_009531, exon 12 of 16)	19399	NM_028766	74122	Mm.38801	NM_028766	ENSMUSG00000030095	Tmem43	1200015A22Rik|LUMA	transmembrane protein 43	protein-coding
mm_101914.1	chr11	49712734	49712744	-	1	NA	promoter-TSS (NM_212484)	promoter-TSS (NM_212484)	-17	NM_212484	104625	Mm.247113	NM_212484	ENSMUSG00000020362	Cnot6	CCR4	CCR4-NOT transcription complex, subunit 6	protein-coding
mm_87440.1	chr10	51480840	51480850	+	1	NA	intron (NM_001291892, intron 1 of 8)	intron (NM_001291892, intron 1 of 8)	233	NM_001291892	14727	Mm.439661	NM_008147	ENSMUSG00000062593	Lilr4b	Gp49a|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4B	protein-coding
mm_55192.1	chr6	52191384	52191393	-	1	NA	exon (NM_008265, exon 1 of 2)	exon (NM_008265, exon 1 of 2)	315	NM_008265	15401	Mm.439647	NM_008265	ENSMUSG00000000942	Hoxa4	AV206827|Hox-1.4	homeobox A4	protein-coding
mm_99405.1	chr11	102248843	102248888	+	1	NA	promoter-TSS (NM_153544)	promoter-TSS (NM_153544)	-17	NM_153544	217216	Mm.247335	NM_153544	ENSMUSG00000034773	BC030867	-	cDNA sequence BC030867	protein-coding
mm_116397.1	chr13	41220334	41220344	-	1	NA	promoter-TSS (NM_019423)	promoter-TSS (NM_019423)	64	NM_019423	54326	Mm.2567	NM_019423	ENSMUSG00000021364	Elovl2	AI317360|Ssc2	elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 2	protein-coding
mm_11312.1	chr2	30286407	30286442	+	1	NA	promoter-TSS (NM_177648)	promoter-TSS (NM_177648)	-9	NM_198304	227699	Mm.330119	NM_198304	ENSMUSG00000052533	Nup188	BC025526|U89435|mKIAA0169	nucleoporin 188	protein-coding
mm_72085.1	chr8	71579264	71579300	+	1	NA	intron (NM_011977, intron 3 of 13)	intron (NM_011977, intron 3 of 13)	10355	NM_011977	26457	Mm.38165	NM_011977	ENSMUSG00000031808	Slc27a1	FATP1|Fatp	solute carrier family 27 (fatty acid transporter), member 1	protein-coding
mm_64079.1	chr7	140941551	140941615	+	1	NA	promoter-TSS (NM_145387)	promoter-TSS (NM_145387)	2	NM_145387	212974	Mm.260139	NM_145387	ENSMUSG00000062031	Pgghg	5730511L01Rik|Athl1|BC023151	protein glucosylgalactosylhydroxylysine glucosidase	protein-coding
mm_117914.1	chr13	99431433	99431443	-	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-18612	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_88803.1	chr10	80752572	80752607	+	1	NA	Intergenic	Intergenic	-2617	NM_199322	208266	Mm.152371	NM_199322	ENSMUSG00000061589	Dot1l	A630076O07|AW907654|Dot1|KMT4|mDot1	DOT1-like, histone H3 methyltransferase (S. cerevisiae)	protein-coding
mm_153265.1	chr19	37077438	37077449	-	1	NA	intron (NM_001290826, intron 7 of 10)	intron (NM_001290826, intron 7 of 10)	-96400	NR_045329	319931	Mm.446730	NR_045329	ENSMUSG00000097591	A330032B11Rik	-	RIKEN cDNA A330032B11 gene	ncRNA
mm_140522.1	chr17	6122161	6122203	-	1	NA	intron (NM_001103181, intron 1 of 13)	intron (NM_001103181, intron 1 of 13)	15352	NM_001103181	68842	Mm.449307	NM_054040	ENSMUSG00000034377	Tulp4	1110057P05Rik|2210038L17Rik|Tusp	tubby like protein 4	protein-coding
mm_64043.1	chr7	140834912	140834947	+	1	NA	promoter-TSS (NM_029821)	promoter-TSS (NM_029821)	-209	NM_001347605	76974	Mm.272359	NM_029821	ENSMUSG00000025481	Urah	1190003J15Rik|2810420C16Rik	urate (5-hydroxyiso-) hydrolase	protein-coding
mm_80138.1	chr9	70729911	70729912	+	1	NA	intron (NM_007399, intron 4 of 15)	intron (NM_007399, intron 4 of 15)	50929	NM_007399	11487	Mm.3037	NM_007399	ENSMUSG00000054693	Adam10	1700031C13Rik|MADM|kuz|kuzbanian	a disintegrin and metallopeptidase domain 10	protein-coding
mm_27360.1	chr3	50429835	50429838	-	1	NA	intron (NM_011990, intron 3 of 11)	intron (NM_011990, intron 3 of 11)	13777	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_82699.1	chr9	22445530	22445547	-	1	NA	TTS (NM_026739)	TTS (NM_026739)	22818	NM_018739	55934	Mm.38235	NM_018739	ENSMUSG00000032239	Rp9	PAP-1|Rp9h	retinitis pigmentosa 9 (human)	protein-coding
mm_115444.1	chr13	117947122	117947123	+	1	NA	intron (NM_010408, intron 6 of 7)	intron (NM_010408, intron 6 of 7)	-227111	NR_045508	71100	Mm.414841	NR_045508	ENSMUSG00000079048	4933413L06Rik	-	RIKEN cDNA 4933413L06 gene	ncRNA
mm_18575.1	chr2	65567506	65567527	-	1	NA	promoter-TSS (NM_018732)	promoter-TSS (NM_018732)	-24	NM_018732	20269	Mm.330256	NM_018732	ENSMUSG00000057182	Scn3a	Gm1000|Nav1.3	sodium channel, voltage-gated, type III, alpha	protein-coding
mm_24782.1	chr3	95540268	95540318	+	1	NA	intron (NM_001267695, intron 3 of 7)	B2_Mm1t|SINE|B2	13507	NM_001267695	13040	Mm.3619	NM_021281	ENSMUSG00000038642	Ctss	Cats	cathepsin S	protein-coding
mm_25378.1	chr3	107211449	107211456	+	1	NA	exon (NM_001111143, exon 9 of 9)	exon (NM_001111143, exon 9 of 9)	10280	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_150946.1	chr19	46308836	46308846	+	1	NA	intron (NM_001177369, intron 12 of 22)	intron (NM_001177369, intron 12 of 22)	2911	NM_001177370	18034	Mm.102365	NM_019408	ENSMUSG00000025225	Nfkb2	NF-kappaB2|lyt|p49|p49/p100|p50B|p52	nuclear factor of kappa light polypeptide gene enhancer in B cells 2, p49/p100	protein-coding
mm_141462.1	chr17	30576242	30576312	-	1	NA	promoter-TSS (NM_027060)	promoter-TSS (NM_027060)	10	NM_172618	224671	Mm.41220	NM_027060	ENSMUSG00000062202	Btbd9	1700023F20Rik|4930402L05|AI464421	BTB (POZ) domain containing 9	protein-coding
mm_5317.1	chr1	22783511	22783535	-	1	NA	intron (NM_001012623, intron 1 of 14).2	intron (NM_001012623, intron 1 of 14).2	22201	NM_001012625	116837	Mm.60061	NM_053270	ENSMUSG00000041670	Rims1	C030033M19Rik|RIM1|RIM1a|RIM1alpha|Rab3ip1|Rim|Serg1|mKIAA0340	regulating synaptic membrane exocytosis 1	protein-coding
mm_63231.1	chr7	126459647	126459689	+	1	NA	exon (NM_007504, exon 5 of 23)	exon (NM_007504, exon 5 of 23)	3405	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_108032.1	chr12	73741942	73741979	+	1	NA	intron (NM_001313977, intron 11 of 14)	intron (NM_001313977, intron 11 of 14)	157164	NM_008856	18755	Mm.341677	NM_008856	ENSMUSG00000021108	Prkch	Pkch	protein kinase C, eta	protein-coding
mm_122743.1	chr14	54149249	54149259	-	1	NA	Intergenic	Intergenic	104675	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_95975.1	chr11	58961911	58961933	+	1	NA	exon (NM_001318003, exon 1 of 1)	exon (NM_001318003, exon 1 of 1)	211	NM_001318003	382523		NM_001318003		Gm12260	H3t|OTTMUSG00000005773	predicted gene 12260	protein-coding
mm_2738.1	chr1	128256182	128256203	+	1	NA	exon (NM_026390, exon 4 of 13)	exon (NM_026390, exon 4 of 13)	12011	NM_026390	67812	Mm.293321	NM_026390	ENSMUSG00000026353	Ubxn4	1300013G12Rik|Ubxd2|mKIAA0242	UBX domain protein 4	protein-coding
mm_127842.1	chr15	6874308	6874318	-	1	NA	promoter-TSS (NM_011019)	promoter-TSS (NM_011019)	0	NM_011019	18414	Mm.10760	NM_011019	ENSMUSG00000022146	Osmr	OSMRB	oncostatin M receptor	protein-coding
mm_6399.1	chr1	72861662	72861672	-	1	NA	3' UTR (NM_010518, exon 4 of 4)	3' UTR (NM_010518, exon 4 of 4)	13198	NM_010518	16011	Mm.405761	NM_010518	ENSMUSG00000026185	Igfbp5	AI256729|AW208790|IGFBP-5|IGFBP-5P	insulin-like growth factor binding protein 5	protein-coding
mm_5214.1	chr1	13660477	13660554	-	1	NA	promoter-TSS (NM_145381)	promoter-TSS (NM_145381)	-6	NM_145381	212442	Mm.89572	NM_145381	ENSMUSG00000025937	Lactb2	Cgi-83|E430032H21Rik	lactamase, beta 2	protein-coding
mm_44510.1	chr5	24266716	24266752	-	1	NA	Intergenic	Intergenic	9206	NR_030454	735274		NR_030454	ENSMUSG00000106252	Mir684-1	Mirn684-1	microRNA 684-1	ncRNA
mm_139492.1	chr17	56134269	56134282	+	1	NA	promoter-TSS (NM_013662)	promoter-TSS (NM_013662)	-423	NM_013662	20359	Mm.8029	NM_013662	ENSMUSG00000001227	Sema6b	Sema|Seman|VIb|semaZ	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B	protein-coding
mm_101887.1	chr11	48992306	48992320	-	1	NA	promoter-TSS (NM_011579)	promoter-TSS (NM_011579)	-67	NM_011579	21822	Mm.15793	NM_011579	ENSMUSG00000078922	Tgtp1	Gtp2|Irgb6|Mg21|Tgtp	T cell specific GTPase 1	protein-coding
mm_80402.1	chr9	77636537	77636547	+	1	NA	promoter-TSS (NM_172925)	promoter-TSS (NM_172925)	-190	NM_172925	244923	Mm.138238	NM_172925	ENSMUSG00000044938	Klhl31	9830147P19Rik|D930047P17Rik|Kbtbd1	kelch-like 31	protein-coding
mm_40439.1	chr5	53590722	53590722	+	1	NA	exon (NM_001080927, exon 1 of 11)	exon (NM_001080927, exon 1 of 11)	236	NM_001080927	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_41246.1	chr5	88782030	88782040	+	1	NA	3' UTR (NM_007832, exon 7 of 7)	3' UTR (NM_007832, exon 7 of 7)	17022	NM_007832	13178	Mm.298892	NM_007832	ENSMUSG00000029366	Dck	-	deoxycytidine kinase	protein-coding
mm_57756.1	chr6	129229238	129229245	-	1	NA	Intergenic	Intergenic	8804	NR_040265	76432	Mm.261738	NR_040265	ENSMUSG00000097354	2310001H17Rik	AI646108	RIKEN cDNA 2310001H17 gene	ncRNA
mm_88961.1	chr10	81393831	81393841	+	1	NA	exon (NM_001099917, exon 2 of 4)	exon (NM_001099917, exon 2 of 4)	772	NM_001099917	72273	Mm.253147	NM_001099917	ENSMUSG00000078439	Smim24	2210404O07Rik	small integral membrane protein 24	protein-coding
mm_9781.1	chr1	181211717	181211796	-	1	NA	5' UTR (NM_145514, exon 1 of 14)	5' UTR (NM_145514, exon 1 of 14)	222	NM_145514	226757	Mm.289082	NM_145514	ENSMUSG00000038733	Wdr26	1600024A01Rik|AA693241|AI447817|AU044014|C77982|Gid7	WD repeat domain 26	protein-coding
mm_112784.1	chr13	20098187	20098189	+	1	NA	intron (NM_080288, intron 1 of 21)	intron (NM_080288, intron 1 of 21)	7681	NM_080288	140580	Mm.342392	NM_080288	ENSMUSG00000041112	Elmo1	6330578D22Rik|C230095H21Rik|CED-12	engulfment and cell motility 1	protein-coding
mm_90212.1	chr10	120787257	120787264	+	1	NA	intron (NM_177092, intron 6 of 6)	intron (NM_177092, intron 6 of 6)	21528	NR_038003	70874	Mm.427286	NR_038000	ENSMUSG00000044544	4921513I03Rik	-	RIKEN cDNA 4921513I03 gene	ncRNA
mm_13147.1	chr2	92246208	92246226	+	1	NA	intron (NM_001346704, intron 6 of 18)	intron (NM_001346704, intron 6 of 18)	24655	NM_001109690	192285	Mm.330408	NM_138755	ENSMUSG00000058318	Phf21a	80kDa|Bhc|Bhc80|D030065N23Rik|PFTF1	PHD finger protein 21A	protein-coding
mm_25806.1	chr3	127789867	127789877	+	1	NA	promoter-TSS (NM_145133)	promoter-TSS (NM_145133)	-41	NM_145133	211550	Mm.31852	NM_145133	ENSMUSG00000046688	Tifa	T2bp	TRAF-interacting protein with forkhead-associated domain	protein-coding
mm_31847.1	chr4	74259646	74259662	+	1	NA	intron (NM_144787, intron 1 of 21)	RMER5|LTR|ERV1	7775	NM_144787	76804	Mm.209059	NM_144787	ENSMUSG00000028397	Kdm4c	2410141F18Rik|AA517467|Gasc1|Jmjd2c	lysine (K)-specific demethylase 4C	protein-coding
mm_172685.1	chr8	57183548	57183566	+	1	NA	Intergenic	L1Md_T|LINE|L1	137302	NR_110474	102636514		NR_110474	ENSMUSG00000100510	Uph	-	upperhand	ncRNA
mm_56958.1	chr6	120037888	120037914	-	1	NA	5' UTR (NM_001185020, exon 1 of 26)	5' UTR (NM_001185020, exon 1 of 26)	754	NM_001199083	232341	Mm.333349	NM_198703	ENSMUSG00000045962	Wnk1	6430573H23Rik|EG406236|Hsn2|Prkwnk1|mKIAA0344	WNK lysine deficient protein kinase 1	protein-coding
mm_100063.1	chr11	115334789	115334849	+	1	NA	promoter-TSS (NM_027132)	promoter-TSS (NM_027132)	85	NM_027132	69602	Mm.101844	NM_027132	ENSMUSG00000018862	Otop3	2310011E08Rik	otopetrin 3	protein-coding
mm_155846.1	chrX	101266887	101266903	+	1	NA	intron (NM_013563, intron 4 of 7)	intron (NM_013563, intron 4 of 7)	1360	NM_001308535	16186	Mm.2923	NM_013563	ENSMUSG00000031304	Il2rg	CD132|[g]c|gamma(c)|gc|p64	interleukin 2 receptor, gamma chain	protein-coding
mm_132484.1	chr16	36887339	36887357	+	1	NA	exon (NM_030035, exon 3 of 22)	exon (NM_030035, exon 3 of 22)	2337	NM_030035	224139	Mm.244815	NM_030035	ENSMUSG00000034243	Golgb1	4930428L02Rik|628101|6330407A06Rik|AU042952|C130074L01Rik|F730017E11Rik|Gm6840|mKIAA4151	golgi autoantigen, golgin subfamily b, macrogolgin 1	protein-coding
mm_141889.1	chr17	34861169	34861179	-	1	NA	exon (NM_008198, exon 3 of 18)	exon (NM_008198, exon 3 of 18)	1340	NM_001142706	14962	Mm.653	NM_008198	ENSMUSG00000090231	Cfb	AI195813|AI255840|B|Bf|C2|Fb|H2-Bf	complement factor B	protein-coding
mm_64235.1	chr7	141697188	141697195	+	1	NA	exon (NM_023566, exon 16 of 46)	exon (NM_023566, exon 16 of 46)	6851	NM_023566	17831	Mm.2041	NM_023566		Muc2	2010015E03Rik|MCM|wnn	mucin 2	protein-coding
mm_69430.1	chr7	132813681	132813702	-	1	NA	promoter-TSS (NM_212473)	promoter-TSS (NM_212473)	-495	NM_212473	77938	Mm.225649	NM_175268	ENSMUSG00000030956	Fam53b	A930008G19Rik|mKIAA0140	family with sequence similarity 53, member B	protein-coding
mm_134785.1	chr16	23988601	23988607	-	1	NA	promoter-TSS (NM_009744)	promoter-TSS (NM_009744)	8	NM_009744	12053	Mm.347398	NM_009744	ENSMUSG00000022508	Bcl6	Bcl5	B cell leukemia/lymphoma 6	protein-coding
mm_118166.1	chr13	105294658	105294666	-	1	NA	Intergenic	Intergenic	-1648	NM_027934	71816	Mm.317015	NM_027934	ENSMUSG00000021720	Rnf180	3110001E11Rik|Rines	ring finger protein 180	protein-coding
mm_154610.1	chrX	7651983	7651996	+	1	NA	3' UTR (NM_009305, exon 7 of 7)	3' UTR (NM_009305, exon 7 of 7)	-5390	NM_001290624	54630	Mm.232232	NM_175097	ENSMUSG00000031145	Prickle3	Lmo6|Sfc16	prickle planar cell polarity protein 3	protein-coding
mm_112951.1	chr13	21166179	21166183	+	1	NA	Intergenic	MT2B1|LTR|ERVL	-13750	NM_009054	19720	Mm.314056	NM_009054	ENSMUSG00000021326	Trim27	AW538890|Gm19403|Rfp	tripartite motif-containing 27	protein-coding
mm_149150.1	chr19	9010616	9010635	+	1	NA	exon (NM_009643, exon 5 of 5)	exon (NM_009643, exon 5 of 5)	-7279	NR_105786	102465190		NR_105786	ENSMUSG00000099308	Mir6367	Gm27467|mmu-mir-6367	microRNA 6367	ncRNA
mm_140112.1	chr17	78840960	78840988	+	1	NA	exon (NM_181649, exon 6 of 10)	exon (NM_181649, exon 6 of 10)	5458	NM_181649	53951	Mm.220253	NM_181649	ENSMUSG00000050668	Gpatch11	2310002B06Rik|C80922|Ccdc75|L26697	G patch domain containing 11	protein-coding
mm_13640.1	chr2	114048175	114048208	+	1	NA	exon (NM_009608, exon 6 of 7)	exon (NM_009608, exon 6 of 7)	4684	NM_009608	11464	Mm.686	NM_009608	ENSMUSG00000068614	Actc1	Actc-1	actin, alpha, cardiac muscle 1	protein-coding
mm_167316.1	chr8	66386338	66386346	+	1	NA	promoter-TSS (NM_001166375)	promoter-TSS (NM_001166375)	41	NM_001166375	72925	Mm.380457	NM_175188	ENSMUSG00000036469	March1	2900024D24Rik|BB085186	membrane-associated ring finger (C3HC4) 1	protein-coding
mm_100873.1	chr11	5950000	5950009	-	1	NA	promoter-TSS (NM_010292)	promoter-TSS (NM_010292)	77	NM_010292	103988	Mm.220358	NM_010292	ENSMUSG00000041798	Gck	GLK|Gk|Gls006|HK4|HKIV|HXKP|Hlb62|MODY2	glucokinase	protein-coding
mm_160830.1	chr11	46312826	46312826	-	1	NA	promoter-TSS (NM_001252459)	promoter-TSS (NM_001252459)	33	NM_001252459	76884	Mm.154358	NM_133769	ENSMUSG00000020340	Cyfip2	1500004I01Rik|6430511D02Rik|AA930218|AU022376|Pir121|mKIAA1168	cytoplasmic FMR1 interacting protein 2	protein-coding
mm_46855.1	chr5	113724772	113724788	-	1	NA	promoter-TSS (NR_033216)	promoter-TSS (NR_033216)	-8	NR_033216	381707	Mm.159016	NR_033216	ENSMUSG00000042184	1700069L16Rik	1700096P12Rik	RIKEN cDNA 1700069L16 gene	ncRNA
mm_88191.1	chr10	70060151	70060162	+	1	NA	Intergenic	Intergenic	-36965	NM_001111121	76551	Mm.281741	NM_001111121	ENSMUSG00000048701	Ccdc6	2810012H18Rik|AA536681|AA960498|AW061011	coiled-coil domain containing 6	protein-coding
mm_37898.1	chr4	132617890	132617938	-	1	NA	Intergenic	Intergenic	-21132	NM_210071	14050	Mm.227733	NM_010166	ENSMUSG00000028886	Eya3	AI844637	EYA transcriptional coactivator and phosphatase 3	protein-coding
mm_88784.1	chr10	80603283	80603297	+	1	NA	intron (NM_019575, intron 1 of 6)	intron (NM_019575, intron 1 of 6)	408	NM_019575	56214	Mm.273170	NM_019575	ENSMUSG00000078441	Scamp4	2410022D05Rik|AI448940|AU022392|AW742369|Sc4	secretory carrier membrane protein 4	protein-coding
mm_59971.1	chr7	30454553	30454559	+	1	NA	exon (NM_172898, exon 5 of 15)	exon (NM_172898, exon 5 of 15)	2959	NM_172898	243911	Mm.113908	NM_172898	ENSMUSG00000036915	Kirrel2	C330019F22Rik|NEPH3|NLG1	kin of IRRE like 2 (Drosophila)	protein-coding
mm_43134.1	chr5	125389329	125389339	+	1	NA	intron (NM_019639, intron 1 of 1)	CpG	683	NM_019639	22190	Mm.331	NM_019639	ENSMUSG00000008348	Ubc	2700054O04Rik|AI194771|Rps27a|TI-225|Uba52|Ubb	ubiquitin C	protein-coding
mm_93744.1	chr10	120159480	120159546	-	1	NA	intron (NM_028679, intron 8 of 11)	MLTR18_MM|LTR|ERVK	42024	NM_028679	73914	Mm.146194	NM_028679	ENSMUSG00000020227	Irak3	4833428C18Rik|AI563835|IRAK-M	interleukin-1 receptor-associated kinase 3	protein-coding
mm_63155.1	chr7	123418256	123418276	+	1	NA	exon (NM_025304, exon 7 of 11)	exon (NM_025304, exon 7 of 11)	40284	NM_025304	30949	Mm.260527	NM_025304	ENSMUSG00000030763	Lcmt1	AL033290|LCMT-1|Lcmt	leucine carboxyl methyltransferase 1	protein-coding
mm_151871.1	chr19	5798033	5798037	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	-2054	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_123646.1	chr14	68655778	68655784	-	1	NA	promoter-TSS (NM_010082)	promoter-TSS (NM_010082)	61	NM_010082	13522	Mm.117450	NM_010082	ENSMUSG00000014725	Adam28	C130072N01Rik|D430033C21Rik|Dtgn1|MDC-L|MDCL|TECADAM|eMDCII	a disintegrin and metallopeptidase domain 28	protein-coding
mm_36586.1	chr4	88418265	88418281	-	1	NA	intron (NM_025760, intron 6 of 6)	intron (NM_025760, intron 6 of 6)	20653	NM_025760	66775	Mm.386788	NM_025760	ENSMUSG00000028497	Hacd4	4933428I03Rik|Hcad4|Ptplad2	3-hydroxyacyl-CoA dehydratase 4	protein-coding
mm_99889.1	chr11	109488575	109488588	+	1	NA	intron (NM_028710, intron 3 of 13)	ID_B1|SINE|B4	-14985	NM_001029842	104681	Mm.265874	NM_134038	ENSMUSG00000041920	Slc16a6	AW743111|ESTM12|MCT 6|MCT 7|MCT6	solute carrier family 16 (monocarboxylic acid transporters), member 6	protein-coding
mm_137567.1	chr17	27825280	27825300	+	1	NA	Intergenic	RMER4B|LTR|ERVK	-4748	NM_001271511	224647	Mm.196577	NM_001033279	ENSMUSG00000056692	D17Wsu92e	AU020189|C030010A15|C80239	DNA segment, Chr 17, Wayne State University 92, expressed	protein-coding
mm_85270.1	chr9	99436584	99436609	-	1	NA	5' UTR (NM_008624, exon 1 of 6)	5' UTR (NM_008624, exon 1 of 6)	116	NM_008624	17532	Mm.2045	NM_008624	ENSMUSG00000032470	Mras	2900078C09Rik|AI326250	muscle and microspikes RAS	protein-coding
mm_150366.1	chr19	34649754	34649784	+	1	NA	3' UTR (NM_008331, exon 2 of 2)	3' UTR (NM_008331, exon 2 of 2)	8880	NM_008331	15957	Mm.439751	NM_008331	ENSMUSG00000034459	Ifit1	ISG56|Ifi56|P56	interferon-induced protein with tetratricopeptide repeats 1	protein-coding
mm_28905.1	chr3	98382380	98382421	-	1	NA	promoter-TSS (NM_172863)	promoter-TSS (NM_172863)	-81	NM_172863	242109	Mm.358911	NM_172863	ENSMUSG00000050064	Zfp697	9430053K19|AI467503|Znf697	zinc finger protein 697	protein-coding
mm_135619.1	chr16	52271760	52271770	-	1	NA	intron (NM_009655, intron 11 of 15)	Lx7|LINE|L1	181316	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_22050.1	chr2	168281097	168281118	-	1	NA	Intergenic	CpG	-11776	NM_001081134	241794	Mm.425102	NM_001081134	ENSMUSG00000074575	Kcng1	AW536275|OTTMUSG00000016048	potassium voltage-gated channel, subfamily G, member 1	protein-coding
mm_63874.1	chr7	136268319	136268337	+	1	NA	promoter-TSS (NR_102277)	promoter-TSS (NR_102277)	4	NR_102277	77383	Mm.227745	NR_102277	ENSMUSG00000110027	C030029H02Rik	-	RIKEN cDNA C030029H02 gene	ncRNA
mm_168879.1	chr12	42745801	42745801	-	1	NA	Intergenic	L1Md_T|LINE|L1	-1259744	NM_010733	16981	Mm.404786	NM_010733	ENSMUSG00000036295	Lrrn3	NLRR-3	leucine rich repeat protein 3, neuronal	protein-coding
mm_95184.1	chr11	42420759	42420779	+	1	NA	promoter-TSS (NM_001347314)	promoter-TSS (NM_001347314)	-581	NM_001347314	14401	Mm.338723	NM_008070	ENSMUSG00000007653	Gabrb2	AI834970|C030002O17Rik|C030021G16Rik|Gabrab2|Gabrb-2	gamma-aminobutyric acid (GABA) A receptor, subunit beta 2	protein-coding
mm_164789.1	chr18	12490783	12490790	+	1	NA	intron (NM_010680, intron 32 of 74)	intron (NM_010680, intron 32 of 74)	-13413	NM_001347461	16774	Mm.42012	NM_010680	ENSMUSG00000024421	Lama3	Lama3B|[a]3B	laminin, alpha 3	protein-coding
mm_20322.1	chr2	127335862	127335879	-	1	NA	promoter-TSS (NM_010090)	promoter-TSS (NM_010090)	-289	NM_010090	13537	Mm.4729	NM_010090	ENSMUSG00000027368	Dusp2	PAC1	dual specificity phosphatase 2	protein-coding
mm_14748.1	chr2	144527792	144527802	+	1	NA	promoter-TSS (NM_029763)	promoter-TSS (NM_029763)	52	NM_029763	70408	Mm.389351	NM_029763	ENSMUSG00000027427	Polr3f	2810411G20Rik|3010019O03Rik|3110032A07Rik|RPC39|RPC6	polymerase (RNA) III (DNA directed) polypeptide F	protein-coding
mm_121943.1	chr14	24081986	24081988	-	1	NA	Intergenic	Intergenic	-6890	NR_106069	102465697		NR_106069	ENSMUSG00000105723	Mir7210	mir-7210|mmu-mir-7210	microRNA 7210	ncRNA
mm_182.1	chr1	14869731	14869733	+	1	NA	Intergenic	Intergenic	49130	NM_177781	277328	Mm.186329	NM_177781	ENSMUSG00000032769	Trpa1	Anktm1|TRPA1b	transient receptor potential cation channel, subfamily A, member 1	protein-coding
mm_105623.1	chr11	106789158	106789192	-	1	NA	promoter-TSS (NM_177088)	promoter-TSS (NM_177088)	-77	NM_177088	320162	Mm.30524	NM_177088	ENSMUSG00000018372	Cep95	4732496G21Rik|AI118346|AI448335|Ccdc45|D330027A14Rik|F630025I20Rik	centrosomal protein 95	protein-coding
mm_154147.1	chr19	58454330	58454373	-	1	NA	non-coding (NR_104342, exon 2 of 12)	non-coding (NR_104342, exon 2 of 12)	1047	NM_001285457	14585	Mm.88367	NM_010279	ENSMUSG00000025089	Gfra1	AU042498	glial cell line derived neurotrophic factor family receptor alpha 1	protein-coding
mm_11544.1	chr2	32646640	32646674	+	1	NA	promoter-TSS (NM_001146350)	promoter-TSS (NM_001146350)	62	NM_001146348	13805	Mm.225297	NM_007932	ENSMUSG00000026814	Eng	AI528660|AI662476|CD105|Endo|S-endoglin	endoglin	protein-coding
mm_13959.1	chr2	121359559	121359569	+	1	NA	intron (NM_009897, intron 1 of 8)	intron (NM_009897, intron 1 of 8)	923	NM_009897	12716	Mm.252145	NM_009897	ENSMUSG00000000308	Ckmt1	Mt-CK|ScCKmit|UbCKmit|mi-CK	creatine kinase, mitochondrial 1, ubiquitous	protein-coding
mm_2909.1	chr1	132007607	132007634	+	1	NA	promoter-TSS (NM_007923)	promoter-TSS (NM_007923)	15	NM_007923	13714	Mm.254233	NM_007923	ENSMUSG00000026436	Elk4	2310011G17Rik|A130026I01Rik|BB162516|SAP-1|Sap1	ELK4, member of ETS oncogene family	protein-coding
mm_94689.1	chr11	19924404	19924458	+	1	NA	promoter-TSS (NM_033523)	promoter-TSS (NM_033523)	-11	NM_033523	114716	Mm.266627	NM_033523	ENSMUSG00000045671	Spred2	C79158	sprouty-related, EVH1 domain containing 2	protein-coding
mm_65864.1	chr7	29443551	29443552	-	1	NA	intron (NM_001081028, intron 2 of 22)	B1_Mur1|SINE|Alu	61909	NM_001081028	74206	Mm.447042	NM_001081028	ENSMUSG00000030583	Sipa1l3	2610511M17Rik	signal-induced proliferation-associated 1 like 3	protein-coding
mm_153984.1	chr19	47918922	47918930	-	1	NA	intron (NM_001001738, intron 1 of 1)	intron (NM_001001738, intron 1 of 1)	373	NM_001001738	414801	Mm.29457	NM_001001738	ENSMUSG00000044948	Itprip	4833424O12Rik|DANGER|mKIAA1754	inositol 1,4,5-triphosphate receptor interacting protein	protein-coding
mm_169613.1	chr15	3748132	3748138	-	1	NA	Intergenic	RLTR9D|LTR|ERVK	-164783	NM_010284	14600	Mm.3986	NM_010284	ENSMUSG00000055737	Ghr	GHBP|GHR/BP	growth hormone receptor	protein-coding
mm_97544.1	chr11	78924211	78924217	+	1	NA	promoter-TSS (NM_001313921)	promoter-TSS (NM_001313921)	-526	NM_001313921	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_65946.1	chr7	30417571	30417581	-	1	NA	TTS (NM_011827)	TTS (NM_011827)	2278	NM_011827	23900	Mm.379050	NM_011827	ENSMUSG00000064109	Hcst	DAP10|KAP10	hematopoietic cell signal transducer	protein-coding
mm_167210.1	chr8	3353723	3353731	+	1	NA	exon (NM_001033378, exon 1 of 11)	exon (NM_001033378, exon 1 of 11)	312	NM_001033378	319493	Mm.234565	NM_001033378	ENSMUSG00000074497	A430078G23Rik	-	RIKEN cDNA A430078G23 gene	protein-coding
mm_66025.1	chr7	30612762	30612771	-	1	NA	promoter-TSS (NM_026815)	promoter-TSS (NM_026815)	-32	NM_026815	109637	Mm.25471	NM_026815	ENSMUSG00000006313	Upk1a	1110031P12Rik|AU019298|C87192|Tspan21|Upk1	uroplakin 1A	protein-coding
mm_20188.1	chr2	122609843	122609853	-	1	NA	exon (NM_025961, exon 2 of 9)	exon (NM_025961, exon 2 of 9)	1429	NM_025961	67092	Mm.29975	NM_025961	ENSMUSG00000027199	Gatm	1810003P21Rik|AI314789|AT	glycine amidinotransferase (L-arginine:glycine amidinotransferase)	protein-coding
mm_19484.1	chr2	93046431	93046465	-	1	NA	promoter-TSS (NM_001177536)	promoter-TSS (NM_001177536)	-304	NM_001177536	100042784	Mm.102816	NM_001177536	ENSMUSG00000075028	Prdm11	8030443D09Rik|AA163972|Gm707	PR domain containing 11	protein-coding
mm_12937.1	chr2	85136344	85136354	+	1	NA	promoter-TSS (NM_011784)	promoter-TSS (NM_011784)	-11	NM_011784	23796	Mm.29368	NM_011784	ENSMUSG00000044338	Aplnr	APJ|Agtrl1|msr/apj	apelin receptor	protein-coding
mm_51107.1	chr6	67282088	67282091	+	1	NA	intron (NM_001113564, intron 7 of 7)	intron (NM_001113564, intron 7 of 7)	15110	NM_025814	66870	Mm.240490	NM_025814	ENSMUSG00000036371	Serbp1	1200009K13Rik|9330147J08Rik|AL022786|Pairbp1	serpine1 mRNA binding protein 1	protein-coding
mm_155825.1	chrX	100729837	100729846	+	1	NA	promoter-TSS (NM_023608)	promoter-TSS (NM_023608)	-6	NM_023608	71584	Mm.283495	NM_023608	ENSMUSG00000019359	Gdpd2	9130017L10Rik|Gde3|Obdpf	glycerophosphodiester phosphodiesterase domain containing 2	protein-coding
mm_172962.1	chr9	88599448	88599466	-	1	NA	promoter-TSS (NR_040766)	promoter-TSS (NR_040766)	-214	NR_040766	320692	Mm.427378	NR_040766	ENSMUSG00000097073	9430037G07Rik	-	RIKEN cDNA 9430037G07 gene	ncRNA
mm_59085.1	chr7	19691890	19691916	+	1	NA	exon (NM_001110009, exon 3 of 4)	exon (NM_001110009, exon 3 of 4)	756	NM_001110009	11812	Mm.182440	NM_007469	ENSMUSG00000040564	Apoc1	Apo-CIB|ApoC-IB|apo-CI|apoC-I	apolipoprotein C-I	protein-coding
mm_113169.1	chr13	24813493	24813505	+	1	NA	TTS (NM_024473)	TTS (NM_024473)	11842	NM_024473	79555	Mm.266668	NM_024473	ENSMUSG00000019132	BC005537	8030460C05Rik|C78201	cDNA sequence BC005537	protein-coding
mm_51945.1	chr6	91726073	91726088	+	1	NA	exon (NM_009320, exon 5 of 15)	exon (NM_009320, exon 5 of 15)	42013	NM_009320	21366	Mm.395650	NM_009320	ENSMUSG00000030096	Slc6a6	AA589629|C80501|Taut	solute carrier family 6 (neurotransmitter transporter, taurine), member 6	protein-coding
mm_133891.1	chr16	97391337	97391342	+	1	NA	intron (NM_019517, intron 1 of 8)	intron (NM_019517, intron 1 of 8)	34611	NM_019517	56175	Mm.97885	NM_019517	ENSMUSG00000040605	Bace2	1110059C24Rik|AEPLC|AI850424|ALP56|ARP1|ASP1|ASP21|BAE2|CDA13|CEAP1|DRAP	beta-site APP-cleaving enzyme 2	protein-coding
mm_63547.1	chr7	128068105	128068138	+	1	NA	intron (NM_001082960, intron 2 of 29)	intron (NM_001082960, intron 2 of 29)	5481	NM_008401	16409	Mm.262106	NM_008401	ENSMUSG00000030786	Itgam	CD11b/CD18|CR3|CR3A|Cd11b|F730045J24Rik|Ly-40|MAC1|Mac-1|Mac-1a	integrin alpha M	protein-coding
mm_135388.1	chr16	44332670	44332686	-	1	NA	5' UTR (NM_001159419, exon 1 of 26)	5' UTR (NM_001159419, exon 1 of 26)	160	NM_198034	320007	Mm.242144	NM_198034	ENSMUSG00000022696	Sidt1	AW045928|B830021E24Rik	SID1 transmembrane family, member 1	protein-coding
mm_136689.1	chr17	6828363	6828373	+	1	NA	Intergenic	Intergenic	-45588	NM_009510	22350	Mm.277812	NM_009510	ENSMUSG00000052397	Ezr	AW146364|R75297|Vil2|p81	ezrin	protein-coding
mm_161175.1	chr13	41110063	41110063	-	1	NA	promoter-TSS (NM_008104)	promoter-TSS (NM_008104)	-75	NM_008104	107889	Mm.1399	NM_008104	ENSMUSG00000021362	Gcm2	Gcm-rs1|Gcm1|Gcm1-rs2	glial cells missing homolog 2 (Drosophila)	protein-coding
mm_49294.1	chr6	17694006	17694025	+	1	NA	promoter-TSS (NM_001289625)	promoter-TSS (NM_001289625)	21	NM_001289625	64213	Mm.12051	NM_022332	ENSMUSG00000029534	St7	9430001H04Rik|Fam4a2|HELG|RAY1|SEN4|TSG7	suppression of tumorigenicity 7	protein-coding
mm_121412.1	chr14	119513142	119513143	+	1	NA	intron (NM_015820, intron 1 of 1)	ID_B1|SINE|B4	-236085	NR_045621	75432	Mm.443277	NR_045621	ENSMUSG00000100274	1700006F04Rik	-	RIKEN cDNA 1700006F04 gene	ncRNA
mm_127207.1	chr15	99224546	99224573	+	1	NA	promoter-TSS (NM_010601)	promoter-TSS (NM_010601)	-417	NM_010601	16512	Mm.374793	NM_010601	ENSMUSG00000037579	Kcnh3	AU019351|C030044P22Rik|Elk2|Kv12.2|Melk2	potassium voltage-gated channel, subfamily H (eag-related), member 3	protein-coding
mm_78829.1	chr9	44107744	44107761	+	1	NA	5' UTR (NM_001190313, exon 13 of 14)	5' UTR (NM_001190313, exon 13 of 14)	443	NM_001190319	235312	Mm.227110	NM_145613	ENSMUSG00000079592	C1qtnf5	Ctrp5	C1q and tumor necrosis factor related protein 5	protein-coding
mm_154492.1	chrM	6224	6252	-	1	NA	NA	Intergenic	NA	NA								
mm_71226.1	chr8	40902527	40902542	+	1	NA	exon (NM_001044740, exon 4 of 12)	exon (NM_001044740, exon 4 of 12)	-23699	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_150749.1	chr19	43788398	43788427	+	1	NA	intron (NM_013806, intron 2 of 31)	HAL1ME|LINE|L1	6104	NM_013806	12780	Mm.39054	NM_013806	ENSMUSG00000025194	Abcc2	AI173996|Abc30|Cmoat|Mrp2|cMRP	ATP-binding cassette, sub-family C (CFTR/MRP), member 2	protein-coding
mm_81969.1	chr9	120959962	120959978	+	1	NA	3' UTR (NM_007614, exon 15 of 15)	3' UTR (NM_007614, exon 15 of 15)	4884	NR_106058	102465661		NR_106058	ENSMUSG00000106193	Mir7090	mmu-mir-7090	microRNA 7090	ncRNA
mm_92048.1	chr10	62497834	62497853	-	1	NA	exon (NM_011157, exon 2 of 3)	exon (NM_011157, exon 2 of 3)	9912	NM_011157	19073	Mm.338790	NM_011157	ENSMUSG00000020077	Srgn	Prg|Prg1|Sgc	serglycin	protein-coding
mm_57131.1	chr6	122602405	122602422	-	1	NA	promoter-TSS (NM_031159)	promoter-TSS (NM_031159)	31	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_45903.1	chr5	88720770	88720782	-	1	NA	promoter-TSS (NM_026735)	promoter-TSS (NM_026735)	-95	NM_026735	68473	Mm.35764	NM_026735	ENSMUSG00000006262	Mob1b	1110003E08Rik|AU015450|B230364F10|Mobkl1a	MOB kinase activator 1B	protein-coding
mm_77968.1	chr9	7790975	7791023	+	1	NA	exon (NM_133739, exon 3 of 5)	exon (NM_133739, exon 3 of 5)	6609	NR_049191	100885830		NR_049191	ENSMUSG00000093615	Mir5618	Gm23685|mmu-mir-5618	microRNA 5618	ncRNA
mm_68473.1	chr7	110785130	110785135	-	1	NA	intron (NM_001276301, intron 2 of 14)	intron (NM_001276301, intron 2 of 14)	12528	NM_009667	11717	Mm.3238	NM_009667	ENSMUSG00000005686	Ampd3	-	adenosine monophosphate deaminase 3	protein-coding
mm_14520.1	chr2	132686945	132686982	+	1	NA	Intergenic	CpG	-3320	NM_028637	73747	Mm.284114	NM_028637	ENSMUSG00000044991	1110034G24Rik	-	RIKEN cDNA 1110034G24 gene	protein-coding
mm_27450.1	chr3	52009170	52009181	-	1	NA	intron (NM_001004176, intron 1 of 4)	intron (NM_001004176, intron 1 of 4)	95831	NM_001004176	433586	Mm.234972	NM_001004176	ENSMUSG00000061143	Maml3	AV234550|BC049812|Mam-2|mKIAA1816	mastermind like 3 (Drosophila)	protein-coding
mm_33585.1	chr4	132553296	132553304	+	1	NA	3' UTR (NM_172400, exon 9 of 9)	3' UTR (NM_172400, exon 9 of 9)	-10767	NM_001081211	19204	Mm.89389	NM_001081211	ENSMUSG00000056529	Ptafr	PAFR	platelet-activating factor receptor	protein-coding
mm_188.1	chr1	15545477	15545480	+	1	NA	intron (NM_001098528, intron 1 of 1)	Lx3_Mus|LINE|L1	233026	NM_001098528	98741	Mm.156081	NM_001033195	ENSMUSG00000092083	Kcnb2	9630047L19Rik|BB130875|Kv2.2	potassium voltage gated channel, Shab-related subfamily, member 2	protein-coding
mm_53632.1	chr6	140591608	140591617	+	1	NA	intron (NM_144920, intron 29 of 30)	intron (NM_144920, intron 29 of 30)	-31051	NM_178803	11569	Mm.86453	NM_009637	ENSMUSG00000030232	Aebp2	AU023766|B230313N05Rik	AE binding protein 2	protein-coding
mm_148651.1	chr19	5493725	5493737	+	1	NA	3' UTR (NM_007687, exon 4 of 4)	3' UTR (NM_007687, exon 4 of 4)	3276	NM_007687	12631	Mm.329655	NM_007687	ENSMUSG00000056201	Cfl1	AA959946|Cof	cofilin 1, non-muscle	protein-coding
mm_7791.1	chr1	131495390	131495416	-	1	NA	intron (NM_001081011, intron 2 of 22)	B4|SINE|B4	31958	NM_001081011	14270	Mm.276259	NM_019520	ENSMUSG00000026425	Srgap2	9930124L22Rik|AI448945|FBP2|Fnbp2|srGAP3	SLIT-ROBO Rho GTPase activating protein 2	protein-coding
mm_28171.1	chr3	87996356	87996368	-	1	NA	intron (NM_007529, intron 4 of 13)	RLTR20C1_MM|LTR|ERVK	3994	NM_007529	12032	Mm.4598	NM_007529	ENSMUSG00000004892	Bcan	Cspg7	brevican	protein-coding
mm_102198.1	chr11	54531034	54531052	-	1	NA	intron (NM_175258, intron 1 of 27)	ORR1A4-int|LTR|ERVL-MaLR	8198	NM_001252496	192786	Mm.254404	NM_175258	ENSMUSG00000037533	Rapgef6	A530068K01|AI844632|BB085664|C030018K18Rik|PDZ-GEF2|Pdzgef2|RA-GEF-2|Ragef2|mKIAA4052	Rap guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_37353.1	chr4	120286986	120286988	-	1	NA	exon (NM_194060, exon 1 of 2)	exon (NM_194060, exon 1 of 2)	274	NM_194060	329934	Mm.277090	NM_194060	ENSMUSG00000052135	Foxo6	-	forkhead box O6	protein-coding
mm_43669.1	chr5	138770201	138770208	+	1	NA	intron (NM_030565, intron 3 of 9)	B4A|SINE|B4	15123	NM_030565	80752	Mm.320355	NM_030565	ENSMUSG00000025854	Fam20c	C76981|DMP-4|DMP4|GEF-CK|mKIAA4081	family with sequence similarity 20, member C	protein-coding
mm_58393.1	chr7	3207056	3207069	+	1	NA	Intergenic	Intergenic	-11564	NR_029640	100049710		NR_029640	ENSMUSG00000077815	Mir290a	Mir290|Mirn290|mir-290a|mmu-miR-290|mmu-mir-290a	microRNA 290a	ncRNA
mm_26603.1	chr3	152210455	152210465	+	1	NA	promoter-TSS (NM_027287)	promoter-TSS (NM_027287)	2	NM_057172	51886	Mm.278922	NM_057172	ENSMUSG00000028034	Fubp1	9530027K12Rik|D3Ertd330e|FBP|Fubp|Fubp4	far upstream element (FUSE) binding protein 1	protein-coding
mm_70438.1	chr8	11713260	11713268	+	1	NA	Intergenic	Intergenic	-14841	NM_001113517	54126	Mm.244068	NM_017402	ENSMUSG00000031511	Arhgef7	Cool|PIX|Pak3bp|betaPix|betaPix-b|betaPix-c|cool-1|mKIAA0142|p85Cool1|p85SPR	Rho guanine nucleotide exchange factor (GEF7)	protein-coding
mm_52304.1	chr6	108822337	108822340	+	1	NA	3' UTR (NM_026011, exon 7 of 7)	3' UTR (NM_026011, exon 7 of 7)	-6303	NM_138677	192193	Mm.21596	NM_138677	ENSMUSG00000030104	Edem1	A130059K23Rik|EDEM|mKIAA0212	ER degradation enhancer, mannosidase alpha-like 1	protein-coding
mm_132059.1	chr16	29843616	29843621	+	1	NA	Intergenic	Intergenic	135506	NR_037689	328657	Mm.425982	NM_001033403		Gm1968	-	predicted gene 1968	ncRNA
mm_19332.1	chr2	90579370	90579406	-	1	NA	intron (NM_008982, intron 1 of 23)	A-rich|Low_complexity|Low_complexity	1259	NM_008982	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_46190.1	chr5	97980679	97980694	-	1	NA	intron (NM_133738, intron 7 of 16)	intron (NM_133738, intron 7 of 16)	50276	NM_133738	71914	Mm.24842	NM_133738	ENSMUSG00000029338	Antxr2	2310046B19Rik|AW561899|CMG-2|CMG2|cI-35	anthrax toxin receptor 2	protein-coding
mm_165224.1	chr2	51528879	51528880	+	1	NA	Intergenic	(CTATA)n|Simple_repeat|Simple_repeat	-90979	NR_130155	73375	Mm.396227	NR_130155	ENSMUSG00000086007	1700057H21Rik	-	RIKEN cDNA 1700057H21 gene	ncRNA
mm_134759.1	chr16	23226769	23226780	-	1	NA	intron (NM_001252505, intron 1 of 7)	intron (NM_001252505, intron 1 of 7)	753	NM_001252505	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_142081.1	chr17	35703972	35703994	-	1	NA	5' UTR (NM_172962, exon 1 of 17)	5' UTR (NM_172962, exon 1 of 17)	156	NM_007584	12305	Mm.5021	NM_007584	ENSMUSG00000003534	Ddr1	6030432F18|AI323681|CD167a|Cak|Nep|PTK3A	discoidin domain receptor family, member 1	protein-coding
mm_77510.1	chr8	122892996	122893026	-	1	NA	non-coding (NR_037865, exon 10 of 14)	non-coding (NR_037865, exon 10 of 14)	44637	NM_007662	12555	Mm.1976	NM_007662	ENSMUSG00000031962	Cdh15	AI323380|Cdh14|Mcad	cadherin 15	protein-coding
mm_127824.1	chr15	5244179	5244192	-	1	NA	promoter-TSS (NM_001136079)	promoter-TSS (NM_001136079)	2	NM_001136079	19219	Mm.18509	NM_008965	ENSMUSG00000039942	Ptger4	EP4|Ptgerep4	prostaglandin E receptor 4 (subtype EP4)	protein-coding
mm_91018.1	chr10	17696575	17696578	-	1	NA	Intergenic	Intergenic	-26652	NM_010828	17684	Mm.272321	NM_010828	ENSMUSG00000039910	Cited2	AI835299|ER154-like|Mrg1|Msg2|p35srj	Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 2	protein-coding
mm_4794.1	chr1	184729514	184729532	+	1	NA	intron (NM_008250, intron 3 of 3)	intron (NM_008250, intron 3 of 3)	2970	NM_008250	15284	Mm.1347	NM_008250	ENSMUSG00000039377	Hlx	Hlx1	H2.0-like homeobox	protein-coding
mm_147618.1	chr18	57551874	57551905	-	1	NA	promoter-TSS (NR_027945)	promoter-TSS (NR_027945)	-22	NR_027945	75084	Mm.243841	NR_015494	ENSMUSG00000086607	4930511M06Rik	-	RIKEN cDNA 4930511M06 gene	ncRNA
mm_163279.1	chr11	116359269	116359282	-	1	NA	exon (NM_027258, exon 6 of 19)	exon (NM_027258, exon 6 of 19)	-23921	NM_008240	15223	Mm.378938	NM_008240	ENSMUSG00000034227	Foxj1	FKHL-13|HFH-4|Hfh4	forkhead box J1	protein-coding
mm_97703.1	chr11	80177968	80177993	+	1	NA	intron (NM_172133, intron 10 of 10)	B1_Mur2|SINE|Alu	-5892	NM_028019	71956	Mm.22985	NM_028019	ENSMUSG00000020707	Rnf135	0610037N03Rik|2410006N06Rik	ring finger protein 135	protein-coding
mm_45817.1	chr5	87680889	87680899	-	1	NA	exon (NM_007784, exon 32 of 34)	exon (NM_007784, exon 32 of 34)	14686	NM_001286016	12990	Mm.427467	NM_007784	ENSMUSG00000070702	Csn1s1	AA959832|AW212882|Csna	casein alpha s1	protein-coding
mm_166420.1	chr5	137151709	137151728	-	1	NA	Intergenic	Intergenic	-35511	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_38765.1	chr4	147904644	147904658	-	1	NA	promoter-TSS (NM_001285923)	promoter-TSS (NM_001285923)	47	NM_001285923	170731	Mm.154312	NM_133201	ENSMUSG00000029020	Mfn2	D630023P19Rik|Fzo	mitofusin 2	protein-coding
mm_91141.1	chr10	19851513	19851568	-	1	NA	promoter-TSS (NM_029529)	promoter-TSS (NM_029529)	-81	NM_029529	76157	Mm.74324	NM_029529	ENSMUSG00000050473	Slc35d3	6230421J19Rik|Frcl1	solute carrier family 35, member D3	protein-coding
mm_4857.1	chr1	187609029	187609047	+	1	NA	promoter-TSS (NM_001243792)	promoter-TSS (NM_001243792)	32	NM_001243792	26381	Mm.89989	NM_011935	ENSMUSG00000026610	Esrrg	ERR3|Errg|NR3B3|mKIAA0832	estrogen-related receptor gamma	protein-coding
mm_141611.1	chr17	32810674	32810682	-	1	NA	promoter-TSS (NM_001267583)	promoter-TSS (NM_001267583)	-747	NM_183177	240063	Mm.30675	NM_183177	ENSMUSG00000055202	Zfp811	BC052046	zinc finger protein 811	protein-coding
mm_4552.1	chr1	177442495	177442523	+	1	NA	Intergenic	CpG	-2152	NM_001012330	30928	Mm.330700	NM_013915	ENSMUSG00000063659	Zbtb18	RP58|Zfp238|Znf238	zinc finger and BTB domain containing 18	protein-coding
mm_103784.1	chr11	82781040	82781082	-	1	NA	promoter-TSS (NM_010716)	promoter-TSS (NM_010716)	-19	NR_126067	100503272	Mm.486964	NR_126067	ENSMUSG00000085175	Gm11423	-	predicted gene 11423	ncRNA
mm_60509.1	chr7	44479589	44479594	+	1	NA	Intergenic	L1MC4|LINE|L1	-4926	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_95786.1	chr11	54956196	54956202	+	1	NA	intron (NM_001199275, intron 1 of 18)	CpG-1959	6741	NM_021327	57783	Mm.259671	NM_021327	ENSMUSG00000020400	Tnip1	ABIN|ABIN-1|ABIN1|AU018810|Naf1|Nef|VAN	TNFAIP3 interacting protein 1	protein-coding
mm_30094.1	chr3	138239659	138239665	-	1	NA	promoter-TSS (NR_045760)	promoter-TSS (NR_045760)	1	NR_045760	68369	Mm.441136	NR_045760	ENSMUSG00000099146	0610031O16Rik	-	RIKEN cDNA 0610031O16 gene	ncRNA
mm_1875.1	chr1	85601036	85601070	+	1	NA	5' UTR (NM_001013817, exon 1 of 17)	5' UTR (NM_001013817, exon 1 of 17)	350	NM_001013817	434484	Mm.445821	NM_001013817	ENSMUSG00000070031	Sp140	-	Sp140 nuclear body protein	protein-coding
mm_90632.1	chr10	128485022	128485028	+	1	NA	intron (NM_198160, intron 24 of 27)	(T)n|Simple_repeat|Simple_repeat	7984	NM_001317220	17904	Mm.337074	NM_010860	ENSMUSG00000090841	Myl6	ESMLC|LC17|LC17-GI|MLC-3|MLC1SM|Myln	myosin, light polypeptide 6, alkali, smooth muscle and non-muscle	protein-coding
mm_25481.1	chr3	109080464	109080487	+	1	NA	promoter-TSS (NM_029054)	promoter-TSS (NM_029054)	-24	NM_029054	74686	Mm.307948	NM_029054	ENSMUSG00000027880	Slc25a54	4930443G12Rik|SCaMC-1like	solute carrier family 25, member 54	protein-coding
mm_46175.1	chr5	96922142	96922156	-	1	NA	intron (NR_131152, intron 2 of 2)	intron (NR_131152, intron 2 of 2)	877	NR_131152	666266	Mm.32442	NR_131152	ENSMUSG00000106357	Gm8013	EG666266	predicted gene 8013	ncRNA
mm_136480.1	chr16	96006798	96006812	-	1	NA	intron (NM_001103179, intron 38 of 40)	MTC-int|LTR|ERVL-MaLR	-15902	NM_019537	56088	Mm.396248	NM_019537	ENSMUSG00000022913	Psmg1	AW552102|Dscr2	proteasome (prosome, macropain) assembly chaperone 1	protein-coding
mm_152599.1	chr19	11640845	11640856	-	1	NA	promoter-TSS (NM_133246)	promoter-TSS (NM_133246)	1	NM_133246	170813	Mm.240438	NM_133246	ENSMUSG00000024681	Ms4a3	HTm4	membrane-spanning 4-domains, subfamily A, member 3	protein-coding
mm_37976.1	chr4	133598798	133598830	-	1	NA	Intergenic	Intergenic	3354	NM_018754	55948	Mm.44482	NM_018754	ENSMUSG00000047281	Sfn	Er|Mme1|Ywhas	stratifin	protein-coding
mm_120785.1	chr14	74689141	74689150	+	1	NA	intron (NM_172812, intron 2 of 2)	MLT1D|LTR|ERVL-MaLR	-43152	NM_001285423	13885	Mm.38055	NM_016903	ENSMUSG00000021996	Esd	Es-10|Es10|FGH|sid478	esterase D/formylglutathione hydrolase	protein-coding
mm_128917.1	chr15	73707388	73707414	-	1	NA	5' UTR (NM_173365, exon 1 of 2)	5' UTR (NM_173365, exon 1 of 2)	104	NM_173365	239530	Mm.122997	NM_173365	ENSMUSG00000045281	Gpr20	A430106B11Rik	G protein-coupled receptor 20	protein-coding
mm_9036.1	chr1	167236623	167236653	-	1	NA	exon (NM_030724, exon 3 of 7)	exon (NM_030724, exon 3 of 7)	48489	NM_030724	80914	Mm.280895	NM_030724	ENSMUSG00000026558	Uck2	AA407809|AI481316|AU018180|AU020720|TSA903|UK|UMK|Umpk	uridine-cytidine kinase 2	protein-coding
mm_168644.1	chr1	185155542	185155546	+	1	NA	Intergenic	RMER4A|LTR|ERVK	-48624	NM_001163754	98732	Mm.275841	NM_172649	ENSMUSG00000039318	Rab3gap2	1110059F07Rik|2010002H18Rik|5830469C09|AI851069|AW743433|RAB3-GAP150|mKIAA0839	RAB3 GTPase activating protein subunit 2	protein-coding
mm_17828.1	chr2	33887863	33887877	-	1	NA	promoter-TSS (NM_175184)	promoter-TSS (NM_175184)	76	NM_175184	72543	Mm.254914	NM_175184	ENSMUSG00000038740	Mvb12b	2610200O14Rik|2610528K11Rik|AI414895|Fam125b	multivesicular body subunit 12B	protein-coding
mm_13270.1	chr2	98667049	98667077	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	1199406	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_166267.1	chr5	88815861	88815868	+	1	NA	Intergenic	Intergenic	50851	NM_007832	13178	Mm.298892	NM_007832	ENSMUSG00000029366	Dck	-	deoxycytidine kinase	protein-coding
mm_7983.1	chr1	134105846	134105861	-	1	NA	Intergenic	Intergenic	-5389	NM_001284524	71884	Mm.328268	NM_027979	ENSMUSG00000026450	Chit1	2300002L19Rik	chitinase 1 (chitotriosidase)	protein-coding
mm_96693.1	chr11	69600014	69600040	+	1	NA	3' UTR (NM_013415, exon 7 of 7)	3' UTR (NM_013415, exon 7 of 7)	5933	NM_013415	11932	Mm.235204	NM_013415	ENSMUSG00000041329	Atp1b2	Amog|Atpb-2	ATPase, Na+/K+ transporting, beta 2 polypeptide	protein-coding
mm_135023.1	chr16	32520536	32520546	-	1	NA	Intergenic	Intergenic	24260	NM_199309	245308	Mm.76859	NM_199309	ENSMUSG00000052363	Zdhhc19	Gm1744|Gm616	zinc finger, DHHC domain containing 19	protein-coding
mm_140495.1	chr17	3557743	3557775	-	1	NA	promoter-TSS (NR_045303)	promoter-TSS (NR_045303)	-46	NM_146074	224481	Mm.226554	NM_146074	ENSMUSG00000036983	Tfb1m	AI429207	transcription factor B1, mitochondrial	protein-coding
mm_145001.1	chr18	38406458	38406467	+	1	NA	Intergenic	Intergenic	-12513	NM_022996	65113	Mm.102496	NM_022996	ENSMUSG00000024425	Ndfip1	0610010M22Rik|N4wbp5	Nedd4 family interacting protein 1	protein-coding
mm_155393.1	chrX	72825191	72825213	+	1	NA	promoter-TSS (NM_001290435)	promoter-TSS (NM_001290435)	24	NM_020488	57249	Mm.117125	NM_020488	ENSMUSG00000031344	Gabrq	-	gamma-aminobutyric acid (GABA) A receptor, subunit theta	protein-coding
mm_7720.1	chr1	130661566	130661583	-	1	NA	promoter-TSS (NM_007576)	promoter-TSS (NM_007576)	44	NM_007576	12269	Mm.306720	NM_007576	ENSMUSG00000026405	C4bp	AI195242|C4bpa	complement component 4 binding protein	protein-coding
mm_100067.1	chr11	115403735	115403777	+	1	NA	promoter-TSS (NM_026729)	promoter-TSS (NM_026729)	4	NM_001347645	68572	Mm.271062	NM_026729	ENSMUSG00000018858	Mrpl58	1110001A02Rik|1110002E03Rik|Ict1|MRP-L58	mitochondrial ribosomal protein L58	protein-coding
mm_71501.1	chr8	46806497	46806512	+	1	NA	exon (NM_008391, exon 3 of 9)	exon (NM_008391, exon 3 of 9)	66759	NM_008391	16363	Mm.1149	NM_008391	ENSMUSG00000031627	Irf2	9830146E22Rik|AI646973|Irf-2	interferon regulatory factor 2	protein-coding
mm_111806.1	chr12	105032241	105032258	-	1	NA	promoter-TSS (NR_003145)	promoter-TSS (NR_003145)	30	NR_003145	69434	Mm.380736	NR_003145		Snhg10	1700026B20Rik|AI642517	small nucleolar RNA host gene 10	ncRNA
mm_162115.1	chrX	53724681	53724681	+	1	NA	promoter-TSS (NM_029142)	promoter-TSS (NM_029142)	-150	NM_029142	75013	Mm.336332	NM_029142	ENSMUSG00000055555	4930502E18Rik	Ct55	RIKEN cDNA 4930502E18 gene	protein-coding
mm_103568.1	chr11	77893008	77893023	-	1	NA	intron (NM_008952, intron 1 of 7)	intron (NM_008952, intron 1 of 7)	857	NM_008952	19193	Mm.8543	NM_008952	ENSMUSG00000017453	Pipox	LPIPOX|Pso	pipecolic acid oxidase	protein-coding
mm_4333.1	chr1	171855030	171855037	+	1	NA	TTS (NM_001252472)	TTS (NM_001252472)	15336	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_140489.1	chr17	3283187	3283197	-	1	NA	Intergenic	Intergenic	-43381	NM_001122998	24001	Mm.137134	NM_011878	ENSMUSG00000023800	Tiam2	3000002F19Rik|STEF|mKIAA2016	T cell lymphoma invasion and metastasis 2	protein-coding
mm_51496.1	chr6	83078607	83078669	+	1	NA	intron (NM_197992, intron 1 of 8)	CpG	248	NM_197992	69837	Mm.12261	NM_197992	ENSMUSG00000069678	Pcgf1	2010002K04Rik|AU024121|Nspc1	polycomb group ring finger 1	protein-coding
mm_106600.1	chr11	120731087	120731107	-	1	NA	exon (NM_007621, exon 2 of 8)	exon (NM_007621, exon 2 of 8)	924	NM_007621	12409	Mm.21454	NM_007621	ENSMUSG00000025150	Cbr2	MLCR	carbonyl reductase 2	protein-coding
mm_138581.1	chr17	35470864	35470881	+	1	NA	exon (NM_010391, exon 3 of 7)	exon (NM_010391, exon 3 of 7)	783	NM_010391	15007	Mm.88795	NM_010391	ENSMUSG00000067235	H2-Q10	H-2Q10|Q10|Qa10	histocompatibility 2, Q region locus 10	protein-coding
mm_126839.1	chr15	89059713	89059760	+	1	NA	promoter-TSS (NM_001002005)	promoter-TSS (NM_001002005)	10	NM_001002005	406218	Mm.483059	NM_001002005	ENSMUSG00000058441	Panx2	-	pannexin 2	protein-coding
mm_15777.1	chr2	164333389	164333396	+	1	NA	exon (NM_009301, exon 2 of 3)	exon (NM_009301, exon 2 of 3)	627	NM_009301	20944	Mm.140154	NM_009301	ENSMUSG00000017004	Svs5	BB115186|Semg1|Svp-1|Svp1|Svp5	seminal vesicle secretory protein 5	protein-coding
mm_70649.1	chr8	14326631	14326634	+	1	NA	intron (NM_172910, intron 3 of 15)	intron (NM_172910, intron 3 of 15)	230757	NM_172910	244310	Mm.404697	NM_172910	ENSMUSG00000047495	Dlgap2	6430596N04Rik|Dap-2|Dap2|Sapap2	discs, large (Drosophila) homolog-associated protein 2	protein-coding
mm_43296.1	chr5	134582721	134582727	+	1	NA	promoter-TSS (NM_020022)	promoter-TSS (NM_020022)	34	NM_020022	19718	Mm.332739	NM_020022	ENSMUSG00000023104	Rfc2	2610008M13Rik|40kDa|AI326953|Recc2	replication factor C (activator 1) 2	protein-coding
mm_128196.1	chr15	35150731	35150736	-	1	NA	intron (NM_019635, intron 1 of 10)	intron (NM_019635, intron 1 of 10)	5073	NM_019635	56274	Mm.262330	NM_019635	ENSMUSG00000022329	Stk3	0610042I06Rik|MST|Mst2|Mst3|Ste20|mess1	serine/threonine kinase 3	protein-coding
mm_94226.1	chr11	3266507	3266534	+	1	NA	promoter-TSS (NM_007879)	promoter-TSS (NM_007879)	-134	NM_007879	13494	Mm.3250	NM_007879	ENSMUSG00000020457	Drg1	AA408859|AI132520|Nedd3	developmentally regulated GTP binding protein 1	protein-coding
mm_104101.1	chr11	86704174	86704219	-	1	NA	exon (NM_001003908, exon 26 of 32)	exon (NM_001003908, exon 26 of 32)	20115	NM_001098810	217057	Mm.24868	NM_175004	ENSMUSG00000072582	Ptrh2	A230072I16Rik|Bit1|CGI-147	peptidyl-tRNA hydrolase 2	protein-coding
mm_131193.1	chr16	7341520	7341524	+	1	NA	intron (NM_021477, intron 12 of 16)	intron (NM_021477, intron 12 of 16)	271687	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_134464.1	chr16	18426475	18426503	-	1	NA	promoter-TSS (NM_013711)	promoter-TSS (NM_013711)	72	NM_013711	26462	Mm.390906	NM_013711	ENSMUSG00000075704	Txnrd2	AA118373|ESTM573010|TGR|Tr3|Trxr2|Trxrd2	thioredoxin reductase 2	protein-coding
mm_18865.1	chr2	75705105	75705116	-	1	NA	promoter-TSS (NM_010902)	promoter-TSS (NM_010902)	-447	NM_010902	18024	Mm.1025	NM_010902	ENSMUSG00000015839	Nfe2l2	Nrf2	nuclear factor, erythroid derived 2, like 2	protein-coding
mm_74623.1	chr8	13105354	13105376	-	1	NA	promoter-TSS (NM_178708)	promoter-TSS (NM_178708)	-22	NM_178708	234069	Mm.103427	NM_178708	ENSMUSG00000038542	Pcid2	A730042J05Rik	PCI domain containing 2	protein-coding
mm_28451.1	chr3	90514406	90514420	-	1	NA	promoter-TSS (NM_009113)	promoter-TSS (NM_009113)	-22	NM_009113	20196	Mm.6523	NM_009113	ENSMUSG00000042312	S100a13	-	S100 calcium binding protein A13	protein-coding
mm_85955.1	chr9	112121374	112121384	-	1	NA	intron (NM_001177617, intron 13 of 14)	B3|SINE|B2	-2668	NR_029823	723815		NR_029823	ENSMUSG00000065441	Mir128-2	Mirn128-2|Mirn128b|mir-128-2|mir-128b	microRNA 128-2	ncRNA
mm_49995.1	chr6	41047517	41047539	+	1	NA	Intergenic	Intergenic	-12019	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_168992.1	chr12	99645319	99645329	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-17350	NR_045288	73457	Mm.383439	NR_045288	ENSMUSG00000100211	1700064M15Rik	-	RIKEN cDNA 1700064M15 gene	ncRNA
mm_54962.1	chr6	48708264	48708274	-	1	NA	promoter-TSS (NM_153175)	promoter-TSS (NM_153175)	-25	NM_153175	231931	Mm.321047	NM_153175	ENSMUSG00000047867	Gimap6	4833419H03Rik|Ian6|mFLJ00102	GTPase, IMAP family member 6	protein-coding
mm_155656.1	chrX	85871724	85871728	+	1	NA	intron (NM_001163539, intron 1 of 1)	PB1D10|SINE|Alu	1453	NM_001163539	71398	Mm.185296	NM_001163539	ENSMUSG00000025058	5430427O19Rik	-	RIKEN cDNA 5430427O19 gene	protein-coding
mm_146883.1	chr18	25680192	25680203	-	1	NA	intron (NM_001146292, intron 1 of 12)	intron (NM_001146292, intron 1 of 12)	73786	NM_133195	108013	Mm.266435	NM_133195	ENSMUSG00000024268	Celf4	A230070D14Rik|BRUNOL-4|Brul4|Brunol4|C130060B05Rik	CUGBP, Elav-like family member 4	protein-coding
mm_59853.1	chr7	29941546	29941575	+	1	NA	intron (NM_178384, intron 2 of 4)	intron (NM_178384, intron 2 of 4)	10333	NM_178384	72723	Mm.371648	NM_178384	ENSMUSG00000059975	Zfp74	2810054M15Rik|KRAB8|Zfp66|Znf569|mszf21|mszf77	zinc finger protein 74	protein-coding
mm_146655.1	chr18	11052345	11052358	-	1	NA	promoter-TSS (NM_010258)	promoter-TSS (NM_010258)	-159	NM_010258	14465	Mm.329287	NM_010258	ENSMUSG00000005836	Gata6	AA410133|GATA-6	GATA binding protein 6	protein-coding
mm_127814.1	chr15	5108174	5108196	-	1	NA	exon (NM_001163138, exon 2 of 4)	exon (NM_001163138, exon 2 of 4)	348	NM_001163138	239319	Mm.31252	NM_001163138	ENSMUSG00000041849	Card6	D730008L15	caspase recruitment domain family, member 6	protein-coding
mm_140827.1	chr17	23644980	23644996	-	1	NA	5' UTR (NM_001033339, exon 1 of 10)	5' UTR (NM_001033339, exon 1 of 10)	281	NM_001033339	240047	Mm.235343	NM_001033339	ENSMUSG00000023903	Mmp25	F730048C11Rik|Leukolysin|MMP20|MT6-MMP	matrix metallopeptidase 25	protein-coding
mm_82647.1	chr9	22017883	22017897	-	1	NA	3' UTR (NM_010487, exon 7 of 7)	3' UTR (NM_010487, exon 7 of 7)	14902	NM_008925	19089	Mm.214593	NM_008925	ENSMUSG00000003402	Prkcsh	80K-H|PKCSH	protein kinase C substrate 80K-H	protein-coding
mm_105406.1	chr11	103504930	103504937	-	1	NA	Intergenic	Intergenic	-92269	NM_183034	353047	Mm.18556	NM_183034	ENSMUSG00000034247	Plekhm1	AP162|B2|BC038943|D330036J23Rik	pleckstrin homology domain containing, family M (with RUN domain) member 1	protein-coding
mm_70529.1	chr8	13026025	13026056	+	1	NA	promoter-TSS (NM_010172)	promoter-TSS (NM_010172)	6	NM_010172	14068	Mm.4827	NM_010172	ENSMUSG00000031443	F7	AI132620|Cf7|FVII	coagulation factor VII	protein-coding
mm_72094.1	chr8	71585931	71585957	+	1	NA	exon (NM_011977, exon 14 of 14)	exon (NM_011977, exon 14 of 14)	-6240	NM_025396	66171	Mm.282284	NM_025396	ENSMUSG00000031807	Pgls	1110030K05Rik|AI447866|Plgs	6-phosphogluconolactonase	protein-coding
mm_59066.1	chr7	19463294	19463308	+	1	NA	Intergenic	Intergenic	-4807	NM_172279	232944	Mm.260504	NM_172279	ENSMUSG00000030397	Mark4	2410090P21Rik|C79806|Markl1	MAP/microtubule affinity regulating kinase 4	protein-coding
mm_4101.1	chr1	167350277	167350285	+	1	NA	exon (NM_019993, exon 1 of 11)	exon (NM_019993, exon 1 of 11)	290	NM_019993	56752	Mm.292539	NM_019993	ENSMUSG00000026687	Aldh9a1	AA139417|Abaldh|ESTM40|TMABA-DH|Tmabadh	aldehyde dehydrogenase 9, subfamily A1	protein-coding
mm_38267.1	chr4	136880699	136880728	-	1	NA	exon (NM_009777, exon 3 of 3)	exon (NM_009777, exon 3 of 3)	5464	NM_009777	12260	Mm.2570	NM_009777	ENSMUSG00000036905	C1qb	-	complement component 1, q subcomponent, beta polypeptide	protein-coding
mm_76255.1	chr8	83740062	83740070	-	1	NA	intron (NM_001163031, intron 1 of 17)	intron (NM_001163031, intron 1 of 17)	1245	NM_001163029	26364	Mm.334648	NM_011925	ENSMUSG00000002885	Adgre5	AA409984|Cd97|TM7LN1	adhesion G protein-coupled receptor E5	protein-coding
mm_54160.1	chr6	23096109	23096112	-	1	NA	intron (NM_013930, intron 13 of 23)	intron (NM_013930, intron 13 of 23)	36876	NM_013930	30956	Mm.18651	NM_013930	ENSMUSG00000029695	Aass	LKR|LKR/SDH|LOR|LOR/SDH|Lorsdh|SDH	aminoadipate-semialdehyde synthase	protein-coding
mm_157039.1	chrX	7967803	7967812	-	1	NA	5' UTR (NM_008089, exon 1 of 6)	5' UTR (NM_008089, exon 1 of 6)	103	NM_008089	14460	Mm.335973	NM_008089	ENSMUSG00000031162	Gata1	Gata-1|Gf-1|eryf1	GATA binding protein 1	protein-coding
mm_173140.1	chrX	21504557	21504559	+	1	NA	Intergenic	RLTR10B2|LTR|ERVK	19934	NM_007429	11609	Mm.2679	NM_007429	ENSMUSG00000068122	Agtr2	AI316812|AW107640	angiotensin II receptor, type 2	protein-coding
mm_116050.1	chr13	27435097	27435100	-	1	NA	intron (NM_001271379, intron 3 of 4)	intron (NM_001271379, intron 3 of 4)	3590	NM_001271379	19112	Mm.142728	NM_011167	ENSMUSG00000021345	Prl8a6	Ghd13|PLP-C1|PLP-Ca|PLP-calpha|Prlpc|Prlpc1	prolactin family 8, subfamily a, member 6	protein-coding
mm_19252.1	chr2	84773429	84773464	-	1	NA	exon (NM_009776, exon 3 of 8)	exon (NM_009776, exon 3 of 8)	1983	NM_009776	12258	Mm.38888	NM_009776	ENSMUSG00000023224	Serping1	C1INH|C1nh	serine (or cysteine) peptidase inhibitor, clade G, member 1	protein-coding
mm_36910.1	chr4	108032070	108032098	-	1	NA	promoter-TSS (NM_172874)	promoter-TSS (NM_172874)	6	NM_001285958	242608	Mm.74710	NM_172874	ENSMUSG00000028600	Podn	9430070G18|Pcan|SLRR5A	podocan	protein-coding
mm_104630.1	chr11	97435173	97435181	-	1	NA	Intergenic	Intergenic	-14983	NM_021493	58996	Mm.394118	NM_021493	ENSMUSG00000049807	Arhgap23	A330041B18Rik	Rho GTPase activating protein 23	protein-coding
mm_72947.1	chr8	92189451	92189466	+	1	NA	Intergenic	Intergenic	166662	NR_110452	71296	Mm.86664	NR_033641	ENSMUSG00000031736	Crnde	4933436C20Rik	colorectal neoplasia differentially expressed (non-protein coding)	ncRNA
mm_164817.1	chr18	34624601	34624602	-	1	NA	promoter-TSS (NM_009004)	promoter-TSS (NM_009004)	-23	NM_001166407	19348	Mm.258846	NM_009004	ENSMUSG00000003779	Kif20a	AA415432|Rab6kifl	kinesin family member 20A	protein-coding
mm_34007.1	chr4	137963825	137963838	+	1	NA	3' UTR (NM_199307, exon 20 of 20)	3' UTR (NM_199307, exon 20 of 20)	-29625	NM_001256198	230861	Mm.268903	NM_172703	ENSMUSG00000028760	Eif4g3	1500002J22Rik|4930523M17Rik|G1-419-52|eIF4GII|repro8	eukaryotic translation initiation factor 4 gamma, 3	protein-coding
mm_166063.1	chr4	134060755	134060774	+	1	NA	Intergenic	Intergenic	-7688	NM_001162970	230806	Mm.240080	NM_001162970	ENSMUSG00000012123	Aim1l	-	absent in melanoma 1-like	protein-coding
mm_55783.1	chr6	82052611	82052621	-	1	NA	intron (NM_145570, intron 1 of 2)	intron (NM_145570, intron 1 of 2)	10988	NM_145570	232146	Mm.489683	NM_145570	ENSMUSG00000035104	Eva1a	BC014699|Fam176a|Tmem166	eva-1 homolog A (C. elegans)	protein-coding
mm_5202.1	chr1	13374397	13374411	-	1	NA	promoter-TSS (NM_008678)	promoter-TSS (NM_008678)	-321	NM_008678	17978	Mm.2537	NM_008678	ENSMUSG00000005886	Ncoa2	D1Ertd433e|GRIP-1|Grip1|KAT13C|NCoA-2|SRC-2|TIF2|bHLHe75	nuclear receptor coactivator 2	protein-coding
mm_95896.1	chr11	58190198	58190245	+	1	NA	TTS (NM_001135115)	TTS (NM_001135115)	6378	NM_001135115	631323	Mm.394103	NM_001135115		Gm12250	Irgb10|OTTMUSG00000005723	predicted gene 12250	protein-coding
mm_86521.1	chr10	7753564	7753575	+	1	NA	intron (NM_011835, intron 7 of 10)	B3A|SINE|B2	27348	NM_145418	215751	Mm.471825	NM_145418	ENSMUSG00000040006	Ginm1	AA589616	glycoprotein integral membrane 1	protein-coding
mm_74476.1	chr8	4259258	4259283	-	1	NA	promoter-TSS (NM_183315)	promoter-TSS (NM_183315)	4	NM_183315	330695	Mm.34210	NM_183315	ENSMUSG00000048644	Ctxn1	BC028881|Ctxn	cortexin 1	protein-coding
mm_84344.1	chr9	64230773	64230778	-	1	NA	intron (NM_008927, intron 1 of 10)	B4|SINE|B4	-4426	NM_033607	93841	Mm.390180	NM_033607	ENSMUSG00000035337	Uchl4	-	ubiquitin carboxyl-terminal esterase L4	protein-coding
mm_69376.1	chr7	131146307	131146322	-	1	NA	promoter-TSS (NM_173409)	promoter-TSS (NM_173409)	-31	NM_173409	233918	Mm.78341	NM_173409	ENSMUSG00000013668	4933402N03Rik	4930412O05	RIKEN cDNA 4933402N03 gene	protein-coding
mm_137337.1	chr17	25133386	25133434	+	1	NA	promoter-TSS (NM_011930)	promoter-TSS (NM_011930)	19	NM_011930	26373	Mm.270587	NM_011930	ENSMUSG00000036636	Clcn7	ClC-7|D17Wsu51e	chloride channel, voltage-sensitive 7	protein-coding
mm_41704.1	chr5	101720779	101720782	+	1	NA	Intergenic	Intergenic	-44350	NM_173370	74596	Mm.46764	NM_173370	ENSMUSG00000029330	Cds1	4833409J18Rik|AI314024|AW125888	CDP-diacylglycerol synthase 1	protein-coding
mm_120775.1	chr14	74451536	74451536	+	1	NA	Intergenic	Intergenic	96009	NR_046059	74425	Mm.399498	NR_046059		4933402J15Rik	-	RIKEN cDNA 4933402J15 gene	ncRNA
mm_12559.1	chr2	72476214	72476224	+	1	NA	promoter-TSS (NM_025866)	promoter-TSS (NM_025866)	0	NM_025866	66953	Mm.270676	NM_025866	ENSMUSG00000055612	Cdca7	2310021G01Rik|AU044109|JPO1	cell division cycle associated 7	protein-coding
mm_59267.1	chr7	24899123	24899133	+	1	NA	exon (NM_007655, exon 2 of 5)	exon (NM_007655, exon 2 of 5)	1617	NM_007655	12518	Mm.1355	NM_007655	ENSMUSG00000003379	Cd79a	Ig-alpha|Iga|Igalpha|Ly-54|Ly54|mb-1	CD79A antigen (immunoglobulin-associated alpha)	protein-coding
mm_73935.1	chr8	120002721	120002741	+	1	NA	intron (NM_030209, intron 1 of 14)	intron (NM_030209, intron 1 of 14)	10293	NM_001310635	78892	Mm.264680	NM_030209	ENSMUSG00000031825	Crispld2	1810049K24Rik|Lcrisp2|Lgl1|coffeecrisp	cysteine-rich secretory protein LCCL domain containing 2	protein-coding
mm_58015.1	chr6	136558719	136558736	-	1	NA	intron (NM_019426, intron 1 of 14)	MTE2b|LTR|ERVL-MaLR	39876	NM_019426	54343	Mm.173271	NM_019426	ENSMUSG00000030213	Atf7ip	2610204M12Rik|AM|Mcaf1	activating transcription factor 7 interacting protein	protein-coding
mm_158609.1	chrX	152368681	152368740	-	1	NA	promoter-TSS (NM_001313748)	promoter-TSS (NM_001313748)	-6	NR_132633	70771	Mm.158445	NM_027543	ENSMUSG00000056679	Gpr173	3230401K02Rik|Sreb3	G-protein coupled receptor 173	protein-coding
mm_92703.1	chr10	80714049	80714067	-	1	NA	exon (NM_007460, exon 19 of 31)	exon (NM_007460, exon 19 of 31)	11365	NM_027829	71564	Mm.35802	NM_027829	ENSMUSG00000055862	Izumo4	9030607L17Rik|AI550407	IZUMO family member 4	protein-coding
mm_109914.1	chr12	8482107	8482107	-	1	NA	Intergenic	Intergenic	17878	NM_007483	11852	Mm.687	NM_007483	ENSMUSG00000054364	Rhob	AA017882|Arh6|Arhb	ras homolog family member B	protein-coding
mm_73441.1	chr8	106201331	106201334	+	1	NA	intron (NM_001007567, intron 4 of 4)	B2_Mm2|SINE|B2	9601	NM_001007567	66432	Mm.269029	NM_001007567	ENSMUSG00000033106	Slc7a6os	2010007L18Rik|2400002F02Rik	solute carrier family 7, member 6 opposite strand	protein-coding
mm_95055.1	chr11	32398008	32398045	+	1	NA	intron (NM_177364, intron 6 of 12)	ID2|SINE|ID	50215	NM_177364	268396	Mm.227616	NM_177364	ENSMUSG00000040711	Sh3pxd2b	G431001E03Rik|TSK4|fad49	SH3 and PX domains 2B	protein-coding
mm_79493.1	chr9	57076396	57076411	+	1	NA	promoter-TSS (NM_011378)	promoter-TSS (NM_011378)	27	NM_011378	20466	Mm.15755	NM_011378	ENSMUSG00000042557	Sin3a	AW553200|Sin3|mKIAA4126|mSin3A	transcriptional regulator, SIN3A (yeast)	protein-coding
mm_83777.1	chr9	52141630	52141647	-	1	NA	intron (NM_001162921, intron 2 of 5)	intron (NM_001162921, intron 2 of 5)	26015	NR_105750	102465150		NR_105750	ENSMUSG00000099311	Mir6244	Gm27368|mmu-mir-6244	microRNA 6244	ncRNA
mm_29893.1	chr3	131303145	131303223	-	1	NA	promoter-TSS (NM_027816)	promoter-TSS (NM_027816)	43	NM_027816	71519	Mm.473179	NM_027816	ENSMUSG00000027983	Cyp2u1	8430436A10Rik	cytochrome P450, family 2, subfamily u, polypeptide 1	protein-coding
mm_14781.1	chr2	145851120	145851124	+	1	NA	intron (NM_028724, intron 6 of 12)	intron (NM_028724, intron 6 of 12)	-52119	NM_026425	67877	Mm.151168	NM_026425	ENSMUSG00000002728	Naa20	1500004D14Rik|2900026I01Rik|AU041458|D2Ertd186e|Nat5	N(alpha)-acetyltransferase 20, NatB catalytic subunit	protein-coding
mm_48501.1	chr5	142815813	142815861	-	1	NA	intron (NM_178242, intron 1 of 15)	CpG-11746	1550	NM_178242	231861	Mm.354649	NM_178242	ENSMUSG00000039477	Tnrc18	BC025631|EG381742|Zfp469	trinucleotide repeat containing 18	protein-coding
mm_72824.1	chr8	88199453	88199463	+	1	NA	intron (NM_001164498, intron 1 of 12)	CpG	245	NM_001164498	214627	Mm.491211	NM_001164497	ENSMUSG00000036779	Papd5	5730445M16Rik|5830428A09	PAP associated domain containing 5	protein-coding
mm_2879.1	chr1	131828074	131828079	+	1	NA	promoter-TSS (NM_173865)	promoter-TSS (NM_173865)	64	NM_173865	98396	Mm.389181	NM_173865	ENSMUSG00000013275	Slc41a1	AI573938|B230315F01Rik	solute carrier family 41, member 1	protein-coding
mm_103677.1	chr11	79243382	79243430	-	1	NA	promoter-TSS (NM_001042565)	promoter-TSS (NM_001042565)	-382	NM_001042565	78889	Mm.307022	NM_019653	ENSMUSG00000017677	Wsb1	1110056B13Rik|2700038M07Rik	WD repeat and SOCS box-containing 1	protein-coding
mm_5179.1	chr1	12814450	12814457	-	1	NA	intron (NM_172294, intron 7 of 21)	intron (NM_172294, intron 7 of 21)	95908	NM_172294	240725	Mm.45563	NM_172294	ENSMUSG00000016918	Sulf1	AI467640|AW121680|mKIAA1077	sulfatase 1	protein-coding
mm_15072.1	chr2	153108490	153108542	+	1	NA	promoter-TSS (NM_010407)	promoter-TSS (NM_010407)	48	NM_010407	15162	Mm.715	NM_010407	ENSMUSG00000003283	Hck	AI849071|Bmk	hemopoietic cell kinase	protein-coding
mm_116724.1	chr13	51703111	51703131	-	1	NA	exon (NM_001281880, exon 17 of 17)	exon (NM_001281880, exon 17 of 17)	51413	NM_029279	75420	Mm.275981	NM_029279	ENSMUSG00000035139	Secisbp2	2210413N07Rik|2810012K13Rik|SBP2	SECIS binding protein 2	protein-coding
mm_31302.1	chr4	46031379	46031381	+	1	NA	intron (NM_146142, intron 16 of 16)	L1MCa|LINE|L1	-7842	NM_021883	21916	Mm.249594	NM_021883	ENSMUSG00000028328	Tmod1	E-Tmod|Tmod	tropomodulin 1	protein-coding
mm_133924.1	chr16	97997314	97997362	+	1	NA	promoter-TSS (NR_130962)	promoter-TSS (NR_130962)	-9	NR_130962	245305	Mm.148033	NR_130962		B230307C23Rik	EG245305|OTTMUSG00000028475	RIKEN cDNA B230307C23 gene	ncRNA
mm_94186.1	chr10	128960613	128960639	-	1	NA	exon (NM_027853, exon 1 of 2)	exon (NM_027853, exon 1 of 2)	362	NM_027853	71664	Mm.337232	NM_027853	ENSMUSG00000025347	Mettl7b	0610006F02Rik|AI266817	methyltransferase like 7B	protein-coding
mm_170816.1	chr2	176289878	176289889	+	1	NA	promoter-TSS (NR_040256)	promoter-TSS (NR_040256)	-60	NR_040256	626877	Mm.490744	NR_040256		Gm14405	OTTMUSG00000016573	predicted gene 14405	pseudo
mm_90581.1	chr10	128268647	128268651	+	1	NA	5' UTR (NM_133997, exon 1 of 2)	5' UTR (NM_133997, exon 1 of 2)	652	NM_133997	103161	Mm.26513	NM_133997	ENSMUSG00000047631	Apof	AI255964	apolipoprotein F	protein-coding
mm_111092.1	chr12	80436793	80436825	-	1	NA	promoter-TSS (NM_177267)	promoter-TSS (NM_177267)	-208	NM_177267	320808	Mm.220310	NM_177267	ENSMUSG00000049106	Dcaf5	9430020B07Rik|AI325023|AI430035|AI848110|AW124614|BCRG2|BCRP2|Wdr22	DDB1 and CUL4 associated factor 5	protein-coding
mm_131084.1	chr16	4762617	4762631	+	1	NA	exon (NM_001136066, exon 2 of 6)	exon (NM_001136066, exon 2 of 6)	21011	NM_010443	15369	Mm.272866	NM_010443	ENSMUSG00000004070	Hmox2	HO-2|HO2	heme oxygenase 2	protein-coding
mm_84305.1	chr9	63602465	63602494	-	1	NA	promoter-TSS (NM_025857)	promoter-TSS (NM_025857)	14	NM_030068	78250	Mm.444612	NM_030068	ENSMUSG00000037801	Iqch	4921504K03Rik	IQ motif containing H	protein-coding
mm_97047.1	chr11	72435537	72435558	+	1	NA	promoter-TSS (NM_027819)	promoter-TSS (NM_027819)	21	NM_027819	71522	Mm.23336	NM_027819	ENSMUSG00000040471	Ggt6	9030405D14Rik|AI427679|AW490214	gamma-glutamyltransferase 6	protein-coding
mm_90539.1	chr10	128091139	128091158	+	1	NA	TTS (NM_016774)	TTS (NM_016774)	-1635	NM_054078	116848	Mm.252213	NM_054078	ENSMUSG00000040054	Baz2a	AA415431|C030005G16Rik|C78388|Tip5|Walp3|mKIAA0314	bromodomain adjacent to zinc finger domain, 2A	protein-coding
mm_28251.1	chr3	88512605	88512620	-	1	NA	Intergenic	Intergenic	-9260	NM_001002011	16905	Mm.243014	NM_019390	ENSMUSG00000028063	Lmna	Dhe	lamin A	protein-coding
mm_32907.1	chr4	119120415	119120459	+	1	NA	exon (NM_011400, exon 2 of 10)	exon (NM_011400, exon 2 of 10)	11692	NM_011400	20525	Mm.21002	NM_011400	ENSMUSG00000028645	Slc2a1	Glut-1|Glut1	solute carrier family 2 (facilitated glucose transporter), member 1	protein-coding
mm_65430.1	chr7	25367651	25367670	-	1	NA	TTS (NM_028219)	TTS (NM_028219)	2064	NM_001081375	72383	Mm.34382	NM_028219	ENSMUSG00000063651	Cnfn	2210418J09Rik	cornifelin	protein-coding
mm_6987.1	chr1	86357228	86357269	-	1	NA	promoter-TSS (NR_002851)	promoter-TSS (NR_002851)	-921	NR_002851	80828		NR_002851	ENSMUSG00000064823	Snord82	Rnu82|U82|Z25	small nucleolar RNA, C/D box 82	snoRNA
mm_159412.1	chr3	103913881	103913881	+	1	NA	promoter-TSS (NM_172684)	promoter-TSS (NM_172684)	-239	NM_172684	229675	Mm.29366	NM_172684	ENSMUSG00000044098	Rsbn1	C230004D03Rik|E330004N01|Rosbin|Rsbn|Rsbp|mKIAA3002	rosbin, round spermatid basic protein 1	protein-coding
mm_5856.1	chr1	53548881	53548881	-	1	NA	intron (NM_001252070, intron 28 of 65)	intron (NM_001252070, intron 28 of 65)	157903	NM_001252070	627872	Mm.184692	NM_001252070	ENSMUSG00000096141	Dnah7a	Dnahc7|Dnahc7a|Gm992	dynein, axonemal, heavy chain 7A	protein-coding
mm_33171.1	chr4	126031796	126031816	+	1	NA	exon (NM_007782, exon 5 of 17)	exon (NM_007782, exon 5 of 17)	7147	NM_001252651	12986	Mm.271701	NM_007782	ENSMUSG00000028859	Csf3r	Cd114|Csfgr|G-CSF-R|G-CSFR	colony stimulating factor 3 receptor (granulocyte)	protein-coding
mm_162595.1	chr1	182565013	182565021	+	1	NA	promoter-TSS (NM_001145806)	promoter-TSS (NM_001145806)	10	NM_130890	170725	Mm.189201	NM_130890	ENSMUSG00000038599	Capn8	nCL-2|nCL-2'	calpain 8	protein-coding
mm_114794.1	chr13	89584525	89584543	+	1	NA	intron (NM_013500, intron 1 of 4)	intron (NM_013500, intron 1 of 4)	43898	NM_013500	12950	Mm.266790	NM_013500	ENSMUSG00000021613	Hapln1	BB099155|CLP|Crtl1|Crtl1l|LP|LP-1	hyaluronan and proteoglycan link protein 1	protein-coding
mm_138634.1	chr17	35861281	35861296	+	1	NA	promoter-TSS (NM_134122)	promoter-TSS (NM_134122)	-30	NM_134122	106582	Mm.390992	NM_134122	ENSMUSG00000059791	Nrm	2610307M02Rik|AI429796	nurim (nuclear envelope membrane protein)	protein-coding
mm_155472.1	chrX	73640162	73640172	+	1	NA	intron (NM_029352, intron 1 of 3)	CpG	726	NM_029352	75590	Mm.16479	NM_029352	ENSMUSG00000031383	Dusp9	Dusp4|Mpk4|Pyst3	dual specificity phosphatase 9	protein-coding
mm_31093.1	chr4	41755488	41755498	+	1	NA	promoter-TSS (NM_001302511)	promoter-TSS (NM_001302511)	265	NM_016658	14430	Mm.439669	NM_016658	ENSMUSG00000036073	Galt	AW553376	galactose-1-phosphate uridyl transferase	protein-coding
mm_45641.1	chr5	76905464	76905507	-	1	NA	promoter-TSS (NM_173765)	promoter-TSS (NM_173765)	29	NM_173765	231326	Mm.39271	NM_173765	ENSMUSG00000055923	Aasdh	A230062G08Rik|A830035E16|Acsf4|U26	aminoadipate-semialdehyde dehydrogenase	protein-coding
mm_134477.1	chr16	18588881	18588909	-	1	NA	intron (NM_001285472, intron 1 of 8)	CpG	1776	NM_001285472	21380	Mm.295194	NM_011532	ENSMUSG00000009097	Tbx1	-	T-box 1	protein-coding
mm_88811.1	chr10	80780810	80780813	+	1	NA	intron (NM_199322, intron 9 of 27)	intron (NM_199322, intron 9 of 27)	17815	NM_023900	78670	Mm.41479	NM_023900	ENSMUSG00000035278	Plekhj1	9530063M10Rik	pleckstrin homology domain containing, family J member 1	protein-coding
mm_78313.1	chr9	23223609	23223621	+	1	NA	5' UTR (NM_028472, exon 1 of 15)	5' UTR (NM_028472, exon 1 of 15)	539	NM_028472	73230	Mm.335020	NM_028472	ENSMUSG00000031963	Bmper	3110056H04Rik|CV-2|Crim3|Cv2	BMP-binding endothelial regulator	protein-coding
mm_19665.1	chr2	103283769	103283802	-	1	NA	intron (NM_007914, intron 1 of 8)	intron (NM_007914, intron 1 of 8)	19411	NM_007914	13661	Mm.10724	NM_007914	ENSMUSG00000012350	Ehf	9030625L19Rik|AU019492	ets homologous factor	protein-coding
mm_170321.1	chr18	4197050	4197054	-	1	NA	Intergenic	B3A|SINE|B2	31220	NM_026092	67328	Mm.158148	NM_026092	ENSMUSG00000024233	Lyzl1	1700038F02Rik|Lyc2|Lyzd1	lysozyme-like 1	protein-coding
mm_108247.1	chr12	78226587	78226620	+	1	NA	promoter-TSS (NM_172952)	promoter-TSS (NM_172952)	-52	NM_172952	268566	Mm.341742	NM_145965	ENSMUSG00000047454	Gphn	5730552E08Rik|AI662856|BC027112|C230040D23|GPH|GPHRYN|geph	gephyrin	protein-coding
mm_81073.1	chr9	106212175	106212204	+	1	NA	intron (NM_011876, intron 3 of 8)	intron (NM_011876, intron 3 of 8)	9081	NM_011876	23999	Mm.274346	NM_011876	ENSMUSG00000023277	Twf2	A6-related|AU014993|Ptk9l|Ptk9r	twinfilin actin binding protein 2	protein-coding
mm_52078.1	chr6	97828240	97828249	+	1	NA	intron (NM_001113198, intron 1 of 9)	intron (NM_001113198, intron 1 of 9)	21186	NM_001113198	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_126187.1	chr15	78615927	78615952	+	1	NA	intron (NM_028195, intron 9 of 12)	intron (NM_028195, intron 9 of 12)	18892	NM_028195	72318	Mm.32911	NM_028195	ENSMUSG00000018008	Cyth4	2510004M07Rik|5830469K17Rik|AI467541|Pscd4|mFLJ00017	cytohesin 4	protein-coding
mm_109272.1	chr12	109545783	109545795	+	1	NA	non-coding (NR_003633, exon 1 of 5)	non-coding (NR_003633, exon 1 of 5)	391	NR_003633	17263	Mm.289645	NM_144513	ENSMUSG00000021268	Meg3	2900016C05Rik|3110050O07Rik|6330408G06Rik|AI425946|AW108224|D12Bwg1266e|Gtl2|R74756|R75394	maternally expressed 3	ncRNA
mm_126557.1	chr15	82147566	82147615	+	1	NA	intron (NM_033218, intron 1 of 18)	CpG	321	NM_033218	20788	Mm.9002	NM_033218	ENSMUSG00000022463	Srebf2	AI608257|SREBP-2|SREBP2|SREBP2gc|bHLHd2|lop13|nuc	sterol regulatory element binding factor 2	protein-coding
mm_87442.1	chr10	51481619	51481656	+	1	NA	exon (NM_008147, exon 4 of 9)	exon (NM_008147, exon 4 of 9)	1025	NM_001291892	14727	Mm.439661	NM_008147	ENSMUSG00000062593	Lilr4b	Gp49a|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4B	protein-coding
mm_28534.1	chr3	92709074	92709075	-	1	NA	promoter-TSS (NM_026811)	promoter-TSS (NM_026811)	0	NM_026811	68694	Mm.290624	NM_026811	ENSMUSG00000068889	Lce1e	1110031B11Rik|AI507275	late cornified envelope 1E	protein-coding
mm_165404.1	chr2	138279050	138279061	+	1	NA	exon (NM_145534, exon 1 of 4)	exon (NM_145534, exon 1 of 4)	562	NM_145534	228662	Mm.153405	NM_145534	ENSMUSG00000062098	Btbd3	mKIAA0952	BTB (POZ) domain containing 3	protein-coding
mm_113086.1	chr13	23870285	23870308	+	1	NA	promoter-TSS (NM_009198)	promoter-TSS (NM_009198)	23	NM_001170638	20504	Mm.2656	NM_009198	ENSMUSG00000021335	Slc17a1	NAPI-1|Napi1|Npt1	solute carrier family 17 (sodium phosphate), member 1	protein-coding
mm_165940.1	chr4	77310728	77310732	+	1	NA	intron (NM_011211, intron 6 of 39)	RLTR9D|LTR|ERVK	901165	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding
mm_16652.1	chr2	6542729	6542745	-	1	NA	3' UTR (NM_001110228, exon 14 of 14)	3' UTR (NM_001110228, exon 14 of 14)	178925	NM_001310447	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_68141.1	chr7	102240060	102240148	-	1	NA	exon (NM_019566, exon 2 of 2)	exon (NM_019566, exon 2 of 2)	10014	NM_019566	56212	Mm.259795	NM_019566	ENSMUSG00000073982	Rhog	2810426G09Rik|Arhg|Sid10750	ras homolog family member G	protein-coding
mm_127929.1	chr15	10470491	10470527	-	1	NA	promoter-TSS (NM_030046)	promoter-TSS (NM_030046)	7	NM_030046	78244	Mm.297862	NM_030046	ENSMUSG00000044224	Dnajc21	4930461P20Rik|9930116P15Rik	DnaJ heat shock protein family (Hsp40) member C21	protein-coding
mm_36411.1	chr4	78069485	78069496	-	1	NA	intron (NM_011211, intron 1 of 39)	Lx|LINE|L1	142405	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding
mm_110097.1	chr12	25189662	25189673	-	1	NA	Intergenic	Intergenic	60493	NR_045844	432641	Mm.112955	NR_045844		Gm17746	-	predicted gene, 17746	ncRNA
mm_171290.1	chr3	90086566	90086578	-	1	NA	exon (NM_001293748, exon 3 of 10)	exon (NM_001293748, exon 3 of 10)	7051	NM_001293749	59069	Mm.240839	NM_022314	ENSMUSG00000027940	Tpm3	TM30nm|TMnm|Tm5NM|Tpm-5|Tpm5|Trop-5|gamma-TM|hTM30nm|hTMnm	tropomyosin 3, gamma	protein-coding
mm_80975.1	chr9	103181389	103181429	+	1	NA	3' UTR (NM_173781, exon 8 of 8)	3' UTR (NM_173781, exon 8 of 8)	20656	NM_009275	20818	Mm.273053	NM_009275	ENSMUSG00000032553	Srprb	AA409543	signal recognition particle receptor, B subunit	protein-coding
mm_97907.1	chr11	83439954	83439967	+	1	NA	TTS (NM_080453)	TTS (NM_080453)	2266	NM_025492	66330	Mm.44800	NM_025492	ENSMUSG00000035085	1700020L24Rik	-	RIKEN cDNA 1700020L24 gene	protein-coding
mm_129593.1	chr15	79804456	79804503	-	1	NA	exon (NM_030689, exon 1 of 5)	exon (NM_030689, exon 1 of 5)	230	NM_030689	73340	Mm.38438	NM_030689	ENSMUSG00000022421	Nptxr	1200009K17Rik|1700036C17Rik|5730406O18Rik|AI452369|AI785356|D15Bwg0580e|NPR|Npcd	neuronal pentraxin receptor	protein-coding
mm_130635.1	chr15	100480584	100480588	-	1	NA	3' UTR (NM_153407, exon 5 of 5)	3' UTR (NM_153407, exon 5 of 5)	11552	NM_134093	68614	Mm.275272	NM_134093	ENSMUSG00000037353	Letmd1	1110019O13Rik|AI593524|BB130465|BB235638|HCCR-2|HCCR1|MCC-32|Mccr	LETM1 domain containing 1	protein-coding
mm_171864.1	chr5	23434420	23434422	+	1	NA	promoter-TSS (NM_026984)	promoter-TSS (NM_026984)	-8	NM_026984	69188	Mm.205190	NM_026984	ENSMUSG00000029004	Kmt2e	1810033J14Rik|9530077A04Rik|D230038D11Rik|Mll5|NKp44L	lysine (K)-specific methyltransferase 2E	protein-coding
mm_157718.1	chrX	70344275	70344285	-	1	NA	3' UTR (NM_010498, exon 9 of 9)	3' UTR (NM_010498, exon 9 of 9)	20805	NM_010498	15931	Mm.233083	NM_010498	ENSMUSG00000035847	Ids	AW214631	iduronate 2-sulfatase	protein-coding
mm_165582.1	chr3	28956372	28956378	+	1	NA	Intergenic	Intergenic	63758	NM_001033479	385263	Mm.60893	NM_001033479	ENSMUSG00000074655	Gm1527	Gm1136	predicted gene 1527	protein-coding
mm_26620.1	chr3	152396665	152396702	+	1	NA	promoter-TSS (NM_001287139)	promoter-TSS (NM_001287139)	-1	NM_001287139	108946	Mm.379292	NM_198416	ENSMUSG00000039068	Zzz3	3110065C23Rik|6430567E01Rik|AA408566|AI481057|AW556059|R75514	zinc finger, ZZ domain containing 3	protein-coding
mm_96133.1	chr11	60878362	60878375	+	1	NA	intron (NM_001168507, intron 1 of 2)	CpG	670	NM_173453	216821	Mm.28063	NM_173453	ENSMUSG00000043284	Tmem11	5730466P16Rik|AA409091	transmembrane protein 11	protein-coding
mm_38349.1	chr4	137770005	137770025	-	1	NA	intron (NM_007431, intron 1 of 11)	intron (NM_007431, intron 1 of 11)	-3540	NM_001287172	11647	Mm.288186	NM_007431	ENSMUSG00000028766	Alpl	ALP|APTNAP|Akp-2|Akp2|TNAP|TNSALP	alkaline phosphatase, liver/bone/kidney	protein-coding
mm_100928.1	chr11	6475882	6475917	-	1	NA	5' UTR (NM_011221, exon 1 of 1)	5' UTR (NM_011221, exon 1 of 1)	177	NM_011221	19291	Mm.296150	NM_011221	ENSMUSG00000094483	Purb	2310015K15Rik|AA114818|Cager-2|D11Bwg0414e	purine rich element binding protein B	protein-coding
mm_122647.1	chr14	51905806	51905816	-	1	NA	3' UTR (NM_001145959, exon 15 of 15)	3' UTR (NM_001145959, exon 15 of 15)	7677	NM_001145959	29811	Mm.26722	NM_013864	ENSMUSG00000004558	Ndrg2	AI182517|AU040374|Ndr2|SYLD	N-myc downstream regulated gene 2	protein-coding
mm_93610.1	chr10	117238574	117238582	-	1	NA	exon (NM_029906, exon 1 of 4)	exon (NM_029906, exon 1 of 4)	103	NM_029906	77397	Mm.118350	NM_029906	ENSMUSG00000020177	9530003J23Rik	Lyzf1	RIKEN cDNA 9530003J23 gene	protein-coding
mm_54611.1	chr6	38354103	38354137	-	1	NA	exon (NM_028421, exon 1 of 12)	exon (NM_028421, exon 1 of 12)	483	NM_028864	78781	Mm.25243	NM_028421	ENSMUSG00000029826	Zc3hav1	1200014N16Rik|2900058M19Rik|9130009D18Rik|9830115L13Rik|ARTD13|D6Bwg1452e|ZAP	zinc finger CCCH type, antiviral 1	protein-coding
mm_78000.1	chr9	8901536	8901549	+	1	NA	exon (NM_008829, exon 1 of 8)	exon (NM_008829, exon 1 of 8)	1709	NM_008829	18667	Mm.12798	NM_008829	ENSMUSG00000031870	Pgr	9930019P03Rik|BB114106|ENSMUSG00000074510|NR3C3|PR|PR-A|PR-B	progesterone receptor	protein-coding
mm_82096.1	chr9	123056592	123056593	+	1	NA	exon (NM_177911, exon 10 of 14)	exon (NM_177911, exon 10 of 14)	21851	NM_177911	331046	Mm.195309	NM_177911	ENSMUSG00000025787	Tgm4	9530008N10Rik|Eapa1|TGP	transglutaminase 4 (prostate)	protein-coding
mm_83002.1	chr9	36726628	36726636	-	1	NA	promoter-TSS (NM_007691)	promoter-TSS (NM_007691)	26	NM_007691	12649	Mm.16753	NM_007691	ENSMUSG00000032113	Chek1	C85740|Chk1|rad27	checkpoint kinase 1	protein-coding
mm_99902.1	chr11	109662622	109662628	+	1	NA	intron (NM_001313973, intron 7 of 11)	MIR|SINE|MIR	11704	NM_001313976	19084	Mm.30039	NM_021880	ENSMUSG00000020612	Prkar1a	1300018C22Rik|RIalpha|Tse-1|Tse1	protein kinase, cAMP dependent regulatory, type I, alpha	protein-coding
mm_64027.1	chr7	140769105	140769109	+	1	NA	exon (NM_021282, exon 3 of 9)	exon (NM_021282, exon 3 of 9)	5275	NM_021282	13106	Mm.21758	NM_021282	ENSMUSG00000025479	Cyp2e1	Cyp2e	cytochrome P450, family 2, subfamily e, polypeptide 1	protein-coding
mm_123096.1	chr14	55788760	55788793	-	1	NA	promoter-TSS (NM_019955)	promoter-TSS (NM_019955)	81	NM_001164107	56532	Mm.46612	NM_019955	ENSMUSG00000022221	Ripk3	2610528K09Rik|AW107945|Rip3	receptor-interacting serine-threonine kinase 3	protein-coding
mm_13563.1	chr2	112265862	112265925	+	1	NA	promoter-TSS (NM_133649)	promoter-TSS (NM_133649)	-421	NM_133649	107723	Mm.491155	NM_133648	ENSMUSG00000027130	Slc12a6	9530023I19Rik|KCC3|gaxp	solute carrier family 12, member 6	protein-coding
mm_172002.1	chr6	107140641	107140651	+	1	NA	Intergenic	L1Md_Gf|LINE|L1	-340559	NM_175357	58799	Mm.290085	NM_021449	ENSMUSG00000005362	Crbn	2610203G15Rik|2900045O07Rik|AF229032|AW108261|piL	cereblon	protein-coding
mm_107914.1	chr12	71015931	71015950	+	1	NA	promoter-TSS (NR_045056)	promoter-TSS (NR_045056)	-27	NM_001081195	238247	Mm.241601	NM_001081195	ENSMUSG00000048118	Arid4a	A630009N03|A630067N03Rik|MmRBBP1|Rbbp1	AT rich interactive domain 4A (RBP1-like)	protein-coding
mm_136483.1	chr16	96068009	96068011	-	1	NA	3' UTR (NM_176928, exon 5 of 5)	3' UTR (NM_176928, exon 5 of 5)	14418	NM_001103179	93871	Mm.240871	NM_145125	ENSMUSG00000022914	Brwd1	5330419I02Rik|D530019K20Rik|G1-403-16|Wdr9|repro5	bromodomain and WD repeat domain containing 1	protein-coding
mm_70907.1	chr8	25649398	25649415	+	1	NA	intron (NM_001001735, intron 3 of 9)	CT-rich|Low_complexity|Low_complexity	8829	NM_001081269	234135	Mm.217337	NM_001001735	ENSMUSG00000054823	Whsc1l1	6720429E03|A530023P05|AI528490|NSD3|WHISTLE	Wolf-Hirschhorn syndrome candidate 1-like 1 (human)	protein-coding
mm_162242.1	chrX	155148077	155148077	-	1	NA	promoter-TSS (NM_001081671)	promoter-TSS (NM_001081671)	-228	NM_001081671	73347	Mm.63848	NM_001081671	ENSMUSG00000057402	Cldn34b2	1700042B14Rik	claudin 34B2	protein-coding
mm_166361.1	chr5	123344930	123344933	+	1	NA	intron (NM_029850, intron 1 of 5)	CpG	483	NM_029850	77045	Mm.151960	NM_029850	ENSMUSG00000029438	Bcl7a	4432415N06Rik|AI448316	B cell CLL/lymphoma 7A	protein-coding
mm_55737.1	chr6	77476596	77476608	-	1	NA	intron (NM_001109764, intron 8 of 19)	intron (NM_001109764, intron 8 of 19)	-94127	NR_045141	70753	Mm.490700	NR_045141	ENSMUSG00000108077	6330415B21Rik	-	RIKEN cDNA 6330415B21 gene	ncRNA
mm_19712.1	chr2	103945052	103945069	-	1	NA	Intergenic	Intergenic	-12935	NM_001142337	16909	Mm.29266	NM_008505	ENSMUSG00000032698	Lmo2	Rbtn-2|Rbtn2|Rhom-2|Ttg2	LIM domain only 2	protein-coding
mm_113807.1	chr13	46502114	46502140	+	1	NA	5' UTR (NM_026056, exon 1 of 13)	5' UTR (NM_026056, exon 1 of 13)	224	NM_026056	67252	Mm.44529	NM_026056	ENSMUSG00000021373	Cap2	2810452G09Rik|AV045235	CAP, adenylate cyclase-associated protein, 2 (yeast)	protein-coding
mm_123534.1	chr14	66805246	66805262	-	1	NA	3' UTR (NM_009955, exon 14 of 14)	3' UTR (NM_009955, exon 14 of 14)	63346	NM_009955	12934	Mm.352648	NM_009955	ENSMUSG00000022048	Dpysl2	AI851130|Crmp2|DRP2|Musunc33|TOAD-64|Ulip2	dihydropyrimidinase-like 2	protein-coding
mm_8174.1	chr1	137969214	137969243	-	1	NA	Intergenic	Intergenic	2589	NR_029820	723890		NR_029820	ENSMUSG00000065458	Mir181b-1	Mirn181b-1|mir-181b-1	microRNA 181b-1	ncRNA
mm_14442.1	chr2	130910832	130910837	+	1	NA	intron (NM_009730, intron 1 of 28)	intron (NM_009730, intron 1 of 28)	4339	NM_009730	11990	Mm.119936	NM_009730	ENSMUSG00000027312	Atrn	AW558010|Mgca|mg	attractin	protein-coding
mm_80484.1	chr9	78230680	78230691	+	1	NA	promoter-TSS (NM_008181)	promoter-TSS (NM_008181)	16	NM_008181	14857	Mm.467426	NM_008181	ENSMUSG00000074183	Gsta1	Gst2-1|OTTMUSG00000031890	glutathione S-transferase, alpha 1 (Ya)	protein-coding
mm_14076.1	chr2	124089962	124090018	+	1	NA	promoter-TSS (NM_001290997)	promoter-TSS (NM_001290997)	21	NM_001290997	214968	Mm.330536	NM_172537	ENSMUSG00000027200	Sema6d	1110067B02Rik|AA409156|D330011G23|mKIAA1479	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	protein-coding
mm_116367.1	chr13	40730996	40731029	-	1	NA	promoter-TSS (NM_001122948)	promoter-TSS (NM_001122948)	-555	NM_001122948	21418	Mm.85544	NM_011547	ENSMUSG00000021359	Tfap2a	AP-2|AP2alpha|Ap-2 (a)|Ap2|Ap2tf|Tcfap2a	transcription factor AP-2, alpha	protein-coding
mm_121076.1	chr14	98905128	98905143	+	1	NA	Intergenic	Lx5c|LINE|L1	141001	NM_175245	76789	Mm.38912	NM_175245	ENSMUSG00000033186	Mzt1	2410129H14Rik|AI120158|Mozart1	mitotic spindle organizing protein 1	protein-coding
mm_12341.1	chr2	69723072	69723093	+	1	NA	promoter-TSS (NM_001081086)	promoter-TSS (NM_001081086)	-6	NM_001081086	228005	Mm.11815	NM_001081086	ENSMUSG00000042133	Ppig	AU019516|AU022200|B230312B02Rik|CYP|SRCyp	peptidyl-prolyl isomerase G (cyclophilin G)	protein-coding
mm_64377.1	chr7	142460835	142460886	+	1	NA	promoter-TSS (NM_001271509)	promoter-TSS (NM_001271509)	48	NM_001136071	16985	Mm.234003	NM_019391	ENSMUSG00000018819	Lsp1	Lsp-1|WP34|p50|pp52	lymphocyte specific 1	protein-coding
mm_120113.1	chr14	59478933	59478991	+	1	NA	intron (NM_026908, intron 3 of 10)	intron (NM_026908, intron 3 of 10)	37981	NM_026908	69008	Mm.179091	NM_026908	ENSMUSG00000021981	Cab39l	1500031K13Rik|2810425O13Rik|4930520C08Rik|AA589432|MO2L	calcium binding protein 39-like	protein-coding
mm_77064.1	chr8	109752250	109752267	-	1	NA	Intergenic	Intergenic	-14519	NM_001080930	52335	Mm.276770	NM_001080930	ENSMUSG00000069895	Atxn1l	AW558552|Boat|C330011L24Rik|D6Mgi37|D8Ertd587e|ENSMUSG00000069895	ataxin 1-like	protein-coding
mm_8150.1	chr1	136580582	136580589	-	1	NA	Intergenic	Intergenic	-44316	NM_177643	226442	Mm.62521	NM_177643	ENSMUSG00000041483	Zfp281	Znf281	zinc finger protein 281	protein-coding
mm_75882.1	chr8	70792393	70792451	-	1	NA	promoter-TSS (NM_199308)	promoter-TSS (NM_199308)	11	NM_199308	546071	Mm.250731	NM_199308	ENSMUSG00000031833	Mast3	BC024265|mKIAA0561	microtubule associated serine/threonine kinase 3	protein-coding
mm_80392.1	chr9	75775356	75775378	+	1	NA	promoter-TSS (NM_007555)	promoter-TSS (NM_007555)	2	NM_007555	12160	Mm.428950	NM_007555	ENSMUSG00000032179	Bmp5	AU023399|se	bone morphogenetic protein 5	protein-coding
mm_53162.1	chr6	125321391	125321406	+	1	NA	promoter-TSS (NM_011324)	promoter-TSS (NM_011324)	58	NM_011324	20276	Mm.144114	NM_011324	ENSMUSG00000030340	Scnn1a	ENaC|SCNEA|Scnn1|mENaC	sodium channel, nonvoltage-gated 1 alpha	protein-coding
mm_41161.1	chr5	87929959	87929961	+	1	NA	exon (NM_007786, exon 4 of 5)	exon (NM_007786, exon 4 of 5)	4327	NM_007786	12994	Mm.296303	NM_007786	ENSMUSG00000001622	Csn3	AW208918|CSN10|Csnk	casein kappa	protein-coding
mm_63003.1	chr7	120842839	120842910	+	1	NA	promoter-TSS (NM_001267710)	promoter-TSS (NM_001267710)	43	NM_007908	13631	Mm.25997	NM_007908	ENSMUSG00000035064	Eef2k	C86191|eEF-2K	eukaryotic elongation factor-2 kinase	protein-coding
mm_68957.1	chr7	126566181	126566209	-	1	NA	5' UTR (NM_146200, exon 2 of 21)	5' UTR (NM_146200, exon 2 of 21)	171	NM_146200	56347	Mm.22776	NM_146200	ENSMUSG00000030738	Eif3c	110kDa|3230401O13Rik|Eif3s8|NIPIL(A3)|NipilA3|Xs|Xsl	eukaryotic translation initiation factor 3, subunit C	protein-coding
mm_38391.1	chr4	138819243	138819247	-	1	NA	promoter-TSS (NM_011110)	promoter-TSS (NM_011110)	12	NM_011110	18784	Mm.486532	NM_011110	ENSMUSG00000041193	Pla2g5	PLA2|sPLA2	phospholipase A2, group V	protein-coding
mm_30242.1	chr3	146499722	146499803	-	1	NA	promoter-TSS (NM_001316756)	promoter-TSS (NM_001316756)	-9	NM_027617	70951	Mm.383235	NM_027617	ENSMUSG00000028188	Spata1	4921536I21Rik|AV266943|SP-2	spermatogenesis associated 1	protein-coding
mm_145384.1	chr18	57133053	57133063	+	1	NA	promoter-TSS (NM_001001979)	promoter-TSS (NM_001001979)	-32	NM_001001979	70417	Mm.297863	NM_001001979	ENSMUSG00000024593	Megf10	3000002B06Rik|Gm331	multiple EGF-like-domains 10	protein-coding
mm_39433.1	chr5	16553800	16553821	+	1	NA	promoter-TSS (NM_001289461)	promoter-TSS (NM_001289461)	-91	NM_001289461	15234	Mm.267078	NM_010427	ENSMUSG00000028864	Hgf	C230052L06Rik|HGF/SF|NK1|NK2|SF|SF/HGF	hepatocyte growth factor	protein-coding
mm_120619.1	chr14	70443519	70443530	+	1	NA	promoter-TSS (NM_025945)	promoter-TSS (NM_025945)	14	NR_029802	723838		NR_029802	ENSMUSG00000065528	Mir320	Mirn320|mir-320|mmu-mir-320	microRNA 320	ncRNA
mm_104000.1	chr11	84870813	84870823	-	1	NA	promoter-TSS (NM_153144)	promoter-TSS (NM_153144)	-80	NM_153144	217039	Mm.356653	NM_153144	ENSMUSG00000020530	Ggnbp2	AI451896|C75939|D330017P12Rik|DIF-3|Zfp403	gametogenetin binding protein 2	protein-coding
mm_109831.1	chr12	4038775	4038855	-	1	NA	promoter-TSS (NM_001082483)	promoter-TSS (NM_001082483)	100	NM_001082483	668212	Mm.210266	NM_001082483	ENSMUSG00000020658	Efr3b	AI852640|C030014M07Rik|mKIAA0953	EFR3 homolog B	protein-coding
mm_36204.1	chr4	62360557	62360576	-	1	NA	promoter-TSS (NM_001045528)	promoter-TSS (NM_001045528)	-18	NM_001045528	338355	Mm.357792	NM_001045528	ENSMUSG00000066151	Fkbp15	BB131447|C430014M02Rik|FKBO133|FKBP-133|FKBP-15|FKBP133|mKIAA0674	FK506 binding protein 15	protein-coding
mm_8513.1	chr1	154726689	154726700	-	1	NA	promoter-TSS (NM_009782)	promoter-TSS (NM_009782)	-774	NM_009782	12290	Mm.267517	NM_009782	ENSMUSG00000004110	Cacna1e	A430040I15|BII|Cach6|Cacnl1a6|Cav2.3|Cchra1|alpha1E	calcium channel, voltage-dependent, R type, alpha 1E subunit	protein-coding
mm_80655.1	chr9	90054456	90054458	+	1	NA	5' UTR (NM_007801, exon 1 of 12)	5' UTR (NM_007801, exon 1 of 12)	190	NM_001312649	13036	Mm.2277	NM_007801	ENSMUSG00000032359	Ctsh	AL022844	cathepsin H	protein-coding
mm_47131.1	chr5	120472818	120472830	-	1	NA	promoter-TSS (NM_133902)	promoter-TSS (NM_133902)	-61	NM_133902	257635	Mm.5162	NM_133902	ENSMUSG00000029596	Sdsl	4432411H13Rik|AI504310|SDH1|SDS-RS1|TDH	serine dehydratase-like	protein-coding
mm_119211.1	chr14	32991413	32991423	+	1	NA	promoter-TSS (NM_001146021)	promoter-TSS (NM_001146021)	36	NM_026253	67580	Mm.46115	NM_026253	ENSMUSG00000041673	Lrrc18	4930442L21Rik|MTLR1	leucine rich repeat containing 18	protein-coding
mm_16426.1	chr2	180332391	180332402	+	1	NA	promoter-TSS (NR_045877)	promoter-TSS (NR_045877)	-461	NR_045877	100036520	Mm.98950	NR_045877	ENSMUSG00000056061	Gata5os	Gm14318|OTTMUSG00000016300	GATA binding protein 5, opposite strand	ncRNA
mm_31301.1	chr4	46000449	46000474	+	1	NA	intron (NM_146142, intron 6 of 16)	intron (NM_146142, intron 6 of 16)	28164	NM_146142	100121	Mm.275413	NM_146142	ENSMUSG00000035517	Tdrd7	5730495N10Rik|AI447470|PCTAIRE2BP	tudor domain containing 7	protein-coding
mm_6999.1	chr1	86389370	86389429	-	1	NA	promoter-TSS (NM_001319227)	promoter-TSS (NM_001319227)	-38	NM_001319227	14767	Mm.389159	NM_010341	ENSMUSG00000026237	Nmur1	FM-3|Gpr66|NMU-R1|NMU1R|NmU-R	neuromedin U receptor 1	protein-coding
mm_6695.1	chr1	80755809	80755821	-	1	NA	intron (NM_175291, intron 1 of 55)	intron (NM_175291, intron 1 of 55)	2738	NM_175291	210293	Mm.133473	NM_175291	ENSMUSG00000038608	Dock10	9330153B10Rik|A630054M16Rik|Jr4|Jr5|R75174|ZIZ3|Zizimin3|mKIAA0694	dedicator of cytokinesis 10	protein-coding
mm_60323.1	chr7	44225431	44225451	+	1	NA	promoter-TSS (NM_010639)	promoter-TSS (NM_010639)	81	NM_001320331	16612	Mm.142722	NM_010639	ENSMUSG00000063903	Klk1	0610007D04Rik|KAL-B|Kal|Klk1b6|Klk6|mGk-6	kallikrein 1	protein-coding
mm_56640.1	chr6	113307768	113307786	-	1	NA	intron (NM_001282128, intron 1 of 13)	intron (NM_001282128, intron 1 of 13)	640	NM_001282126	78783	Mm.356059	NM_030178	ENSMUSG00000001632	Brpf1	4833438B11Rik|4930540D11Rik|Brpf2	bromodomain and PHD finger containing, 1	protein-coding
mm_999.1	chr1	58713447	58713457	+	1	NA	5' UTR (NM_207653, exon 1 of 10)	5' UTR (NM_207653, exon 1 of 10)	166	NM_207653	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_167276.1	chr8	34152347	34152350	+	1	NA	Intergenic	Intergenic	-2215	NM_026432	67887	Mm.290353	NM_026432	ENSMUSG00000031532	Saraf	1810045K07Rik|Tmem66	store-operated calcium entry-associated regulatory factor	protein-coding
mm_4661.1	chr1	180365378	180365420	+	1	NA	intron (NM_001081175, intron 2 of 7)	intron (NM_001081175, intron 2 of 7)	-34850	NR_003623	277333	Mm.389223	NM_199472		Gm5069	EG277333	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_94850.1	chr11	23771585	23771598	+	1	NA	promoter-TSS (NM_009044)	promoter-TSS (NM_009044)	-621	NM_009044	19696	Mm.4869	NM_009044	ENSMUSG00000020275	Rel	c-Rel	reticuloendotheliosis oncogene	protein-coding
mm_98463.1	chr11	94948364	94948388	+	1	NA	exon (NM_007742, exon 41 of 51)	exon (NM_007742, exon 41 of 51)	12152	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_18041.1	chr2	39005127	39005145	-	1	NA	promoter-TSS (NM_025592)	promoter-TSS (NM_025592)	-5	NM_025592	66489	Mm.345333	NM_025592	ENSMUSG00000062997	Rpl35	2410039E09Rik	ribosomal protein L35	protein-coding
mm_157301.1	chrX	20928773	20928783	-	1	NA	exon (NM_008823, exon 4 of 9)	exon (NM_008823, exon 4 of 9)	2777	NM_008823	18636	Mm.3064	NM_008823	ENSMUSG00000001128	Cfp	BCFG|Pfc	complement factor properdin	protein-coding
mm_164130.1	chr15	41751485	41751495	+	1	NA	intron (NM_001130166, intron 3 of 16)	intron (NM_001130166, intron 3 of 16)	-37544	NM_001130165	170719	Mm.254267	NM_130885	ENSMUSG00000022307	Oxr1	2210416C20Rik|C7|C7B	oxidation resistance 1	protein-coding
mm_143283.1	chr17	65777567	65777576	-	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-4819	NM_133685	106572	Mm.29274	NM_133685	ENSMUSG00000056515	Rab31	1700093E07Rik|AI415285|Rab22B	RAB31, member RAS oncogene family	protein-coding
mm_122284.1	chr14	34503241	34503250	-	1	NA	promoter-TSS (NM_009758)	promoter-TSS (NM_009758)	-699	NM_009758	12166	Mm.237825	NM_009758	ENSMUSG00000021796	Bmpr1a	1110037I22Rik|ALK3|AU045487|BMPR-IA|Bmpr	bone morphogenetic protein receptor, type 1A	protein-coding
mm_27731.1	chr3	69044698	69044763	-	1	NA	promoter-TSS (NM_025863)	promoter-TSS (NM_025863)	12	NM_025863	66949	Mm.176695	NM_025863	ENSMUSG00000034317	Trim59	2310035M22Rik|2700022F13Rik|Mrf1|TSBF1	tripartite motif-containing 59	protein-coding
mm_79784.1	chr9	63077195	63077198	+	1	NA	Intergenic	MTE2a|LTR|ERVL-MaLR	69784	NM_172446	207667	Mm.36349	NM_172446	ENSMUSG00000022245	Skor1	AV273001|C230094B15Rik|Corl1|Lbxcor1	SKI family transcriptional corepressor 1	protein-coding
mm_77628.1	chr8	124020935	124020955	-	1	NA	intron (NM_133966, intron 1 of 4)	CpG	364	NM_133966	102162	Mm.291777	NM_133966	ENSMUSG00000038697	Taf5l	1110005N04Rik|AI849020	TATA-box binding protein associated factor 5 like	protein-coding
mm_66426.1	chr7	44625691	44625719	-	1	NA	intron (NM_001271538, intron 26 of 40)	ORR1E|LTR|ERVL-MaLR	34819	NM_001290682	16504	Mm.40312	NM_008422	ENSMUSG00000062785	Kcnc3	KShIIID|Kcr2-3|Kv3.3	potassium voltage gated channel, Shaw-related subfamily, member 3	protein-coding
mm_43833.1	chr5	142972368	142972393	+	1	NA	3' UTR (NM_007984, exon 5 of 5)	3' UTR (NM_007984, exon 5 of 5)	12025	NM_007984	14086	Mm.289707	NM_007984	ENSMUSG00000029581	Fscn1	AI663989|Fan1|fascin-1	fascin actin-bundling protein 1	protein-coding
mm_128104.1	chr15	27968261	27968267	-	1	NA	intron (NM_001081302, intron 1 of 56)	intron (NM_001081302, intron 1 of 56)	57584	NM_001081302	223435	Mm.485422	NM_001081302	ENSMUSG00000022263	Trio	6720464I07Rik|AA408740|Solo	triple functional domain (PTPRF interacting)	protein-coding
mm_141725.1	chr17	34115577	34115593	-	1	NA	intron (NR_037970, intron 5 of 12)	intron (NR_037970, intron 5 of 12)	4315	NR_037970	14312	Mm.3444	NM_010238	ENSMUSG00000024335	Brd2	AW228947|D17H6S113E|Frg-1|Fsrg-1|Fsrg1|Nat|Ring3|Rnf3|mKIAA4005	bromodomain containing 2	protein-coding
mm_22249.1	chr2	174849988	174849993	-	1	NA	Intergenic	Intergenic	89371	NM_007903	13616	Mm.9478	NM_007903	ENSMUSG00000027524	Edn3	ET-3|PPET3|ls|tmgc48	endothelin 3	protein-coding
mm_111452.1	chr12	98385861	98385867	-	1	NA	Intergenic	Intergenic	117229	NM_008152	14744	Mm.378924	NM_008152	ENSMUSG00000021886	Gpr65	Dig1|Gpcr25|TDAG8	G-protein coupled receptor 65	protein-coding
mm_13143.1	chr2	92185408	92185436	+	1	NA	promoter-TSS (NM_001109691)	promoter-TSS (NM_001109691)	-61	NM_001109691	192285	Mm.330408	NM_138755	ENSMUSG00000058318	Phf21a	80kDa|Bhc|Bhc80|D030065N23Rik|PFTF1	PHD finger protein 21A	protein-coding
mm_14230.1	chr2	127587215	127587263	+	1	NA	promoter-TSS (NM_029963)	promoter-TSS (NM_029963)	-187	NM_029963	77721	Mm.274601	NM_029963	ENSMUSG00000027374	Mrps5	1620401I16Rik|AI850294	mitochondrial ribosomal protein S5	protein-coding
mm_148124.1	chr18	75377544	75377548	-	1	NA	intron (NM_001042660, intron 3 of 3)	intron (NM_001042660, intron 3 of 3)	10181	NM_001042660	17131	Mm.34407	NM_008543	ENSMUSG00000025880	Smad7	Madh7	SMAD family member 7	protein-coding
mm_30702.1	chr4	11761011	11761013	+	1	NA	intron (NM_019753, intron 1 of 17)	intron (NM_019753, intron 1 of 17)	2855	NM_019753	12557	Mm.33402	NM_019753	ENSMUSG00000028217	Cdh17	HPT-1|HPT-1/LI	cadherin 17	protein-coding
mm_69276.1	chr7	127946725	127946731	-	1	NA	promoter-TSS (NM_001319147)	promoter-TSS (NM_001319147)	-3	NM_001319147	77613	Mm.334253	NM_001081374	ENSMUSG00000070371	Prss36	C330007D15Rik	protease, serine 36	protein-coding
mm_81549.1	chr9	110305186	110305229	+	1	NA	promoter-TSS (NM_001081381)	promoter-TSS (NM_001081381)	15	NM_001081381	72341	Mm.374250	NM_001081381	ENSMUSG00000054836	Elp6	2610001P13Rik|2610002I17Rik|AV159994|Tmem103	elongator acetyltransferase complex subunit 6	protein-coding
mm_25587.1	chr3	116886131	116886145	+	1	NA	intron (NM_009146, intron 7 of 16)	PB1D10|SINE|Alu	24458	NM_009146	20321	Mm.66293	NM_009146	ENSMUSG00000033386	Frrs1	AI131732|Sdfr2	ferric-chelate reductase 1	protein-coding
mm_147180.1	chr18	36770185	36770196	-	1	NA	exon (NM_008214, exon 10 of 13)	exon (NM_008214, exon 10 of 13)	-3976	NM_173383	213236	Mm.234464	NM_173383	ENSMUSG00000044595	Dnd1	BC034897|RBMS4|Ter	DND microRNA-mediated repression inhibitor 1	protein-coding
mm_31814.1	chr4	66827736	66827766	+	1	NA	5' UTR (NM_021297, exon 1 of 3)	5' UTR (NM_021297, exon 1 of 3)	200	NM_021297	21898	Mm.38049	NM_021297	ENSMUSG00000039005	Tlr4	Lps|Ly87|Ran/M1|Rasl2-8	toll-like receptor 4	protein-coding
mm_41221.1	chr5	88584000	88584005	+	1	NA	5' UTR (NM_027530, exon 1 of 13)	5' UTR (NM_027530, exon 1 of 13)	489	NM_027530	52822	Mm.270469	NM_027530	ENSMUSG00000029291	Rufy3	2810428M05Rik|6330416M07Rik|AW455998|AW538594|D5Bwg0860e|Ripx|Rpipx	RUN and FYVE domain containing 3	protein-coding
mm_117240.1	chr13	64312677	64312746	-	1	NA	promoter-TSS (NM_025370)	promoter-TSS (NM_025370)	-1	NM_025370	66129	Mm.491110	NM_025370	ENSMUSG00000021482	Aaed1	1110018J18Rik|AI849003	AhpC/TSA antioxidant enzyme domain containing 1	protein-coding
mm_141213.1	chr17	27133907	27133924	-	1	NA	promoter-TSS (NM_026063)	promoter-TSS (NM_026063)	-24	NM_026063	67267	Mm.272389	NM_026063	ENSMUSG00000024208	Uqcc2	2900010M23Rik|Cbp6|M19|Mnf1	ubiquinol-cytochrome c reductase complex assembly factor 2	protein-coding
mm_153841.1	chr19	46328433	46328452	-	1	NA	5' UTR (NM_133694, exon 1 of 4)	5' UTR (NM_133694, exon 1 of 4)	258	NM_133694	68431	Mm.19973	NM_133694	ENSMUSG00000025226	Fbxl15	0710008C12Rik|Fbxo37	F-box and leucine-rich repeat protein 15	protein-coding
mm_45417.1	chr5	66492119	66492148	-	1	NA	5' UTR (NM_009686, exon 3 of 18)	5' UTR (NM_009686, exon 3 of 18)	126684	NM_009686	11787	Mm.5159	NM_009686	ENSMUSG00000029207	Apbb2	2310007D03Rik|FE65L1|Rirl1|TR2L|Zfra	amyloid beta (A4) precursor protein-binding, family B, member 2	protein-coding
mm_141806.1	chr17	34549332	34549348	-	1	NA	Intergenic	Intergenic	-14955	NM_010929	18132	Mm.173813	NM_010929	ENSMUSG00000015468	Notch4	Int-3|Int3|N4	notch 4	protein-coding
mm_71088.1	chr8	34807614	34807615	+	1	NA	promoter-TSS (NM_176933)	promoter-TSS (NM_176933)	4	NM_176933	319520	Mm.170276	NM_176933	ENSMUSG00000031530	Dusp4	2700078F24Rik|AI844617|BB104621|E130306H24Rik|MKP2	dual specificity phosphatase 4	protein-coding
mm_57285.1	chr6	124415018	124415026	-	1	NA	promoter-TSS (NM_008995)	promoter-TSS (NM_008995)	45	NM_008995	19305	Mm.22418	NM_008995	ENSMUSG00000005069	Pex5	AW212715|ESTM1|PTS1R|Pxr1|X83306	peroxisomal biogenesis factor 5	protein-coding
mm_111062.1	chr12	80113231	80113232	-	1	NA	promoter-TSS (NM_007564)	promoter-TSS (NM_007564)	-218	NM_007564	12192	Mm.235132	NM_007564	ENSMUSG00000021127	Zfp36l1	AW742437|AW743212|Berg36|Brf1|D530020L18Rik|ERF1|TIS11b|cMG1	zinc finger protein 36, C3H type-like 1	protein-coding
mm_41989.1	chr5	107725934	107725940	+	1	NA	promoter-TSS (NM_001267621)	promoter-TSS (NM_001267621)	-132	NM_001267621	14581	Mm.2078	NM_010278	ENSMUSG00000029275	Gfi1	AW495828|Gfi-1|Pal-1|Pal1	growth factor independent 1	protein-coding
mm_85548.1	chr9	106685654	106685674	-	1	NA	5' UTR (NM_011573, exon 1 of 6)	5' UTR (NM_011573, exon 1 of 6)	152	NM_011573	21767	Mm.22266	NM_011573	ENSMUSG00000040813	Tex264	TEG-264	testis expressed gene 264	protein-coding
mm_72939.1	chr8	91387356	91387359	+	1	NA	intron (NM_011936, intron 1 of 8)	B1F|SINE|Alu	73832	NM_011936	26383	Mm.4375	NM_011936	ENSMUSG00000055932	Fto	AW743446|mKIAA1752	fat mass and obesity associated	protein-coding
mm_137369.1	chr17	25471704	25471717	+	1	NA	5' UTR (NM_027951, exon 1 of 6)	5' UTR (NM_027951, exon 1 of 6)	120	NM_027951	71840	Mm.282330	NM_027951	ENSMUSG00000024175	Tekt4	1700010L19Rik	tektin 4	protein-coding
mm_12568.1	chr2	72979504	72979520	+	1	NA	promoter-TSS (NR_045269)	promoter-TSS (NR_045269)	80	NR_045269	100503849	Mm.389285	NM_183265		Sp3os	1700011J10Rik	trans-acting transcription factor 3, opposite strand	ncRNA
mm_86364.1	chr9	123792070	123792072	-	1	NA	3' UTR (NM_001110253, exon 18 of 18)	3' UTR (NM_001110253, exon 18 of 18)	-14406	NM_030712	80901	Mm.124289	NM_030712	ENSMUSG00000048521	Cxcr6	BB217514|BONZO|STRL33	chemokine (C-X-C motif) receptor 6	protein-coding
mm_43724.1	chr5	139543890	139543904	+	1	NA	promoter-TSS (NM_013702)	promoter-TSS (NM_013702)	-1	NM_013702	22255	Mm.42190	NM_013702	ENSMUSG00000029546	Uncx	Chx4|Uncx4.1	UNC homeobox	protein-coding
mm_170019.1	chr1	7190228	7190239	+	1	NA	Intergenic	Intergenic	101313	NM_183028	319263	Mm.21539	NM_183028	ENSMUSG00000051285	Pcmtd1	8430411F12Rik|A030012M09Rik	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding
mm_116217.1	chr13	32806985	32807020	-	1	NA	intron (NM_030215, intron 3 of 6)	intron (NM_030215, intron 3 of 6)	4972	NM_030215	78903	Mm.286680	NM_030215	ENSMUSG00000021400	Wrnip1	4833444L21Rik|WHIP|Wrnip	Werner helicase interacting protein 1	protein-coding
mm_47751.1	chr5	130955725	130955727	-	1	NA	intron (NM_145218, intron 6 of 10)	PB1D9|SINE|Alu	351796	NM_145218	212996	Mm.299204	NM_145218	ENSMUSG00000034040	Wbscr17	AA388321|E330012B09Rik	Williams-Beuren syndrome chromosome region 17 homolog (human)	protein-coding
mm_42283.1	chr5	114289246	114289258	+	1	NA	Intergenic	Intergenic	-15491	NM_148935	116810	Mm.17709	NM_148935	ENSMUSG00000042002	Foxn4	-	forkhead box N4	protein-coding
mm_34557.1	chr4	149634692	149634711	+	1	NA	exon (NM_023051, exon 8 of 19)	exon (NM_023051, exon 8 of 19)	20866	NR_105990	102465983		NR_105990	ENSMUSG00000098580	Mir7023	Gm27912|mmu-mir-7023	microRNA 7023	ncRNA
mm_5957.1	chr1	56971695	56971709	-	1	NA	promoter-TSS (NM_139146)	promoter-TSS (NM_139146)	233	NR_024325	329160	Mm.419039	NR_024325	ENSMUSG00000087022	9130024F11Rik	B530002L08|EG329160	RIKEN cDNA 9130024F11 gene	ncRNA
mm_111460.1	chr12	98420037	98420071	-	1	NA	Intergenic	Intergenic	-103790	NR_136759	105245437	Mm.446375	NR_136759		Gm40893	-	predicted gene, 40893	ncRNA
mm_25905.1	chr3	131112465	131112483	+	1	NA	promoter-TSS (NM_001276403)	promoter-TSS (NM_001276403)	-317	NM_001276403	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_34031.1	chr4	138096818	138096835	+	1	NA	exon (NM_001256198, exon 7 of 33)	exon (NM_001256198, exon 7 of 33)	41692	NR_126429	73563	Mm.444294	NR_126429	ENSMUSG00000084804	1700095J12Rik	-	RIKEN cDNA 1700095J12 gene	ncRNA
mm_92263.1	chr10	71115157	71115160	-	1	NA	intron (NM_031397, intron 1 of 20)	intron (NM_031397, intron 1 of 20)	44532	NM_031397	83675	Mm.286834	NM_031397	ENSMUSG00000014329	Bicc1	Bic-C|bpk|jcpk	BicC family RNA binding protein 1	protein-coding
mm_81650.1	chr9	110953759	110953787	+	1	NA	intron (NM_028838, intron 1 of 8)	CpG	2228	NM_028838	74249	Mm.307615	NM_028838	ENSMUSG00000032495	Lrrc2	2400002D05Rik|4933431K03Rik	leucine rich repeat containing 2	protein-coding
mm_21753.1	chr2	164837404	164837450	-	1	NA	exon (NM_008906, exon 11 of 15)	exon (NM_008906, exon 11 of 15)	3654	NM_008906	19025	Mm.359633	NM_008906	ENSMUSG00000017760	Ctsa	AU019505|PPCA|Ppgb	cathepsin A	protein-coding
mm_58457.1	chr7	3332790	3332837	+	1	NA	Intergenic	Intergenic	-3772	NM_133189	81904	Mm.214994	NM_133189	ENSMUSG00000069806	Cacng7	-	calcium channel, voltage-dependent, gamma subunit 7	protein-coding
mm_24397.1	chr3	90293354	90293380	+	1	NA	Intergenic	Intergenic	23218	NR_105979	102465612		NR_105979	ENSMUSG00000099199	Mir7012	Gm27370|mmu-mir-7012	microRNA 7012	ncRNA
mm_67412.1	chr7	80113971	80114009	-	1	NA	intron (NM_173011, intron 1 of 10)	intron (NM_173011, intron 1 of 10)	1360	NM_173011	269951	Mm.246432	NM_173011	ENSMUSG00000030541	Idh2	E430004F23|IDPm|Idh-2	isocitrate dehydrogenase 2 (NADP+), mitochondrial	protein-coding
mm_147321.1	chr18	42249466	42249468	-	1	NA	intron (NM_134137, intron 4 of 31)	ID_B1|SINE|B4	12604	NM_134137	107045	Mm.312170	NM_134137	ENSMUSG00000024493	Lars	2310045K21Rik|3110009L02Rik|AW536573|mKIAA1352	leucyl-tRNA synthetase	protein-coding
mm_159883.1	chr6	21216258	21216258	+	1	NA	5' UTR (NM_019697, exon 1 of 6)	5' UTR (NM_019697, exon 1 of 6)	149	NM_019697	16508	Mm.425316	NM_019697	ENSMUSG00000060882	Kcnd2	AI839615|AW555701|Kv4.2|R75121|mKIAA1044	potassium voltage-gated channel, Shal-related family, member 2	protein-coding
mm_15352.1	chr2	156202470	156202473	+	1	NA	intron (NM_172674, intron 1 of 17)	intron (NM_172674, intron 1 of 17)	5824	NM_172674	228829	Mm.427078	NM_172674	ENSMUSG00000038116	Phf20	6820402O20Rik	PHD finger protein 20	protein-coding
mm_102458.1	chr11	59839746	59839763	-	1	NA	promoter-TSS (NM_011991)	promoter-TSS (NM_011991)	13	NM_011991	26572	Mm.40	NM_011991	ENSMUSG00000019373	Cops3	Csn3|Sgn3	COP9 signalosome subunit 3	protein-coding
mm_117764.1	chr13	96132701	96132711	-	1	NA	promoter-TSS (NM_029210)	promoter-TSS (NM_029210)	-129	NM_029210	75209	Mm.40436	NM_029210	ENSMUSG00000051111	Sv2c	4930527L09Rik|AI841971	synaptic vesicle glycoprotein 2c	protein-coding
mm_111620.1	chr12	102413553	102413570	-	1	NA	exon (NM_011175, exon 3 of 14)	exon (NM_011175, exon 3 of 14)	26252	NM_011175	19141	Mm.17185	NM_011175	ENSMUSG00000021190	Lgmn	AEP|AI746452|AU022324|Prsc1	legumain	protein-coding
mm_109284.1	chr12	109550909	109550913	+	1	NA	intron (NR_027651, intron 7 of 8)	intron (NR_027651, intron 7 of 8)	5513	NR_003633	17263	Mm.289645	NM_144513	ENSMUSG00000021268	Meg3	2900016C05Rik|3110050O07Rik|6330408G06Rik|AI425946|AW108224|D12Bwg1266e|Gtl2|R74756|R75394	maternally expressed 3	ncRNA
mm_141436.1	chr17	29549589	29549598	-	1	NA	promoter-TSS (NM_001162901)	promoter-TSS (NM_001162901)	0	NM_001162901	71138	Mm.158581	NM_001162901	ENSMUSG00000079580	Tmem217	4933413N12Rik|EG622644	transmembrane protein 217	protein-coding
mm_11269.1	chr2	30061839	30061841	+	1	NA	promoter-TSS (NM_023871)	promoter-TSS (NM_023871)	-156	NM_023871	56086	Mm.326055	NM_023871	ENSMUSG00000054766	Set	2610030F17Rik|5730420M11Rik|AA407739|I-2PP2A|StF-IT-1|TAF-I	SET nuclear oncogene	protein-coding
mm_64527.1	chr7	143978429	143978444	+	1	NA	intron (NR_037302, intron 5 of 5)	CpG	-30818	NR_037292	100526562		NR_037292	ENSMUSG00000093221	Mir3105	mmu-mir-3105	microRNA 3105	ncRNA
mm_61129.1	chr7	55853079	55853084	+	1	NA	intron (NM_011370, intron 1 of 30)	intron (NM_011370, intron 1 of 30)	11010	NM_001164661	20430	Mm.37249	NM_011370	ENSMUSG00000030447	Cyfip1	E030028J09Rik|P140SRA-1|P140sra1|Shyc|Sra-1|Sra1|l(7)1Rl|l71Rl|l7Rl1|mKIAA0068|pl-1	cytoplasmic FMR1 interacting protein 1	protein-coding
mm_120763.1	chr14	73368377	73368406	+	1	NA	exon (NM_008410, exon 2 of 6)	exon (NM_008410, exon 2 of 6)	16880	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_101936.1	chr11	50207447	50207476	-	1	NA	exon (NM_011018, exon 3 of 8)	exon (NM_011018, exon 3 of 8)	3359	NM_001290769	18412	Mm.40828	NM_011018	ENSMUSG00000015837	Sqstm1	A170|OSF-6|Osi|STAP|STONE14|p62	sequestosome 1	protein-coding
mm_40084.1	chr5	34525798	34525869	+	1	NA	promoter-TSS (NM_011893)	promoter-TSS (NM_011893)	49	NM_011893	24055	Mm.5012	NM_011893	ENSMUSG00000054520	Sh3bp2	3BP2	SH3-domain binding protein 2	protein-coding
mm_53223.1	chr6	126990541	126990585	+	1	NA	Intergenic	Intergenic	-24979	NM_010204	14177	Mm.3403	NM_010204	ENSMUSG00000000183	Fgf6	Fgf-6|HSTF-2	fibroblast growth factor 6	protein-coding
mm_15246.1	chr2	154672430	154672434	+	1	NA	intron (NM_029362, intron 1 of 4)	intron (NM_029362, intron 1 of 4)	15406	NM_029362	75608	Mm.262480	NM_029362	ENSMUSG00000038467	Chmp4b	2010012F05Rik|C76846|Snf7-2	charged multivesicular body protein 4B	protein-coding
mm_71721.1	chr8	61963645	61963654	+	1	NA	exon (NM_001293783, exon 13 of 38)	exon (NM_001293783, exon 13 of 38)	35562	NM_001293783	234311	Mm.275233	NM_144928	ENSMUSG00000037921	Ddx60	9830118M07	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	protein-coding
mm_116799.1	chr13	53639226	53639236	-	1	NA	promoter-TSS (NR_131079)	promoter-TSS (NR_131079)	-30	NR_131079	77398	Mm.174307	NR_131079		9530014B07Rik	-	RIKEN cDNA 9530014B07 gene	ncRNA
mm_72664.1	chr8	84872767	84872774	+	1	NA	non-coding (NR_031759, exon 2 of 4)	non-coding (NR_031759, exon 2 of 4)	512	NM_001168244	71846	Mm.229128	NM_027954	ENSMUSG00000003824	Syce2	1700013H19Rik|AA407907|Cesc1	synaptonemal complex central element protein 2	protein-coding
mm_85800.1	chr9	110117380	110117445	-	1	NA	5' UTR (NM_001252682, exon 1 of 23)	5' UTR (NM_001252682, exon 1 of 23)	204	NM_001252682	72831	Mm.276305	NM_133347	ENSMUSG00000032480	Dhx30	2810477H02Rik|C130058C04Rik|Ddx30|HELG|Ret-CoR	DEAH (Asp-Glu-Ala-His) box polypeptide 30	protein-coding
mm_72065.1	chr8	71470406	71470420	+	1	NA	intron (NM_001294259, intron 1 of 3)	intron (NM_001294259, intron 1 of 3)	1219	NR_122114	66498	Mm.260360	NM_025600	ENSMUSG00000074247	Dda1	1500034J01Rik|1700095J19Rik|R74921	DET1 and DDB1 associated 1	protein-coding
mm_65466.1	chr7	25476484	25476500	-	1	NA	exon (NM_001039186, exon 2 of 8)	exon (NM_001039186, exon 2 of 8)	1133	NM_001039185	26365	Mm.322502	NM_011926	ENSMUSG00000074272	Ceacam1	Bgp|Bgp1|C-CAM|CD66a|Cc1|Cea-1|Cea-7|Cea1|Cea7|Hv-2|Hv2|MHVR|MHVR1|Mhv-1|bb-1|mCEA1|mmCGM1|mmCGM1a|mmCGM2	carcinoembryonic antigen-related cell adhesion molecule 1	protein-coding
mm_120545.1	chr14	67299345	67299348	+	1	NA	intron (NM_010095, intron 7 of 16)	intron (NM_010095, intron 7 of 16)	15365	NM_001037931	628416	Mm.390723	NM_001037931		Gm6878	EG628416	predicted gene 6878	protein-coding
mm_142501.1	chr17	46032118	46032131	-	1	NA	5' UTR (NM_001025250, exon 1 of 8)	5' UTR (NM_001025250, exon 1 of 8)	253	NM_001287058	22339	Mm.282184	NM_009505	ENSMUSG00000023951	Vegfa	Vegf|Vpf	vascular endothelial growth factor A	protein-coding
mm_40264.1	chr5	38344403	38344423	+	1	NA	promoter-TSS (NR_046191)	promoter-TSS (NR_046191)	24	NR_046191	78172	Mm.243835	NR_046191	ENSMUSG00000106932	4930487D11Rik	-	RIKEN cDNA 4930487D11 gene	ncRNA
mm_83421.1	chr9	44965520	44965586	-	1	NA	promoter-TSS (NM_145400)	promoter-TSS (NM_145400)	47	NM_001346698	140630	Mm.215069	NM_145400	ENSMUSG00000059890	Ube4a	4732444G18Rik|9930123J21Rik|UFD2b	ubiquitination factor E4A	protein-coding
mm_92325.1	chr10	75764183	75764238	-	1	NA	5' UTR (NM_172549, exon 1 of 37)	5' UTR (NM_172549, exon 1 of 37)	147	NM_172549	104248	Mm.257404	NM_172549	ENSMUSG00000020196	Cabin1	A330070M20Rik|Cain|Ppp3in	calcineurin binding protein 1	protein-coding
mm_102853.1	chr11	69395664	69395712	-	1	NA	promoter-TSS (NM_030083)	promoter-TSS (NM_030083)	-103	NM_030083	78304	Mm.45683	NM_030083	ENSMUSG00000059278	Naa38	1500034E06Rik|Lsmd1	N(alpha)-acetyltransferase 38, NatC auxiliary subunit	protein-coding
mm_125701.1	chr15	67176991	67177055	+	1	NA	promoter-TSS (NM_009177)	promoter-TSS (NM_009177)	-141	NM_009177	20442	Mm.248334	NM_009177	ENSMUSG00000013846	St3gal1	5330418N22Rik|AI467004|ST3GalI|Siat4|Siat4a|St3gal-1	ST3 beta-galactoside alpha-2,3-sialyltransferase 1	protein-coding
mm_128485.1	chr15	50890095	50890108	-	1	NA	promoter-TSS (NR_035444)	promoter-TSS (NR_035444)	-60	NM_032000	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_86115.1	chr9	115499642	115499659	-	1	NA	Intergenic	Intergenic	117831	NR_130329	100316675		NR_130329	ENSMUSG00000080409	Mir467h	Mirn467h|mmu-mir-467h	microRNA 467h	ncRNA
mm_132275.1	chr16	32930094	32930106	+	1	NA	intron (NM_001310674, intron 1 of 21)	B3A|SINE|B2	16000	NM_001310672	70144	Mm.491178	NM_001081255	ENSMUSG00000022801	Lrch3	2210409B11Rik|AW215594|Gm1742	leucine-rich repeats and calponin homology (CH) domain containing 3	protein-coding
mm_45337.1	chr5	65697968	65697990	-	1	NA	promoter-TSS (NM_001081321)	promoter-TSS (NM_001081321)	-123	NM_001081321	71521	Mm.278974	NM_027818	ENSMUSG00000029202	Pds5a	9030416H16Rik|E230024D05Rik|mKIAA0648	PDS5 cohesin associated factor A	protein-coding
mm_42961.1	chr5	123104166	123104179	+	1	NA	intron (NM_001039723, intron 5 of 11)	intron (NM_001039723, intron 5 of 11)	27897	NM_001039723	330189	Mm.391872	NM_001039723	ENSMUSG00000054434	Tmem120b	-	transmembrane protein 120B	protein-coding
mm_61541.1	chr7	79297106	79297139	+	1	NA	exon (NM_018811, exon 3 of 11)	exon (NM_018811, exon 3 of 11)	23856	NM_018811	54608	Mm.365490	NM_018811	ENSMUSG00000039202	Abhd2	2210009N18Rik|LABH2|Labh-2	abhydrolase domain containing 2	protein-coding
mm_8857.1	chr1	162715457	162715484	-	1	NA	exon (NM_001081290, exon 9 of 35)	exon (NM_001081290, exon 9 of 35)	25086	NM_001081290	226562	Mm.245446	NM_001081290	ENSMUSG00000040225	Prrc2c	1810043M20Rik|9630039I18Rik|A630006J20|Bat2d|Bat2d1|Bat2l2|E130112L15Rik|Prrc3|mKIAA1096	proline-rich coiled-coil 2C	protein-coding
mm_123340.1	chr14	63136464	63136505	-	1	NA	exon (NM_007798, exon 5 of 10)	exon (NM_007798, exon 5 of 10)	14022	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_38870.1	chr4	149663188	149663202	-	1	NA	exon (NM_001164049, exon 3 of 24)	exon (NM_001164049, exon 3 of 24)	121	NM_001164052	18707	Mm.229108	NM_008840	ENSMUSG00000039936	Pik3cd	2410099E07Rik|2610208K16Rik|AW545373|p110delta	phosphatidylinositol 3-kinase catalytic delta polypeptide	protein-coding
mm_15569.1	chr2	158624883	158624896	+	1	NA	promoter-TSS (NM_175419)	promoter-TSS (NM_175419)	-24	NM_175419	109275	Mm.27747	NM_175419	ENSMUSG00000037761	Actr5	AA545173|B430109J19Rik	ARP5 actin-related protein 5	protein-coding
mm_39581.1	chr5	23465137	23465148	+	1	NA	intron (NM_026984, intron 4 of 25)	intron (NM_026984, intron 4 of 25)	30713	NM_026984	69188	Mm.205190	NM_026984	ENSMUSG00000029004	Kmt2e	1810033J14Rik|9530077A04Rik|D230038D11Rik|Mll5|NKp44L	lysine (K)-specific methyltransferase 2E	protein-coding
mm_120096.1	chr14	58036607	58036617	+	1	NA	Intergenic	Intergenic	-36074	NM_013518	14180	Mm.8846	NM_013518	ENSMUSG00000021974	Fgf9	Eks	fibroblast growth factor 9	protein-coding
mm_36054.1	chr4	57339002	57339009	-	1	NA	Intergenic	Intergenic	25287	NR_038179	73349	Mm.393774	NR_038178		1700042G15Rik	-	RIKEN cDNA 1700042G15 gene	ncRNA
mm_94237.1	chr11	3292444	3292452	+	1	NA	intron (NM_019574, intron 1 of 3)	intron (NM_019574, intron 1 of 3)	1991	NM_019574	56218	Mm.275563	NM_019574	ENSMUSG00000020453	Patz1	8430401L15Rik|AI447519|Mazr|Patz|Zfp278	POZ (BTB) and AT hook containing zinc finger 1	protein-coding
mm_165427.1	chr2	152907856	152907859	+	1	NA	Intergenic	Intergenic	-3495	NM_001081044	228785	Mm.250604	NM_001081044	ENSMUSG00000027470	Mylk2	9830004H17Rik|BB138278	myosin, light polypeptide kinase 2, skeletal muscle	protein-coding
mm_121599.1	chr14	7994564	7994584	-	1	NA	promoter-TSS (NM_007870)	promoter-TSS (NM_007870)	-392	NM_007870	13421	Mm.272258	NM_007870	ENSMUSG00000025279	Dnase1l3	DNasegamma|Dhp2|Lsd	deoxyribonuclease 1-like 3	protein-coding
mm_42364.1	chr5	114922443	114922476	+	1	NA	promoter-TSS (NM_145209)	promoter-TSS (NM_145209)	-781	NM_145209	231655	Mm.95479	NM_145209	ENSMUSG00000041827	Oasl1	7530414C13Rik|oasl9	2'-5' oligoadenylate synthetase-like 1	protein-coding
mm_99121.1	chr11	100145578	100145626	+	1	NA	exon (NM_008471, exon 1 of 6)	exon (NM_008471, exon 1 of 6)	324	NM_008471	16669	Mm.439699	NM_008471	ENSMUSG00000020911	Krt19	AI663979|CK-19|EndoC|K19|Krt-1.19|Krt1-19	keratin 19	protein-coding
mm_16265.1	chr2	173522664	173522671	+	1	NA	promoter-TSS (NM_028158)	promoter-TSS (NM_028158)	75	NM_028158	72221	Mm.46132	NM_028158	ENSMUSG00000027518	1700021F07Rik	-	RIKEN cDNA 1700021F07 gene	protein-coding
mm_92479.1	chr10	78283123	78283139	-	1	NA	exon (NM_053014, exon 6 of 10)	exon (NM_053014, exon 6 of 10)	-38489	NM_001081055	216131	Mm.27539	NM_001081055	ENSMUSG00000000374	Trappc10	B230307C21Rik|Gm870|Tmem1	trafficking protein particle complex 10	protein-coding
mm_126271.1	chr15	79141311	79141321	+	1	NA	promoter-TSS (NM_001310576)	promoter-TSS (NM_001310576)	-9	NM_027231	69833	Mm.279861	NM_027231	ENSMUSG00000033020	Polr2f	1810060D16Rik|RPB6	polymerase (RNA) II (DNA directed) polypeptide F	protein-coding
mm_67523.1	chr7	80947737	80947764	-	1	NA	promoter-TSS (NM_019951)	promoter-TSS (NM_019951)	-200	NM_019951	56529	Mm.43760	NM_019951	ENSMUSG00000025724	Sec11a	1810012E07Rik|18kDa|Sec11l1|Sid2895p|Spc18|sid2895	SEC11 homolog A, signal peptidase complex subunit	protein-coding
mm_33191.1	chr4	126256657	126256662	+	1	NA	promoter-TSS (NM_144941)	promoter-TSS (NM_144941)	-340	NM_001145970	245877	Mm.266716	NM_144941	ENSMUSG00000028849	Map7d1	AV028413|BC019977|Mtap7d1|Parcc1|Rprc1|mKIAA1187	MAP7 domain containing 1	protein-coding
mm_87926.1	chr10	62543816	62543826	+	1	NA	Intergenic	Intergenic	34636	NM_028197	72320	Mm.258955	NM_028197	ENSMUSG00000036955	Kif1bp	0710007C18Rik|2510003E04Rik|KBP|mKIAA1279	KIF1 binding protein	protein-coding
mm_54186.1	chr6	24103985	24104021	-	1	NA	intron (NM_019481, intron 9 of 14)	intron (NM_019481, intron 9 of 14)	64089	NM_019481	55961	Mm.19299	NM_019481	ENSMUSG00000029700	Slc13a1	AI314066|AI987826|NaSi-1|Nas1	solute carrier family 13 (sodium/sulfate symporters), member 1	protein-coding
mm_74214.1	chr8	123949447	123949465	+	1	NA	promoter-TSS (NM_172288)	promoter-TSS (NM_172288)	-191	NM_172288	234865	Mm.267812	NM_172288	ENSMUSG00000039509	Nup133	mermaid	nucleoporin 133	protein-coding
mm_32988.1	chr4	120291344	120291354	+	1	NA	Intergenic	Intergenic	-4088	NM_194060	329934	Mm.277090	NM_194060	ENSMUSG00000052135	Foxo6	-	forkhead box O6	protein-coding
mm_50866.1	chr6	55376375	55376379	+	1	NA	promoter-TSS (NM_001003685)	promoter-TSS (NM_001003685)	82	NM_001003685	14602	Mm.89928	NM_001003685	ENSMUSG00000004654	Ghrhr	Ghrfr|lit|little	growth hormone releasing hormone receptor	protein-coding
mm_16501.1	chr2	181212587	181212603	+	1	NA	exon (NM_011481, exon 1 of 8)	exon (NM_011481, exon 1 of 8)	576	NM_011481	20811	Mm.4752	NM_011481	ENSMUSG00000027579	Srms	A230069J08Rik|srm	src-related kinase lacking C-terminal regulatory tyrosine and N-terminal myristylation sites	protein-coding
mm_107262.1	chr12	28898603	28898649	+	1	NA	Intergenic	Intergenic	146798	NM_201357	380752	Mm.273724	NM_201357	ENSMUSG00000036613	Tssc1	D12Ertd604e|Eipr1	tumor suppressing subtransferable candidate 1	protein-coding
mm_169812.1	chr16	19342012	19342015	-	1	NA	Intergenic	L1Md_T|LINE|L1	-55272	NM_146451	258443	Mm.377506	NM_146451	ENSMUSG00000050742	Olfr164	MOR279-2	olfactory receptor 164	protein-coding
mm_148633.1	chr19	5460649	5460655	+	1	NA	promoter-TSS (NM_021438)	promoter-TSS (NM_021438)	45	NM_021438	58249	Mm.329656	NM_021438	ENSMUSG00000024911	Fibp	2010004G08Rik|2010005N21Rik|3010027N18Rik	fibroblast growth factor (acidic) intracellular binding protein	protein-coding
mm_79224.1	chr9	49954869	49954891	+	1	NA	Intergenic	Intergenic	-155487	NM_001311065	17967	Mm.4974	NM_010875	ENSMUSG00000039542	Ncam1	CD56|E-NCAM|NCAM-1|Ncam	neural cell adhesion molecule 1	protein-coding
mm_143111.1	chr17	57194171	57194190	-	1	NA	promoter-TSS (NM_019418)	promoter-TSS (NM_019418)	1	NM_019418	50930	Mm.483369	NM_019418	ENSMUSG00000005824	Tnfsf14	HVEM-L|HVEML|LIGHT|LTg|Ly113|Tnlg1d	tumor necrosis factor (ligand) superfamily, member 14	protein-coding
mm_29524.1	chr3	116634974	116634984	-	1	NA	exon (NM_008246, exon 10 of 12)	exon (NM_008246, exon 10 of 12)	-20392	NM_030016	229780	Mm.259648	NM_030016	ENSMUSG00000033439	Trmt13	4631408H19Rik|A330067P21|A930028L21Rik|Ccdc76	tRNA methyltransferase 13	protein-coding
mm_171576.1	chr4	147364574	147364590	+	1	NA	intron (NM_001039209, intron 1 of 2)	intron (NM_001039209, intron 1 of 2)	-188695	NM_001014397	433804	Mm.332047	NM_001014397	ENSMUSG00000065999	Zfp985	Gm13154|OTTMUSG00000010673	zinc finger protein 985	protein-coding
mm_74594.1	chr8	11626804	11626812	-	1	NA	intron (NM_001281975, intron 3 of 6)	intron (NM_001281975, intron 3 of 6)	8228	NR_030781	102334	Mm.12459	NM_133971	ENSMUSG00000031508	Ankrd10	4833425P12Rik|AW549277	ankyrin repeat domain 10	protein-coding
mm_134550.1	chr16	19982960	19982964	-	1	NA	promoter-TSS (NM_183390)	promoter-TSS (NM_183390)	87	NM_183390	239743	Mm.86699	NM_183390	ENSMUSG00000043008	Klhl6	-	kelch-like 6	protein-coding
mm_144128.1	chr18	4920624	4920642	+	1	NA	Intergenic	CpG	108147	NR_045881	100038439	Mm.387569	NR_045881	ENSMUSG00000097043	Gm10556	ENSMUSG00000073646	predicted gene 10556	ncRNA
mm_7609.1	chr1	126492841	126492848	-	1	NA	promoter-TSS (NM_172484)	promoter-TSS (NM_172484)	83	NM_172484	210356	Mm.377234	NM_172484	ENSMUSG00000049690	Nckap5	8430408F21|D130011D22Rik|E030049G20Rik|Erih1|Erih2|Gm1548|Nap5	NCK-associated protein 5	protein-coding
mm_121295.1	chr14	105499819	105499853	+	1	NA	intron (NR_045921, intron 1 of 2)	intron (NR_045921, intron 1 of 2)	1048	NR_045921	74864	Mm.159344	NR_045921	ENSMUSG00000022116	4930449E01Rik	-	RIKEN cDNA 4930449E01 gene	ncRNA
mm_51452.1	chr6	80566151	80566154	+	1	NA	intron (NM_001347261, intron 2 of 2)	intron (NM_001347261, intron 2 of 2)	546509	NM_178731	243499	Mm.483425	NM_178731	ENSMUSG00000052581	Lrrtm4	7530419J18Rik|A230052N11	leucine rich repeat transmembrane neuronal 4	protein-coding
mm_22488.1	chr3	5750804	5750804	+	1	NA	Intergenic	L1_Mus2|LINE|L1	-174556	NM_001163305	19302	Mm.132336	NM_008994	ENSMUSG00000040374	Pex2	D3Ertd138e|PAF-1|PMP35|Pxmp3	peroxisomal biogenesis factor 2	protein-coding
mm_5374.1	chr1	30873838	30873925	-	1	NA	Intergenic	CpG	-10625	NM_001081080	213109	Mm.194486	NM_025871	ENSMUSG00000048874	Phf3	2310061N19Rik|mKIAA0244	PHD finger protein 3	protein-coding
mm_160374.1	chr8	36505352	36505352	+	1	NA	intron (NM_176952, intron 2 of 3)	intron (NM_176952, intron 2 of 3)	16161	NM_176952	319582	Mm.180924	NM_176952	ENSMUSG00000039620	6430573F11Rik	Kiaa1456|TRM9L	RIKEN cDNA 6430573F11 gene	protein-coding
mm_145987.1	chr18	68272833	68272841	+	1	NA	intron (NM_153794, intron 2 of 3)	intron (NM_153794, intron 2 of 3)	-11864	NR_106078	102465702		NR_106078	ENSMUSG00000098253	Mir7219	Gm27613|mmu-mir-7219	microRNA 7219	ncRNA
mm_146889.1	chr18	25753853	25753927	-	1	NA	promoter-TSS (NM_001146295)	promoter-TSS (NM_001146295)	93	NM_133195	108013	Mm.266435	NM_133195	ENSMUSG00000024268	Celf4	A230070D14Rik|BRUNOL-4|Brul4|Brunol4|C130060B05Rik	CUGBP, Elav-like family member 4	protein-coding
mm_91442.1	chr10	33933160	33933170	-	1	NA	intron (NM_028287, intron 6 of 9)	intron (NM_028287, intron 6 of 9)	18047	NM_028287	72580	Mm.248081	NM_028287	ENSMUSG00000039531	Zufsp	2700019D07Rik	zinc finger with UFM1-specific peptidase domain	protein-coding
mm_149153.1	chr19	9015386	9015431	+	1	NA	exon (NM_009643, exon 5 of 5)	exon (NM_009643, exon 5 of 5)	-2496	NR_105786	102465190		NR_105786	ENSMUSG00000099308	Mir6367	Gm27467|mmu-mir-6367	microRNA 6367	ncRNA
mm_136625.1	chr17	5547889	5547901	+	1	NA	intron (NM_146073, intron 1 of 8)	intron (NM_146073, intron 1 of 8)	55295	NM_146073	224454	Mm.487663	NM_146073	ENSMUSG00000034265	Zdhhc14	B530001K09Rik|New1cp	zinc finger, DHHC domain containing 14	protein-coding
mm_149167.1	chr19	9060352	9060392	+	1	NA	intron (NM_001286518, intron 6 of 6)	intron (NM_001286518, intron 6 of 6)	27584	NM_011681	22287	Mm.2258	NM_011681	ENSMUSG00000024653	Scgb1a1	CC10|CC16|CCSP|PCB-BP|UG|UGB|Utg	secretoglobin, family 1A, member 1 (uteroglobin)	protein-coding
mm_32949.1	chr4	119544043	119544046	+	1	NA	intron (NM_172699, intron 1 of 12)	B1_Mur2|SINE|Alu	4383	NM_172699	230700	Mm.259227	NM_172699	ENSMUSG00000032998	Foxj3	C330039G02Rik|Fhd6	forkhead box J3	protein-coding
mm_51203.1	chr6	71325455	71325463	+	1	NA	intron (NM_009858, intron 1 of 5)	intron (NM_009858, intron 1 of 5)	2647	NM_009858	12526	Mm.333148	NM_009858	ENSMUSG00000053044	Cd8b1	Cd8b|Ly-3|Ly-C|Lyt-3	CD8 antigen, beta chain 1	protein-coding
mm_39075.1	chr4	154300008	154300028	-	1	NA	promoter-TSS (NM_001112744)	promoter-TSS (NM_001112744)	-123	NM_001112744	230972	Mm.38481	NM_001112744	ENSMUSG00000029032	Arhgef16	-	Rho guanine nucleotide exchange factor (GEF) 16	protein-coding
mm_163612.1	chr13	51838511	51838519	+	1	NA	Intergenic	B4|SINE|B4	-8160	NM_011817	23882	Mm.281298	NM_011817	ENSMUSG00000021453	Gadd45g	AI327420|C86281|CR6|DDIT2|OIG37	growth arrest and DNA-damage-inducible 45 gamma	protein-coding
mm_46876.1	chr5	113843066	113843075	-	1	NA	3' UTR (NM_011779, exon 11 of 11)	3' UTR (NM_011779, exon 11 of 11)	-12569	NM_009151	20345	Mm.332590	NM_009151	ENSMUSG00000048163	Selplg	CD162|Psgl-1|Psgl1|Selp1|Selpl	selectin, platelet (p-selectin) ligand	protein-coding
mm_153642.1	chr19	44146434	44146447	-	1	NA	promoter-TSS (NM_028607)	promoter-TSS (NM_028607)	6	NM_028607	73689	Mm.124685	NM_028607	ENSMUSG00000057506	Bloc1s2	2410089B13Rik|BLOS2|Bloc1s2a	biogenesis of lysosomal organelles complex-1, subunit 2	protein-coding
mm_92401.1	chr10	76709103	76709119	-	1	NA	3' UTR (NM_009933, exon 35 of 35)	3' UTR (NM_009933, exon 35 of 35)	16933	NM_009933	12833	Mm.2509	NM_009933	ENSMUSG00000001119	Col6a1	AI747156|Col6a-1	collagen, type VI, alpha 1	protein-coding
mm_131599.1	chr16	19035890	19035918	+	1	NA	Intergenic	RLTR9D|LTR|ERVK	159154	NM_010435	15260	Mm.15694	NM_010435	ENSMUSG00000022702	Hira	AA138857|D16Ertd95e|Gm15797|N28177|OTTMUSG00000026264|Tuple1	histone cell cycle regulator	protein-coding
mm_97639.1	chr11	79087066	79087066	+	1	NA	intron (NM_013571, intron 1 of 17)	intron (NM_013571, intron 1 of 17)	59288	NM_013571	16706	Mm.4745	NM_013571	ENSMUSG00000018334	Ksr1	AW492498|B-KSR1|D11Bhm183e|D11Bhm184e|Ksr|RSU2|hb	kinase suppressor of ras 1	protein-coding
mm_150421.1	chr19	37377621	37377622	+	1	NA	intron (NM_010615, intron 1 of 21)	intron (NM_010615, intron 1 of 21)	1218	NM_010615	16551	Mm.42203	NM_010615	ENSMUSG00000012443	Kif11	Eg5|Kif8|Kifl1|Knsl1	kinesin family member 11	protein-coding
mm_17643.1	chr2	31239482	31239486	-	1	NA	Intergenic	MTEa|LTR|ERVL-MaLR	-6439	NM_019681	14299	Mm.249318	NM_019681	ENSMUSG00000062661	Ncs1	9430075O15Rik|A730032G13Rik|AI836659|Freq|Mfreq|NCS-1	neuronal calcium sensor 1	protein-coding
mm_30285.1	chr3	148989349	148989351	-	1	NA	Intergenic	CpG	-34715	NM_001081298	99633	Mm.9776	NM_001081298	ENSMUSG00000028184	Adgrl2	AI450192|CIRL-2|Gm619|Lec1|Lphh1|Lphn2|mKIAA0786	adhesion G protein-coupled receptor L2	protein-coding
mm_144878.1	chr18	36783237	36783271	+	1	NA	promoter-TSS (NM_080636)	promoter-TSS (NM_080636)	45	NM_080636	70791	Mm.282700	NM_080636	ENSMUSG00000019143	Hars2	4631412B19Rik|HARSR|HO3|Harsl	histidyl-tRNA synthetase 2	protein-coding
mm_39946.1	chr5	31877691	31877695	+	1	NA	intron (NM_144541, intron 6 of 11)	B1_Mus1|SINE|Alu	179643	NM_144541	107976	Mm.482126	NM_144541	ENSMUSG00000052139	Bre	6030405P19Rik|AI429776|B830038C02Rik	brain and reproductive organ-expressed protein	protein-coding
mm_72230.1	chr8	74872752	74872763	+	1	NA	promoter-TSS (NM_027837)	promoter-TSS (NM_027837)	-417	NM_027837	71597	Mm.158735	NM_027837	ENSMUSG00000031621	Isx	9130012O13Rik|Pix-1	intestine specific homeobox	protein-coding
mm_163512.1	chr12	113360555	113360574	-	1	NA	Intergenic	Intergenic	-129001	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_114166.1	chr13	55464238	55464319	+	1	NA	promoter-TSS (NM_001030296)	promoter-TSS (NM_001030296)	11	NM_001030296	432763	Mm.315457	NM_001030296	ENSMUSG00000034686	Prr7	XM_484263	proline rich 7 (synaptic)	protein-coding
mm_74131.1	chr8	123194015	123194025	+	1	NA	intron (NM_007876, intron 1 of 10)	intron (NM_007876, intron 1 of 10)	7785	NM_007876	13479	Mm.20388	NM_007876	ENSMUSG00000019278	Dpep1	AI327012|MBD	dipeptidase 1 (renal)	protein-coding
mm_68196.1	chr7	104379939	104379945	-	1	NA	Intergenic	Intergenic	-21296	NM_175648	244183	Mm.347647	NM_175648	ENSMUSG00000052749	Trim30b	A530023O14Rik|Trim30-1	tripartite motif-containing 30B	protein-coding
mm_60322.1	chr7	44225329	44225359	+	1	NA	promoter-TSS (NM_010639)	promoter-TSS (NM_010639)	-16	NM_001320332	16612	Mm.142722	NM_010639	ENSMUSG00000063903	Klk1	0610007D04Rik|KAL-B|Kal|Klk1b6|Klk6|mGk-6	kallikrein 1	protein-coding
mm_129845.1	chr15	83160903	83160915	-	1	NA	exon (NM_029787, exon 5 of 9)	exon (NM_029787, exon 5 of 9)	11264	NR_004432	104307	Mm.471434	NR_004432	ENSMUSG00000065176	Rnu12	-	RNA U12, small nuclear	snRNA
mm_44940.1	chr5	36484235	36484302	-	1	NA	promoter-TSS (NM_001170454)	promoter-TSS (NM_001170454)	17	NM_001170454	231151	Mm.421558	NM_001170454	ENSMUSG00000029196	Tada2b	AA474455|Gm145	transcriptional adaptor 2B	protein-coding
mm_4255.1	chr1	171411306	171411337	+	1	NA	promoter-TSS (NM_001305678)	promoter-TSS (NM_001305678)	8	NM_001305676	22278	Mm.8	NM_009480	ENSMUSG00000026641	Usf1	bHLHb11	upstream transcription factor 1	protein-coding
mm_163669.1	chr13	80883541	80883550	+	1	NA	5' UTR (NM_001042591, exon 1 of 8)	5' UTR (NM_001042591, exon 1 of 8)	123	NM_001042591	105171	Mm.423137	NM_001042591	ENSMUSG00000074794	Arrdc3	AI450344|mKIAA1376	arrestin domain containing 3	protein-coding
mm_74591.1	chr8	11550690	11550755	-	1	NA	promoter-TSS (NM_024248)	promoter-TSS (NM_024248)	49	NM_024248	71941	Mm.196576	NM_024248	ENSMUSG00000056228	Cars2	2310051N18Rik|2410044A07Rik|D530030H10Rik	cysteinyl-tRNA synthetase 2 (mitochondrial)(putative)	protein-coding
mm_90047.1	chr10	116018353	116018421	+	1	NA	promoter-TSS (NM_011217)	promoter-TSS (NM_011217)	24	NM_011217	19279	Mm.336316	NM_011217	ENSMUSG00000020151	Ptprr	Gmcp1|PTP-SL|PTPBR7|RPTPRR|mPTP213	protein tyrosine phosphatase, receptor type, R	protein-coding
mm_118906.1	chr14	26656083	26656099	+	1	NA	3' UTR (NM_007479, exon 6 of 6)	3' UTR (NM_007479, exon 6 of 6)	13517	NR_106132	102465773		NR_106132	ENSMUSG00000098751	Mir7672	Gm27314|mmu-mir-7672	microRNA 7672	ncRNA
mm_128407.1	chr15	44706493	44706505	-	1	NA	promoter-TSS (NM_001285844)	promoter-TSS (NM_001285844)	-11	NM_001285843	319613	Mm.207715	NM_176998	ENSMUSG00000022340	Sybu	Golsyn	syntabulin (syntaxin-interacting)	protein-coding
mm_3391.1	chr1	140904037	140904038	+	1	NA	Intergenic	L1Md_T|LINE|L1	-247635	NR_040604	75910	Mm.483845	NR_040604	ENSMUSG00000102368	4930590L20Rik	-	RIKEN cDNA 4930590L20 gene	ncRNA
mm_172093.1	chr6	22288193	22288194	+	1	NA	promoter-TSS (NM_053116)	promoter-TSS (NM_053116)	-34	NM_053116	93735	Mm.137403	NM_053116	ENSMUSG00000029671	Wnt16	E130309I19Rik	wingless-type MMTV integration site family, member 16	protein-coding
mm_105351.1	chr11	103017074	103017152	-	1	NA	promoter-TSS (NM_026551)	promoter-TSS (NM_026551)	34	NM_026551	68087	Mm.277449	NM_026551	ENSMUSG00000020935	Dcakd	3010024O21Rik|6720485C15Rik|AI849483	dephospho-CoA kinase domain containing	protein-coding
mm_49580.1	chr6	30642330	30642342	+	1	NA	exon (NM_025350, exon 7 of 10)	exon (NM_025350, exon 7 of 10)	3118	NM_025350	109697	Mm.25377	NM_025350	ENSMUSG00000054446	Cpa1	0910001L12Rik|Cpa	carboxypeptidase A1, pancreatic	protein-coding
mm_75765.1	chr8	69974262	69974315	-	1	NA	promoter-TSS (NM_001113346)	promoter-TSS (NM_001113346)	95	NM_001113346	234366	Mm.270044	NM_145596	ENSMUSG00000036180	Gatad2a	1110066C11Rik|BC031407|C80248	GATA zinc finger domain containing 2A	protein-coding
mm_142681.1	chr17	47733028	47733050	-	1	NA	exon (NM_025973, exon 7 of 9)	exon (NM_025973, exon 7 of 9)	-3998	NM_001161722	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_111912.1	chr12	108835787	108835792	-	1	NA	promoter-TSS (NM_181328)	promoter-TSS (NM_181328)	87	NM_181328	214663	Mm.266264	NM_181328	ENSMUSG00000021265	Slc25a29	C030003J19Rik|CACL|mCACL	solute carrier family 25 (mitochondrial carrier, palmitoylcarnitine transporter), member 29	protein-coding
mm_45918.1	chr5	89441596	89441613	-	1	NA	exon (NM_008096, exon 5 of 13)	exon (NM_008096, exon 5 of 13)	16294	NM_008096	14473	Mm.196595	NM_008096	ENSMUSG00000035540	Gc	DBP|VDB	group specific component	protein-coding
mm_98558.1	chr11	95309871	95309911	+	1	NA	intron (NM_177619, intron 1 of 12)	CpG	355	NM_001195004	217127	Mm.90213	NM_177619	ENSMUSG00000038909	Kat7	Hbo1|Hboa|Myst2	K(lysine) acetyltransferase 7	protein-coding
mm_3203.1	chr1	135818843	135818849	+	1	NA	5' UTR (NM_133664, exon 1 of 10)	5' UTR (NM_133664, exon 1 of 10)	248	NM_133664	16763	Mm.36726	NM_133664	ENSMUSG00000041782	Lad1	-	ladinin	protein-coding
mm_129503.1	chr15	78899666	78899716	-	1	NA	promoter-TSS (NM_009164)	promoter-TSS (NM_009164)	-77	NR_133564	20401	Mm.4462	NM_009164	ENSMUSG00000022436	Sh3bp1	3BP-1	SH3-domain binding protein 1	protein-coding
mm_154100.1	chr19	57008570	57008580	-	1	NA	promoter-TSS (NM_001177797)	promoter-TSS (NM_001177797)	0	NM_146102	226250	Mm.226284	NM_146102	ENSMUSG00000025083	Afap1l2	AU041783|C86904|mKIAA1914	actin filament associated protein 1-like 2	protein-coding
mm_48824.1	chr5	149051699	149051708	-	1	NA	promoter-TSS (NM_001313894)	promoter-TSS (NM_001313894)	-87	NM_001313894	15289	Mm.207047	NM_010439	ENSMUSG00000066551	Hmgb1	HMG-1|Hmg1|SBP-1|p30	high mobility group box 1	protein-coding
mm_160202.1	chr7	81571870	81571870	+	1	NA	exon (NM_001004185, exon 1 of 10)	exon (NM_001004185, exon 1 of 10)	578	NM_001004185	434204	Mm.181641	NM_001004185	ENSMUSG00000045795	Whamm	BB081391|Whdc1|mKIAA1971	WAS protein homolog associated with actin, golgi membranes and microtubules	protein-coding
mm_66014.1	chr7	30598820	30598826	-	1	NA	Intergenic	Intergenic	-5881	NM_021397	58206	Mm.116789	NM_021397	ENSMUSG00000006310	Zbtb32	4930524C15Rik|FAXF|FAZF|PLZP|Rog|Tzfp	zinc finger and BTB domain containing 32	protein-coding
mm_160699.1	chr10	41587530	41587530	-	1	NA	intron (NM_001303469, intron 4 of 20)	intron (NM_001303469, intron 4 of 20)	19065	NM_001303469	75973	Mm.228517	NM_029493	ENSMUSG00000075225	Ccdc162	5033413D22Rik|Ccdc162p|Gm29096|Gm61|Gm6976	coiled-coil domain containing 162	protein-coding
mm_52387.1	chr6	113282303	113282316	+	1	NA	promoter-TSS (NM_170673)	promoter-TSS (NM_170673)	2	NM_170673	211232	Mm.65597	NM_170673	ENSMUSG00000030270	Cpne9	A730016F12Rik|mKIAA4217	copine family member IX	protein-coding
mm_128741.1	chr15	64312547	64312584	-	1	NA	5' UTR (NM_001276463, exon 1 of 28)	5' UTR (NM_001276463, exon 1 of 28)	108	NM_001276462	13196	Mm.277236	NM_010026	ENSMUSG00000022377	Asap1	AV239055|DEF-1|Ddef1|PAP|mKIAA1249|s19	ArfGAP with SH3 domain, ankyrin repeat and PH domain1	protein-coding
mm_25492.1	chr3	109340672	109340692	+	1	NA	promoter-TSS (NM_020505)	promoter-TSS (NM_020505)	-1	NM_020505	57257	Mm.282257	NM_020505	ENSMUSG00000033721	Vav3	A530094I06Rik|AA986410|Idd18.1	vav 3 oncogene	protein-coding
mm_79520.1	chr9	57560935	57560989	+	1	NA	promoter-TSS (NM_022813)	promoter-TSS (NM_022813)	18	NM_022813	24044	Mm.286069	NM_022813	ENSMUSG00000040188	Scamp2	AI875466|Sc2	secretory carrier membrane protein 2	protein-coding
mm_118750.1	chr14	22350622	22350632	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	192171	NR_046307	74896	Mm.444661	NR_046307		4930405A10Rik	4930456G20Rik	RIKEN cDNA 4930405A10 gene	ncRNA
mm_92791.1	chr10	81343303	81343314	-	1	NA	promoter-TSS (NM_148951)	promoter-TSS (NM_148951)	-42	NM_148951	209047	Mm.218755	NM_148951	ENSMUSG00000034872	Gipc3	Ahl5|Rgs19ip3	GIPC PDZ domain containing family, member 3	protein-coding
mm_82104.1	chr9	123067193	123067198	+	1	NA	3' UTR (NM_177911, exon 14 of 14)	3' UTR (NM_177911, exon 14 of 14)	32454	NM_177911	331046	Mm.195309	NM_177911	ENSMUSG00000025787	Tgm4	9530008N10Rik|Eapa1|TGP	transglutaminase 4 (prostate)	protein-coding
mm_172777.1	chr8	9552322	9552322	+	1	NA	intron (NM_001347127, intron 1 of 3)	L1Md_Gf|LINE|L1	218701	NM_173446	270028	Mm.268163	NM_173446	ENSMUSG00000079157	Fam155a	6430500D16|AW121567|Tmem28	family with sequence similarity 155, member A	protein-coding
mm_78368.1	chr9	27030719	27030772	+	1	NA	promoter-TSS (NM_178027)	promoter-TSS (NM_178027)	570	NM_178113	78658	Mm.251777	NM_178113	ENSMUSG00000035024	Ncapd3	2810487N22Rik|4632407J06Rik|AI195468|AU018739|B130055D15Rik|mKIAA0056	non-SMC condensin II complex, subunit D3	protein-coding
mm_53090.1	chr6	125002772	125002789	+	1	NA	3' UTR (NM_001145926, exon 6 of 6)	3' UTR (NM_001145926, exon 6 of 6)	4170	NM_001145926	319352	Mm.295327	NM_175696	ENSMUSG00000030329	Pianp	AI255183|AU067746|C530028O21Rik|Panp	PILR alpha associated neural protein	protein-coding
mm_124394.1	chr14	111674759	111674814	-	1	NA	promoter-TSS (NM_198865)	promoter-TSS (NM_198865)	-329	NM_198865	75409	Mm.235097	NM_029273	ENSMUSG00000033214	Slitrk5	2610019D03Rik	SLIT and NTRK-like family, member 5	protein-coding
mm_165603.1	chr3	50407052	50407062	+	1	NA	intron (NM_011990, intron 6 of 11)	intron (NM_011990, intron 6 of 11)	36556	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_168654.1	chr11	87462281	87462301	+	1	NA	intron (NM_001199293, intron 2 of 30)	U3|snRNA|snRNA	34700	NM_001199293	83560	Mm.440758	NM_031386	ENSMUSG00000010342	Tex14	C85585	testis expressed gene 14	protein-coding
mm_101770.1	chr11	43901188	43901242	-	1	NA	promoter-TSS (NM_001284381)	promoter-TSS (NM_001284381)	22	NM_001284380	11548	Mm.39086	NM_007416	ENSMUSG00000050541	Adra1b	[a]1b	adrenergic receptor, alpha 1b	protein-coding
mm_125894.1	chr15	75889833	75889839	+	1	NA	Intergenic	ORR1C2|LTR|ERVL-MaLR	-1113	NM_001282443	223645		NM_001282443	ENSMUSG00000098678	Mroh6	Gm19570	maestro heat-like repeat family member 6	protein-coding
mm_46313.1	chr5	100572193	100572211	-	1	NA	promoter-TSS (NM_139198)	promoter-TSS (NM_139198)	3	NM_139198	231507	Mm.34609	NM_139198	ENSMUSG00000029322	Plac8	C15|D5Wsu111e	placenta-specific 8	protein-coding
mm_103211.1	chr11	70653233	70653305	-	1	NA	intron (NM_011072, intron 1 of 2)	intron (NM_011072, intron 1 of 2)	1381	NM_011072	18643	Mm.2647	NM_011072	ENSMUSG00000018293	Pfn1	Pfn	profilin 1	protein-coding
mm_98128.1	chr11	87405037	87405045	+	1	NA	promoter-TSS (NM_001291440)	promoter-TSS (NM_001291440)	-24	NM_031386	83560	Mm.440758	NM_031386	ENSMUSG00000010342	Tex14	C85585	testis expressed gene 14	protein-coding
mm_15456.1	chr2	157424256	157424322	+	1	NA	promoter-TSS (NM_001025395)	promoter-TSS (NM_001025395)	-4	NM_009271	20779	Mm.22845	NM_009271	ENSMUSG00000027646	Src	AW259666|pp60c-src	Rous sarcoma oncogene	protein-coding
mm_85987.1	chr9	112185957	112185967	-	1	NA	promoter-TSS (NM_001177618)	promoter-TSS (NM_001177618)	-13	NM_001177618	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_65356.1	chr7	25000597	25000607	-	1	NA	exon (NM_001290469, exon 4 of 23)	exon (NM_001290469, exon 4 of 23)	5335	NM_001290469	232975	Mm.44101	NM_144921	ENSMUSG00000040907	Atp1a3	Atpa-2	ATPase, Na+/K+ transporting, alpha 3 polypeptide	protein-coding
mm_114265.1	chr13	58071522	58071530	+	1	NA	intron (NM_001195075, intron 6 of 16)	intron (NM_001195075, intron 6 of 16)	30902	NM_001195075	100503085	Mm.379256	NM_001195075	ENSMUSG00000014164	Klhl3	7530408C15Rik|AI430941|EG627648	kelch-like 3	protein-coding
mm_135857.1	chr16	59632551	59632555	-	1	NA	intron (NM_001347244, intron 1 of 8)	intron (NM_001347244, intron 1 of 8)	-4392	NR_040564	75145	Mm.399348	NR_040564		4930547E14Rik	-	RIKEN cDNA 4930547E14 gene	ncRNA
mm_26700.1	chr3	157566869	157566891	+	1	NA	promoter-TSS (NM_011196)	promoter-TSS (NM_011196)	-12	NM_011196	19218	Mm.30424	NM_011196	ENSMUSG00000040016	Ptger3	EP3|Pgerep3|Ptgerep3	prostaglandin E receptor 3 (subtype EP3)	protein-coding
mm_129102.1	chr15	76014319	76014346	-	1	NA	promoter-TSS (NM_134087)	promoter-TSS (NM_134087)	4	NM_134087	105732	Mm.267178	NM_134087	ENSMUSG00000046761	Fam83h	AA409316	family with sequence similarity 83, member H	protein-coding
mm_60169.1	chr7	40898948	40898960	+	1	NA	promoter-TSS (NM_021387)	promoter-TSS (NM_021387)	-324	NM_021387	58188	Mm.150675	NM_021387	ENSMUSG00000039257	Vstm2b	2900093B09Rik|AB030198	V-set and transmembrane domain containing 2B	protein-coding
mm_26013.1	chr3	135348031	135348085	+	1	NA	promoter-TSS (NM_028946)	promoter-TSS (NM_028946)	21	NM_028946	74446	Mm.85000	NM_028946	ENSMUSG00000050150	Slc9b1	1700094G20Rik|4933424B12Rik|4933425K02Rik|Nhedc1|mtsNHE	solute carrier family 9, subfamily B (NHA1, cation proton antiporter 1), member 1	protein-coding
mm_33402.1	chr4	129821566	129821620	+	1	NA	intron (NM_001164745, intron 1 of 5)	intron (NM_001164745, intron 1 of 5)	885	NM_001164745	19244	Mm.193688	NM_008974	ENSMUSG00000028788	Ptp4a2	Prl-2	protein tyrosine phosphatase 4a2	protein-coding
mm_34771.1	chr4	153957231	153957241	+	1	NA	promoter-TSS (NM_001163019)	promoter-TSS (NM_001163019)	-1	NM_175287	97159	Mm.7066	NM_175287	ENSMUSG00000047613	A430005L14Rik	C79672	RIKEN cDNA A430005L14 gene	protein-coding
mm_48592.1	chr5	143909783	143909841	-	1	NA	promoter-TSS (NM_146165)	promoter-TSS (NM_146165)	27	NM_001172146	231872	Mm.200499	NM_146165	ENSMUSG00000029610	Aimp2	AA407136|AA407225|Aimp2(p38)|Jtv1	aminoacyl tRNA synthetase complex-interacting multifunctional protein 2	protein-coding
mm_78873.1	chr9	44482741	44482779	+	1	NA	Intergenic	CpG	-16376	NM_030256	80288	Mm.370270	NM_030256	ENSMUSG00000063382	Bcl9l	B9L|BC003321|BCL9-2|DLNB11	B cell CLL/lymphoma 9-like	protein-coding
mm_159568.1	chr4	112613639	112613639	+	1	NA	promoter-TSS (NM_001285965)	promoter-TSS (NM_001285965)	-101	NM_001285965	329919	Mm.259806	NM_177865	ENSMUSG00000034359	Skint2	A430070M19|B7S3|OTTMUSG00000008540|Skint-2	selection and upkeep of intraepithelial T cells 2	protein-coding
mm_35259.1	chr4	19881331	19881345	-	1	NA	exon (NM_175406, exon 6 of 8)	exon (NM_175406, exon 6 of 8)	41228	NM_175406	242341	Mm.19298	NM_175406	ENSMUSG00000028238	Atp6v0d2	1620401A02Rik|AI324824|V-ATPase	ATPase, H+ transporting, lysosomal V0 subunit D2	protein-coding
mm_52740.1	chr6	120463321	120463335	+	1	NA	5' UTR (NM_008359, exon 1 of 13)	5' UTR (NM_008359, exon 1 of 13)	131	NM_008359	16172	Mm.4481	NM_008359	ENSMUSG00000002897	Il17ra	AW538159|Cdw217|Il17r|VDw217	interleukin 17 receptor A	protein-coding
mm_96709.1	chr11	69655809	69655819	+	1	NA	TTS (NR_125917)	TTS (NR_125917)	777	NM_009235	20670	Mm.347499	NM_009235	ENSMUSG00000041287	Sox15	-	SRY (sex determining region Y)-box 15	protein-coding
mm_124199.1	chr14	98169465	98169479	-	1	NA	5' UTR (NM_001038610, exon 1 of 11)	5' UTR (NM_001038610, exon 1 of 11)	293	NM_001038610	13134	Mm.320593	NM_007826	ENSMUSG00000055639	Dach1	Dac|Dach	dachshund 1 (Drosophila)	protein-coding
mm_35367.1	chr4	32864601	32864616	-	1	NA	intron (NM_001012451, intron 1 of 15)	intron (NM_001012451, intron 1 of 15)	58897	NM_080471	140577	Mm.214766	NM_080471	ENSMUSG00000040183	Ankrd6	-	ankyrin repeat domain 6	protein-coding
mm_131452.1	chr16	16870743	16870816	+	1	NA	promoter-TSS (NM_011624)	promoter-TSS (NM_011624)	43	NM_011624	21976	Mm.326089	NM_011624	ENSMUSG00000022779	Top3b	-	topoisomerase (DNA) III beta	protein-coding
mm_150051.1	chr19	29380538	29380550	+	1	NA	exon (NM_021893, exon 4 of 7)	exon (NM_021893, exon 4 of 7)	13106	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_16384.1	chr2	178414513	178414591	+	1	NA	promoter-TSS (NM_001081289)	promoter-TSS (NM_001081289)	18	NM_001081289	71532	Mm.40216	NM_001081289	ENSMUSG00000070476	Fam217b	9030418K01Rik|AI851938	family with sequence similarity 217, member B	protein-coding
mm_143745.1	chr17	81513094	81513105	-	1	NA	intron (NR_104580, intron 2 of 8)	intron (NR_104580, intron 2 of 8)	225288	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_14452.1	chr2	131170963	131170971	+	1	NA	3' UTR (NM_027641, exon 7 of 7)	3' UTR (NM_027641, exon 7 of 7)	3843	NM_027641	70997	Mm.252722	NM_027641	ENSMUSG00000027329	Spef1	4931426K16Rik|Clamp	sperm flagellar 1	protein-coding
mm_107261.1	chr12	28834702	28834714	+	1	NA	intron (NM_201357, intron 4 of 8)	intron (NM_201357, intron 4 of 8)	82880	NM_201357	380752	Mm.273724	NM_201357	ENSMUSG00000036613	Tssc1	D12Ertd604e|Eipr1	tumor suppressing subtransferable candidate 1	protein-coding
mm_98053.1	chr11	85821858	85821865	+	1	NA	intron (NR_077059, intron 1 of 4)	intron (NR_077059, intron 1 of 4)	10527	NR_077059	69909	Mm.440214	NR_077059	ENSMUSG00000087013	2610027K06Rik	-	RIKEN cDNA 2610027K06 gene	ncRNA
mm_31859.1	chr4	78774042	78774054	+	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	180001	NR_131142	623726		NR_131142		A430085M09Rik	EG623726	RIKEN cDNA A430085M09 gene	ncRNA
mm_160733.1	chr10	78042439	78042439	+	1	NA	intron (NM_001081695, intron 1 of 13)	intron (NM_001081695, intron 1 of 13)	152	NM_001081695	54427	Mm.13433	NM_019448	ENSMUSG00000000730	Dnmt3l	D6Ertd14e|ecat7	DNA (cytosine-5-)-methyltransferase 3-like	protein-coding
mm_21000.1	chr2	152343910	152343922	-	1	NA	5' UTR (NM_175093, exon 1 of 4)	5' UTR (NM_175093, exon 1 of 4)	144	NM_175093	228775	Mm.276018	NM_144554	ENSMUSG00000032715	Trib3	Ifld2|Nipk|SINK|SKIP3|TRB-3|Trb3	tribbles pseudokinase 3	protein-coding
mm_34858.1	chr4	155543057	155543076	+	1	NA	exon (NM_008142, exon 7 of 12)	exon (NM_008142, exon 7 of 12)	-19326	NM_138671	192185	Mm.28347	NM_138671	ENSMUSG00000029063	Nadk	4432404C02Rik|BC004012	NAD kinase	protein-coding
mm_95350.1	chr11	48802310	48802352	+	1	NA	promoter-TSS (NR_028564)	promoter-TSS (NR_028564)	298	NR_028563	100216534		NR_028563	ENSMUSG00000064725	Snord96a	U96	small nucleolar RNA, C/D box 96A	snoRNA
mm_80493.1	chr9	78448193	78448228	+	1	NA	promoter-TSS (NM_026658)	promoter-TSS (NM_026658)	0	NM_026658	68291	Mm.291779	NM_026658	ENSMUSG00000032342	Mto1	2310039H01Rik|5730419A02Rik	mitochondrial tRNA translation optimization 1	protein-coding
mm_71628.1	chr8	57455899	57455904	+	1	NA	promoter-TSS (NM_009136)	promoter-TSS (NM_009136)	-22	NM_009136	20284	Mm.12886	NM_009136	ENSMUSG00000031610	Scrg1	AW124307	scrapie responsive gene 1	protein-coding
mm_171513.1	chr4	146501939	146501939	+	1	NA	promoter-TSS (NM_001243138)	promoter-TSS (NM_001243138)	-61	NM_001243138	100041433	Mm.441741	NM_001243138	ENSMUSG00000056300	Zfp981	Gm13247|OTTMUSG00000011075	zinc finger protein 981	protein-coding
mm_77453.1	chr8	121851052	121851068	-	1	NA	Intergenic	Intergenic	-21491	NM_145605	234825	Mm.209329	NM_145605	ENSMUSG00000040263	Klhdc4	AA408426|AV352552|BC012312|G430025P05Rik	kelch domain containing 4	protein-coding
mm_73222.1	chr8	99664003	99664009	+	1	NA	intron (NR_132435, intron 1 of 4)	intron (NR_132435, intron 1 of 4)	247332	NR_132435	234624	Mm.124595	NM_175479	ENSMUSG00000052479	A330008L17Rik	-	RIKEN cDNA A330008L17 gene	ncRNA
mm_57307.1	chr6	124718809	124718835	-	1	NA	promoter-TSS (NR_029554)	promoter-TSS (NR_029554)	-432	NR_029792	723944		NR_029792	ENSMUSG00000065462	Mir200c	Mirn200c|mir-200c	microRNA 200c	ncRNA
mm_107140.1	chr12	21417196	21417210	+	1	NA	5' UTR (NM_011739, exon 1 of 5)	5' UTR (NM_011739, exon 1 of 5)	233	NM_011739	22630	Mm.289630	NM_011739	ENSMUSG00000076432	Ywhaq	2700028P07Rik|AA409740|AU021156|R74690	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide	protein-coding
mm_120330.1	chr14	63317733	63317748	+	1	NA	Intergenic	Intergenic	-72469	NM_001310610	14463	Mm.247669	NM_008092	ENSMUSG00000021944	Gata4	Gata-4	GATA binding protein 4	protein-coding
mm_142211.1	chr17	37023218	37023230	-	1	NA	5' UTR (NM_010814, exon 1 of 8)	5' UTR (NM_010814, exon 1 of 8)	174	NM_010814	17441	Mm.210857	NM_010814	ENSMUSG00000076439	Mog	B230317G11Rik	myelin oligodendrocyte glycoprotein	protein-coding
mm_126886.1	chr15	89454169	89454217	+	1	NA	5' UTR (NM_021921, exon 1 of 12)	5' UTR (NM_021921, exon 1 of 12)	282	NM_021921	60597	Mm.173337	NM_021921	ENSMUSG00000022619	Mapk8ip2	3230402N03Rik|AI847694|AW049958|IB2|Jip2|R75148	mitogen-activated protein kinase 8 interacting protein 2	protein-coding
mm_167018.1	chr7	63938798	63938807	-	1	NA	5' UTR (NM_021366, exon 1 of 2)	5' UTR (NM_021366, exon 1 of 2)	113	NM_021366	50794	Mm.240473	NM_021366	ENSMUSG00000052040	Klf13	0610043C13Rik|9430029L20Rik|Bteb3|FKLF-2|FKLF2|NSLP1|RFLAT-1|RFLAT1	Kruppel-like factor 13	protein-coding
mm_149498.1	chr19	11912332	11912355	+	1	NA	promoter-TSS (NM_172635)	promoter-TSS (NM_172635)	-56	NM_172635	225929	Mm.42711	NM_172635	ENSMUSG00000046139	Patl1	AV312086|Pat1b	protein associated with topoisomerase II homolog 1 (yeast)	protein-coding
mm_88600.1	chr10	79793659	79793673	+	1	NA	promoter-TSS (NM_001161747)	promoter-TSS (NM_001161747)	94	NM_001161747	18483	Mm.34650	NM_023128	ENSMUSG00000035863	Palm	-	paralemmin	protein-coding
mm_6581.1	chr1	75219854	75219891	-	1	NA	promoter-TSS (NM_001313724)	promoter-TSS (NM_001313724)	-578	NM_001313724	22145	Mm.1155	NM_009447	ENSMUSG00000026202	Tuba4a	M[a]4|Tuba4	tubulin, alpha 4A	protein-coding
mm_82280.1	chr9	7358681	7358685	-	1	NA	3' UTR (NM_008605, exon 10 of 10)	3' UTR (NM_008605, exon 10 of 10)	11309	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_63565.1	chr7	128116041	128116062	+	1	NA	exon (NM_008401, exon 26 of 30)	exon (NM_008401, exon 26 of 30)	-13517	NM_021334	16411	Mm.22378	NM_021334	ENSMUSG00000030789	Itgax	AI449405|Cd11c|Cr4|N418	integrin alpha X	protein-coding
mm_92589.1	chr10	80075276	80075301	-	1	NA	intron (NM_183426, intron 4 of 31)	intron (NM_183426, intron 4 of 31)	21269	NM_001037741	625249	Mm.332810	NM_008162	ENSMUSG00000075706	Gpx4	GPx-4|GSHPx-4|PHGPx|mtPHGPx|snGPx	glutathione peroxidase 4	protein-coding
mm_148292.1	chr18	82585069	82585087	-	1	NA	3' UTR (NM_010777, exon 7 of 7)	3' UTR (NM_010777, exon 7 of 7)	30570	NM_001025254	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_165241.1	chr2	64043769	64043771	+	1	NA	intron (NM_001267846, intron 2 of 3)	intron (NM_001267846, intron 2 of 3)	54268	NM_001267846	60344	Mm.130769	NM_021716	ENSMUSG00000075324	Fign	fi|fidget	fidgetin	protein-coding
mm_92903.1	chr10	83337484	83337532	-	1	NA	intron (NM_177388, intron 1 of 10)	CpG	309	NM_177388	338365	Mm.67073	NM_177388	ENSMUSG00000034591	Slc41a2	A230035L05Rik|SLC41A1-L1	solute carrier family 41, member 2	protein-coding
mm_6702.1	chr1	81835768	81835769	-	1	NA	Intergenic	Intergenic	-296148	NR_105762	102466629		NR_105762	ENSMUSG00000098797	Mir6344	Gm27840|mmu-mir-6344	microRNA 6344	ncRNA
mm_64977.1	chr7	16874846	16874889	-	1	NA	promoter-TSS (NM_001081655)	promoter-TSS (NM_001081655)	-450	NM_001081655	629378	Mm.491123	NM_001081655	ENSMUSG00000078794	Dact3	EG666671|naa-3	dishevelled-binding antagonist of beta-catenin 3	protein-coding
mm_141220.1	chr17	27204451	27204477	-	1	NA	promoter-TSS (NM_146075)	promoter-TSS (NM_146075)	-26	NM_146075	224640	Mm.29689	NM_146075	ENSMUSG00000044857	Lemd2	BC026588|Lem2|NET25	LEM domain containing 2	protein-coding
mm_147556.1	chr18	54961680	54961691	-	1	NA	intron (NM_175751, intron 2 of 9)	intron (NM_175751, intron 2 of 9)	28495	NM_175751	269023	Mm.192984	NM_175751	ENSMUSG00000052713	Zfp608	4932417D18Rik|D430007A19Rik|Znf608	zinc finger protein 608	protein-coding
mm_130926.1	chr15	102979297	102979329	-	1	NA	intron (NM_008272, intron 1 of 2)	intron (NM_008272, intron 1 of 2)	2281	NM_008272	15427	Mm.4765	NM_008272	ENSMUSG00000036139	Hoxc9	Hox-3.2	homeobox C9	protein-coding
mm_171076.1	chr3	120926837	120926837	-	1	NA	Intergenic	L1Md_A|LINE|L1	-40105	NR_130170	320739	Mm.388474	NR_130170		6530403H02Rik	-	RIKEN cDNA 6530403H02 gene	ncRNA
mm_73084.1	chr8	94480699	94480712	+	1	NA	intron (NM_001033207, intron 6 of 48)	intron (NM_001033207, intron 6 of 48)	7942	NM_001033207	434341	Mm.334720	NM_001033207	ENSMUSG00000074151	Nlrc5	AI451557|AK220210|NOD27	NLR family, CARD domain containing 5	protein-coding
mm_158517.1	chrX	143483044	143483052	-	1	NA	Intergenic	SYNREP_MM|Satellite|Satellite	-35543	NM_001195048	18481	Mm.40035	NM_008778	ENSMUSG00000031284	Pak3	PAK-3|Pak65alpha|Pak65beta|Stk4	p21 protein (Cdc42/Rac)-activated kinase 3	protein-coding
mm_166927.1	chr7	33527358	33527360	+	1	NA	Intergenic	Intergenic	-6904	NM_001310615	626970		NM_001310615	ENSMUSG00000099900	Scgb2b21	Abpbg21|EG626970|Gm6725	secretoglobin, family 2B, member 21	protein-coding
mm_69562.1	chr7	135700400	135700420	-	1	NA	exon (NM_001081117, exon 12 of 14)	exon (NM_001081117, exon 12 of 14)	15969	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_64656.1	chr7	4150372	4150376	-	1	NA	promoter-TSS (NM_175529)	promoter-TSS (NM_175529)	-502	NM_175529	243813	Mm.347643	NM_175529	ENSMUSG00000043432	Leng9	9530024C23Rik|F630035L11Rik	leukocyte receptor cluster (LRC) member 9	protein-coding
mm_58785.1	chr7	16119869	16119907	+	1	NA	promoter-TSS (NM_133727)	promoter-TSS (NM_133727)	12	NM_133727	70394	Mm.41101	NM_133727	ENSMUSG00000006021	Kptn	2310042D10Rik|2E4|C030013F01Rik	kaptin	protein-coding
mm_58241.1	chr6	145047726	145047757	-	1	NA	intron (NM_007532, intron 1 of 10)	intron (NM_007532, intron 1 of 10)	1071	NM_001024468	12035	Mm.4606	NM_007532	ENSMUSG00000030268	Bcat1	BCATc|Eca39	branched chain aminotransferase 1, cytosolic	protein-coding
mm_122890.1	chr14	54948742	54948766	-	1	NA	TTS (NR_029724)	TTS (NR_029724)	388	NR_029724	387204		NR_029724	ENSMUSG00000065432	Mir208a	Mirn208|Mirn208a|mir-208|mir-208a|mmu-mir-208	microRNA 208a	ncRNA
mm_64777.1	chr7	5013282	5013302	-	1	NA	promoter-TSS (NM_001110330)	promoter-TSS (NM_001110330)	-50	NM_001110330	23877	Mm.38911	NM_011813	ENSMUSG00000061374	Fiz1	AI790204|mFLJ00416	Flt3 interacting zinc finger protein 1	protein-coding
mm_167847.1	chrX	6415698	6415712	+	1	NA	promoter-TSS (NM_001313764)	promoter-TSS (NM_001313764)	-37	NM_001313764	208431	Mm.23208	NM_001040459	ENSMUSG00000068270	Shroom4	D430043L16Rik|Gm724|Shrm4	shroom family member 4	protein-coding
mm_142910.1	chr17	53463297	53463314	-	1	NA	promoter-TSS (NM_172497)	promoter-TSS (NM_172497)	16	NM_172497	211482	Mm.60887	NM_172497	ENSMUSG00000023931	Efhb	4921525D22Rik	EF hand domain family, member B	protein-coding
mm_39126.1	chr4	155056785	155056827	-	1	NA	Intergenic	Intergenic	-10224	NM_001042407	668173	Mm.133114	NM_001042407	ENSMUSG00000029047	Pex10	AV128229|Gm142	peroxisomal biogenesis factor 10	protein-coding
mm_97126.1	chr11	74926082	74926133	+	1	NA	promoter-TSS (NM_001163311)	promoter-TSS (NM_001163311)	235	NM_001002764	103677	Mm.288460	NM_001002764	ENSMUSG00000038290	Smg6	AI317223|AU041178	Smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans)	protein-coding
mm_25041.1	chr3	98291116	98291126	+	1	NA	exon (NM_008256, exon 2 of 10)	exon (NM_008256, exon 2 of 10)	10690	NM_008256	15360	Mm.289131	NM_008256	ENSMUSG00000027875	Hmgcs2	1300002P16|mHS	3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2	protein-coding
mm_157359.1	chrX	37100126	37100129	-	1	NA	exon (NM_026573, exon 6 of 10)	exon (NM_026573, exon 6 of 10)	10195	NM_026573	68134	Mm.271160	NM_026573	ENSMUSG00000036572	Upf3b	5730594O13Rik|AI317193|AW541158|RENT3B|UPF3X	UPF3 regulator of nonsense transcripts homolog B (yeast)	protein-coding
mm_95892.1	chr11	58183827	58183871	+	1	NA	promoter-TSS (NM_001135115)	promoter-TSS (NM_001135115)	6	NM_001135115	631323	Mm.394103	NM_001135115		Gm12250	Irgb10|OTTMUSG00000005723	predicted gene 12250	protein-coding
mm_21397.1	chr2	157571271	157571289	-	1	NA	Intergenic	ORR1B2|LTR|ERVL-MaLR	-4919	NM_016916	53619	Mm.480461	NM_016916	ENSMUSG00000067787	Blcap	AI462828|Bc10	bladder cancer associated protein	protein-coding
mm_18883.1	chr2	76672995	76673003	-	1	NA	promoter-TSS (NM_010222)	promoter-TSS (NM_010222)	99	NM_010222	14231	Mm.24720	NM_010222	ENSMUSG00000002732	Fkbp7	23kDa|FKBP-7|FKBP23	FK506 binding protein 7	protein-coding
mm_18949.1	chr2	76781900	76781910	-	1	NA	exon (NM_011652, exon 229 of 313)	exon (NM_011652, exon 229 of 313)	106590	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_82891.1	chr9	32541590	32541602	-	1	NA	promoter-TSS (NM_008026)	promoter-TSS (NM_008026)	-144	NM_008026	14247	Mm.258908	NM_008026	ENSMUSG00000016087	Fli1	EWSR2|Fli-1|SIC-1|Sic1	Friend leukemia integration 1	protein-coding
mm_26887.1	chr3	18177631	18177636	-	1	NA	intron (NM_007825, intron 1 of 5)	RMER5|LTR|ERV1	65705	NM_007825	13123	Mm.316000	NM_007825	ENSMUSG00000039519	Cyp7b1	AW261589|D3Ertd552e|hct-1	cytochrome P450, family 7, subfamily b, polypeptide 1	protein-coding
mm_105046.1	chr11	100613403	100613407	-	1	NA	intron (NM_019795, intron 1 of 13)	intron (NM_019795, intron 1 of 13)	6763	NM_019795	56354	Mm.402409	NM_019795	ENSMUSG00000014195	Dnajc7	2010003F24Rik|2010004G07Rik|CCRP|Ttc2|mDj11|mTpr2	DnaJ heat shock protein family (Hsp40) member C7	protein-coding
mm_81902.1	chr9	119982733	119982744	+	1	NA	intron (NM_153287, intron 1 of 4)	intron (NM_153287, intron 1 of 4)	1920	NM_153287	215418	Mm.491094	NM_153287	ENSMUSG00000032515	Csrnp1	4931429D10Rik|Axud1|CSRNP-1|URAX1|taip-3	cysteine-serine-rich nuclear protein 1	protein-coding
mm_122085.1	chr14	30622162	30622168	-	1	NA	intron (NM_011103, intron 1 of 17)	intron (NM_011103, intron 1 of 17)	4043	NM_011103	18753	Mm.2314	NM_011103	ENSMUSG00000021948	Prkcd	AI385711|D14Ertd420e|PKC[d]|PKCdelta|Pkcd	protein kinase C, delta	protein-coding
mm_66310.1	chr7	39797721	39797738	-	1	NA	Intergenic	MTEa-int|LTR|ERVL-MaLR	279963	NM_001004139	70227	Mm.333800	NM_001004139	ENSMUSG00000068959	Zfp619	3000002G13Rik	zinc finger protein 619	protein-coding
mm_111943.1	chr12	109053088	109053104	-	1	NA	intron (NM_001163175, intron 1 of 6)	CpG-3504	15121	NM_001163175	380785	Mm.342085	NM_001163175	ENSMUSG00000040867	Begain	BM948371|Gm897	brain-enriched guanylate kinase-associated	protein-coding
mm_34487.1	chr4	148558490	148558500	+	1	NA	promoter-TSS (NR_131062)	promoter-TSS (NR_131062)	68	NR_131061	50912	Mm.266635	NM_016699	ENSMUSG00000017264	Exosc10	PM-Scl|PM/Scl-100|Pmscl2|RRP6|p2|p3|p4	exosome component 10	protein-coding
mm_173345.1	chrY	90812972	90812972	+	1	NA	intron (NM_133362, intron 2 of 3)	(TTAGGG)n|Simple_repeat|Simple_repeat	26434	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_11640.1	chr2	34874487	34874515	+	1	NA	5' UTR (NM_030021, exon 1 of 6)	5' UTR (NM_030021, exon 1 of 6)	105	NM_030021	77996	Mm.215255	NM_030021	ENSMUSG00000026870	Cutal	D730039F16Rik	cutA divalent cation tolerance homolog-like	protein-coding
mm_53216.1	chr6	126853092	126853116	+	1	NA	promoter-TSS (NM_009650)	promoter-TSS (NM_009650)	6	NM_009650	11642	Mm.87748	NM_009650	ENSMUSG00000030344	Akap3	Prka3	A kinase (PRKA) anchor protein 3	protein-coding
mm_33312.1	chr4	129070488	129070500	+	1	NA	intron (NM_029219, intron 1 of 8)	B3|SINE|B2	12223	NM_029219	75234	Mm.259672	NM_029219	ENSMUSG00000028793	Rnf19b	4930534K13Rik|4930555L03Rik|Ibrdc3	ring finger protein 19B	protein-coding
mm_158826.1	chrX	167966636	167966638	-	1	NA	intron (NM_001033330, intron 3 of 19)	intron (NM_001033330, intron 3 of 19)	-111560	NM_001290428	333605	Mm.426168	NM_001033330	ENSMUSG00000049176	Frmpd4	Gm196|PKAP1|Pdzd10|Pdzk10|Preso1|preso	FERM and PDZ domain containing 4	protein-coding
mm_62402.1	chr7	101109314	101109323	+	1	NA	intron (NM_199012, intron 1 of 20)	(T)n|Simple_repeat|Simple_repeat	543	NM_199012	207278	Mm.263041	NM_199012	ENSMUSG00000030691	Fchsd2	BC034086|R74866|Sh3md3|mKIAA0769	FCH and double SH3 domains 2	protein-coding
mm_6091.1	chr1	63214227	63214244	-	1	NA	promoter-TSS (NM_146250)	promoter-TSS (NM_146250)	46	NM_146250	241070	Mm.103354	NM_146250	ENSMUSG00000046856	Gpr1	-	G protein-coupled receptor 1	protein-coding
mm_23551.1	chr3	61367432	61367443	+	1	NA	3' UTR (NM_028712, exon 1 of 1)	3' UTR (NM_028712, exon 1 of 1)	2930	NM_028712	74012	Mm.422674	NM_028712	ENSMUSG00000036894	Rap2b	4021402C18Rik|AA408554	RAP2B, member of RAS oncogene family	protein-coding
mm_41270.1	chr5	89102098	89102127	+	1	NA	intron (NM_001197147, intron 7 of 25)	intron (NM_001197147, intron 7 of 25)	214852	NM_018760	54403	Mm.41044	NM_018760	ENSMUSG00000060961	Slc4a4	AI835705|NBC|NBC1	solute carrier family 4 (anion exchanger), member 4	protein-coding
mm_67503.1	chr7	80779316	80779330	-	1	NA	intron (NM_016721, intron 2 of 37)	intron (NM_016721, intron 2 of 37)	24008	NM_016721	29875	Mm.207619	NM_016721	ENSMUSG00000030536	Iqgap1	AA682088|D7Ertd237e|D7Ertd257e|mKIAA0051	IQ motif containing GTPase activating protein 1	protein-coding
mm_148196.1	chr18	79079660	79079663	-	1	NA	intron (NM_053099, intron 2 of 5)	PB1D10|SINE|Alu	29730	NM_053099	240427	Mm.312871	NM_053099	ENSMUSG00000024548	Setbp1	C130092E12|Seb|mKIAA0437	SET binding protein 1	protein-coding
mm_47695.1	chr5	129779120	129779131	-	1	NA	5' UTR (NM_133900, exon 3 of 8)	5' UTR (NM_133900, exon 3 of 8)	8128	NM_133900	100678	Mm.271784	NM_133900	ENSMUSG00000029446	Psph	AI480570|PSP|PSPase	phosphoserine phosphatase	protein-coding
mm_172531.1	chr7	86342809	86342811	+	1	NA	Intergenic	Lx3_Mus|LINE|L1	-6416	NM_146617	258610	Mm.377592	NM_146617	ENSMUSG00000055610	Olfr307	MOR219-1	olfactory receptor 307	protein-coding
mm_167889.1	chrX	61075362	61075384	+	1	NA	Intergenic	Intergenic	-41005	NR_030706	331424	Mm.127263	NM_177916	ENSMUSG00000071753	C230004F18Rik	-	RIKEN cDNA C230004F18 gene	ncRNA
mm_77686.1	chr8	126475063	126475097	-	1	NA	promoter-TSS (NM_001159907)	promoter-TSS (NM_001159907)	-15	NM_001159907	212728	Mm.482479	NM_001159907	ENSMUSG00000090290	Tarbp1	Gm17296|Gm179	TAR RNA binding protein 1	protein-coding
mm_115431.1	chr13	117249699	117249719	+	1	NA	exon (NM_010330, exon 4 of 9)	exon (NM_010330, exon 4 of 9)	29136	NM_010330	13723	Mm.274926	NM_010330	ENSMUSG00000021728	Emb	AL022799|Gp70	embigin	protein-coding
mm_68263.1	chr7	105592437	105592466	-	1	NA	exon (NM_017371, exon 8 of 10)	exon (NM_017371, exon 8 of 10)	7665	NM_017371	15458	Mm.3485	NM_017371	ENSMUSG00000030895	Hpx	Hpxn|hx	hemopexin	protein-coding
mm_103381.1	chr11	75415107	75415118	-	1	NA	exon (NM_011340, exon 5 of 8)	exon (NM_011340, exon 5 of 8)	7511	NM_011340	20317	Mm.2044	NM_011340	ENSMUSG00000000753	Serpinf1	AI195227|EPC-1|Pedf|Pedfl|Sdf3	serine (or cysteine) peptidase inhibitor, clade F, member 1	protein-coding
mm_134028.1	chr16	5010631	5010640	-	1	NA	intron (NM_133185, intron 6 of 10)	intron (NM_133185, intron 6 of 10)	2918	NM_133185	66049	Mm.27792	NM_133185	ENSMUSG00000022540	Rogdi	0610011C19Rik|AU020118|C76152|Lzf	rogdi homolog	protein-coding
mm_87414.1	chr10	46597930	46597939	+	1	NA	Intergenic	Intergenic	353185	NR_028276	108637		NR_028276	ENSMUSG00000096263	Snord14c	Gm23107|Rnu14|U14	small nucleolar RNA, C/D box 14C	snoRNA
mm_61765.1	chr7	82866331	82866369	+	1	NA	promoter-TSS (NM_175366)	promoter-TSS (NM_175366)	-983	NM_175366	108797	Mm.306789	NM_175366	ENSMUSG00000057706	Mex3b	4931439A04Rik|M-04814|Rkhd3|mKIAA2009	mex3 RNA binding family member B	protein-coding
mm_109090.1	chr12	104752181	104752224	+	1	NA	promoter-TSS (NM_148948)	promoter-TSS (NM_148948)	-250	NM_148948	192119	Mm.21135	NM_148948	ENSMUSG00000041415	Dicer1	1110006F08Rik|D12Ertd7e|mKIAA0928	dicer 1, ribonuclease type III	protein-coding
mm_129943.1	chr15	84923941	84923958	-	1	NA	intron (NM_016714, intron 1 of 7)	CpG	521	NM_016714	18141	Mm.28379	NM_016714	ENSMUSG00000016619	Nup50	1700030K07Rik|AI413123|Npap60	nucleoporin 50	protein-coding
mm_132188.1	chr16	32431024	32431034	+	1	NA	promoter-TSS (NM_001163160)	promoter-TSS (NM_001163160)	9	NM_001163159	13026	Mm.98775	NM_009981	ENSMUSG00000005615	Pcyt1a	CTalpha|Cctalpha|Ctpct|Cttalpha	phosphate cytidylyltransferase 1, choline, alpha isoform	protein-coding
mm_14158.1	chr2	126597658	126597692	+	1	NA	intron (NM_008230, intron 10 of 11)	intron (NM_008230, intron 10 of 11)	21003	NM_008230	15186	Mm.18603	NM_008230	ENSMUSG00000027360	Hdc	AW108189|Hdc-a|Hdc-c|Hdc-e|Hdc-s	histidine decarboxylase	protein-coding
mm_74386.1	chr8	128722374	128722424	+	1	NA	exon (NM_010578, exon 12 of 16)	exon (NM_010578, exon 12 of 16)	36745	NM_010578	16412	Mm.263396	NM_010578	ENSMUSG00000025809	Itgb1	4633401G24Rik|AA409975|AA960159|CD29|ENSMUSG00000051907|Fnrb|Gm9863|gpIIa	integrin beta 1 (fibronectin receptor beta)	protein-coding
mm_99622.1	chr11	104637394	104637402	+	1	NA	intron (NM_016780, intron 5 of 14)	intron (NM_016780, intron 5 of 14)	29398	NM_016780	16416	Mm.87150	NM_016780	ENSMUSG00000020689	Itgb3	CD61|GP3A|INGRB3	integrin beta 3	protein-coding
mm_128763.1	chr15	65993085	65993092	-	1	NA	Intergenic	Intergenic	-16284	NM_001145096	654498	Mm.364550	NM_001145096	ENSMUSG00000072511	Hhla1	F930104E18Rik	HERV-H LTR-associating 1	protein-coding
mm_147677.1	chr18	60653192	60653204	-	1	NA	Intergenic	Intergenic	-10212	NR_045401	328963	Mm.417203	NR_045401		G630071F17Rik	G630071F17	RIKEN cDNA G630071F17 gene	ncRNA
mm_79081.1	chr9	46242445	46242449	+	1	NA	exon (NM_007468, exon 3 of 3)	exon (NM_007468, exon 3 of 3)	1603	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_68604.1	chr7	116238413	116238427	-	1	NA	promoter-TSS (NM_001305186)	promoter-TSS (NM_001305186)	-644	NM_001305186	233765	Mm.3741	NM_172743	ENSMUSG00000045659	Plekha7	A430081P20Rik|AI414265	pleckstrin homology domain containing, family A member 7	protein-coding
mm_104288.1	chr11	90130267	90130277	-	1	NA	Intergenic	Intergenic	99924	NM_026433	67888	Mm.212428	NM_026433	ENSMUSG00000069763	Tmem100	1810057C19Rik|AV011897	transmembrane protein 100	protein-coding
mm_127328.1	chr15	100345764	100345783	+	1	NA	Intergenic	RMER17A|LTR|ERVK	-7427	NM_001024672	554292	Mm.268451	NM_001024672	ENSMUSG00000093789	Methig1	Mettl7a2-Higd1c|Mettl7a2Higd1c|Mettl7a2higd1c|UbiE-YGHL1	methyltransferase hypoxia inducible domain containing 1	protein-coding
mm_24894.1	chr3	96162448	96162477	+	1	NA	intron (NM_181409, intron 1 of 16)	intron (NM_181409, intron 1 of 16)	492	NM_181409	194126	Mm.268536	NM_181409	ENSMUSG00000045934	Mtmr11	AI035306|BC051083|Cra	myotubularin related protein 11	protein-coding
mm_33866.1	chr4	135946448	135946495	+	1	NA	promoter-TSS (NM_008254)	promoter-TSS (NM_008254)	18	NM_008254	15356	Mm.482102	NM_008254	ENSMUSG00000028672	Hmgcl	AW476067|HL	3-hydroxy-3-methylglutaryl-Coenzyme A lyase	protein-coding
mm_149759.1	chr19	22813328	22813328	+	1	NA	intron (NM_001035243, intron 8 of 23)	L1Md_F3|LINE|L1	62723	NR_029591	387200		NR_029591	ENSMUSG00000065507	Mir204	Mirn204|mir-204|mmu-mir-204	microRNA 204	ncRNA
mm_74298.1	chr8	126029272	126029294	+	1	NA	intron (NM_008430, intron 2 of 2)	intron (NM_008430, intron 2 of 2)	34181	NM_008430	16525	Mm.10800	NM_008430	ENSMUSG00000033998	Kcnk1	AI788889|TWIK-1	potassium channel, subfamily K, member 1	protein-coding
mm_46604.1	chr5	107869101	107869123	-	1	NA	intron (NM_007964, intron 1 of 17)	CpG	5995	NM_007964	14020	Mm.35796	NM_007964	ENSMUSG00000011831	Evi5	NB4S	ecotropic viral integration site 5	protein-coding
mm_18545.1	chr2	64975701	64975717	-	1	NA	intron (NM_016719, intron 2 of 13)	intron (NM_016719, intron 2 of 13)	47057	NM_016719	50915	Mm.214554	NM_016719	ENSMUSG00000026888	Grb14	AI505286	growth factor receptor bound protein 14	protein-coding
mm_62319.1	chr7	100319250	100319272	+	1	NA	3' UTR (NM_177161, exon 13 of 13)	3' UTR (NM_177161, exon 13 of 13)	33741	NM_177161	320452	Mm.150294	NM_177161	ENSMUSG00000051048	P4ha3	D930031A02Rik	procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide III	protein-coding
mm_17086.1	chr2	22988203	22988203	-	1	NA	intron (NM_001331043, intron 2 of 10)	intron (NM_001331043, intron 2 of 10)	52038	NM_001077192	11308	Mm.205647	NM_007380	ENSMUSG00000058835	Abi1	E3B1|NAP1|Ssh3bp1|abi-1	abl-interactor 1	protein-coding
mm_24912.1	chr3	96246837	96246850	+	1	NA	TTS (NM_178212).2	TTS (NM_178212).2	143	NM_054045	97114	Mm.358797	NM_054045	ENSMUSG00000081058	Hist2h3c2	H3-614|H3.2-614|Hist2h3c2-ps|Hist2h3ca1|M32461	histone cluster 2, H3c2	protein-coding
mm_31448.1	chr4	48588647	48588650	+	1	NA	intron (NM_021436, intron 1 of 9)	intron (NM_021436, intron 1 of 9)	3455	NM_021436	230157	Mm.422686	NM_021436	ENSMUSG00000028347	Tmeff1	A830033E11|M7365|Tr1	transmembrane protein with EGF-like and two follistatin-like domains 1	protein-coding
mm_130647.1	chr15	100615921	100615938	-	1	NA	promoter-TSS (NR_045701)	promoter-TSS (NR_045701)	267	NM_011873	23994	Mm.486175	NM_011873	ENSMUSG00000000346	Dazap2	AI314727|Brbp|Gcap28|Prtb|gt6-12|mKIAA0058	DAZ associated protein 2	protein-coding
mm_21943.1	chr2	167060839	167060847	-	1	NA	intron (NM_001033196, intron 1 of 13)	intron (NM_001033196, intron 1 of 13)	-2091	NR_138563	68949	Mm.391959	NM_001081005		Zfas1	1500012F01Rik|Zfos1	zinc finger, NFX1-type containing 1, antisense RNA 1	ncRNA
mm_21237.1	chr2	156135378	156135382	-	1	NA	intron (NM_010911, intron 4 of 12)	intron (NM_010911, intron 4 of 12)	-8773	NM_001164216	67067	Mm.371623	NM_025946	ENSMUSG00000067847	Romo1	2010100O12Rik|AI853864	reactive oxygen species modulator 1	protein-coding
mm_158941.1	chr1	78658397	78658397	+	1	NA	promoter-TSS (NM_001136226)	promoter-TSS (NM_001136226)	-43	NM_001136226	195434	Mm.276016	NM_001001981	ENSMUSG00000079470	Utp14b	4932411L21Rik|jsd	UTP14B small subunit processome component	protein-coding
mm_163177.1	chr11	87801018	87801023	+	1	NA	intron (NM_010824, intron 9 of 13)	intron (NM_010824, intron 9 of 13)	7236	NM_010824	17523	Mm.4668	NM_010824	ENSMUSG00000009350	Mpo	mKIAA4033	myeloperoxidase	protein-coding
mm_162027.1	chr19	47865497	47865497	+	1	NA	promoter-TSS (NM_026619)	promoter-TSS (NM_026619)	-48	NM_030051	68214	Mm.63791	NM_026619	ENSMUSG00000025069	Gsto2	1700020F09Rik|4930425C18Rik|GSTO 2-2	glutathione S-transferase omega 2	protein-coding
mm_6549.1	chr1	75133530	75133559	-	1	NA	exon (NM_194333, exon 2 of 12)	exon (NM_194333, exon 2 of 12)	346	NM_194333	22626	Mm.68157	NM_194333	ENSMUSG00000026205	Slc23a3	SVCT3|Yspl1	solute carrier family 23 (nucleobase transporters), member 3	protein-coding
mm_164892.1	chr18	63387046	63387054	-	1	NA	5' UTR (NM_001039485, exon 1 of 54)	5' UTR (NM_001039485, exon 1 of 54)	133	NM_001039485	667742	Mm.158720	NM_172629	ENSMUSG00000041482	Piezo2	5930434P17|9030411M15Rik|9430028L06Rik|Fam38b|Fam38b2	piezo-type mechanosensitive ion channel component 2	protein-coding
mm_114924.1	chr13	95325877	95325879	+	1	NA	promoter-TSS (NM_001302539)	promoter-TSS (NM_001302539)	-889	NM_001302539	72114	Mm.3774	NM_028106	ENSMUSG00000041995	Zbed3	0610037K01Rik|2610005H11Rik|AU018975|AU024588	zinc finger, BED type containing 3	protein-coding
mm_78144.1	chr9	20983530	20983545	+	1	NA	Intergenic	Intergenic	-6744	NM_010333	14739	Mm.46493	NM_010333	ENSMUSG00000043895	S1pr2	1100001A16Rik|Edg5|Gpcr13|H218|LPb2|S1P2	sphingosine-1-phosphate receptor 2	protein-coding
mm_70203.1	chr7	144678852	144678908	-	1	NA	intron (NM_178642, intron 1 of 25)	CpG-13775	59712	NM_178642	101772	Mm.26700	NM_178642	ENSMUSG00000031075	Ano1	Tmem16a	anoctamin 1, calcium activated chloride channel	protein-coding
mm_148150.1	chr18	77561707	77561711	-	1	NA	intron (NM_001164504, intron 1 of 7)	intron (NM_001164504, intron 1 of 7)	3427	NM_001164504	225743	Mm.23293	NM_001164504	ENSMUSG00000025427	Rnf165	2900024M11Rik|AI427432|Akd2|Ark2c|G630064H08Rik|Gm96	ring finger protein 165	protein-coding
mm_146779.1	chr18	20059649	20059660	-	1	NA	promoter-TSS (NM_013505)	promoter-TSS (NM_013505)	-100	NM_001317365	13506	Mm.280547	NM_013505	ENSMUSG00000024331	Dsc2	AW228162	desmocollin 2	protein-coding
mm_76091.1	chr8	79680827	79680829	-	1	NA	Intergenic	Intergenic	30912	NM_015751	24015	Mm.5831	NM_015751	ENSMUSG00000058355	Abce1	C79080|Oabp|RLI|RNS41|Rnaseli	ATP-binding cassette, sub-family E (OABP), member 1	protein-coding
mm_62368.1	chr7	100607837	100607854	+	1	NA	5' UTR (NM_024287, exon 1 of 8)	5' UTR (NM_024287, exon 1 of 8)	151	NR_003559	52443	Mm.473730	NM_198831	ENSMUSG00000030706	Mrpl48	1810030E20Rik|2610028L11Rik|CGI-118|D4Ertd786e	mitochondrial ribosomal protein L48	protein-coding
mm_89613.1	chr10	96037419	96037453	+	1	NA	exon (NM_001001932, exon 24 of 29)	exon (NM_001001932, exon 24 of 29)	96773	NM_001001932	216238	Mm.210035	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding
mm_110818.1	chr12	72408579	72408583	-	1	NA	5' UTR (NM_001286448, exon 1 of 7)	5' UTR (NM_001286448, exon 1 of 7)	473	NM_001286448	104001	Mm.221275	NM_153457	ENSMUSG00000021087	Rtn1	Nsp	reticulon 1	protein-coding
mm_88086.1	chr10	68239251	68239288	+	1	NA	intron (NM_023598, intron 3 of 9)	intron (NM_023598, intron 3 of 9)	39457	NM_023598	71371	Mm.440357	NM_023598	ENSMUSG00000019947	Arid5b	4930580B11|5430435G07Rik|AI467247|Desrt|Mrf2|Mrf2alpha|Mrf2beta	AT rich interactive domain 5B (MRF1-like)	protein-coding
mm_136817.1	chr17	12403092	12403102	+	1	NA	exon (NM_008877, exon 11 of 19)	exon (NM_008877, exon 11 of 19)	24488	NM_008877	18815	Mm.971	NM_008877	ENSMUSG00000059481	Plg	AI649309|Pg	plasminogen	protein-coding
mm_24679.1	chr3	94837703	94837723	+	1	NA	5' UTR (NM_172683, exon 1 of 19)	5' UTR (NM_172683, exon 1 of 19)	146	NM_172683	229584	Mm.274787	NM_172683	ENSMUSG00000038902	Pogz	9530006B08Rik	pogo transposable element with ZNF domain	protein-coding
mm_26760.1	chr3	8667034	8667046	-	1	NA	promoter-TSS (NM_010423)	promoter-TSS (NM_010423)	-2	NM_010423	15213	Mm.29581	NM_010423	ENSMUSG00000040289	Hey1	AI316788|AI414254|CHF2|HRT1|Herp2|Hesr1|bHLHb31|hesr-1	hairy/enhancer-of-split related with YRPW motif 1	protein-coding
mm_90795.1	chr10	7140396	7140408	-	1	NA	exon (NM_172546, exon 6 of 13)	exon (NM_172546, exon 6 of 13)	71835	NM_172546	215748	Mm.37984	NM_172546	ENSMUSG00000015202	Cnksr3	6820402C05|BC024086|Magi1	Cnksr family member 3	protein-coding
mm_169368.1	chr14	3287694	3287697	+	1	NA	intron (NR_038059, intron 3 of 3)	L1Md_T|LINE|L1	25293	NR_038059	73549	Mm.398741	NR_038059	ENSMUSG00000079407	1700110I01Rik	100040740|1700016F01Rik|Gm2938	RIKEN cDNA 1700110I01 gene	ncRNA
mm_89213.1	chr10	86705884	86705892	+	1	NA	promoter-TSS (NM_011631)	promoter-TSS (NM_011631)	77	NM_001003939	103220	Mm.440762	NM_153595	ENSMUSG00000044937	Ttc41	AI449705|AU041509|Gnn	tetratricopeptide repeat domain 41	protein-coding
mm_93163.1	chr10	93265125	93265189	-	1	NA	exon (NM_013508, exon 3 of 5)	exon (NM_013508, exon 3 of 5)	46002	NM_001322268	13713	Mm.4454	NM_013508	ENSMUSG00000008398	Elk3	D430049E23Rik|Erp|Etrp|Net|Sap-2	ELK3, member of ETS oncogene family	protein-coding
mm_43139.1	chr5	125393431	125393454	+	1	NA	Intergenic	Intergenic	-3425	NM_019639	22190	Mm.331	NM_019639	ENSMUSG00000008348	Ubc	2700054O04Rik|AI194771|Rps27a|TI-225|Uba52|Ubb	ubiquitin C	protein-coding
mm_89209.1	chr10	86701956	86701986	+	1	NA	exon (NM_011631, exon 5 of 18)	exon (NM_011631, exon 5 of 18)	3473	NM_011631	22027	Mm.87773	NM_011631	ENSMUSG00000020048	Hsp90b1	ERp99|GRP94|TA-3|Targ2|Tra-1|Tra1|endoplasmin|gp96	heat shock protein 90, beta (Grp94), member 1	protein-coding
mm_117698.1	chr13	94357506	94357521	-	1	NA	non-coding (NR_045619, exon 1 of 1)	non-coding (NR_045619, exon 1 of 1)	1410	NR_045619	328309	Mm.174191	NM_183205		Gm9776	A530089L17|ENSMUSG00000042857	predicted gene 9776	ncRNA
mm_99780.1	chr11	107335943	107335958	+	1	NA	intron (NM_145823, intron 2 of 9)	intron (NM_145823, intron 2 of 9)	134770	NM_145823	71795	Mm.397413	NM_145823	ENSMUSG00000040430	Pitpnc1	1110020B03Rik|5830436L09Rik|AI662802|AI851387|C330017I21Rik|Dnr411|RDGBB|RDGBB1|rdgB-beta	phosphatidylinositol transfer protein, cytoplasmic 1	protein-coding
mm_140736.1	chr17	15706113	15706133	-	1	NA	intron (NM_007690, intron 1 of 35)	intron (NM_007690, intron 1 of 35)	1156	NM_007690	12648	Mm.8137	NM_007690	ENSMUSG00000023852	Chd1	4930525N21Rik|AI851787|AW555109	chromodomain helicase DNA binding protein 1	protein-coding
mm_61536.1	chr7	79273215	79273225	+	1	NA	promoter-TSS (NM_018811)	promoter-TSS (NM_018811)	-46	NM_018811	54608	Mm.365490	NM_018811	ENSMUSG00000039202	Abhd2	2210009N18Rik|LABH2|Labh-2	abhydrolase domain containing 2	protein-coding
mm_7352.1	chr1	106606792	106606794	-	1	NA	intron (NM_009741, intron 1 of 1)	intron (NM_009741, intron 1 of 1)	-60162	NR_106164	102466254		NR_106164	ENSMUSG00000098344	Mir3473f	Gm27846|mmu-mir-3473f	microRNA 3473f	ncRNA
mm_31768.1	chr4	63544871	63544881	+	1	NA	5' UTR (NM_024173, exon 1 of 3)	5' UTR (NM_024173, exon 1 of 3)	111	NM_024173	66290	Mm.371615	NM_024173	ENSMUSG00000039105	Atp6v1g1	1810024D14Rik|AA960677|ATP6J|Atp6g1|VAG1|Vma10	ATPase, H+ transporting, lysosomal V1 subunit G1	protein-coding
mm_27536.1	chr3	57575856	57575864	-	1	NA	promoter-TSS (NM_133784)	promoter-TSS (NM_133784)	16	NM_133784	97064	Mm.405029	NM_133784	ENSMUSG00000027803	Wwtr1	2310058J06Rik|2610021I22Rik|C78399|Taz	WW domain containing transcription regulator 1	protein-coding
mm_67746.1	chr7	90475972	90476003	-	1	NA	promoter-TSS (NM_026734)	promoter-TSS (NM_026734)	8	NM_026734	68472	Mm.289791	NM_026734	ENSMUSG00000030614	Tmem126b	1110001A23Rik	transmembrane protein 126B	protein-coding
mm_62834.1	chr7	113766026	113766039	+	1	NA	promoter-TSS (NM_145584)	promoter-TSS (NM_145584)	34	NM_145584	233744	Mm.334160	NM_145584	ENSMUSG00000038156	Spon1	AI666765|AW455831|BC020531|D330035F22Rik|FSP	spondin 1, (f-spondin) extracellular matrix protein	protein-coding
mm_17426.1	chr2	27463995	27464008	-	1	NA	exon (NM_001113574, exon 2 of 13)	exon (NM_001113574, exon 2 of 13)	11397	NM_023336	67382	Mm.28721	NM_023336	ENSMUSG00000026918	Brd3	2410084F24Rik|AW060456|Fsrg2|ORFX|RINGL3	bromodomain containing 3	protein-coding
mm_78859.1	chr9	44397059	44397128	+	1	NA	promoter-TSS (NM_001293630)	promoter-TSS (NM_001293630)	-2	NM_001293630	14385	Mm.30087	NM_008063	ENSMUSG00000032114	Slc37a4	100043178|G6PT|G6pt1|GSD-1b|mG6PT	solute carrier family 37 (glucose-6-phosphate transporter), member 4	protein-coding
mm_156122.1	chrX	116345734	116345738	+	1	NA	Intergenic	Intergenic	-103208	NM_001033471	382239	Mm.336224	NM_001033471	ENSMUSG00000072995	Cpxcr1	Gm1143	CPX chromosome region, candidate 1	protein-coding
mm_52760.1	chr6	120817768	120817769	+	1	NA	intron (NM_007510, intron 2 of 8)	intron (NM_007510, intron 2 of 8)	4917	NM_007510	11973	Mm.29045	NM_007510	ENSMUSG00000019210	Atp6v1e1	2410029D23Rik|Atp6e|Atp6e2|Atp6v1e|D6Ertd385e|E2|P31|Vma4	ATPase, H+ transporting, lysosomal V1 subunit E1	protein-coding
mm_168297.1	chr11	106028424	106028436	-	1	NA	intron (NM_001037712, intron 12 of 12)	IAPLTR1_Mm|LTR|ERVK	-8442	NM_027946	71833	Mm.307455	NM_027946	ENSMUSG00000049354	Dcaf7	1700012F10Rik|2610037L01Rik|C86529|HAN11|Wdr68	DDB1 and CUL4 associated factor 7	protein-coding
mm_58372.1	chr6	148946147	148946182	-	1	NA	non-coding (NR_144294, exon 1 of 2)	non-coding (NR_144294, exon 1 of 2)	268	NM_019643	56306	Mm.18637	NM_019643	ENSMUSG00000039985	Fam60a	Ppcs1|Pptcs1|Tera	family with sequence similarity 60, member A	protein-coding
mm_101118.1	chr11	12009493	12009495	-	1	NA	intron (NM_010345, intron 1 of 16)	MTE-int|LTR|ERVL-MaLR	18477	NM_001177629	14783	Mm.273117	NM_010345	ENSMUSG00000020176	Grb10	5730571D09Rik|AI325020|Meg1|mKIAA0207	growth factor receptor bound protein 10	protein-coding
mm_76914.1	chr8	105932668	105932693	-	1	NA	TTS (NM_173432)	TTS (NM_173432)	1182	NM_023182	109660	Mm.2745	NM_023182	ENSMUSG00000031896	Ctrl	0910001G08Rik|1810004D15Rik|AV005227|Ctra-1|Ctra1|chymopasin|mFLJ00366	chymotrypsin-like	protein-coding
mm_162596.1	chr1	183058632	183058648	-	1	NA	Intergenic	Intergenic	88917	NM_001278220	68897	Mm.327216	NM_026866	ENSMUSG00000030768	Disp1	1190008H24Rik|DispA	dispatched RND transporter family member 1	protein-coding
mm_35275.1	chr4	19922495	19922550	-	1	NA	promoter-TSS (NM_175406)	promoter-TSS (NM_175406)	44	NM_175406	242341	Mm.19298	NM_175406	ENSMUSG00000028238	Atp6v0d2	1620401A02Rik|AI324824|V-ATPase	ATPase, H+ transporting, lysosomal V0 subunit D2	protein-coding
mm_29439.1	chr3	110142745	110142758	-	1	NA	intron (NM_001163351, intron 1 of 4)	CpG	721	NM_001163348	80883	Mm.39262	NM_030699	ENSMUSG00000059857	Ntng1	A930010C08Rik|AI853992|Lmnt1	netrin G1	protein-coding
mm_78557.1	chr9	35669625	35669678	+	1	NA	promoter-TSS (NM_001033421)	promoter-TSS (NM_001033421)	12	NM_001033421	330921	Mm.479701	NM_001033421	ENSMUSG00000074452	Pate2	Gm846|Pate-M|mANLP1	prostate and testis expressed 2	protein-coding
mm_119132.1	chr14	31160730	31160746	+	1	NA	intron (NM_138672, intron 11 of 68)	intron (NM_138672, intron 11 of 68)	7903	NM_138672	192187	Mm.220821	NM_138672	ENSMUSG00000042286	Stab1	FEEL-1|FELE-1|MFEEL-1|MS-1|STAB-1|mKIAA0246	stabilin 1	protein-coding
mm_92448.1	chr10	77735193	77735195	-	1	NA	intron (NM_001287074, intron 1 of 11)	intron (NM_001287074, intron 1 of 11)	8708	NM_001205033	100502953	Mm.486157	NM_001205033	ENSMUSG00000096421	Gm10100	ENSMUSG00000061452	predicted gene 10100	protein-coding
mm_56200.1	chr6	88874985	88875030	-	1	NA	promoter-TSS (NM_176973)	promoter-TSS (NM_176973)	37	NM_001347327	319655	Mm.302613	NM_176973	ENSMUSG00000033152	Podxl2	D130074J02Rik|PODLX2	podocalyxin-like 2	protein-coding
mm_65595.1	chr7	27337583	27337616	-	1	NA	promoter-TSS (NM_175641)	promoter-TSS (NM_175641)	13	NM_175641	108075	Mm.272251	NM_175641	ENSMUSG00000040488	Ltbp4	2310046A13Rik	latent transforming growth factor beta binding protein 4	protein-coding
mm_69639.1	chr7	138846168	138846199	-	1	NA	promoter-TSS (NM_026391)	promoter-TSS (NM_026391)	84	NM_001045483	69546	Mm.31598	NM_027115	ENSMUSG00000041775	Mapk1ip1	2310009E07Rik|AU043776|MISS	mitogen-activated protein kinase 1 interacting protein 1	protein-coding
mm_23332.1	chr3	54295307	54295317	+	1	NA	intron (NR_046161, intron 6 of 10)	(T)n|Simple_repeat|Simple_repeat	-65795	NM_001198766	50706	Mm.236067	NM_015784	ENSMUSG00000027750	Postn	A630052E07Rik|AI747096|OSF-2|Osf2|PLF|PN	periostin, osteoblast specific factor	protein-coding
mm_42131.1	chr5	111104809	111104811	+	1	NA	intron (NM_001267622, intron 5 of 22)	intron (NM_001267622, intron 5 of 22)	100666	NR_030482	735278		NR_030482	ENSMUSG00000076163	Mir701	Mirn701|mir-701|mmu-mir-701	microRNA 701	ncRNA
mm_77559.1	chr8	123426738	123426739	-	1	NA	Intergenic	MuLV-int|LTR|ERV1	15174	NM_023279	22152	Mm.40068	NM_023279	ENSMUSG00000062380	Tubb3	3200002H15Rik|M(beta)3|M(beta)6	tubulin, beta 3 class III	protein-coding
mm_63520.1	chr7	127877147	127877174	+	1	NA	promoter-TSS (NM_146259)	promoter-TSS (NM_146259)	-337	NM_146259	244219	Mm.207872	NM_146259	ENSMUSG00000049728	Zfp668	BC030314|E130018B19Rik|Znf668	zinc finger protein 668	protein-coding
mm_43971.1	chr5	146079168	146079188	+	1	NA	promoter-TSS (NM_001105160)	promoter-TSS (NM_001105160)	-80	NM_001105160	100041449	Mm.301900	NM_001105160	ENSMUSG00000061292	Cyp3a59	ENSMUSG00000061292	cytochrome P450, family 3, subfamily a, polypeptide 59	protein-coding
mm_136097.1	chr16	85079928	85079942	-	1	NA	exon (NM_001198823, exon 5 of 18)	exon (NM_001198823, exon 5 of 18)	93772	NM_001198825	11820	Mm.277585	NM_007471	ENSMUSG00000022892	App	Abeta|Abpp|Adap|Ag|Cvap|E030013M08Rik|betaApp	amyloid beta (A4) precursor protein	protein-coding
mm_21229.1	chr2	155979446	155979466	-	1	NA	intron (NM_001130000, intron 19 of 32)	intron (NM_001130000, intron 19 of 32)	22898	NM_177217	16328	Mm.288729	NM_008383	ENSMUSG00000038241	Cep250	AW490617|B230210E21Rik|Cep2|Inmp	centrosomal protein 250	protein-coding
mm_3375.1	chr1	139056759	139056763	+	1	NA	intron (NM_181347, intron 6 of 20)	intron (NM_181347, intron 6 of 20)	79104	NR_108103	78229	Mm.437838	NR_108103	ENSMUSG00000104900	4930596I21Rik	-	RIKEN cDNA 4930596I21 gene	ncRNA
mm_105443.1	chr11	104417029	104417052	-	1	NA	intron (NM_001081045, intron 2 of 13)	intron (NM_001081045, intron 2 of 13)	25251	NM_001081045	76719	Mm.136418	NM_001081045	ENSMUSG00000018412	Kansl1	1700081L11Rik|9430041J06Rik|mKIAA1267	KAT8 regulatory NSL complex subunit 1	protein-coding
mm_131915.1	chr16	23308043	23308053	+	1	NA	intron (NM_001252506, intron 1 of 6)	intron (NM_001252506, intron 1 of 6)	17578	NM_001252506	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_146767.1	chr18	20002004	20002014	-	1	NA	promoter-TSS (NM_001291809)	promoter-TSS (NM_001291809)	88	NM_007882	13507	Mm.89935	NM_007882	ENSMUSG00000059898	Dsc3	5430426I24Rik	desmocollin 3	protein-coding
mm_34658.1	chr4	150866473	150866489	+	1	NA	exon (NM_133753, exon 4 of 4)	exon (NM_133753, exon 4 of 4)	11390	NM_133753	74155	Mm.318841	NM_133753	ENSMUSG00000028967	Errfi1	1300002F13Rik|AI788755|Mig-6|Mig6|RALT	ERBB receptor feedback inhibitor 1	protein-coding
mm_25160.1	chr3	103049656	103049667	+	1	NA	exon (NM_001310693, exon 11 of 18)	exon (NM_001310693, exon 11 of 18)	-8624	NM_010937	18176	Mm.400954	NM_010937	ENSMUSG00000027852	Nras	AV095280|N-ras	neuroblastoma ras oncogene	protein-coding
mm_6878.1	chr1	84363775	84363785	-	1	NA	Intergenic	Intergenic	-79135	NM_001003948	98496	Mm.187470	NM_001003948	ENSMUSG00000045658	Pid1	5033414K04Rik|NYGGF4	phosphotyrosine interaction domain containing 1	protein-coding
mm_44035.1	chr5	147468463	147468471	+	1	NA	intron (NM_028291, intron 4 of 18)	intron (NM_028291, intron 4 of 18)	37887	NM_028291	72587	Mm.320469	NM_028291	ENSMUSG00000029647	Pan3	2700050F09Rik|A430027N15Rik|AU014670	PAN3 poly(A) specific ribonuclease subunit	protein-coding
mm_78020.1	chr9	13749155	13749205	+	1	NA	promoter-TSS (NM_023858)	promoter-TSS (NM_023858)	-1	NM_023858	77116	Mm.210405	NM_023858	ENSMUSG00000031918	Mtmr2	6030445P13Rik	myotubularin related protein 2	protein-coding
mm_4173.1	chr1	171121682	171121696	+	1	NA	promoter-TSS (NM_001081275)	promoter-TSS (NM_001081275)	28	NM_001081275	75472	Mm.32760	NM_029301	ENSMUSG00000026649	Cfap126	1700009P17Rik|AV282292|Flattop|Fltp	cilia and flagella associated protein 126	protein-coding
mm_8437.1	chr1	152766282	152766319	-	1	NA	promoter-TSS (NM_026369)	promoter-TSS (NM_026369)	5	NM_001346118	19731	Mm.245270	NM_016846	ENSMUSG00000026482	Rgl1	Rgl|mKIAA0959	ral guanine nucleotide dissociation stimulator,-like 1	protein-coding
mm_4982.1	chr1	191717881	191717904	+	1	NA	promoter-TSS (NM_001134829)	promoter-TSS (NM_001134829)	-132	NM_172266	226856	Mm.277958	NM_172266	ENSMUSG00000026623	Lpgat1	AI649174|AW112037|BC013667	lysophosphatidylglycerol acyltransferase 1	protein-coding
mm_5925.1	chr1	55226523	55226541	-	1	NA	5' UTR (NM_028713, exon 1 of 9)	5' UTR (NM_028713, exon 1 of 9)	250	NM_028713	74013	Mm.292050	NM_028713	ENSMUSG00000025978	Rftn2	2700010E02Rik|3222401M22Rik	raftlin family member 2	protein-coding
mm_153501.1	chr19	41333051	41333094	-	1	NA	intron (NM_031376, intron 2 of 16)	MTE2a|LTR|ERVL-MaLR	51998	NM_031376	83490	Mm.222266	NM_031376	ENSMUSG00000025017	Pik3ap1	1810044J04Rik|BCAP	phosphoinositide-3-kinase adaptor protein 1	protein-coding
mm_7136.1	chr1	91056493	91056508	-	1	NA	intron (NM_001310732, intron 1 of 24)	B3|SINE|B2	3056	NM_008515	16978	Mm.45039	NM_008515	ENSMUSG00000026305	Lrrfip1	AU024550|Fliiap1	leucine rich repeat (in FLII) interacting protein 1	protein-coding
mm_129140.1	chr15	76200553	76200563	-	1	NA	promoter-TSS (NM_201391)	promoter-TSS (NM_201391)	49	NM_201390	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
mm_187.1	chr1	15491438	15491439	+	1	NA	intron (NM_001098528, intron 1 of 1)	intron (NM_001098528, intron 1 of 1)	178986	NM_001098528	98741	Mm.156081	NM_001033195	ENSMUSG00000092083	Kcnb2	9630047L19Rik|BB130875|Kv2.2	potassium voltage gated channel, Shab-related subfamily, member 2	protein-coding
mm_172952.1	chr9	87161833	87161833	-	1	NA	intron (NM_001177731, intron 2 of 4)	L1Md_T|LINE|L1	17527	NM_001101482	244958	Mm.335337	NM_001101482	ENSMUSG00000042761	Mrap2	BB633055	melanocortin 2 receptor accessory protein 2	protein-coding
mm_134382.1	chr16	17201201	17201209	-	1	NA	intron (NM_009456, intron 1 of 3)	CpG	287	NM_009456	22195	Mm.3074	NM_009456	ENSMUSG00000038965	Ube2l3	C79827|UbcM4|Ubce7	ubiquitin-conjugating enzyme E2L 3	protein-coding
mm_144295.1	chr18	12173554	12173567	+	1	NA	intron (NM_029623, intron 3 of 19)	intron (NM_029623, intron 3 of 19)	4830	NM_029623	76482	Mm.196596	NM_029623	ENSMUSG00000024410	3110002H16Rik	2400010D15Rik|Mic-1|Mic1	RIKEN cDNA 3110002H16 gene	protein-coding
mm_80918.1	chr9	100885027	100885030	+	1	NA	intron (NM_009282, intron 15 of 33)	Lx3_Mus|LINE|L1	149856	NM_001311149	66904	Mm.335385	NM_025835	ENSMUSG00000032527	Pccb	1300012P06Rik|AI314687|R74805	propionyl Coenzyme A carboxylase, beta polypeptide	protein-coding
mm_42794.1	chr5	121660643	121660645	+	1	NA	promoter-TSS (NM_001289543)	promoter-TSS (NM_001289543)	81	NM_001289543	72399	Mm.153372	NM_028227	ENSMUSG00000029458	Brap	3010002G07Rik|BRAP2|IMP	BRCA1 associated protein	protein-coding
mm_144016.1	chr17	88792000	88792000	-	1	NA	promoter-TSS (NM_013582)	promoter-TSS (NM_013582)	-24	NM_013582	16867	Mm.1644	NM_013582	ENSMUSG00000024107	Lhcgr	Gpcr19-rs1|LH-R|Lhr	luteinizing hormone/choriogonadotropin receptor	protein-coding
mm_130758.1	chr15	101274372	101274381	-	1	NA	3' UTR (NM_010444, exon 7 of 7)	3' UTR (NM_010444, exon 7 of 7)	7530	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_43496.1	chr5	136967860	136967875	+	1	NA	promoter-TSS (NM_021719)	promoter-TSS (NM_021719)	-2	NM_021719	60363	Mm.87202	NM_021719	ENSMUSG00000001739	Cldn15	2210009B08Rik|BB107105	claudin 15	protein-coding
mm_104364.1	chr11	94321911	94321943	-	1	NA	promoter-TSS (NM_026313)	promoter-TSS (NM_026313)	-16	NM_026313	67684	Mm.30927	NM_026313	ENSMUSG00000020863	Luc7l3	3300001P08Rik|Luc7a	LUC7-like 3 (S. cerevisiae)	protein-coding
mm_144633.1	chr18	32939448	32939458	+	1	NA	exon (NM_009793, exon 1 of 11)	exon (NM_009793, exon 1 of 11)	412	NM_009793	12326	Mm.222329	NM_009793	ENSMUSG00000038128	Camk4	A430110E23Rik|AI666733|CaMKIV|CaMKIV/Gr|D18Bwg0362e	calcium/calmodulin-dependent protein kinase IV	protein-coding
mm_148960.1	chr19	7494021	7494031	+	1	NA	promoter-TSS (NM_001163505)	promoter-TSS (NM_001163505)	-14	NM_001163505	109168	Mm.264016	NM_146091	ENSMUSG00000024759	Atl3	4633402C03Rik|5730596K20Rik|AI465397|AW228836	atlastin GTPase 3	protein-coding
mm_75679.1	chr8	68042688	68042702	-	1	NA	Intergenic	Lx8b|LINE|L1	-68121	NM_177698	234353	Mm.32525	NM_027626	ENSMUSG00000030465	Psd3	4931420C21Rik|AI661273|BC003498|D430018P08|EFA6D	pleckstrin and Sec7 domain containing 3	protein-coding
mm_57860.1	chr6	129533268	129533275	-	1	NA	promoter-TSS (NR_045270)	promoter-TSS (NR_045270)	13	NR_045270	100504641	Mm.398286	NR_045270	ENSMUSG00000097675	1700101I11Rik	-	RIKEN cDNA 1700101I11 gene	ncRNA
mm_71319.1	chr8	44935336	44935347	+	1	NA	Intergenic	CpG	-14867	NM_001081286	14107	Mm.27365	NM_001081286	ENSMUSG00000070047	Fat1	2310038E12Rik|AU023433|Fath|mFat1	FAT atypical cadherin 1	protein-coding
mm_74657.1	chr8	13548951	13548964	-	1	NA	Intergenic	Intergenic	13504	NM_025601	66501	Mm.46136	NM_025601	ENSMUSG00000031452	1700029H14Rik	-	RIKEN cDNA 1700029H14 gene	protein-coding
mm_110836.1	chr12	72907489	72907494	-	1	NA	intron (NM_029444, intron 8 of 17)	intron (NM_029444, intron 8 of 17)	10274	NM_029444	75801	Mm.242892	NM_029444	ENSMUSG00000021098	4930447C04Rik	4921504I02Rik|A930035O15Rik|Six6OS|Six6as|Six6os1	RIKEN cDNA 4930447C04 gene	protein-coding
mm_58863.1	chr7	16908717	16908735	+	1	NA	exon (NM_008967, exon 2 of 2)	exon (NM_008967, exon 2 of 2)	2236	NM_008967	19222	Mm.287572	NM_008967	ENSMUSG00000043017	Ptgir	IP|PGI2	prostaglandin I receptor (IP)	protein-coding
mm_45525.1	chr5	72636228	72636236	-	1	NA	intron (NM_007723, intron 1 of 8)	intron (NM_007723, intron 1 of 8)	6520	NM_007723	12788	Mm.436652	NM_007723	ENSMUSG00000067220	Cnga1	Cncg	cyclic nucleotide gated channel alpha 1	protein-coding
mm_86385.1	chr9	123872965	123872969	-	1	NA	Intergenic	Intergenic	-10938	NM_011798	23832	Mm.390241	NM_011798	ENSMUSG00000060509	Xcr1	Ccxcr1|Gpr5|mXcr1	chemokine (C motif) receptor 1	protein-coding
mm_43745.1	chr5	140321615	140321671	+	1	NA	promoter-TSS (NM_010752)	promoter-TSS (NM_010752)	-91	NM_010752	17120	Mm.27250	NM_010752	ENSMUSG00000029554	Mad1l1	AI173502|AW550425|Mad1	MAD1 mitotic arrest deficient 1-like 1	protein-coding
mm_31707.1	chr4	62619516	62619530	+	1	NA	promoter-TSS (NM_001081650)	promoter-TSS (NM_001081650)	-149	NM_001081650	50780	Mm.286753	NM_019492	ENSMUSG00000059810	Rgs3	4930506N09Rik|C2PA-RGS3|C2pa|PDZ-RGS3|RGS3S	regulator of G-protein signaling 3	protein-coding
mm_136463.1	chr16	95359405	95359417	-	1	NA	3' UTR (NM_133659, exon 11 of 11)	3' UTR (NM_133659, exon 11 of 11)	99937	NM_001302154	13876	Mm.164531	NM_133659	ENSMUSG00000040732	Erg	D030036I24Rik	avian erythroblastosis virus E-26 (v-ets) oncogene related	protein-coding
mm_75486.1	chr8	48843361	48843379	-	1	NA	Intergenic	CpG	-168680	NM_011857	23965	Mm.42191	NM_011857	ENSMUSG00000031561	Tenm3	2610100B16Rik|Odz1|Odz3|Ten-m3|mKIAA1455	teneurin transmembrane protein 3	protein-coding
mm_106059.1	chr11	116131002	116131041	-	1	NA	TTS (NM_024177)	TTS (NM_024177)	107	NM_178802	338364	Mm.439976	NM_178802	ENSMUSG00000054517	Trim65	4732463G12Rik	tripartite motif-containing 65	protein-coding
mm_148680.1	chr19	5646851	5646860	+	1	NA	exon (NM_009045, exon 11 of 11)	exon (NM_009045, exon 11 of 11)	9365	NM_009045	19697	Mm.249966	NM_009045	ENSMUSG00000024927	Rela	p65	v-rel reticuloendotheliosis viral oncogene homolog A (avian)	protein-coding
mm_164922.1	chr18	77185627	77185639	+	1	NA	promoter-TSS (NM_013666)	promoter-TSS (NM_013666)	-214	NM_153124	225742	Mm.365178	NM_013666	ENSMUSG00000025425	St8sia5	ST8SiaV|Siat8e	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 5	protein-coding
mm_117400.1	chr13	73692601	73692640	-	1	NA	intron (NM_028878, intron 2 of 11)	intron (NM_028878, intron 2 of 11)	-7206	NM_027780	71390	Mm.105251	NM_027780		Slc6a19os	5430425J12Rik	solute carrier family 6 (neurotransmitter transporter), member 19, opposite strand	protein-coding
mm_167730.1	chr9	104102579	104102611	-	1	NA	intron (NM_145700, intron 1 of 2)	intron (NM_145700, intron 1 of 2)	24048	NM_145700	252837	Mm.269254	NM_145700	ENSMUSG00000079355	Ackr4	A630091E18Rik|CCBP2|CCR11|CCX-CKR|CCX-CKR1|Ccrl1|Cmkbrl1|PPR1|VSHK1	atypical chemokine receptor 4	protein-coding
mm_171065.1	chr3	112152130	112152130	+	1	NA	Intergenic	L1Md_T|LINE|L1	270227	NR_045362	625585	Mm.389497	NR_045362	ENSMUSG00000104543	Gm6602	-	predicted gene 6602	ncRNA
mm_132660.1	chr16	41801854	41801854	+	1	NA	intron (NM_001347236, intron 1 of 6)	BC1_Mm|scRNA|scRNA	268512	NM_175548	268890	Mm.310524	NM_175548	ENSMUSG00000061080	Lsamp	5430428I19|AW046674|B130007O04Rik|D930023J12Rik|Lam|Lamp	limbic system-associated membrane protein	protein-coding
mm_8002.1	chr1	134549610	134549616	-	1	NA	promoter-TSS (NM_001145300)	promoter-TSS (NM_001145300)	69	NM_001145300	71001	Mm.158529	NM_183292	ENSMUSG00000046367	Mgat4e	4931440L10Rik	MGAT4 family, member E	protein-coding
mm_99813.1	chr11	108404814	108404828	+	1	NA	exon (NM_013475, exon 4 of 8)	exon (NM_013475, exon 4 of 8)	9524	NM_013475	11818	Mm.2266	NM_013475	ENSMUSG00000000049	Apoh	B2GPI|beta-2-GPI|beta2-GPI	apolipoprotein H	protein-coding
mm_94155.1	chr10	128744847	128744887	-	1	NA	promoter-TSS (NM_016811)	promoter-TSS (NM_016811)	-811	NM_016811	13139	Mm.291235	NM_016811	ENSMUSG00000025357	Dgka	80kDa|AW146112|Dagk1	diacylglycerol kinase, alpha	protein-coding
mm_122144.1	chr14	31188734	31188759	-	1	NA	exon (NM_022656, exon 8 of 21)	exon (NM_022656, exon 8 of 21)	18080	NM_022656	64652	Mm.298728	NM_022656	ENSMUSG00000021910	Nisch	1200007D05Rik|3202002H23Rik|AW494485|I-1	nischarin	protein-coding
mm_104413.1	chr11	94653688	94653707	-	1	NA	promoter-TSS (NM_177752)	promoter-TSS (NM_177752)	57	NM_177752	268465	Mm.358937	NM_177752	ENSMUSG00000039055	Eme1	6820428D13	essential meiotic structure-specific endonuclease 1	protein-coding
mm_52457.1	chr6	113690987	113690997	+	1	NA	exon (NM_172161, exon 12 of 13)	exon (NM_172161, exon 12 of 13)	-6058	NM_001347356	381801	Mm.333322	NM_001033463	ENSMUSG00000056952	Tatdn2	AI646012|mKIAA0218	TatD DNase domain containing 2	protein-coding
mm_32402.1	chr4	106911436	106911446	+	1	NA	promoter-TSS (NM_198438)	promoter-TSS (NM_198438)	-29	NM_198438	72475	Mm.195635	NM_023672	ENSMUSG00000061887	Ssbp3	2610021L12Rik|2610200M23Rik|5730488C10Rik|AI854733|AW551939|LAST|SSDP1	single-stranded DNA binding protein 3	protein-coding
mm_35369.1	chr4	32923518	32923530	-	1	NA	promoter-TSS (NM_080471)	promoter-TSS (NM_080471)	-19	NM_001012450	140577	Mm.214766	NM_080471	ENSMUSG00000040183	Ankrd6	-	ankyrin repeat domain 6	protein-coding
mm_141963.1	chr17	35121187	35121197	-	1	NA	promoter-TSS (NM_009975)	promoter-TSS (NM_009975)	100	NM_001303476	13001	Mm.378901	NM_009975	ENSMUSG00000024387	Csnk2b	CK II beta	casein kinase 2, beta polypeptide	protein-coding
mm_103648.1	chr11	78969390	78969401	-	1	NA	intron (NM_001159301, intron 4 of 9)	intron (NM_001159301, intron 4 of 9)	15529	NM_001159301	16859	Mm.341434	NM_010708	ENSMUSG00000001123	Lgals9	AA407335|AI194909|AI265545|LGALS35|Lgals5|gal-9|galectin-9	lectin, galactose binding, soluble 9	protein-coding
mm_41596.1	chr5	95960310	95960314	+	1	NA	3' UTR (NM_018866, exon 4 of 4)	3' UTR (NM_018866, exon 4 of 4)	3373	NM_018866	55985	Mm.10116	NM_018866	ENSMUSG00000023078	Cxcl13	4631412M08Rik|ANGIE2|Angie|BCA-1|BLC|BLR1L|Scyb13	chemokine (C-X-C motif) ligand 13	protein-coding
mm_50699.1	chr6	52026620	52026628	+	1	NA	Intergenic	Intergenic	-14075	NM_018773	54353	Mm.221479	NM_018773	ENSMUSG00000059182	Skap2	2610021A10Rik|AA960083|BB137539|RA70|SKAP-HOM|Saps|Scap2|mSKAP55R	src family associated phosphoprotein 2	protein-coding
mm_148448.1	chr19	3972476	3972503	+	1	NA	5' UTR (NM_001177438, exon 1 of 10)	5' UTR (NM_001177438, exon 1 of 10)	161	NM_001177438	621603	Mm.34137	NM_001177438	ENSMUSG00000075296	Aldh3b2	AI848594|C130048D07Rik	aldehyde dehydrogenase 3 family, member B2	protein-coding
mm_59193.1	chr7	24499600	24499604	+	1	NA	exon (NM_153112, exon 3 of 9)	exon (NM_153112, exon 3 of 9)	-7485	NM_001290461	232969	Mm.181332	NM_146183	ENSMUSG00000064264	Zfp428	2410005H09Rik|AV271806|AW047854|Znf428	zinc finger protein 428	protein-coding
mm_50594.1	chr6	49071205	49071217	+	1	NA	Intergenic	Intergenic	-2584	NM_029353	75593	Mm.439947	NM_029353	ENSMUSG00000029815	Malsu1	2410003K15Rik|Matsu1	mitochondrial assembly of ribosomal large subunit 1	protein-coding
mm_30775.1	chr4	17945954	17945956	+	1	NA	intron (NM_019724, intron 1 of 9)	Lx3A|LINE|L1	92497	NM_019724	17389	Mm.187315	NM_019724	ENSMUSG00000028226	Mmp16	MT-MMP 3|MT3-MMP|Mt3mmp	matrix metallopeptidase 16	protein-coding
mm_19813.1	chr2	110362986	110363001	-	1	NA	promoter-TSS (NM_026271)	promoter-TSS (NM_026271)	0	NM_026271	67606	Mm.291809	NM_026271	ENSMUSG00000074971	Fibin	1110018M03Rik	fin bud initiation factor homolog (zebrafish)	protein-coding
mm_23557.1	chr3	62339025	62339037	+	1	NA	5' UTR (NM_001081295, exon 1 of 14)	5' UTR (NM_001081295, exon 1 of 14)	254	NM_001081295	622434	Mm.153974	NM_001081295	ENSMUSG00000036885	Arhgef26	4631416L12Rik|8430436L14Rik|AI303572|AW491953|SGEF	Rho guanine nucleotide exchange factor (GEF) 26	protein-coding
mm_31272.1	chr4	45342252	45342281	+	1	NA	exon (NM_153167, exon 1 of 7)	exon (NM_153167, exon 1 of 7)	165	NM_153167	242418	Mm.317668	NM_153167	ENSMUSG00000035572	Dcaf10	AA959934|Wdr32	DDB1 and CUL4 associated factor 10	protein-coding
mm_91416.1	chr10	31690583	31690587	-	1	NA	3' UTR (NM_001013411, exon 7 of 7)	3' UTR (NM_001013411, exon 7 of 7)	-80860	NM_001146349	268291	Mm.295212	NM_001146349	ENSMUSG00000063760	Rnf217	AU016819|Ibrdc1	ring finger protein 217	protein-coding
mm_22922.1	chr3	31096841	31096854	+	1	NA	5' UTR (NM_001039090, exon 2 of 7)	5' UTR (NM_001039090, exon 2 of 7)	1789	NM_001039090	20482	Mm.15406	NM_011386	ENSMUSG00000027660	Skil	Skir|SnoN|sno	SKI-like	protein-coding
mm_51838.1	chr6	90302084	90302140	+	1	NA	intron (NM_177738, intron 2 of 4)	intron (NM_177738, intron 2 of 4)	842	NM_177738	243535	Mm.233854	NM_177738	ENSMUSG00000049694	BC048671	-	cDNA sequence BC048671	protein-coding
mm_22292.1	chr2	180257106	180257118	-	1	NA	promoter-TSS (NM_025587)	promoter-TSS (NM_025587)	-267	NM_025587	66481	Mm.289669	NM_025587	ENSMUSG00000039001	Rps21	1810049N11Rik|2410030A14Rik	ribosomal protein S21	protein-coding
mm_31328.1	chr4	46451045	46451051	+	1	NA	5' UTR (NM_130889, exon 1 of 7)	5' UTR (NM_130889, exon 1 of 7)	122	NM_130889	67628	Mm.263913	NM_130889	ENSMUSG00000028333	Anp32b	2410015B15Rik|PAL31|PHAPI2a|Ssp29	acidic (leucine-rich) nuclear phosphoprotein 32 family, member B	protein-coding
mm_4989.1	chr1	191719165	191719229	+	1	NA	intron (NM_001134829, intron 1 of 7)	intron (NM_001134829, intron 1 of 7)	802	NM_001134829	226856	Mm.277958	NM_172266	ENSMUSG00000026623	Lpgat1	AI649174|AW112037|BC013667	lysophosphatidylglycerol acyltransferase 1	protein-coding
mm_167749.1	chr9	109849249	109849259	+	1	NA	exon (NM_009921, exon 1 of 4)	exon (NM_009921, exon 1 of 4)	202	NM_009921	12796	Mm.3834	NM_009921	ENSMUSG00000038357	Camp	CAP18|Cnlp|Cramp|FALL39|MCLP	cathelicidin antimicrobial peptide	protein-coding
mm_59885.1	chr7	30298944	30298960	+	1	NA	exon (NM_001081114, exon 7 of 14)	exon (NM_001081114, exon 7 of 14)	7199	NM_001081114	76686	Mm.159258	NM_001081114	ENSMUSG00000013921	Clip3	1500005P14Rik|AI844915|Clipr-59	CAP-GLY domain containing linker protein 3	protein-coding
mm_138070.1	chr17	33941239	33941280	+	1	NA	promoter-TSS (NM_010385)	promoter-TSS (NM_010385)	536	NM_020603	57315	Mm.2437	NM_020603	ENSMUSG00000024312	Wdr46	2310007I04Rik|Bing4|C78447|C78559	WD repeat domain 46	protein-coding
mm_5021.1	chr1	193153190	193153199	+	1	NA	promoter-TSS (NM_016851)	promoter-TSS (NM_016851)	82	NM_016851	54139	Mm.273695	NM_016851	ENSMUSG00000026638	Irf6	AI876454|E230028I05Rik|mirf6	interferon regulatory factor 6	protein-coding
mm_139588.1	chr17	57223819	57223863	+	1	NA	exon (NM_009778, exon 11 of 41)	exon (NM_009778, exon 11 of 41)	4295	NM_009778	12266	Mm.19131	NM_009778	ENSMUSG00000024164	C3	AI255234|ASP|HSE-MSF|Plp	complement component 3	protein-coding
mm_27716.1	chr3	68761414	68761423	-	1	NA	Intergenic	Intergenic	69994	NM_008351	16159	Mm.103783	NM_008351	ENSMUSG00000027776	Il12a	IL-12p35|Il-12a|Ll12a|p35	interleukin 12a	protein-coding
mm_89180.1	chr10	86345821	86345840	+	1	NA	exon (NM_011595, exon 5 of 5)	exon (NM_011595, exon 5 of 5)	45418	NM_011595	21859	Mm.4871	NM_011595	ENSMUSG00000020044	Timp3	Timp-3	tissue inhibitor of metalloproteinase 3	protein-coding
mm_153868.1	chr19	46675345	46675354	-	1	NA	Intergenic	Intergenic	-2349	NM_007809	13074	Mm.1262	NM_007809	ENSMUSG00000003555	Cyp17a1	Cyp17|p450c17	cytochrome P450, family 17, subfamily a, polypeptide 1	protein-coding
mm_56068.1	chr6	86787542	86787588	-	1	NA	intron (NM_013471, intron 1 of 12)	ID_B1|SINE|B4	6019	NM_013471	11746	Mm.259702	NM_013471	ENSMUSG00000029994	Anxa4	AI265406|AIV|AW106930|Anx4|Xanx-4	annexin A4	protein-coding
mm_25710.1	chr3	122511956	122511958	+	1	NA	intron (NM_013867, intron 6 of 11)	intron (NM_013867, intron 6 of 11)	29724	NR_106117	102465764		NR_106117	ENSMUSG00000104773	Mir7657	mmu-mir-7657	microRNA 7657	ncRNA
mm_4903.1	chr1	189860376	189860386	+	1	NA	intron (NM_008976, intron 15 of 18)	intron (NM_008976, intron 15 of 18)	61907	NM_026796	226830	Mm.156895	NM_026796	ENSMUSG00000026603	Smyd2	1110020E07Rik|4930402C15|KMT3C|Zmynd14	SET and MYND domain containing 2	protein-coding
mm_115593.1	chr13	11827163	11827177	-	1	NA	intron (NM_023868, intron 15 of 104)	intron (NM_023868, intron 15 of 104)	279775	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding
mm_37208.1	chr4	117883429	117883507	-	1	NA	promoter-TSS (NM_001253381)	promoter-TSS (NM_001253381)	8	NR_045570	53418	Mm.123843	NM_017377	ENSMUSG00000028541	B4galt2	Ggtb2	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 2	protein-coding
mm_119482.1	chr14	47358208	47358221	+	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-15646	NM_010705	16854	Mm.248615	NM_010705	ENSMUSG00000050335	Lgals3	GBP|L-34|Mac-2|gal3	lectin, galactose binding, soluble 3	protein-coding
mm_149744.1	chr19	22448179	22448196	+	1	NA	promoter-TSS (NM_177341)	promoter-TSS (NM_177341)	-21	NM_177341	226025	Mm.131943	NM_177341	ENSMUSG00000052387	Trpm3	6330504P12Rik|9330180E14|AU018608|B930001P07Rik|LTRPC3|MLSN2	transient receptor potential cation channel, subfamily M, member 3	protein-coding
mm_67068.1	chr7	67759736	67759759	-	1	NA	promoter-TSS (NM_207663)	promoter-TSS (NM_207663)	-5	NM_207663	233335	Mm.60526	NM_183312	ENSMUSG00000030554	Synm	4930412K21Rik|AI852401|Dmn|E130104F11|Syn|Synemin	synemin, intermediate filament protein	protein-coding
mm_325.1	chr1	24678889	24678937	+	1	NA	promoter-TSS (NM_001310483)	promoter-TSS (NM_001310483)	-5	NM_001310483	68421	Mm.336563	NM_026719	ENSMUSG00000073725	Lmbrd1	0910001K20Rik|AV347960	LMBR1 domain containing 1	protein-coding
mm_131734.1	chr16	21931057	21931059	+	1	NA	3' UTR (NM_172821, exon 13 of 13)	3' UTR (NM_172821, exon 13 of 13)	16494	NM_025693	66664	Mm.46480	NM_025693	ENSMUSG00000022856	Tmem41a	2900010K02Rik|5730578N08Rik	transmembrane protein 41a	protein-coding
mm_17999.1	chr2	38194455	38194475	-	1	NA	intron (NM_146122, intron 2 of 21)	intron (NM_146122, intron 2 of 21)	92919	NM_146122	227801	Mm.314245	NM_146122	ENSMUSG00000035392	Dennd1a	6030446I19Rik|connecdenn	DENN/MADD domain containing 1A	protein-coding
mm_133163.1	chr16	70417608	70417612	+	1	NA	intron (NM_028803, intron 3 of 15)	ORR1B1|LTR|ERVL-MaLR	103661	NM_028803	74185	Mm.396102	NM_028803	ENSMUSG00000022707	Gbe1	2310045H19Rik|2810426P10Rik|D16Ertd536e	glucan (1,4-alpha-), branching enzyme 1	protein-coding
mm_54353.1	chr6	31069878	31069880	-	1	NA	Intergenic	Intergenic	-6786	NR_029532	387223		NR_029532	ENSMUSG00000065604	Mir29b-1	Mirn29b|Mirn29b-1|mir-29b-1	microRNA 29b-1	ncRNA
mm_61947.1	chr7	90191694	90191706	+	1	NA	exon (NM_001252521, exon 17 of 20)	exon (NM_001252521, exon 17 of 20)	61468	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_151078.1	chr19	47585314	47585320	+	1	NA	intron (NM_009289, intron 1 of 18)	HAL1|LINE|L1	5298	NM_001164639	20874	Mm.281011	NM_009289	ENSMUSG00000025060	Slk	9A2|AV021402|AW411554|Etk4|SMAK|Stk2|mKIAA0204|mSLK	STE20-like kinase	protein-coding
mm_59279.1	chr7	24907307	24907326	+	1	NA	intron (NM_001130152, intron 1 of 28)	intron (NM_001130152, intron 1 of 28)	2970	NM_001130152	16801	Mm.3181	NM_008488	ENSMUSG00000040940	Arhgef1	Lbcl2|Lsc	Rho guanine nucleotide exchange factor (GEF) 1	protein-coding
mm_140748.1	chr17	15831229	15831251	-	1	NA	Intergenic	CpG	-4654	NM_178615	68799	Mm.293466	NM_178615	ENSMUSG00000048027	Rgmb	1110059F19Rik|DRAGON	repulsive guidance molecule family member B	protein-coding
mm_37500.1	chr4	123718116	123718145	-	1	NA	promoter-TSS (NR_002445).2	promoter-TSS (NR_002445).2	31	NR_002445	170658	Mm.375824	NR_002445		BC002163	-	NADH dehydrogenase Fe-S protein 5 pseudogene	pseudo
mm_144657.1	chr18	34247686	34247704	+	1	NA	intron (NM_007462, intron 1 of 15)	intron (NM_007462, intron 1 of 15)	-25923	NR_040534	633395	Mm.414290	NR_040534	ENSMUSG00000073607	Gm10548	ENSMUSG00000073607	ribosomal protein L29 pseudogene	pseudo
mm_78033.1	chr9	13827782	13827784	+	1	NA	promoter-TSS (NM_001310721)	promoter-TSS (NM_001310721)	56	NM_176836	72826	Mm.246174	NM_176836	ENSMUSG00000037808	Fam76b	2810485I05Rik|C78303	family with sequence similarity 76, member B	protein-coding
mm_121144.1	chr14	101898531	101898548	+	1	NA	intron (NM_001347628, intron 9 of 26)	intron (NM_001347628, intron 9 of 26)	57916	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_62019.1	chr7	91542966	91542993	+	1	NA	intron (NM_011807, intron 2 of 22)	intron (NM_011807, intron 2 of 22)	452193	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_104535.1	chr11	96347296	96347330	-	1	NA	3' UTR (NM_010458, exon 2 of 2)	3' UTR (NM_010458, exon 2 of 2)	3544	NM_010458	15410	Mm.342481	NM_010458	ENSMUSG00000048763	Hoxb3	Hox-2.7	homeobox B3	protein-coding
mm_115626.1	chr13	12105432	12105442	-	1	NA	intron (NM_023868, intron 1 of 104)	intron (NM_023868, intron 1 of 104)	1508	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding
mm_66173.1	chr7	33944994	33944995	-	1	NA	promoter-TSS (NM_178308)	promoter-TSS (NM_178308)	-9	NM_178308	110187	Mm.155750	NM_178308	ENSMUSG00000066586	Scgb2b26	Abpbg26|Abpbg4|Abpg|C2d|Scgb2b4	secretoglobin, family 2B, member 26	protein-coding
mm_61694.1	chr7	81104940	81104942	+	1	NA	3' UTR (NM_054085, exon 14 of 14)	3' UTR (NM_054085, exon 14 of 14)	-9858	NM_001004184	434203	Mm.389909	NM_001004184	ENSMUSG00000025726	Slc28a1	Cnt1	solute carrier family 28 (sodium-coupled nucleoside transporter), member 1	protein-coding
mm_55742.1	chr6	77545185	77545213	-	1	NA	intron (NM_001109764, intron 8 of 19)	intron (NM_001109764, intron 8 of 19)	-162724	NR_045141	70753	Mm.490700	NR_045141	ENSMUSG00000108077	6330415B21Rik	-	RIKEN cDNA 6330415B21 gene	ncRNA
mm_109397.1	chr12	109947165	109947191	+	1	NA	Intergenic	Intergenic	199300	NR_037233	100499517		NR_037233	ENSMUSG00000093351	Mir3072	mir-3072|mmu-mir-3072	microRNA 3072	ncRNA
mm_138553.1	chr17	35264892	35264895	+	1	NA	intron (NM_010380, intron 3 of 7)	intron (NM_010380, intron 3 of 7)	1770	NM_001267808	14980	Mm.439675	NM_001267808		H2-L	H-2L	histocompatibility 2, D region locus L	protein-coding
mm_13228.1	chr2	97497357	97497358	+	1	NA	intron (NM_001289744, intron 1 of 1)	intron (NM_001289744, intron 1 of 1)	29700	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_139147.1	chr17	47527978	47527992	+	1	NA	intron (NM_001081635, intron 1 of 6)	B1_Mur1|SINE|Alu	22934	NM_001081635	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_47017.1	chr5	115489831	115489840	-	1	NA	Intergenic	PB1D7|SINE|Alu	-5351	NM_133760	75387	Mm.332616	NM_133760	ENSMUSG00000029524	Sirt4	4930596O17Rik	sirtuin 4	protein-coding
mm_92192.1	chr10	68119894	68119900	-	1	NA	intron (NM_023598, intron 7 of 9)	intron (NM_023598, intron 7 of 9)	140299	NM_001081346	170799	Mm.209844	NM_133244	ENSMUSG00000037846	Rtkn2	B130039D23Rik|Mbf|Plekhk1	rhotekin 2	protein-coding
mm_53534.1	chr6	136630197	136630245	+	1	NA	intron (NM_025806, intron 6 of 10)	MLT1F1|LTR|ERVL-MaLR	31672	NM_025806	66857	Mm.3311	NM_025806	ENSMUSG00000030214	Plbd1	1100001H23Rik	phospholipase B domain containing 1	protein-coding
mm_95232.1	chr11	44520403	44520440	+	1	NA	intron (NM_001166553, intron 1 of 5)	intron (NM_001166553, intron 1 of 5)	1044	NM_001166553	74315	Mm.156771	NM_028862	ENSMUSG00000019189	Rnf145	3732413I11Rik|TMRF1	ring finger protein 145	protein-coding
mm_39554.1	chr5	21901580	21901601	+	1	NA	intron (NM_001310464, intron 60 of 63)	intron (NM_001310464, intron 60 of 63)	-35986	NM_030727	80979	Mm.160370	NM_030727	ENSMUSG00000029015	Slc26a5	Pres|prestin	solute carrier family 26, member 5	protein-coding
mm_7023.1	chr1	87098099	87098116	-	1	NA	3' UTR (NM_001081082, exon 11 of 11)	3' UTR (NM_001081082, exon 11 of 11)	3499	NM_001081082	76768	Mm.58068	NM_001081082	ENSMUSG00000079440	Alpi	2010001C14Rik|Akp6|gIAP	alkaline phosphatase, intestinal	protein-coding
mm_11245.1	chr2	29890097	29890107	+	1	NA	promoter-TSS (NM_013615)	promoter-TSS (NM_013615)	39	NM_013615	18286	Mm.330116	NM_013615	ENSMUSG00000026790	Odf2	AI848335|MMTEST29	outer dense fiber of sperm tails 2	protein-coding
mm_37089.1	chr4	116507467	116507492	-	1	NA	promoter-TSS (NM_008389)	promoter-TSS (NM_008389)	-70	NM_008389	16351	Mm.1350	NM_008389	ENSMUSG00000028696	Ipp	D4Jhu8|Mipp	IAP promoted placental gene	protein-coding
mm_68261.1	chr7	105592359	105592383	-	1	NA	exon (NM_017371, exon 8 of 10)	exon (NM_017371, exon 8 of 10)	7745	NM_017371	15458	Mm.3485	NM_017371	ENSMUSG00000030895	Hpx	Hpxn|hx	hemopexin	protein-coding
mm_28848.1	chr3	96727567	96727573	-	1	NA	promoter-TSS (NM_026406)	promoter-TSS (NM_026406)	-41	NM_026406	67845	Mm.386792	NM_026406	ENSMUSG00000028098	Rnf115	2610028E05Rik|AU042696|Zfp364	ring finger protein 115	protein-coding
mm_23709.1	chr3	68869338	68869399	+	1	NA	promoter-TSS (NM_001167996)	promoter-TSS (NM_001167996)	-218	NM_001167996	68725	Mm.45741	NM_001167996	ENSMUSG00000046999	1110032F04Rik	AI115547	RIKEN cDNA 1110032F04 gene	protein-coding
mm_58987.1	chr7	19086273	19086333	+	1	NA	promoter-TSS (NR_037282)	promoter-TSS (NR_037282)	-525	NR_037282	100526504		NR_037282	ENSMUSG00000092659	Mir3100	mir-3100|mmu-mir-3100	microRNA 3100	ncRNA
mm_84109.1	chr9	58313190	58313212	-	1	NA	promoter-TSS (NM_010729)	promoter-TSS (NM_010729)	11	NM_010729	16949	Mm.250492	NM_010729	ENSMUSG00000032334	Loxl1	Loxl	lysyl oxidase-like 1	protein-coding
mm_136300.1	chr16	91548162	91548195	-	1	NA	intron (NM_008338, intron 1 of 6)	MIRb|SINE|MIR	1084	NM_008338	15980	Mm.249364	NM_008338	ENSMUSG00000022965	Ifngr2	Ifgr2|Ifgt	interferon gamma receptor 2	protein-coding
mm_11942.1	chr2	52872122	52872133	+	1	NA	intron (NM_172409, intron 1 of 26)	ID_B1|SINE|B4	14259	NM_172409	71409	Mm.394427	NM_172409	ENSMUSG00000036053	Fmnl2	5430425K04Rik|Man	formin-like 2	protein-coding
mm_47950.1	chr5	135489197	135489237	-	1	NA	intron (NM_146001, intron 1 of 30)	CpG	55905	NM_146001	215114	Mm.280805	NM_146001	ENSMUSG00000039959	Hip1	2610109B09Rik|A930014B11Rik|E130315I21Rik|mKIAA4113	huntingtin interacting protein 1	protein-coding
mm_63581.1	chr7	128118137	128118150	+	1	NA	3' UTR (NM_008401, exon 30 of 30)	3' UTR (NM_008401, exon 30 of 30)	-11425	NM_021334	16411	Mm.22378	NM_021334	ENSMUSG00000030789	Itgax	AI449405|Cd11c|Cr4|N418	integrin alpha X	protein-coding
mm_91079.1	chr10	19011933	19011941	-	1	NA	promoter-TSS (NM_001166402)	promoter-TSS (NM_001166402)	26	NM_001166402	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_87664.1	chr10	58497919	58497970	+	1	NA	promoter-TSS (NM_001162956)	promoter-TSS (NM_001162956)	7	NM_001162956	76138	Mm.211744	NM_001162956	ENSMUSG00000038010	Ccdc138	6230424H07Rik|BC042726	coiled-coil domain containing 138	protein-coding
mm_135483.1	chr16	46010230	46010251	-	1	NA	5' UTR (NM_001134480, exon 1 of 4)	5' UTR (NM_001134480, exon 1 of 4)	173	NM_001134480	433022	Mm.380993	NM_001134480	ENSMUSG00000087141	Plcxd2	AW494639|EG433022	phosphatidylinositol-specific phospholipase C, X domain containing 2	protein-coding
mm_12851.1	chr2	83659551	83659551	+	1	NA	intron (NM_026934, intron 5 of 9)	intron (NM_026934, intron 5 of 9)	14973	NM_026934	69082	Mm.27804	NM_026934	ENSMUSG00000027091	Zc3h15	1700006A17Rik|1810012H02Rik|2610312B22Rik|FM22|Ierepo4	zinc finger CCCH-type containing 15	protein-coding
mm_117545.1	chr13	83729545	83729584	-	1	NA	intron (NR_015561, intron 1 of 3)	intron (NR_015561, intron 1 of 3)	1458	NR_015561	320203	Mm.245636	NM_177100	ENSMUSG00000050334	C130071C03Rik	2810449C10Rik	RIKEN cDNA C130071C03 gene	ncRNA
mm_60160.1	chr7	39552817	39552840	+	1	NA	Intergenic	CpG	35062	NM_001004139	70227	Mm.333800	NM_001004139	ENSMUSG00000068959	Zfp619	3000002G13Rik	zinc finger protein 619	protein-coding
mm_160672.1	chr10	6788080	6788080	+	1	NA	promoter-TSS (NM_001304950)	promoter-TSS (NM_001304950)	-490	NM_001304950	18390	Mm.438000	NM_011013	ENSMUSG00000000766	Oprm1	M-OR-1|MOP-R|MOR-1|MOR-1O|Oprm|mor|muOR	opioid receptor, mu 1	protein-coding
mm_30210.1	chr3	144849302	144849302	-	1	NA	promoter-TSS (NM_139148)	promoter-TSS (NM_139148)	0	NM_139148	229927	Mm.290600	NM_139148	ENSMUSG00000037033	Clca3b	Clca4	chloride channel accessory 3B	protein-coding
mm_104202.1	chr11	87987529	87987537	-	1	NA	promoter-TSS (NM_001168472)	promoter-TSS (NM_001168472)	0	NM_026556	68097	Mm.246436	NM_026556	ENSMUSG00000020483	Dynll2	1700064A15Rik|6720463E02Rik|C87222|DLC8|DLC8b|Dlc2	dynein light chain LC8-type 2	protein-coding
mm_60023.1	chr7	30832485	30832526	+	1	NA	Intergenic	RLTR1B-int|LTR|ERV1	-8730	NM_146187	233079	Mm.97338	NM_146187	ENSMUSG00000051314	Ffar2	GPCR43|Gpr43	free fatty acid receptor 2	protein-coding
mm_100425.1	chr11	119447544	119447582	+	1	NA	Intergenic	PB1D11|SINE|Alu	-43784	NM_001164636	338371	Mm.271946	NM_177394	ENSMUSG00000039850	Endov	A730011L01Rik	endonuclease V	protein-coding
mm_4079.1	chr1	166339421	166339427	+	1	NA	Intergenic	Intergenic	-39743	NM_030245	27878	Mm.100665	NM_030245	ENSMUSG00000026563	Tada1	2900026B15Rik|D1Ertd251e|Staf42|Tada1l	transcriptional adaptor 1	protein-coding
mm_153158.1	chr19	34475144	34475151	-	1	NA	promoter-TSS (NM_009890)	promoter-TSS (NM_009890)	-12	NM_009890	12642	Mm.30824	NM_009890	ENSMUSG00000050370	Ch25h	AI462618|m25OH	cholesterol 25-hydroxylase	protein-coding
mm_30072.1	chr3	137981484	137981494	-	1	NA	promoter-TSS (NM_001310753)	promoter-TSS (NM_001310753)	60	NM_011932	26377	Mm.254835	NM_011932	ENSMUSG00000028159	Dapp1	Bam32	dual adaptor for phosphotyrosine and 3-phosphoinositides 1	protein-coding
mm_37971.1	chr4	133498539	133498556	-	1	NA	promoter-TSS (NM_001081156)	promoter-TSS (NM_001081156)	3	NM_001081156	69539	Mm.151594	NM_001081156	ENSMUSG00000056596	Trnp1	2300002D11Rik|Trnp	TMF1-regulated nuclear protein 1	protein-coding
mm_53268.1	chr6	128399789	128399825	+	1	NA	promoter-TSS (NM_021717)	promoter-TSS (NM_021717)	41	NM_001162858	60345	Mm.269883	NM_021717	ENSMUSG00000001520	Nrip2	AW491344|NIX1	nuclear receptor interacting protein 2	protein-coding
mm_151198.1	chr19	53537491	53537506	+	1	NA	exon (NM_001085390, exon 3 of 4)	exon (NM_001085390, exon 3 of 4)	8180	NM_001085390	240672	Mm.482424	NM_001085390	ENSMUSG00000034765	Dusp5	Gm337	dual specificity phosphatase 5	protein-coding
mm_114098.1	chr13	54718561	54718572	+	1	NA	exon (NM_001033364, exon 12 of 32)	exon (NM_001033364, exon 12 of 32)	17103	NM_001033364	268663	Mm.315382	NM_001033364	ENSMUSG00000034918	Cdhr2	Gm624|PC-LKC|Pcdh24	cadherin-related family member 2	protein-coding
mm_106013.1	chr11	115885232	115885236	-	1	NA	Intergenic	Intergenic	-14905	NM_183259	66528	Mm.275740	NM_183259	ENSMUSG00000048442	Smim5	2210020M01Rik	small integral membrane protein 5	protein-coding
mm_90407.1	chr10	127420326	127420333	+	1	NA	promoter-TSS (NM_001168293)	promoter-TSS (NM_001168293)	-538	NM_027900	71750	Mm.29342	NM_027900	ENSMUSG00000025404	R3hdm2	1300003K24Rik|AU041262|mKIAA1002	R3H domain containing 2	protein-coding
mm_50290.1	chr6	47454434	47454445	+	1	NA	5' UTR (NM_012042, exon 1 of 22)	5' UTR (NM_012042, exon 1 of 22)	115	NM_012042	26965	Mm.87611	NM_012042	ENSMUSG00000029686	Cul1	-	cullin 1	protein-coding
mm_32580.1	chr4	110583928	110583931	+	1	NA	intron (NM_001048189, intron 3 of 12)	intron (NM_001048189, intron 3 of 12)	186231	NM_030231	78933	Mm.435620	NM_030231	ENSMUSG00000061298	Agbl4	4930578N11Rik|4931433A01Rik	ATP/GTP binding protein-like 4	protein-coding
mm_165855.1	chr4	15185399	15185399	+	1	NA	Intergenic	Intergenic	-36268	NM_178617	69352	Mm.389031	NM_178617	ENSMUSG00000040536	Necab1	1700003H21Rik|Efcbp1|STIP-1	N-terminal EF-hand calcium binding protein 1	protein-coding
mm_3071.1	chr1	134189834	134189849	+	1	NA	3' UTR (NM_007695, exon 10 of 10)	3' UTR (NM_007695, exon 10 of 10)	-3607	NM_016749	53311	Mm.379067	NM_016749	ENSMUSG00000042451	Mybph	AI385643|MyBP-H	myosin binding protein H	protein-coding
mm_145611.1	chr18	61105528	61105546	+	1	NA	promoter-TSS (NM_001037859)	promoter-TSS (NM_001037859)	-35	NM_001037859	12978	Mm.22574	NM_007779	ENSMUSG00000024621	Csf1r	AI323359|CD115|CSF-1R|Csfmr|Fim-2|Fim2|Fms|M-CSF-R|M-CSFR	colony stimulating factor 1 receptor	protein-coding
mm_157384.1	chrX	38067310	38067349	-	1	NA	intron (NM_001024850, intron 1 of 2)	intron (NM_001024850, intron 1 of 2)	854	NM_001024850	434769	Mm.244139	NM_001024850	ENSMUSG00000053909	Rhox10	-	reproductive homeobox 10	protein-coding
mm_130135.1	chr15	90898412	90898420	-	1	NA	promoter-TSS (NR_033583)	promoter-TSS (NR_033583)	60	NR_033583	20738	Mm.431547	NR_033583		Spn-ps	Cd43-ps	sialophorin, pseudogene	pseudo
mm_61327.1	chr7	68230296	68230302	+	1	NA	3' UTR (NM_010513, exon 21 of 21)	3' UTR (NM_010513, exon 21 of 21)	33934	NM_030101	78444	Mm.425468	NM_030101	ENSMUSG00000030553	Pgpep1l	C330024D12Rik	pyroglutamyl-peptidase I-like	protein-coding
mm_112544.1	chr13	12133879	12133883	+	1	NA	Intergenic	Intergenic	-26936	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding
mm_59446.1	chr7	27133346	27133378	+	1	NA	exon (NM_007817, exon 10 of 10)	exon (NM_007817, exon 10 of 10)	13407	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_132669.1	chr16	42875806	42875827	+	1	NA	promoter-TSS (NR_040522)	promoter-TSS (NR_040522)	-54	NR_040522	75722	Mm.243747	NR_040521	ENSMUSG00000075070	4932412D23Rik	ENSMUSG00000075070|Gm10809	RIKEN cDNA 4932412D23 gene	ncRNA
mm_82975.1	chr9	35844204	35844219	-	1	NA	promoter-TSS (NM_029863)	promoter-TSS (NM_029863)	-61	NM_029863	77080	Mm.159846	NM_029863	ENSMUSG00000047980	9230110F15Rik	Pate-A|Pate5|mANLP3	RIKEN cDNA 9230110F15 gene	protein-coding
mm_39023.1	chr4	152131788	152131801	-	1	NA	intron (NM_207688, intron 3 of 10)	CpG-10714	-2869	NM_019585	56226	Mm.264215	NM_019585	ENSMUSG00000028943	Espn	je	espin	protein-coding
mm_123389.1	chr14	63377872	63377898	-	1	NA	intron (NM_007549, intron 10 of 12)	intron (NM_007549, intron 10 of 12)	39302	NM_007549	12143	Mm.3962	NM_007549	ENSMUSG00000014453	Blk	-	B lymphoid kinase	protein-coding
mm_150554.1	chr19	39329100	39329115	+	1	NA	exon (NM_007815, exon 8 of 9)	exon (NM_007815, exon 8 of 9)	42022	NM_007815	13095	Mm.20764	NM_007815	ENSMUSG00000003053	Cyp2c29	AHOH|AHOHase|AI159681|AI196010|Ah-2|Ahh-1|Cyp2c|P450-2C	cytochrome P450, family 2, subfamily c, polypeptide 29	protein-coding
mm_111453.1	chr12	98385870	98385874	-	1	NA	Intergenic	Intergenic	117237	NM_008152	14744	Mm.378924	NM_008152	ENSMUSG00000021886	Gpr65	Dig1|Gpcr25|TDAG8	G-protein coupled receptor 65	protein-coding
mm_70671.1	chr8	14898081	14898105	+	1	NA	3' UTR (NM_012000, exon 3 of 3)	3' UTR (NM_012000, exon 3 of 3)	9557	NM_012000	26889	Mm.254027	NM_012000	ENSMUSG00000026317	Cln8	mnd	ceroid-lipofuscinosis, neuronal 8	protein-coding
mm_40143.1	chr5	35166504	35166525	+	1	NA	Intergenic	Intergenic	-60817	NM_013587	16976	Mm.277661	NM_013587	ENSMUSG00000029103	Lrpap1	AA617339|AI790446|AU042172|C77774|HBP44|RAP	low density lipoprotein receptor-related protein associated protein 1	protein-coding
mm_96399.1	chr11	67250606	67250612	+	1	NA	exon (NM_010855, exon 21 of 40)	exon (NM_010855, exon 21 of 40)	12797	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_173187.1	chrX	60426585	60426607	-	1	NA	Intergenic	Intergenic	-22615	NM_001037863	320940	Mm.490394	NM_001001798	ENSMUSG00000062949	Atp11c	A330005H02Rik|AI315324|Ig	ATPase, class VI, type 11C	protein-coding
mm_13599.1	chr2	112618443	112618447	+	1	NA	intron (NM_001165935, intron 1 of 4)	intron (NM_001165935, intron 1 of 4)	58763	NM_001165935	74268	Mm.315125	NM_028844	ENSMUSG00000003604	Aven	1700013A01Rik|1700056A21Rik|mAven-L|mAven-S	apoptosis, caspase activation inhibitor	protein-coding
mm_8333.1	chr1	150099541	150099555	-	1	NA	promoter-TSS (NM_011198)	promoter-TSS (NM_011198)	326	NR_015466	320019	Mm.353072	NR_015466	ENSMUSG00000097028	Ptgs2os	7530420F21Rik	prostaglandin-endoperoxide synthase 2, opposite strand	ncRNA
mm_170723.1	chr2	150181752	150181766	+	1	NA	promoter-TSS (NM_001145863)	promoter-TSS (NM_001145863)	4	NM_001145863	100271882		NM_001145863	ENSMUSG00000079009	Gm14139	OTTMUSG00000015769	predicted gene 14139	protein-coding
mm_75670.1	chr8	67818285	67818320	-	1	NA	promoter-TSS (NM_027626)	promoter-TSS (NM_027626)	-7	NM_027626	234353	Mm.32525	NM_027626	ENSMUSG00000030465	Psd3	4931420C21Rik|AI661273|BC003498|D430018P08|EFA6D	pleckstrin and Sec7 domain containing 3	protein-coding
mm_87371.1	chr10	44268390	44268408	+	1	NA	promoter-TSS (NM_053069)	promoter-TSS (NM_053069)	60	NM_053069	11793	Mm.22264	NM_053069	ENSMUSG00000038160	Atg5	2010107M05Rik|3110067M24Rik|AW319544|Apg5l|Atg5l|C88337|Paddy	autophagy related 5	protein-coding
mm_48368.1	chr5	139473259	139473269	-	1	NA	3' UTR (NM_001159908, exon 7 of 7)	3' UTR (NM_001159908, exon 7 of 7)	11227	NM_133349	100494	Mm.24521	NM_133349	ENSMUSG00000053581	Zfand2a	AA407930|AU016206|Airap	zinc finger, AN1-type domain 2A	protein-coding
mm_134221.1	chr16	11254251	11254264	-	1	NA	promoter-TSS (NM_001130008)	promoter-TSS (NM_001130008)	68	NM_001130008	14852	Mm.325827	NM_146066	ENSMUSG00000062203	Gspt1	AI314175|AI326449|AV307676|C79774|G1st|Gst-1	G1 to S phase transition 1	protein-coding
mm_8191.1	chr1	138101415	138101419	-	1	NA	intron (NM_001111316, intron 11 of 31)	intron (NM_001111316, intron 11 of 31)	73709	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_126980.1	chr15	93441606	93441622	+	1	NA	exon (NM_001083114, exon 4 of 8)	exon (NM_001083114, exon 4 of 8)	43150	NM_001285863	223828	Mm.74208	NM_146062	ENSMUSG00000036167	Pphln1	CR|HSPC206|HSPC232	periphilin 1	protein-coding
mm_56442.1	chr6	97459310	97459320	-	1	NA	promoter-TSS (NM_001346639)	promoter-TSS (NM_001346639)	-29	NM_001346639	232288	Mm.27789	NM_145148	ENSMUSG00000030064	Frmd4b	6030440G05Rik|C87375|GOBLIN|GRSP1|R74720	FERM domain containing 4B	protein-coding
mm_49761.1	chr6	34774240	34774266	+	1	NA	3' UTR (NM_145575, exon 12 of 12)	3' UTR (NM_145575, exon 12 of 12)	-6179	NM_001289657	76223	Mm.150047	NM_178630	ENSMUSG00000038836	Agbl3	2900053G10Rik|4930431N21Rik|6530406M24Rik|CCP3	ATP/GTP binding protein-like 3	protein-coding
mm_90549.1	chr10	128096852	128096899	+	1	NA	intron (NM_054078, intron 2 of 29)	CpG	4092	NM_054078	116848	Mm.252213	NM_054078	ENSMUSG00000040054	Baz2a	AA415431|C030005G16Rik|C78388|Tip5|Walp3|mKIAA0314	bromodomain adjacent to zinc finger domain, 2A	protein-coding
mm_145919.1	chr18	67066609	67066615	+	1	NA	Intergenic	Intergenic	-21686	NM_177137	14680	Mm.440746	NM_010307	ENSMUSG00000024524	Gnal	2610011C15Rik|9630020G10Rik|Galphaolf|Gna10|Golf	guanine nucleotide binding protein, alpha stimulating, olfactory type	protein-coding
mm_20147.1	chr2	121541963	121541966	-	1	NA	intron (NM_001290986, intron 12 of 12)	ID_B1|SINE|B4	35241	NM_001290986	241627	Mm.293284	NM_030234	ENSMUSG00000027242	Wdr76	5830411K18Rik|6030457D09|AA517836	WD repeat domain 76	protein-coding
mm_109819.1	chr12	3835641	3835689	-	1	NA	intron (NM_007872, intron 2 of 22)	intron (NM_007872, intron 2 of 22)	26579	NR_045884	100038522	Mm.417270	NR_045884	ENSMUSG00000073242	Dnmt3aos	ENSMUSG00000073242|Gm10485	DNA methyltransferase 3A, opposite strand	ncRNA
mm_100426.1	chr11	119448749	119448771	+	1	NA	Intergenic	Intergenic	-42587	NM_001164636	338371	Mm.271946	NM_177394	ENSMUSG00000039850	Endov	A730011L01Rik	endonuclease V	protein-coding
mm_106461.1	chr11	120047032	120047061	-	1	NA	promoter-TSS (NM_007377)	promoter-TSS (NM_007377)	99	NM_001198785	11302	Mm.6826	NM_007377	ENSMUSG00000025375	Aatk	AATYK|aatyk1|mKIAA0641	apoptosis-associated tyrosine kinase	protein-coding
mm_110208.1	chr12	27342446	27342457	-	1	NA	5' UTR (NM_009234, exon 1 of 1)	5' UTR (NM_009234, exon 1 of 1)	267	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding
mm_111134.1	chr12	81532841	81532925	-	1	NA	promoter-TSS (NM_025292)	promoter-TSS (NM_025292)	28	NM_001309847	105940408		NM_001309847	ENSMUSG00000021139	Synj2bp-cox16	ARIP2a	Synj2bp-cox16 readthrough	protein-coding
mm_114559.1	chr13	74350300	74350308	+	1	NA	promoter-TSS (NM_024201)	promoter-TSS (NM_024201)	-13	NM_001168659	67433	Mm.101586	NM_024201	ENSMUSG00000021578	Ccdc127	0610011N22Rik|5430420E17Rik|A430066A18|AI256405|AW050060|C130002N06	coiled-coil domain containing 127	protein-coding
mm_144000.1	chr17	88058212	88058214	-	1	NA	intron (NM_001081034, intron 1 of 22)	intron (NM_001081034, intron 1 of 22)	7072	NM_001081034	225055	Mm.386857	NM_001081034	ENSMUSG00000005371	Fbxo11	C80048|Jf	F-box protein 11	protein-coding
mm_69928.1	chr7	141950455	141950465	-	1	NA	intron (NM_001009930, intron 1 of 19)	CpG	709	NM_001009929	75770	Mm.274868	NM_029426	ENSMUSG00000053046	Brsk2	4833424K13Rik|SAD-A|SADA	BR serine/threonine kinase 2	protein-coding
mm_108886.1	chr12	99971666	99971686	+	1	NA	intron (NM_146037, intron 2 of 2)	intron (NM_146037, intron 2 of 2)	7177	NM_001164427	217826	Mm.312335	NM_146037	ENSMUSG00000045404	Kcnk13	BB085247|F730021E22Rik|Gm1570|Gm1685	potassium channel, subfamily K, member 13	protein-coding
mm_120457.1	chr14	65970587	65970591	+	1	NA	intron (NM_013492, intron 1 of 8)	intron (NM_013492, intron 1 of 8)	2106	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_41689.1	chr5	100569521	100569533	+	1	NA	intron (NM_139198, intron 1 of 4)	intron (NM_139198, intron 1 of 4)	2678	NM_139198	231507	Mm.34609	NM_139198	ENSMUSG00000029322	Plac8	C15|D5Wsu111e	placenta-specific 8	protein-coding
mm_155002.1	chrX	41400599	41400603	+	1	NA	promoter-TSS (NM_001290451)	promoter-TSS (NM_001290451)	-700	NM_016886	53623	Mm.327681	NM_016886	ENSMUSG00000001986	Gria3	2900064I19Rik|GluA3|GluR-C|GluR-K3|Glur-3|Glur3|Gluralpha3	glutamate receptor, ionotropic, AMPA3 (alpha 3)	protein-coding
mm_143048.1	chr17	56883852	56883862	-	1	NA	exon (NM_030141, exon 10 of 14)	exon (NM_030141, exon 10 of 14)	8224	NM_030141	78625	Mm.160106	NM_030141	ENSMUSG00000024209	1700061G19Rik	1700026H02|AI507598	RIKEN cDNA 1700061G19 gene	protein-coding
mm_135129.1	chr16	35843977	35843988	-	1	NA	intron (NM_001039530, intron 12 of 16)	RLTR21|LTR|ERVK	27400	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_115999.1	chr13	24415002	24415008	-	1	NA	promoter-TSS (NM_001284520)	promoter-TSS (NM_001284520)	-117	NM_007717	12763	Mm.8396	NM_007717	ENSMUSG00000016756	Cmah	-	cytidine monophospho-N-acetylneuraminic acid hydroxylase	protein-coding
mm_22859.1	chr3	28697902	28697912	+	1	NA	promoter-TSS (NM_031197)	promoter-TSS (NM_031197)	4	NM_031197	20526	Mm.18443	NM_031197	ENSMUSG00000027690	Slc2a2	AI266973|Glut-2|Glut2	solute carrier family 2 (facilitated glucose transporter), member 2	protein-coding
mm_34273.1	chr4	141424249	141424255	+	1	NA	3' UTR (NM_013868, exon 3 of 3)	3' UTR (NM_013868, exon 3 of 3)	3473	NM_013868	29818	Mm.46181	NM_013868	ENSMUSG00000006221	Hspb7	27kDa|Hsp25-2|cvHsp	heat shock protein family, member 7 (cardiovascular)	protein-coding
mm_14682.1	chr2	140056008	140056020	+	1	NA	intron (NR_110350, intron 2 of 12)	intron (NR_110350, intron 2 of 12)	10791	NM_001159640	75812	Mm.293449	NM_175225	ENSMUSG00000039033	Tasp1	4930485D02Rik|AW986064	taspase, threonine aspartase 1	protein-coding
mm_2351.1	chr1	92910902	92910912	+	1	NA	promoter-TSS (NM_181405)	promoter-TSS (NM_181405)	82	NM_181405	108657	Mm.200971	NM_181405	ENSMUSG00000026269	Rnpepl1	1110014H17Rik|AI894167	arginyl aminopeptidase (aminopeptidase B)-like 1	protein-coding
mm_91981.1	chr10	61680281	61680291	-	1	NA	promoter-TSS (NM_009120)	promoter-TSS (NM_009120)	4	NR_126477	75539		NR_126477		1700022H01Rik	-	RIKEN cDNA 1700022H01 gene	ncRNA
mm_155219.1	chrX	56792729	56792760	+	1	NA	3' UTR (NM_010211, exon 7 of 7)	3' UTR (NM_010211, exon 7 of 7)	6217	NM_001287800	14199	Mm.3126	NM_010211	ENSMUSG00000023092	Fhl1	FHL-1|KyoT|RAM14-1|SLIM|SLIM-1	four and a half LIM domains 1	protein-coding
mm_17646.1	chr2	31470848	31470853	-	1	NA	intron (NR_002687, intron 1 of 15)	intron (NR_002687, intron 1 of 15)	542	NR_002687	432466	Mm.333323	NR_002687	ENSMUSG00000046687	Gm5424	EG432466	argininosuccinate synthase pseudogene	pseudo
mm_83536.1	chr9	46233217	46233232	-	1	NA	exon (NM_001289755, exon 4 of 4)	exon (NM_001289755, exon 4 of 4)	2075	NM_001289833	11814	Mm.390161	NM_023114	ENSMUSG00000032081	Apoc3	apo-CIII|apoC-III	apolipoprotein C-III	protein-coding
mm_106141.1	chr11	116494604	116494632	-	1	NA	Intergenic	RSINE1|SINE|B4	-4272	NM_026364	67763	Mm.25125	NM_026364	ENSMUSG00000015869	Prpsap1	5730409F23Rik|PAP39	phosphoribosyl pyrophosphate synthetase-associated protein 1	protein-coding
mm_34444.1	chr4	147986044	147986049	+	1	NA	exon (NM_008726, exon 1 of 3)	exon (NM_008726, exon 1 of 3)	258	NM_001287348	18158	Mm.2740	NM_008726	ENSMUSG00000029019	Nppb	AA408272|BNF|BNP	natriuretic peptide type B	protein-coding
mm_164596.1	chr17	27935116	27935124	-	1	NA	intron (NM_001286040, intron 1 of 24)	intron (NM_001286040, intron 1 of 24)	25814	NM_181413	224650	Mm.32556	NM_181413	ENSMUSG00000024219	Anks1	Anks1a|mKIAA0229	ankyrin repeat and SAM domain containing 1	protein-coding
mm_65182.1	chr7	19696402	19696439	-	1	NA	exon (NM_009696, exon 4 of 4)	exon (NM_009696, exon 4 of 4)	1978	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_143401.1	chr17	70753512	70753517	-	1	NA	intron (NM_001347411, intron 9 of 14)	intron (NM_001347411, intron 9 of 14)	93263	NM_001164077	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_146933.1	chr18	32068159	32068195	-	1	NA	intron (NM_173441, intron 1 of 13)	CpG	443	NM_173441	73473	Mm.66853	NM_173441	ENSMUSG00000024384	Iws1	1700069O15Rik|3000008H23|AL117927|AW214353	IWS1, SUPT6 interacting protein	protein-coding
mm_18220.1	chr2	50297164	50297197	-	1	NA	promoter-TSS (NM_133839)	promoter-TSS (NM_133839)	370	NR_040362	100502624	Mm.382825	NR_040361	ENSMUSG00000085862	Gm13483	OTTMUSG00000012382	predicted gene 13483	ncRNA
mm_40322.1	chr5	43901471	43901519	+	1	NA	exon (NM_007646, exon 3 of 8)	exon (NM_007646, exon 3 of 8)	32686	NM_007646	12494	Mm.249873	NM_007646	ENSMUSG00000029084	Cd38	ADPRC 1|Cd38-rs1|I-19	CD38 antigen	protein-coding
mm_132592.1	chr16	38452797	38452831	+	1	NA	promoter-TSS (NM_007414)	promoter-TSS (NM_007414)	-125	NM_007414	11544	Mm.20047	NM_007414	ENSMUSG00000002844	Adprh	Arh1	ADP-ribosylarginine hydrolase	protein-coding
mm_30001.1	chr3	135594407	135594425	-	1	NA	intron (NM_008689, intron 18 of 24)	intron (NM_008689, intron 18 of 24)	97131	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_47096.1	chr5	118064027	118064030	-	1	NA	TTS (NM_172721)	TTS (NM_172721)	36204	NM_021344	57816	Mm.273285	NM_021344	ENSMUSG00000029359	Tesc	1010001A17Rik|2410011K10Rik|TE-1	tescalcin	protein-coding
mm_142847.1	chr17	51797071	51797080	-	1	NA	intron (NM_009122, intron 5 of 10)	intron (NM_009122, intron 5 of 10)	14979	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_113327.1	chr13	30788127	30788148	+	1	NA	Intergenic	Intergenic	38904	NM_013674	16364	Mm.4677	NM_013674	ENSMUSG00000021356	Irf4	AI385587|IRF-4|LSIRF|NF-EM5|Spip	interferon regulatory factor 4	protein-coding
mm_61567.1	chr7	79710365	79710375	+	1	NA	exon (NM_010626, exon 4 of 18)	exon (NM_010626, exon 4 of 18)	3816	NM_010626	16576	Mm.101633	NM_010626	ENSMUSG00000050382	Kif7	-	kinesin family member 7	protein-coding
mm_5943.1	chr1	56637462	56637480	-	1	NA	promoter-TSS (NM_027661)	promoter-TSS (NM_027661)	-20	NM_027661	71066	Mm.152656	NM_027661	ENSMUSG00000045336	Hsfy2	4933413G11Rik|Hspy2l	heat shock transcription factor, Y-linked 2	protein-coding
mm_101151.1	chr11	16779552	16779561	-	1	NA	intron (NM_207655, intron 1 of 27)	intron (NM_207655, intron 1 of 27)	27353	NM_007912	13649	Mm.8534	NM_007912	ENSMUSG00000020122	Egfr	9030024J15Rik|AI552599|Erbb|Errb1|Errp|Wa5|wa-2|wa2	epidermal growth factor receptor	protein-coding
mm_116462.1	chr13	43423425	43423432	-	1	NA	intron (NM_019930, intron 6 of 13)	Lx|LINE|L1	25052	NM_023554	70078	Mm.439927	NM_023554	ENSMUSG00000063200	Nol7	2210008F15Rik|5730556I21Rik|NOP27|RARG-1	nucleolar protein 7	protein-coding
mm_60318.1	chr7	44209599	44209612	+	1	NA	intron (NM_010915, intron 1 of 4)	intron (NM_010915, intron 1 of 4)	2172	NM_010915	18048	Mm.440886	NM_010915	ENSMUSG00000066513	Klk1b4	Ngfa|alpha-NGF|mGk-4	kallikrein 1-related pepidase b4	protein-coding
mm_126244.1	chr15	79002339	79002352	+	1	NA	TTS (NR_105921)	TTS (NR_105921)	122	NR_105921	102465577		NR_105921	ENSMUSG00000099180	Mir6956	Gm27880|mmu-mir-6956	microRNA 6956	ncRNA
mm_56405.1	chr6	97163546	97163557	-	1	NA	exon (NM_001081111, exon 10 of 17)	exon (NM_001081111, exon 10 of 17)	-14668	NM_175313	101351	Mm.116802	NM_175313	ENSMUSG00000035245	Eogt	A130022J15Rik|AI447490|AW214473|AW259391|Aer61	EGF domain-specific O-linked N-acetylglucosamine (GlcNAc) transferase	protein-coding
mm_51731.1	chr6	87038505	87038524	+	1	NA	Intergenic	Intergenic	-4332	NM_013528	14583	Mm.19893	NM_013528	ENSMUSG00000029992	Gfpt1	2810423A18Rik|AI324119|AI449986|GFA|GFAT|GFAT1|GFAT1m|Gfpt	glutamine fructose-6-phosphate transaminase 1	protein-coding
mm_24398.1	chr3	90294082	90294090	+	1	NA	Intergenic	Intergenic	23937	NR_105979	102465612		NR_105979	ENSMUSG00000099199	Mir7012	Gm27370|mmu-mir-7012	microRNA 7012	ncRNA
mm_51767.1	chr6	88000262	88000296	+	1	NA	3' UTR (NM_009005, exon 6 of 6)	3' UTR (NM_009005, exon 6 of 6)	18596	NR_026990	434064	Mm.371796	NR_026990	ENSMUSG00000084950	Gm5577	EG434064	predicted gene 5577	ncRNA
mm_158621.1	chrX	152689461	152689468	-	1	NA	intron (NM_001290684, intron 2 of 9)	intron (NM_001290684, intron 2 of 9)	-44916	NM_001290685	110380	Mm.40796	NM_172441	ENSMUSG00000045180	Shroom2	4832440C16|Apxl|C630003H05Rik|Shrm2	shroom family member 2	protein-coding
mm_112777.1	chr13	20090453	20090493	+	1	NA	promoter-TSS (NM_080288)	promoter-TSS (NM_080288)	-34	NM_080288	140580	Mm.342392	NM_080288	ENSMUSG00000041112	Elmo1	6330578D22Rik|C230095H21Rik|CED-12	engulfment and cell motility 1	protein-coding
mm_59887.1	chr7	30303907	30303926	+	1	NA	exon (NM_001081114, exon 12 of 14)	exon (NM_001081114, exon 12 of 14)	-4837	NM_198027	233065	Mm.276277	NM_198027	ENSMUSG00000042831	Alkbh6	AI839550|Abh6|C130099A02	alkB homolog 6	protein-coding
mm_65085.1	chr7	19260683	19260702	-	1	NA	intron (NR_104069, intron 4 of 10)	intron (NR_104069, intron 4 of 10)	11162	NM_001282021	22323	Mm.9684	NM_009499	ENSMUSG00000030403	Vasp	-	vasodilator-stimulated phosphoprotein	protein-coding
mm_30772.1	chr4	17853452	17853474	+	1	NA	promoter-TSS (NM_019724)	promoter-TSS (NM_019724)	5	NM_019724	17389	Mm.187315	NM_019724	ENSMUSG00000028226	Mmp16	MT-MMP 3|MT3-MMP|Mt3mmp	matrix metallopeptidase 16	protein-coding
mm_78654.1	chr9	40450366	40450411	+	1	NA	intron (NM_172768, intron 1 of 19)	intron (NM_172768, intron 1 of 19)	5376	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_72951.1	chr8	92357788	92357801	+	1	NA	promoter-TSS (NM_018826)	promoter-TSS (NM_018826)	-2	NM_018826	54352	Mm.101153	NM_018826	ENSMUSG00000031737	Irx5	-	Iroquois related homeobox 5 (Drosophila)	protein-coding
mm_31001.1	chr4	40160049	40160050	+	1	NA	intron (NM_007386, intron 1 of 20)	intron (NM_007386, intron 1 of 20)	16784	NM_007386	11428	Mm.331547	NM_007386	ENSMUSG00000028405	Aco1	Aco-1|Irebp|Irp1	aconitase 1	protein-coding
mm_101472.1	chr11	30649486	30649498	-	1	NA	promoter-TSS (NM_029344)	promoter-TSS (NM_029344)	-96	NM_029344	75572	Mm.390319	NM_029344	ENSMUSG00000060923	Acyp2	2310004B09Rik	acylphosphatase 2, muscle type	protein-coding
mm_11574.1	chr2	32916454	32916482	+	1	NA	intron (NM_146119, intron 5 of 13)	B3|SINE|B2	40334	NM_146119	227737	Mm.301646	NM_146119	ENSMUSG00000026796	Fam129b	9130404D14Rik	family with sequence similarity 129, member B	protein-coding
mm_138831.1	chr17	39848193	39848207	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	5203	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_21679.1	chr2	164426188	164426204	-	1	NA	exon (NM_011521, exon 5 of 5)	exon (NM_011521, exon 5 of 5)	16992	NM_011521	20971	Mm.3815	NM_011521	ENSMUSG00000017009	Sdc4	AA959608|AW108331|S4|Synd4|ryudocan|syndecan-4	syndecan 4	protein-coding
mm_77018.1	chr8	108584328	108584337	-	1	NA	non-coding (NR_077224, exon 1 of 2)	non-coding (NR_077224, exon 1 of 2)	345	NR_077224	109215	Mm.65282	NR_077224	ENSMUSG00000110613	Lncbate1	3010033K07Rik|Lnc-BATE1	brown adipose tissue enriched long non-coding RNA 1	ncRNA
mm_102185.1	chr11	54248482	54248492	-	1	NA	exon (NM_009969, exon 3 of 4)	exon (NM_009969, exon 3 of 4)	1412	NM_009969	12981	Mm.4922	NM_009969	ENSMUSG00000018916	Csf2	Csfgm|GMCSF|Gm-CSf|MGI-IGM	colony stimulating factor 2 (granulocyte-macrophage)	protein-coding
mm_160500.1	chr9	15306458	15306458	-	1	NA	promoter-TSS (NM_001199485)	promoter-TSS (NM_001199485)	-10	NM_001199484	70984	Mm.261842	NM_133732	ENSMUSG00000031938	4931406C07Rik	-	RIKEN cDNA 4931406C07 gene	protein-coding
mm_87913.1	chr10	62340620	62340684	+	1	NA	promoter-TSS (NM_001146100)	promoter-TSS (NM_001146100)	45	NR_038038	70162	Mm.441212	NR_038038		Hk1os	2210417K05Rik	hexokinase 1, opposite strand	ncRNA
mm_49999.1	chr6	41048284	41048299	+	1	NA	Intergenic	Intergenic	-12782	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_120299.1	chr14	63139062	63139063	+	1	NA	exon (NM_007798, exon 8 of 10)	exon (NM_007798, exon 8 of 10)	16600	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_56177.1	chr6	88045191	88045268	-	1	NA	promoter-TSS (NM_009005)	promoter-TSS (NM_009005)	41	NM_001293652	19349	Mm.333233	NM_009005	ENSMUSG00000079477	Rab7	Rab7a	RAB7, member RAS oncogene family	protein-coding
mm_96130.1	chr11	60830691	60830730	+	1	NA	promoter-TSS (NM_001172112)	promoter-TSS (NM_001172112)	79	NM_145428	216820	Mm.21475	NM_145428	ENSMUSG00000042569	Dhrs7b	BC003479|C79874|C80074|PexRAP	dehydrogenase/reductase (SDR family) member 7B	protein-coding
mm_22442.1	chr2	181693711	181693722	-	1	NA	promoter-TSS (NM_001291208)	promoter-TSS (NM_001291208)	94	NM_001291206	56470	Mm.274366	NM_026446	ENSMUSG00000002458	Rgs19	2610042F04Rik|AI324841|AW547781|GAIP	regulator of G-protein signaling 19	protein-coding
mm_26167.1	chr3	138282627	138282646	+	1	NA	exon (NM_007409, exon 5 of 9)	exon (NM_007409, exon 5 of 9)	4991	NM_007409	11522	Mm.2409	NM_007409	ENSMUSG00000074207	Adh1	ADH-AA|AI194826|Adh-1|Adh-1-t|Adh-1e|Adh-1t|Adh-3e|Adh1-e|Adh1-t|Adh1tl|Adh3-e	alcohol dehydrogenase 1 (class I)	protein-coding
mm_173319.1	chrY	90736843	90736857	+	1	NA	Intergenic	Intergenic	18200	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_41441.1	chr5	90905189	90905203	+	1	NA	exon (NM_009140, exon 4 of 4)	exon (NM_009140, exon 4 of 4)	1297	NM_009140	20310	Mm.4979	NM_009140	ENSMUSG00000058427	Cxcl2	CINC-2a|GROb|Gro2|MIP-2|MIP-2a|Mgsa-b|Mip2|Scyb|Scyb2	chemokine (C-X-C motif) ligand 2	protein-coding
mm_48183.1	chr5	137412624	137412627	-	1	NA	exon (NM_011741, exon 52 of 88)	exon (NM_011741, exon 52 of 88)	62516	NM_010144	13846	Mm.34533	NM_010144	ENSMUSG00000029710	Ephb4	AI042935|Htk|MDK2|Myk1|Tyro11	Eph receptor B4	protein-coding
mm_74210.1	chr8	123895938	123895948	+	1	NA	Intergenic	Intergenic	-1168	NM_009606	11459	Mm.214950	NM_009606	ENSMUSG00000031972	Acta1	AA959943|Acta-2|Acts|Actsk-1	actin, alpha 1, skeletal muscle	protein-coding
mm_75805.1	chr8	70212252	70212265	-	1	NA	promoter-TSS (NM_001007570)	promoter-TSS (NM_001007570)	23	NM_001007570	73095	Mm.185413	NM_001007570	ENSMUSG00000002346	Slc25a42	2900084M01Rik	solute carrier family 25, member 42	protein-coding
mm_55518.1	chr6	70260960	70260964	-	1	NA	Intergenic	Intergenic	531213	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_92100.1	chr10	63017590	63017611	-	1	NA	exon (NM_001079824, exon 5 of 10)	exon (NM_001079824, exon 5 of 10)	2700	NM_001347457	432467	Mm.274784	NM_001079824	ENSMUSG00000020069	Hnrnph3	AA693301|AI666703|Hnrph3	heterogeneous nuclear ribonucleoprotein H3	protein-coding
mm_106707.1	chr12	3806537	3806571	+	1	NA	promoter-TSS (NM_001271753)	promoter-TSS (NM_001271753)	-426	NM_007872	13435	Mm.5001	NM_007872	ENSMUSG00000020661	Dnmt3a	MmuIIIA	DNA methyltransferase 3A	protein-coding
mm_136511.1	chr16	97170822	97170836	-	1	NA	promoter-TSS (NM_031174)	promoter-TSS (NM_031174)	-94	NM_031174	13508	Mm.102437	NM_031174	ENSMUSG00000050272	Dscam	4932410A21Rik	Down syndrome cell adhesion molecule	protein-coding
mm_145999.1	chr18	68344774	68344788	+	1	NA	Intergenic	MTC-int|LTR|ERVL-MaLR	7178	NM_013596	17203	Mm.8003	NM_013596	ENSMUSG00000007480	Mc5r	-	melanocortin 5 receptor	protein-coding
mm_11659.1	chr2	35109483	35109538	+	1	NA	promoter-TSS (NM_012018)	promoter-TSS (NM_012018)	18	NM_012018	26920	Mm.231332	NM_012018	ENSMUSG00000057110	Cntrl	6720467O09Rik|AA968343|Cep1|Cep110|IB3/5|Ma2a8|b2b1468.1Clo|b2b1468Clo	centriolin	protein-coding
mm_53734.1	chr6	145121839	145121846	+	1	NA	5' UTR (NM_008511, exon 1 of 19)	5' UTR (NM_008511, exon 1 of 19)	103	NM_008511	16970	Mm.843	NM_008511	ENSMUSG00000030263	Lrmp	D6Int3|D6Int4|D6Int5|D6Int7|D6Int8|Jaw1	lymphoid-restricted membrane protein	protein-coding
mm_170832.1	chr2	177000898	177000914	+	1	NA	Intergenic	Intergenic	-73093	NM_001305133	102639598	Mm.379980	NM_029813	ENSMUSG00000074527	Gm14296	-	predicted gene 14296	protein-coding
mm_77089.1	chr8	110793562	110793584	-	1	NA	intron (NM_029646, intron 1 of 7)	intron (NM_029646, intron 1 of 7)	12351	NM_029646	76527	Mm.77697	NM_029646	ENSMUSG00000031750	Il34	2010004A03Rik|AI593503	interleukin 34	protein-coding
mm_7883.1	chr1	133030581	133030586	-	1	NA	promoter-TSS (NM_001302802)	promoter-TSS (NM_001302802)	4	NM_001302802	17248	Mm.426531	NM_008575	ENSMUSG00000054387	Mdm4	4933417N07Rik|AA414968|AL023055|AU018793|AU021806|C85810|Mdmx	transformed mouse 3T3 cell double minute 4	protein-coding
mm_30238.1	chr3	146378943	146378946	-	1	NA	promoter-TSS (NR_033542)	promoter-TSS (NR_033542)	0	NR_033542	100038607	Mm.365888	NR_033542	ENSMUSG00000105602	Gm10636	ENSMUSG00000074175	predicted gene 10636	ncRNA
mm_130957.1	chr15	103310426	103310444	-	1	NA	promoter-TSS (NM_030720)	promoter-TSS (NM_030720)	3	NM_030720	80910	Mm.160369	NM_030720	ENSMUSG00000063234	Gpr84	EX33	G protein-coupled receptor 84	protein-coding
mm_37839.1	chr4	132075251	132075291	-	1	NA	promoter-TSS (NM_001128607)	promoter-TSS (NM_001128607)	42	NM_001128607	269587	Mm.30038	NM_183428	ENSMUSG00000028906	Epb41	4.1R|AI415518|D4Ertd442e|Elp-1|Elp1|Epb4.1|mKIAA4056	erythrocyte membrane protein band 4.1	protein-coding
mm_88018.1	chr10	67185731	67185768	+	1	NA	promoter-TSS (NM_001242396)	promoter-TSS (NM_001242396)	-1	NM_001242396	108829	Mm.23846	NM_207221	ENSMUSG00000037876	Jmjd1c	5430433L24Rik|D630035I23Rik|Jmjdic|TRIP8	jumonji domain containing 1C	protein-coding
mm_135301.1	chr16	38703685	38703693	-	1	NA	intron (NM_020260, intron 1 of 11)	intron (NM_020260, intron 1 of 11)	9346	NM_020260	12549	Mm.370848	NM_020260	ENSMUSG00000022799	Arhgap31	5830477L08Rik|AU041750|Cdgap|D330026I07Rik	Rho GTPase activating protein 31	protein-coding
mm_164787.1	chr18	10706702	10706768	-	1	NA	promoter-TSS (NM_134130)	promoter-TSS (NM_134130)	-39	NM_134130	106861	Mm.273108	NM_134130	ENSMUSG00000002475	Abhd3	AA675331|LABH3	abhydrolase domain containing 3	protein-coding
mm_79430.1	chr9	55948177	55948185	+	1	NA	Intergenic	(T)n|Simple_repeat|Simple_repeat	-10066	NM_001081341	244891	Mm.86588	NM_175536	ENSMUSG00000034007	Scaper	C430017I08|D530014O03Rik|Zfp291	S phase cyclin A-associated protein in the ER	protein-coding
mm_40811.1	chr5	71699957	71699973	+	1	NA	promoter-TSS (NM_008069)	promoter-TSS (NM_008069)	-51	NM_008069	14400	Mm.38567	NM_008069	ENSMUSG00000029212	Gabrb1	AW061132|B230208N19Rik|Gabrb-1	gamma-aminobutyric acid (GABA) A receptor, subunit beta 1	protein-coding
mm_122446.1	chr14	45295865	45295875	-	1	NA	intron (NM_015774, intron 9 of 15)	intron (NM_015774, intron 9 of 15)	22702	NM_015774	50527	Mm.387108	NM_015774	ENSMUSG00000021831	Ero1l	ERO1-L|Ero1a	ERO1-like (S. cerevisiae)	protein-coding
mm_60612.1	chr7	44590919	44590919	+	1	NA	promoter-TSS (NM_001290682)	promoter-TSS (NM_001290682)	33	NM_001290682	16504	Mm.40312	NM_008422	ENSMUSG00000062785	Kcnc3	KShIIID|Kcr2-3|Kv3.3	potassium voltage gated channel, Shaw-related subfamily, member 3	protein-coding
mm_58065.1	chr6	136875795	136875811	-	1	NA	promoter-TSS (NM_008597)	promoter-TSS (NM_008597)	20	NM_008597	17313	Mm.243085	NM_008597	ENSMUSG00000030218	Mgp	Mglap	matrix Gla protein	protein-coding
mm_9808.1	chr1	181937201	181937212	-	1	NA	intron (NM_010135, intron 3 of 14)	intron (NM_010135, intron 3 of 14)	82774	NM_008680	13800	Mm.87759	NM_008680	ENSMUSG00000022995	Enah	Mena|NDPP-1|Ndpp1|WBP8	enabled homolog (Drosophila)	protein-coding
mm_30409.1	chr3	152255334	152255354	-	1	NA	5' UTR (NM_199465, exon 2 of 13)	5' UTR (NM_199465, exon 2 of 13)	10976	NM_199465	68810	Mm.200188	NM_199465	ENSMUSG00000039103	Nexn	1110046H09Rik|AA553326|NELIN	nexilin	protein-coding
mm_37787.1	chr4	130279218	130279231	-	1	NA	Intergenic	Intergenic	-3638	NM_172702	230779	Mm.45132	NM_172702	ENSMUSG00000023232	Serinc2	2310004K20Rik|AW121759|FKSG84|TDE2|Tde2l	serine incorporator 2	protein-coding
mm_55667.1	chr6	72521672	72521674	-	1	NA	Intergenic	Intergenic	-22718	NM_007599	12332	Mm.18626	NM_007599	ENSMUSG00000056737	Capg	gCap39|mbh1	capping protein (actin filament), gelsolin-like	protein-coding
mm_106937.1	chr12	8674392	8674421	+	1	NA	promoter-TSS (NM_030723)	promoter-TSS (NM_030723)	147	NM_001160220	80913	Mm.341243	NM_030723	ENSMUSG00000020594	Pum2	5730503J23Rik|Pumm2	pumilio RNA-binding family member 2	protein-coding
mm_23260.1	chr3	51415987	51416044	+	1	NA	promoter-TSS (NM_053089)	promoter-TSS (NM_053089)	-1	NM_053089	74838	Mm.275281	NM_053089	ENSMUSG00000063273	Naa15	5730450D16Rik|6330400I15|ASTBDN|Narg1|Tbdn-1|mNAT1	N(alpha)-acetyltransferase 15, NatA auxiliary subunit	protein-coding
mm_127278.1	chr15	99821131	99821170	+	1	NA	intron (NM_001113545, intron 3 of 10)	intron (NM_001113545, intron 3 of 10)	-1001	NM_023063	65970	Mm.33207	NM_023063	ENSMUSG00000023022	Lima1	Eplin	LIM domain and actin binding 1	protein-coding
mm_138987.1	chr17	45495738	45495759	+	1	NA	Intergenic	Intergenic	-11093	NM_198608	224805	Mm.329063	NM_198608	ENSMUSG00000023938	Aars2	Aarsl|AlaRS|Gm89	alanyl-tRNA synthetase 2, mitochondrial	protein-coding
mm_5540.1	chr1	38320260	38320272	-	1	NA	intron (NM_001290814, intron 7 of 21)	intron (NM_001290814, intron 7 of 21)	-190604	NM_019570	56210	Mm.389103	NM_019570	ENSMUSG00000026082	Rev1	1110027I23Rik|AU022044|Rev1l	REV1, DNA directed polymerase	protein-coding
mm_111114.1	chr12	80960600	80960629	-	1	NA	exon (NM_001177561, exon 2 of 5)	exon (NM_001177561, exon 2 of 5)	7465	NM_011387	20493	Mm.486361	NM_011387	ENSMUSG00000021135	Slc10a1	Ntcp	solute carrier family 10 (sodium/bile acid cotransporter family), member 1	protein-coding
mm_120289.1	chr14	63135493	63135505	+	1	NA	intron (NM_007798, intron 3 of 9)	intron (NM_007798, intron 3 of 9)	13037	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_58818.1	chr7	16420954	16420996	+	1	NA	intron (NM_198631, intron 4 of 13)	intron (NM_198631, intron 4 of 13)	19779	NM_198631	330474	Mm.333594	NM_198631	ENSMUSG00000059273	Zc3h4	Bwq1|Gm768|Kiaa1064-hp|mKIAA1064	zinc finger CCCH-type containing 4	protein-coding
mm_106943.1	chr12	8750116	8750153	+	1	NA	non-coding (NR_027670, exon 22 of 22)	non-coding (NR_027670, exon 22 of 22)	-21262	NM_011519	20969	Mm.2580	NM_011519	ENSMUSG00000020592	Sdc1	AA408134|AA409076|CD138|Sstn|Synd|Synd1|syn-1	syndecan 1	protein-coding
mm_24379.1	chr3	90248523	90248533	+	1	NA	intron (NM_013901, intron 1 of 3)	intron (NM_013901, intron 1 of 3)	336	NM_013901	30791	Mm.294709	NM_013901	ENSMUSG00000052310	Slc39a1	Zip1|Zirtl	solute carrier family 39 (zinc transporter), member 1	protein-coding
mm_110726.1	chr12	69683699	69683711	-	1	NA	Intergenic	MER102b|DNA|hAT-Charlie	-1853	NM_001135559	20663	Mm.3770	NM_001135559	ENSMUSG00000034801	Sos2	SOS-2|mSOS-2	son of sevenless homolog 2 (Drosophila)	protein-coding
mm_48872.1	chr5	150594494	150594535	-	1	NA	promoter-TSS (NM_133898)	promoter-TSS (NM_133898)	11	NM_133898	100637	Mm.279932	NM_133898	ENSMUSG00000041132	N4bp2l1	2410024N18Rik|AI428195|B230342M21Rik	NEDD4 binding protein 2-like 1	protein-coding
mm_83412.1	chr9	44802967	44802994	-	1	NA	promoter-TSS (NM_138951)	promoter-TSS (NM_138951)	-29	NM_138951	192653	Mm.325487	NM_138951	ENSMUSG00000039438	Ttc36	-	tetratricopeptide repeat domain 36	protein-coding
mm_113799.1	chr13	46420138	46420141	+	1	NA	intron (NM_001081425, intron 1 of 3)	intron (NM_001081425, intron 1 of 3)	1839	NM_001081425	666794	Mm.38269	NM_001081425	ENSMUSG00000038132	Rbm24	6330546B05Rik|AI606861	RNA binding motif protein 24	protein-coding
mm_155465.1	chrX	73608459	73608461	+	1	NA	Intergenic	ORR1A1|LTR|ERVL-MaLR	-30981	NM_029352	75590	Mm.16479	NM_029352	ENSMUSG00000031383	Dusp9	Dusp4|Mpk4|Pyst3	dual specificity phosphatase 9	protein-coding
mm_136967.1	chr17	15706578	15706586	+	1	NA	intron (NM_007690, intron 1 of 35)	intron (NM_007690, intron 1 of 35)	1615	NM_007690	12648	Mm.8137	NM_007690	ENSMUSG00000023852	Chd1	4930525N21Rik|AI851787|AW555109	chromodomain helicase DNA binding protein 1	protein-coding
mm_58145.1	chr6	142186145	142186153	-	1	NA	promoter-TSS (NM_023718)	promoter-TSS (NM_023718)	0	NM_023718	28254	Mm.38953	NM_023718	ENSMUSG00000079262	Slco1a6	4930422F19Rik|AI790453|Oatp-5|Oatp5|Slc21a13	solute carrier organic anion transporter family, member 1a6	protein-coding
mm_137470.1	chr17	26676406	26676466	+	1	NA	promoter-TSS (NM_025272)	promoter-TSS (NM_025272)	40	NM_025272	11974	Mm.22602	NM_025272	ENSMUSG00000015575	Atp6v0e	Atp6k|Atp6v0e1|M9.2	ATPase, H+ transporting, lysosomal V0 subunit E	protein-coding
mm_140069.1	chr17	75005524	75005565	+	1	NA	promoter-TSS (NM_019919)	promoter-TSS (NM_019919)	15	NM_019919	268977	Mm.269747	NM_019919	ENSMUSG00000001870	Ltbp1	9430031G15Rik|9830146M04|Ltbp-1|Ltbp1L|TGF-beta1-BP-1|Tgfb|b2b1000Clo	latent transforming growth factor beta binding protein 1	protein-coding
mm_7253.1	chr1	93754562	93754678	-	1	NA	promoter-TSS (NM_174874)	promoter-TSS (NM_174874)	218	NM_025920	67026	Mm.272356	NM_025920	ENSMUSG00000026279	Thap4	2010320B01Rik	THAP domain containing 4	protein-coding
mm_96765.1	chr11	69919911	69919915	+	1	NA	intron (NM_001166593, intron 1 of 6)	intron (NM_001166593, intron 1 of 6)	717	NM_001166590	276770	Mm.18026	NM_181582	ENSMUSG00000078812	Eif5a	AA410058|D19Wsu54e|Eif4d|Eif5a1|eIF-4D|eIF-5A|eIF-5A-1|eIF-5A1	eukaryotic translation initiation factor 5A	protein-coding
mm_133492.1	chr16	90385875	90385885	+	1	NA	promoter-TSS (NM_015755)	promoter-TSS (NM_015755)	-517	NM_015755	26559	Mm.125874	NM_015755	ENSMUSG00000053414	Hunk	Bstk1|Mak-v	hormonally upregulated Neu-associated kinase	protein-coding
mm_97506.1	chr11	78499010	78499022	+	1	NA	promoter-TSS (NM_011707)	promoter-TSS (NM_011707)	-104	NM_011707	22370	Mm.3667	NM_011707	ENSMUSG00000017344	Vtn	AI256434|Vn	vitronectin	protein-coding
mm_121278.1	chr14	103699513	103699523	+	1	NA	promoter-TSS (NR_045148)	promoter-TSS (NR_045148)	-86	NR_045148	70898	Mm.27548	NR_045148	ENSMUSG00000089707	Slain1os	4921525B02Rik	SLAIN motif family, member 1, opposite strand	ncRNA
mm_38408.1	chr4	139092959	139092977	-	1	NA	promoter-TSS (NM_008675)	promoter-TSS (NM_008675)	2	NM_008675	17965	Mm.9404	NM_008675	ENSMUSG00000041120	Nbl1	D4H1S1733E|DAN|Dana|NO3	neuroblastoma, suppression of tumorigenicity 1	protein-coding
mm_83491.1	chr9	45945920	45945931	-	1	NA	intron (NM_172257, intron 12 of 25)	intron (NM_172257, intron 12 of 25)	-6335	NR_106055	102465659		NR_106055	ENSMUSG00000098327	Mir7087	Gm27273|mmu-mir-7087	microRNA 7087	ncRNA
mm_61622.1	chr7	80186910	80186932	+	1	NA	promoter-TSS (NM_013659)	promoter-TSS (NM_013659)	80	NM_013659	20352	Mm.275909	NM_013659	ENSMUSG00000030539	Sema4b	SemC|Semac|mKIAA1745	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B	protein-coding
mm_103254.1	chr11	70982948	70982985	-	1	NA	promoter-TSS (NM_007573)	promoter-TSS (NM_007573)	60	NM_007573	12261	Mm.30049	NM_007573	ENSMUSG00000018446	C1qbp	AA407365|AA986492|D11Wsu182e|HABP1|P32|gC1qBP	complement component 1, q subcomponent binding protein	protein-coding
mm_154712.1	chrX	8892444	8892454	+	1	NA	promoter-TSS (NR_045448)	promoter-TSS (NR_045448)	96	NR_045448	102941	Mm.41588	NM_175327	ENSMUSG00000052364	B630019K06Rik	AI843180	novel protein similar to F-box and leucine-rich repeat protein 17 (Fbxl17)	pseudo
mm_53667.1	chr6	141632418	141632432	+	1	NA	intron (NM_020495, intron 1 of 15)	ID_B1|SINE|B4	2907	NM_020495	28253	Mm.272223	NM_020495	ENSMUSG00000030236	Slco1b2	7330442B20Rik|OATP-C|OATP2|Oatp1b2|Oatp4|Slc21a10|Slc21a6|lst-1|mlst-1	solute carrier organic anion transporter family, member 1b2	protein-coding
mm_147071.1	chr18	35215044	35215067	-	1	NA	promoter-TSS (NM_178005)	promoter-TSS (NM_178005)	-31	NM_178005	107065	Mm.39900	NM_178005	ENSMUSG00000071862	Lrrtm2	AI851755|BB129880|C630011A14Rik|mKIAA0416	leucine rich repeat transmembrane neuronal 2	protein-coding
mm_168148.1	chr10	36162685	36162686	+	1	NA	Intergenic	L1Md_A|LINE|L1	-344122	NM_001253355	319415	Mm.332442	NM_001081208	ENSMUSG00000044499	Hs3st5	D930005L05Rik|Gm1151|Hs3ost5	heparan sulfate (glucosamine) 3-O-sulfotransferase 5	protein-coding
mm_77040.1	chr8	109575399	109575415	-	1	NA	exon (NM_017370, exon 5 of 5)	exon (NM_017370, exon 5 of 5)	3765	NM_017370	15439	Mm.26730	NM_017370	ENSMUSG00000031722	Hp	HP-1|preHP2	haptoglobin	protein-coding
mm_47283.1	chr5	122106793	122106803	-	1	NA	TTS (NM_010861)	TTS (NM_010861)	5818	NM_010861	17906	Mm.1529	NM_010861	ENSMUSG00000013936	Myl2	MLC-2|MLC-2s/v|MLC-2v|Mlc2v|Mylpc	myosin, light polypeptide 2, regulatory, cardiac, slow	protein-coding
mm_156418.1	chrX	140907512	140907533	+	1	NA	promoter-TSS (NM_030181)	promoter-TSS (NM_030181)	-86	NM_030181	78789	Mm.244932	NM_026103	ENSMUSG00000031430	Vsig1	1700062D20Rik|4930405J24Rik	V-set and immunoglobulin domain containing 1	protein-coding
mm_90782.1	chr10	6980446	6980490	-	1	NA	promoter-TSS (NM_001170802)	promoter-TSS (NM_001170802)	-3	NM_001170801	320495	Mm.331674	NM_001033391	ENSMUSG00000064065	Ipcef1	A130090K04Rik	interaction protein for cytohesin exchange factors 1	protein-coding
mm_77045.1	chr8	109575774	109575796	-	1	NA	exon (NM_017370, exon 5 of 5)	exon (NM_017370, exon 5 of 5)	3387	NM_017370	15439	Mm.26730	NM_017370	ENSMUSG00000031722	Hp	HP-1|preHP2	haptoglobin	protein-coding
mm_166214.1	chr5	54959307	54959308	+	1	NA	Intergenic	Intergenic	609315	NR_038045	330086	Mm.254449	NM_177871	ENSMUSG00000105912	Gm10440	D130065D13|ENSMUSG00000072936	predicted gene 10440	ncRNA
mm_75575.1	chr8	60965441	60965470	-	1	NA	intron (NM_007711, intron 1 of 11)	MLT1D|LTR|ERVL-MaLR	-10656	NM_173876	12725	Mm.25263	NM_007711	ENSMUSG00000004319	Clcn3	Clc3	chloride channel, voltage-sensitive 3	protein-coding
mm_158377.1	chrX	135210766	135210789	-	1	NA	promoter-TSS (NM_025355)	promoter-TSS (NM_025355)	-90	NM_025355	66104	Mm.336239	NM_025355	ENSMUSG00000031409	Tceal6	1500026B10Rik	transcription elongation factor A (SII)-like 6	protein-coding
mm_157870.1	chrX	75416511	75416528	-	1	NA	promoter-TSS (NM_001166459)	promoter-TSS (NM_001166459)	65	NM_010839	105886298	Mm.16366	NM_010839	ENSMUSG00000090110	Cmc4	Mtcp1nb|p8MTCP1	C-x(9)-C motif containing 4	protein-coding
mm_1255.1	chr1	63113116	63113131	+	1	NA	intron (NM_001081436, intron 1 of 11)	intron (NM_001081436, intron 1 of 11)	1144	NM_001081436	227195	Mm.74718	NM_001081436	ENSMUSG00000040865	Ino80d	7330405I11|A430093A21Rik|BC010584|OTTMUSG00000002594	INO80 complex subunit D	protein-coding
mm_144614.1	chr18	32817028	32817032	+	1	NA	non-coding (NR_033206, exon 1 of 2)	non-coding (NR_033206, exon 1 of 2)	170	NR_033206	53603	Mm.143716	NM_021367	ENSMUSG00000024379	Tslp	-	thymic stromal lymphopoietin	protein-coding
mm_81813.1	chr9	118040510	118040566	+	1	NA	promoter-TSS (NM_013727)	promoter-TSS (NM_013727)	16	NM_013727	27215	Mm.92705	NM_013727	ENSMUSG00000039285	Azi2	AA410145|AZ2	5-azacytidine induced gene 2	protein-coding
mm_45890.1	chr5	88554127	88554189	-	1	NA	promoter-TSS (NM_023054)	promoter-TSS (NM_023054)	-325	NM_023054	65961	Mm.490364	NM_023054	ENSMUSG00000070697	Utp3	2400011K09Rik|AW557551|C87704|Crl1|Crlz1|Sas10	UTP3 small subunit processome component	protein-coding
mm_131423.1	chr16	14708211	14708227	+	1	NA	exon (NM_011415, exon 3 of 3)	exon (NM_011415, exon 3 of 3)	2360	NM_011415	20583	Mm.4272	NM_011415	ENSMUSG00000022676	Snai2	Slug|Slugh|Snail2	snail family zinc finger 2	protein-coding
mm_101800.1	chr11	46254000	46254009	-	1	NA	exon (NM_001252459, exon 18 of 31)	exon (NM_001252459, exon 18 of 31)	18447	NM_177075	320116	Mm.39600	NM_177075	ENSMUSG00000048721	Fndc9	C030019I05Rik	fibronectin type III domain containing 9	protein-coding
mm_100808.1	chr11	5079795	5079800	-	1	NA	TTS (NM_001283063)	TTS (NM_001283063)	-14470	NM_001190406	78926	Mm.44591	NM_030228	ENSMUSG00000034201	Gas2l1	4930500E24Rik|D0Jmb1|Gar22|TU-71.1	growth arrest-specific 2 like 1	protein-coding
mm_142339.1	chr17	43591452	43591463	-	1	NA	promoter-TSS (NR_045445)	promoter-TSS (NR_045445)	52	NR_045445	73504	Mm.9277	NR_045444	ENSMUSG00000090307	1700071M16Rik	-	RIKEN cDNA 1700071M16 gene	ncRNA
mm_31954.1	chr4	86823905	86823910	+	1	NA	intron (NM_184088, intron 21 of 31)	(T)n|Simple_repeat|Simple_repeat	33460	NM_009096	20104	Mm.379007	NM_009096	ENSMUSG00000028495	Rps6	S6R	ribosomal protein S6	protein-coding
mm_148098.1	chr18	73948878	73948883	-	1	NA	intron (NM_172632, intron 2 of 5)	intron (NM_172632, intron 2 of 5)	-69027	NR_045390	77855	Mm.410760	NR_045390	ENSMUSG00000090263	D730045A05Rik	-	RIKEN cDNA D730045A05 gene	ncRNA
mm_9362.1	chr1	172198506	172198516	-	1	NA	3' UTR (NM_001329871, exon 4 of 4)	3' UTR (NM_001329871, exon 4 of 4)	8293	NM_001329871	18611	Mm.544	NM_011063	ENSMUSG00000013698	Pea15a	Mat1|PEA-15|Pea15|Pkcs15	phosphoprotein enriched in astrocytes 15A	protein-coding
mm_74720.1	chr8	17419716	17419720	-	1	NA	intron (NM_053171, intron 1 of 69)	intron (NM_053171, intron 1 of 69)	115667	NM_053171	94109	Mm.436988	NM_053171	ENSMUSG00000060924	Csmd1	B930082H09|mKIAA1890	CUB and Sushi multiple domains 1	protein-coding
mm_1898.1	chr1	85709451	85709461	+	1	NA	3' UTR (NM_013673, exon 20 of 20)	3' UTR (NM_013673, exon 20 of 20)	27150	NM_177055	319997	Mm.116691	NM_177055	ENSMUSG00000052760	A630001G21Rik	-	RIKEN cDNA A630001G21 gene	protein-coding
mm_108431.1	chr12	82245807	82245815	+	1	NA	intron (NM_001167983, intron 2 of 23)	L1M4c|LINE|L1	-65538	NM_172579	217692	Mm.261333	NM_172579	ENSMUSG00000042700	Sipa1l1	4931426N11Rik|AW213287|Spar|mKIAA0440	signal-induced proliferation-associated 1 like 1	protein-coding
mm_99168.1	chr11	100736224	100736235	+	1	NA	intron (NM_024456, intron 1 of 5)	intron (NM_024456, intron 1 of 5)	1986	NM_024456	19345	Mm.29829	NM_024456	ENSMUSG00000019173	Rab5c	AI326010|Rabl	RAB5C, member RAS oncogene family	protein-coding
mm_91888.1	chr10	59950217	59950228	-	1	NA	3' UTR (NM_029083, exon 3 of 3)	3' UTR (NM_029083, exon 3 of 3)	1548	NM_029083	74747	Mm.21697	NM_029083	ENSMUSG00000020108	Ddit4	5830413E08Rik|AA415483|REDD1|Rtp801|dig2	DNA-damage-inducible transcript 4	protein-coding
mm_95775.1	chr11	54909623	54909633	+	1	NA	exon (NM_008161, exon 5 of 5)	exon (NM_008161, exon 5 of 5)	6774	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_139925.1	chr17	71019482	71019498	+	1	NA	promoter-TSS (NM_001083934)	promoter-TSS (NM_001083934)	-67	NM_010867	17929	Mm.4103	NM_010867	ENSMUSG00000024049	Myom1	D430047A17Rik	myomesin 1	protein-coding
mm_131374.1	chr16	13903153	13903211	+	1	NA	promoter-TSS (NM_053181)	promoter-TSS (NM_053181)	21	NM_001289562	93734	Mm.76554	NM_033564	ENSMUSG00000022679	Mpv17l	M-LP	Mpv17 transgene, kidney disease mutant-like	protein-coding
mm_87220.1	chr10	40300943	40300987	+	1	NA	intron (NM_007444, intron 1 of 7)	CpG	1221	NM_007444	100041585	Mm.476925	NM_007444	ENSMUSG00000063953	Amd2	AdoMetDC|Amd1|Amd3|ENSMUSG00000063953	S-adenosylmethionine decarboxylase 2	protein-coding
mm_99932.1	chr11	111023854	111023871	+	1	NA	promoter-TSS (NM_001252208)	promoter-TSS (NM_001252208)	2	NM_001252208	16517	Mm.30176	NM_010604	ENSMUSG00000051497	Kcnj16	6430410F18Rik|AI132396|Kir5.1	potassium inwardly-rectifying channel, subfamily J, member 16	protein-coding
mm_11364.1	chr2	30965842	30965845	+	1	NA	intron (NM_144884, intron 2 of 4)	intron (NM_144884, intron 2 of 4)	2075	NM_144884	30931	Mm.154994	NM_144884	ENSMUSG00000026849	Tor1a	DQ2|Dyt1|torsinA	torsin family 1, member A (torsin A)	protein-coding
mm_131873.1	chr16	23179138	23179142	+	1	NA	Intergenic	RMER1C|Other|Other	32604	NM_009605	11450	Mm.3969	NM_009605	ENSMUSG00000022878	Adipoq	30kDa|APN|Acdc|Acrp30|Ad|GBP28|adipo|apM1	adiponectin, C1Q and collagen domain containing	protein-coding
mm_105324.1	chr11	102894535	102894543	-	1	NA	exon (NM_010277, exon 4 of 9)	exon (NM_010277, exon 4 of 9)	2661	NM_001131020	14580	Mm.1239	NM_010277	ENSMUSG00000020932	Gfap	AI836096	glial fibrillary acidic protein	protein-coding
mm_142934.1	chr17	56000231	56000281	-	1	NA	intron (NM_145934, intron 6 of 12)	intron (NM_145934, intron 6 of 12)	5350	NM_145934	106766	Mm.204991	NM_145934	ENSMUSG00000038781	Stap2	AW049765|STAP-2	signal transducing adaptor family member 2	protein-coding
mm_2332.1	chr1	92831651	92831726	+	1	NA	promoter-TSS (NM_016696)	promoter-TSS (NM_016696)	2	NM_016696	14733	Mm.297976	NM_016696	ENSMUSG00000034220	Gpc1	AI462976	glypican 1	protein-coding
mm_111783.1	chr12	104473367	104473373	-	1	NA	promoter-TSS (NM_010351)	promoter-TSS (NM_010351)	-134	NM_010351	14836	Mm.129	NM_010351	ENSMUSG00000021095	Gsc	-	goosecoid homeobox	protein-coding
mm_128865.1	chr15	72810297	72810332	-	1	NA	promoter-TSS (NR_002864)	promoter-TSS (NR_002864)	10	NR_002864	353342	Mm.440245	NR_002864	ENSMUSG00000106847	Peg13	-	paternally expressed 13	ncRNA
mm_146513.1	chr18	3337615	3337646	-	1	NA	promoter-TSS (NM_001110852)	promoter-TSS (NM_001110852)	-41	NM_001110852	12916	Mm.5244	NM_013498	ENSMUSG00000063889	Crem	ICER|ICERI	cAMP responsive element modulator	protein-coding
mm_160114.1	chr7	26535068	26535068	+	1	NA	promoter-TSS (NM_001048219)	promoter-TSS (NM_001048219)	45	NM_001048219	233001	Mm.11889	NM_194056	ENSMUSG00000054102	Nlrp9a	D7Ertd565e|Nalp-theta|Nalp9a	NLR family, pyrin domain containing 9A	protein-coding
mm_88723.1	chr10	80171347	80171352	+	1	NA	3' UTR (NM_007705, exon 7 of 7)	3' UTR (NM_007705, exon 7 of 7)	-1595	NM_027207	69770	Mm.302754	NM_027207	ENSMUSG00000035595	1600002K03Rik	-	RIKEN cDNA 1600002K03 gene	protein-coding
mm_126584.1	chr15	82294091	82294107	+	1	NA	3' UTR (NM_011889, exon 10 of 10)	3' UTR (NM_011889, exon 10 of 10)	-4885	NM_029066	74716	Mm.159315	NM_029066	ENSMUSG00000022455	Wbp2nl	4930521I23Rik|PAWP	WBP2 N-terminal like	protein-coding
mm_127252.1	chr15	99699898	99699902	+	1	NA	3' UTR (NM_009597, exon 12 of 12)	3' UTR (NM_009597, exon 12 of 12)	-2387	NM_031842	83797	Mm.273756	NM_031842	ENSMUSG00000023018	Smarcd1	AA407987|Baf60a|D15Kz1	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1	protein-coding
mm_68708.1	chr7	119861828	119861863	-	1	NA	intron (NM_001163703, intron 1 of 2)	intron (NM_001163703, intron 1 of 2)	33613	NM_173408	233805	Mm.31539	NM_173408	ENSMUSG00000048787	Dcun1d3	1700020A13Rik|BC030335	DCN1, defective in cullin neddylation 1, domain containing 3 (S. cerevisiae)	protein-coding
mm_65852.1	chr7	29281915	29281935	-	1	NA	promoter-TSS (NM_001082548)	promoter-TSS (NM_001082548)	52	NM_001082548	20733	Mm.295230	NM_011464	ENSMUSG00000074227	Spint2	AL024025|C76321|HAI-2	serine protease inhibitor, Kunitz type 2	protein-coding
mm_47758.1	chr5	131307849	131307932	-	1	NA	promoter-TSS (NM_145218)	promoter-TSS (NM_145218)	-368	NM_145218	212996	Mm.299204	NM_145218	ENSMUSG00000034040	Wbscr17	AA388321|E330012B09Rik	Williams-Beuren syndrome chromosome region 17 homolog (human)	protein-coding
mm_21923.1	chr2	166950896	166950909	-	1	NA	exon (NM_011490, exon 9 of 12)	exon (NM_011490, exon 9 of 12)	13815	NR_111895	20853	Mm.73276	NM_011490	ENSMUSG00000039536	Stau1	5830401L18Rik|AW549911|C85792|Stau	staufen (RNA binding protein) homolog 1 (Drosophila)	protein-coding
mm_39909.1	chr5	31297598	31297602	+	1	NA	promoter-TSS (NM_144909)	promoter-TSS (NM_144909)	19	NM_144909	231103	Mm.100043	NM_144909	ENSMUSG00000059434	Gckr	GKRP	glucokinase regulatory protein	protein-coding
mm_7471.1	chr1	120488562	120488582	-	1	NA	exon (NM_010766, exon 7 of 17)	exon (NM_010766, exon 7 of 17)	16512	NM_010766	17167	Mm.1856	NM_010766	ENSMUSG00000026390	Marco	AI323439|Ly112|Scara2	macrophage receptor with collagenous structure	protein-coding
mm_68278.1	chr7	105599297	105599329	-	1	NA	exon (NM_017371, exon 4 of 10)	exon (NM_017371, exon 4 of 10)	803	NM_017371	15458	Mm.3485	NM_017371	ENSMUSG00000030895	Hpx	Hpxn|hx	hemopexin	protein-coding
mm_1831.1	chr1	82724910	82724943	+	1	NA	promoter-TSS (NM_029409)	promoter-TSS (NM_029409)	36	NM_001310699	75734	Mm.396863	NM_029409	ENSMUSG00000026150	Mff	5230400G24Rik|AI314724	mitochondrial fission factor	protein-coding
mm_138594.1	chr17	35510072	35510092	+	1	NA	exon (NM_001252452, exon 4 of 5)	exon (NM_001252452, exon 4 of 5)	1275	NM_001252452	18999	Mm.17031	NM_013633	ENSMUSG00000024406	Pou5f1	NF-A3|Oct-3|Oct-3/4|Oct-4|Oct3|Oct3/4|Oct4|Otf-3|Otf-4|Otf3|Otf3-rs7|Otf3g|Otf4	POU domain, class 5, transcription factor 1	protein-coding
mm_147893.1	chr18	65220823	65220830	-	1	NA	intron (NR_105742, intron 4 of 6)	intron (NR_105742, intron 4 of 6)	-28035	NR_029600	387231		NR_029600	ENSMUSG00000065402	Mir122	Mir122a|Mirn122a|mir-122|mmu-mir-122	microRNA 122	ncRNA
mm_148240.1	chr18	80608460	80608478	-	1	NA	intron (NM_198429, intron 9 of 9)	intron (NM_198429, intron 9 of 9)	-63923	NR_028424	100039348	Mm.254722	NR_028424		Gm2176	A430076E10Rik	glucosamine-6-phosphate deaminase 1 pseudogene	pseudo
mm_148433.1	chr19	3942369	3942398	+	1	NA	exon (NM_019449, exon 6 of 11)	exon (NM_019449, exon 6 of 11)	7197	NM_001161428	54445	Mm.262094	NM_019449	ENSMUSG00000036908	Unc93b1	Unc-93B1|Unc93b	unc-93 homolog B1 (C. elegans)	protein-coding
mm_31522.1	chr4	54947516	54947543	+	1	NA	promoter-TSS (NM_172867)	promoter-TSS (NM_172867)	-416	NM_172867	242466	Mm.102904	NM_172867	ENSMUSG00000060206	Zfp462	6030417H05|9430078C22Rik|Gt4-2|Zfpip	zinc finger protein 462	protein-coding
mm_102388.1	chr11	58938852	58938923	-	1	NA	promoter-TSS (NM_022423)	promoter-TSS (NM_022423)	19	NM_022423	108660	Mm.249986	NM_022423	ENSMUSG00000020496	Rnf187	2410016F01Rik|AB030190|RACO-1	ring finger protein 187	protein-coding
mm_79121.1	chr9	46913474	46913480	+	1	NA	promoter-TSS (NR_015605)	promoter-TSS (NR_015605)	-126	NR_015605	73040	Mm.265384	NR_015605	ENSMUSG00000099696	2900052N01Rik	AU067665	RIKEN cDNA 2900052N01 gene	ncRNA
mm_5346.1	chr1	24943168	24943169	-	1	NA	Intergenic	Intergenic	264250	NM_001310483	68421	Mm.336563	NM_026719	ENSMUSG00000073725	Lmbrd1	0910001K20Rik|AV347960	LMBR1 domain containing 1	protein-coding
mm_172021.1	chr6	115808719	115808720	-	1	NA	promoter-TSS (NR_028546)	promoter-TSS (NR_028546)	24	NM_172086	19951	Mm.104368	NM_172086	ENSMUSG00000057841	Rpl32	AU020185|rpL32-3A	ribosomal protein L32	protein-coding
mm_130711.1	chr15	100738384	100738390	-	1	NA	Intergenic	Intergenic	-5650	NR_045782	619313	Mm.123436	NR_045781		I730030J21Rik	-	RIKEN cDNA I730030J21 gene	ncRNA
mm_159906.1	chr6	42817282	42817282	+	1	NA	promoter-TSS (NM_146445)	promoter-TSS (NM_146445)	-191	NM_146445	258437	Mm.347658	NM_146445	ENSMUSG00000054431	Olfr450	MOR257-3	olfactory receptor 450	protein-coding
mm_25816.1	chr3	127791267	127791277	+	1	NA	intron (NM_145133, intron 1 of 2)	intron (NM_145133, intron 1 of 2)	1359	NM_145133	211550	Mm.31852	NM_145133	ENSMUSG00000046688	Tifa	T2bp	TRAF-interacting protein with forkhead-associated domain	protein-coding
mm_91830.1	chr10	56982099	56982103	-	1	NA	Intergenic	Intergenic	504252	NR_045353	74928	Mm.416643	NR_045353	ENSMUSG00000097370	4930467K11Rik	-	RIKEN cDNA 4930467K11 gene	ncRNA
mm_162012.1	chr19	44237612	44237612	+	1	NA	intron (NM_024450, intron 4 of 5)	RMER17C2|LTR|ERVK	34324	NM_024450	30049	Mm.480594	NM_024450	ENSMUSG00000025202	Scd3	4930513N16Rik	stearoyl-coenzyme A desaturase 3	protein-coding
mm_83343.1	chr9	44288333	44288409	-	1	NA	promoter-TSS (NM_138955)	promoter-TSS (NM_138955)	-127	NM_138955	192663	Mm.101876	NM_138955	ENSMUSG00000032131	Abcg4	6430517O04Rik	ATP-binding cassette, sub-family G (WHITE), member 4	protein-coding
mm_170483.1	chr19	14791952	14791967	-	1	NA	Intergenic	ERVB7_1-LTR_MM|LTR|ERVK	-193776	NM_001302947	21888	Mm.103638	NM_011600	ENSMUSG00000024642	Tle4	5730411M05Rik|AA792082|Bce-1|Bce1|ESTM13|ESTM14|Grg4|X83332|X83333|grg-4	transducin-like enhancer of split 4	protein-coding
mm_82763.1	chr9	26911816	26911819	-	1	NA	intron (NM_001281475, intron 6 of 20)	intron (NM_001281475, intron 6 of 20)	11264	NM_001281475	382064	Mm.335028	NM_001177509	ENSMUSG00000079644	Gm1110	-	predicted gene 1110	protein-coding
mm_105530.1	chr11	106300845	106300890	-	1	NA	exon (NM_008117, exon 4 of 5)	exon (NM_008117, exon 4 of 5)	1029	NM_008117	14599	Mm.343934	NM_008117	ENSMUSG00000020713	Gh	Gh1|Ghb1	growth hormone	protein-coding
mm_24576.1	chr3	93444674	93444678	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	2346	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_155770.1	chrX	96255555	96255565	+	1	NA	intron (NM_177789, intron 4 of 6)	intron (NM_177789, intron 4 of 6)	12743	NR_029801	723814		NR_029801	ENSMUSG00000076066	Mir223	Mirn223|miR-223|mmu-mir-223	microRNA 223	ncRNA
mm_70386.1	chr8	10484085	10484101	+	1	NA	intron (NM_001319151, intron 23 of 34)	MTEa|LTR|ERVL-MaLR	330182	NM_001319151	244281	Mm.422761	NM_001081397	ENSMUSG00000039057	Myo16	BM140241|C230040D10Rik|Gm1105|NYAP3|mKIAA0865	myosin XVI	protein-coding
mm_105026.1	chr11	100472773	100472788	-	1	NA	promoter-TSS (NM_172565)	promoter-TSS (NM_172565)	2	NM_172565	217194	Mm.183320	NM_172565	ENSMUSG00000048732	Klhl11	BC011167	kelch-like 11	protein-coding
mm_136793.1	chr17	12092711	12092711	+	1	NA	Intergenic	Intergenic	-26573	NM_026644	68262	Mm.258300	NM_026644	ENSMUSG00000023827	Agpat4	1500003P24Rik	1-acylglycerol-3-phosphate O-acyltransferase 4 (lysophosphatidic acid acyltransferase, delta)	protein-coding
mm_119193.1	chr14	32513556	32513560	+	1	NA	promoter-TSS (NM_001081221)	promoter-TSS (NM_001081221)	37	NM_001081221	319955	Mm.318310	NM_177043	ENSMUSG00000054051	Ercc6	4732403I04|C130058G22Rik|CSB	excision repair cross-complementing rodent repair deficiency, complementation group 6	protein-coding
mm_29581.1	chr3	117322001	117322005	-	1	NA	exon (NM_177664, exon 7 of 7)	exon (NM_177664, exon 7 of 7)	38873	NM_177664	229791	Mm.140138	NM_177664	ENSMUSG00000044667	Plppr4	A330086D10|D3Bwg0562e|Lppr4|PRG-1|mKIAA0455	phospholipid phosphatase related 4	protein-coding
mm_103020.1	chr11	69734976	69734987	-	1	NA	exon (NM_001291068, exon 29 of 29)	exon (NM_001291068, exon 29 of 29)	23652	NM_001291068	20020	Mm.16533	NM_009089	ENSMUSG00000005198	Polr2a	220kDa|Rpb1|Rpo2-1	polymerase (RNA) II (DNA directed) polypeptide A	protein-coding
mm_116359.1	chr13	40728942	40728945	-	1	NA	intron (NM_001301674, intron 2 of 7)	intron (NM_001301674, intron 2 of 7)	1135	NR_125899	102633805		NR_125899	ENSMUSG00000097752	Gm26688	Tfap2a-as1	predicted gene, 26688	ncRNA
mm_169907.1	chr16	54511901	54511906	+	1	NA	Intergenic	BGLII|LTR|ERVK	771334	NM_178720	239852	Mm.245045	NM_178720	ENSMUSG00000064310	Zpld1	9430016A21Rik	zona pellucida like domain containing 1	protein-coding
mm_121535.1	chr14	122375234	122375251	+	1	NA	intron (NM_029556, intron 3 of 7)	intron (NM_029556, intron 3 of 7)	75873	NR_033325	328479	Mm.86095	NR_033325	ENSMUSG00000064052	Gm5089	6530402A20|C030005G22Rik|EG328479	predicted gene 5089	ncRNA
mm_105857.1	chr11	113751785	113751806	-	1	NA	promoter-TSS (NM_001163346)	promoter-TSS (NM_001163346)	20	NM_001163346	56699	Mm.293378	NM_020006	ENSMUSG00000041598	Cdc42ep4	1500041M20Rik|Borg4|CEP4	CDC42 effector protein (Rho GTPase binding) 4	protein-coding
mm_172778.1	chr8	95825388	95825394	+	1	NA	Intergenic	CpG	-17929	NM_001205226	234594	Mm.259220	NM_153164	ENSMUSG00000036550	Cnot1	6030411K04Rik|AA815922|D830048B13	CCR4-NOT transcription complex, subunit 1	protein-coding
mm_83914.1	chr9	56418062	56418081	-	1	NA	promoter-TSS (NM_025812)	promoter-TSS (NM_025812)	-21	NM_172924	244895	Mm.490331	NM_172924	ENSMUSG00000074305	Peak1	1110049L02Rik|9530046P14|AA690169|BE132841|C230081A13Rik|SGK269|mKIAA2002	pseudopodium-enriched atypical kinase 1	protein-coding
mm_145826.1	chr18	65437404	65437422	+	1	NA	intron (NM_172833, intron 1 of 15)	B1_Mur1|SINE|Alu	6416	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_46367.1	chr5	103425749	103425761	-	1	NA	intron (NM_011204, intron 1 of 47)	CpG	563	NM_011204	19249	Mm.3414	NM_011204	ENSMUSG00000034573	Ptpn13	AI324989|PTP-BL|PTPL1|Ptpri|RIP	protein tyrosine phosphatase, non-receptor type 13	protein-coding
mm_106049.1	chr11	116080342	116080353	-	1	NA	intron (NM_001347642, intron 4 of 6)	intron (NM_001347642, intron 4 of 6)	-2386	NM_001009573	70450	Mm.259460	NM_001009573	ENSMUSG00000057948	Unc13d	2610108D09Rik|Jinx|Munc13-4|mFLJ00067	unc-13 homolog D (C. elegans)	protein-coding
mm_130077.1	chr15	89373866	89373901	-	1	NA	promoter-TSS (NM_001111288)	promoter-TSS (NM_001111288)	-65	NM_001111288	100126824	Mm.287977	NM_001111288	ENSMUSG00000091780	Sco2	-	SCO2 cytochrome c oxidase assembly protein	protein-coding
mm_59870.1	chr7	30232034	30232050	+	1	NA	promoter-TSS (NM_027259)	promoter-TSS (NM_027259)	-13	NM_025548	66411	Mm.27947	NM_025548	ENSMUSG00000006095	Tbcb	2410007D12Rik|AU041393|CG22|CKAPI|Ckap1	tubulin folding cofactor B	protein-coding
mm_19515.1	chr2	93984858	93984865	-	1	NA	intron (NM_026944, intron 8 of 9)	intron (NM_026944, intron 8 of 9)	4827	NR_045827	70852	Mm.437014	NR_045827	ENSMUSG00000027196	Alkbh3os1	4921507L20Rik	alkB homolog 3, opposite strand 1	ncRNA
mm_6451.1	chr1	74014653	74014694	-	1	NA	intron (NM_027884, intron 4 of 34)	intron (NM_027884, intron 4 of 34)	109774	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_110397.1	chr12	44210062	44210077	-	1	NA	promoter-TSS (NM_013760)	promoter-TSS (NM_013760)	-1	NM_013760	27362	Mm.27432	NM_013760	ENSMUSG00000014905	Dnajb9	AA408011|AA673251|AA673481|AW556981|ERdj4|Mdg1|mDj7	DnaJ heat shock protein family (Hsp40) member B9	protein-coding
mm_38939.1	chr4	150197363	150197385	-	1	NA	exon (NM_009802, exon 3 of 8)	exon (NM_009802, exon 3 of 8)	3761	NM_009802	12353	Mm.232523	NM_009802	ENSMUSG00000028972	Car6	Ca6|DOC1	carbonic anhydrase 6	protein-coding
mm_85079.1	chr9	91364945	91364957	-	1	NA	exon (NM_009573, exon 1 of 3)	exon (NM_009573, exon 1 of 3)	848	NM_009573	22771	Mm.335350	NM_009573	ENSMUSG00000032368	Zic1	ZIC|ZNF201	zinc finger protein of the cerebellum 1	protein-coding
mm_137377.1	chr17	25717490	25717551	+	1	NA	intron (NM_022422, intron 1 of 2)	CpG	348	NM_022422	64337	Mm.171123	NM_022422	ENSMUSG00000025739	Gng13	1500031D04Rik|AB030194|Ggamma13	guanine nucleotide binding protein (G protein), gamma 13	protein-coding
mm_16601.1	chr2	5062945	5062954	-	1	NA	intron (NM_181848, intron 1 of 14)	intron (NM_181848, intron 1 of 14)	989	NM_181848	71648	Mm.116942	NM_181848	ENSMUSG00000026672	Optn	4930441O07Rik|FIP2|HYPL|NRP	optineurin	protein-coding
mm_66269.1	chr7	36696071	36696074	-	1	NA	Intergenic	CpG	-2046	NM_172298	243931	Mm.44141	NM_172298	ENSMUSG00000021217	Tshz3	A630038G13Rik|Tsh3|Zfp537|mKIAA1474|teashirt3	teashirt zinc finger family member 3	protein-coding
mm_173231.1	chrX	79744262	79744266	+	1	NA	Intergenic	L1Md_T|LINE|L1	-72829	NM_028025	71967	Mm.379207	NM_028025	ENSMUSG00000046942	Mageb16	2410003J06Rik	melanoma antigen family B, 16	protein-coding
mm_149258.1	chr19	10525251	10525305	+	1	NA	promoter-TSS (NM_025333)	promoter-TSS (NM_025333)	34	NM_172302	269061	Mm.490260	NM_172302	ENSMUSG00000034820	Cpsf7	5730453I16Rik|AL022757|C330017N18Rik	cleavage and polyadenylation specific factor 7	protein-coding
mm_98080.1	chr11	86545012	86545050	+	1	NA	promoter-TSS (NM_001199045)	promoter-TSS (NM_001199045)	40	NM_001199046	56427	Mm.383207	NM_019756	ENSMUSG00000020513	Tubd1	4930550G19Rik|Tubd	tubulin, delta 1	protein-coding
mm_16460.1	chr2	180598220	180598226	+	1	NA	promoter-TSS (NM_009936)	promoter-TSS (NM_009936)	1	NM_009936	12841	Mm.141312	NM_009936	ENSMUSG00000027570	Col9a3	AV006866	collagen, type IX, alpha 3	protein-coding
mm_166952.1	chr7	44219246	44219278	+	1	NA	intron (NM_008456, intron 2 of 4)	(TCTCTG)n|Simple_repeat|Simple_repeat	2788	NM_008456	16622	Mm.443373	NM_008456	ENSMUSG00000066512	Klk1b5	Klk5|kallikrein|mGK-5	kallikrein 1-related peptidase b5	protein-coding
mm_2748.1	chr1	128705430	128705442	+	1	NA	Intergenic	Intergenic	-113137	NM_009911	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding
mm_31671.1	chr4	60005915	60005922	+	1	NA	intron (NM_001081285, intron 4 of 5)	intron (NM_001081285, intron 4 of 5)	2369	NM_001081285	620807	Mm.464562	NM_001081285	ENSMUSG00000078689	Mup6	Gm12544|Mup2|OTTMUSG00000007423	major urinary protein 6	protein-coding
mm_160379.1	chr8	41293486	41293486	+	1	NA	exon (NM_023662, exon 22 of 38)	exon (NM_023662, exon 22 of 38)	53727	NM_023662	18536	Mm.117896	NM_023662	ENSMUSG00000031592	Pcm1	2600002H09Rik|9430077F19Rik|C030044G17Rik	pericentriolar material 1	protein-coding
mm_140782.1	chr17	17889730	17889734	-	1	NA	intron (NM_008039, intron 1 of 1)	B4A|SINE|B4	1908	NM_008039	14289	Mm.378918	NM_008039	ENSMUSG00000052270	Fpr2	E330010I07Rik|Fpr-rs2	formyl peptide receptor 2	protein-coding
mm_47198.1	chr5	120812485	120812493	-	1	NA	promoter-TSS (NR_003507)	promoter-TSS (NR_003507)	25	NM_033541	114643	Mm.43230	NM_033541	ENSMUSG00000001166	Oas1c	Oasl2|Oasl5	2'-5' oligoadenylate synthetase 1C	protein-coding
mm_10853.1	chr2	25025611	25025615	+	1	NA	intron (NM_146251, intron 20 of 34)	B1_Mur4|SINE|Alu	-28766	NM_001177654	56876	Mm.42956	NM_020276	ENSMUSG00000006476	Nsmf	Jacob|Nelf	NMDA receptor synaptonuclear signaling and neuronal migration factor	protein-coding
mm_74650.1	chr8	13390100	13390103	-	1	NA	exon (NM_009724, exon 3 of 7)	exon (NM_009724, exon 3 of 7)	6677	NM_009724	11945	Mm.154039	NM_009724	ENSMUSG00000031449	Atp4b	AV080843	ATPase, H+/K+ exchanging, beta polypeptide	protein-coding
mm_77630.1	chr8	124021360	124021445	-	1	NA	promoter-TSS (NM_133966)	promoter-TSS (NM_133966)	-93	NM_133966	102162	Mm.291777	NM_133966	ENSMUSG00000038697	Taf5l	1110005N04Rik|AI849020	TATA-box binding protein associated factor 5 like	protein-coding
mm_79687.1	chr9	60334088	60334125	+	1	NA	intron (NM_001040426, intron 6 of 17)	MTE2a|LTR|ERVL-MaLR	176929	NM_001040426	207596	Mm.28791	NM_172444	ENSMUSG00000032289	Thsd4	ADAMTSL-6|ADAMTSL6|AI585901|Adamtsl4|B230114P05Rik	thrombospondin, type I, domain containing 4	protein-coding
mm_155063.1	chrX	42502480	42502489	+	1	NA	promoter-TSS (NM_011364)	promoter-TSS (NM_011364)	-81	NM_011364	20400	Mm.441197	NM_011364	ENSMUSG00000005696	Sh2d1a	Gm686|SAP	SH2 domain containing 1A	protein-coding
mm_24048.1	chr3	87906318	87906326	+	1	NA	promoter-TSS (NM_008231)	promoter-TSS (NM_008231)	1	NM_008231	15191	Mm.292208	NM_008231	ENSMUSG00000004897	Hdgf	AI118077|D3Ertd299e	hepatoma-derived growth factor	protein-coding
mm_148727.1	chr19	5848590	5848668	+	1	NA	Intergenic	Intergenic	-3149	NR_003513	66961	Mm.281895	NR_003513	ENSMUSG00000092274	Neat1	2310043N10Rik|VINC	nuclear paraspeckle assembly transcript 1 (non-protein coding)	ncRNA
mm_40403.1	chr5	53038082	53038085	+	1	NA	Intergenic	Intergenic	-11270	NM_011402	20531	Mm.284891	NM_011402	ENSMUSG00000029188	Slc34a2	AA536683|D5Ertd227e|NaPi-2b|Npt2b	solute carrier family 34 (sodium phosphate), member 2	protein-coding
mm_55202.1	chr6	52208596	52208604	-	1	NA	promoter-TSS (NM_010454)	promoter-TSS (NM_010454)	24	NM_010454	15403	Mm.222030	NM_010454	ENSMUSG00000043219	Hoxa6	Hox-1.2	homeobox A6	protein-coding
mm_30047.1	chr3	136103522	136103526	-	1	NA	intron (NM_001310749, intron 7 of 15)	intron (NM_001310749, intron 7 of 15)	222542	NM_001310749	242248	Mm.30832	NM_001033350	ENSMUSG00000037922	Bank1	A530094C12Rik|AI451642|AVIEF|BANK	B cell scaffold protein with ankyrin repeats 1	protein-coding
mm_1171.1	chr1	60914625	60914660	+	1	NA	exon (NM_009843, exon 4 of 4)	exon (NM_009843, exon 4 of 4)	5617	NM_001281976	12477	Mm.390	NM_009843	ENSMUSG00000026011	Ctla4	Cd152|Ctla-4|Ly-56	cytotoxic T-lymphocyte-associated protein 4	protein-coding
mm_151932.1	chr19	5800291	5800301	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	2376	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_11903.1	chr2	50303276	50303292	+	1	NA	intron (NR_040362, intron 1 of 2)	intron (NR_040362, intron 1 of 2)	6474	NR_040362	100502624	Mm.382825	NR_040361	ENSMUSG00000085862	Gm13483	OTTMUSG00000012382	predicted gene 13483	ncRNA
mm_119953.1	chr14	55055661	55055678	+	1	NA	Intergenic	Intergenic	17207	NR_073535	100151693	Mm.378403	NR_073535	ENSMUSG00000072492	Gm10364	EG545052|ENSMUSG00000072492	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_68866.1	chr7	126416704	126416725	-	1	NA	Intergenic	IMPB_01|Satellite|Satellite	-1844	NM_009844	12478	Mm.4360	NM_009844	ENSMUSG00000030724	Cd19	AW495831	CD19 antigen	protein-coding
mm_42583.1	chr5	117319063	117319109	+	1	NA	promoter-TSS (NM_001033311)	promoter-TSS (NM_001033311)	-180	NM_001033311	231668	Mm.298603	NM_001033311	ENSMUSG00000066894	Vsig10	-	V-set and immunoglobulin domain containing 10	protein-coding
mm_157564.1	chrX	52310108	52310111	-	1	NA	intron (NM_016697, intron 7 of 7)	intron (NM_016697, intron 7 of 7)	68072	NR_105805	102465202		NR_105805	ENSMUSG00000105738	Mir6384	mmu-mir-6384	microRNA 6384	ncRNA
mm_27780.1	chr3	73708328	73708338	-	1	NA	promoter-TSS (NM_009738)	promoter-TSS (NM_009738)	82	NM_009738	12038	Mm.250719	NM_009738	ENSMUSG00000027792	Bche	C730038G20Rik	butyrylcholinesterase	protein-coding
mm_132142.1	chr16	31948625	31948641	+	1	NA	promoter-TSS (NR_027897)	promoter-TSS (NR_027897)	87	NM_026554	68092	Mm.290027	NM_026554	ENSMUSG00000022774	Ncbp2	20kDa|5930413E18Rik|AA536802|AI843301|C79367	nuclear cap binding protein subunit 2	protein-coding
mm_158277.1	chrX	111463455	111463473	-	1	NA	intron (NM_025949, intron 2 of 24)	CpG-15872	74495	NM_025949	67071	Mm.37617	NM_025949	ENSMUSG00000025665	Rps6ka6	2610524K04Rik|RSK4|S6K-alpha-6	ribosomal protein S6 kinase polypeptide 6	protein-coding
mm_18278.1	chr2	52424796	52424806	-	1	NA	promoter-TSS (NM_182994)	promoter-TSS (NM_182994)	73	NM_182994	75423	Mm.314378	NM_182994	ENSMUSG00000036093	Arl5a	2410015N24Rik|2810410P22Rik|AA408731|AW610751|Arl5|T25534	ADP-ribosylation factor-like 5A	protein-coding
mm_22089.1	chr2	168767160	168767162	-	1	NA	promoter-TSS (NM_201396)	promoter-TSS (NM_201396)	40	NM_201395	99377	Mm.434054	NM_175303	ENSMUSG00000027547	Sall4	5730441M18Rik|AA407717|AL022809|AW536104|C330011P20Rik|C78083|C78563|Tex20	sal-like 4 (Drosophila)	protein-coding
mm_45899.1	chr5	88676112	88676129	-	1	NA	promoter-TSS (NM_178700)	promoter-TSS (NM_178700)	51	NM_178700	231413	Mm.332474	NM_178700	ENSMUSG00000044221	Grsf1	BB232551|C80280|D5Wsu31e	G-rich RNA sequence binding factor 1	protein-coding
mm_98303.1	chr11	90033017	90033044	+	1	NA	intron (NM_026433, intron 1 of 2)	intron (NM_026433, intron 1 of 2)	2682	NM_026433	67888	Mm.212428	NM_026433	ENSMUSG00000069763	Tmem100	1810057C19Rik|AV011897	transmembrane protein 100	protein-coding
mm_93495.1	chr10	112160322	112160330	-	1	NA	Intergenic	Intergenic	-3295	NM_001310675	353025	Mm.194428	NM_178278	ENSMUSG00000035694	Caps2	D630005B03Rik	calcyphosphine 2	protein-coding
mm_49705.1	chr6	34384231	34384335	+	1	NA	promoter-TSS (NM_172398)	promoter-TSS (NM_172398)	36	NM_172398	67861	Mm.70371	NM_172398	ENSMUSG00000061758	Akr1b10	2310005E10Rik|Akr1b16	aldo-keto reductase family 1, member B10 (aldose reductase)	protein-coding
mm_33474.1	chr4	130818656	130818677	+	1	NA	exon (NM_011520, exon 3 of 5)	exon (NM_011520, exon 3 of 5)	26129	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_124886.1	chr15	10269002	10269006	+	1	NA	intron (NM_001253781, intron 1 of 9)	intron (NM_001253781, intron 1 of 9)	-24647	NM_001253782	19116	Mm.10516	NM_011169	ENSMUSG00000005268	Prlr	AI987712|Pr-1|Pr-3|Prlr-rs1	prolactin receptor	protein-coding
mm_14397.1	chr2	130012337	130012350	+	1	NA	promoter-TSS (NM_009374)	promoter-TSS (NM_009374)	3	NM_009374	21818	Mm.2961	NM_009374	ENSMUSG00000027401	Tgm3	AI893889|TG E|TG(E)|TGE|TGase E|TGase-3|we	transglutaminase 3, E polypeptide	protein-coding
mm_74831.1	chr8	23191585	23191598	-	1	NA	5' UTR (NM_018743, exon 2 of 13)	5' UTR (NM_018743, exon 2 of 13)	16862	NM_018743	102247	Mm.200898	NM_018743	ENSMUSG00000031545	Gpat4	AU041707|AW545732|Agpat6|Tsarg7	glycerol-3-phosphate acyltransferase 4	protein-coding
mm_30724.1	chr4	13743515	13743534	+	1	NA	5' UTR (NM_001111026, exon 1 of 11)	5' UTR (NM_001111026, exon 1 of 11)	222	NM_001111026	12395	Mm.4909	NM_009822	ENSMUSG00000006586	Runx1t1	Cbfa2t1h|ETO|MTG8	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	protein-coding
mm_108658.1	chr12	86421629	86421662	+	1	NA	promoter-TSS (NM_011934)	promoter-TSS (NM_011934)	1	NM_011934	26380	Mm.235550	NM_011934	ENSMUSG00000021255	Esrrb	Err2|Errb|Estrrb|Nr3b2	estrogen related receptor, beta	protein-coding
mm_113118.1	chr13	24501578	24501598	+	1	NA	Intergenic	Intergenic	-80601	NM_001286100	193385	Mm.217319	NM_029679	ENSMUSG00000036006	Fam65b	-	family with sequence similarity 65, member B	protein-coding
mm_94421.1	chr11	5871772	5871782	+	1	NA	TTS (NM_008894)	TTS (NM_008894)	6479	NM_008894	18972	Mm.35788	NM_008894	ENSMUSG00000020471	Pold2	50kDa|p50|po1D2	polymerase (DNA directed), delta 2, regulatory subunit	protein-coding
mm_56850.1	chr6	117937395	117937435	-	1	NA	promoter-TSS (NM_001173372)	promoter-TSS (NM_001173372)	-80	NM_001173372	108017	Mm.250392	NM_033648	ENSMUSG00000004988	Fxyd4	0610008I02Rik|AI267073|Chif	FXYD domain-containing ion transport regulator 4	protein-coding
mm_124676.1	chr15	6424661	6424664	+	1	NA	exon (NM_001037905, exon 9 of 14)	exon (NM_001037905, exon 9 of 14)	-20671	NM_013485	12279	Mm.29095	NM_013485	ENSMUSG00000022149	C9	-	complement component 9	protein-coding
mm_143324.1	chr17	66357721	66357723	-	1	NA	intron (NM_001114098, intron 9 of 14)	B1_Mur1|SINE|Alu	92028	NM_172963	68617	Mm.33421	NM_172963	ENSMUSG00000052105	Mtcl1	1110012J17Rik|Ccdc165|D130071O13|Kiaa0802|Soga2|mKIAA0802|t8219b25	microtubule crosslinking factor 1	protein-coding
mm_74719.1	chr8	17380956	17380968	-	1	NA	intron (NM_053171, intron 1 of 69)	intron (NM_053171, intron 1 of 69)	154423	NM_053171	94109	Mm.436988	NM_053171	ENSMUSG00000060924	Csmd1	B930082H09|mKIAA1890	CUB and Sushi multiple domains 1	protein-coding
mm_44877.1	chr5	34635012	34635023	-	1	NA	intron (NM_026660, intron 7 of 12)	intron (NM_026660, intron 7 of 12)	2097	NM_026660	68294	Mm.34564	NM_026660	ENSMUSG00000001082	Mfsd10	0610009O03Rik|Tetran	major facilitator superfamily domain containing 10	protein-coding
mm_2329.1	chr1	92831335	92831375	+	1	NA	promoter-TSS (NM_016696)	promoter-TSS (NM_016696)	-331	NM_016696	14733	Mm.297976	NM_016696	ENSMUSG00000034220	Gpc1	AI462976	glypican 1	protein-coding
mm_59377.1	chr7	25755472	25755474	+	1	NA	promoter-TSS (NM_178089)	promoter-TSS (NM_178089)	-753	NM_144922	232989	Mm.254223	NM_144922	ENSMUSG00000040725	Hnrnpul1	E130317O14Rik|E1B-AP5|E1BAP5|Hnrnpul|Hnrpul1	heterogeneous nuclear ribonucleoprotein U-like 1	protein-coding
mm_22069.1	chr2	168741753	168741774	-	1	NA	promoter-TSS (NM_015731)	promoter-TSS (NM_015731)	37	NM_015731	11981	Mm.330819	NM_015731	ENSMUSG00000027546	Atp9a	IIa	ATPase, class II, type 9A	protein-coding
mm_172464.1	chr7	42642612	42642628	-	1	NA	promoter-TSS (NM_001242388)	promoter-TSS (NM_001242388)	-16	NM_001242388	208111	Mm.387841	NM_001034857	ENSMUSG00000074158	Zfp976	9830147E19Rik|C330019L16Rik	zinc finger protein 976	protein-coding
mm_28248.1	chr3	88503599	88503614	-	1	NA	promoter-TSS (NM_001111102)	promoter-TSS (NM_001111102)	-254	NM_001002011	16905	Mm.243014	NM_019390	ENSMUSG00000028063	Lmna	Dhe	lamin A	protein-coding
mm_18970.1	chr2	76812138	76812153	-	1	NA	exon (NM_011652, exon 179 of 313)	exon (NM_011652, exon 179 of 313)	136830	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_68059.1	chr7	101838000	101838014	-	1	NA	promoter-TSS (NM_001122739)	promoter-TSS (NM_001122739)	-183	NM_001122739	16332	Mm.476000	NM_010567	ENSMUSG00000032737	Inppl1	51C|SHIP2	inositol polyphosphate phosphatase-like 1	protein-coding
mm_106172.1	chr11	116679983	116679999	-	1	NA	intron (NM_009180, intron 6 of 8)	intron (NM_009180, intron 6 of 8)	5394	NR_028570	100216538		NR_028570	ENSMUSG00000065094	Snord1a	snR38	small nucleolar RNA, C/D box 1A	snoRNA
mm_131556.1	chr16	18052865	18052881	+	1	NA	promoter-TSS (NM_010047)	promoter-TSS (NM_010047)	13	NM_010047	13353	Mm.27155	NM_010047	ENSMUSG00000003531	Dgcr6	-	DiGeorge syndrome critical region gene 6	protein-coding
mm_81897.1	chr9	119895132	119895148	+	1	NA	intron (NM_026236, intron 1 of 18)	CpG	245	NM_026236	67561	Mm.104789	NM_026236	ENSMUSG00000032512	Wdr48	8430408H12Rik|Uaf1|mKIAA1449	WD repeat domain 48	protein-coding
mm_79388.1	chr9	54801761	54801774	+	1	NA	Intergenic	Intergenic	37019	NM_013496	12903	Mm.34797	NM_013496	ENSMUSG00000032291	Crabp1	AI326249|CRABP-I|Crabp-1|CrabpI|Rbp-5	cellular retinoic acid binding protein I	protein-coding
mm_83301.1	chr9	43521001	43521033	-	1	NA	Intergenic	PB1D10|SINE|Alu	210254	NM_023655	72169	Mm.273277	NM_023655	ENSMUSG00000032013	Trim29	1110047J21Rik|2810431N19Rik|4732461M22Rik|AI119726	tripartite motif-containing 29	protein-coding
mm_94047.1	chr10	128179998	128180006	-	1	NA	5' UTR (NM_001039080, exon 1 of 14)	5' UTR (NM_001039080, exon 1 of 14)	295	NM_001039080	56516	Mm.42247	NM_019711	ENSMUSG00000040043	Rbms2	2610315E04Rik|Scr3	RNA binding motif, single stranded interacting protein 2	protein-coding
mm_156714.1	chrX	159638850	159638876	+	1	NA	intron (NM_001135727, intron 1 of 17)	C-rich|Low_complexity|Low_complexity	11591	NM_001135727	58194	Mm.286495	NM_021389	ENSMUSG00000040990	Sh3kbp1	1200007H22Rik|1700125L08Rik|5830464D22Rik|AI447724|Cin85|IN85|Ruk|Seta	SH3-domain kinase binding protein 1	protein-coding
mm_9998.1	chr1	191403271	191403273	-	1	NA	Intergenic	Intergenic	-6231	NM_144880	226849	Mm.205569	NM_144880	ENSMUSG00000026626	Ppp2r5a	PR61alpha	protein phosphatase 2, regulatory subunit B', alpha	protein-coding
mm_169956.1	chr16	89635987	89635987	+	1	NA	Intergenic	Intergenic	-64804	NM_001113406	16693	Mm.310906	NM_001113406	ENSMUSG00000091212	Krtap11-1	AA162070|AA589467|AV018433|Hacl1|KAP11.1|PRED29	keratin associated protein 11-1	protein-coding
mm_121974.1	chr14	25768793	25768802	-	1	NA	promoter-TSS (NM_001101433)	promoter-TSS (NM_001101433)	59	NM_001101433	71918	Mm.41904	NM_001101433	ENSMUSG00000055538	Zcchc24	2310047A01Rik	zinc finger, CCHC domain containing 24	protein-coding
mm_11294.1	chr2	30133874	30133892	+	1	NA	5' UTR (NM_146252, exon 1 of 12)	5' UTR (NM_146252, exon 1 of 12)	137	NM_146252	70296	Mm.19172	NM_146252	ENSMUSG00000039678	Tbc1d13	2600014A06Rik|BC025586	TBC1 domain family, member 13	protein-coding
mm_91738.1	chr10	46819922	46819930	-	1	NA	Intergenic	RLTR9A|LTR|ERVK	575177	NR_028276	108637		NR_028276	ENSMUSG00000096263	Snord14c	Gm23107|Rnu14|U14	small nucleolar RNA, C/D box 14C	snoRNA
mm_106598.1	chr11	120730893	120730904	-	1	NA	exon (NM_007621, exon 3 of 8)	exon (NM_007621, exon 3 of 8)	1123	NM_007621	12409	Mm.21454	NM_007621	ENSMUSG00000025150	Cbr2	MLCR	carbonyl reductase 2	protein-coding
mm_52829.1	chr6	121359682	121359692	+	1	NA	intron (NM_001347433, intron 9 of 14)	intron (NM_001347433, intron 9 of 14)	12990	NM_133661	14411	Mm.274506	NM_133661	ENSMUSG00000030109	Slc6a12	BGT1|GAT-2|GAT2|Gabt2	solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12	protein-coding
mm_165228.1	chr2	53606376	53606403	+	1	NA	Intergenic	Intergenic	414305	NM_022989	65103	Mm.37623	NM_022989	ENSMUSG00000026960	Arl6ip6	2310057C01Rik|2610529A11Rik|Aip-6	ADP-ribosylation factor-like 6 interacting protein 6	protein-coding
mm_164251.1	chr15	97995602	97995603	-	1	NA	intron (NM_031163, intron 11 of 53)	intron (NM_031163, intron 11 of 53)	9122	NM_031163	12824	Mm.2423	NM_031163	ENSMUSG00000022483	Col2a1	Col2|Col2a|Col2a-1|Del1|Dmm|Lpk|Rgsc856	collagen, type II, alpha 1	protein-coding
mm_74110.1	chr8	122962927	122962933	+	1	NA	intron (NM_001081379, intron 2 of 12)	intron (NM_001081379, intron 2 of 12)	79354	NR_037865	77087	Mm.31567	NM_001081379	ENSMUSG00000035569	Ankrd11	2410104C19Rik|3010027A04Rik|6330578C09Rik|9530048I21Rik|AA930108|Gm176|Yod	ankyrin repeat domain 11	protein-coding
mm_22018.1	chr2	167877597	167877612	-	1	NA	Intergenic	Intergenic	-54723	NM_011201	19246	Mm.277916	NM_011201	ENSMUSG00000027540	Ptpn1	PTP-1B|PTP-HA2|PTP1B	protein tyrosine phosphatase, non-receptor type 1	protein-coding
mm_4607.1	chr1	178525720	178525735	+	1	NA	Intergenic	L1M4a2|LINE|L1	-3398	NM_001161665	269152	Mm.129727	NM_177724	ENSMUSG00000026494	Kif26b	4832420M10|BC056349|D230039L06Rik	kinesin family member 26B	protein-coding
mm_42629.1	chr5	118404884	118404890	+	1	NA	Intergenic	MTC|LTR|ERVL-MaLR	-155832	NM_001347445	76199	Mm.206238	NM_172424	ENSMUSG00000018076	Med13l	2210413I17Rik|6330591G05Rik|9030618F05Rik|Thrap2|Trap240L|mKIAA1025	mediator complex subunit 13-like	protein-coding
mm_112065.1	chr12	111981054	111981064	-	1	NA	promoter-TSS (NM_001127685)	promoter-TSS (NM_001127685)	-308	NM_001127685	217874	Mm.134213	NM_001127685	ENSMUSG00000091402	Rd3l	A930011N13	retinal degeneration 3-like	protein-coding
mm_73513.1	chr8	107368797	107368830	+	1	NA	exon (NM_018823, exon 13 of 15)	exon (NM_018823, exon 13 of 15)	34392	NM_008706	18104	Mm.252	NM_008706	ENSMUSG00000003849	Nqo1	AV001255|Dia4|Dtd|Nmo-1|Nmo1|Nmor1|Ox-1|Ox1|Qr1	NAD(P)H dehydrogenase, quinone 1	protein-coding
mm_170642.1	chr19	8989348	8989348	+	1	NA	promoter-TSS (NM_001286518)	promoter-TSS (NM_001286518)	64	NM_001286518	66395	Mm.203866	NM_009643	ENSMUSG00000069833	Ahnak	DY6	AHNAK nucleoprotein (desmoyokin)	protein-coding
mm_22341.1	chr2	180824597	180824607	-	1	NA	Intergenic	Intergenic	-47702	NM_080641	140489	Mm.134062	NM_080641	ENSMUSG00000045493	Bhlhe23	A930001L02Rik|BETA4|Beta3b|Bhlhb4	basic helix-loop-helix family, member e23	protein-coding
mm_18072.1	chr2	42652844	42652854	-	1	NA	5' UTR (NM_053011, exon 1 of 91)	5' UTR (NM_053011, exon 1 of 91)	749	NM_053011	94217	Mm.441398	NM_053011	ENSMUSG00000049252	Lrp1b	9630004P12Rik|LRP-DIT	low density lipoprotein-related protein 1B (deleted in tumors)	protein-coding
mm_87030.1	chr10	28611948	28611955	+	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	-56409	NM_001305663	210757	Mm.123021	NM_178666	ENSMUSG00000049109	Themis	E430004N04Rik|Gasp|Spot|Tsepa|thylex	thymocyte selection associated	protein-coding
mm_155583.1	chrX	78737738	78737757	+	1	NA	promoter-TSS (NM_001164739)	promoter-TSS (NM_001164739)	-16	NM_001164739	70864	Mm.66681	NM_001164739	ENSMUSG00000078315	Fam47c	4921509A18Rik|Fam47a|Fam47a-ps	family with sequence similarity 47, member C	protein-coding
mm_106669.1	chr11	121519802	121519810	-	1	NA	promoter-TSS (NM_178763)	promoter-TSS (NM_178763)	-464	NM_178763	319530	Mm.11395	NM_178763	ENSMUSG00000039238	Zfp750	A030007D23Rik|Znf750	zinc finger protein 750	protein-coding
mm_153985.1	chr19	47919194	47919235	-	1	NA	promoter-TSS (NM_001001738)	promoter-TSS (NM_001001738)	85	NM_001001738	414801	Mm.29457	NM_001001738	ENSMUSG00000044948	Itprip	4833424O12Rik|DANGER|mKIAA1754	inositol 1,4,5-triphosphate receptor interacting protein	protein-coding
mm_57662.1	chr6	128487483	128487506	-	1	NA	exon (NM_007376, exon 31 of 36)	exon (NM_007376, exon 31 of 36)	39226	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_11473.1	chr2	32376300	32376315	+	1	NA	exon (NM_001252538, exon 15 of 18)	exon (NM_001252538, exon 15 of 18)	5608	NM_198001	73737	Mm.27608	NM_198001	ENSMUSG00000039195	1110008P14Rik	C79326	RIKEN cDNA 1110008P14 gene	protein-coding
mm_134032.1	chr16	5012753	5012777	-	1	NA	intron (NM_133185, intron 2 of 10)	intron (NM_133185, intron 2 of 10)	788	NM_133185	66049	Mm.27792	NM_133185	ENSMUSG00000022540	Rogdi	0610011C19Rik|AU020118|C76152|Lzf	rogdi homolog	protein-coding
mm_21792.1	chr2	164857241	164857273	-	1	NA	intron (NM_011125, intron 1 of 15)	CpG-8831	451	NM_011125	18830	Mm.6105	NM_011125	ENSMUSG00000017754	Pltp	Bpife|OD107	phospholipid transfer protein	protein-coding
mm_80448.1	chr9	77976883	77976893	+	1	NA	exon (NM_134255, exon 5 of 8)	exon (NM_134255, exon 5 of 8)	59523	NM_134255	68801	Mm.430736	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	ELOVL family member 5, elongation of long chain fatty acids (yeast)	protein-coding
mm_107599.1	chr12	49382792	49382802	+	1	NA	promoter-TSS (NM_008241)	promoter-TSS (NM_008241)	-86	NM_001160112	15228	Mm.4704	NM_008241	ENSMUSG00000020950	Foxg1	2900064B05Rik|BF-1|Bf1|Hfh9|Hfhbf1	forkhead box G1	protein-coding
mm_23670.1	chr3	68572427	68572437	+	1	NA	promoter-TSS (NM_013928)	promoter-TSS (NM_013928)	64	NM_013928	30953	Mm.331064	NM_013928	ENSMUSG00000027777	Schip1	Nf2ip|Schip-1	schwannomin interacting protein 1	protein-coding
mm_139725.1	chr17	57476402	57476425	+	1	NA	intron (NM_010130, intron 19 of 21)	MIRc|SINE|MIR	68901	NM_001104591	224916	Mm.469889	NM_001104591	ENSMUSG00000090655	Vmn2r120	EG224916	vomeronasal 2, receptor 120	protein-coding
mm_153789.1	chr19	45840011	45840017	-	1	NA	intron (NM_198296, intron 24 of 25)	L1MB2|LINE|L1	-23951	NM_145703	80906	Mm.213204	NM_030716	ENSMUSG00000025221	Kcnip2	KChIP2	Kv channel-interacting protein 2	protein-coding
mm_89029.1	chr10	82699184	82699197	+	1	NA	exon (NM_001081218, exon 1 of 15)	exon (NM_001081218, exon 1 of 15)	183	NM_001081218	67933	Mm.127405	NM_026462	ENSMUSG00000020246	Hcfc2	1700129L13Rik|AU019838	host cell factor C2	protein-coding
mm_22537.1	chr3	8561097	8561110	+	1	NA	3' UTR (NM_025285, exon 5 of 5)	3' UTR (NM_025285, exon 5 of 5)	51576	NM_025285	20257	Mm.29580	NM_025285	ENSMUSG00000027500	Stmn2	AI159727|SCG10|Scgn10|Stmb2	stathmin-like 2	protein-coding
mm_151291.1	chr19	55316314	55316367	+	1	NA	promoter-TSS (NM_025883)	promoter-TSS (NM_025883)	283	NM_001293686	53611	Mm.258637	NM_016862	ENSMUSG00000024983	Vti1a	1110014F16Rik|1110018K19Rik|4921537J05Rik|MVti1|MVti1a|Vti1|Vti1-rp2	vesicle transport through interaction with t-SNAREs 1A	protein-coding
mm_14421.1	chr2	130479702	130479711	+	1	NA	intron (NM_001163688, intron 1 of 20)	L1MA4|LINE|L1	29428	NM_001163688	19262	Mm.224246	NM_008980	ENSMUSG00000027303	Ptpra	Ptpa|Ptpalpha|Rptpalpha|Rptra|Rptralpha	protein tyrosine phosphatase, receptor type, A	protein-coding
mm_172.1	chr1	13388829	13388854	+	1	NA	Intergenic	Intergenic	-14758	NM_008678	17978	Mm.2537	NM_008678	ENSMUSG00000005886	Ncoa2	D1Ertd433e|GRIP-1|Grip1|KAT13C|NCoA-2|SRC-2|TIF2|bHLHe75	nuclear receptor coactivator 2	protein-coding
mm_141342.1	chr17	28558263	28558324	-	1	NA	TTS (NR_105935)	TTS (NR_105935)	208	NR_105935	102465585		NR_105935	ENSMUSG00000099152	Mir6969	Gm27305|mmu-mir-6969	microRNA 6969	ncRNA
mm_73858.1	chr8	118283654	118283664	+	1	NA	promoter-TSS (NM_019707)	promoter-TSS (NM_019707)	48	NM_019707	12554	Mm.334841	NM_019707	ENSMUSG00000031841	Cdh13	4932416G01Rik|Cdht|Tcad	cadherin 13	protein-coding
mm_116605.1	chr13	48662704	48662748	-	1	NA	promoter-TSS (NM_007526)	promoter-TSS (NM_007526)	-310	NM_007526	12022	Mm.42241	NM_007526	ENSMUSG00000021381	Barx1	-	BarH-like homeobox 1	protein-coding
mm_161747.1	chr17	34048474	34048474	+	1	NA	intron (NM_001317722, intron 7 of 64)	intron (NM_001317722, intron 7 of 64)	9336	NM_001317722	12815	Mm.20230	NM_009926	ENSMUSG00000024330	Col11a2	-	collagen, type XI, alpha 2	protein-coding
mm_142764.1	chr17	49509855	49509877	-	1	NA	intron (NM_001008231, intron 1 of 25)	intron (NM_001008231, intron 1 of 25)	54471	NM_001008231	76441	Mm.211275	NM_001008231	ENSMUSG00000040260	Daam2	2310016D11Rik|AI843643|AW557870	dishevelled associated activator of morphogenesis 2	protein-coding
mm_54680.1	chr6	39419762	39419817	-	1	NA	promoter-TSS (NM_001311109)	promoter-TSS (NM_001311109)	-13	NM_001311109	54484	Mm.270484	NM_018810	ENSMUSG00000029922	Mkrn1	RFP	makorin, ring finger protein, 1	protein-coding
mm_71479.1	chr8	46617390	46617417	+	1	NA	promoter-TSS (NM_001001184)	promoter-TSS (NM_001001184)	112	NM_009810	12367	Mm.34405	NM_009810	ENSMUSG00000031628	Casp3	A830040C14Rik|AC-3|CASP-3|CC3|CPP-32|CPP32|Caspase-3|Lice|SCA-1|Yama|mldy	caspase 3	protein-coding
mm_46812.1	chr5	113081581	113081584	-	1	NA	promoter-TSS (NM_021352)	promoter-TSS (NM_021352)	2	NM_001159650	12962	Mm.378899	NM_021352	ENSMUSG00000029352	Crybb3	AI852419	crystallin, beta B3	protein-coding
mm_125785.1	chr15	74716631	74716660	+	1	NA	3' UTR (NM_028216, exon 3 of 3)	3' UTR (NM_028216, exon 3 of 3)	1806	NM_028216	72373	Mm.46395	NM_028216	ENSMUSG00000022598	Psca	2210408B04Rik	prostate stem cell antigen	protein-coding
mm_102974.1	chr11	69671245	69671284	-	1	NA	intron (NM_001159375, intron 1 of 10)	CpG	1159	NM_144958	13681	Mm.26680	NM_144958	ENSMUSG00000059796	Eif4a1	BM-010|Ddx2a|Eif4	eukaryotic translation initiation factor 4A1	protein-coding
mm_44455.1	chr5	21865607	21865617	-	1	NA	promoter-TSS (NM_030727)	promoter-TSS (NM_030727)	-8	NM_030727	80979	Mm.160370	NM_030727	ENSMUSG00000029015	Slc26a5	Pres|prestin	solute carrier family 26, member 5	protein-coding
mm_12475.1	chr2	71528604	71528645	+	1	NA	promoter-TSS (NM_010053)	promoter-TSS (NM_010053)	-821	NM_010053	13390	Mm.475101	NM_010053	ENSMUSG00000041911	Dlx1	Dlx|Dlx-1	distal-less homeobox 1	protein-coding
mm_761.1	chr1	43969860	43969865	+	1	NA	intron (NM_001310540, intron 11 of 28)	(T)n|Simple_repeat|Simple_repeat	35868	NM_009418	22019	Mm.401675	NM_009418	ENSMUSG00000041763	Tpp2	TPP-2|TppII	tripeptidyl peptidase II	protein-coding
mm_119598.1	chr14	51007942	51007948	+	1	NA	promoter-TSS (NM_029145)	promoter-TSS (NM_029145)	16	NM_029145	75019	Mm.318775	NM_029145	ENSMUSG00000021872	Rnase10	4930474F22Rik|Rah1	ribonuclease, RNase A family, 10 (non-active)	protein-coding
mm_68521.1	chr7	112003824	112003828	-	1	NA	Intergenic	Intergenic	-19680	NM_133758	74996	Mm.16974	NM_133758	ENSMUSG00000059263	Usp47	4930502N04Rik|A630020C16Rik	ubiquitin specific peptidase 47	protein-coding
mm_157713.1	chrX	66876162	66876167	-	1	NA	Intergenic	Intergenic	-37039	NR_030149	723888		NR_030149	ENSMUSG00000070071	Mir465	Mirn465|mir-465a|mmu-mir-465	microRNA 465	ncRNA
mm_44508.1	chr5	24030650	24030707	-	1	NA	promoter-TSS (NM_053090)	promoter-TSS (NM_053090)	12	NM_053090	84652	Mm.304976	NM_053090	ENSMUSG00000028995	Fam126a	AB030242|Drctnnb1a	family with sequence similarity 126, member A	protein-coding
mm_116379.1	chr13	41001133	41001151	-	1	NA	5' UTR (NM_026550, exon 1 of 10)	5' UTR (NM_026550, exon 1 of 10)	132	NM_026550	68083	Mm.24789	NM_026550	ENSMUSG00000038683	Pak1ip1	5830431I15Rik|5930415H02Rik|AA419825|AI314040|AW556169|Gdpd1|PIP1	PAK1 interacting protein 1	protein-coding
mm_19763.1	chr2	105399309	105399315	-	1	NA	promoter-TSS (NM_009037)	promoter-TSS (NM_009037)	7	NM_009037	19672	Mm.4876	NM_009037	ENSMUSG00000005973	Rcn1	Rcn	reticulocalbin 1	protein-coding
mm_77577.1	chr8	123518742	123518810	-	1	NA	promoter-TSS (NM_018855)	promoter-TSS (NM_018855)	-59	NM_018855	104346	Mm.117265	NM_018855	ENSMUSG00000040220	Gas8	Gas11	growth arrest specific 8	protein-coding
mm_117908.1	chr13	99430407	99430417	-	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-17586	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_15013.1	chr2	152604359	152604399	+	1	NA	promoter-TSS (NM_001037247)	promoter-TSS (NM_001037247)	52	NM_001037247	266620	Mm.330669	NM_001037247	ENSMUSG00000044863	Defb36	BD-36|Defb123|mBD-36	defensin beta 36	protein-coding
mm_73202.1	chr8	95678218	95678228	+	1	NA	Intergenic	CpG	-24814	NM_001195006	234593	Mm.29846	NM_145602	ENSMUSG00000036564	Ndrg4	D8Bwg1337e|Ndr1-rs|Ndr4|R74996|SMAP-8	N-myc downstream regulated gene 4	protein-coding
mm_57793.1	chr6	129275089	129275099	-	1	NA	intron (NM_001033122, intron 1 of 4)	intron (NM_001033122, intron 1 of 4)	275	NM_001033122	12515	Mm.74745	NM_001033122	ENSMUSG00000030156	Cd69	5830438K24Rik|AI452015|AIM|VEA	CD69 antigen	protein-coding
mm_92218.1	chr10	68270395	68270399	-	1	NA	intron (NM_023598, intron 2 of 9)	intron (NM_023598, intron 2 of 9)	8329	NM_023598	71371	Mm.440357	NM_023598	ENSMUSG00000019947	Arid5b	4930580B11|5430435G07Rik|AI467247|Desrt|Mrf2|Mrf2alpha|Mrf2beta	AT rich interactive domain 5B (MRF1-like)	protein-coding
mm_44464.1	chr5	22932067	22932076	-	1	NA	intron (NM_001081231, intron 1 of 3)	intron (NM_001081231, intron 1 of 3)	-185187	NR_027362	330052	Mm.459265	NR_027362	ENSMUSG00000105076	A930003O13Rik	-	RIKEN cDNA A930003O13 gene	ncRNA
mm_32719.1	chr4	116221678	116221688	+	1	NA	promoter-TSS (NM_181585)	promoter-TSS (NM_181585)	-231	NM_181585	18710	Mm.253819	NM_181585	ENSMUSG00000028698	Pik3r3	AA414954|p55pik	phosphatidylinositol 3 kinase, regulatory subunit, polypeptide 3 (p55)	protein-coding
mm_105315.1	chr11	102887707	102887717	-	1	NA	TTS (NM_025766)	TTS (NM_025766)	2543	NM_025766	66784	Mm.483216	NM_025766	ENSMUSG00000075510	Fam187a	4933439F11Rik	family with sequence similarity 187, member A	protein-coding
mm_126620.1	chr15	83149643	83149647	+	1	NA	promoter-TSS (NM_178627)	promoter-TSS (NM_178627)	0	NR_004432	104307	Mm.471434	NR_004432	ENSMUSG00000065176	Rnu12	-	RNA U12, small nuclear	snRNA
mm_25766.1	chr3	125587811	125587811	+	1	NA	intron (NM_022565, intron 4 of 13)	ID4|SINE|ID	183720	NM_022565	64580	Mm.444289	NM_022565	ENSMUSG00000027971	Ndst4	4930439H17Rik	N-deacetylase/N-sulfotransferase (heparin glucosaminyl) 4	protein-coding
mm_4565.1	chr1	177447465	177447473	+	1	NA	exon (NM_013915, exon 1 of 1)	exon (NM_013915, exon 1 of 1)	1648	NM_013915	30928	Mm.330700	NM_013915	ENSMUSG00000063659	Zbtb18	RP58|Zfp238|Znf238	zinc finger and BTB domain containing 18	protein-coding
mm_10170.1	chr2	4559702	4559706	+	1	NA	promoter-TSS (NM_001177844)	promoter-TSS (NM_001177844)	-50	NM_001177844	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding
mm_27877.1	chr3	79170473	79170512	-	1	NA	Intergenic	Intergenic	-24617	NM_001099624	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_98467.1	chr11	94949371	94949434	+	1	NA	exon (NM_007742, exon 45 of 51)	exon (NM_007742, exon 45 of 51)	13178	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_129791.1	chr15	82847866	82847868	-	1	NA	intron (NM_001114140, intron 2 of 5)	intron (NM_001114140, intron 2 of 5)	50594	NR_027799	21378	Mm.417272	NR_027799		Tbrg3	TB-11	transforming growth factor beta regulated gene 3	ncRNA
mm_31667.1	chr4	60003479	60003486	+	1	NA	promoter-TSS (NM_001081285)	promoter-TSS (NM_001081285)	-67	NM_001081285	620807	Mm.464562	NM_001081285	ENSMUSG00000078689	Mup6	Gm12544|Mup2|OTTMUSG00000007423	major urinary protein 6	protein-coding
mm_101275.1	chr11	21371144	21371221	-	1	NA	promoter-TSS (NM_139297)	promoter-TSS (NM_139297)	85	NM_001290634	216558	Mm.28877	NM_139297	ENSMUSG00000001891	Ugp2	UDPGP|UGPase	UDP-glucose pyrophosphorylase 2	protein-coding
mm_28745.1	chr3	95754797	95754803	-	1	NA	exon (NM_001163617, exon 1 of 17)	exon (NM_001163617, exon 1 of 17)	177	NM_027931	71807	Mm.271754	NM_027931	ENSMUSG00000028107	Tars2	2610024N01Rik|AI429208|Tarsl1	threonyl-tRNA synthetase 2, mitochondrial (putative)	protein-coding
mm_82644.1	chr9	22016408	22016419	-	1	NA	3' UTR (NM_010487, exon 7 of 7)	3' UTR (NM_010487, exon 7 of 7)	13425	NM_008925	19089	Mm.214593	NM_008925	ENSMUSG00000003402	Prkcsh	80K-H|PKCSH	protein kinase C substrate 80K-H	protein-coding
mm_87972.1	chr10	63457579	63457583	+	1	NA	promoter-TSS (NM_001164376)	promoter-TSS (NM_001164376)	70	NM_001164376	216033	Mm.444692	NM_177612	ENSMUSG00000060843	Ctnna3	4930429L08Rik|4933408A16|Catna3|Vr22	catenin (cadherin associated protein), alpha 3	protein-coding
mm_24336.1	chr3	89662718	89662728	+	1	NA	exon (NM_080466, exon 7 of 8)	exon (NM_080466, exon 7 of 8)	-52299	NM_001038587	56417	Mm.316628	NM_019655	ENSMUSG00000027951	Adar	AV242451|Adar1|Adar1p110|Adar1p150|mZaADAR	adenosine deaminase, RNA-specific	protein-coding
mm_73056.1	chr8	94377883	94377893	+	1	NA	Intergenic	Intergenic	-8612	NM_022331	64209	Mm.29151	NM_022331	ENSMUSG00000031770	Herpud1	Herp|Mifl|SUP	homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1	protein-coding
mm_149683.1	chr19	20492695	20492747	+	1	NA	promoter-TSS (NR_015502)	promoter-TSS (NR_015502)	6	NR_015502	320092	Mm.482524	NR_015502		E030003E18Rik	1700127G21Rik	RIKEN cDNA E030003E18 gene	ncRNA
mm_172153.1	chr6	41475587	41475602	+	1	NA	Intergenic	ETnERV-int|LTR|ERVK	16664	NM_053243	114228	Mm.449428	NM_053243	ENSMUSG00000062751	Prss1	Try-1|Try1|Trygn16	protease, serine 1 (trypsin 1)	protein-coding
mm_86439.1	chr10	3973167	3973178	+	1	NA	promoter-TSS (NM_001170785)	promoter-TSS (NM_001170785)	97	NM_172308	270685	Mm.184752	NM_172308	ENSMUSG00000040675	Mthfd1l	2410004L15Rik|AI647056|Fthfsdc1	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1-like	protein-coding
mm_108791.1	chr12	91400439	91400452	+	1	NA	promoter-TSS (NM_001113404)	promoter-TSS (NM_001113404)	-548	NM_001113404	22095	Mm.173847	NM_011648	ENSMUSG00000020963	Tshr	AI481368|hypothroid|hyt|pet	thyroid stimulating hormone receptor	protein-coding
mm_2408.1	chr1	93811810	93811846	+	1	NA	exon (NM_025454, exon 3 of 8)	exon (NM_025454, exon 3 of 8)	7863	NM_025454	66262	Mm.64065	NM_025454	ENSMUSG00000026283	Ing5	1700001C14Rik|1700027H23Rik|1810018M11Rik|AI225768	inhibitor of growth family, member 5	protein-coding
mm_80337.1	chr9	75071149	75071228	+	1	NA	promoter-TSS (NM_010864)	promoter-TSS (NM_010864)	-18	NM_010864	17918	Mm.3645	NM_010864	ENSMUSG00000034593	Myo5a	9630007J19Rik|AI413174|AI661011|Dbv|MVa|Myo5|MyoVA|Sev-1|d|d-120J|flail|flr	myosin VA	protein-coding
mm_146613.1	chr18	10052153	10052162	-	1	NA	Intergenic	MMERGLN-int|LTR|ERV1	-22008	NM_001038589	59025	Mm.329277	NM_021522	ENSMUSG00000047879	Usp14	2610005K12Rik|2610037B11Rik|AW107924|C78769|ax|nmf375	ubiquitin specific peptidase 14	protein-coding
mm_132748.1	chr16	44159691	44159726	+	1	NA	3' UTR (NM_028108, exon 5 of 5)	3' UTR (NM_028108, exon 5 of 5)	-13689	NM_001029889	207806	Mm.310566	NM_001029889	ENSMUSG00000068284	Usf3	5530400K22Rik|Gm1779|Gm608|mKIAA2018	upstream transcription factor family member 3	protein-coding
mm_88485.1	chr10	77686093	77686096	+	1	NA	promoter-TSS (NM_001287074)	promoter-TSS (NM_001287074)	-475	NM_001287074	252974	Mm.221237	NM_145855	ENSMUSG00000069581	Tspear	C330046G03Rik|ORF65|TSP-EAR|Tnep1	thrombospondin type laminin G domain and EAR repeats	protein-coding
mm_154294.1	chr19	61198750	61198767	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-22449	NM_001177513	633057	Mm.426097	NM_001177513	ENSMUSG00000094649	Gm7102	EG633057	predicted gene 7102	protein-coding
mm_134563.1	chr16	20316803	20316805	-	1	NA	intron (NM_183158, intron 2 of 8)	intron (NM_183158, intron 2 of 8)	8600	NM_183158	224044	Mm.276400	NM_183158	ENSMUSG00000022818	Cyp2ab1	EG224044|F730023N20	cytochrome P450, family 2, subfamily ab, polypeptide 1	protein-coding
mm_109188.1	chr12	108495281	108495284	+	1	NA	intron (NM_001043335, intron 4 of 21)	intron (NM_001043335, intron 4 of 21)	-59438	NM_001163394	14026	Mm.238841	NM_007965	ENSMUSG00000021262	Evl	AI528774	Ena-vasodilator stimulated phosphoprotein	protein-coding
mm_94806.1	chr11	23008522	23008532	+	1	NA	Intergenic	CpG	-4860	NM_028672	73873	Mm.252406	NM_028672	ENSMUSG00000049811	Fam161a	4930430E16Rik	family with sequence similarity 161, member A	protein-coding
mm_120976.1	chr14	78650930	78650938	+	1	NA	intron (NM_001081336, intron 3 of 28)	intron (NM_001081336, intron 3 of 28)	-6483	NR_104044	380921	Mm.89591	NM_001081336	ENSMUSG00000034731	Dgkh	5930402B05Rik|D130015C16|DGK	diacylglycerol kinase, eta	protein-coding
mm_157090.1	chrX	9437084	9437119	-	1	NA	3' UTR (NM_007807, exon 13 of 13)	3' UTR (NM_007807, exon 13 of 13)	32223	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_53702.1	chr6	142882808	142882855	+	1	NA	intron (NM_011374, intron 2 of 4)	intron (NM_011374, intron 2 of 4)	68600	NR_045707	665037	Mm.401493	NR_045707	ENSMUSG00000072683	Gm7457	EG665037|ENSMUSG00000072683	predicted gene 7457	ncRNA
mm_165111.1	chr19	58144020	58144036	+	1	NA	Intergenic	Intergenic	92861	NR_049196	100885835		NR_049196	ENSMUSG00000093757	Mir5623	Gm26068|mir-5623|mmu-mir-5623	microRNA 5623	ncRNA
mm_74032.1	chr8	121806387	121806397	+	1	NA	intron (NM_145605, intron 6 of 11)	intron (NM_145605, intron 6 of 11)	23177	NM_145605	234825	Mm.209329	NM_145605	ENSMUSG00000040263	Klhdc4	AA408426|AV352552|BC012312|G430025P05Rik	kelch domain containing 4	protein-coding
mm_95886.1	chr11	58104083	58104137	+	1	NA	promoter-TSS (NM_026949)	promoter-TSS (NM_026949)	-43	NM_026949	69125	Mm.28910	NM_026949	ENSMUSG00000020515	Cnot8	1500015I04Rik|1810022F04Rik|AA536816|AU015770|AU043059	CCR4-NOT transcription complex, subunit 8	protein-coding
mm_118237.1	chr13	111748224	111748227	-	1	NA	3' UTR (NM_011945, exon 20 of 20)	3' UTR (NM_011945, exon 20 of 20)	60758	NM_011945	26401	Mm.15918	NM_011945	ENSMUSG00000021754	Map3k1	MAPKKK1|MEKK1|Mekk	mitogen-activated protein kinase kinase kinase 1	protein-coding
mm_43967.1	chr5	145371717	145371718	+	1	NA	intron (NM_001100180, intron 7 of 12)	L1M4|LINE|L1	26447	NM_001100180	622127	Mm.359379	NM_001100180	ENSMUSG00000070419	Cyp3a57	EG622127	cytochrome P450, family 3, subfamily a, polypeptide 57	protein-coding
mm_79783.1	chr9	62868705	62868715	+	1	NA	exon (NM_138304, exon 3 of 5)	exon (NM_138304, exon 3 of 5)	-6686	NR_003965	677044	Mm.422004	NR_003965	ENSMUSG00000074250	Gm10653	ENSMUSG00000074250	ribsomal protein S2 pseudogene	pseudo
mm_56835.1	chr6	117175002	117175019	-	1	NA	TTS (NM_021704)	TTS (NM_021704)	6475	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_129573.1	chr15	79729125	79729133	-	1	NA	intron (NM_001205346, intron 10 of 17)	intron (NM_001205346, intron 10 of 17)	13407	NM_194342	223697	Mm.202715	NM_194342	ENSMUSG00000042524	Sun2	B230369L08Rik|C030011B15|Unc84b	Sad1 and UNC84 domain containing 2	protein-coding
mm_11896.1	chr2	49846318	49846356	+	1	NA	intron (NM_027990, intron 1 of 9)	intron (NM_027990, intron 1 of 9)	58651	NM_027990	71897	Mm.41381	NM_027990	ENSMUSG00000026765	Lypd6b	2310010M24Rik|AW049525	LY6/PLAUR domain containing 6B	protein-coding
mm_3701.1	chr1	153762623	153762638	+	1	NA	3' UTR (NM_011882, exon 9 of 9)	3' UTR (NM_011882, exon 9 of 9)	13204	NM_011882	24014	Mm.259254	NM_011882	ENSMUSG00000066800	Rnasel	E230029I04Rik	ribonuclease L (2', 5'-oligoisoadenylate synthetase-dependent)	protein-coding
mm_4791.1	chr1	184536768	184536770	+	1	NA	intron (NR_040472, intron 2 of 5)	intron (NR_040472, intron 2 of 5)	20922	NR_040472	73590	Mm.82792	NR_040472	ENSMUSG00000101574	1700112H15Rik	-	RIKEN cDNA 1700112H15 gene	ncRNA
mm_163908.1	chr14	31210749	31210759	+	1	NA	intron (NM_009393, intron 4 of 5)	B1_Mus1|SINE|Alu	2442	NM_009393	21924	Mm.439921	NM_009393	ENSMUSG00000091898	Tnnc1	AI874626|TnC|cTnC|cTnI|tncc	troponin C, cardiac/slow skeletal	protein-coding
mm_133874.1	chr16	96383899	96383910	+	1	NA	intron (NM_001177886, intron 4 of 8)	intron (NM_001177886, intron 4 of 8)	22140	NM_028078	72058	Mm.119714	NM_028078	ENSMUSG00000000159	Igsf5	2010003D20Rik|JCAM|Jam4	immunoglobulin superfamily, member 5	protein-coding
mm_89701.1	chr10	97646986	97646998	+	1	NA	intron (NM_007884, intron 1 of 7)	intron (NM_007884, intron 1 of 7)	2924	NM_007884	13516	Mm.148886	NM_007884	ENSMUSG00000019936	Epyc	Dspg3|PG-Lb|SLRR3B	epiphycan	protein-coding
mm_126973.1	chr15	93412796	93412812	+	1	NA	intron (NM_175363, intron 2 of 8)	intron (NM_175363, intron 2 of 8)	14340	NM_001285863	223828	Mm.74208	NM_146062	ENSMUSG00000036167	Pphln1	CR|HSPC206|HSPC232	periphilin 1	protein-coding
mm_139668.1	chr17	57411968	57411983	+	1	NA	intron (NM_010130, intron 9 of 21)	ORR1D2|LTR|ERVL-MaLR	53289	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_142721.1	chr17	48146224	48146232	-	1	NA	promoter-TSS (NM_177824)	promoter-TSS (NM_177824)	79	NM_001177897	328829	Mm.466999	NM_177824	ENSMUSG00000073386	9830107B12Rik	Trem5	RIKEN cDNA 9830107B12 gene	protein-coding
mm_32239.1	chr4	102306370	102306372	+	1	NA	intron (NM_019840, intron 1 of 14)	intron (NM_019840, intron 1 of 14)	51432	NM_019840	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_86266.1	chr9	121705349	121705364	-	1	NA	promoter-TSS (NM_178677)	promoter-TSS (NM_178677)	-327	NM_178677	215474	Mm.31421	NM_178677	ENSMUSG00000061536	Sec22c	4932412K21|5930407I15Rik|C530046H07|Sec22l3	SEC22 homolog C, vesicle trafficking protein	protein-coding
mm_44320.1	chr5	9725230	9725248	-	1	NA	5' UTR (NM_181850, exon 1 of 6)	5' UTR (NM_181850, exon 1 of 6)	113	NM_181850	108069	Mm.318966	NM_181850	ENSMUSG00000003974	Grm3	0710001G23Rik|Gprc1c|mGlu3|mGluR3	glutamate receptor, metabotropic 3	protein-coding
mm_43626.1	chr5	138172111	138172132	+	1	NA	promoter-TSS (NM_008568)	promoter-TSS (NM_008568)	100	NM_021392	11781	Mm.113205	NM_021392	ENSMUSG00000019518	Ap4m1	4930443L05Rik|Ap4m4	adaptor-related protein complex AP-4, mu 1	protein-coding
mm_138513.1	chr17	35237674	35237693	+	1	NA	exon (NM_023179, exon 3 of 3)	exon (NM_023179, exon 3 of 3)	1087	NM_023179	66237	Mm.396107	NM_023179	ENSMUSG00000024403	Atp6v1g2	1500002D01Rik|Atp6g2|NG38|VAG2	ATPase, H+ transporting, lysosomal V1 subunit G2	protein-coding
mm_57690.1	chr6	128519496	128519520	-	1	NA	exon (NM_007376, exon 8 of 36)	exon (NM_007376, exon 8 of 36)	7212	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_98136.1	chr11	87566681	87566710	+	1	NA	Intergenic	Intergenic	-11694	NM_001284398	18952	Mm.2214	NM_011129	ENSMUSG00000020486	Sept4	ARTS|Bh5|OTTMUSG00000001265|Pnutl2	septin 4	protein-coding
mm_33794.1	chr4	134924359	134924375	+	1	NA	exon (NM_023665, exon 2 of 5)	exon (NM_023665, exon 2 of 5)	742	NM_023665	27981	Mm.331964	NM_023665	ENSMUSG00000037266	Rsrp1	2700043I21Rik|D4Ucla2|D4Wsu53e	arginine/serine rich protein 1	protein-coding
mm_827.1	chr1	51083516	51083518	+	1	NA	intron (NM_019790, intron 5 of 9)	RMER4B|LTR|ERVK	155994	NM_019790	56363	Mm.245154	NM_019790	ENSMUSG00000026109	Tmeff2	4832418D20Rik|7630402F16Rik|TR-2	transmembrane protein with EGF-like and two follistatin-like domains 2	protein-coding
mm_7443.1	chr1	120120054	120120085	-	1	NA	intron (NM_007830, intron 1 of 3)	intron (NM_007830, intron 1 of 3)	850	NM_001037999	13167	Mm.2785	NM_007830	ENSMUSG00000026385	Dbi	ACBD1|Acbp|EP|endozepine	diazepam binding inhibitor	protein-coding
mm_139351.1	chr17	50509271	50509354	+	1	NA	promoter-TSS (NM_013880)	promoter-TSS (NM_013880)	-235	NM_013880	224860	Mm.217362	NM_013880	ENSMUSG00000038910	Plcl2	PLC-L2|PRIP-2|Plce2|mKIAA1092	phospholipase C-like 2	protein-coding
mm_16137.1	chr2	170526734	170526774	+	1	NA	Intergenic	RLTR17|LTR|ERVK	-14827	NR_040367	100502946	Mm.421284	NR_040367	ENSMUSG00000085495	Gm16796	-	predicted gene, 16796	ncRNA
mm_94496.1	chr11	7063733	7063758	+	1	NA	exon (NM_009622, exon 1 of 20)	exon (NM_009622, exon 1 of 20)	256	NM_009622	432530	Mm.259733	NM_009622	ENSMUSG00000020431	Adcy1	AC1|D11Bwg1392e|I-AC|brl|mKIAA4070	adenylate cyclase 1	protein-coding
mm_115832.1	chr13	21286972	21286972	-	1	NA	3' UTR (NM_010343, exon 5 of 5)	3' UTR (NM_010343, exon 5 of 5)	5714	NM_010343	14780	Mm.1332	NM_010343	ENSMUSG00000004344	Gpx5	AV379049|Arep	glutathione peroxidase 5	protein-coding
mm_33398.1	chr4	129820722	129820786	+	1	NA	promoter-TSS (NM_001164745)	promoter-TSS (NM_001164745)	46	NM_001164745	19244	Mm.193688	NM_008974	ENSMUSG00000028788	Ptp4a2	Prl-2	protein tyrosine phosphatase 4a2	protein-coding
mm_93498.1	chr10	112928404	112928416	-	1	NA	3' UTR (NM_001033474, exon 1 of 1)	3' UTR (NM_001033474, exon 1 of 1)	616	NM_001033474	382423	Mm.431239	NM_001033474	ENSMUSG00000074748	Atxn7l3b	4921506J03Rik|6230409E21Rik|AI315132|ENSMUSG00000074747	ataxin 7-like 3B	protein-coding
mm_133665.1	chr16	92058077	92058086	+	1	NA	promoter-TSS (NM_080456)	promoter-TSS (NM_080456)	-241	NM_017391	53881	Mm.217354	NM_017391	ENSMUSG00000089774	Slc5a3	AA623876|BF642829|Smit1	solute carrier family 5 (inositol transporters), member 3	protein-coding
mm_51154.1	chr6	70719203	70719215	+	1	NA	Intergenic	Intergenic	72966	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_45536.1	chr5	72763744	72763779	-	1	NA	exon (NM_001113460, exon 15 of 19)	exon (NM_001113460, exon 15 of 19)	-10984	NM_001122754	22165	Mm.3264	NM_013698	ENSMUSG00000054892	Txk	A130089B16Rik|Btkl|PTK-RL-18|PTK4|Rlk	TXK tyrosine kinase	protein-coding
mm_31626.1	chr4	59221620	59221632	+	1	NA	3' UTR (NM_011673, exon 9 of 9)	3' UTR (NM_011673, exon 9 of 9)	32076	NM_011673	22234	Mm.198803	NM_011673	ENSMUSG00000028381	Ugcg	AU043821|C80537|Epcs21|GlcT-1|Ugcgl	UDP-glucose ceramide glucosyltransferase	protein-coding
mm_59278.1	chr7	24904417	24904459	+	1	NA	promoter-TSS (NM_001130152)	promoter-TSS (NM_001130152)	92	NM_001130152	16801	Mm.3181	NM_008488	ENSMUSG00000040940	Arhgef1	Lbcl2|Lsc	Rho guanine nucleotide exchange factor (GEF) 1	protein-coding
mm_18345.1	chr2	58157065	58157089	-	1	NA	intron (NM_139200, intron 1 of 7)	intron (NM_139200, intron 1 of 7)	3045	NM_139200	227929	Mm.273905	NM_139200	ENSMUSG00000026832	Cytip	A130053M09Rik|AI462064|C80816|Cbp|Cybr|Pscdbp	cytohesin 1 interacting protein	protein-coding
mm_30887.1	chr4	32250575	32250589	+	1	NA	Intergenic	Intergenic	-166853	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_171129.1	chr3	146499940	146499944	+	1	NA	promoter-TSS (NM_001316756)	promoter-TSS (NM_001316756)	106	NM_010318	14707	Mm.140804	NM_010318	ENSMUSG00000068523	Gng5	G(y)5	guanine nucleotide binding protein (G protein), gamma 5	protein-coding
mm_42848.1	chr5	122206793	122206829	+	1	NA	Intergenic	Intergenic	-2918	NM_001042489	74096	Mm.28804	NM_028752	ENSMUSG00000064267	Hvcn1	0610039P13Rik|AI450555|BTS|HV1|Vsop.|mVSOP	hydrogen voltage-gated channel 1	protein-coding
mm_61961.1	chr7	90302360	90302397	+	1	NA	promoter-TSS (NM_001040085)	promoter-TSS (NM_001040085)	23	NR_110348	83671	Mm.26751	NM_031394	ENSMUSG00000030616	Sytl2	AI266830|Slp2|mKIAA1597	synaptotagmin-like 2	protein-coding
mm_51184.1	chr6	70844584	70844594	+	1	NA	promoter-TSS (NM_010121)	promoter-TSS (NM_010121)	74	NM_001313918	13666	Mm.247167	NM_010121	ENSMUSG00000031668	Eif2ak3	Pek|Perk	eukaryotic translation initiation factor 2 alpha kinase 3	protein-coding
mm_91437.1	chr10	33809572	33809573	-	1	NA	Intergenic	Intergenic	-27457	NM_001101452	215895	Mm.473684	NM_001101452	ENSMUSG00000090298	Sult3a2	EG215895|Gm4794	sulfotransferase family 3A, member 2	protein-coding
mm_18802.1	chr2	73892589	73892616	-	1	NA	promoter-TSS (NM_009715)	promoter-TSS (NM_009715)	37	NM_001284371	11909	Mm.209903	NM_009715	ENSMUSG00000027104	Atf2	Atf-2|CRE-BP|Creb2|D130078H02Rik|D18875|Tg(Gzma-Klra1)7Wum|mXBP	activating transcription factor 2	protein-coding
mm_67540.1	chr7	81455442	81455478	-	1	NA	promoter-TSS (NM_001252526)	promoter-TSS (NM_001252526)	-702	NM_001252526	12877	Mm.273122	NM_007755	ENSMUSG00000025586	Cpeb1	AU024112|Cpeb|mCPEB	cytoplasmic polyadenylation element binding protein 1	protein-coding
mm_20900.1	chr2	149092418	149092426	-	1	NA	Intergenic	Intergenic	-216910	NM_009976	13010	Mm.4263	NM_009976	ENSMUSG00000027447	Cst3	CysC	cystatin C	protein-coding
mm_154336.1	chrM	4006	4014	+	1	NA	NA	Intergenic	NA	NA								
mm_79706.1	chr9	61139187	61139207	+	1	NA	non-coding (NR_045705, exon 1 of 3)	non-coding (NR_045705, exon 1 of 3)	682	NR_045705	619328	Mm.325722	NR_045705	ENSMUSG00000110998	I730028E13Rik	-	RIKEN cDNA I730028E13 gene	ncRNA
mm_56103.1	chr6	87467952	87467977	-	1	NA	exon (NM_001286610, exon 6 of 10)	exon (NM_001286610, exon 6 of 10)	28363	NR_104483	232201	Mm.119564	NM_175476	ENSMUSG00000030047	Arhgap25	A130039I20Rik	Rho GTPase activating protein 25	protein-coding
mm_170859.1	chr2	180725310	180725311	+	1	NA	promoter-TSS (NM_183161)	promoter-TSS (NM_183161)	-29	NM_183161	228993	Mm.87189	NM_183161	ENSMUSG00000023393	Slc17a9	1700019H03Rik|BC019537|Vnut	solute carrier family 17, member 9	protein-coding
mm_131676.1	chr16	20673265	20673362	+	1	NA	intron (NM_001304432, intron 1 of 31)	CpG	586	NM_001304432	208643	Mm.260256	NM_145941	ENSMUSG00000045983	Eif4g1	E030015G23Rik|eIF-4-gamma 1|eIF-4G 1|eIF-4G1|eIF4GI	eukaryotic translation initiation factor 4, gamma 1	protein-coding
mm_136074.1	chr16	84831787	84831799	-	1	NA	intron (NM_001302215, intron 1 of 3)	intron (NM_001302215, intron 1 of 3)	3205	NM_001302216	11957	Mm.353	NM_016755	ENSMUSG00000022890	Atp5j	CF6	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit F	protein-coding
mm_46953.1	chr5	114952751	114952763	-	1	NA	exon (NM_009327, exon 7 of 10)	exon (NM_009327, exon 7 of 10)	10555	NM_028211	72357	Mm.292672	NM_028211	ENSMUSG00000029559	2210016L21Rik	-	RIKEN cDNA 2210016L21 gene	protein-coding
mm_149076.1	chr19	8883866	8883909	+	1	NA	promoter-TSS (NM_001286103)	promoter-TSS (NM_001286103)	9	NM_001286103	102308570	Mm.27503	NM_001286103	ENSMUSG00000096740	Lbhd1	Gm21743	LBH domain containing 1	protein-coding
mm_76842.1	chr8	105289121	105289138	-	1	NA	TTS (NM_177788)	TTS (NM_177788)	399	NM_001166394	74356	Mm.204876	NM_028888	ENSMUSG00000014837	4931428F04Rik	AI426165|Kiaa0895l	RIKEN cDNA 4931428F04 gene	protein-coding
mm_129252.1	chr15	76669866	76669890	-	1	NA	promoter-TSS (NM_007989)	promoter-TSS (NM_007989)	70	NM_007989	14106	Mm.42011	NM_007989	ENSMUSG00000033837	Foxh1	Fast1|Fast2|fast-1|fast-2	forkhead box H1	protein-coding
mm_43204.1	chr5	129096781	129096800	+	1	NA	promoter-TSS (NM_001081342)	promoter-TSS (NM_001081342)	40	NM_001347486	243277	Mm.440501	NM_177734	ENSMUSG00000044017	Adgrd1	E230012M21Rik|Gpr133	adhesion G protein-coupled receptor D1	protein-coding
mm_49176.1	chr6	14901606	14901614	+	1	NA	5' UTR (NM_053242, exon 1 of 19)	5' UTR (NM_053242, exon 1 of 19)	261	NM_053242	114142	Mm.332919	NM_053242	ENSMUSG00000029563	Foxp2	2810043D05Rik|AI449000|CAG-16|D0Kist7	forkhead box P2	protein-coding
mm_168686.1	chr11	96065397	96065397	-	1	NA	promoter-TSS (NM_172300)	promoter-TSS (NM_172300)	-33	NM_172300	268470	Mm.38802	NM_172300	ENSMUSG00000014349	Ube2z	AW049199|C030047H17Rik|D11Moh35	ubiquitin-conjugating enzyme E2Z	protein-coding
mm_65044.1	chr7	18567519	18567523	-	1	NA	promoter-TSS (NM_001037168)	promoter-TSS (NM_001037168)	-216	NM_001037168	545925	Mm.440302	NM_001037168	ENSMUSG00000070797	Psg27	EG545925|cea15	pregnancy-specific glycoprotein 27	protein-coding
mm_58806.1	chr7	16310413	16310444	+	1	NA	intron (NM_133234, intron 1 of 3)	CpG	845	NM_133234	170770	Mm.7660	NM_133234	ENSMUSG00000002083	Bbc3	PUMA|PUMA/JFY1	BCL2 binding component 3	protein-coding
mm_116996.1	chr13	56548535	56548547	-	1	NA	promoter-TSS (NM_010702)	promoter-TSS (NM_010702)	-3	NM_010702	16841	Mm.16973	NM_010702	ENSMUSG00000021539	Lect2	-	leukocyte cell-derived chemotaxin 2	protein-coding
mm_28453.1	chr3	90659424	90659436	-	1	NA	Intergenic	Intergenic	5128	NM_199422	381493	Mm.291525	NM_199422	ENSMUSG00000063767	S100a7a	AY465109|Gm1020|S100A7L1|S100A7f|S100a15|S100a15a|S100a17l1	S100 calcium binding protein A7A	protein-coding
mm_46492.1	chr5	105132356	105132381	-	1	NA	intron (NM_008620, intron 3 of 10)	L1M2|LINE|L1	7184	NM_008620	17472	Mm.440525	NM_008620	ENSMUSG00000079363	Gbp4	AW228052|Mag-2|Mpa-2|Mpa2	guanylate binding protein 4	protein-coding
mm_88395.1	chr10	76562271	76562328	+	1	NA	promoter-TSS (NM_029661)	promoter-TSS (NM_029661)	27	NM_029661	76573	Mm.45611	NM_029661	ENSMUSG00000009115	Spatc1l	1700022B01Rik|1700027D21Rik|AA062323	spermatogenesis and centriole associated 1 like	protein-coding
mm_56170.1	chr6	88000333	88000345	-	1	NA	3' UTR (NM_009005, exon 6 of 6)	3' UTR (NM_009005, exon 6 of 6)	18656	NR_026990	434064	Mm.371796	NR_026990	ENSMUSG00000084950	Gm5577	EG434064	predicted gene 5577	ncRNA
mm_60164.1	chr7	40893673	40893686	+	1	NA	intron (NR_040329, intron 1 of 4)	intron (NR_040329, intron 1 of 4)	4645	NR_040329	320210	Mm.126237	NR_040329	ENSMUSG00000100600	A230077H06Rik	-	RIKEN cDNA A230077H06 gene	ncRNA
mm_121246.1	chr14	103057264	103057275	+	1	NA	TTS (NM_008392)	TTS (NM_008392)	10257	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_12065.1	chr2	59504856	59504858	+	1	NA	3' UTR (NM_029723, exon 4 of 4)	3' UTR (NM_029723, exon 4 of 4)	20204	NM_029723	76747	Mm.275769	NM_029723	ENSMUSG00000026989	Dapl1	2310032F03Rik|EEDA	death associated protein-like 1	protein-coding
mm_74369.1	chr8	128479695	128479706	+	1	NA	intron (NM_008737, intron 10 of 16)	intron (NM_008737, intron 10 of 16)	120459	NR_035436	100316680		NR_035436	ENSMUSG00000084523	Mir1903	Mirn1903|mmu-mir-1903	microRNA 1903	ncRNA
mm_45271.1	chr5	64680328	64680342	-	1	NA	Intergenic	Intergenic	-69636	NR_045078	100042198	Mm.25191	NR_045078	ENSMUSG00000105402	Gm3716	Gm1683	predicted gene 3716	ncRNA
mm_146763.1	chr18	16809234	16809324	-	1	NA	promoter-TSS (NM_007664)	promoter-TSS (NM_007664)	-33	NM_007664	12558	Mm.257437	NM_007664	ENSMUSG00000024304	Cdh2	CDHN|N-CAD|Ncad	cadherin 2	protein-coding
mm_55544.1	chr6	70918916	70918935	-	1	NA	promoter-TSS (NM_028825)	promoter-TSS (NM_028825)	-3	NM_028825	74221	Mm.273326	NM_028825	ENSMUSG00000051896	Tex37	1700011F03Rik	testis expressed 37	protein-coding
mm_95855.1	chr11	57973185	57973199	+	1	NA	Intergenic	Intergenic	-35872	NM_028451	73158	Mm.248843	NM_028451	ENSMUSG00000037331	Larp1	1810024J12Rik|3110040D16Rik|Larp|mKIAA0731	La ribonucleoprotein domain family, member 1	protein-coding
mm_117237.1	chr13	64307065	64307068	-	1	NA	intron (NM_025370, intron 4 of 5)	MTE-int|LTR|ERVL-MaLR	5644	NM_025370	66129	Mm.491110	NM_025370	ENSMUSG00000021482	Aaed1	1110018J18Rik|AI849003	AhpC/TSA antioxidant enzyme domain containing 1	protein-coding
mm_169588.1	chr15	25840634	25840653	-	1	NA	Intergenic	Intergenic	-2655	NM_001034851	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_30234.1	chr3	146108010	146108033	-	1	NA	promoter-TSS (NM_172864)	promoter-TSS (NM_172864)	15	NM_172864	242253	Mm.235040	NM_172864	ENSMUSG00000043020	Wdr63	4931433A13Rik	WD repeat domain 63	protein-coding
mm_146215.1	chr18	76954896	76954906	+	1	NA	intron (NM_001039202, intron 2 of 4)	intron (NM_001039202, intron 2 of 4)	10483	NM_001039201	76987	Mm.236127	NM_029826	ENSMUSG00000025421	Hdhd2	0610039H12Rik|3110052N05Rik	haloacid dehalogenase-like hydrolase domain containing 2	protein-coding
mm_69082.1	chr7	127014586	127014605	-	1	NA	promoter-TSS (NM_080638)	promoter-TSS (NM_080638)	-1	NM_080638	78388	Mm.228797	NM_080638	ENSMUSG00000030681	Mvp	2310009M24Rik|LRP|VAULT1	major vault protein	protein-coding
mm_109658.1	chr12	113014503	113014513	+	1	NA	promoter-TSS (NM_001291445)	promoter-TSS (NM_001291445)	0	NM_001291445	217893	Mm.35754	NM_198165	ENSMUSG00000021143	Pacs2	6720425G15Rik|AW208651|AW489976|E230011J22|Pacs1l|mKIAA0602	phosphofurin acidic cluster sorting protein 2	protein-coding
mm_151033.1	chr19	47015300	47015314	+	1	NA	promoter-TSS (NM_001164363)	promoter-TSS (NM_001164363)	-118	NM_001164363	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_54718.1	chr6	40401772	40401775	-	1	NA	Intergenic	Intergenic	34360	NM_175528	243780	Mm.333006	NM_175528	ENSMUSG00000037172	E330009J07Rik	AI841796|Lchn|mKIAA1147	RIKEN cDNA E330009J07 gene	protein-coding
mm_192.1	chr1	15804358	15804367	+	1	NA	Intergenic	RMER17A|LTR|ERVK	-1284	NM_009352	21749	Mm.4306	NM_009352	ENSMUSG00000025925	Terf1	Pin2|Trbf1|Trf1	telomeric repeat binding factor 1	protein-coding
mm_96760.1	chr11	69914180	69914193	+	1	NA	promoter-TSS (NM_019726)	promoter-TSS (NM_019726)	-6	NM_019726	56310	Mm.477738	NM_019726	ENSMUSG00000023170	Gps2	AI505953	G protein pathway suppressor 2	protein-coding
mm_162744.1	chr10	56389332	56389376	+	1	NA	3' UTR (NM_010288, exon 2 of 2)	3' UTR (NM_010288, exon 2 of 2)	12054	NM_010288	14609	Mm.378921	NM_010288	ENSMUSG00000050953	Gja1	AU042049|AW546267|Cnx43|Cx43|Cx43alpha1|Gja-1|Npm1|connexin43	gap junction protein, alpha 1	protein-coding
mm_112740.1	chr13	19339817	19339829	+	1	NA	Intergenic	Intergenic	55990	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_121781.1	chr14	19890818	19890837	-	1	NA	intron (NM_001038637, intron 4 of 4)	intron (NM_001038637, intron 4 of 4)	51902	NR_105025	52512	Mm.483998	NR_105025		D14Ertd670e	-	DNA segment, Chr 14, ERATO Doi 670, expressed	ncRNA
mm_168389.1	chr11	26650956	26650971	+	1	NA	Intergenic	RLTR9E|LTR|ERVK	-57043	NM_001252447	69922	Mm.285351	NM_027260	ENSMUSG00000064090	Vrk2	2810003O05Rik|AI447698	vaccinia related kinase 2	protein-coding
mm_149874.1	chr19	25175080	25175090	+	1	NA	intron (NM_028785, intron 37 of 47)	intron (NM_028785, intron 37 of 47)	-62117	NM_181404	107351	Mm.260722	NM_181404	ENSMUSG00000032702	Kank1	A930031B09Rik|AU015049|AW121052|Ankrd15|D330024H06Rik|mKIAA0172	KN motif and ankyrin repeat domains 1	protein-coding
mm_70720.1	chr8	15726534	15726536	+	1	NA	Intergenic	Intergenic	442303	NR_037214	100526464		NR_037214	ENSMUSG00000093142	Mir3106	mir-3106|mmu-mir-3106	microRNA 3106	ncRNA
mm_101732.1	chr11	43157806	43157822	-	1	NA	intron (NM_176999, intron 3 of 22)	intron (NM_176999, intron 3 of 22)	7937	NM_176999	319767	Mm.252339	NM_176999	ENSMUSG00000055415	Atp10b	5930426O13Rik|9030605H24Rik	ATPase, class V, type 10B	protein-coding
mm_149801.1	chr19	23687417	23687463	+	1	NA	promoter-TSS (NM_028208)	promoter-TSS (NM_028208)	40	NM_028208	72351	Mm.474795	NM_028208	ENSMUSG00000074925	Ptar1	1700084D09Rik|2010013L17Rik|4930428J16Rik|AI449677	protein prenyltransferase alpha subunit repeat containing 1	protein-coding
mm_126558.1	chr15	82147629	82147660	+	1	NA	intron (NM_033218, intron 1 of 18)	CpG	375	NM_033218	20788	Mm.9002	NM_033218	ENSMUSG00000022463	Srebf2	AI608257|SREBP-2|SREBP2|SREBP2gc|bHLHd2|lop13|nuc	sterol regulatory element binding factor 2	protein-coding
mm_66356.1	chr7	43527845	43527865	-	1	NA	3' UTR (NM_001111058, exon 7 of 7)	3' UTR (NM_001111058, exon 7 of 7)	5316	NM_001111058	12489	Mm.140157	NM_021293	ENSMUSG00000004609	Cd33	Siglec-3|gp67	CD33 antigen	protein-coding
mm_10339.1	chr2	11645731	11645770	+	1	NA	intron (NM_008367, intron 1 of 7)	intron (NM_008367, intron 1 of 7)	2958	NM_008367	16184	Mm.915	NM_008367	ENSMUSG00000026770	Il2ra	CD25|Il2r|Ly-43	interleukin 2 receptor, alpha chain	protein-coding
mm_32974.1	chr4	120097186	120097206	+	1	NA	exon (NM_010657, exon 4 of 9)	exon (NM_010657, exon 4 of 9)	-64010	NM_007902	13615	Mm.284855	NM_007902	ENSMUSG00000028635	Edn2	ET-2|PPET2|VIC	endothelin 2	protein-coding
mm_138381.1	chr17	35027538	35027547	+	1	NA	TTS (NM_138582)	TTS (NM_138582)	474	NR_028258	78376	Mm.390966	NM_023893	ENSMUSG00000036185	Sapcd1	2810436B06Rik|G7d|Ng23	suppressor APC domain containing 1	protein-coding
mm_53932.1	chr6	4747046	4747056	-	1	NA	promoter-TSS (NM_130877)	promoter-TSS (NM_130877)	153	NM_001130188	20392	Mm.8739	NM_011360	ENSMUSG00000004631	Sgce	e-SG	sarcoglycan, epsilon	protein-coding
mm_27448.1	chr3	52009067	52009095	-	1	NA	intron (NM_001004176, intron 1 of 4)	intron (NM_001004176, intron 1 of 4)	95925	NM_001004176	433586	Mm.234972	NM_001004176	ENSMUSG00000061143	Maml3	AV234550|BC049812|Mam-2|mKIAA1816	mastermind like 3 (Drosophila)	protein-coding
mm_115232.1	chr13	109903090	109903110	+	1	NA	promoter-TSS (NR_035442)	promoter-TSS (NR_035442)	-709	NR_035442	100316683		NR_035442	ENSMUSG00000084651	Mir1904	Mirn1904|mmu-mir-1904	microRNA 1904	ncRNA
mm_71329.1	chr8	45007226	45007254	+	1	NA	intron (NM_001081286, intron 2 of 25)	intron (NM_001081286, intron 2 of 25)	57032	NM_001081286	14107	Mm.27365	NM_001081286	ENSMUSG00000070047	Fat1	2310038E12Rik|AU023433|Fath|mFat1	FAT atypical cadherin 1	protein-coding
mm_2470.1	chr1	105669810	105669812	+	1	NA	intron (NM_173187, intron 1 of 28)	intron (NM_173187, intron 1 of 28)	5950	NM_173187	227446	Mm.337339	NM_029349	ENSMUSG00000026319	2310035C23Rik	6430401N10|Kiaa1468|mKIAA1468	RIKEN cDNA 2310035C23 gene	protein-coding
mm_139433.1	chr17	53570238	53570240	+	1	NA	intron (NM_020005, intron 1 of 17)	intron (NM_020005, intron 1 of 17)	3268	NM_020005	18519	Mm.255025	NM_020005	ENSMUSG00000000708	Kat2b	A930006P13Rik|AI461839|AW536563|Pcaf|p/CAF	K(lysine) acetyltransferase 2B	protein-coding
mm_38301.1	chr4	136896344	136896354	-	1	NA	exon (NM_007572, exon 3 of 3)	exon (NM_007572, exon 3 of 3)	2495	NM_007572	12259	Mm.439957	NM_007572	ENSMUSG00000036887	C1qa	AI255395|C1q	complement component 1, q subcomponent, alpha polypeptide	protein-coding
mm_112367.1	chr12	119160914	119160921	-	1	NA	Intergenic	Intergenic	77359	NM_177290	320910	Mm.217000	NM_177290	ENSMUSG00000025321	Itgb8	4832412O06Rik	integrin beta 8	protein-coding
mm_141945.1	chr17	35061492	35061497	-	1	NA	exon (NM_016765, exon 6 of 7)	exon (NM_016765, exon 6 of 7)	2459	NM_016765	51793	Mm.1457	NM_016765	ENSMUSG00000007039	Ddah2	1110003M04Rik|AU019324|AW413173|DDAH-2|DDAHII|Ddah|G6a|NG30	dimethylarginine dimethylaminohydrolase 2	protein-coding
mm_20294.1	chr2	126933216	126933227	-	1	NA	promoter-TSS (NM_023220)	promoter-TSS (NM_023220)	14	NM_023220	66552	Mm.269928	NM_023220	ENSMUSG00000027366	Sppl2a	2010106G01Rik|C130089K23Rik	signal peptide peptidase like 2A	protein-coding
mm_85026.1	chr9	88454266	88454291	-	1	NA	exon (NM_001284328, exon 12 of 12)	exon (NM_001284328, exon 12 of 12)	-15327	NM_172926	244962	Mm.439873	NM_172926	ENSMUSG00000032422	Snx14	B830022K16|C330035N22Rik|YR-14	sorting nexin 14	protein-coding
mm_170412.1	chr18	67934037	67934038	+	1	NA	intron (NM_172631, intron 1 of 5)	CpG	780	NM_172631	52662	Mm.440183	NM_172631	ENSMUSG00000024544	Ldlrad4	8230401C20Rik|A430083H02|A430108L08Rik|C18orf1|D18Ertd653e|D330030L18Rik	low density lipoprotein receptor class A domain containing 4	protein-coding
mm_62892.1	chr7	116031921	116031932	+	1	NA	promoter-TSS (NM_001025560)	promoter-TSS (NM_001025560)	-879	NM_001025560	20679	Mm.323365	NM_011445	ENSMUSG00000051910	Sox6	AI987981|SOX-LZ	SRY (sex determining region Y)-box 6	protein-coding
mm_81342.1	chr9	108548427	108548430	+	1	NA	intron (NM_001114119, intron 7 of 10)	intron (NM_001114119, intron 7 of 10)	-12073	NM_011830	23918	Mm.6065	NM_011830	ENSMUSG00000062867	Impdh2	IMPD	inosine 5'-phosphate dehydrogenase 2	protein-coding
mm_125961.1	chr15	76266950	76266962	+	1	NA	non-coding (NR_045747, exon 3 of 3)	non-coding (NR_045747, exon 3 of 3)	-1133	NM_028852	74281	Mm.159156	NM_028852	ENSMUSG00000049653	Spatc1	1700084J23Rik|speriolin	spermatogenesis and centriole associated 1	protein-coding
mm_141615.1	chr17	32812474	32812474	-	1	NA	Intergenic	RMER5|LTR|ERV1	-2543	NM_183177	240063	Mm.30675	NM_183177	ENSMUSG00000055202	Zfp811	BC052046	zinc finger protein 811	protein-coding
mm_10443.1	chr2	14263309	14263321	+	1	NA	intron (NM_008625, intron 6 of 29)	intron (NM_008625, intron 6 of 29)	2312	NR_030609	100124488		NR_030609	ENSMUSG00000077897	Mir511	Mirn511|mir-511|mmu-mir-511	microRNA 511	ncRNA
mm_59600.1	chr7	28139963	28139971	+	1	NA	exon (NM_001164655, exon 5 of 20)	exon (NM_001164655, exon 5 of 20)	10501	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_5868.1	chr1	53776703	53776707	-	1	NA	intron (NM_133810, intron 1 of 7)	intron (NM_133810, intron 1 of 7)	8510	NM_133810	98267	Mm.25559	NM_133810	ENSMUSG00000026094	Stk17b	3110009A03Rik|AI120141|Drak2	serine/threonine kinase 17b (apoptosis-inducing)	protein-coding
mm_47083.1	chr5	117115910	117115958	-	1	NA	promoter-TSS (NM_178622)	promoter-TSS (NM_178622)	59	NM_001122666	71954	Mm.34456	NM_178622	ENSMUSG00000066900	Suds3	2400003N08Rik|2410008L21Rik|AU067672|mSds3	suppressor of defective silencing 3 homolog (S. cerevisiae)	protein-coding
mm_61563.1	chr7	79660191	79660201	+	1	NA	promoter-TSS (NM_029835)	promoter-TSS (NM_029835)	0	NM_029835	77011	Mm.28132	NM_029835	ENSMUSG00000046591	Ticrr	5730590G19Rik|BC028450|Lrrk1	TOPBP1-interacting checkpoint and replication regulator	protein-coding
mm_97409.1	chr11	77953468	77953479	+	1	NA	exon (NM_021286, exon 2 of 17)	exon (NM_021286, exon 2 of 17)	22634	NM_021286	20370	Mm.229330	NM_021286	ENSMUSG00000000632	Sez6	BSRP-C|D11Bhm177e|sez-6	seizure related gene 6	protein-coding
mm_156155.1	chrX	129955051	129955096	+	1	NA	intron (NM_172493, intron 10 of 26)	intron (NM_172493, intron 10 of 26)	205331	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diaph2	Dia3|Diap2|Drf2|E430022I22Rik	diaphanous related formin 2	protein-coding
mm_33298.1	chr4	128993249	128993290	+	1	NA	promoter-TSS (NM_016895)	promoter-TSS (NM_016895)	45	NM_001033966	11637	Mm.29460	NM_016895	ENSMUSG00000028792	Ak2	Ak-2|D4Ertd220e	adenylate kinase 2	protein-coding
mm_47350.1	chr5	122614487	122614544	-	1	NA	promoter-TSS (NM_009879)	promoter-TSS (NM_009879)	3	NM_009879	12589	Mm.10125	NM_009879	ENSMUSG00000029469	Ift81	AW060663|Cdv-1|Cdv-1r|Cdv1	intraflagellar transport 81	protein-coding
mm_92971.1	chr10	86295054	86295064	-	1	NA	intron (NM_001164495, intron 6 of 6)	intron (NM_001164495, intron 6 of 6)	-5353	NM_011595	21859	Mm.4871	NM_011595	ENSMUSG00000020044	Timp3	Timp-3	tissue inhibitor of metalloproteinase 3	protein-coding
mm_69846.1	chr7	141408541	141408544	-	1	NA	3' UTR (NM_172116, exon 8 of 8)	3' UTR (NM_172116, exon 8 of 8)	5583	NM_172116	213350	Mm.290953	NM_172116	ENSMUSG00000051007	Pddc1	BC023835|D230016J19Rik	Parkinson disease 7 domain containing 1	protein-coding
mm_42641.1	chr5	118561140	118561150	+	1	NA	intron (NM_001347445, intron 1 of 30)	CpG-11438	426	NM_172424	76199	Mm.206238	NM_172424	ENSMUSG00000018076	Med13l	2210413I17Rik|6330591G05Rik|9030618F05Rik|Thrap2|Trap240L|mKIAA1025	mediator complex subunit 13-like	protein-coding
mm_35616.1	chr4	43442959	43442973	-	1	NA	5' UTR (NM_011571, exon 1 of 10)	5' UTR (NM_011571, exon 1 of 10)	689	NM_011571	21754	Mm.485441	NM_011571	ENSMUSG00000028458	Tesk1	AI326901	testis specific protein kinase 1	protein-coding
mm_133461.1	chr16	89151084	89151087	+	1	NA	Intergenic	Intergenic	-54776	NM_001163615	622935	Mm.459837	NM_001163615	ENSMUSG00000091039	Krtap20-2	1190004K03Rik|EG622935|Gm6371	keratin associated protein 20-2	protein-coding
mm_49151.1	chr6	11935189	11935189	+	1	NA	intron (NM_029404, intron 3 of 16)	intron (NM_029404, intron 3 of 16)	9308	NM_001168382	75725	Mm.212411	NM_029404	ENSMUSG00000029629	Phf14	1110001C23Rik|4932409F11Rik|5730446A07Rik|AA623952|AV297001|mKIAA0783	PHD finger protein 14	protein-coding
mm_38124.1	chr4	134563340	134563352	-	1	NA	3' UTR (NM_207237, exon 12 of 12)	3' UTR (NM_207237, exon 12 of 12)	4505	NR_105829	102465216		NR_105829	ENSMUSG00000099289	Mir6403	Gm27992|mmu-mir-6403	microRNA 6403	ncRNA
mm_48629.1	chr5	145136932	145136950	-	1	NA	exon (NM_001033313, exon 2 of 6)	exon (NM_001033313, exon 2 of 6)	3148	NM_001033313	231887	Mm.188851	NM_001033313	ENSMUSG00000029623	Pdap1	HASPP28|PAP|PAP1	PDGFA associated protein 1	protein-coding
mm_46594.1	chr5	107726018	107726040	-	1	NA	promoter-TSS (NM_001267621)	promoter-TSS (NM_001267621)	-224	NM_001267621	14581	Mm.2078	NM_010278	ENSMUSG00000029275	Gfi1	AW495828|Gfi-1|Pal-1|Pal1	growth factor independent 1	protein-coding
mm_50118.1	chr6	41535048	41535067	+	1	NA	Intergenic	Intergenic	13281	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_157304.1	chrX	20929803	20929829	-	1	NA	intron (NM_008823, intron 2 of 8)	intron (NM_008823, intron 2 of 8)	1739	NM_008823	18636	Mm.3064	NM_008823	ENSMUSG00000001128	Cfp	BCFG|Pfc	complement factor properdin	protein-coding
mm_85927.1	chr9	112073869	112073879	-	1	NA	intron (NM_001177618, intron 17 of 18)	MTE2a|LTR|ERVL-MaLR	44837	NR_029823	723815		NR_029823	ENSMUSG00000065441	Mir128-2	Mirn128-2|Mirn128b|mir-128-2|mir-128b	microRNA 128-2	ncRNA
mm_81270.1	chr9	108080468	108080478	+	1	NA	promoter-TSS (NM_008243)	promoter-TSS (NM_008243)	37	NM_008243	15235	Mm.8369	NM_008243	ENSMUSG00000032591	Mst1	D3F15S2h|D9H3F15S2|DNF15S2h|Hgfl	macrophage stimulating 1 (hepatocyte growth factor-like)	protein-coding
mm_14221.1	chr2	127363170	127363193	+	1	NA	promoter-TSS (NM_009633)	promoter-TSS (NM_009633)	-105	NM_009633	11552	Mm.347390	NM_009633	ENSMUSG00000058620	Adra2b	Adra-2b|[a]2B|a2b-AR|alpha2-C2|alpha2B	adrenergic receptor, alpha 2b	protein-coding
mm_97029.1	chr11	72208733	72208760	+	1	NA	exon (NM_026559, exon 3 of 4)	exon (NM_026559, exon 3 of 4)	1192	NM_026559	52700	Mm.27670	NM_026559	ENSMUSG00000020803	Txndc17	4831443O22Rik|D11Ertd672e|TRP14|Txnl5	thioredoxin domain containing 17	protein-coding
mm_80219.1	chr9	72537745	72537748	+	1	NA	intron (NM_001033536, intron 1 of 8)	intron (NM_001033536, intron 1 of 8)	5506	NM_001033536	319758	Mm.32081	NM_001033536	ENSMUSG00000037674	Rfx7	2510005N23Rik|9930116O05Rik|D130086K05Rik|Rfxdc2	regulatory factor X, 7	protein-coding
mm_160848.1	chr11	51756829	51756829	-	1	NA	promoter-TSS (NM_175255)	promoter-TSS (NM_175255)	5	NM_001290785	77371	Mm.33878	NM_175255	ENSMUSG00000036391	Sec24a	-	Sec24 related gene family, member A (S. cerevisiae)	protein-coding
mm_108988.1	chr12	102757966	102758010	+	1	NA	promoter-TSS (NM_001142939)	promoter-TSS (NM_001142939)	13	NM_025666	66622	Mm.34261	NM_025666	ENSMUSG00000041712	Ubr7	5730410I19Rik|AA589405|AW557761	ubiquitin protein ligase E3 component n-recognin 7 (putative)	protein-coding
mm_133455.1	chr16	88924790	88924795	+	1	NA	Intergenic	B3|SINE|B2	7472	NM_133359	170939	Mm.188445	NM_133359	ENSMUSG00000057174	Krtap19-9b	Krtap16-10b|Krtap16.10L	keratin associated protein 19-9B	protein-coding
mm_29589.1	chr3	117868931	117868944	-	1	NA	promoter-TSS (NM_029655)	promoter-TSS (NM_029655)	-1	NM_029655	76561	Mm.33824	NM_029655	ENSMUSG00000028007	Snx7	2510028H01Rik	sorting nexin 7	protein-coding
mm_49544.1	chr6	30401867	30401965	+	1	NA	promoter-TSS (NM_029742)	promoter-TSS (NM_029742)	61	NM_001311087	76788	Mm.277308	NM_029742	ENSMUSG00000029775	Klhdc10	2410127E18Rik|AI593221|mKIAA0265	kelch domain containing 10	protein-coding
mm_62549.1	chr7	102441746	102441756	+	1	NA	promoter-TSS (NM_009103)	promoter-TSS (NM_009103)	56	NM_009103	20133	Mm.197486	NM_009103	ENSMUSG00000030978	Rrm1	RnrM1	ribonucleotide reductase M1	protein-coding
mm_88654.1	chr10	79995079	79995090	+	1	NA	3' UTR (NM_007725, exon 7 of 7)	3' UTR (NM_007725, exon 7 of 7)	-2524	NM_001347081	27403	Mm.103351	NM_013850	ENSMUSG00000035722	Abca7	ABCX|Abc51	ATP-binding cassette, sub-family A (ABC1), member 7	protein-coding
mm_120576.1	chr14	69190669	69190691	+	1	NA	promoter-TSS (NM_010921)	promoter-TSS (NM_010921)	-12	NM_010921	18095	Mm.3520	NM_010921	ENSMUSG00000022061	Nkx3-1	Bax|NKX3.1|NKX3A|Nkx-3.1|bagpipe	NK-3 transcription factor, locus 1 (Drosophila)	protein-coding
mm_89426.1	chr10	90936740	90936751	+	1	NA	intron (NM_001347053, intron 5 of 8)	B4A|SINE|B4	106902	NM_001347053	77531	Mm.440605	NM_181398	ENSMUSG00000058589	Anks1b	AIDA-1b|C030032C09Rik|E530015N03Rik|ENSMUSG00000078431|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding
mm_137722.1	chr17	29135410	29135434	+	1	NA	5' UTR (NM_001002786, exon 1 of 8)	5' UTR (NM_001002786, exon 1 of 8)	366	NM_001002786	442827	Mm.440341	NM_001002786	ENSMUSG00000064147	Rab44	9830134C10Rik	RAB44, member RAS oncogene family	protein-coding
mm_72991.1	chr8	93011599	93011615	+	1	NA	Intergenic	Intergenic	36585	NM_001013764	244595	Mm.390089	NM_001013764	ENSMUSG00000071047	Ces1a	Ces1l|EG244595|Gm4976	carboxylesterase 1A	protein-coding
mm_136519.1	chr16	97454243	97454254	-	1	NA	intron (NM_010846, intron 6 of 10)	intron (NM_010846, intron 6 of 10)	8657	NM_010846	17857	Mm.33996	NM_010846	ENSMUSG00000000386	Mx1	AI893580|Mx|Mx-1	MX dynamin-like GTPase 1	protein-coding
mm_144337.1	chr18	14706137	14706143	+	1	NA	promoter-TSS (NM_001163609)	promoter-TSS (NM_001163609)	-11	NM_001163609	73677	Mm.87277	NM_001163609	ENSMUSG00000036743	Psma8	2410072D24Rik	proteasome (prosome, macropain) subunit, alpha type, 8	protein-coding
mm_51577.1	chr6	83758912	83758920	+	1	NA	TTS (NM_134157)	TTS (NM_134157)	3592	NR_105027	67934	Mm.126190	NR_105027	ENSMUSG00000099354	1700124L16Rik	-	RIKEN cDNA 1700124L16 gene	ncRNA
mm_75076.1	chr8	33862537	33862540	-	1	NA	intron (NM_001042674, intron 4 of 7)	ORR1C2-int|LTR|ERVL-MaLR	67325	NM_019733	19663	Mm.323997	NM_019733	ENSMUSG00000031586	Rbpms	2010300K22Rik|2700019M19Rik|AU017537|RBP-MS|hermes	RNA binding protein gene with multiple splicing	protein-coding
mm_69934.1	chr7	142084671	142084677	-	1	NA	intron (NM_008748, intron 3 of 6)	intron (NM_008748, intron 3 of 6)	10610	NM_008748	18218	Mm.39725	NM_008748	ENSMUSG00000037887	Dusp8	5530400B01Rik|AI593498|Nttp1	dual specificity phosphatase 8	protein-coding
mm_154606.1	chrX	7644233	7644244	+	1	NA	exon (NM_009305, exon 4 of 7)	exon (NM_009305, exon 4 of 7)	5658	NM_009305	20977	Mm.223674	NM_009305	ENSMUSG00000031144	Syp	A230093K24Rik|AI848995|Syn|p38	synaptophysin	protein-coding
mm_54159.1	chr6	23085180	23085187	-	1	NA	intron (NM_013930, intron 18 of 23)	intron (NM_013930, intron 18 of 23)	47803	NM_013930	30956	Mm.18651	NM_013930	ENSMUSG00000029695	Aass	LKR|LKR/SDH|LOR|LOR/SDH|Lorsdh|SDH	aminoadipate-semialdehyde synthase	protein-coding
mm_71233.1	chr8	40906608	40906610	+	1	NA	intron (NM_007514, intron 6 of 11)	intron (NM_007514, intron 6 of 11)	-19624	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_164348.1	chr16	17833773	17833774	-	1	NA	intron (NR_027959, intron 1 of 1)	CpG	654	NR_027959	433004	Mm.310200	NM_001002790		B830017H08Rik	-	RIKEN cDNA B830017H08 gene	ncRNA
mm_40205.1	chr5	37044944	37044958	+	1	NA	Intergenic	Intergenic	-5906	NM_178394	76071	Mm.85280	NM_178394	ENSMUSG00000063646	Jakmip1	5830437M04Rik|C330021K24Rik|Gababrbp|Marlin-1	janus kinase and microtubule interacting protein 1	protein-coding
mm_50528.1	chr6	49045381	49045389	+	1	NA	exon (NM_053110, exon 4 of 11)	exon (NM_053110, exon 4 of 11)	8867	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_9793.1	chr1	181838019	181838046	-	1	NA	intron (NM_133815, intron 2 of 13)	intron (NM_133815, intron 2 of 13)	4369	NM_133815	98386	Mm.4538	NM_133815	ENSMUSG00000004880	Lbr	AI505894|ic	lamin B receptor	protein-coding
mm_150496.1	chr19	39016914	39016930	+	1	NA	intron (NM_028089, intron 3 of 8)	intron (NM_028089, intron 3 of 8)	9903	NM_028089	72082	Mm.142581	NM_028089	ENSMUSG00000025002	Cyp2c55	2010318C06Rik	cytochrome P450, family 2, subfamily c, polypeptide 55	protein-coding
mm_152299.1	chr19	9083792	9083800	-	1	NA	exon (NM_011681, exon 3 of 3)	exon (NM_011681, exon 3 of 3)	4160	NM_011681	22287	Mm.2258	NM_011681	ENSMUSG00000024653	Scgb1a1	CC10|CC16|CCSP|PCB-BP|UG|UGB|Utg	secretoglobin, family 1A, member 1 (uteroglobin)	protein-coding
mm_108411.1	chr12	81859965	81860036	+	1	NA	promoter-TSS (NM_018814)	promoter-TSS (NM_018814)	-30	NM_018814	54604	Mm.86584	NM_018814	ENSMUSG00000021140	Pcnx	2900024E21Rik|3526401J03Rik|AF096286|AI327143|AI413187|Pcnx1|Pcnxl1	pecanex homolog (Drosophila)	protein-coding
mm_81536.1	chr9	110132016	110132102	+	1	NA	promoter-TSS (NM_009211)	promoter-TSS (NM_009211)	35	NM_009211	20588	Mm.85410	NM_009211	ENSMUSG00000032481	Smarcc1	AI115498|BAF155|Rsc8|SRG3|msp3	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 1	protein-coding
mm_103166.1	chr11	70458789	70458802	-	1	NA	promoter-TSS (NM_001029929)	promoter-TSS (NM_001029929)	-827	NM_001029929	574428	Mm.472771	NM_001029929	ENSMUSG00000040829	Zmynd15	-	zinc finger, MYND-type containing 15	protein-coding
mm_72752.1	chr8	85299646	85299667	+	1	NA	promoter-TSS (NM_019716)	promoter-TSS (NM_019716)	24	NR_028268	56452	Mm.29709	NM_019716	ENSMUSG00000031697	Orc6	6720420I10Rik|Orc6l	origin recognition complex, subunit 6	protein-coding
mm_32115.1	chr4	99030879	99030883	+	1	NA	promoter-TSS (NM_013913)	promoter-TSS (NM_013913)	-73	NM_013913	30924	Mm.28341	NM_013913	ENSMUSG00000028553	Angptl3	hypl	angiopoietin-like 3	protein-coding
mm_87290.1	chr10	42502061	42502083	+	1	NA	promoter-TSS (NM_017472)	promoter-TSS (NM_017472)	18	NM_017472	54198	Mm.277870	NM_017472	ENSMUSG00000019804	Snx3	SDP3	sorting nexin 3	protein-coding
mm_97751.1	chr11	80480956	80480965	+	1	NA	3' UTR (NM_009871, exon 1 of 1)	3' UTR (NM_009871, exon 1 of 1)	3914	NM_009871	12569	Mm.142275	NM_009871	ENSMUSG00000048895	Cdk5r1	Cdk5r|D11Bwg0379e|p25|p35	cyclin-dependent kinase 5, regulatory subunit 1 (p35)	protein-coding
mm_133624.1	chr16	91563421	91563458	+	1	NA	3' UTR (NM_008338, exon 7 of 7)	3' UTR (NM_008338, exon 7 of 7)	16345	NM_008338	15980	Mm.249364	NM_008338	ENSMUSG00000022965	Ifngr2	Ifgr2|Ifgt	interferon gamma receptor 2	protein-coding
mm_168983.1	chr12	92891672	92891687	-	1	NA	Intergenic	RLTR3_Mm|LTR|ERVK	553144	NR_126436	75295	Mm.243878	NR_126436		4930559C10Rik	-	RIKEN cDNA 4930559C10 gene	ncRNA
mm_115628.1	chr13	12106839	12106854	-	1	NA	promoter-TSS (NM_023868)	promoter-TSS (NM_023868)	99	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding
mm_137859.1	chr17	31115532	31115543	+	1	NA	3' UTR (NM_009593, exon 15 of 15)	3' UTR (NM_009593, exon 15 of 15)	14074	NM_011575	21786	Mm.4641	NM_011575	ENSMUSG00000024029	Tff3	ITF|mITF	trefoil factor 3, intestinal	protein-coding
mm_36720.1	chr4	98726612	98726661	-	1	NA	promoter-TSS (NM_001081202)	promoter-TSS (NM_001081202)	-118	NM_001081202	381591	Mm.34340	NM_001081202	ENSMUSG00000087166	L1td1	AA546746|AB211064|D76865|ECAT11	LINE-1 type transposase domain containing 1	protein-coding
mm_110175.1	chr12	27336920	27336932	-	1	NA	3' UTR (NM_009234, exon 1 of 1)	3' UTR (NM_009234, exon 1 of 1)	5792	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding
mm_27499.1	chr3	55055089	55055127	-	1	NA	promoter-TSS (NM_007628)	promoter-TSS (NM_007628)	-53	NM_001305221	12427	Mm.4815	NM_007628	ENSMUSG00000027793	Ccna1	-	cyclin A1	protein-coding
mm_10399.1	chr2	13575352	13575360	+	1	NA	intron (NM_011701, intron 1 of 8)	intron (NM_011701, intron 1 of 8)	1045	NM_011701	22352	Mm.268000	NM_011701	ENSMUSG00000026728	Vim	-	vimentin	protein-coding
mm_132208.1	chr16	32608956	32608964	+	1	NA	promoter-TSS (NM_011638)	promoter-TSS (NM_011638)	64	NM_011638	22042	Mm.28683	NM_011638	ENSMUSG00000022797	Tfrc	2610028K12Rik|CD71|E430033M20Rik|Mtvr1|TFR|TFR1|TR|Trfr|p90	transferrin receptor	protein-coding
mm_65538.1	chr7	25816681	25816723	-	1	NA	promoter-TSS (NM_028775)	promoter-TSS (NM_028775)	-172	NM_028775	74134	Mm.275188	NM_028775	ENSMUSG00000040703	Cyp2s1	1200011C15Rik|AU041727|C79779	cytochrome P450, family 2, subfamily s, polypeptide 1	protein-coding
mm_139526.1	chr17	56647736	56647766	+	1	NA	exon (NM_175350, exon 8 of 22)	exon (NM_175350, exon 8 of 22)	19608	NM_175350	106757	Mm.23401	NM_175350	ENSMUSG00000040828	Catsperd	4921529N20Rik|4933402B14Rik|619718|AW045609|Gm6095|Tmem146	catsper channel auxiliary subunit delta	protein-coding
mm_85025.1	chr9	88444081	88444084	-	1	NA	Intergenic	Intergenic	-5131	NM_172926	244962	Mm.439873	NM_172926	ENSMUSG00000032422	Snx14	B830022K16|C330035N22Rik|YR-14	sorting nexin 14	protein-coding
mm_103462.1	chr11	76399108	76399183	-	1	NA	promoter-TSS (NM_008750)	promoter-TSS (NM_008750)	-4	NM_008750	18230	Mm.27915	NM_008750	ENSMUSG00000020844	Nxn	l11Jus13	nucleoredoxin	protein-coding
mm_165038.1	chr19	38040689	38040719	-	1	NA	intron (NM_001302140, intron 1 of 53)	ORR1F|LTR|ERVL-MaLR	2873	NM_001099634	226101	Mm.34674	NM_177035	ENSMUSG00000048612	Myof	2310004N10Rik|2310051D19Rik|E030042N20Rik|Fer1l3	myoferlin	protein-coding
mm_30498.1	chr3	157900423	157900430	-	1	NA	intron (NM_145953, intron 10 of 11)	intron (NM_145953, intron 10 of 11)	24637	NM_145953	107869	Mm.28301	NM_145953	ENSMUSG00000028179	Cth	0610010I13Rik|AI314617|BC019483|CSE|Cys3	cystathionase (cystathionine gamma-lyase)	protein-coding
mm_22041.1	chr2	168207064	168207142	-	1	NA	promoter-TSS (NM_009628)	promoter-TSS (NM_009628)	9	NM_009628	11538	Mm.201322	NM_009628	ENSMUSG00000051149	Adnp	AA589558|mKIAA0784	activity-dependent neuroprotective protein	protein-coding
mm_89947.1	chr10	111284336	111284354	+	1	NA	exon (NM_001003717, exon 17 of 23)	exon (NM_001003717, exon 17 of 23)	-14334	NM_027914	71769	Mm.45256	NM_027914	ENSMUSG00000035759	Bbs10	1300007O09Rik|AI452285	Bardet-Biedl syndrome 10 (human)	protein-coding
mm_96349.1	chr11	66956683	66956693	+	1	NA	promoter-TSS (NR_130315)	promoter-TSS (NR_130315)	50	NR_130315	71576	Mm.340077	NR_130315	ENSMUSG00000085683	9130409J20Rik	-	RIKEN cDNA 9130409J20 gene	ncRNA
mm_60710.1	chr7	45241110	45241114	+	1	NA	5' UTR (NM_001324535, exon 1 of 13)	5' UTR (NM_001324535, exon 1 of 13)	359	NM_001324535	381884	Mm.490944	NM_001324535	ENSMUSG00000094152	Slc6a16	Gm1084	solute carrier family 6, member 16	protein-coding
mm_136912.1	chr17	13017028	13017081	+	1	NA	3' UTR (NM_013671, exon 5 of 5)	3' UTR (NM_013671, exon 5 of 5)	9215	NM_013671	20656	Mm.290876	NM_013671	ENSMUSG00000006818	Sod2	MnSOD|Sod-2	superoxide dismutase 2, mitochondrial	protein-coding
mm_39766.1	chr5	30013384	30013395	+	1	NA	exon (NM_031168, exon 2 of 5)	exon (NM_031168, exon 2 of 5)	275	NM_031168	16193	Mm.1019	NM_031168	ENSMUSG00000025746	Il6	Il-6	interleukin 6	protein-coding
mm_162723.1	chr10	38169833	38169834	+	1	NA	Intergenic	RMER19B2|LTR|ERVK	-5941	NR_131035	75877	Mm.402094	NR_131035	ENSMUSG00000111234	4930591E09Rik	-	RIKEN cDNA 4930591E09 gene	ncRNA
mm_120257.1	chr14	63046843	63046851	+	1	NA	promoter-TSS (NM_001034910)	promoter-TSS (NM_001034910)	-144	NM_001034910	619548	Mm.387101	NM_001034910	ENSMUSG00000054763	Defb42	BD-42|Defb44|mBD-42	defensin beta 42	protein-coding
mm_11204.1	chr2	29181164	29181196	+	1	NA	3' UTR (NM_198033, exon 26 of 26)	3' UTR (NM_198033, exon 26 of 26)	56188	NM_198033	269254	Mm.41867	NM_198033	ENSMUSG00000043535	Setx	A130090N03|A930037J23Rik|AOA2|AW060766|Als4|SCAR1|Sen1|mKIAA0625	senataxin	protein-coding
mm_64071.1	chr7	140906003	140906033	+	1	NA	promoter-TSS (NR_015583)	promoter-TSS (NR_015583)	-46	NR_015583	212965	Mm.387212	NR_015583	ENSMUSG00000109628	BC024386	BC039766	cDNA sequence BC023486	ncRNA
mm_8976.1	chr1	165460517	165460549	-	1	NA	promoter-TSS (NM_028759)	promoter-TSS (NM_028759)	-70	NM_028759	74106	Mm.227605	NM_028759	ENSMUSG00000026571	Dcaf6	1200006M05Rik|Iqwd1|PC326	DDB1 and CUL4 associated factor 6	protein-coding
mm_48000.1	chr5	136161208	136161227	-	1	NA	intron (NM_178751, intron 2 of 2)	RSINE1|SINE|B4	9439	NM_178751	269717	Mm.308396	NM_178751	ENSMUSG00000039747	Orai2	A730041O15Rik|Tmem142b	ORAI calcium release-activated calcium modulator 2	protein-coding
mm_169742.1	chr15	86195008	86195021	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-8873	NM_145475	223753	Mm.222685	NM_145475	ENSMUSG00000035891	Cerk	AI848610|D330016D08Rik|mKIAA1646	ceramide kinase	protein-coding
mm_30551.1	chr4	3693997	3694000	+	1	NA	intron (NM_010747, intron 1 of 12)	PB1D10|SINE|Alu	15877	NM_010747	17096	Mm.317331	NM_010747	ENSMUSG00000042228	Lyn	AA407514|Hck-2|p53Lyn|p56Lyn	LYN proto-oncogene, Src family tyrosine kinase	protein-coding
mm_126843.1	chr15	89075997	89076038	+	1	NA	promoter-TSS (NM_026485)	promoter-TSS (NM_026485)	-47	NM_026485	67976	Mm.284710	NM_026485	ENSMUSG00000015363	Trabd	5730502D15Rik|AL023039	TraB domain containing	protein-coding
mm_58928.1	chr7	17973368	17973380	+	1	NA	exon (NM_023289, exon 2 of 4)	exon (NM_023289, exon 2 of 4)	1207	NM_023289	66996	Mm.36666	NM_023289	ENSMUSG00000030368	Ceacam11	1600015D01Rik	carcinoembryonic antigen-related cell adhesion molecule 11	protein-coding
mm_91062.1	chr10	18996480	18996492	-	1	NA	Intergenic	Intergenic	15477	NM_001166402	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_86543.1	chr10	8903966	8903975	+	1	NA	Intergenic	Intergenic	-17900	NM_175155	70097	Mm.338275	NM_175155	ENSMUSG00000015305	Sash1	1100001C18Rik|2500002E12Rik|A330076K04Rik|mKIAA0790	SAM and SH3 domain containing 1	protein-coding
mm_90006.1	chr10	112931422	112931426	+	1	NA	Intergenic	U1|snRNA|snRNA	-2398	NM_001033474	382423	Mm.431239	NM_001033474	ENSMUSG00000074748	Atxn7l3b	4921506J03Rik|6230409E21Rik|AI315132|ENSMUSG00000074747	ataxin 7-like 3B	protein-coding
mm_88098.1	chr10	68723916	68723931	+	1	NA	exon (NM_177794, exon 1 of 6)	exon (NM_177794, exon 1 of 6)	177	NM_177794	327766	Mm.2479	NM_177794	ENSMUSG00000060044	Tmem26	3230401A06|AI195372	transmembrane protein 26	protein-coding
mm_128964.1	chr15	74832104	74832112	-	1	NA	Intergenic	B3|SINE|B2	9535	NM_001033229	110115	Mm.322606	NM_001033229	ENSMUSG00000075604	Cyp11b1	AA389061|CPN1|Cyp11b|Cyp11b-1|FHI	cytochrome P450, family 11, subfamily b, polypeptide 1	protein-coding
mm_35453.1	chr4	40697341	40697362	-	1	NA	exon (NM_025545, exon 2 of 8)	exon (NM_025545, exon 2 of 8)	5565	NM_025545	66408	Mm.430710	NM_025545	ENSMUSG00000028411	Aptx	2410016G21Rik|AA388047|FHA-HIT	aprataxin	protein-coding
mm_110324.1	chr12	34874803	34874828	-	1	NA	intron (NM_001271386, intron 2 of 27)	MLT1C|LTR|ERVL-MaLR	42280	NM_001271386	79221	Mm.310551	NM_024124	ENSMUSG00000004698	Hdac9	AV022454|D030072B18Rik|HD7B|HD9|HDRP|Hdac7b|Mitr|mKIAA0744	histone deacetylase 9	protein-coding
mm_90529.1	chr10	128086032	128086097	+	1	NA	TTS (NR_030442)	TTS (NR_030442)	778	NR_030442	751518		NR_030442	ENSMUSG00000093245	Mir677	Mirn677|mir-677|mmu-mir-677	microRNA 677	ncRNA
mm_84754.1	chr9	75566727	75566731	-	1	NA	3' UTR (NM_001038710, exon 10 of 10)	3' UTR (NM_001038710, exon 10 of 10)	-7072	NM_016963	50875	Mm.38445	NM_016963	ENSMUSG00000058587	Tmod3	U-Tmod|UTMOD	tropomodulin 3	protein-coding
mm_129978.1	chr15	86004986	86004989	-	1	NA	intron (NM_009886, intron 1 of 34)	intron (NM_009886, intron 1 of 34)	28790	NM_009886	12614	Mm.22680	NM_009886	ENSMUSG00000016028	Celsr1	Adgrc1|Crsh|Scy|crash	cadherin, EGF LAG seven-pass G-type receptor 1	protein-coding
mm_165167.1	chr2	25617780	25617784	+	1	NA	promoter-TSS (NM_029859)	promoter-TSS (NM_029859)	-104	NM_029859	77058	Mm.478493	NM_029859	ENSMUSG00000026940	Ccdc183	4921530D09Rik|Cccd183|Kiaa1984	coiled-coil domain containing 183	protein-coding
mm_71534.1	chr8	46986884	46986891	+	1	NA	promoter-TSS (NM_177304)	promoter-TSS (NM_177304)	0	NM_177304	320981	Mm.211429	NM_177304	ENSMUSG00000038173	Enpp6	4833421B01Rik|B830047L21Rik|D8Ertd514e|E-NPP 6|GPC-Cpde|Npp6	ectonucleotide pyrophosphatase/phosphodiesterase 6	protein-coding
mm_57114.1	chr6	122596466	122596481	-	1	NA	intron (NM_031159, intron 3 of 7)	intron (NM_031159, intron 3 of 7)	5971	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_91714.1	chr10	44423981	44423995	-	1	NA	Intergenic	Intergenic	34760	NM_007548	12142	Mm.4800	NM_007548	ENSMUSG00000038151	Prdm1	Blimp-1|Blimp1|PRDI-BF1|ZNFPR1A1|b2b1765Clo	PR domain containing 1, with ZNF domain	protein-coding
mm_96210.1	chr11	62281458	62281495	+	1	NA	promoter-TSS (NM_028360)	promoter-TSS (NM_028360)	3	NM_029704	72795	Mm.489722	NM_028360	ENSMUSG00000042298	Ttc19	2010204O13Rik|2810460C24Rik|AI505442	tetratricopeptide repeat domain 19	protein-coding
mm_82279.1	chr9	7358334	7358363	-	1	NA	3' UTR (NM_008605, exon 10 of 10)	3' UTR (NM_008605, exon 10 of 10)	10974	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_47992.1	chr5	135962266	135962274	-	1	NA	intron (NM_001160366, intron 9 of 10)	intron (NM_001160366, intron 9 of 10)	12206	NM_001160366	109267	Mm.332750	NM_001160366	ENSMUSG00000029699	Ssc4d	C330016E03Rik|S4D-SRCRB|SRCRB-S4D|Srcrb4d	scavenger receptor cysteine rich family, 4 domains	protein-coding
mm_86042.1	chr9	114496538	114496551	-	1	NA	promoter-TSS (NM_009916)	promoter-TSS (NM_009916)	0	NM_009916	12773	Mm.1337	NM_009916	ENSMUSG00000047898	Ccr4	C-C CKR-4|CHEMR1|Cmkbr4|LESTR|Sdf1r	chemokine (C-C motif) receptor 4	protein-coding
mm_163593.1	chr13	41468362	41468365	-	1	NA	intron (NM_001111324, intron 1 of 7)	intron (NM_001111324, intron 1 of 7)	18997	NM_001111324	18003	Mm.288980	NM_017464	ENSMUSG00000021365	Nedd9	Cas-L|CasL|HEF1|MEF1|Nedd-9|p105	neural precursor cell expressed, developmentally down-regulated gene 9	protein-coding
mm_43402.1	chr5	135851421	135851451	+	1	NA	intron (NM_021403, intron 3 of 14)	intron (NM_021403, intron 3 of 14)	33330	NM_021403	58212	Mm.271230	NM_021403	ENSMUSG00000039860	Srrm3	2900083I11Rik|AB041661|SRm300-like|Srrm2l	serine/arginine repetitive matrix 3	protein-coding
mm_99533.1	chr11	103192695	103192704	+	1	NA	exon (NM_001077698, exon 13 of 26)	exon (NM_001077698, exon 13 of 26)	15849	NM_001254724	69441	Mm.380648	NM_027082	ENSMUSG00000020940	1700023F06Rik	-	RIKEN cDNA 1700023F06 gene	protein-coding
mm_135070.1	chr16	34255430	34255440	-	1	NA	intron (NM_001164268, intron 12 of 33)	MLTR11A|LTR|ERVK	258592	NM_001164268	545156	Mm.82274	NM_177357	ENSMUSG00000061751	Kalrn	2210407G14Rik|AV235988|DUET|E530005C20Rik|Gm539|Hapip|TRAD	kalirin, RhoGEF kinase	protein-coding
mm_103800.1	chr11	82908231	82908249	-	1	NA	intron (NM_145431, intron 1 of 12)	CpG-2340	155	NM_145431	217011	Mm.29176	NM_145431	ENSMUSG00000020692	Nle1	AL022765|BC018399|Nle|l11Jus1|l11Jus4	notchless homolog 1 (Drosophila)	protein-coding
mm_40578.1	chr5	64092926	64092984	+	1	NA	promoter-TSS (NM_025700)	promoter-TSS (NM_025700)	5	NM_025700	66681	Mm.2325	NM_025700	ENSMUSG00000029171	Pgm1	3230402E02Rik|Pgm-1|Pgm2	phosphoglucomutase 1	protein-coding
mm_9729.1	chr1	180199557	180199586	-	1	NA	Intergenic	L2a|LINE|L2	-3551	NM_023341	67426	Mm.38330	NM_023341	ENSMUSG00000026489	Coq8a	4632432J16Rik|AI462003|Adck3|Cabc1|mKIAA0451	coenzyme Q8A	protein-coding
mm_102229.1	chr11	54910370	54910380	-	1	NA	TTS (NM_008161)	TTS (NM_008161)	7521	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_19246.1	chr2	84743750	84743764	-	1	NA	Intergenic	Intergenic	-2579	NR_029544	387149		NR_029544	ENSMUSG00000065484	Mir130a	Mirn130|Mirn130a|mir-130a	microRNA 130a	ncRNA
mm_47424.1	chr5	123171962	123171987	-	1	NA	3' UTR (NM_008277, exon 14 of 14)	3' UTR (NM_008277, exon 14 of 14)	10712	NM_008277	15445	Mm.439709	NM_008277	ENSMUSG00000029445	Hpd	Fla|Flp|Hppd|Laf	4-hydroxyphenylpyruvic acid dioxygenase	protein-coding
mm_110216.1	chr12	28623351	28623371	-	1	NA	promoter-TSS (NM_027866)	promoter-TSS (NM_027866)	-31	NM_027866	71693	Mm.30724	NM_027866	ENSMUSG00000036655	Colec11	CL-K1	collectin sub-family member 11	protein-coding
mm_148653.1	chr19	5493786	5493793	+	1	NA	3' UTR (NM_007687, exon 4 of 4)	3' UTR (NM_007687, exon 4 of 4)	3334	NM_007687	12631	Mm.329655	NM_007687	ENSMUSG00000056201	Cfl1	AA959946|Cof	cofilin 1, non-muscle	protein-coding
mm_85943.1	chr9	112099992	112100006	-	1	NA	intron (NM_001177618, intron 17 of 18)	intron (NM_001177618, intron 17 of 18)	18712	NR_029823	723815		NR_029823	ENSMUSG00000065441	Mir128-2	Mirn128-2|Mirn128b|mir-128-2|mir-128b	microRNA 128-2	ncRNA
mm_166358.1	chr5	122500930	122500931	+	1	NA	intron (NM_001110140, intron 2 of 19)	intron (NM_001110140, intron 2 of 19)	1295	NM_001110140	11938	Mm.227583	NM_009722	ENSMUSG00000029467	Atp2a2	9530097L16Rik|D5Wsu150e|SERCA2|SERCA2B|Serca2a|mKIAA4195	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	protein-coding
mm_28724.1	chr3	95685590	95685607	-	1	NA	5' UTR (NM_001301705, exon 2 of 18)	5' UTR (NM_001301705, exon 2 of 18)	2319	NM_144899	229595	Mm.490574	NM_144899	ENSMUSG00000015850	Adamtsl4	ADAMTSL-4|Tsrc1	ADAMTS-like 4	protein-coding
mm_118228.1	chr13	111482322	111482334	-	1	NA	intron (NM_001122963, intron 2 of 11)	B3A|SINE|B2	7713	NM_028487	73274	Mm.57286	NM_028487	ENSMUSG00000032745	Gpbp1	1700034P14Rik|AU019836|D230035M11Rik|Gpbp|mGPBP	GC-rich promoter binding protein 1	protein-coding
mm_33870.1	chr4	135968659	135968660	+	1	NA	TTS (NM_178389)	TTS (NM_178389)	3494	NM_178389	74246	Mm.247946	NM_178389	ENSMUSG00000028671	Gale	2310002A12Rik|AI323962	galactose-4-epimerase, UDP	protein-coding
mm_167985.1	chrX	169978909	169978931	-	1	NA	promoter-TSS (NR_029457)	promoter-TSS (NR_029457)	-3	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_79959.1	chr9	66189252	66189256	+	1	NA	intron (NM_010019, intron 2 of 11)	intron (NM_010019, intron 2 of 11)	31028	NM_010019	13143	Mm.304472	NM_010019	ENSMUSG00000032380	Dapk2	-	death-associated protein kinase 2	protein-coding
mm_59162.1	chr7	24386557	24386561	+	1	NA	Intergenic	B1_Mur2|SINE|Alu	-13069	NM_028047	71997	Mm.150977	NM_028047	ENSMUSG00000002210	Smg9	1500002O20Rik|AI429693|N28092	smg-9 homolog, nonsense mediated mRNA decay factor (C. elegans)	protein-coding
mm_96747.1	chr11	69847468	69847489	+	1	NA	exon (NM_001168497, exon 3 of 8)	exon (NM_001168497, exon 3 of 8)	834	NR_033133	70310	Mm.28874	NM_023564	ENSMUSG00000019461	Plscr3	2210403O21Rik|2610037N06Rik|ESTM3|X83310	phospholipid scramblase 3	protein-coding
mm_156461.1	chrX	143059107	143059115	+	1	NA	Intergenic	L2c|LINE|L2	-40483	NM_001040434	209540	Mm.297608	NM_001040434	ENSMUSG00000085584	Rgag1	Gm385|Mar9|Mart9	retrotransposon gag domain containing 1	protein-coding
mm_121326.1	chr14	114945994	114946004	+	1	NA	promoter-TSS (NR_126551)	promoter-TSS (NR_126551)	-51	NR_126548	74982		NR_126548		1700100I10Rik	1700085D13Rik|4930481K08Rik	RIKEN cDNA 1700100I10 gene	ncRNA
mm_139751.1	chr17	63863973	63864038	+	1	NA	promoter-TSS (NM_001037997)	promoter-TSS (NM_001037997)	24	NM_001037997	14158	Mm.23039	NM_008000	ENSMUSG00000000127	Fer	AV082135|C330004K01Rik|Fert|Fert2	fer (fms/fps related) protein kinase	protein-coding
mm_20787.1	chr2	143990120	143990150	-	1	NA	exon (NM_133626, exon 2 of 3)	exon (NM_133626, exon 2 of 3)	21128	NM_133626	81910	Mm.13705	NM_024281	ENSMUSG00000027422	Rrbp1	1700087N07Rik|5730465C04Rik|ES/130|mKIAA1398|mRRp0|mRRp1.8|mRRp10|mRRp15a|mRRp15b|mRRp16.8|mRRp2|mRRp41|mRRp47|mRRp5.4|p180	ribosome binding protein 1	protein-coding
mm_169589.1	chr15	26681657	26681657	-	1	NA	intron (NM_176959, intron 2 of 3)	L1Md_T|LINE|L1	213907	NM_176959	448987	Mm.253378	NM_176959	ENSMUSG00000043556	Fbxl7	AL023057|D230018M15Rik|FBL7|Fbl6	F-box and leucine-rich repeat protein 7	protein-coding
mm_154921.1	chrX	23689018	23689020	+	1	NA	Intergenic	Intergenic	-4032	NM_175180	72404	Mm.423	NM_175180	ENSMUSG00000036769	Wdr44	2610034K17Rik|RAB11BP|RPH11	WD repeat domain 44	protein-coding
mm_65377.1	chr7	25088674	25088685	-	1	NA	Intergenic	Intergenic	8496	NR_105855	102465968		NR_105855	ENSMUSG00000098441	Mir6537	Gm27808|mmu-mir-6537	microRNA 6537	ncRNA
mm_3812.1	chr1	158691305	158691315	+	1	NA	3' UTR (NM_001205204, exon 23 of 23)	3' UTR (NM_001205204, exon 23 of 23)	185685	NR_030441	735253		NR_030441	ENSMUSG00000070103	Mir488	Mirn488|mir-488|mmu-mir-488	microRNA 488	ncRNA
mm_151716.1	chr19	4759216	4759217	-	1	NA	intron (NM_025717, intron 2 of 3)	intron (NM_025717, intron 2 of 3)	2691	NM_025717	66704	Mm.396734	NM_025717	ENSMUSG00000033760	Rbm4b	4921506I22Rik|AI504630|AI506404|Lark2|Neosin	RNA binding motif protein 4B	protein-coding
mm_63130.1	chr7	123001793	123001808	+	1	NA	exon (NM_011247, exon 18 of 18)	exon (NM_011247, exon 18 of 18)	31236	NM_175023	19647	Mm.4480	NM_011247	ENSMUSG00000030779	Rbbp6	4933422O15Rik|AI316869|BB233631|C030034J04Rik|C77662|P2P-R|PACT	retinoblastoma binding protein 6	protein-coding
mm_109181.1	chr12	108450413	108450415	+	1	NA	intron (NM_001043335, intron 1 of 21)	L2c|LINE|L2	27598	NM_001043335	68519	Mm.236645	NM_001043335	ENSMUSG00000058070	Eml1	1110008N23Rik|A930030P13Rik|AA171013|AI847476|AI853955|ELP79|EMAP|EMAPL|heco	echinoderm microtubule associated protein like 1	protein-coding
mm_100433.1	chr11	119469055	119469068	+	1	NA	Intergenic	Intergenic	-22286	NM_001164636	338371	Mm.271946	NM_177394	ENSMUSG00000039850	Endov	A730011L01Rik	endonuclease V	protein-coding
mm_26349.1	chr3	142548134	142548153	+	1	NA	3' UTR (NM_001083312, exon 11 of 11)	3' UTR (NM_001083312, exon 11 of 11)	-11909	NM_018734	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_85235.1	chr9	98033248	98033258	-	1	NA	promoter-TSS (NM_022319)	promoter-TSS (NM_022319)	-86	NM_022319	64085	Mm.440903	NM_022319	ENSMUSG00000032452	Clstn2	2900042C18Rik|AI448973|CSTN2|Cs2|Cst-2|mKIAA4134	calsyntenin 2	protein-coding
mm_80430.1	chr9	77921722	77921746	+	1	NA	intron (NM_134255, intron 1 of 7)	intron (NM_134255, intron 1 of 7)	4369	NM_134255	68801	Mm.430736	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	ELOVL family member 5, elongation of long chain fatty acids (yeast)	protein-coding
mm_59859.1	chr7	29983977	29983988	+	1	NA	promoter-TSS (NM_001167873)	promoter-TSS (NM_001167873)	27	NM_001167872	243905	Mm.322432	NM_001033355	ENSMUSG00000074221	Zfp568	C80731|Gm1691|Znf568|chato	zinc finger protein 568	protein-coding
mm_90807.1	chr10	7664140	7664149	-	1	NA	promoter-TSS (NM_008786)	promoter-TSS (NM_008786)	-536	NM_001347228	18537	Mm.258431	NM_008786	ENSMUSG00000019795	Pcmt1	C79501|PIMT	protein-L-isoaspartate (D-aspartate) O-methyltransferase 1	protein-coding
mm_94039.1	chr10	128058791	128058843	-	1	NA	promoter-TSS (NM_019766)	promoter-TSS (NM_019766)	-165	NM_019766	56351	Mm.305816	NM_019766	ENSMUSG00000071072	Ptges3	5730442A20Rik|Ptges|Tebp|cPGES|p23|sid3177	prostaglandin E synthase 3 (cytosolic)	protein-coding
mm_51472.1	chr6	82960541	82960547	+	1	NA	intron (NM_033079, intron 2 of 9)	GA-rich|Low_complexity|Low_complexity	13622	NM_033079	110958	Mm.100652	NM_033079	ENSMUSG00000030041	M1ap	D6Mm5e	meiosis 1 associated protein	protein-coding
mm_145565.1	chr18	60812496	60812504	+	1	NA	TTS (NR_039567)	TTS (NR_039567)	424	NR_039567	100628611		NR_039567	ENSMUSG00000093327	Mir5107	mir-5107|mmu-mir-5107|mu-mir-5107	microRNA 5107	ncRNA
mm_42852.1	chr5	122209971	122209983	+	1	NA	promoter-TSS (NM_028752)	promoter-TSS (NM_028752)	248	NM_001042489	74096	Mm.28804	NM_028752	ENSMUSG00000064267	Hvcn1	0610039P13Rik|AI450555|BTS|HV1|Vsop.|mVSOP	hydrogen voltage-gated channel 1	protein-coding
mm_19435.1	chr2	91963508	91963694	-	1	NA	promoter-TSS (NM_138306)	promoter-TSS (NM_138306)	-38	NM_138306	104418	Mm.314923	NM_138306	ENSMUSG00000040479	Dgkz	E130307B02Rik|ENSMUSG00000075035|F730209L11Rik|mDGK[z]	diacylglycerol kinase zeta	protein-coding
mm_76956.1	chr8	106052552	106052563	-	1	NA	intron (NM_001301176, intron 13 of 14)	intron (NM_001301176, intron 13 of 14)	-7046	NM_010901	18021	Mm.383185	NM_010901	ENSMUSG00000031902	Nfatc3	C80703|D8Ertd281e|NFAT4|NFATx	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 3	protein-coding
mm_69692.1	chr7	139992523	139992533	-	1	NA	promoter-TSS (NM_001291066)	promoter-TSS (NM_001291066)	34	NM_007403	11501	Mm.15969	NM_007403	ENSMUSG00000025473	Adam8	ADAM 8|CD156|CD156a|E430039A18Rik|MS2	a disintegrin and metallopeptidase domain 8	protein-coding
mm_47625.1	chr5	125277836	125277865	-	1	NA	exon (NM_001205082, exon 12 of 12)	exon (NM_001205082, exon 12 of 12)	63244	NM_016741	20778	Mm.282242	NM_016741	ENSMUSG00000037936	Scarb1	AI120173|CD36|Cd36l1|Chohd1|Cla-1|Cla1|D5Ertd460e|Hdlq1|Hlb398|SR-B1|SR-BI|SRBI|Srb1|mSR-BI	scavenger receptor class B, member 1	protein-coding
mm_130147.1	chr15	91017983	91018005	-	1	NA	intron (NM_001109040, intron 1 of 36)	intron (NM_001109040, intron 1 of 36)	31957	NM_001109041	16564	Mm.41379	NM_016705	ENSMUSG00000022629	Kif21a	-	kinesin family member 21A	protein-coding
mm_34565.1	chr4	149854583	149854596	+	1	NA	Intergenic	Intergenic	-80322	NM_027460	70556	Mm.41877	NM_027460	ENSMUSG00000028982	Slc25a33	5730438N18Rik|Pnc1	solute carrier family 25, member 33	protein-coding
mm_87531.1	chr10	53344952	53344971	+	1	NA	3' UTR (NM_001141927, exon 3 of 3)	3' UTR (NM_001141927, exon 3 of 3)	7275	NM_001141927	18821	Mm.34145	NM_023129	ENSMUSG00000038583	Pln	Plb	phospholamban	protein-coding
mm_20136.1	chr2	121410005	121410009	-	1	NA	intron (NM_153075, intron 4 of 12)	ID_B1|SINE|B4	3785	NM_153075	212670	Mm.384318	NM_153075	ENSMUSG00000033486	Catsper2	-	cation channel, sperm associated 2	protein-coding
mm_127017.1	chr15	95965894	95965906	+	1	NA	exon (NM_001253813, exon 19 of 21)	exon (NM_001253813, exon 19 of 21)	113653	NR_126493	402773	Mm.210567	NM_001033483	ENSMUSG00000078925	D030018L15Rik	-	nuclear receptor coactivator 2 pseudogene	pseudo
mm_36017.1	chr4	56947413	56947447	-	1	NA	promoter-TSS (NM_175518)	promoter-TSS (NM_175518)	-1	NM_175518	242474	Mm.296632	NM_175518	ENSMUSG00000055296	Tmem245	A630051L19Rik|AI957324|D730040F13Rik	transmembrane protein 245	protein-coding
mm_141316.1	chr17	28364569	28364584	-	1	NA	intron (NM_021478, intron 2 of 14)	intron (NM_021478, intron 2 of 14)	567	NM_021478	22157	Mm.42102	NM_021478	ENSMUSG00000037446	Tulp1	Tulp1l	tubby like protein 1	protein-coding
mm_60803.1	chr7	45627906	45627910	+	1	NA	TTS (NM_001018013)	TTS (NM_001018013)	371	NM_028544	69903	Mm.181396	NM_028544	ENSMUSG00000044562	Rasip1	1110025D03Rik|2610025P08Rik|AI853551|Rain	Ras interacting protein 1	protein-coding
mm_156393.1	chrX	139806065	139806067	+	1	NA	intron (NM_016675, intron 1 of 1)	intron (NM_016675, intron 1 of 1)	5258	NM_016675	12738	Mm.117068	NM_016675	ENSMUSG00000047230	Cldn2	AL022813	claudin 2	protein-coding
mm_135613.1	chr16	52270711	52270724	-	1	NA	exon (NM_001331110, exon 12 of 15)	exon (NM_001331110, exon 12 of 15)	182364	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_28294.1	chr3	89093370	89093372	-	1	NA	promoter-TSS (NM_001083807)	promoter-TSS (NM_001083807)	-8	NM_028188	72296	Mm.27687	NM_028188	ENSMUSG00000041263	Rusc1	2210403N08Rik|AA408288|NESCA	RUN and SH3 domain containing 1	protein-coding
mm_64028.1	chr7	140769134	140769150	+	1	NA	exon (NM_021282, exon 3 of 9)	exon (NM_021282, exon 3 of 9)	5310	NM_021282	13106	Mm.21758	NM_021282	ENSMUSG00000025479	Cyp2e1	Cyp2e	cytochrome P450, family 2, subfamily e, polypeptide 1	protein-coding
mm_57693.1	chr6	128522045	128522058	-	1	NA	exon (NM_007376, exon 6 of 36)	exon (NM_007376, exon 6 of 36)	4669	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_62566.1	chr7	104218902	104218912	+	1	NA	intron (NM_001013616, intron 1 of 7)	intron (NM_001013616, intron 1 of 7)	112	NM_001013616	94088	Mm.274843	NM_001013616	ENSMUSG00000072244	Trim6	C430046K18Rik|D7Ertd684e	tripartite motif-containing 6	protein-coding
mm_988.1	chr1	58586406	58586446	+	1	NA	promoter-TSS (NM_172513)	promoter-TSS (NM_172513)	29	NM_025597	66495	Mm.2033	NM_025597	ENSMUSG00000026032	Ndufb3	2700033I16Rik|CI-B12	NADH dehydrogenase (ubiquinone) 1 beta subcomplex 3	protein-coding
mm_111292.1	chr12	85471869	85471891	-	1	NA	Intergenic	Intergenic	-2021	NM_010234	14281	Mm.246513	NM_010234	ENSMUSG00000021250	Fos	D12Rfj1|c-fos|cFos	FBJ osteosarcoma oncogene	protein-coding
mm_112554.1	chr13	12565869	12565879	+	1	NA	promoter-TSS (NM_026184)	promoter-TSS (NM_026184)	-9	NM_026184	67475	Mm.358706	NM_026184	ENSMUSG00000057069	Ero1lb	1300013B24Rik|1700065B09Rik|AI447560|Ero1b|ero1-beta	ERO1-like beta (S. cerevisiae)	protein-coding
mm_147293.1	chr18	39490888	39490910	-	1	NA	Intergenic	Intergenic	-3654	NM_008173	14815	Mm.129481	NM_008173	ENSMUSG00000024431	Nr3c1	GR|Grl-1|Grl1	nuclear receptor subfamily 3, group C, member 1	protein-coding
mm_159803.1	chr5	113735828	113735828	+	1	NA	promoter-TSS (NM_001010825)	promoter-TSS (NM_001010825)	46	NM_001010825	231630	Mm.21926	NM_001010825	ENSMUSG00000053334	Ficd	D5Ertd40e|Hype	FIC domain containing	protein-coding
mm_16837.1	chr2	11499562	11499565	-	1	NA	intron (NM_001177758, intron 1 of 14)	ID_B1|SINE|B4	2527	NM_001177754	170768	Mm.19669	NM_133232	ENSMUSG00000026773	Pfkfb3	E330010H22Rik|iPFK-2|uPFK-2	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	protein-coding
mm_124474.1	chr14	121379207	121379269	-	1	NA	promoter-TSS (NM_145465)	promoter-TSS (NM_145465)	-8	NM_145465	223255	Mm.390756	NM_145465	ENSMUSG00000063410	Stk24	1810013H02Rik|C76483|MST-3|Mst3|STE20	serine/threonine kinase 24	protein-coding
mm_130389.1	chr15	97869372	97869382	-	1	NA	exon (NM_009504, exon 6 of 10)	exon (NM_009504, exon 6 of 10)	-24875	NM_001204278	56233	Mm.384027	NM_019572	ENSMUSG00000022475	Hdac7	5830434K02Rik|HD7|HD7a|Hdac7a|mFLJ00062	histone deacetylase 7	protein-coding
mm_29917.1	chr3	131489912	131489936	-	1	NA	Intergenic	Intergenic	-74844	NM_001289479	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_48928.1	chr6	4521388	4521423	+	1	NA	exon (NM_007743, exon 23 of 52)	exon (NM_007743, exon 23 of 52)	15787	NM_007743	12843	Mm.277792	NM_007743	ENSMUSG00000029661	Col1a2	AA960264|AI325291|Col1a-2|Cola-2|Cola2|oim	collagen, type I, alpha 2	protein-coding
mm_35247.1	chr4	19877623	19877627	-	1	NA	3' UTR (NM_175406, exon 8 of 8)	3' UTR (NM_175406, exon 8 of 8)	44941	NM_175406	242341	Mm.19298	NM_175406	ENSMUSG00000028238	Atp6v0d2	1620401A02Rik|AI324824|V-ATPase	ATPase, H+ transporting, lysosomal V0 subunit D2	protein-coding
mm_21478.1	chr2	162661050	162661058	-	1	NA	promoter-TSS (NM_021464)	promoter-TSS (NM_021464)	93	NM_001291151	19281	Mm.235807	NM_021464	ENSMUSG00000053141	Ptprt	R-PTP-T|RPTP-rfo|RPTP-rho|RPTPmam4|RPTPrho|mKIAA0283|mRPTPrho	protein tyrosine phosphatase, receptor type, T	protein-coding
mm_6823.1	chr1	84198426	84198440	-	1	NA	intron (NM_001003948, intron 1 of 2)	intron (NM_001003948, intron 1 of 2)	20528	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_46746.1	chr5	111417126	111417138	-	1	NA	Intergenic	CpG	-1034	NM_001081235	433938	Mm.332576	NM_001081235	ENSMUSG00000070576	Mn1	AA003644|AA009236	meningioma 1	protein-coding
mm_54624.1	chr6	38637221	38637247	-	1	NA	promoter-TSS (NM_001033171)	promoter-TSS (NM_001033171)	5	NM_001033171	74253	Mm.121859	NM_001033171	ENSMUSG00000071537	Klrg2	2310020F24Rik	killer cell lectin-like receptor subfamily G, member 2	protein-coding
mm_86737.1	chr10	19122479	19122491	+	1	NA	Intergenic	Intergenic	-19264	NR_038021	100504265	Mm.383417	NR_038021		Gm20139	-	predicted gene, 20139	ncRNA
mm_138120.1	chr17	34145226	34145230	+	1	NA	promoter-TSS (NM_010388)	promoter-TSS (NM_010388)	-188	NM_010388	15000	Mm.195060	NM_010388	ENSMUSG00000037548	H2-DMb2	H-2Mb2|H2-Mb2	histocompatibility 2, class II, locus Mb2	protein-coding
mm_139575.1	chr17	57062487	57062523	+	1	NA	intron (NM_001347408, intron 1 of 4)	CpG	228	NM_177638	224912	Mm.284447	NM_177638	ENSMUSG00000044279	Crb3	5730439B18|AU015179|AU041752	crumbs family member 3	protein-coding
mm_116198.1	chr13	31820588	31820620	-	1	NA	intron (NM_146041, intron 9 of 10)	intron (NM_146041, intron 9 of 10)	13958	NM_008592	17300	Mm.12949	NM_008592	ENSMUSG00000050295	Foxc1	FREAC3|Fkh1|Mf1|Mf4|ch|fkh-1|frkhda	forkhead box C1	protein-coding
mm_170825.1	chr2	176798570	176798586	+	1	NA	promoter-TSS (NM_001205057)	promoter-TSS (NM_001205057)	-22	NM_001205057	100039123	Mm.389409	NM_001205057	ENSMUSG00000078877	Gm14295	OTTMUSG00000016219	predicted gene 14295	protein-coding
mm_83061.1	chr9	37546059	37546089	-	1	NA	exon (NM_022029, exon 2 of 4)	exon (NM_022029, exon 2 of 4)	6671	NM_022029	64011	Mm.335065	NM_022029	ENSMUSG00000053310	Nrgn	0710001B06Rik|AI838505|NG|NG/RC3|Pss1|R75334|RC3	neurogranin	protein-coding
mm_35392.1	chr4	34050039	34050049	-	1	NA	promoter-TSS (NM_026293)	promoter-TSS (NM_026293)	21	NM_001290443	67652	Mm.55848	NM_026293	ENSMUSG00000028264	Spaca1	1700124L11Rik|4930540L03Rik	sperm acrosome associated 1	protein-coding
mm_157985.1	chrX	94177854	94177864	-	1	NA	Intergenic	CpG	34792	NM_012010	26905	Mm.218851	NM_012010	ENSMUSG00000035150	Eif2s3x	AA409828|AA547477|AI314668|Eif-2gx	eukaryotic translation initiation factor 2, subunit 3, structural gene X-linked	protein-coding
mm_168737.1	chr12	115145969	115145974	-	1	NA	Intergenic	Intergenic	549823	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
mm_15746.1	chr2	164237514	164237520	+	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	824	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_26704.1	chr3	157768100	157768104	+	1	NA	Intergenic	B3|SINE|B2	156961	NM_145953	107869	Mm.28301	NM_145953	ENSMUSG00000028179	Cth	0610010I13Rik|AI314617|BC019483|CSE|Cys3	cystathionase (cystathionine gamma-lyase)	protein-coding
mm_122543.1	chr14	47649215	47649264	-	1	NA	promoter-TSS (NM_001293636)	promoter-TSS (NM_001293636)	-72	NM_001347527	16709	Mm.3110	NM_008477	ENSMUSG00000021843	Ktn1	-	kinectin 1	protein-coding
mm_124438.1	chr14	118706151	118706176	-	1	NA	promoter-TSS (NM_001163676)	promoter-TSS (NM_001163676)	56	NM_001163676	239273	Mm.40537	NM_001033336	ENSMUSG00000032849	Abcc4	ABCC4-N1|D630049P08Rik|MOATB|MRP4	ATP-binding cassette, sub-family C (CFTR/MRP), member 4	protein-coding
mm_63006.1	chr7	120851184	120851194	+	1	NA	promoter-TSS (NM_001267711)	promoter-TSS (NM_001267711)	0	NM_001267711	13631	Mm.25997	NM_007908	ENSMUSG00000035064	Eef2k	C86191|eEF-2K	eukaryotic elongation factor-2 kinase	protein-coding
mm_74852.1	chr8	24674708	24674740	-	1	NA	promoter-TSS (NM_010084)	promoter-TSS (NM_010084)	31	NR_136908	13524	Mm.89943	NM_010084	ENSMUSG00000031552	Adam18	Adam27|Dtgn3|Tmdc3|tMDCIII	a disintegrin and metallopeptidase domain 18	protein-coding
mm_122693.1	chr14	52066162	52066169	-	1	NA	Intergenic	RLTR9D|LTR|ERVK	-3150	NR_028552	100217457		NR_028552	ENSMUSG00000064871	Snord58b	MBII-199	small nucleolar RNA, C/D box 58B	snoRNA
mm_92943.1	chr10	85099409	85099428	-	1	NA	5' UTR (NM_010214, exon 2 of 2)	5' UTR (NM_010214, exon 2 of 2)	3077	NM_010214	14202	Mm.46163	NM_010214	ENSMUSG00000050035	Fhl4	-	four and a half LIM domains 4	protein-coding
mm_153810.1	chr19	46045350	46045360	-	1	NA	promoter-TSS (NM_001113408)	promoter-TSS (NM_001113408)	-144	NM_001113408	16825	Mm.327442	NM_010697	ENSMUSG00000025223	Ldb1	CLIM2|NLI	LIM domain binding 1	protein-coding
mm_18718.1	chr2	72446379	72446388	-	1	NA	Intergenic	Intergenic	-29836	NM_025866	66953	Mm.270676	NM_025866	ENSMUSG00000055612	Cdca7	2310021G01Rik|AU044109|JPO1	cell division cycle associated 7	protein-coding
mm_7368.1	chr1	106724482	106724484	-	1	NA	3' UTR (NM_027534, exon 10 of 10)	3' UTR (NM_027534, exon 10 of 10)	-10193	NM_177410	12043	Mm.257460	NM_009741	ENSMUSG00000057329	Bcl2	AW986256|Bcl-2|C430015F12Rik|D630044D05Rik|D830018M01Rik	B cell leukemia/lymphoma 2	protein-coding
mm_151446.1	chr19	57610946	57610963	+	1	NA	promoter-TSS (NM_181415)	promoter-TSS (NM_181415)	-80	NM_181415	226255	Mm.245340	NM_181415	ENSMUSG00000054843	Atrnl1	AI504415|AW555641|Alp|Atrnl|Atrnlp	attractin like 1	protein-coding
mm_167363.1	chr8	84969709	84969715	+	1	NA	promoter-TSS (NM_011563)	promoter-TSS (NM_011563)	90	NM_011563	21672	Mm.347009	NM_011563	ENSMUSG00000005161	Prdx2	AL022839|Band-8|NkefB|PRP|PrxII|TDX1|TPx|TPx-B|TR|TSA|Tdpx1|Torin	peroxiredoxin 2	protein-coding
mm_126826.1	chr15	88858619	88858632	+	1	NA	Intergenic	Intergenic	-3569	NM_145478	223775	Mm.400129	NM_145478	ENSMUSG00000035828	Pim3	BC026639|Kid1	proviral integration site 3	protein-coding
mm_161877.1	chr18	37294819	37294819	+	1	NA	promoter-TSS (NM_053127)	promoter-TSS (NM_053127)	-21	NM_053127	93873	Mm.197508	NM_053127	ENSMUSG00000051599	Pcdhb2	PcdhbB	protocadherin beta 2	protein-coding
mm_104604.1	chr11	97187649	97187680	-	1	NA	5' UTR (NM_008379, exon 1 of 22)	5' UTR (NM_008379, exon 1 of 22)	228	NM_008379	16211	Mm.251013	NM_008379	ENSMUSG00000001440	Kpnb1	AA409963|IPOB|Impnb	karyopherin (importin) beta 1	protein-coding
mm_52327.1	chr6	108844668	108844670	+	1	NA	intron (NM_138677, intron 4 of 11)	B1F|SINE|Alu	16028	NM_138677	192193	Mm.21596	NM_138677	ENSMUSG00000030104	Edem1	A130059K23Rik|EDEM|mKIAA0212	ER degradation enhancer, mannosidase alpha-like 1	protein-coding
mm_39979.1	chr5	32459017	32459110	+	1	NA	promoter-TSS (NM_172707)	promoter-TSS (NM_172707)	93	NM_172707	19046	Mm.241931	NM_172707	ENSMUSG00000014956	Ppp1cb	1200010B19	protein phosphatase 1, catalytic subunit, beta isoform	protein-coding
mm_30742.1	chr4	14863995	14864018	+	1	NA	promoter-TSS (NM_028264)	promoter-TSS (NM_028264)	-213	NM_028264	72519	Mm.279158	NM_028264	ENSMUSG00000028221	Tmem55a	2610319K07Rik|AI315591|AV001360	transmembrane protein 55A	protein-coding
mm_74797.1	chr8	22398589	22398612	-	1	NA	promoter-TSS (NM_181325)	promoter-TSS (NM_181325)	21	NM_181325	18408	Mm.200907	NM_181325	ENSMUSG00000031482	Slc25a15	D630044L02Rik|Ornt1	solute carrier family 25 (mitochondrial carrier ornithine transporter), member 15	protein-coding
mm_149743.1	chr19	22448120	22448145	+	1	NA	promoter-TSS (NM_177341)	promoter-TSS (NM_177341)	-76	NM_177341	226025	Mm.131943	NM_177341	ENSMUSG00000052387	Trpm3	6330504P12Rik|9330180E14|AU018608|B930001P07Rik|LTRPC3|MLSN2	transient receptor potential cation channel, subfamily M, member 3	protein-coding
mm_112728.1	chr13	19192905	19192945	+	1	NA	Intergenic	MIR3|SINE|MIR	202888	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_95879.1	chr11	58093237	58093257	+	1	NA	Intergenic	Intergenic	-10906	NM_026949	69125	Mm.28910	NM_026949	ENSMUSG00000020515	Cnot8	1500015I04Rik|1810022F04Rik|AA536816|AU015770|AU043059	CCR4-NOT transcription complex, subunit 8	protein-coding
mm_60296.1	chr7	44015954	44015996	+	1	NA	exon (NM_010644, exon 3 of 5)	exon (NM_010644, exon 3 of 5)	3278	NM_010115	13647	Mm.439663	NM_010115		Egfbp2	Egfbp-2|Klk1b26|mGk-13	epidermal growth factor binding protein type B	protein-coding
mm_100345.1	chr11	118419224	118419251	+	1	NA	promoter-TSS (NM_029502)	promoter-TSS (NM_029502)	-119	NM_001267592	76025	Mm.177551	NM_029502	ENSMUSG00000025575	Cant1	5830420C20Rik|Apy1h|D11Bwg0554e|Entpd8|SCAN-1|Shapy	calcium activated nucleotidase 1	protein-coding
mm_146064.1	chr18	69925480	69925537	+	1	NA	promoter-TSS (NM_201362)	promoter-TSS (NM_201362)	-51	NM_201362	381175	Mm.266831	NM_201362	ENSMUSG00000038903	Ccdc68	BC046343	coiled-coil domain containing 68	protein-coding
mm_132055.1	chr16	29579427	29579439	+	1	NA	promoter-TSS (NM_133752)	promoter-TSS (NM_133752)	99	NM_001199177	74143	Mm.274285	NM_133752	ENSMUSG00000038084	Opa1	1200011N24Rik|AI225888|AI847218|lilr3|mKIAA0567	OPA1, mitochondrial dynamin like GTPase	protein-coding
mm_2760.1	chr1	130462273	130462312	+	1	NA	intron (NM_010016, intron 1 of 9)	intron (NM_010016, intron 1 of 9)	452	NM_010016	13136	Mm.101591	NM_010016	ENSMUSG00000026399	Cd55	Daf|Daf-GPI|Daf1|GPI-DAF	CD55 molecule, decay accelerating factor for complement	protein-coding
mm_144607.1	chr18	32407594	32407630	+	1	NA	intron (NM_001083334, intron 2 of 14)	intron (NM_001083334, intron 2 of 14)	-29328	NR_045403	402767	Mm.385109	NR_045403	ENSMUSG00000097413	A830052D11Rik	-	RIKEN cDNA A830052D11 gene	ncRNA
mm_145693.1	chr18	62180120	62180182	+	1	NA	promoter-TSS (NM_007420)	promoter-TSS (NM_007420)	-170	NM_007420	11555	Mm.5598	NM_007420	ENSMUSG00000045730	Adrb2	Adrb-2|Badm|Gpcr7	adrenergic receptor, beta 2	protein-coding
mm_32872.1	chr4	118527034	118527064	+	1	NA	promoter-TSS (NM_025572)	promoter-TSS (NM_025572)	-226	NM_025572	66451	Mm.34431	NM_025572	ENSMUSG00000028536	2610528J11Rik	TEMP	RIKEN cDNA 2610528J11 gene	protein-coding
mm_52318.1	chr6	108836331	108836337	+	1	NA	intron (NM_138677, intron 1 of 11)	intron (NM_138677, intron 1 of 11)	7693	NM_138677	192193	Mm.21596	NM_138677	ENSMUSG00000030104	Edem1	A130059K23Rik|EDEM|mKIAA0212	ER degradation enhancer, mannosidase alpha-like 1	protein-coding
mm_47488.1	chr5	123891790	123891808	-	1	NA	Intergenic	Intergenic	-11779	NM_175520	243270	Mm.33362	NM_175520	ENSMUSG00000049241	Hcar1	Gpr81	hydrocarboxylic acid receptor 1	protein-coding
mm_147232.1	chr18	38250128	38250140	-	1	NA	promoter-TSS (NM_024179)	promoter-TSS (NM_024179)	64	NR_015475	73516	Mm.48776	NR_015475	ENSMUSG00000097080	1700086O06Rik	-	RIKEN cDNA 1700086O06 gene	ncRNA
mm_145068.1	chr18	41579477	41579482	+	1	NA	Intergenic	Lx5c|LINE|L1	371715	NM_029942	77619	Mm.30649	NM_029942	ENSMUSG00000056671	Prelid2	1700003A01Rik|C330008K14Rik	PRELI domain containing 2	protein-coding
mm_36847.1	chr4	106727982	106728001	-	1	NA	promoter-TSS (NM_001126487)	promoter-TSS (NM_001126487)	-61	NM_001126487	381538	Mm.318201	NM_001126487	ENSMUSG00000047502	Mroh7	Gm1027|Heatr8	maestro heat-like repeat family member 7	protein-coding
mm_47692.1	chr5	129670104	129670115	-	1	NA	promoter-TSS (NM_172462)	promoter-TSS (NM_172462)	-21	NM_172462	22648	Mm.135067	NM_172462	ENSMUSG00000051034	Zfp11	6720465D24|Krox-6|Zfp-11	zinc finger protein 11	protein-coding
mm_65207.1	chr7	19697535	19697588	-	1	NA	exon (NM_009696, exon 3 of 4)	exon (NM_009696, exon 3 of 4)	837	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_145007.1	chr18	38428762	38428762	+	1	NA	intron (NM_022996, intron 1 of 7)	intron (NM_022996, intron 1 of 7)	9787	NM_022996	65113	Mm.102496	NM_022996	ENSMUSG00000024425	Ndfip1	0610010M22Rik|N4wbp5	Nedd4 family interacting protein 1	protein-coding
mm_156729.1	chrX	159917226	159917240	+	1	NA	intron (NM_001135728, intron 5 of 12)	intron (NM_001135728, intron 5 of 12)	-25460	NM_001290661	58194	Mm.286495	NM_021389	ENSMUSG00000040990	Sh3kbp1	1200007H22Rik|1700125L08Rik|5830464D22Rik|AI447724|Cin85|IN85|Ruk|Seta	SH3-domain kinase binding protein 1	protein-coding
mm_12521.1	chr2	72145591	72145613	+	1	NA	intron (NM_019688, intron 6 of 29)	intron (NM_019688, intron 6 of 29)	90985	NM_001204166	56508	Mm.196153	NM_019688	ENSMUSG00000049044	Rapgef4	1300003D15Rik|5730402K07Rik|6330581N18Rik|EPAC 2|Epac-2|Epac2|mKIAA4040	Rap guanine nucleotide exchange factor (GEF) 4	protein-coding
mm_13547.1	chr2	112239365	112239409	+	1	NA	promoter-TSS (NM_207206)	promoter-TSS (NM_207206)	-454	NM_207206	99010	Mm.33438	NM_207206	ENSMUSG00000027134	Lpcat4	AI505034|Agpat7|Aytl3|LPEAT2	lysophosphatidylcholine acyltransferase 4	protein-coding
mm_39250.1	chr5	3501998	3502008	+	1	NA	intron (NM_009873, intron 5 of 7)	intron (NM_009873, intron 5 of 7)	-41830	NM_001042501	68152	Mm.240265	NM_026583	ENSMUSG00000058503	Fam133b	2900022K02Rik|5830415L20Rik	family with sequence similarity 133, member B	protein-coding
mm_75630.1	chr8	64693028	64693038	-	1	NA	promoter-TSS (NM_013494)	promoter-TSS (NM_013494)	76	NM_013494	12876	Mm.31395	NM_013494	ENSMUSG00000037852	Cpe	CPH|Cph-1|Cph1|R74677|fat	carboxypeptidase E	protein-coding
mm_124685.1	chr15	6435201	6435214	+	1	NA	exon (NM_001102400, exon 10 of 13)	exon (NM_001102400, exon 10 of 13)	-10126	NM_013485	12279	Mm.29095	NM_013485	ENSMUSG00000022149	C9	-	complement component 9	protein-coding
mm_147462.1	chr18	46612229	46612240	-	1	NA	Intergenic	Intergenic	14530	NM_010120	13664	Mm.262037	NM_010120	ENSMUSG00000057561	Eif1a	C76390|Ef1a|Eftu|Eif4c|eIF-1A|eIF-4C	eukaryotic translation initiation factor 1A	protein-coding
mm_31478.1	chr4	51659192	51659193	+	1	NA	Intergenic	Intergenic	391918	NR_040668	329844	Mm.128934	NR_040668	ENSMUSG00000085515	C630028M04Rik	-	RIKEN cDNA C630028M04 gene	ncRNA
mm_80112.1	chr9	70526881	70526892	+	1	NA	Intergenic	Intergenic	-15892	NM_026337	66660	Mm.22379	NM_025690	ENSMUSG00000032212	Sltm	5730455C01Rik|5730555F13Rik|9130215G10Rik|Met	SAFB-like, transcription modulator	protein-coding
mm_112216.1	chr12	113428790	113428800	-	1	NA	Intergenic	Intergenic	-60770	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_76558.1	chr8	88362155	88362210	-	1	NA	promoter-TSS (NM_012047)	promoter-TSS (NM_012047)	9	NM_012047	26992	Mm.5400	NM_012047	ENSMUSG00000031660	Brd7	BP75|CELTIX1|Ptpn13ip	bromodomain containing 7	protein-coding
mm_12685.1	chr2	75892261	75892292	+	1	NA	intron (NM_172666, intron 13 of 19)	intron (NM_172666, intron 13 of 19)	46186	NM_028235	72421	Mm.275109	NM_028235	ENSMUSG00000075273	Ttc30b	2510042P03Rik|Tcc30b	tetratricopeptide repeat domain 30B	protein-coding
mm_67864.1	chr7	99141069	99141149	-	1	NA	promoter-TSS (NM_178635)	promoter-TSS (NM_178635)	35	NM_178635	78610	Mm.323072	NM_178635	ENSMUSG00000035354	Uvrag	9530039D02Rik|AI648770|BB124205|Uvrag1|Uvragl	UV radiation resistance associated gene	protein-coding
mm_156790.1	chrX	162760368	162760378	+	1	NA	promoter-TSS (NM_009031)	promoter-TSS (NM_009031)	1	NM_009031	245688	Mm.270186	NM_009031	ENSMUSG00000031353	Rbbp7	AA409861|AI173248|AU019541|BB114024|mRbAp46	retinoblastoma binding protein 7	protein-coding
mm_139974.1	chr17	71781243	71781253	+	1	NA	promoter-TSS (NM_030179)	promoter-TSS (NM_030179)	-51	NM_001271483	78785	Mm.196382	NM_030179	ENSMUSG00000024059	Clip4	1700024K14Rik|1700074B05Rik|4833417L20Rik|5830409B12Rik|Rsnl2	CAP-GLY domain containing linker protein family, member 4	protein-coding
mm_103494.1	chr11	76571344	76571364	-	1	NA	promoter-TSS (NM_198895)	promoter-TSS (NM_198895)	30	NM_198895	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_35885.1	chr4	49541179	49541249	-	1	NA	exon (NM_144903, exon 5 of 9)	exon (NM_144903, exon 5 of 9)	8332	NM_144903	230163	Mm.482116	NM_144903	ENSMUSG00000028307	Aldob	Aldo-2|Aldo2|BC016435	aldolase B, fructose-bisphosphate	protein-coding
mm_164312.1	chr15	103897540	103897557	-	1	NA	exon (NM_009267, exon 3 of 4)	exon (NM_009267, exon 3 of 4)	1752	NM_009268	20771	Mm.30276	NM_009268		Mucl1	Spt-2|Spt2	mucin-like 1	protein-coding
mm_52291.1	chr6	108665917	108665926	+	1	NA	3' UTR (NM_011498, exon 5 of 5)	3' UTR (NM_011498, exon 5 of 5)	-4987	NR_104577	75394	Mm.395061	NR_040757	ENSMUSG00000087341	0610040F04Rik	-	RIKEN cDNA 0610040F04 gene	ncRNA
mm_120733.1	chr14	73152589	73152590	+	1	NA	intron (NM_134083, intron 2 of 14)	intron (NM_134083, intron 2 of 14)	9804	NR_033185	105670	Mm.280068	NM_134083	ENSMUSG00000022106	Rcbtb2	2610028E02Rik|2810420M18Rik|AI448345|AW240694|Chc1l|RC/BTB2	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 2	protein-coding
mm_132664.1	chr16	42149189	42149192	+	1	NA	intron (NM_001347236, intron 6 of 6)	intron (NM_001347236, intron 6 of 6)	154279	NR_105858	102466172		NR_105858	ENSMUSG00000098300	Mir6540	Gm27780|mir-6540|mmu-mir-6540	microRNA 6540	ncRNA
mm_123273.1	chr14	61370444	61370480	-	1	NA	exon (NM_008466, exon 15 of 17)	exon (NM_008466, exon 15 of 17)	-10017	NM_026598	68177	Mm.22758	NM_026598	ENSMUSG00000021928	Ebpl	5730442K12Rik|EBRP	emopamil binding protein-like	protein-coding
mm_58031.1	chr6	136662232	136662252	-	1	NA	promoter-TSS (NM_025806)	promoter-TSS (NM_025806)	-349	NM_025806	66857	Mm.3311	NM_025806	ENSMUSG00000030214	Plbd1	1100001H23Rik	phospholipase B domain containing 1	protein-coding
mm_44106.1	chr5	149368414	149368423	+	1	NA	Intergenic	Intergenic	-43388	NM_027519	70717	Mm.252139	NM_027519	ENSMUSG00000029659	Medag	6330406I15Rik|Awms3|MEDA-4|Meda4|mAWMS3	mesenteric estrogen dependent adipogenesis	protein-coding
mm_12672.1	chr2	75768925	75768925	+	1	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	-63252	NM_172666	228061	Mm.31227	NM_172666	ENSMUSG00000042410	Agps	5832437L22|9930035G10Rik|AW123847|Adaps|Adas|Adhaps|Adps|Aldhpsy|bs2	alkylglycerone phosphate synthase	protein-coding
mm_44485.1	chr5	23518796	23518809	-	1	NA	intron (NM_009274, intron 10 of 14)	intron (NM_009274, intron 10 of 14)	84373	NM_026984	69188	Mm.205190	NM_026984	ENSMUSG00000029004	Kmt2e	1810033J14Rik|9530077A04Rik|D230038D11Rik|Mll5|NKp44L	lysine (K)-specific methyltransferase 2E	protein-coding
mm_121442.1	chr14	120430196	120430218	+	1	NA	3' UTR (NM_207515, exon 8 of 8)	3' UTR (NM_207515, exon 8 of 8)	-48254	NM_029519	76108	Mm.261448	NM_029519	ENSMUSG00000051615	Rap2a	5830461H18Rik	RAS related protein 2a	protein-coding
mm_162286.1	chr1	24612684	24612694	+	1	NA	Intergenic	Intergenic	-25252	NM_007733	12823	Mm.329196	NM_007733	ENSMUSG00000026141	Col19a1	-	collagen, type XIX, alpha 1	protein-coding
mm_108609.1	chr12	85475586	85475596	+	1	NA	intron (NM_010234, intron 2 of 3)	intron (NM_010234, intron 2 of 3)	1690	NM_010234	14281	Mm.246513	NM_010234	ENSMUSG00000021250	Fos	D12Rfj1|c-fos|cFos	FBJ osteosarcoma oncogene	protein-coding
mm_2812.1	chr1	130874326	130874333	+	1	NA	exon (NM_026976, exon 2 of 8)	exon (NM_026976, exon 2 of 8)	8552	NM_026976	69169	Mm.46042	NM_026976	ENSMUSG00000042474	Fcmr	1810037B05Rik|Faim3|FcmuR|Toso	Fc fragment of IgM receptor	protein-coding
mm_56863.1	chr6	118350448	118350475	-	1	NA	Intergenic	Intergenic	-41742	NR_110507	102632423	Mm.261755	NR_110507	ENSMUSG00000107933	Gm30498	-	predicted gene, 30498	ncRNA
mm_110589.1	chr12	56529549	56529558	-	1	NA	promoter-TSS (NR_045082)	promoter-TSS (NR_045082)	-133	NR_045082	104798	Mm.310950	NR_045082		E030019B13Rik	AI413669	RIKEN cDNA E030019B13 gene	ncRNA
mm_19859.1	chr2	113829643	113829676	-	1	NA	promoter-TSS (NM_009162)	promoter-TSS (NM_009162)	-568	NM_009162	20394	Mm.4836	NM_009162	ENSMUSG00000023236	Scg5	7B2|AI325031|Sgne-1|Sgne1	secretogranin V	protein-coding
mm_170517.1	chr19	30539774	30539787	-	1	NA	promoter-TSS (NR_003650)	promoter-TSS (NR_003650)	-101	NR_003650	546723	Mm.301509	NM_001037169		Ppp1r2-ps3	EG546723|Gm5972	protein phosphatase 1, regulatory (inhibitor) subunit 2, pseudogene 3	pseudo
mm_173254.1	chrX	94615835	94615842	+	1	NA	Intergenic	Intergenic	-20231	NM_008179	14853	Mm.20826	NM_008179	ENSMUSG00000071723	Gspt2	-	G1 to S phase transition 2	protein-coding
mm_140255.1	chr17	84466350	84466364	+	1	NA	promoter-TSS (NM_183021)	promoter-TSS (NM_183021)	-149	NM_183021	240174	Mm.246767	NM_177826	ENSMUSG00000024251	Thada	6530405K19|A930021O22|AU019899|BC052885|GITA	thyroid adenoma associated	protein-coding
mm_167483.1	chr8	129252920	129252935	+	1	NA	Intergenic	B4A|SINE|B4	-10703	NM_001346808	102635552		NM_001346808		Gm32856	-	predicted gene, 32856	protein-coding
mm_148744.1	chr19	6046105	6046113	+	1	NA	promoter-TSS (NM_028769)	promoter-TSS (NM_028769)	-467	NM_028769	74126	Mm.149870	NM_028769	ENSMUSG00000024807	Syvn1	1200010C09Rik|AW211966|C85322|D530017H19Rik|Hrd1	synovial apoptosis inhibitor 1, synoviolin	protein-coding
mm_40273.1	chr5	41187717	41187717	+	1	NA	Intergenic	Intergenic	519974	NM_001310592	100972	Mm.41555	NM_027295	ENSMUSG00000029128	Rab28	2700023P08Rik|AW496496	RAB28, member RAS oncogene family	protein-coding
mm_112906.1	chr13	20902971	20902983	+	1	NA	intron (NM_012054, intron 5 of 20)	intron (NM_012054, intron 5 of 20)	108864	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_125989.1	chr15	76351304	76351337	+	1	NA	promoter-TSS (NM_026859)	promoter-TSS (NM_026859)	26	NM_026859	68877	Mm.289680	NM_026859	ENSMUSG00000022553	Maf1	1110068E11Rik|AU042856	MAF1 homolog, negative regulator of RNA polymerase III	protein-coding
mm_51251.1	chr6	71831427	71831437	+	1	NA	5' UTR (NM_029673, exon 1 of 15)	5' UTR (NM_029673, exon 1 of 15)	112	NM_001253688	76614	Mm.235123	NM_029673	ENSMUSG00000052337	Immt	1700082C19Rik|D830041H16Rik|HMP|P87|P87/89|P89	inner membrane protein, mitochondrial	protein-coding
mm_133843.1	chr16	96200610	96200620	+	1	NA	5' UTR (NM_015825, exon 1 of 8)	5' UTR (NM_015825, exon 1 of 8)	145	NM_015825	50795	Mm.28638	NM_015825	ENSMUSG00000040666	Sh3bgr	5430437A18Rik	SH3-binding domain glutamic acid-rich protein	protein-coding
mm_122332.1	chr14	37110088	37110106	-	1	NA	promoter-TSS (NM_001206684)	promoter-TSS (NM_001206684)	4	NM_001206684	70045	Mm.271619	NM_001206684	ENSMUSG00000096001	2610528A11Rik	AW494830	RIKEN cDNA 2610528A11 gene	protein-coding
mm_27987.1	chr3	82074640	82074716	-	1	NA	promoter-TSS (NM_001161796)	promoter-TSS (NM_001161796)	33	NM_017469	54195	Mm.9445	NM_017469	ENSMUSG00000028005	Gucy1b3	GC-S-beta-1|GCbeta1	guanylate cyclase 1, soluble, beta 3	protein-coding
mm_79973.1	chr9	66593506	66593550	+	1	NA	promoter-TSS (NM_144937)	promoter-TSS (NM_144937)	-413	NM_001302122	235441	Mm.32465	NM_144937	ENSMUSG00000032376	Usp3	AA409661|BC017156	ubiquitin specific peptidase 3	protein-coding
mm_115013.1	chr13	98354775	98354790	+	1	NA	exon (NM_008242, exon 1 of 1)	exon (NM_008242, exon 1 of 1)	537	NM_008242	15229	Mm.347441	NM_008242	ENSMUSG00000078302	Foxd1	AI385632|BF-2|FREAC4|Hfh10|Hfhbf2	forkhead box D1	protein-coding
mm_16418.1	chr2	180171563	180171573	+	1	NA	promoter-TSS (NM_019822)	promoter-TSS (NM_019822)	-20	NM_019822	56436	Mm.316654	NM_019822	ENSMUSG00000039041	Adrm1	1110063P18Rik|2510006J17Rik|AA408205|ARM-1|AU043535|Arm1|Gp110|Rpn13	adhesion regulating molecule 1	protein-coding
mm_60998.1	chr7	49303822	49303888	+	1	NA	intron (NM_175272, intron 1 of 37)	intron (NM_175272, intron 1 of 37)	57666	NM_175272	78286	Mm.333881	NM_175272	ENSMUSG00000052512	Nav2	5330421F07Rik|AU067780|BQ960892|HELAD1|POMFIL2|RAINB1|RAINB2|Unc53H2|mKIAA3015	neuron navigator 2	protein-coding
mm_51170.1	chr6	70726605	70726607	+	1	NA	Intergenic	Intergenic	65569	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_46964.1	chr5	115148056	115148074	-	1	NA	exon (NM_175403, exon 5 of 5)	exon (NM_175403, exon 5 of 5)	10111	NM_175403	109154	Mm.153963	NM_175403	ENSMUSG00000048578	Mlec	2410014A08Rik|AI850530|ESTM19|X83352|mKIAA0152	malectin	protein-coding
mm_60843.1	chr7	45783884	45783944	+	1	NA	promoter-TSS (NR_110987)	promoter-TSS (NR_110987)	-33	NM_001005511	381983	Mm.44928	NM_001005511	ENSMUSG00000062044	Lmtk3	BC059845|aatyk3	lemur tyrosine kinase 3	protein-coding
mm_117732.1	chr13	95618443	95618475	-	1	NA	promoter-TSS (NM_010169)	promoter-TSS (NM_010169)	-26	NM_010169	14062	Mm.24816	NM_010169	ENSMUSG00000048376	F2r	AI482343|Cf2r|Par1|ThrR	coagulation factor II (thrombin) receptor	protein-coding
mm_71338.1	chr8	45507895	45507905	+	1	NA	5' UTR (NM_001205219, exon 1 of 24)	5' UTR (NM_001205219, exon 1 of 24)	112	NM_001205219	234214	Mm.211096	NM_172752	ENSMUSG00000031626	Sorbs2	2010203O03Rik|9430041O17Rik|A530071H08|Argbp2|mKIAA0777|nArgBP2	sorbin and SH3 domain containing 2	protein-coding
mm_8326.1	chr1	149922340	149922373	-	1	NA	promoter-TSS (NM_001305632)	promoter-TSS (NM_001305632)	83	NM_001305632	18783	Mm.4186	NM_008869	ENSMUSG00000056220	Pla2g4a	Pla2g4|cPLA2|cPLA2-alpha|cPLA2alpha	phospholipase A2, group IVA (cytosolic, calcium-dependent)	protein-coding
mm_66424.1	chr7	44552061	44552071	-	1	NA	exon (NM_009473, exon 5 of 10)	exon (NM_009473, exon 5 of 10)	1899	NM_009473	22260	Mm.968	NM_009473	ENSMUSG00000060601	Nr1h2	AI194859|LXR|LXRB|LXRBSV|LXRbeta|NER1|OR-1|RIP15|UR|Unr|Unr2	nuclear receptor subfamily 1, group H, member 2	protein-coding
mm_71726.1	chr8	61976851	61976868	+	1	NA	intron (NM_001293783, intron 17 of 37)	intron (NM_001293783, intron 17 of 37)	48772	NM_001293783	234311	Mm.275233	NM_144928	ENSMUSG00000037921	Ddx60	9830118M07	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	protein-coding
mm_125456.1	chr15	52040396	52040406	+	1	NA	exon (NM_175503, exon 1 of 2)	exon (NM_175503, exon 1 of 2)	294	NM_175503	239435	Mm.24204	NM_175503	ENSMUSG00000068522	Aard	A5D3|AV328152	alanine and arginine rich domain containing protein	protein-coding
mm_126239.1	chr15	78987128	78987137	+	1	NA	intron (NM_001024716, intron 1 of 13)	intron (NM_001024716, intron 1 of 13)	4076	NM_001024716	110253	Mm.123714	NM_138579	ENSMUSG00000033088	Triobp	AI428493|EST478828|Tara|mKIAA1662	TRIO and F-actin binding protein	protein-coding
mm_63917.1	chr7	139248411	139248456	+	1	NA	promoter-TSS (NM_001098636)	promoter-TSS (NM_001098636)	-49	NM_001033206	101631	Mm.334300	NM_001033206	ENSMUSG00000060260	Pwwp2b	AI594893|D7Ertd517e|D930023J19Rik|Pwwp2	PWWP domain containing 2B	protein-coding
mm_69198.1	chr7	127375960	127375988	-	1	NA	promoter-TSS (NM_175560)	promoter-TSS (NM_175560)	76	NM_175560	269997	Mm.221270	NM_175560	ENSMUSG00000054381	Zfp747	6430604K15Rik	zinc finger protein 747	protein-coding
mm_148539.1	chr19	4604534	4604541	+	1	NA	exon (NM_001162946, exon 9 of 21)	exon (NM_001162946, exon 9 of 21)	10218	NM_008797	18563	Mm.1845	NM_008797	ENSMUSG00000024892	Pcx	Pc|Pcb	pyruvate carboxylase	protein-coding
mm_48551.1	chr5	142906722	142906726	-	1	NA	promoter-TSS (NM_007393)	promoter-TSS (NM_007393)	30	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_163818.1	chr14	19416616	19416656	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	185951	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_79662.1	chr9	59657525	59657581	+	1	NA	intron (NM_001253883, intron 1 of 10)	CpG	1185	NM_001253883	18746	Mm.326167	NM_011099	ENSMUSG00000032294	Pkm	AA414905|AL024370|AL024424|Pk-2|Pk-3|Pk3|Pkm2	pyruvate kinase, muscle	protein-coding
mm_69982.1	chr7	142380818	142380835	-	1	NA	exon (NM_009983, exon 5 of 9)	exon (NM_009983, exon 5 of 9)	7044	NM_009983	13033	Mm.231395	NM_009983	ENSMUSG00000007891	Ctsd	CD|CatD	cathepsin D	protein-coding
mm_118807.1	chr14	25459207	25459225	+	1	NA	promoter-TSS (NM_183208)	promoter-TSS (NM_183208)	31	NM_183208	328365	Mm.227484	NM_183208	ENSMUSG00000007817	Zmiz1	BC065120|E330020C23|ENSMUSG00000072684|Gm10397|I920194n01|Rai17|Zimp10	zinc finger, MIZ-type containing 1	protein-coding
mm_17542.1	chr2	29827027	29827044	-	1	NA	promoter-TSS (NM_026615)	promoter-TSS (NM_026615)	-354	NM_026615	68205	Mm.20273	NM_026615	ENSMUSG00000069020	Urm1	2900073H19Rik	ubiquitin related modifier 1	protein-coding
mm_18462.1	chr2	62343729	62343739	-	1	NA	intron (NM_001159543, intron 23 of 24)	intron (NM_001159543, intron 23 of 24)	68497	NM_010074	13482	Mm.1151	NM_010074	ENSMUSG00000035000	Dpp4	Cd26|Dpp-4|THAM	dipeptidylpeptidase 4	protein-coding
mm_10812.1	chr2	24350301	24350303	+	1	NA	3' UTR (NM_031167, exon 5 of 5)	3' UTR (NM_031167, exon 5 of 5)	4931	NM_001039701	16181	Mm.882	NM_031167	ENSMUSG00000026981	Il1rn	F630041P17Rik|IL-1ra	interleukin 1 receptor antagonist	protein-coding
mm_75866.1	chr8	70760956	70760968	-	1	NA	promoter-TSS (NM_183170)	promoter-TSS (NM_183170)	-41	NM_183170	234384	Mm.213010	NM_183170	ENSMUSG00000035559	Mpv17l2	Fksg24	MPV17 mitochondrial membrane protein-like 2	protein-coding
mm_164004.1	chr14	66859507	66859510	+	1	NA	intron (NM_009955, intron 3 of 13)	intron (NM_009955, intron 3 of 13)	9092	NM_009955	12934	Mm.352648	NM_009955	ENSMUSG00000022048	Dpysl2	AI851130|Crmp2|DRP2|Musunc33|TOAD-64|Ulip2	dihydropyrimidinase-like 2	protein-coding
mm_36262.1	chr4	63495983	63496033	-	1	NA	promoter-TSS (NM_001008793)	promoter-TSS (NM_001008793)	-17	NM_001008791	73750	Mm.300397	NM_028640	ENSMUSG00000039137	Whrn	1110035G07Rik|AW122018|AW742671|C430046P22Rik|Dfnb31|Ush2d|wi	whirlin	protein-coding
mm_172912.1	chr9	63399371	63399375	+	1	NA	promoter-TSS (NM_027090)	promoter-TSS (NM_027090)	-129	NM_027090	69478	Mm.113942	NM_027090	ENSMUSG00000032403	2300009A05Rik	-	RIKEN cDNA 2300009A05 gene	protein-coding
mm_149423.1	chr19	11447489	11447511	+	1	NA	intron (NM_021718, intron 1 of 6)	intron (NM_021718, intron 1 of 6)	3942	NM_021718	60361	Mm.33957	NM_021718	ENSMUSG00000056290	Ms4a4b	AI463180|Chandra|Ly116	membrane-spanning 4-domains, subfamily A, member 4B	protein-coding
mm_152722.1	chr19	18589730	18589761	-	1	NA	exon (NM_017375, exon 7 of 10)	exon (NM_017375, exon 7 of 10)	42068	NM_017375	20409	Mm.172222	NM_017375	ENSMUSG00000024725	Ostf1	C78236|SH3P2|Sh3d3	osteoclast stimulating factor 1	protein-coding
mm_43270.1	chr5	130384693	130384717	+	1	NA	promoter-TSS (NM_198665)	promoter-TSS (NM_198665)	-74	NM_198665	381673	Mm.192133	NM_198665	ENSMUSG00000052014	A330070K13Rik	Gm1051	RIKEN cDNA A330070K13 gene	protein-coding
mm_120662.1	chr14	70545284	70545340	+	1	NA	promoter-TSS (NM_180588)	promoter-TSS (NM_180588)	61	NM_180588	72549	Mm.46742	NM_180588	ENSMUSG00000033589	Reep4	2700029E10Rik	receptor accessory protein 4	protein-coding
mm_79626.1	chr9	59291581	59291613	+	1	NA	promoter-TSS (NM_028121)	promoter-TSS (NM_028121)	25	NM_028121	72141	Mm.22456	NM_028121	ENSMUSG00000025236	Adpgk	2610017G09Rik|Adp-gk|C77577	ADP-dependent glucokinase	protein-coding
mm_29838.1	chr3	129822472	129822482	-	1	NA	promoter-TSS (NM_009102)	promoter-TSS (NM_009102)	28	NM_009102	20132	Mm.278758	NM_009102	ENSMUSG00000028012	Rrh	-	retinal pigment epithelium derived rhodopsin homolog	protein-coding
mm_67629.1	chr7	84152037	84152049	-	1	NA	promoter-TSS (NM_133722)	promoter-TSS (NM_133722)	-150	NM_133722	70178	Mm.23914	NM_133722	ENSMUSG00000038459	Abhd17c	2210412D01Rik|AL023007|Fam108c|Fam108c1	abhydrolase domain containing 17C	protein-coding
mm_115971.1	chr13	24059321	24059324	-	1	NA	intron (NM_001311122, intron 29 of 37)	intron (NM_001311122, intron 29 of 37)	-68108	NM_145399	214189	Mm.255667	NM_145399	ENSMUSG00000021337	Scgn	-	secretagogin, EF-hand calcium binding protein	protein-coding
mm_113158.1	chr13	24802958	24802972	+	1	NA	5' UTR (NM_024473, exon 1 of 5)	5' UTR (NM_024473, exon 1 of 5)	1308	NM_024473	79555	Mm.266668	NM_024473	ENSMUSG00000019132	BC005537	8030460C05Rik|C78201	cDNA sequence BC005537	protein-coding
mm_56635.1	chr6	113077182	113077203	-	1	NA	promoter-TSS (NR_027008)	promoter-TSS (NR_027008)	52	NR_027010	14910	Mm.280950	NR_027008	ENSMUSG00000086429	Gt(ROSA)26Sor	AV258896|Gtrgeo26|Gtrosa26|R26|ROSA26|Thumpd3as1	gene trap ROSA 26, Philippe Soriano	ncRNA
mm_147853.1	chr18	63692342	63692374	-	1	NA	promoter-TSS (NM_016792)	promoter-TSS (NM_016792)	1	NM_016792	53382	Mm.19169	NM_016792	ENSMUSG00000024583	Txnl1	32kDa|TRP32|Txnl	thioredoxin-like 1	protein-coding
mm_168888.1	chr1	24613964	24613974	-	1	NA	Intergenic	Intergenic	-26532	NM_007733	12823	Mm.329196	NM_007733	ENSMUSG00000026141	Col19a1	-	collagen, type XIX, alpha 1	protein-coding
mm_168831.1	chr12	22745698	22745715	-	1	NA	Intergenic	CpG	264537	NR_015504	69732	Mm.391403	NM_028362	ENSMUSG00000073164	2410018L13Rik	2810480C08Rik	RIKEN cDNA 2410018L13 gene	ncRNA
mm_164676.1	chr17	46555199	46555227	+	1	NA	intron (NM_020493, intron 1 of 6)	CpG	949	NM_020493	20807	Mm.45044	NM_020493	ENSMUSG00000015605	Srf	AW049942|AW240594	serum response factor	protein-coding
mm_165452.1	chr2	157320078	157320102	+	1	NA	intron (NM_019642, intron 14 of 16)	intron (NM_019642, intron 14 of 16)	17336	NM_001329683	14601	Mm.389327	NM_010285	ENSMUSG00000027643	Ghrh	GRF|Ghrf	growth hormone releasing hormone	protein-coding
mm_36381.1	chr4	76914707	76914755	-	1	NA	intron (NM_011211, intron 8 of 39)	intron (NM_011211, intron 8 of 39)	1297164	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding
mm_165075.1	chr19	45058309	45058333	-	1	NA	Intergenic	Intergenic	10745	NM_001178013	94280	Mm.36169	NM_053197	ENSMUSG00000025212	Sfxn3	-	sideroflexin 3	protein-coding
mm_111584.1	chr12	101880539	101880550	-	1	NA	intron (NM_028446, intron 11 of 20)	Lx9|LINE|L1	32627	NM_028446	109181	Mm.208618	NM_028446	ENSMUSG00000021188	Trip11	2610511G22Rik|3110031G15Rik|6030460N08Rik|AI450776|GMAP-210|TRIP230	thyroid hormone receptor interactor 11	protein-coding
mm_163721.1	chr13	113071341	113071358	+	1	NA	intron (NM_001281487, intron 5 of 11)	intron (NM_001281487, intron 5 of 11)	-24961	NM_027127	69590	Mm.12715	NM_027127	ENSMUSG00000021760	Gpx8	2310016C16Rik|AU017063	glutathione peroxidase 8 (putative)	protein-coding
mm_18993.1	chr2	76867237	76867248	-	1	NA	intron (NM_011652, intron 107 of 312)	intron (NM_011652, intron 107 of 312)	115305	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_61624.1	chr7	80198565	80198628	+	1	NA	5' UTR (NM_013659, exon 2 of 15)	5' UTR (NM_013659, exon 2 of 15)	11755	NM_013659	20352	Mm.275909	NM_013659	ENSMUSG00000030539	Sema4b	SemC|Semac|mKIAA1745	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B	protein-coding
mm_117541.1	chr13	83609238	83609255	-	1	NA	intron (NM_001347569, intron 3 of 10)	intron (NM_001347569, intron 3 of 10)	35639	NM_001347569	17260	Mm.24001	NM_025282	ENSMUSG00000005583	Mef2c	5430401D19Rik|9930028G15Rik|AV011172|Mef2	myocyte enhancer factor 2C	protein-coding
mm_172988.1	chrM	1160	1160	+	1	NA	NA	Intergenic	NA	NA								
mm_103655.1	chr11	78973168	78973186	-	1	NA	exon (NM_010708, exon 3 of 11)	exon (NM_010708, exon 3 of 11)	11747	NM_001159301	16859	Mm.341434	NM_010708	ENSMUSG00000001123	Lgals9	AA407335|AI194909|AI265545|LGALS35|Lgals5|gal-9|galectin-9	lectin, galactose binding, soluble 9	protein-coding
mm_168871.1	chr12	3691154	3691159	-	1	NA	intron (NR_027869, intron 9 of 20)	RLTR10D2|LTR|ERVK	-115824	NM_007872	13435	Mm.5001	NM_007872	ENSMUSG00000020661	Dnmt3a	MmuIIIA	DNA methyltransferase 3A	protein-coding
mm_48038.1	chr5	136302516	136302537	-	1	NA	intron (NM_001291233, intron 20 of 23)	intron (NM_001291233, intron 20 of 23)	-57586	NM_018825	23921	Mm.425294	NM_018825	ENSMUSG00000005057	Sh2b2	Aps	SH2B adaptor protein 2	protein-coding
mm_162185.1	chrX	103321440	103321440	+	1	NA	promoter-TSS (NM_007674)	promoter-TSS (NM_007674)	42	NM_007674	12592	Mm.4353	NM_007674	ENSMUSG00000031326	Cdx4	Cdx-3|Cdx-4|Cdx3	caudal type homeobox 4	protein-coding
mm_21383.1	chr2	157457268	157457278	-	1	NA	exon (NM_001025395, exon 4 of 14)	exon (NM_001025395, exon 4 of 14)	32980	NM_001025395	20779	Mm.22845	NM_009271	ENSMUSG00000027646	Src	AW259666|pp60c-src	Rous sarcoma oncogene	protein-coding
mm_110870.1	chr12	73725877	73725879	-	1	NA	intron (NM_001313977, intron 11 of 14)	intron (NM_001313977, intron 11 of 14)	141082	NM_008856	18755	Mm.341677	NM_008856	ENSMUSG00000021108	Prkch	Pkch	protein kinase C, eta	protein-coding
mm_72214.1	chr8	72646680	72646725	+	1	NA	promoter-TSS (NM_176940)	promoter-TSS (NM_176940)	-9	NM_176940	319555	Mm.212927	NM_176940	ENSMUSG00000048148	Nwd1	A230063L24Rik	NACHT and WD repeat domain containing 1	protein-coding
mm_141109.1	chr17	26021942	26021959	-	1	NA	promoter-TSS (NM_153140)	promoter-TSS (NM_153140)	-90	NM_153140	215445	Mm.41191	NM_153140	ENSMUSG00000037098	Rab11fip3	Cart1|D030060O14Rik|Rab11-FIP3|mKIAA0665	RAB11 family interacting protein 3 (class II)	protein-coding
mm_4743.1	chr1	182124639	182124649	+	1	NA	promoter-TSS (NM_012058)	promoter-TSS (NM_012058)	-93	NM_012058	27058	Mm.273196	NM_012058	ENSMUSG00000026511	Srp9	9kDa	signal recognition particle 9	protein-coding
mm_161995.1	chr19	37198108	37198108	-	1	NA	promoter-TSS (NM_001290829)	promoter-TSS (NM_001290829)	0	NM_001290829	208922	Mm.391176	NM_198300	ENSMUSG00000039652	Cpeb3	4831444O18Rik|CPE-BP3|mKIAA0940	cytoplasmic polyadenylation element binding protein 3	protein-coding
mm_78652.1	chr9	40341554	40341590	+	1	NA	intron (NM_172768, intron 2 of 19)	intron (NM_172768, intron 2 of 19)	8100	NR_040728	73558	Mm.398307	NR_040728		1700110K17Rik	-	RIKEN cDNA 1700110K17 gene	ncRNA
mm_170443.1	chr18	81137505	81137506	-	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	-150927	NM_178280	20689	Mm.215917	NM_178280	ENSMUSG00000024565	Sall3	B130022O04Rik|Msal|Msal-1|Sal|Salt|Spalt	sal-like 3 (Drosophila)	protein-coding
mm_58246.1	chr6	145048696	145048706	-	1	NA	exon (NM_001024468, exon 1 of 11)	exon (NM_001024468, exon 1 of 11)	111	NM_001024468	12035	Mm.4606	NM_007532	ENSMUSG00000030268	Bcat1	BCATc|Eca39	branched chain aminotransferase 1, cytosolic	protein-coding
mm_61936.1	chr7	90176275	90176288	+	1	NA	exon (NM_001252521, exon 10 of 20)	exon (NM_001252521, exon 10 of 20)	46049	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_6374.1	chr1	72537149	72537172	-	1	NA	promoter-TSS (NM_001045533)	promoter-TSS (NM_001045533)	-596	NM_001045533	381270	Mm.337023	NM_001045533	ENSMUSG00000039372	March4	BC056494|mKIAA1399	membrane-associated ring finger (C3HC4) 4	protein-coding
mm_74548.1	chr8	10695077	10695087	-	1	NA	Intergenic	MTEb|LTR|ERVL-MaLR	187372	NR_040705	320014	Mm.403203	NR_040705	ENSMUSG00000109473	B930025P03Rik	-	RIKEN cDNA B930025P03 gene	ncRNA
mm_93656.1	chr10	117689882	117689901	-	1	NA	3' UTR (NM_010786, exon 12 of 12)	3' UTR (NM_010786, exon 12 of 12)	20867	NM_010786	17246	Mm.22670	NM_010786	ENSMUSG00000020184	Mdm2	1700007J15Rik|AA415488|Mdm-2	transformed mouse 3T3 cell double minute 2	protein-coding
mm_112952.1	chr13	21179425	21179427	+	1	NA	promoter-TSS (NM_009054)	promoter-TSS (NM_009054)	-505	NM_009054	19720	Mm.314056	NM_009054	ENSMUSG00000021326	Trim27	AW538890|Gm19403|Rfp	tripartite motif-containing 27	protein-coding
mm_140765.1	chr17	17624594	17624617	-	1	NA	promoter-TSS (NM_172827)	promoter-TSS (NM_172827)	-116	NM_172827	240028	Mm.328807	NM_172827	ENSMUSG00000023845	Lnpep	2010309L07Rik|4732490P18Rik|CAP|IRAP|PLAP|gp160|vp165	leucyl/cystinyl aminopeptidase	protein-coding
mm_159284.1	chr2	169633597	169633597	+	1	NA	promoter-TSS (NM_080455)	promoter-TSS (NM_080455)	-49	NM_080455	228911	Mm.315789	NM_080455	ENSMUSG00000047907	Tshz2	2900073F20Rik|B830045G17|Mtsh2|Sdccag33l|Tsh2|Zfp218|mKIAA4248|teashirt2	teashirt zinc finger family member 2	protein-coding
mm_94342.1	chr11	4729899	4729907	+	1	NA	intron (NM_026015, intron 3 of 5)	intron (NM_026015, intron 3 of 5)	16875	NM_138948	192650	Mm.207056	NM_138948	ENSMUSG00000009075	Cabp7	-	calcium binding protein 7	protein-coding
mm_131299.1	chr16	11406619	11406675	+	1	NA	intron (NM_001290148, intron 1 of 13)	B1_Mur4|SINE|Alu	999	NM_001290148	74478	Mm.325831	NM_028964	ENSMUSG00000071669	Snx29	4933437K13Rik|ENSMUSG00000079738|Gm11170|Gm1737|Gm930|Rundc2a	sorting nexin 29	protein-coding
mm_63133.1	chr7	123010091	123010107	+	1	NA	Intergenic	Intergenic	39535	NM_175023	19647	Mm.4480	NM_011247	ENSMUSG00000030779	Rbbp6	4933422O15Rik|AI316869|BB233631|C030034J04Rik|C77662|P2P-R|PACT	retinoblastoma binding protein 6	protein-coding
mm_2298.1	chr1	91494707	91494721	+	1	NA	promoter-TSS (NM_028718)	promoter-TSS (NM_028718)	46	NM_028718	74019	Mm.318430	NM_028718	ENSMUSG00000034292	Traf3ip1	3930402D05Rik|AU041749|MIP-T3	TRAF3 interacting protein 1	protein-coding
mm_77316.1	chr8	117748254	117748262	-	1	NA	intron (NM_008290, intron 3 of 4)	B4A|SINE|B4	46312	NM_008290	15486	Mm.276466	NM_008290	ENSMUSG00000031844	Hsd17b2	AI194836|AI194967|AI255511	hydroxysteroid (17-beta) dehydrogenase 2	protein-coding
mm_19461.1	chr2	92392442	92392494	-	1	NA	5' UTR (NM_001202446, exon 1 of 12)	5' UTR (NM_001202446, exon 1 of 12)	215	NM_001202446	19099	Mm.2720	NM_011162	ENSMUSG00000027223	Mapk8ip1	IB1|JIP-1|Jip1|Prkm8ip|Skip|mjip-2a	mitogen-activated protein kinase 8 interacting protein 1	protein-coding
mm_143257.1	chr17	65580697	65580708	-	1	NA	exon (NM_013933, exon 6 of 6)	exon (NM_013933, exon 6 of 6)	32853	NM_013933	30960	Mm.266767	NM_013933	ENSMUSG00000024091	Vapa	33kDa|VAP33	vesicle-associated membrane protein, associated protein A	protein-coding
mm_44496.1	chr5	23684609	23684636	-	1	NA	Intergenic	MLT1F1|LTR|ERVL-MaLR	28045	NR_038090	433855	Mm.205125	NR_015554	ENSMUSG00000105987	AI506816	-	expressed sequence AI506816	ncRNA
mm_67473.1	chr7	80501005	80501023	-	1	NA	intron (NM_001042527, intron 7 of 21)	B3|SINE|B2	33984	NM_007550	12144	Mm.12932	NM_007550	ENSMUSG00000030528	Blm	-	Bloom syndrome, RecQ helicase-like	protein-coding
mm_20833.1	chr2	147185799	147185835	-	1	NA	exon (NM_001077632, exon 1 of 3)	exon (NM_001077632, exon 1 of 3)	585	NM_001077632	18088	Mm.330639	NM_010919	ENSMUSG00000027434	Nkx2-2	Nkx-2.2|Nkx2.2|tinman	NK2 homeobox 2	protein-coding
mm_51887.1	chr6	90602024	90602030	+	1	NA	Intergenic	Intergenic	-2853	NM_027868	71699	Mm.272633	NM_027868	ENSMUSG00000030089	Slc41a3	1010001P06Rik|AI480742|SLC41A1-L2	solute carrier family 41, member 3	protein-coding
mm_13131.1	chr2	91779866	91779869	+	1	NA	intron (NM_172669, intron 7 of 17)	PB1D9|SINE|Alu	49729	NM_001080754	228361	Mm.436667	NM_172669	ENSMUSG00000040506	Ambra1	2310079H06Rik|A130023A14|AA474864|AV021921|D030051N19Rik|mKIAA1736	autophagy/beclin 1 regulator 1	protein-coding
mm_107095.1	chr12	17557715	17557718	+	1	NA	Intergenic	Intergenic	12843	NM_013614	18263	Mm.34102	NM_013614	ENSMUSG00000011179	Odc1	ODC	ornithine decarboxylase, structural 1	protein-coding
mm_95845.1	chr11	57644591	57644617	+	1	NA	promoter-TSS (NM_134189)	promoter-TSS (NM_134189)	-838	NM_134189	171212	Mm.271670	NM_134189	ENSMUSG00000020520	Galnt10	AU018154|C330012K04Rik|GalNAc-T10|GalNAc-T9|Galnt9|ppGaNTase	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 10	protein-coding
mm_141428.1	chr17	29464126	29464161	-	1	NA	Intergenic	Intergenic	-26902	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_144904.1	chr18	37341716	37341728	+	1	NA	promoter-TSS (NM_053132)	promoter-TSS (NM_053132)	20	NM_053132	93878	Mm.44755	NM_053132	ENSMUSG00000045062	Pcdhb7	Pcdhb4B|PcdhbG	protocadherin beta 7	protein-coding
mm_10440.1	chr2	14247544	14247564	+	1	NA	intron (NM_008625, intron 3 of 29)	intron (NM_008625, intron 3 of 29)	-13449	NR_030609	100124488		NR_030609	ENSMUSG00000077897	Mir511	Mirn511|mir-511|mmu-mir-511	microRNA 511	ncRNA
mm_66972.1	chr7	63891425	63891529	-	1	NA	3' UTR (NM_021366, exon 2 of 2)	3' UTR (NM_021366, exon 2 of 2)	-25380	NM_001256311	381994	Mm.425466	NM_001256311	ENSMUSG00000095061	E030018B13Rik	Gm1697	RIKEN cDNA E030018B13 gene	protein-coding
mm_90729.1	chr10	5195037	5195054	-	1	NA	promoter-TSS (NM_001079686)	promoter-TSS (NM_001079686)	-338	NM_001079686	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_96844.1	chr11	70030131	70030141	+	1	NA	intron (NM_001109752, intron 2 of 19)	intron (NM_001109752, intron 2 of 19)	11531	NM_007864	13385	Mm.27256	NM_007864	ENSMUSG00000020886	Dlg4	Dlgh4|PSD-95|PSD95|SAP90|SAP90A	discs, large homolog 4 (Drosophila)	protein-coding
mm_93364.1	chr10	103236346	103236354	-	1	NA	promoter-TSS (NM_001163559)	promoter-TSS (NM_001163559)	-28	NM_029134	74978	Mm.483817	NM_029134	ENSMUSG00000019892	Lrriq1	4930503E15Rik|Gm1557	leucine-rich repeats and IQ motif containing 1	protein-coding
mm_22701.1	chr3	18054393	18054407	+	1	NA	promoter-TSS (NM_021560)	promoter-TSS (NM_021560)	75	NM_021560	59058	Mm.149938	NM_021560	ENSMUSG00000025128	Bhlhe22	Beta3|Beta3a|Bhlhb5	basic helix-loop-helix family, member e22	protein-coding
mm_25818.1	chr3	127798179	127798193	+	1	NA	3' UTR (NM_145133, exon 3 of 3)	3' UTR (NM_145133, exon 3 of 3)	8273	NM_145133	211550	Mm.31852	NM_145133	ENSMUSG00000046688	Tifa	T2bp	TRAF-interacting protein with forkhead-associated domain	protein-coding
mm_58187.1	chr6	142964797	142964839	-	1	NA	promoter-TSS (NM_011374)	promoter-TSS (NM_011374)	-366	NM_011374	20449	Mm.260838	NM_011374	ENSMUSG00000030283	St8sia1	9330109E03Rik|GD3S|Sia-T|Siat8|Siat8a	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 1	protein-coding
mm_110275.1	chr12	32017648	32017656	-	1	NA	intron (NM_011158, intron 2 of 10)	intron (NM_011158, intron 2 of 10)	43627	NM_011158	19088	Mm.25594	NM_011158	ENSMUSG00000002997	Prkar2b	AI451071|AW061005|PKARIIbeta|Pkarb2|RII(beta)	protein kinase, cAMP dependent regulatory, type II beta	protein-coding
mm_103774.1	chr11	82607185	82607185	-	1	NA	Intergenic	Intergenic	-26168	NR_033582	791422	Mm.341562	NR_033582	ENSMUSG00000069796	Gm11426	OTTMUSG00000000913	predicted gene 11426	ncRNA
mm_44816.1	chr5	33649315	33649321	-	1	NA	intron (NM_001289725, intron 2 of 6)	B1_Mus1|SINE|Alu	3256	NM_001289725	20492	Mm.4172	NM_009193	ENSMUSG00000004642	Slbp	-	stem-loop binding protein	protein-coding
mm_88972.1	chr10	81419856	81419866	+	1	NA	intron (NM_026756, intron 2 of 8)	intron (NM_026756, intron 2 of 8)	-3564	NR_106141	102465778		NR_106141	ENSMUSG00000105379	Mir1191b	mmu-mir-1191b	microRNA 1191b	ncRNA
mm_137248.1	chr17	24488774	24488799	+	1	NA	promoter-TSS (NM_027937)	promoter-TSS (NM_027937)	3	NM_027937	268932	Mm.70989	NM_027937	ENSMUSG00000033597	Caskin1	3300002N10Rik|C130061I24|C630036E02Rik|mKIAA1306	CASK interacting protein 1	protein-coding
mm_70902.1	chr8	25602464	25602472	+	1	NA	5' UTR (NM_001308482, exon 1 of 8)	5' UTR (NM_001308482, exon 1 of 8)	184	NM_001308482	234135	Mm.217337	NM_001001735	ENSMUSG00000054823	Whsc1l1	6720429E03|A530023P05|AI528490|NSD3|WHISTLE	Wolf-Hirschhorn syndrome candidate 1-like 1 (human)	protein-coding
mm_41001.1	chr5	77407572	77407583	+	1	NA	exon (NM_008048, exon 1 of 5)	exon (NM_008048, exon 1 of 5)	468	NM_001159518	29817	Mm.233470	NM_008048	ENSMUSG00000036256	Igfbp7	AGM|Fstl2|Mac25	insulin-like growth factor binding protein 7	protein-coding
mm_123892.1	chr14	72847536	72847560	-	1	NA	Intergenic	Intergenic	-137545	NM_207636	319448	Mm.205421	NM_207636	ENSMUSG00000033487	Fndc3a	1700094E19Rik|D14Ertd453e|F730017H24Rik|Fndc3|sys	fibronectin type III domain containing 3A	protein-coding
mm_92198.1	chr10	68136614	68136624	-	1	NA	intron (NM_023598, intron 4 of 9)	intron (NM_023598, intron 4 of 9)	142107	NM_023598	71371	Mm.440357	NM_023598	ENSMUSG00000019947	Arid5b	4930580B11|5430435G07Rik|AI467247|Desrt|Mrf2|Mrf2alpha|Mrf2beta	AT rich interactive domain 5B (MRF1-like)	protein-coding
mm_48904.1	chr6	3523935	3523942	+	1	NA	intron (NM_001167750, intron 8 of 27)	intron (NM_001167750, intron 8 of 27)	25545	NM_001167750	73288	Mm.45539	NM_024260	ENSMUSG00000001376	Vps50	1700034M03Rik|8430415E05Rik|BLM|C87205|Ccdc132|mKIAA1861	VPS50 EARP/GARPII complex subunit	protein-coding
mm_75192.1	chr8	38661453	38661481	-	1	NA	promoter-TSS (NM_145841)	promoter-TSS (NM_145841)	41	NM_145841	244431	Mm.210388	NM_145841	ENSMUSG00000039539	Sgcz	C230085N17Rik	sarcoglycan zeta	protein-coding
mm_52330.1	chr6	109125517	109125517	+	1	NA	Intergenic	Intergenic	296876	NM_138677	192193	Mm.21596	NM_138677	ENSMUSG00000030104	Edem1	A130059K23Rik|EDEM|mKIAA0212	ER degradation enhancer, mannosidase alpha-like 1	protein-coding
mm_88561.1	chr10	79637258	79637296	+	1	NA	intron (NM_001024539, intron 1 of 12)	CpG	641	NM_001024539	216148	Mm.39424	NM_001024539	ENSMUSG00000020312	Shc2	6720466E06|SCK|ShcB|Sli	SHC (Src homology 2 domain containing) transforming protein 2	protein-coding
mm_147937.1	chr18	66022583	66022600	-	1	NA	Intergenic	Intergenic	-19956	NM_001172062	70361	Mm.290857	NM_027400	ENSMUSG00000041891	Lman1	2610020P13Rik|AI326273|AU043785|C730041J05|ERGIC53|F5F8D|MCFD1|MR60|P58|gp58	lectin, mannose-binding, 1	protein-coding
mm_126869.1	chr15	89370527	89370543	+	1	NA	intron (NR_073376, intron 15 of 19)	intron (NR_073376, intron 15 of 19)	3283	NM_001111288	100126824	Mm.287977	NM_001111288	ENSMUSG00000091780	Sco2	-	SCO2 cytochrome c oxidase assembly protein	protein-coding
mm_80616.1	chr9	88359223	88359228	+	1	NA	intron (NM_011851, intron 3 of 8)	intron (NM_011851, intron 3 of 8)	31616	NM_011851	23959	Mm.244235	NM_011851	ENSMUSG00000032420	Nt5e	2210401F01Rik|5'-NT|AI447961|CD73|NT|Nt5|eNT	5' nucleotidase, ecto	protein-coding
mm_137241.1	chr17	24470487	24470503	+	1	NA	promoter-TSS (NM_025954)	promoter-TSS (NM_025954)	22	NM_025954	67078	Mm.28541	NM_025954	ENSMUSG00000043445	Pgp	1700012G19Rik|AI481330|AUM|G3PP	phosphoglycolate phosphatase	protein-coding
mm_56114.1	chr6	87511183	87511194	-	1	NA	intron (NM_001037727, intron 1 of 10)	intron (NM_001037727, intron 1 of 10)	-14861	NM_175476	232201	Mm.119564	NM_175476	ENSMUSG00000030047	Arhgap25	A130039I20Rik	Rho GTPase activating protein 25	protein-coding
mm_44378.1	chr5	17820540	17820570	-	1	NA	exon (NM_001159558, exon 5 of 16)	exon (NM_001159558, exon 5 of 16)	15341	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_90892.1	chr10	10296963	10296967	-	1	NA	Intergenic	MTC|LTR|ERVL-MaLR	175349	NM_001127353	215772	Mm.246573	NM_172547	ENSMUSG00000050994	Adgb	9130014G24Rik	androglobin	protein-coding
mm_55686.1	chr6	72630551	72630559	-	1	NA	intron (NR_040422, intron 3 of 4)	B4|SINE|B4	724	NR_040421	100038714	Mm.321330	NR_040421		Gm15401	ENSMUSG00000072999|OTTMUSG00000021199	predicted gene 15401	ncRNA
mm_131974.1	chr16	24973192	24973203	+	1	NA	intron (NM_001145954, intron 6 of 7)	intron (NM_001145954, intron 6 of 7)	-86442	NR_040374	319487	Mm.137341	NR_040374	ENSMUSG00000096960	A230028O05Rik	-	RIKEN cDNA A230028O05 gene	ncRNA
mm_163325.1	chr12	8015648	8015656	+	1	NA	exon (NM_009693, exon 29 of 29)	exon (NM_009693, exon 29 of 29)	37975	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_165612.1	chr3	54390282	54390294	+	1	NA	exon (NM_015784, exon 22 of 22)	exon (NM_015784, exon 22 of 22)	29181	NM_015784	50706	Mm.236067	NM_015784	ENSMUSG00000027750	Postn	A630052E07Rik|AI747096|OSF-2|Osf2|PLF|PN	periostin, osteoblast specific factor	protein-coding
mm_48323.1	chr5	138994936	138994983	-	1	NA	promoter-TSS (NM_008808)	promoter-TSS (NM_008808)	-6	NM_008808	18590	Mm.2675	NM_008808	ENSMUSG00000025856	Pdgfa	-	platelet derived growth factor, alpha	protein-coding
mm_44439.1	chr5	21424665	21424686	-	1	NA	promoter-TSS (NM_177869)	promoter-TSS (NM_177869)	2	NM_029195	75172	Mm.426695	NM_029195	ENSMUSG00000064280	Ccdc146	4930528G09Rik|mKIAA1505	coiled-coil domain containing 146	protein-coding
mm_49451.1	chr6	29361411	29361425	+	1	NA	exon (NM_007594, exon 3 of 7)	exon (NM_007594, exon 3 of 7)	13312	NM_184053	12321	Mm.392075	NM_007594	ENSMUSG00000029767	Calu	9530075H20Rik	calumenin	protein-coding
mm_75904.1	chr8	71272496	71272512	-	1	NA	promoter-TSS (NM_001142322)	promoter-TSS (NM_001142322)	86	NM_001163042	76478	Mm.27355	NM_029621	ENSMUSG00000035439	Haus8	2410004L22Rik|Hice1	4HAUS augmin-like complex, subunit 8	protein-coding
mm_4742.1	chr1	181877361	181877368	+	1	NA	Intergenic	RMER1B|Other|Other	-34963	NM_133815	98386	Mm.4538	NM_133815	ENSMUSG00000004880	Lbr	AI505894|ic	lamin B receptor	protein-coding
mm_9300.1	chr1	171638766	171638776	-	1	NA	exon (NM_144539, exon 5 of 8)	exon (NM_144539, exon 5 of 8)	3129	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_96577.1	chr11	69059823	69059841	+	1	NA	promoter-TSS (NM_028005)	promoter-TSS (NM_028005)	57	NM_028005	71923	Mm.340257	NM_028005	ENSMUSG00000045176	Borcs6	2310047M10Rik	BLOC-1 related complex subunit 6	protein-coding
mm_77988.1	chr9	7873273	7873277	+	1	NA	promoter-TSS (NM_007464)	promoter-TSS (NM_007464)	-105	NM_007464	11796	Mm.2026	NM_007464	ENSMUSG00000032000	Birc3	AW107670|Api1|Api2|Birc2|C-IAP2|HIAP2|IAP1|IAP2|MIAP1|MIAP2|MIHB|MIHC|RNF49|cIAP-1|cIAP-2|cIAP1|cIAP2	baculoviral IAP repeat-containing 3	protein-coding
mm_101306.1	chr11	22610351	22610371	-	1	NA	Intergenic	Intergenic	98078	NM_153596	103765	Mm.221274	NM_153596	ENSMUSG00000049904	Tmem17	AI503894|AW049890	transmembrane protein 17	protein-coding
mm_103745.1	chr11	80142165	80142177	-	1	NA	promoter-TSS (NM_183275)	promoter-TSS (NM_183275)	-18	NM_183275	68550	Mm.18466	NM_183275	ENSMUSG00000046909	Tefm	1110002N22Rik	transcription elongation factor, mitochondrial	protein-coding
mm_65370.1	chr7	25072804	25072815	-	1	NA	promoter-TSS (NM_008168)	promoter-TSS (NM_008168)	-440	NM_008168	14809	Mm.2879	NM_008168	ENSMUSG00000003378	Grik5	GluK5|GluRgamma2|KA2	glutamate receptor, ionotropic, kainate 5 (gamma 2)	protein-coding
mm_72298.1	chr8	75448771	75448775	+	1	NA	promoter-TSS (NM_027944)	promoter-TSS (NM_027944)	79	NM_001164235	71831	Mm.443238	NM_027944	ENSMUSG00000031620	1700007B14Rik	-	RIKEN cDNA 1700007B14 gene	protein-coding
mm_95161.1	chr11	36548376	36548383	+	1	NA	intron (NM_011856, intron 2 of 28)	RMER17C|LTR|ERVK	395862	NM_001290702	23964	Mm.439889	NM_011856	ENSMUSG00000049336	Tenm2	Odz2|Odz3|Ten-2|Ten-m2	teneurin transmembrane protein 2	protein-coding
mm_156584.1	chrX	152144175	152144190	+	1	NA	promoter-TSS (NM_001114664)	promoter-TSS (NM_001114664)	-86	NM_001114664	245666	Mm.33027	NM_001005475	ENSMUSG00000041115	Iqsec2	Brag1	IQ motif and Sec7 domain 2	protein-coding
mm_47583.1	chr5	124579084	124579095	-	1	NA	promoter-TSS (NM_145371)	promoter-TSS (NM_145371)	42	NM_145371	209354	Mm.28839	NM_145371	ENSMUSG00000029388	Eif2b1	D5Ertd406e|EIF2BA	eukaryotic translation initiation factor 2B, subunit 1 (alpha)	protein-coding
mm_110199.1	chr12	27340720	27340728	-	1	NA	3' UTR (NM_009234, exon 1 of 1)	3' UTR (NM_009234, exon 1 of 1)	1994	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding
mm_103459.1	chr11	76388931	76388938	-	1	NA	intron (NM_008750, intron 1 of 7)	(A)n|Simple_repeat|Simple_repeat	10207	NM_008750	18230	Mm.27915	NM_008750	ENSMUSG00000020844	Nxn	l11Jus13	nucleoredoxin	protein-coding
mm_133276.1	chr16	77399952	77399964	+	1	NA	intron (NR_015543, intron 2 of 4)	intron (NR_015543, intron 2 of 4)	70630	NR_015543	77994	Mm.394688	NR_015543	ENSMUSG00000090386	Mir99ahg	2810055G20Rik|D730043B02Rik	Mir99a and Mirlet7c-1 host gene (non-protein coding)	ncRNA
mm_112570.1	chr13	13576593	13576626	+	1	NA	Intergenic	L1MB3|LINE|L1	-13800	NM_010748	17101	Mm.342337	NM_010748	ENSMUSG00000019726	Lyst	D13Sfk13|beige|bg	lysosomal trafficking regulator	protein-coding
mm_62337.1	chr7	100495988	100496007	+	1	NA	intron (NM_011671, intron 2 of 7)	intron (NM_011671, intron 2 of 7)	2639	NM_011671	22228	Mm.171378	NM_011671	ENSMUSG00000033685	Ucp2	Slc25a8	uncoupling protein 2 (mitochondrial, proton carrier)	protein-coding
mm_78408.1	chr9	29992124	29992124	+	1	NA	Intergenic	Lx8|LINE|L1	-28995	NM_172290	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding
mm_9867.1	chr1	184873555	184873579	-	1	NA	3' UTR (NM_178692, exon 2 of 2)	3' UTR (NM_178692, exon 2 of 2)	9469	NM_178692	226777	Mm.169542	NM_178692	ENSMUSG00000039349	C130074G19Rik	-	RIKEN cDNA C130074G19 gene	protein-coding
mm_58017.1	chr6	136661643	136661663	-	1	NA	exon (NM_025806, exon 1 of 11)	exon (NM_025806, exon 1 of 11)	240	NM_025806	66857	Mm.3311	NM_025806	ENSMUSG00000030214	Plbd1	1100001H23Rik	phospholipase B domain containing 1	protein-coding
mm_35373.1	chr4	33031283	33031294	-	1	NA	promoter-TSS (NM_019586)	promoter-TSS (NM_019586)	35	NR_036602	100504166	Mm.426309	NR_036602	ENSMUSG00000085037	4933421O10Rik	-	RIKEN cDNA 4933421O10 gene	ncRNA
mm_83734.1	chr9	51068103	51068120	-	1	NA	exon (NM_001033534, exon 4 of 8)	exon (NM_001033534, exon 4 of 8)	8983	NM_001033534	244864	Mm.335152	NM_001033534	ENSMUSG00000060594	Layn	E030012M19Rik|Gm511	layilin	protein-coding
mm_86065.1	chr9	114774755	114774758	-	1	NA	intron (NM_001252479, intron 1 of 3)	ID_B1|SINE|B4	7237	NM_133978	102545	Mm.35600	NM_133978	ENSMUSG00000032436	Cmtm7	AI481279|Cklfsf7|LNV	CKLF-like MARVEL transmembrane domain containing 7	protein-coding
mm_43425.1	chr5	136057288	136057298	+	1	NA	promoter-TSS (NM_027158)	promoter-TSS (NM_027158)	26	NM_027158	69665	Mm.75713	NM_027158	ENSMUSG00000006143	Upk3bl	2310043J07Rik	uroplakin 3B-like	protein-coding
mm_60726.1	chr7	45377171	45377197	+	1	NA	non-coding (NR_126539, exon 10 of 10)	non-coding (NR_126539, exon 10 of 10)	-6620	NM_011698	22342	Mm.20472	NM_011698	ENSMUSG00000003872	Lin7b	LIN-7B|MALS-2|Veli2	lin-7 homolog B (C. elegans)	protein-coding
mm_110513.1	chr12	54795661	54795696	-	1	NA	promoter-TSS (NM_026998)	promoter-TSS (NM_026998)	-16	NM_026998	72183	Mm.28240	NM_026998	ENSMUSG00000005656	Snx6	2010006G21Rik|2610032J07Rik|2810425K19Rik|AU018928|C85963	sorting nexin 6	protein-coding
mm_87242.1	chr10	40931920	40931938	+	1	NA	exon (NM_031877, exon 5 of 9)	exon (NM_031877, exon 5 of 9)	48395	NM_031877	83767	Mm.41353	NM_031877	ENSMUSG00000019831	Wasf1	AI195380|AI838537|Scar|WAVE|WAVE-1	WAS protein family, member 1	protein-coding
mm_49727.1	chr6	34685109	34685130	+	1	NA	intron (NM_001347100, intron 2 of 13)	intron (NM_001347100, intron 2 of 13)	-24325	NM_145575	109624	Mm.308134	NM_145575	ENSMUSG00000029761	Cald1	4833423D12Rik|AI195384|AV071549|AW536160|C920027I18Rik	caldesmon 1	protein-coding
mm_9041.1	chr1	167266815	167266817	-	1	NA	intron (NM_030724, intron 1 of 6)	BC1_Mm|scRNA|scRNA	18311	NM_030724	80914	Mm.280895	NM_030724	ENSMUSG00000026558	Uck2	AA407809|AI481316|AU018180|AU020720|TSA903|UK|UMK|Umpk	uridine-cytidine kinase 2	protein-coding
mm_166774.1	chr6	136714219	136714244	-	1	NA	intron (NM_145067, intron 19 of 25)	intron (NM_145067, intron 19 of 25)	-52338	NM_025806	66857	Mm.3311	NM_025806	ENSMUSG00000030214	Plbd1	1100001H23Rik	phospholipase B domain containing 1	protein-coding
mm_65186.1	chr7	19696499	19696505	-	1	NA	exon (NM_009696, exon 4 of 4)	exon (NM_009696, exon 4 of 4)	1896	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_124874.1	chr15	10223797	10223804	+	1	NA	promoter-TSS (NM_001253781)	promoter-TSS (NM_001253781)	-106	NM_001253781	19116	Mm.10516	NM_011169	ENSMUSG00000005268	Prlr	AI987712|Pr-1|Pr-3|Prlr-rs1	prolactin receptor	protein-coding
mm_157724.1	chrX	70345253	70345285	-	1	NA	3' UTR (NM_010498, exon 9 of 9)	3' UTR (NM_010498, exon 9 of 9)	19816	NM_010498	15931	Mm.233083	NM_010498	ENSMUSG00000035847	Ids	AW214631	iduronate 2-sulfatase	protein-coding
mm_64092.1	chr7	140968239	140968256	+	1	NA	5' UTR (NM_001112715, exon 1 of 2)	5' UTR (NM_001112715, exon 1 of 2)	171	NM_001112715	68713	Mm.175661	NM_026820	ENSMUSG00000025491	Ifitm1	1110036C17Rik|DSPA2a|Mil-2|Mil2	interferon induced transmembrane protein 1	protein-coding
mm_111956.1	chr12	109560531	109560549	-	1	NA	non-coding (NR_003633, exon 5 of 5)	non-coding (NR_003633, exon 5 of 5)	-3152	NR_030427	791079		NR_030427	ENSMUSG00000076451	Mir770	Mirn770|mir-770|mmu-mir-770	microRNA 770	ncRNA
mm_48419.1	chr5	140382719	140382757	-	1	NA	intron (NM_172277, intron 1 of 10)	intron (NM_172277, intron 1 of 10)	6570	NM_172277	231834	Mm.27098	NM_172277	ENSMUSG00000029560	Snx8	B130023O14Rik	sorting nexin 8	protein-coding
mm_77459.1	chr8	121944887	121944908	-	1	NA	promoter-TSS (NM_007608)	promoter-TSS (NM_007608)	15	NM_007608	12352	Mm.116761	NM_007608	ENSMUSG00000025317	Car5a	CAV|Ca5a|Car5	carbonic anhydrase 5a, mitochondrial	protein-coding
mm_137435.1	chr17	26503380	26503398	+	1	NA	Intergenic	Intergenic	5083	NM_013642	19252	Mm.239041	NM_013642	ENSMUSG00000024190	Dusp1	3CH134|MKP1|Ptpn16|U19515|erp|mkp-1	dual specificity phosphatase 1	protein-coding
mm_14562.1	chr2	134862964	134862965	+	1	NA	intron (NM_019677, intron 2 of 32)	intron (NM_019677, intron 2 of 32)	76800	NM_001145830	18795	Mm.330607	NM_019677	ENSMUSG00000051177	Plcb1	3110043I21Rik|AI132408|Plcb|mKIAA0581	phospholipase C, beta 1	protein-coding
mm_51729.1	chr6	87009873	87009893	+	1	NA	promoter-TSS (NM_020045)	promoter-TSS (NM_020045)	47	NM_020045	56748	Mm.23809	NM_020045	ENSMUSG00000029993	Nfu1	0610006G17Rik|CGI-33|Hirip5	NFU1 iron-sulfur cluster scaffold	protein-coding
mm_143933.1	chr17	86161981	86162003	-	1	NA	Intergenic	Intergenic	-5793	NM_011104	18754	Mm.24614	NM_011104	ENSMUSG00000045038	Prkce	5830406C15Rik|PKC[e]|PKCepsilon|Pkce|R75156	protein kinase C, epsilon	protein-coding
mm_95351.1	chr11	48803423	48803449	+	1	NA	TTS (NR_028564)	TTS (NR_028564)	297	NR_028564	100216540		NR_028564	ENSMUSG00000064780	Snord95	-	small nucleolar RNA, C/D box 95	snoRNA
mm_76079.1	chr8	79294704	79294736	-	1	NA	promoter-TSS (NR_045823)	promoter-TSS (NR_045823)	236	NM_133823	109136	Mm.26510	NM_133823	ENSMUSG00000037022	Mmaa	2810018E08Rik|AI840684	methylmalonic aciduria (cobalamin deficiency) type A	protein-coding
mm_59420.1	chr7	27121941	27121969	+	1	NA	exon (NM_007817, exon 3 of 10)	exon (NM_007817, exon 3 of 10)	2000	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_56091.1	chr6	87349044	87349073	-	1	NA	exon (NM_025466, exon 3 of 6)	exon (NM_025466, exon 3 of 6)	1857	NM_025466	66283	Mm.46414	NM_025466	ENSMUSG00000030050	Gkn1	2200002K21Rik|AMP-18|BRICD1|Fov	gastrokine 1	protein-coding
mm_44567.1	chr5	24704657	24704671	-	1	NA	intron (NM_016736, intron 11 of 14)	intron (NM_016736, intron 11 of 14)	18849	NM_001305264	53312	Mm.5856	NM_016736	ENSMUSG00000028954	Nub1	4931404D21Rik|6330412F12Rik|BS4|NY-REN-18	negative regulator of ubiquitin-like proteins 1	protein-coding
mm_156421.1	chrX	140923169	140923171	+	1	NA	promoter-TSS (NM_026103)	promoter-TSS (NM_026103)	-19	NM_026103	78789	Mm.244932	NM_026103	ENSMUSG00000031430	Vsig1	1700062D20Rik|4930405J24Rik	V-set and immunoglobulin domain containing 1	protein-coding
mm_72779.1	chr8	86745501	86745515	+	1	NA	promoter-TSS (NR_027829)	promoter-TSS (NR_027829)	-191	NR_027829	666945	Mm.391806	NR_027829		Gm10638	ENSMUSG00000074178	predicted gene 10638	ncRNA
mm_163796.1	chr14	16457174	16457175	+	1	NA	intron (NM_011243, intron 3 of 7)	intron (NM_011243, intron 3 of 7)	91968	NM_009409	21974	Mm.130362	NM_009409	ENSMUSG00000017485	Top2b	D230016L12Rik|Top-2	topoisomerase (DNA) II beta	protein-coding
mm_61487.1	chr7	75702018	75702028	+	1	NA	intron (NM_029332, intron 16 of 36)	intron (NM_029332, intron 16 of 36)	-146315	NM_001122780	207952	Mm.206223	NM_029652	ENSMUSG00000055652	Klhl25	2810402K13Rik|BC027373|Enc-1	kelch-like 25	protein-coding
mm_101739.1	chr11	43379067	43379086	-	1	NA	Intergenic	L1MC4|LINE|L1	-4615	NR_029558	387164		NR_029558	ENSMUSG00000065601	Mir146	Mirn146|miR-146a|mmu-mir-146	microRNA 146	ncRNA
mm_76399.1	chr8	84844712	84844730	-	1	NA	exon (NM_007591, exon 5 of 9)	exon (NM_007591, exon 5 of 9)	2210	NM_007591	12317	Mm.1971	NM_007591	ENSMUSG00000003814	Calr	CRT|Calregulin	calreticulin	protein-coding
mm_128437.1	chr15	50703681	50703727	-	1	NA	intron (NM_001310481, intron 4 of 5)	RSINE1|SINE|B4	185345	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_16345.1	chr2	174346001	174346033	+	1	NA	non-coding (NR_003258, exon 12 of 13)	non-coding (NR_003258, exon 12 of 13)	15928	NM_001077510	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_87728.1	chr10	60115757	60115792	+	1	NA	intron (NM_052994, intron 1 of 10)	intron (NM_052994, intron 1 of 10)	9517	NM_052994	94214	Mm.153429	NM_052994	ENSMUSG00000058297	Spock2	AA407235|Gcap26|mKIAA0275	sparc/osteonectin, cwcv and kazal-like domains proteoglycan 2	protein-coding
mm_146503.1	chr18	3299538	3299567	-	1	NA	promoter-TSS (NM_001110853)	promoter-TSS (NM_001110853)	4	NM_001110853	12916	Mm.5244	NM_013498	ENSMUSG00000063889	Crem	ICER|ICERI	cAMP responsive element modulator	protein-coding
mm_24325.1	chr3	89436880	89436892	+	1	NA	intron (NM_146131, intron 1 of 10)	intron (NM_146131, intron 1 of 10)	182	NM_146131	229534	Mm.65906	NM_146131	ENSMUSG00000042613	Pbxip1	4732463H20Rik	pre B cell leukemia transcription factor interacting protein 1	protein-coding
mm_40641.1	chr5	64917700	64917702	+	1	NA	Intergenic	Intergenic	14998	NM_030682	21897	Mm.273024	NM_030682	ENSMUSG00000044827	Tlr1	-	toll-like receptor 1	protein-coding
mm_171623.1	chr4	154682726	154682729	+	1	NA	Intergenic	RMER16A3|LTR|ERVK	-14860	NM_028513	73353	Mm.30958	NM_028513	ENSMUSG00000051276	Actrt2	1700052K15Rik|Arp-T2|Arpm2	actin-related protein T2	protein-coding
mm_109679.1	chr12	113133177	113133215	+	1	NA	exon (NM_054081, exon 16 of 20)	exon (NM_054081, exon 16 of 20)	-7040	NM_024223	68337	Mm.133825	NM_024223	ENSMUSG00000006356	Crip2	0610010I23Rik|AW743261|C77570|CRP2|CRP4|Crp|ESP1|Hlp	cysteine rich protein 2	protein-coding
mm_59344.1	chr7	25619405	25619446	+	1	NA	promoter-TSS (NM_001290487)	promoter-TSS (NM_001290487)	11	NM_001290487	66349	Mm.159956	NM_025504	ENSMUSG00000057229	Atp5sl	2310004L02Rik|C030044E10Rik	ATP5S-like	protein-coding
mm_47117.1	chr5	119670839	119670844	-	1	NA	promoter-TSS (NM_011535)	promoter-TSS (NM_011535)	-21	NM_198052	21386	Mm.219139	NM_011535	ENSMUSG00000018604	Tbx3	D5Ertd189e	T-box 3	protein-coding
mm_86197.1	chr9	119976054	119976080	-	1	NA	intron (NM_153287, intron 2 of 4)	B1_Mus1|SINE|Alu	8591	NM_153287	215418	Mm.491094	NM_153287	ENSMUSG00000032515	Csrnp1	4931429D10Rik|Axud1|CSRNP-1|URAX1|taip-3	cysteine-serine-rich nuclear protein 1	protein-coding
mm_96565.1	chr11	69026825	69026834	+	1	NA	intron (NM_001143790, intron 7 of 22)	intron (NM_001143790, intron 7 of 22)	10918	NM_001013256	68964	Mm.285785	NM_001013256	ENSMUSG00000020898	Ctc1	1500010J02Rik|AAF-132|AAF132	CTS telomere maintenance complex component 1	protein-coding
mm_19467.1	chr2	92434452	92434454	-	1	NA	promoter-TSS (NM_009963)	promoter-TSS (NM_009963)	-384	NM_009963	12953	Mm.254181	NM_009963	ENSMUSG00000068742	Cry2	AV006279|D130054K12Rik	cryptochrome 2 (photolyase-like)	protein-coding
mm_43557.1	chr5	137615611	137615621	+	1	NA	intron (NM_027708, intron 8 of 9)	intron (NM_027708, intron 8 of 9)	-4212	NM_008788	18542	Mm.262345	NM_008788	ENSMUSG00000029718	Pcolce	Astt-2|Astt2|P14|PCPE-1	procollagen C-endopeptidase enhancer protein	protein-coding
mm_86681.1	chr10	18356319	18356323	+	1	NA	Intergenic	B1_Mur3|SINE|Alu	-51354	NM_173390	215819	Mm.297971	NM_173390	ENSMUSG00000039835	Nhsl1	5730409E15Rik|A630035H13Rik|A730096F01|BC013565|D10Bwg0940e|mKIAA1357	NHS-like 1	protein-coding
mm_82827.1	chr9	31131818	31131836	-	1	NA	promoter-TSS (NM_011176)	promoter-TSS (NM_011176)	-28	NM_011176	19143	Mm.243926	NM_011176	ENSMUSG00000031995	St14	Epithin|MT-SP1|Prss14|Tmprss14|mCAP3|matriptase	suppression of tumorigenicity 14 (colon carcinoma)	protein-coding
mm_38056.1	chr4	134004531	134004539	-	1	NA	3' UTR (NM_145833, exon 4 of 4)	3' UTR (NM_145833, exon 4 of 4)	-3671	NM_026144	67422	Mm.100290	NM_026144	ENSMUSG00000012117	Dhdds	3222401G21Rik|CIT|DS|HDS|W91638	dehydrodolichyl diphosphate synthase	protein-coding
mm_127626.1	chr15	102462371	102462379	+	1	NA	3' UTR (NM_025385, exon 5 of 5)	3' UTR (NM_025385, exon 5 of 5)	3205	NM_025385	66151	Mm.393955	NM_025385	ENSMUSG00000023048	Prr13	1110020C13Rik|2010324E22Rik	proline rich 13	protein-coding
mm_155878.1	chrX	101449079	101449089	+	1	NA	promoter-TSS (NM_013712)	promoter-TSS (NM_013712)	-25	NM_013712	26549	Mm.46232	NM_013712	ENSMUSG00000031312	Itgb1bp2	Chordc3	integrin beta 1 binding protein 2	protein-coding
mm_114656.1	chr13	78024893	78024913	+	1	NA	promoter-TSS (NM_029315)	promoter-TSS (NM_029315)	1	NM_029315	75507	Mm.443255	NM_029315	ENSMUSG00000093668	Pou5f2	1700013G10Rik|SPRM-1|Sprm1	POU domain class 5, transcription factor 2	protein-coding
mm_144113.1	chr18	4353609	4353631	+	1	NA	promoter-TSS (NM_007746)	promoter-TSS (NM_007746)	73	NR_040328	73915	Mm.482777	NR_040328		4833419F23Rik	-	RIKEN cDNA 4833419F23 gene	ncRNA
mm_414.1	chr1	34236586	34236602	+	1	NA	intron (NM_001276764, intron 60 of 102)	intron (NM_001276764, intron 60 of 102)	76264	NM_010081	13518	Mm.336625	NM_010081	ENSMUSG00000026131	Dst	2310001O04Rik|A830042E19Rik|AW554249|BP230|BPAG1-n|Bpag|Bpag1|Macf2|ah|athetoid|dt|mKIAA0728|nmf203|nmf339	dystonin	protein-coding
mm_160314.1	chr7	141981524	141981524	+	1	NA	intron (NM_001009930, intron 1 of 19)	intron (NM_001009930, intron 1 of 19)	-10655	NR_037291	100526509		NR_037291	ENSMUSG00000092652	Mir3104	mir-3104|mmu-mir-3104	microRNA 3104	ncRNA
mm_15287.1	chr2	155276891	155276915	+	1	NA	intron (NR_046364, intron 1 of 2)	CpG	539	NR_046364	66734	Mm.196239	NM_025735	ENSMUSG00000027602	Map1lc3a	1010001H21Rik|4922501H04Rik|LC3|LC3a	microtubule-associated protein 1 light chain 3 alpha	protein-coding
mm_16037.1	chr2	167688957	167688973	+	1	NA	promoter-TSS (NM_009883)	promoter-TSS (NM_009883)	50	NM_001287738	12608	Mm.439656	NM_009883	ENSMUSG00000056501	Cebpb	C/EBPbeta|CRP2|IL-6DBP|LAP|LIP|NF-IL6|NF-M|Nfil6	CCAAT/enhancer binding protein (C/EBP), beta	protein-coding
mm_24137.1	chr3	88277064	88277081	+	1	NA	Intergenic	PB1D10|SINE|Alu	19766	NM_029801	76927	Mm.273330	NM_029801	ENSMUSG00000010538	Tsacc	1700021C14Rik|SIP	TSSK6 activating co-chaperone	protein-coding
mm_37309.1	chr4	119294501	119294518	-	1	NA	promoter-TSS (NM_011732)	promoter-TSS (NM_011732)	4	NM_011732	22608	Mm.258204	NM_011732	ENSMUSG00000028639	Ybx1	1700102N10Rik|C79409|EF1A|MSY1|Nsep1|YB-1|dbpB|mYB-1a	Y box protein 1	protein-coding
mm_113815.1	chr13	46669572	46669582	+	1	NA	promoter-TSS (NM_001033192)	promoter-TSS (NM_001033192)	55	NM_001033192	97863	Mm.275934	NM_001033192	ENSMUSG00000069237	Fam8a1	C78339	family with sequence similarity 8, member A1	protein-coding
mm_139040.1	chr17	46227789	46227799	+	1	NA	exon (NM_028198, exon 18 of 32)	exon (NM_028198, exon 18 of 32)	-3737	NR_030466	751553		NR_030466	ENSMUSG00000076141	Mir693	Mirn693|mir-693|mmu-mir-693	microRNA 693	ncRNA
mm_154801.1	chrX	13289431	13289447	+	1	NA	exon (NM_010028, exon 11 of 17)	exon (NM_010028, exon 11 of 17)	8417	NM_010028	13205	Mm.289662	NM_010028	ENSMUSG00000000787	Ddx3x	D1Pas1-rs2|Ddx3|Fin14	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 3, X-linked	protein-coding
mm_76237.1	chr8	83574795	83574809	-	1	NA	intron (NM_134118, intron 1 of 12)	intron (NM_134118, intron 1 of 12)	8044	NM_025843	66916	Mm.29683	NM_025843	ENSMUSG00000033938	Ndufb7	1110002H15Rik	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 7	protein-coding
mm_64738.1	chr7	4725323	4725404	-	1	NA	promoter-TSS (NM_177887)	promoter-TSS (NM_177887)	-112	NM_177887	330460	Mm.361851	NM_177887	ENSMUSG00000046456	Tmem150b	A630041N19|Tmem224	transmembrane protein 150B	protein-coding
mm_161914.1	chr18	67435706	67435706	-	1	NA	intron (NM_027130, intron 5 of 16)	intron (NM_027130, intron 5 of 16)	13430	NM_027130	69597	Mm.426052	NM_027130	ENSMUSG00000024527	Afg3l2	2310036I02Rik|AW260507|Emv66|par	AFG3-like AAA ATPase 2	protein-coding
mm_167079.1	chr7	100706849	100706854	+	1	NA	5' UTR (NM_178764, exon 1 of 9)	5' UTR (NM_178764, exon 1 of 9)	149	NM_178764	319604	Mm.260362	NM_178764	ENSMUSG00000029461	Fam168a	2610030B18Rik|B930006L02Rik|mKIAA0280	family with sequence similarity 168, member A	protein-coding
mm_67958.1	chr7	100514790	100514799	-	1	NA	promoter-TSS (NM_153527)	promoter-TSS (NM_153527)	21	NM_153527	69387	Mm.278554	NM_153527	ENSMUSG00000030708	Dnajb13	1700014P03Rik|Tsarg	DnaJ heat shock protein family (Hsp40) member B13	protein-coding
mm_33137.1	chr4	125066673	125066715	+	1	NA	promoter-TSS (NM_175246)	promoter-TSS (NM_175246)	1	NM_175246	76793	Mm.22548	NM_175246	ENSMUSG00000050213	Snip1	2410133M08Rik	Smad nuclear interacting protein 1	protein-coding
mm_94260.1	chr11	3488276	3488287	+	1	NA	promoter-TSS (NM_172791)	promoter-TSS (NM_172791)	54	NM_172791	237625	Mm.100476	NM_172791	ENSMUSG00000034579	Pla2g3	-	phospholipase A2, group III	protein-coding
mm_22484.1	chr3	5400651	5400662	+	1	NA	exon (NM_030708, exon 10 of 11)	exon (NM_030708, exon 10 of 11)	175592	NM_001163301	19302	Mm.132336	NM_008994	ENSMUSG00000040374	Pex2	D3Ertd138e|PAF-1|PMP35|Pxmp3	peroxisomal biogenesis factor 2	protein-coding
mm_155334.1	chrX	66649437	66649447	+	1	NA	5' UTR (NM_001161431, exon 1 of 3)	5' UTR (NM_001161431, exon 1 of 3)	124	NM_001161431	245450	Mm.336081	NM_198863	ENSMUSG00000036790	Slitrk2	A930040J07	SLIT and NTRK-like family, member 2	protein-coding
mm_166849.1	chr7	19696725	19696769	+	1	NA	exon (NM_009696, exon 4 of 4)	exon (NM_009696, exon 4 of 4)	1651	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_53476.1	chr6	134929119	134929164	+	1	NA	promoter-TSS (NR_037955)	promoter-TSS (NR_037955)	49	NR_037955	381822	Mm.5935	NR_037955	ENSMUSG00000098318	Lockd	1190002F15Rik|AI120476|Droc	lncRNA downstream of Cdkn1b	ncRNA
mm_141497.1	chr17	31558068	31558082	-	1	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	-6698	NR_027493	18771	Mm.259295	NM_016670	ENSMUSG00000006705	Pknox1	D17Wsu76e|PREP1	Pbx/knotted 1 homeobox	protein-coding
mm_52725.1	chr6	120093349	120093359	+	1	NA	promoter-TSS (NM_016718)	promoter-TSS (NM_016718)	-26	NM_016718	29862	Mm.103668	NM_016718	ENSMUSG00000041377	Ninj2	-	ninjurin 2	protein-coding
mm_7433.1	chr1	119913078	119913086	-	1	NA	promoter-TSS (NM_175106)	promoter-TSS (NM_175106)	86	NM_175106	66343	Mm.49942	NM_175106	ENSMUSG00000036975	Tmem177	2300008B03Rik	transmembrane protein 177	protein-coding
mm_103971.1	chr11	84519274	84519286	-	1	NA	TTS (NM_008498)	TTS (NM_008498)	-5779	NM_019816	56321	Mm.257482	NM_019816	ENSMUSG00000018697	Aatf	4933415H02Rik|5830465M17Rik|Che-1|Trb	apoptosis antagonizing transcription factor	protein-coding
mm_136659.1	chr17	6006491	6006499	+	1	NA	intron (NM_001113352, intron 7 of 25)	intron (NM_001113352, intron 7 of 25)	-1085	NM_001290698	20975	Mm.236068	NM_011523	ENSMUSG00000023805	Synj2	AI481647|SJ2|mKIAA0348	synaptojanin 2	protein-coding
mm_23671.1	chr3	68572465	68572475	+	1	NA	5' UTR (NM_013928, exon 1 of 7)	5' UTR (NM_013928, exon 1 of 7)	102	NM_013928	30953	Mm.331064	NM_013928	ENSMUSG00000027777	Schip1	Nf2ip|Schip-1	schwannomin interacting protein 1	protein-coding
mm_24906.1	chr3	96219832	96219842	+	1	NA	promoter-TSS (NM_178213)	promoter-TSS (NM_178213)	-79	NM_178213	621893		NM_178213	ENSMUSG00000063689	Hist2h2ab	EG621893|H2a-613a	histone cluster 2, H2ab	protein-coding
mm_167237.1	chr8	19113198	19113208	+	1	NA	intron (NM_152802, intron 2 of 2)	RLTR20A4|LTR|ERVK	1630	NM_152802	77674	Mm.281961	NM_152802	ENSMUSG00000043787	Defb12	9230103N16Rik|BD-12	defensin beta 12	protein-coding
mm_61192.1	chr7	63897397	63897425	+	1	NA	intron (NM_021366, intron 1 of 1)	intron (NM_021366, intron 1 of 1)	-19446	NM_001256311	381994	Mm.425466	NM_001256311	ENSMUSG00000095061	E030018B13Rik	Gm1697	RIKEN cDNA E030018B13 gene	protein-coding
mm_139912.1	chr17	70929007	70929007	+	1	NA	Intergenic	Intergenic	61509	NM_023402	67938	Mm.261329	NM_023402	ENSMUSG00000034868	Myl12b	1500001M02Rik|C77744|Mylc2b|RLC-B	myosin, light chain 12B, regulatory	protein-coding
mm_105322.1	chr11	102893135	102893145	-	1	NA	exon (NM_010277, exon 6 of 9)	exon (NM_010277, exon 6 of 9)	4060	NM_001131020	14580	Mm.1239	NM_010277	ENSMUSG00000020932	Gfap	AI836096	glial fibrillary acidic protein	protein-coding
mm_13625.1	chr2	113478893	113478921	+	1	NA	exon (NM_001285459, exon 3 of 17)	exon (NM_001285459, exon 3 of 17)	37843	NM_001285459	14260	Mm.4938	NM_010230	ENSMUSG00000044042	Fmn1	Fmn|formin-1|ld	formin 1	protein-coding
mm_5708.1	chr1	43542426	43542435	-	1	NA	intron (NM_010879, intron 3 of 4)	intron (NM_010879, intron 3 of 4)	96679	NM_010879	17974	Mm.389903	NM_010879	ENSMUSG00000066877	Nck2	4833426I10Rik|Grb4|NCKbeta|Nck-2	non-catalytic region of tyrosine kinase adaptor protein 2	protein-coding
mm_159383.1	chr3	90267375	90267375	+	1	NA	intron (NM_201407, intron 1 of 27)	intron (NM_201407, intron 1 of 27)	861	NM_201407	229541	Mm.30571	NM_201407	ENSMUSG00000042404	Dennd4b	-	DENN/MADD domain containing 4B	protein-coding
mm_33285.1	chr4	128805764	128805779	+	1	NA	intron (NM_001081098, intron 1 of 8)	intron (NM_001081098, intron 1 of 8)	341	NM_001081098	230761	Mm.22616	NM_001081098	ENSMUSG00000028799	Zfp362	-	zinc finger protein 362	protein-coding
mm_164709.1	chr17	53022781	53022781	-	1	NA	Intergenic	Intergenic	420072	NM_001031811	211468	Mm.399068	NM_001031811	ENSMUSG00000035580	Kcnh8	C130090D05Rik|ELK|ELK1|ELK3|Kv12.1	potassium voltage-gated channel, subfamily H (eag-related), member 8	protein-coding
mm_10734.1	chr2	23039291	23039324	+	1	NA	intron (NM_001331043, intron 1 of 10)	intron (NM_001331043, intron 1 of 10)	934	NM_001077192	11308	Mm.205647	NM_007380	ENSMUSG00000058835	Abi1	E3B1|NAP1|Ssh3bp1|abi-1	abl-interactor 1	protein-coding
mm_7941.1	chr1	133914790	133914798	-	1	NA	exon (NM_054077, exon 2 of 3)	exon (NM_054077, exon 2 of 3)	6607	NM_054077	116847	Mm.214514	NM_054077	ENSMUSG00000041577	Prelp	7330409J17Rik|SLRR2A	proline arginine-rich end leucine-rich repeat	protein-coding
mm_64800.1	chr7	6690868	6690886	-	1	NA	intron (NM_011769, intron 2 of 7)	IMPB_01|Satellite|Satellite	5555	NM_011769	22776	Mm.89976	NM_011769	ENSMUSG00000002266	Zim1	-	zinc finger, imprinted 1	protein-coding
mm_86212.1	chr9	120012758	120012770	-	1	NA	TTS (NM_011724)	TTS (NM_011724)	10834	NM_011724	22437	Mm.10117	NM_011724	ENSMUSG00000079243	Xirp1	AI415219|Cmya1	xin actin-binding repeat containing 1	protein-coding
mm_139698.1	chr17	57447820	57447906	+	1	NA	exon (NM_010130, exon 16 of 22)	exon (NM_010130, exon 16 of 22)	89177	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_12349.1	chr2	69749059	69749077	+	1	NA	exon (NM_001081086, exon 13 of 14)	exon (NM_001081086, exon 13 of 14)	25980	NM_001081086	228005	Mm.11815	NM_001081086	ENSMUSG00000042133	Ppig	AU019516|AU022200|B230312B02Rik|CYP|SRCyp	peptidyl-prolyl isomerase G (cyclophilin G)	protein-coding
mm_161822.1	chr17	71781834	71781834	+	1	NA	promoter-TSS (NM_030179)	promoter-TSS (NM_030179)	-113	NM_030179	78785	Mm.196382	NM_030179	ENSMUSG00000024059	Clip4	1700024K14Rik|1700074B05Rik|4833417L20Rik|5830409B12Rik|Rsnl2	CAP-GLY domain containing linker protein family, member 4	protein-coding
mm_120277.1	chr14	63129369	63129382	+	1	NA	intron (NM_007798, intron 1 of 9)	intron (NM_007798, intron 1 of 9)	6913	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_15552.1	chr2	158436997	158437016	+	1	NA	exon (NM_001291138, exon 8 of 30)	exon (NM_001291138, exon 8 of 30)	27153	NM_001291138	228850	Mm.398185	NM_177227	ENSMUSG00000027652	Ralgapb	AI507211|B230339M05Rik|p170	Ral GTPase activating protein, beta subunit (non-catalytic)	protein-coding
mm_22851.1	chr3	28263356	28263386	+	1	NA	5' UTR (NM_001163009, exon 1 of 31)	5' UTR (NM_001163009, exon 1 of 31)	157	NM_001163009	665113	Mm.126193	NM_026910	ENSMUSG00000027692	Tnik	1500031A17Rik|4831440I19Rik|AI451411|C530008O15Rik|C630040K21Rik	TRAF2 and NCK interacting kinase	protein-coding
mm_82074.1	chr9	122923104	122923110	+	1	NA	promoter-TSS (NM_009544)	promoter-TSS (NM_009544)	29	NM_009544	22646	Mm.290595	NM_009544	ENSMUSG00000057895	Zfp105	AW557864	zinc finger protein 105	protein-coding
mm_155255.1	chrX	57224064	57224109	+	1	NA	TTS (NM_011616)	TTS (NM_011616)	11943	NM_011616	21947	Mm.4861	NM_011616	ENSMUSG00000031132	Cd40lg	CD154|CD40-L|Cd40l|HIGM1|IGM|IMD3|Ly-62|Ly62|T-BAM|TRAP|Tnfsf5|Tnlg8b|gp39	CD40 ligand	protein-coding
mm_106411.1	chr11	119053434	119053437	-	1	NA	Intergenic	CpG	-12522	NM_013926	30951	Mm.99953	NM_013926	ENSMUSG00000025578	Cbx8	Pc3	chromobox 8	protein-coding
mm_32295.1	chr4	103119276	103119293	+	1	NA	promoter-TSS (NM_001039081)	promoter-TSS (NM_001039081)	-106	NM_001039081	71148	Mm.288721	NM_027696	ENSMUSG00000028522	Mier1	4933425I22Rik|5830411K19Rik|er1	MEIR1 treanscription regulator	protein-coding
mm_107644.1	chr12	52504098	52504114	+	1	NA	Intergenic	CpG	-11971	NM_009706	11855	Mm.35059	NM_009706	ENSMUSG00000035133	Arhgap5	p190-B|p190B	Rho GTPase activating protein 5	protein-coding
mm_115898.1	chr13	23313355	23313361	-	1	NA	promoter-TSS (NR_126443)	promoter-TSS (NR_126443)	49	NR_126443	75322	Mm.108666	NR_126443	ENSMUSG00000085488	4930557F10Rik	-	RIKEN cDNA 4930557F10 gene	ncRNA
mm_90968.1	chr10	13428713	13428729	-	1	NA	intron (NM_001195065, intron 1 of 12)	intron (NM_001195065, intron 1 of 12)	-39751	NM_001195066	215789	Mm.283359	NM_001033257	ENSMUSG00000062866	Phactr2	AV158170|BC012871	phosphatase and actin regulator 2	protein-coding
mm_59159.1	chr7	24377340	24377352	+	1	NA	exon (NM_001163510, exon 3 of 9)	exon (NM_001163510, exon 3 of 9)	7083	NM_008433	16534	Mm.9911	NM_008433	ENSMUSG00000054342	Kcnn4	IK1|IKCA1|KCA4|KCa3.1|SK4|SKCas|mIKCa1	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4	protein-coding
mm_7646.1	chr1	128299506	128299524	-	1	NA	intron (NM_001081078, intron 8 of 16)	B4|SINE|B4	28803	NM_001081078	226413	Mm.26930	NM_001081078	ENSMUSG00000026354	Lct	Gm100|LAC|LPH|Lphl	lactase	protein-coding
mm_112875.1	chr13	20853898	20853917	+	1	NA	intron (NM_012054, intron 4 of 20)	intron (NM_012054, intron 4 of 20)	59794	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_99367.1	chr11	101733012	101733040	+	1	NA	promoter-TSS (NM_144831)	promoter-TSS (NM_144831)	70	NM_144831	217207	Mm.28186	NM_144831	ENSMUSG00000034931	Dhx8	Ddx8|mDEAH6|mKIAA4096	DEAH (Asp-Glu-Ala-His) box polypeptide 8	protein-coding
mm_75836.1	chr8	70527937	70527942	-	1	NA	promoter-TSS (NM_001199631)	promoter-TSS (NM_001199631)	93	NM_001199631	14232	Mm.141864	NM_010223	ENSMUSG00000019428	Fkbp8	38kDa|FKBP-38|FKBP-8|Fkbp38	FK506 binding protein 8	protein-coding
mm_97351.1	chr11	77493266	77493302	+	1	NA	promoter-TSS (NM_001004144)	promoter-TSS (NM_001004144)	-128	NM_001004144	216963	Mm.290182	NM_001004144	ENSMUSG00000011877	Git1	Cat-1|p95Cat	G protein-coupled receptor kinase-interactor 1	protein-coding
mm_120706.1	chr14	71237390	71237392	+	1	NA	Intergenic	Intergenic	-13882	NR_046075	100043132	Mm.399336	NR_046075		Gm4251	-	predicted gene 4251	ncRNA
mm_83236.1	chr9	42399489	42399495	-	1	NA	intron (NM_009347, intron 1 of 23)	intron (NM_009347, intron 1 of 23)	437	NM_009347	21683	Mm.42209	NM_009347	ENSMUSG00000037705	Tecta	Tctna	tectorin alpha	protein-coding
mm_68354.1	chr7	106510399	106510419	-	1	NA	Intergenic	Intergenic	-69336	NR_003967	209380	Mm.461779	NM_001001318		Gm4759	EG209380	GTPase, very large interferon inducible 1 pseudogene	pseudo
mm_26597.1	chr3	151508032	151508043	+	1	NA	intron (NM_133222, intron 9 of 15)	RSINE1|SINE|B4	70155	NM_133222	170757	Mm.317261	NM_133222	ENSMUSG00000039167	Adgrl4	1110033N21Rik|ETL1|Eltd1|Etl	adhesion G protein-coupled receptor L4	protein-coding
mm_2989.1	chr1	133132649	133132666	+	1	NA	exon (NM_133819, exon 1 of 2)	exon (NM_133819, exon 1 of 2)	1491	NM_133819	108954	Mm.293628	NM_133819	ENSMUSG00000046062	Ppp1r15b	1810033K10Rik|AI606441|C530022L24Rik|CReP	protein phosphatase 1, regulatory (inhibitor) subunit 15b	protein-coding
mm_40285.1	chr5	43233678	43233685	+	1	NA	exon (NM_001177379, exon 1 of 11)	exon (NM_001177379, exon 1 of 11)	218	NM_001177379	231207	Mm.7233	NM_175937	ENSMUSG00000039782	Cpeb2	A630055H10Rik|Cpe-bp2	cytoplasmic polyadenylation element binding protein 2	protein-coding
mm_141679.1	chr17	33929289	33929293	-	1	NA	promoter-TSS (NM_009059)	promoter-TSS (NM_009059)	-603	NM_009059	19732	Mm.43777	NM_009059	ENSMUSG00000041354	Rgl2	KE1.5|Rab2l|Rgt2|Rlf	ral guanine nucleotide dissociation stimulator-like 2	protein-coding
mm_91158.1	chr10	20548362	20548378	-	1	NA	promoter-TSS (NM_001347366)	promoter-TSS (NM_001347366)	-42	NM_001347366	29863	Mm.425617	NM_013875	ENSMUSG00000019990	Pde7b	-	phosphodiesterase 7B	protein-coding
mm_98308.1	chr11	90033583	90033600	+	1	NA	5' UTR (NM_026433, exon 2 of 3)	5' UTR (NM_026433, exon 2 of 3)	3243	NM_026433	67888	Mm.212428	NM_026433	ENSMUSG00000069763	Tmem100	1810057C19Rik|AV011897	transmembrane protein 100	protein-coding
mm_117406.1	chr13	73937720	73937744	-	1	NA	promoter-TSS (NM_027182)	promoter-TSS (NM_027182)	35	NM_027182	69716	Mm.275095	NM_027182	ENSMUSG00000021569	Trip13	2410002G23Rik|D13Ertd328e	thyroid hormone receptor interactor 13	protein-coding
mm_863.1	chr1	52148897	52148924	+	1	NA	exon (NM_001205314, exon 18 of 25)	exon (NM_001205314, exon 18 of 25)	29288	NM_001205313	20846	Mm.277406	NM_009283	ENSMUSG00000026104	Stat1	2010005J02Rik|AA408197	signal transducer and activator of transcription 1	protein-coding
mm_53782.1	chr6	146577535	146577550	+	1	NA	promoter-TSS (NM_026218)	promoter-TSS (NM_026218)	293	NM_138757	71177	Mm.271774	NM_138757	ENSMUSG00000040250	Asun	4933424B01Rik|Spata30	asunder, spermatogenesis regulator	protein-coding
mm_109513.1	chr12	111454246	111454277	+	1	NA	3' UTR (NM_009396, exon 12 of 12)	3' UTR (NM_009396, exon 12 of 12)	11600	NM_009396	21928	Mm.255332	NM_009396	ENSMUSG00000021281	Tnfaip2	B94|Exoc3l3|M-sec|Tnfip2|tnfb94	tumor necrosis factor, alpha-induced protein 2	protein-coding
mm_39410.1	chr5	14669027	14669039	+	1	NA	exon (NM_011995, exon 4 of 25)	exon (NM_011995, exon 4 of 25)	154115	NM_001110796	26875	Mm.146275	NM_011995	ENSMUSG00000061601	Pclo	Acz|Pico	piccolo (presynaptic cytomatrix protein)	protein-coding
mm_28400.1	chr3	90238791	90238805	-	1	NA	intron (NM_030080, intron 5 of 9)	intron (NM_030080, intron 5 of 9)	3752	NM_001307935	78284	Mm.299952	NM_030080	ENSMUSG00000027938	Creb3l4	1700012K17Rik|5330432F22Rik|AIBZIP|AV040530|AV258827|CREB4|JAL|TISP40|acre1	cAMP responsive element binding protein 3-like 4	protein-coding
mm_141888.1	chr17	34861152	34861165	-	1	NA	exon (NM_008198, exon 3 of 18)	exon (NM_008198, exon 3 of 18)	1356	NM_001142706	14962	Mm.653	NM_008198	ENSMUSG00000090231	Cfb	AI195813|AI255840|B|Bf|C2|Fb|H2-Bf	complement factor B	protein-coding
mm_89489.1	chr10	93700686	93700708	+	1	NA	intron (NM_021320, intron 3 of 9)	intron (NM_021320, intron 3 of 9)	-17375	NR_038017	100504069	Mm.391412	NR_038017	ENSMUSG00000085723	Gm15915	OTTMUSG00000027787	predicted gene 15915	ncRNA
mm_136122.1	chr16	85900295	85900309	-	1	NA	5' UTR (NM_011782, exon 1 of 8)	5' UTR (NM_011782, exon 1 of 8)	823	NM_011782	23794	Mm.112933	NM_011782	ENSMUSG00000022894	Adamts5	9530092O11Rik|ADAM-TS5|ADAMTS1|ADAMTS11|ADMP-2|AI481094|ASMP-2	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)	protein-coding
mm_34730.1	chr4	152178238	152178259	+	1	NA	exon (NM_133348, exon 1 of 9)	exon (NM_133348, exon 1 of 9)	148	NM_133348	70025	Mm.296191	NM_133348	ENSMUSG00000028937	Acot7	2410041A17Rik|Ach1|Act|Bach|CTE-IIa|Cte-II|Lach1	acyl-CoA thioesterase 7	protein-coding
mm_53754.1	chr6	145387594	145387601	+	1	NA	promoter-TSS (NR_003625)	promoter-TSS (NR_003625)	-28	NR_003625	381827	Mm.179075	NM_001001987		1700073E17Rik	-	ribosomal protein L7 pseudogene	pseudo
mm_97872.1	chr11	83176255	83176266	+	1	NA	5' UTR (NM_011410, exon 4 of 8)	5' UTR (NM_011410, exon 4 of 8)	1074	NM_001302559	20558	Mm.38192	NM_011410	ENSMUSG00000000204	Slfn4	AI450778	schlafen 4	protein-coding
mm_128664.1	chr15	60149707	60149727	-	1	NA	Intergenic	Intergenic	-133099	NM_027668	71088	Mm.425950	NM_027668	ENSMUSG00000071749	4933412E24Rik	-	RIKEN cDNA 4933412E24 gene	protein-coding
mm_107149.1	chr12	23903124	23903136	+	1	NA	Intergenic	Intergenic	194139	NM_001256489	66808	Mm.379124	NM_001256489	ENSMUSG00000073158	9030624G23Rik	-	RIKEN cDNA 9030624G23 gene	protein-coding
mm_60908.1	chr7	46753417	46753435	+	1	NA	exon (NM_011314, exon 3 of 4)	exon (NM_011314, exon 3 of 4)	1593	NM_011314	20209	Mm.200941	NM_011314	ENSMUSG00000057465	Saa2	AW111173|Saa-2|Saa1	serum amyloid A 2	protein-coding
mm_34485.1	chr4	148536331	148536371	+	1	NA	intron (NM_020009, intron 38 of 57)	intron (NM_020009, intron 38 of 57)	-22076	NM_016699	50912	Mm.266635	NM_016699	ENSMUSG00000017264	Exosc10	PM-Scl|PM/Scl-100|Pmscl2|RRP6|p2|p3|p4	exosome component 10	protein-coding
mm_152856.1	chr19	24174143	24174159	-	1	NA	promoter-TSS (NM_001198985)	promoter-TSS (NM_001198985)	-11	NM_001198985	21873	Mm.104744	NM_011597	ENSMUSG00000024812	Tjp2	ZO-2	tight junction protein 2	protein-coding
mm_131811.1	chr16	22918477	22918491	+	1	NA	5' UTR (NM_001083905, exon 1 of 8)	5' UTR (NM_001083905, exon 1 of 8)	102	NM_001083905	59083	Mm.28461	NM_021564	ENSMUSG00000022871	Fetub	2310011O17Rik|AI255764|D17980|Gugu	fetuin beta	protein-coding
mm_123994.1	chr14	75775495	75775498	-	1	NA	intron (NM_026232, intron 2 of 9)	PB1D10|SINE|Alu	11541	NM_026232	67554	Mm.46067	NM_026232	ENSMUSG00000022003	Slc25a30	4933433D23Rik|AV025504|AV221431|AW319655|KMCP1	solute carrier family 25, member 30	protein-coding
mm_85790.1	chr9	109095814	109095826	-	1	NA	intron (NM_172775, intron 1 of 37)	CpG	384	NM_172775	235611	Mm.53862	NM_172775	ENSMUSG00000053646	Plxnb1	2900002G15Rik|AU042020|mKIAA0407	plexin B1	protein-coding
mm_83945.1	chr9	56852034	56852036	-	1	NA	promoter-TSS (NM_198673)	promoter-TSS (NM_198673)	-72	NM_198673	382075	Mm.335177	NM_198673	ENSMUSG00000045620	Odf3l1	BC049697|Gm1116	outer dense fiber of sperm tails 3-like 1	protein-coding
mm_2004.1	chr1	87127095	87127101	+	1	NA	exon (NM_007432, exon 9 of 11)	exon (NM_007432, exon 9 of 11)	2090	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_92978.1	chr10	86693407	86693428	-	1	NA	exon (NM_011631, exon 14 of 18)	exon (NM_011631, exon 14 of 18)	7890	NR_015572	66263	Mm.392261	NR_015572		1810014B01Rik	-	RIKEN cDNA 1810014B01 gene	pseudo
mm_97434.1	chr11	78165634	78165660	+	1	NA	promoter-TSS (NM_009423)	promoter-TSS (NM_009423)	-97	NM_009423	22032	Mm.390418	NM_009423	ENSMUSG00000017386	Traf4	A530032M13Rik|CART1|msp2	TNF receptor associated factor 4	protein-coding
mm_89422.1	chr10	90915734	90915739	+	1	NA	intron (NM_001177396, intron 6 of 11)	intron (NM_001177396, intron 6 of 11)	85893	NM_001347053	77531	Mm.440605	NM_181398	ENSMUSG00000058589	Anks1b	AIDA-1b|C030032C09Rik|E530015N03Rik|ENSMUSG00000078431|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding
mm_64969.1	chr7	16615267	16615276	-	1	NA	promoter-TSS (NM_172739)	promoter-TSS (NM_172739)	-278	NM_172739	232906	Mm.28646	NM_172739	ENSMUSG00000058230	Arhgap35	6430596G11Rik|AI841135|Grlf1|mKIAA1722|p190A|p190RhoGAP	Rho GTPase activating protein 35	protein-coding
mm_12391.1	chr2	69897256	69897294	+	1	NA	promoter-TSS (NM_177783)	promoter-TSS (NM_177783)	29	NM_177783	68795	Mm.314576	NM_177783	ENSMUSG00000044308	Ubr3	1110059H15Rik|4833421P10Rik|A130030D10Rik|AA409735|AA414972|AA422631|AI646861|AU016126|Zfp650|Znf650	ubiquitin protein ligase E3 component n-recognin 3	protein-coding
mm_146583.1	chr18	7626810	7626880	-	1	NA	promoter-TSS (NM_001161620)	promoter-TSS (NM_001161620)	18	NM_001081287	75739	Mm.133293	NM_001081287	ENSMUSG00000057440	Mpp7	1110068J02Rik|2810038M04Rik|5430426E14Rik|AI415104|Gm955	membrane protein, palmitoylated 7 (MAGUK p55 subfamily member 7)	protein-coding
mm_129711.1	chr15	81858318	81858328	-	1	NA	promoter-TSS (NM_020507)	promoter-TSS (NM_020507)	3	NM_020507	57259	Mm.323595	NM_020507	ENSMUSG00000048546	Tob2	2900090N22Rik|4930545K18Rik|AV071822|mKIAA1663	transducer of ERBB2, 2	protein-coding
mm_143086.1	chr17	57078460	57078484	-	1	NA	promoter-TSS (NM_153551)	promoter-TSS (NM_153551)	38	NM_153551	70785	Mm.284447	NM_153551	ENSMUSG00000002668	Dennd1c	4432409M07Rik	DENN/MADD domain containing 1C	protein-coding
mm_172047.1	chr6	128513330	128513330	-	1	NA	intron (NM_007376, intron 11 of 35)	intron (NM_007376, intron 11 of 35)	13390	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_8945.1	chr1	164438342	164438379	-	1	NA	exon (NM_009721, exon 6 of 6)	exon (NM_009721, exon 6 of 6)	19995	NM_009721	11931	Mm.4550	NM_009721	ENSMUSG00000026576	Atp1b1	Atp4b|Atpb|Atpb-1|NKbeta1	ATPase, Na+/K+ transporting, beta 1 polypeptide	protein-coding
mm_104780.1	chr11	98546199	98546203	-	1	NA	promoter-TSS (NM_011771)	promoter-TSS (NM_011771)	-170	NM_011771	22780	Mm.133367	NM_011771	ENSMUSG00000018168	Ikzf3	5830411O07Rik|Aiolos|Zfpn1a3|Znfn1a3	IKAROS family zinc finger 3	protein-coding
mm_92138.1	chr10	66911470	66911483	-	1	NA	TTS (NR_138560)	TTS (NR_138560)	8908	NR_138560	68488	Mm.338835	NR_138560		1110002J07Rik	-	RIKEN cDNA 1110002J07 gene	ncRNA
mm_147066.1	chr18	35130931	35130935	-	1	NA	intron (NM_009818, intron 1 of 17)	intron (NM_009818, intron 1 of 17)	12021	NM_009818	12385	Mm.18962	NM_009818	ENSMUSG00000037815	Ctnna1	2010010M04Rik|AA517462|AI988031|Catna1	catenin (cadherin associated protein), alpha 1	protein-coding
mm_150426.1	chr19	37436708	37436716	+	1	NA	intron (NM_008245, intron 1 of 3)	intron (NM_008245, intron 1 of 3)	1871	NM_008245	15242	Mm.33896	NM_008245	ENSMUSG00000024986	Hhex	Hex|Hex1|Hhex-rs2|Prh|Prhx	hematopoietically expressed homeobox	protein-coding
mm_33085.1	chr4	124474437	124474441	+	1	NA	intron (NR_040774, intron 2 of 3)	MLT1H|LTR|ERVL-MaLR	11520	NR_040774	78460	Mm.452060	NR_040774		1700057H15Rik	-	RIKEN cDNA 1700057H15 gene	ncRNA
mm_101578.1	chr11	34365875	34365886	-	1	NA	intron (NM_001025382, intron 1 of 3)	MIRc|SINE|MIR	51058	NM_001025382	574403	Mm.444796	NM_001025382	ENSMUSG00000069911	Fam196b	EG574403|Gm6041	family with sequence similarity 196, member B	protein-coding
mm_162057.1	chrX	8413305	8413305	+	1	NA	promoter-TSS (NM_026492)	promoter-TSS (NM_026492)	0	NM_026492	67985	Mm.298030	NM_026492	ENSMUSG00000079705	Ssxb1	4930414C09Rik	synovial sarcoma, X member B1	protein-coding
mm_160277.1	chr7	120145332	120145332	-	1	NA	promoter-TSS (NM_011775)	promoter-TSS (NM_011775)	-41	NM_011775	22787	Mm.6510	NM_011775	ENSMUSG00000030911	Zp2	Zp-2	zona pellucida glycoprotein 2	protein-coding
mm_120493.1	chr14	65980873	65980892	+	1	NA	exon (NM_013492, exon 8 of 9)	exon (NM_013492, exon 8 of 9)	12399	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_164920.1	chr18	77065559	77065572	-	1	NA	promoter-TSS (NM_001164168)	promoter-TSS (NM_001164168)	-115	NM_001164170	17344	Mm.6370	NM_008602	ENSMUSG00000025423	Pias2	6330408K17Rik|AI462206|ARIP3|AU018068|Dib|Miz1|PIASxalpha|PIASxb|PIASxbeta|SIZ2	protein inhibitor of activated STAT 2	protein-coding
mm_151856.1	chr19	5796871	5796894	-	1	NA	promoter-TSS (NR_144621)	promoter-TSS (NR_144621)	-901	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_65426.1	chr7	25297676	25297723	-	1	NA	intron (NM_008776, intron 1 of 5)	CpG-12842	256	NM_008776	18476	Mm.597	NM_008776	ENSMUSG00000005447	Pafah1b3	Pafahg|mus[g]	platelet-activating factor acetylhydrolase, isoform 1b, subunit 3	protein-coding
mm_88299.1	chr10	75316918	75316955	+	1	NA	promoter-TSS (NM_009630)	promoter-TSS (NM_009630)	59	NM_009630	11540	Mm.333734	NM_009630	ENSMUSG00000020178	Adora2a	A2AAR|A2aR|AA2AR	adenosine A2a receptor	protein-coding
mm_162552.1	chr1	171229749	171229762	-	1	NA	3' UTR (NM_010185, exon 5 of 5)	3' UTR (NM_010185, exon 5 of 5)	4594	NM_010185	14127	Mm.22673	NM_010185	ENSMUSG00000058715	Fcer1g	AI573376|CD23|FcR-gamma|FcR[g]|FcRgamma|Fce1g|FcepsilonRI|Ly-50	Fc receptor, IgE, high affinity I, gamma polypeptide	protein-coding
mm_65857.1	chr7	29339189	29339203	-	1	NA	intron (NM_001081028, intron 16 of 22)	intron (NM_001081028, intron 16 of 22)	35191	NM_013874	29861	Mm.101885	NM_013874	ENSMUSG00000030584	Dpf1	Neud4	D4, zinc and double PHD fingers family 1	protein-coding
mm_59242.1	chr7	24780882	24780898	+	1	NA	exon (NM_007675, exon 3 of 4)	exon (NM_007675, exon 3 of 4)	3686	NM_007675	26366	Mm.30300	NM_007675	ENSMUSG00000054169	Ceacam10	Bgp3|Cea10	carcinoembryonic antigen-related cell adhesion molecule 10	protein-coding
mm_62598.1	chr7	105736566	105736589	+	1	NA	promoter-TSS (NM_025897)	promoter-TSS (NM_025897)	7	NM_025897	101867	Mm.231400	NM_025897	ENSMUSG00000030888	Rrp8	1500003O22Rik|2900001K19Rik|AW538116	ribosomal RNA processing 8, methyltransferase, homolog (yeast)	protein-coding
mm_133481.1	chr16	90143983	90143996	+	1	NA	non-coding (NR_033476, exon 1 of 1)	non-coding (NR_033476, exon 1 of 1)	1752	NR_033476	100038709	Mm.484070	NR_033476		Gm10789	ENSMUSG00000074924	predicted gene 10789	ncRNA
mm_154715.1	chrX	9115990	9116022	+	1	NA	Intergenic	L1MB7|LINE|L1	11444	NM_001270700	75775	Mm.50374	NM_001270700	ENSMUSG00000045797	4930402K13Rik	-	RIKEN cDNA 4930402K13 gene	protein-coding
mm_166968.1	chr7	44516961	44516973	+	1	NA	exon (NM_146189, exon 8 of 28)	exon (NM_146189, exon 8 of 28)	7702	NM_146189	233199	Mm.358888	NM_146189	ENSMUSG00000038670	Mybpc2	-	myosin binding protein C, fast-type	protein-coding
mm_172534.1	chr7	93418924	93418924	-	1	NA	Intergenic	L1Md_T|LINE|L1	339045	NM_021427	58238	Mm.113787	NM_021427	ENSMUSG00000051515	Fam181b	A830059I20Rik|AB041569	family with sequence similarity 181, member B	protein-coding
mm_5254.1	chr1	16645802	16645828	-	1	NA	exon (NM_026456, exon 3 of 4)	exon (NM_026456, exon 3 of 4)	11050	NM_026456	67923	Mm.289248	NM_026456	ENSMUSG00000079658	Eloc	2610043E24Rik|2610301I15Rik|AA407206|AI987979|AW049146|Tceb1	elongin C	protein-coding
mm_166851.1	chr7	19696841	19696841	-	1	NA	exon (NM_009696, exon 4 of 4)	exon (NM_009696, exon 4 of 4)	1557	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_70330.1	chr8	4493023	4493045	+	1	NA	promoter-TSS (NM_026058)	promoter-TSS (NM_026058)	-371	NM_026058	67260	Mm.35511	NM_026058	ENSMUSG00000008206	Cers4	2900019C14Rik|Lass4|Trh1	ceramide synthase 4	protein-coding
mm_29938.1	chr3	132683825	132683856	-	1	NA	promoter-TSS (NM_007926)	promoter-TSS (NM_007926)	39	NM_007926	13722	Mm.235137	NM_007926	ENSMUSG00000028029	Aimp1	9830137A06Rik|AIMP1/p43|EMAPII|Emap2|Scye1|p43	aminoacyl tRNA synthetase complex-interacting multifunctional protein 1	protein-coding
mm_15922.1	chr2	165066760	165066768	+	1	NA	intron (NM_170702, intron 6 of 7)	MIRc|SINE|MIR	11128	NM_011611	21939	Mm.271833	NM_011611	ENSMUSG00000017652	Cd40	AI326936|Bp50|GP39|HIGM1|IGM|IMD3|T-BAM|TRAP|Tnfrsf5|p50	CD40 antigen	protein-coding
mm_49456.1	chr6	29397546	29397556	+	1	NA	exon (NM_001347073, exon 2 of 10)	exon (NM_001347073, exon 2 of 10)	967	NM_001347073	232664	Mm.251303	NM_145574	ENSMUSG00000029769	Ccdc136	4921511K06Rik|BC006583	coiled-coil domain containing 136	protein-coding
mm_78104.1	chr9	19629500	19629504	+	1	NA	intron (NM_172918, intron 2 of 8)	intron (NM_172918, intron 2 of 8)	7411	NM_172918	244713	Mm.67366	NM_172918	ENSMUSG00000057551	Zfp317	4932416G03|D230022C05Rik|KRAB9|Zfp67|Zfp75|mszf40	zinc finger protein 317	protein-coding
mm_165248.1	chr2	70135352	70135374	+	1	NA	intron (NM_177376, intron 8 of 34)	L3|LINE|CR1	96237	NM_177376	329421	Mm.99648	NM_177376	ENSMUSG00000042064	Myo3b	A430065P19Rik	myosin IIIB	protein-coding
mm_28866.1	chr3	97610157	97610222	-	1	NA	promoter-TSS (NM_026539)	promoter-TSS (NM_026539)	1	NM_026539	68058	Mm.31761	NM_026539	ENSMUSG00000028089	Chd1l	4432404A22Rik|Alc1|Snf2p	chromodomain helicase DNA binding protein 1-like	protein-coding
mm_36651.1	chr4	94603096	94603193	-	1	NA	5' UTR (NM_172695, exon 1 of 14)	5' UTR (NM_172695, exon 1 of 14)	103	NM_172695	18786	Mm.490101	NM_172695	ENSMUSG00000028577	Plaa	2410007N06|AI536418|AU018445|AW208417|D4Ertd618e|PLA2P|PLAP|Ufd3	phospholipase A2, activating protein	protein-coding
mm_107686.1	chr12	55080529	55080560	+	1	NA	promoter-TSS (NM_011899)	promoter-TSS (NM_011899)	48	NM_011899	24067	Mm.471968	NM_011899	ENSMUSG00000073079	Srp54a	54kDa|Srp54	signal recognition particle 54A	protein-coding
mm_52001.1	chr6	92827635	92827663	+	1	NA	intron (NM_175314, intron 18 of 29)	intron (NM_175314, intron 18 of 29)	73792	NM_175314	101401	Mm.158235	NM_175314	ENSMUSG00000030022	Adamts9	1810011L16Rik|8430403M15Rik|AW743315|E030027K14Rik	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 9	protein-coding
mm_84947.1	chr9	83112596	83112618	-	1	NA	intron (NM_175074, intron 3 of 5)	intron (NM_175074, intron 3 of 5)	34000	NM_175074	94353	Mm.244426	NM_026122	ENSMUSG00000066456	Hmgn3	1110002A15Rik|6330514M13Rik|BB071015|TRIP7	high mobility group nucleosomal binding domain 3	protein-coding
mm_77068.1	chr8	109962128	109962213	-	1	NA	promoter-TSS (NM_028584)	promoter-TSS (NM_028584)	35	NM_212447	73608	Mm.86833	NM_028584	ENSMUSG00000001672	Marveld3	1810006A16Rik|AI642133|Marvd3|Mrvldc3	MARVEL (membrane-associating) domain containing 3	protein-coding
mm_130087.1	chr15	89379165	89379175	-	1	NA	promoter-TSS (NM_001013022)	promoter-TSS (NM_001013022)	84	NM_001013022	70113	Mm.247273	NM_001013022	ENSMUSG00000047394	Odf3b	2010001J22Rik	outer dense fiber of sperm tails 3B	protein-coding
mm_169896.1	chr16	48310469	48310478	+	1	NA	5' UTR (NM_028615, exon 1 of 7)	5' UTR (NM_028615, exon 1 of 7)	199	NM_028615	73703	Mm.27857	NM_028615	ENSMUSG00000072419	Dppa2	2410088E07Rik|C80932|D19Mgi18|ECAT15-2	developmental pluripotency associated 2	protein-coding
mm_98175.1	chr11	87756632	87756635	+	1	NA	promoter-TSS (NR_029555)	promoter-TSS (NR_029555)	-231	NR_029555	387160		NR_029555	ENSMUSG00000105196	Mir142	Mirn142|miR-142|mir-142a|mmu-mir-142|mmu-mir-142a	microRNA 142	ncRNA
mm_141855.1	chr17	34803064	34803072	-	1	NA	exon (NM_009995, exon 6 of 10)	exon (NM_009995, exon 6 of 10)	1358	NM_009995	13079	Mm.440407	NM_009995	ENSMUSG00000024365	Cyp21a1	21-OH|21OH|21OHA|21OHB|CYP21OH-A|Cyp21|Cyp21-ps1|Cyp21B|Cyp21a2-ps|Cyp21a2ps|Oh21-1|Oh21-2	cytochrome P450, family 21, subfamily a, polypeptide 1	protein-coding
mm_144459.1	chr18	23415485	23415492	+	1	NA	promoter-TSS (NM_207650)	promoter-TSS (NM_207650)	79	NM_001285811	13527	Mm.94371	NM_010087	ENSMUSG00000024302	Dtna	2210407P21Rik|DTN-A|Dtn|Gm19389|a-DB-1|adbn	dystrobrevin alpha	protein-coding
mm_59235.1	chr7	24778145	24778152	+	1	NA	exon (NM_007675, exon 2 of 4)	exon (NM_007675, exon 2 of 4)	944	NM_007675	26366	Mm.30300	NM_007675	ENSMUSG00000054169	Ceacam10	Bgp3|Cea10	carcinoembryonic antigen-related cell adhesion molecule 10	protein-coding
mm_9588.1	chr1	174031837	174031845	-	1	NA	promoter-TSS (NM_172648)	promoter-TSS (NM_172648)	-86	NM_172648	226695	Mm.425061	NM_172648	ENSMUSG00000054203	Ifi205	D3|D3cDNA|Ifi205a	interferon activated gene 205	protein-coding
mm_113416.1	chr13	34021649	34021655	+	1	NA	intron (NM_009068, intron 7 of 10)	intron (NM_009068, intron 7 of 10)	-15989	NM_026512	68021	Mm.140243	NM_026512	ENSMUSG00000038286	Bphl	2010012D11Rik|5730533B08Rik|AI115341	biphenyl hydrolase-like (serine hydrolase, breast epithelial mucin-associated antigen)	protein-coding
mm_37367.1	chr4	120825666	120825680	-	1	NA	promoter-TSS (NM_001277095)	promoter-TSS (NM_001277095)	68	NM_001277095	18046	Mm.435590	NM_008692	ENSMUSG00000032897	Nfyc	-	nuclear transcription factor-Y gamma	protein-coding
mm_155603.1	chrX	82949080	82949090	+	1	NA	5' UTR (NM_007868, exon 1 of 79)	5' UTR (NM_007868, exon 1 of 79)	215	NM_007868	13405	Mm.275608	NM_007868	ENSMUSG00000045103	Dmd	DXSmh7|DXSmh9|Dp427|Dp71|dys|mdx|pke	dystrophin, muscular dystrophy	protein-coding
mm_155224.1	chrX	57066032	57066047	+	1	NA	exon (NM_029371, exon 9 of 9)	exon (NM_029371, exon 9 of 9)	12205	NM_029371	72459	Mm.2152	NM_028242	ENSMUSG00000067873	Htatsf1	1600023H17Rik|2600017A12Rik|2700077B20Rik|TAT-SF1	HIV TAT specific factor 1	protein-coding
mm_58710.1	chr7	12978213	12978232	+	1	NA	intron (NM_001168561, intron 1 of 4)	CpG	374	NM_001168561	269870	Mm.62083	NM_175558	ENSMUSG00000033961	Zfp446	A630035I11Rik|A930031C22|AA120513|AV306632	zinc finger protein 446	protein-coding
mm_111234.1	chr12	84766770	84766773	-	1	NA	intron (NM_023409, intron 1 of 3)	intron (NM_023409, intron 1 of 3)	6341	NM_023409	67963	Mm.282556	NM_023409	ENSMUSG00000021242	Npc2	2700012J19Rik|AA408070|AU045843|HE1	Niemann-Pick type C2	protein-coding
mm_119898.1	chr14	54938609	54938615	+	1	NA	exon (NM_026066, exon 3 of 5)	exon (NM_026066, exon 3 of 5)	2115	NM_029390	67272	Mm.41614	NM_026066	ENSMUSG00000040759	Cmtm5	1500005P16Rik|2900052H21Rik|Cklfsf5	CKLF-like MARVEL transmembrane domain containing 5	protein-coding
mm_35423.1	chr4	35206850	35206854	-	1	NA	intron (NM_001081343, intron 6 of 10)	intron (NM_001081343, intron 6 of 10)	19028	NM_001081343	73205	Mm.331544	NM_001081343	ENSMUSG00000028300	3110043O21Rik	AI840585	RIKEN cDNA 3110043O21 gene	protein-coding
mm_46683.1	chr5	109690787	109690813	-	1	NA	Intergenic	Intergenic	-131807	NM_001310694	57914	Mm.35771	NM_016715	ENSMUSG00000033467	Crlf2	CRLM2|Ly114|Tpte2|Tslpr	cytokine receptor-like factor 2	protein-coding
mm_83222.1	chr9	42259761	42259772	-	1	NA	exon (NM_172769, exon 3 of 6)	exon (NM_172769, exon 3 of 6)	4534	NM_172769	235293	Mm.32700	NM_172769	ENSMUSG00000032018	Sc5d	A830037K02|A830073K23Rik|Sc5dl	sterol-C5-desaturase	protein-coding
mm_127608.1	chr15	102459167	102459183	+	1	NA	promoter-TSS (NM_025385)	promoter-TSS (NM_025385)	5	NM_025385	66151	Mm.393955	NM_025385	ENSMUSG00000023048	Prr13	1110020C13Rik|2010324E22Rik	proline rich 13	protein-coding
mm_120345.1	chr14	63783659	63783667	+	1	NA	intron (NM_173393, intron 1 of 2)	intron (NM_173393, intron 1 of 2)	56474	NR_030611	100124452		NR_030611	ENSMUSG00000076049	Mir598	Mirn598|mir-598|mmu-mir-598	microRNA 598	ncRNA
mm_140800.1	chr17	21909620	21909677	-	1	NA	5' UTR (NM_001256493, exon 1 of 5)	5' UTR (NM_001256493, exon 1 of 5)	278	NM_001256493	70081	Mm.245648	NM_001256493	ENSMUSG00000078546	Zfp995	2210404O09Rik	zinc finger protein 995	protein-coding
mm_90558.1	chr10	128194447	128194466	+	1	NA	promoter-TSS (NM_001285779)	promoter-TSS (NM_001285779)	-179	NM_001285777	216456	Mm.30102	NM_001033264	ENSMUSG00000044005	Gls2	A330074B06Rik|AI195532|GA|GLS|Lga	glutaminase 2 (liver, mitochondrial)	protein-coding
mm_85937.1	chr9	112098072	112098085	-	1	NA	intron (NM_001177618, intron 17 of 18)	intron (NM_001177618, intron 17 of 18)	20633	NR_029823	723815		NR_029823	ENSMUSG00000065441	Mir128-2	Mirn128-2|Mirn128b|mir-128-2|mir-128b	microRNA 128-2	ncRNA
mm_171249.1	chr3	7897696	7897704	+	1	NA	Intergenic	B1_Mus1|SINE|Alu	57187	NR_040587	75476	Mm.491752	NR_040587	ENSMUSG00000100010	1700010I02Rik	-	RIKEN cDNA 1700010I02 gene	ncRNA
mm_44215.1	chr5	4757876	4757887	-	1	NA	5' UTR (NM_021457, exon 1 of 1)	5' UTR (NM_021457, exon 1 of 1)	335	NM_021457	14362	Mm.246003	NM_021457	ENSMUSG00000044674	Fzd1	AW227548|FZ-1|Fz1	frizzled class receptor 1	protein-coding
mm_147003.1	chr18	34373314	34373443	-	1	NA	promoter-TSS (NM_007874)	promoter-TSS (NM_007874)	37	NM_007874	13476	Mm.280075	NM_007874	ENSMUSG00000005873	Reep5	AI324241|AU022809|AW495741|DP1/TB2|Dp1|R74856|TB2/DP1	receptor accessory protein 5	protein-coding
mm_152818.1	chr19	23135018	23135034	-	1	NA	Intergenic	CpG	-6200	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_6218.1	chr1	66863266	66863285	-	1	NA	promoter-TSS (NM_007381)	promoter-TSS (NM_007381)	34	NM_007381	11363	Mm.2445	NM_007381	ENSMUSG00000026003	Acadl	AA960361|AU018452|C79855|LCAD	acyl-Coenzyme A dehydrogenase, long-chain	protein-coding
mm_108790.1	chr12	90972846	90972855	+	1	NA	Intergenic	Intergenic	-72998	NR_045858	71349	Mm.442093	NR_045858		5430427M07Rik	-	RIKEN cDNA 5430427M07 gene	ncRNA
mm_8965.1	chr1	165184734	165184737	-	1	NA	intron (NM_145512, intron 4 of 7)	intron (NM_145512, intron 4 of 7)	9698	NM_145512	108735	Mm.288369	NM_145512	ENSMUSG00000040848	Sft2d2	2010005O13Rik|AI506168|AW561909|cI-45	SFT2 domain containing 2	protein-coding
mm_102613.1	chr11	62457854	62457867	-	1	NA	promoter-TSS (NM_177229)	promoter-TSS (NM_177229)	-528	NM_177229	20185	Mm.271814	NM_011308	ENSMUSG00000018501	Ncor1	5730405M06Rik|A230020K14Rik|N-CoR|RIP13|Rxrip13|mKIAA1047	nuclear receptor co-repressor 1	protein-coding
mm_128990.1	chr15	74834744	74834754	-	1	NA	TTS (NM_001033229)	TTS (NM_001033229)	6894	NM_001033229	110115	Mm.322606	NM_001033229	ENSMUSG00000075604	Cyp11b1	AA389061|CPN1|Cyp11b|Cyp11b-1|FHI	cytochrome P450, family 11, subfamily b, polypeptide 1	protein-coding
mm_17710.1	chr2	32385746	32385759	-	1	NA	exon (NM_008491, exon 4 of 6)	exon (NM_008491, exon 4 of 6)	1987	NM_008491	16819	Mm.9537	NM_008491	ENSMUSG00000026822	Lcn2	24p3|AW212229|NRL|Sip24	lipocalin 2	protein-coding
mm_166282.1	chr5	96573797	96573807	+	1	NA	intron (NM_175473, intron 14 of 73)	intron (NM_175473, intron 14 of 73)	199847	NM_175473	231470	Mm.291120	NM_175473	ENSMUSG00000034687	Fras1	E130113P14Rik|bl|mKIAA1500	Fraser extracellular matrix complex subunit 1	protein-coding
mm_56875.1	chr6	118883604	118883623	-	1	NA	intron (NR_046053, intron 3 of 3)	intron (NR_046053, intron 3 of 3)	3455	NR_046053	74363	Mm.399403	NR_046053		4931430N09Rik	-	RIKEN cDNA 4931430N09 gene	ncRNA
mm_67483.1	chr7	80713013	80713014	-	1	NA	3' UTR (NM_016721, exon 38 of 38)	3' UTR (NM_016721, exon 38 of 38)	-24136	NM_173863	70461	Mm.392175	NM_173863	ENSMUSG00000030527	Crtc3	2610312F20Rik|6332415K15Rik|AI429792|BC011210|TORC3	CREB regulated transcription coactivator 3	protein-coding
mm_17824.1	chr2	33887408	33887420	-	1	NA	5' UTR (NM_175184, exon 1 of 10)	5' UTR (NM_175184, exon 1 of 10)	532	NM_175184	72543	Mm.254914	NM_175184	ENSMUSG00000038740	Mvb12b	2610200O14Rik|2610528K11Rik|AI414895|Fam125b	multivesicular body subunit 12B	protein-coding
mm_20843.1	chr2	148034034	148034037	-	1	NA	Intergenic	Intergenic	11429	NM_001291067	15376	Mm.938	NM_010446	ENSMUSG00000037025	Foxa2	HNF3-beta|HNF3beta|Hnf-3b|Hnf3b|Tcf-3b|Tcf3b	forkhead box A2	protein-coding
mm_43464.1	chr5	136692957	136692970	+	1	NA	promoter-TSS (NM_021611)	promoter-TSS (NM_021611)	-183	NM_001303019	59310	Mm.5178	NM_021611	ENSMUSG00000005474	Myl10	1700027I08Rik|Mylc2pl|PLRLC	myosin, light chain 10, regulatory	protein-coding
mm_59930.1	chr7	30423429	30423477	+	1	NA	5' UTR (NM_172142, exon 1 of 11)	5' UTR (NM_172142, exon 1 of 11)	149	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_80096.1	chr9	70270958	70270960	+	1	NA	intron (NM_181072, intron 1 of 27)	intron (NM_181072, intron 1 of 27)	63609	NM_181072	71602	Mm.249311	NM_181072	ENSMUSG00000032220	Myo1e	2310020N23Rik|9130023P14Rik|AA407778|myosin-1e|myr 3	myosin IE	protein-coding
mm_4984.1	chr1	191718036	191718061	+	1	NA	promoter-TSS (NM_001134829)	promoter-TSS (NM_001134829)	24	NM_172266	226856	Mm.277958	NM_172266	ENSMUSG00000026623	Lpgat1	AI649174|AW112037|BC013667	lysophosphatidylglycerol acyltransferase 1	protein-coding
mm_166429.1	chr5	137152699	137152701	-	1	NA	Intergenic	Intergenic	-36493	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_79304.1	chr9	52047153	52047163	+	1	NA	promoter-TSS (NM_009041)	promoter-TSS (NM_009041)	8	NM_001104616	19684	Mm.245746	NM_009041	ENSMUSG00000032050	Rdx	AA516625	radixin	protein-coding
mm_23311.1	chr3	53054678	53054681	+	1	NA	intron (NM_175386, intron 2 of 3)	intron (NM_175386, intron 2 of 3)	13132	NM_175386	108927	Mm.118617	NM_175386	ENSMUSG00000048332	Lhfp	2810489O06Rik|AI194968	lipoma HMGIC fusion partner	protein-coding
mm_56871.1	chr6	118637974	118637983	-	1	NA	intron (NM_001256002, intron 30 of 47)	intron (NM_001256002, intron 30 of 47)	-75722	NM_001081112	232339	Mm.276116	NM_001081112	ENSMUSG00000007827	Ankrd26	5730521P14Rik|BC008111|mKIAA1074	ankyrin repeat domain 26	protein-coding
mm_157474.1	chrX	48098745	48098745	-	1	NA	Intergenic	Intergenic	-9980	NM_001289729	170745	Mm.129279	NM_133213	ENSMUSG00000037005	Xpnpep2	9030008G12Rik|mAPP	X-prolyl aminopeptidase (aminopeptidase P) 2, membrane-bound	protein-coding
mm_145873.1	chr18	65471578	65471588	+	1	NA	intron (NM_172833, intron 13 of 15)	intron (NM_172833, intron 13 of 15)	40586	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_30824.1	chr4	21874017	21874031	+	1	NA	exon (NM_025669, exon 11 of 12)	exon (NM_025669, exon 11 of 12)	-5651	NM_172687	230027	Mm.5662	NM_172687	ENSMUSG00000028247	Coq3	4732433J24|C77934	coenzyme Q3 methyltransferase	protein-coding
mm_8226.1	chr1	138174344	138174348	-	1	NA	intron (NM_001111316, intron 1 of 31)	intron (NM_001111316, intron 1 of 31)	780	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_77584.1	chr8	123858872	123858891	-	1	NA	intron (NM_028536, intron 2 of 3)	intron (NM_028536, intron 2 of 3)	1328	NM_028536	73420	Mm.157746	NM_028536	ENSMUSG00000031971	Ccsap	1700054N08Rik|AI853424	centriole, cilia and spindle associated protein	protein-coding
mm_6402.1	chr1	72862296	72862306	-	1	NA	3' UTR (NM_010518, exon 4 of 4)	3' UTR (NM_010518, exon 4 of 4)	12564	NM_010518	16011	Mm.405761	NM_010518	ENSMUSG00000026185	Igfbp5	AI256729|AW208790|IGFBP-5|IGFBP-5P	insulin-like growth factor binding protein 5	protein-coding
mm_39798.1	chr5	30622454	30622467	+	1	NA	exon (NM_010608, exon 2 of 2)	exon (NM_010608, exon 2 of 2)	-25476	NR_049199	100885838		NR_049199	ENSMUSG00000093710	Mir5625	Gm23930|mmu-mir-5625	microRNA 5625	ncRNA
mm_838.1	chr1	51585353	51585387	+	1	NA	Intergenic	LTR82B|LTR|ERVL	-106971	NM_001310549	109019	Mm.196290	NM_028696	ENSMUSG00000026107	Nabp1	4930434H03Rik|4930442A21Rik|4930488J04Rik|4933440J18Rik|5830411E10Rik|AI852561|Nbp1|Obfc2a|Ssb2	nucleic acid binding protein 1	protein-coding
mm_110979.1	chr12	77055007	77055024	-	1	NA	Intergenic	Intergenic	-92767	NM_001146176	17187	Mm.268548	NM_008558	ENSMUSG00000059436	Max	AA960152|AI875693|bHLHd4|bHLHd5|bHLHd6|bHLHd7|bHLHd8	Max protein	protein-coding
mm_105027.1	chr11	100472795	100472811	-	1	NA	promoter-TSS (NM_172565)	promoter-TSS (NM_172565)	-21	NM_172565	217194	Mm.183320	NM_172565	ENSMUSG00000048732	Klhl11	BC011167	kelch-like 11	protein-coding
mm_169403.1	chr1	45047640	45047651	+	1	NA	Intergenic	L1Md_Gf|LINE|L1	-263893	NM_009930	12825	Mm.249555	NM_009930	ENSMUSG00000026043	Col3a1	AW550625|Col3a-1|Tsk-2|Tsk2	collagen, type III, alpha 1	protein-coding
mm_151512.1	chr19	58734893	58734951	+	1	NA	exon (NM_018874, exon 8 of 13)	exon (NM_018874, exon 8 of 13)	6035	NM_018874	18946	Mm.10753	NM_018874	ENSMUSG00000042179	Pnliprp1	Plrp1	pancreatic lipase related protein 1	protein-coding
mm_12922.1	chr2	84980459	84980462	+	1	NA	promoter-TSS (NM_008920)	promoter-TSS (NM_008920)	-1	NM_008920	19074	Mm.142727	NM_008920	ENSMUSG00000027073	Prg2	EMBP|MBP|mMBP|mMBP-1	proteoglycan 2, bone marrow	protein-coding
mm_70273.1	chr8	3598355	3598369	+	1	NA	intron (NM_001347112, intron 2 of 17)	intron (NM_001347112, intron 2 of 17)	10912	NM_001347111	69697	Mm.390010	NM_027171	ENSMUSG00000044433	Camsap3	2310057J16Rik|Kiaa1543|Nezha	calmodulin regulated spectrin-associated protein family, member 3	protein-coding
mm_105598.1	chr11	106750650	106750660	-	1	NA	promoter-TSS (NM_001271373)	promoter-TSS (NM_001271373)	-571	NM_001271375	380732	Mm.343952	NM_001033435	ENSMUSG00000040528	Milr1	Allergin-1|Gm885|Mca32	mast cell immunoglobulin like receptor 1	protein-coding
mm_112782.1	chr13	20090665	20090679	+	1	NA	5' UTR (NM_080288, exon 1 of 22)	5' UTR (NM_080288, exon 1 of 22)	165	NM_080288	140580	Mm.342392	NM_080288	ENSMUSG00000041112	Elmo1	6330578D22Rik|C230095H21Rik|CED-12	engulfment and cell motility 1	protein-coding
mm_87203.1	chr10	39613188	39613249	+	1	NA	5' UTR (NM_134000, exon 1 of 9)	5' UTR (NM_134000, exon 1 of 9)	284	NM_134000	103213	Mm.436686	NM_134000	ENSMUSG00000019842	Traf3ip2	AI429613|Act1|CIKS	TRAF3 interacting protein 2	protein-coding
mm_70344.1	chr8	4643063	4643070	+	1	NA	Intergenic	Intergenic	29896	NM_145591	233987	Mm.102799	NM_145591	ENSMUSG00000058748	Zfp958	-	zinc finger protein 958	protein-coding
mm_66241.1	chr7	35552947	35552950	-	1	NA	intron (NM_033080, intron 1 of 2)	L1MEc|LINE|L1	2980	NM_033080	110959	Mm.410206	NM_033080	ENSMUSG00000034875	Nudt19	D7Rp2|D7Rp2-r|D7Rp2-s|D7Rp2e|RP2-r|RP2-s	nudix (nucleoside diphosphate linked moiety X)-type motif 19	protein-coding
mm_139222.1	chr17	47730154	47730156	+	1	NA	exon (NM_025973, exon 4 of 9)	exon (NM_025973, exon 4 of 9)	3313	NM_025973	109820	Mm.22957	NM_025973	ENSMUSG00000023987	Pgc	2210410L06Rik|Upg-1|Upg1	progastricsin (pepsinogen C)	protein-coding
mm_59902.1	chr7	30314811	30314870	+	1	NA	promoter-TSS (NM_153577)	promoter-TSS (NM_153577)	24	NM_153577	233066	Mm.227325	NM_153577	ENSMUSG00000019737	Syne4	0610012K07Rik|AI428936|Nesp4	spectrin repeat containing, nuclear envelope family member 4	protein-coding
mm_120530.1	chr14	67176822	67176843	+	1	NA	Intergenic	Intergenic	-56460	NM_010095	13592	Mm.319947	NM_010095	ENSMUSG00000022053	Ebf2	D14Ggc1e|EBF-2|Mmot1|O/E-3|OE-3	early B cell factor 2	protein-coding
mm_150834.1	chr19	44756931	44756942	+	1	NA	promoter-TSS (NM_011037)	promoter-TSS (NM_011037)	-458	NM_011037	18504	Mm.192158	NM_011037	ENSMUSG00000004231	Pax2	Opdc|Pax-2	paired box 2	protein-coding
mm_96013.1	chr11	59542800	59542810	+	1	NA	5' UTR (NM_145827, exon 1 of 10)	5' UTR (NM_145827, exon 1 of 10)	119	NM_145827	216799	Mm.54174	NM_145827	ENSMUSG00000032691	Nlrp3	AGTAVPRL|AII/AVP|Cias1|FCAS|FCU|MWS|Mmig1|NALP3|Pypaf1	NLR family, pyrin domain containing 3	protein-coding
mm_34767.1	chr4	153410825	153410828	+	1	NA	intron (NM_001099299, intron 2 of 5)	intron (NM_001099299, intron 2 of 5)	72004	NM_001099299	230959	Mm.318874	NM_001099299	ENSMUSG00000039546	Ajap1	Gm573	adherens junction associated protein 1	protein-coding
mm_32245.1	chr4	102568868	102568874	+	1	NA	intron (NM_019840, intron 5 of 14)	intron (NM_019840, intron 5 of 14)	-1189	NM_001177980	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_123080.1	chr14	55743847	55743874	-	1	NA	intron (NM_026819, intron 2 of 8)	intron (NM_026819, intron 2 of 8)	1824	NM_026819	52585	Mm.21623	NM_026819	ENSMUSG00000002332	Dhrs1	1110029G07Rik|AW112170|D14Ertd484e	dehydrogenase/reductase (SDR family) member 1	protein-coding
mm_1804.1	chr1	80757739	80757751	+	1	NA	intron (NM_175291, intron 1 of 55)	intron (NM_175291, intron 1 of 55)	808	NM_175291	210293	Mm.133473	NM_175291	ENSMUSG00000038608	Dock10	9330153B10Rik|A630054M16Rik|Jr4|Jr5|R75174|ZIZ3|Zizimin3|mKIAA0694	dedicator of cytokinesis 10	protein-coding
mm_152052.1	chr19	6264409	6264418	-	1	NA	promoter-TSS (NR_029830)	promoter-TSS (NR_029830)	-230	NR_029830	723957		NR_029830	ENSMUSG00000065582	Mir194-2	Mirn194-2|mir-194-2	microRNA 194-2	ncRNA
mm_149922.1	chr19	26621984	26621987	+	1	NA	intron (NM_011416, intron 2 of 32)	intron (NM_011416, intron 2 of 32)	16825	NM_011416	67155	Mm.342988	NM_011416	ENSMUSG00000024921	Smarca2	2610209L14Rik|SNF2alpha|Snf2l2|brahma|brm	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	protein-coding
mm_41880.1	chr5	105274180	105274224	+	1	NA	exon (NM_194336, exon 10 of 11)	exon (NM_194336, exon 10 of 11)	19497	NM_194336	100702	Mm.491210	NM_194336	ENSMUSG00000079362	Gbp6	AI595338|Mpa2l	guanylate binding protein 6	protein-coding
mm_44298.1	chr5	8622985	8622998	-	1	NA	promoter-TSS (NM_198620)	promoter-TSS (NM_198620)	-39	NM_198620	242819	Mm.332192	NM_198620	ENSMUSG00000040570	Rundc3b	Gm440	RUN domain containing 3B	protein-coding
mm_155371.1	chrX	71555980	71556022	+	1	NA	promoter-TSS (NM_008253)	promoter-TSS (NM_008253)	84	NM_001293625	15354	Mm.336087	NM_008253	ENSMUSG00000015217	Hmgb3	Hmg2a|Hmg4	high mobility group box 3	protein-coding
mm_121230.1	chr14	103055751	103055761	+	1	NA	3' UTR (NM_008392, exon 5 of 5)	3' UTR (NM_008392, exon 5 of 5)	8744	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_69207.1	chr7	127422003	127422059	-	1	NA	promoter-TSS (NM_026999)	promoter-TSS (NM_026999)	3	NM_026999	69234	Mm.20301	NM_026999	ENSMUSG00000045251	Zfp688	2810407K09Rik|AI326029	zinc finger protein 688	protein-coding
mm_51996.1	chr6	92306106	92306113	+	1	NA	Intergenic	MLT1B|LTR|ERVL-MaLR	-61459	NM_009426	22044	Mm.1363	NM_009426	ENSMUSG00000005892	Trh	Pro-TRH|Trf	thyrotropin releasing hormone	protein-coding
mm_15502.1	chr2	158028482	158028539	+	1	NA	promoter-TSS (NM_027434)	promoter-TSS (NM_027434)	13	NM_001291135	70470	Mm.290810	NM_027434	ENSMUSG00000027651	Rprd1b	2610304G08Rik|2810446G03Rik|Crept	regulation of nuclear pre-mRNA domain containing 1B	protein-coding
mm_162600.1	chr1	183147550	183147563	-	1	NA	promoter-TSS (NM_001278220)	promoter-TSS (NM_001278220)	1	NM_001278220	68897	Mm.327216	NM_026866	ENSMUSG00000030768	Disp1	1190008H24Rik|DispA	dispatched RND transporter family member 1	protein-coding
mm_160238.1	chr7	103937551	103937551	+	1	NA	exon (NM_147119, exon 1 of 1)	exon (NM_147119, exon 1 of 1)	169	NM_147119	259123	Mm.377861	NM_147119	ENSMUSG00000073938	Olfr632	MOR2-1	olfactory receptor 632	protein-coding
mm_9179.1	chr1	171058375	171058383	-	1	NA	intron (NM_010188, intron 2 of 4)	ID4_|SINE|ID	1024	NM_010188	14131	Mm.22119	NM_010188	ENSMUSG00000059498	Fcgr3	CD16	Fc receptor, IgG, low affinity III	protein-coding
mm_81694.1	chr9	111182301	111182306	+	1	NA	intron (NM_001164838, intron 5 of 14)	intron (NM_001164838, intron 5 of 14)	64192	NM_001164838	71268	Mm.302287	NM_027742	ENSMUSG00000032497	Lrrfip2	5133400F20Rik|AI850587	leucine rich repeat (in FLII) interacting protein 2	protein-coding
mm_49003.1	chr6	4756949	4756960	+	1	NA	exon (NM_130877, exon 2 of 2)	exon (NM_130877, exon 2 of 2)	9648	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_7873.1	chr1	132866802	132866814	-	1	NA	Intergenic	Intergenic	-13547	NM_010732	16980	Mm.39640	NM_010732	ENSMUSG00000026443	Lrrn2	5730406J09Rik|NLRR-2	leucine rich repeat protein 2, neuronal	protein-coding
mm_39951.1	chr5	32133235	32133257	+	1	NA	Intergenic	CpG	-3226	NM_008037	14284	Mm.24684	NM_008037	ENSMUSG00000029135	Fosl2	Fra-2	fos-like antigen 2	protein-coding
mm_53649.1	chr6	140758950	140758956	+	1	NA	Intergenic	B1_Mur2|SINE|Alu	132068	NM_001309436	11569	Mm.86453	NM_009637	ENSMUSG00000030232	Aebp2	AU023766|B230313N05Rik	AE binding protein 2	protein-coding
mm_91708.1	chr10	44148788	44148804	-	1	NA	Intergenic	CpG	-21651	NR_001582	70365	Mm.87073	NR_001582	ENSMUSG00000091358	Speer5-ps1	1700007C10Rik|SPEER-5|Speer5-ps	spermatogenesis associated glutamate (E)-rich protein 5, pseudogene 1	pseudo
mm_169410.1	chr1	45206020	45206021	-	1	NA	Intergenic	Intergenic	-105518	NM_009930	12825	Mm.249555	NM_009930	ENSMUSG00000026043	Col3a1	AW550625|Col3a-1|Tsk-2|Tsk2	collagen, type III, alpha 1	protein-coding
mm_115362.1	chr13	112937555	112937560	+	1	NA	intron (NM_172594, intron 6 of 26)	intron (NM_172594, intron 6 of 26)	9764	NM_172594	218629	Mm.35094	NM_172594	ENSMUSG00000042426	Dhx29	3732415M03|AU043276|Ddxx|E130202M19Rik	DEAH (Asp-Glu-Ala-His) box polypeptide 29	protein-coding
mm_45649.1	chr5	77018841	77018853	-	1	NA	promoter-TSS (NR_077218)	promoter-TSS (NR_077218)	16	NR_077218	68246	Mm.319633	NR_077218	ENSMUSG00000086632	1700112J05Rik	1700110A09Rik	RIKEN cDNA 1700112J05 gene	ncRNA
mm_144044.1	chr17	90400360	90400367	-	1	NA	intron (NM_001346957, intron 14 of 18)	intron (NM_001346957, intron 14 of 18)	55517	NM_001346958	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_144877.1	chr18	36783223	36783235	+	1	NA	promoter-TSS (NM_080636)	promoter-TSS (NM_080636)	20	NM_080636	70791	Mm.282700	NM_080636	ENSMUSG00000019143	Hars2	4631412B19Rik|HARSR|HO3|Harsl	histidyl-tRNA synthetase 2	protein-coding
mm_136998.1	chr17	17402970	17402979	+	1	NA	exon (NM_025681, exon 1 of 6)	exon (NM_025681, exon 1 of 6)	288	NM_025681	66643	Mm.268018	NM_025681	ENSMUSG00000047786	Lix1	5730466L18Rik	limb and CNS expressed 1	protein-coding
mm_18284.1	chr2	52558529	52558537	-	1	NA	promoter-TSS (NM_146123)	promoter-TSS (NM_146123)	78	NM_146123	12298	Mm.330223	NM_146123	ENSMUSG00000017412	Cacnb4	3110038O15Rik|Cchb4|lh	calcium channel, voltage-dependent, beta 4 subunit	protein-coding
mm_82415.1	chr9	14901903	14901911	-	1	NA	intron (NM_022888, intron 2 of 4)	intron (NM_022888, intron 2 of 4)	2044	NM_176807	64931	Mm.86738	NM_022888	ENSMUSG00000031933	Izumo1r	0910001L11Rik|C86255|Folbp3|Folr4|Juno	IZUMO1 receptor, JUNO	protein-coding
mm_88718.1	chr10	80158126	80158129	+	1	NA	3' UTR (NM_001305798, exon 8 of 8)	3' UTR (NM_001305798, exon 8 of 8)	8445	NM_001305799	59090	Mm.143813	NM_021565	ENSMUSG00000035621	Midn	3000003C15Rik	midnolin	protein-coding
mm_57855.1	chr6	129487003	129487012	-	1	NA	3' UTR (NM_138648, exon 8 of 8)	3' UTR (NM_138648, exon 8 of 8)	-14228	NR_132130	56644	Mm.239516	NM_020008	ENSMUSG00000079293	Clec7a	BGR|Clecsf12|beta-GR	C-type lectin domain family 7, member a	protein-coding
mm_38523.1	chr4	141424176	141424200	-	1	NA	3' UTR (NM_013868, exon 3 of 3)	3' UTR (NM_013868, exon 3 of 3)	3409	NM_013868	29818	Mm.46181	NM_013868	ENSMUSG00000006221	Hspb7	27kDa|Hsp25-2|cvHsp	heat shock protein family, member 7 (cardiovascular)	protein-coding
mm_9563.1	chr1	173976953	173976977	-	1	NA	intron (NM_008327, intron 2 of 6)	intron (NM_008327, intron 2 of 6)	5879	NM_008327	26388	Mm.218770	NM_008327	ENSMUSG00000026535	Ifi202b	Ifbip-1|Ifi202|Ifi202a|p202	interferon activated gene 202B	protein-coding
mm_98214.1	chr11	87801042	87801051	+	1	NA	exon (NM_010824, exon 10 of 14)	exon (NM_010824, exon 10 of 14)	7262	NM_010824	17523	Mm.4668	NM_010824	ENSMUSG00000009350	Mpo	mKIAA4033	myeloperoxidase	protein-coding
mm_106910.1	chr12	8016806	8016811	+	1	NA	TTS (NM_009693)	TTS (NM_009693)	39131	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_100963.1	chr11	6638572	6638585	-	1	NA	promoter-TSS (NM_011709)	promoter-TSS (NM_011709)	71	NM_011709	22373	Mm.268094	NM_011709	ENSMUSG00000000381	Wap	-	whey acidic protein	protein-coding
mm_4696.1	chr1	180749812	180749823	+	1	NA	intron (NM_133225, intron 7 of 7)	B1F|SINE|Alu	23774	NM_133225	170760	Mm.272981	NM_133225	ENSMUSG00000026499	Acbd3	60kDa|8430407O11Rik|D1Ertd10e|GCP60|GOLPH1|Gocap1|Pap7	acyl-Coenzyme A binding domain containing 3	protein-coding
mm_53848.1	chr6	149129952	149129955	+	1	NA	Intergenic	Intergenic	-11560	NM_001252096	320204	Mm.274099	NM_177101	ENSMUSG00000039958	Etfbkmt	4833442J19Rik|AI256744|ETFB-KMT|Mettl20	electron transfer flavoprotein beta subunit lysine methyltransferase	protein-coding
mm_100265.1	chr11	117361262	117361277	+	1	NA	3' UTR (NM_001113486, exon 12 of 12)	3' UTR (NM_001113486, exon 12 of 12)	28956	NM_001113488	53860	Mm.38450	NM_017380	ENSMUSG00000059248	Sept9	MSF1|Msf|PNUTL4|Sint1	septin 9	protein-coding
mm_154287.1	chr19	60874473	60874510	-	1	NA	promoter-TSS (NM_007452)	promoter-TSS (NM_007452)	47	NM_007452	11757	Mm.29821	NM_007452	ENSMUSG00000024997	Prdx3	AW822249|Aop1|D0Tohi1|Ef2l|Mer5|Prx3|SP22|TDXM	peroxiredoxin 3	protein-coding
mm_74122.1	chr8	123117448	123117476	+	1	NA	promoter-TSS (NM_170684)	promoter-TSS (NM_170684)	88	NM_170684	102278	Mm.36434	NM_170684	ENSMUSG00000034796	Cpne7	AW047065	copine VII	protein-coding
mm_165287.1	chr2	85048191	85048228	+	1	NA	Intergenic	CpG	-2251	NM_001081260	228140	Mm.23606	NM_001081260	ENSMUSG00000033955	Tnks1bp1	Tab182|mKIAA1741	tankyrase 1 binding protein 1	protein-coding
mm_137561.1	chr17	27685250	27685258	+	1	NA	promoter-TSS (NM_178365)	promoter-TSS (NM_178365)	15	NM_178365	23969	Mm.4926	NM_011861	ENSMUSG00000040276	Pacsin1	A830061D09Rik|H74|mKIAA1379|syndapin	protein kinase C and casein kinase substrate in neurons 1	protein-coding
mm_113050.1	chr13	23621996	23622051	+	1	NA	promoter-TSS (NM_178194)	promoter-TSS (NM_178194)	535	NM_015787	50709	Mm.170587	NM_015787	ENSMUSG00000051627	Hist1h1e	H1-4|H1.4|H1e|H1f4|H1s-4|H1var2	histone cluster 1, H1e	protein-coding
mm_34505.1	chr4	148667206	148667221	+	1	NA	intron (NM_001085505, intron 7 of 10)	intron (NM_001085505, intron 7 of 10)	23896	NM_001085505	230909	Mm.332067	NM_001085505	ENSMUSG00000070577	Gm572	b2b1167Clo	predicted gene 572	protein-coding
mm_106741.1	chr12	3907603	3907619	+	1	NA	exon (NM_153743, exon 18 of 18)	exon (NM_153743, exon 18 of 18)	15867	NM_153743	13435	Mm.5001	NM_007872	ENSMUSG00000020661	Dnmt3a	MmuIIIA	DNA methyltransferase 3A	protein-coding
mm_20181.1	chr2	122595207	122595228	-	1	NA	3' UTR (NM_025961, exon 9 of 9)	3' UTR (NM_025961, exon 9 of 9)	16060	NM_025961	67092	Mm.29975	NM_025961	ENSMUSG00000027199	Gatm	1810003P21Rik|AI314789|AT	glycine amidinotransferase (L-arginine:glycine amidinotransferase)	protein-coding
mm_7346.1	chr1	105990226	105990238	-	1	NA	promoter-TSS (NM_001122675)	promoter-TSS (NM_001122675)	-174	NM_001122676	227449	Mm.210188	NM_001122675	ENSMUSG00000038866	Zcchc2	9930114B20Rik|AW212015	zinc finger, CCHC domain containing 2	protein-coding
mm_98005.1	chr11	84179659	84179687	+	1	NA	Intergenic	CpG	-12197	NM_001037932	628813	Mm.390389	NM_001037932	ENSMUSG00000051452	Gm11437	AI463690|OTTMUSG00000000997	predicted gene 11437	protein-coding
mm_156206.1	chrX	134585645	134585698	+	1	NA	promoter-TSS (NM_019865)	promoter-TSS (NM_019865)	17	NM_019865	19982	Mm.286408	NM_019865	ENSMUSG00000079435	Rpl36a	L44L|Rpl44	ribosomal protein L36A	protein-coding
mm_38333.1	chr4	137593576	137593584	-	1	NA	promoter-TSS (NM_130879)	promoter-TSS (NM_130879)	-609	NM_001347227	170707	Mm.218478	NM_130879	ENSMUSG00000043411	Usp48	2810449C13Rik|AI115503|BC021769|D330022K21Rik|Usp31	ubiquitin specific peptidase 48	protein-coding
mm_32284.1	chr4	102991248	102991277	+	1	NA	promoter-TSS (NM_001163768)	promoter-TSS (NM_001163768)	-533	NM_001163768	67344	Mm.111346	NM_026100	ENSMUSG00000028523	Tctex1d1	1700055O19Rik	Tctex1 domain containing 1	protein-coding
mm_139090.1	chr17	46832393	46832404	+	1	NA	promoter-TSS (NM_001100452)	promoter-TSS (NM_001100452)	-985	NM_001100452	210982	Mm.37642	NM_001100452	ENSMUSG00000036568	Gltscr1l	mKIAA0240	GLTSCR1-like	protein-coding
mm_81679.1	chr9	111058127	111058185	+	1	NA	promoter-TSS (NM_017466)	promoter-TSS (NM_017466)	-638	NM_001302376	54199	Mm.7336	NM_017466	ENSMUSG00000043953	Ccrl2	1810047I05Rik|Ackr5|CCR11|Cmkbr1l2|E01|L-CCR	chemokine (C-C motif) receptor-like 2	protein-coding
mm_12482.1	chr2	71529815	71529841	+	1	NA	TTS (NR_002854)	TTS (NR_002854)	383	NM_010053	13390	Mm.475101	NM_010053	ENSMUSG00000041911	Dlx1	Dlx|Dlx-1	distal-less homeobox 1	protein-coding
mm_168402.1	chr11	29622208	29622208	-	1	NA	Intergenic	Intergenic	-70690	NM_194053	68585	Mm.192580	NM_024226	ENSMUSG00000020458	Rtn4	1110020G17Rik|AA407876|AA409940|AA960376|ASY|C130026I10Rik|NOGO|NSP-CL|NgA|Nogo-A|Nogo-B|Nogo-C|mKIAA0886|mKIAA4153	reticulon 4	protein-coding
mm_142487.1	chr17	45756623	45756628	-	1	NA	Intergenic	Intergenic	-22781	NM_028164	72240	Mm.482897	NM_028164	ENSMUSG00000094690	1600014C23Rik	-	RIKEN cDNA 1600014C23 gene	protein-coding
mm_167674.1	chr9	75410210	75410220	-	1	NA	promoter-TSS (NR_040719)	promoter-TSS (NR_040719)	31	NR_040719	71274	Mm.399152	NR_040719	ENSMUSG00000097021	4933433G15Rik	4921522K19Rik	RIKEN cDNA 4933433G15 gene	ncRNA
mm_136106.1	chr16	85173693	85173718	-	1	NA	promoter-TSS (NM_001198823)	promoter-TSS (NM_001198823)	2	NM_001198825	11820	Mm.277585	NM_007471	ENSMUSG00000022892	App	Abeta|Abpp|Adap|Ag|Cvap|E030013M08Rik|betaApp	amyloid beta (A4) precursor protein	protein-coding
mm_36328.1	chr4	70433432	70433462	-	1	NA	exon (NM_172694, exon 6 of 6)	exon (NM_172694, exon 6 of 6)	-23012	NM_145990	214444	Mm.370777	NM_145990	ENSMUSG00000039298	Cdk5rap2	2900018K03Rik|an|mKIAA1633	CDK5 regulatory subunit associated protein 2	protein-coding
mm_170539.1	chr19	39246660	39246666	-	1	NA	intron (NR_033614, intron 3 of 8)	L1Md_A|LINE|L1	17409	NR_033614	638988	Mm.483843	NR_033614	ENSMUSG00000093610	Cyp2c53-ps	Cyp2c53|EG638988	cytochrome P450, family 2, subfamily c, polypeptide 53-ps	pseudo
mm_67708.1	chr7	89941197	89941213	-	1	NA	promoter-TSS (NM_001291289)	promoter-TSS (NM_001291289)	-1	NM_001291288	67669	Mm.28679	NM_026304	ENSMUSG00000062797	Hikeshi	0610007P06Rik|1110002N09Rik|l(7)6Rn|l7Rn6	heat shock protein nuclear import factor	protein-coding
mm_160216.1	chr7	99448627	99448627	+	1	NA	intron (NM_201352, intron 9 of 17)	intron (NM_201352, intron 9 of 17)	-17377	NM_028145	72184	Mm.153585	NM_028145	ENSMUSG00000035298	Klhl35	2810406K13Rik	kelch-like 35	protein-coding
mm_100531.1	chr11	120608301	120608307	+	1	NA	promoter-TSS (NM_153288)	promoter-TSS (NM_153288)	-173	NM_153288	208990	Mm.29444	NM_153288	ENSMUSG00000044034	Npb	-	neuropeptide B	protein-coding
mm_89708.1	chr10	97693021	97693029	+	1	NA	promoter-TSS (NM_025724)	promoter-TSS (NM_025724)	-34	NM_025724	66716	Mm.56430	NM_025724	ENSMUSG00000047025	Ccer1	4921510H08Rik|AV259683	coiled-coil glutamate-rich protein 1	protein-coding
mm_130263.1	chr15	96643125	96643137	-	1	NA	promoter-TSS (NM_001166456)	promoter-TSS (NM_001166456)	-218	NM_001166458	105727	Mm.103568	NM_134086	ENSMUSG00000023169	Slc38a1	AA408026|AA409865|AL022800|AU015942|NAT2	solute carrier family 38, member 1	protein-coding
mm_51487.1	chr6	83055208	83055233	+	1	NA	promoter-TSS (NM_019752)	promoter-TSS (NM_019752)	-649	NM_019752	64704	Mm.21880	NM_019752	ENSMUSG00000068329	Htra2	AI481710|Omi|Prss25|mnd2	HtrA serine peptidase 2	protein-coding
mm_14848.1	chr2	148397489	148397493	+	1	NA	TTS (NM_009219)	TTS (NM_009219)	2114	NM_009219	20608	Mm.35324	NM_009219	ENSMUSG00000037014	Sstr4	Smstr4|sst4	somatostatin receptor 4	protein-coding
mm_12175.1	chr2	62692614	62692633	+	1	NA	3' UTR (NM_145523, exon 8 of 8)	3' UTR (NM_145523, exon 8 of 8)	28296	NM_145523	227960	Mm.219877	NM_145523	ENSMUSG00000026893	Gca	5133401E04Rik|AI573844	grancalcin	protein-coding
mm_141734.1	chr17	34120379	34120422	-	1	NA	promoter-TSS (NR_037970)	promoter-TSS (NR_037970)	-500	NR_037970	14312	Mm.3444	NM_010238	ENSMUSG00000024335	Brd2	AW228947|D17H6S113E|Frg-1|Fsrg-1|Fsrg1|Nat|Ring3|Rnf3|mKIAA4005	bromodomain containing 2	protein-coding
mm_32282.1	chr4	102986344	102986395	+	1	NA	promoter-TSS (NM_026100)	promoter-TSS (NM_026100)	-10	NM_001163767	67344	Mm.111346	NM_026100	ENSMUSG00000028523	Tctex1d1	1700055O19Rik	Tctex1 domain containing 1	protein-coding
mm_48703.1	chr5	147063295	147063304	-	1	NA	intron (NM_080795, intron 1 of 9)	intron (NM_080795, intron 1 of 9)	13273	NM_080795	140887	Mm.272203	NM_080795	ENSMUSG00000016520	Lnx2	9630046H24|AW209022	ligand of numb-protein X 2	protein-coding
mm_62088.1	chr7	93079913	93079931	+	1	NA	promoter-TSS (NM_021427)	promoter-TSS (NM_021427)	43	NM_021427	58238	Mm.113787	NM_021427	ENSMUSG00000051515	Fam181b	A830059I20Rik|AB041569	family with sequence similarity 181, member B	protein-coding
mm_35391.1	chr4	33513492	33513516	-	1	NA	Intergenic	Intergenic	75423	NR_106198	102465904		NR_106198	ENSMUSG00000098310	Mir8118	Gm27954|mmu-mir-8118	microRNA 8118	ncRNA
mm_104788.1	chr11	98707646	98707656	-	1	NA	exon (NM_011869, exon 20 of 26)	exon (NM_011869, exon 20 of 26)	6338	NM_009971	12985	Mm.1238	NM_009971	ENSMUSG00000038067	Csf3	Csfg|G-CSF|MGI-IG	colony stimulating factor 3 (granulocyte)	protein-coding
mm_94288.1	chr11	4031607	4031614	+	1	NA	promoter-TSS (NM_146013)	promoter-TSS (NM_146013)	-172	NM_146013	103655	Mm.337476	NM_146013	ENSMUSG00000019368	Sec14l4	AI256582|AW536553|SPF|TAP	SEC14-like lipid binding 4	protein-coding
mm_169847.1	chr16	3121226	3121235	-	1	NA	Intergenic	Intergenic	-471168	NM_146860	258859	Mm.377723	NM_146860	ENSMUSG00000051003	Olfr161	MOR131-1|OR912-47M6	olfactory receptor 161	protein-coding
mm_102908.1	chr11	69560171	69560185	-	1	NA	promoter-TSS (NM_007911)	promoter-TSS (NM_007911)	59	NM_007911	13643	Mm.249637	NM_007911	ENSMUSG00000003934	Efnb3	EFL-6|ELF-3|Elk-L3|Epl8|LERK-8|NLERK-2	ephrin B3	protein-coding
mm_2258.1	chr1	91115294	91115310	+	1	NA	exon (NM_001111311, exon 8 of 8)	exon (NM_001111311, exon 8 of 8)	-29801	NM_001033408	329207	Mm.295940	NM_001033408	ENSMUSG00000070732	Rbm44	Gm817	RNA binding motif protein 44	protein-coding
mm_18204.1	chr2	46442867	46442880	-	1	NA	Intergenic	Intergenic	746268	NR_040497	69405	Mm.396184	NR_040497	ENSMUSG00000086202	1700019E08Rik	-	RIKEN cDNA 1700019E08 gene	ncRNA
mm_59450.1	chr7	27133519	27133528	+	1	NA	3' UTR (NM_007817, exon 10 of 10)	3' UTR (NM_007817, exon 10 of 10)	13568	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_62577.1	chr7	104333315	104333321	+	1	NA	intron (NM_001243916, intron 3 of 6)	B2_Mm1a|SINE|B2	3847	NM_001243916	434218	Mm.485757	NM_001243916	ENSMUSG00000090215	Trim34b	Gm15134|OTTMUSG00000019188|Trim34-2	tripartite motif-containing 34B	protein-coding
mm_110682.1	chr12	67110587	67110589	-	1	NA	intron (NM_001193266, intron 1 of 16)	intron (NM_001193266, intron 1 of 16)	111961	NM_001193266	320772	Mm.227680	NM_207010	ENSMUSG00000034912	Mdga2	6720489L24Rik|9330209L04Rik|Adp|Mamdc1	MAM domain containing glycosylphosphatidylinositol anchor 2	protein-coding
mm_116431.1	chr13	41847627	41847642	-	1	NA	promoter-TSS (NM_001145875)	promoter-TSS (NM_001145875)	-18	NM_001145875	109254	Mm.25195	NM_175417	ENSMUSG00000058022	Adtrp	9530008L14Rik	androgen dependent TFPI regulating protein	protein-coding
mm_99026.1	chr11	98939899	98939910	+	1	NA	intron (NM_001177303, intron 1 of 8)	intron (NM_001177303, intron 1 of 8)	193	NM_001177303	19401	Mm.439744	NM_009024	ENSMUSG00000037992	Rara	Nr1b1|RAR|RARalpha1	retinoic acid receptor, alpha	protein-coding
mm_115761.1	chr13	19193586	19193598	-	1	NA	Intergenic	Intergenic	202221	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_104590.1	chr11	97041365	97041392	-	1	NA	promoter-TSS (NM_027026)	promoter-TSS (NM_027026)	-9	NM_027026	69297	Mm.250465	NM_027026	ENSMUSG00000020878	Lrrc46	1700006D24Rik	leucine rich repeat containing 46	protein-coding
mm_99667.1	chr11	105967643	105967662	+	1	NA	promoter-TSS (NM_001281819)	promoter-TSS (NM_001281819)	-293	NM_001281819	11421	Mm.754	NM_009598	ENSMUSG00000020681	Ace	AW208573|CD143	angiotensin I converting enzyme (peptidyl-dipeptidase A) 1	protein-coding
mm_63075.1	chr7	122219470	122219504	+	1	NA	promoter-TSS (NM_027363)	promoter-TSS (NM_027363)	-9	NM_027363	70261	Mm.96997	NM_027363	ENSMUSG00000030865	Chp2	2010110P09Rik|Cbhp2	calcineurin-like EF hand protein 2	protein-coding
mm_162572.1	chr1	174497763	174497770	-	1	NA	Intergenic	Intergenic	-4059	NM_019445	54418	Mm.330620	NM_019445	ENSMUSG00000028354	Fmn2	AU024104	formin 2	protein-coding
mm_80945.1	chr9	102720324	102720336	+	1	NA	exon (NM_019764, exon 2 of 10)	exon (NM_019764, exon 2 of 10)	2526	NM_019764	56332	Mm.21145	NM_019764	ENSMUSG00000032531	Amotl2	AW549739|C79691|Lccp|MASCOT|mKIAA0989	angiomotin-like 2	protein-coding
mm_21524.1	chr2	163636837	163636879	-	1	NA	exon (NM_012032, exon 3 of 10)	exon (NM_012032, exon 3 of 10)	-7992	NR_028113	68386	Mm.410649	NR_028113	ENSMUSG00000058812	0610039K10Rik	-	RIKEN cDNA 0610039K10 gene	ncRNA
mm_61464.1	chr7	75609931	75609940	+	1	NA	exon (NM_029332, exon 7 of 37)	exon (NM_029332, exon 7 of 37)	154401	NM_029332	75547	Mm.216107	NM_029332	ENSMUSG00000066406	Akap13	1700026G02Rik|5730522G15Rik|5830460E08Rik|AKAP-13|AKAP-Lbc|BRX|Ht31|LBC|PROTO-LB|PROTO-LBC	A kinase (PRKA) anchor protein 13	protein-coding
mm_62148.1	chr7	97129224	97129236	+	1	NA	intron (NM_001162477, intron 1 of 9)	intron (NM_001162477, intron 1 of 9)	47479	NM_010248	14389	Mm.42033	NM_010248	ENSMUSG00000004508	Gab2	AI463667|D130058I17Rik|p97	growth factor receptor bound protein 2-associated protein 2	protein-coding
mm_84960.1	chr9	83613945	83613948	-	1	NA	Intergenic	Intergenic	65608	NM_172507	212531	Mm.491246	NM_172507	ENSMUSG00000032261	Sh3bgrl2	A930014C21Rik|AA408038|B930089I21	SH3 domain binding glutamic acid-rich protein like 2	protein-coding
mm_72946.1	chr8	92189430	92189440	+	1	NA	Intergenic	Intergenic	166685	NR_110452	71296	Mm.86664	NR_033641	ENSMUSG00000031736	Crnde	4933436C20Rik	colorectal neoplasia differentially expressed (non-protein coding)	ncRNA
mm_159973.1	chr6	108253050	108253050	+	1	NA	intron (NM_010585, intron 4 of 61)	MIRc|SINE|MIR	39954	NM_010585	16438	Mm.227912	NM_010585	ENSMUSG00000030102	Itpr1	D6Pas2|ENSMUSG00000072853|Gm10429|IP3R 1|IP3R1|InsP3R|Ip3r|Itpr-1|P400|Pcp-1|Pcp1|insP3R1|opt|wblo	inositol 1,4,5-trisphosphate receptor 1	protein-coding
mm_155354.1	chrX	69360307	69360387	+	1	NA	promoter-TSS (NM_008032)	promoter-TSS (NM_008032)	16	NM_008032	14266	Mm.466576	NM_008032	ENSMUSG00000031189	Aff2	FMR2P|Fmr2|Ox19|Oxh	AF4/FMR2 family, member 2	protein-coding
mm_136338.1	chr16	92596147	92596155	-	1	NA	Intergenic	L2a|LINE|L2	98004	NM_172469	209195	Mm.44747	NM_172469	ENSMUSG00000022949	Clic6	5730466J16Rik|AL022908|AW045520|CLIC1L	chloride intracellular channel 6	protein-coding
mm_69022.1	chr7	126792217	126792239	-	1	NA	intron (NM_019674, intron 1 of 8)	CpG-13569	243	NM_019674	56420	Mm.41998	NM_019674	ENSMUSG00000030697	Ppp4c	1110002D08Rik|AU016079|Ppx	protein phosphatase 4, catalytic subunit	protein-coding
mm_64215.1	chr7	141482097	141482118	+	1	NA	intron (NM_001252588, intron 1 of 7)	CpG	5727	NM_001252588	64540	Mm.489619	NM_053082	ENSMUSG00000025511	Tspan4	AI325509|AI746565|D130042I01Rik|NAG-2|Tm4sf7|Tspan-4	tetraspanin 4	protein-coding
mm_8870.1	chr1	162859812	162859825	-	1	NA	5' UTR (NM_001330291, exon 1 of 9)	5' UTR (NM_001330291, exon 1 of 9)	182	NM_001330291	14261	Mm.976	NM_010231	ENSMUSG00000040181	Fmo1	-	flavin containing monooxygenase 1	protein-coding
mm_27996.1	chr3	82548092	82548102	-	1	NA	promoter-TSS (NM_001205099)	promoter-TSS (NM_001205099)	-12	NM_001205099	18167	Mm.1433	NM_008731	ENSMUSG00000028004	Npy2r	NPY2-R	neuropeptide Y receptor Y2	protein-coding
mm_36340.1	chr4	72852601	72852609	-	1	NA	promoter-TSS (NM_001199270)	promoter-TSS (NM_001199270)	29	NM_001199270	353204	Mm.317892	NM_001199270	ENSMUSG00000059343	Aldoart1	4921524E03Rik|Aldo1-ps|Aldo1-ps2|Aldoa-ps2	aldolase 1 A, retrogene 1	protein-coding
mm_163893.1	chr14	27341771	27341781	+	1	NA	intron (NM_001289687, intron 1 of 9)	intron (NM_001289687, intron 1 of 9)	5739	NM_001289687	71704	Mm.248606	NM_027871	ENSMUSG00000021895	Arhgef3	1200004I24Rik|9830169H03Rik|C76747|Xpln	Rho guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_55319.1	chr6	55173475	55173485	-	1	NA	exon (NM_009349, exon 2 of 3)	exon (NM_009349, exon 2 of 3)	1510	NM_009349	21743	Mm.299	NM_009349	ENSMUSG00000003477	Inmt	Temt	indolethylamine N-methyltransferase	protein-coding
mm_25109.1	chr3	101427028	101427075	+	1	NA	exon (NM_207205, exon 4 of 11)	exon (NM_207205, exon 4 of 11)	49926	NM_207205	78908	Mm.257997	NM_207205	ENSMUSG00000042035	Igsf3	1700016K10Rik|2810035F16Rik|4833439O17Rik|mKIAA0466	immunoglobulin superfamily, member 3	protein-coding
mm_92892.1	chr10	82955198	82955200	-	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	-30298	NM_021439	58250	Mm.360747	NM_021439	ENSMUSG00000034612	Chst11	1110020P09Rik|C4ST|C4ST-1|C4ST1|C4s	carbohydrate sulfotransferase 11	protein-coding
mm_17559.1	chr2	30178423	30178473	-	1	NA	promoter-TSS (NM_172660)	promoter-TSS (NM_172660)	11	NM_172660	227695	Mm.4449	NM_172660	ENSMUSG00000039660	Spout1	9930028P05|AL033358|D2Wsu81e	SPOUT domain containing methyltransferase 1	protein-coding
mm_164008.1	chr14	68533808	68533814	-	1	NA	promoter-TSS (NM_007402)	promoter-TSS (NM_007402)	-122	NM_007402	11500	Mm.261495	NM_007402	ENSMUSG00000022056	Adam7	ADAM 7|EAP1|EAPI	a disintegrin and metallopeptidase domain 7	protein-coding
mm_23487.1	chr3	60501258	60501275	+	1	NA	promoter-TSS (NM_001253711)	promoter-TSS (NM_001253711)	87	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_169228.1	chr13	67073030	67073042	+	1	NA	intron (NM_001012449, intron 2 of 2)	MLTR31F_MM|LTR|ERVK	8509	NM_001012448	432769	Mm.458849	NM_001012325	ENSMUSG00000058883	Zfp708	Rslcan11	zinc finger protein 708	protein-coding
mm_108364.1	chr12	80793096	80793110	+	1	NA	intron (NM_001242419, intron 1 of 6)	intron (NM_001242419, intron 1 of 6)	2571	NM_001242419	217684	Mm.341776	NM_178682	ENSMUSG00000021133	Susd6	4933426M11Rik|mKIAA0247	sushi domain containing 6	protein-coding
mm_164288.1	chr15	103751944	103751957	-	1	NA	TTS (NM_009268)	TTS (NM_009268)	3548	NR_126081	20771	Mm.30276	NM_009268		Mucl1	Spt-2|Spt2	mucin-like 1	protein-coding
mm_127594.1	chr15	102392935	102392958	+	1	NA	Intergenic	Intergenic	-13370	NM_013672	20683	Mm.4618	NM_013672	ENSMUSG00000001280	Sp1	1110003E12Rik|AA450830|AI845540|Sp1-1	trans-acting transcription factor 1	protein-coding
mm_13019.1	chr2	91016762	91016772	+	1	NA	3' UTR (NM_198683, exon 14 of 14)	3' UTR (NM_198683, exon 14 of 14)	-18860	NM_009023	19400	Mm.1272	NM_009023	ENSMUSG00000002104	Rapsn	43kDa|Nraps|Raps|rapsyn	receptor-associated protein of the synapse	protein-coding
mm_9820.1	chr1	182341586	182341625	-	1	NA	promoter-TSS (NM_175127)	promoter-TSS (NM_175127)	1	NM_175127	67948	Mm.30737	NM_175127	ENSMUSG00000047539	Fbxo28	4833428J17Rik|5730505P19Rik|D1Ertd578e|Fbx28|mKIAA0483	F-box protein 28	protein-coding
mm_59479.1	chr7	27461441	27461443	+	1	NA	intron (NM_001290525, intron 3 of 4)	B2_Mm2|SINE|B2	9024	NM_001290525	233016	Mm.24021	NM_144923	ENSMUSG00000040466	Blvrb	-	biliverdin reductase B (flavin reductase (NADPH))	protein-coding
mm_80177.1	chr9	72274967	72275013	+	1	NA	5' UTR (NM_146224, exon 1 of 22)	5' UTR (NM_146224, exon 1 of 22)	102	NM_001311105	235469	Mm.242791	NM_146224	ENSMUSG00000038535	Zfp280d	A930005F02Rik|BC027163|Suhw4|ZNF634|Znf280d	zinc finger protein 280D	protein-coding
mm_95789.1	chr11	54960534	54960552	+	1	NA	intron (NM_001199275, intron 1 of 18)	ID_B1|SINE|B4	2397	NM_021327	57783	Mm.259671	NM_021327	ENSMUSG00000020400	Tnip1	ABIN|ABIN-1|ABIN1|AU018810|Naf1|Nef|VAN	TNFAIP3 interacting protein 1	protein-coding
mm_5118.1	chr1	7088741	7088782	-	1	NA	promoter-TSS (NM_183028)	promoter-TSS (NM_183028)	-159	NM_183028	319263	Mm.21539	NM_183028	ENSMUSG00000051285	Pcmtd1	8430411F12Rik|A030012M09Rik	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding
mm_10461.1	chr2	14307037	14307039	+	1	NA	intron (NM_008625, intron 18 of 29)	intron (NM_008625, intron 18 of 29)	46035	NR_030609	100124488		NR_030609	ENSMUSG00000077897	Mir511	Mirn511|mir-511|mmu-mir-511	microRNA 511	ncRNA
mm_157764.1	chrX	73673022	73673035	-	1	NA	promoter-TSS (NM_001142809)	promoter-TSS (NM_001142809)	-105	NM_001142810	102857	Mm.274553	NM_133987	ENSMUSG00000019558	Slc6a8	AA589632|CRT|CRTR|CT1|CTR5|Creat	solute carrier family 6 (neurotransmitter transporter, creatine), member 8	protein-coding
mm_138385.1	chr17	35049725	35049753	+	1	NA	promoter-TSS (NM_033444)	promoter-TSS (NM_033444)	-504	NM_033444	114584	Mm.29524	NM_033444	ENSMUSG00000007041	Clic1	Clcp|G6	chloride intracellular channel 1	protein-coding
mm_153351.1	chr19	39886731	39886760	-	1	NA	promoter-TSS (NM_001104525)	promoter-TSS (NM_001104525)	24	NM_001104525	100043108	Mm.482331	NM_001104525	ENSMUSG00000092008	Cyp2c69	AI098658	cytochrome P450, family 2, subfamily c, polypeptide 69	protein-coding
mm_44389.1	chr5	17829185	17829199	-	1	NA	intron (NM_007643, intron 2 of 14)	intron (NM_007643, intron 2 of 14)	6704	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_150314.1	chr19	34573363	34573410	+	1	NA	exon (NM_008332, exon 3 of 3)	exon (NM_008332, exon 3 of 3)	-10143	NM_010501	15959	Mm.426079	NM_010501	ENSMUSG00000074896	Ifit3	Ifi49|P49	interferon-induced protein with tetratricopeptide repeats 3	protein-coding
mm_30170.1	chr3	144201963	144201969	-	1	NA	exon (NM_010723, exon 2 of 5)	exon (NM_010723, exon 2 of 5)	366	NM_001161770	16911	Mm.29187	NM_010723	ENSMUSG00000028266	Lmo4	A730077C12Rik|Crp3|Etohi4	LIM domain only 4	protein-coding
mm_109013.1	chr12	103388657	103388723	+	1	NA	promoter-TSS (NM_001177841)	promoter-TSS (NM_001177841)	8	NM_001177841	68149	Mm.127378	NM_026580	ENSMUSG00000021203	Otub2	2010015L18Rik|4930586I02Rik|AI413508|AW557219|OTB2|OTU2	OTU domain, ubiquitin aldehyde binding 2	protein-coding
mm_117448.1	chr13	74807885	74807899	-	1	NA	promoter-TSS (NM_009817)	promoter-TSS (NM_009817)	68	NM_009817	12380	Mm.29163	NM_009817	ENSMUSG00000021585	Cast	-	calpastatin	protein-coding
mm_62963.1	chr7	119793742	119793752	+	1	NA	promoter-TSS (NM_028129)	promoter-TSS (NM_028129)	311	NM_027698	71151	Mm.274160	NM_027698	ENSMUSG00000030929	Eri2	4933424N09Rik|Exod1|mKIAA1504	exoribonuclease 2	protein-coding
mm_117117.1	chr13	60672854	60672879	-	1	NA	intron (NM_029653, intron 2 of 25)	intron (NM_029653, intron 2 of 25)	70655	NM_134062	69635	Mm.24103	NM_029653	ENSMUSG00000021559	Dapk1	D13Ucla1|DAP-Kinase	death associated protein kinase 1	protein-coding
mm_137819.1	chr17	30135195	30135210	+	1	NA	intron (NM_148926, intron 2 of 4)	intron (NM_148926, intron 2 of 4)	121333	NR_105839	102465223		NR_105839	ENSMUSG00000098522	Mir6412	Gm27364|mmu-mir-6412	microRNA 6412	ncRNA
mm_83542.1	chr9	46234688	46234743	-	1	NA	exon (NM_001289755, exon 2 of 4)	exon (NM_001289755, exon 2 of 4)	584	NM_001289833	11814	Mm.390161	NM_023114	ENSMUSG00000032081	Apoc3	apo-CIII|apoC-III	apolipoprotein C-III	protein-coding
mm_67551.1	chr7	81566940	81566993	-	1	NA	promoter-TSS (NM_172904)	promoter-TSS (NM_172904)	15	NM_172904	244091	Mm.38773	NM_172904	ENSMUSG00000038663	Fsd2	9830160G03Rik|Spryd1	fibronectin type III and SPRY domain containing 2	protein-coding
mm_20911.1	chr2	150600375	150600383	-	1	NA	intron (NM_027977, intron 1 of 8)	intron (NM_027977, intron 1 of 8)	8144	NM_027977	71881	Mm.26599	NM_027977	ENSMUSG00000033096	Apmap	2310001A20Rik|AI314817	adipocyte plasma membrane associated protein	protein-coding
mm_67053.1	chr7	67363449	67363452	-	1	NA	intron (NM_001291191, intron 1 of 10)	L1MC4|LINE|L1	9408	NM_001291192	17258	Mm.132788	NM_001033713	ENSMUSG00000030557	Mef2a	A430079H05Rik	myocyte enhancer factor 2A	protein-coding
mm_30895.1	chr4	32291784	32291799	+	1	NA	Intergenic	Intergenic	-125644	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_61518.1	chr7	78913795	78913864	+	1	NA	promoter-TSS (NM_020583)	promoter-TSS (NM_020583)	64	NM_020583	57444	Mm.322843	NM_020583	ENSMUSG00000039236	Isg20	1600023I01Rik|2010107M23Rik|20kDa|DnaQL|HEM45	interferon-stimulated protein	protein-coding
mm_15120.1	chr2	153741335	153741375	+	1	NA	promoter-TSS (NM_007896)	promoter-TSS (NM_007896)	68	NM_007896	13589	Mm.143877	NM_007896	ENSMUSG00000027479	Mapre1	5530600P05Rik|AI462499|AI504412|AW260097|BIM1p|D2Ertd459e|Eb1	microtubule-associated protein, RP/EB family, member 1	protein-coding
mm_22076.1	chr2	168749944	168749948	-	1	NA	3' UTR (NM_201396, exon 3 of 3)	3' UTR (NM_201396, exon 3 of 3)	-7810	NM_001289446	11981	Mm.330819	NM_015731	ENSMUSG00000027546	Atp9a	IIa	ATPase, class II, type 9A	protein-coding
mm_69435.1	chr7	132852607	132852655	-	1	NA	promoter-TSS (NM_028095)	promoter-TSS (NM_028095)	16	NM_028095	72096	Mm.28631	NM_028095	ENSMUSG00000030960	Mettl10	2010208K18Rik	methyltransferase like 10	protein-coding
mm_161291.1	chr14	26221906	26221906	+	1	NA	promoter-TSS (NM_001270506).2	promoter-TSS (NM_001270506).2	2	NM_001270506	100039213	Mm.441404	NM_001270506	ENSMUSG00000098463	Cphx2	Gm2104	cytoplasmic polyadenylated homeobox 2	protein-coding
mm_155483.1	chrX	73676714	73676725	+	1	NA	exon (NM_001142809, exon 3 of 13)	exon (NM_001142809, exon 3 of 13)	3586	NM_001142809	102857	Mm.274553	NM_133987	ENSMUSG00000019558	Slc6a8	AA589632|CRT|CRTR|CT1|CTR5|Creat	solute carrier family 6 (neurotransmitter transporter, creatine), member 8	protein-coding
mm_122336.1	chr14	37135090	37135098	-	1	NA	promoter-TSS (NM_001199122)	promoter-TSS (NM_001199122)	45	NM_001199122	66092	Mm.182912	NM_078478	ENSMUSG00000041028	Ghitm	1010001P14Rik|C77840|MICS1|PTD010|Tmbim5	growth hormone inducible transmembrane protein	protein-coding
mm_12745.1	chr2	79122791	79122811	+	1	NA	Intergenic	Intergenic	-132625	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D|Itga4B	integrin alpha 4	protein-coding
mm_60605.1	chr7	44572371	44572416	+	1	NA	promoter-TSS (NM_008437)	promoter-TSS (NM_008437)	-52	NM_008437	16541	Mm.383181	NM_008437	ENSMUSG00000002204	Napsa	KAP|Kdap|NAP1|SNAPA|pronapsin	napsin A aspartic peptidase	protein-coding
mm_38018.1	chr4	133754300	133754316	-	1	NA	promoter-TSS (NM_001080819)	promoter-TSS (NM_001080819)	-697	NM_001080819	93760	Mm.22478	NM_001080819	ENSMUSG00000007880	Arid1a	1110030E03Rik|BAF250a|Osa1|Smarcf1	AT rich interactive domain 1A (SWI-like)	protein-coding
mm_90645.1	chr10	128720235	128720255	+	1	NA	TTS (NM_021882)	TTS (NM_021882)	13987	NM_021882	20431	Mm.16756	NM_021882	ENSMUSG00000025359	Pmel	D10H12S53E|D12S53Eh|Pmel17|Si|Silv|gp100|gp87	premelanosome protein	protein-coding
mm_52328.1	chr6	108857491	108857502	+	1	NA	3' UTR (NM_138677, exon 12 of 12)	3' UTR (NM_138677, exon 12 of 12)	28855	NM_138677	192193	Mm.21596	NM_138677	ENSMUSG00000030104	Edem1	A130059K23Rik|EDEM|mKIAA0212	ER degradation enhancer, mannosidase alpha-like 1	protein-coding
mm_97549.1	chr11	78928591	78928599	+	1	NA	exon (NM_010927, exon 3 of 27)	exon (NM_010927, exon 3 of 27)	3304	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_108220.1	chr12	77066227	77066263	+	1	NA	Intergenic	B1F|SINE|Alu	-103997	NM_001146176	17187	Mm.268548	NM_008558	ENSMUSG00000059436	Max	AA960152|AI875693|bHLHd4|bHLHd5|bHLHd6|bHLHd7|bHLHd8	Max protein	protein-coding
mm_162843.1	chr10	86300631	86300647	+	1	NA	5' UTR (NM_011595, exon 1 of 5)	5' UTR (NM_011595, exon 1 of 5)	227	NM_011595	21859	Mm.4871	NM_011595	ENSMUSG00000020044	Timp3	Timp-3	tissue inhibitor of metalloproteinase 3	protein-coding
mm_39651.1	chr5	24685955	24686004	+	1	NA	exon (NM_001305264, exon 1 of 15)	exon (NM_001305264, exon 1 of 15)	164	NM_001305264	53312	Mm.5856	NM_016736	ENSMUSG00000028954	Nub1	4931404D21Rik|6330412F12Rik|BS4|NY-REN-18	negative regulator of ubiquitin-like proteins 1	protein-coding
mm_66414.1	chr7	44506195	44506210	-	1	NA	exon (NM_146189, exon 23 of 28)	exon (NM_146189, exon 23 of 28)	9614	NM_028169	75538	Mm.258841	NM_028169	ENSMUSG00000051113	Fam71e1	0610007G24Rik|1700021N13Rik|1700021P22Rik|GARI-L5	family with sequence similarity 71, member E1	protein-coding
mm_127515.1	chr15	101850342	101850352	+	1	NA	exon (NM_008473, exon 1 of 9)	exon (NM_008473, exon 1 of 9)	439	NM_008473	16678	Mm.183137	NM_008473	ENSMUSG00000046834	Krt1	Krt-2.1|Krt2-1|Krt86	keratin 1	protein-coding
mm_25429.1	chr3	107895832	107895844	+	1	NA	promoter-TSS (NM_010360)	promoter-TSS (NM_010360)	-16	NM_010360	14866	Mm.282351	NM_010360	ENSMUSG00000004032	Gstm5	-	glutathione S-transferase, mu 5	protein-coding
mm_141694.1	chr17	33978738	33978739	-	1	NA	promoter-TSS (NR_004446)	promoter-TSS (NR_004446)	53	NR_004446	630499	Mm.440940	NM_001081015		H2-K2	EG630499|Gm7035|H-2K1|H-2K1K|H-2K2|H2-K1	histocompatibility 2, K region locus 2	pseudo
mm_112816.1	chr13	20796419	20796467	+	1	NA	intron (NM_012054, intron 1 of 20)	intron (NM_012054, intron 1 of 20)	2330	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_100499.1	chr11	120482334	120482335	+	1	NA	intron (NM_001159328, intron 18 of 21)	intron (NM_001159328, intron 18 of 21)	-2335	NM_027204	56282	Mm.133851	NM_027204	ENSMUSG00000039640	Mrpl12	0610034O11Rik|1500031N16Rik|MRP-L12|Rpml12	mitochondrial ribosomal protein L12	protein-coding
mm_167477.1	chr8	129067107	129067116	+	1	NA	promoter-TSS (NM_029292)	promoter-TSS (NM_029292)	-23	NM_029292	75453	Mm.286964	NM_029292	ENSMUSG00000056018	Ccdc7b	1700008F21Rik	coiled-coil domain containing 7B	protein-coding
mm_3127.1	chr1	134723415	134723418	+	1	NA	intron (NM_009307, intron 2 of 9)	intron (NM_009307, intron 2 of 9)	76735	NM_009307	20980	Mm.5102	NM_009307	ENSMUSG00000026452	Syt2	IP4BP|R74640|mKIAA4194	synaptotagmin II	protein-coding
mm_21587.1	chr2	164237428	164237430	-	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	912	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_159040.1	chr1	180893268	180893268	+	1	NA	exon (NM_177099, exon 1 of 4)	exon (NM_177099, exon 1 of 4)	160	NM_177099	320202	Mm.87078	NM_177099	ENSMUSG00000066652	Lefty2	6030463A22Rik|Ebaf|Lefta|Leftb|lefty-2|lefty-B	left-right determination factor 2	protein-coding
mm_136500.1	chr16	96439638	96439640	-	1	NA	intron (NM_008405, intron 1 of 15)	intron (NM_008405, intron 1 of 15)	3975	NM_008405	16415	Mm.12872	NM_008405	ENSMUSG00000000157	Itgb2l	5033406G21Rik|pactolus	integrin beta 2-like	protein-coding
mm_21173.1	chr2	154738485	154738490	-	1	NA	Intergenic	MTEa|LTR|ERVL-MaLR	-52623	NM_001139512	19383	Mm.221440	NM_023130	ENSMUSG00000027593	Raly	AI663842|Merc	hnRNP-associated with lethal yellow	protein-coding
mm_158531.1	chrX	143861339	143861352	-	1	NA	3' UTR (NM_010025, exon 7 of 7)	3' UTR (NM_010025, exon 7 of 7)	-33933	NM_007603	12338	Mm.30290	NM_007603	ENSMUSG00000067276	Capn6	-	calpain 6	protein-coding
mm_48491.1	chr5	142608749	142608780	-	1	NA	promoter-TSS (NM_175217)	promoter-TSS (NM_175217)	-12	NM_175217	75104	Mm.48712	NM_175217	ENSMUSG00000039533	Mmd2	4930518M15Rik|C88001	monocyte to macrophage differentiation-associated 2	protein-coding
mm_157856.1	chrX	75082320	75082322	-	1	NA	intron (NM_181584, intron 1 of 9)	intron (NM_181584, intron 1 of 9)	2584	NM_181584	210710	Mm.267056	NM_181584	ENSMUSG00000032750	Gab3	5930433H21Rik	growth factor receptor bound protein 2-associated protein 3	protein-coding
mm_110871.1	chr12	73744869	73744882	-	1	NA	intron (NM_001313977, intron 11 of 14)	intron (NM_001313977, intron 11 of 14)	-156449	NM_001313920	15251	Mm.3879	NM_010431	ENSMUSG00000021109	Hif1a	AA959795|HIF-1-alpha|HIF1-alpha|HIF1alpha|MOP1|bHLHe78	hypoxia inducible factor 1, alpha subunit	protein-coding
mm_153674.1	chr19	44396442	44396459	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	11259	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_62977.1	chr7	120116755	120116763	+	1	NA	intron (NM_145586, intron 4 of 4)	intron (NM_145586, intron 4 of 4)	14333	NM_145586	233806	Mm.257952	NM_145586	ENSMUSG00000030917	Tmem159	8430420C20Rik	transmembrane protein 159	protein-coding
mm_103072.1	chr11	69880942	69880963	-	1	NA	promoter-TSS (NM_153143)	promoter-TSS (NM_153143)	33	NM_153143	216858	Mm.239498	NM_153143	ENSMUSG00000046731	Kctd11	AF465352|Ren	potassium channel tetramerisation domain containing 11	protein-coding
mm_161976.1	chr19	13190567	13190567	+	1	NA	promoter-TSS (NM_146693)	promoter-TSS (NM_146693)	-102	NM_146693	258688	Mm.271529	NM_146693	ENSMUSG00000094721	Olfr1462	MOR202-13	olfactory receptor 1462	protein-coding
mm_11096.1	chr2	28001956	28001989	+	1	NA	intron (NM_015734, intron 38 of 65)	intron (NM_015734, intron 38 of 65)	82906	NM_010190	14134	Mm.182935	NM_010190	ENSMUSG00000026835	Fcnb	Fcn2	ficolin B	protein-coding
mm_129501.1	chr15	78855699	78855739	-	1	NA	promoter-TSS (NM_025622)	promoter-TSS (NM_025622)	-190	NM_025622	107753	Mm.390793	NM_025622	ENSMUSG00000043501	Lgals2	2200008F12Rik|AI324147	lectin, galactose-binding, soluble 2	protein-coding
mm_32526.1	chr4	108861689	108861709	+	1	NA	3' UTR (NM_025334, exon 7 of 7)	3' UTR (NM_025334, exon 7 of 7)	13842	NM_029571	100087	Mm.440007	NM_029571	ENSMUSG00000073775	Kti12	1110001A12Rik|AI326810|AU014758	KTI12 homolog, chromatin associated	protein-coding
mm_105939.1	chr11	115187322	115187359	-	1	NA	promoter-TSS (NM_025400)	promoter-TSS (NM_025400)	-24	NM_025400	66176	Mm.86823	NM_025400	ENSMUSG00000015542	Nat9	1110028N05Rik	N-acetyltransferase 9 (GCN5-related, putative)	protein-coding
mm_123866.1	chr14	72556187	72556221	-	1	NA	exon (NM_207636, exon 23 of 26)	exon (NM_207636, exon 23 of 26)	153799	NM_207636	319448	Mm.205421	NM_207636	ENSMUSG00000033487	Fndc3a	1700094E19Rik|D14Ertd453e|F730017H24Rik|Fndc3|sys	fibronectin type III domain containing 3A	protein-coding
mm_159879.1	chr6	8192661	8192661	-	1	NA	promoter-TSS (NM_001037865)	promoter-TSS (NM_001037865)	-44	NM_001037865	213945	Mm.297404	NM_001037865	ENSMUSG00000068794	Col28a1	Col28|Gm466	collagen, type XXVIII, alpha 1	protein-coding
mm_77528.1	chr8	123013224	123013233	-	1	NA	intron (NM_001081379, intron 1 of 12)	intron (NM_001081379, intron 1 of 12)	29056	NR_037865	77087	Mm.31567	NM_001081379	ENSMUSG00000035569	Ankrd11	2410104C19Rik|3010027A04Rik|6330578C09Rik|9530048I21Rik|AA930108|Gm176|Yod	ankyrin repeat domain 11	protein-coding
mm_109413.1	chr12	110484021	110484038	+	1	NA	intron (NM_001135001, intron 3 of 13)	intron (NM_001135001, intron 3 of 13)	-1710	NM_001081457	26931	Mm.240396	NM_012023	ENSMUSG00000017843	Ppp2r5c	2610043M05Rik|2700063L20Rik|AI060890|AW545884|C85228|D12Bwg0916e|mKIAA0044	protein phosphatase 2, regulatory subunit B', gamma	protein-coding
mm_139366.1	chr17	51178700	51178752	+	1	NA	intron (NM_028162, intron 1 of 21)	CpG	626	NM_028162	72238	Mm.120650	NM_028162	ENSMUSG00000023923	Tbc1d5	1600014N05Rik	TBC1 domain family, member 5	protein-coding
mm_150922.1	chr19	46131889	46131904	+	1	NA	promoter-TSS (NM_007703)	promoter-TSS (NM_007703)	-3	NM_007703	12686	Mm.21806	NM_007703	ENSMUSG00000038754	Elovl3	CIN-2|Cig30	elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 3	protein-coding
mm_86224.1	chr9	120135791	120135797	-	1	NA	Intergenic	Intergenic	5360	NR_002902	104433	Mm.453530	NR_002902	ENSMUSG00000064925	Snora62	E2|MBI-13|MBI-136|Rnu108	small nucleolar RNA, H/ACA box 62	snoRNA
mm_81770.1	chr9	114418444	114418479	+	1	NA	intron (NM_009752, intron 2 of 15)	B3|SINE|B2	17366	NM_001200002	100504715	Mm.290516	NM_001200002	ENSMUSG00000079260	Tmppe	-	transmembrane protein with metallophosphoesterase domain	protein-coding
mm_91701.1	chr10	44004430	44004443	-	1	NA	5' UTR (NM_172393, exon 1 of 20)	5' UTR (NM_172393, exon 1 of 20)	410	NM_172393	11630	Mm.292082	NM_172393	ENSMUSG00000019866	Aim1	AI462491|AI463325	absent in melanoma 1	protein-coding
mm_156469.1	chrX	143518672	143518703	+	1	NA	promoter-TSS (NM_001195048)	promoter-TSS (NM_001195048)	96	NM_001195048	18481	Mm.40035	NM_008778	ENSMUSG00000031284	Pak3	PAK-3|Pak65alpha|Pak65beta|Stk4	p21 protein (Cdc42/Rac)-activated kinase 3	protein-coding
mm_15418.1	chr2	156840700	156840740	+	1	NA	intron (NM_173396, intron 1 of 2)	CpG	713	NM_173396	228839	Mm.315625	NM_173396	ENSMUSG00000062175	Tgif2	4921501K24|5730599O09Rik|C80753|C81206	TGFB-induced factor homeobox 2	protein-coding
mm_87272.1	chr10	41810174	41810245	+	1	NA	promoter-TSS (NM_001162908)	promoter-TSS (NM_001162908)	-341	NM_026643	103268	Mm.338605	NM_026643	ENSMUSG00000019813	Cep57l1	2410017P07Rik|4930484D11Rik|AI607327|cep57R	centrosomal protein 57-like 1	protein-coding
mm_51375.1	chr6	72993554	72993577	+	1	NA	Intergenic	Intergenic	-34817	NM_001190327	19240	Mm.3532	NM_025284	ENSMUSG00000079523	Tmsb10	Ptmb10|Tb10	thymosin, beta 10	protein-coding
mm_100037.1	chr11	114983813	114983823	+	1	NA	3' UTR (NM_145437, exon 4 of 4)	3' UTR (NM_145437, exon 4 of 4)	6068	NM_145437	217305	Mm.275986	NM_145437	ENSMUSG00000034641	Cd300ld	4732429D16Rik|CLM5|Cd300ld1|LMIR4|MAIR-IV|clm-5	CD300 molecule like family member d	protein-coding
mm_55125.1	chr6	50566564	50566577	-	1	NA	promoter-TSS (NM_007808)	promoter-TSS (NM_007808)	-73	NR_015581	73183	Mm.430720	NR_015581	ENSMUSG00000085776	5430402O13Rik	3110047M22Rik	RIKEN cDNA 5430402O13 gene	ncRNA
mm_66404.1	chr7	44475753	44475784	-	1	NA	Intergenic	Intergenic	5421	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_105347.1	chr11	102999797	102999810	-	1	NA	TTS (NR_105896)	TTS (NR_105896)	118	NR_105896	102466988		NR_105896	ENSMUSG00000098613	Mir6931	Gm27303|mmu-mir-6931	microRNA 6931	ncRNA
mm_7522.1	chr1	124060568	124060571	-	1	NA	Intergenic	Intergenic	-15010	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_32901.1	chr4	119106018	119106034	+	1	NA	Intergenic	Intergenic	-2719	NM_011400	20525	Mm.21002	NM_011400	ENSMUSG00000028645	Slc2a1	Glut-1|Glut1	solute carrier family 2 (facilitated glucose transporter), member 1	protein-coding
mm_157442.1	chrX	41288880	41288884	-	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	-112419	NM_016886	53623	Mm.327681	NM_016886	ENSMUSG00000001986	Gria3	2900064I19Rik|GluA3|GluR-C|GluR-K3|Glur-3|Glur3|Gluralpha3	glutamate receptor, ionotropic, AMPA3 (alpha 3)	protein-coding
mm_41967.1	chr5	107331158	107331197	+	1	NA	promoter-TSS (NM_054054)	promoter-TSS (NM_054054)	-17	NM_001079873	114642	Mm.182836	NM_054054	ENSMUSG00000029279	Brdt	7420412D09Rik|Brd6|Fsrg3	bromodomain, testis-specific	protein-coding
mm_112985.1	chr13	21362898	21362922	+	1	NA	promoter-TSS (NM_016684)	promoter-TSS (NM_016684)	90	NM_016684	22758	Mm.24124	NM_016684	ENSMUSG00000036721	Zscan12	2510038J07Rik|FPM315|Zfp96|mKIAA0426|zfp-96	zinc finger and SCAN domain containing 12	protein-coding
mm_117644.1	chr13	92576166	92576200	-	1	NA	promoter-TSS (NM_030237)	promoter-TSS (NM_030237)	49	NM_030237	79401	Mm.23520	NM_030237	ENSMUSG00000046957	Spz1	1700027M20Rik|AI429130	spermatogenic leucine zipper 1	protein-coding
mm_68239.1	chr7	105396213	105396224	-	1	NA	intron (NM_001242363, intron 1 of 12)	intron (NM_001242363, intron 1 of 12)	3836	NM_001242364	74349	Mm.30254	NM_199009	ENSMUSG00000044465	Fam160a2	4632419K20Rik|6530415H11Rik|FHIP	family with sequence similarity 160, member A2	protein-coding
mm_102589.1	chr11	61891648	61891663	-	1	NA	intron (NM_019921, intron 10 of 14)	intron (NM_019921, intron 10 of 14)	-36563	NM_013881	29869	Mm.162025	NM_013881	ENSMUSG00000004798	Ulk2	A830085I22Rik|AU015340|Unc51.2|mKIAA0623	unc-51 like kinase 2	protein-coding
mm_171494.1	chr4	146157030	146157035	+	1	NA	promoter-TSS (NM_001177545)	promoter-TSS (NM_001177545)	205	NM_001177546	667666	Mm.459230	NM_001177545	ENSMUSG00000066007	Zfp600	Gm13164|OTTMUSG00000010694	zinc finger protein 600	protein-coding
mm_160361.1	chr8	21858873	21858873	+	1	NA	promoter-TSS (NM_139225)	promoter-TSS (NM_139225)	-28	NM_139225	246085	Mm.220170	NM_139225	ENSMUSG00000044743	Defb10	BD-10|Defb7	defensin beta 10	protein-coding
mm_4340.1	chr1	171856617	171856627	+	1	NA	intron (NM_001289470, intron 3 of 8)	L1_Mur3|LINE|L1	16925	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_8604.1	chr1	156035337	156035340	-	1	NA	promoter-TSS (NM_001160182)	promoter-TSS (NM_001160182)	-326	NM_172843	240832	Mm.253335	NM_022329	ENSMUSG00000050565	Tor1aip2	1110020D10Rik|15kDa|A130072J07|AA103493|AW060462|AW610675|C77739|Ifrg15|Lull1	torsin A interacting protein 2	protein-coding
mm_115456.1	chr13	119408203	119408210	+	1	NA	intron (NM_001308506, intron 1 of 16)	intron (NM_001308506, intron 1 of 16)	805	NM_008710	18115	Mm.132584	NM_008710	ENSMUSG00000025453	Nnt	4930423F13Rik|AI323702|BB168308	nicotinamide nucleotide transhydrogenase	protein-coding
mm_12422.1	chr2	70562855	70562871	+	1	NA	intron (NM_001312900, intron 1 of 6)	CpG	494	NR_040496	68986	Mm.437697	NR_040496	ENSMUSG00000087264	Gad1os	1500002O10Rik	glutamate decarboxylase 1, opposite strand	ncRNA
mm_557.1	chr1	38021705	38021722	+	1	NA	exon (NM_198303, exon 5 of 24)	exon (NM_198303, exon 5 of 24)	23703	NM_198303	226982	Mm.260943	NM_198303	ENSMUSG00000026083	Eif5b	A030003E17Rik|BC018347|IF2	eukaryotic translation initiation factor 5B	protein-coding
mm_45591.1	chr5	74531667	74531754	-	1	NA	promoter-TSS (NM_178672)	promoter-TSS (NM_178672)	32	NM_178672	212986	Mm.134147	NM_178672	ENSMUSG00000062110	Scfd2	E430013M20Rik|STXBP1L1	Sec1 family domain containing 2	protein-coding
mm_81007.1	chr9	103457593	103457607	+	1	NA	intron (NM_001002896, intron 1 of 6)	AT_rich|Low_complexity|Low_complexity	22728	NM_001002896	107993	Mm.335403	NM_001002896	ENSMUSG00000032556	Bfsp2	AI448593|CP49	beaded filament structural protein 2, phakinin	protein-coding
mm_79829.1	chr9	64789664	64789677	+	1	NA	Intergenic	Intergenic	-21341	NM_001162917	102442	Mm.222473	NM_176935	ENSMUSG00000053641	Dennd4a	AI115600|AI851943|F730015K02Rik	DENN/MADD domain containing 4A	protein-coding
mm_19238.1	chr2	84715161	84715218	-	1	NA	promoter-TSS (NM_144887)	promoter-TSS (NM_144887)	-25	NM_144887	228136	Mm.288508	NM_144887	ENSMUSG00000034075	Zdhhc5	1110032A17Rik|AI451382|Zisp	zinc finger, DHHC domain containing 5	protein-coding
mm_146560.1	chr18	6241239	6241307	-	1	NA	5' UTR (NM_008448, exon 1 of 26)	5' UTR (NM_008448, exon 1 of 26)	251	NM_008448	16573	Mm.223744	NM_008448	ENSMUSG00000006740	Kif5b	AL022807|Khc|Khcs|Kns1|Ukhc	kinesin family member 5B	protein-coding
mm_146055.1	chr18	69645328	69645331	+	1	NA	intron (NM_013685, intron 11 of 19)	intron (NM_013685, intron 11 of 19)	-280230	NM_201362	381175	Mm.266831	NM_201362	ENSMUSG00000038903	Ccdc68	BC046343	coiled-coil domain containing 68	protein-coding
mm_43828.1	chr5	142972088	142972100	+	1	NA	exon (NM_007984, exon 5 of 5)	exon (NM_007984, exon 5 of 5)	11739	NM_007984	14086	Mm.289707	NM_007984	ENSMUSG00000029581	Fscn1	AI663989|Fan1|fascin-1	fascin actin-bundling protein 1	protein-coding
mm_8901.1	chr1	163289215	163289235	-	1	NA	intron (NM_001025570, intron 1 of 2)	intron (NM_001025570, intron 1 of 2)	24425	NM_011127	18933	Mm.288642	NM_011127	ENSMUSG00000026586	Prrx1	A230024N07Rik|AA755424|AI385634|AI843499|K-2|Pmx|Pmx1|Prx1|mHox	paired related homeobox 1	protein-coding
mm_138458.1	chr17	35140238	35140249	+	1	NA	exon (NM_001252469, exon 6 of 24)	exon (NM_001252469, exon 6 of 24)	4529	NM_001252469	224727	Mm.203962	NM_057171	ENSMUSG00000024392	Bag6	2410045D21Rik|AA408914|BAG-6|Bat3|D17H6S52E|G3|Scythe	BCL2-associated athanogene 6	protein-coding
mm_27484.1	chr3	54389367	54389384	-	1	NA	exon (NM_015784, exon 21 of 22)	exon (NM_015784, exon 21 of 22)	28268	NM_015784	50706	Mm.236067	NM_015784	ENSMUSG00000027750	Postn	A630052E07Rik|AI747096|OSF-2|Osf2|PLF|PN	periostin, osteoblast specific factor	protein-coding
mm_113763.1	chr13	44782401	44782430	+	1	NA	intron (NM_001205044, intron 2 of 18)	intron (NM_001205044, intron 2 of 18)	51144	NM_001205043	16468	Mm.25059	NM_021878	ENSMUSG00000038518	Jarid2	Jmj|jumonji	jumonji, AT rich interactive domain 2	protein-coding
mm_18685.1	chr2	71376722	71376764	-	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	-9189	NM_172436	78830	Mm.30928	NM_172436	ENSMUSG00000027010	Slc25a12	2610002D09Rik|AI839531|B230107K20Rik|BB129864	solute carrier family 25 (mitochondrial carrier, Aralar), member 12	protein-coding
mm_21404.1	chr2	158028401	158028417	-	1	NA	promoter-TSS (NM_027434)	promoter-TSS (NM_027434)	-88	NM_001291134	70470	Mm.290810	NM_027434	ENSMUSG00000027651	Rprd1b	2610304G08Rik|2810446G03Rik|Crept	regulation of nuclear pre-mRNA domain containing 1B	protein-coding
mm_48547.1	chr5	142905736	142905753	-	1	NA	intron (NM_007393, intron 1 of 5)	CpG	1010	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_124229.1	chr14	101198951	101198959	-	1	NA	exon (NM_029680, exon 3 of 3)	exon (NM_029680, exon 3 of 3)	1114	NM_029680	76627	Mm.31415	NM_029680	ENSMUSG00000042888	Prr30	1700110M21Rik	proline rich 30	protein-coding
mm_34999.1	chr4	156186180	156186188	+	1	NA	intron (NM_021604, intron 2 of 35)	(CGG)n|Simple_repeat|Simple_repeat	11304	NM_021604	11603	Mm.273098	NM_021604	ENSMUSG00000041936	Agrn	Agrin|nmf380	agrin	protein-coding
mm_32855.1	chr4	118289879	118289890	+	1	NA	intron (NM_011213, intron 1 of 32)	intron (NM_011213, intron 1 of 32)	1513	NM_011213	19268	Mm.29855	NM_011213	ENSMUSG00000033295	Ptprf	AA591035|LAR|LARS|RPTP-LAR	protein tyrosine phosphatase, receptor type, F	protein-coding
mm_59124.1	chr7	19915502	19915504	+	1	NA	intron (NM_027514, intron 3 of 7)	MER33|DNA|hAT-Charlie	5640	NM_027514	52118	Mm.227506	NM_027514	ENSMUSG00000040511	Pvr	3830421F03Rik|CD155|D7Ertd458e|HVED|PVS|Taa1|Tage4|mE4|necl-5	poliovirus receptor	protein-coding
mm_24770.1	chr3	95526801	95526811	+	1	NA	promoter-TSS (NM_021281)	promoter-TSS (NM_021281)	20	NM_001267695	13040	Mm.3619	NM_021281	ENSMUSG00000038642	Ctss	Cats	cathepsin S	protein-coding
mm_147505.1	chr18	50135236	50135261	-	1	NA	intron (NM_008292, intron 2 of 23)	intron (NM_008292, intron 2 of 23)	7047	NM_008292	15488	Mm.277857	NM_008292	ENSMUSG00000024507	Hsd17b4	17-beta-HSD|17[b]-HSD|DBP|MFE-2|MFP2|MPF-2|Mfp-2|perMFE-2	hydroxysteroid (17-beta) dehydrogenase 4	protein-coding
mm_159865.1	chr5	143894856	143894856	-	1	NA	exon (NM_025732, exon 1 of 3)	exon (NM_025732, exon 1 of 3)	211	NM_025732	66729	Mm.439817	NM_025732	ENSMUSG00000029607	Ankrd61	4921520G13Rik	ankyrin repeat domain 61	protein-coding
mm_104501.1	chr11	95914855	95914881	-	1	NA	promoter-TSS (NM_008081)	promoter-TSS (NM_008081)	3	NM_008081	14422	Mm.340702	NM_008081	ENSMUSG00000013418	B4galnt2	AI593864|Dlb-1|Dlb1|Galg2|Galgt2|Ggm3|Igf2bp1	beta-1,4-N-acetyl-galactosaminyl transferase 2	protein-coding
mm_62836.1	chr7	113766084	113766098	+	1	NA	promoter-TSS (NM_145584)	promoter-TSS (NM_145584)	93	NM_145584	233744	Mm.334160	NM_145584	ENSMUSG00000038156	Spon1	AI666765|AW455831|BC020531|D330035F22Rik|FSP	spondin 1, (f-spondin) extracellular matrix protein	protein-coding
mm_113235.1	chr13	27249546	27249550	+	1	NA	3' UTR (NM_008865, exon 5 of 5)	3' UTR (NM_008865, exon 5 of 5)	7118	NM_008865	18776	Mm.37203	NM_008865	ENSMUSG00000038891	Prl3b1	Csh2|Ghd8|PL|Pl-2|Pl2|mPL-II|mplII	prolactin family 3, subfamily b, member 1	protein-coding
mm_141928.1	chr17	35027857	35027868	-	1	NA	TTS (NR_130641)	TTS (NR_130641)	154	NR_028258	78376	Mm.390966	NM_023893	ENSMUSG00000036185	Sapcd1	2810436B06Rik|G7d|Ng23	suppressor APC domain containing 1	protein-coding
mm_21457.1	chr2	160860236	160860239	-	1	NA	intron (NM_177263, intron 1 of 3)	AT_rich|Low_complexity|Low_complexity	12753	NM_177263	320799	Mm.436734	NM_177263	ENSMUSG00000035877	Zhx3	1810059C13Rik|4932418O04Rik|9530010N21Rik|Tix1|mKIAA0395	zinc fingers and homeoboxes 3	protein-coding
mm_108547.1	chr12	84409040	84409102	+	1	NA	promoter-TSS (NM_028377)	promoter-TSS (NM_028377)	3	NM_028377	72873	Mm.440428	NM_028377	ENSMUSG00000057265	Bbof1	2900006K08Rik|AI427784|Ccdc176	basal body orientation factor 1	protein-coding
mm_78523.1	chr9	34488788	34488807	+	1	NA	promoter-TSS (NM_001190912)	promoter-TSS (NM_001190912)	66	NM_001190911	67703	Mm.220710	NM_026324	ENSMUSG00000032036	Kirrel3	1500010O20Rik|2900036G11Rik|NEPH2|SST4|mKIAA1867	kin of IRRE like 3 (Drosophila)	protein-coding
mm_74004.1	chr8	121083839	121083859	+	1	NA	promoter-TSS (NM_010426)	promoter-TSS (NM_010426)	-537	NM_010426	15227	Mm.33897	NM_010426	ENSMUSG00000042812	Foxf1	AI450827|FREAC1|Foxf1a|Freac-1|HFH-8|Hfh8	forkhead box F1	protein-coding
mm_164166.1	chr15	73751416	73751439	+	1	NA	5' UTR (NM_008975, exon 2 of 6)	5' UTR (NM_008975, exon 2 of 6)	3401	NM_008975	19245	Mm.390807	NM_008975	ENSMUSG00000059895	Ptp4a3	AV088979|Prl-3|pPtp4a3	protein tyrosine phosphatase 4a3	protein-coding
mm_50140.1	chr6	41543323	41543333	+	1	NA	Intergenic	Intergenic	21552	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_13810.1	chr2	119167759	119167779	+	1	NA	promoter-TSS (NM_177157)	promoter-TSS (NM_177157)	-19	NM_177157	320415	Mm.86373	NM_177157	ENSMUSG00000046814	Gchfr	2010323F13Rik|GFRP|P35	GTP cyclohydrolase I feedback regulator	protein-coding
mm_97173.1	chr11	75532007	75532026	+	1	NA	promoter-TSS (NM_001199283)	promoter-TSS (NM_001199283)	-96	NM_001199283	215113	Mm.11186	NM_173388	ENSMUSG00000038178	Slc43a2	7630402D21Rik|BC042513|Lat4	solute carrier family 43, member 2	protein-coding
mm_148160.1	chr18	77690186	77690189	-	1	NA	intron (NM_178670, intron 1 of 4)	intron (NM_178670, intron 1 of 4)	23823	NM_178670	212163	Mm.23293	NM_178670	ENSMUSG00000047466	8030462N17Rik	Akd2|Ark2N	RIKEN cDNA 8030462N17 gene	protein-coding
mm_102478.1	chr11	60099974	60099993	-	1	NA	Intergenic	Intergenic	-5030	NM_009021	19377	Mm.296366	NM_009021	ENSMUSG00000062115	Rai1	Gt1	retinoic acid induced 1	protein-coding
mm_126834.1	chr15	89019220	89019228	+	1	NA	intron (NM_031260, intron 16 of 26)	U1|snRNA|snRNA	36230	NM_031260	83456	Mm.358791	NM_031260	ENSMUSG00000015365	Mov10l1	CHAMP|Csm	Moloney leukemia virus 10-like 1	protein-coding
mm_150931.1	chr19	46305683	46305741	+	1	NA	promoter-TSS (NM_001177370)	promoter-TSS (NM_001177370)	17	NM_019408	18034	Mm.102365	NM_019408	ENSMUSG00000025225	Nfkb2	NF-kappaB2|lyt|p49|p49/p100|p50B|p52	nuclear factor of kappa light polypeptide gene enhancer in B cells 2, p49/p100	protein-coding
mm_70787.1	chr8	22506464	22506487	+	1	NA	intron (NM_011394, intron 1 of 10)	intron (NM_011394, intron 1 of 10)	-29596	NM_001146117	102032	Mm.378231	NM_001012667	ENSMUSG00000031534	Smim19	AI316807|BG694986|EST-c39	small integral membrane protein 19	protein-coding
mm_102554.1	chr11	61378090	61378092	-	1	NA	promoter-TSS (NM_026183)	promoter-TSS (NM_026183)	-16	NM_026183	67473	Mm.100741	NM_026183	ENSMUSG00000010122	Slc47a1	1300013J15Rik|AI036982|MATE1|mMATE1	solute carrier family 47, member 1	protein-coding
mm_95420.1	chr11	50131318	50131335	+	1	NA	promoter-TSS (NM_001290759)	promoter-TSS (NM_001290759)	-34	NM_001290759	76795	Mm.290975	NM_029745	ENSMUSG00000036644	Tbc1d9b	-	TBC1 domain family, member 9B	protein-coding
mm_148009.1	chr18	68227615	68227633	-	1	NA	intron (NM_172631, intron 3 of 5)	intron (NM_172631, intron 3 of 5)	33349	NR_106078	102465702		NR_106078	ENSMUSG00000098253	Mir7219	Gm27613|mmu-mir-7219	microRNA 7219	ncRNA
mm_12180.1	chr2	64820882	64820883	+	1	NA	Intergenic	Intergenic	201884	NM_016719	50915	Mm.214554	NM_016719	ENSMUSG00000026888	Grb14	AI505286	growth factor receptor bound protein 14	protein-coding
mm_164575.1	chr17	24593140	24593152	+	1	NA	intron (NM_013630, intron 39 of 45)	intron (NM_013630, intron 39 of 45)	39481	NM_011647	22084	Mm.30435	NM_011647	ENSMUSG00000002496	Tsc2	Nafld|Tcs2	tuberous sclerosis 2	protein-coding
mm_104763.1	chr11	98477398	98477419	-	1	NA	intron (NM_011771, intron 6 of 7)	intron (NM_011771, intron 6 of 7)	30574	NM_010346	14786	Mm.276702	NM_010346	ENSMUSG00000019312	Grb7	mKIAA4028	growth factor receptor bound protein 7	protein-coding
mm_130465.1	chr15	98609710	98609744	-	1	NA	Intergenic	CpG	-2094	NM_007405	11512	Mm.157091	NM_007405	ENSMUSG00000022994	Adcy6	AC6|mKIAA0422	adenylate cyclase 6	protein-coding
mm_60826.1	chr7	45706231	45706248	+	1	NA	intron (NM_016974, intron 1 of 3)	intron (NM_016974, intron 1 of 3)	992	NM_016974	13170	Mm.24222	NM_016974	ENSMUSG00000059824	Dbp	-	D site albumin promoter binding protein	protein-coding
mm_106500.1	chr11	120349845	120349862	-	1	NA	intron (NR_038126, intron 1 of 1)	CpG	1175	NR_038126	66838	Mm.375010	NR_038126	ENSMUSG00000043644	0610009L18Rik	-	RIKEN cDNA 0610009L18 gene	ncRNA
mm_92274.1	chr10	71182018	71182058	-	1	NA	promoter-TSS (NR_038040)	promoter-TSS (NR_038040)	2	NR_038040	319572	Mm.211663	NR_038040		C730027H18Rik	-	RIKEN cDNA C730027H18 gene	ncRNA
mm_19485.1	chr2	93162936	93162951	-	1	NA	Intergenic	Intergenic	-24641	NM_001025246	277414	Mm.41033	NM_001025246	ENSMUSG00000068735	Trp53i11	Tp53i11	transformation related protein 53 inducible protein 11	protein-coding
mm_52721.1	chr6	119904256	119904260	+	1	NA	intron (NM_001166381, intron 1 of 11)	intron (NM_001166381, intron 1 of 11)	1560	NM_001166381	19365	Mm.149	NM_011236	ENSMUSG00000030166	Rad52	Rad52yh	RAD52 homolog, DNA repair protein	protein-coding
mm_73594.1	chr8	109997573	109997576	+	1	NA	exon (NM_146214, exon 10 of 12)	exon (NM_146214, exon 10 of 12)	7138	NM_146214	234724	Mm.28110	NM_146214	ENSMUSG00000001670	Tat	-	tyrosine aminotransferase	protein-coding
mm_114005.1	chr13	52596848	52596858	+	1	NA	promoter-TSS (NM_011518)	promoter-TSS (NM_011518)	-29	NM_011518	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_109583.1	chr12	112604033	112604045	+	1	NA	exon (NM_198411, exon 8 of 23)	exon (NM_198411, exon 8 of 23)	15255	NM_198411	70435	Mm.250193	NM_198411	ENSMUSG00000037679	Inf2	2610204M08Rik|AA589465|AW125550|EG629699	inverted formin, FH2 and WH2 domain containing	protein-coding
mm_86328.1	chr9	123061796	123061802	-	1	NA	exon (NM_177911, exon 11 of 14)	exon (NM_177911, exon 11 of 14)	27058	NM_177911	331046	Mm.195309	NM_177911	ENSMUSG00000025787	Tgm4	9530008N10Rik|Eapa1|TGP	transglutaminase 4 (prostate)	protein-coding
mm_56840.1	chr6	117299530	117299547	-	1	NA	Intergenic	Intergenic	131003	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_103796.1	chr11	82889987	82890001	-	1	NA	exon (NM_001277939, exon 2 of 10)	exon (NM_001277939, exon 2 of 10)	630	NR_102719	19364	Mm.9286	NM_011235	ENSMUSG00000018841	Rad51d	R51H3|Rad51l3|TRAD|Trad-d5	RAD51 paralog D	protein-coding
mm_163752.1	chr13	119770201	119770204	-	1	NA	intron (NM_001302550, intron 5 of 6)	ID_B1|SINE|B4	-14320	NM_175538	245269	Mm.403943	NM_175538	ENSMUSG00000095930	Nim1k	E130304F04Rik|Nim1	NIM1 serine/threonine protein kinase	protein-coding
mm_94576.1	chr11	11690186	11690197	+	1	NA	promoter-TSS (NM_001301865)	promoter-TSS (NM_001301865)	14	NM_001301863	22778	Mm.103545	NM_009578	ENSMUSG00000018654	Ikzf1	5832432G11Rik|Ikaros|LyF-1|Zfpn1a1|Znfn1a1|hlk-1|mKIAA4227	IKAROS family zinc finger 1	protein-coding
mm_64492.1	chr7	143109228	143109255	+	1	NA	intron (NM_008434, intron 1 of 15)	intron (NM_008434, intron 1 of 15)	1987	NM_008434	16535	Mm.439769	NM_008434	ENSMUSG00000009545	Kcnq1	AW559127|KVLQT1|Kcna9	potassium voltage-gated channel, subfamily Q, member 1	protein-coding
mm_136851.1	chr17	12792886	12792906	+	1	NA	intron (NR_027784, intron 2 of 2)	intron (NR_027784, intron 2 of 2)	-23190	NM_010515	16004	Mm.26553	NM_010515	ENSMUSG00000023830	Igf2r	AI661837|CD222|CI-MPR|M6P/IGF2R|Mpr300	insulin-like growth factor 2 receptor	protein-coding
mm_132574.1	chr16	38220117	38220127	+	1	NA	exon (NM_019827, exon 9 of 11)	exon (NM_019827, exon 9 of 11)	74702	NM_010936	18171	Mm.8509	NM_010936	ENSMUSG00000022809	Nr1i2	PXR|PXR.1|PXR.2|PXR1|SXR|mPXR	nuclear receptor subfamily 1, group I, member 2	protein-coding
mm_72069.1	chr8	71488765	71488771	+	1	NA	5' UTR (NM_032544, exon 1 of 9)	5' UTR (NM_032544, exon 1 of 9)	665	NM_032544	70359	Mm.142112	NM_032544	ENSMUSG00000007610	Gtpbp3	2410009F13Rik|AI607903	GTP binding protein 3	protein-coding
mm_75812.1	chr8	70302895	70302934	-	1	NA	promoter-TSS (NM_001024922)	promoter-TSS (NM_001024922)	129	NM_021538	59042	Mm.28668	NM_021538	ENSMUSG00000055681	Cope	1110005D17Rik|Cope1	coatomer protein complex, subunit epsilon	protein-coding
mm_12608.1	chr2	74683460	74683468	+	1	NA	intron (NM_008273, intron 1 of 1)	intron (NM_008273, intron 1 of 1)	1141	NM_008273	15431	Mm.207763	NM_008273	ENSMUSG00000042499	Hoxd11	E230017H14Rik|Hox-4.6|Hox-5.4|Hox-5.5	homeobox D11	protein-coding
mm_56332.1	chr6	92640788	92640800	-	1	NA	intron (NM_001081146, intron 2 of 8)	intron (NM_001081146, intron 2 of 8)	65390	NM_001081146	243548	Mm.248820	NM_001081146	ENSMUSG00000030020	Prickle2	6230400G14Rik|6720451F06Rik|mpk2	prickle planar cell polarity protein 2	protein-coding
mm_91677.1	chr10	43530833	43530863	-	1	NA	intron (NM_026411, intron 2 of 3)	intron (NM_026411, intron 2 of 3)	10146	NM_026411	67851	Mm.209953	NM_026411	ENSMUSG00000019797	1700021F05Rik	-	RIKEN cDNA 1700021F05 gene	protein-coding
mm_106980.1	chr12	9574512	9574527	+	1	NA	promoter-TSS (NM_011859)	promoter-TSS (NM_011859)	77	NM_011859	23967	Mm.45055	NM_011859	ENSMUSG00000048387	Osr1	Odd1|Osr	odd-skipped related 1 (Drosophila)	protein-coding
mm_117012.1	chr13	58113596	58113620	-	1	NA	Intergenic	Intergenic	-11180	NM_001195075	100503085	Mm.379256	NM_001195075	ENSMUSG00000014164	Klhl3	7530408C15Rik|AI430941|EG627648	kelch-like 3	protein-coding
mm_59034.1	chr7	19316723	19316736	+	1	NA	Intergenic	Intergenic	-6684	NM_001347586	14282	Mm.248335	NM_008036	ENSMUSG00000003545	Fosb	-	FBJ osteosarcoma oncogene B	protein-coding
mm_116793.1	chr13	53472736	53472787	-	1	NA	promoter-TSS (NM_013601)	promoter-TSS (NM_013601)	19	NM_013601	17702	Mm.1763	NM_013601	ENSMUSG00000021469	Msx2	BB122635|Hox-8|Hox8|Hox8.1	msh homeobox 2	protein-coding
mm_29990.1	chr3	135438658	135438705	-	1	NA	promoter-TSS (NM_025356)	promoter-TSS (NM_025356)	-16	NR_030689	319587	Mm.358971	NR_030689	ENSMUSG00000097032	4930539J05Rik	8030475D13Rik	RIKEN cDNA 4930539J05 gene	ncRNA
mm_9843.1	chr1	184731865	184731882	-	1	NA	exon (NM_008250, exon 1 of 4)	exon (NM_008250, exon 1 of 4)	620	NM_008250	15284	Mm.1347	NM_008250	ENSMUSG00000039377	Hlx	Hlx1	H2.0-like homeobox	protein-coding
mm_14260.1	chr2	128204333	128204347	+	1	NA	Intergenic	Intergenic	76765	NM_001284410	12125	Mm.141083	NM_009754	ENSMUSG00000027381	Bcl2l11	1500006F24Rik|Bim|Bod|bcl2-L-11	BCL2-like 11 (apoptosis facilitator)	protein-coding
mm_25859.1	chr3	129797598	129797623	+	1	NA	intron (NM_001287224, intron 2 of 3)	intron (NM_001287224, intron 2 of 3)	6420	NM_001287224	242235	Mm.302549	NM_001205102	ENSMUSG00000093865	Lrit3	Gm421	leucine-rich repeat, immunoglobulin-like and transmembrane domains 3	protein-coding
mm_51524.1	chr6	83179638	83179650	+	1	NA	promoter-TSS (NM_007835)	promoter-TSS (NM_007835)	55	NM_007835	13191	Mm.6919	NM_007835	ENSMUSG00000031865	Dctn1	AL022633|DAP-150|DP-150|Glued|p150|p150-glued|p150<glued>	dynactin 1	protein-coding
mm_128130.1	chr15	31367491	31367504	-	1	NA	5' UTR (NM_001164441, exon 1 of 4)	5' UTR (NM_001164441, exon 1 of 4)	262	NM_001164441	67434	Mm.102470	NM_026153	ENSMUSG00000022237	Ankrd33b	0610012A05Rik|3021401C12Rik|5730557B15Rik	ankyrin repeat domain 33B	protein-coding
mm_58037.1	chr6	136804415	136804419	-	1	NA	promoter-TSS (NM_175652)	promoter-TSS (NM_175652)	14	NM_175652	320332	Mm.246720	NM_175652	ENSMUSG00000096010	Hist4h4	B130044J01Rik	histone cluster 4, H4	protein-coding
mm_32234.1	chr4	102254994	102255000	+	1	NA	promoter-TSS (NM_019840)	promoter-TSS (NM_019840)	58	NM_019840	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_39437.1	chr5	16870135	16870143	+	1	NA	Intergenic	Intergenic	316238	NM_001289461	15234	Mm.267078	NM_010427	ENSMUSG00000028864	Hgf	C230052L06Rik|HGF/SF|NK1|NK2|SF|SF/HGF	hepatocyte growth factor	protein-coding
mm_5459.1	chr1	36333594	36333598	-	1	NA	Intergenic	Intergenic	15162	NR_105863	102465541		NR_105863	ENSMUSG00000098680	Mir6898	Gm27816|mmu-mir-6898	microRNA 6898	ncRNA
mm_51060.1	chr6	65778995	65779062	+	1	NA	promoter-TSS (NM_027547)	promoter-TSS (NM_027547)	66	NM_029549	70779	Mm.263355	NM_027547	ENSMUSG00000029913	Prdm5	4432417F03Rik|6530401I24Rik|AI197291|E130112L17Rik|PFM2	PR domain containing 5	protein-coding
mm_122842.1	chr14	54724209	54724217	-	1	NA	exon (NM_016972, exon 11 of 11)	exon (NM_016972, exon 11 of 11)	-12039	NM_207131	110794	Mm.236223	NM_207131	ENSMUSG00000052435	Cebpe	C/EBPe|CRP1|Gm294	CCAAT/enhancer binding protein (C/EBP), epsilon	protein-coding
mm_134989.1	chr16	32144434	32144453	-	1	NA	exon (NM_001347181, exon 3 of 3)	exon (NM_001347181, exon 3 of 3)	21033	NM_146069	224109	Mm.33498	NM_146069	ENSMUSG00000052384	Nrros	E430025L02Rik|Lrcc33|Lrrc33	negative regulator of reactive oxygen species	protein-coding
mm_34454.1	chr4	148044253	148044271	+	1	NA	intron (NM_010840, intron 3 of 11)	intron (NM_010840, intron 3 of 11)	3073	NM_001161798	17769	Mm.89959	NM_010840	ENSMUSG00000029009	Mthfr	AI323986	5,10-methylenetetrahydrofolate reductase	protein-coding
mm_79130.1	chr9	47544198	47544219	+	1	NA	intron (NM_001025600, intron 1 of 8)	intron (NM_001025600, intron 1 of 8)	13856	NM_018770	54725	Mm.234832	NM_018770	ENSMUSG00000032076	Cadm1	2900073G06Rik|3100001I08Rik|AI987920|Bl2|Igsf4|Igsf4a|Necl2|RA175|RA175A|RA175B|RA175C|RA175N|ST17|SgIGSF|SynCam|Tslc1	cell adhesion molecule 1	protein-coding
mm_31074.1	chr4	41372319	41372320	+	1	NA	intron (NM_023305, intron 3 of 6)	intron (NM_023305, intron 3 of 6)	23323	NM_023305	67123	Mm.289795	NM_023305	ENSMUSG00000028437	Ubap1	2700092A01Rik|NAG20|UBAP-1|Ubap	ubiquitin-associated protein 1	protein-coding
mm_138788.1	chr17	37271083	37271115	+	1	NA	exon (NM_013819, exon 3 of 8)	exon (NM_013819, exon 3 of 8)	865	NM_013819	14991	Mm.14437	NM_013819	ENSMUSG00000016206	H2-M3	H-2M3|Hmt|M3a|MuprM3|MuprM301|MuprM302|R4B2	histocompatibility 2, M region locus 3	protein-coding
mm_14614.1	chr2	136713541	136713556	+	1	NA	promoter-TSS (NM_001291056)	promoter-TSS (NM_001291056)	98	NM_001291056	20614	Mm.45953	NM_011428	ENSMUSG00000027273	Snap25	Bdr|GENA70|SNAP-25|SUP|sp	synaptosomal-associated protein 25	protein-coding
mm_43340.1	chr5	135089917	135089930	+	1	NA	Intergenic	CpG	-11657	NM_001199677	194309	Mm.44356	NM_177574	ENSMUSG00000043614	Vps37d	Wbscr24	vacuolar protein sorting 37D	protein-coding
mm_155486.1	chrX	73681707	73681742	+	1	NA	3' UTR (NM_001142809, exon 13 of 13)	3' UTR (NM_001142809, exon 13 of 13)	8591	NM_001142809	102857	Mm.274553	NM_133987	ENSMUSG00000019558	Slc6a8	AA589632|CRT|CRTR|CT1|CTR5|Creat	solute carrier family 6 (neurotransmitter transporter, creatine), member 8	protein-coding
mm_57545.1	chr6	126712631	126712680	-	1	NA	intron (NM_013568, intron 1 of 1)	L2a|LINE|L2	28019	NM_013568	16494	Mm.62535	NM_013568	ENSMUSG00000038077	Kcna6	Kv1.6|MK1.6	potassium voltage-gated channel, shaker-related, subfamily, member 6	protein-coding
mm_97611.1	chr11	78951201	78951209	+	1	NA	exon (NM_010927, exon 21 of 27)	exon (NM_010927, exon 21 of 27)	25914	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_87771.1	chr10	60294537	60294565	+	1	NA	exon (NM_011179, exon 5 of 15)	exon (NM_011179, exon 5 of 15)	10090	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_143154.1	chr17	57223236	57223283	-	1	NA	exon (NM_009778, exon 12 of 41)	exon (NM_009778, exon 12 of 41)	4877	NM_009778	12266	Mm.19131	NM_009778	ENSMUSG00000024164	C3	AI255234|ASP|HSE-MSF|Plp	complement component 3	protein-coding
mm_162405.1	chr1	86347640	86347674	-	1	NA	3' UTR (NM_010880, exon 14 of 14)	3' UTR (NM_010880, exon 14 of 14)	3628	NR_028478	100303740	Mm.154378	NR_028478	ENSMUSG00000064837	Snora75	MBI-55	small nucleolar RNA, H/ACA box 75	snoRNA
mm_49985.1	chr6	41033092	41033112	+	1	NA	exon (NM_023333, exon 3 of 5)	exon (NM_023333, exon 3 of 5)	2407	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_42143.1	chr5	111418187	111418203	+	1	NA	promoter-TSS (NM_001081235)	promoter-TSS (NM_001081235)	29	NM_001081235	433938	Mm.332576	NM_001081235	ENSMUSG00000070576	Mn1	AA003644|AA009236	meningioma 1	protein-coding
mm_165171.1	chr2	26916306	26916308	-	1	NA	promoter-TSS (NM_013678)	promoter-TSS (NM_013678)	-114	NM_013678	20931	Mm.389260	NM_013678	ENSMUSG00000014873	Surf2	Surf-2	surfeit gene 2	protein-coding
mm_17409.1	chr2	27246815	27246875	-	1	NA	5' UTR (NM_138665, exon 1 of 21)	5' UTR (NM_138665, exon 1 of 21)	458	NM_138665	192166	Mm.278467	NM_138665	ENSMUSG00000009614	Sardh	-	sarcosine dehydrogenase	protein-coding
mm_94325.1	chr11	4260824	4260824	+	1	NA	intron (NM_008501, intron 1 of 3)	intron (NM_008501, intron 1 of 3)	3256	NM_008501	16878	Mm.4964	NM_008501	ENSMUSG00000034394	Lif	-	leukemia inhibitory factor	protein-coding
mm_171398.1	chr4	122592953	122592971	+	1	NA	Intergenic	Intergenic	-96297	NM_023865	77432	Mm.491436	NM_023865	ENSMUSG00000023263	9530002B09Rik	Aump|Vpp1|Vppl	RIKEN cDNA 9530002B09 gene	protein-coding
mm_19114.1	chr2	79908414	79908415	-	1	NA	promoter-TSS (NM_001009978)	promoter-TSS (NM_001009978)	-15	NM_001009978	18573	Mm.40678	NM_016744	ENSMUSG00000059173	Pde1a	AI987702|AW125737	phosphodiesterase 1A, calmodulin-dependent	protein-coding
mm_139539.1	chr17	56710029	56710039	+	1	NA	intron (NR_045519, intron 14 of 16)	intron (NR_045519, intron 14 of 16)	6887	NM_178926	106639	Mm.37290	NM_178926	ENSMUSG00000054723	Vmac	AI662250	vimentin-type intermediate filament associated coiled-coil protein	protein-coding
mm_40633.1	chr5	64830019	64830045	+	1	NA	TTS (NM_008453)	TTS (NM_008453)	26509	NM_008453	16599	Mm.392759	NM_008453	ENSMUSG00000029178	Klf3	9930027G08Rik|AL024007|Bklf|Tef-2	Kruppel-like factor 3 (basic)	protein-coding
mm_126989.1	chr15	94561584	94561597	+	1	NA	exon (NM_029926, exon 9 of 12)	exon (NM_029926, exon 9 of 12)	17930	NM_029926	266632	Mm.422858	NM_029926	ENSMUSG00000059883	Irak4	8430405M07Rik|9330209D03Rik|IRAK-4|NY-REN-64	interleukin-1 receptor-associated kinase 4	protein-coding
mm_149853.1	chr19	25076536	25076538	+	1	NA	intron (NM_028785, intron 4 of 47)	intron (NM_028785, intron 4 of 47)	77008	NM_028785	76088	Mm.102485	NM_028785	ENSMUSG00000052085	Dock8	1200017A24Rik|5830472H07Rik|A130095G14Rik|AI461977	dedicator of cytokinesis 8	protein-coding
mm_139666.1	chr17	57410770	57410827	+	1	NA	exon (NM_010130, exon 8 of 22)	exon (NM_010130, exon 8 of 22)	52112	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_161197.1	chr13	55213081	55213081	+	1	NA	intron (NM_008739, intron 1 of 22)	intron (NM_008739, intron 1 of 22)	3299	NM_008739	18193	Mm.12964	NM_008739	ENSMUSG00000021488	Nsd1	AI528500|KMT3B	nuclear receptor-binding SET-domain protein 1	protein-coding
mm_74925.1	chr8	25597542	25597598	-	1	NA	promoter-TSS (NM_173012)	promoter-TSS (NM_173012)	-83	NM_173012	270035	Mm.268349	NM_173012	ENSMUSG00000037363	Letm2	6030453H13|D030041N04Rik	leucine zipper-EF-hand containing transmembrane protein 2	protein-coding
mm_125350.1	chr15	39210035	39210035	+	1	NA	intron (NM_001256382, intron 1 of 26)	intron (NM_001256382, intron 1 of 26)	11749	NM_053271	116838	Mm.309296	NM_053271	ENSMUSG00000037386	Rims2	2810036I15Rik|AW048769|RIM2|Rab3ip2|Rim2(+40A)|Rim2(+44A)|Rim2(+4A)|Serg2|Syt3-rs|mKIAA0751	regulating synaptic membrane exocytosis 2	protein-coding
mm_67691.1	chr7	89517535	89517565	-	1	NA	promoter-TSS (NM_029614)	promoter-TSS (NM_029614)	36	NM_029614	76453	Mm.250438	NM_029614	ENSMUSG00000039405	Prss23	2310046G15Rik|4930479H08Rik|AI790574|Spuve	protease, serine 23	protein-coding
mm_133100.1	chr16	64852817	64852864	+	1	NA	5' UTR (NM_178647, exon 2 of 3)	5' UTR (NM_178647, exon 2 of 3)	755	NM_178647	106143	Mm.10160	NM_178647	ENSMUSG00000054604	Cggbp1	AA960172|AL023996|AW045841	CGG triplet repeat binding protein 1	protein-coding
mm_161367.1	chr14	62998016	62998016	+	1	NA	promoter-TSS (NM_001039125)	promoter-TSS (NM_001039125)	-61	NM_001039125	654465	Mm.424929	NM_001039125	ENSMUSG00000075573	Defb47	Defb41|EG654465	defensin beta 47	protein-coding
mm_83269.1	chr9	42966977	42966991	-	1	NA	3' UTR (NM_027144, exon 41 of 41)	3' UTR (NM_027144, exon 41 of 41)	-22613	NM_175481	110637	Mm.370291	NM_175481	ENSMUSG00000032017	Grik4	6330551K01Rik|GluK4|GluRgamma1|KA-1|KA1	glutamate receptor, ionotropic, kainate 4	protein-coding
mm_86058.1	chr9	114584263	114584275	-	1	NA	Intergenic	Intergenic	-19900	NM_001042503	636931	Mm.17857	NM_001042503	ENSMUSG00000079259	Trim71	2610206G21Rik|AL022943|Gm1127|Lin41|lin-41|mLin41|mlin-41	tripartite motif-containing 71	protein-coding
mm_43418.1	chr5	135994797	135994884	+	1	NA	promoter-TSS (NM_001256098)	promoter-TSS (NM_001256098)	40	NM_001256098	74198	Mm.275574	NM_023742	ENSMUSG00000004947	Dtx2	2610524D08Rik|AA408415|AU022494|Deltex2	deltex 2, E3 ubiquitin ligase	protein-coding
mm_153313.1	chr19	38043386	38043418	-	1	NA	5' UTR (NM_001099634, exon 1 of 53)	5' UTR (NM_001099634, exon 1 of 53)	175	NM_001099634	226101	Mm.34674	NM_177035	ENSMUSG00000048612	Myof	2310004N10Rik|2310051D19Rik|E030042N20Rik|Fer1l3	myoferlin	protein-coding
mm_124869.1	chr15	10177664	10177674	+	1	NA	5' UTR (NM_011169, exon 1 of 10)	5' UTR (NM_011169, exon 1 of 10)	431	NM_011169	19116	Mm.10516	NM_011169	ENSMUSG00000005268	Prlr	AI987712|Pr-1|Pr-3|Prlr-rs1	prolactin receptor	protein-coding
mm_142602.1	chr17	46763793	46763808	-	1	NA	promoter-TSS (NM_011195)	promoter-TSS (NM_011195)	-88	NM_011195	19208	Mm.215173	NM_011195	ENSMUSG00000036858	Ptcra	gp33|pT-alpha|pT-alpha-TCR|pT[a]|pTa|pTalpha	pre T cell antigen receptor alpha	protein-coding
mm_63735.1	chr7	130891262	130891292	+	1	NA	intron (NM_001346515, intron 4 of 12)	intron (NM_001346515, intron 4 of 12)	-16991	NR_106028	102466219		NR_106028	ENSMUSG00000104914	Mir7061	mmu-mir-7061	microRNA 7061	ncRNA
mm_8145.1	chr1	136346075	136346145	-	1	NA	promoter-TSS (NM_001081360)	promoter-TSS (NM_001081360)	-6	NM_001347110	67886	Mm.144143	NM_001081360	ENSMUSG00000041570	Camsap2	1600013L13Rik|4930541M15Rik|Camsap1l1|mKIAA1078	calmodulin regulated spectrin-associated protein family, member 2	protein-coding
mm_93529.1	chr10	115332509	115332553	-	1	NA	Intergenic	Intergenic	-16940	NM_024454	216344	Mm.21936	NM_024454	ENSMUSG00000020132	Rab21	9630024B22	RAB21, member RAS oncogene family	protein-coding
mm_84813.1	chr9	77435130	77435158	-	1	NA	exon (NM_001146048, exon 12 of 14)	exon (NM_001146048, exon 12 of 14)	-35728	NR_040378	70487	Mm.58958	NR_040378	ENSMUSG00000099170	5730403I07Rik	-	RIKEN cDNA 5730403I07 gene	ncRNA
mm_165402.1	chr2	137095739	137095776	-	1	NA	intron (NM_013822, intron 6 of 25)	intron (NM_013822, intron 6 of 25)	20763	NM_013822	16449	Mm.22398	NM_013822	ENSMUSG00000027276	Jag1	ABE2|Gsfabe2|Htu|Ozz|Ser-1	jagged 1	protein-coding
mm_11986.1	chr2	55435919	55435949	+	1	NA	promoter-TSS (NM_001304810)	promoter-TSS (NM_001304810)	-36	NM_001304810	16519	Mm.5127	NM_008426	ENSMUSG00000026824	Kcnj3	GIRK-1|GIRK1|Kcnf3|Kir3.1	potassium inwardly-rectifying channel, subfamily J, member 3	protein-coding
mm_60815.1	chr7	45699853	45699894	+	1	NA	promoter-TSS (NM_009800)	promoter-TSS (NM_009800)	-94	NM_009800	12348	Mm.27736	NM_009800	ENSMUSG00000003273	Car11	Ca11	carbonic anhydrase 11	protein-coding
mm_167443.1	chr8	121730010	121730019	+	1	NA	promoter-TSS (NM_020605)	promoter-TSS (NM_020605)	-545	NM_020605	57340	Mm.306870	NM_020605	ENSMUSG00000025318	Jph3	JP-3|Jp3	junctophilin 3	protein-coding
mm_133558.1	chr16	91391744	91391769	+	1	NA	exon (NM_010509, exon 6 of 9)	exon (NM_010509, exon 6 of 9)	-14479	NM_008349	16155	Mm.4154	NM_008349	ENSMUSG00000022969	Il10rb	6620401D04Rik|AI528744|CRF2-4|Crfb4|D16H21S58|D21S58h|IL-10R2|Il10r2	interleukin 10 receptor, beta	protein-coding
mm_8613.1	chr1	156036117	156036139	-	1	NA	promoter-TSS (NM_001160182)	promoter-TSS (NM_001160182)	92	NM_001160182	240832	Mm.253335	NM_022329	ENSMUSG00000050565	Tor1aip2	1110020D10Rik|15kDa|A130072J07|AA103493|AW060462|AW610675|C77739|Ifrg15|Lull1	torsin A interacting protein 2	protein-coding
mm_3278.1	chr1	136579641	136579651	+	1	NA	Intergenic	Intergenic	-45255	NM_177643	226442	Mm.62521	NM_177643	ENSMUSG00000041483	Zfp281	Znf281	zinc finger protein 281	protein-coding
mm_74786.1	chr8	22125031	22125073	-	1	NA	promoter-TSS (NM_177898)	promoter-TSS (NM_177898)	1	NM_177898	330721	Mm.113940	NM_177898	ENSMUSG00000037738	Nek5	6530411J22|BB049667	NIMA (never in mitosis gene a)-related expressed kinase 5	protein-coding
mm_33938.1	chr4	136945625	136945634	+	1	NA	intron (NM_007939, intron 3 of 16)	(CAGC)n|Simple_repeat|Simple_repeat	11187	NM_007939	13842	Mm.1390	NM_007939	ENSMUSG00000028661	Epha8	AW047546|Eek|Hek3|mKIAA1459	Eph receptor A8	protein-coding
mm_130137.1	chr15	90898426	90898430	-	1	NA	promoter-TSS (NR_033583)	promoter-TSS (NR_033583)	48	NR_033583	20738	Mm.431547	NR_033583		Spn-ps	Cd43-ps	sialophorin, pseudogene	pseudo
mm_83501.1	chr9	45955171	45955186	-	1	NA	promoter-TSS (NM_001289668)	promoter-TSS (NM_001289668)	71	NM_172257	214597	Mm.379345	NM_172257	ENSMUSG00000034908	Sidt2	B930096O19|BC023957|CGI-40	SID1 transmembrane family, member 2	protein-coding
mm_6189.1	chr1	65123098	65123104	-	1	NA	5' UTR (NM_001285881, exon 1 of 8)	5' UTR (NM_001285881, exon 1 of 8)	113	NM_175293	98303	Mm.348057	NM_175293	ENSMUSG00000044816	D630023F18Rik	AI314969	RIKEN cDNA D630023F18 gene	protein-coding
mm_31193.1	chr4	43631356	43631414	+	1	NA	promoter-TSS (NM_173788)	promoter-TSS (NM_173788)	-550	NM_173788	230103	Mm.103477	NM_173788	ENSMUSG00000028469	Npr2	GC-B|GC-B2|GC-B3|cn|mNPR-B|pwe	natriuretic peptide receptor 2	protein-coding
mm_139191.1	chr17	47599119	47599129	+	1	NA	TTS (NM_016859)	TTS (NM_016859)	5657	NM_007632	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_65695.1	chr7	28375523	28375584	-	1	NA	Intergenic	Intergenic	-2891	NM_001083912	101497	Mm.235700	NM_138752	ENSMUSG00000037552	Plekhg2	AI194308|Clg|Cslg	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	protein-coding
mm_56923.1	chr6	119417548	119417558	-	1	NA	promoter-TSS (NM_197985)	promoter-TSS (NM_197985)	-70	NM_197985	68465	Mm.291826	NM_197985	ENSMUSG00000030168	Adipor2	1110001I14Rik|ADCR2|AI115388|AW554121|D6Ucla1e|Paqr2	adiponectin receptor 2	protein-coding
mm_127330.1	chr15	100421583	100421590	+	1	NA	intron (NM_008732, intron 1 of 16)	intron (NM_008732, intron 1 of 16)	1469	NM_001146161	18174	Mm.234608	NM_008732	ENSMUSG00000023030	Slc11a2	DCT1|DMT1|Nramp2|mk|van	solute carrier family 11 (proton-coupled divalent metal ion transporters), member 2	protein-coding
mm_144579.1	chr18	31922287	31922304	+	1	NA	Intergenic	Intergenic	-9212	NM_144862	225341	Mm.24551	NM_144862	ENSMUSG00000024395	Lims2	PINCH2	LIM and senescent cell antigen like domains 2	protein-coding
mm_92468.1	chr10	78036122	78036124	-	1	NA	intron (NR_073358, intron 10 of 14)	intron (NR_073358, intron 10 of 14)	-6164	NM_001081695	54427	Mm.13433	NM_019448	ENSMUSG00000000730	Dnmt3l	D6Ertd14e|ecat7	DNA (cytosine-5-)-methyltransferase 3-like	protein-coding
mm_165007.1	chr19	24416036	24416042	+	1	NA	intron (NM_008846, intron 3 of 14)	intron (NM_008846, intron 3 of 14)	61435	NM_026520	68034	Mm.440181	NM_026520	ENSMUSG00000074922	Fam122a	2410124L17Rik|2900009I07Rik|ENSMUSG00000051082|Gm9849	family with sequence similarity 122, member A	protein-coding
mm_27278.1	chr3	41082993	41083024	-	1	NA	promoter-TSS (NM_027558)	promoter-TSS (NM_027558)	38	NM_027558	70804	Mm.40321	NM_027558	ENSMUSG00000049940	Pgrmc2	4631434O19Rik|5730409G06Rik|DG6|PMBP	progesterone receptor membrane component 2	protein-coding
mm_160345.1	chr8	19495081	19495081	+	1	NA	promoter-TSS (NM_139220)	promoter-TSS (NM_139220)	-16	NM_139220	246080	Mm.207067	NM_139220	ENSMUSG00000037790	Defb7	BD-7|Defb15	defensin beta 7	protein-coding
mm_105012.1	chr11	100414674	100414744	-	1	NA	promoter-TSS (NM_010221)	promoter-TSS (NM_010221)	110	NM_176830	66180	Mm.4940	NM_176830	ENSMUSG00000006931	P3h4	1110036O03Rik|AI413214|Leprel4|Sc65	prolyl 3-hydroxylase family member 4 (non-enzymatic)	protein-coding
mm_26554.1	chr3	146450468	146450503	+	1	NA	promoter-TSS (NM_001293672)	promoter-TSS (NM_001293672)	18	NM_001293672	74245	Mm.45396	NM_028836	ENSMUSG00000028189	Ctbs	2210401K11Rik|CTB	chitobiase, di-N-acetyl-	protein-coding
mm_112845.1	chr13	20835904	20835907	+	1	NA	intron (NM_012054, intron 2 of 20)	MTC|LTR|ERVL-MaLR	41792	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_117000.1	chr13	56895775	56895793	-	1	NA	promoter-TSS (NM_012035)	promoter-TSS (NM_012035)	5	NM_001302372	26946	Mm.62409	NM_012035	ENSMUSG00000021541	Trpc7	TRP7|Trrp8	transient receptor potential cation channel, subfamily C, member 7	protein-coding
mm_846.1	chr1	52008211	52008254	+	1	NA	promoter-TSS (NM_011487)	promoter-TSS (NM_011487)	-8	NM_011487	20849	Mm.1550	NM_011487	ENSMUSG00000062939	Stat4	-	signal transducer and activator of transcription 4	protein-coding
mm_115101.1	chr13	102741343	102741347	+	1	NA	intron (NM_175171, intron 27 of 28)	intron (NM_175171, intron 27 of 28)	-18910	NR_130318	76624	Mm.426384	NR_130171	ENSMUSG00000091906	1700099I09Rik	-	RIKEN cDNA 1700099I09 gene	ncRNA
mm_155464.1	chrX	73570405	73570416	+	1	NA	exon (NM_177236, exon 21 of 21)	exon (NM_177236, exon 21 of 21)	67324	NM_177236	320707	Mm.210095	NM_177236	ENSMUSG00000031376	Atp2b3	6430519O13Rik|Pmca3	ATPase, Ca++ transporting, plasma membrane 3	protein-coding
mm_59332.1	chr7	25396447	25396485	+	1	NA	promoter-TSS (NM_010719)	promoter-TSS (NM_010719)	-479	NM_010719	16890	Mm.158548	NM_010719	ENSMUSG00000003123	Lipe	4933403G17Rik|HSL	lipase, hormone sensitive	protein-coding
mm_80153.1	chr9	70931780	70931789	+	1	NA	intron (NM_001324473, intron 1 of 8)	intron (NM_001324473, intron 1 of 8)	3024	NM_008280	15450	Mm.390187	NM_008280	ENSMUSG00000032207	Lipc	AI256194|HL|Hpl	lipase, hepatic	protein-coding
mm_55872.1	chr6	83506839	83506850	-	1	NA	exon (NM_001162521, exon 1 of 6)	exon (NM_001162521, exon 1 of 6)	125	NM_013764	27369	Mm.42234	NM_013764	ENSMUSG00000014554	Dguok	dGK|dGK1|dGK2|dGK3	deoxyguanosine kinase	protein-coding
mm_51300.1	chr6	72309804	72309820	+	1	NA	exon (NM_147779, exon 8 of 12)	exon (NM_147779, exon 8 of 12)	5202	NM_147779	20388	Mm.46033	NM_147779	ENSMUSG00000056370	Sftpb	AI562151|SF-B|SP-B|Sftp-3|Sftp3	surfactant associated protein B	protein-coding
mm_114717.1	chr13	83656714	83656716	+	1	NA	intron (NM_001347581, intron 9 of 9)	intron (NM_001347581, intron 9 of 9)	-71391	NR_015561	320203	Mm.245636	NM_177100	ENSMUSG00000050334	C130071C03Rik	2810449C10Rik	RIKEN cDNA C130071C03 gene	ncRNA
mm_6985.1	chr1	86357151	86357168	-	1	NA	promoter-TSS (NR_002851)	promoter-TSS (NR_002851)	-832	NR_002851	80828		NR_002851	ENSMUSG00000064823	Snord82	Rnu82|U82|Z25	small nucleolar RNA, C/D box 82	snoRNA
mm_150534.1	chr19	39291555	39291559	+	1	NA	intron (NM_007815, intron 3 of 8)	intron (NM_007815, intron 3 of 8)	4472	NM_007815	13095	Mm.20764	NM_007815	ENSMUSG00000003053	Cyp2c29	AHOH|AHOHase|AI159681|AI196010|Ah-2|Ahh-1|Cyp2c|P450-2C	cytochrome P450, family 2, subfamily c, polypeptide 29	protein-coding
mm_85340.1	chr9	102717558	102717581	-	1	NA	promoter-TSS (NM_019764)	promoter-TSS (NM_019764)	-235	NM_019764	56332	Mm.21145	NM_019764	ENSMUSG00000032531	Amotl2	AW549739|C79691|Lccp|MASCOT|mKIAA0989	angiomotin-like 2	protein-coding
mm_92140.1	chr10	66930856	66930869	-	1	NA	Intergenic	Intergenic	-10478	NR_138561	68488	Mm.338835	NR_138560		1110002J07Rik	-	RIKEN cDNA 1110002J07 gene	ncRNA
mm_121912.1	chr14	22013157	22013186	-	1	NA	Intergenic	B1F1|SINE|Alu	-6541	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_22240.1	chr2	174464064	174464099	-	1	NA	promoter-TSS (NM_025983)	promoter-TSS (NM_025983)	20	NM_025983	67126	Mm.20841	NM_025983	ENSMUSG00000016252	Atp5e	2410043G19Rik|ATPE|AV000645	ATP synthase, H+ transporting, mitochondrial F1 complex, epsilon subunit	protein-coding
mm_102712.1	chr11	67052564	67052618	-	1	NA	promoter-TSS (NM_025510)	promoter-TSS (NM_025510)	27	NM_025510	66358	Mm.22511	NM_025510	ENSMUSG00000020910	Adprm	2310004I24Rik|MDS006	ADP-ribose/CDP-alcohol diphosphatase, manganese dependent	protein-coding
mm_107941.1	chr12	71889539	71889556	+	1	NA	promoter-TSS (NM_001286452)	promoter-TSS (NM_001286452)	4	NM_001286452	208846	Mm.87417	NM_026102	ENSMUSG00000034574	Daam1	-	dishevelled associated activator of morphogenesis 1	protein-coding
mm_103598.1	chr11	78386570	78386598	-	1	NA	promoter-TSS (NM_008238)	promoter-TSS (NM_008238)	24	NM_008238	15218	Mm.4496	NM_008238	ENSMUSG00000002057	Foxn1	D11Bhm185e|Fkh19|HFH-11|Hfh11|Whn|nu|nude	forkhead box N1	protein-coding
mm_140059.1	chr17	74668274	74668282	+	1	NA	intron (NM_007566, intron 62 of 72)	intron (NM_007566, intron 62 of 72)	-49472	NM_152817	74196	Mm.209503	NM_152817	ENSMUSG00000024078	Ttc27	2610511O17Rik	tetratricopeptide repeat domain 27	protein-coding
mm_117999.1	chr13	100515136	100515139	-	1	NA	exon (NM_008756, exon 5 of 9)	exon (NM_008756, exon 5 of 9)	-22528	NM_022011	23894	Mm.272533	NM_022011	ENSMUSG00000021639	Gtf2h2	44kDa|BTF2 p44|BTF2-p44|Btf2p44|p44	general transcription factor II H, polypeptide 2	protein-coding
mm_17998.1	chr2	38190865	38190868	-	1	NA	intron (NM_146122, intron 2 of 21)	intron (NM_146122, intron 2 of 21)	96518	NM_146122	227801	Mm.314245	NM_146122	ENSMUSG00000035392	Dennd1a	6030446I19Rik|connecdenn	DENN/MADD domain containing 1A	protein-coding
mm_72268.1	chr8	75098758	75098836	+	1	NA	exon (NM_010442, exon 4 of 5)	exon (NM_010442, exon 4 of 5)	5179	NM_010442	15368	Mm.276389	NM_010442	ENSMUSG00000005413	Hmox1	D8Wsu38e|HO-1|HO1|Hemox|Hmox|Hsp32	heme oxygenase 1	protein-coding
mm_113721.1	chr13	43765536	43765548	+	1	NA	Intergenic	Intergenic	-19570	NM_009856	12522	Mm.57175	NM_009856	ENSMUSG00000015396	Cd83	-	CD83 antigen	protein-coding
mm_109049.1	chr12	104339069	104339101	+	1	NA	intron (NM_011458, intron 1 of 4)	intron (NM_011458, intron 1 of 4)	599	NM_011458	20714	Mm.291569	NM_011458	ENSMUSG00000058207	Serpina3k	1300001I07Rik|D12Rp54|MMCM2|MMSpi2|RP54|Spi-2|Spi2|contrapsin	serine (or cysteine) peptidase inhibitor, clade A, member 3K	protein-coding
mm_133327.1	chr16	78302545	78302548	+	1	NA	intron (NM_001276263, intron 1 of 2)	intron (NM_001276263, intron 1 of 2)	875	NM_001276263	13052	Mm.66222	NM_009988	ENSMUSG00000022865	Cxadr	2610206D03Rik|AU016810|AW553441|CAR|MCAR|MCVADR	coxsackie virus and adenovirus receptor	protein-coding
mm_91375.1	chr10	30200548	30200573	-	1	NA	promoter-TSS (NM_001109747)	promoter-TSS (NM_001109747)	-20	NM_001109747	66311	Mm.251779	NM_001109747	ENSMUSG00000075266	Cenpw	2610036L11Rik|Cug2	centromere protein W	protein-coding
mm_118271.1	chr13	112601800	112601819	-	1	NA	intron (NM_001145885, intron 18 of 21)	intron (NM_001145885, intron 18 of 21)	-21147	NM_139299	218624	Mm.380801	NM_139299	ENSMUSG00000050377	Il31ra	CRL3|GLM-R|GPL|Glmr|NR10	interleukin 31 receptor A	protein-coding
mm_48050.1	chr5	136472022	136472068	-	1	NA	intron (NM_001291239, intron 2 of 22)	intron (NM_001291239, intron 2 of 22)	93936	NM_001291239	13047	Mm.320317	NM_009986	ENSMUSG00000029705	Cux1	CDP|Cutl1|Cux|Cux-1	cut-like homeobox 1	protein-coding
mm_73162.1	chr8	95003369	95003427	+	1	NA	exon (NM_001198894, exon 3 of 14)	exon (NM_001198894, exon 3 of 14)	-14294	NM_173036	54672	Mm.27995	NM_173036	ENSMUSG00000060470	Adgrg3	A030001G24Rik|AW214383|Gpr97|Pb1|Pb99	adhesion G protein-coupled receptor G3	protein-coding
mm_152614.1	chr19	11966156	11966160	-	1	NA	exon (NM_001033174, exon 1 of 14)	exon (NM_001033174, exon 1 of 14)	314	NM_001033174	76303	Mm.291279	NM_001033174	ENSMUSG00000024687	Osbp	1110018F06Rik|AW559088|mKIAA4220	oxysterol binding protein	protein-coding
mm_62505.1	chr7	102065739	102065771	+	1	NA	promoter-TSS (NM_029211)	promoter-TSS (NM_029211)	264	NM_001286689	102443350	Mm.292904	NM_001286689	ENSMUSG00000070425	Xndc1	Xndr	Xrcc1 N-terminal domain containing 1	protein-coding
mm_97543.1	chr11	78922323	78922339	+	1	NA	exon (NM_010927, exon 2 of 27)	exon (NM_010927, exon 2 of 27)	1544	NM_010927	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_123315.1	chr14	62465062	62465072	-	1	NA	Intergenic	Intergenic	-8778	NM_172810	239134	Mm.236557	NM_172810	ENSMUSG00000021933	Gucy1b2	B930025B03|GC-SB2	guanylate cyclase 1, soluble, beta 2	protein-coding
mm_144564.1	chr18	31760582	31760656	+	1	NA	promoter-TSS (NM_001242430)	promoter-TSS (NM_001242430)	3	NM_001242430	225339	Mm.290804	NM_153515	ENSMUSG00000041915	Ammecr1l	5430429D03Rik|AU022236|AU040755|AW111353|E230022H04Rik	AMME chromosomal region gene 1-like	protein-coding
mm_44502.1	chr5	23844086	23844151	-	1	NA	promoter-TSS (NM_025394)	promoter-TSS (NM_025394)	27	NM_025394	66169	Mm.291868	NM_025394	ENSMUSG00000028998	Tomm7	1110020J08Rik|AW047273|Tom7	translocase of outer mitochondrial membrane 7 homolog (yeast)	protein-coding
mm_138798.1	chr17	37534705	37534713	+	1	NA	Intergenic	L1_Mur2|LINE|L1	4752	NM_001005485	545205	Mm.383371	NM_001005485	ENSMUSG00000090675	Olfr111	-	olfactory receptor 111	protein-coding
mm_145359.1	chr18	56676650	56676660	+	1	NA	Intergenic	RMER17C2|LTR|ERVK	-31158	NM_010721	16906	Mm.4105	NM_010721	ENSMUSG00000024590	Lmnb1	-	lamin B1	protein-coding
mm_25852.1	chr3	129553452	129553469	+	1	NA	intron (NM_130450, intron 2 of 4)	B4|SINE|B4	21074	NM_130450	170439	Mm.314113	NM_130450	ENSMUSG00000041220	Elovl6	C77826|FAE|LCE	ELOVL family member 6, elongation of long chain fatty acids (yeast)	protein-coding
mm_83192.1	chr9	41014190	41014205	-	1	NA	3' UTR (NM_176860, exon 14 of 14)	3' UTR (NM_176860, exon 14 of 14)	-9569	NM_019465	54698	Mm.42791	NM_019465	ENSMUSG00000032021	Crtam	-	cytotoxic and regulatory T cell molecule	protein-coding
mm_68419.1	chr7	109723845	109723855	-	1	NA	promoter-TSS (NM_001040700)	promoter-TSS (NM_001040700)	-79	NM_001040700	57355	Mm.358682	NM_020609	ENSMUSG00000031022	BC051019	AA571491|D7H11orf16|ICRFP703B1614Q5.5	cDNA sequence BC051019	protein-coding
mm_133247.1	chr16	77124256	77124260	+	1	NA	Intergenic	Intergenic	110189	NM_013918	30940	Mm.40986	NM_013918	ENSMUSG00000022867	Usp25	-	ubiquitin specific peptidase 25	protein-coding
mm_84026.1	chr9	57761923	57761925	-	1	NA	intron (NM_007713, intron 1 of 12)	intron (NM_007713, intron 1 of 12)	3936	NM_007713	102414	Mm.25720	NM_007713	ENSMUSG00000032316	Clk3	AI256811	CDC-like kinase 3	protein-coding
mm_121864.1	chr14	20733599	20733646	-	1	NA	5' UTR (NM_010811, exon 2 of 15)	5' UTR (NM_010811, exon 2 of 15)	940	NM_010811	17423	Mm.4084	NM_010811	ENSMUSG00000039308	Ndst2	Mndns|NDST-2	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 2	protein-coding
mm_126042.1	chr15	76904536	76904573	+	1	NA	exon (NM_012053, exon 3 of 6)	exon (NM_012053, exon 3 of 6)	483	NM_012053	26961	Mm.30066	NM_012053	ENSMUSG00000003970	Rpl8	-	ribosomal protein L8	protein-coding
mm_53107.1	chr6	125071327	125071345	+	1	NA	promoter-TSS (NM_001163268)	promoter-TSS (NM_001163268)	59	NM_001163268	381810	Mm.333386	NM_001163268	ENSMUSG00000067714	Lpar5	GPR93|Gm1072|Gpr92|LPA5	lysophosphatidic acid receptor 5	protein-coding
mm_103455.1	chr11	76287328	76287346	-	1	NA	intron (NM_008750, intron 1 of 7)	MIR|SINE|MIR	43601	NM_183263	67390	Mm.24886	NM_183263	ENSMUSG00000038046	Rnmtl1	4833420N02Rik|AI255153|HC90|Mrm3	RNA methyltransferase like 1	protein-coding
mm_134901.1	chr16	30039339	30039364	-	1	NA	non-coding (NR_045878, exon 1 of 4)	non-coding (NR_045878, exon 1 of 4)	128	NR_045878	71528	Mm.297640	NR_045878		9030404E10Rik	-	RIKEN cDNA 9030404E10 gene	ncRNA
mm_80813.1	chr9	96525328	96525362	+	1	NA	Intergenic	Intergenic	-46670	NM_001311135	19823	Mm.28235	NM_011279	ENSMUSG00000051234	Rnf7	Rbx2|SAG	ring finger protein 7	protein-coding
mm_125334.1	chr15	38691617	38691640	+	1	NA	exon (NM_025494, exon 13 of 13)	exon (NM_025494, exon 13 of 13)	29724	NM_025494	66335	Mm.276618	NM_025494	ENSMUSG00000022295	Atp6v1c1	1700025B18Rik|U13839	ATPase, H+ transporting, lysosomal V1 subunit C1	protein-coding
mm_57900.1	chr6	131388261	131388344	-	1	NA	5' UTR (NM_011733, exon 1 of 9)	5' UTR (NM_011733, exon 1 of 9)	148	NM_139117	56449	Mm.458000	NM_011733	ENSMUSG00000030189	Ybx3	Csda|Dpba|MSY3|MSY4|Yb2|dbpA|oxyR	Y box protein 3	protein-coding
mm_1234.1	chr1	62792408	62792452	+	1	NA	intron (NR_040601, intron 2 of 2)	intron (NR_040601, intron 2 of 2)	2302	NR_040601	74992	Mm.401979	NR_040601		4930487H11Rik	-	RIKEN cDNA 4930487H11 gene	ncRNA
mm_53006.1	chr6	123270788	123270803	+	1	NA	intron (NM_001163161, intron 5 of 5)	B1F|SINE|Alu	8688	NM_010819	17474	Mm.441101	NM_010819	ENSMUSG00000030144	Clec4d	Clecsf8|Mpcl|mcl	C-type lectin domain family 4, member d	protein-coding
mm_100832.1	chr11	5444839	5444872	-	1	NA	promoter-TSS (NM_001080924)	promoter-TSS (NM_001080924)	-8	NM_001080924	407821	Mm.216313	NM_001080924	ENSMUSG00000041961	Znrf3	Gm1167	zinc and ring finger 3	protein-coding
mm_139381.1	chr17	51879883	51879906	+	1	NA	Intergenic	Intergenic	-2833	NR_045095	100504169	Mm.417731	NR_045095		Gm20098	-	predicted gene, 20098	ncRNA
mm_17502.1	chr2	28915537	28915572	-	1	NA	exon (NM_019446, exon 1 of 3)	exon (NM_019446, exon 1 of 3)	867	NM_019446	54422	Mm.21390	NM_019446	ENSMUSG00000026805	Barhl1	Dres115|MBH2	BarH-like 1 (Drosophila)	protein-coding
mm_94726.1	chr11	20647249	20647253	+	1	NA	intron (NM_001038625, intron 1 of 1)	intron (NM_001038625, intron 1 of 1)	15274	NM_001038625	58172	Mm.339676	NM_021372	ENSMUSG00000049800	Sertad2	AB041541|AU021878|Kiaa0127|MNCb-1504|SEI-2|Sei2|TRIP-Br2|mKIAA0127	SERTA domain containing 2	protein-coding
mm_47525.1	chr5	124152832	124152840	-	1	NA	intron (NM_011256, intron 2 of 24)	MIR3|SINE|MIR	34346	NM_001289472	19679	Mm.44261	NM_011256	ENSMUSG00000029406	Pitpnm2	NIR3|RDGBA2|Rdgb2|mKIAA1457	phosphatidylinositol transfer protein, membrane-associated 2	protein-coding
mm_127375.1	chr15	100810473	100810494	+	1	NA	intron (NM_001347102, intron 19 of 23)	intron (NM_001347102, intron 19 of 23)	29229	NM_001347102	59033	Mm.209856	NM_021530	ENSMUSG00000023032	Slc4a8	AW493845|C230026C11|NDCBE|kNBC-3	solute carrier family 4 (anion exchanger), member 8	protein-coding
mm_60452.1	chr7	44477478	44477488	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-7034	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_152398.1	chr19	10555725	10555761	-	1	NA	promoter-TSS (NM_001277861)	promoter-TSS (NM_001277861)	20	NM_001277861	68642	Mm.31236	NM_026798	ENSMUSG00000024667	Tmem216	1110017C22Rik|2810441K11Rik|4921533J23Rik|A930021F15Rik|AI482550	transmembrane protein 216	protein-coding
mm_93796.1	chr10	120805593	120805613	-	1	NA	intron (NM_177092, intron 5 of 6)	RSINE1|SINE|B4	39871	NR_038003	70874	Mm.427286	NR_038000	ENSMUSG00000044544	4921513I03Rik	-	RIKEN cDNA 4921513I03 gene	ncRNA
mm_102570.1	chr11	61579253	61579264	-	1	NA	intron (NM_001252188, intron 1 of 10)	CpG	429	NM_010148	13855	Mm.139695	NM_010148	ENSMUSG00000001036	Epn2	9530051D10Rik|AA536924|Ibp2	epsin 2	protein-coding
mm_132290.1	chr16	33207026	33207029	+	1	NA	intron (NM_176840, intron 4 of 12)	ID_B1|SINE|B4	21956	NM_176840	106326	Mm.486405	NM_176840	ENSMUSG00000022807	Osbpl11	9430097N02Rik|AI132306|AU019795|ORP-11	oxysterol binding protein-like 11	protein-coding
mm_74267.1	chr8	124898487	124898502	+	1	NA	promoter-TSS (NM_198103)	promoter-TSS (NM_198103)	608	NM_001111141	244666	Mm.482915	NM_001111141	ENSMUSG00000031986	Sprtn	Gm505	SprT-like N-terminal domain	protein-coding
mm_59166.1	chr7	24399675	24399727	+	1	NA	promoter-TSS (NM_028047)	promoter-TSS (NM_028047)	73	NM_028047	71997	Mm.150977	NM_028047	ENSMUSG00000002210	Smg9	1500002O20Rik|AI429693|N28092	smg-9 homolog, nonsense mediated mRNA decay factor (C. elegans)	protein-coding
mm_168993.1	chr12	99645512	99645521	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-17542	NR_045288	73457	Mm.383439	NR_045288	ENSMUSG00000100211	1700064M15Rik	-	RIKEN cDNA 1700064M15 gene	ncRNA
mm_361.1	chr1	33813662	33813673	+	1	NA	intron (NM_001290699, intron 2 of 12)	intron (NM_001290699, intron 2 of 12)	928	NM_133817	98403	Mm.289103	NM_133817	ENSMUSG00000042197	Zfp451	4930515K21Rik|4933435G09Rik|AI596398|COASTER|Kiaa0576-hp|Znf451|mKIAA1702	zinc finger protein 451	protein-coding
mm_7456.1	chr1	120271075	120271085	-	1	NA	promoter-TSS (NM_001085409)	promoter-TSS (NM_001085409)	2	NM_001085409	68428	Mm.181033	NM_133186	ENSMUSG00000026389	Steap3	1010001D01Rik|Tsap6|pHyde	STEAP family member 3	protein-coding
mm_6099.1	chr1	63730307	63730342	-	1	NA	promoter-TSS (NM_172422)	promoter-TSS (NM_172422)	-6	NM_029696	76668	Mm.30494	NM_029696	ENSMUSG00000025963	Mdh1b	1700124B08Rik|AV255588	malate dehydrogenase 1B, NAD (soluble)	protein-coding
mm_15385.1	chr2	156613629	156613639	+	1	NA	promoter-TSS (NM_146128)	promoter-TSS (NM_146128)	-63	NM_146128	228836	Mm.22094	NM_146128	ENSMUSG00000061689	Dlgap4	AI225853|BC024558|DAP-4|DAP4|SAPAP-4|Sapap4|WBP16	discs, large homolog-associated protein 4 (Drosophila)	protein-coding
mm_33741.1	chr4	134127536	134127605	+	1	NA	TTS (NM_026257)	TTS (NM_026257)	1183	NM_080559	73723	Mm.22240	NM_080559	ENSMUSG00000028843	Sh3bgrl3	1110004L05Rik|AU022188	SH3 domain binding glutamic acid-rich protein-like 3	protein-coding
mm_81475.1	chr9	109931837	109931853	+	1	NA	promoter-TSS (NM_008633)	promoter-TSS (NM_008633)	71	NM_008633	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_172392.1	chr7	14086782	14086786	-	1	NA	intron (NM_001101586, intron 3 of 5)	L1Md_T|LINE|L1	36209	NM_001101586	629203	Mm.482066	NM_001101586	ENSMUSG00000074375	Sult2a3	EG629203|Gm6955	sulfotransferase family 2A, dehydroepiandrosterone (DHEA)-preferring, member 3	protein-coding
mm_101317.1	chr11	22853196	22853203	-	1	NA	intron (NM_001169114, intron 1 of 1)	intron (NM_001169114, intron 1 of 1)	6536	NM_016888	53625	Mm.395495	NM_016888	ENSMUSG00000051650	B3gnt2	AA408337|AA409404|AW260308|B3Galt6|B3gnt1|BGnT-1|BGnT-2|BGnT1|BGnT2|Beta3gnt	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 2	protein-coding
mm_108488.1	chr12	83671905	83671925	+	1	NA	exon (NM_027349, exon 13 of 19)	exon (NM_027349, exon 13 of 19)	-16648	NM_008943	19164	Mm.998	NM_008943	ENSMUSG00000019969	Psen1	Ad3h|PS-1|PS1|S182	presenilin 1	protein-coding
mm_80406.1	chr9	77636637	77636711	+	1	NA	promoter-TSS (NM_172925)	promoter-TSS (NM_172925)	-58	NM_172925	244923	Mm.138238	NM_172925	ENSMUSG00000044938	Klhl31	9830147P19Rik|D930047P17Rik|Kbtbd1	kelch-like 31	protein-coding
mm_51341.1	chr6	72544412	72544449	+	1	NA	promoter-TSS (NM_007599)	promoter-TSS (NM_007599)	39	NM_007599	12332	Mm.18626	NM_007599	ENSMUSG00000056737	Capg	gCap39|mbh1	capping protein (actin filament), gelsolin-like	protein-coding
mm_22616.1	chr3	14578787	14578807	+	1	NA	5' UTR (NM_007892, exon 1 of 8)	5' UTR (NM_007892, exon 1 of 8)	126	NM_007892	13559	Mm.153415	NM_007892	ENSMUSG00000027552	E2f5	AU024671|E2F-5	E2F transcription factor 5	protein-coding
mm_149877.1	chr19	25236960	25236982	+	1	NA	promoter-TSS (NM_181404)	promoter-TSS (NM_181404)	-231	NM_181404	107351	Mm.260722	NM_181404	ENSMUSG00000032702	Kank1	A930031B09Rik|AU015049|AW121052|Ankrd15|D330024H06Rik|mKIAA0172	KN motif and ankyrin repeat domains 1	protein-coding
mm_168127.1	chr10	23349885	23349885	-	1	NA	promoter-TSS (NM_001347372)	promoter-TSS (NM_001347372)	5	NM_001347372	14051	Mm.332128	NM_010167	ENSMUSG00000010461	Eya4	B130023L16Rik	EYA transcriptional coactivator and phosphatase 4	protein-coding
mm_149854.1	chr19	25081699	25081704	+	1	NA	intron (NM_028785, intron 6 of 47)	B4|SINE|B4	82172	NM_028785	76088	Mm.102485	NM_028785	ENSMUSG00000052085	Dock8	1200017A24Rik|5830472H07Rik|A130095G14Rik|AI461977	dedicator of cytokinesis 8	protein-coding
mm_73727.1	chr8	113572682	113572685	+	1	NA	Intergenic	RLTR6-int|LTR|ERV1	55401	NR_110476	78048	Mm.252797	NR_110476		4930571O06Rik	-	RIKEN cDNA 4930571O06 gene	ncRNA
mm_126807.1	chr15	87632078	87632085	+	1	NA	intron (NM_134096, intron 1 of 3)	intron (NM_134096, intron 1 of 3)	6851	NM_134096	106014	Mm.244319	NM_134096	ENSMUSG00000054863	Fam19a5	TAFA5|Tafa-5|Tara-5	family with sequence similarity 19, member A5	protein-coding
mm_150674.1	chr19	42052241	42052258	+	1	NA	promoter-TSS (NM_025752)	promoter-TSS (NM_025752)	21	NM_025752	66765	Mm.440412	NM_025752	ENSMUSG00000090369	4933411K16Rik	-	RIKEN cDNA 4933411K16 gene	protein-coding
mm_135414.1	chr16	45148569	45148613	-	1	NA	intron (NM_028756, intron 4 of 6)	intron (NM_028756, intron 4 of 6)	10082	NM_028756	74102	Mm.264984	NM_028756	ENSMUSG00000022664	Slc35a5	1010001J06Rik|AU021179|BB097433|D16Ertd450e|D730043G07Rik	solute carrier family 35, member A5	protein-coding
mm_172891.1	chr9	5555631	5555645	-	1	NA	Intergenic	ERVB4_2-LTR_MM|LTR|ERVK	210162	NM_009808	12364	Mm.42163	NM_009808	ENSMUSG00000025887	Casp12	-	caspase 12	protein-coding
mm_9256.1	chr1	171601857	171601913	-	1	NA	exon (NM_001277968, exon 2 of 9)	exon (NM_001277968, exon 2 of 9)	5449	NR_102726	17085	Mm.560	NM_008534	ENSMUSG00000004707	Ly9	AI893573|CD229|Lgp100|Ly-9|SLAMF3|T100	lymphocyte antigen 9	protein-coding
mm_141975.1	chr17	35159154	35159198	-	1	NA	exon (NM_020027, exon 12 of 31)	exon (NM_020027, exon 12 of 31)	5701	NM_001199044	53761	Mm.272462	NM_020027	ENSMUSG00000024393	Prrc2a	3110039B05Rik|Bat-2|Bat2|D17H6S51E|G2|Wbp12|mKIAA4178	proline-rich coiled-coil 2A	protein-coding
mm_76487.1	chr8	85760307	85760315	-	1	NA	intron (NM_028007, intron 10 of 17)	B3|SINE|B2	59406	NR_106189	102465898		NR_106189	ENSMUSG00000098388	Mir8109	Gm27495|mmu-mir-8109	microRNA 8109	ncRNA
mm_142945.1	chr17	56074933	56075036	-	1	NA	promoter-TSS (NM_024432)	promoter-TSS (NM_024432)	5	NM_024432	66530	Mm.28000	NM_024432	ENSMUSG00000019578	Ubxn6	1200008L11Rik|2210415J11Rik|AU040909|Ubxd1|Ubxdc2	UBX domain protein 6	protein-coding
mm_163183.1	chr11	93885825	93885877	+	1	NA	promoter-TSS (NM_134012)	promoter-TSS (NM_134012)	-85	NM_001013375	217109	Mm.379350	NM_001013375	ENSMUSG00000054079	Utp18	6230425C22Rik|6430513M13|Wdr50	UTP18 small subunit processome component	protein-coding
mm_109137.1	chr12	106147865	106147907	+	1	NA	Intergenic	MLT1E3|LTR|ERVL-MaLR	137623	NM_001029843	22367	Mm.2981	NM_011705	ENSMUSG00000021115	Vrk1	51PK	vaccinia related kinase 1	protein-coding
mm_86392.1	chr9	123968397	123968411	-	1	NA	5' UTR (NM_009912, exon 1 of 2)	5' UTR (NM_009912, exon 1 of 2)	288	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_43752.1	chr5	140436250	140436288	+	1	NA	exon (NM_133916, exon 11 of 19)	exon (NM_133916, exon 11 of 19)	8930	NR_106005	102466792		NR_106005	ENSMUSG00000098319	Mir7038	Gm27955|mmu-mir-7038	microRNA 7038	ncRNA
mm_46089.1	chr5	92347015	92347031	-	1	NA	3' UTR (NM_021274, exon 4 of 4)	3' UTR (NM_021274, exon 4 of 4)	1866	NM_021274	15945	Mm.877	NM_021274	ENSMUSG00000034855	Cxcl10	C7|CRG-2|INP10|IP-10|IP10|Ifi10|Scyb10|gIP-10|mob-1	chemokine (C-X-C motif) ligand 10	protein-coding
mm_65169.1	chr7	19681351	19681357	-	1	NA	exon (NM_007385, exon 1 of 3)	exon (NM_007385, exon 1 of 3)	106	NM_007385	11425	Mm.477720	NM_007385	ENSMUSG00000074336	Apoc4	Acl|apo-CIV|apoC-IV	apolipoprotein C-IV	protein-coding
mm_105029.1	chr11	100477087	100477113	-	1	NA	3' UTR (NM_134037, exon 28 of 28)	3' UTR (NM_134037, exon 28 of 28)	1380	NR_130343	102465671		NR_130343	ENSMUSG00000104854	Mir7116	mmu-mir-7116	microRNA 7116	ncRNA
mm_27557.1	chr3	58525743	58525761	-	1	NA	promoter-TSS (NM_001005509)	promoter-TSS (NM_001005509)	-69	NM_001005509	229317	Mm.21617	NM_001005509	ENSMUSG00000027810	Eif2a	D030048D22|D3Ertd194e	eukaryotic translation initiation factor 2A	protein-coding
mm_156719.1	chrX	159708594	159708612	+	1	NA	promoter-TSS (NM_021389)	promoter-TSS (NM_021389)	2	NR_110970	58194	Mm.286495	NM_021389	ENSMUSG00000040990	Sh3kbp1	1200007H22Rik|1700125L08Rik|5830464D22Rik|AI447724|Cin85|IN85|Ruk|Seta	SH3-domain kinase binding protein 1	protein-coding
mm_158285.1	chrX	112314409	112314420	-	1	NA	intron (NM_001313734, intron 1 of 6)	intron (NM_001313734, intron 1 of 6)	3062	NM_026565	68117	Mm.161014	NM_026565	ENSMUSG00000025525	Apool	6720473G16Rik|9430083G14Rik|E130106L15Rik	apolipoprotein O-like	protein-coding
mm_157547.1	chrX	51450259	51450261	-	1	NA	intron (NM_001077202, intron 3 of 4)	intron (NM_001077202, intron 3 of 4)	230217	NM_001290468	50786	Mm.252561	NM_015819	ENSMUSG00000062184	Hs6st2	6OST2	heparan sulfate 6-O-sulfotransferase 2	protein-coding
mm_159034.1	chr1	177248638	177248638	-	1	NA	intron (NM_011785, intron 1 of 12)	intron (NM_011785, intron 1 of 12)	129	NM_011785	23797	Mm.235194	NM_011785	ENSMUSG00000019699	Akt3	AI851531|D930002M15Rik|Nmf350	thymoma viral proto-oncogene 3	protein-coding
mm_104953.1	chr11	100140853	100140875	-	1	NA	TTS (NM_008471)	TTS (NM_008471)	2835	NM_001313963	16669	Mm.439699	NM_008471	ENSMUSG00000020911	Krt19	AI663979|CK-19|EndoC|K19|Krt-1.19|Krt1-19	keratin 19	protein-coding
mm_124530.1	chr14	122372649	122372654	-	1	NA	intron (NM_029556, intron 3 of 7)	intron (NM_029556, intron 3 of 7)	78464	NR_033325	328479	Mm.86095	NR_033325	ENSMUSG00000064052	Gm5089	6530402A20|C030005G22Rik|EG328479	predicted gene 5089	ncRNA
mm_139414.1	chr17	53354467	53354472	+	1	NA	Intergenic	Intergenic	108852	NM_172497	211482	Mm.60887	NM_172497	ENSMUSG00000023931	Efhb	4921525D22Rik	EF hand domain family, member B	protein-coding
mm_35362.1	chr4	32375203	32375213	-	1	NA	Intergenic	Intergenic	-42227	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_131628.1	chr16	20123822	20123838	+	1	NA	3' UTR (NM_029436, exon 8 of 8)	3' UTR (NM_029436, exon 8 of 8)	-17233	NM_001033237	208146	Mm.390895	NM_001033237	ENSMUSG00000041215	Yeats2	BC042768|mKIAA1197	YEATS domain containing 2	protein-coding
mm_164521.1	chr16	97948673	97948689	-	1	NA	3' UTR (NM_001081684, exon 2 of 2)	3' UTR (NM_001081684, exon 2 of 2)	13941	NM_001081685	114565	Mm.474489	NM_175428	ENSMUSG00000046962	Zbtb21	5430437K12Rik|B430213I24Rik|Zfp295|Znf295|mKIAA1227	zinc finger and BTB domain containing 21	protein-coding
mm_53790.1	chr6	146642573	146642596	+	1	NA	promoter-TSS (NM_025315)	promoter-TSS (NM_025315)	5	NM_025315	108098	Mm.26212	NM_025315	ENSMUSG00000030291	Med21	0610007L03Rik|AI449604|D19234|D6Ertd782e|Srb7|Surb7	mediator complex subunit 21	protein-coding
mm_30512.1	chr3	158036567	158036629	-	1	NA	promoter-TSS (NM_001289525)	promoter-TSS (NM_001289525)	41	NM_001093752	69207	Mm.223946	NM_026989	ENSMUSG00000055436	Srsf11	0610009J05Rik|2610019N13Rik|BF642805|Sfrs11	serine/arginine-rich splicing factor 11	protein-coding
mm_44563.1	chr5	24623473	24623483	-	1	NA	Intergenic	Intergenic	-21476	NM_025891	66993	Mm.436539	NM_025891	ENSMUSG00000028949	Smarcd3	1500001J14Rik|2210409C08Rik|BAF60C	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3	protein-coding
mm_62551.1	chr7	102441832	102441888	+	1	NA	5' UTR (NM_009103, exon 1 of 19)	5' UTR (NM_009103, exon 1 of 19)	165	NM_009103	20133	Mm.197486	NM_009103	ENSMUSG00000030978	Rrm1	RnrM1	ribonucleotide reductase M1	protein-coding
mm_5001.1	chr1	191928589	191928611	+	1	NA	Intergenic	Intergenic	-21073	NR_030669	98736	Mm.379232	NM_001024489	ENSMUSG00000055833	1700034H15Rik	4930557M11Rik|BB016121	RIKEN cDNA 1700034H15 gene	ncRNA
mm_48474.1	chr5	140995575	140995582	-	1	NA	intron (NM_175362, intron 1 of 24)	intron (NM_175362, intron 1 of 24)	5018	NM_175362	108723	Mm.46187	NM_175362	ENSMUSG00000036526	Card11	0610008L17Rik|2410011D02Rik|BIMP3|CARMA1	caspase recruitment domain family, member 11	protein-coding
mm_86985.1	chr10	25473078	25473082	+	1	NA	exon (NM_013511, exon 8 of 20)	exon (NM_013511, exon 8 of 20)	63192	NM_001195596	100504474	Mm.46323	NM_001195596	ENSMUSG00000096546	Smlr1	2010003K15Rik	small leucine-rich protein 1	protein-coding
mm_1677.1	chr1	74817042	74817064	+	1	NA	Intergenic	CpG	25034	NM_009518	22409	Mm.5130	NM_009518	ENSMUSG00000026167	Wnt10a	-	wingless-type MMTV integration site family, member 10A	protein-coding
mm_104985.1	chr11	100265895	100265907	-	1	NA	intron (NM_212483, intron 3 of 7)	intron (NM_212483, intron 3 of 7)	3970	NM_212483	68239	Mm.158190	NM_212483	ENSMUSG00000053654	Krt42	2410039E07Rik|K17n|Ka22|ecat6	keratin 42	protein-coding
mm_125951.1	chr15	76248977	76248988	+	1	NA	TTS (NR_105918)	TTS (NR_105918)	791	NR_105918	102465575		NR_105918	ENSMUSG00000098625	Mir6953	Gm27738|mmu-mir-6953	microRNA 6953	ncRNA
mm_84148.1	chr9	59469115	59469118	-	1	NA	intron (NM_019927, intron 1 of 13)	RMER5|LTR|ERV1	12625	NR_045640	100504377	Mm.446631	NR_045640		Gm20199	-	predicted gene, 20199	ncRNA
mm_125313.1	chr15	38087984	38087988	+	1	NA	Intergenic	Intergenic	-9132	NM_001081359	70790	Mm.476840	NM_027553	ENSMUSG00000037487	Ubr5	Edd|Edd1	ubiquitin protein ligase E3 component n-recognin 5	protein-coding
mm_15633.1	chr2	162987548	162987560	+	1	NA	promoter-TSS (NM_013731)	promoter-TSS (NM_013731)	73	NM_013731	27219	Mm.26462	NM_013731	ENSMUSG00000017868	Sgk2	AI098171|AW146006|Sgkl	serum/glucocorticoid regulated kinase 2	protein-coding
mm_50580.1	chr6	49055611	49055635	+	1	NA	exon (NM_053110, exon 10 of 11)	exon (NM_053110, exon 10 of 11)	-18172	NM_029353	75593	Mm.439947	NM_029353	ENSMUSG00000029815	Malsu1	2410003K15Rik|Matsu1	mitochondrial assembly of ribosomal large subunit 1	protein-coding
mm_40183.1	chr5	36204048	36204063	+	1	NA	promoter-TSS (NM_175249)	promoter-TSS (NM_175249)	34	NM_175249	76943	Mm.44242	NM_175249	ENSMUSG00000043430	Psapl1	2310020A21Rik	prosaposin-like 1	protein-coding
mm_61417.1	chr7	73608938	73608974	+	1	NA	Intergenic	Intergenic	-50561	NR_037569	69170	Mm.34539	NR_037569	ENSMUSG00000101970	1810026B05Rik	-	RIKEN cDNA 1810026B05 gene	ncRNA
mm_91570.1	chr10	40098888	40098905	-	1	NA	intron (NM_001114332, intron 1 of 5)	L1M4|LINE|L1	43358	NM_028247	72472	Mm.186778	NM_028247	ENSMUSG00000019838	Slc16a10	2610103N14Rik|9830169E08|Mct10|PRO0813|TAT1	solute carrier family 16 (monocarboxylic acid transporters), member 10	protein-coding
mm_77765.1	chr9	3002961	3002984	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	35771	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_27116.1	chr3	31079628	31079661	-	1	NA	Intergenic	Intergenic	-15414	NM_011386	20482	Mm.15406	NM_011386	ENSMUSG00000027660	Skil	Skir|SnoN|sno	SKI-like	protein-coding
mm_90276.1	chr10	122802201	122802221	+	1	NA	intron (NM_176919, intron 2 of 8)	intron (NM_176919, intron 2 of 8)	122896	NR_106182	102466884		NR_106182	ENSMUSG00000099225	Mir8104	Gm27380|mmu-mir-8104	microRNA 8104	ncRNA
mm_145105.1	chr18	44104511	44104546	+	1	NA	promoter-TSS (NM_030061)	promoter-TSS (NM_030061)	5	NM_030061	78242	Mm.99782	NM_030061	ENSMUSG00000061144	Spink12	9230117E20Rik	serine peptidase inhibitor, Kazal type 12	protein-coding
mm_38528.1	chr4	141538563	141538626	-	1	NA	promoter-TSS (NM_019763)	promoter-TSS (NM_019763)	3	NM_001347235	56381	Mm.299906	NM_019763	ENSMUSG00000040761	Spen	Mint|mKIAA0929	SPEN homolog, transcriptional regulator (Drosophila)	protein-coding
mm_133052.1	chr16	57572271	57572297	+	1	NA	exon (NM_001040397, exon 5 of 5)	exon (NM_001040397, exon 5 of 5)	23042	NM_001177871	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding
mm_111349.1	chr12	86947329	86947335	-	1	NA	promoter-TSS (NM_173735)	promoter-TSS (NM_173735)	-11	NM_173735	217732	Mm.22337	NM_173735	ENSMUSG00000034157	Cipc	2310044G17Rik|AI842544|AI853744|Kiaa1737|mKIAA1737	CLOCK interacting protein, circadian	protein-coding
mm_20425.1	chr2	129304765	129304776	-	1	NA	exon (NM_010554, exon 5 of 7)	exon (NM_010554, exon 5 of 7)	5202	NM_010554	16175	Mm.15534	NM_010554	ENSMUSG00000027399	Il1a	Il-1a	interleukin 1 alpha	protein-coding
mm_18692.1	chr2	71537892	71537907	-	1	NA	promoter-TSS (NR_002854)	promoter-TSS (NR_002854)	-8	NR_002854	111970	Mm.4543	NR_002854		Dlx1as	Dix1as|Dlx1os	distal-less homeobox 1, antisense	ncRNA
mm_160804.1	chr11	6606020	6606020	-	1	NA	promoter-TSS (NM_001081652)	promoter-TSS (NM_001081652)	34	NM_001081652	192950	Mm.337771	NM_001081652	ENSMUSG00000041073	Nacad	D230024G13Rik|mKIAA0363	NAC alpha domain containing	protein-coding
mm_89157.1	chr10	86033058	86033068	+	1	NA	intron (NM_001347151, intron 4 of 8)	intron (NM_001347151, intron 4 of 8)	10909	NM_001347151	69754	Mm.44236	NM_153195	ENSMUSG00000001786	Fbxo7	2410015K21Rik|A230052G17Rik|AI117679|AW260462|C85118	F-box protein 7	protein-coding
mm_45904.1	chr5	88739772	88739774	-	1	NA	intron (NM_026735, intron 1 of 5)	intron (NM_026735, intron 1 of 5)	18902	NM_026735	68473	Mm.35764	NM_026735	ENSMUSG00000006262	Mob1b	1110003E08Rik|AU015450|B230364F10|Mobkl1a	MOB kinase activator 1B	protein-coding
mm_84641.1	chr9	71168688	71168698	-	1	NA	promoter-TSS (NR_110517)	promoter-TSS (NR_110517)	-83	NR_110517	102635087	Mm.444536	NR_110517	ENSMUSG00000111429	Gm32511	-	predicted gene, 32511	ncRNA
mm_65949.1	chr7	30420353	30420362	-	1	NA	promoter-TSS (NM_011827)	promoter-TSS (NM_011827)	-503	NM_011827	23900	Mm.379050	NM_011827	ENSMUSG00000064109	Hcst	DAP10|KAP10	hematopoietic cell signal transducer	protein-coding
mm_148420.1	chr19	3936355	3936391	+	1	NA	exon (NM_019449, exon 3 of 11)	exon (NM_019449, exon 3 of 11)	1187	NM_001161428	54445	Mm.262094	NM_019449	ENSMUSG00000036908	Unc93b1	Unc-93B1|Unc93b	unc-93 homolog B1 (C. elegans)	protein-coding
mm_80149.1	chr9	70927129	70927130	+	1	NA	intron (NM_001324473, intron 1 of 8)	intron (NM_001324473, intron 1 of 8)	7679	NM_008280	15450	Mm.390187	NM_008280	ENSMUSG00000032207	Lipc	AI256194|HL|Hpl	lipase, hepatic	protein-coding
mm_50749.1	chr6	52903792	52903828	+	1	NA	intron (NM_173406, intron 1 of 4)	intron (NM_173406, intron 1 of 4)	5810	NM_001168277	231986	Mm.386865	NM_173406	ENSMUSG00000063568	Jazf1	AI591476|C820002C15|Jaz1|Tip27	JAZF zinc finger 1	protein-coding
mm_31115.1	chr4	42950370	42950445	+	1	NA	Intergenic	Intergenic	-2687	NM_019874	56323	Mm.20437	NM_019874	ENSMUSG00000036052	Dnajb5	1110058L06Rik|AI462558|Hsc40|Hsp40-3	DnaJ heat shock protein family (Hsp40) member B5	protein-coding
mm_154035.1	chr19	53528896	53528909	-	1	NA	promoter-TSS (NM_001085390)	promoter-TSS (NM_001085390)	-416	NM_001085390	240672	Mm.482424	NM_001085390	ENSMUSG00000034765	Dusp5	Gm337	dual specificity phosphatase 5	protein-coding
mm_55032.1	chr6	48951511	48951527	-	1	NA	Intergenic	Lx8b|LINE|L1	21623	NM_001081273	69761	Mm.333053	NM_001081273	ENSMUSG00000029813	1600015I10Rik	AI429442|Doxl1	RIKEN cDNA 1600015I10 gene	protein-coding
mm_68682.1	chr7	118995213	118995219	-	1	NA	promoter-TSS (NM_001195774)	promoter-TSS (NM_001195774)	-5	NM_001195774	64297	Mm.103439	NM_022420	ENSMUSG00000008734	Gprc5b	AW125761|Raig2	G protein-coupled receptor, family C, group 5, member B	protein-coding
mm_89345.1	chr10	88091071	88091076	+	1	NA	promoter-TSS (NM_029971)	promoter-TSS (NM_029971)	1	NM_029971	110312	Mm.391436	NM_029971	ENSMUSG00000035383	Pmch	A230109K23Rik	pro-melanin-concentrating hormone	protein-coding
mm_169297.1	chr14	100314415	100314417	+	1	NA	Intergenic	Intergenic	-164620	NM_010636	16597	Mm.396499	NM_010636	ENSMUSG00000072294	Klf12	2700063E05Rik|AI225908|AI315654|AP-2rep|B130052C06Rik|D530033K05Rik	Kruppel-like factor 12	protein-coding
mm_74923.1	chr8	25597001	25597038	-	1	NA	intron (NM_173012, intron 1 of 10)	CpG	468	NM_173012	270035	Mm.268349	NM_173012	ENSMUSG00000037363	Letm2	6030453H13|D030041N04Rik	leucine zipper-EF-hand containing transmembrane protein 2	protein-coding
mm_172019.1	chr6	114765596	114765596	-	1	NA	intron (NM_001253718, intron 18 of 19)	L1Md_A|LINE|L1	122499	NM_001253717	74244	Mm.275332	NM_028835	ENSMUSG00000030314	Atg7	1810013K23Rik|Agp7|Apg7l|Atg7l|Gm21553	autophagy related 7	protein-coding
mm_128821.1	chr15	67128921	67128929	-	1	NA	intron (NM_009177, intron 2 of 8)	intron (NM_009177, intron 2 of 8)	47957	NM_009177	20442	Mm.248334	NM_009177	ENSMUSG00000013846	St3gal1	5330418N22Rik|AI467004|ST3GalI|Siat4|Siat4a|St3gal-1	ST3 beta-galactoside alpha-2,3-sialyltransferase 1	protein-coding
mm_4526.1	chr1	175632121	175632133	+	1	NA	promoter-TSS (NM_133809)	promoter-TSS (NM_133809)	-66	NM_133809	98256	Mm.27217	NM_133809	ENSMUSG00000039783	Kmo	AI046660	kynurenine 3-monooxygenase (kynurenine 3-hydroxylase)	protein-coding
mm_171287.1	chr3	90079665	90079665	+	1	NA	5' UTR (NM_001253740, exon 1 of 8)	5' UTR (NM_001253740, exon 1 of 8)	144	NM_001293749	59069	Mm.240839	NM_022314	ENSMUSG00000027940	Tpm3	TM30nm|TMnm|Tm5NM|Tpm-5|Tpm5|Trop-5|gamma-TM|hTM30nm|hTMnm	tropomyosin 3, gamma	protein-coding
mm_149617.1	chr19	16436196	16436209	+	1	NA	5' UTR (NM_008137, exon 1 of 7)	5' UTR (NM_008137, exon 1 of 7)	535	NM_008137	14675	Mm.313181	NM_008137	ENSMUSG00000024697	Gna14	AU023208	guanine nucleotide binding protein, alpha 14	protein-coding
mm_3872.1	chr1	160989650	160989682	+	1	NA	exon (NM_080844, exon 3 of 8)	exon (NM_080844, exon 3 of 8)	11060	NM_080844	11905	Mm.260770	NM_080844	ENSMUSG00000026715	Serpinc1	AI114908|ATIII|At-3|At3	serine (or cysteine) peptidase inhibitor, clade C (antithrombin), member 1	protein-coding
mm_113848.1	chr13	47201636	47201646	+	1	NA	intron (NM_001170643, intron 1 of 7)	intron (NM_001170643, intron 1 of 7)	7638	NM_001170643	218215	Mm.287609	NM_146042	ENSMUSG00000038068	Rnf144b	BC025007|E130105P19Rik|Ibrdc2|Pir2	ring finger protein 144B	protein-coding
mm_129037.1	chr15	74996493	74996529	-	1	NA	exon (NM_001271446, exon 3 of 4)	exon (NM_001271446, exon 3 of 4)	1520	NM_001271417	110454	Mm.425949	NM_010738	ENSMUSG00000075602	Ly6a	Ly-6A.2|Ly-6A/E|Ly-6E.1|Sca-1|Sca1|TAP	lymphocyte antigen 6 complex, locus A	protein-coding
mm_56584.1	chr6	106794618	106794636	-	1	NA	intron (NM_175357, intron 3 of 10)	intron (NM_175357, intron 3 of 10)	5460	NM_021449	58799	Mm.290085	NM_021449	ENSMUSG00000005362	Crbn	2610203G15Rik|2900045O07Rik|AF229032|AW108261|piL	cereblon	protein-coding
mm_136727.1	chr17	8245040	8245050	+	1	NA	promoter-TSS (NM_001190338)	promoter-TSS (NM_001190338)	-13	NM_001190338	12458	Mm.8007	NM_009835	ENSMUSG00000040899	Ccr6	CC-CKR-6|CCR-6|Cmkbr6|KY411	chemokine (C-C motif) receptor 6	protein-coding
mm_8795.1	chr1	161788473	161788483	-	1	NA	promoter-TSS (NM_001205243)	promoter-TSS (NM_001205243)	17	NM_001205243	14103	Mm.3355	NM_010177	ENSMUSG00000000817	Fasl	APT1LG1|CD178|CD95-L|CD95L|Fas-L|Faslg|Tnfsf6|Tnlg1a|gld	Fas ligand (TNF superfamily, member 6)	protein-coding
mm_1409.1	chr1	67154284	67154299	+	1	NA	intron (NM_001080809, intron 7 of 37)	intron (NM_001080809, intron 7 of 37)	31264	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_90284.1	chr10	122986575	122986588	+	1	NA	promoter-TSS (NR_029527)	promoter-TSS (NR_029527)	-857	NR_029527	387251		NR_029527	ENSMUSG00000065406	Mirlet7i	Mirnlet7i|let-7i|mmu-let-7i	microRNA let7i	ncRNA
mm_146885.1	chr18	25753487	25753498	-	1	NA	exon (NM_001146295, exon 1 of 2)	exon (NM_001146295, exon 1 of 2)	491	NM_133195	108013	Mm.266435	NM_133195	ENSMUSG00000024268	Celf4	A230070D14Rik|BRUNOL-4|Brul4|Brunol4|C130060B05Rik	CUGBP, Elav-like family member 4	protein-coding
mm_74083.1	chr8	122546483	122546501	+	1	NA	intron (NM_001037298, intron 1 of 50)	intron (NM_001037298, intron 1 of 50)	4837	NM_001037298	234839	Mm.37324	NM_001037298	ENSMUSG00000014444	Piezo1	9630020g22|Fam38a|mKIAA0233	piezo-type mechanosensitive ion channel component 1	protein-coding
mm_99208.1	chr11	101023069	101023081	+	1	NA	intron (NM_001243050, intron 5 of 20)	ID_B1|SINE|B4	-7265	NR_105893	102466767		NR_105893	ENSMUSG00000098415	Mir6928	Gm27728|mmu-mir-6928	microRNA 6928	ncRNA
mm_96068.1	chr11	59750160	59750187	+	1	NA	intron (NM_012027, intron 13 of 23)	intron (NM_012027, intron 13 of 23)	-10019	NR_045476	69320	Mm.443242	NR_045476	ENSMUSG00000086330	1700007J10Rik	4930573L17Rik	RIKEN cDNA 1700007J10 gene	ncRNA
mm_34304.1	chr4	141757348	141757395	+	1	NA	intron (NM_001081408, intron 4 of 6)	intron (NM_001081408, intron 4 of 6)	10696	NM_001081408	75986	Mm.30032	NM_001081408	ENSMUSG00000040706	Agmat	5033405N08Rik	agmatine ureohydrolase (agmatinase)	protein-coding
mm_83013.1	chr9	36780037	36780055	-	1	NA	3' UTR (NM_001199494, exon 11 of 11)	3' UTR (NM_001199494, exon 11 of 11)	-12468	NM_008408	16430	Mm.2863	NM_008408	ENSMUSG00000032116	Stt3a	AA408947|BB081708|Itm1	STT3, subunit of the oligosaccharyltransferase complex, homolog A (S. cerevisiae)	protein-coding
mm_36408.1	chr4	78043812	78043820	-	1	NA	intron (NM_011211, intron 1 of 39)	intron (NM_011211, intron 1 of 39)	168079	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding
mm_69274.1	chr7	127946489	127946502	-	1	NA	5' UTR (NM_001319147, exon 1 of 15)	5' UTR (NM_001319147, exon 1 of 15)	230	NM_001319147	77613	Mm.334253	NM_001081374	ENSMUSG00000070371	Prss36	C330007D15Rik	protease, serine 36	protein-coding
mm_39429.1	chr5	16553541	16553588	+	1	NA	promoter-TSS (NM_010427)	promoter-TSS (NM_010427)	69	NM_010427	15234	Mm.267078	NM_010427	ENSMUSG00000028864	Hgf	C230052L06Rik|HGF/SF|NK1|NK2|SF|SF/HGF	hepatocyte growth factor	protein-coding
mm_51295.1	chr6	72306782	72306790	+	1	NA	intron (NM_147779, intron 4 of 11)	intron (NM_147779, intron 4 of 11)	2176	NM_147779	20388	Mm.46033	NM_147779	ENSMUSG00000056370	Sftpb	AI562151|SF-B|SP-B|Sftp-3|Sftp3	surfactant associated protein B	protein-coding
mm_135360.1	chr16	43979749	43979825	-	1	NA	promoter-TSS (NM_001007460)	promoter-TSS (NM_001007460)	-737	NM_001007460	332175	Mm.327852	NM_001007460	ENSMUSG00000036304	Zdhhc23	Gm1751|Gm779|nidd	zinc finger, DHHC domain containing 23	protein-coding
mm_8716.1	chr1	159030960	159030969	-	1	NA	Intergenic	Intergenic	-73526	NM_001085376	23850	Mm.458621	NM_001085376	ENSMUSG00000073530	Pappa2	PAPP-A2|PLAC3|Pappe	pappalysin 2	protein-coding
mm_78904.1	chr9	44772952	44772964	+	1	NA	promoter-TSS (NM_023831)	promoter-TSS (NM_023831)	-51	NM_023831	76568	Mm.278597	NM_023831	ENSMUSG00000002031	Ift46	1500035H01Rik|AA408110|AI663846|R75047|c11orf2	intraflagellar transport 46	protein-coding
mm_34982.1	chr4	156016800	156016804	+	1	NA	TTS (NM_011659)	TTS (NM_011659)	3107	NM_011659	22163	Mm.13885	NM_011659	ENSMUSG00000029075	Tnfrsf4	ACT35|CD134|Ly-70|Ox40|TXGP1L|Txgp1	tumor necrosis factor receptor superfamily, member 4	protein-coding
mm_170469.1	chr1	90623169	90623176	-	1	NA	Intergenic	LTRIS2|LTR|ERV1	19747	NM_133805	108679	Mm.119177	NM_133805	ENSMUSG00000034432	Cops8	9430009J09Rik|AA408242|Csn8|Sgn8	COP9 signalosome subunit 8	protein-coding
mm_17591.1	chr2	30594902	30594917	-	1	NA	promoter-TSS (NM_030137)	promoter-TSS (NM_030137)	-135	NM_030137	78617	Mm.40413	NM_030137	ENSMUSG00000047363	Cstad	9530039B02Rik	CSA-conditional, T cell activation-dependent protein	protein-coding
mm_37542.1	chr4	125122540	125122563	-	1	NA	intron (NM_153159, intron 2 of 5)	intron (NM_153159, intron 2 of 5)	5330	NM_153159	230738	Mm.402	NM_153159	ENSMUSG00000042677	Zc3h12a	BC036563|MCPIP|MCPIP-1|Mcpip1|Reg1	zinc finger CCCH type containing 12A	protein-coding
mm_93760.1	chr10	120193381	120193396	-	1	NA	intron (NM_028679, intron 1 of 11)	intron (NM_028679, intron 1 of 11)	8149	NM_028679	73914	Mm.146194	NM_028679	ENSMUSG00000020227	Irak3	4833428C18Rik|AI563835|IRAK-M	interleukin-1 receptor-associated kinase 3	protein-coding
mm_155332.1	chrX	66025486	66025496	+	1	NA	Intergenic	Intergenic	-623827	NM_001161431	245450	Mm.336081	NM_198863	ENSMUSG00000036790	Slitrk2	A930040J07	SLIT and NTRK-like family, member 2	protein-coding
mm_44548.1	chr5	24598635	24598654	-	1	NA	exon (NM_025891, exon 2 of 13)	exon (NM_025891, exon 2 of 13)	3358	NM_025891	66993	Mm.436539	NM_025891	ENSMUSG00000028949	Smarcd3	1500001J14Rik|2210409C08Rik|BAF60C	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3	protein-coding
mm_24715.1	chr3	95228837	95228847	+	1	NA	promoter-TSS (NM_019914)	promoter-TSS (NM_019914)	-101	NM_001038708	57912	Mm.28189	NM_172395	ENSMUSG00000046722	Cdc42se1	1300002M12Rik|AW558204|Cdcse1|SCIP1|Spec1	CDC42 small effector 1	protein-coding
mm_3131.1	chr1	134987787	134987797	+	1	NA	exon (NM_001033409, exon 18 of 18)	exon (NM_001033409, exon 18 of 18)	25227	NM_001278115	67196	Mm.284587	NM_026024	ENSMUSG00000026429	Ube2t	2700084L22Rik|C80607	ubiquitin-conjugating enzyme E2T	protein-coding
mm_110713.1	chr12	69402843	69402847	-	1	NA	Intergenic	MERV1_LTR|LTR|ERV1	30695	NM_007481	11845	Mm.27308	NM_007481	ENSMUSG00000044147	Arf6	AI788669|AW496366	ADP-ribosylation factor 6	protein-coding
mm_24737.1	chr3	95283264	95283294	+	1	NA	5' UTR (NM_133858, exon 1 of 10)	5' UTR (NM_133858, exon 1 of 10)	344	NM_199475	75007	Mm.279287	NM_133858	ENSMUSG00000038712	Fam63a	1810005H09Rik|4930504E06Rik|AA562754|AA960384|AW561904|cI-40|mKIAA1390|ni	family with sequence similarity 63, member A	protein-coding
mm_151456.1	chr19	58119826	58119828	+	1	NA	intron (NM_181415, intron 28 of 28)	intron (NM_181415, intron 28 of 28)	68660	NR_049196	100885835		NR_049196	ENSMUSG00000093757	Mir5623	Gm26068|mir-5623|mmu-mir-5623	microRNA 5623	ncRNA
mm_84152.1	chr9	59486582	59486590	-	1	NA	promoter-TSS (NM_019927)	promoter-TSS (NM_019927)	-212	NM_019927	23806	Mm.305925	NM_019927	ENSMUSG00000025234	Arih1	AU021774|Ari|Ari1|Hari|Hhari|Ubch7bp|Uip77	ariadne RBR E3 ubiquitin protein ligase 1	protein-coding
mm_159984.1	chr6	113697897	113697897	+	1	NA	exon (NM_001347356, exon 2 of 8)	exon (NM_001347356, exon 2 of 8)	847	NM_001033463	381801	Mm.333322	NM_001033463	ENSMUSG00000056952	Tatdn2	AI646012|mKIAA0218	TatD DNase domain containing 2	protein-coding
mm_38620.1	chr4	142015077	142015114	-	1	NA	Intergenic	Intergenic	-2803	NR_131014	78917	Mm.139995	NR_131014	ENSMUSG00000085761	4930455G09Rik	-	RIKEN cDNA 4930455G09 gene	ncRNA
mm_116412.1	chr13	41486999	41487031	-	1	NA	intron (NM_001111324, intron 1 of 7)	intron (NM_001111324, intron 1 of 7)	345	NM_001111324	18003	Mm.288980	NM_017464	ENSMUSG00000021365	Nedd9	Cas-L|CasL|HEF1|MEF1|Nedd-9|p105	neural precursor cell expressed, developmentally down-regulated gene 9	protein-coding
mm_1179.1	chr1	61638943	61638955	+	1	NA	5' UTR (NM_001081050, exon 1 of 23)	5' UTR (NM_001081050, exon 1 of 23)	125	NM_001081050	72823	Mm.35153	NM_001081050	ENSMUSG00000052062	Pard3b	1810008K04Rik|2010002N16Rik|2810455B10Rik|Als2cr19|PAR3B|PAR3L|PAR3beta	par-3 family cell polarity regulator beta	protein-coding
mm_166380.1	chr5	130224164	130224169	+	1	NA	intron (NM_027854, intron 1 of 6)	B3|SINE|B2	1831	NM_027854	71667	Mm.258508	NM_027854	ENSMUSG00000053094	Tmem248	0610007L01Rik|A930023A16Rik|AW557951|G430067H08Rik	transmembrane protein 248	protein-coding
mm_149485.1	chr19	11810636	11810650	+	1	NA	intron (NM_001025307, intron 1 of 10)	intron (NM_001025307, intron 1 of 10)	8760	NM_001286543	20908	Mm.272264	NM_011502	ENSMUSG00000041488	Stx3	Syn-3	syntaxin 3	protein-coding
mm_28361.1	chr3	89870202	89870211	-	1	NA	3' UTR (NM_010559, exon 10 of 10)	3' UTR (NM_010559, exon 10 of 10)	38836	NM_172530	214547	Mm.225	NM_172530	ENSMUSG00000046280	She	9430022A14	src homology 2 domain-containing transforming protein E	protein-coding
mm_165856.1	chr4	19122634	19122642	+	1	NA	Intergenic	Intergenic	-158212	NM_013927	30952	Mm.445778	NM_013927	ENSMUSG00000056494	Cngb3	CCNC2|CNG6|Cngbeta2	cyclic nucleotide gated channel beta 3	protein-coding
mm_1803.1	chr1	80757691	80757707	+	1	NA	intron (NM_175291, intron 1 of 55)	intron (NM_175291, intron 1 of 55)	854	NM_175291	210293	Mm.133473	NM_175291	ENSMUSG00000038608	Dock10	9330153B10Rik|A630054M16Rik|Jr4|Jr5|R75174|ZIZ3|Zizimin3|mKIAA0694	dedicator of cytokinesis 10	protein-coding
mm_44904.1	chr5	35652654	35652679	-	1	NA	3' UTR (NM_030127, exon 9 of 9)	3' UTR (NM_030127, exon 9 of 9)	27114	NM_001042615	78558	Mm.274255	NM_030127	ENSMUSG00000029096	Htra3	2210021K23Rik|9530081K03Rik|Prsp|Tasp	HtrA serine peptidase 3	protein-coding
mm_81092.1	chr9	106368595	106368640	+	1	NA	promoter-TSS (NM_153459)	promoter-TSS (NM_153459)	-15	NM_153459	235584	Mm.275584	NM_153459	ENSMUSG00000053716	Dusp7	AU015694|Mkpx|Pyst2	dual specificity phosphatase 7	protein-coding
mm_32311.1	chr4	103313828	103313856	+	1	NA	promoter-TSS (NM_025909)	promoter-TSS (NM_025909)	-4	NM_025909	67013	Mm.30021	NM_025909	ENSMUSG00000035069	Oma1	2010001O09Rik|MPRP-1|ZMPOMA1	OMA1 zinc metallopeptidase	protein-coding
mm_9136.1	chr1	170857495	170857513	-	1	NA	intron (NM_001081304, intron 1 of 15)	intron (NM_001081304, intron 1 of 15)	10267	NM_001081304	226641	Mm.377046	NM_001081304	ENSMUSG00000026663	Atf6	9130025P16Rik|9630036G24|AA789574|Atf6alpha|ESTM49	activating transcription factor 6	protein-coding
mm_14892.1	chr2	149283604	149283607	+	1	NA	Intergenic	ERVB4_3-LTR_MM|LTR|ERVK	-121644	NM_021405	58214	Mm.117117	NM_021405	ENSMUSG00000033156	Cst10	DD72	cystatin 10 (chondrocytes)	protein-coding
mm_133453.1	chr16	88828986	88829000	+	1	NA	promoter-TSS (NM_013713)	promoter-TSS (NM_013713)	-16	NM_013713	26560	Mm.86430	NM_013713	ENSMUSG00000022931	Krtap15	Krtap15-1|Pmg-2|Pmg2	keratin associated protein 15	protein-coding
mm_4042.1	chr1	165774613	165774623	+	1	NA	3' UTR (NM_011804, exon 4 of 4)	3' UTR (NM_011804, exon 4 of 4)	10838	NM_011804	433375	Mm.294885	NM_011804	ENSMUSG00000040713	Creg1	AA755314|Creg	cellular repressor of E1A-stimulated genes 1	protein-coding
mm_147238.1	chr18	38284392	38284408	-	1	NA	promoter-TSS (NM_017378)	promoter-TSS (NM_017378)	1	NM_017378	53601	Mm.12862	NM_017378	ENSMUSG00000024440	Pcdh12	Pcdh14|VE-cad-2	protocadherin 12	protein-coding
mm_62595.1	chr7	105648204	105648206	+	1	NA	Intergenic	Intergenic	7665	NM_019502	14356	Mm.220330	NM_019502	ENSMUSG00000089847	Timm10b	Fxc1|Tim10b|Tim9b	translocase of inner mitochondrial membrane 10B	protein-coding
mm_36335.1	chr4	72198309	72198319	-	1	NA	intron (NM_001285530, intron 2 of 17)	intron (NM_001285530, intron 2 of 17)	2579	NM_011599	21885	Mm.278444	NM_011599	ENSMUSG00000008305	Tle1	C230057C06Rik|Estm14|Grg-1|Grg1|Tle4l	transducin-like enhancer of split 1	protein-coding
mm_55269.1	chr6	53820765	53820837	-	1	NA	promoter-TSS (NM_025817)	promoter-TSS (NM_025817)	24	NM_025817	66873	Mm.422727	NM_025817	ENSMUSG00000043496	Tril	1200009O22Rik|AI316813|mKIAA0644	TLR4 interactor with leucine-rich repeats	protein-coding
mm_4420.1	chr1	172500266	172500288	+	1	NA	promoter-TSS (NM_178598)	promoter-TSS (NM_178598)	31	NM_178598	21346	Mm.271711	NM_178598	ENSMUSG00000026547	Tagln2	2700094C18Rik|SM22beta|Sm22B|Sm22a	transgelin 2	protein-coding
mm_99615.1	chr11	104607777	104607812	+	1	NA	promoter-TSS (NM_016780)	promoter-TSS (NM_016780)	-206	NM_016780	16416	Mm.87150	NM_016780	ENSMUSG00000020689	Itgb3	CD61|GP3A|INGRB3	integrin beta 3	protein-coding
mm_136208.1	chr16	89833213	89833215	-	1	NA	exon (NM_001145886, exon 15 of 28)	exon (NM_001145886, exon 15 of 28)	-14862	NM_001145887	21844	Mm.310902	NM_009384	ENSMUSG00000002489	Tiam1	AI847750|D16Ium10|D16Ium10e	T cell lymphoma invasion and metastasis 1	protein-coding
mm_154102.1	chr19	57045085	57045086	-	1	NA	intron (NM_001290813, intron 14 of 20)	intron (NM_001290813, intron 14 of 20)	-36510	NM_001177797	226250	Mm.226284	NM_146102	ENSMUSG00000025083	Afap1l2	AU041783|C86904|mKIAA1914	actin filament associated protein 1-like 2	protein-coding
mm_85802.1	chr9	110117536	110117544	-	1	NA	promoter-TSS (NM_001252682)	promoter-TSS (NM_001252682)	76	NM_001252682	72831	Mm.276305	NM_133347	ENSMUSG00000032480	Dhx30	2810477H02Rik|C130058C04Rik|Ddx30|HELG|Ret-CoR	DEAH (Asp-Glu-Ala-His) box polypeptide 30	protein-coding
mm_148398.1	chr19	3769105	3769112	+	1	NA	intron (NM_001167887, intron 2 of 11)	intron (NM_001167887, intron 2 of 11)	1687	NM_001167885	225888	Mm.278578	NM_144871	ENSMUSG00000045098	Kmt5b	AA117471|C630029K18Rik|Suv4-20h1|Suv420h1	lysine methyltransferase 5B	protein-coding
mm_35274.1	chr4	19920770	19920774	-	1	NA	intron (NM_175406, intron 1 of 7)	intron (NM_175406, intron 1 of 7)	1794	NM_175406	242341	Mm.19298	NM_175406	ENSMUSG00000028238	Atp6v0d2	1620401A02Rik|AI324824|V-ATPase	ATPase, H+ transporting, lysosomal V0 subunit D2	protein-coding
mm_67598.1	chr7	83735427	83735436	-	1	NA	promoter-TSS (NM_010551)	promoter-TSS (NM_010551)	59	NM_010551	16170	Mm.10137	NM_010551	ENSMUSG00000001741	Il16	mKIAA4048	interleukin 16	protein-coding
mm_20958.1	chr2	151744143	151744205	-	1	NA	Intergenic	Intergenic	-2864	NM_001305244	228769	Mm.146984	NM_144889	ENSMUSG00000032869	Psmf1	AW048666|BC012260|PI31	proteasome (prosome, macropain) inhibitor subunit 1	protein-coding
mm_89207.1	chr10	86696790	86696808	+	1	NA	exon (NM_011631, exon 8 of 18)	exon (NM_011631, exon 8 of 18)	8645	NM_011631	22027	Mm.87773	NM_011631	ENSMUSG00000020048	Hsp90b1	ERp99|GRP94|TA-3|Targ2|Tra-1|Tra1|endoplasmin|gp96	heat shock protein 90, beta (Grp94), member 1	protein-coding
mm_130053.1	chr15	89169605	89169627	-	1	NA	intron (NM_138749, intron 3 of 37)	intron (NM_138749, intron 3 of 37)	4335	NM_001159521	140570	Mm.267514	NM_138749	ENSMUSG00000036606	Plxnb2	Debt|plexin-B2	plexin B2	protein-coding
mm_99877.1	chr11	109425665	109425677	+	1	NA	promoter-TSS (NM_025275)	promoter-TSS (NM_025275)	-275	NM_025275	13929	Mm.211850	NM_025275	ENSMUSG00000020610	Amz2	AA408420|ESTM12|X83328	archaelysin family metallopeptidase 2	protein-coding
mm_34917.1	chr4	155728343	155728352	+	1	NA	intron (NM_026899, intron 2 of 4)	intron (NM_026899, intron 2 of 4)	-6457	NM_001101506	381582	Mm.379515	NM_001101506	ENSMUSG00000084845	Tmem240	EG381582|Gm5151	transmembrane protein 240	protein-coding
mm_97462.1	chr11	78261718	78261803	+	1	NA	promoter-TSS (NM_001002004)	promoter-TSS (NM_001002004)	6	NM_001002004	72503	Mm.237103	NM_001002004	ENSMUSG00000010277	2610507B11Rik	AU022687|D11Bhm178e|D11Bhm179e|E1|Kiaa0100|mKIAA0100	RIKEN cDNA 2610507B11 gene	protein-coding
mm_49665.1	chr6	31220401	31220429	+	1	NA	promoter-TSS (NR_040262)	promoter-TSS (NR_040262)	64	NR_040261	73652	Mm.441297	NR_040257	ENSMUSG00000087380	2210408F21Rik	-	RIKEN cDNA 2210408F21 gene	ncRNA
mm_125119.1	chr15	30172520	30172567	+	1	NA	promoter-TSS (NM_008729)	promoter-TSS (NM_008729)	-50	NM_008729	18163	Mm.321648	NM_008729	ENSMUSG00000022240	Ctnnd2	Catnd2|Nprap|neurojugin	catenin (cadherin associated protein), delta 2	protein-coding
mm_143913.1	chr17	85614803	85614812	-	1	NA	intron (NR_038084, intron 2 of 3)	intron (NR_038084, intron 2 of 3)	3589	NR_038084	100043902	Mm.150838	NR_015385	ENSMUSG00000093460	Six3os1	D17Mgi26|E130112H22Rik|Rncr1|Six3os	SIX homeobox 3, opposite strand 1	ncRNA
mm_101968.1	chr11	50308867	50308891	-	1	NA	exon (NM_001110500, exon 5 of 15)	exon (NM_001110500, exon 5 of 15)	-16543	NM_175334	103806	Mm.51116	NM_175334	ENSMUSG00000050567	Maml1	AI644666|AW743257|D930008C07Rik|Mam-1|Mam1|mKIAA0200	mastermind like 1 (Drosophila)	protein-coding
mm_151124.1	chr19	47865816	47865835	+	1	NA	promoter-TSS (NM_026619)	promoter-TSS (NM_026619)	31	NM_026619	68214	Mm.63791	NM_026619	ENSMUSG00000025069	Gsto2	1700020F09Rik|4930425C18Rik|GSTO 2-2	glutathione S-transferase omega 2	protein-coding
mm_39147.1	chr4	155361357	155361433	-	1	NA	promoter-TSS (NM_008860)	promoter-TSS (NM_008860)	33	NM_008860	18762	Mm.28561	NM_008860	ENSMUSG00000029053	Prkcz	AI098070|C80388|Pkcz|R74924|aPKCzeta|nPKC-zeta|zetaPKC	protein kinase C, zeta	protein-coding
mm_92086.1	chr10	62792244	62792290	-	1	NA	5' UTR (NM_026201, exon 1 of 25)	5' UTR (NM_026201, exon 1 of 25)	101	NM_026201	67500	Mm.196371	NM_026201	ENSMUSG00000020074	Ccar1	2610511G16Rik|9430036H15Rik|Carp1	cell division cycle and apoptosis regulator 1	protein-coding
mm_30376.1	chr3	152210268	152210320	-	1	NA	promoter-TSS (NM_027287)	promoter-TSS (NM_027287)	-164	NM_057172	51886	Mm.278922	NM_057172	ENSMUSG00000028034	Fubp1	9530027K12Rik|D3Ertd330e|FBP|Fubp|Fubp4	far upstream element (FUSE) binding protein 1	protein-coding
mm_91277.1	chr10	24692396	24692400	-	1	NA	intron (NM_001308327, intron 1 of 24)	intron (NM_001308327, intron 1 of 24)	19761	NM_001308327	18605	Mm.27254	NM_008813	ENSMUSG00000037370	Enpp1	4833416E15Rik|AI428932|C76301|CD203c|E-NPP 1|E-NPP1|Ly-41|M6S1|NPP1|Npps|PC-1|Pca|Pca-1|Pdnp1|ttw|twy	ectonucleotide pyrophosphatase/phosphodiesterase 1	protein-coding
mm_53438.1	chr6	134152275	134152278	+	1	NA	intron (NM_001303102, intron 3 of 8)	intron (NM_001303102, intron 3 of 8)	116576	NM_007961	14011	Mm.269995	NM_007961	ENSMUSG00000030199	Etv6	AW123102|AW557856|Tel	ets variant 6	protein-coding
mm_25322.1	chr3	106547728	106547738	+	1	NA	promoter-TSS (NM_026013)	promoter-TSS (NM_026013)	-65	NM_001286986	67171	Mm.290488	NM_026013	ENSMUSG00000027900	Dram2	2010305N14Rik|2610318G18Rik|AI647667|Tmem77	DNA-damage regulated autophagy modulator 2	protein-coding
mm_20084.1	chr2	120731199	120731211	-	1	NA	intron (NM_026891, intron 1 of 27)	CpG	312	NM_026891	68968	Mm.2289	NM_026891	ENSMUSG00000027284	Cdan1	1500015A01Rik|AI448026|AW492297|CDA-I|CDA1|CDAI	congenital dyserythropoietic anemia, type I (human)	protein-coding
mm_59099.1	chr7	19697012	19697084	+	1	NA	exon (NM_009696, exon 4 of 4)	exon (NM_009696, exon 4 of 4)	1350	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_61025.1	chr7	49517366	49517371	+	1	NA	intron (NM_175272, intron 11 of 37)	intron (NM_175272, intron 11 of 37)	119467	NM_001005232	13172	Mm.307176	NM_001005232	ENSMUSG00000030507	Dbx1	AI426026|Dbx	developing brain homeobox 1	protein-coding
mm_133736.1	chr16	93883959	93883974	+	1	NA	promoter-TSS (NM_028083)	promoter-TSS (NM_028083)	65	NM_028083	110749	Mm.274222	NM_028083	ENSMUSG00000022945	Chaf1b	2600017H24Rik|C76145|CAF-I p60|CAF-Ip60|CAF1|CAF1A|CAF1P60|MPHOSPH7	chromatin assembly factor 1, subunit B (p60)	protein-coding
mm_8582.1	chr1	155947715	155947719	-	1	NA	intron (NM_001039184, intron 6 of 37)	Lx6|LINE|L1	25538	NM_001039184	74081	Mm.260247	NM_001039184	ENSMUSG00000033671	Cep350	4933409L06Rik|6430546F08Rik	centrosomal protein 350	protein-coding
mm_66457.1	chr7	44869844	44869854	-	1	NA	promoter-TSS (NM_133949)	promoter-TSS (NM_133949)	-61	NM_133949	84113	Mm.42855	NM_133949	ENSMUSG00000038502	Ptov1	1110030G05Rik|AU041779|Gcap3	prostate tumor over expressed gene 1	protein-coding
mm_145555.1	chr18	60811419	60811452	+	1	NA	promoter-TSS (NR_039567)	promoter-TSS (NR_039567)	-641	NR_039567	100628611		NR_039567	ENSMUSG00000093327	Mir5107	mir-5107|mmu-mir-5107|mu-mir-5107	microRNA 5107	ncRNA
mm_151499.1	chr19	58728130	58728163	+	1	NA	promoter-TSS (NM_018874)	promoter-TSS (NM_018874)	-741	NM_018874	18946	Mm.10753	NM_018874	ENSMUSG00000042179	Pnliprp1	Plrp1	pancreatic lipase related protein 1	protein-coding
mm_64384.1	chr7	142475045	142475092	+	1	NA	intron (NM_001271508, intron 1 of 10)	intron (NM_001271508, intron 1 of 10)	-1945	NM_001271523	16985	Mm.234003	NM_019391	ENSMUSG00000018819	Lsp1	Lsp-1|WP34|p50|pp52	lymphocyte specific 1	protein-coding
mm_107972.1	chr12	72844478	72844489	+	1	NA	Intergenic	Intergenic	73282	NM_029444	75801	Mm.242892	NM_029444	ENSMUSG00000021098	4930447C04Rik	4921504I02Rik|A930035O15Rik|Six6OS|Six6as|Six6os1	RIKEN cDNA 4930447C04 gene	protein-coding
mm_90700.1	chr10	130332977	130332988	+	1	NA	intron (NM_183264, intron 1 of 8)	RMER17C2|LTR|ERVK	10130	NM_183264	67596	Mm.131264	NM_183264	ENSMUSG00000034833	Tespa1	5830405N20Rik|A430001F24Rik|AI450549	thymocyte expressed, positive selection associated 1	protein-coding
mm_14476.1	chr2	131499266	131499269	+	1	NA	intron (NM_001177836, intron 1 of 7)	intron (NM_001177836, intron 1 of 7)	7405	NM_001177838	228608	Mm.136586	NM_145533	ENSMUSG00000027333	Smox	B130066H01Rik|PAO|PAOh1|SMO	spermine oxidase	protein-coding
mm_116053.1	chr13	27437123	27437133	-	1	NA	exon (NM_011167, exon 2 of 6)	exon (NM_011167, exon 2 of 6)	1560	NM_001271379	19112	Mm.142728	NM_011167	ENSMUSG00000021345	Prl8a6	Ghd13|PLP-C1|PLP-Ca|PLP-calpha|Prlpc|Prlpc1	prolactin family 8, subfamily a, member 6	protein-coding
mm_84556.1	chr9	67710907	67710910	-	1	NA	Intergenic	Intergenic	16872	NR_106100	102466824		NR_106100	ENSMUSG00000098937	Mir7241	Gm27918|mmu-mir-7241	microRNA 7241	ncRNA
mm_41916.1	chr5	105599556	105599586	+	1	NA	intron (NM_133897, intron 3 of 3)	intron (NM_133897, intron 3 of 3)	80100	NM_133897	100604	Mm.319847	NM_133897	ENSMUSG00000054720	Lrrc8c	AD158|AI326115|E430036I04Rik|fad158	leucine rich repeat containing 8 family, member C	protein-coding
mm_101850.1	chr11	48838546	48838559	-	1	NA	intron (NM_001347446, intron 1 of 6)	intron (NM_001347446, intron 1 of 6)	547	NM_001347436	94089	Mm.390335	NM_053166	ENSMUSG00000040350	Trim7	AI790312	tripartite motif-containing 7	protein-coding
mm_126324.1	chr15	79739597	79739610	+	1	NA	intron (NM_001205346, intron 2 of 17)	intron (NM_001205346, intron 2 of 17)	2933	NM_194342	223697	Mm.202715	NM_194342	ENSMUSG00000042524	Sun2	B230369L08Rik|C030011B15|Unc84b	Sad1 and UNC84 domain containing 2	protein-coding
mm_13386.1	chr2	103969529	103969533	+	1	NA	promoter-TSS (NM_008505)	promoter-TSS (NM_008505)	-26	NM_001142336	16909	Mm.29266	NM_008505	ENSMUSG00000032698	Lmo2	Rbtn-2|Rbtn2|Rhom-2|Ttg2	LIM domain only 2	protein-coding
mm_145002.1	chr18	38418910	38418916	+	1	NA	promoter-TSS (NM_022996)	promoter-TSS (NM_022996)	-62	NM_022996	65113	Mm.102496	NM_022996	ENSMUSG00000024425	Ndfip1	0610010M22Rik|N4wbp5	Nedd4 family interacting protein 1	protein-coding
mm_16623.1	chr2	5676063	5676065	-	1	NA	promoter-TSS (NM_001290376)	promoter-TSS (NM_001290376)	-18	NM_001290376	227541	Mm.191949	NM_177343	ENSMUSG00000039145	Camk1d	A630059D12Rik|CKLiK|CaMKIdelta|E030025C11Rik|mCKLiK	calcium/calmodulin-dependent protein kinase ID	protein-coding
mm_38598.1	chr4	141846278	141846293	-	1	NA	promoter-TSS (NM_001033875)	promoter-TSS (NM_001033875)	74	NM_001033875	76701	Mm.489680	NM_001033875	ENSMUSG00000062478	Ctrc	1810044E12Rik	chymotrypsin C (caldecrin)	protein-coding
mm_110243.1	chr12	31265105	31265119	-	1	NA	promoter-TSS (NM_008482)	promoter-TSS (NM_008482)	-182	NM_008482	16777	Mm.172674	NM_008482	ENSMUSG00000002900	Lamb1	C77966|C80098|C81607|D130003D08Rik|Lamb-1|Lamb1-1	laminin B1	protein-coding
mm_99495.1	chr11	102881216	102881246	+	1	NA	promoter-TSS (NM_001109995)	promoter-TSS (NM_001109995)	-13	NM_028492	73293	Mm.67659	NM_028492	ENSMUSG00000020930	Ccdc103	1700039D13Rik	coiled-coil domain containing 103	protein-coding
mm_154014.1	chr19	53195232	53195236	-	1	NA	intron (NM_013758, intron 1 of 15)	intron (NM_013758, intron 1 of 15)	51237	NM_013758	27360	Mm.426080	NM_013758	ENSMUSG00000025026	Add3	AI463285|R75380	adducin 3 (gamma)	protein-coding
mm_144782.1	chr18	35830972	35830973	+	1	NA	intron (NM_133687, intron 1 of 2)	CpG	1154	NM_133687	67393	Mm.94560	NM_133687	ENSMUSG00000046668	Cxxc5	4930415K17Rik	CXXC finger 5	protein-coding
mm_20980.1	chr2	151974150	151974168	-	1	NA	promoter-TSS (NM_001289151)	promoter-TSS (NM_001289151)	-178	NM_028666	73847	Mm.272444	NM_028666	ENSMUSG00000027459	Fam110a	1700008J10Rik|5430432M24Rik|AI747080	family with sequence similarity 110, member A	protein-coding
mm_99686.1	chr11	106036929	106036945	+	1	NA	promoter-TSS (NM_027946)	promoter-TSS (NM_027946)	65	NM_027946	71833	Mm.307455	NM_027946	ENSMUSG00000049354	Dcaf7	1700012F10Rik|2610037L01Rik|C86529|HAN11|Wdr68	DDB1 and CUL4 associated factor 7	protein-coding
mm_44994.1	chr5	38159458	38159491	-	1	NA	promoter-TSS (NM_010942)	promoter-TSS (NM_010942)	-7	NM_010942	18196	Mm.7414	NM_010942	ENSMUSG00000029126	Nsg1	Neep21|m234|p21	neuron specific gene family member 1	protein-coding
mm_117464.1	chr13	75943701	75943760	-	1	NA	promoter-TSS (NM_028493)	promoter-TSS (NM_028493)	94	NM_028493	73296	Mm.276200	NM_028493	ENSMUSG00000021589	Rhobtb3	1700040C17Rik|2610033K01Rik|4930503C18Rik|AI317148|AW208826|mKIAA0878	Rho-related BTB domain containing 3	protein-coding
mm_166478.1	chr5	145042979	145042983	+	1	NA	promoter-TSS (NM_027069)	promoter-TSS (NM_027069)	-9	NM_027069	69396	Mm.45463	NM_027069	ENSMUSG00000029620	1700018F24Rik	AV045857	RIKEN cDNA 1700018F24 gene	protein-coding
mm_88742.1	chr10	80280929	80280976	+	1	NA	exon (NM_133188, exon 7 of 12)	exon (NM_133188, exon 7 of 12)	2788	NR_105876	102466207		NR_105876	ENSMUSG00000098672	Mir6911	Gm27822|mmu-mir-6911	microRNA 6911	ncRNA
mm_31019.1	chr4	40723085	40723104	+	1	NA	promoter-TSS (NR_077226)	promoter-TSS (NR_077226)	164	NM_001164672	15502	Mm.27897	NM_008298	ENSMUSG00000028410	Dnaja1	HSJ-2|Hsj2|Nedd7	DnaJ heat shock protein family (Hsp40) member A1	protein-coding
mm_135770.1	chr16	56831773	56831790	-	1	NA	intron (NM_019631, intron 1 of 5)	intron (NM_019631, intron 1 of 5)	-35923	NM_172825	239853	Mm.258979	NM_172825	ENSMUSG00000022755	Adgrg7	9130020O16Rik|Gpr128	adhesion G protein-coupled receptor G7	protein-coding
mm_124922.1	chr15	12122859	12122860	+	1	NA	intron (NM_011767, intron 2 of 19)	intron (NM_011767, intron 2 of 19)	5008	NM_011767	22763	Mm.273496	NM_011767	ENSMUSG00000022201	Zfr	C920030H05Rik	zinc finger RNA binding protein	protein-coding
mm_151868.1	chr19	5797845	5797853	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	-1868	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_157967.1	chrX	90745232	90745236	-	1	NA	Intergenic	Intergenic	-146908	NM_001101450	212952	Mm.477436	NM_001101450	ENSMUSG00000091497	Gm44	-	predicted gene 44	protein-coding
mm_78947.1	chr9	45138577	45138594	+	1	NA	promoter-TSS (NM_001013390)	promoter-TSS (NM_001013390)	-457	NM_001013390	399548	Mm.335112	NM_001013390	ENSMUSG00000046480	Scn4b	Gm1471	sodium channel, type IV, beta	protein-coding
mm_131863.1	chr16	23112243	23112294	+	1	NA	intron (NM_001347179, intron 10 of 10)	intron (NM_001347179, intron 10 of 10)	1498	NR_034048	100217420	Mm.260084	NR_034048	ENSMUSG00000087935	Snora81	MBI-61	small nucleolar RNA, H/ACA box 81	snoRNA
mm_1144.1	chr1	60746368	60746427	+	1	NA	promoter-TSS (NM_007642)	promoter-TSS (NM_007642)	9	NM_007642	12487	Mm.255003	NM_007642	ENSMUSG00000026012	Cd28	-	CD28 antigen	protein-coding
mm_27972.1	chr3	80802605	80802617	-	1	NA	5' UTR (NM_013540, exon 1 of 16)	5' UTR (NM_013540, exon 1 of 16)	180	NM_013540	14800	Mm.220224	NM_013540	ENSMUSG00000033981	Gria2	GluA2|GluR-B|Glur-2|Glur2	glutamate receptor, ionotropic, AMPA2 (alpha 2)	protein-coding
mm_73334.1	chr8	105304096	105304104	+	1	NA	intron (NM_148952, intron 7 of 9)	intron (NM_148952, intron 7 of 9)	-1501	NM_172760	234683	Mm.237966	NM_172760	ENSMUSG00000014791	Elmo3	9930107J06|BC058752|CED-12|Ced12	engulfment and cell motility 3	protein-coding
mm_65248.1	chr7	19861223	19861225	-	1	NA	promoter-TSS (NM_001033419)	promoter-TSS (NM_001033419)	75	NM_001033419	330483	Mm.260192	NM_001033419	ENSMUSG00000014686	Ceacam16	Gm769	carcinoembryonic antigen-related cell adhesion molecule 16	protein-coding
mm_1197.1	chr1	62706327	62706350	+	1	NA	intron (NM_001077405, intron 1 of 15)	CpG	3021	NM_001077405	18187	Mm.266341	NM_010939	ENSMUSG00000025969	Nrp2	1110048P06Rik|Np-2|Np2|Npn-2|Npn2	neuropilin 2	protein-coding
mm_27312.1	chr3	50366635	50366646	-	1	NA	3' UTR (NM_011990, exon 12 of 12)	3' UTR (NM_011990, exon 12 of 12)	76973	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_118673.1	chr14	22022707	22022710	+	1	NA	intron (NM_028275, intron 1 of 6)	MTD|LTR|ERVL-MaLR	2996	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_45404.1	chr5	66214545	66214545	-	1	NA	Intergenic	RMER17C|LTR|ERVK	-23210	NR_040695	73639	Mm.48851	NR_040695	ENSMUSG00000107014	1700126H18Rik	-	RIKEN cDNA 1700126H18 gene	ncRNA
mm_2172.1	chr1	88306732	88306737	+	1	NA	promoter-TSS (NM_134252)	promoter-TSS (NM_134252)	22	NM_134252	171382	Mm.218753	NM_134252	ENSMUSG00000036251	Trpm8	CMR1|LTRPC6|LTrpC-6|TRPP8|Trp-p8	transient receptor potential cation channel, subfamily M, member 8	protein-coding
mm_114626.1	chr13	76099879	76099881	+	1	NA	intron (NM_001081352, intron 2 of 43)	intron (NM_001081352, intron 2 of 43)	1146	NM_001081352	218343	Mm.277964	NM_001081352	ENSMUSG00000033991	Ttc37	mKIAA0372	tetratricopeptide repeat domain 37	protein-coding
mm_50280.1	chr6	47045046	47045061	+	1	NA	intron (NM_001004357, intron 17 of 23)	intron (NM_001004357, intron 17 of 23)	-199343	NM_025771	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding
mm_80207.1	chr9	72438610	72438616	+	1	NA	promoter-TSS (NM_008613)	promoter-TSS (NM_008613)	84	NM_008613	17427	Mm.387671	NM_008613	ENSMUSG00000032221	Mns1	AW546487	meiosis-specific nuclear structural protein 1	protein-coding
mm_55525.1	chr6	70709898	70709915	-	1	NA	Intergenic	Intergenic	82269	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_150050.1	chr19	29380524	29380534	+	1	NA	exon (NM_021893, exon 4 of 7)	exon (NM_021893, exon 4 of 7)	13091	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_123089.1	chr14	55758344	55758436	-	1	NA	promoter-TSS (NM_009894)	promoter-TSS (NM_009894)	34	NM_009894	12684	Mm.466766	NM_009894	ENSMUSG00000022219	Cideb	1110030C18Rik|AI790179|CIDE-B	cell death-inducing DNA fragmentation factor, alpha subunit-like effector B	protein-coding
mm_145155.1	chr18	46515917	46515925	+	1	NA	intron (NM_173423, intron 2 of 2)	L1MB8|LINE|L1	10050	NM_173423	240263	Mm.38249	NM_173423	ENSMUSG00000033319	Fem1c	2610312A07Rik|3632443A22Rik|AI646567	fem-1 homolog c (C.elegans)	protein-coding
mm_26757.1	chr3	8666834	8666843	-	1	NA	exon (NM_010423, exon 1 of 5)	exon (NM_010423, exon 1 of 5)	200	NM_010423	15213	Mm.29581	NM_010423	ENSMUSG00000040289	Hey1	AI316788|AI414254|CHF2|HRT1|Herp2|Hesr1|bHLHb31|hesr-1	hairy/enhancer-of-split related with YRPW motif 1	protein-coding
mm_10437.1	chr2	14174551	14174564	+	1	NA	promoter-TSS (NM_001081310)	promoter-TSS (NM_001081310)	33	NM_001081310	625286	Mm.158781	NM_001081310	ENSMUSG00000061531	Tmem236	2010003H20Rik|Fam23a|Gm613	transmembrane protein 236	protein-coding
mm_84822.1	chr9	77733284	77733289	-	1	NA	Intergenic	Intergenic	-21249	NM_010295	14629	Mm.89888	NM_010295	ENSMUSG00000032350	Gclc	D9Wsu168e|GLCL-H|Ggcs-hs|Glclc	glutamate-cysteine ligase, catalytic subunit	protein-coding
mm_78755.1	chr9	42673969	42674011	+	1	NA	intron (NM_175481, intron 5 of 20)	intron (NM_175481, intron 5 of 20)	-201764	NM_173038	272589	Mm.34483	NM_173038	ENSMUSG00000037287	Tbcel	D330014K23|E130107N23Rik|Lrrc35	tubulin folding cofactor E-like	protein-coding
mm_35266.1	chr4	19900508	19900515	-	1	NA	intron (NM_175406, intron 2 of 7)	intron (NM_175406, intron 2 of 7)	22055	NM_175406	242341	Mm.19298	NM_175406	ENSMUSG00000028238	Atp6v0d2	1620401A02Rik|AI324824|V-ATPase	ATPase, H+ transporting, lysosomal V0 subunit D2	protein-coding
mm_169043.1	chr13	14951094	14951111	+	1	NA	Intergenic	ERVB7_1-LTR_MM|LTR|ERVK	320844	NM_134067	105351	Mm.41450	NM_134067	ENSMUSG00000039182	AW209491	-	expressed sequence AW209491	protein-coding
mm_130737.1	chr15	101253723	101253740	-	1	NA	Intergenic	Intergenic	-13115	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_164956.1	chr19	5614053	5614053	-	1	NA	Intergenic	Intergenic	-3959	NM_178637	81601	Mm.228930	NM_178637	ENSMUSG00000024926	Kat5	AI839539|CPLA2|Htatip|Htatip1|PLIP|Tip55|Tip60	K(lysine) acetyltransferase 5	protein-coding
mm_169908.1	chr16	54686824	54686842	+	1	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	596404	NM_178720	239852	Mm.245045	NM_178720	ENSMUSG00000064310	Zpld1	9430016A21Rik	zona pellucida like domain containing 1	protein-coding
mm_60111.1	chr7	35449137	35449143	+	1	NA	promoter-TSS (NM_001199016)	promoter-TSS (NM_001199016)	-39	NM_021291	30962	Mm.45874	NM_021291	ENSMUSG00000030492	Slc7a9	CSNU3	solute carrier family 7 (cationic amino acid transporter, y+ system), member 9	protein-coding
mm_56340.1	chr6	92857027	92857031	-	1	NA	intron (NM_175314, intron 16 of 29)	intron (NM_175314, intron 16 of 29)	44412	NM_175314	101401	Mm.158235	NM_175314	ENSMUSG00000030022	Adamts9	1810011L16Rik|8430403M15Rik|AW743315|E030027K14Rik	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 9	protein-coding
mm_117005.1	chr13	57884378	57884391	-	1	NA	intron (NM_001166464, intron 2 of 10)	intron (NM_001166464, intron 2 of 10)	23948	NM_009262	20745	Mm.379020	NM_009262	ENSMUSG00000056222	Spock1	Spock|Ticn1|testican	sparc/osteonectin, cwcv and kazal-like domains proteoglycan 1	protein-coding
mm_107407.1	chr12	33429606	33429649	+	1	NA	promoter-TSS (NM_172253)	promoter-TSS (NM_172253)	3	NM_172253	28071	Mm.196472	NM_172253	ENSMUSG00000020561	Twistnb	2410173G11|2810024J17Rik|D16Wsu83e	twist basic helix-loop-helix transcription factor 1 neighbor	protein-coding
mm_84239.1	chr9	62282159	62282163	-	1	NA	promoter-TSS (NM_025721)	promoter-TSS (NM_025721)	18	NM_025721	66712	Mm.263615	NM_025721	ENSMUSG00000046846	Spesp1	4921508E09Rik|AI428149	sperm equatorial segment protein 1	protein-coding
mm_160660.1	chr9	119552077	119552077	-	1	NA	intron (NM_021544, intron 3 of 27)	intron (NM_021544, intron 3 of 27)	10601	NM_001253860	20271	Mm.103584	NM_021544	ENSMUSG00000032511	Scn5a	Nav1.5|Nav1.5c|SkM1|SkM2|mH1	sodium channel, voltage-gated, type V, alpha	protein-coding
mm_2325.1	chr1	92439708	92439729	+	1	NA	TTS (NM_024197)	TTS (NM_024197)	24824	NR_105865	102465542		NR_105865	ENSMUSG00000098288	Mir6900	Gm27708|mmu-mir-6900	microRNA 6900	ncRNA
mm_47073.1	chr5	116591473	116591483	-	1	NA	5' UTR (NM_026886, exon 1 of 13)	5' UTR (NM_026886, exon 1 of 13)	339	NM_026886	68955	Mm.146779	NM_026886	ENSMUSG00000063919	Srrm4	1500001A10Rik|B230202K19Rik|bv|mKIAA1853|nSR100	serine/arginine repetitive matrix 4	protein-coding
mm_56872.1	chr6	118658743	118658748	-	1	NA	intron (NM_001256002, intron 24 of 47)	intron (NM_001256002, intron 24 of 47)	-96489	NM_001081112	232339	Mm.276116	NM_001081112	ENSMUSG00000007827	Ankrd26	5730521P14Rik|BC008111|mKIAA1074	ankyrin repeat domain 26	protein-coding
mm_10069.1	chr1	193588625	193588665	-	1	NA	Intergenic	Intergenic	-81115	NR_029592	387201		NR_029592	ENSMUSG00000065533	Mir205	Mirn205|mir-205|mmu-mir-205	microRNA 205	ncRNA
mm_77236.1	chr8	115704940	115704959	-	1	NA	3' UTR (NM_001025577, exon 1 of 1)	3' UTR (NM_001025577, exon 1 of 1)	1945	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_131947.1	chr16	24393465	24393528	+	1	NA	non-coding (NR_037954, exon 1 of 2)	non-coding (NR_037954, exon 1 of 2)	146	NM_178665	210126	Mm.209385	NM_178665	ENSMUSG00000033306	Lpp	9430020K16Rik|AA959454|AU024130|B130055L10Rik|C79715|D630048H16	LIM domain containing preferred translocation partner in lipoma	protein-coding
mm_15834.1	chr2	164685081	164685152	+	1	NA	promoter-TSS (NM_001012704)	promoter-TSS (NM_001012704)	9	NM_001012704	408190	Mm.376205	NM_001012704	ENSMUSG00000067704	Wfdc13	Wfdc13l1	WAP four-disulfide core domain 13	protein-coding
mm_107436.1	chr12	36157123	36157133	+	1	NA	promoter-TSS (NM_025840)	promoter-TSS (NM_025840)	4	NM_146033	217473	Mm.130422	NM_146033	ENSMUSG00000036188	Ankmy2	AI035571|ZMYND20	ankyrin repeat and MYND domain containing 2	protein-coding
mm_135014.1	chr16	32487169	32487191	-	1	NA	intron (NM_145932, intron 1 of 8)	intron (NM_145932, intron 1 of 8)	699	NM_145932	106407	Mm.476915	NM_145932	ENSMUSG00000035699	Slc51a	AV001382|AW261577|D630035O19Rik|OSTalpha|Osta	solute carrier family 51, alpha subunit	protein-coding
mm_10536.1	chr2	16431736	16431752	+	1	NA	intron (NM_026162, intron 1 of 13)	intron (NM_026162, intron 1 of 13)	75440	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding
mm_82031.1	chr9	121938100	121938126	+	1	NA	non-coding (NR_033553, exon 2 of 5)	non-coding (NR_033553, exon 2 of 5)	838	NR_033553	69430	Mm.482910	NR_033553	ENSMUSG00000043773	1700048O20Rik	1700022O21Rik	RIKEN cDNA 1700048O20 gene	ncRNA
mm_161153.1	chr13	23763660	23763660	+	1	NA	promoter-TSS (NM_030609)	promoter-TSS (NM_030609)	-8	NM_030609	80838	Mm.480242	NM_030609	ENSMUSG00000049539	Hist1h1a	H1.1|H1a|H1f1|H1var3	histone cluster 1, H1a	protein-coding
mm_10369.1	chr2	11723254	11723276	+	1	NA	intron (NR_073191, intron 3 of 5)	intron (NR_073191, intron 3 of 5)	17553	NM_001271500	16169	Mm.200196	NM_008358	ENSMUSG00000023206	Il15ra	AA690181|IL-15RA	interleukin 15 receptor, alpha chain	protein-coding
mm_6847.1	chr1	84243559	84243581	-	1	NA	intron (NM_001003948, intron 1 of 2)	ORR1F|LTR|ERVL-MaLR	-24609	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_120474.1	chr14	65974838	65974916	+	1	NA	exon (NM_013492, exon 4 of 9)	exon (NM_013492, exon 4 of 9)	6394	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_120562.1	chr14	68123698	68123716	+	1	NA	promoter-TSS (NR_045897)	promoter-TSS (NR_045897)	-45	NR_045897	100043072	Mm.242832	NR_045897		A230070E04Rik	Gm4210	RIKEN cDNA A230070E04 gene	ncRNA
mm_159845.1	chr5	135458099	135458099	-	1	NA	intron (NM_146001, intron 3 of 30)	intron (NM_146001, intron 3 of 30)	-63553	NM_148932	107939	Mm.28399	NM_148932	ENSMUSG00000053293	Pom121	2610027A18Rik|C80273|mKIAA0618	nuclear pore membrane protein 121	protein-coding
mm_107604.1	chr12	49384288	49384316	+	1	NA	5' UTR (NM_008241, exon 2 of 2)	5' UTR (NM_008241, exon 2 of 2)	1295	NM_008241	15228	Mm.4704	NM_008241	ENSMUSG00000020950	Foxg1	2900064B05Rik|BF-1|Bf1|Hfh9|Hfhbf1	forkhead box G1	protein-coding
mm_19861.1	chr2	113848272	113848375	-	1	NA	5' UTR (NM_181416, exon 1 of 12)	5' UTR (NM_181416, exon 1 of 12)	338	NM_181416	228482	Mm.45753	NM_181416	ENSMUSG00000041219	Arhgap11a	6530401L14Rik|mKIAA0013	Rho GTPase activating protein 11A	protein-coding
mm_83490.1	chr9	45945628	45945631	-	1	NA	intron (NM_172257, intron 13 of 25)	intron (NM_172257, intron 13 of 25)	-6039	NR_106055	102465659		NR_106055	ENSMUSG00000098327	Mir7087	Gm27273|mmu-mir-7087	microRNA 7087	ncRNA
mm_51383.1	chr6	76632656	76632656	+	1	NA	Intergenic	Intergenic	-610061	NM_028880	74342	Mm.292568	NM_028880	ENSMUSG00000060780	Lrrtm1	4632401D06Rik|AW125451	leucine rich repeat transmembrane neuronal 1	protein-coding
mm_97696.1	chr11	80165671	80165679	+	1	NA	exon (NM_172133, exon 6 of 11)	exon (NM_172133, exon 6 of 11)	11513	NM_172133	216991	Mm.341520	NM_172133	ENSMUSG00000020709	Adap2	Centa2	ArfGAP with dual PH domains 2	protein-coding
mm_93221.1	chr10	95145829	95145847	-	1	NA	promoter-TSS (NR_131146)	promoter-TSS (NR_131146)	-13	NR_131146	628062		NR_131146		Gm29684	-	predicted gene, 29684	ncRNA
mm_116375.1	chr13	40892674	40892686	-	1	NA	intron (NM_008105, intron 1 of 2)	intron (NM_008105, intron 1 of 2)	5922	NM_008105	14538	Mm.314757	NM_008105	ENSMUSG00000021360	Gcnt2	5330430K10Rik|IGnT|IGnTA|IGnTB|IGnTC	glucosaminyl (N-acetyl) transferase 2, I-branching enzyme	protein-coding
mm_170643.1	chr19	9216860	9216865	+	1	NA	Intergenic	Intergenic	-81296	NM_025610	66514	Mm.272847	NM_025610	ENSMUSG00000024654	Asrgl1	2410004D18Rik|ALP|ALP1|AU040643|AW060375	asparaginase like 1	protein-coding
mm_155272.1	chrX	60030533	60030559	+	1	NA	3' UTR (NM_001305797, exon 7 of 7)	3' UTR (NM_001305797, exon 7 of 7)	31082	NM_001305797	14071	Mm.391283	NM_007979	ENSMUSG00000031138	F9	AW111646|Cf-9|Cf9	coagulation factor IX	protein-coding
mm_87952.1	chr10	63061536	63061548	+	1	NA	promoter-TSS (NM_026701)	promoter-TSS (NM_026701)	-75	NM_026701	68371	Mm.261389	NM_026701	ENSMUSG00000020072	Pbld1	0610038K03Rik|Mawbp|Pbld	phenazine biosynthesis-like protein domain containing 1	protein-coding
mm_122338.1	chr14	37135154	37135172	-	1	NA	promoter-TSS (NM_001199122)	promoter-TSS (NM_001199122)	-24	NM_001199122	66092	Mm.182912	NM_078478	ENSMUSG00000041028	Ghitm	1010001P14Rik|C77840|MICS1|PTD010|Tmbim5	growth hormone inducible transmembrane protein	protein-coding
mm_17169.1	chr2	25305128	25305146	-	1	NA	exon (NM_001177657, exon 6 of 19)	exon (NM_001177657, exon 6 of 19)	13917	NM_001242940	320354	Mm.445875	NM_001242940		Grin1os	E130003G02Rik	glutamate receptor, ionotropic, NMDA1 (zeta 1), opposite strand	protein-coding
mm_150732.1	chr19	43731442	43731461	+	1	NA	3' UTR (NM_053103, exon 13 of 13)	3' UTR (NM_053103, exon 13 of 13)	21549	NM_144874	226139	Mm.248237	NM_144874	ENSMUSG00000040018	Cox15	2900026G05Rik	cytochrome c oxidase assembly protein 15	protein-coding
mm_24138.1	chr3	88278449	88278459	+	1	NA	Intergenic	RMER17C|LTR|ERVK	18384	NM_029801	76927	Mm.273330	NM_029801	ENSMUSG00000010538	Tsacc	1700021C14Rik|SIP	TSSK6 activating co-chaperone	protein-coding
mm_24771.1	chr3	95526820	95526871	+	1	NA	promoter-TSS (NM_021281)	promoter-TSS (NM_021281)	59	NM_001267695	13040	Mm.3619	NM_021281	ENSMUSG00000038642	Ctss	Cats	cathepsin S	protein-coding
mm_157629.1	chrX	56598082	56598107	-	1	NA	promoter-TSS (NM_146234)	promoter-TSS (NM_146234)	-175	NM_146234	236792	Mm.291824	NM_146234	ENSMUSG00000061273	Mmgt1	9630048L06Rik|BC032271|Emc5|Mir5116|Tmem32|mir-5116	membrane magnesium transporter 1	protein-coding
mm_107898.1	chr12	70825451	70825479	+	1	NA	promoter-TSS (NM_028127)	promoter-TSS (NM_028127)	-49	NM_028127	319710	Mm.2962	NM_028127	ENSMUSG00000048285	Frmd6	2610019M19Rik|4930488L10Rik|AW212977|Willin	FERM domain containing 6	protein-coding
mm_63391.1	chr7	127244512	127244578	+	1	NA	promoter-TSS (NM_177362)	promoter-TSS (NM_177362)	19	NM_177362	244216	Mm.41038	NM_177362	ENSMUSG00000054716	Zfp771	G630024C07Rik|Znf771	zinc finger protein 771	protein-coding
mm_31539.1	chr4	55477585	55477595	+	1	NA	Intergenic	ORSL-2a|DNA|hAT-Tip100	54885	NM_010637	16600	Mm.4325	NM_010637	ENSMUSG00000003032	Klf4	EZF|Gklf|Zie	Kruppel-like factor 4 (gut)	protein-coding
mm_113716.1	chr13	43615951	43615991	+	1	NA	5' UTR (NM_183204, exon 1 of 2)	5' UTR (NM_183204, exon 1 of 2)	174	NM_183204	328234	Mm.40588	NM_183204	ENSMUSG00000044164	Rnf182	C630023L15Rik	ring finger protein 182	protein-coding
mm_46860.1	chr5	113805431	113805432	-	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	-5079	NM_146162	231633	Mm.41681	NM_146162	ENSMUSG00000054675	Tmem119	AW208946|BC025600|obif	transmembrane protein 119	protein-coding
mm_59121.1	chr7	19877160	19877161	+	1	NA	3' UTR (NM_177036, exon 7 of 7)	3' UTR (NM_177036, exon 7 of 7)	10805	NM_177036	319930	Mm.215839	NM_177036	ENSMUSG00000049848	Ceacam19	C130022P09Rik|CEAL1	carcinoembryonic antigen-related cell adhesion molecule 19	protein-coding
mm_57041.1	chr6	122340201	122340244	-	1	NA	promoter-TSS (NM_001271579)	promoter-TSS (NM_001271579)	5	NM_001271579	13619	Mm.6822	NM_007905	ENSMUSG00000040669	Phc1	AW557034|Edr|Edr1|Mph1|Rae-28|rae28	polyhomeotic-like 1 (Drosophila)	protein-coding
mm_38371.1	chr4	138396439	138396464	-	1	NA	promoter-TSS (NM_001081672)	promoter-TSS (NM_001081672)	7	NM_001081672	625638	Mm.379091	NM_001081672	ENSMUSG00000078235	Fam43b	OTTMUSG00000009974	family with sequence similarity 43, member B	protein-coding
mm_14632.1	chr2	136781399	136781420	+	1	NA	3' UTR (NM_001291056, exon 8 of 8)	3' UTR (NM_001291056, exon 8 of 8)	67959	NM_001291056	20614	Mm.45953	NM_011428	ENSMUSG00000027273	Snap25	Bdr|GENA70|SNAP-25|SUP|sp	synaptosomal-associated protein 25	protein-coding
mm_9062.1	chr1	167393827	167393835	-	1	NA	promoter-TSS (NM_025569)	promoter-TSS (NM_025569)	-34	NM_025569	66447	Mm.218286	NM_025569	ENSMUSG00000026688	Mgst3	2010012L10Rik|2010306B17Rik|2700004G04Rik|AA516734|GST-III	microsomal glutathione S-transferase 3	protein-coding
mm_13154.1	chr2	92442113	92442117	+	1	NA	Intergenic	Intergenic	-8046	NM_009963	12953	Mm.254181	NM_009963	ENSMUSG00000068742	Cry2	AV006279|D130054K12Rik	cryptochrome 2 (photolyase-like)	protein-coding
mm_51042.1	chr6	65602823	65602855	+	1	NA	intron (NM_001001495, intron 5 of 7)	intron (NM_001001495, intron 5 of 7)	12441	NM_001001495	414084	Mm.117558	NM_001001495	ENSMUSG00000044162	Tnip3	9030611K07Rik|ABIN-3|LIND	TNFAIP3 interacting protein 3	protein-coding
mm_43805.1	chr5	142903685	142903723	+	1	NA	3' UTR (NM_007393, exon 6 of 6)	3' UTR (NM_007393, exon 6 of 6)	3050	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_22356.1	chr2	181013249	181013298	-	1	NA	exon (NM_028518, exon 28 of 36)	exon (NM_028518, exon 28 of 36)	25904	NM_015730	11438	Mm.252369	NM_015730	ENSMUSG00000027577	Chrna4	Acra-4|Acra4|EBN1|ENFL1	cholinergic receptor, nicotinic, alpha polypeptide 4	protein-coding
mm_173206.1	chrX	69606256	69606256	-	1	NA	intron (NM_008032, intron 3 of 19)	intron (NM_008032, intron 3 of 19)	245925	NM_008032	14266	Mm.466576	NM_008032	ENSMUSG00000031189	Aff2	FMR2P|Fmr2|Ox19|Oxh	AF4/FMR2 family, member 2	protein-coding
mm_108607.1	chr12	85474690	85474714	+	1	NA	intron (NM_010234, intron 1 of 3)	CpG	801	NM_010234	14281	Mm.246513	NM_010234	ENSMUSG00000021250	Fos	D12Rfj1|c-fos|cFos	FBJ osteosarcoma oncogene	protein-coding
mm_30051.1	chr3	136325963	136326034	-	1	NA	promoter-TSS (NM_001033350)	promoter-TSS (NM_001033350)	68	NM_001310749	242248	Mm.30832	NM_001033350	ENSMUSG00000037922	Bank1	A530094C12Rik|AI451642|AVIEF|BANK	B cell scaffold protein with ankyrin repeats 1	protein-coding
mm_33003.1	chr4	120532261	120532265	+	1	NA	promoter-TSS (NM_177570)	promoter-TSS (NM_177570)	32	NM_177570	194219	Mm.29788	NM_177570	ENSMUSG00000047518	Slfnl1	4933406A14Rik	schlafen like 1	protein-coding
mm_48320.1	chr5	138977186	138977196	-	1	NA	3' UTR (NM_008808, exon 6 of 6)	3' UTR (NM_008808, exon 6 of 6)	17762	NM_008808	18590	Mm.2675	NM_008808	ENSMUSG00000025856	Pdgfa	-	platelet derived growth factor, alpha	protein-coding
mm_77193.1	chr8	112011272	112011296	-	1	NA	promoter-TSS (NM_001286384)	promoter-TSS (NM_001286384)	70	NM_001286384	85305	Mm.196544	NM_053092	ENSMUSG00000031948	Kars	AA589550|AL024334|AL033315|AL033367|D8Ertd698e|D8Wsu108e|LysRS|mKIAA0070	lysyl-tRNA synthetase	protein-coding
mm_98229.1	chr11	88068302	88068315	+	1	NA	promoter-TSS (NM_016686)	promoter-TSS (NM_016686)	29	NM_016686	22344	Mm.46628	NM_016686	ENSMUSG00000018377	Vezf1	AI848691|AW046909|db1	vascular endothelial zinc finger 1	protein-coding
mm_108669.1	chr12	86505051	86505064	+	1	NA	intron (NM_001159500, intron 3 of 6)	intron (NM_001159500, intron 3 of 6)	83413	NM_011934	26380	Mm.235550	NM_011934	ENSMUSG00000021255	Esrrb	Err2|Errb|Estrrb|Nr3b2	estrogen related receptor, beta	protein-coding
mm_31527.1	chr4	55009280	55009307	+	1	NA	exon (NM_172867, exon 3 of 13)	exon (NM_172867, exon 3 of 13)	61348	NM_172867	242466	Mm.102904	NM_172867	ENSMUSG00000060206	Zfp462	6030417H05|9430078C22Rik|Gt4-2|Zfpip	zinc finger protein 462	protein-coding
mm_92092.1	chr10	62865300	62865328	-	1	NA	intron (NM_027384, intron 1 of 10)	intron (NM_027384, intron 1 of 10)	14700	NM_027384	52463	Mm.17774	NM_027384	ENSMUSG00000047146	Tet1	2510010B09Rik|AA517754|BB001228|Cxxc6|D10Ertd17e|LCX|mKIAA1676	tet methylcytosine dioxygenase 1	protein-coding
mm_128499.1	chr15	51991768	51991778	-	1	NA	promoter-TSS (NM_009009)	promoter-TSS (NM_009009)	-13	NM_009009	19357	Mm.182628	NM_009009	ENSMUSG00000022314	Rad21	SCC1|mKIAA0078	RAD21 cohesin complex component	protein-coding
mm_147547.1	chr18	54840129	54840133	-	1	NA	Intergenic	Intergenic	150049	NM_175751	269023	Mm.192984	NM_175751	ENSMUSG00000052713	Zfp608	4932417D18Rik|D430007A19Rik|Znf608	zinc finger protein 608	protein-coding
mm_74690.1	chr8	14998615	14998618	-	1	NA	intron (NM_172751, intron 28 of 28)	intron (NM_172751, intron 28 of 28)	-12409	NM_029116	74901	Mm.46675	NM_029116	ENSMUSG00000055675	Kbtbd11	2900016B01Rik|4930465M17Rik|mKIAA0711	kelch repeat and BTB (POZ) domain containing 11	protein-coding
mm_16064.1	chr2	167936475	167936483	+	1	NA	intron (NM_011201, intron 1 of 8)	intron (NM_011201, intron 1 of 8)	4152	NM_011201	19246	Mm.277916	NM_011201	ENSMUSG00000027540	Ptpn1	PTP-1B|PTP-HA2|PTP1B	protein tyrosine phosphatase, non-receptor type 1	protein-coding
mm_16558.1	chr2	181864419	181864438	+	1	NA	promoter-TSS (NM_025901)	promoter-TSS (NM_025901)	68	NM_025901	67005	Mm.271986	NM_025901	ENSMUSG00000038628	Polr3k	12.3kDa|1500004O14Rik|AI196849|AU014893|C11|RPC10|RPC11	polymerase (RNA) III (DNA directed) polypeptide K	protein-coding
mm_104026.1	chr11	86173100	86173102	-	1	NA	intron (NM_178309, intron 6 of 19)	intron (NM_178309, intron 6 of 19)	28092	NM_178309	237911	Mm.186143	NM_178309	ENSMUSG00000034329	Brip1	3110009N10Rik|8030460J03Rik|Bach1|FACJ|Fancj|OF	BRCA1 interacting protein C-terminal helicase 1	protein-coding
mm_130943.1	chr15	103251056	103251071	-	1	NA	5' UTR (NM_008685, exon 2 of 3)	5' UTR (NM_008685, exon 2 of 3)	613	NM_001302338	18022	Mm.457989	NM_008685	ENSMUSG00000058794	Nfe2	NF-E2|NF-E2/P45|p45|p45NFE2|p45nf-e2	nuclear factor, erythroid derived 2	protein-coding
mm_115087.1	chr13	102701275	102701296	+	1	NA	intron (NM_008533, intron 1 of 2)	PB1D7|SINE|Alu	7727	NM_008533	17079	Mm.373974	NM_008533	ENSMUSG00000021624	Cd180	F630107B15|Ly78|RP105	CD180 antigen	protein-coding
mm_25758.1	chr3	123508589	123508615	+	1	NA	promoter-TSS (NR_028574)	promoter-TSS (NR_028574)	-266	NR_028574	69895	Mm.260791	NR_028574	ENSMUSG00000104960	Snhg8	1110065M07Rik|2010109N14Rik	small nucleolar RNA host gene 8	ncRNA
mm_102174.1	chr11	53980297	53980350	-	1	NA	promoter-TSS (NM_019723)	promoter-TSS (NM_019723)	-296	NM_019723	56517	Mm.154284	NM_019723	ENSMUSG00000063652	Slc22a21	Octn3|Slc22a9	solute carrier family 22 (organic cation transporter), member 21	protein-coding
mm_124015.1	chr14	76506476	76506508	-	1	NA	exon (NM_207652, exon 3 of 3)	exon (NM_207652, exon 3 of 3)	1982	NM_009366	21807	Mm.153272	NM_009366	ENSMUSG00000022010	Tsc22d1	AA589566|AW105905|Egr5|TSC-22|Tgfb1i4|Tsc|Tsc22	TSC22 domain family, member 1	protein-coding
mm_45786.1	chr5	87337166	87337203	-	1	NA	promoter-TSS (NM_028094)	promoter-TSS (NM_028094)	11	NM_028094	72094	Mm.482739	NM_028094	ENSMUSG00000035780	Ugt2a3	2010321J07Rik	UDP glucuronosyltransferase 2 family, polypeptide A3	protein-coding
mm_162656.1	chr10	4266531	4266531	+	1	NA	exon (NM_031185, exon 1 of 4)	exon (NM_031185, exon 1 of 4)	202	NM_031185	83397	Mm.27481	NM_031185	ENSMUSG00000038587	Akap12	AI317366|SSeCKS|Srcs5|Tsga12	A kinase (PRKA) anchor protein (gravin) 12	protein-coding
mm_93376.1	chr10	105522005	105522017	-	1	NA	intron (NM_177368, intron 1 of 11)	intron (NM_177368, intron 1 of 11)	52468	NM_177368	278279	Mm.25225	NM_177368	ENSMUSG00000036019	Tmtc2	8430438D04Rik|D330034A10Rik	transmembrane and tetratricopeptide repeat containing 2	protein-coding
mm_39835.1	chr5	30869578	30869580	+	1	NA	promoter-TSS (NM_144525)	promoter-TSS (NM_144525)	-68	NM_144525	68796	Mm.205169	NM_144525	ENSMUSG00000038828	Tmem214	1110039B18Rik|4921530J21Rik|AI841294|AU018742|C76280	transmembrane protein 214	protein-coding
mm_36152.1	chr4	59549276	59549303	-	1	NA	promoter-TSS (NM_144904)	promoter-TSS (NM_144904)	75	NM_178164	230257	Mm.331640	NM_144904	ENSMUSG00000028382	Ptbp3	5830471K22Rik|AA407443|AI462022|AW107884|C86549|Rod1	polypyrimidine tract binding protein 3	protein-coding
mm_57862.1	chr6	129533655	129533659	-	1	NA	promoter-TSS (NR_045270)	promoter-TSS (NR_045270)	-373	NR_045270	100504641	Mm.398286	NR_045270	ENSMUSG00000097675	1700101I11Rik	-	RIKEN cDNA 1700101I11 gene	ncRNA
mm_46935.1	chr5	114773358	114773370	-	1	NA	TTS (NR_027872)	TTS (NR_027872)	127	NM_019834	26431	Mm.195632	NM_019834	ENSMUSG00000041890	Git2	1500036H07Rik|5830420E16Rik|6430510B20Rik|9630056M03Rik|B230104M05Rik|CAT2|mKIAA0148	G protein-coupled receptor kinase-interactor 2	protein-coding
mm_61820.1	chr7	87584323	87584327	+	1	NA	5' UTR (NM_001081414, exon 1 of 10)	5' UTR (NM_001081414, exon 1 of 10)	157	NM_001143834	108071	Mm.235018	NM_001033224	ENSMUSG00000049583	Grm5	6430542K11Rik|AI850523|Glu5R|Gprc1e|mGluR5|mGluR5b	glutamate receptor, metabotropic 5	protein-coding
mm_143956.1	chr17	86947868	86947901	-	1	NA	promoter-TSS (NM_029121)	promoter-TSS (NM_029121)	3	NM_029121	74915	Mm.159369	NM_029121	ENSMUSG00000053375	Atp6v1e2	4930500C14Rik|Atp6e1|E1	ATPase, H+ transporting, lysosomal V1 subunit E2	protein-coding
mm_68927.1	chr7	126475056	126475079	-	1	NA	promoter-TSS (NM_001289538)	promoter-TSS (NM_001289538)	63	NM_001289538	20399	Mm.8538	NM_011363	ENSMUSG00000030733	Sh2b1	AI425885|C530001K22Rik|Irip|Psm|SH2-B|SH2-Bb|Sh2bpsm1|mKIAA1299	SH2B adaptor protein 1	protein-coding
mm_61812.1	chr7	87278889	87278892	+	1	NA	intron (NM_001285833, intron 2 of 19)	intron (NM_001285833, intron 2 of 19)	32241	NM_001285833	50490	Mm.31748	NM_015760	ENSMUSG00000030562	Nox4	AI648021	NADPH oxidase 4	protein-coding
mm_107004.1	chr12	11295011	11295031	+	1	NA	exon (NM_001324476, exon 16 of 26)	exon (NM_001324476, exon 16 of 26)	-4866	NR_106136	102465775		NR_106136	ENSMUSG00000098879	Mir7675	Gm27965|mmu-mir-7675	microRNA 7675	ncRNA
mm_171971.1	chr5	88547138	88547138	+	1	NA	Intergenic	L1Md_T|LINE|L1	-7345	NM_023054	65961	Mm.490364	NM_023054	ENSMUSG00000070697	Utp3	2400011K09Rik|AW557551|C87704|Crl1|Crlz1|Sas10	UTP3 small subunit processome component	protein-coding
mm_87779.1	chr10	60296385	60296397	+	1	NA	intron (NM_011179, intron 8 of 14)	intron (NM_011179, intron 8 of 14)	11930	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_146072.1	chr18	70531168	70531175	+	1	NA	promoter-TSS (NM_001136090)	promoter-TSS (NM_001136090)	-850	NM_001289515	26447	Mm.244352	NM_011972	ENSMUSG00000038425	Poli	Rad30b	polymerase (DNA directed), iota	protein-coding
mm_2482.1	chr1	105981556	105981584	+	1	NA	Intergenic	Intergenic	-8836	NM_001122676	227449	Mm.210188	NM_001122675	ENSMUSG00000038866	Zcchc2	9930114B20Rik|AW212015	zinc finger, CCHC domain containing 2	protein-coding
mm_122806.1	chr14	54572852	54572864	-	1	NA	intron (NM_010590, intron 2 of 7)	intron (NM_010590, intron 2 of 7)	4803	NM_010590	16475	Mm.100253	NM_010590	ENSMUSG00000022178	Ajuba	Jub	ajuba LIM protein	protein-coding
mm_111379.1	chr12	87369018	87369034	-	1	NA	exon (NM_011479, exon 2 of 12)	exon (NM_011479, exon 2 of 12)	19329	NM_011479	20773	Mm.565	NM_011479	ENSMUSG00000021036	Sptlc2	LCB2|LCB2a|Spt2	serine palmitoyltransferase, long chain base subunit 2	protein-coding
mm_117903.1	chr13	99430082	99430092	-	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-17261	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_54946.1	chr6	48588452	48588456	-	1	NA	promoter-TSS (NM_183309)	promoter-TSS (NM_183309)	-991	NM_183309	330305	Mm.123868	NM_183309	ENSMUSG00000052730	Gm5111	A630038D02|EG330305	predicted gene 5111	protein-coding
mm_168107.1	chr10	14745943	14745957	-	1	NA	intron (NR_045824, intron 3 of 5)	intron (NR_045824, intron 3 of 5)	-14339	NM_008703	18101	Mm.487342	NM_008703	ENSMUSG00000019865	Nmbr	BB182387	neuromedin B receptor	protein-coding
mm_78434.1	chr9	32032286	32032375	+	1	NA	Intergenic	CpG	-83806	NM_001195632	330914	Mm.46683	NM_177379	ENSMUSG00000041444	Arhgap32	3426406O18Rik|Gc-gap|Grit|Px-rics|Rics|mKIAA0712|p200Rhogap|p250Gap	Rho GTPase activating protein 32	protein-coding
mm_150124.1	chr19	30003778	30003813	+	1	NA	promoter-TSS (NM_025741)	promoter-TSS (NM_025741)	5	NM_025741	66745	Mm.158128	NM_025741	ENSMUSG00000024815	Trpd52l3	4931412G03Rik	tumor protein D52-like 3	protein-coding
mm_94002.1	chr10	127595432	127595445	-	1	NA	exon (NM_008512, exon 7 of 89)	exon (NM_008512, exon 7 of 89)	25710	NM_008512	16971	Mm.271854	NM_008512	ENSMUSG00000040249	Lrp1	A2mr|AI316852|CD91|Lrp|b2b1554Clo	low density lipoprotein receptor-related protein 1	protein-coding
mm_103365.1	chr11	75168153	75168156	-	1	NA	promoter-TSS (NM_001098203)	promoter-TSS (NM_001098203)	-2	NM_001098203	15248	Mm.57250	NM_010430	ENSMUSG00000043099	Hic1	AA408311|HIC-1	hypermethylated in cancer 1	protein-coding
mm_170179.1	chr17	60783681	60783682	+	1	NA	Intergenic	L1Md_T|LINE|L1	-1770359	NM_026497	67993	Mm.36507	NM_026497	ENSMUSG00000024228	Nudt12	0610016O18Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 12	protein-coding
mm_28124.1	chr3	86920831	86920977	-	1	NA	promoter-TSS (NM_001195500)	promoter-TSS (NM_001195500)	-20	NM_001195500	70762	Mm.44490	NM_027539	ENSMUSG00000028078	Dclk2	6330415M09Rik|AU044875|CL2|CLICK2|Click-II|Dcamkl2	doublecortin-like kinase 2	protein-coding
mm_137488.1	chr17	26948402	26948428	+	1	NA	promoter-TSS (NR_037244)	promoter-TSS (NR_037244)	-296	NR_037244	100526534		NR_037244	ENSMUSG00000093118	Mir3083	mir-3083|mmu-mir-3083	microRNA 3083	ncRNA
mm_169754.1	chr15	90882499	90882499	+	1	NA	Intergenic	Intergenic	15977	NR_033583	20738	Mm.431547	NR_033583		Spn-ps	Cd43-ps	sialophorin, pseudogene	pseudo
mm_10606.1	chr2	18997331	18997348	+	1	NA	promoter-TSS (NR_024323)	promoter-TSS (NR_024323)	782	NM_008845	18718	Mm.313977	NM_008845	ENSMUSG00000026737	Pip4k2a	AW742916|Pip5k2a	phosphatidylinositol-5-phosphate 4-kinase, type II, alpha	protein-coding
mm_91266.1	chr10	23787144	23787160	-	1	NA	promoter-TSS (NM_011295)	promoter-TSS (NM_011295)	57	NM_011295	20042	Mm.371846	NM_011295	ENSMUSG00000061983	Rps12	-	ribosomal protein S12	protein-coding
mm_116751.1	chr13	51846285	51846288	-	1	NA	promoter-TSS (NM_011817)	promoter-TSS (NM_011817)	-389	NM_011817	23882	Mm.281298	NM_011817	ENSMUSG00000021453	Gadd45g	AI327420|C86281|CR6|DDIT2|OIG37	growth arrest and DNA-damage-inducible 45 gamma	protein-coding
mm_14687.1	chr2	140395422	140395438	+	1	NA	promoter-TSS (NM_028387)	promoter-TSS (NM_028387)	0	NM_001013802	72899	Mm.229466	NM_028387	ENSMUSG00000068205	Macrod2	1110033L15Rik|2610107G07Rik|2900006F19Rik	MACRO domain containing 2	protein-coding
mm_85842.1	chr9	110532945	110532958	-	1	NA	intron (NM_001081340, intron 1 of 20)	CpG	354	NM_001081340	235626	Mm.288949	NM_001081340	ENSMUSG00000044791	Setd2	4921524K10Rik|BC031601|KMT3A	SET domain containing 2	protein-coding
mm_108709.1	chr12	87026319	87026337	+	1	NA	promoter-TSS (NM_172583)	promoter-TSS (NM_172583)	-236	NM_172583	217733	Mm.110032	NM_172583	ENSMUSG00000034145	Tmem63c	4932420N09|9330187M14Rik	transmembrane protein 63c	protein-coding
mm_53423.1	chr6	134035822	134035897	+	1	NA	5' UTR (NM_007961, exon 1 of 8)	5' UTR (NM_007961, exon 1 of 8)	159	NM_007961	14011	Mm.269995	NM_007961	ENSMUSG00000030199	Etv6	AW123102|AW557856|Tel	ets variant 6	protein-coding
mm_114947.1	chr13	96603064	96603074	+	1	NA	intron (NM_023420, intron 5 of 17)	intron (NM_023420, intron 5 of 17)	60334	NM_023420	68018	Mm.24125	NM_023420	ENSMUSG00000021669	Col4a3bp	2810404O15Rik|9230101K08Rik|AU016711|CERT|GPBP	collagen, type IV, alpha 3 (Goodpasture antigen) binding protein	protein-coding
mm_38826.1	chr4	149099803	149099843	-	1	NA	promoter-TSS (NM_019781)	promoter-TSS (NM_019781)	-11	NM_019781	56273	Mm.184172	NM_019781	ENSMUSG00000028975	Pex14	Pex14p|R75137	peroxisomal biogenesis factor 14	protein-coding
mm_19956.1	chr2	117342832	117342896	-	1	NA	promoter-TSS (NM_011246)	promoter-TSS (NM_011246)	13	NM_011246	19419	Mm.42150	NM_011246	ENSMUSG00000027347	Rasgrp1	Rasgrp	RAS guanyl releasing protein 1	protein-coding
mm_20067.1	chr2	120404094	120404101	-	1	NA	promoter-TSS (NM_173734)	promoter-TSS (NM_173734)	19	NM_173734	211499	Mm.260712	NM_173734	ENSMUSG00000033808	Tmem87a	A930025J12Rik	transmembrane protein 87A	protein-coding
mm_58382.1	chr6	149260915	149260919	-	1	NA	Intergenic	Intergenic	-48497	NM_001289661	67246	Mm.333515	NM_026054	ENSMUSG00000032712	2810474O19Rik	6720435I21Rik|AA536804|AU020969|GET|Kiaa1551	RIKEN cDNA 2810474O19 gene	protein-coding
mm_157863.1	chrX	75130893	75130905	-	1	NA	5' UTR (NM_008621, exon 1 of 12)	5' UTR (NM_008621, exon 1 of 12)	117	NM_008621	17524	Mm.391267	NM_008621	ENSMUSG00000031402	Mpp1	55kDa|C130070C03Rik|p55	membrane protein, palmitoylated	protein-coding
mm_83386.1	chr9	44603469	44603478	-	1	NA	Intergenic	MER89|LTR|ERV1	-1419	NM_001110826	13209	Mm.267061	NM_007841	ENSMUSG00000032097	Ddx6	1110001P04Rik|E230023J21Rik|HLR2|mRCK/P54|p54|rck	DEAD (Asp-Glu-Ala-Asp) box polypeptide 6	protein-coding
mm_87733.1	chr10	60132922	60132961	+	1	NA	3' UTR (NM_052994, exon 11 of 11)	3' UTR (NM_052994, exon 11 of 11)	6165	NR_105871	102465546		NR_105871	ENSMUSG00000105468	Mir6906	mmu-mir-6906	microRNA 6906	ncRNA
mm_117254.1	chr13	64366898	64366937	-	1	NA	exon (NM_009984, exon 5 of 8)	exon (NM_009984, exon 5 of 8)	3603	NM_009984	13039	Mm.930	NM_009984	ENSMUSG00000021477	Ctsl	1190035F06Rik|CatL|Ctsl1|MEP|fs|nkt	cathepsin L	protein-coding
mm_9870.1	chr1	185000000	185000012	-	1	NA	promoter-TSS (NM_145515)	promoter-TSS (NM_145515)	-457	NM_145515	226778	Mm.7445	NM_145515	ENSMUSG00000026620	Mark1	AW491150|B930025N23Rik|Emk3|Par-1c|mKIAA1477|mPar-1c	MAP/microtubule affinity regulating kinase 1	protein-coding
mm_120321.1	chr14	63142904	63142915	+	1	NA	3' UTR (NM_007798, exon 10 of 10)	3' UTR (NM_007798, exon 10 of 10)	20447	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_135458.1	chr16	45724706	45724710	-	1	NA	promoter-TSS (NM_019754)	promoter-TSS (NM_019754)	-177	NM_019754	56370	Mm.24183	NM_019754	ENSMUSG00000022658	Tagln3	2700038H05Rik|2900005O10Rik|AI426007|Np25	transgelin 3	protein-coding
mm_82651.1	chr9	22024421	22024423	-	1	NA	intron (NM_010487, intron 6 of 6)	AT_rich|Low_complexity|Low_complexity	21434	NM_008925	19089	Mm.214593	NM_008925	ENSMUSG00000003402	Prkcsh	80K-H|PKCSH	protein kinase C substrate 80K-H	protein-coding
mm_172608.1	chr8	15520076	15520078	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	462424	NM_008664	17930	Mm.272115	NM_008664	ENSMUSG00000031461	Myom2	AW146149	myomesin 2	protein-coding
mm_84679.1	chr9	72099377	72099380	-	1	NA	intron (NM_001253862, intron 3 of 19)	intron (NM_001253862, intron 3 of 19)	11823	NM_001253862	21406	Mm.171615	NM_011544	ENSMUSG00000032228	Tcf12	A130037E08Rik|ALF1|HEB|HEBAlt|HTF-4|HTF4|ME1|REB|bHLHb20	transcription factor 12	protein-coding
mm_40225.1	chr5	37279662	37279671	+	1	NA	exon (NM_001136058, exon 8 of 14)	exon (NM_001136058, exon 8 of 14)	33902	NM_007765	12933	Mm.290995	NM_007765	ENSMUSG00000029121	Crmp1	CRMP-1|DRP-1|Dpysl1|ULIP-3|Ulip3	collapsin response mediator protein 1	protein-coding
mm_43233.1	chr5	129941950	129941971	+	1	NA	promoter-TSS (NM_001286382)	promoter-TSS (NM_001286382)	-149	NM_001001327	69568	Mm.288718	NM_027121	ENSMUSG00000066735	Vkorc1l1	2310024K08Rik	vitamin K epoxide reductase complex, subunit 1-like 1	protein-coding
mm_161996.1	chr19	37330383	37330383	-	1	NA	intron (NM_031156, intron 1 of 23)	intron (NM_031156, intron 1 of 23)	230	NM_031156	15925	Mm.28366	NM_031156	ENSMUSG00000056999	Ide	1300012G03Rik|4833415K22Rik|AA675336|AI507533	insulin degrading enzyme	protein-coding
mm_106971.1	chr12	8947994	8948004	+	1	NA	promoter-TSS (NM_010770)	promoter-TSS (NM_010770)	70	NM_010770	17182	Mm.42226	NM_010770	ENSMUSG00000020583	Matn3	AV009181	matrilin 3	protein-coding
mm_47667.1	chr5	127281573	127281608	-	1	NA	promoter-TSS (NR_038129)	promoter-TSS (NR_038129)	33	NR_038129	67351	Mm.320172	NR_038127	ENSMUSG00000087104	Tmem132cos	1700085B03Rik	transmembrane protein 132C, opposite strand	ncRNA
mm_167.1	chr1	13069894	13069901	+	1	NA	Intergenic	RMER17C|LTR|ERVK	57266	NM_001081209	383491	Mm.309380	NM_001081209	ENSMUSG00000042414	Prdm14	-	PR domain containing 14	protein-coding
mm_96520.1	chr11	68496502	68496512	+	1	NA	3' UTR (NM_177320, exon 19 of 19)	3' UTR (NM_177320, exon 19 of 19)	-6512	NM_001004435	104709	Mm.234573	NM_001004435	ENSMUSG00000046207	Pik3r6	BB220380|p84|p84 PIKAP|p87(PIKAP)|p87PIKAP	phosphoinositide-3-kinase, regulatory subunit 6	protein-coding
mm_151466.1	chr19	58670359	58670368	+	1	NA	promoter-TSS (NM_026925)	promoter-TSS (NM_026925)	-2	NM_026925	69060	Mm.20407	NM_026925	ENSMUSG00000046008	Pnlip	1810007A24Rik|PL|PTL	pancreatic lipase	protein-coding
mm_57856.1	chr6	129487787	129487796	-	1	NA	exon (NM_138648, exon 8 of 8)	exon (NM_138648, exon 8 of 8)	-15012	NR_132130	56644	Mm.239516	NM_020008	ENSMUSG00000079293	Clec7a	BGR|Clecsf12|beta-GR	C-type lectin domain family 7, member a	protein-coding
mm_108823.1	chr12	95703031	95703058	+	1	NA	intron (NM_201518, intron 1 of 1)	intron (NM_201518, intron 1 of 1)	10818	NM_201518	399558	Mm.341948	NM_201518	ENSMUSG00000047414	Flrt2	-	fibronectin leucine rich transmembrane protein 2	protein-coding
mm_31334.1	chr4	46463853	46463893	+	1	NA	exon (NM_130889, exon 3 of 7)	exon (NM_130889, exon 3 of 7)	12947	NM_130889	67628	Mm.263913	NM_130889	ENSMUSG00000028333	Anp32b	2410015B15Rik|PAL31|PHAPI2a|Ssp29	acidic (leucine-rich) nuclear phosphoprotein 32 family, member B	protein-coding
mm_87341.1	chr10	43479283	43479329	+	1	NA	5' UTR (NM_199028, exon 1 of 4)	5' UTR (NM_199028, exon 1 of 4)	166	NM_199028	331623	Mm.490388	NM_199028	ENSMUSG00000038214	Bend3	mKIAA1553	BEN domain containing 3	protein-coding
mm_99522.1	chr11	103170417	103170427	+	1	NA	promoter-TSS (NM_001077698)	promoter-TSS (NM_001077698)	-716	NM_001077698	57778	Mm.138913	NM_019679	ENSMUSG00000055805	Fmnl1	8030453N10Rik|AI553564|Fmnl|Fnrl|Frls	formin-like 1	protein-coding
mm_68370.1	chr7	107801215	107801238	-	1	NA	promoter-TSS (NM_172908)	promoter-TSS (NM_172908)	-47	NM_172908	244199	Mm.99576	NM_172908	ENSMUSG00000048236	Ovch2	9230106D23Rik|Ovtn	ovochymase 2	protein-coding
mm_93259.1	chr10	95564035	95564062	-	1	NA	5' UTR (NM_027722, exon 1 of 5)	5' UTR (NM_027722, exon 1 of 5)	119	NM_027722	71207	Mm.24397	NM_027722	ENSMUSG00000020029	Nudt4	4933436C10Rik|DIPP2|DIPP2alpha|DIPP2beta|HDCMB47P	nudix (nucleoside diphosphate linked moiety X)-type motif 4	protein-coding
mm_172186.1	chr6	50565271	50565288	+	1	NA	exon (NM_007808, exon 3 of 3)	exon (NM_007808, exon 3 of 3)	1195	NM_007808	13063	Mm.35389	NM_007808	ENSMUSG00000063694	Cycs	-	cytochrome c, somatic	protein-coding
mm_164456.1	chr16	55283236	55283240	-	1	NA	promoter-TSS (NM_178720)	promoter-TSS (NM_178720)	-1	NM_178720	239852	Mm.245045	NM_178720	ENSMUSG00000064310	Zpld1	9430016A21Rik	zona pellucida like domain containing 1	protein-coding
mm_142050.1	chr17	35626635	35626639	-	1	NA	promoter-TSS (NM_001244654)	promoter-TSS (NM_001244654)	0	NM_001244654	672682	Mm.454025	NM_001244654	ENSMUSG00000090588	Gm9573	Muc21	predicted gene 9573	protein-coding
mm_159324.1	chr3	19531237	19531237	+	1	NA	promoter-TSS (NM_001163537)	promoter-TSS (NM_001163537)	-10	NM_001163537	66326	Mm.45615	NM_025489	ENSMUSG00000027606	Dnajc5b	1700008A05Rik	DnaJ heat shock protein family (Hsp40) member C5 beta	protein-coding
mm_28680.1	chr3	95331687	95331690	-	1	NA	intron (NM_001163641, intron 14 of 21)	intron (NM_001163641, intron 14 of 21)	12858	NM_001320492	76893	Mm.181009	NM_029789	ENSMUSG00000015714	Cers2	0610013I17Rik|AI225939|Lass2|TRH3	ceramide synthase 2	protein-coding
mm_165251.1	chr2	71787828	71787829	-	1	NA	intron (NM_001277970, intron 1 of 24)	CpG	889	NM_001277970	16403	Mm.225096	NM_008397	ENSMUSG00000027111	Itga6	5033401O05Rik|AI115430|Cd49f|VLA-6	integrin alpha 6	protein-coding
mm_32221.1	chr4	101717583	101717593	+	1	NA	5' UTR (NM_001122899, exon 1 of 19)	5' UTR (NM_001122899, exon 1 of 19)	181	NM_010704	16847	Mm.259282	NM_010704	ENSMUSG00000057722	Lepr	LEPROT|Leprb|Modb1|OB-RGRP|Obr|db|diabetes|obese-like|obl	leptin receptor	protein-coding
mm_168290.1	chr11	101627210	101627225	+	1	NA	promoter-TSS (NM_025654)	promoter-TSS (NM_025654)	-732	NM_025654	66599	Mm.41449	NM_025654	ENSMUSG00000010362	Rdm1	2410008M22Rik|AW212028|Rad52b	RAD52 motif 1	protein-coding
mm_107935.1	chr12	71361923	71361940	+	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	22277	NR_136902	67348	Mm.54261	NR_136902	ENSMUSG00000100668	1700083H02Rik	100041190|Gm3190	RIKEN cDNA 1700083H02 gene	ncRNA
mm_36819.1	chr4	104876389	104876405	-	1	NA	promoter-TSS (NM_146148)	promoter-TSS (NM_146148)	1	NM_001290645	230558	Mm.197638	NM_146148	ENSMUSG00000035031	C8a	-	complement component 8, alpha polypeptide	protein-coding
mm_60274.1	chr7	43915141	43915147	+	1	NA	Intergenic	Intergenic	-18627	NM_174865	317652	Mm.389896	NM_174865	ENSMUSG00000055193	Klk15	-	kallikrein related-peptidase 15	protein-coding
mm_30329.1	chr3	151732087	151732097	-	1	NA	3' UTR (NM_133871, exon 8 of 8)	3' UTR (NM_133871, exon 8 of 8)	17867	NM_133871	99899	Mm.30756	NM_133871	ENSMUSG00000028037	Ifi44	A430056A10Rik|AW261460|MTAP44|p44	interferon-induced protein 44	protein-coding
mm_23841.1	chr3	82370558	82370558	+	1	NA	intron (NM_001081230, intron 4 of 13)	intron (NM_001081230, intron 4 of 13)	12486	NM_001081230	213582	Mm.271269	NM_001081230	ENSMUSG00000033900	Map9	5033421J10Rik|5330427D05Rik|ASAP|Mtap9	microtubule-associated protein 9	protein-coding
mm_92233.1	chr10	69166858	69166867	-	1	NA	Intergenic	MTE2b|LTR|ERVL-MaLR	-41690	NM_001252636	69288	Mm.26659	NM_001081347	ENSMUSG00000019944	Rhobtb1	1700008H16Rik|3110048G13Rik|AI173445|AI573858|AV350930	Rho-related BTB domain containing 1	protein-coding
mm_113321.1	chr13	30766173	30766179	+	1	NA	3' UTR (NM_013674, exon 9 of 9)	3' UTR (NM_013674, exon 9 of 9)	16943	NM_013674	16364	Mm.4677	NM_013674	ENSMUSG00000021356	Irf4	AI385587|IRF-4|LSIRF|NF-EM5|Spip	interferon regulatory factor 4	protein-coding
mm_38619.1	chr4	142015057	142015069	-	1	NA	Intergenic	Intergenic	-2835	NR_131014	78917	Mm.139995	NR_131014	ENSMUSG00000085761	4930455G09Rik	-	RIKEN cDNA 4930455G09 gene	ncRNA
mm_82010.1	chr9	121710487	121710493	+	1	NA	intron (NM_026794, intron 1 of 2)	CpG	101	NM_026794	26901	Mm.24848	NM_026794	ENSMUSG00000032526	Ss18l2	1110020I04Rik|AI463209|Deb1	SS18, nBAF chromatin remodeling complex subunit like 2	protein-coding
mm_107564.1	chr12	44210372	44210394	+	1	NA	promoter-TSS (NM_013760)	promoter-TSS (NM_013760)	70	NR_049203	100885842		NR_049203	ENSMUSG00000093618	Mir5627	Gm23684|mir-5627|mmu-mir-5627	microRNA 5627	ncRNA
mm_21588.1	chr2	164237441	164237450	-	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	896	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_51000.1	chr6	63553123	63553129	+	1	NA	intron (NM_008167, intron 2 of 15)	B1_Mur4|SINE|Alu	296269	NM_008167	14804	Mm.439651	NM_008167	ENSMUSG00000071424	Grid2	B230104L07Rik|GluD2|GluRdelta2|Lc|Lc<J>|MMS10-AC|Ms10ac|cpr|ho|nmf408|tpr	glutamate receptor, ionotropic, delta 2	protein-coding
mm_159937.1	chr6	72958792	72958792	-	1	NA	promoter-TSS (NM_025284)	promoter-TSS (NM_025284)	-44	NM_001190327	19240	Mm.3532	NM_025284	ENSMUSG00000079523	Tmsb10	Ptmb10|Tb10	thymosin, beta 10	protein-coding
mm_159234.1	chr2	139678029	139678029	+	1	NA	promoter-TSS (NM_001276489)	promoter-TSS (NM_001276489)	-149	NM_001276489	319909	Mm.41113	NM_001126490	ENSMUSG00000074766	Ism1	5430433G21Rik|Ism	isthmin 1, angiogenesis inhibitor	protein-coding
mm_109971.1	chr12	12937982	12937989	-	1	NA	intron (NM_008709, intron 2 of 2)	intron (NM_008709, intron 2 of 2)	3851	NM_008709	18109	Mm.16469	NM_008709	ENSMUSG00000037169	Mycn	N-myc|Nmyc|Nmyc-1|Nmyc1|bHLHe37|c-nmyc	v-myc avian myelocytomatosis viral related oncogene, neuroblastoma derived	protein-coding
mm_105125.1	chr11	101226415	101226455	-	1	NA	promoter-TSS (NM_007970)	promoter-TSS (NM_007970)	28	NM_007970	14055	Mm.5027	NM_007970	ENSMUSG00000006920	Ezh1	ENX-2	enhancer of zeste 1 polycomb repressive complex 2 subunit	protein-coding
mm_112010.1	chr12	110978944	110978956	-	1	NA	promoter-TSS (NM_175207)	promoter-TSS (NM_175207)	71	NM_175207	74251	Mm.250989	NM_175207	ENSMUSG00000037904	Ankrd9	2500003O20Rik	ankyrin repeat domain 9	protein-coding
mm_114920.1	chr13	95325143	95325159	+	1	NA	5' UTR (NM_028106, exon 1 of 2)	5' UTR (NM_028106, exon 1 of 2)	326	NM_028106	72114	Mm.3774	NM_028106	ENSMUSG00000041995	Zbed3	0610037K01Rik|2610005H11Rik|AU018975|AU024588	zinc finger, BED type containing 3	protein-coding
mm_67316.1	chr7	79596560	79596569	-	1	NA	intron (NM_019799, intron 9 of 10)	(TG)n|Simple_repeat|Simple_repeat	21093	NM_019799	56315	Mm.10909	NM_019799	ENSMUSG00000030549	Rhcg	BB065800	Rhesus blood group-associated C glycoprotein	protein-coding
mm_97879.1	chr11	83223562	83223601	+	1	NA	promoter-TSS (NR_015519)	promoter-TSS (NR_015519)	5	NR_015519	100043636	Mm.295569	NR_015519	ENSMUSG00000087107	AI662270	AW496474	expressed sequence AI662270	ncRNA
mm_14972.1	chr2	152095087	152095100	+	1	NA	3' UTR (NM_001160410, exon 2 of 2)	3' UTR (NM_001160410, exon 2 of 2)	-10431	NM_029688	76650	Mm.218639	NM_029688	ENSMUSG00000032802	Srxn1	1700127B04Rik|AI854065|AW488194|Npn3|Srx|Srx1|TX01	sulfiredoxin 1 homolog (S. cerevisiae)	protein-coding
mm_39016.1	chr4	152131334	152131336	-	1	NA	intron (NM_207688, intron 3 of 10)	CpG-10714	-2410	NM_019585	56226	Mm.264215	NM_019585	ENSMUSG00000028943	Espn	je	espin	protein-coding
mm_15513.1	chr2	158262704	158262708	+	1	NA	intron (NM_177850, intron 4 of 14)	intron (NM_177850, intron 4 of 14)	4465	NM_177850	329547	Mm.260883	NM_177850	ENSMUSG00000052922	Bpi	9230105K17Rik|Bpifd1	bactericidal permeablility increasing protein	protein-coding
mm_12326.1	chr2	69394153	69394193	+	1	NA	intron (NM_175512, intron 2 of 4)	intron (NM_175512, intron 2 of 4)	13711	NM_175512	241452	Mm.211655	NM_175512	ENSMUSG00000027068	Dhrs9	C730025I08Rik|Rdh15	dehydrogenase/reductase (SDR family) member 9	protein-coding
mm_156464.1	chrX	143518401	143518414	+	1	NA	promoter-TSS (NM_001195048)	promoter-TSS (NM_001195048)	-184	NM_001195048	18481	Mm.40035	NM_008778	ENSMUSG00000031284	Pak3	PAK-3|Pak65alpha|Pak65beta|Stk4	p21 protein (Cdc42/Rac)-activated kinase 3	protein-coding
mm_139432.1	chr17	53568439	53568460	+	1	NA	intron (NM_020005, intron 1 of 17)	intron (NM_020005, intron 1 of 17)	1478	NM_020005	18519	Mm.255025	NM_020005	ENSMUSG00000000708	Kat2b	A930006P13Rik|AI461839|AW536563|Pcaf|p/CAF	K(lysine) acetyltransferase 2B	protein-coding
mm_17321.1	chr2	26476117	26476128	-	1	NA	exon (NM_008714, exon 15 of 34)	exon (NM_008714, exon 15 of 34)	-6003	NR_105962	102465602		NR_105962	ENSMUSG00000098548	Mir6996	Gm27531|mmu-mir-6996	microRNA 6996	ncRNA
mm_36156.1	chr4	59783801	59783876	-	1	NA	promoter-TSS (NM_001013577)	promoter-TSS (NM_001013577)	17	NM_001013577	66209	Mm.51988	NM_001013577	ENSMUSG00000038544	Inip	1110054O05Rik|2610312O17Rik|AA399876|Ssbip1	INTS3 and NABP interacting protein	protein-coding
mm_134359.1	chr16	16829277	16829349	-	1	NA	promoter-TSS (NM_015773)	promoter-TSS (NM_015773)	50	NM_015773	50525	Mm.31701	NM_015773	ENSMUSG00000022783	Spag6l	PF16|Spag6|Spag6l1	sperm associated antigen 6-like	protein-coding
mm_157083.1	chrX	9436088	9436102	-	1	NA	3' UTR (NM_007807, exon 13 of 13)	3' UTR (NM_007807, exon 13 of 13)	33229	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_113463.1	chr13	36117350	36117367	+	1	NA	promoter-TSS (NM_024274)	promoter-TSS (NM_024274)	-1	NM_201358	380840	Mm.390576	NM_201358	ENSMUSG00000046573	Lyrm4	BC034664|Gm903	LYR motif containing 4	protein-coding
mm_44809.1	chr5	33493405	33493408	-	1	NA	Intergenic	B1_Mur2|SINE|Alu	-59316	NM_011320	672284		NM_011320	ENSMUSG00000029112	Nkx1-1	Nkx-1.1|Sax2	NK1 transcription factor related, locus 1 (Drosophila)	protein-coding
mm_89328.1	chr10	87932427	87932441	+	1	NA	3' UTR (NM_010512, exon 5 of 5)	3' UTR (NM_010512, exon 5 of 5)	-34237	NR_000040	22172	Mm.391420	NR_000040		Tyms-ps	-	thymidylate synthase, pseudogene	pseudo
mm_66699.1	chr7	45920652	45920668	-	1	NA	5' UTR (NM_001146346, exon 1 of 5)	5' UTR (NM_001146346, exon 1 of 5)	189	NM_001146346	13732	Mm.20829	NM_010129	ENSMUSG00000040212	Emp3	H-4|H4|HNMP-1|MI-35|Ymp	epithelial membrane protein 3	protein-coding
mm_108466.1	chr12	83632195	83632203	+	1	NA	promoter-TSS (NM_027349)	promoter-TSS (NM_027349)	-35	NM_027349	67039	Mm.46005	NM_027349	ENSMUSG00000010608	Rbm25	2600011C06Rik|2610015J01Rik|A130095G20Rik|AI159652|AL023075|AU043498|RNPC7	RNA binding motif protein 25	protein-coding
mm_137662.1	chr17	28691791	28691825	+	1	NA	promoter-TSS (NM_001168513)	promoter-TSS (NM_001168513)	466	NM_001168514	26416	Mm.311337	NM_011951	ENSMUSG00000053436	Mapk14	CSBP2|Crk1|Csbp1|Mxi2|PRKM14|PRKM15|p38|p38-alpha|p38MAPK|p38a|p38alpha	mitogen-activated protein kinase 14	protein-coding
mm_83815.1	chr9	53617358	53617362	-	1	NA	3' UTR (NM_001161618, exon 18 of 18)	3' UTR (NM_001161618, exon 18 of 18)	-7010	NM_144784	110446	Mm.293233	NM_144784	ENSMUSG00000032047	Acat1	6330585C21Rik|Acat	acetyl-Coenzyme A acetyltransferase 1	protein-coding
mm_141684.1	chr17	33951047	33951064	-	1	NA	TTS (NM_011296)	TTS (NM_011296)	433	NM_019420	54218	Mm.11132	NM_019420	ENSMUSG00000067370	B3galt4	Gal-T2|Galt2	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 4	protein-coding
mm_36084.1	chr4	58206671	58206673	-	1	NA	promoter-TSS (NM_022814)	promoter-TSS (NM_022814)	-76	NM_022814	64817	Mm.261024	NM_022814	ENSMUSG00000028369	Svep1	1110021D17Rik|4833413O10Rik|AA387071|D430029O09Rik|Polydom	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	protein-coding
mm_145429.1	chr18	58678018	58678040	+	1	NA	3' UTR (NM_025478, exon 5 of 5)	3' UTR (NM_025478, exon 5 of 5)	18547	NM_025478	66307	Mm.182574	NM_025478	ENSMUSG00000024601	Isoc1	2610034N03Rik	isochorismatase domain containing 1	protein-coding
mm_49229.1	chr6	15824981	15824989	+	1	NA	Intergenic	Intergenic	104324	NM_175088	16543	Mm.1314	NM_175088	ENSMUSG00000041390	Mdfic	Kdt1|Mdfid	MyoD family inhibitor domain containing	protein-coding
mm_70839.1	chr8	23411247	23411270	+	1	NA	promoter-TSS (NM_013834)	promoter-TSS (NM_013834)	-244	NM_013834	20377	Mm.281691	NM_013834	ENSMUSG00000031548	Sfrp1	2210415K03Rik|AW011917|AW107218|AW742929|sFRP-1	secreted frizzled-related protein 1	protein-coding
mm_131627.1	chr16	20123603	20123606	+	1	NA	3' UTR (NM_029436, exon 8 of 8)	3' UTR (NM_029436, exon 8 of 8)	-17459	NM_001033237	208146	Mm.390895	NM_001033237	ENSMUSG00000041215	Yeats2	BC042768|mKIAA1197	YEATS domain containing 2	protein-coding
mm_30056.1	chr3	136684653	136684667	-	1	NA	intron (NM_008913, intron 1 of 13)	intron (NM_008913, intron 1 of 13)	14594	NM_001293622	19055	Mm.331389	NM_008913	ENSMUSG00000028161	Ppp3ca	2900074D19Rik|CN|Caln|Calna|CnA	protein phosphatase 3, catalytic subunit, alpha isoform	protein-coding
mm_168591.1	chr1	173879873	173879877	-	1	NA	intron (NM_001170853, intron 2 of 9)	intron (NM_001170853, intron 2 of 9)	312	NM_001170853	100040462	Mm.463437	NM_001170853	ENSMUSG00000090272	Mndal	Gm2785|Ifi212	myeloid nuclear differentiation antigen like	protein-coding
mm_148576.1	chr19	4878672	4878718	+	1	NA	promoter-TSS (NM_001168517)	promoter-TSS (NM_001168517)	5	NM_001168517	70605	Mm.36885	NM_027476	ENSMUSG00000006463	Zdhhc24	5730496N17Rik|Leng4	zinc finger, DHHC domain containing 24	protein-coding
mm_153140.1	chr19	34246177	34246191	-	1	NA	exon (NM_007392, exon 6 of 9)	exon (NM_007392, exon 6 of 9)	9189	NM_007392	11475	Mm.213025	NM_007392	ENSMUSG00000035783	Acta2	0610041G09Rik|Actvs|SMalphaA|a-SMA|alphaSMA	actin, alpha 2, smooth muscle, aorta	protein-coding
mm_10075.1	chr1	195092243	195092253	-	1	NA	promoter-TSS (NM_010778)	promoter-TSS (NM_010778)	0	NR_132621	17221	Mm.12884	NM_010778	ENSMUSG00000016493	Cd46	Mcp	CD46 antigen, complement regulatory protein	protein-coding
mm_15699.1	chr2	163725671	163725693	+	1	NA	TTS (NM_001272052)	TTS (NM_001272052)	24557	NM_007398	11486	Mm.388	NM_007398	ENSMUSG00000017697	Ada	-	adenosine deaminase	protein-coding
mm_77401.1	chr8	120532598	120532638	-	1	NA	intron (NM_198671, intron 1 of 15)	intron (NM_198671, intron 1 of 15)	-3239	NM_001145897	382034	Mm.334856	NM_198671	ENSMUSG00000031822	Gse1	2210013I18Rik|mKIAA0182	genetic suppressor element 1, coiled-coil protein	protein-coding
mm_59916.1	chr7	30418159	30418169	+	1	NA	TTS (NM_011662)	TTS (NM_011662)	1690	NM_011827	23900	Mm.379050	NM_011827	ENSMUSG00000064109	Hcst	DAP10|KAP10	hematopoietic cell signal transducer	protein-coding
mm_143076.1	chr17	57041660	57041662	-	1	NA	promoter-TSS (NM_175333)	promoter-TSS (NM_175333)	-7	NM_175333	103775	Mm.33647	NM_175333	ENSMUSG00000011486	Slc25a41	4933406J04Rik|AI507137	solute carrier family 25, member 41	protein-coding
mm_129907.1	chr15	84065330	84065364	-	1	NA	promoter-TSS (NM_029946)	promoter-TSS (NM_029946)	2	NM_029946	77627	Mm.196288	NM_029946	ENSMUSG00000022441	Efcab6	4931407K02Rik|4932408N08Rik|bM150J22.2|mKIAA1672	EF-hand calcium binding domain 6	protein-coding
mm_153549.1	chr19	42086339	42086375	-	1	NA	promoter-TSS (NM_198108)	promoter-TSS (NM_198108)	13	NM_198108	226123	Mm.259441	NM_198108	ENSMUSG00000049670	Morn4	-	MORN repeat containing 4	protein-coding
mm_135105.1	chr16	35573594	35573604	-	1	NA	intron (NM_013661, intron 1 of 21)	intron (NM_013661, intron 1 of 21)	32237	NM_013661	20357	Mm.42015	NM_013661	ENSMUSG00000052133	Sema5b	AI893641|SemG|Semag|mKIAA1445	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B	protein-coding
mm_31288.1	chr4	45932636	45932668	+	1	NA	intron (NM_198660, intron 30 of 37)	intron (NM_198660, intron 30 of 37)	-32683	NM_001290475	100121	Mm.275413	NM_146142	ENSMUSG00000035517	Tdrd7	5730495N10Rik|AI447470|PCTAIRE2BP	tudor domain containing 7	protein-coding
mm_109202.1	chr12	108667190	108667206	+	1	NA	intron (NM_001163394, intron 3 of 13)	intron (NM_001163394, intron 3 of 13)	8578	NR_029771	723909		NR_029771	ENSMUSG00000065436	Mir342	Mirn342|mmu-mir-342	microRNA 342	ncRNA
mm_159755.1	chr5	88376108	88376108	+	1	NA	promoter-TSS (NM_027793)	promoter-TSS (NM_027793)	0	NM_027793	71421	Mm.79700	NM_027793	ENSMUSG00000029282	Amtn	5430427O21Rik	amelotin	protein-coding
mm_131248.1	chr16	10545341	10545351	+	1	NA	promoter-TSS (NM_177562)	promoter-TSS (NM_177562)	7	NM_001204229	74374	Mm.159176	NM_177562	ENSMUSG00000068663	Clec16a	4932416N17Rik|curt|mKIAA0350	C-type lectin domain family 16, member A	protein-coding
mm_104500.1	chr11	95912607	95912609	-	1	NA	intron (NM_008081, intron 1 of 10)	intron (NM_008081, intron 1 of 10)	2263	NM_008081	14422	Mm.340702	NM_008081	ENSMUSG00000013418	B4galnt2	AI593864|Dlb-1|Dlb1|Galg2|Galgt2|Ggm3|Igf2bp1	beta-1,4-N-acetyl-galactosaminyl transferase 2	protein-coding
mm_137860.1	chr17	31208050	31208112	+	1	NA	promoter-TSS (NM_177823)	promoter-TSS (NM_177823)	15	NM_177823	328795	Mm.387930	NM_177823	ENSMUSG00000042345	Ubash3a	5830413C03Rik|C330001M22|Sts-2|TULA|TULA-1	ubiquitin associated and SH3 domain containing, A	protein-coding
mm_109402.1	chr12	110375514	110375517	+	1	NA	Intergenic	Intergenic	-71664	NM_001135001	26931	Mm.240396	NM_012023	ENSMUSG00000017843	Ppp2r5c	2610043M05Rik|2700063L20Rik|AI060890|AW545884|C85228|D12Bwg0916e|mKIAA0044	protein phosphatase 2, regulatory subunit B', gamma	protein-coding
mm_65455.1	chr7	25463701	25463718	-	1	NA	3' UTR (NM_001039186, exon 8 of 8)	3' UTR (NM_001039186, exon 8 of 8)	13916	NM_001039185	26365	Mm.322502	NM_011926	ENSMUSG00000074272	Ceacam1	Bgp|Bgp1|C-CAM|CD66a|Cc1|Cea-1|Cea-7|Cea1|Cea7|Hv-2|Hv2|MHVR|MHVR1|Mhv-1|bb-1|mCEA1|mmCGM1|mmCGM1a|mmCGM2	carcinoembryonic antigen-related cell adhesion molecule 1	protein-coding
mm_47138.1	chr5	120548267	120548269	-	1	NA	intron (NM_145853, intron 13 of 27)	intron (NM_145853, intron 13 of 27)	37076	NM_001177594	170756	Mm.291070	NM_133221	ENSMUSG00000032754	Slc8b1	AF261233|NCKX6|NCLX|Slc24a6	solute carrier family 8 (sodium/lithium/calcium exchanger), member B1	protein-coding
mm_168695.1	chr11	97450265	97450269	+	1	NA	5' UTR (NM_021493, exon 1 of 19)	5' UTR (NM_021493, exon 1 of 19)	107	NM_021493	58996	Mm.394118	NM_021493	ENSMUSG00000049807	Arhgap23	A330041B18Rik	Rho GTPase activating protein 23	protein-coding
mm_31777.1	chr4	63560218	63560236	+	1	NA	promoter-TSS (NM_144905)	promoter-TSS (NM_144905)	-133	NM_144905	230279	Mm.41523	NM_144905	ENSMUSG00000045917	Tmem268	6330416G13Rik|AW492431|bM230C2.2	transmembrane protein 268	protein-coding
mm_109652.1	chr12	112861107	112861115	+	1	NA	promoter-TSS (NM_019925)	promoter-TSS (NM_019925)	-195	NM_019925	56696	Mm.20455	NM_019925	ENSMUSG00000021298	Gpr132	G2a	G protein-coupled receptor 132	protein-coding
mm_39223.1	chr4	156199721	156199736	-	1	NA	exon (NM_015783, exon 2 of 2)	exon (NM_015783, exon 2 of 2)	1090	NM_015783	100038882	Mm.4950	NM_015783	ENSMUSG00000035692	Isg15	G1p2|IGI15|IP17|Irfp|UCRP	ISG15 ubiquitin-like modifier	protein-coding
mm_83178.1	chr9	40800763	40800786	-	1	NA	promoter-TSS (NM_031165)	promoter-TSS (NM_031165)	-499	NM_031165	15481	Mm.290774	NM_031165	ENSMUSG00000015656	Hspa8	2410008N15Rik|Hsc70|Hsc71|Hsc73|Hsp73|Hspa10	heat shock protein 8	protein-coding
mm_92110.1	chr10	63057445	63057459	-	1	NA	intron (NM_026085, intron 9 of 9)	intron (NM_026085, intron 9 of 9)	-4165	NM_026701	68371	Mm.261389	NM_026701	ENSMUSG00000020072	Pbld1	0610038K03Rik|Mawbp|Pbld	phenazine biosynthesis-like protein domain containing 1	protein-coding
mm_136447.1	chr16	94994949	94994965	-	1	NA	intron (NM_001025584, intron 1 of 4)	intron (NM_001025584, intron 1 of 4)	2739	NM_001025584	16522	Mm.328720	NM_010606	ENSMUSG00000043301	Kcnj6	BIR1|GIRK2|KATP2|KCNJ7|Kir3.2|weaver|wv	potassium inwardly-rectifying channel, subfamily J, member 6	protein-coding
mm_68644.1	chr7	118485643	118485657	-	1	NA	3' UTR (NM_001033380, exon 1 of 1)	3' UTR (NM_001033380, exon 1 of 1)	6325	NM_001033380	319622	Mm.323386	NM_001033380	ENSMUSG00000095115	Itpripl2	C130081G24|E030018N11Rik	inositol 1,4,5-triphosphate receptor interacting protein-like 2	protein-coding
mm_105439.1	chr11	104370018	104370022	-	1	NA	intron (NM_001081045, intron 3 of 13)	AT_rich|Low_complexity|Low_complexity	72271	NM_001081045	76719	Mm.136418	NM_001081045	ENSMUSG00000018412	Kansl1	1700081L11Rik|9430041J06Rik|mKIAA1267	KAT8 regulatory NSL complex subunit 1	protein-coding
mm_100962.1	chr11	6637274	6637302	-	1	NA	exon (NM_011709, exon 2 of 4)	exon (NM_011709, exon 2 of 4)	1361	NM_011709	22373	Mm.268094	NM_011709	ENSMUSG00000000381	Wap	-	whey acidic protein	protein-coding
mm_39129.1	chr4	155080837	155080879	-	1	NA	exon (NM_026395, exon 3 of 7)	exon (NM_026395, exon 3 of 7)	5439	NM_026395	67830	Mm.241604	NM_026395	ENSMUSG00000029048	Rer1	1110060F11Rik|5830454N22Rik|AU043380	retention in endoplasmic reticulum sorting receptor 1	protein-coding
mm_111577.1	chr12	101818997	101819007	-	1	NA	5' UTR (NM_011812, exon 1 of 11)	5' UTR (NM_011812, exon 1 of 11)	117	NM_011812	23876	Mm.288381	NM_011812	ENSMUSG00000021186	Fbln5	A55|DANCE|EVEC	fibulin 5	protein-coding
mm_68180.1	chr7	103853200	103853213	-	1	NA	promoter-TSS (NM_008221)	promoter-TSS (NM_008221)	1	NM_008221	15135	Mm.440164	NM_008221	ENSMUSG00000052187	Hbb-y	Ey|Hby	hemoglobin Y, beta-like embryonic chain	protein-coding
mm_36779.1	chr4	102984209	102984219	-	1	NA	intron (NR_040444, intron 1 of 3)	intron (NR_040444, intron 1 of 3)	-2165	NM_001163767	67344	Mm.111346	NM_026100	ENSMUSG00000028523	Tctex1d1	1700055O19Rik	Tctex1 domain containing 1	protein-coding
mm_93951.1	chr10	127263044	127263050	-	1	NA	5' UTR (NM_001039000, exon 1 of 29)	5' UTR (NM_001039000, exon 1 of 29)	316	NM_008447	16572	Mm.30355	NM_008447	ENSMUSG00000074657	Kif5a	D10Bwg0738e|Khc|Kif5|Kns|mKIAA4086	kinesin family member 5A	protein-coding
mm_129988.1	chr15	86141349	86141386	-	1	NA	3' UTR (NM_145475, exon 13 of 13)	3' UTR (NM_145475, exon 13 of 13)	44774	NM_145475	223753	Mm.222685	NM_145475	ENSMUSG00000035891	Cerk	AI848610|D330016D08Rik|mKIAA1646	ceramide kinase	protein-coding
mm_130784.1	chr15	101562890	101562892	-	1	NA	promoter-TSS (NM_177717)	promoter-TSS (NM_177717)	59	NM_177717	239673	Mm.461267	NM_177717	ENSMUSG00000048699	Krt90	4732456N10Rik|Ket90	keratin 90	protein-coding
mm_142171.1	chr17	36231308	36231325	-	1	NA	Intergenic	CpG	26530	NM_026308	67676	Mm.27131	NM_026308	ENSMUSG00000024446	Rpp21	0610037N01Rik	ribonuclease P 21 subunit	protein-coding
mm_12228.1	chr2	68470845	68470855	+	1	NA	intron (NM_016866, intron 1 of 17)	intron (NM_016866, intron 1 of 17)	1131	NM_016866	53416	Mm.198414	NM_016866	ENSMUSG00000027030	Stk39	AW227544|AW556857|DCHT|RF005|Rnl5|SPAK	serine/threonine kinase 39	protein-coding
mm_59132.1	chr7	19965540	19965543	+	1	NA	intron (NM_027839, intron 1 of 11)	intron (NM_027839, intron 1 of 11)	129	NM_027839	71601	Mm.98097	NM_027839	ENSMUSG00000070777	Ceacam20	9130012D09Rik	carcinoembryonic antigen-related cell adhesion molecule 20	protein-coding
mm_24914.1	chr3	96262438	96262467	+	1	NA	TTS (NM_033596)	TTS (NM_033596)	865	NM_033596	97122	Mm.227295	NM_033596	ENSMUSG00000091405	Hist2h4	H4|X04652	histone cluster 2, H4	protein-coding
mm_73586.1	chr8	109986651	109986676	+	1	NA	Intergenic	Intergenic	-3773	NM_146214	234724	Mm.28110	NM_146214	ENSMUSG00000001670	Tat	-	tyrosine aminotransferase	protein-coding
mm_87524.1	chr10	53337351	53337381	+	1	NA	promoter-TSS (NM_001141927)	promoter-TSS (NM_001141927)	-320	NM_023129	18821	Mm.34145	NM_023129	ENSMUSG00000038583	Pln	Plb	phospholamban	protein-coding
mm_60212.1	chr7	43463109	43463113	+	1	NA	promoter-TSS (NM_001290316)	promoter-TSS (NM_001290316)	-122	NM_001290316	75690	Mm.30200	NM_001290316	ENSMUSG00000070604	Vsig10l	-	V-set and immunoglobulin domain containing 10 like	protein-coding
mm_52750.1	chr6	120666301	120666354	+	1	NA	promoter-TSS (NM_001128151)	promoter-TSS (NM_001128151)	-94	NM_001128151	330409	Mm.333357	NM_001128151	ENSMUSG00000071226	Cecr2	2610101O16Rik|2810409N01Rik|Gtl4|mKIAA1740	cat eye syndrome chromosome region, candidate 2	protein-coding
mm_142989.1	chr17	56290066	56290084	-	1	NA	intron (NM_025836, intron 1 of 7)	intron (NM_025836, intron 1 of 7)	436	NM_025836	66905	Mm.311696	NM_025836	ENSMUSG00000024197	Plin3	1300012C15Rik|M6prbp1|Tip47	perilipin 3	protein-coding
mm_32461.1	chr4	107381143	107381147	+	1	NA	intron (NM_028355, intron 6 of 17)	RSINE1|SINE|B4	13361	NM_028355	72787	Mm.28478	NM_028355	ENSMUSG00000028614	Ndc1	2810475A17Rik|AI450313|Tmem48|sks	NDC1 transmembrane nucleoporin	protein-coding
mm_104973.1	chr11	100207403	100207436	-	1	NA	promoter-TSS (NM_016958)	promoter-TSS (NM_016958)	91	NM_016958	16664	Mm.439898	NM_016958	ENSMUSG00000045545	Krt14	AI626930|CK-14|K14|Krt-1.14|Krt1-14	keratin 14	protein-coding
mm_155863.1	chrX	101377324	101377334	+	1	NA	promoter-TSS (NM_008124)	promoter-TSS (NM_008124)	94	NM_008124	14618	Mm.21198	NM_008124	ENSMUSG00000047797	Gjb1	Cnx32|Cx32|connexin-32	gap junction protein, beta 1	protein-coding
mm_115173.1	chr13	108158724	108158754	+	1	NA	promoter-TSS (NM_001127346)	promoter-TSS (NM_001127346)	1	NM_028042	71991	Mm.212208	NM_028042	ENSMUSG00000021694	Ercc8	2410022P04Rik|2810431L23Rik|4631412O06Rik|B130065P18Rik|Ckn1|Csa	excision repaiross-complementing rodent repair deficiency, complementation group 8	protein-coding
mm_67659.1	chr7	85541244	85541247	-	1	NA	Intergenic	L1_Mur3|LINE|L1	27843	NM_001105183	670940	Mm.469908	NM_001105183	ENSMUSG00000090806	Vmn2r70	EG620835	vomeronasal 2, receptor 70	protein-coding
mm_168100.1	chr10	129593767	129593770	-	1	NA	Intergenic	L1Md_T|LINE|L1	14711	NM_146931	258933	Mm.377755	NM_146931	ENSMUSG00000052012	Olfr796	MOR269-1	olfactory receptor 796	protein-coding
mm_154748.1	chrX	10582135	10582137	+	1	NA	intron (NM_019634, intron 2 of 7)	intron (NM_019634, intron 2 of 7)	97020	NM_019634	21912	Mm.18590	NM_019634	ENSMUSG00000058254	Tspan7	1200014P11Rik|A15|AI323365|Cd231|Mxs1|PE31|R74651|TALLA|Tm4sf2	tetraspanin 7	protein-coding
mm_108770.1	chr12	89772053	89772059	+	1	NA	intron (NM_172544, intron 14 of 19)	intron (NM_172544, intron 14 of 19)	-40427	NM_001252074	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding
mm_141232.1	chr17	27431416	27431458	-	1	NA	exon (NM_001291045, exon 9 of 10)	exon (NM_001291045, exon 9 of 10)	72096	NM_001013385	268934	Mm.358940	NM_001013385	ENSMUSG00000063239	Grm4	Gprc1d|mGluR4	glutamate receptor, metabotropic 4	protein-coding
mm_4503.1	chr1	173729142	173729157	+	1	NA	exon (NM_001204910, exon 5 of 8)	exon (NM_001204910, exon 5 of 8)	12660	NM_001204910	226691	Mm.440876	NM_001204910	ENSMUSG00000073490	Ifi207	AI607873|Pyhin-A	interferon activated gene 207	protein-coding
mm_10645.1	chr2	20559881	20559905	+	1	NA	intron (NM_029895, intron 3 of 18)	intron (NM_029895, intron 3 of 18)	40380	NM_001177631	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding
mm_19030.1	chr2	76969192	76969226	-	1	NA	exon (NM_011652, exon 8 of 313)	exon (NM_011652, exon 8 of 313)	13338	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_14005.1	chr2	122028545	122028563	+	1	NA	promoter-TSS (NM_001256055)	promoter-TSS (NM_001256055)	-26	NM_144545	78655	Mm.458184	NM_144545	ENSMUSG00000027236	Eif3j1	1810016I04Rik|2700079K05Rik|AA409117|AA409446|C78575|Eif3j|Eif3j-1|Eif3j-2|Eif3j2|Eif3s1|eIF-3-alpha-A|eIF-3-alpha-B|eIF3-alpha|eIF3-p35|eIF3j-A|eIF3j-B	eukaryotic translation initiation factor 3, subunit J1	protein-coding
mm_83527.1	chr9	46230116	46230127	-	1	NA	exon (NM_009692, exon 4 of 4)	exon (NM_009692, exon 4 of 4)	1491	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2|apo-AI|apoA-I	apolipoprotein A-I	protein-coding
mm_152046.1	chr19	6141200	6141209	-	1	NA	promoter-TSS (NM_019722)	promoter-TSS (NM_019722)	-67	NM_019722	56327	Mm.21071	NM_019722	ENSMUSG00000024944	Arl2	2610009M23Rik|AI115441|AW553335	ADP-ribosylation factor-like 2	protein-coding
mm_71977.1	chr8	70594402	70594412	+	1	NA	promoter-TSS (NM_023627)	promoter-TSS (NM_023627)	-74	NM_023627	71780	Mm.29357	NM_023627	ENSMUSG00000019139	Isyna1	1300017C10Rik|AU018670	myo-inositol 1-phosphate synthase A1	protein-coding
mm_78222.1	chr9	21568288	21568291	+	1	NA	intron (NM_153141, intron 1 of 14)	intron (NM_153141, intron 1 of 14)	21395	NM_153141	59035	Mm.178115	NM_021531	ENSMUSG00000032185	Carm1	Prmt4	coactivator-associated arginine methyltransferase 1	protein-coding
mm_82605.1	chr9	21367453	21367472	-	1	NA	promoter-TSS (NM_001042707)	promoter-TSS (NM_001042707)	-409	NM_001042708	16201	Mm.440026	NM_010561	ENSMUSG00000032178	Ilf3	MBII-26|MPHOSPH4|NF90|NFAR	interleukin enhancer binding factor 3	protein-coding
mm_104720.1	chr11	98149552	98149621	-	1	NA	promoter-TSS (NM_028149)	promoter-TSS (NM_028149)	30	NM_028149	72194	Mm.218350	NM_028149	ENSMUSG00000020883	Fbxl20	2610511F20Rik|4632423N09Rik|AI849362|AL117906|C86145|Fbl2|Scr|mKIAA4147	F-box and leucine-rich repeat protein 20	protein-coding
mm_80083.1	chr9	70067947	70067955	+	1	NA	Intergenic	RSINE1|SINE|B4	-29863	NM_028087	72077	Mm.195555	NM_028087	ENSMUSG00000032226	Gcnt3	2010013H22Rik|2210021I22Rik|2210401J11Rik	glucosaminyl (N-acetyl) transferase 3, mucin type	protein-coding
mm_39502.1	chr5	21194419	21194433	+	1	NA	exon (NM_175437, exon 2 of 31)	exon (NM_175437, exon 2 of 31)	8159	NM_175437	212167	Mm.121705	NM_175437	ENSMUSG00000039934	Gsap	A530088I07Rik|Pion	gamma-secretase activating protein	protein-coding
mm_159941.1	chr6	83086341	83086341	+	1	NA	promoter-TSS (NM_010692)	promoter-TSS (NM_010692)	-24	NM_010692	16815	Mm.20359	NM_010692	ENSMUSG00000034968	Lbx2	Lbx2h	ladybird homeobox homolog 2 (Drosophila)	protein-coding
mm_93042.1	chr10	88379052	88379073	-	1	NA	promoter-TSS (NM_001004164)	promoter-TSS (NM_001004164)	-350	NM_001004164	432486	Mm.335190	NM_001004164	ENSMUSG00000035311	Gnptab	EG432486|mKIAA1208	N-acetylglucosamine-1-phosphate transferase, alpha and beta subunits	protein-coding
mm_97069.1	chr11	72961181	72961228	+	1	NA	promoter-TSS (NM_001163337)	promoter-TSS (NM_001163337)	35	NM_001163337	53313	Mm.6306	NM_016745	ENSMUSG00000020788	Atp2a3	SERCA3b|Serca3	ATPase, Ca++ transporting, ubiquitous	protein-coding
mm_42142.1	chr5	111417760	111417770	+	1	NA	promoter-TSS (NM_001081235)	promoter-TSS (NM_001081235)	-401	NM_001081235	433938	Mm.332576	NM_001081235	ENSMUSG00000070576	Mn1	AA003644|AA009236	meningioma 1	protein-coding
mm_55475.1	chr6	68863042	68863048	-	1	NA	Intergenic	Intergenic	464129	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_88956.1	chr10	81390312	81390326	+	1	NA	Intergenic	Intergenic	-2745	NM_001099917	72273	Mm.253147	NM_001099917	ENSMUSG00000078439	Smim24	2210404O07Rik	small integral membrane protein 24	protein-coding
mm_82885.1	chr9	32526938	32526941	-	1	NA	intron (NM_008026, intron 1 of 8)	intron (NM_008026, intron 1 of 8)	14513	NM_008026	14247	Mm.258908	NM_008026	ENSMUSG00000016087	Fli1	EWSR2|Fli-1|SIC-1|Sic1	Friend leukemia integration 1	protein-coding
mm_14027.1	chr2	122152640	122152750	+	1	NA	3' UTR (NM_009735, exon 4 of 4)	3' UTR (NM_009735, exon 4 of 4)	5008	NM_009735	12010	Mm.163	NM_009735	ENSMUSG00000060802	B2m	Ly-m11|beta2-m|beta2m	beta-2 microglobulin	protein-coding
mm_55463.1	chr6	67535686	67535697	-	1	NA	exon (NM_020047, exon 1 of 1)	exon (NM_020047, exon 1 of 1)	131	NM_020047	56753	Mm.439913	NM_020047	ENSMUSG00000051397	Tacstd2	C80403|EGP-1|GA733-1|Ly97|TROP2	tumor-associated calcium signal transducer 2	protein-coding
mm_93758.1	chr10	120193341	120193353	-	1	NA	intron (NM_028679, intron 1 of 11)	intron (NM_028679, intron 1 of 11)	8190	NM_028679	73914	Mm.146194	NM_028679	ENSMUSG00000020227	Irak3	4833428C18Rik|AI563835|IRAK-M	interleukin-1 receptor-associated kinase 3	protein-coding
mm_86263.1	chr9	121704687	121704700	-	1	NA	intron (NM_178677, intron 1 of 7)	intron (NM_178677, intron 1 of 7)	336	NM_001164562	215474	Mm.31421	NM_178677	ENSMUSG00000061536	Sec22c	4932412K21|5930407I15Rik|C530046H07|Sec22l3	SEC22 homolog C, vesicle trafficking protein	protein-coding
mm_43623.1	chr5	138162183	138162191	+	1	NA	exon (NM_012002, exon 4 of 10)	exon (NM_012002, exon 4 of 10)	1085	NM_012002	26893	Mm.3981	NM_012002	ENSMUSG00000019494	Cops6	Sgn3|VIP/MOV34	COP9 signalosome subunit 6	protein-coding
mm_8738.1	chr1	160212865	160212873	-	1	NA	promoter-TSS (NM_009786)	promoter-TSS (NM_009786)	23	NM_009786	12301	Mm.10702	NM_009786	ENSMUSG00000014226	Cacybp	SIP	calcyclin binding protein	protein-coding
mm_126084.1	chr15	77840272	77840276	+	1	NA	intron (NM_022410, intron 1 of 40)	intron (NM_022410, intron 1 of 40)	1901	NM_022410	17886	Mm.29677	NM_022410	ENSMUSG00000022443	Myh9	Fltn|Myhn-1|Myhn1|NMHCIIA|NMMHC-A|NMMHC-IIA|TU72.6	myosin, heavy polypeptide 9, non-muscle	protein-coding
mm_76801.1	chr8	104247571	104247574	-	1	NA	intron (NM_021028, intron 2 of 9)	intron (NM_021028, intron 2 of 9)	986	NR_045642	57813	Mm.183110	NM_021028	ENSMUSG00000035824	Tk2	AU024611|mt-TK	thymidine kinase 2, mitochondrial	protein-coding
mm_5771.1	chr1	51473944	51473978	-	1	NA	intron (NM_001310548, intron 3 of 5)	intron (NM_001310548, intron 3 of 5)	4438	NM_028696	109019	Mm.196290	NM_028696	ENSMUSG00000026107	Nabp1	4930434H03Rik|4930442A21Rik|4930488J04Rik|4933440J18Rik|5830411E10Rik|AI852561|Nbp1|Obfc2a|Ssb2	nucleic acid binding protein 1	protein-coding
mm_27020.1	chr3	26046094	26046109	-	1	NA	intron (NM_138666, intron 3 of 7)	intron (NM_138666, intron 3 of 7)	107206	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_59691.1	chr7	28451944	28451989	+	1	NA	promoter-TSS (NM_001141921)	promoter-TSS (NM_001141921)	-19	NM_030562	80749	Mm.483073	NM_030562	ENSMUSG00000030600	Lrfn1	BC004018|SALM2|Semo1	leucine rich repeat and fibronectin type III domain containing 1	protein-coding
mm_138304.1	chr17	34643956	34643959	+	1	NA	promoter-TSS (NM_019873)	promoter-TSS (NM_019873)	-926	NM_019873	56299	Mm.10025	NM_019873	ENSMUSG00000033739	Fkbpl	DIR1|NG7|Ppiase-X|Wisp39	FK506 binding protein-like	protein-coding
mm_129103.1	chr15	76047657	76047701	-	1	NA	intron (NM_001310543, intron 34 of 35)	intron (NM_001310543, intron 34 of 35)	17209	NR_105917	102466772		NR_105917	ENSMUSG00000098451	Mir6952	Gm27948|mmu-mir-6952	microRNA 6952	ncRNA
mm_1060.1	chr1	58973662	58973684	+	1	NA	promoter-TSS (NM_172406)	promoter-TSS (NM_172406)	102	NM_172656	227154	Mm.286006	NM_172656	ENSMUSG00000026027	Stradb	AA792893|Als2cr2|B830008M19|D1Ucla2|ILPIP|ILPIPA|PRO1038|Papk|Syradb	STE20-related kinase adaptor beta	protein-coding
mm_153408.1	chr19	40564974	40564987	-	1	NA	exon (NM_153554, exon 13 of 19)	exon (NM_153554, exon 13 of 19)	23483	NM_019698	56454	Mm.233117	NM_019698	ENSMUSG00000025007	Aldh18a1	2810433K04Rik|AI429789|Pycs	aldehyde dehydrogenase 18 family, member A1	protein-coding
mm_171271.1	chr3	88772514	88772514	-	1	NA	promoter-TSS (NM_018804)	promoter-TSS (NM_018804)	85	NM_018804	229521	Mm.379376	NM_018804	ENSMUSG00000068923	Syt11	1500004A13Rik|3632445O20Rik|5430404N14Rik|6530420C11Rik|AI851970	synaptotagmin XI	protein-coding
mm_124164.1	chr14	93685273	93685283	-	1	NA	intron (NM_001346722, intron 2 of 4)	intron (NM_001346722, intron 2 of 4)	203610	NM_001271800	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding
mm_134647.1	chr16	21947454	21947517	-	1	NA	promoter-TSS (NR_037773)	promoter-TSS (NR_037773)	67	NM_025693	66664	Mm.46480	NM_025693	ENSMUSG00000022856	Tmem41a	2900010K02Rik|5730578N08Rik	transmembrane protein 41a	protein-coding
mm_167222.1	chr8	12314678	12314681	+	1	NA	Intergenic	Intergenic	-71092	NR_027975	434280	Mm.447484	NM_001013812	ENSMUSG00000047935	Gm5607	EG434280	predicted gene 5607	ncRNA
mm_96363.1	chr11	67098569	67098581	+	1	NA	intron (NM_001099635, intron 32 of 40)	intron (NM_001099635, intron 32 of 40)	-1229	NR_105888	102466766		NR_105888	ENSMUSG00000098855	Mir6923	Gm27312|mmu-mir-6923	microRNA 6923	ncRNA
mm_158395.1	chrX	136741121	136741128	-	1	NA	promoter-TSS (NM_001168225)	promoter-TSS (NM_001168225)	31	NM_001168225	56397	Mm.27218	NM_019768	ENSMUSG00000031422	Morf4l2	2410017O14Rik|Mrgx|Sid393p|mKIAA0026	mortality factor 4 like 2	protein-coding
mm_58191.1	chr6	143070029	143070032	-	1	NA	intron (NM_001109688, intron 8 of 24)	intron (NM_001109688, intron 8 of 24)	30122	NM_001286578	74741	Mm.130260	NM_029081	ENSMUSG00000030279	C2cd5	5730419I09Rik|C030008B15Rik|CDP138	C2 calcium-dependent domain containing 5	protein-coding
mm_120082.1	chr14	57746149	57746195	+	1	NA	promoter-TSS (NM_015771)	promoter-TSS (NM_015771)	-49	NM_015771	50523	Mm.347899	NM_015771	ENSMUSG00000021959	Lats2	4932411G09Rik|AV277261|AW228608	large tumor suppressor 2	protein-coding
mm_141982.1	chr17	35164861	35164889	-	1	NA	promoter-TSS (NM_020027)	promoter-TSS (NM_020027)	2	NM_001199044	53761	Mm.272462	NM_020027	ENSMUSG00000024393	Prrc2a	3110039B05Rik|Bat-2|Bat2|D17H6S51E|G2|Wbp12|mKIAA4178	proline-rich coiled-coil 2A	protein-coding
mm_66853.1	chr7	51862217	51862281	-	1	NA	promoter-TSS (NM_001115087)	promoter-TSS (NM_001115087)	18	NM_001115087	100040608	Mm.322643	NM_001115087	ENSMUSG00000092118	Fancf	A730016A17	Fanconi anemia, complementation group F	protein-coding
mm_62175.1	chr7	97400050	97400115	+	1	NA	promoter-TSS (NM_024220)	promoter-TSS (NM_024220)	79	NM_024220	68197	Mm.334031	NM_024220	ENSMUSG00000030647	Ndufc2	1810004I06Rik|2010300P09Rik|G1|R75094	NADH dehydrogenase (ubiquinone) 1, subcomplex unknown, 2	protein-coding
mm_156770.1	chrX	160768138	160768168	+	1	NA	5' UTR (NM_011302, exon 1 of 6)	5' UTR (NM_011302, exon 1 of 6)	140	NM_011302	20147	Mm.41982	NM_011302	ENSMUSG00000031293	Rs1	Rs1h|Xlrs1|tmgc1	retinoschisis (X-linked, juvenile) 1 (human)	protein-coding
mm_77194.1	chr8	112011300	112011310	-	1	NA	promoter-TSS (NM_001286384)	promoter-TSS (NM_001286384)	49	NM_001286384	85305	Mm.196544	NM_053092	ENSMUSG00000031948	Kars	AA589550|AL024334|AL033315|AL033367|D8Ertd698e|D8Wsu108e|LysRS|mKIAA0070	lysyl-tRNA synthetase	protein-coding
mm_98752.1	chr11	96545435	96545449	+	1	NA	intron (NM_001033186, intron 4 of 12)	intron (NM_001033186, intron 4 of 12)	80851	NM_001177898	78473	Mm.395840	NM_001033186	ENSMUSG00000057058	Skap1	1700091G21Rik|Scap1|Skap-55	src family associated phosphoprotein 1	protein-coding
mm_31388.1	chr4	48043546	48043572	+	1	NA	Intergenic	Intergenic	-1746	NM_015743	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_170807.1	chr2	175931079	175931085	-	1	NA	promoter-TSS (NM_001177404).2	promoter-TSS (NM_001177404).2	18	NM_001177407	667962	Mm.422667	NM_001177405	ENSMUSG00000089756	Zfp966	Gm8898|OTTMUSG00000016203	zinc finger protein 966	protein-coding
mm_52541.1	chr6	115931965	115931978	+	1	NA	promoter-TSS (NM_145383)	promoter-TSS (NM_145383)	44	NM_145383	212541	Mm.2965	NM_145383	ENSMUSG00000030324	Rho	Noerg1|Opn2|Ops|RP4	rhodopsin	protein-coding
mm_169308.1	chr14	104715879	104715879	-	1	NA	intron (NR_015593, intron 1 of 5)	LSU-rRNA_Hsa|rRNA|rRNA	76732	NR_015593	320249	Mm.320725	NR_015593		D130009I18Rik	-	RIKEN cDNA D130009I18 gene	ncRNA
mm_21831.1	chr2	165400399	165400410	-	1	NA	promoter-TSS (NM_029021)	promoter-TSS (NM_029021)	-10	NM_029021	74614	Mm.72179	NM_029021	ENSMUSG00000027670	Ocstamp	4833422F24Rik|OC-STAMP	osteoclast stimulatory transmembrane protein	protein-coding
mm_163019.1	chr11	46740217	46740227	+	1	NA	promoter-TSS (NM_001166632)	promoter-TSS (NM_001166632)	-1	NM_001166632	171283	Mm.17771	NM_134248	ENSMUSG00000040405	Havcr1	AI503787|KIM-1|TIM-1|Tim1|Timd1	hepatitis A virus cellular receptor 1	protein-coding
mm_95285.1	chr11	45893895	45893909	+	1	NA	exon (NM_001045520, exon 7 of 12)	exon (NM_001045520, exon 7 of 12)	41938	NM_001045520	216705	Mm.169673	NM_001045520	ENSMUSG00000006169	Clint1	AI642036|AW537616|C530049I24Rik|Enth|Epn4|F630206G17Rik|mKIAA0171	clathrin interactor 1	protein-coding
mm_35555.1	chr4	41520306	41520325	-	1	NA	exon (NM_027993, exon 6 of 6)	exon (NM_027993, exon 6 of 6)	2878	NR_045726	76992	Mm.440546	NR_045726	ENSMUSG00000036162	Fam219aos	1700066J24Rik	family with sequence similarity 219, member A, opposite strand	ncRNA
mm_64997.1	chr7	16924133	16924137	-	1	NA	promoter-TSS (NM_007590)	promoter-TSS (NM_007590)	-103	NM_007590	12315	Mm.288630	NM_007590	ENSMUSG00000019370	Calm3	CaMA|R75142	calmodulin 3	protein-coding
mm_89806.1	chr10	103029133	103029143	+	1	NA	promoter-TSS (NM_172553)	promoter-TSS (NM_172553)	-361	NM_172553	216285	Mm.19287	NM_172553	ENSMUSG00000036602	Alx1	AI314867|C130005I02|Cart1	ALX homeobox 1	protein-coding
mm_172164.1	chr6	44793026	44793027	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-267035	NM_001004357	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding
mm_168387.1	chr1	124922644	124922645	+	1	NA	Intergenic	L1Md_T|LINE|L1	513083	NM_023735	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding
mm_114986.1	chr13	97493577	97493605	+	1	NA	intron (NR_110430, intron 2 of 2)	intron (NR_110430, intron 2 of 2)	10890	NR_110431	100039691	Mm.219358	NR_110430	ENSMUSG00000078952	Lncenc1	ENSMUSG00000078952|Gm11019|Gm2373|Lincenc1|Platr18|linc-Enc1	long non-coding RNA, embryonic stem cells expressed 1	ncRNA
mm_162198.1	chrX	119927212	119927212	+	1	NA	promoter-TSS (NM_053114)	promoter-TSS (NM_053114)	16	NM_053114	93728	Mm.125979	NM_053114	ENSMUSG00000034732	Pabpc5	C820015E17	poly(A) binding protein, cytoplasmic 5	protein-coding
mm_619.1	chr1	40084776	40084784	+	1	NA	promoter-TSS (NM_010555)	promoter-TSS (NM_010555)	12	NM_010555	16178	Mm.1349	NM_010555	ENSMUSG00000026073	Il1r2	CD121b|Il1r-2	interleukin 1 receptor, type II	protein-coding
mm_31569.1	chr4	57594474	57594527	+	1	NA	intron (NM_001304544, intron 1 of 8)	RSINE1|SINE|B4	26252	NM_172868	242481	Mm.331630	NM_172868	ENSMUSG00000090053	Palm2	53-H12|B130066I24|R75368|pEN70	paralemmin 2	protein-coding
mm_36224.1	chr4	62524397	62524412	-	1	NA	promoter-TSS (NM_177607)	promoter-TSS (NM_177607)	610	NM_021498	59001	Mm.27444	NM_021498	ENSMUSG00000028394	Pole3	1810034K18Rik|YBL1	polymerase (DNA directed), epsilon 3 (p17 subunit)	protein-coding
mm_61860.1	chr7	88309923	88309943	+	1	NA	3' UTR (NM_009982, exon 7 of 7)	3' UTR (NM_009982, exon 7 of 7)	31848	NM_001311790	13032	Mm.89295	NM_009982	ENSMUSG00000030560	Ctsc	AI047818|CatC|DPP1|DPPI	cathepsin C	protein-coding
mm_137535.1	chr17	27556581	27556593	+	1	NA	promoter-TSS (NM_001166545)	promoter-TSS (NM_001166545)	13	NM_001166540	15361	Mm.4438	NM_016660	ENSMUSG00000046711	Hmga1	AL023995|Hmga1a|Hmga1b|Hmgi|Hmgiy|Hmgy	high mobility group AT-hook 1	protein-coding
mm_89460.1	chr10	93210082	93210085	+	1	NA	intron (NM_146239, intron 2 of 16)	intron (NM_146239, intron 2 of 16)	47298	NR_035452	100316689		NR_035452	ENSMUSG00000089214	Mir1931	mir-1931|mmu-mir-1931	microRNA 1931	ncRNA
mm_156258.1	chrX	136820042	136820075	+	1	NA	Intergenic	Intergenic	-2688	NM_001290561	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_124457.1	chr14	120042430	120042471	-	1	NA	promoter-TSS (NM_001001490)	promoter-TSS (NM_001001490)	-15	NM_001001490	239283	Mm.138520	NM_001001490	ENSMUSG00000044819	Oxgr1	Cysltr3|Gm299|Gpr80|Gpr99|P2Y15	oxoglutarate (alpha-ketoglutarate) receptor 1	protein-coding
mm_139599.1	chr17	57255961	57255967	+	1	NA	intron (NM_134125, intron 9 of 13)	T-rich|Low_complexity|Low_complexity	6513	NM_001242389	106628	Mm.37368	NM_134125	ENSMUSG00000019487	Trip10	AI646975|Cip4	thyroid hormone receptor interactor 10	protein-coding
mm_87900.1	chr10	62071694	62071717	+	1	NA	Intergenic	Intergenic	39308	NM_027251	69894	Mm.294126	NM_027251	ENSMUSG00000020083	2010107G23Rik	AA545165	RIKEN cDNA 2010107G23 gene	protein-coding
mm_40099.1	chr5	34573809	34573875	+	1	NA	promoter-TSS (NR_106111)	promoter-TSS (NR_106111)	178	NM_001331086	11518	Mm.289106	NM_013457	ENSMUSG00000029106	Add1	AI256389	adducin 1 (alpha)	protein-coding
mm_133692.1	chr16	92539880	92539882	+	1	NA	3' UTR (NM_172469, exon 6 of 6)	3' UTR (NM_172469, exon 6 of 6)	41734	NM_172469	209195	Mm.44747	NM_172469	ENSMUSG00000022949	Clic6	5730466J16Rik|AL022908|AW045520|CLIC1L	chloride intracellular channel 6	protein-coding
mm_98771.1	chr11	96739927	96739927	+	1	NA	intron (NM_001177898, intron 10 of 10)	intron (NM_001177898, intron 10 of 10)	37628	NM_028965	74479	Mm.270781	NM_028965	ENSMUSG00000020876	Snx11	4933439F10Rik|A930041K09Rik|AI117694	sorting nexin 11	protein-coding
mm_124688.1	chr15	6435390	6435412	+	1	NA	exon (NM_001102400, exon 10 of 13)	exon (NM_001102400, exon 10 of 13)	-9932	NM_013485	12279	Mm.29095	NM_013485	ENSMUSG00000022149	C9	-	complement component 9	protein-coding
mm_22743.1	chr3	19957089	19957114	+	1	NA	promoter-TSS (NM_007752)	promoter-TSS (NM_007752)	47	NM_007752	12870	Mm.13787	NM_007752	ENSMUSG00000003617	Cp	D3Ertd555e	ceruloplasmin	protein-coding
mm_33488.1	chr4	130823043	130823047	+	1	NA	3' UTR (NM_011520, exon 5 of 5)	3' UTR (NM_011520, exon 5 of 5)	30508	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_170395.1	chr1	86358170	86358176	-	1	NA	exon (NM_010880, exon 2 of 14)	exon (NM_010880, exon 2 of 14)	1282	NM_010880	17975	Mm.154378	NM_010880	ENSMUSG00000026234	Ncl	B530004O11Rik|C23|D0Nds28|D1Nds28|Nucl	nucleolin	protein-coding
mm_49448.1	chr6	29348144	29348159	+	1	NA	promoter-TSS (NM_184053)	promoter-TSS (NM_184053)	45	NM_184053	12321	Mm.392075	NM_007594	ENSMUSG00000029767	Calu	9530075H20Rik	calumenin	protein-coding
mm_160647.1	chr9	110243747	110243747	+	1	NA	promoter-TSS (NM_013884)	promoter-TSS (NM_013884)	-36	NM_013884	29873	Mm.38496	NM_013884	ENSMUSG00000032482	Cspg5	Caleb|Ngc	chondroitin sulfate proteoglycan 5	protein-coding
mm_40514.1	chr5	57800374	57800386	+	1	NA	intron (NM_001310608, intron 1 of 3)	B1F1|SINE|Alu	82299	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_76736.1	chr8	95142478	95142577	-	1	NA	promoter-TSS (NM_010631)	promoter-TSS (NM_010631)	13	NM_010631	16582	Mm.378951	NM_010631	ENSMUSG00000031788	Kifc3	AI325457|BB123200	kinesin family member C3	protein-coding
mm_55973.1	chr6	85865809	85865810	-	1	NA	3' UTR (NM_053096, exon 3 of 3)	3' UTR (NM_053096, exon 3 of 3)	3328	NM_053096	93673	Mm.24251	NM_053096	ENSMUSG00000033634	Nat8f2	Cml2	N-acetyltransferase 8 (GCN5-related) family member 2	protein-coding
mm_162217.1	chrX	138209608	138209608	-	1	NA	promoter-TSS (NM_026469)	promoter-TSS (NM_026469)	-28	NM_026469	67944	Mm.443280	NM_026469	ENSMUSG00000071686	Tex13a	1700025D03Rik	testis expressed 13A	protein-coding
mm_1653.1	chr1	74662097	74662116	+	1	NA	intron (NM_001014974, intron 1 of 19)	CpG	352	NM_001014974	67534	Mm.260714	NM_001014974	ENSMUSG00000033257	Ttll4	4632407P03Rik|AI451681|mKIAA0173	tubulin tyrosine ligase-like family, member 4	protein-coding
mm_41187.1	chr5	88327847	88327859	+	1	NA	exon (NM_008644, exon 3 of 3)	exon (NM_008644, exon 3 of 3)	10541	NM_008644	17830	Mm.200411	NM_008644	ENSMUSG00000064156	Prol1	Muc10	proline rich, lacrimal 1	protein-coding
mm_87877.1	chr10	61648588	61648636	+	1	NA	promoter-TSS (NM_026438)	promoter-TSS (NM_026438)	-9	NM_026438	67895	Mm.28897	NM_026438	ENSMUSG00000020089	Ppa1	2010317E03Rik|Pyp	pyrophosphatase (inorganic) 1	protein-coding
mm_80739.1	chr9	94713478	94713488	+	1	NA	intron (NM_177909, intron 4 of 15)	RMER12|LTR|ERVK	-38346	NR_106116	102465763		NR_106116	ENSMUSG00000098251	Mir7656	Gm27614|mmu-mir-7656	microRNA 7656	ncRNA
mm_79575.1	chr9	58134805	58134823	+	1	NA	5' UTR (NM_001162479, exon 1 of 19)	5' UTR (NM_001162479, exon 1 of 19)	149	NM_001162479	20897	Mm.10801	NM_009291	ENSMUSG00000032327	Stra6	AI891933	stimulated by retinoic acid gene 6	protein-coding
mm_133469.1	chr16	89226827	89226831	+	1	NA	Intergenic	Intergenic	20968	NM_001163615	622935	Mm.459837	NM_001163615	ENSMUSG00000091039	Krtap20-2	1190004K03Rik|EG622935|Gm6371	keratin associated protein 20-2	protein-coding
mm_104494.1	chr11	95837204	95837219	-	1	NA	exon (NM_025659, exon 2 of 8)	exon (NM_025659, exon 2 of 8)	-5084	NM_023121	14710	Mm.46299	NM_023121	ENSMUSG00000038811	Gngt2	AV096488	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 2	protein-coding
mm_42870.1	chr5	122235401	122235416	+	1	NA	intron (NM_028752, intron 3 of 6)	intron (NM_028752, intron 3 of 6)	25121	NM_028752	74096	Mm.28804	NM_028752	ENSMUSG00000064267	Hvcn1	0610039P13Rik|AI450555|BTS|HV1|Vsop.|mVSOP	hydrogen voltage-gated channel 1	protein-coding
mm_87236.1	chr10	40703679	40703696	+	1	NA	intron (NM_177793, intron 1 of 4)	intron (NM_177793, intron 1 of 4)	20405	NM_177793	327747	Mm.80407	NM_177793	ENSMUSG00000045555	Mettl24	9030224M15Rik	methyltransferase like 24	protein-coding
mm_15737.1	chr2	164237225	164237256	+	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	1101	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_157030.1	chrX	7923168	7923191	-	1	NA	3' UTR (NM_013892, exon 3 of 3)	3' UTR (NM_013892, exon 3 of 3)	3357	NM_013892	30052	Mm.4881	NM_013892	ENSMUSG00000039278	Pcsk1n	AI848336|KEP|PEN|PEN19|PEN20|Pan3|SAAS|SAASCT|bLEN|lLEN|proSAAS	proprotein convertase subtilisin/kexin type 1 inhibitor	protein-coding
mm_119920.1	chr14	54959835	54959851	+	1	NA	exon (NM_010856, exon 14 of 39)	exon (NM_010856, exon 14 of 39)	6764	NM_001164171	17888	Mm.290003	NM_010856	ENSMUSG00000040752	Myh6	A830009F23Rik|AA517445|Myhc-a|Myhca|alpha-MHC	myosin, heavy polypeptide 6, cardiac muscle, alpha	protein-coding
mm_41567.1	chr5	93159840	93159851	+	1	NA	intron (NM_001347377, intron 5 of 10)	Charlie5|DNA|hAT-Charlie	46650	NM_017367	12453	Mm.250419	NM_017367	ENSMUSG00000063015	Ccni	-	cyclin I	protein-coding
mm_406.1	chr1	34187876	34187879	+	1	NA	intron (NM_133833, intron 35 of 92)	AT_rich|Low_complexity|Low_complexity	27547	NM_010081	13518	Mm.336625	NM_010081	ENSMUSG00000026131	Dst	2310001O04Rik|A830042E19Rik|AW554249|BP230|BPAG1-n|Bpag|Bpag1|Macf2|ah|athetoid|dt|mKIAA0728|nmf203|nmf339	dystonin	protein-coding
mm_36934.1	chr4	108579097	108579107	-	1	NA	promoter-TSS (NM_011015)	promoter-TSS (NM_011015)	234	NM_172697	230596	Mm.157534	NM_172697	ENSMUSG00000063800	Prpf38a	2410002M20Rik	PRP38 pre-mRNA processing factor 38 (yeast) domain containing A	protein-coding
mm_131332.1	chr16	13266424	13266429	+	1	NA	intron (NM_181860, intron 1 of 3)	(T)n|Simple_repeat|Simple_repeat	1347	NM_181860	239719	Mm.270643	NM_153588	ENSMUSG00000009569	Mkl2	ENSMUSG00000075401|Gt4-1|MRTF-B|Mrtfb|mKIAA1243	MKL/myocardin-like 2	protein-coding
mm_22132.1	chr2	170427854	170427862	-	1	NA	promoter-TSS (NM_001164369)	promoter-TSS (NM_001164369)	-13	NM_029815	76960	Mm.240850	NM_029815	ENSMUSG00000013523	Bcas1	2210416M21Rik|9030223A09Rik|AI841227|NABC1	breast carcinoma amplified sequence 1	protein-coding
mm_167931.1	chrX	105166688	105166691	+	1	NA	Intergenic	MTEa|LTR|ERVL-MaLR	-1184	NR_002167	279610	Mm.418157	NR_002167		E530001F21Rik	-	RIKEN cDNA E530001F21 gene	pseudo
mm_56705.1	chr6	115037825	115037881	-	1	NA	promoter-TSS (NM_026894)	promoter-TSS (NM_026894)	21	NM_026894	68971	Mm.24937	NM_026894	ENSMUSG00000030316	Tamm41	1500001M20Rik|TAM41	TAM41 mitochondrial translocator assembly and maintenance homolog	protein-coding
mm_96420.1	chr11	67256185	67256191	+	1	NA	exon (NM_010855, exon 34 of 40)	exon (NM_010855, exon 34 of 40)	18376	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_34005.1	chr4	137931198	137931202	+	1	NA	intron (NM_199307, intron 5 of 19)	intron (NM_199307, intron 5 of 19)	-62256	NM_001256198	230861	Mm.268903	NM_172703	ENSMUSG00000028760	Eif4g3	1500002J22Rik|4930523M17Rik|G1-419-52|eIF4GII|repro8	eukaryotic translation initiation factor 4 gamma, 3	protein-coding
mm_156528.1	chrX	151046882	151046905	+	1	NA	promoter-TSS (NM_008001)	promoter-TSS (NM_008001)	-277	NM_008001	14163	Mm.8142	NM_008001	ENSMUSG00000025265	Fgd1	ZFYVE3	FYVE, RhoGEF and PH domain containing 1	protein-coding
mm_9093.1	chr1	168873728	168873734	-	1	NA	Intergenic	Intergenic	383088	NR_105766	102465178		NR_105766	ENSMUSG00000098407	Mir6348	Gm27412|mmu-mir-6348	microRNA 6348	ncRNA
mm_142446.1	chr17	45592454	45592472	-	1	NA	promoter-TSS (NM_022880)	promoter-TSS (NM_022880)	-70	NM_022880	63959	Mm.29744	NM_022880	ENSMUSG00000023942	Slc29a1	1200014D21Rik|AA407560|ENT1	solute carrier family 29 (nucleoside transporters), member 1	protein-coding
mm_155131.1	chrX	49485089	49485122	+	1	NA	intron (NM_001081123, intron 1 of 12)	intron (NM_001081123, intron 1 of 12)	14655	NM_001081123	75404	Mm.44305	NM_001081123	ENSMUSG00000036198	Arhgap36	1100001E04Rik|rho-gap	Rho GTPase activating protein 36	protein-coding
mm_65596.1	chr7	27337668	27337680	-	1	NA	promoter-TSS (NM_175641)	promoter-TSS (NM_175641)	-62	NM_175641	108075	Mm.272251	NM_175641	ENSMUSG00000040488	Ltbp4	2310046A13Rik	latent transforming growth factor beta binding protein 4	protein-coding
mm_155520.1	chrX	74255052	74255062	+	1	NA	intron (NM_007927, intron 1 of 5)	CpG	370	NM_007927	13726	Mm.18892	NM_007927	ENSMUSG00000001964	Emd	AW550900|Sta	emerin	protein-coding
mm_143265.1	chr17	65639787	65639799	-	1	NA	promoter-TSS (NM_153519)	promoter-TSS (NM_153519)	-37	NM_153519	213272	Mm.255732	NM_153519	ENSMUSG00000050612	Txndc2	AU021712|Sptrx-1|Sptrx1|Trx4	thioredoxin domain containing 2 (spermatozoa)	protein-coding
mm_48032.1	chr5	136246580	136246598	-	1	NA	Intergenic	Intergenic	-1649	NM_018825	23921	Mm.425294	NM_018825	ENSMUSG00000005057	Sh2b2	Aps	SH2B adaptor protein 2	protein-coding
mm_23371.1	chr3	55461964	55461977	+	1	NA	5' UTR (NM_001111052, exon 1 of 14)	5' UTR (NM_001111052, exon 1 of 14)	212	NM_001195540	13175	Mm.393242	NM_019978	ENSMUSG00000027797	Dclk1	1700113D08Rik|2810480F11Rik|AI836758|Click-I|Cpg16|Dcamkl1|Dcl|Dclk|mKIAA0369	doublecortin-like kinase 1	protein-coding
mm_103909.1	chr11	83578597	83578619	-	1	NA	promoter-TSS (NM_011338)	promoter-TSS (NM_011338)	28	NM_011338	20308	Mm.416125	NM_011338	ENSMUSG00000019122	Ccl9	CCF18|MRP-2|Scya10|Scya9	chemokine (C-C motif) ligand 9	protein-coding
mm_107421.1	chr12	35047181	35047230	+	1	NA	promoter-TSS (NM_001014973)	promoter-TSS (NM_001014973)	16	NM_001014973	217463	Mm.213991	NM_001014973	ENSMUSG00000020590	Snx13	Rgs-px1|mKIAA0713	sorting nexin 13	protein-coding
mm_71229.1	chr8	40905571	40905620	+	1	NA	exon (NM_001044740, exon 6 of 12)	exon (NM_001044740, exon 6 of 12)	-20638	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_64998.1	chr7	16945650	16945657	-	1	NA	exon (NM_001099636, exon 1 of 1)	exon (NM_001099636, exon 1 of 1)	971	NM_001099636	434128	Mm.483018	NM_001099636	ENSMUSG00000070802	Pnmal2	EG434128	PNMA-like 2	protein-coding
mm_71348.1	chr8	45628113	45628129	+	1	NA	5' UTR (NM_001310707, exon 1 of 24)	5' UTR (NM_001310707, exon 1 of 24)	370	NM_001310707	234214	Mm.211096	NM_172752	ENSMUSG00000031626	Sorbs2	2010203O03Rik|9430041O17Rik|A530071H08|Argbp2|mKIAA0777|nArgBP2	sorbin and SH3 domain containing 2	protein-coding
mm_4654.1	chr1	180345934	180345944	+	1	NA	intron (NM_001081175, intron 2 of 7)	intron (NM_001081175, intron 2 of 7)	-15390	NR_003623	277333	Mm.389223	NM_199472		Gm5069	EG277333	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_67375.1	chr7	79841975	79841997	-	1	NA	exon (NM_008486, exon 1 of 20)	exon (NM_008486, exon 1 of 20)	366	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_103523.1	chr11	76847048	76847052	-	1	NA	promoter-TSS (NM_007754)	promoter-TSS (NM_007754)	-42	NM_007754	12874	Mm.276736	NM_007754	ENSMUSG00000020841	Cpd	AA960140|AW322530|D830034L15Rik	carboxypeptidase D	protein-coding
mm_20735.1	chr2	137116334	137116350	-	1	NA	5' UTR (NM_013822, exon 1 of 26)	5' UTR (NM_013822, exon 1 of 26)	178	NM_013822	16449	Mm.22398	NM_013822	ENSMUSG00000027276	Jag1	ABE2|Gsfabe2|Htu|Ozz|Ser-1	jagged 1	protein-coding
mm_162719.1	chr10	36974521	36974531	+	1	NA	promoter-TSS (NM_008229)	promoter-TSS (NM_008229)	-18	NM_008229	15182	Mm.19806	NM_008229	ENSMUSG00000019777	Hdac2	D10Wsu179e|YAF1|Yy1bp|mRPD3	histone deacetylase 2	protein-coding
mm_163587.1	chr13	38108825	38108826	+	1	NA	Intergenic	Intergenic	-42469	NM_023842	109620	Mm.355327	NM_023842	ENSMUSG00000054889	Dsp	2300002E22Rik|5730453H04Rik|AA407887|AA407888|AW109828|DP|rul	desmoplakin	protein-coding
mm_146260.1	chr18	77814354	77814366	+	1	NA	intron (NM_013831, intron 1 of 14)	B1_Mur4|SINE|Alu	19810	NM_013831	19201	Mm.57174	NM_013831	ENSMUSG00000025429	Pstpip2	MAYP|cmo	proline-serine-threonine phosphatase-interacting protein 2	protein-coding
mm_6503.1	chr1	74295786	74295794	-	1	NA	intron (NM_027154, intron 1 of 11)	intron (NM_027154, intron 1 of 11)	8546	NM_027154	69660	Mm.261182	NM_027154	ENSMUSG00000006301	Tmbim1	2310061B02Rik|AA960455|AU024746|C78899|RECS1|Tmbib1|mKIAA4161	transmembrane BAX inhibitor motif containing 1	protein-coding
mm_98074.1	chr11	86484625	86484643	+	1	NA	promoter-TSS (NM_029788)	promoter-TSS (NM_029788)	-23	NM_029788	76892	Mm.262707	NM_029788	ENSMUSG00000020521	Rnft1	0610013E23Rik|AV007605	ring finger protein, transmembrane 1	protein-coding
mm_151009.1	chr19	46707450	46707511	+	1	NA	promoter-TSS (NM_020577)	promoter-TSS (NM_020577)	37	NM_020577	57344	Mm.28566	NM_020577	ENSMUSG00000003559	As3mt	2310045H08Rik|Cyt19	arsenic (+3 oxidation state) methyltransferase	protein-coding
mm_123143.1	chr14	56811051	56811054	-	1	NA	intron (NM_144842, intron 1 of 7)	intron (NM_144842, intron 1 of 7)	412	NM_001253753	219105	Mm.473172	NM_144842	ENSMUSG00000040123	Zmym5	9830124H08Rik	zinc finger, MYM-type 5	protein-coding
mm_99012.1	chr11	98843799	98843800	+	1	NA	intron (NM_001080925, intron 4 of 14)	intron (NM_001080925, intron 4 of 14)	7014	NM_001080925	268480	Mm.340766	NM_001080925	ENSMUSG00000038020	Rapgefl1	B230105J10	Rap guanine nucleotide exchange factor (GEF)-like 1	protein-coding
mm_55988.1	chr6	85961632	85961671	-	1	NA	promoter-TSS (NM_028099)	promoter-TSS (NM_028099)	16	NM_028099	72102	Mm.24007	NM_028099	ENSMUSG00000030002	Dusp11	2010300F21Rik|AI481497	dual specificity phosphatase 11 (RNA/RNP complex 1-interacting)	protein-coding
mm_24181.1	chr3	88583766	88583783	+	1	NA	intron (NM_025448, intron 2 of 4)	intron (NM_025448, intron 2 of 4)	4103	NM_025448	66256	Mm.7091	NM_025448	ENSMUSG00000041355	Ssr2	1500032E05Rik|AI315033|AU020133|TLAP|TRAPB|TRAPbeta	signal sequence receptor, beta	protein-coding
mm_81774.1	chr9	114688730	114688740	+	1	NA	promoter-TSS (NM_146229)	promoter-TSS (NM_146229)	-96	NM_146229	235661	Mm.128627	NM_146229	ENSMUSG00000032435	Dync1li1	1110053F02Rik|Dnclic1|LIC-1	dynein cytoplasmic 1 light intermediate chain 1	protein-coding
mm_116312.1	chr13	37050238	37050274	-	1	NA	promoter-TSS (NM_001166391)	promoter-TSS (NM_001166391)	-12	NM_001166391	74145	Mm.235105	NM_028784	ENSMUSG00000039109	F13a1	1200014I03Rik|AI462306|F13a	coagulation factor XIII, A1 subunit	protein-coding
mm_131801.1	chr16	22899288	22899290	+	1	NA	non-coding (NR_075099, exon 6 of 6)	non-coding (NR_075099, exon 6 of 6)	-4903	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_4261.1	chr1	171437569	171437584	+	1	NA	promoter-TSS (NM_172647)	promoter-TSS (NM_172647)	15	NM_172647	16456	Mm.294882	NM_172647	ENSMUSG00000038235	F11r	9130004G24|AA638916|ESTM33|JAM|JAM-1|JAM-A|Jcam|Jcam1|Ly106	F11 receptor	protein-coding
mm_114851.1	chr13	93095642	93095663	+	1	NA	exon (NM_023821, exon 2 of 13)	exon (NM_023821, exon 2 of 13)	819	NR_046182	408254	Mm.474857	NR_046182		A630019I02Rik	-	RIKEN cDNA A630019I02 gene	ncRNA
mm_92516.1	chr10	78464946	78464965	-	1	NA	promoter-TSS (NM_172134)	promoter-TSS (NM_172134)	-7	NM_172134	216134	Mm.206159	NM_172134	ENSMUSG00000032788	Pdxk	2310036D04Rik|AA119688|C77999	pyridoxal (pyridoxine, vitamin B6) kinase	protein-coding
mm_75120.1	chr8	34764907	34764924	-	1	NA	Intergenic	Intergenic	-42695	NM_176933	319520	Mm.170276	NM_176933	ENSMUSG00000031530	Dusp4	2700078F24Rik|AI844617|BB104621|E130306H24Rik|MKP2	dual specificity phosphatase 4	protein-coding
mm_115489.1	chr13	3611037	3611062	-	1	NA	promoter-TSS (NM_134063)	promoter-TSS (NM_134063)	59	NM_134063	105203	Mm.221609	NM_134063	ENSMUSG00000033799	Fam208b	AI645998|Pap20|mKIAA2006	family with sequence similarity 208, member B	protein-coding
mm_18684.1	chr2	71367774	71367797	-	1	NA	promoter-TSS (NM_172436)	promoter-TSS (NM_172436)	-231	NM_172436	78830	Mm.30928	NM_172436	ENSMUSG00000027010	Slc25a12	2610002D09Rik|AI839531|B230107K20Rik|BB129864	solute carrier family 25 (mitochondrial carrier, Aralar), member 12	protein-coding
mm_9706.1	chr1	179502115	179502118	-	1	NA	intron (NM_027188, intron 1 of 11)	intron (NM_027188, intron 1 of 11)	15887	NM_027188	69726	Mm.222338	NM_027188	ENSMUSG00000055067	Smyd3	2410008A19Rik|Zmynd1	SET and MYND domain containing 3	protein-coding
mm_101187.1	chr11	17198510	17198559	-	1	NA	3' UTR (NM_024459, exon 6 of 6)	3' UTR (NM_024459, exon 6 of 6)	13055	NM_025443	66249	Mm.27831	NM_025443	ENSMUSG00000020116	Pno1	1810003N24Rik|AA407421|AU015468|AU019495|AU042323|Emi3|Imi3	partner of NOB1 homolog	protein-coding
mm_48955.1	chr6	4540844	4540852	+	1	NA	3' UTR (NM_007743, exon 52 of 52)	3' UTR (NM_007743, exon 52 of 52)	35230	NM_007743	12843	Mm.277792	NM_007743	ENSMUSG00000029661	Col1a2	AA960264|AI325291|Col1a-2|Cola-2|Cola2|oim	collagen, type I, alpha 2	protein-coding
mm_104794.1	chr11	98770318	98770353	-	1	NA	exon (NM_145434, exon 5 of 8)	exon (NM_145434, exon 5 of 8)	5042	NM_145434	217166	Mm.390397	NM_145434	ENSMUSG00000020889	Nr1d1	A530070C09Rik|R75201	nuclear receptor subfamily 1, group D, member 1	protein-coding
mm_24465.1	chr3	90654141	90654149	+	1	NA	promoter-TSS (NM_199422)	promoter-TSS (NM_199422)	-157	NM_199422	381493	Mm.291525	NM_199422	ENSMUSG00000063767	S100a7a	AY465109|Gm1020|S100A7L1|S100A7f|S100a15|S100a15a|S100a17l1	S100 calcium binding protein A7A	protein-coding
mm_131118.1	chr16	5378156	5378170	+	1	NA	Intergenic	Intergenic	-122207	NM_027446	70511	Mm.45780	NM_027446	ENSMUSG00000022544	Eef2kmt	5730409G15Rik|Fam86|Fam86a|eEF2-KMT	eukaryotic elongation factor 2 lysine methyltransferase	protein-coding
mm_37815.1	chr4	131672134	131672146	-	1	NA	Intergenic	Intergenic	166138	NM_011214	19273	Mm.4860	NM_011214	ENSMUSG00000028909	Ptpru	Ftp-1|PCP-2|PTP|PTP-lambda|PTPlambda|Pcp2|Ptpf|Ptprl|R-PTP-U|R-PTP-psi|RPTPlambda	protein tyrosine phosphatase, receptor type, U	protein-coding
mm_11872.1	chr2	49224199	49224200	+	1	NA	intron (NM_029924, intron 6 of 16)	L1_Rod|LINE|L1	-21701	NM_001290656	109241	Mm.440436	NM_029924	ENSMUSG00000036792	Mbd5	9430004D19Rik|AA536666|AI426407|C030040A15Rik|Gm1630|OTTMUSG00000012483	methyl-CpG binding domain protein 5	protein-coding
mm_133940.1	chr16	3907711	3907717	-	1	NA	intron (NM_028484, intron 1 of 2)	intron (NM_028484, intron 1 of 2)	975	NM_028484	73261	Mm.486226	NM_028484	ENSMUSG00000005983	1700037C18Rik	2810022L20Rik	RIKEN cDNA 1700037C18 gene	protein-coding
mm_92948.1	chr10	85103658	85103664	-	1	NA	intron (NM_001013028, intron 1 of 2)	MamRep1879|DNA|hAT-Tip100?	1034	NM_001013028	103266	Mm.335025	NM_001013028	ENSMUSG00000060935	Tmem263	AI597468	transmembrane protein 263	protein-coding
mm_91301.1	chr10	24916146	24916156	-	1	NA	exon (NM_007482, exon 7 of 8)	exon (NM_007482, exon 7 of 8)	5487	NR_105870	102465545		NR_105870	ENSMUSG00000099181	Mir6905	Gm27879|mmu-mir-6905	microRNA 6905	ncRNA
mm_120692.1	chr14	70776172	70776178	+	1	NA	intron (NM_010071, intron 3 of 4)	intron (NM_010071, intron 3 of 4)	1794	NM_010071	13449	Mm.243323	NM_010071	ENSMUSG00000022102	Dok2	DokR|Frip	docking protein 2	protein-coding
mm_73231.1	chr8	104111413	104111432	+	1	NA	intron (NM_009868, intron 1 of 11)	intron (NM_009868, intron 1 of 11)	-5549	NR_131138	546096	Mm.252264	NR_131138	ENSMUSG00000110053	Gm29682	-	predicted gene, 29682	ncRNA
mm_149084.1	chr19	8920359	8920426	+	1	NA	promoter-TSS (NM_024256)	promoter-TSS (NM_024256)	-1	NM_024256	72727	Mm.259	NM_024256	ENSMUSG00000071649	B3gat3	2810405M13Rik	beta-1,3-glucuronyltransferase 3 (glucuronosyltransferase I)	protein-coding
mm_64280.1	chr7	141813731	141813735	+	1	NA	exon (NM_010844, exon 38 of 50)	exon (NM_010844, exon 38 of 50)	24722	NM_010844	17833	Mm.334332	NM_010844	ENSMUSG00000037974	Muc5ac	2210005L13Rik|MGM	mucin 5, subtypes A and C, tracheobronchial/gastric	protein-coding
mm_12698.1	chr2	76499090	76499098	+	1	NA	promoter-TSS (NM_001290735)	promoter-TSS (NM_001290735)	88	NM_001290735	99031	Mm.240435	NM_145525	ENSMUSG00000042359	Osbpl6	1110062M20Rik|AI596402|ORP-6|mKIAA4128	oxysterol binding protein-like 6	protein-coding
mm_152650.1	chr19	12574227	12574252	-	1	NA	intron (NM_001346545, intron 1 of 2)	intron (NM_001346545, intron 1 of 2)	714	NM_026640	107373	Mm.1643	NM_026640	ENSMUSG00000024691	Fam111a	4632417K18Rik|AW413625	family with sequence similarity 111, member A	protein-coding
mm_89421.1	chr10	90907703	90907705	+	1	NA	intron (NM_001347053, intron 3 of 8)	intron (NM_001347053, intron 3 of 8)	77861	NM_001347053	77531	Mm.440605	NM_181398	ENSMUSG00000058589	Anks1b	AIDA-1b|C030032C09Rik|E530015N03Rik|ENSMUSG00000078431|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding
mm_132079.1	chr16	30186541	30186556	+	1	NA	Intergenic	Intergenic	80984	NM_027904	71756	Mm.290614	NM_027904	ENSMUSG00000023176	Cpn2	1300018K11Rik	carboxypeptidase N, polypeptide 2	protein-coding
mm_69329.1	chr7	128740398	128740410	-	1	NA	promoter-TSS (NM_145955)	promoter-TSS (NM_145955)	25	NM_145955	210711	Mm.58882	NM_145955	ENSMUSG00000048170	Mcmbp	1110007A13Rik|AU017382|BC025641|MCM-BP	minichromosome maintenance complex binding protein	protein-coding
mm_103087.1	chr11	69920484	69920519	-	1	NA	5' UTR (NM_001166590, exon 1 of 6)	5' UTR (NM_001166590, exon 1 of 6)	129	NM_001166590	276770	Mm.18026	NM_181582	ENSMUSG00000078812	Eif5a	AA410058|D19Wsu54e|Eif4d|Eif5a1|eIF-4D|eIF-5A|eIF-5A-1|eIF-5A1	eukaryotic translation initiation factor 5A	protein-coding
mm_47967.1	chr5	135778283	135778328	-	1	NA	promoter-TSS (NM_029659)	promoter-TSS (NM_029659)	-4	NM_001289555	76571	Mm.247666	NM_029659	ENSMUSG00000019178	Styxl1	1700011C14Rik|Dusp24|Mkstyx	serine/threonine/tyrosine interacting-like 1	protein-coding
mm_157448.1	chrX	41911878	41911912	-	1	NA	promoter-TSS (NM_001033422)	promoter-TSS (NM_001033422)	6	NM_001033422	331401	Mm.259498	NM_001033422	ENSMUSG00000037475	Thoc2	6330441O12Rik|D130005M13Rik|Gm1139|Gm1793|Tho2	THO complex 2	protein-coding
mm_51438.1	chr6	80019009	80019030	+	1	NA	promoter-TSS (NM_178731)	promoter-TSS (NM_178731)	142	NM_001134743	243499	Mm.483425	NM_178731	ENSMUSG00000052581	Lrrtm4	7530419J18Rik|A230052N11	leucine rich repeat transmembrane neuronal 4	protein-coding
mm_3980.1	chr1	164249296	164249306	+	1	NA	exon (NM_054087, exon 1 of 6)	exon (NM_054087, exon 1 of 6)	255	NM_001276455	116914	Mm.35444	NM_054087	ENSMUSG00000040918	Slc19a2	AV276020|AW322295|DDA1|THTR1|TRMA	solute carrier family 19 (thiamine transporter), member 2	protein-coding
mm_95163.1	chr11	37597156	37597202	+	1	NA	Intergenic	Intergenic	-61810	NR_131154	100039148	Mm.120467	NR_131154	ENSMUSG00000087388	Gm12128	OTTMUSG00000005422	predicted gene 12128	ncRNA
mm_88748.1	chr10	80292454	80292495	+	1	NA	promoter-TSS (NM_009091)	promoter-TSS (NM_009091)	-35	NM_001310726	20054	Mm.643	NM_009091	ENSMUSG00000063457	Rps15	rig	ribosomal protein S15	protein-coding
mm_108696.1	chr12	86947032	86947055	+	1	NA	promoter-TSS (NM_001289430)	promoter-TSS (NM_001289430)	2	NM_001289430	217732	Mm.22337	NM_173735	ENSMUSG00000034157	Cipc	2310044G17Rik|AI842544|AI853744|Kiaa1737|mKIAA1737	CLOCK interacting protein, circadian	protein-coding
mm_115540.1	chr13	6648697	6648703	-	1	NA	promoter-TSS (NM_001291071)	promoter-TSS (NM_001291071)	71	NM_019703	56421	Mm.273874	NM_019703	ENSMUSG00000021196	Pfkp	1200015H23Rik|9330125N24Rik|ATP-PFK|PFK-C|PFK-P	phosphofructokinase, platelet	protein-coding
mm_105976.1	chr11	115536237	115536267	-	1	NA	promoter-TSS (NM_133354)	promoter-TSS (NM_133354)	-22	NM_133354	170930	Mm.29923	NM_133354	ENSMUSG00000020738	Sumo2	SUMO-2|Smt3A|Smt3b|Smt3h2	small ubiquitin-like modifier 2	protein-coding
mm_94853.1	chr11	23894780	23894791	+	1	NA	intron (NM_172555, intron 1 of 21)	CpG	485	NM_172555	216578	Mm.470599	NM_172555	ENSMUSG00000020273	Papolg	9630006B20Rik	poly(A) polymerase gamma	protein-coding
mm_7116.1	chr1	90014605	90014634	-	1	NA	promoter-TSS (NM_139152)	promoter-TSS (NM_139152)	-42	NM_139152	208372	Mm.215164	NM_139152	ENSMUSG00000067081	Asb18	Asb-18	ankyrin repeat and SOCS box-containing 18	protein-coding
mm_105064.1	chr11	100720110	100720127	-	1	NA	5' UTR (NM_001305003, exon 2 of 6)	5' UTR (NM_001305003, exon 2 of 6)	6268	NM_029307	75482	Mm.46175	NM_029307	ENSMUSG00000017832	Hspb9	1700007H20Rik	heat shock protein, alpha-crystallin-related, B9	protein-coding
mm_83990.1	chr9	57440085	57440129	-	1	NA	promoter-TSS (NM_176831)	promoter-TSS (NM_176831)	7	NM_176831	66812	Mm.250508	NM_176831	ENSMUSG00000063849	Ppcdc	1810057I13Rik|8430432M10Rik	phosphopantothenoylcysteine decarboxylase	protein-coding
mm_16819.1	chr2	11425703	11425705	-	1	NA	Intergenic	Intergenic	-27204	NR_040615	77543	Mm.490670	NR_040615	ENSMUSG00000102674	8030442B05Rik	-	RIKEN cDNA 8030442B05 gene	ncRNA
mm_167074.1	chr7	100498749	100498755	+	1	NA	exon (NM_011671, exon 7 of 8)	exon (NM_011671, exon 7 of 8)	5394	NM_011671	22228	Mm.171378	NM_011671	ENSMUSG00000033685	Ucp2	Slc25a8	uncoupling protein 2 (mitochondrial, proton carrier)	protein-coding
mm_163987.1	chr14	61768103	61768106	+	1	NA	Intergenic	Intergenic	-85731	NR_028264	668253	Mm.32886	NR_028264	ENSMUSG00000097589	Dleu2	1810047A16Rik|4932411A06Rik|7730401J12Rik|AI197277|AI788824|Alt1|Gm9069|Leu2	deleted in lymphocytic leukemia, 2	ncRNA
mm_168661.1	chr11	88980703	88980704	+	1	NA	intron (NM_016706, intron 1 of 6)	intron (NM_016706, intron 1 of 6)	6768	NM_016706	12812	Mm.268004	NM_016706	ENSMUSG00000033983	Coil	C79982|Cln80|p80|p80-coilin	coilin	protein-coding
mm_6344.1	chr1	71638538	71638589	-	1	NA	exon (NM_001276413, exon 11 of 44)	exon (NM_001276413, exon 11 of 44)	14671	NM_010233	14268	Mm.193099	NM_010233	ENSMUSG00000026193	Fn1	E330027I09|Fn|Fn-1	fibronectin 1	protein-coding
mm_111638.1	chr12	102647751	102647751	-	1	NA	intron (NM_172584, intron 2 of 9)	intron (NM_172584, intron 2 of 9)	37269	NR_035457	100316812		NR_035457	ENSMUSG00000089324	Mir1936	mir-1936|mmu-mir-1936	microRNA 1936	ncRNA
mm_137255.1	chr17	24550026	24550033	+	1	NA	promoter-TSS (NM_013630)	promoter-TSS (NM_013630)	79	NM_013630	18763	Mm.30435	NM_013630	ENSMUSG00000032855	Pkd1	PC1|mFLJ00285	polycystic kidney disease 1 homolog	protein-coding
mm_153751.1	chr19	45075137	45075160	-	1	NA	promoter-TSS (NM_178929)	promoter-TSS (NM_178929)	-991	NM_178929	107250	Mm.24417	NM_178929	ENSMUSG00000025213	Kazald1	AI842353|Bono1|IGFBP-rP10	Kazal-type serine peptidase inhibitor domain 1	protein-coding
mm_88491.1	chr10	77726450	77726452	+	1	NA	promoter-TSS (NM_001205033)	promoter-TSS (NM_001205033)	-35	NM_001205033	100502953	Mm.486157	NM_001205033	ENSMUSG00000096421	Gm10100	ENSMUSG00000061452	predicted gene 10100	protein-coding
mm_127963.1	chr15	11987692	11987695	-	1	NA	intron (NM_011294, intron 3 of 4)	ORR1B1|LTR|ERVL-MaLR	8314	NM_011294	20024	Mm.41746	NM_011294	ENSMUSG00000022205	Sub1	AI842364|P15|P9|Pc4|Rpo2tc1	SUB1 homolog (S. cerevisiae)	protein-coding
mm_140566.1	chr17	8524853	8524878	-	1	NA	Intergenic	CpG	-1936	NM_001290707	23984	Mm.87161	NM_011866	ENSMUSG00000023868	Pde10a	-	phosphodiesterase 10A	protein-coding
mm_122701.1	chr14	52160926	52160929	-	1	NA	3' UTR (NM_001168515, exon 25 of 25)	3' UTR (NM_001168515, exon 25 of 25)	36312	NM_033618	114741	Mm.21662	NM_033618	ENSMUSG00000035726	Supt16	Cdc68|Fact140|Spt16|Supt16h	suppressor of Ty 16	protein-coding
mm_58603.1	chr7	5051516	5051557	+	1	NA	promoter-TSS (NM_026900)	promoter-TSS (NM_026900)	4	NM_026900	68992	Mm.41484	NM_026900	ENSMUSG00000055633	Zfp580	1500015O20Rik|AI838225|Znf580	zinc finger protein 580	protein-coding
mm_129769.1	chr15	82707357	82707375	-	1	NA	Intergenic	Intergenic	-17308	NR_033515	627860	Mm.486636	NR_033515		Cyp2d37-ps	EG627860|Gm6800	cytochrome P450, family 2, subfamily d, polypeptide 37, pseudogene	pseudo
mm_163479.1	chr12	105678447	105678488	+	1	NA	intron (NM_029654, intron 1 of 41)	ORR1B1|LTR|ERVL-MaLR	6774	NM_029654	76559	Mm.114362	NM_029654	ENSMUSG00000041341	Atg2b	2410024A21Rik|AI047755|AI503411|AW558123|C030004M05Rik|C630028L02Rik|mKIAA4067	autophagy related 2B	protein-coding
mm_16310.1	chr2	174297328	174297353	+	1	NA	promoter-TSS (NM_001077507)	promoter-TSS (NM_001077507)	-519	NM_001077507	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_93139.1	chr10	92164745	92164754	-	1	NA	non-coding (NR_028262, exon 2 of 13)	non-coding (NR_028262, exon 2 of 13)	429	NR_028262	110333	Mm.429764	NR_028262		Rmst	100041799|AI853140|C230053E11Rik|D930049J19Rik|Dmt2|Gm3515|M2|Ncrms	rhabdomyosarcoma 2 associated transcript (non-coding RNA)	ncRNA
mm_147644.1	chr18	60273267	60273277	-	1	NA	promoter-TSS (NM_001034859)	promoter-TSS (NM_001034859)	-5	NM_001034859	225594	Mm.329460	NM_001034859	ENSMUSG00000068606	Gm4841	EG225594|Ifgga3	predicted gene 4841	protein-coding
mm_97716.1	chr11	80183887	80183905	+	1	NA	promoter-TSS (NM_028019)	promoter-TSS (NM_028019)	24	NM_028019	71956	Mm.22985	NM_028019	ENSMUSG00000020707	Rnf135	0610037N03Rik|2410006N06Rik	ring finger protein 135	protein-coding
mm_52547.1	chr6	115935119	115935128	+	1	NA	exon (NM_145383, exon 3 of 5)	exon (NM_145383, exon 3 of 5)	3196	NM_145383	212541	Mm.2965	NM_145383	ENSMUSG00000030324	Rho	Noerg1|Opn2|Ops|RP4	rhodopsin	protein-coding
mm_142490.1	chr17	45828854	45828882	-	1	NA	Intergenic	Intergenic	-95024	NM_028164	72240	Mm.482897	NM_028164	ENSMUSG00000094690	1600014C23Rik	-	RIKEN cDNA 1600014C23 gene	protein-coding
mm_126307.1	chr15	79533834	79533848	+	1	NA	promoter-TSS (NM_152806)	promoter-TSS (NM_152806)	-924	NM_152806	67040	Mm.29644	NM_152806	ENSMUSG00000055065	Ddx17	2610007K22Rik|A430025E01Rik|AI047725|C80929|Gm926|p72	DEAD (Asp-Glu-Ala-Asp) box polypeptide 17	protein-coding
mm_37164.1	chr4	117156123	117156143	-	1	NA	promoter-TSS (NR_030704)	promoter-TSS (NR_030704)	-1	NM_009098	20116	Mm.260904	NM_009098	ENSMUSG00000047675	Rps8	-	ribosomal protein S8	protein-coding
mm_119633.1	chr14	51853768	51853772	+	1	NA	promoter-TSS (NM_017385)	promoter-TSS (NM_017385)	2	NM_053111	93719	Mm.221324	NM_053111	ENSMUSG00000062148	Ear6	-	eosinophil-associated, ribonuclease A family, member 6	protein-coding
mm_18325.1	chr2	57122102	57122102	-	1	NA	intron (NM_001139509, intron 1 of 7)	intron (NM_001139509, intron 1 of 7)	1901	NM_001139509	18227	Mm.3507	NM_013613	ENSMUSG00000026826	Nr4a2	HZF-3|NOT|Nurr1|RNR-1|TINOR|TINUR	nuclear receptor subfamily 4, group A, member 2	protein-coding
mm_19810.1	chr2	110314526	110314571	-	1	NA	Intergenic	Intergenic	-8823	NM_130452	170442	Mm.27335	NM_130452	ENSMUSG00000041660	Bbox1	AI874739	butyrobetaine (gamma), 2-oxoglutarate dioxygenase 1 (gamma-butyrobetaine hydroxylase)	protein-coding
mm_46798.1	chr5	112966393	112966397	-	1	NA	intron (NM_177078, intron 5 of 20)	intron (NM_177078, intron 5 of 20)	49143	NM_001285806	320129	Mm.285619	NM_177078	ENSMUSG00000042249	Grk3	4833444A01Rik|AI851927|AW551196|Adrbk-2|Adrbk2|Bark-2	G protein-coupled receptor kinase 3	protein-coding
mm_81864.1	chr9	118926639	118926654	+	1	NA	5' UTR (NM_133710, exon 1 of 8)	5' UTR (NM_133710, exon 1 of 8)	110	NM_133710	69274	Mm.439928	NM_133710	ENSMUSG00000047409	Ctdspl	2810418J22Rik|AI426263|HYA22|SCP3	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase-like	protein-coding
mm_3921.1	chr1	162570598	162570656	+	1	NA	promoter-TSS (NM_016796)	promoter-TSS (NM_016796)	-201	NM_016796	53330	Mm.10699	NM_016796	ENSMUSG00000026696	Vamp4	D1Ertd147e	vesicle-associated membrane protein 4	protein-coding
mm_7041.1	chr1	87101631	87101636	-	1	NA	promoter-TSS (NM_001081082)	promoter-TSS (NM_001081082)	-27	NM_001081082	76768	Mm.58068	NM_001081082	ENSMUSG00000079440	Alpi	2010001C14Rik|Akp6|gIAP	alkaline phosphatase, intestinal	protein-coding
mm_36766.1	chr4	101390556	101390573	-	1	NA	intron (NR_040640, intron 3 of 3)	intron (NR_040640, intron 3 of 3)	-28725	NM_001177602	11639	Mm.42040	NM_009647	ENSMUSG00000028527	Ak4	AK 4|Ak-3|Ak-4|Ak3|Ak3l1|D4Ertd274e	adenylate kinase 4	protein-coding
mm_72882.1	chr8	89003853	89003863	+	1	NA	Intergenic	Intergenic	-20877	NR_106190	102465899		NR_106190	ENSMUSG00000099078	Mir8110	Gm27571|mmu-mir-8110	microRNA 8110	ncRNA
mm_11947.1	chr2	52927613	52927642	+	1	NA	intron (NM_172409, intron 1 of 26)	intron (NM_172409, intron 1 of 26)	69759	NM_172409	71409	Mm.394427	NM_172409	ENSMUSG00000036053	Fmnl2	5430425K04Rik|Man	formin-like 2	protein-coding
mm_6856.1	chr1	84262538	84262589	-	1	NA	intron (NM_001003948, intron 1 of 2)	intron (NM_001003948, intron 1 of 2)	22082	NM_001003948	98496	Mm.187470	NM_001003948	ENSMUSG00000045658	Pid1	5033414K04Rik|NYGGF4	phosphotyrosine interaction domain containing 1	protein-coding
mm_134558.1	chr16	20292133	20292143	-	1	NA	intron (NM_001005767, intron 4 of 9)	intron (NM_001005767, intron 4 of 9)	10224	NM_001005767	381038	Mm.371737	NM_001005767	ENSMUSG00000033918	Parl	D16Ertd607e|PRO2207|PSARL1|PSENIP2|Psarl	presenilin associated, rhomboid-like	protein-coding
mm_116888.1	chr13	55321898	55321911	-	1	NA	promoter-TSS (NM_025596)	promoter-TSS (NM_025596)	76	NM_009000	19336	Mm.220923	NM_009000	ENSMUSG00000034789	Rab24	6530406O07Rik	RAB24, member RAS oncogene family	protein-coding
mm_24760.1	chr3	95496734	95496735	+	1	NA	3' UTR (NM_001037737, exon 22 of 22)	3' UTR (NM_001037737, exon 22 of 22)	-2476	NM_007802	13038	Mm.272085	NM_007802	ENSMUSG00000028111	Ctsk	AI323530|MMS10-Q|Ms10q|catK	cathepsin K	protein-coding
mm_31982.1	chr4	89123332	89123347	+	1	NA	Intergenic	Intergenic	-14031	NM_024433	66902	Mm.28500	NM_024433	ENSMUSG00000062937	Mtap	1300019I21Rik|MSAP	methylthioadenosine phosphorylase	protein-coding
mm_13999.1	chr2	121956438	121956480	+	1	NA	promoter-TSS (NM_008545)	promoter-TSS (NM_008545)	-367	NM_008545	17147	Mm.389349	NM_008545	ENSMUSG00000074881	Mageb3	Mage-b3|Mage-ps1|Mage-rs3|Smage3	melanoma antigen, family B, 3	protein-coding
mm_159464.1	chr4	3871886	3871886	-	1	NA	5' UTR (NM_020021, exon 1 of 1)	5' UTR (NM_020021, exon 1 of 1)	219	NM_020021	17451	Mm.459300	NM_020021	ENSMUSG00000078365	Mos	c-mos	Moloney sarcoma oncogene	protein-coding
mm_147389.1	chr18	44173719	44173722	-	1	NA	intron (NM_183123, intron 2 of 4)	intron (NM_183123, intron 2 of 4)	1353	NM_183123	77424	Mm.99224	NM_183123	ENSMUSG00000053729	Spinkl	9530002K18Rik	serine protease inhibitor, Kazal type-like	protein-coding
mm_75290.1	chr8	41041882	41041913	-	1	NA	promoter-TSS (NM_001005865)	promoter-TSS (NM_001005865)	34	NM_001005865	102103	Mm.149438	NM_001005863	ENSMUSG00000045636	Mtus1	AI481402|ATBP135|Atip1|B430010I23Rik|B430305I03Rik|C85752|Cctsg1-440|MD44|MTSG1|mKIAA1288	mitochondrial tumor suppressor 1	protein-coding
mm_110765.1	chr12	70227659	70227669	-	1	NA	promoter-TSS (NR_045174)	promoter-TSS (NR_045174)	19	NM_133198	110095	Mm.256926	NM_133198	ENSMUSG00000021069	Pygl	-	liver glycogen phosphorylase	protein-coding
mm_125844.1	chr15	74958890	74958900	+	1	NA	3' UTR (NM_001164036, exon 4 of 4)	3' UTR (NM_001164036, exon 4 of 4)	3789	NM_001164040	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_75469.1	chr8	47990491	47990534	-	1	NA	promoter-TSS (NM_133791)	promoter-TSS (NM_133791)	39	NM_133791	52357	Mm.235074	NM_133791	ENSMUSG00000031563	Wwc2	5330431C14Rik|AU022508|C85457|D8Ertd594e	WW, C2 and coiled-coil domain containing 2	protein-coding
mm_161640.1	chr16	94570853	94570853	+	1	NA	promoter-TSS (NM_001113389)	promoter-TSS (NM_001113389)	-54	NM_001113389	13548	Mm.310973	NM_007890	ENSMUSG00000022897	Dyrk1a	2310043O08Rik|D16Ertd272e|D16Ertd493e|Dyrk|ENSMUSG00000074897|Gm10783|Mnbh|Mp86|mmb	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1a	protein-coding
mm_164597.1	chr17	28513972	28514009	+	1	NA	Intergenic	Intergenic	-16871	NM_026290	67645	Mm.46170	NM_026290	ENSMUSG00000024223	Armc12	4930511I11Rik|AV041658	armadillo repeat containing 12	protein-coding
mm_144268.1	chr18	11054063	11054074	+	1	NA	5' UTR (NM_010258, exon 2 of 7)	5' UTR (NM_010258, exon 2 of 7)	-1501	NR_105023	68434	Mm.57626	NR_105022	ENSMUSG00000097222	1010001N08Rik	Gata6as	RIKEN cDNA 1010001N08 gene	ncRNA
mm_63813.1	chr7	133747583	133747604	+	1	NA	intron (NM_133941, intron 3 of 11)	intron (NM_133941, intron 3 of 11)	12676	NM_001286030	101437	Mm.199223	NM_133941	ENSMUSG00000030986	Dhx32	3110079L04Rik|4732469F02Rik|AA408140|Ddx32	DEAH (Asp-Glu-Ala-His) box polypeptide 32	protein-coding
mm_142927.1	chr17	53846375	53846390	-	1	NA	promoter-TSS (NM_026935)	promoter-TSS (NM_026935)	-424	NM_026935	69083	Mm.19320	NM_026935	ENSMUSG00000023122	Sult1c2	1810008N17Rik|ST1C1|ST1C2|Sult1c1	sulfotransferase family, cytosolic, 1C, member 2	protein-coding
mm_60005.1	chr7	30720282	30720290	+	1	NA	exon (NM_018731, exon 14 of 22)	exon (NM_018731, exon 14 of 22)	8077	NM_001290627	11944	Mm.12821	NM_018731	ENSMUSG00000005553	Atp4a	-	ATPase, H+/K+ exchanging, gastric, alpha polypeptide	protein-coding
mm_87715.1	chr10	60105899	60105910	+	1	NA	promoter-TSS (NM_052994)	promoter-TSS (NM_052994)	-353	NM_052994	94214	Mm.153429	NM_052994	ENSMUSG00000058297	Spock2	AA407235|Gcap26|mKIAA0275	sparc/osteonectin, cwcv and kazal-like domains proteoglycan 2	protein-coding
mm_56866.1	chr6	118419389	118419441	-	1	NA	promoter-TSS (NM_194339)	promoter-TSS (NM_194339)	2	NM_194339	213895	Mm.25269	NM_194339	ENSMUSG00000030138	Bms1	AA408648|AU020092|AU043373|BB007109|BC030906|Bms1l|mKIAA0187	BMS1, ribosome biogenesis factor	protein-coding
mm_63845.1	chr7	135652379	135652382	+	1	NA	promoter-TSS (NR_015548)	promoter-TSS (NR_015548)	-66	NR_015548	67765	Mm.445272	NR_015548	ENSMUSG00000097471	5830432E09Rik	-	RIKEN cDNA 5830432E09 gene	ncRNA
mm_139410.1	chr17	52602398	52602437	+	1	NA	promoter-TSS (NM_001031811)	promoter-TSS (NM_001031811)	-292	NM_001031811	211468	Mm.399068	NM_001031811	ENSMUSG00000035580	Kcnh8	C130090D05Rik|ELK|ELK1|ELK3|Kv12.1	potassium voltage-gated channel, subfamily H (eag-related), member 8	protein-coding
mm_147882.1	chr18	64660982	64661010	-	1	NA	promoter-TSS (NM_001001488)	promoter-TSS (NM_001001488)	4	NM_001001488	54670	Mm.270043	NM_001001488	ENSMUSG00000039529	Atp8b1	AI451886|FIC1|Ic	ATPase, class I, type 8B, member 1	protein-coding
mm_12276.1	chr2	68999965	68999975	+	1	NA	intron (NM_172856, intron 3 of 9)	intron (NM_172856, intron 3 of 9)	-135830	NM_181547	329416	Mm.90047	NM_181547	ENSMUSG00000034738	Nostrin	Daip2|mDaIP2	nitric oxide synthase trafficker	protein-coding
mm_83411.1	chr9	44802953	44802961	-	1	NA	promoter-TSS (NM_138951)	promoter-TSS (NM_138951)	-6	NM_138951	192653	Mm.325487	NM_138951	ENSMUSG00000039438	Ttc36	-	tetratricopeptide repeat domain 36	protein-coding
mm_54949.1	chr6	48648086	48648090	-	1	NA	intron (NM_001077410, intron 2 of 5)	intron (NM_001077410, intron 2 of 5)	727	NM_212486	243374	Mm.86514	NM_212486	ENSMUSG00000064262	Gimap8	Gm457|IAN9|IMAP8	GTPase, IMAP family member 8	protein-coding
mm_31651.1	chr4	59728047	59728051	+	1	NA	intron (NM_001015681, intron 2 of 3)	intron (NM_001015681, intron 2 of 3)	55806	NM_001013577	66209	Mm.51988	NM_001013577	ENSMUSG00000038544	Inip	1110054O05Rik|2610312O17Rik|AA399876|Ssbip1	INTS3 and NABP interacting protein	protein-coding
mm_134736.1	chr16	22899434	22899441	-	1	NA	TTS (NM_001276450)	TTS (NM_001276450)	-5051	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_113461.1	chr13	35968468	35968471	+	1	NA	5' UTR (NM_029628, exon 2 of 2)	5' UTR (NM_029628, exon 2 of 2)	563	NM_029628	76487	Mm.44745	NM_029628	ENSMUSG00000050423	Ppp1r3g	1600032L17Rik	protein phosphatase 1, regulatory (inhibitor) subunit 3G	protein-coding
mm_155903.1	chrX	101680062	101680077	+	1	NA	intron (NM_139144, intron 21 of 21)	PB1D11|SINE|Alu	39851	NM_001290535	108155	Mm.487332	NM_139144	ENSMUSG00000034160	Ogt	1110038P24Rik|4831420N21Rik|AI115525|Ogtl	O-linked N-acetylglucosamine (GlcNAc) transferase (UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase)	protein-coding
mm_141353.1	chr17	28689759	28689764	-	1	NA	5' UTR (NM_001290320, exon 1 of 20)	5' UTR (NM_001290320, exon 1 of 20)	226	NM_001290320	224661		NM_146076	ENSMUSG00000036196	Slc26a8	-	solute carrier family 26, member 8	protein-coding
mm_89437.1	chr10	91165992	91166016	+	1	NA	exon (NM_001080132, exon 2 of 6)	exon (NM_001080132, exon 2 of 6)	4546	NM_001283048	21917	Mm.159684	NM_011605	ENSMUSG00000019961	Tmpo	5630400D24Rik|AI195756|AI606875|AW214352|AW547477|LAP2|TP	thymopoietin	protein-coding
mm_85777.1	chr9	109057716	109057723	-	1	NA	TTS (NM_026381)	TTS (NM_026381)	1532	NM_001012236	22040	Mm.439964	NM_011637	ENSMUSG00000049734	Trex1	AU041952	three prime repair exonuclease 1	protein-coding
mm_170945.1	chr2	51876508	51876527	+	1	NA	Intergenic	IAP1-MM_LTR|LTR|ERVK	58127	NM_001141982	71684	Mm.28309	NM_030243	ENSMUSG00000036249	Rbm43	0610033I05Rik	RNA binding motif protein 43	protein-coding
mm_41791.1	chr5	103753053	103753102	+	1	NA	Intergenic	Charlie1a|DNA|hAT-Charlie	-1085	NM_133919	17355	Mm.6949	NM_133919	ENSMUSG00000029313	Aff1	9630032B01Rik|AW319193|Af4|Mllt2h|Rob	AF4/FMR2 family, member 1	protein-coding
mm_86634.1	chr10	14046176	14046182	+	1	NA	intron (NM_010437, intron 1 of 8)	intron (NM_010437, intron 1 of 8)	79800	NM_010437	15273	Mm.42157	NM_010437	ENSMUSG00000015501	Hivep2	Gm20114|MIBP1|Schnurri-2|Shn-2	human immunodeficiency virus type I enhancer binding protein 2	protein-coding
mm_112171.1	chr12	113419995	113420006	-	1	NA	Intergenic	Intergenic	-69565	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_21555.1	chr2	164079561	164079580	-	1	NA	exon (NM_021420, exon 2 of 11)	exon (NM_021420, exon 2 of 11)	5392	NM_021420	58231	Mm.234472	NM_021420	ENSMUSG00000018209	Stk4	AI447339|AU020804|Kas-2|Mst1|Ysk3	serine/threonine kinase 4	protein-coding
mm_76414.1	chr8	84937379	84937392	-	1	NA	promoter-TSS (NM_019945)	promoter-TSS (NM_019945)	-32	NM_019945	56527	Mm.154614	NM_019945	ENSMUSG00000053693	Mast1	9430008B02Rik|SAST|SAST170	microtubule associated serine/threonine kinase 1	protein-coding
mm_39944.1	chr5	31873080	31873084	+	1	NA	intron (NM_144541, intron 6 of 11)	intron (NM_144541, intron 6 of 11)	175032	NM_144541	107976	Mm.482126	NM_144541	ENSMUSG00000052139	Bre	6030405P19Rik|AI429776|B830038C02Rik	brain and reproductive organ-expressed protein	protein-coding
mm_31670.1	chr4	60005493	60005502	+	1	NA	exon (NM_001081285, exon 4 of 6)	exon (NM_001081285, exon 4 of 6)	1948	NM_001081285	620807	Mm.464562	NM_001081285	ENSMUSG00000078689	Mup6	Gm12544|Mup2|OTTMUSG00000007423	major urinary protein 6	protein-coding
mm_53844.1	chr6	148983851	148983859	+	1	NA	Intergenic	RMER17C2|LTR|ERVK	-37423	NM_019643	56306	Mm.18637	NM_019643	ENSMUSG00000039985	Fam60a	Ppcs1|Pptcs1|Tera	family with sequence similarity 60, member A	protein-coding
mm_96719.1	chr11	69665638	69665674	+	1	NA	exon (NM_001291058, exon 2 of 6)	exon (NM_001291058, exon 2 of 6)	514	NM_001291058	12514	Mm.15819	NM_009853	ENSMUSG00000018774	Cd68	Lamp4|Scard1|gp110	CD68 antigen	protein-coding
mm_63931.1	chr7	139482391	139482392	+	1	NA	intron (NM_183144, intron 4 of 15)	intron (NM_183144, intron 4 of 15)	93282	NM_001127363	212111	Mm.28308	NM_183144	ENSMUSG00000025477	Inpp5a	-	inositol polyphosphate-5-phosphatase A	protein-coding
mm_163470.1	chr12	103338415	103338421	-	1	NA	intron (NM_023049, intron 2 of 9)	intron (NM_023049, intron 2 of 9)	17583	NM_023049	65256	Mm.27159	NM_023049	ENSMUSG00000021200	Asb2	1110008E15Rik	ankyrin repeat and SOCS box-containing 2	protein-coding
mm_137003.1	chr17	17491513	17491534	+	1	NA	Intergenic	Intergenic	88837	NM_025681	66643	Mm.268018	NM_025681	ENSMUSG00000047786	Lix1	5730466L18Rik	limb and CNS expressed 1	protein-coding
mm_98648.1	chr11	96251240	96251253	+	1	NA	promoter-TSS (NR_037977)	promoter-TSS (NR_037977)	-414	NR_037977	193022	Mm.169508	NR_037977		Gm53	-	predicted gene 53	ncRNA
mm_84094.1	chr9	58247125	58247141	-	1	NA	exon (NM_008884, exon 2 of 8)	exon (NM_008884, exon 2 of 8)	2653	NM_178087	18854	Mm.392123	NM_008884	ENSMUSG00000036986	Pml	1200009E24Rik|AI661194|Trim19	promyelocytic leukemia	protein-coding
mm_21893.1	chr2	166155582	166155621	-	1	NA	promoter-TSS (NM_028072)	promoter-TSS (NM_028072)	82	NM_001252579	72043	Mm.1011	NM_028072	ENSMUSG00000006800	Sulf2	2010004N24Rik|AU020235|MSulf-2|mKIAA1247	sulfatase 2	protein-coding
mm_110564.1	chr12	55821099	55821110	-	1	NA	5' UTR (NM_019994, exon 1 of 41)	5' UTR (NM_019994, exon 1 of 41)	412	NM_019994	56784	Mm.292180	NM_019994	ENSMUSG00000021027	Ralgapa1	2310003F20Rik|4930400K19Rik|AI563624|GRIPE|Garnl1|Tulip1|mKIAA0884	Ral GTPase activating protein, alpha subunit 1	protein-coding
mm_62686.1	chr7	110023110	110023119	+	1	NA	intron (NM_181517, intron 1 of 24)	B1_Mus2|SINE|Alu	4689	NM_181517	233726	Mm.222328	NM_181517	ENSMUSG00000066232	Ipo7	A330055O14Rik|C330016G14|Imp7|Ranbp7	importin 7	protein-coding
mm_126552.1	chr15	82127917	82128001	+	1	NA	promoter-TSS (NM_172428)	promoter-TSS (NM_172428)	-16	NR_137170	76457	Mm.440373	NM_172428	ENSMUSG00000068114	Ccdc134	2310042L06Rik|AW208859	coiled-coil domain containing 134	protein-coding
mm_154967.1	chrX	37126778	37126795	+	1	NA	promoter-TSS (NM_025937)	promoter-TSS (NM_025937)	23	NM_025937	67050	Mm.55422	NM_025937	ENSMUSG00000016409	Nkap	2610020O08Rik|AA987160|AI849147|AL024236	NFKB activating protein	protein-coding
mm_75855.1	chr8	70699822	70699869	-	1	NA	exon (NM_001286944, exon 1 of 1)	exon (NM_001286944, exon 1 of 1)	2106	NM_001286944	16478	Mm.419851	NM_010592	ENSMUSG00000071076	Jund	Jund1	jun D proto-oncogene	protein-coding
mm_130636.1	chr15	100486607	100486630	-	1	NA	intron (NM_153407, intron 3 of 4)	intron (NM_153407, intron 3 of 4)	8621	NM_153407	207785	Mm.294969	NM_153407	ENSMUSG00000044636	Csrnp2	CSRNP-2|Csnrp2|taip-12	cysteine-serine-rich nuclear protein 2	protein-coding
mm_38370.1	chr4	138396388	138396437	-	1	NA	promoter-TSS (NM_001081672)	promoter-TSS (NM_001081672)	46	NM_001081672	625638	Mm.379091	NM_001081672	ENSMUSG00000078235	Fam43b	OTTMUSG00000009974	family with sequence similarity 43, member B	protein-coding
mm_108415.1	chr12	81959122	81959133	+	1	NA	intron (NM_018814, intron 14 of 35)	ID4|SINE|ID	99097	NM_018814	54604	Mm.86584	NM_018814	ENSMUSG00000021140	Pcnx	2900024E21Rik|3526401J03Rik|AF096286|AI327143|AI413187|Pcnx1|Pcnxl1	pecanex homolog (Drosophila)	protein-coding
mm_164540.1	chr17	7879851	7879875	+	1	NA	Intergenic	Intergenic	-46137	NM_145968	72536	Mm.119680	NM_145968	ENSMUSG00000033450	Tagap	2610315E15Rik	T cell activation Rho GTPase activating protein	protein-coding
mm_47058.1	chr5	116381649	116381653	-	1	NA	Intergenic	MLT1B|LTR|ERVL-MaLR	41213	NM_030704	80888	Mm.21549	NM_030704	ENSMUSG00000041548	Hspb8	AU018630|AW413033|Cryac|D5Ucla4|E2IG1|H11|H11K|HSP20-like|HSP22	heat shock protein 8	protein-coding
mm_155643.1	chrX	85269508	85269560	+	1	NA	5' UTR (NM_028046, exon 2 of 2)	5' UTR (NM_028046, exon 2 of 2)	19857	NM_028046	71996	Mm.20201	NM_028046	ENSMUSG00000035491	Fthl17a	1600014K23Rik|AI324104	ferritin, heavy polypeptide-like 17, member A	protein-coding
mm_173136.1	chrX	20617823	20617832	+	1	NA	promoter-TSS (NM_145627)	promoter-TSS (NM_145627)	68	NM_145627	236732	Mm.279194	NM_145627	ENSMUSG00000031060	Rbm10	E430039K10Rik	RNA binding motif protein 10	protein-coding
mm_139359.1	chr17	50528952	50528967	+	1	NA	intron (NM_013880, intron 1 of 5)	ID4|SINE|ID	19412	NM_013880	224860	Mm.217362	NM_013880	ENSMUSG00000038910	Plcl2	PLC-L2|PRIP-2|Plce2|mKIAA1092	phospholipase C-like 2	protein-coding
mm_46519.1	chr5	105328958	105328962	-	1	NA	intron (NR_132129, intron 5 of 10)	intron (NR_132129, intron 5 of 10)	17512	NM_001039647	634650	Mm.458435	NM_001039647	ENSMUSG00000092021	Gbp11	EG634650|Gm7141	guanylate binding protein 11	protein-coding
mm_29165.1	chr3	106483436	106483437	-	1	NA	intron (NR_033207, intron 1 of 1)	intron (NR_033207, intron 1 of 1)	986	NM_001278941	72121	Mm.14816	NM_028110	ENSMUSG00000027901	Dennd2d	2010308M01Rik|AI451421	DENN/MADD domain containing 2D	protein-coding
mm_83865.1	chr9	54824770	54824796	-	1	NA	Intergenic	Intergenic	-38972	NM_022655	64602	Mm.208991	NM_022655	ENSMUSG00000032293	Ireb2	D9Ertd85e|Irp2	iron responsive element binding protein 2	protein-coding
mm_122268.1	chr14	34358256	34358264	-	1	NA	Intergenic	Intergenic	-2867	NM_183278	69134	Mm.27156	NM_183278	ENSMUSG00000043681	Fam25c	2200001I15Rik|Fam25	family with sequence similarity 25, member C	protein-coding
mm_155775.1	chrX	96341734	96341742	+	1	NA	intron (NM_001310755, intron 2 of 10)	L1_Mur3|LINE|L1	26181	NM_001310754	245525	Mm.166749	NM_172931	ENSMUSG00000045802	Hsf3	B230358A15Rik|HSF 3|HSTF 3	heat shock transcription factor 3	protein-coding
mm_156243.1	chrX	136245118	136245175	+	1	NA	promoter-TSS (NM_011712)	promoter-TSS (NM_011712)	66	NM_011712	22381	Mm.512	NM_011712	ENSMUSG00000042712	Wbp5	AL024233|Tceal9	WW domain binding protein 5	protein-coding
mm_10605.1	chr2	18906348	18906352	+	1	NA	intron (NM_008845, intron 2 of 9)	intron (NM_008845, intron 2 of 9)	91771	NM_008845	18718	Mm.313977	NM_008845	ENSMUSG00000026737	Pip4k2a	AW742916|Pip5k2a	phosphatidylinositol-5-phosphate 4-kinase, type II, alpha	protein-coding
mm_151224.1	chr19	53700866	53700887	+	1	NA	intron (NM_001170847, intron 1 of 13)	Lx7|LINE|L1	23570	NM_001170847	73713	Mm.313695	NM_001170847	ENSMUSG00000043639	Rbm20	1110018J23Rik|2010003H22Rik|AI646761	RNA binding motif protein 20	protein-coding
mm_152461.1	chr19	10881678	10881717	-	1	NA	promoter-TSS (NM_134142)	promoter-TSS (NM_134142)	46	NM_134142	68539	Mm.251890	NM_134142	ENSMUSG00000034659	Tmem109	1110006I15Rik|AA958958|C77652	transmembrane protein 109	protein-coding
mm_116133.1	chr13	28953428	28953438	-	1	NA	5' UTR (NM_009238, exon 1 of 1)	5' UTR (NM_009238, exon 1 of 1)	249	NM_009238	20677	Mm.240627	NM_009238	ENSMUSG00000076431	Sox4	AA682046|Sox-4	SRY (sex determining region Y)-box 4	protein-coding
mm_12286.1	chr2	69008606	69008615	+	1	NA	intron (NM_172856, intron 4 of 9)	RMER30|DNA|hAT-Charlie	-127190	NM_181547	329416	Mm.90047	NM_181547	ENSMUSG00000034738	Nostrin	Daip2|mDaIP2	nitric oxide synthase trafficker	protein-coding
mm_24700.1	chr3	95126207	95126213	+	1	NA	intron (NM_016712, intron 3 of 9)	PB1D10|SINE|Alu	1696	NM_016712	50874	Mm.71935	NM_016712	ENSMUSG00000005628	Tmod4	MTMOD|Sk-Tmod	tropomodulin 4	protein-coding
mm_97623.1	chr11	78957506	78957527	+	1	NA	exon (NM_010927, exon 26 of 27)	exon (NM_010927, exon 26 of 27)	27408	NM_001159301	16859	Mm.341434	NM_010708	ENSMUSG00000001123	Lgals9	AA407335|AI194909|AI265545|LGALS35|Lgals5|gal-9|galectin-9	lectin, galactose binding, soluble 9	protein-coding
mm_44777.1	chr5	32122514	32122522	-	1	NA	Intergenic	Intergenic	-13954	NM_008037	14284	Mm.24684	NM_008037	ENSMUSG00000029135	Fosl2	Fra-2	fos-like antigen 2	protein-coding
mm_128774.1	chr15	66702584	66702612	-	1	NA	intron (NM_009375, intron 20 of 47)	intron (NM_009375, intron 20 of 47)	31828	NM_009375	21819	Mm.441333	NM_009375	ENSMUSG00000053469	Tg	Tgn|cog	thyroglobulin	protein-coding
mm_39470.1	chr5	19907503	19907551	+	1	NA	promoter-TSS (NM_001170745)	promoter-TSS (NM_001170745)	9	NM_015823	50791	Mm.332231	NM_015823	ENSMUSG00000040003	Magi2	AIP-1|Acvri1|Acvrinp1|Acvrip1|Magi-2|S-SCAM|mKIAA0705	membrane associated guanylate kinase, WW and PDZ domain containing 2	protein-coding
mm_91942.1	chr10	60831453	60831472	-	1	NA	5' UTR (NM_029770, exon 1 of 17)	5' UTR (NM_029770, exon 1 of 17)	119	NM_029770	107449	Mm.290433	NM_029770	ENSMUSG00000020099	Unc5b	6330415E02Rik|A630020F16|D10Bwg0792e|Unc5h2	unc-5 netrin receptor B	protein-coding
mm_89202.1	chr10	86348966	86349004	+	1	NA	3' UTR (NM_011595, exon 5 of 5)	3' UTR (NM_011595, exon 5 of 5)	48573	NM_011595	21859	Mm.4871	NM_011595	ENSMUSG00000020044	Timp3	Timp-3	tissue inhibitor of metalloproteinase 3	protein-coding
mm_142130.1	chr17	35901544	35901569	-	1	NA	exon (NM_028476, exon 9 of 10)	exon (NM_028476, exon 9 of 10)	-4178	NM_001033630	69662	Mm.260159	NM_001033630	ENSMUSG00000050705	2310061I04Rik	-	RIKEN cDNA 2310061I04 gene	protein-coding
mm_117469.1	chr13	76056340	76056353	-	1	NA	exon (NM_175495, exon 1 of 1)	exon (NM_175495, exon 1 of 1)	650	NM_175495	238725	Mm.167172	NM_175495	ENSMUSG00000045509	Gpr150	C030001A19Rik|PGR11	G protein-coupled receptor 150	protein-coding
mm_46747.1	chr5	111417141	111417159	-	1	NA	Intergenic	CpG	-1016	NM_001081235	433938	Mm.332576	NM_001081235	ENSMUSG00000070576	Mn1	AA003644|AA009236	meningioma 1	protein-coding
mm_72028.1	chr8	70758109	70758134	+	1	NA	TTS (NM_183170)	TTS (NM_183170)	2800	NM_183170	234384	Mm.213010	NM_183170	ENSMUSG00000035559	Mpv17l2	Fksg24	MPV17 mitochondrial membrane protein-like 2	protein-coding
mm_57512.1	chr6	125481780	125481788	-	1	NA	intron (NM_007657, intron 1 of 7)	intron (NM_007657, intron 1 of 7)	12971	NM_007657	12527	Mm.210676	NM_007657	ENSMUSG00000030342	Cd9	Tspan29	CD9 antigen	protein-coding
mm_14786.1	chr2	145860233	145860246	+	1	NA	exon (NM_028724, exon 9 of 13)	exon (NM_028724, exon 9 of 13)	-43002	NM_026425	67877	Mm.151168	NM_026425	ENSMUSG00000002728	Naa20	1500004D14Rik|2900026I01Rik|AU041458|D2Ertd186e|Nat5	N(alpha)-acetyltransferase 20, NatB catalytic subunit	protein-coding
mm_31881.1	chr4	82065826	82065835	+	1	NA	non-coding (NR_040659, exon 1 of 3)	non-coding (NR_040659, exon 1 of 3)	450	NR_040659	545641	Mm.216028	NR_040659	ENSMUSG00000085022	Gm5860	EG545641	predicted gene 5860	ncRNA
mm_159615.1	chr4	133212639	133212639	-	1	NA	promoter-TSS (NM_008154)	promoter-TSS (NM_008154)	-103	NM_008154	14748	Mm.4721	NM_008154	ENSMUSG00000049649	Gpr3	Gpcr20|Gpcr21|Gpcr3	G-protein coupled receptor 3	protein-coding
mm_5936.1	chr1	55363463	55363475	-	1	NA	promoter-TSS (NM_029267)	promoter-TSS (NM_029267)	0	NM_029267	75388	Mm.483408	NM_029267	ENSMUSG00000025977	Boll	4930554P13Rik|4930597B14Rik	bol, boule-like (Drosophila)	protein-coding
mm_22491.1	chr3	5860669	5860718	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-284445	NM_001163305	19302	Mm.132336	NM_008994	ENSMUSG00000040374	Pex2	D3Ertd138e|PAF-1|PMP35|Pxmp3	peroxisomal biogenesis factor 2	protein-coding
mm_52906.1	chr6	122811190	122811221	+	1	NA	Intergenic	CpG	-8979	NM_021899	60611	Mm.87142	NM_021899	ENSMUSG00000003154	Foxj2	Fhx	forkhead box J2	protein-coding
mm_82639.1	chr9	21992091	21992106	-	1	NA	intron (NM_001163787, intron 8 of 12)	intron (NM_001163787, intron 8 of 12)	-2645	NM_023622	71746	Mm.110594	NM_023622	ENSMUSG00000040146	Rgl3	1300003D20Rik|mFLJ00153	ral guanine nucleotide dissociation stimulator-like 3	protein-coding
mm_43357.1	chr5	135187508	135187595	+	1	NA	5' UTR (NM_011714, exon 1 of 19)	5' UTR (NM_011714, exon 1 of 19)	228	NM_011714	22385	Mm.40331	NM_011714	ENSMUSG00000002748	Baz1b	C87820|WSTF|Wbscr9	bromodomain adjacent to zinc finger domain, 1B	protein-coding
mm_72346.1	chr8	79639493	79639519	+	1	NA	promoter-TSS (NM_001256033)	promoter-TSS (NM_001256033)	-170	NM_001256033	73945	Mm.34348	NM_001081164	ENSMUSG00000036990	Otud4	4930431L18Rik|AI449692|D8Ertd69e|mKIAA1046	OTU domain containing 4	protein-coding
mm_119566.1	chr14	49066709	49066743	+	1	NA	promoter-TSS (NM_207214)	promoter-TSS (NM_207214)	-59	NM_207214	105504	Mm.31607	NM_207214	ENSMUSG00000061244	Exoc5	AI447711|AI448003|Gm76|PRO1912|SEC10|Sec10l1	exocyst complex component 5	protein-coding
mm_101536.1	chr11	33513672	33513682	-	1	NA	promoter-TSS (NR_110973)	promoter-TSS (NR_110973)	69	NR_110973	66011	Mm.383775	NM_023146	ENSMUSG00000040594	Ranbp17	-	RAN binding protein 17	protein-coding
mm_129504.1	chr15	78924990	78924991	-	1	NA	Intergenic	PB1D10|SINE|Alu	-1735	NM_008495	16852	Mm.43831	NM_008495	ENSMUSG00000068220	Lgals1	AA410090|Gal-1|Galbp|L-14.5|L14|Lect14|galectin-1	lectin, galactose binding, soluble 1	protein-coding
mm_137193.1	chr17	23824462	23824483	+	1	NA	TTS (NM_026305)	TTS (NM_026305)	4637	NM_026305	67673	Mm.153758	NM_026305	ENSMUSG00000055839	Elob	0610040H15Rik|Tceb2	elongin B	protein-coding
mm_19839.1	chr2	112510227	112510236	-	1	NA	intron (NM_028844, intron 1 of 5)	intron (NM_028844, intron 1 of 5)	17267	NM_028844	74268	Mm.315125	NM_028844	ENSMUSG00000003604	Aven	1700013A01Rik|1700056A21Rik|mAven-L|mAven-S	apoptosis, caspase activation inhibitor	protein-coding
mm_58154.1	chr6	142386988	142387002	-	1	NA	promoter-TSS (NM_001204907)	promoter-TSS (NM_001204907)	92	NM_001204906	19691	Mm.27407	NM_023042	ENSMUSG00000030243	Recql	RecQ1	RecQ protein-like	protein-coding
mm_54355.1	chr6	31088214	31088222	-	1	NA	Intergenic	Intergenic	-25125	NR_029532	387223		NR_029532	ENSMUSG00000065604	Mir29b-1	Mirn29b|Mirn29b-1|mir-29b-1	microRNA 29b-1	ncRNA
mm_161763.1	chr17	36058422	36058422	-	1	NA	promoter-TSS (NM_001199967)	promoter-TSS (NM_001199967)	-51	NM_001199967	100529082	Mm.484641	NM_001199967	ENSMUSG00000079492	Gm11127	ENSMUSG00000079492	predicted gene 11127	protein-coding
mm_91952.1	chr10	61099815	61099854	-	1	NA	3' UTR (NM_001316673, exon 15 of 15)	3' UTR (NM_001316673, exon 15 of 15)	10503	NM_025273	13180	Mm.39473	NM_025273	ENSMUSG00000020098	Pcbd1	Dcoh|Pcbd|Pcd|Phs	pterin 4 alpha carbinolamine dehydratase/dimerization cofactor of hepatocyte nuclear factor 1 alpha (TCF1) 1	protein-coding
mm_1718.1	chr1	75247190	75247197	+	1	NA	3' UTR (NM_008985, exon 23 of 23)	3' UTR (NM_008985, exon 23 of 23)	10491	NM_001159885	56812	Mm.489660	NM_020266	ENSMUSG00000026203	Dnajb2	2700059H22Rik|Dnajb10|Hsj1|mDj8	DnaJ heat shock protein family (Hsp40) member B2	protein-coding
mm_1012.1	chr1	58728616	58728626	+	1	NA	intron (NM_001293804, intron 3 of 9)	intron (NM_001293804, intron 3 of 9)	-1931	NM_001293805	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_112466.1	chr13	5867916	5867931	+	1	NA	3' UTR (NM_011803, exon 4 of 4)	3' UTR (NM_011803, exon 4 of 4)	6434	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_9778.1	chr1	181144199	181144209	-	1	NA	promoter-TSS (NM_026171)	promoter-TSS (NM_026171)	0	NM_026171	67459	Mm.263464	NM_026171	ENSMUSG00000026516	Nvl	1200009I24Rik	nuclear VCP-like	protein-coding
mm_141044.1	chr17	25408205	25408208	-	1	NA	intron (NM_001163691, intron 2 of 34)	intron (NM_001163691, intron 2 of 34)	25577	NM_021415	58226	Mm.268378	NM_021415	ENSMUSG00000024112	Cacna1h	Cav3.2|MNCb-1209|alpha13.2	calcium channel, voltage-dependent, T type, alpha 1H subunit	protein-coding
mm_127900.1	chr15	9507114	9507125	-	1	NA	3' UTR (NM_008372, exon 8 of 8)	3' UTR (NM_008372, exon 8 of 8)	22757	NM_008372	16197	Mm.389	NM_008372	ENSMUSG00000003882	Il7r	CD127|IL-7Ralpha	interleukin 7 receptor	protein-coding
mm_130966.1	chr15	103318263	103318274	-	1	NA	intron (NM_013866, intron 3 of 7)	intron (NM_013866, intron 3 of 7)	-7830	NM_030720	80910	Mm.160369	NM_030720	ENSMUSG00000063234	Gpr84	EX33	G protein-coupled receptor 84	protein-coding
mm_79207.1	chr9	48991988	48992005	+	1	NA	intron (NM_175482, intron 1 of 23)	intron (NM_175482, intron 1 of 23)	6611	NM_175482	235323	Mm.21630	NM_175482	ENSMUSG00000032267	Usp28	9830148O20Rik|AU022237|mKIAA1515	ubiquitin specific peptidase 28	protein-coding
mm_95141.1	chr11	35121127	35121141	+	1	NA	promoter-TSS (NM_011412)	promoter-TSS (NM_011412)	-322	NM_011412	20564	Mm.478604	NM_011412	ENSMUSG00000056427	Slit3	Slil2|Slit1|b2b2362.1Clo	slit homolog 3 (Drosophila)	protein-coding
mm_104538.1	chr11	96350189	96350199	-	1	NA	Intergenic	Intergenic	-1438	NM_134032	103889	Mm.281153	NM_134032	ENSMUSG00000075588	Hoxb2	AI894218|Hox-2.8|Hoxbes2	homeobox B2	protein-coding
mm_122394.1	chr14	40966947	40966966	-	1	NA	promoter-TSS (NM_145928)	promoter-TSS (NM_145928)	-60	NM_145928	52588	Mm.28876	NM_145928	ENSMUSG00000037824	Tspan14	AA958793|D14Ertd226e|Tm4sf14|tspan-14	tetraspanin 14	protein-coding
mm_123299.1	chr14	61633135	61633138	-	1	NA	intron (NR_028264, intron 3 of 6)	intron (NR_028264, intron 3 of 6)	-1026	NR_029733	387174		NR_029733	ENSMUSG00000093007	Mir15a	Mirn15a|mir-15a|mmu-mir-15a	microRNA 15a	ncRNA
mm_153030.1	chr19	31764964	31764990	-	1	NA	promoter-TSS (NM_001013833)	promoter-TSS (NM_001013833)	56	NM_001013833	19091	Mm.381170	NM_011160	ENSMUSG00000052920	Prkg1	AW125416|CGKI|Gm19690|Prkg1b|Prkgr1b	protein kinase, cGMP-dependent, type I	protein-coding
mm_155889.1	chrX	101649387	101649401	+	1	NA	intron (NM_139144, intron 3 of 21)	intron (NM_139144, intron 3 of 21)	9176	NM_001290535	108155	Mm.487332	NM_139144	ENSMUSG00000034160	Ogt	1110038P24Rik|4831420N21Rik|AI115525|Ogtl	O-linked N-acetylglucosamine (GlcNAc) transferase (UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase)	protein-coding
mm_58902.1	chr7	17163364	17163372	+	1	NA	TTS (NM_054059)	TTS (NM_054059)	12968	NM_054059	384557	Mm.486145	NM_054059	ENSMUSG00000053228	Ceacam3	EG384557|Psg24|cea12	carcinoembryonic antigen-related cell adhesion molecule 3	protein-coding
mm_75625.1	chr8	64689478	64689488	-	1	NA	intron (NM_013494, intron 1 of 8)	B4A|SINE|B4	3626	NM_013494	12876	Mm.31395	NM_013494	ENSMUSG00000037852	Cpe	CPH|Cph-1|Cph1|R74677|fat	carboxypeptidase E	protein-coding
mm_166798.1	chr7	3330902	3330921	+	1	NA	3' UTR (NM_011102, exon 18 of 18)	3' UTR (NM_011102, exon 18 of 18)	-5674	NM_133189	81904	Mm.214994	NM_133189	ENSMUSG00000069806	Cacng7	-	calcium channel, voltage-dependent, gamma subunit 7	protein-coding
mm_28565.1	chr3	93444872	93444918	-	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	2565	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_30091.1	chr3	138193825	138193851	-	1	NA	Intergenic	Intergenic	-7125	NM_001163386	67741	Mm.383221	NM_001163385	ENSMUSG00000012042	4930579F01Rik	-	RIKEN cDNA 4930579F01 gene	protein-coding
mm_93521.1	chr10	115288325	115288334	-	1	NA	Intergenic	Intergenic	27262	NM_024454	216344	Mm.21936	NM_024454	ENSMUSG00000020132	Rab21	9630024B22	RAB21, member RAS oncogene family	protein-coding
mm_169562.1	chr15	14697412	14697427	-	1	NA	Intergenic	RLTR9D|LTR|ERVK	-1523744	NM_007666	12563	Mm.57048	NM_007666	ENSMUSG00000039385	Cdh6	cad6	cadherin 6	protein-coding
mm_79792.1	chr9	63876193	63876202	+	1	NA	Intergenic	Intergenic	-118203	NM_016769	17127	Mm.7320	NM_016769	ENSMUSG00000032402	Smad3	AU022421|Madh3	SMAD family member 3	protein-coding
mm_52880.1	chr6	122513420	122513459	+	1	NA	promoter-TSS (NM_015776)	promoter-TSS (NM_015776)	-145	NM_001347434	50530	Mm.41931	NM_015776	ENSMUSG00000030116	Mfap5	MAGP-2|MFAP-5	microfibrillar associated protein 5	protein-coding
mm_128381.1	chr15	42676954	42676954	-	1	NA	promoter-TSS (NM_001286062)	promoter-TSS (NM_001286062)	23	NM_001286062	11600	Mm.309336	NM_009640	ENSMUSG00000022309	Angpt1	1110046O21Rik|Ang-1|Ang1	angiopoietin 1	protein-coding
mm_31605.1	chr4	58286065	58286068	+	1	NA	5' UTR (NM_010944, exon 1 of 14)	5' UTR (NM_010944, exon 1 of 14)	104	NM_010944	18198	Mm.16148	NM_010944	ENSMUSG00000057280	Musk	Mdk4|Mlk|Nsk1|Nsk2|Nsk3	muscle, skeletal, receptor tyrosine kinase	protein-coding
mm_95318.1	chr11	46437032	46437050	+	1	NA	promoter-TSS (NM_025426)	promoter-TSS (NM_025426)	80	NM_025426	66213	Mm.24159	NM_025426	ENSMUSG00000020397	Med7	1110063B05Rik|Crsp33|Crsp9	mediator complex subunit 7	protein-coding
mm_113705.1	chr13	43365459	43365522	+	1	NA	Intergenic	CpG	-5226	NM_178848	68346	Mm.35325	NM_178848	ENSMUSG00000054021	Sirt5	0610012J09Rik|1500032M05Rik|AV001953	sirtuin 5	protein-coding
mm_66904.1	chr7	59980935	59980947	-	1	NA	Intergenic	Intergenic	-2085	NR_028529	100217429		NR_028529		Snord64	MBII-13	small nucleolar RNA, C/D box 64	snoRNA
mm_108840.1	chr12	97124505	97124527	+	1	NA	Intergenic	Intergenic	-1077294	NR_103800	69423	Mm.46121	NM_027076		1700019M22Rik	-	NFX-like protein	pseudo
mm_116763.1	chr13	52573235	52573255	-	1	NA	promoter-TSS (NR_046069)	promoter-TSS (NR_046069)	-20	NR_046069	100040572	Mm.278873	NR_046069		Gm2848	-	predicted gene 2848	ncRNA
mm_115624.1	chr13	12104520	12104525	-	1	NA	intron (NM_023868, intron 1 of 104)	intron (NM_023868, intron 1 of 104)	2423	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding
mm_70002.1	chr7	142387821	142387845	-	1	NA	promoter-TSS (NM_009983)	promoter-TSS (NM_009983)	37	NM_009983	13033	Mm.231395	NM_009983	ENSMUSG00000007891	Ctsd	CD|CatD	cathepsin D	protein-coding
mm_61756.1	chr7	82771511	82771527	+	1	NA	intron (NM_175317, intron 18 of 19)	intron (NM_175317, intron 18 of 19)	-15875	NR_046004	77800	Mm.444811	NR_046004	ENSMUSG00000086690	4933406J10Rik	A930009F24Rik	RIKEN cDNA 4933406J10 gene	ncRNA
mm_167356.1	chr8	84198764	84198786	+	1	NA	Intergenic	Intergenic	-9743	NR_029740	387216		NR_029740	ENSMUSG00000065611	Mir23a	Mirn23a|mir-23a|mmu-mir-23a	microRNA 23a	ncRNA
mm_121574.1	chr14	122891880	122891880	+	1	NA	intron (NM_145466, intron 2 of 2)	intron (NM_145466, intron 2 of 2)	21285	NM_145466	223267	Mm.379358	NM_145466	ENSMUSG00000041625	Ggact	A2ld1	gamma-glutamylamine cyclotransferase	protein-coding
mm_145414.1	chr18	57878621	57878637	+	1	NA	promoter-TSS (NM_009194)	promoter-TSS (NM_009194)	-49	NM_009194	20496	Mm.399997	NM_009194	ENSMUSG00000024597	Slc12a2	9330166H04Rik|Nkcc1|mBSC2|sy-ns	solute carrier family 12, member 2	protein-coding
mm_159499.1	chr4	43668916	43668916	+	1	NA	promoter-TSS (NM_175517)	promoter-TSS (NM_175517)	-55	NM_001085508	242409	Mm.171489	NM_001085508	ENSMUSG00000078716	Tmem8b	4930500O05Rik	transmembrane protein 8B	protein-coding
mm_164613.1	chr17	31161432	31161436	-	1	NA	TTS (NM_009362)	TTS (NM_009362)	3619	NM_009362	21784	Mm.2854	NM_009362	ENSMUSG00000024032	Tff1	Bcei|PS2	trefoil factor 1	protein-coding
mm_83911.1	chr9	56360986	56361007	-	1	NA	intron (NM_172924, intron 2 of 6)	intron (NM_172924, intron 2 of 6)	57054	NM_172924	244895	Mm.490331	NM_172924	ENSMUSG00000074305	Peak1	1110049L02Rik|9530046P14|AA690169|BE132841|C230081A13Rik|SGK269|mKIAA2002	pseudopodium-enriched atypical kinase 1	protein-coding
mm_9235.1	chr1	171287917	171287929	-	1	NA	promoter-TSS (NM_013919)	promoter-TSS (NM_013919)	38	NM_013919	30941	Mm.27510	NM_013919	ENSMUSG00000053483	Usp21	ESTM28|Usp16|Usp23|W53272	ubiquitin specific peptidase 21	protein-coding
mm_171757.1	chr5	105093102	105093106	-	1	NA	intron (NM_172777, intron 5 of 10)	L1Md_T|LINE|L1	17188	NM_172777	236573	Mm.425261	NM_172777	ENSMUSG00000029298	Gbp9	-	guanylate-binding protein 9	protein-coding
mm_78016.1	chr9	13662194	13662194	+	1	NA	promoter-TSS (NM_173776)	promoter-TSS (NM_173776)	-266	NM_173776	270118	Mm.116898	NM_173776	ENSMUSG00000031925	Maml2	5930431H10|BC032967	mastermind like 2 (Drosophila)	protein-coding
mm_25140.1	chr3	102520256	102520263	+	1	NA	exon (NM_013609, exon 4 of 4)	exon (NM_013609, exon 4 of 4)	50340	NM_013609	18049	Mm.1259	NM_013609	ENSMUSG00000027859	Ngf	Ngfb	nerve growth factor	protein-coding
mm_40575.1	chr5	63840274	63840281	+	1	NA	intron (NM_029554, intron 1 of 3)	intron (NM_029554, intron 1 of 3)	27782	NM_029554	76261	Mm.38143	NM_029554	ENSMUSG00000060512	0610040J01Rik	AI662686	RIKEN cDNA 0610040J01 gene	protein-coding
mm_75424.1	chr8	46941286	46941321	-	1	NA	Intergenic	Intergenic	-45584	NM_177304	320981	Mm.211429	NM_177304	ENSMUSG00000038173	Enpp6	4833421B01Rik|B830047L21Rik|D8Ertd514e|E-NPP 6|GPC-Cpde|Npp6	ectonucleotide pyrophosphatase/phosphodiesterase 6	protein-coding
mm_134913.1	chr16	30283252	30283266	-	1	NA	promoter-TSS (NM_028973)	promoter-TSS (NM_028973)	-5	NM_028973	74488	Mm.290677	NM_028973	ENSMUSG00000052316	Lrrc15	5430427N11Rik|LIB	leucine rich repeat containing 15	protein-coding
mm_39794.1	chr5	30588191	30588220	+	1	NA	promoter-TSS (NM_010608)	promoter-TSS (NM_010608)	35	NM_010608	16527	Mm.439936	NM_010608	ENSMUSG00000049265	Kcnk3	TASK|Task-1|cTBAK-1	potassium channel, subfamily K, member 3	protein-coding
mm_17240.1	chr2	25608422	25608432	-	1	NA	promoter-TSS (NM_001024616)	promoter-TSS (NM_001024616)	19	NM_001024616	227624	Mm.29600	NM_001024616	ENSMUSG00000015087	Rabl6	B230208H17Rik|Rbel1|Rbel1a|Rbel1b|parf	RAB, member RAS oncogene family-like 6	protein-coding
mm_47734.1	chr5	130172574	130172585	-	1	NA	intron (NM_001199059, intron 1 of 8)	intron (NM_001199059, intron 1 of 8)	760	NM_001199059	56715	Mm.288639	NM_019983	ENSMUSG00000025340	Rabgef1	Rab5ef|Rabex5|Rin2	RAB guanine nucleotide exchange factor (GEF) 1	protein-coding
mm_84864.1	chr9	78587969	78588047	-	1	NA	promoter-TSS (NM_172773)	promoter-TSS (NM_172773)	37	NM_172773	235504	Mm.46932	NM_172773	ENSMUSG00000049624	Slc17a5	4631416G20Rik|4732491M05|AST|ISSD|NSD|SD|SIALIN|SIASD|SLD	solute carrier family 17 (anion/sugar transporter), member 5	protein-coding
mm_88794.1	chr10	80644574	80644590	+	1	NA	intron (NM_145361, intron 6 of 8)	intron (NM_145361, intron 6 of 8)	12489	NM_145361	208198	Mm.60720	NM_145361	ENSMUSG00000003344	Btbd2	2610037C03Rik|4930512K17Rik	BTB (POZ) domain containing 2	protein-coding
mm_126161.1	chr15	78430118	78430127	+	1	NA	exon (NM_001289671, exon 2 of 8)	exon (NM_001289671, exon 2 of 8)	1558	NR_110357	72844	Mm.390816	NM_001081367	ENSMUSG00000033287	Kctd17	2900008M13Rik|AA414907|AW742389|N28155	potassium channel tetramerisation domain containing 17	protein-coding
mm_133543.1	chr16	91225410	91225426	+	1	NA	promoter-TSS (NM_016967)	promoter-TSS (NM_016967)	-132	NM_016967	50913	Mm.37289	NM_016967	ENSMUSG00000039830	Olig2	AI604895|Bhlhb1|Olg-2|Oligo2|RK17|bHLHe19	oligodendrocyte transcription factor 2	protein-coding
mm_29238.1	chr3	107215962	107215974	-	1	NA	exon (NM_001111143, exon 5 of 9)	exon (NM_001111143, exon 5 of 9)	5764	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_52324.1	chr6	108836692	108836698	+	1	NA	intron (NM_138677, intron 1 of 11)	intron (NM_138677, intron 1 of 11)	8054	NM_138677	192193	Mm.21596	NM_138677	ENSMUSG00000030104	Edem1	A130059K23Rik|EDEM|mKIAA0212	ER degradation enhancer, mannosidase alpha-like 1	protein-coding
mm_30039.1	chr3	135691513	135691564	-	1	NA	promoter-TSS (NM_008689)	promoter-TSS (NM_008689)	9	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_97936.1	chr11	83648602	83648606	+	1	NA	exon (NM_011337, exon 2 of 3)	exon (NM_011337, exon 2 of 3)	774	NM_011337	20302	Mm.1282	NM_011337	ENSMUSG00000000982	Ccl3	AI323804|G0S19-1|LD78alpha|MIP-1alpha|MIP1-(a)|MIP1-alpha|Mip1a|Scya3	chemokine (C-C motif) ligand 3	protein-coding
mm_128892.1	chr15	73185271	73185283	-	1	NA	promoter-TSS (NM_153178)	promoter-TSS (NM_153178)	-330	NM_153178	239528	Mm.23095	NM_153178	ENSMUSG00000036698	Ago2	1110029L17Rik|2310051F07Rik|AI225898|AL022874|AW546247|ENSMUSG00000072493|Eif2c2|Gerp95|Gm10365|mKIAA4215	argonaute RISC catalytic subunit 2	protein-coding
mm_137547.1	chr17	27556978	27556989	+	1	NA	5' UTR (NM_001039356, exon 2 of 6)	5' UTR (NM_001039356, exon 2 of 6)	330	NM_001166477	111241	Mm.426212	NM_001166476	ENSMUSG00000078249	Hmga1-rs1	ENSMUSG00000041059|Hmgi-rs1	high mobility group AT-hook I, related sequence 1	protein-coding
mm_116313.1	chr13	37050291	37050301	-	1	NA	promoter-TSS (NM_001166391)	promoter-TSS (NM_001166391)	-52	NM_001166391	74145	Mm.235105	NM_028784	ENSMUSG00000039109	F13a1	1200014I03Rik|AI462306|F13a	coagulation factor XIII, A1 subunit	protein-coding
mm_139269.1	chr17	48065302	48065307	+	1	NA	non-coding (NR_110485, exon 3 of 3)	non-coding (NR_110485, exon 3 of 3)	-24328	NM_026625	68224	Mm.138490	NM_026625	ENSMUSG00000021545	1700067P10Rik	-	RIKEN cDNA 1700067P10 gene	protein-coding
mm_127068.1	chr15	97373980	97373988	+	1	NA	5' UTR (NM_172293, exon 5 of 6)	5' UTR (NM_172293, exon 5 of 6)	-126697	NM_001164602	105827	Mm.24005	NM_178114	ENSMUSG00000048218	Amigo2	AI415330|AMIGO-2|AW208913|Ali1	adhesion molecule with Ig like domain 2	protein-coding
mm_147301.1	chr18	39519283	39519303	-	1	NA	Intergenic	Intergenic	-32048	NM_008173	14815	Mm.129481	NM_008173	ENSMUSG00000024431	Nr3c1	GR|Grl-1|Grl1	nuclear receptor subfamily 3, group C, member 1	protein-coding
mm_5612.1	chr1	39650941	39650991	-	1	NA	5' UTR (NM_170597, exon 1 of 4)	5' UTR (NM_170597, exon 1 of 4)	216	NM_170597	263764	Mm.122091	NM_170597	ENSMUSG00000050967	Creg2	A830098L22Rik	cellular repressor of E1A-stimulated genes 2	protein-coding
mm_168045.1	chrY	90811406	90811419	+	1	NA	intron (NM_133362, intron 2 of 3)	IMPB_01|Satellite|Satellite	25970	NM_133362	170942	Mm.76062	NM_133362	ENSMUSG00000096768	Erdr1	edr	erythroid differentiation regulator 1	protein-coding
mm_136882.1	chr17	13008242	13008252	+	1	NA	exon (NM_013671, exon 2 of 5)	exon (NM_013671, exon 2 of 5)	408	NM_013671	20656	Mm.290876	NM_013671	ENSMUSG00000006818	Sod2	MnSOD|Sod-2	superoxide dismutase 2, mitochondrial	protein-coding
mm_94686.1	chr11	19924169	19924184	+	1	NA	promoter-TSS (NM_033523)	promoter-TSS (NM_033523)	-266	NM_033523	114716	Mm.266627	NM_033523	ENSMUSG00000045671	Spred2	C79158	sprouty-related, EVH1 domain containing 2	protein-coding
mm_10490.1	chr2	14824078	14824088	+	1	NA	promoter-TSS (NM_001252533)	promoter-TSS (NM_001252533)	-9	NM_001252533	12296	Mm.313930	NM_023116	ENSMUSG00000057914	Cacnb2	AW060387|CAB2|Cavbeta2|Cchb2	calcium channel, voltage-dependent, beta 2 subunit	protein-coding
mm_5458.1	chr1	36309620	36309623	-	1	NA	intron (NM_001172206, intron 1 of 6)	intron (NM_001172206, intron 1 of 6)	1888	NM_001172205	214855	Mm.34316	NM_145996	ENSMUSG00000037447	Arid5a	D430024K22Rik|Mrf1	AT rich interactive domain 5A (MRF1-like)	protein-coding
mm_133565.1	chr16	91399341	91399350	+	1	NA	exon (NM_010509, exon 8 of 9)	exon (NM_010509, exon 8 of 9)	-6890	NM_008349	16155	Mm.4154	NM_008349	ENSMUSG00000022969	Il10rb	6620401D04Rik|AI528744|CRF2-4|Crfb4|D16H21S58|D21S58h|IL-10R2|Il10r2	interleukin 10 receptor, beta	protein-coding
mm_60443.1	chr7	44477080	44477090	+	1	NA	Intergenic	L1MEd|LINE|L1	6738	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_9654.1	chr1	177763413	177763440	-	1	NA	3' UTR (NM_007422, exon 13 of 13)	3' UTR (NM_007422, exon 13 of 13)	33083	NM_007422	11566	Mm.338021	NM_007422	ENSMUSG00000015961	Adss	AI314886|AS|Adss2	adenylosuccinate synthetase, non muscle	protein-coding
mm_171303.1	chr3	93908134	93908141	+	1	NA	Intergenic	MT2B1|LTR|ERVL	35406	NM_001163730	668359	Mm.80593	NM_001163730	ENSMUSG00000094328	Gm9125	EG668359	predicted gene 9125	protein-coding
mm_23092.1	chr3	37063613	37063616	+	1	NA	promoter-TSS (NM_009350)	promoter-TSS (NM_009350)	-42	NM_009350	21744	Mm.8122	NM_009350	ENSMUSG00000027719	Adad1	Tenr	adenosine deaminase domain containing 1 (testis specific)	protein-coding
mm_25190.1	chr3	103484714	103484755	+	1	NA	Intergenic	MTB_Mm|LTR|ERVL-MaLR	-90548	NM_001276679	54524	Mm.88818	NM_018800	ENSMUSG00000027849	Syt6	3110037A08Rik|AW048930|sytVI	synaptotagmin VI	protein-coding
mm_102840.1	chr11	69350716	69350719	-	1	NA	intron (NM_146019, intron 28 of 39)	intron (NM_146019, intron 28 of 39)	9948	NR_027827	80515	Mm.5324	NM_020591	ENSMUSG00000043419	Chd3os	2310043C11Rik|A030009H04Rik|AA589459|AB041807|MNCb-2875|RNF21	chromodomain helicase DNA binding protein 3, opposite strand	ncRNA
mm_89953.1	chr10	111293594	111293614	+	1	NA	3' UTR (NM_001003717, exon 23 of 23)	3' UTR (NM_001003717, exon 23 of 23)	-5075	NM_027914	71769	Mm.45256	NM_027914	ENSMUSG00000035759	Bbs10	1300007O09Rik|AI452285	Bardet-Biedl syndrome 10 (human)	protein-coding
mm_100630.1	chr11	121706595	121706604	+	1	NA	intron (NM_144797, intron 1 of 3)	intron (NM_144797, intron 1 of 3)	4172	NM_144797	210029	Mm.153566	NM_144797	ENSMUSG00000039208	Metrnl	9430048M07Rik|BC019776	meteorin, glial cell differentiation regulator-like	protein-coding
mm_5319.1	chr1	22783622	22783635	-	1	NA	intron (NM_001012623, intron 1 of 14).2	intron (NM_001012623, intron 1 of 14).2	22096	NM_001012625	116837	Mm.60061	NM_053270	ENSMUSG00000041670	Rims1	C030033M19Rik|RIM1|RIM1a|RIM1alpha|Rab3ip1|Rim|Serg1|mKIAA0340	regulating synaptic membrane exocytosis 1	protein-coding
mm_100916.1	chr11	6274819	6274829	-	1	NA	promoter-TSS (NM_134020)	promoter-TSS (NM_134020)	13	NM_134020	103694	Mm.254495	NM_134020	ENSMUSG00000004394	Tmed4	1110014L17Rik|AI326346	transmembrane p24 trafficking protein 4	protein-coding
mm_136969.1	chr17	15731971	15731983	+	1	NA	exon (NM_007690, exon 8 of 36)	exon (NM_007690, exon 8 of 36)	27010	NM_007690	12648	Mm.8137	NM_007690	ENSMUSG00000023852	Chd1	4930525N21Rik|AI851787|AW555109	chromodomain helicase DNA binding protein 1	protein-coding
mm_88295.1	chr10	75303618	75303624	+	1	NA	intron (NM_153406, intron 13 of 15)	intron (NM_153406, intron 13 of 15)	-13256	NM_009630	11540	Mm.333734	NM_009630	ENSMUSG00000020178	Adora2a	A2AAR|A2aR|AA2AR	adenosine A2a receptor	protein-coding
mm_118146.1	chr13	105054827	105054847	-	1	NA	promoter-TSS (NM_029879)	promoter-TSS (NM_029879)	93	NM_029879	52882	Mm.100348	NM_029879	ENSMUSG00000021719	Rgs7bp	A930030I01Rik|AI842293|D13Bwg1146e|R7bp	regulator of G-protein signalling 7 binding protein	protein-coding
mm_142556.1	chr17	46637245	46637249	-	1	NA	intron (NM_029091, intron 6 of 15)	intron (NM_029091, intron 6 of 15)	-7743	NM_175168	71461	Mm.181833	NM_175168	ENSMUSG00000023972	Ptk7	8430404F20Rik|chz|mPTK7/CCK4	PTK7 protein tyrosine kinase 7	protein-coding
mm_155671.1	chrX	90744736	90744754	+	1	NA	Intergenic	Intergenic	-147397	NM_001101450	212952	Mm.477436	NM_001101450	ENSMUSG00000091497	Gm44	-	predicted gene 44	protein-coding
mm_41085.1	chr5	87680809	87680826	+	1	NA	intron (NM_001286016, intron 31 of 33)	intron (NM_001286016, intron 31 of 33)	14609	NM_001286016	12990	Mm.427467	NM_007784	ENSMUSG00000070702	Csn1s1	AA959832|AW212882|Csna	casein alpha s1	protein-coding
mm_113355.1	chr13	31899624	31899632	+	1	NA	intron (NM_146041, intron 9 of 10)	intron (NM_146041, intron 9 of 10)	92982	NM_008592	17300	Mm.12949	NM_008592	ENSMUSG00000050295	Foxc1	FREAC3|Fkh1|Mf1|Mf4|ch|fkh-1|frkhda	forkhead box C1	protein-coding
mm_29510.1	chr3	116253500	116253506	-	1	NA	promoter-TSS (NM_022427)	promoter-TSS (NM_022427)	-19	NM_022427	64378	Mm.40025	NM_022427	ENSMUSG00000068696	Gpr88	AW061286|Strg	G-protein coupled receptor 88	protein-coding
mm_84797.1	chr9	77229462	77229471	-	1	NA	intron (NM_027150, intron 2 of 7)	intron (NM_027150, intron 2 of 7)	118404	NM_027150	69642	Mm.35008	NM_027150	ENSMUSG00000032355	Mlip	2310046A06Rik|AI931782|CIP	muscular LMNA-interacting protein	protein-coding
mm_61664.1	chr7	80778604	80778643	+	1	NA	intron (NM_016721, intron 2 of 37)	MIR|SINE|MIR	24708	NM_016721	29875	Mm.207619	NM_016721	ENSMUSG00000030536	Iqgap1	AA682088|D7Ertd237e|D7Ertd257e|mKIAA0051	IQ motif containing GTPase activating protein 1	protein-coding
mm_158235.1	chrX	106485192	106485212	-	1	NA	promoter-TSS (NM_001007580)	promoter-TSS (NM_001007580)	27	NM_001007580	333564	Mm.298000	NM_001007580	ENSMUSG00000033737	Fndc3c1	Fndc3c|Gm784	fibronectin type III domain containing 3C1	protein-coding
mm_90478.1	chr10	127866526	127866538	+	1	NA	promoter-TSS (NM_145424)	promoter-TSS (NM_145424)	56	NM_145424	216454	Mm.214923	NM_145424	ENSMUSG00000074639	BC089597	CRAD-L	cDNA sequence BC089597	protein-coding
mm_119090.1	chr14	30892032	30892052	+	1	NA	exon (NM_001289633, exon 9 of 22)	exon (NM_001289633, exon 9 of 22)	5566	NM_001289632	16427	Mm.34819	NM_018746	ENSMUSG00000021922	Itih4	ITI-HC4|Itih-4|PK-120	inter alpha-trypsin inhibitor, heavy chain 4	protein-coding
mm_134150.1	chr16	10785187	10785195	-	1	NA	intron (NM_001271603, intron 1 of 1)	CpG	345	NM_009896	12703	Mm.130	NM_009896	ENSMUSG00000038037	Socs1	Cish1|Cish7|JAB|SOCS-1|SSI-1	suppressor of cytokine signaling 1	protein-coding
mm_68639.1	chr7	118326910	118326926	-	1	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	83011	NR_027879	67745	Mm.483404	NM_183267	ENSMUSG00000055159	4930583K01Rik	-	RIKEN cDNA 4930583K01 gene	ncRNA
mm_96892.1	chr11	70437282	70437311	+	1	NA	promoter-TSS (NR_106064)	promoter-TSS (NR_106064)	-959	NR_106064	102465670		NR_106064	ENSMUSG00000099109	Mir7115	Gm27902|mmu-mir-7115	microRNA 7115	ncRNA
mm_1203.1	chr1	62719019	62719047	+	1	NA	exon (NM_001077407, exon 2 of 16)	exon (NM_001077407, exon 2 of 16)	15716	NM_001077405	18187	Mm.266341	NM_010939	ENSMUSG00000025969	Nrp2	1110048P06Rik|Np-2|Np2|Npn-2|Npn2	neuropilin 2	protein-coding
mm_5297.1	chr1	21291527	21291543	-	1	NA	intron (NR_002858, intron 3 of 5)	intron (NR_002858, intron 3 of 5)	6777	NR_002858	241041	Mm.290634	NR_002858	ENSMUSG00000025936	Gm4956	EG241041	predicted gene 4956	pseudo
mm_18163.1	chr2	45099473	45099486	-	1	NA	intron (NM_001289521, intron 1 of 8)	intron (NM_001289521, intron 1 of 8)	10798	NM_001289521	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_128958.1	chr15	74799809	74799852	-	1	NA	5' UTR (NM_029627, exon 1 of 4)	5' UTR (NM_029627, exon 1 of 4)	138	NM_029627	76486	Mm.273319	NM_029627	ENSMUSG00000044678	Ly6k	2410015A16Rik|3110035B01Rik|mLy-6K	lymphocyte antigen 6 complex, locus K	protein-coding
mm_394.1	chr1	34121251	34121288	+	1	NA	intron (NM_001276764, intron 8 of 102)	intron (NM_001276764, intron 8 of 102)	3910	NR_105861	102466987		NR_105861	ENSMUSG00000105982	Mir6896	mmu-mir-6896	microRNA 6896	ncRNA
mm_80621.1	chr9	88553228	88553235	+	1	NA	intron (NM_001142943, intron 2 of 5)	intron (NM_001142943, intron 2 of 5)	5211	NM_001163061	71640	Mm.259988	NM_001142943	ENSMUSG00000032425	Zfp949	4930422I07Rik	zinc finger protein 949	protein-coding
mm_1517.1	chr1	72711322	72711330	+	1	NA	promoter-TSS (NM_009084)	promoter-TSS (NM_009084)	66	NM_009084	19981	Mm.21529	NM_009084	ENSMUSG00000046330	Rpl37a	-	ribosomal protein L37a	protein-coding
mm_112000.1	chr12	110815020	110815047	-	1	NA	intron (NM_011973, intron 5 of 11)	intron (NM_011973, intron 5 of 11)	25906	NM_011973	26448	Mm.140948	NM_011973	ENSMUSG00000056458	Mok	RAGE1|Rage|Stk30	MOK protein kinase	protein-coding
mm_147755.1	chr18	61211624	61211634	-	1	NA	promoter-TSS (NM_007885)	promoter-TSS (NM_007885)	-33	NM_007885	13521	Mm.24803	NM_007885	ENSMUSG00000034320	Slc26a2	Dtd|ST-OB	solute carrier family 26 (sulfate transporter), member 2	protein-coding
mm_3800.1	chr1	157526079	157526092	+	1	NA	promoter-TSS (NM_001159986)	promoter-TSS (NM_001159986)	-85	NM_001159986	89867	Mm.87114	NM_033354	ENSMUSG00000026589	Sec16b	Lztr2|Rgpr|Rgpr-p117	SEC16 homolog B (S. cerevisiae)	protein-coding
mm_57667.1	chr6	128487995	128488009	-	1	NA	exon (NM_007376, exon 30 of 36)	exon (NM_007376, exon 30 of 36)	38718	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_129558.1	chr15	79534202	79534209	-	1	NA	TTS (NM_199079)	TTS (NM_199079)	-1288	NM_152806	67040	Mm.29644	NM_152806	ENSMUSG00000055065	Ddx17	2610007K22Rik|A430025E01Rik|AI047725|C80929|Gm926|p72	DEAD (Asp-Glu-Ala-Asp) box polypeptide 17	protein-coding
mm_156244.1	chrX	136270259	136270269	+	1	NA	promoter-TSS (NM_009750)	promoter-TSS (NM_009750)	11	NM_001110234	12070	Mm.90787	NM_009750	ENSMUSG00000046432	Bex3	AL033356|DXWsu67e|Gcap27|Nade|Ngfrap1	brain expressed X-linked 3	protein-coding
mm_40622.1	chr5	64806362	64806364	+	1	NA	intron (NM_008453, intron 1 of 5)	intron (NM_008453, intron 1 of 5)	2840	NM_008453	16599	Mm.392759	NM_008453	ENSMUSG00000029178	Klf3	9930027G08Rik|AL024007|Bklf|Tef-2	Kruppel-like factor 3 (basic)	protein-coding
mm_71816.1	chr8	68884541	68884561	+	1	NA	intron (NM_008509, intron 1 of 9)	intron (NM_008509, intron 1 of 9)	3996	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_147035.1	chr18	34751543	34751560	-	1	NA	promoter-TSS (NM_009860)	promoter-TSS (NM_009860)	-18	NM_009860	12532	Mm.286602	NM_009860	ENSMUSG00000044201	Cdc25c	Cdc25	cell division cycle 25C	protein-coding
mm_167723.1	chr9	101074123	101074140	+	1	NA	promoter-TSS (NM_001100451)	promoter-TSS (NM_001100451)	-631	NM_001100451	77853	Mm.326206	NM_001100451	ENSMUSG00000066415	Msl2	E130103E02Rik|Msl2l1|Rnf184	male-specific lethal 2 homolog (Drosophila)	protein-coding
mm_170513.1	chr19	29160050	29160058	+	1	NA	Intergenic	Intergenic	24775	NR_029778	724062		NR_029778	ENSMUSG00000065556	Mir101b	Mirn101b|mir-101b	microRNA 101b	ncRNA
mm_9754.1	chr1	180813550	180813583	-	1	NA	promoter-TSS (NM_008210)	promoter-TSS (NM_008210)	39	NM_008210	15078	Mm.138832	NM_008210	ENSMUSG00000060743	H3f3a	H3.3A	H3 histone, family 3A	protein-coding
mm_156109.1	chrX	114474388	114474399	+	1	NA	promoter-TSS (NM_001290478)	promoter-TSS (NM_001290478)	60	NM_001290477	237010	Mm.132583	NM_172781	ENSMUSG00000025597	Klhl4	B130014A11|C130018J01Rik	kelch-like 4	protein-coding
mm_119585.1	chr14	50926709	50926741	+	1	NA	TTS (NM_001033271)	TTS (NM_001033271)	1776	NM_009687	11792	Mm.203	NM_009687	ENSMUSG00000035960	Apex1	APE|Apex|HAP1|Ref-1	apurinic/apyrimidinic endonuclease 1	protein-coding
mm_121673.1	chr14	12467084	12467100	-	1	NA	exon (NM_001042617, exon 21 of 31)	exon (NM_001042617, exon 21 of 31)	-121227	NM_080433	54713	Mm.34644	NM_080433	ENSMUSG00000021743	Fezf2	AI451466|AI852056|Fez|Fezl|Zfp312	Fez family zinc finger 2	protein-coding
mm_103062.1	chr11	69837501	69837514	-	1	NA	Intergenic	CpG	-1018	NM_026982	69186	Mm.248772	NM_026982	ENSMUSG00000070394	Tmem256	1810027O10Rik|3110009M16Rik	transmembrane protein 256	protein-coding
mm_82013.1	chr9	121719173	121719278	+	1	NA	promoter-TSS (NM_010918)	promoter-TSS (NM_010918)	44	NM_010918	18087	Mm.32842	NM_010918	ENSMUSG00000032525	Nktr	5330401F18Rik|D9Wsu172e	natural killer tumor recognition sequence	protein-coding
mm_100580.1	chr11	120784309	120784345	+	1	NA	promoter-TSS (NM_145370)	promoter-TSS (NM_145370)	55	NM_001177874	209318	Mm.30195	NM_145370	ENSMUSG00000025156	Gps1	Cops1|Csn1|R75577|Sgn1	G protein pathway suppressor 1	protein-coding
mm_30630.1	chr4	8785652	8785688	+	1	NA	exon (NM_001277149, exon 3 of 38)	exon (NM_001277149, exon 3 of 38)	95264	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_131465.1	chr16	17035584	17035596	+	1	NA	intron (NM_011949, intron 7 of 8)	intron (NM_011949, intron 7 of 8)	-34549	NM_023249	106369	Mm.237941	NM_023249	ENSMUSG00000022773	Ypel1	0610009L05Rik|1700016N17Rik|1700019O22Rik|4921520K19Rik|4930511F14Rik|AV118478|DGL-1|Dgl1|Ppil2|mdgl-1	yippee-like 1 (Drosophila)	protein-coding
mm_95271.1	chr11	45703795	45703831	+	1	NA	Intergenic	Intergenic	-104270	NR_045876	100009664	Mm.415439	NR_045876		F630206G17Rik	-	RIKEN cDNA F630206G17 gene	ncRNA
mm_149856.1	chr19	25095396	25095410	+	1	NA	intron (NM_028785, intron 10 of 47)	intron (NM_028785, intron 10 of 47)	95874	NM_028785	76088	Mm.102485	NM_028785	ENSMUSG00000052085	Dock8	1200017A24Rik|5830472H07Rik|A130095G14Rik|AI461977	dedicator of cytokinesis 8	protein-coding
mm_124626.1	chr15	3303288	3303290	+	1	NA	intron (NM_001166063, intron 1 of 8)	intron (NM_001166063, intron 1 of 8)	237	NM_001166063	100039139	Mm.455610	NM_001166063	ENSMUSG00000091119	Ccdc152	ENSMUSG00000071814	coiled-coil domain containing 152	protein-coding
mm_28941.1	chr3	98882313	98882323	-	1	NA	intron (NM_019545, intron 4 of 8)	intron (NM_019545, intron 4 of 8)	10912	NM_019545	56185	Mm.281874	NM_019545	ENSMUSG00000027870	Hao2	AI325478|Hao-2|Hao3|Haox3	hydroxyacid oxidase 2	protein-coding
mm_101201.1	chr11	19018818	19018828	-	1	NA	5' UTR (NM_010789, exon 1 of 12)	5' UTR (NM_010789, exon 1 of 12)	146	NM_001193271	17268	Mm.356578	NM_010789	ENSMUSG00000020160	Meis1	C530044H18Rik|Evi8	Meis homeobox 1	protein-coding
mm_98547.1	chr11	95010385	95010419	+	1	NA	5' UTR (NM_146025, exon 1 of 10)	5' UTR (NM_146025, exon 1 of 10)	523	NM_146025	217125	Mm.297199	NM_146025	ENSMUSG00000047181	Samd14	AI839049|AI854782|BC034054	sterile alpha motif domain containing 14	protein-coding
mm_150533.1	chr19	39291495	39291501	+	1	NA	intron (NM_007815, intron 3 of 8)	intron (NM_007815, intron 3 of 8)	4413	NM_007815	13095	Mm.20764	NM_007815	ENSMUSG00000003053	Cyp2c29	AHOH|AHOHase|AI159681|AI196010|Ah-2|Ahh-1|Cyp2c|P450-2C	cytochrome P450, family 2, subfamily c, polypeptide 29	protein-coding
mm_63665.1	chr7	129593599	129593604	+	1	NA	intron (NM_172255, intron 2 of 28)	ORR1A2|LTR|ERVL-MaLR	1738	NM_172255	207425	Mm.229323	NM_172255	ENSMUSG00000042055	Wdr11	2900055P10Rik|AW489876|Brwd2|mKIAA1351	WD repeat domain 11	protein-coding
mm_139913.1	chr17	70963660	70963667	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	26853	NM_023402	67938	Mm.261329	NM_023402	ENSMUSG00000034868	Myl12b	1500001M02Rik|C77744|Mylc2b|RLC-B	myosin, light chain 12B, regulatory	protein-coding
mm_168803.1	chr12	20417680	20417682	+	1	NA	Intergenic	Intergenic	398098	NR_015521	69513	Mm.273972	NR_015521	ENSMUSG00000099759	1700030C10Rik	-	RIKEN cDNA 1700030C10 gene	ncRNA
mm_67175.1	chr7	73595159	73595187	-	1	NA	Intergenic	Intergenic	-36778	NR_037569	69170	Mm.34539	NR_037569	ENSMUSG00000101970	1810026B05Rik	-	RIKEN cDNA 1810026B05 gene	ncRNA
mm_20535.1	chr2	131041389	131041471	-	1	NA	exon (NM_020014, exon 2 of 6)	exon (NM_020014, exon 2 of 6)	-1032	NR_105969	102465606		NR_105969	ENSMUSG00000098686	Mir6973b	Gm27815|mmu-mir-6973b	microRNA 6973b	ncRNA
mm_120985.1	chr14	78966865	78966868	+	1	NA	intron (NM_173758, intron 12 of 25)	intron (NM_173758, intron 12 of 25)	117688	NM_173758	219189	Mm.159651	NM_027906	ENSMUSG00000058997	Vwa8	1300010F03Rik|4932416F07Rik|AI957255|Kiaa0564|mKIAA0564	von Willebrand factor A domain containing 8	protein-coding
mm_137690.1	chr17	28895746	28895754	+	1	NA	TTS (NM_172450)	TTS (NM_172450)	-9515	NR_045457	74179	Mm.248931	NR_045457	ENSMUSG00000085333	1700030A11Rik	-	RIKEN cDNA 1700030A11 gene	ncRNA
mm_170536.1	chr19	38704283	38704292	-	1	NA	intron (NM_019588, intron 5 of 31)	intron (NM_019588, intron 5 of 31)	114950	NM_021315	57753	Mm.86482	NM_021315	ENSMUSG00000024999	Noc3l	AF233884|Fad24	NOC3 like DNA replication regulator	protein-coding
mm_45548.1	chr5	73024656	73024658	-	1	NA	intron (NM_028194, intron 60 of 62)	intron (NM_028194, intron 60 of 62)	17753	NM_173403	231290	Mm.491387	NM_173403	ENSMUSG00000029219	Slc10a4	E130304D01	solute carrier family 10 (sodium/bile acid cotransporter family), member 4	protein-coding
mm_23884.1	chr3	83031127	83031129	+	1	NA	exon (NM_010196, exon 5 of 5)	exon (NM_010196, exon 5 of 5)	4975	NM_001111048	14161	Mm.88793	NM_010196	ENSMUSG00000028001	Fga	ENSMUSG00000059807|Fib	fibrinogen alpha chain	protein-coding
mm_114290.1	chr13	58807694	58807700	+	1	NA	promoter-TSS (NM_001025074)	promoter-TSS (NM_001025074)	0	NM_001025074	18212	Mm.130054	NM_008745	ENSMUSG00000055254	Ntrk2	GP145-TrkB/GP95-TrkB|Tkrb|trk-B|trkB	neurotrophic tyrosine kinase, receptor, type 2	protein-coding
mm_44635.1	chr5	27817827	27817827	-	1	NA	Intergenic	Intergenic	-24120	NM_008314	15563	Mm.4835	NM_008314	ENSMUSG00000039106	Htr5a	Htr5	5-hydroxytryptamine (serotonin) receptor 5A	protein-coding
mm_21944.1	chr2	167060850	167060892	-	1	NA	intron (NM_001033196, intron 1 of 13)	intron (NM_001033196, intron 1 of 13)	-2063	NR_138563	68949	Mm.391959	NM_001081005		Zfas1	1500012F01Rik|Zfos1	zinc finger, NFX1-type containing 1, antisense RNA 1	ncRNA
mm_89273.1	chr10	87860825	87860830	+	1	NA	promoter-TSS (NM_001111276)	promoter-TSS (NM_001111276)	-284	NM_001111274	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_59227.1	chr7	24638785	24638797	+	1	NA	intron (NM_133743, intron 3 of 4)	PB1D11|SINE|Alu	2221	NM_133743	72434	Mm.281093	NM_133743	ENSMUSG00000057454	Lypd3	2310061G07Rik|C4.4a	Ly6/Plaur domain containing 3	protein-coding
mm_139791.1	chr17	65886353	65886394	+	1	NA	promoter-TSS (NM_009067)	promoter-TSS (NM_009067)	-618	NM_009067	19765	Mm.17009	NM_009067	ENSMUSG00000024096	Ralbp1	RLIP76|Rip1	ralA binding protein 1	protein-coding
mm_153460.1	chr19	41232428	41232449	-	1	NA	exon (NM_133352, exon 9 of 15)	exon (NM_133352, exon 9 of 15)	-25664	NM_011904	24087	Mm.89983	NM_011904	ENSMUSG00000025013	Tll2	-	tolloid-like 2	protein-coding
mm_158456.1	chrX	140599107	140599154	-	1	NA	intron (NM_001077364, intron 1 of 3)	CpG	1392	NM_001077364	14605	Mm.22216	NM_010286	ENSMUSG00000031431	Tsc22d3	DIP|Dsip1|Gilz|TSC-22R|Tilz3	TSC22 domain family, member 3	protein-coding
mm_101310.1	chr11	22765583	22765604	-	1	NA	Intergenic	Intergenic	94142	NM_016888	53625	Mm.395495	NM_016888	ENSMUSG00000051650	B3gnt2	AA408337|AA409404|AW260308|B3Galt6|B3gnt1|BGnT-1|BGnT-2|BGnT1|BGnT2|Beta3gnt	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 2	protein-coding
mm_40192.1	chr5	36695794	36695798	+	1	NA	intron (NM_001081232, intron 1 of 8)	CpG	225	NM_001081232	320661	Mm.26480	NM_177221	ENSMUSG00000029190	D5Ertd579e	9030221A05Rik|A930018H20Rik|Kiaa0232	DNA segment, Chr 5, ERATO Doi 579, expressed	protein-coding
mm_157679.1	chrX	59568057	59568067	-	1	NA	intron (NM_001290414, intron 1 of 6)	CpG	17510	NM_001290414	14168	Mm.7995	NM_010200	ENSMUSG00000031137	Fgf13	Fhf2	fibroblast growth factor 13	protein-coding
mm_114763.1	chr13	87663476	87663478	+	1	NA	Intergenic	ERVB4_3-LTR_MM|LTR|ERVK	-1157995	NM_010103	13612	Mm.125580	NM_010103	ENSMUSG00000034488	Edil3	Del-1|Del1	EGF-like repeats and discoidin I-like domains 3	protein-coding
mm_139020.1	chr17	46110983	46111022	+	1	NA	promoter-TSS (NM_026768)	promoter-TSS (NM_026768)	-2	NM_026768	68565	Mm.287443	NM_026768	ENSMUSG00000023967	Mrps18a	1110004O20Rik|C79712	mitochondrial ribosomal protein S18A	protein-coding
mm_55959.1	chr6	85451830	85451843	-	1	NA	promoter-TSS (NM_001163427)	promoter-TSS (NM_001163427)	134	NR_028081	73327	Mm.379221	NM_028505	ENSMUSG00000030008	Pradc1	1700040I03Rik|Pap21	protease-associated domain containing 1	protein-coding
mm_153891.1	chr19	46969541	46969555	-	1	NA	promoter-TSS (NM_001164365)	promoter-TSS (NM_001164365)	19	NM_001164365	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_31898.1	chr4	83435089	83435096	+	1	NA	intron (NM_029949, intron 3 of 8)	intron (NM_029949, intron 3 of 8)	17348	NM_029949	77634	Mm.271985	NM_029949	ENSMUSG00000028483	Snapc3	1810020H02Rik|4930558A07Rik|5031401C21Rik|AI414457|E030018J20Rik	small nuclear RNA activating complex, polypeptide 3	protein-coding
mm_97571.1	chr11	78940002	78940016	+	1	NA	exon (NM_010927, exon 10 of 27)	exon (NM_010927, exon 10 of 27)	14718	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_59810.1	chr7	29170241	29170249	+	1	NA	promoter-TSS (NM_182696)	promoter-TSS (NM_182696)	35	NM_182694	243897	Mm.389886	NM_182694	ENSMUSG00000031493	Ggn	AI593290	gametogenetin	protein-coding
mm_55433.1	chr6	66875428	66875434	-	1	NA	Intergenic	Intergenic	-20966	NM_001177557	14701	Mm.234342	NM_025278	ENSMUSG00000036402	Gng12	2010305F15Rik|AA536815|AI115529|AI314170|AI842738	guanine nucleotide binding protein (G protein), gamma 12	protein-coding
mm_1753.1	chr1	75507415	75507455	+	1	NA	promoter-TSS (NM_178884)	promoter-TSS (NM_178884)	-174	NM_001329843	16322	Mm.1100	NM_010564	ENSMUSG00000032968	Inha	AW555078	inhibin alpha	protein-coding
mm_123696.1	chr14	69707508	69707543	-	1	NA	promoter-TSS (NM_001146012)	promoter-TSS (NM_001146012)	-32	NM_001301652	71843	Mm.27738	NM_001146012	ENSMUSG00000034194	R3hcc1	1700020M16Rik|AA407796	R3H domain and coiled-coil containing 1	protein-coding
mm_138626.1	chr17	35841699	35841721	+	1	NA	intron (NM_001010833, intron 1 of 15)	intron (NM_001010833, intron 1 of 15)	212	NM_001010833	240087	Mm.218511	NM_001010833	ENSMUSG00000061607	Mdc1	6820401C03|AA413496|Nfbd1|mKIAA0170	mediator of DNA damage checkpoint 1	protein-coding
mm_42098.1	chr5	110344713	110344734	+	1	NA	promoter-TSS (NM_001310709)	promoter-TSS (NM_001310709)	-7	NR_132326	381667	Mm.332572	NM_001033459	ENSMUSG00000072754	Lrcol1	Clpsl3|Gm1679	leucine rich colipase-like 1	protein-coding
mm_130717.1	chr15	101052179	101052206	-	1	NA	3' UTR (NM_001214911, exon 1 of 1)	3' UTR (NM_001214911, exon 1 of 1)	2207	NM_001214911	668225	Mm.385011	NM_001214911	ENSMUSG00000095440	Fignl2	EG668225	fidgetin-like 2	protein-coding
mm_89299.1	chr10	87913705	87913736	+	1	NA	exon (NM_010512, exon 3 of 5)	exon (NM_010512, exon 3 of 5)	52609	NM_001111276	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_129483.1	chr15	78770990	78771000	-	1	NA	intron (NM_008595, intron 1 of 7)	intron (NM_008595, intron 1 of 7)	2450	NM_008595	17305	Mm.149235	NM_008595	ENSMUSG00000018169	Mfng	AW546563	MFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	protein-coding
mm_17657.1	chr2	32065357	32065363	-	1	NA	Intergenic	Intergenic	14414	NR_106135	102466844		NR_106135	ENSMUSG00000099075	Mir7674	Gm27563|mmu-mir-7674	microRNA 7674	ncRNA
mm_3514.1	chr1	150107409	150107417	+	1	NA	3' UTR (NM_011198, exon 10 of 10)	3' UTR (NM_011198, exon 10 of 10)	7382	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_120107.1	chr14	59201419	59201495	+	1	NA	5' UTR (NM_027764, exon 1 of 12)	5' UTR (NM_027764, exon 1 of 12)	229	NM_027764	71330	Mm.234195	NM_027764	ENSMUSG00000035469	Rcbtb1	5430409I18Rik|AW111883|CLLD7|CLLL7	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 1	protein-coding
mm_128487.1	chr15	50890232	50890257	-	1	NA	promoter-TSS (NM_032000)	promoter-TSS (NM_032000)	-203	NM_032000	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_168307.1	chr11	107492066	107492069	+	1	NA	exon (NM_025894, exon 7 of 11)	exon (NM_025894, exon 7 of 11)	12539	NM_025894	66997	Mm.491171	NM_025894	ENSMUSG00000020720	Psmd12	1500002F15Rik|AI480719|P55	proteasome (prosome, macropain) 26S subunit, non-ATPase, 12	protein-coding
mm_41016.1	chr5	81102966	81102970	+	1	NA	intron (NM_001347369, intron 2 of 25)	intron (NM_001347369, intron 2 of 25)	81375	NM_198702	319387	Mm.273631	NM_198702	ENSMUSG00000037605	Adgrl3	5430402I23Rik|CIRL-3|D130075K09Rik|Gm1379|LEC3|Lphn3|mKIAA0768	adhesion G protein-coupled receptor L3	protein-coding
mm_1868.1	chr1	85598131	85598149	+	1	NA	intron (NM_175397, intron 2 of 12)	intron (NM_175397, intron 2 of 12)	670	NM_030194	109032	Mm.335802	NM_030194	ENSMUSG00000070034	Sp110	5031415C07Rik|52kDa|5830484A20Rik|ENSMUSG00000075603|Ifi75|Ipr1	Sp110 nuclear body protein	protein-coding
mm_122852.1	chr14	54781907	54781925	-	1	NA	promoter-TSS (NM_016972)	promoter-TSS (NM_016972)	-30	NM_016972	50934	Mm.276831	NM_016972	ENSMUSG00000022180	Slc7a8	AA408822|LAT2	solute carrier family 7 (cationic amino acid transporter, y+ system), member 8	protein-coding
mm_102255.1	chr11	55185030	55185082	-	1	NA	promoter-TSS (NM_153170)	promoter-TSS (NM_153170)	21	NM_153170	246049	Mm.291280	NM_153170	ENSMUSG00000020264	Slc36a2	A530067G19Rik|PAT2|Tramd1	solute carrier family 36 (proton/amino acid symporter), member 2	protein-coding
mm_69071.1	chr7	126975401	126975416	-	1	NA	promoter-TSS (NM_026638)	promoter-TSS (NM_026638)	-506	NM_026638	52858	Mm.28219	NM_026638	ENSMUSG00000030682	Cdipt	9530042F15Rik|D7Bwg0575e|Pis|Pis1	CDP-diacylglycerol--inositol 3-phosphatidyltransferase (phosphatidylinositol synthase)	protein-coding
mm_166522.1	chr6	24597714	24597722	+	1	NA	promoter-TSS (NM_053098)	promoter-TSS (NM_053098)	-53	NM_053098	93677	Mm.332941	NM_053098	ENSMUSG00000029683	Lmod2	C-Lmod	leiomodin 2 (cardiac)	protein-coding
mm_67044.1	chr7	67266009	67266031	-	1	NA	exon (NM_001291196, exon 7 of 12)	exon (NM_001291196, exon 7 of 12)	43404	NM_001191051	75099	Mm.121691	NM_175215	ENSMUSG00000043831	Lysmd4	4930506D23Rik	LysM, putative peptidoglycan-binding, domain containing 4	protein-coding
mm_129903.1	chr15	83936075	83936081	-	1	NA	promoter-TSS (NM_001161628)	promoter-TSS (NM_001161628)	17	NM_001161628	77627	Mm.196288	NM_029946	ENSMUSG00000022441	Efcab6	4931407K02Rik|4932408N08Rik|bM150J22.2|mKIAA1672	EF-hand calcium binding domain 6	protein-coding
mm_8849.1	chr1	162707829	162707843	-	1	NA	exon (NM_001081290, exon 15 of 35)	exon (NM_001081290, exon 15 of 35)	32720	NM_001081290	226562	Mm.245446	NM_001081290	ENSMUSG00000040225	Prrc2c	1810043M20Rik|9630039I18Rik|A630006J20|Bat2d|Bat2d1|Bat2l2|E130112L15Rik|Prrc3|mKIAA1096	proline-rich coiled-coil 2C	protein-coding
mm_4189.1	chr1	171213970	171214007	+	1	NA	promoter-TSS (NM_001243062)	promoter-TSS (NM_001243062)	18	NM_001243063	12355	Mm.486506	NM_009803	ENSMUSG00000005677	Nr1i3	AA209988|AI551208|CAR|CAR-beta|Care2|ESTM32|MB67	nuclear receptor subfamily 1, group I, member 3	protein-coding
mm_32010.1	chr4	94739449	94739455	+	1	NA	5' UTR (NM_001290551, exon 1 of 22)	5' UTR (NM_001290551, exon 1 of 22)	163	NM_001290551	21687	Mm.14313	NM_013690	ENSMUSG00000006386	Tek	AA517024|Cd202b|Hyk|STK1|Tie-2|Tie2	endothelial-specific receptor tyrosine kinase	protein-coding
mm_52354.1	chr6	112459654	112459669	+	1	NA	5' UTR (NM_007617, exon 1 of 2)	5' UTR (NM_007617, exon 1 of 2)	156	NM_007617	12391	Mm.3924	NM_007617	ENSMUSG00000062694	Cav3	AI385751|Cav-3|M-cav	caveolin 3	protein-coding
mm_114867.1	chr13	93841480	93841484	+	1	NA	intron (NM_009712, intron 4 of 7)	(CTGTG)n|Simple_repeat|Simple_repeat	50705	NR_049198	100885837		NR_049198	ENSMUSG00000093480	Mir5624	Gm25075|mir-5624|mmu-mir-5624	microRNA 5624	ncRNA
mm_28979.1	chr3	101110375	101110469	-	1	NA	promoter-TSS (NM_011197)	promoter-TSS (NM_011197)	-256	NM_011197	19221	Mm.24807	NM_011197	ENSMUSG00000027864	Ptgfrn	4833445A08Rik|AU042434|CD9P-1|FPRP|Trim45	prostaglandin F2 receptor negative regulator	protein-coding
mm_54551.1	chr6	37016724	37016734	-	1	NA	intron (NM_001347104, intron 17 of 32)	intron (NM_001347104, intron 17 of 32)	-205368	NM_008973	19242	Mm.279690	NM_008973	ENSMUSG00000029838	Ptn	HARP|HB-GAM|HBBN|HBGF-8|HBNF|OSF|Osf-1|Osf1	pleiotrophin	protein-coding
mm_97559.1	chr11	78935351	78935357	+	1	NA	exon (NM_010927, exon 6 of 27)	exon (NM_010927, exon 6 of 27)	10063	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_9108.1	chr1	170110745	170110823	-	1	NA	Intergenic	Intergenic	-21840	NM_022563	18214	Mm.229249	NM_022563	ENSMUSG00000026674	Ddr2	AW495251|Ntrkr3|tyro10	discoidin domain receptor family, member 2	protein-coding
mm_68980.1	chr7	126589300	126589304	-	1	NA	TTS (NM_138310)	TTS (NM_138310)	-3485	NM_001146311	12752	Mm.268930	NM_009907	ENSMUSG00000030720	Cln3	AI323623	ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease)	protein-coding
mm_141773.1	chr17	34284435	34284521	-	1	NA	exon (NM_010378, exon 2 of 5)	exon (NM_010378, exon 2 of 5)	3293	NM_010378	14960	Mm.235338	NM_010378	ENSMUSG00000036594	H2-Aa	Aalpha|H-2Aa|H2Aa|I-Aalpha|IAalpha|Ia-1|Ia1	histocompatibility 2, class II antigen A, alpha	protein-coding
mm_147274.1	chr18	39137917	39137919	-	1	NA	intron (NM_175164, intron 10 of 22)	intron (NM_175164, intron 10 of 22)	144773	NM_175164	71302	Mm.329396	NM_175164	ENSMUSG00000036452	Arhgap26	1810044B20Rik|2610010G17Rik|4933432P15Rik|AI853435|mKIAA0621	Rho GTPase activating protein 26	protein-coding
mm_110043.1	chr12	17329367	17329369	-	1	NA	Intergenic	Intergenic	-4638	NM_001159632	68775	Mm.178798	NM_133699	ENSMUSG00000020566	Atp6v1c2	1110038G14Rik	ATPase, H+ transporting, lysosomal V1 subunit C2	protein-coding
mm_152647.1	chr19	12540750	12540760	-	1	NA	Intergenic	Intergenic	-32755	NM_001346545	107373	Mm.1643	NM_026640	ENSMUSG00000024691	Fam111a	4632417K18Rik|AW413625	family with sequence similarity 111, member A	protein-coding
mm_84413.1	chr9	65562182	65562190	-	1	NA	intron (NM_153119, intron 3 of 5)	intron (NM_153119, intron 3 of 5)	17901	NM_153119	102595	Mm.247303	NM_153119	ENSMUSG00000050721	Plekho2	AI840980|Plekhq1	pleckstrin homology domain containing, family O member 2	protein-coding
mm_50960.1	chr6	58909176	58909179	+	1	NA	intron (NM_028705, intron 22 of 24)	intron (NM_028705, intron 22 of 24)	-2051	NM_021432	58243	Mm.389747	NM_021432	ENSMUSG00000055430	Nap1l5	1110020M21Rik	nucleosome assembly protein 1-like 5	protein-coding
mm_32968.1	chr4	120032536	120032547	+	1	NA	intron (NM_010657, intron 2 of 8)	intron (NM_010657, intron 2 of 8)	-128665	NM_007902	13615	Mm.284855	NM_007902	ENSMUSG00000028635	Edn2	ET-2|PPET2|VIC	endothelin 2	protein-coding
mm_147821.1	chr18	61911534	61911610	-	1	NA	5' UTR (NM_198649, exon 1 of 23)	5' UTR (NM_198649, exon 1 of 23)	252	NM_198649	319713	Mm.329478	NM_198649	ENSMUSG00000032735	Ablim3	AW990719|D930036B08Rik	actin binding LIM protein family, member 3	protein-coding
mm_159033.1	chr1	176275265	176275265	-	1	NA	promoter-TSS (NM_176916)	promoter-TSS (NM_176916)	47	NM_176916	319455	Mm.338001	NM_176916	ENSMUSG00000055214	Pld5	B230365F16Rik	phospholipase D family, member 5	protein-coding
mm_147760.1	chr18	61331503	61331515	-	1	NA	intron (NM_133249, intron 1 of 11)	intron (NM_133249, intron 1 of 11)	68922	NM_133249	170826	Mm.415302	NM_133249	ENSMUSG00000033871	Ppargc1b	4631412G21Rik|Perc	peroxisome proliferative activated receptor, gamma, coactivator 1 beta	protein-coding
mm_20389.1	chr2	129019685	129019687	-	1	NA	Intergenic	ORR1C2|LTR|ERVL-MaLR	-46261	NM_027192	69737	Mm.33909	NM_027192	ENSMUSG00000027394	Ttl	2410003M22Rik|2700049H19Rik|AI848570	tubulin tyrosine ligase	protein-coding
mm_21564.1	chr2	164190577	164190590	-	1	NA	promoter-TSS (NM_138684)	promoter-TSS (NM_138684)	-25	NM_138684	192200	Mm.6433	NM_138684	ENSMUSG00000042845	Wfdc12	Swam2|WAP2	WAP four-disulfide core domain 12	protein-coding
mm_16811.1	chr2	11212009	11212025	-	1	NA	intron (NM_008859, intron 1 of 17)	intron (NM_008859, intron 1 of 17)	39635	NM_008859	18761	Mm.329993	NM_008859	ENSMUSG00000026778	Prkcq	A130035A12Rik|AW494342|PKC-0|PKC-theta|PKCtheta|Pkcq	protein kinase C, theta	protein-coding
mm_15517.1	chr2	158313265	158313288	+	1	NA	intron (NM_008489, intron 3 of 14)	intron (NM_008489, intron 3 of 14)	6783	NM_008489	16803	Mm.218846	NM_008489	ENSMUSG00000016024	Lbp	Bpifd2|Ly88	lipopolysaccharide binding protein	protein-coding
mm_157273.1	chrX	20291729	20291775	-	1	NA	promoter-TSS (NM_177353)	promoter-TSS (NM_177353)	12	NM_177353	236727	Mm.132983	NM_177353	ENSMUSG00000037341	Slc9a7	A530087D17Rik|NHE7	solute carrier family 9 (sodium/hydrogen exchanger), member 7	protein-coding
mm_35043.1	chr4	4138992	4139024	-	1	NA	promoter-TSS (NM_001002927)	promoter-TSS (NM_001002927)	-563	NM_001002927	18619	Mm.475097	NM_001002927	ENSMUSG00000045573	Penk	AI326464|ENK|PPA|Penk1	preproenkephalin	protein-coding
mm_80445.1	chr9	77962302	77962307	+	1	NA	intron (NM_134255, intron 3 of 7)	L1MEd|LINE|L1	44939	NM_134255	68801	Mm.430736	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	ELOVL family member 5, elongation of long chain fatty acids (yeast)	protein-coding
mm_142541.1	chr17	46556022	46556028	-	1	NA	5' UTR (NM_020493, exon 1 of 7)	5' UTR (NM_020493, exon 1 of 7)	137	NM_020493	20807	Mm.45044	NM_020493	ENSMUSG00000015605	Srf	AW049942|AW240594	serum response factor	protein-coding
mm_36669.1	chr4	95487414	95487454	-	1	NA	Intergenic	Intergenic	-70073	NM_001113412	75578	Mm.276098	NM_029347	ENSMUSG00000028573	Fggy	2310009E04Rik	FGGY carbohydrate kinase domain containing	protein-coding
mm_5951.1	chr1	56969828	56969850	-	1	NA	5' UTR (NM_139146, exon 2 of 11)	5' UTR (NM_139146, exon 2 of 11)	1495	NM_139146	212712	Mm.145599	NM_139146	ENSMUSG00000038331	Satb2	mKIAA1034	special AT-rich sequence binding protein 2	protein-coding
mm_108787.1	chr12	90738733	90738777	+	1	NA	5' UTR (NM_010050, exon 1 of 2)	5' UTR (NM_010050, exon 1 of 2)	282	NM_010050	13371	Mm.21389	NM_010050	ENSMUSG00000007682	Dio2	5DII|AI324267|DIOII	deiodinase, iodothyronine, type II	protein-coding
mm_10381.1	chr2	12301020	12301032	+	1	NA	promoter-TSS (NR_040353)	promoter-TSS (NR_040353)	-220	NR_040353	338535	Mm.483275	NR_040353	ENSMUSG00000086843	E030013I19Rik	-	RIKEN cDNA E030013I19 gene	ncRNA
mm_167334.1	chr8	71367431	71367443	-	1	NA	intron (NM_001145780, intron 2 of 8)	CpG	220	NM_025917	67023	Mm.41890	NM_025917	ENSMUSG00000002395	Use1	2010315L10Rik|5730403H22Rik|AV002165|D12|Ed2|Q-snare|p31	unconventional SNARE in the ER 1 homolog (S. cerevisiae)	protein-coding
mm_123174.1	chr14	57525570	57525645	-	1	NA	intron (NM_145837, intron 2 of 2)	CpG-4526	778	NM_145837	239114	Mm.390726	NM_145837	ENSMUSG00000050222	Il17d	AI462269|IL-17D	interleukin 17D	protein-coding
mm_157044.1	chrX	7978028	7978040	-	1	NA	Intergenic	Intergenic	-10124	NM_008089	14460	Mm.335973	NM_008089	ENSMUSG00000031162	Gata1	Gata-1|Gf-1|eryf1	GATA binding protein 1	protein-coding
mm_115683.1	chr13	13526002	13526017	-	1	NA	Intergenic	Intergenic	-64400	NM_010748	17101	Mm.342337	NM_010748	ENSMUSG00000019726	Lyst	D13Sfk13|beige|bg	lysosomal trafficking regulator	protein-coding
mm_22034.1	chr2	168186098	168186101	-	1	NA	intron (NM_001310086, intron 4 of 4)	B1_Mur3|SINE|Alu	21013	NM_009628	11538	Mm.201322	NM_009628	ENSMUSG00000051149	Adnp	AA589558|mKIAA0784	activity-dependent neuroprotective protein	protein-coding
mm_61740.1	chr7	82175207	82175243	+	1	NA	Intergenic	CpG	-84683	NM_001277955	20408	Mm.736	NM_017400	ENSMUSG00000030638	Sh3gl3	EEN-B2|SH3P13|Sh3d2c|Sh3d2c2	SH3-domain GRB2-like 3	protein-coding
mm_165260.1	chr2	73038069	73038075	-	1	NA	Intergenic	Intergenic	-57626	NM_001018042	20687	Mm.124328	NM_011450	ENSMUSG00000027109	Sp3	D130027J01Rik	trans-acting transcription factor 3	protein-coding
mm_145015.1	chr18	38637182	38637189	+	1	NA	Intergenic	Intergenic	-35917	NM_011898	24066	Mm.42038	NM_011898	ENSMUSG00000024427	Spry4	A030006O18Rik|sprouty4	sprouty homolog 4 (Drosophila)	protein-coding
mm_44597.1	chr5	25059618	25059627	-	1	NA	intron (NM_145401, intron 1 of 15)	intron (NM_145401, intron 1 of 15)	41020	NM_145401	108099	Mm.33649	NM_145401	ENSMUSG00000028944	Prkag2	2410051C13Rik|AAKG|AAKG2|AI854673|H91620p|WPWS	protein kinase, AMP-activated, gamma 2 non-catalytic subunit	protein-coding
mm_70350.1	chr8	5080193	5080204	+	1	NA	Intergenic	Intergenic	25089	NM_011388	20494	Mm.3500	NM_011388	ENSMUSG00000023073	Slc10a2	9130221J18Rik|AI605518|ASBT|IBAT|ISBT	solute carrier family 10, member 2	protein-coding
mm_29450.1	chr3	113156743	113156762	-	1	NA	promoter-TSS (NM_001190404)	promoter-TSS (NM_001190404)	-25	NM_001190403	545562	Mm.462977	NM_001190403		Amy2b	Amy-X|Amy2-2|OTTMUSG00000022462|mAmy2-1	amylase 2b	protein-coding
mm_10624.1	chr2	19488556	19488573	+	1	NA	intron (NM_027600, intron 10 of 16)	intron (NM_027600, intron 10 of 16)	-41890	NR_131924	102637107	Mm.406835	NR_131924	ENSMUSG00000085388	Ptf1aos	Gm13336|OTTMUSG00000011493	pancreas specific transcription factor 1a, opposite strand	ncRNA
mm_90387.1	chr10	127295445	127295448	+	1	NA	TTS (NM_001171582)	TTS (NM_001171582)	4653	NM_001290183	13198	Mm.110220	NM_007837	ENSMUSG00000025408	Ddit3	CHOP-10|CHOP10|chop|gadd153	DNA-damage inducible transcript 3	protein-coding
mm_169204.1	chr13	66402120	66402125	+	1	NA	Intergenic	Intergenic	38996	NM_183119	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
mm_106784.1	chr12	4769119	4769125	+	1	NA	promoter-TSS (NM_028376)	promoter-TSS (NM_028376)	145	NM_175431	207921	Mm.184898	NM_175431	ENSMUSG00000050545	Fam228b	A830093I24Rik	family with sequence similarity 228, member B	protein-coding
mm_116037.1	chr13	26770128	26770150	-	1	NA	promoter-TSS (NM_008232)	promoter-TSS (NM_008232)	26	NM_008232	15192	Mm.7411	NM_008232	ENSMUSG00000045835	Hdgfl1	4921520N01Rik|HRP-1|Hdgfrp1|Pwwp1	hepatoma derived growth factor-like 1	protein-coding
mm_40445.1	chr5	53591530	53591540	+	1	NA	intron (NM_001080927, intron 1 of 10)	intron (NM_001080927, intron 1 of 10)	1049	NM_001080927	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_98597.1	chr11	95825136	95825149	+	1	NA	intron (NM_153104, intron 1 of 2)	intron (NM_153104, intron 1 of 2)	642	NM_153104	237928	Mm.133075	NM_153104	ENSMUSG00000050860	Phospho1	D11Moh36|Phospo1	phosphatase, orphan 1	protein-coding
mm_22300.1	chr2	180334706	180334716	-	1	NA	promoter-TSS (NM_008093)	promoter-TSS (NM_008093)	-32	NM_008093	14464	Mm.388880	NM_008093	ENSMUSG00000015627	Gata5	-	GATA binding protein 5	protein-coding
mm_144033.1	chr17	90088195	90088227	-	1	NA	5' UTR (NM_001347419, exon 1 of 3)	5' UTR (NM_001347419, exon 1 of 3)	157	NM_001346962	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_10662.1	chr2	20737324	20737329	+	1	NA	intron (NM_029895, intron 6 of 18)	intron (NM_029895, intron 6 of 18)	217813	NM_001177631	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding
mm_35450.1	chr4	40269779	40269849	-	1	NA	promoter-TSS (NM_134097)	promoter-TSS (NM_134097)	27	NM_134097	106021	Mm.251548	NM_134097	ENSMUSG00000036822	Topors	AW105885|LUN|TP53BPL|p53BP3/LUN	topoisomerase I binding, arginine/serine-rich	protein-coding
mm_84003.1	chr9	57606195	57606205	-	1	NA	promoter-TSS (NM_146223)	promoter-TSS (NM_146223)	81	NM_146223	235415	Mm.35242	NM_146223	ENSMUSG00000039714	Cplx3	BC016632|CpxIII|ERGIC-53L|ERGL|Lamn1l|Lman1l	complexin 3	protein-coding
mm_88584.1	chr10	79710078	79710100	+	1	NA	exon (NM_001077184, exon 3 of 7)	exon (NM_001077184, exon 3 of 7)	5731	NM_009768	12215	Mm.726	NM_009768	ENSMUSG00000023175	Bsg	AI115436|AI325119|CD147|EMMPRIN|HT-7	basigin	protein-coding
mm_96930.1	chr11	70519157	70519161	+	1	NA	promoter-TSS (NM_146020)	promoter-TSS (NM_146020)	-50	NM_146020	216871	Mm.22551	NM_146020	ENSMUSG00000046811	Gltpd2	C730027E14Rik	glycolipid transfer protein domain containing 2	protein-coding
mm_95628.1	chr11	53631824	53631856	+	1	NA	3' UTR (NM_008355, exon 4 of 4)	3' UTR (NM_008355, exon 4 of 4)	2862	NM_008355	16163	Mm.1284	NM_008355	ENSMUSG00000020383	Il13	Il-13	interleukin 13	protein-coding
mm_144311.1	chr18	12642597	12642609	+	1	NA	promoter-TSS (NM_028341)	promoter-TSS (NM_028341)	-930	NM_028341	72747	Mm.52526	NM_028341	ENSMUSG00000024424	Ttc39c	1700008N02Rik|2810439F02Rik	tetratricopeptide repeat domain 39C	protein-coding
mm_151805.1	chr19	5425036	5425046	-	1	NA	promoter-TSS (NM_024176)	promoter-TSS (NM_024176)	-62	NM_001291080	66556	Mm.275446	NM_024176	ENSMUSG00000024914	Drap1	2310074H19Rik|NC2-alpha	Dr1 associated protein 1 (negative cofactor 2 alpha)	protein-coding
mm_138680.1	chr17	35916913	35916914	+	1	NA	promoter-TSS (NM_025878)	promoter-TSS (NM_025878)	-283	NM_001163818	52040	Mm.29385	NM_175934	ENSMUSG00000039220	Ppp1r10	2610025H06Rik|Cat53|D17Ertd808e|Fb19|Pnuts	protein phosphatase 1, regulatory subunit 10	protein-coding
mm_67157.1	chr7	73541426	73541432	-	1	NA	non-coding (NR_037569, exon 5 of 5)	non-coding (NR_037569, exon 5 of 5)	317	NM_001081345	244059	Mm.34539	NM_001081345	ENSMUSG00000078671	Chd2	2810013C04Rik|2810040A01Rik|5630401D06Rik|AI851092|BC029703|CHD-2	chromodomain helicase DNA binding protein 2	protein-coding
mm_53858.1	chr6	149309445	149309482	+	1	NA	promoter-TSS (NM_001289662)	promoter-TSS (NM_001289662)	49	NM_001289662	67246	Mm.333515	NM_026054	ENSMUSG00000032712	2810474O19Rik	6720435I21Rik|AA536804|AU020969|GET|Kiaa1551	RIKEN cDNA 2810474O19 gene	protein-coding
mm_3023.1	chr1	133610398	133610417	+	1	NA	promoter-TSS (NM_009227)	promoter-TSS (NM_009227)	-127	NM_009227	20643	Mm.249110	NM_009227	ENSMUSG00000090553	Snrpe	AL022645|C76690|SME	small nuclear ribonucleoprotein E	protein-coding
mm_20517.1	chr2	130667721	130667750	-	1	NA	promoter-TSS (NM_025922)	promoter-TSS (NM_025922)	-106	NM_025922	16434	Mm.21399	NM_025922	ENSMUSG00000074797	Itpa	2010016I08Rik|AU020102|Itp	inosine triphosphatase (nucleoside triphosphate pyrophosphatase)	protein-coding
mm_45811.1	chr5	87671544	87671559	-	1	NA	intron (NM_001286016, intron 8 of 33)	intron (NM_001286016, intron 8 of 33)	5343	NM_001286016	12990	Mm.427467	NM_007784	ENSMUSG00000070702	Csn1s1	AA959832|AW212882|Csna	casein alpha s1	protein-coding
mm_119826.1	chr14	54259228	54259241	+	1	NA	promoter-TSS (NM_134076)	promoter-TSS (NM_134076)	2	NM_134076	105501	Mm.28771	NM_134076	ENSMUSG00000040997	Abhd4	1110035H23Rik|AI429574|Abh4	abhydrolase domain containing 4	protein-coding
mm_121174.1	chr14	103033839	103033850	+	1	NA	promoter-TSS (NR_045657)	promoter-TSS (NR_045657)	-41	NR_045657	71264	Mm.399572	NR_045657		4933432I03Rik	-	RIKEN cDNA 4933432I03 gene	ncRNA
mm_95252.1	chr11	44621183	44621192	+	1	NA	exon (NM_001290710, exon 3 of 15)	exon (NM_001290710, exon 3 of 15)	3087	NM_001290710	13591	Mm.439662	NM_007897	ENSMUSG00000057098	Ebf1	Ebf|O/E-1|OE-1|Olf-1|Olf1	early B cell factor 1	protein-coding
mm_165267.1	chr2	74736397	74736435	+	1	NA	intron (NM_010468, intron 1 of 2)	intron (NM_010468, intron 1 of 2)	10346	NR_029566	387144		NR_029566	ENSMUSG00000065500	Mir10b	Mirn10b|mir-10b|mmu-mir-10b	microRNA 10b	ncRNA
mm_139851.1	chr17	69421804	69421845	+	1	NA	Intergenic	Intergenic	5377	NR_026848	77533	Mm.266592	NR_026848		C030034I22Rik	-	RIKEN cDNA C030034I22 gene	ncRNA
mm_70117.1	chr7	142968205	142968225	-	1	NA	exon (NM_008554, exon 2 of 3)	exon (NM_008554, exon 2 of 3)	1049	NM_008554	17173	Mm.196417	NM_008554	ENSMUSG00000009248	Ascl2	2410083I15Rik|Mash2|bHLHa45	achaete-scute family bHLH transcription factor 2	protein-coding
mm_32954.1	chr4	119637705	119637721	+	1	NA	promoter-TSS (NM_008190)	promoter-TSS (NM_008190)	-19	NM_008190	14915	Mm.2614	NM_008190	ENSMUSG00000023247	Guca2a	Guca2	guanylate cyclase activator 2a (guanylin)	protein-coding
mm_44999.1	chr5	38220383	38220396	-	1	NA	promoter-TSS (NM_029162)	promoter-TSS (NM_029162)	39	NM_029162	75079	Mm.258741	NM_029162	ENSMUSG00000029127	Zbtb49	4930518A03Rik|Zfp509|Znf509	zinc finger and BTB domain containing 49	protein-coding
mm_102976.1	chr11	69672335	69672359	-	1	NA	promoter-TSS (NM_144958)	promoter-TSS (NM_144958)	76	NM_144958	13681	Mm.26680	NM_144958	ENSMUSG00000059796	Eif4a1	BM-010|Ddx2a|Eif4	eukaryotic translation initiation factor 4A1	protein-coding
mm_122873.1	chr14	54925797	54925807	-	1	NA	5' UTR (NM_010112, exon 1 of 6)	5' UTR (NM_010112, exon 1 of 6)	986	NM_010112	13644	Mm.236438	NM_010112	ENSMUSG00000022203	Efs	-	embryonal Fyn-associated substrate	protein-coding
mm_85344.1	chr9	103208895	103208971	-	1	NA	TTS (NM_133977)	TTS (NM_133977)	-6868	NM_009275	20818	Mm.273053	NM_009275	ENSMUSG00000032553	Srprb	AA409543	signal recognition particle receptor, B subunit	protein-coding
mm_1287.1	chr1	64150126	64150126	+	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-28737	NM_033563	93691	Mm.29466	NM_033563	ENSMUSG00000025959	Klf7	9830124P08Rik	Kruppel-like factor 7 (ubiquitous)	protein-coding
mm_147112.1	chr18	35722063	35722073	-	1	NA	promoter-TSS (NM_001033141)	promoter-TSS (NM_001033141)	-577	NM_001033141	68545	Mm.329362	NM_001033141	ENSMUSG00000073599	Ecscr	1110006O17Rik|ARIA	endothelial cell surface expressed chemotaxis and apoptosis regulator	protein-coding
mm_70536.1	chr8	13037977	13037985	+	1	NA	intron (NM_001242368, intron 2 of 8)	intron (NM_001242368, intron 2 of 8)	673	NM_001242368	14058	Mm.262589	NM_007972	ENSMUSG00000031444	F10	Cf10|fX	coagulation factor X	protein-coding
mm_142038.1	chr17	35263592	35263618	-	1	NA	exon (NM_001267808, exon 6 of 11)	exon (NM_001267808, exon 6 of 11)	482	NM_001267808	14980	Mm.439675	NM_001267808		H2-L	H-2L	histocompatibility 2, D region locus L	protein-coding
mm_6176.1	chr1	65100628	65100638	-	1	NA	exon (NM_007774, exon 3 of 3)	exon (NM_007774, exon 3 of 3)	2730	NM_007774	12964	Mm.26904	NM_007774	ENSMUSG00000044429	Cryga	Cryg-4|DGcry-4	crystallin, gamma A	protein-coding
mm_19630.1	chr2	102813857	102813867	-	1	NA	3' UTR (NM_009851, exon 19 of 19)	3' UTR (NM_009851, exon 19 of 19)	87803	NM_001177785	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_94851.1	chr11	23771619	23771627	+	1	NA	promoter-TSS (NM_009044)	promoter-TSS (NM_009044)	-653	NM_009044	19696	Mm.4869	NM_009044	ENSMUSG00000020275	Rel	c-Rel	reticuloendotheliosis oncogene	protein-coding
mm_110192.1	chr12	27340274	27340284	-	1	NA	3' UTR (NM_009234, exon 1 of 1)	3' UTR (NM_009234, exon 1 of 1)	2439	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding
mm_163767.1	chr13	120017973	120017983	+	1	NA	Intergenic	Intergenic	34226	NM_001302966	100861753	Mm.165042	NM_001302966	ENSMUSG00000095609	Gm21188	-	predicted gene, 21188	protein-coding
mm_85973.1	chr9	112160457	112160467	-	1	NA	3' UTR (NM_001177623, exon 10 of 10)	3' UTR (NM_001177623, exon 10 of 10)	25487	NM_001177618	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_103368.1	chr11	75178793	75178830	-	1	NA	promoter-TSS (NM_027136)	promoter-TSS (NM_027136)	-3	NM_027136	246257	Mm.41496	NM_027136	ENSMUSG00000038268	Ovca2	9030414M07Rik	candidate tumor suppressor in ovarian cancer 2	protein-coding
mm_107464.1	chr12	37241900	37241904	+	1	NA	5' UTR (NM_178767, exon 1 of 13)	5' UTR (NM_178767, exon 1 of 13)	263	NM_178767	319660	Mm.485540	NM_178767	ENSMUSG00000050103	Agmo	A530016O06Rik|AI790538|Tmem195	alkylglycerol monooxygenase	protein-coding
mm_162741.1	chr10	56389075	56389079	+	1	NA	3' UTR (NM_010288, exon 2 of 2)	3' UTR (NM_010288, exon 2 of 2)	11777	NM_010288	14609	Mm.378921	NM_010288	ENSMUSG00000050953	Gja1	AU042049|AW546267|Cnx43|Cx43|Cx43alpha1|Gja-1|Npm1|connexin43	gap junction protein, alpha 1	protein-coding
mm_12771.1	chr2	79325584	79325595	+	1	NA	exon (NM_010576, exon 27 of 28)	exon (NM_010576, exon 27 of 28)	70163	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D|Itga4B	integrin alpha 4	protein-coding
mm_35347.1	chr4	32250686	32250695	-	1	NA	Intergenic	Intergenic	-166745	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_1223.1	chr1	62738428	62738443	+	1	NA	exon (NM_001077407, exon 3 of 16)	exon (NM_001077407, exon 3 of 16)	35118	NM_001077405	18187	Mm.266341	NM_010939	ENSMUSG00000025969	Nrp2	1110048P06Rik|Np-2|Np2|Npn-2|Npn2	neuropilin 2	protein-coding
mm_148544.1	chr19	4711260	4711270	+	1	NA	promoter-TSS (NM_021287)	promoter-TSS (NM_021287)	42	NM_021287	20743	Mm.329668	NM_021287	ENSMUSG00000067889	Sptbn2	Spnb3|mKIAA0302	spectrin beta, non-erythrocytic 2	protein-coding
mm_166434.1	chr5	137187945	137187964	-	1	NA	Intergenic	Intergenic	-71747	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_152425.1	chr19	10676431	10676438	-	1	NA	intron (NM_021453, intron 2 of 8)	B4A|SINE|B4	1637	NM_021453	58803	Mm.34037	NM_021453	ENSMUSG00000024738	Pga5	1110035E17Rik|Pepf	pepsinogen 5, group I	protein-coding
mm_144848.1	chr18	36610417	36610443	+	1	NA	intron (NM_175375, intron 10 of 33)	intron (NM_175375, intron 10 of 33)	49827	NM_175375	108857	Mm.482287	NM_175375	ENSMUSG00000024483	Ankhd1	1110004O12Rik|4933432B13Rik|9130019P20Rik|A530027J04Rik|A630021B20Rik|AA571404|Mask|mFLJ00246|mKIAA1085	ankyrin repeat and KH domain containing 1	protein-coding
mm_49843.1	chr6	38354660	38354673	+	1	NA	promoter-TSS (NM_028421)	promoter-TSS (NM_028421)	-63	NM_028421	78781	Mm.25243	NM_028421	ENSMUSG00000029826	Zc3hav1	1200014N16Rik|2900058M19Rik|9130009D18Rik|9830115L13Rik|ARTD13|D6Bwg1452e|ZAP	zinc finger CCCH type, antiviral 1	protein-coding
mm_3453.1	chr1	150103246	150103255	+	1	NA	intron (NM_011198, intron 5 of 9)	intron (NM_011198, intron 5 of 9)	3219	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_23761.1	chr3	73066297	73066329	+	1	NA	promoter-TSS (NR_040557)	promoter-TSS (NR_040557)	-38	NR_040557	626082	Mm.428099	NR_040557	ENSMUSG00000103428	Gm20754	-	predicted gene, 20754	ncRNA
mm_92319.1	chr10	75560082	75560099	-	1	NA	exon (NM_198860, exon 1 of 4)	exon (NM_198860, exon 1 of 4)	240	NM_198860	192734	Mm.259320	NM_198860	ENSMUSG00000046807	Lrrc75b	AI646023|Fam211b	leucine rich repeat containing 75B	protein-coding
mm_87338.1	chr10	43478813	43478863	+	1	NA	promoter-TSS (NM_199028)	promoter-TSS (NM_199028)	-302	NM_199028	331623	Mm.490388	NM_199028	ENSMUSG00000038214	Bend3	mKIAA1553	BEN domain containing 3	protein-coding
mm_144164.1	chr18	6101643	6101644	+	1	NA	intron (NM_029277, intron 3 of 17)	intron (NM_029277, intron 3 of 17)	34455	NM_029277	75415	Mm.239675	NM_029277	ENSMUSG00000041225	Arhgap12	2810011M08Rik	Rho GTPase activating protein 12	protein-coding
mm_51379.1	chr6	73248634	73248695	+	1	NA	exon (NM_019879, exon 1 of 9)	exon (NM_019879, exon 1 of 9)	159	NM_019879	56451	Mm.29845	NM_019879	ENSMUSG00000052738	Suclg1	1500000I01Rik|Sucla1	succinate-CoA ligase, GDP-forming, alpha subunit	protein-coding
mm_29102.1	chr3	104818179	104818187	-	1	NA	5' UTR (NM_008619, exon 1 of 20)	5' UTR (NM_008619, exon 1 of 20)	122	NM_008619	17454	Mm.1597	NM_008619	ENSMUSG00000002227	Mov10	C77703|Mov-10	Moloney leukemia virus 10	protein-coding
mm_54839.1	chr6	42586392	42586398	-	1	NA	TTS (NM_203396)	TTS (NM_203396)	10977	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_102403.1	chr11	59139248	59139280	-	1	NA	Intergenic	Intergenic	-2889	NM_199152	380698	Mm.339542	NM_199152	ENSMUSG00000061462	Obscn	BC046431|Gm878|OTTMUSG00000005786|UNC89	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	protein-coding
mm_105527.1	chr11	106300811	106300811	-	1	NA	exon (NM_008117, exon 4 of 5)	exon (NM_008117, exon 4 of 5)	1085	NM_008117	14599	Mm.343934	NM_008117	ENSMUSG00000020713	Gh	Gh1|Ghb1	growth hormone	protein-coding
mm_150341.1	chr19	34583529	34583533	+	1	NA	promoter-TSS (NM_010501)	promoter-TSS (NM_010501)	2	NM_010501	15959	Mm.426079	NM_010501	ENSMUSG00000074896	Ifit3	Ifi49|P49	interferon-induced protein with tetratricopeptide repeats 3	protein-coding
mm_116466.1	chr13	43481022	43481038	-	1	NA	promoter-TSS (NM_019930)	promoter-TSS (NM_019930)	-57	NM_019930	56705	Mm.148781	NM_019930	ENSMUSG00000038546	Ranbp9	IBAP-1|Ibap1|RanBPM	RAN binding protein 9	protein-coding
mm_35962.1	chr4	53142757	53142769	-	1	NA	intron (NM_013454, intron 2 of 49)	Charlie29a|DNA|hAT-Charlie	17132	NM_013454	11303	Mm.277376	NM_013454	ENSMUSG00000015243	Abca1	ABC-1|Abc1	ATP-binding cassette, sub-family A (ABC1), member 1	protein-coding
mm_105660.1	chr11	107337872	107337898	-	1	NA	intron (NM_145823, intron 1 of 9)	intron (NM_145823, intron 1 of 9)	132835	NM_145823	71795	Mm.397413	NM_145823	ENSMUSG00000040430	Pitpnc1	1110020B03Rik|5830436L09Rik|AI662802|AI851387|C330017I21Rik|Dnr411|RDGBB|RDGBB1|rdgB-beta	phosphatidylinositol transfer protein, cytoplasmic 1	protein-coding
mm_86549.1	chr10	10234969	10234974	+	1	NA	Intergenic	Intergenic	237343	NM_001127353	215772	Mm.246573	NM_172547	ENSMUSG00000050994	Adgb	9130014G24Rik	androglobin	protein-coding
mm_125057.1	chr15	25910465	25910490	+	1	NA	intron (NM_001034851, intron 3 of 8)	intron (NM_001034851, intron 3 of 8)	-23075	NM_001277318	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_7289.1	chr1	97769877	97769907	-	1	NA	promoter-TSS (NM_001310773)	promoter-TSS (NM_001310773)	200	NM_173760	227399	Mm.220817	NM_173760	ENSMUSG00000040648	Ppip5k2	AW555814|Cfap160|D330021B20|Hisppd1|Vip2|mKIAA0433	diphosphoinositol pentakisphosphate kinase 2	protein-coding
mm_63599.1	chr7	128144659	128144683	+	1	NA	exon (NM_021334, exon 21 of 30)	exon (NM_021334, exon 21 of 30)	15103	NM_021334	16411	Mm.22378	NM_021334	ENSMUSG00000030789	Itgax	AI449405|Cd11c|Cr4|N418	integrin alpha X	protein-coding
mm_103389.1	chr11	75416336	75416353	-	1	NA	exon (NM_011340, exon 3 of 8)	exon (NM_011340, exon 3 of 8)	6279	NM_011340	20317	Mm.2044	NM_011340	ENSMUSG00000000753	Serpinf1	AI195227|EPC-1|Pedf|Pedfl|Sdf3	serine (or cysteine) peptidase inhibitor, clade F, member 1	protein-coding
mm_46358.1	chr5	103211110	103211128	-	1	NA	5' UTR (NM_001081567, exon 1 of 14)	5' UTR (NM_001081567, exon 1 of 14)	215	NM_001081567	26414	Mm.39253	NM_009158	ENSMUSG00000046709	Mapk10	C230008H04Rik|JNK3|JNK3B1|JNK3B2|SAPK(beta)|Serk2|p493F12|p54bSAPK	mitogen-activated protein kinase 10	protein-coding
mm_139348.1	chr17	50508249	50508260	+	1	NA	Intergenic	Intergenic	-1293	NM_013880	224860	Mm.217362	NM_013880	ENSMUSG00000038910	Plcl2	PLC-L2|PRIP-2|Plce2|mKIAA1092	phospholipase C-like 2	protein-coding
mm_37415.1	chr4	122861453	122861466	-	1	NA	intron (NM_001301067, intron 12 of 12)	intron (NM_001301067, intron 12 of 12)	24598	NM_007598	12331	Mm.8687	NM_007598	ENSMUSG00000028656	Cap1	-	CAP, adenylate cyclase-associated protein 1 (yeast)	protein-coding
mm_62305.1	chr7	100178680	100178704	+	1	NA	promoter-TSS (NM_001190950)	promoter-TSS (NM_001190950)	9	NM_001190871	57442	Mm.282386	NM_020574	ENSMUSG00000035165	Kcne3	2210017H05Rik|MiRP2	potassium voltage-gated channel, Isk-related subfamily, gene 3	protein-coding
mm_59869.1	chr7	30231885	30231901	+	1	NA	promoter-TSS (NM_027259)	promoter-TSS (NM_027259)	136	NM_025548	66411	Mm.27947	NM_025548	ENSMUSG00000006095	Tbcb	2410007D12Rik|AU041393|CG22|CKAPI|Ckap1	tubulin folding cofactor B	protein-coding
mm_169425.1	chr14	53369986	53369990	+	1	NA	Intergenic	Intergenic	-874293	NM_001170918	57269	Mm.88822	NM_020512	ENSMUSG00000059887	Olfr1507	MOR244-1|Mor28|Or28	olfactory receptor 1507	protein-coding
mm_110464.1	chr12	51800765	51800777	-	1	NA	exon (NM_144788, exon 8 of 43)	exon (NM_144788, exon 8 of 43)	28765	NM_144788	207304	Mm.249391	NM_144788	ENSMUSG00000035247	Hectd1	A630086P08Rik|AI844876|b2b327Clo|opm	HECT domain containing 1	protein-coding
mm_170909.1	chr2	32628241	32628252	+	1	NA	promoter-TSS (NM_001198792)	promoter-TSS (NM_001198792)	-144	NM_001198792	11636	Mm.29189	NM_021515	ENSMUSG00000026817	Ak1	Ak-1|B430205N08Rik	adenylate kinase 1	protein-coding
mm_76907.1	chr8	105846746	105846776	-	1	NA	exon (NM_177150, exon 9 of 13)	exon (NM_177150, exon 9 of 13)	5247	NM_177150	320394	Mm.334775	NM_177150	ENSMUSG00000036672	Cenpt	G630055P03Rik	centromere protein T	protein-coding
mm_58272.1	chr6	145434047	145434054	-	1	NA	intron (NM_028742, intron 1 of 9)	intron (NM_028742, intron 1 of 9)	875	NM_028742	74071	Mm.441497	NM_028742	ENSMUSG00000054966	Lmntd1	4933403M22Rik|AI482300|Ifltd1|Lmna-rs1|Lmna1|OTTMUSG00000022798	lamin tail domain containing 1	protein-coding
mm_62906.1	chr7	117380997	117381014	+	1	NA	promoter-TSS (NM_175645)	promoter-TSS (NM_175645)	26	NM_175645	233781	Mm.461427	NM_175645	ENSMUSG00000030657	Xylt1	8030490L12	xylosyltransferase 1	protein-coding
mm_118823.1	chr14	25576139	25576152	+	1	NA	exon (NM_183208, exon 5 of 24)	exon (NM_183208, exon 5 of 24)	-10659	NR_033492	77592	Mm.444871	NM_175264		4931406H21Rik	-	RIKEN cDNA 4931406H21 gene	ncRNA
mm_94711.1	chr11	20532073	20532087	+	1	NA	Intergenic	Intergenic	-11173	NM_021372	58172	Mm.339676	NM_021372	ENSMUSG00000049800	Sertad2	AB041541|AU021878|Kiaa0127|MNCb-1504|SEI-2|Sei2|TRIP-Br2|mKIAA0127	SERTA domain containing 2	protein-coding
mm_107999.1	chr12	73352454	73352467	+	1	NA	exon (NM_001037717, exon 16 of 16)	exon (NM_001037717, exon 16 of 16)	57103	NR_046013	380765	Mm.490476	NR_046013		D830013O20Rik	Gm891	RIKEN cDNA D830013O20 gene	ncRNA
mm_82263.1	chr9	6266563	6266590	-	1	NA	promoter-TSS (NM_027942)	promoter-TSS (NM_027942)	-29	NM_027942	71829	Mm.141452	NM_027942	ENSMUSG00000047619	Ddi1	1700011N24Rik	DNA-damage inducible 1	protein-coding
mm_82672.1	chr9	22131607	22131620	-	1	NA	intron (NM_001102405, intron 1 of 4)	intron (NM_001102405, intron 1 of 4)	252	NM_001102404	11433	Mm.46354	NM_007388	ENSMUSG00000001348	Acp5	TRACP|TRAP	acid phosphatase 5, tartrate resistant	protein-coding
mm_93451.1	chr10	110000935	110000943	-	1	NA	promoter-TSS (NM_001081035)	promoter-TSS (NM_001081035)	-720	NM_001081035	260315	Mm.225050	NM_177797	ENSMUSG00000020181	Nav3	4732483H20Rik|9630020C08Rik|POMFIL1|Pomfil1p|mKIAA0938|unc53H3	neuron navigator 3	protein-coding
mm_82913.1	chr9	35005777	35005818	-	1	NA	intron (NM_001190913, intron 6 of 13)	ORR1F|LTR|ERVL-MaLR	-110931	NR_029475	78934	Mm.391688	NR_029475	ENSMUSG00000070315	4930581F22Rik	-	RIKEN cDNA 4930581F22 gene	ncRNA
mm_110005.1	chr12	15865730	15865732	-	1	NA	Intergenic	Intergenic	-48946	NM_144551	217410	Mm.491136	NM_144551	ENSMUSG00000020601	Trib2	AW319517|TRB-2|TRB2	tribbles pseudokinase 2	protein-coding
mm_17600.1	chr2	30828183	30828194	-	1	NA	5' UTR (NM_133346, exon 1 of 6)	5' UTR (NM_133346, exon 1 of 6)	112	NM_133346	72323	Mm.27656	NM_133346	ENSMUSG00000039483	Asb6	2510004M11Rik|AA409356	ankyrin repeat and SOCS box-containing 6	protein-coding
mm_131057.1	chr16	4265699	4265706	+	1	NA	Intergenic	ID_B1|SINE|B4	36473	NR_003628	436332	Mm.478141	NM_001013830	ENSMUSG00000089645	Gm5766	EG436332	ribosomal protein L7a pseudogene	pseudo
mm_172209.1	chr6	59129495	59129499	-	1	NA	Intergenic	L1Md_T|LINE|L1	-79373	NM_001081145	68140	Mm.25843	NM_001081145	ENSMUSG00000049232	Tigd2	3632410O17Rik	tigger transposable element derived 2	protein-coding
mm_61424.1	chr7	73618900	73618941	+	1	NA	Intergenic	Intergenic	-60525	NR_037569	69170	Mm.34539	NR_037569	ENSMUSG00000101970	1810026B05Rik	-	RIKEN cDNA 1810026B05 gene	ncRNA
mm_59830.1	chr7	29298289	29298290	+	1	NA	Intergenic	Intergenic	-5716	NM_013874	29861	Mm.101885	NM_013874	ENSMUSG00000030584	Dpf1	Neud4	D4, zinc and double PHD fingers family 1	protein-coding
mm_84181.1	chr9	60063030	60063031	-	1	NA	intron (NM_001040426, intron 7 of 17)	intron (NM_001040426, intron 7 of 17)	78190	NM_172444	207596	Mm.28791	NM_172444	ENSMUSG00000032289	Thsd4	ADAMTSL-6|ADAMTSL6|AI585901|Adamtsl4|B230114P05Rik	thrombospondin, type I, domain containing 4	protein-coding
mm_2928.1	chr1	132265990	132265993	+	1	NA	Intergenic	MMERGLN_LTR|LTR|ERV1	-32635	NM_144810	213417	Mm.39723	NM_144810	ENSMUSG00000042115	Klhdc8a	A630065K24Rik	kelch domain containing 8A	protein-coding
mm_155631.1	chrX	84772724	84772730	+	1	NA	intron (NM_007868, intron 55 of 78)	intron (NM_007868, intron 55 of 78)	-275568	NM_001314038	13405	Mm.275608	NM_007868	ENSMUSG00000045103	Dmd	DXSmh7|DXSmh9|Dp427|Dp71|dys|mdx|pke	dystrophin, muscular dystrophy	protein-coding
mm_123535.1	chr14	66805288	66805316	-	1	NA	3' UTR (NM_009955, exon 14 of 14)	3' UTR (NM_009955, exon 14 of 14)	63298	NM_009955	12934	Mm.352648	NM_009955	ENSMUSG00000022048	Dpysl2	AI851130|Crmp2|DRP2|Musunc33|TOAD-64|Ulip2	dihydropyrimidinase-like 2	protein-coding
mm_47375.1	chr5	122988488	122988526	-	1	NA	promoter-TSS (NR_045820)	promoter-TSS (NR_045820)	592	NM_001003953	30841	Mm.86406	NM_013910	ENSMUSG00000029475	Kdm2b	Cxxc2|Fbl10|Fbxl10|Jhdm1b|PCCX2	lysine (K)-specific demethylase 2B	protein-coding
mm_156159.1	chrX	129981994	129982000	+	1	NA	intron (NM_172493, intron 17 of 26)	intron (NM_172493, intron 17 of 26)	232255	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diaph2	Dia3|Diap2|Drf2|E430022I22Rik	diaphanous related formin 2	protein-coding
mm_156157.1	chrX	129962919	129962959	+	1	NA	exon (NM_172493, exon 14 of 27)	exon (NM_172493, exon 14 of 27)	213197	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diaph2	Dia3|Diap2|Drf2|E430022I22Rik	diaphanous related formin 2	protein-coding
mm_163330.1	chr12	8500185	8500216	+	1	NA	promoter-TSS (NM_007483)	promoter-TSS (NM_007483)	-215	NM_007483	11852	Mm.687	NM_007483	ENSMUSG00000054364	Rhob	AA017882|Arh6|Arhb	ras homolog family member B	protein-coding
mm_47880.1	chr5	134703155	134703174	-	1	NA	3' UTR (NM_007925, exon 37 of 37)	3' UTR (NM_007925, exon 37 of 37)	-14574	NM_010717	16885	Mm.15409	NM_010717	ENSMUSG00000029674	Limk1	KIZ-1|LIMK-1|Limk	LIM-domain containing, protein kinase	protein-coding
mm_70315.1	chr8	4243368	4243387	+	1	NA	exon (NM_001164172, exon 3 of 12)	exon (NM_001164172, exon 3 of 12)	3272	NM_001291778	26400	Mm.3906	NM_011944	ENSMUSG00000002948	Map2k7	5930412N11Rik|JNKK 2|Jnkk2|MAPKK 7|MEK 7|Mapkk7|Mek7|Mkk7|Prkmk7|sek2	mitogen-activated protein kinase kinase 7	protein-coding
mm_147141.1	chr18	36454524	36454535	-	1	NA	promoter-TSS (NM_026027)	promoter-TSS (NM_026027)	-34	NM_026027	67199	Mm.30184	NM_026027	ENSMUSG00000024346	Pfdn1	2700086I23Rik|AA408327|AU044714	prefoldin 1	protein-coding
mm_1291.1	chr1	64301830	64301861	+	1	NA	Intergenic	Intergenic	-180456	NM_033563	93691	Mm.29466	NM_033563	ENSMUSG00000025959	Klf7	9830124P08Rik	Kruppel-like factor 7 (ubiquitous)	protein-coding
mm_118936.1	chr14	27210336	27210350	+	1	NA	intron (NM_001289686, intron 3 of 12)	intron (NM_001289686, intron 3 of 12)	-27667	NM_027871	71704	Mm.248606	NM_027871	ENSMUSG00000021895	Arhgef3	1200004I24Rik|9830169H03Rik|C76747|Xpln	Rho guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_98202.1	chr11	87796084	87796093	+	1	NA	exon (NM_010824, exon 6 of 14)	exon (NM_010824, exon 6 of 14)	2304	NM_010824	17523	Mm.4668	NM_010824	ENSMUSG00000009350	Mpo	mKIAA4033	myeloperoxidase	protein-coding
mm_101355.1	chr11	23739956	23739985	-	1	NA	Intergenic	Intergenic	31000	NM_009044	19696	Mm.4869	NM_009044	ENSMUSG00000020275	Rel	c-Rel	reticuloendotheliosis oncogene	protein-coding
mm_13265.1	chr2	98666750	98666784	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	1199110	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_141477.1	chr17	31144252	31144265	-	1	NA	promoter-TSS (NM_009363)	promoter-TSS (NM_009363)	24	NM_009363	21785	Mm.1825	NM_009363	ENSMUSG00000024028	Tff2	SP|mSP	trefoil factor 2 (spasmolytic protein 1)	protein-coding
mm_126470.1	chr15	81301792	81301803	+	1	NA	Intergenic	Intergenic	-49935	NR_077230	78102	Mm.296832	NR_077229		8430426J06Rik	-	RIKEN cDNA 8430426J06 gene	ncRNA
mm_81578.1	chr9	110422420	110422444	+	1	NA	3' UTR (NM_008694, exon 4 of 4)	3' UTR (NM_008694, exon 4 of 4)	2624	NM_008694	18054	Mm.236225	NM_008694	ENSMUSG00000032484	Ngp	bectenecin	neutrophilic granule protein	protein-coding
mm_71383.1	chr8	45992653	45992653	+	1	NA	intron (NM_138668, intron 9 of 11)	intron (NM_138668, intron 9 of 11)	7197	NM_001039562	654824	Mm.334517	NM_001039562	ENSMUSG00000050914	Ankrd37	-	ankyrin repeat domain 37	protein-coding
mm_98438.1	chr11	94938566	94938587	+	1	NA	exon (NM_007742, exon 5 of 51)	exon (NM_007742, exon 5 of 51)	2352	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_15442.1	chr2	157367107	157367137	+	1	NA	promoter-TSS (NM_026968)	promoter-TSS (NM_026968)	-472	NM_026968	69161	Mm.228619	NM_026968	ENSMUSG00000063019	Manbal	1810024K12Rik|AI836500	mannosidase, beta A, lysosomal-like	protein-coding
mm_40179.1	chr5	36048656	36048660	+	1	NA	intron (NM_030889, intron 10 of 26)	intron (NM_030889, intron 10 of 26)	155339	NM_027373	70292	Mm.125167	NM_027373	ENSMUSG00000029094	Afap1	2600003E23Rik|9630044L16Rik|AI848729|Afap|mKIAA3018	actin filament associated protein 1	protein-coding
mm_144809.1	chr18	36286363	36286419	+	1	NA	intron (NM_008989, intron 1 of 1)	intron (NM_008989, intron 1 of 1)	5229	NM_008989	19290	Mm.231802	NM_008989	ENSMUSG00000043991	Pura	CAGER-1|Pur-alpha|ssCRE-BP	purine rich element binding protein A	protein-coding
mm_29814.1	chr3	127896221	127896233	-	1	NA	promoter-TSS (NM_027482)	promoter-TSS (NM_027482)	96	NM_027482	70617	Mm.317049	NM_027482	ENSMUSG00000050549	5730508B09Rik	2700063A17Rik|C80506	RIKEN cDNA 5730508B09 gene	protein-coding
mm_86189.1	chr9	119403476	119403486	-	1	NA	intron (NM_001313757, intron 1 of 10)	CpG	1303	NM_007397	11481	Mm.8940	NM_007397	ENSMUSG00000061393	Acvr2b	4930516B21Rik|ActRIIB	activin receptor IIB	protein-coding
mm_43549.1	chr5	137569857	137569879	+	1	NA	promoter-TSS (NM_001289507)	promoter-TSS (NM_001289507)	28	NM_015799	50765	Mm.21757	NM_015799	ENSMUSG00000029716	Tfr2	Trfr2	transferrin receptor 2	protein-coding
mm_131293.1	chr16	11397194	11397217	+	1	NA	intron (NM_028964, intron 5 of 20)	B4|SINE|B4	-8443	NM_001290148	74478	Mm.325831	NM_028964	ENSMUSG00000071669	Snx29	4933437K13Rik|ENSMUSG00000079738|Gm11170|Gm1737|Gm930|Rundc2a	sorting nexin 29	protein-coding
mm_76530.1	chr8	87804391	87804402	-	1	NA	promoter-TSS (NM_001310520)	promoter-TSS (NM_001310520)	43	NM_001310520	94187	Mm.23452	NM_033327	ENSMUSG00000045333	Zfp423	Ebfaz|Roaz|Zfp104|Znf423|ataxia1|mKIAA0760|nur12	zinc finger protein 423	protein-coding
mm_59212.1	chr7	24547168	24547244	+	1	NA	promoter-TSS (NM_009532)	promoter-TSS (NM_009532)	56	NM_009532	22594	Mm.4347	NM_009532	ENSMUSG00000051768	Xrcc1	Xrcc-1	X-ray repair complementing defective repair in Chinese hamster cells 1	protein-coding
mm_92008.1	chr10	62340111	62340121	-	1	NA	promoter-TSS (NR_038038)	promoter-TSS (NR_038038)	305	NM_001146100	15275	Mm.196605	NM_010438	ENSMUSG00000037012	Hk1	BB404130|Hk-1|Hk1-s|dea|mHk1-s	hexokinase 1	protein-coding
mm_148313.1	chr18	83768069	83768084	-	1	NA	Intergenic	Intergenic	318486	NM_001081300	110796	Mm.102136	NM_001081300	ENSMUSG00000046982	Tshz1	5730407I04Rik|D18Bwg1409e|Mtsh1|NY-CO-33|Sdccag33|Tsh1|mKIAA4206|teashirt1	teashirt zinc finger family member 1	protein-coding
mm_98928.1	chr11	98355310	98355320	+	1	NA	intron (NR_045477, intron 2 of 2)	intron (NR_045477, intron 2 of 2)	2968	NR_045477	69338	Mm.398308	NR_045477	ENSMUSG00000085944	1700003D09Rik	-	RIKEN cDNA 1700003D09 gene	ncRNA
mm_55001.1	chr6	48835573	48835595	-	1	NA	exon (NM_001164209, exon 6 of 8)	exon (NM_001164209, exon 6 of 8)	5404	NM_023056	65963	Mm.28385	NM_023056	ENSMUSG00000029810	Tmem176b	1810009M01Rik|Clast1|Lr8	transmembrane protein 176B	protein-coding
mm_90286.1	chr10	123265032	123265053	+	1	NA	non-coding (NR_045514, exon 1 of 6)	non-coding (NR_045514, exon 1 of 6)	966	NM_001252387	268354	Mm.51939	NM_182807	ENSMUSG00000044071	Fam19a2	6330575M02|FAM19A2 TAFA-2|TAFA2|Tafa-2	family with sequence similarity 19, member A2	protein-coding
mm_90456.1	chr10	127725393	127725407	+	1	NA	promoter-TSS (NM_009312)	promoter-TSS (NM_009312)	8	NM_009312	21334	Mm.2374	NM_009312	ENSMUSG00000025400	Tac2	PPT-B|Tac3	tachykinin 2	protein-coding
mm_7094.1	chr1	88700539	88700555	-	1	NA	3' UTR (NM_177305, exon 1 of 1)	3' UTR (NM_177305, exon 1 of 1)	1644	NM_177305	320982	Mm.27968	NM_177305	ENSMUSG00000049866	Arl4c	A630084M22Rik|Arl7|LAK	ADP-ribosylation factor-like 4C	protein-coding
mm_105952.1	chr11	115297522	115297580	-	1	NA	promoter-TSS (NM_178035)	promoter-TSS (NM_178035)	-5	NM_178035	328035	Mm.21995	NM_178035	ENSMUSG00000044788	Fads6	BC044804|OTTMUSG00000021749	fatty acid desaturase domain family, member 6	protein-coding
mm_54748.1	chr6	41033030	41033041	-	1	NA	exon (NM_023333, exon 3 of 5)	exon (NM_023333, exon 3 of 5)	2474	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_139806.1	chr17	66233548	66233571	+	1	NA	Intergenic	Intergenic	110039	NM_001003919	320209	Mm.259605	NM_001003919	ENSMUSG00000035842	Ddx11	4732462I11Rik|CHL1|CHLR1|KRG2|essa15a	DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11	protein-coding
mm_110842.1	chr12	72945444	72945466	-	1	NA	TTS (NM_011384)	TTS (NM_011384)	5573	NM_011384	20476	Mm.57138	NM_011384	ENSMUSG00000021099	Six6	Optx2|Six9	sine oculis-related homeobox 6	protein-coding
mm_14332.1	chr2	129588256	129588292	+	1	NA	Intergenic	Intergenic	-4565	NM_001291020	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_127379.1	chr15	100870671	100870702	+	1	NA	promoter-TSS (NM_001077499)	promoter-TSS (NM_001077499)	41	NM_001077499	20273	Mm.385012	NM_011323	ENSMUSG00000023033	Scn8a	AI853486|C630029C19Rik|NaCh6|Nav1.6|dmu|med|mnd-2|mnd2|nmf2|nmf335|nmf58|nur14|seal	sodium channel, voltage-gated, type VIII, alpha	protein-coding
mm_141134.1	chr17	26206458	26206466	-	1	NA	intron (NM_001081069, intron 9 of 16)	intron (NM_001081069, intron 9 of 16)	3500	NM_001081069	50782	Mm.109840	NM_001081069	ENSMUSG00000024186	Rgs11	C78048	regulator of G-protein signaling 11	protein-coding
mm_85952.1	chr9	112120175	112120188	-	1	NA	intron (NM_001177617, intron 13 of 14)	B4|SINE|B4	-1470	NR_029823	723815		NR_029823	ENSMUSG00000065441	Mir128-2	Mirn128-2|Mirn128b|mir-128-2|mir-128b	microRNA 128-2	ncRNA
mm_143359.1	chr17	67308281	67308284	-	1	NA	intron (NM_008984, intron 1 of 30)	PB1D10|SINE|Alu	46177	NM_008984	19274	Mm.311809	NM_008984	ENSMUSG00000033278	Ptprm	RPTPmu|mKIAA4044	protein tyrosine phosphatase, receptor type, M	protein-coding
mm_77671.1	chr8	124874680	124874688	-	1	NA	intron (NM_010322, intron 4 of 15)	MTC|LTR|ERVL-MaLR	11651	NM_010322	14712	Mm.29114	NM_010322	ENSMUSG00000031985	Gnpat	AU019525|D1Ertd819e|DHAPAT	glyceronephosphate O-acyltransferase	protein-coding
mm_5900.1	chr1	54732716	54732719	-	1	NA	intron (NM_001081433, intron 13 of 27)	intron (NM_001081433, intron 13 of 27)	-175033	NM_001163314	241062	Mm.103539	NM_175508	ENSMUSG00000073678	Pgap1	5033403E17Rik|9030223K07Rik|A530084K22|D230012E17Rik|oto	post-GPI attachment to proteins 1	protein-coding
mm_168680.1	chr11	95310235	95310236	-	1	NA	promoter-TSS (NM_001195004)	promoter-TSS (NM_001195004)	11	NM_001195004	217127	Mm.90213	NM_177619	ENSMUSG00000038909	Kat7	Hbo1|Hboa|Myst2	K(lysine) acetyltransferase 7	protein-coding
mm_16783.1	chr2	9889587	9889596	-	1	NA	promoter-TSS (NR_040511)	promoter-TSS (NR_040511)	-51	NR_040511	77682	Mm.488621	NR_040511	ENSMUSG00000079602	9230102O04Rik	-	RIKEN cDNA 9230102O04 gene	ncRNA
mm_91630.1	chr10	42068607	42068617	-	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	-50230	NM_001034858	213402	Mm.211320	NM_001034858	ENSMUSG00000071324	Armc2	2610018I05Rik	armadillo repeat containing 2	protein-coding
mm_37872.1	chr4	132353624	132353641	-	1	NA	promoter-TSS (NR_003270)	promoter-TSS (NR_003270)	54	NR_003270	399101	Mm.486919	NR_002904	ENSMUSG00000085241	Snhg3	Rnu17d|U17HG	small nucleolar RNA host gene 3	ncRNA
mm_126542.1	chr15	82028026	82028046	+	1	NA	intron (NM_010247, intron 7 of 12)	intron (NM_010247, intron 7 of 12)	11667	NM_010247	14375	Mm.288809	NM_010247	ENSMUSG00000022471	Xrcc6	70kDa|G22p1|Ku70	X-ray repair complementing defective repair in Chinese hamster cells 6	protein-coding
mm_155426.1	chrX	73492727	73492738	+	1	NA	exon (NM_007542, exon 5 of 8)	exon (NM_007542, exon 5 of 8)	9131	NM_007542	12111	Mm.2608	NM_007542	ENSMUSG00000031375	Bgn	BG|DSPG1|PG-S1|PGI|SLRR1A	biglycan	protein-coding
mm_159963.1	chr6	90178679	90178679	+	1	NA	promoter-TSS (NM_053222)	promoter-TSS (NM_053222)	-37	NM_053222	113849	Mm.435482	NM_053222	ENSMUSG00000060816	Vmn1r52	V1ra7|VN3	vomeronasal 1 receptor 52	protein-coding
mm_33677.1	chr4	133240779	133240827	+	1	NA	promoter-TSS (NM_016693)	promoter-TSS (NM_016693)	-15	NM_016693	53608	Mm.36640	NM_016693	ENSMUSG00000028862	Map3k6	Ask2|MAPKKK6|MEKK6	mitogen-activated protein kinase kinase kinase 6	protein-coding
mm_130688.1	chr15	100681953	100681957	-	1	NA	intron (NM_033612, intron 5 of 7)	B1_Mur2|SINE|Alu	5965	NM_033612	109901	Mm.2131	NM_033612	ENSMUSG00000023031	Cela1	1810009A17Rik|1810062B19Rik|Ela-1|Ela1|PC-TsF	chymotrypsin-like elastase family, member 1	protein-coding
mm_43097.1	chr5	124460757	124460768	+	1	NA	3' UTR (NM_001310723, exon 7 of 7)	3' UTR (NM_001310723, exon 7 of 7)	14058	NM_001310727	67956	Mm.137966	NM_030241	ENSMUSG00000049327	Kmt5a	2410195B05Rik|AA617402|AW536475|PR-SET7|PR/SET07|Setd8	lysine methyltransferase 5A	protein-coding
mm_94668.1	chr11	17221354	17221378	+	1	NA	intron (NM_178909, intron 2 of 7)	LSU-rRNA_Hsa|rRNA|rRNA	9473	NM_178909	103784	Mm.298132	NM_178909	ENSMUSG00000078970	Wdr92	AI553587|HZGJ	WD repeat domain 92	protein-coding
mm_45874.1	chr5	88328008	88328013	-	1	NA	exon (NM_008644, exon 3 of 3)	exon (NM_008644, exon 3 of 3)	10698	NM_008644	17830	Mm.200411	NM_008644	ENSMUSG00000064156	Prol1	Muc10	proline rich, lacrimal 1	protein-coding
mm_68099.1	chr7	102015684	102015698	-	1	NA	TTS (NM_133947)	TTS (NM_133947)	2464	NM_010531	16068	Mm.422756	NM_010531	ENSMUSG00000070427	Il18bp	IL-18BP|Igifbp|MC54L	interleukin 18 binding protein	protein-coding
mm_9690.1	chr1	178337101	178337118	-	1	NA	exon (NM_016805, exon 1 of 14)	exon (NM_016805, exon 1 of 14)	675	NM_016805	51810	Mm.86589	NM_016805	ENSMUSG00000039630	Hnrnpu	AA408410|AI256620|AL024194|AL024437|AW557595|C86794|Hnrpu|SAFA|Sp120|hnRNP U	heterogeneous nuclear ribonucleoprotein U	protein-coding
mm_90194.1	chr10	120208804	120208808	+	1	NA	promoter-TSS (NM_026617)	promoter-TSS (NM_026617)	-20	NM_026617	68212	Mm.157426	NM_026617	ENSMUSG00000020225	Tmbim4	0610007H07Rik|AU022431	transmembrane BAX inhibitor motif containing 4	protein-coding
mm_112673.1	chr13	16027582	16027592	+	1	NA	3' UTR (NM_008380, exon 5 of 5)	3' UTR (NM_008380, exon 5 of 5)	15736	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_18631.1	chr2	69342559	69342570	-	1	NA	promoter-TSS (NM_021022)	promoter-TSS (NM_021022)	52	NM_021022	27413	Mm.439855	NM_021022	ENSMUSG00000027048	Abcb11	ABC16|Bsep|Lith1|PFIC2|PGY4|SPGP	ATP-binding cassette, sub-family B (MDR/TAP), member 11	protein-coding
mm_66388.1	chr7	44105653	44105659	-	1	NA	exon (NM_010642, exon 3 of 5)	exon (NM_010642, exon 3 of 5)	3364	NM_010642	16616	Mm.443292	NM_010642	ENSMUSG00000066516	Klk1b21	Klk21|mGk-21	kallikrein 1-related peptidase b21	protein-coding
mm_104696.1	chr11	97954957	97954972	-	1	NA	intron (NM_001163608, intron 5 of 13)	intron (NM_001163608, intron 5 of 13)	31482	NM_028199	72324	Mm.39617	NM_028199	ENSMUSG00000017417	Plxdc1	2410003I07Rik|AI848450|Tem7	plexin domain containing 1	protein-coding
mm_60440.1	chr7	44477004	44477022	+	1	NA	Intergenic	L1MEd|LINE|L1	6666	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_150297.1	chr19	34550665	34550702	+	1	NA	promoter-TSS (NM_008332)	promoter-TSS (NM_008332)	-11	NM_008332	15958	Mm.2036	NM_008332	ENSMUSG00000045932	Ifit2	AV302338|Ifi54|P54	interferon-induced protein with tetratricopeptide repeats 2	protein-coding
mm_137612.1	chr17	28262117	28262126	+	1	NA	intron (NM_011145, intron 2 of 7)	(T)n|Simple_repeat|Simple_repeat	-9587	NR_045427	69050	Mm.486938	NR_045427	ENSMUSG00000002250	1810013A23Rik	-	RIKEN cDNA 1810013A23 gene	ncRNA
mm_79005.1	chr9	45426631	45426648	+	1	NA	intron (NR_040732, intron 1 of 4)	MIRb|SINE|MIR	-3654	NM_001081270	114873	Mm.325499	NM_001081270	ENSMUSG00000032087	Dscaml1	4921507G06Rik|4930435C18Rik|BB239540|mKIAA1132	Down syndrome cell adhesion molecule like 1	protein-coding
mm_95411.1	chr11	50024949	50025021	+	1	NA	promoter-TSS (NM_021540)	promoter-TSS (NM_021540)	-346	NM_021540	59044	Mm.359004	NM_021540	ENSMUSG00000020376	Rnf130	2510042A13Rik|G1RZFP|G1rp|GOLIATH|GP	ring finger protein 130	protein-coding
mm_170900.1	chr2	30069341	30069358	+	1	NA	exon (NM_001204875, exon 4 of 8)	exon (NM_001204875, exon 4 of 8)	2875	NM_001204875	56086	Mm.326055	NM_023871	ENSMUSG00000054766	Set	2610030F17Rik|5730420M11Rik|AA407739|I-2PP2A|StF-IT-1|TAF-I	SET nuclear oncogene	protein-coding
mm_120878.1	chr14	75284344	75284390	+	1	NA	promoter-TSS (NM_026083)	promoter-TSS (NM_026083)	-6	NM_026083	67302	Mm.74704	NM_026083	ENSMUSG00000022000	Zc3h13	2600010B19Rik|3110050K21Rik|4930570G11Rik|C87618	zinc finger CCCH type containing 13	protein-coding
mm_135212.1	chr16	36626539	36626551	-	1	NA	intron (NM_019388, intron 2 of 7)	intron (NM_019388, intron 2 of 7)	39532	NM_019388	12524	Mm.1452	NM_019388	ENSMUSG00000022901	Cd86	B7|B7-2|B7.2|B70|CLS1|Cd28l2|ETC-1|Ly-58|Ly58|MB7|MB7-2|TS/A-2	CD86 antigen	protein-coding
mm_104462.1	chr11	95076658	95076722	-	1	NA	promoter-TSS (NM_013565)	promoter-TSS (NM_013565)	24	NM_013565	16400	Mm.57035	NM_013565	ENSMUSG00000001507	Itga3	AA407068|CD49C|GAPB3	integrin alpha 3	protein-coding
mm_31217.1	chr4	43983497	43983523	+	1	NA	promoter-TSS (NM_001002787)	promoter-TSS (NM_001002787)	6	NM_001002787	442829	Mm.348215	NM_001002787	ENSMUSG00000070999	Ccin	4933417A14Rik	calicin	protein-coding
mm_169979.1	chr17	14989865	14989883	-	1	NA	intron (NM_001123370, intron 11 of 11)	BGLII|LTR|ERVK	11010	NM_001123370	100041574	Mm.393767	NM_001123370	ENSMUSG00000036552	9030025P20Rik	D17Zt9e	RIKEN cDNA 9030025P20 gene	protein-coding
mm_10291.1	chr2	10371352	10371355	+	1	NA	intron (NM_001198808, intron 1 of 22)	intron (NM_001198808, intron 1 of 22)	902	NM_001198808	353282	Mm.329991	NM_177386	ENSMUSG00000061186	Sfmbt2	D2Wsu23e|D330030P06Rik	Scm-like with four mbt domains 2	protein-coding
mm_553.1	chr1	38019262	38019280	+	1	NA	exon (NM_198303, exon 4 of 24)	exon (NM_198303, exon 4 of 24)	21261	NM_198303	226982	Mm.260943	NM_198303	ENSMUSG00000026083	Eif5b	A030003E17Rik|BC018347|IF2	eukaryotic translation initiation factor 5B	protein-coding
mm_142503.1	chr17	46032367	46032383	-	1	NA	promoter-TSS (NM_001025250)	promoter-TSS (NM_001025250)	2	NM_001287058	22339	Mm.282184	NM_009505	ENSMUSG00000023951	Vegfa	Vegf|Vpf	vascular endothelial growth factor A	protein-coding
mm_150042.1	chr19	29378015	29378181	+	1	NA	intron (NM_021893, intron 3 of 6)	intron (NM_021893, intron 3 of 6)	10660	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_34442.1	chr4	147940927	147940931	+	1	NA	promoter-TSS (NM_029841)	promoter-TSS (NM_029841)	34	NM_029841	77034	Mm.183076	NM_029841	ENSMUSG00000044496	2510039O18Rik	Kiaa2013	RIKEN cDNA 2510039O18 gene	protein-coding
mm_6126.1	chr1	64527784	64527788	-	1	NA	Intergenic	Intergenic	-5018	NM_133828	12912	Mm.422634	NM_009952	ENSMUSG00000025958	Creb1	2310001E10Rik|3526402H21Rik|AV083133|Creb|Creb-1	cAMP responsive element binding protein 1	protein-coding
mm_164393.1	chr16	33746995	33747014	+	1	NA	intron (NM_175256, intron 10 of 14)	B1_Mur4|SINE|Alu	-47033	NM_010739	17063	Mm.3177	NM_010739	ENSMUSG00000022824	Muc13	114/A10|14/A10|AI159736|Lrrp|Ly64|NJ-1	mucin 13, epithelial transmembrane	protein-coding
mm_140966.1	chr17	24658540	24658557	-	1	NA	promoter-TSS (NM_001099664)	promoter-TSS (NM_001099664)	-123	NM_001099664	381073	Mm.291772	NM_001099664	ENSMUSG00000071230	Npw	Gm935	neuropeptide W	protein-coding
mm_75823.1	chr8	70487215	70487225	-	1	NA	exon (NM_182991, exon 1 of 8)	exon (NM_182991, exon 1 of 8)	138	NM_182991	67937	Mm.23002	NM_182991	ENSMUSG00000035964	Tmem59l	5330410G16Rik	transmembrane protein 59-like	protein-coding
mm_86475.1	chr10	4612052	4612067	+	1	NA	promoter-TSS (NR_126357)	promoter-TSS (NR_126357)	70	NM_007956	13982	Mm.9213	NM_007956	ENSMUSG00000019768	Esr1	ER|ER-alpha|ERa|ERalpha|ESR|Estr|Estra|Nr3a1	estrogen receptor 1 (alpha)	protein-coding
mm_88921.1	chr10	81192487	81192518	+	1	NA	exon (NM_001190474, exon 9 of 9)	exon (NM_001190474, exon 9 of 9)	-2189	NR_015477	69678	Mm.81562	NR_015477		Atcayos	2310050B05Rik	ataxia, cerebellar, Cayman type, opposite strand	ncRNA
mm_137279.1	chr17	24727820	24727839	+	1	NA	promoter-TSS (NM_001163945)	promoter-TSS (NM_001163945)	0	NM_001163945	66211	Mm.46198	NM_025425	ENSMUSG00000002500	Rpl3l	1110057H16Rik	ribosomal protein L3-like	protein-coding
mm_31067.1	chr4	41348998	41349008	+	1	NA	promoter-TSS (NM_001290454)	promoter-TSS (NM_001290454)	7	NM_023305	67123	Mm.289795	NM_023305	ENSMUSG00000028437	Ubap1	2700092A01Rik|NAG20|UBAP-1|Ubap	ubiquitin-associated protein 1	protein-coding
mm_123718.1	chr14	70151298	70151341	-	1	NA	exon (NM_146055, exon 6 of 21)	exon (NM_146055, exon 6 of 21)	2472	NM_146055	219158	Mm.218284	NM_146055	ENSMUSG00000033712	Ccar2	2610301G19Rik|Dbc1|mKIAA1967	cell cycle activator and apoptosis regulator 2	protein-coding
mm_55866.1	chr6	83457181	83457217	-	1	NA	promoter-TSS (NM_001347313)	promoter-TSS (NM_001347313)	-807	NM_001347313	194388	Mm.211030	NM_183138	ENSMUSG00000034832	Tet3	B430006D22Rik|BC037432|D230004J03Rik	tet methylcytosine dioxygenase 3	protein-coding
mm_141728.1	chr17	34116292	34116309	-	1	NA	exon (NM_001204973, exon 4 of 13)	exon (NM_001204973, exon 4 of 13)	3600	NR_037970	14312	Mm.3444	NM_010238	ENSMUSG00000024335	Brd2	AW228947|D17H6S113E|Frg-1|Fsrg-1|Fsrg1|Nat|Ring3|Rnf3|mKIAA4005	bromodomain containing 2	protein-coding
mm_145160.1	chr18	46598620	46598642	+	1	NA	intron (NM_010120, intron 1 of 2)	intron (NM_010120, intron 1 of 2)	927	NM_010120	13664	Mm.262037	NM_010120	ENSMUSG00000057561	Eif1a	C76390|Ef1a|Eftu|Eif4c|eIF-1A|eIF-4C	eukaryotic translation initiation factor 1A	protein-coding
mm_45645.1	chr5	76951561	76951589	-	1	NA	promoter-TSS (NM_172146)	promoter-TSS (NM_172146)	3	NM_172146	231327	Mm.202337	NM_172146	ENSMUSG00000029246	Ppat	5730454C12Rik|AA408689|AA675351|AI507113|C79945	phosphoribosyl pyrophosphate amidotransferase	protein-coding
mm_163695.1	chr13	100448727	100448731	-	1	NA	intron (NM_008670, intron 1 of 15)	MTD|LTR|ERVL-MaLR	4135	NM_008670	17940	Mm.6898	NM_008670	ENSMUSG00000021640	Naip1	AV364616|Birc1a|D13Lsd1|Naip|Naip-rs1	NLR family, apoptosis inhibitory protein 1	protein-coding
mm_91243.1	chr10	22306556	22306586	-	1	NA	promoter-TSS (NR_015465)	promoter-TSS (NR_015465)	-149	NR_015465	606736	Mm.387042	NR_015465	ENSMUSG00000097352	C920009B18Rik	-	RIKEN cDNA C920009B18 gene	ncRNA
mm_150723.1	chr19	43612393	43612416	+	1	NA	promoter-TSS (NM_008699)	promoter-TSS (NM_008699)	79	NM_008699	18089	Mm.56994	NM_008699	ENSMUSG00000044220	Nkx2-3	Nkx-2.3|Nkx2.3|tinman	NK2 homeobox 3	protein-coding
mm_118312.1	chr13	113101963	113101972	-	1	NA	promoter-TSS (NM_010370)	promoter-TSS (NM_010370)	-986	NM_010370	14938	Mm.15510	NM_010370	ENSMUSG00000023132	Gzma	AW494114|Ctla-3|Ctla3|Hf|Hf1|SE1|TSP-1|TSP1	granzyme A	protein-coding
mm_52798.1	chr6	121318239	121318256	+	1	NA	exon (NM_144512, exon 3 of 15)	exon (NM_144512, exon 3 of 15)	17951	NM_144512	14412	Mm.258596	NM_144512	ENSMUSG00000030108	Slc6a13	GAT3|Gabt3|Gat2	solute carrier family 6 (neurotransmitter transporter, GABA), member 13	protein-coding
mm_146012.1	chr18	69347062	69347064	+	1	NA	intron (NM_001083967, intron 1 of 19)	intron (NM_001083967, intron 1 of 19)	1342	NM_001083967	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding
mm_49880.1	chr6	38608970	38608976	+	1	NA	3' UTR (NM_001170848, exon 9 of 9)	3' UTR (NM_001170848, exon 9 of 9)	28266	NM_001033171	74253	Mm.121859	NM_001033171	ENSMUSG00000071537	Klrg2	2310020F24Rik	killer cell lectin-like receptor subfamily G, member 2	protein-coding
mm_92754.1	chr10	81025805	81025821	-	1	NA	promoter-TSS (NM_145217)	promoter-TSS (NM_145217)	-436	NM_145217	208666	Mm.44995	NM_145217	ENSMUSG00000043670	Diras1	Di-Ras1|Gbts1|RIG	DIRAS family, GTP-binding RAS-like 1	protein-coding
mm_138979.1	chr17	45456927	45456941	+	1	NA	intron (NM_027649, intron 4 of 7)	intron (NM_027649, intron 4 of 7)	18004	NM_027649	71020	Mm.44257	NM_027649	ENSMUSG00000023935	Spats1	1700011H05Rik|4933400B06Rik|Daip2|Ddip|Srsp1	spermatogenesis associated, serine-rich 1	protein-coding
mm_28850.1	chr3	96830971	96830975	-	1	NA	non-coding (NR_015596, exon 2 of 2)	non-coding (NR_015596, exon 2 of 2)	908	NM_021517	59020	Mm.489677	NM_021517	ENSMUSG00000038298	Pdzk1	1700023D20Rik|2610507N21Rik|4921513F16Rik|AI267131|AI314638|AL022680|D3Ertd537e|Pdzd1|mPDZK1	PDZ domain containing 1	protein-coding
mm_127936.1	chr15	10558637	10558641	-	1	NA	promoter-TSS (NM_029430)	promoter-TSS (NM_029430)	29	NM_029430	75777	Mm.48812	NM_029430	ENSMUSG00000022249	Ttc23l	4930401A09Rik	tetratricopeptide repeat domain 23-like	protein-coding
mm_164174.1	chr15	76196237	76196241	+	1	NA	promoter-TSS (NM_201394)	promoter-TSS (NM_201394)	-529	NM_201394	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
mm_36780.1	chr4	102989472	102989477	-	1	NA	intron (NM_001163767, intron 2 of 4)	intron (NM_001163767, intron 2 of 4)	281	NR_040444	100504717	Mm.394445	NR_040444	ENSMUSG00000085181	Gm12709	OTTMUSG00000008056	predicted gene 12709	ncRNA
mm_66325.1	chr7	42505742	42505758	-	1	NA	promoter-TSS (NM_001309388)	promoter-TSS (NM_001309388)	3	NM_001309389	434178	Mm.333810	NM_001309388	ENSMUSG00000092416	Zfp141	-	zinc finger protein 141	protein-coding
mm_158121.1	chrX	102252189	102252197	-	1	NA	promoter-TSS (NM_001276466)	promoter-TSS (NM_001276466)	-12	NM_001276466	12705	Mm.2390	NM_007709	ENSMUSG00000051159	Cited1	AI316840|AU019144|Msg1	Cbp/p300-interacting transactivator with Glu/Asp-rich carboxy-terminal domain 1	protein-coding
mm_44804.1	chr5	33218230	33218243	-	1	NA	promoter-TSS (NM_133903)	promoter-TSS (NM_133903)	2	NM_133903	100689	Mm.34694	NM_133903	ENSMUSG00000037379	Spon2	2310045I24Rik|AI504350|M-spondin|Mindin|Mspondin	spondin 2, extracellular matrix protein	protein-coding
mm_11053.1	chr2	27182211	27182232	+	1	NA	intron (NM_138942, intron 11 of 11)	intron (NM_138942, intron 11 of 11)	16714	NM_138942	13166	Mm.167781	NM_138942	ENSMUSG00000000889	Dbh	-	dopamine beta hydroxylase	protein-coding
mm_20104.1	chr2	121085779	121085794	-	1	NA	promoter-TSS (NM_028799)	promoter-TSS (NM_028799)	-27	NM_028799	74176	Mm.20187	NM_028799	ENSMUSG00000053675	Tgm5	2310007C07Rik|TGMX|TGx	transglutaminase 5	protein-coding
mm_27586.1	chr3	59122973	59122995	-	1	NA	intron (NM_001287119, intron 1 of 2)	B3|SINE|B2	7778	NM_001008497	140795	Mm.439021	NM_133200	ENSMUSG00000036381	P2ry14	A330108O13Rik|Gpr105|P2Y14	purinergic receptor P2Y, G-protein coupled, 14	protein-coding
mm_32554.1	chr4	109415632	109415648	+	1	NA	promoter-TSS (NM_001145948)	promoter-TSS (NM_001145948)	-7	NM_001145948	230603	Mm.33091	NM_153392	ENSMUSG00000028555	Ttc39a	4922503N01Rik	tetratricopeptide repeat domain 39A	protein-coding
mm_173119.1	chrX	161926349	161926350	-	1	NA	intron (NM_001081052, intron 1 of 7)	intron (NM_001081052, intron 1 of 7)	208796	NM_198409	24004	Mm.328503	NM_198409	ENSMUSG00000043518	Rai2	3f8	retinoic acid induced 2	protein-coding
mm_152519.1	chr19	11302204	11302215	-	1	NA	Intergenic	Intergenic	-18396	NM_183190	269063	Mm.268940	NM_183190	ENSMUSG00000054523	Ms4a5	-	membrane-spanning 4-domains, subfamily A, member 5	protein-coding
mm_13825.1	chr2	119237726	119237740	+	1	NA	5' UTR (NM_016907, exon 2 of 11)	5' UTR (NM_016907, exon 2 of 11)	373	NM_016907	20732	Mm.104955	NM_016907	ENSMUSG00000027315	Spint1	HAI-1	serine protease inhibitor, Kunitz type 1	protein-coding
mm_86840.1	chr10	21396172	21396183	+	1	NA	3' UTR (NM_178713, exon 7 of 7)	3' UTR (NM_178713, exon 7 of 7)	18877	NM_178713	237320	Mm.90181	NM_178713	ENSMUSG00000037542	Aldh8a1	Raldh4	aldehyde dehydrogenase 8 family, member A1	protein-coding
mm_89516.1	chr10	94311945	94311978	+	1	NA	Intergenic	CpG	-13258	NR_033209	215472	Mm.255656	NM_174999	ENSMUSG00000053420	Gm4792	E130012K09|EG215472	predicted gene 4792	ncRNA
mm_68407.1	chr7	109616796	109616819	-	1	NA	promoter-TSS (NR_037617)	promoter-TSS (NR_037617)	-239	NR_037617	76954	Mm.252009	NM_029811	ENSMUSG00000031024	St5	2010004M01Rik|2610305K15Rik	suppression of tumorigenicity 5	protein-coding
mm_58151.1	chr6	142323027	142323040	-	1	NA	promoter-TSS (NM_130861)	promoter-TSS (NM_130861)	-52	NM_130861	108096	Mm.206599	NM_130861	ENSMUSG00000063975	Slco1a5	Oatp-3|Oatp3|Slc21a7	solute carrier organic anion transporter family, member 1a5	protein-coding
mm_152659.1	chr19	12795517	12795567	-	1	NA	non-coding (NR_024093, exon 1 of 13)	non-coding (NR_024093, exon 1 of 13)	581	NR_024093	664779	Mm.290924	NM_001039718	ENSMUSG00000024695	Gm44505	Zfp91-Cntf|Zfp91Cntf	predicted readthrough transcript (NMD candidate), 44505	ncRNA
mm_108928.1	chr12	101007659	101007673	+	1	NA	intron (NM_026681, intron 3 of 29)	intron (NM_026681, intron 3 of 29)	14102	NR_035421	100316805		NR_035421	ENSMUSG00000080575	Mir1190	Mirn1190|mmu-mir-1190	microRNA 1190	ncRNA
mm_32621.1	chr4	114406718	114406733	+	1	NA	promoter-TSS (NM_001085549)	promoter-TSS (NM_001085549)	1	NM_001085549	666048	Mm.331779	NM_001085549	ENSMUSG00000070867	Trabd2b	Gm12824|Hkat|OTTMUSG00000008561	TraB domain containing 2B	protein-coding
mm_63692.1	chr7	130601383	130601418	+	1	NA	intron (NM_001004468, intron 1 of 21)	(TTCCC)n|Simple_repeat|Simple_repeat	23916	NM_206856	57752	Mm.86322	NM_021314	ENSMUSG00000030852	Tacc2	mKIAA4180	transforming, acidic coiled-coil containing protein 2	protein-coding
mm_9188.1	chr1	171129861	171129900	-	1	NA	exon (NM_025321, exon 6 of 6)	exon (NM_025321, exon 6 of 6)	8219	NM_001081275	75472	Mm.32760	NM_029301	ENSMUSG00000026649	Cfap126	1700009P17Rik|AV282292|Flattop|Fltp	cilia and flagella associated protein 126	protein-coding
mm_51792.1	chr6	88222280	88222295	+	1	NA	promoter-TSS (NM_019964)	promoter-TSS (NM_019964)	19	NM_019964	56691	Mm.272871	NM_019964	ENSMUSG00000048206	Dnajb8	1700016F14Rik|1700031F10Rik|AI326313|mDj6	DnaJ heat shock protein family (Hsp40) member B8	protein-coding
mm_172166.1	chr6	44793140	44793140	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-266921	NM_001004357	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding
mm_28395.1	chr3	90052433	90052459	-	1	NA	promoter-TSS (NM_001165987)	promoter-TSS (NM_001165987)	29	NM_001165983	74383	Mm.25610	NM_028475	ENSMUSG00000042520	Ubap2l	3110083O19Rik|4932431F02Rik|A430103N23Rik|C77168|Nice-4|mKIAA0144	ubiquitin-associated protein 2-like	protein-coding
mm_13543.1	chr2	110731593	110731601	+	1	NA	exon (NM_001290786, exon 2 of 4)	exon (NM_001290786, exon 2 of 4)	10103	NM_172979	269328	Mm.32566	NM_172979	ENSMUSG00000050808	Muc15	4732460E09|D730046L02Rik|MUC-15	mucin 15	protein-coding
mm_126132.1	chr15	78336430	78336442	+	1	NA	exon (NM_007780, exon 3 of 14)	exon (NM_007780, exon 3 of 14)	10446	NM_007780	12983	Mm.235324	NM_007780	ENSMUSG00000071713	Csf2rb	AI848964|AIC2B|Bc|CDw131|Csf2rb1|Csfgmrb|Il3r|Il3rb|Il3rb1|Il5rb	colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage)	protein-coding
mm_23276.1	chr3	51660397	51660406	+	1	NA	promoter-TSS (NM_174995)	promoter-TSS (NM_174995)	-778	NM_174995	211666	Mm.24679	NM_174995	ENSMUSG00000074604	Mgst2	GST2|MGST-II	microsomal glutathione S-transferase 2	protein-coding
mm_96437.1	chr11	67305680	67305707	+	1	NA	exon (NM_177369, exon 36 of 40)	exon (NM_177369, exon 36 of 40)	-21410	NM_001081250	544791	Mm.461064	NM_001081250	ENSMUSG00000060180	Myh13	MyHC-eo	myosin, heavy polypeptide 13, skeletal muscle	protein-coding
mm_141496.1	chr17	31558030	31558066	-	1	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	-6725	NR_027493	18771	Mm.259295	NM_016670	ENSMUSG00000006705	Pknox1	D17Wsu76e|PREP1	Pbx/knotted 1 homeobox	protein-coding
mm_70901.1	chr8	25602237	25602315	+	1	NA	promoter-TSS (NM_001308482)	promoter-TSS (NM_001308482)	-8	NM_001001735	234135	Mm.217337	NM_001001735	ENSMUSG00000054823	Whsc1l1	6720429E03|A530023P05|AI528490|NSD3|WHISTLE	Wolf-Hirschhorn syndrome candidate 1-like 1 (human)	protein-coding
mm_66257.1	chr7	35647128	35647143	-	1	NA	intron (NM_019746, intron 1 of 5)	CpG	347	NM_019746	56330	Mm.371609	NM_019746	ENSMUSG00000030417	Pdcd5	2200003D22Rik|AA408513|Tfar19	programmed cell death 5	protein-coding
mm_127392.1	chr15	101115797	101115805	+	1	NA	promoter-TSS (NM_144790)	promoter-TSS (NM_144790)	46	NM_144790	208258	Mm.152952	NM_144790	ENSMUSG00000047034	Ankrd33	A930021G21Rik|Panky|Panky-a	ankyrin repeat domain 33	protein-coding
mm_37251.1	chr4	118269731	118269737	-	1	NA	intron (NM_011213, intron 3 of 32)	intron (NM_011213, intron 3 of 32)	21663	NM_011213	19268	Mm.29855	NM_011213	ENSMUSG00000033295	Ptprf	AA591035|LAR|LARS|RPTP-LAR	protein tyrosine phosphatase, receptor type, F	protein-coding
mm_119831.1	chr14	54361293	54361349	+	1	NA	intron (NM_026936, intron 1 of 9)	CpG	480	NM_026936	69089	Mm.182340	NM_026936	ENSMUSG00000000959	Oxa1l	1810020M02Rik|AI894287	oxidase assembly 1-like	protein-coding
mm_79529.1	chr9	57708535	57708608	+	1	NA	promoter-TSS (NM_153799)	promoter-TSS (NM_153799)	2	NM_153799	353190	Mm.268104	NM_153799	ENSMUSG00000038957	Edc3	AA517853|Lsm16|Yjdc	enhancer of mRNA decapping 3	protein-coding
mm_77250.1	chr8	115705699	115705706	-	1	NA	3' UTR (NM_001025577, exon 1 of 1)	3' UTR (NM_001025577, exon 1 of 1)	1192	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_114992.1	chr13	97559995	97560008	+	1	NA	promoter-TSS (NR_046157)	promoter-TSS (NR_046157)	1	NR_046157	328314	Mm.138047	NR_046157	ENSMUSG00000110235	Gm5086	B230311A21|EG328314	predicted gene 5086	ncRNA
mm_27988.1	chr3	82093457	82093470	-	1	NA	3' UTR (NM_021896, exon 9 of 9)	3' UTR (NM_021896, exon 9 of 9)	12846	NR_105977	102466991		NR_105977	ENSMUSG00000098712	Mir7010	Gm28029|mmu-mir-7010	microRNA 7010	ncRNA
mm_158049.1	chrX	99467385	99467395	-	1	NA	exon (NM_001290556, exon 3 of 3)	exon (NM_001290556, exon 3 of 3)	3345	NM_001083110	18744	Mm.8211	NM_008853	ENSMUSG00000034403	Pja1	praja-1	praja ring finger 1, E3 ubiquitin protein ligase	protein-coding
mm_70398.1	chr8	11217946	11217970	+	1	NA	exon (NM_009931, exon 37 of 52)	exon (NM_009931, exon 37 of 52)	-94847	NM_009932	12827	Mm.181021	NM_009932	ENSMUSG00000031503	Col4a2	Col4a-2	collagen, type IV, alpha 2	protein-coding
mm_72205.1	chr8	72584086	72584116	+	1	NA	intron (NM_144534, intron 4 of 5)	intron (NM_144534, intron 4 of 5)	11998	NM_144534	74166	Mm.212927	NM_144534	ENSMUSG00000031791	Tmem38a	1110001E17Rik|AI413399|TRIC-A|mg33a	transmembrane protein 38A	protein-coding
mm_132917.1	chr16	49739224	49739226	+	1	NA	intron (NM_028680, intron 6 of 10)	Lx2|LINE|L1	39931	NM_028680	73916	Mm.241276	NM_028680	ENSMUSG00000032965	Ift57	4833420A15Rik|Esrrbl1|Hippi|MHS4R2	intraflagellar transport 57	protein-coding
mm_69116.1	chr7	127025878	127025889	-	1	NA	exon (NM_010772, exon 2 of 5)	exon (NM_010772, exon 2 of 5)	596	NM_010772	17188	Mm.378964	NM_010772	ENSMUSG00000030678	Maz	MAZI|PUR1|Pur-1|SAF-1|SAF-2	MYC-associated zinc finger protein (purine-binding transcription factor)	protein-coding
mm_32035.1	chr4	95681642	95681649	+	1	NA	intron (NM_001113412, intron 5 of 15)	intron (NM_001113412, intron 5 of 15)	102224	NM_029347	75578	Mm.276098	NM_029347	ENSMUSG00000028573	Fggy	2310009E04Rik	FGGY carbohydrate kinase domain containing	protein-coding
mm_105290.1	chr11	102469735	102469752	-	1	NA	5' UTR (NM_010575, exon 1 of 30)	5' UTR (NM_010575, exon 1 of 30)	140	NM_010575	16399	Mm.26646	NM_010575	ENSMUSG00000034664	Itga2b	AI172977|CD41|CD41B|GpIIb|alphaIIb	integrin alpha 2b	protein-coding
mm_159549.1	chr4	101717430	101717430	+	1	NA	promoter-TSS (NM_001122899)	promoter-TSS (NM_001122899)	23	NM_010704	16847	Mm.259282	NM_010704	ENSMUSG00000057722	Lepr	LEPROT|Leprb|Modb1|OB-RGRP|Obr|db|diabetes|obese-like|obl	leptin receptor	protein-coding
mm_168914.1	chr12	55877900	55877900	-	1	NA	Intergenic	RLTR44C|LTR|ERVK	41534	NM_001037756	52592	Mm.24761	NM_027867	ENSMUSG00000012076	Brms1l	0710008O11Rik|AI159718|BRMS1|D12Ertd407e	breast cancer metastasis-suppressor 1-like	protein-coding
mm_64098.1	chr7	141009585	141009596	+	1	NA	TTS (NM_025378)	TTS (NM_025378)	1154	NM_025378	66141	Mm.141021	NM_025378	ENSMUSG00000025492	Ifitm3	1110004C05Rik|Cd225|Cdw217|DSPA2b|Fgls|IP15|mil-1	interferon induced transmembrane protein 3	protein-coding
mm_24177.1	chr3	88578010	88578040	+	1	NA	Intergenic	PB1D9|SINE|Alu	-1646	NM_025448	66256	Mm.7091	NM_025448	ENSMUSG00000041355	Ssr2	1500032E05Rik|AI315033|AU020133|TLAP|TRAPB|TRAPbeta	signal sequence receptor, beta	protein-coding
mm_119807.1	chr14	54222238	54222256	+	1	NA	Intergenic	Intergenic	31682	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_116582.1	chr13	47106120	47106128	-	1	NA	promoter-TSS (NM_025900)	promoter-TSS (NM_025900)	97	NM_025900	110052	Mm.131150	NM_025900	ENSMUSG00000021377	Dek	1810019E15Rik|D13H6S231E	DEK oncogene (DNA binding)	protein-coding
mm_109152.1	chr12	107996455	107996460	+	1	NA	intron (NM_001079883, intron 1 of 3)	intron (NM_001079883, intron 1 of 3)	6957	NM_001079883	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_171972.1	chr5	88547511	88547524	+	1	NA	Intergenic	L1Md_T|LINE|L1	-6966	NM_023054	65961	Mm.490364	NM_023054	ENSMUSG00000070697	Utp3	2400011K09Rik|AW557551|C87704|Crl1|Crlz1|Sas10	UTP3 small subunit processome component	protein-coding
mm_48414.1	chr5	140264324	140264328	-	1	NA	intron (NM_010752, intron 9 of 17)	intron (NM_010752, intron 9 of 17)	57226	NM_010752	17120	Mm.27250	NM_010752	ENSMUSG00000029554	Mad1l1	AI173502|AW550425|Mad1	MAD1 mitotic arrest deficient 1-like 1	protein-coding
mm_93564.1	chr10	116535821	116535833	-	1	NA	intron (NM_001037846, intron 2 of 15)	intron (NM_001037846, intron 2 of 15)	45684	NM_001037848	72068	Mm.351553	NM_028082	ENSMUSG00000020166	Cnot2	2600016M12Rik|2810470K03Rik|AA537049|AA959607|AW557563|C79650	CCR4-NOT transcription complex, subunit 2	protein-coding
mm_131790.1	chr16	22898880	22898918	+	1	NA	exon (NM_001276450, exon 7 of 7)	exon (NM_001276450, exon 7 of 7)	-4513	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_73006.1	chr8	93810931	93810951	+	1	NA	TTS (NR_026888)	TTS (NR_026888)	103	NM_001113384	14681	Mm.251445	NM_010308	ENSMUSG00000031748	Gnao1	AW050213|Galphao|Gnao|alphaO	guanine nucleotide binding protein, alpha O	protein-coding
mm_92990.1	chr10	86701978	86701995	-	1	NA	exon (NM_011631, exon 5 of 18)	exon (NM_011631, exon 5 of 18)	3458	NM_011631	22027	Mm.87773	NM_011631	ENSMUSG00000020048	Hsp90b1	ERp99|GRP94|TA-3|Targ2|Tra-1|Tra1|endoplasmin|gp96	heat shock protein 90, beta (Grp94), member 1	protein-coding
mm_4304.1	chr1	171840573	171840598	+	1	NA	5' UTR (NM_013489, exon 2 of 9)	5' UTR (NM_013489, exon 2 of 9)	888	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_12318.1	chr2	69380482	69380503	+	1	NA	promoter-TSS (NM_175512)	promoter-TSS (NM_175512)	30	NM_175512	241452	Mm.211655	NM_175512	ENSMUSG00000027068	Dhrs9	C730025I08Rik|Rdh15	dehydrogenase/reductase (SDR family) member 9	protein-coding
mm_42772.1	chr5	121288112	121288117	+	1	NA	intron (NM_181421, intron 13 of 75)	intron (NM_181421, intron 13 of 75)	67895	NM_181421	269700	Mm.184589	NM_181421	ENSMUSG00000042744	Gm15800	A130010L24|AU042671|BC019639|EG545802|OTTMUSG00000026283|mKIAA0614	predicted gene 15800	protein-coding
mm_141186.1	chr17	26939372	26939397	-	1	NA	promoter-TSS (NR_104458)	promoter-TSS (NR_104458)	74	NR_104458	67675	Mm.439919	NM_026307	ENSMUSG00000024194	Cuta	0610039D01Rik|1810022E02Rik|1810060C03Rik|2700094G22Rik|AI326454	cutA divalent cation tolerance homolog	protein-coding
mm_49758.1	chr6	34768781	34768783	+	1	NA	intron (NM_001347100, intron 12 of 13)	intron (NM_001347100, intron 12 of 13)	-11650	NM_001289657	76223	Mm.150047	NM_178630	ENSMUSG00000038836	Agbl3	2900053G10Rik|4930431N21Rik|6530406M24Rik|CCP3	ATP/GTP binding protein-like 3	protein-coding
mm_104599.1	chr11	97142927	97142930	-	1	NA	intron (NM_198100, intron 6 of 8)	PB1D9|SINE|Alu	3491	NR_106094	102466822		NR_106094	ENSMUSG00000099286	Mir7235	Gm27986|mmu-mir-7235	microRNA 7235	ncRNA
mm_148972.1	chr19	7557453	7557465	+	1	NA	promoter-TSS (NM_139269)	promoter-TSS (NM_139269)	0	NM_139269	225845	Mm.274810	NM_139269	ENSMUSG00000060675	Pla2g16	C78643|HRSL3|Hrasls3|Hrev107|MLP-3	phospholipase A2, group XVI	protein-coding
mm_170689.1	chr2	131127375	131127376	+	1	NA	promoter-TSS (NM_028306)	promoter-TSS (NM_028306)	-37	NM_028306	72630	Mm.277465	NM_028306	ENSMUSG00000074793	Hspa12b	2700081N06Rik	heat shock protein 12B	protein-coding
mm_116264.1	chr13	34345640	34345674	-	1	NA	promoter-TSS (NM_001033167)	promoter-TSS (NM_001033167)	-475	NM_001033167	73102	Mm.23932	NM_001033167	ENSMUSG00000038267	Slc22a23	3110004L20Rik	solute carrier family 22, member 23	protein-coding
mm_87095.1	chr10	33083226	33083234	+	1	NA	promoter-TSS (NM_029726)	promoter-TSS (NM_029726)	-253	NM_029726	76757	Mm.338508	NM_029726	ENSMUSG00000019787	Trdn	2310045H21Rik|EG432451|TDN	triadin	protein-coding
mm_79465.1	chr9	56424417	56424419	+	1	NA	intron (NM_025812, intron 1 of 9)	intron (NM_025812, intron 1 of 9)	5572	NM_025812	66867	Mm.150856	NM_025812	ENSMUSG00000032329	Hmg20a	1200004E06Rik|5730490E10Rik|Hmgxb1|Ibraf	high mobility group 20A	protein-coding
mm_159607.1	chr4	130138542	130138542	-	1	NA	promoter-TSS (NM_001163027)	promoter-TSS (NM_001163027)	9	NM_001163027	230777	Mm.246595	NM_198959	ENSMUSG00000028778	Hcrtr1	Ox1r|ox-1-R|ox1-R	hypocretin (orexin) receptor 1	protein-coding
mm_113805.1	chr13	46502038	46502048	+	1	NA	5' UTR (NM_026056, exon 1 of 13)	5' UTR (NM_026056, exon 1 of 13)	140	NM_026056	67252	Mm.44529	NM_026056	ENSMUSG00000021373	Cap2	2810452G09Rik|AV045235	CAP, adenylate cyclase-associated protein, 2 (yeast)	protein-coding
mm_127377.1	chr15	100814292	100814338	+	1	NA	intron (NM_001347102, intron 22 of 23)	intron (NM_001347102, intron 22 of 23)	33061	NM_001347102	59033	Mm.209856	NM_021530	ENSMUSG00000023032	Slc4a8	AW493845|C230026C11|NDCBE|kNBC-3	solute carrier family 4 (anion exchanger), member 8	protein-coding
mm_136405.1	chr16	93711268	93711270	-	1	NA	promoter-TSS (NM_026700)	promoter-TSS (NM_026700)	-638	NM_026700	70028	Mm.23230	NM_026700	ENSMUSG00000022946	Dopey2	0610038M01Rik|2610510B01Rik|AI503246|C21orf5|mKIAA0933	dopey family member 2	protein-coding
mm_51883.1	chr6	90601932	90601938	+	1	NA	Intergenic	Intergenic	-2945	NM_027868	71699	Mm.272633	NM_027868	ENSMUSG00000030089	Slc41a3	1010001P06Rik|AI480742|SLC41A1-L2	solute carrier family 41, member 3	protein-coding
mm_93252.1	chr10	95501922	95501953	-	1	NA	promoter-TSS (NM_026065)	promoter-TSS (NM_026065)	-10	NM_026065	67270	Mm.30008	NM_026065	ENSMUSG00000062981	Mrpl42	2700009F22Rik|2900055D03Rik|D10Ertd322e|HSPC204|L31mt|MRP-L31|PTD007|Rpml31	mitochondrial ribosomal protein L42	protein-coding
mm_17741.1	chr2	32712729	32712793	-	1	NA	promoter-TSS (NM_130860)	promoter-TSS (NM_130860)	23	NM_130860	107951	Mm.27557	NM_130860	ENSMUSG00000009555	Cdk9	PITALRE	cyclin-dependent kinase 9 (CDC2-related kinase)	protein-coding
mm_124770.1	chr15	6800076	6800080	+	1	NA	3' UTR (NM_030168, exon 38 of 38)	3' UTR (NM_030168, exon 38 of 38)	74235	NM_011019	18414	Mm.10760	NM_011019	ENSMUSG00000022146	Osmr	OSMRB	oncostatin M receptor	protein-coding
mm_146445.1	chr18	85071768	85071774	+	1	NA	Intergenic	Intergenic	-120247	NM_025969	67105	Mm.250617	NM_025969	ENSMUSG00000024645	Timm21	1700034H14Rik|2700002I20Rik	tranlocase of inner mitochondrial membrane 21	protein-coding
mm_113704.1	chr13	43250933	43250938	+	1	NA	intron (NM_001033399, intron 1 of 1)	intron (NM_001033399, intron 1 of 1)	53237	NM_001033399	328232	Mm.441399	NM_001033399	ENSMUSG00000051335	Gfod1	9630032O13|AI850995	glucose-fructose oxidoreductase domain containing 1	protein-coding
mm_92700.1	chr10	80701937	80701986	-	1	NA	promoter-TSS (NM_027829)	promoter-TSS (NM_027829)	-141	NM_172457	208228	Mm.49309	NM_172457	ENSMUSG00000003348	Mob3a	5330417K06Rik|A630029F06|AV218468|Mobkl2a	MOB kinase activator 3A	protein-coding
mm_104438.1	chr11	94973448	94973471	-	1	NA	5' UTR (NM_009161, exon 2 of 11)	5' UTR (NM_009161, exon 2 of 11)	2868	NM_009161	20391	Mm.18709	NM_009161	ENSMUSG00000001508	Sgca	50DAG|Asg	sarcoglycan, alpha (dystrophin-associated glycoprotein)	protein-coding
mm_108045.1	chr12	73907975	73908015	+	1	NA	5' UTR (NM_010431, exon 1 of 15)	5' UTR (NM_010431, exon 1 of 15)	128	NM_001313919	15251	Mm.3879	NM_010431	ENSMUSG00000021109	Hif1a	AA959795|HIF-1-alpha|HIF1-alpha|HIF1alpha|MOP1|bHLHe78	hypoxia inducible factor 1, alpha subunit	protein-coding
mm_165449.1	chr2	156475892	156475894	+	1	NA	5' UTR (NM_001006664, exon 1 of 22)	5' UTR (NM_001006664, exon 1 of 22)	359	NM_001006664	13821	Mm.20852	NM_013510	ENSMUSG00000027624	Epb41l1	4.1N|Epb4.1l1|NBL1|mKIAA0338	erythrocyte membrane protein band 4.1 like 1	protein-coding
mm_10456.1	chr2	14289150	14289160	+	1	NA	exon (NM_008625, exon 12 of 30)	exon (NM_008625, exon 12 of 30)	28152	NR_030609	100124488		NR_030609	ENSMUSG00000077897	Mir511	Mirn511|mir-511|mmu-mir-511	microRNA 511	ncRNA
mm_170957.1	chr2	5379374	5379375	-	1	NA	promoter-TSS (NR_030601)	promoter-TSS (NR_030601)	-16	NR_030601	100124465		NR_030601	ENSMUSG00000078031	Mir466d	Mirn466d	microRNA 466d	ncRNA
mm_135387.1	chr16	44332626	44332668	-	1	NA	5' UTR (NM_001159419, exon 1 of 26)	5' UTR (NM_001159419, exon 1 of 26)	191	NM_198034	320007	Mm.242144	NM_198034	ENSMUSG00000022696	Sidt1	AW045928|B830021E24Rik	SID1 transmembrane family, member 1	protein-coding
mm_39574.1	chr5	23433954	23433979	+	1	NA	promoter-TSS (NM_026984)	promoter-TSS (NM_026984)	387	NR_040469	269630	Mm.425231	NR_040469	ENSMUSG00000073147	5031425E22Rik	-	RIKEN cDNA 5031425E22 gene	ncRNA
mm_152559.1	chr19	11491947	11491979	-	1	NA	promoter-TSS (NM_001164202)	promoter-TSS (NM_001164202)	-75	NM_001164202	666926	Mm.486382	NM_001164202	ENSMUSG00000058470	Gm8369	EG666926	predicted gene 8369	protein-coding
mm_15020.1	chr2	152677572	152677594	+	1	NA	exon (NM_001159553, exon 2 of 3)	exon (NM_001159553, exon 2 of 3)	8122	NM_001159552	14950	Mm.277327	NM_010376	ENSMUSG00000019188	H13	1200006O09Rik|4930443L17Rik|5031424B04Rik|AV020344|H-13|Hm13|PSL3|Spp	histocompatibility 13	protein-coding
mm_10933.1	chr2	25467876	25467897	+	1	NA	exon (NM_008963, exon 5 of 7)	exon (NM_008963, exon 5 of 7)	1863	NM_008963	19215	Mm.1008	NM_008963	ENSMUSG00000015090	Ptgds	21kDa|L-PGDS|PGD2|PGDS|PGDS2|Ptgs3	prostaglandin D2 synthase (brain)	protein-coding
mm_89649.1	chr10	97479437	97479463	+	1	NA	promoter-TSS (NM_001190451)	promoter-TSS (NM_001190451)	-50	NM_001190451	13179	Mm.56769	NM_007833	ENSMUSG00000019929	Dcn	DC|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding
mm_35316.1	chr4	25666415	25666418	-	1	NA	intron (NM_010243, intron 2 of 2)	intron (NM_010243, intron 2 of 2)	133587	NM_010243	14348	Mm.39101	NM_010243	ENSMUSG00000055373	Fut9	AI746471|AU067636|mFUT9|mFuc-TIX	fucosyltransferase 9	protein-coding
mm_12847.1	chr2	83644502	83644521	+	1	NA	promoter-TSS (NM_026934)	promoter-TSS (NM_026934)	-67	NM_026934	69082	Mm.27804	NM_026934	ENSMUSG00000027091	Zc3h15	1700006A17Rik|1810012H02Rik|2610312B22Rik|FM22|Ierepo4	zinc finger CCCH-type containing 15	protein-coding
mm_104635.1	chr11	97523211	97523218	-	1	NA	exon (NM_018873, exon 18 of 20)	exon (NM_018873, exon 18 of 20)	-22874	NM_001289118	100141474	Mm.482426	NM_001289118	ENSMUSG00000047988	4933428G20Rik	-	RIKEN cDNA 4933428G20 gene	protein-coding
mm_88682.1	chr10	80053998	80054026	+	1	NA	promoter-TSS (NM_001037741)	promoter-TSS (NM_001037741)	-7	NM_001037741	625249	Mm.332810	NM_008162	ENSMUSG00000075706	Gpx4	GPx-4|GSHPx-4|PHGPx|mtPHGPx|snGPx	glutathione peroxidase 4	protein-coding
mm_43690.1	chr5	139150140	139150146	+	1	NA	promoter-TSS (NM_001081265)	promoter-TSS (NM_001081265)	-80	NM_001081265	433956	Mm.5547	NM_001081265	ENSMUSG00000025857	Dnaaf5	BC053401|C76907|Heatr2	dynein, axonemal assembly factor 5	protein-coding
mm_113431.1	chr13	34734872	34734882	+	1	NA	Intergenic	Intergenic	-4765	NM_138746	108161	Mm.41991	NM_138746	ENSMUSG00000038246	Fam50b	D0H6S2654E|X5L|XAP-5-like	family with sequence similarity 50, member B	protein-coding
mm_39540.1	chr5	21475198	21475201	+	1	NA	intron (NM_177869, intron 7 of 7)	intron (NM_177869, intron 7 of 7)	50296	NM_177869	330050	Mm.40655	NM_177869	ENSMUSG00000047221	Fam185a	4631428I10|AI847670	family with sequence similarity 185, member A	protein-coding
mm_82557.1	chr9	21028254	21028284	-	1	NA	3' UTR (NM_010493, exon 7 of 7)	3' UTR (NM_010493, exon 7 of 7)	-1104	NM_023892	78369	Mm.30220	NM_023892	ENSMUSG00000001014	Icam4	1810015M19Rik|Cd242|ICAM-4	intercellular adhesion molecule 4, Landsteiner-Wiener blood group	protein-coding
mm_101973.1	chr11	50325580	50325589	-	1	NA	promoter-TSS (NM_001110500)	promoter-TSS (NM_001110500)	89	NM_001110499	12330	Mm.248827	NM_007597	ENSMUSG00000020368	Canx	1110069N15Rik|AI988026|Cnx|D11Ertd153e	calnexin	protein-coding
mm_77422.1	chr8	121083053	121083083	-	1	NA	promoter-TSS (NR_045471)	promoter-TSS (NR_045471)	42	NR_045471	68790	Mm.246916	NR_045471	ENSMUSG00000097336	Fendrr	1110050K14Rik|LL66|linc-Foxf1a|lincFoxf1	Foxf1 adjacent non-coding developmental regulatory RNA	ncRNA
mm_82862.1	chr9	31913319	31913333	-	1	NA	promoter-TSS (NM_013800)	promoter-TSS (NM_013800)	-41	NM_013800	12023	Mm.261044	NM_013800	ENSMUSG00000032033	Barx2	2310006E12Rik|Barx2b	BarH-like homeobox 2	protein-coding
mm_119478.1	chr14	47319496	47319539	+	1	NA	3' UTR (NM_178684, exon 4 of 4)	3' UTR (NM_178684, exon 4 of 4)	21203	NM_178684	218975	Mm.212297	NM_178684	ENSMUSG00000021840	Mapk1ip1l	9130202B12|C130032J12Rik	mitogen-activated protein kinase 1 interacting protein 1-like	protein-coding
mm_137646.1	chr17	28549472	28549482	+	1	NA	promoter-TSS (NM_001034871)	promoter-TSS (NM_001034871)	-10	NM_001034871	328788	Mm.99400	NM_001034871	ENSMUSG00000024224	Clpsl2	Gm749	colipase-like 2	protein-coding
mm_33968.1	chr4	137594942	137594968	+	1	NA	intron (NM_001347227, intron 1 of 26)	intron (NM_001347227, intron 1 of 26)	766	NM_130879	170707	Mm.218478	NM_130879	ENSMUSG00000043411	Usp48	2810449C13Rik|AI115503|BC021769|D330022K21Rik|Usp31	ubiquitin specific peptidase 48	protein-coding
mm_96541.1	chr11	68692098	68692126	+	1	NA	5' UTR (NM_175260, exon 1 of 41)	5' UTR (NM_175260, exon 1 of 41)	197	NM_175260	77579	Mm.218233	NM_175260	ENSMUSG00000020900	Myh10	5730504C04Rik|9330167F11Rik|Fltn|Myhn-2|Myhn2|NMHC II-B|NMHC-B|NMHCII-B|NMMHC II-b|NMMHC-B|NMMHC-IIB|SMemb|mKIAA3005	myosin, heavy polypeptide 10, non-muscle	protein-coding
mm_119942.1	chr14	54983551	54983573	+	1	NA	exon (NM_080728, exon 24 of 41)	exon (NM_080728, exon 24 of 41)	-7786	NR_030607	100124433		NR_030607	ENSMUSG00000077928	Mir208b	Mirn208b|mir-208b	microRNA 208b	ncRNA
mm_150040.1	chr19	29377915	29377927	+	1	NA	intron (NM_021893, intron 3 of 6)	intron (NM_021893, intron 3 of 6)	10483	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_170092.1	chr17	36121420	36121438	-	1	NA	promoter-TSS (NM_010395)	promoter-TSS (NM_010395)	6	NM_010395	15024	Mm.426031	NM_010395	ENSMUSG00000079491	H2-T10	H-2T10	histocompatibility 2, T region locus 10	protein-coding
mm_82182.1	chr9	123933919	123933931	+	1	NA	Intergenic	Intergenic	34767	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_59613.1	chr7	28142590	28142596	+	1	NA	exon (NM_001164655, exon 6 of 20)	exon (NM_001164655, exon 6 of 20)	13127	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_36493.1	chr4	83273747	83273797	-	1	NA	intron (NM_027238, intron 2 of 19)	RMER17B|LTR|ERVK	50417	NM_027238	69863	Mm.5540	NM_025782	ENSMUSG00000038172	Ttc39b	1810054D07Rik|9130422G05Rik|AI450603|AV103077|AW215585	tetratricopeptide repeat domain 39B	protein-coding
mm_63626.1	chr7	128340414	128340446	+	1	NA	Intergenic	Intergenic	-42299	NM_145590	233913	Mm.220880	NM_145590	ENSMUSG00000030780	BC017158	-	cDNA sequence BC017158	protein-coding
mm_5047.1	chr1	194626908	194626912	+	1	NA	intron (NM_008882, intron 1 of 31)	intron (NM_008882, intron 1 of 31)	7081	NM_008882	18845	Mm.2251	NM_008882	ENSMUSG00000026640	Plxna2	2810428A13Rik|AA589422|AW457381|OCT|PlexA2|Plxn2|mKIAA0463	plexin A2	protein-coding
mm_112384.1	chr12	119238130	119238137	-	1	NA	5' UTR (NM_177290, exon 1 of 14)	5' UTR (NM_177290, exon 1 of 14)	143	NM_177290	320910	Mm.217000	NM_177290	ENSMUSG00000025321	Itgb8	4832412O06Rik	integrin beta 8	protein-coding
mm_102267.1	chr11	55394563	55394599	-	1	NA	3' UTR (NM_009242, exon 10 of 10)	3' UTR (NM_009242, exon 10 of 10)	25499	NM_009242	20692	Mm.291442	NM_009242	ENSMUSG00000018593	Sparc	BM-40|ON	secreted acidic cysteine rich glycoprotein	protein-coding
mm_37529.1	chr4	124850671	124850691	-	1	NA	promoter-TSS (NM_001142727)	promoter-TSS (NM_001142727)	49	NM_001142727	68920	Mm.272397	NM_001142727	ENSMUSG00000078570	1110065P20Rik	C530005M16Rik	RIKEN cDNA 1110065P20 gene	protein-coding
mm_130878.1	chr15	102246305	102246326	-	1	NA	5' UTR (NM_001042727, exon 1 of 8)	5' UTR (NM_001042727, exon 1 of 8)	185	NM_001042727	19411	Mm.1273	NM_011244	ENSMUSG00000001288	Rarg	Nr1b3|RAR-gamma|RARD|RARgamma2	retinoic acid receptor, gamma	protein-coding
mm_25128.1	chr3	102144165	102144175	+	1	NA	exon (NM_009814, exon 10 of 11)	exon (NM_009814, exon 10 of 11)	57715	NM_009814	12373	Mm.15343	NM_009814	ENSMUSG00000027861	Casq2	AA033488|AW146219|Csq2|ESTM52|cCSQ	calsequestrin 2	protein-coding
mm_54017.1	chr6	8509102	8509144	-	1	NA	promoter-TSS (NR_040452)	promoter-TSS (NR_040452)	38	NR_040452	320312	Mm.374890	NR_040452	ENSMUSG00000087305	A430035B10Rik	2810488G03Rik	RIKEN cDNA A430035B10 gene	ncRNA
mm_151784.1	chr19	5366599	5366611	-	1	NA	promoter-TSS (NM_027236)	promoter-TSS (NM_027236)	-208	NM_027236	69860	Mm.299167	NM_027236	ENSMUSG00000024841	Eif1ad	2010003J03Rik|AI131644	eukaryotic translation initiation factor 1A domain containing	protein-coding
mm_141791.1	chr17	34342126	34342141	-	1	NA	TTS (NM_010381)	TTS (NM_010381)	2512	NM_010381	100504404	Mm.15680	NM_010381		H2-Ea-ps	AI323765|E-alpha-f|H-2Ea|H2-Ea|I-Ealpha|Ia-3|Ia3|MHC-H2-Ea	histocompatibility 2, class II antigen E alpha, pseudogene	protein-coding
mm_149195.1	chr19	9954843	9954855	+	1	NA	Intergenic	Intergenic	-25751	NR_073181	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
mm_21874.1	chr2	166074443	166074463	-	1	NA	3' UTR (NM_028072, exon 21 of 21)	3' UTR (NM_028072, exon 21 of 21)	80832	NM_001252578	72043	Mm.1011	NM_028072	ENSMUSG00000006800	Sulf2	2010004N24Rik|AU020235|MSulf-2|mKIAA1247	sulfatase 2	protein-coding
mm_102504.1	chr11	60723414	60723434	-	1	NA	exon (NM_022009, exon 4 of 30)	exon (NM_022009, exon 4 of 30)	3839	NM_022009	14248	Mm.339755	NM_022009	ENSMUSG00000002812	Flii	3632430F08Rik|Fliih	flightless I actin binding protein	protein-coding
mm_31254.1	chr4	45012169	45012204	+	1	NA	5' UTR (NM_001163284, exon 1 of 2)	5' UTR (NM_001163284, exon 1 of 2)	226	NM_001163284	230119	Mm.44222	NM_173399	ENSMUSG00000049657	Zbtb5	5930421I10|9430083K24Rik|AI646847|mKIAA0354	zinc finger and BTB domain containing 5	protein-coding
mm_162691.1	chr10	19644991	19644994	+	1	NA	Intergenic	MLTR25C|LTR|ERVK	22964	NM_178258	237310	Mm.331979	NM_178258	ENSMUSG00000039760	Il22ra2	CRF2-10|CRF2-s1|CRF2X|Il-22bp	interleukin 22 receptor, alpha 2	protein-coding
mm_10222.1	chr2	5957461	5957473	+	1	NA	intron (NM_001081132, intron 1 of 21)	intron (NM_001081132, intron 1 of 21)	5998	NM_001081132	326622	Mm.31102	NM_001081132	ENSMUSG00000043241	Upf2	-	UPF2 regulator of nonsense transcripts homolog (yeast)	protein-coding
mm_88858.1	chr10	80930821	80930838	+	1	NA	intron (NM_008655, intron 2 of 3)	intron (NM_008655, intron 2 of 3)	738	NM_008655	17873	Mm.1360	NM_008655	ENSMUSG00000015312	Gadd45b	AI323528|Myd118	growth arrest and DNA-damage-inducible 45 beta	protein-coding
mm_162678.1	chr10	10203122	10203125	+	1	NA	Intergenic	Intergenic	269191	NM_001127353	215772	Mm.246573	NM_172547	ENSMUSG00000050994	Adgb	9130014G24Rik	androglobin	protein-coding
mm_150370.1	chr19	34746301	34746313	+	1	NA	intron (NM_172838, intron 1 of 6)	intron (NM_172838, intron 1 of 6)	804	NM_172838	240638	Mm.74636	NM_172838	ENSMUSG00000009378	Slc16a12	3230401A21|AW210596	solute carrier family 16 (monocarboxylic acid transporters), member 12	protein-coding
mm_66188.1	chr7	34196179	34196192	-	1	NA	intron (NM_026549, intron 2 of 6)	intron (NM_026549, intron 2 of 6)	462	NM_026549	68079	Mm.38173	NM_026549	ENSMUSG00000002635	Pdcd2l	6030457N17Rik	programmed cell death 2-like	protein-coding
mm_92592.1	chr10	80075412	80075453	-	1	NA	intron (NM_183426, intron 4 of 31)	intron (NM_183426, intron 4 of 31)	21413	NM_001037741	625249	Mm.332810	NM_008162	ENSMUSG00000075706	Gpx4	GPx-4|GSHPx-4|PHGPx|mtPHGPx|snGPx	glutathione peroxidase 4	protein-coding
mm_29630.1	chr3	121571606	121571615	-	1	NA	Intergenic	Intergenic	-39266	NM_145394	213603	Mm.33062	NM_145394	ENSMUSG00000039865	Slc44a3	BC010552	solute carrier family 44, member 3	protein-coding
mm_160655.1	chr9	117629914	117629914	-	1	NA	promoter-TSS (NM_001172121)	promoter-TSS (NM_001172121)	-1	NM_001172121	207181	Mm.326411	NM_178660	ENSMUSG00000039607	Rbms3	6720477E09Rik|8430436O14Rik	RNA binding motif, single stranded interacting protein	protein-coding
mm_85357.1	chr9	103215220	103215270	-	1	NA	exon (NM_133977, exon 14 of 17)	exon (NM_133977, exon 14 of 17)	-13180	NM_009275	20818	Mm.273053	NM_009275	ENSMUSG00000032553	Srprb	AA409543	signal recognition particle receptor, B subunit	protein-coding
mm_139837.1	chr17	69156854	69156860	+	1	NA	promoter-TSS (NM_013813)	promoter-TSS (NM_013813)	47	NM_013813	13823	Mm.131135	NM_013813	ENSMUSG00000024044	Epb41l3	4.1B|DAL1P|Dal1|Epb4.1l3|NBL3	erythrocyte membrane protein band 4.1 like 3	protein-coding
mm_154539.1	chrM	14061	14074	-	1	NA	NA	Intergenic	NA	NA								
mm_156667.1	chrX	159210338	159210358	+	1	NA	Intergenic	Intergenic	-45434	NM_148945	110651	Mm.328476	NM_148945	ENSMUSG00000031309	Rps6ka3	MAPKAPK-1b|MPK-9|Rsk2|S6K-alpha3|p90RSK3|pp90RSK2	ribosomal protein S6 kinase polypeptide 3	protein-coding
mm_144920.1	chr18	37661772	37661776	+	1	NA	promoter-TSS (NM_033584)	promoter-TSS (NM_033584)	-171	NM_033584	93709	Mm.247203	NM_033584	ENSMUSG00000103144	Pcdhga1	-	protocadherin gamma subfamily A, 1	protein-coding
mm_6693.1	chr1	80715706	80715709	-	1	NA	intron (NM_175291, intron 1 of 55)	intron (NM_175291, intron 1 of 55)	42846	NM_175291	210293	Mm.133473	NM_175291	ENSMUSG00000038608	Dock10	9330153B10Rik|A630054M16Rik|Jr4|Jr5|R75174|ZIZ3|Zizimin3|mKIAA0694	dedicator of cytokinesis 10	protein-coding
mm_54090.1	chr6	15846155	15846173	-	1	NA	Intergenic	LTR33A_|LTR|ERVL	125503	NM_175088	16543	Mm.1314	NM_175088	ENSMUSG00000041390	Mdfic	Kdt1|Mdfid	MyoD family inhibitor domain containing	protein-coding
mm_63768.1	chr7	131236877	131236880	+	1	NA	intron (NM_175166, intron 15 of 22)	intron (NM_175166, intron 15 of 22)	62476	NM_175166	71395	Mm.118845	NM_175166	ENSMUSG00000006204	5430419D17Rik	-	RIKEN cDNA 5430419D17 gene	protein-coding
mm_170414.1	chr18	68692162	68692162	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-47238	NR_105774	102465183		NR_105774	ENSMUSG00000099300	Mir6356	Gm27461|mmu-mir-6356	microRNA 6356	ncRNA
mm_41039.1	chr5	86086189	86086219	+	1	NA	intron (NM_001310639, intron 3 of 7)	B1_Mur3|SINE|Alu	14458	NM_001310639	56792	Mm.131237	NM_019992	ENSMUSG00000029254	Stap1	AI586015|Brdg1|STAP-1	signal transducing adaptor family member 1	protein-coding
mm_45360.1	chr5	65991235	65991246	-	1	NA	intron (NR_027961, intron 4 of 6)	intron (NR_027961, intron 4 of 6)	13045	NR_027961	231253	Mm.436542	NM_177679	ENSMUSG00000054598	9130230L23Rik	-	RIKEN cDNA 9130230L23 gene	ncRNA
mm_157170.1	chrX	9469289	9469331	-	1	NA	promoter-TSS (NM_007807)	promoter-TSS (NM_007807)	14	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_157350.1	chrX	36989658	36989674	-	1	NA	promoter-TSS (NM_001253706)	promoter-TSS (NM_001253706)	29	NM_001177324	56526	Mm.260036	NM_019942	ENSMUSG00000050379	Sept6	2810035H17Rik|C920001C06Rik|Sep6|mKIAA0128	septin 6	protein-coding
mm_77142.1	chr8	111537380	111537390	-	1	NA	promoter-TSS (NM_001168623)	promoter-TSS (NM_001168623)	745	NM_001168621	170737	Mm.271578	NM_133206	ENSMUSG00000033545	Znrf1	B830022L21Rik|Rnf42|Zrfp1|nin283	zinc and ring finger 1	protein-coding
mm_17963.1	chr2	37430809	37430821	-	1	NA	5' UTR (NM_146253, exon 1 of 2)	5' UTR (NM_146253, exon 1 of 2)	104	NM_146253	241322	Mm.330182	NM_146253	ENSMUSG00000066798	Zbtb6	A830092L04Rik|ZID|Zfp482	zinc finger and BTB domain containing 6	protein-coding
mm_45524.1	chr5	72636207	72636218	-	1	NA	intron (NM_007723, intron 1 of 8)	intron (NM_007723, intron 1 of 8)	6540	NM_007723	12788	Mm.436652	NM_007723	ENSMUSG00000067220	Cnga1	Cncg	cyclic nucleotide gated channel alpha 1	protein-coding
mm_156615.1	chrX	153499369	153499381	+	1	NA	exon (NM_018798, exon 1 of 1)	exon (NM_018798, exon 1 of 1)	1143	NM_018798	54609	Mm.430772	NM_018798	ENSMUSG00000050148	Ubqln2	Chap1|Dsk2|HRIHFB2157|Plic-2|Plic2	ubiquilin 2	protein-coding
mm_149787.1	chr19	23140957	23140967	+	1	NA	promoter-TSS (NM_010638)	promoter-TSS (NM_010638)	-264	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_45711.1	chr5	84067186	84067204	-	1	NA	intron (NM_007937, intron 15 of 15)	intron (NM_007937, intron 15 of 15)	350187	NM_007937	13839	Mm.137991	NM_007937	ENSMUSG00000029245	Epha5	AI854630|AW125296|Cek7|Ehk1|Els1|Hek7|Rek7|bsk	Eph receptor A5	protein-coding
mm_114430.1	chr13	65033047	65033065	+	1	NA	promoter-TSS (NM_001083890)	promoter-TSS (NM_001083890)	-2	NM_001083890	238683	Mm.295543	NM_001083890	ENSMUSG00000074849	Spata31d1c	4932441B19Rik|Fam75d1c	spermatogenesis associated 31 subfamily D, member 1C	protein-coding
mm_20034.1	chr2	119760410	119760421	-	1	NA	promoter-TSS (NM_203345)	promoter-TSS (NM_203345)	16	NM_203345	17005	Mm.1740	NM_008523	ENSMUSG00000027297	Ltk	-	leukocyte tyrosine kinase	protein-coding
mm_44270.1	chr5	5694025	5694109	-	1	NA	promoter-TSS (NM_001103156)	promoter-TSS (NM_001103156)	22	NM_001285471	74051	Mm.274956	NM_028734	ENSMUSG00000015653	Steap2	4921538B17Rik|AI930049|AW045895|IPCA-1|IPCA1|PCANAP1|STAMP1|STMP	six transmembrane epithelial antigen of prostate 2	protein-coding
mm_63122.1	chr7	122969875	122969885	+	1	NA	promoter-TSS (NM_175023)	promoter-TSS (NM_175023)	579	NR_045614	73951	Mm.389936	NR_045614		4930413G21Rik	-	RIKEN cDNA 4930413G21 gene	ncRNA
mm_102762.1	chr11	67771116	67771134	-	1	NA	promoter-TSS (NM_175681)	promoter-TSS (NM_175681)	28	NM_175681	93896	Mm.118883	NM_175681	ENSMUSG00000049928	Glp2r	9530092J08Rik|GLP-2	glucagon-like peptide 2 receptor	protein-coding
mm_42197.1	chr5	112288735	112288768	+	1	NA	intron (NM_001326590, intron 1 of 5)	intron (NM_001326590, intron 1 of 5)	12060	NM_009419	22022	Mm.250631	NM_009419	ENSMUSG00000029344	Tpst2	AI448750|D5Ucla3|Tango13b|grm|grt	protein-tyrosine sulfotransferase 2	protein-coding
mm_79692.1	chr9	60671961	60671965	+	1	NA	intron (NM_001311095, intron 5 of 15)	intron (NM_001311095, intron 5 of 15)	15571	NM_001311095	102747	Mm.269413	NM_145616	ENSMUSG00000047766	Lrrc49	AI430817|AW050057|D430025H09Rik|PGs4|p79	leucine rich repeat containing 49	protein-coding
mm_160293.1	chr7	129257013	129257013	+	1	NA	promoter-TSS (NM_001080963)	promoter-TSS (NM_001080963)	-81	NM_001080963	381925	Mm.39184	NM_001080963	ENSMUSG00000070366	Plpp4	C030048B12Rik|Gm1090|Ppapdc1a	phospholipid phosphatase 4	protein-coding
mm_11097.1	chr2	28032056	28032073	+	1	NA	intron (NM_015734, intron 64 of 65)	intron (NM_015734, intron 64 of 65)	52814	NM_010190	14134	Mm.182935	NM_010190	ENSMUSG00000026835	Fcnb	Fcn2	ficolin B	protein-coding
mm_58805.1	chr7	16309578	16309641	+	1	NA	promoter-TSS (NM_133234)	promoter-TSS (NM_133234)	26	NM_133234	170770	Mm.7660	NM_133234	ENSMUSG00000002083	Bbc3	PUMA|PUMA/JFY1	BCL2 binding component 3	protein-coding
mm_146746.1	chr18	16115369	16115383	-	1	NA	Intergenic	MIRb|SINE|MIR	-397330	NM_199055	71367	Mm.329304	NM_199055	ENSMUSG00000047161	Chst9	5430438D01Rik	carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 9	protein-coding
mm_10134.1	chr2	4017758	4017768	+	1	NA	promoter-TSS (NM_001347086)	promoter-TSS (NM_001347086)	80	NM_001347086	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding
mm_76110.1	chr8	80700632	80700636	-	1	NA	3' UTR (NM_053124, exon 24 of 24)	3' UTR (NM_053124, exon 24 of 24)	38825	NM_053124	93762	Mm.246803	NM_053124	ENSMUSG00000031715	Smarca5	4933427E24Rik|D030040M08Rik|D330027N15Rik|MommeD4|Snf2h	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5	protein-coding
mm_90174.1	chr10	119672682	119672706	+	1	NA	intron (NM_133442, intron 1 of 21)	intron (NM_133442, intron 1 of 21)	89005	NR_045359	75321	Mm.402041	NR_045359	ENSMUSG00000084764	Grip1os2	4930564G21Rik	glutamate receptor interacting protein 1, opposite strand 2	ncRNA
mm_137092.1	chr17	21535531	21535545	+	1	NA	promoter-TSS (NM_144515)	promoter-TSS (NM_144515)	-1	NM_144515	22710	Mm.296100	NM_144515	ENSMUSG00000051341	Zfp52	KRAB11|Zfp-52|Zfp76|mszf23-2|mszf24|mszf34|mszf75|zfec29	zinc finger protein 52	protein-coding
mm_11562.1	chr2	32845918	32845942	+	1	NA	intron (NM_009295, intron 1 of 18)	intron (NM_009295, intron 1 of 18)	1302	NM_009295	20910	Mm.278865	NM_009295	ENSMUSG00000026797	Stxbp1	AI317162|AI326233|MMS10-G|Ms10g|Munc-18a|Munc18-1|N-sec1|Rb-sec1|Sxtbp1|Unc18-1|Unc18h|nsec1	syntaxin binding protein 1	protein-coding
mm_301.1	chr1	23761750	23761759	+	1	NA	promoter-TSS (NM_172124)	promoter-TSS (NM_172124)	-172	NM_172124	280645	Mm.471661	NM_172124	ENSMUSG00000026156	B3gat2	GlcAT-S|Glcats	beta-1,3-glucuronyltransferase 2 (glucuronosyltransferase S)	protein-coding
mm_133458.1	chr16	89129202	89129205	+	1	NA	Intergenic	Intergenic	-65201	NM_001276278	68637	Mm.384089	NM_001276278	ENSMUSG00000068073	1110025L11Rik	-	RIKEN cDNA 1110025L11 gene	protein-coding
mm_18244.1	chr2	52188738	52188761	-	1	NA	exon (NM_010889, exon 121 of 157)	exon (NM_010889, exon 121 of 157)	-102253	NR_040620	78049	Mm.243883	NR_040620		4930573O16Rik	-	RIKEN cDNA 4930573O16 gene	ncRNA
mm_97007.1	chr11	70884804	70884824	+	1	NA	exon (NM_019400, exon 3 of 18)	exon (NM_019400, exon 3 of 18)	40053	NM_001291142	54189	Mm.7087	NM_019400	ENSMUSG00000020817	Rabep1	Rab5ep|rabaptin-5|rabaptin-5alpha	rabaptin, RAB GTPase binding effector protein 1	protein-coding
mm_155615.1	chrX	83082411	83082416	+	1	NA	intron (NM_007868, intron 1 of 78)	B4A|SINE|B4	133543	NM_007868	13405	Mm.275608	NM_007868	ENSMUSG00000045103	Dmd	DXSmh7|DXSmh9|Dp427|Dp71|dys|mdx|pke	dystrophin, muscular dystrophy	protein-coding
mm_82633.1	chr9	21962387	21962397	-	1	NA	intron (NM_010149, intron 1 of 7)	intron (NM_010149, intron 1 of 7)	1184	NM_010149	13857	Mm.2653	NM_010149	ENSMUSG00000006235	Epor	-	erythropoietin receptor	protein-coding
mm_39033.1	chr4	152291664	152291672	-	1	NA	promoter-TSS (NM_008237)	promoter-TSS (NM_008237)	-6	NM_008237	15207	Mm.3516	NM_008237	ENSMUSG00000028946	Hes3	Hes-3|bHLHb43	hairy and enhancer of split 3 (Drosophila)	protein-coding
mm_54764.1	chr6	41311306	41311317	-	1	NA	TTS (NM_001003405)	TTS (NM_001003405)	3399	NM_001003405	103964	Mm.333022	NM_001003405	ENSMUSG00000036938	Try5	1810049H19Rik|Tc|Tesp4	trypsin 5	protein-coding
mm_90935.1	chr10	12869631	12869641	-	1	NA	Intergenic	CpG	-7901	NM_011682	22288	Mm.331784	NM_011682	ENSMUSG00000019820	Utrn	AA589569|DRP|Dmdl	utrophin	protein-coding
mm_28329.1	chr3	89365192	89365194	-	1	NA	promoter-TSS (NM_029974)	promoter-TSS (NM_029974)	60	NM_029974	77772	Mm.164013	NM_029974	ENSMUSG00000042672	Dcst1	A330106H01Rik	DC-STAMP domain containing 1	protein-coding
mm_168220.1	chr10	77169505	77169505	-	1	NA	Intergenic	Intergenic	-2975	NM_009929	12822	Mm.4352	NM_009929	ENSMUSG00000001435	Col18a1	-	collagen, type XVIII, alpha 1	protein-coding
mm_2037.1	chr1	87214302	87214369	+	1	NA	5' UTR (NM_001039169, exon 1 of 7)	5' UTR (NM_001039169, exon 1 of 7)	396	NM_001039169	26987	Mm.227183	NM_023314	ENSMUSG00000026254	Eif4e2	2700069E09Rik|AI036339|AV129531|D0H0S6743E|Eif4el3	eukaryotic translation initiation factor 4E member 2	protein-coding
mm_133385.1	chr16	84773856	84773875	+	1	NA	promoter-TSS (NM_023844)	promoter-TSS (NM_023844)	-258	NM_023844	67374	Mm.41758	NM_023844	ENSMUSG00000053062	Jam2	1110002N23Rik|2410030G21Rik|2410167M24Rik|JAM-2|JAM-B|Jcam2|VE-JAM	junction adhesion molecule 2	protein-coding
mm_128099.1	chr15	27876456	27876478	-	1	NA	intron (NM_001081302, intron 10 of 56)	intron (NM_001081302, intron 10 of 56)	149381	NM_001081302	223435	Mm.485422	NM_001081302	ENSMUSG00000022263	Trio	6720464I07Rik|AA408740|Solo	triple functional domain (PTPRF interacting)	protein-coding
mm_103863.1	chr11	83393234	83393248	-	1	NA	intron (NM_027915, intron 19 of 20)	intron (NM_027915, intron 19 of 20)	-16831	NM_001013386	276952	Mm.66275	NM_001013386	ENSMUSG00000020684	Rasl10b	B230331P10Rik|Gm729|VTS58635	RAS-like, family 10, member B	protein-coding
mm_75673.1	chr8	67910912	67910935	-	1	NA	promoter-TSS (NM_030263)	promoter-TSS (NM_030263)	23	NM_030263	234353	Mm.32525	NM_027626	ENSMUSG00000030465	Psd3	4931420C21Rik|AI661273|BC003498|D430018P08|EFA6D	pleckstrin and Sec7 domain containing 3	protein-coding
mm_143363.1	chr17	67350040	67350045	-	1	NA	intron (NM_008984, intron 1 of 30)	AT_rich|Low_complexity|Low_complexity	4417	NM_008984	19274	Mm.311809	NM_008984	ENSMUSG00000033278	Ptprm	RPTPmu|mKIAA4044	protein tyrosine phosphatase, receptor type, M	protein-coding
mm_76600.1	chr8	90301363	90301366	-	1	NA	intron (NM_172913, intron 1 of 6)	intron (NM_172913, intron 1 of 6)	46888	NM_172913	244579	Mm.302755	NM_172913	ENSMUSG00000043668	Tox3	500-9|BC052044|C230068E13|CAGF9|Tnrc9	TOX high mobility group box family member 3	protein-coding
mm_113025.1	chr13	22049835	22049858	+	1	NA	Intergenic	Lx8|LINE|L1	6616	NM_178198	319183	Mm.371766	NM_178198	ENSMUSG00000069300	Hist1h2bj	-	histone cluster 1, H2bj	protein-coding
mm_93297.1	chr10	96595610	96595617	-	1	NA	Intergenic	Intergenic	-21388	NM_007569	12226	Mm.23811	NM_007569	ENSMUSG00000036478	Btg1	AI426953|AW546738	B cell translocation gene 1, anti-proliferative	protein-coding
mm_96020.1	chr11	59543063	59543071	+	1	NA	intron (NM_145827, intron 1 of 9)	intron (NM_145827, intron 1 of 9)	381	NM_145827	216799	Mm.54174	NM_145827	ENSMUSG00000032691	Nlrp3	AGTAVPRL|AII/AVP|Cias1|FCAS|FCU|MWS|Mmig1|NALP3|Pypaf1	NLR family, pyrin domain containing 3	protein-coding
mm_102582.1	chr11	61808647	61808650	-	1	NA	intron (NM_013881, intron 14 of 26)	intron (NM_013881, intron 14 of 26)	46444	NM_013881	29869	Mm.162025	NM_013881	ENSMUSG00000004798	Ulk2	A830085I22Rik|AU015340|Unc51.2|mKIAA0623	unc-51 like kinase 2	protein-coding
mm_29359.1	chr3	108562154	108562178	-	1	NA	intron (NM_026198, intron 1 of 2)	CpG	300	NM_026198	67495	Mm.32615	NM_026198	ENSMUSG00000068732	Tmem167b	2010200O16Rik	transmembrane protein 167B	protein-coding
mm_135542.1	chr16	49783440	49783446	-	1	NA	Intergenic	Intergenic	-72211	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_151436.1	chr19	57360752	57360762	+	1	NA	promoter-TSS (NM_145505)	promoter-TSS (NM_145505)	142	NR_040316	320879	Mm.375089	NR_040316	ENSMUSG00000097785	B230217O12Rik	-	RIKEN cDNA B230217O12 gene	ncRNA
mm_2708.1	chr1	128103298	128103311	+	1	NA	promoter-TSS (NM_001285945)	promoter-TSS (NM_001285945)	-2	NM_181750	226412	Mm.221041	NM_181750	ENSMUSG00000056211	R3hdm1	R3hdm	R3H domain containing 1	protein-coding
mm_102622.1	chr11	62466569	62466570	-	1	NA	intron (NM_001039536, intron 1 of 6)	intron (NM_001039536, intron 1 of 6)	8109	NM_001039536	327942	Mm.390358	NM_199026	ENSMUSG00000014245	Pigl	Gm737	phosphatidylinositol glycan anchor biosynthesis, class L	protein-coding
mm_94367.1	chr11	5039153	5039164	+	1	NA	exon (NM_001243043, exon 18 of 23)	exon (NM_001243043, exon 18 of 23)	-18970	NM_145216	75668	Mm.374836	NM_145216	ENSMUSG00000034209	Rasl10a	2210403B10Rik|AI852688	RAS-like, family 10, member A	protein-coding
mm_63347.1	chr7	126975616	126975624	+	1	NA	promoter-TSS (NM_026638)	promoter-TSS (NM_026638)	-294	NM_026638	52858	Mm.28219	NM_026638	ENSMUSG00000030682	Cdipt	9530042F15Rik|D7Bwg0575e|Pis|Pis1	CDP-diacylglycerol--inositol 3-phosphatidyltransferase (phosphatidylinositol synthase)	protein-coding
mm_96263.1	chr11	62648767	62648781	+	1	NA	promoter-TSS (NM_198861)	promoter-TSS (NM_198861)	110	NM_175002	216829	Mm.295306	NM_175002	ENSMUSG00000048497	Mmgt2	AI852046	membrane magnesium transporter 2	protein-coding
mm_136962.1	chr17	15597896	15597911	+	1	NA	Intergenic	Intergenic	-33885	NR_045431	71008	Mm.399492	NR_045431		4933401D09Rik	-	RIKEN cDNA 4933401D09 gene	ncRNA
mm_19975.1	chr2	118296927	118296938	-	1	NA	intron (NM_201367, intron 1 of 2)	intron (NM_201367, intron 1 of 2)	-7982	NR_045919	73358	Mm.437192	NR_045919	ENSMUSG00000085889	1700054M17Rik	-	RIKEN cDNA 1700054M17 gene	ncRNA
mm_25138.1	chr3	102506620	102506635	+	1	NA	intron (NM_001112698, intron 1 of 2)	T-rich|Low_complexity|Low_complexity	36708	NM_013609	18049	Mm.1259	NM_013609	ENSMUSG00000027859	Ngf	Ngfb	nerve growth factor	protein-coding
mm_46316.1	chr5	100599264	100599268	-	1	NA	Intergenic	RMER19C|LTR|ERVK	-27061	NM_139198	231507	Mm.34609	NM_139198	ENSMUSG00000029322	Plac8	C15|D5Wsu111e	placenta-specific 8	protein-coding
mm_72945.1	chr8	92097312	92097317	+	1	NA	Intergenic	MLT1H|LTR|ERVL-MaLR	258806	NR_110452	71296	Mm.86664	NR_033641	ENSMUSG00000031736	Crnde	4933436C20Rik	colorectal neoplasia differentially expressed (non-protein coding)	ncRNA
mm_124109.1	chr14	79467379	79467399	-	1	NA	exon (NM_018765, exon 8 of 10)	exon (NM_018765, exon 8 of 10)	-13805	NM_007920	13709	Mm.20938	NM_007920	ENSMUSG00000036461	Elf1	Elf-1|Sts1|mElf-1|p70	E74-like factor 1	protein-coding
mm_30826.1	chr4	21874102	21874121	+	1	NA	exon (NM_025669, exon 11 of 12)	exon (NM_025669, exon 11 of 12)	-5564	NM_172687	230027	Mm.5662	NM_172687	ENSMUSG00000028247	Coq3	4732433J24|C77934	coenzyme Q3 methyltransferase	protein-coding
mm_78724.1	chr9	41580704	41580717	+	1	NA	promoter-TSS (NR_015483)	promoter-TSS (NR_015483)	-543	NR_015483	73144	Mm.38166	NM_001033153	ENSMUSG00000074415	3110039I08Rik	2610203C20Rik|AI848448|D230004N17Rik|D3Mgi9|Mir100hg	RIKEN cDNA 3110039I08 gene	ncRNA
mm_128074.1	chr15	27663423	27663440	-	1	NA	intron (NM_001242423, intron 4 of 7)	intron (NM_001242423, intron 4 of 7)	18111	NM_001242424	223433	Mm.266485	NM_198301	ENSMUSG00000056069	Fam105a	9830126M18	family with sequence similarity 105, member A	protein-coding
mm_66366.1	chr7	43533178	43533191	-	1	NA	promoter-TSS (NM_001111058)	promoter-TSS (NM_001111058)	-13	NM_021293	12489	Mm.140157	NM_021293	ENSMUSG00000004609	Cd33	Siglec-3|gp67	CD33 antigen	protein-coding
mm_122371.1	chr14	39472903	39472956	-	1	NA	non-coding (NR_131973, exon 1 of 1)	non-coding (NR_131973, exon 1 of 1)	159	NM_001190187	18183	Mm.258705	NM_008734	ENSMUSG00000041014	Nrg3	ska	neuregulin 3	protein-coding
mm_2765.1	chr1	130551007	130551021	+	1	NA	Intergenic	Intergenic	78592	NM_009581	22789	Mm.4644	NM_009581	ENSMUSG00000042554	Zp3r	AV264399|SP56	zona pellucida 3 receptor	protein-coding
mm_81773.1	chr9	114515714	114515750	+	1	NA	intron (NM_001042503, intron 3 of 3)	intron (NM_001042503, intron 3 of 3)	-19188	NM_009916	12773	Mm.1337	NM_009916	ENSMUSG00000047898	Ccr4	C-C CKR-4|CHEMR1|Cmkbr4|LESTR|Sdf1r	chemokine (C-C motif) receptor 4	protein-coding
mm_91592.1	chr10	40348639	40348677	-	1	NA	promoter-TSS (NM_001168304)	promoter-TSS (NM_001168304)	-650	NM_001291817	78334	Mm.200924	NM_198164	ENSMUSG00000038481	Cdk19	2700084L06Rik|AI845279|AW228747|CDK11|Cdc2l6|mKIAA1028	cyclin-dependent kinase 19	protein-coding
mm_125348.1	chr15	39198108	39198123	+	1	NA	promoter-TSS (NM_053271)	promoter-TSS (NM_053271)	-171	NM_001256382	116838	Mm.309296	NM_053271	ENSMUSG00000037386	Rims2	2810036I15Rik|AW048769|RIM2|Rab3ip2|Rim2(+40A)|Rim2(+44A)|Rim2(+4A)|Serg2|Syt3-rs|mKIAA0751	regulating synaptic membrane exocytosis 2	protein-coding
mm_147052.1	chr18	34932017	34932020	-	1	NA	promoter-TSS (NM_144866)	promoter-TSS (NM_144866)	-15	NM_144866	225363	Mm.329353	NM_144866	ENSMUSG00000024360	Etf1	AI463371|D6Ertd109e|ERF|ERF1|SUP45L1|TB3-1	eukaryotic translation termination factor 1	protein-coding
mm_84615.1	chr9	70457884	70457899	-	1	NA	exon (NM_033604, exon 6 of 15)	exon (NM_033604, exon 6 of 15)	-36337	NM_007630	12442	Mm.22592	NM_007630	ENSMUSG00000032218	Ccnb2	CycB2	cyclin B2	protein-coding
mm_152742.1	chr19	19050952	19050954	-	1	NA	intron (NM_001043354, intron 1 of 9)	intron (NM_001043354, intron 1 of 9)	-49836	NM_001289921	225998	Mm.234641	NM_146095	ENSMUSG00000036192	Rorb	Nr1f2|RZR-beta|RZRB|Rorbeta|hstp	RAR-related orphan receptor beta	protein-coding
mm_123167.1	chr14	57328381	57328381	-	1	NA	intron (NM_030004, intron 3 of 7)	B1_Mus1|SINE|Alu	70102	NM_030004	68631	Mm.25539	NM_030004	ENSMUSG00000021947	Cryl1	1110025H08Rik|A230106J09Rik|C85932|gul3dh	crystallin, lambda 1	protein-coding
mm_134621.1	chr16	21369734	21369763	-	1	NA	Intergenic	Intergenic	-36392	NR_131983	76222	Mm.86031	NR_131983		Magef1	6430590I03Rik	melanoma antigen family F, 1	pseudo
mm_7953.1	chr1	133915415	133915421	-	1	NA	5' UTR (NM_054077, exon 2 of 3)	5' UTR (NM_054077, exon 2 of 3)	5983	NM_054077	116847	Mm.214514	NM_054077	ENSMUSG00000041577	Prelp	7330409J17Rik|SLRR2A	proline arginine-rich end leucine-rich repeat	protein-coding
mm_166287.1	chr5	98167366	98167408	+	1	NA	Intergenic	CpG	-13482	NM_029947	77630	Mm.332511	NM_029947	ENSMUSG00000035456	Prdm8	4930565F05Rik|PFM5	PR domain containing 8	protein-coding
mm_103350.1	chr11	74829892	74829902	-	1	NA	Intergenic	Intergenic	-1027	NM_010813	17428	Mm.3759	NM_010813	ENSMUSG00000000282	Mnt	Rox|bHLHd3	max binding protein	protein-coding
mm_20663.1	chr2	132118765	132118775	-	1	NA	intron (NM_018824, intron 1 of 15)	intron (NM_018824, intron 1 of 15)	26338	NM_018824	54338	Mm.103581	NM_018824	ENSMUSG00000027340	Slc23a2	AI844736|NBTL1|SVCT2|Slc23a1|YSPL2|YSPL3|mKIAA0238	solute carrier family 23 (nucleobase transporters), member 2	protein-coding
mm_48440.1	chr5	140629465	140629483	-	1	NA	exon (NM_175274, exon 11 of 14)	exon (NM_175274, exon 11 of 14)	19557	NM_001308040	78339	Mm.28947	NM_175274	ENSMUSG00000036565	Ttyh3	2900029G13Rik|AI414930|TTY3|mTTY3	tweety family member 3	protein-coding
mm_89002.1	chr10	81620548	81620558	+	1	NA	Intergenic	Intergenic	6769	NM_001163430	50721	Mm.25643	NM_181586	ENSMUSG00000034748	Sirt6	2810449N18Rik|AI043036|Sir2l6	sirtuin 6	protein-coding
mm_89276.1	chr10	87861296	87861306	+	1	NA	5' UTR (NM_001111276, exon 1 of 4)	5' UTR (NM_001111276, exon 1 of 4)	190	NM_001111276	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_54426.1	chr6	33248876	33248894	-	1	NA	promoter-TSS (NM_009148)	promoter-TSS (NM_009148)	-205	NM_001347089	20336	Mm.265512	NM_009148	ENSMUSG00000029763	Exoc4	C78892|Sec8|Sec8l1	exocyst complex component 4	protein-coding
mm_144716.1	chr18	35118908	35118926	+	1	NA	promoter-TSS (NM_009818)	promoter-TSS (NM_009818)	5	NM_009818	12385	Mm.18962	NM_009818	ENSMUSG00000037815	Ctnna1	2010010M04Rik|AA517462|AI988031|Catna1	catenin (cadherin associated protein), alpha 1	protein-coding
mm_5036.1	chr1	193326004	193326006	+	1	NA	exon (NM_001277928, exon 8 of 23)	exon (NM_001277928, exon 8 of 23)	23762	NM_001277928	16780	Mm.435441	NM_008484	ENSMUSG00000026639	Lamb3	-	laminin, beta 3	protein-coding
mm_51485.1	chr6	83053874	83053893	+	1	NA	promoter-TSS (NR_125891)	promoter-TSS (NR_125891)	-638	NR_125891	11993	Mm.386752	NM_007517	ENSMUSG00000068328	Aup1	AA589454	ancient ubiquitous protein 1	protein-coding
mm_138918.1	chr17	43607260	43607335	+	1	NA	exon (NM_013737, exon 10 of 12)	exon (NM_013737, exon 10 of 12)	-15788	NR_045444	73504	Mm.9277	NR_045444	ENSMUSG00000090307	1700071M16Rik	-	RIKEN cDNA 1700071M16 gene	ncRNA
mm_111422.1	chr12	91589954	91589968	-	1	NA	promoter-TSS (NM_031391)	promoter-TSS (NM_031391)	-312	NM_031391	83602	Mm.275728	NM_031391	ENSMUSG00000020962	Gtf2a1	6330549H03Rik|AA536742|AA959775|AW060250|TfIIAa/b|Tfiia1	general transcription factor II A, 1	protein-coding
mm_85029.1	chr9	88463013	88463024	-	1	NA	exon (NM_001284328, exon 8 of 12)	exon (NM_001284328, exon 8 of 12)	19379	NM_019666	56403	Mm.260545	NM_019666	ENSMUSG00000032423	Syncrip	2610109K23Rik|4632417O19Rik|GRY-RBP|Nsap1|Nsap1l|hnRNP Q|pp68	synaptotagmin binding, cytoplasmic RNA interacting protein	protein-coding
mm_148015.1	chr18	68300330	68300336	-	1	NA	promoter-TSS (NM_026440)	promoter-TSS (NM_026440)	0	NM_153794	108654	Mm.125857	NM_153794	ENSMUSG00000038121	Fam210a	4933403F05Rik|AA987140|AV134576|AW491926	family with sequence similarity 210, member A	protein-coding
mm_170840.1	chr2	177294430	177294441	+	1	NA	Intergenic	Intergenic	-170307	NM_001177568	628308	Mm.460436	NM_001177568	ENSMUSG00000078866	Zfp970	Gm14420|OTTMUSG00000016588	zinc finger protein 970	protein-coding
mm_32868.1	chr4	118429742	118429764	+	1	NA	promoter-TSS (NM_001039176)	promoter-TSS (NM_001039176)	52	NM_001039176	54325	Mm.282096	NM_019422	ENSMUSG00000006390	Elovl1	AA407424|BB151133|Ssc1	elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 1	protein-coding
mm_1284.1	chr1	64088191	64088197	+	1	NA	intron (NM_033563, intron 1 of 3)	intron (NM_033563, intron 1 of 3)	33195	NM_033563	93691	Mm.29466	NM_033563	ENSMUSG00000025959	Klf7	9830124P08Rik	Kruppel-like factor 7 (ubiquitous)	protein-coding
mm_164241.1	chr15	94137759	94137793	-	1	NA	Intergenic	Intergenic	-109426	NR_045629	328594	Mm.135523	NR_045629		D630010B17Rik	Gm811	RIKEN cDNA D630010B17 gene	ncRNA
mm_34831.1	chr4	155235487	155235522	+	1	NA	Intergenic	Intergenic	-12969	NM_011385	20481	Mm.28520	NM_011385	ENSMUSG00000029050	Ski	2310012I02Rik|2610001A11Rik|AA062172|AA589460|BC004088	ski sarcoma viral oncogene homolog (avian)	protein-coding
mm_105926.1	chr11	115066653	115066669	-	1	NA	Intergenic	Intergenic	-4622	NM_172050	217306	Mm.222667	NM_172050	ENSMUSG00000048498	Cd300e	BC034097|CLM2|Cd300le|TREM5	CD300E molecule	protein-coding
mm_69438.1	chr7	132910959	132910967	-	1	NA	Intergenic	Intergenic	-38659	NM_207302	360216	Mm.389984	NM_207302	ENSMUSG00000030967	Zranb1	9330160G10Rik|D7Wsu87e|Gm1956|Trabid	zinc finger, RAN-binding domain containing 1	protein-coding
mm_14396.1	chr2	129832070	129832075	+	1	NA	3' UTR (NM_183262, exon 4 of 4)	3' UTR (NM_183262, exon 4 of 4)	-30613	NR_029452	654409	Mm.305555	NR_029452		4932416H05Rik	-	RIKEN cDNA 4932416H05 gene	ncRNA
mm_153011.1	chr19	30549517	30549520	-	1	NA	promoter-TSS (NM_010051)	promoter-TSS (NM_010051)	-22	NM_010051	13380	Mm.214717	NM_010051	ENSMUSG00000024868	Dkk1	mdkk-1	dickkopf WNT signaling pathway inhibitor 1	protein-coding
mm_172135.1	chr6	35118301	35118310	-	1	NA	intron (NM_016877, intron 1 of 10)	U2|snRNA|snRNA	15432	NM_001164412	53621	Mm.214525	NM_016877	ENSMUSG00000038784	Cnot4	Not4|Not4h|Not4hp	CCR4-NOT transcription complex, subunit 4	protein-coding
mm_40349.1	chr5	45670005	45670006	+	1	NA	promoter-TSS (NM_019438)	promoter-TSS (NM_019438)	80	NM_019438	54392	Mm.32012	NM_019438	ENSMUSG00000015880	Ncapg	5730507H05Rik|Hcapg|MFT.M05.13	non-SMC condensin I complex, subunit G	protein-coding
mm_69247.1	chr7	127824470	127824580	-	1	NA	promoter-TSS (NM_024414)	promoter-TSS (NM_024414)	6	NM_024414	56216	Mm.439759	NM_024414	ENSMUSG00000030806	Stx1b	Stx1b2|Stx1bl|Syn1b	syntaxin 1B	protein-coding
mm_102453.1	chr11	59810027	59810044	-	1	NA	promoter-TSS (NM_001271357)	promoter-TSS (NM_001271357)	4	NM_001271356	216805	Mm.339640	NM_146018	ENSMUSG00000032633	Flcn	AU014660|B430214A04Rik|Bhd|FLCL	folliculin	protein-coding
mm_5080.1	chr1	4409224	4409240	-	1	NA	promoter-TSS (NM_001195662)	promoter-TSS (NM_001195662)	9	NM_001195662	19888	Mm.294263	NM_011283	ENSMUSG00000025900	Rp1	Dcdc3|Orp1|Rp1h|mG145	retinitis pigmentosa 1 (human)	protein-coding
mm_166667.1	chr6	90754981	90754997	-	1	NA	intron (NM_001134384, intron 1 of 13)	intron (NM_001134384, intron 1 of 13)	-38460	NM_001134383	232227	Mm.196943	NM_182784	ENSMUSG00000034312	Iqsec1	AW561907|BC026481|BRAG2|D6Ertd349e|cI-43	IQ motif and Sec7 domain 1	protein-coding
mm_137895.1	chr17	31681319	31681331	+	1	NA	3' UTR (NM_001278570, exon 3 of 3)	3' UTR (NM_001278570, exon 3 of 3)	3394	NM_001278570	12954	Mm.1228	NM_013501	ENSMUSG00000024041	Cryaa	Acry-1|Crya-1|Crya1|DAcry-1|lop18	crystallin, alpha A	protein-coding
mm_96186.1	chr11	61684079	61684096	+	1	NA	promoter-TSS (NM_178618)	promoter-TSS (NM_178618)	-323	NM_178618	69640	Mm.458559	NM_178618	ENSMUSG00000042377	Fam83g	2310040C09Rik|AI506990|wly	family with sequence similarity 83, member G	protein-coding
mm_159785.1	chr5	107331103	107331103	+	1	NA	promoter-TSS (NM_054054)	promoter-TSS (NM_054054)	-91	NM_001079873	114642	Mm.182836	NM_054054	ENSMUSG00000029279	Brdt	7420412D09Rik|Brd6|Fsrg3	bromodomain, testis-specific	protein-coding
mm_143226.1	chr17	63312957	63312963	-	1	NA	promoter-TSS (NR_130176)	promoter-TSS (NR_130176)	13	NR_130176	414079	Mm.444282	NR_130176	ENSMUSG00000090565	4930405O22Rik	-	RIKEN cDNA 4930405O22 gene	ncRNA
mm_26496.1	chr3	145576455	145576492	+	1	NA	exon (NM_001081094, exon 1 of 10)	exon (NM_001081094, exon 1 of 10)	257	NM_001346521	229937	Mm.24586	NM_001081094	ENSMUSG00000074182	Znhit6	2410019A14Rik	zinc finger, HIT type 6	protein-coding
mm_94991.1	chr11	31871503	31871513	+	1	NA	5' UTR (NM_026252, exon 1 of 10)	5' UTR (NM_026252, exon 1 of 10)	568	NM_026252	67579	Mm.339792	NM_026252	ENSMUSG00000020300	Cpeb4	Cpe-bp4|Cpeb-4|mCPEB-4	cytoplasmic polyadenylation element binding protein 4	protein-coding
mm_112894.1	chr13	20885283	20885292	+	1	NA	intron (NM_012054, intron 4 of 20)	MLT1D|LTR|ERVL-MaLR	91174	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_121036.1	chr14	79898442	79898448	+	1	NA	Intergenic	Intergenic	-29269	NR_033535	100038734	Mm.387484	NR_033535		Gm10845	ENSMUSG00000075496	predicted gene 10845	ncRNA
mm_158521.1	chrX	143827379	143827386	-	1	NA	promoter-TSS (NM_007603)	promoter-TSS (NM_007603)	30	NM_007603	12338	Mm.30290	NM_007603	ENSMUSG00000067276	Capn6	-	calpain 6	protein-coding
mm_57119.1	chr6	122596808	122596833	-	1	NA	intron (NM_001134391, intron 2 of 7)	intron (NM_001134391, intron 2 of 7)	5624	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_5739.1	chr1	45345045	45345061	-	1	NA	exon (NM_009930, exon 47 of 51)	exon (NM_009930, exon 47 of 51)	33515	NM_009930	12825	Mm.249555	NM_009930	ENSMUSG00000026043	Col3a1	AW550625|Col3a-1|Tsk-2|Tsk2	collagen, type III, alpha 1	protein-coding
mm_95078.1	chr11	32674488	32674491	+	1	NA	intron (NM_001271349, intron 1 of 11)	intron (NM_001271349, intron 1 of 11)	31934	NM_001271347	103583	Mm.28017	NM_134015	ENSMUSG00000020271	Fbxw11	2310065A07Rik|AA536858|BTRC2|BTRCP2|Fbxw1b|HOS	F-box and WD-40 domain protein 11	protein-coding
mm_155417.1	chrX	73490850	73490875	+	1	NA	exon (NM_007542, exon 2 of 8)	exon (NM_007542, exon 2 of 8)	7261	NM_007542	12111	Mm.2608	NM_007542	ENSMUSG00000031375	Bgn	BG|DSPG1|PG-S1|PGI|SLRR1A	biglycan	protein-coding
mm_33950.1	chr4	137424860	137424870	+	1	NA	exon (NM_026419, exon 4 of 8)	exon (NM_026419, exon 4 of 8)	5655	NM_026419	67868	Mm.297477	NM_026419	ENSMUSG00000023433	Cela3b	0910001F22Rik|2310074F01Rik|AI504000|Ela3|Ela3b	chymotrypsin-like elastase family, member 3B	protein-coding
mm_62428.1	chr7	101348141	101348149	+	1	NA	promoter-TSS (NM_001040111)	promoter-TSS (NM_001040111)	76	NM_001040111	69710	Mm.277687	NM_027180	ENSMUSG00000032812	Arap1	2410002L19Rik|Centd2|mKIAA0782	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	protein-coding
mm_153217.1	chr19	34747435	34747449	-	1	NA	promoter-TSS (NM_172838)	promoter-TSS (NM_172838)	-331	NM_172838	240638	Mm.74636	NM_172838	ENSMUSG00000009378	Slc16a12	3230401A21|AW210596	solute carrier family 16 (monocarboxylic acid transporters), member 12	protein-coding
mm_79942.1	chr9	65914331	65914331	+	1	NA	intron (NM_173185, intron 1 of 13)	intron (NM_173185, intron 1 of 13)	5321	NM_173185	214897	Mm.325816	NM_173185	ENSMUSG00000032384	Csnk1g1	9130020E21Rik	casein kinase 1, gamma 1	protein-coding
mm_132553.1	chr16	37883872	37883902	+	1	NA	3' UTR (NM_177093, exon 4 of 4)	3' UTR (NM_177093, exon 4 of 4)	15487	NM_177093	320184	Mm.390882	NM_177093	ENSMUSG00000034158	Lrrc58	1810012N18Rik|C330018J07Rik	leucine rich repeat containing 58	protein-coding
mm_79203.1	chr9	48817578	48817582	+	1	NA	intron (NM_001033324, intron 2 of 6)	intron (NM_001033324, intron 2 of 6)	18365	NM_001033324	235320	Mm.457803	NM_001033324	ENSMUSG00000066687	Zbtb16	AI467657|PLZF|Zfp145|lu	zinc finger and BTB domain containing 16	protein-coding
mm_145642.1	chr18	61117662	61117672	+	1	NA	TTS (NR_105949)	TTS (NR_105949)	199	NR_105949	102466212		NR_105949	ENSMUSG00000098389	Mir6983	Gm27496|mmu-mir-6983	microRNA 6983	ncRNA
mm_13441.1	chr2	105126827	105126833	+	1	NA	promoter-TSS (NR_015462)	promoter-TSS (NR_015462)	301	NM_144783	22431	Mm.389339	NM_144783	ENSMUSG00000016458	Wt1	D630046I19Rik|Wt-1	Wilms tumor 1 homolog	protein-coding
mm_64528.1	chr7	143978929	143978965	+	1	NA	intron (NR_037302, intron 5 of 5)	CpG	-30307	NR_037292	100526562		NR_037292	ENSMUSG00000093221	Mir3105	mmu-mir-3105	microRNA 3105	ncRNA
mm_16955.1	chr2	17390891	17390899	-	1	NA	intron (NM_028757, intron 4 of 6)	intron (NM_028757, intron 4 of 6)	-172619	NR_105847	102465964		NR_105847	ENSMUSG00000099161	Mir6419	Gm27713|mmu-mir-6419	microRNA 6419	ncRNA
mm_84595.1	chr9	70037952	70037960	-	1	NA	intron (NM_028087, intron 1 of 2)	intron (NM_028087, intron 1 of 2)	132	NM_028087	72077	Mm.195555	NM_028087	ENSMUSG00000032226	Gcnt3	2010013H22Rik|2210021I22Rik|2210401J11Rik	glucosaminyl (N-acetyl) transferase 3, mucin type	protein-coding
mm_67383.1	chr7	79842318	79842328	-	1	NA	promoter-TSS (NM_008486)	promoter-TSS (NM_008486)	29	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_20743.1	chr2	140019459	140019464	-	1	NA	intron (NR_110352, intron 3 of 12)	intron (NR_110352, intron 3 of 12)	47344	NM_001159640	75812	Mm.293449	NM_175225	ENSMUSG00000039033	Tasp1	4930485D02Rik|AW986064	taspase, threonine aspartase 1	protein-coding
mm_41955.1	chr5	105816658	105816663	+	1	NA	Intergenic	(T)n|Simple_repeat|Simple_repeat	-59908	NR_030777	54367	Mm.248876	NM_018759	ENSMUSG00000029290	Zfp326	5730470H14Rik|ZAN75|Znf326	zinc finger protein 326	protein-coding
mm_2272.1	chr1	91250298	91250310	+	1	NA	promoter-TSS (NM_026454)	promoter-TSS (NM_026454)	-15	NM_026454	67921	Mm.337238	NM_026454	ENSMUSG00000034343	Ube2f	2510010F15Rik|AI851109	ubiquitin-conjugating enzyme E2F (putative)	protein-coding
mm_155515.1	chrX	74204915	74204926	+	1	NA	exon (NM_031379, exon 10 of 13)	exon (NM_031379, exon 10 of 13)	27661	NM_031379	83553	Mm.25057	NM_031379	ENSMUSG00000031397	Tktl1	C79967	transketolase-like 1	protein-coding
mm_146468.1	chr18	87756281	87756288	+	1	NA	Intergenic	Intergenic	1044219	NM_172633	12405	Mm.70775	NM_172633	ENSMUSG00000024647	Cbln2	6330593N19Rik|A730004O05	cerebellin 2 precursor protein	protein-coding
mm_116569.1	chr13	47098242	47098276	-	1	NA	exon (NM_025900, exon 7 of 11)	exon (NM_025900, exon 7 of 11)	7962	NM_025900	110052	Mm.131150	NM_025900	ENSMUSG00000021377	Dek	1810019E15Rik|D13H6S231E	DEK oncogene (DNA binding)	protein-coding
mm_22726.1	chr3	19644518	19644529	+	1	NA	promoter-TSS (NM_001081281)	promoter-TSS (NM_001081281)	63	NM_001081281	381485	Mm.35419	NM_001081281	ENSMUSG00000060913	Trim55	D830041C10Rik|Murf2|Rnf29	tripartite motif-containing 55	protein-coding
mm_91936.1	chr10	60724336	60724357	-	1	NA	intron (NM_023596, intron 3 of 5)	intron (NM_023596, intron 3 of 5)	-27856	NM_023370	22295	Mm.440327	NM_023370	ENSMUSG00000012819	Cdh23	4930542A03Rik|USH1D|ahl|ahl1|bob|bus|mdfw|nmf112|nmf181|nmf252|sals|v	cadherin 23 (otocadherin)	protein-coding
mm_43081.1	chr5	124447148	124447158	+	1	NA	intron (NM_001310727, intron 1 of 6)	intron (NM_001310727, intron 1 of 6)	449	NM_001310727	67956	Mm.137966	NM_030241	ENSMUSG00000049327	Kmt5a	2410195B05Rik|AA617402|AW536475|PR-SET7|PR/SET07|Setd8	lysine methyltransferase 5A	protein-coding
mm_149009.1	chr19	8725095	8725097	+	1	NA	promoter-TSS (NR_004445)	promoter-TSS (NR_004445)	-770	NR_004445	100127111	Mm.292489	NR_004445	ENSMUSG00000065087	Snord22	Rnu22|U22	small nucleolar RNA, C/D box 22	snoRNA
mm_104427.1	chr11	94944626	94944641	-	1	NA	exon (NM_007742, exon 27 of 51)	exon (NM_007742, exon 27 of 51)	8409	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_151773.1	chr19	5295398	5295430	-	1	NA	promoter-TSS (NM_030109)	promoter-TSS (NM_030109)	41	NM_030109	319322	Mm.196532	NM_030109	ENSMUSG00000024853	Sf3b2	145kDa|2610311M13Rik|2810441F20Rik|B230398H18Rik|SAP145|SF3b1|SF3b145|SF3b150	splicing factor 3b, subunit 2	protein-coding
mm_106610.1	chr11	120807857	120807859	-	1	NA	exon (NM_007988, exon 43 of 43)	exon (NM_007988, exon 43 of 43)	-11463	NM_026824	68730	Mm.180622	NM_026824	ENSMUSG00000025155	Dus1l	1110032N12Rik	dihydrouridine synthase 1-like (S. cerevisiae)	protein-coding
mm_62599.1	chr7	105736645	105736698	+	1	NA	promoter-TSS (NM_025897)	promoter-TSS (NM_025897)	-54	NM_010562	16202	Mm.274846	NM_010562	ENSMUSG00000030890	Ilk	AA511515|ESTM24	integrin linked kinase	protein-coding
mm_66348.1	chr7	43518547	43518561	-	1	NA	Intergenic	Intergenic	-12616	NM_028737	74054	Mm.195732	NM_028737	ENSMUSG00000013353	4931406B18Rik	4930538L19Rik	RIKEN cDNA 4931406B18 gene	protein-coding
mm_144929.1	chr18	37707196	37707226	+	1	NA	promoter-TSS (NM_033589)	promoter-TSS (NM_033589)	-18	NM_033589	93714	Mm.247203	NM_033589	ENSMUSG00000103793	Pcdhga6	-	protocadherin gamma subfamily A, 6	protein-coding
mm_59755.1	chr7	28825302	28825314	+	1	NA	promoter-TSS (NM_016772)	promoter-TSS (NM_016772)	-30	NM_016772	51798	Mm.291776	NM_016772	ENSMUSG00000053898	Ech1	AA617331	enoyl coenzyme A hydratase 1, peroxisomal	protein-coding
mm_8921.1	chr1	163314439	163314464	-	1	NA	promoter-TSS (NM_175686)	promoter-TSS (NM_175686)	-801	NM_175686	18933	Mm.288642	NM_011127	ENSMUSG00000026586	Prrx1	A230024N07Rik|AA755424|AI385634|AI843499|K-2|Pmx|Pmx1|Prx1|mHox	paired related homeobox 1	protein-coding
mm_112320.1	chr12	115194120	115194126	-	1	NA	Intergenic	Intergenic	501671	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
mm_141821.1	chr17	34615966	34615978	-	1	NA	promoter-TSS (NM_152922)	promoter-TSS (NM_152922)	-1	NM_152922	81701	Mm.231343	NM_152922	ENSMUSG00000015467	Egfl8	Ng3	EGF-like domain 8	protein-coding
mm_147243.1	chr18	38349940	38349946	-	1	NA	Intergenic	Intergenic	-10950	NM_011937	26384	Mm.22374	NM_011937	ENSMUSG00000052102	Gnpda1	GNPDA|Gnp1|Gnpi|oscillin	glucosamine-6-phosphate deaminase 1	protein-coding
mm_8724.1	chr1	160047511	160047517	-	1	NA	intron (NM_001162896, intron 1 of 2)	intron (NM_001162896, intron 1 of 2)	3134	NM_001162896	67647	Mm.171518	NM_001024470	ENSMUSG00000090394	4930523C07Rik	-	RIKEN cDNA 4930523C07 gene	protein-coding
mm_135280.1	chr16	38447447	38447490	-	1	NA	exon (NM_007414, exon 3 of 4)	exon (NM_007414, exon 3 of 4)	5221	NM_007414	11544	Mm.20047	NM_007414	ENSMUSG00000002844	Adprh	Arh1	ADP-ribosylarginine hydrolase	protein-coding
mm_167951.1	chrX	139807511	139807512	+	1	NA	intron (NM_016675, intron 1 of 1)	B3|SINE|B2	6703	NM_016675	12738	Mm.117068	NM_016675	ENSMUSG00000047230	Cldn2	AL022813	claudin 2	protein-coding
mm_86093.1	chr9	115035026	115035031	-	1	NA	Intergenic	Intergenic	-32251	NM_148958	74486	Mm.458474	NM_148958	ENSMUSG00000040875	Osbpl10	4933433D06Rik|C820004B04Rik|OPR-10|ORP-10	oxysterol binding protein-like 10	protein-coding
mm_56928.1	chr6	119480460	119480494	-	1	NA	exon (NM_133940, exon 1 of 1)	exon (NM_133940, exon 1 of 1)	809	NM_133940	101358	Mm.125477	NM_133940	ENSMUSG00000030019	Fbxl14	AW322056|Fbx14l	F-box and leucine-rich repeat protein 14	protein-coding
mm_43453.1	chr5	136171560	136171584	+	1	NA	promoter-TSS (NM_178751)	promoter-TSS (NM_178751)	-916	NM_178751	269717	Mm.308396	NM_178751	ENSMUSG00000039747	Orai2	A730041O15Rik|Tmem142b	ORAI calcium release-activated calcium modulator 2	protein-coding
mm_48092.1	chr5	137032411	137032442	-	1	NA	exon (NM_001039385, exon 2 of 2)	exon (NM_001039385, exon 2 of 2)	2131	NM_001039385	381677	Mm.389697	NM_001039385	ENSMUSG00000037428	Vgf	Gm1052	VGF nerve growth factor inducible	protein-coding
mm_71257.1	chr8	40917583	40917593	+	1	NA	3' UTR (NM_001044740, exon 12 of 12)	3' UTR (NM_001044740, exon 12 of 12)	-8645	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_138879.1	chr17	43360364	43360382	+	1	NA	Intergenic	Intergenic	-29093	NM_001081178	224792	Mm.23478	NM_001081178	ENSMUSG00000056492	Adgrf5	8430401C09Rik|9330185D23|AI528491|Gpr116|mKIAA0758	adhesion G protein-coupled receptor F5	protein-coding
mm_25793.1	chr3	127545084	127545098	+	1	NA	promoter-TSS (NR_029653)	promoter-TSS (NR_029653)	-137	NR_030403	723948		NR_030403	ENSMUSG00000076252	Mir302b	Mirn302b|mir-302b	microRNA 302b	ncRNA
mm_167402.1	chr8	103590942	103590943	-	1	NA	Intergenic	Lx5|LINE|L1	-12857	NR_045730	71058	Mm.67707	NR_045730	ENSMUSG00000110336	4933400L20Rik	-	RIKEN cDNA 4933400L20 gene	ncRNA
mm_24801.1	chr3	95550126	95550129	+	1	NA	exon (NM_021281, exon 7 of 8)	exon (NM_021281, exon 7 of 8)	-9550	NM_026489	67981	Mm.179050	NM_026489	ENSMUSG00000028109	Hormad1	4921522K05Rik|Nohma	HORMA domain containing 1	protein-coding
mm_104504.1	chr11	95961680	95961683	-	1	NA	3' UTR (NM_009951, exon 15 of 15)	3' UTR (NM_009951, exon 15 of 15)	1702	NR_037223	100526468		NR_037223	ENSMUSG00000093358	Mir3063	mmu-mir-3063	microRNA 3063	ncRNA
mm_13026.1	chr2	91044941	91044967	+	1	NA	exon (NM_009023, exon 7 of 8)	exon (NM_009023, exon 7 of 8)	-9062	NM_008948	19182	Mm.289832	NM_008948	ENSMUSG00000002102	Psmc3	TBP-1	proteasome (prosome, macropain) 26S subunit, ATPase 3	protein-coding
mm_159480.1	chr4	35152029	35152029	+	1	NA	promoter-TSS (NM_199157)	promoter-TSS (NM_199157)	-26	NM_199157	387510	Mm.386929	NM_199157	ENSMUSG00000042993	Ifnk	-	interferon kappa	protein-coding
mm_53985.1	chr6	6869490	6869503	-	1	NA	promoter-TSS (NR_015388)	promoter-TSS (NR_015388)	37	NR_015388	320038	Mm.94021	NR_015388		Dlx6os1	A230055N17Rik|Dlx6as1|Evf-1|Evf-2|Evf1|Evf1/2|Evf2|Shhrs|mEvf-1	distal-less homeobox 6, opposite strand 1	ncRNA
mm_113642.1	chr13	42149353	42149355	+	1	NA	intron (NM_007772, intron 3 of 8)	B4A|SINE|B4	97333	NM_007772	110521	Mm.4808	NM_007772	ENSMUSG00000021366	Hivep1	Cryabp1	human immunodeficiency virus type I enhancer binding protein 1	protein-coding
mm_130766.1	chr15	101373733	101373733	-	1	NA	Intergenic	Intergenic	-3608	NM_028770	74127	Mm.440055	NM_028770	ENSMUSG00000037185	Krt80	1200016G03Rik|2310041I20Rik|Kb20	keratin 80	protein-coding
mm_159756.1	chr5	88487961	88487961	+	1	NA	promoter-TSS (NM_017468)	promoter-TSS (NM_017468)	-14	NM_017468	13801	Mm.8014	NM_017468	ENSMUSG00000029286	Enam	abte	enamelin	protein-coding
mm_112927.1	chr13	20956714	20956727	+	1	NA	intron (NM_012054, intron 12 of 20)	B4A|SINE|B4	116579	NM_146535	258528	Mm.377554	NM_146535	ENSMUSG00000042869	Olfr1370	MOR256-14	olfactory receptor 1370	protein-coding
mm_6092.1	chr1	63214248	63214264	-	1	NA	promoter-TSS (NM_146250)	promoter-TSS (NM_146250)	25	NM_146250	241070	Mm.103354	NM_146250	ENSMUSG00000046856	Gpr1	-	G protein-coupled receptor 1	protein-coding
mm_82926.1	chr9	35117695	35117757	-	1	NA	promoter-TSS (NM_009178)	promoter-TSS (NM_009178)	-916	NM_009178	20443	Mm.275973	NM_009178	ENSMUSG00000032038	St3gal4	Siat4c	ST3 beta-galactoside alpha-2,3-sialyltransferase 4	protein-coding
mm_142431.1	chr17	45570326	45570382	-	1	NA	exon (NM_008302, exon 6 of 11)	exon (NM_008302, exon 6 of 11)	2907	NM_008302	15516	Mm.2180	NM_008302	ENSMUSG00000023944	Hsp90ab1	90kDa|AL022974|C81438|Hsp84|Hsp84-1|Hsp90|Hspcb	heat shock protein 90 alpha (cytosolic), class B member 1	protein-coding
mm_133713.1	chr16	93607817	93607829	+	1	NA	promoter-TSS (NM_007620)	promoter-TSS (NM_007620)	-14	NM_007620	12408	Mm.26940	NM_007620	ENSMUSG00000051483	Cbr1	AW261796|CR|Cbr	carbonyl reductase 1	protein-coding
mm_74746.1	chr8	18991029	18991041	-	1	NA	promoter-TSS (NM_181683)	promoter-TSS (NM_181683)	20	NM_181683	353320	Mm.270483	NM_181683	ENSMUSG00000053695	Defb37	BD-37	defensin beta 37	protein-coding
mm_88818.1	chr10	80802399	80802403	+	1	NA	exon (NM_013651, exon 4 of 9)	exon (NM_013651, exon 4 of 9)	-2847	NM_007445	11705	Mm.376094	NM_007445	ENSMUSG00000035262	Amh	MIS	anti-Mullerian hormone	protein-coding
mm_82569.1	chr9	21078635	21078658	-	1	NA	intron (NR_038081, intron 9 of 16)	B4|SINE|B4	-3058	NR_106050	102465656		NR_106050	ENSMUSG00000098907	Mir7082	Gm27933|mmu-mir-7082	microRNA 7082	ncRNA
mm_25213.1	chr3	103846808	103846818	+	1	NA	intron (NM_001142960, intron 3 of 3)	intron (NM_001142960, intron 3 of 3)	-12982	NR_104070	19260	Mm.395	NM_008979	ENSMUSG00000027843	Ptpn22	70zpep|PEP|Ptpn8	protein tyrosine phosphatase, non-receptor type 22 (lymphoid)	protein-coding
mm_53986.1	chr6	6869518	6869539	-	1	NA	promoter-TSS (NR_015388)	promoter-TSS (NR_015388)	5	NR_015388	320038	Mm.94021	NR_015388		Dlx6os1	A230055N17Rik|Dlx6as1|Evf-1|Evf-2|Evf1|Evf1/2|Evf2|Shhrs|mEvf-1	distal-less homeobox 6, opposite strand 1	ncRNA
mm_3397.1	chr1	143641297	143641310	+	1	NA	5' UTR (NM_020025, exon 1 of 2)	5' UTR (NM_020025, exon 1 of 2)	606	NM_020025	26878	Mm.285580	NM_020025	ENSMUSG00000033849	B3galt2	-	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 2	protein-coding
mm_157607.1	chrX	53670509	53670540	-	1	NA	promoter-TSS (NM_001018063)	promoter-TSS (NM_001018063)	-116	NM_001018063	553127	Mm.328602	NM_001018063	ENSMUSG00000067924	Cxx1b	Mart8c	CAAX box 1B	protein-coding
mm_82747.1	chr9	26804446	26804457	-	1	NA	intron (NM_153803, intron 1 of 19)	intron (NM_153803, intron 1 of 19)	1966	NM_153803	244757	Mm.293696	NM_153803	ENSMUSG00000036395	Glb1l2	-	galactosidase, beta 1-like 2	protein-coding
mm_37327.1	chr4	119492548	119492561	-	1	NA	promoter-TSS (NM_177572)	promoter-TSS (NM_177572)	44	NM_177572	194237	Mm.206201	NM_177572	ENSMUSG00000048899	Rimkla	B930030J24|NAAGS|NAAGS-II|Rimk	ribosomal modification protein rimK-like family member A	protein-coding
mm_126354.1	chr15	79932885	79932897	+	1	NA	promoter-TSS (NM_144811)	promoter-TSS (NM_144811)	-245	NM_144811	52609	Mm.323442	NM_144811	ENSMUSG00000053411	Cbx7	1600014J01Rik|AI851678|D15Ertd417e	chromobox 7	protein-coding
mm_143864.1	chr17	84186635	84186655	-	1	NA	exon (NM_001001806, exon 2 of 2)	exon (NM_001001806, exon 2 of 2)	1302	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_25891.1	chr3	131110351	131110357	+	1	NA	promoter-TSS (NM_001276402)	promoter-TSS (NM_001276402)	57	NM_001276402	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_55812.1	chr6	83033337	83033347	-	1	NA	promoter-TSS (NM_013586)	promoter-TSS (NM_013586)	129	NM_010070	13448	Mm.156	NM_010070	ENSMUSG00000068335	Dok1	AW557123|p62DOK	docking protein 1	protein-coding
mm_104642.1	chr11	97536935	97536944	-	1	NA	intron (NM_018873, intron 5 of 19)	intron (NM_018873, intron 5 of 19)	-36599	NM_001289118	100141474	Mm.482426	NM_001289118	ENSMUSG00000047988	4933428G20Rik	-	RIKEN cDNA 4933428G20 gene	protein-coding
mm_39263.1	chr5	3571591	3571610	+	1	NA	promoter-TSS (NM_029843)	promoter-TSS (NM_029843)	-116	NM_029843	77036	Mm.389069	NM_029843	ENSMUSG00000008307	1700109H08Rik	-	RIKEN cDNA 1700109H08 gene	protein-coding
mm_29669.1	chr3	122619738	122619748	-	1	NA	promoter-TSS (NM_001114665)	promoter-TSS (NM_001114665)	-29	NM_153118	214459	Mm.209491	NM_153118	ENSMUSG00000039735	Fnbp1l	2610318I01Rik|AW548221|TOCA1|toca-1	formin binding protein 1-like	protein-coding
mm_97796.1	chr11	82951347	82951360	+	1	NA	promoter-TSS (NM_183201)	promoter-TSS (NM_183201)	-749	NM_183201	327978	Mm.42147	NM_183201	ENSMUSG00000054404	Slfn5	AI956840	schlafen 5	protein-coding
mm_31737.1	chr4	63152642	63152653	+	1	NA	exon (NM_007443, exon 2 of 10)	exon (NM_007443, exon 2 of 10)	1525	NM_007443	11699	Mm.2197	NM_007443	ENSMUSG00000028356	Ambp	AI194774|ASPI|HI-30|Intin4|Itil|UTI	alpha 1 microglobulin/bikunin	protein-coding
mm_69626.1	chr7	137314395	137314445	-	1	NA	promoter-TSS (NM_001113414)	promoter-TSS (NM_001113414)	25	NM_001113415	13593	Mm.258708	NM_010096	ENSMUSG00000010476	Ebf3	3110018A08Rik|O/E-2|mKIAA4201	early B cell factor 3	protein-coding
mm_92306.1	chr10	75150098	75150103	-	1	NA	intron (NM_001081412, intron 8 of 22)	RMER17C|LTR|ERVK	-61973	NM_153406	74392	Mm.27716	NM_153406	ENSMUSG00000033444	Specc1l	4930470P14Rik|4932439K10Rik|9530057A13Rik|AI317249|Cytsa|mKIAA0376	sperm antigen with calponin homology and coiled-coil domains 1-like	protein-coding
mm_67449.1	chr7	80396962	80396978	-	1	NA	exon (NM_001081454, exon 6 of 16)	exon (NM_001081454, exon 6 of 16)	5842	NM_011046	18550	Mm.5241	NM_011046	ENSMUSG00000030530	Furin	9130404I01Rik|Fur|PACE|Pcsk3|SPC1	furin (paired basic amino acid cleaving enzyme)	protein-coding
mm_20809.1	chr2	144331409	144331414	-	1	NA	promoter-TSS (NM_152947)	promoter-TSS (NM_152947)	-49	NM_152947	107586	Mm.252750	NM_026924	ENSMUSG00000037279	Ovol2	1700108N11Rik|1810007D21Rik|M-OVO|M-OVO-A|M-OVO-B|MOVO|Ovo2|Zfp339|movo2	ovo like zinc finger 2	protein-coding
mm_153338.1	chr19	38342647	38342654	-	1	NA	Intergenic	Intergenic	-53330	NM_175507	240660	Mm.262085	NM_175507	ENSMUSG00000044026	Slc35g1	AA590464|D330039I19Rik|Tmem20	solute carrier family 35, member G1	protein-coding
mm_153330.1	chr19	38124638	38124677	-	1	NA	intron (NM_001159487, intron 1 of 5)	CpG-7486	154	NM_011255	19662	Mm.2605	NM_011255	ENSMUSG00000024990	Rbp4	Rbp-4	retinol binding protein 4, plasma	protein-coding
mm_51722.1	chr6	86943244	86943251	+	1	NA	intron (NM_001040106, intron 4 of 20)	intron (NM_001040106, intron 4 of 20)	-66589	NM_001170591	56748	Mm.23809	NM_020045	ENSMUSG00000029993	Nfu1	0610006G17Rik|CGI-33|Hirip5	NFU1 iron-sulfur cluster scaffold	protein-coding
mm_18433.1	chr2	60842333	60842349	-	1	NA	exon (NM_001141932, exon 2 of 15)	exon (NM_001141932, exon 2 of 15)	39097	NM_001141932	56878	Mm.259667	NM_020296	ENSMUSG00000026970	Rbms1	2600014B10Rik|AI255215|MSSP-1|MSSP-2|MSSP-3|YC1	RNA binding motif, single stranded interacting protein 1	protein-coding
mm_118235.1	chr13	111490122	111490139	-	1	NA	promoter-TSS (NM_028487)	promoter-TSS (NM_028487)	-89	NM_001122963	73274	Mm.57286	NM_028487	ENSMUSG00000032745	Gpbp1	1700034P14Rik|AU019836|D230035M11Rik|Gpbp|mGPBP	GC-rich promoter binding protein 1	protein-coding
mm_77141.1	chr8	111536403	111536439	-	1	NA	promoter-TSS (NM_133206)	promoter-TSS (NM_133206)	-219	NM_001168622	170737	Mm.271578	NM_133206	ENSMUSG00000033545	Znrf1	B830022L21Rik|Rnf42|Zrfp1|nin283	zinc and ring finger 1	protein-coding
mm_12919.1	chr2	84937653	84937678	+	1	NA	5' UTR (NM_021398, exon 2 of 13)	5' UTR (NM_021398, exon 2 of 13)	1019	NM_021398	58207	Mm.290729	NM_021398	ENSMUSG00000027074	Slc43a3	Eeg1|SEEEG-1	solute carrier family 43, member 3	protein-coding
mm_78838.1	chr9	44326533	44326576	+	1	NA	promoter-TSS (NM_007875)	promoter-TSS (NM_007875)	-291	NM_007875	13478	Mm.18353	NM_007875	ENSMUSG00000032123	Dpagt1	AU021132|Dpagt2|GPT|Gnpta	dolichyl-phosphate (UDP-N-acetylglucosamine) acetylglucosaminephosphotransferase 1 (GlcNAc-1-P transferase)	protein-coding
mm_106747.1	chr12	3954944	3954957	+	1	NA	promoter-TSS (NM_008895)	promoter-TSS (NM_008895)	5	NM_001278583	18976	Mm.277996	NM_008895	ENSMUSG00000020660	Pomc	ACTH|BE|Beta-LPH|Clip|Gamma-LPH|Npp|Pomc-1|Pomc1|alpha-MSH|alphaMSH|beta-MSH|gamma-MSH	pro-opiomelanocortin-alpha	protein-coding
mm_10529.1	chr2	16402027	16402040	+	1	NA	intron (NM_026162, intron 1 of 13)	intron (NM_026162, intron 1 of 13)	45729	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding
mm_117355.1	chr13	69772624	69772636	-	1	NA	Intergenic	MLTR73|LTR|ERV1	-32733	NM_001145162	76980	Mm.23960	NM_001145162	ENSMUSG00000052981	Ube2ql1	3110006E14Rik	ubiquitin-conjugating enzyme E2Q family-like 1	protein-coding
mm_71949.1	chr8	70493118	70493128	+	1	NA	promoter-TSS (NM_018827)	promoter-TSS (NM_018827)	-8	NM_018827	12931	Mm.335584	NM_018827	ENSMUSG00000007888	Crlf1	CLF-1|CRLM-3|CRLM3|NR6|NR6.1	cytokine receptor-like factor 1	protein-coding
mm_121804.1	chr14	20263434	20263460	-	1	NA	intron (NM_029006, intron 3 of 4)	intron (NM_029006, intron 3 of 4)	5715	NM_029006	74571	Mm.105571	NM_029006	ENSMUSG00000023387	Kcnk16	4731413G05Rik|TALK-1|TALK1	potassium channel, subfamily K, member 16	protein-coding
mm_156702.1	chrX	159532763	159532775	+	1	NA	5' UTR (NM_001033472, exon 1 of 12)	5' UTR (NM_001033472, exon 1 of 12)	101	NM_001033472	382252	Mm.296254	NM_001033472	ENSMUSG00000044150	A830080D01Rik	2310067E24Rik|Gm1146	RIKEN cDNA A830080D01 gene	protein-coding
mm_82504.1	chr9	20480838	20480856	-	1	NA	intron (NM_146221, intron 1 of 6)	B4|SINE|B4	11899	NM_146221	235028	Mm.297660	NM_146221	ENSMUSG00000059475	Zfp426	2900057C04Rik|KRAB1|Zfo61|Zfp68-rs1|Znf426|mKIAA4237	zinc finger protein 426	protein-coding
mm_146197.1	chr18	76241421	76241464	+	1	NA	promoter-TSS (NM_010754)	promoter-TSS (NM_010754)	-259	NM_010754	17126	Mm.152699	NM_010754	ENSMUSG00000024563	Smad2	7120426M23Rik|Madh2|Madr2|Smad-2|mMad2	SMAD family member 2	protein-coding
mm_134826.1	chr16	26073997	26074010	-	1	NA	intron (NM_173379, intron 1 of 14)	RSINE1|SINE|B4	31781	NM_173379	210530	Mm.326869	NM_173379	ENSMUSG00000038168	P3h2	4832416N06|AW553532|Leprel1|Mlat4	prolyl 3-hydroxylase 2	protein-coding
mm_18423.1	chr2	60751792	60751814	-	1	NA	TTS (NM_001141932)	TTS (NM_001141932)	-29200	NM_001159564	16420	Mm.98193	NM_021359	ENSMUSG00000026971	Itgb6	2210409C20Rik|4831415H04Rik	integrin beta 6	protein-coding
mm_149467.1	chr19	11586604	11586610	+	1	NA	TTS (NM_026835)	TTS (NM_026835)	18197	NM_026835	68774	Mm.290390	NM_026835	ENSMUSG00000024679	Ms4a6d	1110058E16Rik|AI447446|Ms4a11	membrane-spanning 4-domains, subfamily A, member 6D	protein-coding
mm_17734.1	chr2	32567742	32567751	-	1	NA	3' UTR (NM_153560, exon 11 of 11)	3' UTR (NM_153560, exon 11 of 11)	-3112	NM_010073	13481	Mm.22001	NM_010073	ENSMUSG00000026810	Dpm2	AW557993|R75484	dolichol-phosphate (beta-D) mannosyltransferase 2	protein-coding
mm_112012.1	chr12	110978982	110979028	-	1	NA	promoter-TSS (NM_175207)	promoter-TSS (NM_175207)	16	NM_175207	74251	Mm.250989	NM_175207	ENSMUSG00000037904	Ankrd9	2500003O20Rik	ankyrin repeat domain 9	protein-coding
mm_84066.1	chr9	58201357	58201383	-	1	NA	exon (NM_001161535, exon 1 of 2)	exon (NM_001161535, exon 1 of 2)	345	NM_001161535	320563	Mm.186499	NM_177193	ENSMUSG00000051243	Islr2	B930052A04Rik|Linx|Mbu-3|mKIAA1465	immunoglobulin superfamily containing leucine-rich repeat 2	protein-coding
mm_1498.1	chr1	72087817	72087820	+	1	NA	Intergenic	Intergenic	-82623	NR_040454	71134	Mm.370574	NR_040454	ENSMUSG00000101848	4933417E11Rik	-	RIKEN cDNA 4933417E11 gene	ncRNA
mm_135261.1	chr16	37861176	37861191	-	1	NA	Intergenic	Intergenic	-7217	NM_177093	320184	Mm.390882	NM_177093	ENSMUSG00000034158	Lrrc58	1810012N18Rik|C330018J07Rik	leucine rich repeat containing 58	protein-coding
mm_38815.1	chr4	148500307	148500338	-	1	NA	5' UTR (NM_001039554, exon 1 of 5)	5' UTR (NM_001039554, exon 1 of 5)	140	NM_001039554	654812	Mm.388929	NM_001039554	ENSMUSG00000028989	Angptl7	-	angiopoietin-like 7	protein-coding
mm_94785.1	chr11	22001844	22001846	+	1	NA	promoter-TSS (NM_011023)	promoter-TSS (NM_011023)	-194	NM_011023	18423	Mm.129663	NM_011023	ENSMUSG00000005917	Otx1	A730044F23Rik|jv	orthodenticle homeobox 1	protein-coding
mm_105405.1	chr11	103504918	103504928	-	1	NA	Intergenic	Intergenic	-92259	NM_183034	353047	Mm.18556	NM_183034	ENSMUSG00000034247	Plekhm1	AP162|B2|BC038943|D330036J23Rik	pleckstrin homology domain containing, family M (with RUN domain) member 1	protein-coding
mm_24114.1	chr3	88145583	88145600	+	1	NA	intron (NM_133665, intron 1 of 10)	intron (NM_133665, intron 1 of 10)	3219	NM_001310593	17261	Mm.28184	NM_133665	ENSMUSG00000001419	Mef2d	C80750	myocyte enhancer factor 2D	protein-coding
mm_129028.1	chr15	74958848	74958878	-	1	NA	3' UTR (NM_001164036, exon 4 of 4)	3' UTR (NM_001164036, exon 4 of 4)	3757	NM_001164040	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_44709.1	chr5	30907681	30907691	-	1	NA	5' UTR (NM_001134692, exon 1 of 2)	5' UTR (NM_001134692, exon 1 of 2)	102	NM_001134692	67695	Mm.21450	NM_024460	ENSMUSG00000038803	Ost4	2310016E02Rik	oligosaccharyltransferase complex subunit 4 (non-catalytic)	protein-coding
mm_166815.1	chr7	16400894	16400932	+	1	NA	promoter-TSS (NM_198631)	promoter-TSS (NM_198631)	-283	NM_198631	330474	Mm.333594	NM_198631	ENSMUSG00000059273	Zc3h4	Bwq1|Gm768|Kiaa1064-hp|mKIAA1064	zinc finger CCCH-type containing 4	protein-coding
mm_33366.1	chr4	129513398	129513409	+	1	NA	promoter-TSS (NM_010807)	promoter-TSS (NM_010807)	-178	NM_010807	17357	Mm.424974	NM_010807	ENSMUSG00000047945	Marcksl1	AL022768|AW215397|AW536807|D4Bc1|F52|MacMARCKS|Macs2|Macs3|Mlp|Mrp	MARCKS-like 1	protein-coding
mm_90548.1	chr10	128093244	128093265	+	1	NA	intron (NM_054078, intron 1 of 29)	CpG	471	NM_054078	116848	Mm.252213	NM_054078	ENSMUSG00000040054	Baz2a	AA415431|C030005G16Rik|C78388|Tip5|Walp3|mKIAA0314	bromodomain adjacent to zinc finger domain, 2A	protein-coding
mm_124859.1	chr15	9554587	9554597	+	1	NA	Intergenic	Intergenic	-24716	NM_008372	16197	Mm.389	NM_008372	ENSMUSG00000003882	Il7r	CD127|IL-7Ralpha	interleukin 7 receptor	protein-coding
mm_31464.1	chr4	49521215	49521296	+	1	NA	promoter-TSS (NM_001289901)	promoter-TSS (NM_001289901)	79	NM_001289901	230162	Mm.186994	NM_145547	ENSMUSG00000039634	Zfp189	BB131811|C430015I23Rik	zinc finger protein 189	protein-coding
mm_56564.1	chr6	101377377	101377388	-	1	NA	exon (NM_018884, exon 1 of 10)	exon (NM_018884, exon 1 of 10)	515	NM_018884	55983	Mm.321654	NM_018884	ENSMUSG00000035357	Pdzrn3	1110020C07Rik|AI429718|AL023082|LNX3|SEMACAP3|Semcap3	PDZ domain containing RING finger 3	protein-coding
mm_3959.1	chr1	164115332	164115347	+	1	NA	promoter-TSS (NM_011347)	promoter-TSS (NM_011347)	75	NM_011347	20344	Mm.3337	NM_011347	ENSMUSG00000026580	Selp	CD62P|GMP-140|Grmp|LECAM3|PADGEM	selectin, platelet	protein-coding
mm_7335.1	chr1	105356770	105356788	-	1	NA	promoter-TSS (NM_001160368)	promoter-TSS (NM_001160368)	-69	NM_001160368	320311	Mm.389162	NM_178779	ENSMUSG00000047496	Rnf152	A930029B02Rik	ring finger protein 152	protein-coding
mm_103914.1	chr11	83588710	83588712	-	1	NA	3' UTR (NM_009139, exon 4 of 4)	3' UTR (NM_009139, exon 4 of 4)	4376	NM_009139	20305	Mm.137	NM_009139	ENSMUSG00000018927	Ccl6	MRP-1|Scya6|c10	chemokine (C-C motif) ligand 6	protein-coding
mm_84338.1	chr9	64177789	64177811	-	1	NA	exon (NM_024212, exon 8 of 10)	exon (NM_024212, exon 8 of 10)	-1497	NM_183316	330959	Mm.24082	NM_183316	ENSMUSG00000032398	Snapc5	2010103A03Rik	small nuclear RNA activating complex, polypeptide 5	protein-coding
mm_90762.1	chr10	5550799	5550807	-	1	NA	promoter-TSS (NM_153399)	promoter-TSS (NM_153399)	-111	NM_001347732	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_38990.1	chr4	151108245	151108277	-	1	NA	intron (NM_001081557, intron 11 of 23)	CpG	18691	NM_001308446	105704528	Mm.415128	NM_001308446	ENSMUSG00000078491	Gm13090	OTTMUSG00000010356	predicted gene 13090	protein-coding
mm_43154.1	chr5	125532542	125532544	+	1	NA	5' UTR (NM_001190352, exon 1 of 9)	5' UTR (NM_001190352, exon 1 of 9)	125	NM_001190352	208151	Mm.40397	NM_001190352	ENSMUSG00000070498	Tmem132b	AK220418|mKIAA1786	transmembrane protein 132B	protein-coding
mm_137548.1	chr17	27557462	27557507	+	1	NA	intron (NM_001166537, intron 1 of 4)	CpG-6152	831	NM_001166477	111241	Mm.426212	NM_001166476	ENSMUSG00000078249	Hmga1-rs1	ENSMUSG00000041059|Hmgi-rs1	high mobility group AT-hook I, related sequence 1	protein-coding
mm_143450.1	chr17	70920012	70920017	-	1	NA	Intergenic	Intergenic	-66482	NM_001164074	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_52046.1	chr6	97210383	97210412	+	1	NA	promoter-TSS (NM_022992)	promoter-TSS (NM_022992)	-395	NM_022992	65106	Mm.291014	NM_022992	ENSMUSG00000035199	Arl6ip5	5930404D22Rik|AV001879|Aip-5|Gtrap3-18|addiscin	ADP-ribosylation factor-like 6 interacting protein 5	protein-coding
mm_150505.1	chr19	39023379	39023388	+	1	NA	intron (NM_028089, intron 4 of 8)	Lx6|LINE|L1	16364	NM_028089	72082	Mm.142581	NM_028089	ENSMUSG00000025002	Cyp2c55	2010318C06Rik	cytochrome P450, family 2, subfamily c, polypeptide 55	protein-coding
mm_18459.1	chr2	62343634	62343653	-	1	NA	intron (NM_001159543, intron 23 of 24)	intron (NM_001159543, intron 23 of 24)	68588	NM_010074	13482	Mm.1151	NM_010074	ENSMUSG00000035000	Dpp4	Cd26|Dpp-4|THAM	dipeptidylpeptidase 4	protein-coding
mm_122387.1	chr14	40907470	40907484	-	1	NA	3' UTR (NM_001316748, exon 9 of 9)	3' UTR (NM_001316748, exon 9 of 9)	-14512	NM_177816	328381	Mm.235694	NM_177816	ENSMUSG00000037833	Sh2d4b	A430109M18Rik|D030001E08	SH2 domain containing 4B	protein-coding
mm_165941.1	chr4	78092209	78092212	-	1	NA	intron (NM_011211, intron 1 of 39)	intron (NM_011211, intron 1 of 39)	119685	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding
mm_38863.1	chr4	149446047	149446048	-	1	NA	Intergenic	Intergenic	8921	NM_022020	63954	Mm.46023	NM_022020	ENSMUSG00000028996	Rbp7	1110002J23Rik|CRBP-III	retinol binding protein 7, cellular	protein-coding
mm_792.1	chr1	45338707	45338740	+	1	NA	exon (NM_009930, exon 34 of 51)	exon (NM_009930, exon 34 of 51)	27185	NM_009930	12825	Mm.249555	NM_009930	ENSMUSG00000026043	Col3a1	AW550625|Col3a-1|Tsk-2|Tsk2	collagen, type III, alpha 1	protein-coding
mm_141214.1	chr17	27167706	27167736	-	1	NA	promoter-TSS (NM_173027)	promoter-TSS (NM_173027)	43	NM_173027	271424	Mm.209679	NM_173027	ENSMUSG00000024210	Ip6k3	D830007E07Rik|Ihpk3	inositol hexaphosphate kinase 3	protein-coding
mm_55592.1	chr6	71608130	71608177	-	1	NA	intron (NM_001038695, intron 11 of 26)	intron (NM_001038695, intron 11 of 26)	24533	NM_173001	104263	Mm.260479	NM_173001	ENSMUSG00000053470	Kdm3a	1700105C21Rik|C230043E16Rik|JHDM2a|Jmjd1|Jmjd1a|KDM2A|TGSA|Tsga	lysine (K)-specific demethylase 3A	protein-coding
mm_123867.1	chr14	72561641	72561654	-	1	NA	exon (NM_207636, exon 17 of 26)	exon (NM_207636, exon 17 of 26)	148356	NM_207636	319448	Mm.205421	NM_207636	ENSMUSG00000033487	Fndc3a	1700094E19Rik|D14Ertd453e|F730017H24Rik|Fndc3|sys	fibronectin type III domain containing 3A	protein-coding
mm_167025.1	chr7	67212388	67212390	+	1	NA	intron (NR_131044, intron 2 of 2)	intron (NR_131044, intron 2 of 2)	10069	NR_131044	76628	Mm.384589	NR_131043	ENSMUSG00000097527	1700112J16Rik	-	RIKEN cDNA 1700112J16 gene	ncRNA
mm_123229.1	chr14	60027057	60027061	-	1	NA	intron (NM_015803, intron 10 of 35)	intron (NM_015803, intron 10 of 35)	59775	NM_015803	50769	Mm.319599	NM_015803	ENSMUSG00000021983	Atp8a2	AI415030|Atpc1b|agil|wl	ATPase, aminophospholipid transporter-like, class I, type 8A, member 2	protein-coding
mm_22197.1	chr2	173291176	173291180	-	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-14645	NM_022995	65112	Mm.73682	NM_022995	ENSMUSG00000038400	Pmepa1	2210418I02Rik|AW455466|Erg1.2|N4wbp4|Stag1|Tmepai	prostate transmembrane protein, androgen induced 1	protein-coding
mm_44052.1	chr5	147894953	147894990	+	1	NA	promoter-TSS (NM_027872)	promoter-TSS (NM_027872)	-169	NM_027872	71706	Mm.153218	NM_027872	ENSMUSG00000029650	Slc46a3	1200006F02Rik	solute carrier family 46, member 3	protein-coding
mm_93059.1	chr10	88765490	88765492	-	1	NA	exon (NM_175158, exon 44 of 62)	exon (NM_175158, exon 44 of 62)	34077	NM_025859	104303	Mm.291247	NM_025859	ENSMUSG00000060904	Arl1	2310008D22Rik|AU019749	ADP-ribosylation factor-like 1	protein-coding
mm_140194.1	chr17	83355067	83355073	+	1	NA	intron (NM_001114362, intron 1 of 21)	intron (NM_001114362, intron 1 of 21)	4139	NM_001114362	78798	Mm.295565	NM_199466	ENSMUSG00000032624	Eml4	4930443C24Rik|AI644019	echinoderm microtubule associated protein like 4	protein-coding
mm_94249.1	chr11	3330782	3330812	+	1	NA	promoter-TSS (NM_178149)	promoter-TSS (NM_178149)	66	NM_178149	216505	Mm.390323	NM_178149	ENSMUSG00000034614	Pik3ip1	1500004A08Rik|5830455E04Rik|Crkd|Hgfl	phosphoinositide-3-kinase interacting protein 1	protein-coding
mm_125791.1	chr15	74721692	74721694	+	1	NA	exon (NM_198607, exon 1 of 2)	exon (NM_198607, exon 1 of 2)	459	NM_198607	223626	Mm.268603	NM_198607	ENSMUSG00000056665	Them6	4930572J05Rik	thioesterase superfamily member 6	protein-coding
mm_172249.1	chr6	69438793	69438797	-	1	NA	Intergenic	Intergenic	-111621	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_169491.1	chr14	75284592	75284594	+	1	NA	5' UTR (NM_026083, exon 1 of 19)	5' UTR (NM_026083, exon 1 of 19)	220	NM_026083	67302	Mm.74704	NM_026083	ENSMUSG00000022000	Zc3h13	2600010B19Rik|3110050K21Rik|4930570G11Rik|C87618	zinc finger CCCH type containing 13	protein-coding
mm_166139.1	chr4	156241332	156241372	+	1	NA	exon (NM_021303, exon 10 of 19)	exon (NM_021303, exon 10 of 19)	5342	NM_021303	57741	Mm.423051	NM_021303	ENSMUSG00000095567	Noc2l	AA410003|AF155546|NIR	NOC2 like nucleolar associated transcriptional repressor	protein-coding
mm_131571.1	chr16	18248938	18248948	+	1	NA	promoter-TSS (NM_011239)	promoter-TSS (NM_011239)	60	NM_001081000	15547	Mm.271798	NM_008307	ENSMUSG00000022721	Trmt2a	Htf9c	TRM2 tRNA methyltransferase 2A	protein-coding
mm_53849.1	chr6	149139792	149139807	+	1	NA	Intergenic	Intergenic	-1714	NM_001252096	320204	Mm.274099	NM_177101	ENSMUSG00000039958	Etfbkmt	4833442J19Rik|AI256744|ETFB-KMT|Mettl20	electron transfer flavoprotein beta subunit lysine methyltransferase	protein-coding
mm_155114.1	chrX	48519782	48519790	+	1	NA	exon (NM_011228, exon 1 of 2)	exon (NM_011228, exon 1 of 2)	501	NM_011228	19337	Mm.2015	NM_011228	ENSMUSG00000031104	Rab33a	Rabs10	RAB33A, member RAS oncogene family	protein-coding
mm_37640.1	chr4	128051168	128051170	-	1	NA	intron (NM_001281955, intron 1 of 70)	intron (NM_001281955, intron 1 of 70)	63125	NM_001281955	329942	Mm.421342	NM_001281955	ENSMUSG00000028804	Csmd2	Gm139	CUB and Sushi multiple domains 2	protein-coding
mm_151250.1	chr19	53906574	53906593	+	1	NA	intron (NM_001168491, intron 1 of 11)	intron (NM_001168491, intron 1 of 11)	3232	NM_001168491	18569	Mm.1605	NM_011050	ENSMUSG00000024975	Pdcd4	D19Ucla1|Ma3|Tis	programmed cell death 4	protein-coding
mm_70146.1	chr7	143458824	143458856	-	1	NA	3' UTR (NM_001161624, exon 4 of 4)	3' UTR (NM_001161624, exon 4 of 4)	2210	NM_009876	12577	Mm.168789	NM_009876	ENSMUSG00000037664	Cdkn1c	AL024410|CDKI|Kip2|p57(kip2)|p57Kip2	cyclin-dependent kinase inhibitor 1C (P57)	protein-coding
mm_1149.1	chr1	60768209	60768212	+	1	NA	intron (NM_007642, intron 3 of 3)	intron (NM_007642, intron 3 of 3)	21822	NM_007642	12487	Mm.255003	NM_007642	ENSMUSG00000026012	Cd28	-	CD28 antigen	protein-coding
mm_160836.1	chr11	48979377	48979377	-	1	NA	promoter-TSS (NM_173434).2	promoter-TSS (NM_173434).2	4	NM_001114679	667214	Mm.441306	NM_001114679	ENSMUSG00000069893	9930111J21Rik1	9930111J21Rik|Iigp	RIKEN cDNA 9930111J21 gene 1	protein-coding
mm_121400.1	chr14	119156365	119156383	+	1	NA	intron (NM_015820, intron 1 of 1)	MER74A|LTR|ERVL	18109	NM_015820	50787	Mm.445777	NM_015820	ENSMUSG00000053465	Hs6st3	6OST3|HS6ST-3	heparan sulfate 6-O-sulfotransferase 3	protein-coding
mm_50627.1	chr6	50261934	50261960	+	1	NA	promoter-TSS (NM_018769)	promoter-TSS (NM_018769)	-178	NM_018769	54722	Mm.248361	NM_018769	ENSMUSG00000029821	Dfna5	2310037D07Rik|4932441K13Rik|Dfna5h|EG14210|Fin15	deafness, autosomal dominant 5 (human)	protein-coding
mm_255.1	chr1	20356454	20356485	+	1	NA	promoter-TSS (NR_045734)	promoter-TSS (NR_045734)	15	NR_045734	75028	Mm.417820	NR_045734	ENSMUSG00000089914	4930486I03Rik	-	RIKEN cDNA 4930486I03 gene	ncRNA
mm_66207.1	chr7	34305487	34305497	-	1	NA	Intergenic	Intergenic	-19883	NM_172741	233103	Mm.491097	NM_172741	ENSMUSG00000066571	4931406P16Rik	AA553327|mKIAA0355	RIKEN cDNA 4931406P16 gene	protein-coding
mm_316.1	chr1	24615895	24615913	+	1	NA	Intergenic	Intergenic	-28467	NM_007733	12823	Mm.329196	NM_007733	ENSMUSG00000026141	Col19a1	-	collagen, type XIX, alpha 1	protein-coding
mm_134538.1	chr16	19706306	19706333	-	1	NA	promoter-TSS (NM_177356)	promoter-TSS (NM_177356)	46	NM_177356	239739	Mm.258059	NM_177356	ENSMUSG00000041247	Lamp3	1200002D17Rik|Cd208|DC-LAMP|DCLAMP|LAMP|TSC403	lysosomal-associated membrane protein 3	protein-coding
mm_128091.1	chr15	27788313	27788421	-	1	NA	intron (NM_001081302, intron 34 of 56)	intron (NM_001081302, intron 34 of 56)	-106825	NM_001242423	223433	Mm.266485	NM_198301	ENSMUSG00000056069	Fam105a	9830126M18	family with sequence similarity 105, member A	protein-coding
mm_19742.1	chr2	104780583	104780586	-	1	NA	intron (NM_001123327, intron 3 of 11)	(A)n|Simple_repeat|Simple_repeat	36112	NM_001123327	99003	Mm.274314	NM_001123327	ENSMUSG00000074994	Qser1	4732486I23Rik|AI502974	glutamine and serine rich 1	protein-coding
mm_8765.1	chr1	160792882	160792892	-	1	NA	promoter-TSS (NM_013862)	promoter-TSS (NM_013862)	51	NM_013862	29809	Mm.25833	NM_013862	ENSMUSG00000026721	Rabgap1l	5830411O09Rik|8430421H08Rik|9630005B12Rik|AW049894|HHL|Hh1|mKIAA0471	RAB GTPase activating protein 1-like	protein-coding
mm_93991.1	chr10	127522429	127522454	-	1	NA	promoter-TSS (NM_028230)	promoter-TSS (NM_028230)	3	NM_001252316	108037	Mm.29890	NM_028230	ENSMUSG00000025403	Shmt2	2700043D08Rik|AA408223|AA986903	serine hydroxymethyltransferase 2 (mitochondrial)	protein-coding
mm_155253.1	chrX	57224031	57224037	+	1	NA	TTS (NM_011616)	TTS (NM_011616)	11891	NM_011616	21947	Mm.4861	NM_011616	ENSMUSG00000031132	Cd40lg	CD154|CD40-L|Cd40l|HIGM1|IGM|IMD3|Ly-62|Ly62|T-BAM|TRAP|Tnfsf5|Tnlg8b|gp39	CD40 ligand	protein-coding
mm_53080.1	chr6	124939303	124939319	+	1	NA	Intergenic	Intergenic	7923	NM_001170341	30853	Mm.29737	NM_145385	ENSMUSG00000030120	Mlf2	AI256856|AU018944|C77284	myeloid leukemia factor 2	protein-coding
mm_102985.1	chr11	69681995	69682005	-	1	NA	promoter-TSS (NM_001163571)	promoter-TSS (NM_001163571)	-30	NM_030702	80886	Mm.284592	NM_030702	ENSMUSG00000005204	Senp3	AA408656|Smt3ip|Smt3ip1	SUMO/sentrin specific peptidase 3	protein-coding
mm_138047.1	chr17	33925733	33925764	+	1	NA	exon (NM_009318, exon 4 of 8)	exon (NM_009318, exon 4 of 8)	-4146	NM_009059	19732	Mm.43777	NM_009059	ENSMUSG00000041354	Rgl2	KE1.5|Rab2l|Rgt2|Rlf	ral guanine nucleotide dissociation stimulator-like 2	protein-coding
mm_92202.1	chr10	68136703	68136708	-	1	NA	intron (NM_023598, intron 4 of 9)	intron (NM_023598, intron 4 of 9)	142021	NM_023598	71371	Mm.440357	NM_023598	ENSMUSG00000019947	Arid5b	4930580B11|5430435G07Rik|AI467247|Desrt|Mrf2|Mrf2alpha|Mrf2beta	AT rich interactive domain 5B (MRF1-like)	protein-coding
mm_13915.1	chr2	120567653	120567678	+	1	NA	promoter-TSS (NM_001177793)	promoter-TSS (NM_001177793)	-6	NM_001177792	20619	Mm.245715	NM_009222	ENSMUSG00000027287	Snap23	23kDa|AA408749|SNAP-23|Sndt|Syndet	synaptosomal-associated protein 23	protein-coding
mm_46187.1	chr5	97919879	97919883	-	1	NA	intron (NM_133738, intron 16 of 16)	intron (NM_133738, intron 16 of 16)	111081	NM_133738	71914	Mm.24842	NM_133738	ENSMUSG00000029338	Antxr2	2310046B19Rik|AW561899|CMG-2|CMG2|cI-35	anthrax toxin receptor 2	protein-coding
mm_73390.1	chr8	105701625	105701693	+	1	NA	promoter-TSS (NM_019695)	promoter-TSS (NM_019695)	12	NM_001286345	56513	Mm.472753	NM_019695	ENSMUSG00000005699	Pard6a	0710008C04Rik|2610010A15Rik|PAR-6A|PAR6alpha|Par-6|Par6|Par6c|TAX40|Tip-40	par-6 family cell polarity regulator alpha	protein-coding
mm_66466.1	chr7	44929411	44929521	-	1	NA	promoter-TSS (NM_001077264)	promoter-TSS (NM_001077264)	24	NM_007458	11771	Mm.6877	NM_007458	ENSMUSG00000060279	Ap2a1	Adtaa	adaptor-related protein complex 2, alpha 1 subunit	protein-coding
mm_81510.1	chr9	110034836	110034847	+	1	NA	exon (NM_008633, exon 7 of 19)	exon (NM_008633, exon 7 of 19)	-17180	NM_001311163	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_39163.1	chr4	155624561	155624574	-	1	NA	promoter-TSS (NM_007661)	promoter-TSS (NM_007661)	188	NR_040441	100502734	Mm.306018	NR_040441	ENSMUSG00000086682	Gm16023	OTTMUSG00000029160	predicted gene 16023	ncRNA
mm_1018.1	chr1	58738975	58738997	+	1	NA	intron (NM_001293805, intron 4 of 7)	B4A|SINE|B4	8434	NM_001293805	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_112005.1	chr12	110858912	110858945	-	1	NA	intron (NM_001199785, intron 2 of 6)	intron (NM_001199785, intron 2 of 6)	8649	NM_028365	72805	Mm.443524	NM_028365	ENSMUSG00000021271	Zfp839	2810455K09Rik	zinc finger protein 839	protein-coding
mm_83547.1	chr9	46237404	46237408	-	1	NA	Intergenic	Intergenic	-1770	NM_001289756	11814	Mm.390161	NM_023114	ENSMUSG00000032081	Apoc3	apo-CIII|apoC-III	apolipoprotein C-III	protein-coding
mm_77575.1	chr8	123515334	123515437	-	1	NA	promoter-TSS (NM_028146)	promoter-TSS (NM_028146)	70	NM_001170975	72185	Mm.27925	NM_028146	ENSMUSG00000031970	Dbndd1	2810427I04Rik|D8Ertd590e	dysbindin (dystrobrevin binding protein 1) domain containing 1	protein-coding
mm_1623.1	chr1	74393270	74393280	+	1	NA	intron (NM_153088, intron 1 of 6)	intron (NM_153088, intron 1 of 6)	-1035	NR_029743	387219		NR_029743	ENSMUSG00000065468	Mir26b	Mirn26b|mir-26b|mmu-mir-26b	microRNA 26b	ncRNA
mm_74821.1	chr8	23035443	23035488	-	1	NA	intron (NM_001277284, intron 1 of 42)	intron (NM_001277284, intron 1 of 42)	366	NM_001277284	11733	Mm.334444	NM_031158	ENSMUSG00000031543	Ank1	Ank-1|nb|pale	ankyrin 1, erythroid	protein-coding
mm_16888.1	chr2	13011673	13011686	-	1	NA	promoter-TSS (NM_153155)	promoter-TSS (NM_153155)	-815	NM_153155	227580	Mm.229322	NM_153155	ENSMUSG00000049630	C1ql3	1110065A22Rik|AI661623|C1ql|C1qtnf13|CTRP13|K100	C1q-like 3	protein-coding
mm_123440.1	chr14	64949331	64949370	-	1	NA	promoter-TSS (NM_001253731)	promoter-TSS (NM_001253731)	507	NM_177338	219150	Mm.344074	NM_177338	ENSMUSG00000021972	Hmbox1	AI451877|AI604847|F830020C16Rik	homeobox containing 1	protein-coding
mm_153563.1	chr19	42307103	42307116	-	1	NA	intron (NM_145123, intron 6 of 14)	intron (NM_145123, intron 6 of 14)	-26939	NR_037246	100526549		NR_037246	ENSMUSG00000093234	Mir3085	mir-3085|mmu-mir-3085	microRNA 3085	ncRNA
mm_31603.1	chr4	57956925	57956967	+	1	NA	promoter-TSS (NM_011660)	promoter-TSS (NM_011660)	-535	NM_011660	22166	Mm.260618	NM_011660	ENSMUSG00000028367	Txn1	ADF|AW550880|Trx1|Txn	thioredoxin 1	protein-coding
mm_67462.1	chr7	80404030	80404041	-	1	NA	intron (NM_001081454, intron 1 of 15)	intron (NM_001081454, intron 1 of 15)	-1223	NM_011046	18550	Mm.5241	NM_011046	ENSMUSG00000030530	Furin	9130404I01Rik|Fur|PACE|Pcsk3|SPC1	furin (paired basic amino acid cleaving enzyme)	protein-coding
mm_20822.1	chr2	145934683	145934738	-	1	NA	promoter-TSS (NM_025820)	promoter-TSS (NM_025820)	-10	NM_025820	66877	Mm.248755	NM_025820	ENSMUSG00000001767	Crnkl1	1200013P10Rik|5730590A01Rik|C80326|crn	Crn, crooked neck-like 1 (Drosophila)	protein-coding
mm_105667.1	chr11	107428071	107428082	-	1	NA	intron (NM_145823, intron 1 of 9)	intron (NM_145823, intron 1 of 9)	42644	NM_145823	71795	Mm.397413	NM_145823	ENSMUSG00000040430	Pitpnc1	1110020B03Rik|5830436L09Rik|AI662802|AI851387|C330017I21Rik|Dnr411|RDGBB|RDGBB1|rdgB-beta	phosphatidylinositol transfer protein, cytoplasmic 1	protein-coding
mm_167526.1	chr9	21288040	21288069	+	1	NA	promoter-TSS (NM_145416)	promoter-TSS (NM_145416)	-85	NM_145416	215194	Mm.290690	NM_145416	ENSMUSG00000035047	Kri1	-	KRI1 homolog	protein-coding
mm_57697.1	chr6	128524051	128524132	-	1	NA	exon (NM_007376, exon 3 of 36)	exon (NM_007376, exon 3 of 36)	2629	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_108152.1	chr12	76319058	76319061	+	1	NA	intron (NM_138745, intron 27 of 27)	HAL1|LINE|L1	-5832	NM_001101471	238276	Mm.311452	NM_001101471	ENSMUSG00000021057	Akap5	3526401B18Rik|AKAP 150|AKAP-5|AKAP150|BB098886|Gm258|P150	A kinase (PRKA) anchor protein 5	protein-coding
mm_130975.1	chr15	103340086	103340100	-	1	NA	promoter-TSS (NM_013866)	promoter-TSS (NM_013866)	-7	NM_013866	29813	Mm.14099	NM_013866	ENSMUSG00000000552	Zfp385a	Hzf|Zfp385|Znf385a	zinc finger protein 385A	protein-coding
mm_111426.1	chr12	91686090	91686104	-	1	NA	intron (NM_175367, intron 4 of 6)	intron (NM_175367, intron 4 of 6)	-95610	NM_175335	83602	Mm.275728	NM_031391	ENSMUSG00000020962	Gtf2a1	6330549H03Rik|AA536742|AA959775|AW060250|TfIIAa/b|Tfiia1	general transcription factor II A, 1	protein-coding
mm_129513.1	chr15	79062704	79062706	-	1	NA	exon (NM_144849, exon 1 of 8)	exon (NM_144849, exon 1 of 8)	154	NM_144849	223690	Mm.24262	NM_144849	ENSMUSG00000033055	Ankrd54	C730048E16Rik|EST1068184|EST475269|Liar	ankyrin repeat domain 54	protein-coding
mm_102070.1	chr11	52260594	52260625	-	1	NA	exon (NM_009331, exon 4 of 10)	exon (NM_009331, exon 4 of 10)	21986	NM_009331	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_7925.1	chr1	133899153	133899173	-	1	NA	intron (NM_054076, intron 5 of 6)	MIRb|SINE|MIR	8010	NM_054076	269120	Mm.59985	NM_054076	ENSMUSG00000010311	Optc	-	opticin	protein-coding
mm_110131.1	chr12	26444799	26444809	-	1	NA	3' UTR (NM_021384, exon 6 of 6)	3' UTR (NM_021384, exon 6 of 6)	11648	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_167549.1	chr9	32143420	32143421	+	1	NA	intron (NM_001195632, intron 2 of 21)	B2_Mm2|SINE|B2	27284	NM_001195632	330914	Mm.46683	NM_177379	ENSMUSG00000041444	Arhgap32	3426406O18Rik|Gc-gap|Grit|Px-rics|Rics|mKIAA0712|p200Rhogap|p250Gap	Rho GTPase activating protein 32	protein-coding
mm_82162.1	chr9	123781601	123781621	+	1	NA	3' UTR (NM_001166625, exon 4 of 4)	3' UTR (NM_001166625, exon 4 of 4)	14400	NM_001166625	12769	Mm.440604	NM_009913	ENSMUSG00000029530	Ccr9	A130091K22Rik|Cmkbr10|GPR-9-6	chemokine (C-C motif) receptor 9	protein-coding
mm_128175.1	chr15	34443230	34443272	-	1	NA	promoter-TSS (NR_028101)	promoter-TSS (NR_028101)	-18	NR_028101	666899	Mm.439801	NR_028101		Gm12191	OTTMUSG00000005566	ribosomal protein L30 pseudogene	pseudo
mm_53246.1	chr6	127577946	127577957	+	1	NA	promoter-TSS (NM_001033464)	promoter-TSS (NM_001033464)	-24	NM_001033464	381812	Mm.296093	NM_001033464	ENSMUSG00000061414	Cracr2a	Efcab4b|Gm1073|Gm462	calcium release activated channel regulator 2A	protein-coding
mm_146508.1	chr18	3337342	3337399	-	1	NA	intron (NR_033457, intron 1 of 1)	CpG	219	NM_001110851	12916	Mm.5244	NM_013498	ENSMUSG00000063889	Crem	ICER|ICERI	cAMP responsive element modulator	protein-coding
mm_113693.1	chr13	43122850	43122869	+	1	NA	promoter-TSS (NM_001005748)	promoter-TSS (NM_001005748)	20	NM_001005748	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding
mm_43891.1	chr5	143981080	143981105	+	1	NA	Intergenic	Intergenic	33761	NM_177682	231874	Mm.320432	NM_177682	ENSMUSG00000029617	Ccz1	AU022870	CCZ1 vacuolar protein trafficking and biogenesis associated	protein-coding
mm_133522.1	chr16	90831130	90831150	+	1	NA	non-coding (NR_133572, exon 1 of 6)	non-coding (NR_133572, exon 1 of 6)	281	NM_001316761	70967	Mm.253077	NM_027627	ENSMUSG00000039903	Eva1c	1700092M14Rik|4931408A02Rik|Fam176c	eva-1 homolog C (C. elegans)	protein-coding
mm_139309.1	chr17	48351137	48351170	+	1	NA	exon (NM_031254, exon 3 of 5)	exon (NM_031254, exon 3 of 5)	4752	NM_001272078	83433	Mm.261623	NM_031254	ENSMUSG00000023992	Trem2	TREM-2|Trem2a|Trem2b|Trem2c	triggering receptor expressed on myeloid cells 2	protein-coding
mm_103605.1	chr11	78437292	78437292	-	1	NA	Intergenic	Intergenic	-15107	NM_022411	20500	Mm.274058	NM_022411	ENSMUSG00000001095	Slc13a2	Nadc1|mNaDC-1	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 2	protein-coding
mm_104785.1	chr11	98683410	98683418	-	1	NA	intron (NM_009439, intron 1 of 11)	intron (NM_009439, intron 1 of 11)	860	NM_009439	22123	Mm.12194	NM_009439	ENSMUSG00000017221	Psmd3	AI255837|AntP91a|D11Bwg1349e|Psd3|Tstap91a	proteasome (prosome, macropain) 26S subunit, non-ATPase, 3	protein-coding
mm_83763.1	chr9	51963610	51963616	-	1	NA	promoter-TSS (NM_007996)	promoter-TSS (NM_007996)	-11	NM_001301728	14148	Mm.1061	NM_007996	ENSMUSG00000032051	Fdx1	-	ferredoxin 1	protein-coding
mm_145929.1	chr18	67133548	67133585	+	1	NA	promoter-TSS (NM_010307)	promoter-TSS (NM_010307)	6	NM_010307	14680	Mm.440746	NM_010307	ENSMUSG00000024524	Gnal	2610011C15Rik|9630020G10Rik|Galphaolf|Gna10|Golf	guanine nucleotide binding protein, alpha stimulating, olfactory type	protein-coding
mm_161349.1	chr14	54912661	54912661	-	1	NA	5' UTR (NM_021551, exon 2 of 9)	5' UTR (NM_021551, exon 2 of 9)	471	NM_021551	59049	Mm.27435	NM_021551	ENSMUSG00000022199	Slc22a17	1700094C23Rik|24p3R|AU041908|AW555662|BOIT|Boct	solute carrier family 22 (organic cation transporter), member 17	protein-coding
mm_44647.1	chr5	28209917	28209935	-	1	NA	5' UTR (NM_001310511, exon 1 of 3)	5' UTR (NM_001310511, exon 1 of 3)	242	NM_001310511	269637	Mm.68286	NM_175651	ENSMUSG00000044681	Cnpy1	1500012D20Rik|9630008K15Rik|AI853839	canopy FGF signaling regulator 1	protein-coding
mm_118941.1	chr14	27307972	27307983	+	1	NA	intron (NM_001289686, intron 4 of 12)	B1F1|SINE|Alu	-28060	NM_001289687	71704	Mm.248606	NM_027871	ENSMUSG00000021895	Arhgef3	1200004I24Rik|9830169H03Rik|C76747|Xpln	Rho guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_106759.1	chr12	4234087	4234118	+	1	NA	promoter-TSS (NM_001204912)	promoter-TSS (NM_001204912)	75	NM_001204912	69709	Mm.250552	NM_001204912	ENSMUSG00000096199	Ptrhd1	2410017P09Rik	peptidyl-tRNA hydrolase domain containing 1	protein-coding
mm_157115.1	chrX	9439924	9439946	-	1	NA	exon (NM_007807, exon 12 of 13)	exon (NM_007807, exon 12 of 13)	29389	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_170120.1	chr17	39846790	39846797	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	3796	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_102700.1	chr11	66149317	66149321	-	1	NA	intron (NM_001099633, intron 4 of 68)	intron (NM_001099633, intron 4 of 68)	19232	NM_001099633	237806	Mm.264210	NM_001099633	ENSMUSG00000056752	Dnah9	9030022M04|A230091C01|C230051G16|D11Ertd686e|Dnahc9|mKIAA0357	dynein, axonemal, heavy chain 9	protein-coding
mm_24933.1	chr3	96559744	96559756	+	1	NA	exon (NM_023719, exon 5 of 8)	exon (NM_023719, exon 5 of 8)	1793	NM_023719	56338	Mm.410189	NM_023719	ENSMUSG00000038393	Txnip	1200008J08Rik|AA682105|Hyplip1|THIF|Tbp-2|VDUP1	thioredoxin interacting protein	protein-coding
mm_37956.1	chr4	133339185	133339234	-	1	NA	5' UTR (NM_199306, exon 1 of 16)	5' UTR (NM_199306, exon 1 of 16)	106	NM_199306	230796	Mm.226576	NM_199306	ENSMUSG00000037622	Wdtc1	Gm695|adipose|adp	WD and tetratricopeptide repeats 1	protein-coding
mm_92500.1	chr10	78352078	78352095	-	1	NA	promoter-TSS (NM_053014)	promoter-TSS (NM_053014)	-386	NM_053014	28169	Mm.141230	NM_053014	ENSMUSG00000001211	Agpat3	AW061257|AW493985|D10Jhu12e|lpaat3	1-acylglycerol-3-phosphate O-acyltransferase 3	protein-coding
mm_29500.1	chr3	116007341	116007396	-	1	NA	promoter-TSS (NM_021388)	promoter-TSS (NM_021388)	38	NM_023214	66500	Mm.34550	NM_023214	ENSMUSG00000054414	Slc30a7	1810059J10Rik|2610034N15Rik|4833428C12Rik|AI467242|ZnT-7|ZnT7|Zntl2	solute carrier family 30 (zinc transporter), member 7	protein-coding
mm_40985.1	chr5	77266157	77266171	+	1	NA	intron (NM_011263, intron 1 of 3)	CpG	670	NM_011263	19712	Mm.28840	NM_011263	ENSMUSG00000029249	Rest	2610008J04Rik|AA407358|NRSF|REST4	RE1-silencing transcription factor	protein-coding
mm_89146.1	chr10	86021882	86021954	+	1	NA	promoter-TSS (NM_153195)	promoter-TSS (NM_153195)	-11	NM_153195	69754	Mm.44236	NM_153195	ENSMUSG00000001786	Fbxo7	2410015K21Rik|A230052G17Rik|AI117679|AW260462|C85118	F-box protein 7	protein-coding
mm_77222.1	chr8	115703038	115703059	-	1	NA	TTS (NM_001025577)	TTS (NM_001025577)	3846	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_7892.1	chr1	133332269	133332270	-	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	5057	NM_178260	280287	Mm.458301	NM_178260	ENSMUSG00000098306	Kiss1	kisspeptin|metastatin	KiSS-1 metastasis-suppressor	protein-coding
mm_112198.1	chr12	113425925	113425969	-	1	NA	Intergenic	Intergenic	-63618	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_138162.1	chr17	34261802	34261829	+	1	NA	Intergenic	Intergenic	-1412	NM_207105	14961	Mm.254067	NM_207105	ENSMUSG00000073421	H2-Ab1	AI845868|Abeta|H-2Ab|H2-Ab|I-Abeta|IAb|Ia-2|Ia2|Rmcs1	histocompatibility 2, class II antigen A, beta 1	protein-coding
mm_504.1	chr1	37100661	37100672	+	1	NA	Intergenic	Intergenic	-117612	NM_001282010	12790	Mm.214224	NM_009918	ENSMUSG00000026114	Cnga3	CNG3	cyclic nucleotide gated channel alpha 3	protein-coding
mm_9748.1	chr1	180694083	180694083	-	1	NA	3' UTR (NM_013729, exon 2 of 2)	3' UTR (NM_013729, exon 2 of 2)	2951	NM_013729	27217	Mm.103647	NM_013729	ENSMUSG00000026497	Mixl1	Mm1|Mml	Mix1 homeobox-like 1 (Xenopus laevis)	protein-coding
mm_149136.1	chr19	9002802	9002837	+	1	NA	exon (NM_009643, exon 5 of 5)	exon (NM_009643, exon 5 of 5)	13535	NM_001286518	66395	Mm.203866	NM_009643	ENSMUSG00000069833	Ahnak	DY6	AHNAK nucleoprotein (desmoyokin)	protein-coding
mm_30478.1	chr3	154821770	154821773	-	1	NA	intron (NM_177066, intron 23 of 24)	intron (NM_177066, intron 23 of 24)	110638	NM_175176	209601	Mm.331454	NM_175176	ENSMUSG00000078161	Erich3	1700013E18Rik|4922501L14Rik|5031409G23Rik|AI596448|Gm133	glutamate rich 3	protein-coding
mm_6829.1	chr1	84204793	84204832	-	1	NA	intron (NM_001003948, intron 1 of 2)	(CCCA)n|Simple_repeat|Simple_repeat	14149	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_42683.1	chr5	119832085	119832097	+	1	NA	Intergenic	Intergenic	-2572	NM_011537	21388	Mm.103636	NM_011537	ENSMUSG00000018263	Tbx5	-	T-box 5	protein-coding
mm_89892.1	chr10	110793730	110793747	+	1	NA	Intergenic	Intergenic	48273	NM_178609	52679	Mm.11747	NM_178609	ENSMUSG00000020185	E2f7	A630014C11Rik|D10Ertd739e	E2F transcription factor 7	protein-coding
mm_9816.1	chr1	182020258	182020291	-	1	NA	promoter-TSS (NM_010135)	promoter-TSS (NM_010135)	-294	NM_010135	13800	Mm.87759	NM_008680	ENSMUSG00000022995	Enah	Mena|NDPP-1|Ndpp1|WBP8	enabled homolog (Drosophila)	protein-coding
mm_166517.1	chr6	17306375	17306379	+	1	NA	promoter-TSS (NM_007616)	promoter-TSS (NM_007616)	42	NM_007616	12389	Mm.28278	NM_007616	ENSMUSG00000007655	Cav1	Cav|Cav-1	caveolin 1, caveolae protein	protein-coding
mm_37891.1	chr4	132533360	132533395	-	1	NA	exon (NM_007512, exon 3 of 4)	exon (NM_007512, exon 3 of 4)	2037	NM_007512	11983	Mm.2171	NM_007512	ENSMUSG00000054428	Atpif1	Atpi|IF(1)|If1	ATPase inhibitory factor 1	protein-coding
mm_78214.1	chr9	21510593	21510626	+	1	NA	promoter-TSS (NM_010744)	promoter-TSS (NM_010744)	-375	NM_010744	17083	Mm.196618	NM_010744	ENSMUSG00000032180	Tmed1	Il1rl1l|Ly84l|St2l	transmembrane p24 trafficking protein 1	protein-coding
mm_155747.1	chrX	96167071	96167084	+	1	NA	3' UTR (NM_010833, exon 13 of 13)	3' UTR (NM_010833, exon 13 of 13)	71032	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_154935.1	chrX	35891239	35891242	+	1	NA	intron (NM_001009947, intron 1 of 52)	intron (NM_001009947, intron 1 of 52)	2408	NM_001009947	75974	Mm.32873	NM_177745	ENSMUSG00000031093	Dock11	5033414A21Rik|8030476J24|Zizimin2|sph238	dedicator of cytokinesis 11	protein-coding
mm_25256.1	chr3	104780822	104780829	+	1	NA	promoter-TSS (NM_027982)	promoter-TSS (NM_027982)	-231	NM_027982	71887	Mm.379204	NM_027982	ENSMUSG00000002228	Ppm1j	2310008J22Rik|PP2Czeta|Ppp2cz	protein phosphatase 1J	protein-coding
mm_163254.1	chr11	109427018	109427027	+	1	NA	5' UTR (NM_025275, exon 3 of 9)	5' UTR (NM_025275, exon 3 of 9)	802	NM_001252193	13929	Mm.211850	NM_025275	ENSMUSG00000020610	Amz2	AA408420|ESTM12|X83328	archaelysin family metallopeptidase 2	protein-coding
mm_85042.1	chr9	89092683	89092691	-	1	NA	5' UTR (NM_001170884, exon 1 of 7)	5' UTR (NM_001170884, exon 1 of 7)	148	NM_001170884	666747	Mm.425592	NM_001170884	ENSMUSG00000079162	Trim43b	EG666747|Gm8269	tripartite motif-containing 43B	protein-coding
mm_35451.1	chr4	40279341	40279381	-	1	NA	promoter-TSS (NM_001033305)	promoter-TSS (NM_001033305)	60	NM_001033305	230075	Mm.1103	NM_001033305	ENSMUSG00000071014	Ndufb6	CI-B17|Gm137	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 6	protein-coding
mm_95003.1	chr11	31874320	31874345	+	1	NA	intron (NM_001290676, intron 1 of 8)	intron (NM_001290676, intron 1 of 8)	3392	NM_026252	67579	Mm.339792	NM_026252	ENSMUSG00000020300	Cpeb4	Cpe-bp4|Cpeb-4|mCPEB-4	cytoplasmic polyadenylation element binding protein 4	protein-coding
mm_16587.1	chr2	3726788	3726808	-	1	NA	intron (NM_025626, intron 1 of 3)	intron (NM_025626, intron 1 of 3)	13340	NM_025626	66540	Mm.277864	NM_025626	ENSMUSG00000026655	Fam107b	3110001A13Rik|AA589595|AA959793|AI132312	family with sequence similarity 107, member B	protein-coding
mm_103823.1	chr11	83012136	83012147	-	1	NA	intron (NM_181545, intron 4 of 5)	Lx7|LINE|L1	8581	NM_001167743	276950	Mm.491599	NM_181545	ENSMUSG00000035208	Slfn8	-	schlafen 8	protein-coding
mm_118591.1	chr14	20655242	20655273	+	1	NA	intron (NM_021508, intron 2 of 5)	intron (NM_021508, intron 2 of 5)	1283	NM_021508	59011	Mm.439911	NM_021508	ENSMUSG00000068697	Myoz1	2310001N11Rik|AV090278|FATZ|Myoz	myozenin 1	protein-coding
mm_128817.1	chr15	67114889	67114909	-	1	NA	intron (NM_009177, intron 3 of 8)	intron (NM_009177, intron 3 of 8)	61983	NM_009177	20442	Mm.248334	NM_009177	ENSMUSG00000013846	St3gal1	5330418N22Rik|AI467004|ST3GalI|Siat4|Siat4a|St3gal-1	ST3 beta-galactoside alpha-2,3-sialyltransferase 1	protein-coding
mm_149342.1	chr19	10850424	10850439	+	1	NA	intron (NM_023044, intron 2 of 7)	MTD|LTR|ERVL-MaLR	7887	NM_023044	65221	Mm.27387	NM_023044	ENSMUSG00000024737	Slc15a3	Ci1|cI-1	solute carrier family 15, member 3	protein-coding
mm_153373.1	chr19	40356617	40356654	-	1	NA	intron (NM_001034963, intron 8 of 22)	intron (NM_001034963, intron 8 of 22)	45675	NM_001034964	20411	Mm.210815	NM_009166	ENSMUSG00000025006	Sorbs1	2310065E01Rik|9530001P15Rik|CAP|SH3P12|Sh3d5|mKIAA1296	sorbin and SH3 domain containing 1	protein-coding
mm_153769.1	chr19	45631123	45631157	-	1	NA	intron (NM_013907, intron 4 of 8)	intron (NM_013907, intron 4 of 8)	29053	NM_013907	30838	Mm.254739	NM_013907	ENSMUSG00000040913	Fbxw4	Dac|Fbw4|SHFM3|SHSF3|dactylin|dactylyn	F-box and WD-40 domain protein 4	protein-coding
mm_138022.1	chr17	33910424	33910445	+	1	NA	5' UTR (NM_001199733, exon 2 of 8)	5' UTR (NM_001199733, exon 2 of 8)	833	NM_001199733	13163	Mm.271809	NM_007829	ENSMUSG00000002307	Daxx	-	Fas death domain-associated protein	protein-coding
mm_39017.1	chr4	152131411	152131420	-	1	NA	intron (NM_207688, intron 3 of 10)	CpG-10714	-2490	NM_019585	56226	Mm.264215	NM_019585	ENSMUSG00000028943	Espn	je	espin	protein-coding
mm_150676.1	chr19	42052284	42052284	+	1	NA	promoter-TSS (NM_025752)	promoter-TSS (NM_025752)	56	NM_025752	66765	Mm.440412	NM_025752	ENSMUSG00000090369	4933411K16Rik	-	RIKEN cDNA 4933411K16 gene	protein-coding
mm_75609.1	chr8	62123107	62123123	-	1	NA	promoter-TSS (NM_001136089)	promoter-TSS (NM_001136089)	78	NM_001136089	26359	Mm.42179	NM_011922	ENSMUSG00000031635	Anxa10	-	annexin A10	protein-coding
mm_123317.1	chr14	62497336	62497342	-	1	NA	Intergenic	Lx8|LINE|L1	-41050	NM_172810	239134	Mm.236557	NM_172810	ENSMUSG00000021933	Gucy1b2	B930025B03|GC-SB2	guanylate cyclase 1, soluble, beta 2	protein-coding
mm_110352.1	chr12	38730826	38730832	-	1	NA	Intergenic	RMER17A2|LTR|ERVK	-49253	NM_001347379	14009	Mm.4866	NM_007960	ENSMUSG00000004151	Etv1	ER81|Etsrp81	ets variant 1	protein-coding
mm_159700.1	chr5	26817397	26817397	+	1	NA	promoter-TSS (NM_010075)	promoter-TSS (NM_010075)	40	NM_010075	13483	Mm.42078	NM_010075	ENSMUSG00000061576	Dpp6	B930011P16Rik|D5Buc3|D5Buc4|D5Buc5|DPP VI|Dpp-6|Gm1377|In(5)6H-p|Peplb|Rw	dipeptidylpeptidase 6	protein-coding
mm_166212.1	chr5	52190537	52190543	-	1	NA	promoter-TSS (NM_001042620)	promoter-TSS (NM_001042620)	6	NR_104311	13204	Mm.993	NM_007839	ENSMUSG00000029169	Dhx15	DBP1|DEAH9|Ddx15|HRH2|mDEAH9	DEAH (Asp-Glu-Ala-His) box polypeptide 15	protein-coding
mm_46868.1	chr5	113830391	113830418	-	1	NA	promoter-TSS (NM_009151)	promoter-TSS (NM_009151)	97	NM_009151	20345	Mm.332590	NM_009151	ENSMUSG00000048163	Selplg	CD162|Psgl-1|Psgl1|Selp1|Selpl	selectin, platelet (p-selectin) ligand	protein-coding
mm_76124.1	chr8	80869245	80869255	-	1	NA	intron (NM_021356, intron 1 of 9)	intron (NM_021356, intron 1 of 9)	11229	NM_021356	14388	Mm.277409	NM_021356	ENSMUSG00000031714	Gab1	AA408973|AW107238	growth factor receptor bound protein 2-associated protein 1	protein-coding
mm_33206.1	chr4	126429701	126429763	+	1	NA	promoter-TSS (NM_153402)	promoter-TSS (NM_153402)	-190	NM_153402	214150	Mm.440915	NM_153402	ENSMUSG00000028842	Ago3	AW048688|C130014L07Rik|Eif2c3	argonaute RISC catalytic subunit 3	protein-coding
mm_52197.1	chr6	100527351	100527395	+	1	NA	promoter-TSS (NR_040525)	promoter-TSS (NR_040525)	-27	NR_040525	73395	Mm.69413	NR_040525	ENSMUSG00000101553	1700049E22Rik	-	RIKEN cDNA 1700049E22 gene	ncRNA
mm_69714.1	chr7	140154643	140154698	-	1	NA	promoter-TSS (NM_183147)	promoter-TSS (NM_183147)	-11	NM_183147	212518	Mm.246858	NM_183147	ENSMUSG00000045733	Sprn	C630041J07	shadow of prion protein	protein-coding
mm_91070.1	chr10	19008374	19008394	-	1	NA	intron (NM_001166402, intron 1 of 7)	intron (NM_001166402, intron 1 of 7)	3579	NM_001166402	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_58787.1	chr7	16130146	16130170	+	1	NA	5' UTR (NM_148946, exon 1 of 10)	5' UTR (NM_148946, exon 1 of 10)	332	NM_148946	110891	Mm.241147	NM_148946	ENSMUSG00000030376	Slc8a2	Ncx2	solute carrier family 8 (sodium/calcium exchanger), member 2	protein-coding
mm_146023.1	chr18	69519798	69519807	+	1	NA	intron (NM_013685, intron 5 of 19)	intron (NM_013685, intron 5 of 19)	174081	NM_001083967	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding
mm_1726.1	chr1	75375272	75375325	+	1	NA	promoter-TSS (NM_007463)	promoter-TSS (NM_007463)	1	NM_007463	11790	Mm.275397	NM_007463	ENSMUSG00000026207	Speg	AW125581|Apeg1|BPEG|D1Bwg1450e|SPEGalpha|SPEGbeta|mKIAA1297	SPEG complex locus	protein-coding
mm_93082.1	chr10	89533551	89533590	-	1	NA	promoter-TSS (NM_001163504)	promoter-TSS (NM_001163504)	52	NM_001163504	20186	Mm.3095	NM_009108	ENSMUSG00000047638	Nr1h4	AI957360|Fxr|HRR1|RIP14|Rxrip14	nuclear receptor subfamily 1, group H, member 4	protein-coding
mm_31946.1	chr4	86711090	86711114	+	1	NA	Intergenic	MLTR25A|LTR|ERVK	-37453	NM_184088	329877	Mm.273718	NM_184088	ENSMUSG00000038024	Dennd4c	1700065A05Rik|AA420392	DENN/MADD domain containing 4C	protein-coding
mm_45706.1	chr5	83355121	83355127	-	1	NA	promoter-TSS (NM_153801)	promoter-TSS (NM_153801)	71	NM_153801	243078	Mm.126783	NM_153801	ENSMUSG00000049537	Tecrl	D330017N19Rik|Srd5a2l2	trans-2,3-enoyl-CoA reductase-like	protein-coding
mm_69785.1	chr7	141094889	141094949	-	1	NA	5' UTR (NM_023059, exon 2 of 10)	5' UTR (NM_023059, exon 2 of 10)	5627	NM_023059	24058	Mm.38017	NM_023059	ENSMUSG00000025494	Sigirr	AI256711|TIR8	single immunoglobulin and toll-interleukin 1 receptor (TIR) domain	protein-coding
mm_63846.1	chr7	135652484	135652499	+	1	NA	promoter-TSS (NR_015548)	promoter-TSS (NR_015548)	-177	NR_015548	67765	Mm.445272	NR_015548	ENSMUSG00000097471	5830432E09Rik	-	RIKEN cDNA 5830432E09 gene	ncRNA
mm_123995.1	chr14	75786967	75786980	-	1	NA	promoter-TSS (NM_026232)	promoter-TSS (NM_026232)	64	NM_026232	67554	Mm.46067	NM_026232	ENSMUSG00000022003	Slc25a30	4933433D23Rik|AV025504|AV221431|AW319655|KMCP1	solute carrier family 25, member 30	protein-coding
mm_133410.1	chr16	85056372	85056391	+	1	NA	exon (NM_001198823, exon 6 of 18)	exon (NM_001198823, exon 6 of 18)	84170	NR_045889	100038614	Mm.441351	NR_045889		Gm10791	ENSMUSG00000074933	predicted gene 10791	ncRNA
mm_141752.1	chr17	34261589	34261593	-	1	NA	Intergenic	Intergenic	-1636	NM_207105	14961	Mm.254067	NM_207105	ENSMUSG00000073421	H2-Ab1	AI845868|Abeta|H-2Ab|H2-Ab|I-Abeta|IAb|Ia-2|Ia2|Rmcs1	histocompatibility 2, class II antigen A, beta 1	protein-coding
mm_146530.1	chr18	5334310	5334331	-	1	NA	intron (NM_178722, intron 1 of 4)	CpG	119	NM_178722	240186	Mm.118257	NM_178722	ENSMUSG00000050945	Zfp438	9430031G09|9430091M14Rik|B830013J05Rik	zinc finger protein 438	protein-coding
mm_162441.1	chr1	113194260	113194267	+	1	NA	Intergenic	MTE2a|LTR|ERVL-MaLR	-1329345	NM_001081316	319901	Mm.103468	NM_001081316	ENSMUSG00000038702	Dsel	9330132E09Rik|DS-epi2	dermatan sulfate epimerase-like	protein-coding
mm_170131.1	chr17	39847265	39847265	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	4268	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_144637.1	chr18	32978596	32978600	+	1	NA	intron (NM_009793, intron 1 of 10)	L1Md_T|LINE|L1	39557	NM_009793	12326	Mm.222329	NM_009793	ENSMUSG00000038128	Camk4	A430110E23Rik|AI666733|CaMKIV|CaMKIV/Gr|D18Bwg0362e	calcium/calmodulin-dependent protein kinase IV	protein-coding
mm_55479.1	chr6	68910981	68910998	-	1	NA	Intergenic	Intergenic	416185	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_11966.1	chr2	53192167	53192177	+	1	NA	promoter-TSS (NM_018785)	promoter-TSS (NM_018785)	88	NM_022989	65103	Mm.37623	NM_022989	ENSMUSG00000026960	Arl6ip6	2310057C01Rik|2610529A11Rik|Aip-6	ADP-ribosylation factor-like 6 interacting protein 6	protein-coding
mm_14372.1	chr2	129630112	129630134	+	1	NA	exon (NM_001291022, exon 5 of 5)	exon (NM_001291022, exon 5 of 5)	36954	NM_001291022	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_134698.1	chr16	22657085	22657096	-	1	NA	5' UTR (NM_138650, exon 1 of 25)	5' UTR (NM_138650, exon 1 of 25)	141	NM_138650	110197	Mm.194986	NM_138650	ENSMUSG00000022861	Dgkg	2900055E17Rik|90kDa|AI854428|Dagk3|E430001K23Rik|mKIAA4131	diacylglycerol kinase, gamma	protein-coding
mm_147473.1	chr18	46741545	46741584	-	1	NA	promoter-TSS (NM_026217)	promoter-TSS (NM_026217)	15	NM_026217	67526	Mm.9852	NM_026217	ENSMUSG00000032905	Atg12	4931423H11Rik|A330058M13Rik|Apg12l|Atg12l	autophagy related 12	protein-coding
mm_45722.1	chr5	86065477	86065501	-	1	NA	promoter-TSS (NM_001345902)	promoter-TSS (NM_001345902)	94	NM_001345902	12617	Mm.4649	NM_007683	ENSMUSG00000029253	Cenpc1	CENP-C|Cenpc	centromere protein C1	protein-coding
mm_172830.1	chr9	20584741	20584752	-	1	NA	intron (NM_172919, intron 1 of 5)	RLTR11B|LTR|ERVK	3418	NM_172919	244721	Mm.86627	NM_172919	ENSMUSG00000058192	Zfp846	2210010B09Rik|9130221F13|Znf846	zinc finger protein 846	protein-coding
mm_141851.1	chr17	34801889	34801904	-	1	NA	exon (NM_009995, exon 10 of 10)	exon (NM_009995, exon 10 of 10)	2530	NM_009995	13079	Mm.440407	NM_009995	ENSMUSG00000024365	Cyp21a1	21-OH|21OH|21OHA|21OHB|CYP21OH-A|Cyp21|Cyp21-ps1|Cyp21B|Cyp21a2-ps|Cyp21a2ps|Oh21-1|Oh21-2	cytochrome P450, family 21, subfamily a, polypeptide 1	protein-coding
mm_25653.1	chr3	121484737	121484744	+	1	NA	intron (NM_145394, intron 12 of 14)	intron (NM_145394, intron 12 of 14)	47604	NM_145394	213603	Mm.33062	NM_145394	ENSMUSG00000039865	Slc44a3	BC010552	solute carrier family 44, member 3	protein-coding
mm_35289.1	chr4	21767174	21767217	-	1	NA	promoter-TSS (NM_029840)	promoter-TSS (NM_029840)	16	NM_029840	77032	Mm.87238	NM_029840	ENSMUSG00000028251	Tstd3	2610029I01Rik	thiosulfate sulfurtransferase (rhodanese)-like domain containing 3	protein-coding
mm_153292.1	chr19	37376230	37376242	-	1	NA	promoter-TSS (NM_010615)	promoter-TSS (NM_010615)	-167	NM_010615	16551	Mm.42203	NM_010615	ENSMUSG00000012443	Kif11	Eg5|Kif8|Kifl1|Knsl1	kinesin family member 11	protein-coding
mm_109227.1	chr12	108793932	108793945	+	1	NA	exon (NM_009537, exon 1 of 5)	exon (NM_009537, exon 1 of 5)	627	NM_009537	22632	Mm.3868	NM_009537	ENSMUSG00000021264	Yy1	AW488674|NF-E1	YY1 transcription factor	protein-coding
mm_163467.1	chr12	102423680	102423695	-	1	NA	exon (NM_011175, exon 2 of 14)	exon (NM_011175, exon 2 of 14)	16126	NM_011175	19141	Mm.17185	NM_011175	ENSMUSG00000021190	Lgmn	AEP|AI746452|AU022324|Prsc1	legumain	protein-coding
mm_95588.1	chr11	53324675	53324704	+	1	NA	promoter-TSS (NM_026479)	promoter-TSS (NM_026479)	0	NM_026479	67966	Mm.288072	NM_026479	ENSMUSG00000018239	Zcchc10	2410141K03Rik|AA675321|D11Ertd416e	zinc finger, CCHC domain containing 10	protein-coding
mm_10753.1	chr2	23197392	23197395	+	1	NA	3' UTR (NM_013771, exon 19 of 19)	3' UTR (NM_013771, exon 19 of 19)	-10083	NM_027635	70981	Mm.314026	NM_027635	ENSMUSG00000026774	4931423N10Rik	-	RIKEN cDNA 4931423N10 gene	protein-coding
mm_165631.1	chr3	68584133	68584141	+	1	NA	intron (NM_013928, intron 1 of 6)	intron (NM_013928, intron 1 of 6)	11769	NM_013928	30953	Mm.331064	NM_013928	ENSMUSG00000027777	Schip1	Nf2ip|Schip-1	schwannomin interacting protein 1	protein-coding
mm_152217.1	chr19	8257647	8257649	-	1	NA	Intergenic	Intergenic	-38748	NM_001347426	236293	Mm.440581	NM_172776	ENSMUSG00000075044	Slc22a29	D630002G06Rik	solute carrier family 22. member 29	protein-coding
mm_111443.1	chr12	98203665	98203687	-	1	NA	3' UTR (NM_008079, exon 17 of 17)	3' UTR (NM_008079, exon 17 of 17)	55783	NM_008079	14420	Mm.5120	NM_008079	ENSMUSG00000021003	Galc	2310068B06Rik|A930008M05Rik|AW212969|AW413532|Gacy|twi|twitcher	galactosylceramidase	protein-coding
mm_47555.1	chr5	124392024	124392040	-	1	NA	exon (NM_001081203, exon 20 of 32)	exon (NM_001081203, exon 20 of 32)	33882	NM_001081203	243272	Mm.23879	NM_001081203	ENSMUSG00000038095	Sbno1	9330180L10Rik|AI849128|AW557836|BC021875|Sbno|mSno1|sno	strawberry notch homolog 1 (Drosophila)	protein-coding
mm_3367.1	chr1	138304771	138304783	+	1	NA	Intergenic	Intergenic	31039	NM_177397	338375	Mm.114424	NM_177397	ENSMUSG00000026394	Atp6v1g3	-	ATPase, H+ transporting, lysosomal V1 subunit G3	protein-coding
mm_138899.1	chr17	43568607	43568639	+	1	NA	5' UTR (NM_013737, exon 1 of 12)	5' UTR (NM_013737, exon 1 of 12)	172	NM_013737	27226	Mm.9277	NM_013737	ENSMUSG00000023913	Pla2g7	PAF-AH|R75400	phospholipase A2, group VII (platelet-activating factor acetylhydrolase, plasma)	protein-coding
mm_126829.1	chr15	88862468	88862484	+	1	NA	5' UTR (NM_145478, exon 1 of 6)	5' UTR (NM_145478, exon 1 of 6)	282	NM_145478	223775	Mm.400129	NM_145478	ENSMUSG00000035828	Pim3	BC026639|Kid1	proviral integration site 3	protein-coding
mm_10106.1	chr2	3636895	3636901	+	1	NA	Intergenic	Intergenic	-76560	NM_025626	66540	Mm.277864	NM_025626	ENSMUSG00000026655	Fam107b	3110001A13Rik|AA589595|AA959793|AI132312	family with sequence similarity 107, member B	protein-coding
mm_10271.1	chr2	9882124	9882134	+	1	NA	TTS (NR_040511)	TTS (NR_040511)	883	NR_024257	381347	Mm.441450	NR_024257		4930412O13Rik	ENSMUSG00000075535|Gm10853	RIKEN cDNA 4930412O13 gene	ncRNA
mm_98971.1	chr11	98685893	98685901	+	1	NA	intron (NM_009439, intron 2 of 11)	intron (NM_009439, intron 2 of 11)	3343	NM_009439	22123	Mm.12194	NM_009439	ENSMUSG00000017221	Psmd3	AI255837|AntP91a|D11Bwg1349e|Psd3|Tstap91a	proteasome (prosome, macropain) 26S subunit, non-ATPase, 3	protein-coding
mm_120979.1	chr14	78703540	78703585	+	1	NA	intron (NM_001081336, intron 1 of 28)	B3|SINE|B2	21527	NM_001081336	380921	Mm.89591	NM_001081336	ENSMUSG00000034731	Dgkh	5930402B05Rik|D130015C16|DGK	diacylglycerol kinase, eta	protein-coding
mm_11940.1	chr2	52866643	52866645	+	1	NA	intron (NM_172409, intron 1 of 26)	intron (NM_172409, intron 1 of 26)	8776	NM_172409	71409	Mm.394427	NM_172409	ENSMUSG00000036053	Fmnl2	5430425K04Rik|Man	formin-like 2	protein-coding
mm_127782.1	chr15	3542398	3542408	-	1	NA	intron (NM_001048178, intron 1 of 8)	Tigger7|DNA|TcMar-Tigger	39439	NM_001286370	14600	Mm.3986	NM_010284	ENSMUSG00000055737	Ghr	GHBP|GHR/BP	growth hormone receptor	protein-coding
mm_167944.1	chrX	132146960	132146960	+	1	NA	Intergenic	Lx8b|LINE|L1	1542033	NM_001105245	279653	Mm.39738	NM_001105245	ENSMUSG00000051323	Pcdh19	B530002L05Rik|Gm717|mKIAA1313	protocadherin 19	protein-coding
mm_120773.1	chr14	73798880	73798882	+	1	NA	Intergenic	Intergenic	246095	NM_011506	20916	Mm.38951	NM_011506	ENSMUSG00000022110	Sucla2	4930547K18Rik|A-SCS	succinate-Coenzyme A ligase, ADP-forming, beta subunit	protein-coding
mm_38367.1	chr4	138367882	138367892	-	1	NA	promoter-TSS (NM_028176)	promoter-TSS (NM_028176)	68	NM_028176	72269	Mm.46182	NM_028176	ENSMUSG00000028755	Cda	2210401N16Rik	cytidine deaminase	protein-coding
mm_65086.1	chr7	19260926	19260943	-	1	NA	exon (NM_001282022, exon 6 of 13)	exon (NM_001282022, exon 6 of 13)	10920	NM_001282021	22323	Mm.9684	NM_009499	ENSMUSG00000030403	Vasp	-	vasodilator-stimulated phosphoprotein	protein-coding
mm_142656.1	chr17	47629111	47629113	-	1	NA	Intergenic	Intergenic	-1578	NM_198421	224836	Mm.59393	NM_198421	ENSMUSG00000090115	Usp49	C330046L10Rik|Gm545	ubiquitin specific peptidase 49	protein-coding
mm_32326.1	chr4	103978864	103978865	+	1	NA	Intergenic	Intergenic	-388674	NR_104385	13131	Mm.289682	NM_010014	ENSMUSG00000028519	Dab1	AI956902|C630028C02Rik|scm|scr|scrambler|yot	disabled 1	protein-coding
mm_18451.1	chr2	60962858	60962926	-	1	NA	5' UTR (NM_020296, exon 1 of 14)	5' UTR (NM_020296, exon 1 of 14)	312	NM_020296	56878	Mm.259667	NM_020296	ENSMUSG00000026970	Rbms1	2600014B10Rik|AI255215|MSSP-1|MSSP-2|MSSP-3|YC1	RNA binding motif, single stranded interacting protein 1	protein-coding
mm_78675.1	chr9	40781129	40781177	+	1	NA	exon (NM_133733, exon 6 of 7)	exon (NM_133733, exon 6 of 7)	-20120	NM_031165	15481	Mm.290774	NM_031165	ENSMUSG00000015656	Hspa8	2410008N15Rik|Hsc70|Hsc71|Hsc73|Hsp73|Hspa10	heat shock protein 8	protein-coding
mm_70487.1	chr8	12396321	12396363	+	1	NA	5' UTR (NM_009233, exon 1 of 1)	5' UTR (NM_009233, exon 1 of 1)	823	NM_009233	20664	Mm.39088	NM_009233	ENSMUSG00000096014	Sox1	BB176347|Sox-1	SRY (sex determining region Y)-box 1	protein-coding
mm_98641.1	chr11	96194337	96194351	+	1	NA	promoter-TSS (NM_008267)	promoter-TSS (NM_008267)	-17	NM_008267	15408	Mm.57221	NM_008267	ENSMUSG00000049604	Hoxb13	-	homeobox B13	protein-coding
mm_103502.1	chr11	76578007	76578019	-	1	NA	promoter-TSS (NM_198894)	promoter-TSS (NM_198894)	-274	NM_198894	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_25853.1	chr3	129612858	129612868	+	1	NA	intron (NM_130450, intron 3 of 4)	intron (NM_130450, intron 3 of 4)	80477	NM_130450	170439	Mm.314113	NM_130450	ENSMUSG00000041220	Elovl6	C77826|FAE|LCE	ELOVL family member 6, elongation of long chain fatty acids (yeast)	protein-coding
mm_12012.1	chr2	57367495	57367528	+	1	NA	3' UTR (NM_010274, exon 17 of 17)	3' UTR (NM_010274, exon 17 of 17)	129129	NM_010274	14571	Mm.3711	NM_010274	ENSMUSG00000026827	Gpd2	AA408484|AI448216|AU021455|AW494132|GPDH|Gdm1|Gpd-m|Gpdh-m|TISP38	glycerol phosphate dehydrogenase 2, mitochondrial	protein-coding
mm_32191.1	chr4	101292250	101292278	+	1	NA	Intergenic	CpG	-26982	NM_146145	16451	Mm.289657	NM_146145	ENSMUSG00000028530	Jak1	AA960307|BAP004|C130039L05Rik	Janus kinase 1	protein-coding
mm_113175.1	chr13	24814048	24814052	+	1	NA	Intergenic	Intergenic	12393	NM_024473	79555	Mm.266668	NM_024473	ENSMUSG00000019132	BC005537	8030460C05Rik|C78201	cDNA sequence BC005537	protein-coding
mm_37478.1	chr4	123565584	123565608	-	1	NA	intron (NM_001199136, intron 1 of 97)	intron (NM_001199136, intron 1 of 97)	-50824	NR_105824	102465214		NR_105824	ENSMUSG00000099005	Mir6398	Gm27657|mmu-mir-6398	microRNA 6398	ncRNA
mm_119159.1	chr14	31641052	31641082	+	1	NA	promoter-TSS (NM_019975)	promoter-TSS (NM_019975)	10	NM_025295	26363	Mm.282679	NM_025295	ENSMUSG00000021900	Btd	-	biotinidase	protein-coding
mm_106796.1	chr12	4907811	4907824	+	1	NA	promoter-TSS (NM_145441)	promoter-TSS (NM_145441)	-297	NM_145441	217379	Mm.259170	NM_145441	ENSMUSG00000020634	Ubxn2a	6330407P03Rik|Ubxd4	UBX domain protein 2A	protein-coding
mm_94000.1	chr10	127594389	127594438	-	1	NA	intron (NM_008512, intron 8 of 88)	intron (NM_008512, intron 8 of 88)	26735	NM_008512	16971	Mm.271854	NM_008512	ENSMUSG00000040249	Lrp1	A2mr|AI316852|CD91|Lrp|b2b1554Clo	low density lipoprotein receptor-related protein 1	protein-coding
mm_124165.1	chr14	93700818	93700835	-	1	NA	intron (NM_001346722, intron 2 of 4)	intron (NM_001346722, intron 2 of 4)	188062	NM_001271800	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding
mm_116534.1	chr13	45875843	45875853	-	1	NA	intron (NM_001199304, intron 2 of 6)	B4|SINE|B4	89143	NM_001199304	20238	Mm.342683	NM_009124	ENSMUSG00000046876	Atxn1	2900016G23Rik|Atx1|C85907|ENSMUSG00000074917|Gm10786|Sca1	ataxin 1	protein-coding
mm_53353.1	chr6	129350349	129350374	+	1	NA	5' UTR (NM_177686, exon 1 of 6)	5' UTR (NM_177686, exon 1 of 6)	117	NM_177686	232413	Mm.90241	NM_177686	ENSMUSG00000053063	Clec12a	CLL-1|D230024O04|KLRL1|Micl	C-type lectin domain family 12, member a	protein-coding
mm_166533.1	chr6	30079942	30079946	+	1	NA	intron (NM_001164229, intron 1 of 12)	intron (NM_001164229, intron 1 of 12)	3623	NM_001164229	18181	Mm.259258	NM_010938	ENSMUSG00000058440	Nrf1	C87038|D6Ertd415e	nuclear respiratory factor 1	protein-coding
mm_64304.1	chr7	141861992	141862000	+	1	NA	exon (NM_028801, exon 31 of 49)	exon (NM_028801, exon 31 of 49)	22924	NM_028801	74180	Mm.200752	NM_028801	ENSMUSG00000066108	Muc5b	2300002I04Rik|A130042M24|AV085033|MUC5|MUC9|mucin 5b	mucin 5, subtype B, tracheobronchial	protein-coding
mm_83793.1	chr9	52288027	52288034	-	1	NA	Intergenic	Intergenic	-119919	NM_001162921	244871	Mm.295686	NM_001162921	ENSMUSG00000035164	Zc3h12c	A230108E06|C230027N18Rik|mKIAA1726	zinc finger CCCH type containing 12C	protein-coding
mm_73544.1	chr8	108724728	108724733	+	1	NA	intron (NM_007496, intron 1 of 9)	intron (NM_007496, intron 1 of 9)	10086	NM_007496	11906	Mm.416972	NM_007496	ENSMUSG00000038872	Zfhx3	A230102L03Rik|Atbf1|Sci|WBP9|mKIAA4228	zinc finger homeobox 3	protein-coding
mm_75877.1	chr8	70765059	70765083	-	1	NA	exon (NM_023065, exon 2 of 8)	exon (NM_023065, exon 2 of 8)	1592	NM_023065	65972	Mm.30241	NM_023065	ENSMUSG00000031838	Ifi30	GILT|IP30	interferon gamma inducible protein 30	protein-coding
mm_103229.1	chr11	70671599	70671608	-	1	NA	exon (NM_001190378, exon 18 of 22)	exon (NM_001190378, exon 18 of 22)	-2187	NM_001167669	216873	Mm.432524	NM_172561	ENSMUSG00000018287	Spag7	5730443G10|ACRP|FSA-1|Fsa1l	sperm associated antigen 7	protein-coding
mm_15713.1	chr2	164018095	164018128	+	1	NA	3' UTR (NM_018753, exon 6 of 6)	3' UTR (NM_018753, exon 6 of 6)	-7113	NM_001114079	381404	Mm.82301	NM_001114079	ENSMUSG00000054582	Pabpc1l	1810053B01Rik|Epab	poly(A) binding protein, cytoplasmic 1-like	protein-coding
mm_78980.1	chr9	45379898	45379903	+	1	NA	intron (NM_022004, intron 1 of 7)	intron (NM_022004, intron 1 of 7)	9715	NM_022004	59095	Mm.208287	NM_022004	ENSMUSG00000066705	Fxyd6	0610030I18Rik|Php	FXYD domain-containing ion transport regulator 6	protein-coding
mm_97041.1	chr11	72306561	72306575	+	1	NA	exon (NM_001037713, exon 4 of 6)	exon (NM_001037713, exon 4 of 6)	4939	NM_001037713	327959	Mm.291131	NM_001037713	ENSMUSG00000040483	Xaf1	Fbox39	XIAP associated factor 1	protein-coding
mm_98433.1	chr11	94937583	94937603	+	1	NA	intron (NM_007742, intron 1 of 50)	intron (NM_007742, intron 1 of 50)	1369	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_68495.1	chr7	111076218	111076231	-	1	NA	intron (NM_001040131, intron 13 of 20)	intron (NM_001040131, intron 13 of 20)	6806	NM_001040131	13690	Mm.185453	NM_013507	ENSMUSG00000005610	Eif4g2	DAP-5|E130105L11Rik|Nat1|Natm1|p97	eukaryotic translation initiation factor 4, gamma 2	protein-coding
mm_72931.1	chr8	91313281	91313293	+	1	NA	promoter-TSS (NM_173431)	promoter-TSS (NM_173431)	-65	NM_173431	244585	Mm.324592	NM_173431	ENSMUSG00000033282	Rpgrip1l	1700047E16Rik|4931437C01|Ftm|Nphp8	Rpgrip1-like	protein-coding
mm_135971.1	chr16	75016104	75016116	-	1	NA	Intergenic	Intergenic	569951	NM_001252513	320355	Mm.99517	NM_177142	ENSMUSG00000032948	Lipi	D930038D03Rik|lpd1	lipase, member I	protein-coding
mm_57547.1	chr6	126738218	126738238	-	1	NA	3' UTR (NM_013568, exon 1 of 2)	3' UTR (NM_013568, exon 1 of 2)	2446	NM_013568	16494	Mm.62535	NM_013568	ENSMUSG00000038077	Kcna6	Kv1.6|MK1.6	potassium voltage-gated channel, shaker-related, subfamily, member 6	protein-coding
mm_120793.1	chr14	74733679	74733691	+	1	NA	intron (NM_001285423, intron 1 of 8)	intron (NM_001285423, intron 1 of 8)	1388	NM_016903	13885	Mm.38055	NM_016903	ENSMUSG00000021996	Esd	Es-10|Es10|FGH|sid478	esterase D/formylglutathione hydrolase	protein-coding
mm_137121.1	chr17	22674333	22674342	+	1	NA	Intergenic	Intergenic	73189	NM_001104575	628185	Mm.390947	NM_001104575	ENSMUSG00000094921	Vmn2r112	EG628185|V2rp1	vomeronasal 2, receptor 112	protein-coding
mm_10737.1	chr2	23069058	23069089	+	1	NA	promoter-TSS (NM_001102438)	promoter-TSS (NM_001102438)	1	NM_001102438	74159	Mm.181973	NM_028793	ENSMUSG00000026781	Acbd5	1300014E15Rik	acyl-Coenzyme A binding domain containing 5	protein-coding
mm_168907.1	chr12	55155415	55155419	+	1	NA	5' UTR (NM_001100109, exon 1 of 16).2	5' UTR (NM_001100109, exon 1 of 16).2	313	NM_001100109	665155	Mm.12848	NM_001100109	ENSMUSG00000079108	Srp54b	-	signal recognition particle 54B	protein-coding
mm_19797.1	chr2	110032388	110032428	-	1	NA	exon (NM_026613, exon 3 of 6)	exon (NM_026613, exon 3 of 6)	14591	NM_026613	68201	Mm.181767	NM_026613	ENSMUSG00000027160	Ccdc34	2810027O19Rik|4930522P10Rik|AI596202	coiled-coil domain containing 34	protein-coding
mm_37594.1	chr4	126533562	126533613	-	1	NA	promoter-TSS (NM_153177)	promoter-TSS (NM_153177)	-129	NM_153177	76850	Mm.86705	NM_153177	ENSMUSG00000042500	Ago4	5730550L01Rik|AI481660|Eif2c4	argonaute RISC catalytic subunit 4	protein-coding
mm_129165.1	chr15	76246610	76246634	-	1	NA	promoter-TSS (NM_023168)	promoter-TSS (NM_023168)	-185	NM_023168	66168	Mm.41665	NM_023168	ENSMUSG00000022564	Grina	1110025J15Rik|Lag|Tmbim3	glutamate receptor, ionotropic, N-methyl D-aspartate-associated protein 1 (glutamate binding)	protein-coding
mm_40542.1	chr5	58004882	58004895	+	1	NA	intron (NM_001310608, intron 3 of 3)	B3|SINE|B2	286807	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_108191.1	chr12	76765528	76765584	+	1	NA	promoter-TSS (NM_206534)	promoter-TSS (NM_206534)	-17	NM_206534	211151	Mm.80970	NM_206534	ENSMUSG00000090258	Churc1	1700030P15Rik|My015|chch	churchill domain containing 1	protein-coding
mm_119780.1	chr14	54181422	54181438	+	1	NA	Intergenic	Intergenic	72499	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_32137.1	chr4	99224492	99224494	+	1	NA	exon (NM_001145967, exon 7 of 11)	exon (NM_001145967, exon 7 of 11)	30346	NM_001145967	242557	Mm.241663	NM_175029	ENSMUSG00000028550	Atg4c	Apg4-C|Apg4c|Atg4cl|Autl1	autophagy related 4C, cysteine peptidase	protein-coding
mm_37681.1	chr4	129222378	129222391	-	1	NA	exon (NM_001285867, exon 6 of 7)	exon (NM_001285867, exon 6 of 7)	5527	NM_001285866	97130	Mm.331907	NM_001033189	ENSMUSG00000050390	C77080	Kiaa1522|mKIAA1522	expressed sequence C77080	protein-coding
mm_84927.1	chr9	81633771	81633787	-	1	NA	intron (NR_040396, intron 1 of 4)	intron (NR_040396, intron 1 of 4)	-1227	NM_010482	15551	Mm.445308	NM_010482	ENSMUSG00000049511	Htr1b	-	5-hydroxytryptamine (serotonin) receptor 1B	protein-coding
mm_111894.1	chr12	108636818	108636830	-	1	NA	intron (NM_001163396, intron 2 of 14)	intron (NM_001163396, intron 2 of 14)	1071	NM_001163396	14026	Mm.238841	NM_007965	ENSMUSG00000021262	Evl	AI528774	Ena-vasodilator stimulated phosphoprotein	protein-coding
mm_160044.1	chr6	140543725	140543725	+	1	NA	exon (NM_144920, exon 11 of 31)	exon (NM_144920, exon 11 of 31)	-78938	NM_178803	11569	Mm.86453	NM_009637	ENSMUSG00000030232	Aebp2	AU023766|B230313N05Rik	AE binding protein 2	protein-coding
mm_130303.1	chr15	97019925	97019937	-	1	NA	intron (NM_027052, intron 1 of 15)	intron (NM_027052, intron 1 of 15)	36025	NM_027052	69354	Mm.250980	NM_027052	ENSMUSG00000022464	Slc38a4	1110012E16Rik|1700012A18Rik|Ata3|mATA3|mNAT3	solute carrier family 38, member 4	protein-coding
mm_7088.1	chr1	88576598	88576609	-	1	NA	Intergenic	Intergenic	25086	NR_037971	100503197	Mm.99352	NR_037971	ENSMUSG00000100798	Gm19589	-	predicted gene, 19589	ncRNA
mm_87466.1	chr10	51491112	51491128	+	1	NA	intron (NM_001291894, intron 1 of 8)	intron (NM_001291894, intron 1 of 8)	222	NM_013532	14728	Mm.34408	NM_013532	ENSMUSG00000062593	Lilrb4a	CD85K|Gp49b|HM18|ILT3|LIR-5|Lilrb4|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4A	protein-coding
mm_74464.1	chr8	4217114	4217126	-	1	NA	5' UTR (NM_207203, exon 1 of 7)	5' UTR (NM_207203, exon 1 of 7)	192	NM_207203	73072	Mm.477379	NM_207203	ENSMUSG00000064125	Prr36	-	proline rich 36	protein-coding
mm_84320.1	chr9	63758172	63758190	-	1	NA	promoter-TSS (NM_016769)	promoter-TSS (NM_016769)	-187	NM_016769	17127	Mm.7320	NM_016769	ENSMUSG00000032402	Smad3	AU022421|Madh3	SMAD family member 3	protein-coding
mm_96536.1	chr11	68691907	68691911	+	1	NA	promoter-TSS (NM_175260)	promoter-TSS (NM_175260)	-6	NM_175260	77579	Mm.218233	NM_175260	ENSMUSG00000020900	Myh10	5730504C04Rik|9330167F11Rik|Fltn|Myhn-2|Myhn2|NMHC II-B|NMHC-B|NMHCII-B|NMMHC II-b|NMMHC-B|NMMHC-IIB|SMemb|mKIAA3005	myosin, heavy polypeptide 10, non-muscle	protein-coding
mm_156372.1	chrX	139651700	139651718	+	1	NA	intron (NM_001254761, intron 2 of 6)	intron (NM_001254761, intron 2 of 6)	-33287	NM_001081499	245638	Mm.275869	NM_001081499	ENSMUSG00000042473	Tbc1d8b	4921505D17Rik|9030605E16Rik	TBC1 domain family, member 8B	protein-coding
mm_60784.1	chr7	45566723	45566736	+	1	NA	exon (NM_025330, exon 9 of 9)	exon (NM_025330, exon 9 of 9)	-3424	NM_009737	12036	Mm.24210	NM_009737	ENSMUSG00000030826	Bcat2	Bcat-2|Eca40	branched chain aminotransferase 2, mitochondrial	protein-coding
mm_49107.1	chr6	8259367	8259378	+	1	NA	promoter-TSS (NM_026632)	promoter-TSS (NM_026632)	84	NM_001302353	100036521	Mm.446106	NM_001302353	ENSMUSG00000089862	Umad1	Gm16039|OTTMUSG00000029336	UMAP1-MVP12 associated (UMA) domain containing 1	protein-coding
mm_82200.1	chr9	124080056	124080100	+	1	NA	Intergenic	Intergenic	-22105	NM_009915	12772	Mm.6272	NM_009915	ENSMUSG00000049103	Ccr2	Cc-ckr-2|Ccr2a|Ccr2b|Ckr2|Ckr2a|Ckr2b|Cmkbr2|mJe-r	chemokine (C-C motif) receptor 2	protein-coding
mm_39963.1	chr5	32136976	32136977	+	1	NA	intron (NM_008037, intron 1 of 3)	T-rich|Low_complexity|Low_complexity	504	NM_008037	14284	Mm.24684	NM_008037	ENSMUSG00000029135	Fosl2	Fra-2	fos-like antigen 2	protein-coding
mm_126428.1	chr15	80572675	80572681	+	1	NA	promoter-TSS (NM_001289442)	promoter-TSS (NM_001289442)	81	NM_001289442	17444	Mm.12947	NM_010815	ENSMUSG00000042351	Grap2	GRAP-2|GRB2L|GRBLG|GRID|Gads|GrbX|Grf40|GrpL|Mona|P38	GRB2-related adaptor protein 2	protein-coding
mm_139393.1	chr17	52282633	52282645	+	1	NA	Intergenic	Intergenic	-320070	NM_001031811	211468	Mm.399068	NM_001031811	ENSMUSG00000035580	Kcnh8	C130090D05Rik|ELK|ELK1|ELK3|Kv12.1	potassium voltage-gated channel, subfamily H (eag-related), member 8	protein-coding
mm_135584.1	chr16	50578408	50578420	-	1	NA	Intergenic	Intergenic	-12089	NR_040566	75211	Mm.399337	NR_040566		4930542D17Rik	-	RIKEN cDNA 4930542D17 gene	ncRNA
mm_137867.1	chr17	31319858	31319882	+	1	NA	intron (NM_001242427, intron 6 of 19)	MER2|DNA|TcMar-Tigger	23646	NM_001242427	224674	Mm.311395	NM_153062	ENSMUSG00000024036	Slc37a1	G3PP	solute carrier family 37 (glycerol-3-phosphate transporter), member 1	protein-coding
mm_110533.1	chr12	55014356	55014373	-	1	NA	Intergenic	Intergenic	-28028	NM_013815	217578	Mm.479583	NM_013815	ENSMUSG00000035021	Baz1a	Acf1|B930060C03|BC065123|Gtl5|Wcrf180|cbp146	bromodomain adjacent to zinc finger domain 1A	protein-coding
mm_33735.1	chr4	134118115	134118122	+	1	NA	intron (NR_045571, intron 8 of 13)	intron (NR_045571, intron 8 of 13)	10635	NM_080559	73723	Mm.22240	NM_080559	ENSMUSG00000028843	Sh3bgrl3	1110004L05Rik|AU022188	SH3 domain binding glutamic acid-rich protein-like 3	protein-coding
mm_33052.1	chr4	123105147	123105168	+	1	NA	promoter-TSS (NM_007559)	promoter-TSS (NM_007559)	-4	NM_007559	12164	Mm.439764	NM_007559	ENSMUSG00000002384	Bmp8b	Op3	bone morphogenetic protein 8b	protein-coding
mm_7767.1	chr1	131199988	131199992	-	1	NA	5' UTR (NM_001311094, exon 1 of 5)	5' UTR (NM_001311094, exon 1 of 5)	195	NM_001311094	54354	Mm.248291	NM_018750	ENSMUSG00000026430	Rassf5	1300019G20Rik|Maxp1|Nore1|Nore1A|Nore1B|Rapl	Ras association (RalGDS/AF-6) domain family member 5	protein-coding
mm_125937.1	chr15	76247908	76247923	+	1	NA	promoter-TSS (NR_105918)	promoter-TSS (NR_105918)	-276	NR_105918	102465575		NR_105918	ENSMUSG00000098625	Mir6953	Gm27738|mmu-mir-6953	microRNA 6953	ncRNA
mm_142460.1	chr17	45596658	45596666	-	1	NA	promoter-TSS (NM_001199114)	promoter-TSS (NM_001199114)	-760	NM_001199114	63959	Mm.29744	NM_022880	ENSMUSG00000023942	Slc29a1	1200014D21Rik|AA407560|ENT1	solute carrier family 29 (nucleoside transporters), member 1	protein-coding
mm_148921.1	chr19	6976475	6976497	+	1	NA	intron (NM_008889, intron 1 of 3)	intron (NM_008889, intron 1 of 3)	1438	NM_008889	18938	Mm.140	NM_008889	ENSMUSG00000056612	Ppp1r14b	AOM172|PHI-1|PLCB3N|Png	protein phosphatase 1, regulatory (inhibitor) subunit 14B	protein-coding
mm_3626.1	chr1	152766694	152766710	+	1	NA	promoter-TSS (NM_001346117)	promoter-TSS (NM_001346117)	160	NM_026369	67771	Mm.288974	NM_026369	ENSMUSG00000008475	Arpc5	5830443F10Rik|p16-Arc	actin related protein 2/3 complex, subunit 5	protein-coding
mm_118913.1	chr14	26691662	26691671	+	1	NA	Intergenic	Intergenic	-21820	NM_178668	211948	Mm.290758	NM_178668	ENSMUSG00000043702	Pde12	2'-PDE|E430028B21Rik	phosphodiesterase 12	protein-coding
mm_94525.1	chr11	9049048	9049061	+	1	NA	promoter-TSS (NM_001290520)	promoter-TSS (NM_001290520)	-63	NM_177576	194974	Mm.79210	NM_177576	ENSMUSG00000040985	Sun3	Sunc1	Sad1 and UNC84 domain containing 3	protein-coding
mm_44891.1	chr5	35094981	35094996	-	1	NA	exon (NM_013587, exon 7 of 8)	exon (NM_013587, exon 7 of 8)	10709	NM_013587	16976	Mm.277661	NM_013587	ENSMUSG00000029103	Lrpap1	AA617339|AI790446|AU042172|C77774|HBP44|RAP	low density lipoprotein receptor-related protein associated protein 1	protein-coding
mm_107062.1	chr12	16657903	16657917	+	1	NA	intron (NM_008747, intron 2 of 3)	intron (NM_008747, intron 2 of 3)	4440	NM_008747	18217	Mm.281715	NM_008747	ENSMUSG00000020591	Ntsr2	NT2R|NTRL	neurotensin receptor 2	protein-coding
mm_117741.1	chr13	95883404	95883410	-	1	NA	intron (NM_027711, intron 1 of 35)	intron (NM_027711, intron 1 of 35)	8515	NM_027711	544963	Mm.38878	NM_027711	ENSMUSG00000021676	Iqgap2	4933417J23Rik|A630053O10|AI788777	IQ motif containing GTPase activating protein 2	protein-coding
mm_98077.1	chr11	86484740	86484750	+	1	NA	promoter-TSS (NM_029788)	promoter-TSS (NM_029788)	88	NM_029788	76892	Mm.262707	NM_029788	ENSMUSG00000020521	Rnft1	0610013E23Rik|AV007605	ring finger protein, transmembrane 1	protein-coding
mm_148557.1	chr19	4721185	4721195	+	1	NA	intron (NM_021287, intron 2 of 36)	intron (NM_021287, intron 2 of 36)	9967	NM_021287	20743	Mm.329668	NM_021287	ENSMUSG00000067889	Sptbn2	Spnb3|mKIAA0302	spectrin beta, non-erythrocytic 2	protein-coding
mm_22654.1	chr3	14871546	14871546	+	1	NA	exon (NM_007606, exon 7 of 7)	exon (NM_007606, exon 7 of 7)	8008	NM_007606	12350	Mm.300	NM_007606	ENSMUSG00000027559	Car3	BB219044|Ca3|Car-3	carbonic anhydrase 3	protein-coding
mm_2923.1	chr1	132116597	132116612	+	1	NA	exon (NM_008795, exon 12 of 16)	exon (NM_008795, exon 12 of 16)	23081	NM_008795	18557	Mm.28130	NM_008795	ENSMUSG00000026437	Cdk18	AA682070|Ctk18|Pctk3	cyclin-dependent kinase 18	protein-coding
mm_119049.1	chr14	30631413	30631424	+	1	NA	Intergenic	Intergenic	-5210	NM_011103	18753	Mm.2314	NM_011103	ENSMUSG00000021948	Prkcd	AI385711|D14Ertd420e|PKC[d]|PKCdelta|Pkcd	protein kinase C, delta	protein-coding
mm_146963.1	chr18	33438335	33438348	-	1	NA	3' UTR (NM_001267717, exon 5 of 5)	3' UTR (NM_001267717, exon 5 of 5)	25293	NM_001267717	27528	Mm.407415	NM_053078	ENSMUSG00000042834	Nrep	AI325076|D0H4S114|Harp|P311|PTZ17|SEZ17	neuronal regeneration related protein	protein-coding
mm_2559.1	chr1	112950839	112950842	+	1	NA	Intergenic	Intergenic	-1085922	NM_001081316	319901	Mm.103468	NM_001081316	ENSMUSG00000038702	Dsel	9330132E09Rik|DS-epi2	dermatan sulfate epimerase-like	protein-coding
mm_139578.1	chr17	57080248	57080285	+	1	NA	3' UTR (NM_009451, exon 4 of 4)	3' UTR (NM_009451, exon 4 of 4)	-1756	NM_153551	70785	Mm.284447	NM_153551	ENSMUSG00000002668	Dennd1c	4432409M07Rik	DENN/MADD domain containing 1C	protein-coding
mm_80389.1	chr9	75625843	75625885	+	1	NA	exon (NM_027309, exon 1 of 3)	exon (NM_027309, exon 1 of 3)	132	NM_027309	70082	Mm.19119	NM_027309	ENSMUSG00000032184	Lysmd2	2210402C18Rik|AV033872|AW538442	LysM, putative peptidoglycan-binding, domain containing 2	protein-coding
mm_137572.1	chr17	27847970	27847983	+	1	NA	exon (NM_011432, exon 5 of 6)	exon (NM_011432, exon 5 of 6)	7889	NM_011432	20630	Mm.103949	NM_011432	ENSMUSG00000024217	Snrpc	Snrp1c|U1-C|U1C	U1 small nuclear ribonucleoprotein C	protein-coding
mm_118077.1	chr13	103096819	103096869	-	1	NA	intron (NM_175171, intron 3 of 28)	intron (NM_175171, intron 3 of 28)	237648	NM_175171	328329	Mm.202606	NM_175171	ENSMUSG00000034751	Mast4	4930420O11Rik|AI642422|mKIAA0303	microtubule associated serine/threonine kinase family member 4	protein-coding
mm_102679.1	chr11	65261810	65261818	-	1	NA	intron (NM_146386, intron 1 of 12)	intron (NM_146386, intron 1 of 12)	8175	NM_145136	214384	Mm.32257	NM_145136	ENSMUSG00000020542	Myocd	BSAC2A|Srfcp	myocardin	protein-coding
mm_107549.1	chr12	41024097	41024134	+	1	NA	promoter-TSS (NM_053122)	promoter-TSS (NM_053122)	25	NM_053122	93757	Mm.363813	NM_053122	ENSMUSG00000056899	Immp2l	AI853880|IMP2	IMP2 inner mitochondrial membrane peptidase-like (S. cerevisiae)	protein-coding
mm_117078.1	chr13	59557231	59557346	-	1	NA	promoter-TSS (NM_001284219)	promoter-TSS (NM_001284219)	59	NM_001284218	67269	Mm.153008	NM_023328	ENSMUSG00000021557	Agtpbp1	1700020N17Rik|2310001G17Rik|2900054O13Rik|4930445M19Rik|5730402G09Rik|CCP1|Nna1|nmf243|pcd	ATP/GTP binding protein 1	protein-coding
mm_15195.1	chr2	154205417	154205438	+	1	NA	exon (NM_153418, exon 4 of 16)	exon (NM_153418, exon 4 of 16)	5047	NM_153418	228801	Mm.3783	NM_153418	ENSMUSG00000027485	Bpifb1	Lplunc1	BPI fold containing family B, member 1	protein-coding
mm_135174.1	chr16	35938913	35938938	-	1	NA	5' UTR (NM_030253, exon 1 of 11)	5' UTR (NM_030253, exon 1 of 11)	102	NM_001013371	209200	Mm.390852	NM_001013371	ENSMUSG00000049502	Dtx3l	AU042200|BC023741	deltex 3-like, E3 ubiquitin ligase	protein-coding
mm_142589.1	chr17	46736156	46736169	-	1	NA	3' UTR (NM_001305990, exon 4 of 4)	3' UTR (NM_001305990, exon 4 of 4)	-6997	NM_010321	14711	Mm.29395	NM_010321	ENSMUSG00000002769	Gnmt	-	glycine N-methyltransferase	protein-coding
mm_62769.1	chr7	112310601	112310604	+	1	NA	intron (NM_001193305, intron 6 of 25)	MLT1C|LTR|ERVL-MaLR	-57706	NM_027587	100504195	Mm.291129	NM_027587	ENSMUSG00000030771	Micalcl	4921517J23Rik	MICAL C-terminal like	protein-coding
mm_144667.1	chr18	34409364	34409371	+	1	NA	promoter-TSS (NM_016927)	promoter-TSS (NM_016927)	-56	NM_001163004	53871	Mm.445792	NM_016927	ENSMUSG00000014503	Pkd2l2	TRPP5	polycystic kidney disease 2-like 2	protein-coding
mm_153417.1	chr19	40612161	40612255	-	1	NA	promoter-TSS (NM_026260)	promoter-TSS (NM_026260)	7	NM_026260	67590	Mm.60758	NM_026260	ENSMUSG00000025008	Tctn3	4930521E07Rik|AI197391|Tect3	tectonic family member 3	protein-coding
mm_124766.1	chr15	6665855	6665866	+	1	NA	TTS (NM_001278269)	TTS (NM_001278269)	-42521	NM_030168	78757	Mm.275811	NM_030168	ENSMUSG00000050310	Rictor	4921505C17Rik|6030405M08Rik|AVO3|AW492497|D530039E11Rik	RPTOR independent companion of MTOR, complex 2	protein-coding
mm_128409.1	chr15	44746575	44746597	-	1	NA	intron (NM_178765, intron 2 of 7)	intron (NM_178765, intron 2 of 7)	2086	NM_001285840	319613	Mm.207715	NM_176998	ENSMUSG00000022340	Sybu	Golsyn	syntabulin (syntaxin-interacting)	protein-coding
mm_6425.1	chr1	73930786	73930795	-	1	NA	intron (NM_001289895, intron 22 of 32)	intron (NM_001289895, intron 22 of 32)	-66324	NR_045311	109198	Mm.359721	NR_045311	ENSMUSG00000100301	6030407O03Rik	-	RIKEN cDNA 6030407O03 gene	ncRNA
mm_65727.1	chr7	28381027	28381042	-	1	NA	Intergenic	Intergenic	-1806	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_45106.1	chr5	44799686	44799692	-	1	NA	promoter-TSS (NM_010698)	promoter-TSS (NM_010698)	57	NM_001347349	16826	Mm.25785	NM_010698	ENSMUSG00000039706	Ldb2	AI035351|AW146358|CLIM1|CLP-36|Ldb3	LIM domain binding 2	protein-coding
mm_99574.1	chr11	104132833	104132839	+	1	NA	promoter-TSS (NM_007762)	promoter-TSS (NM_007762)	55	NM_001313929	12921	Mm.1892	NM_007762	ENSMUSG00000018634	Crhr1	CRF1R|CRFR1|Crhr	corticotropin releasing hormone receptor 1	protein-coding
mm_172959.1	chr9	88482183	88482194	-	1	NA	5' UTR (NM_001284328, exon 1 of 12)	5' UTR (NM_001284328, exon 1 of 12)	209	NM_019666	56403	Mm.260545	NM_019666	ENSMUSG00000032423	Syncrip	2610109K23Rik|4632417O19Rik|GRY-RBP|Nsap1|Nsap1l|hnRNP Q|pp68	synaptotagmin binding, cytoplasmic RNA interacting protein	protein-coding
mm_153656.1	chr19	44394871	44394871	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	12838	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_38557.1	chr4	141642824	141642834	-	1	NA	intron (NM_001347237, intron 1 of 18)	intron (NM_001347237, intron 1 of 18)	-18995	NM_001013780	384071	Mm.295682	NM_001013780	ENSMUSG00000040740	Slc25a34	Gm1369	solute carrier family 25, member 34	protein-coding
mm_84815.1	chr9	77535509	77535519	-	1	NA	intron (NM_001146048, intron 1 of 13)	intron (NM_001146048, intron 1 of 13)	8545	NM_172528	214345	Mm.28534	NM_172528	ENSMUSG00000032352	Lrrc1	A430093J20Rik|AU016091|D030059I21|mKIAA4018	leucine rich repeat containing 1	protein-coding
mm_37428.1	chr4	122886074	122886074	-	1	NA	promoter-TSS (NM_007598)	promoter-TSS (NM_007598)	-17	NM_001301067	12331	Mm.8687	NM_007598	ENSMUSG00000028656	Cap1	-	CAP, adenylate cyclase-associated protein 1 (yeast)	protein-coding
mm_37722.1	chr4	129558335	129558345	-	1	NA	promoter-TSS (NM_010693)	promoter-TSS (NM_010693)	32	NM_001162432	16818	Mm.293753	NM_010693	ENSMUSG00000000409	Lck	Hck-3|Lsk|Lskt|p56<lck>|p56Lck	lymphocyte protein tyrosine kinase	protein-coding
mm_57274.1	chr6	123290359	123290371	-	1	NA	promoter-TSS (NM_019948)	promoter-TSS (NM_019948)	-494	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_7736.1	chr1	130851804	130851823	-	1	NA	3' UTR (NM_011082, exon 11 of 11)	3' UTR (NM_011082, exon 11 of 11)	-13964	NM_026976	69169	Mm.46042	NM_026976	ENSMUSG00000042474	Fcmr	1810037B05Rik|Faim3|FcmuR|Toso	Fc fragment of IgM receptor	protein-coding
mm_136740.1	chr17	8340602	8340608	+	1	NA	promoter-TSS (NM_178774)	promoter-TSS (NM_178774)	-134	NM_178774	320111	Mm.442510	NM_178774	ENSMUSG00000055945	Prr18	9630019K15Rik	proline rich 18	protein-coding
mm_49659.1	chr6	31126738	31126742	+	1	NA	intron (NR_110471, intron 3 of 3)	intron (NR_110471, intron 3 of 3)	-63647	NR_029532	387223		NR_029532	ENSMUSG00000065604	Mir29b-1	Mirn29b|Mirn29b-1|mir-29b-1	microRNA 29b-1	ncRNA
mm_128614.1	chr15	58823611	58823621	-	1	NA	promoter-TSS (NM_175212)	promoter-TSS (NM_175212)	-189	NM_175212	74868	Mm.293754	NM_175212	ENSMUSG00000062373	Tmem65	2610029O13Rik|4930438D12Rik	transmembrane protein 65	protein-coding
mm_101399.1	chr11	26593673	26593685	-	1	NA	5' UTR (NM_027260, exon 1 of 13)	5' UTR (NM_027260, exon 1 of 13)	241	NM_027260	69922	Mm.285351	NM_027260	ENSMUSG00000064090	Vrk2	2810003O05Rik|AI447698	vaccinia related kinase 2	protein-coding
mm_149077.1	chr19	8883911	8883928	+	1	NA	promoter-TSS (NM_001286103)	promoter-TSS (NM_001286103)	41	NM_001286103	102308570	Mm.27503	NM_001286103	ENSMUSG00000096740	Lbhd1	Gm21743	LBH domain containing 1	protein-coding
mm_85037.1	chr9	88526787	88526797	-	1	NA	Intergenic	U4|snRNA|snRNA	-3895	NR_040721	72655	Mm.21798	NR_040721	ENSMUSG00000097195	Snhg5	2810026P18Rik|4933428I09Rik|mU50HG-b	small nucleolar RNA host gene 5	ncRNA
mm_95938.1	chr11	58382747	58382789	+	1	NA	exon (NM_001083884, exon 4 of 7)	exon (NM_001083884, exon 4 of 7)	2122	NM_001330197	70163	Mm.24119	NM_027339	ENSMUSG00000013643	Lypd8	2210415F13Rik	LY6/PLAUR domain containing 8	protein-coding
mm_153899.1	chr19	47068379	47068402	-	1	NA	intron (NM_177342, intron 1 of 10)	CpG	642	NM_177342	226182	Mm.301522	NM_177342	ENSMUSG00000025049	Taf5	6330528C20Rik|AV117817	TATA-box binding protein associated factor 5	protein-coding
mm_98869.1	chr11	97799575	97799581	+	1	NA	promoter-TSS (NM_010688)	promoter-TSS (NM_010688)	-94	NM_010688	16796	Mm.271967	NM_010688	ENSMUSG00000038366	Lasp1	AA408629|Def-4|SH3P6|Tg(Col1a1-lacZ)1Ngma	LIM and SH3 protein 1	protein-coding
mm_41134.1	chr5	87808115	87808115	+	1	NA	promoter-TSS (NM_009973)	promoter-TSS (NM_009973)	-6	NM_001301334	12992	Mm.153308	NM_009973	ENSMUSG00000061388	Csn1s2b	AW987150|Csnd|Csne	casein alpha s2-like B	protein-coding
mm_85678.1	chr9	107815961	107815965	-	1	NA	intron (NM_011251, intron 6 of 20)	B3A|SINE|B2	-44961	NM_148930	83486	Mm.259197	NM_148930	ENSMUSG00000032580	Rbm5	D030069N10Rik	RNA binding motif protein 5	protein-coding
mm_122389.1	chr14	40949746	40949753	-	1	NA	intron (NM_145928, intron 1 of 8)	intron (NM_145928, intron 1 of 8)	-1540	NM_001316748	52588	Mm.28876	NM_145928	ENSMUSG00000037824	Tspan14	AA958793|D14Ertd226e|Tm4sf14|tspan-14	tetraspanin 14	protein-coding
mm_141476.1	chr17	31129603	31129619	-	1	NA	promoter-TSS (NM_011575)	promoter-TSS (NM_011575)	0	NM_011575	21786	Mm.4641	NM_011575	ENSMUSG00000024029	Tff3	ITF|mITF	trefoil factor 3, intestinal	protein-coding
mm_52149.1	chr6	97991777	97991790	+	1	NA	promoter-TSS (NM_008601)	promoter-TSS (NM_008601)	0	NM_008601	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_40414.1	chr5	53070014	53070027	+	1	NA	3' UTR (NM_011402, exon 13 of 13)	3' UTR (NM_011402, exon 13 of 13)	20667	NM_011402	20531	Mm.284891	NM_011402	ENSMUSG00000029188	Slc34a2	AA536683|D5Ertd227e|NaPi-2b|Npt2b	solute carrier family 34 (sodium phosphate), member 2	protein-coding
mm_50698.1	chr6	51598933	51598961	+	1	NA	Intergenic	B3A|SINE|B2	54424	NM_001127348	71982	Mm.294166	NM_028035	ENSMUSG00000038301	Snx10	2410004M09Rik	sorting nexin 10	protein-coding
mm_16732.1	chr2	9176056	9176059	-	1	NA	Intergenic	B1F|SINE|Alu	-13458	NR_038180	73438	Mm.23558	NR_038180	ENSMUSG00000085580	1700061F12Rik	-	RIKEN cDNA 1700061F12 gene	ncRNA
mm_65042.1	chr7	18567319	18567345	-	1	NA	promoter-TSS (NM_001037168)	promoter-TSS (NM_001037168)	-27	NM_001037168	545925	Mm.440302	NM_001037168	ENSMUSG00000070797	Psg27	EG545925|cea15	pregnancy-specific glycoprotein 27	protein-coding
mm_97679.1	chr11	79993063	79993122	+	1	NA	promoter-TSS (NM_001163018)	promoter-TSS (NM_001163018)	-14	NM_001163018	52615	Mm.283410	NM_199196	ENSMUSG00000017548	Suz12	2610028O16Rik|AI195385|AU016842|AW536442|D11Ertd530e|mKIAA0160	suppressor of zeste 12 homolog (Drosophila)	protein-coding
mm_116352.1	chr13	38960847	38960883	-	1	NA	promoter-TSS (NM_001170431)	promoter-TSS (NM_001170431)	10	NM_001170431	108652	Mm.255506	NM_134060	ENSMUSG00000021432	Slc35b3	4921526O06Rik|AI428480|CGI-19|PABST2|PAPST2	solute carrier family 35, member B3	protein-coding
mm_44029.1	chr5	147430408	147430545	+	1	NA	promoter-TSS (NM_028291)	promoter-TSS (NM_028291)	-104	NM_028291	72587	Mm.320469	NM_028291	ENSMUSG00000029647	Pan3	2700050F09Rik|A430027N15Rik|AU014670	PAN3 poly(A) specific ribonuclease subunit	protein-coding
mm_87048.1	chr10	28807575	28807585	+	1	NA	intron (NM_001305663, intron 5 of 5)	Lx|LINE|L1	115927	NR_033601	114676	Mm.390292	NR_033601		4930519F09Rik	-	pyruvate dehydrogenase E1 alpha 1 pseudogene	pseudo
mm_23706.1	chr3	68790710	68790720	+	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	-78871	NM_001167996	68725	Mm.45741	NM_001167996	ENSMUSG00000046999	1110032F04Rik	AI115547	RIKEN cDNA 1110032F04 gene	protein-coding
mm_30300.1	chr3	149077180	149077193	-	1	NA	Intergenic	Intergenic	-122551	NM_001081298	99633	Mm.9776	NM_001081298	ENSMUSG00000028184	Adgrl2	AI450192|CIRL-2|Gm619|Lec1|Lphh1|Lphn2|mKIAA0786	adhesion G protein-coupled receptor L2	protein-coding
mm_78204.1	chr9	21424902	21424981	+	1	NA	promoter-TSS (NM_001039520)	promoter-TSS (NM_001039520)	33	NM_001039520	13430	Mm.433257	NM_007871	ENSMUSG00000033335	Dnm2	Dyn2|Udnm|b2b2159Clo	dynamin 2	protein-coding
mm_7064.1	chr1	87573906	87573934	-	1	NA	promoter-TSS (NM_001160164)	promoter-TSS (NM_001160164)	-50	NM_001111314	53972	Mm.435439	NM_019867	ENSMUSG00000026259	Ngef	Tims2|ephexin	neuronal guanine nucleotide exchange factor	protein-coding
mm_147980.1	chr18	67508587	67508589	-	1	NA	intron (NM_194355, intron 6 of 14)	B1_Mur2|SINE|Alu	40585	NM_176832	68166	Mm.208723	NM_176832	ENSMUSG00000024533	Spire1	6030430B19Rik|AI415299|AU022898|AW550622|Spir-1	spire homolog 1 (Drosophila)	protein-coding
mm_66446.1	chr7	44865607	44865622	-	1	NA	exon (NM_133949, exon 6 of 12)	exon (NM_133949, exon 6 of 12)	4174	NM_133949	84113	Mm.42855	NM_133949	ENSMUSG00000038502	Ptov1	1110030G05Rik|AU041779|Gcap3	prostate tumor over expressed gene 1	protein-coding
mm_151862.1	chr19	5797289	5797301	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	-1314	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_79124.1	chr9	46913575	46913585	+	1	NA	promoter-TSS (NR_015605)	promoter-TSS (NR_015605)	-23	NR_015605	73040	Mm.265384	NR_015605	ENSMUSG00000099696	2900052N01Rik	AU067665	RIKEN cDNA 2900052N01 gene	ncRNA
mm_8470.1	chr1	153332997	153333013	-	1	NA	promoter-TSS (NM_010683)	promoter-TSS (NM_010683)	-219	NM_010683	226519	Mm.1249	NM_010683	ENSMUSG00000026478	Lamc1	Lamb2	laminin, gamma 1	protein-coding
mm_166856.1	chr7	20009641	20009649	+	1	NA	intron (NM_194058, intron 1 of 9)	intron (NM_194058, intron 1 of 9)	1622	NM_194058	243874	Mm.277114	NM_194058	ENSMUSG00000060508	Nlrp9b	Nalp-delta|Nalp9b|Nlrp9	NLR family, pyrin domain containing 9B	protein-coding
mm_130453.1	chr15	98564439	98564442	-	1	NA	intron (NM_009833, intron 2 of 8)	intron (NM_009833, intron 2 of 8)	-2884	NR_028442	100048895	Mm.471074	NR_028442		9330020H09Rik	ENSMUSG00000075426	RIKEN cDNA 9330020H09 gene	ncRNA
mm_99232.1	chr11	101063052	101063074	+	1	NA	3' UTR (NM_001243049, exon 21 of 21)	3' UTR (NM_001243049, exon 21 of 21)	-7031	NM_013792	27419	Mm.95452	NM_013792	ENSMUSG00000001751	Naglu	-	alpha-N-acetylglucosaminidase (Sanfilippo disease IIIB)	protein-coding
mm_23798.1	chr3	79852895	79852913	+	1	NA	Intergenic	MLT1F|LTR|ERVL-MaLR	-10242	NM_027495	70652	Mm.46635	NM_027495	ENSMUSG00000027956	Tmem144	1110057I03Rik|5730537D05Rik	transmembrane protein 144	protein-coding
mm_172576.1	chr8	113571545	113571545	-	1	NA	Intergenic	RLTR6-int|LTR|ERV1	54263	NR_110476	78048	Mm.252797	NR_110476		4930571O06Rik	-	RIKEN cDNA 4930571O06 gene	ncRNA
mm_89537.1	chr10	94550866	94550876	+	1	NA	intron (NM_172051, intron 1 of 3)	intron (NM_172051, intron 1 of 3)	-24386	NM_001168684	319880	Mm.23047	NM_172051	ENSMUSG00000020023	Tmcc3	AW488095|C630016B22Rik|C88213|Tmcc1	transmembrane and coiled coil domains 3	protein-coding
mm_17188.1	chr2	25461070	25461080	-	1	NA	promoter-TSS (NM_153557)	promoter-TSS (NM_153557)	19	NM_153557	227622	Mm.261780	NM_153557	ENSMUSG00000047617	BC029214	D930050G13Rik|Paxx	cDNA sequence BC029214	protein-coding
mm_33253.1	chr4	127168532	127168551	+	1	NA	promoter-TSS (NM_198618)	promoter-TSS (NM_198618)	-663	NM_198618	242667	Mm.331885	NM_198618	ENSMUSG00000042388	Dlgap3	BC058433|DAP-3|DAP3|Prpl8|Sapap3	discs, large (Drosophila) homolog-associated protein 3	protein-coding
mm_134807.1	chr16	24608296	24608326	-	1	NA	exon (NM_178665, exon 5 of 13)	exon (NM_178665, exon 5 of 13)	78997	NR_038091	624582	Mm.439775	NR_038091		Morf4l1-ps1	A730098P11Rik	mortality factor 4 like 1, pseudogene 1	pseudo
mm_95314.1	chr11	46396549	46396575	+	1	NA	intron (NR_105955, intron 2 of 4)	intron (NR_105955, intron 2 of 4)	-7047	NM_001281965	16428	Mm.339927	NM_010583	ENSMUSG00000020395	Itk	Emt|Tcsk|Tsk	IL2 inducible T cell kinase	protein-coding
mm_114574.1	chr13	75089847	75089886	+	1	NA	promoter-TSS (NM_013628)	promoter-TSS (NM_013628)	-121	NM_013628	18548	Mm.1333	NM_013628	ENSMUSG00000021587	Pcsk1	Nec-1|Nec1|PC1|PC3|Phpp-1|SPC3	proprotein convertase subtilisin/kexin type 1	protein-coding
mm_144956.1	chr18	37813175	37813234	+	1	NA	intron (NM_033581, intron 1 of 3)	intron (NM_033581, intron 1 of 3)	-1875	NM_033582	93707	Mm.247203	NM_033582	ENSMUSG00000023036	Pcdhgc4	-	protocadherin gamma subfamily C, 4	protein-coding
mm_29449.1	chr3	113149371	113149388	-	1	NA	intron (NM_001190403, intron 9 of 9)	intron (NM_001190403, intron 9 of 9)	7348	NM_001190404	545562	Mm.462977	NM_001190403		Amy2b	Amy-X|Amy2-2|OTTMUSG00000022462|mAmy2-1	amylase 2b	protein-coding
mm_37222.1	chr4	117926754	117926760	-	1	NA	exon (NM_001284191, exon 6 of 6)	exon (NM_001284191, exon 6 of 6)	3006	NM_001284191	11876	Mm.56897	NM_009711	ENSMUSG00000028539	Artn	neublastin	artemin	protein-coding
mm_81045.1	chr9	105470515	105470525	+	1	NA	intron (NM_001253831, intron 1 of 26)	intron (NM_001253831, intron 1 of 26)	24613	NM_175025	235574	Mm.326247	NM_175025	ENSMUSG00000032570	Atp2c1	1700121J11Rik|ATP2C1A|AW061228|BCPM|D930003G21Rik|HHD|SPCA|pmr1	ATPase, Ca++-sequestering	protein-coding
mm_96245.1	chr11	62574524	62574552	+	1	NA	promoter-TSS (NM_011706)	promoter-TSS (NM_011706)	52	NM_011706	22368	Mm.288064	NM_011706	ENSMUSG00000018507	Trpv2	GRC|OTRPC2|VRL-1|Vrl1	transient receptor potential cation channel, subfamily V, member 2	protein-coding
mm_157931.1	chrX	80197276	80197280	-	1	NA	Intergenic	Intergenic	-525843	NM_028025	71967	Mm.379207	NM_028025	ENSMUSG00000046942	Mageb16	2410003J06Rik	melanoma antigen family B, 16	protein-coding
mm_116430.1	chr13	41847600	41847625	-	1	NA	promoter-TSS (NM_001145875)	promoter-TSS (NM_001145875)	4	NM_001145875	109254	Mm.25195	NM_175417	ENSMUSG00000058022	Adtrp	9530008L14Rik	androgen dependent TFPI regulating protein	protein-coding
mm_33075.1	chr4	123859652	123859700	+	1	NA	Intergenic	Intergenic	-45337	NM_019660	56309	Mm.446553	NM_019660	ENSMUSG00000028647	Mycbp	5730488M09Rik|AW552132|AW742590|Amy-1	MYC binding protein	protein-coding
mm_10851.1	chr2	24992633	24992651	+	1	NA	intron (NM_146251, intron 8 of 34)	(T)n|Simple_repeat|Simple_repeat	16609	NM_146251	241274	Mm.389243	NM_146251	ENSMUSG00000036833	Pnpla7	BC027342|E430013P11Rik|Nre	patatin-like phospholipase domain containing 7	protein-coding
mm_50991.1	chr6	63256108	63256126	+	1	NA	promoter-TSS (NM_008167)	promoter-TSS (NM_008167)	-740	NM_008167	14804	Mm.439651	NM_008167	ENSMUSG00000071424	Grid2	B230104L07Rik|GluD2|GluRdelta2|Lc|Lc<J>|MMS10-AC|Ms10ac|cpr|ho|nmf408|tpr	glutamate receptor, ionotropic, delta 2	protein-coding
mm_125790.1	chr15	74721563	74721674	+	1	NA	exon (NM_198607, exon 1 of 2)	exon (NM_198607, exon 1 of 2)	384	NM_198607	223626	Mm.268603	NM_198607	ENSMUSG00000056665	Them6	4930572J05Rik	thioesterase superfamily member 6	protein-coding
mm_168709.1	chr11	99932445	99932459	+	1	NA	Intergenic	Intergenic	-3839	NM_001025244	432602	Mm.246878	NM_001025244	ENSMUSG00000051481	Krtap31-2	OTTMUSG00000002177	keratin associated protein 31-2	protein-coding
mm_156737.1	chrX	159942923	159942945	+	1	NA	5' UTR (NM_001290664, exon 1 of 6)	5' UTR (NM_001290664, exon 1 of 6)	241	NM_001290664	58194	Mm.286495	NM_021389	ENSMUSG00000040990	Sh3kbp1	1200007H22Rik|1700125L08Rik|5830464D22Rik|AI447724|Cin85|IN85|Ruk|Seta	SH3-domain kinase binding protein 1	protein-coding
mm_19577.1	chr2	101644182	101644192	-	1	NA	exon (NM_009019, exon 2 of 2)	exon (NM_009019, exon 2 of 2)	5345	NM_009019	19373	Mm.828	NM_009019	ENSMUSG00000061311	Rag1	Rag-1	recombination activating gene 1	protein-coding
mm_97586.1	chr11	78945683	78945694	+	1	NA	exon (NM_010927, exon 14 of 27)	exon (NM_010927, exon 14 of 27)	20397	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_116897.1	chr13	55400799	55400832	-	1	NA	exon (NM_011392, exon 3 of 13)	exon (NM_011392, exon 3 of 13)	1167	NM_011392	20505	Mm.276355	NM_011392	ENSMUSG00000021490	Slc34a1	NaPi-IIa|Npt2|Npt2a|Slc17a2	solute carrier family 34 (sodium phosphate), member 1	protein-coding
mm_46013.1	chr5	90897523	90897527	-	1	NA	Intergenic	Intergenic	6280	NM_008176	14825	Mm.21013	NM_008176	ENSMUSG00000029380	Cxcl1	Fsp|Gro1|KC|Mgsa|N51|Scyb1|gro	chemokine (C-X-C motif) ligand 1	protein-coding
mm_163455.1	chr12	96047179	96047183	-	1	NA	promoter-TSS (NR_103800)	promoter-TSS (NR_103800)	41	NR_103800	69423	Mm.46121	NM_027076		1700019M22Rik	-	NFX-like protein	pseudo
mm_10420.1	chr2	13580680	13580689	+	1	NA	intron (NM_011701, intron 7 of 8)	intron (NM_011701, intron 7 of 8)	6373	NM_011701	22352	Mm.268000	NM_011701	ENSMUSG00000026728	Vim	-	vimentin	protein-coding
mm_23065.1	chr3	36065985	36066004	+	1	NA	promoter-TSS (NM_172678)	promoter-TSS (NM_172678)	-6	NM_172678	229211	Mm.260997	NM_172678	ENSMUSG00000027710	Acad9	2600017P15Rik|4732402K02|C630012L17Rik|NPD002	acyl-Coenzyme A dehydrogenase family, member 9	protein-coding
mm_86980.1	chr10	25436966	25437002	+	1	NA	intron (NM_013511, intron 1 of 19)	intron (NM_013511, intron 1 of 19)	28616	NM_013511	13822	Mm.306026	NM_013511	ENSMUSG00000019978	Epb41l2	4.1G|AW555191|D10Ertd398e|Epb4.1l2|NBL2	erythrocyte membrane protein band 4.1 like 2	protein-coding
mm_76223.1	chr8	83572709	83572740	-	1	NA	exon (NM_027179, exon 7 of 12)	exon (NM_027179, exon 7 of 12)	5966	NM_025843	66916	Mm.29683	NM_025843	ENSMUSG00000033938	Ndufb7	1110002H15Rik	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 7	protein-coding
mm_38219.1	chr4	135972621	135972631	-	1	NA	promoter-TSS (NM_011942)	promoter-TSS (NM_011942)	-32	NM_011942	26394	Mm.34302	NM_011942	ENSMUSG00000028670	Lypla2	LysoII	lysophospholipase 2	protein-coding
mm_86183.1	chr9	119322331	119322358	-	1	NA	promoter-TSS (NM_133985)	promoter-TSS (NM_133985)	83	NR_045693	108737	Mm.293565	NM_133985	ENSMUSG00000036737	Oxsr1	2210022N24Rik|2810422B09Rik|AI462649|AW209236|Osr1|mKIAA1101	oxidative-stress responsive 1	protein-coding
mm_43543.1	chr5	137531285	137531291	+	1	NA	intron (NM_010312, intron 1 of 9)	CpG	-1694	NR_105846	102465227		NR_105846	ENSMUSG00000098597	Mir6418	Gm27629|mir-6418|mmu-mir-6418	microRNA 6418	ncRNA
mm_150202.1	chr19	32762111	32762114	+	1	NA	intron (NM_008960, intron 1 of 8)	intron (NM_008960, intron 1 of 8)	4535	NM_008960	19211	Mm.245395	NM_008960	ENSMUSG00000013663	Pten	2310035O07Rik|A130070J02Rik|AI463227|B430203M17Rik|MMAC1|TEP1	phosphatase and tensin homolog	protein-coding
mm_11555.1	chr2	32741439	32741447	+	1	NA	promoter-TSS (NM_027529)	promoter-TSS (NM_027529)	-427	NM_027529	70730	Mm.401360	NM_027529	ENSMUSG00000009551	6330409D20Rik	AA517851	RIKEN cDNA 6330409D20 gene	protein-coding
mm_115682.1	chr13	13393593	13393597	-	1	NA	promoter-TSS (NM_031999)	promoter-TSS (NM_031999)	29	NM_031999	83924	Mm.379269	NM_031999	ENSMUSG00000021306	Gpr137b	AI788917|AU016435|AW546472|C730041E01|C80550|C80741|D13Abb1e|Tm7sf1	G protein-coupled receptor 137B	protein-coding
mm_56222.1	chr6	89595648	89595658	-	1	NA	promoter-TSS (NM_001167736)	promoter-TSS (NM_001167736)	-1	NM_001167736	66098	Mm.20313	NM_025351	ENSMUSG00000030086	Chchd6	0710001P09Rik|1700021B03Rik	coiled-coil-helix-coiled-coil-helix domain containing 6	protein-coding
mm_138456.1	chr17	35136573	35136576	+	1	NA	intron (NM_057171, intron 2 of 24)	AT_rich|Low_complexity|Low_complexity	860	NM_001252469	224727	Mm.203962	NM_057171	ENSMUSG00000024392	Bag6	2410045D21Rik|AA408914|BAG-6|Bat3|D17H6S52E|G3|Scythe	BCL2-associated athanogene 6	protein-coding
mm_44322.1	chr5	9725278	9725297	-	1	NA	promoter-TSS (NM_181850)	promoter-TSS (NM_181850)	65	NM_181850	108069	Mm.318966	NM_181850	ENSMUSG00000003974	Grm3	0710001G23Rik|Gprc1c|mGlu3|mGluR3	glutamate receptor, metabotropic 3	protein-coding
mm_150074.1	chr19	29386828	29386840	+	1	NA	3' UTR (NM_021893, exon 7 of 7)	3' UTR (NM_021893, exon 7 of 7)	19396	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_38015.1	chr4	133753962	133754019	-	1	NA	promoter-TSS (NM_001080819)	promoter-TSS (NM_001080819)	-379	NM_001080819	93760	Mm.22478	NM_001080819	ENSMUSG00000007880	Arid1a	1110030E03Rik|BAF250a|Osa1|Smarcf1	AT rich interactive domain 1A (SWI-like)	protein-coding
mm_110130.1	chr12	26444784	26444794	-	1	NA	3' UTR (NM_021384, exon 6 of 6)	3' UTR (NM_021384, exon 6 of 6)	11663	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_112186.1	chr12	113422533	113422548	-	1	NA	Intergenic	Intergenic	-67025	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_13596.1	chr2	112571442	112571462	+	1	NA	intron (NM_001165935, intron 1 of 4)	intron (NM_001165935, intron 1 of 4)	11770	NM_001165935	74268	Mm.315125	NM_028844	ENSMUSG00000003604	Aven	1700013A01Rik|1700056A21Rik|mAven-L|mAven-S	apoptosis, caspase activation inhibitor	protein-coding
mm_41525.1	chr5	92571545	92571563	+	1	NA	promoter-TSS (NM_001170571)	promoter-TSS (NM_001170571)	17	NM_001170571	384198	Mm.76757	NM_001033478	ENSMUSG00000057068	Fam47e	C730043O17|Gm1381	family with sequence similarity 47, member E	protein-coding
mm_93772.1	chr10	120370199	120370201	-	1	NA	intron (NM_010441, intron 4 of 4)	intron (NM_010441, intron 4 of 4)	-19323	NR_040626	320626	Mm.446091	NR_040626	ENSMUSG00000090191	9230105E05Rik	-	RIKEN cDNA 9230105E05 gene	ncRNA
mm_138441.1	chr17	35126317	35126423	+	1	NA	promoter-TSS (NM_033477)	promoter-TSS (NM_033477)	-32	NM_033477	114585	Mm.42070	NM_033477	ENSMUSG00000043311	D17H6S53E	G4|NG34	DNA segment, Chr 17, human D6S53E	protein-coding
mm_144329.1	chr18	12974504	12974586	+	1	NA	intron (NM_008378, intron 1 of 10)	intron (NM_008378, intron 1 of 10)	2293	NM_008378	16210	Mm.8154	NM_008378	ENSMUSG00000024423	Impact	E430016J11Rik	impact, RWD domain protein	protein-coding
mm_52869.1	chr6	122339975	122340002	+	1	NA	promoter-TSS (NM_007905)	promoter-TSS (NM_007905)	239	NM_001271579	13619	Mm.6822	NM_007905	ENSMUSG00000040669	Phc1	AW557034|Edr|Edr1|Mph1|Rae-28|rae28	polyhomeotic-like 1 (Drosophila)	protein-coding
mm_140073.1	chr17	75162929	75162932	+	1	NA	intron (NM_019919, intron 4 of 33)	intron (NM_019919, intron 4 of 33)	-15851	NM_001331236	268977	Mm.269747	NM_019919	ENSMUSG00000001870	Ltbp1	9430031G15Rik|9830146M04|Ltbp-1|Ltbp1L|TGF-beta1-BP-1|Tgfb|b2b1000Clo	latent transforming growth factor beta binding protein 1	protein-coding
mm_73153.1	chr8	94994694	94994721	+	1	NA	intron (NM_018882, intron 1 of 13)	intron (NM_018882, intron 1 of 13)	10308	NM_018882	14766	Mm.290834	NM_018882	ENSMUSG00000031785	Adgrg1	Cyt28|Gpr56|TM7LN4|TM7XN1	adhesion G protein-coupled receptor G1	protein-coding
mm_131661.1	chr16	20611586	20611635	+	1	NA	promoter-TSS (NM_025462)	promoter-TSS (NM_025462)	9	NM_025462	107522	Mm.263319	NM_025462	ENSMUSG00000022842	Ece2	1810009K13Rik|6330509A19Rik|9630025D12Rik|BB127715|Ece-2	endothelin converting enzyme 2	protein-coding
mm_25732.1	chr3	122834755	122834771	+	1	NA	intron (NM_153422, intron 14 of 20)	intron (NM_153422, intron 14 of 20)	-32783	NR_045168	71647	Mm.449992	NR_045168	ENSMUSG00000106583	4930447N08Rik	-	RIKEN cDNA 4930447N08 gene	ncRNA
mm_17486.1	chr2	28582978	28582996	-	1	NA	5' UTR (NM_001290484, exon 1 of 12)	5' UTR (NM_001290484, exon 1 of 12)	292	NM_148928	70239	Mm.274120	NM_148928	ENSMUSG00000026816	Gtf3c5	2700084A09Rik|TFIIIC63|TFiiiC2-63	general transcription factor IIIC, polypeptide 5	protein-coding
mm_80238.1	chr9	72693580	72693609	+	1	NA	intron (NM_010890, intron 6 of 28)	intron (NM_010890, intron 6 of 28)	31247	NM_010890	17999	Mm.279923	NM_010890	ENSMUSG00000032216	Nedd4	AA959633|AL023035|AU019897|E430025J12Rik|Nedd4-1|Nedd4a|mKIAA0093	neural precursor cell expressed, developmentally down-regulated 4	protein-coding
mm_4302.1	chr1	171839716	171839731	+	1	NA	promoter-TSS (NM_013489)	promoter-TSS (NM_013489)	26	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_163604.1	chr13	48968237	48968251	-	1	NA	promoter-TSS (NM_001033268)	promoter-TSS (NM_001033268)	132	NR_015601	68128	Mm.426304	NR_015601		Fam120aos	C030044B11Rik	family with sequence similarity 120A, opposite strand	ncRNA
mm_103595.1	chr11	78301485	78301530	-	1	NA	promoter-TSS (NM_017407)	promoter-TSS (NM_017407)	-84	NM_017407	54141	Mm.24250	NM_017407	ENSMUSG00000002055	Spag5	AI874642|D11Bhm180e|Deepest|MAP126|Mastrin|S17	sperm associated antigen 5	protein-coding
mm_114616.1	chr13	75849375	75849383	+	1	NA	3' UTR (NM_053108, exon 3 of 3)	3' UTR (NM_053108, exon 3 of 3)	9493	NM_053108	93692	Mm.25844	NM_053108	ENSMUSG00000021591	Glrx	C86710|D13Wsu156e|Glrx1|Grx1|TTase	glutaredoxin	protein-coding
mm_119405.1	chr14	44988165	44988178	+	1	NA	promoter-TSS (NM_008964)	promoter-TSS (NM_008964)	60	NM_008964	19217	Mm.4630	NM_008964	ENSMUSG00000037759	Ptger2	EP2|Ptgerep2	prostaglandin E receptor 2 (subtype EP2)	protein-coding
mm_3267.1	chr1	136415268	136415278	+	1	NA	promoter-TSS (NM_026500)	promoter-TSS (NM_026500)	2	NM_026500	67997	Mm.385462	NM_026500	ENSMUSG00000026404	Ddx59	1210002B07Rik|4833411G06Rik	DEAD (Asp-Glu-Ala-Asp) box polypeptide 59	protein-coding
mm_162582.1	chr1	178337805	178337816	-	1	NA	promoter-TSS (NM_016805)	promoter-TSS (NM_016805)	-26	NM_016805	51810	Mm.86589	NM_016805	ENSMUSG00000039630	Hnrnpu	AA408410|AI256620|AL024194|AL024437|AW557595|C86794|Hnrpu|SAFA|Sp120|hnRNP U	heterogeneous nuclear ribonucleoprotein U	protein-coding
mm_14390.1	chr2	129800669	129800698	+	1	NA	exon (NM_183262, exon 1 of 4)	exon (NM_183262, exon 1 of 4)	166	NM_001038635	67333	Mm.389329	NM_183262	ENSMUSG00000037885	Stk35	1700054C12Rik|CLIK1|Stk35l1	serine/threonine kinase 35	protein-coding
mm_76753.1	chr8	95434885	95434901	-	1	NA	promoter-TSS (NM_008187)	promoter-TSS (NM_008187)	-24	NM_008187	14894	Mm.2080	NM_008187	ENSMUSG00000031796	Cfap20	2600014O15Rik|AL024127|Gtl3|T10-2A2	cilia and flagella associated protein 20	protein-coding
mm_122966.1	chr14	54973846	54973854	-	1	NA	exon (NM_080728, exon 35 of 41)	exon (NM_080728, exon 35 of 41)	1926	NR_030607	100124433		NR_030607	ENSMUSG00000077928	Mir208b	Mirn208b|mir-208b	microRNA 208b	ncRNA
mm_33172.1	chr4	126035176	126035214	+	1	NA	intron (NR_045561, intron 7 of 15)	B2_Mm2|SINE|B2	10536	NM_001252651	12986	Mm.271701	NM_007782	ENSMUSG00000028859	Csf3r	Cd114|Csfgr|G-CSF-R|G-CSFR	colony stimulating factor 3 receptor (granulocyte)	protein-coding
mm_48102.1	chr5	137067883	137067894	-	1	NA	exon (NM_008871, exon 4 of 9)	exon (NM_008871, exon 4 of 9)	4384	NM_008871	18787	Mm.250422	NM_008871	ENSMUSG00000037411	Serpine1	PAI-1|PAI1|Planh1	serine (or cysteine) peptidase inhibitor, clade E, member 1	protein-coding
mm_126049.1	chr15	76948226	76948314	+	1	NA	promoter-TSS (NM_054099)	promoter-TSS (NM_054099)	9	NM_001347540	117171	Mm.322968	NM_054099	ENSMUSG00000063236	1110038F14Rik	-	RIKEN cDNA 1110038F14 gene	protein-coding
mm_147961.1	chr18	67066474	67066485	-	1	NA	Intergenic	Intergenic	-21819	NM_177137	14680	Mm.440746	NM_010307	ENSMUSG00000024524	Gnal	2610011C15Rik|9630020G10Rik|Galphaolf|Gna10|Golf	guanine nucleotide binding protein, alpha stimulating, olfactory type	protein-coding
mm_74453.1	chr8	4214289	4214303	-	1	NA	exon (NM_207203, exon 6 of 7)	exon (NM_207203, exon 6 of 7)	3016	NM_207203	73072	Mm.477379	NM_207203	ENSMUSG00000064125	Prr36	-	proline rich 36	protein-coding
mm_3505.1	chr1	150107075	150107081	+	1	NA	3' UTR (NM_011198, exon 10 of 10)	3' UTR (NM_011198, exon 10 of 10)	7047	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_50123.1	chr6	41535546	41535576	+	1	NA	Intergenic	Intergenic	13785	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_50156.1	chr6	41546571	41546577	+	1	NA	Intergenic	Intergenic	24798	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_151315.1	chr19	55845947	55845973	+	1	NA	intron (NR_138565, intron 4 of 15)	intron (NR_138565, intron 4 of 15)	-49361	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_48922.1	chr6	4047678	4047711	+	1	NA	promoter-TSS (NR_131108)	promoter-TSS (NR_131108)	-110	NR_131108	78034	Mm.243851	NR_131108	ENSMUSG00000107681	4930528H21Rik	-	RIKEN cDNA 4930528H21 gene	ncRNA
mm_42825.1	chr5	122100785	122100807	+	1	NA	promoter-TSS (NM_010861)	promoter-TSS (NM_010861)	-184	NM_010861	17906	Mm.1529	NM_010861	ENSMUSG00000013936	Myl2	MLC-2|MLC-2s/v|MLC-2v|Mlc2v|Mylpc	myosin, light polypeptide 2, regulatory, cardiac, slow	protein-coding
mm_149210.1	chr19	9982849	9982852	+	1	NA	non-coding (NR_073181, exon 2 of 5)	non-coding (NR_073181, exon 2 of 5)	204	NM_010239	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
mm_133355.1	chr16	84640170	84640174	+	1	NA	Intergenic	LTR33C|LTR|ERVL	-39617	NR_040537	78023	Mm.243853	NR_040537		4930529L06Rik	-	RIKEN cDNA 4930529L06 gene	ncRNA
mm_48237.1	chr5	137741047	137741062	-	1	NA	5' UTR (NM_001347505, exon 1 of 7)	5' UTR (NM_001347505, exon 1 of 7)	114	NM_001347505	243300	Mm.74750	NM_175521	ENSMUSG00000045348	Nyap1	6430598A04Rik	neuronal tyrosine-phosphorylated phosphoinositide 3-kinase adaptor 1	protein-coding
mm_50966.1	chr6	59710717	59710736	+	1	NA	Intergenic	Intergenic	-284436	NM_183183	243385	Mm.138080	NM_183183	ENSMUSG00000045441	Gprin3	C030038J10Rik|C730021L23	GPRIN family member 3	protein-coding
mm_150761.1	chr19	44236994	44237020	+	1	NA	intron (NM_024450, intron 4 of 5)	intron (NM_024450, intron 4 of 5)	33719	NM_024450	30049	Mm.480594	NM_024450	ENSMUSG00000025202	Scd3	4930513N16Rik	stearoyl-coenzyme A desaturase 3	protein-coding
mm_68459.1	chr7	110164869	110164875	-	1	NA	Intergenic	Intergenic	42813	NM_009516	22390	Mm.287173	NM_009516	ENSMUSG00000031016	Wee1	Wee1A	WEE 1 homolog 1 (S. pombe)	protein-coding
mm_17953.1	chr2	37351073	37351090	-	1	NA	3' UTR (NM_026176, exon 4 of 4)	3' UTR (NM_026176, exon 4 of 4)	8251	NM_026176	67466	Mm.30709	NM_026176	ENSMUSG00000009030	Pdcl	1200011E13Rik|AW108059|PhLP1	phosducin-like	protein-coding
mm_48229.1	chr5	137684589	137684603	-	1	NA	5' UTR (NM_178162, exon 1 of 12)	5' UTR (NM_178162, exon 1 of 12)	157	NM_001303271	231801	Mm.260869	NM_145566	ENSMUSG00000029722	Agfg2	A630095P14Rik|Hrbl|RAB-R|RABR	ArfGAP with FG repeats 2	protein-coding
mm_59976.1	chr7	30459714	30459745	+	1	NA	promoter-TSS (NM_019459)	promoter-TSS (NM_019459)	-329	NM_019459	54631	Mm.437830	NM_019459	ENSMUSG00000006649	Nphs1	NephrinB|nephrin	nephrosis 1, nephrin	protein-coding
mm_61426.1	chr7	73640748	73640749	+	1	NA	Intergenic	Intergenic	45815	NR_033604	244061	Mm.484605	NR_033604	ENSMUSG00000108337	Gm4971	EG244061	Smad nuclear interacting protein 1 pseudogene	pseudo
mm_97500.1	chr11	78394479	78394489	+	1	NA	promoter-TSS (NR_003282)	promoter-TSS (NR_003282)	-1	NR_003282	790911	Mm.457257	NR_003282	ENSMUSG00000085747	Slc13a2os	Gm11194|OTTMUSG00000000132	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 2, opposite strand	ncRNA
mm_60762.1	chr7	45529593	45529640	+	1	NA	intron (NM_148927, intron 1 of 19)	GA-rich|Low_complexity|Low_complexity	3286	NM_148927	69217	Mm.274158	NM_148927	ENSMUSG00000040428	Plekha4	2410005C22Rik|C88169|Pepp1	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 4	protein-coding
mm_85435.1	chr9	104002351	104002362	-	1	NA	promoter-TSS (NM_028721)	promoter-TSS (NM_028721)	-188	NM_172460	74025	Mm.479273	NM_028721	ENSMUSG00000032558	Nphp3	3632410F03Rik|AI550417|C230078J01|D330020E01Rik|pcy	nephronophthisis 3 (adolescent)	protein-coding
mm_47655.1	chr5	125392959	125392975	-	1	NA	Intergenic	Intergenic	-2950	NM_019639	22190	Mm.331	NM_019639	ENSMUSG00000008348	Ubc	2700054O04Rik|AI194771|Rps27a|TI-225|Uba52|Ubb	ubiquitin C	protein-coding
mm_33956.1	chr4	137454779	137454784	+	1	NA	exon (NM_027063, exon 2 of 2)	exon (NM_027063, exon 2 of 2)	1485	NM_027063	69380	Mm.272519	NM_027063	ENSMUSG00000041399	1700013G24Rik	AI507018	RIKEN cDNA 1700013G24 gene	protein-coding
mm_8488.1	chr1	153723422	153723428	-	1	NA	non-coding (NR_046171, exon 3 of 3)	non-coding (NR_046171, exon 3 of 3)	14404	NR_046171	329271	Mm.384841	NR_046171	ENSMUSG00000100334	C230024C17Rik	C230024C17	RIKEN cDNA C230024C17 gene	ncRNA
mm_22486.1	chr3	5515452	5515473	+	1	NA	Intergenic	RMER17A2|LTR|ERVK	60786	NM_001163301	19302	Mm.132336	NM_008994	ENSMUSG00000040374	Pex2	D3Ertd138e|PAF-1|PMP35|Pxmp3	peroxisomal biogenesis factor 2	protein-coding
mm_144435.1	chr18	21091164	21091189	+	1	NA	exon (NM_008586, exon 10 of 15)	exon (NM_008586, exon 10 of 15)	18832	NM_008586	17288	Mm.2682	NM_008586	ENSMUSG00000024313	Mep1b	Mep-1b	meprin 1 beta	protein-coding
mm_156245.1	chrX	136270279	136270283	+	1	NA	promoter-TSS (NM_009750)	promoter-TSS (NM_009750)	28	NM_001110234	12070	Mm.90787	NM_009750	ENSMUSG00000046432	Bex3	AL033356|DXWsu67e|Gcap27|Nade|Ngfrap1	brain expressed X-linked 3	protein-coding
mm_104430.1	chr11	94951297	94951321	-	1	NA	exon (NM_007742, exon 50 of 51)	exon (NM_007742, exon 50 of 51)	15085	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_54453.1	chr6	34746383	34746393	-	1	NA	intron (NM_001347100, intron 5 of 13)	GA-rich|Low_complexity|Low_complexity	-34044	NM_001289657	76223	Mm.150047	NM_178630	ENSMUSG00000038836	Agbl3	2900053G10Rik|4930431N21Rik|6530406M24Rik|CCP3	ATP/GTP binding protein-like 3	protein-coding
mm_89354.1	chr10	88201118	88201156	+	1	NA	promoter-TSS (NM_001122960)	promoter-TSS (NM_001122960)	40	NM_027487	67282	Mm.208465	NM_026070	ENSMUSG00000020056	Washc3	2900091E11Rik|5730495F03Rik|Ccdc53	WASH complex subunit 3	protein-coding
mm_50183.1	chr6	41605652	41605671	+	1	NA	5' UTR (NM_001146351, exon 1 of 18)	5' UTR (NM_001146351, exon 1 of 18)	179	NM_007680	13848	Mm.271976	NM_007680	ENSMUSG00000029869	Ephb6	Cekl|Mep	Eph receptor B6	protein-coding
mm_172921.1	chr9	67253106	67253106	-	1	NA	intron (NM_001081242, intron 50 of 57)	intron (NM_001081242, intron 50 of 57)	-16380	NR_029576	387185		NR_029576	ENSMUSG00000076379	Mir190a	Mir190|Mirn190|mir-190|mir-190a|mmu-mir-190|mmu-mir-190a	microRNA 190a	ncRNA
mm_148116.1	chr18	74961253	74961268	-	1	NA	promoter-TSS (NM_010720)	promoter-TSS (NM_010720)	3	NM_010720	16891	Mm.299647	NM_010720	ENSMUSG00000053846	Lipg	3110013K01Rik|EL|lipase|mEDL	lipase, endothelial	protein-coding
mm_5375.1	chr1	30875912	30875923	-	1	NA	Intergenic	Intergenic	-12661	NM_001081080	213109	Mm.194486	NM_025871	ENSMUSG00000048874	Phf3	2310061N19Rik|mKIAA0244	PHD finger protein 3	protein-coding
mm_120210.1	chr14	62413557	62413567	+	1	NA	intron (NM_172810, intron 10 of 16)	L1MB3|LINE|L1	42727	NM_001204340	239134	Mm.236557	NM_172810	ENSMUSG00000021933	Gucy1b2	B930025B03|GC-SB2	guanylate cyclase 1, soluble, beta 2	protein-coding
mm_63189.1	chr7	125594135	125594147	+	1	NA	Intergenic	Intergenic	-9288	NM_021887	60504	Mm.155643	NM_021887	ENSMUSG00000030745	Il21r	NILR	interleukin 21 receptor	protein-coding
mm_33973.1	chr4	137626693	137626707	+	1	NA	intron (NM_001347227, intron 14 of 26)	intron (NM_001347227, intron 14 of 26)	32511	NM_130879	170707	Mm.218478	NM_130879	ENSMUSG00000043411	Usp48	2810449C13Rik|AI115503|BC021769|D330022K21Rik|Usp31	ubiquitin specific peptidase 48	protein-coding
mm_5736.1	chr1	45339386	45339402	-	1	NA	exon (NM_009930, exon 35 of 51)	exon (NM_009930, exon 35 of 51)	27856	NM_009930	12825	Mm.249555	NM_009930	ENSMUSG00000026043	Col3a1	AW550625|Col3a-1|Tsk-2|Tsk2	collagen, type III, alpha 1	protein-coding
mm_38851.1	chr4	149314007	149314022	-	1	NA	Intergenic	Intergenic	-6281	NM_001290995	16561	Mm.402393	NM_008441	ENSMUSG00000063077	Kif1b	A530096N05Rik|AI448212|AI506502|D4Mil1e|KIF1Bp130|KIF1Bp204	kinesin family member 1B	protein-coding
mm_137097.1	chr17	21537083	21537095	+	1	NA	intron (NM_144515, intron 1 of 4)	RLTR19|LTR|ERVK	-1211	NR_131123	319870	Mm.488274	NR_131123	ENSMUSG00000097781	9330136K24Rik	-	RIKEN cDNA 9330136K24 gene	ncRNA
mm_51385.1	chr6	77242645	77242697	+	1	NA	promoter-TSS (NM_028880)	promoter-TSS (NM_028880)	-46	NM_028880	74342	Mm.292568	NM_028880	ENSMUSG00000060780	Lrrtm1	4632401D06Rik|AW125451	leucine rich repeat transmembrane neuronal 1	protein-coding
mm_7605.1	chr1	126470842	126470867	-	1	NA	intron (NM_001081756, intron 3 of 16)	intron (NM_001081756, intron 3 of 16)	22073	NM_172484	210356	Mm.377234	NM_172484	ENSMUSG00000049690	Nckap5	8430408F21|D130011D22Rik|E030049G20Rik|Erih1|Erih2|Gm1548|Nap5	NCK-associated protein 5	protein-coding
mm_128716.1	chr15	63998072	63998101	-	1	NA	intron (NM_144846, intron 1 of 11)	CpG	62362	NM_144846	223601	Mm.246108	NM_144846	ENSMUSG00000022378	Fam49b	0910001A06Rik|AW122079	family with sequence similarity 49, member B	protein-coding
mm_88507.1	chr10	77893414	77893431	+	1	NA	promoter-TSS (NR_015547)	promoter-TSS (NR_015547)	2	NR_015547	75188	Mm.348012	NM_029200	ENSMUSG00000096573	1700009J07Rik	4930535B06Rik	RIKEN cDNA 1700009J07 gene	ncRNA
mm_4745.1	chr1	182124803	182124818	+	1	NA	promoter-TSS (NM_012058)	promoter-TSS (NM_012058)	73	NM_012058	27058	Mm.273196	NM_012058	ENSMUSG00000026511	Srp9	9kDa	signal recognition particle 9	protein-coding
mm_103258.1	chr11	71018499	71018521	-	1	NA	intron (NM_001291146, intron 1 of 6)	intron (NM_001291146, intron 1 of 6)	793	NM_001291147	116891	Mm.28131	NM_033562	ENSMUSG00000018442	Derl2	CGI-101|Derlin-2|F-lana|Flana	Der1-like domain family, member 2	protein-coding
mm_100017.1	chr11	114890216	114890226	+	1	NA	5' UTR (NM_170758, exon 1 of 7)	5' UTR (NM_170758, exon 1 of 7)	180	NM_170758	217303	Mm.294439	NM_170758	ENSMUSG00000034652	Cd300a	B230315M08Rik|Clm8|LMIR1|MAIR-I|MAIR-Ia|MMAC8|Pigr4|mcpir1	CD300A molecule	protein-coding
mm_167359.1	chr8	84665099	84665138	+	1	NA	Intergenic	Intergenic	-2266	NM_010499	15936	Mm.399	NM_010499	ENSMUSG00000053560	Ier2	AI317238|Ch1|Pip92	immediate early response 2	protein-coding
mm_93839.1	chr10	121626168	121626178	-	1	NA	5' UTR (NM_001081056, exon 1 of 25)	5' UTR (NM_001081056, exon 1 of 25)	143	NM_001081056	73192	Mm.25042	NM_001081056	ENSMUSG00000034667	Xpot	1110004L07Rik|3110065H13Rik|AI452076|C79645|EXPORTIN-T	exportin, tRNA (nuclear export receptor for tRNAs)	protein-coding
mm_46719.1	chr5	110653129	110653137	-	1	NA	promoter-TSS (NM_027156)	promoter-TSS (NM_027156)	249	NM_153570	100608	Mm.29960	NM_153570	ENSMUSG00000033294	Noc4l	AI326906	NOC4 like	protein-coding
mm_24578.1	chr3	93444707	93444715	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	2381	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_63351.1	chr7	126976433	126976466	+	1	NA	5' UTR (NM_026638, exon 1 of 6)	5' UTR (NM_026638, exon 1 of 6)	535	NM_001347656	52858	Mm.28219	NM_026638	ENSMUSG00000030682	Cdipt	9530042F15Rik|D7Bwg0575e|Pis|Pis1	CDP-diacylglycerol--inositol 3-phosphatidyltransferase (phosphatidylinositol synthase)	protein-coding
mm_113434.1	chr13	34875521	34875562	+	1	NA	promoter-TSS (NM_013830)	promoter-TSS (NM_013830)	47	NM_013830	19134	Mm.10027	NM_013830	ENSMUSG00000021413	Prpf4b	2610037H07|Prp4|Prp4k|Prpk|cbp143	pre-mRNA processing factor 4B	protein-coding
mm_68265.1	chr7	105595530	105595539	-	1	NA	exon (NM_017371, exon 6 of 10)	exon (NM_017371, exon 6 of 10)	4582	NM_017371	15458	Mm.3485	NM_017371	ENSMUSG00000030895	Hpx	Hpxn|hx	hemopexin	protein-coding
mm_84618.1	chr9	70503330	70503378	-	1	NA	intron (NM_033604, intron 1 of 14)	CpG	371	NM_033604	93836	Mm.29783	NM_033604	ENSMUSG00000032217	Rnf111	ARK|Arkadia	ring finger 111	protein-coding
mm_9711.1	chr1	179546262	179546276	-	1	NA	promoter-TSS (NM_146105)	promoter-TSS (NM_146105)	7	NM_001331055	15278	Mm.293529	NM_008249	ENSMUSG00000026492	Tfb2m	Hkp1	transcription factor B2, mitochondrial	protein-coding
mm_135626.1	chr16	52287684	52287705	-	1	NA	intron (NM_009655, intron 8 of 15)	intron (NM_009655, intron 8 of 15)	165387	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_3551.1	chr1	150414515	150414527	+	1	NA	exon (NM_133780, exon 17 of 52)	exon (NM_133780, exon 17 of 52)	-21466	NM_145511	226499	Mm.222093	NM_145511	ENSMUSG00000006010	BC003331	1810053E15Rik|Odr4|odr-4	cDNA sequence BC003331	protein-coding
mm_161562.1	chr16	17915100	17915100	-	1	NA	promoter-TSS (NM_029469)	promoter-TSS (NM_029469)	-41	NM_029469	195333	Mm.463003	NM_029469	ENSMUSG00000022738	Gsc2	4930568H22Rik|GSC-2|Gscl	goosecoid homebox 2	protein-coding
mm_50709.1	chr6	52166518	52166524	+	1	NA	intron (NR_131182, intron 1 of 2)	intron (NR_131182, intron 1 of 2)	847	NR_131182	105242657	Mm.490651	NR_131182	ENSMUSG00000056445	Hoxaas2	2810043O09Rik|5730446D14Rik	Hoxa cluster antisense RNA 2	ncRNA
mm_96275.1	chr11	62847112	62847132	+	1	NA	promoter-TSS (NM_001291441)	promoter-TSS (NM_001291441)	-1	NM_001033669	213980	Mm.482259	NM_001033669	ENSMUSG00000090173	Fbxw10	Fbw10|HREP|SM25H2|SM2SH2	F-box and WD-40 domain protein 10	protein-coding
mm_164660.1	chr17	39406347	39406355	+	1	NA	promoter-TSS (NM_001244763)	promoter-TSS (NM_001244763)	-8	NM_001244763	100126774	Mm.350534	NM_001244763	ENSMUSG00000094024	Esp18	Gm20579	exocrine gland secreted peptide 18	protein-coding
mm_49714.1	chr6	34423076	34423091	+	1	NA	TTS (NM_009731)	TTS (NM_009731)	10721	NM_009731	11997	Mm.482073	NM_009731	ENSMUSG00000052131	Akr1b7	AR|Avdp|MVDP	aldo-keto reductase family 1, member B7	protein-coding
mm_113609.1	chr13	41250129	41250211	+	1	NA	5' UTR (NM_001135577, exon 1 of 2)	5' UTR (NM_001135577, exon 1 of 2)	326	NM_001135577	108934	Mm.38578	NM_001135577	ENSMUSG00000091264	Smim13	2900036K02Rik	small integral membrane protein 13	protein-coding
mm_10895.1	chr2	25264305	25264313	+	1	NA	exon (NM_175286, exon 1 of 4)	exon (NM_175286, exon 1 of 4)	1711	NM_175286	97031	Mm.308539	NM_175286	ENSMUSG00000048707	Tprn	C430004E15Rik|C87750	taperin	protein-coding
mm_154608.1	chrX	7648719	7648729	+	1	NA	exon (NM_009305, exon 6 of 7)	exon (NM_009305, exon 6 of 7)	-8655	NM_001290624	54630	Mm.232232	NM_175097	ENSMUSG00000031145	Prickle3	Lmo6|Sfc16	prickle planar cell polarity protein 3	protein-coding
mm_101080.1	chr11	11699530	11699536	-	1	NA	intron (NM_001301866, intron 1 of 5)	intron (NM_001301866, intron 1 of 5)	9356	NM_001301863	22778	Mm.103545	NM_009578	ENSMUSG00000018654	Ikzf1	5832432G11Rik|Ikaros|LyF-1|Zfpn1a1|Znfn1a1|hlk-1|mKIAA4227	IKAROS family zinc finger 1	protein-coding
mm_61252.1	chr7	65804067	65804082	+	1	NA	promoter-TSS (NR_045301)	promoter-TSS (NR_045301)	22	NR_045301	100503969	Mm.383527	NR_045301		1810008I18Rik	-	RIKEN cDNA 1810008I18 gene	ncRNA
mm_109292.1	chr12	109559504	109559518	+	1	NA	non-coding (NR_003633, exon 5 of 5)	non-coding (NR_003633, exon 5 of 5)	-4181	NR_030427	791079		NR_030427	ENSMUSG00000076451	Mir770	Mirn770|mir-770|mmu-mir-770	microRNA 770	ncRNA
mm_118851.1	chr14	25694148	25694166	+	1	NA	promoter-TSS (NM_134084)	promoter-TSS (NM_134084)	-13	NM_134084	105675	Mm.41656	NM_134084	ENSMUSG00000021868	Ppif	AW457192|CyP-D|CyP-F|CypD|PPIase	peptidylprolyl isomerase F (cyclophilin F)	protein-coding
mm_32184.1	chr4	101068975	101068988	+	1	NA	promoter-TSS (NM_183024)	promoter-TSS (NM_183024)	-57	NM_183024	242570	Mm.185636	NM_183024	ENSMUSG00000035275	Raver2	A430091O22Rik	ribonucleoprotein, PTB-binding 2	protein-coding
mm_120225.1	chr14	62857423	62857438	+	1	NA	intron (NM_175546, intron 1 of 11)	intron (NM_175546, intron 1 of 11)	-8112	NR_105860	102465311		NR_105860	ENSMUSG00000098858	Mir6541	Gm27311|mmu-mir-6541	microRNA 6541	ncRNA
mm_101240.1	chr11	20700848	20700851	-	1	NA	intron (NM_001290545, intron 6 of 9)	intron (NM_001290545, intron 6 of 9)	40707	NM_001290545	216549	Mm.356580	NM_181411	ENSMUSG00000049659	Aftph	-	aftiphilin	protein-coding
mm_166206.1	chr5	44073788	44073798	-	1	NA	intron (NM_001163582, intron 1 of 21)	intron (NM_001163582, intron 1 of 21)	20975	NM_001163581	19126	Mm.6250	NM_008935	ENSMUSG00000029086	Prom1	4932416E19Rik|AC133|CD133|Prom|Prom-1|Proml1	prominin 1	protein-coding
mm_104223.1	chr11	88540454	88540468	-	1	NA	intron (NM_054043, intron 6 of 13)	intron (NM_054043, intron 6 of 13)	-78790	NR_131025	68397	Mm.426889	NR_131025		0610039H22Rik	-	RIKEN cDNA 0610039H22 gene	ncRNA
mm_59956.1	chr7	30427155	30427169	+	1	NA	exon (NM_172142, exon 9 of 11)	exon (NM_172142, exon 9 of 11)	3858	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_14439.1	chr2	130840215	130840232	+	1	NA	promoter-TSS (NM_001311147)	promoter-TSS (NM_001311147)	-78	NM_029432	228602	Mm.271990	NM_028367	ENSMUSG00000027309	4930402H24Rik	2810487F15Rik|AI413763|C78926	RIKEN cDNA 4930402H24 gene	protein-coding
mm_5567.1	chr1	38898038	38898058	-	1	NA	5' UTR (NM_145142, exon 1 of 7)	5' UTR (NM_145142, exon 1 of 7)	112	NM_145142	98388	Mm.260054	NM_145142	ENSMUSG00000026080	Chst10	AI507003|AU041319|Hnk-1st|ST	carbohydrate sulfotransferase 10	protein-coding
mm_53680.1	chr6	142303578	142303586	+	1	NA	3' UTR (NM_010491, exon 3 of 3)	3' UTR (NM_010491, exon 3 of 3)	5157	NM_010491	15874	Mm.415	NM_010491	ENSMUSG00000041681	Iapp	DAP	islet amyloid polypeptide	protein-coding
mm_132110.1	chr16	31455121	31455134	+	1	NA	exon (NM_001122683, exon 6 of 7)	exon (NM_001122683, exon 6 of 7)	26374	NM_001122683	71911	Mm.293470	NM_175177	ENSMUSG00000046598	Bdh1	2310032J20Rik|AI327223|Bdh	3-hydroxybutyrate dehydrogenase, type 1	protein-coding
mm_38949.1	chr4	150566865	150566876	-	1	NA	intron (NM_001085492, intron 11 of 22)	ID_B1|SINE|B4	85304	NM_173774	242773	Mm.29280	NM_173774	ENSMUSG00000039838	Slc45a1	C230078B22|Dnb5	solute carrier family 45, member 1	protein-coding
mm_100700.1	chr11	3539229	3539267	-	1	NA	promoter-TSS (NM_001284429)	promoter-TSS (NM_001284429)	44	NM_013870	29856	Mm.188516	NM_013870	ENSMUSG00000020439	Smtn	smsmo	smoothelin	protein-coding
mm_120634.1	chr14	70466854	70466860	+	1	NA	exon (NM_145981, exon 5 of 5)	exon (NM_145981, exon 5 of 5)	9340	NM_145981	105653	Mm.192598	NM_145981	ENSMUSG00000003469	Phyhip	AW049870|C630010D02Rik|Lnap1ip|PAHX-AP#1|PAHX-AP1	phytanoyl-CoA hydroxylase interacting protein	protein-coding
mm_106760.1	chr12	4234124	4234154	+	1	NA	exon (NM_001204912, exon 1 of 2)	exon (NM_001204912, exon 1 of 2)	112	NM_001204912	69709	Mm.250552	NM_001204912	ENSMUSG00000096199	Ptrhd1	2410017P09Rik	peptidyl-tRNA hydrolase domain containing 1	protein-coding
mm_41529.1	chr5	92683311	92683335	+	1	NA	promoter-TSS (NM_015756)	promoter-TSS (NM_015756)	-112	NM_015756	27428	Mm.46014	NM_015756	ENSMUSG00000029381	Shroom3	AL022960|D5Ertd287e|Shrm|Shrm3	shroom family member 3	protein-coding
mm_79166.1	chr9	47850289	47850317	+	1	NA	exon (NM_018770, exon 10 of 10)	exon (NM_018770, exon 10 of 10)	-32095	NR_046048	100038460	Mm.447649	NR_046048		Gm10677	ENSMUSG00000074363	predicted gene 10677	ncRNA
mm_72620.1	chr8	84638539	84638592	+	1	NA	intron (NM_001252059, intron 44 of 45)	intron (NM_001252059, intron 44 of 45)	24287	NM_010499	15936	Mm.399	NM_010499	ENSMUSG00000053560	Ier2	AI317238|Ch1|Pip92	immediate early response 2	protein-coding
mm_158210.1	chrX	105875069	105875087	-	1	NA	exon (NM_009530, exon 9 of 35)	exon (NM_009530, exon 9 of 35)	54294	NM_009530	22589	Mm.10141	NM_009530	ENSMUSG00000031229	Atrx	4833408C14Rik|AI447451|ATR2|DXHXS6677E|HP1-BP38|Hp1bp2|Hp1bp38|MRXS3|RAD54L|Rad54|XH2|Xnp|ZNF-HX	alpha thalassemia/mental retardation syndrome X-linked	protein-coding
mm_118593.1	chr14	20674312	20674371	+	1	NA	promoter-TSS (NM_172596)	promoter-TSS (NM_172596)	20	NM_001168273	218811	Mm.173119	NM_172596	ENSMUSG00000039367	Sec24c	2610204K03Rik|mKIAA0079	Sec24 related gene family, member C (S. cerevisiae)	protein-coding
mm_98485.1	chr11	94951175	94951228	+	1	NA	exon (NM_007742, exon 50 of 51)	exon (NM_007742, exon 50 of 51)	14977	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_75218.1	chr8	39605751	39605761	-	1	NA	3' UTR (NM_031195, exon 9 of 9)	3' UTR (NM_031195, exon 9 of 9)	36922	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_153059.1	chr19	32182144	32182156	-	1	NA	intron (NM_001168525, intron 5 of 9)	intron (NM_001168525, intron 5 of 9)	28863	NM_001168526	208449	Mm.329810	NM_144792	ENSMUSG00000040451	Sgms1	9530058O11Rik|AI841905|C80702|Mob|Sms1|Sor1|Tmem23	sphingomyelin synthase 1	protein-coding
mm_137355.1	chr17	25274364	25274396	+	1	NA	promoter-TSS (NM_011665)	promoter-TSS (NM_011665)	-70	NM_011665	22196	Mm.240044	NM_011665	ENSMUSG00000015120	Ube2i	5830467E05Rik|F830028O17Rik|UBC9|Ubce2i|Ubce9	ubiquitin-conjugating enzyme E2I	protein-coding
mm_50738.1	chr6	52720320	52720324	+	1	NA	intron (NM_025816, intron 1 of 17)	intron (NM_025816, intron 1 of 17)	6593	NM_025816	52440	Mm.389757	NM_025816	ENSMUSG00000004535	Tax1bp1	1200003J11Rik|1700069J21Rik|AA930106|D6Ertd404e|D6Ertd772e|T6bp|TXBP151	Tax1 (human T cell leukemia virus type I) binding protein 1	protein-coding
mm_136658.1	chr17	6005540	6005550	+	1	NA	intron (NM_001113352, intron 7 of 25)	intron (NM_001113352, intron 7 of 25)	-2035	NM_001290698	20975	Mm.236068	NM_011523	ENSMUSG00000023805	Synj2	AI481647|SJ2|mKIAA0348	synaptojanin 2	protein-coding
mm_9990.1	chr1	191363115	191363121	-	1	NA	intron (NM_144880, intron 3 of 12)	RSINE1|SINE|B4	33923	NM_144880	226849	Mm.205569	NM_144880	ENSMUSG00000026626	Ppp2r5a	PR61alpha	protein phosphatase 2, regulatory subunit B', alpha	protein-coding
mm_24654.1	chr3	94413245	94413296	+	1	NA	promoter-TSS (NM_028307)	promoter-TSS (NM_028307)	-48	NM_028307	72634	Mm.331198	NM_028307	ENSMUSG00000041912	Tdrkh	2700091C21Rik|Tdrd2	tudor and KH domain containing protein	protein-coding
mm_163022.1	chr11	47282894	47282895	+	1	NA	intron (NM_011891, intron 2 of 7)	intron (NM_011891, intron 2 of 7)	96408	NM_011891	24052	Mm.338890	NM_011891	ENSMUSG00000020354	Sgcd	35kDa|delta-SG	sarcoglycan, delta (dystrophin-associated glycoprotein)	protein-coding
mm_140582.1	chr17	10212159	10212170	-	1	NA	3' UTR (NM_001159516, exon 7 of 7)	3' UTR (NM_001159516, exon 7 of 7)	107197	NM_021881	19317	Mm.130694	NM_021881	ENSMUSG00000062078	Qk	1110003F05Rik|1500005P18|QkI|l(17)-1Wis|l17Wis1	quaking	protein-coding
mm_98758.1	chr11	96545691	96545697	+	1	NA	intron (NM_001033186, intron 4 of 12)	intron (NM_001033186, intron 4 of 12)	81103	NM_001177898	78473	Mm.395840	NM_001033186	ENSMUSG00000057058	Skap1	1700091G21Rik|Scap1|Skap-55	src family associated phosphoprotein 1	protein-coding
mm_36587.1	chr4	88419001	88419013	-	1	NA	intron (NM_025760, intron 6 of 6)	PB1D9|SINE|Alu	19919	NM_025760	66775	Mm.386788	NM_025760	ENSMUSG00000028497	Hacd4	4933428I03Rik|Hcad4|Ptplad2	3-hydroxyacyl-CoA dehydratase 4	protein-coding
mm_172789.1	chr9	106512396	106512397	+	1	NA	Intergenic	ORR1A1|LTR|ERVL-MaLR	-2177	NM_029300	75470	Mm.63799	NM_029300	ENSMUSG00000066382	Iqcf5	1700007L12Rik	IQ motif containing F5	protein-coding
mm_2801.1	chr1	130851691	130851705	+	1	NA	3' UTR (NM_011082, exon 11 of 11)	3' UTR (NM_011082, exon 11 of 11)	-14079	NM_026976	69169	Mm.46042	NM_026976	ENSMUSG00000042474	Fcmr	1810037B05Rik|Faim3|FcmuR|Toso	Fc fragment of IgM receptor	protein-coding
mm_109670.1	chr12	113052398	113052410	+	1	NA	intron (NM_001291444, intron 8 of 23)	intron (NM_001291444, intron 8 of 23)	-22098	NM_029381	75671	Mm.23377	NM_029381	ENSMUSG00000012211	Tex22	1700028O09Rik|AV210422|Tep22	testis expressed gene 22	protein-coding
mm_126002.1	chr15	76520928	76520937	+	1	NA	intron (NM_130893, intron 1 of 1)	intron (NM_130893, intron 1 of 1)	1197	NM_130893	170729	Mm.218747	NM_130893	ENSMUSG00000048385	Scrt1	-	scratch family zinc finger 1	protein-coding
mm_3809.1	chr1	158362498	158362511	+	1	NA	5' UTR (NM_001205204, exon 1 of 23)	5' UTR (NM_001205204, exon 1 of 23)	200	NM_001205204	11899	Mm.329586	NM_007495	ENSMUSG00000026587	Astn1	Astn|GC14|mKIAA0289	astrotactin 1	protein-coding
mm_61161.1	chr7	59228744	59228769	+	1	NA	promoter-TSS (NM_001033962)	promoter-TSS (NM_001033962)	4	NM_011668	22215	Mm.9002	NM_011668	ENSMUSG00000025326	Ube3a	4732496B02|5830462N02Rik|A130086L21Rik|Hpve6a|mKIAA4216	ubiquitin protein ligase E3A	protein-coding
mm_94697.1	chr11	20113060	20113094	+	1	NA	promoter-TSS (NM_146243)	promoter-TSS (NM_146243)	-126	NM_146243	66713	Mm.259045	NM_146243	ENSMUSG00000020152	Actr2	4921510D23Rik|AA409782|Arp2|D6Ertd746e	ARP2 actin-related protein 2	protein-coding
mm_11361.1	chr2	30930020	30930037	+	1	NA	Intergenic	Intergenic	-22973	NM_133673	30934	Mm.249164	NM_133673	ENSMUSG00000026848	Tor1b	2610016F05Rik|DQ1|torsinB	torsin family 1, member B	protein-coding
mm_40740.1	chr5	66676232	66676257	+	1	NA	non-coding (NR_102714, exon 1 of 5)	non-coding (NR_102714, exon 1 of 5)	123	NM_011670	22223	Mm.29807	NM_011670	ENSMUSG00000029223	Uchl1	AW822034|C88048|PGP 9.5|PGP9.5|R75593|UCH-L1|UCHL-1|gad	ubiquitin carboxy-terminal hydrolase L1	protein-coding
mm_94637.1	chr11	16901831	16901835	+	1	NA	intron (NM_207655, intron 20 of 27)	intron (NM_207655, intron 20 of 27)	49449	NR_110421	72735	Mm.268598	NR_015469		Eldr	2810442I21Rik|4930500E12Rik|Fabl	Egfr long non-coding downstream RNA	ncRNA
mm_78183.1	chr9	21225364	21225388	+	1	NA	intron (NR_106127, intron 1 of 3)	intron (NR_106127, intron 1 of 3)	905	NR_106127	102465769		NR_106127	ENSMUSG00000098764	Mir7667	Gm27756|mmu-mir-7667	microRNA 7667	ncRNA
mm_71375.1	chr8	45803701	45803703	+	1	NA	exon (NM_001205219, exon 19 of 24)	exon (NM_001205219, exon 19 of 24)	15595	NR_045739	319940	Mm.441720	NR_045739	ENSMUSG00000085440	Sorbs2os	D330022K07Rik	sorbin and SH3 domain containing 2, opposite strand	ncRNA
mm_68253.1	chr7	105581201	105581271	-	1	NA	5' UTR (NM_001253886, exon 1 of 14)	5' UTR (NM_001253886, exon 1 of 14)	255	NM_001253885	11785	Mm.38469	NM_009685	ENSMUSG00000037032	Apbb1	Fe65|Rir	amyloid beta (A4) precursor protein-binding, family B, member 1	protein-coding
mm_57240.1	chr6	123283058	123283075	-	1	NA	3' UTR (NM_019948, exon 6 of 6)	3' UTR (NM_019948, exon 6 of 6)	6805	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_172100.1	chr6	31088199	31088200	-	1	NA	Intergenic	Intergenic	-25106	NR_029532	387223		NR_029532	ENSMUSG00000065604	Mir29b-1	Mirn29b|Mirn29b-1|mir-29b-1	microRNA 29b-1	ncRNA
mm_73.1	chr1	6673376	6673380	+	1	NA	intron (NM_001244693, intron 2 of 22)	L1VL2|LINE|L1	-56673	NR_045189	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding
mm_105155.1	chr11	101466159	101466216	-	1	NA	promoter-TSS (NM_012037)	promoter-TSS (NM_012037)	12	NM_012037	26949	Mm.29210	NM_012037	ENSMUSG00000034993	Vat1	VAT-1	vesicle amine transport 1	protein-coding
mm_16133.1	chr2	170349294	170349331	+	1	NA	exon (NM_001164369, exon 11 of 12)	exon (NM_001164369, exon 11 of 12)	-7049	NR_040610	73303	Mm.443297	NR_040610	ENSMUSG00000086999	Bcas1os2	1700040N02Rik	breast carcinoma amplified sequence 1, opposite strand 2	ncRNA
mm_156278.1	chrX	136836964	136836974	+	1	NA	3' UTR (NM_011123, exon 7 of 7)	3' UTR (NM_011123, exon 7 of 7)	14223	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_156225.1	chrX	135796114	135796164	+	1	NA	intron (NM_001005385, intron 5 of 9)	CpG	-42895	NM_001163016	245607	Mm.489763	NM_001163015	ENSMUSG00000072966	Gprasp2	5330440H13Rik|GASP-2|GASP2|Prpl5	G protein-coupled receptor associated sorting protein 2	protein-coding
mm_157900.1	chrX	77848005	77848017	-	1	NA	exon (NM_017471, exon 2 of 7)	exon (NM_017471, exon 2 of 7)	5489	NM_017471	54192	Mm.8034	NM_017471	ENSMUSG00000000003	Pbsn	PB|Prbs	probasin	protein-coding
mm_99660.1	chr11	105784813	105784825	+	1	NA	intron (NM_181071, intron 6 of 25)	L1_Mus3|LINE|L1	159328	NM_007805	13056	Mm.149403	NM_007805	ENSMUSG00000019590	Cyb561	-	cytochrome b-561	protein-coding
mm_80526.1	chr9	80126365	80126384	+	1	NA	exon (NM_146003, exon 15 of 23)	exon (NM_146003, exon 15 of 23)	-38660	NM_001039546	17920	Mm.4040	NM_008662	ENSMUSG00000033577	Myo6	BC029719|Tlc|sv	myosin VI	protein-coding
mm_142188.1	chr17	36890035	36890050	-	1	NA	promoter-TSS (NM_001172168)	promoter-TSS (NM_001172168)	83	NM_001033235	195359	Mm.32606	NM_001033235	ENSMUSG00000073399	Trim40	Gm319|Gm35|Gm865	tripartite motif-containing 40	protein-coding
mm_119698.1	chr14	53665913	53665946	+	1	NA	Intergenic	Intergenic	588000	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_137726.1	chr17	29268909	29268974	+	1	NA	5' UTR (NM_030561, exon 1 of 9)	5' UTR (NM_030561, exon 1 of 9)	153	NM_030561	80748	Mm.290116	NM_030561	ENSMUSG00000052712	BC004004	2400006G15Rik	cDNA sequence BC004004	protein-coding
mm_53611.1	chr6	139662685	139662696	+	1	NA	Intergenic	RSINE1|SINE|B4	-53169	NM_207683	18705	Mm.333471	NM_011084	ENSMUSG00000030228	Pik3c2g	C80387|PI3K-C2-gamma	phosphatidylinositol 3-kinase, C2 domain containing, gamma polypeptide	protein-coding
mm_72086.1	chr8	71579307	71579320	+	1	NA	intron (NM_011977, intron 3 of 13)	intron (NM_011977, intron 3 of 13)	10386	NM_011977	26457	Mm.38165	NM_011977	ENSMUSG00000031808	Slc27a1	FATP1|Fatp	solute carrier family 27 (fatty acid transporter), member 1	protein-coding
mm_160194.1	chr7	63444787	63444787	+	1	NA	promoter-TSS (NM_130880)	promoter-TSS (NM_130880)	15	NM_130880	170711	Mm.156872	NM_130880	ENSMUSG00000033510	Otud7a	AJ430384|Otud7	OTU domain containing 7A	protein-coding
mm_169985.1	chr17	15022785	15022786	+	1	NA	TTS (NM_001123372)	TTS (NM_001123372)	-12601	NM_001123367	100041639	Mm.440445	NM_001123367	ENSMUSG00000079710	Gm3448	-	predicted gene 3448	protein-coding
mm_53934.1	chr6	4747171	4747184	-	1	NA	promoter-TSS (NM_001130188)	promoter-TSS (NM_001130188)	27	NM_001130188	20392	Mm.8739	NM_011360	ENSMUSG00000004631	Sgce	e-SG	sarcoglycan, epsilon	protein-coding
mm_40243.1	chr5	38039198	38039219	+	1	NA	promoter-TSS (NM_026959)	promoter-TSS (NM_026959)	-22	NM_001289536	71116	Mm.18959	NM_026959	ENSMUSG00000029125	Stx18	1810035L21Rik|4933425D03Rik|AU041562	syntaxin 18	protein-coding
mm_72212.1	chr8	72646617	72646628	+	1	NA	promoter-TSS (NM_176940)	promoter-TSS (NM_176940)	-89	NM_176940	319555	Mm.212927	NM_176940	ENSMUSG00000048148	Nwd1	A230063L24Rik	NACHT and WD repeat domain containing 1	protein-coding
mm_64584.1	chr7	145300890	145300910	+	1	NA	promoter-TSS (NM_145379)	promoter-TSS (NM_145379)	-9	NM_145379	211577	Mm.215151	NM_145379	ENSMUSG00000031070	Mrgprf	BC019711|Mgrc|MrgF	MAS-related GPR, member F	protein-coding
mm_86375.1	chr9	123835978	123835995	-	1	NA	intron (NM_148925, intron 5 of 18)	intron (NM_148925, intron 5 of 18)	15675	NM_148925	17281	Mm.252941	NM_148925	ENSMUSG00000025241	Fyco1	2810409M01Rik|Mem2|RUFY3|ZFYVE7	FYVE and coiled-coil domain containing 1	protein-coding
mm_100468.1	chr11	119928602	119928614	+	1	NA	intron (NR_039557, intron 2 of 2)	intron (NR_039557, intron 2 of 2)	-14484	NM_001037754	108100	Mm.197534	NM_130862	ENSMUSG00000025372	Baiap2	IRSp53|R75030	brain-specific angiogenesis inhibitor 1-associated protein 2	protein-coding
mm_43735.1	chr5	139793995	139794005	+	1	NA	intron (NM_010757, intron 1 of 2)	intron (NM_010757, intron 1 of 2)	2464	NM_010757	17135	Mm.157313	NM_010757	ENSMUSG00000018143	Mafk	AW061068|NF-E2|Nfe2u	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein K (avian)	protein-coding
mm_162462.1	chr1	128767189	128767195	+	1	NA	Intergenic	Intergenic	-174893	NM_009911	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding
mm_15862.1	chr2	164832863	164832878	+	1	NA	promoter-TSS (NM_008906)	promoter-TSS (NM_008906)	-2	NM_001038492	19025	Mm.359633	NM_008906	ENSMUSG00000017760	Ctsa	AU019505|PPCA|Ppgb	cathepsin A	protein-coding
mm_66354.1	chr7	43527701	43527713	-	1	NA	3' UTR (NM_001111058, exon 7 of 7)	3' UTR (NM_001111058, exon 7 of 7)	5464	NM_001111058	12489	Mm.140157	NM_021293	ENSMUSG00000004609	Cd33	Siglec-3|gp67	CD33 antigen	protein-coding
mm_113172.1	chr13	24813555	24813570	+	1	NA	TTS (NM_024473)	TTS (NM_024473)	11905	NM_024473	79555	Mm.266668	NM_024473	ENSMUSG00000019132	BC005537	8030460C05Rik|C78201	cDNA sequence BC005537	protein-coding
mm_48498.1	chr5	142802985	142802987	-	1	NA	intron (NM_178242, intron 2 of 15)	intron (NM_178242, intron 2 of 15)	14401	NM_178242	231861	Mm.354649	NM_178242	ENSMUSG00000039477	Tnrc18	BC025631|EG381742|Zfp469	trinucleotide repeat containing 18	protein-coding
mm_60606.1	chr7	44572585	44572617	+	1	NA	5' UTR (NM_008437, exon 1 of 9)	5' UTR (NM_008437, exon 1 of 9)	156	NM_008437	16541	Mm.383181	NM_008437	ENSMUSG00000002204	Napsa	KAP|Kdap|NAP1|SNAPA|pronapsin	napsin A aspartic peptidase	protein-coding
mm_151526.1	chr19	58744037	58744066	+	1	NA	exon (NM_018874, exon 13 of 13)	exon (NM_018874, exon 13 of 13)	15164	NM_018874	18946	Mm.10753	NM_018874	ENSMUSG00000042179	Pnliprp1	Plrp1	pancreatic lipase related protein 1	protein-coding
mm_17574.1	chr2	30413271	30413299	-	1	NA	intron (NM_007760, intron 1 of 13)	intron (NM_007760, intron 1 of 13)	2463	NM_007760	12908	Mm.20396	NM_007760	ENSMUSG00000026853	Crat	AW107812|CARAT	carnitine acetyltransferase	protein-coding
mm_146162.1	chr18	75056869	75056885	+	1	NA	intron (NM_027727, intron 5 of 16)	RSINE1|SINE|B4	38105	NM_027727	69190	Mm.173826	NM_027727	ENSMUSG00000035765	Dym	1810041M12Rik|4933427L07Rik|C030019K18Rik	dymeclin	protein-coding
mm_131595.1	chr16	18876710	18876739	+	1	NA	promoter-TSS (NM_010922)	promoter-TSS (NM_010922)	-26	NM_010435	15260	Mm.15694	NM_010435	ENSMUSG00000022702	Hira	AA138857|D16Ertd95e|Gm15797|N28177|OTTMUSG00000026264|Tuple1	histone cell cycle regulator	protein-coding
mm_83575.1	chr9	47708444	47708467	-	1	NA	intron (NM_001025600, intron 1 of 8)	intron (NM_001025600, intron 1 of 8)	109753	NR_046048	100038460	Mm.447649	NR_046048		Gm10677	ENSMUSG00000074363	predicted gene 10677	ncRNA
mm_94321.1	chr11	4237786	4237803	+	1	NA	intron (NM_001013365, intron 1 of 2)	intron (NM_001013365, intron 1 of 2)	1009	NM_001013365	18413	Mm.131422	NM_001013365	ENSMUSG00000058755	Osm	OncoM	oncostatin M	protein-coding
mm_138279.1	chr17	34608980	34608980	+	1	NA	promoter-TSS (NM_018862)	promoter-TSS (NM_018862)	-34	NM_018862	55979	Mm.8684	NM_018862	ENSMUSG00000034254	Agpat1	1-AGP|1-AGPAT|AW047140	1-acylglycerol-3-phosphate O-acyltransferase 1 (lysophosphatidic acid acyltransferase, alpha)	protein-coding
mm_107001.1	chr12	11280333	11280377	+	1	NA	exon (NM_025695, exon 6 of 27)	exon (NM_025695, exon 6 of 27)	14469	NM_025695	67241	Mm.173953	NM_025695	ENSMUSG00000020608	Smc6	2810489L22Rik|3830418C19Rik|AA990493|AU018782|AW742439|SMC-6|Smc6l1|mKIAA4103	structural maintenance of chromosomes 6	protein-coding
mm_125079.1	chr15	26308792	26308800	+	1	NA	promoter-TSS (NM_001310774)	promoter-TSS (NM_001310774)	-252	NM_177597	211147	Mm.54257	NM_177597	ENSMUSG00000022269	March11	9630025C22	membrane-associated ring finger (C3HC4) 11	protein-coding
mm_80227.1	chr9	72662474	72662523	+	1	NA	5' UTR (NM_010890, exon 1 of 29)	5' UTR (NM_010890, exon 1 of 29)	151	NM_010890	17999	Mm.279923	NM_010890	ENSMUSG00000032216	Nedd4	AA959633|AL023035|AU019897|E430025J12Rik|Nedd4-1|Nedd4a|mKIAA0093	neural precursor cell expressed, developmentally down-regulated 4	protein-coding
mm_78965.1	chr9	45274894	45274906	+	1	NA	Intergenic	Intergenic	-5751	NM_001324486	16154	Mm.379327	NM_008348	ENSMUSG00000032089	Il10ra	AW553859|CDw210|CDw210a|IL-10R1|IL-10RA|Il10r|mIL-10R	interleukin 10 receptor, alpha	protein-coding
mm_164015.1	chr14	70994437	70994463	-	1	NA	Intergenic	Intergenic	104343	NM_001302094	14586	Mm.32619	NM_008115	ENSMUSG00000022103	Gfra2	-	glial cell line derived neurotrophic factor family receptor alpha 2	protein-coding
mm_84804.1	chr9	77261435	77261452	-	1	NA	intron (NM_027150, intron 1 of 7)	intron (NM_027150, intron 1 of 7)	86427	NM_027150	69642	Mm.35008	NM_027150	ENSMUSG00000032355	Mlip	2310046A06Rik|AI931782|CIP	muscular LMNA-interacting protein	protein-coding
mm_109746.1	chr12	117625079	117625085	+	1	NA	intron (NM_175930, intron 9 of 27)	intron (NM_175930, intron 9 of 27)	108603	NM_175930	217944	Mm.227642	NM_175930	ENSMUSG00000041992	Rapgef5	4932413M22|C86120|D030051B22Rik|GFR|Mrgef|mKIAA0277|mmr-gef	Rap guanine nucleotide exchange factor (GEF) 5	protein-coding
mm_112456.1	chr13	5864751	5864768	+	1	NA	intron (NM_011803, intron 1 of 3)	intron (NM_011803, intron 1 of 3)	3270	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_34815.1	chr4	154937186	154937199	+	1	NA	Intergenic	Intergenic	-9115	NM_178931	230979	Mm.215147	NM_178931	ENSMUSG00000042333	Tnfrsf14	Atar|HveA|Hvem|Tnfrs14	tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)	protein-coding
mm_76797.1	chr8	102865869	102865876	-	1	NA	Intergenic	Intergenic	-80761	NM_009866	12552	Mm.1571	NM_009866	ENSMUSG00000031673	Cdh11	Cad11|OSF-4	cadherin 11	protein-coding
mm_102155.1	chr11	53707270	53707332	-	1	NA	promoter-TSS (NM_009012)	promoter-TSS (NM_009012)	18	NM_009012	19360	Mm.4888	NM_009012	ENSMUSG00000020380	Rad50	Mrell|Rad50l	RAD50 double strand break repair protein	protein-coding
mm_123813.1	chr14	70523386	70523405	-	1	NA	intron (NM_011359, intron 1 of 5)	RSINE1|SINE|B4	686	NM_011359	20389	Mm.24040	NM_011359	ENSMUSG00000022097	Sftpc	Bricd6|SP-C|SP5|SPC|Sftp-2|Sftp2|pro-SpC	surfactant associated protein C	protein-coding
mm_53286.1	chr6	128960598	128960600	+	1	NA	intron (NR_045009, intron 1 of 1)	intron (NR_045009, intron 1 of 1)	-10561	NM_001168224	70809	Mm.439891	NM_027562	ENSMUSG00000000248	Clec2g	4632413B12Rik|Clr-c|Clr-d|Clrc|Clrd|Clrx|Ddv10|Ocilrp1	C-type lectin domain family 2, member g	protein-coding
mm_112940.1	chr13	20986332	20986352	+	1	NA	intron (NM_012054, intron 13 of 20)	MT2B|LTR|ERVL	86957	NM_146535	258528	Mm.377554	NM_146535	ENSMUSG00000042869	Olfr1370	MOR256-14	olfactory receptor 1370	protein-coding
mm_6920.1	chr1	84840259	84840274	-	1	NA	promoter-TSS (NM_133975)	promoter-TSS (NM_133975)	425	NM_025386	66153	Mm.381192	NM_025386	ENSMUSG00000073633	Fbxo36	0610008D19Rik|1110020F21Rik|2410002G19Rik|D1Ertd757e	F-box protein 36	protein-coding
mm_64432.1	chr7	142577966	142577974	+	1	NA	promoter-TSS (NR_030416)	promoter-TSS (NR_030416)	176	NR_130974	14955	Mm.14802	NR_001592	ENSMUSG00000000031	H19	AI747191	H19, imprinted maternally expressed transcript	ncRNA
mm_43177.1	chr5	127657496	127657500	+	1	NA	intron (NM_177005, intron 4 of 11)	intron (NM_177005, intron 4 of 11)	25236	NM_177005	319804	Mm.237888	NM_177005	ENSMUSG00000049971	Glt1d1	5730455A04Rik	glycosyltransferase 1 domain containing 1	protein-coding
mm_107010.1	chr12	11802133	11802133	+	1	NA	Intergenic	Intergenic	80766	NR_003964	627110	Mm.194735	NR_003964		Tubb2a-ps2	C79445	tubulin, beta 2a, pseudogene 2	pseudo
mm_41157.1	chr5	87929875	87929878	+	1	NA	exon (NM_007786, exon 4 of 5)	exon (NM_007786, exon 4 of 5)	4243	NM_007786	12994	Mm.296303	NM_007786	ENSMUSG00000001622	Csn3	AW208918|CSN10|Csnk	casein kappa	protein-coding
mm_70444.1	chr8	11728071	11728095	+	1	NA	promoter-TSS (NM_001113517)	promoter-TSS (NM_001113517)	-22	NM_001113517	54126	Mm.244068	NM_017402	ENSMUSG00000031511	Arhgef7	Cool|PIX|Pak3bp|betaPix|betaPix-b|betaPix-c|cool-1|mKIAA0142|p85Cool1|p85SPR	Rho guanine nucleotide exchange factor (GEF7)	protein-coding
mm_101327.1	chr11	22972848	22972860	-	1	NA	5' UTR (NM_011663, exon 1 of 1)	5' UTR (NM_011663, exon 1 of 1)	849	NM_011663	22183	Mm.29542	NM_011663	ENSMUSG00000044068	Zrsr1	D11Ncvs75|Irlgs2|SP2|U2af1-rs1|U2afbp-rs	zinc finger (CCCH type), RNA binding motif and serine/arginine rich 1	protein-coding
mm_172524.1	chr7	83755987	83755991	+	1	NA	Intergenic	Intergenic	-20499	NM_010551	16170	Mm.10137	NM_010551	ENSMUSG00000001741	Il16	mKIAA4048	interleukin 16	protein-coding
mm_53619.1	chr6	140424087	140424138	+	1	NA	promoter-TSS (NM_144920)	promoter-TSS (NM_144920)	13	NM_144920	109135	Mm.247670	NM_144920	ENSMUSG00000030231	Plekha5	2810431N21Rik|AI428202|AK129423|AMH-Cre|Ayu21-9|Gt(pU21)9Imeg|Pepp2|Tg(AMH-cre)1Flor	pleckstrin homology domain containing, family A member 5	protein-coding
mm_132162.1	chr16	32247222	32247283	+	1	NA	promoter-TSS (NM_026898)	promoter-TSS (NM_026898)	-1	NM_026898	68980	Mm.159860	NM_026898	ENSMUSG00000022787	Wdr53	1500002B03Rik|AI848860	WD repeat domain 53	protein-coding
mm_79263.1	chr9	50753165	50753167	+	1	NA	promoter-TSS (NM_024441)	promoter-TSS (NM_024441)	195	NM_009964	12955	Mm.178	NM_009964	ENSMUSG00000032060	Cryab	Crya-2|Crya2|HspB5|P23	crystallin, alpha B	protein-coding
mm_89978.1	chr10	111595909	111595918	+	1	NA	Intergenic	Intergenic	-1640	NR_045344	71321	Mm.410785	NR_045344	ENSMUSG00000097082	4933440J02Rik	-	RIKEN cDNA 4933440J02 gene	ncRNA
mm_142634.1	chr17	47414706	47414725	-	1	NA	promoter-TSS (NM_001172091)	promoter-TSS (NM_001172091)	-4	NM_001172091	75462	Mm.46129	NM_029296	ENSMUSG00000047150	1700001C19Rik	-	RIKEN cDNA 1700001C19 gene	protein-coding
mm_110282.1	chr12	32061306	32061317	-	1	NA	promoter-TSS (NM_011158)	promoter-TSS (NM_011158)	-32	NM_011158	19088	Mm.25594	NM_011158	ENSMUSG00000002997	Prkar2b	AI451071|AW061005|PKARIIbeta|Pkarb2|RII(beta)	protein kinase, cAMP dependent regulatory, type II beta	protein-coding
mm_138044.1	chr17	33925401	33925445	+	1	NA	exon (NM_009318, exon 4 of 8)	exon (NM_009318, exon 4 of 8)	-4471	NM_009059	19732	Mm.43777	NM_009059	ENSMUSG00000041354	Rgl2	KE1.5|Rab2l|Rgt2|Rlf	ral guanine nucleotide dissociation stimulator-like 2	protein-coding
mm_70944.1	chr8	26158187	26158252	+	1	NA	promoter-TSS (NM_199042)	promoter-TSS (NM_199042)	50	NM_199042	73754	Mm.383241	NM_199042	ENSMUSG00000037214	Thap1	4833431A01Rik|AW490810	THAP domain containing, apoptosis associated protein 1	protein-coding
mm_98451.1	chr11	94945363	94945387	+	1	NA	exon (NM_007742, exon 30 of 51)	exon (NM_007742, exon 30 of 51)	9151	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_98099.1	chr11	86630242	86630246	+	1	NA	intron (NM_029478, intron 7 of 11)	ID4_|SINE|ID	-25827	NR_106195	102465902		NR_106195	ENSMUSG00000099324	Mir8115	Gm28012|mmu-mir-8115	microRNA 8115	ncRNA
mm_49579.1	chr6	30642306	30642327	+	1	NA	exon (NM_025350, exon 7 of 10)	exon (NM_025350, exon 7 of 10)	3098	NM_025350	109697	Mm.25377	NM_025350	ENSMUSG00000054446	Cpa1	0910001L12Rik|Cpa	carboxypeptidase A1, pancreatic	protein-coding
mm_13677.1	chr2	116878687	116878696	+	1	NA	promoter-TSS (NM_026104)	promoter-TSS (NM_026104)	0	NM_026104	67356	Mm.131623	NM_026104	ENSMUSG00000027355	Tmco5	1700095F04Rik|Tmco5a	transmembrane and coiled-coil domains 5	protein-coding
mm_111771.1	chr12	104035832	104035852	-	1	NA	intron (NM_026535, intron 2 of 4)	intron (NM_026535, intron 2 of 4)	8601	NM_026535	68054	Mm.20286	NM_026535	ENSMUSG00000041567	Serpina12	4632419J12Rik	serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 12	protein-coding
mm_104803.1	chr11	98775195	98775210	-	1	NA	5' UTR (NM_145434, exon 1 of 8)	5' UTR (NM_145434, exon 1 of 8)	175	NM_145434	217166	Mm.390397	NM_145434	ENSMUSG00000020889	Nr1d1	A530070C09Rik|R75201	nuclear receptor subfamily 1, group D, member 1	protein-coding
mm_127245.1	chr15	99601230	99601268	+	1	NA	promoter-TSS (NM_175087)	promoter-TSS (NM_175087)	-151	NM_175087	11831	Mm.202309	NM_175087	ENSMUSG00000043144	Aqp6	AI790337	aquaporin 6	protein-coding
mm_7259.1	chr1	93803771	93803817	-	1	NA	promoter-TSS (NM_025454)	promoter-TSS (NM_025454)	-171	NM_025454	66262	Mm.64065	NM_025454	ENSMUSG00000026283	Ing5	1700001C14Rik|1700027H23Rik|1810018M11Rik|AI225768	inhibitor of growth family, member 5	protein-coding
mm_17093.1	chr2	23040093	23040127	-	1	NA	5' UTR (NM_001077190, exon 1 of 11)	5' UTR (NM_001077190, exon 1 of 11)	131	NM_001077192	11308	Mm.205647	NM_007380	ENSMUSG00000058835	Abi1	E3B1|NAP1|Ssh3bp1|abi-1	abl-interactor 1	protein-coding
mm_3730.1	chr1	155083708	155083733	+	1	NA	Intergenic	Intergenic	15916	NM_010500	15939	Mm.12246	NM_010500	ENSMUSG00000056708	Ier5	-	immediate early response 5	protein-coding
mm_138042.1	chr17	33920523	33920554	+	1	NA	intron (NM_001025313, intron 3 of 7)	CpG	1060	NM_009318	21356	Mm.154457	NM_009318	ENSMUSG00000024308	Tapbp	D17Wsu91e|TPN	TAP binding protein	protein-coding
mm_125954.1	chr15	76249238	76249266	+	1	NA	TTS (NR_105918)	TTS (NR_105918)	1061	NR_105918	102465575		NR_105918	ENSMUSG00000098625	Mir6953	Gm27738|mmu-mir-6953	microRNA 6953	ncRNA
mm_134680.1	chr16	22411861	22411875	-	1	NA	exon (NM_023794, exon 7 of 13)	exon (NM_023794, exon 7 of 13)	27702	NM_023794	104156	Mm.155708	NM_023794	ENSMUSG00000013089	Etv5	1110005E01Rik|8430401F14Rik|ERM	ets variant 5	protein-coding
mm_27185.1	chr3	34649848	34649875	-	1	NA	promoter-TSS (NM_011443)	promoter-TSS (NM_011443)	-134	NM_011443	20674	Mm.65396	NM_011443	ENSMUSG00000074637	Sox2	Sox-2|lcc|ysb	SRY (sex determining region Y)-box 2	protein-coding
mm_56587.1	chr6	107438316	107438316	-	1	NA	Intergenic	Intergenic	-91410	NM_008516	16979	Mm.428543	NM_008516	ENSMUSG00000034648	Lrrn1	2810047E21Rik|NLRR-1	leucine rich repeat protein 1, neuronal	protein-coding
mm_108529.1	chr12	84151220	84151235	+	1	NA	3' UTR (NM_001163501, exon 13 of 13)	3' UTR (NM_001163501, exon 13 of 13)	-2738	NM_027438	70481	Mm.444348	NM_027438	ENSMUSG00000054383	Pnma1	5730402C15Rik	paraneoplastic antigen MA1	protein-coding
mm_169448.1	chr14	59414575	59414585	-	1	NA	intron (NR_135463, intron 8 of 13)	intron (NR_135463, intron 8 of 13)	-21068	NM_001164289	628705	Mm.479244	NM_001164289	ENSMUSG00000091144	Phf11c	EG628705|Gm6907|Phf11	PHD finger protein 11C	protein-coding
mm_38323.1	chr4	137344061	137344070	-	1	NA	intron (NM_009861, intron 1 of 5)	MERVL_2A-int|LTR|ERVL	13694	NM_009861	12540	Mm.1022	NM_009861	ENSMUSG00000006699	Cdc42	AI747189|AU018915	cell division cycle 42	protein-coding
mm_97473.1	chr11	78322966	78322996	+	1	NA	promoter-TSS (NM_001303423)	promoter-TSS (NM_001303423)	-92	NM_001303423	11676	Mm.7729	NM_009657	ENSMUSG00000017390	Aldoc	AI847350|AU040929|Aldo3|Scrg2	aldolase C, fructose-bisphosphate	protein-coding
mm_124292.1	chr14	103054849	103054869	-	1	NA	exon (NM_008392, exon 5 of 5)	exon (NM_008392, exon 5 of 5)	7847	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_57636.1	chr6	128358198	128358202	-	1	NA	intron (NM_001326587, intron 3 of 3)	intron (NM_001326587, intron 3 of 3)	-2349	NM_011657	22158	Mm.291783	NM_011657	ENSMUSG00000001521	Tulp3	2310022L06Rik|AI316887	tubby-like protein 3	protein-coding
mm_83229.1	chr9	42343884	42343893	-	1	NA	exon (NM_001324548, exon 16 of 24)	exon (NM_001324548, exon 16 of 24)	56041	NM_009347	21683	Mm.42209	NM_009347	ENSMUSG00000037705	Tecta	Tctna	tectorin alpha	protein-coding
mm_145717.1	chr18	62994876	62994886	+	1	NA	intron (NM_028017, intron 10 of 11)	intron (NM_028017, intron 10 of 11)	16965	NM_028017	108123	Mm.292687	NM_028017	ENSMUSG00000024581	Napg	2400003O04Rik|SNARE	N-ethylmaleimide sensitive fusion protein attachment protein gamma	protein-coding
mm_152132.1	chr19	7020939	7020961	-	1	NA	3' UTR (NM_016737, exon 14 of 14)	3' UTR (NM_016737, exon 14 of 14)	-1481	NM_153795	108101	Mm.157591	NM_153795	ENSMUSG00000024965	Fermt3	C79673|Kindlin3	fermitin family member 3	protein-coding
mm_15458.1	chr2	157426405	157426427	+	1	NA	intron (NM_009271, intron 1 of 14)	intron (NM_009271, intron 1 of 14)	2123	NM_001025395	20779	Mm.22845	NM_009271	ENSMUSG00000027646	Src	AW259666|pp60c-src	Rous sarcoma oncogene	protein-coding
mm_26105.1	chr3	137341104	137341146	+	1	NA	promoter-TSS (NM_016885)	promoter-TSS (NM_016885)	47	NM_016885	59308	Mm.27343	NM_016885	ENSMUSG00000054690	Emcn	0610012K22Rik|AI315669|Muc14	endomucin	protein-coding
mm_127514.1	chr15	101850144	101850164	+	1	NA	exon (NM_008473, exon 1 of 9)	exon (NM_008473, exon 1 of 9)	632	NM_008473	16678	Mm.183137	NM_008473	ENSMUSG00000046834	Krt1	Krt-2.1|Krt2-1|Krt86	keratin 1	protein-coding
mm_15647.1	chr2	163068214	163068222	+	1	NA	TTS (NR_105970)	TTS (NR_105970)	128	NR_105970	102465607		NR_105970	ENSMUSG00000099091	Mir7003	Gm27340|mmu-mir-7003	microRNA 7003	ncRNA
mm_58039.1	chr6	136821563	136821591	-	1	NA	exon (NM_021714, exon 6 of 12)	exon (NM_021714, exon 6 of 12)	6639	NM_021714	60321	Mm.141197	NM_021714	ENSMUSG00000030216	Wbp11	2510026P17Rik|D6Wsu113e|Npwbp|SIPP1	WW domain binding protein 11	protein-coding
mm_135116.1	chr16	35841112	35841122	-	1	NA	exon (NM_001039530, exon 14 of 17)	exon (NM_001039530, exon 14 of 17)	30265	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_86107.1	chr9	115310460	115310484	-	1	NA	promoter-TSS (NM_024222)	promoter-TSS (NM_024222)	-51	NM_024222	68292	Mm.296158	NM_024222	ENSMUSG00000032437	Stt3b	1300006C19Rik|Simp	STT3, subunit of the oligosaccharyltransferase complex, homolog B (S. cerevisiae)	protein-coding
mm_83492.1	chr9	45945942	45945960	-	1	NA	intron (NM_172257, intron 12 of 25)	intron (NM_172257, intron 12 of 25)	-6361	NR_106055	102465659		NR_106055	ENSMUSG00000098327	Mir7087	Gm27273|mmu-mir-7087	microRNA 7087	ncRNA
mm_100032.1	chr11	114931309	114931345	+	1	NA	intron (NM_199221, intron 1 of 3)	intron (NM_199221, intron 1 of 3)	3059	NM_001347651	217304	Mm.185355	NM_199221	ENSMUSG00000063193	Cd300lb	CLM-7|Clm7|Gm253|LMIR5	CD300 molecule like family member B	protein-coding
mm_2596.1	chr1	119526182	119526197	+	1	NA	promoter-TSS (NM_146103)	promoter-TSS (NM_146103)	35	NM_146103	226351	Mm.439806	NM_146103	ENSMUSG00000098923	Tmem185b	2500001K11Rik	transmembrane protein 185B	protein-coding
mm_68468.1	chr7	110648730	110648738	-	1	NA	Intergenic	Intergenic	21065	NM_009627	11535	Mm.1408	NM_009627	ENSMUSG00000030790	Adm	AM	adrenomedullin	protein-coding
mm_161368.1	chr14	63509337	63509337	-	1	NA	promoter-TSS (NM_021480)	promoter-TSS (NM_021480)	-245	NM_021480	58865	Mm.354229	NM_021480	ENSMUSG00000021953	Tdh	-	L-threonine dehydrogenase	protein-coding
mm_159604.1	chr4	129118782	129118782	-	1	NA	intron (NM_001286081, intron 1 of 3)	intron (NM_001286081, intron 1 of 3)	1390	NM_001286083	15444	Mm.384452	NM_010471	ENSMUSG00000028785	Hpca	-	hippocalcin	protein-coding
mm_63635.1	chr7	128523649	128523667	+	1	NA	promoter-TSS (NM_013863)	promoter-TSS (NM_013863)	75	NM_013863	29810	Mm.84073	NM_013863	ENSMUSG00000030847	Bag3	AA407278|Bis|mg638	BCL2-associated athanogene 3	protein-coding
mm_137901.1	chr17	31820349	31820357	+	1	NA	Intergenic	Intergenic	35439	NM_010831	17691	Mm.290941	NM_010831	ENSMUSG00000024042	Sik1	Msk|Sik|Snf1lk	salt inducible kinase 1	protein-coding
mm_79096.1	chr9	46243002	46243012	+	1	NA	exon (NM_007468, exon 3 of 3)	exon (NM_007468, exon 3 of 3)	2163	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_49365.1	chr6	23248539	23248548	+	1	NA	promoter-TSS (NM_028462)	promoter-TSS (NM_028462)	-279	NM_028462	73191	Mm.55115	NM_028462	ENSMUSG00000029697	Fezf1	3110069A13Rik|Fez|Zfp312-like|fez-like	Fez family zinc finger 1	protein-coding
mm_50602.1	chr6	49244742	49244744	+	1	NA	intron (NM_001347209, intron 7 of 7)	intron (NM_001347209, intron 7 of 7)	19309	NM_001347209	101214	Mm.196598	NM_198102	ENSMUSG00000029817	Tra2a	1500010G04Rik|AL022798|G430041M01Rik|mAWMS1	transformer 2 alpha homolog (Drosophila)	protein-coding
mm_81623.1	chr9	110834654	110834663	+	1	NA	promoter-TSS (NM_153172)	promoter-TSS (NM_153172)	70	NM_153172	260408	Mm.79114	NM_153172	ENSMUSG00000047257	Prss45	Tespl|Tessp5	protease, serine 45	protein-coding
mm_77245.1	chr8	115705385	115705399	-	1	NA	3' UTR (NM_001025577, exon 1 of 1)	3' UTR (NM_001025577, exon 1 of 1)	1502	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_76027.1	chr8	75109331	75109373	-	1	NA	promoter-TSS (NM_008566)	promoter-TSS (NM_008566)	-157	NM_001302540	17218	Mm.5048	NM_008566	ENSMUSG00000005410	Mcm5	AA617332|AI324988|AL033333|Cdc46|Mcmd5|P1-CDC46	minichromosome maintenance complex component 5	protein-coding
mm_162962.1	chr11	6547210	6547220	+	1	NA	intron (NM_001190343, intron 1 of 8)	CpG	328	NM_001190343	216527	Mm.221271	NM_146014	ENSMUSG00000000378	Ccm2	BC029157	cerebral cavernous malformation 2	protein-coding
mm_73269.1	chr8	104540771	104540784	+	1	NA	promoter-TSS (NM_053070)	promoter-TSS (NM_053070)	-30	NM_053070	12354	Mm.129265	NM_053070	ENSMUSG00000031883	Car7	AV343731|Ca7	carbonic anhydrase 7	protein-coding
mm_125166.1	chr15	31273193	31273218	+	1	NA	exon (NM_146057, exon 4 of 4)	exon (NM_146057, exon 4 of 4)	48820	NM_146057	223453	Mm.222867	NM_146057	ENSMUSG00000039168	Dap	4921531N22Rik|AI789753|AU040360	death-associated protein	protein-coding
mm_82209.1	chr9	124103797	124103808	+	1	NA	intron (NM_009915, intron 1 of 2)	intron (NM_009915, intron 1 of 2)	1619	NM_009915	12772	Mm.6272	NM_009915	ENSMUSG00000049103	Ccr2	Cc-ckr-2|Ccr2a|Ccr2b|Ckr2|Ckr2a|Ckr2b|Cmkbr2|mJe-r	chemokine (C-C motif) receptor 2	protein-coding
mm_16546.1	chr2	181715006	181715082	+	1	NA	promoter-TSS (NM_011012)	promoter-TSS (NM_011012)	28	NM_001318923	18389	Mm.285075	NM_011012	ENSMUSG00000027584	Oprl1	KOR-3|KOR3|LC132|MOR-C|NOP|ORGC|ORL1|Oprl|XOR1|morc	opioid receptor-like 1	protein-coding
mm_106062.1	chr11	116131111	116131131	-	1	NA	promoter-TSS (NM_178802)	promoter-TSS (NM_178802)	7	NM_178802	338364	Mm.439976	NM_178802	ENSMUSG00000054517	Trim65	4732463G12Rik	tripartite motif-containing 65	protein-coding
mm_130569.1	chr15	99457743	99457753	-	1	NA	promoter-TSS (NM_001001884)	promoter-TSS (NM_001001884)	0	NM_001001884	380969	Mm.22915	NM_001001884	ENSMUSG00000023009	Nckap5l	C230021P08Rik|Cep169	NCK-associated protein 5-like	protein-coding
mm_151834.1	chr19	5719307	5719315	-	1	NA	exon (NM_001114597, exon 9 of 19)	exon (NM_001114597, exon 9 of 19)	7006	NM_001114595	114601	Mm.210447	NM_053252	ENSMUSG00000024937	Ehbp1l1	G430002G23Rik	EH domain binding protein 1-like 1	protein-coding
mm_102423.1	chr11	59413089	59413095	-	1	NA	intron (NM_144521, intron 4 of 4)	intron (NM_144521, intron 4 of 4)	36864	NM_144521	67826	Mm.26680	NM_144521	ENSMUSG00000009894	Snap47	1110031B06Rik|SNAP-47	synaptosomal-associated protein, 47	protein-coding
mm_169935.1	chr16	60760325	60760330	-	1	NA	Intergenic	BGLII|LTR|ERVK	-154796	NM_007938	13840	Mm.455790	NM_007938	ENSMUSG00000055540	Epha6	Ehk2|Hek12|m-ehk2	Eph receptor A6	protein-coding
mm_15098.1	chr2	153345991	153346073	+	1	NA	promoter-TSS (NM_001039939)	promoter-TSS (NM_001039939)	-107	NM_001039939	228790	Mm.330677	NM_001039939	ENSMUSG00000042548	Asxl1	mKIAA0978	additional sex combs like 1	protein-coding
mm_20197.1	chr2	124222356	124222375	-	1	NA	promoter-TSS (NR_040612)	promoter-TSS (NR_040612)	-7	NR_040612	75946	Mm.415059	NR_040612	ENSMUSG00000086954	4930583P06Rik	-	RIKEN cDNA 4930583P06 gene	ncRNA
mm_104069.1	chr11	86586209	86586221	-	1	NA	intron (NM_029478, intron 11 of 11)	intron (NM_029478, intron 11 of 11)	-2057	NR_029738	387140		NR_029738	ENSMUSG00000065455	Mir21a	Mir21|Mirn21|mmu-mir-21|mmu-mir-21a	microRNA 21a	ncRNA
mm_51768.1	chr6	88045386	88045392	+	1	NA	promoter-TSS (NM_009005)	promoter-TSS (NM_009005)	-119	NM_009005	19349	Mm.333233	NM_009005	ENSMUSG00000079477	Rab7	Rab7a	RAB7, member RAS oncogene family	protein-coding
mm_172481.1	chr7	50033850	50033850	-	1	NA	intron (NM_001037906, intron 2 of 19)	intron (NM_001037906, intron 2 of 19)	58500	NM_001037906	338352	Mm.383528	NM_001037906	ENSMUSG00000055409	Nell1	B230343H07Rik|l7R6	NEL-like 1	protein-coding
mm_136140.1	chr16	87432598	87432613	-	1	NA	promoter-TSS (NM_001081068)	promoter-TSS (NM_001081068)	1	NM_001081068	78913	Mm.249005	NM_001081068	ENSMUSG00000052299	Ltn1	4930528H02Rik|AV266914|C87237|Listerin|Rnf160|Zfp294	listerin E3 ubiquitin protein ligase 1	protein-coding
mm_44198.1	chr5	3647721	3647733	-	1	NA	5' UTR (NM_026033, exon 1 of 5)	5' UTR (NM_026033, exon 1 of 5)	209	NM_026033	67210	Mm.178424	NM_026033	ENSMUSG00000007415	Gatad1	2310031E19Rik|2810047M21Rik|8430439A17Rik|9130430G15Rik|B330017N08Rik|ENSMUSG00000073241|Odag	GATA zinc finger domain containing 1	protein-coding
mm_78531.1	chr9	35116741	35116767	+	1	NA	promoter-TSS (NR_029475)	promoter-TSS (NR_029475)	26	NR_029475	78934	Mm.391688	NR_029475	ENSMUSG00000070315	4930581F22Rik	-	RIKEN cDNA 4930581F22 gene	ncRNA
mm_165989.1	chr4	109117766	109117779	-	1	NA	intron (NM_001346502, intron 4 of 23)	intron (NM_001346502, intron 4 of 23)	264	NM_173350	100273	Mm.366315	NM_133885	ENSMUSG00000028559	Osbpl9	2600011I06Rik|AU015843|Orp-9	oxysterol binding protein-like 9	protein-coding
mm_92682.1	chr10	80590293	80590329	-	1	NA	promoter-TSS (NM_145421)	promoter-TSS (NM_145421)	30	NM_145421	216169	Mm.29802	NM_145421	ENSMUSG00000003346	Abhd17a	1700013O15Rik|BC005632|D10Bwg1364e|Fam108a	abhydrolase domain containing 17A	protein-coding
mm_137162.1	chr17	23803616	23803684	+	1	NA	intron (NM_175229, intron 1 of 13)	CpG	463	NM_175229	75956	Mm.5222	NM_175229	ENSMUSG00000039218	Srrm2	5033413A03Rik|AA410130|SRm300|mKIAA0324	serine/arginine repetitive matrix 2	protein-coding
mm_151824.1	chr19	5637376	5637391	-	1	NA	promoter-TSS (NM_009045)	promoter-TSS (NM_009045)	-107	NM_009045	19697	Mm.249966	NM_009045	ENSMUSG00000024927	Rela	p65	v-rel reticuloendotheliosis viral oncogene homolog A (avian)	protein-coding
mm_79748.1	chr9	62368032	62368040	+	1	NA	intron (NM_009672, intron 1 of 6)	intron (NM_009672, intron 1 of 6)	26693	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	protein-coding
mm_35923.1	chr4	53032106	53032139	-	1	NA	3' UTR (NM_013454, exon 50 of 50)	3' UTR (NM_013454, exon 50 of 50)	20242	NM_025623	66536	Mm.38244	NM_025623	ENSMUSG00000015247	Nipsnap3b	2700063N13Rik|Nipsnap3a	nipsnap homolog 3B (C. elegans)	protein-coding
mm_37477.1	chr4	123565558	123565565	-	1	NA	intron (NM_001199136, intron 1 of 97)	intron (NM_001199136, intron 1 of 97)	-50859	NR_105824	102465214		NR_105824	ENSMUSG00000099005	Mir6398	Gm27657|mmu-mir-6398	microRNA 6398	ncRNA
mm_150293.1	chr19	34493361	34493388	+	1	NA	3' UTR (NM_021460, exon 10 of 10)	3' UTR (NM_021460, exon 10 of 10)	-18239	NM_009890	12642	Mm.30824	NM_009890	ENSMUSG00000050370	Ch25h	AI462618|m25OH	cholesterol 25-hydroxylase	protein-coding
mm_58960.1	chr7	18925864	18925899	+	1	NA	promoter-TSS (NM_001029877)	promoter-TSS (NM_001029877)	-7	NM_001029877	384569	Mm.262724	NM_001029877	ENSMUSG00000030411	Nova2	Gm1424	neuro-oncological ventral antigen 2	protein-coding
mm_80969.1	chr9	103112039	103112045	+	1	NA	promoter-TSS (NM_173781)	promoter-TSS (NM_173781)	-32	NM_173781	270192	Mm.490252	NM_173781	ENSMUSG00000032549	Rab6b	9630015C03|AI844641|C330006L04Rik|D9Bwg0185e	RAB6B, member RAS oncogene family	protein-coding
mm_62403.1	chr7	101110736	101110747	+	1	NA	exon (NM_001146010, exon 2 of 20)	exon (NM_001146010, exon 2 of 20)	1966	NM_199012	207278	Mm.263041	NM_199012	ENSMUSG00000030691	Fchsd2	BC034086|R74866|Sh3md3|mKIAA0769	FCH and double SH3 domains 2	protein-coding
mm_44638.1	chr5	28123649	28123660	-	1	NA	Intergenic	Intergenic	-42042	NM_010134	13799	Mm.4298	NM_010134	ENSMUSG00000039095	En2	BB131122|En-2	engrailed 2	protein-coding
mm_4683.1	chr1	180583809	180583823	+	1	NA	exon (NM_007415, exon 7 of 23)	exon (NM_007415, exon 7 of 23)	-3385	NR_105869	102466761		NR_105869	ENSMUSG00000098926	Mir6904	Gm27426|mmu-mir-6904	microRNA 6904	ncRNA
mm_45671.1	chr5	77211464	77211484	-	1	NA	promoter-TSS (NM_001289764)	promoter-TSS (NM_001289764)	-3	NM_001289768	69982	Mm.46106	NM_183284	ENSMUSG00000053030	Spink2	1700007F22Rik|AV038945|HUSI-II	serine peptidase inhibitor, Kazal type 2	protein-coding
mm_65378.1	chr7	25089894	25089919	-	1	NA	Intergenic	Intergenic	7269	NR_105855	102465968		NR_105855	ENSMUSG00000098441	Mir6537	Gm27808|mmu-mir-6537	microRNA 6537	ncRNA
mm_106767.1	chr12	4592993	4593087	+	1	NA	promoter-TSS (NM_001198969)	promoter-TSS (NM_001198969)	32	NM_001198968	20403	Mm.341204	NM_011365	ENSMUSG00000020640	Itsn2	AI327390|Ese2|Sh3d1B|Sh3p18|mKIAA1256	intersectin 2	protein-coding
mm_139663.1	chr17	57406976	57407000	+	1	NA	intron (NM_010130, intron 6 of 21)	intron (NM_010130, intron 6 of 21)	48302	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_73223.1	chr8	100160607	100160610	+	1	NA	Intergenic	Intergenic	743934	NR_132435	234624	Mm.124595	NM_175479	ENSMUSG00000052479	A330008L17Rik	-	RIKEN cDNA A330008L17 gene	ncRNA
mm_150501.1	chr19	39022049	39022057	+	1	NA	intron (NM_028089, intron 4 of 8)	B3|SINE|B2	15034	NM_028089	72082	Mm.142581	NM_028089	ENSMUSG00000025002	Cyp2c55	2010318C06Rik	cytochrome P450, family 2, subfamily c, polypeptide 55	protein-coding
mm_37188.1	chr4	117375496	117375501	-	1	NA	promoter-TSS (NM_001310729)	promoter-TSS (NM_001310729)	-37	NM_001310729	66743	Mm.318331	NM_025739	ENSMUSG00000028677	Rnf220	4732477A13|4931406I20Rik|5730503K05Rik|AV302541	ring finger protein 220	protein-coding
mm_55836.1	chr6	83143259	83143264	-	1	NA	intron (NM_009106, intron 2 of 12)	intron (NM_009106, intron 2 of 12)	6177	NM_009106	20166	Mm.4139	NM_009106	ENSMUSG00000034930	Rtkn	-	rhotekin	protein-coding
mm_80328.1	chr9	75037713	75037737	+	1	NA	promoter-TSS (NM_021548)	promoter-TSS (NM_021548)	-7	NM_021548	59046	Mm.247837	NM_021548	ENSMUSG00000007656	Arpp19	19kDa|2700024H10Rik|ARPP-19|AW559096|Arpp12	cAMP-regulated phosphoprotein 19	protein-coding
mm_79760.1	chr9	62409253	62409295	+	1	NA	Intergenic	Intergenic	67931	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	protein-coding
mm_46567.1	chr5	107173417	107173419	-	1	NA	intron (NM_011578, intron 4 of 16)	intron (NM_011578, intron 4 of 16)	116177	NM_011578	21814	Mm.200775	NM_011578	ENSMUSG00000029287	Tgfbr3	1110036H20Rik|AU015626|AW215636|TBRIII	transforming growth factor, beta receptor III	protein-coding
mm_43804.1	chr5	142903117	142903140	+	1	NA	TTS (NM_007393)	TTS (NM_007393)	3626	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_67872.1	chr7	99180266	99180319	-	1	NA	intron (NM_026384, intron 1 of 7)	intron (NM_026384, intron 1 of 7)	2421	NM_026384	67800	Mm.180189	NM_026384	ENSMUSG00000030747	Dgat2	0610010B06Rik|ARAT|DGAT-2	diacylglycerol O-acyltransferase 2	protein-coding
mm_109184.1	chr12	108477012	108477015	+	1	NA	intron (NM_001043335, intron 3 of 21)	MTD|LTR|ERVL-MaLR	54197	NM_001043335	68519	Mm.236645	NM_001043335	ENSMUSG00000058070	Eml1	1110008N23Rik|A930030P13Rik|AA171013|AI847476|AI853955|ELP79|EMAP|EMAPL|heco	echinoderm microtubule associated protein like 1	protein-coding
mm_8563.1	chr1	155280435	155280438	-	1	NA	3' UTR (NM_011273, exon 15 of 15)	3' UTR (NM_011273, exon 15 of 15)	121733	NM_021433	58244	Mm.66264	NM_021433	ENSMUSG00000026470	Stx6	2310039E05Rik|2410005I16Rik|AA437559|AI415714|AI845861	syntaxin 6	protein-coding
mm_3004.1	chr1	133256114	133256155	+	1	NA	non-coding (NR_037984, exon 3 of 4)	non-coding (NR_037984, exon 3 of 4)	10037	NM_182930	240753	Mm.253559	NM_182930	ENSMUSG00000041757	Plekha6	9530028L01Rik|AU042621|Pepp3	pleckstrin homology domain containing, family A member 6	protein-coding
mm_117138.1	chr13	60940235	60940246	-	1	NA	exon (NM_009411, exon 3 of 5)	exon (NM_009411, exon 3 of 5)	1695	NM_009411	21984	Mm.2372	NM_009411	ENSMUSG00000033834	Tpbpa	AV033951|Tb-1|Tb1|Tpbp|b2b1247Clo	trophoblast specific protein alpha	protein-coding
mm_51297.1	chr6	72306909	72306927	+	1	NA	exon (NM_001282071, exon 5 of 11)	exon (NM_001282071, exon 5 of 11)	2308	NM_147779	20388	Mm.46033	NM_147779	ENSMUSG00000056370	Sftpb	AI562151|SF-B|SP-B|Sftp-3|Sftp3	surfactant associated protein B	protein-coding
mm_64206.1	chr7	141475267	141475292	+	1	NA	promoter-TSS (NM_025593)	promoter-TSS (NM_025593)	43	NM_053082	64540	Mm.489619	NM_053082	ENSMUSG00000025511	Tspan4	AI325509|AI746565|D130042I01Rik|NAG-2|Tm4sf7|Tspan-4	tetraspanin 4	protein-coding
mm_48934.1	chr6	4537945	4537956	+	1	NA	exon (NM_007743, exon 49 of 52)	exon (NM_007743, exon 49 of 52)	32332	NM_007743	12843	Mm.277792	NM_007743	ENSMUSG00000029661	Col1a2	AA960264|AI325291|Col1a-2|Cola-2|Cola2|oim	collagen, type I, alpha 2	protein-coding
mm_89554.1	chr10	94846981	94846984	+	1	NA	intron (NM_018797, intron 12 of 30)	intron (NM_018797, intron 12 of 30)	97596	NM_018797	54712	Mm.256712	NM_018797	ENSMUSG00000074785	Plxnc1	2510048K12Rik|AW742158|CD232|Vespr	plexin C1	protein-coding
mm_70853.1	chr8	23669654	23669671	+	1	NA	promoter-TSS (NM_177086)	promoter-TSS (NM_177086)	1	NM_177086	320158	Mm.121274	NM_177086	ENSMUSG00000037492	Zmat4	9630048M01Rik	zinc finger, matrin type 4	protein-coding
mm_52009.1	chr6	93234057	93234069	+	1	NA	Intergenic	Intergenic	293481	NR_015530	330385	Mm.483472	NR_015530	ENSMUSG00000097462	9530026P05Rik	B430306B02	RIKEN cDNA 9530026P05 gene	ncRNA
mm_160461.1	chr8	109647484	109647484	+	1	NA	exon (NM_001286454, exon 19 of 33)	exon (NM_001286454, exon 19 of 33)	32967	NM_181544	244646	Mm.436810	NM_181544	ENSMUSG00000048827	Pkd1l3	-	polycystic kidney disease 1 like 3	protein-coding
mm_118762.1	chr14	22433042	22433054	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	109750	NR_046307	74896	Mm.444661	NR_046307		4930405A10Rik	4930456G20Rik	RIKEN cDNA 4930405A10 gene	ncRNA
mm_135223.1	chr16	36784747	36784758	-	1	NA	exon (NM_021301, exon 1 of 22)	exon (NM_021301, exon 1 of 22)	210	NM_001145899	57738	Mm.281804	NM_021301	ENSMUSG00000022899	Slc15a2	8430408C16Rik|C78862|Pept2	solute carrier family 15 (H+/peptide transporter), member 2	protein-coding
mm_167634.1	chr9	62868733	62868733	+	1	NA	exon (NM_138304, exon 3 of 5)	exon (NM_138304, exon 3 of 5)	-6709	NR_003965	677044	Mm.422004	NR_003965	ENSMUSG00000074250	Gm10653	ENSMUSG00000074250	ribsomal protein S2 pseudogene	pseudo
mm_113955.1	chr13	51101204	51101231	+	1	NA	promoter-TSS (NR_029463)	promoter-TSS (NR_029463)	-330	NM_001283029	20729	Mm.188432	NM_011462	ENSMUSG00000021395	Spin1	Spin	spindlin 1	protein-coding
mm_38034.1	chr4	133875261	133875274	-	1	NA	promoter-TSS (NM_001285506)	promoter-TSS (NM_001285506)	-536	NM_001285506	20111	Mm.301827	NM_009097	ENSMUSG00000003644	Rps6ka1	Mapkapk-1a|Rsk|Rsk-1|Rsk1|S6K-alpha-1|p90-Rsk1|p90Rsk1|p90S6K|p90rsk	ribosomal protein S6 kinase polypeptide 1	protein-coding
mm_84203.1	chr9	60680976	60680979	-	1	NA	intron (NM_145616, intron 3 of 16)	intron (NM_145616, intron 3 of 16)	6557	NM_001311095	102747	Mm.269413	NM_145616	ENSMUSG00000047766	Lrrc49	AI430817|AW050057|D430025H09Rik|PGs4|p79	leucine rich repeat containing 49	protein-coding
mm_60134.1	chr7	37447604	37447608	+	1	NA	Intergenic	Tigger5b|DNA|TcMar-Tigger	322146	NM_172385	243937	Mm.322505	NM_172385	ENSMUSG00000043456	Zfp536	9630010P11Rik|Znf536|mKIAA0390	zinc finger protein 536	protein-coding
mm_167885.1	chrX	53460315	53460325	+	1	NA	Intergenic	Intergenic	25402	NR_034074	69501	Mm.63828	NM_175147	ENSMUSG00000060967	Etd	1700030K02Rik	embryonic testis differentiation	ncRNA
mm_113294.1	chr13	30381340	30381364	+	1	NA	exon (NM_177322, exon 3 of 3)	exon (NM_177322, exon 3 of 3)	44996	NM_177322	11607	Mm.35062	NM_177322	ENSMUSG00000049115	Agtr1a	1810074K20Rik|AG2S|AI551199|AT1|AT1a|AT2R1|AT2R1A|Agtr-1a|Agtr1|Angtr-1a	angiotensin II receptor, type 1a	protein-coding
mm_58201.1	chr6	143221421	143221431	-	1	NA	Intergenic	Intergenic	-24462	NR_027803	52285	Mm.354898	NM_001033129		D6Ertd474e	1700001I24Rik|AU023129	DNA segment, Chr 6, ERATO Doi 474, expressed	ncRNA
mm_74383.1	chr8	128697997	128698000	+	1	NA	intron (NM_010578, intron 1 of 15)	PB1D10|SINE|Alu	12344	NM_010578	16412	Mm.263396	NM_010578	ENSMUSG00000025809	Itgb1	4633401G24Rik|AA409975|AA960159|CD29|ENSMUSG00000051907|Fnrb|Gm9863|gpIIa	integrin beta 1 (fibronectin receptor beta)	protein-coding
mm_56984.1	chr6	120493903	120493913	-	1	NA	promoter-TSS (NM_033567)	promoter-TSS (NM_033567)	-101	NM_033567	94047	Mm.23088	NM_033567	ENSMUSG00000094626	Cecr6	AW048664	cat eye syndrome chromosome region, candidate 6	protein-coding
mm_149821.1	chr19	24300664	24300673	+	1	NA	intron (NM_008846, intron 14 of 14)	intron (NM_008846, intron 14 of 14)	-20082	NM_008044	14297	Mm.7319	NM_008044	ENSMUSG00000059363	Fxn	FA|FARR|Frda|X25	frataxin	protein-coding
mm_40002.1	chr5	32838096	32838107	+	1	NA	intron (NM_194340, intron 3 of 10)	intron (NM_194340, intron 3 of 10)	16129	NM_194340	215476	Mm.248721	NM_194340	ENSMUSG00000054280	Prr14l	6030436E02Rik|C330019G07Rik|Prl14l	proline rich 14-like	protein-coding
mm_37846.1	chr4	132184388	132184391	-	1	NA	TTS (NM_145393)	TTS (NM_145393)	27867	NM_145393	213541	Mm.23998	NM_145393	ENSMUSG00000040025	Ythdf2	9430020E02Rik|HGRG8|NY-REN-2	YTH domain family 2	protein-coding
mm_134209.1	chr16	11176026	11176038	-	1	NA	intron (NM_145931, intron 1 of 22)	CpG	361	NR_027502	106205	Mm.226860	NM_145931	ENSMUSG00000037965	Zc3h7a	A430104C18Rik|AI447294|AW556219|HSPC055|Zc3h7|Zc3hdc7	zinc finger CCCH type containing 7 A	protein-coding
mm_149431.1	chr19	11470680	11470708	+	1	NA	intron (NM_001166376, intron 1 of 2)	intron (NM_001166376, intron 1 of 2)	1326	NM_028595	73656	Mm.440719	NM_028595	ENSMUSG00000079419	Ms4a6c	2200009H22Rik|2210417N07Rik	membrane-spanning 4-domains, subfamily A, member 6C	protein-coding
mm_44808.1	chr5	33335797	33335804	-	1	NA	intron (NM_021500, intron 1 of 8)	CpG	228	NM_021500	59003	Mm.138617	NM_021500	ENSMUSG00000079562	Maea	1110030D19Rik|EMP|Gid9	macrophage erythroblast attacher	protein-coding
mm_77178.1	chr8	111691129	111691141	-	1	NA	promoter-TSS (NM_025583)	promoter-TSS (NM_025583)	-125	NM_025583	66473	Mm.34374	NM_025583	ENSMUSG00000031957	Ctrb1	2200008D09Rik|AI504462|Ctrb|Prt-2	chymotrypsinogen B1	protein-coding
mm_105247.1	chr11	102349970	102349986	-	1	NA	3' UTR (NM_011403, exon 20 of 20)	3' UTR (NM_011403, exon 20 of 20)	15303	NM_011403	20533	Mm.7248	NM_011403	ENSMUSG00000006574	Slc4a1	Ae1|CD233|Empb3|l11Jus51	solute carrier family 4 (anion exchanger), member 1	protein-coding
mm_14729.1	chr2	144266078	144266095	+	1	NA	non-coding (NR_030762, exon 1 of 1)	non-coding (NR_030762, exon 1 of 1)	116	NR_030762	100313519	Mm.453538	NR_030762	ENSMUSG00000077714	Snord17	MBI-43	small nucleolar RNA, C/D box 17	snoRNA
mm_169570.1	chr1	5197500	5197504	+	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	114416	NM_001310442	108664	Mm.27082	NM_133826	ENSMUSG00000033793	Atp6v1h	0710001F19Rik|AU022349|CGI-11|SFD|SFDalpha|SFDbeta|VMA13	ATPase, H+ transporting, lysosomal V1 subunit H	protein-coding
mm_151876.1	chr19	5798393	5798399	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	-2415	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_55968.1	chr6	85820982	85820990	-	1	NA	promoter-TSS (NM_023493)	promoter-TSS (NM_023493)	-14	NM_023493	69049	Mm.441449	NM_023493	ENSMUSG00000079494	Nat8f5	1810018F03Rik|Cml5	N-acetyltransferase 8 (GCN5-related) family member 5	protein-coding
mm_133828.1	chr16	95900449	95900488	+	1	NA	intron (NR_040484, intron 1 of 3)	L1MC5|LINE|L1	-1755	NR_040485	69776	Mm.120470	NR_040484	ENSMUSG00000086899	1600002D24Rik	-	RIKEN cDNA 1600002D24 gene	ncRNA
mm_53606.1	chr6	138325312	138325318	+	1	NA	Intergenic	Intergenic	-97790	NR_126073	319702	Mm.403785	NR_126072	ENSMUSG00000089957	A830011K09Rik	-	RIKEN cDNA A830011K09 gene	ncRNA
mm_99868.1	chr11	109397643	109397664	+	1	NA	3' UTR (NM_010303, exon 4 of 4)	3' UTR (NM_010303, exon 4 of 4)	-28293	NM_025275	13929	Mm.211850	NM_025275	ENSMUSG00000020610	Amz2	AA408420|ESTM12|X83328	archaelysin family metallopeptidase 2	protein-coding
mm_137064.1	chr17	19445237	19445237	+	1	NA	Intergenic	RLTR50A|LTR|ERVK	-59574	NM_001104562	627537	Mm.469858	NM_001104562	ENSMUSG00000091859	Vmn2r100	EG627537	vomeronasal 2, receptor 100	protein-coding
mm_8548.1	chr1	155146792	155146820	-	1	NA	promoter-TSS (NM_008209)	promoter-TSS (NM_008209)	-26	NM_008209	15064	Mm.7580	NM_008209	ENSMUSG00000026471	Mr1	H2ls	major histocompatibility complex, class I-related	protein-coding
mm_160118.1	chr7	27446685	27446685	-	1	NA	promoter-TSS (NM_032610)	promoter-TSS (NM_032610)	-96	NM_032610	80297	Mm.459123	NM_032610	ENSMUSG00000011751	Sptbn4	1700022P15Rik|5830426A08Rik|ROSA62|SpbIV|Spnb4|dyn|lnd|nmf261|nmf379|qv	spectrin beta, non-erythrocytic 4	protein-coding
mm_118355.1	chr13	115090124	115090241	-	1	NA	promoter-TSS (NM_134058)	promoter-TSS (NM_134058)	-24	NM_134058	105083	Mm.486295	NM_134058	ENSMUSG00000042275	Pelo	AA409897|AI852218	pelota homolog (Drosophila)	protein-coding
mm_133507.1	chr16	90738269	90738282	+	1	NA	promoter-TSS (NM_029844)	promoter-TSS (NM_029844)	-49	NM_029844	77037	Mm.22455	NM_029844	ENSMUSG00000039956	Mrap	1110025G12Rik|Falp|ORF61	melanocortin 2 receptor accessory protein	protein-coding
mm_20672.1	chr2	132247748	132247787	-	1	NA	promoter-TSS (NM_027478)	promoter-TSS (NM_027478)	21	NM_027478	70612	Mm.30116	NM_027478	ENSMUSG00000027341	Tmem230	5730494N06Rik|AA407821	transmembrane protein 230	protein-coding
mm_58018.1	chr6	136661678	136661691	-	1	NA	5' UTR (NM_025806, exon 1 of 11)	5' UTR (NM_025806, exon 1 of 11)	209	NM_025806	66857	Mm.3311	NM_025806	ENSMUSG00000030214	Plbd1	1100001H23Rik	phospholipase B domain containing 1	protein-coding
mm_122862.1	chr14	54907579	54907597	-	1	NA	exon (NM_021551, exon 8 of 9)	exon (NM_021551, exon 8 of 9)	5544	NM_021551	59049	Mm.27435	NM_021551	ENSMUSG00000022199	Slc22a17	1700094C23Rik|24p3R|AU041908|AW555662|BOIT|Boct	solute carrier family 22 (organic cation transporter), member 17	protein-coding
mm_43684.1	chr5	138809579	138809597	+	1	NA	3' UTR (NM_030565, exon 10 of 10)	3' UTR (NM_030565, exon 10 of 10)	-10492	NM_001195128	384244	Mm.485002	NM_001195128	ENSMUSG00000094504	Gm5294	EG384244	predicted gene 5294	protein-coding
mm_157271.1	chrX	20146138	20146149	-	1	NA	intron (NM_177353, intron 12 of 16)	Lx|LINE|L1	86573	NM_021715	60322	Mm.44827	NM_021715	ENSMUSG00000037347	Chst7	2600013M07Rik|C6ST-2|GST5|Gn6st-4|glcNAc6ST-4	carbohydrate (N-acetylglucosamino) sulfotransferase 7	protein-coding
mm_41406.1	chr5	90786598	90786635	+	1	NA	exon (NM_203320, exon 3 of 4)	exon (NM_203320, exon 3 of 4)	515	NM_203320	330122	Mm.244289	NM_203320	ENSMUSG00000029379	Cxcl3	Dcip1|Gm1960	chemokine (C-X-C motif) ligand 3	protein-coding
mm_1707.1	chr1	75236440	75236469	+	1	NA	promoter-TSS (NM_001159883)	promoter-TSS (NM_001159883)	31	NM_001159883	56812	Mm.489660	NM_020266	ENSMUSG00000026203	Dnajb2	2700059H22Rik|Dnajb10|Hsj1|mDj8	DnaJ heat shock protein family (Hsp40) member B2	protein-coding
mm_126978.1	chr15	93435944	93435954	+	1	NA	intron (NM_175363, intron 3 of 8)	intron (NM_175363, intron 3 of 8)	37485	NM_001285863	223828	Mm.74208	NM_146062	ENSMUSG00000036167	Pphln1	CR|HSPC206|HSPC232	periphilin 1	protein-coding
mm_101896.1	chr11	49119748	49119755	-	1	NA	intron (NM_010999, intron 3 of 5)	intron (NM_010999, intron 3 of 5)	-5994	NM_146337	258334	Mm.390388	NM_146337	ENSMUSG00000047511	Olfr1396	MOR276-2	olfactory receptor 1396	protein-coding
mm_81306.1	chr9	108347828	108347926	+	1	NA	promoter-TSS (NM_011678)	promoter-TSS (NM_011678)	46	NM_011678	22258	Mm.3974	NM_011678	ENSMUSG00000032612	Usp4	F730026I20Rik|Unp|mKIAA4155	ubiquitin specific peptidase 4 (proto-oncogene)	protein-coding
mm_151433.1	chr19	57216156	57216165	+	1	NA	promoter-TSS (NM_178688)	promoter-TSS (NM_178688)	-128	NM_178688	226251	Mm.217161	NM_178688	ENSMUSG00000025085	Ablim1	2210411C18Rik|2610209L21Rik|4833406P10Rik|9330196J19Rik|AV079770|AW060987|AW215784|Limab1|mKIAA0059	actin-binding LIM protein 1	protein-coding
mm_160549.1	chr9	45803568	45803568	-	1	NA	intron (NM_001081373, intron 4 of 29)	intron (NM_001081373, intron 4 of 29)	25070	NM_001081373	214552	Mm.260103	NM_172531	ENSMUSG00000043987	Cep164	AI450905|BC027092|D030051D21|mKIAA1052	centrosomal protein 164	protein-coding
mm_26673.1	chr3	154796221	154796231	+	1	NA	intron (NM_177066, intron 23 of 24)	intron (NM_177066, intron 23 of 24)	85093	NM_175176	209601	Mm.331454	NM_175176	ENSMUSG00000078161	Erich3	1700013E18Rik|4922501L14Rik|5031409G23Rik|AI596448|Gm133	glutamate rich 3	protein-coding
mm_54701.1	chr6	39558132	39558139	-	1	NA	promoter-TSS (NM_172477)	promoter-TSS (NM_172477)	-301	NM_172477	209773	Mm.440021	NM_172477	ENSMUSG00000038456	Dennd2a	B930096L08Rik|C130031G22|mKIAA1277	DENN/MADD domain containing 2A	protein-coding
mm_73677.1	chr8	111536625	111536633	+	1	NA	promoter-TSS (NM_133206)	promoter-TSS (NM_133206)	-11	NM_001168622	170737	Mm.271578	NM_133206	ENSMUSG00000033545	Znrf1	B830022L21Rik|Rnf42|Zrfp1|nin283	zinc and ring finger 1	protein-coding
mm_111368.1	chr12	87225090	87225128	-	1	NA	intron (NM_027744, intron 4 of 7)	intron (NM_027744, intron 4 of 7)	13492	NM_027744	71275	Mm.79198	NM_027744	ENSMUSG00000072919	Noxred1	4933437F05Rik	NADP+ dependent oxidoreductase domain containing 1	protein-coding
mm_127905.1	chr15	9524093	9524104	-	1	NA	intron (NM_008372, intron 2 of 7)	intron (NM_008372, intron 2 of 7)	5778	NM_008372	16197	Mm.389	NM_008372	ENSMUSG00000003882	Il7r	CD127|IL-7Ralpha	interleukin 7 receptor	protein-coding
mm_145269.1	chr18	52768135	52768149	+	1	NA	promoter-TSS (NM_001199153)	promoter-TSS (NM_001199153)	-2	NM_001199154	67847	Mm.292168	NM_026408	ENSMUSG00000024534	Sncaip	2810407O15Rik|4933427B05Rik|BB104594|SYPH1	synuclein, alpha interacting protein (synphilin)	protein-coding
mm_42077.1	chr5	110136015	110136019	+	1	NA	intron (NM_001289579, intron 1 of 18)	CpG	187	NM_001289580	231600	Mm.30264	NM_172717	ENSMUSG00000014668	Chfr	5730484M20Rik|C230082M18|RNF116	checkpoint with forkhead and ring finger domains	protein-coding
mm_126260.1	chr15	79108729	79108780	+	1	NA	promoter-TSS (NM_177461)	promoter-TSS (NM_177461)	-229	NM_177461	27008	Mm.196480	NM_177461	ENSMUSG00000033039	Micall1	AI448246|D15Mit260|D15N2e|EST573322|EST820961|MIRab13|mKIAA1668	microtubule associated monooxygenase, calponin and LIM domain containing -like 1	protein-coding
mm_168185.1	chr10	59806511	59806512	+	1	NA	intron (NM_001291443, intron 9 of 12)	intron (NM_001291443, intron 9 of 12)	-73080	NM_019965	56709	Mm.103610	NM_019965	ENSMUSG00000020109	Dnajb12	Dj10|mDj10	DnaJ heat shock protein family (Hsp40) member B12	protein-coding
mm_170800.1	chr2	175606130	175606136	-	1	NA	Intergenic	Intergenic	-34258	NM_001177543	100039060	Mm.289463	NM_001177543	ENSMUSG00000078886	0610010B08Rik	Gm2026	RIKEN cDNA 0610010B08 gene	protein-coding
mm_9913.1	chr1	189007830	189007852	-	1	NA	promoter-TSS (NM_172650)	promoter-TSS (NM_172650)	-1	NM_172650	226823	Mm.209880	NM_172650	ENSMUSG00000026608	Kctd3	4930438A20Rik|9330185B06|E330032J19Rik|NY-REN-45	potassium channel tetramerisation domain containing 3	protein-coding
mm_32886.1	chr4	118961943	118961961	+	1	NA	promoter-TSS (NM_133892)	promoter-TSS (NM_133892)	-15	NM_133892	100470	Mm.26698	NM_133892	ENSMUSG00000024903	Lao1	AW990848	L-amino acid oxidase 1	protein-coding
mm_51147.1	chr6	70642364	70642385	+	1	NA	Intergenic	Intergenic	149801	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_134145.1	chr16	10784748	10784754	-	1	NA	exon (NM_001271603, exon 2 of 2)	exon (NM_001271603, exon 2 of 2)	785	NM_009896	12703	Mm.130	NM_009896	ENSMUSG00000038037	Socs1	Cish1|Cish7|JAB|SOCS-1|SSI-1	suppressor of cytokine signaling 1	protein-coding
mm_156839.1	chrX	164373516	164373549	+	1	NA	promoter-TSS (NM_010216)	promoter-TSS (NM_010216)	10	NM_010216	14205	Mm.297978	NM_010216	ENSMUSG00000031380	Vegfd	AI325264|Figf|VEGF-D	vascular endothelial growth factor D	protein-coding
mm_63359.1	chr7	127021352	127021362	+	1	NA	promoter-TSS (NM_001102563)	promoter-TSS (NM_001102563)	-146	NM_001102563	69017	Mm.392047	NM_001102563	ENSMUSG00000045114	Prrt2	1500031I19Rik|AI195361|DSPB3	proline-rich transmembrane protein 2	protein-coding
mm_69998.1	chr7	142385929	142385937	-	1	NA	intron (NM_009983, intron 1 of 8)	intron (NM_009983, intron 1 of 8)	1937	NM_009983	13033	Mm.231395	NM_009983	ENSMUSG00000007891	Ctsd	CD|CatD	cathepsin D	protein-coding
mm_81124.1	chr9	106463514	106463551	+	1	NA	TTS (NM_001159652)	TTS (NM_001159652)	2408	NM_001159652	436090	Mm.482905	NM_001159652	ENSMUSG00000091735	Gpr62	4933402E03Rik	G protein-coupled receptor 62	protein-coding
mm_50357.1	chr6	48647209	48647219	+	1	NA	promoter-TSS (NM_001286629)	promoter-TSS (NM_001286629)	-20	NM_001077410	243374	Mm.86514	NM_212486	ENSMUSG00000064262	Gimap8	Gm457|IAN9|IMAP8	GTPase, IMAP family member 8	protein-coding
mm_61282.1	chr7	66839753	66839770	+	1	NA	promoter-TSS (NM_001033877)	promoter-TSS (NM_001033877)	26	NM_001033877	233332	Mm.445763	NM_001033877	ENSMUSG00000058145	Adamts17	AU023434	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 17	protein-coding
mm_90988.1	chr10	13868933	13869004	-	1	NA	promoter-TSS (NM_025446)	promoter-TSS (NM_025446)	-11	NM_001347362	66253	Mm.45755	NM_025446	ENSMUSG00000019806	Aig1	1500031O19Rik|AV064870|AW413422|CGI-103	androgen-induced 1	protein-coding
mm_145159.1	chr18	46598534	46598613	+	1	NA	intron (NM_010120, intron 1 of 2)	intron (NM_010120, intron 1 of 2)	869	NM_010120	13664	Mm.262037	NM_010120	ENSMUSG00000057561	Eif1a	C76390|Ef1a|Eftu|Eif4c|eIF-1A|eIF-4C	eukaryotic translation initiation factor 1A	protein-coding
mm_27699.1	chr3	66981280	66981304	-	1	NA	promoter-TSS (NM_001302359)	promoter-TSS (NM_001302359)	-151	NM_001302359	20429	Mm.39093	NM_013665	ENSMUSG00000027833	Shox2	6330543G17Rik|OG12|Og12x|Prx3|SHOT	short stature homeobox 2	protein-coding
mm_153838.1	chr19	46327107	46327114	-	1	NA	promoter-TSS (NM_001347454)	promoter-TSS (NM_001347454)	46	NM_028627	73728	Mm.268532	NM_028627	ENSMUSG00000037126	Psd	1110007H17Rik|A930015K15|Efa6|Efa6a|Psdl|mKIAA2011	pleckstrin and Sec7 domain containing	protein-coding
mm_69279.1	chr7	127993703	127993762	-	1	NA	5' UTR (NM_023258, exon 1 of 3)	5' UTR (NM_023258, exon 1 of 3)	135	NM_023258	66824	Mm.24163	NM_023258	ENSMUSG00000030793	Pycard	9130417A21Rik|Asc|CARD5|TMS-1|TNS1|masc	PYD and CARD domain containing	protein-coding
mm_130531.1	chr15	98933923	98933937	-	1	NA	intron (NM_011654, intron 1 of 3)	CpG	460	NM_011654	22143	Mm.392113	NM_011654	ENSMUSG00000023004	Tuba1b	Tuba2	tubulin, alpha 1B	protein-coding
mm_5446.1	chr1	36098553	36098561	-	1	NA	intron (NM_015818, intron 1 of 1)	intron (NM_015818, intron 1 of 1)	30157	NM_015818	50785	Mm.213566	NM_015818	ENSMUSG00000045216	Hs6st1	6Ost1	heparan sulfate 6-O-sulfotransferase 1	protein-coding
mm_129673.1	chr15	81374874	81374896	-	1	NA	exon (NM_133726, exon 8 of 12)	exon (NM_133726, exon 8 of 12)	-14120	NM_011399	20524	Mm.222536	NM_011399	ENSMUSG00000022404	Slc25a17	34kDa|47kDa|PMP34|Pmp47	solute carrier family 25 (mitochondrial carrier, peroxisomal membrane protein), member 17	protein-coding
mm_22009.1	chr2	167775205	167775216	-	1	NA	Intergenic	L2a|LINE|L2	84033	NR_015500	329562	Mm.123101	NM_177851	ENSMUSG00000006462	A530013C23Rik	-	RIKEN cDNA A530013C23 gene	ncRNA
mm_18436.1	chr2	60881185	60881206	-	1	NA	5' UTR (NM_001141932, exon 1 of 15)	5' UTR (NM_001141932, exon 1 of 15)	243	NM_001141932	56878	Mm.259667	NM_020296	ENSMUSG00000026970	Rbms1	2600014B10Rik|AI255215|MSSP-1|MSSP-2|MSSP-3|YC1	RNA binding motif, single stranded interacting protein 1	protein-coding
mm_35544.1	chr4	41490060	41490062	-	1	NA	Intergenic	B1_Mur2|SINE|Alu	13014	NM_001085515	329828	Mm.27054	NM_001085515	ENSMUSG00000046312	AI464131	AA408153|AI604836|Gm762|Kiaa1161|NET37	expressed sequence AI464131	protein-coding
mm_151572.1	chr19	60811837	60811879	+	1	NA	intron (NM_001347464, intron 1 of 7)	CpG	288	NM_001167829	67894	Mm.26148	NM_026437	ENSMUSG00000024993	Fam45a	1810055E12Rik	family with sequence similarity 45, member A	protein-coding
mm_94219.1	chr11	3198583	3198608	+	1	NA	Intergenic	RMER6B|LTR|ERVK	-3758	NM_001166548	74203	Mm.255649	NM_023743	ENSMUSG00000020454	Eif4enif1	2610509L04Rik|A930019J01Rik|AA410001|AU021239|Clast4|D11Ertd166e	eukaryotic translation initiation factor 4E nuclear import factor 1	protein-coding
mm_114698.1	chr13	83504161	83504227	+	1	NA	5' UTR (NM_025282, exon 1 of 11)	5' UTR (NM_025282, exon 1 of 11)	160	NM_001347564	17260	Mm.24001	NM_025282	ENSMUSG00000005583	Mef2c	5430401D19Rik|9930028G15Rik|AV011172|Mef2	myocyte enhancer factor 2C	protein-coding
mm_149015.1	chr19	8740740	8740767	+	1	NA	promoter-TSS (NM_001177347)	promoter-TSS (NM_001177347)	35	NM_001177347	74307	Mm.48791	NM_001177347	ENSMUSG00000090840	1700092M07Rik	-	RIKEN cDNA 1700092M07 gene	protein-coding
mm_167622.1	chr9	59291398	59291412	-	1	NA	promoter-TSS (NM_028121)	promoter-TSS (NM_028121)	-167	NM_028121	72141	Mm.22456	NM_028121	ENSMUSG00000025236	Adpgk	2610017G09Rik|Adp-gk|C77577	ADP-dependent glucokinase	protein-coding
mm_126787.1	chr15	86234873	86234885	+	1	NA	intron (NM_145476, intron 2 of 12)	intron (NM_145476, intron 2 of 12)	20420	NM_145476	223754	Mm.28904	NM_145476	ENSMUSG00000051864	Tbc1d22a	BC023106|D15Ertd781e	TBC1 domain family, member 22a	protein-coding
mm_80073.1	chr9	69761089	69761093	+	1	NA	promoter-TSS (NR_040765)	promoter-TSS (NR_040765)	-55	NR_040765	319970	Mm.186434	NR_040765	ENSMUSG00000097623	B230323A14Rik	-	RIKEN cDNA B230323A14 gene	ncRNA
mm_170277.1	chr18	27463144	27463144	-	1	NA	Intergenic	Intergenic	-1097020	NR_045398	320624	Mm.50107	NR_045398		4930474G06Rik	-	RIKEN cDNA 4930474G06 gene	ncRNA
mm_67723.1	chr7	90068025	90068027	-	1	NA	Intergenic	Intergenic	38867	NR_110364	319711	Mm.31753	NR_015614	ENSMUSG00000097585	E230029C05Rik	AI452102|B230337J15	RIKEN cDNA E230029C05 gene	ncRNA
mm_109109.1	chr12	105395579	105395580	+	1	NA	non-coding (NR_045085, exon 3 of 3)	non-coding (NR_045085, exon 3 of 3)	8181	NR_045085	100040339	Mm.240751	NR_045085		Gm2721	-	predicted gene 2721	ncRNA
mm_66319.1	chr7	41393320	41393356	-	1	NA	promoter-TSS (NM_001199330)	promoter-TSS (NM_001199330)	41	NM_001199330	233168	Mm.379390	NM_183167	ENSMUSG00000056383	AI987944	-	expressed sequence AI987944	protein-coding
mm_68388.1	chr7	109493628	109493641	-	1	NA	5' UTR (NM_001170913, exon 1 of 20)	5' UTR (NM_001170913, exon 1 of 20)	104	NM_001170913	330627	Mm.183528	NM_181853	ENSMUSG00000031026	Trim66	Kiaa0298-hp|Tif1d	tripartite motif-containing 66	protein-coding
mm_24288.1	chr3	89243823	89243849	+	1	NA	exon (NM_183037, exon 3 of 10)	exon (NM_183037, exon 3 of 10)	1177	NR_121683	360213	Mm.331156	NM_183037	ENSMUSG00000042766	Trim46	TRIFIC	tripartite motif-containing 46	protein-coding
mm_91163.1	chr10	20607350	20607375	-	1	NA	intron (NM_013875, intron 2 of 12)	intron (NM_013875, intron 2 of 12)	-59034	NM_001347366	29863	Mm.425617	NM_013875	ENSMUSG00000019990	Pde7b	-	phosphodiesterase 7B	protein-coding
mm_135540.1	chr16	49771837	49771848	-	1	NA	Intergenic	L2b|LINE|L2	72548	NM_028680	73916	Mm.241276	NM_028680	ENSMUSG00000032965	Ift57	4833420A15Rik|Esrrbl1|Hippi|MHS4R2	intraflagellar transport 57	protein-coding
mm_56459.1	chr6	98342729	98342734	-	1	NA	promoter-TSS (NM_001128092)	promoter-TSS (NM_001128092)	23	NM_001128092	330390	Mm.484161	NM_001128092	ENSMUSG00000090667	Gm765	-	predicted gene 765	protein-coding
mm_132428.1	chr16	35770383	35770396	+	1	NA	promoter-TSS (NM_175111)	promoter-TSS (NM_175111)	3	NM_175111	66667	Mm.45272	NM_175111	ENSMUSG00000022849	Hspbap1	3830421G21Rik	Hspb associated protein 1	protein-coding
mm_169044.1	chr13	14951112	14951112	+	1	NA	Intergenic	ERVB7_1-LTR_MM|LTR|ERVK	320854	NM_134067	105351	Mm.41450	NM_134067	ENSMUSG00000039182	AW209491	-	expressed sequence AW209491	protein-coding
mm_163228.1	chr11	102653141	102653145	+	1	NA	Intergenic	B3A|SINE|B2	-12442	NM_001127576	268491	Mm.447643	NM_001127576	ENSMUSG00000051455	Meioc	Gm1564|Gm663	meiosis specific with coiled-coil domain	protein-coding
mm_167662.1	chr9	71395688	71395688	-	1	NA	Intergenic	Intergenic	89270	NM_001164793	28015	Mm.21094	NM_178602	ENSMUSG00000032199	Polr2m	AA407243|AA408799|AI303746|AW553238|D9Wsu138e|Grinl1a|mKIAA4185	polymerase (RNA) II (DNA directed) polypeptide M	protein-coding
mm_51479.1	chr6	83026273	83026305	+	1	NA	exon (NM_033079, exon 8 of 10)	exon (NM_033079, exon 8 of 10)	7182	NM_010070	13448	Mm.156	NM_010070	ENSMUSG00000068335	Dok1	AW557123|p62DOK	docking protein 1	protein-coding
mm_137453.1	chr17	26551441	26551476	+	1	NA	Intergenic	Intergenic	-10054	NM_026170	67458	Mm.30496	NM_026170	ENSMUSG00000001576	Ergic1	1200007D18Rik|maa-136	endoplasmic reticulum-golgi intermediate compartment (ERGIC) 1	protein-coding
mm_56976.1	chr6	120294282	120294316	-	1	NA	intron (NM_198884, intron 1 of 19)	CpG	260	NM_198884	330406	Mm.321840	NM_198884	ENSMUSG00000041372	B4galnt3	AB114826|B4GalNAcT3|C330047A21	beta-1,4-N-acetyl-galactosaminyl transferase 3	protein-coding
mm_101581.1	chr11	34407066	34407078	-	1	NA	intron (NM_001025382, intron 3 of 3)	intron (NM_001025382, intron 3 of 3)	92250	NM_001025382	574403	Mm.444796	NM_001025382	ENSMUSG00000069911	Fam196b	EG574403|Gm6041	family with sequence similarity 196, member B	protein-coding
mm_140450.1	chr17	88626550	88626566	+	1	NA	promoter-TSS (NM_029858)	promoter-TSS (NM_029858)	3	NM_029858	77057	Mm.482203	NM_029858	ENSMUSG00000033855	Ston1	4921524J06Rik|C86231|Salf|Sblf	stonin 1	protein-coding
mm_51828.1	chr6	89392102	89392140	+	1	NA	intron (NM_025351, intron 6 of 7)	intron (NM_025351, intron 6 of 7)	-29508	NM_008881	18844	Mm.3789	NM_008881	ENSMUSG00000030084	Plxna1	2600013D04Rik|NOV|PlexA1|Plxn1|mKIAA4053	plexin A1	protein-coding
mm_136336.1	chr16	92522047	92522053	-	1	NA	intron (NM_172469, intron 1 of 5)	intron (NM_172469, intron 1 of 5)	23903	NM_172469	209195	Mm.44747	NM_172469	ENSMUSG00000022949	Clic6	5730466J16Rik|AL022908|AW045520|CLIC1L	chloride intracellular channel 6	protein-coding
mm_102624.1	chr11	62510937	62510958	-	1	NA	intron (NM_001039536, intron 5 of 6)	MLTR25A|LTR|ERVK	28314	NM_028448	73139	Mm.390409	NM_028448	ENSMUSG00000018509	Cenpv	3110013H01Rik|AA671303|Prr6	centromere protein V	protein-coding
mm_78091.1	chr9	18292345	18292360	+	1	NA	promoter-TSS (NM_025844)	promoter-TSS (NM_025844)	85	NM_025844	66917	Mm.103534	NM_025844	ENSMUSG00000001774	Chordc1	1110001O09Rik|AA409036|Chp-1|morgana	cysteine and histidine-rich domain (CHORD)-containing, zinc-binding protein 1	protein-coding
mm_63275.1	chr7	126762905	126762926	+	1	NA	intron (NM_011952, intron 2 of 8)	intron (NM_011952, intron 2 of 8)	3289	NM_011952	26417	Mm.8385	NM_011952	ENSMUSG00000063065	Mapk3	Erk-1|Erk1|Ert2|Esrk1|Mnk1|Mtap2k|Prkm3|p44|p44erk1|p44mapk	mitogen-activated protein kinase 3	protein-coding
mm_100605.1	chr11	121260113	121260121	+	1	NA	5' UTR (NM_001080932, exon 1 of 9)	5' UTR (NM_001080932, exon 1 of 9)	130	NM_001080932	68837	Mm.209750	NM_001080932	ENSMUSG00000039275	Foxk2	1110054H05Rik|5730434B08Rik|6230415M23Rik|ILF|Ilf1	forkhead box K2	protein-coding
mm_10869.1	chr2	25214707	25214755	+	1	NA	promoter-TSS (NM_028961)	promoter-TSS (NM_028961)	-101	NM_028961	74472	Mm.176944	NM_028961	ENSMUSG00000036770	Stpg3	4933433C11Rik	sperm tail PG rich repeat containing 3	protein-coding
mm_167567.1	chr9	42122537	42122574	-	1	NA	intron (NM_011436, intron 1 of 47)	intron (NM_011436, intron 1 of 47)	1734	NM_011436	20660	Mm.121920	NM_011436	ENSMUSG00000049313	Sorl1	2900010L19Rik|AI596264|AW261561|LR11|SorLA|gp250|mSorLA	sortilin-related receptor, LDLR class A repeats-containing	protein-coding
mm_26395.1	chr3	142594805	142594816	+	1	NA	promoter-TSS (NM_010259)	promoter-TSS (NM_010259)	-37	NM_010259	14468	Mm.457978	NM_010259	ENSMUSG00000040264	Gbp2b	Gbp-1|Gbp1|Mag-1|Mpa-1|Mpa1	guanylate binding protein 2b	protein-coding
mm_146961.1	chr18	33384988	33385008	-	1	NA	Intergenic	Intergenic	78636	NM_001267717	27528	Mm.407415	NM_053078	ENSMUSG00000042834	Nrep	AI325076|D0H4S114|Harp|P311|PTZ17|SEZ17	neuronal regeneration related protein	protein-coding
mm_83842.1	chr9	54434964	54434968	-	1	NA	intron (NM_172771, intron 13 of 43)	intron (NM_172771, intron 13 of 43)	66660	NM_172771	235380	Mm.93636	NM_172771	ENSMUSG00000041268	Dmxl2	6330586A12|6430411K14Rik|E130119P06Rik|mKIAA0856	Dmx-like 2	protein-coding
mm_80353.1	chr9	75186039	75186054	+	1	NA	exon (NM_010864, exon 28 of 41)	exon (NM_010864, exon 28 of 41)	-45968	NM_001081322	208943	Mm.41339	NM_001081322	ENSMUSG00000033590	Myo5c	9130003O20Rik|BB085560|C330029I24	myosin VC	protein-coding
mm_59690.1	chr7	28444940	28444969	+	1	NA	intron (NM_001039192, intron 5 of 6)	intron (NM_001039192, intron 5 of 6)	4017	NM_001039192	63986	Mm.194536	NM_022024	ENSMUSG00000060791	Gmfg	0610039G16Rik|2310057N07Rik|AI324845	glia maturation factor, gamma	protein-coding
mm_52611.1	chr6	117173769	117173787	+	1	NA	3' UTR (NM_021704, exon 3 of 3)	3' UTR (NM_021704, exon 3 of 3)	5243	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_139870.1	chr17	70561740	70561750	+	1	NA	promoter-TSS (NM_001128181)	promoter-TSS (NM_001128181)	-2	NM_001128181	224997	Mm.311840	NM_027712	ENSMUSG00000003279	Dlgap1	4933422O14Rik|9630002F18|AI845682|AI848168|BB075781|D17Bwg0511e|GKAP/SAPAP|GKPA/SAPAP|Gkap|Sapap1|mKIAA4162	discs, large (Drosophila) homolog-associated protein 1	protein-coding
mm_56588.1	chr6	107877520	107877520	-	1	NA	Intergenic	Intergenic	-187525	NM_001276356	74729	Mm.56539	NM_178391	ENSMUSG00000034639	Setmar	5830404F24Rik|Etet2	SET domain without mariner transposase fusion	protein-coding
mm_5956.1	chr1	56971339	56971347	-	1	NA	promoter-TSS (NR_024325)	promoter-TSS (NR_024325)	-9	NM_139146	212712	Mm.145599	NM_139146	ENSMUSG00000038331	Satb2	mKIAA1034	special AT-rich sequence binding protein 2	protein-coding
mm_140010.1	chr17	73158529	73158532	+	1	NA	intron (NM_001081071, intron 1 of 5)	intron (NM_001081071, intron 1 of 5)	50545	NM_001177967	225010	Mm.329194	NM_001081071	ENSMUSG00000054469	Lclat1	AI181996|Agpat8|Alcat1|Gm91|Lycat	lysocardiolipin acyltransferase 1	protein-coding
mm_113424.1	chr13	34046817	34046821	+	1	NA	exon (NM_026512, exon 3 of 7)	exon (NM_026512, exon 3 of 7)	9178	NM_026512	68021	Mm.140243	NM_026512	ENSMUSG00000038286	Bphl	2010012D11Rik|5730533B08Rik|AI115341	biphenyl hydrolase-like (serine hydrolase, breast epithelial mucin-associated antigen)	protein-coding
mm_147328.1	chr18	42579762	42579790	-	1	NA	promoter-TSS (NM_181543)	promoter-TSS (NM_181543)	-124	NM_181543	240239	Mm.186779	NM_181543	ENSMUSG00000042816	Gpr151	C130082O03Rik|GalRL|PGR7|nGPCR-2037	G protein-coupled receptor 151	protein-coding
mm_141240.1	chr17	27445159	27445207	-	1	NA	intron (NM_001013385, intron 5 of 8)	intron (NM_001013385, intron 5 of 8)	58350	NM_001013385	268934	Mm.358940	NM_001013385	ENSMUSG00000063239	Grm4	Gprc1d|mGluR4	glutamate receptor, metabotropic 4	protein-coding
mm_158014.1	chrX	95658417	95658447	-	1	NA	promoter-TSS (NM_001003916)	promoter-TSS (NM_001003916)	77	NM_001289696	245522	Mm.336158	NM_001003916	ENSMUSG00000035062	Zc4h2	Gm372|mKIAA1166	zinc finger, C4H2 domain containing	protein-coding
mm_11982.1	chr2	55411814	55411819	+	1	NA	Intergenic	Intergenic	-24154	NM_001304810	16519	Mm.5127	NM_008426	ENSMUSG00000026824	Kcnj3	GIRK-1|GIRK1|Kcnf3|Kir3.1	potassium inwardly-rectifying channel, subfamily J, member 3	protein-coding
mm_28233.1	chr3	88455331	88455347	-	1	NA	intron (NM_001163489, intron 1 of 14)	intron (NM_001163489, intron 1 of 14)	422	NM_013658	20351	Mm.439752	NM_013658	ENSMUSG00000028064	Sema4a	AI132332|SemB|Semab	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A	protein-coding
mm_119004.1	chr14	29018237	29018243	+	1	NA	promoter-TSS (NM_176920)	promoter-TSS (NM_176920)	32	NM_176920	319476	Mm.95780	NM_176920	ENSMUSG00000045776	Lrtm1	A930016D02Rik	leucine-rich repeats and transmembrane domains 1	protein-coding
mm_11670.1	chr2	35284699	35284709	+	1	NA	exon (NM_001206369, exon 3 of 17)	exon (NM_001206369, exon 3 of 17)	2324	NM_146120	227753	Mm.443	NM_146120	ENSMUSG00000026879	Gsn	ADF	gelsolin	protein-coding
mm_6994.1	chr1	86358971	86358997	-	1	NA	promoter-TSS (NR_015507)	promoter-TSS (NR_015507)	471	NM_010880	17975	Mm.154378	NM_010880	ENSMUSG00000026234	Ncl	B530004O11Rik|C23|D0Nds28|D1Nds28|Nucl	nucleolin	protein-coding
mm_32622.1	chr4	114445119	114445122	+	1	NA	intron (NM_001085549, intron 2 of 6)	intron (NM_001085549, intron 2 of 6)	38396	NM_001085549	666048	Mm.331779	NM_001085549	ENSMUSG00000070867	Trabd2b	Gm12824|Hkat|OTTMUSG00000008561	TraB domain containing 2B	protein-coding
mm_150474.1	chr19	38836562	38836612	+	1	NA	promoter-TSS (NM_145952)	promoter-TSS (NM_145952)	8	NM_145952	209478	Mm.391153	NM_145952	ENSMUSG00000048720	Tbc1d12	BC033574	TBC1D12: TBC1 domain family, member 12	protein-coding
mm_163239.1	chr11	104329918	104329928	+	1	NA	3' UTR (NM_010838, exon 10 of 10)	3' UTR (NM_010838, exon 10 of 10)	98487	NM_001285454	17762	Mm.1287	NM_010838	ENSMUSG00000018411	Mapt	AI413597|AW045860|Mtapt|Tau	microtubule-associated protein tau	protein-coding
mm_149247.1	chr19	10389000	10389063	+	1	NA	promoter-TSS (NM_018801)	promoter-TSS (NM_018801)	-59	NM_018801	54525	Mm.182654	NM_018801	ENSMUSG00000024743	Syt7	AI851541|B230112P13Rik	synaptotagmin VII	protein-coding
mm_67789.1	chr7	97645121	97645135	-	1	NA	promoter-TSS (NR_126461)	promoter-TSS (NR_126461)	-16	NR_126461	75448	Mm.439818	NR_126461	ENSMUSG00000086433	Rsf1os1	1700006D18Rik	remodeling and spacing factor 1, opposite strand 1	ncRNA
mm_132195.1	chr16	32488094	32488131	+	1	NA	promoter-TSS (NM_145932)	promoter-TSS (NM_145932)	-233	NM_145932	106407	Mm.476915	NM_145932	ENSMUSG00000035699	Slc51a	AV001382|AW261577|D630035O19Rik|OSTalpha|Osta	solute carrier family 51, alpha subunit	protein-coding
mm_171733.1	chr4	93889208	93889225	+	1	NA	Intergenic	L1Md_T|LINE|L1	-553705	NM_026954	69136	Mm.171558	NM_026954	ENSMUSG00000054000	Tusc1	2200001D17Rik|TSG-9	tumor suppressor candidate 1	protein-coding
mm_130059.1	chr15	89180964	89181032	-	1	NA	promoter-TSS (NM_001284506)	promoter-TSS (NM_001284506)	-210	NM_138749	140570	Mm.267514	NM_138749	ENSMUSG00000036606	Plxnb2	Debt|plexin-B2	plexin B2	protein-coding
mm_164507.1	chr16	93547776	93547779	+	1	NA	Intergenic	Intergenic	56038	NM_145482	224440	Mm.10628	NM_145482	ENSMUSG00000022948	Setd4	AY037804|C21orf18|ORF21	SET domain containing 4	protein-coding
mm_86731.1	chr10	19065528	19065543	+	1	NA	Intergenic	Intergenic	-50125	NM_009397	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_50755.1	chr6	53433970	53433982	+	1	NA	intron (NM_001327821, intron 4 of 10)	U1|snRNA|snRNA	-139398	NM_172728	231991	Mm.227444	NM_172728	ENSMUSG00000053007	Creb5	9430076C15Rik|CRE-BPa|Crebpa|D430026C09Rik	cAMP responsive element binding protein 5	protein-coding
mm_99246.1	chr11	101082609	101082642	+	1	NA	promoter-TSS (NM_001305982)	promoter-TSS (NM_001305982)	60	NM_001305982	71743	Mm.182271	NM_027896	ENSMUSG00000001755	Coasy	1300003G02Rik|Dpck|Ppat|Ukr1	Coenzyme A synthase	protein-coding
mm_93192.1	chr10	94035772	94035787	-	1	NA	promoter-TSS (NM_053072)	promoter-TSS (NM_053072)	20	NM_172538	215008	Mm.124177	NM_172538	ENSMUSG00000036099	Vezt	A630071D13Rik|AI848282	vezatin, adherens junctions transmembrane protein	protein-coding
mm_101644.1	chr11	36498796	36498807	-	1	NA	intron (NM_011856, intron 2 of 28)	intron (NM_011856, intron 2 of 28)	445440	NM_001290702	23964	Mm.439889	NM_011856	ENSMUSG00000049336	Tenm2	Odz2|Odz3|Ten-2|Ten-m2	teneurin transmembrane protein 2	protein-coding
mm_88745.1	chr10	80285254	80285278	+	1	NA	exon (NM_133188, exon 11 of 12)	exon (NM_133188, exon 11 of 12)	7102	NR_105876	102466207		NR_105876	ENSMUSG00000098672	Mir6911	Gm27822|mmu-mir-6911	microRNA 6911	ncRNA
mm_129954.1	chr15	85042309	85042318	-	1	NA	intron (NM_133750, intron 1 of 8)	intron (NM_133750, intron 1 of 8)	5251	NM_133750	73225	Mm.247535	NM_133750	ENSMUSG00000022434	Fam118a	-	family with sequence similarity 118, member A	protein-coding
mm_149791.1	chr19	23141127	23141137	+	1	NA	promoter-TSS (NM_010638)	promoter-TSS (NM_010638)	-94	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_101837.1	chr11	48752503	48752505	-	1	NA	Intergenic	Intergenic	-47856	NM_008143	14694	Mm.5305	NM_008143	ENSMUSG00000020372	Rack1	AL033335|GB-like|Gnb2-rs1|Gnb2l1|p205	receptor for activated C kinase 1	protein-coding
mm_32959.1	chr4	119813057	119813103	+	1	NA	Intergenic	Intergenic	-1598	NM_010657	16656	Mm.302758	NM_010657	ENSMUSG00000028634	Hivep3	2900056N03Rik|A130075N07|AI848000|E030045D18Rik|KBP-1|KBP1|Krc|Rc|Schnurri-3|Shn3|Zas3	human immunodeficiency virus type I enhancer binding protein 3	protein-coding
mm_6288.1	chr1	69687227	69687256	-	1	NA	Intergenic	Intergenic	-1281	NM_011770	22779	Mm.106343	NM_011770	ENSMUSG00000025997	Ikzf2	A730095J18Rik|Helios|Zfpn1a2|Znfn1a2	IKAROS family zinc finger 2	protein-coding
mm_98595.1	chr11	95824514	95824549	+	1	NA	promoter-TSS (NM_153104)	promoter-TSS (NM_153104)	31	NM_153104	237928	Mm.133075	NM_153104	ENSMUSG00000050860	Phospho1	D11Moh36|Phospo1	phosphatase, orphan 1	protein-coding
mm_150003.1	chr19	29287944	29287960	+	1	NA	exon (NM_008413, exon 11 of 25)	exon (NM_008413, exon 11 of 25)	36149	NM_008413	16452	Mm.275839	NM_008413	ENSMUSG00000024789	Jak2	Fd17	Janus kinase 2	protein-coding
mm_64914.1	chr7	16235400	16235403	-	1	NA	3' UTR (NM_176912, exon 2 of 2)	3' UTR (NM_176912, exon 2 of 2)	6930	NM_001146005	319430	Mm.239570	NM_176912	ENSMUSG00000074361	C5ar2	C5L2|E030029A11Rik|Gpr77	complement component 5a receptor 2	protein-coding
mm_56778.1	chr6	116633345	116633355	-	1	NA	3' UTR (NM_178045, exon 11 of 11)	3' UTR (NM_178045, exon 11 of 11)	-4351	NM_026057	67255	Mm.18810	NM_026057	ENSMUSG00000059878	Zfp422	2900028O21Rik|AU041373|KOX15|Krox-25-2|Krox-26|Krox25|Krox26|Znf22	zinc finger protein 422	protein-coding
mm_96037.1	chr11	59556398	59556411	+	1	NA	intron (NM_145827, intron 6 of 9)	ID_B1|SINE|B4	13718	NM_145827	216799	Mm.54174	NM_145827	ENSMUSG00000032691	Nlrp3	AGTAVPRL|AII/AVP|Cias1|FCAS|FCU|MWS|Mmig1|NALP3|Pypaf1	NLR family, pyrin domain containing 3	protein-coding
mm_31051.1	chr4	41136093	41136103	+	1	NA	promoter-TSS (NM_026275)	promoter-TSS (NM_026275)	77	NM_026275	67615	Mm.389540	NM_026275	ENSMUSG00000036241	Ube2r2	1200003M11Rik|Cdc34b|Ubc3b	ubiquitin-conjugating enzyme E2R 2	protein-coding
mm_103313.1	chr11	73137992	73138003	-	1	NA	exon (NM_010353, exon 1 of 1)	exon (NM_010353, exon 1 of 1)	297	NM_010353	14841	Mm.42045	NM_010353	ENSMUSG00000050107	Gsg2	Haspin	germ cell associated 2, haspin	protein-coding
mm_17848.1	chr2	34692560	34692563	-	1	NA	intron (NM_025709, intron 20 of 26)	AT_rich|Low_complexity|Low_complexity	62671	NM_025709	66691	Mm.156452	NM_025709	ENSMUSG00000026867	Gapvd1	2010005B09Rik|4432404J10Rik|AW108497|Gapex-5|RAP6|RME-6|mKIAA1521	GTPase activating protein and VPS9 domains 1	protein-coding
mm_86504.1	chr10	7212381	7212390	+	1	NA	promoter-TSS (NM_172546)	promoter-TSS (NM_172546)	-148	NM_172546	215748	Mm.37984	NM_172546	ENSMUSG00000015202	Cnksr3	6820402C05|BC024086|Magi1	Cnksr family member 3	protein-coding
mm_30371.1	chr3	152193774	152193797	-	1	NA	promoter-TSS (NM_025926)	promoter-TSS (NM_025926)	60	NM_025926	67035	Mm.46746	NM_025926	ENSMUSG00000028035	Dnajb4	1700029A20Rik|2010306G19Rik|5730460G06Rik	DnaJ heat shock protein family (Hsp40) member B4	protein-coding
mm_57992.1	chr6	136172331	136172333	-	1	NA	intron (NM_008171, intron 2 of 14)	intron (NM_008171, intron 2 of 14)	1179	NM_008171	14812	Mm.436649	NM_008171	ENSMUSG00000030209	Grin2b	AW490526|GluN2B|NR2B|Nmdar2b	glutamate receptor, ionotropic, NMDA2B (epsilon 2)	protein-coding
mm_130225.1	chr15	96264051	96264053	-	1	NA	Intergenic	Intergenic	-9368	NR_130160	75768	Mm.212701	NR_130160	ENSMUSG00000097619	4833422M21Rik	4933406G12Rik	RIKEN cDNA 4833422M21 gene	ncRNA
mm_77386.1	chr8	120116112	120116128	-	1	NA	intron (NM_172286, intron 1 of 12)	intron (NM_172286, intron 1 of 12)	1968	NM_001163761	234797	Mm.101958	NM_172286	ENSMUSG00000031824	6430548M08Rik	AW049007|Kiaa0513|mKIAA0513	RIKEN cDNA 6430548M08 gene	protein-coding
mm_111927.1	chr12	108884399	108884411	-	1	NA	intron (NM_011710, intron 2 of 10)	intron (NM_011710, intron 2 of 10)	8793	NM_001164488	22375	Mm.38433	NM_011710	ENSMUSG00000021266	Wars	TrpRS|WRS	tryptophanyl-tRNA synthetase	protein-coding
mm_44296.1	chr5	8622856	8622921	-	1	NA	promoter-TSS (NM_198620)	promoter-TSS (NM_198620)	64	NM_001347311	242819	Mm.332192	NM_198620	ENSMUSG00000040570	Rundc3b	Gm440	RUN domain containing 3B	protein-coding
mm_172292.1	chr6	9610109	9610112	+	1	NA	Intergenic	L1Md_T|LINE|L1	660091	NM_008751	18231	Mm.46954	NM_008751	ENSMUSG00000046178	Nxph1	C130005L03Rik	neurexophilin 1	protein-coding
mm_66951.1	chr7	62209484	62209494	-	1	NA	Intergenic	Intergenic	-124179	NR_049204	100885843		NR_049204	ENSMUSG00000095154	Mir344i	Gm26031|mir-344i|mmu-mir-344i	microRNA 344i	ncRNA
mm_162698.1	chr10	20441906	20441907	+	1	NA	intron (NM_001347366, intron 3 of 11)	intron (NM_001347366, intron 3 of 11)	94087	NM_027930	71804	Mm.262151	NM_027930	ENSMUSG00000019992	Mtfr2	2610016C23Rik|4933412C16Rik|Dufd1|Fam54a	mitochondrial fission regulator 2	protein-coding
mm_135401.1	chr16	44559455	44559462	-	1	NA	promoter-TSS (NM_172506)	promoter-TSS (NM_172506)	-588	NM_172506	117606	Mm.41561	NM_172506	ENSMUSG00000022687	Boc	4732455C11|mFLJ00376	biregional cell adhesion molecule-related/down-regulated by oncogenes (Cdon) binding protein	protein-coding
mm_29573.1	chr3	116968828	116968834	-	1	NA	5' UTR (NM_023245, exon 1 of 8)	5' UTR (NM_023245, exon 1 of 8)	121	NM_023245	114301	Mm.253736	NM_023245	ENSMUSG00000033377	Palmd	4631423C22Rik|PALML	palmdelphin	protein-coding
mm_48196.1	chr5	137531065	137531078	-	1	NA	intron (NM_010312, intron 1 of 9)	CpG	-1477	NR_105846	102465227		NR_105846	ENSMUSG00000098597	Mir6418	Gm27629|mir-6418|mmu-mir-6418	microRNA 6418	ncRNA
mm_154544.1	chrM	14677	14692	-	1	NA	NA	Intergenic	NA	NA								
mm_101142.1	chr11	14599195	14599207	-	1	NA	promoter-TSS (NM_001164166)	promoter-TSS (NM_001164166)	24	NR_045918	73307	Mm.399291	NR_045918	ENSMUSG00000085561	1700046C09Rik	-	RIKEN cDNA 1700046C09 gene	ncRNA
mm_40807.1	chr5	71658041	71658058	+	1	NA	5' UTR (NM_010251, exon 1 of 9)	5' UTR (NM_010251, exon 1 of 9)	259	NM_010251	14397	Mm.248731	NM_010251	ENSMUSG00000029211	Gabra4	Gabra-4	gamma-aminobutyric acid (GABA) A receptor, subunit alpha 4	protein-coding
mm_108951.1	chr12	102354760	102354821	+	1	NA	intron (NM_177620, intron 4 of 9)	intron (NM_177620, intron 4 of 9)	71149	NM_001161365	217835	Mm.24145	NM_177620	ENSMUSG00000044456	Rin3	6430500K07|C86933	Ras and Rab interactor 3	protein-coding
mm_140256.1	chr17	84511551	84511561	+	1	NA	promoter-TSS (NM_177606)	promoter-TSS (NM_177606)	-339	NM_177606	213556	Mm.215159	NM_177606	ENSMUSG00000040852	Plekhh2	AI256725|E030001K05|mKIAA2028	pleckstrin homology domain containing, family H (with MyTH4 domain) member 2	protein-coding
mm_144356.1	chr18	16274572	16274588	+	1	NA	Intergenic	Intergenic	534666	NM_007664	12558	Mm.257437	NM_007664	ENSMUSG00000024304	Cdh2	CDHN|N-CAD|Ncad	cadherin 2	protein-coding
mm_77965.1	chr9	7764201	7764211	+	1	NA	5' UTR (NM_133739, exon 1 of 5)	5' UTR (NM_133739, exon 1 of 5)	129	NM_133739	71929	Mm.283293	NM_133739	ENSMUSG00000050912	Tmem123	2310075C12Rik	transmembrane protein 123	protein-coding
mm_58630.1	chr7	5083923	5083946	+	1	NA	exon (NM_001252454, exon 2 of 11)	exon (NM_001252454, exon 2 of 11)	3699	NM_001252454	13854	Mm.3091	NM_010147	ENSMUSG00000035203	Epn1	AA269831|Ibp1	epsin 1	protein-coding
mm_130410.1	chr15	97977371	97977389	-	1	NA	intron (NM_031163, intron 51 of 53)	intron (NM_031163, intron 51 of 53)	13151	NM_001252153	380967	Mm.196630	NM_201359	ENSMUSG00000052369	Tmem106c	AI046681|BC046621|D15Ertd405e	transmembrane protein 106C	protein-coding
mm_171070.1	chr3	11590439	11590454	+	1	NA	Intergenic	Intergenic	253913	NR_040751	100038545	Mm.388494	NR_040751	ENSMUSG00000104015	Gm10745	ENSMUSG00000074696	predicted gene 10745	ncRNA
mm_2745.1	chr1	128591320	128591361	+	1	NA	intron (NM_009911, intron 1 of 1)	CpG	959	NM_009911	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding
mm_75938.1	chr8	71558991	71559011	-	1	NA	promoter-TSS (NM_001100462)	promoter-TSS (NM_001100462)	-130	NM_001100462	434325	Mm.33613	NM_001100462	ENSMUSG00000043664	Tmem221	-	transmembrane protein 221	protein-coding
mm_9915.1	chr1	189007895	189007910	-	1	NA	promoter-TSS (NM_172650)	promoter-TSS (NM_172650)	-62	NM_172650	226823	Mm.209880	NM_172650	ENSMUSG00000026608	Kctd3	4930438A20Rik|9330185B06|E330032J19Rik|NY-REN-45	potassium channel tetramerisation domain containing 3	protein-coding
mm_124548.1	chr14	122475203	122475219	-	1	NA	promoter-TSS (NR_045046)	promoter-TSS (NR_045046)	-12	NR_045046	69248	Mm.235369	NR_045046	ENSMUSG00000085555	2610035F20Rik	-	RIKEN cDNA 2610035F20 gene	ncRNA
mm_21668.1	chr2	164425520	164425532	-	1	NA	3' UTR (NM_011521, exon 5 of 5)	3' UTR (NM_011521, exon 5 of 5)	17662	NM_011521	20971	Mm.3815	NM_011521	ENSMUSG00000017009	Sdc4	AA959608|AW108331|S4|Synd4|ryudocan|syndecan-4	syndecan 4	protein-coding
mm_7789.1	chr1	131477836	131477854	-	1	NA	intron (NM_001081011, intron 2 of 22)	intron (NM_001081011, intron 2 of 22)	49516	NM_001081011	14270	Mm.276259	NM_019520	ENSMUSG00000026425	Srgap2	9930124L22Rik|AI448945|FBP2|Fnbp2|srGAP3	SLIT-ROBO Rho GTPase activating protein 2	protein-coding
mm_19657.1	chr2	102967531	102967537	-	1	NA	Intergenic	Intergenic	-65869	NM_001039150	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_77795.1	chr9	3029656	3029676	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	9077	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_2880.1	chr1	131828316	131828341	+	1	NA	5' UTR (NM_173865, exon 1 of 11)	5' UTR (NM_173865, exon 1 of 11)	316	NM_173865	98396	Mm.389181	NM_173865	ENSMUSG00000013275	Slc41a1	AI573938|B230315F01Rik	solute carrier family 41, member 1	protein-coding
mm_18181.1	chr2	45111130	45111136	-	1	NA	promoter-TSS (NM_001289521)	promoter-TSS (NM_001289521)	-5	NR_110572	433424	Mm.441408	NR_110571	ENSMUSG00000052248	Zeb2os	Gm13476|OTTMUSG00000012358|Zeb2nat	zinc finger E-box binding homeobox 2, opposite strand	ncRNA
mm_79894.1	chr9	65332555	65332570	+	1	NA	Intergenic	Intergenic	-13506	NM_016688	50996	Mm.29193	NM_016688	ENSMUSG00000041837	Pdcd7	C80112|ES18	programmed cell death 7	protein-coding
mm_92787.1	chr10	81298792	81298841	-	1	NA	intron (NM_008844, intron 1 of 17)	L1MB7|LINE|L1	5853	NM_001146687	18717	Mm.24222	NM_008844	ENSMUSG00000034902	Pip5k1c	AI115456|AI835305|Pip5kIgamma	phosphatidylinositol-4-phosphate 5-kinase, type 1 gamma	protein-coding
mm_144934.1	chr18	37730966	37730989	+	1	NA	promoter-TSS (NM_033577)	promoter-TSS (NM_033577)	-177	NM_033577	93702	Mm.247203	NM_033577	ENSMUSG00000103749	Pcdhgb5	-	protocadherin gamma subfamily B, 5	protein-coding
mm_16572.1	chr2	3422609	3422633	-	1	NA	promoter-TSS (NM_008579)	promoter-TSS (NM_008579)	27	NM_008579	104362	Mm.2688	NM_008579	ENSMUSG00000026650	Meig1	MLZ-278|Meg1	meiosis expressed gene 1	protein-coding
mm_165840.1	chr3	159495441	159495454	+	1	NA	promoter-TSS (NM_001172093)	promoter-TSS (NM_001172093)	14	NM_001172093	76131	Mm.371655	NM_029523	ENSMUSG00000028175	Depdc1a	5830484J08Rik|Depdc1	DEP domain containing 1a	protein-coding
mm_134374.1	chr16	17132378	17132388	-	1	NA	promoter-TSS (NM_022324)	promoter-TSS (NM_022324)	0	NM_022324	64136	Mm.30222	NM_022324	ENSMUSG00000022769	Sdf2l1	-	stromal cell-derived factor 2-like 1	protein-coding
mm_168217.1	chr10	7617459	7617462	-	1	NA	intron (NM_172784, intron 6 of 6)	B2_Mm1a|SINE|B2	27660	NM_172784	237253	Mm.206759	NM_172784	ENSMUSG00000019796	Lrp11	1700034J19Rik|6330533B21|9830160H19Rik	low density lipoprotein receptor-related protein 11	protein-coding
mm_155838.1	chrX	100795450	100795476	+	1	NA	intron (NM_001177780, intron 1 of 11)	intron (NM_001177780, intron 1 of 11)	18192	NM_001177780	53310	Mm.4615	NM_016747	ENSMUSG00000000881	Dlg3	Dlgh3|SAP102|mKIAA1232	discs, large homolog 3 (Drosophila)	protein-coding
mm_160399.1	chr8	70783509	70783509	-	1	NA	exon (NM_199308, exon 19 of 26)	exon (NM_199308, exon 19 of 26)	6647	NR_029440	72093	Mm.271208	NR_029440		2010320M18Rik	-	RIKEN cDNA 2010320M18 gene	ncRNA
mm_14873.1	chr2	148799743	148799756	+	1	NA	intron (NM_009978, intron 1 of 3)	RSINE1|SINE|B4	910	NM_009978	13012	Mm.20435	NM_009978	ENSMUSG00000027442	Cst8	Cres|Cst-rs1	cystatin 8 (cystatin-related epididymal spermatogenic)	protein-coding
mm_172088.1	chr6	17656356	17656370	-	1	NA	exon (NM_007604, exon 5 of 10)	exon (NM_007604, exon 5 of 10)	19265	NM_007604	12343	Mm.392504	NM_007604	ENSMUSG00000015733	Capza2	1110053K06Rik|AW208808|Cappa2	capping protein (actin filament) muscle Z-line, alpha 2	protein-coding
mm_13238.1	chr2	98662467	98662476	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	1194814	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_147824.1	chr18	61911881	61911888	-	1	NA	promoter-TSS (NM_001164491)	promoter-TSS (NM_001164491)	-32	NM_001164491	319713	Mm.329478	NM_198649	ENSMUSG00000032735	Ablim3	AW990719|D930036B08Rik	actin binding LIM protein family, member 3	protein-coding
mm_114063.1	chr13	54379759	54379776	+	1	NA	3' UTR (NM_009946, exon 4 of 4)	3' UTR (NM_009946, exon 4 of 4)	8418	NM_009946	12890	Mm.268902	NM_009946	ENSMUSG00000025867	Cplx2	921-L|AI413745|AW492120	complexin 2	protein-coding
mm_115713.1	chr13	15853134	15853153	-	1	NA	Intergenic	Intergenic	45900	NR_046131	328190	Mm.446957	NR_046131		A530046M15Rik	A530046M15	RIKEN cDNA A530046M15 gene	ncRNA
mm_62964.1	chr7	119793988	119794012	+	1	NA	promoter-TSS (NM_028129)	promoter-TSS (NM_028129)	58	NM_027698	71151	Mm.274160	NM_027698	ENSMUSG00000030929	Eri2	4933424N09Rik|Exod1|mKIAA1504	exoribonuclease 2	protein-coding
mm_57002.1	chr6	121027447	121027459	-	1	NA	intron (NR_138097, intron 11 of 18)	intron (NR_138097, intron 11 of 18)	-37011	NR_138098	100043793	Mm.448053	NR_138098		Gm4651	-	predicted gene 4651	ncRNA
mm_51034.1	chr6	65590417	65590432	+	1	NA	promoter-TSS (NM_001001495)	promoter-TSS (NM_001001495)	26	NM_001001495	414084	Mm.117558	NM_001001495	ENSMUSG00000044162	Tnip3	9030611K07Rik|ABIN-3|LIND	TNFAIP3 interacting protein 3	protein-coding
mm_66708.1	chr7	45923420	45923426	-	1	NA	Intergenic	Intergenic	-1997	NM_010129	13732	Mm.20829	NM_010129	ENSMUSG00000040212	Emp3	H-4|H4|HNMP-1|MI-35|Ymp	epithelial membrane protein 3	protein-coding
mm_34724.1	chr4	152178017	152178030	+	1	NA	promoter-TSS (NM_133348)	promoter-TSS (NM_133348)	-77	NM_133348	70025	Mm.296191	NM_133348	ENSMUSG00000028937	Acot7	2410041A17Rik|Ach1|Act|Bach|CTE-IIa|Cte-II|Lach1	acyl-CoA thioesterase 7	protein-coding
mm_53813.1	chr6	147032587	147032597	+	1	NA	promoter-TSS (NM_025620)	promoter-TSS (NM_025620)	55	NM_025620	66532	Mm.45888	NM_025620	ENSMUSG00000040121	Rep15	2210417D09Rik	RAB15 effector protein	protein-coding
mm_35113.1	chr4	9917378	9917400	-	1	NA	promoter-TSS (NR_004448)	promoter-TSS (NR_004448)	8	NR_004448	74662	Mm.483401	NR_004448	ENSMUSG00000082843	4930448K20Rik	1700009K09Rik	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_50942.1	chr6	57824538	57824557	+	1	NA	intron (NM_146168, intron 1 of 4)	CpG	578	NM_146168	232023	Mm.24642	NM_146168	ENSMUSG00000037788	Vopp1	AW146242|Ecop	vesicular, overexpressed in cancer, prosurvival protein 1	protein-coding
mm_169674.1	chr15	66057091	66057102	+	1	NA	intron (NM_152923, intron 1 of 14)	L1Md_T|LINE|L1	-80292	NM_001145096	654498	Mm.364550	NM_001145096	ENSMUSG00000072511	Hhla1	F930104E18Rik	HERV-H LTR-associating 1	protein-coding
mm_73091.1	chr8	94533010	94533074	+	1	NA	promoter-TSS (NM_153507)	promoter-TSS (NM_153507)	14	NM_153507	234577	Mm.291815	NM_153507	ENSMUSG00000034361	Cpne2	3322401K10Rik	copine II	protein-coding
mm_96966.1	chr11	70647614	70647635	+	1	NA	promoter-TSS (NM_024211)	promoter-TSS (NM_024211)	337	NM_027445	70510	Mm.261818	NM_027445	ENSMUSG00000040746	Rnf167	0610010G05Rik|5730408C10Rik|AU019305|AV328608	ring finger protein 167	protein-coding
mm_69818.1	chr7	141264516	141264526	-	1	NA	exon (NM_001252601, exon 6 of 10)	exon (NM_001252601, exon 6 of 10)	1903	NM_001252601	54123	Mm.3233	NM_016850	ENSMUSG00000025498	Irf7	-	interferon regulatory factor 7	protein-coding
mm_121675.1	chr14	12822638	12822649	-	1	NA	exon (NM_001042617, exon 1 of 31)	exon (NM_001042617, exon 1 of 31)	436	NM_001042617	27062	Mm.260881	NM_012061	ENSMUSG00000054423	Cadps	AU067781|CAPS|CAPS1|mKIAA1121	Ca2+-dependent secretion activator	protein-coding
mm_149425.1	chr19	11454653	11454664	+	1	NA	exon (NM_021718, exon 3 of 7)	exon (NM_021718, exon 3 of 7)	11100	NM_021718	60361	Mm.33957	NM_021718	ENSMUSG00000056290	Ms4a4b	AI463180|Chandra|Ly116	membrane-spanning 4-domains, subfamily A, member 4B	protein-coding
mm_14539.1	chr2	132792529	132792542	+	1	NA	exon (NM_007694, exon 4 of 5)	exon (NM_007694, exon 4 of 5)	11257	NM_007694	12653	Mm.255241	NM_007694	ENSMUSG00000027350	Chgb	Scg-1	chromogranin B	protein-coding
mm_170747.1	chr2	155963709	155963714	+	1	NA	intron (NM_001130000, intron 3 of 32)	intron (NM_001130000, intron 3 of 32)	7153	NM_177217	16328	Mm.288729	NM_008383	ENSMUSG00000038241	Cep250	AW490617|B230210E21Rik|Cep2|Inmp	centrosomal protein 250	protein-coding
mm_42810.1	chr5	121835193	121835197	+	1	NA	intron (NM_001306127, intron 1 of 8)	intron (NM_001306127, intron 1 of 8)	909	NM_001306126	16923	Mm.65493	NM_008507	ENSMUSG00000042594	Sh2b3	AI429800|Lnk	SH2B adaptor protein 3	protein-coding
mm_171945.1	chr5	72933008	72933025	-	1	NA	intron (NM_153567, intron 1 of 8)	intron (NM_153567, intron 1 of 8)	18654	NM_153567	75991	Mm.121285	NM_153567	ENSMUSG00000036087	Slain2	5033405K12Rik|8030444K12Rik|AI596370	SLAIN motif family, member 2	protein-coding
mm_45401.1	chr5	66151858	66151866	-	1	NA	promoter-TSS (NM_001127382)	promoter-TSS (NM_001127382)	92	NM_001127382	245945	Mm.36863	NM_139065	ENSMUSG00000070780	Rbm47	9530077J19Rik	RNA binding motif protein 47	protein-coding
mm_71277.1	chr8	40919674	40919722	+	1	NA	3' UTR (NM_001044740, exon 12 of 12)	3' UTR (NM_001044740, exon 12 of 12)	-6535	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_34264.1	chr4	141421786	141421798	+	1	NA	exon (NM_013868, exon 1 of 3)	exon (NM_013868, exon 1 of 3)	1013	NM_013868	29818	Mm.46181	NM_013868	ENSMUSG00000006221	Hspb7	27kDa|Hsp25-2|cvHsp	heat shock protein family, member 7 (cardiovascular)	protein-coding
mm_105708.1	chr11	108290169	108290172	-	1	NA	intron (NM_011101, intron 2 of 16)	B4A|SINE|B4	53718	NM_011101	18750	Mm.222178	NM_011101	ENSMUSG00000050965	Prkca	AI875142|Pkca	protein kinase C, alpha	protein-coding
mm_11830.1	chr2	45085950	45085979	+	1	NA	intron (NM_001289521, intron 1 of 8)	intron (NM_001289521, intron 1 of 8)	24313	NM_001289521	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_31042.1	chr4	41135544	41135554	+	1	NA	promoter-TSS (NM_026275)	promoter-TSS (NM_026275)	-472	NM_026275	67615	Mm.389540	NM_026275	ENSMUSG00000036241	Ube2r2	1200003M11Rik|Cdc34b|Ubc3b	ubiquitin-conjugating enzyme E2R 2	protein-coding
mm_160525.1	chr9	36258323	36258323	-	1	NA	Intergenic	Intergenic	-122693	NR_030729	100041618	Mm.484847	NR_030729	ENSMUSG00000098390	Gm3434	-	predicted gene 3434	ncRNA
mm_19446.1	chr2	91982839	91982858	-	1	NA	3' UTR (NM_011957, exon 12 of 12)	3' UTR (NM_011957, exon 12 of 12)	-19285	NM_138306	104418	Mm.314923	NM_138306	ENSMUSG00000040479	Dgkz	E130307B02Rik|ENSMUSG00000075035|F730209L11Rik|mDGK[z]	diacylglycerol kinase zeta	protein-coding
mm_45471.1	chr5	69341700	69341714	-	1	NA	promoter-TSS (NM_175519)	promoter-TSS (NM_175519)	2	NM_175519	243043	Mm.234821	NM_175519	ENSMUSG00000037653	Kctd8	A730087N02Rik	potassium channel tetramerisation domain containing 8	protein-coding
mm_18262.1	chr2	52292864	52292885	-	1	NA	exon (NM_010889, exon 31 of 157)	exon (NM_010889, exon 31 of 157)	1872	NR_040620	78049	Mm.243883	NR_040620		4930573O16Rik	-	RIKEN cDNA 4930573O16 gene	ncRNA
mm_75366.1	chr8	45294868	45294872	-	1	NA	promoter-TSS (NM_008455)	promoter-TSS (NM_008455)	-35	NM_008455	16621	Mm.482691	NM_008455	ENSMUSG00000109764	Klkb1	APS|Kal-3|Kal3|Klk3|PSA	kallikrein B, plasma 1	protein-coding
mm_147714.1	chr18	60812496	60812529	-	1	NA	TTS (NR_039567)	TTS (NR_039567)	436	NR_039567	100628611		NR_039567	ENSMUSG00000093327	Mir5107	mir-5107|mmu-mir-5107|mu-mir-5107	microRNA 5107	ncRNA
mm_150438.1	chr19	37576971	37577002	+	1	NA	exon (NM_175353, exon 6 of 22)	exon (NM_175353, exon 6 of 22)	26568	NM_175353	107371	Mm.24865	NM_175353	ENSMUSG00000053799	Exoc6	4833405E05Rik|AW413330|C430002C19|Sec15|Sec15l1|hbd|msec15	exocyst complex component 6	protein-coding
mm_51697.1	chr6	86578313	86578323	+	1	NA	Intergenic	Intergenic	-49856	NM_026414	67855	Mm.183043	NM_026414	ENSMUSG00000033508	Asprv1	2300003P22Rik|AA986851|SASP|SASPase|Taps	aspartic peptidase, retroviral-like 1	protein-coding
mm_83946.1	chr9	56860476	56860507	-	1	NA	Intergenic	Intergenic	-4613	NM_139001	121021	Mm.41329	NM_139001	ENSMUSG00000032911	Cspg4	4732461B14Rik|AN2|NG2	chondroitin sulfate proteoglycan 4	protein-coding
mm_9937.1	chr1	190144552	190144561	-	1	NA	intron (NM_008937, intron 4 of 4)	MIRc|SINE|MIR	26124	NM_008937	19130	Mm.132579	NM_008937	ENSMUSG00000010175	Prox1	A230003G05Rik	prospero homeobox 1	protein-coding
mm_55069.1	chr6	49051113	49051128	-	1	NA	exon (NM_053110, exon 8 of 11)	exon (NM_053110, exon 8 of 11)	14602	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_118279.1	chr13	112652358	112652370	-	1	NA	promoter-TSS (NM_010029)	promoter-TSS (NM_010029)	-54	NM_001145885	13206	Mm.12818	NM_010029	ENSMUSG00000021758	Ddx4	AV206478|Mvh|VASA	DEAD (Asp-Glu-Ala-Asp) box polypeptide 4	protein-coding
mm_11591.1	chr2	33216110	33216124	+	1	NA	5' UTR (NM_011923, exon 1 of 5)	5' UTR (NM_011923, exon 1 of 5)	156	NM_011923	26360	Mm.208919	NM_011923	ENSMUSG00000004105	Angptl2	AI593246|AW260363|Arp2	angiopoietin-like 2	protein-coding
mm_104138.1	chr11	86993653	86993674	-	1	NA	promoter-TSS (NM_001005341)	promoter-TSS (NM_001005341)	99	NM_001005341	77864	Mm.191894	NM_001005341	ENSMUSG00000018427	Ypel2	6430570G24|E130113K08Rik	yippee-like 2 (Drosophila)	protein-coding
mm_153932.1	chr19	47416318	47416328	-	1	NA	intron (NM_001164717, intron 2 of 13)	intron (NM_001164717, intron 2 of 13)	48088	NM_001164717	14218	Mm.127560	NM_008018	ENSMUSG00000053617	Sh3pxd2a	2310014D11Rik|AA589508|AI256723|AI413738|C230050L11|EG329070|Fish|Gm5098|Sh3md1|TSK5|Tks5	SH3 and PX domains 2A	protein-coding
mm_15525.1	chr2	158382570	158382588	+	1	NA	3' UTR (NM_175692, exon 5 of 5)	3' UTR (NM_175692, exon 5 of 5)	6941	NM_175692	319317	Mm.294494	NM_175692	ENSMUSG00000044349	Snhg11	A930034L06Rik|AI854265|AL022637|AW319638|E130013N09Rik	small nucleolar RNA host gene 11	protein-coding
mm_25306.1	chr3	105987378	105987380	+	1	NA	TTS (NM_007696)	TTS (NM_007696)	13577	NM_007696	12659	Mm.431947	NM_007696	ENSMUSG00000074340	Ovgp1	120kDa|AU016433|AU019448|Chit5|MOGP|OGP|muc9	oviductal glycoprotein 1	protein-coding
mm_123353.1	chr14	63142498	63142524	-	1	NA	3' UTR (NM_007798, exon 10 of 10)	3' UTR (NM_007798, exon 10 of 10)	20049	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_172847.1	chr9	3532752	3532755	+	1	NA	5' UTR (NM_001033322, exon 1 of 8)	5' UTR (NM_001033322, exon 1 of 8)	404	NM_001033322	234889	Mm.91240	NM_001033322	ENSMUSG00000041624	Gucy1a2	6330407I18Rik|A230060L24Rik	guanylate cyclase 1, soluble, alpha 2	protein-coding
mm_11858.1	chr2	48813999	48814013	+	1	NA	promoter-TSS (NM_007396)	promoter-TSS (NM_007396)	-103	NM_007396	11480	Mm.314338	NM_007396	ENSMUSG00000052155	Acvr2a	ActrIIa|Acvr2|TactrII	activin receptor IIA	protein-coding
mm_96374.1	chr11	67237853	67237864	+	1	NA	promoter-TSS (NM_010855)	promoter-TSS (NM_010855)	46	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_127460.1	chr15	101272178	101272202	+	1	NA	exon (NM_010444, exon 4 of 7)	exon (NM_010444, exon 4 of 7)	5344	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_61894.1	chr7	90025220	90025228	+	1	NA	Intergenic	Intergenic	-3935	NR_110365	319711	Mm.31753	NR_015614	ENSMUSG00000097585	E230029C05Rik	AI452102|B230337J15	RIKEN cDNA E230029C05 gene	ncRNA
mm_940.1	chr1	56087017	56087029	+	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	68045	NR_126076	69356	Mm.393775	NR_126075	ENSMUSG00000100372	1700003I22Rik	-	RIKEN cDNA 1700003I22 gene	ncRNA
mm_32317.1	chr4	103563528	103563549	+	1	NA	Intergenic	Intergenic	181038	NR_040673	622167	Mm.244115	NR_040673	ENSMUSG00000086136	Gm12718	OTTMUSG00000008109	predicted gene 12718	ncRNA
mm_32243.1	chr4	102511133	102511137	+	1	NA	intron (NM_019840, intron 5 of 14)	intron (NM_019840, intron 5 of 14)	-58925	NM_001177980	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_48704.1	chr5	147065791	147065796	-	1	NA	intron (NM_080795, intron 1 of 9)	intron (NM_080795, intron 1 of 9)	10779	NM_080795	140887	Mm.272203	NM_080795	ENSMUSG00000016520	Lnx2	9630046H24|AW209022	ligand of numb-protein X 2	protein-coding
mm_1528.1	chr1	72849109	72849144	+	1	NA	exon (NM_008342, exon 2 of 4)	exon (NM_008342, exon 2 of 4)	23739	NM_001310659	16008	Mm.141936	NM_008342	ENSMUSG00000039323	Igfbp2	AI255832|IBP-2|Igfbp-2|mIGFBP-2	insulin-like growth factor binding protein 2	protein-coding
mm_132401.1	chr16	35001396	35001408	+	1	NA	3' UTR (NM_139300, exon 32 of 32)	3' UTR (NM_139300, exon 32 of 32)	-21019	NM_023587	70757	Mm.27286	NM_023587	ENSMUSG00000035376	Hacd2	6330408J20Rik|AI255777|AI481689|Hcad2|Ptplb	3-hydroxyacyl-CoA dehydratase 2	protein-coding
mm_113405.1	chr13	33964664	33964674	+	1	NA	promoter-TSS (NM_001163241)	promoter-TSS (NM_001163241)	10	NM_001163241	18105	Mm.264036	NM_020282	ENSMUSG00000046949	Nqo2	NMO2|Nmor2|Ox2	NAD(P)H dehydrogenase, quinone 2	protein-coding
mm_41530.1	chr5	92683627	92683648	+	1	NA	5' UTR (NM_015756, exon 1 of 11)	5' UTR (NM_015756, exon 1 of 11)	202	NM_015756	27428	Mm.46014	NM_015756	ENSMUSG00000029381	Shroom3	AL022960|D5Ertd287e|Shrm|Shrm3	shroom family member 3	protein-coding
mm_77757.1	chr8	128686322	128686339	-	1	NA	intron (NM_010578, intron 1 of 15)	CpG	676	NM_010578	16412	Mm.263396	NM_010578	ENSMUSG00000025809	Itgb1	4633401G24Rik|AA409975|AA960159|CD29|ENSMUSG00000051907|Fnrb|Gm9863|gpIIa	integrin beta 1 (fibronectin receptor beta)	protein-coding
mm_152262.1	chr19	8798386	8798395	-	1	NA	intron (NM_026329, intron 1 of 7)	intron (NM_026329, intron 1 of 7)	167	NM_026329	67710	Mm.22117	NM_026329	ENSMUSG00000071662	Polr2g	2410046K11Rik|A230108L04Rik|C76415|RBP7|Rpo2-7l	polymerase (RNA) II (DNA directed) polypeptide G	protein-coding
mm_27243.1	chr3	36571953	36572003	-	1	NA	promoter-TSS (NM_009828)	promoter-TSS (NM_009828)	18	NM_009828	12428	Mm.4189	NM_009828	ENSMUSG00000027715	Ccna2	AA408589|Ccn-1|Ccn1|Ccna|CycA2|Cyca	cyclin A2	protein-coding
mm_22619.1	chr3	14641723	14641754	+	1	NA	promoter-TSS (NM_024495)	promoter-TSS (NM_024495)	11	NM_024495	71934	Mm.158776	NM_024495	ENSMUSG00000027555	Car13	2310075C21Rik|Ca13	carbonic anhydrase 13	protein-coding
mm_164220.1	chr15	84987855	84987857	-	1	NA	5' UTR (NM_001033273, exon 1 of 10)	5' UTR (NM_001033273, exon 1 of 10)	115	NM_001033273	223739	Mm.323925	NM_001033273	ENSMUSG00000036046	5031439G07Rik	AW554572|mKIAA0930	RIKEN cDNA 5031439G07 gene	protein-coding
mm_97038.1	chr11	72301614	72301671	+	1	NA	promoter-TSS (NM_001291153)	promoter-TSS (NM_001291153)	13	NM_001037713	327959	Mm.291131	NM_001037713	ENSMUSG00000040483	Xaf1	Fbox39	XIAP associated factor 1	protein-coding
mm_58447.1	chr7	3303572	3303584	+	1	NA	promoter-TSS (NM_011102)	promoter-TSS (NM_011102)	46	NM_011102	18752	Mm.7980	NM_011102	ENSMUSG00000078816	Prkcg	PKCgamma|Pkcc|Prkcc	protein kinase C, gamma	protein-coding
mm_123733.1	chr14	70175357	70175395	-	1	NA	intron (NM_145978, intron 1 of 9)	intron (NM_145978, intron 1 of 9)	1439	NM_001253736	213019	Mm.283968	NM_145978	ENSMUSG00000022090	Pdlim2	4732462F18Rik|Slim	PDZ and LIM domain 2	protein-coding
mm_99073.1	chr11	99280224	99280251	+	1	NA	exon (NM_029393, exon 8 of 8)	exon (NM_029393, exon 8 of 8)	5001	NM_029393	75706	Mm.46378	NM_029393	ENSMUSG00000020913	Krt24	2310058N18Rik|2310075C18Rik	keratin 24	protein-coding
mm_157606.1	chrX	53670398	53670456	-	1	NA	promoter-TSS (NM_001018063)	promoter-TSS (NM_001018063)	-19	NM_001018063	553127	Mm.328602	NM_001018063	ENSMUSG00000067924	Cxx1b	Mart8c	CAAX box 1B	protein-coding
mm_4030.1	chr1	165769822	165769830	+	1	NA	exon (NM_011804, exon 2 of 4)	exon (NM_011804, exon 2 of 4)	6046	NM_011804	433375	Mm.294885	NM_011804	ENSMUSG00000040713	Creg1	AA755314|Creg	cellular repressor of E1A-stimulated genes 1	protein-coding
mm_140576.1	chr17	9775863	9775872	-	1	NA	promoter-TSS (NR_045433)	promoter-TSS (NR_045433)	-1	NR_045433	71092	Mm.243827	NR_045433		4930452A19Rik	4933424P20Rik	RIKEN cDNA 4930452A19 gene	ncRNA
mm_70623.1	chr8	13600625	13600643	+	1	NA	intron (NM_009025, intron 4 of 23)	intron (NM_009025, intron 4 of 23)	-38173	NM_001080781	66501	Mm.46136	NM_025601	ENSMUSG00000031452	1700029H14Rik	-	RIKEN cDNA 1700029H14 gene	protein-coding
mm_59532.1	chr7	27731374	27731397	+	1	NA	promoter-TSS (NM_029531)	promoter-TSS (NM_029531)	-24	NM_029531	22718	Mm.66913	NM_009560	ENSMUSG00000037640	Zfp60	6330516O17Rik|AI426106|AI449354|Mfg-3|Mfg3	zinc finger protein 60	protein-coding
mm_49061.1	chr6	5390388	5390423	+	1	NA	intron (NM_023048, intron 1 of 5)	intron (NM_023048, intron 1 of 5)	7019	NM_023048	65255	Mm.51340	NM_023048	ENSMUSG00000042607	Asb4	8430401O13Rik|AV117194|AW060255	ankyrin repeat and SOCS box-containing 4	protein-coding
mm_867.1	chr1	52151007	52151017	+	1	NA	intron (NM_001205313, intron 19 of 24)	intron (NM_001205313, intron 19 of 24)	31390	NM_001205313	20846	Mm.277406	NM_009283	ENSMUSG00000026104	Stat1	2010005J02Rik|AA408197	signal transducer and activator of transcription 1	protein-coding
mm_105434.1	chr11	104302392	104302412	-	1	NA	exon (NM_010838, exon 4 of 10)	exon (NM_010838, exon 4 of 10)	70966	NM_001285454	17762	Mm.1287	NM_010838	ENSMUSG00000018411	Mapt	AI413597|AW045860|Mtapt|Tau	microtubule-associated protein tau	protein-coding
mm_27609.1	chr3	59195124	59195137	-	1	NA	promoter-TSS (NM_001302203)	promoter-TSS (NM_001302203)	-26	NM_001302203	84111	Mm.60267	NM_032399	ENSMUSG00000051431	Gpr87	-	G protein-coupled receptor 87	protein-coding
mm_117849.1	chr13	98695025	98695038	-	1	NA	promoter-TSS (NM_001025606)	promoter-TSS (NM_001025606)	-200	NM_001025606	380863	Mm.28264	NM_001025606	ENSMUSG00000052485	Tmem171	Gm905	transmembrane protein 171	protein-coding
mm_154243.1	chr19	60766412	60766423	-	1	NA	exon (NM_010123, exon 19 of 22)	exon (NM_010123, exon 19 of 22)	7968	NR_034047	100217439		NR_034047		Snora19	MBI-51	small nucleolar RNA, H/ACA box 19	snoRNA
mm_70500.1	chr8	12842844	12842886	+	1	NA	exon (NM_001293667, exon 18 of 30)	exon (NM_001293667, exon 18 of 30)	-10946	NR_045775	100504249	Mm.441494	NR_045775	ENSMUSG00000084780	Gm15350	OTTMUSG00000020611	predicted gene 15350	ncRNA
mm_102365.1	chr11	58390152	58390158	-	1	NA	exon (NM_001083884, exon 7 of 7)	exon (NM_001083884, exon 7 of 7)	9509	NM_001330197	70163	Mm.24119	NM_027339	ENSMUSG00000013643	Lypd8	2210415F13Rik	LY6/PLAUR domain containing 8	protein-coding
mm_72173.1	chr8	72311504	72311511	+	1	NA	Intergenic	Intergenic	-7555	NM_008452	16598	Mm.26938	NM_008452	ENSMUSG00000055148	Klf2	Lklf	Kruppel-like factor 2 (lung)	protein-coding
mm_133240.1	chr16	77077122	77077132	+	1	NA	exon (NM_013918, exon 14 of 24)	exon (NM_013918, exon 14 of 24)	63058	NM_013918	30940	Mm.40986	NM_013918	ENSMUSG00000022867	Usp25	-	ubiquitin specific peptidase 25	protein-coding
mm_76096.1	chr8	80057507	80057564	-	1	NA	5' UTR (NM_020259, exon 1 of 13)	5' UTR (NM_020259, exon 1 of 13)	473	NM_020259	15245	Mm.254493	NM_020259	ENSMUSG00000064325	Hhip	Hhip1	Hedgehog-interacting protein	protein-coding
mm_127216.1	chr15	99295212	99295279	+	1	NA	promoter-TSS (NM_018786)	promoter-TSS (NM_018786)	-164	NM_018786	54614	Mm.358668	NM_018786	ENSMUSG00000023007	Prpf40b	2610317D23Rik|Hypc	pre-mRNA processing factor 40B	protein-coding
mm_139490.1	chr17	56082119	56082139	+	1	NA	exon (NM_001304785, exon 2 of 16)	exon (NM_001304785, exon 2 of 16)	2498	NM_001304785	15193	Mm.12966	NM_008233	ENSMUSG00000002833	Hdgfrp2	HRP-2	hepatoma-derived growth factor, related protein 2	protein-coding
mm_170641.1	chr19	8989256	8989259	+	1	NA	promoter-TSS (NM_001286518)	promoter-TSS (NM_001286518)	-27	NR_104460	66395	Mm.203866	NM_009643	ENSMUSG00000069833	Ahnak	DY6	AHNAK nucleoprotein (desmoyokin)	protein-coding
mm_92163.1	chr10	67548743	67548793	-	1	NA	exon (NM_001005419, exon 1 of 1)	exon (NM_001005419, exon 1 of 1)	187	NM_001005419	211488	Mm.297250	NM_001005419	ENSMUSG00000057134	Ado	Gm237	2-aminoethanethiol (cysteamine) dioxygenase	protein-coding
mm_81063.1	chr9	106171181	106171226	+	1	NA	5' UTR (NM_029896, exon 1 of 9)	5' UTR (NM_029896, exon 1 of 9)	274	NM_029896	77305	Mm.265125	NM_029896	ENSMUSG00000020257	Wdr82	9430077D24Rik|CDW5/WDR82	WD repeat domain containing 82	protein-coding
mm_129170.1	chr15	76249360	76249381	-	1	NA	3' UTR (NM_023168, exon 7 of 7)	3' UTR (NM_023168, exon 7 of 7)	1179	NR_105918	102465575		NR_105918	ENSMUSG00000098625	Mir6953	Gm27738|mmu-mir-6953	microRNA 6953	ncRNA
mm_49648.1	chr6	30806311	30806328	+	1	NA	intron (NM_017478, intron 20 of 23)	intron (NM_017478, intron 20 of 23)	65020	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_17104.1	chr2	24048829	24048846	-	1	NA	intron (NM_080462, intron 1 of 6)	intron (NM_080462, intron 1 of 6)	542	NM_080462	140483	Mm.33120	NM_080462	ENSMUSG00000026986	Hnmt	1500031F01Rik|AI788969	histamine N-methyltransferase	protein-coding
mm_71934.1	chr8	70302755	70302760	+	1	NA	promoter-TSS (NM_021538)	promoter-TSS (NM_021538)	-28	NM_021538	59042	Mm.28668	NM_021538	ENSMUSG00000055681	Cope	1110005D17Rik|Cope1	coatomer protein complex, subunit epsilon	protein-coding
mm_19729.1	chr2	104493757	104493769	-	1	NA	intron (NM_010434, intron 1 of 15)	CpG	726	NM_010434	15259	Mm.257925	NM_010434	ENSMUSG00000027177	Hipk3	DYRK6|FIST3|PKY|mir-1902	homeodomain interacting protein kinase 3	protein-coding
mm_39325.1	chr5	8567114	8567123	+	1	NA	intron (NM_001347311, intron 4 of 10)	intron (NM_001347311, intron 4 of 10)	55834	NM_001347311	242819	Mm.332192	NM_198620	ENSMUSG00000040570	Rundc3b	Gm440	RUN domain containing 3B	protein-coding
mm_67118.1	chr7	70361579	70361583	-	1	NA	promoter-TSS (NM_009697)	promoter-TSS (NM_009697)	-988	NM_009697	11819	Mm.158143	NM_009697	ENSMUSG00000030551	Nr2f2	2700033K02Rik|9430015G03Rik|ARP-1|Aporp1|COUP-TF2|COUP-TFII|COUPTFB|EAR3|SVP40|Tcfcoup2	nuclear receptor subfamily 2, group F, member 2	protein-coding
mm_86829.1	chr10	21186935	21186966	+	1	NA	Intergenic	MER102b|DNA|hAT-Charlie	-25966	NM_010848	17863	Mm.52109	NM_010848	ENSMUSG00000019982	Myb	AI550390|M16449|c-myb	myeloblastosis oncogene	protein-coding
mm_107125.1	chr12	19954236	19954237	+	1	NA	Intergenic	CpG	861543	NR_015521	69513	Mm.273972	NR_015521	ENSMUSG00000099759	1700030C10Rik	-	RIKEN cDNA 1700030C10 gene	ncRNA
mm_10498.1	chr2	15049430	15049447	+	1	NA	promoter-TSS (NM_001165942)	promoter-TSS (NM_001165942)	-126	NM_028950	74455	Mm.478923	NM_028950	ENSMUSG00000026707	Nsun6	4933403D21Rik|4933414E04Rik|NOPD1	NOL1/NOP2/Sun domain family member 6	protein-coding
mm_66355.1	chr7	43527795	43527806	-	1	NA	3' UTR (NM_001111058, exon 7 of 7)	3' UTR (NM_001111058, exon 7 of 7)	5371	NM_001111058	12489	Mm.140157	NM_021293	ENSMUSG00000004609	Cd33	Siglec-3|gp67	CD33 antigen	protein-coding
mm_118875.1	chr14	25857634	25857635	+	1	NA	intron (NM_013469, intron 1 of 14)	intron (NM_013469, intron 1 of 14)	15479	NM_013469	11744	Mm.294083	NM_013469	ENSMUSG00000021866	Anxa11	A830099O17Rik|Anx11	annexin A11	protein-coding
mm_62035.1	chr7	92143085	92143092	+	1	NA	intron (NM_011807, intron 13 of 22)	intron (NM_011807, intron 13 of 22)	-23577	NR_131016	75845	Mm.437835	NR_131016	ENSMUSG00000109382	4930567K12Rik	-	RIKEN cDNA 4930567K12 gene	ncRNA
mm_697.1	chr1	40580493	40580510	+	1	NA	5' UTR (NM_177084, exon 1 of 12)	5' UTR (NM_177084, exon 1 of 12)	274	NM_177084	110895	Mm.108602	NM_177084	ENSMUSG00000026065	Slc9a4	AW990558|D730009J23Rik|NHE4	solute carrier family 9 (sodium/hydrogen exchanger), member 4	protein-coding
mm_137557.1	chr17	27655573	27655622	+	1	NA	promoter-TSS (NM_001286743)	promoter-TSS (NM_001286743)	6	NM_001286743	23969	Mm.4926	NM_011861	ENSMUSG00000040276	Pacsin1	A830061D09Rik|H74|mKIAA1379|syndapin	protein kinase C and casein kinase substrate in neurons 1	protein-coding
mm_160527.1	chr9	36843827	36843827	+	1	NA	exon (NM_183171, exon 1 of 9)	exon (NM_183171, exon 1 of 9)	168	NM_183171	235180	Mm.5264	NM_183171	ENSMUSG00000032118	Fez1	UNC-76|UNC76	fasciculation and elongation protein zeta 1 (zygin I)	protein-coding
mm_2888.1	chr1	131867277	131867296	+	1	NA	promoter-TSS (NM_144875)	promoter-TSS (NM_144875)	9	NM_144875	226422	Mm.34027	NM_144875	ENSMUSG00000026433	Rab29	Rab7l1	RAB29, member RAS oncogene family	protein-coding
mm_166142.1	chr5	3340966	3340970	+	1	NA	Intergenic	Intergenic	-2925	NM_009873	12571	Mm.31672	NM_009873	ENSMUSG00000040274	Cdk6	AI504062|Crk2	cyclin-dependent kinase 6	protein-coding
mm_154741.1	chrX	10312475	10312493	+	1	NA	exon (NM_008769, exon 9 of 10)	exon (NM_008769, exon 9 of 10)	60179	NM_008769	18416	Mm.2611	NM_008769	ENSMUSG00000031173	Otc	AI265390|Sf|spf	ornithine transcarbamylase	protein-coding
mm_4177.1	chr1	171125316	171125324	+	1	NA	exon (NM_001081275, exon 4 of 6)	exon (NM_001081275, exon 4 of 6)	3659	NM_001081275	75472	Mm.32760	NM_029301	ENSMUSG00000026649	Cfap126	1700009P17Rik|AV282292|Flattop|Fltp	cilia and flagella associated protein 126	protein-coding
mm_138812.1	chr17	39846619	39846657	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	3641	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_171219.1	chr3	59767225	59767229	+	1	NA	Intergenic	L1Md_F3|LINE|L1	37441	NM_001101531	433597	Mm.297801	NM_001101531	ENSMUSG00000090527	Gm5538	-	predicted gene 5538	protein-coding
mm_16602.1	chr2	5063933	5063971	-	1	NA	promoter-TSS (NM_181848)	promoter-TSS (NM_181848)	-14	NM_181848	71648	Mm.116942	NM_181848	ENSMUSG00000026672	Optn	4930441O07Rik|FIP2|HYPL|NRP	optineurin	protein-coding
mm_52709.1	chr6	119479505	119479530	+	1	NA	promoter-TSS (NM_133940)	promoter-TSS (NM_133940)	-151	NM_133940	101358	Mm.125477	NM_133940	ENSMUSG00000030019	Fbxl14	AW322056|Fbx14l	F-box and leucine-rich repeat protein 14	protein-coding
mm_111809.1	chr12	105222735	105222745	-	1	NA	promoter-TSS (NR_110339)	promoter-TSS (NR_110339)	-3	NM_001289468	21432	Mm.18154	NM_009337	ENSMUSG00000041359	Tcl1	Tcl1a	T cell lymphoma breakpoint 1	protein-coding
mm_157211.1	chrX	12762091	12762113	-	1	NA	promoter-TSS (NM_001048208)	promoter-TSS (NM_001048208)	-129	NM_001048208	26896	Mm.17616	NM_012005	ENSMUSG00000064127	Med14	9930001L01Rik|AU041628|Crsp2|ENSMUSG00000073278|Gm641|ORF1|Trap170	mediator complex subunit 14	protein-coding
mm_166246.1	chr5	77095277	77095277	-	1	NA	promoter-TSS (NM_001159901)	promoter-TSS (NM_001159901)	-10	NM_001159900	74318	Mm.181852	NM_175606	ENSMUSG00000059325	Hopx	1110018K11Rik|1200015P04Rik|2300002F06Rik|AI848177|AW490897|Cameo|Hdop|Hod|Hop|Ob1|Obl|Toto	HOP homeobox	protein-coding
mm_128814.1	chr15	67105064	67105085	-	1	NA	3' UTR (NM_009177, exon 9 of 9)	3' UTR (NM_009177, exon 9 of 9)	71808	NM_009177	20442	Mm.248334	NM_009177	ENSMUSG00000013846	St3gal1	5330418N22Rik|AI467004|ST3GalI|Siat4|Siat4a|St3gal-1	ST3 beta-galactoside alpha-2,3-sialyltransferase 1	protein-coding
mm_76391.1	chr8	84844127	84844145	-	1	NA	exon (NM_007591, exon 7 of 9)	exon (NM_007591, exon 7 of 9)	2795	NM_007591	12317	Mm.1971	NM_007591	ENSMUSG00000003814	Calr	CRT|Calregulin	calreticulin	protein-coding
mm_147151.1	chr18	36679112	36679135	-	1	NA	promoter-TSS (NM_026404)	promoter-TSS (NM_026404)	-92	NM_001083317	67843	Mm.273350	NM_026404	ENSMUSG00000033272	Slc35a4	2610030J16Rik	solute carrier family 35, member A4	protein-coding
mm_79365.1	chr9	54534121	54534127	+	1	NA	Intergenic	Intergenic	-4860	NM_173778	244885	Mm.358924	NM_173778	ENSMUSG00000046460	Sh2d7	4933412E14Rik	SH2 domain containing 7	protein-coding
mm_158679.1	chrX	159758245	159758248	-	1	NA	intron (NR_110969, intron 1 of 16)	intron (NR_110969, intron 1 of 16)	49645	NR_110970	58194	Mm.286495	NM_021389	ENSMUSG00000040990	Sh3kbp1	1200007H22Rik|1700125L08Rik|5830464D22Rik|AI447724|Cin85|IN85|Ruk|Seta	SH3-domain kinase binding protein 1	protein-coding
mm_141961.1	chr17	35120536	35120559	-	1	NA	promoter-TSS (NM_001128597)	promoter-TSS (NM_001128597)	745	NM_001303476	13001	Mm.378901	NM_009975	ENSMUSG00000024387	Csnk2b	CK II beta	casein kinase 2, beta polypeptide	protein-coding
mm_135627.1	chr16	52298762	52298772	-	1	NA	intron (NM_009655, intron 3 of 15)	B1_Mur3|SINE|Alu	154314	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_79235.1	chr9	50499210	50499222	+	1	NA	exon (NM_029639, exon 2 of 4)	exon (NM_029639, exon 2 of 4)	4691	NM_029639	76509	Mm.29959	NM_029639	ENSMUSG00000032068	Plet1	0610037B23Rik|1600029D21Rik|AA407923|AU043048	placenta expressed transcript 1	protein-coding
mm_1127.1	chr1	60231341	60231343	+	1	NA	intron (NM_173444, intron 11 of 54)	intron (NM_173444, intron 11 of 54)	50743	NM_173444	269198	Mm.205224	NM_173444	ENSMUSG00000073664	Nbeal1	2310076G13Rik|A530050O19Rik|A530083I02Rik|AI662228|ALS2CR17	neurobeachin like 1	protein-coding
mm_15123.1	chr2	153779241	153779251	+	1	NA	Intergenic	CpG	-1633	NR_036629	100504221	Mm.246778	NM_177849	ENSMUSG00000044083	Efcab8	A630008I04|EG329541	EF-hand calcium binding domain 8	ncRNA
mm_108082.1	chr12	73964482	73964542	+	1	NA	promoter-TSS (NM_178392)	promoter-TSS (NM_178392)	-18	NM_178392	75627	Mm.25937	NM_178392	ENSMUSG00000021113	Snapc1	2700033G17Rik|AU015787	small nuclear RNA activating complex, polypeptide 1	protein-coding
mm_93681.1	chr10	117792664	117792717	-	1	NA	promoter-TSS (NM_134010)	promoter-TSS (NM_134010)	15	NM_134010	103468	Mm.12568	NM_134010	ENSMUSG00000052798	Nup107	AW541137|C76801	nucleoporin 107	protein-coding
mm_92878.1	chr10	82623075	82623123	-	1	NA	5' UTR (NM_001135567, exon 1 of 3)	5' UTR (NM_001135567, exon 1 of 3)	129	NM_001135569	544717	Mm.334867	NM_001135567	ENSMUSG00000063320	1190007I07Rik	-	RIKEN cDNA 1190007I07 gene	protein-coding
mm_78259.1	chr9	21848227	21848237	+	1	NA	intron (NM_177030, intron 1 of 49)	intron (NM_177030, intron 1 of 49)	4403	NM_177030	319899	Mm.128153	NM_177030	ENSMUSG00000032198	Dock6	2410095B20Rik|4931431C02Rik|C330023D02Rik|mKIAA1395	dedicator of cytokinesis 6	protein-coding
mm_171669.1	chr4	48273742	48273751	-	1	NA	intron (NM_029572, intron 1 of 11)	B1_Mus2|SINE|Alu	5843	NM_029572	76299	Mm.317701	NM_029572	ENSMUSG00000028343	Erp44	1110001E24Rik|AI849526|AL033348|Txndc4	endoplasmic reticulum protein 44	protein-coding
mm_79354.1	chr9	53850244	53850257	+	1	NA	promoter-TSS (NM_025540)	promoter-TSS (NM_025540)	-1	NM_025540	66402	Mm.29132	NM_025540	ENSMUSG00000042045	Sln	2310045A07Rik	sarcolipin	protein-coding
mm_73671.1	chr8	111431386	111431392	+	1	NA	Intergenic	Intergenic	-18811	NR_105819	102466970		NR_105819	ENSMUSG00000098410	Mir1957b	Gm27725|mmu-mir-1957b	microRNA 1957b	ncRNA
mm_86711.1	chr10	18853568	18853618	+	1	NA	exon (NM_022032, exon 2 of 3)	exon (NM_022032, exon 2 of 3)	8522	NM_022032	64058	Mm.28209	NM_022032	ENSMUSG00000019851	Perp	1110017A08Rik|KCP1|KRTCAP1|PIGPC1|THW	PERP, TP53 apoptosis effector	protein-coding
mm_32466.1	chr4	107688490	107688493	+	1	NA	Intergenic	Intergenic	-4329	NM_019872	56296	Mm.141324	NM_019872	ENSMUSG00000028610	Dmrtb1	Dmrt6|Prp13	DMRT-like family B with proline-rich C-terminal, 1	protein-coding
mm_133333.1	chr16	78695007	78695017	+	1	NA	Intergenic	Lx8|LINE|L1	-118324	NM_025967	67102	Mm.37332	NM_025967	ENSMUSG00000022864	D16Ertd472e	1700010I10Rik|2310009O17Rik|E330003K22Rik|Eurl	DNA segment, Chr 16, ERATO Doi 472, expressed	protein-coding
mm_88542.1	chr10	78574493	78574545	+	1	NA	promoter-TSS (NM_173751)	promoter-TSS (NM_173751)	19	NM_173751	216136	Mm.2644	NM_173751	ENSMUSG00000032763	Ilvbl	5830463I21|AI415009	ilvB (bacterial acetolactate synthase)-like	protein-coding
mm_129982.1	chr15	86034017	86034027	-	1	NA	promoter-TSS (NM_009886)	promoter-TSS (NM_009886)	-245	NM_009886	12614	Mm.22680	NM_009886	ENSMUSG00000016028	Celsr1	Adgrc1|Crsh|Scy|crash	cadherin, EGF LAG seven-pass G-type receptor 1	protein-coding
mm_137471.1	chr17	26682672	26682697	+	1	NA	exon (NM_025272, exon 2 of 4)	exon (NM_025272, exon 2 of 4)	6288	NM_025272	11974	Mm.22602	NM_025272	ENSMUSG00000015575	Atp6v0e	Atp6k|Atp6v0e1|M9.2	ATPase, H+ transporting, lysosomal V0 subunit E	protein-coding
mm_85598.1	chr9	107541817	107541830	-	1	NA	promoter-TSS (NM_019720)	promoter-TSS (NM_019720)	42	NM_019720	56368	Mm.24833	NM_019720	ENSMUSG00000037190	Cyb561d2	AW049681|Tsp10	cytochrome b-561 domain containing 2	protein-coding
mm_16588.1	chr2	3731319	3731327	-	1	NA	intron (NM_025626, intron 1 of 3)	intron (NM_025626, intron 1 of 3)	17865	NM_025626	66540	Mm.277864	NM_025626	ENSMUSG00000026655	Fam107b	3110001A13Rik|AA589595|AA959793|AI132312	family with sequence similarity 107, member B	protein-coding
mm_130730.1	chr15	101225164	101225178	-	1	NA	promoter-TSS (NR_045328)	promoter-TSS (NR_045328)	15	NR_045328	380977	Mm.399924	NR_045326	ENSMUSG00000097915	A330009N23Rik	-	RIKEN cDNA A330009N23 gene	ncRNA
mm_114910.1	chr13	94957392	94957393	+	1	NA	Intergenic	Intergenic	-18952	NM_172590	218460	Mm.33856	NM_172590	ENSMUSG00000042015	Wdr41	B830029I03Rik|MSTP048	WD repeat domain 41	protein-coding
mm_141900.1	chr17	34951289	34951292	-	1	NA	promoter-TSS (NR_028527)	promoter-TSS (NR_028527)	-282	NR_028527	100217427		NR_028527	ENSMUSG00000093009	Snord52	MBII-297	small nucleolar RNA, C/D box 52	snoRNA
mm_155037.1	chrX	42108373	42108384	+	1	NA	non-coding (NR_125870, exon 6 of 6)	non-coding (NR_125870, exon 6 of 6)	37136	NM_001301641	11798	Mm.259879	NM_009688	ENSMUSG00000025860	Xiap	1110015C02Rik|Aipa|Api3|Birc4|IAP3|ILP-1|MIHA	X-linked inhibitor of apoptosis	protein-coding
mm_69602.1	chr7	135773728	135773764	-	1	NA	Intergenic	B4A|SINE|B4	-57367	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_78695.1	chr9	40873982	40873998	+	1	NA	promoter-TSS (NM_178245)	promoter-TSS (NM_178245)	-137	NM_178245	244813	Mm.261652	NM_178245	ENSMUSG00000054360	Bsx	Bsx1a|Bsx1b	brain specific homeobox	protein-coding
mm_94166.1	chr10	128803947	128803995	-	1	NA	intron (NM_178066, intron 1 of 4)	intron (NM_178066, intron 1 of 4)	399	NM_178066	73827	Mm.24630	NM_178066	ENSMUSG00000047090	Tmem198b	1110012D08Rik	transmembrane protein 198b	protein-coding
mm_77105.1	chr8	111061815	111061822	-	1	NA	Intergenic	Intergenic	5479	NM_028274	72544	Mm.24174	NM_028274	ENSMUSG00000109941	Exosc6	2610510N21Rik|C76919|Mtr3	exosome component 6	protein-coding
mm_119089.1	chr14	30891707	30891746	+	1	NA	exon (NM_001289633, exon 8 of 22)	exon (NM_001289633, exon 8 of 22)	5250	NM_001289632	16427	Mm.34819	NM_018746	ENSMUSG00000021922	Itih4	ITI-HC4|Itih-4|PK-120	inter alpha-trypsin inhibitor, heavy chain 4	protein-coding
mm_135480.1	chr16	46001808	46001818	-	1	NA	intron (NM_001134480, intron 1 of 3)	intron (NM_001134480, intron 1 of 3)	8600	NM_001134480	433022	Mm.380993	NM_001134480	ENSMUSG00000087141	Plcxd2	AW494639|EG433022	phosphatidylinositol-specific phospholipase C, X domain containing 2	protein-coding
mm_78162.1	chr9	21028144	21028155	+	1	NA	3' UTR (NM_010493, exon 7 of 7)	3' UTR (NM_010493, exon 7 of 7)	-1224	NM_023892	78369	Mm.30220	NM_023892	ENSMUSG00000001014	Icam4	1810015M19Rik|Cd242|ICAM-4	intercellular adhesion molecule 4, Landsteiner-Wiener blood group	protein-coding
mm_122596.1	chr14	50930833	50930878	-	1	NA	promoter-TSS (NM_001033271)	promoter-TSS (NM_001033271)	-6	NM_001310507	219024	Mm.239117	NM_001033271	ENSMUSG00000035953	Tmem55b	BC039161	transmembrane protein 55b	protein-coding
mm_119896.1	chr14	54938483	54938493	+	1	NA	intron (NM_026066, intron 2 of 4)	intron (NM_026066, intron 2 of 4)	1991	NM_029390	67272	Mm.41614	NM_026066	ENSMUSG00000040759	Cmtm5	1500005P16Rik|2900052H21Rik|Cklfsf5	CKLF-like MARVEL transmembrane domain containing 5	protein-coding
mm_20327.1	chr2	127482542	127482577	-	1	NA	promoter-TSS (NM_001111331)	promoter-TSS (NM_001111331)	-60	NM_001111331	56461	Mm.315292	NM_019789	ENSMUSG00000079056	Kcnip3	4933407H12Rik|AI413860|Csen|DREAM|KChIP3|R74849	Kv channel interacting protein 3, calsenilin	protein-coding
mm_98432.1	chr11	94936247	94936260	+	1	NA	promoter-TSS (NM_007742)	promoter-TSS (NM_007742)	29	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_124664.1	chr15	6301309	6301319	+	1	NA	intron (NM_001008702, intron 1 of 13)	MER5A|DNA|hAT-Charlie	1525	NM_001008702	13132	Mm.240830	NM_023118	ENSMUSG00000022150	Dab2	5730435J12Rik|AA960054|AI957090|D15Wsu122e|D630005B22Rik|Doc-2|Doc2|p96	disabled 2, mitogen-responsive phosphoprotein	protein-coding
mm_163907.1	chr14	31187126	31187145	-	1	NA	exon (NM_022656, exon 10 of 21)	exon (NM_022656, exon 10 of 21)	-18494	NM_138672	192187	Mm.220821	NM_138672	ENSMUSG00000042286	Stab1	FEEL-1|FELE-1|MFEEL-1|MS-1|STAB-1|mKIAA0246	stabilin 1	protein-coding
mm_135268.1	chr16	38376848	38376853	-	1	NA	intron (NM_001081984, intron 3 of 3)	intron (NM_001081984, intron 3 of 3)	14660	NM_022318	64082	Mm.390856	NM_022318	ENSMUSG00000022803	Popdc2	AV006127|Pop2	popeye domain containing 2	protein-coding
mm_21692.1	chr2	164461576	164461586	-	1	NA	intron (NM_025575, intron 2 of 3)	CpG-8820	610	NM_025575	66460	Mm.44218	NM_025575	ENSMUSG00000045503	Sys1	2610042O14Rik|AI266964|C87389	SYS1 Golgi-localized integral membrane protein homolog (S. cerevisiae)	protein-coding
mm_24393.1	chr3	90266493	90266501	+	1	NA	promoter-TSS (NM_201407)	promoter-TSS (NM_201407)	-17	NM_201407	229541	Mm.30571	NM_201407	ENSMUSG00000042404	Dennd4b	-	DENN/MADD domain containing 4B	protein-coding
mm_25568.1	chr3	116598213	116598234	+	1	NA	intron (NM_030016, intron 1 of 11)	intron (NM_030016, intron 1 of 11)	3265	NM_001289571	72776	Mm.440836	NM_028349	ENSMUSG00000027959	Sass6	2810453L12Rik	SAS-6 centriolar assembly protein	protein-coding
mm_19236.1	chr2	84715111	84715121	-	1	NA	promoter-TSS (NM_144887)	promoter-TSS (NM_144887)	48	NM_144887	228136	Mm.288508	NM_144887	ENSMUSG00000034075	Zdhhc5	1110032A17Rik|AI451382|Zisp	zinc finger, DHHC domain containing 5	protein-coding
mm_141305.1	chr17	28217725	28217735	-	1	NA	exon (NM_027185, exon 3 of 11)	exon (NM_027185, exon 3 of 11)	9952	NM_027185	23853	Mm.204731	NM_027185	ENSMUSG00000002257	Def6	2410003F05Rik|6430538D02Rik|AV094905|Ibp|Slat|Slat2|Slat6	differentially expressed in FDCP 6	protein-coding
mm_48989.1	chr6	4755984	4756002	+	1	NA	exon (NM_130877, exon 2 of 2)	exon (NM_130877, exon 2 of 2)	8687	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_5373.1	chr1	30873585	30873657	-	1	NA	Intergenic	CpG	-10365	NM_001081080	213109	Mm.194486	NM_025871	ENSMUSG00000048874	Phf3	2310061N19Rik|mKIAA0244	PHD finger protein 3	protein-coding
mm_109105.1	chr12	105336923	105336970	+	1	NA	promoter-TSS (NR_125773)	promoter-TSS (NR_125773)	-47	NR_125773	69952	Mm.158311	NR_045047	ENSMUSG00000097929	Tunar	2810011L19Rik|Tuna	Tcl1 upstream neural differentiation associated RNA	ncRNA
mm_26998.1	chr3	25833032	25833042	-	1	NA	intron (NM_001163387, intron 3 of 5)	intron (NM_001163387, intron 3 of 5)	320270	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_32450.1	chr4	107357760	107357783	+	1	NA	intron (NM_145550, intron 9 of 9)	intron (NM_145550, intron 9 of 9)	-10013	NM_028355	72787	Mm.28478	NM_028355	ENSMUSG00000028614	Ndc1	2810475A17Rik|AI450313|Tmem48|sks	NDC1 transmembrane nucleoporin	protein-coding
mm_84659.1	chr9	71723568	71723578	-	1	NA	exon (NM_026599, exon 3 of 19)	exon (NM_026599, exon 3 of 19)	48029	NM_026599	68178	Mm.99961	NM_026599	ENSMUSG00000032232	Cgnl1	4933421H10Rik|9930020M10Rik|AI503810|Jacop	cingulin-like 1	protein-coding
mm_110143.1	chr12	26448574	26448586	-	1	NA	intron (NM_021384, intron 4 of 5)	intron (NM_021384, intron 4 of 5)	7872	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_124163.1	chr14	93685188	93685198	-	1	NA	intron (NM_001346722, intron 2 of 4)	intron (NM_001346722, intron 2 of 4)	203695	NM_001271800	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding
mm_136331.1	chr16	92399743	92399746	-	1	NA	intron (NM_001081549, intron 1 of 3)	intron (NM_001081549, intron 1 of 3)	334	NM_019466	54720	Mm.265744	NM_019466	ENSMUSG00000022951	Rcan1	Adapt78|CALP1L|CSP1|DSC1|Dscr1|MCIP1|RCN1	regulator of calcineurin 1	protein-coding
mm_31441.1	chr4	48585082	48585134	+	1	NA	promoter-TSS (NM_021436)	promoter-TSS (NM_021436)	-85	NM_021436	230157	Mm.422686	NM_021436	ENSMUSG00000028347	Tmeff1	A830033E11|M7365|Tr1	transmembrane protein with EGF-like and two follistatin-like domains 1	protein-coding
mm_83350.1	chr9	44342333	44342344	-	1	NA	promoter-TSS (NM_001110251)	promoter-TSS (NM_001110251)	43	NM_001110251	15288	Mm.247676	NM_013551	ENSMUSG00000032126	Hmbs	PBGD|T25658|Ups|Uros1	hydroxymethylbilane synthase	protein-coding
mm_160448.1	chr8	105296023	105296023	-	1	NA	promoter-TSS (NM_177788)	promoter-TSS (NM_177788)	75	NM_177788	277978	Mm.40228	NM_177788	ENSMUSG00000043251	Exoc3l	C730015A04Rik|Exoc3l1	exocyst complex component 3-like	protein-coding
mm_7526.1	chr1	124208261	124208276	-	1	NA	Intergenic	Intergenic	-162709	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_107216.1	chr12	26445355	26445408	+	1	NA	3' UTR (NM_021384, exon 6 of 6)	3' UTR (NM_021384, exon 6 of 6)	11071	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_57124.1	chr6	122600142	122600152	-	1	NA	intron (NM_001134391, intron 1 of 7)	MRLTR33|LTR|ERVK	2297	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_15190.1	chr2	154202667	154202690	+	1	NA	exon (NM_153418, exon 2 of 16)	exon (NM_153418, exon 2 of 16)	2298	NM_153418	228801	Mm.3783	NM_153418	ENSMUSG00000027485	Bpifb1	Lplunc1	BPI fold containing family B, member 1	protein-coding
mm_132818.1	chr16	45224075	45224085	+	1	NA	promoter-TSS (NM_001037719)	promoter-TSS (NM_001037719)	-257	NM_001037719	208154	Mm.38199	NM_177584	ENSMUSG00000052013	Btla	A630002H24	B and T lymphocyte associated	protein-coding
mm_56407.1	chr6	97179101	97179159	-	1	NA	promoter-TSS (NM_001081111)	promoter-TSS (NM_001081111)	-6	NM_001081111	232286	Mm.30893	NM_001081111	ENSMUSG00000030059	Tmf1	7030402D04Rik|Gm153|Tmf1`	TATA element modulatory factor 1	protein-coding
mm_157732.1	chrX	70867546	70867548	-	1	NA	Intergenic	MTE-int|LTR|ERVL-MaLR	-182709	NM_001256048	333639	Mm.371730	NM_001081354	ENSMUSG00000059401	Mamld1	G630014P10Rik	mastermind-like domain containing 1	protein-coding
mm_67587.1	chr7	83632473	83632475	-	1	NA	intron (NM_023377, intron 1 of 5)	intron (NM_023377, intron 1 of 5)	457	NM_023377	170460	Mm.357953	NM_023377	ENSMUSG00000046027	Stard5	2310058G22Rik|AI607880|D7Ertd152e	StAR-related lipid transfer (START) domain containing 5	protein-coding
mm_20947.1	chr2	151632622	151632632	-	1	NA	promoter-TSS (NM_198214)	promoter-TSS (NM_198214)	-34	NM_001291076	241727	Mm.39312	NM_198214	ENSMUSG00000027457	Snph	6430515A01|AW045671|AW556958|AW743098|mKIAA0374	syntaphilin	protein-coding
mm_69840.1	chr7	141327676	141327694	-	1	NA	promoter-TSS (NM_001282076)	promoter-TSS (NM_001282076)	40	NM_016874	54006	Mm.28392	NM_016874	ENSMUSG00000058886	Deaf1	AU042387|C230009B13Rik|NUDR	deformed epidermal autoregulatory factor 1 (Drosophila)	protein-coding
mm_129479.1	chr15	78726749	78726764	-	1	NA	Intergenic	MER45A|DNA|hAT-Tip100	-8643	NM_183141	207393	Mm.323188	NM_183141	ENSMUSG00000043460	Elfn2	6330514E13|AW048948|BC094219|Lrrc62|Ppp1r29	leucine rich repeat and fibronectin type III, extracellular 2	protein-coding
mm_48539.1	chr5	142905129	142905153	-	1	NA	intron (NM_007393, intron 3 of 5)	intron (NM_007393, intron 3 of 5)	1613	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_19635.1	chr2	102825540	102825588	-	1	NA	intron (NM_001039150, intron 11 of 13)	intron (NM_001039150, intron 11 of 13)	76101	NM_001177785	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_29401.1	chr3	108905301	108905343	-	1	NA	exon (NM_025845, exon 5 of 6)	exon (NM_025845, exon 5 of 6)	6382	NM_025845	66921	Mm.51049	NM_025845	ENSMUSG00000027881	Prpf38b	1110021E09Rik|AU018955	PRP38 pre-mRNA processing factor 38 (yeast) domain containing B	protein-coding
mm_123976.1	chr14	75176650	75176682	-	1	NA	intron (NM_008879, intron 1 of 16)	intron (NM_008879, intron 1 of 16)	40241	NM_008879	18826	Mm.153911	NM_008879	ENSMUSG00000021998	Lcp1	AW536232|D14Ertd310e|LCP-1|Pls2|pp65	lymphocyte cytosolic protein 1	protein-coding
mm_22772.1	chr3	20262407	20262444	+	1	NA	exon (NM_029706, exon 9 of 11)	exon (NM_029706, exon 9 of 11)	13308	NM_029706	76703	Mm.34692	NM_029706	ENSMUSG00000011463	Cpb1	0910001A18Rik|1810063F02Rik|2210008M23Rik|AI504870	carboxypeptidase B1 (tissue)	protein-coding
mm_3257.1	chr1	136220731	136220734	+	1	NA	intron (NM_028872, intron 6 of 9)	intron (NM_028872, intron 6 of 9)	-7904	NM_001329610	76422	Mm.159735	NM_001329610		Mroh3	2310006M14Rik	maestro heat-like repeat family member 3	protein-coding
mm_2062.1	chr1	87588782	87588786	+	1	NA	intron (NM_001160165, intron 1 of 2)	intron (NM_001160165, intron 1 of 2)	4762	NM_001160165	23956	Mm.143717	NM_015750	ENSMUSG00000079434	Neu2	MBS|MSS|MTS	neuraminidase 2	protein-coding
mm_6726.1	chr1	82587035	82587055	-	1	NA	promoter-TSS (NM_007735)	promoter-TSS (NM_007735)	124	NM_007734	12828	Mm.389135	NM_007734	ENSMUSG00000079465	Col4a3	[a]3(IV)|alpha3(IV)	collagen, type IV, alpha 3	protein-coding
mm_18583.1	chr2	66256577	66256645	-	1	NA	promoter-TSS (NM_001290669)	promoter-TSS (NM_001290669)	6	NM_001047604	73668	Mm.250868	NM_001047604	ENSMUSG00000034848	Ttc21b	2410066K11Rik|Thm1|aln|mKIAA1992	tetratricopeptide repeat domain 21B	protein-coding
mm_153235.1	chr19	35924489	35924508	-	1	NA	Intergenic	Intergenic	132862	NM_001347442	15566	Mm.254266	NM_008315	ENSMUSG00000024798	Htr7	5-HT7	5-hydroxytryptamine (serotonin) receptor 7	protein-coding
mm_7635.1	chr1	127854997	127855030	-	1	NA	Intergenic	Intergenic	-13760	NM_178690	226407	Mm.489713	NM_178690	ENSMUSG00000036104	Rab3gap1	1700003B17Rik|4732493F09Rik|AL117896|Rab3gap|p130	RAB3 GTPase activating protein subunit 1	protein-coding
mm_137436.1	chr17	26506254	26506371	+	1	NA	exon (NM_013642, exon 4 of 4)	exon (NM_013642, exon 4 of 4)	2160	NM_013642	19252	Mm.239041	NM_013642	ENSMUSG00000024190	Dusp1	3CH134|MKP1|Ptpn16|U19515|erp|mkp-1	dual specificity phosphatase 1	protein-coding
mm_41973.1	chr5	107403592	107403611	+	1	NA	promoter-TSS (NM_001001804)	promoter-TSS (NM_001001804)	88	NM_001001804	384214	Mm.489863	NM_001001804	ENSMUSG00000033805	Ephx4	Abhd7|Ephxrp|Gm1382	epoxide hydrolase 4	protein-coding
mm_80241.1	chr9	72721529	72721557	+	1	NA	exon (NM_010890, exon 12 of 29)	exon (NM_010890, exon 12 of 29)	59196	NM_010890	17999	Mm.279923	NM_010890	ENSMUSG00000032216	Nedd4	AA959633|AL023035|AU019897|E430025J12Rik|Nedd4-1|Nedd4a|mKIAA0093	neural precursor cell expressed, developmentally down-regulated 4	protein-coding
mm_80164.1	chr9	71215808	71215831	+	1	NA	promoter-TSS (NM_009022)	promoter-TSS (NM_009022)	30	NM_009022	19378	Mm.42016	NM_009022	ENSMUSG00000013584	Aldh1a2	AV116159|Aldh1a7|Raldh1|Raldh2	aldehyde dehydrogenase family 1, subfamily A2	protein-coding
mm_146997.1	chr18	34371965	34371987	-	1	NA	intron (NM_007874, intron 2 of 4)	B1F|SINE|Alu	1439	NM_007874	13476	Mm.280075	NM_007874	ENSMUSG00000005873	Reep5	AI324241|AU022809|AW495741|DP1/TB2|Dp1|R74856|TB2/DP1	receptor accessory protein 5	protein-coding
mm_76495.1	chr8	86580665	86580675	-	1	NA	Intergenic	Intergenic	-14080	NM_172912	244562	Mm.67485	NM_172912	ENSMUSG00000036872	Abcc12	4930467B22Rik|MRP9	ATP-binding cassette, sub-family C (CFTR/MRP), member 12	protein-coding
mm_163465.1	chr12	101975884	101975886	-	1	NA	promoter-TSS (NM_016856)	promoter-TSS (NM_016856)	-89	NM_016856	51786	Mm.716	NM_016856	ENSMUSG00000041781	Cpsf2	100kDa|2610024B04Rik|AI662483|Cpsf|MCPSF|mKIAA1367	cleavage and polyadenylation specific factor 2	protein-coding
mm_36024.1	chr4	57011625	57011644	-	1	NA	Intergenic	Intergenic	-21243	NM_001142965	230235	Mm.207654	NM_001142965	ENSMUSG00000045589	Frrs1l	6430704M03Rik	ferric-chelate reductase 1 like	protein-coding
mm_137215.1	chr17	24169737	24169805	+	1	NA	promoter-TSS (NM_009729)	promoter-TSS (NM_009729)	-342	NM_009729	11984	Mm.30155	NM_009729	ENSMUSG00000024121	Atp6v0c	Atp6c|Atp6c2|Atp6l|Atpl|Atpl-rs1|PL16|VATL|Vma3	ATPase, H+ transporting, lysosomal V0 subunit C	protein-coding
mm_163700.1	chr13	103992848	103992848	-	1	NA	Intergenic	Intergenic	-72262	NM_001005868	59079	Mm.277354	NM_021563	ENSMUSG00000021709	Erbin	1700028E05Rik|Erbb2ip|mKIAA1225	Erbb2 interacting protein	protein-coding
mm_133054.1	chr16	57572334	57572349	+	1	NA	exon (NM_001040397, exon 5 of 5)	exon (NM_001040397, exon 5 of 5)	23099	NM_001177871	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding
mm_136389.1	chr16	93142079	93142092	-	1	NA	Intergenic	Intergenic	211104	NR_040486	69857	Mm.81192	NR_040486	ENSMUSG00000100277	1810053B23Rik	1810008L18Rik|1810056K14Rik	RIKEN cDNA 1810053B23 gene	ncRNA
mm_137444.1	chr17	26514927	26514952	+	1	NA	Intergenic	Intergenic	-6467	NM_013642	19252	Mm.239041	NM_013642	ENSMUSG00000024190	Dusp1	3CH134|MKP1|Ptpn16|U19515|erp|mkp-1	dual specificity phosphatase 1	protein-coding
mm_63811.1	chr7	133747554	133747554	+	1	NA	intron (NM_133941, intron 3 of 11)	intron (NM_133941, intron 3 of 11)	12715	NM_001286030	101437	Mm.199223	NM_133941	ENSMUSG00000030986	Dhx32	3110079L04Rik|4732469F02Rik|AA408140|Ddx32	DEAH (Asp-Glu-Ala-His) box polypeptide 32	protein-coding
mm_62731.1	chr7	110806160	110806186	+	1	NA	intron (NM_001276301, intron 12 of 14)	intron (NM_001276301, intron 12 of 14)	33569	NM_009667	11717	Mm.3238	NM_009667	ENSMUSG00000005686	Ampd3	-	adenosine monophosphate deaminase 3	protein-coding
mm_148730.1	chr19	5877875	5877885	+	1	NA	promoter-TSS (NM_134154)	promoter-TSS (NM_134154)	-586	NM_134154	107375	Mm.5323	NM_134154	ENSMUSG00000024818	Slc25a45	AW491445	solute carrier family 25, member 45	protein-coding
mm_167416.1	chr8	109494029	109494033	+	1	NA	promoter-TSS (NM_019938)	promoter-TSS (NM_019938)	4	NM_019938	56523	Mm.42166	NM_019938	ENSMUSG00000031727	Pmfbp1	1700016D22Rik|F77|Stap	polyamine modulated factor 1 binding protein 1	protein-coding
mm_99609.1	chr11	104580373	104580383	+	1	NA	intron (NM_010858, intron 3 of 8)	intron (NM_010858, intron 3 of 8)	-18180	NR_130177	100415912	Mm.446786	NR_130177		Gm11665	Gm11664|OTTMUSG00000003182|OTTMUSG00000003183	predicted gene 11665	ncRNA
mm_7013.1	chr1	86504056	86504080	-	1	NA	Intergenic	CpG	-22668	NM_008972	19231	Mm.19187	NM_008972	ENSMUSG00000026238	Ptma	Thym	prothymosin alpha	protein-coding
mm_10883.1	chr2	25255440	25255486	+	1	NA	promoter-TSS (NM_001082476)	promoter-TSS (NM_001082476)	24	NM_177344	227615	Mm.213925	NM_177344	ENSMUSG00000078201	Tmem203	C730025P13Rik|Hbebp1	transmembrane protein 203	protein-coding
mm_124119.1	chr14	79526178	79526180	-	1	NA	intron (NM_001286411, intron 1 of 8)	intron (NM_001286411, intron 1 of 8)	10505	NM_001286411	13709	Mm.20938	NM_007920	ENSMUSG00000036461	Elf1	Elf-1|Sts1|mElf-1|p70	E74-like factor 1	protein-coding
mm_87133.1	chr10	34283874	34283877	+	1	NA	3' UTR (NM_009433, exon 1 of 1)	3' UTR (NM_009433, exon 1 of 1)	1685	NM_009433	22110	Mm.20445	NM_009433	ENSMUSG00000047514	Tspyl1	Tspyl	testis-specific protein, Y-encoded-like 1	protein-coding
mm_134426.1	chr16	17921903	17921922	-	1	NA	Intergenic	CpG	6307	NM_153150	13358	Mm.229291	NM_153150	ENSMUSG00000003528	Slc25a1	1300019P08Rik|2610100G11Rik|AI194714|Ctp|Dgsj|Slc20a3	solute carrier family 25 (mitochondrial carrier, citrate transporter), member 1	protein-coding
mm_49128.1	chr6	8550371	8550375	+	1	NA	intron (NM_133236, intron 2 of 7)	U2|snRNA|snRNA	30315	NM_001286729	170772	Mm.210787	NM_133236	ENSMUSG00000029638	Glcci1	2310047L21Rik|A130036A18Rik|Fam117c|Gig18|Tssn1	glucocorticoid induced transcript 1	protein-coding
mm_22228.1	chr2	174429076	174429132	-	1	NA	exon (NM_022325, exon 4 of 6)	exon (NM_022325, exon 4 of 6)	9935	NM_022325	64138	Mm.156919	NM_022325	ENSMUSG00000016256	Ctsz	AI787083|AU019819|CTSX|D2Wsu143e	cathepsin Z	protein-coding
mm_106446.1	chr11	119917182	119917206	-	1	NA	intron (NM_001085498, intron 6 of 7)	intron (NM_001085498, intron 6 of 7)	3384	NM_001085498	208092	Mm.306673	NM_001085498	ENSMUSG00000025371	Chmp6	2400004G01Rik	charged multivesicular body protein 6	protein-coding
mm_163184.1	chr11	93995821	93995853	-	1	NA	promoter-TSS (NM_001199204)	promoter-TSS (NM_001199204)	-254	NM_001199203	70834	Mm.260737	NM_027569	ENSMUSG00000020859	Spag9	3110018C07Rik|4733401I23Rik|4831406C20Rik|AW552012|JLP|JSAP2|JSAP2a|Jip4|Mapk8ip4|syd1	sperm associated antigen 9	protein-coding
mm_144103.1	chr18	3507982	3507992	+	1	NA	promoter-TSS (NM_026505)	promoter-TSS (NM_026505)	30	NM_026505	68010	Mm.284863	NM_026505	ENSMUSG00000024232	Bambi	2610003H06Rik	BMP and activin membrane-bound inhibitor	protein-coding
mm_149631.1	chr19	17222574	17222589	+	1	NA	3' UTR (NM_181348, exon 20 of 20)	3' UTR (NM_181348, exon 20 of 20)	116924	NM_001136484	14537	Mm.244825	NM_010265	ENSMUSG00000038843	Gcnt1	5630400D21Rik|B130048E03|C2 GlcNAcT|C2GNT|IGnT	glucosaminyl (N-acetyl) transferase 1, core 2	protein-coding
mm_24763.1	chr3	95499257	95499265	+	1	NA	promoter-TSS (NM_007802)	promoter-TSS (NM_007802)	51	NM_007802	13038	Mm.272085	NM_007802	ENSMUSG00000028111	Ctsk	AI323530|MMS10-Q|Ms10q|catK	cathepsin K	protein-coding
mm_84446.1	chr9	66300864	66300871	-	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	-49583	NM_145617	235439	Mm.244179	NM_145617	ENSMUSG00000038664	Herc1	2810449H11Rik|B230218H07|D130015N03Rik|tbl	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	protein-coding
mm_41806.1	chr5	103754219	103754229	+	1	NA	promoter-TSS (NM_133919)	promoter-TSS (NM_133919)	62	NM_133919	17355	Mm.6949	NM_133919	ENSMUSG00000029313	Aff1	9630032B01Rik|AW319193|Af4|Mllt2h|Rob	AF4/FMR2 family, member 1	protein-coding
mm_53943.1	chr6	5182785	5182788	-	1	NA	intron (NM_011134, intron 4 of 8)	intron (NM_011134, intron 4 of 8)	11160	NM_011134	18979	Mm.237657	NM_011134	ENSMUSG00000002588	Pon1	Pon	paraoxonase 1	protein-coding
mm_8254.1	chr1	138842466	138842477	-	1	NA	promoter-TSS (NM_001042577)	promoter-TSS (NM_001042577)	-27	NM_001042577	16876	Mm.250732	NM_010714	ENSMUSG00000019230	Lhx9	3110009O07Rik|BB104635|LH2B	LIM homeobox protein 9	protein-coding
mm_156040.1	chrX	107816501	107816520	+	1	NA	promoter-TSS (NM_025921)	promoter-TSS (NM_025921)	33	NM_001163104	213449	Mm.444635	NM_001163104	ENSMUSG00000073007	Fam46d	Gm377	family with sequence similarity 46, member D	protein-coding
mm_160072.1	chr7	6502091	6502091	-	1	NA	exon (NM_146913, exon 1 of 1)	exon (NM_146913, exon 1 of 1)	133	NM_146913	258915	Mm.223321	NM_146913	ENSMUSG00000093877	Olfr1348	MOR103-9	olfactory receptor 1348	protein-coding
mm_133803.1	chr16	95298798	95298820	+	1	NA	non-coding (NR_073406, exon 6 of 6)	non-coding (NR_073406, exon 6 of 6)	41251	NM_001271690	16516	Mm.272239	NM_019664	ENSMUSG00000062609	Kcnj15	4930414N08Rik|AI182284|AI267127|IRKK|Kir4.2	potassium inwardly-rectifying channel, subfamily J, member 15	protein-coding
mm_1511.1	chr1	72459459	72459463	+	1	NA	intron (NM_001045533, intron 1 of 3)	intron (NM_001045533, intron 1 of 3)	77103	NM_001045533	381270	Mm.337023	NM_001045533	ENSMUSG00000039372	March4	BC056494|mKIAA1399	membrane-associated ring finger (C3HC4) 4	protein-coding
mm_86473.1	chr10	4611946	4611958	+	1	NA	promoter-TSS (NR_126357)	promoter-TSS (NR_126357)	-37	NM_001302532	13982	Mm.9213	NM_007956	ENSMUSG00000019768	Esr1	ER|ER-alpha|ERa|ERalpha|ESR|Estr|Estra|Nr3a1	estrogen receptor 1 (alpha)	protein-coding
mm_62921.1	chr7	118592485	118592505	+	1	NA	promoter-TSS (NM_001331203)	promoter-TSS (NM_001331203)	49	NM_001331203	381914	Mm.291232	NM_001331201	ENSMUSG00000109284	B230311B06Rik	Gm1695	RIKEN cDNA B230311B06 gene	protein-coding
mm_18155.1	chr2	45091347	45091355	-	1	NA	intron (NM_001289521, intron 1 of 8)	intron (NM_001289521, intron 1 of 8)	18926	NM_001289521	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_85438.1	chr9	104102343	104102363	-	1	NA	5' UTR (NM_145700, exon 2 of 3)	5' UTR (NM_145700, exon 2 of 3)	24290	NM_145700	252837	Mm.269254	NM_145700	ENSMUSG00000079355	Ackr4	A630091E18Rik|CCBP2|CCR11|CCX-CKR|CCX-CKR1|Ccrl1|Cmkbrl1|PPR1|VSHK1	atypical chemokine receptor 4	protein-coding
mm_24520.1	chr3	92944484	92944487	+	1	NA	promoter-TSS (NM_033175)	promoter-TSS (NM_033175)	-1	NM_033175	94060	Mm.301748	NM_033175	ENSMUSG00000045475	Lce3c	2300007B01Rik|AV076207|Eig3|Sprrl1	late cornified envelope 3C	protein-coding
mm_143887.1	chr17	84355007	84355020	-	1	NA	intron (NM_183021, intron 26 of 37)	RMER1A|Other|Other	111195	NM_183021	240174	Mm.246767	NM_177826	ENSMUSG00000024251	Thada	6530405K19|A930021O22|AU019899|BC052885|GITA	thyroid adenoma associated	protein-coding
mm_24303.1	chr3	89391825	89391870	+	1	NA	promoter-TSS (NR_040403)	promoter-TSS (NR_040403)	-17	NR_040403	545539	Mm.393389	NR_040403	ENSMUSG00000074466	Gm15417	ENSMUSG00000074466|OTTMUSG00000021274	predicted gene 15417	ncRNA
mm_119398.1	chr14	41151529	41151535	+	1	NA	promoter-TSS (NM_010775)	promoter-TSS (NM_010775)	76	NM_010775	17194	Mm.281805	NM_010775	ENSMUSG00000037780	Mbl1	MBL-A|MBP-A|S-MBP	mannose-binding lectin (protein A) 1	protein-coding
mm_2127.1	chr1	88025142	88025158	+	1	NA	Intergenic	Intergenic	-16599	NM_001033291	227334	Mm.80484	NM_001033291	ENSMUSG00000005501	Usp40	B230215L03Rik|C730029K03	ubiquitin specific peptidase 40	protein-coding
mm_92162.1	chr10	67547769	67547796	-	1	NA	3' UTR (NM_001005419, exon 1 of 1)	3' UTR (NM_001005419, exon 1 of 1)	1173	NM_001005419	211488	Mm.297250	NM_001005419	ENSMUSG00000057134	Ado	Gm237	2-aminoethanethiol (cysteamine) dioxygenase	protein-coding
mm_151964.1	chr19	5801716	5801732	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	948	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_111505.1	chr12	99457896	99457918	-	1	NA	Intergenic	Intergenic	-7833	NM_183186	71375	Mm.341972	NM_183186	ENSMUSG00000033713	Foxn3	5430426H20Rik|AA589593|AW556347|Ches1|Ches1l|HTLFL1	forkhead box N3	protein-coding
mm_58876.1	chr7	16987025	16987063	+	1	NA	Intergenic	RSINE1|SINE|B4	-7544	NM_001101535	434130	Mm.459162	NM_001101535	ENSMUSG00000041117	Ccdc8	ENSMUSG00000041117	coiled-coil domain containing 8	protein-coding
mm_44954.1	chr5	36695993	36696041	-	1	NA	promoter-TSS (NM_001081232)	promoter-TSS (NM_001081232)	4	NM_001081232	320661	Mm.26480	NM_177221	ENSMUSG00000029190	D5Ertd579e	9030221A05Rik|A930018H20Rik|Kiaa0232	DNA segment, Chr 5, ERATO Doi 579, expressed	protein-coding
mm_89568.1	chr10	95418683	95418687	+	1	NA	intron (NR_045339, intron 1 of 4)	intron (NR_045339, intron 1 of 4)	1310	NR_045338	70523	Mm.158398	NR_045338	ENSMUSG00000097766	5730420D15Rik	-	RIKEN cDNA 5730420D15 gene	ncRNA
mm_54619.1	chr6	38433720	38433732	-	1	NA	promoter-TSS (NM_177185)	promoter-TSS (NM_177185)	-199	NM_177185	320538	Mm.302831	NM_177185	ENSMUSG00000038538	Ubn2	2900060J04Rik|6030408G03Rik|BC060116|D130059P03Rik|mKIAA2030	ubinuclein 2	protein-coding
mm_123387.1	chr14	63349525	63349526	-	1	NA	Intergenic	B4A|SINE|B4	67662	NM_007549	12143	Mm.3962	NM_007549	ENSMUSG00000014453	Blk	-	B lymphoid kinase	protein-coding
mm_87895.1	chr10	62071268	62071293	+	1	NA	Intergenic	Intergenic	39733	NM_027251	69894	Mm.294126	NM_027251	ENSMUSG00000020083	2010107G23Rik	AA545165	RIKEN cDNA 2010107G23 gene	protein-coding
mm_158432.1	chrX	139871638	139871670	-	1	NA	promoter-TSS (NM_001193309)	promoter-TSS (NM_001193309)	0	NM_029413	75746	Mm.23269	NM_029413	ENSMUSG00000031434	Morc4	1600017G11Rik|5630401M14Rik|AA117449|Zcwcc2	microrchidia 4	protein-coding
mm_103467.1	chr11	76468475	76468486	-	1	NA	promoter-TSS (NM_001291186)	promoter-TSS (NM_001291186)	-15	NM_001291186	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_101394.1	chr11	26387406	26387442	-	1	NA	intron (NM_001277273, intron 1 of 13)	CpG	340	NR_102382	67030	Mm.18875	NM_025923	ENSMUSG00000004018	Fancl	2010322C19Rik|AW554273|B230118H11Rik|Phf9|Pog|gcd	Fanconi anemia, complementation group L	protein-coding
mm_87845.1	chr10	60892295	60892297	+	1	NA	Intergenic	Intergenic	-30727	NR_105835	102466158		NR_105835	ENSMUSG00000099279	Mir6408	Gm27451|mmu-mir-6408	microRNA 6408	ncRNA
mm_140154.1	chr17	80127778	80127824	+	1	NA	exon (NM_176963, exon 1 of 7)	exon (NM_176963, exon 1 of 7)	330	NM_176963	319625	Mm.29098	NM_176963	ENSMUSG00000035473	Galm	A530057M15Rik|AU015645|AU020959	galactose mutarotase	protein-coding
mm_64755.1	chr7	4843825	4843835	-	1	NA	intron (NM_001290291, intron 1 of 4)	intron (NM_001290291, intron 1 of 4)	866	NM_001290291	232813	Mm.44666	NM_172737	ENSMUSG00000053550	Shisa7	ckamp59	shisa family member 7	protein-coding
mm_149052.1	chr19	8837677	8837721	+	1	NA	5' UTR (NM_001136064, exon 1 of 12)	5' UTR (NM_001136064, exon 1 of 12)	232	NM_001136064	14705	Mm.345134	NM_008144	ENSMUSG00000071657	Bscl2	2900097C17Rik|AI046355|Gng3lg	Berardinelli-Seip congenital lipodystrophy 2 (seipin)	protein-coding
mm_58628.1	chr7	5081923	5081928	+	1	NA	intron (NM_001252454, intron 1 of 10)	intron (NM_001252454, intron 1 of 10)	1690	NM_001252454	13854	Mm.3091	NM_010147	ENSMUSG00000035203	Epn1	AA269831|Ibp1	epsin 1	protein-coding
mm_4431.1	chr1	172506612	172506623	+	1	NA	exon (NM_178598, exon 5 of 5)	exon (NM_178598, exon 5 of 5)	6371	NM_178598	21346	Mm.271711	NM_178598	ENSMUSG00000026547	Tagln2	2700094C18Rik|SM22beta|Sm22B|Sm22a	transgelin 2	protein-coding
mm_80318.1	chr9	74866475	74866489	+	1	NA	intron (NM_008262, intron 1 of 1)	intron (NM_008262, intron 1 of 1)	4561	NM_008262	15379	Mm.303355	NM_008262	ENSMUSG00000043013	Onecut1	D9Ertd423e|HNF-6|Hfh12|Hnf6|Hnf6b|OC-1|Oc1	one cut domain, family member 1	protein-coding
mm_123108.1	chr14	55884224	55884237	-	1	NA	promoter-TSS (NM_019820)	promoter-TSS (NM_019820)	26	NM_019820	56410	Mm.97163	NM_019820	ENSMUSG00000040380	Cbln3	-	cerebellin 3 precursor protein	protein-coding
mm_126269.1	chr15	79124482	79124518	+	1	NA	intron (NM_177461, intron 6 of 15)	intron (NM_177461, intron 6 of 15)	15517	NM_177461	27008	Mm.196480	NM_177461	ENSMUSG00000033039	Micall1	AI448246|D15Mit260|D15N2e|EST573322|EST820961|MIRab13|mKIAA1668	microtubule associated monooxygenase, calponin and LIM domain containing -like 1	protein-coding
mm_23980.1	chr3	86017232	86017245	+	1	NA	Intergenic	Intergenic	-14747	NM_001001650	368202	Mm.253822	NM_001001650	ENSMUSG00000049013	Prss48	Esspl|Gm1019	protease, serine 48	protein-coding
mm_121819.1	chr14	20452218	20452241	-	1	NA	promoter-TSS (NM_001163638)	promoter-TSS (NM_001163638)	-4	NM_001163639	76670	Mm.159759	NM_029698	ENSMUSG00000039543	Cfap70	Ttc18	cilia and flagella associated protein 70	protein-coding
mm_131657.1	chr16	20540664	20540766	+	1	NA	intron (NM_009679, intron 4 of 10)	intron (NM_009679, intron 4 of 10)	5235	NM_009679	11773	Mm.18946	NM_009679	ENSMUSG00000022841	Ap2m1	-	adaptor-related protein complex 2, mu 1 subunit	protein-coding
mm_15891.1	chr2	164880046	164880061	+	1	NA	intron (NM_146129, intron 1 of 16)	CpG	685	NM_146129	228866	Mm.241134	NM_146129	ENSMUSG00000039849	Pcif1	2310022K11Rik|C20orf67|F730014I05Rik	PDX1 C-terminal inhibiting factor 1	protein-coding
mm_171078.1	chr3	121249936	121249941	-	1	NA	intron (NM_178936, intron 1 of 7)	LSU-rRNA_Hsa|rRNA|rRNA	13378	NM_178936	99887	Mm.26088	NM_178936	ENSMUSG00000028132	Tmem56	4930577M16Rik|AU018104|AW109744|C730036B01Rik	transmembrane protein 56	protein-coding
mm_37221.1	chr4	117915194	117915198	-	1	NA	promoter-TSS (NM_146152)	promoter-TSS (NM_146152)	-197	NM_146152	230673	Mm.287810	NM_146152	ENSMUSG00000033365	Ipo13	Imp13|Kap13|Ranbp13	importin 13	protein-coding
mm_109638.1	chr12	112794276	112794289	+	1	NA	Intergenic	Intergenic	-14693	NM_145450	217887	Mm.186678	NM_145450	ENSMUSG00000037594	BC022687	AW050009|C130001I08Rik|Flj20080	cDNA sequence BC022687	protein-coding
mm_136761.1	chr17	8801641	8801682	+	1	NA	promoter-TSS (NM_011866)	promoter-TSS (NM_011866)	-84	NM_011866	23984	Mm.87161	NM_011866	ENSMUSG00000023868	Pde10a	-	phosphodiesterase 10A	protein-coding
mm_83126.1	chr9	40423639	40423654	-	1	NA	intron (NM_172768, intron 1 of 19)	intron (NM_172768, intron 1 of 19)	32118	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_66309.1	chr7	39517956	39517993	-	1	NA	intron (NM_001004139, intron 1 of 3)	CpG	208	NM_001004139	70227	Mm.333800	NM_001004139	ENSMUSG00000068959	Zfp619	3000002G13Rik	zinc finger protein 619	protein-coding
mm_116100.1	chr13	28884253	28884306	-	1	NA	intron (NR_045053, intron 1 of 8)	intron (NR_045053, intron 1 of 8)	1143	NR_045054	72518	Mm.37454	NR_045053		2610307P16Rik	AI666457	RIKEN cDNA 2610307P16 gene	ncRNA
mm_122526.1	chr14	47380247	47380265	-	1	NA	exon (NM_010705, exon 3 of 6)	exon (NM_010705, exon 3 of 6)	6396	NM_001145953	16854	Mm.248615	NM_010705	ENSMUSG00000050335	Lgals3	GBP|L-34|Mac-2|gal3	lectin, galactose binding, soluble 3	protein-coding
mm_142960.1	chr17	56120672	56120681	-	1	NA	exon (NM_029796, exon 2 of 2)	exon (NM_029796, exon 2 of 2)	1270	NM_029796	76905	Mm.348025	NM_029796	ENSMUSG00000037095	Lrg1	1300008B03Rik|2310031E04Rik|Lrg|Lrhg	leucine-rich alpha-2-glycoprotein 1	protein-coding
mm_14048.1	chr2	122313790	122313806	+	1	NA	promoter-TSS (NM_001305262)	promoter-TSS (NM_001305262)	-68	NM_001305262	213696	Mm.247121	NM_145395	ENSMUSG00000027224	Duoxa1	BC019755|Nip|Nip1	dual oxidase maturation factor 1	protein-coding
mm_36089.1	chr4	58458933	58458939	-	1	NA	intron (NM_001290486, intron 2 of 2)	intron (NM_001290486, intron 2 of 2)	-17838	NR_037278	100526502		NR_037278	ENSMUSG00000093293	Mir3095	mir-3095|mmu-mir-3095	microRNA 3095	ncRNA
mm_102334.1	chr11	57829316	57829325	-	1	NA	3' UTR (NM_008213, exon 2 of 2)	3' UTR (NM_008213, exon 2 of 2)	2827	NM_008213	15110	Mm.4746	NM_008213	ENSMUSG00000037335	Hand1	Ehand1|Hxt|Th1|Thing1|bHLHa27|eHAND	heart and neural crest derivatives expressed transcript 1	protein-coding
mm_113052.1	chr13	23684193	23684208	+	1	NA	promoter-TSS (NM_178189)	promoter-TSS (NM_178189)	1	NM_023422	68024	Mm.261676	NM_023422	ENSMUSG00000018102	Hist1h2bc	2610022J01Rik|H2bfs|R74621	histone cluster 1, H2bc	protein-coding
mm_149408.1	chr19	11404736	11404770	+	1	NA	Intergenic	Intergenic	-2908	NM_029499	64380	Mm.440715	NM_029499	ENSMUSG00000024675	Ms4a4c	5830413L19Rik|AI449185|Ms4a9	membrane-spanning 4-domains, subfamily A, member 4C	protein-coding
mm_36559.1	chr4	87161619	87161629	-	1	NA	intron (NM_172426, intron 2 of 10)	intron (NM_172426, intron 2 of 10)	66339	NM_001110240	76376	Mm.490487	NM_172426	ENSMUSG00000037996	Slc24a2	2810021B17Rik|6330417K15Rik|AI847460|Nckx2	solute carrier family 24 (sodium/potassium/calcium exchanger), member 2	protein-coding
mm_56942.1	chr6	119948492	119948547	-	1	NA	exon (NM_001185020, exon 17 of 26)	exon (NM_001185020, exon 17 of 26)	45821	NM_001166381	19365	Mm.149	NM_011236	ENSMUSG00000030166	Rad52	Rad52yh	RAD52 homolog, DNA repair protein	protein-coding
mm_71119.1	chr8	36168941	36168981	+	1	NA	Intergenic	Intergenic	74133	NM_172911	244418	Mm.244971	NM_172911	ENSMUSG00000050271	Prag1	9830148H23|D8Ertd82e|NACK|Sgk223|mFLJ00269	PEAK1 related kinase activating pseudokinase 1	protein-coding
mm_5755.1	chr1	46853884	46853916	-	1	NA	promoter-TSS (NM_172653)	promoter-TSS (NM_172653)	-391	NM_172653	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|mKIAA1265	solute carrier family 39 (zinc transporter), member 10	protein-coding
mm_45331.1	chr5	65537140	65537173	-	1	NA	promoter-TSS (NM_016786)	promoter-TSS (NM_016786)	-89	NM_016786	53323	Mm.319512	NM_016786	ENSMUSG00000029203	Ube2k	AW492011|D5Ertd601e|E2-25k|HIP-2|Hip2|Hypg|Lig	ubiquitin-conjugating enzyme E2K	protein-coding
mm_27770.1	chr3	72904428	72904459	-	1	NA	exon (NM_001081137, exon 41 of 47)	exon (NM_001081137, exon 41 of 47)	62423	NM_001081137	69983	Mm.261054	NM_001081137	ENSMUSG00000027790	Sis	2010204N08Rik|SI|Si-s	sucrase isomaltase (alpha-glucosidase)	protein-coding
mm_154499.1	chrM	11704	11714	-	1	NA	NA	Intergenic	NA	NA								
mm_80613.1	chr9	88327593	88327622	+	1	NA	promoter-TSS (NM_011851)	promoter-TSS (NM_011851)	-2	NM_011851	23959	Mm.244235	NM_011851	ENSMUSG00000032420	Nt5e	2210401F01Rik|5'-NT|AI447961|CD73|NT|Nt5|eNT	5' nucleotidase, ecto	protein-coding
mm_106161.1	chr11	116626952	116626960	-	1	NA	promoter-TSS (NM_172572)	promoter-TSS (NM_172572)	63	NM_172572	217344	Mm.89695	NM_172572	ENSMUSG00000020806	Rhbdf2	4732465I17Rik|Rhbdl6|cub	rhomboid 5 homolog 2	protein-coding
mm_84949.1	chr9	83146502	83146506	-	1	NA	5' UTR (NM_026122, exon 1 of 6)	5' UTR (NM_026122, exon 1 of 6)	103	NM_175074	94353	Mm.244426	NM_026122	ENSMUSG00000066456	Hmgn3	1110002A15Rik|6330514M13Rik|BB071015|TRIP7	high mobility group nucleosomal binding domain 3	protein-coding
mm_67176.1	chr7	73596245	73596275	-	1	NA	Intergenic	Intergenic	-37865	NR_037569	69170	Mm.34539	NR_037569	ENSMUSG00000101970	1810026B05Rik	-	RIKEN cDNA 1810026B05 gene	ncRNA
mm_20536.1	chr2	131041478	131041554	-	1	NA	exon (NM_020014, exon 2 of 6)	exon (NM_020014, exon 2 of 6)	-1118	NR_105969	102465606		NR_105969	ENSMUSG00000098686	Mir6973b	Gm27815|mmu-mir-6973b	microRNA 6973b	ncRNA
mm_29345.1	chr3	108284538	108284547	-	1	NA	intron (NM_001271599, intron 1 of 20)	intron (NM_001271599, intron 1 of 20)	478	NM_019972	20661	Mm.157119	NM_019972	ENSMUSG00000068747	Sort1	2900053A11Rik|AI852375|Ntr3|Ntsr3	sortilin 1	protein-coding
mm_38679.1	chr4	144998328	144998343	-	1	NA	intron (NM_001276502, intron 66 of 68)	intron (NM_001276502, intron 66 of 68)	105198	NM_011303	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding
mm_152206.1	chr19	7711236	7711246	-	1	NA	promoter-TSS (NM_144785)	promoter-TSS (NM_144785)	69	NM_144785	207151	Mm.21365	NM_144785	ENSMUSG00000024757	Slc22a19	D630043A20Rik|OAT-5|Oat5|Slc22a9	solute carrier family 22 (organic anion transporter), member 19	protein-coding
mm_69318.1	chr7	128461328	128461387	-	1	NA	5' UTR (NM_009383, exon 1 of 12)	5' UTR (NM_009383, exon 1 of 12)	156	NM_009383	21843	Mm.242072	NM_009383	ENSMUSG00000030846	Tial1	5330433G13Rik|AL033329|TIAR|mTIAR	Tia1 cytotoxic granule-associated RNA binding protein-like 1	protein-coding
mm_107239.1	chr12	26478854	26478872	+	1	NA	3' UTR (NM_020557, exon 5 of 5)	3' UTR (NM_020557, exon 5 of 5)	9648	NM_020557	22169	Mm.271839	NM_020557	ENSMUSG00000020638	Cmpk2	1200004E04Rik|TDKI|Tyki	cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial	protein-coding
mm_33828.1	chr4	135578731	135578743	+	1	NA	Intergenic	Intergenic	-5117	NM_001013756	230824	Mm.331972	NM_001013756	ENSMUSG00000037188	Grhl3	AI561912|Get1|Som|Tfcp2l4|ct	grainyhead-like 3 (Drosophila)	protein-coding
mm_64007.1	chr7	140203725	140203736	+	1	NA	promoter-TSS (NM_001011814)	promoter-TSS (NM_001011814)	-962	NM_001011814	258055	Mm.377339	NM_001011814	ENSMUSG00000050366	Olfr524	MOR103-14P	olfactory receptor 524	protein-coding
mm_172489.1	chr7	53890202	53890202	+	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	1687	NR_105746	102466619		NR_105746	ENSMUSG00000099176	Mir6238	Gm27982|mmu-mir-6238	microRNA 6238	ncRNA
mm_154422.1	chrM	251	313	-	1	NA	NA	Intergenic	NA	NA								
mm_82197.1	chr9	124022111	124022123	+	1	NA	5' UTR (NM_009914, exon 1 of 2)	5' UTR (NM_009914, exon 1 of 2)	146	NM_009914	12771	Mm.57050	NM_009914	ENSMUSG00000035448	Ccr3	CC-CKR3|CKR3|Cmkbr1l2|Cmkbr3	chemokine (C-C motif) receptor 3	protein-coding
mm_169424.1	chr14	53318762	53318778	+	1	NA	Intergenic	Intergenic	-823075	NM_001170918	57269	Mm.88822	NM_020512	ENSMUSG00000059887	Olfr1507	MOR244-1|Mor28|Or28	olfactory receptor 1507	protein-coding
mm_72082.1	chr8	71570727	71570823	+	1	NA	exon (NM_011977, exon 3 of 14)	exon (NM_011977, exon 3 of 14)	1848	NM_011977	26457	Mm.38165	NM_011977	ENSMUSG00000031808	Slc27a1	FATP1|Fatp	solute carrier family 27 (fatty acid transporter), member 1	protein-coding
mm_105609.1	chr11	106782934	106782954	-	1	NA	promoter-TSS (NR_037224)	promoter-TSS (NR_037224)	-185	NR_037224	100526469		NR_037224	ENSMUSG00000093273	Mir3064	mir-3064|mmu-mir-3064	microRNA 3064	ncRNA
mm_147738.1	chr18	61107648	61107698	-	1	NA	intron (NM_001037859, intron 2 of 21)	intron (NM_001037859, intron 2 of 21)	2101	NM_001037859	12978	Mm.22574	NM_007779	ENSMUSG00000024621	Csf1r	AI323359|CD115|CSF-1R|Csfmr|Fim-2|Fim2|Fms|M-CSF-R|M-CSFR	colony stimulating factor 1 receptor	protein-coding
mm_30921.1	chr4	32723004	32723016	+	1	NA	exon (NM_001081392, exon 48 of 102)	exon (NM_001081392, exon 48 of 102)	65891	NM_001081392	100019	Mm.24627	NM_133874	ENSMUSG00000058006	Mdn1	4833432B22Rik|A130070M06|AA958993|D4Abb1e|Gm135	midasin AAA ATPase 1	protein-coding
mm_9538.1	chr1	173875857	173875866	-	1	NA	intron (NM_001170853, intron 2 of 9)	intron (NM_001170853, intron 2 of 9)	4326	NM_001170853	100040462	Mm.463437	NM_001170853	ENSMUSG00000090272	Mndal	Gm2785|Ifi212	myeloid nuclear differentiation antigen like	protein-coding
mm_107396.1	chr12	33315491	33315501	+	1	NA	intron (NM_001033436, intron 1 of 7)	intron (NM_001033436, intron 1 of 7)	12981	NM_001033436	380753	Mm.41540	NM_028139	ENSMUSG00000020564	Atxn7l1	2810423G08Rik|Atxn7l4	ataxin 7-like 1	protein-coding
mm_92477.1	chr10	78234737	78234740	-	1	NA	intron (NM_001081055, intron 1 of 22)	intron (NM_001081055, intron 1 of 22)	9904	NM_001081055	216131	Mm.27539	NM_001081055	ENSMUSG00000000374	Trappc10	B230307C21Rik|Gm870|Tmem1	trafficking protein particle complex 10	protein-coding
mm_81118.1	chr9	106460651	106460657	+	1	NA	exon (NM_021567, exon 5 of 13)	exon (NM_021567, exon 5 of 13)	5286	NM_001159652	436090	Mm.482905	NM_001159652	ENSMUSG00000091735	Gpr62	4933402E03Rik	G protein-coupled receptor 62	protein-coding
mm_125257.1	chr15	35329172	35329192	+	1	NA	promoter-TSS (NR_045280)	promoter-TSS (NR_045280)	-647	NR_045280	100126269	Mm.247402	NR_045280		BC048602	-	cDNA sequence BC048602	ncRNA
mm_135803.1	chr16	57265502	57265513	-	1	NA	TTS (NM_027651)	TTS (NM_027651)	27344	NM_027651	71027	Mm.158563	NM_027651	ENSMUSG00000022753	Tmem30c	4933401B01Rik|4933409A18Rik|Cdc50c	transmembrane protein 30C	protein-coding
mm_153597.1	chr19	43751707	43751708	-	1	NA	intron (NM_144874, intron 1 of 8)	intron (NM_144874, intron 1 of 8)	1293	NM_144874	226139	Mm.248237	NM_144874	ENSMUSG00000040018	Cox15	2900026G05Rik	cytochrome c oxidase assembly protein 15	protein-coding
mm_154046.1	chr19	55076212	55076215	-	1	NA	intron (NM_008149, intron 17 of 20)	intron (NM_008149, intron 17 of 20)	23234	NM_008149	14732	Mm.210196	NM_008149	ENSMUSG00000024978	Gpam	GPAT|GPAT1	glycerol-3-phosphate acyltransferase, mitochondrial	protein-coding
mm_25514.1	chr3	113162560	113162565	+	1	NA	Intergenic	Intergenic	-5835	NM_001190403	545562	Mm.462977	NM_001190403		Amy2b	Amy-X|Amy2-2|OTTMUSG00000022462|mAmy2-1	amylase 2b	protein-coding
mm_80530.1	chr9	80165062	80165076	+	1	NA	promoter-TSS (NM_001039546)	promoter-TSS (NM_001039546)	35	NM_001039546	17920	Mm.4040	NM_008662	ENSMUSG00000033577	Myo6	BC029719|Tlc|sv	myosin VI	protein-coding
mm_56272.1	chr6	91024082	91024086	-	1	NA	intron (NM_018815, intron 33 of 39)	intron (NM_018815, intron 33 of 39)	92742	NM_018815	54563	Mm.28162	NM_018815	ENSMUSG00000030091	Nup210	9830001L10|AI836801|Pom210|gp190|gp210	nucleoporin 210	protein-coding
mm_42416.1	chr5	115279674	115279716	+	1	NA	promoter-TSS (NM_026504)	promoter-TSS (NM_026504)	-7	NM_026504	52064	Mm.290142	NM_026504	ENSMUSG00000041733	Coq5	1810014G04Rik|D5Ertd33e	coenzyme Q5 methyltransferase	protein-coding
mm_110896.1	chr12	75599333	75599333	-	1	NA	Intergenic	Intergenic	-3133	NM_012024	26932	Mm.259626	NM_012024	ENSMUSG00000021051	Ppp2r5e	4633401M22Rik|AI449017|B56beta	protein phosphatase 2, regulatory subunit B', epsilon	protein-coding
mm_44164.1	chr5	150684308	150684310	+	1	NA	intron (NM_001346503, intron 1 of 34)	B1F2|SINE|Alu	10482	NM_001346503	100710	Mm.32959	NM_175310	ENSMUSG00000034021	Pds5b	AI646570|AS3|AW212954|Aprin|Tg(Wap-ERBB2)229Wzw|WAP-Her-2|mKIAA0979	PDS5 cohesin associated factor B	protein-coding
mm_31439.1	chr4	48540382	48540411	+	1	NA	promoter-TSS (NM_028137)	promoter-TSS (NM_028137)	-103	NM_028137	66665	Mm.140749	NM_028137	ENSMUSG00000039693	Msantd3	2410046L14Rik|2810429P03Rik|5730528L13Rik|Mysantd3	Myb/SANT-like DNA-binding domain containing 3	protein-coding
mm_11475.1	chr2	32384655	32384693	+	1	NA	TTS (NM_008491)	TTS (NM_008491)	-2759	NM_198001	73737	Mm.27608	NM_198001	ENSMUSG00000039195	1110008P14Rik	C79326	RIKEN cDNA 1110008P14 gene	protein-coding
mm_88261.1	chr10	73821959	73821973	+	1	NA	promoter-TSS (NM_001142743)	promoter-TSS (NM_001142743)	99	NM_001142735	11994	Mm.338933	NM_023115	ENSMUSG00000052613	Pcdh15	BB078305|ENSMUSG00000046980|Gm9815|Ush1f|av|nmf19|roda	protocadherin 15	protein-coding
mm_44130.1	chr5	149678247	149678304	+	1	NA	promoter-TSS (NM_001081204)	promoter-TSS (NM_001081204)	18	NM_001081204	381694	Mm.45060	NM_001081204	ENSMUSG00000051950	B3glct	B3galtl|Gm1057	beta-3-glucosyltransferase	protein-coding
mm_152293.1	chr19	9003497	9003539	-	1	NA	exon (NM_009643, exon 5 of 5)	exon (NM_009643, exon 5 of 5)	14234	NM_001286518	66395	Mm.203866	NM_009643	ENSMUSG00000069833	Ahnak	DY6	AHNAK nucleoprotein (desmoyokin)	protein-coding
mm_104601.1	chr11	97162007	97162010	-	1	NA	3' UTR (NM_008379, exon 22 of 22)	3' UTR (NM_008379, exon 22 of 22)	-12296	NM_198100	73174	Mm.27882	NM_198100	ENSMUSG00000038517	Tbkbp1	3110043L15Rik|ProSAPiP2|SINTBAD	TBK1 binding protein 1	protein-coding
mm_18630.1	chr2	69237452	69237464	-	1	NA	TTS (NM_021022)	TTS (NM_021022)	17509	NM_001289857	14378	Mm.140768	NM_021331	ENSMUSG00000005232	G6pc2	G6pc-rs|IGRP	glucose-6-phosphatase, catalytic, 2	protein-coding
mm_8210.1	chr1	138136474	138136498	-	1	NA	intron (NM_001111316, intron 1 of 31)	intron (NM_001111316, intron 1 of 31)	38640	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_31714.1	chr4	62634398	62634413	+	1	NA	intron (NM_134257, intron 6 of 15)	intron (NM_134257, intron 6 of 15)	14733	NM_134257	50780	Mm.286753	NM_019492	ENSMUSG00000059810	Rgs3	4930506N09Rik|C2PA-RGS3|C2pa|PDZ-RGS3|RGS3S	regulator of G-protein signaling 3	protein-coding
mm_96015.1	chr11	59542962	59542967	+	1	NA	intron (NM_145827, intron 1 of 9)	intron (NM_145827, intron 1 of 9)	278	NM_145827	216799	Mm.54174	NM_145827	ENSMUSG00000032691	Nlrp3	AGTAVPRL|AII/AVP|Cias1|FCAS|FCU|MWS|Mmig1|NALP3|Pypaf1	NLR family, pyrin domain containing 3	protein-coding
mm_95209.1	chr11	43598570	43598591	+	1	NA	exon (NM_008375, exon 2 of 4)	exon (NM_008375, exon 2 of 4)	2982	NM_008375	16204	Mm.142716	NM_008375	ENSMUSG00000020405	Fabp6	GT|I-15P|I-BABP|ILBP|ILBP3|Illbp	fatty acid binding protein 6, ileal (gastrotropin)	protein-coding
mm_144279.1	chr18	11787193	11787196	+	1	NA	Intergenic	MYSERV16_I-int|LTR|ERVK	-52080	NM_022021	63955	Mm.40717	NM_022021	ENSMUSG00000040957	Cables1	Cables|ik3-1	CDK5 and Abl enzyme substrate 1	protein-coding
mm_89680.1	chr10	97517610	97517629	+	1	NA	exon (NM_007833, exon 8 of 8)	exon (NM_007833, exon 8 of 8)	35288	NM_007833	13179	Mm.56769	NM_007833	ENSMUSG00000019929	Dcn	DC|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding
mm_15690.1	chr2	163658530	163658534	+	1	NA	promoter-TSS (NM_001164053)	promoter-TSS (NM_001164053)	74	NM_001164053	18769	Mm.10091	NM_011106	ENSMUSG00000035268	Pkig	PKIgamma	protein kinase inhibitor, gamma	protein-coding
mm_114671.1	chr13	80158663	80158665	+	1	NA	Intergenic	U4|snRNA|snRNA	-724758	NM_001042591	105171	Mm.423137	NM_001042591	ENSMUSG00000074794	Arrdc3	AI450344|mKIAA1376	arrestin domain containing 3	protein-coding
mm_39530.1	chr5	21308441	21308444	+	1	NA	intron (NM_029195, intron 11 of 18)	intron (NM_029195, intron 11 of 18)	-64231	NM_008013	14190	Mm.292100	NM_008013	ENSMUSG00000039899	Fgl2	AI385601|musfiblp	fibrinogen-like protein 2	protein-coding
mm_146424.1	chr18	84848944	84848950	+	1	NA	Intergenic	MLTR14|LTR|ERV1	-2467	NM_025797	109672	Mm.31018	NM_025797	ENSMUSG00000024646	Cyb5a	0610009N12Rik|Cyb5	cytochrome b5 type A (microsomal)	protein-coding
mm_15058.1	chr2	152931939	152931945	+	1	NA	TTS (NM_010226)	TTS (NM_010226)	1266	NM_010226	14239	Mm.205798	NM_010226	ENSMUSG00000074676	Foxs1	FREAC10|Fkh3|Fkhl18	forkhead box S1	protein-coding
mm_23988.1	chr3	86224200	86224243	+	1	NA	promoter-TSS (NM_030695)	promoter-TSS (NM_030695)	-469	NM_001077688	80877	Mm.439825	NM_030695	ENSMUSG00000028080	Lrba	C80285|D3Ertd775e|Lab300|Lba	LPS-responsive beige-like anchor	protein-coding
mm_80932.1	chr9	102626565	102626603	+	1	NA	promoter-TSS (NM_001081122)	promoter-TSS (NM_001081122)	288	NM_181394	69010	Mm.2000	NM_181394	ENSMUSG00000035048	Anapc13	1810004D07Rik|APC13|SWM1	anaphase promoting complex subunit 13	protein-coding
mm_72791.1	chr8	86895129	86895138	+	1	NA	Intergenic	RMER15|LTR|ERVL	-9875	NM_030563	80750	Mm.25117	NM_030563	ENSMUSG00000031652	N4bp1	AI481586|C81621	NEDD4 binding protein 1	protein-coding
mm_59725.1	chr7	28788224	28788239	+	1	NA	promoter-TSS (NM_177158)	promoter-TSS (NM_177158)	-738	NM_177158	320435	Mm.74632	NM_177158	ENSMUSG00000051735	Rinl	5830482F20Rik|9930116N10Rik	Ras and Rab interactor-like	protein-coding
mm_123724.1	chr14	70153686	70153733	-	1	NA	promoter-TSS (NM_146055)	promoter-TSS (NM_146055)	82	NM_146055	219158	Mm.218284	NM_146055	ENSMUSG00000033712	Ccar2	2610301G19Rik|Dbc1|mKIAA1967	cell cycle activator and apoptosis regulator 2	protein-coding
mm_32068.1	chr4	97777926	97777940	+	1	NA	5' UTR (NM_001122953, exon 1 of 10)	5' UTR (NM_001122953, exon 1 of 10)	307	NM_010905	18027	Mm.31274	NM_010905	ENSMUSG00000028565	Nfia	1110047K16Rik|9430022M17Rik|CTF|NF1-A|NF1A	nuclear factor I/A	protein-coding
mm_37402.1	chr4	121215072	121215114	-	1	NA	promoter-TSS (NM_001346660)	promoter-TSS (NM_001346660)	-9	NM_001346660	109263	Mm.215745	NM_001081013	ENSMUSG00000049878	Rlf	9230110M18Rik|AI195322|MommeD8	rearranged L-myc fusion sequence	protein-coding
mm_53584.1	chr6	137464453	137464453	+	1	NA	3' UTR (NM_011216, exon 27 of 27)	3' UTR (NM_011216, exon 27 of 27)	53732	NM_001164403	19277	Mm.186361	NM_011216	ENSMUSG00000030223	Ptpro	D28|GLEPP1|PTPBK|PTPROt|PTPU2|PTPoc|PTPphi|Ptpn15|R-PTP-O	protein tyrosine phosphatase, receptor type, O	protein-coding
mm_76913.1	chr8	105932595	105932604	-	1	NA	TTS (NM_173432)	TTS (NM_173432)	1263	NM_023182	109660	Mm.2745	NM_023182	ENSMUSG00000031896	Ctrl	0910001G08Rik|1810004D15Rik|AV005227|Ctra-1|Ctra1|chymopasin|mFLJ00366	chymotrypsin-like	protein-coding
mm_45259.1	chr5	63953640	63953648	-	1	NA	intron (NM_145923, intron 1 of 6)	intron (NM_145923, intron 1 of 6)	15253	NM_145923	100532	Mm.243632	NM_145923	ENSMUSG00000047881	Rell1	AA536743	RELT-like 1	protein-coding
mm_72464.1	chr8	83290624	83290670	+	1	NA	exon (NM_009463, exon 1 of 6)	exon (NM_009463, exon 1 of 6)	299	NM_009463	22227	Mm.4177	NM_009463	ENSMUSG00000031710	Ucp1	AI385626|Slc25a7|Ucp	uncoupling protein 1 (mitochondrial, proton carrier)	protein-coding
mm_106033.1	chr11	116077607	116077632	-	1	NA	TTS (NM_016852)	TTS (NM_016852)	342	NM_001009573	70450	Mm.259460	NM_001009573	ENSMUSG00000057948	Unc13d	2610108D09Rik|Jinx|Munc13-4|mFLJ00067	unc-13 homolog D (C. elegans)	protein-coding
mm_137342.1	chr17	25136661	25136664	+	1	NA	promoter-TSS (NM_001317404)	promoter-TSS (NM_001317404)	31	NM_001317404	26373	Mm.270587	NM_011930	ENSMUSG00000036636	Clcn7	ClC-7|D17Wsu51e	chloride channel, voltage-sensitive 7	protein-coding
mm_376.1	chr1	34011258	34011268	+	1	NA	promoter-TSS (NM_134448)	promoter-TSS (NM_134448)	-562	NM_133833	13518	Mm.336625	NM_010081	ENSMUSG00000026131	Dst	2310001O04Rik|A830042E19Rik|AW554249|BP230|BPAG1-n|Bpag|Bpag1|Macf2|ah|athetoid|dt|mKIAA0728|nmf203|nmf339	dystonin	protein-coding
mm_155294.1	chrX	61183917	61183933	+	1	NA	3' UTR (NM_001166658, exon 1 of 1)	3' UTR (NM_001166658, exon 1 of 1)	1633	NM_001166658	631990	Mm.401324	NM_001166658	ENSMUSG00000090546	Cdr1	100039759|Cdr|Cdr34|EG631990|Gm2409|Gm7077	cerebellar degeneration related antigen 1	protein-coding
mm_112599.1	chr13	14142972	14142997	+	1	NA	exon (NM_194262, exon 8 of 24)	exon (NM_194262, exon 8 of 24)	79200	NM_198122	94246	Mm.439784	NM_194262	ENSMUSG00000039219	Arid4b	BCAA|BRCAA1|RBBP1L1|Rbp1l1|SAP180	AT rich interactive domain 4B (RBP1-like)	protein-coding
mm_147296.1	chr18	39514151	39514165	-	1	NA	Intergenic	Intergenic	-26913	NM_008173	14815	Mm.129481	NM_008173	ENSMUSG00000024431	Nr3c1	GR|Grl-1|Grl1	nuclear receptor subfamily 3, group C, member 1	protein-coding
mm_108909.1	chr12	100206149	100206165	+	1	NA	exon (NM_009790, exon 5 of 6)	exon (NM_009790, exon 5 of 6)	6013	NM_001313934	12313	Mm.285993	NM_009790	ENSMUSG00000001175	Calm1	AI256814|AI327027|AI461935|AL024000|CaM|Calm	calmodulin 1	protein-coding
mm_171509.1	chr4	146286993	146287001	+	1	NA	intron (NM_001083918, intron 3 of 6).2	intron (NM_001083918, intron 3 of 6).2	16612	NM_001083918	666532	Mm.392861	NM_001083918	ENSMUSG00000067916	Zfp991	Gm13139|OTTMUSG00000010657	zinc finger protein 991	protein-coding
mm_56737.1	chr6	115759022	115759036	-	1	NA	promoter-TSS (NM_144805)	promoter-TSS (NM_144805)	-30	NM_144805	94346	Mm.29739	NM_144805	ENSMUSG00000059900	Tmem40	9030407H20Rik|AV091463|W64236	transmembrane protein 40	protein-coding
mm_84235.1	chr9	62122655	62122665	-	1	NA	promoter-TSS (NR_039595)	promoter-TSS (NR_039595)	-66	NR_039595	100628602		NR_039595	ENSMUSG00000092696	Mir5133	mir-5133|mmu-mir-5133|mu-mir-5133	microRNA 5133	ncRNA
mm_123379.1	chr14	63271655	63271679	-	1	NA	Intergenic	Intergenic	-26396	NM_001310610	14463	Mm.247669	NM_008092	ENSMUSG00000021944	Gata4	Gata-4	GATA binding protein 4	protein-coding
mm_88119.1	chr10	69219329	69219346	+	1	NA	intron (NM_001252637, intron 2 of 10)	intron (NM_001252637, intron 2 of 10)	6143	NM_001252638	69288	Mm.26659	NM_001081347	ENSMUSG00000019944	Rhobtb1	1700008H16Rik|3110048G13Rik|AI173445|AI573858|AV350930	Rho-related BTB domain containing 1	protein-coding
mm_140560.1	chr17	7987238	7987239	-	1	NA	Intergenic	Intergenic	41624	NM_025789	66832	Mm.29830	NM_025789	ENSMUSG00000073471	Rsph3a	1700012G05Rik|4930524H12Rik|R74860|Rshl2|Rshl2a	radial spoke 3A homolog (Chlamydomonas)	protein-coding
mm_21195.1	chr2	155443080	155443081	-	1	NA	Intergenic	Intergenic	-2297	NM_019825	56406	Mm.27592	NM_019825	ENSMUSG00000038369	Ncoa6	AIB3|ASC-2|ASC2|NRC|Ncoa7|PRIP|RAP250|mKIAA0181	nuclear receptor coactivator 6	protein-coding
mm_41667.1	chr5	99336777	99336784	+	1	NA	intron (NR_030692, intron 3 of 3)	intron (NR_030692, intron 3 of 3)	-83853	NM_145839	320292	Mm.259074	NM_145839	ENSMUSG00000089809	Rasgef1b	4732452O09Rik|GPIgamma4|Gpig4	RasGEF domain family, member 1B	protein-coding
mm_70527.1	chr8	12997162	12997184	+	1	NA	intron (NM_001159486, intron 6 of 29)	intron (NM_001159486, intron 6 of 29)	-28861	NM_010172	14068	Mm.4827	NM_010172	ENSMUSG00000031443	F7	AI132620|Cf7|FVII	coagulation factor VII	protein-coding
mm_82381.1	chr9	14643524	14643542	-	1	NA	Intergenic	Intergenic	-28533	NM_001081395	75723	Mm.159552	NM_001081395	ENSMUSG00000013076	Amotl1	2310010G08Rik|2310067L22Rik|4932416D09Rik|JEAP|mFLJ00155	angiomotin-like 1	protein-coding
mm_34257.1	chr4	141398827	141398842	+	1	NA	promoter-TSS (NM_024412)	promoter-TSS (NM_024412)	-128	NM_024412	12733	Mm.167900	NM_024412	ENSMUSG00000033770	Clcnka	C75963|CLC-K1|Clcnk1	chloride channel, voltage-sensitive Ka	protein-coding
mm_139978.1	chr17	71782588	71782632	+	1	NA	intron (NM_030179, intron 1 of 15)	CpG	663	NM_030179	78785	Mm.196382	NM_030179	ENSMUSG00000024059	Clip4	1700024K14Rik|1700074B05Rik|4833417L20Rik|5830409B12Rik|Rsnl2	CAP-GLY domain containing linker protein family, member 4	protein-coding
mm_162903.1	chr10	115817180	115817188	+	1	NA	promoter-TSS (NM_001168680)	promoter-TSS (NM_001168680)	-100	NM_001168680	216350	Mm.22270	NM_146010	ENSMUSG00000034127	Tspan8	C76990|E330007O21Rik|Tm4sf3	tetraspanin 8	protein-coding
mm_83939.1	chr9	56795767	56795824	-	1	NA	Intergenic	CpG	56168	NM_198673	382075	Mm.335177	NM_198673	ENSMUSG00000045620	Odf3l1	BC049697|Gm1116	outer dense fiber of sperm tails 3-like 1	protein-coding
mm_99398.1	chr11	102189652	102189734	+	1	NA	promoter-TSS (NM_175935)	promoter-TSS (NM_175935)	-6	NM_175935	68401	Mm.22385	NM_175935	ENSMUSG00000034793	G6pc3	0710001K01Rik|AU019276|AU045429|AV128920|AW545836|UGRP	glucose 6 phosphatase, catalytic, 3	protein-coding
mm_108167.1	chr12	76403912	76403922	+	1	NA	promoter-TSS (NM_001002012)	promoter-TSS (NM_001002012)	-259	NM_001002012	15512	Mm.296181	NM_008301	ENSMUSG00000059970	Hspa2	70kDa|HSP70.2|HSP70A2|Hsp70-2	heat shock protein 2	protein-coding
mm_62781.1	chr7	112427716	112427718	+	1	NA	promoter-TSS (NM_020606)	promoter-TSS (NM_020606)	11	NM_020606	57342	Mm.143763	NM_020606	ENSMUSG00000030770	Parva	2010012A22Rik|5430400F08Rik|AI225929|AU042898|Actp|CH-ILKBP|Parvin	parvin, alpha	protein-coding
mm_122334.1	chr14	37121634	37121649	-	1	NA	3' UTR (NM_001199122, exon 9 of 9)	3' UTR (NM_001199122, exon 9 of 9)	-11540	NM_001206684	70045	Mm.271619	NM_001206684	ENSMUSG00000096001	2610528A11Rik	AW494830	RIKEN cDNA 2610528A11 gene	protein-coding
mm_159146.1	chr2	87191606	87191606	+	1	NA	promoter-TSS (NM_146661)	promoter-TSS (NM_146661)	-83	NM_146661	258655	Mm.377618	NM_146661	ENSMUSG00000044487	Olfr1112	MOR264-6	olfactory receptor 1112	protein-coding
mm_95755.1	chr11	54902918	54902932	+	1	NA	promoter-TSS (NM_008161)	promoter-TSS (NM_008161)	71	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_127113.1	chr15	97964278	97964306	+	1	NA	promoter-TSS (NM_201359)	promoter-TSS (NM_201359)	63	NM_001252153	380967	Mm.196630	NM_201359	ENSMUSG00000052369	Tmem106c	AI046681|BC046621|D15Ertd405e	transmembrane protein 106C	protein-coding
mm_33202.1	chr4	126296172	126296174	+	1	NA	intron (NM_199473, intron 1 of 3)	PB1D9|SINE|Alu	9379	NM_199473	329941	Mm.296327	NM_199473	ENSMUSG00000056174	Col8a2	AI429819	collagen, type VIII, alpha 2	protein-coding
mm_89521.1	chr10	94356977	94357038	+	1	NA	Intergenic	Intergenic	-58304	NR_033209	215472	Mm.255656	NM_174999	ENSMUSG00000053420	Gm4792	E130012K09|EG215472	predicted gene 4792	ncRNA
mm_132411.1	chr16	35025647	35025667	+	1	NA	intron (NM_023587, intron 1 of 6)	ORR1F|LTR|ERVL-MaLR	3236	NM_023587	70757	Mm.27286	NM_023587	ENSMUSG00000035376	Hacd2	6330408J20Rik|AI255777|AI481689|Hcad2|Ptplb	3-hydroxyacyl-CoA dehydratase 2	protein-coding
mm_56998.1	chr6	121003035	121003052	-	1	NA	intron (NM_001270475, intron 17 of 31)	intron (NM_001270475, intron 17 of 31)	44199	NR_138099	215458	Mm.122399	NR_138099		LOC215458	-	uncharacterized LOC215458	ncRNA
mm_111041.1	chr12	79249759	79249769	-	1	NA	intron (NM_001008550, intron 31 of 41)	intron (NM_001008550, intron 31 of 41)	40851	NM_030017	77974	Mm.274373	NM_030017	ENSMUSG00000021123	Rdh12	-	retinol dehydrogenase 12	protein-coding
mm_106766.1	chr12	4592901	4592945	+	1	NA	promoter-TSS (NM_001198969)	promoter-TSS (NM_001198969)	-85	NM_001198969	20403	Mm.341204	NM_011365	ENSMUSG00000020640	Itsn2	AI327390|Ese2|Sh3d1B|Sh3p18|mKIAA1256	intersectin 2	protein-coding
mm_41988.1	chr5	107725160	107725169	+	1	NA	promoter-TSS (NM_010278)	promoter-TSS (NM_010278)	641	NM_001267621	14581	Mm.2078	NM_010278	ENSMUSG00000029275	Gfi1	AW495828|Gfi-1|Pal-1|Pal1	growth factor independent 1	protein-coding
mm_164237.1	chr15	91641974	91641978	+	1	NA	Intergenic	Intergenic	-31248	NM_025730	66725	Mm.37558	NM_025730	ENSMUSG00000036273	Lrrk2	4921513O20Rik|9330188B09Rik|AW561911|D630001M17Rik|Gm927|cI-46	leucine-rich repeat kinase 2	protein-coding
mm_19398.1	chr2	91635803	91635812	-	1	NA	exon (NM_010168, exon 2 of 14)	exon (NM_010168, exon 2 of 14)	650	NM_010168	14061	Mm.89048	NM_010168	ENSMUSG00000027249	F2	Cf-2|Cf2|FII	coagulation factor II	protein-coding
mm_65892.1	chr7	30072873	30072924	-	1	NA	promoter-TSS (NM_001252519)	promoter-TSS (NM_001252519)	-75	NM_001253385	330502	Mm.295906	NM_177889	ENSMUSG00000098022	Zfp82	A030010D05|Krab16|Mszf3|Zfp-82	zinc finger protein 82	protein-coding
mm_107476.1	chr12	37880664	37880679	+	1	NA	promoter-TSS (NM_178681)	promoter-TSS (NM_178681)	-34	NM_178681	217480	Mm.126525	NM_178681	ENSMUSG00000036095	Dgkb	6430574F24|90kda|C630029D13Rik|DAGK2|DGK|DGK-beta|mKIAA0718	diacylglycerol kinase, beta	protein-coding
mm_43118.1	chr5	124637489	124637501	+	1	NA	exon (NM_011596, exon 4 of 20)	exon (NM_011596, exon 4 of 20)	8443	NM_011596	21871	Mm.1158	NM_011596	ENSMUSG00000038023	Atp6v0a2	8430408C20Rik|AI385560|ATP6a2|AW489264|Atp6n1d|Atp6n2|C76904|ISF|J6B7|SHIF|Stv1|TJ6M|TJ6s|Tj6|V-ATPase 116 kDa|V-ATPase a2	ATPase, H+ transporting, lysosomal V0 subunit A2	protein-coding
mm_144963.1	chr18	37821532	37821539	+	1	NA	exon (NM_033583, exon 1 of 4)	exon (NM_033583, exon 1 of 4)	1989	NM_033583	93708	Mm.247203	NM_033583	ENSMUSG00000102543	Pcdhgc5	-	protocadherin gamma subfamily C, 5	protein-coding
mm_13434.1	chr2	105126309	105126322	+	1	NA	promoter-TSS (NM_144783)	promoter-TSS (NM_144783)	195	NR_015462	329480	Mm.246679	NR_015462	ENSMUSG00000074987	Wt1os	6030498F17|AI314831|Wt1-as	Wilms tumor 1 homolog, opposite strand	ncRNA
mm_55420.1	chr6	65127992	65128005	-	1	NA	intron (NM_019455, intron 4 of 5)	U2|snRNA|snRNA	16732	NM_019455	54486	Mm.410688	NM_019455	ENSMUSG00000029919	Hpgds	H-PGDS|Ptgds2	hematopoietic prostaglandin D synthase	protein-coding
mm_47756.1	chr5	131307440	131307454	-	1	NA	promoter-TSS (NM_145218)	promoter-TSS (NM_145218)	75	NM_145218	212996	Mm.299204	NM_145218	ENSMUSG00000034040	Wbscr17	AA388321|E330012B09Rik	Williams-Beuren syndrome chromosome region 17 homolog (human)	protein-coding
mm_100052.1	chr11	115180028	115180040	+	1	NA	exon (NM_012030, exon 5 of 6)	exon (NM_012030, exon 5 of 6)	7282	NM_025400	66176	Mm.86823	NM_025400	ENSMUSG00000015542	Nat9	1110028N05Rik	N-acetyltransferase 9 (GCN5-related, putative)	protein-coding
mm_16302.1	chr2	174289620	174289638	+	1	NA	intron (NR_002846, intron 1 of 4)	(CA)n|Simple_repeat|Simple_repeat	5309	NM_022000	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_100148.1	chr11	116030305	116030385	+	1	NA	promoter-TSS (NM_001286006)	promoter-TSS (NM_001286006)	29	NM_172569	217331	Mm.297706	NM_172569	ENSMUSG00000020770	Unk	B230379M23Rik|Zc3h5|Zc3hdc5|mKIAA1753	unkempt family zinc finger	protein-coding
mm_76242.1	chr8	83583414	83583420	-	1	NA	intron (NM_134118, intron 1 of 12)	intron (NM_134118, intron 1 of 12)	11074	NM_027179	106529	Mm.352239	NM_027179	ENSMUSG00000031708	Tecr	2410016D23Rik|A230102P12Rik|AI173355|D17Ertd178e|Gpsn2|SC2	trans-2,3-enoyl-CoA reductase	protein-coding
mm_28958.1	chr3	100665219	100665230	-	1	NA	intron (NM_010763, intron 1 of 12)	B2_Mm2|SINE|B2	20249	NM_010763	17156	Mm.271617	NM_010763	ENSMUSG00000008763	Man1a2	AI428775|AI528764|AI854422|Man1b|PCR2	mannosidase, alpha, class 1A, member 2	protein-coding
mm_172424.1	chr7	28174520	28174523	+	1	NA	exon (NM_007991, exon 2 of 9)	exon (NM_007991, exon 2 of 9)	4773	NM_007991	14113	Mm.4595	NM_007991	ENSMUSG00000046865	Fbl	AL022665|FIB|FLRN|RNU3IP1	fibrillarin	protein-coding
mm_91984.1	chr10	61784015	61784017	-	1	NA	promoter-TSS (NM_207000)	promoter-TSS (NM_207000)	-152	NM_207000	404634	Mm.272870	NM_207000	ENSMUSG00000020086	H2afy2	macroH2A2	H2A histone family, member Y2	protein-coding
mm_11216.1	chr2	29643739	29643757	+	1	NA	intron (NM_001039087, intron 1 of 25)	intron (NM_001039087, intron 1 of 25)	24028	NM_001039086	107746	Mm.298274	NM_054050	ENSMUSG00000039844	Rapgef1	4932418O06Rik|C3G|Grf2	Rap guanine nucleotide exchange factor (GEF) 1	protein-coding
mm_100443.1	chr11	119486503	119486513	+	1	NA	Intergenic	Intergenic	-4839	NM_001164636	338371	Mm.271946	NM_177394	ENSMUSG00000039850	Endov	A730011L01Rik	endonuclease V	protein-coding
mm_6828.1	chr1	84203100	84203103	-	1	NA	intron (NM_001003948, intron 1 of 2)	intron (NM_001003948, intron 1 of 2)	15860	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_93939.1	chr10	127189982	127190071	-	1	NA	promoter-TSS (NM_028027)	promoter-TSS (NM_028027)	28	NM_028027	52666	Mm.272230	NM_028027	ENSMUSG00000019467	Arhgef25	2410008H17Rik|D10Ertd610e|GEFT	Rho guanine nucleotide exchange factor (GEF) 25	protein-coding
mm_12966.1	chr2	90679370	90679412	+	1	NA	5' UTR (NM_021512, exon 2 of 37)	5' UTR (NM_021512, exon 2 of 37)	2176	NM_021512	59015	Mm.24532	NM_021512	ENSMUSG00000051329	Nup160	160kDa|2810011M03Rik|AA414952|AU020188|Gtl-13|Gtl1-13|Gtl13|mKIAA0197	nucleoporin 160	protein-coding
mm_109199.1	chr12	108648400	108648410	+	1	NA	exon (NM_007965, exon 2 of 13)	exon (NM_007965, exon 2 of 13)	-10215	NR_029771	723909		NR_029771	ENSMUSG00000065436	Mir342	Mirn342|mmu-mir-342	microRNA 342	ncRNA
mm_120449.1	chr14	65968604	65968607	+	1	NA	5' UTR (NM_013492, exon 1 of 9)	5' UTR (NM_013492, exon 1 of 9)	122	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_146964.1	chr18	33438622	33438636	-	1	NA	3' UTR (NM_001267717, exon 5 of 5)	3' UTR (NM_001267717, exon 5 of 5)	25005	NM_001267717	27528	Mm.407415	NM_053078	ENSMUSG00000042834	Nrep	AI325076|D0H4S114|Harp|P311|PTZ17|SEZ17	neuronal regeneration related protein	protein-coding
mm_105085.1	chr11	100848136	100848181	-	1	NA	intron (NM_001113563, intron 1 of 18)	intron (NM_001113563, intron 1 of 18)	2427	NM_001113563	20851	Mm.34064	NM_011489	ENSMUSG00000020919	Stat5b	-	signal transducer and activator of transcription 5B	protein-coding
mm_155305.1	chrX	61185995	61186009	+	1	NA	promoter-TSS (NM_001166658)	promoter-TSS (NM_001166658)	-444	NM_001166658	631990	Mm.401324	NM_001166658	ENSMUSG00000090546	Cdr1	100039759|Cdr|Cdr34|EG631990|Gm2409|Gm7077	cerebellar degeneration related antigen 1	protein-coding
mm_35553.1	chr4	41517302	41517323	-	1	NA	promoter-TSS (NM_001048005)	promoter-TSS (NM_001048005)	21	NM_001048005	73721	Mm.45614	NM_028624	ENSMUSG00000028441	1110017D15Rik	Cbe1|Smrp1	RIKEN cDNA 1110017D15 gene	protein-coding
mm_66448.1	chr7	44868669	44868698	-	1	NA	intron (NM_133949, intron 1 of 11)	intron (NM_133949, intron 1 of 11)	1105	NM_133949	84113	Mm.42855	NM_133949	ENSMUSG00000038502	Ptov1	1110030G05Rik|AU041779|Gcap3	prostate tumor over expressed gene 1	protein-coding
mm_84257.1	chr9	62536771	62536832	-	1	NA	5' UTR (NM_175484, exon 1 of 12)	5' UTR (NM_175484, exon 1 of 12)	243	NM_175484	235431	Mm.335229	NM_175484	ENSMUSG00000041729	Coro2b	CLIPINC|E130012P22Rik	coronin, actin binding protein, 2B	protein-coding
mm_15174.1	chr2	154130368	154130374	+	1	NA	promoter-TSS (NM_028528)	promoter-TSS (NM_028528)	35	NM_028528	73388	Mm.71904	NM_028528	ENSMUSG00000027482	Bpifa3	1700058C13Rik|Splunc3	BPI fold containing family A, member 3	protein-coding
mm_41617.1	chr5	96824903	96824916	+	1	NA	exon (NM_013470, exon 7 of 13)	exon (NM_013470, exon 7 of 13)	31524	NM_013470	11745	Mm.7214	NM_013470	ENSMUSG00000029484	Anxa3	Anx3	annexin A3	protein-coding
mm_87001.1	chr10	26797933	26797962	+	1	NA	intron (NM_176837, intron 1 of 14)	intron (NM_176837, intron 1 of 14)	25435	NM_176837	73910	Mm.356496	NM_176837	ENSMUSG00000039031	Arhgap18	4833419J07Rik|AI314906|AI843501	Rho GTPase activating protein 18	protein-coding
mm_47654.1	chr5	125392947	125392955	-	1	NA	Intergenic	Intergenic	-2934	NM_019639	22190	Mm.331	NM_019639	ENSMUSG00000008348	Ubc	2700054O04Rik|AI194771|Rps27a|TI-225|Uba52|Ubb	ubiquitin C	protein-coding
mm_105832.1	chr11	113444690	113444716	-	1	NA	intron (NM_027216, intron 5 of 9)	intron (NM_027216, intron 5 of 9)	121112	NM_001166503	69806	Mm.341021	NM_027216	ENSMUSG00000041654	Slc39a11	1810074D23Rik	solute carrier family 39 (metal ion transporter), member 11	protein-coding
mm_42460.1	chr5	115436642	115436657	+	1	NA	intron (NM_008629, intron 6 of 14)	CpG	6964	NM_008629	17690	Mm.5077	NM_008629	ENSMUSG00000054256	Msi1	Msi1h|Musahi1|m-Msi-1	musashi RNA-binding protein 1	protein-coding
mm_110257.1	chr12	31654768	31654840	-	1	NA	promoter-TSS (NM_001163126)	promoter-TSS (NM_001163126)	22	NM_028002	71916	Mm.62979	NM_028002	ENSMUSG00000020648	Dus4l	2310069P03Rik|2700089B10Rik|AI482040|Pp35	dihydrouridine synthase 4-like (S. cerevisiae)	protein-coding
mm_167278.1	chr8	35209121	35209143	-	1	NA	Intergenic	MT2A|LTR|ERVL	-166609	NM_177741	244416	Mm.247126	NM_177741	ENSMUSG00000046794	Ppp1r3b	6430576E21|AW821953|GL|PTG	protein phosphatase 1, regulatory (inhibitor) subunit 3B	protein-coding
mm_63287.1	chr7	126795247	126795290	+	1	NA	TTS (NM_001177307)	TTS (NM_001177307)	-2797	NM_019674	56420	Mm.41998	NM_019674	ENSMUSG00000030697	Ppp4c	1110002D08Rik|AU016079|Ppx	protein phosphatase 4, catalytic subunit	protein-coding
mm_98939.1	chr11	98371975	98371985	+	1	NA	intron (NM_021547, intron 1 of 14)	intron (NM_021547, intron 1 of 14)	-11831	NM_011540	21393	Mm.10762	NM_011540	ENSMUSG00000007877	Tcap	AI503981|AJ223855	titin-cap	protein-coding
mm_166914.1	chr7	30394371	30394380	-	1	NA	Intergenic	Intergenic	-19413	NM_011662	22177	Mm.46301	NM_011662	ENSMUSG00000030579	Tyrobp	DAP12|KARAP|Ly83	TYRO protein tyrosine kinase binding protein	protein-coding
mm_94314.1	chr11	4223693	4223710	+	1	NA	Intergenic	Intergenic	5450	NM_028022	71962	Mm.7852	NM_028022	ENSMUSG00000020424	Gatsl3	2410008K03Rik	GATS protein-like 3	protein-coding
mm_80597.1	chr9	86467164	86467170	+	1	NA	promoter-TSS (NM_177208)	promoter-TSS (NM_177208)	13	NM_177208	320615	Mm.245500	NM_177208	ENSMUSG00000034973	Dopey1	B130005I07Rik|BC035275|C130028L17|D9Ertd809e	dopey family member 1	protein-coding
mm_108349.1	chr12	80480275	80480284	+	1	NA	intron (NM_133798, intron 2 of 8)	intron (NM_133798, intron 2 of 8)	17184	NM_133798	97827	Mm.206631	NM_133798	ENSMUSG00000032705	Exd2	4930539P14Rik|C85658|Exdl2	exonuclease 3'-5' domain containing 2	protein-coding
mm_24838.1	chr3	95659623	95659713	+	1	NA	intron (NM_008562, intron 1 of 2)	intron (NM_008562, intron 1 of 2)	947	NM_008562	17210	Mm.1639	NM_008562	ENSMUSG00000038612	Mcl1	AW556805|Mcl-1	myeloid cell leukemia sequence 1	protein-coding
mm_16805.1	chr2	10126204	10126285	-	1	NA	exon (NM_010582, exon 4 of 21)	exon (NM_010582, exon 4 of 21)	4439	NM_010582	16425	Mm.182043	NM_010582	ENSMUSG00000037254	Itih2	AI747202|Intin2|Itih-2	inter-alpha trypsin inhibitor, heavy chain 2	protein-coding
mm_90506.1	chr10	128039473	128039482	+	1	NA	exon (NM_001113199, exon 3 of 9)	exon (NM_001113199, exon 3 of 9)	4131	NM_001113199	17938	Mm.3746	NM_013608	ENSMUSG00000061315	Naca	AL022831|AL024382|Gm1878|mKIAA0363|skNAC	nascent polypeptide-associated complex alpha polypeptide	protein-coding
mm_70323.1	chr8	4253131	4253136	+	1	NA	promoter-TSS (NM_133968)	promoter-TSS (NM_133968)	31	NM_133968	102209	Mm.28452	NM_133968	ENSMUSG00000011837	Snapc2	0610007H10Rik|AU015675	small nuclear RNA activating complex, polypeptide 2	protein-coding
mm_49198.1	chr6	15197088	15197102	+	1	NA	exon (NM_001286607, exon 2 of 17)	exon (NM_001286607, exon 2 of 17)	11589	NM_001286607	114142	Mm.332919	NM_053242	ENSMUSG00000029563	Foxp2	2810043D05Rik|AI449000|CAG-16|D0Kist7	forkhead box P2	protein-coding
mm_43124.1	chr5	125071577	125071583	+	1	NA	intron (NM_011424, intron 14 of 46)	ORR1B1|LTR|ERVL-MaLR	68105	NM_028443	73121	Mm.296138	NM_028443	ENSMUSG00000037962	Rflna	3110032G18Rik|Fam101a|cfm|cfm2	refilin A	protein-coding
mm_38286.1	chr4	136890327	136890343	-	1	NA	exon (NM_007574, exon 3 of 3)	exon (NM_007574, exon 3 of 3)	2579	NM_007574	12262	Mm.439732	NM_007574	ENSMUSG00000036896	C1qc	AI385742|C1qg|Ciqc	complement component 1, q subcomponent, C chain	protein-coding
mm_50486.1	chr6	48988574	48988580	+	1	NA	exon (NM_172888, exon 1 of 5)	exon (NM_172888, exon 1 of 5)	1716	NM_172888	243377	Mm.446302	NM_172888	ENSMUSG00000039215	Svs1	9530003A11	seminal vesicle secretory protein 1	protein-coding
mm_106272.1	chr11	117987214	117987232	-	1	NA	intron (NM_133757, intron 1 of 9)	CpG	366	NM_133757	74451	Mm.28864	NM_133757	ENSMUSG00000017715	Pgs1	2610019F11Rik|4933424M23Rik|SAF	phosphatidylglycerophosphate synthase 1	protein-coding
mm_156956.1	chrX	169989010	169989025	+	1	NA	exon (NM_001290504, exon 10 of 10)	exon (NM_001290504, exon 10 of 10)	-10100	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_85020.1	chr9	88380245	88380262	-	1	NA	exon (NM_172926, exon 26 of 28)	exon (NM_172926, exon 26 of 28)	52644	NM_011851	23959	Mm.244235	NM_011851	ENSMUSG00000032420	Nt5e	2210401F01Rik|5'-NT|AI447961|CD73|NT|Nt5|eNT	5' nucleotidase, ecto	protein-coding
mm_83813.1	chr9	53610286	53610328	-	1	NA	promoter-TSS (NM_144784)	promoter-TSS (NM_144784)	43	NM_144784	110446	Mm.293233	NM_144784	ENSMUSG00000032047	Acat1	6330585C21Rik|Acat	acetyl-Coenzyme A acetyltransferase 1	protein-coding
mm_43865.1	chr5	143474667	143474701	+	1	NA	exon (NM_144915, exon 4 of 15)	exon (NM_144915, exon 4 of 15)	10191	NM_144915	231871	Mm.469963	NM_144915	ENSMUSG00000039206	Daglb	E330036I19Rik	diacylglycerol lipase, beta	protein-coding
mm_111963.1	chr12	109604416	109604420	-	1	NA	intron (NR_028261, intron 1 of 20)	intron (NR_028261, intron 1 of 20)	473	NR_028261	75745	Mm.293263	NR_028261		Rian	5530401N18Rik|C130089L09Rik|Meg8	RNA imprinted and accumulated in nucleus	ncRNA
mm_68377.1	chr7	109170045	109170064	-	1	NA	5' UTR (NM_057173, exon 1 of 4)	5' UTR (NM_057173, exon 1 of 4)	458	NM_001302206	109594	Mm.360145	NM_057173	ENSMUSG00000036111	Lmo1	Rbtn-1|Rbtn1|Ttg1	LIM domain only 1	protein-coding
mm_85118.1	chr9	95407768	95407779	-	1	NA	promoter-TSS (NM_018763)	promoter-TSS (NM_018763)	-503	NM_018763	54371	Mm.212446	NM_018763	ENSMUSG00000033350	Chst2	AI428561|AW121776|C130041E03Rik|Chts2|GST-2|GlcNAc6ST|Gn6st	carbohydrate sulfotransferase 2	protein-coding
mm_69517.1	chr7	135525300	135525305	-	1	NA	intron (NM_178669, intron 1 of 2)	ORR1E|LTR|ERVL-MaLR	3352	NM_178669	212070	Mm.39721	NM_178669	ENSMUSG00000050866	Clrn3	AI649392|Tmem12	clarin 3	protein-coding
mm_68533.1	chr7	113368544	113368549	-	1	NA	intron (NM_133700, intron 2 of 10)	intron (NM_133700, intron 2 of 10)	793	NM_133700	68815	Mm.238034	NM_133700	ENSMUSG00000038187	Btbd10	1110056N09Rik|Gmrp1	BTB (POZ) domain containing 10	protein-coding
mm_26181.1	chr3	138341934	138341938	+	1	NA	Intergenic	RMER15|LTR|ERVL	28650	NM_026945	69117	Mm.46265	NM_026945	ENSMUSG00000053054	Adh6a	1810009C16Rik|Adh5a	alcohol dehydrogenase 6A (class V)	protein-coding
mm_44609.1	chr5	25436345	25436347	-	1	NA	intron (NM_001081383, intron 2 of 58)	PB1D9|SINE|Alu	62437	NM_001081383	231051	Mm.332268	NM_001081383	ENSMUSG00000038056	Kmt2c	E330008K23Rik|HALR|Mll3|mKIAA1506	lysine (K)-specific methyltransferase 2C	protein-coding
mm_88530.1	chr10	78352544	78352548	+	1	NA	promoter-TSS (NM_053014)	promoter-TSS (NM_053014)	-846	NM_053014	28169	Mm.141230	NM_053014	ENSMUSG00000001211	Agpat3	AW061257|AW493985|D10Jhu12e|lpaat3	1-acylglycerol-3-phosphate O-acyltransferase 3	protein-coding
mm_45656.1	chr5	77095280	77095290	-	1	NA	promoter-TSS (NM_001159901)	promoter-TSS (NM_001159901)	-18	NM_001159900	74318	Mm.181852	NM_175606	ENSMUSG00000059325	Hopx	1110018K11Rik|1200015P04Rik|2300002F06Rik|AI848177|AW490897|Cameo|Hdop|Hod|Hop|Ob1|Obl|Toto	HOP homeobox	protein-coding
mm_170301.1	chr18	33394898	33394902	+	1	NA	Intergenic	L1Md_T|LINE|L1	68734	NM_001267717	27528	Mm.407415	NM_053078	ENSMUSG00000042834	Nrep	AI325076|D0H4S114|Harp|P311|PTZ17|SEZ17	neuronal regeneration related protein	protein-coding
mm_65165.1	chr7	19676783	19676800	-	1	NA	5' UTR (NM_001277944, exon 2 of 5)	5' UTR (NM_001277944, exon 2 of 5)	1150	NM_001277944	11813	Mm.28394	NM_001277944	ENSMUSG00000002992	Apoc2	apo-CII|apoC-II	apolipoprotein C-II	protein-coding
mm_172431.1	chr7	28961485	28961491	-	1	NA	intron (NM_021895, intron 1 of 20)	intron (NM_021895, intron 1 of 20)	792	NM_021895	60595	Mm.81144	NM_021895	ENSMUSG00000054808	Actn4	C77391	actinin alpha 4	protein-coding
mm_62258.1	chr7	99313394	99313423	+	1	NA	intron (NM_001048167, intron 1 of 2)	intron (NM_001048167, intron 1 of 2)	39831	NM_009825	12406	Mm.22708	NM_009825	ENSMUSG00000070436	Serpinh1	BERF-1|Cbp1|Cbp2|Hsp47|J6|Serpinh2|gp46	serine (or cysteine) peptidase inhibitor, clade H, member 1	protein-coding
mm_122429.1	chr14	44989903	44989926	-	1	NA	intron (NM_008964, intron 1 of 1)	intron (NM_008964, intron 1 of 1)	1803	NM_008964	19217	Mm.4630	NM_008964	ENSMUSG00000037759	Ptger2	EP2|Ptgerep2	prostaglandin E receptor 2 (subtype EP2)	protein-coding
mm_165918.1	chr4	59035251	59035261	+	1	NA	promoter-TSS (NM_025277)	promoter-TSS (NM_025277)	100	NM_025277	14700	Mm.41780	NM_025277	ENSMUSG00000038607	Gng10	AV006524	guanine nucleotide binding protein (G protein), gamma 10	protein-coding
mm_23892.1	chr3	83031494	83031550	+	1	NA	exon (NM_010196, exon 5 of 5)	exon (NM_010196, exon 5 of 5)	5369	NM_001111048	14161	Mm.88793	NM_010196	ENSMUSG00000028001	Fga	ENSMUSG00000059807|Fib	fibrinogen alpha chain	protein-coding
mm_73767.1	chr8	115715920	115715924	+	1	NA	Intergenic	Intergenic	-9028	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_119881.1	chr14	54892493	54892500	+	1	NA	Intergenic	B1_Mur1|SINE|Alu	-1647	NM_019402	54196	Mm.7723	NM_019402	ENSMUSG00000022194	Pabpn1	PAB2|Pabp3|mPABII	poly(A) binding protein, nuclear 1	protein-coding
mm_47400.1	chr5	123128513	123128523	-	1	NA	intron (NM_175092, intron 2 of 4)	intron (NM_175092, intron 2 of 4)	4111	NM_175092	23912	Mm.253876	NM_175092	ENSMUSG00000029449	Rhof	AI845056|AV026554|Arhf|Ifld1|Rif	ras homolog family member F (in filopodia)	protein-coding
mm_317.1	chr1	24678353	24678381	+	1	NA	promoter-TSS (NM_026719)	promoter-TSS (NM_026719)	-177	NM_026719	68421	Mm.336563	NM_026719	ENSMUSG00000073725	Lmbrd1	0910001K20Rik|AV347960	LMBR1 domain containing 1	protein-coding
mm_30948.1	chr4	33132504	33132513	+	1	NA	promoter-TSS (NM_008075)	promoter-TSS (NM_008075)	-48	NM_008075	14408	Mm.14116	NM_008075	ENSMUSG00000028280	Gabrr1	GABA-C	gamma-aminobutyric acid (GABA) C receptor, subunit rho 1	protein-coding
mm_151709.1	chr19	4615454	4615512	-	1	NA	5' UTR (NM_153388, exon 1 of 3)	5' UTR (NM_153388, exon 1 of 3)	184	NM_153388	225875	Mm.329675	NM_153388	ENSMUSG00000045045	Lrfn4	BC023156|Salm3	leucine rich repeat and fibronectin type III domain containing 4	protein-coding
mm_105030.1	chr11	100494163	100494175	-	1	NA	intron (NM_001199296, intron 17 of 28)	intron (NM_001199296, intron 17 of 28)	-15689	NR_130343	102465671		NR_130343	ENSMUSG00000104854	Mir7116	mmu-mir-7116	microRNA 7116	ncRNA
mm_40959.1	chr5	76951628	76951638	+	1	NA	promoter-TSS (NM_172146)	promoter-TSS (NM_172146)	-55	NM_172146	231327	Mm.202337	NM_172146	ENSMUSG00000029246	Ppat	5730454C12Rik|AA408689|AA675351|AI507113|C79945	phosphoribosyl pyrophosphate amidotransferase	protein-coding
mm_146360.1	chr18	82584251	82584272	+	1	NA	3' UTR (NM_010777, exon 7 of 7)	3' UTR (NM_010777, exon 7 of 7)	29753	NM_001025254	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_131349.1	chr16	13671981	13672032	+	1	NA	5' UTR (NM_001177552, exon 1 of 6)	5' UTR (NM_001177552, exon 1 of 6)	148	NM_025653	67118	Mm.223689	NM_025653	ENSMUSG00000022684	Bfar	3010001A07Rik|3110001I22Rik|AI666707|AW107665|Bar|Rnf47	bifunctional apoptosis regulator	protein-coding
mm_36582.1	chr4	88033278	88033288	-	1	NA	5' UTR (NM_027326, exon 1 of 11)	5' UTR (NM_027326, exon 1 of 11)	124	NM_027326	70122	Mm.288898	NM_027326	ENSMUSG00000028496	Mllt3	2210011H10Rik|2610012I03Rik|3830408D16Rik|Af9|D4Ertd321e	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 3	protein-coding
mm_164049.1	chr14	102225547	102225548	+	1	NA	Intergenic	Intergenic	384924	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_139829.1	chr17	69075700	69075745	+	1	NA	Intergenic	CpG	-81088	NM_013813	13823	Mm.131135	NM_013813	ENSMUSG00000024044	Epb41l3	4.1B|DAL1P|Dal1|Epb4.1l3|NBL3	erythrocyte membrane protein band 4.1 like 3	protein-coding
mm_52352.1	chr6	112459624	112459639	+	1	NA	5' UTR (NM_007617, exon 1 of 2)	5' UTR (NM_007617, exon 1 of 2)	126	NM_007617	12391	Mm.3924	NM_007617	ENSMUSG00000062694	Cav3	AI385751|Cav-3|M-cav	caveolin 3	protein-coding
mm_145305.1	chr18	53463499	53463519	+	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	-1037	NM_001033281	225518	Mm.297645	NM_001033281	ENSMUSG00000069378	Prdm6	Gm92|PRISM	PR domain containing 6	protein-coding
mm_59584.1	chr7	28129513	28129513	+	1	NA	promoter-TSS (NM_001164655)	promoter-TSS (NM_001164655)	47	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_26812.1	chr3	10208570	10208586	-	1	NA	promoter-TSS (NM_024406)	promoter-TSS (NM_024406)	-2	NM_024406	11770	Mm.582	NM_024406	ENSMUSG00000062515	Fabp4	422/aP2|ALBP/Ap2|Ap2|Lbpl	fatty acid binding protein 4, adipocyte	protein-coding
mm_140945.1	chr17	24514978	24515013	-	1	NA	intron (NM_153792, intron 4 of 20)	intron (NM_153792, intron 4 of 20)	12943	NM_153792	224619	Mm.275150	NM_153792	ENSMUSG00000052752	Traf7	RFWD1	TNF receptor-associated factor 7	protein-coding
mm_7618.1	chr1	126830429	126830437	-	1	NA	5' UTR (NM_176957, exon 1 of 13)	5' UTR (NM_176957, exon 1 of 13)	199	NM_001081756	210356	Mm.377234	NM_172484	ENSMUSG00000049690	Nckap5	8430408F21|D130011D22Rik|E030049G20Rik|Erih1|Erih2|Gm1548|Nap5	NCK-associated protein 5	protein-coding
mm_107500.1	chr12	38861028	38861066	+	1	NA	intron (NM_001347379, intron 10 of 11)	intron (NM_001347379, intron 10 of 11)	77336	NM_001163154	14009	Mm.4866	NM_007960	ENSMUSG00000004151	Etv1	ER81|Etsrp81	ets variant 1	protein-coding
mm_99998.1	chr11	114851123	114851140	+	1	NA	promoter-TSS (NM_147217)	promoter-TSS (NM_147217)	-401	NM_001110337	70355	Mm.242413	NM_147217	ENSMUSG00000051043	Gprc5c	1110028I06Rik|3200002M13Rik|Raig3	G protein-coupled receptor, family C, group 5, member C	protein-coding
mm_169500.1	chr1	47658695	47658710	+	1	NA	Intergenic	Intergenic	-191577	NR_105768	102466969		NR_105768	ENSMUSG00000098876	Mir6350	Gm27958|mmu-mir-6350	microRNA 6350	ncRNA
mm_53800.1	chr6	146796074	146796091	+	1	NA	Intergenic	CpG	-9448	NM_172309	272322	Mm.333500	NM_172309	ENSMUSG00000040187	Arntl2	4632430A05Rik|BMAL2|CLIF|MOP9|bHLHe6	aryl hydrocarbon receptor nuclear translocator-like 2	protein-coding
mm_126999.1	chr15	95790861	95790874	+	1	NA	promoter-TSS (NM_001253813)	promoter-TSS (NM_001253813)	24	NM_001253813	105722	Mm.38087	NM_175344	ENSMUSG00000064210	Ano6	2900059G15Rik|AA407480|AW554778|F730003B03Rik|Tmem16f	anoctamin 6	protein-coding
mm_15417.1	chr2	156840154	156840164	+	1	NA	5' UTR (NM_001291124, exon 1 of 4)	5' UTR (NM_001291124, exon 1 of 4)	152	NM_173396	228839	Mm.315625	NM_173396	ENSMUSG00000062175	Tgif2	4921501K24|5730599O09Rik|C80753|C81206	TGFB-induced factor homeobox 2	protein-coding
mm_17913.1	chr2	35367731	35367737	-	1	NA	promoter-TSS (NM_029463)	promoter-TSS (NM_029463)	-5	NM_029463	75859	Mm.159604	NM_029463	ENSMUSG00000026882	4930568D16Rik	Ggta1l1	RIKEN cDNA 4930568D16 gene	protein-coding
mm_102562.1	chr11	61469388	61469392	-	1	NA	Intergenic	Intergenic	-15398	NM_001291024	22671	Mm.89201	NM_009548	ENSMUSG00000010086	Rnf112	ZNF179|Zfp179|bfp|neurolastin	ring finger protein 112	protein-coding
mm_105687.1	chr11	107733944	107733971	-	1	NA	TTS (NM_019431)	TTS (NM_019431)	-17481	NM_007582	12299	Mm.57093	NM_007582	ENSMUSG00000020722	Cacng1	-	calcium channel, voltage-dependent, gamma subunit 1	protein-coding
mm_142804.1	chr17	50455877	50455918	-	1	NA	Intergenic	Intergenic	-53650	NM_013880	224860	Mm.217362	NM_013880	ENSMUSG00000038910	Plcl2	PLC-L2|PRIP-2|Plce2|mKIAA1092	phospholipase C-like 2	protein-coding
mm_154083.1	chr19	56663656	56663697	-	1	NA	Intergenic	Intergenic	-58696	NM_007419	11554	Mm.46797	NM_007419	ENSMUSG00000035283	Adrb1	Adrb-1|beta-AR	adrenergic receptor, beta 1	protein-coding
mm_32728.1	chr4	116557669	116557724	+	1	NA	promoter-TSS (NM_029868)	promoter-TSS (NM_029868)	-31	NM_029868	77110	Mm.41715	NM_029868	ENSMUSG00000034042	Gpbp1l1	5330440M15Rik|BC002292	GC-rich promoter binding protein 1-like 1	protein-coding
mm_41332.1	chr5	90492689	90492718	+	1	NA	exon (NM_007423, exon 3 of 15)	exon (NM_007423, exon 3 of 15)	1989	NM_007423	11576	Mm.358570	NM_007423	ENSMUSG00000054932	Afp	-	alpha fetoprotein	protein-coding
mm_37383.1	chr4	120980090	120980102	-	1	NA	intron (NM_133716, intron 4 of 9)	B3A|SINE|B2	-6774	NR_105982	102465614		NR_105982	ENSMUSG00000106436	Mir7015	mmu-mir-7015	microRNA 7015	ncRNA
mm_138141.1	chr17	34200708	34200729	+	1	NA	exon (NM_010724, exon 5 of 6)	exon (NM_010724, exon 5 of 6)	2523	NM_010724	16913	Mm.180191	NM_010724	ENSMUSG00000024338	Psmb8	Lmp-7|Lmp7	proteasome (prosome, macropain) subunit, beta type 8 (large multifunctional peptidase 7)	protein-coding
mm_26913.1	chr3	20122474	20122478	-	1	NA	3' UTR (NM_013755, exon 7 of 7)	3' UTR (NM_013755, exon 7 of 7)	32640	NM_013755	27357	Mm.6375	NM_013755	ENSMUSG00000019528	Gyg	AU017667|Gyg1	glycogenin	protein-coding
mm_62264.1	chr7	99478882	99478916	+	1	NA	TTS (NR_002173)	TTS (NR_002173)	808	NR_002173	449631	Mm.236868	NR_002173	ENSMUSG00000064966	Snord15b	Gm5775|Rnu15-b|Rnu15b|U15B	small nucleolar RNA, C/D box 14B	snoRNA
mm_111374.1	chr12	87260695	87260708	-	1	NA	exon (NM_001142580, exon 3 of 20)	exon (NM_001142580, exon 3 of 20)	3543	NM_134044	104799	Mm.208750	NM_134044	ENSMUSG00000021038	Vipas39	6720456H09Rik|9330175H22Rik|AI413782|SPE-39|Spe39|Vipar|hSPE-39	VPS33B interacting protein, apical-basolateral polarity regulator, spe-39 homolog	protein-coding
mm_13277.1	chr2	101581552	101581593	+	1	NA	intron (NM_026592, intron 5 of 6)	intron (NM_026592, intron 5 of 6)	-43176	NM_009020	19374	Mm.4988	NM_009020	ENSMUSG00000032864	Rag2	Rag-2	recombination activating gene 2	protein-coding
mm_96149.1	chr11	61142458	61142471	+	1	NA	intron (NM_021349, intron 2 of 3)	intron (NM_021349, intron 2 of 3)	1629	NM_021349	57916	Mm.265915	NM_021349	ENSMUSG00000010142	Tnfrsf13b	1200009E08Rik|Taci	tumor necrosis factor receptor superfamily, member 13b	protein-coding
mm_145970.1	chr18	67933288	67933307	+	1	NA	promoter-TSS (NM_172631)	promoter-TSS (NM_172631)	40	NM_172631	52662	Mm.440183	NM_172631	ENSMUSG00000024544	Ldlrad4	8230401C20Rik|A430083H02|A430108L08Rik|C18orf1|D18Ertd653e|D330030L18Rik	low density lipoprotein receptor class A domain containing 4	protein-coding
mm_128432.1	chr15	50682467	50682485	-	1	NA	intron (NM_001310481, intron 4 of 5)	intron (NM_001310481, intron 4 of 5)	206573	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_16758.1	chr2	9869804	9869827	-	1	NA	intron (NM_008091, intron 3 of 5)	intron (NM_008091, intron 3 of 5)	8785	NM_008091	14462	Mm.313866	NM_008091	ENSMUSG00000015619	Gata3	Gata-3|jal	GATA binding protein 3	protein-coding
mm_41430.1	chr5	90903688	90903709	+	1	NA	promoter-TSS (NM_009140)	promoter-TSS (NM_009140)	-201	NM_009140	20310	Mm.4979	NM_009140	ENSMUSG00000058427	Cxcl2	CINC-2a|GROb|Gro2|MIP-2|MIP-2a|Mgsa-b|Mip2|Scyb|Scyb2	chemokine (C-X-C motif) ligand 2	protein-coding
mm_73961.1	chr8	120487653	120487666	+	1	NA	Intergenic	CpG	-1207	NM_198671	382034	Mm.334856	NM_198671	ENSMUSG00000031822	Gse1	2210013I18Rik|mKIAA0182	genetic suppressor element 1, coiled-coil protein	protein-coding
mm_76025.1	chr8	75098834	75098848	-	1	NA	exon (NM_010442, exon 4 of 5)	exon (NM_010442, exon 4 of 5)	5223	NM_010442	15368	Mm.276389	NM_010442	ENSMUSG00000005413	Hmox1	D8Wsu38e|HO-1|HO1|Hemox|Hmox|Hsp32	heme oxygenase 1	protein-coding
mm_16846.1	chr2	11535520	11535557	-	1	NA	intron (NM_001177758, intron 1 of 14)	CpG	18391	NM_001177758	170768	Mm.19669	NM_133232	ENSMUSG00000026773	Pfkfb3	E330010H22Rik|iPFK-2|uPFK-2	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	protein-coding
mm_171680.1	chr4	54447814	54447815	-	1	NA	Intergenic	L1Md_F2|LINE|L1	-500131	NM_172867	242466	Mm.102904	NM_172867	ENSMUSG00000060206	Zfp462	6030417H05|9430078C22Rik|Gt4-2|Zfpip	zinc finger protein 462	protein-coding
mm_164430.1	chr16	46120259	46120261	-	1	NA	promoter-TSS (NM_032465)	promoter-TSS (NM_032465)	-12	NM_032465	84544	Mm.29204	NM_032465	ENSMUSG00000022657	Cd96	1700109I12Rik|Tactile	CD96 antigen	protein-coding
mm_66391.1	chr7	44236099	44236124	-	1	NA	promoter-TSS (NR_029436)	promoter-TSS (NR_029436)	11	NR_029436	70004	Mm.158317	NR_029436	ENSMUSG00000038782	1700028J19Rik	-	RIKEN cDNA 1700028J19 gene	ncRNA
mm_137509.1	chr17	27038135	27038136	+	1	NA	Intergenic	Intergenic	8876	NM_027544	70772	Mm.440437	NM_027544	ENSMUSG00000048731	Ggnbp1	0610031G08Rik|mdf	gametogenetin binding protein 1	protein-coding
mm_164651.1	chr17	35649731	35649735	+	1	NA	promoter-TSS (NM_001163194)	promoter-TSS (NM_001163194)	25	NM_001163194	433102	Mm.136760	NM_001163194	ENSMUSG00000090509	Sfta2	EG433102	surfactant associated 2	protein-coding
mm_40779.1	chr5	67287442	67287446	+	1	NA	3' UTR (NM_030108, exon 9 of 9)	3' UTR (NM_030108, exon 9 of 9)	-19511	NM_178651	109108	Mm.234455	NM_178651	ENSMUSG00000029221	Slc30a9	2310024J23Rik|AL024256|GAC63|HUEL|znT-9	solute carrier family 30 (zinc transporter), member 9	protein-coding
mm_159375.1	chr3	89387649	89387649	-	1	NA	intron (NM_009565, intron 1 of 2)	intron (NM_009565, intron 1 of 2)	-4215	NR_040403	545539	Mm.393389	NR_040403	ENSMUSG00000074466	Gm15417	ENSMUSG00000074466|OTTMUSG00000021274	predicted gene 15417	ncRNA
mm_3428.1	chr1	150100094	150100106	+	1	NA	promoter-TSS (NM_011198)	promoter-TSS (NM_011198)	69	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_89626.1	chr10	96280570	96280583	+	1	NA	Intergenic	Intergenic	54369	NR_110448	74881	Mm.410819	NR_110448		4930459C07Rik	-	RIKEN cDNA 4930459C07 gene	ncRNA
mm_47152.1	chr5	120606971	120606991	-	1	NA	exon (NM_029408, exon 5 of 5)	exon (NM_029408, exon 5 of 5)	5608	NM_029096	100764	Mm.9654	NM_029096	ENSMUSG00000029600	Rita1	1110008J03Rik|AI853657|C86297|Rita	RBPJ interacting and tubulin associated 1	protein-coding
mm_63748.1	chr7	131032062	131032074	+	1	NA	promoter-TSS (NM_007769)	promoter-TSS (NM_007769)	-8	NM_001347632	12945	Mm.4138	NM_007769	ENSMUSG00000047517	Dmbt1	CRP|CRP-[a]|CRP-[b]|Crpd|DBMT1|gp300|p80	deleted in malignant brain tumors 1	protein-coding
mm_87578.1	chr10	56389466	56389479	+	1	NA	3' UTR (NM_010288, exon 2 of 2)	3' UTR (NM_010288, exon 2 of 2)	12172	NM_010288	14609	Mm.378921	NM_010288	ENSMUSG00000050953	Gja1	AU042049|AW546267|Cnx43|Cx43|Cx43alpha1|Gja-1|Npm1|connexin43	gap junction protein, alpha 1	protein-coding
mm_49721.1	chr6	34598596	34598606	+	1	NA	promoter-TSS (NM_001347100)	promoter-TSS (NM_001347100)	97	NM_001347100	109624	Mm.308134	NM_145575	ENSMUSG00000029761	Cald1	4833423D12Rik|AI195384|AV071549|AW536160|C920027I18Rik	caldesmon 1	protein-coding
mm_122983.1	chr14	54983771	54983791	-	1	NA	exon (NM_080728, exon 24 of 41)	exon (NM_080728, exon 24 of 41)	-8005	NR_030607	100124433		NR_030607	ENSMUSG00000077928	Mir208b	Mirn208b|mir-208b	microRNA 208b	ncRNA
mm_129864.1	chr15	83367007	83367016	-	1	NA	non-coding (NR_027980, exon 1 of 4)	non-coding (NR_027980, exon 1 of 4)	286	NR_027980	69291	Mm.66794	NM_001033147		1700001L05Rik	-	RIKEN cDNA 1700001L05 gene	ncRNA
mm_136589.1	chr17	4995665	4995693	+	1	NA	exon (NM_001085355, exon 1 of 20)	exon (NM_001085355, exon 1 of 20)	605	NM_001085355	239985	Mm.133401	NM_001085355	ENSMUSG00000069729	Arid1b	8030481M12|9330189K18Rik|AI836955|Ardi1b|B230217J03Rik|mKIAA1235	AT rich interactive domain 1B (SWI-like)	protein-coding
mm_150383.1	chr19	36348318	36348353	+	1	NA	Intergenic	(CCG)n|Simple_repeat|Simple_repeat	-30732	NM_029508	76073	Mm.259180	NM_029508	ENSMUSG00000024805	Pcgf5	0610009F02Rik|1110054A01Rik|5830406C17Rik|5830443C21Rik|9530023M17Rik|AI324127	polycomb group ring finger 5	protein-coding
mm_138801.1	chr17	37997329	37997330	+	1	NA	Intergenic	Intergenic	-44307	NM_001011829	258094	Mm.377348	NM_001011829	ENSMUSG00000109376	Olfr761	MOR218-12|MOR218-5P|MOR218-6P|Olfr1552-ps1	olfactory receptor 761	protein-coding
mm_38388.1	chr4	138819132	138819149	-	1	NA	5' UTR (NM_011110, exon 1 of 5)	5' UTR (NM_011110, exon 1 of 5)	117	NM_011110	18784	Mm.486532	NM_011110	ENSMUSG00000041193	Pla2g5	PLA2|sPLA2	phospholipase A2, group V	protein-coding
mm_159933.1	chr6	71399315	71399315	-	1	NA	intron (NM_024288, intron 4 of 8)	intron (NM_024288, intron 4 of 8)	25888	NM_001081110	12525	Mm.1858	NM_009857	ENSMUSG00000053977	Cd8a	BB154331|Ly-2|Ly-35|Ly-B|Lyt-2	CD8 antigen, alpha chain	protein-coding
mm_9931.1	chr1	189922253	189922327	-	1	NA	promoter-TSS (NM_026796)	promoter-TSS (NM_026796)	-2	NM_026796	226830	Mm.156895	NM_026796	ENSMUSG00000026603	Smyd2	1110020E07Rik|4930402C15|KMT3C|Zmynd14	SET and MYND domain containing 2	protein-coding
mm_121469.1	chr14	120911165	120911173	+	1	NA	promoter-TSS (NM_023579)	promoter-TSS (NM_023579)	-25	NM_023579	70572	Mm.221452	NM_023579	ENSMUSG00000030662	Ipo5	1110011C18Rik|5730478E03Rik|AA409333|C76941|IMB3|Kpnb3|Ranbp5	importin 5	protein-coding
mm_151236.1	chr19	53793398	53793411	+	1	NA	intron (NM_001170847, intron 1 of 13)	intron (NM_001170847, intron 1 of 13)	-98827	NM_011050	18569	Mm.1605	NM_011050	ENSMUSG00000024975	Pdcd4	D19Ucla1|Ma3|Tis	programmed cell death 4	protein-coding
mm_45647.1	chr5	76974594	76974636	-	1	NA	promoter-TSS (NM_025691)	promoter-TSS (NM_025691)	-86	NM_025691	66661	Mm.296976	NM_025691	ENSMUSG00000036323	Srp72	5730576P14Rik|72kDa|AI132477|BC019196|C77589	signal recognition particle 72	protein-coding
mm_11564.1	chr2	32876137	32876241	+	1	NA	promoter-TSS (NM_146119)	promoter-TSS (NM_146119)	55	NM_146119	227737	Mm.301646	NM_146119	ENSMUSG00000026796	Fam129b	9130404D14Rik	family with sequence similarity 129, member B	protein-coding
mm_52256.1	chr6	107530138	107530196	+	1	NA	5' UTR (NM_008516, exon 1 of 2)	5' UTR (NM_008516, exon 1 of 2)	441	NM_008516	16979	Mm.428543	NM_008516	ENSMUSG00000034648	Lrrn1	2810047E21Rik|NLRR-1	leucine rich repeat protein 1, neuronal	protein-coding
mm_60478.1	chr7	44478349	44478355	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-6165	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_133642.1	chr16	91738930	91738963	+	1	NA	intron (NM_001110275, intron 1 of 28)	intron (NM_001110275, intron 1 of 28)	9575	NM_010587	16443	Mm.40546	NM_010587	ENSMUSG00000022957	Itsn1	AA517634|AA545208|AI316805|AI839402|AI848451|Ehsh1|Ese1|Itsn|Sh3p17	intersectin 1 (SH3 domain protein 1A)	protein-coding
mm_155474.1	chrX	73640371	73640377	+	1	NA	exon (NM_029352, exon 2 of 4)	exon (NM_029352, exon 2 of 4)	933	NM_029352	75590	Mm.16479	NM_029352	ENSMUSG00000031383	Dusp9	Dusp4|Mpk4|Pyst3	dual specificity phosphatase 9	protein-coding
mm_72959.1	chr8	92827274	92827395	+	1	NA	promoter-TSS (NM_008610)	promoter-TSS (NM_008610)	37	NM_008610	17390	Mm.29564	NM_008610	ENSMUSG00000031740	Mmp2	Clg4a|GelA|MMP-2	matrix metallopeptidase 2	protein-coding
mm_17557.1	chr2	30124775	30124807	-	1	NA	promoter-TSS (NM_178694)	promoter-TSS (NM_178694)	-180	NM_001290503	227693	Mm.44526	NM_178694	ENSMUSG00000039686	Zer1	C230075L19Rik|Zyg11bl	zyg-11 related, cell cycle regulator	protein-coding
mm_89263.1	chr10	87859594	87859612	+	1	NA	intron (NM_001314010, intron 2 of 4)	intron (NM_001314010, intron 2 of 4)	551	NM_010512	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_162058.1	chrX	8803913	8803913	+	1	NA	intron (NM_199319, intron 1 of 6)	intron (NM_199319, intron 1 of 6)	222	NM_199319	387586	Mm.227643	NM_199319	ENSMUSG00000071816	Ssxb5	-	synovial sarcoma, X member B5	protein-coding
mm_136438.1	chr16	94526397	94526451	-	1	NA	5' UTR (NM_007834, exon 1 of 8)	5' UTR (NM_007834, exon 1 of 8)	205	NM_007834	13185	Mm.7472	NM_007834	ENSMUSG00000022898	Dscr3	AW538125|Dcra	Down syndrome critical region gene 3	protein-coding
mm_99084.1	chr11	99417223	99417268	+	1	NA	intron (NM_010661, intron 6 of 7)	intron (NM_010661, intron 6 of 7)	5014	NM_010661	268482	Mm.436651	NM_010661	ENSMUSG00000020912	Krt12	AI835216|K12|Krt-12|Krt1-12	keratin 12	protein-coding
mm_48915.1	chr6	4004041	4004057	+	1	NA	promoter-TSS (NM_025331)	promoter-TSS (NM_025331)	62	NM_025331	66066	Mm.25547	NM_025331	ENSMUSG00000032766	Gng11	0610037B21Rik	guanine nucleotide binding protein (G protein), gamma 11	protein-coding
mm_148105.1	chr18	74065658	74065681	-	1	NA	promoter-TSS (NM_172632)	promoter-TSS (NM_172632)	-720	NM_172632	225724	Mm.254517	NM_172632	ENSMUSG00000024558	Mapk4	A330097D03Rik|Erk3|Prkm4|p63Mapk	mitogen-activated protein kinase 4	protein-coding
mm_81844.1	chr9	118538876	118538905	+	1	NA	exon (NM_018748, exon 11 of 24)	exon (NM_018748, exon 11 of 24)	32572	NM_018748	54214	Mm.10409	NM_018748	ENSMUSG00000038708	Golga4	AI225887|AU019508|Olp-1	golgi autoantigen, golgin subfamily a, 4	protein-coding
mm_106662.1	chr11	121333574	121333577	-	1	NA	intron (NM_025793, intron 6 of 9)	intron (NM_025793, intron 6 of 9)	20872	NM_025793	66840	Mm.103986	NM_025793	ENSMUSG00000025173	Wdr45b	0610008N23Rik|AA408735|D16Bwg0193e|WIPI-3|Wdr45l	WD repeat domain 45B	protein-coding
mm_170570.1	chr19	51142566	51142581	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-463927	NM_001290356	58178	Mm.313672	NM_021377	ENSMUSG00000043531	Sorcs1	Sorcs|mSorCS	sortilin-related VPS10 domain containing receptor 1	protein-coding
mm_156782.1	chrX	161717462	161717496	+	1	NA	promoter-TSS (NM_198409)	promoter-TSS (NM_198409)	-74	NM_198409	24004	Mm.328503	NM_198409	ENSMUSG00000043518	Rai2	3f8	retinoic acid induced 2	protein-coding
mm_17816.1	chr2	33733361	33733380	-	1	NA	3' UTR (NM_175184, exon 10 of 10)	3' UTR (NM_175184, exon 10 of 10)	-72446	NR_045729	320482	Mm.442057	NR_045729	ENSMUSG00000086484	Nron	A630071L07Rik|Gm24353	non-protein coding RNA, repressor of NFAT	ncRNA
mm_46121.1	chr5	92435220	92435235	-	1	NA	promoter-TSS (NM_183392)	promoter-TSS (NM_183392)	-28	NM_183392	269113	Mm.275289	NM_183392	ENSMUSG00000034826	Nup54	3110079L04Rik|54kDa	nucleoporin 54	protein-coding
mm_88692.1	chr10	80121940	80121950	+	1	NA	intron (NR_126043, intron 1 of 10)	intron (NR_126043, intron 1 of 10)	6142	NM_001301854	20869	Mm.44231	NM_011492	ENSMUSG00000003068	Stk11	AA408040|Lkb1|Par-4|R75140	serine/threonine kinase 11	protein-coding
mm_114558.1	chr13	74208760	74208795	+	1	NA	promoter-TSS (NM_177333)	promoter-TSS (NM_177333)	-77	NM_177333	211446	Mm.261859	NM_177333	ENSMUSG00000034152	Exoc3	2810050O03Rik|E430013E20Rik|Sec6|Sec6l1	exocyst complex component 3	protein-coding
mm_138781.1	chr17	37270262	37270278	+	1	NA	promoter-TSS (NM_013819)	promoter-TSS (NM_013819)	36	NM_013819	14991	Mm.14437	NM_013819	ENSMUSG00000016206	H2-M3	H-2M3|Hmt|M3a|MuprM3|MuprM301|MuprM302|R4B2	histocompatibility 2, M region locus 3	protein-coding
mm_48589.1	chr5	143894987	143894993	-	1	NA	promoter-TSS (NM_001310772)	promoter-TSS (NM_001310772)	77	NM_025732	66729	Mm.439817	NM_025732	ENSMUSG00000029607	Ankrd61	4921520G13Rik	ankyrin repeat domain 61	protein-coding
mm_140084.1	chr17	75435864	75435885	+	1	NA	promoter-TSS (NM_001166493)	promoter-TSS (NM_001166493)	-31	NM_001166493	240168	Mm.329203	NM_207246	ENSMUSG00000071042	Rasgrp3	BC066069|Gm327	RAS, guanyl releasing protein 3	protein-coding
mm_5349.1	chr1	25165154	25165158	-	1	NA	intron (NM_175642, intron 19 of 30)	intron (NM_175642, intron 19 of 30)	112798	NM_001204913	100504323	Mm.484176	NM_001204913		Gm20172	-	predicted gene, 20172	protein-coding
mm_154015.1	chr19	53199141	53199145	-	1	NA	intron (NM_013758, intron 1 of 15)	intron (NM_013758, intron 1 of 15)	55146	NM_013758	27360	Mm.426080	NM_013758	ENSMUSG00000025026	Add3	AI463285|R75380	adducin 3 (gamma)	protein-coding
mm_159839.1	chr5	134456679	134456679	-	1	NA	promoter-TSS (NM_001081464)	promoter-TSS (NM_001081464)	37	NM_001081468	57080	Mm.332735	NM_020331	ENSMUSG00000023079	Gtf2ird1	1700012P16Rik|BEN|Cream1|ESTM9|GTF3|Gtf2il|MusTRD1|Tg(Alb1-Myc)166.8Sst|WBSCR11|X83320	general transcription factor II I repeat domain-containing 1	protein-coding
mm_138400.1	chr17	35059042	35059130	+	1	NA	promoter-TSS (NM_016765)	promoter-TSS (NM_016765)	51	NM_016765	51793	Mm.1457	NM_016765	ENSMUSG00000007039	Ddah2	1110003M04Rik|AU019324|AW413173|DDAH-2|DDAHII|Ddah|G6a|NG30	dimethylarginine dimethylaminohydrolase 2	protein-coding
mm_29815.1	chr3	127896248	127896270	-	1	NA	promoter-TSS (NM_027482)	promoter-TSS (NM_027482)	64	NM_027482	70617	Mm.317049	NM_027482	ENSMUSG00000050549	5730508B09Rik	2700063A17Rik|C80506	RIKEN cDNA 5730508B09 gene	protein-coding
mm_136221.1	chr16	90138267	90138313	-	1	NA	Intergenic	Intergenic	-3947	NR_033476	100038709	Mm.484070	NR_033476		Gm10789	ENSMUSG00000074924	predicted gene 10789	ncRNA
mm_37133.1	chr4	116807533	116807573	-	1	NA	promoter-TSS (NM_026654)	promoter-TSS (NM_026654)	6	NM_026654	68276	Mm.30534	NM_026654	ENSMUSG00000028688	Toe1	4930584N22Rik|4933424D16Rik|AI413517	target of EGR1, member 1 (nuclear)	protein-coding
mm_60571.1	chr7	44481545	44481555	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-2967	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_103670.1	chr11	79140088	79140091	-	1	NA	intron (NM_013571, intron 1 of 17)	intron (NM_013571, intron 1 of 17)	6265	NM_013571	16706	Mm.4745	NM_013571	ENSMUSG00000018334	Ksr1	AW492498|B-KSR1|D11Bhm183e|D11Bhm184e|Ksr|RSU2|hb	kinase suppressor of ras 1	protein-coding
mm_49300.1	chr6	17743595	17743613	+	1	NA	promoter-TSS (NM_001289629)	promoter-TSS (NM_001289629)	12	NM_001289627	64213	Mm.12051	NM_022332	ENSMUSG00000029534	St7	9430001H04Rik|Fam4a2|HELG|RAY1|SEN4|TSG7	suppression of tumorigenicity 7	protein-coding
mm_104533.1	chr11	96306902	96306915	-	1	NA	promoter-TSS (NR_131758)	promoter-TSS (NR_131758)	2	NR_131758	75395	Mm.440014	NR_131758	ENSMUSG00000085645	Hoxb5os	0610040B09Rik|AV302770|Hoxb5/6as	homeobox B5 and homeobox B6, opposite strand	ncRNA
mm_123560.1	chr14	66868422	66868432	-	1	NA	promoter-TSS (NM_001034881)	promoter-TSS (NM_001034881)	173	NM_009955	12934	Mm.352648	NM_009955	ENSMUSG00000022048	Dpysl2	AI851130|Crmp2|DRP2|Musunc33|TOAD-64|Ulip2	dihydropyrimidinase-like 2	protein-coding
mm_155749.1	chrX	96167247	96167255	+	1	NA	3' UTR (NM_010833, exon 13 of 13)	3' UTR (NM_010833, exon 13 of 13)	71206	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_73000.1	chr8	93810772	93810778	+	1	NA	promoter-TSS (NM_010308)	promoter-TSS (NM_010308)	-63	NM_010308	14681	Mm.251445	NM_010308	ENSMUSG00000031748	Gnao1	AW050213|Galphao|Gnao|alphaO	guanine nucleotide binding protein, alpha O	protein-coding
mm_73585.1	chr8	109868587	109868609	+	1	NA	promoter-TSS (NM_001122594)	promoter-TSS (NM_001122594)	-5	NM_001122594	244650	Mm.23494	NM_001122594	ENSMUSG00000031732	Phlpp2	AI481772|C130044A18Rik|Phlppl	PH domain and leucine rich repeat protein phosphatase 2	protein-coding
mm_38882.1	chr4	149701582	149701602	-	1	NA	promoter-TSS (NM_001029837)	promoter-TSS (NM_001029837)	37	NM_001029837	18707	Mm.229108	NM_008840	ENSMUSG00000039936	Pik3cd	2410099E07Rik|2610208K16Rik|AW545373|p110delta	phosphatidylinositol 3-kinase catalytic delta polypeptide	protein-coding
mm_58106.1	chr6	137649179	137649192	-	1	NA	promoter-TSS (NM_007945)	promoter-TSS (NM_007945)	100	NM_001271588	13860	Mm.235346	NM_007945	ENSMUSG00000015766	Eps8	AW261790	epidermal growth factor receptor pathway substrate 8	protein-coding
mm_99776.1	chr11	107201917	107201930	+	1	NA	Intergenic	Intergenic	-12542	NM_001161329	68979	Mm.294617	NM_133702	ENSMUSG00000018433	Nol11	1500002M01Rik|AU015220|AU019874	nucleolar protein 11	protein-coding
mm_122900.1	chr14	54952990	54953023	-	1	NA	exon (NM_010856, exon 23 of 39)	exon (NM_010856, exon 23 of 39)	-3864	NR_029724	387204		NR_029724	ENSMUSG00000065432	Mir208a	Mirn208|Mirn208a|mir-208|mir-208a|mmu-mir-208	microRNA 208a	ncRNA
mm_15363.1	chr2	156420838	156420862	+	1	NA	promoter-TSS (NM_001291121)	promoter-TSS (NM_001291121)	-59	NM_001291122	13821	Mm.20852	NM_013510	ENSMUSG00000027624	Epb41l1	4.1N|Epb4.1l1|NBL1|mKIAA0338	erythrocyte membrane protein band 4.1 like 1	protein-coding
mm_43054.1	chr5	124175415	124175430	+	1	NA	intron (NM_011256, intron 2 of 24)	intron (NM_011256, intron 2 of 24)	11760	NM_001289472	19679	Mm.44261	NM_011256	ENSMUSG00000029406	Pitpnm2	NIR3|RDGBA2|Rdgb2|mKIAA1457	phosphatidylinositol transfer protein, membrane-associated 2	protein-coding
mm_59539.1	chr7	27804883	27804894	+	1	NA	Intergenic	Intergenic	-2308	NM_027703	71163	Mm.440493	NM_027703	ENSMUSG00000030604	Zfp626	4833408D11Rik|4933426I21Rik|7630402I04Rik	zinc finger protein 626	protein-coding
mm_136010.1	chr16	75906846	75906860	-	1	NA	intron (NM_023380, intron 1 of 7)	intron (NM_023380, intron 1 of 7)	2413	NM_023380	67742	Mm.131406	NM_023380	ENSMUSG00000022876	Samsn1	4930571B16Rik|930571B16Rik|Hacs1|SLy2	SAM domain, SH3 domain and nuclear localization signals, 1	protein-coding
mm_141042.1	chr17	25345560	25345563	-	1	NA	promoter-TSS (NM_031187)	promoter-TSS (NM_031187)	1	NM_031187	100503895	Mm.3301	NM_031187	ENSMUSG00000024173	Tpsab1	MMCP-7|Mcp-7|Mcp7|Mcpt7	tryptase alpha/beta 1	protein-coding
mm_56886.1	chr6	119031257	119031273	-	1	NA	intron (NM_001256002, intron 3 of 47)	L1ME3D|LINE|L1	77230	NM_001159534	12288	Mm.41628	NM_009781	ENSMUSG00000051331	Cacna1c	Cav1.2|Cchl1a1|D930026N18Rik|MBC|MELC-CC	calcium channel, voltage-dependent, L type, alpha 1C subunit	protein-coding
mm_119748.1	chr14	54153147	54153164	+	1	NA	Intergenic	Intergenic	100774	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_77808.1	chr9	3036357	3036387	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	2371	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_83712.1	chr9	50746502	50746597	-	1	NA	promoter-TSS (NM_025865)	promoter-TSS (NM_025865)	-28	NM_025865	66952	Mm.273375	NM_025865	ENSMUSG00000032062	2310030G06Rik	2610024D04Rik|AV017521	RIKEN cDNA 2310030G06 gene	protein-coding
mm_153104.1	chr19	32756410	32756426	-	1	NA	Intergenic	CpG	-1159	NM_008960	19211	Mm.245395	NM_008960	ENSMUSG00000013663	Pten	2310035O07Rik|A130070J02Rik|AI463227|B430203M17Rik|MMAC1|TEP1	phosphatase and tensin homolog	protein-coding
mm_100635.1	chr11	121718509	121718526	+	1	NA	Intergenic	Intergenic	16090	NM_144797	210029	Mm.153566	NM_144797	ENSMUSG00000039208	Metrnl	9430048M07Rik|BC019776	meteorin, glial cell differentiation regulator-like	protein-coding
mm_14428.1	chr2	130539527	130539534	+	1	NA	intron (NM_001163688, intron 10 of 20)	intron (NM_001163688, intron 10 of 20)	24219	NR_040348	321014	Mm.442588	NR_040348	ENSMUSG00000060029	4930473A02Rik	-	RIKEN cDNA 4930473A02 gene	ncRNA
mm_28032.1	chr3	83049798	83049817	-	1	NA	promoter-TSS (NM_181849)	promoter-TSS (NM_181849)	56	NM_181849	110135	Mm.30063	NM_181849	ENSMUSG00000033831	Fgb	2510049G14Rik	fibrinogen beta chain	protein-coding
mm_102955.1	chr11	69664388	69664459	-	1	NA	non-coding (NR_110993, exon 5 of 5)	non-coding (NR_110993, exon 5 of 5)	1380	NR_035455	100316840		NR_035455	ENSMUSG00000088752	Mir1934	mir-1934|mmu-mir-1934	microRNA 1934	ncRNA
mm_76815.1	chr8	104443002	104443025	-	1	NA	promoter-TSS (NM_001013380)	promoter-TSS (NM_001013380)	34	NM_001013380	234663	Mm.289583	NM_001013380	ENSMUSG00000035770	Dync1li2	AA409702|C920003I06|Dncli2|Dnclic2|LIC2	dynein, cytoplasmic 1 light intermediate chain 2	protein-coding
mm_20090.1	chr2	120850429	120850445	-	1	NA	promoter-TSS (NM_001024856)	promoter-TSS (NM_001024856)	-19	NM_001024856	140810	Mm.275698	NM_080788	ENSMUSG00000090100	Ttbk2	2610507N02Rik|AI326283|B930008N24Rik|TTK|Ttbk|Ttbk1|mKIAA0847	tau tubulin kinase 2	protein-coding
mm_46325.1	chr5	100813496	100813538	-	1	NA	intron (NM_172405, intron 4 of 8)	intron (NM_172405, intron 4 of 8)	7418	NM_172405	70681	Mm.486560	NM_172405	ENSMUSG00000035234	Fam175a	3830405G04Rik|5630400M01Rik|AI506069|AL024423|AV118690|Ccdc98	family with sequence similarity 175, member A	protein-coding
mm_30776.1	chr4	18193521	18193522	+	1	NA	Intergenic	Intergenic	340063	NM_019724	17389	Mm.187315	NM_019724	ENSMUSG00000028226	Mmp16	MT-MMP 3|MT3-MMP|Mt3mmp	matrix metallopeptidase 16	protein-coding
mm_135098.1	chr16	35234921	35234926	-	1	NA	intron (NM_001012765, intron 1 of 20)	U4|snRNA|snRNA	79287	NM_001012765	224129	Mm.41137	NM_001012765	ENSMUSG00000022840	Adcy5	AW121902|Ac5	adenylate cyclase 5	protein-coding
mm_144009.1	chr17	88388465	88388471	-	1	NA	Intergenic	Intergenic	-52244	NM_180974	14236	Mm.112824	NM_180974	ENSMUSG00000034998	Foxn2	3230402J05Rik|6030465J18Rik|Fkh19|Foxn1|HTLF	forkhead box N2	protein-coding
mm_154620.1	chrX	7722268	7722287	+	1	NA	promoter-TSS (NM_172372)	promoter-TSS (NM_172372)	57	NM_001290792	54636	Mm.305725	NM_172372	ENSMUSG00000039382	Wdr45	C79260|DXImx38e|JM5|Sfc19|WIPI-4|Wdrx1	WD repeat domain 45	protein-coding
mm_140283.1	chr17	85033617	85033635	+	1	NA	intron (NM_009205, intron 3 of 9)	intron (NM_009205, intron 3 of 9)	5279	NM_009205	20532	Mm.227176	NM_009205	ENSMUSG00000024131	Slc3a1	D2H|NBAT|NTAA|RBAT	solute carrier family 3, member 1	protein-coding
mm_92663.1	chr10	80421848	80421876	-	1	NA	intron (NM_001164148, intron 3 of 18)	intron (NM_001164148, intron 3 of 18)	11791	NM_001164150	21423	Mm.3406	NM_011548	ENSMUSG00000020167	Tcf3	A1|AA408400|ALF2|AW209082|E12|E12/E47|E2A|E47|KA1|ME2|Pan1|Pan2|TCF-3|Tcfe2a|VDIR|bHLHb21	transcription factor 3	protein-coding
mm_4394.1	chr1	172341420	172341425	+	1	NA	5' UTR (NM_001039484, exon 1 of 2)	5' UTR (NM_001039484, exon 1 of 2)	212	NM_001039484	16513	Mm.254563	NM_020269	ENSMUSG00000044708	Kcnj10	BIR10|BIRK-1|Kir1.2|Kir4.1	potassium inwardly-rectifying channel, subfamily J, member 10	protein-coding
mm_23827.1	chr3	81037138	81037205	+	1	NA	5' UTR (NM_019971, exon 1 of 6)	5' UTR (NM_019971, exon 1 of 6)	755	NM_019971	54635	Mm.331089	NM_019971	ENSMUSG00000028019	Pdgfc	1110064L01Rik|AI647969|PDGF-C	platelet-derived growth factor, C polypeptide	protein-coding
mm_32528.1	chr4	108879093	108879116	+	1	NA	promoter-TSS (NM_023537)	promoter-TSS (NM_023537)	34	NM_023537	69908	Mm.41580	NM_023537	ENSMUSG00000003411	Rab3b	2610528C18Rik	RAB3B, member RAS oncogene family	protein-coding
mm_74890.1	chr8	25103015	25103030	-	1	NA	Intergenic	CpG	-1211	NM_031257	83436	Mm.261122	NM_031257	ENSMUSG00000031557	Plekha2	6430512N22Rik|AI851530|AU041791|TAPP2|W91773	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 2	protein-coding
mm_95378.1	chr11	49095852	49095865	+	1	NA	exon (NM_001271677, exon 3 of 3)	exon (NM_001271677, exon 3 of 3)	8841	NM_008330	15953	Mm.24769	NM_008330	ENSMUSG00000078920	Ifi47	47kDa|IRG-47|Ifggc1|Igrd|Iigp4|Iipg4|Irgd	interferon gamma inducible protein 47	protein-coding
mm_14394.1	chr2	129801393	129801396	+	1	NA	promoter-TSS (NR_029452)	promoter-TSS (NR_029452)	65	NR_029452	654409	Mm.305555	NR_029452		4932416H05Rik	-	RIKEN cDNA 4932416H05 gene	ncRNA
mm_34841.1	chr4	155398166	155398197	+	1	NA	promoter-TSS (NM_008072)	promoter-TSS (NM_008072)	-112	NM_008072	14403	Mm.388925	NM_008072	ENSMUSG00000029054	Gabrd	AI853201	gamma-aminobutyric acid (GABA) A receptor, subunit delta	protein-coding
mm_96764.1	chr11	69917301	69917314	+	1	NA	TTS (NM_019726)	TTS (NM_019726)	3115	NM_019726	56310	Mm.477738	NM_019726	ENSMUSG00000023170	Gps2	AI505953	G protein pathway suppressor 2	protein-coding
mm_10404.1	chr2	13578627	13578671	+	1	NA	exon (NM_011701, exon 4 of 9)	exon (NM_011701, exon 4 of 9)	4338	NM_011701	22352	Mm.268000	NM_011701	ENSMUSG00000026728	Vim	-	vimentin	protein-coding
mm_18067.1	chr2	42169872	42169883	-	1	NA	intron (NM_053011, intron 2 of 90)	intron (NM_053011, intron 2 of 90)	277691	NR_105754	102465171		NR_105754	ENSMUSG00000098660	Mir6336	Gm27584|mmu-mir-6336	microRNA 6336	ncRNA
mm_91934.1	chr10	60696472	60696506	-	1	NA	promoter-TSS (NM_001252635)	promoter-TSS (NM_001252635)	1	NM_001252635	22295	Mm.440327	NM_023370	ENSMUSG00000012819	Cdh23	4930542A03Rik|USH1D|ahl|ahl1|bob|bus|mdfw|nmf112|nmf181|nmf252|sals|v	cadherin 23 (otocadherin)	protein-coding
mm_142052.1	chr17	35638123	35638133	-	1	NA	exon (NM_001033366, exon 2 of 3)	exon (NM_001033366, exon 2 of 3)	5567	NM_001033366	268949	Mm.296301	NM_001033366	ENSMUSG00000073408	Dpcr1	Gm630	diffuse panbronchiolitis critical region 1 (human)	protein-coding
mm_173271.1	chrX	97604227	97604227	+	1	NA	Intergenic	L1_Mur2|LINE|L1	-227018	NM_001161433	245527	Mm.189270	NM_175540	ENSMUSG00000034457	Eda2r	9430060M22Rik|TNFRSF27|Xedar	ectodysplasin A2 receptor	protein-coding
mm_23118.1	chr3	37639986	37639986	+	1	NA	promoter-TSS (NM_011896)	promoter-TSS (NM_011896)	39	NM_001305442	24063	Mm.330986	NM_011896	ENSMUSG00000037211	Spry1	sprouty1|spry-1	sprouty homolog 1 (Drosophila)	protein-coding
mm_165302.1	chr2	92915069	92915071	+	1	NA	promoter-TSS (NM_030725)	promoter-TSS (NM_030725)	-31	NM_030725	80976	Mm.33490	NM_030725	ENSMUSG00000027220	Syt13	5730409J20Rik|AI549909|mKIAA1427	synaptotagmin XIII	protein-coding
mm_139528.1	chr17	56673224	56673232	+	1	NA	promoter-TSS (NM_027933)	promoter-TSS (NM_027933)	3	NM_027933	71810	Mm.29608	NM_027933	ENSMUSG00000002372	Ranbp3	2610024N24Rik|AA408221	RAN binding protein 3	protein-coding
mm_50964.1	chr6	59233463	59233486	+	1	NA	Intergenic	Intergenic	24604	NM_001081145	68140	Mm.25843	NM_001081145	ENSMUSG00000049232	Tigd2	3632410O17Rik	tigger transposable element derived 2	protein-coding
mm_86143.1	chr9	117093285	117093297	-	1	NA	intron (NM_001172122, intron 2 of 13)	intron (NM_001172122, intron 2 of 13)	159192	NM_001172123	207181	Mm.326411	NM_178660	ENSMUSG00000039607	Rbms3	6720477E09Rik|8430436O14Rik	RNA binding motif, single stranded interacting protein	protein-coding
mm_43503.1	chr5	136987389	136987414	+	1	NA	promoter-TSS (NM_001310748)	promoter-TSS (NM_001310748)	382	NM_011962	26433	Mm.251003	NM_011962	ENSMUSG00000004846	Plod3	AI414586|LH3	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3	protein-coding
mm_172154.1	chr6	42020545	42020547	-	1	NA	Intergenic	ETnERV-int|LTR|ERVK	-17848	NM_009299	20939	Mm.4119	NM_009299	ENSMUSG00000023289	Sva	-	seminal vesicle antigen	protein-coding
mm_18312.1	chr2	54085543	54085559	-	1	NA	promoter-TSS (NM_023396)	promoter-TSS (NM_023396)	1	NM_023396	67874	Mm.27086	NM_023396	ENSMUSG00000075334	Rprm	2410012A13Rik|Reprimo	reprimo, TP53 dependent G2 arrest mediator candidate	protein-coding
mm_87201.1	chr10	39558168	39558179	+	1	NA	intron (NM_001122892, intron 12 of 12)	intron (NM_001122892, intron 12 of 12)	-54761	NM_134000	103213	Mm.436686	NM_134000	ENSMUSG00000019842	Traf3ip2	AI429613|Act1|CIKS	TRAF3 interacting protein 2	protein-coding
mm_131291.1	chr16	11387594	11387607	+	1	NA	intron (NM_028964, intron 4 of 20)	B1_Mur3|SINE|Alu	-18048	NM_001290148	74478	Mm.325831	NM_028964	ENSMUSG00000071669	Snx29	4933437K13Rik|ENSMUSG00000079738|Gm11170|Gm1737|Gm930|Rundc2a	sorting nexin 29	protein-coding
mm_166810.1	chr7	10536718	10536719	+	1	NA	Intergenic	Lx8|LINE|L1	-8549	NM_001172072	628580	Mm.480301	NM_001172072	ENSMUSG00000047031	Vmn1r68	EG628580|Gm6898	vomeronasal 1 receptor 68	protein-coding
mm_158726.1	chrX	163761324	163761344	-	1	NA	promoter-TSS (NM_028842)	promoter-TSS (NM_028842)	-2	NM_028842	74264	Mm.39304	NM_028842	ENSMUSG00000083695	Rnf138rt1	-	ring finger protein 138, retrogene 1	protein-coding
mm_123861.1	chr14	72539066	72539076	-	1	NA	3' UTR (NM_207636, exon 26 of 26)	3' UTR (NM_207636, exon 26 of 26)	170932	NM_207636	319448	Mm.205421	NM_207636	ENSMUSG00000033487	Fndc3a	1700094E19Rik|D14Ertd453e|F730017H24Rik|Fndc3|sys	fibronectin type III domain containing 3A	protein-coding
mm_37041.1	chr4	115781013	115781023	-	1	NA	promoter-TSS (NM_029196)	promoter-TSS (NM_029196)	16	NM_029196	75173	Mm.331798	NM_029196	ENSMUSG00000044556	Tex38	4930544O15Rik|Theg4	testis expressed 38	protein-coding
mm_24566.1	chr3	93443953	93443959	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	1626	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_5186.1	chr1	13096104	13096111	-	1	NA	Intergenic	Intergenic	31056	NM_001081209	383491	Mm.309380	NM_001081209	ENSMUSG00000042414	Prdm14	-	PR domain containing 14	protein-coding
mm_37254.1	chr4	118291420	118291430	-	1	NA	promoter-TSS (NM_011213)	promoter-TSS (NM_011213)	-28	NM_011213	19268	Mm.29855	NM_011213	ENSMUSG00000033295	Ptprf	AA591035|LAR|LARS|RPTP-LAR	protein tyrosine phosphatase, receptor type, F	protein-coding
mm_32981.1	chr4	120134960	120134971	+	1	NA	3' UTR (NM_010657, exon 9 of 9)	3' UTR (NM_010657, exon 9 of 9)	-26241	NM_007902	13615	Mm.284855	NM_007902	ENSMUSG00000028635	Edn2	ET-2|PPET2|VIC	endothelin 2	protein-coding
mm_147683.1	chr18	60718689	60718706	-	1	NA	Intergenic	Intergenic	-5308	NM_008306	15531	Mm.181862	NM_008306	ENSMUSG00000054008	Ndst1	1200015G06Rik|HSNST|HSNST 1|Hsst|N-HSST|N-HSST 1|NDST-1|b2b2230Clo	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 1	protein-coding
mm_101726.1	chr11	42182859	42182882	-	1	NA	promoter-TSS (NM_010250)	promoter-TSS (NM_010250)	60	NM_010250	14394	Mm.439668	NM_010250	ENSMUSG00000010803	Gabra1	Gabra-1	gamma-aminobutyric acid (GABA) A receptor, subunit alpha 1	protein-coding
mm_149886.1	chr19	25383504	25383517	+	1	NA	intron (NM_181404, intron 4 of 13)	intron (NM_181404, intron 4 of 13)	-122196	NM_015826	50796	Mm.391208	NM_015826	ENSMUSG00000024837	Dmrt1	-	doublesex and mab-3 related transcription factor 1	protein-coding
mm_22179.1	chr2	173216868	173216883	-	1	NA	exon (NM_021394, exon 2 of 8)	exon (NM_021394, exon 2 of 8)	2047	NM_021394	58203	Mm.116687	NM_021394	ENSMUSG00000027514	Zbp1	2010010H03Rik|Dai|Dlm1|mZaDLM	Z-DNA binding protein 1	protein-coding
mm_168671.1	chr11	92842841	92842843	-	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-256448	NM_028296	72605	Mm.342160	NM_028296	ENSMUSG00000056158	Car10	2700029L05Rik|BB085816|Ca10	carbonic anhydrase 10	protein-coding
mm_132815.1	chr16	45184765	45184790	+	1	NA	intron (NM_026402, intron 10 of 11)	intron (NM_026402, intron 10 of 11)	25948	NM_026402	67841	Mm.41775	NM_026402	ENSMUSG00000022663	Atg3	2610016C12Rik|APG3|Apg3l|Atg3l|PC3-96	autophagy related 3	protein-coding
mm_106728.1	chr12	3873166	3873175	+	1	NA	intron (NM_007872, intron 5 of 22)	intron (NM_007872, intron 5 of 22)	-10926	NR_045884	100038522	Mm.417270	NR_045884	ENSMUSG00000073242	Dnmt3aos	ENSMUSG00000073242|Gm10485	DNA methyltransferase 3A, opposite strand	ncRNA
mm_68270.1	chr7	105595646	105595656	-	1	NA	exon (NM_017371, exon 6 of 10)	exon (NM_017371, exon 6 of 10)	4465	NM_017371	15458	Mm.3485	NM_017371	ENSMUSG00000030895	Hpx	Hpxn|hx	hemopexin	protein-coding
mm_14035.1	chr2	122153013	122153047	+	1	NA	TTS (NM_009735)	TTS (NM_009735)	5343	NM_009735	12010	Mm.163	NM_009735	ENSMUSG00000060802	B2m	Ly-m11|beta2-m|beta2m	beta-2 microglobulin	protein-coding
mm_24716.1	chr3	95228960	95228980	+	1	NA	promoter-TSS (NM_019914)	promoter-TSS (NM_019914)	27	NM_001038708	57912	Mm.28189	NM_172395	ENSMUSG00000046722	Cdc42se1	1300002M12Rik|AW558204|Cdcse1|SCIP1|Spec1	CDC42 small effector 1	protein-coding
mm_143415.1	chr17	70834831	70834855	-	1	NA	Intergenic	Intergenic	11934	NM_001164077	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_3404.1	chr1	143803654	143803657	+	1	NA	intron (NM_019562, intron 10 of 10)	intron (NM_019562, intron 10 of 10)	26377	NM_019562	56207	Mm.261004	NM_019562	ENSMUSG00000018189	Uchl5	5830413B11Rik|Uch37	ubiquitin carboxyl-terminal esterase L5	protein-coding
mm_45543.1	chr5	72852776	72852782	-	1	NA	intron (NM_001113461, intron 1 of 17)	PB1D10|SINE|Alu	15669	NM_001113461	21682	Mm.319581	NM_013689	ENSMUSG00000029217	Tec	-	tec protein tyrosine kinase	protein-coding
mm_50255.1	chr6	42586011	42586045	+	1	NA	Intergenic	Intergenic	11344	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_100925.1	chr11	6471474	6471493	-	1	NA	3' UTR (NM_011221, exon 1 of 1)	3' UTR (NM_011221, exon 1 of 1)	4593	NM_011221	19291	Mm.296150	NM_011221	ENSMUSG00000094483	Purb	2310015K15Rik|AA114818|Cager-2|D11Bwg0414e	purine rich element binding protein B	protein-coding
mm_49051.1	chr6	4923496	4923512	+	1	NA	intron (NM_181595, intron 2 of 15)	intron (NM_181595, intron 2 of 15)	20184	NM_181595	243725	Mm.332901	NM_181595	ENSMUSG00000032827	Ppp1r9a	2810430P21Rik|4930518N04Rik|5330407E15|A230094E16Rik|BB181831|NRB|mKIAA1222|neurabin-I	protein phosphatase 1, regulatory (inhibitor) subunit 9A	protein-coding
mm_59273.1	chr7	24903012	24903080	+	1	NA	promoter-TSS (NM_008488)	promoter-TSS (NM_008488)	60	NM_001130151	16801	Mm.3181	NM_008488	ENSMUSG00000040940	Arhgef1	Lbcl2|Lsc	Rho guanine nucleotide exchange factor (GEF) 1	protein-coding
mm_93072.1	chr10	89410839	89410851	-	1	NA	3' UTR (NM_001284344, exon 12 of 12)	3' UTR (NM_001284344, exon 12 of 12)	33122	NM_001284344	237436	Mm.11982	NM_001033331	ENSMUSG00000074802	Gas2l3	8430435B07Rik|Gm240	growth arrest-specific 2 like 3	protein-coding
mm_147823.1	chr18	61911784	61911854	-	1	NA	promoter-TSS (NM_001164491)	promoter-TSS (NM_001164491)	5	NM_198649	319713	Mm.329478	NM_198649	ENSMUSG00000032735	Ablim3	AW990719|D930036B08Rik	actin binding LIM protein family, member 3	protein-coding
mm_3317.1	chr1	137906844	137906857	+	1	NA	Intergenic	Intergenic	-59605	NR_029795	735252		NR_029795	ENSMUSG00000065565	Mir181a-1	Mirn181a-1|Mirn213|miR-213|mir-181a-1|mmu-mir-213	microRNA 181a-1	ncRNA
mm_126866.1	chr15	89355717	89355727	+	1	NA	promoter-TSS (NM_001271601)	promoter-TSS (NM_001271601)	3	NM_001271601	52683	Mm.143167	NM_001115132	ENSMUSG00000008690	Ncaph2	-	non-SMC condensin II complex, subunit H2	protein-coding
mm_38501.1	chr4	141088217	141088223	-	1	NA	promoter-TSS (NM_177867)	promoter-TSS (NM_177867)	-125	NM_177867	329972	Mm.247201	NM_177867	ENSMUSG00000045004	Spata21	4933414G08	spermatogenesis associated 21	protein-coding
mm_99501.1	chr11	102925600	102925644	+	1	NA	promoter-TSS (NM_197959)	promoter-TSS (NM_197959)	-498	NM_197959	70218	Mm.32084	NM_197959	ENSMUSG00000051378	Kif18b	3000004C01Rik	kinesin family member 18B	protein-coding
mm_16825.1	chr2	11474207	11474219	-	1	NA	3' UTR (NM_001177754, exon 16 of 16)	3' UTR (NM_001177754, exon 16 of 16)	27877	NM_001177754	170768	Mm.19669	NM_133232	ENSMUSG00000026773	Pfkfb3	E330010H22Rik|iPFK-2|uPFK-2	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	protein-coding
mm_25877.1	chr3	130247037	130247039	+	1	NA	intron (NM_029838, intron 2 of 37)	MTC|LTR|ERVL-MaLR	66193	NM_001244952	77018	Mm.91728	NM_029838	ENSMUSG00000058897	Col25a1	2700062B08Rik|CLAC-P	collagen, type XXV, alpha 1	protein-coding
mm_48710.1	chr5	147235545	147235557	-	1	NA	intron (NR_038157, intron 3 of 5)	intron (NR_038157, intron 3 of 5)	-34580	NM_008814	18609	Mm.389714	NM_008814	ENSMUSG00000029644	Pdx1	IDX-1|IPF-1|Ipf1|Mody4|STF-1|pdx-1	pancreatic and duodenal homeobox 1	protein-coding
mm_57829.1	chr6	129464463	129464473	-	1	NA	intron (NR_132130, intron 5 of 5)	intron (NR_132130, intron 5 of 5)	8311	NM_001309637	56644	Mm.239516	NM_020008	ENSMUSG00000079293	Clec7a	BGR|Clecsf12|beta-GR	C-type lectin domain family 7, member a	protein-coding
mm_111462.1	chr12	98432167	98432170	-	1	NA	3' UTR (NM_001316665, exon 7 of 7)	3' UTR (NM_001316665, exon 7 of 7)	-91676	NR_136759	105245437	Mm.446375	NR_136759		Gm40893	-	predicted gene, 40893	ncRNA
mm_101683.1	chr11	40692667	40692679	-	1	NA	promoter-TSS (NM_134017)	promoter-TSS (NM_134017)	9	NM_134017	108645	Mm.293771	NM_134017	ENSMUSG00000042032	Mat2b	1110064C04Rik|2410018D16Rik|AI182287|AU022853|MAT-II|MATIIbeta|TGR	methionine adenosyltransferase II, beta	protein-coding
mm_35040.1	chr4	4138775	4138798	-	1	NA	promoter-TSS (NM_001002927)	promoter-TSS (NM_001002927)	-341	NM_001002927	18619	Mm.475097	NM_001002927	ENSMUSG00000045573	Penk	AI326464|ENK|PPA|Penk1	preproenkephalin	protein-coding
mm_33305.1	chr4	129035377	129035399	+	1	NA	Intergenic	Intergenic	-22883	NM_029219	75234	Mm.259672	NM_029219	ENSMUSG00000028793	Rnf19b	4930534K13Rik|4930555L03Rik|Ibrdc3	ring finger protein 19B	protein-coding
mm_82640.1	chr9	22002581	22002598	-	1	NA	promoter-TSS (NM_029939)	promoter-TSS (NM_029939)	45	NM_001163787	77609	Mm.159953	NM_029939	ENSMUSG00000039632	Ccdc151	AI644415|C330001K17Rik|b2b1885Clo	coiled-coil domain containing 151	protein-coding
mm_108449.1	chr12	82451259	82451284	+	1	NA	3' UTR (NM_001167983, exon 24 of 24)	3' UTR (NM_001167983, exon 24 of 24)	139922	NM_172579	217692	Mm.261333	NM_172579	ENSMUSG00000042700	Sipa1l1	4931426N11Rik|AW213287|Spar|mKIAA0440	signal-induced proliferation-associated 1 like 1	protein-coding
mm_147959.1	chr18	67062998	67063001	-	1	NA	Intergenic	Intergenic	-25299	NM_177137	14680	Mm.440746	NM_010307	ENSMUSG00000024524	Gnal	2610011C15Rik|9630020G10Rik|Galphaolf|Gna10|Golf	guanine nucleotide binding protein, alpha stimulating, olfactory type	protein-coding
mm_14552.1	chr2	133497895	133497895	+	1	NA	Intergenic	Intergenic	-54264	NM_007553	12156	Mm.103205	NM_007553	ENSMUSG00000027358	Bmp2	AI467020|Bmp2a	bone morphogenetic protein 2	protein-coding
mm_110237.1	chr12	30373339	30373351	-	1	NA	promoter-TSS (NM_172951)	promoter-TSS (NM_172951)	30	NM_172951	268534	Mm.279765	NM_172951	ENSMUSG00000020672	Sntg2	2210008K22Rik|9530013L23|BB121248|G2syn|Syn5	syntrophin, gamma 2	protein-coding
mm_61029.1	chr7	49522864	49522888	+	1	NA	intron (NM_175272, intron 11 of 37)	intron (NM_175272, intron 11 of 37)	113959	NM_001005232	13172	Mm.307176	NM_001005232	ENSMUSG00000030507	Dbx1	AI426026|Dbx	developing brain homeobox 1	protein-coding
mm_45192.1	chr5	52184604	52184615	-	1	NA	exon (NM_001042620, exon 2 of 12)	exon (NM_001042620, exon 2 of 12)	5937	NR_104311	13204	Mm.993	NM_007839	ENSMUSG00000029169	Dhx15	DBP1|DEAH9|Ddx15|HRH2|mDEAH9	DEAH (Asp-Glu-Ala-His) box polypeptide 15	protein-coding
mm_111182.1	chr12	83956063	83956068	-	1	NA	Intergenic	Intergenic	5457	NM_023633	71952	Mm.251483	NM_023633	ENSMUSG00000046791	2410016O06Rik	MAPJD|NO66	RIKEN cDNA 2410016O06 gene	protein-coding
mm_19036.1	chr2	76975062	76975080	-	1	NA	exon (NM_011652, exon 4 of 313)	exon (NM_011652, exon 4 of 313)	7476	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_111504.1	chr12	99445555	99445558	-	1	NA	intron (NM_183186, intron 1 of 5)	intron (NM_183186, intron 1 of 5)	4518	NM_183186	71375	Mm.341972	NM_183186	ENSMUSG00000033713	Foxn3	5430426H20Rik|AA589593|AW556347|Ches1|Ches1l|HTLFL1	forkhead box N3	protein-coding
mm_28619.1	chr3	95015215	95015246	-	1	NA	promoter-TSS (NM_030074)	promoter-TSS (NM_030074)	8	NM_030074	78266	Mm.389478	NM_030074	ENSMUSG00000019338	Zfp687	4931408L03Rik|Znf687|mKIAA1441	zinc finger protein 687	protein-coding
mm_104602.1	chr11	97182658	97182661	-	1	NA	intron (NM_008379, intron 3 of 21)	intron (NM_008379, intron 3 of 21)	5233	NM_008379	16211	Mm.251013	NM_008379	ENSMUSG00000001440	Kpnb1	AA409963|IPOB|Impnb	karyopherin (importin) beta 1	protein-coding
mm_169104.1	chr13	44869625	44869625	-	1	NA	intron (NM_001205044, intron 4 of 18)	LSU-rRNA_Hsa|rRNA|rRNA	132471	NM_025772	94245	Mm.352311	NM_025772	ENSMUSG00000057531	Dtnbp1	5430437B18Rik|AW048963|Bloc1s8|dysbindin|sdy	dystrobrevin binding protein 1	protein-coding
mm_77201.1	chr8	113843840	113843845	-	1	NA	intron (NM_172466, intron 3 of 22)	intron (NM_172466, intron 3 of 22)	4997	NM_172466	208936	Mm.167471	NM_172466	ENSMUSG00000053399	Adamts18	9630038L21|ADAMTS21|E130314N14Rik	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 18	protein-coding
mm_101078.1	chr11	11689764	11689769	-	1	NA	promoter-TSS (NM_001301865)	promoter-TSS (NM_001301865)	-411	NM_001301865	22778	Mm.103545	NM_009578	ENSMUSG00000018654	Ikzf1	5832432G11Rik|Ikaros|LyF-1|Zfpn1a1|Znfn1a1|hlk-1|mKIAA4227	IKAROS family zinc finger 1	protein-coding
mm_54149.1	chr6	22355991	22356007	-	1	NA	promoter-TSS (NM_138587)	promoter-TSS (NM_138587)	82	NM_138587	27999	Mm.490307	NM_138587	ENSMUSG00000029672	Fam3c	D6Wsu176e|Ilei	family with sequence similarity 3, member C	protein-coding
mm_1481.1	chr1	71564479	71564491	+	1	NA	exon (NM_026195, exon 6 of 16)	exon (NM_026195, exon 6 of 16)	7329	NM_026195	108147	Mm.38010	NM_026195	ENSMUSG00000026192	Atic	2610509C24Rik|AA536954|AW212393	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	protein-coding
mm_10262.1	chr2	9595627	9595634	+	1	NA	Intergenic	Intergenic	282970	NM_008091	14462	Mm.313866	NM_008091	ENSMUSG00000015619	Gata3	Gata-3|jal	GATA binding protein 3	protein-coding
mm_80443.1	chr9	77960950	77960960	+	1	NA	exon (NM_134255, exon 3 of 8)	exon (NM_134255, exon 3 of 8)	43590	NM_134255	68801	Mm.430736	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	ELOVL family member 5, elongation of long chain fatty acids (yeast)	protein-coding
mm_163444.1	chr12	86833764	86833798	-	1	NA	Intergenic	Intergenic	51033	NM_145836	238330	Mm.248358	NM_145836	ENSMUSG00000034168	Irf2bpl	6430527G18Rik|Eap1	interferon regulatory factor 2 binding protein-like	protein-coding
mm_154573.1	chrX	7067517	7067534	+	1	NA	promoter-TSS (NM_009651)	promoter-TSS (NM_009651)	10	NM_009651	11643	Mm.1498	NM_009651	ENSMUSG00000050089	Akap4	AKAP-4|AKAP82|Fsc1|PRKA4|mAKAP82|p82	A kinase (PRKA) anchor protein 4	protein-coding
mm_123065.1	chr14	55672170	55672179	-	1	NA	promoter-TSS (NM_177992)	promoter-TSS (NM_177992)	-61	NM_177992	105446	Mm.390685	NM_177992	ENSMUSG00000002326	Gmpr2	1810008P16Rik|5730544D12Rik|AA959850|GMPR 2	guanosine monophosphate reductase 2	protein-coding
mm_126969.1	chr15	93397983	93397993	+	1	NA	promoter-TSS (NM_001083114)	promoter-TSS (NM_001083114)	302	NM_026025	67197	Mm.293181	NM_026025	ENSMUSG00000022635	Zcrb1	2700088M22Rik|Madp-1	zinc finger CCHC-type and RNA binding motif 1	protein-coding
mm_30149.1	chr3	142547640	142547650	-	1	NA	3' UTR (NM_001083312, exon 11 of 11)	3' UTR (NM_001083312, exon 11 of 11)	-12407	NM_018734	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_156006.1	chrX	106703965	106703975	+	1	NA	intron (NM_001033541, intron 3 of 3)	intron (NM_001033541, intron 3 of 3)	-100291	NM_001281859	58861	Mm.287166	NM_021476	ENSMUSG00000052821	Cysltr1	BB147369|CysLT1R|Cyslt1	cysteinyl leukotriene receptor 1	protein-coding
mm_137711.1	chr17	29099638	29099652	+	1	NA	3' UTR (NM_007669, exon 3 of 3)	3' UTR (NM_007669, exon 3 of 3)	5876	NM_007669	12575	Mm.195663	NM_007669	ENSMUSG00000023067	Cdkn1a	CAP20|CDKI|CIP1|Cdkn1|P21|SDI1|Waf1|mda6|p21Cip1|p21WAF	cyclin-dependent kinase inhibitor 1A (P21)	protein-coding
mm_153821.1	chr19	46304605	46304605	-	1	NA	promoter-TSS (NM_001177369)	promoter-TSS (NM_001177369)	-132	NM_001177369	18034	Mm.102365	NM_019408	ENSMUSG00000025225	Nfkb2	NF-kappaB2|lyt|p49|p49/p100|p50B|p52	nuclear factor of kappa light polypeptide gene enhancer in B cells 2, p49/p100	protein-coding
mm_35953.1	chr4	53127925	53127953	-	1	NA	intron (NM_013454, intron 4 of 49)	intron (NM_013454, intron 4 of 49)	31956	NM_013454	11303	Mm.277376	NM_013454	ENSMUSG00000015243	Abca1	ABC-1|Abc1	ATP-binding cassette, sub-family A (ABC1), member 1	protein-coding
mm_156726.1	chrX	159878061	159878074	+	1	NA	intron (NM_001135728, intron 2 of 12)	intron (NM_001135728, intron 2 of 12)	37599	NM_001135728	58194	Mm.286495	NM_021389	ENSMUSG00000040990	Sh3kbp1	1200007H22Rik|1700125L08Rik|5830464D22Rik|AI447724|Cin85|IN85|Ruk|Seta	SH3-domain kinase binding protein 1	protein-coding
mm_42134.1	chr5	111139932	111139935	+	1	NA	intron (NM_001267622, intron 5 of 22)	intron (NM_001267622, intron 5 of 22)	135789	NR_030482	735278		NR_030482	ENSMUSG00000076163	Mir701	Mirn701|mir-701|mmu-mir-701	microRNA 701	ncRNA
mm_68040.1	chr7	101361865	101361888	-	1	NA	intron (NM_001040111, intron 1 of 33)	intron (NM_001040111, intron 1 of 33)	13807	NM_001040111	69710	Mm.277687	NM_027180	ENSMUSG00000032812	Arap1	2410002L19Rik|Centd2|mKIAA0782	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	protein-coding
mm_94075.1	chr10	128409320	128409374	-	1	NA	5' UTR (NM_027257, exon 2 of 7)	5' UTR (NM_027257, exon 2 of 7)	449	NM_027257	69917	Mm.46614	NM_027257	ENSMUSG00000025374	Nabp2	2610036N15Rik|Obfc2b|SSB1	nucleic acid binding protein 2	protein-coding
mm_114296.1	chr13	58906319	58906319	+	1	NA	intron (NM_001025074, intron 12 of 17)	intron (NM_001025074, intron 12 of 17)	98622	NM_001025074	18212	Mm.130054	NM_008745	ENSMUSG00000055254	Ntrk2	GP145-TrkB/GP95-TrkB|Tkrb|trk-B|trkB	neurotrophic tyrosine kinase, receptor, type 2	protein-coding
mm_18033.1	chr2	38712837	38712861	-	1	NA	promoter-TSS (NM_001316687)	promoter-TSS (NM_001316687)	-615	NM_001316687	26423	Mm.31387	NM_139051	ENSMUSG00000026751	Nr5a1	Ad4BP|ELP|ELP-3|Ftz-F1|Ftzf1|SF-1|SF1|STF-1	nuclear receptor subfamily 5, group A, member 1	protein-coding
mm_113271.1	chr13	29016268	29016303	+	1	NA	promoter-TSS (NR_045075)	promoter-TSS (NR_045075)	30	NR_045075	77920	Mm.197051	NR_045073	ENSMUSG00000086363	A330102I10Rik	-	RIKEN cDNA A330102I10 gene	ncRNA
mm_153596.1	chr19	43751663	43751681	-	1	NA	intron (NM_144874, intron 1 of 8)	intron (NM_144874, intron 1 of 8)	1328	NM_144874	226139	Mm.248237	NM_144874	ENSMUSG00000040018	Cox15	2900026G05Rik	cytochrome c oxidase assembly protein 15	protein-coding
mm_45282.1	chr5	64933551	64933606	-	1	NA	promoter-TSS (NM_030682)	promoter-TSS (NM_030682)	-20	NM_001276445	21897	Mm.273024	NM_030682	ENSMUSG00000044827	Tlr1	-	toll-like receptor 1	protein-coding
mm_83379.1	chr9	44561850	44561854	-	1	NA	Intergenic	L1M2|LINE|L1	-35431	NM_007551	12145	Mm.6246	NM_007551	ENSMUSG00000047880	Cxcr5	Blr1|CXC-R5|CXCR-5|Gpcr6|MDR15	chemokine (C-X-C motif) receptor 5	protein-coding
mm_76523.1	chr8	87472366	87472381	-	1	NA	promoter-TSS (NR_125722)	promoter-TSS (NR_125722)	219	NM_019626	12404	Mm.4880	NM_019626	ENSMUSG00000031654	Cbln1	AI323299	cerebellin 1 precursor protein	protein-coding
mm_128672.1	chr15	60187336	60187340	-	1	NA	Intergenic	Intergenic	-170720	NM_027668	71088	Mm.425950	NM_027668	ENSMUSG00000071749	4933412E24Rik	-	RIKEN cDNA 4933412E24 gene	protein-coding
mm_814.1	chr1	45881726	45881736	+	1	NA	Intergenic	Intergenic	43863	NM_016917	53945	Mm.28756	NM_016917	ENSMUSG00000025993	Slc40a1	Dusg|Fpn1|IREG1|MTP|MTP1|Ol5|Pcm|Slc11a3|Slc39a1	solute carrier family 40 (iron-regulated transporter), member 1	protein-coding
mm_129325.1	chr15	77771175	77771191	-	1	NA	exon (NM_022410, exon 27 of 41)	exon (NM_022410, exon 27 of 41)	-15954	NM_001081970	239552	Mm.125650	NM_001081970	ENSMUSG00000056656	Apol8	9830006J20Rik|APOL-II|Apol2	apolipoprotein L 8	protein-coding
mm_72913.1	chr8	90955510	90955519	+	1	NA	intron (NM_001310530, intron 1 of 37)	intron (NM_001310530, intron 1 of 37)	23265	NM_001310530	109151	Mm.100615	NM_177224	ENSMUSG00000056608	Chd9	1810014J18Rik|9030205D12Rik|A330063D19Rik|AD013|PRIC320|mKIAA0308	chromodomain helicase DNA binding protein 9	protein-coding
mm_4140.1	chr1	170868677	170868707	+	1	NA	promoter-TSS (NM_001081304)	promoter-TSS (NM_001081304)	-921	NM_001081304	226641	Mm.377046	NM_001081304	ENSMUSG00000026663	Atf6	9130025P16Rik|9630036G24|AA789574|Atf6alpha|ESTM49	activating transcription factor 6	protein-coding
mm_103665.1	chr11	79059816	79059842	-	1	NA	intron (NM_013571, intron 2 of 17)	intron (NM_013571, intron 2 of 17)	36232	NR_045873	790910	Mm.440410	NR_045873		Gm11201	ENSMUSG00000072637|OTTMUSG00000000169	predicted gene 11201	ncRNA
mm_13474.1	chr2	105683015	105683018	+	1	NA	intron (NM_001310146, intron 1 of 9)	intron (NM_001310146, intron 1 of 9)	553	NM_001310145	18508	Mm.3608	NM_013627	ENSMUSG00000027168	Pax6	1500038E17Rik|AEY11|Dey|Gsfaey11|Pax-6|Sey	paired box 6	protein-coding
mm_82457.1	chr9	15627871	15627884	-	1	NA	promoter-TSS (NM_181816)	promoter-TSS (NM_181816)	56	NM_181816	234964	Mm.32237	NM_181816	ENSMUSG00000039977	Ccdc67	4933401K09Rik|Deup1	coiled-coil domain containing 67	protein-coding
mm_92177.1	chr10	67695930	67695959	-	1	NA	Intergenic	Intergenic	-146989	NM_001005419	211488	Mm.297250	NM_001005419	ENSMUSG00000057134	Ado	Gm237	2-aminoethanethiol (cysteamine) dioxygenase	protein-coding
mm_50999.1	chr6	63546759	63546760	+	1	NA	intron (NM_008167, intron 2 of 15)	intron (NM_008167, intron 2 of 15)	289902	NM_008167	14804	Mm.439651	NM_008167	ENSMUSG00000071424	Grid2	B230104L07Rik|GluD2|GluRdelta2|Lc|Lc<J>|MMS10-AC|Ms10ac|cpr|ho|nmf408|tpr	glutamate receptor, ionotropic, delta 2	protein-coding
mm_9804.1	chr1	181917225	181917243	-	1	NA	exon (NM_010135, exon 11 of 15)	exon (NM_010135, exon 11 of 15)	-74833	NM_133815	98386	Mm.4538	NM_133815	ENSMUSG00000004880	Lbr	AI505894|ic	lamin B receptor	protein-coding
mm_123789.1	chr14	70429098	70429116	-	1	NA	promoter-TSS (NM_021308)	promoter-TSS (NM_021308)	-13	NM_021308	57746	Mm.85253	NM_021308	ENSMUSG00000033644	Piwil2	Piwil1l|mili	piwi-like RNA-mediated gene silencing 2	protein-coding
mm_170175.1	chr17	57248441	57248458	-	1	NA	promoter-TSS (NM_030084)	promoter-TSS (NM_030084)	-760	NM_030084	78308	Mm.28468	NM_030084	ENSMUSG00000005823	Gpr108	1810015L19Rik|AA589464|C79132|Lustr2	G protein-coupled receptor 108	protein-coding
mm_146645.1	chr18	11048651	11048662	-	1	NA	intron (NR_105023, intron 3 of 5)	intron (NR_105023, intron 3 of 5)	-3854	NM_010258	14465	Mm.329287	NM_010258	ENSMUSG00000005836	Gata6	AA410133|GATA-6	GATA binding protein 6	protein-coding
mm_17459.1	chr2	28557646	28557689	-	1	NA	exon (NM_009885, exon 9 of 11)	exon (NM_009885, exon 9 of 11)	5736	NM_009885	12613	Mm.236017	NM_009885	ENSMUSG00000026818	Cel	1810036E18Rik|BAL	carboxyl ester lipase	protein-coding
mm_27541.1	chr3	57576486	57576494	-	1	NA	promoter-TSS (NM_133784)	promoter-TSS (NM_133784)	-580	NM_001168281	97064	Mm.405029	NM_133784	ENSMUSG00000027803	Wwtr1	2310058J06Rik|2610021I22Rik|C78399|Taz	WW domain containing transcription regulator 1	protein-coding
mm_170037.1	chr17	23260602	23260614	-	1	NA	Intergenic	L1Md_A|LINE|L1	51705	NM_001102584	666002	Mm.469838	NM_001102584	ENSMUSG00000091945	Vmn2r114	EG666002|V2Rp3	vomeronasal 2, receptor 114	protein-coding
mm_106198.1	chr11	116842876	116842893	-	1	NA	promoter-TSS (NM_028865)	promoter-TSS (NM_028865)	565	NM_033398	107817	Mm.481684	NM_033398	ENSMUSG00000056962	Jmjd6	5730436I23Rik|D11Ertd195e|PSR|PtdSerR|Ptdsr|mKIAA0585	jumonji domain containing 6	protein-coding
mm_16653.1	chr2	6543978	6544006	-	1	NA	3' UTR (NM_001110228, exon 14 of 14)	3' UTR (NM_001110228, exon 14 of 14)	177670	NM_001310447	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_169837.1	chr16	26866447	26866447	+	1	NA	Intergenic	L1Md_F2|LINE|L1	101798	NM_001285916	239789	Mm.326909	NM_001013761	ENSMUSG00000068428	Gmnc	Gemc1|Gm1778|Gm606	geminin coiled-coil domain containing	protein-coding
mm_25791.1	chr3	126844674	126844677	+	1	NA	3' UTR (NM_001293663, exon 20 of 20)	3' UTR (NM_001293663, exon 20 of 20)	98711	NM_001034168	109676	Mm.220242	NM_178655	ENSMUSG00000032826	Ank2	100043364|AI835472|AW491075|Ank-2|Gm4392	ankyrin 2, brain	protein-coding
mm_119379.1	chr14	41134305	41134315	+	1	NA	exon (NM_023134, exon 6 of 6)	exon (NM_023134, exon 6 of 6)	2522	NM_023134	20387	Mm.46062	NM_023134	ENSMUSG00000021789	Sftpa1	SP-A|Sftp-1|Sftp1	surfactant associated protein A1	protein-coding
mm_152514.1	chr19	11279631	11279637	-	1	NA	intron (NM_183190, intron 1 of 4)	intron (NM_183190, intron 1 of 4)	4179	NM_183190	269063	Mm.268940	NM_183190	ENSMUSG00000054523	Ms4a5	-	membrane-spanning 4-domains, subfamily A, member 5	protein-coding
mm_32043.1	chr4	95967385	95967403	+	1	NA	promoter-TSS (NR_045777)	promoter-TSS (NR_045777)	15	NM_030014	77963	Mm.49994	NM_030014	ENSMUSG00000028572	Hook1	A930033L17Rik|azh	hook microtubule tethering protein 1	protein-coding
mm_167259.1	chr8	25813762	25813772	+	1	NA	3' UTR (NM_011485, exon 7 of 7)	3' UTR (NM_011485, exon 7 of 7)	5293	NM_011485	20845	Mm.293314	NM_011485	ENSMUSG00000031574	Star	AV363654|D8Ertd419e|stARD1	steroidogenic acute regulatory protein	protein-coding
mm_57611.1	chr6	128124361	128124384	-	1	NA	intron (NM_175414, intron 1 of 8)	intron (NM_175414, intron 1 of 8)	19206	NM_175414	109246	Mm.21814	NM_175414	ENSMUSG00000030352	Tspan9	6720474K14Rik|9430079M16Rik|AU018597	tetraspanin 9	protein-coding
mm_143009.1	chr17	56441937	56441940	-	1	NA	intron (NM_001252455, intron 6 of 27)	intron (NM_001252455, intron 6 of 27)	20283	NM_001252456	19280	Mm.258771	NM_011218	ENSMUSG00000013236	Ptprs	AL022616|PTP|PTP-NU3|PTPNU-3|PTPsigma|Ptpt9|R-PTP-S|RPTPsigma	protein tyrosine phosphatase, receptor type, S	protein-coding
mm_27679.1	chr3	65945130	65945138	-	1	NA	Intergenic	AT_rich|Low_complexity|Low_complexity	13091	NM_019937	56706	Mm.175612	NM_019937	ENSMUSG00000027829	Ccnl1	2610030E23Rik|AU018493|Ccnl|ania-6a	cyclin L1	protein-coding
mm_84620.1	chr9	70542680	70542691	-	1	NA	promoter-TSS (NM_025690)	promoter-TSS (NM_025690)	-93	NM_026337	66660	Mm.22379	NM_025690	ENSMUSG00000032212	Sltm	5730455C01Rik|5730555F13Rik|9130215G10Rik|Met	SAFB-like, transcription modulator	protein-coding
mm_76807.1	chr8	104395766	104395858	-	1	NA	promoter-TSS (NM_153582)	promoter-TSS (NM_153582)	-5	NM_153582	97487	Mm.29658	NM_153582	ENSMUSG00000096188	Cmtm4	Cklfsf4|D19397|ENSMUSG00000051554|Gm9853	CKLF-like MARVEL transmembrane domain containing 4	protein-coding
mm_71767.1	chr8	66426861	66426901	+	1	NA	intron (NM_175188, intron 6 of 7)	MIR3|SINE|MIR	40580	NM_001166375	72925	Mm.380457	NM_175188	ENSMUSG00000036469	March1	2900024D24Rik|BB085186	membrane-associated ring finger (C3HC4) 1	protein-coding
mm_59654.1	chr7	28179994	28180028	+	1	NA	promoter-TSS (NM_001271370)	promoter-TSS (NM_001271370)	-305	NM_001271370	13549	Mm.57249	NM_010092	ENSMUSG00000002409	Dyrk1b	Mirk	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1b	protein-coding
mm_161229.1	chr13	78199198	78199198	-	1	NA	promoter-TSS (NM_010151)	promoter-TSS (NM_010151)	-325	NM_010151	13865	Mm.439653	NM_010151	ENSMUSG00000069171	Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR-3|EAR3|Erbal3|SVP44|Tcfcoup1	nuclear receptor subfamily 2, group F, member 1	protein-coding
mm_119786.1	chr14	54185991	54186004	+	1	NA	Intergenic	Intergenic	67932	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_29392.1	chr3	108904317	108904325	-	1	NA	exon (NM_025845, exon 6 of 6)	exon (NM_025845, exon 6 of 6)	7383	NM_025845	66921	Mm.51049	NM_025845	ENSMUSG00000027881	Prpf38b	1110021E09Rik|AU018955	PRP38 pre-mRNA processing factor 38 (yeast) domain containing B	protein-coding
mm_54299.1	chr6	29415549	29415554	-	1	NA	exon (NM_001201378, exon 12 of 15)	exon (NM_001201378, exon 12 of 15)	16625	NM_001201378	232664	Mm.251303	NM_145574	ENSMUSG00000029769	Ccdc136	4921511K06Rik|BC006583	coiled-coil domain containing 136	protein-coding
mm_74215.1	chr8	123954011	123954041	+	1	NA	3' UTR (NM_019552, exon 13 of 13)	3' UTR (NM_019552, exon 13 of 13)	-4761	NM_172288	234865	Mm.267812	NM_172288	ENSMUSG00000039509	Nup133	mermaid	nucleoporin 133	protein-coding
mm_165569.1	chr3	19217652	19217653	+	1	NA	intron (NR_045575, intron 7 of 8)	B1_Mus2|SINE|Alu	29431	NR_045575	67472	Mm.45125	NM_026182	ENSMUSG00000027601	Mtfr1	1300002C08Rik|1700080D04Rik|2810026O10Rik|4930579E05Rik|Chppr|Fam54a2	mitochondrial fission regulator 1	protein-coding
mm_167692.1	chr9	87734922	87734928	-	1	NA	Intergenic	Intergenic	-3665	NM_023814	76365	Mm.158789	NM_023814	ENSMUSG00000032419	Tbx18	2810012F10Rik|2810404D13Rik	T-box18	protein-coding
mm_13545.1	chr2	112000102	112000105	+	1	NA	Intergenic	Intergenic	9081	NM_146449	258441	Mm.377504	NM_146449	ENSMUSG00000108827	Olfr1310	MOR245-3	olfactory receptor 1310	protein-coding
mm_29454.1	chr3	113206695	113206698	-	1	NA	Intergenic	Intergenic	-49969	NM_001190403	545562	Mm.462977	NM_001190403		Amy2b	Amy-X|Amy2-2|OTTMUSG00000022462|mAmy2-1	amylase 2b	protein-coding
mm_65346.1	chr7	24989841	24989850	-	1	NA	exon (NM_001290469, exon 13 of 23)	exon (NM_001290469, exon 13 of 23)	-2178	NR_106014	102465634		NR_106014	ENSMUSG00000099258	Mir7047	Gm27270|mmu-mir-7047	microRNA 7047	ncRNA
mm_17094.1	chr2	23040139	23040174	-	1	NA	promoter-TSS (NM_001077190)	promoter-TSS (NM_001077190)	85	NM_001077192	11308	Mm.205647	NM_007380	ENSMUSG00000058835	Abi1	E3B1|NAP1|Ssh3bp1|abi-1	abl-interactor 1	protein-coding
mm_88522.1	chr10	78055328	78055365	+	1	NA	promoter-TSS (NM_001284200)	promoter-TSS (NM_001284200)	11	NM_001284200	54427	Mm.13433	NM_019448	ENSMUSG00000000730	Dnmt3l	D6Ertd14e|ecat7	DNA (cytosine-5-)-methyltransferase 3-like	protein-coding
mm_70946.1	chr8	26698889	26698925	+	1	NA	Intergenic	Intergenic	125516	NR_045904	72316	Mm.490534	NR_045904	ENSMUSG00000100335	2310008N11Rik	-	RIKEN cDNA 2310008N11 gene	ncRNA
mm_7843.1	chr1	132358901	132358903	-	1	NA	intron (NM_001311107, intron 4 of 4)	intron (NM_001311107, intron 4 of 4)	9046	NM_001311108	68875	Mm.273785	NM_178874	ENSMUSG00000042066	Tmcc2	1110063G11Rik	transmembrane and coiled-coil domains 2	protein-coding
mm_3820.1	chr1	159256749	159256761	+	1	NA	intron (NM_011931, intron 6 of 19)	MTD|LTR|ERVL-MaLR	24429	NM_011931	26374	Mm.328135	NM_011931	ENSMUSG00000040782	Rfwd2	AI316802|C80879|Cop1	ring finger and WD repeat domain 2	protein-coding
mm_92834.1	chr10	81487186	81487229	-	1	NA	3' UTR (NM_134009, exon 14 of 14)	3' UTR (NM_134009, exon 14 of 14)	-4498	NM_001311124	319586	Mm.152689	NM_176954	ENSMUSG00000034818	Celf5	4930565A21Rik|Brunol5	CUGBP, Elav-like family member 5	protein-coding
mm_132299.1	chr16	33518304	33518340	+	1	NA	promoter-TSS (NM_134251)	promoter-TSS (NM_134251)	-7	NM_134251	171286	Mm.35253	NM_134251	ENSMUSG00000035506	Slc12a8	CCC9|E330020C02Rik	solute carrier family 12 (potassium/chloride transporters), member 8	protein-coding
mm_113493.1	chr13	37403978	37403987	+	1	NA	intron (NM_010745, intron 3 of 4)	intron (NM_010745, intron 3 of 4)	58637	NM_010745	17084	Mm.2639	NM_010745	ENSMUSG00000021423	Ly86	MD-1|MD1|ly86_tv2	lymphocyte antigen 86	protein-coding
mm_98095.1	chr11	86613339	86613372	+	1	NA	intron (NM_029478, intron 7 of 11)	U1|snRNA|snRNA	-29197	NR_029738	387140		NR_029738	ENSMUSG00000065455	Mir21a	Mir21|Mirn21|mmu-mir-21|mmu-mir-21a	microRNA 21a	ncRNA
mm_159996.1	chr6	118758027	118758027	-	1	NA	promoter-TSS (NM_001290335)	promoter-TSS (NM_001290335)	-53	NM_001290335	12288	Mm.41628	NM_009781	ENSMUSG00000051331	Cacna1c	Cav1.2|Cchl1a1|D930026N18Rik|MBC|MELC-CC	calcium channel, voltage-dependent, L type, alpha 1C subunit	protein-coding
mm_103089.1	chr11	69920538	69920580	-	1	NA	promoter-TSS (NM_001166590)	promoter-TSS (NM_001166590)	71	NM_001166590	276770	Mm.18026	NM_181582	ENSMUSG00000078812	Eif5a	AA410058|D19Wsu54e|Eif4d|Eif5a1|eIF-4D|eIF-5A|eIF-5A-1|eIF-5A1	eukaryotic translation initiation factor 5A	protein-coding
mm_160107.1	chr7	24546448	24546448	+	1	NA	promoter-TSS (NM_009532)	promoter-TSS (NM_009532)	-443	NM_001037143	641361	Mm.333661	NM_001037143	ENSMUSG00000011632	Pinlyp	2310033E01Rik	phospholipase A2 inhibitor and LY6/PLAUR domain containing	protein-coding
mm_78402.1	chr9	28921089	28921095	+	1	NA	3' UTR (NM_177906, exon 8 of 8)	3' UTR (NM_177906, exon 8 of 8)	1042037	NM_172290	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding
mm_3009.1	chr1	133354211	133354239	+	1	NA	exon (NM_031193, exon 2 of 9)	exon (NM_031193, exon 2 of 9)	3551	NM_031192	19701	Mm.220955	NM_031192	ENSMUSG00000070645	Ren1	D19352|Ren|Ren-1|Ren-A|Ren1c|Ren1d|Rn-1|Rnr	renin 1 structural	protein-coding
mm_103200.1	chr11	70652077	70652087	-	1	NA	TTS (NM_001316728)	TTS (NM_001316728)	2568	NM_011072	18643	Mm.2647	NM_011072	ENSMUSG00000018293	Pfn1	Pfn	profilin 1	protein-coding
mm_90110.1	chr10	117277330	117277340	+	1	NA	TTS (NM_017372)	TTS (NM_017372)	4937	NM_017372	17105	Mm.45436	NM_017372	ENSMUSG00000069516	Lyz2	AI326280|Lys|Lysm|Lyzf2|Lyzs|Lzm|Lzm-s1|Lzp	lysozyme 2	protein-coding
mm_150849.1	chr19	44990061	44990092	+	1	NA	intron (NM_011976, intron 1 of 14)	intron (NM_011976, intron 1 of 14)	732	NM_011976	26456	Mm.34404	NM_011976	ENSMUSG00000025207	Sema4g	AI507908|AW554132	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4G	protein-coding
mm_157394.1	chrX	38406800	38406812	-	1	NA	intron (NM_001017959, intron 8 of 8)	L1M3|LINE|L1	49654	NM_010685	16784	Mm.486	NM_010685	ENSMUSG00000016534	Lamp2	CD107b|LGP-B|Lamp II|Lamp-2|Lamp-2a|Lamp-2b|Lamp-2c|Mac3	lysosomal-associated membrane protein 2	protein-coding
mm_78081.1	chr9	15730858	15730900	+	1	NA	intron (NM_172289, intron 8 of 10)	intron (NM_172289, intron 8 of 10)	21110	NM_172289	234967	Mm.138815	NM_172289	ENSMUSG00000043885	Slc36a4	6330573I15Rik|PAT4	solute carrier family 36 (proton/amino acid symporter), member 4	protein-coding
mm_156117.1	chrX	114904983	114904994	+	1	NA	promoter-TSS (NM_001276396)	promoter-TSS (NM_001276396)	-24	NM_001276396	237009	Mm.302216	NM_207241	ENSMUSG00000050435	Ube2dnl1	Ube2dnl	ubiquitin-conjugating enzyme E2D N-terminal like 1	protein-coding
mm_148927.1	chr19	6996213	6996232	+	1	NA	promoter-TSS (NM_153597)	promoter-TSS (NM_153597)	91	NR_027351	107328	Mm.391161	NM_153597	ENSMUSG00000047656	Trpt1	AU079016|AW045591|Tpt1|Tpt1h	tRNA phosphotransferase 1	protein-coding
mm_4532.1	chr1	175698587	175698600	+	1	NA	promoter-TSS (NM_029453)	promoter-TSS (NM_029453)	0	NM_029453	75820	Mm.50361	NM_029453	ENSMUSG00000026523	Wdr64	4930415O10Rik|4930511H01Rik	WD repeat domain 64	protein-coding
mm_84134.1	chr9	59036388	59036460	-	1	NA	promoter-TSS (NM_008684)	promoter-TSS (NM_008684)	17	NM_008684	18007	Mm.42249	NM_008684	ENSMUSG00000032340	Neo1	2610028H22Rik|AI327052|D930014N22Rik|Igdcc2	neogenin	protein-coding
mm_60459.1	chr7	44477677	44477702	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-6828	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_164706.1	chr17	52350043	52350047	-	1	NA	Intergenic	Intergenic	-252664	NM_001031811	211468	Mm.399068	NM_001031811	ENSMUSG00000035580	Kcnh8	C130090D05Rik|ELK|ELK1|ELK3|Kv12.1	potassium voltage-gated channel, subfamily H (eag-related), member 8	protein-coding
mm_15314.1	chr2	155568175	155568179	+	1	NA	intron (NM_008180, intron 9 of 12)	B1_Mur1|SINE|Alu	-11247	NR_040613	74945	Mm.401956	NR_040613	ENSMUSG00000086529	Acss2os	4930471I20Rik	acyl-CoA synthetase short-chain family member 2, opposite strand	ncRNA
mm_31007.1	chr4	40193741	40193745	+	1	NA	exon (NM_007386, exon 19 of 21)	exon (NM_007386, exon 19 of 21)	46082	NM_172689	230073	Mm.86382	NM_172689	ENSMUSG00000040296	Ddx58	6430573D20Rik|C330021E21|RIG-I|RLR-1	DEAD (Asp-Glu-Ala-Asp) box polypeptide 58	protein-coding
mm_71728.1	chr8	61977572	61977586	+	1	NA	intron (NM_001293783, intron 17 of 37)	B1_Mus1|SINE|Alu	49492	NM_001293783	234311	Mm.275233	NM_144928	ENSMUSG00000037921	Ddx60	9830118M07	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	protein-coding
mm_118274.1	chr13	112620738	112620746	-	1	NA	exon (NM_010029, exon 14 of 21)	exon (NM_010029, exon 14 of 21)	31568	NM_010029	13206	Mm.12818	NM_010029	ENSMUSG00000021758	Ddx4	AV206478|Mvh|VASA	DEAD (Asp-Glu-Ala-Asp) box polypeptide 4	protein-coding
mm_29201.1	chr3	106766727	106766743	-	1	NA	intron (NM_007651, intron 5 of 7)	MIR|SINE|MIR	23414	NM_007651	12508	Mm.316861	NM_007651	ENSMUSG00000040747	Cd53	AI323659|Ox-44|Tspan25	CD53 antigen	protein-coding
mm_131245.1	chr16	10526430	10526440	+	1	NA	3' UTR (NM_001243761, exon 19 of 19)	3' UTR (NM_001243761, exon 19 of 19)	16619	NM_021428	58239	Mm.353006	NM_021428	ENSMUSG00000038055	Dexi	1810029J14Rik|AI836170|AW413143|D16Bwg0586e|Myle	dexamethasone-induced transcript	protein-coding
mm_23257.1	chr3	51340204	51340213	+	1	NA	intron (NM_023502, intron 1 of 9)	CpG	436	NM_001291059	69257	Mm.131038	NM_023502	ENSMUSG00000037174	Elf2	2610036A20Rik|A230104O07Rik|AW111824|BB183398|EU32|NERF|NERF-1A|NERF-1B|NERF-2	E74-like factor 2	protein-coding
mm_83130.1	chr9	40435030	40435061	-	1	NA	intron (NM_172768, intron 1 of 19)	intron (NM_172768, intron 1 of 19)	20719	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_144696.1	chr18	34862497	34862521	+	1	NA	exon (NM_007913, exon 2 of 2)	exon (NM_007913, exon 2 of 2)	1302	NM_007913	13653	Mm.181959	NM_007913	ENSMUSG00000038418	Egr1	A530045N19Rik|ETR103|Egr-1|Krox-1|Krox-24|Krox24|NGF1-A|NGFI-A|NGFIA|TIS8|Zenk|Zfp-6|Zif268|egr	early growth response 1	protein-coding
mm_42684.1	chr5	119832103	119832127	+	1	NA	Intergenic	Intergenic	-2548	NM_011537	21388	Mm.103636	NM_011537	ENSMUSG00000018263	Tbx5	-	T-box 5	protein-coding
mm_9011.1	chr1	166047824	166047834	-	1	NA	Intergenic	Intergenic	-45195	NM_011137	18986	Mm.245261	NM_011137	ENSMUSG00000026565	Pou2f1	2810482H01Rik|NF-A1|Oct-1|Oct1|Otf-1|Otf1	POU domain, class 2, transcription factor 1	protein-coding
mm_146636.1	chr18	10610125	10610144	-	1	NA	5' UTR (NM_001081222, exon 1 of 11)	5' UTR (NM_001081222, exon 1 of 11)	218	NM_001081222	77805	Mm.210996	NM_144542	ENSMUSG00000024293	Esco1	A930014I12Rik	establishment of sister chromatid cohesion N-acetyltransferase 1	protein-coding
mm_97206.1	chr11	75607883	75607895	+	1	NA	intron (NM_008850, intron 4 of 11)	intron (NM_008850, intron 4 of 11)	-7658	NR_110477	654359	Mm.439961	NR_110477		Gm12338	OTTMUSG00000006216	cytochrome c oxidase, subunit VIIc pseudogene	pseudo
mm_92.1	chr1	7111647	7111660	+	1	NA	intron (NM_183028, intron 1 of 5)	intron (NM_183028, intron 1 of 5)	22733	NM_183028	319263	Mm.21539	NM_183028	ENSMUSG00000051285	Pcmtd1	8430411F12Rik|A030012M09Rik	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding
mm_13529.1	chr2	110557139	110557142	+	1	NA	Intergenic	Intergenic	-40159	NM_001003915	241612	Mm.277148	NM_001003915	ENSMUSG00000041644	Slc5a12	AI315119|D630015G19|SMCT2	solute carrier family 5 (sodium/glucose cotransporter), member 12	protein-coding
mm_124697.1	chr15	6439229	6439240	+	1	NA	3' UTR (NM_001102400, exon 13 of 13)	3' UTR (NM_001102400, exon 13 of 13)	-6099	NM_013485	12279	Mm.29095	NM_013485	ENSMUSG00000022149	C9	-	complement component 9	protein-coding
mm_137329.1	chr17	25045362	25045370	+	1	NA	intron (NM_134126, intron 13 of 29)	intron (NM_134126, intron 13 of 29)	29280	NM_134126	106633	Mm.32802	NM_134126	ENSMUSG00000024169	Ift140	AI661311|Tce5|Wdtc2|mKIAA0590	intraflagellar transport 140	protein-coding
mm_65229.1	chr7	19715396	19715460	-	1	NA	promoter-TSS (NM_001109748)	promoter-TSS (NM_001109748)	1	NM_001109748	53333	Mm.61682	NM_016871	ENSMUSG00000002984	Tomm40	AW539759|Mom35|Tom40	translocase of outer mitochondrial membrane 40 homolog (yeast)	protein-coding
mm_58579.1	chr7	4915203	4915230	+	1	NA	promoter-TSS (NM_170759)	promoter-TSS (NM_170759)	-1	NM_170759	232816	Mm.27442	NM_170759	ENSMUSG00000074406	Zfp628	Zec|Znf628	zinc finger protein 628	protein-coding
mm_53793.1	chr6	146657223	146657230	+	1	NA	promoter-TSS (NR_046277)	promoter-TSS (NR_046277)	8	NR_046277	74925	Mm.386304	NR_046277	ENSMUSG00000085238	4930479D17Rik	-	RIKEN cDNA 4930479D17 gene	ncRNA
mm_100041.1	chr11	114998913	114998927	+	1	NA	intron (NM_134158, intron 2 of 3)	ID_B1|SINE|B4	2960	NM_134158	140497	Mm.2699	NM_134158	ENSMUSG00000044811	Cd300c2	CLM4|Cd300c|Cd300d|DIgR1|Igsf7|Lmir2|MAIR-II	CD300C molecule 2	protein-coding
mm_11188.1	chr2	29099902	29099918	+	1	NA	Intergenic	RLTR34D_MM|LTR|ERVK	-25082	NM_198033	269254	Mm.41867	NM_198033	ENSMUSG00000043535	Setx	A130090N03|A930037J23Rik|AOA2|AW060766|Als4|SCAR1|Sen1|mKIAA0625	senataxin	protein-coding
mm_16232.1	chr2	173156205	173156221	+	1	NA	intron (NM_011044, intron 6 of 9)	intron (NM_011044, intron 6 of 9)	3140	NM_011044	18534	Mm.266867	NM_011044	ENSMUSG00000027513	Pck1	AI265463|PEPCK|Pck-1	phosphoenolpyruvate carboxykinase 1, cytosolic	protein-coding
mm_29363.1	chr3	108653796	108653827	-	1	NA	promoter-TSS (NM_145543)	promoter-TSS (NM_145543)	-102	NM_145543	229725	Mm.214545	NM_145543	ENSMUSG00000027884	Clcc1	Mclc	chloride channel CLIC-like 1	protein-coding
mm_115590.1	chr13	11827100	11827118	-	1	NA	intron (NM_023868, intron 15 of 104)	intron (NM_023868, intron 15 of 104)	279836	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding
mm_78818.1	chr9	44085030	44085047	+	1	NA	5' UTR (NM_198091, exon 1 of 12)	5' UTR (NM_198091, exon 1 of 12)	118	NM_198091	53376	Mm.272770	NM_016808	ENSMUSG00000032010	Usp2	B930035K21Rik|Ubp41	ubiquitin specific peptidase 2	protein-coding
mm_104653.1	chr11	97575211	97575236	-	1	NA	promoter-TSS (NM_018873)	promoter-TSS (NM_018873)	-97	NM_018873	56013	Mm.342665	NM_018873	ENSMUSG00000038453	Srcin1	P140|SNIP|mKIAA1684|p140Cap	SRC kinase signaling inhibitor 1	protein-coding
mm_82300.1	chr9	7864255	7864300	-	1	NA	intron (NM_007464, intron 1 of 8)	intron (NM_007464, intron 1 of 8)	8893	NM_007464	11796	Mm.2026	NM_007464	ENSMUSG00000032000	Birc3	AW107670|Api1|Api2|Birc2|C-IAP2|HIAP2|IAP1|IAP2|MIAP1|MIAP2|MIHB|MIHC|RNF49|cIAP-1|cIAP-2|cIAP1|cIAP2	baculoviral IAP repeat-containing 3	protein-coding
mm_68877.1	chr7	126447485	126447495	-	1	NA	exon (NM_007504, exon 19 of 23)	exon (NM_007504, exon 19 of 23)	15583	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_139027.1	chr17	46160562	46160577	+	1	NA	promoter-TSS (NM_019581)	promoter-TSS (NM_019581)	-463	NM_019581	56055	Mm.22147	NM_019581	ENSMUSG00000023952	Gtpbp2	nmf205	GTP binding protein 2	protein-coding
mm_97261.1	chr11	75764629	75764639	+	1	NA	exon (NM_009536, exon 6 of 6)	exon (NM_009536, exon 6 of 6)	-31175	NR_136933	102641247	Mm.411386	NR_136932		Gm12339	OTTMUSG00000006218	predicted gene 12339	ncRNA
mm_5409.1	chr1	33814396	33814406	-	1	NA	5' UTR (NM_001290700, exon 1 of 4)	5' UTR (NM_001290700, exon 1 of 4)	194	NM_133817	98403	Mm.289103	NM_133817	ENSMUSG00000042197	Zfp451	4930515K21Rik|4933435G09Rik|AI596398|COASTER|Kiaa0576-hp|Znf451|mKIAA1702	zinc finger protein 451	protein-coding
mm_8685.1	chr1	156939629	156939657	-	1	NA	promoter-TSS (NM_001159968)	promoter-TSS (NM_001159968)	-17	NM_023884	78255	Mm.28376	NM_023884	ENSMUSG00000026594	Ralgps2	1810020P17Rik|2210408F11Rik|4921528G01Rik|9130014M22Rik|AU043409|AW046161	Ral GEF with PH domain and SH3 binding motif 2	protein-coding
mm_146283.1	chr18	77938453	77938477	+	1	NA	promoter-TSS (NM_001195633)	promoter-TSS (NM_001195633)	-2	NM_001195633	100502841	Mm.297782	NM_001195633	ENSMUSG00000039840	Epg5	4732475F16|5430411K18Rik|AI661957|AW456499|mKIAA1632	ectopic P-granules autophagy protein 5 homolog (C. elegans)	protein-coding
mm_75753.1	chr8	69902016	69902024	-	1	NA	promoter-TSS (NM_032004)	promoter-TSS (NM_032004)	-164	NM_032004	83984	Mm.432504	NM_032004	ENSMUSG00000047654	Tssk6	Sstk|TSK-6|TSSK-6	testis-specific serine kinase 6	protein-coding
mm_133451.1	chr16	88777830	88777835	+	1	NA	Intergenic	Intergenic	-3626	NM_027170	69696	Mm.358728	NM_027170	ENSMUSG00000048830	2310057N15Rik	Krtap13-1	RIKEN cDNA 2310057N15 gene	protein-coding
mm_22117.1	chr2	170151667	170151685	-	1	NA	Intergenic	Intergenic	-9001	NM_001159683	228913	Mm.22858	NM_001033299	ENSMUSG00000052056	Zfp217	4933431C08Rik|AW987152|Gm562|ZABC1|Znf217	zinc finger protein 217	protein-coding
mm_37348.1	chr4	119966886	119966892	-	1	NA	intron (NM_010657, intron 1 of 8)	intron (NM_010657, intron 1 of 8)	152211	NM_010657	16656	Mm.302758	NM_010657	ENSMUSG00000028634	Hivep3	2900056N03Rik|A130075N07|AI848000|E030045D18Rik|KBP-1|KBP1|Krc|Rc|Schnurri-3|Shn3|Zas3	human immunodeficiency virus type I enhancer binding protein 3	protein-coding
mm_25589.1	chr3	116886207	116886213	+	1	NA	intron (NM_009146, intron 7 of 16)	intron (NM_009146, intron 7 of 16)	24530	NM_009146	20321	Mm.66293	NM_009146	ENSMUSG00000033386	Frrs1	AI131732|Sdfr2	ferric-chelate reductase 1	protein-coding
mm_140491.1	chr17	3283277	3283284	-	1	NA	Intergenic	Intergenic	-43293	NM_001122998	24001	Mm.137134	NM_011878	ENSMUSG00000023800	Tiam2	3000002F19Rik|STEF|mKIAA2016	T cell lymphoma invasion and metastasis 2	protein-coding
mm_122432.1	chr14	45158448	45158450	-	1	NA	intron (NM_001310534, intron 14 of 20)	L1_Mur3|LINE|L1	60976	NM_172597	70561	Mm.28129	NM_172597	ENSMUSG00000021830	Txndc16	5730420B22Rik|C77647	thioredoxin domain containing 16	protein-coding
mm_35472.1	chr4	40823576	40823595	-	1	NA	exon (NM_022305, exon 2 of 6)	exon (NM_022305, exon 2 of 6)	26553	NR_039584	100628614		NR_039584	ENSMUSG00000096377	Mir5123	mmu-mir-5123|mu-mir-5123	microRNA 5123	ncRNA
mm_110446.1	chr12	51134906	51134925	-	1	NA	Intergenic	Intergenic	129759	NR_126468	75494	Mm.416848	NR_126468		1700008C04Rik	-	RIKEN cDNA 1700008C04 gene	ncRNA
mm_83956.1	chr9	56928351	56928392	-	1	NA	promoter-TSS (NM_175483)	promoter-TSS (NM_175483)	0	NM_175483	235406	Mm.191459	NM_175483	ENSMUSG00000032733	Snx33	E130307J07Rik|Sh3px3	sorting nexin 33	protein-coding
mm_75997.1	chr8	72464245	72464257	-	1	NA	exon (NM_138585, exon 10 of 18)	exon (NM_138585, exon 10 of 18)	5838	NR_106036	102465647		NR_106036	ENSMUSG00000099079	Mir7068	Gm27570|mmu-mir-7068	microRNA 7068	ncRNA
mm_84162.1	chr9	59563918	59563957	-	1	NA	exon (NM_010421, exon 13 of 14)	exon (NM_010421, exon 13 of 14)	-14400	NM_175235	76183	Mm.265415	NM_175235	ENSMUSG00000032297	Celf6	6330569O16Rik|Brunol6	CUGBP, Elav-like family member 6	protein-coding
mm_150190.1	chr19	32665766	32665785	+	1	NA	3' UTR (NM_011864, exon 13 of 13)	3' UTR (NM_011864, exon 13 of 13)	45770	NM_011864	23972	Mm.203916	NM_011864	ENSMUSG00000024899	Papss2	1810018P12Rik|AI159688|AtpsU2|Atpsk2|Sk2|bm	3'-phosphoadenosine 5'-phosphosulfate synthase 2	protein-coding
mm_50783.1	chr6	53698099	53698101	+	1	NA	3' UTR (NM_001327821, exon 11 of 11)	3' UTR (NM_001327821, exon 11 of 11)	122725	NM_025817	66873	Mm.422727	NM_025817	ENSMUSG00000043496	Tril	1200009O22Rik|AI316813|mKIAA0644	TLR4 interactor with leucine-rich repeats	protein-coding
mm_136518.1	chr16	97454211	97454224	-	1	NA	exon (NM_010846, exon 7 of 11)	exon (NM_010846, exon 7 of 11)	8688	NM_010846	17857	Mm.33996	NM_010846	ENSMUSG00000000386	Mx1	AI893580|Mx|Mx-1	MX dynamin-like GTPase 1	protein-coding
mm_71754.1	chr8	65966639	65966645	+	1	NA	intron (NM_001166372, intron 2 of 7)	intron (NM_001166372, intron 2 of 7)	348117	NM_175188	72925	Mm.380457	NM_175188	ENSMUSG00000036469	March1	2900024D24Rik|BB085186	membrane-associated ring finger (C3HC4) 1	protein-coding
mm_166987.1	chr7	45731947	45731950	-	1	NA	intron (NM_017465, intron 5 of 6)	intron (NM_017465, intron 5 of 6)	-6132	NM_027055	69363	Mm.45607	NM_027055	ENSMUSG00000070563	Spaca4	1700008E09Rik|AV043694|Samp14	sperm acrosome associated 4	protein-coding
mm_114020.1	chr13	52618712	52618756	+	1	NA	intron (NM_001198977, intron 3 of 13)	intron (NM_001198977, intron 3 of 13)	21852	NM_011518	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_95480.1	chr11	51262550	51262576	+	1	NA	promoter-TSS (NM_007714)	promoter-TSS (NM_007714)	388	NM_177567	193286	Mm.80975	NM_177567	ENSMUSG00000045942	BC049762	4930503F14	cDNA sequence BC049762	protein-coding
mm_69248.1	chr7	127824766	127824777	-	1	NA	promoter-TSS (NM_024414)	promoter-TSS (NM_024414)	-240	NM_024414	56216	Mm.439759	NM_024414	ENSMUSG00000030806	Stx1b	Stx1b2|Stx1bl|Syn1b	syntaxin 1B	protein-coding
mm_129768.1	chr15	82693092	82693114	-	1	NA	Intergenic	Intergenic	-3045	NR_033515	627860	Mm.486636	NR_033515		Cyp2d37-ps	EG627860|Gm6800	cytochrome P450, family 2, subfamily d, polypeptide 37, pseudogene	pseudo
mm_52092.1	chr6	97835170	97835183	+	1	NA	intron (NM_001113198, intron 1 of 9)	intron (NM_001113198, intron 1 of 9)	28118	NM_001113198	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_75086.1	chr8	33927472	33927474	-	1	NA	intron (NM_001042674, intron 1 of 7)	intron (NM_001042674, intron 1 of 7)	2390	NM_019733	19663	Mm.323997	NM_019733	ENSMUSG00000031586	Rbpms	2010300K22Rik|2700019M19Rik|AU017537|RBP-MS|hermes	RNA binding protein gene with multiple splicing	protein-coding
mm_14989.1	chr2	152243343	152243343	+	1	NA	intron (NM_007788, intron 1 of 12)	intron (NM_007788, intron 1 of 12)	16503	NM_007788	12995	Mm.23692	NM_007788	ENSMUSG00000074698	Csnk2a1	Csnk2a1-rs4	casein kinase 2, alpha 1 polypeptide	protein-coding
mm_15372.1	chr2	156432994	156433006	+	1	NA	intron (NM_013510, intron 1 of 21)	intron (NM_013510, intron 1 of 21)	12091	NM_001291123	13821	Mm.20852	NM_013510	ENSMUSG00000027624	Epb41l1	4.1N|Epb4.1l1|NBL1|mKIAA0338	erythrocyte membrane protein band 4.1 like 1	protein-coding
mm_33611.1	chr4	132608518	132608531	+	1	NA	Intergenic	MLT1A1|LTR|ERVL-MaLR	-30522	NM_210071	14050	Mm.227733	NM_010166	ENSMUSG00000028886	Eya3	AI844637	EYA transcriptional coactivator and phosphatase 3	protein-coding
mm_54206.1	chr6	25688768	25688781	-	1	NA	exon (NM_010338, exon 1 of 2)	exon (NM_010338, exon 1 of 2)	1206	NM_010338	14763	Mm.409670	NM_010338	ENSMUSG00000039904	Gpr37	AI848630|Pael-R	G protein-coupled receptor 37	protein-coding
mm_142422.1	chr17	45568994	45569013	-	1	NA	exon (NM_008302, exon 9 of 11)	exon (NM_008302, exon 9 of 11)	4258	NM_008302	15516	Mm.2180	NM_008302	ENSMUSG00000023944	Hsp90ab1	90kDa|AL022974|C81438|Hsp84|Hsp84-1|Hsp90|Hspcb	heat shock protein 90 alpha (cytosolic), class B member 1	protein-coding
mm_25237.1	chr3	103901811	103901821	+	1	NA	intron (NR_104070, intron 18 of 22)	MTE2b|LTR|ERVL-MaLR	-12304	NM_172684	229675	Mm.29366	NM_172684	ENSMUSG00000044098	Rsbn1	C230004D03Rik|E330004N01|Rosbin|Rsbn|Rsbp|mKIAA3002	rosbin, round spermatid basic protein 1	protein-coding
mm_25708.1	chr3	122511200	122511220	+	1	NA	intron (NM_013867, intron 5 of 11)	intron (NM_013867, intron 5 of 11)	30471	NR_106117	102465764		NR_106117	ENSMUSG00000104773	Mir7657	mmu-mir-7657	microRNA 7657	ncRNA
mm_114944.1	chr13	96542728	96542775	+	1	NA	promoter-TSS (NM_001164222)	promoter-TSS (NM_001164222)	16	NM_023420	68018	Mm.24125	NM_023420	ENSMUSG00000021669	Col4a3bp	2810404O15Rik|9230101K08Rik|AU016711|CERT|GPBP	collagen, type IV, alpha 3 (Goodpasture antigen) binding protein	protein-coding
mm_150800.1	chr19	44305920	44305946	+	1	NA	3' UTR (NM_009128, exon 6 of 6)	3' UTR (NM_009128, exon 6 of 6)	2762	NR_039574	100628619		NR_039574	ENSMUSG00000093315	Mir5114	mmu-mir-5114|mu-mir-5114	microRNA 5114	ncRNA
mm_30041.1	chr3	135696816	135696828	-	1	NA	Intergenic	Intergenic	-5275	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_30792.1	chr4	19708584	19708599	+	1	NA	intron (NR_074089, intron 1 of 23)	CpG	413	NM_177327	107568	Mm.78312	NM_177327	ENSMUSG00000041058	Wwp1	8030445B08Rik|AIP5|SDRP1|Tiul1	WW domain containing E3 ubiquitin protein ligase 1	protein-coding
mm_28740.1	chr3	95737832	95737871	-	1	NA	exon (NM_007899, exon 4 of 11)	exon (NM_007899, exon 4 of 11)	1718	NM_007899	13601	Mm.3433	NM_007899	ENSMUSG00000028108	Ecm1	AI663821|p85	extracellular matrix protein 1	protein-coding
mm_61354.1	chr7	68338338	68338340	+	1	NA	intron (NM_001013811, intron 5 of 8)	MER47B|DNA|TcMar-Tigger	-61745	NR_040340	100504026	Mm.426764	NR_040340	ENSMUSG00000086628	Gm16157	OTTMUSG00000031023	predicted gene 16157	ncRNA
mm_165420.1	chr2	148522375	148522375	+	1	NA	Intergenic	Intergenic	-78840	NM_010740	17064	Mm.681	NM_010740	ENSMUSG00000027435	Cd93	6030404G09Rik|AA145088|AA4.1|AW555904|C1qr1|C1qrp|Ly68	CD93 antigen	protein-coding
mm_147153.1	chr18	36679228	36679250	-	1	NA	promoter-TSS (NM_026404)	promoter-TSS (NM_026404)	24	NM_026404	67843	Mm.273350	NM_026404	ENSMUSG00000033272	Slc35a4	2610030J16Rik	solute carrier family 35, member A4	protein-coding
mm_55677.1	chr6	72598382	72598424	-	1	NA	promoter-TSS (NM_026159)	promoter-TSS (NM_026159)	10	NM_144917	232089	Mm.167232	NM_144917	ENSMUSG00000056698	Elmod3	AI844780|C330008I15Rik|RBM29|Rbed1	ELMO/CED-12 domain containing 3	protein-coding
mm_158436.1	chrX	140062449	140062460	-	1	NA	promoter-TSS (NM_177921)	promoter-TSS (NM_177921)	114	NM_001081668	279706	Mm.102590	NM_001081668	ENSMUSG00000072944	Nup62cl	Gm719	nucleoporin 62 C-terminal like	protein-coding
mm_75183.1	chr8	36952415	36952473	-	1	NA	promoter-TSS (NM_001194940)	promoter-TSS (NM_001194940)	-2	NM_001194940	50768	Mm.125155	NM_015802	ENSMUSG00000031523	Dlc1	A730069N07Rik|Arhgap7|HP|STARD12|dlc-1	deleted in liver cancer 1	protein-coding
mm_94144.1	chr10	128737599	128737616	-	1	NA	intron (NM_016811, intron 1 of 23)	intron (NM_016811, intron 1 of 23)	6449	NM_016811	13139	Mm.291235	NM_016811	ENSMUSG00000025357	Dgka	80kDa|AW146112|Dagk1	diacylglycerol kinase, alpha	protein-coding
mm_160523.1	chr9	35844126	35844126	-	1	NA	promoter-TSS (NM_029863)	promoter-TSS (NM_029863)	24	NM_029863	77080	Mm.159846	NM_029863	ENSMUSG00000047980	9230110F15Rik	Pate-A|Pate5|mANLP3	RIKEN cDNA 9230110F15 gene	protein-coding
mm_140203.1	chr17	83729193	83729202	+	1	NA	intron (NM_001171053, intron 3 of 13)	intron (NM_001171053, intron 3 of 13)	23034	NM_001171052	116871	Mm.277668	NM_054082	ENSMUSG00000055817	Mta3	1110002J22Rik|mKIAA1266	metastasis associated 3	protein-coding
mm_117862.1	chr13	98839555	98839569	-	1	NA	Intergenic	Intergenic	-24113	NM_172591	218503	Mm.23928	NM_172591	ENSMUSG00000041685	Fcho2	5832424M12Rik|AA387320	FCH domain only 2	protein-coding
mm_45533.1	chr5	72752764	72752784	-	1	NA	promoter-TSS (NM_001289495)	promoter-TSS (NM_001289495)	3	NM_001289494	22165	Mm.3264	NM_013698	ENSMUSG00000054892	Txk	A130089B16Rik|Btkl|PTK-RL-18|PTK4|Rlk	TXK tyrosine kinase	protein-coding
mm_153129.1	chr19	34166038	34166092	-	1	NA	promoter-TSS (NM_024204)	promoter-TSS (NM_024204)	-24	NM_024204	52024	Mm.183030	NM_024204	ENSMUSG00000024774	Ankrd22	5430429D21Rik|D19Ertd675e	ankyrin repeat domain 22	protein-coding
mm_81766.1	chr9	114401448	114401474	+	1	NA	intron (NR_108101, intron 1 of 14)	CpG	366	NM_001200002	100504715	Mm.290516	NM_001200002	ENSMUSG00000079260	Tmppe	-	transmembrane protein with metallophosphoesterase domain	protein-coding
mm_18455.1	chr2	60963197	60963251	-	1	NA	promoter-TSS (NM_020296)	promoter-TSS (NM_020296)	-20	NM_020296	56878	Mm.259667	NM_020296	ENSMUSG00000026970	Rbms1	2600014B10Rik|AI255215|MSSP-1|MSSP-2|MSSP-3|YC1	RNA binding motif, single stranded interacting protein 1	protein-coding
mm_81351.1	chr9	108569952	108569960	+	1	NA	promoter-TSS (NM_026378)	promoter-TSS (NM_026378)	64	NM_026378	67789	Mm.458081	NM_026378	ENSMUSG00000019039	Dalrd3	6330580J24Rik|C77829|mir-425	DALR anticodon binding domain containing 3	protein-coding
mm_103888.1	chr11	83574981	83574994	-	1	NA	3' UTR (NM_011338, exon 4 of 4)	3' UTR (NM_011338, exon 4 of 4)	3649	NM_011338	20308	Mm.416125	NM_011338	ENSMUSG00000019122	Ccl9	CCF18|MRP-2|Scya10|Scya9	chemokine (C-C motif) ligand 9	protein-coding
mm_10383.1	chr2	12301230	12301250	+	1	NA	promoter-TSS (NR_040353)	promoter-TSS (NR_040353)	-6	NR_040353	338535	Mm.483275	NR_040353	ENSMUSG00000086843	E030013I19Rik	-	RIKEN cDNA E030013I19 gene	ncRNA
mm_135025.1	chr16	32522305	32522319	-	1	NA	Intergenic	Intergenic	26031	NM_199309	245308	Mm.76859	NM_199309	ENSMUSG00000052363	Zdhhc19	Gm1744|Gm616	zinc finger, DHHC domain containing 19	protein-coding
mm_111329.1	chr12	86726103	86726140	-	1	NA	promoter-TSS (NR_136890)	promoter-TSS (NR_136890)	-186	NR_136890	102635405		NR_136890		Gm32755	-	predicted gene, 32755	ncRNA
mm_52182.1	chr6	99433480	99433491	+	1	NA	intron (NM_001347345, intron 2 of 19)	intron (NM_001347345, intron 2 of 19)	1860	NM_053202	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_143448.1	chr17	70919855	70919889	-	1	NA	Intergenic	Intergenic	-66340	NM_001164074	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_13185.1	chr2	93187543	93187553	+	1	NA	promoter-TSS (NM_001025246)	promoter-TSS (NM_001025246)	-36	NM_001025246	277414	Mm.41033	NM_001025246	ENSMUSG00000068735	Trp53i11	Tp53i11	transformation related protein 53 inducible protein 11	protein-coding
mm_58170.1	chr6	142702223	142702255	-	1	NA	promoter-TSS (NM_011511)	promoter-TSS (NM_011511)	35	NM_021041	20928	Mm.35670	NM_011511	ENSMUSG00000030249	Abcc9	AI414027|AI449286|SUR2A|SUR2B|Sur2	ATP-binding cassette, sub-family C (CFTR/MRP), member 9	protein-coding
mm_167486.1	chr8	129263597	129263631	+	1	NA	promoter-TSS (NM_001346808)	promoter-TSS (NM_001346808)	-16	NM_001346808	102635552		NM_001346808		Gm32856	-	predicted gene, 32856	protein-coding
mm_107648.1	chr12	52516267	52516281	+	1	NA	exon (NM_009706, exon 1 of 6)	exon (NM_009706, exon 1 of 6)	197	NM_009706	11855	Mm.35059	NM_009706	ENSMUSG00000035133	Arhgap5	p190-B|p190B	Rho GTPase activating protein 5	protein-coding
mm_162162.1	chrX	94724627	94724627	+	1	NA	promoter-TSS (NM_001081473)	promoter-TSS (NM_001081473)	58	NM_001081473	668166	Mm.426145	NM_001081473	ENSMUSG00000073062	Zxdb	Zxda	zinc finger, X-linked, duplicated B	protein-coding
mm_41492.1	chr5	92137941	92137974	+	1	NA	promoter-TSS (NM_019490)	promoter-TSS (NM_019490)	19	NM_019490	56041	Mm.15868	NM_019490	ENSMUSG00000029407	Uso1	115kDa|TAP|Vdp	USO1 vesicle docking factor	protein-coding
mm_39435.1	chr5	16553860	16553886	+	1	NA	promoter-TSS (NM_001289461)	promoter-TSS (NM_001289461)	-28	NM_001289461	15234	Mm.267078	NM_010427	ENSMUSG00000028864	Hgf	C230052L06Rik|HGF/SF|NK1|NK2|SF|SF/HGF	hepatocyte growth factor	protein-coding
mm_111978.1	chr12	110278933	110278956	-	1	NA	promoter-TSS (NR_002866)	promoter-TSS (NR_002866)	-286	NM_172119	107585	Mm.154427	NM_172119	ENSMUSG00000075707	Dio3	-	deiodinase, iodothyronine type III	protein-coding
mm_25169.1	chr3	103074036	103074048	+	1	NA	promoter-TSS (NM_001033303)	promoter-TSS (NM_001033303)	28	NM_001033303	229665	Mm.331272	NM_001033303	ENSMUSG00000070385	Ampd1	AI553520|Ampd-1	adenosine monophosphate deaminase 1	protein-coding
mm_47578.1	chr5	124541082	124541095	-	1	NA	intron (NM_019770, intron 1 of 3)	CpG	297	NM_019770	56334	Mm.325307	NM_019770	ENSMUSG00000029390	Tmed2	1110032D12Rik|1810020N21Rik|Rnp24|Sid394|p24beta1	transmembrane p24 trafficking protein 2	protein-coding
mm_74793.1	chr8	22398261	22398276	-	1	NA	promoter-TSS (NR_045473)	promoter-TSS (NR_045473)	353	NM_181325	18408	Mm.200907	NM_181325	ENSMUSG00000031482	Slc25a15	D630044L02Rik|Ornt1	solute carrier family 25 (mitochondrial carrier ornithine transporter), member 15	protein-coding
mm_152535.1	chr19	11327129	11327139	-	1	NA	intron (NM_027836, intron 3 of 6)	intron (NM_027836, intron 3 of 6)	7561	NM_001276398	109225	Mm.491251	NM_027836	ENSMUSG00000024672	Ms4a7	9130422I10Rik|A430103C15Rik|CD20l4|CFFMA	membrane-spanning 4-domains, subfamily A, member 7	protein-coding
mm_55680.1	chr6	72610511	72610532	-	1	NA	TTS (NM_009444)	TTS (NM_009444)	6227	NM_009444	22135	Mm.246563	NM_009444		Tgoln2	TGN38B|TGN41|TGN46|Ttgn2	trans-golgi network protein 2	protein-coding
mm_102063.1	chr11	52256837	52256856	-	1	NA	exon (NM_009331, exon 8 of 10)	exon (NM_009331, exon 8 of 10)	24851	NM_011543	21402	Mm.42944	NM_011543	ENSMUSG00000036309	Skp1a	15kDa|2610043E24Rik|2610206H23Rik|EMC19|OCP-II|OCP2|SKP1|Tceb1l|p19A|p19Skp1	S-phase kinase-associated protein 1A	protein-coding
mm_29798.1	chr3	127780195	127780222	-	1	NA	5' UTR (NM_027808, exon 1 of 14)	5' UTR (NM_027808, exon 1 of 14)	319	NM_027808	71481	Mm.158704	NM_027808	ENSMUSG00000028028	Alpk1	8430410J10Rik|LAK	alpha-kinase 1	protein-coding
mm_83730.1	chr9	51056702	51056703	-	1	NA	TTS (NM_001033534)	TTS (NM_001033534)	20392	NM_001033534	244864	Mm.335152	NM_001033534	ENSMUSG00000060594	Layn	E030012M19Rik|Gm511	layilin	protein-coding
mm_59384.1	chr7	26189877	26189895	+	1	NA	intron (NM_010000, intron 4 of 8)	Lx4A|LINE|L1	16477	NM_010000	13094	Mm.14413	NM_010000	ENSMUSG00000040660	Cyp2b9	Cyp2b	cytochrome P450, family 2, subfamily b, polypeptide 9	protein-coding
mm_105278.1	chr11	102407923	102407951	-	1	NA	promoter-TSS (NM_026542)	promoter-TSS (NM_026542)	-420	NM_026542	68066	Mm.44226	NM_026542	ENSMUSG00000018677	Slc25a39	3010027G13Rik|D11Ertd333e	solute carrier family 25, member 39	protein-coding
mm_305.1	chr1	23761977	23761999	+	1	NA	promoter-TSS (NM_172124)	promoter-TSS (NM_172124)	62	NM_172124	280645	Mm.471661	NM_172124	ENSMUSG00000026156	B3gat2	GlcAT-S|Glcats	beta-1,3-glucuronyltransferase 2 (glucuronosyltransferase S)	protein-coding
mm_140032.1	chr17	74338764	74338772	+	1	NA	promoter-TSS (NM_001162870)	promoter-TSS (NM_001162870)	-219	NM_001162870	50850	Mm.19804	NM_016962	ENSMUSG00000024068	Spast	Spg4|mKIAA1083	spastin	protein-coding
mm_29121.1	chr3	105052917	105052938	-	1	NA	promoter-TSS (NM_001163333)	promoter-TSS (NM_001163333)	26	NM_001163333	80281	Mm.200327	NM_030249	ENSMUSG00000062127	Cttnbp2nl	AA552995|AA589392|AU018624|BC003236|mKIAA1433	CTTNBP2 N-terminal like	protein-coding
mm_63116.1	chr7	122671379	122671396	+	1	NA	promoter-TSS (NM_019430)	promoter-TSS (NM_019430)	-357	NM_019430	54376	Mm.444212	NM_019430	ENSMUSG00000066189	Cacng3	-	calcium channel, voltage-dependent, gamma subunit 3	protein-coding
mm_4671.1	chr1	180388000	180388004	+	1	NA	intron (NM_001081175, intron 2 of 7)	intron (NM_001081175, intron 2 of 7)	-57453	NR_003623	277333	Mm.389223	NM_199472		Gm5069	EG277333	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_170500.1	chr19	24290193	24290201	-	1	NA	Intergenic	(CCA)n|Simple_repeat|Simple_repeat	-9611	NM_008044	14297	Mm.7319	NM_008044	ENSMUSG00000059363	Fxn	FA|FARR|Frda|X25	frataxin	protein-coding
mm_78759.1	chr9	43303232	43303240	+	1	NA	Intergenic	Intergenic	-7527	NM_023655	72169	Mm.273277	NM_023655	ENSMUSG00000032013	Trim29	1110047J21Rik|2810431N19Rik|4732461M22Rik|AI119726	tripartite motif-containing 29	protein-coding
mm_27147.1	chr3	32949790	32949811	-	1	NA	3' UTR (NM_021483, exon 15 of 15)	3' UTR (NM_021483, exon 15 of 15)	35279	NM_001163517	58869	Mm.151332	NM_021483	ENSMUSG00000027674	Pex5l	1700016J08Rik|PXR2|Pex2|TRIP8b|pex5Rp	peroxisomal biogenesis factor 5-like	protein-coding
mm_25214.1	chr3	103846836	103846855	+	1	NA	intron (NM_001142960, intron 3 of 3)	intron (NM_001142960, intron 3 of 3)	-12950	NR_104070	19260	Mm.395	NM_008979	ENSMUSG00000027843	Ptpn22	70zpep|PEP|Ptpn8	protein tyrosine phosphatase, non-receptor type 22 (lymphoid)	protein-coding
mm_43783.1	chr5	142441107	142441110	+	1	NA	intron (NM_199068, intron 2 of 8)	intron (NM_199068, intron 2 of 8)	-22823	NM_172725	231855	Mm.78250	NM_172725	ENSMUSG00000039623	Ap5z1	C330006K01Rik	adaptor-related protein complex 5, zeta 1 subunit	protein-coding
mm_80428.1	chr9	77921486	77921500	+	1	NA	intron (NM_134255, intron 1 of 7)	intron (NM_134255, intron 1 of 7)	4128	NM_134255	68801	Mm.430736	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	ELOVL family member 5, elongation of long chain fatty acids (yeast)	protein-coding
mm_68959.1	chr7	126566365	126566416	-	1	NA	promoter-TSS (NM_146200)	promoter-TSS (NM_146200)	-24	NM_146200	56347	Mm.22776	NM_146200	ENSMUSG00000030738	Eif3c	110kDa|3230401O13Rik|Eif3s8|NIPIL(A3)|NipilA3|Xs|Xsl	eukaryotic translation initiation factor 3, subunit C	protein-coding
mm_61071.1	chr7	51511125	51511190	+	1	NA	non-coding (NR_073508, exon 1 of 21)	non-coding (NR_073508, exon 1 of 21)	128	NM_001271879	233246	Mm.254431	NM_177694	ENSMUSG00000055489	Ano5	9330162L24|Gdd1|Tmem16e	anoctamin 5	protein-coding
mm_107789.1	chr12	61610461	61610471	+	1	NA	intron (NM_178714, intron 1 of 3)	RLTR20C|LTR|ERVK	87299	NM_001310586	238205	Mm.28802	NM_178714	ENSMUSG00000035653	Lrfn5	AI427653|AI604817|C130061B21|mKIAA4208	leucine rich repeat and fibronectin type III domain containing 5	protein-coding
mm_118156.1	chr13	105250450	105250479	-	1	NA	exon (NM_027934, exon 4 of 8)	exon (NM_027934, exon 4 of 8)	42550	NM_027934	71816	Mm.317015	NM_027934	ENSMUSG00000021720	Rnf180	3110001E11Rik|Rines	ring finger protein 180	protein-coding
mm_22986.1	chr3	33621579	33621590	+	1	NA	Intergenic	L1Md_A|LINE|L1	-178599	NM_027619	67120	Mm.275710	NM_025978	ENSMUSG00000027677	Ttc14	2700016E08Rik|4930434D01Rik|4931403I22Rik|4933402I15Rik|AI662468|AU014779|AW561908|cI-44|mKIAA1980	tetratricopeptide repeat domain 14	protein-coding
mm_1405.1	chr1	67152468	67152477	+	1	NA	intron (NM_001080809, intron 7 of 37)	intron (NM_001080809, intron 7 of 37)	29445	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_61296.1	chr7	67660917	67660923	+	1	NA	intron (NM_001168476, intron 1 of 9)	intron (NM_001168476, intron 1 of 9)	13510	NM_025905	67009	Mm.249356	NM_025905	ENSMUSG00000030555	Ttc23	1600012K10Rik	tetratricopeptide repeat domain 23	protein-coding
mm_120071.1	chr14	57058216	57058221	+	1	NA	promoter-TSS (NM_016975)	promoter-TSS (NM_016975)	-188	NM_016975	14611	Mm.57207	NM_016975	ENSMUSG00000048582	Gja3	Cnx46|Cx43|Cx46|Gja-3	gap junction protein, alpha 3	protein-coding
mm_76944.1	chr8	105966039	105966120	-	1	NA	promoter-TSS (NM_001253804)	promoter-TSS (NM_001253804)	36	NM_001253804	20498	Mm.292447	NM_009195	ENSMUSG00000017765	Slc12a4	AW546649|KCC1|RBCKCC1	solute carrier family 12, member 4	protein-coding
mm_54209.1	chr6	25689496	25689506	-	1	NA	5' UTR (NM_010338, exon 1 of 2)	5' UTR (NM_010338, exon 1 of 2)	479	NM_010338	14763	Mm.409670	NM_010338	ENSMUSG00000039904	Gpr37	AI848630|Pael-R	G protein-coupled receptor 37	protein-coding
mm_72709.1	chr8	84986364	84986380	+	1	NA	Intergenic	Intergenic	-4223	NM_133255	170833	Mm.247775	NM_133255	ENSMUSG00000052566	Hook2	A630054I03Rik	hook microtubule tethering protein 2	protein-coding
mm_171922.1	chr5	58281214	58281223	+	1	NA	Intergenic	RLTR10D2|LTR|ERVK	171780	NR_046190	78163	Mm.243828	NR_046190	ENSMUSG00000105234	4930459L07Rik	-	RIKEN cDNA 4930459L07 gene	ncRNA
mm_93007.1	chr10	87057916	87057934	-	1	NA	promoter-TSS (NM_029685)	promoter-TSS (NM_029685)	-121	NM_029685	76640	Mm.78423	NM_029685	ENSMUSG00000047129	1700113H08Rik	-	RIKEN cDNA 1700113H08 gene	protein-coding
mm_30449.1	chr3	153852415	153852428	-	1	NA	promoter-TSS (NR_040373)	promoter-TSS (NR_040373)	3	NR_040373	72317	Mm.440147	NR_040373	ENSMUSG00000086438	Asb17os	2510003D18Rik	ankyrin repeat and SOCS box-containing 17, opposite strand	ncRNA
mm_36421.1	chr4	81361464	81361500	-	1	NA	exon (NM_001305286, exon 16 of 46)	exon (NM_001305286, exon 16 of 46)	81333	NM_010820	17475	Mm.153039	NM_010820	ENSMUSG00000028402	Mpdz	AI225843|B930003D11Rik|MUPP1	multiple PDZ domain protein	protein-coding
mm_6885.1	chr1	84695768	84695778	-	1	NA	promoter-TSS (NR_039588)	promoter-TSS (NR_039588)	-66	NR_039588	100628595		NR_039588	ENSMUSG00000093254	Mir5126	mir-5126|mmu-mir-5126|mu-mir-5126	microRNA 5126	ncRNA
mm_137403.1	chr17	25919342	25919368	+	1	NA	intron (NM_139154, intron 2 of 6)	CpG	359	NM_139154	224624	Mm.328872	NM_139154	ENSMUSG00000025730	Rab40c	RAR3	Rab40C, member RAS oncogene family	protein-coding
mm_67202.1	chr7	74302544	74302559	-	1	NA	intron (NM_001038643, intron 8 of 10)	B4|SINE|B4	252229	NM_023908	108116	Mm.425467	NM_023908	ENSMUSG00000025790	Slco3a1	5830414C08Rik|Anr1|MJAM|OATP-D|R75096|Slc21a11	solute carrier organic anion transporter family, member 3a1	protein-coding
mm_20776.1	chr2	143948428	143948444	-	1	NA	exon (NM_024281, exon 23 of 24)	exon (NM_024281, exon 23 of 24)	33105	NM_019771	56431	Mm.28919	NM_019771	ENSMUSG00000015932	Dstn	2610043P17Rik|ADF|AU042046|Dsn|corn1|sid23p	destrin	protein-coding
mm_51036.1	chr6	65594777	65594780	+	1	NA	intron (NM_001001495, intron 2 of 7)	intron (NM_001001495, intron 2 of 7)	4380	NM_001001495	414084	Mm.117558	NM_001001495	ENSMUSG00000044162	Tnip3	9030611K07Rik|ABIN-3|LIND	TNFAIP3 interacting protein 3	protein-coding
mm_2355.1	chr1	92934807	92934818	+	1	NA	non-coding (NR_015525, exon 2 of 2)	non-coding (NR_015525, exon 2 of 2)	404	NM_011796	23830	Mm.294315	NM_011796	ENSMUSG00000026270	Capn10	AW049679|Capn8|mKIAA1845	calpain 10	protein-coding
mm_16722.1	chr2	7328292	7328296	-	1	NA	intron (NM_001110231, intron 2 of 15)	intron (NM_001110231, intron 2 of 15)	67706	NM_001110232	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_162482.1	chr1	134406052	134406062	+	1	NA	promoter-TSS (NM_028057)	promoter-TSS (NM_028057)	67	NM_028057	72017	Mm.280230	NM_028057	ENSMUSG00000026456	Cyb5r1	1500005G05Rik|B5R.1|C80155|Nqo3a2	cytochrome b5 reductase 1	protein-coding
mm_70262.1	chr8	3522581	3522591	+	1	NA	intron (NM_001122818, intron 10 of 34)	intron (NM_001122818, intron 10 of 34)	7202	NM_015801	50767	Mm.23085	NM_015801	ENSMUSG00000004565	Pnpla6	AI661849|MSws|Nte	patatin-like phospholipase domain containing 6	protein-coding
mm_64847.1	chr7	13023206	13023223	-	1	NA	promoter-TSS (NM_011588)	promoter-TSS (NM_011588)	-938	NM_011588	21849	Mm.15701	NM_011588	ENSMUSG00000005566	Trim28	AA408787|KAP-1|KRIP-1|MommeD9|Tif1b|Tif1beta	tripartite motif-containing 28	protein-coding
mm_112452.1	chr13	5863816	5863826	+	1	NA	intron (NM_011803, intron 1 of 3)	intron (NM_011803, intron 1 of 3)	2332	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_135802.1	chr16	57265483	57265491	-	1	NA	TTS (NM_027651)	TTS (NM_027651)	27364	NM_027651	71027	Mm.158563	NM_027651	ENSMUSG00000022753	Tmem30c	4933401B01Rik|4933409A18Rik|Cdc50c	transmembrane protein 30C	protein-coding
mm_84611.1	chr9	70413234	70413274	-	1	NA	exon (NM_007630, exon 4 of 9)	exon (NM_007630, exon 4 of 9)	-7501	NR_049200	100885839		NR_049200	ENSMUSG00000093763	Mir5626	Gm25590|mir-5626|mmu-mir-5626	microRNA 5626	ncRNA
mm_57080.1	chr6	122581784	122581795	-	1	NA	intron (NM_001134391, intron 5 of 7)	intron (NM_001134391, intron 5 of 7)	20655	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_132351.1	chr16	34120082	34120093	+	1	NA	intron (NM_177357, intron 33 of 59)	intron (NM_177357, intron 33 of 59)	-153084	NM_009471	22247	Mm.13145	NM_009471	ENSMUSG00000022814	Umps	1700095D23Rik|AA408257|AL033308|BB164745	uridine monophosphate synthetase	protein-coding
mm_34678.1	chr4	150945332	150945337	+	1	NA	3' UTR (NM_001077508, exon 7 of 7)	3' UTR (NM_001077508, exon 7 of 7)	17335	NM_001077509	21942	Mm.244187	NM_011612	ENSMUSG00000028965	Tnfrsf9	4-1BB|A930040I11Rik|AA408498|AI325004|CDw137|Cd137|ILA|Ly63	tumor necrosis factor receptor superfamily, member 9	protein-coding
mm_78823.1	chr9	44101723	44101735	+	1	NA	promoter-TSS (NM_001190314)	promoter-TSS (NM_001190314)	-41	NM_001190314	259172	Mm.227110	NM_147126	ENSMUSG00000034739	Mfrp	rd6	membrane frizzled-related protein	protein-coding
mm_161684.1	chr17	20419230	20419230	+	1	NA	promoter-TSS (NM_001166735)	promoter-TSS (NM_001166735)	67	NM_001166735	665525	Mm.480265	NM_001166735	ENSMUSG00000091151	Vmn1r224	EG665525|Gm7673	vomeronasal 1 receptor 224	protein-coding
mm_82478.1	chr9	16502494	16502505	-	1	NA	Intergenic	Intergenic	-124268	NM_001080814	270120	Mm.195010	NM_001080814	ENSMUSG00000074505	Fat3	9430076A06Rik|D430038H04Rik|Gm1132|Gm510|MFAT3F	FAT atypical cadherin 3	protein-coding
mm_154865.1	chrX	20671348	20671365	+	1	NA	exon (NM_009457, exon 9 of 26)	exon (NM_009457, exon 9 of 26)	8460	NM_001136085	22201	Mm.1104	NM_009457	ENSMUSG00000001924	Uba1	A1S9|Sbx|Ube-1|Ube1x	ubiquitin-like modifier activating enzyme 1	protein-coding
mm_131208.1	chr16	8680792	8680794	+	1	NA	promoter-TSS (NM_001324517)	promoter-TSS (NM_001324517)	23	NM_001324517	436336	Mm.357666	NM_001324517		Gm5767	EG436336	predicted gene 5767	protein-coding
mm_4599.1	chr1	178406032	178406034	+	1	NA	5' UTR (NM_026626, exon 1 of 7)	5' UTR (NM_026626, exon 1 of 7)	152	NM_026626	68226	Mm.252132	NM_026626	ENSMUSG00000026495	Efcab2	1700073K01Rik|D830011E08Rik	EF-hand calcium binding domain 2	protein-coding
mm_57595.1	chr6	127769701	127769708	-	1	NA	promoter-TSS (NM_201371)	promoter-TSS (NM_201371)	-545	NM_201371	381813	Mm.39750	NM_201371	ENSMUSG00000030350	Prmt8	Hrmt1l3|Hrmt1l4	protein arginine N-methyltransferase 8	protein-coding
mm_106885.1	chr12	8012076	8012085	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	34403	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_145311.1	chr18	53877725	53877756	+	1	NA	intron (NM_152809, intron 1 of 12)	intron (NM_152809, intron 1 of 12)	15627	NM_152809	70425	Mm.368668	NM_152809	ENSMUSG00000073563	Csnk1g3	3300002K07Rik|C330049O21Rik	casein kinase 1, gamma 3	protein-coding
mm_97381.1	chr11	77718727	77718749	+	1	NA	TTS (NM_001024205)	TTS (NM_001024205)	6555	NM_001313933	12957	Mm.22830	NM_009965	ENSMUSG00000000724	Cryba1	BA3/A1|Cryb	crystallin, beta A1	protein-coding
mm_1311.1	chr1	65029829	65029841	+	1	NA	intron (NM_001310617, intron 1 of 8)	Lx9|LINE|L1	2924	NM_027582	70861	Mm.18725	NM_027582	ENSMUSG00000025955	Akr1cl	4921521F21Rik|AI451536|AI503553	aldo-keto reductase family 1, member C-like	protein-coding
mm_45957.1	chr5	90464024	90464035	-	1	NA	exon (NM_009654, exon 4 of 15)	exon (NM_009654, exon 4 of 15)	3159	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_81967.1	chr9	120959553	120959573	+	1	NA	3' UTR (NM_007614, exon 15 of 15)	3' UTR (NM_007614, exon 15 of 15)	4477	NR_106058	102465661		NR_106058	ENSMUSG00000106193	Mir7090	mmu-mir-7090	microRNA 7090	ncRNA
mm_24410.1	chr3	90466086	90466090	+	1	NA	promoter-TSS (NM_008727)	promoter-TSS (NM_008727)	-222	NM_008727	18160	Mm.4627	NM_008727	ENSMUSG00000027931	Npr1	AI893888|GC-A|NPR-A|NPRA|Pndr	natriuretic peptide receptor 1	protein-coding
mm_163837.1	chr14	19417832	19417899	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	184722	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_114872.1	chr13	94083491	94083500	+	1	NA	intron (NM_172589, intron 1 of 3)	intron (NM_172589, intron 1 of 3)	25699	NM_172589	218454	Mm.316553	NM_172589	ENSMUSG00000045312	Lhfpl2	6030465B15|AI447312|AW050335|mKIAA0206|vgim	lipoma HMGIC fusion partner-like 2	protein-coding
mm_13641.1	chr2	114049170	114049178	+	1	NA	exon (NM_009608, exon 5 of 7)	exon (NM_009608, exon 5 of 7)	3701	NM_009608	11464	Mm.686	NM_009608	ENSMUSG00000068614	Actc1	Actc-1	actin, alpha, cardiac muscle 1	protein-coding
mm_79320.1	chr9	52172816	52172829	+	1	NA	Intergenic	Intergenic	-4711	NM_001162921	244871	Mm.295686	NM_001162921	ENSMUSG00000035164	Zc3h12c	A230108E06|C230027N18Rik|mKIAA1726	zinc finger CCCH type containing 12C	protein-coding
mm_128806.1	chr15	66949051	66949068	-	1	NA	intron (NM_008681, intron 3 of 15)	intron (NM_008681, intron 3 of 15)	20582	NM_008681	17988	Mm.30837	NM_008681	ENSMUSG00000005125	Ndrg1	CAP43|CMT4D|DRG1|HMSNL|NMSL|Ndr1|Ndrl|PROXY1|RTP|TDD5	N-myc downstream regulated gene 1	protein-coding
mm_83666.1	chr9	49714159	49714169	-	1	NA	intron (NM_001081445, intron 1 of 17)	intron (NM_001081445, intron 1 of 17)	84905	NM_001081445	17967	Mm.4974	NM_010875	ENSMUSG00000039542	Ncam1	CD56|E-NCAM|NCAM-1|Ncam	neural cell adhesion molecule 1	protein-coding
mm_110912.1	chr12	76216876	76216897	-	1	NA	intron (NM_001159532, intron 5 of 8)	intron (NM_001159532, intron 5 of 8)	29860	NM_019784	80384	Mm.78551	NM_019784	ENSMUSG00000021056	Tex21	4931406F04Rik|4931412D23Rik|4931421K24Rik|tsec-2	testis expressed gene 21	protein-coding
mm_103527.1	chr11	77078405	77078442	-	1	NA	promoter-TSS (NR_030756)	promoter-TSS (NR_030756)	14	NM_001012309	237859	Mm.156195	NM_001012309	ENSMUSG00000037958	Nsrp1	8030451K07|AI851076|AL022898|Ccdc55|NSpr70|NSrp70	nuclear speckle regulatory protein 1	protein-coding
mm_54421.1	chr6	32993645	32993649	-	1	NA	intron (NM_025336, intron 3 of 7)	intron (NM_025336, intron 3 of 7)	66505	NM_025336	66075	Mm.21501	NM_025336	ENSMUSG00000053768	Chchd3	0610041L09Rik|1700039J09Rik|AW558177	coiled-coil-helix-coiled-coil-helix domain containing 3	protein-coding
mm_132698.1	chr16	43363040	43363073	+	1	NA	intron (NM_181058, intron 2 of 6)	LFSINE_Vert|SINE|tRNA	57140	NR_046026	626693	Mm.447083	NR_046026	ENSMUSG00000085499	Gm15713	OTTMUSG00000025617	predicted gene 15713	ncRNA
mm_17902.1	chr2	35200797	35200825	-	1	NA	5' UTR (NM_026697, exon 1 of 8)	5' UTR (NM_026697, exon 1 of 8)	309	NM_026697	68365	Mm.198264	NM_026697	ENSMUSG00000026878	Rab14	0610030G24Rik|2810475J17Rik|A830021G03Rik|AI314285|AI649155|D030017L14Rik	RAB14, member RAS oncogene family	protein-coding
mm_115404.1	chr13	114048488	114048492	+	1	NA	intron (NM_172595, intron 4 of 4)	L1MDa|LINE|L1	103102	NR_045836	319803	Mm.386896	NM_177004		A430090L17Rik	-	RIKEN cDNA A430090L17 gene	ncRNA
mm_152724.1	chr19	18630907	18630909	-	1	NA	intron (NM_017375, intron 1 of 9)	intron (NM_017375, intron 1 of 9)	905	NM_017375	20409	Mm.172222	NM_017375	ENSMUSG00000024725	Ostf1	C78236|SH3P2|Sh3d3	osteoclast stimulating factor 1	protein-coding
mm_139151.1	chr17	47538690	47538695	+	1	NA	intron (NM_001081635, intron 1 of 6)	intron (NM_001081635, intron 1 of 6)	33641	NM_001081635	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_5651.1	chr1	40534391	40534393	-	1	NA	intron (NM_010553, intron 7 of 12)	ORR1A2|LTR|ERVL-MaLR	19030	NM_010553	16174	Mm.20466	NM_010553	ENSMUSG00000026068	Il18rap	AcPL|IL-18R-beta|IL-18RAcP|IL-18Rbeta|IL-1RAcPL	interleukin 18 receptor accessory protein	protein-coding
mm_52310.1	chr6	108828606	108828616	+	1	NA	promoter-TSS (NM_138677)	promoter-TSS (NM_138677)	-30	NM_138677	192193	Mm.21596	NM_138677	ENSMUSG00000030104	Edem1	A130059K23Rik|EDEM|mKIAA0212	ER degradation enhancer, mannosidase alpha-like 1	protein-coding
mm_162761.1	chr10	61881956	61881956	-	1	NA	intron (NM_001304757, intron 16 of 37)	intron (NM_001304757, intron 16 of 37)	97152	NM_001304757	12817	Mm.300931	NM_007731	ENSMUSG00000058806	Col13a1	-	collagen, type XIII, alpha 1	protein-coding
mm_133908.1	chr16	97550864	97550875	+	1	NA	intron (NM_013606, intron 7 of 13)	intron (NM_013606, intron 7 of 13)	14786	NM_013606	17858	Mm.14157	NM_013606	ENSMUSG00000023341	Mx2	AI528743|Mx-2	MX dynamin-like GTPase 2	protein-coding
mm_84746.1	chr9	75409283	75409336	-	1	NA	promoter-TSS (NR_040719)	promoter-TSS (NR_040719)	50	NM_027418	50772	Mm.480076	NM_015806	ENSMUSG00000042688	Mapk6	2610021I23Rik|D130053K17Rik|Erk3|Mapk4|Mapk63|Prkm4|Prkm6	mitogen-activated protein kinase 6	protein-coding
mm_148963.1	chr19	7494428	7494462	+	1	NA	promoter-TSS (NM_146091)	promoter-TSS (NM_146091)	7	NM_146091	109168	Mm.264016	NM_146091	ENSMUSG00000024759	Atl3	4633402C03Rik|5730596K20Rik|AI465397|AW228836	atlastin GTPase 3	protein-coding
mm_109925.1	chr12	8641009	8641039	-	1	NA	Intergenic	CpG	-33110	NM_001160221	80913	Mm.341243	NM_030723	ENSMUSG00000020594	Pum2	5730503J23Rik|Pumm2	pumilio RNA-binding family member 2	protein-coding
mm_3343.1	chr1	137971171	137971186	+	1	NA	Intergenic	(TTTC)n|Simple_repeat|Simple_repeat	4539	NR_029820	723890		NR_029820	ENSMUSG00000065458	Mir181b-1	Mirn181b-1|mir-181b-1	microRNA 181b-1	ncRNA
mm_118651.1	chr14	21745487	21745512	+	1	NA	intron (NM_001007268, intron 3 of 7)	intron (NM_001007268, intron 3 of 7)	-2620	NM_013849	27389	Mm.390674	NM_013849	ENSMUSG00000021768	Dusp13	DUSP13A|DUSP13B|Gm1203|LMW-DSP6|MDSP|TMDP|TS-DSP6	dual specificity phosphatase 13	protein-coding
mm_133549.1	chr16	91372787	91372864	+	1	NA	promoter-TSS (NM_010509)	promoter-TSS (NM_010509)	42	NM_001110498	15976	Mm.6834	NM_010509	ENSMUSG00000022971	Ifnar2	AI747302|Ifnar-2	interferon (alpha and beta) receptor 2	protein-coding
mm_36749.1	chr4	101179887	101179900	-	1	NA	intron (NM_146145, intron 6 of 24)	intron (NM_146145, intron 6 of 24)	85389	NM_146145	16451	Mm.289657	NM_146145	ENSMUSG00000028530	Jak1	AA960307|BAP004|C130039L05Rik	Janus kinase 1	protein-coding
mm_126292.1	chr15	79347584	79347598	+	1	NA	promoter-TSS (NM_010755)	promoter-TSS (NM_010755)	71	NM_010755	17133	Mm.86646	NM_010755	ENSMUSG00000042622	Maff	-	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein F (avian)	protein-coding
mm_126213.1	chr15	78899845	78899853	+	1	NA	promoter-TSS (NM_009164)	promoter-TSS (NM_009164)	81	NM_009164	20401	Mm.4462	NM_009164	ENSMUSG00000022436	Sh3bp1	3BP-1	SH3-domain binding protein 1	protein-coding
mm_11482.1	chr2	32385712	32385732	+	1	NA	exon (NM_008491, exon 4 of 6)	exon (NM_008491, exon 4 of 6)	2017	NM_008491	16819	Mm.9537	NM_008491	ENSMUSG00000026822	Lcn2	24p3|AW212229|NRL|Sip24	lipocalin 2	protein-coding
mm_92158.1	chr10	67537700	67537711	-	1	NA	promoter-TSS (NM_010118)	promoter-TSS (NM_010118)	-164	NM_010118	13654	Mm.290421	NM_010118	ENSMUSG00000037868	Egr2	Egr-2|Krox-20|Krox20|NGF1-B|Zfp-25|Zfp-6	early growth response 2	protein-coding
mm_144906.1	chr18	37400846	37400886	+	1	NA	promoter-TSS (NM_053134)	promoter-TSS (NM_053134)	11	NM_053134	93880	Mm.286019	NM_053134	ENSMUSG00000051242	Pcdhb9	Pcdhb4C|PcdhbI	protocadherin beta 9	protein-coding
mm_59606.1	chr7	28141001	28141015	+	1	NA	intron (NM_001164655, intron 5 of 19)	intron (NM_001164655, intron 5 of 19)	11542	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_53032.1	chr6	124512645	124512668	+	1	NA	promoter-TSS (NM_023143)	promoter-TSS (NM_023143)	35	NM_023143	50909	Mm.333375	NM_023143	ENSMUSG00000055172	C1ra	AI132558|C1r|mC1rA	complement component 1, r subcomponent A	protein-coding
mm_71155.1	chr8	40124658	40124671	+	1	NA	intron (NR_035426, intron 1 of 5)	intron (NR_035426, intron 1 of 5)	103123	NR_035426	100316806		NR_035426	ENSMUSG00000080653	Mir669e	Mirn669e|mmu-mir-669e	microRNA 669e	ncRNA
mm_15480.1	chr2	157561718	157561731	+	1	NA	exon (NM_001291129, exon 3 of 3)	exon (NM_001291129, exon 3 of 3)	1646	NM_180960	18111	Mm.34330	NM_010923	ENSMUSG00000067786	Nnat	5730414I02Rik|AW107673|Peg5	neuronatin	protein-coding
mm_24995.1	chr3	97159080	97159101	+	1	NA	5' UTR (NM_019800, exon 1 of 10)	5' UTR (NM_019800, exon 1 of 10)	313	NM_019800	66659	Mm.101368	NM_019800	ENSMUSG00000028093	Acp6	5730559A09Rik|ACPL1|AU022842|mPACPL1	acid phosphatase 6, lysophosphatidic	protein-coding
mm_54582.1	chr6	38124542	38124557	-	1	NA	promoter-TSS (NM_080467)	promoter-TSS (NM_080467)	37	NM_080467	140494	Mm.462308	NM_080467	ENSMUSG00000038600	Atp6v0a4	Atp6n1b|a4	ATPase, H+ transporting, lysosomal V0 subunit A4	protein-coding
mm_16637.1	chr2	5925269	5925272	-	1	NA	intron (NM_001081131, intron 4 of 16)	intron (NM_001081131, intron 4 of 16)	17522	NM_001081131	209692	Mm.222517	NM_001081131	ENSMUSG00000025815	Dhtkd1	C330018I04Rik	dehydrogenase E1 and transketolase domain containing 1	protein-coding
mm_140701.1	chr17	14398932	14398941	-	1	NA	promoter-TSS (NR_027986)	promoter-TSS (NR_027986)	6	NR_027986	74917	Mm.32228	NM_183107		4930474M22Rik	-	RIKEN cDNA 4930474M22 gene	ncRNA
mm_21247.1	chr2	156176787	156176818	-	1	NA	intron (NM_133242, intron 3 of 16)	intron (NM_133242, intron 3 of 16)	2778	NM_001291115	170791	Mm.392436	NM_133242	ENSMUSG00000027620	Rbm39	1500012C14Rik|2310040E03Rik|B330012G18Rik|C79248|R75070|Rnpc2|caper	RNA binding motif protein 39	protein-coding
mm_48012.1	chr5	136165243	136165253	-	1	NA	intron (NM_178751, intron 1 of 2)	B3A|SINE|B2	5408	NM_178751	269717	Mm.308396	NM_178751	ENSMUSG00000039747	Orai2	A730041O15Rik|Tmem142b	ORAI calcium release-activated calcium modulator 2	protein-coding
mm_93977.1	chr10	127341584	127341614	-	1	NA	promoter-TSS (NM_010296)	promoter-TSS (NM_010296)	-20	NM_010296	14632	Mm.391450	NM_010296	ENSMUSG00000025407	Gli1	AV235269|Zfp-5|Zfp5	GLI-Kruppel family member GLI1	protein-coding
mm_145836.1	chr18	65442382	65442393	+	1	NA	intron (NM_172833, intron 2 of 15)	intron (NM_172833, intron 2 of 15)	11390	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_77637.1	chr8	124273957	124273966	-	1	NA	intron (NM_139272, intron 1 of 15)	intron (NM_139272, intron 1 of 15)	42567	NM_139272	108148	Mm.33808	NM_139272	ENSMUSG00000089704	Galnt2	AI480629	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2	protein-coding
mm_678.1	chr1	40466295	40466302	+	1	NA	TTS (NM_001025602)	TTS (NM_001025602)	292	NM_008365	16182	Mm.253664	NM_008365	ENSMUSG00000026070	Il18r1	Il18ralpha|Il1rrp	interleukin 18 receptor 1	protein-coding
mm_5121.1	chr1	9298500	9298512	-	1	NA	5' UTR (NM_001290390, exon 1 of 21)	5' UTR (NM_001290390, exon 1 of 21)	1371	NM_001290390	71096	Mm.336395	NM_027671	ENSMUSG00000025909	Sntg1	4933426D16Rik|G1SYN|SYN4	syntrophin, gamma 1	protein-coding
mm_172713.1	chr8	70477541	70477545	+	1	NA	promoter-TSS (NM_001122830)	promoter-TSS (NM_001122830)	-600	NM_178771	234378	Mm.187090	NM_172052	ENSMUSG00000055707	Klhl26	C630013N10Rik|Klkl26	kelch-like 26	protein-coding
mm_149540.1	chr19	12564464	12564490	+	1	NA	Intergenic	Intergenic	-9033	NM_001346545	107373	Mm.1643	NM_026640	ENSMUSG00000024691	Fam111a	4632417K18Rik|AW413625	family with sequence similarity 111, member A	protein-coding
mm_57604.1	chr6	128009238	128009241	-	1	NA	intron (NM_175414, intron 3 of 8)	intron (NM_175414, intron 3 of 8)	121617	NM_026743	68498	Mm.174368	NM_026743	ENSMUSG00000030351	Tspan11	1110014F12Rik|AU067806	tetraspanin 11	protein-coding
mm_23553.1	chr3	62159192	62159209	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-179577	NM_001081295	622434	Mm.153974	NM_001081295	ENSMUSG00000036885	Arhgef26	4631416L12Rik|8430436L14Rik|AI303572|AW491953|SGEF	Rho guanine nucleotide exchange factor (GEF) 26	protein-coding
mm_168941.1	chr12	71302180	71302183	-	1	NA	Intergenic	Intergenic	-7703	NM_021532	59036	Mm.46662	NM_021532	ENSMUSG00000044548	Dact1	4921528D17Rik|AI115603|DAPPER|DAPPER1|FRODO|Frd1|Frodo1|MDpr1|MTNG3|THYEX3	dishevelled-binding antagonist of beta-catenin 1	protein-coding
mm_163432.1	chr12	85281341	85281344	+	1	NA	promoter-TSS (NM_025421)	promoter-TSS (NM_025421)	-907	NM_025421	66204	Mm.311985	NM_025421	ENSMUSG00000008822	Acyp1	1110039O14Rik|AI325944	acylphosphatase 1, erythrocyte (common) type	protein-coding
mm_276.1	chr1	21240632	21240642	+	1	NA	promoter-TSS (NM_010356)	promoter-TSS (NM_010356)	52	NM_010356	14859	Mm.394593	NM_010356	ENSMUSG00000025934	Gsta3	Gst2-3	glutathione S-transferase, alpha 3	protein-coding
mm_84501.1	chr9	66919167	66919197	-	1	NA	intron (NM_173413, intron 1 of 7)	intron (NM_173413, intron 1 of 7)	523	NM_173413	235442	Mm.260376	NM_173413	ENSMUSG00000036943	Rab8b	5930437D16|D330025I23Rik	RAB8B, member RAS oncogene family	protein-coding
mm_1607.1	chr1	74382352	74382364	+	1	NA	intron (NM_013612, intron 9 of 14)	intron (NM_013612, intron 9 of 14)	7155	NM_013612	18173	Mm.2913	NM_013612	ENSMUSG00000026177	Slc11a1	Bcg|Ity|Ity1|Lsh|Nramp|Nramp1|ity	solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1	protein-coding
mm_144094.1	chr18	3337907	3337917	+	1	NA	promoter-TSS (NM_001110852)	promoter-TSS (NM_001110852)	-323	NM_001110852	12916	Mm.5244	NM_013498	ENSMUSG00000063889	Crem	ICER|ICERI	cAMP responsive element modulator	protein-coding
mm_149834.1	chr19	24875663	24875667	+	1	NA	Intergenic	Intergenic	-13823	NM_175013	226041	Mm.105222	NM_175013	ENSMUSG00000041731	Pgm5	4833423B07|9530034F03Rik|D830025G17|aciculin	phosphoglucomutase 5	protein-coding
mm_53278.1	chr6	128662380	128662396	+	1	NA	promoter-TSS (NM_053165)	promoter-TSS (NM_053165)	3	NM_053165	94071	Mm.197689	NM_053165	ENSMUSG00000030364	Clec2h	Clrf|clr-f	C-type lectin domain family 2, member h	protein-coding
mm_173157.1	chrX	35860188	35860193	+	1	NA	Intergenic	L1Md_A|LINE|L1	-28642	NM_001009947	75974	Mm.32873	NM_177745	ENSMUSG00000031093	Dock11	5033414A21Rik|8030476J24|Zizimin2|sph238	dedicator of cytokinesis 11	protein-coding
mm_100279.1	chr11	117790890	117790927	+	1	NA	exon (NM_181856, exon 12 of 16)	exon (NM_181856, exon 12 of 16)	-6752	NM_029964	77727	Mm.159981	NM_029964	ENSMUSG00000025573	6030468B19Rik	-	RIKEN cDNA 6030468B19 gene	protein-coding
mm_55132.1	chr6	51059703	51059745	-	1	NA	Intergenic	Intergenic	210186	NR_029719	387166		NR_029719	ENSMUSG00000065505	Mir148a	Mirn148|Mirn148a|mir-148a	microRNA 148a	ncRNA
mm_49716.1	chr6	34486259	34486292	+	1	NA	intron (NM_007563, intron 1 of 2)	intron (NM_007563, intron 1 of 2)	9919	NM_007563	12183	Mm.282863	NM_007563	ENSMUSG00000038871	Bpgm	AI323730|AL022789|C86192	2,3-bisphosphoglycerate mutase	protein-coding
mm_140836.1	chr17	23670786	23670792	-	1	NA	intron (NM_001008425, intron 2 of 12)	intron (NM_001008425, intron 2 of 12)	-2819	NM_181821	353502	Mm.359030	NM_181821	ENSMUSG00000023904	Hcfc1r1	HPIP	host cell factor C1 regulator 1 (XPO1-dependent)	protein-coding
mm_123192.1	chr14	57925466	57925484	-	1	NA	intron (NM_028643, intron 8 of 11)	B4A|SINE|B4	-35213	NM_029492	75965	Mm.29044	NM_029492	ENSMUSG00000021969	Zdhhc20	4930542A17Rik|5033406L14Rik|AI448102|B230110O18Rik|ENSMUSG00000055956|HK11	zinc finger, DHHC domain containing 20	protein-coding
mm_34899.1	chr4	155630522	155630533	+	1	NA	intron (NM_001347308, intron 6 of 20)	MTEb|LTR|ERVL-MaLR	5658	NM_007661	12537	Mm.267410	NM_007661	ENSMUSG00000029062	Cdk11b	AA989746|CDK11-p110|CDK11-p46|CDK11-p58|Cdc11b|Cdc2l1|Cdc2l2|Cdk11|p58	cyclin-dependent kinase 11B	protein-coding
mm_19767.1	chr2	105399595	105399642	-	1	NA	promoter-TSS (NM_009037)	promoter-TSS (NM_009037)	-299	NM_009037	19672	Mm.4876	NM_009037	ENSMUSG00000005973	Rcn1	Rcn	reticulocalbin 1	protein-coding
mm_172838.1	chr9	26408234	26408234	-	1	NA	Intergenic	L1Md_T|LINE|L1	-325574	NM_001310766	76898	Mm.218788	NM_029792	ENSMUSG00000045994	B3gat1	0710007K08Rik|AI846286|GlcAT-P|Glcatp|Hnk1	beta-1,3-glucuronyltransferase 1 (glucuronosyltransferase P)	protein-coding
mm_89889.1	chr10	109137295	109137297	+	1	NA	Intergenic	Intergenic	-126321	NM_001252341	20979	Mm.289702	NM_009306	ENSMUSG00000035864	Syt1	AW124717|G630098F17Rik|SytI	synaptotagmin I	protein-coding
mm_137398.1	chr17	25829037	25829076	+	1	NA	promoter-TSS (NM_028101)	promoter-TSS (NM_028101)	13	NM_028101	72106	Mm.277599	NM_028101	ENSMUSG00000025736	Jmjd8	2610003J06Rik	jumonji domain containing 8	protein-coding
mm_56082.1	chr6	87287269	87287282	-	1	NA	intron (NM_054041, intron 5 of 17)	intron (NM_054041, intron 5 of 17)	48500	NM_054041	69538	Mm.232525	NM_054041	ENSMUSG00000033420	Antxr1	2310008J16Rik|2810405N18Rik|Antrx1|Tem8	anthrax toxin receptor 1	protein-coding
mm_92841.1	chr10	81508067	81508099	-	1	NA	intron (NM_010304, intron 5 of 6)	intron (NM_010304, intron 5 of 6)	-7946	NM_010102	13611	Mm.33065	NM_010102	ENSMUSG00000044199	S1pr4	Edg6|Lpc1|S1p4	sphingosine-1-phosphate receptor 4	protein-coding
mm_87367.1	chr10	44016143	44016148	+	1	NA	Intergenic	L2b|LINE|L2	-11299	NM_172393	11630	Mm.292082	NM_172393	ENSMUSG00000019866	Aim1	AI462491|AI463325	absent in melanoma 1	protein-coding
mm_54761.1	chr6	41197008	41197021	-	1	NA	Intergenic	L1ME3D|LINE|L1	-105258	NM_011646	22074	Mm.383263	NM_011646	ENSMUSG00000054106	Try4	0910001B19Rik|Td	trypsin 4	protein-coding
mm_74242.1	chr8	124793014	124793056	+	1	NA	promoter-TSS (NM_198632)	promoter-TSS (NM_198632)	16	NM_198632	330863	Mm.422769	NM_198632	ENSMUSG00000036913	Trim67	D130049O21Rik|TNL	tripartite motif-containing 67	protein-coding
mm_99865.1	chr11	109397377	109397400	+	1	NA	3' UTR (NM_010303, exon 4 of 4)	3' UTR (NM_010303, exon 4 of 4)	-28558	NM_025275	13929	Mm.211850	NM_025275	ENSMUSG00000020610	Amz2	AA408420|ESTM12|X83328	archaelysin family metallopeptidase 2	protein-coding
mm_145374.1	chr18	56734069	56734082	+	1	NA	intron (NM_010721, intron 5 of 10)	(CCTG)n|Simple_repeat|Simple_repeat	26262	NM_010721	16906	Mm.4105	NM_010721	ENSMUSG00000024590	Lmnb1	-	lamin B1	protein-coding
mm_158552.1	chrX	147428775	147428818	-	1	NA	5' UTR (NM_008356, exon 1 of 14)	5' UTR (NM_008356, exon 1 of 14)	396	NM_001306059	16165	Mm.368330	NM_008356	ENSMUSG00000031289	Il13ra2	CD213a2|IL-13R-alpha-2	interleukin 13 receptor, alpha 2	protein-coding
mm_115970.1	chr13	24059290	24059313	-	1	NA	intron (NM_001311122, intron 29 of 37)	intron (NM_001311122, intron 29 of 37)	-68087	NM_145399	214189	Mm.255667	NM_145399	ENSMUSG00000021337	Scgn	-	secretagogin, EF-hand calcium binding protein	protein-coding
mm_159881.1	chr6	17693303	17693303	+	1	NA	promoter-TSS (NM_001289625)	promoter-TSS (NM_001289625)	-691	NM_001289624	64213	Mm.12051	NM_022332	ENSMUSG00000029534	St7	9430001H04Rik|Fam4a2|HELG|RAY1|SEN4|TSG7	suppression of tumorigenicity 7	protein-coding
mm_57936.1	chr6	134791328	134791339	-	1	NA	intron (NM_001048054, intron 1 of 6)	intron (NM_001048054, intron 1 of 6)	1295	NM_130447	70686	Mm.491182	NM_130447	ENSMUSG00000030203	Dusp16	3830417M17Rik|AW558566|D6Ertd213e|MKP-7|MKP7|Mkpm	dual specificity phosphatase 16	protein-coding
mm_127148.1	chr15	98541385	98541389	+	1	NA	Intergenic	Intergenic	-7118	NM_001289440	69612	Mm.229107	NM_133714	ENSMUSG00000022992	Kansl2	2310037I24Rik|B930009D17	KAT8 regulatory NSL complex subunit 2	protein-coding
mm_34740.1	chr4	152241969	152241977	+	1	NA	intron (NM_001146057, intron 6 of 8)	intron (NM_001146057, intron 6 of 8)	-32389	NM_178406	100129	Mm.23235	NM_178406	ENSMUSG00000042804	Gpr153	1110065N12Rik|AI449320|PGR1	G protein-coupled receptor 153	protein-coding
mm_119075.1	chr14	30880115	30880146	+	1	NA	intron (NM_181390, intron 1 of 2)	intron (NM_181390, intron 1 of 2)	873	NM_181390	66175	Mm.220895	NM_181390	ENSMUSG00000042485	Mustn1	1110028G01Rik|Mustang	musculoskeletal, embryonic nuclear protein 1	protein-coding
mm_84934.1	chr9	82928874	82928882	-	1	NA	intron (NM_001081216, intron 11 of 39)	intron (NM_001081216, intron 11 of 39)	46611	NM_001081216	83946	Mm.221688	NM_031879	ENSMUSG00000032253	Phip	2810004D21Rik|4632404O06Rik|Ndrp|Wdr11	pleckstrin homology domain interacting protein	protein-coding
mm_89650.1	chr10	97479471	97479481	+	1	NA	promoter-TSS (NM_001190451)	promoter-TSS (NM_001190451)	-24	NM_001190451	13179	Mm.56769	NM_007833	ENSMUSG00000019929	Dcn	DC|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding
mm_7887.1	chr1	133133579	133133585	-	1	NA	exon (NM_133819, exon 1 of 2)	exon (NM_133819, exon 1 of 2)	2416	NM_133819	108954	Mm.293628	NM_133819	ENSMUSG00000046062	Ppp1r15b	1810033K10Rik|AI606441|C530022L24Rik|CReP	protein phosphatase 1, regulatory (inhibitor) subunit 15b	protein-coding
mm_69408.1	chr7	132323574	132323584	-	1	NA	Intergenic	Intergenic	-6424	NM_029935	77590	Mm.213582	NM_029935	ENSMUSG00000030930	Chst15	4631426J05Rik|BRAG|GalNAcS-6ST|MAd5|mKIAA0598	carbohydrate (N-acetylgalactosamine 4-sulfate 6-O) sulfotransferase 15	protein-coding
mm_64957.1	chr7	16500328	16500330	-	1	NA	intron (NM_172739, intron 5 of 6)	intron (NM_172739, intron 5 of 6)	-23549	NM_008718	18142	Mm.145821	NM_008718	ENSMUSG00000001988	Npas1	MOP5|bHLHe11	neuronal PAS domain protein 1	protein-coding
mm_95243.1	chr11	44617648	44617660	+	1	NA	promoter-TSS (NM_001290711)	promoter-TSS (NM_001290711)	-446	NM_001290711	13591	Mm.439662	NM_007897	ENSMUSG00000057098	Ebf1	Ebf|O/E-1|OE-1|Olf-1|Olf1	early B cell factor 1	protein-coding
mm_142443.1	chr17	45573263	45573272	-	1	NA	promoter-TSS (NM_008302)	promoter-TSS (NM_008302)	-6	NM_008302	15516	Mm.2180	NM_008302	ENSMUSG00000023944	Hsp90ab1	90kDa|AL022974|C81438|Hsp84|Hsp84-1|Hsp90|Hspcb	heat shock protein 90 alpha (cytosolic), class B member 1	protein-coding
mm_10468.1	chr2	14331110	14331131	+	1	NA	exon (NM_008625, exon 30 of 30)	exon (NM_008625, exon 30 of 30)	-57278	NM_001012305	277468	Mm.44662	NM_001012305	ENSMUSG00000036949	Slc39a12	AW046938|Gm731	solute carrier family 39 (zinc transporter), member 12	protein-coding
mm_148695.1	chr19	5741860	5741887	+	1	NA	5' UTR (NM_008520, exon 2 of 28)	5' UTR (NM_008520, exon 2 of 28)	969	NM_008520	16998	Mm.182396	NM_008520	ENSMUSG00000024940	Ltbp3	Ltbp2|mFLJ00070	latent transforming growth factor beta binding protein 3	protein-coding
mm_88984.1	chr10	81564086	81564122	+	1	NA	exon (NM_010347, exon 3 of 7)	exon (NM_010347, exon 3 of 7)	4660	NM_001276288	14797	Mm.180013	NM_010347	ENSMUSG00000054452	Aes	AL024115|Esp1|Grg|Grg-5|Grg5|Tle5	amino-terminal enhancer of split	protein-coding
mm_151659.1	chr19	4125866	4125895	-	1	NA	promoter-TSS (NM_016666)	promoter-TSS (NM_016666)	-22	NM_016666	11632	Mm.10433	NM_016666	ENSMUSG00000024847	Aip	AA408703|AW476050|Ara9|D19Bwg1412e|Fkbp16|Xap2	aryl-hydrocarbon receptor-interacting protein	protein-coding
mm_149074.1	chr19	8873560	8873584	+	1	NA	exon (NM_146093, exon 6 of 10)	exon (NM_146093, exon 6 of 10)	2013	NM_146093	225896	Mm.27839	NM_146093	ENSMUSG00000071655	Ubxn1	2B28|4930455J02Rik|D19Ertd721e|T25529	UBX domain protein 1	protein-coding
mm_160300.1	chr7	135410455	135410455	+	1	NA	promoter-TSS (NM_183193)	promoter-TSS (NM_183193)	88	NM_183193	270004	Mm.132547	NM_183193	ENSMUSG00000048377	Foxi2	B130055A05Rik	forkhead box I2	protein-coding
mm_56943.1	chr6	119948687	119948704	-	1	NA	exon (NM_001185020, exon 17 of 26)	exon (NM_001185020, exon 17 of 26)	45997	NM_001166381	19365	Mm.149	NM_011236	ENSMUSG00000030166	Rad52	Rad52yh	RAD52 homolog, DNA repair protein	protein-coding
mm_99190.1	chr11	100939858	100939871	+	1	NA	promoter-TSS (NM_011486)	promoter-TSS (NM_011486)	-324	NM_011486	20848	Mm.249934	NM_011486	ENSMUSG00000004040	Stat3	1110034C02Rik|AW109958|Aprf	signal transducer and activator of transcription 3	protein-coding
mm_170789.1	chr2	175077903	175077914	+	1	NA	Intergenic	Intergenic	-10139	NM_001085546	664987		NM_001085546	ENSMUSG00000078905	Gm14393	OTTMUSG00000016546	predicted gene 14393	protein-coding
mm_132631.1	chr16	38931891	38931895	+	1	NA	intron (NM_170599, intron 1 of 6)	intron (NM_170599, intron 1 of 6)	29548	NM_170599	207683	Mm.245564	NM_170599	ENSMUSG00000022790	Igsf11	1700025L02Rik|BT-IgSF|Igsf13	immunoglobulin superfamily, member 11	protein-coding
mm_139827.1	chr17	68837063	68837093	+	1	NA	promoter-TSS (NM_001206661)	promoter-TSS (NM_001206661)	-58	NM_001206661	622645	Mm.86422	NM_001206661	ENSMUSG00000095407	Tmem200c	EG622645|Gm6338	transmembrane protein 200C	protein-coding
mm_172125.1	chr6	3201367	3201367	+	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	-87152	NR_036696	667335	Mm.380219	NR_036696	ENSMUSG00000106779	Gm8579	EG667335	spermatogenesis associated glutamate (E)-rich protein 4a pseudogene	pseudo
mm_51700.1	chr6	86609563	86609573	+	1	NA	Intergenic	Intergenic	-18606	NM_026414	67855	Mm.183043	NM_026414	ENSMUSG00000033508	Asprv1	2300003P22Rik|AA986851|SASP|SASPase|Taps	aspartic peptidase, retroviral-like 1	protein-coding
mm_113613.1	chr13	41473765	41473776	+	1	NA	intron (NM_001111324, intron 1 of 7)	MER68|LTR|ERVL	13590	NM_001111324	18003	Mm.288980	NM_017464	ENSMUSG00000021365	Nedd9	Cas-L|CasL|HEF1|MEF1|Nedd-9|p105	neural precursor cell expressed, developmentally down-regulated gene 9	protein-coding
mm_85013.1	chr9	87731164	87731172	-	1	NA	promoter-TSS (NM_023814)	promoter-TSS (NM_023814)	92	NM_023814	76365	Mm.158789	NM_023814	ENSMUSG00000032419	Tbx18	2810012F10Rik|2810404D13Rik	T-box18	protein-coding
mm_138402.1	chr17	35059159	35059169	+	1	NA	TTS (NM_033444)	TTS (NM_033444)	129	NM_016765	51793	Mm.1457	NM_016765	ENSMUSG00000007039	Ddah2	1110003M04Rik|AU019324|AW413173|DDAH-2|DDAHII|Ddah|G6a|NG30	dimethylarginine dimethylaminohydrolase 2	protein-coding
mm_33642.1	chr4	133011484	133011492	+	1	NA	promoter-TSS (NM_146155)	promoter-TSS (NM_146155)	-18	NM_146155	230793	Mm.31816	NM_146155	ENSMUSG00000037692	Ahdc1	D030015G18Rik	AT hook, DNA binding motif, containing 1	protein-coding
mm_128430.1	chr15	50417426	50417472	-	1	NA	Intergenic	Intergenic	471600	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_136131.1	chr16	86472909	86472915	-	1	NA	Intergenic	BC1_Mm|scRNA|scRNA	-571787	NM_011782	23794	Mm.112933	NM_011782	ENSMUSG00000022894	Adamts5	9530092O11Rik|ADAM-TS5|ADAMTS1|ADAMTS11|ADMP-2|AI481094|ASMP-2	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)	protein-coding
mm_167502.1	chr9	13297953	13297999	+	1	NA	Intergenic	Intergenic	51020	NM_025534	66396	Mm.290620	NM_025534	ENSMUSG00000079084	Ccdc82	2310043N13Rik	coiled-coil domain containing 82	protein-coding
mm_131895.1	chr16	23237361	23237368	+	1	NA	intron (NM_001252505, intron 1 of 7)	intron (NM_001252505, intron 1 of 7)	11343	NM_001252505	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_100060.1	chr11	115307156	115307164	+	1	NA	promoter-TSS (NM_172801)	promoter-TSS (NM_172801)	-3	NM_172801	237987	Mm.44542	NM_172801	ENSMUSG00000050201	Otop2	4732464P15	otopetrin 2	protein-coding
mm_19890.1	chr2	114050586	114050615	-	1	NA	exon (NM_009608, exon 3 of 7)	exon (NM_009608, exon 3 of 7)	2275	NM_009608	11464	Mm.686	NM_009608	ENSMUSG00000068614	Actc1	Actc-1	actin, alpha, cardiac muscle 1	protein-coding
mm_44056.1	chr5	148264902	148264918	+	1	NA	intron (NM_029920, intron 7 of 14)	intron (NM_029920, intron 7 of 14)	127905	NM_001301424	11987	Mm.275489	NM_007513	ENSMUSG00000041313	Slc7a1	4831426K01Rik|AI447493|Atrc-1|Atrc1|Cat1|Rec-1|Rev-1|mCAT-1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 1	protein-coding
mm_34808.1	chr4	154878081	154878120	+	1	NA	intron (NM_013783, intron 2 of 23)	ORR1E|LTR|ERVL-MaLR	8515	NM_013783	27390	Mm.116944	NM_013783	ENSMUSG00000058183	Mmel1	Mell1|NEP2|NEPII|Nl1|SEP	membrane metallo-endopeptidase-like 1	protein-coding
mm_129356.1	chr15	77945718	77945733	-	1	NA	exon (NM_001017983, exon 8 of 9)	exon (NM_001017983, exon 8 of 9)	10997	NM_001168260	239554	Mm.295605	NM_001017983	ENSMUSG00000016552	Foxred2	A430097D04Rik|D15Bwg0759e|Gm304	FAD-dependent oxidoreductase domain containing 2	protein-coding
mm_42360.1	chr5	114911885	114911899	+	1	NA	3' UTR (NM_011854, exon 6 of 6)	3' UTR (NM_011854, exon 6 of 6)	-11348	NM_145209	231655	Mm.95479	NM_145209	ENSMUSG00000041827	Oasl1	7530414C13Rik|oasl9	2'-5' oligoadenylate synthetase-like 1	protein-coding
mm_48506.1	chr5	142817655	142817668	-	1	NA	promoter-TSS (NM_001122730)	promoter-TSS (NM_001122730)	-274	NM_001122730	231861	Mm.354649	NM_178242	ENSMUSG00000039477	Tnrc18	BC025631|EG381742|Zfp469	trinucleotide repeat containing 18	protein-coding
mm_86522.1	chr10	7758695	7758701	+	1	NA	intron (NM_011835, intron 7 of 10)	intron (NM_011835, intron 7 of 10)	22219	NM_145418	215751	Mm.471825	NM_145418	ENSMUSG00000040006	Ginm1	AA589616	glycoprotein integral membrane 1	protein-coding
mm_73598.1	chr8	109998827	109998842	+	1	NA	exon (NM_146214, exon 12 of 12)	exon (NM_146214, exon 12 of 12)	8398	NM_146214	234724	Mm.28110	NM_146214	ENSMUSG00000001670	Tat	-	tyrosine aminotransferase	protein-coding
mm_123798.1	chr14	70520071	70520135	-	1	NA	TTS (NM_011359)	TTS (NM_011359)	157	NM_009755	12153	Mm.27757	NM_009755	ENSMUSG00000022098	Bmp1	Pcp|Tld	bone morphogenetic protein 1	protein-coding
mm_138082.1	chr17	33996014	33996040	+	1	NA	TTS (NM_001001892)	TTS (NM_001001892)	4306	NM_001001892	14972	Mm.422886	NM_001001892	ENSMUSG00000061232	H2-K1	H-2K|H-2K(d)|H2-K|K-f	histocompatibility 2, K1, K region	protein-coding
mm_93803.1	chr10	120899027	120899037	-	1	NA	promoter-TSS (NM_177092)	promoter-TSS (NM_177092)	-61	NM_177092	320183	Mm.169755	NM_177092	ENSMUSG00000051236	Msrb3	D430026P16Rik|I-8-23|MsrB2	methionine sulfoxide reductase B3	protein-coding
mm_34419.1	chr4	145274169	145274179	+	1	NA	intron (NM_009401, intron 12 of 12)	intron (NM_009401, intron 12 of 12)	-27304	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_85853.1	chr9	110684129	110684140	-	1	NA	intron (NM_028312, intron 1 of 6)	intron (NM_028312, intron 1 of 6)	27631	NM_028312	72654	Mm.249115	NM_028312	ENSMUSG00000019659	Ccdc12	2700094L05Rik|C76605	coiled-coil domain containing 12	protein-coding
mm_23025.1	chr3	34640221	34640225	+	1	NA	intron (NR_015580, intron 3 of 4)	intron (NR_015580, intron 3 of 4)	1759	NR_035433	100316679		NR_035433	ENSMUSG00000104797	Mir1897	Mirn1897|mmu-mir-1897	microRNA 1897	ncRNA
mm_88061.1	chr10	67644440	67644450	+	1	NA	Intergenic	Intergenic	-95490	NM_001005419	211488	Mm.297250	NM_001005419	ENSMUSG00000057134	Ado	Gm237	2-aminoethanethiol (cysteamine) dioxygenase	protein-coding
mm_45326.1	chr5	65492791	65492868	-	1	NA	promoter-TSS (NM_133697)	promoter-TSS (NM_133697)	6	NM_133697	68552	Mm.10709	NM_133697	ENSMUSG00000037822	Smim14	1110003E01Rik|1700127H04Rik|5430439C17Rik|MAd4	small integral membrane protein 14	protein-coding
mm_159799.1	chr5	112465994	112465994	-	1	NA	exon (NM_001253916, exon 6 of 17)	exon (NM_001253916, exon 6 of 17)	16568	NM_001177504	625464	Mm.389676	NM_001177504	ENSMUSG00000072722	Gm6588	EG625464	predicted gene 6588	protein-coding
mm_53851.1	chr6	149141655	149141663	+	1	NA	5' UTR (NM_001252096, exon 1 of 4)	5' UTR (NM_001252096, exon 1 of 4)	146	NM_177101	320204	Mm.274099	NM_177101	ENSMUSG00000039958	Etfbkmt	4833442J19Rik|AI256744|ETFB-KMT|Mettl20	electron transfer flavoprotein beta subunit lysine methyltransferase	protein-coding
mm_8603.1	chr1	156034858	156034864	-	1	NA	promoter-TSS (NM_001160180)	promoter-TSS (NM_001160180)	-44	NM_001160019	208263	Mm.211654	NM_144791	ENSMUSG00000026466	Tor1aip1	LAP1|Lap1B	torsin A interacting protein 1	protein-coding
mm_15904.1	chr2	164968265	164968317	+	1	NA	5' UTR (NM_020333, exon 1 of 26)	5' UTR (NM_020333, exon 1 of 26)	303	NM_020333	57138	Mm.252987	NM_020333	ENSMUSG00000017740	Slc12a5	KCC2|mKIAA1176	solute carrier family 12, member 5	protein-coding
mm_9702.1	chr1	179139420	179139423	-	1	NA	intron (NM_027188, intron 5 of 11)	intron (NM_027188, intron 5 of 11)	378582	NM_027188	69726	Mm.222338	NM_027188	ENSMUSG00000055067	Smyd3	2410008A19Rik|Zmynd1	SET and MYND domain containing 3	protein-coding
mm_29139.1	chr3	105825784	105825816	-	1	NA	Intergenic	Intergenic	10233	NR_045845	433637	Mm.331285	NR_045845	ENSMUSG00000104835	Gm5547	EG433637	predicted gene 5547	ncRNA
mm_170644.1	chr19	9422521	9422522	+	1	NA	Intergenic	RLTR9F|LTR|ERVK	136727	NR_073559	619371	Mm.316894	NM_001030317		Stxbp3-ps	Munc18c(L)|Stxbp3-1|Stxbp3b	syntaxin-binding protein 3, pseudogene	pseudo
mm_109592.1	chr12	112633960	112633992	+	1	NA	intron (NM_007421, intron 5 of 12)	intron (NM_007421, intron 5 of 12)	-10852	NM_001161737	30954	Mm.289812	NM_013929	ENSMUSG00000064326	Siva1	CD27bp|Siva	SIVA1, apoptosis-inducing factor	protein-coding
mm_132127.1	chr16	31754770	31754784	+	1	NA	5' UTR (NM_001252436, exon 1 of 23)	5' UTR (NM_001252436, exon 1 of 23)	427	NM_001252436	13383	Mm.382	NM_007862	ENSMUSG00000022770	Dlg1	B130052P05Rik|Dlgh1|E-dlg/SAP97|SAP-97|SAP97|mKIAA4187	discs, large homolog 1 (Drosophila)	protein-coding
mm_110016.1	chr12	16646992	16647002	-	1	NA	Intergenic	Intergenic	-6473	NM_008747	18217	Mm.281715	NM_008747	ENSMUSG00000020591	Ntsr2	NT2R|NTRL	neurotensin receptor 2	protein-coding
mm_10111.1	chr2	3713441	3713443	+	1	NA	promoter-TSS (NM_025626)	promoter-TSS (NM_025626)	-16	NM_025626	66540	Mm.277864	NM_025626	ENSMUSG00000026655	Fam107b	3110001A13Rik|AA589595|AA959793|AI132312	family with sequence similarity 107, member B	protein-coding
mm_68517.1	chr7	111736048	111736064	-	1	NA	intron (NM_173739, intron 1 of 10)	intron (NM_173739, intron 1 of 10)	43921	NM_173739	233733	Mm.323322	NM_173739	ENSMUSG00000038296	Galnt18	2900011G21Rik|BC024988|Galntl4	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 18	protein-coding
mm_61924.1	chr7	90160527	90160551	+	1	NA	exon (NM_001252521, exon 2 of 20)	exon (NM_001252521, exon 2 of 20)	30307	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_37611.1	chr4	126967993	126967999	-	1	NA	promoter-TSS (NM_001114399)	promoter-TSS (NM_001114399)	-73	NM_001114399	67785	Mm.165401	NM_001114399	ENSMUSG00000042446	Zmym4	6330503C17Rik|AI480785|AW493829|CDIR|D630001M21|MYM|Zfp262|Znf262|mKIAA0425	zinc finger, MYM-type 4	protein-coding
mm_105289.1	chr11	102447648	102447677	-	1	NA	promoter-TSS (NM_199200)	promoter-TSS (NM_199200)	1	NM_199200	217219	Mm.259924	NM_199200	ENSMUSG00000034685	Fam171a2	-	family with sequence similarity 171, member A2	protein-coding
mm_49656.1	chr6	31123237	31123239	+	1	NA	intron (NR_110471, intron 3 of 3)	ORR1F|LTR|ERVL-MaLR	-60145	NR_029532	387223		NR_029532	ENSMUSG00000065604	Mir29b-1	Mirn29b|Mirn29b-1|mir-29b-1	microRNA 29b-1	ncRNA
mm_13272.1	chr2	99454547	99454549	+	1	NA	Intergenic	Intergenic	1986891	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_8684.1	chr1	156939554	156939615	-	1	NA	promoter-TSS (NM_001159968)	promoter-TSS (NM_001159968)	42	NM_001159968	78255	Mm.28376	NM_023884	ENSMUSG00000026594	Ralgps2	1810020P17Rik|2210408F11Rik|4921528G01Rik|9130014M22Rik|AU043409|AW046161	Ral GEF with PH domain and SH3 binding motif 2	protein-coding
mm_39116.1	chr4	154936604	154936610	-	1	NA	Intergenic	Intergenic	-8530	NM_178931	230979	Mm.215147	NM_178931	ENSMUSG00000042333	Tnfrsf14	Atar|HveA|Hvem|Tnfrs14	tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)	protein-coding
mm_108490.1	chr12	83672834	83672859	+	1	NA	exon (NM_027349, exon 14 of 19)	exon (NM_027349, exon 14 of 19)	-15717	NM_008943	19164	Mm.998	NM_008943	ENSMUSG00000019969	Psen1	Ad3h|PS-1|PS1|S182	presenilin 1	protein-coding
mm_136280.1	chr16	91069143	91069159	-	1	NA	promoter-TSS (NM_028905)	promoter-TSS (NM_028905)	-6	NM_028905	74387	Mm.236220	NM_028905	ENSMUSG00000039851	4932438H23Rik	4931406G06Rik|AI550392	RIKEN cDNA 4932438H23 gene	protein-coding
mm_107942.1	chr12	71889714	71889723	+	1	NA	5' UTR (NM_001286452, exon 1 of 25)	5' UTR (NM_001286452, exon 1 of 25)	175	NM_001286452	208846	Mm.87417	NM_026102	ENSMUSG00000034574	Daam1	-	dishevelled associated activator of morphogenesis 1	protein-coding
mm_8957.1	chr1	164537561	164537569	-	1	NA	Intergenic	Intergenic	-79210	NM_009721	11931	Mm.4550	NM_009721	ENSMUSG00000026576	Atp1b1	Atp4b|Atpb|Atpb-1|NKbeta1	ATPase, Na+/K+ transporting, beta 1 polypeptide	protein-coding
mm_100538.1	chr11	120633720	120633761	+	1	NA	promoter-TSS (NM_010756)	promoter-TSS (NM_010756)	-193	NM_010756	17134	Mm.268010	NM_010756	ENSMUSG00000051510	Mafg	AA545192|C630022N07Rik	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein G (avian)	protein-coding
mm_15407.1	chr2	156749160	156749205	+	1	NA	exon (NM_001042488, exon 4 of 7)	exon (NM_001042488, exon 4 of 7)	-26282	NM_172118	98932	Mm.271770	NM_172118	ENSMUSG00000067818	Myl9	AI327049|MLC20|Mylc2c|RLC-C	myosin, light polypeptide 9, regulatory	protein-coding
mm_84045.1	chr9	58025122	58025154	-	1	NA	exon (NM_001346787, exon 7 of 10)	exon (NM_001346787, exon 7 of 10)	-7136	NM_001243265	330951	Mm.406992	NM_001243265		Gm16130	E330033L03|OTTMUSG00000030814	predicted gene 16130	protein-coding
mm_26387.1	chr3	142570533	142570548	+	1	NA	exon (NM_018734, exon 9 of 11)	exon (NM_018734, exon 9 of 11)	10044	NM_001289493	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_79925.1	chr9	65630688	65630703	+	1	NA	5' UTR (NM_028030, exon 1 of 8)	5' UTR (NM_028030, exon 1 of 8)	113	NM_028030	71973	Mm.29148	NM_028030	ENSMUSG00000032387	Rbpms2	2400008B06Rik|AI316523	RNA binding protein with multiple splicing 2	protein-coding
mm_30399.1	chr3	152252829	152252849	-	1	NA	exon (NM_199465, exon 4 of 13)	exon (NM_199465, exon 4 of 13)	13481	NM_199465	68810	Mm.200188	NM_199465	ENSMUSG00000039103	Nexn	1110046H09Rik|AA553326|NELIN	nexilin	protein-coding
mm_24935.1	chr3	96560243	96560263	+	1	NA	exon (NM_023719, exon 7 of 8)	exon (NM_023719, exon 7 of 8)	2296	NM_023719	56338	Mm.410189	NM_023719	ENSMUSG00000038393	Txnip	1200008J08Rik|AA682105|Hyplip1|THIF|Tbp-2|VDUP1	thioredoxin interacting protein	protein-coding
mm_24668.1	chr3	94591314	94591320	+	1	NA	Intergenic	RMER19B2|LTR|ERVK	-8601	NM_029721	76742	Mm.28160	NM_029721	ENSMUSG00000028136	Snx27	5730552M22Rik|ESTM45|ESTM47|R75405	sorting nexin family member 27	protein-coding
mm_6350.1	chr1	71648084	71648105	-	1	NA	exon (NM_001276413, exon 5 of 44)	exon (NM_001276413, exon 5 of 44)	5140	NM_010233	14268	Mm.193099	NM_010233	ENSMUSG00000026193	Fn1	E330027I09|Fn|Fn-1	fibronectin 1	protein-coding
mm_10209.1	chr2	5413247	5413248	+	1	NA	intron (NR_030601, intron 1 of 1)	intron (NR_030601, intron 1 of 1)	33857	NR_030601	100124465		NR_030601	ENSMUSG00000078031	Mir466d	Mirn466d	microRNA 466d	ncRNA
mm_3012.1	chr1	133363585	133363623	+	1	NA	promoter-TSS (NM_175443)	promoter-TSS (NM_175443)	32	NM_175443	214253	Mm.52111	NM_175443	ENSMUSG00000070644	Etnk2	4933417N20Rik|AI197444|EKI 2|Eki2|Tuc1	ethanolamine kinase 2	protein-coding
mm_1973.1	chr1	86522710	86522727	+	1	NA	Intergenic	Intergenic	-4018	NM_008972	19231	Mm.19187	NM_008972	ENSMUSG00000026238	Ptma	Thym	prothymosin alpha	protein-coding
mm_20074.1	chr2	120563745	120563755	-	1	NA	promoter-TSS (NM_011743)	promoter-TSS (NM_011743)	81	NM_011743	20402	Mm.485295	NM_011743	ENSMUSG00000027288	Zfp106	Cd-1|D2Dcr28|H3a|Sh3bp3|Znf106|sirm	zinc finger protein 106	protein-coding
mm_75719.1	chr8	69027651	69027693	-	1	NA	Intergenic	LTR48|LTR|ERV1	-61064	NM_007509	11966	Mm.249096	NM_007509	ENSMUSG00000006273	Atp6v1b2	AI194269|AI790362|Atp6b2|HO57|R74844	ATPase, H+ transporting, lysosomal V1 subunit B2	protein-coding
mm_47697.1	chr5	129779205	129779283	-	1	NA	5' UTR (NM_133900, exon 3 of 8)	5' UTR (NM_133900, exon 3 of 8)	8009	NM_133900	100678	Mm.271784	NM_133900	ENSMUSG00000029446	Psph	AI480570|PSP|PSPase	phosphoserine phosphatase	protein-coding
mm_60748.1	chr7	45461065	45461100	+	1	NA	TTS (NM_007527)	TTS (NM_007527)	-1196	NM_010240	14325	Mm.30357	NM_010240	ENSMUSG00000050708	Ftl1	Ftl|Ftl-1|L-ferritin	ferritin light polypeptide 1	protein-coding
mm_76813.1	chr8	104442945	104442955	-	1	NA	promoter-TSS (NM_001013380)	promoter-TSS (NM_001013380)	97	NM_001013380	234663	Mm.289583	NM_001013380	ENSMUSG00000035770	Dync1li2	AA409702|C920003I06|Dncli2|Dnclic2|LIC2	dynein, cytoplasmic 1 light intermediate chain 2	protein-coding
mm_72675.1	chr8	84911335	84911349	+	1	NA	TTS (NM_019945)	TTS (NM_019945)	-1993	NR_103491	100503676	Mm.437155	NR_103491	ENSMUSG00000003812	Gm38426	-	predicted gene, 38426	ncRNA
mm_123998.1	chr14	75834830	75834837	-	1	NA	Intergenic	Intergenic	10131	NR_045294	100043189	Mm.426329	NR_045294		Gm4285	-	predicted gene 4285	ncRNA
mm_169220.1	chr13	66744849	66744867	-	1	NA	Intergenic	Intergenic	160492	NM_026219	67530	Mm.379136	NM_026219	ENSMUSG00000021520	Uqcrb	2210415M14Rik|QP-C|QPC|UQBC|UQBP|UQPC	ubiquinol-cytochrome c reductase binding protein	protein-coding
mm_42503.1	chr5	115491971	115491988	+	1	NA	Intergenic	CpG	-7495	NM_133760	75387	Mm.332616	NM_133760	ENSMUSG00000029524	Sirt4	4930596O17Rik	sirtuin 4	protein-coding
mm_98442.1	chr11	94942006	94942047	+	1	NA	exon (NM_007742, exon 17 of 51)	exon (NM_007742, exon 17 of 51)	5802	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_39674.1	chr5	25516058	25516058	+	1	NA	promoter-TSS (NM_198621)	promoter-TSS (NM_198621)	-9	NM_198621	242891	Mm.291521	NM_198621	ENSMUSG00000038044	Cct8l1	Gm443	chaperonin containing TCP1, subunit 8 (theta)-like 1	protein-coding
mm_53397.1	chr6	129588364	129588393	+	1	NA	Intergenic	Intergenic	-3433	NM_010654	16643	Mm.391515	NM_010654	ENSMUSG00000030165	Klrd1	CD94	killer cell lectin-like receptor, subfamily D, member 1	protein-coding
mm_136671.1	chr17	6106881	6106907	+	1	NA	promoter-TSS (NM_001103181)	promoter-TSS (NM_001103181)	64	NM_001103181	68842	Mm.449307	NM_054040	ENSMUSG00000034377	Tulp4	1110057P05Rik|2210038L17Rik|Tusp	tubby like protein 4	protein-coding
mm_37807.1	chr4	130818770	130818919	-	1	NA	exon (NM_011520, exon 3 of 5)	exon (NM_011520, exon 3 of 5)	26307	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_3247.1	chr1	136131364	136131381	+	1	NA	promoter-TSS (NM_001039472)	promoter-TSS (NM_001039472)	-29	NM_001039472	16565	Mm.276135	NM_019962	ENSMUSG00000041642	Kif21b	2610511N21Rik|mKIAA0449	kinesin family member 21B	protein-coding
mm_3485.1	chr1	150105683	150105695	+	1	NA	exon (NM_011198, exon 10 of 10)	exon (NM_011198, exon 10 of 10)	5658	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_38085.1	chr4	134154460	134154482	-	1	NA	intron (NM_144527, intron 4 of 13)	intron (NM_144527, intron 4 of 13)	-25718	NM_080559	73723	Mm.22240	NM_080559	ENSMUSG00000028843	Sh3bgrl3	1110004L05Rik|AU022188	SH3 domain binding glutamic acid-rich protein-like 3	protein-coding
mm_122127.1	chr14	31156124	31156139	-	1	NA	intron (NM_138672, intron 21 of 68)	B2_Mm2|SINE|B2	12510	NM_138672	192187	Mm.220821	NM_138672	ENSMUSG00000042286	Stab1	FEEL-1|FELE-1|MFEEL-1|MS-1|STAB-1|mKIAA0246	stabilin 1	protein-coding
mm_55170.1	chr6	51920244	51920273	-	1	NA	intron (NM_018773, intron 6 of 12)	MIR|SINE|MIR	92291	NM_018773	54353	Mm.221479	NM_018773	ENSMUSG00000059182	Skap2	2610021A10Rik|AA960083|BB137539|RA70|SKAP-HOM|Saps|Scap2|mSKAP55R	src family associated phosphoprotein 2	protein-coding
mm_23701.1	chr3	68761431	68761455	+	1	NA	Intergenic	Intergenic	70019	NM_008351	16159	Mm.103783	NM_008351	ENSMUSG00000027776	Il12a	IL-12p35|Il-12a|Ll12a|p35	interleukin 12a	protein-coding
mm_136611.1	chr17	5334823	5334831	+	1	NA	intron (NM_001085355, intron 16 of 19)	intron (NM_001085355, intron 16 of 19)	83940	NM_175349	106557	Mm.432764	NM_175349	ENSMUSG00000101959	Ldhal6b	4933402O15Rik|AI326310|LDHL|Ldhal	lactate dehydrogenase A-like 6B	protein-coding
mm_93043.1	chr10	88380157	88380180	-	1	NA	intron (NM_001004164, intron 1 of 20)	intron (NM_001004164, intron 1 of 20)	756	NM_001004164	432486	Mm.335190	NM_001004164	ENSMUSG00000035311	Gnptab	EG432486|mKIAA1208	N-acetylglucosamine-1-phosphate transferase, alpha and beta subunits	protein-coding
mm_169541.1	chr15	100421369	100421373	-	1	NA	intron (NM_008732, intron 1 of 16)	intron (NM_008732, intron 1 of 16)	1684	NM_001146161	18174	Mm.234608	NM_008732	ENSMUSG00000023030	Slc11a2	DCT1|DMT1|Nramp2|mk|van	solute carrier family 11 (proton-coupled divalent metal ion transporters), member 2	protein-coding
mm_25980.1	chr3	133310094	133310145	+	1	NA	promoter-TSS (NM_001293641)	promoter-TSS (NM_001293641)	9	NM_146141	74776	Mm.210305	NM_146141	ENSMUSG00000028013	Ppa2	1110013G13Rik|Sid6306	pyrophosphatase (inorganic) 2	protein-coding
mm_104855.1	chr11	99350004	99350019	-	1	NA	intron (NM_010666, intron 1 of 7)	intron (NM_010666, intron 1 of 7)	1107	NM_010666	16675	Mm.440476	NM_010666	ENSMUSG00000017588	Krt27	CK-27|Krt1-c29|mIRSa3.1|stpm	keratin 27	protein-coding
mm_91169.1	chr10	20697782	20697797	-	1	NA	intron (NM_013875, intron 1 of 12)	intron (NM_013875, intron 1 of 12)	27289	NM_013875	29863	Mm.425617	NM_013875	ENSMUSG00000019990	Pde7b	-	phosphodiesterase 7B	protein-coding
mm_28398.1	chr3	90213578	90213630	-	1	NA	promoter-TSS (NM_001293741)	promoter-TSS (NM_001293741)	43	NM_001190258	100043813	Mm.270283	NM_001190258	ENSMUSG00000050621	Rps27rt	ENSMUSG00000050621|Gm9846|Rps27l2	ribosomal protein S27, retrogene	protein-coding
mm_43284.1	chr5	133475080	133475080	+	1	NA	Intergenic	Intergenic	-624668	NM_030719	80909	Mm.45218	NM_030719	ENSMUSG00000015944	Gatsl2	7530428J21Rik|AW742413|Gats|Gatsl1	GATS protein-like 2	protein-coding
mm_142870.1	chr17	51815826	51815834	-	1	NA	intron (NM_001163632, intron 1 of 10)	intron (NM_001163632, intron 1 of 10)	-3776	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_46095.1	chr5	92347267	92347285	-	1	NA	3' UTR (NM_021274, exon 4 of 4)	3' UTR (NM_021274, exon 4 of 4)	1613	NM_021274	15945	Mm.877	NM_021274	ENSMUSG00000034855	Cxcl10	C7|CRG-2|INP10|IP-10|IP10|Ifi10|Scyb10|gIP-10|mob-1	chemokine (C-X-C motif) ligand 10	protein-coding
mm_7785.1	chr1	131281894	131281903	-	1	NA	Intergenic	RMER6A|LTR|ERVK	-2335	NM_019777	56489	Mm.386783	NM_019777	ENSMUSG00000042349	Ikbke	AW558201|IKK-i|IKKepsilon|Ikki	inhibitor of kappaB kinase epsilon	protein-coding
mm_45140.1	chr5	49024675	49024675	-	1	NA	intron (NM_001199244, intron 1 of 7)	intron (NM_001199244, intron 1 of 7)	-135118	NM_030265	80334	Mm.160172	NM_030265	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding
mm_73786.1	chr8	117157951	117157967	+	1	NA	promoter-TSS (NM_001081151)	promoter-TSS (NM_001081151)	-176	NM_001081151	209239	Mm.132992	NM_001081151	ENSMUSG00000052557	Gan	A330045G18|gigaxonin	giant axonal neuropathy	protein-coding
mm_76863.1	chr8	105471482	105471487	-	1	NA	promoter-TSS (NM_026481)	promoter-TSS (NM_026481)	-62	NM_026481	67971	Mm.29358	NM_026481	ENSMUSG00000014846	Tppp3	2700055K07Rik|CGI-38|Ceacam9|mmCGM8	tubulin polymerization-promoting protein family member 3	protein-coding
mm_22597.1	chr3	13946369	13946379	+	1	NA	promoter-TSS (NM_001163330)	promoter-TSS (NM_001163330)	2	NM_001163330	76897	Mm.422625	NM_178631	ENSMUSG00000039717	Ralyl	0710005M24Rik	RALY RNA binding protein-like	protein-coding
mm_69409.1	chr7	132365860	132365871	-	1	NA	Intergenic	Intergenic	-48710	NM_029935	77590	Mm.213582	NM_029935	ENSMUSG00000030930	Chst15	4631426J05Rik|BRAG|GalNAcS-6ST|MAd5|mKIAA0598	carbohydrate (N-acetylgalactosamine 4-sulfate 6-O) sulfotransferase 15	protein-coding
mm_27901.1	chr3	79479675	79479678	-	1	NA	intron (NM_001162999, intron 13 of 16)	intron (NM_001162999, intron 13 of 16)	88003	NM_001162999	329679	Mm.244005	NM_001162999	ENSMUSG00000061175	Fnip2	D630023B12Rik|mKIAA1450	folliculin interacting protein 2	protein-coding
mm_156094.1	chrX	112311352	112311363	+	1	NA	promoter-TSS (NM_026565)	promoter-TSS (NM_026565)	5	NM_026565	68117	Mm.161014	NM_026565	ENSMUSG00000025525	Apool	6720473G16Rik|9430083G14Rik|E130106L15Rik	apolipoprotein O-like	protein-coding
mm_63314.1	chr7	126863425	126863444	+	1	NA	exon (NM_172746, exon 4 of 7)	exon (NM_172746, exon 4 of 7)	1462	NM_172746	233876	Mm.363427	NM_172746	ENSMUSG00000042606	Hirip3	B130036O03|C86302	HIRA interacting protein 3	protein-coding
mm_94312.1	chr11	4223620	4223638	+	1	NA	Intergenic	Intergenic	5378	NM_028022	71962	Mm.7852	NM_028022	ENSMUSG00000020424	Gatsl3	2410008K03Rik	GATS protein-like 3	protein-coding
mm_151978.1	chr19	5828166	5828267	-	1	NA	non-coding (NR_131212, exon 1 of 1)	non-coding (NR_131212, exon 1 of 1)	17262	NR_131212	66961	Mm.281895	NR_003513	ENSMUSG00000092274	Neat1	2310043N10Rik|VINC	nuclear paraspeckle assembly transcript 1 (non-protein coding)	ncRNA
mm_46355.1	chr5	103026929	103026971	-	1	NA	intron (NM_001318102, intron 4 of 13)	intron (NM_001318102, intron 4 of 13)	31442	NM_001310686	26414	Mm.39253	NM_009158	ENSMUSG00000046709	Mapk10	C230008H04Rik|JNK3|JNK3B1|JNK3B2|SAPK(beta)|Serk2|p493F12|p54bSAPK	mitogen-activated protein kinase 10	protein-coding
mm_57570.1	chr6	127130182	127130203	-	1	NA	3' UTR (NM_009829, exon 5 of 5)	3' UTR (NM_009829, exon 5 of 5)	-19197	NR_040274	77558	Mm.358918	NR_040273	ENSMUSG00000097166	9330179D12Rik	-	RIKEN cDNA 9330179D12 gene	ncRNA
mm_7447.1	chr1	120121059	120121073	-	1	NA	promoter-TSS (NM_001172074)	promoter-TSS (NM_001172074)	30	NM_007830	13167	Mm.2785	NM_007830	ENSMUSG00000026385	Dbi	ACBD1|Acbp|EP|endozepine	diazepam binding inhibitor	protein-coding
mm_31307.1	chr4	46077173	46077177	+	1	NA	intron (NM_021883, intron 2 of 9)	intron (NM_021883, intron 2 of 9)	37953	NM_021883	21916	Mm.249594	NM_021883	ENSMUSG00000028328	Tmod1	E-Tmod|Tmod	tropomodulin 1	protein-coding
mm_54706.1	chr6	39637870	39637880	-	1	NA	intron (NM_139294, intron 16 of 21)	ORR1C2|LTR|ERVL-MaLR	45292	NM_026612	68198	Mm.29415	NM_026612	ENSMUSG00000002416	Ndufb2	1810011O01Rik|8kDa|AGGG|AI325567|CI-AGGG	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 2	protein-coding
mm_116504.1	chr13	45001829	45001846	-	1	NA	intron (NM_025772, intron 1 of 9)	CpG	259	NM_025772	94245	Mm.352311	NM_025772	ENSMUSG00000057531	Dtnbp1	5430437B18Rik|AW048963|Bloc1s8|dysbindin|sdy	dystrobrevin binding protein 1	protein-coding
mm_151718.1	chr19	4793855	4793905	-	1	NA	promoter-TSS (NM_009032)	promoter-TSS (NM_009032)	21	NM_009032	19653	Mm.426069	NM_009032	ENSMUSG00000094936	Rbm4	4921506I22Rik|Lark1|Mlark|Rbm4a|lark	RNA binding motif protein 4	protein-coding
mm_146371.1	chr18	82584701	82584734	+	1	NA	3' UTR (NM_010777, exon 7 of 7)	3' UTR (NM_010777, exon 7 of 7)	30209	NM_001025254	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_77970.1	chr9	7792718	7792739	+	1	NA	3' UTR (NM_133739, exon 5 of 5)	3' UTR (NM_133739, exon 5 of 5)	8338	NR_049191	100885830		NR_049191	ENSMUSG00000093615	Mir5618	Gm23685|mmu-mir-5618	microRNA 5618	ncRNA
mm_76918.1	chr8	105933186	105933197	-	1	NA	exon (NM_023182, exon 2 of 7)	exon (NM_023182, exon 2 of 7)	671	NM_023182	109660	Mm.2745	NM_023182	ENSMUSG00000031896	Ctrl	0910001G08Rik|1810004D15Rik|AV005227|Ctra-1|Ctra1|chymopasin|mFLJ00366	chymotrypsin-like	protein-coding
mm_54809.1	chr6	42323329	42323339	-	1	NA	intron (NM_001286584, intron 1 of 6)	intron (NM_001286584, intron 1 of 6)	1306	NM_001286584	76156	Mm.234314	NM_029528	ENSMUSG00000029861	Fam131b	6330503C03Rik|6530406I18Rik|AV277466	family with sequence similarity 131, member B	protein-coding
mm_63098.1	chr7	122415715	122415720	+	1	NA	intron (NM_001316672, intron 2 of 16)	MIR|SINE|MIR	126592	NM_008855	18751	Mm.207496	NM_008855	ENSMUSG00000052889	Prkcb	PKC-B|PKC-Beta|Pkcb|Prkcb1|Prkcb2	protein kinase C, beta	protein-coding
mm_164461.1	chr16	58499848	58499857	-	1	NA	intron (NM_018784, intron 2 of 10)	intron (NM_018784, intron 2 of 10)	23460	NM_018784	54613	Mm.212742	NM_018784	ENSMUSG00000022747	St3gal6	1700023B24Rik|AI930218|AW552396|Siat10|St3galVI	ST3 beta-galactoside alpha-2,3-sialyltransferase 6	protein-coding
mm_71812.1	chr8	68884348	68884350	+	1	NA	intron (NM_008509, intron 1 of 9)	intron (NM_008509, intron 1 of 9)	3794	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_156337.1	chrX	139009793	139009803	+	1	NA	TTS (NM_013724)	TTS (NM_013724)	75438	NM_177920	331535	Mm.211704	NM_177920	ENSMUSG00000031271	Serpina7	C730040N12Rik|Tbg	serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 7	protein-coding
mm_5556.1	chr1	38665024	38665034	-	1	NA	Intergenic	Intergenic	-37785	NM_001290814	16764	Mm.336679	NM_010678	ENSMUSG00000037138	Aff3	3222402O04Rik|A730046J16|LAF-4|Laf4	AF4/FMR2 family, member 3	protein-coding
mm_22226.1	chr2	174428693	174428705	-	1	NA	exon (NM_022325, exon 5 of 6)	exon (NM_022325, exon 5 of 6)	10340	NM_022325	64138	Mm.156919	NM_022325	ENSMUSG00000016256	Ctsz	AI787083|AU019819|CTSX|D2Wsu143e	cathepsin Z	protein-coding
mm_14600.1	chr2	136060785	136060796	+	1	NA	intron (NM_029530, intron 4 of 5)	intron (NM_029530, intron 4 of 5)	2863	NM_029530	76161	Mm.41638	NM_029530	ENSMUSG00000027270	Lamp5	3110035N03Rik|6330527O06Rik|BAD-LAMP|LAMP-5	lysosomal-associated membrane protein family, member 5	protein-coding
mm_146325.1	chr18	80707263	80707269	+	1	NA	intron (NM_198429, intron 1 of 9)	intron (NM_198429, intron 1 of 9)	907	NM_001164111	18018	Mm.329560	NM_016791	ENSMUSG00000033016	Nfatc1	2210017P03Rik|AI449492|AV076380|NF-ATc|NFAT2|NFATc|Nfatcb	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 1	protein-coding
mm_85970.1	chr9	112156462	112156473	-	1	NA	intron (NM_001177619, intron 10 of 10)	intron (NM_001177619, intron 10 of 10)	29482	NM_001177618	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_94494.1	chr11	7063402	7063404	+	1	NA	promoter-TSS (NM_009622)	promoter-TSS (NM_009622)	-86	NM_009622	432530	Mm.259733	NM_009622	ENSMUSG00000020431	Adcy1	AC1|D11Bwg1392e|I-AC|brl|mKIAA4070	adenylate cyclase 1	protein-coding
mm_139764.1	chr17	64601282	64601293	+	1	NA	promoter-TSS (NM_008549)	promoter-TSS (NM_008549)	-362	NM_008549	17158	Mm.2433	NM_008549	ENSMUSG00000024085	Man2a1	Mana-2|Mana2|Map-2	mannosidase 2, alpha 1	protein-coding
mm_106538.1	chr11	120578844	120578864	-	1	NA	3' UTR (NM_133796, exon 6 of 6)	3' UTR (NM_133796, exon 6 of 6)	2766	NM_133796	192662	Mm.30016	NM_133796	ENSMUSG00000025132	Arhgdia	5330430M07Rik|Gdi-1|Rho-GDI|RhoDGI|RhoGDI-1	Rho GDP dissociation inhibitor (GDI) alpha	protein-coding
mm_59020.1	chr7	19271949	19271953	+	1	NA	promoter-TSS (NM_001282022)	promoter-TSS (NM_001282022)	-97	NM_001282022	22323	Mm.9684	NM_009499	ENSMUSG00000030403	Vasp	-	vasodilator-stimulated phosphoprotein	protein-coding
mm_2720.1	chr1	128167930	128167941	+	1	NA	exon (NM_181750, exon 6 of 27)	exon (NM_181750, exon 6 of 27)	-34426	NR_029543	387147		NR_029543	ENSMUSG00000065520	Mir128-1	Mirn128|Mirn128-1|Mirn128a|mir-128-1	microRNA 128-1	ncRNA
mm_25349.1	chr3	106788760	106788771	+	1	NA	intron (NM_007651, intron 1 of 7)	intron (NM_007651, intron 1 of 7)	1384	NM_007651	12508	Mm.316861	NM_007651	ENSMUSG00000040747	Cd53	AI323659|Ox-44|Tspan25	CD53 antigen	protein-coding
mm_16010.1	chr2	167384063	167384073	+	1	NA	Intergenic	Intergenic	-34890	NM_019835	56336	Mm.200886	NM_019835	ENSMUSG00000017929	B4galt5	9430078I07Rik|AW049941|AW539721	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 5	protein-coding
mm_48222.1	chr5	137625070	137625079	-	1	NA	promoter-TSS (NM_027708)	promoter-TSS (NM_027708)	4	NM_027708	71176	Mm.474695	NM_027708	ENSMUSG00000089984	Fbxo24	4933422D21Rik|Fbx24	F-box protein 24	protein-coding
mm_73158.1	chr8	94995684	94995694	+	1	NA	intron (NM_018882, intron 1 of 13)	intron (NM_018882, intron 1 of 13)	11290	NM_018882	14766	Mm.290834	NM_018882	ENSMUSG00000031785	Adgrg1	Cyt28|Gpr56|TM7LN4|TM7XN1	adhesion G protein-coupled receptor G1	protein-coding
mm_30034.1	chr3	135691326	135691370	-	1	NA	5' UTR (NM_008689, exon 1 of 25)	5' UTR (NM_008689, exon 1 of 25)	199	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_71321.1	chr8	44935397	44935408	+	1	NA	Intergenic	CpG	-14806	NM_001081286	14107	Mm.27365	NM_001081286	ENSMUSG00000070047	Fat1	2310038E12Rik|AU023433|Fath|mFat1	FAT atypical cadherin 1	protein-coding
mm_111129.1	chr12	81475349	81475355	-	1	NA	intron (NR_132134, intron 2 of 3)	intron (NR_132134, intron 2 of 3)	9499	NR_132135	66272	Mm.439970	NM_025461	ENSMUSG00000091803	Cox16	1810020G14Rik|1810055I05Rik|BB388670	cytochrome c oxidase assembly protein 16	protein-coding
mm_36041.1	chr4	57249113	57249124	-	1	NA	intron (NM_011207, intron 8 of 25)	intron (NM_011207, intron 8 of 25)	52719	NM_011207	545622	Mm.246552	NM_011207	ENSMUSG00000038764	Ptpn3	9530011I20Rik|PTP-H1|PTPCL	protein tyrosine phosphatase, non-receptor type 3	protein-coding
mm_26438.1	chr3	142621274	142621291	+	1	NA	intron (NM_010260, intron 1 of 10)	Lx8|LINE|L1	619	NM_010260	14469	Mm.24038	NM_010260	ENSMUSG00000028270	Gbp2	-	guanylate binding protein 2	protein-coding
mm_156748.1	chrX	159988224	159988251	+	1	NA	promoter-TSS (NM_001163085)	promoter-TSS (NM_001163085)	-196	NM_001163085	270672	Mm.386889	NM_001163085	ENSMUSG00000031303	Map3k15	BC031147|MEKK15	mitogen-activated protein kinase kinase kinase 15	protein-coding
mm_14813.1	chr2	146101675	146101679	+	1	NA	Intergenic	Intergenic	-120320	NM_016889	53626	Mm.379070	NM_016889	ENSMUSG00000068154	Insm1	IA-1	insulinoma-associated 1	protein-coding
mm_41273.1	chr5	89236280	89236289	+	1	NA	3' UTR (NM_001136260, exon 25 of 25)	3' UTR (NM_001136260, exon 25 of 25)	221614	NM_008096	14473	Mm.196595	NM_008096	ENSMUSG00000035540	Gc	DBP|VDB	group specific component	protein-coding
mm_64843.1	chr7	13010035	13010054	-	1	NA	promoter-TSS (NM_001024699)	promoter-TSS (NM_001024699)	-244	NM_001024699	232879	Mm.279272	NM_001024699	ENSMUSG00000049600	Zbtb45	BB161562|Gm157|Zfp499	zinc finger and BTB domain containing 45	protein-coding
mm_127580.1	chr15	102326133	102326152	+	1	NA	promoter-TSS (NM_027044)	promoter-TSS (NM_027044)	26	NM_027044	56612	Mm.158264	NM_020031	ENSMUSG00000001289	Pfdn5	1190001O17Rik|1700010A06Rik|D15Ertd697e|Eig1|MM-1	prefoldin 5	protein-coding
mm_153515.1	chr19	41474928	41474933	-	1	NA	Intergenic	Intergenic	-50322	NM_001326287	627352	Mm.395111	NM_001326287		Morf4l1b	EG627352|Gm6747	mortality factor 4 like 1B	protein-coding
mm_154883.1	chrX	20703909	20703909	+	1	NA	promoter-TSS (NM_145628)	promoter-TSS (NM_145628)	0	NM_145628	236733	Mm.34489	NM_145628	ENSMUSG00000031066	Usp11	6230415D12Rik|mKIAA4085	ubiquitin specific peptidase 11	protein-coding
mm_125340.1	chr15	39076886	39076938	+	1	NA	promoter-TSS (NM_026778)	promoter-TSS (NM_026778)	-20	NM_026778	68588	Mm.41556	NM_026778	ENSMUSG00000054196	Cthrc1	1110014B07Rik	collagen triple helix repeat containing 1	protein-coding
mm_84451.1	chr9	66514541	66514563	-	1	NA	promoter-TSS (NM_175206)	promoter-TSS (NM_175206)	41	NM_175206	74165	Mm.297998	NM_175206	ENSMUSG00000050503	Fbxl22	1110004B15Rik	F-box and leucine-rich repeat protein 22	protein-coding
mm_39014.1	chr4	152125993	152126001	-	1	NA	intron (NM_207688, intron 8 of 10)	CpG	2928	NM_019585	56226	Mm.264215	NM_019585	ENSMUSG00000028943	Espn	je	espin	protein-coding
mm_41811.1	chr5	103782069	103782071	+	1	NA	intron (NM_001080798, intron 1 of 19)	intron (NM_001080798, intron 1 of 19)	27497	NM_001080798	17355	Mm.6949	NM_133919	ENSMUSG00000029313	Aff1	9630032B01Rik|AW319193|Af4|Mllt2h|Rob	AF4/FMR2 family, member 1	protein-coding
mm_101090.1	chr11	11853588	11853601	-	1	NA	intron (NM_001190448, intron 6 of 14)	MER2B|DNA|TcMar-Tigger	-14529	NR_045178	73321	Mm.443306	NR_045178	ENSMUSG00000086391	1700042O10Rik	-	RIKEN cDNA 1700042O10 gene	ncRNA
mm_13674.1	chr2	116067934	116067975	+	1	NA	promoter-TSS (NM_001346047)	promoter-TSS (NM_001346047)	-510	NM_001346047	17536	Mm.247566	NM_010825	ENSMUSG00000027210	Meis2	A430109D20Rik|Mrg1|Stra10	Meis homeobox 2	protein-coding
mm_172491.1	chr7	56013930	56013952	+	1	NA	intron (NM_153578, intron 1 of 4)	intron (NM_153578, intron 1 of 4)	5632	NM_153578	233280	Mm.389901	NM_153578	ENSMUSG00000047037	Nipa1	1110027G09Rik|A830014A18Rik|FSP3|Spg6	non imprinted in Prader-Willi/Angelman syndrome 1 homolog (human)	protein-coding
mm_136780.1	chr17	10456294	10456298	+	1	NA	promoter-TSS (NR_077237)	promoter-TSS (NR_077237)	80	NR_077238	319750	Mm.383485	NR_077237	ENSMUSG00000089633	A230009B12Rik	-	RIKEN cDNA A230009B12 gene	ncRNA
mm_64912.1	chr7	16213185	16213205	-	1	NA	intron (NM_001285931, intron 5 of 16)	intron (NM_001285931, intron 5 of 16)	8798	NM_001285931	71723	Mm.75259	NM_027883	ENSMUSG00000006019	Dhx34	1200013B07Rik|1810012L18Rik|Ddx34|mKIAA0134	DEAH (Asp-Glu-Ala-His) box polypeptide 34	protein-coding
mm_51786.1	chr6	88200136	88200149	+	1	NA	intron (NM_008090, intron 2 of 5)	intron (NM_008090, intron 2 of 5)	1478	NM_008090	14461	Mm.491156	NM_008090	ENSMUSG00000015053	Gata2	Gata-2	GATA binding protein 2	protein-coding
mm_117656.1	chr13	93192218	93192237	-	1	NA	promoter-TSS (NM_133905)	promoter-TSS (NM_133905)	56	NM_133905	100715	Mm.242865	NM_133905	ENSMUSG00000042167	Papd4	8030446C20Rik|AI649009|GLD-2|Gld2	PAP associated domain containing 4	protein-coding
mm_24479.1	chr3	91114358	91114361	+	1	NA	Intergenic	Intergenic	-23554	NM_001101461	229550	Mm.98335	NM_001101461	ENSMUSG00000091175	9130204L05Rik	Gm127	RIKEN cDNA 9130204L05 gene	protein-coding
mm_45425.1	chr5	66618773	66618807	-	1	NA	promoter-TSS (NM_009686)	promoter-TSS (NM_009686)	27	NM_009686	11787	Mm.5159	NM_009686	ENSMUSG00000029207	Apbb2	2310007D03Rik|FE65L1|Rirl1|TR2L|Zfra	amyloid beta (A4) precursor protein-binding, family B, member 2	protein-coding
mm_387.1	chr1	34077281	34077290	+	1	NA	intron (NM_133833, intron 1 of 92)	intron (NM_133833, intron 1 of 92)	-40074	NR_105861	102466987		NR_105861	ENSMUSG00000105982	Mir6896	mmu-mir-6896	microRNA 6896	ncRNA
mm_124311.1	chr14	103156393	103156403	-	1	NA	exon (NM_207215, exon 58 of 85)	exon (NM_207215, exon 58 of 85)	-56832	NM_001347600	50789	Mm.214746	NM_015822	ENSMUSG00000022124	Fbxl3	AU041772|AW212966|FBK|Fbl3a|Fbxl3a|Ovtm|Play68	F-box and leucine-rich repeat protein 3	protein-coding
mm_20219.1	chr2	125767985	125767988	-	1	NA	intron (NM_177608, intron 5 of 17)	intron (NM_177608, intron 5 of 17)	14884	NM_177608	70354	Mm.138091	NM_133725	ENSMUSG00000035093	Secisbp2l	3110001I20Rik|AI504340|C630011I23	SECIS binding protein 2-like	protein-coding
mm_51548.1	chr6	83239240	83239279	+	1	NA	intron (NM_001166067, intron 1 of 24)	intron (NM_001166067, intron 1 of 24)	1884	NM_001166067	232156	Mm.333189	NM_001166067	ENSMUSG00000068323	Slc4a5	C330006M16|C330016K18Rik	solute carrier family 4, sodium bicarbonate cotransporter, member 5	protein-coding
mm_54145.1	chr6	22326463	22326465	-	1	NA	intron (NM_138587, intron 5 of 9)	intron (NM_138587, intron 5 of 9)	29617	NM_138587	27999	Mm.490307	NM_138587	ENSMUSG00000029672	Fam3c	D6Wsu176e|Ilei	family with sequence similarity 3, member C	protein-coding
mm_173162.1	chrX	39738842	39738842	+	1	NA	Intergenic	L1Md_F2|LINE|L1	124762	NM_001191032	100504400	Mm.373409	NM_001191032	ENSMUSG00000095240	Cypt14	-	cysteine-rich perinuclear theca 14	protein-coding
mm_130010.1	chr15	86574492	86574499	-	1	NA	Intergenic	Intergenic	360036	NM_145476	223754	Mm.28904	NM_145476	ENSMUSG00000051864	Tbc1d22a	BC023106|D15Ertd781e	TBC1 domain family, member 22a	protein-coding
mm_104663.1	chr11	97629367	97629381	-	1	NA	5' UTR (NM_175332, exon 1 of 1)	5' UTR (NM_175332, exon 1 of 1)	342	NM_175332	103551	Mm.24506	NM_175332	ENSMUSG00000043439	Epop	AA409164|AI413509|AW539173|E13|E130012A19Rik|esPRC2p48	elongin BC and polycomb repressive complex 2 associated protein	protein-coding
mm_139554.1	chr17	56875472	56875489	+	1	NA	promoter-TSS (NM_030141)	promoter-TSS (NM_030141)	-153	NM_030141	78625	Mm.160106	NM_030141	ENSMUSG00000024209	1700061G19Rik	1700026H02|AI507598	RIKEN cDNA 1700061G19 gene	protein-coding
mm_15653.1	chr2	163203153	163203169	+	1	NA	Intergenic	CpG	-22293	NM_001098799	269389	Mm.207709	NM_001098799	ENSMUSG00000074607	Tox2	AI851523|AV026525|BI987407|Gcx1|RxHMG1	TOX high mobility group box family member 2	protein-coding
mm_110034.1	chr12	16999965	16999977	-	1	NA	5' UTR (NM_001161111, exon 1 of 6)	5' UTR (NM_001161111, exon 1 of 6)	147	NM_172574	217430	Mm.379451	NM_172574	ENSMUSG00000045679	Pqlc3	C78076|E030024M05Rik	PQ loop repeat containing	protein-coding
mm_44873.1	chr5	34634707	34634729	-	1	NA	intron (NM_026660, intron 8 of 12)	intron (NM_026660, intron 8 of 12)	2396	NM_026660	68294	Mm.34564	NM_026660	ENSMUSG00000001082	Mfsd10	0610009O03Rik|Tetran	major facilitator superfamily domain containing 10	protein-coding
mm_122828.1	chr14	54686927	54686970	-	1	NA	promoter-TSS (NM_023190)	promoter-TSS (NM_023190)	-17	NM_023190	56215	Mm.297078	NM_019567	ENSMUSG00000022185	Acin1	2610036I19Rik|2610510L13Rik|Acinus|Acn|C79325|acinusL|acinusS|mKIAA0670	apoptotic chromatin condensation inducer 1	protein-coding
mm_73242.1	chr8	104239745	104239779	+	1	NA	intron (NM_021028, intron 4 of 9)	intron (NM_021028, intron 4 of 9)	8796	NR_045642	57813	Mm.183110	NM_021028	ENSMUSG00000035824	Tk2	AU024611|mt-TK	thymidine kinase 2, mitochondrial	protein-coding
mm_143709.1	chr17	80700752	80700779	-	1	NA	intron (NM_001290345, intron 1 of 33)	intron (NM_001290345, intron 1 of 33)	27260	NM_001290345	225028	Mm.311948	NM_001081357	ENSMUSG00000024242	Map4k3	4833416M01Rik|4833416M07Rik|9530052P13Rik|Glk|MAPKKKK3|MEKKK 3|MEKKK3|RAB8IPL1	mitogen-activated protein kinase kinase kinase kinase 3	protein-coding
mm_106475.1	chr11	120139437	120139448	-	1	NA	intron (NM_024249, intron 4 of 16)	intron (NM_024249, intron 4 of 16)	11909	NM_001164799	72055	Mm.253403	NM_024249	ENSMUSG00000061306	Slc38a10	1810073N04Rik	solute carrier family 38, member 10	protein-coding
mm_110598.1	chr12	56535254	56535269	-	1	NA	intron (NM_009385, intron 1 of 2)	CpG-3195	1647	NM_009385	21869	Mm.89972	NM_009385	ENSMUSG00000001496	Nkx2-1	AV026640|Nkx2.1|T/EBP|Titf1|Ttf-1	NK2 homeobox 1	protein-coding
mm_30218.1	chr3	145018943	145018969	-	1	NA	intron (NM_017474, intron 4 of 13)	intron (NM_017474, intron 4 of 13)	13820	NM_017474	23844	Mm.33483	NM_017474	ENSMUSG00000028255	Clca1	Clca2|Clca3|gob-5|gob5	chloride channel accessory 1	protein-coding
mm_134483.1	chr16	18626397	18626414	-	1	NA	intron (NM_213614, intron 2 of 11)	CpG	3533	NM_213614	18951	Mm.20365	NM_213614	ENSMUSG00000072214	Sept5	Cdcrel-1|Cdcrel1|Pnutl1	septin 5	protein-coding
mm_95446.1	chr11	50252439	50252454	+	1	NA	Intergenic	RLTR23|LTR|ERV1	-13914	NR_132733	17001	Mm.245151	NM_008521	ENSMUSG00000020377	Ltc4s	-	leukotriene C4 synthase	protein-coding
mm_160282.1	chr7	122997167	122997167	+	1	NA	exon (NM_011247, exon 15 of 18)	exon (NM_011247, exon 15 of 18)	26603	NM_175023	19647	Mm.4480	NM_011247	ENSMUSG00000030779	Rbbp6	4933422O15Rik|AI316869|BB233631|C030034J04Rik|C77662|P2P-R|PACT	retinoblastoma binding protein 6	protein-coding
mm_108321.1	chr12	79762374	79762388	+	1	NA	intron (NM_009014, intron 8 of 10)	intron (NM_009014, intron 8 of 10)	162352	NR_131075	77290	Mm.395042	NR_131073		9430078K24Rik	-	RIKEN cDNA 9430078K24 gene	ncRNA
mm_18505.1	chr2	62611799	62611815	-	1	NA	exon (NM_027835, exon 6 of 16)	exon (NM_027835, exon 6 of 16)	34448	NM_027835	71586	Mm.136224	NM_027835	ENSMUSG00000026896	Ifih1	9130009C22Rik|Helicard|Hlcd|MDA5|RLR-2	interferon induced with helicase C domain 1	protein-coding
mm_110112.1	chr12	26443640	26443642	-	1	NA	3' UTR (NM_021384, exon 6 of 6)	3' UTR (NM_021384, exon 6 of 6)	12811	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_48662.1	chr5	145980378	145980385	-	1	NA	intron (NR_030782, intron 11 of 11)	MER5B|DNA|hAT-Charlie	29236	NM_019792	56388	Mm.301900	NM_019792	ENSMUSG00000029630	Cyp3a25	AI327008	cytochrome P450, family 3, subfamily a, polypeptide 25	protein-coding
mm_120403.1	chr14	64950315	64950323	+	1	NA	promoter-TSS (NM_001347626)	promoter-TSS (NM_001347626)	274	NM_001253731	210925	Mm.71332	NM_153414	ENSMUSG00000021975	Ints9	BC028953|D14Ertd231e	integrator complex subunit 9	protein-coding
mm_5427.1	chr1	34485925	34485946	-	1	NA	Intergenic	Intergenic	-12495	NM_009355	21755	Mm.10725	NM_009355	ENSMUSG00000026125	Prss39	Tesp1	protease, serine 39	protein-coding
mm_115557.1	chr13	9076382	9076392	-	1	NA	Intergenic	Lx4B|LINE|L1	-17494	NM_001311117	217980	Mm.234944	NM_172585	ENSMUSG00000033499	Larp4b	A630096F19|AI256361|D13Wsu64e|Larp5	La ribonucleoprotein domain family, member 4B	protein-coding
mm_88847.1	chr10	80930131	80930137	+	1	NA	promoter-TSS (NM_008655)	promoter-TSS (NM_008655)	43	NM_008655	17873	Mm.1360	NM_008655	ENSMUSG00000015312	Gadd45b	AI323528|Myd118	growth arrest and DNA-damage-inducible 45 beta	protein-coding
mm_116557.1	chr13	46727671	46727683	-	1	NA	5' UTR (NM_175749, exon 1 of 22)	5' UTR (NM_175749, exon 1 of 22)	172	NM_175749	218210	Mm.255398	NM_175749	ENSMUSG00000021374	Nup153	B130015D15Rik|C88147	nucleoporin 153	protein-coding
mm_34795.1	chr4	154601300	154601302	+	1	NA	intron (NM_001177995, intron 1 of 15)	intron (NM_001177995, intron 1 of 15)	35066	NR_045643	320939	Mm.436738	NR_045643		5930403L14Rik	-	RIKEN cDNA 5930403L14 gene	ncRNA
mm_48416.1	chr5	140331874	140331897	-	1	NA	promoter-TSS (NM_026510)	promoter-TSS (NM_026510)	13	NM_026510	68017	Mm.38894	NM_026510	ENSMUSG00000029557	Mrm2	2310037B18Rik|Ftsj2	mitochondrial rRNA methyltransferase 2	protein-coding
mm_95033.1	chr11	32058843	32058863	+	1	NA	3' UTR (NM_008741, exon 5 of 5)	3' UTR (NM_008741, exon 5 of 5)	42375	NR_130637	104692	Mm.414035	NR_130637	ENSMUSG00000086386	Gm12108	BB052462|OTTMUSG00000005365	predicted gene 12108	ncRNA
mm_132567.1	chr16	38109735	38109738	+	1	NA	intron (NM_001347232, intron 1 of 11)	intron (NM_001347232, intron 1 of 11)	-20476	NR_033221	414072	Mm.483602	NR_033221		BC031361	-	cDNA sequence BC031361	ncRNA
mm_116167.1	chr13	30792207	30792225	-	1	NA	Intergenic	Intergenic	42983	NM_013674	16364	Mm.4677	NM_013674	ENSMUSG00000021356	Irf4	AI385587|IRF-4|LSIRF|NF-EM5|Spip	interferon regulatory factor 4	protein-coding
mm_169982.1	chr17	15010236	15010255	+	1	NA	promoter-TSS (NM_001123367)	promoter-TSS (NM_001123367)	-61	NM_001123367	100041639	Mm.440445	NM_001123367	ENSMUSG00000079710	Gm3448	-	predicted gene 3448	protein-coding
mm_10555.1	chr2	16751386	16751404	+	1	NA	3' UTR (NM_026162, exon 14 of 14)	3' UTR (NM_026162, exon 14 of 14)	262331	NR_040632	75069	Mm.50378	NR_040632		4930515L03Rik	-	RIKEN cDNA 4930515L03 gene	ncRNA
mm_7327.1	chr1	102628197	102628234	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	1472447	NR_037989	100504525	Mm.87065	NR_037989	ENSMUSG00000100684	Gm20268	-	predicted gene, 20268	ncRNA
mm_2410.1	chr1	93825271	93825305	+	1	NA	promoter-TSS (NM_001310767)	promoter-TSS (NM_001310767)	48	NM_001310767	98314	Mm.383401	NM_178882	ENSMUSG00000073609	D2hgdh	AA408776|AA408778|AI325464	D-2-hydroxyglutarate dehydrogenase	protein-coding
mm_14387.1	chr2	129800296	129800319	+	1	NA	promoter-TSS (NM_183262)	promoter-TSS (NM_183262)	-210	NM_183262	67333	Mm.389329	NM_183262	ENSMUSG00000037885	Stk35	1700054C12Rik|CLIK1|Stk35l1	serine/threonine kinase 35	protein-coding
mm_37269.1	chr4	118543211	118543251	-	1	NA	intron (NM_172383, intron 2 of 3)	intron (NM_172383, intron 2 of 3)	495	NM_172383	230678	Mm.23639	NM_172383	ENSMUSG00000050854	Tmem125	6330530A05Rik|AV223516	transmembrane protein 125	protein-coding
mm_64050.1	chr7	140835491	140835501	+	1	NA	promoter-TSS (NM_029821)	promoter-TSS (NM_029821)	0	NM_029821	76974	Mm.272359	NM_029821	ENSMUSG00000025481	Urah	1190003J15Rik|2810420C16Rik	urate (5-hydroxyiso-) hydrolase	protein-coding
mm_110186.1	chr12	27338503	27338518	-	1	NA	3' UTR (NM_009234, exon 1 of 1)	3' UTR (NM_009234, exon 1 of 1)	4208	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding
mm_148019.1	chr18	68429281	68429293	-	1	NA	promoter-TSS (NM_001271716)	promoter-TSS (NM_001271716)	33	NM_001301372	17200	Mm.426053	NM_008560	ENSMUSG00000045569	Mc2r	ACTH-R|ACTHR|MC2-R	melanocortin 2 receptor	protein-coding
mm_67486.1	chr7	80719288	80719291	-	1	NA	intron (NM_016721, intron 36 of 37)	PB1|SINE|Alu	-30412	NM_173863	70461	Mm.392175	NM_173863	ENSMUSG00000030527	Crtc3	2610312F20Rik|6332415K15Rik|AI429792|BC011210|TORC3	CREB regulated transcription coactivator 3	protein-coding
mm_153541.1	chr19	41981120	41981150	-	1	NA	promoter-TSS (NM_028152)	promoter-TSS (NM_028152)	1	NM_028152	72199	Mm.218940	NM_028152	ENSMUSG00000025159	Mms19	2410001K24Rik|2610042O15Rik|AI316855|C79368|C86341|Mms19l	MMS19 (MET18 S. cerevisiae)	protein-coding
mm_20846.1	chr2	148045892	148045905	-	1	NA	promoter-TSS (NM_001291067)	promoter-TSS (NM_001291067)	50	NM_001291065	15376	Mm.938	NM_010446	ENSMUSG00000037025	Foxa2	HNF3-beta|HNF3beta|Hnf-3b|Hnf3b|Tcf-3b|Tcf3b	forkhead box A2	protein-coding
mm_91115.1	chr10	19187562	19187588	-	1	NA	intron (NR_038022, intron 1 of 1)	L2|LINE|L2	20337	NR_038022	100504265	Mm.383417	NR_038021		Gm20139	-	predicted gene, 20139	ncRNA
mm_159327.1	chr3	32531308	32531308	+	1	NA	intron (NM_024200, intron 1 of 17)	B3|SINE|B2	1826	NM_024200	67414	Mm.290414	NM_024200	ENSMUSG00000027668	Mfn1	2310002F04Rik|6330416C07Rik|D3Ertd265e|HR2|mKIAA4032	mitofusin 1	protein-coding
mm_80692.1	chr9	91380690	91380706	+	1	NA	intron (NM_009576, intron 3 of 4)	intron (NM_009576, intron 3 of 4)	11726	NM_009576	22774	Mm.8062	NM_009576	ENSMUSG00000036972	Zic4	-	zinc finger protein of the cerebellum 4	protein-coding
mm_105744.1	chr11	109414862	109414872	-	1	NA	Intergenic	B3|SINE|B2	-11079	NM_025275	13929	Mm.211850	NM_025275	ENSMUSG00000020610	Amz2	AA408420|ESTM12|X83328	archaelysin family metallopeptidase 2	protein-coding
mm_172744.1	chr8	80582402	80582405	-	1	NA	Intergenic	MLTR31C_MM|LTR|ERVK	-28636	NM_001167898	333315	Mm.134296	NM_001167898	ENSMUSG00000042353	Frem3	Gm795|NV2	Fras1 related extracellular matrix protein 3	protein-coding
mm_7749.1	chr1	131097432	131097455	-	1	NA	exon (NM_008551, exon 1 of 10)	exon (NM_008551, exon 1 of 10)	400	NM_008551	17164	Mm.221235	NM_008551	ENSMUSG00000016528	Mapkapk2	AA960234|MAPKAP-K2|MK-2|MK2|Rps6kc1	MAP kinase-activated protein kinase 2	protein-coding
mm_142223.1	chr17	37480637	37480647	-	1	NA	TTS (NM_008204)	TTS (NM_008204)	2887	NM_008204	14990	Mm.329041	NM_008204	ENSMUSG00000016283	H2-M2	H-2M2|Thy19.4	histocompatibility 2, M region locus 2	protein-coding
mm_77779.1	chr9	3021257	3021283	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	17473	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_150611.1	chr19	40894153	40894163	+	1	NA	promoter-TSS (NR_106167)	promoter-TSS (NR_106167)	-545	NR_106167	102466881		NR_106167	ENSMUSG00000099118	Mir8092	Gm27407|mmu-mir-8092	microRNA 8092	ncRNA
mm_63033.1	chr7	121074667	121074673	+	1	NA	promoter-TSS (NM_030691)	promoter-TSS (NM_030691)	-140	NM_030691	80719	Mm.160384	NM_030691	ENSMUSG00000035004	Igsf6	-	immunoglobulin superfamily, member 6	protein-coding
mm_113625.1	chr13	41662930	41662935	+	1	NA	Intergenic	Intergenic	12170	NM_001145878	328231	Mm.227476	NM_177808	ENSMUSG00000054258	Gm5082	A030008J09|EG328231	predicted gene 5082	protein-coding
mm_142819.1	chr17	51751169	51751176	-	1	NA	intron (NM_009122, intron 9 of 10)	intron (NM_009122, intron 9 of 10)	60882	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_5530.1	chr1	37996920	37996950	-	1	NA	intron (NM_172054, intron 1 of 4)	intron (NM_172054, intron 1 of 4)	273	NM_172054	98258	Mm.28438	NM_172054	ENSMUSG00000058407	Txndc9	AI098020|APACD	thioredoxin domain containing 9	protein-coding
mm_114707.1	chr13	83525692	83525700	+	1	NA	intron (NM_001347566, intron 1 of 10)	intron (NM_001347566, intron 1 of 10)	953	NM_001347580	17260	Mm.24001	NM_025282	ENSMUSG00000005583	Mef2c	5430401D19Rik|9930028G15Rik|AV011172|Mef2	myocyte enhancer factor 2C	protein-coding
mm_72208.1	chr8	72646421	72646430	+	1	NA	promoter-TSS (NM_176940)	promoter-TSS (NM_176940)	-286	NM_176940	319555	Mm.212927	NM_176940	ENSMUSG00000048148	Nwd1	A230063L24Rik	NACHT and WD repeat domain containing 1	protein-coding
mm_99430.1	chr11	102407720	102407733	+	1	NA	promoter-TSS (NM_026542)	promoter-TSS (NM_026542)	-209	NM_026542	68066	Mm.44226	NM_026542	ENSMUSG00000018677	Slc25a39	3010027G13Rik|D11Ertd333e	solute carrier family 25, member 39	protein-coding
mm_83359.1	chr9	44407082	44407111	-	1	NA	promoter-TSS (NM_024266)	promoter-TSS (NM_024266)	452	NM_021789	60409	Mm.29814	NM_021789	ENSMUSG00000032112	Trappc4	1500017G03Rik|AI303617|HSPC172|PTD009|Sbd|Sbdn|Sdcbp2|TRS23	trafficking protein particle complex 4	protein-coding
mm_106950.1	chr12	8774570	8774573	+	1	NA	intron (NM_011519, intron 1 of 4)	intron (NM_011519, intron 1 of 4)	3175	NM_011519	20969	Mm.2580	NM_011519	ENSMUSG00000020592	Sdc1	AA408134|AA409076|CD138|Sstn|Synd|Synd1|syn-1	syndecan 1	protein-coding
mm_36219.1	chr4	62516707	62516721	-	1	NA	intron (NM_008525, intron 1 of 11)	intron (NM_008525, intron 1 of 11)	3195	NM_001276446	17025	Mm.6988	NM_008525	ENSMUSG00000028393	Alad	ALADH|Lv	aminolevulinate, delta-, dehydratase	protein-coding
mm_38678.1	chr4	144983455	144983472	-	1	NA	intron (NM_001276502, intron 66 of 68)	intron (NM_001276502, intron 66 of 68)	90326	NM_011303	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding
mm_66246.1	chr7	35555958	35555968	-	1	NA	promoter-TSS (NM_033080)	promoter-TSS (NM_033080)	-35	NM_033080	110959	Mm.410206	NM_033080	ENSMUSG00000034875	Nudt19	D7Rp2|D7Rp2-r|D7Rp2-s|D7Rp2e|RP2-r|RP2-s	nudix (nucleoside diphosphate linked moiety X)-type motif 19	protein-coding
mm_5137.1	chr1	9721405	9721416	-	1	NA	3' UTR (NM_173443, exon 3 of 3)	3' UTR (NM_173443, exon 3 of 3)	-21201	NM_008651	17864	Mm.479	NM_008651	ENSMUSG00000025912	Mybl1	A-myb|G1-419-6|repro9	myeloblastosis oncogene-like 1	protein-coding
mm_96537.1	chr11	68691927	68691944	+	1	NA	promoter-TSS (NM_175260)	promoter-TSS (NM_175260)	20	NM_175260	77579	Mm.218233	NM_175260	ENSMUSG00000020900	Myh10	5730504C04Rik|9330167F11Rik|Fltn|Myhn-2|Myhn2|NMHC II-B|NMHC-B|NMHCII-B|NMMHC II-b|NMMHC-B|NMMHC-IIB|SMemb|mKIAA3005	myosin, heavy polypeptide 10, non-muscle	protein-coding
mm_105122.1	chr11	101171197	101171207	-	1	NA	promoter-TSS (NM_146030)	promoter-TSS (NM_146030)	100	NM_146030	217198	Mm.273254	NM_146030	ENSMUSG00000035172	Plekhh3	BC020025	pleckstrin homology domain containing, family H (with MyTH4 domain) member 3	protein-coding
mm_113922.1	chr13	49582669	49582707	+	1	NA	promoter-TSS (NM_012050)	promoter-TSS (NM_012050)	-59	NM_012050	27047	Mm.390589	NM_012050	ENSMUSG00000048368	Omd	OSAD|SLRR2C	osteomodulin	protein-coding
mm_127427.1	chr15	101268028	101268051	+	1	NA	intron (NM_010444, intron 1 of 6)	intron (NM_010444, intron 1 of 6)	1193	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_93039.1	chr10	88356971	88356985	-	1	NA	promoter-TSS (NM_027878)	promoter-TSS (NM_027878)	97	NM_027878	71712	Mm.35450	NM_027878	ENSMUSG00000020057	Dram1	1200002N14Rik|Dram	DNA-damage regulated autophagy modulator 1	protein-coding
mm_63431.1	chr7	127478844	127478874	+	1	NA	Intergenic	CpG	-6362	NM_010183	14123	Mm.323505	NM_010183	ENSMUSG00000042423	Fbrs	Fbs|Fbs1	fibrosin	protein-coding
mm_9014.1	chr1	166121142	166121145	-	1	NA	intron (NM_001033344, intron 2 of 5)	L1ME1|LINE|L1	6755	NM_001033344	240892	Mm.35315	NM_001033344	ENSMUSG00000026564	Dusp27	C130085G02Rik|Gm209	dual specificity phosphatase 27 (putative)	protein-coding
mm_162291.1	chr1	30052617	30052617	+	1	NA	Intergenic	Lx8b|LINE|L1	631129	NR_105760	102465174		NR_105760	ENSMUSG00000099257	Mir6342	Gm27268|mmu-mir-6342	microRNA 6342	ncRNA
mm_152182.1	chr19	7426823	7426835	-	1	NA	TTS (NM_175381)	TTS (NM_175381)	4256	NR_105957	102466781		NR_105957	ENSMUSG00000098293	Mir6991	Gm27966|mmu-mir-6991	microRNA 6991	ncRNA
mm_83378.1	chr9	44551238	44551264	-	1	NA	Intergenic	Intergenic	-24830	NM_007551	12145	Mm.6246	NM_007551	ENSMUSG00000047880	Cxcr5	Blr1|CXC-R5|CXCR-5|Gpcr6|MDR15	chemokine (C-X-C motif) receptor 5	protein-coding
mm_128291.1	chr15	37233122	37233149	-	1	NA	promoter-TSS (NM_026496)	promoter-TSS (NM_026496)	99	NM_026496	252973	Mm.244612	NM_026496	ENSMUSG00000022286	Grhl2	0610015A08Rik|BOM|Tcfcp2l3|clft3	grainyhead-like 2 (Drosophila)	protein-coding
mm_53538.1	chr6	136803943	136803959	+	1	NA	TTS (NM_175652)	TTS (NM_175652)	480	NM_175652	320332	Mm.246720	NM_175652	ENSMUSG00000096010	Hist4h4	B130044J01Rik	histone cluster 4, H4	protein-coding
mm_76472.1	chr8	85408016	85408019	-	1	NA	TTS (NM_025722)	TTS (NM_025722)	24824	NR_033144	66714	Mm.272748	NM_025722	ENSMUSG00000036934	4921524J17Rik	-	RIKEN cDNA 4921524J17 gene	protein-coding
mm_113973.1	chr13	51651710	51651746	+	1	NA	promoter-TSS (NM_029279)	promoter-TSS (NM_029279)	20	NM_029279	75420	Mm.275981	NM_029279	ENSMUSG00000035139	Secisbp2	2210413N07Rik|2810012K13Rik|SBP2	SECIS binding protein 2	protein-coding
mm_100544.1	chr11	120677326	120677355	+	1	NA	intron (NM_198223, intron 1 of 14)	intron (NM_198223, intron 1 of 14)	679	NM_001164224	68938	Mm.294020	NM_026877	ENSMUSG00000025142	Aspscr1	1190006K01Rik|ASPC|ASPCR1|ASPL|ASPS|RCC17|TUG	alveolar soft part sarcoma chromosome region, candidate 1 (human)	protein-coding
mm_169789.1	chr16	14067725	14067737	+	1	NA	intron (NM_144518, intron 2 of 5)	intron (NM_144518, intron 2 of 5)	-80864	NM_001270718	74482	Mm.484026	NM_028968	ENSMUSG00000065968	Ifitm7	4933438K12Rik|Mil4	interferon induced transmembrane protein 7	protein-coding
mm_16281.1	chr2	173800053	173800054	+	1	NA	Intergenic	Intergenic	62482	NM_019806	56491	Mm.260456	NM_019806	ENSMUSG00000054455	Vapb	AI225786|AI840687|AI848259|D2Abb2e|R75548|VAP33b|Vamp33b	vesicle-associated membrane protein, associated protein B and C	protein-coding
mm_123657.1	chr14	69243577	69243615	-	1	NA	3' UTR (NM_026331, exon 4 of 4)	3' UTR (NM_026331, exon 4 of 4)	41507	NM_026331	67712	Mm.293635	NM_026331	ENSMUSG00000034248	Slc25a37	1700020E22Rik|4930513O14Rik|4930526G11Rik|AI848481|C330015G08Rik|Mfrn|Mfrn1|Mscp|frascati|mitoferrin	solute carrier family 25, member 37	protein-coding
mm_59230.1	chr7	24709230	24709234	+	1	NA	promoter-TSS (NM_199150)	promoter-TSS (NM_199150)	-27	NM_199150	232972	Mm.293074	NM_199150	ENSMUSG00000045587	BC049730	Lypd10	cDNA sequence BC049730	protein-coding
mm_16584.1	chr2	3715580	3715598	-	1	NA	intron (NM_025626, intron 1 of 3)	intron (NM_025626, intron 1 of 3)	2131	NM_025626	66540	Mm.277864	NM_025626	ENSMUSG00000026655	Fam107b	3110001A13Rik|AA589595|AA959793|AI132312	family with sequence similarity 107, member B	protein-coding
mm_129774.1	chr15	82791117	82791133	-	1	NA	exon (NM_029562, exon 7 of 9)	exon (NM_029562, exon 7 of 9)	3120	NM_029562	76279	Mm.439931	NM_029562	ENSMUSG00000022445	Cyp2d26	1300006E06Rik	cytochrome P450, family 2, subfamily d, polypeptide 26	protein-coding
mm_113448.1	chr13	35738488	35738530	+	1	NA	intron (NM_009881, intron 3 of 9)	intron (NM_009881, intron 3 of 9)	-2893	NM_001123386	12593	Mm.29002	NM_009881	ENSMUSG00000059288	Cdyl	AI325931	chromodomain protein, Y chromosome-like	protein-coding
mm_121798.1	chr14	20138510	20138519	-	1	NA	Intergenic	Intergenic	43268	NM_021542	16529	Mm.68998	NM_021542	ENSMUSG00000023243	Kcnk5	KCNK5b|TASK-2	potassium channel, subfamily K, member 5	protein-coding
mm_109676.1	chr12	113074820	113074822	+	1	NA	TTS (NM_001291445)	TTS (NM_001291445)	319	NM_029381	75671	Mm.23377	NM_029381	ENSMUSG00000012211	Tex22	1700028O09Rik|AV210422|Tep22	testis expressed gene 22	protein-coding
mm_64404.1	chr7	142510656	142510675	+	1	NA	exon (NM_001163669, exon 10 of 17)	exon (NM_001163669, exon 10 of 17)	-3894	NR_033261	677289	Mm.350054	NR_033261	ENSMUSG00000043795	Prr33	ENSMUSG00000043795|Gm14492|OTTMUSG00000016823	proline rich 33	ncRNA
mm_889.1	chr1	52845072	52845094	+	1	NA	promoter-TSS (NM_146108)	promoter-TSS (NM_146108)	45	NM_146108	227095	Mm.222063	NM_146108	ENSMUSG00000041426	Hibch	2610509I15Rik|HIBYL-COA-H	3-hydroxyisobutyryl-Coenzyme A hydrolase	protein-coding
mm_142389.1	chr17	44814650	44814660	-	1	NA	promoter-TSS (NM_009820)	promoter-TSS (NM_009820)	-28	NM_001146038	12393	Mm.391013	NM_009820	ENSMUSG00000039153	Runx2	AML3|Cbf|Cbfa-1|Cbfa1|LS3|Osf2|PEBP2aA|Pebp2a1|Pebpa2a	runt related transcription factor 2	protein-coding
mm_54225.1	chr6	28133905	28133934	-	1	NA	intron (NM_008174, intron 1 of 10)	intron (NM_008174, intron 1 of 10)	450	NM_008174	14823	Mm.320732	NM_008174	ENSMUSG00000024211	Grm8	A230002O04|Gprc1h|mGluR8	glutamate receptor, metabotropic 8	protein-coding
mm_107094.1	chr12	17547693	17547714	+	1	NA	exon (NM_013614, exon 4 of 12)	exon (NM_013614, exon 4 of 12)	2830	NM_013614	18263	Mm.34102	NM_013614	ENSMUSG00000011179	Odc1	ODC	ornithine decarboxylase, structural 1	protein-coding
mm_117313.1	chr13	67553100	67553176	-	1	NA	promoter-TSS (NR_131100)	promoter-TSS (NR_131100)	14	NM_001035231	212276	Mm.422831	NM_183145	ENSMUSG00000095432	Zfp748	KRAB-O|Rslcan20/21|Zfp208|mszf54	zinc finger protein 748	protein-coding
mm_74103.1	chr8	122848368	122848400	+	1	NA	promoter-TSS (NM_007662)	promoter-TSS (NM_007662)	10	NM_007662	12555	Mm.1976	NM_007662	ENSMUSG00000031962	Cdh15	AI323380|Cdh14|Mcad	cadherin 15	protein-coding
mm_79089.1	chr9	46242657	46242665	+	1	NA	exon (NM_007468, exon 3 of 3)	exon (NM_007468, exon 3 of 3)	1817	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_127156.1	chr15	98626632	98626641	+	1	NA	Intergenic	Intergenic	-5692	NM_001044741	12297	Mm.3544	NM_007581	ENSMUSG00000003352	Cacnb3	Beta3|CAB3|Ca(v)beta3|Cchb3	calcium channel, voltage-dependent, beta 3 subunit	protein-coding
mm_3667.1	chr1	153652931	153652931	+	1	NA	promoter-TSS (NM_026380)	promoter-TSS (NM_026380)	-106	NM_026380	67792	Mm.379143	NM_026380	ENSMUSG00000042671	Rgs8	6530413N01Rik	regulator of G-protein signaling 8	protein-coding
mm_25331.1	chr3	106573726	106573737	+	1	NA	3' UTR (NM_026013, exon 9 of 9)	3' UTR (NM_026013, exon 9 of 9)	-25929	NM_133869	99712	Mm.429443	NM_133869	ENSMUSG00000040774	Cept1	9930118K05Rik|mCEPT1	choline/ethanolaminephosphotransferase 1	protein-coding
mm_137399.1	chr17	25833108	25833154	+	1	NA	5' UTR (NM_019719, exon 1 of 7)	5' UTR (NM_019719, exon 1 of 7)	230	NM_019719	56424	Mm.277599	NM_019719	ENSMUSG00000039615	Stub1	0610033N24Rik|2210017D18Rik|2310040B03Rik|AW046544|Chip	STIP1 homology and U-Box containing protein 1	protein-coding
mm_39730.1	chr5	28373089	28373092	+	1	NA	intron (NM_028234, intron 10 of 18)	intron (NM_028234, intron 10 of 18)	55901	NM_028234	381626	Mm.304075	NM_028234	ENSMUSG00000048271	Rbm33	3200001K10Rik|6430512A10Rik|AA386890|Prr8	RNA binding motif protein 33	protein-coding
mm_88701.1	chr10	80145416	80145465	+	1	NA	exon (NM_025313, exon 4 of 4)	exon (NM_025313, exon 4 of 4)	-2832	NM_001305798	59090	Mm.143813	NM_021565	ENSMUSG00000035621	Midn	3000003C15Rik	midnolin	protein-coding
mm_101574.1	chr11	34311794	34311811	-	1	NA	intron (NM_033374, intron 28 of 51)	intron (NM_033374, intron 28 of 51)	-3020	NM_001025382	574403	Mm.444796	NM_001025382	ENSMUSG00000069911	Fam196b	EG574403|Gm6041	family with sequence similarity 196, member B	protein-coding
mm_96674.1	chr11	69411356	69411383	+	1	NA	intron (NM_001017426, intron 1 of 22)	CpG	2306	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_22460.1	chr3	3298330	3298331	+	1	NA	Intergenic	Intergenic	-209700	NM_013920	30942	Mm.330897	NM_013920	ENSMUSG00000017688	Hnf4g	NR2A2	hepatocyte nuclear factor 4, gamma	protein-coding
mm_164095.1	chr15	11334760	11334765	+	1	NA	intron (NM_175501, intron 22 of 23)	intron (NM_175501, intron 22 of 23)	64896	NM_033074	110960	Mm.286061	NM_033074	ENSMUSG00000022241	Tars	D15Wsu59e|ThrRS	threonyl-tRNA synthetase	protein-coding
mm_88215.1	chr10	70245241	70245254	+	1	NA	promoter-TSS (NM_025807)	promoter-TSS (NM_025807)	-29	NM_025807	66859	Mm.19325	NM_025807	ENSMUSG00000037762	Slc16a9	1200003C15Rik|4930425B13Rik|AI552636	solute carrier family 16 (monocarboxylic acid transporters), member 9	protein-coding
mm_5629.1	chr1	40397529	40397539	-	1	NA	Intergenic	Intergenic	-32036	NM_001294171	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_93704.1	chr10	118141566	118141610	-	1	NA	promoter-TSS (NM_010785)	promoter-TSS (NM_010785)	-199	NM_001162904	17245	Mm.101191	NM_010785	ENSMUSG00000020212	Mdm1	Arrd2|Mdm-1	transformed mouse 3T3 cell double minute 1	protein-coding
mm_162052.1	chrX	7658309	7658309	+	1	NA	intron (NM_001290624, intron 1 of 8)	intron (NM_001290624, intron 1 of 8)	930	NM_001290624	54630	Mm.232232	NM_175097	ENSMUSG00000031145	Prickle3	Lmo6|Sfc16	prickle planar cell polarity protein 3	protein-coding
mm_80788.1	chr9	95954821	95954843	+	1	NA	promoter-TSS (NM_001311130)	promoter-TSS (NM_001311130)	72	NM_001311130	24127	Mm.291179	NM_011916	ENSMUSG00000032410	Xrn1	Dhm2|exo|mXrn1	5'-3' exoribonuclease 1	protein-coding
mm_102656.1	chr11	63919631	63919634	-	1	NA	intron (NM_018805, intron 1 of 1)	intron (NM_018805, intron 1 of 1)	2652	NM_018805	54710	Mm.274426	NM_018805	ENSMUSG00000070407	Hs3st3b1	3-OST-3B|3OST3B1|3Ost3b|AU041882|AW536289|Hs3st3b|m3-OST-3B	heparan sulfate (glucosamine) 3-O-sulfotransferase 3B1	protein-coding
mm_117271.1	chr13	64903950	64903995	-	1	NA	promoter-TSS (NM_001081129)	promoter-TSS (NM_001081129)	-84	NM_001081129	238680	Mm.390590	NM_001081129	ENSMUSG00000033063	Cntnap3	-	contactin associated protein-like 3	protein-coding
mm_21876.1	chr2	166083566	166083576	-	1	NA	intron (NM_001252579, intron 10 of 20)	intron (NM_001252579, intron 10 of 20)	71714	NM_001252578	72043	Mm.1011	NM_028072	ENSMUSG00000006800	Sulf2	2010004N24Rik|AU020235|MSulf-2|mKIAA1247	sulfatase 2	protein-coding
mm_81938.1	chr9	120303966	120304021	+	1	NA	promoter-TSS (NM_144557)	promoter-TSS (NM_144557)	-80	NM_144557	245049	Mm.100936	NM_144557	ENSMUSG00000041794	Myrip	A230081N12Rik|Slac2-c|Slac2c	myosin VIIA and Rab interacting protein	protein-coding
mm_79822.1	chr9	64396628	64396632	+	1	NA	intron (NM_172522, intron 1 of 22)	ID_B1|SINE|B4	11004	NM_001134399	214058	Mm.127721	NM_172522	ENSMUSG00000036466	Megf11	2410080H04Rik|D130061K05	multiple EGF-like-domains 11	protein-coding
mm_18227.1	chr2	51447706	51447752	-	1	NA	Intergenic	Lx5|LINE|L1	-9829	NR_130155	73375	Mm.396227	NR_130155	ENSMUSG00000086007	1700057H21Rik	-	RIKEN cDNA 1700057H21 gene	ncRNA
mm_71082.1	chr8	34760874	34760876	+	1	NA	Intergenic	Intergenic	-46735	NM_176933	319520	Mm.170276	NM_176933	ENSMUSG00000031530	Dusp4	2700078F24Rik|AI844617|BB104621|E130306H24Rik|MKP2	dual specificity phosphatase 4	protein-coding
mm_136169.1	chr16	88563202	88563214	-	1	NA	promoter-TSS (NM_018778)	promoter-TSS (NM_018778)	-25	NM_018778	54420	Mm.25836	NM_018778	ENSMUSG00000050520	Cldn8	AI648025	claudin 8	protein-coding
mm_61280.1	chr7	66822203	66822206	+	1	NA	3' UTR (NM_001164201, exon 11 of 11)	3' UTR (NM_001164201, exon 11 of 11)	-17531	NM_001033877	233332	Mm.445763	NM_001033877	ENSMUSG00000058145	Adamts17	AU023434	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 17	protein-coding
mm_2234.1	chr1	91044466	91044480	+	1	NA	intron (NM_001111312, intron 1 of 12)	intron (NM_001111312, intron 1 of 12)	-8971	NM_001310732	16978	Mm.45039	NM_008515	ENSMUSG00000026305	Lrrfip1	AU024550|Fliiap1	leucine rich repeat (in FLII) interacting protein 1	protein-coding
mm_11437.1	chr2	32006429	32006461	+	1	NA	intron (NM_172268, intron 17 of 35)	intron (NM_172268, intron 17 of 35)	31995	NM_172268	227720	Mm.289686	NM_172268	ENSMUSG00000001855	Nup214	BC039282|CAN|D2H9S46E	nucleoporin 214	protein-coding
mm_56026.1	chr6	86607627	86607638	-	1	NA	Intergenic	Intergenic	-20542	NM_026414	67855	Mm.183043	NM_026414	ENSMUSG00000033508	Asprv1	2300003P22Rik|AA986851|SASP|SASPase|Taps	aspartic peptidase, retroviral-like 1	protein-coding
mm_32422.1	chr4	107126618	107126622	+	1	NA	Intergenic	Intergenic	29729	NM_172873	242603	Mm.257231	NM_172873	ENSMUSG00000047636	Cdcp2	D030010E02Rik	CUB domain containing protein 2	protein-coding
mm_75936.1	chr8	71558907	71558919	-	1	NA	promoter-TSS (NM_001100462)	promoter-TSS (NM_001100462)	-42	NM_001100462	434325	Mm.33613	NM_001100462	ENSMUSG00000043664	Tmem221	-	transmembrane protein 221	protein-coding
mm_157004.1	chrX	7583934	7583955	-	1	NA	intron (NM_001199348, intron 1 of 12)	intron (NM_001199348, intron 1 of 12)	3461	NM_001199348	20371	Mm.182291	NM_054039	ENSMUSG00000039521	Foxp3	JM2|scurfin|sf	forkhead box P3	protein-coding
mm_48470.1	chr5	140841970	140841985	-	1	NA	Intergenic	Intergenic	-11546	NM_010302	14673	Mm.370185	NM_010302	ENSMUSG00000000149	Gna12	AI414047|AI504261|Galpha12	guanine nucleotide binding protein, alpha 12	protein-coding
mm_57515.1	chr6	125483499	125483508	-	1	NA	intron (NM_007657, intron 1 of 7)	intron (NM_007657, intron 1 of 7)	11252	NM_007657	12527	Mm.210676	NM_007657	ENSMUSG00000030342	Cd9	Tspan29	CD9 antigen	protein-coding
mm_12750.1	chr2	79237251	79237271	+	1	NA	Intergenic	Intergenic	-18165	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D|Itga4B	integrin alpha 4	protein-coding
mm_11256.1	chr2	29914446	29914449	+	1	NA	exon (NM_001113213, exon 11 of 21)	exon (NM_001113213, exon 11 of 21)	-20962	NM_028923	74412	Mm.275121	NM_028923	ENSMUSG00000019715	Gle1	4933405K21Rik|AA553313|Gle1l	GLE1 RNA export mediator (yeast)	protein-coding
mm_109787.1	chr12	3248590	3248610	-	1	NA	3' UTR (NM_016676, exon 6 of 6)	3' UTR (NM_016676, exon 6 of 6)	12809	NR_015551	74173	Mm.309774	NM_028796	ENSMUSG00000079179	Rab10os	1700012B15Rik|1810036A22Rik	RAB10, member RAS oncogene family, opposite strand	ncRNA
mm_64133.1	chr7	141172915	141172957	+	1	NA	promoter-TSS (NM_001172100)	promoter-TSS (NM_001172100)	-85	NM_001172100	107702	Mm.197493	NM_145135	ENSMUSG00000038650	Rnh1	AW546468|C80305|RNH	ribonuclease/angiogenin inhibitor 1	protein-coding
mm_38534.1	chr4	141566385	141566393	-	1	NA	Intergenic	Intergenic	20227	NR_030695	320456	Mm.32859	NM_177163		B330016D10Rik	-	RIKEN cDNA B330016D10 gene	ncRNA
mm_27109.1	chr3	30699856	30699872	-	1	NA	promoter-TSS (NM_001309233)	promoter-TSS (NM_001309233)	-21	NM_001309233	320352	Mm.229153	NM_001309233	ENSMUSG00000074653	Lrrc31	E230002P03Rik	leucine rich repeat containing 31	protein-coding
mm_348.1	chr1	31176405	31176413	+	1	NA	promoter-TSS (NM_153601)	promoter-TSS (NM_153601)	-26	NM_153601	266744	Mm.389093	NM_153601	ENSMUSG00000050217	Lgsn	Gluld1|Lgs|lengsin	lengsin, lens protein with glutamine synthetase domain	protein-coding
mm_81035.1	chr9	104854458	104854474	+	1	NA	intron (NM_028719, intron 2 of 15)	intron (NM_028719, intron 2 of 15)	-198802	NM_053159	94062	Mm.29746	NM_053159	ENSMUSG00000032563	Mrpl3	2010320L16Rik|5930422H18Rik|AA407889	mitochondrial ribosomal protein L3	protein-coding
mm_98140.1	chr11	87578499	87578500	+	1	NA	5' UTR (NM_001284398, exon 1 of 11)	5' UTR (NM_001284398, exon 1 of 11)	110	NM_001284398	18952	Mm.2214	NM_011129	ENSMUSG00000020486	Sept4	ARTS|Bh5|OTTMUSG00000001265|Pnutl2	septin 4	protein-coding
mm_88710.1	chr10	80150984	80151000	+	1	NA	intron (NM_001347117, intron 2 of 7)	CpG-1261	1310	NM_001305799	59090	Mm.143813	NM_021565	ENSMUSG00000035621	Midn	3000003C15Rik	midnolin	protein-coding
mm_59582.1	chr7	28129460	28129479	+	1	NA	promoter-TSS (NM_001164655)	promoter-TSS (NM_001164655)	3	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_158501.1	chrX	142390395	142390428	-	1	NA	5' UTR (NM_207625, exon 1 of 16)	5' UTR (NM_207625, exon 1 of 16)	124	NM_001033600	50790	Mm.391337	NM_019477	ENSMUSG00000031278	Acsl4	9430020A05Rik|ACS4|AU018108|Facl4|Lacs4	acyl-CoA synthetase long-chain family member 4	protein-coding
mm_147143.1	chr18	36515799	36515812	-	1	NA	promoter-TSS (NM_010415)	promoter-TSS (NM_010415)	0	NM_010415	15200	Mm.289681	NM_010415	ENSMUSG00000024486	Hbegf	AW047313|Dtr|Dts|Hegfl	heparin-binding EGF-like growth factor	protein-coding
mm_5493.1	chr1	36939603	36939655	-	1	NA	promoter-TSS (NM_018872)	promoter-TSS (NM_018872)	-102	NM_018872	56030	Mm.186943	NM_018872	ENSMUSG00000026116	Tmem131	2610524E03Rik|CC28|D1Bwg0491e|Neg|RW1|YR-23|mKIAA0257	transmembrane protein 131	protein-coding
mm_49811.1	chr6	36389322	36389334	+	1	NA	intron (NM_203491, intron 2 of 2)	intron (NM_203491, intron 2 of 2)	-1094	NR_015589	319472	Mm.226434	NR_015589	ENSMUSG00000073154	9330158H04Rik	-	RIKEN cDNA 9330158H04 gene	ncRNA
mm_155210.1	chrX	56779700	56779718	+	1	NA	promoter-TSS (NM_001077362)	promoter-TSS (NM_001077362)	26	NM_001077362	14199	Mm.3126	NM_010211	ENSMUSG00000023092	Fhl1	FHL-1|KyoT|RAM14-1|SLIM|SLIM-1	four and a half LIM domains 1	protein-coding
mm_55567.1	chr6	71371180	71371202	-	1	NA	Intergenic	Intergenic	-2236	NM_009857	12525	Mm.1858	NM_009857	ENSMUSG00000053977	Cd8a	BB154331|Ly-2|Ly-35|Ly-B|Lyt-2	CD8 antigen, alpha chain	protein-coding
mm_108376.1	chr12	80854049	80854061	+	1	NA	intron (NM_001242419, intron 3 of 6)	intron (NM_001242419, intron 3 of 6)	63523	NM_001242419	217684	Mm.341776	NM_178682	ENSMUSG00000021133	Susd6	4933426M11Rik|mKIAA0247	sushi domain containing 6	protein-coding
mm_78604.1	chr9	37531122	37531138	+	1	NA	intron (NR_136939, intron 1 of 6)	intron (NR_136939, intron 1 of 6)	3041	NM_027102	69524	Mm.41751	NM_027102	ENSMUSG00000001946	Esam	2310008D05Rik|Esam1|W117m	endothelial cell-specific adhesion molecule	protein-coding
mm_39053.1	chr4	153632215	153632222	-	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-149388	NM_001099299	230959	Mm.318874	NM_001099299	ENSMUSG00000039546	Ajap1	Gm573	adherens junction associated protein 1	protein-coding
mm_76473.1	chr8	85425696	85425699	-	1	NA	intron (NR_033144, intron 1 of 2)	intron (NR_033144, intron 1 of 2)	7144	NR_033144	66714	Mm.272748	NM_025722	ENSMUSG00000036934	4921524J17Rik	-	RIKEN cDNA 4921524J17 gene	protein-coding
mm_112604.1	chr13	14186899	14186912	+	1	NA	exon (NM_194262, exon 20 of 24)	exon (NM_194262, exon 20 of 24)	123121	NM_198122	94246	Mm.439784	NM_194262	ENSMUSG00000039219	Arid4b	BCAA|BRCAA1|RBBP1L1|Rbp1l1|SAP180	AT rich interactive domain 4B (RBP1-like)	protein-coding
mm_65393.1	chr7	25094826	25094864	-	1	NA	exon (NM_001163556, exon 12 of 14)	exon (NM_001163556, exon 12 of 14)	2330	NR_105855	102465968		NR_105855	ENSMUSG00000098441	Mir6537	Gm27808|mmu-mir-6537	microRNA 6537	ncRNA
mm_59678.1	chr7	28393038	28393042	+	1	NA	promoter-TSS (NM_019458)	promoter-TSS (NM_019458)	44	NM_019458	54624	Mm.7916	NM_019458	ENSMUSG00000003437	Paf1	5730511K23Rik|AA675045	Paf1, RNA polymerase II complex component	protein-coding
mm_79764.1	chr9	62753366	62753413	+	1	NA	intron (NM_176922, intron 12 of 29)	intron (NM_176922, intron 12 of 29)	58259	NM_010193	14155	Mm.24069	NM_010193	ENSMUSG00000032244	Fem1b	mKIAA0396	feminization 1 homolog b (C. elegans)	protein-coding
mm_72749.1	chr8	85096764	85096782	+	1	NA	exon (NM_010764, exon 22 of 24)	exon (NM_010764, exon 22 of 24)	13504	NM_010764	17159	Mm.4219	NM_010764	ENSMUSG00000005142	Man2b1	AW107687|LAMAN	mannosidase 2, alpha B1	protein-coding
mm_19751.1	chr2	104849757	104849800	-	1	NA	promoter-TSS (NM_178695)	promoter-TSS (NM_178695)	72	NM_178695	228413	Mm.259609	NM_178695	ENSMUSG00000027171	Prrg4	9930111I18Rik|TMG4	proline rich Gla (G-carboxyglutamic acid) 4 (transmembrane)	protein-coding
mm_145969.1	chr18	67933039	67933101	+	1	NA	promoter-TSS (NM_172631)	promoter-TSS (NM_172631)	-187	NM_172631	52662	Mm.440183	NM_172631	ENSMUSG00000024544	Ldlrad4	8230401C20Rik|A430083H02|A430108L08Rik|C18orf1|D18Ertd653e|D330030L18Rik	low density lipoprotein receptor class A domain containing 4	protein-coding
mm_149836.1	chr19	24900432	24900450	+	1	NA	exon (NM_008022, exon 1 of 1)	exon (NM_008022, exon 1 of 1)	868	NM_008022	14237	Mm.377080	NM_008022	ENSMUSG00000051490	Foxd4	FREAC5|Fkh2	forkhead box D4	protein-coding
mm_63237.1	chr7	126563681	126563726	+	1	NA	exon (NM_146200, exon 5 of 21)	exon (NM_146200, exon 5 of 21)	2663	NM_146200	56347	Mm.22776	NM_146200	ENSMUSG00000030738	Eif3c	110kDa|3230401O13Rik|Eif3s8|NIPIL(A3)|NipilA3|Xs|Xsl	eukaryotic translation initiation factor 3, subunit C	protein-coding
mm_37305.1	chr4	119282254	119282280	-	1	NA	exon (NM_011732, exon 5 of 8)	exon (NM_011732, exon 5 of 8)	12246	NM_011732	22608	Mm.258204	NM_011732	ENSMUSG00000028639	Ybx1	1700102N10Rik|C79409|EF1A|MSY1|Nsep1|YB-1|dbpB|mYB-1a	Y box protein 1	protein-coding
mm_136492.1	chr16	96127465	96127496	-	1	NA	intron (NM_008251, intron 1 of 5)	CpG-5899	245	NM_008251	15312	Mm.2756	NM_008251	ENSMUSG00000040681	Hmgn1	HMG-14|Hmg14	high mobility group nucleosomal binding domain 1	protein-coding
mm_99173.1	chr11	100849628	100849638	+	1	NA	intron (NM_001113563, intron 1 of 18)	intron (NM_001113563, intron 1 of 18)	952	NM_001113563	20851	Mm.34064	NM_011489	ENSMUSG00000020919	Stat5b	-	signal transducer and activator of transcription 5B	protein-coding
mm_2225.1	chr1	90603461	90603511	+	1	NA	promoter-TSS (NM_133805)	promoter-TSS (NM_133805)	61	NM_133805	108679	Mm.119177	NM_133805	ENSMUSG00000034432	Cops8	9430009J09Rik|AA408242|Csn8|Sgn8	COP9 signalosome subunit 8	protein-coding
mm_6499.1	chr1	74284378	74284436	-	1	NA	promoter-TSS (NM_025580)	promoter-TSS (NM_025580)	331	NM_146110	227290	Mm.379371	NM_146110	ENSMUSG00000006299	Aamp	AU040907|Aamp-rs	angio-associated migratory protein	protein-coding
mm_151653.1	chr19	4121439	4121486	-	1	NA	5' UTR (NM_016666, exon 2 of 7)	5' UTR (NM_016666, exon 2 of 7)	113	NM_001276284	11632	Mm.10433	NM_016666	ENSMUSG00000024847	Aip	AA408703|AW476050|Ara9|D19Bwg1412e|Fkbp16|Xap2	aryl-hydrocarbon receptor-interacting protein	protein-coding
mm_128897.1	chr15	73268492	73268528	-	1	NA	intron (NM_001130409, intron 18 of 29)	intron (NM_001130409, intron 18 of 29)	-13628	NR_029561	387169		NR_029561	ENSMUSG00000065612	Mir151	Mirn151|mir-151|mmu-mir-151	microRNA 151	ncRNA
mm_132478.1	chr16	36722541	36722568	+	1	NA	exon (NM_134109, exon 7 of 8)	exon (NM_134109, exon 7 of 8)	28576	NM_001285791	106347	Mm.17807	NM_134109	ENSMUSG00000022900	Ildr1	AU041483|AU044638	immunoglobulin-like domain containing receptor 1	protein-coding
mm_53191.1	chr6	125493313	125493332	+	1	NA	intron (NM_007657, intron 1 of 7)	intron (NM_007657, intron 1 of 7)	1433	NM_007657	12527	Mm.210676	NM_007657	ENSMUSG00000030342	Cd9	Tspan29	CD9 antigen	protein-coding
mm_169496.1	chr14	75931526	75931545	-	1	NA	intron (NM_026816, intron 5 of 7)	intron (NM_026816, intron 5 of 7)	-23468	NM_026214	67516	Mm.390712	NM_026214	ENSMUSG00000046523	Kctd4	2210017A09Rik|AU017169	potassium channel tetramerisation domain containing 4	protein-coding
mm_118789.1	chr14	24118862	24118870	+	1	NA	Intergenic	Intergenic	29989	NR_106069	102465697		NR_106069	ENSMUSG00000105723	Mir7210	mir-7210|mmu-mir-7210	microRNA 7210	ncRNA
mm_158019.1	chrX	95965071	95965093	-	1	NA	Intergenic	Intergenic	-8108	NM_152822	76130	Mm.274318	NM_152822	ENSMUSG00000057421	Las1l	1810030A06Rik|5830482G23Rik	LAS1-like (S. cerevisiae)	protein-coding
mm_72940.1	chr8	91467696	91467725	+	1	NA	intron (NM_011936, intron 4 of 8)	intron (NM_011936, intron 4 of 8)	154185	NM_011936	26383	Mm.4375	NM_011936	ENSMUSG00000055932	Fto	AW743446|mKIAA1752	fat mass and obesity associated	protein-coding
mm_116514.1	chr13	45689047	45689050	-	1	NA	intron (NM_001199304, intron 5 of 6)	ID_B1|SINE|B4	181604	NM_025508	66355	Mm.290802	NM_025508	ENSMUSG00000000253	Gmpr	2310004P21Rik|AV028449|GMPR 1	guanosine monophosphate reductase	protein-coding
mm_16778.1	chr2	9887748	9887769	-	1	NA	TTS (NR_024257)	TTS (NR_024257)	1782	NR_040511	77682	Mm.488621	NR_040511	ENSMUSG00000079602	9230102O04Rik	-	RIKEN cDNA 9230102O04 gene	ncRNA
mm_67293.1	chr7	78895733	78895739	-	1	NA	promoter-TSS (NM_001162939)	promoter-TSS (NM_001162939)	-191	NM_026531	68048	Mm.34109	NM_026531	ENSMUSG00000030609	Aen	2700083B06Rik|Isg20l1	apoptosis enhancing nuclease	protein-coding
mm_20653.1	chr2	132094588	132094608	-	1	NA	intron (NM_018824, intron 2 of 15)	intron (NM_018824, intron 2 of 15)	50510	NM_018824	54338	Mm.103581	NM_018824	ENSMUSG00000027340	Slc23a2	AI844736|NBTL1|SVCT2|Slc23a1|YSPL2|YSPL3|mKIAA0238	solute carrier family 23 (nucleobase transporters), member 2	protein-coding
mm_139661.1	chr17	57406832	57406919	+	1	NA	exon (NM_010130, exon 6 of 22)	exon (NM_010130, exon 6 of 22)	48189	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_114612.1	chr13	75845627	75845632	+	1	NA	intron (NM_053108, intron 1 of 2)	intron (NM_053108, intron 1 of 2)	5743	NM_053108	93692	Mm.25844	NM_053108	ENSMUSG00000021591	Glrx	C86710|D13Wsu156e|Glrx1|Grx1|TTase	glutaredoxin	protein-coding
mm_75621.1	chr8	64617640	64617650	-	1	NA	exon (NM_013494, exon 3 of 9)	exon (NM_013494, exon 3 of 9)	75464	NM_013494	12876	Mm.31395	NM_013494	ENSMUSG00000037852	Cpe	CPH|Cph-1|Cph1|R74677|fat	carboxypeptidase E	protein-coding
mm_121137.1	chr14	101886886	101886896	+	1	NA	intron (NM_001347628, intron 6 of 26)	intron (NM_001347628, intron 6 of 26)	46268	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_143021.1	chr17	56512477	56512509	-	1	NA	promoter-TSS (NM_011483)	promoter-TSS (NM_011483)	-10	NM_011483	20834	Mm.76862	NM_011483	ENSMUSG00000044526	Znrf4	1700094M01Rik|Ssrzf1|spzn	zinc and ring finger 4	protein-coding
mm_13685.1	chr2	117120435	117120441	+	1	NA	promoter-TSS (NM_001277256)	promoter-TSS (NM_001277256)	-633	NM_001277256	114715	Mm.245890	NM_033524	ENSMUSG00000027351	Spred1	5730461F13Rik|AL024345|AW047647	sprouty protein with EVH-1 domain 1, related sequence	protein-coding
mm_124135.1	chr14	86148246	86148246	-	1	NA	Intergenic	Intergenic	-97724	NR_040457	75155	Mm.399239	NR_040457		4930529K09Rik	4930507G21Rik	RIKEN cDNA 4930529K09 gene	ncRNA
mm_149903.1	chr19	25599496	25599496	+	1	NA	intron (NM_015826, intron 4 of 4)	intron (NM_015826, intron 4 of 4)	-11041	NM_177360	240590	Mm.62785	NM_177360	ENSMUSG00000042372	Dmrt3	-	doublesex and mab-3 related transcription factor 3	protein-coding
mm_24680.1	chr3	94864154	94864165	+	1	NA	exon (NM_172683, exon 6 of 19)	exon (NM_172683, exon 6 of 19)	22799	NM_008945	19172	Mm.368	NM_008945	ENSMUSG00000005779	Psmb4	Pros-27	proteasome (prosome, macropain) subunit, beta type 4	protein-coding
mm_29540.1	chr3	116711867	116711882	-	1	NA	intron (NM_144902, intron 1 of 7)	CpG	406	NM_144902	229782	Mm.190758	NM_144902	ENSMUSG00000027957	Slc35a3	2310050P13Rik	solute carrier family 35 (UDP-N-acetylglucosamine (UDP-GlcNAc) transporter), member 3	protein-coding
mm_71820.1	chr8	68894619	68894716	+	1	NA	exon (NM_008509, exon 4 of 10)	exon (NM_008509, exon 4 of 10)	14112	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_10968.1	chr2	25706722	25706730	+	1	NA	promoter-TSS (NM_023326)	promoter-TSS (NM_023326)	-153	NM_023326	107771	Mm.330057	NM_023326	ENSMUSG00000049086	Bmyc	2900002K07Rik|AW060705|Mycb	brain expressed myelocytomatosis oncogene	protein-coding
mm_108893.1	chr12	100072437	100072443	+	1	NA	Intergenic	Lx7|LINE|L1	-39891	NM_008947	19179	Mm.157105	NM_008947	ENSMUSG00000021178	Psmc1	AI325227|P26s4|Rpt2/S4|S4|rpt2	protease (prosome, macropain) 26S subunit, ATPase 1	protein-coding
mm_123242.1	chr14	60251355	60251365	-	1	NA	promoter-TSS (NM_170591)	promoter-TSS (NM_170591)	18	NM_170591	71844	Mm.258051	NM_170591	ENSMUSG00000063895	Nupl1	1700017F11Rik|Nup58|mKIAA0410	nucleoporin like 1	protein-coding
mm_94285.1	chr11	3989925	3989946	+	1	NA	promoter-TSS (NM_001177691)	promoter-TSS (NM_001177691)	2	NM_001177691	53897	Mm.103414	NM_016922	ENSMUSG00000049721	Gal3st1	Cst|Gcst	galactose-3-O-sulfotransferase 1	protein-coding
mm_63595.1	chr7	128140462	128140472	+	1	NA	exon (NM_021334, exon 17 of 30)	exon (NM_021334, exon 17 of 30)	10899	NM_021334	16411	Mm.22378	NM_021334	ENSMUSG00000030789	Itgax	AI449405|Cd11c|Cr4|N418	integrin alpha X	protein-coding
mm_25437.1	chr3	108092852	108092858	+	1	NA	promoter-TSS (NM_008141)	promoter-TSS (NM_008141)	-211	NM_008141	14686	Mm.439652	NM_008141	ENSMUSG00000009108	Gnat2	AW490837|Gnat-2|Gt-2|Tcalpha	guanine nucleotide binding protein, alpha transducing 2	protein-coding
mm_92844.1	chr10	81508920	81508965	-	1	NA	intron (NM_010304, intron 5 of 6)	intron (NM_010304, intron 5 of 6)	-8805	NM_010102	13611	Mm.33065	NM_010102	ENSMUSG00000044199	S1pr4	Edg6|Lpc1|S1p4	sphingosine-1-phosphate receptor 4	protein-coding
mm_105084.1	chr11	100846057	100846064	-	1	NA	intron (NM_001113563, intron 1 of 18)	intron (NM_001113563, intron 1 of 18)	4525	NM_001113563	20851	Mm.34064	NM_011489	ENSMUSG00000020919	Stat5b	-	signal transducer and activator of transcription 5B	protein-coding
mm_3422.1	chr1	146495645	146495679	+	1	NA	promoter-TSS (NM_153539)	promoter-TSS (NM_153539)	-4	NM_153539	215378	Mm.441817	NM_153539	ENSMUSG00000035131	Brinp3	B830045N13Rik|Fam5c	bone morphogenetic protein/retinoic acid inducible neural specific 3	protein-coding
mm_72404.1	chr8	81770683	81770689	+	1	NA	intron (NM_001024617, intron 6 of 24)	intron (NM_001024617, intron 6 of 24)	428124	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_155547.1	chrX	74313243	74313253	+	1	NA	exon (NM_138607, exon 1 of 13)	exon (NM_138607, exon 1 of 13)	215	NM_138607	108160	Mm.4370	NM_138607	ENSMUSG00000001962	Fam50a	D0HXS9928E|XAP-5	family with sequence similarity 50, member A	protein-coding
mm_84623.1	chr9	70623692	70623706	-	1	NA	intron (NM_172772, intron 5 of 8)	intron (NM_172772, intron 5 of 8)	33475	NM_172772	235461	Mm.170855	NM_172772	ENSMUSG00000042444	Fam63b	AI465301|B230380D07Rik|mKIAA1164	family with sequence similarity 63, member B	protein-coding
mm_7685.1	chr1	128590846	128590894	-	1	NA	intron (NM_009911, intron 1 of 1)	intron (NM_009911, intron 1 of 1)	1429	NM_009911	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding
mm_112354.1	chr12	118657860	118657878	-	1	NA	Intergenic	ID_B1|SINE|B4	-127676	NR_045947	100384890	Mm.484658	NR_045947		D230030E09Rik	Npe	Riken cDNA D230030E09 gene	ncRNA
mm_138126.1	chr17	34187022	34187028	+	1	NA	promoter-TSS (NM_001161730)	promoter-TSS (NM_001161730)	305	NM_013585	16912	Mm.390983	NM_013585	ENSMUSG00000096727	Psmb9	Lmp-2|Lmp2	proteasome (prosome, macropain) subunit, beta type 9 (large multifunctional peptidase 2)	protein-coding
mm_77969.1	chr9	7792680	7792695	+	1	NA	3' UTR (NM_133739, exon 5 of 5)	3' UTR (NM_133739, exon 5 of 5)	8297	NR_049191	100885830		NR_049191	ENSMUSG00000093615	Mir5618	Gm23685|mmu-mir-5618	microRNA 5618	ncRNA
mm_172917.1	chr9	65201835	65201847	-	1	NA	Intergenic	U5|snRNA|snRNA	-12849	NM_177460	214424	Mm.31129	NM_177460	ENSMUSG00000032392	Parp16	ARTD15|BC055447|C79952|PARP-16	poly (ADP-ribose) polymerase family, member 16	protein-coding
mm_66471.1	chr7	44974782	44974824	-	1	NA	promoter-TSS (NM_153679)	promoter-TSS (NM_153679)	48	NM_153679	78070	Mm.231465	NM_153679	ENSMUSG00000007783	Cpt1c	6530437J22Rik|9630004I06Rik	carnitine palmitoyltransferase 1c	protein-coding
mm_32754.1	chr4	116687175	116687185	+	1	NA	intron (NM_011034, intron 1 of 5)	intron (NM_011034, intron 1 of 5)	-1158	NR_040442	100502959	Mm.395400	NR_040442		AV051173	-	expressed sequence AV051173	ncRNA
mm_107591.1	chr12	47834049	47834062	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	467407	NR_039586	100628593		NR_039586	ENSMUSG00000092981	Mir5125	mmu-mir-5125|mu-mir-5125	microRNA 5125	ncRNA
mm_110172.1	chr12	27336557	27336567	-	1	NA	3' UTR (NM_009234, exon 1 of 1)	3' UTR (NM_009234, exon 1 of 1)	6156	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding
mm_19812.1	chr2	110362956	110362963	-	1	NA	promoter-TSS (NM_026271)	promoter-TSS (NM_026271)	34	NM_026271	67606	Mm.291809	NM_026271	ENSMUSG00000074971	Fibin	1110018M03Rik	fin bud initiation factor homolog (zebrafish)	protein-coding
mm_27741.1	chr3	69107612	69107621	-	1	NA	intron (NM_008467, intron 1 of 16)	B3|SINE|B2	19476	NM_008467	16649	Mm.30601	NM_008467	ENSMUSG00000027782	Kpna4	1110058D08Rik|IPOA3	karyopherin (importin) alpha 4	protein-coding
mm_136858.1	chr17	12806116	12806147	+	1	NA	intron (NR_027784, intron 2 of 2)	B2_Mm1t|SINE|B2	-36425	NM_010515	16004	Mm.26553	NM_010515	ENSMUSG00000023830	Igf2r	AI661837|CD222|CI-MPR|M6P/IGF2R|Mpr300	insulin-like growth factor 2 receptor	protein-coding
mm_29652.1	chr3	122391228	122391267	-	1	NA	Intergenic	Intergenic	-28533	NM_013867	29815	Mm.45815	NM_013867	ENSMUSG00000028121	Bcar3	AI131758|AND-34	breast cancer anti-estrogen resistance 3	protein-coding
mm_88578.1	chr10	79682371	79682408	+	1	NA	5' UTR (NM_177613, exon 1 of 5)	5' UTR (NM_177613, exon 1 of 5)	194	NM_177613	216150	Mm.21981	NM_177613	ENSMUSG00000020307	Cdc34	AI327276|UBE2R1	cell division cycle 34	protein-coding
mm_74895.1	chr8	25158026	25158040	-	1	NA	3' UTR (NM_177089, exon 13 of 13)	3' UTR (NM_177089, exon 13 of 13)	1200	NR_106187	102467006		NR_106187	ENSMUSG00000099142	Mir8108	Gm27484|mmu-mir-8108	microRNA 8108	ncRNA
mm_56499.1	chr6	99266495	99266540	-	1	NA	promoter-TSS (NM_001197321)	promoter-TSS (NM_001197321)	-2	NM_001197321	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_77922.1	chr9	7352871	7352907	+	1	NA	exon (NM_008605, exon 5 of 10)	exon (NM_008605, exon 5 of 10)	5515	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_72554.1	chr8	84066420	84066431	+	1	NA	promoter-TSS (NM_009055)	promoter-TSS (NM_009055)	-411	NM_009055	19724	Mm.7892	NM_009055	ENSMUSG00000031706	Rfx1	AI047719|AI385641	regulatory factor X, 1 (influences HLA class II expression)	protein-coding
mm_124346.1	chr14	103998252	103998260	-	1	NA	intron (NR_045953, intron 1 of 2)	Lx9|LINE|L1	28886	NR_045953	73877	Mm.399172	NR_045953		4930432J09Rik	-	RIKEN cDNA 4930432J09 gene	ncRNA
mm_150261.1	chr19	34193253	34193312	+	1	NA	intron (NM_029682, intron 1 of 10)	intron (NM_029682, intron 1 of 10)	1012	NM_029682	76630	Mm.130952	NM_029682	ENSMUSG00000024776	Stambpl1	1700095N21Rik|8230401J17Rik|ALMalpha|AMSH-FP	STAM binding protein like 1	protein-coding
mm_98855.1	chr11	97663102	97663141	+	1	NA	promoter-TSS (NM_139311)	promoter-TSS (NM_139311)	-291	NM_139311	246198	Mm.23685	NM_139311	ENSMUSG00000038437	Mllt6	AI315037|Af17	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 6	protein-coding
mm_37116.1	chr4	116651420	116651426	-	1	NA	5' UTR (NM_021473, exon 1 of 9)	5' UTR (NM_021473, exon 1 of 9)	251	NM_021473	58810	Mm.30085	NM_021473	ENSMUSG00000028692	Akr1a1	2610201A18Rik|Akr1a4	aldo-keto reductase family 1, member A1 (aldehyde reductase)	protein-coding
mm_32985.1	chr4	120136312	120136326	+	1	NA	TTS (NM_010657)	TTS (NM_010657)	-24887	NM_007902	13615	Mm.284855	NM_007902	ENSMUSG00000028635	Edn2	ET-2|PPET2|VIC	endothelin 2	protein-coding
mm_27704.1	chr3	67463781	67463791	-	1	NA	5' UTR (NM_016753, exon 1 of 6)	5' UTR (NM_016753, exon 1 of 6)	121	NM_016753	17035	Mm.2632	NM_016753	ENSMUSG00000047557	Lxn	-	latexin	protein-coding
mm_171305.1	chr3	93982824	93982831	-	1	NA	Intergenic	MT2B1|LTR|ERVL	-21513	NM_207273	399676	Mm.454051	NM_207273	ENSMUSG00000094163	Tdpoz5	-	TD and POZ domain containing 5	protein-coding
mm_67656.1	chr7	84689981	84689991	-	1	NA	intron (NR_038175, intron 1 of 4)	intron (NR_038175, intron 1 of 4)	346	NR_038175	72495	Mm.382914	NR_038175	ENSMUSG00000085236	2610206C17Rik	-	RIKEN cDNA 2610206C17 gene	ncRNA
mm_131730.1	chr16	21855128	21855142	+	1	NA	Intergenic	B4A|SINE|B4	-36834	NM_172821	71751	Mm.420837	NM_172821	ENSMUSG00000033618	Map3k13	C130026N12Rik|LZK	mitogen-activated protein kinase kinase kinase 13	protein-coding
mm_106664.1	chr11	121388187	121388267	-	1	NA	promoter-TSS (NM_139147)	promoter-TSS (NM_139147)	24	NM_139147	217371	Mm.281639	NM_139147	ENSMUSG00000025170	Rab40b	SEC4L|rar	Rab40B, member RAS oncogene family	protein-coding
mm_110509.1	chr12	54695830	54695884	-	1	NA	promoter-TSS (NM_001331162)	promoter-TSS (NM_001331162)	37	NM_001331162	66266	Mm.156440	NM_025456	ENSMUSG00000054302	Eapp	1810011O16Rik	E2F-associated phosphoprotein	protein-coding
mm_102080.1	chr11	52277361	52277371	-	1	NA	intron (NM_001313981, intron 3 of 10)	RLTR34C_MM|LTR|ERVK	5229	NM_009331	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_6802.1	chr1	84152963	84152975	-	1	NA	intron (NM_001003948, intron 2 of 2)	ORR1G|LTR|ERVL-MaLR	65992	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_95504.1	chr11	51915767	51915774	+	1	NA	Intergenic	Intergenic	-51861	NM_029976	52626	Mm.289456	NM_029976	ENSMUSG00000020392	Cdkn2aipnl	A430101B06Rik|AA409260|D11Ertd497e|MNCb-1520	CDKN2A interacting protein N-terminal like	protein-coding
mm_144228.1	chr18	10181400	10181409	+	1	NA	5' UTR (NM_009071, exon 1 of 33)	5' UTR (NM_009071, exon 1 of 33)	388	NM_009071	19877	Mm.6710	NM_009071	ENSMUSG00000024290	Rock1	1110055K06Rik|Rock-I	Rho-associated coiled-coil containing protein kinase 1	protein-coding
mm_18678.1	chr2	71338200	71338253	-	1	NA	intron (NM_172436, intron 3 of 17)	intron (NM_172436, intron 3 of 17)	29328	NM_172436	78830	Mm.30928	NM_172436	ENSMUSG00000027010	Slc25a12	2610002D09Rik|AI839531|B230107K20Rik|BB129864	solute carrier family 25 (mitochondrial carrier, Aralar), member 12	protein-coding
mm_112900.1	chr13	20897629	20897649	+	1	NA	intron (NM_012054, intron 4 of 20)	intron (NM_012054, intron 4 of 20)	103526	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_149257.1	chr19	10435191	10435206	+	1	NA	intron (NM_173068, intron 5 of 10)	intron (NM_173068, intron 5 of 10)	22249	NM_001111140	278795	Mm.490638	NM_001111140	ENSMUSG00000090291	Lrrc10b	Gm705|SerdinR	leucine rich repeat containing 10B	protein-coding
mm_18599.1	chr2	66785238	66785248	-	1	NA	promoter-TSS (NM_009135)	promoter-TSS (NM_009135)	-333	NM_009135	20272	Mm.38127	NM_009135	ENSMUSG00000034810	Scn7a	1110034K09Rik|AI642000|NaG|Nav2|Nav2.3|Nax|Scn6a	sodium channel, voltage-gated, type VII, alpha	protein-coding
mm_7826.1	chr1	132067957	132067974	-	1	NA	promoter-TSS (NM_001114662)	promoter-TSS (NM_001114662)	97	NM_172510	213006	Mm.208445	NM_172510	ENSMUSG00000059149	Mfsd4a	A230072B04|A930031D07Rik|AI850289|Mfsd4	major facilitator superfamily domain containing 4A	protein-coding
mm_111971.1	chr12	109949639	109949686	-	1	NA	Intergenic	Intergenic	201784	NR_037233	100499517		NR_037233	ENSMUSG00000093351	Mir3072	mir-3072|mmu-mir-3072	microRNA 3072	ncRNA
mm_150725.1	chr19	43675174	43675192	+	1	NA	promoter-TSS (NR_045645)	promoter-TSS (NR_045645)	5	NR_045645	100502982	Mm.313570	NR_045645		BC037704	-	cDNA sequence BC037704	ncRNA
mm_128583.1	chr15	58034309	58034335	-	1	NA	promoter-TSS (NM_029418)	promoter-TSS (NM_029418)	-28	NM_029418	75758	Mm.455792	NM_029418	ENSMUSG00000101892	9130401M01Rik	AI849328	RIKEN cDNA 9130401M01 gene	protein-coding
mm_137081.1	chr17	21450362	21450397	+	1	NA	promoter-TSS (NM_009558)	promoter-TSS (NM_009558)	5	NM_009558	22709	Mm.293030	NM_009558	ENSMUSG00000023892	Zfp51	Zfp-51|zfec12	zinc finger protein 51	protein-coding
mm_133827.1	chr16	95900422	95900446	+	1	NA	intron (NR_040484, intron 1 of 3)	intron (NR_040484, intron 1 of 3)	-1721	NR_040485	69776	Mm.120470	NR_040484	ENSMUSG00000086899	1600002D24Rik	-	RIKEN cDNA 1600002D24 gene	ncRNA
mm_68810.1	chr7	125552056	125552065	-	1	NA	promoter-TSS (NM_001008700)	promoter-TSS (NM_001008700)	-222	NM_001008700	16190	Mm.233802	NM_010557	ENSMUSG00000030748	Il4ra	CD124|Il4r	interleukin 4 receptor, alpha	protein-coding
mm_62835.1	chr7	113766045	113766063	+	1	NA	promoter-TSS (NM_145584)	promoter-TSS (NM_145584)	56	NM_145584	233744	Mm.334160	NM_145584	ENSMUSG00000038156	Spon1	AI666765|AW455831|BC020531|D330035F22Rik|FSP	spondin 1, (f-spondin) extracellular matrix protein	protein-coding
mm_103973.1	chr11	84525515	84525542	-	1	NA	promoter-TSS (NM_008498)	promoter-TSS (NM_008498)	6	NM_008498	16869	Mm.4965	NM_008498	ENSMUSG00000018698	Lhx1	Lim1	LIM homeobox protein 1	protein-coding
mm_38146.1	chr4	134896310	134896319	-	1	NA	TTS (NM_011270)	TTS (NM_011270)	18602	NM_027935	71817	Mm.88349	NM_027935	ENSMUSG00000028822	Tmem50a	3200001F09Rik|CAM|Smp1	transmembrane protein 50A	protein-coding
mm_138911.1	chr17	43594858	43594891	+	1	NA	exon (NM_013737, exon 4 of 12)	exon (NM_013737, exon 4 of 12)	-3365	NR_045444	73504	Mm.9277	NR_045444	ENSMUSG00000090307	1700071M16Rik	-	RIKEN cDNA 1700071M16 gene	ncRNA
mm_36384.1	chr4	77151962	77151974	-	1	NA	intron (NM_011211, intron 7 of 39)	IAPEY_LTR|LTR|ERVK	1059927	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding
mm_104746.1	chr11	98463383	98463391	-	1	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	16553	NM_010346	14786	Mm.276702	NM_010346	ENSMUSG00000019312	Grb7	mKIAA4028	growth factor receptor bound protein 7	protein-coding
mm_97340.1	chr11	77349269	77349279	+	1	NA	intron (NM_001291190, intron 1 of 13)	intron (NM_001291190, intron 1 of 13)	994	NM_001291190	237860	Mm.440381	NM_177710	ENSMUSG00000037926	Ssh2	SSH-2|SSH-2L|mSSH-2L	slingshot homolog 2 (Drosophila)	protein-coding
mm_80067.1	chr9	69464470	69464474	+	1	NA	5' UTR (NM_007585, exon 2 of 13)	5' UTR (NM_007585, exon 2 of 13)	7528	NR_037296	100526560		NR_037296	ENSMUSG00000093042	Mir3109	mir-3109|mmu-mir-3109	microRNA 3109	ncRNA
mm_123652.1	chr14	69221658	69221680	-	1	NA	Intergenic	Intergenic	30977	NM_010921	18095	Mm.3520	NM_010921	ENSMUSG00000022061	Nkx3-1	Bax|NKX3.1|NKX3A|Nkx-3.1|bagpipe	NK-3 transcription factor, locus 1 (Drosophila)	protein-coding
mm_156830.1	chrX	164269573	164269612	+	1	NA	5' UTR (NM_027153, exon 1 of 10)	5' UTR (NM_027153, exon 1 of 10)	161	NM_027153	69656	Mm.293463	NM_027153	ENSMUSG00000031379	Pir	2310042L19Rik|Pirnl	pirin	protein-coding
mm_74512.1	chr8	8683092	8683099	-	1	NA	intron (NM_176849, intron 2 of 3)	AT_rich|Low_complexity|Low_complexity	7067	NR_106114	102465762		NR_106114	ENSMUSG00000098917	Mir7654	Gm27748|mmu-mir-7654	microRNA 7654	ncRNA
mm_85690.1	chr9	108072063	108072066	-	1	NA	intron (NM_001311152, intron 3 of 38)	B4|SINE|B4	7237	NM_001311152	84585	Mm.379272	NM_032543	ENSMUSG00000041528	Rnf123	BC003945|Kpc1	ring finger protein 123	protein-coding
mm_79373.1	chr9	54698901	54698907	+	1	NA	promoter-TSS (NM_021422)	promoter-TSS (NM_021422)	-655	NM_021422	58233	Mm.489676	NM_021422	ENSMUSG00000032285	Dnaja4	1110021L12Rik|AV358213|Dj4|Hsj4|mmDjA4	DnaJ heat shock protein family (Hsp40) member A4	protein-coding
mm_65840.1	chr7	29238100	29238106	-	1	NA	promoter-TSS (NM_001110201)	promoter-TSS (NM_001110201)	-220	NM_001110201	77254	Mm.36699	NM_029887	ENSMUSG00000030588	Yif1b	9430029K10Rik|Yip1b	Yip1 interacting factor homolog B (S. cerevisiae)	protein-coding
mm_147150.1	chr18	36678270	36678273	-	1	NA	promoter-TSS (NM_026404)	promoter-TSS (NM_026404)	-944	NM_001083317	67843	Mm.273350	NM_026404	ENSMUSG00000033272	Slc35a4	2610030J16Rik	solute carrier family 35, member A4	protein-coding
mm_114233.1	chr13	56609333	56609358	+	1	NA	promoter-TSS (NM_009369)	promoter-TSS (NM_009369)	-258	NM_009369	21810	Mm.14455	NM_009369	ENSMUSG00000035493	Tgfbi	68kDa|AI181842|AI747162|Beta-ig|big-h3	transforming growth factor, beta induced	protein-coding
mm_40247.1	chr5	38076520	38076534	+	1	NA	intron (NM_001289536, intron 1 of 9)	intron (NM_001289536, intron 1 of 9)	37297	NM_026959	71116	Mm.18959	NM_026959	ENSMUSG00000029125	Stx18	1810035L21Rik|4933425D03Rik|AU041562	syntaxin 18	protein-coding
mm_48357.1	chr5	139382277	139382326	-	1	NA	intron (NM_030258, intron 1 of 1)	intron (NM_030258, intron 1 of 1)	1634	NM_030258	80290	Mm.270003	NM_030258	ENSMUSG00000044197	Gpr146	BC003323|PGR8	G protein-coupled receptor 146	protein-coding
mm_44220.1	chr5	4758027	4758045	-	1	NA	5' UTR (NM_021457, exon 1 of 1)	5' UTR (NM_021457, exon 1 of 1)	180	NM_021457	14362	Mm.246003	NM_021457	ENSMUSG00000044674	Fzd1	AW227548|FZ-1|Fz1	frizzled class receptor 1	protein-coding
mm_31893.1	chr4	82692769	82692776	+	1	NA	Intergenic	Intergenic	166889	NM_026647	68268	Mm.32047	NM_026647	ENSMUSG00000028403	Zdhhc21	9130404H11Rik|AL024349|D130004H04Rik|dep	zinc finger, DHHC domain containing 21	protein-coding
mm_137515.1	chr17	27084974	27084980	+	1	NA	intron (NM_080553, intron 3 of 57)	intron (NM_080553, intron 3 of 57)	-6268	NR_106142	102465779		NR_106142	ENSMUSG00000098826	Mir7677	Gm27400|mmu-mir-7677	microRNA 7677	ncRNA
mm_143918.1	chr17	85615455	85615462	-	1	NA	intron (NR_038084, intron 2 of 3)	intron (NR_038084, intron 2 of 3)	2938	NR_038084	100043902	Mm.150838	NR_015385	ENSMUSG00000093460	Six3os1	D17Mgi26|E130112H22Rik|Rncr1|Six3os	SIX homeobox 3, opposite strand 1	ncRNA
mm_115773.1	chr13	19308522	19308534	-	1	NA	Intergenic	Intergenic	87285	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_74963.1	chr8	26158546	26158580	-	1	NA	intron (NM_199042, intron 1 of 2)	CpG	394	NM_199042	73754	Mm.383241	NM_199042	ENSMUSG00000037214	Thap1	4833431A01Rik|AW490810	THAP domain containing, apoptosis associated protein 1	protein-coding
mm_93493.1	chr10	112160283	112160303	-	1	NA	Intergenic	Intergenic	-3328	NM_001310675	353025	Mm.194428	NM_178278	ENSMUSG00000035694	Caps2	D630005B03Rik	calcyphosphine 2	protein-coding
mm_142535.1	chr17	46520671	46520719	-	1	NA	intron (NM_001081335, intron 23 of 40)	G-rich|Low_complexity|Low_complexity	23906	NM_207161	381101	Mm.35801	NM_207161	ENSMUSG00000040658	Dnph1	C76683|Rcl	2'-deoxynucleoside 5'-phosphate N-hydrolase 1	protein-coding
mm_52791.1	chr6	121264029	121264042	+	1	NA	intron (NM_011909, intron 8 of 10)	MTD|LTR|ERVL-MaLR	18129	NM_011909	24110	Mm.326911	NM_011909	ENSMUSG00000030107	Usp18	1110058H21Rik|AW047653|UBP43|Ubp15	ubiquitin specific peptidase 18	protein-coding
mm_131893.1	chr16	23231003	23231006	+	1	NA	intron (NM_001252505, intron 1 of 7)	intron (NM_001252505, intron 1 of 7)	4983	NM_001252505	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_155930.1	chrX	103482699	103482702	+	1	NA	non-coding (NR_002844, exon 4 of 4)	non-coding (NR_002844, exon 4 of 4)	533	NR_001570	213742	Mm.274770	NR_001463	ENSMUSG00000086503	Xist	A430022B11|AI314753	inactive X specific transcripts	ncRNA
mm_108591.1	chr12	85351040	85351062	+	1	NA	intron (NM_026775, intron 2 of 4)	intron (NM_026775, intron 2 of 4)	-11689	NM_145138	217718	Mm.29071	NM_145138	ENSMUSG00000034290	Nek9	C130021H08Rik	NIMA (never in mitosis gene a)-related expressed kinase 9	protein-coding
mm_113145.1	chr13	24721693	24721701	+	1	NA	exon (NM_029679, exon 20 of 23)	exon (NM_029679, exon 20 of 23)	40240	NM_020567	57441	Mm.12239	NM_020567	ENSMUSG00000006715	Gmnn	AW546347|Gem	geminin	protein-coding
mm_169536.1	chr14	95055266	95055275	+	1	NA	Intergenic	L1Md_A|LINE|L1	-825996	NM_025733	66732	Mm.75060	NM_025733	ENSMUSG00000034689	4921530L21Rik	-	RIKEN cDNA 4921530L21 gene	protein-coding
mm_148756.1	chr19	6058322	6058359	+	1	NA	promoter-TSS (NM_026246)	promoter-TSS (NM_026246)	373	NM_001190436	14109	Mm.329631	NM_007990	ENSMUSG00000038274	Fau	MNSFbeta	Finkel-Biskis-Reilly murine sarcoma virus (FBR-MuSV) ubiquitously expressed (fox derived)	protein-coding
mm_40446.1	chr5	53591597	53591607	+	1	NA	intron (NM_001080927, intron 1 of 10)	intron (NM_001080927, intron 1 of 10)	1116	NM_001080927	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_15711.1	chr2	164017939	164018028	+	1	NA	3' UTR (NM_018753, exon 6 of 6)	3' UTR (NM_018753, exon 6 of 6)	-7241	NM_001114079	381404	Mm.82301	NM_001114079	ENSMUSG00000054582	Pabpc1l	1810053B01Rik|Epab	poly(A) binding protein, cytoplasmic 1-like	protein-coding
mm_28755.1	chr3	95819347	95819380	-	1	NA	promoter-TSS (NM_001081293)	promoter-TSS (NM_001081293)	-410	NM_001081293	75137	Mm.196275	NM_028328	ENSMUSG00000028106	Rprd2	2810036A19Rik|4930535B03Rik|6720469I21Rik|AL022841|AL022940|AU021304|BB077382|mKIAA0460	regulation of nuclear pre-mRNA domain containing 2	protein-coding
mm_119848.1	chr14	54440766	54440778	+	1	NA	3' UTR (NM_008608, exon 10 of 10)	3' UTR (NM_008608, exon 10 of 10)	9174	NM_008608	17387	Mm.280175	NM_008608	ENSMUSG00000000957	Mmp14	AI325305|MMP-X1|MT-MMP-1|MT1-MMP|sabe	matrix metallopeptidase 14 (membrane-inserted)	protein-coding
mm_150048.1	chr19	29380464	29380490	+	1	NA	exon (NM_021893, exon 4 of 7)	exon (NM_021893, exon 4 of 7)	13039	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_32454.1	chr4	107368040	107368057	+	1	NA	5' UTR (NM_028355, exon 1 of 18)	5' UTR (NM_028355, exon 1 of 18)	264	NM_028355	72787	Mm.28478	NM_028355	ENSMUSG00000028614	Ndc1	2810475A17Rik|AI450313|Tmem48|sks	NDC1 transmembrane nucleoporin	protein-coding
mm_74113.1	chr8	123042560	123042654	+	1	NA	promoter-TSS (NR_045268)	promoter-TSS (NR_045268)	32	NR_045268	100503178	Mm.294938	NR_045268	ENSMUSG00000099881	2810013P06Rik	-	RIKEN cDNA 2810013P06 gene	ncRNA
mm_48195.1	chr5	137530991	137531049	-	1	NA	intron (NM_010312, intron 1 of 9)	CpG	-1426	NR_105846	102465227		NR_105846	ENSMUSG00000098597	Mir6418	Gm27629|mir-6418|mmu-mir-6418	microRNA 6418	ncRNA
mm_168839.1	chr12	23315333	23315350	-	1	NA	Intergenic	CpG	-305098	NR_015504	69732	Mm.391403	NM_028362	ENSMUSG00000073164	2410018L13Rik	2810480C08Rik	RIKEN cDNA 2410018L13 gene	ncRNA
mm_139783.1	chr17	65794166	65794211	+	1	NA	intron (NM_001114131, intron 2 of 19)	MT2A|LTR|ERVL	10833	NR_104465	70351	Mm.48686	NM_146081	ENSMUSG00000061950	Ppp4r1	3110001J10Rik|Pp4r1	protein phosphatase 4, regulatory subunit 1	protein-coding
mm_31304.1	chr4	46039218	46039280	+	1	NA	promoter-TSS (NM_021883)	promoter-TSS (NM_021883)	27	NM_021883	21916	Mm.249594	NM_021883	ENSMUSG00000028328	Tmod1	E-Tmod|Tmod	tropomodulin 1	protein-coding
mm_45784.1	chr5	87337120	87337131	-	1	NA	promoter-TSS (NM_028094)	promoter-TSS (NM_028094)	70	NM_028094	72094	Mm.482739	NM_028094	ENSMUSG00000035780	Ugt2a3	2010321J07Rik	UDP glucuronosyltransferase 2 family, polypeptide A3	protein-coding
mm_51432.1	chr6	78466813	78466825	+	1	NA	exon (NM_011260, exon 5 of 6)	exon (NM_011260, exon 5 of 6)	2055	NM_011260	19695	Mm.252385	NM_011260	ENSMUSG00000030017	Reg3g	AI449515|REG-3-gamma|reg III-gamma	regenerating islet-derived 3 gamma	protein-coding
mm_94610.1	chr11	16257868	16257878	+	1	NA	5' UTR (NM_001290539, exon 1 of 5)	5' UTR (NM_001290539, exon 1 of 5)	149	NM_145967	211739	Mm.284015	NM_145967	ENSMUSG00000048834	Vstm2a	Vstm2	V-set and transmembrane domain containing 2A	protein-coding
mm_121602.1	chr14	8004051	8004057	-	1	NA	intron (NM_001331064, intron 1 of 8)	intron (NM_001331064, intron 1 of 8)	1088	NM_001331064	66082	Mm.181473	NM_025341	ENSMUSG00000025277	Abhd6	0610041D24Rik|AA673485|AV065425	abhydrolase domain containing 6	protein-coding
mm_4002.1	chr1	164796632	164796649	+	1	NA	promoter-TSS (NM_019759)	promoter-TSS (NM_019759)	-92	NM_019759	56429	Mm.28935	NM_019759	ENSMUSG00000026574	Dpt	1810032B19Rik|5033416F05Rik|EQ-1|Eq1	dermatopontin	protein-coding
mm_138398.1	chr17	35053015	35053023	+	1	NA	intron (NM_033444, intron 3 of 5)	intron (NM_033444, intron 3 of 5)	2776	NM_033444	114584	Mm.29524	NM_033444	ENSMUSG00000007041	Clic1	Clcp|G6	chloride intracellular channel 1	protein-coding
mm_111285.1	chr12	85374697	85374719	-	1	NA	promoter-TSS (NM_026775)	promoter-TSS (NM_026775)	9	NM_026775	68581	Mm.379159	NM_026775	ENSMUSG00000021248	Tmed10	1110014C03Rik|Tmp21|p23|p24delta1	transmembrane p24 trafficking protein 10	protein-coding
mm_6078.1	chr1	62703781	62703831	-	1	NA	5' UTR (NM_001077407, exon 1 of 16)	5' UTR (NM_001077407, exon 1 of 16)	489	NM_001077405	18187	Mm.266341	NM_010939	ENSMUSG00000025969	Nrp2	1110048P06Rik|Np-2|Np2|Npn-2|Npn2	neuropilin 2	protein-coding
mm_94227.1	chr11	3289169	3289194	+	1	NA	promoter-TSS (NR_045109)	promoter-TSS (NR_045109)	50	NR_045109	56218	Mm.275563	NM_019574	ENSMUSG00000020453	Patz1	8430401L15Rik|AI447519|Mazr|Patz|Zfp278	POZ (BTB) and AT hook containing zinc finger 1	protein-coding
mm_132688.1	chr16	43230734	43230771	+	1	NA	intron (NM_001285805, intron 2 of 10)	intron (NM_001285805, intron 2 of 10)	-16532	NM_181058	56490	Mm.136238	NM_019778	ENSMUSG00000022708	Zbtb20	1300017A20Rik|7330412A13Rik|A930017C21Rik|D16Wsu73e|DPZF|HOF|ODA-8S|Oda8|Zfp288	zinc finger and BTB domain containing 20	protein-coding
mm_97842.1	chr11	83065243	83065253	+	1	NA	5' UTR (NM_011408, exon 1 of 2)	5' UTR (NM_011408, exon 1 of 2)	136	NM_011408	20556	Mm.278689	NM_011408	ENSMUSG00000072620	Slfn2	Shlf2	schlafen 2	protein-coding
mm_123790.1	chr14	70429372	70429414	-	1	NA	promoter-TSS (NM_021308)	promoter-TSS (NM_021308)	-299	NM_021308	57746	Mm.85253	NM_021308	ENSMUSG00000033644	Piwil2	Piwil1l|mili	piwi-like RNA-mediated gene silencing 2	protein-coding
mm_96873.1	chr11	70214106	70214132	+	1	NA	5' UTR (NM_153081, exon 1 of 5)	5' UTR (NM_153081, exon 1 of 5)	209	NM_153081	216867	Mm.289238	NM_153081	ENSMUSG00000040938	Slc16a11	AB041591|MCT 11|MNCb-2717	solute carrier family 16 (monocarboxylic acid transporters), member 11	protein-coding
mm_110342.1	chr12	36156725	36156735	-	1	NA	promoter-TSS (NM_025840)	promoter-TSS (NM_025840)	95	NM_025840	66912	Mm.288669	NM_025840	ENSMUSG00000020547	Bzw2	1110001I24Rik|Bdm2|HSPC028	basic leucine zipper and W2 domains 2	protein-coding
mm_147257.1	chr18	38635828	38635848	-	1	NA	Intergenic	Intergenic	-34570	NM_011898	24066	Mm.42038	NM_011898	ENSMUSG00000024427	Spry4	A030006O18Rik|sprouty4	sprouty homolog 4 (Drosophila)	protein-coding
mm_44349.1	chr5	17787710	17787748	-	1	NA	exon (NM_001159558, exon 14 of 16)	exon (NM_001159558, exon 14 of 16)	48167	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_115973.1	chr13	24135085	24135097	-	1	NA	intron (NM_001311122, intron 11 of 37)	B1_Mus2|SINE|Alu	-143877	NM_145399	214189	Mm.255667	NM_145399	ENSMUSG00000021337	Scgn	-	secretagogin, EF-hand calcium binding protein	protein-coding
mm_109266.1	chr12	109545197	109545219	+	1	NA	promoter-TSS (NR_003633)	promoter-TSS (NR_003633)	-190	NR_003633	17263	Mm.289645	NM_144513	ENSMUSG00000021268	Meg3	2900016C05Rik|3110050O07Rik|6330408G06Rik|AI425946|AW108224|D12Bwg1266e|Gtl2|R74756|R75394	maternally expressed 3	ncRNA
mm_155532.1	chrX	74302387	74302401	+	1	NA	exon (NM_018794, exon 7 of 10)	exon (NM_018794, exon 7 of 10)	-2618	NM_010273	14567	Mm.205830	NM_010273	ENSMUSG00000015291	Gdi1	GDIA|GDIalpha	guanosine diphosphate (GDP) dissociation inhibitor 1	protein-coding
mm_129615.1	chr15	80013965	80013983	-	1	NA	exon (NM_011057, exon 1 of 7)	exon (NM_011057, exon 1 of 7)	834	NM_011057	18591	Mm.144089	NM_011057	ENSMUSG00000000489	Pdgfb	PDGF-B|Sis	platelet derived growth factor, B polypeptide	protein-coding
mm_66585.1	chr7	45386760	45386763	-	1	NA	intron (NM_009224, intron 6 of 9)	intron (NM_009224, intron 6 of 9)	8981	NM_009224	20637	Mm.216386	NM_009224	ENSMUSG00000063511	Snrnp70	2700022N21Rik|3200002N22Rik|AI325098|R74807|Rnu1p70|Rnulp70|Snrp70|Srnp70|U1-70|U1-70K	small nuclear ribonucleoprotein 70 (U1)	protein-coding
mm_71355.1	chr8	45658667	45658728	+	1	NA	intron (NM_001310707, intron 1 of 23)	intron (NM_001310707, intron 1 of 23)	-3296	NM_001310708	234214	Mm.211096	NM_172752	ENSMUSG00000031626	Sorbs2	2010203O03Rik|9430041O17Rik|A530071H08|Argbp2|mKIAA0777|nArgBP2	sorbin and SH3 domain containing 2	protein-coding
mm_126413.1	chr15	80257166	80257186	+	1	NA	exon (NM_009716, exon 3 of 3)	exon (NM_009716, exon 3 of 3)	1992	NM_009716	11911	Mm.641	NM_009716	ENSMUSG00000042406	Atf4	Atf-4|C/ATF|CREB2|TAXREB67	activating transcription factor 4	protein-coding
mm_119842.1	chr14	54436201	54436218	+	1	NA	exon (NM_008608, exon 3 of 10)	exon (NM_008608, exon 3 of 10)	4611	NM_008608	17387	Mm.280175	NM_008608	ENSMUSG00000000957	Mmp14	AI325305|MMP-X1|MT-MMP-1|MT1-MMP|sabe	matrix metallopeptidase 14 (membrane-inserted)	protein-coding
mm_142007.1	chr17	35200288	35200299	-	1	NA	exon (NM_013693, exon 4 of 4)	exon (NM_013693, exon 4 of 4)	1714	NM_013693	21926	Mm.1293	NM_013693	ENSMUSG00000024401	Tnf	DIF|TNF-a|TNF-alpha|TNFSF2|TNFalpha|Tnfa|Tnfsf1a|Tnlg1f	tumor necrosis factor	protein-coding
mm_8294.1	chr1	143666853	143666858	-	1	NA	intron (NM_145991, intron 10 of 16)	intron (NM_145991, intron 10 of 16)	26158	NM_020025	26878	Mm.285580	NM_020025	ENSMUSG00000033849	B3galt2	-	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 2	protein-coding
mm_108290.1	chr12	79145848	79145857	+	1	NA	intron (NM_009705, intron 2 of 7)	intron (NM_009705, intron 2 of 7)	15064	NM_009705	11847	Mm.3506	NM_009705	ENSMUSG00000021125	Arg2	AII|AU022422	arginase type II	protein-coding
mm_127716.1	chr15	103034618	103034642	+	1	NA	5' UTR (NM_013553, exon 1 of 2)	5' UTR (NM_013553, exon 1 of 2)	235	NM_013553	15423	Mm.1351	NM_013553	ENSMUSG00000075394	Hoxc4	Hox-3.5	homeobox C4	protein-coding
mm_143591.1	chr17	74459224	74459233	-	1	NA	promoter-TSS (NM_001033367)	promoter-TSS (NM_001033367)	-120	NM_001033367	268973	Mm.311884	NM_001033367	ENSMUSG00000039193	Nlrc4	9530011P19Rik|CLAN|CLAN1|CLANA|CLANB|CLANC|CLAND|Card12|IPAF	NLR family, CARD domain containing 4	protein-coding
mm_53333.1	chr6	129234908	129234917	+	1	NA	intron (NR_040265, intron 1 of 2)	RMER17C|LTR|ERVK	3133	NR_040265	76432	Mm.261738	NR_040265	ENSMUSG00000097354	2310001H17Rik	AI646108	RIKEN cDNA 2310001H17 gene	ncRNA
mm_153514.1	chr19	41385090	41385109	-	1	NA	promoter-TSS (NM_031376)	promoter-TSS (NM_031376)	-29	NM_031376	83490	Mm.222266	NM_031376	ENSMUSG00000025017	Pik3ap1	1810044J04Rik|BCAP	phosphoinositide-3-kinase adaptor protein 1	protein-coding
mm_34870.1	chr4	155558796	155558808	+	1	NA	3' UTR (NM_008142, exon 12 of 12)	3' UTR (NM_008142, exon 12 of 12)	-3590	NM_138671	192185	Mm.28347	NM_138671	ENSMUSG00000029063	Nadk	4432404C02Rik|BC004012	NAD kinase	protein-coding
mm_147661.1	chr18	60600437	60600461	-	1	NA	3' UTR (NM_001109975, exon 2 of 2)	3' UTR (NM_001109975, exon 2 of 2)	-8733	NM_133363	170947	Mm.159257	NM_133363	ENSMUSG00000049173	Myoz3	4833419K08Rik|Fatz-3	myozenin 3	protein-coding
mm_72513.1	chr8	83900707	83900717	+	1	NA	5' UTR (NM_181039, exon 1 of 23)	5' UTR (NM_181039, exon 1 of 23)	614	NM_181039	330814	Mm.260733	NM_181039	ENSMUSG00000013033	Adgrl1	2900070I05Rik|AI182398|CLIBA|Lec2|Lphn1|mKIAA0821	adhesion G protein-coupled receptor L1	protein-coding
mm_35377.1	chr4	33189391	33189409	-	1	NA	5' UTR (NM_001034867, exon 1 of 7)	5' UTR (NM_001034867, exon 1 of 7)	337	NM_001034867	242377	Mm.372465	NM_001034867	ENSMUSG00000054659	Pm20d2	Acy1l2|Gm424	peptidase M20 domain containing 2	protein-coding
mm_57464.1	chr6	125191622	125191663	-	1	NA	promoter-TSS (NM_025595)	promoter-TSS (NM_025595)	-56	NM_146171	68298	Mm.257590	NM_146171	ENSMUSG00000038252	Ncapd2	2810406C15Rik|2810465G24Rik|CAP-D2|CNAP1|mKIAA0159	non-SMC condensin I complex, subunit D2	protein-coding
mm_87890.1	chr10	61845712	61845732	+	1	NA	intron (NM_001304757, intron 35 of 37)	intron (NM_001304757, intron 35 of 37)	-61858	NM_207000	404634	Mm.272870	NM_207000	ENSMUSG00000020086	H2afy2	macroH2A2	H2A histone family, member Y2	protein-coding
mm_76526.1	chr8	87472604	87472614	-	1	NA	promoter-TSS (NM_019626)	promoter-TSS (NM_019626)	-17	NM_019626	12404	Mm.4880	NM_019626	ENSMUSG00000031654	Cbln1	AI323299	cerebellin 1 precursor protein	protein-coding
mm_142364.1	chr17	44105729	44105767	-	1	NA	promoter-TSS (NM_199016)	promoter-TSS (NM_199016)	60	NM_199016	224794	Mm.255971	NM_199016	ENSMUSG00000023961	Enpp4	4933413N07Rik|AA986363|AI195364|E-NPP 4|Gm90|mKIAA0879	ectonucleotide pyrophosphatase/phosphodiesterase 4	protein-coding
mm_108923.1	chr12	100856075	100856082	+	1	NA	intron (NM_145448, intron 9 of 12)	ID_B1|SINE|B4	43446	NM_001177674	238377	Mm.32160	NM_175493	ENSMUSG00000047415	Gpr68	BB131428|Ogr1	G protein-coupled receptor 68	protein-coding
mm_12612.1	chr2	74691861	74691869	+	1	NA	promoter-TSS (NM_013554)	promoter-TSS (NM_013554)	-26	NM_013554	15430	Mm.24420	NM_013554	ENSMUSG00000050368	Hoxd10	AI385591|AI874987|Hox-4.5|Hox-5.3	homeobox D10	protein-coding
mm_122965.1	chr14	54973823	54973840	-	1	NA	exon (NM_080728, exon 35 of 41)	exon (NM_080728, exon 35 of 41)	1945	NR_030607	100124433		NR_030607	ENSMUSG00000077928	Mir208b	Mirn208b|mir-208b	microRNA 208b	ncRNA
mm_110591.1	chr12	56532943	56532984	-	1	NA	3' UTR (NM_009385, exon 3 of 3)	3' UTR (NM_009385, exon 3 of 3)	-3543	NR_045082	104798	Mm.310950	NR_045082		E030019B13Rik	AI413669	RIKEN cDNA E030019B13 gene	ncRNA
mm_21204.1	chr2	155592709	155592770	-	1	NA	promoter-TSS (NM_001291111)	promoter-TSS (NM_001291111)	71	NM_001291111	14854	Mm.252316	NM_008180	ENSMUSG00000027610	Gss	AI314904|GS-A/GS-B|GSH-S	glutathione synthetase	protein-coding
mm_79384.1	chr9	54772880	54772886	+	1	NA	3' UTR (NM_001284507, exon 3 of 3)	3' UTR (NM_001284507, exon 3 of 3)	8135	NM_013496	12903	Mm.34797	NM_013496	ENSMUSG00000032291	Crabp1	AI326249|CRABP-I|Crabp-1|CrabpI|Rbp-5	cellular retinoic acid binding protein I	protein-coding
mm_15459.1	chr2	157441970	157441972	+	1	NA	intron (NM_009271, intron 2 of 14)	intron (NM_009271, intron 2 of 14)	17678	NM_001025395	20779	Mm.22845	NM_009271	ENSMUSG00000027646	Src	AW259666|pp60c-src	Rous sarcoma oncogene	protein-coding
mm_44913.1	chr5	35671514	35671574	-	1	NA	intron (NM_030127, intron 1 of 8)	intron (NM_030127, intron 1 of 8)	8236	NM_001042615	78558	Mm.274255	NM_030127	ENSMUSG00000029096	Htra3	2210021K23Rik|9530081K03Rik|Prsp|Tasp	HtrA serine peptidase 3	protein-coding
mm_123263.1	chr14	61305318	61305340	-	1	NA	promoter-TSS (NR_033788)	promoter-TSS (NR_033788)	5	NR_033788	67355	Mm.193728	NR_033788	ENSMUSG00000101505	1700109G14Rik	1700126G13Rik	RIKEN cDNA 1700109G14 gene	ncRNA
mm_95082.1	chr11	32745463	32745499	+	1	NA	3' UTR (NM_134015, exon 14 of 14)	3' UTR (NM_134015, exon 14 of 14)	79113	NM_027050	69351	Mm.65488	NM_027050	ENSMUSG00000020270	Smim23	1700008A04Rik	small integral membrane protein 23	protein-coding
mm_111476.1	chr12	98683698	98683706	-	1	NA	intron (NM_011877, intron 13 of 18)	intron (NM_011877, intron 13 of 18)	50943	NM_011877	24000	Mm.4420	NM_011877	ENSMUSG00000021009	Ptpn21	PTPD1|PTPRL10	protein tyrosine phosphatase, non-receptor type 21	protein-coding
mm_170987.1	chr2	7404248	7404260	+	1	NA	Intergenic	IAPLTR1_Mm|LTR|ERVK	-8056	NM_001110231	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_161280.1	chr14	19768349	19768349	+	1	NA	exon (NM_008695, exon 4 of 21)	exon (NM_008695, exon 4 of 21)	17092	NM_008695	18074	Mm.20348	NM_008695	ENSMUSG00000021806	Nid2	AW547149|Ly111|NID-2|entactin-2|nidogen-2	nidogen 2	protein-coding
mm_105696.1	chr11	107915042	107915069	-	1	NA	promoter-TSS (NM_001199301)	promoter-TSS (NM_001199301)	0	NM_001199301	140723	Mm.87663	NM_080644	ENSMUSG00000040373	Cacng5	-	calcium channel, voltage-dependent, gamma subunit 5	protein-coding
mm_124824.1	chr15	9073025	9073038	+	1	NA	intron (NM_001040395, intron 1 of 12)	intron (NM_001040395, intron 1 of 12)	1771	NM_001040395	68646	Mm.244226	NM_001040395	ENSMUSG00000022253	Nadk2	MNADK|Nadkd1	NAD kinase 2, mitochondrial	protein-coding
mm_62726.1	chr7	110774241	110774252	+	1	NA	intron (NM_009667, intron 1 of 14)	intron (NM_009667, intron 1 of 14)	1642	NM_009667	11717	Mm.3238	NM_009667	ENSMUSG00000005686	Ampd3	-	adenosine monophosphate deaminase 3	protein-coding
mm_17792.1	chr2	33087170	33087207	-	1	NA	promoter-TSS (NM_178888)	promoter-TSS (NM_178888)	16	NM_178888	99326	Mm.41290	NM_178888	ENSMUSG00000038860	Garnl3	AW120551	GTPase activating RANGAP domain-like 3	protein-coding
mm_14190.1	chr2	127081557	127081560	+	1	NA	intron (NM_026678, intron 2 of 7)	intron (NM_026678, intron 2 of 7)	10901	NM_026678	109778	Mm.22028	NM_026678	ENSMUSG00000001999	Blvra	0610006A11Rik|2500001N03Rik|Blvr	biliverdin reductase A	protein-coding
mm_104230.1	chr11	88625630	88625661	-	1	NA	intron (NM_054043, intron 5 of 13)	intron (NM_054043, intron 5 of 13)	6394	NR_131025	68397	Mm.426889	NR_131025		0610039H22Rik	-	RIKEN cDNA 0610039H22 gene	ncRNA
mm_103131.1	chr11	70237571	70237600	-	1	NA	TTS (NM_173742)	TTS (NM_173742)	329	NM_001177601	104457	Mm.30016	NM_026757	ENSMUSG00000020831	0610010K14Rik	1110020A23Rik|AL033328|AU045833|Bap18	RIKEN cDNA 0610010K14 gene	protein-coding
mm_155894.1	chrX	101652531	101652562	+	1	NA	intron (NM_139144, intron 4 of 21)	intron (NM_139144, intron 4 of 21)	12328	NM_001290535	108155	Mm.487332	NM_139144	ENSMUSG00000034160	Ogt	1110038P24Rik|4831420N21Rik|AI115525|Ogtl	O-linked N-acetylglucosamine (GlcNAc) transferase (UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase)	protein-coding
mm_100988.1	chr11	7213944	7213990	-	1	NA	promoter-TSS (NM_008343)	promoter-TSS (NM_008343)	-44	NM_008343	16009	Mm.29254	NM_008343	ENSMUSG00000020427	Igfbp3	AI649005|IGFBP-3|IGgfbp3	insulin-like growth factor binding protein 3	protein-coding
mm_63892.1	chr7	138846382	138846429	+	1	NA	promoter-TSS (NM_026391)	promoter-TSS (NM_026391)	19	NM_026391	52432	Mm.258739	NM_026391	ENSMUSG00000041769	Ppp2r2d	1300017E19Rik|D7Ertd753e|MDS026	protein phosphatase 2, regulatory subunit B, delta	protein-coding
mm_89872.1	chr10	108264862	108264876	+	1	NA	intron (NM_027892, intron 19 of 25)	intron (NM_027892, intron 19 of 25)	-67320	NM_054056	114774	Mm.391419	NM_054056	ENSMUSG00000035873	Pawr	2310001G03Rik|PAR4|Par-4	PRKC, apoptosis, WT1, regulator	protein-coding
mm_7595.1	chr1	125450364	125450368	-	1	NA	Intergenic	Intergenic	-14639	NM_001205386	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding
mm_97273.1	chr11	75960995	75961019	+	1	NA	Intergenic	ORR1B2|LTR|ERVL-MaLR	-35116	NM_001291159	380714	Mm.425697	NM_029548	ENSMUSG00000020847	Rph3al	Gm1753|Noc2	rabphilin 3A-like (without C2 domains)	protein-coding
mm_145207.1	chr18	50024337	50024345	+	1	NA	intron (NM_001177759, intron 1 of 1)	intron (NM_001177759, intron 1 of 1)	-28941	NM_134131	106869	Mm.27740	NM_134131	ENSMUSG00000062210	Tnfaip8	AA987150|E130304C20Rik|ENSMUSG00000073567|Gg2-1|Gm10539|Nded|Ssc-2|Tipe	tumor necrosis factor, alpha-induced protein 8	protein-coding
mm_100278.1	chr11	117790703	117790703	+	1	NA	exon (NM_181856, exon 11 of 16)	exon (NM_181856, exon 11 of 16)	-6957	NM_029964	77727	Mm.159981	NM_029964	ENSMUSG00000025573	6030468B19Rik	-	RIKEN cDNA 6030468B19 gene	protein-coding
mm_124578.1	chr14	124621902	124621912	-	1	NA	intron (NM_207667, intron 1 of 4)	intron (NM_207667, intron 1 of 4)	55220	NM_207667	14169	Mm.206362	NM_010201	ENSMUSG00000025551	Fgf14	FHF-4|Fhf4|mFHF-4(1B)	fibroblast growth factor 14	protein-coding
mm_139928.1	chr17	71019549	71019562	+	1	NA	promoter-TSS (NM_001083934)	promoter-TSS (NM_001083934)	-2	NM_010867	17929	Mm.4103	NM_010867	ENSMUSG00000024049	Myom1	D430047A17Rik	myomesin 1	protein-coding
mm_48964.1	chr6	4600733	4600770	+	1	NA	promoter-TSS (NM_145398)	promoter-TSS (NM_145398)	-315	NM_145398	213819	Mm.270703	NM_145398	ENSMUSG00000015189	Casd1	Cas1|Cast1	CAS1 domain containing 1	protein-coding
mm_140113.1	chr17	78882004	78882027	+	1	NA	intron (NM_011163, intron 1 of 15)	intron (NM_011163, intron 1 of 15)	557	NM_011163	19106	Mm.378990	NM_011163	ENSMUSG00000024079	Eif2ak2	2310047A08Rik|4732414G15Rik|AI467567|AI747578|Pkr|Prkr|Tik	eukaryotic translation initiation factor 2-alpha kinase 2	protein-coding
mm_50008.1	chr6	41059339	41059391	+	1	NA	Intergenic	Intergenic	-23856	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_73668.1	chr8	111259292	111259314	+	1	NA	promoter-TSS (NM_009149)	promoter-TSS (NM_009149)	-101	NM_009149	20340	Mm.276271	NM_009149	ENSMUSG00000003316	Glg1	AI593353|AW537898|CFR|CFR-1|ESL-1|MG-160|MG160|Selel	golgi apparatus protein 1	protein-coding
mm_34232.1	chr4	141096939	141096950	+	1	NA	exon (NM_177867, exon 6 of 15)	exon (NM_177867, exon 6 of 15)	8599	NM_177867	329972	Mm.247201	NM_177867	ENSMUSG00000045004	Spata21	4933414G08	spermatogenesis associated 21	protein-coding
mm_80577.1	chr9	84041316	84041319	+	1	NA	intron (NM_001305935, intron 8 of 10)	intron (NM_001305935, intron 8 of 10)	92536	NM_199195	12040	Mm.12819	NM_199195	ENSMUSG00000032263	Bckdhb	BCKDE1B|BCKDH E1-beta	branched chain ketoacid dehydrogenase E1, beta polypeptide	protein-coding
mm_118125.1	chr13	104228803	104228828	-	1	NA	promoter-TSS (NM_021790)	promoter-TSS (NM_021790)	29	NM_172807	238831	Mm.98910	NM_172807	ENSMUSG00000021713	Ppwd1	4632422M10Rik|A330090G21Rik	peptidylprolyl isomerase domain and WD repeat containing 1	protein-coding
mm_72874.1	chr8	88697023	88697033	+	1	NA	promoter-TSS (NM_001128171)	promoter-TSS (NM_001128171)	0	NM_001128170	74256	Mm.490395	NM_173369	ENSMUSG00000036712	Cyld	2010013M14Rik|2900009M21Rik|C130039D01Rik|CDMT|CYLD1|EAC|mKIAA0849	CYLD lysine 63 deubiquitinase	protein-coding
mm_20876.1	chr2	148732369	148732372	-	1	NA	promoter-TSS (NM_019632)	promoter-TSS (NM_019632)	50	NM_019632	17957	Mm.274308	NM_019632	ENSMUSG00000027438	Napb	Brp14|E161|I47|SNARE|b-SNAP	N-ethylmaleimide sensitive fusion protein attachment protein beta	protein-coding
mm_38780.1	chr4	148075417	148075423	-	1	NA	Intergenic	Intergenic	12644	NM_009642	11610	Mm.46247	NM_009642	ENSMUSG00000029007	Agtrap	3300002E14Rik|AT1R|Atrap|D4Wsu124e	angiotensin II, type I receptor-associated protein	protein-coding
mm_21676.1	chr2	164425992	164426046	-	1	NA	3' UTR (NM_011521, exon 5 of 5)	3' UTR (NM_011521, exon 5 of 5)	17169	NM_011521	20971	Mm.3815	NM_011521	ENSMUSG00000017009	Sdc4	AA959608|AW108331|S4|Synd4|ryudocan|syndecan-4	syndecan 4	protein-coding
mm_51909.1	chr6	91212788	91212798	+	1	NA	promoter-TSS (NM_001081437)	promoter-TSS (NM_001081437)	29	NM_007992	14115	Mm.249146	NM_007992	ENSMUSG00000064080	Fbln2	5730577E14Rik|FIBL-2	fibulin 2	protein-coding
mm_87863.1	chr10	61180475	61180478	+	1	NA	3' UTR (NM_001017407, exon 4 of 4)	3' UTR (NM_001017407, exon 4 of 4)	5214	NM_023064	65971	Mm.30227	NM_023064	ENSMUSG00000020096	Tbata	1700021K02Rik|AI428928|Spatial|Titest	thymus, brain and testes associated	protein-coding
mm_93928.1	chr10	127165680	127165692	-	1	NA	promoter-TSS (NM_027739)	promoter-TSS (NM_027739)	-145	NM_027739	14421	Mm.386762	NM_008080	ENSMUSG00000006731	B4galnt1	4933429D13Rik|Gal-NAc-T|GalNAc-T|GalNAcT|Galgt1|Ggm-2|Ggm2	beta-1,4-N-acetyl-galactosaminyl transferase 1	protein-coding
mm_10794.1	chr2	24349503	24349508	+	1	NA	exon (NM_031167, exon 5 of 5)	exon (NM_031167, exon 5 of 5)	4134	NM_001039701	16181	Mm.882	NM_031167	ENSMUSG00000026981	Il1rn	F630041P17Rik|IL-1ra	interleukin 1 receptor antagonist	protein-coding
mm_44168.1	chr5	150764853	150764859	+	1	NA	intron (NM_001346503, intron 17 of 34)	intron (NM_001346503, intron 17 of 34)	91029	NM_001346503	100710	Mm.32959	NM_175310	ENSMUSG00000034021	Pds5b	AI646570|AS3|AW212954|Aprin|Tg(Wap-ERBB2)229Wzw|WAP-Her-2|mKIAA0979	PDS5 cohesin associated factor B	protein-coding
mm_10672.1	chr2	21205720	21205781	+	1	NA	promoter-TSS (NM_027728)	promoter-TSS (NM_027728)	26	NM_177588	208967	Mm.268841	NM_177588	ENSMUSG00000048550	Thnsl1	AW413632	threonine synthase-like 1 (bacterial)	protein-coding
mm_10789.1	chr2	24347704	24347743	+	1	NA	intron (NM_001159562, intron 3 of 4)	intron (NM_001159562, intron 3 of 4)	2352	NM_001039701	16181	Mm.882	NM_031167	ENSMUSG00000026981	Il1rn	F630041P17Rik|IL-1ra	interleukin 1 receptor antagonist	protein-coding
mm_36576.1	chr4	88019528	88019531	-	1	NA	intron (NM_027326, intron 2 of 10)	intron (NM_027326, intron 2 of 10)	13878	NM_027326	70122	Mm.288898	NM_027326	ENSMUSG00000028496	Mllt3	2210011H10Rik|2610012I03Rik|3830408D16Rik|Af9|D4Ertd321e	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 3	protein-coding
mm_111045.1	chr12	79646629	79646664	-	1	NA	intron (NM_009014, intron 7 of 10)	intron (NM_009014, intron 7 of 10)	278087	NR_131075	77290	Mm.395042	NR_131073		9430078K24Rik	-	RIKEN cDNA 9430078K24 gene	ncRNA
mm_88306.1	chr10	75324983	75324989	+	1	NA	5' UTR (NM_001331096, exon 1 of 3)	5' UTR (NM_001331096, exon 1 of 3)	128	NM_001331096	11540	Mm.333734	NM_009630	ENSMUSG00000020178	Adora2a	A2AAR|A2aR|AA2AR	adenosine A2a receptor	protein-coding
mm_57485.1	chr6	125265328	125265342	-	1	NA	promoter-TSS (NR_015527)	promoter-TSS (NR_015527)	-190	NR_015527	73870	Mm.440681	NR_015527	ENSMUSG00000108129	4930417O13Rik	-	RIKEN cDNA 4930417O13 gene	ncRNA
mm_148472.1	chr19	4097446	4097451	+	1	NA	promoter-TSS (NM_026373)	promoter-TSS (NM_026373)	97	NM_026373	52004	Mm.29609	NM_026373	ENSMUSG00000024856	Cdk2ap2	5830466O21Rik|D19Ertd144e|Doc-1r	CDK2-associated protein 2	protein-coding
mm_55079.1	chr6	49214586	49214592	-	1	NA	5' UTR (NM_023670, exon 1 of 15)	5' UTR (NM_023670, exon 1 of 15)	365	NM_023670	140488	Mm.281018	NM_023670	ENSMUSG00000029814	Igf2bp3	2610101N11Rik|AA522010|AL022933|AU045931|IMP-3|IMP3|Koc13|Neilsen|mimp3	insulin-like growth factor 2 mRNA binding protein 3	protein-coding
mm_73943.1	chr8	120109422	120109451	+	1	NA	Intergenic	Intergenic	-4716	NM_001163762	234797	Mm.101958	NM_172286	ENSMUSG00000031824	6430548M08Rik	AW049007|Kiaa0513|mKIAA0513	RIKEN cDNA 6430548M08 gene	protein-coding
mm_145145.1	chr18	45559889	45559905	+	1	NA	promoter-TSS (NM_080465)	promoter-TSS (NM_080465)	-257	NM_080465	140492	Mm.411614	NM_080465	ENSMUSG00000054477	Kcnn2	KCa2.2|SK2|SKCA2|bc|fri	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2	protein-coding
mm_42166.1	chr5	112259626	112259659	+	1	NA	intron (NM_023695, intron 3 of 5)	intron (NM_023695, intron 3 of 5)	3822	NM_001312893	12960	Mm.29488	NM_023695	ENSMUSG00000029343	Crybb1	3110006K12Rik|BB1CRY	crystallin, beta B1	protein-coding
mm_147043.1	chr18	34887363	34887394	-	1	NA	Intergenic	GC_rich|Low_complexity|Low_complexity	26171	NM_007913	13653	Mm.181959	NM_007913	ENSMUSG00000038418	Egr1	A530045N19Rik|ETR103|Egr-1|Krox-1|Krox-24|Krox24|NGF1-A|NGFI-A|NGFIA|TIS8|Zenk|Zfp-6|Zif268|egr	early growth response 1	protein-coding
mm_120672.1	chr14	70554499	70554503	+	1	NA	intron (NM_021877, intron 1 of 19)	CpG	445	NM_021877	15460	Mm.7598	NM_021877	ENSMUSG00000022096	Hr	ALUNC|AU|N|ba|bldy|hr|rh|rh-bmh|rhino	hairless	protein-coding
mm_69882.1	chr7	141636881	141636910	-	1	NA	intron (NM_001330001, intron 31 of 33)	intron (NM_001330001, intron 31 of 33)	16194	NR_106030	102466798		NR_106030	ENSMUSG00000098759	Mir7063	Gm27654|mmu-mir-7063	microRNA 7063	ncRNA
mm_53517.1	chr6	136463670	136463693	+	1	NA	Intergenic	ID_B1|SINE|B4	-48112	NM_001201390	100502936	Mm.21182	NM_001201390	ENSMUSG00000045291	E330021D16Rik	C85549	RIKEN cDNA E330021D16 gene	protein-coding
mm_127398.1	chr15	101134599	101134630	+	1	NA	5' UTR (NM_009612, exon 3 of 11)	5' UTR (NM_009612, exon 3 of 11)	6092	NM_001277257	11482	Mm.279542	NM_009612	ENSMUSG00000000530	Acvrl1	AI115505|AI427544|Acvrlk1|Alk1	activin A receptor, type II-like 1	protein-coding
mm_28090.1	chr3	85887343	85887355	-	1	NA	5' UTR (NM_177130, exon 1 of 2)	5' UTR (NM_177130, exon 1 of 2)	169	NM_177130	320302	Mm.482978	NM_177130	ENSMUSG00000031286	Glt28d2	4732486J07Rik|Glt28d1l	glycosyltransferase 28 domain containing 2	protein-coding
mm_67879.1	chr7	99238565	99238623	-	1	NA	promoter-TSS (NM_177448)	promoter-TSS (NM_177448)	17	NM_177448	233549	Mm.208030	NM_177448	ENSMUSG00000052396	Mogat2	DGAT2L5|MGAT2|Mgat1l	monoacylglycerol O-acyltransferase 2	protein-coding
mm_122051.1	chr14	30160783	30160788	-	1	NA	intron (NM_001302637, intron 8 of 48)	intron (NM_001302637, intron 8 of 48)	138152	NM_175343	218865	Mm.259916	NM_172264	ENSMUSG00000015970	Chdh	AU041472|D630034H06Rik	choline dehydrogenase	protein-coding
mm_159646.1	chr4	144378120	144378120	-	1	NA	promoter-TSS (NM_001115077)	promoter-TSS (NM_001115077)	-187	NM_001115077	627009	Mm.473686	NM_001115077	ENSMUSG00000073721	Gm13125	EG627009|OTTMUSG00000010547	predicted gene 13125	protein-coding
mm_5673.1	chr1	43092439	43092498	-	1	NA	intron (NM_001013025, intron 2 of 12)	CpG	6154	NM_001013025	73122	Mm.246069	NM_001013025	ENSMUSG00000070939	Tgfbrap1	3110018K12Rik|AU024090|AU042859|AW742551|Trap1	transforming growth factor, beta receptor associated protein 1	protein-coding
mm_99375.1	chr11	101984344	101984354	+	1	NA	intron (NM_028207, intron 1 of 2)	intron (NM_028207, intron 1 of 2)	442	NM_028207	72349	Mm.196295	NM_028207	ENSMUSG00000003518	Dusp3	2210015O03Rik|5031436O03Rik|T-DSP11|VHR	dual specificity phosphatase 3 (vaccinia virus phosphatase VH1-related)	protein-coding
mm_960.1	chr1	57995981	57996059	+	1	NA	promoter-TSS (NM_199007)	promoter-TSS (NM_199007)	46	NM_199007	68549	Mm.32800	NM_199007	ENSMUSG00000026039	Sgol2a	1110007N04Rik|4932411A20Rik|5730576N04Rik|AU018846|AV008062|D1Ertd8e|Sgol2|Tripin	shugoshin-like 2a (S. pombe)	protein-coding
mm_125619.1	chr15	61987680	61987753	+	1	NA	exon (NM_001177354, exon 2 of 3)	exon (NM_001177354, exon 2 of 3)	2375	NM_001177352	17869	Mm.2444	NM_010849	ENSMUSG00000022346	Myc	AU016757|Myc2|Niard|Nird|bHLHe39	myelocytomatosis oncogene	protein-coding
mm_15969.1	chr2	166072202	166072223	+	1	NA	3' UTR (NM_008679, exon 23 of 23)	3' UTR (NM_008679, exon 23 of 23)	79575	NM_008679	17979	Mm.469663	NM_008679	ENSMUSG00000027678	Ncoa3	2010305B15Rik|AW321064|Actr|Aib1|KAT13B|Rac3|Src3|Tram-1|Tram1|bHLHe42|p/Cip|pCip	nuclear receptor coactivator 3	protein-coding
mm_71862.1	chr8	69088717	69088727	+	1	NA	promoter-TSS (NM_007509)	promoter-TSS (NM_007509)	-14	NM_007509	11966	Mm.249096	NM_007509	ENSMUSG00000006273	Atp6v1b2	AI194269|AI790362|Atp6b2|HO57|R74844	ATPase, H+ transporting, lysosomal V1 subunit B2	protein-coding
mm_142626.1	chr17	47395399	47395416	-	1	NA	intron (NM_008189, intron 2 of 3)	intron (NM_008189, intron 2 of 3)	5199	NM_008189	14913	Mm.16224	NM_008189	ENSMUSG00000023982	Guca1a	GC-A|Gcap1|Guca1|mGCAP1	guanylate cyclase activator 1a (retina)	protein-coding
mm_152538.1	chr19	11327959	11327982	-	1	NA	exon (NM_001276398, exon 3 of 7)	exon (NM_001276398, exon 3 of 7)	6725	NM_001276398	109225	Mm.491251	NM_027836	ENSMUSG00000024672	Ms4a7	9130422I10Rik|A430103C15Rik|CD20l4|CFFMA	membrane-spanning 4-domains, subfamily A, member 7	protein-coding
mm_47705.1	chr5	129887289	129887305	-	1	NA	5' UTR (NM_024166, exon 1 of 4)	5' UTR (NM_024166, exon 1 of 4)	173	NM_024166	14004	Mm.30133	NM_024166	ENSMUSG00000070493	Chchd2	AL033347|Etohi6	coiled-coil-helix-coiled-coil-helix domain containing 2	protein-coding
mm_29288.1	chr3	107742559	107742595	-	1	NA	3' UTR (NM_007778, exon 9 of 9)	3' UTR (NM_007778, exon 9 of 9)	17892	NM_001113530	12977	Mm.795	NM_007778	ENSMUSG00000014599	Csf1	C87615|Csfm|MCSF|op	colony stimulating factor 1 (macrophage)	protein-coding
mm_142326.1	chr17	43490342	43490347	-	1	NA	intron (NM_008585, intron 7 of 13)	intron (NM_008585, intron 7 of 13)	12429	NM_008585	17287	Mm.5346	NM_008585	ENSMUSG00000023914	Mep1a	AI098089|AW107200|Mep-1|Mep-1a|Mep1	meprin 1 alpha	protein-coding
mm_11089.1	chr2	27886417	27886440	+	1	NA	promoter-TSS (NM_015734)	promoter-TSS (NM_015734)	3	NM_015734	12831	Mm.7281	NM_015734	ENSMUSG00000026837	Col5a1	AI413331	collagen, type V, alpha 1	protein-coding
mm_2623.1	chr1	120602512	120602522	+	1	NA	promoter-TSS (NM_010133)	promoter-TSS (NM_010133)	30	NM_010133	13798	Mm.2657	NM_010133	ENSMUSG00000058665	En1	En-1|Mo-en.1|engrailed-1	engrailed 1	protein-coding
mm_107797.1	chr12	64917839	64917870	+	1	NA	promoter-TSS (NM_001025605)	promoter-TSS (NM_001025605)	-57	NM_001025605	217648	Mm.341586	NM_001025605	ENSMUSG00000047227	Gm527	-	predicted gene 527	protein-coding
mm_8784.1	chr1	161251129	161251139	-	1	NA	promoter-TSS (NM_007453)	promoter-TSS (NM_007453)	76	NR_130150	11758	Mm.186185	NM_007453	ENSMUSG00000026701	Prdx6	1-Cys Prx|1-cysPrx|9430088D19Rik|AA690119|Aop2|Brp-12|CP-3|GPx|Ltw-4|Ltw4|Lvtw-4|NSGPx|ORF06|Prdx5|aiPLA2	peroxiredoxin 6	protein-coding
mm_143185.1	chr17	58908540	58908549	-	1	NA	intron (NM_027001, intron 8 of 12)	intron (NM_027001, intron 8 of 12)	82831	NM_027001	69239	Mm.246732	NM_027001	ENSMUSG00000024227	Pdzph1	2610034M16Rik|AV114557	PDZ and pleckstrin homology domains 1	protein-coding
mm_27983.1	chr3	81968284	81968285	-	1	NA	intron (NM_019911, intron 5 of 11)	intron (NM_019911, intron 5 of 11)	7444	NM_019911	56720	Mm.258622	NM_019911	ENSMUSG00000028011	Tdo2	AA407491|TDO|TO|chky	tryptophan 2,3-dioxygenase	protein-coding
mm_129912.1	chr15	84132036	84132040	-	1	NA	Intergenic	Intergenic	-8863	NM_029427	75772	Mm.159565	NM_029427	ENSMUSG00000018868	Pnpla5	4833426H19Rik|GS2L	patatin-like phospholipase domain containing 5	protein-coding
mm_99332.1	chr11	101465303	101465317	+	1	NA	intron (NM_012037, intron 1 of 5)	intron (NM_012037, intron 1 of 5)	889	NM_012037	26949	Mm.29210	NM_012037	ENSMUSG00000034993	Vat1	VAT-1	vesicle amine transport 1	protein-coding
mm_43905.1	chr5	144255286	144255299	+	1	NA	promoter-TSS (NM_018772)	promoter-TSS (NM_018772)	67	NM_018772	55950	Mm.38011	NM_018772	ENSMUSG00000047843	Bri3	I3	brain protein I3	protein-coding
mm_153647.1	chr19	44280790	44280806	-	1	NA	Intergenic	Intergenic	-12878	NM_009128	20250	Mm.487021	NM_009128	ENSMUSG00000025203	Scd2	Mir5114|Scd-2|mir-5114|swty	stearoyl-Coenzyme A desaturase 2	protein-coding
mm_142135.1	chr17	35910033	35910076	-	1	NA	promoter-TSS (NM_028476)	promoter-TSS (NM_028476)	14	NM_001142745	73242	Mm.273155	NM_028476	ENSMUSG00000024426	Atat1	0610011P08Rik|2610008K08Rik|2610110G12Rik|3110080J08Rik|Mec17|TAT	alpha tubulin acetyltransferase 1	protein-coding
mm_141842.1	chr17	34729983	34730016	-	1	NA	intron (NM_009780, intron 35 of 40)	intron (NM_009780, intron 35 of 40)	13898	NM_009780	12268	Mm.477109	NM_009780	ENSMUSG00000073418	C4b	C4|Ss	complement component 4B (Chido blood group)	protein-coding
mm_95388.1	chr11	49245525	49245539	+	1	NA	5' UTR (NM_010794, exon 2 of 3)	5' UTR (NM_010794, exon 2 of 3)	1341	NM_001110148	17308	Mm.196933	NM_010794	ENSMUSG00000020346	Mgat1	Mgat-1	mannoside acetylglucosaminyltransferase 1	protein-coding
mm_10334.1	chr2	11626174	11626202	+	1	NA	Intergenic	Intergenic	-16604	NM_008367	16184	Mm.915	NM_008367	ENSMUSG00000026770	Il2ra	CD25|Il2r|Ly-43	interleukin 2 receptor, alpha chain	protein-coding
mm_77992.1	chr9	8544228	8544258	+	1	NA	5' UTR (NM_001282087, exon 1 of 3)	5' UTR (NM_001282087, exon 1 of 3)	101	NM_001282087	22068	Mm.325086	NM_013838	ENSMUSG00000031997	Trpc6	AV025995|LLHWJM002|LLHWJM003|LLHWJM004|TRP-6|Trrp6|mtrp6	transient receptor potential cation channel, subfamily C, member 6	protein-coding
mm_96411.1	chr11	67254674	67254683	+	1	NA	exon (NM_010855, exon 30 of 40)	exon (NM_010855, exon 30 of 40)	16866	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_112890.1	chr13	20885073	20885083	+	1	NA	intron (NM_012054, intron 4 of 20)	B4|SINE|B4	90965	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_37918.1	chr4	132785369	132785381	-	1	NA	exon (NM_001033308, exon 4 of 6)	exon (NM_001033308, exon 4 of 6)	10989	NM_001033308	230787	Mm.290912	NM_001033308	ENSMUSG00000037731	Themis2	ICB-1	thymocyte selection associated family member 2	protein-coding
mm_124765.1	chr15	6665297	6665318	+	1	NA	3' UTR (NM_001278269, exon 17 of 17)	3' UTR (NM_001278269, exon 17 of 17)	-43074	NM_030168	78757	Mm.275811	NM_030168	ENSMUSG00000050310	Rictor	4921505C17Rik|6030405M08Rik|AVO3|AW492497|D530039E11Rik	RPTOR independent companion of MTOR, complex 2	protein-coding
mm_29674.1	chr3	122802020	122802045	-	1	NA	promoter-TSS (NR_045168)	promoter-TSS (NR_045168)	-52	NR_045168	71647	Mm.449992	NR_045168	ENSMUSG00000106583	4930447N08Rik	-	RIKEN cDNA 4930447N08 gene	ncRNA
mm_66361.1	chr7	43530336	43530342	-	1	NA	intron (NM_021293, intron 3 of 5)	intron (NM_021293, intron 3 of 5)	2832	NM_001111058	12489	Mm.140157	NM_021293	ENSMUSG00000004609	Cd33	Siglec-3|gp67	CD33 antigen	protein-coding
mm_125658.1	chr15	64024088	64024094	+	1	NA	intron (NM_144846, intron 1 of 11)	intron (NM_144846, intron 1 of 11)	36357	NM_144846	223601	Mm.246108	NM_144846	ENSMUSG00000022378	Fam49b	0910001A06Rik|AW122079	family with sequence similarity 49, member B	protein-coding
mm_129647.1	chr15	80650053	80650060	-	1	NA	3' UTR (NM_001289442, exon 8 of 8)	3' UTR (NM_001289442, exon 8 of 8)	3983	NR_105922	102466773		NR_105922	ENSMUSG00000098631	Mir6957	Gm27895|mmu-mir-6957	microRNA 6957	ncRNA
mm_129662.1	chr15	81111500	81111505	-	1	NA	intron (NM_001082536, intron 2 of 13)	intron (NM_001082536, intron 2 of 13)	-6455	NM_153049	223701	Mm.439814	NM_153049	ENSMUSG00000042292	Mkl1	AMKL|Bsac|Mal|Mrtf-A	MKL (megakaryoblastic leukemia)/myocardin-like 1	protein-coding
mm_149406.1	chr19	11392787	11392793	+	1	NA	exon (NM_001310331, exon 7 of 7)	exon (NM_001310331, exon 7 of 7)	-14871	NM_029499	64380	Mm.440715	NM_029499	ENSMUSG00000024675	Ms4a4c	5830413L19Rik|AI449185|Ms4a9	membrane-spanning 4-domains, subfamily A, member 4C	protein-coding
mm_723.1	chr1	42851254	42851295	+	1	NA	promoter-TSS (NM_023514)	promoter-TSS (NM_023514)	41	NM_023514	69527	Mm.252982	NM_023514	ENSMUSG00000060679	Mrps9	2310002A08Rik|AW322516|Mrp-S9|S9mt|mg637	mitochondrial ribosomal protein S9	protein-coding
mm_151098.1	chr19	47855019	47855021	+	1	NA	promoter-TSS (NM_010362)	promoter-TSS (NM_010362)	47	NM_010362	14873	Mm.378931	NM_010362	ENSMUSG00000025068	Gsto1	AA407097|AI194287|AU018802|Gsto-1|Gstx|Spg-r|p28	glutathione S-transferase omega 1	protein-coding
mm_137473.1	chr17	26699325	26699337	+	1	NA	3' UTR (NM_025272, exon 4 of 4)	3' UTR (NM_025272, exon 4 of 4)	-16319	NM_029870	77128	Mm.275414	NM_029870	ENSMUSG00000048249	Crebrf	A930001N09Rik|LRF	CREB3 regulatory factor	protein-coding
mm_33549.1	chr4	130934835	130934846	+	1	NA	3' UTR (NM_010686, exon 8 of 8)	3' UTR (NM_010686, exon 8 of 8)	-9545	NM_010769	17180	Mm.271796	NM_010769	ENSMUSG00000040533	Matn1	CMP|Crtm|Mat1|matrilin-1	matrilin 1, cartilage matrix protein	protein-coding
mm_141285.1	chr17	27910201	27910249	-	1	NA	intron (NM_001286040, intron 1 of 24)	intron (NM_001286040, intron 1 of 24)	919	NM_181413	224650	Mm.32556	NM_181413	ENSMUSG00000024219	Anks1	Anks1a|mKIAA0229	ankyrin repeat and SAM domain containing 1	protein-coding
mm_17123.1	chr2	24763137	24763153	-	1	NA	promoter-TSS (NM_001042528)	promoter-TSS (NM_001042528)	7	NM_001042528	12287	Mm.4424	NM_007579	ENSMUSG00000004113	Cacna1b	AW050276|AW060892|AW822256|BIII|Cav2.2|Cchn1a|alpha(1B)	calcium channel, voltage-dependent, N type, alpha 1B subunit	protein-coding
mm_84390.1	chr9	65423245	65423256	-	1	NA	promoter-TSS (NM_178933)	promoter-TSS (NM_178933)	-477	NM_178933	330962	Mm.335247	NM_178933	ENSMUSG00000053862	Slc51b	Ostb	solute carrier family 51, beta subunit	protein-coding
mm_57971.1	chr6	135346498	135346511	-	1	NA	Intergenic	Intergenic	-16427	NM_010128	13730	Mm.182785	NM_010128	ENSMUSG00000030208	Emp1	I-8-09|TMP	epithelial membrane protein 1	protein-coding
mm_142266.1	chr17	39845900	39845939	-	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	2922	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_41750.1	chr5	102845151	102845200	+	1	NA	5' UTR (NM_001346585, exon 1 of 7)	5' UTR (NM_001346585, exon 1 of 7)	168	NM_001346585	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding
mm_26950.1	chr3	20274855	20274860	-	1	NA	intron (NM_029706, intron 2 of 10)	intron (NM_029706, intron 2 of 10)	876	NM_029706	76703	Mm.34692	NM_029706	ENSMUSG00000011463	Cpb1	0910001A18Rik|1810063F02Rik|2210008M23Rik|AI504870	carboxypeptidase B1 (tissue)	protein-coding
mm_50773.1	chr6	53629932	53629961	+	1	NA	intron (NM_001327821, intron 7 of 10)	MLTR14|LTR|ERV1	56572	NM_172728	231991	Mm.227444	NM_172728	ENSMUSG00000053007	Creb5	9430076C15Rik|CRE-BPa|Crebpa|D430026C09Rik	cAMP responsive element binding protein 5	protein-coding
mm_146869.1	chr18	25168863	25168884	-	1	NA	promoter-TSS (NM_001142698)	promoter-TSS (NM_001142698)	4	NM_001142698	66648	Mm.263189	NM_001004361	ENSMUSG00000024269	Tpgs2	5730437P09Rik|5730494M16Rik|AI666318|Pgs2	tubulin polyglutamylase complex subunit 2	protein-coding
mm_157434.1	chrX	38635004	38635012	-	1	NA	5' UTR (NM_021550, exon 1 of 2)	5' UTR (NM_021550, exon 1 of 2)	135	NM_021550	59048	Mm.441410	NM_021550	ENSMUSG00000048970	C1galt1c1	1500002I11Rik|AB030184|C1GalT2|C81205|Cosmc	C1GALT1-specific chaperone 1	protein-coding
mm_43062.1	chr5	124327632	124327642	+	1	NA	promoter-TSS (NM_001134717)	promoter-TSS (NM_001134717)	335	NM_001081323	269702	Mm.60224	NM_001081323	ENSMUSG00000038126	Mphosph9	4930548D04Rik|9630025B04Rik|AW413446|AW547060|B930097C17Rik|C87456|MPP-9|MPP9	M-phase phosphoprotein 9	protein-coding
mm_76507.1	chr8	86885175	86885189	-	1	NA	promoter-TSS (NM_030563)	promoter-TSS (NM_030563)	76	NM_030563	80750	Mm.25117	NM_030563	ENSMUSG00000031652	N4bp1	AI481586|C81621	NEDD4 binding protein 1	protein-coding
mm_133552.1	chr16	91373210	91373253	+	1	NA	intron (NM_001347258, intron 1 of 7)	CpG	448	NM_001110498	15976	Mm.6834	NM_010509	ENSMUSG00000022971	Ifnar2	AI747302|Ifnar-2	interferon (alpha and beta) receptor 2	protein-coding
mm_5145.1	chr1	9748278	9748320	-	1	NA	promoter-TSS (NM_173443)	promoter-TSS (NM_173443)	83	NM_173443	70675	Mm.274493	NM_173443	ENSMUSG00000045210	Vcpip1	4932442A08|5730421J18Rik|5730538E15Rik|VCIP135|mKIAA1850	valosin containing protein (p97)/p47 complex interacting protein 1	protein-coding
mm_32932.1	chr4	119236903	119236905	+	1	NA	exon (NM_019782, exon 3 of 16)	exon (NM_019782, exon 3 of 16)	3075	NM_001042411	56401	Mm.27961	NM_019782	ENSMUSG00000028641	P3h1	2410024C15Rik|Gros1|Lepre1	prolyl 3-hydroxylase 1	protein-coding
mm_75067.1	chr8	33806861	33806885	-	1	NA	intron (NM_001042674, intron 5 of 7)	intron (NM_001042674, intron 5 of 7)	-59103	NM_001206849	72632	Mm.443483	NM_001206849	ENSMUSG00000094500	Smim18	2700090O03Rik|AI835723	small integral membrane protein 18	protein-coding
mm_116323.1	chr13	37992100	37992116	-	1	NA	exon (NM_025965, exon 2 of 8)	exon (NM_025965, exon 2 of 8)	2082	NM_025965	107513	Mm.426670	NM_025965	ENSMUSG00000021427	Ssr1	2510001K09Rik|6330400D04|AI159733|AI452176|SSR|TRAPA	signal sequence receptor, alpha	protein-coding
mm_15467.1	chr2	157464335	157464338	+	1	NA	intron (NM_009271, intron 8 of 14)	intron (NM_009271, intron 8 of 14)	40043	NM_001025395	20779	Mm.22845	NM_009271	ENSMUSG00000027646	Src	AW259666|pp60c-src	Rous sarcoma oncogene	protein-coding
mm_69353.1	chr7	130266238	130266261	-	1	NA	5' UTR (NM_010207, exon 1 of 18)	5' UTR (NM_010207, exon 1 of 18)	559	NM_010207	14183	Mm.16340	NM_010207	ENSMUSG00000030849	Fgfr2	AU043015|AW556123|Bek|Fgfr-2|Fgfr-7|Fgfr7|KGFR|KGFRTr|svs	fibroblast growth factor receptor 2	protein-coding
mm_67506.1	chr7	80782286	80782301	-	1	NA	intron (NM_016721, intron 2 of 37)	intron (NM_016721, intron 2 of 37)	21038	NM_016721	29875	Mm.207619	NM_016721	ENSMUSG00000030536	Iqgap1	AA682088|D7Ertd237e|D7Ertd257e|mKIAA0051	IQ motif containing GTPase activating protein 1	protein-coding
mm_59666.1	chr7	28375771	28375792	+	1	NA	Intergenic	Intergenic	-3119	NM_001083912	101497	Mm.235700	NM_138752	ENSMUSG00000037552	Plekhg2	AI194308|Clg|Cslg	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	protein-coding
mm_97476.1	chr11	78323121	78323145	+	1	NA	promoter-TSS (NM_001303423)	promoter-TSS (NM_001303423)	60	NM_001303423	11676	Mm.7729	NM_009657	ENSMUSG00000017390	Aldoc	AI847350|AU040929|Aldo3|Scrg2	aldolase C, fructose-bisphosphate	protein-coding
mm_4226.1	chr1	171345670	171345680	+	1	NA	promoter-TSS (NM_012049)	promoter-TSS (NM_012049)	-24	NM_011070	18637	Mm.10756	NM_011070	ENSMUSG00000006412	Pfdn2	ESTM27|W48336	prefoldin 2	protein-coding
mm_147768.1	chr18	61375476	61375492	-	1	NA	intron (NM_133249, intron 1 of 11)	intron (NM_133249, intron 1 of 11)	24947	NM_133249	170826	Mm.415302	NM_133249	ENSMUSG00000033871	Ppargc1b	4631412G21Rik|Perc	peroxisome proliferative activated receptor, gamma, coactivator 1 beta	protein-coding
mm_159171.1	chr2	104230570	104230570	-	1	NA	intron (NM_001033347, intron 9 of 20)	intron (NM_001033347, intron 9 of 20)	107801	NM_026634	68243	Mm.158191	NM_026634	ENSMUSG00000032671	A930018P22Rik	-	RIKEN cDNA A930018P22 gene	protein-coding
mm_106991.1	chr12	11139499	11139499	+	1	NA	intron (NM_001168564, intron 1 of 2)	intron (NM_001168564, intron 1 of 2)	10874	NM_173417	238076	Mm.113278	NM_173417	ENSMUSG00000043673	Kcns3	-	potassium voltage-gated channel, delayed-rectifier, subfamily S, member 3	protein-coding
mm_26718.1	chr3	158897608	158897610	+	1	NA	Intergenic	Intergenic	-178755	NR_040750	624759	Mm.491054	NR_040750	ENSMUSG00000106053	Gm20752	-	predicted gene, 20752	ncRNA
mm_133899.1	chr16	97547311	97547317	+	1	NA	intron (NM_013606, intron 6 of 13)	intron (NM_013606, intron 6 of 13)	11231	NM_013606	17858	Mm.14157	NM_013606	ENSMUSG00000023341	Mx2	AI528743|Mx-2	MX dynamin-like GTPase 2	protein-coding
mm_96944.1	chr11	70540830	70540840	+	1	NA	intron (NM_001302475, intron 1 of 24)	intron (NM_001302475, intron 1 of 24)	563	NM_001302476	18806	Mm.260177	NM_008876	ENSMUSG00000020828	Pld2	PLD1C	phospholipase D2	protein-coding
mm_170856.1	chr2	180246684	180246689	-	1	NA	Intergenic	RLTR1B|LTR|ERV1	-10693	NM_025587	66481	Mm.289669	NM_025587	ENSMUSG00000039001	Rps21	1810049N11Rik|2410030A14Rik	ribosomal protein S21	protein-coding
mm_171276.1	chr3	88831436	88831436	+	1	NA	intron (NR_015498, intron 1 of 1)	intron (NR_015498, intron 1 of 1)	1051	NR_015498	319830	Mm.400394	NR_015498		1500004A13Rik	5430404N14Rik|BB132176	RIKEN cDNA 1500004A13 gene	ncRNA
mm_44217.1	chr5	4757927	4757936	-	1	NA	5' UTR (NM_021457, exon 1 of 1)	5' UTR (NM_021457, exon 1 of 1)	285	NM_021457	14362	Mm.246003	NM_021457	ENSMUSG00000044674	Fzd1	AW227548|FZ-1|Fz1	frizzled class receptor 1	protein-coding
mm_154723.1	chrX	9435494	9435499	+	1	NA	3' UTR (NM_007807, exon 13 of 13)	3' UTR (NM_007807, exon 13 of 13)	33828	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_111523.1	chr12	100187437	100187448	-	1	NA	promoter-TSS (NR_045282)	promoter-TSS (NR_045282)	-526	NR_045282	100038378	Mm.387075	NR_045282	ENSMUSG00000072884	Gm10433	ENSMUSG00000072884	predicted gene 10433	ncRNA
mm_112127.1	chr12	112929763	112929778	-	1	NA	promoter-TSS (NM_010588)	promoter-TSS (NM_010588)	-275	NM_010588	16450	Mm.186146	NM_010588	ENSMUSG00000002799	Jag2	D12Ggc2e|Serh|mJagged2-1|sm	jagged 2	protein-coding
mm_18283.1	chr2	52530638	52530640	-	1	NA	intron (NM_001285426, intron 2 of 13)	B4A|SINE|B4	27972	NM_146123	12298	Mm.330223	NM_146123	ENSMUSG00000017412	Cacnb4	3110038O15Rik|Cchb4|lh	calcium channel, voltage-dependent, beta 4 subunit	protein-coding
mm_58243.1	chr6	145048602	145048642	-	1	NA	exon (NM_001024468, exon 1 of 11)	exon (NM_001024468, exon 1 of 11)	190	NM_001024468	12035	Mm.4606	NM_007532	ENSMUSG00000030268	Bcat1	BCATc|Eca39	branched chain aminotransferase 1, cytosolic	protein-coding
mm_93742.1	chr10	120142841	120142862	-	1	NA	exon (NM_028679, exon 12 of 12)	exon (NM_028679, exon 12 of 12)	-29886	NM_080446	117599	Mm.214703	NM_080446	ENSMUSG00000020228	Helb	AI447783|D10Ertd664e	helicase (DNA) B	protein-coding
mm_135983.1	chr16	75092564	75092604	-	1	NA	Intergenic	Intergenic	493477	NM_001252513	320355	Mm.99517	NM_177142	ENSMUSG00000032948	Lipi	D930038D03Rik|lpd1	lipase, member I	protein-coding
mm_151713.1	chr19	4625273	4625321	-	1	NA	TTS (NM_001033447)	TTS (NM_001033447)	320	NM_023131	19671	Mm.391143	NM_023131	ENSMUSG00000024889	Rce1	D19Ertd283e|D19Ertd98e	Ras converting CAAX endopeptidase 1	protein-coding
mm_61555.1	chr7	79499977	79499987	+	1	NA	promoter-TSS (NR_040314)	promoter-TSS (NR_040314)	-44	NR_040311	101694	Mm.41661	NR_040311	ENSMUSG00000097023	Mir9-3hg	AI854517	Mir9-3 host gene	ncRNA
mm_145150.1	chr18	46227081	46227092	+	1	NA	Intergenic	Intergenic	-14479	NM_178872	28105	Mm.277382	NM_178872	ENSMUSG00000033949	Trim36	D18Wsu100e|haprin	tripartite motif-containing 36	protein-coding
mm_4139.1	chr1	170644786	170644837	+	1	NA	5' UTR (NM_177068, exon 1 of 8)	5' UTR (NM_177068, exon 1 of 8)	279	NM_177068	320078	Mm.287131	NM_177068	ENSMUSG00000038463	Olfml2b	1110018N05Rik|4832415H08Rik|AI467542	olfactomedin-like 2B	protein-coding
mm_37182.1	chr4	117277677	117277683	-	1	NA	intron (NM_025739, intron 10 of 14)	intron (NM_025739, intron 10 of 14)	11775	NM_001310730	66743	Mm.318331	NM_025739	ENSMUSG00000028677	Rnf220	4732477A13|4931406I20Rik|5730503K05Rik|AV302541	ring finger protein 220	protein-coding
mm_66175.1	chr7	34013301	34013312	-	1	NA	exon (NM_001276475, exon 2 of 3)	exon (NM_001276475, exon 2 of 3)	636	NM_001276475	233099	Mm.110829	NM_001100464	ENSMUSG00000066584	Scgb2b27	Abpbg27|Abpbg5|Scgb2b5	secretoglobin, family 2B, member 27	protein-coding
mm_33648.1	chr4	133039483	133039495	+	1	NA	intron (NM_146155, intron 2 of 6)	CpG	27983	NM_146155	230793	Mm.31816	NM_146155	ENSMUSG00000037692	Ahdc1	D030015G18Rik	AT hook, DNA binding motif, containing 1	protein-coding
mm_94866.1	chr11	24078112	24078134	+	1	NA	promoter-TSS (NM_001242934)	promoter-TSS (NM_001242934)	67	NM_001159289	14025	Mm.53687	NM_016707	ENSMUSG00000000861	Bcl11a	2810047E18Rik|BCL-11A|Ctip1|D930021L15Rik|Evi9|Evi9a|Evi9b|Evi9c|mKIAA1809	B cell CLL/lymphoma 11A (zinc finger protein)	protein-coding
mm_70533.1	chr8	13037358	13037362	+	1	NA	promoter-TSS (NM_007972)	promoter-TSS (NM_007972)	52	NM_001242368	14058	Mm.262589	NM_007972	ENSMUSG00000031444	F10	Cf10|fX	coagulation factor X	protein-coding
mm_110841.1	chr12	72939764	72939775	-	1	NA	promoter-TSS (NM_011384)	promoter-TSS (NM_011384)	-113	NM_011384	20476	Mm.57138	NM_011384	ENSMUSG00000021099	Six6	Optx2|Six9	sine oculis-related homeobox 6	protein-coding
mm_117599.1	chr13	89893234	89893235	-	1	NA	intron (NM_028012, intron 7 of 7)	L1_Mur2|LINE|L1	-150722	NM_001134475	13003	Mm.158700	NM_019389	ENSMUSG00000021614	Vcan	5430420N07Rik|9430051N09|Cspg2|DPEAAE|NG2|PG-M|PG-M(V0)|PG-M(V1)|hdf	versican	protein-coding
mm_50921.1	chr6	57606117	57606124	+	1	NA	intron (NM_025992, intron 6 of 22)	Lx8b|LINE|L1	25128	NM_025992	67138	Mm.297393	NM_025992	ENSMUSG00000029798	Herc6	1700121D12Rik|2510038N07Rik|4930427L17Rik|AI451296|CEB1|Herc5	hect domain and RLD 6	protein-coding
mm_2683.1	chr1	127306625	127306637	+	1	NA	intron (NM_145128, intron 2 of 17)	intron (NM_145128, intron 2 of 17)	101645	NM_145128	107895	Mm.214682	NM_145128	ENSMUSG00000036155	Mgat5	4930471A21Rik|5330407H02Rik|AI480971|GlcNAc-TV	mannoside acetylglucosaminyltransferase 5	protein-coding
mm_86355.1	chr9	123678853	123678863	-	1	NA	promoter-TSS (NM_139142)	promoter-TSS (NM_139142)	-26	NM_139142	102680	Mm.440867	NM_139142	ENSMUSG00000036814	Slc6a20a	A730081N20Rik|AU022428|Xt3s1|Xtrp3s1	solute carrier family 6 (neurotransmitter transporter), member 20A	protein-coding
mm_43715.1	chr5	139406402	139406435	+	1	NA	promoter-TSS (NM_177000)	promoter-TSS (NM_177000)	31	NM_177000	319772	Mm.440271	NM_177000	ENSMUSG00000044092	C130050O18Rik	-	RIKEN cDNA C130050O18 gene	protein-coding
mm_32359.1	chr4	105157594	105157604	+	1	NA	5' UTR (NM_080555, exon 1 of 6)	5' UTR (NM_080555, exon 1 of 6)	252	NM_080555	67916	Mm.348326	NM_080555	ENSMUSG00000028517	Plpp3	1110003O22Rik|2610002D05Rik|AV025606|D4Bwg0538e|D4Bwg1535e|Lpp3|Ppab2b|Ppap2b	phospholipid phosphatase 3	protein-coding
mm_46478.1	chr5	105131798	105131804	-	1	NA	intron (NM_008620, intron 3 of 10)	A-rich|Low_complexity|Low_complexity	7751	NM_008620	17472	Mm.440525	NM_008620	ENSMUSG00000079363	Gbp4	AW228052|Mag-2|Mpa-2|Mpa2	guanylate binding protein 4	protein-coding
mm_51494.1	chr6	83058069	83058104	+	1	NA	TTS (NR_125891)	TTS (NR_125891)	242	NM_033606	93838	Mm.140332	NM_033606	ENSMUSG00000009145	Dqx1	2310066E11Rik	DEAQ RNA-dependent ATPase	protein-coding
mm_102954.1	chr11	69664367	69664382	-	1	NA	non-coding (NR_110993, exon 5 of 5)	non-coding (NR_110993, exon 5 of 5)	1331	NR_035455	100316840		NR_035455	ENSMUSG00000088752	Mir1934	mir-1934|mmu-mir-1934	microRNA 1934	ncRNA
mm_137741.1	chr17	29368958	29368983	+	1	NA	intron (NM_001159538, intron 8 of 15)	RMER17C|LTR|ERVK	8056	NM_001159538	26382	Mm.279187	NM_013710	ENSMUSG00000024013	Fgd2	Tcd-2|Tcd2|ZFYVE4|tcs-2|tcs2	FYVE, RhoGEF and PH domain containing 2	protein-coding
mm_48655.1	chr5	145872467	145872478	-	1	NA	intron (NM_007818, intron 4 of 12)	Lx5|LINE|L1	7382	NM_007818	13112	Mm.332844	NM_007818	ENSMUSG00000056035	Cyp3a11	AI256190|Cyp3a|IIIAm1|Pcn	cytochrome P450, family 3, subfamily a, polypeptide 11	protein-coding
mm_167932.1	chrX	105655542	105655544	+	1	NA	Intergenic	Intergenic	-108934	NM_030614	80903	Mm.154768	NM_030614	ENSMUSG00000031230	Fgf16	-	fibroblast growth factor 16	protein-coding
mm_29200.1	chr3	106766672	106766692	-	1	NA	intron (NM_007651, intron 5 of 7)	intron (NM_007651, intron 5 of 7)	23467	NM_007651	12508	Mm.316861	NM_007651	ENSMUSG00000040747	Cd53	AI323659|Ox-44|Tspan25	CD53 antigen	protein-coding
mm_84117.1	chr9	58526172	58526185	-	1	NA	3' UTR (NM_133983, exon 7 of 7)	3' UTR (NM_133983, exon 7 of 7)	14762	NM_133983	102657	Mm.5356	NM_133983	ENSMUSG00000035914	Cd276	6030411F23Rik|AU016588|B7RP-2|B7h3	CD276 antigen	protein-coding
mm_48999.1	chr6	4756732	4756742	+	1	NA	exon (NM_130877, exon 2 of 2)	exon (NM_130877, exon 2 of 2)	9431	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_92154.1	chr10	67535545	67535549	-	1	NA	Intergenic	CpG	-2322	NM_010118	13654	Mm.290421	NM_010118	ENSMUSG00000037868	Egr2	Egr-2|Krox-20|Krox20|NGF1-B|Zfp-25|Zfp-6	early growth response 2	protein-coding
mm_67618.1	chr7	83972423	83972428	-	1	NA	intron (NM_030728, intron 13 of 28)	intron (NM_030728, intron 13 of 28)	80425	NM_023403	67943	Mm.117365	NM_023403	ENSMUSG00000038503	Mesdc2	2210015O11Rik|AW537813|mKIAA0081|mesd|msd	mesoderm development candidate 2	protein-coding
mm_92831.1	chr10	81482638	81482644	-	1	NA	promoter-TSS (NM_176954)	promoter-TSS (NM_176954)	68	NM_176954	319586	Mm.152689	NM_176954	ENSMUSG00000034818	Celf5	4930565A21Rik|Brunol5	CUGBP, Elav-like family member 5	protein-coding
mm_32484.1	chr4	107890220	107890270	+	1	NA	intron (NM_001347160, intron 2 of 7)	intron (NM_001347160, intron 2 of 7)	346	NM_028754	74098	Mm.274853	NM_028754	ENSMUSG00000028608	0610037L13Rik	1110008H16Rik	RIKEN cDNA 0610037L13 gene	protein-coding
mm_61970.1	chr7	90451134	90451137	+	1	NA	intron (NM_025460, intron 4 of 4)	intron (NM_025460, intron 4 of 4)	6073	NM_025460	66271	Mm.28963	NM_025460	ENSMUSG00000030615	Tmem126a	1810020E01Rik	transmembrane protein 126A	protein-coding
mm_146474.1	chr18	89176966	89176989	+	1	NA	Intergenic	Intergenic	-20450	NM_178687	225825	Mm.139293	NM_178687	ENSMUSG00000034028	Cd226	BC051526|DNAM-1|DNAM1|Pta1|TLiSA1	CD226 antigen	protein-coding
mm_62275.1	chr7	99579695	99579709	+	1	NA	intron (NM_177231, intron 1 of 15)	MLT1O|LTR|ERVL-MaLR	27433	NR_029760	723840		NR_029760	ENSMUSG00000065571	Mir326	Mirn326|mir-326|mmu-mir-326	microRNA 326	ncRNA
mm_27840.1	chr3	79152859	79152878	-	1	NA	Intergenic	Intergenic	-6993	NM_001099624	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_118161.1	chr13	105294291	105294302	-	1	NA	Intergenic	CpG	-1282	NM_027934	71816	Mm.317015	NM_027934	ENSMUSG00000021720	Rnf180	3110001E11Rik|Rines	ring finger protein 180	protein-coding
mm_138955.1	chr17	44188604	44188618	+	1	NA	promoter-TSS (NM_172621)	promoter-TSS (NM_172621)	39	NM_172621	224796	Mm.37666	NM_172621	ENSMUSG00000023959	Clic5	5730531E12Rik|B330005L24|Gm322|jbg	chloride intracellular channel 5	protein-coding
mm_154058.1	chr19	55119811	55119815	-	1	NA	Intergenic	Intergenic	-20366	NM_008149	14732	Mm.210196	NM_008149	ENSMUSG00000024978	Gpam	GPAT|GPAT1	glycerol-3-phosphate acyltransferase, mitochondrial	protein-coding
mm_33825.1	chr4	135495970	135495974	+	1	NA	promoter-TSS (NM_030189)	promoter-TSS (NM_030189)	-15	NM_030189	78806	Mm.374844	NM_030189	ENSMUSG00000028801	Stpg1	4930403G18Rik|4930555I21Rik|Mapo2	sperm tail PG rich repeat containing 1	protein-coding
mm_48091.1	chr5	136987857	136987866	-	1	NA	promoter-TSS (NM_001310748)	promoter-TSS (NM_001310748)	98	NM_027318	70103	Mm.273147	NM_027318	ENSMUSG00000059518	Znhit1	2700001K05Rik|ZNFN4A1	zinc finger, HIT domain containing 1	protein-coding
mm_2586.1	chr1	118675573	118675596	+	1	NA	exon (NM_023755, exon 14 of 15)	exon (NM_023755, exon 14 of 15)	47639	NM_023755	81879	Mm.24621	NM_023755	ENSMUSG00000026380	Tfcp2l1	1810030F05Rik|4932442M07Rik|AA575098|Cp2l1|Crtr-1|D930018N21Rik|LBP-9|Tcfcp2l1	transcription factor CP2-like 1	protein-coding
mm_166038.1	chr4	129491267	129491274	+	1	NA	promoter-TSS (NM_080442)	promoter-TSS (NM_080442)	80	NM_001085491	68233	Mm.424983	NM_001085491	ENSMUSG00000078554	Fam229a	1700125D06Rik	family with sequence similarity 229, member A	protein-coding
mm_164798.1	chr18	21026305	21026308	+	1	NA	3' UTR (NM_207623, exon 7 of 7)	3' UTR (NM_207623, exon 7 of 7)	24349	NM_207623	56515	Mm.253542	NM_019706	ENSMUSG00000024317	Rnf138	2410015A17Rik|2810480D20Rik|STRIN|Trif|Trif-d	ring finger protein 138	protein-coding
mm_140671.1	chr17	12940318	12940370	-	1	NA	promoter-TSS (NM_153151)	promoter-TSS (NM_153151)	52	NM_153151	224530	Mm.490312	NM_153151	ENSMUSG00000062480	Acat3	ACTL	acetyl-Coenzyme A acetyltransferase 3	protein-coding
mm_168682.1	chr11	95761448	95761454	+	1	NA	intron (NM_201609, intron 4 of 4)	intron (NM_201609, intron 4 of 4)	12384	NM_201609	268469	Mm.389038	NM_201609	ENSMUSG00000075595	Zfp652	9530033F24Rik|ZNF652	zinc finger protein 652	protein-coding
mm_64774.1	chr7	4996123	4996141	-	1	NA	promoter-TSS (NM_026741)	promoter-TSS (NM_026741)	-31	NM_026741	68490	Mm.76400	NM_026741	ENSMUSG00000051550	Zfp579	1110003A17Rik|Znf579	zinc finger protein 579	protein-coding
mm_13945.1	chr2	121289723	121289736	+	1	NA	exon (NM_032393, exon 1 of 7)	exon (NM_032393, exon 1 of 7)	127	NM_032393	17754	Mm.36501	NM_032393	ENSMUSG00000027254	Map1a	6330416M19Rik|AI853608|Mtap-1|Mtap1|Mtap1a|moth1	microtubule-associated protein 1 A	protein-coding
mm_36230.1	chr4	63149451	63149466	-	1	NA	exon (NM_007443, exon 5 of 10)	exon (NM_007443, exon 5 of 10)	4714	NM_007443	11699	Mm.2197	NM_007443	ENSMUSG00000028356	Ambp	AI194774|ASPI|HI-30|Intin4|Itil|UTI	alpha 1 microglobulin/bikunin	protein-coding
mm_136690.1	chr17	6828470	6828483	+	1	NA	Intergenic	Intergenic	-45696	NM_009510	22350	Mm.277812	NM_009510	ENSMUSG00000052397	Ezr	AW146364|R75297|Vil2|p81	ezrin	protein-coding
mm_45702.1	chr5	83354947	83354973	-	1	NA	exon (NM_153801, exon 1 of 12)	exon (NM_153801, exon 1 of 12)	235	NM_153801	243078	Mm.126783	NM_153801	ENSMUSG00000049537	Tecrl	D330017N19Rik|Srd5a2l2	trans-2,3-enoyl-CoA reductase-like	protein-coding
mm_76768.1	chr8	95807459	95807471	-	1	NA	promoter-TSS (NM_178078)	promoter-TSS (NM_178078)	-3	NM_001205226	234594	Mm.259220	NM_153164	ENSMUSG00000036550	Cnot1	6030411K04Rik|AA815922|D830048B13	CCR4-NOT transcription complex, subunit 1	protein-coding
mm_119264.1	chr14	34017075	34017089	+	1	NA	Intergenic	Intergenic	-23996	NM_001034880	432838	Mm.318383	NM_001034880	ENSMUSG00000072624	Gm5460	EG432838	predicted gene 5460	protein-coding
mm_23277.1	chr3	51661002	51661005	+	1	NA	promoter-TSS (NM_174995)	promoter-TSS (NM_174995)	-176	NM_174995	211666	Mm.24679	NM_174995	ENSMUSG00000074604	Mgst2	GST2|MGST-II	microsomal glutathione S-transferase 2	protein-coding
mm_159436.1	chr3	119740783	119740783	-	1	NA	intron (NM_001310711, intron 7 of 13)	intron (NM_001310711, intron 7 of 13)	42605	NM_001310711	56195	Mm.29966	NM_019550	ENSMUSG00000028134	Ptbp2	Ptb2|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding
mm_42446.1	chr5	115432008	115432018	+	1	NA	intron (NM_008629, intron 4 of 14)	intron (NM_008629, intron 4 of 14)	2328	NM_008629	17690	Mm.5077	NM_008629	ENSMUSG00000054256	Msi1	Msi1h|Musahi1|m-Msi-1	musashi RNA-binding protein 1	protein-coding
mm_68344.1	chr7	106506515	106506533	-	1	NA	Intergenic	Intergenic	-65451	NR_003967	209380	Mm.461779	NM_001001318		Gm4759	EG209380	GTPase, very large interferon inducible 1 pseudogene	pseudo
mm_3401.1	chr1	143739574	143739642	+	1	NA	promoter-TSS (NM_023505)	promoter-TSS (NM_023505)	-7	NM_023505	69367	Mm.272727	NM_023505	ENSMUSG00000018196	Glrx2	1700010P22Rik|AI645710|Grx2	glutaredoxin 2 (thioltransferase)	protein-coding
mm_149450.1	chr19	11491904	11491908	+	1	NA	promoter-TSS (NM_001164202)	promoter-TSS (NM_001164202)	-132	NM_001164202	666926	Mm.486382	NM_001164202	ENSMUSG00000058470	Gm8369	EG666926	predicted gene 8369	protein-coding
mm_128034.1	chr15	25363972	25363983	-	1	NA	3' UTR (NM_027395, exon 2 of 2)	3' UTR (NM_027395, exon 2 of 2)	49787	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	brain abundant, membrane attached signal protein 1	protein-coding
mm_61443.1	chr7	75475088	75475090	+	1	NA	intron (NM_029332, intron 1 of 36)	intron (NM_029332, intron 1 of 36)	19555	NM_029332	75547	Mm.216107	NM_029332	ENSMUSG00000066406	Akap13	1700026G02Rik|5730522G15Rik|5830460E08Rik|AKAP-13|AKAP-Lbc|BRX|Ht31|LBC|PROTO-LB|PROTO-LBC	A kinase (PRKA) anchor protein 13	protein-coding
mm_99708.1	chr11	106216929	106216968	+	1	NA	promoter-TSS (NM_026009)	promoter-TSS (NM_026009)	22	NM_028074	72047	Mm.41367	NM_028074	ENSMUSG00000020705	Ddx42	1810047H21Rik|AW319508|AW556242|B430002H05Rik|RHELP|RNAHP|SF3b125	DEAD (Asp-Glu-Ala-Asp) box polypeptide 42	protein-coding
mm_15720.1	chr2	164074123	164074218	+	1	NA	promoter-TSS (NM_021420)	promoter-TSS (NM_021420)	-8	NM_021420	58231	Mm.234472	NM_021420	ENSMUSG00000018209	Stk4	AI447339|AU020804|Kas-2|Mst1|Ysk3	serine/threonine kinase 4	protein-coding
mm_79678.1	chr9	59750933	59750935	+	1	NA	promoter-TSS (NM_001172071)	promoter-TSS (NM_001172071)	-240	NM_173018	270163	Mm.249545	NM_173018	ENSMUSG00000039585	Myo9a	4732465J09Rik|C130068I12Rik|C230003M11	myosin IXa	protein-coding
mm_114931.1	chr13	95765122	95765138	+	1	NA	intron (NM_027711, intron 2 of 35)	intron (NM_027711, intron 2 of 35)	68210	NM_010170	14064	Mm.440952	NM_010170	ENSMUSG00000021675	F2rl2	F730031A08|PAR3	coagulation factor II (thrombin) receptor-like 2	protein-coding
mm_13457.1	chr2	105668944	105668950	+	1	NA	promoter-TSS (NM_001244198)	promoter-TSS (NM_001244198)	51	NM_001244201	18508	Mm.3608	NM_013627	ENSMUSG00000027168	Pax6	1500038E17Rik|AEY11|Dey|Gsfaey11|Pax-6|Sey	paired box 6	protein-coding
mm_77723.1	chr8	126839427	126839440	-	1	NA	Intergenic	Intergenic	106488	NM_024214	67952	Mm.6932	NM_024214	ENSMUSG00000093904	Tomm20	1810060K07Rik|BB284719|Gm19268|MAS20|MOM19|TOM20|mKIAA0016	translocase of outer mitochondrial membrane 20 homolog (yeast)	protein-coding
mm_147613.1	chr18	57244115	57244123	-	1	NA	intron (NM_001001979, intron 7 of 24)	intron (NM_001001979, intron 7 of 24)	-110614	NM_028447	73137	Mm.29889	NM_028447	ENSMUSG00000024594	Prrc1	1190002C06Rik|2310058D16Rik|3110038B19Rik|9430085A19Rik	proline-rich coiled-coil 1	protein-coding
mm_155459.1	chrX	73503118	73503135	+	1	NA	promoter-TSS (NM_177236)	promoter-TSS (NM_177236)	40	NM_177236	320707	Mm.210095	NM_177236	ENSMUSG00000031376	Atp2b3	6430519O13Rik|Pmca3	ATPase, Ca++ transporting, plasma membrane 3	protein-coding
mm_104683.1	chr11	97716908	97716923	-	1	NA	3' UTR (NM_054051, exon 10 of 10)	3' UTR (NM_054051, exon 10 of 10)	13481	NM_011971	26446	Mm.21874	NM_011971	ENSMUSG00000069744	Psmb3	AL033320|C10-II	proteasome (prosome, macropain) subunit, beta type 3	protein-coding
mm_47729.1	chr5	130171571	130171590	-	1	NA	promoter-TSS (NM_001199059)	promoter-TSS (NM_001199059)	-239	NM_001199059	56715	Mm.288639	NM_019983	ENSMUSG00000025340	Rabgef1	Rab5ef|Rabex5|Rin2	RAB guanine nucleotide exchange factor (GEF) 1	protein-coding
mm_143212.1	chr17	62881678	62881729	-	1	NA	promoter-TSS (NM_207654)	promoter-TSS (NM_207654)	-386	NM_010109	13640	Mm.7978	NM_010109	ENSMUSG00000048915	Efna5	AL-1|AV158822|EFL-5|Ephrin-A5|Epl7|LERK-7|RAGS	ephrin A5	protein-coding
mm_98543.1	chr11	95010245	95010276	+	1	NA	5' UTR (NM_146025, exon 1 of 10)	5' UTR (NM_146025, exon 1 of 10)	381	NM_146025	217125	Mm.297199	NM_146025	ENSMUSG00000047181	Samd14	AI839049|AI854782|BC034054	sterile alpha motif domain containing 14	protein-coding
mm_77956.1	chr9	7571458	7571489	+	1	NA	promoter-TSS (NM_001310717)	promoter-TSS (NM_001310717)	77	NM_001310717	234911	Mm.334940	NM_001030289	ENSMUSG00000070323	Mmp27	Gm180	matrix metallopeptidase 27	protein-coding
mm_146519.1	chr18	4336290	4336298	-	1	NA	intron (NM_007746, intron 5 of 7)	intron (NM_007746, intron 5 of 7)	16659	NM_007746	26410	Mm.3275	NM_007746	ENSMUSG00000024235	Map3k8	Cot|Cot/Tpl2|Est|Estf|Tpl-2|Tpl2|c-COT	mitogen-activated protein kinase kinase kinase 8	protein-coding
mm_52587.1	chr6	116652231	116652263	+	1	NA	exon (NM_001166580, exon 2 of 2)	exon (NM_001166580, exon 2 of 2)	1563	NM_001166580	213393	Mm.38231	NM_145980	ENSMUSG00000048489	8430408G22Rik	Depp|Fseg	RIKEN cDNA 8430408G22 gene	protein-coding
mm_58050.1	chr6	136835427	136835447	-	1	NA	promoter-TSS (NM_001039558)	promoter-TSS (NM_001039558)	13	NM_001039558	654818	Mm.386899	NM_001039558	ENSMUSG00000043298	Smco3	C030030A07Rik	single-pass membrane protein with coiled-coil domains 3	protein-coding
mm_170526.1	chr19	33456508	33456510	-	1	NA	Intergenic	RLTR9D|LTR|ERVK	61261	NM_001323386	628236		NM_001323386	ENSMUSG00000079344	Lipo4	Gm6857	lipase, member O4	protein-coding
mm_47512.1	chr5	124075753	124075794	-	1	NA	intron (NM_019875, intron 9 of 11)	intron (NM_019875, intron 9 of 11)	20025	NM_019875	56325	Mm.254839	NM_019875	ENSMUSG00000029408	Abcb9	TAPL|mKIAA1520	ATP-binding cassette, sub-family B (MDR/TAP), member 9	protein-coding
mm_146567.1	chr18	6490902	6490926	-	1	NA	promoter-TSS (NM_001276350)	promoter-TSS (NM_001276350)	-57	NM_027497	13831	Mm.312133	NM_007935	ENSMUSG00000024240	Epc1	2400007E14Rik|5730566F07Rik|A930032N02Rik|mir-1893	enhancer of polycomb homolog 1 (Drosophila)	protein-coding
mm_83984.1	chr9	57421374	57421386	-	1	NA	intron (NM_176831, intron 3 of 6)	intron (NM_176831, intron 3 of 6)	18734	NM_176831	66812	Mm.250508	NM_176831	ENSMUSG00000063849	Ppcdc	1810057I13Rik|8430432M10Rik	phosphopantothenoylcysteine decarboxylase	protein-coding
mm_112492.1	chr13	6558469	6558474	+	1	NA	intron (NM_145131, intron 9 of 26)	AT_rich|Low_complexity|Low_complexity	10314	NM_145131	69617	Mm.41933	NM_145131	ENSMUSG00000021193	Pitrm1	2310012C15Rik|AA410010|MP-1|MP1|Ntup1|PreP|mKIAA1104	pitrilysin metallepetidase 1	protein-coding
mm_47016.1	chr5	115489554	115489583	-	1	NA	Intergenic	U4|snRNA|snRNA	-5084	NM_133760	75387	Mm.332616	NM_133760	ENSMUSG00000029524	Sirt4	4930596O17Rik	sirtuin 4	protein-coding
mm_103765.1	chr11	81593115	81593118	-	1	NA	intron (NM_001034013, intron 1 of 9)	intron (NM_001034013, intron 1 of 9)	-19577	NM_001033765	237880	Mm.435528	NM_001033765		1700071K01Rik	-	RIKEN cDNA 1700071K01 gene	protein-coding
mm_151890.1	chr19	5798751	5798755	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	-2772	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_150536.1	chr19	39300067	39300070	+	1	NA	intron (NM_007815, intron 3 of 8)	L1_Mus3|LINE|L1	12983	NM_007815	13095	Mm.20764	NM_007815	ENSMUSG00000003053	Cyp2c29	AHOH|AHOHase|AI159681|AI196010|Ah-2|Ahh-1|Cyp2c|P450-2C	cytochrome P450, family 2, subfamily c, polypeptide 29	protein-coding
mm_170564.1	chr19	46957940	46957940	-	1	NA	intron (NM_001164363, intron 1 of 17)	Lx9|LINE|L1	4411	NM_029810	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_146930.1	chr18	31998131	31998157	-	1	NA	exon (NM_032394, exon 14 of 47)	exon (NM_032394, exon 14 of 47)	38787	NM_032394	17922	Mm.440013	NM_032394	ENSMUSG00000024388	Myo7b	-	myosin VIIB	protein-coding
mm_154022.1	chr19	53390536	53390544	-	1	NA	promoter-TSS (NM_172429)	promoter-TSS (NM_172429)	33	NM_172429	76479	Mm.313687	NM_172429	ENSMUSG00000025024	Smndc1	2410004J23Rik|4933440I19Rik	survival motor neuron domain containing 1	protein-coding
mm_3495.1	chr1	150106610	150106616	+	1	NA	3' UTR (NM_011198, exon 10 of 10)	3' UTR (NM_011198, exon 10 of 10)	6582	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_151774.1	chr19	5302501	5302502	-	1	NA	5' UTR (NM_001024717, exon 2 of 3)	5' UTR (NM_001024717, exon 2 of 3)	4170	NM_001024717	545276	Mm.447174	NM_001024717	ENSMUSG00000047658	Gal3st3	-	galactose-3-O-sulfotransferase 3	protein-coding
mm_21979.1	chr2	167383560	167383572	-	1	NA	Intergenic	B1_Mur1|SINE|Alu	-34388	NM_019835	56336	Mm.200886	NM_019835	ENSMUSG00000017929	B4galt5	9430078I07Rik|AW049941|AW539721	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 5	protein-coding
mm_166464.1	chr5	140830312	140830321	-	1	NA	5' UTR (NM_010302, exon 1 of 4)	5' UTR (NM_010302, exon 1 of 4)	115	NM_010302	14673	Mm.370185	NM_010302	ENSMUSG00000000149	Gna12	AI414047|AI504261|Galpha12	guanine nucleotide binding protein, alpha 12	protein-coding
mm_172109.1	chr6	3200879	3200886	+	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	-87637	NR_036696	667335	Mm.380219	NR_036696	ENSMUSG00000106779	Gm8579	EG667335	spermatogenesis associated glutamate (E)-rich protein 4a pseudogene	pseudo
mm_74539.1	chr8	9976216	9976254	-	1	NA	promoter-TSS (NM_176953)	promoter-TSS (NM_176953)	88	NM_176953	319583	Mm.80584	NM_176953	ENSMUSG00000049717	Lig4	5830471N16Rik|tiny	ligase IV, DNA, ATP-dependent	protein-coding
mm_92735.1	chr10	80918049	80918060	-	1	NA	exon (NM_010722, exon 1 of 12)	exon (NM_010722, exon 1 of 12)	191	NM_010722	16907	Mm.7362	NM_010722	ENSMUSG00000062075	Lmnb2	-	lamin B2	protein-coding
mm_24011.1	chr3	87377957	87377960	+	1	NA	intron (NM_001310545, intron 1 of 10)	intron (NM_001310545, intron 1 of 10)	1571	NM_001136236	229499	Mm.255203	NM_153090	ENSMUSG00000059994	Fcrl1	A230020G22Rik|Bxmas1|Bxmh1|Bxmh1b|Fcrh1|Fcrh1l|Fcrh1s|Ifgp1	Fc receptor-like 1	protein-coding
mm_80264.1	chr9	72925084	72925097	+	1	NA	promoter-TSS (NM_028116)	promoter-TSS (NM_028116)	-560	NM_028116	72135	Mm.273605	NM_028116	ENSMUSG00000034910	Pygo1	2600014C22Rik	pygopus 1	protein-coding
mm_67843.1	chr7	98562334	98562351	-	1	NA	Intergenic	Intergenic	68120	NM_001113379	434215	Mm.323057	NM_001113379	ENSMUSG00000090958	Lrrc32	AI426318|D11S833Eh|D7H11S833E|EG434215|Garp	leucine rich repeat containing 32	protein-coding
mm_37866.1	chr4	132345687	132345708	-	1	NA	promoter-TSS (NM_133878)	promoter-TSS (NM_133878)	53	NM_001197082	100088	Mm.255045	NM_133878	ENSMUSG00000028896	Rcc1	4931417M11Rik|AI326872|Chc1	regulator of chromosome condensation 1	protein-coding
mm_78822.1	chr9	44093866	44093885	+	1	NA	3' UTR (NM_198091, exon 12 of 12)	3' UTR (NM_198091, exon 12 of 12)	-7895	NM_001190314	259172	Mm.227110	NM_147126	ENSMUSG00000034739	Mfrp	rd6	membrane frizzled-related protein	protein-coding
mm_149032.1	chr19	8802540	8802558	+	1	NA	promoter-TSS (NM_001098237)	promoter-TSS (NM_001098237)	19	NM_001098237	75291	Mm.23423	NM_133759	ENSMUSG00000071661	Zbtb3	4930563M09Rik	zinc finger and BTB domain containing 3	protein-coding
mm_66009.1	chr7	30563265	30563275	-	1	NA	promoter-TSS (NM_025498)	promoter-TSS (NM_025498)	-70	NM_170760	233073	Mm.34790	NM_170760	ENSMUSG00000078765	U2af1l4	AA407033|AF419339|AI451269|AW553050|U2af26	U2 small nuclear RNA auxiliary factor 1-like 4	protein-coding
mm_47623.1	chr5	125277157	125277165	-	1	NA	TTS (NM_001205082)	TTS (NM_001205082)	63933	NM_016741	20778	Mm.282242	NM_016741	ENSMUSG00000037936	Scarb1	AI120173|CD36|Cd36l1|Chohd1|Cla-1|Cla1|D5Ertd460e|Hdlq1|Hlb398|SR-B1|SR-BI|SRBI|Srb1|mSR-BI	scavenger receptor class B, member 1	protein-coding
mm_114041.1	chr13	53448252	53448257	+	1	NA	intron (NR_037991, intron 6 of 7)	intron (NR_037991, intron 6 of 7)	24526	NM_013601	17702	Mm.1763	NM_013601	ENSMUSG00000021469	Msx2	BB122635|Hox-8|Hox8|Hox8.1	msh homeobox 2	protein-coding
mm_27948.1	chr3	79825466	79825478	-	1	NA	intron (NM_027495, intron 7 of 11)	intron (NM_027495, intron 7 of 11)	17190	NM_027495	70652	Mm.46635	NM_027495	ENSMUSG00000027956	Tmem144	1110057I03Rik|5730537D05Rik	transmembrane protein 144	protein-coding
mm_9547.1	chr1	173921249	173921298	-	1	NA	3' UTR (NM_001302650, exon 9 of 9)	3' UTR (NM_001302650, exon 9 of 9)	-8227	NM_001033450	381308	Mm.490248	NM_001033450	ENSMUSG00000026536	Ifi211	A730048F03|Ifi205b|Mnda|ifi-205-B	interferon activated gene 211	protein-coding
mm_9638.1	chr1	177064485	177064505	-	1	NA	intron (NM_011785, intron 8 of 12)	Lx3B|LINE|L1	184272	NM_011785	23797	Mm.235194	NM_011785	ENSMUSG00000019699	Akt3	AI851531|D930002M15Rik|Nmf350	thymoma viral proto-oncogene 3	protein-coding
mm_156357.1	chrX	139335891	139335901	+	1	NA	intron (NM_011635, intron 1 of 2)	intron (NM_011635, intron 1 of 2)	2213	NM_011635	22037	Mm.1297	NM_011635	ENSMUSG00000051257	Trap1a	Tra-P1A	tumor rejection antigen P1A	protein-coding
mm_103864.1	chr11	83429808	83429832	-	1	NA	promoter-TSS (NM_001013759)	promoter-TSS (NM_001013759)	-299	NM_001013759	237891	Mm.340523	NM_001013759	ENSMUSG00000020686	Gas2l2	-	growth arrest-specific 2 like 2	protein-coding
mm_20867.1	chr2	148441772	148441829	-	1	NA	exon (NM_010740, exon 1 of 2)	exon (NM_010740, exon 1 of 2)	1735	NM_010740	17064	Mm.681	NM_010740	ENSMUSG00000027435	Cd93	6030404G09Rik|AA145088|AA4.1|AW555904|C1qr1|C1qrp|Ly68	CD93 antigen	protein-coding
mm_79918.1	chr9	65551288	65551303	+	1	NA	Intergenic	Intergenic	28792	NM_153119	102595	Mm.247303	NM_153119	ENSMUSG00000050721	Plekho2	AI840980|Plekhq1	pleckstrin homology domain containing, family O member 2	protein-coding
mm_1418.1	chr1	67160892	67160916	+	1	NA	exon (NM_001080809, exon 12 of 38)	exon (NM_001080809, exon 12 of 38)	37877	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_58396.1	chr7	3213808	3213822	+	1	NA	Intergenic	Intergenic	-4811	NR_029640	100049710		NR_029640	ENSMUSG00000077815	Mir290a	Mir290|Mirn290|mir-290a|mmu-miR-290|mmu-mir-290a	microRNA 290a	ncRNA
mm_123109.1	chr14	55884251	55884255	-	1	NA	promoter-TSS (NM_019820)	promoter-TSS (NM_019820)	3	NM_019820	56410	Mm.97163	NM_019820	ENSMUSG00000040380	Cbln3	-	cerebellin 3 precursor protein	protein-coding
mm_136786.1	chr17	10807828	10807841	+	1	NA	intron (NM_027032, intron 1 of 4)	intron (NM_027032, intron 1 of 4)	32357	NM_027032	69310	Mm.18889	NM_027032	ENSMUSG00000037196	Pacrg	1700008H23Rik	PARK2 co-regulated	protein-coding
mm_156205.1	chrX	134465977	134465979	+	1	NA	exon (NM_028958, exon 10 of 13)	exon (NM_028958, exon 10 of 13)	10512	NM_028958	74469	Mm.103259	NM_028958	ENSMUSG00000009596	Taf7l	4933438I11Rik|Taf2q	TATA-box binding protein associated factor 7 like	protein-coding
mm_144627.1	chr18	32938917	32938928	+	1	NA	promoter-TSS (NM_009793)	promoter-TSS (NM_009793)	-119	NM_009793	12326	Mm.222329	NM_009793	ENSMUSG00000038128	Camk4	A430110E23Rik|AI666733|CaMKIV|CaMKIV/Gr|D18Bwg0362e	calcium/calmodulin-dependent protein kinase IV	protein-coding
mm_46669.1	chr5	108775022	108775032	-	1	NA	Intergenic	CpG	11185	NR_040691	73295	Mm.416858	NR_040691	ENSMUSG00000101762	1700047L14Rik	-	RIKEN cDNA 1700047L14 gene	ncRNA
mm_118059.1	chr13	102693376	102693381	-	1	NA	promoter-TSS (NM_008533)	promoter-TSS (NM_008533)	-180	NM_008533	17079	Mm.373974	NM_008533	ENSMUSG00000021624	Cd180	F630107B15|Ly78|RP105	CD180 antigen	protein-coding
mm_64228.1	chr7	141691199	141691209	+	1	NA	exon (NM_023566, exon 2 of 46)	exon (NM_023566, exon 2 of 46)	864	NM_023566	17831	Mm.2041	NM_023566		Muc2	2010015E03Rik|MCM|wnn	mucin 2	protein-coding
mm_103202.1	chr11	70652165	70652194	-	1	NA	TTS (NM_001316728)	TTS (NM_001316728)	2471	NM_011072	18643	Mm.2647	NM_011072	ENSMUSG00000018293	Pfn1	Pfn	profilin 1	protein-coding
mm_97676.1	chr11	79962590	79962611	+	1	NA	promoter-TSS (NM_144826)	promoter-TSS (NM_144826)	-213	NM_144826	216987	Mm.274961	NM_144826	ENSMUSG00000035575	Utp6	4732497O03Rik|HCA66	UTP6 small subunit processome component	protein-coding
mm_122434.1	chr14	45218984	45218997	-	1	NA	promoter-TSS (NM_027518)	promoter-TSS (NM_027518)	435	NM_172597	70561	Mm.28129	NM_172597	ENSMUSG00000021830	Txndc16	5730420B22Rik|C77647	thioredoxin domain containing 16	protein-coding
mm_146618.1	chr18	10100947	10100955	-	1	NA	exon (NM_009071, exon 17 of 33)	exon (NM_009071, exon 17 of 33)	-70802	NM_001038589	59025	Mm.329277	NM_021522	ENSMUSG00000047879	Usp14	2610005K12Rik|2610037B11Rik|AW107924|C78769|ax|nmf375	ubiquitin specific peptidase 14	protein-coding
mm_74044.1	chr8	122006916	122006936	+	1	NA	intron (NM_001285983, intron 8 of 12)	intron (NM_001285983, intron 8 of 12)	28902	NR_106096	102466915		NR_106096	ENSMUSG00000099140	Mir7237	Gm27482|mmu-mir-7237	microRNA 7237	ncRNA
mm_146348.1	chr18	82543950	82543952	+	1	NA	intron (NM_001025245, intron 3 of 3)	intron (NM_001025245, intron 3 of 3)	-10512	NM_001025256	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_132325.1	chr16	33794346	33794356	+	1	NA	intron (NM_010739, intron 1 of 12)	intron (NM_010739, intron 1 of 12)	314	NM_010739	17063	Mm.3177	NM_010739	ENSMUSG00000022824	Muc13	114/A10|14/A10|AI159736|Lrrp|Ly64|NJ-1	mucin 13, epithelial transmembrane	protein-coding
mm_12920.1	chr2	84952581	84952583	+	1	NA	intron (NM_021398, intron 10 of 12)	L1MC5a|LINE|L1	15936	NM_021398	58207	Mm.290729	NM_021398	ENSMUSG00000027074	Slc43a3	Eeg1|SEEEG-1	solute carrier family 43, member 3	protein-coding
mm_165530.1	chr2	178455538	178455543	+	1	NA	intron (NM_001291189, intron 3 of 13)	intron (NM_001291189, intron 3 of 13)	25025	NM_198656	381409	Mm.330860	NM_198656	ENSMUSG00000039155	Cdh26	Gm1010	cadherin-like 26	protein-coding
mm_169726.1	chr15	80781420	80781428	-	1	NA	intron (NM_144812, intron 3 of 24)	RLTR23|LTR|ERV1	-17186	NM_177124	213988	Mm.131328	NM_144812	ENSMUSG00000047888	Tnrc6b	2700090M07Rik|A730065C02Rik|AI848765|D230019K20Rik	trinucleotide repeat containing 6b	protein-coding
mm_168863.1	chr12	30911549	30911549	-	1	NA	promoter-TSS (NM_013709)	promoter-TSS (NM_013709)	63	NM_021330	11431	Mm.359831	NM_021330	ENSMUSG00000044573	Acp1	4632432E04Rik|AI427468|Acp-1|LMW-PTP|Lmptp	acid phosphatase 1, soluble	protein-coding
mm_9839.1	chr1	184034297	184034308	-	1	NA	promoter-TSS (NM_028516)	promoter-TSS (NM_028516)	-159	NM_022019	63953	Mm.404024	NM_022019	ENSMUSG00000039384	Dusp10	2610306G15Rik|AI158871|MKP-5|MKP5	dual specificity phosphatase 10	protein-coding
mm_115972.1	chr13	24094465	24094539	-	1	NA	exon (NM_026825, exon 22 of 38)	exon (NM_026825, exon 22 of 38)	-103288	NM_145399	214189	Mm.255667	NM_145399	ENSMUSG00000021337	Scgn	-	secretagogin, EF-hand calcium binding protein	protein-coding
mm_135403.1	chr16	44745932	44745954	-	1	NA	intron (NM_001159329, intron 1 of 5)	CpG	420	NM_001159329	66067	Mm.34520	NM_025332	ENSMUSG00000022668	Gtpbp8	0610037H22Rik	GTP-binding protein 8 (putative)	protein-coding
mm_127161.1	chr15	98634744	98634778	+	1	NA	promoter-TSS (NM_007581)	promoter-TSS (NM_007581)	-6	NM_007581	12297	Mm.3544	NM_007581	ENSMUSG00000003352	Cacnb3	Beta3|CAB3|Ca(v)beta3|Cchb3	calcium channel, voltage-dependent, beta 3 subunit	protein-coding
mm_81144.1	chr9	106839699	106839701	+	1	NA	intron (NM_001015507, intron 8 of 22)	intron (NM_001015507, intron 8 of 22)	17724	NM_001015507	321006	Mm.440089	NM_001015507	ENSMUSG00000040325	Vprbp	AI447437|B930007L02Rik|mKIAA0800	Vpr (HIV-1) binding protein	protein-coding
mm_59738.1	chr7	28814010	28814023	+	1	NA	exon (NM_177301, exon 3 of 13)	exon (NM_177301, exon 3 of 13)	3126	NM_177301	15388	Mm.9043	NM_177301	ENSMUSG00000015165	Hnrnpl	C79783|D830027H13Rik|Hnrpl	heterogeneous nuclear ribonucleoprotein L	protein-coding
mm_71625.1	chr8	57436433	57436446	+	1	NA	Intergenic	Intergenic	-19484	NM_009136	20284	Mm.12886	NM_009136	ENSMUSG00000031610	Scrg1	AW124307	scrapie responsive gene 1	protein-coding
mm_106809.1	chr12	6005799	6005799	+	1	NA	Intergenic	Intergenic	629297	NR_015579	72669	Mm.10434	NM_028318		2810032G03Rik	AI461720	RIKEN cDNA 2810032G03 gene	ncRNA
mm_15712.1	chr2	164018076	164018089	+	1	NA	3' UTR (NM_018753, exon 6 of 6)	3' UTR (NM_018753, exon 6 of 6)	-7142	NM_001114079	381404	Mm.82301	NM_001114079	ENSMUSG00000054582	Pabpc1l	1810053B01Rik|Epab	poly(A) binding protein, cytoplasmic 1-like	protein-coding
mm_171634.1	chr4	20971765	20971768	-	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	-193098	NM_172987	269513	Mm.317473	NM_172987	ENSMUSG00000055761	Nkain3	C530048M05|E130310K16Rik	Na+/K+ transporting ATPase interacting 3	protein-coding
mm_36000.1	chr4	56673979	56673989	-	1	NA	Intergenic	Intergenic	67441	NM_025271	11471	Mm.251434	NM_025271	ENSMUSG00000070980	Actl7b	Tact1	actin-like 7b	protein-coding
mm_126489.1	chr15	81626365	81626389	+	1	NA	exon (NM_177821, exon 13 of 31)	exon (NM_177821, exon 13 of 31)	-37512	NM_001289712	214669	Mm.280768	NM_145993	ENSMUSG00000022394	L3mbtl2	4732493N06Rik|M4mbt	l(3)mbt-like 2 (Drosophila)	protein-coding
mm_155649.1	chrX	85776935	85776958	+	1	NA	promoter-TSS (NM_212444)	promoter-TSS (NM_212444)	-127	NM_001294138	14933	Mm.246682	NM_008194	ENSMUSG00000025059	Gk	D930012N15Rik|Gyk	glycerol kinase	protein-coding
mm_147753.1	chr18	61211479	61211494	-	1	NA	5' UTR (NM_007885, exon 1 of 4)	5' UTR (NM_007885, exon 1 of 4)	110	NM_007885	13521	Mm.24803	NM_007885	ENSMUSG00000034320	Slc26a2	Dtd|ST-OB	solute carrier family 26 (sulfate transporter), member 2	protein-coding
mm_64927.1	chr7	16273928	16273960	-	1	NA	promoter-TSS (NM_001136270)	promoter-TSS (NM_001136270)	-252	NM_001136270	66300	Mm.218698	NM_001136270	ENSMUSG00000091811	Inafm1	2610014I16Rik|Prr24	InaF motif containing 1	protein-coding
mm_169573.1	chr15	21656481	21656498	+	1	NA	Intergenic	(TTAGGG)n|Simple_repeat|Simple_repeat	545037	NM_001008420	215654	Mm.300909	NM_001008420	ENSMUSG00000040452	Cdh12	Cdhb	cadherin 12	protein-coding
mm_148255.1	chr18	80743034	80743040	-	1	NA	intron (NM_001201569, intron 26 of 29)	intron (NM_001201569, intron 26 of 29)	-29966	NM_001164109	18018	Mm.329560	NM_016791	ENSMUSG00000033016	Nfatc1	2210017P03Rik|AI449492|AV076380|NF-ATc|NFAT2|NFATc|Nfatcb	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 1	protein-coding
mm_32279.1	chr4	102833678	102833679	+	1	NA	intron (NM_001285852, intron 1 of 25)	intron (NM_001285852, intron 1 of 25)	73543	NM_001285859	73094	Mm.54201	NM_144906	ENSMUSG00000028524	Sgip1	3110007P09Rik|SGIP1alpha|gag	SH3-domain GRB2-like (endophilin) interacting protein 1	protein-coding
mm_134825.1	chr16	26073956	26073987	-	1	NA	intron (NM_173379, intron 1 of 14)	RSINE1|SINE|B4	31813	NM_173379	210530	Mm.326869	NM_173379	ENSMUSG00000038168	P3h2	4832416N06|AW553532|Leprel1|Mlat4	prolyl 3-hydroxylase 2	protein-coding
mm_146040.1	chr18	69592945	69592953	+	1	NA	intron (NM_013685, intron 8 of 19)	(GA)n|Simple_repeat|Simple_repeat	247228	NM_001083967	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding
mm_19217.1	chr2	84650470	84650487	-	1	NA	promoter-TSS (NM_001085453)	promoter-TSS (NM_001085453)	32	NM_001085453	12388	Mm.35738	NM_007615	ENSMUSG00000034101	Ctnnd1	AA409437|AU019353|Catns|Ctnnd|P120|mKIAA0384	catenin (cadherin associated protein), delta 1	protein-coding
mm_112543.1	chr13	11939484	11939491	+	1	NA	intron (NM_023868, intron 2 of 104)	intron (NM_023868, intron 2 of 104)	167458	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding
mm_121724.1	chr14	16575457	16575501	-	1	NA	promoter-TSS (NM_001289762)	promoter-TSS (NM_001289762)	-3	NM_001289762	218772	Mm.259318	NM_011243	ENSMUSG00000017491	Rarb	A830025K23|Hap|Nr1b2	retinoic acid receptor, beta	protein-coding
mm_33788.1	chr4	134923617	134923628	+	1	NA	promoter-TSS (NM_023665)	promoter-TSS (NM_023665)	-3	NM_023665	27981	Mm.331964	NM_023665	ENSMUSG00000037266	Rsrp1	2700043I21Rik|D4Ucla2|D4Wsu53e	arginine/serine rich protein 1	protein-coding
mm_88676.1	chr10	80047010	80047030	+	1	NA	promoter-TSS (NR_110342)	promoter-TSS (NR_110342)	-146	NR_110342	625249	Mm.332810	NM_008162	ENSMUSG00000075706	Gpx4	GPx-4|GSHPx-4|PHGPx|mtPHGPx|snGPx	glutathione peroxidase 4	protein-coding
mm_162941.1	chr10	128492895	128492901	-	1	NA	intron (NM_001317217, intron 2 of 6)	intron (NM_001317217, intron 2 of 6)	111	NM_001317220	17904	Mm.337074	NM_010860	ENSMUSG00000090841	Myl6	ESMLC|LC17|LC17-GI|MLC-3|MLC1SM|Myln	myosin, light polypeptide 6, alkali, smooth muscle and non-muscle	protein-coding
mm_161799.1	chr17	54298805	54298805	-	1	NA	5' UTR (NM_022025, exon 1 of 9)	5' UTR (NM_022025, exon 1 of 9)	229	NM_022025	63993	Mm.155241	NM_022025	ENSMUSG00000023945	Slc5a7	CHT1	solute carrier family 5 (choline transporter), member 7	protein-coding
mm_134196.1	chr16	10993136	10993138	-	1	NA	promoter-TSS (NM_019980)	promoter-TSS (NM_019980)	-16	NM_019980	56722	Mm.294753	NM_019980	ENSMUSG00000022500	Litaf	3222402J11Rik|C85531|N4WBP3|TBX1	LPS-induced TN factor	protein-coding
mm_123009.1	chr14	54994542	54994557	-	1	NA	promoter-TSS (NM_080728)	promoter-TSS (NM_080728)	0	NM_080728	140781	Mm.457983	NM_080728	ENSMUSG00000053093	Myh7	B-MHC|MyHC-I|Myhc-b|Myhcb|beta-MHC	myosin, heavy polypeptide 7, cardiac muscle, beta	protein-coding
mm_131765.1	chr16	22892751	22892777	+	1	NA	intron (NR_075099, intron 1 of 5)	intron (NR_075099, intron 1 of 5)	749	NM_001276449	11625	Mm.197554	NM_013465	ENSMUSG00000022868	Ahsg	-	alpha-2-HS-glycoprotein	protein-coding
mm_17563.1	chr2	30205675	30205693	-	1	NA	promoter-TSS (NM_172404)	promoter-TSS (NM_172404)	15	NM_172404	70266	Mm.216089	NM_172404	ENSMUSG00000039648	Kyat1	2010009K05Rik|AI182306|Ccbl1|Gtk|Kat1|KatI	kynurenine aminotransferase 1	protein-coding
mm_53315.1	chr6	129183112	129183131	+	1	NA	exon (NM_053109, exon 2 of 5)	exon (NM_053109, exon 2 of 5)	2506	NM_053109	93694	Mm.197536	NM_053109	ENSMUSG00000030157	Clec2d	Clr-b|Clrb|Ocil	C-type lectin domain family 2, member d	protein-coding
mm_99869.1	chr11	109398861	109398891	+	1	NA	3' UTR (NM_010303, exon 4 of 4)	3' UTR (NM_010303, exon 4 of 4)	-27070	NM_025275	13929	Mm.211850	NM_025275	ENSMUSG00000020610	Amz2	AA408420|ESTM12|X83328	archaelysin family metallopeptidase 2	protein-coding
mm_109291.1	chr12	109559485	109559499	+	1	NA	non-coding (NR_003633, exon 5 of 5)	non-coding (NR_003633, exon 5 of 5)	-4200	NR_030427	791079		NR_030427	ENSMUSG00000076451	Mir770	Mirn770|mir-770|mmu-mir-770	microRNA 770	ncRNA
mm_67949.1	chr7	100495678	100495695	-	1	NA	intron (NM_011671, intron 2 of 7)	intron (NM_011671, intron 2 of 7)	2328	NM_011671	22228	Mm.171378	NM_011671	ENSMUSG00000033685	Ucp2	Slc25a8	uncoupling protein 2 (mitochondrial, proton carrier)	protein-coding
mm_90766.1	chr10	5804599	5804623	-	1	NA	intron (NM_025995, intron 1 of 4)	intron (NM_025995, intron 1 of 4)	854	NM_025995	67141	Mm.197520	NM_025995	ENSMUSG00000019773	Fbxo5	2510044I10Rik|C85305|Emi1|Fbxo31	F-box protein 5	protein-coding
mm_154382.1	chrM	11352	11362	+	1	NA	NA	Intergenic	NA	NA								
mm_95724.1	chr11	54568199	54568213	+	1	NA	intron (NM_175258, intron 5 of 27)	intron (NM_175258, intron 5 of 27)	-27940	NM_001252498	192786	Mm.254404	NM_175258	ENSMUSG00000037533	Rapgef6	A530068K01|AI844632|BB085664|C030018K18Rik|PDZ-GEF2|Pdzgef2|RA-GEF-2|Ragef2|mKIAA4052	Rap guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_46336.1	chr5	101851489	101851495	-	1	NA	intron (NM_172882, intron 59 of 66)	intron (NM_172882, intron 59 of 66)	86362	NM_173370	74596	Mm.46764	NM_173370	ENSMUSG00000029330	Cds1	4833409J18Rik|AI314024|AW125888	CDP-diacylglycerol synthase 1	protein-coding
mm_168384.1	chr1	123477190	123477206	+	1	NA	intron (NM_199021, intron 7 of 25)	RLTR31D_MM|LTR|ERVK	568361	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_144178.1	chr18	6765118	6765123	+	1	NA	promoter-TSS (NM_181070)	promoter-TSS (NM_181070)	-47	NM_181070	19330	Mm.132802	NM_181070	ENSMUSG00000073639	Rab18	AA959686	RAB18, member RAS oncogene family	protein-coding
mm_53352.1	chr6	129350334	129350338	+	1	NA	promoter-TSS (NM_177686)	promoter-TSS (NM_177686)	92	NM_177686	232413	Mm.90241	NM_177686	ENSMUSG00000053063	Clec12a	CLL-1|D230024O04|KLRL1|Micl	C-type lectin domain family 12, member a	protein-coding
mm_93035.1	chr10	88338628	88338630	-	1	NA	intron (NM_027878, intron 3 of 6)	intron (NM_027878, intron 3 of 6)	18446	NM_027878	71712	Mm.35450	NM_027878	ENSMUSG00000020057	Dram1	1200002N14Rik|Dram	DNA-damage regulated autophagy modulator 1	protein-coding
mm_28900.1	chr3	98315000	98315003	-	1	NA	intron (NM_016966, intron 10 of 11)	intron (NM_016966, intron 10 of 11)	24968	NM_016966	236539	Mm.16898	NM_016966	ENSMUSG00000053398	Phgdh	3-PGDH|3PGDH|4930479N23|A10|PGAD|PGD|PGDH|SERA	3-phosphoglycerate dehydrogenase	protein-coding
mm_81649.1	chr9	110953727	110953756	+	1	NA	intron (NM_028838, intron 1 of 8)	intron (NM_028838, intron 1 of 8)	2196	NM_028838	74249	Mm.307615	NM_028838	ENSMUSG00000032495	Lrrc2	2400002D05Rik|4933431K03Rik	leucine rich repeat containing 2	protein-coding
mm_114923.1	chr13	95325259	95325300	+	1	NA	5' UTR (NM_028106, exon 1 of 2)	5' UTR (NM_028106, exon 1 of 2)	454	NM_028106	72114	Mm.3774	NM_028106	ENSMUSG00000041995	Zbed3	0610037K01Rik|2610005H11Rik|AU018975|AU024588	zinc finger, BED type containing 3	protein-coding
mm_7343.1	chr1	105988830	105988841	-	1	NA	Intergenic	Intergenic	-1571	NM_001122676	227449	Mm.210188	NM_001122675	ENSMUSG00000038866	Zcchc2	9930114B20Rik|AW212015	zinc finger, CCHC domain containing 2	protein-coding
mm_127918.1	chr15	9555949	9555964	-	1	NA	Intergenic	Lx9|LINE|L1	-26080	NM_008372	16197	Mm.389	NM_008372	ENSMUSG00000003882	Il7r	CD127|IL-7Ralpha	interleukin 7 receptor	protein-coding
mm_19923.1	chr2	116049110	116049129	-	1	NA	exon (NM_010825, exon 7 of 12)	exon (NM_010825, exon 7 of 12)	15500	NM_001346044	17536	Mm.247566	NM_010825	ENSMUSG00000027210	Meis2	A430109D20Rik|Mrg1|Stra10	Meis homeobox 2	protein-coding
mm_120867.1	chr14	75229910	75229922	+	1	NA	3' UTR (NM_001247984, exon 16 of 16)	3' UTR (NM_001247984, exon 16 of 16)	-12371	NM_019775	56373	Mm.24242	NM_019775	ENSMUSG00000021999	Cpb2	1110032P04Rik|4930405E17Rik|AI255929|CPR|Cpu|TAFI	carboxypeptidase B2 (plasma)	protein-coding
mm_9137.1	chr1	170867734	170867742	-	1	NA	promoter-TSS (NM_001081304)	promoter-TSS (NM_001081304)	33	NM_001081304	226641	Mm.377046	NM_001081304	ENSMUSG00000026663	Atf6	9130025P16Rik|9630036G24|AA789574|Atf6alpha|ESTM49	activating transcription factor 6	protein-coding
mm_5227.1	chr1	14309862	14309879	-	1	NA	5' UTR (NM_001252192, exon 1 of 17)	5' UTR (NM_001252192, exon 1 of 17)	329	NM_001310459	14048	Mm.250185	NM_010164	ENSMUSG00000025932	Eya1	bor	EYA transcriptional coactivator and phosphatase 1	protein-coding
mm_81100.1	chr9	106429465	106429479	+	1	NA	promoter-TSS (NM_001324533)	promoter-TSS (NM_001324533)	61	NM_009082	19944	Mm.288696	NM_009082	ENSMUSG00000048758	Rpl29	Rpl43	ribosomal protein L29	protein-coding
mm_147082.1	chr18	35627224	35627249	-	1	NA	promoter-TSS (NM_011397)	promoter-TSS (NM_011397)	-9	NM_011397	20522	Mm.22702	NM_011397	ENSMUSG00000024354	Slc23a1	D18Ucla2|SVCT1|Slc23a2|YSPL3	solute carrier family 23 (nucleobase transporters), member 1	protein-coding
mm_101539.1	chr11	33527350	33527360	-	1	NA	Intergenic	Intergenic	-13609	NM_023146	66011	Mm.383775	NM_023146	ENSMUSG00000040594	Ranbp17	-	RAN binding protein 17	protein-coding
mm_24596.1	chr3	93445305	93445320	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	2982	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_24377.1	chr3	90231666	90231708	+	1	NA	promoter-TSS (NM_206924)	promoter-TSS (NM_206924)	90	NM_206924	23922	Mm.13912	NM_206924	ENSMUSG00000027937	Jtb	Gm622	jumping translocation breakpoint	protein-coding
mm_113599.1	chr13	41016324	41016335	+	1	NA	promoter-TSS (NM_025387)	promoter-TSS (NM_025387)	79	NM_025387	66154	Mm.30005	NM_025387	ENSMUSG00000021361	Tmem14c	1110021D01Rik|AU020193|HSPC194	transmembrane protein 14C	protein-coding
mm_170049.1	chr17	26922811	26922824	+	1	NA	intron (NM_053173, intron 5 of 10)	intron (NM_053173, intron 5 of 10)	1855	NR_105933	102466211		NR_105933	ENSMUSG00000098586	Gm27775	Mir6967|Mir6967-1|mmu-mir-6967|mmu-mir-6967-1	predicted gene, 27775	ncRNA
mm_2398.1	chr1	93685907	93685929	+	1	NA	intron (NM_016778, intron 1 of 4)	CpG	343	NM_016778	51800	Mm.3295	NM_016778	ENSMUSG00000026278	Bok	matador|mtd	BCL2-related ovarian killer	protein-coding
mm_157349.1	chrX	36989524	36989537	-	1	NA	5' UTR (NM_001253706, exon 1 of 11)	5' UTR (NM_001253706, exon 1 of 11)	165	NM_001177324	56526	Mm.260036	NM_019942	ENSMUSG00000050379	Sept6	2810035H17Rik|C920001C06Rik|Sep6|mKIAA0128	septin 6	protein-coding
mm_91594.1	chr10	40350028	40350101	-	1	NA	intron (NM_001291816, intron 1 of 11)	CpG	756	NM_001291816	78334	Mm.200924	NM_198164	ENSMUSG00000038481	Cdk19	2700084L06Rik|AI845279|AW228747|CDK11|Cdc2l6|mKIAA1028	cyclin-dependent kinase 19	protein-coding
mm_127670.1	chr15	102671904	102671922	+	1	NA	promoter-TSS (NR_030460)	promoter-TSS (NR_030460)	-47	NR_030460	751542		NR_030460	ENSMUSG00000076009	Mir688	Mirn688|mmu-mir-688	microRNA 688	ncRNA
mm_10344.1	chr2	11655537	11655550	+	1	NA	intron (NM_008367, intron 1 of 7)	intron (NM_008367, intron 1 of 7)	12751	NM_008367	16184	Mm.915	NM_008367	ENSMUSG00000026770	Il2ra	CD25|Il2r|Ly-43	interleukin 2 receptor, alpha chain	protein-coding
mm_63274.1	chr7	126762885	126762900	+	1	NA	intron (NM_011952, intron 2 of 8)	MIR3|SINE|MIR	3266	NM_011952	26417	Mm.8385	NM_011952	ENSMUSG00000063065	Mapk3	Erk-1|Erk1|Ert2|Esrk1|Mnk1|Mtap2k|Prkm3|p44|p44erk1|p44mapk	mitogen-activated protein kinase 3	protein-coding
mm_102488.1	chr11	60222833	60222852	-	1	NA	Intergenic	CpG	-2215	NM_001313979	20787	Mm.278701	NM_011480	ENSMUSG00000020538	Srebf1	ADD1|SREBP-1a|SREBP1|SREBP1c|bHLHd1	sterol regulatory element binding transcription factor 1	protein-coding
mm_170562.1	chr19	45993571	45993579	-	1	NA	intron (NM_198296, intron 1 of 25)	ERVB7_2B-LTR_MM|LTR|ERVK	4913	NM_198296	71617	Mm.210949	NM_198296	ENSMUSG00000039901	9130011E15Rik	AI431055|AW050122	RIKEN cDNA 9130011E15 gene	protein-coding
mm_43287.1	chr5	134099768	134099797	+	1	NA	promoter-TSS (NM_030719)	promoter-TSS (NM_030719)	34	NM_030719	80909	Mm.45218	NM_030719	ENSMUSG00000015944	Gatsl2	7530428J21Rik|AW742413|Gats|Gatsl1	GATS protein-like 2	protein-coding
mm_169989.1	chr17	15052530	15052548	-	1	NA	promoter-TSS (NM_001034891)	promoter-TSS (NM_001034891)	-520	NM_001034891	381062	Mm.393767	NM_183133	ENSMUSG00000036552	Ermard	2210404J11Rik|2410011O22Rik|AI448938	ER membrane associated RNA degradation	protein-coding
mm_44648.1	chr5	28209962	28209979	-	1	NA	5' UTR (NM_001310511, exon 1 of 3)	5' UTR (NM_001310511, exon 1 of 3)	198	NM_001310511	269637	Mm.68286	NM_175651	ENSMUSG00000044681	Cnpy1	1500012D20Rik|9630008K15Rik|AI853839	canopy FGF signaling regulator 1	protein-coding
mm_31467.1	chr4	49549670	49549705	+	1	NA	promoter-TSS (NM_144903)	promoter-TSS (NM_144903)	-141	NM_144903	230163	Mm.482116	NM_144903	ENSMUSG00000028307	Aldob	Aldo-2|Aldo2|BC016435	aldolase B, fructose-bisphosphate	protein-coding
mm_119178.1	chr14	32165820	32165831	+	1	NA	promoter-TSS (NM_019744)	promoter-TSS (NM_019744)	36	NM_019744	27057	Mm.371598	NM_019744	ENSMUSG00000056234	Ncoa4	ARA70|Rfg	nuclear receptor coactivator 4	protein-coding
mm_61061.1	chr7	49975011	49975102	+	1	NA	promoter-TSS (NM_001037906)	promoter-TSS (NM_001037906)	-294	NM_001037906	338352	Mm.383528	NM_001037906	ENSMUSG00000055409	Nell1	B230343H07Rik|l7R6	NEL-like 1	protein-coding
mm_91137.1	chr10	19718687	19718723	-	1	NA	intron (NM_172786, intron 1 of 6)	intron (NM_172786, intron 1 of 6)	6118	NM_172786	237313	Mm.234667	NM_172786	ENSMUSG00000020007	Il20ra	E230031K19	interleukin 20 receptor, alpha	protein-coding
mm_18330.1	chr2	57238759	57238764	-	1	NA	intron (NM_010274, intron 1 of 16)	intron (NM_010274, intron 1 of 16)	379	NM_010274	14571	Mm.3711	NM_010274	ENSMUSG00000026827	Gpd2	AA408484|AI448216|AU021455|AW494132|GPDH|Gdm1|Gpd-m|Gpdh-m|TISP38	glycerol phosphate dehydrogenase 2, mitochondrial	protein-coding
mm_15787.1	chr2	164425228	164425251	+	1	NA	3' UTR (NM_011521, exon 5 of 5)	3' UTR (NM_011521, exon 5 of 5)	17949	NM_011521	20971	Mm.3815	NM_011521	ENSMUSG00000017009	Sdc4	AA959608|AW108331|S4|Synd4|ryudocan|syndecan-4	syndecan 4	protein-coding
mm_6174.1	chr1	65100424	65100447	-	1	NA	TTS (NM_007774)	TTS (NM_007774)	2928	NM_007774	12964	Mm.26904	NM_007774	ENSMUSG00000044429	Cryga	Cryg-4|DGcry-4	crystallin, gamma A	protein-coding
mm_2302.1	chr1	91540007	91540009	+	1	NA	promoter-TSS (NM_001039126)	promoter-TSS (NM_001039126)	-557	NM_001039126	65247	Mm.234152	NM_023046	ENSMUSG00000026311	Asb1	1700029O08Rik|1700054C17Rik|AI426616|AI851378|mKIAA1146	ankyrin repeat and SOCS box-containing 1	protein-coding
mm_12571.1	chr2	72997270	72997277	+	1	NA	Intergenic	Intergenic	-16827	NM_001018042	20687	Mm.124328	NM_011450	ENSMUSG00000027109	Sp3	D130027J01Rik	trans-acting transcription factor 3	protein-coding
mm_7672.1	chr1	128588841	128588858	-	1	NA	exon (NM_009911, exon 2 of 2)	exon (NM_009911, exon 2 of 2)	3450	NM_009911	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding
mm_107938.1	chr12	71876034	71876064	+	1	NA	intron (NM_026102, intron 1 of 25)	intron (NM_026102, intron 1 of 25)	-13494	NM_001286452	208846	Mm.87417	NM_026102	ENSMUSG00000034574	Daam1	-	dishevelled associated activator of morphogenesis 1	protein-coding
mm_115708.1	chr13	14523179	14523202	-	1	NA	promoter-TSS (NM_001081348)	promoter-TSS (NM_001081348)	36	NM_001081348	94253	Mm.125298	NM_153130	ENSMUSG00000021301	Hecw1	9330116H24Rik|AV273951|E130207I19Rik|Nedl1	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	protein-coding
mm_56767.1	chr6	116193427	116193501	-	1	NA	promoter-TSS (NM_177412)	promoter-TSS (NM_177412)	-90	NM_177412	330401	Mm.425352	NM_177412	ENSMUSG00000030126	Tmcc1	3632431M01Rik|mKIAA0779	transmembrane and coiled coil domains 1	protein-coding
mm_128483.1	chr15	50890043	50890064	-	1	NA	promoter-TSS (NR_035444)	promoter-TSS (NR_035444)	-12	NM_032000	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_25670.1	chr3	121953214	121953295	+	1	NA	promoter-TSS (NM_172525)	promoter-TSS (NM_172525)	-72	NM_172525	214137	Mm.229287	NM_172525	ENSMUSG00000039831	Arhgap29	6720461J18Rik|A830014I19|AU040217|B130017I01Rik|C76601|Parg1	Rho GTPase activating protein 29	protein-coding
mm_156743.1	chrX	159944409	159944412	+	1	NA	intron (NR_110969, intron 13 of 16)	intron (NR_110969, intron 13 of 16)	1717	NM_001290664	58194	Mm.286495	NM_021389	ENSMUSG00000040990	Sh3kbp1	1200007H22Rik|1700125L08Rik|5830464D22Rik|AI447724|Cin85|IN85|Ruk|Seta	SH3-domain kinase binding protein 1	protein-coding
mm_72954.1	chr8	92358004	92358011	+	1	NA	5' UTR (NM_018826, exon 1 of 3)	5' UTR (NM_018826, exon 1 of 3)	211	NM_018826	54352	Mm.101153	NM_018826	ENSMUSG00000031737	Irx5	-	Iroquois related homeobox 5 (Drosophila)	protein-coding
mm_141119.1	chr17	26090252	26090315	-	1	NA	promoter-TSS (NM_011933)	promoter-TSS (NM_011933)	-119	NM_011933	26378	Mm.292869	NM_011933	ENSMUSG00000036775	Decr2	-	2-4-dienoyl-Coenzyme A reductase 2, peroxisomal	protein-coding
mm_36950.1	chr4	109102639	109102660	-	1	NA	intron (NM_133885, intron 4 of 22)	intron (NM_133885, intron 4 of 22)	15387	NM_173350	100273	Mm.366315	NM_133885	ENSMUSG00000028559	Osbpl9	2600011I06Rik|AU015843|Orp-9	oxysterol binding protein-like 9	protein-coding
mm_113757.1	chr13	44736673	44736675	+	1	NA	intron (NM_001205044, intron 2 of 18)	B1_Mus1|SINE|Alu	5403	NM_001205043	16468	Mm.25059	NM_021878	ENSMUSG00000038518	Jarid2	Jmj|jumonji	jumonji, AT rich interactive domain 2	protein-coding
mm_50588.1	chr6	49059989	49060004	+	1	NA	Intergenic	Intergenic	-13799	NM_029353	75593	Mm.439947	NM_029353	ENSMUSG00000029815	Malsu1	2410003K15Rik|Matsu1	mitochondrial assembly of ribosomal large subunit 1	protein-coding
mm_53928.1	chr6	4717209	4717223	-	1	NA	intron (NM_011360, intron 3 of 10)	intron (NM_011360, intron 3 of 10)	29988	NM_001130188	20392	Mm.8739	NM_011360	ENSMUSG00000004631	Sgce	e-SG	sarcoglycan, epsilon	protein-coding
mm_4270.1	chr1	171559133	171559150	+	1	NA	promoter-TSS (NM_018729)	promoter-TSS (NM_018729)	-52	NM_018729	18106	Mm.2299	NM_018729	ENSMUSG00000004709	Cd244	2B4|C9.1|F730046O15Rik|Ly90|NAIL|NKR2B4|Nmrk|SLAMF4	CD244 natural killer cell receptor 2B4	protein-coding
mm_158990.1	chr1	133610250	133610250	-	1	NA	promoter-TSS (NM_009227)	promoter-TSS (NM_009227)	30	NM_009227	20643	Mm.249110	NM_009227	ENSMUSG00000090553	Snrpe	AL022645|C76690|SME	small nuclear ribonucleoprotein E	protein-coding
mm_2395.1	chr1	93685575	93685678	+	1	NA	promoter-TSS (NM_016778)	promoter-TSS (NM_016778)	51	NM_016778	51800	Mm.3295	NM_016778	ENSMUSG00000026278	Bok	matador|mtd	BCL2-related ovarian killer	protein-coding
mm_110303.1	chr12	32820058	32820076	-	1	NA	promoter-TSS (NM_021524)	promoter-TSS (NM_021524)	-268	NM_021524	59027	Mm.202727	NM_021524	ENSMUSG00000020572	Nampt	1110035O14Rik|AI314458|AI480535|NAmPRTase|Pbef|Pbef1|Visfatin	nicotinamide phosphoribosyltransferase	protein-coding
mm_112730.1	chr13	19208820	19208839	+	1	NA	Intergenic	Intergenic	186984	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_75140.1	chr8	35394210	35394216	-	1	NA	Intergenic	Intergenic	18472	NM_177741	244416	Mm.247126	NM_177741	ENSMUSG00000046794	Ppp1r3b	6430576E21|AW821953|GL|PTG	protein phosphatase 1, regulatory (inhibitor) subunit 3B	protein-coding
mm_9298.1	chr1	171638718	171638736	-	1	NA	exon (NM_144539, exon 5 of 8)	exon (NM_144539, exon 5 of 8)	3173	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_38482.1	chr4	140742640	140742644	-	1	NA	promoter-TSS (NM_153106)	promoter-TSS (NM_153106)	1	NM_153106	242726	Mm.271661	NM_153106	ENSMUSG00000040935	Padi6	Pad6|Padi5|ePAD	peptidyl arginine deiminase, type VI	protein-coding
mm_848.1	chr1	52008611	52008651	+	1	NA	5' UTR (NM_011487, exon 1 of 24)	5' UTR (NM_011487, exon 1 of 24)	391	NM_011487	20849	Mm.1550	NM_011487	ENSMUSG00000062939	Stat4	-	signal transducer and activator of transcription 4	protein-coding
mm_126319.1	chr15	79690922	79690924	+	1	NA	promoter-TSS (NM_013818)	promoter-TSS (NM_013818)	27	NM_013818	14904	Mm.19080	NM_013818	ENSMUSG00000042535	Gtpbp1	AL022987|AW045683|C85212|GP-1|Gtpbp	GTP binding protein 1	protein-coding
mm_39757.1	chr5	29735992	29736011	+	1	NA	promoter-TSS (NR_028426)	promoter-TSS (NR_028426)	-65	NR_028426	332993	Mm.473746	NR_028426		Gm5129	EG332993|ENSMUSG00000053121	predicted gene 5129	ncRNA
mm_100253.1	chr11	117326640	117326661	+	1	NA	intron (NM_001113487, intron 2 of 10)	intron (NM_001113487, intron 2 of 10)	-5065	NM_017380	53860	Mm.38450	NM_017380	ENSMUSG00000059248	Sept9	MSF1|Msf|PNUTL4|Sint1	septin 9	protein-coding
mm_5435.1	chr1	34819928	34819964	-	1	NA	exon (NM_001160236, exon 4 of 7)	exon (NM_001160236, exon 4 of 7)	18224	NM_183019	226970	Mm.41604	NM_183019	ENSMUSG00000037509	Arhgef4	9330140K16Rik|Asef|ENSMUSG00000070955	Rho guanine nucleotide exchange factor (GEF) 4	protein-coding
mm_148545.1	chr19	4711277	4711287	+	1	NA	promoter-TSS (NM_021287)	promoter-TSS (NM_021287)	59	NM_021287	20743	Mm.329668	NM_021287	ENSMUSG00000067889	Sptbn2	Spnb3|mKIAA0302	spectrin beta, non-erythrocytic 2	protein-coding
mm_128570.1	chr15	57693771	57693783	-	1	NA	promoter-TSS (NM_199449)	promoter-TSS (NM_199449)	-890	NM_199449	387609	Mm.36557	NM_199449	ENSMUSG00000071757	Zhx2	Afr-1|Afr1|Raf|mKIAA0854	zinc fingers and homeoboxes 2	protein-coding
mm_168806.1	chr12	20615062	20615063	+	1	NA	Intergenic	CpG	200717	NR_015521	69513	Mm.273972	NR_015521	ENSMUSG00000099759	1700030C10Rik	-	RIKEN cDNA 1700030C10 gene	ncRNA
mm_134265.1	chr16	13780636	13780657	-	1	NA	promoter-TSS (NM_001039521)	promoter-TSS (NM_001039521)	-53	NM_001039521	106298	Mm.288606	NM_001039521	ENSMUSG00000022682	Rrn3	AL023001|E130302O19Rik|R75565|TIF-1A|Tif1a	RRN3 RNA polymerase I transcription factor homolog (yeast)	protein-coding
mm_11076.1	chr2	27677318	27677340	+	1	NA	5' UTR (NM_011305, exon 1 of 10)	5' UTR (NM_011305, exon 1 of 10)	128	NM_011305	20181	Mm.24624	NM_011305	ENSMUSG00000015846	Rxra	9530071D11Rik|Nr2b1|RXRalpha1	retinoid X receptor alpha	protein-coding
mm_77678.1	chr8	125474952	125474980	-	1	NA	exon (NM_001081337, exon 4 of 21)	exon (NM_001081337, exon 4 of 21)	17744	NM_001081337	244668	Mm.271668	NM_001081337	ENSMUSG00000001995	Sipa1l2	BC058408|mKIAA1389	signal-induced proliferation-associated 1 like 2	protein-coding
mm_28936.1	chr3	98882223	98882227	-	1	NA	intron (NM_019545, intron 4 of 8)	intron (NM_019545, intron 4 of 8)	11005	NM_019545	56185	Mm.281874	NM_019545	ENSMUSG00000027870	Hao2	AI325478|Hao-2|Hao3|Haox3	hydroxyacid oxidase 2	protein-coding
mm_129041.1	chr15	75087036	75087049	-	1	NA	Intergenic	RLTR11A|LTR|ERVK	24907	NM_001099217	100041546	Mm.482110	NM_001099217	ENSMUSG00000022584	Ly6c2	Ly-6C.2|Ly-6C2	lymphocyte antigen 6 complex, locus C2	protein-coding
mm_87640.1	chr10	58371410	58371499	+	1	NA	promoter-TSS (NM_201242)	promoter-TSS (NM_201242)	0	NM_201242	110829	Mm.57734	NM_026148	ENSMUSG00000019920	Lims1	2310016J22Rik|4921524A02Rik|AI507642|AU021743|AW551584|C430041B13Rik|Lims1l|PINCH|PINCH1	LIM and senescent cell antigen-like domains 1	protein-coding
mm_17451.1	chr2	28555924	28555940	-	1	NA	3' UTR (NM_009885, exon 11 of 11)	3' UTR (NM_009885, exon 11 of 11)	7471	NM_009885	12613	Mm.236017	NM_009885	ENSMUSG00000026818	Cel	1810036E18Rik|BAL	carboxyl ester lipase	protein-coding
mm_30253.1	chr3	146615588	146615604	-	1	NA	promoter-TSS (NM_019957)	promoter-TSS (NM_019957)	2	NM_019957	56629	Mm.25853	NM_019957	ENSMUSG00000028185	Dnase2b	AI526873|Dlad|DnaseIIb	deoxyribonuclease II beta	protein-coding
mm_148242.1	chr18	80611194	80611221	-	1	NA	intron (NM_198429, intron 9 of 9)	intron (NM_198429, intron 9 of 9)	-66661	NR_028424	100039348	Mm.254722	NR_028424		Gm2176	A430076E10Rik	glucosamine-6-phosphate deaminase 1 pseudogene	pseudo
mm_170835.1	chr2	177065455	177065466	-	1	NA	Intergenic	Intergenic	-137647	NM_001305133	102639598	Mm.379980	NM_029813	ENSMUSG00000074527	Gm14296	-	predicted gene 14296	protein-coding
mm_49993.1	chr6	41047467	41047490	+	1	NA	Intergenic	Intergenic	-11969	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_83466.1	chr9	45268861	45268872	-	1	NA	intron (NM_008348, intron 1 of 6)	intron (NM_008348, intron 1 of 6)	283	NM_008348	16154	Mm.379327	NM_008348	ENSMUSG00000032089	Il10ra	AW553859|CDw210|CDw210a|IL-10R1|IL-10RA|Il10r|mIL-10R	interleukin 10 receptor, alpha	protein-coding
mm_68773.1	chr7	122021144	122021206	-	1	NA	promoter-TSS (NM_028758)	promoter-TSS (NM_028758)	23	NM_028758	74105	Mm.29619	NM_028758	ENSMUSG00000030872	Gga2	1200007E24Rik|mKIAA1080	golgi associated, gamma adaptin ear containing, ARF binding protein 2	protein-coding
mm_28302.1	chr3	89214241	89214254	-	1	NA	promoter-TSS (NM_013604)	promoter-TSS (NM_013604)	88	NM_001161824	17827	Mm.280943	NM_013604	ENSMUSG00000064068	Mtx1	Gcap6|Mtx	metaxin 1	protein-coding
mm_210.1	chr1	16661569	16661574	+	1	NA	intron (NR_037998, intron 3 of 3)	RLTR30D2_MM|LTR|ERV1	-3620	NM_027415	70397	Mm.194225	NM_026392	ENSMUSG00000025940	Tmem70	1110020A09Rik|2210416J16Rik	transmembrane protein 70	protein-coding
mm_52372.1	chr6	113077355	113077382	+	1	NA	promoter-TSS (NR_027008)	promoter-TSS (NR_027008)	-124	NR_027008	14910	Mm.280950	NR_027008	ENSMUSG00000086429	Gt(ROSA)26Sor	AV258896|Gtrgeo26|Gtrosa26|R26|ROSA26|Thumpd3as1	gene trap ROSA 26, Philippe Soriano	ncRNA
mm_8058.1	chr1	135375224	135375228	-	1	NA	promoter-TSS (NM_175259)	promoter-TSS (NM_175259)	-163	NM_175259	77552	Mm.41407	NM_175259	ENSMUSG00000041889	Shisa4	9330132O05Rik|Tmem58|mShisa4	shisa family member 4	protein-coding
mm_62980.1	chr7	120173903	120173914	+	1	NA	promoter-TSS (NM_028085)	promoter-TSS (NM_028085)	50	NM_028085	72074	Mm.23165	NM_028085	ENSMUSG00000030909	Anks4b	2010013E14Rik|AI956809|Harp	ankyrin repeat and sterile alpha motif domain containing 4B	protein-coding
mm_75584.1	chr8	61549787	61549822	-	1	NA	exon (NM_001293774, exon 2 of 12)	exon (NM_001293774, exon 2 of 12)	41365	NM_001293774	72333	Mm.29933	NM_001081390	ENSMUSG00000058056	Palld	2410003B16Rik|6030492A02	palladin, cytoskeletal associated protein	protein-coding
mm_124087.1	chr14	78732701	78732775	-	1	NA	Intergenic	CpG	-7649	NM_001081336	380921	Mm.89591	NM_001081336	ENSMUSG00000034731	Dgkh	5930402B05Rik|D130015C16|DGK	diacylglycerol kinase, eta	protein-coding
mm_31013.1	chr4	40721128	40721136	+	1	NA	non-coding (NR_077226, exon 3 of 3)	non-coding (NR_077226, exon 3 of 3)	1185	NR_077221	622208	Mm.471544	NR_077221		Gm6297	-	predicted gene 6297	ncRNA
mm_28596.1	chr3	94472893	94472930	-	1	NA	exon (NM_025506, exon 3 of 7)	exon (NM_025506, exon 3 of 7)	680	NM_025506	66353	Mm.46405	NM_025506	ENSMUSG00000028139	Riiad1	2310007A19Rik|Ncrna00166	regulatory subunit of type II PKA R-subunit (RIIa) domain containing 1	protein-coding
mm_72051.1	chr8	71367211	71367238	+	1	NA	promoter-TSS (NM_025917)	promoter-TSS (NM_025917)	7	NM_025917	67023	Mm.41890	NM_025917	ENSMUSG00000002395	Use1	2010315L10Rik|5730403H22Rik|AV002165|D12|Ed2|Q-snare|p31	unconventional SNARE in the ER 1 homolog (S. cerevisiae)	protein-coding
mm_130797.1	chr15	101692568	101692575	-	1	NA	exon (NM_008476, exon 4 of 9)	exon (NM_008476, exon 4 of 9)	1734	NM_008476	16687	Mm.302399	NM_008476	ENSMUSG00000058354	Krt6a	2310016L08Rik|Krt2-6a|Krt2-6c|MK6a|mK6[a]	keratin 6A	protein-coding
mm_20168.1	chr2	122305622	122305628	-	1	NA	exon (NM_001305262, exon 7 of 10)	exon (NM_001305262, exon 7 of 10)	6725	NM_025777	66811	Mm.171333	NM_025777	ENSMUSG00000027225	Duoxa2	9030623N16Rik|Nip2	dual oxidase maturation factor 2	protein-coding
mm_165619.1	chr3	60501862	60501880	+	1	NA	intron (NM_001253710, intron 1 of 7)	intron (NM_001253710, intron 1 of 7)	692	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_71590.1	chr8	54954970	54954974	+	1	NA	5' UTR (NM_153581, exon 1 of 7)	5' UTR (NM_153581, exon 1 of 7)	244	NM_001253756	234267	Mm.241700	NM_153581	ENSMUSG00000031517	Gpm6a	Gpm6|M6A	glycoprotein m6a	protein-coding
mm_120081.1	chr14	57744781	57744803	+	1	NA	intron (NM_015771, intron 1 of 7)	intron (NM_015771, intron 1 of 7)	1331	NM_015771	50523	Mm.347899	NM_015771	ENSMUSG00000021959	Lats2	4932411G09Rik|AV277261|AW228608	large tumor suppressor 2	protein-coding
mm_173167.1	chrX	41994997	41995012	-	1	NA	Intergenic	L1Md_T|LINE|L1	-72832	NM_009688	11798	Mm.259879	NM_009688	ENSMUSG00000025860	Xiap	1110015C02Rik|Aipa|Api3|Birc4|IAP3|ILP-1|MIHA	X-linked inhibitor of apoptosis	protein-coding
mm_172382.1	chr7	13124245	13124253	-	1	NA	Intergenic	Intergenic	8109	NM_134227	171261	Mm.377215	NM_134227	ENSMUSG00000070815	Vmn1r87	V1rk1	vomeronasal 1 receptor 87	protein-coding
mm_85461.1	chr9	105494963	105494997	-	1	NA	5' UTR (NM_175025, exon 1 of 28)	5' UTR (NM_175025, exon 1 of 28)	153	NM_175025	235574	Mm.326247	NM_175025	ENSMUSG00000032570	Atp2c1	1700121J11Rik|ATP2C1A|AW061228|BCPM|D930003G21Rik|HHD|SPCA|pmr1	ATPase, Ca++-sequestering	protein-coding
mm_91033.1	chr10	18210820	18210831	-	1	NA	promoter-TSS (NM_001195036)	promoter-TSS (NM_001195036)	65	NM_001195036	100045792	Mm.380617	NM_001195036	ENSMUSG00000071392	Ect2l	C330021H03Rik|ENSMUSG00000071392|Gm10331	epithelial cell transforming sequence 2 oncogene-like	protein-coding
mm_38844.1	chr4	149178190	149178218	-	1	NA	3' UTR (NM_001290995, exon 49 of 49)	3' UTR (NM_001290995, exon 49 of 49)	-11497	NM_001081274	110208	Mm.252080	NM_025801	ENSMUSG00000028961	Pgd	0610042A05Rik|AU019875|C78335	phosphogluconate dehydrogenase	protein-coding
mm_2087.1	chr1	87694865	87694870	+	1	NA	intron (NM_010566, intron 10 of 26)	intron (NM_010566, intron 10 of 26)	-61144	NM_029846	77040	Mm.272972	NM_029846	ENSMUSG00000026289	Atg16l1	1500009K01Rik|Apg16l|Atg16l|WDR30	autophagy related 16-like 1 (S. cerevisiae)	protein-coding
mm_86074.1	chr9	114778923	114778926	-	1	NA	intron (NM_001252479, intron 1 of 3)	intron (NM_001252479, intron 1 of 3)	3069	NM_133978	102545	Mm.35600	NM_133978	ENSMUSG00000032436	Cmtm7	AI481279|Cklfsf7|LNV	CKLF-like MARVEL transmembrane domain containing 7	protein-coding
mm_82957.1	chr9	35570423	35570440	-	1	NA	promoter-TSS (NM_029762)	promoter-TSS (NM_029762)	-362	NM_029762	76832	Mm.482285	NM_029762	ENSMUSG00000050555	Hyls1	3010015K02Rik	hydrolethalus syndrome 1	protein-coding
mm_132316.1	chr16	33752633	33752637	+	1	NA	intron (NM_175256, intron 12 of 14)	B1_Mur1|SINE|Alu	-41402	NM_010739	17063	Mm.3177	NM_010739	ENSMUSG00000022824	Muc13	114/A10|14/A10|AI159736|Lrrp|Ly64|NJ-1	mucin 13, epithelial transmembrane	protein-coding
mm_15357.1	chr2	156312590	156312625	+	1	NA	promoter-TSS (NM_020255)	promoter-TSS (NM_020255)	97	NM_020255	19018	Mm.389346	NM_020255	ENSMUSG00000046229	Scand1	2310003H23Rik|Leap1|PGC-2|Ppargc2	SCAN domain-containing 1	protein-coding
mm_43434.1	chr5	136084084	136084101	+	1	NA	5' UTR (NM_133914, exon 1 of 21)	5' UTR (NM_133914, exon 1 of 21)	176	NM_001039103	54153	Mm.290655	NM_133914	ENSMUSG00000004952	Rasa4	AA793972|AW112107|BB079060|CAPRI|GAPL	RAS p21 protein activator 4	protein-coding
mm_86978.1	chr10	25432577	25432619	+	1	NA	intron (NM_013511, intron 1 of 19)	intron (NM_013511, intron 1 of 19)	24230	NM_013511	13822	Mm.306026	NM_013511	ENSMUSG00000019978	Epb41l2	4.1G|AW555191|D10Ertd398e|Epb4.1l2|NBL2	erythrocyte membrane protein band 4.1 like 2	protein-coding
mm_138547.1	chr17	35263865	35263885	+	1	NA	exon (NM_001267808, exon 7 of 11)	exon (NM_001267808, exon 7 of 11)	752	NM_001267808	14980	Mm.439675	NM_001267808		H2-L	H-2L	histocompatibility 2, D region locus L	protein-coding
mm_51865.1	chr6	90550530	90550570	+	1	NA	promoter-TSS (NM_027406)	promoter-TSS (NM_027406)	-298	NM_027406	107747	Mm.30035	NM_027406	ENSMUSG00000030088	Aldh1l1	1810048F20Rik|FDH|Fthfd|Neut2	aldehyde dehydrogenase 1 family, member L1	protein-coding
mm_52139.1	chr6	97957080	97957086	+	1	NA	intron (NM_001113198, intron 2 of 9)	intron (NM_001113198, intron 2 of 9)	27266	NM_001178049	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_96235.1	chr11	62551462	62551477	+	1	NA	promoter-TSS (NR_002875).2	promoter-TSS (NR_002875).2	-35	NR_002875	218963	Mm.282093	NR_002875		Gm1821	-	ubiquitin pseudogene	pseudo
mm_158640.1	chrX	155216375	155216405	-	1	NA	promoter-TSS (NM_009121)	promoter-TSS (NM_009121)	59	NM_009121	20229	Mm.2734	NM_009121	ENSMUSG00000025283	Sat1	AA617398|SSAT|Sat	spermidine/spermine N1-acetyl transferase 1	protein-coding
mm_64728.1	chr7	4684917	4684960	-	1	NA	promoter-TSS (NM_024172)	promoter-TSS (NM_024172)	25	NM_024172	66245	Mm.6803	NM_024172	ENSMUSG00000063802	Hspbp1	1500019G21Rik	HSPA (heat shock 70kDa) binding protein, cytoplasmic cochaperone 1	protein-coding
mm_21238.1	chr2	156144139	156144192	-	1	NA	promoter-TSS (NM_025946)	promoter-TSS (NM_025946)	12	NM_001164217	67067	Mm.371623	NM_025946	ENSMUSG00000067847	Romo1	2010100O12Rik|AI853864	reactive oxygen species modulator 1	protein-coding
mm_6139.1	chr1	64737709	64737726	-	1	NA	promoter-TSS (NM_001042659)	promoter-TSS (NM_001042659)	33	NM_001042659	14367	Mm.150813	NM_022721	ENSMUSG00000045005	Fzd5	5330434N09Rik|AI427138|Fz-5|Fz5|mFz5	frizzled class receptor 5	protein-coding
mm_110913.1	chr12	76216948	76216985	-	1	NA	exon (NM_019784, exon 5 of 10)	exon (NM_019784, exon 5 of 10)	29780	NM_019784	80384	Mm.78551	NM_019784	ENSMUSG00000021056	Tex21	4931406F04Rik|4931412D23Rik|4931421K24Rik|tsec-2	testis expressed gene 21	protein-coding
mm_125148.1	chr15	30646668	30646686	+	1	NA	intron (NM_008729, intron 6 of 22)	CpG	-392449	NR_045186	73784	Mm.66947	NR_045186		4930430F21Rik	-	RIKEN cDNA 4930430F21 gene	ncRNA
mm_166355.1	chr5	121233146	121233148	+	1	NA	intron (NM_181421, intron 1 of 75)	B1_Mm|SINE|Alu	12928	NM_181421	269700	Mm.184589	NM_181421	ENSMUSG00000042744	Gm15800	A130010L24|AU042671|BC019639|EG545802|OTTMUSG00000026283|mKIAA0614	predicted gene 15800	protein-coding
mm_104124.1	chr11	86757338	86757344	-	1	NA	5' UTR (NM_001003908, exon 1 of 32)	5' UTR (NM_001003908, exon 1 of 32)	151	NM_001003908	67300	Mm.254588	NM_001003908	ENSMUSG00000047126	Cltc	3110065L21Rik|CHC|R74732	clathrin, heavy polypeptide (Hc)	protein-coding
mm_4022.1	chr1	165723095	165723100	+	1	NA	Intergenic	Intergenic	-15003	NM_001038846	226594	Mm.265552	NM_178593	ENSMUSG00000040723	Rcsd1	A430105K13Rik|BC025872|CapZIP	RCSD domain containing 1	protein-coding
mm_52772.1	chr6	121210713	121210719	+	1	NA	promoter-TSS (NM_017379)	promoter-TSS (NM_017379)	-18	NM_017379	53857	Mm.32884	NM_017379	ENSMUSG00000030137	Tuba8	-	tubulin, alpha 8	protein-coding
mm_77023.1	chr8	108584648	108584658	-	1	NA	promoter-TSS (NR_077224)	promoter-TSS (NR_077224)	24	NR_077224	109215	Mm.65282	NR_077224	ENSMUSG00000110613	Lncbate1	3010033K07Rik|Lnc-BATE1	brown adipose tissue enriched long non-coding RNA 1	ncRNA
mm_131530.1	chr16	17646593	17646620	+	1	NA	exon (NM_001166164, exon 1 of 8)	exon (NM_001166164, exon 1 of 8)	136	NM_001166164	72315	Mm.297777	NM_001166164	ENSMUSG00000041617	Ccdc74a	2310015A05Rik	coiled-coil domain containing 74A	protein-coding
mm_100179.1	chr11	116624389	116624405	+	1	NA	promoter-TSS (NM_001167680)	promoter-TSS (NM_001167680)	-145	NM_001167680	217344	Mm.89695	NM_172572	ENSMUSG00000020806	Rhbdf2	4732465I17Rik|Rhbdl6|cub	rhomboid 5 homolog 2	protein-coding
mm_161353.1	chr14	55511389	55511389	+	1	NA	promoter-TSS (NM_009947)	promoter-TSS (NM_009947)	29	NM_009947	12891	Mm.5249	NM_009947	ENSMUSG00000022212	Cpne6	AU067659|BB076446	copine VI	protein-coding
mm_165677.1	chr3	90587276	90587290	+	1	NA	Intergenic	Intergenic	-2964	NM_001195760	628324	Mm.33816	NM_001195760	ENSMUSG00000094018	S100a2	CaN19|EG628324|S100L	S100 calcium binding protein A2	protein-coding
mm_68727.1	chr7	120202105	120202123	-	1	NA	promoter-TSS (NM_016669)	promoter-TSS (NM_016669)	-126	NM_016669	12971	Mm.9114	NM_016669	ENSMUSG00000030905	Crym	-	crystallin, mu	protein-coding
mm_166824.1	chr7	18402892	18402917	-	1	NA	Intergenic	CpG	29151	NM_054063	114871	Mm.362025	NM_054063	ENSMUSG00000030373	Psg28	cea16	pregnancy-specific glycoprotein 28	protein-coding
mm_98835.1	chr11	97436276	97436320	+	1	NA	Intergenic	Intergenic	-13862	NM_021493	58996	Mm.394118	NM_021493	ENSMUSG00000049807	Arhgap23	A330041B18Rik	Rho GTPase activating protein 23	protein-coding
mm_100844.1	chr11	5762045	5762053	-	1	NA	promoter-TSS (NR_015577)	promoter-TSS (NR_015577)	-101	NR_015577	76508	Mm.260203	NR_015577	ENSMUSG00000083844	Ube2d-ps	1600028I17Rik|2210015D19Rik|AI596465	ubiquitin-conjugating enzyme E2D, pseudogene	ncRNA
mm_141597.1	chr17	32425281	32425295	-	1	NA	Intergenic	B1F|SINE|Alu	-1121	NM_001271478	57757	Mm.86752	NM_021319	ENSMUSG00000079563	Pglyrp2	C730002N09Rik|PGRP-L|Pglyrpl|tagL	peptidoglycan recognition protein 2	protein-coding
mm_35111.1	chr4	9661095	9661105	-	1	NA	intron (NM_001290367, intron 1 of 22)	intron (NM_001290367, intron 1 of 22)	8062	NM_023066	65973	Mm.222206	NM_023066	ENSMUSG00000028207	Asph	2310005F16Rik|3110001L23Rik|AI848629|AW261690|AW561901|BAH|C79816|cI-37	aspartate-beta-hydroxylase	protein-coding
mm_103295.1	chr11	72475009	72475032	-	1	NA	promoter-TSS (NM_001276383)	promoter-TSS (NM_001276383)	7	NM_001276383	216892	Mm.212812	NM_153060	ENSMUSG00000040447	Spns2	-	spinster homolog 2	protein-coding
mm_102577.1	chr11	61720088	61720125	-	1	NA	intron (NM_001033227, intron 1 of 15)	intron (NM_001033227, intron 1 of 15)	693	NM_001033227	109342	Mm.441070	NM_001033227	ENSMUSG00000042371	Slc5a10	C330021F16Rik|SGLT5	solute carrier family 5 (sodium/glucose cotransporter), member 10	protein-coding
mm_23141.1	chr3	38885877	38885887	+	1	NA	Intergenic	CpG	-1058	NM_183221	329628	Mm.316210	NM_183221	ENSMUSG00000046743	Fat4	6030410K14Rik|9430004M15	FAT atypical cadherin 4	protein-coding
mm_110092.1	chr12	25097240	25097283	-	1	NA	Intergenic	Intergenic	-1169	NM_010496	15902	Mm.34871	NM_010496	ENSMUSG00000020644	Id2	AI255428|C78922|Idb2|bHLHb26	inhibitor of DNA binding 2	protein-coding
mm_83097.1	chr9	40321271	40321293	-	1	NA	intron (NM_172768, intron 4 of 19)	intron (NM_172768, intron 4 of 19)	-12190	NR_040728	73558	Mm.398307	NR_040728		1700110K17Rik	-	RIKEN cDNA 1700110K17 gene	ncRNA
mm_169209.1	chr13	66487952	66487971	-	1	NA	Intergenic	Intergenic	-46843	NM_001290196	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
mm_19689.1	chr2	103467743	103467789	-	1	NA	exon (NM_009804, exon 7 of 13)	exon (NM_009804, exon 7 of 13)	17387	NM_009804	12359	Mm.4215	NM_009804	ENSMUSG00000027187	Cat	2210418N07|Cas-1|Cas1|Cs-1	catalase	protein-coding
mm_108905.1	chr12	100203634	100203673	+	1	NA	exon (NM_009790, exon 3 of 6)	exon (NM_009790, exon 3 of 6)	3509	NM_001313934	12313	Mm.285993	NM_009790	ENSMUSG00000001175	Calm1	AI256814|AI327027|AI461935|AL024000|CaM|Calm	calmodulin 1	protein-coding
mm_17406.1	chr2	27246756	27246777	-	1	NA	5' UTR (NM_138665, exon 1 of 21)	5' UTR (NM_138665, exon 1 of 21)	537	NM_138665	192166	Mm.278467	NM_138665	ENSMUSG00000009614	Sardh	-	sarcosine dehydrogenase	protein-coding
mm_26892.1	chr3	19140490	19140510	-	1	NA	intron (NM_028840, intron 4 of 6)	intron (NM_028840, intron 4 of 6)	22565	NM_028840	74252	Mm.200383	NM_028840	ENSMUSG00000027599	Armc1	2310016N05Rik|2900046P06Rik|3110009G21Rik|AA409258|AW048872|Arcp|C330014L16Rik	armadillo repeat containing 1	protein-coding
mm_24160.1	chr3	88531495	88531527	+	1	NA	promoter-TSS (NM_001029890)	promoter-TSS (NM_001029890)	-884	NM_001029890	72640	Mm.275154	NM_001029890	ENSMUSG00000074480	Mex3a	2700083E18Rik|Gm411|Rkhd4	mex3 RNA binding family member A	protein-coding
mm_80378.1	chr9	75410146	75410176	+	1	NA	promoter-TSS (NR_040719)	promoter-TSS (NR_040719)	-23	NR_040719	71274	Mm.399152	NR_040719	ENSMUSG00000097021	4933433G15Rik	4921522K19Rik	RIKEN cDNA 4933433G15 gene	ncRNA
mm_126174.1	chr15	78565979	78565996	+	1	NA	exon (NM_009008, exon 3 of 7)	exon (NM_009008, exon 3 of 7)	6796	NM_009008	19354	Mm.1972	NM_009008	ENSMUSG00000033220	Rac2	AI323801|AI452260	RAS-related C3 botulinum substrate 2	protein-coding
mm_161568.1	chr16	20325176	20325176	-	1	NA	intron (NM_183158, intron 1 of 8)	Lx7|LINE|L1	228	NM_183158	224044	Mm.276400	NM_183158	ENSMUSG00000022818	Cyp2ab1	EG224044|F730023N20	cytochrome P450, family 2, subfamily ab, polypeptide 1	protein-coding
mm_154119.1	chr19	57197351	57197366	-	1	NA	5' UTR (NM_001103177, exon 1 of 22)	5' UTR (NM_001103177, exon 1 of 22)	273	NM_001103177	226251	Mm.217161	NM_178688	ENSMUSG00000025085	Ablim1	2210411C18Rik|2610209L21Rik|4833406P10Rik|9330196J19Rik|AV079770|AW060987|AW215784|Limab1|mKIAA0059	actin-binding LIM protein 1	protein-coding
mm_24794.1	chr3	95545499	95545513	+	1	NA	exon (NM_021281, exon 5 of 8)	exon (NM_021281, exon 5 of 8)	-14171	NM_026489	67981	Mm.179050	NM_026489	ENSMUSG00000028109	Hormad1	4921522K05Rik|Nohma	HORMA domain containing 1	protein-coding
mm_41242.1	chr5	88765201	88765211	+	1	NA	5' UTR (NM_007832, exon 1 of 7)	5' UTR (NM_007832, exon 1 of 7)	193	NM_007832	13178	Mm.298892	NM_007832	ENSMUSG00000029366	Dck	-	deoxycytidine kinase	protein-coding
mm_101354.1	chr11	23739931	23739952	-	1	NA	Intergenic	Intergenic	31029	NM_009044	19696	Mm.4869	NM_009044	ENSMUSG00000020275	Rel	c-Rel	reticuloendotheliosis oncogene	protein-coding
mm_167119.1	chr7	119597258	119597264	+	1	NA	3' UTR (NM_146197, exon 14 of 14)	3' UTR (NM_146197, exon 14 of 14)	-20567	NM_054094	117147	Mm.427560	NM_054094	ENSMUSG00000033533	Acsm1	Acas3|Bucs1|Macs	acyl-CoA synthetase medium-chain family member 1	protein-coding
mm_17951.1	chr2	37146568	37146572	-	1	NA	Intergenic	Intergenic	-40922	NM_147051	259053	Mm.377810	NM_147051	ENSMUSG00000075377	Olfr362	MOR158-1	olfactory receptor 362	protein-coding
mm_77383.1	chr8	120101287	120101336	-	1	NA	5' UTR (NM_133967, exon 1 of 8)	5' UTR (NM_133967, exon 1 of 8)	161	NM_133967	102193	Mm.240076	NM_133967	ENSMUSG00000031823	Zdhhc7	AL024087|Gramp2	zinc finger, DHHC domain containing 7	protein-coding
mm_75544.1	chr8	57487737	57487795	-	1	NA	promoter-TSS (NM_021788)	promoter-TSS (NM_021788)	94	NM_021788	60406	Mm.118	NM_021788	ENSMUSG00000031609	Sap30	30kDa	sin3 associated polypeptide	protein-coding
mm_82958.1	chr9	35570444	35570450	-	1	NA	promoter-TSS (NM_029762)	promoter-TSS (NM_029762)	-378	NM_029762	76832	Mm.482285	NM_029762	ENSMUSG00000050555	Hyls1	3010015K02Rik	hydrolethalus syndrome 1	protein-coding
mm_167243.1	chr8	20892666	20892668	+	1	NA	promoter-TSS (NM_001039119)	promoter-TSS (NM_001039119)	0	NM_001039119	654453	Mm.237840	NM_001039119	ENSMUSG00000074454	Defb33	BD-33|EG654453	defensin beta 33	protein-coding
mm_140314.1	chr17	86223681	86223691	+	1	NA	intron (NM_011104, intron 1 of 14)	intron (NM_011104, intron 1 of 14)	55901	NM_011104	18754	Mm.24614	NM_011104	ENSMUSG00000045038	Prkce	5830406C15Rik|PKC[e]|PKCepsilon|Pkce|R75156	protein kinase C, epsilon	protein-coding
mm_57867.1	chr6	129623899	129623907	-	1	NA	promoter-TSS (NM_001286018)	promoter-TSS (NM_001286018)	-39	NM_001286018	27007	Mm.8217	NM_033078	ENSMUSG00000030149	Klrk1	D6H12S2489E|NKG2-D|Nkg2d	killer cell lectin-like receptor subfamily K, member 1	protein-coding
mm_34271.1	chr4	141424072	141424097	+	1	NA	3' UTR (NM_013868, exon 3 of 3)	3' UTR (NM_013868, exon 3 of 3)	3305	NM_013868	29818	Mm.46181	NM_013868	ENSMUSG00000006221	Hspb7	27kDa|Hsp25-2|cvHsp	heat shock protein family, member 7 (cardiovascular)	protein-coding
mm_90295.1	chr10	125388536	125388556	+	1	NA	Intergenic	Intergenic	-60011	NM_011391	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|Mct2	solute carrier family 16 (monocarboxylic acid transporters), member 7	protein-coding
mm_1448.1	chr1	67230542	67230555	+	1	NA	3' UTR (NM_001080809, exon 38 of 38)	3' UTR (NM_001080809, exon 38 of 38)	107521	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_47066.1	chr5	116422825	116422836	-	1	NA	promoter-TSS (NM_030704)	promoter-TSS (NM_030704)	34	NM_030704	80888	Mm.21549	NM_030704	ENSMUSG00000041548	Hspb8	AU018630|AW413033|Cryac|D5Ucla4|E2IG1|H11|H11K|HSP20-like|HSP22	heat shock protein 8	protein-coding
mm_135709.1	chr16	55523669	55523679	-	1	NA	Intergenic	Intergenic	28943	NR_039578	100628589		NR_039578	ENSMUSG00000093292	Mir5118	mmu-mir-5118|mu-mir-5118	microRNA 5118	ncRNA
mm_141834.1	chr17	34632373	34632410	-	1	NA	TTS (NM_030890)	TTS (NM_030890)	2705	NM_030890	260297	Mm.390965	NM_030890	ENSMUSG00000015476	Prrt1	Bat-4|Bat4|D17H6S54E|DSPD1|G5b|NG5|ORF31	proline-rich transmembrane protein 1	protein-coding
mm_24476.1	chr3	90692878	90692897	+	1	NA	exon (NM_001281852, exon 3 of 3)	exon (NM_001281852, exon 3 of 3)	2834	NM_001281852	20202	Mm.2128	NM_009114	ENSMUSG00000056071	S100a9	60B8Ag|AW546964|BEE22|Cagb|GAGB|L1Ag|MRP14|p14	S100 calcium binding protein A9 (calgranulin B)	protein-coding
mm_125044.1	chr15	25812714	25812725	+	1	NA	3' UTR (NM_019472, exon 41 of 41)	3' UTR (NM_019472, exon 41 of 41)	-30579	NM_001034851	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_32496.1	chr4	108391450	108391461	+	1	NA	Intergenic	Intergenic	-7800	NM_001099303	545667	Mm.380025	NM_001099303	ENSMUSG00000059816	Fam159a	OTTMUSG00000008243	family with sequence similarity 159, member A	protein-coding
mm_96185.1	chr11	61672196	61672218	+	1	NA	TTS (NM_001033227)	TTS (NM_001033227)	-12203	NM_178618	69640	Mm.458559	NM_178618	ENSMUSG00000042377	Fam83g	2310040C09Rik|AI506990|wly	family with sequence similarity 83, member G	protein-coding
mm_116938.1	chr13	56074046	56074059	-	1	NA	3' UTR (NM_001159515, exon 9 of 9)	3' UTR (NM_001159515, exon 9 of 9)	61498	NM_012015	26914	Mm.283802	NM_012015	ENSMUSG00000015937	H2afy	H2AF12M|mH2a1|macroH2A1	H2A histone family, member Y	protein-coding
mm_78239.1	chr9	21625945	21625959	+	1	NA	intron (NM_001174079, intron 1 of 33)	intron (NM_001174079, intron 1 of 33)	9783	NM_001174078	20586	Mm.286593	NM_011417	ENSMUSG00000032187	Smarca4	Brg1|HP1-BP72|SNF2beta|SW1/SNF|b2b508.1Clo|b2b692Clo	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	protein-coding
mm_143658.1	chr17	79713706	79713725	-	1	NA	exon (NM_009994, exon 2 of 3)	exon (NM_009994, exon 2 of 3)	1326	NM_009994	13078	Mm.214016	NM_009994	ENSMUSG00000024087	Cyp1b1	CP1B|P4501b1	cytochrome P450, family 1, subfamily b, polypeptide 1	protein-coding
mm_121851.1	chr14	20660872	20660888	-	1	NA	exon (NM_175132, exon 4 of 4)	exon (NM_175132, exon 4 of 4)	3694	NM_001310432	68760	Mm.35789	NM_175132	ENSMUSG00000039376	Synpo2l	1110054M18Rik|Chap	synaptopodin 2-like	protein-coding
mm_119348.1	chr14	41105545	41105569	+	1	NA	5' UTR (NM_133653, exon 2 of 10)	5' UTR (NM_133653, exon 2 of 10)	524	NM_133653	11720	Mm.14064	NM_133653	ENSMUSG00000037798	Mat1a	AI046368|AdoMet|Ams|MAT|MATA1|SAMS|SAMS1	methionine adenosyltransferase I, alpha	protein-coding
mm_92383.1	chr10	76442759	76442813	-	1	NA	5' UTR (NM_001282992, exon 1 of 42)	5' UTR (NM_001282992, exon 1 of 42)	126	NM_008787	18541	Mm.251794	NM_008787	ENSMUSG00000001151	Pcnt	AW476095|C86676|KEN|Pcnt2|kendrin|m239Asp|m275Asp	pericentrin (kendrin)	protein-coding
mm_128980.1	chr15	74833540	74833558	-	1	NA	Intergenic	B3|SINE|B2	8094	NM_001033229	110115	Mm.322606	NM_001033229	ENSMUSG00000075604	Cyp11b1	AA389061|CPN1|Cyp11b|Cyp11b-1|FHI	cytochrome P450, family 11, subfamily b, polypeptide 1	protein-coding
mm_131220.1	chr16	8850814	8850817	+	1	NA	intron (NM_001081400, intron 3 of 3)	intron (NM_001081400, intron 3 of 3)	20715	NM_001081400	69053	Mm.390868	NM_001081400	ENSMUSG00000022507	1810013L24Rik	1110017P05Rik|3010002C02Rik|AA792997|AW124177|Gm19906|R74903	RIKEN cDNA 1810013L24 gene	protein-coding
mm_152921.1	chr19	28011083	28011089	-	1	NA	promoter-TSS (NM_011265)	promoter-TSS (NM_011265)	80	NM_011265	19726	Mm.313321	NM_011265	ENSMUSG00000040929	Rfx3	C230093O12Rik|MRFX3	regulatory factor X, 3 (influences HLA class II expression)	protein-coding
mm_44727.1	chr5	31047880	31047886	-	1	NA	promoter-TSS (NM_027855)	promoter-TSS (NM_027855)	196	NM_177870	330064	Mm.205463	NM_177870	ENSMUSG00000006641	Slc5a6	E430023I20	solute carrier family 5 (sodium-dependent vitamin transporter), member 6	protein-coding
mm_134858.1	chr16	28445684	28445694	-	1	NA	5' UTR (NM_183064, exon 1 of 5)	5' UTR (NM_183064, exon 1 of 5)	386	NM_183064	14167	Mm.7996	NM_010199	ENSMUSG00000022523	Fgf12	AV114868|B230343J05Rik|FGF-12|FHF-1|Fhf1	fibroblast growth factor 12	protein-coding
mm_127644.1	chr15	102484154	102484188	+	1	NA	exon (NM_001174073, exon 8 of 13)	exon (NM_001174073, exon 8 of 13)	13539	NM_001174073	18521	Mm.236513	NM_011042	ENSMUSG00000056851	Pcbp2	AW412548|Hnrpx|alphaCP-2	poly(rC) binding protein 2	protein-coding
mm_75498.1	chr8	52197040	52197071	-	1	NA	Intergenic	Intergenic	-1314647	NM_001205054	11593	Mm.334535	NM_001005847	ENSMUSG00000031521	Aga	AW060726	aspartylglucosaminidase	protein-coding
mm_165273.1	chr2	76370336	76370366	+	1	NA	exon (NM_153405, exon 1 of 10)	exon (NM_153405, exon 1 of 10)	367	NM_153405	241490	Mm.33310	NM_153405	ENSMUSG00000042369	Rbm45	Drb1|Drbp1|G430095G15Rik	RNA binding motif protein 45	protein-coding
mm_97489.1	chr11	78326305	78326332	+	1	NA	exon (NM_009657, exon 8 of 8)	exon (NM_009657, exon 8 of 8)	-2104	NM_201406	276846	Mm.295908	NM_201406	ENSMUSG00000041958	Pigs	BC058979|Gm393|Gm689	phosphatidylinositol glycan anchor biosynthesis, class S	protein-coding
mm_167357.1	chr8	84237009	84237014	-	1	NA	promoter-TSS (NM_172503)	promoter-TSS (NM_172503)	31	NM_172503	212168	Mm.117094	NM_172503	ENSMUSG00000035671	Zswim4	D330002I24|E130119J17Rik	zinc finger SWIM-type containing 4	protein-coding
mm_153171.1	chr19	34493626	34493640	-	1	NA	3' UTR (NM_021460, exon 10 of 10)	3' UTR (NM_021460, exon 10 of 10)	-18498	NM_009890	12642	Mm.30824	NM_009890	ENSMUSG00000050370	Ch25h	AI462618|m25OH	cholesterol 25-hydroxylase	protein-coding
mm_5605.1	chr1	39577318	39577331	-	1	NA	promoter-TSS (NM_001033135)	promoter-TSS (NM_001033135)	23	NM_001033135	67702	Mm.28614	NM_001033135	ENSMUSG00000048234	Rnf149	1600023E10Rik|AV037261|C76763|Gm15832|Greul4|OTTMUSG00000026591	ring finger protein 149	protein-coding
mm_116142.1	chr13	29690801	29690804	-	1	NA	intron (NR_131896, intron 8 of 16)	intron (NR_131896, intron 8 of 16)	164871	NR_131896	68916	Mm.212227	NM_144536	ENSMUSG00000006191	Cdkal1	1190005B03Rik|6620401C13Rik	CDK5 regulatory subunit associated protein 1-like 1	protein-coding
mm_54635.1	chr6	38737469	38737483	-	1	NA	exon (NM_010433, exon 7 of 15)	exon (NM_010433, exon 7 of 15)	74407	NM_001101507	665180	Mm.349066	NM_001101507	ENSMUSG00000079598	Clec2l	AI414054|AW122724|Gm1064	C-type lectin domain family 2, member L	protein-coding
mm_36052.1	chr4	57301792	57301828	-	1	NA	promoter-TSS (NM_011207)	promoter-TSS (NM_011207)	27	NM_011207	545622	Mm.246552	NM_011207	ENSMUSG00000038764	Ptpn3	9530011I20Rik|PTP-H1|PTPCL	protein tyrosine phosphatase, non-receptor type 3	protein-coding
mm_1103.1	chr1	59763685	59763685	+	1	NA	promoter-TSS (NM_007561)	promoter-TSS (NM_007561)	-594	NM_007561	12168	Mm.7106	NM_007561	ENSMUSG00000067336	Bmpr2	2610024H22Rik|AL117858|AW546137|BB189135|BMP-2|BMPR-2|BMPR-II|BMPRII|BRK-3|Gm20272	bone morphogenetic protein receptor, type II (serine/threonine kinase)	protein-coding
mm_169693.1	chr15	74955690	74955692	+	1	NA	5' UTR (NM_001164036, exon 1 of 4)	5' UTR (NM_001164036, exon 1 of 4)	585	NM_001164040	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_146802.1	chr18	20741029	20741042	-	1	NA	intron (NM_019737, intron 1 of 8)	intron (NM_019737, intron 1 of 8)	5369	NM_019737	56386	Mm.393827	NM_019737	ENSMUSG00000056124	B4galt6	AA536803|AU022389	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 6	protein-coding
mm_63528.1	chr7	127918045	127918051	+	1	NA	intron (NM_026370, intron 3 of 10)	ID_B1|SINE|B4	5531	NM_026370	67773	Mm.425492	NM_026370	ENSMUSG00000030801	Kat8	2010203C02Rik|5830450F21Rik|D7Ertd629e|MOF|Myst1	K(lysine) acetyltransferase 8	protein-coding
mm_96923.1	chr11	70509692	70509793	+	1	NA	intron (NM_029360, intron 1 of 4)	intron (NM_029360, intron 1 of 4)	4468	NM_029360	75604	Mm.24400	NM_029360	ENSMUSG00000018919	Tm4sf5	2010003F10Rik|AI323987	transmembrane 4 superfamily member 5	protein-coding
mm_44550.1	chr5	24598905	24598918	-	1	NA	intron (NM_025891, intron 1 of 12)	CpG-10886	3091	NM_025891	66993	Mm.436539	NM_025891	ENSMUSG00000028949	Smarcd3	1500001J14Rik|2210409C08Rik|BAF60C	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3	protein-coding
mm_114648.1	chr13	77135065	77135114	+	1	NA	promoter-TSS (NM_001145676)	promoter-TSS (NM_001145676)	379	NM_134071	105377	Mm.209730	NM_134071	ENSMUSG00000021597	Slf1	2700017A04Rik|AW545819|Ankrd32|Brctd1|Brctx|C730024G01Rik	SMC5-SMC6 complex localization factor 1	protein-coding
mm_108238.1	chr12	77332037	77332050	+	1	NA	non-coding (NR_045554, exon 4 of 12)	non-coding (NR_045554, exon 4 of 12)	-56821	NM_001252615	53618	Mm.35628	NM_016893	ENSMUSG00000021065	Fut8	-	fucosyltransferase 8	protein-coding
mm_81704.1	chr9	111271951	111271963	+	1	NA	promoter-TSS (NM_026810)	promoter-TSS (NM_026810)	112	NM_175266	77781	Mm.209005	NM_175266	ENSMUSG00000046785	Epm2aip1	A930003G21Rik|mKIAA0766	EPM2A (laforin) interacting protein 1	protein-coding
mm_77789.1	chr9	3026653	3026682	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	12076	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_77202.1	chr8	113846120	113846125	-	1	NA	intron (NM_172466, intron 2 of 22)	intron (NM_172466, intron 2 of 22)	2717	NM_172466	208936	Mm.167471	NM_172466	ENSMUSG00000053399	Adamts18	9630038L21|ADAMTS21|E130314N14Rik	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 18	protein-coding
mm_66416.1	chr7	44529608	44529618	-	1	NA	intron (NM_019866, intron 3 of 5)	intron (NM_019866, intron 3 of 5)	2458	NM_019866	272382	Mm.8012	NM_019866	ENSMUSG00000008193	Spib	Spi-B	Spi-B transcription factor (Spi-1/PU.1 related)	protein-coding
mm_150632.1	chr19	41475930	41475933	+	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-49321	NM_001326287	627352	Mm.395111	NM_001326287		Morf4l1b	EG627352|Gm6747	mortality factor 4 like 1B	protein-coding
mm_104294.1	chr11	90389686	90389699	-	1	NA	intron (NM_172563, intron 1 of 3)	CpG	1225	NM_172563	217082	Mm.158903	NM_172563	ENSMUSG00000003949	Hlf	E230015K02Rik	hepatic leukemia factor	protein-coding
mm_90737.1	chr10	5367637	5367659	-	1	NA	exon (NM_153399, exon 15 of 32)	exon (NM_153399, exon 15 of 32)	120666	NM_001347711	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_7392.1	chr1	111864942	111864952	-	1	NA	promoter-TSS (NM_001081316)	promoter-TSS (NM_001081316)	-29	NM_001081316	319901	Mm.103468	NM_001081316	ENSMUSG00000038702	Dsel	9330132E09Rik|DS-epi2	dermatan sulfate epimerase-like	protein-coding
mm_31106.1	chr4	42916648	42916712	+	1	NA	promoter-TSS (NM_172690)	promoter-TSS (NM_172690)	-563	NM_001346526	230085	Mm.240965	NM_172690	ENSMUSG00000036062	Phf24	GINIP|N28178	PHD finger protein 24	protein-coding
mm_169379.1	chr14	37742491	37742494	-	1	NA	Intergenic	RLTR9D|LTR|ERVK	-607170	NM_078478	66092	Mm.182912	NM_078478	ENSMUSG00000041028	Ghitm	1010001P14Rik|C77840|MICS1|PTD010|Tmbim5	growth hormone inducible transmembrane protein	protein-coding
mm_141649.1	chr17	33663249	33663289	-	1	NA	exon (NM_001109913, exon 10 of 17)	exon (NM_001109913, exon 10 of 17)	22189	NM_001109913	76936	Mm.311439	NM_029804	ENSMUSG00000059208	Hnrnpm	2610023M21Rik|AA409009|Hnrpm|mKIAA4193	heterogeneous nuclear ribonucleoprotein M	protein-coding
mm_167083.1	chr7	101500643	101500649	+	1	NA	intron (NM_001243758, intron 7 of 30)	intron (NM_001243758, intron 7 of 30)	25270	NR_029791	387157		NR_029791	ENSMUSG00000065446	Mir139	Mirn139|mir-139|mmu-mir-139	microRNA 139	ncRNA
mm_56090.1	chr6	87346349	87346367	-	1	NA	exon (NM_025466, exon 6 of 6)	exon (NM_025466, exon 6 of 6)	4557	NM_025466	66283	Mm.46414	NM_025466	ENSMUSG00000030050	Gkn1	2200002K21Rik|AMP-18|BRICD1|Fov	gastrokine 1	protein-coding
mm_61697.1	chr7	81114817	81114847	+	1	NA	promoter-TSS (NM_001004184)	promoter-TSS (NM_001004184)	33	NM_001004184	434203	Mm.389909	NM_001004184	ENSMUSG00000025726	Slc28a1	Cnt1	solute carrier family 28 (sodium-coupled nucleoside transporter), member 1	protein-coding
mm_119675.1	chr14	52638453	52638472	+	1	NA	Intergenic	Intergenic	-142767	NM_001170918	57269	Mm.88822	NM_020512	ENSMUSG00000059887	Olfr1507	MOR244-1|Mor28|Or28	olfactory receptor 1507	protein-coding
mm_53938.1	chr6	4816306	4816320	-	1	NA	Intergenic	Intergenic	69007	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_161704.1	chr17	24474149	24474149	+	1	NA	5' UTR (NM_175682, exon 1 of 5)	5' UTR (NM_175682, exon 1 of 5)	265	NM_175682	319259	Mm.258355	NM_175682	ENSMUSG00000045744	Bricd5	9930021D14Rik	BRICHOS domain containing 5	protein-coding
mm_46909.1	chr5	114372626	114372656	-	1	NA	intron (NM_026145, intron 2 of 6)	intron (NM_026145, intron 2 of 6)	7864	NM_001159941	330171	Mm.238285	NM_026145	ENSMUSG00000001098	Kctd10	AW536343|C87062|mBACURD3	potassium channel tetramerisation domain containing 10	protein-coding
mm_142784.1	chr17	50156232	50156252	-	1	NA	intron (NM_181397, intron 2 of 9)	B1_Mus2|SINE|Alu	34255	NM_181397	76438	Mm.41854	NM_181397	ENSMUSG00000039316	Rftn1	2310015N21Rik|AI853526	raftlin lipid raft linker 1	protein-coding
mm_28196.1	chr3	88161305	88161324	-	1	NA	exon (NM_001310593, exon 7 of 11)	exon (NM_001310593, exon 7 of 11)	16471	NR_045997	76642	Mm.424420	NR_045997	ENSMUSG00000096935	1700113A16Rik	2210408E11Rik|AA408983	RIKEN cDNA 1700113A16 gene	ncRNA
mm_45590.1	chr5	74405096	74405132	-	1	NA	intron (NM_001286437, intron 4 of 7)	MLT1D|LTR|ERVL-MaLR	126628	NM_178672	212986	Mm.134147	NM_178672	ENSMUSG00000062110	Scfd2	E430013M20Rik|STXBP1L1	Sec1 family domain containing 2	protein-coding
mm_126089.1	chr15	77905555	77905596	+	1	NA	Intergenic	Intergenic	23419	NM_019913	56551	Mm.291917	NM_019913	ENSMUSG00000005354	Txn2	2510006J11Rik|AI788873|Trx2	thioredoxin 2	protein-coding
mm_52159.1	chr6	98019013	98019029	+	1	NA	3' UTR (NM_001178049, exon 10 of 10)	3' UTR (NM_001178049, exon 10 of 10)	27238	NM_008601	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_115373.1	chr13	113048391	113048401	+	1	NA	intron (NM_001281487, intron 2 of 11)	intron (NM_001281487, intron 2 of 11)	-2008	NM_027127	69590	Mm.12715	NM_027127	ENSMUSG00000021760	Gpx8	2310016C16Rik|AU017063	glutathione peroxidase 8 (putative)	protein-coding
mm_75434.1	chr8	47289395	47289411	-	1	NA	promoter-TSS (NM_001286376)	promoter-TSS (NM_001286376)	-1	NM_001114311	71069	Mm.23973	NM_175162	ENSMUSG00000038143	Stox2	4933409N07Rik|AI449080|AI835114|mKIAA1392	storkhead box 2	protein-coding
mm_120009.1	chr14	55672251	55672298	+	1	NA	promoter-TSS (NM_177992)	promoter-TSS (NM_177992)	39	NM_177992	105446	Mm.390685	NM_177992	ENSMUSG00000002326	Gmpr2	1810008P16Rik|5730544D12Rik|AA959850|GMPR 2	guanosine monophosphate reductase 2	protein-coding
mm_60711.1	chr7	45277345	45277351	+	1	NA	Intergenic	Intergenic	-5525	NM_001033176	76713	Mm.425445	NM_001033176	ENSMUSG00000070568	Slc6a21	1700039E15Rik|Gm19188	solute carrier family 6 member 21	protein-coding
mm_104701.1	chr11	97995864	97995935	-	1	NA	5' UTR (NM_207231, exon 1 of 6)	5' UTR (NM_207231, exon 1 of 6)	274	NM_207231	217151	Mm.277896	NM_207231	ENSMUSG00000038352	Arl5c	Arl12|BC065791	ADP-ribosylation factor-like 5C	protein-coding
mm_154075.1	chr19	56424592	56424592	-	1	NA	intron (NM_007611, intron 2 of 6)	intron (NM_007611, intron 2 of 6)	27463	NM_007611	12369	Mm.35687	NM_007611	ENSMUSG00000025076	Casp7	AI314680|CMH-1|ICE-IAP3|Mch3|caspase-7|mCASP-7	caspase 7	protein-coding
mm_18185.1	chr2	45111839	45111862	-	1	NA	promoter-TSS (NR_110571)	promoter-TSS (NR_110571)	-410	NR_110571	433424	Mm.441408	NR_110571	ENSMUSG00000052248	Zeb2os	Gm13476|OTTMUSG00000012358|Zeb2nat	zinc finger E-box binding homeobox 2, opposite strand	ncRNA
mm_159966.1	chr6	91986759	91986759	+	1	NA	intron (NM_172731, intron 1 of 20)	intron (NM_172731, intron 1 of 20)	7794	NM_172731	232237	Mm.295740	NM_172731	ENSMUSG00000034037	Fgd5	C330025N11Rik|ZFYVE23|mFLJ00274	FYVE, RhoGEF and PH domain containing 5	protein-coding
mm_125531.1	chr15	57976140	57976150	+	1	NA	Intergenic	Intergenic	-9758	NM_173862	239463	Mm.221241	NM_173862	ENSMUSG00000051225	Fam83a	-	family with sequence similarity 83, member A	protein-coding
mm_164304.1	chr15	103897428	103897442	-	1	NA	exon (NM_009267, exon 3 of 4)	exon (NM_009267, exon 3 of 4)	1865	NM_009268	20771	Mm.30276	NM_009268		Mucl1	Spt-2|Spt2	mucin-like 1	protein-coding
mm_109279.1	chr12	109547444	109547455	+	1	NA	intron (NR_027651, intron 5 of 8)	intron (NR_027651, intron 5 of 8)	2051	NR_003633	17263	Mm.289645	NM_144513	ENSMUSG00000021268	Meg3	2900016C05Rik|3110050O07Rik|6330408G06Rik|AI425946|AW108224|D12Bwg1266e|Gtl2|R74756|R75394	maternally expressed 3	ncRNA
mm_153719.1	chr19	44406531	44406582	-	1	NA	exon (NM_009127, exon 2 of 6)	exon (NM_009127, exon 2 of 6)	1153	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_55362.1	chr6	57535369	57535395	-	1	NA	promoter-TSS (NM_175523)	promoter-TSS (NM_175523)	44	NM_175523	243382	Mm.396893	NM_175523	ENSMUSG00000037826	Ppm1k	2900063A19Rik|A930026L03Rik|PP2Cm	protein phosphatase 1K (PP2C domain containing)	protein-coding
mm_80327.1	chr9	75037657	75037701	+	1	NA	promoter-TSS (NM_001142655)	promoter-TSS (NM_001142655)	-53	NM_021548	59046	Mm.247837	NM_021548	ENSMUSG00000007656	Arpp19	19kDa|2700024H10Rik|ARPP-19|AW559096|Arpp12	cAMP-regulated phosphoprotein 19	protein-coding
mm_63513.1	chr7	127875832	127875851	+	1	NA	intron (NM_146259, intron 1 of 2)	CpG	982	NM_146259	244219	Mm.207872	NM_146259	ENSMUSG00000049728	Zfp668	BC030314|E130018B19Rik|Znf668	zinc finger protein 668	protein-coding
mm_171337.1	chr4	102645806	102645807	-	1	NA	Intergenic	(TCTCCC)n|Simple_repeat|Simple_repeat	55963	NM_001177981	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_41202.1	chr5	88328420	88328424	+	1	NA	exon (NM_008644, exon 3 of 3)	exon (NM_008644, exon 3 of 3)	11110	NM_008644	17830	Mm.200411	NM_008644	ENSMUSG00000064156	Prol1	Muc10	proline rich, lacrimal 1	protein-coding
mm_97444.1	chr11	78188453	78188483	+	1	NA	promoter-TSS (NM_001159482)	promoter-TSS (NM_001159482)	41	NM_001159482	19376	Mm.275864	NM_033475	ENSMUSG00000002059	Rab34	AI326479|Narr|Rah|Rah1	RAB34, member RAS oncogene family	protein-coding
mm_163843.1	chr14	19418023	19418040	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	184556	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_168738.1	chr12	115158853	115158853	-	1	NA	Intergenic	Intergenic	536941	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
mm_151520.1	chr19	58739446	58739451	+	1	NA	intron (NM_018874, intron 10 of 12)	intron (NM_018874, intron 10 of 12)	10561	NM_018874	18946	Mm.10753	NM_018874	ENSMUSG00000042179	Pnliprp1	Plrp1	pancreatic lipase related protein 1	protein-coding
mm_91735.1	chr10	45578122	45578127	-	1	NA	exon (NM_172473, exon 1 of 24)	exon (NM_172473, exon 1 of 24)	295	NM_172473	209462	Mm.458633	NM_172473	ENSMUSG00000038822	Hace1	1700042J16Rik|A730034A22Rik|BC025474	HECT domain and ankyrin repeat containing, E3 ubiquitin protein ligase 1	protein-coding
mm_142690.1	chr17	47739356	47739364	-	1	NA	intron (NM_001161723, intron 1 of 8)	intron (NM_001161723, intron 1 of 8)	1429	NM_001161723	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_30419.1	chr3	152266123	152266152	-	1	NA	intron (NM_199465, intron 1 of 12)	intron (NM_199465, intron 1 of 12)	183	NM_199465	68810	Mm.200188	NM_199465	ENSMUSG00000039103	Nexn	1110046H09Rik|AA553326|NELIN	nexilin	protein-coding
mm_138560.1	chr17	35320530	35320557	+	1	NA	promoter-TSS (NM_010390)	promoter-TSS (NM_010390)	-15	NM_010390	15006	Mm.466882	NM_010390	ENSMUSG00000079507	H2-Q1	H-2Q1|Q1|Q1b|Q1d|Q1k|Qa-1|Qa1|Qed-1	histocompatibility 2, Q region locus 1	protein-coding
mm_79552.1	chr9	57972513	57972526	+	1	NA	Intergenic	Intergenic	-25505	NM_001346787	13070	Mm.302865	NM_019779	ENSMUSG00000032323	Cyp11a1	Cyp11a|Cypxia1|D9Ertd411e|P450scc|Scc|cscc	cytochrome P450, family 11, subfamily a, polypeptide 1	protein-coding
mm_24669.1	chr3	94681060	94681066	+	1	NA	Intergenic	MMERGLN-int|LTR|ERV1	-12510	NM_019414	20342	Mm.225405	NM_019414	ENSMUSG00000068877	Selenbp2	AP56|Lpsb2	selenium binding protein 2	protein-coding
mm_147464.1	chr18	46636329	46636333	-	1	NA	Intergenic	MER5A|DNA|hAT-Charlie	38627	NM_010120	13664	Mm.262037	NM_010120	ENSMUSG00000057561	Eif1a	C76390|Ef1a|Eftu|Eif4c|eIF-1A|eIF-4C	eukaryotic translation initiation factor 1A	protein-coding
mm_5336.1	chr1	23922395	23922438	-	1	NA	promoter-TSS (NM_028534)	promoter-TSS (NM_028534)	-35	NM_028534	98366	Mm.329963	NM_028534	ENSMUSG00000026155	Smap1	1700056O10Rik|4921514B13Rik|4921525H11Rik|AI462175	small ArfGAP 1	protein-coding
mm_31459.1	chr4	49059232	49059247	+	1	NA	promoter-TSS (NM_178756)	promoter-TSS (NM_178756)	-223	NM_178756	272031	Mm.299460	NM_178756	ENSMUSG00000063446	Plppr1	E130309F12Rik|Lppr1|PRG-3|mKIAA4247	phospholipid phosphatase related 1	protein-coding
mm_87189.1	chr10	39413527	39413536	+	1	NA	intron (NM_001122892, intron 2 of 12)	L1MB2|LINE|L1	43732	NM_001122893	14360	Mm.4848	NM_008054	ENSMUSG00000019843	Fyn	AI448320|AW552119	Fyn proto-oncogene	protein-coding
mm_141787.1	chr17	34305704	34305714	-	1	NA	promoter-TSS (NM_010382)	promoter-TSS (NM_010382)	-158	NM_010382	14969	Mm.22564	NM_010382	ENSMUSG00000060586	H2-Eb1	Eb|H-2Eb|H2Eb|Ia-4|Ia4	histocompatibility 2, class II antigen E beta	protein-coding
mm_38727.1	chr4	145236769	145236796	-	1	NA	intron (NM_011610, intron 1 of 9)	intron (NM_011610, intron 1 of 9)	10088	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_47404.1	chr5	123132273	123132283	-	1	NA	exon (NM_175092, exon 1 of 5)	exon (NM_175092, exon 1 of 5)	351	NM_175092	23912	Mm.253876	NM_175092	ENSMUSG00000029449	Rhof	AI845056|AV026554|Arhf|Ifld1|Rif	ras homolog family member F (in filopodia)	protein-coding
mm_161631.1	chr16	88932208	88932208	-	1	NA	promoter-TSS (NM_133359)	promoter-TSS (NM_133359)	56	NM_133359	170939	Mm.188445	NM_133359	ENSMUSG00000057174	Krtap19-9b	Krtap16-10b|Krtap16.10L	keratin associated protein 19-9B	protein-coding
mm_137370.1	chr17	25518469	25518484	+	1	NA	Intergenic	Intergenic	-21188	NM_001191008	20609	Mm.353282	NM_011425	ENSMUSG00000050824	Sstr5	Smstr5|sst5	somatostatin receptor 5	protein-coding
mm_131323.1	chr16	12450355	12450355	+	1	NA	Intergenic	Intergenic	-361035	NR_040507	75493	Mm.396146	NR_040507	ENSMUSG00000101565	1700003L19Rik	-	RIKEN cDNA 1700003L19 gene	ncRNA
mm_94927.1	chr11	29548210	29548255	+	1	NA	promoter-TSS (NM_024277)	promoter-TSS (NM_024277)	-192	NM_001033865	78294	Mm.180003	NM_024277	ENSMUSG00000020460	Rps27a	0610006J14Rik|Uba52|Ubb|Ubc	ribosomal protein S27A	protein-coding
mm_34436.1	chr4	147553258	147553276	+	1	NA	promoter-TSS (NM_001014397)	promoter-TSS (NM_001014397)	-10	NM_001014397	433804	Mm.332047	NM_001014397	ENSMUSG00000065999	Zfp985	Gm13154|OTTMUSG00000010673	zinc finger protein 985	protein-coding
mm_113669.1	chr13	42709651	42709739	+	1	NA	exon (NM_001005740, exon 1 of 13)	exon (NM_001005740, exon 1 of 13)	114	NM_001005740	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding
mm_26490.1	chr3	145292510	145292536	+	1	NA	promoter-TSS (NM_027770)	promoter-TSS (NM_027770)	51	NM_001317733	71355	Mm.235570	NM_027770	ENSMUSG00000028197	Col24a1	5430404K19Rik	collagen, type XXIV, alpha 1	protein-coding
mm_49232.1	chr6	17198102	17198110	+	1	NA	promoter-TSS (NR_102304)	promoter-TSS (NR_102304)	-1	NR_102304	319682	Mm.136046	NR_102304	ENSMUSG00000085171	D830026I12Rik	-	RIKEN cDNA D830026I12 gene	ncRNA
mm_157885.1	chrX	75843223	75843236	-	1	NA	promoter-TSS (NM_001346520)	promoter-TSS (NM_001346520)	-166	NM_001346520	102866	Mm.28777	NM_145629	ENSMUSG00000016382	Pls3	AI115446|AL024105	plastin 3 (T-isoform)	protein-coding
mm_116593.1	chr13	48537828	48537834	-	1	NA	promoter-TSS (NR_029731)	promoter-TSS (NR_029731)	86	NR_029731	387252		NR_029731	ENSMUSG00000105621	Mirlet7f-1	Mirlet7f1|Mirnlet7f1|let-7f-1	microRNA let7f-1	ncRNA
mm_112798.1	chr13	20445285	20445289	+	1	NA	intron (NM_080288, intron 15 of 21)	intron (NM_080288, intron 15 of 21)	-27703	NM_198093	140580	Mm.342392	NM_080288	ENSMUSG00000041112	Elmo1	6330578D22Rik|C230095H21Rik|CED-12	engulfment and cell motility 1	protein-coding
mm_79051.1	chr9	46229163	46229191	+	1	NA	exon (NM_009692, exon 3 of 4)	exon (NM_009692, exon 3 of 4)	547	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2|apo-AI|apoA-I	apolipoprotein A-I	protein-coding
mm_7172.1	chr1	92127937	92127963	-	1	NA	intron (NM_207225, intron 2 of 26)	L1M4|LINE|L1	52391	NM_207225	208727	Mm.318567	NM_207225	ENSMUSG00000026313	Hdac4	4932408F19Rik|HD4	histone deacetylase 4	protein-coding
mm_73128.1	chr8	94857475	94857494	+	1	NA	promoter-TSS (NM_009090)	promoter-TSS (NM_009090)	34	NM_009090	20021	Mm.292492	NM_009090	ENSMUSG00000031783	Polr2c	33kDa|RPB3|Rpo2-3|mRBP31	polymerase (RNA) II (DNA directed) polypeptide C	protein-coding
mm_89441.1	chr10	91171759	91171770	+	1	NA	promoter-TSS (NM_001080132)	promoter-TSS (NM_001080132)	-145	NM_001080130	21917	Mm.159684	NM_011605	ENSMUSG00000019961	Tmpo	5630400D24Rik|AI195756|AI606875|AW214352|AW547477|LAP2|TP	thymopoietin	protein-coding
mm_99972.1	chr11	113751977	113751997	+	1	NA	promoter-TSS (NM_001163346)	promoter-TSS (NM_001163346)	-172	NM_001163346	56699	Mm.293378	NM_020006	ENSMUSG00000041598	Cdc42ep4	1500041M20Rik|Borg4|CEP4	CDC42 effector protein (Rho GTPase binding) 4	protein-coding
mm_173226.1	chrX	7671311	7671330	-	1	NA	promoter-TSS (NM_019755)	promoter-TSS (NM_019755)	70	NM_019755	18824	Mm.18565	NM_019755	ENSMUSG00000031146	Plp2	mIMA4	proteolipid protein 2	protein-coding
mm_4238.1	chr1	171388921	171388935	+	1	NA	promoter-TSS (NM_001005508)	promoter-TSS (NM_001005508)	-32	NM_001005508	226652	Mm.251048	NM_001005508	ENSMUSG00000048865	Arhgap30	6030405P05Rik|Gm102|mFLJ00267	Rho GTPase activating protein 30	protein-coding
mm_129087.1	chr15	75909290	75909311	-	1	NA	promoter-TSS (NM_001285430)	promoter-TSS (NM_001285430)	44	NM_001285433	66656	Mm.258927	NM_023240	ENSMUSG00000055762	Eef1d	EF-1-delta	eukaryotic translation elongation factor 1 delta (guanine nucleotide exchange protein)	protein-coding
mm_104979.1	chr11	100248954	100248969	-	1	NA	promoter-TSS (NM_008470)	promoter-TSS (NM_008470)	-59	NM_008470	16666	Mm.422799	NM_008470	ENSMUSG00000053797	Krt16	AI324768|CK-16|K16|Krt1-16	keratin 16	protein-coding
mm_137492.1	chr17	26951658	26951684	+	1	NA	intron (NM_001281491, intron 3 of 18)	intron (NM_001281491, intron 3 of 18)	-3552	NR_037244	100526534		NR_037244	ENSMUSG00000093118	Mir3083	mir-3083|mmu-mir-3083	microRNA 3083	ncRNA
mm_101823.1	chr11	46699050	46699075	-	1	NA	promoter-TSS (NM_001161355)	promoter-TSS (NM_001161355)	-232	NM_001161355	171284	Mm.234654	NM_134249	ENSMUSG00000040413	Timd2	AA816106|AU019358|AU019662|C78111|G9D3|TIM-2|Tim2	T cell immunoglobulin and mucin domain containing 2	protein-coding
mm_14041.1	chr2	122234834	122234841	+	1	NA	promoter-TSS (NM_146126)	promoter-TSS (NM_146126)	-2	NM_146126	20322	Mm.371580	NM_146126	ENSMUSG00000027227	Sord	Sdh-1|Sdh1|Sodh-1	sorbitol dehydrogenase	protein-coding
mm_33806.1	chr4	135120641	135120660	+	1	NA	promoter-TSS (NM_019732)	promoter-TSS (NM_019732)	5	NM_019732	12399	Mm.378894	NM_019732	ENSMUSG00000070691	Runx3	AML2|Cbfa3|Pebp2a3	runt related transcription factor 3	protein-coding
mm_47862.1	chr5	134611886	134611897	-	1	NA	intron (NM_020044, intron 1 of 12)	intron (NM_020044, intron 1 of 12)	3134	NM_022964	56743	Mm.391375	NM_020044	ENSMUSG00000040751	Lat2	AW125574|LAB|NTAL|WSCR5|Wbscr15|Wbscr5	linker for activation of T cells family, member 2	protein-coding
mm_74205.1	chr8	123892941	123892961	+	1	NA	exon (NM_009606, exon 4 of 7)	exon (NM_009606, exon 4 of 7)	1824	NM_001272041	11459	Mm.214950	NM_009606	ENSMUSG00000031972	Acta1	AA959943|Acta-2|Acts|Actsk-1	actin, alpha 1, skeletal muscle	protein-coding
mm_54853.1	chr6	42592357	42592362	-	1	NA	intron (NM_203396, intron 3 of 6)	intron (NM_203396, intron 3 of 6)	5013	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_166885.1	chr7	27487128	27487162	+	1	NA	intron (NM_018820, intron 1 of 1)	CpG	192	NM_018820	55942	Mm.153684	NM_018820	ENSMUSG00000008384	Sertad1	1110032C13Rik|AV000455|AW456625|Sei-1|Sei1|TRIP-Br1	SERTA domain containing 1	protein-coding
mm_72630.1	chr8	84663000	84663006	+	1	NA	promoter-TSS (NM_010499)	promoter-TSS (NM_010499)	-151	NM_010499	15936	Mm.399	NM_010499	ENSMUSG00000053560	Ier2	AI317238|Ch1|Pip92	immediate early response 2	protein-coding
mm_64450.1	chr7	142658911	142658953	+	1	NA	promoter-TSS (NM_010514)	promoter-TSS (NM_010514)	-128	NM_010514	16002	Mm.3862	NM_010514	ENSMUSG00000048583	Igf2	AL033362|Igf-2|Igf-II|M6pr|Mpr|Peg2	insulin-like growth factor 2	protein-coding
mm_57221.1	chr6	123261978	123262036	-	1	NA	promoter-TSS (NM_010819)	promoter-TSS (NM_010819)	-100	NM_001163161	17474	Mm.441101	NM_010819	ENSMUSG00000030144	Clec4d	Clecsf8|Mpcl|mcl	C-type lectin domain family 4, member d	protein-coding
mm_136368.1	chr16	92817031	92817055	-	1	NA	intron (NM_001111022, intron 2 of 6)	B3A|SINE|B2	9031	NM_001111021	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_16833.1	chr2	11494010	11494020	-	1	NA	exon (NM_001177754, exon 2 of 16)	exon (NM_001177754, exon 2 of 16)	8075	NM_001177754	170768	Mm.19669	NM_133232	ENSMUSG00000026773	Pfkfb3	E330010H22Rik|iPFK-2|uPFK-2	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	protein-coding
mm_33203.1	chr4	126314136	126314139	+	1	NA	3' UTR (NM_199473, exon 4 of 4)	3' UTR (NM_199473, exon 4 of 4)	7566	NM_133883	100206	Mm.11285	NM_133883	ENSMUSG00000042558	Adprhl2	AI836109|Arh3	ADP-ribosylhydrolase like 2	protein-coding
mm_19798.1	chr2	110050469	110050482	-	1	NA	promoter-TSS (NR_040508)	promoter-TSS (NR_040508)	4	NR_040508	75517	Mm.363927	NR_040508	ENSMUSG00000086186	Ccdc34os	1700024P03Rik	coiled-coil domain containing 34, opposite strand	ncRNA
mm_120413.1	chr14	65266705	65266752	+	1	NA	promoter-TSS (NM_015795)	promoter-TSS (NM_015795)	27	NM_015795	50759	Mm.65308	NM_015795	ENSMUSG00000034532	Fbxo16	4932435C24Rik|Fbx16	F-box protein 16	protein-coding
mm_50958.1	chr6	58862965	58862976	+	1	NA	intron (NM_028705, intron 8 of 24)	intron (NM_028705, intron 8 of 24)	29270	NM_028705	73998	Mm.191892	NM_028705	ENSMUSG00000029804	Herc3	5730409F18Rik|AI646603|mKIAA0032	hect domain and RLD 3	protein-coding
mm_124842.1	chr15	9370698	9370704	+	1	NA	3' UTR (NM_144845, exon 7 of 7)	3' UTR (NM_144845, exon 7 of 7)	35103	NM_144845	223337	Mm.422853	NM_144845	ENSMUSG00000049152	Ugt3a2	AI313915	UDP glycosyltransferases 3 family, polypeptide A2	protein-coding
mm_18851.1	chr2	75676239	75676272	-	1	NA	exon (NM_010902, exon 5 of 5)	exon (NM_010902, exon 5 of 5)	16965	NR_033513	627828	Mm.459502	NR_033513	ENSMUSG00000092086	Gm6793	EG627828	heterogeneous nuclear ribonucleoprotein A3 pseudogene	pseudo
mm_144652.1	chr18	34220979	34221020	+	1	NA	promoter-TSS (NM_007462)	promoter-TSS (NM_007462)	15	NM_007462	11789	Mm.384171	NM_007462	ENSMUSG00000005871	Apc	AI047805|AU020952|AW124434|CC1|Min|mAPC	adenomatosis polyposis coli	protein-coding
mm_33877.1	chr4	136172368	136172395	+	1	NA	5' UTR (NM_177733, exon 1 of 7)	5' UTR (NM_177733, exon 1 of 7)	107	NM_177733	242705	Mm.307932	NM_177733	ENSMUSG00000018983	E2f2	E2F-2	E2F transcription factor 2	protein-coding
mm_21008.1	chr2	152376570	152376637	-	1	NA	promoter-TSS (NM_001009948)	promoter-TSS (NM_001009948)	-37	NM_001009948	228777	Mm.330667	NM_001009948	ENSMUSG00000059361	Nrsn2	Gm123|Neurensin-2	neurensin 2	protein-coding
mm_107443.1	chr12	36326303	36326345	+	1	NA	Intergenic	L1MB1|LINE|L1	12155	NM_025312	66042	Mm.43375	NM_025312	ENSMUSG00000036169	Sostdc1	0610006G05Rik|Sostl|USAG-1|Wise|ectodin	sclerostin domain containing 1	protein-coding
mm_58422.1	chr7	3293127	3293135	+	1	NA	5' UTR (NM_001093766, exon 1 of 2)	5' UTR (NM_001093766, exon 1 of 2)	103	NM_001093766	50918	Mm.29874	NM_016969	ENSMUSG00000068566	Myadm	D7Wsu62e	myeloid-associated differentiation marker	protein-coding
mm_164983.1	chr19	10077447	10077450	+	1	NA	intron (NM_019699, intron 5 of 11)	MTE2b-int|LTR|ERVL-MaLR	24055	NM_019699	56473	Mm.38901	NM_019699	ENSMUSG00000024665	Fads2	2900042M13Rik|Fadsd2	fatty acid desaturase 2	protein-coding
mm_99060.1	chr11	99155173	99155185	+	1	NA	promoter-TSS (NM_007719)	promoter-TSS (NM_007719)	-102	NM_007719	12775	Mm.2932	NM_007719	ENSMUSG00000037944	Ccr7	CC-CKR-7|CCR-7|CD197|Cdw197|Cmkbr7|EBI1|Ebi1h	chemokine (C-C motif) receptor 7	protein-coding
mm_160584.1	chr9	63602514	63602514	-	1	NA	promoter-TSS (NM_025857)	promoter-TSS (NM_025857)	-21	NM_001311098	78250	Mm.444612	NM_030068	ENSMUSG00000037801	Iqch	4921504K03Rik	IQ motif containing H	protein-coding
mm_99435.1	chr11	102432787	102432802	+	1	NA	intron (NM_008175, intron 1 of 12)	intron (NM_008175, intron 1 of 12)	2472	NM_008175	14824	Mm.1568	NM_008175	ENSMUSG00000034708	Grn	Pgrn|epithelin	granulin	protein-coding
mm_133225.1	chr16	76403326	76403378	+	1	NA	Intergenic	Intergenic	-30303	NM_173440	268903	Mm.74711	NM_173440	ENSMUSG00000048490	Nrip1	6030458L20Rik|8430438I05Rik|9630050P12|AA959574|AW456757|RIP140	nuclear receptor interacting protein 1	protein-coding
mm_30161.1	chr3	144186518	144186521	-	1	NA	Intergenic	Intergenic	15813	NM_001161770	16911	Mm.29187	NM_010723	ENSMUSG00000028266	Lmo4	A730077C12Rik|Crp3|Etohi4	LIM domain only 4	protein-coding
mm_78338.1	chr9	25277553	25277614	+	1	NA	exon (NM_001205367, exon 3 of 13)	exon (NM_001205367, exon 3 of 13)	25144	NM_001205367	235072	Mm.270259	NM_009859	ENSMUSG00000001833	Sept7	Cdc10|E430034N22	septin 7	protein-coding
mm_73930.1	chr8	119918314	119918337	+	1	NA	intron (NM_001310630, intron 1 of 13)	intron (NM_001310630, intron 1 of 13)	7965	NM_001310630	22224	Mm.256910	NM_009462	ENSMUSG00000031826	Usp10	2610014N07Rik|UBPO|Uchrp|mKIAA0190	ubiquitin specific peptidase 10	protein-coding
mm_150156.1	chr19	32224205	32224207	+	1	NA	intron (NM_001168525, intron 4 of 9)	intron (NM_001168525, intron 4 of 9)	-13193	NM_001168526	208449	Mm.329810	NM_144792	ENSMUSG00000040451	Sgms1	9530058O11Rik|AI841905|C80702|Mob|Sms1|Sor1|Tmem23	sphingomyelin synthase 1	protein-coding
mm_37711.1	chr4	129491086	129491095	-	1	NA	promoter-TSS (NM_080442)	promoter-TSS (NM_080442)	-100	NM_001085491	68233	Mm.424983	NM_001085491	ENSMUSG00000078554	Fam229a	1700125D06Rik	family with sequence similarity 229, member A	protein-coding
mm_119149.1	chr14	31494349	31494367	+	1	NA	promoter-TSS (NM_028932)	promoter-TSS (NM_028932)	619	NM_025907	67011	Mm.291731	NM_025907	ENSMUSG00000021891	Mettl6	1600013P15Rik|AI467521|AU020711	methyltransferase like 6	protein-coding
mm_60822.1	chr7	45705411	45705423	+	1	NA	TTS (NM_009800)	TTS (NM_009800)	170	NM_016974	13170	Mm.24222	NM_016974	ENSMUSG00000059824	Dbp	-	D site albumin promoter binding protein	protein-coding
mm_70788.1	chr8	22506494	22506509	+	1	NA	intron (NM_011394, intron 1 of 10)	intron (NM_011394, intron 1 of 10)	-29622	NM_001146117	102032	Mm.378231	NM_001012667	ENSMUSG00000031534	Smim19	AI316807|BG694986|EST-c39	small integral membrane protein 19	protein-coding
mm_116242.1	chr13	33920897	33920899	-	1	NA	intron (NM_001243192, intron 6 of 7)	intron (NM_001243192, intron 6 of 7)	-15134	NR_040707	68808	Mm.443347	NR_040707	ENSMUSG00000085457	1110046J04Rik	-	RIKEN cDNA 1110046J04 gene	ncRNA
mm_107636.1	chr12	52216657	52216660	+	1	NA	intron (NM_029760, intron 6 of 10)	intron (NM_029760, intron 6 of 10)	118912	NM_029760	76826	Mm.244781	NM_029760	ENSMUSG00000035142	Nubpl	2410170E07Rik	nucleotide binding protein-like	protein-coding
mm_140855.1	chr17	23700182	23700201	-	1	NA	Intergenic	CpG	-16165	NM_020293	56863	Mm.491368	NM_020293	ENSMUSG00000066720	Cldn9	nmf329	claudin 9	protein-coding
mm_28343.1	chr3	89402651	89402669	-	1	NA	promoter-TSS (NM_020517)	promoter-TSS (NM_020517)	-10	NM_020517	57275	Mm.482283	NM_020517	ENSMUSG00000078173	Lenep	AU018355|Lep503	lens epithelial protein	protein-coding
mm_119006.1	chr14	29021404	29021413	+	1	NA	intron (NM_176920, intron 1 of 2)	intron (NM_176920, intron 1 of 2)	3200	NM_176920	319476	Mm.95780	NM_176920	ENSMUSG00000045776	Lrtm1	A930016D02Rik	leucine-rich repeats and transmembrane domains 1	protein-coding
mm_56171.1	chr6	88000511	88000533	-	1	NA	exon (NM_009005, exon 6 of 6)	exon (NM_009005, exon 6 of 6)	18839	NR_026990	434064	Mm.371796	NR_026990	ENSMUSG00000084950	Gm5577	EG434064	predicted gene 5577	ncRNA
mm_119228.1	chr14	33294047	33294050	+	1	NA	intron (NM_153800, intron 3 of 10)	intron (NM_153800, intron 3 of 10)	77225	NM_153800	239027	Mm.318350	NM_153800	ENSMUSG00000063506	Arhgap22	B230341L19Rik|RHOGAP2|p68RacGAP	Rho GTPase activating protein 22	protein-coding
mm_55174.1	chr6	51987837	51987844	-	1	NA	intron (NM_018773, intron 4 of 12)	L1MB7|LINE|L1	24709	NM_018773	54353	Mm.221479	NM_018773	ENSMUSG00000059182	Skap2	2610021A10Rik|AA960083|BB137539|RA70|SKAP-HOM|Saps|Scap2|mSKAP55R	src family associated phosphoprotein 2	protein-coding
mm_80561.1	chr9	83587954	83587968	+	1	NA	intron (NM_172507, intron 2 of 3)	intron (NM_172507, intron 2 of 3)	39623	NM_172507	212531	Mm.491246	NM_172507	ENSMUSG00000032261	Sh3bgrl2	A930014C21Rik|AA408038|B930089I21	SH3 domain binding glutamic acid-rich protein like 2	protein-coding
mm_162342.1	chr1	48582685	48582689	+	1	NA	Intergenic	Intergenic	-1115562	NR_105768	102466969		NR_105768	ENSMUSG00000098876	Mir6350	Gm27958|mmu-mir-6350	microRNA 6350	ncRNA
mm_86983.1	chr10	25441412	25441450	+	1	NA	intron (NM_013511, intron 1 of 19)	intron (NM_013511, intron 1 of 19)	33063	NM_013511	13822	Mm.306026	NM_013511	ENSMUSG00000019978	Epb41l2	4.1G|AW555191|D10Ertd398e|Epb4.1l2|NBL2	erythrocyte membrane protein band 4.1 like 2	protein-coding
mm_79988.1	chr9	67013063	67013074	+	1	NA	Intergenic	Intergenic	30803	NM_001164252	22003	Mm.121878	NM_024427	ENSMUSG00000032366	Tpm1	AA986836|AI854628|TM2|Tm3|Tmpa|Tpm-1|alpha-TM	tropomyosin 1, alpha	protein-coding
mm_147723.1	chr18	60848912	60848976	-	1	NA	promoter-TSS (NM_011552)	promoter-TSS (NM_011552)	20	NM_011552	21453	Mm.486251	NM_011552	ENSMUSG00000024613	Tcof1	AA408847|AW209012|treacle	treacle ribosome biogenesis factor 1	protein-coding
mm_46823.1	chr5	113163918	113163921	-	1	NA	promoter-TSS (NM_172884)	promoter-TSS (NM_172884)	-606	NM_172884	243219	Mm.160131	NM_172884	ENSMUSG00000051339	2900026A02Rik	8430408O14Rik|A530094D01|AW539426|Gm449|Kiaa1671|mKIAA1671	RIKEN cDNA 2900026A02 gene	protein-coding
mm_69330.1	chr7	128740413	128740423	-	1	NA	promoter-TSS (NM_145955)	promoter-TSS (NM_145955)	11	NM_145955	210711	Mm.58882	NM_145955	ENSMUSG00000048170	Mcmbp	1110007A13Rik|AU017382|BC025641|MCM-BP	minichromosome maintenance complex binding protein	protein-coding
mm_161610.1	chr16	44943690	44943690	+	1	NA	promoter-TSS (NM_029018)	promoter-TSS (NM_029018)	12	NM_001128132	74603	Mm.297337	NM_027578	ENSMUSG00000036172	Cd200r3	4733401I18Rik|4833409J19Rik|AI505817|BB106877|mCD200RLb	CD200 receptor 3	protein-coding
mm_118478.1	chr14	11697054	11697057	+	1	NA	intron (NM_008981, intron 1 of 29)	intron (NM_008981, intron 1 of 29)	143502	NM_008981	19270	Mm.431266	NM_008981	ENSMUSG00000021745	Ptprg	5430405N12Rik|AW046354|AW549872|RPTPgamma	protein tyrosine phosphatase, receptor type, G	protein-coding
mm_151350.1	chr19	55897942	55897950	+	1	NA	intron (NM_001142924, intron 1 of 11)	intron (NM_001142924, intron 1 of 11)	2625	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_160980.1	chr11	102604748	102604748	+	1	NA	exon (NM_020510, exon 1 of 1)	exon (NM_020510, exon 1 of 1)	317	NM_020510	57265	Mm.36416	NM_020510	ENSMUSG00000050288	Fzd2	AL033370|AW456835|Fz10|Fzd10|Mfz10|Mfz10a	frizzled class receptor 2	protein-coding
mm_115044.1	chr13	99939580	99939613	+	1	NA	Intergenic	Intergenic	-38913	NM_001081493	27220	Mm.75498	NM_013732	ENSMUSG00000021647	Cartpt	Cart	CART prepropeptide	protein-coding
mm_170675.1	chr2	121480984	121480996	+	1	NA	Intergenic	Intergenic	-6967	NM_001081975	100034361	Mm.270393	NM_001081975	ENSMUSG00000048222	Mfap1b	-	microfibrillar-associated protein 1B	protein-coding
mm_141444.1	chr17	29842343	29842355	-	1	NA	exon (NM_001081160, exon 9 of 16)	exon (NM_001081160, exon 9 of 16)	45533	NM_001081160	74762	Mm.40901	NM_001081160	ENSMUSG00000043557	Mdga1	1200011I03Rik|GPIM|Mamdc3	MAM domain containing glycosylphosphatidylinositol anchor 1	protein-coding
mm_146878.1	chr18	25505052	25505077	-	1	NA	intron (NM_001146293, intron 3 of 12)	intron (NM_001146293, intron 3 of 12)	248919	NM_133195	108013	Mm.266435	NM_133195	ENSMUSG00000024268	Celf4	A230070D14Rik|BRUNOL-4|Brul4|Brunol4|C130060B05Rik	CUGBP, Elav-like family member 4	protein-coding
mm_163854.1	chr14	19418427	19418476	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	184136	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_76783.1	chr8	99416398	99416462	-	1	NA	promoter-TSS (NM_001285913)	promoter-TSS (NM_001285913)	41	NM_001285913	12564	Mm.441131	NM_007667	ENSMUSG00000036510	Cdh8	AI851472|cad8	cadherin 8	protein-coding
mm_40281.1	chr5	43103976	43103987	+	1	NA	Intergenic	Intergenic	-129482	NM_175937	231207	Mm.7233	NM_175937	ENSMUSG00000039782	Cpeb2	A630055H10Rik|Cpe-bp2	cytoplasmic polyadenylation element binding protein 2	protein-coding
mm_537.1	chr1	37998098	37998114	+	1	NA	promoter-TSS (NM_172054)	promoter-TSS (NM_172054)	96	NM_198303	226982	Mm.260943	NM_198303	ENSMUSG00000026083	Eif5b	A030003E17Rik|BC018347|IF2	eukaryotic translation initiation factor 5B	protein-coding
mm_154188.1	chr19	58822439	58822447	-	1	NA	intron (NM_001327998, intron 5 of 12)	intron (NM_001327998, intron 5 of 12)	-28029	NM_026208	67507	Mm.27027	NM_026208	ENSMUSG00000026931	1700019N19Rik	-	RIKEN cDNA 1700019N19 gene	protein-coding
mm_16918.1	chr2	13573558	13573565	-	1	NA	promoter-TSS (NM_011701)	promoter-TSS (NM_011701)	-750	NM_011701	22352	Mm.268000	NM_011701	ENSMUSG00000026728	Vim	-	vimentin	protein-coding
mm_134747.1	chr16	23108105	23108118	-	1	NA	promoter-TSS (NR_030705)	promoter-TSS (NR_030705)	643	NR_110335	13682	Mm.260084	NM_013506	ENSMUSG00000022884	Eif4a2	4833432N07Rik|BM-010|Ddx2b|Eif4|eIF-4A-II|eIF4A-II	eukaryotic translation initiation factor 4A2	protein-coding
mm_16859.1	chr2	11651497	11651500	-	1	NA	intron (NM_008367, intron 1 of 7)	ID_B1|SINE|B4	8706	NM_008367	16184	Mm.915	NM_008367	ENSMUSG00000026770	Il2ra	CD25|Il2r|Ly-43	interleukin 2 receptor, alpha chain	protein-coding
mm_128766.1	chr15	66286766	66286802	-	1	NA	promoter-TSS (NM_152923)	promoter-TSS (NM_152923)	-560	NM_152923	110862	Mm.255585	NM_152923	ENSMUSG00000056258	Kcnq3	-	potassium voltage-gated channel, subfamily Q, member 3	protein-coding
mm_151219.1	chr19	53677328	53677340	+	1	NA	promoter-TSS (NM_001170847)	promoter-TSS (NM_001170847)	28	NM_001170847	73713	Mm.313695	NM_001170847	ENSMUSG00000043639	Rbm20	1110018J23Rik|2010003H22Rik|AI646761	RNA binding motif protein 20	protein-coding
mm_81839.1	chr9	118481266	118481287	+	1	NA	exon (NM_010136, exon 3 of 6)	exon (NM_010136, exon 3 of 6)	3087	NM_010136	13813	Mm.200692	NM_010136	ENSMUSG00000032446	Eomes	C77258|TBR-2|Tbr2	eomesodermin	protein-coding
mm_107161.1	chr12	24581500	24581529	+	1	NA	exon (NM_001161406, exon 4 of 16)	exon (NM_001161406, exon 4 of 16)	795	NM_145890	195733	Mm.263068	NM_145890	ENSMUSG00000020656	Grhl1	LBP-32|MGR|Tcfcp2l2	grainyhead-like 1 (Drosophila)	protein-coding
mm_14345.1	chr2	129593361	129593377	+	1	NA	5' UTR (NM_001291022, exon 1 of 5)	5' UTR (NM_001291022, exon 1 of 5)	200	NM_001291022	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_3039.1	chr1	134040253	134040262	+	1	NA	exon (NM_021355, exon 2 of 3)	exon (NM_021355, exon 2 of 3)	2742	NM_021355	14264	Mm.287146	NM_021355	ENSMUSG00000041559	Fmod	AI131919|AU041740|SLRR2E	fibromodulin	protein-coding
mm_131634.1	chr16	20188810	20188811	+	1	NA	intron (NM_001033237, intron 10 of 29)	RLTR40|LTR|ERVK	-12576	NR_030454	735274		NR_030454	ENSMUSG00000106252	Mir684-1	Mirn684-1	microRNA 684-1	ncRNA
mm_48517.1	chr5	142895234	142895242	-	1	NA	promoter-TSS (NM_001033312)	promoter-TSS (NM_001033312)	0	NM_001033312	231863	Mm.89753	NM_001033312	ENSMUSG00000066640	Fbxl18	AI427077|B130019G13Rik|C330021B20Rik	F-box and leucine-rich repeat protein 18	protein-coding
mm_63971.1	chr7	139944748	139944763	+	1	NA	exon (NM_009482, exon 2 of 2)	exon (NM_009482, exon 2 of 2)	899	NM_009482	22286	Mm.10205	NM_009482	ENSMUSG00000047751	Utf1	AI505934	undifferentiated embryonic cell transcription factor 1	protein-coding
mm_79746.1	chr9	62367872	62367883	+	1	NA	intron (NM_009672, intron 1 of 6)	intron (NM_009672, intron 1 of 6)	26534	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	protein-coding
mm_5622.1	chr1	40130474	40130476	-	1	NA	Intergenic	Intergenic	-44624	NR_037980	100047133	Mm.447052	NR_037980	ENSMUSG00000097899	Gm16894	-	predicted gene, 16894	ncRNA
mm_67489.1	chr7	80723939	80723965	-	1	NA	exon (NM_016721, exon 34 of 38)	exon (NM_016721, exon 34 of 38)	-35075	NM_173863	70461	Mm.392175	NM_173863	ENSMUSG00000030527	Crtc3	2610312F20Rik|6332415K15Rik|AI429792|BC011210|TORC3	CREB regulated transcription coactivator 3	protein-coding
mm_20849.1	chr2	148046985	148046991	-	1	NA	promoter-TSS (NM_010446)	promoter-TSS (NM_010446)	-19	NM_010446	15376	Mm.938	NM_010446	ENSMUSG00000037025	Foxa2	HNF3-beta|HNF3beta|Hnf-3b|Hnf3b|Tcf-3b|Tcf3b	forkhead box A2	protein-coding
mm_105891.1	chr11	114934293	114934299	-	1	NA	promoter-TSS (NM_199221)	promoter-TSS (NM_199221)	90	NM_001347651	217304	Mm.185355	NM_199221	ENSMUSG00000063193	Cd300lb	CLM-7|Clm7|Gm253|LMIR5	CD300 molecule like family member B	protein-coding
mm_41182.1	chr5	88317288	88317306	+	1	NA	promoter-TSS (NM_008644)	promoter-TSS (NM_008644)	-15	NM_008644	17830	Mm.200411	NM_008644	ENSMUSG00000064156	Prol1	Muc10	proline rich, lacrimal 1	protein-coding
mm_61137.1	chr7	56107439	56107443	+	1	NA	intron (NM_010418, intron 16 of 92)	Lx3C|LINE|L1	57286	NM_010418	15204	Mm.20929	NM_010418	ENSMUSG00000030451	Herc2	D15F32S1h|D7H15F32S1|D7H15F37S1|jdf2|mKIAA0393|rjs	HECT and RLD domain containing E3 ubiquitin protein ligase 2	protein-coding
mm_104919.1	chr11	99838070	99838073	-	1	NA	promoter-TSS (NM_001195383)	promoter-TSS (NM_001195383)	-5	NM_001195383	100502865	Mm.476649	NM_001195383	ENSMUSG00000078257	2300003K06Rik	-	RIKEN cDNA 2300003K06 gene	protein-coding
mm_30174.1	chr3	144204859	144204878	-	1	NA	5' UTR (NM_010723, exon 1 of 5)	5' UTR (NM_010723, exon 1 of 5)	387	NM_010723	16911	Mm.29187	NM_010723	ENSMUSG00000028266	Lmo4	A730077C12Rik|Crp3|Etohi4	LIM domain only 4	protein-coding
mm_161087.1	chr12	87102347	87102347	-	1	NA	5' UTR (NM_022414, exon 1 of 4)	5' UTR (NM_022414, exon 1 of 4)	192	NM_022414	64242	Mm.41395	NM_022414	ENSMUSG00000021032	Ngb	-	neuroglobin	protein-coding
mm_17677.1	chr2	32260139	32260152	-	1	NA	promoter-TSS (NM_011675)	promoter-TSS (NM_011675)	-40	NM_011675	22245	Mm.425076	NM_011675	ENSMUSG00000002550	Uck1	URK1|Umpk	uridine-cytidine kinase 1	protein-coding
mm_148393.1	chr19	3767362	3767384	+	1	NA	promoter-TSS (NM_001167886)	promoter-TSS (NM_001167886)	-48	NM_001167889	225888	Mm.278578	NM_144871	ENSMUSG00000045098	Kmt5b	AA117471|C630029K18Rik|Suv4-20h1|Suv420h1	lysine methyltransferase 5B	protein-coding
mm_19906.1	chr2	114175275	114175293	-	1	NA	promoter-TSS (NM_009702)	promoter-TSS (NM_009702)	55	NM_009702	11834	Mm.2545	NM_009702	ENSMUSG00000040383	Aqr	AW495846|mKIAA0560	aquarius	protein-coding
mm_80081.1	chr9	70020252	70020263	+	1	NA	intron (NR_104093, intron 5 of 5)	intron (NR_104093, intron 5 of 5)	7709	NM_001282083	235459	Mm.293117	NM_199151	ENSMUSG00000033543	Gtf2a2	TFIIA-gamma|TfIIg|Tfiia2	general transcription factor II A, 2	protein-coding
mm_3616.1	chr1	152399883	152399891	+	1	NA	promoter-TSS (NM_177756)	promoter-TSS (NM_177756)	20	NM_177756	269132	Mm.23782	NM_177756	ENSMUSG00000032649	Colgalt2	AI427652|D730024P12|Glt25d2	collagen beta(1-O)galactosyltransferase 2	protein-coding
mm_25933.1	chr3	131368990	131369000	+	1	NA	Intergenic	Intergenic	-24072	NM_028943	74442	Mm.273360	NM_028943	ENSMUSG00000050931	Sgms2	4933405A16Rik|5133401H06Rik|AI854299	sphingomyelin synthase 2	protein-coding
mm_44762.1	chr5	31576615	31576631	-	1	NA	Intergenic	Intergenic	-5226	NR_102275	100740	Mm.23370	NR_102275		AI839979	-	expressed sequence AI839979	ncRNA
mm_87331.1	chr10	42934911	42934917	+	1	NA	intron (NM_172938, intron 5 of 8)	intron (NM_172938, intron 5 of 8)	74402	NM_172938	268297	Mm.98731	NM_172938	ENSMUSG00000044770	Scml4	9330161D17|mFLJ00197	sex comb on midleg-like 4 (Drosophila)	protein-coding
mm_60590.1	chr7	44483008	44483018	+	1	NA	Intergenic	Intergenic	-1504	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_27738.1	chr3	69085439	69085452	-	1	NA	intron (NM_008467, intron 12 of 16)	intron (NM_008467, intron 12 of 16)	-40703	NM_025863	66949	Mm.176695	NM_025863	ENSMUSG00000034317	Trim59	2310035M22Rik|2700022F13Rik|Mrf1|TSBF1	tripartite motif-containing 59	protein-coding
mm_68837.1	chr7	126327208	126327232	-	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	40825	NR_106025	102466797		NR_106025	ENSMUSG00000099017	Mir7058	Gm27766|mmu-mir-7058	microRNA 7058	ncRNA
mm_145066.1	chr18	40721508	40721516	+	1	NA	Intergenic	Lx8|LINE|L1	463151	NM_026135	383348	Mm.76366	NM_026135	ENSMUSG00000051401	Kctd16	4930434H12Rik|Gm1267	potassium channel tetramerisation domain containing 16	protein-coding
mm_115083.1	chr13	102693523	102693586	+	1	NA	promoter-TSS (NM_008533)	promoter-TSS (NM_008533)	-4	NM_008533	17079	Mm.373974	NM_008533	ENSMUSG00000021624	Cd180	F630107B15|Ly78|RP105	CD180 antigen	protein-coding
mm_39257.1	chr5	3543813	3543853	+	1	NA	promoter-TSS (NM_001042501)	promoter-TSS (NM_001042501)	0	NM_001042501	68152	Mm.240265	NM_026583	ENSMUSG00000058503	Fam133b	2900022K02Rik|5830415L20Rik	family with sequence similarity 133, member B	protein-coding
mm_151103.1	chr19	47859422	47859510	+	1	NA	exon (NM_010362, exon 4 of 6)	exon (NM_010362, exon 4 of 6)	4493	NM_010362	14873	Mm.378931	NM_010362	ENSMUSG00000025068	Gsto1	AA407097|AI194287|AU018802|Gsto-1|Gstx|Spg-r|p28	glutathione S-transferase omega 1	protein-coding
mm_130318.1	chr15	97369280	97369288	-	1	NA	intron (NM_172293, intron 4 of 5)	intron (NM_172293, intron 4 of 5)	-121997	NM_001164602	105827	Mm.24005	NM_178114	ENSMUSG00000048218	Amigo2	AI415330|AMIGO-2|AW208913|Ali1	adhesion molecule with Ig like domain 2	protein-coding
mm_8973.1	chr1	165329813	165329816	-	1	NA	3' UTR (NM_028759, exon 19 of 19)	3' UTR (NM_028759, exon 19 of 19)	27191	NM_001310430	240888	Mm.329929	NM_001081126	ENSMUSG00000040836	Gpr161	Gm208|Gm208Gpr|vl	G protein-coupled receptor 161	protein-coding
mm_128594.1	chr15	58132316	58132342	-	1	NA	exon (NM_027435, exon 2 of 28)	exon (NM_027435, exon 2 of 28)	2753	NM_027435	70472	Mm.221758	NM_027435	ENSMUSG00000022360	Atad2	2610509G12Rik	ATPase family, AAA domain containing 2	protein-coding
mm_64479.1	chr7	143064949	143064959	+	1	NA	intron (NM_133655, intron 2 of 7)	intron (NM_133655, intron 2 of 7)	-4414	NM_020285	56844	Mm.139675	NM_020285	ENSMUSG00000045752	Tssc4	AA241958|ESTM671070	tumor-suppressing subchromosomal transferable fragment 4	protein-coding
mm_85095.1	chr9	92436526	92436539	-	1	NA	Intergenic	RMER6C|LTR|ERVK	-20846	NM_178711	235527	Mm.55289	NM_178711	ENSMUSG00000032377	Plscr4	AV245873	phospholipid scramblase 4	protein-coding
mm_31634.1	chr4	59352172	59352214	+	1	NA	intron (NM_001163288, intron 10 of 16)	intron (NM_001163288, intron 10 of 16)	86440	NM_001163288	634731	Mm.483589	NM_001163288	ENSMUSG00000038578	Susd1	A530080P10|Gm12528|OTTMUSG00000007332	sushi domain containing 1	protein-coding
mm_125727.1	chr15	73155572	73155578	+	1	NA	intron (NM_153178, intron 1 of 18)	intron (NM_153178, intron 1 of 18)	29372	NM_153178	239528	Mm.23095	NM_153178	ENSMUSG00000036698	Ago2	1110029L17Rik|2310051F07Rik|AI225898|AL022874|AW546247|ENSMUSG00000072493|Eif2c2|Gerp95|Gm10365|mKIAA4215	argonaute RISC catalytic subunit 2	protein-coding
mm_59936.1	chr7	30424287	30424302	+	1	NA	5' UTR (NM_172142, exon 3 of 11)	5' UTR (NM_172142, exon 3 of 11)	990	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_57796.1	chr6	129284411	129284427	-	1	NA	Intergenic	MIRc|SINE|MIR	-9050	NM_001033122	12515	Mm.74745	NM_001033122	ENSMUSG00000030156	Cd69	5830438K24Rik|AI452015|AIM|VEA	CD69 antigen	protein-coding
mm_100124.1	chr11	115912002	115912025	+	1	NA	promoter-TSS (NM_001162998)	promoter-TSS (NM_001162998)	-4	NM_001162998	68528	Mm.441893	NM_001162998	ENSMUSG00000075420	Smim6	1110017F19Rik	small integral membrane protein 6	protein-coding
mm_110788.1	chr12	72071068	72071079	-	1	NA	promoter-TSS (NM_181752)	promoter-TSS (NM_181752)	-82	NM_181752	238252	Mm.390508	NM_181752	ENSMUSG00000043398	Gpr135	PAFR	G protein-coupled receptor 135	protein-coding
mm_160025.1	chr6	130231737	130231737	-	1	NA	promoter-TSS (NM_014194)	promoter-TSS (NM_014194)	-50	NM_014194	16638	Mm.441781	NM_014194	ENSMUSG00000067599	Klra7	LGL-1|Ly-49G.1|Ly-49G.2|Ly-49G.3|Ly49G.4|Ly49g|Ly49g1|Ly49g2	killer cell lectin-like receptor, subfamily A, member 7	protein-coding
mm_41223.1	chr5	88584214	88584230	+	1	NA	exon (NM_027530, exon 1 of 13)	exon (NM_027530, exon 1 of 13)	709	NM_027530	52822	Mm.270469	NM_027530	ENSMUSG00000029291	Rufy3	2810428M05Rik|6330416M07Rik|AW455998|AW538594|D5Bwg0860e|Ripx|Rpipx	RUN and FYVE domain containing 3	protein-coding
mm_128443.1	chr15	50752311	50752345	-	1	NA	intron (NM_001310481, intron 4 of 5)	intron (NM_001310481, intron 4 of 5)	136721	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_125237.1	chr15	34238109	34238177	+	1	NA	5' UTR (NM_033521, exon 1 of 7)	5' UTR (NM_033521, exon 1 of 7)	117	NM_033521	114128	Mm.197518	NM_033521	ENSMUSG00000022257	Laptm4b	C330023P13Rik|LAPTM4beta	lysosomal-associated protein transmembrane 4B	protein-coding
mm_163116.1	chr11	74649957	74649966	+	1	NA	intron (NM_001081158, intron 1 of 25)	CpG	466	NM_001081158	74148	Mm.214574	NM_001081158	ENSMUSG00000020741	Cluh	1300001I01Rik|Kiaa0664|mKIAA0664	clustered mitochondria (cluA/CLU1) homolog	protein-coding
mm_66655.1	chr7	45713564	45713589	-	1	NA	exon (NM_001172561, exon 2 of 6)	exon (NM_001172561, exon 2 of 6)	1631	NM_020011	56632	Mm.24222	NM_020011	ENSMUSG00000057342	Sphk2	C76851	sphingosine kinase 2	protein-coding
mm_13914.1	chr2	120502511	120502532	+	1	NA	intron (NM_001109761, intron 15 of 20)	intron (NM_001109761, intron 15 of 20)	25612	NM_001109761	12335	Mm.458021	NM_007601	ENSMUSG00000079110	Capn3	AI323605|Capa-3|Capa3|Lp82|p94	calpain 3	protein-coding
mm_14361.1	chr2	129616387	129616408	+	1	NA	exon (NM_007547, exon 4 of 8)	exon (NM_007547, exon 4 of 8)	23228	NM_001291022	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_42269.1	chr5	114146294	114146317	+	1	NA	Intergenic	Intergenic	15149	NM_011677	22256	Mm.1393	NM_011677	ENSMUSG00000029591	Ung	UNG1|UNG2	uracil DNA glycosylase	protein-coding
mm_105729.1	chr11	109144341	109144377	-	1	NA	promoter-TSS (NR_037978)	promoter-TSS (NR_037978)	10	NR_037978	268498	Mm.227970	NM_001085512	ENSMUSG00000078605	E030025P04Rik	Gm664	RIKEN cDNA E030025P04 gene	ncRNA
mm_21508.1	chr2	163624865	163624971	-	1	NA	3' UTR (NM_012032, exon 10 of 10)	3' UTR (NM_012032, exon 10 of 10)	17706	NM_001305803	76080	Mm.89828	NM_029512	ENSMUSG00000017679	Ttpal	3110080A02Rik|5830472M02Rik	tocopherol (alpha) transfer protein-like	protein-coding
mm_71171.1	chr8	40584937	40584954	+	1	NA	intron (NM_001040699, intron 6 of 13)	intron (NM_001040699, intron 6 of 13)	49847	NM_001040699	54384	Mm.294871	NM_019433	ENSMUSG00000039431	Mtmr7	-	myotubularin related protein 7	protein-coding
mm_157487.1	chrX	48249214	48249217	-	1	NA	Intergenic	MTA_Mm-int|LTR|ERVL-MaLR	-7719	NM_028276	72554	Mm.336045	NM_028276	ENSMUSG00000063785	Utp14a	2700066J21Rik|JsdX|NY-CO-16|SDCCAG16|T25628|mKIAA0266	UTP14A small subunit processome component	protein-coding
mm_52056.1	chr6	97232659	97232683	+	1	NA	3' UTR (NM_022992, exon 3 of 3)	3' UTR (NM_022992, exon 3 of 3)	20109	NM_001081157	320502	Mm.68163	NM_001081157	ENSMUSG00000044086	Lmod3	5430424A14Rik	leiomodin 3 (fetal)	protein-coding
mm_50056.1	chr6	41178409	41178453	+	1	NA	Intergenic	Intergenic	-123841	NM_011646	22074	Mm.383263	NM_011646	ENSMUSG00000054106	Try4	0910001B19Rik|Td	trypsin 4	protein-coding
mm_68189.1	chr7	104164830	104164832	-	1	NA	promoter-TSS (NM_172905)	promoter-TSS (NM_172905)	-15	NM_172905	244180	Mm.17149	NM_172905	ENSMUSG00000044265	Olfm5	E030002O03Rik	olfactomedin 5	protein-coding
mm_103981.1	chr11	84826284	84826301	-	1	NA	intron (NM_177564, intron 1 of 6)	intron (NM_177564, intron 1 of 6)	2711	NM_177564	192970	Mm.192213	NM_177564	ENSMUSG00000034449	Dhrs11	-	dehydrogenase/reductase (SDR family) member 11	protein-coding
mm_134787.1	chr16	24013221	24013226	-	1	NA	Intergenic	Intergenic	-24611	NM_009744	12053	Mm.347398	NM_009744	ENSMUSG00000022508	Bcl6	Bcl5	B cell leukemia/lymphoma 6	protein-coding
mm_145665.1	chr18	61131032	61131055	+	1	NA	TTS (NM_178277)	TTS (NM_178277)	13575	NR_105949	102466212		NR_105949	ENSMUSG00000098389	Mir6983	Gm27496|mmu-mir-6983	microRNA 6983	ncRNA
mm_80024.1	chr9	67996619	67996676	+	1	NA	Intergenic	Intergenic	29067	NR_045745	434412	Mm.490707	NR_045745	ENSMUSG00000111841	Gm20745	-	predicted gene, 20745	ncRNA
mm_26575.1	chr3	146852360	146852438	+	1	NA	promoter-TSS (NM_001302958)	promoter-TSS (NM_001302958)	32	NM_001302958	70892	Mm.187793	NM_027594	ENSMUSG00000036745	Ttll7	1110049N09Rik|4921517B04Rik|C630030B20|mTTLL7	tubulin tyrosine ligase-like family, member 7	protein-coding
mm_650.1	chr1	40429137	40429177	+	1	NA	promoter-TSS (NM_001294171)	promoter-TSS (NM_001294171)	-413	NM_001294171	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_168705.1	chr11	98067587	98067596	+	1	NA	Intergenic	RLTR27|LTR|ERVK	-14129	NM_146028	217154	Mm.181008	NM_146028	ENSMUSG00000017400	Stac2	24b2|24b2/STAC2|AW240854	SH3 and cysteine rich domain 2	protein-coding
mm_143698.1	chr17	80480464	80480474	-	1	NA	promoter-TSS (NM_009231)	promoter-TSS (NM_009231)	-16	NM_009231	20662	Mm.60975	NM_009231	ENSMUSG00000024241	Sos1	4430401P03Rik|9630010N06|AI449023	son of sevenless homolog 1 (Drosophila)	protein-coding
mm_76421.1	chr8	84976313	84976337	-	1	NA	TTS (NM_008416)	TTS (NM_008416)	2423	NM_008416	16477	Mm.1167	NM_008416	ENSMUSG00000052837	Junb	-	jun B proto-oncogene	protein-coding
mm_142770.1	chr17	49550102	49550117	-	1	NA	intron (NM_001008231, intron 1 of 25)	intron (NM_001008231, intron 1 of 25)	14228	NM_001008231	76441	Mm.211275	NM_001008231	ENSMUSG00000040260	Daam2	2310016D11Rik|AI843643|AW557870	dishevelled associated activator of morphogenesis 2	protein-coding
mm_124279.1	chr14	103046828	103046868	-	1	NA	promoter-TSS (NM_008392)	promoter-TSS (NM_008392)	-164	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_149691.1	chr19	21271851	21271890	+	1	NA	promoter-TSS (NM_009551)	promoter-TSS (NM_009551)	-408	NM_009551	22682	Mm.292405	NM_009551	ENSMUSG00000024750	Zfand5	2310057A04Rik|5830475F03Rik|AA415485|Za20d2|Zfp216	zinc finger, AN1-type domain 5	protein-coding
mm_129266.1	chr15	76904958	76905004	-	1	NA	exon (NM_012053, exon 4 of 6)	exon (NM_012053, exon 4 of 6)	910	NM_012053	26961	Mm.30066	NM_012053	ENSMUSG00000003970	Rpl8	-	ribosomal protein L8	protein-coding
mm_122135.1	chr14	31162496	31162506	-	1	NA	exon (NM_138672, exon 6 of 69)	exon (NM_138672, exon 6 of 69)	6140	NM_138672	192187	Mm.220821	NM_138672	ENSMUSG00000042286	Stab1	FEEL-1|FELE-1|MFEEL-1|MS-1|STAB-1|mKIAA0246	stabilin 1	protein-coding
mm_46557.1	chr5	106696760	106696784	-	1	NA	promoter-TSS (NM_026856)	promoter-TSS (NM_026856)	58	NM_026856	52397	Mm.249474	NM_026856	ENSMUSG00000049606	Zfp644	1110068L01Rik|AA408882|BM-005|D5Ertd689e|Zep-2	zinc finger protein 644	protein-coding
mm_99448.1	chr11	102433961	102433991	+	1	NA	exon (NM_008175, exon 5 of 13)	exon (NM_008175, exon 5 of 13)	3654	NM_008175	14824	Mm.1568	NM_008175	ENSMUSG00000034708	Grn	Pgrn|epithelin	granulin	protein-coding
mm_167292.1	chr8	45749003	45749010	+	1	NA	intron (NM_172752, intron 6 of 22)	intron (NM_172752, intron 6 of 22)	70291	NR_045739	319940	Mm.441720	NR_045739	ENSMUSG00000085440	Sorbs2os	D330022K07Rik	sorbin and SH3 domain containing 2, opposite strand	ncRNA
mm_55097.1	chr6	49424969	49424969	-	1	NA	intron (NM_029916, intron 10 of 23)	intron (NM_029916, intron 10 of 23)	29365	NM_029916	77485	Mm.128054	NM_029916	ENSMUSG00000023403	Stk31	C330007K24Rik	serine threonine kinase 31	protein-coding
mm_154333.1	chrM	3376	3390	+	1	NA	NA	Intergenic	NA	NA								
mm_82851.1	chr9	31211806	31211824	-	1	NA	promoter-TSS (NM_009691)	promoter-TSS (NM_009691)	0	NM_001102455	11804	Mm.19133	NM_009691	ENSMUSG00000031996	Aplp2	AI790698|APLP-2	amyloid beta (A4) precursor-like protein 2	protein-coding
mm_134790.1	chr16	24090033	24090046	-	1	NA	Intergenic	Intergenic	-101427	NM_009744	12053	Mm.347398	NM_009744	ENSMUSG00000022508	Bcl6	Bcl5	B cell leukemia/lymphoma 6	protein-coding
mm_153128.1	chr19	34166014	34166030	-	1	NA	promoter-TSS (NM_024204)	promoter-TSS (NM_024204)	19	NM_024204	52024	Mm.183030	NM_024204	ENSMUSG00000024774	Ankrd22	5430429D21Rik|D19Ertd675e	ankyrin repeat domain 22	protein-coding
mm_146865.1	chr18	24603465	24603530	-	1	NA	promoter-TSS (NM_021448)	promoter-TSS (NM_021448)	320	NM_139143	106957	Mm.21688	NM_139143	ENSMUSG00000024270	Slc39a6	Ermelin	solute carrier family 39 (metal ion transporter), member 6	protein-coding
mm_70189.1	chr7	143780424	143780430	-	1	NA	3' UTR (NM_175534, exon 2 of 2)	3' UTR (NM_175534, exon 2 of 2)	4073	NM_175534	244238	Mm.183561	NM_175534	ENSMUSG00000048965	Mrgpre	C130069N09Rik|Ebrt3|Mgrf|MrgE	MAS-related GPR, member E	protein-coding
mm_143038.1	chr17	56717682	56717709	-	1	NA	promoter-TSS (NM_027244)	promoter-TSS (NM_027244)	4	NM_001166474	106639	Mm.37290	NM_178926	ENSMUSG00000054723	Vmac	AI662250	vimentin-type intermediate filament associated coiled-coil protein	protein-coding
mm_141318.1	chr17	28365111	28365136	-	1	NA	promoter-TSS (NM_021478)	promoter-TSS (NM_021478)	20	NM_021478	22157	Mm.42102	NM_021478	ENSMUSG00000037446	Tulp1	Tulp1l	tubby like protein 1	protein-coding
mm_30005.1	chr3	135608402	135608412	-	1	NA	intron (NM_008689, intron 12 of 24)	intron (NM_008689, intron 12 of 24)	83140	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_63554.1	chr7	128076189	128076200	+	1	NA	intron (NM_001082960, intron 6 of 29)	intron (NM_001082960, intron 6 of 29)	13554	NM_008401	16409	Mm.262106	NM_008401	ENSMUSG00000030786	Itgam	CD11b/CD18|CR3|CR3A|Cd11b|F730045J24Rik|Ly-40|MAC1|Mac-1|Mac-1a	integrin alpha M	protein-coding
mm_51848.1	chr6	90363905	90363920	+	1	NA	3' UTR (NM_144940, exon 20 of 20)	3' UTR (NM_144940, exon 20 of 20)	-5582	NM_173002	80292	Mm.100116	NM_030260	ENSMUSG00000034430	Zxdc	A930012H20|B930086F11Rik|BC003332	ZXD family zinc finger C	protein-coding
mm_94955.1	chr11	30153089	30153093	+	1	NA	intron (NM_175836, intron 3 of 34)	intron (NM_175836, intron 3 of 34)	45166	NM_009260	20742	Mm.123110	NM_009260	ENSMUSG00000020315	Sptbn1	9930031C03Rik|AL033301|SPTB2|Spnb-2|Spnb2|elf1|elf3|mKIAA4049	spectrin beta, non-erythrocytic 1	protein-coding
mm_121343.1	chr14	115942596	115942598	+	1	NA	intron (NM_175500, intron 7 of 7)	Lx3A|LINE|L1	-533045	NR_045761	75088	Mm.444706	NR_045761	ENSMUSG00000093551	4930505G20Rik	-	RIKEN cDNA 4930505G20 gene	ncRNA
mm_124274.1	chr14	103029187	103029191	-	1	NA	intron (NR_045657, intron 2 of 2)	intron (NR_045657, intron 2 of 2)	4614	NR_045657	71264	Mm.399572	NR_045657		4933432I03Rik	-	RIKEN cDNA 4933432I03 gene	ncRNA
mm_134952.1	chr16	31303465	31303491	-	1	NA	exon (NM_007470, exon 4 of 6)	exon (NM_007470, exon 4 of 6)	11330	NM_001301353	11815	Mm.2082	NM_007470	ENSMUSG00000022548	Apod	-	apolipoprotein D	protein-coding
mm_15425.1	chr2	157085070	157085076	+	1	NA	Intergenic	Intergenic	-1982	NM_001177439	383766	Mm.480305	NM_001177439	ENSMUSG00000074628	Tldc2	Gm1332	TBC/LysM associated domain containing 2	protein-coding
mm_133652.1	chr16	91804654	91804661	+	1	NA	intron (NM_001110275, intron 7 of 28)	intron (NM_001110275, intron 7 of 28)	75286	NM_010587	16443	Mm.40546	NM_010587	ENSMUSG00000022957	Itsn1	AA517634|AA545208|AI316805|AI839402|AI848451|Ehsh1|Ese1|Itsn|Sh3p17	intersectin 1 (SH3 domain protein 1A)	protein-coding
mm_73041.1	chr8	94267087	94267101	+	1	NA	intron (NM_172410, intron 4 of 22)	intron (NM_172410, intron 4 of 22)	52493	NM_172410	71805	Mm.458170	NM_172410	ENSMUSG00000032939	Nup93	2410008G02Rik	nucleoporin 93	protein-coding
mm_125824.1	chr15	74957181	74957209	+	1	NA	intron (NM_001164039, intron 2 of 4)	intron (NM_001164039, intron 2 of 4)	2089	NM_001164040	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_155083.1	chrX	48056560	48056561	+	1	NA	Intergenic	Intergenic	-21707	NM_013912	30878	Mm.29262	NM_013912	ENSMUSG00000037010	Apln	6030430G11Rik|Apel	apelin	protein-coding
mm_78041.1	chr9	14381054	14381088	+	1	NA	5' UTR (NM_028013, exon 1 of 2)	5' UTR (NM_028013, exon 1 of 2)	171	NM_028013	71946	Mm.41423	NM_028013	ENSMUSG00000037419	Endod1	2210414F18Rik|2310067E08Rik|C85344	endonuclease domain containing 1	protein-coding
mm_103530.1	chr11	77200949	77200955	-	1	NA	Intergenic	Intergenic	-11984	NM_176965	319634	Mm.108786	NM_176965	ENSMUSG00000050944	Efcab5	4930563A03Rik	EF-hand calcium binding domain 5	protein-coding
mm_102393.1	chr11	58999239	58999281	-	1	NA	exon (NM_001171512, exon 93 of 104)	exon (NM_001171512, exon 93 of 104)	21167	NM_053168	94091	Mm.248049	NM_053168	ENSMUSG00000020455	Trim11	-	tripartite motif-containing 11	protein-coding
mm_25338.1	chr3	106721673	106721733	+	1	NA	promoter-TSS (NM_001039488)	promoter-TSS (NM_001039488)	21	NM_001286685	321000	Mm.259638	NM_028081	ENSMUSG00000056260	Lrif1	2010012G17Rik|4933421E11Rik|AI450568	ligand dependent nuclear receptor interacting factor 1	protein-coding
mm_48886.1	chr5	151233819	151233851	-	1	NA	Intergenic	CpG	-43642	NM_146258	243362	Mm.209272	NM_146258	ENSMUSG00000016128	Stard13	DLC2|GT650	StAR-related lipid transfer (START) domain containing 13	protein-coding
mm_100774.1	chr11	4789816	4789828	-	1	NA	exon (NM_001252253, exon 12 of 15)	exon (NM_001252253, exon 12 of 15)	-43044	NM_138948	192650	Mm.207056	NM_138948	ENSMUSG00000009075	Cabp7	-	calcium binding protein 7	protein-coding
mm_26719.1	chr3	158960376	158960377	+	1	NA	Intergenic	Intergenic	-115988	NR_040750	624759	Mm.491054	NR_040750	ENSMUSG00000106053	Gm20752	-	predicted gene, 20752	ncRNA
mm_67185.1	chr7	73940034	73940044	-	1	NA	3' UTR (NM_009181, exon 6 of 6)	3' UTR (NM_009181, exon 6 of 6)	73643	NM_009181	20450	Mm.4954	NM_009181	ENSMUSG00000025789	St8sia2	AI323367|ST8SiaII|STX|Siat8b	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 2	protein-coding
mm_20545.1	chr2	131068530	131068543	-	1	NA	TTS (NM_011426)	TTS (NM_011426)	-4722	NM_001163529	110751	Mm.108550	NM_033615	ENSMUSG00000027318	Adam33	Adaml	a disintegrin and metallopeptidase domain 33	protein-coding
mm_48646.1	chr5	145854961	145854971	-	1	NA	3' UTR (NM_007818, exon 13 of 13)	3' UTR (NM_007818, exon 13 of 13)	24888	NM_007818	13112	Mm.332844	NM_007818	ENSMUSG00000056035	Cyp3a11	AI256190|Cyp3a|IIIAm1|Pcn	cytochrome P450, family 3, subfamily a, polypeptide 11	protein-coding
mm_118016.1	chr13	100775845	100775893	-	1	NA	promoter-TSS (NM_021886)	promoter-TSS (NM_021886)	30	NM_021886	26886	Mm.273502	NM_021886	ENSMUSG00000045273	Cenph	1700021I11Rik|2410018A12Rik|2610042E16Rik|2810046K12Rik|AU044255|CENP-H|ENP	centromere protein H	protein-coding
mm_91443.1	chr10	33933178	33933189	-	1	NA	intron (NM_028287, intron 6 of 9)	intron (NM_028287, intron 6 of 9)	18029	NM_028287	72580	Mm.248081	NM_028287	ENSMUSG00000039531	Zufsp	2700019D07Rik	zinc finger with UFM1-specific peptidase domain	protein-coding
mm_9228.1	chr1	171241046	171241059	-	1	NA	exon (NM_153064, exon 3 of 13)	exon (NM_153064, exon 3 of 13)	6070	NM_153064	226646	Mm.21669	NM_153064	ENSMUSG00000013593	Ndufs2	CI-49kD	NADH dehydrogenase (ubiquinone) Fe-S protein 2	protein-coding
mm_6083.1	chr1	63088482	63088495	-	1	NA	intron (NM_001081436, intron 4 of 11)	intron (NM_001081436, intron 4 of 11)	25779	NM_001081436	227195	Mm.74718	NM_001081436	ENSMUSG00000040865	Ino80d	7330405I11|A430093A21Rik|BC010584|OTTMUSG00000002594	INO80 complex subunit D	protein-coding
mm_140042.1	chr17	74489493	74489575	+	1	NA	promoter-TSS (NM_026417)	promoter-TSS (NM_026417)	41	NM_026417	67864	Mm.41891	NM_026417	ENSMUSG00000024072	Yipf4	2310034L04Rik	Yip1 domain family, member 4	protein-coding
mm_42627.1	chr5	118318968	118318972	+	1	NA	Intergenic	Intergenic	73743	NM_001081236	76792	Mm.103428	NM_001081236	ENSMUSG00000032840	2410131K14Rik	-	RIKEN cDNA 2410131K14 gene	protein-coding
mm_157410.1	chrX	38440273	38440301	-	1	NA	exon (NM_001017959, exon 3 of 9)	exon (NM_001017959, exon 3 of 9)	16173	NM_010685	16784	Mm.486	NM_010685	ENSMUSG00000016534	Lamp2	CD107b|LGP-B|Lamp II|Lamp-2|Lamp-2a|Lamp-2b|Lamp-2c|Mac3	lysosomal-associated membrane protein 2	protein-coding
mm_131442.1	chr16	16213123	16213138	+	1	NA	promoter-TSS (NM_026163)	promoter-TSS (NM_026163)	-215	NM_026163	67451	Mm.2252	NM_026163	ENSMUSG00000041957	Pkp2	1200008D14Rik|1200012P04Rik|AA516617|Pkp2l	plakophilin 2	protein-coding
mm_40793.1	chr5	67607874	67607889	+	1	NA	promoter-TSS (NM_001033415)	promoter-TSS (NM_001033415)	-2	NM_001033415	330096	Mm.442747	NM_001033415	ENSMUSG00000050010	Shisa3	D830007B15Rik	shisa family member 3	protein-coding
mm_61621.1	chr7	80186836	80186904	+	1	NA	promoter-TSS (NM_013659)	promoter-TSS (NM_013659)	29	NM_013659	20352	Mm.275909	NM_013659	ENSMUSG00000030539	Sema4b	SemC|Semac|mKIAA1745	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B	protein-coding
mm_20359.1	chr2	128257706	128257743	-	1	NA	Intergenic	Intergenic	130149	NM_001284410	12125	Mm.141083	NM_009754	ENSMUSG00000027381	Bcl2l11	1500006F24Rik|Bim|Bod|bcl2-L-11	BCL2-like 11 (apoptosis facilitator)	protein-coding
mm_27590.1	chr3	59130630	59130640	-	1	NA	5' UTR (NM_001287124, exon 1 of 2)	5' UTR (NM_001287124, exon 1 of 2)	127	NM_001008497	140795	Mm.439021	NM_133200	ENSMUSG00000036381	P2ry14	A330108O13Rik|Gpr105|P2Y14	purinergic receptor P2Y, G-protein coupled, 14	protein-coding
mm_53020.1	chr6	124068123	124068170	+	1	NA	Intergenic	RMER16-int|LTR|ERVK	43388	NM_019917	56552	Mm.23795	NM_019917	ENSMUSG00000096630	Vmn2r26	V2R1|V2r1b	vomeronasal 2, receptor 26	protein-coding
mm_87506.1	chr10	52388964	52388977	+	1	NA	Intergenic	Intergenic	-2638	NM_025684	66650	Mm.90950	NM_025684	ENSMUSG00000038624	Nepn	5730521E12Rik|Npn|periolin	nephrocan	protein-coding
mm_164462.1	chr16	58499874	58499885	-	1	NA	intron (NM_018784, intron 2 of 10)	intron (NM_018784, intron 2 of 10)	23433	NM_018784	54613	Mm.212742	NM_018784	ENSMUSG00000022747	St3gal6	1700023B24Rik|AI930218|AW552396|Siat10|St3galVI	ST3 beta-galactoside alpha-2,3-sialyltransferase 6	protein-coding
mm_119040.1	chr14	30568177	30568209	+	1	NA	exon (NM_009388, exon 7 of 14)	exon (NM_009388, exon 7 of 14)	-3956	NR_037237	100526475		NR_037237	ENSMUSG00000093156	Mir3076	mir-3076|mmu-mir-3076	microRNA 3076	ncRNA
mm_32299.1	chr4	103119462	103119464	+	1	NA	promoter-TSS (NM_001039081)	promoter-TSS (NM_001039081)	73	NM_001039081	71148	Mm.288721	NM_027696	ENSMUSG00000028522	Mier1	4933425I22Rik|5830411K19Rik|er1	MEIR1 treanscription regulator	protein-coding
mm_54720.1	chr6	40435151	40435157	-	1	NA	intron (NM_175528, intron 1 of 7)	intron (NM_175528, intron 1 of 7)	979	NM_175528	243780	Mm.333006	NM_175528	ENSMUSG00000037172	E330009J07Rik	AI841796|Lchn|mKIAA1147	RIKEN cDNA E330009J07 gene	protein-coding
mm_1452.1	chr1	67230644	67230653	+	1	NA	3' UTR (NM_001080809, exon 38 of 38)	3' UTR (NM_001080809, exon 38 of 38)	107621	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_66710.1	chr7	45973367	45973395	-	1	NA	Intergenic	Intergenic	44983	NM_001033243	211535	Mm.227539	NM_001033243	ENSMUSG00000040189	Ccdc114	-	coiled-coil domain containing 114	protein-coding
mm_123911.1	chr14	73325913	73325943	-	1	NA	promoter-TSS (NM_009029)	promoter-TSS (NM_009029)	-137	NM_009029	19645	Mm.273862	NM_009029	ENSMUSG00000022105	Rb1	Rb|Rb-1|pRb	retinoblastoma 1	protein-coding
mm_149671.1	chr19	18855669	18855672	+	1	NA	intron (NM_153417, intron 26 of 38)	Lx7|LINE|L1	105687	NM_153417	225997	Mm.215171	NM_153417	ENSMUSG00000024727	Trpm6	CHAK2|TRPM6/CHAK2	transient receptor potential cation channel, subfamily M, member 6	protein-coding
mm_69271.1	chr7	127930019	127930040	-	1	NA	promoter-TSS (NM_133351)	promoter-TSS (NM_133351)	84	NM_133351	76560	Mm.5875	NM_133351	ENSMUSG00000030800	Prss8	2410039E18Rik|AI313909|C79772|CAP1|fr|mCAP1	protease, serine 8 (prostasin)	protein-coding
mm_118548.1	chr14	17659764	17659779	+	1	NA	Intergenic	Intergenic	-1189	NM_001113417	21834	Mm.32563	NM_009380	ENSMUSG00000021779	Thrb	Nr1a2|T3R[b]|T3Rbeta|Thrb1|Thrb2|c-erbAbeta	thyroid hormone receptor beta	protein-coding
mm_55004.1	chr6	48836257	48836282	-	1	NA	exon (NM_001164209, exon 4 of 8)	exon (NM_001164209, exon 4 of 8)	4719	NM_023056	65963	Mm.28385	NM_023056	ENSMUSG00000029810	Tmem176b	1810009M01Rik|Clast1|Lr8	transmembrane protein 176B	protein-coding
mm_3811.1	chr1	158551587	158551589	+	1	NA	intron (NM_007495, intron 8 of 22)	intron (NM_007495, intron 8 of 22)	45963	NR_030441	735253		NR_030441	ENSMUSG00000070103	Mir488	Mirn488|mir-488|mmu-mir-488	microRNA 488	ncRNA
mm_116581.1	chr13	47106102	47106110	-	1	NA	5' UTR (NM_025900, exon 1 of 11)	5' UTR (NM_025900, exon 1 of 11)	115	NM_025900	110052	Mm.131150	NM_025900	ENSMUSG00000021377	Dek	1810019E15Rik|D13H6S231E	DEK oncogene (DNA binding)	protein-coding
mm_142369.1	chr17	44618576	44618579	-	1	NA	intron (NR_073392, intron 6 of 7)	intron (NR_073392, intron 6 of 7)	117599	NR_073425	12393	Mm.391013	NM_009820	ENSMUSG00000039153	Runx2	AML3|Cbf|Cbfa-1|Cbfa1|LS3|Osf2|PEBP2aA|Pebp2a1|Pebpa2a	runt related transcription factor 2	protein-coding
mm_126836.1	chr15	89020329	89020339	+	1	NA	exon (NM_031260, exon 17 of 27)	exon (NM_031260, exon 17 of 27)	37340	NM_031260	83456	Mm.358791	NM_031260	ENSMUSG00000015365	Mov10l1	CHAMP|Csm	Moloney leukemia virus 10-like 1	protein-coding
mm_142361.1	chr17	43744578	43744595	-	1	NA	intron (NM_018887, intron 10 of 11)	intron (NM_018887, intron 10 of 11)	-57265	NM_207649	53901	Mm.251242	NM_030598	ENSMUSG00000039601	Rcan2	Csp2|Dscr1l1|MCIP2|ZAKI-4	regulator of calcineurin 2	protein-coding
mm_40951.1	chr5	76855491	76855491	+	1	NA	intron (NM_001163793, intron 5 of 8)	intron (NM_001163793, intron 5 of 8)	14892	NM_001163793	320827	Mm.101504	NM_001163793	ENSMUSG00000036377	C530008M17Rik	2810489J07Rik|4930529A19Rik|4931405B09Rik|Kiaa1211|mKIAA1211	RIKEN cDNA C530008M17 gene	protein-coding
mm_144196.1	chr18	7905441	7905459	+	1	NA	exon (NM_001146298, exon 5 of 13)	exon (NM_001146298, exon 5 of 13)	36253	NM_153085	225131	Mm.204524	NM_153085	ENSMUSG00000024283	Wac	1110067P07Rik|A230035H12Rik|AI256735|AI256776|Wwp4	WW domain containing adaptor with coiled-coil	protein-coding
mm_145142.1	chr18	45559590	45559600	+	1	NA	promoter-TSS (NM_080465)	promoter-TSS (NM_080465)	-559	NM_080465	140492	Mm.411614	NM_080465	ENSMUSG00000054477	Kcnn2	KCa2.2|SK2|SKCA2|bc|fri	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2	protein-coding
mm_106262.1	chr11	117968058	117968072	-	1	NA	exon (NM_007707, exon 2 of 2)	exon (NM_007707, exon 2 of 2)	1301	NM_007707	12702	Mm.3468	NM_007707	ENSMUSG00000053113	Socs3	Cis3|Cish3|EF-10|Ef10|SSI-3|Ssi3	suppressor of cytokine signaling 3	protein-coding
mm_74294.1	chr8	125995342	125995346	+	1	NA	5' UTR (NM_008430, exon 1 of 3)	5' UTR (NM_008430, exon 1 of 3)	242	NM_008430	16525	Mm.10800	NM_008430	ENSMUSG00000033998	Kcnk1	AI788889|TWIK-1	potassium channel, subfamily K, member 1	protein-coding
mm_47125.1	chr5	119807651	119807666	-	1	NA	Intergenic	Intergenic	-27005	NM_011537	21388	Mm.103636	NM_011537	ENSMUSG00000018263	Tbx5	-	T-box 5	protein-coding
mm_44949.1	chr5	36582382	36582399	-	1	NA	promoter-TSS (NM_133910)	promoter-TSS (NM_133910)	7	NM_133910	100855	Mm.486203	NM_133910	ENSMUSG00000029192	Tbc1d14	2810413P16Rik|AU043625|C86258|D5Ertd110e|mKIAA1322	TBC1 domain family, member 14	protein-coding
mm_156031.1	chrX	107256067	107256087	+	1	NA	promoter-TSS (NM_001033251)	promoter-TSS (NM_001033251)	49	NM_001033251	213439	Mm.383562	NM_001033251	ENSMUSG00000073008	Gpr174	Gm376|Lypsr3	G protein-coupled receptor 174	protein-coding
mm_167518.1	chr9	15279923	15279927	-	1	NA	promoter-TSS (NM_144933)	promoter-TSS (NM_144933)	-58	NM_144933	234959	Mm.44151	NM_144933	ENSMUSG00000031935	Med17	77kDa|C330002H14Rik|Crsp6|Trap80	mediator complex subunit 17	protein-coding
mm_130517.1	chr15	98871176	98871187	-	1	NA	promoter-TSS (NM_001033276)	promoter-TSS (NM_001033276)	24	NM_001033276	381022	Mm.264889	NM_001033276	ENSMUSG00000048154	Kmt2d	ALR|BC032281|BC058659|C430014K11Rik|KMT2B|Mll2|Mll4	lysine (K)-specific methyltransferase 2D	protein-coding
mm_88131.1	chr10	69398752	69398765	+	1	NA	Intergenic	CpG	-45846	NM_007659	12534	Mm.281367	NM_007659	ENSMUSG00000019942	Cdk1	Cdc2|Cdc2a|p34<CDC2>	cyclin-dependent kinase 1	protein-coding
mm_142797.1	chr17	50190536	50190542	-	1	NA	promoter-TSS (NM_181397)	promoter-TSS (NM_181397)	-42	NM_181397	76438	Mm.41854	NM_181397	ENSMUSG00000039316	Rftn1	2310015N21Rik|AI853526	raftlin lipid raft linker 1	protein-coding
mm_59418.1	chr7	27121842	27121897	+	1	NA	exon (NM_007817, exon 3 of 10)	exon (NM_007817, exon 3 of 10)	1914	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_149724.1	chr19	21778643	21778651	+	1	NA	5' UTR (NM_031997, exon 1 of 25)	5' UTR (NM_031997, exon 1 of 25)	307	NM_031997	83921	Mm.329776	NM_031997	ENSMUSG00000024754	Tmem2	-	transmembrane protein 2	protein-coding
mm_66774.1	chr7	46833389	46833393	-	1	NA	Intergenic	Intergenic	-12413	NM_010699	16828	Mm.29324	NM_010699	ENSMUSG00000063229	Ldha	Ldh1|Ldhm|l7R2	lactate dehydrogenase A	protein-coding
mm_51278.1	chr6	72142173	72142191	+	1	NA	exon (NM_011375, exon 4 of 7)	exon (NM_011375, exon 4 of 7)	-18985	NR_045165	71265	Mm.442035	NR_045163	ENSMUSG00000108709	4933431G14Rik	4930565C19Rik	RIKEN cDNA 4933431G14 gene	ncRNA
mm_47225.1	chr5	121373414	121373432	-	1	NA	exon (NM_001163470, exon 10 of 12)	exon (NM_001163470, exon 10 of 12)	12192	NM_001163470	231712	Mm.20488	NM_172275	ENSMUSG00000042726	Trafd1	1110008K06Rik|Fln29	TRAF type zinc finger domain containing 1	protein-coding
mm_86008.1	chr9	112233313	112233323	-	1	NA	promoter-TSS (NM_001177616)	promoter-TSS (NM_001177616)	-817	NM_001177616	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_103272.1	chr11	72037514	72037525	-	1	NA	promoter-TSS (NM_053245)	promoter-TSS (NM_053245)	-10	NM_053245	114230	Mm.95707	NM_053245	ENSMUSG00000040554	Aipl1	A930007I01Rik	aryl hydrocarbon receptor-interacting protein-like 1	protein-coding
mm_29480.1	chr3	115712604	115712613	-	1	NA	exon (NM_007901, exon 2 of 2)	exon (NM_007901, exon 2 of 2)	2447	NM_007901	13609	Mm.982	NM_007901	ENSMUSG00000045092	S1pr1	AI849002|Edg1|Lpb1|S1p|S1p1	sphingosine-1-phosphate receptor 1	protein-coding
mm_86046.1	chr9	114497338	114497351	-	1	NA	promoter-TSS (NM_009916)	promoter-TSS (NM_009916)	-800	NM_009916	12773	Mm.1337	NM_009916	ENSMUSG00000047898	Ccr4	C-C CKR-4|CHEMR1|Cmkbr4|LESTR|Sdf1r	chemokine (C-C motif) receptor 4	protein-coding
mm_4311.1	chr1	171845680	171845684	+	1	NA	intron (NM_001289470, intron 2 of 8)	intron (NM_001289470, intron 2 of 8)	5985	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_43406.1	chr5	135887906	135887923	+	1	NA	promoter-TSS (NM_013560)	promoter-TSS (NM_013560)	-5	NM_013560	15507	Mm.13849	NM_013560	ENSMUSG00000004951	Hspb1	27kDa|Hsp25	heat shock protein 1	protein-coding
mm_90346.1	chr10	127150707	127150715	+	1	NA	Intergenic	Intergenic	-14445	NR_045166	14421	Mm.386762	NM_008080	ENSMUSG00000006731	B4galnt1	4933429D13Rik|Gal-NAc-T|GalNAc-T|GalNAcT|Galgt1|Ggm-2|Ggm2	beta-1,4-N-acetyl-galactosaminyl transferase 1	protein-coding
mm_154195.1	chr19	58943558	58943572	-	1	NA	exon (NM_178689, exon 1 of 14)	exon (NM_178689, exon 1 of 14)	107	NM_001327998	73442	Mm.39739	NM_175199	ENSMUSG00000025092	Hspa12a	1700063D12Rik|AI118035|AI840429|AW048913|AW556406|D5Mgi40|Gm19925|mKIAA0417	heat shock protein 12A	protein-coding
mm_144542.1	chr18	27598583	27598585	+	1	NA	Intergenic	Intergenic	-961580	NR_045398	320624	Mm.50107	NR_045398		4930474G06Rik	-	RIKEN cDNA 4930474G06 gene	ncRNA
mm_25777.1	chr3	126596994	126597038	+	1	NA	promoter-TSS (NM_001293663)	promoter-TSS (NM_001293663)	65	NM_023813	108058	Mm.255822	NM_023813	ENSMUSG00000053819	Camk2d	2810011D23Rik|8030469K03Rik|CaMK II|[d]-CaMKII	calcium/calmodulin-dependent protein kinase II, delta	protein-coding
mm_86607.1	chr10	13832795	13832800	+	1	NA	intron (NM_001347362, intron 1 of 5)	intron (NM_001347362, intron 1 of 5)	36160	NM_025446	66253	Mm.45755	NM_025446	ENSMUSG00000019806	Aig1	1500031O19Rik|AV064870|AW413422|CGI-103	androgen-induced 1	protein-coding
mm_123677.1	chr14	69484711	69484723	-	1	NA	Intergenic	Intergenic	27832	NM_173420	239167	Mm.259889	NM_173420	ENSMUSG00000047977	Synb	D930020E02Rik|syncytin-B	syncytin b	protein-coding
mm_47296.1	chr5	122248085	122248093	-	1	NA	intron (NR_104441, intron 8 of 12)	intron (NR_104441, intron 8 of 12)	16371	NR_104441	654470	Mm.28804	NM_001039153	ENSMUSG00000038593	Tctn1	G730031O11Rik|Tect1	tectonic family member 1	protein-coding
mm_50103.1	chr6	41533221	41533227	+	1	NA	Intergenic	Intergenic	11448	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_27.1	chr1	6214685	6214722	+	1	NA	promoter-TSS (NM_009826)	promoter-TSS (NM_009826)	41	NM_009826	12421	Mm.293811	NM_009826	ENSMUSG00000025907	Rb1cc1	2900055E04Rik|5930404L04Rik|Cc1|FIP200|LaXp180	RB1-inducible coiled-coil 1	protein-coding
mm_102193.1	chr11	54353248	54353259	-	1	NA	intron (NM_001033597, intron 20 of 20)	intron (NM_001033597, intron 20 of 20)	-17399	NM_029105	74847	Mm.486538	NM_029105	ENSMUSG00000020332	Meikin	4930404A10Rik	meiotic kinetochore factor	protein-coding
mm_121039.1	chr14	80006268	80006276	+	1	NA	exon (NM_001030294, exon 2 of 7)	exon (NM_001030294, exon 2 of 7)	5970	NM_001030294	380924	Mm.26456	NM_001030294	ENSMUSG00000022026	Olfm4	GC1|GW112|Gm296|Gm913|OlfD|pPD4	olfactomedin 4	protein-coding
mm_83714.1	chr9	50752291	50752337	-	1	NA	promoter-TSS (NM_001289784)	promoter-TSS (NM_001289784)	40	NM_001164708	69253	Mm.1980	NM_024441	ENSMUSG00000038086	Hspb2	27kDa|2810021G24Rik|HSP27|MKBP	heat shock protein 2	protein-coding
mm_117274.1	chr13	65066519	65066529	-	1	NA	3' UTR (NM_001083901, exon 13 of 13)	3' UTR (NM_001083901, exon 13 of 13)	33466	NM_001083890	238683	Mm.295543	NM_001083890	ENSMUSG00000074849	Spata31d1c	4932441B19Rik|Fam75d1c	spermatogenesis associated 31 subfamily D, member 1C	protein-coding
mm_92211.1	chr10	68218849	68218852	-	1	NA	intron (NM_023598, intron 3 of 9)	intron (NM_023598, intron 3 of 9)	59876	NM_023598	71371	Mm.440357	NM_023598	ENSMUSG00000019947	Arid5b	4930580B11|5430435G07Rik|AI467247|Desrt|Mrf2|Mrf2alpha|Mrf2beta	AT rich interactive domain 5B (MRF1-like)	protein-coding
mm_1493.1	chr1	71888056	71888067	+	1	NA	promoter-TSS (NR_027659)	promoter-TSS (NR_027659)	-51	NR_027658	667931	Mm.214128	NR_027658	ENSMUSG00000099707	Gm8883	EG667931|Gm554	predicted gene 8883	ncRNA
mm_131005.1	chr15	103562826	103562833	-	1	NA	TTS (NM_008134)	TTS (NM_008134)	2252	NM_001289587	14663	Mm.219621	NM_008134	ENSMUSG00000022491	Glycam1	MC26|Sgp50|glyCAM-1	glycosylation dependent cell adhesion molecule 1	protein-coding
mm_81518.1	chr9	110051997	110052010	+	1	NA	promoter-TSS (NM_001311164)	promoter-TSS (NM_001311164)	-18	NM_001311163	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_93906.1	chr10	126978443	126978445	-	1	NA	promoter-TSS (NM_001113470)	promoter-TSS (NM_001113470)	-273	NM_001113470	52468	Mm.29490	NM_146012	ENSMUSG00000078429	Ctdsp2	AI586070|D10Ertd73e|OS-4|OS4|SCP2	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 2	protein-coding
mm_143551.1	chr17	74047851	74047867	-	1	NA	promoter-TSS (NM_053188)	promoter-TSS (NM_053188)	57	NM_053188	94224	Mm.38933	NM_053188	ENSMUSG00000038541	Srd5a2	5ART2|S5AR 2	steroid 5 alpha-reductase 2	protein-coding
mm_59411.1	chr7	27121492	27121500	+	1	NA	intron (NM_007817, intron 1 of 9)	intron (NM_007817, intron 1 of 9)	1541	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_131602.1	chr16	19063588	19063614	+	1	NA	Intergenic	Intergenic	186851	NM_010435	15260	Mm.15694	NM_010435	ENSMUSG00000022702	Hira	AA138857|D16Ertd95e|Gm15797|N28177|OTTMUSG00000026264|Tuple1	histone cell cycle regulator	protein-coding
mm_165620.1	chr3	61409919	61409950	+	1	NA	Intergenic	Intergenic	45427	NM_028712	74012	Mm.422674	NM_028712	ENSMUSG00000036894	Rap2b	4021402C18Rik|AA408554	RAP2B, member of RAS oncogene family	protein-coding
mm_148359.1	chr18	85666792	85666824	-	1	NA	Intergenic	Intergenic	-715284	NM_025969	67105	Mm.250617	NM_025969	ENSMUSG00000024645	Timm21	1700034H14Rik|2700002I20Rik	tranlocase of inner mitochondrial membrane 21	protein-coding
mm_166363.1	chr5	123832288	123832294	-	1	NA	Intergenic	Intergenic	33225	NM_030701	80885	Mm.440567	NM_030701	ENSMUSG00000045502	Hcar2	Gpr109a|Gpr109b|HM74|Niacr1|PUMA-G|Pumag|mHM74b	hydroxycarboxylic acid receptor 2	protein-coding
mm_110139.1	chr12	26447948	26447958	-	1	NA	intron (NM_021384, intron 4 of 5)	ID_B1|SINE|B4	8499	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_87580.1	chr10	56504496	56504520	+	1	NA	Intergenic	Intergenic	127208	NM_010288	14609	Mm.378921	NM_010288	ENSMUSG00000050953	Gja1	AU042049|AW546267|Cnx43|Cx43|Cx43alpha1|Gja-1|Npm1|connexin43	gap junction protein, alpha 1	protein-coding
mm_30417.1	chr3	152265862	152265878	-	1	NA	intron (NM_199465, intron 1 of 12)	CpG	450	NM_199465	68810	Mm.200188	NM_199465	ENSMUSG00000039103	Nexn	1110046H09Rik|AA553326|NELIN	nexilin	protein-coding
mm_47693.1	chr5	129682321	129682323	-	1	NA	Intergenic	MYSERV6-int|LTR|ERVK	-12234	NM_172462	22648	Mm.135067	NM_172462	ENSMUSG00000051034	Zfp11	6720465D24|Krox-6|Zfp-11	zinc finger protein 11	protein-coding
mm_163303.1	chr11	120941988	120941994	-	1	NA	Intergenic	L1MB8|LINE|L1	-6493	NM_030696	80879	Mm.28632	NM_030696	ENSMUSG00000025161	Slc16a3	Mct3|Mct4	solute carrier family 16 (monocarboxylic acid transporters), member 3	protein-coding
mm_122973.1	chr14	54975365	54975405	-	1	NA	TTS (NR_030607)	TTS (NR_030607)	391	NR_030607	100124433		NR_030607	ENSMUSG00000077928	Mir208b	Mirn208b|mir-208b	microRNA 208b	ncRNA
mm_138551.1	chr17	35264777	35264787	+	1	NA	intron (NM_010380, intron 3 of 7)	B1_Mm|SINE|Alu	1659	NM_001267808	14980	Mm.439675	NM_001267808		H2-L	H-2L	histocompatibility 2, D region locus L	protein-coding
mm_60483.1	chr7	44478421	44478438	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-6088	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_122846.1	chr14	54733250	54733263	-	1	NA	exon (NM_016972, exon 7 of 11)	exon (NM_016972, exon 7 of 11)	-21082	NM_207131	110794	Mm.236223	NM_207131	ENSMUSG00000052435	Cebpe	C/EBPe|CRP1|Gm294	CCAAT/enhancer binding protein (C/EBP), epsilon	protein-coding
mm_165615.1	chr3	57312445	57312446	-	1	NA	Intergenic	Intergenic	-10526	NM_008536	17112	Mm.856	NM_008536	ENSMUSG00000027800	Tm4sf1	L6|M3s1	transmembrane 4 superfamily member 1	protein-coding
mm_143339.1	chr17	66504209	66504217	-	1	NA	intron (NM_024448, intron 2 of 5)	AT_rich|Low_complexity|Low_complexity	15457	NM_024448	19328	Mm.248313	NM_024448	ENSMUSG00000023460	Rab12	2900054P15Rik|AW555448|C77700	RAB12, member RAS oncogene family	protein-coding
mm_165132.1	chr2	9882653	9882661	+	1	NA	TTS (NR_040511)	TTS (NR_040511)	1411	NR_024257	381347	Mm.441450	NR_024257		4930412O13Rik	ENSMUSG00000075535|Gm10853	RIKEN cDNA 4930412O13 gene	ncRNA
mm_156073.1	chrX	109161631	109161657	+	1	NA	3' UTR (NM_019989, exon 4 of 4)	3' UTR (NM_019989, exon 4 of 4)	-35112	NM_001037917	622976	Mm.482747	NM_001037917	ENSMUSG00000048621	Gm6377	EG622976	predicted gene 6377	protein-coding
mm_8313.1	chr1	144249050	144249067	-	1	NA	promoter-TSS (NM_015811)	promoter-TSS (NM_015811)	46	NM_015811	50778	Mm.103701	NM_015811	ENSMUSG00000026358	Rgs1	BL34	regulator of G-protein signaling 1	protein-coding
mm_61884.1	chr7	89632876	89632912	+	1	NA	promoter-TSS (NM_181407)	promoter-TSS (NM_181407)	76	NM_181407	109264	Mm.334011	NM_181407	ENSMUSG00000030621	Me3	1700020C08Rik|B230207H15Rik	malic enzyme 3, NADP(+)-dependent, mitochondrial	protein-coding
mm_102686.1	chr11	65356384	65356396	-	1	NA	Intergenic	B1_Mus2|SINE|Alu	-68557	NR_040280	327946	Mm.383301	NR_040280	ENSMUSG00000085162	Gm12295	A730013G04|OTTMUSG00000005904	predicted gene 12295	ncRNA
mm_134988.1	chr16	32144046	32144084	-	1	NA	exon (NM_001347181, exon 3 of 3)	exon (NM_001347181, exon 3 of 3)	21411	NM_146069	224109	Mm.33498	NM_146069	ENSMUSG00000052384	Nrros	E430025L02Rik|Lrcc33|Lrrc33	negative regulator of reactive oxygen species	protein-coding
mm_14846.1	chr2	148395370	148395413	+	1	NA	promoter-TSS (NM_009219)	promoter-TSS (NM_009219)	14	NM_009219	20608	Mm.35324	NM_009219	ENSMUSG00000037014	Sstr4	Smstr4|sst4	somatostatin receptor 4	protein-coding
mm_135367.1	chr16	44061470	44061479	-	1	NA	Intergenic	Intergenic	-33529	NM_001172107	207798	Mm.19316	NM_153528	ENSMUSG00000036292	Gramd1c	4921521N14Rik	GRAM domain containing 1C	protein-coding
mm_54183.1	chr6	23839492	23839514	-	1	NA	promoter-TSS (NM_153163)	promoter-TSS (NM_153163)	-82	NM_001252105	320405	Mm.259632	NM_153163	ENSMUSG00000017978	Cadps2	A230044C21Rik|Caps-2|Caps2|Cpd2	Ca2+-dependent activator protein for secretion 2	protein-coding
mm_104382.1	chr11	94474089	94474112	-	1	NA	promoter-TSS (NM_001177890)	promoter-TSS (NM_001177890)	98	NM_001177888	12291	Mm.29585	NM_009783	ENSMUSG00000020866	Cacna1g	Cav3.1d|[a]1G|a1G|alpha-1G|mKIAA1123	calcium channel, voltage-dependent, T type, alpha 1G subunit	protein-coding
mm_19053.1	chr2	77278869	77278876	-	1	NA	intron (NM_175465, intron 1 of 17)	(A)n|Simple_repeat|Simple_repeat	1720	NM_175465	228071	Mm.27120	NM_175465	ENSMUSG00000042272	Sestd1	1500031J16Rik|A930010O20|Solo/Trio8	SEC14 and spectrin domains 1	protein-coding
mm_57273.1	chr6	123289863	123289876	-	1	NA	promoter-TSS (NM_019948)	promoter-TSS (NM_019948)	2	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_6558.1	chr1	75141532	75141544	-	1	NA	intron (NM_026977, intron 1 of 8)	CpG	830	NM_026977	69171	Mm.28193	NM_026977	ENSMUSG00000033159	Cnppd1	1810031K17Rik|AU043960	cyclin Pas1/PHO80 domain containing 1	protein-coding
mm_34509.1	chr4	148804451	148804494	+	1	NA	promoter-TSS (NM_001159344)	promoter-TSS (NM_001159344)	80	NM_027195	69743	Mm.233879	NM_027195	ENSMUSG00000028977	Casz1	2410019P08Rik|AV096627|BC040081|Cst|D4Ertd432e	castor zinc finger 1	protein-coding
mm_128029.1	chr15	25363521	25363541	-	1	NA	3' UTR (NM_027395, exon 2 of 2)	3' UTR (NM_027395, exon 2 of 2)	50233	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	brain abundant, membrane attached signal protein 1	protein-coding
mm_167952.1	chrX	140598925	140598925	+	1	NA	intron (NM_001077364, intron 1 of 3)	CpG	1597	NM_001077364	14605	Mm.22216	NM_010286	ENSMUSG00000031431	Tsc22d3	DIP|Dsip1|Gilz|TSC-22R|Tilz3	TSC22 domain family, member 3	protein-coding
mm_100703.1	chr11	3648072	3648099	-	1	NA	promoter-TSS (NR_110490)	promoter-TSS (NR_110490)	-549	NR_002322	544752	Mm.390314	NR_002321	ENSMUSG00000056579	Tug1	AI316828	taurine upregulated gene 1	ncRNA
mm_147911.1	chr18	65427808	65427809	-	1	NA	intron (NR_105742, intron 3 of 6)	7SLRNA|srpRNA|srpRNA	-3189	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_38285.1	chr4	136890304	136890315	-	1	NA	exon (NM_007574, exon 3 of 3)	exon (NM_007574, exon 3 of 3)	2605	NM_007574	12262	Mm.439732	NM_007574	ENSMUSG00000036896	C1qc	AI385742|C1qg|Ciqc	complement component 1, q subcomponent, C chain	protein-coding
mm_108846.1	chr12	98268679	98268690	+	1	NA	promoter-TSS (NM_008152)	promoter-TSS (NM_008152)	49	NM_008152	14744	Mm.378924	NM_008152	ENSMUSG00000021886	Gpr65	Dig1|Gpcr25|TDAG8	G-protein coupled receptor 65	protein-coding
mm_111680.1	chr12	103382567	103382577	-	1	NA	intron (NR_033587, intron 1 of 5)	ORR1A2|LTR|ERVL-MaLR	5678	NR_033587	68149	Mm.127378	NM_026580	ENSMUSG00000021203	Otub2	2010015L18Rik|4930586I02Rik|AI413508|AW557219|OTB2|OTU2	OTU domain, ubiquitin aldehyde binding 2	protein-coding
mm_101555.1	chr11	33843677	33843687	-	1	NA	promoter-TSS (NM_001290690)	promoter-TSS (NM_001290690)	-97	NM_001290690	70357	Mm.252514	NM_027398	ENSMUSG00000053519	Kcnip1	KCHIP1|Kchip1.2	Kv channel-interacting protein 1	protein-coding
mm_39724.1	chr5	28316929	28317008	+	1	NA	promoter-TSS (NM_028234)	promoter-TSS (NM_028234)	-221	NM_028234	381626	Mm.304075	NM_028234	ENSMUSG00000048271	Rbm33	3200001K10Rik|6430512A10Rik|AA386890|Prr8	RNA binding motif protein 33	protein-coding
mm_98333.1	chr11	90675968	90675978	+	1	NA	intron (NM_028011, intron 3 of 15)	intron (NM_028011, intron 3 of 15)	11628	NM_028011	71943	Mm.167868	NM_028011	ENSMUSG00000020541	Tom1l1	2310045L10Rik|C80573|Srcasm	target of myb1-like 1 (chicken)	protein-coding
mm_151441.1	chr19	57452901	57452926	+	1	NA	promoter-TSS (NM_029839)	promoter-TSS (NM_029839)	7	NM_028115	72133	Mm.258404	NM_028115	ENSMUSG00000025086	Trub1	2610009I02Rik|9030425C13Rik|AI448235|BB118943|C76870	TruB pseudouridine (psi) synthase family member 1	protein-coding
mm_120216.1	chr14	62760465	62760484	+	1	NA	promoter-TSS (NR_045503)	promoter-TSS (NR_045503)	-27	NR_045503	71000	Mm.399410	NR_045503	ENSMUSG00000097775	4931440J10Rik	-	RIKEN cDNA 4931440J10 gene	ncRNA
mm_8940.1	chr1	164437877	164437904	-	1	NA	TTS (NM_001293313)	TTS (NM_001293313)	20465	NM_009721	11931	Mm.4550	NM_009721	ENSMUSG00000026576	Atp1b1	Atp4b|Atpb|Atpb-1|NKbeta1	ATPase, Na+/K+ transporting, beta 1 polypeptide	protein-coding
mm_31417.1	chr4	48051255	48051268	+	1	NA	promoter-TSS (NM_001307989)	promoter-TSS (NM_001307989)	15	NM_001307989	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_91879.1	chr10	59613144	59613148	-	1	NA	intron (NM_001033259, intron 1 of 7)	intron (NM_001033259, intron 1 of 7)	3546	NM_001033259	215999	Mm.296470	NM_001033259	ENSMUSG00000009647	Mcu	2010012O16Rik|AV064928|C10orf42|Ccdc109a|D130073L02Rik|Gm64	mitochondrial calcium uniporter	protein-coding
mm_47353.1	chr5	122744930	122744948	-	1	NA	intron (NM_145358, intron 11 of 15)	intron (NM_145358, intron 11 of 15)	34471	NM_001199676	207565	Mm.289237	NM_145358	ENSMUSG00000029471	Camkk2	6330570N16Rik|AW061083|mKIAA0787	calcium/calmodulin-dependent protein kinase kinase 2, beta	protein-coding
mm_173198.1	chrX	65367094	65367094	-	1	NA	Intergenic	Intergenic	319450	NM_027302	70062	Mm.45791	NM_027302	ENSMUSG00000031181	Ctag2	1700030B21Rik	cancer/testis antigen 2	protein-coding
mm_67572.1	chr7	81934632	81934650	-	1	NA	promoter-TSS (NM_013886)	promoter-TSS (NM_013886)	-182	NM_013886	29877	Mm.392934	NM_013886	ENSMUSG00000025104	Hdgfrp3	2700022B06Rik|HRP-3	hepatoma-derived growth factor, related protein 3	protein-coding
mm_20932.1	chr2	150856108	150856129	-	1	NA	intron (NM_024465, intron 2 of 12)	B1_Mur1|SINE|Alu	48613	NM_024465	76192	Mm.112632	NM_024465	ENSMUSG00000032046	Abhd12	1500011G07Rik|6330583M11Rik|AI431047|AW547313	abhydrolase domain containing 12	protein-coding
mm_53228.1	chr6	127152570	127152574	+	1	NA	intron (NR_040275, intron 1 of 1)	intron (NR_040275, intron 1 of 1)	-1524	NM_009829	12444	Mm.333406	NM_009829	ENSMUSG00000000184	Ccnd2	2600016F06Rik|AI256817|BF642806|C86853|Vin-1|Vin1|cD2	cyclin D2	protein-coding
mm_36951.1	chr4	109107997	109108006	-	1	NA	intron (NM_001346502, intron 4 of 23)	intron (NM_001346502, intron 4 of 23)	10035	NM_173350	100273	Mm.366315	NM_133885	ENSMUSG00000028559	Osbpl9	2600011I06Rik|AU015843|Orp-9	oxysterol binding protein-like 9	protein-coding
mm_13943.1	chr2	121289590	121289606	+	1	NA	promoter-TSS (NM_032393)	promoter-TSS (NM_032393)	-4	NM_032393	17754	Mm.36501	NM_032393	ENSMUSG00000027254	Map1a	6330416M19Rik|AI853608|Mtap-1|Mtap1|Mtap1a|moth1	microtubule-associated protein 1 A	protein-coding
mm_132123.1	chr16	31749156	31749161	+	1	NA	intron (NR_045516, intron 5 of 24)	intron (NR_045516, intron 5 of 24)	-5192	NM_001252436	13383	Mm.382	NM_007862	ENSMUSG00000022770	Dlg1	B130052P05Rik|Dlgh1|E-dlg/SAP97|SAP-97|SAP97|mKIAA4187	discs, large homolog 1 (Drosophila)	protein-coding
mm_68518.1	chr7	111736142	111736153	-	1	NA	intron (NM_173739, intron 1 of 10)	intron (NM_173739, intron 1 of 10)	43830	NM_173739	233733	Mm.323322	NM_173739	ENSMUSG00000038296	Galnt18	2900011G21Rik|BC024988|Galntl4	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 18	protein-coding
mm_143821.1	chr17	83846871	83846879	-	1	NA	promoter-TSS (NM_025325)	promoter-TSS (NM_025325)	-85	NM_025325	107766	Mm.30100	NM_025325	ENSMUSG00000000673	Haao	0610007K21Rik|0610012J07Rik|3-HAO|3-HAOxase|3HAO	3-hydroxyanthranilate 3,4-dioxygenase	protein-coding
mm_149057.1	chr19	8839387	8839400	+	1	NA	promoter-TSS (NM_008144)	promoter-TSS (NM_008144)	65	NM_008144	14705	Mm.345134	NM_008144	ENSMUSG00000071657	Bscl2	2900097C17Rik|AI046355|Gng3lg	Berardinelli-Seip congenital lipodystrophy 2 (seipin)	protein-coding
mm_107446.1	chr12	36607465	36607468	+	1	NA	intron (NM_178629, intron 9 of 9)	intron (NM_178629, intron 9 of 9)	191850	NR_037309	100499526		NR_037309	ENSMUSG00000092917	Mir3472	mmu-mir-3472	microRNA 3472	ncRNA
mm_189.1	chr1	15803205	15803236	+	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	-2426	NM_009352	21749	Mm.4306	NM_009352	ENSMUSG00000025925	Terf1	Pin2|Trbf1|Trf1	telomeric repeat binding factor 1	protein-coding
mm_124753.1	chr15	6642575	6642588	+	1	NA	intron (NM_011815, intron 9 of 17)	intron (NM_011815, intron 9 of 17)	62734	NM_011815	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_58418.1	chr7	3292976	3292990	+	1	NA	promoter-TSS (NM_001093766)	promoter-TSS (NM_001093766)	-45	NM_001093766	50918	Mm.29874	NM_016969	ENSMUSG00000068566	Myadm	D7Wsu62e	myeloid-associated differentiation marker	protein-coding
mm_5482.1	chr1	36799404	36799406	-	1	NA	intron (NM_018872, intron 33 of 40)	intron (NM_018872, intron 33 of 40)	20421	NM_001289612	22637	Mm.8038	NM_009539	ENSMUSG00000026117	Zap70	Srk|ZAP-70|mrtle|mur	zeta-chain (TCR) associated protein kinase	protein-coding
mm_13668.1	chr2	115581652	115581665	+	1	NA	promoter-TSS (NM_207264)	promoter-TSS (NM_207264)	-58	NM_207264	399568	Mm.134929	NM_207264	ENSMUSG00000040282	BC052040	-	cDNA sequence BC052040	protein-coding
mm_12721.1	chr2	78293161	78293311	+	1	NA	intron (NM_177843, intron 3 of 5)	RMER19C|LTR|ERVK	55689	NM_177843	329436	Mm.235448	NM_177843		Gm14461	A830093M07|OTTMUSG00000016703	predicted gene 14461	protein-coding
mm_133359.1	chr16	84702164	84702182	+	1	NA	Intergenic	Intergenic	-10850	NR_132106	100653389	Mm.261808	NR_132106	ENSMUSG00000097418	Mir155hg	Bic|Gm26667	Mir155 host gene (non-protein coding)	ncRNA
mm_39812.1	chr5	30666891	30666963	+	1	NA	promoter-TSS (NM_007681)	promoter-TSS (NM_007681)	41	NR_126074	12615	Mm.290563	NM_007681	ENSMUSG00000029177	Cenpa	Cenp-A	centromere protein A	protein-coding
mm_128450.1	chr15	50772542	50772563	-	1	NA	intron (NM_001310485, intron 5 of 7)	intron (NM_001310485, intron 5 of 7)	116497	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_16901.1	chr2	13413585	13413597	-	1	NA	intron (NM_001081084, intron 27 of 66)	intron (NM_001081084, intron 27 of 66)	78285	NM_001081084	65969	Mm.313915	NM_001081084	ENSMUSG00000026726	Cubn	AA408369|AL022750|D2Wsu88e	cubilin (intrinsic factor-cobalamin receptor)	protein-coding
mm_78479.1	chr9	32695752	32695775	+	1	NA	promoter-TSS (NM_001038642)	promoter-TSS (NM_001038642)	-279	NM_011808	23871	Mm.292415	NM_011808	ENSMUSG00000032035	Ets1	AI196000|AI448617|D230050P06|Ets-1|Tpl1|vs	E26 avian leukemia oncogene 1, 5' domain	protein-coding
mm_165870.1	chr4	39740759	39740759	+	1	NA	Intergenic	Intergenic	290466	NM_001081095	75471	Mm.23522	NM_001081095	ENSMUSG00000028287	1700009N14Rik	AI429145	RIKEN cDNA 1700009N14 gene	protein-coding
mm_69183.1	chr7	127233125	127233235	-	1	NA	promoter-TSS (NM_146201)	promoter-TSS (NM_146201)	-50	NR_030674	100043580	Mm.482209	NR_030674	ENSMUSG00000000486	Gm4532	-	predicted gene 4532	ncRNA
mm_4926.1	chr1	191036813	191036825	+	1	NA	promoter-TSS (NM_029336)	promoter-TSS (NM_029336)	-3	NM_029336	75558	Mm.383398	NM_029336	ENSMUSG00000057072	Spata45	1700022P22Rik	spermatogenesis associated 45	protein-coding
mm_168772.1	chr12	17459366	17459384	-	1	NA	Intergenic	RLTR9D|LTR|ERVK	-85498	NM_013614	18263	Mm.34102	NM_013614	ENSMUSG00000011179	Odc1	ODC	ornithine decarboxylase, structural 1	protein-coding
mm_24785.1	chr3	95541699	95541717	+	1	NA	intron (NM_001267695, intron 3 of 7)	intron (NM_001267695, intron 3 of 7)	14922	NM_001267695	13040	Mm.3619	NM_021281	ENSMUSG00000038642	Ctss	Cats	cathepsin S	protein-coding
mm_5413.1	chr1	33814592	33814600	-	1	NA	promoter-TSS (NM_001290700)	promoter-TSS (NM_001290700)	-1	NM_001290699	98403	Mm.289103	NM_133817	ENSMUSG00000042197	Zfp451	4930515K21Rik|4933435G09Rik|AI596398|COASTER|Kiaa0576-hp|Znf451|mKIAA1702	zinc finger protein 451	protein-coding
mm_5865.1	chr1	53775650	53775673	-	1	NA	intron (NM_133810, intron 2 of 7)	intron (NM_133810, intron 2 of 7)	9554	NM_133810	98267	Mm.25559	NM_133810	ENSMUSG00000026094	Stk17b	3110009A03Rik|AI120141|Drak2	serine/threonine kinase 17b (apoptosis-inducing)	protein-coding
mm_123320.1	chr14	62700655	62700701	-	1	NA	exon (NM_008715, exon 15 of 19)	exon (NM_008715, exon 15 of 19)	37011	NM_001199945	319433	Mm.483827	NM_001199945	ENSMUSG00000091155	Serpine3	E130113E03Rik	serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 3	protein-coding
mm_44688.1	chr5	30154957	30154986	-	1	NA	promoter-TSS (NM_001289798)	promoter-TSS (NM_001289798)	9	NM_178878	97212	Mm.200497	NM_178878	ENSMUSG00000025745	Hadha	C77020|Mtpa	hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), alpha subunit	protein-coding
mm_111801.1	chr12	105006873	105006876	-	1	NA	intron (NM_172500, intron 1 of 16)	ID_B1|SINE|B4	2935	NM_172500	212073	Mm.212688	NM_172500	ENSMUSG00000054150	Syne3	nesprin-3	spectrin repeat containing, nuclear envelope family member 3	protein-coding
mm_145784.1	chr18	65083610	65083624	+	1	NA	intron (NM_001114386, intron 5 of 30)	intron (NM_001114386, intron 5 of 30)	60090	NM_031881	83814	Mm.98668	NM_031881	ENSMUSG00000024589	Nedd4l	1300012C07Rik|Nedd4-2|Nedd4b	neural precursor cell expressed, developmentally down-regulated gene 4-like	protein-coding
mm_116828.1	chr13	54611333	54611387	-	1	NA	promoter-TSS (NM_028870)	promoter-TSS (NM_028870)	13	NM_028870	74325	Mm.290026	NM_028870	ENSMUSG00000047547	Cltb	2310046E19Rik|lcb	clathrin, light polypeptide (Lcb)	protein-coding
mm_162528.1	chr1	163887822	163887832	+	1	NA	intron (NM_001305643, intron 18 of 19)	intron (NM_001305643, intron 18 of 19)	-41273	NM_001286002	240880	Mm.389213	NM_028776	ENSMUSG00000026584	Scyl3	1200016D23Rik|6030457O16|AW214499|Pace1	SCY1-like 3 (S. cerevisiae)	protein-coding
mm_14213.1	chr2	127333500	127333510	+	1	NA	Intergenic	Intergenic	-2654	NM_010090	13537	Mm.4729	NM_010090	ENSMUSG00000027368	Dusp2	PAC1	dual specificity phosphatase 2	protein-coding
mm_114236.1	chr13	56609517	56609606	+	1	NA	promoter-TSS (NM_009369)	promoter-TSS (NM_009369)	-42	NM_009369	21810	Mm.14455	NM_009369	ENSMUSG00000035493	Tgfbi	68kDa|AI181842|AI747162|Beta-ig|big-h3	transforming growth factor, beta induced	protein-coding
mm_12450.1	chr2	71211796	71211812	+	1	NA	promoter-TSS (NM_001198877)	promoter-TSS (NM_001198877)	98	NM_001198876	13427	Mm.249479	NM_010064	ENSMUSG00000027012	Dync1i2	3110079H08Rik|AW554389|Dncic2	dynein cytoplasmic 1 intermediate chain 2	protein-coding
mm_41288.1	chr5	90463391	90463397	+	1	NA	intron (NM_009654, intron 3 of 14)	Lx9|LINE|L1	2524	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_77000.1	chr8	107388683	107388685	-	1	NA	3' UTR (NM_008706, exon 6 of 6)	3' UTR (NM_008706, exon 6 of 6)	14521	NM_008706	18104	Mm.252	NM_008706	ENSMUSG00000003849	Nqo1	AV001255|Dia4|Dtd|Nmo-1|Nmo1|Nmor1|Ox-1|Ox1|Qr1	NAD(P)H dehydrogenase, quinone 1	protein-coding
mm_73983.1	chr8	120549291	120549292	+	1	NA	intron (NM_001145896, intron 1 of 15)	intron (NM_001145896, intron 1 of 15)	10595	NR_106159	102466849		NR_106159	ENSMUSG00000098280	Mir7687	Gm27573|mmu-mir-7687	microRNA 7687	ncRNA
mm_14693.1	chr2	141180000	141180006	+	1	NA	intron (NM_001013802, intron 5 of 18)	intron (NM_001013802, intron 5 of 18)	-508527	NM_178382	71436	Mm.426781	NM_178382	ENSMUSG00000051379	Flrt3	5530600M07Rik|C430047I10Rik|mKIAA1469	fibronectin leucine rich transmembrane protein 3	protein-coding
mm_22414.1	chr2	181483587	181483652	-	1	NA	Intergenic	Intergenic	-9587	NM_183181	241850	Mm.87455	NM_183181	ENSMUSG00000055882	Abhd16b	1700095H12	abhydrolase domain containing 16B	protein-coding
mm_44964.1	chr5	36713337	36713399	-	1	NA	Intergenic	Intergenic	-17347	NM_001081232	320661	Mm.26480	NM_177221	ENSMUSG00000029190	D5Ertd579e	9030221A05Rik|A930018H20Rik|Kiaa0232	DNA segment, Chr 5, ERATO Doi 579, expressed	protein-coding
mm_76454.1	chr8	85220568	85220593	-	1	NA	Intergenic	Intergenic	-9917	NM_146859	258858	Mm.354727	NM_146859	ENSMUSG00000051952	Olfr371	MOR141-3	olfactory receptor 371	protein-coding
mm_5877.1	chr1	53824977	53824987	-	1	NA	intron (NM_001001883, intron 28 of 28)	intron (NM_001001883, intron 28 of 28)	-24442	NR_106149	102465783		NR_106149	ENSMUSG00000098443	Mir7681	Gm27806|mmu-mir-7681	microRNA 7681	ncRNA
mm_8809.1	chr1	161876781	161876821	-	1	NA	promoter-TSS (NM_172645)	promoter-TSS (NM_172645)	-140	NM_172645	226551	Mm.170002	NM_172645	ENSMUSG00000040297	Suco	4732491B11|AI848100|AU016931|Opt	SUN domain containing ossification factor	protein-coding
mm_118585.1	chr14	20348160	20348244	+	1	NA	promoter-TSS (NM_172379)	promoter-TSS (NM_172379)	40	NM_001177633	105428	Mm.206990	NM_172379	ENSMUSG00000039599	Fam149b	AA536717|AI428773|Fam149b1|mKIAA0974	family with sequence similarity 149, member B	protein-coding
mm_137795.1	chr17	29679248	29679270	+	1	NA	intron (NR_132314, intron 10 of 27)	intron (NR_132314, intron 10 of 27)	18664	NM_028791	74157	Mm.390979	NM_028791	ENSMUSG00000024019	Cmtr1	1300018I05Rik|AI451264|Ftsjd2|MTr1	cap methyltransferase 1	protein-coding
mm_150887.1	chr19	45151595	45151595	+	1	NA	intron (NM_021901, intron 1 of 2)	CpG	880	NM_021901	21908	Mm.391203	NM_021901	ENSMUSG00000025215	Tlx1	Hox-11|Hox11|Tlx-1	T cell leukemia, homeobox 1	protein-coding
mm_32019.1	chr4	95052858	95052873	+	1	NA	promoter-TSS (NM_010591)	promoter-TSS (NM_010591)	-643	NM_010591	16476	Mm.275071	NM_010591	ENSMUSG00000052684	Jun	AP-1|Junc|c-jun	jun proto-oncogene	protein-coding
mm_66126.1	chr7	31054355	31054383	-	1	NA	exon (NM_019503, exon 2 of 8)	exon (NM_019503, exon 2 of 8)	484	NM_052991	56188	Mm.1491	NM_019503	ENSMUSG00000036570	Fxyd1	0610012C17Rik|1110006M24Rik|Plm|Pml	FXYD domain-containing ion transport regulator 1	protein-coding
mm_95621.1	chr11	53567362	53567428	+	1	NA	promoter-TSS (NM_008443)	promoter-TSS (NM_008443)	26	NM_001290806	16568	Mm.88694	NM_008443	ENSMUSG00000018395	Kif3a	Kif3|Kifl|Kns3	kinesin family member 3A	protein-coding
mm_92239.1	chr10	69352887	69352929	-	1	NA	promoter-TSS (NM_007659)	promoter-TSS (NM_007659)	4	NM_007659	12534	Mm.281367	NM_007659	ENSMUSG00000019942	Cdk1	Cdc2|Cdc2a|p34<CDC2>	cyclin-dependent kinase 1	protein-coding
mm_114780.1	chr13	88821944	88821976	+	1	NA	5' UTR (NM_001037987, exon 1 of 11)	5' UTR (NM_001037987, exon 1 of 11)	488	NM_001037987	13612	Mm.125580	NM_010103	ENSMUSG00000034488	Edil3	Del-1|Del1	EGF-like repeats and discoidin I-like domains 3	protein-coding
mm_24513.1	chr3	92679246	92679247	+	1	NA	promoter-TSS (NM_028622)	promoter-TSS (NM_028622)	-1	NM_028622	73719	Mm.292458	NM_028622	ENSMUSG00000042092	Lce1c	1110014K05Rik	late cornified envelope 1C	protein-coding
mm_104588.1	chr11	97026156	97026179	-	1	NA	non-coding (NR_133649, exon 1 of 2)	non-coding (NR_133649, exon 1 of 2)	251	NR_133649	100127433	Mm.156282	NR_133649	ENSMUSG00000087067	Gm11532	OTTMUSG00000001860|Sp6os	predicted gene 11532	ncRNA
mm_112938.1	chr13	20986224	20986235	+	1	NA	intron (NM_012054, intron 13 of 20)	MT2B|LTR|ERVL	87070	NM_146535	258528	Mm.377554	NM_146535	ENSMUSG00000042869	Olfr1370	MOR256-14	olfactory receptor 1370	protein-coding
mm_64436.1	chr7	142653077	142653110	+	1	NA	3' UTR (NM_010514, exon 4 of 4)	3' UTR (NM_010514, exon 4 of 4)	1903	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_164180.1	chr15	76269162	76269170	-	1	NA	intron (NR_045747, intron 1 of 2)	intron (NR_045747, intron 1 of 2)	673	NR_045747	100038659	Mm.448549	NR_045747		Mirt2	ENSMUSG00000075583|Gm10872|Gm24562	myocardial infraction associated transcript 2	ncRNA
mm_78593.1	chr9	37400217	37400223	+	1	NA	Intergenic	Intergenic	-1677	NM_028783	74144	Mm.485070	NM_028783	ENSMUSG00000032125	Robo4	1200012D01Rik|AI593217	roundabout guidance receptor 4	protein-coding
mm_75162.1	chr8	36570079	36570082	-	1	NA	3' UTR (NM_015802, exon 14 of 14)	3' UTR (NM_015802, exon 14 of 14)	43863	NM_015802	50768	Mm.125155	NM_015802	ENSMUSG00000031523	Dlc1	A730069N07Rik|Arhgap7|HP|STARD12|dlc-1	deleted in liver cancer 1	protein-coding
mm_53822.1	chr6	147257082	147257088	+	1	NA	exon (NM_008970, exon 3 of 4)	exon (NM_008970, exon 3 of 4)	6928	NM_008970	19227	Mm.28440	NM_008970	ENSMUSG00000048776	Pthlh	PLP|PTH-like|Pthrp	parathyroid hormone-like peptide	protein-coding
mm_10126.1	chr2	3770640	3770664	+	1	NA	intron (NM_025626, intron 1 of 3)	intron (NM_025626, intron 1 of 3)	57194	NM_025626	66540	Mm.277864	NM_025626	ENSMUSG00000026655	Fam107b	3110001A13Rik|AA589595|AA959793|AI132312	family with sequence similarity 107, member B	protein-coding
mm_166127.1	chr4	154754915	154754916	+	1	NA	Intergenic	Intergenic	-87048	NM_028513	73353	Mm.30958	NM_028513	ENSMUSG00000051276	Actrt2	1700052K15Rik|Arp-T2|Arpm2	actin-related protein T2	protein-coding
mm_127479.1	chr15	101274122	101274131	+	1	NA	exon (NM_010444, exon 7 of 7)	exon (NM_010444, exon 7 of 7)	7280	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_49673.1	chr6	31532187	31532200	+	1	NA	intron (NM_013723, intron 1 of 7)	ORR1C2|LTR|ERVL-MaLR	31744	NM_013723	27205	Mm.89918	NM_013723	ENSMUSG00000025608	Podxl	AW121214|Ly102|PC|PCLP-1|Pclp1	podocalyxin-like	protein-coding
mm_100915.1	chr11	6274441	6274459	-	1	NA	exon (NM_134020, exon 2 of 5)	exon (NM_134020, exon 2 of 5)	387	NM_134020	103694	Mm.254495	NM_134020	ENSMUSG00000004394	Tmed4	1110014L17Rik|AI326346	transmembrane p24 trafficking protein 4	protein-coding
mm_14849.1	chr2	148397530	148397538	+	1	NA	TTS (NM_009219)	TTS (NM_009219)	2157	NM_009219	20608	Mm.35324	NM_009219	ENSMUSG00000037014	Sstr4	Smstr4|sst4	somatostatin receptor 4	protein-coding
mm_60847.1	chr7	45800685	45800728	+	1	NA	intron (NM_001005511, intron 14 of 15)	intron (NM_001005511, intron 14 of 15)	13610	NM_011181	19158	Mm.272130	NM_011181	ENSMUSG00000003269	Cyth2	ARNO|CLM2|Pscd2	cytohesin 2	protein-coding
mm_58424.1	chr7	3296785	3296804	+	1	NA	exon (NM_016969, exon 3 of 3)	exon (NM_016969, exon 3 of 3)	3766	NM_001093766	50918	Mm.29874	NM_016969	ENSMUSG00000068566	Myadm	D7Wsu62e	myeloid-associated differentiation marker	protein-coding
mm_153711.1	chr19	44398094	44398118	-	1	NA	exon (NM_009127, exon 6 of 6)	exon (NM_009127, exon 6 of 6)	9603	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_163757.1	chr13	119791112	119791128	-	1	NA	promoter-TSS (NM_028245)	promoter-TSS (NM_028245)	2	NM_001302550	72465	Mm.139115	NM_028245	ENSMUSG00000094870	Zfp131	2610109I01Rik|AW558871|Znf131	zinc finger protein 131	protein-coding
mm_123219.1	chr14	59441312	59441317	-	1	NA	promoter-TSS (NM_001320721)	promoter-TSS (NM_001320721)	333	NM_026908	69008	Mm.179091	NM_026908	ENSMUSG00000021981	Cab39l	1500031K13Rik|2810425O13Rik|4930520C08Rik|AA589432|MO2L	calcium binding protein 39-like	protein-coding
mm_133400.1	chr16	84834881	84834887	+	1	NA	promoter-TSS (NM_008065)	promoter-TSS (NM_008065)	114	NM_001302216	11957	Mm.353	NM_016755	ENSMUSG00000022890	Atp5j	CF6	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit F	protein-coding
mm_126225.1	chr15	78929645	78929686	+	1	NA	exon (NM_008495, exon 3 of 4)	exon (NM_008495, exon 3 of 4)	2940	NM_008495	16852	Mm.43831	NM_008495	ENSMUSG00000068220	Lgals1	AA410090|Gal-1|Galbp|L-14.5|L14|Lect14|galectin-1	lectin, galactose binding, soluble 1	protein-coding
mm_149426.1	chr19	11465438	11465442	+	1	NA	Intergenic	Intergenic	-3928	NM_001166376	73656	Mm.440719	NM_028595	ENSMUSG00000079419	Ms4a6c	2200009H22Rik|2210417N07Rik	membrane-spanning 4-domains, subfamily A, member 6C	protein-coding
mm_97226.1	chr11	75651200	75651210	+	1	NA	promoter-TSS (NM_001080774)	promoter-TSS (NM_001080774)	-304	NM_008659	17913	Mm.234502	NM_008659	ENSMUSG00000017774	Myo1c	C80397|MMIb|MYO1E|NMI|mm1beta|myr2	myosin IC	protein-coding
mm_20125.1	chr2	121271404	121271410	-	1	NA	promoter-TSS (NM_013735)	promoter-TSS (NM_013735)	0	NM_001290830	27223	Mm.215389	NM_013735	ENSMUSG00000043909	Trp53bp1	53BP1|Tp53bp1|m53BP1|p53BP1	transformation related protein 53 binding protein 1	protein-coding
mm_168675.1	chr11	94037658	94037680	-	1	NA	intron (NM_001199203, intron 3 of 29)	intron (NM_001199203, intron 3 of 29)	-6536	NM_001025430	70834	Mm.260737	NM_027569	ENSMUSG00000020859	Spag9	3110018C07Rik|4733401I23Rik|4831406C20Rik|AW552012|JLP|JSAP2|JSAP2a|Jip4|Mapk8ip4|syd1	sperm associated antigen 9	protein-coding
mm_125756.1	chr15	73761421	73761428	+	1	NA	Intergenic	Intergenic	13398	NM_008975	19245	Mm.390807	NM_008975	ENSMUSG00000059895	Ptp4a3	AV088979|Prl-3|pPtp4a3	protein tyrosine phosphatase 4a3	protein-coding
mm_76009.1	chr8	72723902	72723942	-	1	NA	intron (NM_001113248, intron 1 of 6)	CpG	652	NM_009188	20467	Mm.2137	NM_009188	ENSMUSG00000031622	Sin3b	2810430C10Rik	transcriptional regulator, SIN3B (yeast)	protein-coding
mm_158670.1	chrX	157595598	157595607	-	1	NA	intron (NM_172307, intron 1 of 10)	intron (NM_172307, intron 1 of 10)	3113	NM_172307	270669	Mm.37577	NM_172307	ENSMUSG00000046873	Mbtps2	9630032G22Rik|AI662535	membrane-bound transcription factor peptidase, site 2	protein-coding
mm_55307.1	chr6	54972429	54972466	-	1	NA	promoter-TSS (NM_001171007)	promoter-TSS (NM_001171007)	165	NM_172729	107607	Mm.28498	NM_172729	ENSMUSG00000038058	Nod1	C230079P11|Card4|F830007N14Rik|Nlrc1	nucleotide-binding oligomerization domain containing 1	protein-coding
mm_93614.1	chr10	117238666	117238676	-	1	NA	promoter-TSS (NM_029906)	promoter-TSS (NM_029906)	10	NM_029906	77397	Mm.118350	NM_029906	ENSMUSG00000020177	9530003J23Rik	Lyzf1	RIKEN cDNA 9530003J23 gene	protein-coding
mm_25987.1	chr3	133534417	133534426	+	1	NA	intron (NM_001040400, intron 1 of 10)	intron (NM_001040400, intron 1 of 10)	9969	NM_001346736	214133	Mm.347816	NM_145989	ENSMUSG00000040943	Tet2	Ayu17-449|E130014J05Rik|mKIAA1546	tet methylcytosine dioxygenase 2	protein-coding
mm_1139.1	chr1	60703976	60704014	+	1	NA	Intergenic	Intergenic	-42393	NM_007642	12487	Mm.255003	NM_007642	ENSMUSG00000026012	Cd28	-	CD28 antigen	protein-coding
mm_161359.1	chr14	56886856	56886856	+	1	NA	promoter-TSS (NM_029498)	promoter-TSS (NM_029498)	-939	NM_029498	76007	Mm.31417	NM_029498	ENSMUSG00000021945	Zmym2	5830413P05Rik|FIM|MYM|RAMP|SCLL|Zfp198|Znf198	zinc finger, MYM-type 2	protein-coding
mm_144288.1	chr18	12128820	12128828	+	1	NA	promoter-TSS (NM_024182)	promoter-TSS (NM_024182)	-26	NM_024182	66878	Mm.28551	NM_024182	ENSMUSG00000024404	Riok3	1200013N13Rik|D18Ertd331e|E130306C24Rik|Sudd	RIO kinase 3	protein-coding
mm_100854.1	chr11	5837746	5837758	-	1	NA	5' UTR (NM_017401, exon 1 of 11)	5' UTR (NM_017401, exon 1 of 11)	264	NM_017401	54125	Mm.260194	NM_017401	ENSMUSG00000020474	Polm	AI462166|B230309I03Rik|Tdt-N	polymerase (DNA directed), mu	protein-coding
mm_46904.1	chr5	114273773	114273786	-	1	NA	promoter-TSS (NM_148935)	promoter-TSS (NM_148935)	-18	NM_148935	116810	Mm.17709	NM_148935	ENSMUSG00000042002	Foxn4	-	forkhead box N4	protein-coding
mm_154844.1	chrX	20364673	20364683	+	1	NA	non-coding (NR_110966, exon 1 of 8)	non-coding (NR_110966, exon 1 of 8)	197	NR_110967	19889	Mm.288141	NM_133669	ENSMUSG00000060090	Rp2	AI662636|Rp2h	retinitis pigmentosa 2 homolog	protein-coding
mm_114724.1	chr13	83715276	83715302	+	1	NA	Intergenic	Intergenic	-12817	NR_015561	320203	Mm.245636	NM_177100	ENSMUSG00000050334	C130071C03Rik	2810449C10Rik	RIKEN cDNA C130071C03 gene	ncRNA
mm_143304.1	chr17	65986119	65986130	-	1	NA	exon (NM_001025572, exon 9 of 13)	exon (NM_001025572, exon 9 of 13)	-34937	NM_023053	65960	Mm.10153	NM_023053	ENSMUSG00000024098	Twsg1	1810013J15Rik|9030422N06Rik|AW552143|D17Ertd403e|Tsg|Twg	twisted gastrulation BMP signaling modulator 1	protein-coding
mm_27234.1	chr3	36468953	36468965	-	1	NA	intron (NM_009673, intron 2 of 12)	intron (NM_009673, intron 2 of 12)	6565	NR_105976	102466786		NR_105976	ENSMUSG00000098808	Mir7009	Gm27472|mmu-mir-7009	microRNA 7009	ncRNA
mm_39613.1	chr5	24256708	24256728	+	1	NA	promoter-TSS (NR_030454).4	promoter-TSS (NR_030454).4	-810	NR_030454	735274		NR_030454	ENSMUSG00000106252	Mir684-1	Mirn684-1	microRNA 684-1	ncRNA
mm_162696.1	chr10	20148889	20148901	+	1	NA	promoter-TSS (NM_008635)	promoter-TSS (NM_008635)	-25	NM_008635	17761	Mm.20928	NM_008635	ENSMUSG00000019996	Map7	E-MAP-115|MAP-7|Mtap7|R75000|mshi|mste|ste	microtubule-associated protein 7	protein-coding
mm_131594.1	chr16	18836574	18836583	+	1	NA	promoter-TSS (NM_001033164)	promoter-TSS (NM_001033164)	-2	NM_001033164	72307	Mm.36907	NM_001033164	ENSMUSG00000071632	2510002D24Rik	2410043I01Rik|AA163535|AA409624|DXMgi27	RIKEN cDNA 2510002D24 gene	protein-coding
mm_29426.1	chr3	109021809	109021815	-	1	NA	intron (NM_001163567, intron 1 of 10)	intron (NM_001163567, intron 1 of 10)	5795	NM_001163567	329739	Mm.69013	NM_001163567	ENSMUSG00000040339	Fam102b	1600010D10Rik|B430201A12Rik	family with sequence similarity 102, member B	protein-coding
mm_67561.1	chr7	81862511	81862521	-	1	NA	promoter-TSS (NM_001291282)	promoter-TSS (NM_001291282)	-171	NM_001291282	107769	Mm.221412	NM_145375	ENSMUSG00000038623	Tm6sf1	AI428514|BC023123|C630016D09Rik	transmembrane 6 superfamily member 1	protein-coding
mm_102293.1	chr11	55410208	55410212	-	1	NA	intron (NM_001290817, intron 1 of 9)	MER113|DNA|hAT-Charlie	9870	NM_009242	20692	Mm.291442	NM_009242	ENSMUSG00000018593	Sparc	BM-40|ON	secreted acidic cysteine rich glycoprotein	protein-coding
mm_20921.1	chr2	150837389	150837437	-	1	NA	exon (NM_024465, exon 10 of 13)	exon (NM_024465, exon 10 of 13)	50617	NM_153781	110078	Mm.222584	NM_153781	ENSMUSG00000033059	Pygb	-	brain glycogen phosphorylase	protein-coding
mm_113686.1	chr13	42866383	42866410	+	1	NA	5' UTR (NM_001302636, exon 1 of 13)	5' UTR (NM_001302636, exon 1 of 13)	149	NM_001302636	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding
mm_135155.1	chr16	35858062	35858073	-	1	NA	exon (NM_001039530, exon 6 of 17)	exon (NM_001039530, exon 6 of 17)	13315	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_135379.1	chr16	44139260	44139283	-	1	NA	promoter-TSS (NM_007508)	promoter-TSS (NM_007508)	-252	NM_007508	11964	Mm.217787	NM_007508	ENSMUSG00000052459	Atp6v1a	AI647066|Atp6a1|Atp6a2|Atp6v1a1|VA68|VPP2	ATPase, H+ transporting, lysosomal V1 subunit A	protein-coding
mm_143434.1	chr17	70851711	70851738	-	1	NA	promoter-TSS (NM_001164075)	promoter-TSS (NM_001164075)	10	NM_001164075	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_2588.1	chr1	118683463	118683473	+	1	NA	3' UTR (NM_023755, exon 15 of 15)	3' UTR (NM_023755, exon 15 of 15)	55523	NM_023755	81879	Mm.24621	NM_023755	ENSMUSG00000026380	Tfcp2l1	1810030F05Rik|4932442M07Rik|AA575098|Cp2l1|Crtr-1|D930018N21Rik|LBP-9|Tcfcp2l1	transcription factor CP2-like 1	protein-coding
mm_134112.1	chr16	9995807	9995818	-	1	NA	Intergenic	Intergenic	-3279	NM_008170	14811	Mm.2953	NM_008170	ENSMUSG00000059003	Grin2a	GluN2A|NMDAR2A|NR2A	glutamate receptor, ionotropic, NMDA2A (epsilon 1)	protein-coding
mm_166123.1	chr4	152224343	152224383	+	1	NA	intron (NM_001146057, intron 4 of 8)	intron (NM_001146057, intron 4 of 8)	24519	NM_001146058	70025	Mm.296191	NM_133348	ENSMUSG00000028937	Acot7	2410041A17Rik|Ach1|Act|Bach|CTE-IIa|Cte-II|Lach1	acyl-CoA thioesterase 7	protein-coding
mm_75529.1	chr8	57314621	57314623	-	1	NA	intron (NR_110474, intron 2 of 4)	intron (NR_110474, intron 2 of 4)	6237	NR_110474	102636514		NR_110474	ENSMUSG00000100510	Uph	-	upperhand	ncRNA
mm_26600.1	chr3	152120311	152120320	+	1	NA	intron (NM_016867, intron 3 of 5)	B4A|SINE|B4	45585	NM_016867	54120	Mm.97	NM_016867	ENSMUSG00000039131	Gipc2	2200002N01Rik|AU021850|Semcap2	GIPC PDZ domain containing family, member 2	protein-coding
mm_166407.1	chr5	136581699	136581703	-	1	NA	Intergenic	Intergenic	-14211	NM_001291238	13047	Mm.320317	NM_009986	ENSMUSG00000029705	Cux1	CDP|Cutl1|Cux|Cux-1	cut-like homeobox 1	protein-coding
mm_79044.1	chr9	46225491	46225517	+	1	NA	Intergenic	Intergenic	-3126	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2|apo-AI|apoA-I	apolipoprotein A-I	protein-coding
mm_65073.1	chr7	19037213	19037221	-	1	NA	intron (NM_026605, intron 8 of 26)	MLT1K|LTR|ERVL-MaLR	12840	NM_026605	68188	Mm.130902	NM_026605	ENSMUSG00000023118	Sympk	1500016F02Rik|4632415H16Rik|AA125406|AI449890|SPK|SYM	symplekin	protein-coding
mm_13966.1	chr2	121424583	121424593	+	1	NA	exon (NM_007952, exon 3 of 13)	exon (NM_007952, exon 3 of 13)	10686	NM_007952	14827	Mm.263177	NM_007952	ENSMUSG00000027248	Pdia3	58kDa|ERp57|ERp60|ERp61|Erp|Grp58|PDI|PDI-Q2|PI-PLC|PLC[a]|Plca	protein disulfide isomerase associated 3	protein-coding
mm_113933.1	chr13	49623530	49623534	+	1	NA	3' UTR (NM_008760, exon 7 of 7)	3' UTR (NM_008760, exon 7 of 7)	15461	NM_008760	18295	Mm.4258	NM_008760	ENSMUSG00000021390	Ogn	3110079A16Rik|OG|OIF|SLRR3A|mimecan|mimican	osteoglycin	protein-coding
mm_167818.1	chr9	124282915	124282930	+	1	NA	Intergenic	RMER10A|LTR|ERVL	29772	NM_001243118	630836	Mm.458553	NM_001243117	ENSMUSG00000074829	2010315B03Rik	BC029716	RIKEN cDNA 2010315B03 gene	protein-coding
mm_146864.1	chr18	24603447	24603459	-	1	NA	promoter-TSS (NM_021448)	promoter-TSS (NM_021448)	364	NM_139143	106957	Mm.21688	NM_139143	ENSMUSG00000024270	Slc39a6	Ermelin	solute carrier family 39 (metal ion transporter), member 6	protein-coding
mm_6626.1	chr1	78174735	78174740	-	1	NA	intron (NM_001159520, intron 4 of 8)	intron (NM_001159520, intron 4 of 8)	22399	NM_008781	18505	Mm.1371	NM_008781	ENSMUSG00000004872	Pax3	Pax-3|Sp|Splchl2|splotch	paired box 3	protein-coding
mm_84662.1	chr9	71896048	71896102	-	1	NA	promoter-TSS (NM_001253864)	promoter-TSS (NM_001253864)	21	NM_001253864	21406	Mm.171615	NM_011544	ENSMUSG00000032228	Tcf12	A130037E08Rik|ALF1|HEB|HEBAlt|HTF-4|HTF4|ME1|REB|bHLHb20	transcription factor 12	protein-coding
mm_135273.1	chr16	38406811	38406830	-	1	NA	intron (NM_134102, intron 7 of 10)	intron (NM_134102, intron 7 of 10)	26325	NM_134102	85031	Mm.279805	NM_134102	ENSMUSG00000002847	Pla1a	AA986889|Ps-pla1|Pspla1	phospholipase A1 member A	protein-coding
mm_57565.1	chr6	127125826	127125842	-	1	NA	3' UTR (NM_009829, exon 5 of 5)	3' UTR (NM_009829, exon 5 of 5)	-16282	NM_177003	319801	Mm.101836	NM_177003	ENSMUSG00000038028	Tigar	9630033F20Rik|AA793651|AI595337|C79710|C85509	Trp53 induced glycolysis repulatory phosphatase	protein-coding
mm_118147.1	chr13	105054850	105054864	-	1	NA	promoter-TSS (NM_029879)	promoter-TSS (NM_029879)	73	NM_029879	52882	Mm.100348	NM_029879	ENSMUSG00000021719	Rgs7bp	A930030I01Rik|AI842293|D13Bwg1146e|R7bp	regulator of G-protein signalling 7 binding protein	protein-coding
mm_135841.1	chr16	58524240	58524249	-	1	NA	promoter-TSS (NM_018784)	promoter-TSS (NM_018784)	-932	NM_018784	54613	Mm.212742	NM_018784	ENSMUSG00000022747	St3gal6	1700023B24Rik|AI930218|AW552396|Siat10|St3galVI	ST3 beta-galactoside alpha-2,3-sialyltransferase 6	protein-coding
mm_41675.1	chr5	99682431	99682452	+	1	NA	intron (NR_030692, intron 1 of 3)	intron (NR_030692, intron 1 of 3)	46619	NR_030692	319818	Mm.295233	NR_030692	ENSMUSG00000089809	A930011G23Rik	-	RIKEN cDNA A930011G23 gene	ncRNA
mm_60848.1	chr7	45813989	45814000	+	1	NA	intron (NM_011181, intron 1 of 11)	CpG	322	NM_011181	19158	Mm.272130	NM_011181	ENSMUSG00000003269	Cyth2	ARNO|CLM2|Pscd2	cytohesin 2	protein-coding
mm_151780.1	chr19	5364894	5364918	-	1	NA	non-coding (NR_104482, exon 2 of 2)	non-coding (NR_104482, exon 2 of 2)	1457	NM_001038231	23825	Mm.358649	NM_011793	ENSMUSG00000024844	Banf1	Baf|Bcrp1|L2bp1/Baf	barrier to autointegration factor 1	protein-coding
mm_77936.1	chr9	7355305	7355314	+	1	NA	intron (NM_001320077, intron 8 of 10)	intron (NM_001320077, intron 8 of 10)	7935	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_55820.1	chr6	83054332	83054342	-	1	NA	promoter-TSS (NR_125891)	promoter-TSS (NR_125891)	-184	NR_125891	11993	Mm.386752	NM_007517	ENSMUSG00000068328	Aup1	AA589454	ancient ubiquitous protein 1	protein-coding
mm_94183.1	chr10	128923949	128923957	-	1	NA	promoter-TSS (NM_015740)	promoter-TSS (NM_015740)	-429	NM_015740	14533	Mm.30118	NM_015740	ENSMUSG00000090247	Bloc1s1	AI839753|BLOS1|Gcn5l1	biogenesis of lysosomal organelles complex-1, subunit 1	protein-coding
mm_381.1	chr1	34022791	34022803	+	1	NA	intron (NM_133833, intron 1 of 92)	PB1D10|SINE|Alu	10972	NM_134448	13518	Mm.336625	NM_010081	ENSMUSG00000026131	Dst	2310001O04Rik|A830042E19Rik|AW554249|BP230|BPAG1-n|Bpag|Bpag1|Macf2|ah|athetoid|dt|mKIAA0728|nmf203|nmf339	dystonin	protein-coding
mm_130272.1	chr15	96698797	96698808	-	1	NA	5' UTR (NM_175121, exon 2 of 16)	5' UTR (NM_175121, exon 2 of 16)	896	NM_175121	67760	Mm.46754	NM_175121	ENSMUSG00000022462	Slc38a2	5033402L14Rik|AI316867|ATA2|SAT2|mKIAA1382	solute carrier family 38, member 2	protein-coding
mm_99463.1	chr11	102435316	102435329	+	1	NA	exon (NM_008175, exon 10 of 13)	exon (NM_008175, exon 10 of 13)	5000	NM_008175	14824	Mm.1568	NM_008175	ENSMUSG00000034708	Grn	Pgrn|epithelin	granulin	protein-coding
mm_10609.1	chr2	19007842	19007850	+	1	NA	Intergenic	Lx7|LINE|L1	9527	NR_024323	74629	Mm.117687	NR_024323	ENSMUSG00000026736	4930426L09Rik	-	RIKEN cDNA 4930426L09 gene	ncRNA
mm_129293.1	chr15	77245517	77245562	-	1	NA	intron (NM_053104, intron 1 of 13)	intron (NM_053104, intron 1 of 13)	61514	NM_001110827	93686	Mm.202774	NM_053104	ENSMUSG00000033565	Rbfox2	Fbm2|Fxh|Hrnbp2|Rbm9	RNA binding protein, fox-1 homolog (C. elegans) 2	protein-coding
mm_66762.1	chr7	46728747	46728765	-	1	NA	3' UTR (NM_011316, exon 4 of 4)	3' UTR (NM_011316, exon 4 of 4)	3847	NM_011316	20211	Mm.3489	NM_011316	ENSMUSG00000040017	Saa4	Saa-4|Saa-5	serum amyloid A 4	protein-coding
mm_113446.1	chr13	35662134	35662138	+	1	NA	intron (NM_009881, intron 1 of 9)	U1|snRNA|snRNA	2274	NM_009881	12593	Mm.29002	NM_009881	ENSMUSG00000059288	Cdyl	AI325931	chromodomain protein, Y chromosome-like	protein-coding
mm_54854.1	chr6	42593277	42593293	-	1	NA	exon (NM_203396, exon 2 of 7)	exon (NM_203396, exon 2 of 7)	4087	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_61271.1	chr7	66324528	66324531	+	1	NA	intron (NM_146191, intron 6 of 33)	intron (NM_146191, intron 6 of 33)	57195	NR_106024	102465640		NR_106024	ENSMUSG00000098353	Mir7057	Gm27550|mmu-mir-7057	microRNA 7057	ncRNA
mm_127876.1	chr15	8465309	8465321	-	1	NA	Intergenic	Intergenic	-20852	NM_201232	71175	Mm.240329	NM_027707	ENSMUSG00000022141	Nipbl	Idn3	Nipped-B homolog (Drosophila)	protein-coding
mm_138611.1	chr17	35799715	35799721	+	1	NA	Intergenic	Intergenic	-21995	NM_133662	15937	Mm.25613	NM_133662	ENSMUSG00000003541	Ier3	AI663993|IEX-1|cI-3|gly96	immediate early response 3	protein-coding
mm_165683.1	chr3	90694172	90694211	-	1	NA	intron (NM_009114, intron 2 of 2)	intron (NM_009114, intron 2 of 2)	1530	NM_001281852	20202	Mm.2128	NM_009114	ENSMUSG00000056071	S100a9	60B8Ag|AW546964|BEE22|Cagb|GAGB|L1Ag|MRP14|p14	S100 calcium binding protein A9 (calgranulin B)	protein-coding
mm_69679.1	chr7	139985875	139985885	-	1	NA	TTS (NR_106029)	TTS (NR_106029)	994	NR_106029	102465643		NR_106029	ENSMUSG00000099092	Mir7062	Gm27339|mmu-mir-7062	microRNA 7062	ncRNA
mm_154541.1	chrM	14288	14300	-	1	NA	NA	Intergenic	NA	NA								
mm_171661.1	chr4	44123325	44123342	+	1	NA	non-coding (NR_040414, exon 1 of 1)	non-coding (NR_040414, exon 1 of 1)	1440	NR_040414	623796	Mm.490409	NR_040414	ENSMUSG00000084274	Gm12504	OTTMUSG00000007209	prothymosin alpha pseudogene	pseudo
mm_92911.1	chr10	83624924	83624927	-	1	NA	intron (NM_145220, intron 4 of 20)	intron (NM_145220, intron 4 of 20)	23739	NM_145220	216190	Mm.282985	NM_145220	ENSMUSG00000020263	Appl2	Dip3b	adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 2	protein-coding
mm_37073.1	chr4	116163702	116163722	-	1	NA	exon (NM_133681, exon 6 of 8)	exon (NM_133681, exon 6 of 8)	3886	NM_133681	66805	Mm.45994	NM_133681	ENSMUSG00000028699	Tspan1	9030418M05Rik	tetraspanin 1	protein-coding
mm_2821.1	chr1	131097943	131097966	+	1	NA	promoter-TSS (NM_008551)	promoter-TSS (NM_008551)	-111	NM_008551	17164	Mm.221235	NM_008551	ENSMUSG00000016528	Mapkapk2	AA960234|MAPKAP-K2|MK-2|MK2|Rps6kc1	MAP kinase-activated protein kinase 2	protein-coding
mm_126424.1	chr15	80572495	80572499	+	1	NA	promoter-TSS (NM_001289442)	promoter-TSS (NM_001289442)	-100	NM_001289442	17444	Mm.12947	NM_010815	ENSMUSG00000042351	Grap2	GRAP-2|GRB2L|GRBLG|GRID|Gads|GrbX|Grf40|GrpL|Mona|P38	GRB2-related adaptor protein 2	protein-coding
mm_131388.1	chr16	14209584	14209619	+	1	NA	exon (NM_013607, exon 28 of 42)	exon (NM_013607, exon 28 of 42)	46326	NM_001114085	67203	Mm.24105	NM_023317	ENSMUSG00000022678	Nde1	2810027M15Rik|AU042936|AW822251|Nude|mNudE	nudE neurodevelopment protein 1	protein-coding
mm_952.1	chr1	57732963	57732980	+	1	NA	Intergenic	(TTGTG)n|Simple_repeat|Simple_repeat	-41890	NM_144882	67198	Mm.159989	NM_144882	ENSMUSG00000038305	Spats2l	2810022L02Rik|A230104H11Rik|AA987173|AI480531|AI842453|AW413586	spermatogenesis associated, serine-rich 2-like	protein-coding
mm_41686.1	chr5	100518359	100518369	+	1	NA	promoter-TSS (NM_012001)	promoter-TSS (NM_012001)	55	NM_012001	26891	Mm.957	NM_012001	ENSMUSG00000035297	Cops4	AW208976|D5Ertd774e	COP9 signalosome subunit 4	protein-coding
mm_159070.1	chr2	25236821	25236821	-	1	NA	promoter-TSS (NM_001033410)	promoter-TSS (NM_001033410)	-34	NM_001033410	329360	Mm.244652	NM_001033410	ENSMUSG00000089953	Rnf224	Gm757	ring finger protein 224	protein-coding
mm_35288.1	chr4	21767145	21767164	-	1	NA	promoter-TSS (NM_029840)	promoter-TSS (NM_029840)	57	NM_029840	77032	Mm.87238	NM_029840	ENSMUSG00000028251	Tstd3	2610029I01Rik	thiosulfate sulfurtransferase (rhodanese)-like domain containing 3	protein-coding
mm_4726.1	chr1	181285796	181285828	+	1	NA	Intergenic	Intergenic	-66816	NM_028408	72978	Mm.338083	NM_028408	ENSMUSG00000026514	Cnih3	2900075G08Rik|CNIH-3	cornichon family AMPA receptor auxiliary protein 3	protein-coding
mm_114938.1	chr13	96388306	96388338	+	1	NA	promoter-TSS (NM_026173)	promoter-TSS (NM_026173)	28	NM_026173	67463	Mm.86472	NM_026173	ENSMUSG00000021671	Poc5	1200014M14Rik|AV144706	POC5 centriolar protein	protein-coding
mm_147777.1	chr18	61536523	61536558	-	1	NA	promoter-TSS (NM_177828)	promoter-TSS (NM_177828)	-4	NM_177828	328967	Mm.488098	NM_177828	ENSMUSG00000045094	Arhgef37	4933429F08Rik	Rho guanine nucleotide exchange factor (GEF) 37	protein-coding
mm_136235.1	chr16	90726801	90726805	-	1	NA	intron (NM_025642, intron 1 of 4)	intron (NM_025642, intron 1 of 4)	568	NM_025642	66578	Mm.180363	NM_025642	ENSMUSG00000022978	Mis18a	2610039C10Rik|2810018N07Rik	MIS18 kinetochore protein A	protein-coding
mm_27517.1	chr3	57234621	57234623	-	1	NA	Intergenic	Intergenic	67297	NM_008536	17112	Mm.856	NM_008536	ENSMUSG00000027800	Tm4sf1	L6|M3s1	transmembrane 4 superfamily member 1	protein-coding
mm_74007.1	chr8	121116164	121116177	+	1	NA	promoter-TSS (NM_013519)	promoter-TSS (NM_013519)	-1	NM_013519	14234	Mm.14092	NM_013519	ENSMUSG00000046714	Foxc2	Fkh14|Hfhbf3|MFH-1|Mfh1	forkhead box C2	protein-coding
mm_27329.1	chr3	50369677	50369689	-	1	NA	3' UTR (NM_011990, exon 12 of 12)	3' UTR (NM_011990, exon 12 of 12)	73930	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_70519.1	chr8	12949417	12949428	+	1	NA	promoter-TSS (NM_001159485)	promoter-TSS (NM_001159485)	4	NM_001159485	17207	Mm.334413	NM_178076	ENSMUSG00000031442	Mcf2l	C130040G20Rik|Dbs|Ost|mKIAA0362	mcf.2 transforming sequence-like	protein-coding
mm_103942.1	chr11	83850533	83850547	-	1	NA	promoter-TSS (NM_001291268)	promoter-TSS (NM_001291268)	-329	NM_001291268	21410	Mm.7226	NM_009330	ENSMUSG00000020679	Hnf1b	HNF-1-beta|HNF-1B|HNF-1Beta|Hnf1beta|LFB3|Tcf-2|Tcf2|vHNF1	HNF1 homeobox B	protein-coding
mm_69780.1	chr7	141063046	141063046	-	1	NA	intron (NM_177897, intron 1 of 19)	intron (NM_177897, intron 1 of 19)	1772	NM_177897	330671	Mm.133741	NM_177897	ENSMUSG00000055629	B4galnt4	BC038881|Gm1095|beta4GalNAcT4	beta-1,4-N-acetyl-galactosaminyl transferase 4	protein-coding
mm_114237.1	chr13	56609609	56609628	+	1	NA	promoter-TSS (NM_009369)	promoter-TSS (NM_009369)	15	NM_009369	21810	Mm.14455	NM_009369	ENSMUSG00000035493	Tgfbi	68kDa|AI181842|AI747162|Beta-ig|big-h3	transforming growth factor, beta induced	protein-coding
mm_148397.1	chr19	3768113	3768207	+	1	NA	5' UTR (NM_001167886, exon 2 of 11)	5' UTR (NM_001167886, exon 2 of 11)	739	NM_001167885	225888	Mm.278578	NM_144871	ENSMUSG00000045098	Kmt5b	AA117471|C630029K18Rik|Suv4-20h1|Suv420h1	lysine methyltransferase 5B	protein-coding
mm_33121.1	chr4	124791423	124791452	+	1	NA	intron (NR_126474, intron 16 of 24)	intron (NR_126474, intron 16 of 24)	-11112	NM_008636	17764	Mm.272397	NM_008636	ENSMUSG00000028890	Mtf1	MTF-1|Thyls	metal response element binding transcription factor 1	protein-coding
mm_112175.1	chr12	113421423	113421441	-	1	NA	Intergenic	Intergenic	-68133	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_14501.1	chr2	132094719	132094744	+	1	NA	intron (NM_018824, intron 2 of 15)	intron (NM_018824, intron 2 of 15)	50377	NM_018824	54338	Mm.103581	NM_018824	ENSMUSG00000027340	Slc23a2	AI844736|NBTL1|SVCT2|Slc23a1|YSPL2|YSPL3|mKIAA0238	solute carrier family 23 (nucleobase transporters), member 2	protein-coding
mm_80178.1	chr9	72275020	72275026	+	1	NA	5' UTR (NM_146224, exon 1 of 22)	5' UTR (NM_146224, exon 1 of 22)	135	NM_001311105	235469	Mm.242791	NM_146224	ENSMUSG00000038535	Zfp280d	A930005F02Rik|BC027163|Suhw4|ZNF634|Znf280d	zinc finger protein 280D	protein-coding
mm_56419.1	chr6	97252748	97252765	-	1	NA	promoter-TSS (NM_001081157)	promoter-TSS (NM_001081157)	24	NM_001081157	320502	Mm.68163	NM_001081157	ENSMUSG00000044086	Lmod3	5430424A14Rik	leiomodin 3 (fetal)	protein-coding
mm_63872.1	chr7	135952731	135952737	+	1	NA	Intergenic	Intergenic	-236355	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_44241.1	chr5	5314594	5314603	-	1	NA	intron (NM_011074, intron 2 of 14)	intron (NM_011074, intron 2 of 14)	-48530	NM_001310448	18647	Mm.389061	NM_011074	ENSMUSG00000028926	Cdk14	Pftk1|mKIAA0834	cyclin-dependent kinase 14	protein-coding
mm_100541.1	chr11	120673019	120673066	+	1	NA	promoter-TSS (NM_026877)	promoter-TSS (NM_026877)	69	NM_026877	68938	Mm.294020	NM_026877	ENSMUSG00000025142	Aspscr1	1190006K01Rik|ASPC|ASPCR1|ASPL|ASPS|RCC17|TUG	alveolar soft part sarcoma chromosome region, candidate 1 (human)	protein-coding
mm_34520.1	chr4	148951128	148951140	+	1	NA	intron (NM_001159344, intron 20 of 20)	AmnSINE1|SINE|Deu	146742	NM_027195	69743	Mm.233879	NM_027195	ENSMUSG00000028977	Casz1	2410019P08Rik|AV096627|BC040081|Cst|D4Ertd432e	castor zinc finger 1	protein-coding
mm_46660.1	chr5	108675595	108675626	-	1	NA	promoter-TSS (NM_001310692)	promoter-TSS (NM_001310692)	-245	NM_174870	231583	Mm.440571	NM_174870	ENSMUSG00000046959	Slc26a1	Sat1	solute carrier family 26 (sulfate transporter), member 1	protein-coding
mm_119034.1	chr14	30549164	30549188	+	1	NA	promoter-TSS (NM_009388)	promoter-TSS (NM_009388)	45	NM_009388	21881	Mm.290692	NM_009388	ENSMUSG00000021957	Tkt	p68	transketolase	protein-coding
mm_62735.1	chr7	110955962	110955975	+	1	NA	intron (NM_194464, intron 1 of 20)	intron (NM_194464, intron 1 of 20)	-9781	NM_010826	17540	Mm.250023	NM_010826	ENSMUSG00000005611	Mrvi1	BB115629|Irag|Ris1	MRV integration site 1	protein-coding
mm_56448.1	chr6	97578094	97578125	-	1	NA	intron (NM_145148, intron 1 of 23)	intron (NM_145148, intron 1 of 23)	39548	NM_145148	232288	Mm.27789	NM_145148	ENSMUSG00000030064	Frmd4b	6030440G05Rik|C87375|GOBLIN|GRSP1|R74720	FERM domain containing 4B	protein-coding
mm_135440.1	chr16	45408933	45408950	-	1	NA	5' UTR (NM_010818, exon 1 of 6)	5' UTR (NM_010818, exon 1 of 6)	112	NM_010818	17470	Mm.245851	NM_010818	ENSMUSG00000022661	Cd200	Mox2|OX2	CD200 antigen	protein-coding
mm_37696.1	chr4	129268771	129268828	-	1	NA	Intergenic	Intergenic	-7395	NM_001285867	97130	Mm.331907	NM_001033189	ENSMUSG00000050390	C77080	Kiaa1522|mKIAA1522	expressed sequence C77080	protein-coding
mm_45196.1	chr5	52369201	52369219	-	1	NA	3' UTR (NM_011435, exon 2 of 2)	3' UTR (NM_011435, exon 2 of 2)	5406	NM_011435	20657	Mm.2407	NM_011435	ENSMUSG00000072941	Sod3	AI314465|EC-SOD	superoxide dismutase 3, extracellular	protein-coding
mm_167229.1	chr8	13192355	13192359	-	1	NA	intron (NM_025768, intron 2 of 7)	intron (NM_025768, intron 2 of 7)	-3259	NR_035494	100316713		NR_035494	ENSMUSG00000088054	Mir1968	mir-1968|mmu-mir-1968	microRNA 1968	ncRNA
mm_17619.1	chr2	30967847	30967856	-	1	NA	promoter-TSS (NM_144884)	promoter-TSS (NM_144884)	67	NM_144884	30931	Mm.154994	NM_144884	ENSMUSG00000026849	Tor1a	DQ2|Dyt1|torsinA	torsin family 1, member A (torsin A)	protein-coding
mm_92189.1	chr10	68102085	68102098	-	1	NA	exon (NM_023598, exon 9 of 10)	exon (NM_023598, exon 9 of 10)	122493	NM_001081346	170799	Mm.209844	NM_133244	ENSMUSG00000037846	Rtkn2	B130039D23Rik|Mbf|Plekhk1	rhotekin 2	protein-coding
mm_109155.1	chr12	108178852	108178860	+	1	NA	promoter-TSS (NM_009832)	promoter-TSS (NM_009832)	428	NM_028262	52690	Mm.159185	NM_028262	ENSMUSG00000056770	Setd3	2610102I01Rik|2610305M23Rik|6030490B17Rik|D12Ertd771e	SET domain containing 3	protein-coding
mm_135980.1	chr16	75053724	75053727	-	1	NA	Intergenic	Lx5|LINE|L1	532336	NM_001252513	320355	Mm.99517	NM_177142	ENSMUSG00000032948	Lipi	D930038D03Rik|lpd1	lipase, member I	protein-coding
mm_18561.1	chr2	65238626	65238643	-	1	NA	promoter-TSS (NM_177025)	promoter-TSS (NM_177025)	-8	NM_027225	319876	Mm.34159	NM_027225	ENSMUSG00000034903	Cobll1	1810047P18Rik|Coblr1|D430044D16Rik	Cobl-like 1	protein-coding
mm_107820.1	chr12	67651374	67651376	+	1	NA	Intergenic	RMER19A|LTR|ERVK	-428826	NM_207010	320772	Mm.227680	NM_207010	ENSMUSG00000034912	Mdga2	6720489L24Rik|9330209L04Rik|Adp|Mamdc1	MAM domain containing glycosylphosphatidylinositol anchor 2	protein-coding
mm_35797.1	chr4	46538390	46538408	-	1	NA	3' UTR (NM_001164804, exon 12 of 12)	3' UTR (NM_001164804, exon 12 of 12)	-2258	NM_029077	74735	Mm.240252	NM_029077	ENSMUSG00000039853	Trim14	5830400N10Rik|pub	tripartite motif-containing 14	protein-coding
mm_44285.1	chr5	8353482	8353487	-	1	NA	intron (NM_001310440, intron 2 of 30)	(A)n|Simple_repeat|Simple_repeat	14676	NM_001007221	11496	Mm.275895	NM_001007220	ENSMUSG00000040537	Adam22	2900022I03Rik|AI854032|MDC2	a disintegrin and metallopeptidase domain 22	protein-coding
mm_13573.1	chr2	112305749	112305754	+	1	NA	intron (NM_133648, intron 1 of 24)	B1F2|SINE|Alu	21063	NM_133648	107723	Mm.491155	NM_133648	ENSMUSG00000027130	Slc12a6	9530023I19Rik|KCC3|gaxp	solute carrier family 12, member 6	protein-coding
mm_4746.1	chr1	182125392	182125395	+	1	NA	intron (NM_012058, intron 1 of 2)	intron (NM_012058, intron 1 of 2)	656	NM_012058	27058	Mm.273196	NM_012058	ENSMUSG00000026511	Srp9	9kDa	signal recognition particle 9	protein-coding
mm_139589.1	chr17	57223935	57223940	+	1	NA	exon (NM_009778, exon 11 of 41)	exon (NM_009778, exon 11 of 41)	4199	NM_009778	12266	Mm.19131	NM_009778	ENSMUSG00000024164	C3	AI255234|ASP|HSE-MSF|Plp	complement component 3	protein-coding
mm_151008.1	chr19	46689903	46689943	+	1	NA	promoter-TSS (NM_025563)	promoter-TSS (NM_025563)	17	NM_025563	66439	Mm.87163	NM_025563	ENSMUSG00000062376	Borcs7	2010012O05Rik|4930569L17Rik|AI413851|AI467257	BLOC-1 related complex subunit 7	protein-coding
mm_91752.1	chr10	50520946	50520959	-	1	NA	Intergenic	RMER17A|LTR|ERVK	-71717	NM_198007	77987	Mm.222497	NM_198007	ENSMUSG00000038774	Ascc3	ASC1p200|B630009I04Rik|BC023451|D430001L07Rik|D630041L21|Helic1|RNAH	activating signal cointegrator 1 complex subunit 3	protein-coding
mm_14083.1	chr2	125068119	125068133	+	1	NA	promoter-TSS (NM_175034)	promoter-TSS (NM_175034)	-1	NM_175034	317750	Mm.330538	NM_175034	ENSMUSG00000035183	Slc24a5	F630045L20Rik|JSX|NCKX5|NCX5|Oca6	solute carrier family 24, member 5	protein-coding
mm_96651.1	chr11	69368290	69368300	+	1	NA	intron (NM_146019, intron 1 of 39)	intron (NM_146019, intron 1 of 39)	1131	NM_146019	216848	Mm.178246	NM_146019	ENSMUSG00000018474	Chd3	2600010P09Rik|AF020312|Chd7|Prp7|Prp9-1	chromodomain helicase DNA binding protein 3	protein-coding
mm_89461.1	chr10	93309711	93309724	+	1	NA	intron (NM_013508, intron 1 of 4)	intron (NM_013508, intron 1 of 4)	1442	NM_001322268	13713	Mm.4454	NM_013508	ENSMUSG00000008398	Elk3	D430049E23Rik|Erp|Etrp|Net|Sap-2	ELK3, member of ETS oncogene family	protein-coding
mm_37044.1	chr4	115781116	115781121	-	1	NA	promoter-TSS (NM_029196)	promoter-TSS (NM_029196)	-84	NM_029196	75173	Mm.331798	NM_029196	ENSMUSG00000044556	Tex38	4930544O15Rik|Theg4	testis expressed 38	protein-coding
mm_131942.1	chr16	24012745	24012750	+	1	NA	Intergenic	Intergenic	-24135	NM_009744	12053	Mm.347398	NM_009744	ENSMUSG00000022508	Bcl6	Bcl5	B cell leukemia/lymphoma 6	protein-coding
mm_144335.1	chr18	14331856	14331867	+	1	NA	Intergenic	Intergenic	99555	NR_045373	74529	Mm.400519	NR_045373		8430422H06Rik	-	RIKEN cDNA 8430422H06 gene	ncRNA
mm_119263.1	chr14	34017057	34017067	+	1	NA	Intergenic	Intergenic	-24016	NM_001034880	432838	Mm.318383	NM_001034880	ENSMUSG00000072624	Gm5460	EG432838	predicted gene 5460	protein-coding
mm_5185.1	chr1	13096061	13096082	-	1	NA	Intergenic	Intergenic	31092	NM_001081209	383491	Mm.309380	NM_001081209	ENSMUSG00000042414	Prdm14	-	PR domain containing 14	protein-coding
mm_106875.1	chr12	8010756	8010773	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	33087	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_149478.1	chr19	11750254	11750263	+	1	NA	exon (NM_008118, exon 4 of 9)	exon (NM_008118, exon 4 of 9)	2699	NM_008118	14603	Mm.456	NM_008118	ENSMUSG00000024682	Gif	AV073125	gastric intrinsic factor	protein-coding
mm_83231.1	chr9	42398648	42398656	-	1	NA	intron (NM_009347, intron 1 of 23)	intron (NM_009347, intron 1 of 23)	1277	NM_009347	21683	Mm.42209	NM_009347	ENSMUSG00000037705	Tecta	Tctna	tectorin alpha	protein-coding
mm_129093.1	chr15	75928647	75928688	-	1	NA	intron (NM_031201, intron 2 of 10)	intron (NM_031201, intron 2 of 10)	1063	NM_031201	22122	Mm.22596	NM_031201	ENSMUSG00000022570	Tsta3	AI256181|FX|Tstap35b	tissue specific transplantation antigen P35B	protein-coding
mm_45290.1	chr5	65019144	65019150	-	1	NA	intron (NM_026667, intron 7 of 13)	intron (NM_026667, intron 7 of 13)	48829	NR_030577	100124451		NR_030577	ENSMUSG00000077042	Mir574	Mirn574|mir-574|mmu-mir-574	microRNA 574	ncRNA
mm_76955.1	chr8	106011423	106011470	-	1	NA	promoter-TSS (NM_025518)	promoter-TSS (NM_025518)	-32	NM_025518	66369	Mm.287500	NM_025518	ENSMUSG00000031901	Dus2	2310016K04Rik|Dus2l	dihydrouridine synthase 2	protein-coding
mm_94599.1	chr11	11829398	11829410	+	1	NA	intron (NM_001190448, intron 9 of 14)	MLTR14|LTR|ERV1	-20442	NM_001163360	60530	Mm.236114	NM_021891	ENSMUSG00000035455	Fignl1	-	fidgetin-like 1	protein-coding
mm_152013.1	chr19	5989167	5989185	-	1	NA	3' UTR (NM_007600, exon 22 of 22)	3' UTR (NM_007600, exon 22 of 22)	-3033	NM_198650	381203	Mm.329638	NM_198650	ENSMUSG00000037451	Slc22a20	Gm963|OAT1-L|mOAT6	solute carrier family 22 (organic anion transporter), member 20	protein-coding
mm_135177.1	chr16	35939083	35939109	-	1	NA	promoter-TSS (NM_001013371)	promoter-TSS (NM_001013371)	-69	NM_001013371	209200	Mm.390852	NM_001013371	ENSMUSG00000049502	Dtx3l	AU042200|BC023741	deltex 3-like, E3 ubiquitin ligase	protein-coding
mm_24178.1	chr3	88578507	88578513	+	1	NA	Intergenic	RMER17C|LTR|ERVK	-1161	NM_025448	66256	Mm.7091	NM_025448	ENSMUSG00000041355	Ssr2	1500032E05Rik|AI315033|AU020133|TLAP|TRAPB|TRAPbeta	signal sequence receptor, beta	protein-coding
mm_35097.1	chr4	8823242	8823251	-	1	NA	intron (NM_001277149, intron 8 of 37)	intron (NM_001277149, intron 8 of 37)	132840	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_24780.1	chr3	95540065	95540083	+	1	NA	intron (NM_001267695, intron 3 of 7)	intron (NM_001267695, intron 3 of 7)	13288	NM_001267695	13040	Mm.3619	NM_021281	ENSMUSG00000038642	Ctss	Cats	cathepsin S	protein-coding
mm_100939.1	chr11	6522849	6522854	-	1	NA	Intergenic	Intergenic	-1893	NM_178440	246177	Mm.239554	NM_178440	ENSMUSG00000020437	Myo1g	E430002D17Rik	myosin IG	protein-coding
mm_147562.1	chr18	54989599	54989619	-	1	NA	intron (NM_175751, intron 1 of 9)	intron (NM_175751, intron 1 of 9)	571	NM_175751	269023	Mm.192984	NM_175751	ENSMUSG00000052713	Zfp608	4932417D18Rik|D430007A19Rik|Znf608	zinc finger protein 608	protein-coding
mm_151581.1	chr19	61224472	61224483	+	1	NA	TTS (NM_009970)	TTS (NM_009970)	3941	NM_009970	12982	Mm.287228	NM_009970	ENSMUSG00000059326	Csf2ra	CD116|Csfgmra|GM-CSF-Ra|GM-CSFR	colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)	protein-coding
mm_24381.1	chr3	90248858	90248870	+	1	NA	intron (NM_013901, intron 1 of 3)	intron (NM_013901, intron 1 of 3)	672	NM_013901	30791	Mm.294709	NM_013901	ENSMUSG00000052310	Slc39a1	Zip1|Zirtl	solute carrier family 39 (zinc transporter), member 1	protein-coding
mm_100372.1	chr11	119126739	119126744	+	1	NA	Intergenic	Intergenic	27396	NR_105899	102465563		NR_105899	ENSMUSG00000098704	Mir6934	Gm27523|mmu-mir-6934	microRNA 6934	ncRNA
mm_168234.1	chr10	81687399	81687413	+	1	NA	Intergenic	CpG	-17419	NM_001243067	73610	Mm.490466	NM_001243067	ENSMUSG00000096795	Zfp433	1700123A16Rik	zinc finger protein 433	protein-coding
mm_62270.1	chr7	99535653	99535740	+	1	NA	5' UTR (NM_178220, exon 1 of 15)	5' UTR (NM_178220, exon 1 of 15)	210	NM_177231	109689	Mm.260193	NM_177231	ENSMUSG00000018909	Arrb1	1200006I17Rik|AW208571|G430100A01Rik	arrestin, beta 1	protein-coding
mm_43345.1	chr5	135128660	135128670	+	1	NA	exon (NM_021455, exon 8 of 17)	exon (NM_021455, exon 8 of 17)	-21046	NM_013763	27368	Mm.36746	NM_013763	ENSMUSG00000005374	Tbl2	C76179|WS-bTRP	transducin (beta)-like 2	protein-coding
mm_40753.1	chr5	66857733	66857756	+	1	NA	intron (NM_001001980, intron 1 of 25)	intron (NM_001001980, intron 1 of 25)	-110672	NM_001256122	77569	Mm.374778	NM_001001980	ENSMUSG00000037736	Limch1	3732412D22Rik|mKIAA1102	LIM and calponin homology domains 1	protein-coding
mm_105504.1	chr11	106161571	106161579	-	1	NA	Intergenic	Intergenic	-1433	NM_172397	67803	Mm.21687	NM_172397	ENSMUSG00000040699	Limd2	0610025L06Rik|AI413966	LIM domain containing 2	protein-coding
mm_159989.1	chr6	115944828	115944828	+	1	NA	promoter-TSS (NM_138311)	promoter-TSS (NM_138311)	-103	NM_001346702	171506	Mm.21899	NM_138311	ENSMUSG00000042279	H1foo	C86609|H1.8|H1fo|H1oo	H1 histone family, member O, oocyte-specific	protein-coding
mm_102606.1	chr11	62416317	62416321	-	1	NA	intron (NM_011308, intron 4 of 44)	PB1D7|SINE|Alu	22196	NM_001252313	20185	Mm.271814	NM_011308	ENSMUSG00000018501	Ncor1	5730405M06Rik|A230020K14Rik|N-CoR|RIP13|Rxrip13|mKIAA1047	nuclear receptor co-repressor 1	protein-coding
mm_157453.1	chrX	43152749	43152753	-	1	NA	intron (NM_011855, intron 2 of 32)	intron (NM_011855, intron 2 of 32)	122033	NM_011855	23963	Mm.327698	NM_011855	ENSMUSG00000016150	Tenm1	Odz1|Odz2|TCAP-1|Ten-m1|ten-1	teneurin transmembrane protein 1	protein-coding
mm_85297.1	chr9	100486463	100486492	-	1	NA	promoter-TSS (NM_001033543)	promoter-TSS (NM_001033543)	-4	NM_001033543	213208	Mm.242896	NM_001033543	ENSMUSG00000044244	Il20rb	AV228068|Fndc6|Gm186|Il20R2	interleukin 20 receptor beta	protein-coding
mm_150776.1	chr19	44294266	44294273	+	1	NA	5' UTR (NM_009128, exon 1 of 6)	5' UTR (NM_009128, exon 1 of 6)	593	NM_009128	20250	Mm.487021	NM_009128	ENSMUSG00000025203	Scd2	Mir5114|Scd-2|mir-5114|swty	stearoyl-Coenzyme A desaturase 2	protein-coding
mm_95853.1	chr11	57831695	57831703	+	1	NA	exon (NM_008213, exon 1 of 2)	exon (NM_008213, exon 1 of 2)	448	NM_008213	15110	Mm.4746	NM_008213	ENSMUSG00000037335	Hand1	Ehand1|Hxt|Th1|Thing1|bHLHa27|eHAND	heart and neural crest derivatives expressed transcript 1	protein-coding
mm_12507.1	chr2	71875082	71875090	+	1	NA	intron (NM_172665, intron 1 of 10)	intron (NM_172665, intron 1 of 10)	1862	NM_172665	228026	Mm.34411	NM_172665	ENSMUSG00000006494	Pdk1	B830012B01|D530020C15Rik	pyruvate dehydrogenase kinase, isoenzyme 1	protein-coding
mm_22853.1	chr3	28263424	28263428	+	1	NA	5' UTR (NM_001163009, exon 1 of 31)	5' UTR (NM_001163009, exon 1 of 31)	212	NM_001163009	665113	Mm.126193	NM_026910	ENSMUSG00000027692	Tnik	1500031A17Rik|4831440I19Rik|AI451411|C530008O15Rik|C630040K21Rik	TRAF2 and NCK interacting kinase	protein-coding
mm_117770.1	chr13	96542435	96542445	-	1	NA	promoter-TSS (NM_001164222)	promoter-TSS (NM_001164222)	139	NM_012048	27015	Mm.89926	NM_012048	ENSMUSG00000021668	Polk	DINP|Dinb1	polymerase (DNA directed), kappa	protein-coding
mm_125508.1	chr15	55557555	55557574	+	1	NA	promoter-TSS (NM_026759)	promoter-TSS (NM_026759)	156	NM_001168250	105837	Mm.390829	NM_134092	ENSMUSG00000022369	Mtbp	AI429604|MDM2BP	Mdm2, transformed 3T3 cell double minute p53 binding protein	protein-coding
mm_147374.1	chr18	43546838	43546882	-	1	NA	intron (NM_001163637, intron 19 of 21)	intron (NM_001163637, intron 19 of 21)	-108574	NM_001291455	22240	Mm.8180	NM_009468	ENSMUSG00000024501	Dpysl3	CRMP-4|DRP-3|TUC4|ULIP-1|Ulip|Ulip1	dihydropyrimidinase-like 3	protein-coding
mm_2990.1	chr1	133163852	133163921	+	1	NA	Intergenic	CpG	32720	NM_133819	108954	Mm.293628	NM_133819	ENSMUSG00000046062	Ppp1r15b	1810033K10Rik|AI606441|C530022L24Rik|CReP	protein phosphatase 1, regulatory (inhibitor) subunit 15b	protein-coding
mm_129122.1	chr15	76119294	76119315	-	1	NA	TTS (NM_001142968)	TTS (NM_001142968)	891	NM_144848	223650	Mm.259929	NM_144848		Eppk1	6230424I18Rik|EPIPL|EPIPL1|EPPK	epiplakin 1	protein-coding
mm_121047.1	chr14	80022710	80022718	+	1	NA	TTS (NM_001030294)	TTS (NM_001030294)	22412	NM_001030294	380924	Mm.26456	NM_001030294	ENSMUSG00000022026	Olfm4	GC1|GW112|Gm296|Gm913|OlfD|pPD4	olfactomedin 4	protein-coding
mm_83230.1	chr9	42394601	42394601	-	1	NA	intron (NM_009347, intron 3 of 23)	intron (NM_009347, intron 3 of 23)	5328	NM_009347	21683	Mm.42209	NM_009347	ENSMUSG00000037705	Tecta	Tctna	tectorin alpha	protein-coding
mm_22684.1	chr3	16214692	16214705	+	1	NA	non-coding (NR_027375, exon 6 of 6)	non-coding (NR_027375, exon 6 of 6)	31515	NM_001145919	229096	Mm.23834	NM_172677	ENSMUSG00000047213	Ythdf3	9130022A11Rik	YTH domain family 3	protein-coding
mm_137303.1	chr17	24850706	24850706	+	1	NA	promoter-TSS (NM_023480)	promoter-TSS (NM_023480)	39	NM_001159626	14651	Mm.43784	NM_024284	ENSMUSG00000024158	Hagh	BC019817|Glo-2|Glo2|Rsp29	hydroxyacyl glutathione hydrolase	protein-coding
mm_130680.1	chr15	100678115	100678122	-	1	NA	intron (NM_033612, intron 6 of 7)	intron (NM_033612, intron 6 of 7)	-8618	NM_001270537	668218	Mm.451225	NM_001270537	ENSMUSG00000098112	Bin2	-	bridging integrator 2	protein-coding
mm_148002.1	chr18	67724527	67724559	-	1	NA	promoter-TSS (NM_001127177)	promoter-TSS (NM_001127177)	78	NM_001127177	19255	Mm.260433	NM_008977	ENSMUSG00000024539	Ptpn2	AI325124|Ptpt|TC-PTP	protein tyrosine phosphatase, non-receptor type 2	protein-coding
mm_454.1	chr1	36132013	36132025	+	1	NA	Intergenic	Intergenic	12294	NR_105862	102465540		NR_105862	ENSMUSG00000098752	Mir6897	Gm27652|mmu-mir-6897	microRNA 6897	ncRNA
mm_264.1	chr1	20917841	20917854	+	1	NA	intron (NM_028829, intron 1 of 2)	intron (NM_028829, intron 1 of 2)	27225	NM_028829	74229	Mm.40780	NM_028829	ENSMUSG00000025931	Paqr8	1700019B16Rik|3110001D06Rik	progestin and adipoQ receptor family member VIII	protein-coding
mm_64960.1	chr7	16614614	16614623	-	1	NA	5' UTR (NM_172739, exon 1 of 7)	5' UTR (NM_172739, exon 1 of 7)	375	NM_172739	232906	Mm.28646	NM_172739	ENSMUSG00000058230	Arhgap35	6430596G11Rik|AI841135|Grlf1|mKIAA1722|p190A|p190RhoGAP	Rho GTPase activating protein 35	protein-coding
mm_55843.1	chr6	83317539	83317588	-	1	NA	promoter-TSS (NM_008638)	promoter-TSS (NM_008638)	41	NM_008638	17768	Mm.443	NM_008638	ENSMUSG00000005667	Mthfd2	AW558851|NMDMC	methylenetetrahydrofolate dehydrogenase (NAD+ dependent), methenyltetrahydrofolate cyclohydrolase	protein-coding
mm_148250.1	chr18	80713063	80713080	-	1	NA	promoter-TSS (NM_001164109)	promoter-TSS (NM_001164109)	0	NM_198429	18018	Mm.329560	NM_016791	ENSMUSG00000033016	Nfatc1	2210017P03Rik|AI449492|AV076380|NF-ATc|NFAT2|NFATc|Nfatcb	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 1	protein-coding
mm_56517.1	chr6	99484188	99484197	-	1	NA	intron (NM_001347345, intron 1 of 19)	B4|SINE|B4	36801	NM_001347345	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_140610.1	chr17	10839992	10840000	-	1	NA	promoter-TSS (NM_016694)	promoter-TSS (NM_016694)	195	NM_027032	69310	Mm.18889	NM_027032	ENSMUSG00000037196	Pacrg	1700008H23Rik	PARK2 co-regulated	protein-coding
mm_20313.1	chr2	127277789	127277789	-	1	NA	intron (NM_139308, intron 1 of 7)	intron (NM_139308, intron 1 of 7)	7560	NM_139308	99138	Mm.41271	NM_139308	ENSMUSG00000027367	Stard7	AI852671|AL022671|AW544915	START domain containing 7	protein-coding
mm_88022.1	chr10	67189273	67189286	+	1	NA	intron (NM_001242396, intron 1 of 24)	intron (NM_001242396, intron 1 of 24)	3529	NM_001242396	108829	Mm.23846	NM_207221	ENSMUSG00000037876	Jmjd1c	5430433L24Rik|D630035I23Rik|Jmjdic|TRIP8	jumonji domain containing 1C	protein-coding
mm_55716.1	chr6	73221626	73221664	-	1	NA	promoter-TSS (NM_001164669)	promoter-TSS (NM_001164669)	-14	NM_001164669	330355	Mm.333166	NM_001164669	ENSMUSG00000052861	Dnah6	9830168K20|A730004I20Rik|Dnahc6|mKIAA1697|mdhc6	dynein, axonemal, heavy chain 6	protein-coding
mm_47660.1	chr5	125434054	125434131	-	1	NA	promoter-TSS (NM_203319)	promoter-TSS (NM_203319)	-44	NM_203319	208144	Mm.296385	NM_203319	ENSMUSG00000029480	Dhx37	Gm1050|Gm451|mKIAA1517	DEAH (Asp-Glu-Ala-His) box polypeptide 37	protein-coding
mm_152095.1	chr19	6909600	6909626	-	1	NA	promoter-TSS (NM_026306)	promoter-TSS (NM_026306)	32	NM_012021	54683	Mm.279782	NM_012021	ENSMUSG00000024953	Prdx5	AOEB166|AOPP|Pmp20|Prdx6|PrxV	peroxiredoxin 5	protein-coding
mm_70689.1	chr8	15011431	15011437	+	1	NA	intron (NM_029116, intron 1 of 1)	CpG	409	NM_029116	74901	Mm.46675	NM_029116	ENSMUSG00000055675	Kbtbd11	2900016B01Rik|4930465M17Rik|mKIAA0711	kelch repeat and BTB (POZ) domain containing 11	protein-coding
mm_94097.1	chr10	128549126	128549170	-	1	NA	promoter-TSS (NM_018860)	promoter-TSS (NM_018860)	20	NM_018860	67945	Mm.290786	NM_018860	ENSMUSG00000093674	Rpl41	1810055P16Rik|2210411K19Rik	ribosomal protein L41	protein-coding
mm_73631.1	chr8	110721463	110721486	+	1	NA	promoter-TSS (NM_198625)	promoter-TSS (NM_198625)	-2	NM_198625	244654	Mm.490385	NM_198625	ENSMUSG00000033763	Mtss1l	ABBA	metastasis suppressor 1-like	protein-coding
mm_88944.1	chr10	81321256	81321270	+	1	NA	exon (NM_027381, exon 1 of 9)	exon (NM_027381, exon 1 of 9)	160	NM_027381	70312	Mm.87628	NM_027381	ENSMUSG00000034889	Cactin	2510012J08Rik	cactin, spliceosome C complex subunit	protein-coding
mm_52837.1	chr6	121636269	121636279	+	1	NA	5' UTR (NM_175628, exon 1 of 36)	5' UTR (NM_175628, exon 1 of 36)	101	NM_175628	232345	Mm.30151	NM_175628	ENSMUSG00000030111	A2m	A2mp	alpha-2-macroglobulin	protein-coding
mm_81188.1	chr9	107542219	107542258	+	1	NA	promoter-TSS (NM_019720)	promoter-TSS (NM_019720)	29	NM_018879	56032	Mm.11337	NM_018879	ENSMUSG00000010057	Nprl2	2810446G01Rik|G21|NPR2L|Tusc4	nitrogen permease regulator-like 2	protein-coding
mm_119571.1	chr14	50357886	50357898	+	1	NA	promoter-TSS (NM_205819)	promoter-TSS (NM_205819)	-22	NM_205819	239081	Mm.291512	NM_205819	ENSMUSG00000051969	Tlr11	Gm287	toll-like receptor 11	protein-coding
mm_1786.1	chr1	78602343	78602364	+	1	NA	Intergenic	RLTR41|LTR|ERV1	-55472	NM_001033606	74205	Mm.276016	NM_028817	ENSMUSG00000032883	Acsl3	2610510B12Rik|Acs3|C85929|Facl3|Pro2194	acyl-CoA synthetase long-chain family member 3	protein-coding
mm_103623.1	chr11	78696497	78696541	-	1	NA	5' UTR (NM_008702, exon 1 of 11)	5' UTR (NM_008702, exon 1 of 11)	906	NM_008702	18099	Mm.9001	NM_008702	ENSMUSG00000017376	Nlk	AI194375	nemo like kinase	protein-coding
mm_169015.1	chr13	108509179	108509188	-	1	NA	Intergenic	L1Md_T|LINE|L1	-144994	NM_011056	238871	Mm.434429	NM_011056	ENSMUSG00000021699	Pde4d	9630011N22Rik|Dpde3	phosphodiesterase 4D, cAMP specific	protein-coding
mm_3291.1	chr1	136678141	136678154	+	1	NA	Intergenic	Intergenic	-5249	NR_045324	100503460	Mm.30630	NR_045324	ENSMUSG00000097113	Gm19705	-	predicted gene, 19705	ncRNA
mm_146493.1	chr18	3270756	3270799	-	1	NA	intron (NM_001311066, intron 3 of 3)	intron (NM_001311066, intron 3 of 3)	10355	NM_001311066	12916	Mm.5244	NM_013498	ENSMUSG00000063889	Crem	ICER|ICERI	cAMP responsive element modulator	protein-coding
mm_12179.1	chr2	63221853	63221853	+	1	NA	Intergenic	Intergenic	-37566	NM_133207	170738	Mm.242532	NM_133207	ENSMUSG00000059742	Kcnh7	9330137I11Rik|Kv11.3|erg3	potassium voltage-gated channel, subfamily H (eag-related), member 7	protein-coding
mm_82527.1	chr9	20667854	20667919	-	1	NA	TTS (NM_173777)	TTS (NM_173777)	15756	NM_023371	23988	Mm.7906	NM_023371	ENSMUSG00000032171	Pin1	0610025L01Rik|D9Bwg1161e	protein (peptidyl-prolyl cis/trans isomerase) NIMA-interacting 1	protein-coding
mm_10110.1	chr2	3704788	3704798	+	1	NA	Intergenic	Intergenic	-8665	NM_025626	66540	Mm.277864	NM_025626	ENSMUSG00000026655	Fam107b	3110001A13Rik|AA589595|AA959793|AI132312	family with sequence similarity 107, member B	protein-coding
mm_57800.1	chr6	129331739	129331779	-	1	NA	promoter-TSS (NM_199034)	promoter-TSS (NM_199034)	22	NM_199034	381816	Mm.46114	NM_199034	ENSMUSG00000047720	4922502D21Rik	Clec2m|Gm1074|SPATA78	RIKEN cDNA 4922502D21 gene	protein-coding
mm_143274.1	chr17	65674430	65674432	-	1	NA	intron (NM_133685, intron 5 of 6)	intron (NM_133685, intron 5 of 6)	-32227	NM_001146002	213272	Mm.255732	NM_153519	ENSMUSG00000050612	Txndc2	AU021712|Sptrx-1|Sptrx1|Trx4	thioredoxin domain containing 2 (spermatozoa)	protein-coding
mm_146302.1	chr18	80253275	80253286	+	1	NA	Intergenic	RLTR35B_MM|LTR|ERVL	-1965	NM_001164420	66943	Mm.29247	NM_025861	ENSMUSG00000034006	Pqlc1	2310009N05Rik|4933425L21Rik|5730564E11Rik|C78974	PQ loop repeat containing 1	protein-coding
mm_15663.1	chr2	163323333	163323341	+	1	NA	TTS (NM_001098799)	TTS (NM_001098799)	74636	NM_021566	59091	Mm.34459	NM_021566	ENSMUSG00000017817	Jph2	1110002E14Rik|JP-2|Jp2	junctophilin 2	protein-coding
mm_64546.1	chr7	144321120	144321173	+	1	NA	intron (NM_001113373, intron 7 of 15)	(CA)n|Simple_repeat|Simple_repeat	36761	NM_001081370	210274	Mm.483624	NM_001081370	ENSMUSG00000037541	Shank2	ProSAP1|mKIAA1022	SH3/ankyrin domain gene 2	protein-coding
mm_17716.1	chr2	32387056	32387065	-	1	NA	exon (NM_008491, exon 2 of 6)	exon (NM_008491, exon 2 of 6)	679	NM_008491	16819	Mm.9537	NM_008491	ENSMUSG00000026822	Lcn2	24p3|AW212229|NRL|Sip24	lipocalin 2	protein-coding
mm_40167.1	chr5	35814357	35814371	+	1	NA	intron (NM_001177696, intron 6 of 21)	intron (NM_001177696, intron 6 of 21)	56484	NM_001177698	231148	Mm.254446	NM_177678	ENSMUSG00000029095	Ablim2	AI606905|C230091L11	actin-binding LIM protein 2	protein-coding
mm_142074.1	chr17	35700521	35700606	-	1	NA	promoter-TSS (NM_001198833)	promoter-TSS (NM_001198833)	27	NM_001198833	12305	Mm.5021	NM_007584	ENSMUSG00000003534	Ddr1	6030432F18|AI323681|CD167a|Cak|Nep|PTK3A	discoidin domain receptor family, member 1	protein-coding
mm_141905.1	chr17	34957124	34957147	-	1	NA	exon (NM_010478, exon 1 of 1)	exon (NM_010478, exon 1 of 1)	2103	NM_010478	15511	Mm.372314	NM_010478	ENSMUSG00000090877	Hspa1b	Hsp70|Hsp70-1|Hsp70.1|hsp68	heat shock protein 1B	protein-coding
mm_16227.1	chr2	173155941	173155952	+	1	NA	exon (NM_011044, exon 6 of 10)	exon (NM_011044, exon 6 of 10)	2873	NM_011044	18534	Mm.266867	NM_011044	ENSMUSG00000027513	Pck1	AI265463|PEPCK|Pck-1	phosphoenolpyruvate carboxykinase 1, cytosolic	protein-coding
mm_125124.1	chr15	30172923	30172938	+	1	NA	5' UTR (NM_008729, exon 1 of 23)	5' UTR (NM_008729, exon 1 of 23)	337	NM_008729	18163	Mm.321648	NM_008729	ENSMUSG00000022240	Ctnnd2	Catnd2|Nprap|neurojugin	catenin (cadherin associated protein), delta 2	protein-coding
mm_151649.1	chr19	4064096	4064099	-	1	NA	Intergenic	MMVL30-int|LTR|ERV1	-4803	NM_144869	225884	Mm.440201	NM_144869	ENSMUSG00000058216	Gstp3	-	glutathione S-transferase pi 3	protein-coding
mm_69362.1	chr7	130539923	130539971	-	1	NA	exon (NM_001162855, exon 4 of 11)	exon (NM_001162855, exon 4 of 11)	7434	NM_001162855	67872	Mm.21714	NM_001162855	ENSMUSG00000040331	Nsmce4a	2410003A14Rik	NSE4 homolog A, SMC5-SMC6 complex component	protein-coding
mm_55849.1	chr6	83386736	83386739	-	1	NA	intron (NM_001347313, intron 4 of 11)	L1MB3|LINE|L1	14365	NR_105793	102465194		NR_105793	ENSMUSG00000099045	Mir6374	Gm27292|mmu-mir-6374	microRNA 6374	ncRNA
mm_105986.1	chr11	115627703	115627709	-	1	NA	5' UTR (NM_001252384, exon 2 of 8)	5' UTR (NM_001252384, exon 2 of 8)	589	NM_001252394	67283	Mm.383426	NM_026071	ENSMUSG00000020744	Slc25a19	2900089E13Rik|DNC|MUP1|TPC	solute carrier family 25 (mitochondrial thiamine pyrophosphate carrier), member 19	protein-coding
mm_79310.1	chr9	52048903	52048912	+	1	NA	promoter-TSS (NR_023357)	promoter-TSS (NR_023357)	-202	NR_023357	629557	Mm.422775	NR_023357		Gm6981	EG629557	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_137759.1	chr17	29489231	29489237	+	1	NA	Intergenic	Intergenic	-1811	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_149068.1	chr19	8850940	8850954	+	1	NA	5' UTR (NM_001013019, exon 1 of 2)	5' UTR (NM_001013019, exon 1 of 2)	162	NM_001013019	68852	Mm.265792	NM_001013019	ENSMUSG00000071656	Lrrn4cl	1110067I12Rik	LRRN4 C-terminal like	protein-coding
mm_98950.1	chr11	98447118	98447126	+	1	NA	5' UTR (NM_010346, exon 1 of 15)	5' UTR (NM_010346, exon 1 of 15)	288	NM_010346	14786	Mm.276702	NM_010346	ENSMUSG00000019312	Grb7	mKIAA4028	growth factor receptor bound protein 7	protein-coding
mm_95361.1	chr11	48901300	48901313	+	1	NA	intron (NM_001024230, intron 2 of 4)	B1_Mur1|SINE|Alu	846	NM_001024230	432555	Mm.338931	NM_001024230	ENSMUSG00000058163	Gm5431	EG432555|Irgb9b8	predicted gene 5431	protein-coding
mm_173313.1	chrY	90735109	90735114	+	1	NA	Intergenic	IMPB_01|Satellite|Satellite	19939	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_98830.1	chr11	97415555	97415576	+	1	NA	Intergenic	CpG	-34595	NM_021493	58996	Mm.394118	NM_021493	ENSMUSG00000049807	Arhgap23	A330041B18Rik	Rho GTPase activating protein 23	protein-coding
mm_74899.1	chr8	25201316	25201344	-	1	NA	5' UTR (NM_177089, exon 1 of 13)	5' UTR (NM_177089, exon 1 of 13)	212	NM_199323	320165	Mm.308452	NM_177089	ENSMUSG00000065954	Tacc1	4833447E04Rik|AA960202|B230378H13Rik	transforming, acidic coiled-coil containing protein 1	protein-coding
mm_113482.1	chr13	37345339	37345365	+	1	NA	promoter-TSS (NM_010745)	promoter-TSS (NM_010745)	7	NM_010745	17084	Mm.2639	NM_010745	ENSMUSG00000021423	Ly86	MD-1|MD1|ly86_tv2	lymphocyte antigen 86	protein-coding
mm_90005.1	chr10	112837718	112837732	+	1	NA	Intergenic	Intergenic	91301	NM_001033474	382423	Mm.431239	NM_001033474	ENSMUSG00000074748	Atxn7l3b	4921506J03Rik|6230409E21Rik|AI315132|ENSMUSG00000074747	ataxin 7-like 3B	protein-coding
mm_135571.1	chr16	50330980	50330980	-	1	NA	intron (NM_001347240, intron 3 of 16)	intron (NM_001347240, intron 3 of 16)	101409	NM_027444	70508	Mm.28940	NM_027444	ENSMUSG00000022641	Bbx	5530401J07Rik|5730403O13Rik	bobby sox HMG box containing	protein-coding
mm_1169.1	chr1	60913667	60913672	+	1	NA	intron (NM_009843, intron 3 of 3)	intron (NM_009843, intron 3 of 3)	4644	NM_001281976	12477	Mm.390	NM_009843	ENSMUSG00000026011	Ctla4	Cd152|Ctla-4|Ly-56	cytotoxic T-lymphocyte-associated protein 4	protein-coding
mm_75648.1	chr8	65129318	65129328	-	1	NA	non-coding (NR_033217, exon 1 of 3)	non-coding (NR_033217, exon 1 of 3)	214	NR_033217	407795	Mm.387876	NR_033217	ENSMUSG00000074300	BC030870	-	cDNA sequence BC030870	ncRNA
mm_27504.1	chr3	55539970	55539972	-	1	NA	TTS (NM_001111052)	TTS (NM_001111052)	78213	NM_001195540	13175	Mm.393242	NM_019978	ENSMUSG00000027797	Dclk1	1700113D08Rik|2810480F11Rik|AI836758|Click-I|Cpg16|Dcamkl1|Dcl|Dclk|mKIAA0369	doublecortin-like kinase 1	protein-coding
mm_125543.1	chr15	58405831	58405845	+	1	NA	Intergenic	ID_B1|SINE|B4	-9630	NM_145959	210998	Mm.3224	NM_145959	ENSMUSG00000037119	Fam91a1	AV220772|BC033609|D15Ertd621e|SKIN|mKIAA0493	family with sequence similarity 91, member A1	protein-coding
mm_164938.1	chr18	86433021	86433032	+	1	NA	intron (NM_144946, intron 4 of 10)	RSINE1|SINE|B4	38074	NM_144946	246317	Mm.329578	NM_144946	ENSMUSG00000050321	Neto1	AI851453|Btcl1|C130005O10Rik	neuropilin (NRP) and tolloid (TLL)-like 1	protein-coding
mm_171025.1	chr2	84650651	84650652	-	1	NA	promoter-TSS (NM_001085449)	promoter-TSS (NM_001085449)	89	NM_001085449	12388	Mm.35738	NM_007615	ENSMUSG00000034101	Ctnnd1	AA409437|AU019353|Catns|Ctnnd|P120|mKIAA0384	catenin (cadherin associated protein), delta 1	protein-coding
mm_132719.1	chr16	43510268	43510280	+	1	NA	intron (NM_181058, intron 3 of 6)	intron (NM_181058, intron 3 of 6)	-90078	NR_046026	626693	Mm.447083	NR_046026	ENSMUSG00000085499	Gm15713	OTTMUSG00000025617	predicted gene 15713	ncRNA
mm_143872.1	chr17	84187028	84187066	-	1	NA	exon (NM_001001806, exon 2 of 2)	exon (NM_001001806, exon 2 of 2)	900	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_99395.1	chr11	102146340	102146383	+	1	NA	intron (NM_145829, intron 1 of 6)	intron (NM_145829, intron 1 of 6)	848	NM_145829	217214	Mm.31686	NM_145829	ENSMUSG00000048217	Nags	1700120E20Rik|argA	N-acetylglutamate synthase	protein-coding
mm_37595.1	chr4	126736237	126736245	-	1	NA	promoter-TSS (NM_198960)	promoter-TSS (NM_198960)	28	NM_198960	332937	Mm.331881	NM_198960	ENSMUSG00000042477	Tfap2e	AI505200|AP-2e|Tcfap2e	transcription factor AP-2, epsilon	protein-coding
mm_31339.1	chr4	46469961	46469985	+	1	NA	exon (NM_130889, exon 5 of 7)	exon (NM_130889, exon 5 of 7)	19047	NM_130889	67628	Mm.263913	NM_130889	ENSMUSG00000028333	Anp32b	2410015B15Rik|PAL31|PHAPI2a|Ssp29	acidic (leucine-rich) nuclear phosphoprotein 32 family, member B	protein-coding
mm_18315.1	chr2	57107935	57107944	-	1	NA	3' UTR (NM_013613, exon 8 of 8)	3' UTR (NM_013613, exon 8 of 8)	7099	NM_013613	18227	Mm.3507	NM_013613	ENSMUSG00000026826	Nr4a2	HZF-3|NOT|Nurr1|RNR-1|TINOR|TINUR	nuclear receptor subfamily 4, group A, member 2	protein-coding
mm_83271.1	chr9	42985727	42985731	-	1	NA	intron (NM_027144, intron 28 of 40)	intron (NM_027144, intron 28 of 40)	-41358	NM_175481	110637	Mm.370291	NM_175481	ENSMUSG00000032017	Grik4	6330551K01Rik|GluK4|GluRgamma1|KA-1|KA1	glutamate receptor, ionotropic, kainate 4	protein-coding
mm_145825.1	chr18	65437380	65437391	+	1	NA	intron (NM_172833, intron 1 of 15)	B1_Mur1|SINE|Alu	6388	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_156069.1	chrX	109161229	109161301	+	1	NA	3' UTR (NM_019989, exon 4 of 4)	3' UTR (NM_019989, exon 4 of 4)	-35491	NM_001037917	622976	Mm.482747	NM_001037917	ENSMUSG00000048621	Gm6377	EG622976	predicted gene 6377	protein-coding
mm_51972.1	chr6	91758551	91758567	+	1	NA	3' UTR (NM_009320, exon 15 of 15)	3' UTR (NM_009320, exon 15 of 15)	48834	NM_001159507	243547	Mm.333264	NM_001033353	ENSMUSG00000030098	Grip2	-	glutamate receptor interacting protein 2	protein-coding
mm_42192.1	chr5	112276684	112276693	+	1	NA	promoter-TSS (NM_009419)	promoter-TSS (NM_009419)	-3	NM_001326590	22022	Mm.250631	NM_009419	ENSMUSG00000029344	Tpst2	AI448750|D5Ucla3|Tango13b|grm|grt	protein-tyrosine sulfotransferase 2	protein-coding
mm_103174.1	chr11	70459833	70459841	-	1	NA	5' UTR (NM_001029929, exon 1 of 14)	5' UTR (NM_001029929, exon 1 of 14)	147	NM_023158	66102	Mm.425692	NM_023158	ENSMUSG00000018920	Cxcl16	0910001K24Rik|AV290116|BB024863|CXCL16v1|CXCL16v2|SR-PSOX|Zmynd15|b2b498Clo	chemokine (C-X-C motif) ligand 16	protein-coding
mm_95765.1	chr11	54907186	54907200	+	1	NA	exon (NM_008161, exon 2 of 5)	exon (NM_008161, exon 2 of 5)	4339	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_128128.1	chr15	31338693	31338703	-	1	NA	intron (NM_027496, intron 1 of 3)	ORR1D2|LTR|ERVL-MaLR	29061	NM_001164441	67434	Mm.102470	NM_026153	ENSMUSG00000022237	Ankrd33b	0610012A05Rik|3021401C12Rik|5730557B15Rik	ankyrin repeat domain 33B	protein-coding
mm_151757.1	chr19	5106968	5107023	-	1	NA	promoter-TSS (NM_029576)	promoter-TSS (NM_029576)	1	NM_029576	76308	Mm.182563	NM_029576	ENSMUSG00000024870	Rab1b	1110011F09Rik	RAB1B, member RAS oncogene family	protein-coding
mm_36198.1	chr4	62348127	62348130	-	1	NA	intron (NM_001045528, intron 2 of 27)	intron (NM_001045528, intron 2 of 27)	12420	NM_001045528	338355	Mm.357792	NM_001045528	ENSMUSG00000066151	Fkbp15	BB131447|C430014M02Rik|FKBO133|FKBP-133|FKBP-15|FKBP133|mKIAA0674	FK506 binding protein 15	protein-coding
mm_124489.1	chr14	121738630	121738653	-	1	NA	5' UTR (NM_001128307, exon 1 of 56)	5' UTR (NM_001128307, exon 1 of 56)	288	NM_001128308	105445	Mm.378591	NM_134074	ENSMUSG00000025558	Dock9	AA959601|AW538057|B230309H04Rik|D14Wsu89e|Zizimin1|mKIAA1058	dedicator of cytokinesis 9	protein-coding
mm_154476.1	chrM	4228	4244	-	1	NA	NA	Intergenic	NA	NA								
mm_164308.1	chr15	103897461	103897466	+	1	NA	exon (NM_009267, exon 3 of 4)	exon (NM_009267, exon 3 of 4)	1837	NM_009268	20771	Mm.30276	NM_009268		Mucl1	Spt-2|Spt2	mucin-like 1	protein-coding
mm_76618.1	chr8	91629708	91629734	-	1	NA	intron (NM_011936, intron 8 of 8)	intron (NM_011936, intron 8 of 8)	171933	NM_001253822	16373	Mm.238044	NM_008393	ENSMUSG00000031734	Irx3	AI894186	Iroquois related homeobox 3	protein-coding
mm_42495.1	chr5	115474674	115474682	+	1	NA	TTS (NM_011107)	TTS (NM_011107)	8412	NM_011107	18778	Mm.20190	NM_011107	ENSMUSG00000029522	Pla2g1b	Pla2a|sPLA2IB	phospholipase A2, group IB, pancreas	protein-coding
mm_137739.1	chr17	29360957	29360968	+	1	NA	promoter-TSS (NM_013710)	promoter-TSS (NM_013710)	48	NM_001159538	26382	Mm.279187	NM_013710	ENSMUSG00000024013	Fgd2	Tcd-2|Tcd2|ZFYVE4|tcs-2|tcs2	FYVE, RhoGEF and PH domain containing 2	protein-coding
mm_164991.1	chr19	12076029	12076029	+	1	NA	intron (NR_030566, intron 2 of 3)	intron (NR_030566, intron 2 of 3)	-1399	NM_001011853	258155	Mm.377363	NM_001011853	ENSMUSG00000067526	Olfr1425	MOR239-7	olfactory receptor 1425	protein-coding
mm_54148.1	chr6	22343711	22343720	-	1	NA	intron (NM_138587, intron 1 of 9)	intron (NM_138587, intron 1 of 9)	12366	NM_138587	27999	Mm.490307	NM_138587	ENSMUSG00000029672	Fam3c	D6Wsu176e|Ilei	family with sequence similarity 3, member C	protein-coding
mm_98536.1	chr11	95009899	95009919	+	1	NA	promoter-TSS (NM_146025)	promoter-TSS (NM_146025)	30	NM_146025	217125	Mm.297199	NM_146025	ENSMUSG00000047181	Samd14	AI839049|AI854782|BC034054	sterile alpha motif domain containing 14	protein-coding
mm_171359.1	chr4	117154486	117154494	-	1	NA	promoter-TSS (NR_028524)	promoter-TSS (NR_028524)	84	NR_028524	100217424		NR_028524	ENSMUSG00000065680	Snord38a	MBII-329	small nucleolar RNA, C/D box 38A	snoRNA
mm_67866.1	chr7	99157052	99157078	-	1	NA	exon (NM_026384, exon 7 of 8)	exon (NM_026384, exon 7 of 8)	-15921	NM_178635	78610	Mm.323072	NM_178635	ENSMUSG00000035354	Uvrag	9530039D02Rik|AI648770|BB124205|Uvrag1|Uvragl	UV radiation resistance associated gene	protein-coding
mm_101011.1	chr11	8505036	8505045	-	1	NA	intron (NM_001083587, intron 16 of 30)	intron (NM_001083587, intron 16 of 30)	159495	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_46993.1	chr5	115334270	115334280	-	1	NA	3' UTR (NM_029645, exon 3 of 3)	3' UTR (NM_029645, exon 3 of 3)	6886	NM_029645	384281	Mm.229308	NM_029645	ENSMUSG00000029536	Gatc	2010003O18Rik	glutamyl-tRNA(Gln) amidotransferase, subunit C	protein-coding
mm_167812.1	chr9	123931876	123931904	+	1	NA	Intergenic	Intergenic	36802	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_127938.1	chr15	10589032	10589068	-	1	NA	intron (NM_001166408, intron 11 of 17)	ID4_|SINE|ID	-11243	NR_033541	100038608	Mm.450744	NR_033541		Gm10389	ENSMUSG00000072658	predicted gene 10389	ncRNA
mm_17483.1	chr2	28562434	28562452	-	1	NA	intron (NM_009885, intron 1 of 10)	intron (NM_009885, intron 1 of 10)	960	NM_009885	12613	Mm.236017	NM_009885	ENSMUSG00000026818	Cel	1810036E18Rik|BAL	carboxyl ester lipase	protein-coding
mm_45380.1	chr5	66122648	66122658	-	1	NA	intron (NM_001127382, intron 2 of 7)	intron (NM_001127382, intron 2 of 7)	-24474	NM_139065	245945	Mm.36863	NM_139065	ENSMUSG00000070780	Rbm47	9530077J19Rik	RNA binding motif protein 47	protein-coding
mm_88158.1	chr10	69681632	69681636	+	1	NA	intron (NM_170730, intron 1 of 17)	intron (NM_170730, intron 1 of 17)	147926	NM_146005	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_40553.1	chr5	58396659	58396660	+	1	NA	Intergenic	Intergenic	56339	NR_046190	78163	Mm.243828	NR_046190	ENSMUSG00000105234	4930459L07Rik	-	RIKEN cDNA 4930459L07 gene	ncRNA
mm_52485.1	chr6	114643107	114643169	+	1	NA	promoter-TSS (NM_028835)	promoter-TSS (NM_028835)	41	NM_001253717	74244	Mm.275332	NM_028835	ENSMUSG00000030314	Atg7	1810013K23Rik|Agp7|Apg7l|Atg7l|Gm21553	autophagy related 7	protein-coding
mm_138509.1	chr17	35236609	35236617	+	1	NA	promoter-TSS (NM_010909)	promoter-TSS (NM_010909)	17	NM_023179	66237	Mm.396107	NM_023179	ENSMUSG00000024403	Atp6v1g2	1500002D01Rik|Atp6g2|NG38|VAG2	ATPase, H+ transporting, lysosomal V1 subunit G2	protein-coding
mm_91114.1	chr10	19186461	19186471	-	1	NA	intron (NR_038022, intron 1 of 1)	intron (NR_038022, intron 1 of 1)	19228	NR_038022	100504265	Mm.383417	NR_038021		Gm20139	-	predicted gene, 20139	ncRNA
mm_91624.1	chr10	41752212	41752267	-	1	NA	intron (NM_001243074, intron 2 of 10)	intron (NM_001243074, intron 2 of 10)	57424	NM_001243075	103268	Mm.338605	NM_026643	ENSMUSG00000019813	Cep57l1	2410017P07Rik|4930484D11Rik|AI607327|cep57R	centrosomal protein 57-like 1	protein-coding
mm_13324.1	chr2	102781804	102781812	+	1	NA	3' UTR (NM_001077514, exon 11 of 11)	3' UTR (NM_001077514, exon 11 of 11)	75370	NM_001077515	20511	Mm.267547	NM_011393	ENSMUSG00000005089	Slc1a2	1700091C19Rik|2900019G14Rik|AI159670|Eaat2|GLT-1|GLT1|MGLT1	solute carrier family 1 (glial high affinity glutamate transporter), member 2	protein-coding
mm_28809.1	chr3	96256262	96256268	-	1	NA	Intergenic	Intergenic	7052	NM_033596	97122	Mm.227295	NM_033596	ENSMUSG00000091405	Hist2h4	H4|X04652	histone cluster 2, H4	protein-coding
mm_166870.1	chr7	24766000	24766002	-	1	NA	Intergenic	Intergenic	-5690	NM_026862	68891	Mm.292848	NM_026862	ENSMUSG00000052212	Cd177	1190003K14Rik|Pdp3	CD177 antigen	protein-coding
mm_62748.1	chr7	111122176	111122196	+	1	NA	intron (NR_015573, intron 1 of 2)	CpG	489	NR_015573	75479	Mm.381620	NR_015573	ENSMUSG00000110424	1700012D14Rik	-	RIKEN cDNA 1700012D14 gene	ncRNA
mm_58402.1	chr7	3218396	3218407	+	1	NA	promoter-TSS (NR_029640)	promoter-TSS (NR_029640)	-225	NR_029640	100049710		NR_029640	ENSMUSG00000077815	Mir290a	Mir290|Mirn290|mir-290a|mmu-miR-290|mmu-mir-290a	microRNA 290a	ncRNA
mm_130608.1	chr15	99821049	99821078	-	1	NA	promoter-TSS (NM_023063)	promoter-TSS (NM_023063)	-914	NM_023063	65970	Mm.33207	NM_023063	ENSMUSG00000023022	Lima1	Eplin	LIM domain and actin binding 1	protein-coding
mm_88613.1	chr10	79826007	79826023	+	1	NA	exon (NM_030218, exon 2 of 5)	exon (NM_030218, exon 2 of 5)	4994	NM_030218	78906	Mm.33087	NM_030218	ENSMUSG00000035852	Misp	9130017N09Rik	mitotic spindle positioning	protein-coding
mm_32778.1	chr4	116708123	116708133	+	1	NA	promoter-TSS (NM_026714)	promoter-TSS (NM_026714)	257	NM_025962	67096	Mm.252785	NM_025962	ENSMUSG00000028690	Mmachc	1810037K07Rik|CblC	methylmalonic aciduria cblC type, with homocystinuria	protein-coding
mm_131593.1	chr16	18832177	18832183	+	1	NA	intron (NR_028403, intron 11 of 11)	MLT1B|LTR|ERVL-MaLR	-4400	NM_001033164	72307	Mm.36907	NM_001033164	ENSMUSG00000071632	2510002D24Rik	2410043I01Rik|AA163535|AA409624|DXMgi27	RIKEN cDNA 2510002D24 gene	protein-coding
mm_73863.1	chr8	118354248	118354250	+	1	NA	intron (NM_019707, intron 1 of 13)	B4|SINE|B4	70638	NM_019707	12554	Mm.334841	NM_019707	ENSMUSG00000031841	Cdh13	4932416G01Rik|Cdht|Tcad	cadherin 13	protein-coding
mm_65157.1	chr7	19643090	19643122	-	1	NA	exon (NM_019649, exon 5 of 14)	exon (NM_019649, exon 5 of 14)	-13668	NM_009046	19698	Mm.1741	NM_009046	ENSMUSG00000002983	Relb	shep	avian reticuloendotheliosis viral (v-rel) oncogene related B	protein-coding
mm_42371.1	chr5	114925414	114925426	+	1	NA	intron (NM_145209, intron 2 of 6)	intron (NM_145209, intron 2 of 6)	2180	NM_145209	231655	Mm.95479	NM_145209	ENSMUSG00000041827	Oasl1	7530414C13Rik|oasl9	2'-5' oligoadenylate synthetase-like 1	protein-coding
mm_62789.1	chr7	112679379	112679387	+	1	NA	promoter-TSS (NM_001166584)	promoter-TSS (NM_001166584)	63	NM_009346	21676	Mm.24685	NM_009346	ENSMUSG00000055320	Tead1	2610024B07Rik|B230114H05Rik|Gtrgeo5|TEAD-1|TEF-1|Tcf13|mTEF-1	TEA domain family member 1	protein-coding
mm_104162.1	chr11	87325062	87325073	-	1	NA	intron (NR_106195, intron 6 of 8)	B2_Mm2|SINE|B2	33927	NM_177167	320472	Mm.341988	NM_177167	ENSMUSG00000046442	Ppm1e	AW049266|B930008A12Rik|POPX1|PP2CH|mKIAA1072	protein phosphatase 1E (PP2C domain containing)	protein-coding
mm_140616.1	chr17	10840316	10840323	-	1	NA	promoter-TSS (NM_016694)	promoter-TSS (NM_016694)	-40	NM_001317726	50873	Mm.311110	NM_016694	ENSMUSG00000023826	Park2	PRKN	Parkinson disease (autosomal recessive, juvenile) 2, parkin	protein-coding
mm_166988.1	chr7	45917567	45917576	+	1	NA	TTS (NM_144801)	TTS (NM_144801)	3278	NM_001146346	13732	Mm.20829	NM_010129	ENSMUSG00000040212	Emp3	H-4|H4|HNMP-1|MI-35|Ymp	epithelial membrane protein 3	protein-coding
mm_116287.1	chr13	35027034	35027055	-	1	NA	Intergenic	Intergenic	-32900	NM_001110331	23986	Mm.491141	NM_011868	ENSMUSG00000021417	Eci2	Acbd2|Drs1|Hca88|Peci	enoyl-Coenzyme A delta isomerase 2	protein-coding
mm_63484.1	chr7	127746738	127746747	+	1	NA	promoter-TSS (NM_172748)	promoter-TSS (NM_172748)	-33	NM_172748	233902	Mm.259353	NM_172748	ENSMUSG00000030811	Fbxl19	6030430O11|BC059812|Fbl19	F-box and leucine-rich repeat protein 19	protein-coding
mm_10214.1	chr2	5848121	5848134	+	1	NA	intron (NM_016918, intron 1 of 9)	intron (NM_016918, intron 1 of 9)	3093	NM_016918	53893	Mm.251904	NM_016918	ENSMUSG00000025817	Nudt5	-	nudix (nucleoside diphosphate linked moiety X)-type motif 5	protein-coding
mm_132170.1	chr16	32303810	32303813	+	1	NA	Intergenic	Intergenic	26350	NM_027355	70238	Mm.228263	NM_027355	ENSMUSG00000014074	Rnf168	3110001H15Rik	ring finger protein 168	protein-coding
mm_85667.1	chr9	107675993	107676000	-	1	NA	exon (NM_008140, exon 8 of 9)	exon (NM_008140, exon 8 of 9)	3596	NM_008140	14685	Mm.284853	NM_008140	ENSMUSG00000034837	Gnat1	Gnat-1|Ird1|Ird2|Tralpha|irdc|irdr|transducin	guanine nucleotide binding protein, alpha transducing 1	protein-coding
mm_100789.1	chr11	4939536	4939546	-	1	NA	exon (NM_010904, exon 4 of 4)	exon (NM_010904, exon 4 of 4)	-7980	NM_001243043	11764	Mm.274816	NM_007454	ENSMUSG00000009090	Ap1b1	Adtb1|b2b1660Clo	adaptor protein complex AP-1, beta 1 subunit	protein-coding
mm_149415.1	chr19	11426223	11426257	+	1	NA	exon (NM_029499, exon 7 of 7)	exon (NM_029499, exon 7 of 7)	-17318	NM_021718	60361	Mm.33957	NM_021718	ENSMUSG00000056290	Ms4a4b	AI463180|Chandra|Ly116	membrane-spanning 4-domains, subfamily A, member 4B	protein-coding
mm_10314.1	chr2	11172357	11172367	+	1	NA	promoter-TSS (NM_008859)	promoter-TSS (NM_008859)	-20	NM_008859	18761	Mm.329993	NM_008859	ENSMUSG00000026778	Prkcq	A130035A12Rik|AW494342|PKC-0|PKC-theta|PKCtheta|Pkcq	protein kinase C, theta	protein-coding
mm_154259.1	chr19	60768901	60768911	-	1	NA	intron (NM_010123, intron 16 of 21)	intron (NM_010123, intron 16 of 21)	5479	NR_034047	100217439		NR_034047		Snora19	MBI-51	small nucleolar RNA, H/ACA box 19	snoRNA
mm_110066.1	chr12	21373607	21373617	-	1	NA	promoter-TSS (NM_009615)	promoter-TSS (NM_009615)	20	NR_102380	11491	Mm.27681	NM_009615	ENSMUSG00000052593	Adam17	CD156b|Tace	a disintegrin and metallopeptidase domain 17	protein-coding
mm_23937.1	chr3	84189986	84190022	+	1	NA	intron (NM_001271725, intron 6 of 11)	intron (NM_001271725, intron 6 of 11)	15366	NR_036654	624713	Mm.442604	NR_036654		Gm6525	EG624713	ribosomal protein L36a pseudogene	pseudo
mm_88565.1	chr10	79665468	79665470	+	1	NA	exon (NM_013591, exon 3 of 5)	exon (NM_013591, exon 3 of 5)	895	NM_013591	17123	Mm.391556	NM_013591	ENSMUSG00000020310	Madcam1	AV211525	mucosal vascular addressin cell adhesion molecule 1	protein-coding
mm_1810.1	chr1	81093983	81093989	+	1	NA	intron (NM_172849, intron 2 of 4)	intron (NM_172849, intron 2 of 4)	16669	NM_172849	241134	Mm.313904	NM_172849	ENSMUSG00000054976	Nyap2	9430031J16Rik|Jr6|Kiaa1486	neuronal tyrosine-phophorylated phosphoinositide 3-kinase adaptor 2	protein-coding
mm_168602.1	chr1	174609777	174609779	+	1	NA	exon (NM_019445, exon 5 of 18)	exon (NM_019445, exon 5 of 18)	107953	NM_019445	54418	Mm.330620	NM_019445	ENSMUSG00000028354	Fmn2	AU024104	formin 2	protein-coding
mm_14753.1	chr2	144697332	144697333	+	1	NA	intron (NM_025314, intron 4 of 5)	B1_Mus1|SINE|Alu	97379	NM_025314	66044	Mm.28109	NM_025314	ENSMUSG00000027430	Dtd1	0610006H08Rik|DUE-B|Hars2	D-tyrosyl-tRNA deacylase 1	protein-coding
mm_133224.1	chr16	76373194	76373213	+	1	NA	promoter-TSS (NM_173440)	promoter-TSS (NM_173440)	-154	NM_173440	268903	Mm.74711	NM_173440	ENSMUSG00000048490	Nrip1	6030458L20Rik|8430438I05Rik|9630050P12|AA959574|AW456757|RIP140	nuclear receptor interacting protein 1	protein-coding
mm_93786.1	chr10	120476946	120477022	-	1	NA	promoter-TSS (NM_010441)	promoter-TSS (NM_010441)	-515	NM_010441	15364	Mm.157190	NM_010441	ENSMUSG00000056758	Hmga2	9430083A20Rik|HMGI-C|Hmgic|pg|pygmy	high mobility group AT-hook 2	protein-coding
mm_125970.1	chr15	76294344	76294355	+	1	NA	promoter-TSS (NM_001195537)	promoter-TSS (NM_001195537)	-85	NM_001195537	100503915	Mm.393455	NM_001195537	ENSMUSG00000071724	Smpd5	ENSMUSG00000071724|Gm10345|MA-nSMase	sphingomyelin phosphodiesterase 5	protein-coding
mm_94870.1	chr11	24078292	24078323	+	1	NA	5' UTR (NM_001242934, exon 1 of 4)	5' UTR (NM_001242934, exon 1 of 4)	251	NM_001159289	14025	Mm.53687	NM_016707	ENSMUSG00000000861	Bcl11a	2810047E18Rik|BCL-11A|Ctip1|D930021L15Rik|Evi9|Evi9a|Evi9b|Evi9c|mKIAA1809	B cell CLL/lymphoma 11A (zinc finger protein)	protein-coding
mm_25456.1	chr3	108415980	108415989	+	1	NA	promoter-TSS (NM_017392)	promoter-TSS (NM_017392)	-490	NM_001004177	53883	Mm.39728	NM_017392	ENSMUSG00000068740	Celsr2	Adgrc2|EGFL2|Flamingo1|flamingo|mKIAA0279|mfmi1	cadherin, EGF LAG seven-pass G-type receptor 2	protein-coding
mm_139031.1	chr17	46161150	46161168	+	1	NA	exon (NM_019581, exon 1 of 12)	exon (NM_019581, exon 1 of 12)	127	NM_001145979	56055	Mm.22147	NM_019581	ENSMUSG00000023952	Gtpbp2	nmf205	GTP binding protein 2	protein-coding
mm_3326.1	chr1	137924989	137925010	+	1	NA	Intergenic	Intergenic	-41456	NR_029795	735252		NR_029795	ENSMUSG00000065565	Mir181a-1	Mirn181a-1|Mirn213|miR-213|mir-181a-1|mmu-mir-213	microRNA 181a-1	ncRNA
mm_141582.1	chr17	32389365	32389411	-	1	NA	promoter-TSS (NM_011717)	promoter-TSS (NM_011717)	51	NR_033525	22404	Mm.274948	NM_011717	ENSMUSG00000024050	Wiz	-	widely-interspaced zinc finger motifs	protein-coding
mm_63952.1	chr7	139894919	139894985	+	1	NA	5' UTR (NM_177261, exon 1 of 31)	5' UTR (NM_177261, exon 1 of 31)	256	NM_177261	76484	Mm.44442	NM_177261	ENSMUSG00000066129	Kndc1	2410012C07Rik|B830014K08Rik|VKIND|very-kind	kinase non-catalytic C-lobe domain (KIND) containing 1	protein-coding
mm_143738.1	chr17	81493446	81493457	-	1	NA	intron (NR_104580, intron 2 of 8)	intron (NR_104580, intron 2 of 8)	244936	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_143199.1	chr17	62761140	62761144	-	1	NA	intron (NM_010109, intron 1 of 3)	intron (NM_010109, intron 1 of 3)	120175	NM_207654	13640	Mm.7978	NM_010109	ENSMUSG00000048915	Efna5	AL-1|AV158822|EFL-5|Ephrin-A5|Epl7|LERK-7|RAGS	ephrin A5	protein-coding
mm_154961.1	chrX	36877585	36877585	+	1	NA	intron (NM_019668, intron 3 of 5)	B1_Mus1|SINE|Alu	3290	NM_019668	22209	Mm.395649	NM_019668	ENSMUSG00000016308	Ube2a	HHR6A|HR6A|Mhr6a	ubiquitin-conjugating enzyme E2A	protein-coding
mm_140903.1	chr17	24150887	24150907	-	1	NA	promoter-TSS (NM_001286662)	promoter-TSS (NM_001286662)	25	NM_001286662	18607	Mm.10504	NM_011062	ENSMUSG00000024122	Pdpk1	Pdk1	3-phosphoinositide dependent protein kinase 1	protein-coding
mm_160642.1	chr9	108985914	108985914	+	1	NA	promoter-TSS (NM_145077)	promoter-TSS (NM_145077)	-249	NM_145077	171530	Mm.388865	NM_145077	ENSMUSG00000049699	Ucn2	Ucn II|Ucn-2|ucn-II	urocortin 2	protein-coding
mm_46202.1	chr5	98031298	98031316	-	1	NA	promoter-TSS (NM_133738)	promoter-TSS (NM_133738)	-345	NM_133738	71914	Mm.24842	NM_133738	ENSMUSG00000029338	Antxr2	2310046B19Rik|AW561899|CMG-2|CMG2|cI-35	anthrax toxin receptor 2	protein-coding
mm_140168.1	chr17	80307318	80307327	+	1	NA	promoter-TSS (NM_001145452)	promoter-TSS (NM_001145452)	-85	NM_001145452	381112	Mm.360004	NM_001145452	ENSMUSG00000054901	Arhgef33	Gm941	Rho guanine nucleotide exchange factor (GEF) 33	protein-coding
mm_6760.1	chr1	84072056	84072082	-	1	NA	intron (NM_001003948, intron 2 of 2)	intron (NM_001003948, intron 2 of 2)	146892	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_153199.1	chr19	34602061	34602075	-	1	NA	promoter-TSS (NM_001101605)	promoter-TSS (NM_001101605)	-100	NM_001101605	667373	Mm.371956	NM_001101605	ENSMUSG00000079339	Ifit1bl1	Gm14446|Ifit1c|OTTMUSG00000016644	interferon induced protein with tetratricpeptide repeats 1B like 1	protein-coding
mm_46740.1	chr5	110836041	110836063	-	1	NA	exon (NM_153571, exon 3 of 6)	exon (NM_153571, exon 3 of 6)	3725	NM_153571	100900	Mm.200231	NM_153571	ENSMUSG00000043510	Hscb	AI325508|AW049829|Hsc20	HscB iron-sulfur cluster co-chaperone	protein-coding
mm_138949.1	chr17	44134731	44134748	+	1	NA	Intergenic	Intergenic	-28931	NM_199016	224794	Mm.255971	NM_199016	ENSMUSG00000023961	Enpp4	4933413N07Rik|AA986363|AI195364|E-NPP 4|Gm90|mKIAA0879	ectonucleotide pyrophosphatase/phosphodiesterase 4	protein-coding
mm_100559.1	chr11	120729667	120729688	+	1	NA	3' UTR (NM_007621, exon 8 of 8)	3' UTR (NM_007621, exon 8 of 8)	2344	NM_007621	12409	Mm.21454	NM_007621	ENSMUSG00000025150	Cbr2	MLCR	carbonyl reductase 2	protein-coding
mm_66134.1	chr7	31076657	31076675	-	1	NA	promoter-TSS (NM_008557)	promoter-TSS (NM_008557)	31	NM_008557	17178	Mm.263847	NM_008557	ENSMUSG00000057092	Fxyd3	Mat8	FXYD domain-containing ion transport regulator 3	protein-coding
mm_129817.1	chr15	83030947	83030958	-	1	NA	intron (NM_001271411, intron 1 of 5)	intron (NM_001271411, intron 1 of 5)	-1002	NM_001271413	74039	Mm.32584	NM_028728	ENSMUSG00000058099	Nfam1	4921501M20Rik|Cnaip	Nfat activating molecule with ITAM motif 1	protein-coding
mm_33623.1	chr4	132731827	132731843	+	1	NA	intron (NM_201368, intron 1 of 2)	intron (NM_201368, intron 1 of 2)	711	NM_201368	381560	Mm.44558	NM_201368	ENSMUSG00000037752	Xkr8	4931440N07Rik|AI597014|Gm1031|XRG8|mXkr8	X-linked Kx blood group related 8	protein-coding
mm_141869.1	chr17	34823437	34823451	-	1	NA	promoter-TSS (NM_011413)	promoter-TSS (NM_011413)	10	NM_011413	625018	Mm.439678	NM_011413		C4a	Slp|SlpA	complement component 4A (Rodgers blood group)	protein-coding
mm_9676.1	chr1	178331457	178331478	-	1	NA	exon (NM_016805, exon 9 of 14)	exon (NM_016805, exon 9 of 14)	6317	NM_016805	51810	Mm.86589	NM_016805	ENSMUSG00000039630	Hnrnpu	AA408410|AI256620|AL024194|AL024437|AW557595|C86794|Hnrpu|SAFA|Sp120|hnRNP U	heterogeneous nuclear ribonucleoprotein U	protein-coding
mm_49788.1	chr6	35178120	35178139	+	1	NA	intron (NM_027513, intron 1 of 42)	CpG	513	NM_027513	70699	Mm.261208	NM_027513	ENSMUSG00000038759	Nup205	3830404O05Rik|AV248391|mKIAA0225	nucleoporin 205	protein-coding
mm_117736.1	chr13	95659648	95659650	-	1	NA	intron (NM_027711, intron 27 of 35)	intron (NM_027711, intron 27 of 35)	-37271	NM_010170	14064	Mm.440952	NM_010170	ENSMUSG00000021675	F2rl2	F730031A08|PAR3	coagulation factor II (thrombin) receptor-like 2	protein-coding
mm_42297.1	chr5	114450860	114450864	+	1	NA	intron (NM_023556, intron 5 of 10)	intron (NM_023556, intron 5 of 10)	6593	NM_023556	17855	Mm.28088	NM_023556	ENSMUSG00000041939	Mvk	2310010A05Rik|AI256848|AI414037|MK	mevalonate kinase	protein-coding
mm_92780.1	chr10	81230774	81230825	-	1	NA	promoter-TSS (NM_178662)	promoter-TSS (NM_178662)	-20	NM_178662	16467	Mm.127681	NM_178662	ENSMUSG00000034958	Atcay	3322401A10Rik|BB077577|BNIP-H|CLAC|hes|ji	ataxia, cerebellar, Cayman type	protein-coding
mm_4234.1	chr1	171370346	171370359	+	1	NA	5' UTR (NM_027893, exon 1 of 9)	5' UTR (NM_027893, exon 1 of 9)	179	NM_001122680	71740	Mm.263414	NM_027893	ENSMUSG00000006411	Nectin4	1200017F15Rik|Prr4|Pvrl4	nectin cell adhesion molecule 4	protein-coding
mm_72780.1	chr8	86745537	86745554	+	1	NA	promoter-TSS (NR_027829)	promoter-TSS (NR_027829)	-154	NR_027829	666945	Mm.391806	NR_027829		Gm10638	ENSMUSG00000074178	predicted gene 10638	ncRNA
mm_46349.1	chr5	102502486	102502498	-	1	NA	intron (NM_146161, intron 1 of 8)	intron (NM_146161, intron 1 of 8)	21101	NM_029270	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding
mm_94297.1	chr11	4077350	4077353	+	1	NA	3' UTR (NM_001029937, exon 12 of 12)	3' UTR (NM_001029937, exon 12 of 12)	12498	NM_001029937	380683	Mm.296806	NM_001029937	ENSMUSG00000054986	Sec14l3	1110069O07Rik	SEC14-like lipid binding 3	protein-coding
mm_15011.1	chr2	152573743	152573754	+	1	NA	intron (NM_207276, intron 1 of 2)	intron (NM_207276, intron 1 of 2)	1004	NM_207276	403172	Mm.84518	NM_207276	ENSMUSG00000056544	Defb21	4930525K10Rik|Gm121	defensin beta 21	protein-coding
mm_82339.1	chr9	10904745	10904765	-	1	NA	promoter-TSS (NM_001170787)	promoter-TSS (NM_001170787)	20	NM_001170787	244682	Mm.187021	NM_001033359	ENSMUSG00000039488	Cntn5	6720426O10Rik|A830025P08Rik|Gm507|NB-2	contactin 5	protein-coding
mm_65498.1	chr7	25718977	25719062	-	1	NA	promoter-TSS (NM_028771)	promoter-TSS (NM_028771)	34	NM_028771	52132	Mm.278798	NM_028771	ENSMUSG00000002608	Ccdc97	1200014H14Rik|2810446P04Rik|AA545218|D7Ertd462e	coiled-coil domain containing 97	protein-coding
mm_104168.1	chr11	87404467	87404509	-	1	NA	promoter-TSS (NM_053269)	promoter-TSS (NM_053269)	7	NM_053269	114714	Mm.37376	NM_053269	ENSMUSG00000007646	Rad51c	R51H3|Rad51l2	RAD51 paralog C	protein-coding
mm_39894.1	chr5	31195588	31195592	+	1	NA	intron (NM_153680, intron 4 of 14)	intron (NM_153680, intron 4 of 14)	2286	NM_153680	266781	Mm.6118	NM_153680	ENSMUSG00000029146	Snx17	5830447M19Rik|AI790646|D5Ertd260e|b2b1625.1Clo|mKIAA0064	sorting nexin 17	protein-coding
mm_4648.1	chr1	180330496	180330536	+	1	NA	promoter-TSS (NR_003623)	promoter-TSS (NR_003623)	33	NR_003623	277333	Mm.389223	NM_199472		Gm5069	EG277333	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_18571.1	chr2	65529276	65529278	-	1	NA	intron (NM_018732, intron 4 of 26)	intron (NM_018732, intron 4 of 26)	38215	NM_018732	20269	Mm.330256	NM_018732	ENSMUSG00000057182	Scn3a	Gm1000|Nav1.3	sodium channel, voltage-gated, type III, alpha	protein-coding
mm_26979.1	chr3	25536795	25536795	-	1	NA	intron (NM_001163387, intron 3 of 5)	intron (NM_001163387, intron 3 of 5)	616512	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_165329.1	chr2	112587414	112587415	+	1	NA	intron (NM_001165935, intron 1 of 4)	intron (NM_001165935, intron 1 of 4)	27732	NM_001165935	74268	Mm.315125	NM_028844	ENSMUSG00000003604	Aven	1700013A01Rik|1700056A21Rik|mAven-L|mAven-S	apoptosis, caspase activation inhibitor	protein-coding
mm_146363.1	chr18	82584413	82584455	+	1	NA	3' UTR (NM_010777, exon 7 of 7)	3' UTR (NM_010777, exon 7 of 7)	29926	NM_001025254	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_110665.1	chr12	61521806	61521818	-	1	NA	promoter-TSS (NR_045049)	promoter-TSS (NR_045049)	8	NR_045049	100504101	Mm.235026	NR_045049		Gm20063	-	predicted gene, 20063	ncRNA
mm_108371.1	chr12	80827608	80827619	+	1	NA	intron (NM_001242419, intron 1 of 6)	intron (NM_001242419, intron 1 of 6)	37081	NM_001242419	217684	Mm.341776	NM_178682	ENSMUSG00000021133	Susd6	4933426M11Rik|mKIAA0247	sushi domain containing 6	protein-coding
mm_148322.1	chr18	83828490	83828517	-	1	NA	Intergenic	Intergenic	258059	NM_001081300	110796	Mm.102136	NM_001081300	ENSMUSG00000046982	Tshz1	5730407I04Rik|D18Bwg1409e|Mtsh1|NY-CO-33|Sdccag33|Tsh1|mKIAA4206|teashirt1	teashirt zinc finger family member 1	protein-coding
mm_11565.1	chr2	32877949	32877978	+	1	NA	intron (NM_146119, intron 1 of 13)	intron (NM_146119, intron 1 of 13)	1829	NM_146119	227737	Mm.301646	NM_146119	ENSMUSG00000026796	Fam129b	9130404D14Rik	family with sequence similarity 129, member B	protein-coding
mm_112651.1	chr13	16019920	16019935	+	1	NA	intron (NM_008380, intron 4 of 4)	intron (NM_008380, intron 4 of 4)	8076	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_64647.1	chr7	4062684	4062688	-	1	NA	intron (NM_001302683, intron 1 of 6)	Lx8b|LINE|L1	518	NM_001302677	52855	Mm.290880	NM_178611	ENSMUSG00000055541	Lair1	5133400O11Rik|BB115266|D7Bwg0421e|Lair-1	leukocyte-associated Ig-like receptor 1	protein-coding
mm_10289.1	chr2	10370495	10370517	+	1	NA	promoter-TSS (NM_001198808)	promoter-TSS (NM_001198808)	55	NM_001198808	353282	Mm.329991	NM_177386	ENSMUSG00000061186	Sfmbt2	D2Wsu23e|D330030P06Rik	Scm-like with four mbt domains 2	protein-coding
mm_87071.1	chr10	29146700	29146741	+	1	NA	exon (NM_026138, exon 2 of 7)	exon (NM_026138, exon 2 of 7)	2724	NM_026138	67412	Mm.390264	NM_026138	ENSMUSG00000038916	Soga3	6330407J23Rik	SOGA family member 3	protein-coding
mm_110758.1	chr12	70111575	70111588	-	1	NA	promoter-TSS (NR_104398)	promoter-TSS (NR_104398)	48	NR_104398	18080	Mm.244047	NM_008697	ENSMUSG00000021068	Nin	3110068G20Rik|AI385615|AU024711|mKIAA1565	ninein	protein-coding
mm_164227.1	chr15	86234708	86234728	+	1	NA	intron (NM_145476, intron 1 of 12)	intron (NM_145476, intron 1 of 12)	20259	NM_145476	223754	Mm.28904	NM_145476	ENSMUSG00000051864	Tbc1d22a	BC023106|D15Ertd781e	TBC1 domain family, member 22a	protein-coding
mm_69971.1	chr7	142377046	142377060	-	1	NA	exon (NM_009983, exon 7 of 9)	exon (NM_009983, exon 7 of 9)	-3307	NM_001347541	320802	Mm.154486	NM_177265	ENSMUSG00000045777	Ifitm10	6330512M04Rik|AI848576|DSPA3	interferon induced transmembrane protein 10	protein-coding
mm_112357.1	chr12	118966391	118966393	-	1	NA	promoter-TSS (NM_029961)	promoter-TSS (NM_029961)	29	NM_029961	77706	Mm.261496	NM_029961	ENSMUSG00000072791	Abcb5	9230106F14Rik	ATP-binding cassette, sub-family B (MDR/TAP), member 5	protein-coding
mm_12578.1	chr2	73274714	73274725	+	1	NA	3' UTR (NM_001005343, exon 2 of 2)	3' UTR (NM_001005343, exon 2 of 2)	2793	NM_001005343	381373	Mm.330293	NM_001005343	ENSMUSG00000068859	Sp9	-	trans-acting transcription factor 9	protein-coding
mm_71896.1	chr8	69996739	69996807	+	1	NA	promoter-TSS (NM_001286450)	promoter-TSS (NM_001286450)	-389	NM_145596	234366	Mm.270044	NM_145596	ENSMUSG00000036180	Gatad2a	1110066C11Rik|BC031407|C80248	GATA zinc finger domain containing 2A	protein-coding
mm_46637.1	chr5	108525423	108525433	-	1	NA	exon (NM_007756, exon 3 of 4)	exon (NM_007756, exon 3 of 4)	24599	NM_007756	12889	Mm.5195	NM_007756	ENSMUSG00000033615	Cplx1	921-S	complexin 1	protein-coding
mm_94056.1	chr10	128211789	128211823	-	1	NA	promoter-TSS (NM_025716)	promoter-TSS (NM_025716)	-12	NM_025716	66701	Mm.29694	NM_025716	ENSMUSG00000051346	Spryd4	4633402N23Rik|AA114801	SPRY domain containing 4	protein-coding
mm_8169.1	chr1	137325836	137325841	-	1	NA	Intergenic	Intergenic	-365390	NM_030676	26424	Mm.16794	NM_030676	ENSMUSG00000026398	Nr5a2	AU020803|D1Ertd308e|Ftf|LRH-1|UF2-H3B	nuclear receptor subfamily 5, group A, member 2	protein-coding
mm_164641.1	chr17	34804466	34804474	-	1	NA	promoter-TSS (NM_009995)	promoter-TSS (NM_009995)	-44	NM_009995	13079	Mm.440407	NM_009995	ENSMUSG00000024365	Cyp21a1	21-OH|21OH|21OHA|21OHB|CYP21OH-A|Cyp21|Cyp21-ps1|Cyp21B|Cyp21a2-ps|Cyp21a2ps|Oh21-1|Oh21-2	cytochrome P450, family 21, subfamily a, polypeptide 1	protein-coding
mm_136716.1	chr17	7945586	7945636	+	1	NA	promoter-TSS (NM_025789)	promoter-TSS (NM_025789)	-3	NM_025789	66832	Mm.29830	NM_025789	ENSMUSG00000073471	Rsph3a	1700012G05Rik|4930524H12Rik|R74860|Rshl2|Rshl2a	radial spoke 3A homolog (Chlamydomonas)	protein-coding
mm_119430.1	chr14	46084025	46084026	+	1	NA	promoter-TSS (NR_002875)	promoter-TSS (NR_002875)	-2	NR_002875	218963	Mm.282093	NR_002875		Gm1821	-	ubiquitin pseudogene	pseudo
mm_87514.1	chr10	52686845	52686846	+	1	NA	Intergenic	ORR1B2-int|LTR|ERVL-MaLR	-3656	NM_178675	215085	Mm.338690	NM_178675	ENSMUSG00000038602	Slc35f1	Duf6|E130016L02	solute carrier family 35, member F1	protein-coding
mm_170514.1	chr19	29367435	29367436	+	1	NA	promoter-TSS (NM_021893)	promoter-TSS (NM_021893)	-3	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_40842.1	chr5	73292795	73292819	+	1	NA	promoter-TSS (NM_001159889)	promoter-TSS (NM_001159889)	13	NM_001159888	68095	Mm.247039	NM_023429	ENSMUSG00000029152	Ociad1	6030432N09Rik|AI481327|AW557942|Asrij|B230209J16Rik|BB021357|Emi2|Imi2|OCIA|TPA018	OCIA domain containing 1	protein-coding
mm_16153.1	chr2	172353290	172353296	+	1	NA	3' UTR (NM_025912, exon 3 of 3)	3' UTR (NM_025912, exon 3 of 3)	7716	NM_025912	67017	Mm.30013	NM_025912	ENSMUSG00000027495	Fam210b	2010011I20Rik|AI430961|AV108736	family with sequence similarity 210, member B	protein-coding
mm_36182.1	chr4	62208675	62208698	-	1	NA	promoter-TSS (NM_009554)	promoter-TSS (NM_009554)	-140	NM_001290350	22696	Mm.5011	NM_009554	ENSMUSG00000028389	Zfp37	Tzn|Zfp-37	zinc finger protein 37	protein-coding
mm_4314.1	chr1	171845847	171845848	+	1	NA	intron (NM_001289470, intron 2 of 8)	intron (NM_001289470, intron 2 of 8)	6150	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_157153.1	chrX	9462880	9462890	-	1	NA	intron (NM_007807, intron 3 of 12)	intron (NM_007807, intron 3 of 12)	6439	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_146356.1	chr18	82575597	82575612	+	1	NA	exon (NM_001025251, exon 5 of 7)	exon (NM_001025251, exon 5 of 7)	21096	NM_001025254	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_109000.1	chr12	103232623	103232626	+	1	NA	intron (NM_133364, intron 3 of 4)	intron (NM_133364, intron 3 of 4)	9522	NM_133364	170952	Mm.217019	NM_133364	ENSMUSG00000041669	Prima1	B230212M13Rik|BB120497|PRiMA	proline rich membrane anchor 1	protein-coding
mm_20436.1	chr2	129306639	129306649	-	1	NA	exon (NM_010554, exon 4 of 7)	exon (NM_010554, exon 4 of 7)	3328	NM_010554	16175	Mm.15534	NM_010554	ENSMUSG00000027399	Il1a	Il-1a	interleukin 1 alpha	protein-coding
mm_66084.1	chr7	30957221	30957267	-	1	NA	promoter-TSS (NM_011680)	promoter-TSS (NM_011680)	-441	NM_011680	22282	Mm.322453	NM_011680	ENSMUSG00000058239	Usf2	Usf-2|bHLHb12	upstream transcription factor 2	protein-coding
mm_94548.1	chr11	11115785	11115790	+	1	NA	intron (NM_177033, intron 1 of 3)	CpG	1771	NM_177033	319922	Mm.337851	NM_177033	ENSMUSG00000050830	Vwc2	A930041G11Rik|G11|PSST739|UNQ739|cradin	von Willebrand factor C domain containing 2	protein-coding
mm_125303.1	chr15	37233311	37233337	+	1	NA	5' UTR (NM_026496, exon 1 of 16)	5' UTR (NM_026496, exon 1 of 16)	288	NM_026496	252973	Mm.244612	NM_026496	ENSMUSG00000022286	Grhl2	0610015A08Rik|BOM|Tcfcp2l3|clft3	grainyhead-like 2 (Drosophila)	protein-coding
mm_172448.1	chr7	31280128	31280128	-	1	NA	Intergenic	L1Md_T|LINE|L1	11688	NM_020563	57426	Mm.6205	NM_020563	ENSMUSG00000062556	Scgb1b2	Abpa2|Abph|Apbh|LGP|Mja1l|Scgb1b1	secretoglobin, family 1B, member 2	protein-coding
mm_40646.1	chr5	65013383	65013387	+	1	NA	intron (NM_026667, intron 6 of 13)	RMER10B|LTR|ERVL	43067	NR_030577	100124451		NR_030577	ENSMUSG00000077042	Mir574	Mirn574|mir-574|mmu-mir-574	microRNA 574	ncRNA
mm_103375.1	chr11	75344321	75344324	-	1	NA	intron (NM_001164223, intron 1 of 17)	PB1|SINE|Alu	4061	NM_001164223	68275	Mm.102574	NM_026653	ENSMUSG00000000751	Rpa1	5031405K23Rik|70kDa|AA589576|AW557552|RF-A|RP-A|Rpa	replication protein A1	protein-coding
mm_127532.1	chr15	102102199	102102242	+	1	NA	promoter-TSS (NM_153533)	promoter-TSS (NM_153533)	-768	NM_153533	209039	Mm.29389	NM_153533	ENSMUSG00000037003	Tns2	C1-ten|Tenc1|nep|nph	tensin 2	protein-coding
mm_96451.1	chr11	67559832	67559834	+	1	NA	intron (NM_008088, intron 1 of 13)	intron (NM_008088, intron 1 of 13)	-26667	NM_001109657	14457	Mm.40338	NM_008088	ENSMUSG00000033066	Gas7	AW124766|B230343A10Rik|Gas7-cb	growth arrest specific 7	protein-coding
mm_19777.1	chr2	106650353	106650374	-	1	NA	promoter-TSS (NR_137201)	promoter-TSS (NR_137201)	1	NR_137201	102640562	Mm.404175	NR_137201	ENSMUSG00000085218	BB218582	-	expressed sequence BB218582	ncRNA
mm_4355.1	chr1	171917490	171917503	+	1	NA	promoter-TSS (NM_030710)	promoter-TSS (NM_030710)	34	NM_001347186	30925	Mm.486404	NM_030710	ENSMUSG00000015314	Slamf6	KAL1|KAL1b|Ly108|NTB-A|NTBA|SF2000	SLAM family member 6	protein-coding
mm_8619.1	chr1	156037396	156037414	-	1	NA	promoter-TSS (NM_144791)	promoter-TSS (NM_144791)	-925	NM_001160018	208263	Mm.211654	NM_144791	ENSMUSG00000026466	Tor1aip1	LAP1|Lap1B	torsin A interacting protein 1	protein-coding
mm_53917.1	chr6	4047574	4047580	-	1	NA	promoter-TSS (NR_131108)	promoter-TSS (NR_131108)	7	NR_131108	78034	Mm.243851	NR_131108	ENSMUSG00000107681	4930528H21Rik	-	RIKEN cDNA 4930528H21 gene	ncRNA
mm_127646.1	chr15	102485971	102485990	+	1	NA	exon (NM_011042, exon 9 of 14)	exon (NM_011042, exon 9 of 14)	15348	NM_001174073	18521	Mm.236513	NM_011042	ENSMUSG00000056851	Pcbp2	AW412548|Hnrpx|alphaCP-2	poly(rC) binding protein 2	protein-coding
mm_52357.1	chr6	112459752	112459758	+	1	NA	5' UTR (NM_007617, exon 1 of 2)	5' UTR (NM_007617, exon 1 of 2)	250	NM_007617	12391	Mm.3924	NM_007617	ENSMUSG00000062694	Cav3	AI385751|Cav-3|M-cav	caveolin 3	protein-coding
mm_161721.1	chr17	27556653	27556653	+	1	NA	promoter-TSS (NM_001166545)	promoter-TSS (NM_001166545)	0	NM_001166476	111241	Mm.426212	NM_001166476	ENSMUSG00000078249	Hmga1-rs1	ENSMUSG00000041059|Hmgi-rs1	high mobility group AT-hook I, related sequence 1	protein-coding
mm_167806.1	chr9	123928797	123928840	-	1	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	39874	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_130690.1	chr15	100682029	100682041	-	1	NA	intron (NM_033612, intron 5 of 7)	B3A|SINE|B2	5885	NM_033612	109901	Mm.2131	NM_033612	ENSMUSG00000023031	Cela1	1810009A17Rik|1810062B19Rik|Ela-1|Ela1|PC-TsF	chymotrypsin-like elastase family, member 1	protein-coding
mm_149260.1	chr19	10525585	10525605	+	1	NA	promoter-TSS (NM_025333)	promoter-TSS (NM_025333)	351	NM_172302	269061	Mm.490260	NM_172302	ENSMUSG00000034820	Cpsf7	5730453I16Rik|AL022757|C330017N18Rik	cleavage and polyadenylation specific factor 7	protein-coding
mm_151368.1	chr19	55931465	55931480	+	1	NA	exon (NM_001142921, exon 12 of 12)	exon (NM_001142921, exon 12 of 12)	36151	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_60937.1	chr7	46861482	46861494	+	1	NA	intron (NM_013580, intron 1 of 7)	intron (NM_013580, intron 1 of 7)	225	NM_013580	16833	Mm.16563	NM_013580	ENSMUSG00000030851	Ldhc	LDH-C4|Ldh-3|Ldh-x|Ldh3|Ldhc4	lactate dehydrogenase C	protein-coding
mm_137821.1	chr17	30169839	30169843	+	1	NA	intron (NM_148926, intron 3 of 4)	MYSERV6-int|LTR|ERVK	86694	NR_105839	102465223		NR_105839	ENSMUSG00000098522	Mir6412	Gm27364|mmu-mir-6412	microRNA 6412	ncRNA
mm_31860.1	chr4	79327664	79327665	+	1	NA	Intergenic	L1_Mur2|LINE|L1	733617	NR_131142	623726		NR_131142		A430085M09Rik	EG623726	RIKEN cDNA A430085M09 gene	ncRNA
mm_122688.1	chr14	52020641	52020653	-	1	NA	promoter-TSS (NM_001253694)	promoter-TSS (NM_001253694)	86	NM_001253696	69890	Mm.475652	NM_027248	ENSMUSG00000049295	Zfp219	2010302A17Rik	zinc finger protein 219	protein-coding
mm_31191.1	chr4	43578710	43578772	+	1	NA	promoter-TSS (NM_172866)	promoter-TSS (NM_172866)	6	NM_172866	242406	Mm.259311	NM_172866	ENSMUSG00000028468	Rgp1	1110029E03Rik|AI527196|F730001J03|mKIAA0258	RAB6A GEF compex partner 1	protein-coding
mm_167051.1	chr7	83659418	83659427	-	1	NA	intron (NM_010551, intron 12 of 18)	intron (NM_010551, intron 12 of 18)	27405	NM_023377	170460	Mm.357953	NM_023377	ENSMUSG00000046027	Stard5	2310058G22Rik|AI607880|D7Ertd152e	StAR-related lipid transfer (START) domain containing 5	protein-coding
mm_24399.1	chr3	90294093	90294104	+	1	NA	Intergenic	Intergenic	23949	NR_105979	102465612		NR_105979	ENSMUSG00000099199	Mir7012	Gm27370|mmu-mir-7012	microRNA 7012	ncRNA
mm_113104.1	chr13	24397412	24397422	+	1	NA	intron (NM_001284519, intron 3 of 17)	intron (NM_001284519, intron 3 of 17)	-17705	NM_007717	12763	Mm.8396	NM_007717	ENSMUSG00000016756	Cmah	-	cytidine monophospho-N-acetylneuraminic acid hydroxylase	protein-coding
mm_30315.1	chr3	151731465	151731482	-	1	NA	3' UTR (NM_133871, exon 8 of 8)	3' UTR (NM_133871, exon 8 of 8)	18486	NM_133871	99899	Mm.30756	NM_133871	ENSMUSG00000028037	Ifi44	A430056A10Rik|AW261460|MTAP44|p44	interferon-induced protein 44	protein-coding
mm_55293.1	chr6	54566500	54566508	-	1	NA	promoter-TSS (NM_027268)	promoter-TSS (NM_027268)	-122	NM_027268	69938	Mm.41557	NM_027268	ENSMUSG00000019124	Scrn1	2810019K23Rik|6330535A03Rik|AI852905|SES1|mKIAA0193	secernin 1	protein-coding
mm_108551.1	chr12	84411161	84411163	+	1	NA	exon (NM_028377, exon 2 of 12)	exon (NM_028377, exon 2 of 12)	2094	NM_028377	72873	Mm.440428	NM_028377	ENSMUSG00000057265	Bbof1	2900006K08Rik|AI427784|Ccdc176	basal body orientation factor 1	protein-coding
mm_147795.1	chr18	61652450	61652464	-	1	NA	intron (NR_045402, intron 2 of 4)	intron (NR_045402, intron 2 of 4)	-3199	NR_029601	387161		NR_029601	ENSMUSG00000065445	Mir143	Mirn143|mir-143|mmu-mir-143	microRNA 143	ncRNA
mm_60869.1	chr7	45924203	45924242	+	1	NA	Intergenic	Intergenic	-2796	NM_010129	13732	Mm.20829	NM_010129	ENSMUSG00000040212	Emp3	H-4|H4|HNMP-1|MI-35|Ymp	epithelial membrane protein 3	protein-coding
mm_18422.1	chr2	60751654	60751680	-	1	NA	TTS (NM_001141932)	TTS (NM_001141932)	-29064	NM_001159564	16420	Mm.98193	NM_021359	ENSMUSG00000026971	Itgb6	2210409C20Rik|4831415H04Rik	integrin beta 6	protein-coding
mm_88679.1	chr10	80053560	80053570	+	1	NA	promoter-TSS (NM_008162)	promoter-TSS (NM_008162)	77	NM_008162	625249	Mm.332810	NM_008162	ENSMUSG00000075706	Gpx4	GPx-4|GSHPx-4|PHGPx|mtPHGPx|snGPx	glutathione peroxidase 4	protein-coding
mm_138483.1	chr17	35195533	35195545	+	1	NA	TTS (NR_105939)	TTS (NR_105939)	567	NR_105939	102465588		NR_105939	ENSMUSG00000098291	Mir6973a	Gm27967|mmu-mir-6973a	microRNA 6973a	ncRNA
mm_149115.1	chr19	8967080	8967102	+	1	NA	promoter-TSS (NM_026007)	promoter-TSS (NM_026007)	50	NM_026007	67160	Mm.247762	NM_026007	ENSMUSG00000071644	Eef1g	2610301D06Rik|AA407312|EF1G	eukaryotic translation elongation factor 1 gamma	protein-coding
mm_85307.1	chr9	100987977	100988004	-	1	NA	intron (NM_025835, intron 9 of 14)	intron (NM_025835, intron 9 of 14)	46894	NM_001311149	66904	Mm.335385	NM_025835	ENSMUSG00000032527	Pccb	1300012P06Rik|AI314687|R74805	propionyl Coenzyme A carboxylase, beta polypeptide	protein-coding
mm_64051.1	chr7	140835525	140835537	+	1	NA	promoter-TSS (NM_029821)	promoter-TSS (NM_029821)	35	NM_029821	76974	Mm.272359	NM_029821	ENSMUSG00000025481	Urah	1190003J15Rik|2810420C16Rik	urate (5-hydroxyiso-) hydrolase	protein-coding
mm_107233.1	chr12	26478162	26478189	+	1	NA	3' UTR (NM_020557, exon 5 of 5)	3' UTR (NM_020557, exon 5 of 5)	8960	NM_020557	22169	Mm.271839	NM_020557	ENSMUSG00000020638	Cmpk2	1200004E04Rik|TDKI|Tyki	cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial	protein-coding
mm_123690.1	chr14	69637026	69637029	-	1	NA	intron (NM_033325, intron 2 of 13)	B4|SINE|B4	27551	NM_033325	94352	Mm.116714	NM_033325	ENSMUSG00000034205	Loxl2	1110004B06Rik|4930526G11Rik|9430067E15Rik	lysyl oxidase-like 2	protein-coding
mm_28364.1	chr3	89871054	89871067	-	1	NA	3' UTR (NM_010559, exon 10 of 10)	3' UTR (NM_010559, exon 10 of 10)	39690	NM_172530	214547	Mm.225	NM_172530	ENSMUSG00000046280	She	9430022A14	src homology 2 domain-containing transforming protein E	protein-coding
mm_85427.1	chr9	103499321	103499326	-	1	NA	exon (NM_178638, exon 4 of 6)	exon (NM_178638, exon 4 of 6)	-18995	NM_001002896	107993	Mm.335403	NM_001002896	ENSMUSG00000032556	Bfsp2	AI448593|CP49	beaded filament structural protein 2, phakinin	protein-coding
mm_59546.1	chr7	27927593	27927597	+	1	NA	intron (NM_028538, intron 1 of 3)	intron (NM_028538, intron 1 of 3)	1835	NM_028538	73430	Mm.379224	NM_028538	ENSMUSG00000070709	Zfp974	1700049G17Rik|AV321011|BB026409	zinc finger protein 974	protein-coding
mm_90928.1	chr10	12827291	12827307	-	1	NA	intron (NM_011682, intron 1 of 73)	intron (NM_011682, intron 1 of 73)	34436	NM_011682	22288	Mm.331784	NM_011682	ENSMUSG00000019820	Utrn	AA589569|DRP|Dmdl	utrophin	protein-coding
mm_74292.1	chr8	125960288	125960314	+	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	-34801	NM_008430	16525	Mm.10800	NM_008430	ENSMUSG00000033998	Kcnk1	AI788889|TWIK-1	potassium channel, subfamily K, member 1	protein-coding
mm_17416.1	chr2	27248336	27248346	-	1	NA	Intergenic	Intergenic	-1038	NM_138665	192166	Mm.278467	NM_138665	ENSMUSG00000009614	Sardh	-	sarcosine dehydrogenase	protein-coding
mm_144847.1	chr18	36606174	36606189	+	1	NA	intron (NM_175375, intron 10 of 33)	Lx8|LINE|L1	45578	NM_175375	108857	Mm.482287	NM_175375	ENSMUSG00000024483	Ankhd1	1110004O12Rik|4933432B13Rik|9130019P20Rik|A530027J04Rik|A630021B20Rik|AA571404|Mask|mFLJ00246|mKIAA1085	ankyrin repeat and KH domain containing 1	protein-coding
mm_32861.1	chr4	118410871	118410882	+	1	NA	intron (NM_020000, intron 1 of 6)	intron (NM_020000, intron 1 of 6)	1539	NM_020000	80509	Mm.259567	NM_020000	ENSMUSG00000006392	Med8	2210021A15Rik|AB041805|ARC32	mediator complex subunit 8	protein-coding
mm_134784.1	chr16	23988564	23988574	-	1	NA	promoter-TSS (NM_009744)	promoter-TSS (NM_009744)	43	NM_009744	12053	Mm.347398	NM_009744	ENSMUSG00000022508	Bcl6	Bcl5	B cell leukemia/lymphoma 6	protein-coding
mm_139857.1	chr17	69969318	69969326	+	1	NA	5' UTR (NM_001347412, exon 1 of 14)	5' UTR (NM_001347412, exon 1 of 14)	249	NM_001347411	224997	Mm.311840	NM_027712	ENSMUSG00000003279	Dlgap1	4933422O14Rik|9630002F18|AI845682|AI848168|BB075781|D17Bwg0511e|GKAP/SAPAP|GKPA/SAPAP|Gkap|Sapap1|mKIAA4162	discs, large (Drosophila) homolog-associated protein 1	protein-coding
mm_83988.1	chr9	57434938	57434953	-	1	NA	exon (NM_176831, exon 3 of 7)	exon (NM_176831, exon 3 of 7)	5169	NM_176831	66812	Mm.250508	NM_176831	ENSMUSG00000063849	Ppcdc	1810057I13Rik|8430432M10Rik	phosphopantothenoylcysteine decarboxylase	protein-coding
mm_10973.1	chr2	25706978	25706999	+	1	NA	exon (NM_023326, exon 1 of 1)	exon (NM_023326, exon 1 of 1)	109	NM_023326	107771	Mm.330057	NM_023326	ENSMUSG00000049086	Bmyc	2900002K07Rik|AW060705|Mycb	brain expressed myelocytomatosis oncogene	protein-coding
mm_37842.1	chr4	132078497	132078499	-	1	NA	Intergenic	YREP_Mm|Unknown|Unknown	-3185	NM_001128607	269587	Mm.30038	NM_183428	ENSMUSG00000028906	Epb41	4.1R|AI415518|D4Ertd442e|Elp-1|Elp1|Epb4.1|mKIAA4056	erythrocyte membrane protein band 4.1	protein-coding
mm_165671.1	chr3	89245228	89245263	-	1	NA	promoter-TSS (NM_001039466)	promoter-TSS (NM_001039466)	-46	NM_001039466	360213	Mm.331156	NM_183037	ENSMUSG00000042766	Trim46	TRIFIC	tripartite motif-containing 46	protein-coding
mm_144256.1	chr18	11034681	11034684	+	1	NA	Intergenic	PB1D10|SINE|Alu	-17828	NM_010258	14465	Mm.329287	NM_010258	ENSMUSG00000005836	Gata6	AA410133|GATA-6	GATA binding protein 6	protein-coding
mm_88452.1	chr10	77554034	77554045	+	1	NA	intron (NM_008404, intron 8 of 15)	intron (NM_008404, intron 8 of 15)	23691	NM_008404	16414	Mm.1137	NM_008404	ENSMUSG00000000290	Itgb2	2E6|AI528527|Cd18|LAD|LCAMB|Lfa1|MF17	integrin beta 2	protein-coding
mm_134320.1	chr16	16073393	16073399	-	1	NA	intron (NM_146068, intron 5 of 19)	intron (NM_146068, intron 5 of 19)	73455	NM_146068	224008	Mm.244703	NM_146068	ENSMUSG00000041974	Spidr	2310008H04Rik|Kiaa0146	scaffolding protein involved in DNA repair	protein-coding
mm_136513.1	chr16	97171066	97171103	-	1	NA	promoter-TSS (NM_031174)	promoter-TSS (NM_031174)	-349	NM_031174	13508	Mm.102437	NM_031174	ENSMUSG00000050272	Dscam	4932410A21Rik	Down syndrome cell adhesion molecule	protein-coding
mm_152335.1	chr19	9978425	9978431	-	1	NA	Intergenic	Intergenic	-2172	NR_073181	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
mm_88750.1	chr10	80299085	80299126	+	1	NA	intron (NR_038088, intron 1 of 4)	intron (NR_038088, intron 1 of 4)	-2715	NM_011789	23805	Mm.57247	NM_011789	ENSMUSG00000020135	Apc2	AI852447|APCL|R75424	adenomatosis polyposis coli 2	protein-coding
mm_110668.1	chr12	64965497	64965538	-	1	NA	promoter-TSS (NM_177805)	promoter-TSS (NM_177805)	19	NM_025707	66689	Mm.248678	NM_025707	ENSMUSG00000020948	Klhl28	2810440N09Rik|4122402F11Rik|4931401E10Rik|Btbd5	kelch-like 28	protein-coding
mm_2233.1	chr1	91044451	91044462	+	1	NA	intron (NM_001111312, intron 1 of 12)	intron (NM_001111312, intron 1 of 12)	-8988	NM_001310732	16978	Mm.45039	NM_008515	ENSMUSG00000026305	Lrrfip1	AU024550|Fliiap1	leucine rich repeat (in FLII) interacting protein 1	protein-coding
mm_73899.1	chr8	119437140	119437154	+	1	NA	promoter-TSS (NM_027950)	promoter-TSS (NM_027950)	-15	NM_027950	71839	Mm.272357	NM_027950	ENSMUSG00000074063	Osgin1	1700012B18Rik|Okl38	oxidative stress induced growth inhibitor 1	protein-coding
mm_7014.1	chr1	86504083	86504101	-	1	NA	Intergenic	CpG	-22644	NM_008972	19231	Mm.19187	NM_008972	ENSMUSG00000026238	Ptma	Thym	prothymosin alpha	protein-coding
mm_91912.1	chr10	60294693	60294744	-	1	NA	exon (NM_011179, exon 5 of 15)	exon (NM_011179, exon 5 of 15)	10257	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_131850.1	chr16	23060448	23060454	+	1	NA	exon (NM_001102411, exon 2 of 10)	exon (NM_001102411, exon 2 of 10)	2151	NM_001102412	16644	Mm.2160	NM_023125	ENSMUSG00000022875	Kng1	Kng	kininogen 1	protein-coding
mm_30020.1	chr3	135665368	135665378	-	1	NA	intron (NM_008689, intron 3 of 24)	intron (NM_008689, intron 3 of 24)	26174	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_86132.1	chr9	116366304	116366330	-	1	NA	Intergenic	Intergenic	-190954	NM_009371	21813	Mm.172346	NM_009371	ENSMUSG00000032440	Tgfbr2	1110020H15Rik|AU042018|DNIIR|RIIDN|TBR-II|TbetaR-II|TbetaRII	transforming growth factor, beta receptor II	protein-coding
mm_98171.1	chr11	87751909	87751924	+	1	NA	Intergenic	Intergenic	-4948	NR_029555	387160		NR_029555	ENSMUSG00000105196	Mir142	Mirn142|miR-142|mir-142a|mmu-mir-142|mmu-mir-142a	microRNA 142	ncRNA
mm_84402.1	chr9	65555128	65555148	-	1	NA	3' UTR (NM_153119, exon 6 of 6)	3' UTR (NM_153119, exon 6 of 6)	24949	NM_153119	102595	Mm.247303	NM_153119	ENSMUSG00000050721	Plekho2	AI840980|Plekhq1	pleckstrin homology domain containing, family O member 2	protein-coding
mm_74406.1	chr8	3467618	3467662	-	1	NA	promoter-TSS (NM_026951)	promoter-TSS (NM_026951)	8	NM_026951	69129	Mm.45279	NM_026951	ENSMUSG00000069633	Pex11g	1810022F11Rik|1810049N02Rik|Pex11c|Pex11gamma	peroxisomal biogenesis factor 11 gamma	protein-coding
mm_98893.1	chr11	97844518	97844531	+	1	NA	Intergenic	Intergenic	3744	NM_001080935	68127	Mm.110270	NM_001080935	ENSMUSG00000050538	B230217C12Rik	AI840637	RIKEN cDNA B230217C12 gene	protein-coding
mm_101181.1	chr11	17000389	17000400	-	1	NA	intron (NM_019549, intron 1 of 9)	intron (NM_019549, intron 1 of 9)	8324	NM_019549	56193	Mm.98232	NM_019549	ENSMUSG00000020120	Plek	2010300B13Rik	pleckstrin	protein-coding
mm_172526.1	chr7	84835040	84835040	-	1	NA	Intergenic	Intergenic	-18531	NM_146415	258410	Mm.484702	NM_146415	ENSMUSG00000070460	Olfr291	MOR254-2	olfactory receptor 291	protein-coding
mm_33329.1	chr4	129107773	129107794	+	1	NA	intron (NM_025452, intron 1 of 5)	intron (NM_025452, intron 1 of 5)	2235	NM_001290706	66260	Mm.25295	NM_025452	ENSMUSG00000028786	Tmem54	1810017F10Rik|AI507302	transmembrane protein 54	protein-coding
mm_5015.1	chr1	192854917	192854937	+	1	NA	promoter-TSS (NR_131748)	promoter-TSS (NR_131748)	-1	NR_131748	100503471	Mm.380305	NR_131748		Gm15867	OTTMUSG00000027054	predicted gene 15867	ncRNA
mm_18431.1	chr2	60807413	60807426	-	1	NA	intron (NM_020296, intron 2 of 13)	intron (NM_020296, intron 2 of 13)	74019	NM_001141932	56878	Mm.259667	NM_020296	ENSMUSG00000026970	Rbms1	2600014B10Rik|AI255215|MSSP-1|MSSP-2|MSSP-3|YC1	RNA binding motif, single stranded interacting protein 1	protein-coding
mm_73905.1	chr8	119447039	119447135	+	1	NA	TTS (NM_027950)	TTS (NM_027950)	368	NM_054095	117148	Mm.356184	NM_054095	ENSMUSG00000031837	Necab2	Efcbp2	N-terminal EF-hand calcium binding protein 2	protein-coding
mm_171105.1	chr3	133544378	133544379	-	1	NA	promoter-TSS (NM_001346736)	promoter-TSS (NM_001346736)	12	NM_001346736	214133	Mm.347816	NM_145989	ENSMUSG00000040943	Tet2	Ayu17-449|E130014J05Rik|mKIAA1546	tet methylcytosine dioxygenase 2	protein-coding
mm_95947.1	chr11	58386816	58386824	+	1	NA	exon (NM_001083884, exon 6 of 7)	exon (NM_001083884, exon 6 of 7)	6174	NM_001330197	70163	Mm.24119	NM_027339	ENSMUSG00000013643	Lypd8	2210415F13Rik	LY6/PLAUR domain containing 8	protein-coding
mm_88203.1	chr10	70169157	70169169	+	1	NA	exon (NM_001111121, exon 5 of 9)	exon (NM_001111121, exon 5 of 9)	-35501	NM_001304739	69563	Mm.64672	NM_001304739	ENSMUSG00000019933	Mrln	2310015B20Rik|Mln	myoregulin	protein-coding
mm_96493.1	chr11	67922371	67922387	+	1	NA	promoter-TSS (NM_173754)	promoter-TSS (NM_173754)	-226	NM_173754	216835	Mm.158885	NM_173754	ENSMUSG00000020905	Usp43	-	ubiquitin specific peptidase 43	protein-coding
mm_56892.1	chr6	119109006	119109017	-	1	NA	promoter-TSS (NM_001159534)	promoter-TSS (NM_001159534)	-516	NM_001256002	12288	Mm.41628	NM_009781	ENSMUSG00000051331	Cacna1c	Cav1.2|Cchl1a1|D930026N18Rik|MBC|MELC-CC	calcium channel, voltage-dependent, L type, alpha 1C subunit	protein-coding
mm_3387.1	chr1	140246013	140246044	+	1	NA	promoter-TSS (NM_001081027)	promoter-TSS (NM_001081027)	-229	NM_001081027	240776	Mm.483845	NM_001081027	ENSMUSG00000052726	Kcnt2	E330038N15Rik|Slick	potassium channel, subfamily T, member 2	protein-coding
mm_32523.1	chr4	108847828	108847895	+	1	NA	promoter-TSS (NM_029571)	promoter-TSS (NM_029571)	4	NM_029571	100087	Mm.440007	NM_029571	ENSMUSG00000073775	Kti12	1110001A12Rik|AI326810|AU014758	KTI12 homolog, chromatin associated	protein-coding
mm_110560.1	chr12	55492588	55492605	-	1	NA	promoter-TSS (NM_010907)	promoter-TSS (NM_010907)	51	NM_010907	18035	Mm.170515	NM_010907	ENSMUSG00000021025	Nfkbia	AI462015|Nfkbi	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, alpha	protein-coding
mm_128974.1	chr15	74832463	74832471	-	1	NA	Intergenic	Intergenic	9176	NM_001033229	110115	Mm.322606	NM_001033229	ENSMUSG00000075604	Cyp11b1	AA389061|CPN1|Cyp11b|Cyp11b-1|FHI	cytochrome P450, family 11, subfamily b, polypeptide 1	protein-coding
mm_116561.1	chr13	46736887	46736925	-	1	NA	Intergenic	Intergenic	-9057	NM_175749	218210	Mm.255398	NM_175749	ENSMUSG00000021374	Nup153	B130015D15Rik|C88147	nucleoporin 153	protein-coding
mm_151102.1	chr19	47857992	47858007	+	1	NA	exon (NM_010362, exon 3 of 6)	exon (NM_010362, exon 3 of 6)	3026	NM_010362	14873	Mm.378931	NM_010362	ENSMUSG00000025068	Gsto1	AA407097|AI194287|AU018802|Gsto-1|Gstx|Spg-r|p28	glutathione S-transferase omega 1	protein-coding
mm_85961.1	chr9	112139067	112139077	-	1	NA	intron (NM_001177617, intron 10 of 14)	intron (NM_001177617, intron 10 of 14)	-20361	NR_029823	723815		NR_029823	ENSMUSG00000065441	Mir128-2	Mirn128-2|Mirn128b|mir-128-2|mir-128b	microRNA 128-2	ncRNA
mm_22369.1	chr2	181147355	181147396	-	1	NA	TTS (NM_007906)	TTS (NM_007906)	9640	NM_007906	13628	Mm.2645	NM_007906	ENSMUSG00000016349	Eef1a2	Eef1a|S1|wasted|wst	eukaryotic translation elongation factor 1 alpha 2	protein-coding
mm_56494.1	chr6	99204489	99204497	-	1	NA	intron (NM_001347345, intron 4 of 19)	intron (NM_001347345, intron 4 of 19)	62022	NM_001197321	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_33774.1	chr4	134496967	134496988	+	1	NA	promoter-TSS (NM_001285849)	promoter-TSS (NM_001285849)	-64	NM_001285849	71904	Mm.142343	NM_027995	ENSMUSG00000037348	Paqr7	2310021M12Rik|AV001994|BB007237|Mpra|PGLP|mPR	progestin and adipoQ receptor family member VII	protein-coding
mm_47633.1	chr5	125300531	125300540	-	1	NA	exon (NM_001205082, exon 4 of 12)	exon (NM_001205082, exon 4 of 12)	40559	NM_016741	20778	Mm.282242	NM_016741	ENSMUSG00000037936	Scarb1	AI120173|CD36|Cd36l1|Chohd1|Cla-1|Cla1|D5Ertd460e|Hdlq1|Hlb398|SR-B1|SR-BI|SRBI|Srb1|mSR-BI	scavenger receptor class B, member 1	protein-coding
mm_112382.1	chr12	119238065	119238092	-	1	NA	5' UTR (NM_177290, exon 1 of 14)	5' UTR (NM_177290, exon 1 of 14)	198	NM_177290	320910	Mm.217000	NM_177290	ENSMUSG00000025321	Itgb8	4832412O06Rik	integrin beta 8	protein-coding
mm_109294.1	chr12	109559606	109559629	+	1	NA	non-coding (NR_003633, exon 5 of 5)	non-coding (NR_003633, exon 5 of 5)	-4075	NR_030427	791079		NR_030427	ENSMUSG00000076451	Mir770	Mirn770|mir-770|mmu-mir-770	microRNA 770	ncRNA
mm_87226.1	chr10	40444834	40444858	+	1	NA	intron (NM_001291817, intron 4 of 11)	intron (NM_001291817, intron 4 of 11)	95538	NM_001291816	78334	Mm.200924	NM_198164	ENSMUSG00000038481	Cdk19	2700084L06Rik|AI845279|AW228747|CDK11|Cdc2l6|mKIAA1028	cyclin-dependent kinase 19	protein-coding
mm_30586.1	chr4	5644217	5644240	+	1	NA	promoter-TSS (NM_173426)	promoter-TSS (NM_173426)	49	NM_173426	242297	Mm.331470	NM_173426	ENSMUSG00000049119	Fam110b	1700012H17Rik|5031405P22|AW049855	family with sequence similarity 110, member B	protein-coding
mm_52235.1	chr6	104493050	104493111	+	1	NA	promoter-TSS (NM_017383)	promoter-TSS (NM_017383)	36	NM_017383	53870	Mm.321671	NM_017383	ENSMUSG00000030092	Cntn6	NB-3	contactin 6	protein-coding
mm_170209.1	chr17	70898200	70898204	-	1	NA	Intergenic	B2_Mm1t|SINE|B2	-44670	NM_001164074	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_28241.1	chr3	88461197	88461226	-	1	NA	promoter-TSS (NM_001163489)	promoter-TSS (NM_001163489)	-29	NM_001163489	20351	Mm.439752	NM_013658	ENSMUSG00000028064	Sema4a	AI132332|SemB|Semab	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A	protein-coding
mm_166817.1	chr7	17750548	17750551	+	1	NA	exon (NM_028480, exon 5 of 9)	exon (NM_028480, exon 5 of 9)	37297	NM_028480	73250	Mm.244138	NM_028480	ENSMUSG00000008789	Ceacam5	1600029H12Rik|Psg30	carcinoembryonic antigen-related cell adhesion molecule 5	protein-coding
mm_148446.1	chr19	3972424	3972433	+	1	NA	promoter-TSS (NM_001177438)	promoter-TSS (NM_001177438)	100	NM_001177438	621603	Mm.34137	NM_001177438	ENSMUSG00000075296	Aldh3b2	AI848594|C130048D07Rik	aldehyde dehydrogenase 3 family, member B2	protein-coding
mm_46021.1	chr5	90905242	90905264	-	1	NA	3' UTR (NM_009140, exon 4 of 4)	3' UTR (NM_009140, exon 4 of 4)	1354	NM_009140	20310	Mm.4979	NM_009140	ENSMUSG00000058427	Cxcl2	CINC-2a|GROb|Gro2|MIP-2|MIP-2a|Mgsa-b|Mip2|Scyb|Scyb2	chemokine (C-X-C motif) ligand 2	protein-coding
mm_99509.1	chr11	103101690	103101726	+	1	NA	promoter-TSS (NM_025988)	promoter-TSS (NM_025988)	20	NM_025988	67131	Mm.390367	NM_025988	ENSMUSG00000056938	Acbd4	2010009P05Rik|2010015A21Rik|AI849317	acyl-Coenzyme A binding domain containing 4	protein-coding
mm_87722.1	chr10	60106304	60106318	+	1	NA	promoter-TSS (NM_052994)	promoter-TSS (NM_052994)	54	NM_052994	94214	Mm.153429	NM_052994	ENSMUSG00000058297	Spock2	AA407235|Gcap26|mKIAA0275	sparc/osteonectin, cwcv and kazal-like domains proteoglycan 2	protein-coding
mm_119779.1	chr14	54179713	54179722	+	1	NA	Intergenic	Intergenic	74212	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_114479.1	chr13	69141220	69141234	+	1	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	-141686	NM_153534	210044	Mm.390617	NM_153534	ENSMUSG00000021536	Adcy2	mKIAA1060	adenylate cyclase 2	protein-coding
mm_19698.1	chr2	103761164	103761172	-	1	NA	promoter-TSS (NM_153126)	promoter-TSS (NM_153126)	82	NM_153126	98956	Mm.288005	NM_153126	ENSMUSG00000027185	Nat10	AI429152	N-acetyltransferase 10	protein-coding
mm_171868.1	chr5	24974422	24974427	-	1	NA	intron (NM_145401, intron 3 of 15)	(TTCC)n|Simple_repeat|Simple_repeat	21329	NM_001310480	108099	Mm.33649	NM_145401	ENSMUSG00000028944	Prkag2	2410051C13Rik|AAKG|AAKG2|AI854673|H91620p|WPWS	protein kinase, AMP-activated, gamma 2 non-catalytic subunit	protein-coding
mm_167977.1	chrX	159456412	159456424	+	1	NA	intron (NM_001313751, intron 3 of 15)	L1_Rod|LINE|L1	-2707	NM_001313752	78283	Mm.160079	NM_001081124	ENSMUSG00000041020	Map7d2	1600028E09Rik|2900002G04Rik|5330432J06Rik|C030036K04Rik|Mtap7d2	MAP7 domain containing 2	protein-coding
mm_71372.1	chr8	45763958	45763970	+	1	NA	intron (NM_172752, intron 8 of 22)	intron (NM_172752, intron 8 of 22)	55333	NR_045739	319940	Mm.441720	NR_045739	ENSMUSG00000085440	Sorbs2os	D330022K07Rik	sorbin and SH3 domain containing 2, opposite strand	ncRNA
mm_33663.1	chr4	133174526	133174537	+	1	NA	intron (NM_153423, intron 1 of 8)	intron (NM_153423, intron 1 of 8)	-21124	NR_105984	102466215		NR_105984	ENSMUSG00000099202	Mir7017	Gm27945|mmu-mir-7017	microRNA 7017	ncRNA
mm_151.1	chr1	11414090	11414146	+	1	NA	promoter-TSS (NM_001160369)	promoter-TSS (NM_001160369)	13	NM_001160371	320492	Mm.52021	NM_177173	ENSMUSG00000057715	A830018L16Rik	-	RIKEN cDNA A830018L16 gene	protein-coding
mm_110781.1	chr12	71015547	71015553	-	1	NA	promoter-TSS (NM_001081195)	promoter-TSS (NM_001081195)	273	NR_045056	73204	Mm.363770	NR_045055	ENSMUSG00000085622	3110056K07Rik	4921536K06Rik	RIKEN cDNA 3110056K07 gene	ncRNA
mm_166857.1	chr7	20782172	20782175	+	1	NA	Intergenic	ERVB4_1-I_MM-int|LTR|ERVK	-5112	NM_001166716	436135	Mm.480278	NM_001166716	ENSMUSG00000091638	Vmn1r113	EG436135|Gm5748	vomeronasal 1 receptor 113	protein-coding
mm_26946.1	chr3	20266509	20266520	-	1	NA	exon (NM_029706, exon 4 of 11)	exon (NM_029706, exon 4 of 11)	9219	NM_029706	76703	Mm.34692	NM_029706	ENSMUSG00000011463	Cpb1	0910001A18Rik|1810063F02Rik|2210008M23Rik|AI504870	carboxypeptidase B1 (tissue)	protein-coding
mm_159076.1	chr2	25863850	25863850	+	1	NA	promoter-TSS (NM_001145403)	promoter-TSS (NM_001145403)	55	NM_001145403	227632	Mm.119462	NM_175462	ENSMUSG00000058740	Kcnt1	C030030G16Rik|Slack|Slo2.2|slo2	potassium channel, subfamily T, member 1	protein-coding
mm_84656.1	chr9	71631134	71631142	-	1	NA	intron (NM_001304362, intron 16 of 18)	intron (NM_001304362, intron 16 of 18)	-38778	NM_001033208	102371	Mm.27585	NM_001033208	ENSMUSG00000041361	Myzap	AA407270|AV006038|Gcom1|Gm640|Grinl1a7|Myozap	myocardial zonula adherens protein	protein-coding
mm_28630.1	chr3	95142347	95142362	-	1	NA	promoter-TSS (NM_027206)	promoter-TSS (NM_027206)	6	NM_027206	69769	Mm.34368	NM_027206	ENSMUSG00000013707	Tnfaip8l2	1810019A08Rik|AW610835|TIPE2	tumor necrosis factor, alpha-induced protein 8-like 2	protein-coding
mm_166296.1	chr5	104113876	104113902	-	1	NA	5' UTR (NM_010097, exon 1 of 11)	5' UTR (NM_010097, exon 1 of 11)	199	NM_010097	13602	Mm.29027	NM_010097	ENSMUSG00000029309	Sparcl1	Ecm2|Sc1|hevin|mast9	SPARC-like 1	protein-coding
mm_88339.1	chr10	75589364	75589390	+	1	NA	promoter-TSS (NM_011820)	promoter-TSS (NM_011820)	-4	NM_011820	23887	Mm.257927	NM_011820	ENSMUSG00000006344	Ggt5	AI551243|GGL|GGT-REL|Ggtla1	gamma-glutamyltransferase 5	protein-coding
mm_124789.1	chr15	8109323	8109356	+	1	NA	promoter-TSS (NM_133227)	promoter-TSS (NM_133227)	26	NM_133227	170762	Mm.295168	NM_133227	ENSMUSG00000022142	Nup155	D930027M19Rik|mKIAA0791	nucleoporin 155	protein-coding
mm_31502.1	chr4	53440389	53440502	+	1	NA	promoter-TSS (NM_001159633)	promoter-TSS (NM_001159633)	32	NM_133891	100434	Mm.482207	NM_133891	ENSMUSG00000028412	Slc44a1	2210409B22Rik|4833416H08Rik|AW547365|CHTL1|CTL1|Cdw92	solute carrier family 44, member 1	protein-coding
mm_30823.1	chr4	21873777	21873786	+	1	NA	exon (NM_025669, exon 11 of 12)	exon (NM_025669, exon 11 of 12)	-5894	NM_172687	230027	Mm.5662	NM_172687	ENSMUSG00000028247	Coq3	4732433J24|C77934	coenzyme Q3 methyltransferase	protein-coding
mm_39785.1	chr5	30232616	30232680	+	1	NA	promoter-TSS (NM_027652)	promoter-TSS (NM_027652)	67	NR_137634	28042	Mm.168854	NM_027652	ENSMUSG00000075703	Selenoi	4933402G07Rik|AI448296|AI452230|C79563|D5Wsu178e|Ept1|SELI|mKIAA1724	selenoprotein I	protein-coding
mm_16044.1	chr2	167721703	167721726	+	1	NA	Intergenic	Intergenic	30537	NR_015500	329562	Mm.123101	NM_177851	ENSMUSG00000006462	A530013C23Rik	-	RIKEN cDNA A530013C23 gene	ncRNA
mm_37788.1	chr4	130307510	130307519	-	1	NA	Intergenic	PB1D10|SINE|Alu	-1264	NM_010174	14077	Mm.388886	NM_010174	ENSMUSG00000028773	Fabp3	Fabph-1|Fabph-4|Fabph1|Fabph4|H-FABP|Mdgi	fatty acid binding protein 3, muscle and heart	protein-coding
mm_71411.1	chr8	46471937	46471953	+	1	NA	intron (NM_007981, intron 1 of 20)	intron (NM_007981, intron 1 of 20)	908	NM_007981	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_159311.1	chr2	181493183	181493183	+	1	NA	promoter-TSS (NM_183181)	promoter-TSS (NM_183181)	-23	NM_183181	241850	Mm.87455	NM_183181	ENSMUSG00000055882	Abhd16b	1700095H12	abhydrolase domain containing 16B	protein-coding
mm_26367.1	chr3	142560352	142560354	+	1	NA	promoter-TSS (NM_001289493)	promoter-TSS (NM_001289493)	-143	NM_001289493	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_87677.1	chr10	59136998	59137013	+	1	NA	3' UTR (NM_172788, exon 10 of 10)	3' UTR (NM_172788, exon 10 of 10)	84842	NM_001024911	103080	Mm.346842	NM_001024910	ENSMUSG00000019917	Sept10	4921515A04Rik|9430099J10Rik|AA408298|AI874685	septin 10	protein-coding
mm_5343.1	chr1	24595488	24595488	-	1	NA	Intergenic	Lx2B|LINE|L1	-8051	NM_007733	12823	Mm.329196	NM_007733	ENSMUSG00000026141	Col19a1	-	collagen, type XIX, alpha 1	protein-coding
mm_77258.1	chr8	115706995	115707018	-	1	NA	promoter-TSS (NM_001025577)	promoter-TSS (NM_001025577)	-112	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_90309.1	chr10	126997512	126997524	+	1	NA	promoter-TSS (NR_030259)	promoter-TSS (NR_030259)	-922	NR_030259	723882		NR_030259	ENSMUSG00000072837	Mir546	Mirn546|mmu-mir-546	microRNA 546	ncRNA
mm_114450.1	chr13	66933377	66933383	+	1	NA	promoter-TSS (NM_025547)	promoter-TSS (NM_025547)	-308	NM_025547	66410	Mm.347939	NM_025547	ENSMUSG00000021519	Mterf3	2410017I18Rik|Mterfd1	mitochondrial transcription termination factor 3	protein-coding
mm_97877.1	chr11	83191342	83191357	+	1	NA	promoter-TSS (NM_011409)	promoter-TSS (NM_011409)	19	NM_011409	20557	Mm.290922	NM_011409	ENSMUSG00000018986	Slfn3	-	schlafen 3	protein-coding
mm_25985.1	chr3	133534370	133534381	+	1	NA	intron (NM_001040400, intron 1 of 10)	intron (NM_001040400, intron 1 of 10)	10015	NM_001346736	214133	Mm.347816	NM_145989	ENSMUSG00000040943	Tet2	Ayu17-449|E130014J05Rik|mKIAA1546	tet methylcytosine dioxygenase 2	protein-coding
mm_125657.1	chr15	63718342	63718373	+	1	NA	Intergenic	(CCA)n|Simple_repeat|Simple_repeat	90382	NM_031378	83492	Mm.335619	NM_031378	ENSMUSG00000079025	Gsdmc	Gsdmc1|Mlze	gasdermin C	protein-coding
mm_143931.1	chr17	86075331	86075335	-	1	NA	intron (NM_030133, intron 14 of 20)	intron (NM_030133, intron 14 of 20)	69842	NM_030133	78586	Mm.146236	NM_030133	ENSMUSG00000024135	Srbd1	AI461933|C85414|D530025C17Rik	S1 RNA binding domain 1	protein-coding
mm_14512.1	chr2	132281155	132281197	+	1	NA	intron (NM_138651, intron 1 of 12)	intron (NM_138651, intron 1 of 12)	-4763	NM_001291039	110911	Mm.284503	NM_138651	ENSMUSG00000058793	Cds2	5730450N06Rik|5730460C18Rik|AI854580|D2Wsu127e	CDP-diacylglycerol synthase (phosphatidate cytidylyltransferase) 2	protein-coding
mm_168302.1	chr11	106724411	106724411	-	1	NA	Intergenic	RLTR11B|LTR|ERVK	-9130	NM_001305157	18613	Mm.343951	NM_008816	ENSMUSG00000020717	Pecam1	C85791|Cd31|PECAM-1|Pecam	platelet/endothelial cell adhesion molecule 1	protein-coding
mm_90182.1	chr10	119992917	119992958	+	1	NA	promoter-TSS (NM_001277295)	promoter-TSS (NM_001277295)	15	NR_102387	74053	Mm.196692	NM_028736	ENSMUSG00000034813	Grip1	4931400F03Rik|GRIP|eb	glutamate receptor interacting protein 1	protein-coding
mm_43394.1	chr5	135778629	135778645	+	1	NA	promoter-TSS (NM_029659)	promoter-TSS (NM_029659)	-12	NM_008617	17448	Mm.297096	NM_008617	ENSMUSG00000019179	Mdh2	MDH|Mdh-2|Mor-1|Mor1	malate dehydrogenase 2, NAD (mitochondrial)	protein-coding
mm_29987.1	chr3	135428474	135428477	-	1	NA	Intergenic	Intergenic	-5042	NM_025902	67006	Mm.269993	NM_025902	ENSMUSG00000028165	Cisd2	1500009M05Rik|1500026J14Rik|1500031D15Rik|AI848398|B630006A20Rik|Miner1|Naf-1|Noxp70|Zcd2	CDGSH iron sulfur domain 2	protein-coding
mm_141604.1	chr17	32788239	32788260	-	1	NA	promoter-TSS (NM_172458)	promoter-TSS (NM_172458)	38	NM_172458	208292	Mm.38813	NM_172458	ENSMUSG00000024298	Zfp871	4732483N19|9030612M13Rik|AI118577|AI265322|mKIAA3006	zinc finger protein 871	protein-coding
mm_30304.1	chr3	149326766	149326768	-	1	NA	Intergenic	Intergenic	52030	NR_040591	381482	Mm.393866	NR_040591		Gm1653	-	predicted gene 1653	ncRNA
mm_32119.1	chr4	99031197	99031208	+	1	NA	exon (NM_013913, exon 1 of 7)	exon (NM_013913, exon 1 of 7)	248	NM_013913	30924	Mm.28341	NM_013913	ENSMUSG00000028553	Angptl3	hypl	angiopoietin-like 3	protein-coding
mm_94542.1	chr11	9191791	9191799	+	1	NA	promoter-TSS (NM_178259)	promoter-TSS (NM_178259)	-147	NM_178259	268379	Mm.39270	NM_178259	ENSMUSG00000004668	Abca13	9830132L24|A930002G16Rik|AI956815	ATP-binding cassette, sub-family A (ABC1), member 13	protein-coding
mm_96226.1	chr11	62512153	62512163	+	1	NA	exon (NM_001039536, exon 6 of 7)	exon (NM_001039536, exon 6 of 7)	27103	NM_028448	73139	Mm.390409	NM_028448	ENSMUSG00000018509	Cenpv	3110013H01Rik|AA671303|Prr6	centromere protein V	protein-coding
mm_19054.1	chr2	77280555	77280565	-	1	NA	promoter-TSS (NM_175465)	promoter-TSS (NM_175465)	32	NM_175465	228071	Mm.27120	NM_175465	ENSMUSG00000042272	Sestd1	1500031J16Rik|A930010O20|Solo/Trio8	SEC14 and spectrin domains 1	protein-coding
mm_78466.1	chr9	32594746	32594747	+	1	NA	Intergenic	Intergenic	-53294	NM_008026	14247	Mm.258908	NM_008026	ENSMUSG00000016087	Fli1	EWSR2|Fli-1|SIC-1|Sic1	Friend leukemia integration 1	protein-coding
mm_135995.1	chr16	75284839	75284845	-	1	NA	Intergenic	Intergenic	301219	NM_001252513	320355	Mm.99517	NM_177142	ENSMUSG00000032948	Lipi	D930038D03Rik|lpd1	lipase, member I	protein-coding
mm_24642.1	chr3	94377487	94377497	+	1	NA	promoter-TSS (NM_001293734)	promoter-TSS (NM_001293734)	60	NR_121656	19885	Mm.4372	NM_011281	ENSMUSG00000028150	Rorc	Nr1f3|RORgamma|TOR|Thor	RAR-related orphan receptor gamma	protein-coding
mm_14043.1	chr2	122264752	122264764	+	1	NA	3' UTR (NM_146126, exon 9 of 9)	3' UTR (NM_146126, exon 9 of 9)	29919	NM_146126	20322	Mm.371580	NM_146126	ENSMUSG00000027227	Sord	Sdh-1|Sdh1|Sodh-1	sorbitol dehydrogenase	protein-coding
mm_145583.1	chr18	60984389	60984400	+	1	NA	exon (NM_001286809, exon 5 of 6)	exon (NM_001286809, exon 5 of 6)	20840	NM_001286809	12322	Mm.131530	NM_009792	ENSMUSG00000024617	Camk2a	CaMKII|R74975|mKIAA0968	calcium/calmodulin-dependent protein kinase II alpha	protein-coding
mm_117466.1	chr13	76017547	76017563	-	1	NA	5' UTR (NM_178916, exon 1 of 4)	5' UTR (NM_178916, exon 1 of 4)	1007	NM_178916	218341	Mm.266515	NM_178916	ENSMUSG00000043190	Rfesd	AI256775|D030068K09	Rieske (Fe-S) domain containing	protein-coding
mm_104835.1	chr11	99155019	99155037	-	1	NA	promoter-TSS (NM_007719)	promoter-TSS (NM_007719)	49	NM_001301713	12775	Mm.2932	NM_007719	ENSMUSG00000037944	Ccr7	CC-CKR-7|CCR-7|CD197|Cdw197|Cmkbr7|EBI1|Ebi1h	chemokine (C-C motif) receptor 7	protein-coding
mm_120599.1	chr14	70078010	70078045	+	1	NA	5' UTR (NM_001289925, exon 2 of 3)	5' UTR (NM_001289925, exon 2 of 3)	232	NM_001289927	13655	Mm.103737	NM_018781	ENSMUSG00000033730	Egr3	Pilot	early growth response 3	protein-coding
mm_47783.1	chr5	131993284	131993286	-	1	NA	intron (NM_177047, intron 4 of 18)	intron (NM_177047, intron 4 of 18)	113016	NR_040704	75369	Mm.389696	NR_040704	ENSMUSG00000105773	4930563F08Rik	-	RIKEN cDNA 4930563F08 gene	ncRNA
mm_100308.1	chr11	117976304	117976318	+	1	NA	Intergenic	Intergenic	-6945	NM_007707	12702	Mm.3468	NM_007707	ENSMUSG00000053113	Socs3	Cis3|Cish3|EF-10|Ef10|SSI-3|Ssi3	suppressor of cytokine signaling 3	protein-coding
mm_169645.1	chr15	51607885	51607886	+	1	NA	Intergenic	L1Md_Gf|LINE|L1	-212275	NR_045092	100502643	Mm.131987	NR_045092		Gm19303	-	predicted gene, 19303	ncRNA
mm_59624.1	chr7	28154641	28154651	+	1	NA	exon (NM_001164655, exon 13 of 20)	exon (NM_001164655, exon 13 of 20)	-15102	NM_007991	14113	Mm.4595	NM_007991	ENSMUSG00000046865	Fbl	AL022665|FIB|FLRN|RNU3IP1	fibrillarin	protein-coding
mm_130486.1	chr15	98763137	98763190	-	1	NA	promoter-TSS (NM_007478)	promoter-TSS (NM_007478)	-45	NM_007478	11842	Mm.221298	NM_007478	ENSMUSG00000051853	Arf3	5430400P17Rik|AI854770	ADP-ribosylation factor 3	protein-coding
mm_164465.1	chr16	59557490	59557504	+	1	NA	Intergenic	Intergenic	-1745	NM_174848	224273	Mm.246424	NM_174848	ENSMUSG00000022723	Crybg3	5031404N19|AU022790|Gm9581	beta-gamma crystallin domain containing 3	protein-coding
mm_130479.1	chr15	98740155	98740184	-	1	NA	3' UTR (NM_007478, exon 5 of 5)	3' UTR (NM_007478, exon 5 of 5)	-11971	NM_024169	66120	Mm.30729	NM_024169	ENSMUSG00000003355	Fkbp11	1110002O23Rik|FKBP-11	FK506 binding protein 11	protein-coding
mm_21203.1	chr2	155582657	155582668	-	1	NA	intron (NM_001291111, intron 1 of 11)	intron (NM_001291111, intron 1 of 11)	10148	NM_001291111	14854	Mm.252316	NM_008180	ENSMUSG00000027610	Gss	AI314904|GS-A/GS-B|GSH-S	glutathione synthetase	protein-coding
mm_159673.1	chr4	154882258	154882258	+	1	NA	intron (NM_013783, intron 3 of 23)	intron (NM_013783, intron 3 of 23)	12673	NM_013783	27390	Mm.116944	NM_013783	ENSMUSG00000058183	Mmel1	Mell1|NEP2|NEPII|Nl1|SEP	membrane metallo-endopeptidase-like 1	protein-coding
mm_167092.1	chr7	106264063	106264072	+	1	NA	Intergenic	IAPLTR4|LTR|ERVK	-48727	NM_029000	74558	Mm.458429	NM_029000	ENSMUSG00000045868	Gvin1	9130002C22Rik|9830104F22Rik|Iigs1|VLIG|VLIG-1	GTPase, very large interferon inducible 1	protein-coding
mm_119829.1	chr14	54360827	54360851	+	1	NA	promoter-TSS (NM_026936)	promoter-TSS (NM_026936)	-2	NM_026936	69089	Mm.182340	NM_026936	ENSMUSG00000000959	Oxa1l	1810020M02Rik|AI894287	oxidase assembly 1-like	protein-coding
mm_107661.1	chr12	52818509	52818529	+	1	NA	intron (NM_198111, intron 2 of 13)	intron (NM_198111, intron 2 of 13)	119136	NM_198111	238161	Mm.310822	NM_198111	ENSMUSG00000061603	Akap6	AI482140|Akapalpha|Akapbeta|PRKA	A kinase (PRKA) anchor protein 6	protein-coding
mm_20362.1	chr2	128306593	128306605	-	1	NA	intron (NR_028589, intron 2 of 2)	intron (NR_028589, intron 2 of 2)	122752	NR_028591	100043424	Mm.297222	NR_028589		Gm14005	OTTMUSG00000015351	predicted gene 14005	ncRNA
mm_50793.1	chr6	54040079	54040091	+	1	NA	5' UTR (NM_001163640, exon 1 of 13)	5' UTR (NM_001163640, exon 1 of 13)	153	NM_001163640	69993	Mm.321147	NM_023543	ENSMUSG00000004633	Chn2	1700026N20Rik|4930557O16Rik|ARHGAP3|Bch	chimerin 2	protein-coding
mm_136032.1	chr16	77329526	77329551	-	1	NA	non-coding (NR_015543, exon 1 of 5)	non-coding (NR_015543, exon 1 of 5)	210	NR_015543	77994	Mm.394688	NR_015543	ENSMUSG00000090386	Mir99ahg	2810055G20Rik|D730043B02Rik	Mir99a and Mirlet7c-1 host gene (non-protein coding)	ncRNA
mm_20028.1	chr2	119477618	119477705	-	1	NA	promoter-TSS (NM_026574)	promoter-TSS (NM_026574)	-32	NM_026574	68142	Mm.330496	NM_026574	ENSMUSG00000034154	Ino80	2310079N15Rik|4632409L19Rik|Inoc1	INO80 complex subunit	protein-coding
mm_143004.1	chr17	56425135	56425181	-	1	NA	intron (NM_001252455, intron 10 of 27)	CpG	-6249	NR_105943	102465590		NR_105943	ENSMUSG00000098339	Mir6977	Gm27922|mmu-mir-6977	microRNA 6977	ncRNA
mm_165642.1	chr3	75890626	75890642	-	1	NA	intron (NM_001291069, intron 11 of 15)	intron (NM_001291069, intron 11 of 15)	66315	NM_175193	73124	Mm.249232	NM_175193	ENSMUSG00000034109	Golim4	3110027H23Rik|GIMPC|GPP130|Golph4|P138	golgi integral membrane protein 4	protein-coding
mm_29626.1	chr3	121548031	121548035	-	1	NA	Intergenic	Intergenic	-15689	NM_145394	213603	Mm.33062	NM_145394	ENSMUSG00000039865	Slc44a3	BC010552	solute carrier family 44, member 3	protein-coding
mm_82858.1	chr9	31464240	31464252	-	1	NA	promoter-TSS (NM_144936)	promoter-TSS (NM_144936)	-8	NM_144936	235135	Mm.390134	NM_144936	ENSMUSG00000041737	Tmem45b	BC018222	transmembrane protein 45b	protein-coding
mm_123395.1	chr14	63417126	63417138	-	1	NA	promoter-TSS (NM_007549)	promoter-TSS (NM_007549)	55	NM_007549	12143	Mm.3962	NM_007549	ENSMUSG00000014453	Blk	-	B lymphoid kinase	protein-coding
mm_154030.1	chr19	53441472	53441479	-	1	NA	non-coding (NR_028427, exon 10 of 10)	non-coding (NR_028427, exon 10 of 10)	23321	NR_028427	381232	Mm.248624	NR_028427	ENSMUSG00000097636	Mirt1	4833407H14Rik|5430437C04Rik|5830416P10Rik|ENSMUSG00000074788|Gm10758	myocardial infarction associated transcript 1	ncRNA
mm_160812.1	chr11	21135586	21135586	+	1	NA	intron (NM_023324, intron 1 of 6)	L1MDa|LINE|L1	44262	NM_023324	67245	Mm.28957	NM_023324	ENSMUSG00000020134	Peli1	2810468L03Rik|A930031K15Rik|AA409794|AI586297|D11Ertd676e	pellino 1	protein-coding
mm_62610.1	chr7	107166988	107166991	+	1	NA	promoter-TSS (NM_001002894)	promoter-TSS (NM_001002894)	-1	NM_001002894	76858	Mm.35644	NM_001002894	ENSMUSG00000016626	Nlrp14	4921520L01Rik|GC-LRR|Nalp-iota|Nalp14|Nalp14l	NLR family, pyrin domain containing 14	protein-coding
mm_11540.1	chr2	32646532	32646541	+	1	NA	promoter-TSS (NM_001146350)	promoter-TSS (NM_001146350)	-59	NM_007932	13805	Mm.225297	NM_007932	ENSMUSG00000026814	Eng	AI528660|AI662476|CD105|Endo|S-endoglin	endoglin	protein-coding
mm_24638.1	chr3	94372887	94372887	+	1	NA	promoter-TSS (NM_011281)	promoter-TSS (NM_011281)	93	NM_011281	19885	Mm.4372	NM_011281	ENSMUSG00000028150	Rorc	Nr1f3|RORgamma|TOR|Thor	RAR-related orphan receptor gamma	protein-coding
mm_89688.1	chr10	97565579	97565597	+	1	NA	promoter-TSS (NM_008524)	promoter-TSS (NM_008524)	87	NM_008524	17022	Mm.18888	NM_008524	ENSMUSG00000036446	Lum	Ldc|SLRR2D	lumican	protein-coding
mm_61298.1	chr7	67679108	67679117	+	1	NA	intron (NM_001168475, intron 6 of 10)	intron (NM_001168475, intron 6 of 10)	31702	NM_025905	67009	Mm.249356	NM_025905	ENSMUSG00000030555	Ttc23	1600012K10Rik	tetratricopeptide repeat domain 23	protein-coding
mm_44092.1	chr5	149245942	149245967	+	1	NA	Intergenic	Intergenic	-19050	NM_001308462	11690	Mm.19844	NM_009663	ENSMUSG00000060063	Alox5ap	Flap	arachidonate 5-lipoxygenase activating protein	protein-coding
mm_133222.1	chr16	76342012	76342015	+	1	NA	intron (NM_173440, intron 2 of 3)	RMER15-int|LTR|ERVL	31036	NM_173440	268903	Mm.74711	NM_173440	ENSMUSG00000048490	Nrip1	6030458L20Rik|8430438I05Rik|9630050P12|AA959574|AW456757|RIP140	nuclear receptor interacting protein 1	protein-coding
mm_43372.1	chr5	135632697	135632727	+	1	NA	promoter-TSS (NM_146002)	promoter-TSS (NM_146002)	58	NM_146002	215160	Mm.295438	NM_031398	ENSMUSG00000039917	Rhbdd2	0610011L13Rik|AI480532|Rhbdl7|Usmg1	rhomboid domain containing 2	protein-coding
mm_17082.1	chr2	22950689	22950707	-	1	NA	intron (NM_001331043, intron 8 of 10)	intron (NM_001331043, intron 8 of 10)	55176	NM_019501	56075	Mm.249752	NM_019501	ENSMUSG00000026784	Pdss1	2610203G20Rik|2700031G06Rik|TPT|TPT 1|Tprt|mDLP1|mSPS1	prenyl (solanesyl) diphosphate synthase, subunit 1	protein-coding
mm_102637.1	chr11	62550994	62551019	-	1	NA	promoter-TSS (NR_002875).2	promoter-TSS (NR_002875).2	-165	NM_011664	22187	Mm.371592	NM_011664	ENSMUSG00000019505	Ubb	AL033289|Rps27a|Uba52|Ubb2|Ubc	ubiquitin B	protein-coding
mm_127403.1	chr15	101224323	101224338	+	1	NA	promoter-TSS (NR_045326)	promoter-TSS (NR_045326)	123	NM_019518	56149	Mm.276573	NM_019518	ENSMUSG00000000531	Grasp	tamalin	GRP1 (general receptor for phosphoinositides 1)-associated scaffold protein	protein-coding
mm_107399.1	chr12	33333236	33333250	+	1	NA	intron (NM_001033436, intron 2 of 7)	intron (NM_001033436, intron 2 of 7)	30728	NM_001033436	380753	Mm.41540	NM_028139	ENSMUSG00000020564	Atxn7l1	2810423G08Rik|Atxn7l4	ataxin 7-like 1	protein-coding
mm_45122.1	chr5	45857474	45857511	-	1	NA	promoter-TSS (NM_172153)	promoter-TSS (NM_172153)	48	NM_001163073	209707	Mm.71498	NM_172153	ENSMUSG00000015882	Lcorl	Mlr1	ligand dependent nuclear receptor corepressor-like	protein-coding
mm_70521.1	chr8	12949481	12949491	+	1	NA	promoter-TSS (NM_001159485)	promoter-TSS (NM_001159485)	68	NM_001159485	17207	Mm.334413	NM_178076	ENSMUSG00000031442	Mcf2l	C130040G20Rik|Dbs|Ost|mKIAA0362	mcf.2 transforming sequence-like	protein-coding
mm_136865.1	chr17	12867025	12867037	+	1	NA	intron (NM_008552, intron 1 of 8)	MLT1N2|LTR|ERVL-MaLR	1112	NM_008552	17171	Mm.425994	NM_008552	ENSMUSG00000068037	Mas1	Mas-1|Mgra	MAS1 oncogene	protein-coding
mm_70615.1	chr8	13435469	13435503	+	1	NA	promoter-TSS (NM_001143672)	promoter-TSS (NM_001143672)	27	NM_001143672	272465	Mm.250502	NM_001143671	ENSMUSG00000038457	Tmem255b	Fam70b|Gm687	transmembrane protein 255B	protein-coding
mm_105874.1	chr11	114923585	114923600	-	1	NA	3' UTR (NM_199221, exon 4 of 4)	3' UTR (NM_199221, exon 4 of 4)	10794	NM_001347651	217304	Mm.185355	NM_199221	ENSMUSG00000063193	Cd300lb	CLM-7|Clm7|Gm253|LMIR5	CD300 molecule like family member B	protein-coding
mm_106118.1	chr11	116359293	116359349	-	1	NA	intron (NM_027258, intron 5 of 18)	intron (NM_027258, intron 5 of 18)	-23967	NM_008240	15223	Mm.378938	NM_008240	ENSMUSG00000034227	Foxj1	FKHL-13|HFH-4|Hfh4	forkhead box J1	protein-coding
mm_155159.1	chrX	52988076	52988078	+	1	NA	promoter-TSS (NM_013556)	promoter-TSS (NM_013556)	-1	NM_013556	15452	Mm.299381	NM_013556	ENSMUSG00000025630	Hprt	C81579|HPGRT|Hprt1	hypoxanthine guanine phosphoribosyl transferase	protein-coding
mm_153469.1	chr19	41264346	41264363	-	1	NA	promoter-TSS (NM_133352)	promoter-TSS (NM_133352)	-350	NM_133352	107358	Mm.246440	NM_133352	ENSMUSG00000025016	Tm9sf3	1810073M23Rik|2810031D16Rik|AI115521|AI413748|AW146116|AW549777|Smbp|mKIAA4036	transmembrane 9 superfamily member 3	protein-coding
mm_115111.1	chr13	103919435	103919455	+	1	NA	intron (NM_001005868, intron 1 of 26)	intron (NM_001005868, intron 1 of 26)	1141	NM_001289473	59079	Mm.277354	NM_021563	ENSMUSG00000021709	Erbin	1700028E05Rik|Erbb2ip|mKIAA1225	Erbb2 interacting protein	protein-coding
mm_101928.1	chr11	50202934	50202952	-	1	NA	exon (NM_011018, exon 6 of 8)	exon (NM_011018, exon 6 of 8)	7877	NM_001290769	18412	Mm.40828	NM_011018	ENSMUSG00000015837	Sqstm1	A170|OSF-6|Osi|STAP|STONE14|p62	sequestosome 1	protein-coding
mm_103833.1	chr11	83020351	83020361	-	1	NA	intron (NM_181545, intron 1 of 5)	intron (NM_181545, intron 1 of 5)	366	NM_001167743	276950	Mm.491599	NM_181545	ENSMUSG00000035208	Slfn8	-	schlafen 8	protein-coding
mm_142287.1	chr17	40242286	40242289	-	1	NA	promoter-TSS (NM_009639)	promoter-TSS (NM_009639)	-29	NM_009639	11572	Mm.14138	NM_009639	ENSMUSG00000025433	Crisp3	Aeg2|CRISP-3|CRS3|SGP28	cysteine-rich secretory protein 3	protein-coding
mm_153600.1	chr19	43879712	43879729	-	1	NA	promoter-TSS (NM_001306088)	promoter-TSS (NM_001306088)	48	NM_001306088	71972	Mm.159024	NM_028029	ENSMUSG00000025195	Dnmbp	2410003L07Rik|2410003M15Rik|TUBA	dynamin binding protein	protein-coding
mm_134305.1	chr16	15736678	15736679	-	1	NA	intron (NM_011159, intron 47 of 85)	intron (NM_011159, intron 47 of 85)	98812	NM_011159	19090	Mm.71	NM_011159	ENSMUSG00000022672	Prkdc	AI326420|AU019811|DNA-PKcs|DNAPDcs|DNAPK|DNPK1|DOXNPH|HYRC1|XRCC7|dxnph|p460|scid|slip	protein kinase, DNA activated, catalytic polypeptide	protein-coding
mm_108375.1	chr12	80854028	80854031	+	1	NA	intron (NM_001242419, intron 3 of 6)	intron (NM_001242419, intron 3 of 6)	63497	NM_001242419	217684	Mm.341776	NM_178682	ENSMUSG00000021133	Susd6	4933426M11Rik|mKIAA0247	sushi domain containing 6	protein-coding
mm_150751.1	chr19	43794452	43794455	+	1	NA	intron (NM_013806, intron 2 of 31)	B1_Mus2|SINE|Alu	12145	NM_013806	12780	Mm.39054	NM_013806	ENSMUSG00000025194	Abcc2	AI173996|Abc30|Cmoat|Mrp2|cMRP	ATP-binding cassette, sub-family C (CFTR/MRP), member 2	protein-coding
mm_109697.1	chr12	113152772	113152800	+	1	NA	intron (NM_007763, intron 1 of 4)	intron (NM_007763, intron 1 of 4)	774	NM_007763	12925	Mm.272368	NM_007763	ENSMUSG00000006360	Crip1	CRHP|CRP1|Crip	cysteine-rich protein 1 (intestinal)	protein-coding
mm_148122.1	chr18	75342614	75342625	-	1	NA	Intergenic	CpG	-24746	NM_001042660	17131	Mm.34407	NM_008543	ENSMUSG00000025880	Smad7	Madh7	SMAD family member 7	protein-coding
mm_69783.1	chr7	141094083	141094094	-	1	NA	intron (NM_023059, intron 2 of 9)	intron (NM_023059, intron 2 of 9)	6458	NM_023059	24058	Mm.38017	NM_023059	ENSMUSG00000025494	Sigirr	AI256711|TIR8	single immunoglobulin and toll-interleukin 1 receptor (TIR) domain	protein-coding
mm_167999.1	chrX	170018253	170018259	+	1	NA	Intergenic	B2_Mm1a|SINE|B2	-39339	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_114661.1	chr13	78121035	78121044	+	1	NA	intron (NM_001163420, intron 8 of 8)	intron (NM_001163420, intron 8 of 8)	75410	NM_001347538	13865	Mm.439653	NM_010151	ENSMUSG00000069171	Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR-3|EAR3|Erbal3|SVP44|Tcfcoup1	nuclear receptor subfamily 2, group F, member 1	protein-coding
mm_27326.1	chr3	50368282	50368293	-	1	NA	3' UTR (NM_011990, exon 12 of 12)	3' UTR (NM_011990, exon 12 of 12)	75326	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_156470.1	chrX	143518707	143518717	+	1	NA	5' UTR (NM_001195048, exon 1 of 16)	5' UTR (NM_001195048, exon 1 of 16)	121	NM_001195048	18481	Mm.40035	NM_008778	ENSMUSG00000031284	Pak3	PAK-3|Pak65alpha|Pak65beta|Stk4	p21 protein (Cdc42/Rac)-activated kinase 3	protein-coding
mm_29138.1	chr3	105801324	105801377	-	1	NA	promoter-TSS (NM_145541)	promoter-TSS (NM_145541)	31	NM_145541	109905	Mm.101922	NM_145541	ENSMUSG00000068798	Rap1a	AI848598|G-22K|Krev-1|Rap1	RAS-related protein-1a	protein-coding
mm_50933.1	chr6	57702547	57702558	+	1	NA	promoter-TSS (NM_133737)	promoter-TSS (NM_133737)	97	NM_133737	71835	Mm.274904	NM_133737	ENSMUSG00000062190	Lancl2	1700003F10Rik	LanC (bacterial lantibiotic synthetase component C)-like 2	protein-coding
mm_165339.1	chr2	117989473	117989481	+	1	NA	intron (NR_126479, intron 8 of 9)	intron (NR_126479, intron 8 of 9)	121725	NR_126479	329496	Mm.235844	NR_126479	ENSMUSG00000087203	Gm13986	C230060E24|OTTMUSG00000015236	predicted gene 13986	ncRNA
mm_127726.1	chr15	103240443	103240453	+	1	NA	promoter-TSS (NM_010447)	promoter-TSS (NM_010447)	-6	NR_002883	434858	Mm.391346	NR_002883		Gm5643	EG434858	heterogeneous nuclear ribonucleoprotein A1 pseudogene	pseudo
mm_74687.1	chr8	14989672	14989675	-	1	NA	intron (NM_172751, intron 26 of 28)	intron (NM_172751, intron 26 of 28)	-21352	NM_029116	74901	Mm.46675	NM_029116	ENSMUSG00000055675	Kbtbd11	2900016B01Rik|4930465M17Rik|mKIAA0711	kelch repeat and BTB (POZ) domain containing 11	protein-coding
mm_88362.1	chr10	75937163	75937174	+	1	NA	TTS (NM_001277132)	TTS (NM_001277132)	1595	NM_175329	103172	Mm.333849	NM_175329	ENSMUSG00000049422	Chchd10	1620401E04Rik|AI267078|Ndg2	coiled-coil-helix-coiled-coil-helix domain containing 10	protein-coding
mm_124056.1	chr14	77875094	77875108	-	1	NA	promoter-TSS (NM_025384)	promoter-TSS (NM_025384)	-184	NM_025384	66148	Mm.248046	NM_025384	ENSMUSG00000022013	Dnajc15	1110003P16Rik|Dnajd1	DnaJ heat shock protein family (Hsp40) member C15	protein-coding
mm_109945.1	chr12	11326443	11326461	-	1	NA	exon (NM_012038, exon 4 of 4)	exon (NM_012038, exon 4 of 4)	26565	NR_106136	102465775		NR_106136	ENSMUSG00000098879	Mir7675	Gm27965|mmu-mir-7675	microRNA 7675	ncRNA
mm_18454.1	chr2	60963138	60963169	-	1	NA	promoter-TSS (NM_020296)	promoter-TSS (NM_020296)	51	NM_020296	56878	Mm.259667	NM_020296	ENSMUSG00000026970	Rbms1	2600014B10Rik|AI255215|MSSP-1|MSSP-2|MSSP-3|YC1	RNA binding motif, single stranded interacting protein 1	protein-coding
mm_66705.1	chr7	45921262	45921312	-	1	NA	promoter-TSS (NM_001146346)	promoter-TSS (NM_001146346)	139	NM_010129	13732	Mm.20829	NM_010129	ENSMUSG00000040212	Emp3	H-4|H4|HNMP-1|MI-35|Ymp	epithelial membrane protein 3	protein-coding
mm_144175.1	chr18	6733954	6733960	+	1	NA	Intergenic	MIR|SINE|MIR	-31210	NM_181070	19330	Mm.132802	NM_181070	ENSMUSG00000073639	Rab18	AA959686	RAB18, member RAS oncogene family	protein-coding
mm_140248.1	chr17	84182004	84182014	+	1	NA	Intergenic	Intergenic	5938	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_85957.1	chr9	112124413	112124424	-	1	NA	intron (NM_001177617, intron 13 of 14)	B4|SINE|B4	-5707	NR_029823	723815		NR_029823	ENSMUSG00000065441	Mir128-2	Mirn128-2|Mirn128b|mir-128-2|mir-128b	microRNA 128-2	ncRNA
mm_78262.1	chr9	21927686	21927697	+	1	NA	promoter-TSS (NM_178577)	promoter-TSS (NM_178577)	-156	NM_001253870	235043	Mm.253329	NM_178577	ENSMUSG00000040883	Tmem205	-	transmembrane protein 205	protein-coding
mm_32890.1	chr4	118964193	118964200	+	1	NA	exon (NM_133892, exon 3 of 7)	exon (NM_133892, exon 3 of 7)	2229	NM_133892	100470	Mm.26698	NM_133892	ENSMUSG00000024903	Lao1	AW990848	L-amino acid oxidase 1	protein-coding
mm_79054.1	chr9	46229910	46229986	+	1	NA	exon (NM_009692, exon 4 of 4)	exon (NM_009692, exon 4 of 4)	1318	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2|apo-AI|apoA-I	apolipoprotein A-I	protein-coding
mm_83189.1	chr9	41004696	41004714	-	1	NA	promoter-TSS (NM_019465)	promoter-TSS (NM_019465)	-77	NM_019465	54698	Mm.42791	NM_019465	ENSMUSG00000032021	Crtam	-	cytotoxic and regulatory T cell molecule	protein-coding
mm_67773.1	chr7	97081498	97081511	-	1	NA	promoter-TSS (NM_010248)	promoter-TSS (NM_010248)	-247	NM_001162477	14389	Mm.42033	NM_010248	ENSMUSG00000004508	Gab2	AI463667|D130058I17Rik|p97	growth factor receptor bound protein 2-associated protein 2	protein-coding
mm_138335.1	chr17	34898277	34898315	+	1	NA	promoter-TSS (NM_001286575)	promoter-TSS (NM_001286575)	-196	NM_001286575	110147	Mm.35345	NM_145830	ENSMUSG00000013787	Ehmt2	Bat8|D17Ertd710e|G9a|KMT1C|NG36	euchromatic histone lysine N-methyltransferase 2	protein-coding
mm_71451.1	chr8	46521659	46521665	+	1	NA	intron (NM_001302163, intron 11 of 20)	intron (NM_001302163, intron 11 of 20)	-30407	NM_027973	71876	Mm.22108	NM_027973	ENSMUSG00000031629	Cenpu	1700029A22Rik|Mlf1ip	centromere protein U	protein-coding
mm_116971.1	chr13	56178798	56178811	-	1	NA	promoter-TSS (NM_001168615)	promoter-TSS (NM_001168615)	81	NM_145976	212937	Mm.116697	NM_145976	ENSMUSG00000049625	Tifab	-	TRAF-interacting protein with forkhead-associated domain, family member B	protein-coding
mm_36151.1	chr4	59538076	59538087	-	1	NA	intron (NM_178164, intron 1 of 13)	intron (NM_178164, intron 1 of 13)	11283	NM_178164	230257	Mm.331640	NM_144904	ENSMUSG00000028382	Ptbp3	5830471K22Rik|AA407443|AI462022|AW107884|C86549|Rod1	polypyrimidine tract binding protein 3	protein-coding
mm_106572.1	chr11	120661185	120661199	-	1	NA	promoter-TSS (NM_175263)	promoter-TSS (NM_175263)	-355	NM_175263	77583	Mm.32839	NM_175263	ENSMUSG00000042988	Notum	5730593N15Rik	notum pectinacetylesterase homolog (Drosophila)	protein-coding
mm_89868.1	chr10	108230546	108230549	+	1	NA	exon (NM_027892, exon 4 of 26)	exon (NM_027892, exon 4 of 26)	68147	NM_027892	17931	Mm.422959	NM_027892	ENSMUSG00000019907	Ppp1r12a	1200015F06Rik|5730577I22Rik|AA792106|AV099298|D10Ertd625e|Mypt1	protein phosphatase 1, regulatory (inhibitor) subunit 12A	protein-coding
mm_142722.1	chr17	48146235	48146294	-	1	NA	promoter-TSS (NM_177824)	promoter-TSS (NM_177824)	43	NM_001177897	328829	Mm.466999	NM_177824	ENSMUSG00000073386	9830107B12Rik	Trem5	RIKEN cDNA 9830107B12 gene	protein-coding
mm_88535.1	chr10	78425691	78425729	+	1	NA	promoter-TSS (NM_007793)	promoter-TSS (NM_007793)	40	NM_007793	13014	Mm.6095	NM_007793	ENSMUSG00000005054	Cstb	AA960480|Stfb	cystatin B	protein-coding
mm_21407.1	chr2	158091791	158091795	-	1	NA	promoter-TSS (NR_040609)	promoter-TSS (NR_040609)	4	NR_040609	72340	Mm.443395	NR_040609	ENSMUSG00000100860	2010009K17Rik	-	RIKEN cDNA 2010009K17 gene	ncRNA
mm_135467.1	chr16	45844229	45844236	-	1	NA	5' UTR (NM_153412, exon 1 of 18)	5' UTR (NM_153412, exon 1 of 18)	146	NM_153412	208177	Mm.211477	NM_153412	ENSMUSG00000033149	Phldb2	AV253284|C820004H04Rik|LL5b|LL5beta	pleckstrin homology like domain, family B, member 2	protein-coding
mm_121447.1	chr14	120430674	120430687	+	1	NA	3' UTR (NM_207515, exon 8 of 8)	3' UTR (NM_207515, exon 8 of 8)	-47781	NM_029519	76108	Mm.261448	NM_029519	ENSMUSG00000051615	Rap2a	5830461H18Rik	RAS related protein 2a	protein-coding
mm_35996.1	chr4	55651205	55651218	-	1	NA	Intergenic	CpG	-118736	NM_010637	16600	Mm.4325	NM_010637	ENSMUSG00000003032	Klf4	EZF|Gklf|Zie	Kruppel-like factor 4 (gut)	protein-coding
mm_114521.1	chr13	73328486	73328509	+	1	NA	promoter-TSS (NM_010888)	promoter-TSS (NM_010888)	-15	NM_010888	407785	Mm.29897	NM_010888	ENSMUSG00000021606	Ndufs6	BC059730|IP13	NADH dehydrogenase (ubiquinone) Fe-S protein 6	protein-coding
mm_49798.1	chr6	35411972	35411978	+	1	NA	Intergenic	Intergenic	81129	NR_040526	73409	Mm.69443	NR_040526	ENSMUSG00000107341	1700065J11Rik	-	RIKEN cDNA 1700065J11 gene	ncRNA
mm_57438.1	chr6	124920092	124920121	-	1	NA	Intergenic	Intergenic	-2160	NM_026988	69202	Mm.142187	NM_026988	ENSMUSG00000030122	Ptms	2610009E16Rik	parathymosin	protein-coding
mm_84535.1	chr9	67250893	67250899	-	1	NA	intron (NM_001081242, intron 50 of 57)	intron (NM_001081242, intron 50 of 57)	-14170	NR_029576	387185		NR_029576	ENSMUSG00000076379	Mir190a	Mir190|Mirn190|mir-190|mir-190a|mmu-mir-190|mmu-mir-190a	microRNA 190a	ncRNA
mm_119139.1	chr14	31209432	31209442	+	1	NA	intron (NM_009393, intron 1 of 5)	intron (NM_009393, intron 1 of 5)	1125	NM_009393	21924	Mm.439921	NM_009393	ENSMUSG00000091898	Tnnc1	AI874626|TnC|cTnC|cTnI|tncc	troponin C, cardiac/slow skeletal	protein-coding
mm_165783.1	chr3	131127567	131127578	+	1	NA	intron (NM_001276403, intron 3 of 11)	intron (NM_001276403, intron 3 of 11)	14781	NM_001276403	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_25778.1	chr3	126597103	126597113	+	1	NA	5' UTR (NM_001293663, exon 1 of 20)	5' UTR (NM_001293663, exon 1 of 20)	157	NM_023813	108058	Mm.255822	NM_023813	ENSMUSG00000053819	Camk2d	2810011D23Rik|8030469K03Rik|CaMK II|[d]-CaMKII	calcium/calmodulin-dependent protein kinase II, delta	protein-coding
mm_167167.1	chr7	136305097	136305097	+	1	NA	intron (NR_102277, intron 3 of 3)	intron (NR_102277, intron 3 of 3)	36773	NR_102277	77383	Mm.227745	NR_102277	ENSMUSG00000110027	C030029H02Rik	-	RIKEN cDNA C030029H02 gene	ncRNA
mm_42997.1	chr5	123394783	123394826	+	1	NA	promoter-TSS (NM_177582)	promoter-TSS (NM_177582)	6	NM_177582	208104	Mm.83277	NM_133917	ENSMUSG00000038342	Mlxip	AW228700|Mir|bHLHe36	MLX interacting protein	protein-coding
mm_68882.1	chr7	126447896	126447902	-	1	NA	exon (NM_007504, exon 17 of 23)	exon (NM_007504, exon 17 of 23)	15174	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_116473.1	chr13	43481456	43481515	-	1	NA	promoter-TSS (NM_019930)	promoter-TSS (NM_019930)	-512	NM_019930	56705	Mm.148781	NM_019930	ENSMUSG00000038546	Ranbp9	IBAP-1|Ibap1|RanBPM	RAN binding protein 9	protein-coding
mm_96339.1	chr11	66380392	66380394	+	1	NA	intron (NM_001034874, intron 2 of 4)	intron (NM_001034874, intron 2 of 4)	145733	NM_001034874	380702	Mm.351764	NM_001034874	ENSMUSG00000053930	Shisa6	Gm879|ckamp52	shisa family member 6	protein-coding
mm_146720.1	chr18	15064145	15064155	-	1	NA	promoter-TSS (NM_001142731)	promoter-TSS (NM_001142731)	-568	NM_001142731	106931	Mm.329299	NM_134112	ENSMUSG00000036225	Kctd1	4933402K10Rik|AI661543|AW553000	potassium channel tetramerisation domain containing 1	protein-coding
mm_98069.1	chr11	85889834	85889848	+	1	NA	promoter-TSS (NM_011536)	promoter-TSS (NM_011536)	-222	NM_011536	21387	Mm.275336	NM_011536	ENSMUSG00000000094	Tbx4	3930401C23	T-box 4	protein-coding
mm_154805.1	chrX	13422359	13422366	+	1	NA	Intergenic	RMER19B|LTR|ERVK	-45310	NM_173415	236690	Mm.90233	NM_173415	ENSMUSG00000051228	Nyx	CLNP|CSNB1|CSNB4|nob	nyctalopin	protein-coding
mm_154763.1	chrX	12079261	12079270	+	1	NA	intron (NM_001168321, intron 1 of 13)	CpG	1288	NM_175045	71458	Mm.196328	NM_029510	ENSMUSG00000040363	Bcor	2900008C10Rik|5830466J11Rik|8430401K06Rik|BcorR|D930024N20Rik|mKIAA1575	BCL6 interacting corepressor	protein-coding
mm_3438.1	chr1	150102170	150102189	+	1	NA	intron (NM_011198, intron 4 of 9)	intron (NM_011198, intron 4 of 9)	2148	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_111052.1	chr12	80109775	80109798	-	1	NA	exon (NM_007564, exon 2 of 2)	exon (NM_007564, exon 2 of 2)	3227	NM_007564	12192	Mm.235132	NM_007564	ENSMUSG00000021127	Zfp36l1	AW742437|AW743212|Berg36|Brf1|D530020L18Rik|ERF1|TIS11b|cMG1	zinc finger protein 36, C3H type-like 1	protein-coding
mm_73744.1	chr8	114289366	114289388	+	1	NA	exon (NM_173016, exon 7 of 9)	exon (NM_173016, exon 7 of 9)	62101	NR_045831	71122	Mm.437539	NR_045831		4933408N05Rik	-	RIKEN cDNA 4933408N05 gene	ncRNA
mm_90391.1	chr10	127322002	127322026	+	1	NA	promoter-TSS (NM_001285785)	promoter-TSS (NM_001285785)	50	NM_001285785	216445	Mm.227198	NM_146011	ENSMUSG00000040345	Arhgap9	AU043488	Rho GTPase activating protein 9	protein-coding
mm_55179.1	chr6	52014076	52014093	-	1	NA	Intergenic	RMER17C2|LTR|ERVK	-1535	NM_018773	54353	Mm.221479	NM_018773	ENSMUSG00000059182	Skap2	2610021A10Rik|AA960083|BB137539|RA70|SKAP-HOM|Saps|Scap2|mSKAP55R	src family associated phosphoprotein 2	protein-coding
mm_74416.1	chr8	3625207	3625212	-	1	NA	promoter-TSS (NM_001129804)	promoter-TSS (NM_001129804)	73	NM_008790	18545	Mm.440882	NM_008790	ENSMUSG00000004630	Pcp2	L7|Pcp-2	Purkinje cell protein 2 (L7)	protein-coding
mm_137228.1	chr17	24351955	24351968	+	1	NA	promoter-TSS (NM_001039581)	promoter-TSS (NM_001039581)	-62	NM_013855	27410	Mm.239470	NM_013855	ENSMUSG00000024130	Abca3	1810036E22Rik|ABC-C|Abc3	ATP-binding cassette, sub-family A (ABC1), member 3	protein-coding
mm_68444.1	chr7	109986310	109986346	-	1	NA	promoter-TSS (NM_153525)	promoter-TSS (NM_153525)	-98	NM_153525	233724	Mm.43212	NM_153525	ENSMUSG00000047554	Tmem41b	1500015G02Rik|1500031M19Rik|AU018901|D7Ertd70e|D7Ertd743e	transmembrane protein 41B	protein-coding
mm_6013.1	chr1	59014087	59014093	-	1	NA	Intergenic	Intergenic	40519	NM_172656	227154	Mm.286006	NM_172656	ENSMUSG00000026027	Stradb	AA792893|Als2cr2|B830008M19|D1Ucla2|ILPIP|ILPIPA|PRO1038|Papk|Syradb	STE20-related kinase adaptor beta	protein-coding
mm_118801.1	chr14	24622152	24622158	+	1	NA	Intergenic	Intergenic	131474	NM_011297	20088	Mm.16775	NM_011297	ENSMUSG00000025290	Rps24	-	ribosomal protein S24	protein-coding
mm_74773.1	chr8	21703643	21703649	-	1	NA	promoter-TSS (NM_001007582)	promoter-TSS (NM_001007582)	1	NM_001007582	382000	Mm.14269	NM_001007582	ENSMUSG00000058618	AY761184	CRS1C-3|CRS1C-6	cDNA sequence AY761184	protein-coding
mm_58748.1	chr7	13285350	13285371	+	1	NA	exon (NM_010715, exon 4 of 29)	exon (NM_010715, exon 4 of 29)	6095	NM_001083188	16881	Mm.288179	NM_010715	ENSMUSG00000056394	Lig1	AL033288|LigI	ligase I, DNA, ATP-dependent	protein-coding
mm_48946.1	chr6	4539656	4539677	+	1	NA	exon (NM_007743, exon 51 of 52)	exon (NM_007743, exon 51 of 52)	34048	NM_007743	12843	Mm.277792	NM_007743	ENSMUSG00000029661	Col1a2	AA960264|AI325291|Col1a-2|Cola-2|Cola2|oim	collagen, type I, alpha 2	protein-coding
mm_61734.1	chr7	81932876	81932895	+	1	NA	intron (NM_013886, intron 1 of 5)	intron (NM_013886, intron 1 of 5)	1574	NM_013886	29877	Mm.392934	NM_013886	ENSMUSG00000025104	Hdgfrp3	2700022B06Rik|HRP-3	hepatoma-derived growth factor, related protein 3	protein-coding
mm_1147.1	chr1	60751717	60751719	+	1	NA	intron (NM_007642, intron 1 of 3)	intron (NM_007642, intron 1 of 3)	5330	NM_007642	12487	Mm.255003	NM_007642	ENSMUSG00000026012	Cd28	-	CD28 antigen	protein-coding
mm_161915.1	chr18	67464844	67464844	+	1	NA	promoter-TSS (NM_144867)	promoter-TSS (NM_144867)	-5	NM_144867	225655	Mm.221420	NM_144867	ENSMUSG00000024530	Slmo1	A230074A19Rik|BC019561|Prelid3a	slowmo homolog 1 (Drosophila)	protein-coding
mm_108445.1	chr12	82450592	82450603	+	1	NA	3' UTR (NM_001167983, exon 24 of 24)	3' UTR (NM_001167983, exon 24 of 24)	139248	NM_172579	217692	Mm.261333	NM_172579	ENSMUSG00000042700	Sipa1l1	4931426N11Rik|AW213287|Spar|mKIAA0440	signal-induced proliferation-associated 1 like 1	protein-coding
mm_60414.1	chr7	44476168	44476178	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	5826	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_117713.1	chr13	95250269	95250331	-	1	NA	promoter-TSS (NM_172263)	promoter-TSS (NM_172263)	4	NM_172263	218461	Mm.100167	NM_172263	ENSMUSG00000021684	Pde8b	B230331L10Rik|C030047E14Rik	phosphodiesterase 8B	protein-coding
mm_173220.1	chrX	74622280	74622280	-	1	NA	Intergenic	Intergenic	23355	NM_001099302	434797	Mm.391298	NM_001099302	ENSMUSG00000079534	Gm5640	EG434797	predicted gene 5640	protein-coding
mm_140054.1	chr17	74556782	74556786	+	1	NA	intron (NM_007566, intron 3 of 72)	ID4|SINE|ID	28489	NM_007566	12211	Mm.442564	NM_007566	ENSMUSG00000024073	Birc6	A430032G04Rik|A430040A19Rik|AA501170|Bruce|D630005A10Rik|mKIAA1289	baculoviral IAP repeat-containing 6	protein-coding
mm_166257.1	chr5	87672158	87672190	+	1	NA	intron (NM_001286016, intron 8 of 33)	intron (NM_001286016, intron 8 of 33)	5966	NM_001286016	12990	Mm.427467	NM_007784	ENSMUSG00000070702	Csn1s1	AA959832|AW212882|Csna	casein alpha s1	protein-coding
mm_25836.1	chr3	129210005	129210012	+	1	NA	intron (NM_011098, intron 3 of 4)	intron (NM_011098, intron 3 of 4)	-3924	NM_001042502	18741	Mm.246804	NM_011098	ENSMUSG00000028023	Pitx2	9430085M16Rik|Brx1|Brx1b|Munc30|Otlx2|Ptx2|Rieg	paired-like homeodomain transcription factor 2	protein-coding
mm_110704.1	chr12	69318571	69318581	-	1	NA	intron (NM_025441, intron 25 of 32)	intron (NM_025441, intron 25 of 32)	21895	NM_027117	69554	Mm.234368	NM_027117	ENSMUSG00000020978	Klhdc2	2310022K15Rik|D12Ertd522e|HCLP-1|LCP	kelch domain containing 2	protein-coding
mm_137018.1	chr17	17838390	17838443	+	1	NA	exon (NM_001162909, exon 8 of 9)	exon (NM_001162909, exon 8 of 9)	7441	NM_001162909	75202	Mm.227456	NM_029205	ENSMUSG00000080316	Spaca6	4930546H06Rik|9530079D04Rik|B230206P06Rik|Ncrna00085|SPACA6A|let-7e|mir-125a|mir-99b	sperm acrosome associated 6	protein-coding
mm_89556.1	chr10	95117892	95117896	+	1	NA	Intergenic	Intergenic	27931	NR_131146	628062		NR_131146		Gm29684	-	predicted gene, 29684	ncRNA
mm_97592.1	chr11	78947840	78947850	+	1	NA	intron (NM_001313921, intron 14 of 25)	intron (NM_001313921, intron 14 of 25)	22554	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_16902.1	chr2	13424753	13424763	-	1	NA	exon (NM_001081084, exon 27 of 67)	exon (NM_001081084, exon 27 of 67)	67118	NM_001081084	65969	Mm.313915	NM_001081084	ENSMUSG00000026726	Cubn	AA408369|AL022750|D2Wsu88e	cubilin (intrinsic factor-cobalamin receptor)	protein-coding
mm_56827.1	chr6	117173724	117173752	-	1	NA	3' UTR (NM_021704, exon 3 of 3)	3' UTR (NM_021704, exon 3 of 3)	5203	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_48859.1	chr5	149769486	149769523	-	1	NA	Intergenic	Intergenic	42247	NR_077242	100861794	Mm.402054	NR_077242	ENSMUSG00000106740	Gm21221	-	predicted gene, 21221	ncRNA
mm_99033.1	chr11	98959757	98959771	+	1	NA	promoter-TSS (NM_001176528)	promoter-TSS (NM_001176528)	-707	NM_001176528	19401	Mm.439744	NM_009024	ENSMUSG00000037992	Rara	Nr1b1|RAR|RARalpha1	retinoic acid receptor, alpha	protein-coding
mm_121789.1	chr14	19977218	19977246	-	1	NA	promoter-TSS (NM_001285911)	promoter-TSS (NM_001285911)	17	NM_001038637	14702	Mm.41737	NM_010315	ENSMUSG00000043004	Gng2	-	guanine nucleotide binding protein (G protein), gamma 2	protein-coding
mm_130142.1	chr15	90898542	90898542	-	1	NA	promoter-TSS (NR_033583)	promoter-TSS (NR_033583)	-66	NR_033583	20738	Mm.431547	NR_033583		Spn-ps	Cd43-ps	sialophorin, pseudogene	pseudo
mm_107981.1	chr12	72945764	72945774	+	1	NA	TTS (NM_011384)	TTS (NM_011384)	5887	NM_011384	20476	Mm.57138	NM_011384	ENSMUSG00000021099	Six6	Optx2|Six9	sine oculis-related homeobox 6	protein-coding
mm_70572.1	chr8	13159577	13159589	+	1	NA	intron (NM_010684, intron 1 of 8)	L1MDb|LINE|L1	422	NM_010684	16783	Mm.16716	NM_010684	ENSMUSG00000031447	Lamp1	CD107a|LGP-120|LGP-A|Lamp-1|P2B	lysosomal-associated membrane protein 1	protein-coding
mm_98960.1	chr11	98575918	98575929	+	1	NA	Intergenic	Intergenic	11322	NM_025661	66612	Mm.180546	NM_025661	ENSMUSG00000038150	Ormdl3	2810011N17Rik|AI315223	ORM1-like 3 (S. cerevisiae)	protein-coding
mm_163657.1	chr13	73870746	73870747	+	1	NA	Intergenic	Intergenic	-23115	NM_001347535	72293	Mm.45506	NM_028186	ENSMUSG00000021567	Nkd2	2210403L10Rik|AW212591|mNkd2	naked cuticle 2 homolog (Drosophila)	protein-coding
mm_123256.1	chr14	61046495	61046523	-	1	NA	5' UTR (NM_013869, exon 1 of 10)	5' UTR (NM_013869, exon 1 of 10)	346	NM_013869	29820	Mm.281356	NM_013869	ENSMUSG00000060548	Tnfrsf19	AL023044|AW123854|TAJ|TAJ-ALPHA|TRADE|Troy	tumor necrosis factor receptor superfamily, member 19	protein-coding
mm_56733.1	chr6	115731078	115731090	-	1	NA	intron (NM_144805, intron 9 of 11)	intron (NM_144805, intron 9 of 11)	27915	NM_144805	94346	Mm.29739	NM_144805	ENSMUSG00000059900	Tmem40	9030407H20Rik|AV091463|W64236	transmembrane protein 40	protein-coding
mm_56009.1	chr6	86516177	86516209	-	1	NA	Intergenic	MIR3|SINE|MIR	9972	NM_011865	23983	Mm.274146	NM_011865	ENSMUSG00000051695	Pcbp1	WBP17|[a]CP-1|alphaCP-1|hnRNP E1	poly(rC) binding protein 1	protein-coding
mm_127185.1	chr15	98993251	98993289	+	1	NA	Intergenic	CpG	7305	NR_045991	75951	Mm.441657	NR_045991	ENSMUSG00000097587	4930578M01Rik	3010001K12Rik	RIKEN cDNA 4930578M01 gene	ncRNA
mm_150649.1	chr19	41911921	41911934	+	1	NA	promoter-TSS (NM_023418)	promoter-TSS (NM_023418)	56	NM_023418	18648	Mm.16783	NM_023418	ENSMUSG00000011752	Pgam1	2310050F24Rik|Pgam-1	phosphoglycerate mutase 1	protein-coding
mm_102361.1	chr11	58330239	58330253	-	1	NA	promoter-TSS (NM_024480)	promoter-TSS (NM_024480)	93	NM_001256520	319475	Mm.72124	NM_178761	ENSMUSG00000049755	Zfp672	4930488P06Rik|4930511N19Rik|Znf672	zinc finger protein 672	protein-coding
mm_96200.1	chr11	62028655	62028657	+	1	NA	intron (NM_001310526, intron 1 of 7)	intron (NM_001310526, intron 1 of 7)	-48368	NM_001029936	432572	Mm.438022	NM_001029936	ENSMUSG00000042331	Specc1	2810012G08Rik|B230396K10Rik|Cytsb	sperm antigen with calponin homology and coiled-coil domains 1	protein-coding
mm_89906.1	chr10	111164888	111164898	+	1	NA	promoter-TSS (NM_001003717)	promoter-TSS (NM_001003717)	91	NM_175489	237542	Mm.220204	NM_175489	ENSMUSG00000020189	Osbpl8	AA536976|AA536995|C730029P18Rik|D330025H14Rik|ORP-8	oxysterol binding protein-like 8	protein-coding
mm_118007.1	chr13	100616938	100616981	-	1	NA	promoter-TSS (NM_001038602)	promoter-TSS (NM_001038602)	12	NM_001038602	218518	Mm.25300	NM_178410	ENSMUSG00000021636	Marveld2	BC003296|MARVD2|Mrvldc2|Tric|Trica|Tricb|Tricc	MARVEL (membrane-associating) domain containing 2	protein-coding
mm_149039.1	chr19	8820066	8820076	+	1	NA	promoter-TSS (NM_027412)	promoter-TSS (NM_027412)	670	NM_001081196	68693	Mm.476519	NM_001081196	ENSMUSG00000071659	Hnrnpul2	1110031M08Rik|AI465155|Hnrpul2	heterogeneous nuclear ribonucleoprotein U-like 2	protein-coding
mm_97855.1	chr11	83069862	83069878	+	1	NA	exon (NM_011408, exon 2 of 2)	exon (NM_011408, exon 2 of 2)	4758	NM_011408	20556	Mm.278689	NM_011408	ENSMUSG00000072620	Slfn2	Shlf2	schlafen 2	protein-coding
mm_108771.1	chr12	89812349	89812351	+	1	NA	promoter-TSS (NM_001252074)	promoter-TSS (NM_001252074)	-133	NM_001252074	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding
mm_83173.1	chr9	40687907	40687911	-	1	NA	intron (NM_133733, intron 1 of 6)	intron (NM_133733, intron 1 of 6)	1945	NM_133733	71566	Mm.280560	NM_133733	ENSMUSG00000032024	Clmp	9030425E11Rik|ACAM|ASP5|AW557819	CXADR-like membrane protein	protein-coding
mm_172111.1	chr6	3200912	3200916	+	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	-87605	NR_036696	667335	Mm.380219	NR_036696	ENSMUSG00000106779	Gm8579	EG667335	spermatogenesis associated glutamate (E)-rich protein 4a pseudogene	pseudo
mm_62472.1	chr7	101836589	101836640	+	1	NA	exon (NM_010567, exon 2 of 29)	exon (NM_010567, exon 2 of 29)	1210	NM_001122739	16332	Mm.476000	NM_010567	ENSMUSG00000032737	Inppl1	51C|SHIP2	inositol polyphosphate phosphatase-like 1	protein-coding
mm_148991.1	chr19	8618047	8618056	+	1	NA	promoter-TSS (NM_008766)	promoter-TSS (NM_008766)	55	NM_008766	18399	Mm.30090	NM_008766	ENSMUSG00000024650	Slc22a6	NKT|Oat1|Orctl1|mOat1	solute carrier family 22 (organic anion transporter), member 6	protein-coding
mm_136081.1	chr16	84835327	84835336	-	1	NA	promoter-TSS (NM_001302216)	promoter-TSS (NM_001302216)	207	NM_008065	14390	Mm.18974	NM_008065	ENSMUSG00000008976	Gabpa	GABPalpha	GA repeat binding protein, alpha	protein-coding
mm_148323.1	chr18	84012363	84012396	-	1	NA	3' UTR (NM_001081300, exon 2 of 2)	3' UTR (NM_001081300, exon 2 of 2)	74183	NM_001081300	110796	Mm.102136	NM_001081300	ENSMUSG00000046982	Tshz1	5730407I04Rik|D18Bwg1409e|Mtsh1|NY-CO-33|Sdccag33|Tsh1|mKIAA4206|teashirt1	teashirt zinc finger family member 1	protein-coding
mm_153683.1	chr19	44396709	44396712	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	10999	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_53622.1	chr6	140479777	140479788	+	1	NA	intron (NM_144920, intron 3 of 30)	L1MA4|LINE|L1	55683	NM_144920	109135	Mm.247670	NM_144920	ENSMUSG00000030231	Plekha5	2810431N21Rik|AI428202|AK129423|AMH-Cre|Ayu21-9|Gt(pU21)9Imeg|Pepp2|Tg(AMH-cre)1Flor	pleckstrin homology domain containing, family A member 5	protein-coding
mm_156778.1	chrX	161297768	161297778	+	1	NA	Intergenic	Intergenic	135023	NM_001290651	107815	Mm.159173	NM_133194	ENSMUSG00000000037	Scml2	4932420G07Rik	sex comb on midleg-like 2 (Drosophila)	protein-coding
mm_52236.1	chr6	104493162	104493216	+	1	NA	5' UTR (NM_017383, exon 1 of 23)	5' UTR (NM_017383, exon 1 of 23)	145	NM_017383	53870	Mm.321671	NM_017383	ENSMUSG00000030092	Cntn6	NB-3	contactin 6	protein-coding
mm_28841.1	chr3	96592742	96592790	-	1	NA	intron (NM_027241, intron 1 of 7)	intron (NM_027241, intron 1 of 7)	1415	NM_001293701	69870	Mm.292739	NM_027241	ENSMUSG00000028104	Polr3gl	2010003I19Rik	polymerase (RNA) III (DNA directed) polypeptide G like	protein-coding
mm_84849.1	chr9	78443222	78443253	-	1	NA	promoter-TSS (NM_173386)	promoter-TSS (NM_173386)	0	NR_125721	214763	Mm.101559	NM_173386	ENSMUSG00000032344	Mb21d1	E330016A19Rik|cGAS	Mab-21 domain containing 1	protein-coding
mm_106671.1	chr11	121673070	121673102	-	1	NA	promoter-TSS (NM_178664)	promoter-TSS (NM_178664)	65	NM_178664	210004	Mm.386847	NM_178664	ENSMUSG00000046605	B3gntl1	6030413G23Rik	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase-like 1	protein-coding
mm_6249.1	chr1	68766571	68766572	-	1	NA	intron (NM_010154, intron 1 of 26)	B1_Mur3|SINE|Alu	341488	NM_010154	13869	Mm.442420	NM_010154	ENSMUSG00000062209	Erbb4	Her4|c-erbB-4	erb-b2 receptor tyrosine kinase 4	protein-coding
mm_166440.1	chr5	137211103	137211121	-	1	NA	Intergenic	Intergenic	-77142	NM_009599	11423	Mm.255464	NM_009599	ENSMUSG00000023328	Ache	-	acetylcholinesterase	protein-coding
mm_44394.1	chr5	17833441	17833456	-	1	NA	intron (NM_001159556, intron 1 of 14)	RMER6C|LTR|ERVK	2448	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_49089.1	chr6	7036910	7036913	+	1	NA	intron (NM_001077713, intron 1 of 1)	intron (NM_001077713, intron 1 of 1)	80893	NM_001077713	71238	Mm.389086	NM_001077713	ENSMUSG00000042505	Sdhaf3	0610005M07Rik|4933430A16Rik|Acn9	succinate dehydrogenase complex assembly factor 3	protein-coding
mm_78639.1	chr9	40269275	40269303	+	1	NA	promoter-TSS (NM_001083917)	promoter-TSS (NM_001083917)	73	NM_178227	235281	Mm.290083	NM_153522	ENSMUSG00000049281	Scn3b	1110001K16Rik|4833414B02Rik|Scnb3	sodium channel, voltage-gated, type III, beta	protein-coding
mm_67922.1	chr7	99863357	99863374	-	1	NA	intron (NM_001164258, intron 2 of 18)	intron (NM_001164258, intron 2 of 18)	4147	NM_001164258	446101	Mm.440757	NM_001164258	ENSMUSG00000035211	Xrra1	AI449753	X-ray radiation resistance associated 1	protein-coding
mm_141765.1	chr17	34282888	34282896	-	1	NA	3' UTR (NM_010378, exon 5 of 5)	3' UTR (NM_010378, exon 5 of 5)	4879	NM_010378	14960	Mm.235338	NM_010378	ENSMUSG00000036594	H2-Aa	Aalpha|H-2Aa|H2Aa|I-Aalpha|IAalpha|Ia-1|Ia1	histocompatibility 2, class II antigen A, alpha	protein-coding
mm_126200.1	chr15	78877173	78877196	+	1	NA	promoter-TSS (NM_145929)	promoter-TSS (NM_145929)	-6	NM_145929	106039	Mm.251331	NM_145929	ENSMUSG00000033128	Gga1	4930406E12Rik|AU016030|AW209092	golgi associated, gamma adaptin ear containing, ARF binding protein 1	protein-coding
mm_8354.1	chr1	150392709	150392713	-	1	NA	promoter-TSS (NM_133780)	promoter-TSS (NM_133780)	-127	NM_133780	108989	Mm.174256	NM_133780	ENSMUSG00000006005	Tpr	2610029M07Rik|C77892	translocated promoter region, nuclear basket protein	protein-coding
mm_40886.1	chr5	74614503	74614503	+	1	NA	intron (NM_001159577, intron 6 of 10)	PB1D10|SINE|Alu	63369	NM_001159580	16924	Mm.440403	NM_010727	ENSMUSG00000029228	Lnx1	Lnx	ligand of numb-protein X 1	protein-coding
mm_144144.1	chr18	4994891	4994901	+	1	NA	Intergenic	Intergenic	-51693	NM_153153	225115	Mm.136791	NM_153153	ENSMUSG00000024236	Svil	AU024053|B430302E16Rik	supervillin	protein-coding
mm_146850.1	chr18	24020750	24020813	-	1	NA	promoter-TSS (NM_021559)	promoter-TSS (NM_021559)	-10	NM_021559	59057	Mm.417427	NM_021559	ENSMUSG00000051469	Zfp24	3526401F17Rik|5033419P20Rik|AI480505|AI642085|AL024422|KOX17|ZF-12|Zfp191|Znf191|Znf24|Znp191	zinc finger protein 24	protein-coding
mm_73769.1	chr8	115830530	115830540	+	1	NA	Intergenic	Intergenic	-123641	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_112219.1	chr12	113429137	113429148	-	1	NA	Intergenic	Intergenic	-60423	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_70102.1	chr7	142661255	142661269	-	1	NA	promoter-TSS (NM_001122736)	promoter-TSS (NM_001122736)	9	NM_001122736	16002	Mm.3862	NM_010514	ENSMUSG00000048583	Igf2	AL033362|Igf-2|Igf-II|M6pr|Mpr|Peg2	insulin-like growth factor 2	protein-coding
mm_30052.1	chr3	136326039	136326060	-	1	NA	promoter-TSS (NM_001033350)	promoter-TSS (NM_001033350)	17	NM_001310749	242248	Mm.30832	NM_001033350	ENSMUSG00000037922	Bank1	A530094C12Rik|AI451642|AVIEF|BANK	B cell scaffold protein with ankyrin repeats 1	protein-coding
mm_118609.1	chr14	20929393	20929403	+	1	NA	promoter-TSS (NM_009502)	promoter-TSS (NM_009502)	-35	NM_009502	22330	Mm.279361	NM_009502	ENSMUSG00000021823	Vcl	9430097D22|AA571387|AI462105|AW545629	vinculin	protein-coding
mm_168633.1	chr1	182629876	182629879	+	1	NA	intron (NM_130890, intron 19 of 20)	(TTAGGG)n|Simple_repeat|Simple_repeat	64870	NM_130890	170725	Mm.189201	NM_130890	ENSMUSG00000038599	Capn8	nCL-2|nCL-2'	calpain 8	protein-coding
mm_161519.1	chr15	99528243	99528243	-	1	NA	promoter-TSS (NM_028224)	promoter-TSS (NM_028224)	-78	NM_001038658	72393	Mm.39760	NM_028224	ENSMUSG00000023011	Faim2	2900002L20Rik|Lfg|Lfg2|NMP25|Nmp35|Tmbim2	Fas apoptotic inhibitory molecule 2	protein-coding
mm_154270.1	chr19	60772889	60772941	-	1	NA	exon (NM_010123, exon 12 of 22)	exon (NM_010123, exon 12 of 22)	1470	NR_034047	100217439		NR_034047		Snora19	MBI-51	small nucleolar RNA, H/ACA box 19	snoRNA
mm_45091.1	chr5	44101952	44101965	-	1	NA	promoter-TSS (NM_008935)	promoter-TSS (NM_008935)	-222	NM_001163577	19126	Mm.6250	NM_008935	ENSMUSG00000029086	Prom1	4932416E19Rik|AC133|CD133|Prom|Prom-1|Proml1	prominin 1	protein-coding
mm_33161.1	chr4	125949983	125950006	+	1	NA	Intergenic	Intergenic	-27684	NR_015560	72395	Mm.112888	NR_015560	ENSMUSG00000085562	2610028E06Rik	BB043107	RIKEN cDNA 2610028E06 gene	ncRNA
mm_2538.1	chr1	107420191	107420197	+	1	NA	Intergenic	Intergenic	-2495	NM_027548	116872	Mm.66015	NM_027548	ENSMUSG00000067001	Serpinb7	4631416M05Rik|megsin|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 7	protein-coding
mm_84780.1	chr9	75971026	75971031	-	1	NA	Intergenic	Intergenic	-43949	NM_173731	208982	Mm.82306	NM_173731	ENSMUSG00000007908	Hmgcll1	BC037381	3-hydroxymethyl-3-methylglutaryl-Coenzyme A lyase-like 1	protein-coding
mm_168618.1	chr11	77763255	77763269	+	1	NA	Intergenic	CpG	-13973	NM_001291213	360013	Mm.341248	NM_011586	ENSMUSG00000000631	Myo18a	MAJN|MyoPDZ|MysPDZ|SP-R210	myosin XVIIIA	protein-coding
mm_77215.1	chr8	114723347	114723355	-	1	NA	intron (NM_019573, intron 8 of 8)	intron (NM_019573, intron 8 of 8)	283699	NM_019573	80707	Mm.440420	NM_019573	ENSMUSG00000004637	Wwox	5330426P09Rik|9030416C10Rik|WOX1	WW domain-containing oxidoreductase	protein-coding
mm_9912.1	chr1	189000365	189000405	-	1	NA	intron (NM_172650, intron 3 of 17)	intron (NM_172650, intron 3 of 17)	7455	NM_172650	226823	Mm.209880	NM_172650	ENSMUSG00000026608	Kctd3	4930438A20Rik|9330185B06|E330032J19Rik|NY-REN-45	potassium channel tetramerisation domain containing 3	protein-coding
mm_153809.1	chr19	46045332	46045347	-	1	NA	promoter-TSS (NM_001113408)	promoter-TSS (NM_001113408)	-128	NM_001113408	16825	Mm.327442	NM_010697	ENSMUSG00000025223	Ldb1	CLIM2|NLI	LIM domain binding 1	protein-coding
mm_147888.1	chr18	64888777	64888783	-	1	NA	intron (NM_001114386, intron 1 of 30)	intron (NM_001114386, intron 1 of 30)	1024	NM_001114386	83814	Mm.98668	NM_031881	ENSMUSG00000024589	Nedd4l	1300012C07Rik|Nedd4-2|Nedd4b	neural precursor cell expressed, developmentally down-regulated gene 4-like	protein-coding
mm_135078.1	chr16	34263050	34263065	-	1	NA	intron (NM_001164268, intron 10 of 33)	intron (NM_001164268, intron 10 of 33)	250970	NM_001164268	545156	Mm.82274	NM_177357	ENSMUSG00000061751	Kalrn	2210407G14Rik|AV235988|DUET|E530005C20Rik|Gm539|Hapip|TRAD	kalirin, RhoGEF kinase	protein-coding
mm_48329.1	chr5	138997611	138997627	-	1	NA	Intergenic	CpG	-2666	NM_008808	18590	Mm.2675	NM_008808	ENSMUSG00000025856	Pdgfa	-	platelet derived growth factor, alpha	protein-coding
mm_77829.1	chr9	4309720	4309748	+	1	NA	promoter-TSS (NM_026962)	promoter-TSS (NM_026962)	-9	NM_001164574	69149	Mm.25946	NM_026962	ENSMUSG00000025893	Kbtbd3	2200003A07Rik|Bklhd3	kelch repeat and BTB (POZ) domain containing 3	protein-coding
mm_12671.1	chr2	75729529	75729533	+	1	NA	Intergenic	B1_Mur2|SINE|Alu	-24868	NM_010902	18024	Mm.1025	NM_010902	ENSMUSG00000015839	Nfe2l2	Nrf2	nuclear factor, erythroid derived 2, like 2	protein-coding
mm_140730.1	chr17	15527282	15527315	-	1	NA	promoter-TSS (NM_008799)	promoter-TSS (NM_008799)	3	NM_008799	18567	Mm.323	NM_008799	ENSMUSG00000014771	Pdcd2	AI528543|Pcd2|RP-8	programmed cell death 2	protein-coding
mm_123384.1	chr14	63321533	63321543	-	1	NA	Intergenic	B1F1|SINE|Alu	-76267	NM_001310610	14463	Mm.247669	NM_008092	ENSMUSG00000021944	Gata4	Gata-4	GATA binding protein 4	protein-coding
mm_48816.1	chr5	149015807	149015818	-	1	NA	Intergenic	CpG	8850	NR_040429	100503307	Mm.188008	NR_040429	ENSMUSG00000086610	Gm15408	OTTMUSG00000021225	predicted gene 15408	ncRNA
mm_105083.1	chr11	100846008	100846018	-	1	NA	intron (NM_001113563, intron 1 of 18)	intron (NM_001113563, intron 1 of 18)	4572	NM_001113563	20851	Mm.34064	NM_011489	ENSMUSG00000020919	Stat5b	-	signal transducer and activator of transcription 5B	protein-coding
mm_15076.1	chr2	153125504	153125535	+	1	NA	intron (NM_001172117, intron 2 of 12)	IMPB_01|Satellite|Satellite	17051	NM_010407	15162	Mm.715	NM_010407	ENSMUSG00000003283	Hck	AI849071|Bmk	hemopoietic cell kinase	protein-coding
mm_24419.1	chr3	90526857	90526859	+	1	NA	promoter-TSS (NM_001163526)	promoter-TSS (NM_001163526)	9	NM_001163526	66166	Mm.24006	NM_025393	ENSMUSG00000042306	S100a14	1110013O05Rik|S100a15|S114	S100 calcium binding protein A14	protein-coding
mm_39697.1	chr5	27111382	27111395	+	1	NA	intron (NM_207282, intron 1 of 25)	intron (NM_207282, intron 1 of 25)	62189	NM_207282	13483	Mm.42078	NM_010075	ENSMUSG00000061576	Dpp6	B930011P16Rik|D5Buc3|D5Buc4|D5Buc5|DPP VI|Dpp-6|Gm1377|In(5)6H-p|Peplb|Rw	dipeptidylpeptidase 6	protein-coding
mm_94406.1	chr11	5797512	5797526	+	1	NA	intron (NM_013810, intron 8 of 12)	intron (NM_013810, intron 8 of 12)	6277	NM_018870	56012	Mm.219627	NM_018870	ENSMUSG00000020475	Pgam2	-	phosphoglycerate mutase 2	protein-coding
mm_78815.1	chr9	44076121	44076151	+	1	NA	exon (NM_016808, exon 2 of 13)	exon (NM_016808, exon 2 of 13)	6707	NM_016808	53376	Mm.272770	NM_016808	ENSMUSG00000032010	Usp2	B930035K21Rik|Ubp41	ubiquitin specific peptidase 2	protein-coding
mm_106404.1	chr11	118909796	118909806	-	1	NA	promoter-TSS (NM_001039167)	promoter-TSS (NM_001039167)	-229	NM_001039167	52897	Mm.341103	NM_001024931	ENSMUSG00000025576	Rbfox3	Fox-3|Hrnbp3|NeuN|Neuna60	RNA binding protein, fox-1 homolog (C. elegans) 3	protein-coding
mm_73420.1	chr8	106078800	106078818	+	1	NA	exon (NM_010901, exon 2 of 10)	exon (NM_010901, exon 2 of 10)	19206	NM_010901	18021	Mm.383185	NM_010901	ENSMUSG00000031902	Nfatc3	C80703|D8Ertd281e|NFAT4|NFATx	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 3	protein-coding
mm_13369.1	chr2	103566343	103566351	+	1	NA	promoter-TSS (NM_178890)	promoter-TSS (NM_178890)	37	NM_178890	99382	Mm.35850	NM_178890	ENSMUSG00000032724	Abtb2	AW539457|BPOZ-2	ankyrin repeat and BTB (POZ) domain containing 2	protein-coding
mm_73567.1	chr8	109614229	109614239	+	1	NA	promoter-TSS (NM_001286454)	promoter-TSS (NM_001286454)	-283	NM_001286454	244646	Mm.436810	NM_181544	ENSMUSG00000048827	Pkd1l3	-	polycystic kidney disease 1 like 3	protein-coding
mm_103646.1	chr11	78967469	78967502	-	1	NA	exon (NM_010708, exon 7 of 11)	exon (NM_010708, exon 7 of 11)	17439	NM_001159301	16859	Mm.341434	NM_010708	ENSMUSG00000001123	Lgals9	AA407335|AI194909|AI265545|LGALS35|Lgals5|gal-9|galectin-9	lectin, galactose binding, soluble 9	protein-coding
mm_118559.1	chr14	17981634	17981639	+	1	NA	promoter-TSS (NM_009380)	promoter-TSS (NM_009380)	-8	NM_009380	21834	Mm.32563	NM_009380	ENSMUSG00000021779	Thrb	Nr1a2|T3R[b]|T3Rbeta|Thrb1|Thrb2|c-erbAbeta	thyroid hormone receptor beta	protein-coding
mm_22449.1	chr2	181698434	181698447	-	1	NA	promoter-TSS (NM_199023)	promoter-TSS (NM_199023)	2	NM_199023	277496	Mm.212749	NM_199023	ENSMUSG00000045794	Lkaaear1	4930526D03Rik|Gm692	LKAAEAR motif containing 1 (IKAAEAR murine motif)	protein-coding
mm_107996.1	chr12	73336692	73336711	+	1	NA	intron (NM_001037717, intron 6 of 15)	B1F|SINE|Alu	49853	NM_001037717	625098	Mm.32075	NM_001037717	ENSMUSG00000044712	Slc38a6	AW322671|EG625098	solute carrier family 38, member 6	protein-coding
mm_47047.1	chr5	116083181	116083189	-	1	NA	promoter-TSS (NM_001101546)	promoter-TSS (NM_001101546)	61	NM_001101546	545798	Mm.483995	NM_001101546	ENSMUSG00000079278	Tmem233	DSPB2|Gm13843|OTTMUSG00000014722	transmembrane protein 233	protein-coding
mm_79570.1	chr9	58134275	58134281	+	1	NA	promoter-TSS (NM_001162479)	promoter-TSS (NM_001162479)	203	NM_001162476	20897	Mm.10801	NM_009291	ENSMUSG00000032327	Stra6	AI891933	stimulated by retinoic acid gene 6	protein-coding
mm_170958.1	chr2	54385025	54385028	+	1	NA	Intergenic	Intergenic	-51361	NM_173030	271786	Mm.330227	NM_173030	ENSMUSG00000060988	Galnt13	A230002A12|A230020F20|BB182356	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13	protein-coding
mm_139029.1	chr17	46161075	46161085	+	1	NA	promoter-TSS (NM_019581)	promoter-TSS (NM_019581)	48	NM_001145979	56055	Mm.22147	NM_019581	ENSMUSG00000023952	Gtpbp2	nmf205	GTP binding protein 2	protein-coding
mm_56997.1	chr6	121003006	121003012	-	1	NA	intron (NM_001270475, intron 17 of 31)	intron (NM_001270475, intron 17 of 31)	44165	NR_138099	215458	Mm.122399	NR_138099		LOC215458	-	uncharacterized LOC215458	ncRNA
mm_17186.1	chr2	25460994	25461004	-	1	NA	promoter-TSS (NM_153557)	promoter-TSS (NM_153557)	95	NM_153557	227622	Mm.261780	NM_153557	ENSMUSG00000047617	BC029214	D930050G13Rik|Paxx	cDNA sequence BC029214	protein-coding
mm_9763.1	chr1	180894414	180894436	-	1	NA	intron (NM_177099, intron 2 of 3)	CpG	1317	NM_177099	320202	Mm.87078	NM_177099	ENSMUSG00000066652	Lefty2	6030463A22Rik|Ebaf|Lefta|Leftb|lefty-2|lefty-B	left-right determination factor 2	protein-coding
mm_74499.1	chr8	7580204	7580211	-	1	NA	Intergenic	Intergenic	1080566	NM_010111	13642	Mm.209813	NM_010111	ENSMUSG00000001300	Efnb2	ELF-2|Epl5|Eplg5|Htk-L|LERK-5|Lerk5|NLERK-1	ephrin B2	protein-coding
mm_106622.1	chr11	120824099	120824116	-	1	NA	5' UTR (NM_007988, exon 1 of 43)	5' UTR (NM_007988, exon 1 of 43)	440	NM_007988	14104	Mm.236443	NM_007988	ENSMUSG00000025153	Fasn	A630082H08Rik|FAS	fatty acid synthase	protein-coding
mm_113085.1	chr13	23870260	23870266	+	1	NA	promoter-TSS (NM_009198)	promoter-TSS (NM_009198)	-10	NM_009198	20504	Mm.2656	NM_009198	ENSMUSG00000021335	Slc17a1	NAPI-1|Napi1|Npt1	solute carrier family 17 (sodium phosphate), member 1	protein-coding
mm_34960.1	chr4	156002274	156002276	+	1	NA	intron (NM_001302468, intron 4 of 6)	PB1D7|SINE|Alu	8938	NM_001302468	20318	Mm.293517	NM_011341	ENSMUSG00000029076	Sdf4	Cab45	stromal cell derived factor 4	protein-coding
mm_167366.1	chr8	87472527	87472529	-	1	NA	promoter-TSS (NM_019626)	promoter-TSS (NM_019626)	64	NM_019626	12404	Mm.4880	NM_019626	ENSMUSG00000031654	Cbln1	AI323299	cerebellin 1 precursor protein	protein-coding
mm_150406.1	chr19	36834305	36834309	+	1	NA	promoter-TSS (NM_001163635)	promoter-TSS (NM_001163635)	75	NM_001163635	74493	Mm.249310	NM_001163635	ENSMUSG00000024811	Tnks2	5430432P15Rik|AA517131|AI662480|ARTD6|TNKS-2|Tank2	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase 2	protein-coding
mm_65011.1	chr7	17082328	17082350	-	1	NA	intron (NM_001310628, intron 1 of 5)	intron (NM_001310628, intron 1 of 5)	8299	NM_007676	26436	Mm.143686	NM_007676	ENSMUSG00000066760	Psg16	Cea11|PSG|bCEA	pregnancy specific glycoprotein 16	protein-coding
mm_58680.1	chr7	12512489	12512512	+	1	NA	promoter-TSS (NM_028434)	promoter-TSS (NM_028434)	-51	NM_028434	73090	Mm.84622	NM_028434	ENSMUSG00000030385	2900092C05Rik	-	RIKEN cDNA 2900092C05 gene	protein-coding
mm_99760.1	chr11	106755149	106755184	+	1	NA	intron (NM_001271375, intron 3 of 6)	intron (NM_001271375, intron 3 of 6)	3940	NM_001033435	380732	Mm.343952	NM_001033435	ENSMUSG00000040528	Milr1	Allergin-1|Gm885|Mca32	mast cell immunoglobulin like receptor 1	protein-coding
mm_130830.1	chr15	101846412	101846422	-	1	NA	intron (NM_008473, intron 7 of 8)	intron (NM_008473, intron 7 of 8)	4369	NM_008473	16678	Mm.183137	NM_008473	ENSMUSG00000046834	Krt1	Krt-2.1|Krt2-1|Krt86	keratin 1	protein-coding
mm_92928.1	chr10	84441301	84441360	-	1	NA	promoter-TSS (NM_001004363)	promoter-TSS (NM_001004363)	-859	NM_001004363	77976	Mm.25874	NM_001004363	ENSMUSG00000020032	Nuak1	AU014801|AW494241|B230104P22Rik|Omphk1	NUAK family, SNF1-like kinase, 1	protein-coding
mm_140419.1	chr17	87673331	87673340	+	1	NA	intron (NM_008628, intron 1 of 15)	intron (NM_008628, intron 1 of 15)	778	NM_008628	17685	Mm.4619	NM_008628	ENSMUSG00000024151	Msh2	AI788990	mutS homolog 2	protein-coding
mm_170833.1	chr2	177000949	177000956	+	1	NA	Intergenic	Intergenic	-73139	NM_001305133	102639598	Mm.379980	NM_029813	ENSMUSG00000074527	Gm14296	-	predicted gene 14296	protein-coding
mm_153162.1	chr19	34493006	34493084	-	1	NA	3' UTR (NM_021460, exon 10 of 10)	3' UTR (NM_021460, exon 10 of 10)	-17910	NM_009890	12642	Mm.30824	NM_009890	ENSMUSG00000050370	Ch25h	AI462618|m25OH	cholesterol 25-hydroxylase	protein-coding
mm_108902.1	chr12	100199562	100199578	+	1	NA	promoter-TSS (NM_001313934)	promoter-TSS (NM_001313934)	135	NM_009790	12313	Mm.285993	NM_009790	ENSMUSG00000001175	Calm1	AI256814|AI327027|AI461935|AL024000|CaM|Calm	calmodulin 1	protein-coding
mm_42640.1	chr5	118561105	118561128	+	1	NA	intron (NM_001347445, intron 1 of 30)	CpG-11438	397	NM_172424	76199	Mm.206238	NM_172424	ENSMUSG00000018076	Med13l	2210413I17Rik|6330591G05Rik|9030618F05Rik|Thrap2|Trap240L|mKIAA1025	mediator complex subunit 13-like	protein-coding
mm_88477.1	chr10	77613732	77613770	+	1	NA	promoter-TSS (NR_125903)	promoter-TSS (NR_125903)	42	NR_125903	20610	Mm.24433	NM_019929	ENSMUSG00000020265	Sumo3	2810014B19Rik|D10Ertd345e|SMT3A|SUMO-3|Smt3h1	small ubiquitin-like modifier 3	protein-coding
mm_171256.1	chr3	81711867	81711869	-	1	NA	Intergenic	L1Md_T|LINE|L1	-90157	NR_138586	320566	Mm.208417	NR_138586	ENSMUSG00000103695	A830029E22Rik	-	RIKEN cDNA A830029E22 gene	ncRNA
mm_49826.1	chr6	37805973	37805979	+	1	NA	Intergenic	Intergenic	-64835	NM_001272064	21848	Mm.41063	NM_145076	ENSMUSG00000029833	Trim24	A130082H20Rik|AI447469|D430004I05Rik|TIF1|TIF1-alpha|TIF1alpha|Tif1a	tripartite motif-containing 24	protein-coding
mm_128989.1	chr15	74834709	74834719	-	1	NA	TTS (NM_001033229)	TTS (NM_001033229)	6929	NM_001033229	110115	Mm.322606	NM_001033229	ENSMUSG00000075604	Cyp11b1	AA389061|CPN1|Cyp11b|Cyp11b-1|FHI	cytochrome P450, family 11, subfamily b, polypeptide 1	protein-coding
mm_146739.1	chr18	15403641	15403657	-	1	NA	promoter-TSS (NM_001308647)	promoter-TSS (NM_001308647)	109	NM_001317729	11829	Mm.250786	NM_009700	ENSMUSG00000024411	Aqp4	WCH4	aquaporin 4	protein-coding
mm_131198.1	chr16	8594678	8594680	+	1	NA	intron (NM_172961, intron 6 of 15)	L1ME3A|LINE|L1	43022	NM_025708	66690	Mm.10068	NM_025708	ENSMUSG00000043140	Tmem186	2810440M13Rik|4432406C05Rik|AI648175|AW210586	transmembrane protein 186	protein-coding
mm_164850.1	chr18	46074940	46074942	+	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-29681	NR_040342	107003	Mm.395148	NR_040342		A330093E20Rik	AU043608	RIKEN cDNA A330093E20 gene	ncRNA
mm_26831.1	chr3	10440055	10440127	-	1	NA	promoter-TSS (NM_001127191)	promoter-TSS (NM_001127191)	39	NM_029068	74718	Mm.440548	NM_029068	ENSMUSG00000027534	Snx16	4930522N22Rik|AI117577|AI747675	sorting nexin 16	protein-coding
mm_128844.1	chr15	71444064	71444067	-	1	NA	Intergenic	Intergenic	283773	NM_177819	70363	Mm.126450	NM_177819	ENSMUSG00000036800	Fam135b	1700010C24Rik|A830008O07Rik	family with sequence similarity 135, member B	protein-coding
mm_73853.1	chr8	117739067	117739067	+	1	NA	intron (NM_008290, intron 2 of 4)	Lx7|LINE|L1	37121	NM_008290	15486	Mm.276466	NM_008290	ENSMUSG00000031844	Hsd17b2	AI194836|AI194967|AI255511	hydroxysteroid (17-beta) dehydrogenase 2	protein-coding
mm_47246.1	chr5	121568990	121569002	-	1	NA	exon (NM_009656, exon 12 of 13)	exon (NM_009656, exon 12 of 13)	-23104	NM_010765	17165	Mm.272206	NM_010765	ENSMUSG00000029454	Mapkapk5	MK5|PRAK	MAP kinase-activated protein kinase 5	protein-coding
mm_121774.1	chr14	19889244	19889255	-	1	NA	intron (NM_001038637, intron 4 of 4)	AT_rich|Low_complexity|Low_complexity	50324	NR_105025	52512	Mm.483998	NR_105025		D14Ertd670e	-	DNA segment, Chr 14, ERATO Doi 670, expressed	ncRNA
mm_38079.1	chr4	134128053	134128076	-	1	NA	exon (NM_080559, exon 2 of 3)	exon (NM_080559, exon 2 of 3)	689	NM_080559	73723	Mm.22240	NM_080559	ENSMUSG00000028843	Sh3bgrl3	1110004L05Rik|AU022188	SH3 domain binding glutamic acid-rich protein-like 3	protein-coding
mm_159915.1	chr6	48612940	48612940	+	1	NA	promoter-TSS (NM_173429)	promoter-TSS (NM_173429)	-240	NM_173429	243372	Mm.435190	NM_173429	ENSMUSG00000007216	Zfp775	C130032F08Rik|Znf775	zinc finger protein 775	protein-coding
mm_62277.1	chr7	99594581	99594604	+	1	NA	intron (NM_177231, intron 10 of 15)	intron (NM_177231, intron 10 of 15)	32511	NM_001195529	100503386	Mm.180719	NM_001195529	ENSMUSG00000096606	Tpbgl	EG245190|Gm4980	trophoblast glycoprotein-like	protein-coding
mm_96904.1	chr11	70455859	70455892	+	1	NA	exon (NM_023158, exon 4 of 5)	exon (NM_023158, exon 4 of 5)	-3747	NM_001029929	574428	Mm.472771	NM_001029929	ENSMUSG00000040829	Zmynd15	-	zinc finger, MYND-type containing 15	protein-coding
mm_165047.1	chr19	40476536	40476570	-	1	NA	intron (NM_178362, intron 1 of 28)	L2c|LINE|L2	-25155	NM_001034963	20411	Mm.210815	NM_009166	ENSMUSG00000025006	Sorbs1	2310065E01Rik|9530001P15Rik|CAP|SH3P12|Sh3d5|mKIAA1296	sorbin and SH3 domain containing 1	protein-coding
mm_3697.1	chr1	153760910	153760914	+	1	NA	intron (NM_011882, intron 8 of 8)	intron (NM_011882, intron 8 of 8)	11486	NM_011882	24014	Mm.259254	NM_011882	ENSMUSG00000066800	Rnasel	E230029I04Rik	ribonuclease L (2', 5'-oligoisoadenylate synthetase-dependent)	protein-coding
mm_123254.1	chr14	61046296	61046306	-	1	NA	5' UTR (NM_013869, exon 1 of 10)	5' UTR (NM_013869, exon 1 of 10)	554	NM_013869	29820	Mm.281356	NM_013869	ENSMUSG00000060548	Tnfrsf19	AL023044|AW123854|TAJ|TAJ-ALPHA|TRADE|Troy	tumor necrosis factor receptor superfamily, member 19	protein-coding
mm_141028.1	chr17	25240113	25240158	-	1	NA	promoter-TSS (NM_001163718)	promoter-TSS (NM_001163718)	5	NM_001346737	214505	Mm.38607	NM_172529	ENSMUSG00000035521	Gnptg	6430527N14Rik|A830081F19|AU067667|AU067744|Mdcp1|Tce7	N-acetylglucosamine-1-phosphotransferase, gamma subunit	protein-coding
mm_98062.1	chr11	85832762	85832776	+	1	NA	promoter-TSS (NR_077059)	promoter-TSS (NR_077059)	154	NM_009324	21385	Mm.287052	NM_009324	ENSMUSG00000000093	Tbx2	-	T-box 2	protein-coding
mm_149915.1	chr19	26606434	26606457	+	1	NA	intron (NM_011416, intron 1 of 32)	CpG	1285	NM_011416	67155	Mm.342988	NM_011416	ENSMUSG00000024921	Smarca2	2610209L14Rik|SNF2alpha|Snf2l2|brahma|brm	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	protein-coding
mm_40042.1	chr5	33821095	33821116	+	1	NA	Intergenic	CpG	-22007	NM_175231	107823	Mm.19892	NM_175231	ENSMUSG00000057406	Whsc1	5830445G22Rik|9430010A17Rik|AW555663|C130020C13Rik|D030027O06Rik|D930023B08Rik|MMSET|NSD2|Whsc1l|mKIAA1090	Wolf-Hirschhorn syndrome candidate 1 (human)	protein-coding
mm_14351.1	chr2	129602202	129602217	+	1	NA	intron (NM_001291022, intron 1 of 4)	intron (NM_001291022, intron 1 of 4)	9040	NM_001291022	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_12503.1	chr2	71873267	71873272	+	1	NA	promoter-TSS (NM_172665)	promoter-TSS (NM_172665)	45	NM_172665	228026	Mm.34411	NM_172665	ENSMUSG00000006494	Pdk1	B830012B01|D530020C15Rik	pyruvate dehydrogenase kinase, isoenzyme 1	protein-coding
mm_20966.1	chr2	151972876	151972895	-	1	NA	intron (NM_146127, intron 1 of 1)	intron (NM_146127, intron 1 of 1)	509	NM_001289151	73847	Mm.272444	NM_028666	ENSMUSG00000027459	Fam110a	1700008J10Rik|5430432M24Rik|AI747080	family with sequence similarity 110, member A	protein-coding
mm_161942.1	chr19	4139745	4139745	+	1	NA	promoter-TSS (NM_206973)	promoter-TSS (NM_206973)	-54	NM_206973	269053	Mm.131677	NM_206973	ENSMUSG00000044724	Gpr152	A930009H15Rik|Gm673	G protein-coupled receptor 152	protein-coding
mm_65333.1	chr7	24978410	24978419	-	1	NA	3' UTR (NM_001290469, exon 23 of 23)	3' UTR (NM_001290469, exon 23 of 23)	-5686	NM_010261	14470	Mm.22473	NM_010261	ENSMUSG00000003380	Rabac1	2310040I06Rik|Gbpap1|PRA1|prenylin	Rab acceptor 1 (prenylated)	protein-coding
mm_167102.1	chr7	110859661	110859691	-	1	NA	exon (NM_053247, exon 2 of 6)	exon (NM_053247, exon 2 of 6)	3277	NM_053247	114332	Mm.396078	NM_053247	ENSMUSG00000030787	Lyve1	1200012G08Rik|Crsbp-1|Lyve-1|Xlkd1	lymphatic vessel endothelial hyaluronan receptor 1	protein-coding
mm_5393.1	chr1	33605826	33605833	-	1	NA	intron (NM_008922, intron 7 of 13)	intron (NM_008922, intron 7 of 13)	63965	NM_008922	19076	Mm.27705	NM_008922	ENSMUSG00000026134	Prim2	AI323589	DNA primase, p58 subunit	protein-coding
mm_89056.1	chr10	82881801	82881828	+	1	NA	exon (NM_001042523, exon 8 of 15)	exon (NM_001042523, exon 8 of 15)	15188	NM_025499	66341	Mm.443284	NM_025499	ENSMUSG00000109864	Eid3	1700027M21Rik|NS4EB	EP300 interacting inhibitor of differentiation 3	protein-coding
mm_88083.1	chr10	68137004	68137027	+	1	NA	intron (NM_023598, intron 4 of 9)	intron (NM_023598, intron 4 of 9)	141711	NM_023598	71371	Mm.440357	NM_023598	ENSMUSG00000019947	Arid5b	4930580B11|5430435G07Rik|AI467247|Desrt|Mrf2|Mrf2alpha|Mrf2beta	AT rich interactive domain 5B (MRF1-like)	protein-coding
mm_171805.1	chr5	126318455	126318463	+	1	NA	Intergenic	(TTAGGG)n|Simple_repeat|Simple_repeat	-712330	NR_040685	71247	Mm.399586	NR_040685	ENSMUSG00000105490	4933438B17Rik	-	RIKEN cDNA 4933438B17 gene	ncRNA
mm_132500.1	chr16	36951137	36951154	+	1	NA	exon (NM_008225, exon 6 of 14)	exon (NM_008225, exon 6 of 14)	16162	NM_008225	15163	Mm.4091	NM_008225	ENSMUSG00000022831	Hcls1	AW213261|HS1	hematopoietic cell specific Lyn substrate 1	protein-coding
mm_35712.1	chr4	44233842	44233848	-	1	NA	Intergenic	CpG	-12578	NR_039565	100628618		NR_039565	ENSMUSG00000092677	Mir5106	mir-5106|mmu-mir-5106|mu-mir-5106	microRNA 5106	ncRNA
mm_60543.1	chr7	44480521	44480529	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-3992	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_26839.1	chr3	14533779	14533818	-	1	NA	promoter-TSS (NM_028915)	promoter-TSS (NM_028915)	10	NM_028915	71710	Mm.257449	NM_028915	ENSMUSG00000027550	Lrrcc1	1200008A14Rik|4932441F23Rik|AI195358|AI447421	leucine rich repeat and coiled-coil domain containing 1	protein-coding
mm_130883.1	chr15	102252613	102252628	-	1	NA	5' UTR (NM_011244, exon 3 of 10)	5' UTR (NM_011244, exon 3 of 10)	4902	NM_011244	19411	Mm.1273	NM_011244	ENSMUSG00000001288	Rarg	Nr1b3|RAR-gamma|RARD|RARgamma2	retinoic acid receptor, gamma	protein-coding
mm_73497.1	chr8	107165910	107165925	+	1	NA	intron (NM_025558, intron 1 of 4)	intron (NM_025558, intron 1 of 4)	15256	NM_025558	66427	Mm.20242	NM_025558	ENSMUSG00000031924	Cyb5b	1810044O22Rik|AU015618|Cyb5m	cytochrome b5 type B	protein-coding
mm_141026.1	chr17	25211899	25211910	-	1	NA	intron (NM_001290736, intron 8 of 14)	intron (NM_001290736, intron 8 of 14)	-10678	NM_028789	74154	Mm.267353	NM_028789	ENSMUSG00000015127	Unkl	1300004G08Rik	unkempt family like zinc finger	protein-coding
mm_22874.1	chr3	29198769	29198770	+	1	NA	intron (NM_001167748, intron 4 of 12)	intron (NM_001167748, intron 4 of 12)	116192	NM_029412	75740	Mm.330948	NM_029412	ENSMUSG00000063600	Egfem1	6130401L20Rik|Efcab11	EGF-like and EMI domain containing 1	protein-coding
mm_132782.1	chr16	44811771	44811821	+	1	NA	Intergenic	Intergenic	-8932	NM_207244	239849	Mm.445045	NM_207244	ENSMUSG00000062082	Cd200r4	F630107N04Rik|MCD200RLa	CD200 receptor 4	protein-coding
mm_73510.1	chr8	107368294	107368305	+	1	NA	exon (NM_018823, exon 13 of 15)	exon (NM_018823, exon 13 of 15)	34906	NM_008706	18104	Mm.252	NM_008706	ENSMUSG00000003849	Nqo1	AV001255|Dia4|Dtd|Nmo-1|Nmo1|Nmor1|Ox-1|Ox1|Qr1	NAD(P)H dehydrogenase, quinone 1	protein-coding
mm_147658.1	chr18	60591784	60591867	-	1	NA	promoter-TSS (NM_133363)	promoter-TSS (NM_133363)	-109	NM_133363	170947	Mm.159257	NM_133363	ENSMUSG00000049173	Myoz3	4833419K08Rik|Fatz-3	myozenin 3	protein-coding
mm_14284.1	chr2	128802297	128802308	+	1	NA	TTS (NM_008587)	TTS (NM_008587)	-16001	NM_028248	72477	Mm.259688	NM_028248	ENSMUSG00000014353	Tmem87b	2610301K12Rik|2810431I02Rik|AU014804	transmembrane protein 87B	protein-coding
mm_138454.1	chr17	35135927	35135944	+	1	NA	intron (NM_001252469, intron 1 of 23)	intron (NM_001252469, intron 1 of 23)	221	NM_001252469	224727	Mm.203962	NM_057171	ENSMUSG00000024392	Bag6	2410045D21Rik|AA408914|BAG-6|Bat3|D17H6S52E|G3|Scythe	BCL2-associated athanogene 6	protein-coding
mm_140516.1	chr17	6007481	6007484	-	1	NA	promoter-TSS (NM_001290698)	promoter-TSS (NM_001290698)	-98	NM_001290698	20975	Mm.236068	NM_011523	ENSMUSG00000023805	Synj2	AI481647|SJ2|mKIAA0348	synaptojanin 2	protein-coding
mm_154736.1	chrX	9862131	9862143	+	1	NA	Intergenic	Intergenic	12434	NM_029229	385317	Mm.108656	NM_029229	ENSMUSG00000048994	H2al3	4930557A04Rik	H2A histone family member L3	protein-coding
mm_60699.1	chr7	45175580	45175615	+	1	NA	TTS (NM_001195255)	TTS (NM_001195255)	2294	NR_106022	102465638		NR_106022	ENSMUSG00000106470	Mir7055	mmu-mir-7055	microRNA 7055	ncRNA
mm_61889.1	chr7	89736678	89736685	+	1	NA	exon (NM_181407, exon 2 of 14)	exon (NM_181407, exon 2 of 14)	103863	NM_181407	109264	Mm.334011	NM_181407	ENSMUSG00000030621	Me3	1700020C08Rik|B230207H15Rik	malic enzyme 3, NADP(+)-dependent, mitochondrial	protein-coding
mm_85569.1	chr9	107261032	107261050	-	1	NA	intron (NM_001316691, intron 4 of 7)	intron (NM_001316691, intron 4 of 7)	28355	NM_001316691	102626	Mm.222612	NM_178907	ENSMUSG00000032577	Mapkapk3	3PK|AI874665|MAPKAP-K3|MAPKAP3|MK-3|MK3|MapkKapk3	mitogen-activated protein kinase-activated protein kinase 3	protein-coding
mm_59881.1	chr7	30291942	30291968	+	1	NA	intron (NM_001081114, intron 1 of 13)	intron (NM_001081114, intron 1 of 13)	202	NM_001081114	76686	Mm.159258	NM_001081114	ENSMUSG00000013921	Clip3	1500005P14Rik|AI844915|Clipr-59	CAP-GLY domain containing linker protein 3	protein-coding
mm_24256.1	chr3	89186734	89186744	+	1	NA	intron (NM_001014995, intron 7 of 11)	intron (NM_001014995, intron 7 of 11)	3514	NM_001014995	68521	Mm.274708	NM_001014995	ENSMUSG00000032657	Fam189b	1110013L07Rik	family with sequence similarity 189, member B	protein-coding
mm_11914.1	chr2	52071544	52071552	+	1	NA	Intergenic	Intergenic	-1289	NM_175238	51869	Mm.254530	NM_175238	ENSMUSG00000036202	Rif1	5730435J01Rik|6530403D07Rik|AU016181|AW549474|D2Ertd145e	replication timing regulatory factor 1	protein-coding
mm_75228.1	chr8	39618653	39618666	-	1	NA	intron (NM_001113326, intron 5 of 9)	intron (NM_001113326, intron 5 of 9)	24019	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_69076.1	chr7	126976133	126976142	-	1	NA	5' UTR (NM_026638, exon 1 of 6)	5' UTR (NM_026638, exon 1 of 6)	223	NM_001347656	52858	Mm.28219	NM_026638	ENSMUSG00000030682	Cdipt	9530042F15Rik|D7Bwg0575e|Pis|Pis1	CDP-diacylglycerol--inositol 3-phosphatidyltransferase (phosphatidylinositol synthase)	protein-coding
mm_130544.1	chr15	98953598	98953607	-	1	NA	promoter-TSS (NM_011653)	promoter-TSS (NM_011653)	-101	NM_011653	22142	Mm.405359	NM_011653	ENSMUSG00000072235	Tuba1a	Tuba-1|Tuba1	tubulin, alpha 1A	protein-coding
mm_104551.1	chr11	96780342	96780355	-	1	NA	Intergenic	B3A|SINE|B2	-2793	NM_001163389	74479	Mm.270781	NM_028965	ENSMUSG00000020876	Snx11	4933439F10Rik|A930041K09Rik|AI117694	sorting nexin 11	protein-coding
mm_115551.1	chr13	8871752	8871762	-	1	NA	promoter-TSS (NM_172445)	promoter-TSS (NM_172445)	-21	NM_001039388	207615	Mm.284654	NM_172445	ENSMUSG00000021147	Wdr37	-	WD repeat domain 37	protein-coding
mm_66859.1	chr7	54412522	54412530	-	1	NA	Intergenic	Intergenic	-422719	NM_178705	233271	Mm.387344	NM_178705	ENSMUSG00000063297	Luzp2	9330154K17Rik|D130073E01	leucine zipper protein 2	protein-coding
mm_96255.1	chr11	62602958	62602991	+	1	NA	promoter-TSS (NR_028526)	promoter-TSS (NR_028526)	97	NR_030738	69221	Mm.270874	NR_030738	ENSMUSG00000086841	2410006H16Rik	-	RIKEN cDNA 2410006H16 gene	ncRNA
mm_3561.1	chr1	150426864	150426894	+	1	NA	exon (NM_133780, exon 30 of 52)	exon (NM_133780, exon 30 of 52)	-33824	NM_145511	226499	Mm.222093	NM_145511	ENSMUSG00000006010	BC003331	1810053E15Rik|Odr4|odr-4	cDNA sequence BC003331	protein-coding
mm_27819.1	chr3	79063546	79063548	-	1	NA	3' UTR (NM_001099624, exon 24 of 24)	3' UTR (NM_001099624, exon 24 of 24)	81340	NM_001310536	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_165837.1	chr3	156852201	156852202	+	1	NA	intron (NM_177274, intron 1 of 6)	intron (NM_177274, intron 1 of 6)	290407	NM_001039094	320840	Mm.317293	NM_177274	ENSMUSG00000040037	Negr1	5330422G01Rik|KILON|Ntra	neuronal growth regulator 1	protein-coding
mm_36828.1	chr4	106145791	106145833	-	1	NA	Intergenic	ORR1C1|LTR|ERVL-MaLR	-170401	NM_183225	329908	Mm.234544	NM_183225	ENSMUSG00000028514	Usp24	2700066K03Rik|2810030C21Rik|AI414051|B130021E18|C79851	ubiquitin specific peptidase 24	protein-coding
mm_132301.1	chr16	33518550	33518559	+	1	NA	promoter-TSS (NM_001083902)	promoter-TSS (NM_001083902)	-41	NM_001083902	171286	Mm.35253	NM_134251	ENSMUSG00000035506	Slc12a8	CCC9|E330020C02Rik	solute carrier family 12 (potassium/chloride transporters), member 8	protein-coding
mm_120546.1	chr14	67316119	67316121	+	1	NA	intron (NM_010095, intron 7 of 16)	intron (NM_010095, intron 7 of 16)	-1409	NM_001037931	628416	Mm.390723	NM_001037931		Gm6878	EG628416	predicted gene 6878	protein-coding
mm_101792.1	chr11	46166329	46166384	-	1	NA	promoter-TSS (NM_172524)	promoter-TSS (NM_172524)	3	NM_172524	214112	Mm.225253	NM_172524	ENSMUSG00000020411	Nipal4	9530066K23Rik	NIPA-like domain containing 4	protein-coding
mm_91113.1	chr10	19186452	19186456	-	1	NA	intron (NR_038022, intron 1 of 1)	intron (NR_038022, intron 1 of 1)	19216	NR_038022	100504265	Mm.383417	NR_038021		Gm20139	-	predicted gene, 20139	ncRNA
mm_37292.1	chr4	119184008	119184025	-	1	NA	exon (NM_013848, exon 6 of 13)	exon (NM_013848, exon 6 of 13)	5995	NM_013848	27028	Mm.290753	NM_013848	ENSMUSG00000028644	Ermap	AA409279|AI666418	erythroblast membrane-associated protein	protein-coding
mm_162492.1	chr1	135924363	135924366	+	1	NA	Intergenic	Intergenic	-5157	NM_019645	18772	Mm.4494	NM_019645	ENSMUSG00000026413	Pkp1	-	plakophilin 1	protein-coding
mm_13919.1	chr2	120609378	120609391	+	1	NA	promoter-TSS (NM_025475)	promoter-TSS (NM_025475)	2	NM_025475	66296	Mm.221900	NM_025475	ENSMUSG00000027285	Haus2	1700101G24Rik|2410007P03Rik|AU020217|Cep27	HAUS augmin-like complex, subunit 2	protein-coding
mm_124687.1	chr15	6435307	6435361	+	1	NA	exon (NM_001102400, exon 10 of 13)	exon (NM_001102400, exon 10 of 13)	-9999	NM_013485	12279	Mm.29095	NM_013485	ENSMUSG00000022149	C9	-	complement component 9	protein-coding
mm_57000.1	chr6	121003100	121003134	-	1	NA	intron (NM_001270475, intron 17 of 31)	intron (NM_001270475, intron 17 of 31)	44273	NR_138099	215458	Mm.122399	NR_138099		LOC215458	-	uncharacterized LOC215458	ncRNA
mm_29750.1	chr3	127027554	127027585	-	1	NA	intron (NM_001327938, intron 13 of 47)	B4A|SINE|B4	-29117	NM_178655	109676	Mm.220242	NM_178655	ENSMUSG00000032826	Ank2	100043364|AI835472|AW491075|Ank-2|Gm4392	ankyrin 2, brain	protein-coding
mm_115875.1	chr13	21746317	21746348	-	1	NA	Intergenic	RLTR22_Mur|LTR|ERVK	4221	NM_178211	319160	Mm.255646	NM_178211	ENSMUSG00000064288	Hist1h4k	-	histone cluster 1, H4k	protein-coding
mm_129415.1	chr15	78388739	78388749	-	1	NA	promoter-TSS (NM_001163613)	promoter-TSS (NM_001163613)	25	NM_001163613	73376	Mm.73222	NM_028522	ENSMUSG00000062154	Tex33	1700061J05Rik|Ean57	testis expressed 33	protein-coding
mm_91497.1	chr10	37136016	37136052	-	1	NA	3' UTR (NM_008538, exon 2 of 2)	3' UTR (NM_008538, exon 2 of 2)	2892	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_72110.1	chr8	71612145	71612163	+	1	NA	exon (NM_146211, exon 2 of 12)	exon (NM_146211, exon 2 of 12)	1130	NM_146211	234407	Mm.240885	NM_146211	ENSMUSG00000034807	Colgalt1	2810024B22Rik|Glt25d1	collagen beta(1-O)galactosyltransferase 1	protein-coding
mm_95267.1	chr11	45005089	45005096	+	1	NA	3' UTR (NM_001290711, exon 16 of 16)	3' UTR (NM_001290711, exon 16 of 16)	111836	NR_045100	100504255	Mm.123608	NR_045100	ENSMUSG00000084773	Gm12159	OTTMUSG00000005475	predicted gene 12159	ncRNA
mm_133960.1	chr16	4087742	4087761	-	1	NA	exon (NM_001025432, exon 30 of 31)	exon (NM_001025432, exon 30 of 31)	-9941	NM_026508	68015	Mm.123366	NM_026508	ENSMUSG00000005981	Trap1	2410002K23Rik|HSP75	TNF receptor-associated protein 1	protein-coding
mm_98282.1	chr11	89060668	89060672	+	1	NA	promoter-TSS (NM_019505)	promoter-TSS (NM_019505)	78	NM_019505	56077	Mm.153695	NM_019505	ENSMUSG00000000276	Dgke	C87606|DAGK6|DGK	diacylglycerol kinase, epsilon	protein-coding
mm_30818.1	chr4	21848040	21848077	+	1	NA	non-coding (NR_028384, exon 1 of 1)	non-coding (NR_028384, exon 1 of 1)	390	NR_028384	67735	Mm.391650	NR_028384		4930528A17Rik	-	RIKEN cDNA 4930528A17 gene	ncRNA
mm_17894.1	chr2	35067015	35067030	-	1	NA	Intergenic	Intergenic	-5581	NM_010406	15139	Mm.2168	NM_010406	ENSMUSG00000026874	Hc	C5|C5a|He	hemolytic complement	protein-coding
mm_44094.1	chr5	149247440	149247454	+	1	NA	Intergenic	Intergenic	-17557	NM_001308462	11690	Mm.19844	NM_009663	ENSMUSG00000060063	Alox5ap	Flap	arachidonate 5-lipoxygenase activating protein	protein-coding
mm_90522.1	chr10	128059097	128059153	+	1	NA	5' UTR (NM_019766, exon 1 of 8)	5' UTR (NM_019766, exon 1 of 8)	143	NM_019766	56351	Mm.305816	NM_019766	ENSMUSG00000071072	Ptges3	5730442A20Rik|Ptges|Tebp|cPGES|p23|sid3177	prostaglandin E synthase 3 (cytosolic)	protein-coding
mm_117869.1	chr13	98877879	98877882	-	1	NA	intron (NM_001048267, intron 5 of 23)	PB1D10|SINE|Alu	13162	NM_001048267	238799	Mm.173286	NM_178716	ENSMUSG00000009470	Tnpo1	AU021749|D13Ertd688e|IPO2|Kpnb2|MIP|MIP1|TRN	transportin 1	protein-coding
mm_37183.1	chr4	117277713	117277723	-	1	NA	intron (NM_025739, intron 10 of 14)	intron (NM_025739, intron 10 of 14)	11737	NM_001310730	66743	Mm.318331	NM_025739	ENSMUSG00000028677	Rnf220	4732477A13|4931406I20Rik|5730503K05Rik|AV302541	ring finger protein 220	protein-coding
mm_158765.1	chrX	166546510	166546514	-	1	NA	exon (NM_019397, exon 7 of 12)	exon (NM_019397, exon 7 of 12)	-36034	NM_001007577	245695	Mm.336318	NM_001007577	ENSMUSG00000051224	Tceanc	A630018P17Rik|Gm390	transcription elongation factor A (SII) N-terminal and central domain containing	protein-coding
mm_38011.1	chr4	133753031	133753044	-	1	NA	exon (NM_001080819, exon 1 of 20)	exon (NM_001080819, exon 1 of 20)	574	NM_001080819	93760	Mm.22478	NM_001080819	ENSMUSG00000007880	Arid1a	1110030E03Rik|BAF250a|Osa1|Smarcf1	AT rich interactive domain 1A (SWI-like)	protein-coding
mm_140323.1	chr17	86753668	86753672	+	1	NA	promoter-TSS (NM_010137)	promoter-TSS (NM_010137)	-194	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_159471.1	chr4	12140301	12140301	+	1	NA	5' UTR (NM_028226, exon 1 of 3)	5' UTR (NM_028226, exon 1 of 3)	184	NM_028226	72397	Mm.430709	NM_028226	ENSMUSG00000046667	Rbm12b1	3000004N20Rik|Rbm12b|Rbm12ba	RNA binding motif protein 12 B1	protein-coding
mm_70550.1	chr8	13056149	13056156	+	1	NA	3' UTR (NM_007972, exon 9 of 9)	3' UTR (NM_007972, exon 9 of 9)	-4756	NM_025834	66901	Mm.441140	NM_025834	ENSMUSG00000031445	Proz	1300015B06Rik	protein Z, vitamin K-dependent plasma glycoprotein	protein-coding
mm_73796.1	chr8	117265905	117265909	+	1	NA	intron (NM_001163262, intron 1 of 20)	PB1D10|SINE|Alu	8888	NM_001163262	74440	Mm.233181	NM_028941	ENSMUSG00000034390	Cmip	4933407C03Rik|5830471E12Rik|AI314065|AI464126	c-Maf inducing protein	protein-coding
mm_9210.1	chr1	171229876	171229893	-	1	NA	exon (NM_010185, exon 5 of 5)	exon (NM_010185, exon 5 of 5)	4465	NM_010185	14127	Mm.22673	NM_010185	ENSMUSG00000058715	Fcer1g	AI573376|CD23|FcR-gamma|FcR[g]|FcRgamma|Fce1g|FcepsilonRI|Ly-50	Fc receptor, IgE, high affinity I, gamma polypeptide	protein-coding
mm_166404.1	chr5	136179751	136179787	+	1	NA	TTS (NM_025774)	TTS (NM_025774)	-9113	NM_178751	269717	Mm.308396	NM_178751	ENSMUSG00000039747	Orai2	A730041O15Rik|Tmem142b	ORAI calcium release-activated calcium modulator 2	protein-coding
mm_133806.1	chr16	95700556	95700559	+	1	NA	Intergenic	Intergenic	-1850	NM_011809	23872	Mm.290207	NM_011809	ENSMUSG00000022895	Ets2	AU022856|Ets-2	E26 avian leukemia oncogene 2, 3' domain	protein-coding
mm_143542.1	chr17	74016999	74017006	-	1	NA	TTS (NM_053188)	TTS (NM_053188)	30914	NM_053188	94224	Mm.38933	NM_053188	ENSMUSG00000038541	Srd5a2	5ART2|S5AR 2	steroid 5 alpha-reductase 2	protein-coding
mm_55555.1	chr6	71270732	71270748	-	1	NA	promoter-TSS (NR_106192)	promoter-TSS (NR_106192)	-931	NR_106192	102465900		NR_106192	ENSMUSG00000098623	Mir8112	Gm27739|mmu-mir-8112	microRNA 8112	ncRNA
mm_20879.1	chr2	148771402	148771435	-	1	NA	promoter-TSS (NM_030059)	promoter-TSS (NM_030059)	79	NM_030059	78240	Mm.99424	NM_030059	ENSMUSG00000036958	Cst11	9230101F08Rik|BB067629|CRES2|mCSTE1	cystatin 11	protein-coding
mm_133645.1	chr16	91793562	91793572	+	1	NA	intron (NM_001110275, intron 4 of 28)	intron (NM_001110275, intron 4 of 28)	64196	NM_010587	16443	Mm.40546	NM_010587	ENSMUSG00000022957	Itsn1	AA517634|AA545208|AI316805|AI839402|AI848451|Ehsh1|Ese1|Itsn|Sh3p17	intersectin 1 (SH3 domain protein 1A)	protein-coding
mm_63745.1	chr7	130943447	130943464	+	1	NA	intron (NM_019564, intron 1 of 8)	intron (NM_019564, intron 1 of 8)	7252	NM_019564	56213	Mm.30156	NM_019564	ENSMUSG00000006205	Htra1	AI429470|HTRA|L56|Prss11|RSPP11	HtrA serine peptidase 1	protein-coding
mm_53787.1	chr6	146589134	146589146	+	1	NA	intron (NM_001347513, intron 3 of 5)	intron (NM_001347513, intron 3 of 5)	11229	NM_026218	67529	Mm.333499	NM_026218	ENSMUSG00000040242	Fgfr1op2	1500031J01Rik	FGFR1 oncogene partner 2	protein-coding
mm_118878.1	chr14	25868828	25868856	+	1	NA	intron (NM_013469, intron 1 of 14)	intron (NM_013469, intron 1 of 14)	26687	NM_013469	11744	Mm.294083	NM_013469	ENSMUSG00000021866	Anxa11	A830099O17Rik|Anx11	annexin A11	protein-coding
mm_79318.1	chr9	52104237	52104260	+	1	NA	Intergenic	Intergenic	-11375	NR_105750	102465150		NR_105750	ENSMUSG00000099311	Mir6244	Gm27368|mmu-mir-6244	microRNA 6244	ncRNA
mm_88101.1	chr10	68780255	68780274	+	1	NA	3' UTR (NM_177794, exon 6 of 6)	3' UTR (NM_177794, exon 6 of 6)	56518	NM_177794	327766	Mm.2479	NM_177794	ENSMUSG00000060044	Tmem26	3230401A06|AI195372	transmembrane protein 26	protein-coding
mm_167504.1	chr9	13298186	13298201	+	1	NA	Intergenic	Intergenic	51237	NM_025534	66396	Mm.290620	NM_025534	ENSMUSG00000079084	Ccdc82	2310043N13Rik	coiled-coil domain containing 82	protein-coding
mm_53197.1	chr6	125539709	125539716	+	1	NA	Intergenic	Lx8|LINE|L1	-13236	NM_011708	22371	Mm.22339	NM_011708	ENSMUSG00000001930	Vwf	6820430P06Rik|AI551257|B130011O06Rik|C630030D09|F8VWF|VWD	Von Willebrand factor	protein-coding
mm_167708.1	chr9	96636752	96636772	+	1	NA	Intergenic	Intergenic	-5259	NM_053268	114713	Mm.124502	NM_053268	ENSMUSG00000032413	Rasa2	5430433H21Rik|AA517451|AU023900|GAP1m	RAS p21 protein activator 2	protein-coding
mm_103450.1	chr11	76202636	76202639	-	1	NA	intron (NM_027773, intron 2 of 4)	intron (NM_027773, intron 2 of 4)	581	NM_027773	116972	Mm.188413	NM_027773	ENSMUSG00000069808	Fam57a	2310047D13Rik|4932415L08Rik|5430402E13Rik|5430420K21Rik|Wdt3	family with sequence similarity 57, member A	protein-coding
mm_49562.1	chr6	30580876	30580886	+	1	NA	intron (NM_027926, intron 5 of 10)	intron (NM_027926, intron 5 of 10)	12512	NM_027926	71791	Mm.105759	NM_027926	ENSMUSG00000039070	Cpa4	1110019K20Rik|AV009555	carboxypeptidase A4	protein-coding
mm_127327.1	chr15	100304943	100304991	+	1	NA	exon (NM_027334, exon 1 of 2)	exon (NM_027334, exon 1 of 2)	150	NM_027334	70152	Mm.488086	NM_027334	ENSMUSG00000054619	Mettl7a1	2210414H16Rik|3300001H21Rik|Aam-B|Mettl7a|UbiE1	methyltransferase like 7A1	protein-coding
mm_96978.1	chr11	70654095	70654131	+	1	NA	intron (NM_011072, intron 1 of 2)	CpG	537	NM_011072	18643	Mm.2647	NM_011072	ENSMUSG00000018293	Pfn1	Pfn	profilin 1	protein-coding
mm_86426.1	chr10	3834877	3834904	+	1	NA	intron (NM_001159942, intron 2 of 16)	intron (NM_001159942, intron 2 of 16)	-37777	NM_001033253	213783	Mm.150831	NM_001033253	ENSMUSG00000040624	Plekhg1	D10Ertd733e|Gm521|mKIAA1209	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	protein-coding
mm_110149.1	chr12	26450580	26450658	-	1	NA	exon (NM_021384, exon 3 of 6)	exon (NM_021384, exon 3 of 6)	5833	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_67158.1	chr7	73541497	73541505	-	1	NA	non-coding (NR_037569, exon 5 of 5)	non-coding (NR_037569, exon 5 of 5)	245	NM_001081345	244059	Mm.34539	NM_001081345	ENSMUSG00000078671	Chd2	2810013C04Rik|2810040A01Rik|5630401D06Rik|AI851092|BC029703|CHD-2	chromodomain helicase DNA binding protein 2	protein-coding
mm_135276.1	chr16	38432880	38432919	-	1	NA	5' UTR (NM_134102, exon 1 of 11)	5' UTR (NM_134102, exon 1 of 11)	246	NM_134102	85031	Mm.279805	NM_134102	ENSMUSG00000002847	Pla1a	AA986889|Ps-pla1|Pspla1	phospholipase A1 member A	protein-coding
mm_20518.1	chr2	130697463	130697481	-	1	NA	promoter-TSS (NM_001081162)	promoter-TSS (NM_001081162)	47	NM_001081162	269356	Mm.441391	NM_001081162	ENSMUSG00000074796	Slc4a11	AI503023|BTR1|NaBC1	solute carrier family 4, sodium bicarbonate transporter-like, member 11	protein-coding
mm_149157.1	chr19	9017119	9017133	+	1	NA	promoter-TSS (NR_105786)	promoter-TSS (NR_105786)	-778	NR_105786	102465190		NR_105786	ENSMUSG00000099308	Mir6367	Gm27467|mmu-mir-6367	microRNA 6367	ncRNA
mm_1683.1	chr1	74856543	74856552	+	1	NA	3' UTR (NM_009872, exon 1 of 1)	3' UTR (NM_009872, exon 1 of 1)	1518	NM_009872	12570	Mm.153833	NM_009872	ENSMUSG00000090071	Cdk5r2	B230310J22Rik|p39	cyclin-dependent kinase 5, regulatory subunit 2 (p39)	protein-coding
mm_2496.1	chr1	106026380	106026382	+	1	NA	intron (NM_001122676, intron 11 of 13)	intron (NM_001122676, intron 11 of 13)	35975	NM_001122675	227449	Mm.210188	NM_001122675	ENSMUSG00000038866	Zcchc2	9930114B20Rik|AW212015	zinc finger, CCHC domain containing 2	protein-coding
mm_166360.1	chr5	123248698	123248728	+	1	NA	3' UTR (NM_026000, exon 6 of 6)	3' UTR (NM_026000, exon 6 of 6)	20523	NM_026000	67151	Mm.278997	NM_026000	ENSMUSG00000029440	Psmd9	1500011J20Rik|2610202L11Rik|Bridge-1|P27	proteasome (prosome, macropain) 26S subunit, non-ATPase, 9	protein-coding
mm_155934.1	chrX	103493770	103493782	+	1	NA	intron (NR_015508, intron 1 of 2)	CpG	218	NR_015508	70252	Mm.380486	NR_015508	ENSMUSG00000097571	Jpx	2010000I03Rik|2510040I06Rik|Enox	Jpx transcript, Xist activator (non-protein coding)	ncRNA
mm_106397.1	chr11	118797980	118797989	-	1	NA	intron (NM_001039168, intron 2 of 14)	intron (NM_001039168, intron 2 of 14)	-36943	NM_001285438	52897	Mm.341103	NM_001024931	ENSMUSG00000025576	Rbfox3	Fox-3|Hrnbp3|NeuN|Neuna60	RNA binding protein, fox-1 homolog (C. elegans) 3	protein-coding
mm_118385.1	chr13	117242698	117242709	-	1	NA	intron (NM_010330, intron 2 of 8)	MIR|SINE|MIR	22130	NM_010330	13723	Mm.274926	NM_010330	ENSMUSG00000021728	Emb	AL022799|Gp70	embigin	protein-coding
mm_82473.1	chr9	16501986	16502089	-	1	NA	Intergenic	CpG	-123806	NM_001080814	270120	Mm.195010	NM_001080814	ENSMUSG00000074505	Fat3	9430076A06Rik|D430038H04Rik|Gm1132|Gm510|MFAT3F	FAT atypical cadherin 3	protein-coding
mm_154066.1	chr19	55315981	55316038	-	1	NA	promoter-TSS (NM_025883)	promoter-TSS (NM_025883)	23	NM_025883	66980	Mm.386789	NM_025883	ENSMUSG00000024982	Zdhhc6	2400007G07Rik|5930409M18Rik|AI462345|C77369	zinc finger, DHHC domain containing 6	protein-coding
mm_147977.1	chr18	67449084	67449205	-	1	NA	promoter-TSS (NM_027130)	promoter-TSS (NM_027130)	-8	NM_027130	69597	Mm.426052	NM_027130	ENSMUSG00000024527	Afg3l2	2310036I02Rik|AW260507|Emv66|par	AFG3-like AAA ATPase 2	protein-coding
mm_153203.1	chr19	34640717	34640729	-	1	NA	promoter-TSS (NM_053217)	promoter-TSS (NM_053217)	20	NM_053217	112419	Mm.440727	NM_053217	ENSMUSG00000067297	Ifit1bl2	2010002M12Rik|AW412491|Ifit1b	interferon induced protein with tetratricopeptide repeats 1B like 2	protein-coding
mm_118686.1	chr14	22122164	22122174	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	102457	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_138096.1	chr17	34048399	34048411	+	1	NA	intron (NM_001317722, intron 7 of 64)	intron (NM_001317722, intron 7 of 64)	9267	NM_001317722	12815	Mm.20230	NM_009926	ENSMUSG00000024330	Col11a2	-	collagen, type XI, alpha 2	protein-coding
mm_35641.1	chr4	43519256	43519299	-	1	NA	exon (NM_009416, exon 5 of 9)	exon (NM_009416, exon 5 of 9)	4277	NM_009416	22004	Mm.646	NM_009416	ENSMUSG00000028464	Tpm2	Tpm-2|Trop-2	tropomyosin 2, beta	protein-coding
mm_90962.1	chr10	13324251	13324318	-	1	NA	promoter-TSS (NM_001195096)	promoter-TSS (NM_001195096)	-124	NM_001033257	215789	Mm.283359	NM_001033257	ENSMUSG00000062866	Phactr2	AV158170|BC012871	phosphatase and actin regulator 2	protein-coding
mm_85887.1	chr9	111053834	111053848	-	1	NA	TTS (NM_017466)	TTS (NM_017466)	3403	NM_001302377	54199	Mm.7336	NM_017466	ENSMUSG00000043953	Ccrl2	1810047I05Rik|Ackr5|CCR11|Cmkbr1l2|E01|L-CCR	chemokine (C-C motif) receptor-like 2	protein-coding
mm_123264.1	chr14	61305359	61305370	-	1	NA	promoter-TSS (NR_033788)	promoter-TSS (NR_033788)	-30	NR_033788	67355	Mm.193728	NR_033788	ENSMUSG00000101505	1700109G14Rik	1700126G13Rik	RIKEN cDNA 1700109G14 gene	ncRNA
mm_118734.1	chr14	22275191	22275201	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	255484	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_8526.1	chr1	154884394	154884417	-	1	NA	Intergenic	Intergenic	-158485	NM_009782	12290	Mm.267517	NM_009782	ENSMUSG00000004110	Cacna1e	A430040I15|BII|Cach6|Cacnl1a6|Cav2.3|Cchra1|alpha1E	calcium channel, voltage-dependent, R type, alpha 1E subunit	protein-coding
mm_149605.1	chr19	16359302	16359320	+	1	NA	intron (NM_008139, intron 5 of 6)	intron (NM_008139, intron 5 of 6)	-44307	NR_105832	102465218		NR_105832	ENSMUSG00000098718	Mir496b	Gm28028|mmu-mir-496b	microRNA 496b	ncRNA
mm_154908.1	chrX	21360835	21360851	+	1	NA	promoter-TSS (NR_045668)	promoter-TSS (NR_045668)	-22	NR_045668	331392	Mm.23126	NM_198633	ENSMUSG00000051537	Gm5124	EG331392	nucleolar and coiled-body phosphoprotein 1 pseudogene	pseudo
mm_116422.1	chr13	41828338	41828402	-	1	NA	exon (NM_175417, exon 2 of 7)	exon (NM_175417, exon 2 of 7)	19118	NM_175417	109254	Mm.25195	NM_175417	ENSMUSG00000058022	Adtrp	9530008L14Rik	androgen dependent TFPI regulating protein	protein-coding
mm_127126.1	chr15	98112049	98112066	+	1	NA	promoter-TSS (NM_021514)	promoter-TSS (NM_021514)	-3	NM_021514	18642	Mm.272582	NM_021514	ENSMUSG00000033065	Pfkm	AI131669|ATP-PFK|PFK-A|PFK-M|Pfk-4|Pfk4|Pfka|Pfkx	phosphofructokinase, muscle	protein-coding
mm_23053.1	chr3	35723056	35723078	+	1	NA	Intergenic	PB1|SINE|Alu	-31071	NM_029570	76295	Mm.239416	NM_029570	ENSMUSG00000037400	Atp11b	1110019I14Rik|ATPIF|ATPIR|mKIAA0956	ATPase, class VI, type 11B	protein-coding
mm_94293.1	chr11	4064882	4064898	+	1	NA	promoter-TSS (NM_001029937)	promoter-TSS (NM_001029937)	37	NM_001029937	380683	Mm.296806	NM_001029937	ENSMUSG00000054986	Sec14l3	1110069O07Rik	SEC14-like lipid binding 3	protein-coding
mm_118724.1	chr14	22220629	22220631	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	200918	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_125122.1	chr15	30172679	30172731	+	1	NA	5' UTR (NM_008729, exon 1 of 23)	5' UTR (NM_008729, exon 1 of 23)	112	NM_008729	18163	Mm.321648	NM_008729	ENSMUSG00000022240	Ctnnd2	Catnd2|Nprap|neurojugin	catenin (cadherin associated protein), delta 2	protein-coding
mm_47549.1	chr5	124351268	124351286	-	1	NA	intron (NM_013812, intron 1 of 3)	intron (NM_013812, intron 1 of 3)	3351	NM_013812	13445	Mm.391838	NM_013812	ENSMUSG00000029394	Cdk2ap1	Apc10|Cdkap1|DORC1|Doc1|ST19|doc-1|p12	CDK2 (cyclin-dependent kinase 2)-associated protein 1	protein-coding
mm_145983.1	chr18	68227929	68227975	+	1	NA	intron (NM_172631, intron 3 of 5)	(CA)n|Simple_repeat|Simple_repeat	33021	NR_106078	102465702		NR_106078	ENSMUSG00000098253	Mir7219	Gm27613|mmu-mir-7219	microRNA 7219	ncRNA
mm_93588.1	chr10	117063336	117063366	-	1	NA	intron (NM_007636, intron 1 of 15)	CpG	463	NM_007636	12461	Mm.247788	NM_007636	ENSMUSG00000034024	Cct2	Cctb	chaperonin containing Tcp1, subunit 2 (beta)	protein-coding
mm_59097.1	chr7	19696944	19696959	+	1	NA	exon (NM_009696, exon 4 of 4)	exon (NM_009696, exon 4 of 4)	1447	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_142900.1	chr17	52162632	52162640	-	1	NA	Intergenic	Intergenic	279909	NR_045095	100504169	Mm.417731	NR_045095		Gm20098	-	predicted gene, 20098	ncRNA
mm_98816.1	chr11	97309681	97309700	+	1	NA	Intergenic	Intergenic	-6026	NM_025927	67036	Mm.5381	NM_025927	ENSMUSG00000018882	Mrpl45	2600005P05Rik|AU043542|R75241	mitochondrial ribosomal protein L45	protein-coding
mm_113972.1	chr13	51651692	51651702	+	1	NA	promoter-TSS (NM_029279)	promoter-TSS (NM_029279)	-11	NM_001308448	75420	Mm.275981	NM_029279	ENSMUSG00000035139	Secisbp2	2210413N07Rik|2810012K13Rik|SBP2	SECIS binding protein 2	protein-coding
mm_134172.1	chr16	10796816	10796830	-	1	NA	promoter-TSS (NM_013637)	promoter-TSS (NM_013637)	0	NM_013637	19118	Mm.42733	NM_013637	ENSMUSG00000022501	Prm1	Prm-1	protamine 1	protein-coding
mm_62844.1	chr7	114290338	114290354	+	1	NA	Intergenic	Intergenic	-14230	NM_011965	26440	Mm.121265	NM_011965	ENSMUSG00000030751	Psma1	C2|HC2|Pros-30|alpha-type	proteasome (prosome, macropain) subunit, alpha type 1	protein-coding
mm_113621.1	chr13	41625965	41625992	+	1	NA	intron (NM_001163572, intron 1 of 2)	MTE-int|LTR|ERVL-MaLR	19762	NM_001163572	621976	Mm.259830	NM_001163572	ENSMUSG00000087370	Tmem170b	EG621976	transmembrane protein 170B	protein-coding
mm_73055.1	chr8	94377869	94377881	+	1	NA	Intergenic	Intergenic	-8625	NM_022331	64209	Mm.29151	NM_022331	ENSMUSG00000031770	Herpud1	Herp|Mifl|SUP	homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1	protein-coding
mm_56471.1	chr6	99028252	99028295	-	1	NA	promoter-TSS (NM_001197322)	promoter-TSS (NM_001197322)	25	NM_001197322	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_162947.1	chr11	3330755	3330759	+	1	NA	promoter-TSS (NM_178149)	promoter-TSS (NM_178149)	26	NM_178149	216505	Mm.390323	NM_178149	ENSMUSG00000034614	Pik3ip1	1500004A08Rik|5830455E04Rik|Crkd|Hgfl	phosphoinositide-3-kinase interacting protein 1	protein-coding
mm_155803.1	chrX	99042990	99043017	+	1	NA	intron (NM_199018, intron 1 of 13)	CpG	422	NM_199018	236920	Mm.236928	NM_199018	ENSMUSG00000031216	Stard8	Dlc3|mKIAA0189	START domain containing 8	protein-coding
mm_63556.1	chr7	128077819	128077826	+	1	NA	intron (NM_001082960, intron 6 of 29)	Lx3A|LINE|L1	15182	NM_008401	16409	Mm.262106	NM_008401	ENSMUSG00000030786	Itgam	CD11b/CD18|CR3|CR3A|Cd11b|F730045J24Rik|Ly-40|MAC1|Mac-1|Mac-1a	integrin alpha M	protein-coding
mm_126203.1	chr15	78877542	78877585	+	1	NA	5' UTR (NM_145929, exon 1 of 17)	5' UTR (NM_145929, exon 1 of 17)	373	NM_145929	106039	Mm.251331	NM_145929	ENSMUSG00000033128	Gga1	4930406E12Rik|AU016030|AW209092	golgi associated, gamma adaptin ear containing, ARF binding protein 1	protein-coding
mm_45878.1	chr5	88328269	88328301	-	1	NA	exon (NM_008644, exon 3 of 3)	exon (NM_008644, exon 3 of 3)	10973	NM_008644	17830	Mm.200411	NM_008644	ENSMUSG00000064156	Prol1	Muc10	proline rich, lacrimal 1	protein-coding
mm_167867.1	chrX	23232404	23232408	+	1	NA	intron (NM_001310466, intron 5 of 6)	BC1_Mm|scRNA|scRNA	34396	NM_001310466	67455	Mm.224306	NM_026167	ENSMUSG00000036782	Klhl13	1200009K10Rik|AI451128|Bklhd2|D130072F20Rik	kelch-like 13	protein-coding
mm_121648.1	chr14	9634365	9634398	-	1	NA	intron (NM_001308286, intron 5 of 6)	RMER17C|LTR|ERVK	-249714	NR_030680	100042415	Mm.235938	NR_030680		Mnd1-ps	Gm3833	Mnd1 retrotransposed pseudogene	pseudo
mm_27994.1	chr3	82425164	82425164	-	1	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	67092	NM_001081230	213582	Mm.271269	NM_001081230	ENSMUSG00000033900	Map9	5033421J10Rik|5330427D05Rik|ASAP|Mtap9	microtubule-associated protein 9	protein-coding
mm_47238.1	chr5	121452463	121452518	-	1	NA	promoter-TSS (NM_029912)	promoter-TSS (NM_029912)	-16	NM_026129	67397	Mm.154570	NM_026129	ENSMUSG00000029616	Erp29	1200015M03Rik|2810446M09Rik|AW209030|Erp28|Erp31|PDI-Db	endoplasmic reticulum protein 29	protein-coding
mm_124524.1	chr14	122106941	122106989	-	1	NA	promoter-TSS (NM_080556)	promoter-TSS (NM_080556)	9	NR_015586	319727	Mm.215552	NR_015586		A330035P11Rik	-	RIKEN cDNA A330035P11 gene	ncRNA
mm_21495.1	chr2	163397947	163398000	-	1	NA	promoter-TSS (NM_001205076)	promoter-TSS (NM_001205076)	0	NM_021566	59091	Mm.34459	NM_021566	ENSMUSG00000017817	Jph2	1110002E14Rik|JP-2|Jp2	junctophilin 2	protein-coding
mm_18902.1	chr2	76718125	76718139	-	1	NA	exon (NM_011652, exon 301 of 313)	exon (NM_011652, exon 301 of 313)	42817	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_16006.1	chr2	167363613	167363652	+	1	NA	Intergenic	MLT-int|LTR|ERVL-MaLR	-14454	NM_019835	56336	Mm.200886	NM_019835	ENSMUSG00000017929	B4galt5	9430078I07Rik|AW049941|AW539721	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 5	protein-coding
mm_46047.1	chr5	92065636	92065640	-	1	NA	intron (NM_001080795, intron 6 of 10)	intron (NM_001080795, intron 6 of 10)	17279	NM_001080797	23881	Mm.290530	NM_011816	ENSMUSG00000029405	G3bp2	AA409541|E430034L04Rik|G3BP|mKIAA0660	GTPase activating protein (SH3 domain) binding protein 2	protein-coding
mm_73193.1	chr8	95496447	95496469	+	1	NA	Intergenic	MLT1D|LTR|ERVL-MaLR	-7638	NM_009974	13000	Mm.51136	NM_009974	ENSMUSG00000046707	Csnk2a2	1110035J23Rik|C77789|CK2	casein kinase 2, alpha prime polypeptide	protein-coding
mm_58107.1	chr6	137649212	137649294	-	1	NA	promoter-TSS (NM_007945)	promoter-TSS (NM_007945)	32	NM_001271588	13860	Mm.235346	NM_007945	ENSMUSG00000015766	Eps8	AW261790	epidermal growth factor receptor pathway substrate 8	protein-coding
mm_20780.1	chr2	143988975	143988985	-	1	NA	exon (NM_133626, exon 2 of 3)	exon (NM_133626, exon 2 of 3)	22283	NM_133626	81910	Mm.13705	NM_024281	ENSMUSG00000027422	Rrbp1	1700087N07Rik|5730465C04Rik|ES/130|mKIAA1398|mRRp0|mRRp1.8|mRRp10|mRRp15a|mRRp15b|mRRp16.8|mRRp2|mRRp41|mRRp47|mRRp5.4|p180	ribosome binding protein 1	protein-coding
mm_77878.1	chr9	7184515	7184567	+	1	NA	promoter-TSS (NM_029775)	promoter-TSS (NM_029775)	-25	NM_029775	76863	Mm.27293	NM_029775	ENSMUSG00000032002	Dcun1d5	3110001A18Rik|4833420K19Rik|AW060460|D430047L21Rik	DCN1, defective in cullin neddylation 1, domain containing 5 (S. cerevisiae)	protein-coding
mm_101464.1	chr11	30471856	30471860	-	1	NA	promoter-TSS (NM_001100394)	promoter-TSS (NM_001100394)	-29	NM_001100394	75087	Mm.159422	NM_001100394	ENSMUSG00000040919	4930505A04Rik	-	RIKEN cDNA 4930505A04 gene	protein-coding
mm_113213.1	chr13	25151723	25151745	+	1	NA	intron (NM_177577, intron 7 of 9)	intron (NM_177577, intron 7 of 9)	95730	NM_177577	195208	Mm.284719	NM_177577	ENSMUSG00000035910	Dcdc2a	AW492955|Dcdc2|RU2	doublecortin domain containing 2a	protein-coding
mm_114916.1	chr13	95021827	95021863	+	1	NA	3' UTR (NM_172590, exon 13 of 13)	3' UTR (NM_172590, exon 13 of 13)	45501	NM_172590	218460	Mm.33856	NM_172590	ENSMUSG00000042015	Wdr41	B830029I03Rik|MSTP048	WD repeat domain 41	protein-coding
mm_31427.1	chr4	48084223	48084242	+	1	NA	3' UTR (NM_015743, exon 8 of 8)	3' UTR (NM_015743, exon 8 of 8)	32986	NM_001307989	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_12097.1	chr2	60921204	60921207	+	1	NA	intron (NM_020296, intron 1 of 13)	intron (NM_020296, intron 1 of 13)	-39767	NM_001141931	56878	Mm.259667	NM_020296	ENSMUSG00000026970	Rbms1	2600014B10Rik|AI255215|MSSP-1|MSSP-2|MSSP-3|YC1	RNA binding motif, single stranded interacting protein 1	protein-coding
mm_135006.1	chr16	32246880	32246947	-	1	NA	promoter-TSS (NM_026898)	promoter-TSS (NM_026898)	112	NM_173439	268882	Mm.256137	NM_173439	ENSMUSG00000035764	Fbxo45	2610017J04Rik|AI463119|BC026799	F-box protein 45	protein-coding
mm_149169.1	chr19	9083638	9083648	+	1	NA	TTS (NM_011681)	TTS (NM_011681)	4313	NM_011681	22287	Mm.2258	NM_011681	ENSMUSG00000024653	Scgb1a1	CC10|CC16|CCSP|PCB-BP|UG|UGB|Utg	secretoglobin, family 1A, member 1 (uteroglobin)	protein-coding
mm_65561.1	chr7	27166733	27166765	-	1	NA	promoter-TSS (NM_053208)	promoter-TSS (NM_053208)	53	NM_053208	112406	Mm.29978	NM_053208	ENSMUSG00000058709	Egln2	0610011A13Rik|C85656|Hif-p4h-1|Ier4|Phd1|SM-20	egl-9 family hypoxia-inducible factor 2	protein-coding
mm_12295.1	chr2	69071394	69071410	+	1	NA	exon (NM_001347161, exon 8 of 11)	exon (NM_001347161, exon 8 of 11)	-64398	NM_181547	329416	Mm.90047	NM_181547	ENSMUSG00000034738	Nostrin	Daip2|mDaIP2	nitric oxide synthase trafficker	protein-coding
mm_26914.1	chr3	20132514	20132516	-	1	NA	intron (NM_013755, intron 5 of 6)	intron (NM_013755, intron 5 of 6)	22601	NM_013755	27357	Mm.6375	NM_013755	ENSMUSG00000019528	Gyg	AU017667|Gyg1	glycogenin	protein-coding
mm_5184.1	chr1	13023270	13023319	-	1	NA	Intergenic	Intergenic	-32159	NM_172841	240726	Mm.24481	NM_172841	ENSMUSG00000025938	Slco5a1	4732454B15|A630033C23Rik|AA407151	solute carrier organic anion transporter family, member 5A1	protein-coding
mm_112193.1	chr12	113425477	113425498	-	1	NA	Intergenic	(CAGCT)n|Simple_repeat|Simple_repeat	-64078	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_27720.1	chr3	68902777	68902797	-	1	NA	intron (NM_026641, intron 18 of 19)	intron (NM_026641, intron 18 of 19)	33201	NM_001167996	68725	Mm.45741	NM_001167996	ENSMUSG00000046999	1110032F04Rik	AI115547	RIKEN cDNA 1110032F04 gene	protein-coding
mm_129569.1	chr15	79658855	79658888	-	1	NA	promoter-TSS (NM_028634)	promoter-TSS (NM_028634)	85	NM_029407	75729	Mm.78946	NM_029407	ENSMUSG00000042564	Fam227a	4933432B09Rik	family with sequence similarity 227, member A	protein-coding
mm_30574.1	chr4	3938894	3938898	+	1	NA	promoter-TSS (NM_019969)	promoter-TSS (NM_019969)	8	NM_001285804	66433	Mm.27406	NM_181391	ENSMUSG00000042198	Chchd7	1810049H20Rik	coiled-coil-helix-coiled-coil-helix domain containing 7	protein-coding
mm_114299.1	chr13	59419362	59419397	+	1	NA	Intergenic	Intergenic	125072	NM_001284221	67269	Mm.153008	NM_023328	ENSMUSG00000021557	Agtpbp1	1700020N17Rik|2310001G17Rik|2900054O13Rik|4930445M19Rik|5730402G09Rik|CCP1|Nna1|nmf243|pcd	ATP/GTP binding protein 1	protein-coding
mm_164640.1	chr17	34804404	34804410	-	1	NA	promoter-TSS (NM_009995)	promoter-TSS (NM_009995)	19	NM_009995	13079	Mm.440407	NM_009995	ENSMUSG00000024365	Cyp21a1	21-OH|21OH|21OHA|21OHB|CYP21OH-A|Cyp21|Cyp21-ps1|Cyp21B|Cyp21a2-ps|Cyp21a2ps|Oh21-1|Oh21-2	cytochrome P450, family 21, subfamily a, polypeptide 1	protein-coding
mm_82154.1	chr9	123776504	123776511	+	1	NA	intron (NM_009913, intron 2 of 2)	intron (NM_009913, intron 2 of 2)	9296	NM_001166625	12769	Mm.440604	NM_009913	ENSMUSG00000029530	Ccr9	A130091K22Rik|Cmkbr10|GPR-9-6	chemokine (C-C motif) receptor 9	protein-coding
mm_40483.1	chr5	54377557	54377566	+	1	NA	Intergenic	Lx9|LINE|L1	27569	NR_038045	330086	Mm.254449	NM_177871	ENSMUSG00000105912	Gm10440	D130065D13|ENSMUSG00000072936	predicted gene 10440	ncRNA
mm_80252.1	chr9	72749417	72749443	+	1	NA	3' UTR (NM_010890, exon 29 of 29)	3' UTR (NM_010890, exon 29 of 29)	-57844	NM_175485	235472	Mm.31696	NM_175485	ENSMUSG00000036030	Prtg	A230098A12Rik|Igdcc5	protogenin	protein-coding
mm_98986.1	chr11	98744204	98744225	+	1	NA	intron (NM_178060, intron 1 of 8)	intron (NM_178060, intron 1 of 8)	2429	NM_001313983	21833	Mm.265917	NM_178060	ENSMUSG00000058756	Thra	6430529J03Rik|AW259572|Erba|Nr1a1|Rvr|T3R[a]|T3Ralpha|Thra1|Thra2|c-erbA-1|c-erbA-alpha|c-erbAalpha	thyroid hormone receptor alpha	protein-coding
mm_59847.1	chr7	29783959	29784028	+	1	NA	promoter-TSS (NM_013705)	promoter-TSS (NM_013705)	-797	NM_013705	22693	Mm.292690	NM_013705	ENSMUSG00000047473	Zfp30	2610306P15Rik|Zfp-30	zinc finger protein 30	protein-coding
mm_16504.1	chr2	181287764	181287820	+	1	NA	intron (NM_198169, intron 1 of 9)	CpG	174	NM_198169	229004	Mm.220423	NM_198169	ENSMUSG00000038705	Gmeb2	AI839884	glucocorticoid modulatory element binding protein 2	protein-coding
mm_143635.1	chr17	78985406	78985426	-	1	NA	intron (NM_001171004, intron 2 of 18)	intron (NM_001171004, intron 2 of 18)	23089	NM_001171005	75292	Mm.252776	NM_029239	ENSMUSG00000024070	Prkd3	4930557O20Rik|5730497N19Rik|PKD3|Pkcnu|Prkcn	protein kinase D3	protein-coding
mm_160515.1	chr9	22036413	22036413	-	1	NA	exon (NM_010487, exon 3 of 7)	exon (NM_010487, exon 3 of 7)	15610	NM_010487	15571	Mm.390167	NM_010487	ENSMUSG00000003410	Elavl3	2600009P04Rik|Huc|PLE21|mHuC	ELAV (embryonic lethal, abnormal vision, Drosophila)-like 3 (Hu antigen C)	protein-coding
mm_163286.1	chr11	117991851	117991859	-	1	NA	intron (NM_133757, intron 1 of 9)	intron (NM_133757, intron 1 of 9)	4998	NM_133757	74451	Mm.28864	NM_133757	ENSMUSG00000017715	Pgs1	2610019F11Rik|4933424M23Rik|SAF	phosphatidylglycerophosphate synthase 1	protein-coding
mm_10707.1	chr2	22774318	22774337	+	1	NA	promoter-TSS (NM_019456)	promoter-TSS (NM_019456)	0	NM_019456	54519	Mm.14255	NM_019456	ENSMUSG00000026786	Apbb1ip	9930118P07Rik|Prp48	amyloid beta (A4) precursor protein-binding, family B, member 1 interacting protein	protein-coding
mm_172278.1	chr6	87119518	87119531	-	1	NA	Intergenic	RLTR44C|LTR|ERVK	14778	NM_001167937	52372	Mm.282851	NM_001167937	ENSMUSG00000090891	D6Ertd527e	AU043841	DNA segment, Chr 6, ERATO Doi 527, expressed	protein-coding
mm_137385.1	chr17	25786586	25786613	+	1	NA	promoter-TSS (NM_001165929)	promoter-TSS (NM_001165929)	19	NM_001165929	381077	Mm.328867	NM_001165929	ENSMUSG00000071202	Ccdc78	Gm938|Gm950	coiled-coil domain containing 78	protein-coding
mm_47496.1	chr5	124031019	124031022	-	1	NA	intron (NM_177876, intron 1 of 3)	intron (NM_177876, intron 1 of 3)	1240	NM_177876	330192	Mm.4079	NM_177876	ENSMUSG00000066278	Vps37b	2300007F24Rik|AI415429|BC026744	vacuolar protein sorting 37B	protein-coding
mm_96249.1	chr11	62575898	62575933	+	1	NA	intron (NM_011706, intron 1 of 15)	intron (NM_011706, intron 1 of 15)	1429	NM_011706	22368	Mm.288064	NM_011706	ENSMUSG00000018507	Trpv2	GRC|OTRPC2|VRL-1|Vrl1	transient receptor potential cation channel, subfamily V, member 2	protein-coding
mm_99593.1	chr11	104310481	104310491	+	1	NA	exon (NM_010838, exon 6 of 10)	exon (NM_010838, exon 6 of 10)	79050	NM_001285454	17762	Mm.1287	NM_010838	ENSMUSG00000018411	Mapt	AI413597|AW045860|Mtapt|Tau	microtubule-associated protein tau	protein-coding
mm_11077.1	chr2	27677393	27677403	+	1	NA	5' UTR (NM_011305, exon 1 of 10)	5' UTR (NM_011305, exon 1 of 10)	197	NM_011305	20181	Mm.24624	NM_011305	ENSMUSG00000015846	Rxra	9530071D11Rik|Nr2b1|RXRalpha1	retinoid X receptor alpha	protein-coding
mm_78224.1	chr9	21588181	21588202	+	1	NA	TTS (NM_138303)	TTS (NM_138303)	-4531	NM_178619	69773	Mm.39704	NM_178619	ENSMUSG00000048429	Timm29	1810026J23Rik	translocase of inner mitochondrial membrane 29	protein-coding
mm_46782.1	chr5	112577150	112577177	-	1	NA	promoter-TSS (NM_001253916)	promoter-TSS (NM_001253916)	35	NM_001253917	56747	Mm.143742	NM_019982	ENSMUSG00000058153	Sez6l	AI843918|AIG1|AW539724|Acig1|BSRP-B|mKIAA0927	seizure related 6 homolog like	protein-coding
mm_99736.1	chr11	106374800	106374807	+	1	NA	promoter-TSS (NM_029345)	promoter-TSS (NM_029345)	-23	NM_029345	75573	Mm.159539	NM_029345	ENSMUSG00000009210	Prr29	2310007L24Rik	proline rich 29	protein-coding
mm_120261.1	chr14	63055086	63055093	+	1	NA	promoter-TSS (NR_046019)	promoter-TSS (NR_046019)	16	NR_046019	72609	Mm.387101	NR_046019		2700070H01Rik	-	RIKEN cDNA 2700070H01 gene	ncRNA
mm_73201.1	chr8	95678207	95678216	+	1	NA	Intergenic	CpG	-24826	NM_001195006	234593	Mm.29846	NM_145602	ENSMUSG00000036564	Ndrg4	D8Bwg1337e|Ndr1-rs|Ndr4|R74996|SMAP-8	N-myc downstream regulated gene 4	protein-coding
mm_112755.1	chr13	19342728	19342739	+	1	NA	Intergenic	Intergenic	53080	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_64529.1	chr7	143979416	143979432	+	1	NA	intron (NR_037302, intron 5 of 5)	intron (NR_037302, intron 5 of 5)	-29830	NR_037292	100526562		NR_037292	ENSMUSG00000093221	Mir3105	mmu-mir-3105	microRNA 3105	ncRNA
mm_116003.1	chr13	24603860	24603867	-	1	NA	intron (NR_024599, intron 1 of 1)	intron (NR_024599, intron 1 of 1)	904	NR_024599	76024	Mm.440710	NR_024599		Gm11346	5830431A10Rik|AI447617|Gm11347|OTTMUSG00000000601|OTTMUSG00000000602	X-linked lymphocyte-regulated 5 pseudogene	pseudo
mm_163249.1	chr11	106788918	106788972	+	1	NA	promoter-TSS (NM_177088)	promoter-TSS (NM_177088)	-307	NM_177088	320162	Mm.30524	NM_177088	ENSMUSG00000018372	Cep95	4732496G21Rik|AI118346|AI448335|Ccdc45|D330027A14Rik|F630025I20Rik	centrosomal protein 95	protein-coding
mm_70874.1	chr8	25101073	25101104	+	1	NA	intron (NM_031257, intron 1 of 11)	intron (NM_031257, intron 1 of 11)	723	NM_031257	83436	Mm.261122	NM_031257	ENSMUSG00000031557	Plekha2	6430512N22Rik|AI851530|AU041791|TAPP2|W91773	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 2	protein-coding
mm_97303.1	chr11	76622316	76622362	+	1	NA	Intergenic	CpG	-44600	NM_198894	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_172606.1	chr8	15520043	15520043	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	462390	NM_008664	17930	Mm.272115	NM_008664	ENSMUSG00000031461	Myom2	AW146149	myomesin 2	protein-coding
mm_91455.1	chr10	34019629	34019638	-	1	NA	promoter-TSS (NM_025614)	promoter-TSS (NM_025614)	-17	NM_025614	66521	Mm.28528	NM_025614	ENSMUSG00000019782	Rwdd1	0710001K08Rik|2610002D06Rik|2700069A07Rik|IH1	RWD domain containing 1	protein-coding
mm_172773.1	chr8	94434404	94434405	+	1	NA	non-coding (NR_015514, exon 2 of 3)	non-coding (NR_015514, exon 2 of 3)	699	NR_015514	320377	Mm.486022	NR_015514		9330175E14Rik	A630085K21	RIKEN cDNA 9330175E14 gene	ncRNA
mm_51916.1	chr6	91233795	91233806	+	1	NA	exon (NM_001081437, exon 2 of 17)	exon (NM_001081437, exon 2 of 17)	21036	NM_007992	14115	Mm.249146	NM_007992	ENSMUSG00000064080	Fbln2	5730577E14Rik|FIBL-2	fibulin 2	protein-coding
mm_100908.1	chr11	6228414	6228449	-	1	NA	exon (NM_207242, exon 2 of 19)	exon (NM_207242, exon 2 of 19)	1814	NM_207242	237636	Mm.212492	NM_207242	ENSMUSG00000020447	Npc1l1	9130221N23Rik|Gm243	NPC1-like 1	protein-coding
mm_145630.1	chr18	61109841	61109851	+	1	NA	exon (NM_001037859, exon 3 of 22)	exon (NM_001037859, exon 3 of 22)	4274	NM_001037859	12978	Mm.22574	NM_007779	ENSMUSG00000024621	Csf1r	AI323359|CD115|CSF-1R|Csfmr|Fim-2|Fim2|Fms|M-CSF-R|M-CSFR	colony stimulating factor 1 receptor	protein-coding
mm_63969.1	chr7	139944667	139944679	+	1	NA	exon (NM_009482, exon 2 of 2)	exon (NM_009482, exon 2 of 2)	817	NM_009482	22286	Mm.10205	NM_009482	ENSMUSG00000047751	Utf1	AI505934	undifferentiated embryonic cell transcription factor 1	protein-coding
mm_67583.1	chr7	82971421	82971423	-	1	NA	promoter-TSS (NR_045855)	promoter-TSS (NR_045855)	-31	NR_045855	71285	Mm.76818	NR_045855	ENSMUSG00000109106	4933430H16Rik	-	RIKEN cDNA 4933430H16 gene	ncRNA
mm_20943.1	chr2	151542343	151542354	-	1	NA	promoter-TSS (NM_008019)	promoter-TSS (NM_008019)	-135	NR_126058	14225	Mm.278458	NM_008019	ENSMUSG00000032966	Fkbp1a	FKBP12|Fkbp|Fkbp1	FK506 binding protein 1a	protein-coding
mm_41387.1	chr5	90768634	90768646	+	1	NA	exon (NM_023785, exon 1 of 3)	exon (NM_023785, exon 1 of 3)	122	NM_023785	57349	Mm.293614	NM_023785	ENSMUSG00000029372	Ppbp	2400003M24Rik|AI854500|CTAP3|CTAPIII|Cxcl7|LA-PF4|LDGF|MDGF|NAP-2|NAP-2-L1|Scyb7|TGB|TGB1|THBGB1|b-TG1|beta-TG	pro-platelet basic protein	protein-coding
mm_98853.1	chr11	97663016	97663034	+	1	NA	promoter-TSS (NM_139311)	promoter-TSS (NM_139311)	-387	NM_139311	246198	Mm.23685	NM_139311	ENSMUSG00000038437	Mllt6	AI315037|Af17	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 6	protein-coding
mm_134670.1	chr16	22265921	22265949	-	1	NA	promoter-TSS (NM_001330554)	promoter-TSS (NM_001330554)	70	NM_001330554	20462	Mm.210352	NM_009186	ENSMUSG00000022858	Tra2b	5730405G21Rik|D16Ertd266e|SIG-41|Sfrs10|Silg41|TRA2beta	transformer 2 beta homolog (Drosophila)	protein-coding
mm_9325.1	chr1	171844175	171844185	-	1	NA	intron (NM_001289470, intron 2 of 8)	intron (NM_001289470, intron 2 of 8)	4483	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_52482.1	chr6	114315728	114315737	+	1	NA	3' UTR (NM_178703, exon 16 of 16)	3' UTR (NM_178703, exon 16 of 16)	33097	NM_178703	232333	Mm.5260	NM_178703	ENSMUSG00000030310	Slc6a1	A730043E01|GABATHG|GABATR|GAT-1|Gabt|Gabt1|Gat1|XT-1|Xtrp1	solute carrier family 6 (neurotransmitter transporter, GABA), member 1	protein-coding
mm_148823.1	chr19	6306539	6306553	+	1	NA	promoter-TSS (NM_001033342)	promoter-TSS (NM_001033342)	89	NM_001033342	240505	Mm.329622	NM_001033342	ENSMUSG00000024769	Cdc42bpg	BC046418|MRCKgamma	CDC42 binding protein kinase gamma (DMPK-like)	protein-coding
mm_167176.1	chr7	140096733	140096737	+	1	NA	exon (NM_009475, exon 4 of 5)	exon (NM_009475, exon 4 of 5)	3339	NM_009475	22264	Mm.439707	NM_009475	ENSMUSG00000025467	Prap1	Upa	proline-rich acidic protein 1	protein-coding
mm_121195.1	chr14	103051314	103051502	+	1	NA	exon (NM_008392, exon 4 of 5)	exon (NM_008392, exon 4 of 5)	4396	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_12511.1	chr2	72009396	72009399	+	1	NA	intron (NM_001204165, intron 1 of 30)	MTC|LTR|ERVL-MaLR	28182	NM_019688	56508	Mm.196153	NM_019688	ENSMUSG00000049044	Rapgef4	1300003D15Rik|5730402K07Rik|6330581N18Rik|EPAC 2|Epac-2|Epac2|mKIAA4040	Rap guanine nucleotide exchange factor (GEF) 4	protein-coding
mm_32757.1	chr4	116687250	116687260	+	1	NA	intron (NM_011034, intron 1 of 5)	intron (NM_011034, intron 1 of 5)	-1233	NR_040442	100502959	Mm.395400	NR_040442		AV051173	-	expressed sequence AV051173	ncRNA
mm_127844.1	chr15	7115790	7115808	-	1	NA	Intergenic	Intergenic	-13773	NM_001113386	16880	Mm.149720	NM_013584	ENSMUSG00000054263	Lifr	A230075M04Rik|AW061234|LIF	leukemia inhibitory factor receptor	protein-coding
mm_157986.1	chrX	94212639	94212662	-	1	NA	promoter-TSS (NM_012010)	promoter-TSS (NM_012010)	1	NM_012010	26905	Mm.218851	NM_012010	ENSMUSG00000035150	Eif2s3x	AA409828|AA547477|AI314668|Eif-2gx	eukaryotic translation initiation factor 2, subunit 3, structural gene X-linked	protein-coding
mm_70094.1	chr7	142658758	142658767	-	1	NA	promoter-TSS (NM_010514)	promoter-TSS (NM_010514)	42	NM_010514	16002	Mm.3862	NM_010514	ENSMUSG00000048583	Igf2	AL033362|Igf-2|Igf-II|M6pr|Mpr|Peg2	insulin-like growth factor 2	protein-coding
mm_115023.1	chr13	98904196	98904199	+	1	NA	intron (NM_178716, intron 1 of 23)	intron (NM_178716, intron 1 of 23)	-13155	NM_001048267	238799	Mm.173286	NM_178716	ENSMUSG00000009470	Tnpo1	AU021749|D13Ertd688e|IPO2|Kpnb2|MIP|MIP1|TRN	transportin 1	protein-coding
mm_71961.1	chr8	70527994	70528018	+	1	NA	5' UTR (NM_001199631, exon 1 of 9)	5' UTR (NM_001199631, exon 1 of 9)	160	NM_001199631	14232	Mm.141864	NM_010223	ENSMUSG00000019428	Fkbp8	38kDa|FKBP-38|FKBP-8|Fkbp38	FK506 binding protein 8	protein-coding
mm_66252.1	chr7	35586938	35586949	-	1	NA	intron (NM_145633, intron 1 of 28)	intron (NM_145633, intron 1 of 28)	696	NM_178263	245886	Mm.272620	NM_145633	ENSMUSG00000034867	Ankrd27	AA408090|BC016493|D330003H11Rik|Varp	ankyrin repeat domain 27 (VPS9 domain)	protein-coding
mm_3852.1	chr1	160906373	160906460	+	1	NA	promoter-TSS (NM_001024952)	promoter-TSS (NM_001024952)	5	NM_001024952	381305	Mm.329667	NM_001024952	ENSMUSG00000040423	Rc3h1	5730557L09Rik|Gm551|N28103|mKIAA2025	RING CCCH (C3H) domains 1	protein-coding
mm_6609.1	chr1	75479126	75479142	-	1	NA	promoter-TSS (NM_177056)	promoter-TSS (NM_177056)	337	NM_001001565	74241	Mm.260577	NM_001001565	ENSMUSG00000032997	Chpf	1700028N03Rik|AI414328|D1Bwg1363e	chondroitin polymerizing factor	protein-coding
mm_79066.1	chr9	46233272	46233297	+	1	NA	exon (NM_001289755, exon 4 of 4)	exon (NM_001289755, exon 4 of 4)	2015	NM_001289833	11814	Mm.390161	NM_023114	ENSMUSG00000032081	Apoc3	apo-CIII|apoC-III	apolipoprotein C-III	protein-coding
mm_27224.1	chr3	36053513	36053531	-	1	NA	promoter-TSS (NM_178418)	promoter-TSS (NM_178418)	25	NM_178418	241943	Mm.269018	NM_178418	ENSMUSG00000047696	Ccdc144b	-	coiled-coil domain containing 144B	protein-coding
mm_44847.1	chr5	34187871	34187896	-	1	NA	promoter-TSS (NM_010753)	promoter-TSS (NM_010753)	-173	NM_010753	17122	Mm.259260	NM_010753	ENSMUSG00000037235	Mxd4	2810410A03Rik|Mad4|bHLHc12	Max dimerization protein 4	protein-coding
mm_167874.1	chrX	36894102	36894105	+	1	NA	intron (NM_029891, intron 1 of 2)	B4A|SINE|B4	8796	NM_029891	77286	Mm.21649	NM_029891	ENSMUSG00000044149	Nkrf	9430034D17Rik|AW124770|C80287	NF-kappaB repressing factor	protein-coding
mm_127168.1	chr15	98740253	98740312	+	1	NA	3' UTR (NM_007478, exon 5 of 5)	3' UTR (NM_007478, exon 5 of 5)	-12084	NM_024169	66120	Mm.30729	NM_024169	ENSMUSG00000003355	Fkbp11	1110002O23Rik|FKBP-11	FK506 binding protein 11	protein-coding
mm_130979.1	chr15	103344639	103344656	-	1	NA	3' UTR (NM_010577, exon 30 of 30)	3' UTR (NM_010577, exon 30 of 30)	-4561	NM_013866	29813	Mm.14099	NM_013866	ENSMUSG00000000552	Zfp385a	Hzf|Zfp385|Znf385a	zinc finger protein 385A	protein-coding
mm_74906.1	chr8	25203895	25203923	-	1	NA	Intergenic	Intergenic	-2367	NM_177089	320165	Mm.308452	NM_177089	ENSMUSG00000065954	Tacc1	4833447E04Rik|AA960202|B230378H13Rik	transforming, acidic coiled-coil containing protein 1	protein-coding
mm_169187.1	chr13	66027482	66027493	-	1	NA	Intergenic	Intergenic	-85966	NM_001177832	628709	Mm.390595	NM_001177832	ENSMUSG00000095909	Gm10324	ENSMUSG00000071302	predicted gene 10324	protein-coding
mm_149261.1	chr19	10535436	10535444	+	1	NA	exon (NM_172302, exon 6 of 10)	exon (NM_172302, exon 6 of 10)	10196	NM_172302	269061	Mm.490260	NM_172302	ENSMUSG00000034820	Cpsf7	5730453I16Rik|AL022757|C330017N18Rik	cleavage and polyadenylation specific factor 7	protein-coding
mm_2171.1	chr1	88259428	88259438	+	1	NA	3' UTR (NM_198652, exon 8 of 8)	3' UTR (NM_198652, exon 8 of 8)	9975	NR_040291	78605	Mm.384762	NR_040291		6430706D22Rik	-	RIKEN cDNA 6430706D22 gene	ncRNA
mm_142178.1	chr17	36271116	36271145	-	1	NA	intron (NM_024468, intron 1 of 6)	CpG	303	NM_178281	79263	Mm.40624	NM_024468	ENSMUSG00000045409	Trim39	1100001D15Rik|E130103K13Rik|RBCC-B30.2|Rnf23|mKIAA4179|tfp	tripartite motif-containing 39	protein-coding
mm_80965.1	chr9	103111742	103111866	+	1	NA	promoter-TSS (NM_173781)	promoter-TSS (NM_173781)	-270	NM_173781	270192	Mm.490252	NM_173781	ENSMUSG00000032549	Rab6b	9630015C03|AI844641|C330006L04Rik|D9Bwg0185e	RAB6B, member RAS oncogene family	protein-coding
mm_24207.1	chr3	88621275	88621285	+	1	NA	promoter-TSS (NM_001198913)	promoter-TSS (NM_001198913)	-114	NM_001198913	16800	Mm.239329	NM_008487	ENSMUSG00000028059	Arhgef2	AA408978|GEF|GEF-H1|GEFH1|LFP40|Lbcl1|Lfc|P40|mKIAA0651	rho/rac guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_120624.1	chr14	70457548	70457550	+	1	NA	promoter-TSS (NM_145981)	promoter-TSS (NM_145981)	32	NM_145981	105653	Mm.192598	NM_145981	ENSMUSG00000003469	Phyhip	AW049870|C630010D02Rik|Lnap1ip|PAHX-AP#1|PAHX-AP1	phytanoyl-CoA hydroxylase interacting protein	protein-coding
mm_64428.1	chr7	142577602	142577654	+	1	NA	promoter-TSS (NR_030416)	promoter-TSS (NR_030416)	-481	NR_030416	735280		NR_030416	ENSMUSG00000076275	Mir675	Mirn675|mir-675|mmu-mir-675	microRNA 675	ncRNA
mm_88817.1	chr10	80798903	80798952	+	1	NA	promoter-TSS (NM_023900)	promoter-TSS (NM_023900)	192	NM_013651	20222	Mm.358633	NM_013651	ENSMUSG00000020211	Sf3a2	66kDa|AW047242|PRP11|SFA66|Sap62	splicing factor 3a, subunit 2	protein-coding
mm_39596.1	chr5	23501999	23502017	+	1	NA	exon (NM_026984, exon 26 of 26)	exon (NM_026984, exon 26 of 26)	67579	NM_026984	69188	Mm.205190	NM_026984	ENSMUSG00000029004	Kmt2e	1810033J14Rik|9530077A04Rik|D230038D11Rik|Mll5|NKp44L	lysine (K)-specific methyltransferase 2E	protein-coding
mm_133733.1	chr16	93833272	93833277	+	1	NA	intron (NM_001045529, intron 1 of 16)	intron (NM_001045529, intron 1 of 16)	1153	NM_001045529	338467	Mm.287329	NM_001045529	ENSMUSG00000039456	Morc3	1110051N18Rik|AI452146|BF318192|D16Jhu32e|NXP2|Zcwcc3	microrchidia 3	protein-coding
mm_23253.1	chr3	51232920	51232921	+	1	NA	intron (NM_009834, intron 1 of 2)	Cheshire|DNA|hAT-Charlie	8473	NM_009834	12457	Mm.86541	NM_009834	ENSMUSG00000023087	Noct	AU043840|Ccr4|Ccrn4l	nocturnin	protein-coding
mm_129332.1	chr15	77813204	77813237	-	1	NA	5' UTR (NM_022410, exon 2 of 41)	5' UTR (NM_022410, exon 2 of 41)	28955	NM_022410	17886	Mm.29677	NM_022410	ENSMUSG00000022443	Myh9	Fltn|Myhn-1|Myhn1|NMHCIIA|NMMHC-A|NMMHC-IIA|TU72.6	myosin, heavy polypeptide 9, non-muscle	protein-coding
mm_96875.1	chr11	70214954	70214964	+	1	NA	exon (NM_153081, exon 3 of 5)	exon (NM_153081, exon 3 of 5)	1049	NM_153081	216867	Mm.289238	NM_153081	ENSMUSG00000040938	Slc16a11	AB041591|MCT 11|MNCb-2717	solute carrier family 16 (monocarboxylic acid transporters), member 11	protein-coding
mm_133127.1	chr16	65816024	65816038	+	1	NA	intron (NM_028572, intron 1 of 3)	intron (NM_028572, intron 1 of 3)	398	NM_028572	73569	Mm.25670	NM_028572	ENSMUSG00000091243	Vgll3	1700110N18Rik|4832416J22|C80713|Vgl-3|Vito-2	vestigial like family member 3	protein-coding
mm_67037.1	chr7	67044335	67044344	-	1	NA	intron (NM_001033877, intron 13 of 22)	intron (NM_001033877, intron 13 of 22)	178119	NR_131044	76628	Mm.384589	NR_131043	ENSMUSG00000097527	1700112J16Rik	-	RIKEN cDNA 1700112J16 gene	ncRNA
mm_88918.1	chr10	81183057	81183070	+	1	NA	promoter-TSS (NM_001190474)	promoter-TSS (NM_001190474)	56	NM_001190474	13144	Mm.10294	NM_007828	ENSMUSG00000034974	Dapk3	ZIPK|dlk	death-associated protein kinase 3	protein-coding
mm_71314.1	chr8	43308442	43308466	+	1	NA	Intergenic	Intergenic	-1445	NM_009556	22702	Mm.285848	NM_009556	ENSMUSG00000051176	Zfp42	Rex-1|Rex1|Zfp-42	zinc finger protein 42	protein-coding
mm_118399.1	chr13	119399744	119399747	-	1	NA	intron (NM_001308506, intron 2 of 16)	B3|SINE|B2	9266	NM_008710	18115	Mm.132584	NM_008710	ENSMUSG00000025453	Nnt	4930423F13Rik|AI323702|BB168308	nicotinamide nucleotide transhydrogenase	protein-coding
mm_45167.1	chr5	51458076	51458100	-	1	NA	non-coding (NR_027710, exon 13 of 13)	non-coding (NR_027710, exon 13 of 13)	95833	NR_027710	19017	Mm.259072	NM_008904	ENSMUSG00000029167	Ppargc1a	A830037N07Rik|ENSMUSG00000079510|Gm11133|PGC-1|PPARGC-1-alpha|Pgc-1alpha|Pgc1|Pgco1|Ppargc1	peroxisome proliferative activated receptor, gamma, coactivator 1 alpha	protein-coding
mm_12131.1	chr2	61652069	61652074	+	1	NA	intron (NM_011529, intron 7 of 7)	intron (NM_011529, intron 7 of 7)	58974	NM_001164071	21353	Mm.244393	NM_011529	ENSMUSG00000064289	Tank	C86182|E430026L09Rik|I-TRAF	TRAF family member-associated Nf-kappa B activator	protein-coding
mm_20468.1	chr2	129370308	129370354	-	1	NA	5' UTR (NM_008361, exon 2 of 7)	5' UTR (NM_008361, exon 2 of 7)	429	NR_015474	329514	Mm.207315	NM_177848	ENSMUSG00000074805	Il1bos	9430083I22|Gm14047|OTTMUSG00000015529	interleukin 1 beta, opposite strand	ncRNA
mm_80410.1	chr9	77657395	77657399	+	1	NA	3' UTR (NM_172925, exon 3 of 3)	3' UTR (NM_172925, exon 3 of 3)	20665	NM_172925	244923	Mm.138238	NM_172925	ENSMUSG00000044938	Klhl31	9830147P19Rik|D930047P17Rik|Kbtbd1	kelch-like 31	protein-coding
mm_8244.1	chr1	138582371	138582379	-	1	NA	intron (NM_001311148, intron 1 of 7)	LTR16A|LTR|ERVL	37382	NM_021605	59125	Mm.143817	NM_021605	ENSMUSG00000026393	Nek7	2810460C19Rik|AU020186	NIMA (never in mitosis gene a)-related expressed kinase 7	protein-coding
mm_142974.1	chr17	56140315	56140327	-	1	NA	promoter-TSS (NM_001130456)	promoter-TSS (NM_001130456)	22	NM_001130456	20359	Mm.8029	NM_013662	ENSMUSG00000001227	Sema6b	Sema|Seman|VIb|semaZ	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B	protein-coding
mm_20760.1	chr2	140773553	140773555	-	1	NA	intron (NM_001013802, intron 3 of 18)	intron (NM_001013802, intron 3 of 18)	-102078	NM_178382	71436	Mm.426781	NM_178382	ENSMUSG00000051379	Flrt3	5530600M07Rik|C430047I10Rik|mKIAA1469	fibronectin leucine rich transmembrane protein 3	protein-coding
mm_161683.1	chr17	20285662	20285662	-	1	NA	promoter-TSS (NM_001104568)	promoter-TSS (NM_001104568)	-232	NM_001104568	224576	Mm.469854	NM_001104568	ENSMUSG00000091656	Vmn2r106	EG224576	vomeronasal 2, receptor 106	protein-coding
mm_155328.1	chrX	65047639	65047649	+	1	NA	promoter-TSS (NM_027302)	promoter-TSS (NM_027302)	0	NM_027302	70062	Mm.45791	NM_027302	ENSMUSG00000031181	Ctag2	1700030B21Rik	cancer/testis antigen 2	protein-coding
mm_61902.1	chr7	90130228	90130279	+	1	NA	promoter-TSS (NM_001252521)	promoter-TSS (NM_001252521)	21	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_50504.1	chr6	49036558	49036564	+	1	NA	promoter-TSS (NM_053110)	promoter-TSS (NM_053110)	43	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_122826.1	chr14	54686273	54686283	-	1	NA	5' UTR (NM_021437, exon 1 of 2)	5' UTR (NM_021437, exon 1 of 2)	107	NM_021437	58248	Mm.197509	NM_021437	ENSMUSG00000040822	1700123O20Rik	MNCb-2990	RIKEN cDNA 1700123O20 gene	protein-coding
mm_45891.1	chr5	88564819	88564829	-	1	NA	promoter-TSS (NM_001289775)	promoter-TSS (NM_001289775)	-216	NM_001289774	52822	Mm.270469	NM_027530	ENSMUSG00000029291	Rufy3	2810428M05Rik|6330416M07Rik|AW455998|AW538594|D5Bwg0860e|Ripx|Rpipx	RUN and FYVE domain containing 3	protein-coding
mm_79456.1	chr9	56248868	56248873	+	1	NA	intron (NM_172924, intron 4 of 6)	intron (NM_172924, intron 4 of 6)	-87800	NM_019793	56434	Mm.28484	NM_019793	ENSMUSG00000032324	Tspan3	1700055K04Rik|TM4-A|Tm4sf8	tetraspanin 3	protein-coding
mm_124849.1	chr15	9524348	9524358	+	1	NA	intron (NM_008372, intron 2 of 7)	intron (NM_008372, intron 2 of 7)	5523	NM_008372	16197	Mm.389	NM_008372	ENSMUSG00000003882	Il7r	CD127|IL-7Ralpha	interleukin 7 receptor	protein-coding
mm_89750.1	chr10	99263225	99263240	+	1	NA	promoter-TSS (NM_026268)	promoter-TSS (NM_026268)	1	NM_026268	67603	Mm.1791	NM_026268	ENSMUSG00000019960	Dusp6	1300019I03Rik|MKP-3|MKP3|PYST1	dual specificity phosphatase 6	protein-coding
mm_42167.1	chr5	112261586	112261596	+	1	NA	intron (NM_023695, intron 3 of 5)	MIRb|SINE|MIR	5771	NM_001312893	12960	Mm.29488	NM_023695	ENSMUSG00000029343	Crybb1	3110006K12Rik|BB1CRY	crystallin, beta B1	protein-coding
mm_149535.1	chr19	12465742	12465761	+	1	NA	TTS (NM_010821)	TTS (NM_010821)	4972	NM_010821	17476	Mm.3999	NM_010821	ENSMUSG00000046805	Mpeg1	MPS1|Mpg-1	macrophage expressed gene 1	protein-coding
mm_148614.1	chr19	5366966	5367037	+	1	NA	promoter-TSS (NM_011793)	promoter-TSS (NM_011793)	-125	NM_011793	23825	Mm.358649	NM_011793	ENSMUSG00000024844	Banf1	Baf|Bcrp1|L2bp1/Baf	barrier to autointegration factor 1	protein-coding
mm_13098.1	chr2	91259823	91259860	+	1	NA	intron (NM_028733, intron 1 of 10)	intron (NM_028733, intron 1 of 10)	2512	NM_028733	80708	Mm.236650	NM_028733	ENSMUSG00000027257	Pacsin3	4921507A02Rik|6330413E15Rik|AW413130	protein kinase C and casein kinase substrate in neurons 3	protein-coding
mm_64339.1	chr7	142376844	142376878	+	1	NA	exon (NM_009983, exon 8 of 9)	exon (NM_009983, exon 8 of 9)	-3115	NM_001347541	320802	Mm.154486	NM_177265	ENSMUSG00000045777	Ifitm10	6330512M04Rik|AI848576|DSPA3	interferon induced transmembrane protein 10	protein-coding
mm_112574.1	chr13	13590460	13590471	+	1	NA	promoter-TSS (NM_010748)	promoter-TSS (NM_010748)	56	NM_010748	17101	Mm.342337	NM_010748	ENSMUSG00000019726	Lyst	D13Sfk13|beige|bg	lysosomal trafficking regulator	protein-coding
mm_155355.1	chrX	69360395	69360411	+	1	NA	promoter-TSS (NM_008032)	promoter-TSS (NM_008032)	72	NM_008032	14266	Mm.466576	NM_008032	ENSMUSG00000031189	Aff2	FMR2P|Fmr2|Ox19|Oxh	AF4/FMR2 family, member 2	protein-coding
mm_84550.1	chr9	67573227	67573269	-	1	NA	Intergenic	Intergenic	-13545	NM_001081242	70549	Mm.33645	NM_027458	ENSMUSG00000052698	Tln2	5730421P04Rik|AI507121|AI787438|AL118320|mKIAA0320	talin 2	protein-coding
mm_41910.1	chr5	105591293	105591300	+	1	NA	intron (NM_133897, intron 3 of 3)	B4|SINE|B4	71825	NM_133897	100604	Mm.319847	NM_133897	ENSMUSG00000054720	Lrrc8c	AD158|AI326115|E430036I04Rik|fad158	leucine rich repeat containing 8 family, member C	protein-coding
mm_53593.1	chr6	138115098	138115101	+	1	NA	Intergenic	Intergenic	-25438	NM_019946	56615	Mm.14796	NM_019946	ENSMUSG00000008540	Mgst1	1500002K10Rik|Gst	microsomal glutathione S-transferase 1	protein-coding
mm_144800.1	chr18	36109812	36109816	+	1	NA	non-coding (NR_015571, exon 2 of 2)	non-coding (NR_015571, exon 2 of 2)	3611	NR_015571	74966	Mm.379238	NM_030089		4930471G03Rik	1700007N01Rik	RIKEN cDNA 4930471G03 gene	ncRNA
mm_157088.1	chrX	9436662	9436664	-	1	NA	3' UTR (NM_007807, exon 13 of 13)	3' UTR (NM_007807, exon 13 of 13)	32661	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_83025.1	chr9	37233676	37233693	-	1	NA	exon (NM_001145960, exon 16 of 19)	exon (NM_001145960, exon 16 of 19)	22054	NM_020258	56857	Mm.440037	NM_020258	ENSMUSG00000032122	Slc37a2	G3PP|Slc37a1|cI-2|ci2	solute carrier family 37 (glycerol-3-phosphate transporter), member 2	protein-coding
mm_60041.1	chr7	31059361	31059382	+	1	NA	promoter-TSS (NM_144556)	promoter-TSS (NM_144556)	-564	NM_144556	243914	Mm.389870	NM_144556	ENSMUSG00000036560	Lgi4	Lgil3|clp	leucine-rich repeat LGI family, member 4	protein-coding
mm_6544.1	chr1	75128578	75128600	-	1	NA	exon (NM_194333, exon 10 of 12)	exon (NM_194333, exon 10 of 12)	5301	NM_194333	22626	Mm.68157	NM_194333	ENSMUSG00000026205	Slc23a3	SVCT3|Yspl1	solute carrier family 23 (nucleobase transporters), member 3	protein-coding
mm_142333.1	chr17	43538959	43538967	-	1	NA	exon (NM_001254953, exon 2 of 3)	exon (NM_001254953, exon 2 of 3)	4676	NM_001254953	100043332	Mm.17626	NM_001254953	ENSMUSG00000096140	Ankrd66	AU041848|D730048J04Rik|Gm4368	ankyrin repeat domain 66	protein-coding
mm_75844.1	chr8	70618775	70618809	-	1	NA	intron (NM_153074, intron 2 of 2)	intron (NM_153074, intron 2 of 2)	1948	NM_153074	211228	Mm.132939	NM_153074	ENSMUSG00000049988	Lrrc25	Mapa	leucine rich repeat containing 25	protein-coding
mm_101983.1	chr11	50431289	50431321	-	1	NA	promoter-TSS (NM_172557)	promoter-TSS (NM_172557)	-194	NM_172557	216724	Mm.390400	NM_172557	ENSMUSG00000020375	Rufy1	3000002E04Rik|Rabip4|ZFYVE12	RUN and FYVE domain containing 1	protein-coding
mm_156510.1	chrX	150547438	150547452	+	1	NA	promoter-TSS (NR_106147)	promoter-TSS (NR_106147)	0	NR_106147	102465782		NR_106147	ENSMUSG00000099172	Mir3620	Gm27984|mmu-mir-3620	microRNA 3620	ncRNA
mm_33083.1	chr4	123928299	123928319	+	1	NA	intron (NM_017475, intron 5 of 6)	intron (NM_017475, intron 5 of 6)	10876	NM_017475	54170	Mm.220922	NM_017475	ENSMUSG00000028646	Rragc	AU041672|Gtr2|RAGC|TIB929|YGR163W	Ras-related GTP binding C	protein-coding
mm_46057.1	chr5	92256294	92256304	-	1	NA	Intergenic	Intergenic	-3140	NM_011148	19023	Mm.87155	NM_011148	ENSMUSG00000029410	Ppef2	-	protein phosphatase, EF hand calcium-binding domain 2	protein-coding
mm_57336.1	chr6	124742676	124742729	-	1	NA	3' UTR (NM_007881, exon 10 of 10)	3' UTR (NM_007881, exon 10 of 10)	-1623	NM_013535	14790	Mm.439877	NM_013535	ENSMUSG00000072772	Grcc10	2310033H05Rik|C10	gene rich cluster, C10 gene	protein-coding
mm_65062.1	chr7	18890356	18890371	-	1	NA	TTS (NM_009402)	TTS (NM_009402)	5673	NM_009402	21946	Mm.21855	NM_009402	ENSMUSG00000030413	Pglyrp1	PGRP|PGRP-S|Pglyrp|Tag7|Tasg7|Tnfsf3l	peptidoglycan recognition protein 1	protein-coding
mm_62034.1	chr7	92129709	92129712	+	1	NA	intron (NM_011807, intron 13 of 22)	intron (NM_011807, intron 13 of 22)	-10199	NR_131016	75845	Mm.437835	NR_131016	ENSMUSG00000109382	4930567K12Rik	-	RIKEN cDNA 4930567K12 gene	ncRNA
mm_66903.1	chr7	59978871	59978874	-	1	NA	promoter-TSS (NR_028529)	promoter-TSS (NR_028529)	-16	NR_028529	100217429		NR_028529		Snord64	MBII-13	small nucleolar RNA, C/D box 64	snoRNA
mm_158562.1	chrX	150440836	150440846	-	1	NA	promoter-TSS (NM_001164686)	promoter-TSS (NM_001164686)	64	NM_001164686	382245	Mm.277309	NM_001164683	ENSMUSG00000041353	Tmem29	2700081K05Rik|6330540D07Rik|CXorf44-like	transmembrane protein 29	protein-coding
mm_43933.1	chr5	145104474	145104492	+	1	NA	exon (NM_019767, exon 7 of 10)	exon (NM_019767, exon 7 of 10)	-9773	NM_023142	11867	Mm.30010	NM_023142	ENSMUSG00000029622	Arpc1b	41kDa|AA408064|AA408534|AA571392|AF007010|AW208418|L72|SOP2Hs|p41-ARC	actin related protein 2/3 complex, subunit 1B	protein-coding
mm_149072.1	chr19	8871618	8871628	+	1	NA	promoter-TSS (NM_146093)	promoter-TSS (NM_146093)	64	NM_146093	225896	Mm.27839	NM_146093	ENSMUSG00000071655	Ubxn1	2B28|4930455J02Rik|D19Ertd721e|T25529	UBX domain protein 1	protein-coding
mm_142861.1	chr17	51813826	51813832	-	1	NA	intron (NM_001163632, intron 1 of 10)	intron (NM_001163632, intron 1 of 10)	-1775	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_23106.1	chr3	37420274	37420335	+	1	NA	promoter-TSS (NM_001291044)	promoter-TSS (NM_001291044)	354	NM_021343	57815	Mm.172679	NM_021343	ENSMUSG00000027722	Spata5	2510048F20Rik|C78064|Spaf	spermatogenesis associated 5	protein-coding
mm_36190.1	chr4	62298248	62298280	-	1	NA	3' UTR (NM_025286, exon 4 of 4)	3' UTR (NM_025286, exon 4 of 4)	6717	NM_001290518	20530	Mm.292539	NM_025286	ENSMUSG00000066152	Slc31a2	AI604396|CTR2	solute carrier family 31, member 2	protein-coding
mm_62397.1	chr7	101108549	101108579	+	1	NA	promoter-TSS (NM_001146010)	promoter-TSS (NM_001146010)	-211	NM_001146010	207278	Mm.263041	NM_199012	ENSMUSG00000030691	Fchsd2	BC034086|R74866|Sh3md3|mKIAA0769	FCH and double SH3 domains 2	protein-coding
mm_89094.1	chr10	84440827	84440850	+	1	NA	promoter-TSS (NM_001004363)	promoter-TSS (NM_001004363)	-367	NM_001004363	77976	Mm.25874	NM_001004363	ENSMUSG00000020032	Nuak1	AU014801|AW494241|B230104P22Rik|Omphk1	NUAK family, SNF1-like kinase, 1	protein-coding
mm_14827.1	chr2	147014761	147014764	+	1	NA	intron (NM_011917, intron 1 of 29)	intron (NM_011917, intron 1 of 29)	1702	NM_011917	24128	Mm.3065	NM_011917	ENSMUSG00000027433	Xrn2	-	5'-3' exoribonuclease 2	protein-coding
mm_44319.1	chr5	9725152	9725163	-	1	NA	5' UTR (NM_181850, exon 1 of 6)	5' UTR (NM_181850, exon 1 of 6)	195	NM_181850	108069	Mm.318966	NM_181850	ENSMUSG00000003974	Grm3	0710001G23Rik|Gprc1c|mGlu3|mGluR3	glutamate receptor, metabotropic 3	protein-coding
mm_160390.1	chr8	54600848	54600848	+	1	NA	promoter-TSS (NM_133711)	promoter-TSS (NM_133711)	67	NM_133711	69281	Mm.45833	NM_133711	ENSMUSG00000031518	Spata4	1700001N01Rik|Srg2|TSARG2	spermatogenesis associated 4	protein-coding
mm_131177.1	chr16	7069950	7069958	+	1	NA	5' UTR (NM_183188, exon 1 of 13)	5' UTR (NM_183188, exon 1 of 13)	119	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_88930.1	chr10	81257348	81257362	+	1	NA	promoter-TSS (NM_001285854)	promoter-TSS (NM_001285854)	56	NM_001285853	17179	Mm.2918	NM_010768	ENSMUSG00000004933	Matk	CHK|HYL|Ntk|p56ntk	megakaryocyte-associated tyrosine kinase	protein-coding
mm_125450.1	chr15	51713642	51713659	+	1	NA	Intergenic	MLTR11B|LTR|ERVK	151811	NM_080635	68135	Mm.289800	NM_080635	ENSMUSG00000022312	Eif3h	1110008A16Rik|40kD|9430017H16Rik|EIF3-P40|EIF3-gamma|Eif3s3	eukaryotic translation initiation factor 3, subunit H	protein-coding
mm_29611.1	chr3	121263298	121263310	-	1	NA	promoter-TSS (NM_178936)	promoter-TSS (NM_178936)	12	NM_178936	99887	Mm.26088	NM_178936	ENSMUSG00000028132	Tmem56	4930577M16Rik|AU018104|AW109744|C730036B01Rik	transmembrane protein 56	protein-coding
mm_33039.1	chr4	122886239	122886293	+	1	NA	promoter-TSS (NM_007598)	promoter-TSS (NM_007598)	-209	NM_001301067	12331	Mm.8687	NM_007598	ENSMUSG00000028656	Cap1	-	CAP, adenylate cyclase-associated protein 1 (yeast)	protein-coding
mm_105894.1	chr11	114960492	114960509	-	1	NA	promoter-TSS (NM_199225)	promoter-TSS (NM_199225)	-83	NM_199225	387565	Mm.351450	NM_199225	ENSMUSG00000058728	Cd300c	Clm6	CD300C molecule	protein-coding
mm_149002.1	chr19	8667760	8667762	+	1	NA	intron (NM_001112697, intron 2 of 2)	intron (NM_001112697, intron 2 of 2)	3756	NM_001112697	12669	Mm.240607	NM_007698	ENSMUSG00000032773	Chrm1	Chrm-1|M1|M1R	cholinergic receptor, muscarinic 1, CNS	protein-coding
mm_93275.1	chr10	95842905	95842915	-	1	NA	Intergenic	Intergenic	-97753	NM_001001932	216238	Mm.210035	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding
mm_17337.1	chr2	26594934	26594945	-	1	NA	intron (NM_026212, intron 4 of 5)	intron (NM_026212, intron 4 of 5)	-3519	NR_106155	102465787		NR_106155	ENSMUSG00000105799	Mir126b	mmu-mir-126b	microRNA 126b	ncRNA
mm_40636.1	chr5	64899114	64899139	+	1	NA	Intergenic	Intergenic	33573	NM_030682	21897	Mm.273024	NM_030682	ENSMUSG00000044827	Tlr1	-	toll-like receptor 1	protein-coding
mm_171041.1	chr2	96960701	96960718	-	1	NA	intron (NM_001289743, intron 3 of 6)	L1Md_T|LINE|L1	-506948	NM_001289744	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_67940.1	chr7	100121513	100121524	-	1	NA	promoter-TSS (NM_133692)	promoter-TSS (NM_133692)	-18	NM_133692	67967	Mm.37562	NM_133692	ENSMUSG00000030726	Pold3	2410142G14Rik|C85233|P66|P68	polymerase (DNA-directed), delta 3, accessory subunit	protein-coding
mm_395.1	chr1	34121338	34121348	+	1	NA	intron (NM_001276764, intron 8 of 102)	intron (NM_001276764, intron 8 of 102)	3984	NR_105861	102466987		NR_105861	ENSMUSG00000105982	Mir6896	mmu-mir-6896	microRNA 6896	ncRNA
mm_162273.1	chr1	10335551	10335554	+	1	NA	intron (NM_177834, intron 9 of 10)	B4A|SINE|B4	-102882	NM_001102430	211673	Mm.229141	NM_001102430	ENSMUSG00000067851	Arfgef1	ARFGEP1|BIG1|D130059B05Rik|D730028O18Rik|P200	ADP-ribosylation factor guanine nucleotide-exchange factor 1(brefeldin A-inhibited)	protein-coding
mm_14031.1	chr2	122152863	122152895	+	1	NA	3' UTR (NM_009735, exon 4 of 4)	3' UTR (NM_009735, exon 4 of 4)	5192	NM_009735	12010	Mm.163	NM_009735	ENSMUSG00000060802	B2m	Ly-m11|beta2-m|beta2m	beta-2 microglobulin	protein-coding
mm_95436.1	chr11	50224749	50224760	+	1	NA	promoter-TSS (NM_145926)	promoter-TSS (NM_145926)	-581	NM_145926	103534	Mm.86759	NM_145926	ENSMUSG00000036620	Mgat4b	AA407995|GnTIVb	mannoside acetylglucosaminyltransferase 4, isoenzyme B	protein-coding
mm_23987.1	chr3	86143132	86143159	+	1	NA	promoter-TSS (NM_016959)	promoter-TSS (NM_016959)	-477	NM_016959	20091	Mm.391785	NM_016959	ENSMUSG00000028081	Rps3a1	Rps3a	ribosomal protein S3A1	protein-coding
mm_76878.1	chr8	105579856	105579864	-	1	NA	promoter-TSS (NM_001271806)	promoter-TSS (NM_001271806)	-15	NM_001271806	11604	Mm.441696	NM_007427	ENSMUSG00000005705	Agrp	Agrt|Art	agouti related neuropeptide	protein-coding
mm_57143.1	chr6	122633492	122633504	-	1	NA	Intergenic	Lx5c|LINE|L1	7074	NM_139218	73708	Mm.27982	NM_139218	ENSMUSG00000046323	Dppa3	2410075G02Rik|PCG7|PGC7|Stella	developmental pluripotency-associated 3	protein-coding
mm_164443.1	chr16	49855371	49855387	+	1	NA	promoter-TSS (NM_010581)	promoter-TSS (NM_010581)	-275	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_19851.1	chr2	113758639	113758655	-	1	NA	promoter-TSS (NM_011824)	promoter-TSS (NM_011824)	1	NM_011824	23892	Mm.166318	NM_011824	ENSMUSG00000074934	Grem1	Cktsf1b1|Drm|Grem|ld	gremlin 1, DAN family BMP antagonist	protein-coding
mm_108412.1	chr12	81860074	81860121	+	1	NA	promoter-TSS (NM_018814)	promoter-TSS (NM_018814)	67	NM_018814	54604	Mm.86584	NM_018814	ENSMUSG00000021140	Pcnx	2900024E21Rik|3526401J03Rik|AF096286|AI327143|AI413187|Pcnx1|Pcnxl1	pecanex homolog (Drosophila)	protein-coding
mm_15628.1	chr2	162987428	162987436	+	1	NA	promoter-TSS (NM_013731)	promoter-TSS (NM_013731)	-49	NM_001291154	27219	Mm.26462	NM_013731	ENSMUSG00000017868	Sgk2	AI098171|AW146006|Sgkl	serum/glucocorticoid regulated kinase 2	protein-coding
mm_8323.1	chr1	149449964	149449974	-	1	NA	Intergenic	Intergenic	472470	NM_001305632	18783	Mm.4186	NM_008869	ENSMUSG00000056220	Pla2g4a	Pla2g4|cPLA2|cPLA2-alpha|cPLA2alpha	phospholipase A2, group IVA (cytosolic, calcium-dependent)	protein-coding
mm_150233.1	chr19	34008248	34008269	+	1	NA	promoter-TSS (NM_172837)	promoter-TSS (NM_172837)	4	NM_001205349	240633	Mm.58924	NM_172837	ENSMUSG00000024771	Lipk	9930115F20|BC055815|Lipl2	lipase, family member K	protein-coding
mm_26761.1	chr3	8667050	8667056	-	1	NA	promoter-TSS (NM_010423)	promoter-TSS (NM_010423)	-15	NM_010423	15213	Mm.29581	NM_010423	ENSMUSG00000040289	Hey1	AI316788|AI414254|CHF2|HRT1|Herp2|Hesr1|bHLHb31|hesr-1	hairy/enhancer-of-split related with YRPW motif 1	protein-coding
mm_22396.1	chr2	181234083	181234128	-	1	NA	exon (NM_183162, exon 9 of 19)	exon (NM_183162, exon 9 of 19)	7922	NM_183162	229003	Mm.315872	NM_183162	ENSMUSG00000027580	Helz2	PDIP1|Pric285|mKIAA1769|mPDIP1	helicase with zinc finger 2, transcriptional coactivator	protein-coding
mm_61262.1	chr7	66079779	66079798	+	1	NA	exon (NM_024439, exon 1 of 6)	exon (NM_024439, exon 1 of 6)	139	NM_024439	109815	Mm.482127	NM_024439	ENSMUSG00000075701	Selenos	1500011E07Rik|C78786|H-4|H-47|H4|H47|Sels|Vimp	selenoprotein S	protein-coding
mm_52538.1	chr6	115931898	115931919	+	1	NA	promoter-TSS (NM_145383)	promoter-TSS (NM_145383)	-19	NM_145383	212541	Mm.2965	NM_145383	ENSMUSG00000030324	Rho	Noerg1|Opn2|Ops|RP4	rhodopsin	protein-coding
mm_38646.1	chr4	143267903	143267906	-	1	NA	3' UTR (NM_010329, exon 6 of 6)	3' UTR (NM_010329, exon 6 of 6)	31660	NM_010329	14726	Mm.2976	NM_010329	ENSMUSG00000028583	Pdpn	Gp38|OTS-8|RANDAM-2|T1-alpha|T1a|T1alpha	podoplanin	protein-coding
mm_94843.1	chr11	23699579	23699582	+	1	NA	intron (NM_028304, intron 4 of 17)	ID_B1|SINE|B4	33604	NM_028304	74467	Mm.29536	NM_028304	ENSMUSG00000020280	Pus10	2810013G11Rik|4933435A13Rik|AU014648|C77560|Ccdc139	pseudouridylate synthase 10	protein-coding
mm_68985.1	chr7	126590057	126590084	-	1	NA	TTS (NM_138310)	TTS (NM_138310)	-4253	NM_001146311	12752	Mm.268930	NM_009907	ENSMUSG00000030720	Cln3	AI323623	ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease)	protein-coding
mm_46530.1	chr5	105693397	105693439	-	1	NA	Intergenic	Intergenic	-6551	NM_001122768	231549	Mm.23837	NM_178701	ENSMUSG00000046079	Lrrc8d	2810473G09Rik|4930525N13Rik|A930019F03|Lrrc5	leucine rich repeat containing 8D	protein-coding
mm_143091.1	chr17	57080608	57080625	-	1	NA	3' UTR (NM_009451, exon 4 of 4)	3' UTR (NM_009451, exon 4 of 4)	-2106	NM_153551	70785	Mm.284447	NM_153551	ENSMUSG00000002668	Dennd1c	4432409M07Rik	DENN/MADD domain containing 1C	protein-coding
mm_111969.1	chr12	109895133	109895133	-	1	NA	Intergenic	Intergenic	147255	NR_037233	100499517		NR_037233	ENSMUSG00000093351	Mir3072	mir-3072|mmu-mir-3072	microRNA 3072	ncRNA
mm_28479.1	chr3	92429404	92429426	-	1	NA	Intergenic	Intergenic	-3167	NM_011477	20765	Mm.57085	NM_011477	ENSMUSG00000054215	Sprr2k	-	small proline-rich protein 2K	protein-coding
mm_9558.1	chr1	173971345	173971357	-	1	NA	intron (NM_008327, intron 5 of 6)	intron (NM_008327, intron 5 of 6)	11493	NM_008327	26388	Mm.218770	NM_008327	ENSMUSG00000026535	Ifi202b	Ifbip-1|Ifi202|Ifi202a|p202	interferon activated gene 202B	protein-coding
mm_44416.1	chr5	18005376	18005383	-	1	NA	intron (NM_001081143, intron 5 of 7)	RMER17A2|LTR|ERVK	42809	NM_001081143	242851	Mm.332230	NM_001081143	ENSMUSG00000028777	Gnat3	Ggust|Gtn	guanine nucleotide binding protein, alpha transducing 3	protein-coding
mm_26432.1	chr3	142618883	142618891	+	1	NA	3' UTR (NM_010259, exon 11 of 11)	3' UTR (NM_010259, exon 11 of 11)	-1776	NM_010260	14469	Mm.24038	NM_010260	ENSMUSG00000028270	Gbp2	-	guanylate binding protein 2	protein-coding
mm_95397.1	chr11	49663648	49663658	+	1	NA	promoter-TSS (NM_054037)	promoter-TSS (NM_054037)	58	NM_170727	68662	Mm.22802	NM_054037	ENSMUSG00000064057	Scgb3a1	HIN-1|LuLeu2|Pnsp2|UGRP2|Utgrp2	secretoglobin, family 3A, member 1	protein-coding
mm_70374.1	chr8	10006429	10006455	+	1	NA	promoter-TSS (NM_033622)	promoter-TSS (NM_033622)	-25	NM_001347309	24099	Mm.28835	NM_033622	ENSMUSG00000031497	Tnfsf13b	BAFF|BLyS|D8Ertd387e|TALL-1|TALL1|THANK|TNFSF20|Tnlg7a|zTNF4	tumor necrosis factor (ligand) superfamily, member 13b	protein-coding
mm_103034.1	chr11	69758178	69758201	-	1	NA	exon (NM_001291068, exon 1 of 29)	exon (NM_001291068, exon 1 of 29)	444	NM_001291068	20020	Mm.16533	NM_009089	ENSMUSG00000005198	Polr2a	220kDa|Rpb1|Rpo2-1	polymerase (RNA) II (DNA directed) polypeptide A	protein-coding
mm_78922.1	chr9	45042566	45042623	+	1	NA	5' UTR (NM_007962, exon 1 of 6)	5' UTR (NM_007962, exon 1 of 6)	250	NM_007962	14012	Mm.33240	NM_007962	ENSMUSG00000032092	Mpzl2	Eva|Eva1	myelin protein zero-like 2	protein-coding
mm_58278.1	chr6	145746271	145746274	-	1	NA	Intergenic	Intergenic	-62111	NM_027760	71323	Mm.158669	NM_027760	ENSMUSG00000030259	Rassf8	5133400D11Rik|AA815821|AW123240|Hoj1|mHoj-1	Ras association (RalGDS/AF-6) domain family (N-terminal) member 8	protein-coding
mm_105833.1	chr11	113464351	113464352	-	1	NA	intron (NM_001166503, intron 4 of 9)	intron (NM_001166503, intron 4 of 9)	101464	NM_001166503	69806	Mm.341021	NM_027216	ENSMUSG00000041654	Slc39a11	1810074D23Rik	solute carrier family 39 (metal ion transporter), member 11	protein-coding
mm_170180.1	chr17	60784105	60784105	+	1	NA	Intergenic	L1Md_T|LINE|L1	-1770783	NM_026497	67993	Mm.36507	NM_026497	ENSMUSG00000024228	Nudt12	0610016O18Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 12	protein-coding
mm_37596.1	chr4	126744111	126744121	-	1	NA	3' UTR (NM_011986, exon 7 of 7)	3' UTR (NM_011986, exon 7 of 7)	-7847	NM_198960	332937	Mm.331881	NM_198960	ENSMUSG00000042477	Tfap2e	AI505200|AP-2e|Tcfap2e	transcription factor AP-2, epsilon	protein-coding
mm_112637.1	chr13	16014398	16014408	+	1	NA	intron (NM_008380, intron 2 of 4)	intron (NM_008380, intron 2 of 4)	2552	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_163412.1	chr12	77418413	77418420	+	1	NA	intron (NR_045554, intron 8 of 11)	intron (NR_045554, intron 8 of 11)	8275	NM_001252616	53618	Mm.35628	NM_016893	ENSMUSG00000021065	Fut8	-	fucosyltransferase 8	protein-coding
mm_137591.1	chr17	28069618	28069642	+	1	NA	exon (NM_013687, exon 7 of 10)	exon (NM_013687, exon 7 of 10)	10954	NM_013687	21463	Mm.29758	NM_013687	ENSMUSG00000062859	Tcp11	D17Ken1|Tcp-11	t-complex protein 11	protein-coding
mm_144260.1	chr18	11052488	11052510	+	1	NA	promoter-TSS (NR_105023)	promoter-TSS (NR_105023)	-11	NM_010258	14465	Mm.329287	NM_010258	ENSMUSG00000005836	Gata6	AA410133|GATA-6	GATA binding protein 6	protein-coding
mm_95704.1	chr11	54438274	54438284	+	1	NA	promoter-TSS (NM_173753)	promoter-TSS (NM_173753)	100	NM_173753	216742	Mm.34087	NM_173753	ENSMUSG00000035992	Fnip1	A730024A03Rik|AI838773|AW557298	folliculin interacting protein 1	protein-coding
mm_105635.1	chr11	106998450	106998463	-	1	NA	intron (NM_010655, intron 1 of 10)	intron (NM_010655, intron 1 of 10)	1069	NM_010655	16647	Mm.12508	NM_010655	ENSMUSG00000018362	Kpna2	2410044B12Rik|IPOA1|PTAC58|Rch1	karyopherin (importin) alpha 2	protein-coding
mm_35036.1	chr4	4134196	4134210	-	1	NA	exon (NM_001002927, exon 2 of 2)	exon (NM_001002927, exon 2 of 2)	4242	NM_001002927	18619	Mm.475097	NM_001002927	ENSMUSG00000045573	Penk	AI326464|ENK|PPA|Penk1	preproenkephalin	protein-coding
mm_171457.1	chr4	145514895	145514911	+	1	NA	intron (NM_001324553, intron 1 of 3)	intron (NM_001324553, intron 1 of 3)	4144	NM_001324553	101056073	Mm.276881	NM_001324553	ENSMUSG00000078503	LOC101056073	-	zinc finger protein 501-like	protein-coding
mm_148284.1	chr18	82527769	82527773	-	1	NA	intron (NM_001025245, intron 3 of 3)	intron (NM_001025245, intron 3 of 3)	-26692	NM_001025256	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_150740.1	chr19	43782298	43782313	+	1	NA	promoter-TSS (NM_013806)	promoter-TSS (NM_013806)	-3	NM_013806	12780	Mm.39054	NM_013806	ENSMUSG00000025194	Abcc2	AI173996|Abc30|Cmoat|Mrp2|cMRP	ATP-binding cassette, sub-family C (CFTR/MRP), member 2	protein-coding
mm_3148.1	chr1	135146783	135146871	+	1	NA	promoter-TSS (NM_026823)	promoter-TSS (NM_026823)	-7	NM_026823	68724	Mm.174998	NM_026823	ENSMUSG00000026426	Arl8a	1110033P22Rik|Arl10b|gie2	ADP-ribosylation factor-like 8A	protein-coding
mm_105925.1	chr11	115062159	115062169	-	1	NA	promoter-TSS (NM_172050)	promoter-TSS (NM_172050)	-125	NM_172050	217306	Mm.222667	NM_172050	ENSMUSG00000048498	Cd300e	BC034097|CLM2|Cd300le|TREM5	CD300E molecule	protein-coding
mm_7040.1	chr1	87101591	87101617	-	1	NA	promoter-TSS (NM_001081082)	promoter-TSS (NM_001081082)	2	NM_001081082	76768	Mm.58068	NM_001081082	ENSMUSG00000079440	Alpi	2010001C14Rik|Akp6|gIAP	alkaline phosphatase, intestinal	protein-coding
mm_23647.1	chr3	67473447	67473455	+	1	NA	intron (NM_138591, intron 15 of 17)	intron (NM_138591, intron 15 of 17)	-9544	NM_016753	17035	Mm.2632	NM_016753	ENSMUSG00000047557	Lxn	-	latexin	protein-coding
mm_171097.1	chr3	131338114	131338121	+	1	NA	intron (NM_028943, intron 2 of 5)	RLTR1B|LTR|ERV1	6806	NM_028943	74442	Mm.273360	NM_028943	ENSMUSG00000050931	Sgms2	4933405A16Rik|5133401H06Rik|AI854299	sphingomyelin synthase 2	protein-coding
mm_17908.1	chr2	35315496	35315506	-	1	NA	3' UTR (NM_013515, exon 7 of 7)	3' UTR (NM_013515, exon 7 of 7)	21508	NM_013515	13830	Mm.295284	NM_013515	ENSMUSG00000026880	Stom	Epb7.2	stomatin	protein-coding
mm_145786.1	chr18	65143607	65143621	+	1	NA	intron (NM_001114386, intron 5 of 30)	intron (NM_001114386, intron 5 of 30)	-105247	NR_029600	387231		NR_029600	ENSMUSG00000065402	Mir122	Mir122a|Mirn122a|mir-122|mmu-mir-122	microRNA 122	ncRNA
mm_17142.1	chr2	25095126	25095138	-	1	NA	promoter-TSS (NM_001163626)	promoter-TSS (NM_001163626)	73	NM_001163626	241275	Mm.218774	NM_172204	ENSMUSG00000036805	Noxa1	NY-CO-31|SDCCAG31	NADPH oxidase activator 1	protein-coding
mm_132713.1	chr16	43503608	43503626	+	1	NA	intron (NM_181058, intron 3 of 6)	intron (NM_181058, intron 3 of 6)	-83421	NR_046026	626693	Mm.447083	NR_046026	ENSMUSG00000085499	Gm15713	OTTMUSG00000025617	predicted gene 15713	ncRNA
mm_58694.1	chr7	12925440	12925455	+	1	NA	exon (NM_009095, exon 3 of 6)	exon (NM_009095, exon 3 of 6)	-1969	NM_029809	381845	Mm.439896	NM_029809	ENSMUSG00000033967	Rnf225	2310014L17Rik|AV237412|C77118	ring finger protein 225	protein-coding
mm_6551.1	chr1	75133867	75133888	-	1	NA	promoter-TSS (NM_194333)	promoter-TSS (NM_194333)	13	NM_194333	22626	Mm.68157	NM_194333	ENSMUSG00000026205	Slc23a3	SVCT3|Yspl1	solute carrier family 23 (nucleobase transporters), member 3	protein-coding
mm_44961.1	chr5	36712111	36712111	-	1	NA	Intergenic	Intergenic	-16090	NM_001081232	320661	Mm.26480	NM_177221	ENSMUSG00000029190	D5Ertd579e	9030221A05Rik|A930018H20Rik|Kiaa0232	DNA segment, Chr 5, ERATO Doi 579, expressed	protein-coding
mm_27255.1	chr3	37174673	37174680	-	1	NA	Intergenic	Intergenic	-48722	NM_008366	16183	Mm.14190	NM_008366	ENSMUSG00000027720	Il2	Il-2	interleukin 2	protein-coding
mm_40160.1	chr5	35588051	35588052	+	1	NA	non-coding (NR_045807, exon 2 of 4)	non-coding (NR_045807, exon 2 of 4)	712	NR_045807	74364	Mm.473123	NM_175208	ENSMUSG00000055061	4931431C16Rik	-	RIKEN cDNA 4931431C16 gene	ncRNA
mm_3070.1	chr1	134189722	134189732	+	1	NA	3' UTR (NM_007695, exon 10 of 10)	3' UTR (NM_007695, exon 10 of 10)	-3721	NM_016749	53311	Mm.379067	NM_016749	ENSMUSG00000042451	Mybph	AI385643|MyBP-H	myosin binding protein H	protein-coding
mm_59241.1	chr7	24780866	24780871	+	1	NA	intron (NM_007675, intron 2 of 3)	intron (NM_007675, intron 2 of 3)	3664	NM_007675	26366	Mm.30300	NM_007675	ENSMUSG00000054169	Ceacam10	Bgp3|Cea10	carcinoembryonic antigen-related cell adhesion molecule 10	protein-coding
mm_143849.1	chr17	84145884	84145894	-	1	NA	Intergenic	Intergenic	42058	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_108519.1	chr12	84052148	84052157	+	1	NA	promoter-TSS (NM_134246)	promoter-TSS (NM_134246)	1	NM_134246	171281	Mm.202331	NM_134246	ENSMUSG00000021228	Acot3	AW108394|PTE-Ia|Pte2a	acyl-CoA thioesterase 3	protein-coding
mm_47720.1	chr5	130003001	130003012	-	1	NA	promoter-TSS (NM_010368)	promoter-TSS (NM_010368)	-178	NM_010368	110006	Mm.3317	NM_010368	ENSMUSG00000025534	Gusb	AI747421|Gur|Gus|Gus-r|Gus-s|Gus-t|Gus-u|Gut|asd|g	glucuronidase, beta	protein-coding
mm_150182.1	chr19	32643081	32643083	+	1	NA	intron (NM_001201470, intron 7 of 11)	intron (NM_001201470, intron 7 of 11)	23077	NM_011864	23972	Mm.203916	NM_011864	ENSMUSG00000024899	Papss2	1810018P12Rik|AI159688|AtpsU2|Atpsk2|Sk2|bm	3'-phosphoadenosine 5'-phosphosulfate synthase 2	protein-coding
mm_169344.1	chr14	15094143	15094159	-	1	NA	Intergenic	L1Md_T|LINE|L1	273336	NM_001195229	674895	Mm.317563	NM_001034865	ENSMUSG00000042567	Nek10	Gm282	NIMA (never in mitosis gene a)- related kinase 10	protein-coding
mm_30915.1	chr4	32615490	32615505	+	1	NA	promoter-TSS (NM_011997)	promoter-TSS (NM_011997)	27	NM_011997	26885	Mm.22279	NM_011997	ENSMUSG00000028282	Casp8ap2	D4Ertd659e|FLASH	caspase 8 associated protein 2	protein-coding
mm_5733.1	chr1	45334621	45334637	-	1	NA	exon (NM_009930, exon 25 of 51)	exon (NM_009930, exon 25 of 51)	23091	NM_009930	12825	Mm.249555	NM_009930	ENSMUSG00000026043	Col3a1	AW550625|Col3a-1|Tsk-2|Tsk2	collagen, type III, alpha 1	protein-coding
mm_71576.1	chr8	54550385	54550397	+	1	NA	promoter-TSS (NM_029569)	promoter-TSS (NM_029569)	60	NM_029569	76294	Mm.33171	NM_029569	ENSMUSG00000031519	Asb5	1110018D09Rik	ankyrin repeat and SOCs box-containing 5	protein-coding
mm_1402.1	chr1	67144903	67144927	+	1	NA	intron (NM_001080809, intron 4 of 37)	intron (NM_001080809, intron 4 of 37)	21888	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_172455.1	chr7	3579126	3579144	-	1	NA	Intergenic	RLTR11B|LTR|ERVK	37022	NM_175632	232790	Mm.358882	NM_175632	ENSMUSG00000054594	Oscar	mOSCAR|mOSCAR-M1|mOSCAR-M2|mOSCAR-M3	osteoclast associated receptor	protein-coding
mm_98228.1	chr11	88068243	88068289	+	1	NA	promoter-TSS (NM_016686)	promoter-TSS (NM_016686)	-13	NM_016686	22344	Mm.46628	NM_016686	ENSMUSG00000018377	Vezf1	AI848691|AW046909|db1	vascular endothelial zinc finger 1	protein-coding
mm_14161.1	chr2	126606412	126606423	+	1	NA	exon (NM_008230, exon 4 of 12)	exon (NM_008230, exon 4 of 12)	12261	NM_008230	15186	Mm.18603	NM_008230	ENSMUSG00000027360	Hdc	AW108189|Hdc-a|Hdc-c|Hdc-e|Hdc-s	histidine decarboxylase	protein-coding
mm_79134.1	chr9	47569210	47569232	+	1	NA	intron (NM_001025600, intron 1 of 8)	(TTTC)n|Simple_repeat|Simple_repeat	38869	NM_018770	54725	Mm.234832	NM_018770	ENSMUSG00000032076	Cadm1	2900073G06Rik|3100001I08Rik|AI987920|Bl2|Igsf4|Igsf4a|Necl2|RA175|RA175A|RA175B|RA175C|RA175N|ST17|SgIGSF|SynCam|Tslc1	cell adhesion molecule 1	protein-coding
mm_101587.1	chr11	34681694	34681712	-	1	NA	intron (NM_033374, intron 22 of 51)	RLTR44-int|LTR|ERVK	102202	NM_033374	94176	Mm.380679	NM_033374	ENSMUSG00000020143	Dock2	AI662014|AW122239|CED-5|Hch|MBC	dedicator of cyto-kinesis 2	protein-coding
mm_168704.1	chr11	98033149	98033150	-	1	NA	Intergenic	B1_Mm|SINE|Alu	6225	NM_009078	19921	Mm.10247	NM_009078	ENSMUSG00000017404	Rpl19	-	ribosomal protein L19	protein-coding
mm_16088.1	chr2	168771726	168771754	+	1	NA	Intergenic	Intergenic	-4539	NM_175303	99377	Mm.434054	NM_175303	ENSMUSG00000027547	Sall4	5730441M18Rik|AA407717|AL022809|AW536104|C330011P20Rik|C78083|C78563|Tex20	sal-like 4 (Drosophila)	protein-coding
mm_70515.1	chr8	12947936	12947962	+	1	NA	promoter-TSS (NR_128567)	promoter-TSS (NR_128567)	8	NR_128567	104797311		NR_128567	ENSMUSG00000105030	Gm38671	Mir9768|mmu-mir-9768	predicted gene, 38671	ncRNA
mm_133290.1	chr16	77484945	77484983	+	1	NA	intron (NR_015543, intron 3 of 4)	intron (NR_015543, intron 3 of 4)	-113972	NR_029535	387229		NR_029535	ENSMUSG00000065530	Mir99a	Mirn99a|mir-99a|mmu-mir-99a	microRNA 99a	ncRNA
mm_168378.1	chr1	122086625	122086625	+	1	NA	Intergenic	L1Md_T|LINE|L1	-518645	NM_025860	66942	Mm.44219	NM_025860	ENSMUSG00000001674	Ddx18	2310005B10Rik	DEAD (Asp-Glu-Ala-Asp) box polypeptide 18	protein-coding
mm_8893.1	chr1	162898377	162898393	-	1	NA	intron (NM_018881, intron 1 of 8)	intron (NM_018881, intron 1 of 8)	327	NM_018881	55990	Mm.10929	NM_018881	ENSMUSG00000040170	Fmo2	2310008D08Rik|2310042I22Rik|AW107733	flavin containing monooxygenase 2	protein-coding
mm_104898.1	chr11	99610428	99610434	-	1	NA	promoter-TSS (NM_001099346)	promoter-TSS (NM_001099346)	-242	NM_001099346	100041488	Mm.465212	NM_001099346	ENSMUSG00000058725	Gm11937	-	predicted gene 11937	protein-coding
mm_49462.1	chr6	29419273	29419282	+	1	NA	exon (NM_145574, exon 15 of 16)	exon (NM_145574, exon 15 of 16)	-13876	NM_001081185	68794	Mm.39046	NM_026839	ENSMUSG00000068699	Flnc	1110055E19Rik|ABP-280|ABPL|Fln2	filamin C, gamma	protein-coding
mm_152794.1	chr19	21472513	21472533	-	1	NA	5' UTR (NM_010266, exon 1 of 14)	5' UTR (NM_010266, exon 1 of 14)	138	NM_010266	14544	Mm.45054	NM_010266	ENSMUSG00000058624	Gda	AU015411|AW047581|GAH	guanine deaminase	protein-coding
mm_65708.1	chr7	28378108	28378110	-	1	NA	exon (NM_011756, exon 2 of 2)	exon (NM_011756, exon 2 of 2)	1119	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_146481.1	chr18	89206559	89206573	+	1	NA	intron (NM_001039149, intron 1 of 5)	intron (NM_001039149, intron 1 of 5)	9139	NM_001039149	225825	Mm.139293	NM_178687	ENSMUSG00000034028	Cd226	BC051526|DNAM-1|DNAM1|Pta1|TLiSA1	CD226 antigen	protein-coding
mm_160403.1	chr8	71290253	71290253	+	1	NA	5' UTR (NM_001142322, exon 2 of 40)	5' UTR (NM_001142322, exon 2 of 40)	17539	NM_001142323	17925	Mm.33779	NM_015742	ENSMUSG00000004677	Myo9b	-	myosin IXb	protein-coding
mm_34114.1	chr4	139199266	139199295	+	1	NA	intron (NM_001271405, intron 1 of 8)	intron (NM_001271405, intron 1 of 8)	5169	NM_001271405	12345	Mm.2945	NM_009798	ENSMUSG00000028745	Capzb	1700120C01Rik|AI325129|CPB1|CPB2|CPbeat2|CPbeta1|CPbeta2|Cappb1	capping protein (actin filament) muscle Z-line, beta	protein-coding
mm_107849.1	chr12	69373494	69373507	+	1	NA	3' UTR (NM_007481, exon 2 of 2)	3' UTR (NM_007481, exon 2 of 2)	1350	NM_007481	11845	Mm.27308	NM_007481	ENSMUSG00000044147	Arf6	AI788669|AW496366	ADP-ribosylation factor 6	protein-coding
mm_12514.1	chr2	72054656	72054676	+	1	NA	promoter-TSS (NM_001204166)	promoter-TSS (NM_001204166)	49	NM_001204166	56508	Mm.196153	NM_019688	ENSMUSG00000049044	Rapgef4	1300003D15Rik|5730402K07Rik|6330581N18Rik|EPAC 2|Epac-2|Epac2|mKIAA4040	Rap guanine nucleotide exchange factor (GEF) 4	protein-coding
mm_76635.1	chr8	92355496	92355506	-	1	NA	intron (NR_110452, intron 1 of 3)	intron (NR_110452, intron 1 of 3)	619	NR_110452	71296	Mm.86664	NR_033641	ENSMUSG00000031736	Crnde	4933436C20Rik	colorectal neoplasia differentially expressed (non-protein coding)	ncRNA
mm_97617.1	chr11	78952967	78952982	+	1	NA	exon (NM_010927, exon 22 of 27)	exon (NM_010927, exon 22 of 27)	27683	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_124755.1	chr15	6643716	6643733	+	1	NA	exon (NM_001278269, exon 10 of 17)	exon (NM_001278269, exon 10 of 17)	63877	NM_011815	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_129236.1	chr15	76617130	76617146	-	1	NA	promoter-TSS (NM_028064)	promoter-TSS (NM_028064)	-286	NM_028064	72027	Mm.276829	NM_028064	ENSMUSG00000063354	Slc39a4	1600025H15Rik|AU041686|AWMS2|ZIP4	solute carrier family 39 (zinc transporter), member 4	protein-coding
mm_106324.1	chr11	118303849	118303906	-	1	NA	exon (NM_011594, exon 5 of 5)	exon (NM_011594, exon 5 of 5)	-13633	NM_001033528	72344	Mm.232293	NM_001033528	ENSMUSG00000033909	Usp36	2700002L06Rik|mKIAA1453	ubiquitin specific peptidase 36	protein-coding
mm_109020.1	chr12	103532487	103532503	+	1	NA	promoter-TSS (NM_028980)	promoter-TSS (NM_028980)	-70	NM_028980	74521	Mm.248619	NM_028980	ENSMUSG00000021209	Ppp4r4	8430415E04Rik|mKIAA1622	protein phosphatase 4, regulatory subunit 4	protein-coding
mm_19029.1	chr2	76969165	76969187	-	1	NA	exon (NM_011652, exon 8 of 313)	exon (NM_011652, exon 8 of 313)	13371	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_46522.1	chr5	105345928	105345932	-	1	NA	intron (NR_132129, intron 1 of 10)	intron (NR_132129, intron 1 of 10)	542	NM_001039647	634650	Mm.458435	NM_001039647	ENSMUSG00000092021	Gbp11	EG634650|Gm7141	guanylate binding protein 11	protein-coding
mm_105209.1	chr11	102156340	102156414	-	1	NA	promoter-TSS (NM_029649)	promoter-TSS (NM_029649)	30	NM_029649	76547	Mm.46529	NM_029649	ENSMUSG00000020921	Tmem101	2610511E22Rik	transmembrane protein 101	protein-coding
mm_112974.1	chr13	21287376	21287382	+	1	NA	exon (NM_010343, exon 5 of 5)	exon (NM_010343, exon 5 of 5)	5307	NM_010343	14780	Mm.1332	NM_010343	ENSMUSG00000004344	Gpx5	AV379049|Arep	glutathione peroxidase 5	protein-coding
mm_120310.1	chr14	63142312	63142340	+	1	NA	exon (NM_007798, exon 10 of 10)	exon (NM_007798, exon 10 of 10)	19864	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_127434.1	chr15	101270178	101270187	+	1	NA	exon (NM_010444, exon 2 of 7)	exon (NM_010444, exon 2 of 7)	3336	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_142763.1	chr17	49479771	49479782	-	1	NA	exon (NM_001008231, exon 14 of 26)	exon (NM_001008231, exon 14 of 26)	51412	NM_020042	56738	Mm.22256	NM_020042	ENSMUSG00000064120	Mocs1	3110045D15Rik|AI043170|AW536397	molybdenum cofactor synthesis 1	protein-coding
mm_13497.1	chr2	107011051	107011070	+	1	NA	Intergenic	Intergenic	-36663	NM_001025102	212772	Mm.381231	NM_173750	ENSMUSG00000027122	Arl14ep	2700007P21Rik|4930448O08Rik|ARF7EP	ADP-ribosylation factor-like 14 effector protein	protein-coding
mm_27459.1	chr3	52105046	52105056	-	1	NA	promoter-TSS (NM_001004176)	promoter-TSS (NM_001004176)	-45	NM_001004176	433586	Mm.234972	NM_001004176	ENSMUSG00000061143	Maml3	AV234550|BC049812|Mam-2|mKIAA1816	mastermind like 3 (Drosophila)	protein-coding
mm_149082.1	chr19	8904987	8905015	+	1	NA	exon (NM_008060, exon 4 of 25)	exon (NM_008060, exon 4 of 25)	6944	NM_008060	14376	Mm.3196	NM_008060	ENSMUSG00000071650	Ganab	AU042638|G2an|GluII|mKIAA0088	alpha glucosidase 2 alpha neutral subunit	protein-coding
mm_5529.1	chr1	37957758	37957760	-	1	NA	promoter-TSS (NM_027111)	promoter-TSS (NM_027111)	0	NM_027111	69541	Mm.389117	NM_027111	ENSMUSG00000026085	Lyg1	2300002O18Rik	lysozyme G-like 1	protein-coding
mm_132097.1	chr16	31325258	31325269	+	1	NA	Intergenic	Intergenic	-10455	NM_001301354	11815	Mm.2082	NM_007470	ENSMUSG00000022548	Apod	-	apolipoprotein D	protein-coding
mm_169198.1	chr13	66244139	66244144	-	1	NA	Intergenic	Intergenic	130688	NM_001177832	628709	Mm.390595	NM_001177832	ENSMUSG00000095909	Gm10324	ENSMUSG00000071302	predicted gene 10324	protein-coding
mm_150097.1	chr19	29470185	29470233	+	1	NA	intron (NM_021396, intron 5 of 5)	B3A|SINE|B2	51778	NR_015567	77779	Mm.458738	NR_015567	ENSMUSG00000097855	A930007I19Rik	-	RIKEN cDNA A930007I19 gene	ncRNA
mm_43784.1	chr5	142453959	142453991	+	1	NA	exon (NM_199068, exon 7 of 9)	exon (NM_199068, exon 7 of 9)	-9956	NM_172725	231855	Mm.78250	NM_172725	ENSMUSG00000039623	Ap5z1	C330006K01Rik	adaptor-related protein complex 5, zeta 1 subunit	protein-coding
mm_106030.1	chr11	116077471	116077511	-	1	NA	exon (NM_001009573, exon 2 of 33)	exon (NM_001009573, exon 2 of 33)	470	NM_001009573	70450	Mm.259460	NM_001009573	ENSMUSG00000057948	Unc13d	2610108D09Rik|Jinx|Munc13-4|mFLJ00067	unc-13 homolog D (C. elegans)	protein-coding
mm_58788.1	chr7	16130179	16130189	+	1	NA	5' UTR (NM_148946, exon 1 of 10)	5' UTR (NM_148946, exon 1 of 10)	358	NM_148946	110891	Mm.241147	NM_148946	ENSMUSG00000030376	Slc8a2	Ncx2	solute carrier family 8 (sodium/calcium exchanger), member 2	protein-coding
mm_139796.1	chr17	66005670	66005682	+	1	NA	intron (NM_001025572, intron 8 of 12)	intron (NM_001025572, intron 8 of 12)	-54489	NM_023053	65960	Mm.10153	NM_023053	ENSMUSG00000024098	Twsg1	1810013J15Rik|9030422N06Rik|AW552143|D17Ertd403e|Tsg|Twg	twisted gastrulation BMP signaling modulator 1	protein-coding
mm_75077.1	chr8	33863030	33863051	-	1	NA	exon (NM_019733, exon 4 of 9)	exon (NM_019733, exon 4 of 9)	66823	NM_019733	19663	Mm.323997	NM_019733	ENSMUSG00000031586	Rbpms	2010300K22Rik|2700019M19Rik|AU017537|RBP-MS|hermes	RNA binding protein gene with multiple splicing	protein-coding
mm_50330.1	chr6	48411614	48411624	+	1	NA	intron (NM_001347153, intron 11 of 17)	intron (NM_001347153, intron 11 of 17)	16033	NM_001347153	77827	Mm.107646	NM_133922	ENSMUSG00000042810	Krba1	A930040G15Rik|AI448780	KRAB-A domain containing 1	protein-coding
mm_119558.1	chr14	48670286	48670334	+	1	NA	non-coding (NR_029384, exon 2 of 5)	non-coding (NR_029384, exon 2 of 5)	1022	NR_029384	606497	Mm.165199	NR_029384	ENSMUSG00000098682	Otx2os1	-	orthodenticle homeobox 2 opposite strand 1	ncRNA
mm_105698.1	chr11	108227007	108227011	-	1	NA	intron (NM_011101, intron 2 of 16)	intron (NM_011101, intron 2 of 16)	116879	NM_011101	18750	Mm.222178	NM_011101	ENSMUSG00000050965	Prkca	AI875142|Pkca	protein kinase C, alpha	protein-coding
mm_141769.1	chr17	34283177	34283188	-	1	NA	exon (NM_010378, exon 4 of 5)	exon (NM_010378, exon 4 of 5)	4589	NM_010378	14960	Mm.235338	NM_010378	ENSMUSG00000036594	H2-Aa	Aalpha|H-2Aa|H2Aa|I-Aalpha|IAalpha|Ia-1|Ia1	histocompatibility 2, class II antigen A, alpha	protein-coding
mm_8751.1	chr1	160307421	160307437	-	1	NA	intron (NM_001038621, intron 2 of 8)	intron (NM_001038621, intron 2 of 8)	-11457	NR_035448	100316784		NR_035448	ENSMUSG00000089204	Mir1927	mmu-mir-1927	microRNA 1927	ncRNA
mm_159710.1	chr5	31048930	31048930	-	1	NA	promoter-TSS (NM_177870)	promoter-TSS (NM_177870)	-6	NM_001177622	330064	Mm.205463	NM_177870	ENSMUSG00000006641	Slc5a6	E430023I20	solute carrier family 5 (sodium-dependent vitamin transporter), member 6	protein-coding
mm_77282.1	chr8	116732828	116732899	-	1	NA	5' UTR (NM_029441, exon 1 of 7)	5' UTR (NM_029441, exon 1 of 7)	128	NM_029441	75796	Mm.159575	NM_029441	ENSMUSG00000031758	Cdyl2	1700029M19Rik|4930453I21Rik|Gm20194	chromodomain protein, Y chromosome-like 2	protein-coding
mm_98385.1	chr11	94209870	94209898	+	1	NA	Intergenic	Intergenic	-1570	NM_009427	22057	Mm.259673	NM_009427	ENSMUSG00000037573	Tob1	Tob|Trob	transducer of ErbB-2.1	protein-coding
mm_37120.1	chr4	116651597	116651636	-	1	NA	promoter-TSS (NM_021473)	promoter-TSS (NM_021473)	58	NM_021473	58810	Mm.30085	NM_021473	ENSMUSG00000028692	Akr1a1	2610201A18Rik|Akr1a4	aldo-keto reductase family 1, member A1 (aldehyde reductase)	protein-coding
mm_19330.1	chr2	90577832	90577843	-	1	NA	intron (NM_008982, intron 1 of 23)	ID4|SINE|ID	2810	NM_008982	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_15416.1	chr2	156840082	156840141	+	1	NA	5' UTR (NM_001291124, exon 1 of 4)	5' UTR (NM_001291124, exon 1 of 4)	104	NM_173396	228839	Mm.315625	NM_173396	ENSMUSG00000062175	Tgif2	4921501K24|5730599O09Rik|C80753|C81206	TGFB-induced factor homeobox 2	protein-coding
mm_163435.1	chr12	85455165	85455175	-	1	NA	Intergenic	Intergenic	-18731	NM_010234	14281	Mm.246513	NM_010234	ENSMUSG00000021250	Fos	D12Rfj1|c-fos|cFos	FBJ osteosarcoma oncogene	protein-coding
mm_69135.1	chr7	127042383	127042389	-	1	NA	promoter-TSS (NM_145588)	promoter-TSS (NM_145588)	34	NM_145588	110033	Mm.286488	NM_145588	ENSMUSG00000030677	Kif22	AU021460|C81217|Kid|Kif22a	kinesin family member 22	protein-coding
mm_48415.1	chr5	140321525	140321585	-	1	NA	promoter-TSS (NM_010752)	promoter-TSS (NM_010752)	-3	NM_010752	17120	Mm.27250	NM_010752	ENSMUSG00000029554	Mad1l1	AI173502|AW550425|Mad1	MAD1 mitotic arrest deficient 1-like 1	protein-coding
mm_90756.1	chr10	5550550	5550562	-	1	NA	5' UTR (NM_153399, exon 1 of 32)	5' UTR (NM_153399, exon 1 of 32)	136	NM_153399	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_11357.1	chr2	30919515	30919525	+	1	NA	Intergenic	B1_Mur2|SINE|Alu	-16223	NM_022415	64292	Mm.28768	NM_022415	ENSMUSG00000050737	Ptges	2410099E23Rik|D2Ertd369e|Pges|mPGES|mPGES-1	prostaglandin E synthase	protein-coding
mm_109946.1	chr12	11326475	11326490	-	1	NA	exon (NM_012038, exon 4 of 4)	exon (NM_012038, exon 4 of 4)	26595	NR_106136	102465775		NR_106136	ENSMUSG00000098879	Mir7675	Gm27965|mmu-mir-7675	microRNA 7675	ncRNA
mm_145060.1	chr18	40333236	40333239	+	1	NA	intron (NM_026135, intron 1 of 1)	intron (NM_026135, intron 1 of 1)	74876	NM_026135	383348	Mm.76366	NM_026135	ENSMUSG00000051401	Kctd16	4930434H12Rik|Gm1267	potassium channel tetramerisation domain containing 16	protein-coding
mm_19113.1	chr2	79908390	79908403	-	1	NA	promoter-TSS (NM_001009978)	promoter-TSS (NM_001009978)	3	NM_001009979	18573	Mm.40678	NM_016744	ENSMUSG00000059173	Pde1a	AI987702|AW125737	phosphodiesterase 1A, calmodulin-dependent	protein-coding
mm_82695.1	chr9	22376289	22376317	-	1	NA	exon (NM_028390, exon 4 of 24)	exon (NM_028390, exon 4 of 24)	2920	NR_030448	751551		NR_030448	ENSMUSG00000076117	Mir680-2	Mirn680-2	microRNA 680-2	ncRNA
mm_44604.1	chr5	25100891	25100932	-	1	NA	promoter-TSS (NM_145401)	promoter-TSS (NM_145401)	-64	NR_027851	67261	Mm.461781	NM_026059	ENSMUSG00000043833	2900005J15Rik	-	RIKEN cDNA 2900005J15 gene	ncRNA
mm_131993.1	chr16	25048156	25048195	+	1	NA	Intergenic	Intergenic	-11464	NR_040374	319487	Mm.137341	NR_040374	ENSMUSG00000096960	A230028O05Rik	-	RIKEN cDNA A230028O05 gene	ncRNA
mm_154790.1	chrX	13072000	13072039	+	1	NA	intron (NM_009481, intron 1 of 44)	CpG	521	NM_009481	22284	Mm.242646	NM_009481	ENSMUSG00000031010	Usp9x	5730589N07Rik|AA407302|AA407699|AL022658|AL022749|Dffrx|FAF-X|Fafl	ubiquitin specific peptidase 9, X chromosome	protein-coding
mm_15877.1	chr2	164837001	164837032	+	1	NA	exon (NM_008906, exon 9 of 15)	exon (NM_008906, exon 9 of 15)	3243	NM_008906	19025	Mm.359633	NM_008906	ENSMUSG00000017760	Ctsa	AU019505|PPCA|Ppgb	cathepsin A	protein-coding
mm_31641.1	chr4	59581558	59581568	+	1	NA	promoter-TSS (NM_024255)	promoter-TSS (NM_024255)	0	NM_001301367	72479	Mm.272905	NM_024255	ENSMUSG00000028383	Hsdl2	2610207I16Rik	hydroxysteroid dehydrogenase like 2	protein-coding
mm_62462.1	chr7	101581219	101581231	+	1	NA	promoter-TSS (NM_019915)	promoter-TSS (NM_019915)	-64	NM_019915	11872	Mm.57008	NM_019915	ENSMUSG00000030651	Art2b	ART2.2|ARTC2|Art|Ly92b|Rt-6|Rt6|Rt6-2	ADP-ribosyltransferase 2b	protein-coding
mm_18805.1	chr2	73911008	73911056	-	1	NA	5' UTR (NM_175015, exon 2 of 5)	5' UTR (NM_175015, exon 2 of 5)	294	NM_175015	228033	Mm.2966	NM_175015	ENSMUSG00000018770	Atp5g3	6030447M23	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit C3 (subunit 9)	protein-coding
mm_50862.1	chr6	55336280	55336314	+	1	NA	promoter-TSS (NM_007472)	promoter-TSS (NM_007472)	-2	NM_007472	11826	Mm.18625	NM_007472	ENSMUSG00000004655	Aqp1	CHIP28	aquaporin 1	protein-coding
mm_99749.1	chr11	106686067	106686068	+	1	NA	intron (NM_001305157, intron 7 of 15)	intron (NM_001305157, intron 7 of 15)	29214	NM_001305158	18613	Mm.343951	NM_008816	ENSMUSG00000020717	Pecam1	C85791|Cd31|PECAM-1|Pecam	platelet/endothelial cell adhesion molecule 1	protein-coding
mm_4633.1	chr1	179668299	179668354	+	1	NA	promoter-TSS (NM_178653)	promoter-TSS (NM_178653)	95	NM_178653	109232	Mm.136458	NM_178653	ENSMUSG00000038936	Sccpdh	AW214504|C330023F11Rik	saccharopine dehydrogenase (putative)	protein-coding
mm_70512.1	chr8	12931719	12931750	+	1	NA	intron (NM_178076, intron 1 of 30)	intron (NM_178076, intron 1 of 30)	15841	NM_178076	17207	Mm.334413	NM_178076	ENSMUSG00000031442	Mcf2l	C130040G20Rik|Dbs|Ost|mKIAA0362	mcf.2 transforming sequence-like	protein-coding
mm_153286.1	chr19	37291680	37291690	-	1	NA	intron (NM_031156, intron 13 of 23)	intron (NM_031156, intron 13 of 23)	-27590	NR_040298	77059	Mm.251476	NR_040298		4931408D14Rik	-	RIKEN cDNA 4931408D14 gene	ncRNA
mm_110416.1	chr12	46784315	46784318	-	1	NA	intron (NM_021361, intron 2 of 4)	intron (NM_021361, intron 2 of 4)	34459	NM_021361	664883	Mm.247195	NM_021361	ENSMUSG00000021047	Nova1	9430099M15Rik|G630039L02|Nova-1	neuro-oncological ventral antigen 1	protein-coding
mm_8325.1	chr1	149840972	149840976	-	1	NA	intron (NM_001305632, intron 15 of 16)	intron (NM_001305632, intron 15 of 16)	81465	NM_001305632	18783	Mm.4186	NM_008869	ENSMUSG00000056220	Pla2g4a	Pla2g4|cPLA2|cPLA2-alpha|cPLA2alpha	phospholipase A2, group IVA (cytosolic, calcium-dependent)	protein-coding
mm_99276.1	chr11	101260570	101260622	+	1	NA	promoter-TSS (NM_175638)	promoter-TSS (NM_175638)	29	NM_175638	69847	Mm.23656	NM_175638	ENSMUSG00000035112	Wnk4	2010002J11Rik|Pha2b|Prkwnk4	WNK lysine deficient protein kinase 4	protein-coding
mm_72372.1	chr8	81015195	81015211	+	1	NA	promoter-TSS (NM_027554)	promoter-TSS (NM_027554)	-297	NM_027554	74841	Mm.246018	NM_027554	ENSMUSG00000038250	Usp38	4631402N15Rik|4833420O05Rik|AA536967|AU044701|AW544820|mKIAA1891	ubiquitin specific peptidase 38	protein-coding
mm_44273.1	chr5	5694481	5694491	-	1	NA	promoter-TSS (NM_001103156)	promoter-TSS (NM_001103156)	82	NM_028734	74051	Mm.274956	NM_028734	ENSMUSG00000015653	Steap2	4921538B17Rik|AI930049|AW045895|IPCA-1|IPCA1|PCANAP1|STAMP1|STMP	six transmembrane epithelial antigen of prostate 2	protein-coding
mm_49239.1	chr6	17306381	17306407	+	1	NA	promoter-TSS (NM_007616)	promoter-TSS (NM_007616)	59	NM_007616	12389	Mm.28278	NM_007616	ENSMUSG00000007655	Cav1	Cav|Cav-1	caveolin 1, caveolae protein	protein-coding
mm_111030.1	chr12	79172413	79172473	-	1	NA	promoter-TSS (NM_016800)	promoter-TSS (NM_016800)	15	NM_016800	53612	Mm.265929	NM_016800	ENSMUSG00000021124	Vti1b	AU015348|GES30|MVti1b|SNARE|Vti1-rp1	vesicle transport through interaction with t-SNAREs 1B	protein-coding
mm_15684.1	chr2	163630929	163630941	+	1	NA	exon (NM_012032, exon 6 of 10)	exon (NM_012032, exon 6 of 10)	-13915	NR_028113	68386	Mm.410649	NR_028113	ENSMUSG00000058812	0610039K10Rik	-	RIKEN cDNA 0610039K10 gene	ncRNA
mm_78760.1	chr9	43303254	43303268	+	1	NA	Intergenic	Intergenic	-7502	NM_023655	72169	Mm.273277	NM_023655	ENSMUSG00000032013	Trim29	1110047J21Rik|2810431N19Rik|4732461M22Rik|AI119726	tripartite motif-containing 29	protein-coding
mm_99363.1	chr11	101682858	101682869	+	1	NA	Intergenic	Intergenic	17322	NM_025404	80981	Mm.266840	NM_025404	ENSMUSG00000034936	Arl4d	1110036H21Rik|ARL6|AW456149|Arf4l|Arfl4|Arl5	ADP-ribosylation factor-like 4D	protein-coding
mm_20481.1	chr2	129630623	129630651	-	1	NA	3' UTR (NM_001291022, exon 5 of 5)	3' UTR (NM_001291022, exon 5 of 5)	37468	NM_001291022	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_31148.1	chr4	43392104	43392110	+	1	NA	intron (NM_001037709, intron 1 of 11)	MIRb|SINE|MIR	10125	NM_001037709	100213	Mm.235730	NM_199057	ENSMUSG00000035969	Rusc2	AI840675|mKIAA0375	RUN and SH3 domain containing 2	protein-coding
mm_62218.1	chr7	98371738	98371745	+	1	NA	Intergenic	RMER17C2|LTR|ERVK	-10413	NM_001168539	244152	Mm.25317	NM_001024619	ENSMUSG00000049580	Tsku	9530051K01Rik|E2ig4|Lrrc54|Tsk	tsukushi, small leucine rich proteoglycan	protein-coding
mm_132014.1	chr16	25866090	25866092	+	1	NA	exon (NM_001127262, exon 6 of 11)	exon (NM_001127262, exon 6 of 11)	64175	NM_001127264	22061	Mm.20894	NM_011641	ENSMUSG00000022510	Trp63	AI462811|Ket|P51/P63|P63|P73l|Tp63|Trp53rp1	transformation related protein 63	protein-coding
mm_72926.1	chr8	91106555	91106561	+	1	NA	intron (NM_011250, intron 15 of 21)	intron (NM_011250, intron 15 of 21)	27469	NM_001302337	14339	Mm.324588	NM_010241	ENSMUSG00000031667	Aktip	AL023020|Fif|Ft|Ft1|Fts	thymoma viral proto-oncogene 1 interacting protein	protein-coding
mm_104673.1	chr11	97663674	97663703	-	1	NA	intron (NM_139311, intron 1 of 19)	intron (NM_139311, intron 1 of 19)	276	NM_139311	246198	Mm.23685	NM_139311	ENSMUSG00000038437	Mllt6	AI315037|Af17	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 6	protein-coding
mm_170224.1	chr17	80568057	80568066	+	1	NA	Intergenic	RLTR10A|LTR|ERVK	-4227	NM_001033443	381113	Mm.329216	NM_001033443	ENSMUSG00000033966	Cdkl4	AU067824|Gm942	cyclin-dependent kinase-like 4	protein-coding
mm_155369.1	chrX	71364746	71364794	+	1	NA	promoter-TSS (NM_016985)	promoter-TSS (NM_016985)	10	NM_001313706	53332	Mm.219672	NM_016985	ENSMUSG00000015214	Mtmr1	AW049210	myotubularin related protein 1	protein-coding
mm_78753.1	chr9	42466016	42466053	+	1	NA	intron (NM_173038, intron 1 of 7)	intron (NM_173038, intron 1 of 7)	6192	NM_173038	272589	Mm.34483	NM_173038	ENSMUSG00000037287	Tbcel	D330014K23|E130107N23Rik|Lrrc35	tubulin folding cofactor E-like	protein-coding
mm_71471.1	chr8	46534965	46535002	+	1	NA	3' UTR (NM_007981, exon 21 of 21)	3' UTR (NM_007981, exon 21 of 21)	-17086	NM_027973	71876	Mm.22108	NM_027973	ENSMUSG00000031629	Cenpu	1700029A22Rik|Mlf1ip	centromere protein U	protein-coding
mm_10778.1	chr2	24322387	24322399	+	1	NA	Intergenic	RLTR43C|LTR|ERVK	-14467	NM_031167	16181	Mm.882	NM_031167	ENSMUSG00000026981	Il1rn	F630041P17Rik|IL-1ra	interleukin 1 receptor antagonist	protein-coding
mm_69580.1	chr7	135704125	135704155	-	1	NA	exon (NM_001081117, exon 10 of 14)	exon (NM_001081117, exon 10 of 14)	12239	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_24467.1	chr3	90654192	90654205	+	1	NA	promoter-TSS (NM_199422)	promoter-TSS (NM_199422)	-104	NM_199422	381493	Mm.291525	NM_199422	ENSMUSG00000063767	S100a7a	AY465109|Gm1020|S100A7L1|S100A7f|S100a15|S100a15a|S100a17l1	S100 calcium binding protein A7A	protein-coding
mm_150653.1	chr19	41917774	41917805	+	1	NA	3' UTR (NM_023418, exon 4 of 4)	3' UTR (NM_023418, exon 4 of 4)	5918	NM_023418	18648	Mm.16783	NM_023418	ENSMUSG00000011752	Pgam1	2310050F24Rik|Pgam-1	phosphoglycerate mutase 1	protein-coding
mm_144237.1	chr18	10618041	10618051	+	1	NA	intron (NM_009226, intron 1 of 3)	CpG	250	NM_009226	20641	Mm.603	NM_009226	ENSMUSG00000002477	Snrpd1	AA407109|AL023031|SMD1	small nuclear ribonucleoprotein D1	protein-coding
mm_75175.1	chr8	36827993	36828005	-	1	NA	intron (NM_001194940, intron 4 of 17)	intron (NM_001194940, intron 4 of 17)	-94945	NM_001194941	50768	Mm.125155	NM_015802	ENSMUSG00000031523	Dlc1	A730069N07Rik|Arhgap7|HP|STARD12|dlc-1	deleted in liver cancer 1	protein-coding
mm_49351.1	chr6	21986379	21986435	+	1	NA	5' UTR (NM_001081351, exon 1 of 22)	5' UTR (NM_001081351, exon 1 of 22)	497	NM_001081351	214642	Mm.221404	NM_001081351	ENSMUSG00000062980	Cped1	6720481P07|A430107O13Rik|AI552584	cadherin-like and PC-esterase domain containing 1	protein-coding
mm_113862.1	chr13	48261107	48261123	+	1	NA	promoter-TSS (NM_031166)	promoter-TSS (NM_031166)	-312	NM_031166	15904	Mm.458006	NM_031166	ENSMUSG00000021379	Id4	Idb4|bHLHb27	inhibitor of DNA binding 4	protein-coding
mm_80730.1	chr9	93853898	93853898	+	1	NA	Intergenic	Lx8|LINE|L1	684183	NM_001033145	68861	Mm.258746	NM_001033145	ENSMUSG00000045414	1190002N15Rik	GoPro49|HASF	RIKEN cDNA 1190002N15 gene	protein-coding
mm_137450.1	chr17	26532966	26532972	+	1	NA	Intergenic	Intergenic	-24497	NM_013642	19252	Mm.239041	NM_013642	ENSMUSG00000024190	Dusp1	3CH134|MKP1|Ptpn16|U19515|erp|mkp-1	dual specificity phosphatase 1	protein-coding
mm_14023.1	chr2	122151013	122151026	+	1	NA	exon (NM_009735, exon 2 of 4)	exon (NM_009735, exon 2 of 4)	3332	NM_009735	12010	Mm.163	NM_009735	ENSMUSG00000060802	B2m	Ly-m11|beta2-m|beta2m	beta-2 microglobulin	protein-coding
mm_130178.1	chr15	93398193	93398201	-	1	NA	promoter-TSS (NM_026025)	promoter-TSS (NM_026025)	93	NM_026025	67197	Mm.293181	NM_026025	ENSMUSG00000022635	Zcrb1	2700088M22Rik|Madp-1	zinc finger CCHC-type and RNA binding motif 1	protein-coding
mm_95399.1	chr11	49720104	49720120	+	1	NA	Intergenic	Intergenic	-7390	NM_212484	104625	Mm.247113	NM_212484	ENSMUSG00000020362	Cnot6	CCR4	CCR4-NOT transcription complex, subunit 6	protein-coding
mm_141967.1	chr17	35121424	35121434	-	1	NA	promoter-TSS (NM_009975)	promoter-TSS (NM_009975)	0	NM_001303445	13001	Mm.378901	NM_009975	ENSMUSG00000024387	Csnk2b	CK II beta	casein kinase 2, beta polypeptide	protein-coding
mm_146868.1	chr18	25168616	25168731	-	1	NA	promoter-TSS (NM_001033532)	promoter-TSS (NM_001033532)	204	NM_001142698	66648	Mm.263189	NM_001004361	ENSMUSG00000024269	Tpgs2	5730437P09Rik|5730494M16Rik|AI666318|Pgs2	tubulin polyglutamylase complex subunit 2	protein-coding
mm_82635.1	chr9	21963569	21963592	-	1	NA	promoter-TSS (NM_010149)	promoter-TSS (NM_010149)	-4	NM_010149	13857	Mm.2653	NM_010149	ENSMUSG00000006235	Epor	-	erythropoietin receptor	protein-coding
mm_162730.1	chr10	43438474	43438474	+	1	NA	intron (NM_001168289, intron 7 of 7)	B1_Mur4|SINE|Alu	-40666	NM_199028	331623	Mm.490388	NM_199028	ENSMUSG00000038214	Bend3	mKIAA1553	BEN domain containing 3	protein-coding
mm_14234.1	chr2	127590743	127590759	+	1	NA	exon (NM_029963, exon 2 of 12)	exon (NM_029963, exon 2 of 12)	3325	NM_029963	77721	Mm.274601	NM_029963	ENSMUSG00000027374	Mrps5	1620401I16Rik|AI850294	mitochondrial ribosomal protein S5	protein-coding
mm_8259.1	chr1	138876931	138876952	-	1	NA	promoter-TSS (NR_138576)	promoter-TSS (NR_138576)	9	NR_138576	75546	Mm.71176	NR_138576	ENSMUSG00000099808	1700019P21Rik	-	RIKEN cDNA 1700019P21 gene	ncRNA
mm_152896.1	chr19	24862242	24862291	-	1	NA	promoter-TSS (NM_175013)	promoter-TSS (NM_175013)	-424	NM_175013	226041	Mm.105222	NM_175013	ENSMUSG00000041731	Pgm5	4833423B07|9530034F03Rik|D830025G17|aciculin	phosphoglucomutase 5	protein-coding
mm_48400.1	chr5	140201156	140201175	-	1	NA	intron (NM_010752, intron 10 of 17)	intron (NM_010752, intron 10 of 17)	120387	NM_010752	17120	Mm.27250	NM_010752	ENSMUSG00000029554	Mad1l1	AI173502|AW550425|Mad1	MAD1 mitotic arrest deficient 1-like 1	protein-coding
mm_163523.1	chr12	116047814	116047825	+	1	NA	promoter-TSS (NM_019565)	promoter-TSS (NM_019565)	95	NM_019565	56220	Mm.254997	NM_019565	ENSMUSG00000042063	Zfp386	Kzf1|mKIAA4205	zinc finger protein 386 (Kruppel-like)	protein-coding
mm_85797.1	chr9	109902342	109902347	-	1	NA	Intergenic	Intergenic	12701	NR_106057	102465660		NR_106057	ENSMUSG00000098490	Mir7089	Gm27418|mmu-mir-7089	microRNA 7089	ncRNA
mm_38175.1	chr4	135264022	135264048	-	1	NA	intron (NM_013885, intron 1 of 5)	ID_B1|SINE|B4	8725	NM_013885	29876	Mm.257765	NM_013885	ENSMUSG00000037242	Clic4	D0Jmb3|TU-74|mc3s5|mtCLIC	chloride intracellular channel 4 (mitochondrial)	protein-coding
mm_153057.1	chr19	32155352	32155365	-	1	NA	intron (NM_001168526, intron 2 of 5)	RSINE1|SINE|B4	-52218	NM_018830	54447	Mm.491229	NM_018830	ENSMUSG00000024887	Asah2	AI585898	N-acylsphingosine amidohydrolase 2	protein-coding
mm_14610.1	chr2	136532267	136532287	+	1	NA	promoter-TSS (NM_175667)	promoter-TSS (NM_175667)	-44	NM_175667	319196	Mm.477841	NM_175667	ENSMUSG00000074771	Ankef1	AV276460|Ankrd5	ankyrin repeat and EF-hand domain containing 1	protein-coding
mm_15297.1	chr2	155383072	155383080	+	1	NA	intron (NM_178111, intron 1 of 3)	intron (NM_178111, intron 1 of 3)	1220	NM_178111	68728	Mm.293605	NM_178111	ENSMUSG00000038375	Trp53inp2	1110029F20Rik|Tp53inp2	transformation related protein 53 inducible nuclear protein 2	protein-coding
mm_135425.1	chr16	45372628	45372638	-	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	36420	NM_010818	17470	Mm.245851	NM_010818	ENSMUSG00000022661	Cd200	Mox2|OX2	CD200 antigen	protein-coding
mm_112288.1	chr12	114479507	114479521	-	1	NA	Intergenic	Intergenic	-10048	NR_106062	102465663		NR_106062	ENSMUSG00000105438	Mir7094-1	mmu-mir-7094-1	microRNA 7094-1	ncRNA
mm_141614.1	chr17	32810788	32810801	-	1	NA	promoter-TSS (NM_001267583)	promoter-TSS (NM_001267583)	-863	NM_183177	240063	Mm.30675	NM_183177	ENSMUSG00000055202	Zfp811	BC052046	zinc finger protein 811	protein-coding
mm_56326.1	chr6	92481643	92481646	-	1	NA	promoter-TSS (NM_001134460)	promoter-TSS (NM_001134460)	-252	NM_001134460	243548	Mm.248820	NM_001081146	ENSMUSG00000030020	Prickle2	6230400G14Rik|6720451F06Rik|mpk2	prickle planar cell polarity protein 2	protein-coding
mm_139746.1	chr17	63499011	63499033	+	1	NA	intron (NM_015794, intron 1 of 8)	CpG	1558	NM_015794	50758	Mm.136366	NM_015794	ENSMUSG00000023965	Fbxl17	6330576B01Rik|AI452053|BB073797|C130023C01Rik|Fbx13|Fbxo13	F-box and leucine-rich repeat protein 17	protein-coding
mm_141014.1	chr17	25015767	25015791	-	1	NA	promoter-TSS (NM_020608)	promoter-TSS (NM_020608)	-307	NM_134126	106633	Mm.32802	NM_134126	ENSMUSG00000024169	Ift140	AI661311|Tce5|Wdtc2|mKIAA0590	intraflagellar transport 140	protein-coding
mm_45789.1	chr5	87482279	87482283	-	1	NA	promoter-TSS (NM_001024148)	promoter-TSS (NM_001024148)	-23	NM_001024148	552899	Mm.26794	NM_001024148	ENSMUSG00000029268	Ugt2a2	-	UDP glucuronosyltransferase 2 family, polypeptide A2	protein-coding
mm_76267.1	chr8	84044983	84044995	-	1	NA	promoter-TSS (NM_173184)	promoter-TSS (NM_173184)	-10	NM_173184	212108	Mm.261583	NM_173184	ENSMUSG00000045232	Rln3	M3|insl7	relaxin 3	protein-coding
mm_130253.1	chr15	96642187	96642197	-	1	NA	promoter-TSS (NM_134086)	promoter-TSS (NM_134086)	151	NM_001166456	105727	Mm.103568	NM_134086	ENSMUSG00000023169	Slc38a1	AA408026|AA409865|AL022800|AU015942|NAT2	solute carrier family 38, member 1	protein-coding
mm_7461.1	chr1	120476668	120476688	-	1	NA	exon (NM_010766, exon 16 of 17)	exon (NM_010766, exon 16 of 17)	28406	NM_010766	17167	Mm.1856	NM_010766	ENSMUSG00000026390	Marco	AI323439|Ly112|Scara2	macrophage receptor with collagenous structure	protein-coding
mm_85554.1	chr9	106685893	106685961	-	1	NA	promoter-TSS (NM_001081654)	promoter-TSS (NM_001081654)	25	NR_104459	21767	Mm.22266	NM_011573	ENSMUSG00000040813	Tex264	TEG-264	testis expressed gene 264	protein-coding
mm_39164.1	chr4	155624578	155624634	-	1	NA	promoter-TSS (NM_007661)	promoter-TSS (NM_007661)	149	NR_040441	100502734	Mm.306018	NR_040441	ENSMUSG00000086682	Gm16023	OTTMUSG00000029160	predicted gene 16023	ncRNA
mm_72615.1	chr8	84615484	84615499	+	1	NA	intron (NM_001252059, intron 36 of 45)	T-rich|Low_complexity|Low_complexity	47361	NM_010499	15936	Mm.399	NM_010499	ENSMUSG00000053560	Ier2	AI317238|Ch1|Pip92	immediate early response 2	protein-coding
mm_24040.1	chr3	87846779	87846788	+	1	NA	promoter-TSS (NM_021309)	promoter-TSS (NM_021309)	28	NM_021309	27371	Mm.86361	NM_021309	ENSMUSG00000028071	Sh2d2a	Lad|Ribp|Tsad	SH2 domain containing 2A	protein-coding
mm_119503.1	chr14	47380347	47380360	+	1	NA	exon (NM_010705, exon 3 of 6)	exon (NM_010705, exon 3 of 6)	6493	NM_001145953	16854	Mm.248615	NM_010705	ENSMUSG00000050335	Lgals3	GBP|L-34|Mac-2|gal3	lectin, galactose binding, soluble 3	protein-coding
mm_116400.1	chr13	41358991	41359006	-	1	NA	promoter-TSS (NM_017464)	promoter-TSS (NM_017464)	3	NM_017464	18003	Mm.288980	NM_017464	ENSMUSG00000021365	Nedd9	Cas-L|CasL|HEF1|MEF1|Nedd-9|p105	neural precursor cell expressed, developmentally down-regulated gene 9	protein-coding
mm_142516.1	chr17	46264934	46264953	-	1	NA	5' UTR (NM_028751, exon 4 of 11)	5' UTR (NM_028751, exon 4 of 11)	10778	NM_001111142	224813	Mm.70999	NM_001111142	ENSMUSG00000071073	Lrrc73	Gm88	leucine rich repeat containing 73	protein-coding
mm_18187.1	chr2	45112116	45112134	-	1	NA	promoter-TSS (NR_110571)	promoter-TSS (NR_110571)	-135	NR_110571	433424	Mm.441408	NR_110571	ENSMUSG00000052248	Zeb2os	Gm13476|OTTMUSG00000012358|Zeb2nat	zinc finger E-box binding homeobox 2, opposite strand	ncRNA
mm_5183.1	chr1	12992731	12992747	-	1	NA	Intergenic	CpG	-1604	NM_172841	240726	Mm.24481	NM_172841	ENSMUSG00000025938	Slco5a1	4732454B15|A630033C23Rik|AA407151	solute carrier organic anion transporter family, member 5A1	protein-coding
mm_7495.1	chr1	121346194	121346215	-	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-13615	NM_178082	72999	Mm.27136	NM_133748	ENSMUSG00000003721	Insig2	2900053I11Rik|C730043J18Rik|Insig-2	insulin induced gene 2	protein-coding
mm_151610.1	chr19	3897101	3897112	-	1	NA	exon (NM_001136091, exon 16 of 20)	exon (NM_001136091, exon 16 of 20)	8124	NM_016921	27060	Mm.271689	NM_016921	ENSMUSG00000001750	Tcirg1	ATP6N1C|ATP6a3|Atp6i|OC-116|OPTB1|Stv1|TIRC7|Vph1|oc	T cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 protein A3	protein-coding
mm_61850.1	chr7	88297205	88297217	+	1	NA	exon (NM_009982, exon 3 of 7)	exon (NM_009982, exon 3 of 7)	19126	NM_001311790	13032	Mm.89295	NM_009982	ENSMUSG00000030560	Ctsc	AI047818|CatC|DPP1|DPPI	cathepsin C	protein-coding
mm_3955.1	chr1	164063288	164063304	+	1	NA	intron (NM_011346, intron 2 of 8)	T-rich|Low_complexity|Low_complexity	1220	NM_001164059	20343	Mm.1461	NM_011346	ENSMUSG00000026581	Sell	AI528707|CD62L|L-selectin|LECAM-1|Lnhr|Ly-22|Ly-m22|Lyam-1|Lyam1	selectin, lymphocyte	protein-coding
mm_154522.1	chrM	13344	13371	-	1	NA	NA	Intergenic	NA	NA								
mm_165198.1	chr2	32587050	32587056	+	1	NA	promoter-TSS (NM_011373)	promoter-TSS (NM_011373)	-25	NM_001276425	20448	Mm.27446	NM_011373	ENSMUSG00000079442	St6galnac4	SIAT7-D|ST6GalNAcIV|Siat7d	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 4	protein-coding
mm_40933.1	chr5	76588816	76588837	+	1	NA	Intergenic	CpG	-2888	NM_199032	381644	Mm.332452	NM_199032	ENSMUSG00000036403	Cep135	BC062951|Cep4|Gm1044	centrosomal protein 135	protein-coding
mm_88935.1	chr10	81268208	81268270	+	1	NA	promoter-TSS (NM_018758)	promoter-TSS (NM_018758)	67	NM_018758	57267	Mm.293931	NM_018758	ENSMUSG00000004931	Apba3	AW208791|Mint-3|X11gamma|lin-10|mint3	amyloid beta (A4) precursor protein-binding, family A, member 3	protein-coding
mm_149519.1	chr19	12440402	12440416	+	1	NA	Intergenic	Intergenic	12504	NM_019540	56093	Mm.285849	NM_019540	ENSMUSG00000040065	Pfpl	Epcs5|Epcs50	pore forming protein-like	protein-coding
mm_71941.1	chr8	70373542	70373558	+	1	NA	promoter-TSS (NM_016685)	promoter-TSS (NM_016685)	2	NM_016685	12845	Mm.45071	NM_016685	ENSMUSG00000031849	Comp	TSP5	cartilage oligomeric matrix protein	protein-coding
mm_154486.1	chrM	4757	4799	-	1	NA	NA	Intergenic	NA	NA								
mm_124671.1	chr15	6392500	6392505	+	1	NA	intron (NM_001310446, intron 1 of 13)	intron (NM_001310446, intron 1 of 13)	5754	NM_001310446	13132	Mm.240830	NM_023118	ENSMUSG00000022150	Dab2	5730435J12Rik|AA960054|AI957090|D15Wsu122e|D630005B22Rik|Doc-2|Doc2|p96	disabled 2, mitogen-responsive phosphoprotein	protein-coding
mm_55330.1	chr6	56157168	56157206	-	1	NA	intron (NM_001025568, intron 8 of 16)	intron (NM_001025568, intron 8 of 16)	139672	NM_011153	19051	Mm.42096	NM_011153	ENSMUSG00000002930	Ppp1r17	G-substrate|Gsbs|Ppp1r2	protein phosphatase 1, regulatory subunit 17	protein-coding
mm_32286.1	chr4	102991816	102991837	+	1	NA	promoter-TSS (NM_001163768)	promoter-TSS (NM_001163768)	31	NM_001163768	67344	Mm.111346	NM_026100	ENSMUSG00000028523	Tctex1d1	1700055O19Rik	Tctex1 domain containing 1	protein-coding
mm_110182.1	chr12	27337598	27337606	-	1	NA	3' UTR (NM_009234, exon 1 of 1)	3' UTR (NM_009234, exon 1 of 1)	5116	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding
mm_54956.1	chr6	48689351	48689354	-	1	NA	intron (NM_174990, intron 2 of 2)	RLTR53_Mm|LTR|ERVK	4774	NM_174990	107526	Mm.333048	NM_174990	ENSMUSG00000054435	Gimap4	AU019574|E430007K16Rik|Ian-1|Ian1|Imap4	GTPase, IMAP family member 4	protein-coding
mm_14294.1	chr2	128863922	128863999	+	1	NA	promoter-TSS (NM_024237)	promoter-TSS (NM_024237)	28	NM_024237	70370	Mm.5107	NM_024237	ENSMUSG00000027386	Fbln7	1600015H20Rik|AI464334|TM14	fibulin 7	protein-coding
mm_102242.1	chr11	55021816	55021863	-	1	NA	intron (NR_138556, intron 1 of 24)	intron (NR_138556, intron 1 of 24)	11632	NR_138556	11749	Mm.265347	NM_013472	ENSMUSG00000018340	Anxa6	AW107198|Anx6|AnxVI|Cabm|Camb	annexin A6	protein-coding
mm_167665.1	chr9	72536411	72536414	+	1	NA	intron (NM_001033536, intron 1 of 8)	intron (NM_001033536, intron 1 of 8)	4172	NM_001033536	319758	Mm.32081	NM_001033536	ENSMUSG00000037674	Rfx7	2510005N23Rik|9930116O05Rik|D130086K05Rik|Rfxdc2	regulatory factor X, 7	protein-coding
mm_167202.1	chr7	143166046	143166047	+	1	NA	intron (NM_008434, intron 2 of 15)	L1M5|LINE|L1	58792	NM_008434	16535	Mm.439769	NM_008434	ENSMUSG00000009545	Kcnq1	AW559127|KVLQT1|Kcna9	potassium voltage-gated channel, subfamily Q, member 1	protein-coding
mm_162525.1	chr1	160987123	160987131	+	1	NA	intron (NM_080844, intron 1 of 7)	intron (NM_080844, intron 1 of 7)	8521	NM_080844	11905	Mm.260770	NM_080844	ENSMUSG00000026715	Serpinc1	AI114908|ATIII|At-3|At3	serine (or cysteine) peptidase inhibitor, clade C (antithrombin), member 1	protein-coding
mm_144006.1	chr17	88113390	88113399	-	1	NA	Intergenic	L1M5|LINE|L1	-12118	NM_001190356	225058	Mm.312053	NM_001190356		Gm4832	EG225058	predicted gene 4832	protein-coding
mm_125193.1	chr15	32691799	32691851	+	1	NA	3' UTR (NM_009154, exon 23 of 23)	3' UTR (NM_009154, exon 23 of 23)	-228898	NM_008304	15529	Mm.234266	NM_008304	ENSMUSG00000022261	Sdc2	4833414L08Rik|AA960457|Hspg1|Synd2|syndecan-2	syndecan 2	protein-coding
mm_116496.1	chr13	44947132	44947157	-	1	NA	intron (NM_025772, intron 7 of 9)	intron (NM_025772, intron 7 of 9)	54952	NM_025772	94245	Mm.352311	NM_025772	ENSMUSG00000057531	Dtnbp1	5430437B18Rik|AW048963|Bloc1s8|dysbindin|sdy	dystrobrevin binding protein 1	protein-coding
mm_146375.1	chr18	82584878	82584884	+	1	NA	3' UTR (NM_010777, exon 7 of 7)	3' UTR (NM_010777, exon 7 of 7)	30373	NM_001025254	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_48546.1	chr5	142905697	142905718	-	1	NA	intron (NM_007393, intron 1 of 5)	CpG	1047	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_109388.1	chr12	109738912	109738926	+	1	NA	promoter-TSS (NR_030437)	promoter-TSS (NR_030437)	-200	NR_030437	751524		NR_030437	ENSMUSG00000070136	Mir496a	Mir496|Mirn496|mir-496a|mmu-mir-496|mmu-mir-496a	microRNA 496a	ncRNA
mm_124929.1	chr15	12179720	12179735	+	1	NA	intron (NM_011767, intron 17 of 19)	B1F|SINE|Alu	8235	NR_035443	100316684		NR_035443	ENSMUSG00000084592	Mir1898	Mirn1898|mmu-mir-1898	microRNA 1898	ncRNA
mm_18306.1	chr2	53191196	53191209	-	1	NA	promoter-TSS (NM_018785)	promoter-TSS (NM_018785)	-15	NM_018785	56194	Mm.257474	NM_018785	ENSMUSG00000061136	Prpf40a	2810012K09Rik|FBP-11|FBP11|Fnbp11|Fnbp3	pre-mRNA processing factor 40A	protein-coding
mm_46532.1	chr5	105696155	105696179	-	1	NA	Intergenic	Intergenic	-3802	NM_001122768	231549	Mm.23837	NM_178701	ENSMUSG00000046079	Lrrc8d	2810473G09Rik|4930525N13Rik|A930019F03|Lrrc5	leucine rich repeat containing 8D	protein-coding
mm_12952.1	chr2	89911348	89911351	+	1	NA	Intergenic	ERVB4_3-LTR_MM|LTR|ERVK	-18462	NM_146978	258980	Mm.223370	NM_146978	ENSMUSG00000049149	Olfr1258	MOR232-3	olfactory receptor 1258	protein-coding
mm_102058.1	chr11	52253483	52253493	-	1	NA	3' UTR (NM_009331, exon 10 of 10)	3' UTR (NM_009331, exon 10 of 10)	21493	NM_011543	21402	Mm.42944	NM_011543	ENSMUSG00000036309	Skp1a	15kDa|2610043E24Rik|2610206H23Rik|EMC19|OCP-II|OCP2|SKP1|Tceb1l|p19A|p19Skp1	S-phase kinase-associated protein 1A	protein-coding
mm_63883.1	chr7	137429794	137429797	+	1	NA	Intergenic	Intergenic	-7853	NM_023140	30926	Mm.267692	NM_023140	ENSMUSG00000031068	Glrx3	PICOT|Txnl2	glutaredoxin 3	protein-coding
mm_58256.1	chr6	145076091	145076103	-	1	NA	promoter-TSS (NM_007532)	promoter-TSS (NM_007532)	60	NM_007532	12035	Mm.4606	NM_007532	ENSMUSG00000030268	Bcat1	BCATc|Eca39	branched chain aminotransferase 1, cytosolic	protein-coding
mm_11359.1	chr2	30927648	30927671	+	1	NA	Intergenic	Intergenic	-24362	NM_022415	64292	Mm.28768	NM_022415	ENSMUSG00000050737	Ptges	2410099E23Rik|D2Ertd369e|Pges|mPGES|mPGES-1	prostaglandin E synthase	protein-coding
mm_61630.1	chr7	80246431	80246434	+	1	NA	promoter-TSS (NM_177765)	promoter-TSS (NM_177765)	56	NM_177765	269954	Mm.276780	NM_177765	ENSMUSG00000045467	Ttll13	1700111A04Rik|4921538O11|BC024578	tubulin tyrosine ligase-like family, member 13	protein-coding
mm_57167.1	chr6	122801727	122801740	-	1	NA	Intergenic	CpG	-18451	NM_021899	60611	Mm.87142	NM_021899	ENSMUSG00000003154	Foxj2	Fhx	forkhead box J2	protein-coding
mm_118457.1	chr14	8615910	8615913	+	1	NA	intron (NM_028934, intron 4 of 15)	intron (NM_028934, intron 4 of 15)	50379	NM_028934	74430	Mm.271901	NM_028934	ENSMUSG00000021747	4930452B06Rik	4933406L09Rik|AI854000	RIKEN cDNA 4930452B06 gene	protein-coding
mm_44805.1	chr5	33270642	33270660	-	1	NA	intron (NM_001198860, intron 1 of 9)	intron (NM_001198860, intron 1 of 9)	4353	NM_001310535	13016	Mm.7286	NM_013502	ENSMUSG00000037373	Ctbp1	BARS|CtBP3/BARS|D4S115h|D5H4S115|D5H4S115E	C-terminal binding protein 1	protein-coding
mm_24218.1	chr3	88647413	88647432	+	1	NA	3' UTR (NM_001198913, exon 22 of 22)	3' UTR (NM_001198913, exon 22 of 22)	5720	NM_181817	242093	Mm.269130	NM_181817	ENSMUSG00000049741	Rxfp4	GPCR142|Gpr100|Rln3r2|SALPR	relaxin family peptide receptor 4	protein-coding
mm_37526.1	chr4	124752164	124752193	-	1	NA	intron (NR_126474, intron 7 of 24)	intron (NR_126474, intron 7 of 24)	8397	NR_030480	735263		NR_030480	ENSMUSG00000076119	Mir698	Mirn698|mir-698|mmu-mir-698	microRNA 698	ncRNA
mm_30060.1	chr3	137564384	137564425	-	1	NA	Intergenic	Intergenic	-11782	NM_177665	229862	Mm.246591	NM_177665	ENSMUSG00000055138	Gm4861	9230109N16|EG229862	predicted gene 4861	protein-coding
mm_142698.1	chr17	47834542	47834556	-	1	NA	5' UTR (NM_001109973, exon 1 of 5)	5' UTR (NM_001109973, exon 1 of 5)	142	NM_001109973	17240	Mm.329100	NM_010783	ENSMUSG00000032717	Mdfi	I-mf|I-mfa	MyoD family inhibitor	protein-coding
mm_12758.1	chr2	79255511	79255552	+	1	NA	5' UTR (NM_010576, exon 1 of 28)	5' UTR (NM_010576, exon 1 of 28)	105	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D|Itga4B	integrin alpha 4	protein-coding
mm_159721.1	chr5	34420838	34420838	+	1	NA	exon (NM_001243123, exon 4 of 21)	exon (NM_001243123, exon 4 of 21)	50905	NM_001243123	231128	Mm.286885	NM_001030306	ENSMUSG00000037210	Fam193a	-	family with sequence similarity 193, member A	protein-coding
mm_68317.1	chr7	106352675	106352688	-	1	NA	Intergenic	Intergenic	-28153	NR_030720	668128	Mm.484022	NR_030720		Gm8989	EG668128|Gm21911	very large inducible GTPase 1 pseudogene	pseudo
mm_62541.1	chr7	102299547	102299550	+	1	NA	intron (NM_009287, intron 1 of 11)	L1MB5|LINE|L1	31724	NM_009287	20866	Mm.645	NM_009287	ENSMUSG00000030987	Stim1	SIM	stromal interaction molecule 1	protein-coding
mm_127493.1	chr15	101373340	101373358	+	1	NA	Intergenic	Intergenic	-3224	NM_028770	74127	Mm.440055	NM_028770	ENSMUSG00000037185	Krt80	1200016G03Rik|2310041I20Rik|Kb20	keratin 80	protein-coding
mm_139729.1	chr17	57477207	57477218	+	1	NA	intron (NM_010130, intron 19 of 21)	intron (NM_010130, intron 19 of 21)	68102	NM_001104591	224916	Mm.469889	NM_001104591	ENSMUSG00000090655	Vmn2r120	EG224916	vomeronasal 2, receptor 120	protein-coding
mm_21600.1	chr2	164237904	164237911	-	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	434	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_9948.1	chr1	190979145	190979154	-	1	NA	promoter-TSS (NM_144879)	promoter-TSS (NM_144879)	147	NR_027352	226841	Mm.22856	NM_144879	ENSMUSG00000037568	Vash2	B130052G07Rik	vasohibin 2	protein-coding
mm_35532.1	chr4	41314707	41314723	-	1	NA	5' UTR (NM_026893, exon 1 of 9)	5' UTR (NM_026893, exon 1 of 9)	186	NM_026893	68970	Mm.28891	NM_026893	ENSMUSG00000028436	Dcaf12	1500001L20Rik|5830424K06Rik|AA420338|AI851081|Wdr40a	DDB1 and CUL4 associated factor 12	protein-coding
mm_78047.1	chr9	14643648	14643657	+	1	NA	Intergenic	Intergenic	-28652	NM_001081395	75723	Mm.159552	NM_001081395	ENSMUSG00000013076	Amotl1	2310010G08Rik|2310067L22Rik|4932416D09Rik|JEAP|mFLJ00155	angiomotin-like 1	protein-coding
mm_67256.1	chr7	75641921	75641929	-	1	NA	intron (NM_029332, intron 8 of 36)	intron (NM_029332, intron 8 of 36)	186391	NM_029332	75547	Mm.216107	NM_029332	ENSMUSG00000066406	Akap13	1700026G02Rik|5730522G15Rik|5830460E08Rik|AKAP-13|AKAP-Lbc|BRX|Ht31|LBC|PROTO-LB|PROTO-LBC	A kinase (PRKA) anchor protein 13	protein-coding
mm_103232.1	chr11	70681767	70681774	-	1	NA	intron (NM_178116, intron 8 of 22)	intron (NM_178116, intron 8 of 22)	6335	NM_001190376	216874	Mm.473726	NM_178116	ENSMUSG00000040712	Camta2	Kiaa0909-hp|mKIAA0909	calmodulin binding transcription activator 2	protein-coding
mm_20616.1	chr2	131855414	131855440	-	1	NA	3' UTR (NM_001166206, exon 2 of 2)	3' UTR (NM_001166206, exon 2 of 2)	4320	NM_001166206	71995	Mm.22	NM_028045	ENSMUSG00000037482	Erv3	1600014E20Rik|AA389086|AI426069|AI448024|D19349	endogenous retroviral sequence 3	protein-coding
mm_22088.1	chr2	168767137	168767151	-	1	NA	promoter-TSS (NM_201396)	promoter-TSS (NM_201396)	57	NM_201395	99377	Mm.434054	NM_175303	ENSMUSG00000027547	Sall4	5730441M18Rik|AA407717|AL022809|AW536104|C330011P20Rik|C78083|C78563|Tex20	sal-like 4 (Drosophila)	protein-coding
mm_6212.1	chr1	66837350	66837381	-	1	NA	intron (NM_007381, intron 9 of 10)	intron (NM_007381, intron 9 of 10)	-19770	NM_001122738	68691	Mm.240912	NM_177645	ENSMUSG00000026004	Kansl1l	1110028C15Rik|1190030G24|AI427598|C430010P07Rik|mKIAA4189	KAT8 regulatory NSL complex subunit 1-like	protein-coding
mm_157672.1	chrX	59134422	59134445	-	1	NA	promoter-TSS (NM_010200)	promoter-TSS (NM_010200)	3	NM_010200	14168	Mm.7995	NM_010200	ENSMUSG00000031137	Fgf13	Fhf2	fibroblast growth factor 13	protein-coding
mm_29580.1	chr3	117321763	117321764	-	1	NA	3' UTR (NM_177664, exon 7 of 7)	3' UTR (NM_177664, exon 7 of 7)	39113	NM_177664	229791	Mm.140138	NM_177664	ENSMUSG00000044667	Plppr4	A330086D10|D3Bwg0562e|Lppr4|PRG-1|mKIAA0455	phospholipid phosphatase related 4	protein-coding
mm_49237.1	chr6	17281305	17281364	+	1	NA	5' UTR (NM_001277756, exon 1 of 2)	5' UTR (NM_001277756, exon 1 of 2)	149	NM_016900	12390	Mm.396075	NM_016900	ENSMUSG00000000058	Cav2	AI447843	caveolin 2	protein-coding
mm_50031.1	chr6	41130156	41130171	+	1	NA	Intergenic	Intergenic	-94654	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_72829.1	chr8	88263171	88263175	+	1	NA	Intergenic	Intergenic	-9230	NM_007406	11513	Mm.288206	NM_007406	ENSMUSG00000031659	Adcy7	AA407758	adenylate cyclase 7	protein-coding
mm_98814.1	chr11	97309588	97309625	+	1	NA	Intergenic	Intergenic	-6110	NM_025927	67036	Mm.5381	NM_025927	ENSMUSG00000018882	Mrpl45	2600005P05Rik|AU043542|R75241	mitochondrial ribosomal protein L45	protein-coding
mm_50706.1	chr6	52158429	52158456	+	1	NA	promoter-TSS (NM_010449)	promoter-TSS (NM_010449)	-82	NR_131181	105242658	Mm.372521	NR_131181	ENSMUSG00000087658	Hotairm1	Gm15051|Hoxaas1|OTTMUSG00000018870	Hoxa transcript antisense RNA, myeloid-specific 1	ncRNA
mm_121214.1	chr14	103054596	103054614	+	1	NA	exon (NM_008392, exon 5 of 5)	exon (NM_008392, exon 5 of 5)	7593	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_58822.1	chr7	16700819	16700826	+	1	NA	Intergenic	RMER19B2|LTR|ERVK	-21107	NM_011927	26368	Mm.27096	NM_011927	ENSMUSG00000007209	Ceacam9	AA410097|AW545709|Cea-5|Cea5|mmCGM8	carcinoembryonic antigen-related cell adhesion molecule 9	protein-coding
mm_21071.1	chr2	152830219	152830256	-	1	NA	intron (NM_009743, intron 1 of 2)	intron (NM_009743, intron 1 of 2)	480	NM_001289716	12048	Mm.238213	NM_009743	ENSMUSG00000007659	Bcl2l1	Bcl(X)L|Bcl-XL|Bcl2l|BclX|bcl-x|bcl2-L-1	BCL2-like 1	protein-coding
mm_50043.1	chr6	41151168	41151194	+	1	NA	Intergenic	Intergenic	-115672	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_87754.1	chr10	60277994	60278006	+	1	NA	intron (NM_001146120, intron 1 of 13)	intron (NM_001146120, intron 1 of 13)	372	NM_001146121	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_45442.1	chr5	67425633	67425654	-	1	NA	intron (NM_001164806, intron 1 of 4)	HAL1b|LINE|L1	2156	NM_001164806	666938	Mm.101339	NM_001164806	ENSMUSG00000092060	Bend4	D330027G24Rik|EG666938	BEN domain containing 4	protein-coding
mm_7208.1	chr1	93076227	93076238	-	1	NA	exon (NM_008440, exon 6 of 48)	exon (NM_008440, exon 6 of 48)	6248	NM_001294150	16560	Mm.276408	NM_008440	ENSMUSG00000014602	Kif1a	ATSV|C630002N23Rik|Gm1626|Kns1	kinesin family member 1A	protein-coding
mm_68390.1	chr7	109516687	109516723	-	1	NA	Intergenic	Intergenic	-2490	NM_011975	26451	Mm.305750	NM_011975	ENSMUSG00000046364	Rpl27a	L27'|L27A|L29	ribosomal protein L27A	protein-coding
mm_170594.1	chr19	5802196	5802196	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	476	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_17752.1	chr2	32716739	32716759	-	1	NA	Intergenic	RMER19B|LTR|ERVK	-3777	NR_039536	100628606		NR_039536	ENSMUSG00000105841	Mir3960	mmu-mir-3960	microRNA 3960	ncRNA
mm_104449.1	chr11	95040507	95040543	-	1	NA	intron (NM_133667, intron 1 of 10)	intron (NM_133667, intron 1 of 10)	846	NM_133667	18604	Mm.29768	NM_133667	ENSMUSG00000038967	Pdk2	-	pyruvate dehydrogenase kinase, isoenzyme 2	protein-coding
mm_124774.1	chr15	7140529	7140535	+	1	NA	promoter-TSS (NM_013584)	promoter-TSS (NM_013584)	-10	NM_013584	16880	Mm.149720	NM_013584	ENSMUSG00000054263	Lifr	A230075M04Rik|AW061234|LIF	leukemia inhibitory factor receptor	protein-coding
mm_157202.1	chrX	12457293	12457302	-	1	NA	Intergenic	B3A|SINE|B2	-102301	NR_045321	100043946	Mm.211985	NR_045321	ENSMUSG00000087591	Gm14635	OTTMUSG00000017536	predicted gene 14635	ncRNA
mm_50080.1	chr6	41458924	41458936	+	1	NA	promoter-TSS (NM_053243)	promoter-TSS (NM_053243)	0	NM_053243	114228	Mm.449428	NM_053243	ENSMUSG00000062751	Prss1	Try-1|Try1|Trygn16	protease, serine 1 (trypsin 1)	protein-coding
mm_60837.1	chr7	45721184	45721233	+	1	NA	promoter-TSS (NM_001033170)	promoter-TSS (NM_001033170)	-12	NM_001033170	73813	Mm.322591	NM_001033170	ENSMUSG00000054161	Fam83e	4930403C10Rik	family with sequence similarity 83, member E	protein-coding
mm_110772.1	chr12	70346855	70346867	-	1	NA	exon (NM_001110203, exon 1 of 9)	exon (NM_001110203, exon 1 of 9)	753	NM_001286386	94090	Mm.184012	NM_053167	ENSMUSG00000021071	Trim9	-	tripartite motif-containing 9	protein-coding
mm_34225.1	chr4	141005086	141005102	+	1	NA	exon (NM_029097, exon 24 of 29)	exon (NM_029097, exon 24 of 29)	-5330	NM_001161799	17150	Mm.7386	NM_008546	ENSMUSG00000060572	Mfap2	AI893631|Magp|Magp1	microfibrillar-associated protein 2	protein-coding
mm_64150.1	chr7	141327841	141327882	+	1	NA	promoter-TSS (NM_001282076)	promoter-TSS (NM_001282076)	-136	NM_001282076	54006	Mm.28392	NM_016874	ENSMUSG00000058886	Deaf1	AU042387|C230009B13Rik|NUDR	deformed epidermal autoregulatory factor 1 (Drosophila)	protein-coding
mm_130198.1	chr15	94588085	94588087	-	1	NA	intron (NM_008971, intron 2 of 8)	intron (NM_008971, intron 2 of 8)	1738	NM_008971	19230	Mm.490250	NM_008971	ENSMUSG00000022451	Twf1	A6|Ptk9|twinfilin	twinfilin actin binding protein 1	protein-coding
mm_43328.1	chr5	135009634	135009699	+	1	NA	non-coding (NR_033794, exon 1 of 5)	non-coding (NR_033794, exon 1 of 5)	210	NR_033794	68758	Mm.389700	NM_145215	ENSMUSG00000040532	Abhd11	1110054D16Rik|A630008N09Rik|Wbscr21	abhydrolase domain containing 11	protein-coding
mm_148137.1	chr18	76044280	76044284	-	1	NA	intron (NM_145356, intron 3 of 4)	intron (NM_145356, intron 3 of 4)	54189	NR_045365	73009	Mm.443541	NR_045365		2900057B20Rik	-	RIKEN cDNA 2900057B20 gene	ncRNA
mm_68209.1	chr7	104400794	104400802	-	1	NA	Intergenic	Intergenic	-42152	NM_175648	244183	Mm.347647	NM_175648	ENSMUSG00000052749	Trim30b	A530023O14Rik|Trim30-1	tripartite motif-containing 30B	protein-coding
mm_53069.1	chr6	124914671	124914686	+	1	NA	exon (NM_026988, exon 3 of 5)	exon (NM_026988, exon 3 of 5)	-2973	NM_008479	16768	Mm.4528	NM_008479	ENSMUSG00000030124	Lag3	CD223|LAG-3|Ly66	lymphocyte-activation gene 3	protein-coding
mm_85255.1	chr9	99304753	99304758	-	1	NA	Intergenic	Intergenic	53775	NM_177775	272636	Mm.490440	NM_177775	ENSMUSG00000037681	Esyt3	D930024E11|D9Ertd280e|Fam62c|mKIAA4186	extended synaptotagmin-like protein 3	protein-coding
mm_11941.1	chr2	52868430	52868439	+	1	NA	intron (NM_172409, intron 1 of 26)	intron (NM_172409, intron 1 of 26)	10566	NM_172409	71409	Mm.394427	NM_172409	ENSMUSG00000036053	Fmnl2	5430425K04Rik|Man	formin-like 2	protein-coding
mm_18563.1	chr2	65239040	65239058	-	1	NA	promoter-TSS (NM_177025)	promoter-TSS (NM_177025)	-423	NM_027225	319876	Mm.34159	NM_027225	ENSMUSG00000034903	Cobll1	1810047P18Rik|Coblr1|D430044D16Rik	Cobl-like 1	protein-coding
mm_26841.1	chr3	14611251	14611275	-	1	NA	promoter-TSS (NM_001347206)	promoter-TSS (NM_001347206)	-7	NM_001099674	69126	Mm.389020	NM_001099674	ENSMUSG00000078784	1810022K09Rik	AI746582|AL023036	RIKEN cDNA 1810022K09 gene	protein-coding
mm_65063.1	chr7	18890418	18890424	-	1	NA	TTS (NM_009402)	TTS (NM_009402)	5731	NM_009402	21946	Mm.21855	NM_009402	ENSMUSG00000030413	Pglyrp1	PGRP|PGRP-S|Pglyrp|Tag7|Tasg7|Tnfsf3l	peptidoglycan recognition protein 1	protein-coding
mm_118995.1	chr14	28505818	28505835	+	1	NA	5' UTR (NM_009524, exon 1 of 5)	5' UTR (NM_009524, exon 1 of 5)	353	NM_009524	22418	Mm.287544	NM_009524	ENSMUSG00000021994	Wnt5a	8030457G12Rik|Wnt-5a	wingless-type MMTV integration site family, member 5A	protein-coding
mm_45226.1	chr5	53421357	53421370	-	1	NA	Intergenic	Intergenic	-134416	NM_001080928	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_169263.1	chr13	83631665	83631669	+	1	NA	intron (NM_001347569, intron 4 of 10)	B1_Mus1|SINE|Alu	58060	NM_001347569	17260	Mm.24001	NM_025282	ENSMUSG00000005583	Mef2c	5430401D19Rik|9930028G15Rik|AV011172|Mef2	myocyte enhancer factor 2C	protein-coding
mm_103737.1	chr11	80063410	80063428	-	1	NA	intron (NM_001277106, intron 2 of 6)	intron (NM_001277106, intron 2 of 6)	17572	NM_001277106	54394	Mm.272093	NM_018776	ENSMUSG00000017561	Crlf3	BB164954|Creme9|Cytor4	cytokine receptor-like factor 3	protein-coding
mm_163723.1	chr13	113614210	113614225	+	1	NA	intron (NM_130796, intron 1 of 1)	MER3|DNA|hAT-Charlie	4347	NM_130796	170625	Mm.33721	NM_130796	ENSMUSG00000042364	Snx18	Snag1	sorting nexin 18	protein-coding
mm_143432.1	chr17	70851219	70851232	-	1	NA	promoter-TSS (NM_009372)	promoter-TSS (NM_009372)	-15	NM_009372	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_166496.1	chr5	151488484	151488484	+	1	NA	Intergenic	Lx2|LINE|L1	81980	NR_131166	100042166	Mm.443286	NR_131166	ENSMUSG00000097321	Gm3704	-	predicted gene 3704	ncRNA
mm_122810.1	chr14	54577544	54577558	-	1	NA	5' UTR (NM_010590, exon 1 of 8)	5' UTR (NM_010590, exon 1 of 8)	110	NM_010590	16475	Mm.100253	NM_010590	ENSMUSG00000022178	Ajuba	Jub	ajuba LIM protein	protein-coding
mm_129091.1	chr15	75921227	75921274	-	1	NA	intron (NM_025412, intron 1 of 5)	intron (NM_025412, intron 1 of 5)	310	NM_025412	66194	Mm.250599	NM_025412	ENSMUSG00000022571	Pycrl	1110058B13Rik|2700073G24Rik	pyrroline-5-carboxylate reductase-like	protein-coding
mm_137425.1	chr17	26252916	26252983	+	1	NA	promoter-TSS (NM_025881)	promoter-TSS (NM_025881)	39	NR_037905	66978	Mm.440216	NM_025881	ENSMUSG00000024188	Luc7l	1810045C04Rik|2410018D03Rik	Luc7-like	protein-coding
mm_107432.1	chr12	35925662	35925671	+	1	NA	promoter-TSS (NM_207531)	promoter-TSS (NM_207531)	45	NM_207531	403205	Mm.190508	NM_207531	ENSMUSG00000036231	Agr3	BCMP11|E030025L21Rik|Gm888	anterior gradient 3	protein-coding
mm_151413.1	chr19	56703460	56703509	+	1	NA	Intergenic	Intergenic	-18888	NM_007419	11554	Mm.46797	NM_007419	ENSMUSG00000035283	Adrb1	Adrb-1|beta-AR	adrenergic receptor, beta 1	protein-coding
mm_38602.1	chr4	141859618	141859705	-	1	NA	3' UTR (NM_025994, exon 4 of 4)	3' UTR (NM_025994, exon 4 of 4)	-13302	NM_001033875	76701	Mm.489680	NM_001033875	ENSMUSG00000062478	Ctrc	1810044E12Rik	chymotrypsin C (caldecrin)	protein-coding
mm_97368.1	chr11	77521184	77521187	+	1	NA	TTS (NM_026185)	TTS (NM_026185)	6068	NM_026185	67477	Mm.432526	NM_026185	ENSMUSG00000000686	Abhd15	1300007F04Rik	abhydrolase domain containing 15	protein-coding
mm_100714.1	chr11	3863717	3863727	-	1	NA	exon (NM_152818, exon 1 of 14)	exon (NM_152818, exon 1 of 14)	181	NM_152818	74309	Mm.61022	NM_152818	ENSMUSG00000020435	Osbp2	1700095P05Rik|C630001G20Rik|Gm244|ORP-4|OSBPL1	oxysterol binding protein 2	protein-coding
mm_139878.1	chr17	70748297	70748329	+	1	NA	intron (NM_001347411, intron 9 of 14)	intron (NM_001347411, intron 9 of 14)	98464	NM_001164077	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_142441.1	chr17	45572496	45572506	-	1	NA	intron (NM_008302, intron 1 of 10)	CpG	760	NM_008302	15516	Mm.2180	NM_008302	ENSMUSG00000023944	Hsp90ab1	90kDa|AL022974|C81438|Hsp84|Hsp84-1|Hsp90|Hspcb	heat shock protein 90 alpha (cytosolic), class B member 1	protein-coding
mm_28519.1	chr3	92586201	92586205	-	1	NA	intron (NM_008574, intron 1 of 1)	intron (NM_008574, intron 1 of 1)	2821	NM_008574	17235	Mm.331192	NM_008574		Smcp	Mcs|Mcsp	sperm mitochondria-associated cysteine-rich protein	protein-coding
mm_62998.1	chr7	120739914	120739925	+	1	NA	5' UTR (NM_177697, exon 1 of 34)	5' UTR (NM_177697, exon 1 of 34)	362	NM_177697	233813	Mm.389939	NM_177697	ENSMUSG00000030889	Vwa3a	E030013G06Rik	von Willebrand factor A domain containing 3A	protein-coding
mm_170974.1	chr2	64313588	64313590	+	1	NA	Intergenic	L1Md_T|LINE|L1	-215551	NM_001267847	60344	Mm.130769	NM_021716	ENSMUSG00000075324	Fign	fi|fidget	fidgetin	protein-coding
mm_91522.1	chr10	37138801	37138814	-	1	NA	5' UTR (NM_008538, exon 1 of 2)	5' UTR (NM_008538, exon 1 of 2)	119	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_162238.1	chrX	154579362	154579362	-	1	NA	promoter-TSS (NM_001037167)	promoter-TSS (NM_001037167)	-32	NM_001037167	434881	Mm.357614	NM_001037167	ENSMUSG00000072888	Samt2	EG434881|Gm5647	spermatogenesis associated multipass transmembrane protein 2	protein-coding
mm_61971.1	chr7	90457275	90457285	+	1	NA	promoter-TSS (NM_025460)	promoter-TSS (NM_025460)	-72	NM_025460	66271	Mm.28963	NM_025460	ENSMUSG00000030615	Tmem126a	1810020E01Rik	transmembrane protein 126A	protein-coding
mm_102635.1	chr11	62544813	62544827	-	1	NA	Intergenic	Intergenic	-5559	NM_028448	73139	Mm.390409	NM_028448	ENSMUSG00000018509	Cenpv	3110013H01Rik|AA671303|Prr6	centromere protein V	protein-coding
mm_65279.1	chr7	24355810	24355824	-	1	NA	Intergenic	MTE2b|LTR|ERVL-MaLR	6593	NM_029806	76942	Mm.261468	NM_029806	ENSMUSG00000030484	Lypd5	2210003I03Rik	Ly6/Plaur domain containing 5	protein-coding
mm_75327.1	chr8	43143025	43143043	-	1	NA	Intergenic	Intergenic	-1548	NM_177742	244448	Mm.64542	NM_177742	ENSMUSG00000031651	Triml1	4933403D14|BC050188	tripartite motif family-like 1	protein-coding
mm_16269.1	chr2	173659835	173659871	+	1	NA	promoter-TSS (NM_024436)	promoter-TSS (NM_024436)	8	NM_024436	19334	Mm.275304	NM_024436	ENSMUSG00000027519	Rab22a	3732413A17Rik|AI662177|AW319644|AW550514|E130120E14Rik|Rab22	RAB22A, member RAS oncogene family	protein-coding
mm_138803.1	chr17	38816432	38816438	+	1	NA	Intergenic	Lx2|LINE|L1	176988	NM_001177586	100126768	Mm.471528	NM_001177586	ENSMUSG00000092342	Esp31	Gm20516	exocrine gland secreted peptide 31	protein-coding
mm_170366.1	chr1	85272381	85272385	+	1	NA	Intergenic	Intergenic	-1817	NM_001037909	620078	Mm.386456	NM_175219	ENSMUSG00000052477	C130026I21Rik	4930565N07Rik|OTTMUSG00000029174	RIKEN cDNA C130026I21 gene	protein-coding
mm_6562.1	chr1	75141793	75141803	-	1	NA	promoter-TSS (NM_170755)	promoter-TSS (NM_170755)	570	NM_026977	69171	Mm.28193	NM_026977	ENSMUSG00000033159	Cnppd1	1810031K17Rik|AU043960	cyclin Pas1/PHO80 domain containing 1	protein-coding
mm_111857.1	chr12	107945573	107945576	-	1	NA	intron (NM_001286343, intron 1 of 1)	intron (NM_001286343, intron 1 of 1)	57840	NM_001079883	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_97134.1	chr11	75172445	75172455	+	1	NA	promoter-TSS (NR_029794)	promoter-TSS (NR_029794)	-938	NR_029794	387208		NR_029794	ENSMUSG00000065590	Mir212	Mirn212|mir-212|mmu-mir-212	microRNA 212	ncRNA
mm_34086.1	chr4	138832657	138832683	+	1	NA	non-coding (NR_002926, exon 2 of 5)	non-coding (NR_002926, exon 2 of 5)	794	NM_001082531	18780	Mm.4675	NM_011108	ENSMUSG00000058908	Pla2g2a	EF|Mom1|Pla2|sPLA2|sPla2-IIA	phospholipase A2, group IIA (platelets, synovial fluid)	protein-coding
mm_7195.1	chr1	92993601	92993603	-	1	NA	Intergenic	Intergenic	-12732	NM_177587	208760	Mm.235537	NM_177587	ENSMUSG00000045091	Aqp12	AB084104|mAQP12	aquaporin 12	protein-coding
mm_87819.1	chr10	60306969	60306994	+	1	NA	intron (NR_045556, intron 61 of 68)	intron (NR_045556, intron 61 of 68)	22520	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_125121.1	chr15	30172655	30172665	+	1	NA	promoter-TSS (NM_008729)	promoter-TSS (NM_008729)	67	NM_008729	18163	Mm.321648	NM_008729	ENSMUSG00000022240	Ctnnd2	Catnd2|Nprap|neurojugin	catenin (cadherin associated protein), delta 2	protein-coding
mm_40024.1	chr5	33368694	33368718	+	1	NA	exon (NM_021500, exon 6 of 9)	exon (NM_021500, exon 6 of 9)	-9990	NM_001081101	71101	Mm.132178	NM_001081101	ENSMUSG00000037355	Uvssa	4933407H18Rik|D330017J19Rik|Kiaa1530|mKIAA1530	UV stimulated scaffold protein A	protein-coding
mm_68124.1	chr7	102151416	102151421	-	1	NA	intron (NM_022979, intron 18 of 22)	B2_Mm2|SINE|B2	-34705	NM_001081424	504186	Mm.334074	NM_001081424	ENSMUSG00000066279	Chrna10	-	cholinergic receptor, nicotinic, alpha polypeptide 10	protein-coding
mm_100155.1	chr11	116198854	116198903	+	1	NA	promoter-TSS (NM_027107)	promoter-TSS (NM_027107)	23	NM_027107	69535	Mm.390347	NM_027107	ENSMUSG00000020778	Ten1	2310004N24Rik	TEN1 telomerase capping complex subunit	protein-coding
mm_118108.1	chr13	103921057	103921084	-	1	NA	promoter-TSS (NM_001289475)	promoter-TSS (NM_001289475)	-484	NM_001005868	59079	Mm.277354	NM_021563	ENSMUSG00000021709	Erbin	1700028E05Rik|Erbb2ip|mKIAA1225	Erbb2 interacting protein	protein-coding
mm_162336.1	chr1	45349600	45349602	+	1	NA	3' UTR (NM_009930, exon 51 of 51)	3' UTR (NM_009930, exon 51 of 51)	38063	NM_009930	12825	Mm.249555	NM_009930	ENSMUSG00000026043	Col3a1	AW550625|Col3a-1|Tsk-2|Tsk2	collagen, type III, alpha 1	protein-coding
mm_143205.1	chr17	62816081	62816088	-	1	NA	intron (NM_010109, intron 1 of 3)	intron (NM_010109, intron 1 of 3)	65233	NM_207654	13640	Mm.7978	NM_010109	ENSMUSG00000048915	Efna5	AL-1|AV158822|EFL-5|Ephrin-A5|Epl7|LERK-7|RAGS	ephrin A5	protein-coding
mm_6520.1	chr1	74438893	74438902	-	1	NA	3' UTR (NM_001310662, exon 24 of 24)	3' UTR (NM_001310662, exon 24 of 24)	29513	NM_009509	22349	Mm.471601	NM_009509	ENSMUSG00000026175	Vil1	Vil	villin 1	protein-coding
mm_170314.1	chr18	36561011	36561019	+	1	NA	exon (NM_175375, exon 1 of 34)	exon (NM_175375, exon 1 of 34)	412	NM_175375	108857	Mm.482287	NM_175375	ENSMUSG00000024483	Ankhd1	1110004O12Rik|4933432B13Rik|9130019P20Rik|A530027J04Rik|A630021B20Rik|AA571404|Mask|mFLJ00246|mKIAA1085	ankyrin repeat and KH domain containing 1	protein-coding
mm_114748.1	chr13	84244111	84244114	+	1	NA	intron (NR_029418, intron 1 of 10)	intron (NR_029418, intron 1 of 10)	21816	NM_175187	72745	Mm.295063	NM_175187	ENSMUSG00000035762	Tmem161b	2810446P07Rik|AI843389	transmembrane protein 161B	protein-coding
mm_40408.1	chr5	53059175	53059189	+	1	NA	exon (NM_011402, exon 4 of 13)	exon (NM_011402, exon 4 of 13)	9829	NM_011402	20531	Mm.284891	NM_011402	ENSMUSG00000029188	Slc34a2	AA536683|D5Ertd227e|NaPi-2b|Npt2b	solute carrier family 34 (sodium phosphate), member 2	protein-coding
mm_61339.1	chr7	68279197	68279201	+	1	NA	intron (NM_001013811, intron 1 of 8)	intron (NM_001013811, intron 1 of 8)	-2605	NR_040340	100504026	Mm.426764	NR_040340	ENSMUSG00000086628	Gm16157	OTTMUSG00000031023	predicted gene 16157	ncRNA
mm_99951.1	chr11	112786868	112786877	+	1	NA	3' UTR (NM_011448, exon 3 of 3)	3' UTR (NM_011448, exon 3 of 3)	4662	NM_011448	20682	Mm.286407	NM_011448	ENSMUSG00000000567	Sox9	2010306G03Rik|AV220920|mKIAA4243	SRY (sex determining region Y)-box 9	protein-coding
mm_137696.1	chr17	29032665	29032681	+	1	NA	promoter-TSS (NM_013663)	promoter-TSS (NM_013663)	13	NR_036613	20383	Mm.6787	NM_013663	ENSMUSG00000071172	Srsf3	AL024116|Sfrs3|X16	serine/arginine-rich splicing factor 3	protein-coding
mm_43169.1	chr5	127302608	127302611	+	1	NA	intron (NM_175432, intron 1 of 8)	B4A|SINE|B4	-20986	NR_038128	67351	Mm.320172	NR_038127	ENSMUSG00000087104	Tmem132cos	1700085B03Rik	transmembrane protein 132C, opposite strand	ncRNA
mm_52207.1	chr6	100839123	100839149	+	1	NA	intron (NM_182939, intron 2 of 8)	RMER15|LTR|ERVL	5498	NM_182939	232314	Mm.27223	NM_182939	ENSMUSG00000052144	Ppp4r2	BE691708|C230060M08Rik	protein phosphatase 4, regulatory subunit 2	protein-coding
mm_163964.1	chr14	54966468	54966473	-	1	NA	intron (NM_001164171, intron 1 of 38)	intron (NM_001164171, intron 1 of 38)	137	NM_001164171	17888	Mm.290003	NM_010856	ENSMUSG00000040752	Myh6	A830009F23Rik|AA517445|Myhc-a|Myhca|alpha-MHC	myosin, heavy polypeptide 6, cardiac muscle, alpha	protein-coding
mm_155445.1	chrX	73495063	73495075	+	1	NA	3' UTR (NM_007542, exon 8 of 8)	3' UTR (NM_007542, exon 8 of 8)	-8017	NM_001310537	320707	Mm.210095	NM_177236	ENSMUSG00000031376	Atp2b3	6430519O13Rik|Pmca3	ATPase, Ca++ transporting, plasma membrane 3	protein-coding
mm_61980.1	chr7	90887597	90887607	+	1	NA	Intergenic	Intergenic	-203184	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_77994.1	chr9	8859330	8859332	+	1	NA	Intergenic	Intergenic	-40502	NM_008829	18667	Mm.12798	NM_008829	ENSMUSG00000031870	Pgr	9930019P03Rik|BB114106|ENSMUSG00000074510|NR3C3|PR|PR-A|PR-B	progesterone receptor	protein-coding
mm_168598.1	chr1	173942491	173942491	-	1	NA	promoter-TSS (NM_001302651)	promoter-TSS (NM_001302651)	1	NM_001302649	15950	Mm.463437	NM_008328	ENSMUSG00000039997	Ifi203	Mndal	interferon activated gene 203	protein-coding
mm_70663.1	chr8	14881630	14881657	+	1	NA	Intergenic	Intergenic	-6893	NM_012000	26889	Mm.254027	NM_012000	ENSMUSG00000026317	Cln8	mnd	ceroid-lipofuscinosis, neuronal 8	protein-coding
mm_116503.1	chr13	44982990	44983004	-	1	NA	intron (NM_025772, intron 4 of 9)	intron (NM_025772, intron 4 of 9)	19099	NM_025772	94245	Mm.352311	NM_025772	ENSMUSG00000057531	Dtnbp1	5430437B18Rik|AW048963|Bloc1s8|dysbindin|sdy	dystrobrevin binding protein 1	protein-coding
mm_64897.1	chr7	15950283	15950321	-	1	NA	exon (NM_153068, exon 6 of 6)	exon (NM_153068, exon 6 of 6)	-4194	NM_133831	68077	Mm.277634	NM_133831	ENSMUSG00000041560	Gltscr2	5330430H08Rik|9430097C02Rik|AU041936|AW536441|PICT-1|R74911	glioma tumor suppressor candidate region gene 2	protein-coding
mm_69534.1	chr7	135694438	135694463	-	1	NA	exon (NM_001081117, exon 12 of 14)	exon (NM_001081117, exon 12 of 14)	21929	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_26448.1	chr3	142637420	142637430	+	1	NA	exon (NM_010260, exon 11 of 11)	exon (NM_010260, exon 11 of 11)	-13479	NR_105802	102465200		NR_105802	ENSMUSG00000098871	Mir6381	Gm27963|mmu-mir-6381	microRNA 6381	ncRNA
mm_156819.1	chrX	164140448	164140495	+	1	NA	promoter-TSS (NM_027286)	promoter-TSS (NM_027286)	-9	NM_027286	70008	Mm.13451	NM_027286	ENSMUSG00000015405	Ace2	2010305L05Rik	angiotensin I converting enzyme (peptidyl-dipeptidase A) 2	protein-coding
mm_88008.1	chr10	67097030	67097050	+	1	NA	promoter-TSS (NM_001204915)	promoter-TSS (NM_001204915)	-52	NM_178606	28193	Mm.41272	NM_178606	ENSMUSG00000019873	Reep3	D10Ucla1	receptor accessory protein 3	protein-coding
mm_99838.1	chr11	109269773	109269812	+	1	NA	intron (NM_001165934, intron 7 of 16)	intron (NM_001165934, intron 7 of 16)	28389	NM_001165934	19739	Mm.38548	NM_011268	ENSMUSG00000020599	Rgs9	RGS9-1|Rgs9-2	regulator of G-protein signaling 9	protein-coding
mm_21969.1	chr2	167302212	167302221	-	1	NA	intron (NM_019835, intron 7 of 8)	intron (NM_019835, intron 7 of 8)	46962	NM_019835	56336	Mm.200886	NM_019835	ENSMUSG00000017929	B4galt5	9430078I07Rik|AW049941|AW539721	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 5	protein-coding
mm_13157.1	chr2	92541175	92541181	+	1	NA	Intergenic	Intergenic	-51028	NR_106080	102466819		NR_106080	ENSMUSG00000099223	Mir7221	Gm27378|mmu-mir-7221	microRNA 7221	ncRNA
mm_75531.1	chr8	57320347	57320359	-	1	NA	promoter-TSS (NM_010402)	promoter-TSS (NM_010402)	506	NR_110474	102636514		NR_110474	ENSMUSG00000100510	Uph	-	upperhand	ncRNA
mm_101141.1	chr11	14448656	14448659	-	1	NA	Intergenic	Intergenic	150568	NR_045918	73307	Mm.399291	NR_045918	ENSMUSG00000085561	1700046C09Rik	-	RIKEN cDNA 1700046C09 gene	ncRNA
mm_114295.1	chr13	58808684	58808752	+	1	NA	5' UTR (NM_008745, exon 2 of 13)	5' UTR (NM_008745, exon 2 of 13)	1021	NM_001025074	18212	Mm.130054	NM_008745	ENSMUSG00000055254	Ntrk2	GP145-TrkB/GP95-TrkB|Tkrb|trk-B|trkB	neurotrophic tyrosine kinase, receptor, type 2	protein-coding
mm_55989.1	chr6	85961673	85961683	-	1	NA	promoter-TSS (NM_028099)	promoter-TSS (NM_028099)	-11	NM_028099	72102	Mm.24007	NM_028099	ENSMUSG00000030002	Dusp11	2010300F21Rik|AI481497	dual specificity phosphatase 11 (RNA/RNP complex 1-interacting)	protein-coding
mm_161872.1	chr18	37005222	37005222	+	1	NA	promoter-TSS (NM_009961)	promoter-TSS (NM_009961)	-98	NM_009961	12943	Mm.308500	NM_009961	ENSMUSG00000007440	Pcdha10	Cnr3|Cnr8|Crnr3|Crnr8|Pcdha14	protocadherin alpha 10	protein-coding
mm_160056.1	chr7	4122239	4122239	+	1	NA	intron (NM_001305822, intron 1 of 13)	intron (NM_001305822, intron 1 of 13)	-1511	NR_033568	77323	Mm.378791	NR_033568	ENSMUSG00000086155	9430041J12Rik	-	RIKEN cDNA 9430041J12 gene	ncRNA
mm_68605.1	chr7	116264256	116264265	-	1	NA	intron (NM_001305185, intron 3 of 26)	intron (NM_001305185, intron 3 of 26)	-26484	NM_001305186	233765	Mm.3741	NM_172743	ENSMUSG00000045659	Plekha7	A430081P20Rik|AI414265	pleckstrin homology domain containing, family A member 7	protein-coding
mm_145382.1	chr18	57132970	57133003	+	1	NA	promoter-TSS (NM_001001979)	promoter-TSS (NM_001001979)	-104	NM_001001979	70417	Mm.297863	NM_001001979	ENSMUSG00000024593	Megf10	3000002B06Rik|Gm331	multiple EGF-like-domains 10	protein-coding
mm_119485.1	chr14	47373906	47373923	+	1	NA	promoter-TSS (NM_010705)	promoter-TSS (NM_010705)	54	NM_001145953	16854	Mm.248615	NM_010705	ENSMUSG00000050335	Lgals3	GBP|L-34|Mac-2|gal3	lectin, galactose binding, soluble 3	protein-coding
mm_99258.1	chr11	101181330	101181378	+	1	NA	exon (NM_016782, exon 9 of 24)	exon (NM_016782, exon 9 of 24)	5237	NM_016782	53321	Mm.474527	NM_016782	ENSMUSG00000017167	Cntnap1	AI841080|Caspr|NCP1|Nrxn4|p190|shm	contactin associated protein-like 1	protein-coding
mm_117465.1	chr13	75943813	75943950	-	1	NA	promoter-TSS (NM_028493)	promoter-TSS (NM_028493)	-57	NM_028493	73296	Mm.276200	NM_028493	ENSMUSG00000021589	Rhobtb3	1700040C17Rik|2610033K01Rik|4930503C18Rik|AI317148|AW208826|mKIAA0878	Rho-related BTB domain containing 3	protein-coding
mm_15714.1	chr2	164036983	164036996	+	1	NA	intron (NM_001114079, intron 6 of 13)	intron (NM_001114079, intron 6 of 13)	11765	NM_001114079	381404	Mm.82301	NM_001114079	ENSMUSG00000054582	Pabpc1l	1810053B01Rik|Epab	poly(A) binding protein, cytoplasmic 1-like	protein-coding
mm_118532.1	chr14	15437648	15437677	+	1	NA	intron (NM_146052, intron 1 of 1)	intron (NM_146052, intron 1 of 1)	1325	NM_146052	218763	Mm.138039	NM_146052	ENSMUSG00000045201	Lrrc3b	BC019794|LRP15	leucine rich repeat containing 3B	protein-coding
mm_147530.1	chr18	52891986	52891987	-	1	NA	intron (NM_001199154, intron 6 of 10)	intron (NM_001199154, intron 6 of 10)	10661	NR_035420	100316749		NR_035420	ENSMUSG00000080573	Mir467f	Mirn467f|mmu-mir-467f	microRNA 467f	ncRNA
mm_39558.1	chr5	22746181	22746268	+	1	NA	promoter-TSS (NM_029990)	promoter-TSS (NM_029990)	31	NM_029990	269629	Mm.371712	NM_029990	ENSMUSG00000106379	Lhfpl3	A930031L14Rik	lipoma HMGIC fusion partner-like 3	protein-coding
mm_2669.1	chr1	127205300	127205319	+	1	NA	5' UTR (NM_145128, exon 1 of 18)	5' UTR (NM_145128, exon 1 of 18)	323	NM_145128	107895	Mm.214682	NM_145128	ENSMUSG00000036155	Mgat5	4930471A21Rik|5330407H02Rik|AI480971|GlcNAc-TV	mannoside acetylglucosaminyltransferase 5	protein-coding
mm_151209.1	chr19	53609368	53609371	+	1	NA	intron (NM_007790, intron 2 of 28)	Lx8|LINE|L1	8973	NM_007790	13006	Mm.14910	NM_007790	ENSMUSG00000024974	Smc3	Bamacan|Cspg6|HCAP|Mmip1|SMC-3|SmcD	structural maintenance of chromosomes 3	protein-coding
mm_62458.1	chr7	101460925	101460947	+	1	NA	intron (NM_001243758, intron 2 of 30)	intron (NM_001243758, intron 2 of 30)	9684	NM_001243757	207728	Mm.247564	NM_001008548	ENSMUSG00000030653	Pde2a	CGS-PDE|cGSPDE	phosphodiesterase 2A, cGMP-stimulated	protein-coding
mm_89391.1	chr10	89873009	89873058	+	1	NA	promoter-TSS (NM_001128086)	promoter-TSS (NM_001128086)	-476	NM_001128086	77531	Mm.440605	NM_181398	ENSMUSG00000058589	Anks1b	AIDA-1b|C030032C09Rik|E530015N03Rik|ENSMUSG00000078431|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding
mm_45135.1	chr5	48889532	48889553	-	1	NA	promoter-TSS (NM_030265)	promoter-TSS (NM_030265)	15	NM_030265	80334	Mm.160172	NM_030265	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding
mm_167350.1	chr8	83740107	83740113	-	1	NA	intron (NM_001163031, intron 1 of 17)	intron (NM_001163031, intron 1 of 17)	1201	NM_001163029	26364	Mm.334648	NM_011925	ENSMUSG00000002885	Adgre5	AA409984|Cd97|TM7LN1	adhesion G protein-coupled receptor E5	protein-coding
mm_164431.1	chr16	48771968	48771976	-	1	NA	promoter-TSS (NM_198297)	promoter-TSS (NM_198297)	-16	NM_198297	77647	Mm.167298	NM_198297	ENSMUSG00000030775	Trat1	C030046M14Rik|Tcrim|Trim	T cell receptor associated transmembrane adaptor 1	protein-coding
mm_29075.1	chr3	103868091	103868099	-	1	NA	intron (NR_104070, intron 3 of 22)	intron (NR_104070, intron 3 of 22)	7818	NM_008979	19260	Mm.395	NM_008979	ENSMUSG00000027843	Ptpn22	70zpep|PEP|Ptpn8	protein tyrosine phosphatase, non-receptor type 22 (lymphoid)	protein-coding
mm_104772.1	chr11	98545851	98545863	-	1	NA	5' UTR (NM_011771, exon 1 of 8)	5' UTR (NM_011771, exon 1 of 8)	174	NM_011771	22780	Mm.133367	NM_011771	ENSMUSG00000018168	Ikzf3	5830411O07Rik|Aiolos|Zfpn1a3|Znfn1a3	IKAROS family zinc finger 3	protein-coding
mm_159291.1	chr2	174076852	174076852	+	1	NA	promoter-TSS (NM_001102425)	promoter-TSS (NM_001102425)	-199	NM_172675	228960	Mm.277977	NM_172675	ENSMUSG00000027522	Stx16	4930401D03|5430410K23Rik|6330500A18Rik|AI648908|AW553605|Syn16	syntaxin 16	protein-coding
mm_70358.1	chr8	5640793	5640806	+	1	NA	Intergenic	Intergenic	-535512	NM_011388	20494	Mm.3500	NM_011388	ENSMUSG00000023073	Slc10a2	9130221J18Rik|AI605518|ASBT|IBAT|ISBT	solute carrier family 10, member 2	protein-coding
mm_128095.1	chr15	27788608	27788618	-	1	NA	intron (NM_001081302, intron 34 of 56)	intron (NM_001081302, intron 34 of 56)	-107071	NM_001242423	223433	Mm.266485	NM_198301	ENSMUSG00000056069	Fam105a	9830126M18	family with sequence similarity 105, member A	protein-coding
mm_158594.1	chrX	151017227	151017249	-	1	NA	promoter-TSS (NM_198110)	promoter-TSS (NM_198110)	55	NM_001168600	237107	Mm.45987	NM_198110	ENSMUSG00000025266	Gnl3l	BC020354	guanine nucleotide binding protein-like 3 (nucleolar)-like	protein-coding
mm_160725.1	chr10	75061080	75061080	+	1	NA	exon (NM_001081412, exon 1 of 23)	exon (NM_001081412, exon 1 of 23)	184	NM_001081412	110279	Mm.333722	NM_001081412	ENSMUSG00000009681	Bcr	5133400C09Rik|AI561783|AI853148|mKIAA3017	breakpoint cluster region	protein-coding
mm_119129.1	chr14	31138812	31138847	+	1	NA	TTS (NM_138672)	TTS (NM_138672)	3976	NM_027289	70021	Mm.261681	NM_027289	ENSMUSG00000071547	Nt5dc2	2510015F01Rik	5'-nucleotidase domain containing 2	protein-coding
mm_14891.1	chr2	149257012	149257029	+	1	NA	Intergenic	Intergenic	-148229	NM_021405	58214	Mm.117117	NM_021405	ENSMUSG00000033156	Cst10	DD72	cystatin 10 (chondrocytes)	protein-coding
mm_7876.1	chr1	133011869	133011871	-	1	NA	intron (NM_001302801, intron 3 of 10)	intron (NM_001302801, intron 3 of 10)	13546	NR_126506	17248	Mm.426531	NM_008575	ENSMUSG00000054387	Mdm4	4933417N07Rik|AA414968|AL023055|AU018793|AU021806|C85810|Mdmx	transformed mouse 3T3 cell double minute 4	protein-coding
mm_10406.1	chr2	13578747	13578758	+	1	NA	intron (NM_011701, intron 4 of 8)	intron (NM_011701, intron 4 of 8)	4441	NM_011701	22352	Mm.268000	NM_011701	ENSMUSG00000026728	Vim	-	vimentin	protein-coding
mm_128630.1	chr15	59079840	59079846	-	1	NA	intron (NM_001146180, intron 1 of 13)	intron (NM_001146180, intron 1 of 13)	2183	NM_001146180	211401	Mm.215481	NM_144800	ENSMUSG00000022353	Mtss1	2310003N14Rik|BC024131|D130001D01Rik|Mim|mKIAA0429	metastasis suppressor 1	protein-coding
mm_99929.1	chr11	110997494	110997504	+	1	NA	promoter-TSS (NM_001252209)	promoter-TSS (NM_001252209)	12	NM_001252209	16517	Mm.30176	NM_010604	ENSMUSG00000051497	Kcnj16	6430410F18Rik|AI132396|Kir5.1	potassium inwardly-rectifying channel, subfamily J, member 16	protein-coding
mm_109609.1	chr12	112722511	112722534	+	1	NA	intron (NM_001024602, intron 1 of 18)	CpG	348	NM_001024602	217882	Mm.23689	NM_001024602	ENSMUSG00000072825	Cep170b	AI466840|AW555464|Kiaa0284|mKIAA0284	centrosomal protein 170B	protein-coding
mm_107212.1	chr12	26444935	26444945	+	1	NA	3' UTR (NM_021384, exon 6 of 6)	3' UTR (NM_021384, exon 6 of 6)	11512	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_15954.1	chr2	165992609	165992619	+	1	NA	promoter-TSS (NM_008679)	promoter-TSS (NM_008679)	-23	NM_008679	17979	Mm.469663	NM_008679	ENSMUSG00000027678	Ncoa3	2010305B15Rik|AW321064|Actr|Aib1|KAT13B|Rac3|Src3|Tram-1|Tram1|bHLHe42|p/Cip|pCip	nuclear receptor coactivator 3	protein-coding
mm_146105.1	chr18	74216168	74216173	+	1	NA	promoter-TSS (NM_028868)	promoter-TSS (NM_028868)	-42	NM_028868	74322	Mm.17537	NM_028868	ENSMUSG00000024560	Cxxc1	2410002I16Rik|5830420C16Rik|AI426635|Cfp1|Cgbp|PHF18	CXXC finger 1 (PHD domain)	protein-coding
mm_90595.1	chr10	128298434	128298434	+	1	NA	promoter-TSS (NM_031252)	promoter-TSS (NM_031252)	-350	NM_031252	83430	Mm.125482	NM_031252	ENSMUSG00000025383	Il23a	IL-23|p19	interleukin 23, alpha subunit p19	protein-coding
mm_87090.1	chr10	31976744	31976752	+	1	NA	intron (NM_001013411, intron 3 of 6)	intron (NM_001013411, intron 3 of 6)	-367023	NM_001146349	268291	Mm.295212	NM_001146349	ENSMUSG00000063760	Rnf217	AU016819|Ibrdc1	ring finger protein 217	protein-coding
mm_146444.1	chr18	85071747	85071765	+	1	NA	Intergenic	Intergenic	-120232	NM_025969	67105	Mm.250617	NM_025969	ENSMUSG00000024645	Timm21	1700034H14Rik|2700002I20Rik	tranlocase of inner mitochondrial membrane 21	protein-coding
mm_22448.1	chr2	181698408	181698415	-	1	NA	promoter-TSS (NM_199023)	promoter-TSS (NM_199023)	31	NM_199023	277496	Mm.212749	NM_199023	ENSMUSG00000045794	Lkaaear1	4930526D03Rik|Gm692	LKAAEAR motif containing 1 (IKAAEAR murine motif)	protein-coding
mm_6624.1	chr1	77515049	77515102	-	1	NA	promoter-TSS (NM_007936)	promoter-TSS (NM_007936)	13	NM_007936	13838	Mm.400747	NM_007936	ENSMUSG00000026235	Epha4	2900005C20Rik|AI385584|Cek8|Hek8|Sek|Sek1|Tyro1|rb	Eph receptor A4	protein-coding
mm_92055.1	chr10	62506906	62506910	-	1	NA	intron (NM_011157, intron 1 of 2)	intron (NM_011157, intron 1 of 2)	847	NM_011157	19073	Mm.338790	NM_011157	ENSMUSG00000020077	Srgn	Prg|Prg1|Sgc	serglycin	protein-coding
mm_142573.1	chr17	46680727	46680734	-	1	NA	promoter-TSS (NM_010787)	promoter-TSS (NM_010787)	-53	NM_001277311	17256	Mm.329083	NM_010787	ENSMUSG00000002768	Mea1	Mea-1	male enhanced antigen 1	protein-coding
mm_32257.1	chr4	102570664	102570679	+	1	NA	exon (NM_001177980, exon 1 of 10)	exon (NM_001177980, exon 1 of 10)	611	NM_001177980	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_48489.1	chr5	142551028	142551110	-	1	NA	promoter-TSS (NM_178702)	promoter-TSS (NM_178702)	29	NM_178702	231858	Mm.33766	NM_178702	ENSMUSG00000029576	Radil	AI536456|D930005D10Rik	Ras association and DIL domains	protein-coding
mm_92101.1	chr10	63018086	63018111	-	1	NA	exon (NM_001079824, exon 4 of 10)	exon (NM_001079824, exon 4 of 10)	2202	NM_001347457	432467	Mm.274784	NM_001079824	ENSMUSG00000020069	Hnrnph3	AA693301|AI666703|Hnrph3	heterogeneous nuclear ribonucleoprotein H3	protein-coding
mm_2975.1	chr1	133103539	133103564	+	1	NA	intron (NM_001099276, intron 30 of 32)	intron (NM_001099276, intron 30 of 32)	-27615	NM_133819	108954	Mm.293628	NM_133819	ENSMUSG00000046062	Ppp1r15b	1810033K10Rik|AI606441|C530022L24Rik|CReP	protein phosphatase 1, regulatory (inhibitor) subunit 15b	protein-coding
mm_123356.1	chr14	63142656	63142679	-	1	NA	3' UTR (NM_007798, exon 10 of 10)	3' UTR (NM_007798, exon 10 of 10)	20205	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_69902.1	chr7	141639060	141639075	-	1	NA	intron (NM_001330001, intron 31 of 33)	intron (NM_001330001, intron 31 of 33)	16252	NM_001330001	353328	Mm.246621	NM_181729	ENSMUSG00000048191	Muc6	-	mucin 6, gastric	protein-coding
mm_105911.1	chr11	114983598	114983611	-	1	NA	3' UTR (NM_145437, exon 4 of 4)	3' UTR (NM_145437, exon 4 of 4)	6282	NM_145437	217305	Mm.275986	NM_145437	ENSMUSG00000034641	Cd300ld	4732429D16Rik|CLM5|Cd300ld1|LMIR4|MAIR-IV|clm-5	CD300 molecule like family member d	protein-coding
mm_41485.1	chr5	92112997	92113015	+	1	NA	Intergenic	Intergenic	-24932	NM_019490	56041	Mm.15868	NM_019490	ENSMUSG00000029407	Uso1	115kDa|TAP|Vdp	USO1 vesicle docking factor	protein-coding
mm_117075.1	chr13	59508684	59508698	-	1	NA	intron (NM_001048008, intron 11 of 17)	intron (NM_001048008, intron 11 of 17)	35760	NM_001284221	67269	Mm.153008	NM_023328	ENSMUSG00000021557	Agtpbp1	1700020N17Rik|2310001G17Rik|2900054O13Rik|4930445M19Rik|5730402G09Rik|CCP1|Nna1|nmf243|pcd	ATP/GTP binding protein 1	protein-coding
mm_90735.1	chr10	5312531	5312571	-	1	NA	intron (NM_001347732, intron 44 of 145)	intron (NM_001347732, intron 44 of 145)	-117844	NM_001079686	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_149636.1	chr19	17394038	17394091	+	1	NA	promoter-TSS (NM_019437)	promoter-TSS (NM_019437)	21	NM_019437	54391	Mm.7013	NM_019437	ENSMUSG00000024712	Rfk	0610038L10Rik|AF031381|KOI-4	riboflavin kinase	protein-coding
mm_68307.1	chr7	105747772	105747787	-	1	NA	exon (NM_009906, exon 10 of 13)	exon (NM_009906, exon 10 of 13)	-3441	NM_020024	24075	Mm.274846	NM_020024	ENSMUSG00000043866	Taf10	30kDa|AU041226|TAFII30|Taf2h	TATA-box binding protein associated factor 10	protein-coding
mm_51940.1	chr6	91705805	91705832	+	1	NA	intron (NM_009320, intron 2 of 14)	ID_B1|SINE|B4	21751	NM_009320	21366	Mm.395650	NM_009320	ENSMUSG00000030096	Slc6a6	AA589629|C80501|Taut	solute carrier family 6 (neurotransmitter transporter, taurine), member 6	protein-coding
mm_103151.1	chr11	70352030	70352032	-	1	NA	promoter-TSS (NM_009660)	promoter-TSS (NM_009660)	0	NM_009660	11687	Mm.4584	NM_009660	ENSMUSG00000018924	Alox15	12-LO|12/15-LO|15-LOX|Alox12l|L-12LO	arachidonate 15-lipoxygenase	protein-coding
mm_49147.1	chr6	11925959	11925969	+	1	NA	promoter-TSS (NM_001168382)	promoter-TSS (NM_001168382)	83	NM_001168382	75725	Mm.212411	NM_029404	ENSMUSG00000029629	Phf14	1110001C23Rik|4932409F11Rik|5730446A07Rik|AA623952|AV297001|mKIAA0783	PHD finger protein 14	protein-coding
mm_135267.1	chr16	38341865	38341871	-	1	NA	promoter-TSS (NM_001081025)	promoter-TSS (NM_001081025)	-8	NM_001081025	320214	Mm.294342	NM_177104	ENSMUSG00000022805	Maats1	4932425I24Rik|Aat1|Spata26	MYCBP-associated, testis expressed 1	protein-coding
mm_42022.1	chr5	108269648	108269660	+	1	NA	exon (NM_026106, exon 1 of 3)	exon (NM_026106, exon 1 of 3)	757	NM_026106	13486	Mm.303534	NM_026106	ENSMUSG00000029265	Dr1	1700121L09Rik|Dr1l|NC2|NC2beta	down-regulator of transcription 1	protein-coding
mm_140395.1	chr17	87603629	87603674	+	1	NA	Intergenic	Intergenic	-32328	NM_008532	17075	Mm.4259	NM_008532	ENSMUSG00000045394	Epcam	CD326|EGP|EGP-2|Egp314|Ep-CAM|EpCAM1|GA733-2|Ly74|TROP1|Tacsd1|Tacstd1|gp40	epithelial cell adhesion molecule	protein-coding
mm_1937.1	chr1	86132694	86132739	+	1	NA	exon (NM_027357, exon 22 of 25)	exon (NM_027357, exon 22 of 25)	-20746	NM_008311	15559	Mm.439747	NM_008311	ENSMUSG00000026228	Htr2b	5-HT2B|AJ012488|AV377389	5-hydroxytryptamine (serotonin) receptor 2B	protein-coding
mm_142579.1	chr17	46681902	46681905	-	1	NA	promoter-TSS (NM_027910)	promoter-TSS (NM_027910)	723	NM_001277312	17256	Mm.329083	NM_010787	ENSMUSG00000002768	Mea1	Mea-1	male enhanced antigen 1	protein-coding
mm_65930.1	chr7	30322379	30322392	-	1	NA	promoter-TSS (NM_001033140)	promoter-TSS (NM_001033140)	-10	NM_001033140	68332	Mm.6844	NM_001033140	ENSMUSG00000074211	Sdhaf1	0610010E21Rik|AI430885|AW490662|Lyrm8	succinate dehydrogenase complex assembly factor 1	protein-coding
mm_125994.1	chr15	76368885	76368936	+	1	NA	promoter-TSS (NM_021555)	promoter-TSS (NM_021555)	12	NM_021555	59053	Mm.133202	NM_021555	ENSMUSG00000022554	Hgh1	Brp16|D15Ertd741e|Fam203a|MNCb-5873	HGH1 homolog	protein-coding
mm_123325.1	chr14	62966192	62966200	-	1	NA	Intergenic	Intergenic	18314	NM_001037751	432867	Mm.99387	NM_001037751	ENSMUSG00000075574	Defb48	Defb42|EG432867	defensin beta 48	protein-coding
mm_157757.1	chrX	73494942	73495036	-	1	NA	3' UTR (NM_007542, exon 8 of 8)	3' UTR (NM_007542, exon 8 of 8)	-8097	NM_001310537	320707	Mm.210095	NM_177236	ENSMUSG00000031376	Atp2b3	6430519O13Rik|Pmca3	ATPase, Ca++ transporting, plasma membrane 3	protein-coding
mm_61519.1	chr7	78913892	78913902	+	1	NA	promoter-TSS (NM_001113527)	promoter-TSS (NM_001113527)	132	NM_020583	57444	Mm.322843	NM_020583	ENSMUSG00000039236	Isg20	1600023I01Rik|2010107M23Rik|20kDa|DnaQL|HEM45	interferon-stimulated protein	protein-coding
mm_101824.1	chr11	46707061	46707077	-	1	NA	promoter-TSS (NM_134249)	promoter-TSS (NM_134249)	35	NM_134249	171284	Mm.234654	NM_134249	ENSMUSG00000040413	Timd2	AA816106|AU019358|AU019662|C78111|G9D3|TIM-2|Tim2	T cell immunoglobulin and mucin domain containing 2	protein-coding
mm_162900.1	chr10	115251378	115251389	-	1	NA	exon (NM_025706, exon 1 of 17)	exon (NM_025706, exon 1 of 17)	110	NM_025706	66687	Mm.22252	NM_025706	ENSMUSG00000020130	Tbc1d15	4432405K22Rik|AU022358|AU023730|AW557774|Ly6dl|Rab7-GAP	TBC1 domain family, member 15	protein-coding
mm_147188.1	chr18	37618739	37618774	-	1	NA	intron (NM_001301259, intron 1 of 3)	intron (NM_001301259, intron 1 of 3)	19967	NM_001159275	83885	Mm.193029	NM_001159275	ENSMUSG00000050304	Slc25a2	Ornt2	solute carrier family 25 (mitochondrial carrier, ornithine transporter) member 2	protein-coding
mm_97162.1	chr11	75486814	75486866	+	1	NA	promoter-TSS (NM_138659)	promoter-TSS (NM_138659)	63	NM_138659	192159	Mm.3757	NM_138659	ENSMUSG00000020850	Prpf8	AU019467|D11Bwg0410e|DBF3/PRP8|Prp8|Sfprp8l	pre-mRNA processing factor 8	protein-coding
mm_53629.1	chr6	140516435	140516443	+	1	NA	intron (NM_144920, intron 3 of 30)	intron (NM_144920, intron 3 of 30)	92340	NM_144920	109135	Mm.247670	NM_144920	ENSMUSG00000030231	Plekha5	2810431N21Rik|AI428202|AK129423|AMH-Cre|Ayu21-9|Gt(pU21)9Imeg|Pepp2|Tg(AMH-cre)1Flor	pleckstrin homology domain containing, family A member 5	protein-coding
mm_110546.1	chr12	55398678	55398744	-	1	NA	promoter-TSS (NM_011968)	promoter-TSS (NM_011968)	-114	NM_011968	26443	Mm.30210	NM_011968	ENSMUSG00000021024	Psma6	IOTA	proteasome (prosome, macropain) subunit, alpha type 6	protein-coding
mm_159537.1	chr4	88121262	88121262	+	1	NA	promoter-TSS (NR_030478)	promoter-TSS (NR_030478)	-778	NR_030478	735282		NR_030478	ENSMUSG00000070077	Mir491	Mirn491|mir-491|mmu-mir-491	microRNA 491	ncRNA
mm_80673.1	chr9	90243302	90243312	+	1	NA	intron (NM_194334, intron 2 of 12)	intron (NM_194334, intron 2 of 12)	27462	NM_194334	67016	Mm.335347	NM_194334	ENSMUSG00000037410	Tbc1d2b	1810061M12Rik|AI480956|AV021536|AV023399|AW491493|mKIAA1055	TBC1 domain family, member 2B	protein-coding
mm_99677.1	chr11	105985755	105985778	+	1	NA	promoter-TSS (NR_104047)	promoter-TSS (NR_104047)	-72	NR_104047	100379610	Mm.754	NR_104047	ENSMUSG00000085297	Gm11651	OTTMUSG00000003114	predicted gene 11651	ncRNA
mm_41260.1	chr5	89027960	89027967	+	1	NA	intron (NM_001197147, intron 3 of 25)	intron (NM_001197147, intron 3 of 25)	140703	NM_018760	54403	Mm.41044	NM_018760	ENSMUSG00000060961	Slc4a4	AI835705|NBC|NBC1	solute carrier family 4 (anion exchanger), member 4	protein-coding
mm_106732.1	chr12	3891811	3891829	+	1	NA	promoter-TSS (NM_153743)	promoter-TSS (NM_153743)	76	NM_153743	13435	Mm.5001	NM_007872	ENSMUSG00000020661	Dnmt3a	MmuIIIA	DNA methyltransferase 3A	protein-coding
mm_153722.1	chr19	44406719	44406768	-	1	NA	exon (NM_009127, exon 2 of 6)	exon (NM_009127, exon 2 of 6)	966	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_60146.1	chr7	38183877	38183885	+	1	NA	promoter-TSS (NM_028166)	promoter-TSS (NM_028166)	94	NM_028166	72244	Mm.187554	NM_028166		1600014C10Rik	AI428873	RIKEN cDNA 1600014C10 gene	protein-coding
mm_144440.1	chr18	21652275	21652323	+	1	NA	promoter-TSS (NM_001081403)	promoter-TSS (NM_001081403)	69	NM_001081403	225266	Mm.436836	NM_001081403	ENSMUSG00000042514	Klhl14	6330403N15Rik|AI785250|printor	kelch-like 14	protein-coding
mm_54603.1	chr6	38308265	38308267	-	1	NA	intron (NM_001347122, intron 12 of 12)	MTEa-int|LTR|ERVL-MaLR	-9007	NM_172467	209032	Mm.101389	NM_172467	ENSMUSG00000047749	Zc3hav1l	B130055L09Rik|E430016P22Rik	zinc finger CCCH-type, antiviral 1-like	protein-coding
mm_68724.1	chr7	120201951	120201967	-	1	NA	promoter-TSS (NM_016669)	promoter-TSS (NM_016669)	29	NM_016669	12971	Mm.9114	NM_016669	ENSMUSG00000030905	Crym	-	crystallin, mu	protein-coding
mm_12943.1	chr2	85136542	85136546	+	1	NA	5' UTR (NM_011784, exon 1 of 1)	5' UTR (NM_011784, exon 1 of 1)	184	NM_011784	23796	Mm.29368	NM_011784	ENSMUSG00000044338	Aplnr	APJ|Agtrl1|msr/apj	apelin receptor	protein-coding
mm_124371.1	chr14	105897718	105897728	-	1	NA	promoter-TSS (NM_011897)	promoter-TSS (NM_011897)	-904	NM_011897	24064	Mm.89982	NM_011897	ENSMUSG00000022114	Spry2	sprouty2	sprouty homolog 2 (Drosophila)	protein-coding
mm_60234.1	chr7	43694997	43695035	+	1	NA	exon (NM_174866, exon 5 of 5)	exon (NM_174866, exon 5 of 5)	4598	NM_174866	317653	Mm.247377	NM_174866	ENSMUSG00000044737	Klk14	GK14	kallikrein related-peptidase 14	protein-coding
mm_81789.1	chr9	114978480	114978506	+	1	NA	Intergenic	CpG	-44506	NM_175380	333433	Mm.38198	NM_175380	ENSMUSG00000050627	Gpd1l	2210409H23Rik|D9Ertd660e	glycerol-3-phosphate dehydrogenase 1-like	protein-coding
mm_36987.1	chr4	109666771	109666790	-	1	NA	promoter-TSS (NM_001301368)	promoter-TSS (NM_001301368)	-24	NM_001301368	12580	Mm.1912	NM_007671	ENSMUSG00000028551	Cdkn2c	C77269|INK4c|p18|p18-INK4c|p18-INK6|p18INK4c	cyclin-dependent kinase inhibitor 2C (p18, inhibits CDK4)	protein-coding
mm_94662.1	chr11	17199400	17199403	+	1	NA	3' UTR (NM_024459, exon 6 of 6)	3' UTR (NM_024459, exon 6 of 6)	12188	NM_025443	66249	Mm.27831	NM_025443	ENSMUSG00000020116	Pno1	1810003N24Rik|AA407421|AU015468|AU019495|AU042323|Emi3|Imi3	partner of NOB1 homolog	protein-coding
mm_84261.1	chr9	62537006	62537016	-	1	NA	promoter-TSS (NM_175484)	promoter-TSS (NM_175484)	33	NM_175484	235431	Mm.335229	NM_175484	ENSMUSG00000041729	Coro2b	CLIPINC|E130012P22Rik	coronin, actin binding protein, 2B	protein-coding
mm_41621.1	chr5	96841996	96842026	+	1	NA	intron (NM_013470, intron 12 of 12)	intron (NM_013470, intron 12 of 12)	48626	NM_013470	11745	Mm.7214	NM_013470	ENSMUSG00000029484	Anxa3	Anx3	annexin A3	protein-coding
mm_144981.1	chr18	37997674	37997706	+	1	NA	promoter-TSS (NM_139206)	promoter-TSS (NM_139206)	-116	NM_139206	106952	Mm.247642	NM_139206	ENSMUSG00000024451	Arap3	Centd3|Drag1|E030006K04Rik|cnt-d3	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3	protein-coding
mm_102995.1	chr11	69686917	69686928	-	1	NA	exon (NM_011614, exon 7 of 7)	exon (NM_011614, exon 7 of 7)	-1368	NM_023517	69583	Mm.8983	NM_023517	ENSMUSG00000089669	Tnfsf13	2310026N09Rik|April|Tall2|Tnlg7b|Trdl1	tumor necrosis factor (ligand) superfamily, member 13	protein-coding
mm_151460.1	chr19	58511982	58512009	+	1	NA	promoter-TSS (NM_029372)	promoter-TSS (NM_029372)	-7	NM_029372	75645	Mm.159542	NM_029372	ENSMUSG00000025090	Ccdc172	1700011F14Rik	coiled-coil domain containing 172	protein-coding
mm_27755.1	chr3	69598823	69598874	-	1	NA	5' UTR (NM_020026, exon 1 of 3)	5' UTR (NM_020026, exon 1 of 3)	112	NM_020026	26879	Mm.153710	NM_020026	ENSMUSG00000043300	B3galnt1	B3galt3|b3GT3	UDP-GalNAc:betaGlcNAc beta 1,3-galactosaminyltransferase, polypeptide 1	protein-coding
mm_5977.1	chr1	57970068	57970094	-	1	NA	promoter-TSS (NM_001159864)	promoter-TSS (NM_001159864)	3	NM_001159864	51960	Mm.339711	NM_030211	ENSMUSG00000054770	Kctd18	4932411A20Rik|6530404F10Rik	potassium channel tetramerisation domain containing 18	protein-coding
mm_80132.1	chr9	70658159	70658160	+	1	NA	promoter-TSS (NM_172772)	promoter-TSS (NM_172772)	-985	NM_172772	235461	Mm.170855	NM_172772	ENSMUSG00000042444	Fam63b	AI465301|B230380D07Rik|mKIAA1164	family with sequence similarity 63, member B	protein-coding
mm_63152.1	chr7	123378006	123378086	+	1	NA	promoter-TSS (NM_025304)	promoter-TSS (NM_025304)	64	NM_025304	30949	Mm.260527	NM_025304	ENSMUSG00000030763	Lcmt1	AL033290|LCMT-1|Lcmt	leucine carboxyl methyltransferase 1	protein-coding
mm_43255.1	chr5	130222303	130222316	+	1	NA	promoter-TSS (NM_027854)	promoter-TSS (NM_027854)	-26	NM_027854	71667	Mm.258508	NM_027854	ENSMUSG00000053094	Tmem248	0610007L01Rik|A930023A16Rik|AW557951|G430067H08Rik	transmembrane protein 248	protein-coding
mm_166940.1	chr7	43376818	43376822	-	1	NA	Intergenic	Intergenic	25479	NM_145581	233186	Mm.290569	NM_145581	ENSMUSG00000039013	Siglecf	Siglec5|mSiglec-F	sialic acid binding Ig-like lectin F	protein-coding
mm_68.1	chr1	6637849	6637873	+	1	NA	intron (NM_001244693, intron 2 of 22)	intron (NM_001244693, intron 2 of 22)	-92190	NR_045189	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding
mm_151762.1	chr19	5134362	5134366	-	1	NA	3' UTR (NM_153129, exon 24 of 24)	3' UTR (NM_153129, exon 24 of 24)	-15956	NM_008451	16594	Mm.271648	NM_008451	ENSMUSG00000024862	Klc2	8030455F02Rik|AW212649|KLC 2|KLC-2	kinesin light chain 2	protein-coding
mm_134004.1	chr16	4790188	4790203	-	1	NA	promoter-TSS (NM_025670)	promoter-TSS (NM_025670)	-260	NM_025670	66626	Mm.157648	NM_025670	ENSMUSG00000004071	Cdip1	2700048O17Rik|5730403B10Rik|AU018521|AW742692|CDIP	cell death inducing Trp53 target 1	protein-coding
mm_45083.1	chr5	44038830	44038839	-	1	NA	intron (NM_001163582, intron 6 of 21)	MLTR31F_MM|LTR|ERVK	55934	NM_001163581	19126	Mm.6250	NM_008935	ENSMUSG00000029086	Prom1	4932416E19Rik|AC133|CD133|Prom|Prom-1|Proml1	prominin 1	protein-coding
mm_154319.1	chrM	2201	2211	+	1	NA	NA	Intergenic	NA	NA								
mm_148370.1	chr18	88894324	88894371	-	1	NA	promoter-TSS (NM_018821)	promoter-TSS (NM_018821)	-140	NM_018821	54607	Mm.91920	NM_018821	ENSMUSG00000056153	Socs6	1500012M23Rik|5830401B18Rik|AI447482|Cis4|Cish4|HSPC060|SOCS-4|SOCS-6|SSI4|STAI4|STATI4|Socs4	suppressor of cytokine signaling 6	protein-coding
mm_97241.1	chr11	75679629	75679637	+	1	NA	exon (NM_133656, exon 1 of 3)	exon (NM_133656, exon 1 of 3)	374	NM_001277221	12928	Mm.280125	NM_133656	ENSMUSG00000017776	Crk	Crk-I|Crk-II|Crk-III|Crk3|CrkIII|Crko|c-Crk|p38	v-crk avian sarcoma virus CT10 oncogene homolog	protein-coding
mm_50160.1	chr6	41547429	41547435	+	1	NA	Intergenic	Intergenic	25656	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_73407.1	chr8	105971559	105971576	+	1	NA	Intergenic	ORR1C2|LTR|ERVL-MaLR	-5452	NR_045594	20498	Mm.292447	NM_009195	ENSMUSG00000017765	Slc12a4	AW546649|KCC1|RBCKCC1	solute carrier family 12, member 4	protein-coding
mm_115752.1	chr13	19185507	19185518	-	1	NA	Intergenic	Intergenic	210301	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_71224.1	chr8	40900619	40900627	+	1	NA	intron (NM_007514, intron 3 of 11)	intron (NM_007514, intron 3 of 11)	-25610	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_103893.1	chr11	83575215	83575232	-	1	NA	3' UTR (NM_011338, exon 4 of 4)	3' UTR (NM_011338, exon 4 of 4)	3413	NM_011338	20308	Mm.416125	NM_011338	ENSMUSG00000019122	Ccl9	CCF18|MRP-2|Scya10|Scya9	chemokine (C-C motif) ligand 9	protein-coding
mm_151472.1	chr19	58673073	58673085	+	1	NA	intron (NM_026925, intron 3 of 12)	intron (NM_026925, intron 3 of 12)	2714	NM_026925	69060	Mm.20407	NM_026925	ENSMUSG00000046008	Pnlip	1810007A24Rik|PL|PTL	pancreatic lipase	protein-coding
mm_41081.1	chr5	87677589	87677621	+	1	NA	exon (NM_007784, exon 28 of 34)	exon (NM_007784, exon 28 of 34)	11397	NM_001286016	12990	Mm.427467	NM_007784	ENSMUSG00000070702	Csn1s1	AA959832|AW212882|Csna	casein alpha s1	protein-coding
mm_79037.1	chr9	46207608	46207622	+	1	NA	intron (NM_027498, intron 15 of 24)	intron (NM_027498, intron 15 of 24)	-21015	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2|apo-AI|apoA-I	apolipoprotein A-I	protein-coding
mm_170775.1	chr2	166252713	166252717	-	1	NA	Intergenic	ORR1A0|LTR|ERVL-MaLR	-21193	NR_033467	670775	Mm.384326	NR_033467	ENSMUSG00000084840	Gm11468	OTTMUSG00000001131	predicted gene 11468	ncRNA
mm_54099.1	chr6	16846282	16846305	-	1	NA	intron (NM_031198, intron 2 of 6)	L1_Mur2|LINE|L1	52148	NM_031198	21426	Mm.36217	NM_031198	ENSMUSG00000029553	Tfec	BB107417|Tcfec|bHLHe34	transcription factor EC	protein-coding
mm_93882.1	chr10	125308844	125308853	-	1	NA	intron (NM_011391, intron 1 of 6)	intron (NM_011391, intron 1 of 6)	19687	NM_011391	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|Mct2	solute carrier family 16 (monocarboxylic acid transporters), member 7	protein-coding
mm_100967.1	chr11	6660232	6660240	-	1	NA	promoter-TSS (NR_028586)	promoter-TSS (NR_028586)	0	NR_028586	100041311	Mm.388018	NR_028586	ENSMUSG00000086373	Gm11978	OTTMUSG00000005125|OTTMUSG00000005127	predicted gene 11978	pseudo
mm_168540.1	chr11	62389693	62389706	-	1	NA	exon (NM_001252313, exon 13 of 45)	exon (NM_001252313, exon 13 of 45)	48816	NM_001252313	20185	Mm.271814	NM_011308	ENSMUSG00000018501	Ncor1	5730405M06Rik|A230020K14Rik|N-CoR|RIP13|Rxrip13|mKIAA1047	nuclear receptor co-repressor 1	protein-coding
mm_9768.1	chr1	180996094	180996104	-	1	NA	exon (NM_010145, exon 4 of 9)	exon (NM_010145, exon 4 of 9)	21470	NM_010145	13849	Mm.9075	NM_010145	ENSMUSG00000038776	Ephx1	EH|Eph-1|Eph1|Epxh1|mEH	epoxide hydrolase 1, microsomal	protein-coding
mm_24959.1	chr3	96696380	96696396	+	1	NA	promoter-TSS (NM_001165949)	promoter-TSS (NM_001165949)	13	NM_146135	229615	Mm.1635	NM_018812	ENSMUSG00000028101	Pias3	Pias3l	protein inhibitor of activated STAT 3	protein-coding
mm_138645.1	chr17	35866822	35866832	+	1	NA	5' UTR (NM_175242, exon 1 of 3)	5' UTR (NM_175242, exon 1 of 3)	212	NM_175242	76448	Mm.359982	NM_175242	ENSMUSG00000034595	Ppp1r18	2310014H01Rik|AA407849|AI450394	protein phosphatase 1, regulatory subunit 18	protein-coding
mm_46889.1	chr5	113974831	113974850	-	1	NA	intron (NM_198109, intron 2 of 14)	intron (NM_198109, intron 2 of 14)	18917	NM_198109	231637	Mm.389682	NM_198109	ENSMUSG00000042121	Ssh1	AW551225|Gm1394|Gm1395|SSH-1|SSH-1L	slingshot homolog 1 (Drosophila)	protein-coding
mm_60445.1	chr7	44477143	44477160	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	6804	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_16406.1	chr2	180035082	180035085	+	1	NA	3' UTR (NM_177727, exon 9 of 9)	3' UTR (NM_177727, exon 9 of 9)	7381	NM_001289476	26444	Mm.21728	NM_011969	ENSMUSG00000027566	Psma7	C6-I	proteasome (prosome, macropain) subunit, alpha type 7	protein-coding
mm_39381.1	chr5	13125475	13125512	+	1	NA	Intergenic	Intergenic	-271291	NM_001243072	20346	Mm.372039	NM_009152	ENSMUSG00000028883	Sema3a	Hsema-I|SEMA1|SemD|Semad|coll-1	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	protein-coding
mm_135758.1	chr16	56037729	56037810	-	1	NA	promoter-TSS (NM_029092)	promoter-TSS (NM_029092)	5	NM_029092	52575	Mm.288742	NM_029092	ENSMUSG00000044763	Trmt10c	1300018J16Rik|D16Ertd454e|Rg9mtd1|Rnmtd1	tRNA methyltransferase 10C	protein-coding
mm_18290.1	chr2	52676085	52676099	-	1	NA	promoter-TSS (NM_001285428)	promoter-TSS (NM_001285428)	51	NM_001285426	12298	Mm.330223	NM_146123	ENSMUSG00000017412	Cacnb4	3110038O15Rik|Cchb4|lh	calcium channel, voltage-dependent, beta 4 subunit	protein-coding
mm_164006.1	chr14	67107237	67107238	+	1	NA	Intergenic	Intergenic	-34766	NM_001205188	71978	Mm.273997	NM_028032	ENSMUSG00000022052	Ppp2r2a	2410004D02Rik|mKIAA1541	protein phosphatase 2, regulatory subunit B, alpha	protein-coding
mm_126295.1	chr15	79347938	79348030	+	1	NA	promoter-TSS (NM_001304832)	promoter-TSS (NM_001304832)	-77	NM_001304831	17133	Mm.86646	NM_010755	ENSMUSG00000042622	Maff	-	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein F (avian)	protein-coding
mm_164773.1	chr17	89099963	89099974	+	1	NA	intron (NM_013523, intron 1 of 9)	(T)n|Simple_repeat|Simple_repeat	100707	NM_013523	14309	Mm.57155	NM_013523	ENSMUSG00000032937	Fshr	-	follicle stimulating hormone receptor	protein-coding
mm_29388.1	chr3	108889868	108889894	-	1	NA	5' UTR (NM_177091, exon 1 of 13)	5' UTR (NM_177091, exon 1 of 13)	127	NM_177091	320181	Mm.244233	NM_177091	ENSMUSG00000045326	Fndc7	E230011A21Rik	fibronectin type III domain containing 7	protein-coding
mm_153268.1	chr19	37127708	37127710	-	1	NA	intron (NM_001290828, intron 3 of 10)	intron (NM_001290828, intron 3 of 10)	-46134	NR_045329	319931	Mm.446730	NR_045329	ENSMUSG00000097591	A330032B11Rik	-	RIKEN cDNA A330032B11 gene	ncRNA
mm_82659.1	chr9	22085381	22085389	-	1	NA	promoter-TSS (NM_012029)	promoter-TSS (NM_012029)	42	NM_001253897	26940	Mm.425568	NM_012029	ENSMUSG00000066839	Ecsit	Sitpec	ECSIT signalling integrator	protein-coding
mm_48718.1	chr5	147322340	147322362	-	1	NA	promoter-TSS (NM_001039678)	promoter-TSS (NM_001039678)	89	NM_001039678	231903	Mm.291286	NM_001039678	ENSMUSG00000075543	Urad	EG231903|Prhoxnb	ureidoimidazoline (2-oxo-4-hydroxy-4-carboxy-5) decarboxylase	protein-coding
mm_148130.1	chr18	75697507	75697522	-	1	NA	5' UTR (NM_201354, exon 1 of 12)	5' UTR (NM_201354, exon 1 of 12)	182	NM_201354	269037	Mm.36745	NM_201354	ENSMUSG00000052928	Ctif	Gm672	CBP80/20-dependent translation initiation factor	protein-coding
mm_97290.1	chr11	76217648	76217670	+	1	NA	promoter-TSS (NM_177367)	promoter-TSS (NM_177367)	46	NM_021294	13168	Mm.347413	NM_021294	ENSMUSG00000038057	Dbil5	ELP	diazepam binding inhibitor-like 5	protein-coding
mm_8032.1	chr1	135155321	135155340	-	1	NA	3' UTR (NM_026823, exon 7 of 7)	3' UTR (NM_026823, exon 7 of 7)	8496	NM_026823	68724	Mm.174998	NM_026823	ENSMUSG00000026426	Arl8a	1110033P22Rik|Arl10b|gie2	ADP-ribosylation factor-like 8A	protein-coding
mm_157737.1	chrX	72274748	72274757	-	1	NA	promoter-TSS (NM_017369)	promoter-TSS (NM_017369)	-31	NM_017369	14404	Mm.391288	NM_017369	ENSMUSG00000031340	Gabre	-	gamma-aminobutyric acid (GABA) A receptor, subunit epsilon	protein-coding
mm_134139.1	chr16	10683625	10683633	-	1	NA	intron (NM_001204229, intron 18 of 22)	L1ME3G|LINE|L1	101907	NM_009896	12703	Mm.130	NM_009896	ENSMUSG00000038037	Socs1	Cish1|Cish7|JAB|SOCS-1|SSI-1	suppressor of cytokine signaling 1	protein-coding
mm_167128.1	chr7	126777129	126777135	+	1	NA	5' UTR (NM_026875, exon 1 of 5)	5' UTR (NM_026875, exon 1 of 5)	157	NM_025347	66090	Mm.27114	NM_025347	ENSMUSG00000042675	Ypel3	0610043B10Rik|1190001G19Rik|Suap	yippee-like 3 (Drosophila)	protein-coding
mm_53139.1	chr6	125221725	125221735	+	1	NA	3' UTR (NM_001080557, exon 4 of 4)	3' UTR (NM_001080557, exon 4 of 4)	6149	NM_001080557	22317	Mm.32321	NM_009496	ENSMUSG00000030337	Vamp1	Syb-1|Syb1|VAMP-1|lew	vesicle-associated membrane protein 1	protein-coding
mm_103185.1	chr11	70587158	70587160	-	1	NA	intron (NM_016713, intron 1 of 30)	RMER15|LTR|ERVL	24278	NM_016713	50932	Mm.42967	NM_016713	ENSMUSG00000020827	Mink1	B55|MINK|Map4k6|Ysk2	misshapen-like kinase 1 (zebrafish)	protein-coding
mm_43815.1	chr5	142909314	142909359	+	1	NA	Intergenic	Intergenic	-2582	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_132481.1	chr16	36875120	36875205	+	1	NA	promoter-TSS (NM_134111)	promoter-TSS (NM_134111)	-336	NM_134111	106389	Mm.432078	NM_134111	ENSMUSG00000022838	Eaf2	AW048865|FESTA-L|FESTA-S|Festa|Traits|U19	ELL associated factor 2	protein-coding
mm_28692.1	chr3	95524816	95524839	-	1	NA	Intergenic	Intergenic	-1959	NM_021281	13040	Mm.3619	NM_021281	ENSMUSG00000038642	Ctss	Cats	cathepsin S	protein-coding
mm_124521.1	chr14	122058063	122058083	-	1	NA	Intergenic	Intergenic	23399	NM_001037744	223262	Mm.297637	NM_001037744	ENSMUSG00000071229	Timm8a2	-	translocase of inner mitochondrial membrane 8A2	protein-coding
mm_140279.1	chr17	84965032	84965050	+	1	NA	intron (NM_001159496, intron 1 of 5)	PB1|SINE|Alu	7040	NM_001159496	19043	Mm.249695	NM_011151	ENSMUSG00000061130	Ppm1b	PP2CB	protein phosphatase 1B, magnesium dependent, beta isoform	protein-coding
mm_122218.1	chr14	32388302	32388309	-	1	NA	promoter-TSS (NM_001034037)	promoter-TSS (NM_001034037)	68	NM_001034037	67085	Mm.109099	NM_001034037	ENSMUSG00000072473	1700024G13Rik	C10orf53	RIKEN cDNA 1700024G13 gene	protein-coding
mm_73119.1	chr8	94750449	94750457	+	1	NA	3' UTR (NM_009137, exon 3 of 3)	3' UTR (NM_009137, exon 3 of 3)	4769	NM_009137	20299	Mm.12895	NM_009137	ENSMUSG00000031779	Ccl22	ABCD-1|DCBCK|MDC|Scya22	chemokine (C-C motif) ligand 22	protein-coding
mm_71743.1	chr8	64619491	64619510	+	1	NA	exon (NM_013494, exon 2 of 9)	exon (NM_013494, exon 2 of 9)	73609	NM_013494	12876	Mm.31395	NM_013494	ENSMUSG00000037852	Cpe	CPH|Cph-1|Cph1|R74677|fat	carboxypeptidase E	protein-coding
mm_157820.1	chrX	74073486	74073489	-	1	NA	intron (NM_001081979, intron 1 of 2)	ID_B1|SINE|B4	12203	NM_010788	17257	Mm.131408	NM_010788	ENSMUSG00000031393	Mecp2	1500041B07Rik|D630021H01Rik|Mbd5|WBP10	methyl CpG binding protein 2	protein-coding
mm_151547.1	chr19	59344494	59344512	+	1	NA	intron (NM_001033222, intron 1 of 4)	intron (NM_001033222, intron 1 of 4)	1277	NM_001033222	107368	Mm.27250	NM_001033222	ENSMUSG00000074746	Pdzd8	A630041P07Rik|AV329468|AW228944|Pdzk8	PDZ domain containing 8	protein-coding
mm_29477.1	chr3	115711210	115711245	-	1	NA	3' UTR (NM_007901, exon 2 of 2)	3' UTR (NM_007901, exon 2 of 2)	3828	NM_007901	13609	Mm.982	NM_007901	ENSMUSG00000045092	S1pr1	AI849002|Edg1|Lpb1|S1p|S1p1	sphingosine-1-phosphate receptor 1	protein-coding
mm_136327.1	chr16	92346387	92346419	-	1	NA	3' UTR (NM_008424, exon 2 of 2)	3' UTR (NM_008424, exon 2 of 2)	13065	NM_008424	16509	Mm.299425	NM_008424	ENSMUSG00000039639	Kcne1	Isk|MinK|nmf190	potassium voltage-gated channel, Isk-related subfamily, member 1	protein-coding
mm_153732.1	chr19	44408765	44408776	-	1	NA	Intergenic	MIR3|SINE|MIR	-1061	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_136514.1	chr16	97447661	97447664	-	1	NA	non-coding (NR_003520, exon 9 of 9)	non-coding (NR_003520, exon 9 of 9)	15243	NM_010846	17857	Mm.33996	NM_010846	ENSMUSG00000000386	Mx1	AI893580|Mx|Mx-1	MX dynamin-like GTPase 1	protein-coding
mm_112002.1	chr12	110840851	110840861	-	1	NA	promoter-TSS (NM_011973)	promoter-TSS (NM_011973)	83	NM_011973	26448	Mm.140948	NM_011973	ENSMUSG00000056458	Mok	RAGE1|Rage|Stk30	MOK protein kinase	protein-coding
mm_13155.1	chr2	92483834	92483876	+	1	NA	Intergenic	Intergenic	-23337	NM_145832	228368	Mm.273990	NM_145832	ENSMUSG00000049922	Slc35c1	E430007K15Rik|fuct1	solute carrier family 35, member C1	protein-coding
mm_11113.1	chr2	28193220	28193236	+	1	NA	5' UTR (NM_001038613, exon 1 of 6)	5' UTR (NM_001038613, exon 1 of 6)	135	NM_001038614	56177	Mm.43278	NM_019498	ENSMUSG00000026833	Olfm1	AMY|AW742568|Noe1|OlfA|Pancortin|Pancortin3	olfactomedin 1	protein-coding
mm_61896.1	chr7	90030030	90030072	+	1	NA	intron (NR_110365, intron 1 of 5)	intron (NR_110365, intron 1 of 5)	892	NR_110364	319711	Mm.31753	NR_015614	ENSMUSG00000097585	E230029C05Rik	AI452102|B230337J15	RIKEN cDNA E230029C05 gene	ncRNA
mm_5971.1	chr1	57391482	57391491	-	1	NA	exon (NM_001037742, exon 6 of 8)	exon (NM_001037742, exon 6 of 8)	13866	NM_028546	73467	Mm.263673	NM_028546	ENSMUSG00000038323	1700066M21Rik	AI428479	RIKEN cDNA 1700066M21 gene	protein-coding
mm_31647.1	chr4	59618286	59618289	+	1	NA	3' UTR (NM_024255, exon 11 of 11)	3' UTR (NM_024255, exon 11 of 11)	-7924	NM_001015681	230259	Mm.45688	NM_153158	ENSMUSG00000045071	E130308A19Rik	-	RIKEN cDNA E130308A19 gene	protein-coding
mm_137219.1	chr17	24170976	24171007	+	1	NA	Intergenic	Intergenic	-1562	NM_009729	11984	Mm.30155	NM_009729	ENSMUSG00000024121	Atp6v0c	Atp6c|Atp6c2|Atp6l|Atpl|Atpl-rs1|PL16|VATL|Vma3	ATPase, H+ transporting, lysosomal V0 subunit C	protein-coding
mm_155163.1	chrX	52988210	52988211	+	1	NA	5' UTR (NM_013556, exon 1 of 9)	5' UTR (NM_013556, exon 1 of 9)	132	NM_013556	15452	Mm.299381	NM_013556	ENSMUSG00000025630	Hprt	C81579|HPGRT|Hprt1	hypoxanthine guanine phosphoribosyl transferase	protein-coding
mm_120185.1	chr14	61492692	61492700	+	1	NA	promoter-TSS (NR_045714)	promoter-TSS (NR_045714)	8	NR_045714	75349	Mm.233613	NR_045714		4930556J02Rik	-	RIKEN cDNA 4930556J02 gene	ncRNA
mm_84570.1	chr9	68969556	68969569	-	1	NA	intron (NM_013646, intron 1 of 10)	intron (NM_013646, intron 1 of 10)	204216	NR_033299	320440	Mm.483129	NM_177159		9530091C08Rik	-	RIKEN cDNA 9530091C08 gene	ncRNA
mm_41930.1	chr5	105700215	105700223	+	1	NA	promoter-TSS (NM_178701)	promoter-TSS (NM_178701)	250	NM_001122768	231549	Mm.23837	NM_178701	ENSMUSG00000046079	Lrrc8d	2810473G09Rik|4930525N13Rik|A930019F03|Lrrc5	leucine rich repeat containing 8D	protein-coding
mm_166408.1	chr5	136883096	136883101	-	1	NA	promoter-TSS (NM_024474)	promoter-TSS (NM_024474)	9	NM_024474	140709	Mm.295020	NM_024474	ENSMUSG00000004415	Col26a1	9430032K24Rik|BC002218|Col26a|Emid2|Emu2	collagen, type XXVI, alpha 1	protein-coding
mm_161885.1	chr18	37742063	37742063	+	1	NA	promoter-TSS (NM_033578)	promoter-TSS (NM_033578)	-31	NM_033578	93703	Mm.247203	NM_033578	ENSMUSG00000103088	Pcdhgb6	-	protocadherin gamma subfamily B, 6	protein-coding
mm_85932.1	chr9	112097667	112097715	-	1	NA	intron (NM_001177618, intron 17 of 18)	intron (NM_001177618, intron 17 of 18)	21020	NR_029823	723815		NR_029823	ENSMUSG00000065441	Mir128-2	Mirn128-2|Mirn128b|mir-128-2|mir-128b	microRNA 128-2	ncRNA
mm_82360.1	chr9	14500364	14500377	-	1	NA	promoter-TSS (NM_023153)	promoter-TSS (NM_023153)	112	NM_173433	244694	Mm.240457	NM_173433	ENSMUSG00000053914	Kdm4d	4932416A15|Jmjd2d	lysine (K)-specific demethylase 4D	protein-coding
mm_146946.1	chr18	32462491	32462504	-	1	NA	Intergenic	Intergenic	-84213	NR_045403	402767	Mm.385109	NR_045403	ENSMUSG00000097413	A830052D11Rik	-	RIKEN cDNA A830052D11 gene	ncRNA
mm_89109.1	chr10	84622313	84622360	+	1	NA	promoter-TSS (NM_027423)	promoter-TSS (NM_027423)	-101	NM_027423	70428	Mm.335007	NM_027423	ENSMUSG00000034453	Polr3b	2700078H01Rik|A330032P03Rik|C85372|RPC2	polymerase (RNA) III (DNA directed) polypeptide B	protein-coding
mm_90901.1	chr10	10688944	10688956	-	1	NA	3' UTR (NM_001114333, exon 10 of 10)	3' UTR (NM_001114333, exon 10 of 10)	-62096	NR_046010	78056	Mm.271285	NR_046010		4930567K20Rik	1700038H22Rik	RIKEN cDNA 4930567K20 gene	ncRNA
mm_152303.1	chr19	9085356	9085408	-	1	NA	intron (NM_011681, intron 1 of 2)	intron (NM_011681, intron 1 of 2)	2574	NM_011681	22287	Mm.2258	NM_011681	ENSMUSG00000024653	Scgb1a1	CC10|CC16|CCSP|PCB-BP|UG|UGB|Utg	secretoglobin, family 1A, member 1 (uteroglobin)	protein-coding
mm_54502.1	chr6	35510549	35510570	-	1	NA	3' UTR (NM_008098, exon 4 of 4)	3' UTR (NM_008098, exon 4 of 4)	29329	NM_008098	14489	Mm.182746	NM_008098	ENSMUSG00000029840	Mtpn	5033418D15Rik|Gcdp|V1	myotrophin	protein-coding
mm_81070.1	chr9	106203191	106203201	+	1	NA	promoter-TSS (NM_011876)	promoter-TSS (NM_011876)	88	NM_011876	23999	Mm.274346	NM_011876	ENSMUSG00000023277	Twf2	A6-related|AU014993|Ptk9l|Ptk9r	twinfilin actin binding protein 2	protein-coding
mm_119971.1	chr14	55540373	55540446	+	1	NA	exon (NM_028994, exon 1 of 10)	exon (NM_028994, exon 1 of 10)	143	NM_028994	74551	Mm.29856	NM_028994	ENSMUSG00000040618	Pck2	1810010O14Rik|9130022B02Rik|PEPCK-M	phosphoenolpyruvate carboxykinase 2 (mitochondrial)	protein-coding
mm_77944.1	chr9	7358213	7358375	+	1	NA	exon (NM_008605, exon 10 of 10)	exon (NM_008605, exon 10 of 10)	10920	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_136018.1	chr16	76249459	76249467	-	1	NA	Intergenic	Intergenic	123586	NM_173440	268903	Mm.74711	NM_173440	ENSMUSG00000048490	Nrip1	6030458L20Rik|8430438I05Rik|9630050P12|AA959574|AW456757|RIP140	nuclear receptor interacting protein 1	protein-coding
mm_18938.1	chr2	76754049	76754052	-	1	NA	exon (NM_011652, exon 273 of 313)	exon (NM_011652, exon 273 of 313)	78735	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_20186.1	chr2	122602543	122602562	-	1	NA	exon (NM_025961, exon 4 of 9)	exon (NM_025961, exon 4 of 9)	8725	NM_025961	67092	Mm.29975	NM_025961	ENSMUSG00000027199	Gatm	1810003P21Rik|AI314789|AT	glycine amidinotransferase (L-arginine:glycine amidinotransferase)	protein-coding
mm_98794.1	chr11	96944287	96944299	+	1	NA	promoter-TSS (NM_134021)	promoter-TSS (NM_134021)	147	NR_003293	319371	Mm.436865	NR_003293	ENSMUSG00000078700	D030028A08Rik	-	RIKEN cDNA D030028A08 gene	ncRNA
mm_160006.1	chr6	124755966	124755966	-	1	NA	intron (NM_007881, intron 1 of 9)	intron (NM_007881, intron 1 of 9)	521	NM_007881	13498	Mm.333380	NM_007881	ENSMUSG00000004263	Atn1	Atr1|Drpla|atrophin-1	atrophin 1	protein-coding
mm_110234.1	chr12	30373275	30373285	-	1	NA	promoter-TSS (NM_172951)	promoter-TSS (NM_172951)	95	NM_172951	268534	Mm.279765	NM_172951	ENSMUSG00000020672	Sntg2	2210008K22Rik|9530013L23|BB121248|G2syn|Syn5	syntrophin, gamma 2	protein-coding
mm_155487.1	chrX	73716578	73716618	+	1	NA	promoter-TSS (NM_012060)	promoter-TSS (NM_012060)	1	NM_007435	11666	Mm.365	NM_007435	ENSMUSG00000031378	Abcd1	ALDP|Ald|Aldgh	ATP-binding cassette, sub-family D (ALD), member 1	protein-coding
mm_81001.1	chr9	103426586	103426606	+	1	NA	non-coding (NR_040466, exon 2 of 6)	non-coding (NR_040466, exon 2 of 6)	3018	NR_040466	100529079	Mm.437003	NR_040466	ENSMUSG00000086236	5830418P13Rik	-	RIKEN cDNA 5830418P13 gene	ncRNA
mm_133077.1	chr16	58727998	58728059	+	1	NA	non-coding (NR_045518, exon 1 of 4)	non-coding (NR_045518, exon 1 of 4)	118	NM_001252451	224250	Mm.29482	NM_171826	ENSMUSG00000022744	Cldnd1	1110019C08Rik|AA407103|AI849195|AW489850|Cldn25	claudin domain containing 1	protein-coding
mm_62830.1	chr7	113556775	113556823	+	1	NA	intron (NR_126544, intron 1 of 5)	intron (NR_126544, intron 1 of 5)	8188	NR_126544	69295	Mm.396150	NR_126544	ENSMUSG00000084984	Far1os	1700006P19Rik	fatty acyl CoA reductase 1, opposite strand	ncRNA
mm_2219.1	chr1	89930212	89930249	+	1	NA	intron (NM_010262, intron 1 of 1)	CpG	946	NM_010262	14472	Mm.204730	NM_010262	ENSMUSG00000034486	Gbx2	D130058E05Rik|Gbx-2|MMoxA|Stra7	gastrulation brain homeobox 2	protein-coding
mm_112098.1	chr12	112785218	112785235	-	1	NA	Intergenic	Intergenic	-23749	NM_145450	217887	Mm.186678	NM_145450	ENSMUSG00000037594	BC022687	AW050009|C130001I08Rik|Flj20080	cDNA sequence BC022687	protein-coding
mm_30081.1	chr3	138091132	138091155	-	1	NA	exon (NM_001163457, exon 20 of 20)	exon (NM_001163457, exon 20 of 20)	-23755	NR_037975	329763	Mm.169710	NM_177860	ENSMUSG00000049349	Gm5105	D830013H12|EG329763	predicted gene 5105	ncRNA
mm_16671.1	chr2	6722238	6722249	-	1	NA	promoter-TSS (NM_001310447)	promoter-TSS (NM_001310447)	-581	NM_001310447	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_144.1	chr1	11004524	11004525	+	1	NA	intron (NM_029525, intron 1 of 39)	intron (NM_029525, intron 1 of 39)	11059	NM_029525	109294	Mm.123247	NM_029525	ENSMUSG00000048960	Prex2	6230420N16Rik|AI316880|AI553603|C030045D06Rik|D430013K02|Depdc2|P-Rex2	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	protein-coding
mm_102162.1	chr11	53763961	53763974	-	1	NA	promoter-TSS (NR_106131)	promoter-TSS (NR_106131)	-313	NR_106131	102465772		NR_106131	ENSMUSG00000099153	Mir7671	Gm27802|mmu-mir-7671	microRNA 7671	ncRNA
mm_148204.1	chr18	79110358	79110390	-	1	NA	promoter-TSS (NM_053099)	promoter-TSS (NM_053099)	-983	NM_053099	240427	Mm.312871	NM_053099	ENSMUSG00000024548	Setbp1	C130092E12|Seb|mKIAA0437	SET binding protein 1	protein-coding
mm_33276.1	chr4	128711844	128711879	+	1	NA	intron (NM_001195130, intron 6 of 14)	intron (NM_001195130, intron 6 of 14)	-15710	NM_001195083	54383	Mm.473738	NM_018774	ENSMUSG00000028796	Phc2	A3galt2|AA415044|D130050K19Rik|D4Ertd810e|Edr2|Mph2|p36	polyhomeotic-like 2 (Drosophila)	protein-coding
mm_113787.1	chr13	45538807	45538839	+	1	NA	intron (NM_025508, intron 6 of 8)	intron (NM_025508, intron 6 of 8)	31379	NM_025508	66355	Mm.290802	NM_025508	ENSMUSG00000000253	Gmpr	2310004P21Rik|AV028449|GMPR 1	guanosine monophosphate reductase	protein-coding
mm_140384.1	chr17	87145620	87145622	+	1	NA	Intergenic	Intergenic	37942	NM_019654	56468	Mm.126885	NM_019654	ENSMUSG00000037104	Socs5	1810018L08Rik|Cish5|mKIAA0671	suppressor of cytokine signaling 5	protein-coding
mm_798.1	chr1	45347633	45347694	+	1	NA	exon (NM_009930, exon 50 of 51)	exon (NM_009930, exon 50 of 51)	36125	NM_009930	12825	Mm.249555	NM_009930	ENSMUSG00000026043	Col3a1	AW550625|Col3a-1|Tsk-2|Tsk2	collagen, type III, alpha 1	protein-coding
mm_152624.1	chr19	12469061	12469065	-	1	NA	3' UTR (NM_172442, exon 9 of 9)	3' UTR (NM_172442, exon 9 of 9)	8284	NM_010821	17476	Mm.3999	NM_010821	ENSMUSG00000046805	Mpeg1	MPS1|Mpg-1	macrophage expressed gene 1	protein-coding
mm_119243.1	chr14	33589239	33589267	+	1	NA	promoter-TSS (NM_008978)	promoter-TSS (NM_008978)	-17	NM_008978	19256	Mm.8019	NM_008978	ENSMUSG00000021940	Ptpn20	typ	protein tyrosine phosphatase, non-receptor type 20	protein-coding
mm_44582.1	chr5	24902446	24902456	-	1	NA	promoter-TSS (NR_040684)	promoter-TSS (NR_040684)	-118	NR_040684	71161	Mm.443533	NR_040684	ENSMUSG00000086446	Prkag2os1	4933426D04Rik	protein kinase, AMP-activated, gamma 2 non-catalytic subunit, opposite strand 1	ncRNA
mm_133669.1	chr16	92075445	92075450	+	1	NA	intron (NM_080456, intron 1 of 2)	intron (NM_080456, intron 1 of 2)	17111	NM_080456	121022	Mm.217354	NM_080456	ENSMUSG00000039680	Mrps6	AW046321	mitochondrial ribosomal protein S6	protein-coding
mm_98179.1	chr11	87760899	87760903	+	1	NA	5' UTR (NM_172449, exon 1 of 32)	5' UTR (NM_172449, exon 1 of 32)	360	NM_172449	207777	Mm.342019	NM_172449	ENSMUSG00000034156	Bzrap1	D230016K05|PRAX-1|Tspoap1|mKIAA0612	benzodiazepine receptor associated protein 1	protein-coding
mm_31143.1	chr4	43383452	43383515	+	1	NA	intron (NM_001037709, intron 1 of 11)	intron (NM_001037709, intron 1 of 11)	1501	NM_001037709	100213	Mm.235730	NM_199057	ENSMUSG00000035969	Rusc2	AI840675|mKIAA0375	RUN and SH3 domain containing 2	protein-coding
mm_130119.1	chr15	89523635	89523645	-	1	NA	intron (NM_021423, intron 10 of 21)	intron (NM_021423, intron 10 of 21)	23783	NM_021423	58234	Mm.146855	NM_021423	ENSMUSG00000022623	Shank3	AI841104|SHANK3c-3|SHANK3c-4|Shank3b	SH3/ankyrin domain gene 3	protein-coding
mm_120889.1	chr14	75834490	75834512	+	1	NA	Intergenic	Intergenic	10463	NR_045294	100043189	Mm.426329	NR_045294		Gm4285	-	predicted gene 4285	ncRNA
mm_124012.1	chr14	76110821	76110831	-	1	NA	promoter-TSS (NM_013745)	promoter-TSS (NM_013745)	-11	NM_026177	67467	Mm.260767	NM_026177	ENSMUSG00000022008	Gpalpp1	1200011I18Rik|Kiaa1704	GPALPP motifs containing 1	protein-coding
mm_75236.1	chr8	39629640	39629650	-	1	NA	intron (NM_001113326, intron 3 of 9)	intron (NM_001113326, intron 3 of 9)	13033	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_70805.1	chr8	22974887	22974903	+	1	NA	promoter-TSS (NM_001110783)	promoter-TSS (NM_001110783)	59	NM_001277280	11733	Mm.334444	NM_031158	ENSMUSG00000031543	Ank1	Ank-1|nb|pale	ankyrin 1, erythroid	protein-coding
mm_34393.1	chr4	145000437	145000442	+	1	NA	intron (NM_001276502, intron 66 of 68)	intron (NM_001276502, intron 66 of 68)	107302	NM_011303	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding
mm_42066.1	chr5	109600942	109600946	+	1	NA	Intergenic	Intergenic	-41951	NM_001310694	57914	Mm.35771	NM_016715	ENSMUSG00000033467	Crlf2	CRLM2|Ly114|Tpte2|Tslpr	cytokine receptor-like factor 2	protein-coding
mm_84447.1	chr9	66511726	66511774	-	1	NA	exon (NM_175206, exon 2 of 2)	exon (NM_175206, exon 2 of 2)	2843	NM_175206	74165	Mm.297998	NM_175206	ENSMUSG00000050503	Fbxl22	1110004B15Rik	F-box and leucine-rich repeat protein 22	protein-coding
mm_41807.1	chr5	103754459	103754529	+	1	NA	promoter-TSS (NM_001080798)	promoter-TSS (NM_001080798)	-79	NM_001080798	17355	Mm.6949	NM_133919	ENSMUSG00000029313	Aff1	9630032B01Rik|AW319193|Af4|Mllt2h|Rob	AF4/FMR2 family, member 1	protein-coding
mm_111401.1	chr12	90969799	90969811	-	1	NA	Intergenic	RMER1C|Other|Other	-76043	NR_045858	71349	Mm.442093	NR_045858		5430427M07Rik	-	RIKEN cDNA 5430427M07 gene	ncRNA
mm_99897.1	chr11	109650535	109650554	+	1	NA	promoter-TSS (NM_021880)	promoter-TSS (NM_021880)	-377	NM_021880	19084	Mm.30039	NM_021880	ENSMUSG00000020612	Prkar1a	1300018C22Rik|RIalpha|Tse-1|Tse1	protein kinase, cAMP dependent regulatory, type I, alpha	protein-coding
mm_126016.1	chr15	76660565	76660610	+	1	NA	promoter-TSS (NM_019396)	promoter-TSS (NM_019396)	-54	NM_010630	16581	Mm.378950	NM_010630	ENSMUSG00000004187	Kifc2	-	kinesin family member C2	protein-coding
mm_146614.1	chr18	10065839	10065840	-	1	NA	3' UTR (NM_009071, exon 33 of 33)	3' UTR (NM_009071, exon 33 of 33)	-35690	NM_001038589	59025	Mm.329277	NM_021522	ENSMUSG00000047879	Usp14	2610005K12Rik|2610037B11Rik|AW107924|C78769|ax|nmf375	ubiquitin specific peptidase 14	protein-coding
mm_29295.1	chr3	107852807	107852817	-	1	NA	Intergenic	Intergenic	-24418	NM_133867	99662	Mm.108491	NM_133867	ENSMUSG00000040600	Eps8l3	AI504489|Eps8r3	EPS8-like 3	protein-coding
mm_112789.1	chr13	20185323	20185364	+	1	NA	intron (NM_080288, intron 1 of 21)	intron (NM_080288, intron 1 of 21)	94836	NM_080288	140580	Mm.342392	NM_080288	ENSMUSG00000041112	Elmo1	6330578D22Rik|C230095H21Rik|CED-12	engulfment and cell motility 1	protein-coding
mm_160352.1	chr8	21191562	21191562	+	1	NA	promoter-TSS (NM_007848).2	promoter-TSS (NM_007848).2	-11	NM_007848	13226	Mm.442051	NM_007848	ENSMUSG00000074442	Defa31	CRS4C-2|CRS4C2|CRS4C2b|CRS4C2c|CRS4C2d|CRS4C3a|CRS4C3a2|CRS4C3b|CRS4C3c|CRS4C3d|CRS4C3e|Defa-rs7|Defcr-rs7	defensin, alpha, 31	protein-coding
mm_114080.1	chr13	54575009	54575017	+	1	NA	promoter-TSS (NM_019968)	promoter-TSS (NM_019968)	0	NM_019968	56795	Mm.89484	NM_019968	ENSMUSG00000025870	Arl10	Arl10a|Arm1	ADP-ribosylation factor-like 10	protein-coding
mm_30521.1	chr3	158561584	158561592	-	1	NA	5' UTR (NM_001291453, exon 1 of 26)	5' UTR (NM_001291453, exon 1 of 26)	633	NM_001291453	242274	Mm.132162	NM_001081358	ENSMUSG00000028176	Lrrc7	AK122498|densin|mKIAA1365	leucine rich repeat containing 7	protein-coding
mm_131635.1	chr16	20188823	20188831	+	1	NA	intron (NM_001033237, intron 10 of 29)	RLTR40|LTR|ERVK	-12593	NR_030454	735274		NR_030454	ENSMUSG00000106252	Mir684-1	Mirn684-1	microRNA 684-1	ncRNA
mm_140389.1	chr17	87282999	87283012	+	1	NA	promoter-TSS (NR_015506)	promoter-TSS (NR_015506)	119	NM_028639	225049	Mm.77396	NM_028639	ENSMUSG00000036918	Ttc7	1110035E02Rik|1700007L07Rik|Ttc7a|fsn|hea	tetratricopeptide repeat domain 7	protein-coding
mm_63616.1	chr7	128237512	128237554	+	1	NA	5' UTR (NM_177001, exon 1 of 1)	5' UTR (NM_177001, exon 1 of 1)	176	NM_146205	233912	Mm.475117	NM_146205	ENSMUSG00000042178	Armc5	AW049683|BC032200	armadillo repeat containing 5	protein-coding
mm_157531.1	chrX	51018610	51018683	-	1	NA	promoter-TSS (NM_172413)	promoter-TSS (NM_172413)	-628	NM_172413	72065	Mm.43152	NM_172413	ENSMUSG00000050029	Rap2c	2010200P20Rik|AI194294|AL022976	RAP2C, member of RAS oncogene family	protein-coding
mm_10300.1	chr2	10593178	10593191	+	1	NA	3' UTR (NM_177386, exon 23 of 23)	3' UTR (NM_177386, exon 23 of 23)	75580	NR_035417	100316668		NR_035417	ENSMUSG00000080657	Mir669i	Mirn669i|mir-669i|mmu-mir-669i	microRNA 669i	ncRNA
mm_123584.1	chr14	67062838	67062839	-	1	NA	intron (NM_001205188, intron 2 of 9)	intron (NM_001205188, intron 2 of 9)	9633	NM_028032	71978	Mm.273997	NM_028032	ENSMUSG00000022052	Ppp2r2a	2410004D02Rik|mKIAA1541	protein phosphatase 2, regulatory subunit B, alpha	protein-coding
mm_82344.1	chr9	13818671	13818689	-	1	NA	intron (NM_026665, intron 3 of 10)	intron (NM_026665, intron 3 of 10)	8373	NR_037622	74360	Mm.157212	NM_026665	ENSMUSG00000031922	Cep57	3110002L15Rik|4921510P06Rik|4931428M20Rik|AI467480|Tsp57|mKIAA0092	centrosomal protein 57	protein-coding
mm_131200.1	chr16	8619410	8619421	+	1	NA	3' UTR (NM_001170978, exon 15 of 15)	3' UTR (NM_001170978, exon 15 of 15)	18286	NM_025708	66690	Mm.10068	NM_025708	ENSMUSG00000043140	Tmem186	2810440M13Rik|4432406C05Rik|AI648175|AW210586	transmembrane protein 186	protein-coding
mm_39486.1	chr5	20886191	20886198	+	1	NA	5' UTR (NM_177601, exon 2 of 2)	5' UTR (NM_177601, exon 2 of 2)	3741	NM_177601	212090	Mm.347525	NM_177601	ENSMUSG00000045435	Tmem60	BC027828	transmembrane protein 60	protein-coding
mm_169335.1	chr14	120941867	120941882	+	1	NA	exon (NM_023579, exon 21 of 26)	exon (NM_023579, exon 21 of 26)	30680	NM_023579	70572	Mm.221452	NM_023579	ENSMUSG00000030662	Ipo5	1110011C18Rik|5730478E03Rik|AA409333|C76941|IMB3|Kpnb3|Ranbp5	importin 5	protein-coding
mm_80317.1	chr9	74865636	74865653	+	1	NA	intron (NM_008262, intron 1 of 1)	intron (NM_008262, intron 1 of 1)	3723	NM_008262	15379	Mm.303355	NM_008262	ENSMUSG00000043013	Onecut1	D9Ertd423e|HNF-6|Hfh12|Hnf6|Hnf6b|OC-1|Oc1	one cut domain, family member 1	protein-coding
mm_28074.1	chr3	84304763	84304782	-	1	NA	promoter-TSS (NM_001271726)	promoter-TSS (NM_001271726)	3	NM_001271726	80890	Mm.44876	NM_030706	ENSMUSG00000027993	Trim2	mKIAA0517|narf	tripartite motif-containing 2	protein-coding
mm_99684.1	chr11	106036858	106036866	+	1	NA	promoter-TSS (NM_027946)	promoter-TSS (NM_027946)	-10	NM_027946	71833	Mm.307455	NM_027946	ENSMUSG00000049354	Dcaf7	1700012F10Rik|2610037L01Rik|C86529|HAN11|Wdr68	DDB1 and CUL4 associated factor 7	protein-coding
mm_147645.1	chr18	60392626	60392626	-	1	NA	TTS (NM_001146275)	TTS (NM_001146275)	16597	NM_001146275	60440	Mm.261140	NM_021792	ENSMUSG00000054072	Iigp1	2900074L10Rik|AI046432|AW111922|Ifgga1|Iigp|Irga6	interferon inducible GTPase 1	protein-coding
mm_77741.1	chr8	126971043	126971056	-	1	NA	promoter-TSS (NM_172762)	promoter-TSS (NM_172762)	30	NM_172762	52202	Mm.28199	NM_172762	ENSMUSG00000033931	Rbm34	4930547K05Rik|6330444B11|D8Ertd233e	RNA binding motif protein 34	protein-coding
mm_131106.1	chr16	5007660	5007693	+	1	NA	intron (NR_045596, intron 1 of 2)	intron (NR_045596, intron 1 of 2)	360	NR_045596	432995	Mm.271618	NM_001253796	ENSMUSG00000096215	Smim22	EG432995|Gm5480	small integral membrane protein 22	protein-coding
mm_8069.1	chr1	135479956	135479969	-	1	NA	intron (NM_173437, intron 3 of 28)	L2c|LINE|L2	-25279	NR_049188	100885827		NR_049188	ENSMUSG00000093515	Mir1231	Gm23720|mir-1231|mmu-mir-1231	microRNA 1231	ncRNA
mm_132356.1	chr16	34649949	34649957	+	1	NA	Intergenic	Intergenic	-1258	NM_030744	76378	Mm.23515	NM_030744	ENSMUSG00000022832	Ropn1	1700008N21Rik|ODF6|RHPNAP1|Rppn|ropporin	ropporin, rhophilin associated protein 1	protein-coding
mm_9595.1	chr1	174921814	174921827	-	1	NA	promoter-TSS (NM_011825)	promoter-TSS (NM_011825)	-1	NM_011825	23893	Mm.25760	NM_011825	ENSMUSG00000050069	Grem2	Gremlin2|Prdc	gremlin 2, DAN family BMP antagonist	protein-coding
mm_7248.1	chr1	93654145	93654155	-	1	NA	Intergenic	MT2B1|LTR|ERVL	-18423	NM_021537	59041	Mm.28761	NM_021537	ENSMUSG00000026277	Stk25	1500019J11Rik|AU018434|C86992|Ste20-like|Ysk1	serine/threonine kinase 25 (yeast)	protein-coding
mm_5302.1	chr1	21325737	21325740	-	1	NA	Intergenic	LTR10_RN|LTR|ERVK	-23939	NM_183322	368204	Mm.26006	NM_183322	ENSMUSG00000067750	Khdc1a	AU014713|C88118|Ndg1	KH domain containing 1A	protein-coding
mm_25721.1	chr3	122729851	122729869	+	1	NA	intron (NM_153422, intron 1 of 20)	CpG	702	NM_153422	242202	Mm.134911	NM_153422	ENSMUSG00000053965	Pde5a	Cgbpde|Cn5n|PDE5a2|Pde5|Pde5a1	phosphodiesterase 5A, cGMP-specific	protein-coding
mm_65819.1	chr7	29155937	29155956	-	1	NA	exon (NM_001146023, exon 2 of 8)	exon (NM_001146023, exon 2 of 8)	264	NM_001146023	73833	Mm.260890	NM_028661	ENSMUSG00000030590	Fam98c	1110006G06Rik|AI836081|AV026483|B230110F21Rik	family with sequence similarity 98, member C	protein-coding
mm_144600.1	chr18	32377366	32377368	+	1	NA	5' UTR (NM_009668, exon 1 of 19)	5' UTR (NM_009668, exon 1 of 19)	150	NM_009668	30948	Mm.4383	NM_009668	ENSMUSG00000024381	Bin1	ALP-1|Amphl|BRAMP-2|SH3P9	bridging integrator 1	protein-coding
mm_92958.1	chr10	85916903	85917006	-	1	NA	promoter-TSS (NM_181650)	promoter-TSS (NM_181650)	32	NM_001302886	72843	Mm.25307	NM_181650	ENSMUSG00000035529	Prdm4	1700031E19Rik|2810470D21Rik|AW552272|SC-1|SC1	PR domain containing 4	protein-coding
mm_18558.1	chr2	65238442	65238497	-	1	NA	5' UTR (NM_177025, exon 1 of 14)	5' UTR (NM_177025, exon 1 of 14)	157	NM_177025	319876	Mm.34159	NM_027225	ENSMUSG00000034903	Cobll1	1810047P18Rik|Coblr1|D430044D16Rik	Cobl-like 1	protein-coding
mm_16464.1	chr2	180604883	180604896	+	1	NA	intron (NM_009936, intron 10 of 31)	intron (NM_009936, intron 10 of 31)	6667	NM_009936	12841	Mm.141312	NM_009936	ENSMUSG00000027570	Col9a3	AV006866	collagen, type IX, alpha 3	protein-coding
mm_155196.1	chrX	56469279	56469300	+	1	NA	intron (NM_172779, intron 2 of 16)	PB1D10|SINE|Alu	14450	NM_172779	236790	Mm.474772	NM_172779	ENSMUSG00000035967	Ints6l	4930535D10Rik|6330505F04Rik|D130066O12|Ddx26b	integrator complex subunit 6 like	protein-coding
mm_108793.1	chr12	91400991	91401022	+	1	NA	promoter-TSS (NM_001113404)	promoter-TSS (NM_001113404)	13	NM_011648	22095	Mm.173847	NM_011648	ENSMUSG00000020963	Tshr	AI481368|hypothroid|hyt|pet	thyroid stimulating hormone receptor	protein-coding
mm_10977.1	chr2	25777016	25777021	+	1	NA	promoter-TSS (NM_001100455)	promoter-TSS (NM_001100455)	1	NM_001100455	227630	Mm.27838	NM_001100455	ENSMUSG00000069080	Lcn11	Gm109	lipocalin 11	protein-coding
mm_99692.1	chr11	106084578	106084623	+	1	NA	promoter-TSS (NM_011947)	promoter-TSS (NM_011947)	-302	NM_011947	26406	Mm.27041	NM_011947	ENSMUSG00000020700	Map3k3	AW548911|MAPKKK3|Mekk3|mKIAA4031	mitogen-activated protein kinase kinase kinase 3	protein-coding
mm_157835.1	chrX	74275015	74275059	-	1	NA	promoter-TSS (NR_106059)	promoter-TSS (NR_106059)	-932	NR_106059	102466804		NR_106059	ENSMUSG00000099226	Mir7091	Gm27381|mmu-mir-7091	microRNA 7091	ncRNA
mm_58773.1	chr7	16004685	16004696	+	1	NA	Intergenic	Intergenic	-5195	NM_001081418	243842	Mm.440249	NM_001081418	ENSMUSG00000070808	Gltscr1	-	glioma tumor suppressor candidate region gene 1	protein-coding
mm_125802.1	chr15	74914699	74914709	+	1	NA	Intergenic	Intergenic	-33000	NM_025929	67038	Mm.154566	NM_025929	ENSMUSG00000063522	2010109I03Rik	Ly6m	RIKEN cDNA 2010109I03 gene	protein-coding
mm_170333.1	chr18	45032711	45032716	-	1	NA	Intergenic	L1Md_A|LINE|L1	204048	NM_001163013	240255	Mm.244482	NM_001163013	ENSMUSG00000034653	Ythdc2	3010002F02Rik|BC037178	YTH domain containing 2	protein-coding
mm_158988.1	chr1	133272242	133272242	+	1	NA	exon (NM_001160268, exon 8 of 23)	exon (NM_001160268, exon 8 of 23)	-2434	NR_037984	100502933	Mm.487491	NR_037984	ENSMUSG00000101693	Gm19461	-	predicted gene, 19461	ncRNA
mm_127101.1	chr15	97791474	97791493	+	1	NA	3' UTR (NM_026353, exon 3 of 3)	3' UTR (NM_026353, exon 3 of 3)	7118	NM_026353	67739	Mm.28955	NM_026353	ENSMUSG00000081534	Slc48a1	4930570C03Rik	solute carrier family 48 (heme transporter), member 1	protein-coding
mm_98766.1	chr11	96633768	96633795	+	1	NA	intron (NM_001033186, intron 4 of 12)	(T)n|Simple_repeat|Simple_repeat	143774	NM_028965	74479	Mm.270781	NM_028965	ENSMUSG00000020876	Snx11	4933439F10Rik|A930041K09Rik|AI117694	sorting nexin 11	protein-coding
mm_110511.1	chr12	54701730	54701730	-	1	NA	Intergenic	Intergenic	-5836	NM_025456	66266	Mm.156440	NM_025456	ENSMUSG00000054302	Eapp	1810011O16Rik	E2F-associated phosphoprotein	protein-coding
mm_63943.1	chr7	139834247	139834265	+	1	NA	promoter-TSS (NM_177469)	promoter-TSS (NM_177469)	82	NM_177469	52389	Mm.39863	NM_177469	ENSMUSG00000025475	Adgra1	2900059M17Rik|D7Ertd680e|Gpr123	adhesion G protein-coupled receptor A1	protein-coding
mm_39216.1	chr4	156186094	156186145	-	1	NA	intron (NM_021604, intron 2 of 35)	intron (NM_021604, intron 2 of 35)	11369	NM_021604	11603	Mm.273098	NM_021604	ENSMUSG00000041936	Agrn	Agrin|nmf380	agrin	protein-coding
mm_166086.1	chr4	138879402	138879410	+	1	NA	intron (NM_012044, intron 1 of 4)	intron (NM_012044, intron 1 of 4)	1464	NM_012044	26970	Mm.296007	NM_012044	ENSMUSG00000028751	Pla2g2e	-	phospholipase A2, group IIE	protein-coding
mm_27581.1	chr3	59101736	59101746	-	1	NA	promoter-TSS (NM_173398)	promoter-TSS (NM_173398)	80	NM_173398	229323	Mm.123648	NM_173398	ENSMUSG00000050075	Gpr171	A630006E05|F730001G15Rik|H963	G protein-coupled receptor 171	protein-coding
mm_41673.1	chr5	99682405	99682412	+	1	NA	intron (NR_030692, intron 1 of 3)	intron (NR_030692, intron 1 of 3)	46652	NR_030692	319818	Mm.295233	NR_030692	ENSMUSG00000089809	A930011G23Rik	-	RIKEN cDNA A930011G23 gene	ncRNA
mm_33433.1	chr4	130061145	130061164	+	1	NA	intron (NM_028266, intron 23 of 69)	intron (NM_028266, intron 23 of 69)	13314	NM_028266	107581	Mm.41860	NM_028266	ENSMUSG00000040690	Col16a1	2700007F12Rik|A530052M23Rik|AI838662|CA1F	collagen, type XVI, alpha 1	protein-coding
mm_80895.1	chr9	99629856	99629876	+	1	NA	5' UTR (NM_001311142, exon 1 of 16)	5' UTR (NM_001311142, exon 1 of 16)	288	NM_001311142	72507	Mm.221455	NM_028258	ENSMUSG00000037784	Dzip1l	2610524A10Rik|AI663976	DAZ interacting protein 1-like	protein-coding
mm_81340.1	chr9	108533586	108533609	+	1	NA	exon (NM_175143, exon 3 of 10)	exon (NM_175143, exon 3 of 10)	16510	NM_175143	69232	Mm.335449	NM_175143	ENSMUSG00000006673	Qrich1	2610028H07Rik	glutamine-rich 1	protein-coding
mm_24987.1	chr3	97032395	97032408	+	1	NA	promoter-TSS (NM_008121)	promoter-TSS (NM_008121)	-1	NM_001271628	14613	Mm.281816	NM_008121	ENSMUSG00000057123	Gja5	5730555N10Rik|Cnx40|Cx40|Gja-5	gap junction protein, alpha 5	protein-coding
mm_166634.1	chr6	80185715	80185747	-	1	NA	intron (NM_001347261, intron 2 of 2)	intron (NM_001347261, intron 2 of 2)	166088	NM_178731	243499	Mm.483425	NM_178731	ENSMUSG00000052581	Lrrtm4	7530419J18Rik|A230052N11	leucine rich repeat transmembrane neuronal 4	protein-coding
mm_162777.1	chr10	69534185	69534202	+	1	NA	5' UTR (NM_170688, exon 1 of 43)	5' UTR (NM_170688, exon 1 of 43)	485	NM_146005	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_118446.1	chr14	8213998	8214039	+	1	NA	promoter-TSS (NM_001305936)	promoter-TSS (NM_001305936)	-63	NM_027782	71393	Mm.292712	NM_027782	ENSMUSG00000021752	Kctd6	5430433B02Rik|AU044285	potassium channel tetramerisation domain containing 6	protein-coding
mm_157141.1	chrX	9459442	9459463	-	1	NA	intron (NM_007807, intron 3 of 12)	intron (NM_007807, intron 3 of 12)	9872	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_5034.1	chr1	193302067	193302082	+	1	NA	promoter-TSS (NM_001277928)	promoter-TSS (NM_001277928)	80	NM_008484	16780	Mm.435441	NM_008484	ENSMUSG00000026639	Lamb3	-	laminin, beta 3	protein-coding
mm_49763.1	chr6	34780837	34780905	+	1	NA	5' UTR (NM_001289656, exon 1 of 20)	5' UTR (NM_001289656, exon 1 of 20)	439	NM_001289656	76223	Mm.150047	NM_178630	ENSMUSG00000038836	Agbl3	2900053G10Rik|4930431N21Rik|6530406M24Rik|CCP3	ATP/GTP binding protein-like 3	protein-coding
mm_127086.1	chr15	97731275	97731278	+	1	NA	5' UTR (NM_001168693, exon 1 of 10)	5' UTR (NM_001168693, exon 1 of 10)	129	NM_001168693	19011	Mm.1001	NM_008902	ENSMUSG00000022468	Endou	Pp11r|Tcl-30	endonuclease, polyU-specific	protein-coding
mm_81612.1	chr9	110766229	110766242	+	1	NA	intron (NM_010859, intron 1 of 6)	intron (NM_010859, intron 1 of 6)	2554	NM_010859	17897	Mm.7353	NM_010859	ENSMUSG00000059741	Myl3	MLC1s|MLC1v|Mylc|VLC1	myosin, light polypeptide 3	protein-coding
mm_123225.1	chr14	59597965	59597973	-	1	NA	promoter-TSS (NM_027986)	promoter-TSS (NM_027986)	-10	NM_001168536	71891	Mm.439850	NM_027986	ENSMUSG00000021982	Cdadc1	2310010M10Rik|AI449174|AI463398|BB130816|NYD-SP15	cytidine and dCMP deaminase domain containing 1	protein-coding
mm_10168.1	chr2	4559603	4559629	+	1	NA	promoter-TSS (NM_001177844)	promoter-TSS (NM_001177844)	-138	NM_001177844	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding
mm_133164.1	chr16	70437682	70437685	+	1	NA	intron (NM_028803, intron 6 of 15)	intron (NM_028803, intron 6 of 15)	123734	NM_028803	74185	Mm.396102	NM_028803	ENSMUSG00000022707	Gbe1	2310045H19Rik|2810426P10Rik|D16Ertd536e	glucan (1,4-alpha-), branching enzyme 1	protein-coding
mm_114125.1	chr13	55210316	55210357	+	1	NA	intron (NM_008739, intron 1 of 22)	CpG	554	NM_008739	18193	Mm.12964	NM_008739	ENSMUSG00000021488	Nsd1	AI528500|KMT3B	nuclear receptor-binding SET-domain protein 1	protein-coding
mm_155076.1	chrX	46328971	46328979	+	1	NA	promoter-TSS (NR_045440)	promoter-TSS (NR_045440)	-32	NM_028514	73360	Mm.60929	NM_028514	ENSMUSG00000046615	Actrt1	1700061J02Rik|Arp-T1	actin-related protein T1	protein-coding
mm_84510.1	chr9	67031475	67031527	-	1	NA	exon (NM_001164251, exon 7 of 10)	exon (NM_001164251, exon 7 of 10)	12370	NM_001164252	22003	Mm.121878	NM_024427	ENSMUSG00000032366	Tpm1	AA986836|AI854628|TM2|Tm3|Tmpa|Tpm-1|alpha-TM	tropomyosin 1, alpha	protein-coding
mm_140870.1	chr17	23786092	23786122	-	1	NA	promoter-TSS (NM_029798)	promoter-TSS (NM_029798)	-30	NM_029798	76917	Mm.269613	NM_029798	ENSMUSG00000023911	Flywch2	2810417J12Rik|3010014L17Rik|AW548203	FLYWCH family member 2	protein-coding
mm_119196.1	chr14	32599385	32599400	+	1	NA	promoter-TSS (NM_001001796)	promoter-TSS (NM_001001796)	-16	NM_001347590	107751	Mm.119274	NM_001001796	ENSMUSG00000041730	Prrxl1	Drg11|Drgx	paired related homeobox protein-like 1	protein-coding
mm_66503.1	chr7	45091684	45091705	-	1	NA	intron (NM_026555, intron 1 of 6)	intron (NM_026555, intron 1 of 6)	519	NM_026555	52377	Mm.29997	NM_026555	ENSMUSG00000019539	Rcn3	6030455P07Rik|D530026G20Rik|D7Ertd671e|RLP49	reticulocalbin 3, EF-hand calcium binding domain	protein-coding
mm_124840.1	chr15	9370381	9370391	+	1	NA	3' UTR (NM_144845, exon 7 of 7)	3' UTR (NM_144845, exon 7 of 7)	34788	NM_144845	223337	Mm.422853	NM_144845	ENSMUSG00000049152	Ugt3a2	AI313915	UDP glycosyltransferases 3 family, polypeptide A2	protein-coding
mm_116489.1	chr13	44480320	44480333	-	1	NA	Intergenic	Intergenic	40599	NR_045489	69491	Mm.392410	NR_045489	ENSMUSG00000098144	1700029N11Rik	-	RIKEN cDNA 1700029N11 gene	ncRNA
mm_57074.1	chr6	122578452	122578462	-	1	NA	3' UTR (NM_031159, exon 8 of 8)	3' UTR (NM_031159, exon 8 of 8)	23987	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_41539.1	chr5	92856472	92856511	+	1	NA	intron (NM_001077595, intron 1 of 9)	intron (NM_001077595, intron 1 of 9)	-41502	NM_001077596	27428	Mm.46014	NM_015756	ENSMUSG00000029381	Shroom3	AL022960|D5Ertd287e|Shrm|Shrm3	shroom family member 3	protein-coding
mm_75945.1	chr8	71579045	71579049	-	1	NA	intron (NM_011977, intron 3 of 13)	ZP3AR|Satellite|Satellite	10120	NM_011977	26457	Mm.38165	NM_011977	ENSMUSG00000031808	Slc27a1	FATP1|Fatp	solute carrier family 27 (fatty acid transporter), member 1	protein-coding
mm_71108.1	chr8	35602915	35602920	+	1	NA	intron (NM_001081279, intron 1 of 2)	B1F|SINE|Alu	-13897	NR_040376	100504714	Mm.381744	NR_040376	ENSMUSG00000097357	Gm16793	-	predicted gene, 16793	ncRNA
mm_31977.1	chr4	88868475	88868500	+	1	NA	Intergenic	Intergenic	11714	NM_177348	230405	Mm.246593	NM_177348	ENSMUSG00000045364	Ifne	Ifn-tau-1|Ifne1|Ifnt1|Infe1	interferon epsilon	protein-coding
mm_122079.1	chr14	30607780	30607804	-	1	NA	intron (NM_011103, intron 3 of 17)	intron (NM_011103, intron 3 of 17)	2518	NM_001310682	18753	Mm.2314	NM_011103	ENSMUSG00000021948	Prkcd	AI385711|D14Ertd420e|PKC[d]|PKCdelta|Pkcd	protein kinase C, delta	protein-coding
mm_87920.1	chr10	62505858	62505860	+	1	NA	intron (NM_011157, intron 1 of 2)	B1_Mur2|SINE|Alu	1896	NM_011157	19073	Mm.338790	NM_011157	ENSMUSG00000020077	Srgn	Prg|Prg1|Sgc	serglycin	protein-coding
mm_114382.1	chr13	63240546	63240567	+	1	NA	intron (NR_110520, intron 2 of 5)	intron (NR_110520, intron 2 of 5)	527	NR_110521	72061	Mm.188105	NM_028079	ENSMUSG00000021458	2010111I01Rik	2300006M17Rik|AP-O|AW742919|Aopep|ApO|mir-23b|mir-24-1|mir-27b	RIKEN cDNA 2010111I01 gene	protein-coding
mm_64142.1	chr7	141216627	141216644	+	1	NA	intron (NM_025886, intron 1 of 5)	intron (NM_025886, intron 1 of 5)	775	NM_025886	66985	Mm.21202	NM_025886	ENSMUSG00000038618	Rassf7	2400009B11Rik|AW210608	Ras association (RalGDS/AF-6) domain family (N-terminal) member 7	protein-coding
mm_82698.1	chr9	22390481	22390510	-	1	NA	Intergenic	Intergenic	-1289	NM_028390	68743	Mm.282751	NM_028390	ENSMUSG00000036777	Anln	1110037A17Rik|2900037I21Rik|C78101|Scraps	anillin, actin binding protein	protein-coding
mm_171826.1	chr5	143086270	143086288	-	1	NA	intron (NM_080561, intron 6 of 16)	intron (NM_080561, intron 6 of 16)	26741	NM_207110	108086	Mm.381440	NM_080561	ENSMUSG00000045078	Rnf216	2810055G22Rik|AI647468|AU019462|C86502|F830018F18Rik|TRIAD3|UIP83|Ubce7ip1	ring finger protein 216	protein-coding
mm_137743.1	chr17	29369182	29369202	+	1	NA	intron (NM_001159538, intron 8 of 15)	intron (NM_001159538, intron 8 of 15)	8278	NM_001159538	26382	Mm.279187	NM_013710	ENSMUSG00000024013	Fgd2	Tcd-2|Tcd2|ZFYVE4|tcs-2|tcs2	FYVE, RhoGEF and PH domain containing 2	protein-coding
mm_149755.1	chr19	22733539	22733543	+	1	NA	intron (NM_001035243, intron 6 of 23)	intron (NM_001035243, intron 6 of 23)	-17064	NR_029591	387200		NR_029591	ENSMUSG00000065507	Mir204	Mirn204|mir-204|mmu-mir-204	microRNA 204	ncRNA
mm_81537.1	chr9	110197721	110197725	+	1	NA	exon (NM_009211, exon 21 of 28)	exon (NM_009211, exon 21 of 28)	-46060	NM_013884	29873	Mm.38496	NM_013884	ENSMUSG00000032482	Cspg5	Caleb|Ngc	chondroitin sulfate proteoglycan 5	protein-coding
mm_34381.1	chr4	144906986	144907115	+	1	NA	intron (NM_011303, intron 1 of 5)	intron (NM_011303, intron 1 of 5)	13913	NM_011303	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding
mm_22023.1	chr2	168010656	168010663	-	1	NA	promoter-TSS (NM_001080708)	promoter-TSS (NM_001080708)	-66	NM_001080708	69553	Mm.68454	NM_001080708	ENSMUSG00000074577	Fam65c	2310033K02Rik|Gm124	family with sequence similarity 65, member C	protein-coding
mm_74644.1	chr8	13306661	13306661	-	1	NA	intron (NM_172282, intron 7 of 12)	intron (NM_172282, intron 7 of 12)	-18535	NM_001042650	102323	Mm.368890	NM_001024504	ENSMUSG00000038506	Dcun1d2	AW495713|mFLJ10704	DCN1, defective in cullin neddylation 1, domain containing 2 (S. cerevisiae)	protein-coding
mm_61432.1	chr7	73816569	73816579	+	1	NA	promoter-TSS (NR_077222)	promoter-TSS (NR_077222)	-71	NR_077222	100579147	Mm.109205	NR_077222	ENSMUSG00000074067	Gm10619	4932443D20|ENSMUSG00000074067	predicted gene 10619	ncRNA
mm_103305.1	chr11	72608449	72608475	-	1	NA	intron (NM_025985, intron 1 of 5)	CpG	1201	NM_025985	67128	Mm.458052	NM_025985	ENSMUSG00000020794	Ube2g1	2700059C12Rik|AI256795|AU014992|AW552068|D130023C12Rik	ubiquitin-conjugating enzyme E2G 1	protein-coding
mm_92551.1	chr10	79762510	79762536	-	1	NA	exon (NM_144528, exon 3 of 9)	exon (NM_144528, exon 3 of 9)	4429	NM_144528	70294	Mm.466670	NM_144528	ENSMUSG00000035890	Rnf126	2610010O19Rik	ring finger protein 126	protein-coding
mm_24378.1	chr3	90248196	90248228	+	1	NA	promoter-TSS (NM_013901)	promoter-TSS (NM_013901)	20	NM_013901	30791	Mm.294709	NM_013901	ENSMUSG00000052310	Slc39a1	Zip1|Zirtl	solute carrier family 39 (zinc transporter), member 1	protein-coding
mm_56239.1	chr6	90670470	90670495	-	1	NA	exon (NM_001134384, exon 9 of 14)	exon (NM_001134384, exon 9 of 14)	46047	NM_001134383	232227	Mm.196943	NM_182784	ENSMUSG00000034312	Iqsec1	AW561907|BC026481|BRAG2|D6Ertd349e|cI-43	IQ motif and Sec7 domain 1	protein-coding
mm_93996.1	chr10	127539372	127539378	-	1	NA	exon (NM_008512, exon 88 of 89)	exon (NM_008512, exon 88 of 89)	-4816	NM_183297	104080	Mm.437200	NM_183297	ENSMUSG00000040258	Nxph4	1110036M10Rik|AI851051	neurexophilin 4	protein-coding
mm_156846.1	chrX	164391729	164391735	+	1	NA	exon (NM_010216, exon 3 of 7)	exon (NM_010216, exon 3 of 7)	18210	NM_010216	14205	Mm.297978	NM_010216	ENSMUSG00000031380	Vegfd	AI325264|Figf|VEGF-D	vascular endothelial growth factor D	protein-coding
mm_80844.1	chr9	98287450	98287460	+	1	NA	Intergenic	RLTR10B|LTR|ERVK	-9128	NM_144533	74080	Mm.294082	NM_144533	ENSMUSG00000032456	Nmnat3	4933408N02Rik|PNAT3	nicotinamide nucleotide adenylyltransferase 3	protein-coding
mm_2927.1	chr1	132226314	132226348	+	1	NA	promoter-TSS (NM_001311102)	promoter-TSS (NM_001311102)	17	NM_001311103	213409	Mm.426321	NM_001033250	ENSMUSG00000079330	Lemd1	4930540I23Rik|6430514M23Rik|AI428128|LEMP-1	LEM domain containing 1	protein-coding
mm_91278.1	chr10	24692415	24692429	-	1	NA	intron (NM_001308327, intron 1 of 24)	intron (NM_001308327, intron 1 of 24)	19737	NM_001308327	18605	Mm.27254	NM_008813	ENSMUSG00000037370	Enpp1	4833416E15Rik|AI428932|C76301|CD203c|E-NPP 1|E-NPP1|Ly-41|M6S1|NPP1|Npps|PC-1|Pca|Pca-1|Pdnp1|ttw|twy	ectonucleotide pyrophosphatase/phosphodiesterase 1	protein-coding
mm_107316.1	chr12	31265473	31265484	+	1	NA	exon (NM_008482, exon 1 of 33)	exon (NM_008482, exon 1 of 33)	184	NM_008482	16777	Mm.172674	NM_008482	ENSMUSG00000002900	Lamb1	C77966|C80098|C81607|D130003D08Rik|Lamb-1|Lamb1-1	laminin B1	protein-coding
mm_112597.1	chr13	14091011	14091016	+	1	NA	intron (NM_198122, intron 2 of 22)	B1_Mm|SINE|Alu	27229	NM_198122	94246	Mm.439784	NM_194262	ENSMUSG00000039219	Arid4b	BCAA|BRCAA1|RBBP1L1|Rbp1l1|SAP180	AT rich interactive domain 4B (RBP1-like)	protein-coding
mm_99809.1	chr11	108381205	108381229	+	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	-14080	NM_013475	11818	Mm.2266	NM_013475	ENSMUSG00000000049	Apoh	B2GPI|beta-2-GPI|beta2-GPI	apolipoprotein H	protein-coding
mm_120694.1	chr14	70890032	70890038	+	1	NA	promoter-TSS (NM_008115)	promoter-TSS (NM_008115)	-72	NM_001302095	14586	Mm.32619	NM_008115	ENSMUSG00000022103	Gfra2	-	glial cell line derived neurotrophic factor family receptor alpha 2	protein-coding
mm_129197.1	chr15	76509650	76509683	-	1	NA	intron (NM_010046, intron 1 of 16)	intron (NM_010046, intron 1 of 16)	2152	NM_010046	13350	Mm.22633	NM_010046	ENSMUSG00000022555	Dgat1	ARAT|C75990|D15Ertd23e|Dgat	diacylglycerol O-acyltransferase 1	protein-coding
mm_152286.1	chr19	8929324	8929337	-	1	NA	promoter-TSS (NM_144872)	promoter-TSS (NM_144872)	26	NM_009073	19881	Mm.426094	NM_009073	ENSMUSG00000071648	Rom1	M101156|Rgsc1156|Rom-1|Rosp1|Tspan23	rod outer segment membrane protein 1	protein-coding
mm_14592.1	chr2	136058081	136058102	+	1	NA	5' UTR (NM_029530, exon 1 of 6)	5' UTR (NM_029530, exon 1 of 6)	164	NM_029530	76161	Mm.41638	NM_029530	ENSMUSG00000027270	Lamp5	3110035N03Rik|6330527O06Rik|BAD-LAMP|LAMP-5	lysosomal-associated membrane protein family, member 5	protein-coding
mm_133975.1	chr16	4475162	4475222	-	1	NA	Intergenic	CpG	47861	NM_175347	106393	Mm.35811	NM_175347	ENSMUSG00000022519	Srl	9830004M20Rik|AW108387|sar	sarcalumenin	protein-coding
mm_39061.1	chr4	154025658	154025686	-	1	NA	TTS (NM_001033455)	TTS (NM_001033455)	372	NM_001163722	68859	Mm.477488	NM_001033144	ENSMUSG00000078350	Smim1	0610011H04Rik|1190007F08Rik|2700009I11Rik	small integral membrane protein 1	protein-coding
mm_165398.1	chr2	136012009	136012014	+	1	NA	intron (NM_013829, intron 36 of 36)	intron (NM_013829, intron 36 of 36)	-45916	NM_029530	76161	Mm.41638	NM_029530	ENSMUSG00000027270	Lamp5	3110035N03Rik|6330527O06Rik|BAD-LAMP|LAMP-5	lysosomal-associated membrane protein family, member 5	protein-coding
mm_76514.1	chr8	87469906	87469922	-	1	NA	3' UTR (NM_019626, exon 3 of 3)	3' UTR (NM_019626, exon 3 of 3)	2678	NM_019626	12404	Mm.4880	NM_019626	ENSMUSG00000031654	Cbln1	AI323299	cerebellin 1 precursor protein	protein-coding
mm_36761.1	chr4	101356360	101356503	-	1	NA	promoter-TSS (NR_040708)	promoter-TSS (NR_040708)	-183	NR_040708	77866	Mm.137053	NR_040708	ENSMUSG00000086782	E130102H24Rik	-	RIKEN cDNA E130102H24 gene	ncRNA
mm_101125.1	chr11	12037392	12037407	-	1	NA	promoter-TSS (NM_010345)	promoter-TSS (NM_010345)	21	NM_010345	14783	Mm.273117	NM_010345	ENSMUSG00000020176	Grb10	5730571D09Rik|AI325020|Meg1|mKIAA0207	growth factor receptor bound protein 10	protein-coding
mm_115036.1	chr13	99369759	99369764	+	1	NA	intron (NM_173757, intron 4 of 10)	intron (NM_173757, intron 4 of 10)	24975	NM_173757	218506	Mm.30208	NM_173757	ENSMUSG00000041632	Mrps27	2610028H14Rik	mitochondrial ribosomal protein S27	protein-coding
mm_10386.1	chr2	12924054	12924113	+	1	NA	promoter-TSS (NM_008961)	promoter-TSS (NM_008961)	42	NM_001305437	19212	Mm.229322	NM_008961	ENSMUSG00000026730	Pter	AI790318|Mpr56-1	phosphotriesterase related	protein-coding
mm_28332.1	chr3	89382948	89382960	-	1	NA	intron (NM_009565, intron 1 of 2)	MIRb|SINE|MIR	-8910	NR_040403	545539	Mm.393389	NR_040403	ENSMUSG00000074466	Gm15417	ENSMUSG00000074466|OTTMUSG00000021274	predicted gene 15417	ncRNA
mm_6375.1	chr1	72537186	72537199	-	1	NA	promoter-TSS (NM_001045533)	promoter-TSS (NM_001045533)	-628	NM_001045533	381270	Mm.337023	NM_001045533	ENSMUSG00000039372	March4	BC056494|mKIAA1399	membrane-associated ring finger (C3HC4) 4	protein-coding
mm_172653.1	chr8	3584234	3584252	-	1	NA	exon (NM_001024728, exon 6 of 6)	exon (NM_001024728, exon 6 of 6)	-3207	NM_001347112	69697	Mm.390010	NM_027171	ENSMUSG00000044433	Camsap3	2310057J16Rik|Kiaa1543|Nezha	calmodulin regulated spectrin-associated protein family, member 3	protein-coding
mm_8241.1	chr1	138494175	138494200	-	1	NA	intron (NM_001311148, intron 7 of 7)	intron (NM_001311148, intron 7 of 7)	125570	NM_021605	59125	Mm.143817	NM_021605	ENSMUSG00000026393	Nek7	2810460C19Rik|AU020186	NIMA (never in mitosis gene a)-related expressed kinase 7	protein-coding
mm_70437.1	chr8	11644662	11644664	+	1	NA	Intergenic	RLTR1B|LTR|ERV1	-8906	NM_001281974	102334	Mm.12459	NM_133971	ENSMUSG00000031508	Ankrd10	4833425P12Rik|AW549277	ankyrin repeat domain 10	protein-coding
mm_161031.1	chr12	13362298	13362298	+	1	NA	intron (NM_027706, intron 24 of 51)	intron (NM_027706, intron 24 of 51)	93171	NM_027706	71169	Mm.177520	NM_027706	ENSMUSG00000020576	Nbas	4933425L03Rik|Nag	neuroblastoma amplified sequence	protein-coding
mm_5835.1	chr1	52817797	52817823	-	1	NA	promoter-TSS (NM_008384)	promoter-TSS (NM_008384)	-122	NM_008384	16329	Mm.917	NM_008384	ENSMUSG00000026102	Inpp1	2300002C06Rik|AV137389	inositol polyphosphate-1-phosphatase	protein-coding
mm_8551.1	chr1	155230192	155230200	-	1	NA	Intergenic	Intergenic	71493	NM_021433	58244	Mm.66264	NM_021433	ENSMUSG00000026470	Stx6	2310039E05Rik|2410005I16Rik|AA437559|AI415714|AI845861	syntaxin 6	protein-coding
mm_21502.1	chr2	163509631	163509644	-	1	NA	intron (NM_001312907, intron 1 of 10)	intron (NM_001312907, intron 1 of 10)	2780	NM_001312907	15378	Mm.202383	NM_008261	ENSMUSG00000017950	Hnf4a	HNF-4|Hnf4|Hnf4alpha|MODY1|Nr2a1|TCF-14|Tcf14	hepatic nuclear factor 4, alpha	protein-coding
mm_114077.1	chr13	54503787	54503800	+	1	NA	promoter-TSS (NM_176987)	promoter-TSS (NM_176987)	-12	NM_176987	319719	Mm.376151	NM_176987	ENSMUSG00000043183	Simc1	4732471D19Rik	SUMO-interacting motifs containing 1	protein-coding
mm_73131.1	chr8	94923688	94923708	+	1	NA	promoter-TSS (NM_001145972)	promoter-TSS (NM_001145972)	4	NM_001145972	382045	Mm.334726	NM_001033468	ENSMUSG00000061577	Adgrg5	Gm1109|Gpr114|PGR27	adhesion G protein-coupled receptor G5	protein-coding
mm_99904.1	chr11	109668581	109668668	+	1	NA	3' UTR (NM_001313974, exon 11 of 11)	3' UTR (NM_001313974, exon 11 of 11)	17703	NM_001313976	19084	Mm.30039	NM_021880	ENSMUSG00000020612	Prkar1a	1300018C22Rik|RIalpha|Tse-1|Tse1	protein kinase, cAMP dependent regulatory, type I, alpha	protein-coding
mm_12377.1	chr2	69822951	69822969	+	1	NA	intron (NM_177784, intron 1 of 3)	CpG	590	NM_177784	277396	Mm.138073	NM_177784	ENSMUSG00000042155	Klhl23	C130068N17Rik	kelch-like 23	protein-coding
mm_83753.1	chr9	51278541	51278576	-	1	NA	promoter-TSS (NM_001195681)	promoter-TSS (NM_001195681)	-4	NM_001195681	100502940	Mm.235705	NM_001195681	ENSMUSG00000079559	Gm684	-	predicted gene 684	protein-coding
mm_135914.1	chr16	67602558	67602578	-	1	NA	intron (NM_178721, intron 1 of 9)	intron (NM_178721, intron 1 of 9)	18340	NM_001347247	239857	Mm.394300	NM_178721	ENSMUSG00000064115	Cadm2	2900078E11Rik|9330131D06|A830029E02Rik|Igdf4d|Igsf4d|NECL3|SynCAM 2|SynCAM2	cell adhesion molecule 2	protein-coding
mm_11554.1	chr2	32737359	32737389	+	1	NA	intron (NM_027529, intron 2 of 2)	MIR|SINE|MIR	3642	NM_027529	70730	Mm.401360	NM_027529	ENSMUSG00000009551	6330409D20Rik	AA517851	RIKEN cDNA 6330409D20 gene	protein-coding
mm_66995.1	chr7	64374072	64374109	-	1	NA	promoter-TSS (NM_177893)	promoter-TSS (NM_177893)	5	NM_177893	330554	Mm.236510	NM_177893	ENSMUSG00000033458	Fan1	6030441H18Rik|Mtmr15|mFAN1	FANCD2/FANCI-associated nuclease 1	protein-coding
mm_99530.1	chr11	103181699	103181702	+	1	NA	intron (NM_019679, intron 3 of 26)	intron (NM_019679, intron 3 of 26)	10562	NM_019679	57778	Mm.138913	NM_019679	ENSMUSG00000055805	Fmnl1	8030453N10Rik|AI553564|Fmnl|Fnrl|Frls	formin-like 1	protein-coding
mm_28632.1	chr3	95190763	95190767	-	1	NA	intron (NM_029885, intron 7 of 9)	intron (NM_029885, intron 7 of 9)	26426	NM_011351	20360	Mm.23662	NM_011351	ENSMUSG00000038777	Sema6c	Semay|mKIAA1869	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C	protein-coding
mm_13065.1	chr2	91115694	91115702	+	1	NA	TTS (NM_011355)	TTS (NM_011355)	-2446	NM_008653	17868	Mm.10728	NM_008653	ENSMUSG00000002100	Mybpc3	-	myosin binding protein C, cardiac	protein-coding
mm_67685.1	chr7	89338913	89338919	-	1	NA	promoter-TSS (NM_028343)	promoter-TSS (NM_028343)	-129	NM_028343	72759	Mm.208477	NM_028343	ENSMUSG00000039428	Tmem135	2810439K08Rik|AW319712|PMP52	transmembrane protein 135	protein-coding
mm_30488.1	chr3	155093194	155093240	-	1	NA	promoter-TSS (NM_028938)	promoter-TSS (NM_028938)	161	NM_029330	75540	Mm.35218	NM_029330	ENSMUSG00000053870	Fpgt	1700016E03Rik	fucose-1-phosphate guanylyltransferase	protein-coding
mm_17115.1	chr2	24472596	24472601	-	1	NA	intron (NM_011040, intron 2 of 11)	intron (NM_011040, intron 2 of 11)	3001	NM_011040	18510	Mm.2533	NM_011040	ENSMUSG00000026976	Pax8	Pax-8	paired box 8	protein-coding
mm_17819.1	chr2	33755268	33755285	-	1	NA	intron (NM_175184, intron 7 of 9)	intron (NM_175184, intron 7 of 9)	-50540	NR_045729	320482	Mm.442057	NR_045729	ENSMUSG00000086484	Nron	A630071L07Rik|Gm24353	non-protein coding RNA, repressor of NFAT	ncRNA
mm_47095.1	chr5	117909519	117909523	-	1	NA	intron (NM_008712, intron 10 of 27)	ORR1A1|LTR|ERVL-MaLR	42682	NM_008712	18125	Mm.44249	NM_008712	ENSMUSG00000029361	Nos1	2310005C01Rik|N-NOS|NC-NOS|NO|NOS|NOS-I|Nos-1|bNOS|nNOS	nitric oxide synthase 1, neuronal	protein-coding
mm_2403.1	chr1	93754953	93755029	+	1	NA	promoter-TSS (NM_025920)	promoter-TSS (NM_025920)	-42	NM_174874	66615	Mm.29087	NM_174874	ENSMUSG00000026280	Atg4b	2510009N07Rik|AW048066|Apg4b|Atg4bl|Autl1	autophagy related 4B, cysteine peptidase	protein-coding
mm_143036.1	chr17	56709841	56709889	-	1	NA	intron (NR_045519, intron 14 of 16)	intron (NR_045519, intron 14 of 16)	7056	NM_178926	106639	Mm.37290	NM_178926	ENSMUSG00000054723	Vmac	AI662250	vimentin-type intermediate filament associated coiled-coil protein	protein-coding
mm_10333.1	chr2	11554024	11554040	+	1	NA	promoter-TSS (NM_001177758)	promoter-TSS (NM_001177758)	-103	NM_001177758	170768	Mm.19669	NM_133232	ENSMUSG00000026773	Pfkfb3	E330010H22Rik|iPFK-2|uPFK-2	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	protein-coding
mm_145715.1	chr18	62977855	62977931	+	1	NA	promoter-TSS (NM_028017)	promoter-TSS (NM_028017)	-23	NM_028017	108123	Mm.292687	NM_028017	ENSMUSG00000024581	Napg	2400003O04Rik|SNARE	N-ethylmaleimide sensitive fusion protein attachment protein gamma	protein-coding
mm_49528.1	chr6	30047980	30048049	+	1	NA	promoter-TSS (NM_001164227)	promoter-TSS (NM_001164227)	26	NM_001164226	18181	Mm.259258	NM_010938	ENSMUSG00000058440	Nrf1	C87038|D6Ertd415e	nuclear respiratory factor 1	protein-coding
mm_97193.1	chr11	75576938	75576950	+	1	NA	3' UTR (NM_001199283, exon 14 of 14)	3' UTR (NM_001199283, exon 14 of 14)	-11135	NM_008850	18738	Mm.3128	NM_008850	ENSMUSG00000017781	Pitpna	Pitpn|vb|vibrator	phosphatidylinositol transfer protein, alpha	protein-coding
mm_15288.1	chr2	155276917	155276930	+	1	NA	intron (NR_046364, intron 1 of 2)	CpG	559	NR_046364	66734	Mm.196239	NM_025735	ENSMUSG00000027602	Map1lc3a	1010001H21Rik|4922501H04Rik|LC3|LC3a	microtubule-associated protein 1 light chain 3 alpha	protein-coding
mm_130242.1	chr15	96638186	96638199	-	1	NA	intron (NM_001166458, intron 1 of 15)	intron (NM_001166458, intron 1 of 15)	3770	NM_134086	105727	Mm.103568	NM_134086	ENSMUSG00000023169	Slc38a1	AA408026|AA409865|AL022800|AU015942|NAT2	solute carrier family 38, member 1	protein-coding
mm_101032.1	chr11	8587259	8587306	-	1	NA	intron (NM_001083587, intron 3 of 30)	intron (NM_001083587, intron 3 of 30)	77253	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_136116.1	chr16	85801281	85801284	-	1	NA	intron (NM_009621, intron 1 of 8)	intron (NM_009621, intron 1 of 8)	1831	NM_009621	11504	Mm.1421	NM_009621	ENSMUSG00000022893	Adamts1	ADAM-TS1|ADAMTS|ADAMTS-1|C3-C5|METH-1|METH1	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 1	protein-coding
mm_2122.1	chr1	87900467	87900489	+	1	NA	intron (NM_177646, intron 3 of 29)	Lx7|LINE|L1	-46179	NR_136921	100503175	Mm.426422	NR_136921	ENSMUSG00000101942	Gm19582	-	predicted gene, 19582	ncRNA
mm_117964.1	chr13	99516538	99516579	-	1	NA	promoter-TSS (NM_008634)	promoter-TSS (NM_008634)	44	NM_008634	17755	Mm.4173	NM_008634	ENSMUSG00000052727	Map1b	A230055D22|AI843217|LC1|MAP5|Mtap-5|Mtap1b|Mtap5	microtubule-associated protein 1B	protein-coding
mm_134934.1	chr16	31142079	31142104	-	1	NA	intron (NM_030138, intron 4 of 22)	intron (NM_030138, intron 4 of 22)	59147	NM_030138	78618	Mm.274646	NM_030138	ENSMUSG00000049076	Acap2	4832442G16|9530039J15Rik|CNT-B2|Centb2|mKIAA0041	ArfGAP with coiled-coil, ankyrin repeat and PH domains 2	protein-coding
mm_104347.1	chr11	94253845	94253878	-	1	NA	Intergenic	Intergenic	-11282	NM_181819	278507	Mm.342216	NM_181819	ENSMUSG00000044177	Wfikkn2	2610304F08Rik|AY100450|Gasp1|WFIKKNRP	WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 2	protein-coding
mm_100812.1	chr11	5099085	5099095	-	1	NA	promoter-TSS (NM_177370)	promoter-TSS (NM_177370)	-2	NM_001283061	14030	Mm.142822	NM_007968	ENSMUSG00000009079	Ewsr1	Ews|Ewsh	Ewing sarcoma breakpoint region 1	protein-coding
mm_62501.1	chr7	101993262	101993276	+	1	NA	exon (NM_133947, exon 7 of 25)	exon (NM_133947, exon 7 of 25)	23426	NM_133947	101706	Mm.27259	NM_133947	ENSMUSG00000066306	Numa1	6720401E04Rik|AA764025|AL022610|AU014979|NuMA	nuclear mitotic apparatus protein 1	protein-coding
mm_120959.1	chr14	77520141	77520169	+	1	NA	intron (NM_001253759, intron 7 of 19)	RLTR25A|LTR|ERVK	-13287	NR_033141	629678	Mm.390721	NM_001037935	ENSMUSG00000067973	Gm6994	EG629678	predicted gene 6994	ncRNA
mm_5953.1	chr1	56971268	56971278	-	1	NA	promoter-TSS (NR_024325)	promoter-TSS (NR_024325)	61	NM_139146	212712	Mm.145599	NM_139146	ENSMUSG00000038331	Satb2	mKIAA1034	special AT-rich sequence binding protein 2	protein-coding
mm_96530.1	chr11	68539603	68539627	+	1	NA	intron (NM_001004435, intron 13 of 19)	intron (NM_001004435, intron 13 of 19)	-16571	NM_146004	215723	Mm.131205	NM_146004	ENSMUSG00000048329	Mfsd6l	-	major facilitator superfamily domain containing 6-like	protein-coding
mm_160698.1	chr10	41071658	41071658	-	1	NA	promoter-TSS (NM_199058)	promoter-TSS (NM_199058)	-74	NM_199058	140741	Mm.290693	NM_199058	ENSMUSG00000046922	Gpr6	AI852874|Gm233	G protein-coupled receptor 6	protein-coding
mm_23040.1	chr3	34764144	34764152	+	1	NA	Intergenic	Intergenic	-7927	NR_110488	102638436	Mm.261793	NR_110488	ENSMUSG00000106519	Gm38509	Peril	predicted gene, 38509	ncRNA
mm_85489.1	chr9	106133514	106133519	-	1	NA	Intergenic	RMER15|LTR|ERVL	-20608	NR_029549	387153		NR_029549	ENSMUSG00000065407	Mir135a-1	Mir135a01|Mirn135|Mirn135a-1|mir-135a-1	microRNA 135a-1	ncRNA
mm_161426.1	chr15	44196189	44196189	+	1	NA	promoter-TSS (NM_013696)	promoter-TSS (NM_013696)	54	NM_013696	22045	Mm.309350	NM_013696	ENSMUSG00000038760	Trhr	TRH-R1	thyrotropin releasing hormone receptor	protein-coding
mm_145807.1	chr18	65386056	65386099	+	1	NA	intron (NM_001037294, intron 1 of 12)	ID4_|SINE|ID	7811	NM_001037294	225638	Mm.296528	NM_001037294	ENSMUSG00000032845	Alpk2	Gm549|Hak	alpha-kinase 2	protein-coding
mm_156208.1	chrX	134601212	134601266	+	1	NA	promoter-TSS (NM_001313716)	promoter-TSS (NM_001313716)	60	NM_001313717	56258	Mm.315909	NM_019868	ENSMUSG00000045427	Hnrnph2	DXHXS1271E|Ftp-3|Ftp3|H'|HNRNP|Hnrph2	heterogeneous nuclear ribonucleoprotein H2	protein-coding
mm_109781.1	chr12	119390691	119390692	+	1	NA	Intergenic	Intergenic	-52719	NM_001163136	238455	Mm.31376	NM_001163136	ENSMUSG00000041886	Macc1	4732474O15Rik|Gm267	metastasis associated in colon cancer 1	protein-coding
mm_156679.1	chrX	159341708	159341710	+	1	NA	intron (NM_001346675, intron 16 of 23)	B3A|SINE|B2	-30486	NM_025437	66235	Mm.294623	NM_025437	ENSMUSG00000067194	Eif1ax	1500010B24Rik|AI426898|Eif1ay	eukaryotic translation initiation factor 1A, X-linked	protein-coding
mm_10829.1	chr2	24386376	24386386	+	1	NA	intron (NM_177611, intron 1 of 16)	intron (NM_177611, intron 1 of 16)	984	NM_177611	215632	Mm.490434	NM_177611	ENSMUSG00000026979	Psd4	BC046518|EFA6B	pleckstrin and Sec7 domain containing 4	protein-coding
mm_31910.1	chr4	84884419	84884457	+	1	NA	5' UTR (NM_177385, exon 1 of 5)	5' UTR (NM_177385, exon 1 of 5)	129	NM_177385	338349	Mm.440562	NM_175275	ENSMUSG00000038070	Cntln	AI448092|B430108F07Rik|D530005L17Rik	centlein, centrosomal protein	protein-coding
mm_36648.1	chr4	94556738	94556802	-	1	NA	promoter-TSS (NM_026368)	promoter-TSS (NM_026368)	26	NM_026368	67770	Mm.35170	NM_026368	ENSMUSG00000028578	Caap1	5830433M19Rik|AI536248|CAAP	caspase activity and apoptosis inhibitor 1	protein-coding
mm_42362.1	chr5	114922212	114922234	+	1	NA	Intergenic	L2|LINE|L2	-1017	NM_145209	231655	Mm.95479	NM_145209	ENSMUSG00000041827	Oasl1	7530414C13Rik|oasl9	2'-5' oligoadenylate synthetase-like 1	protein-coding
mm_94995.1	chr11	31871685	31871710	+	1	NA	5' UTR (NM_026252, exon 1 of 10)	5' UTR (NM_026252, exon 1 of 10)	757	NM_026252	67579	Mm.339792	NM_026252	ENSMUSG00000020300	Cpeb4	Cpe-bp4|Cpeb-4|mCPEB-4	cytoplasmic polyadenylation element binding protein 4	protein-coding
mm_27489.1	chr3	54807738	54807746	-	1	NA	promoter-TSS (NM_133231)	promoter-TSS (NM_133231)	49	NM_133231	170767	Mm.185735	NM_133231	ENSMUSG00000036615	Rfxap	5730495K23Rik	regulatory factor X-associated protein	protein-coding
mm_126897.1	chr15	89500117	89500145	+	1	NA	intron (NM_021423, intron 1 of 21)	CpG-5250	274	NM_021423	58234	Mm.146855	NM_021423	ENSMUSG00000022623	Shank3	AI841104|SHANK3c-3|SHANK3c-4|Shank3b	SH3/ankyrin domain gene 3	protein-coding
mm_159315.1	chr3	10183928	10183928	-	1	NA	promoter-TSS (NM_001030305)	promoter-TSS (NM_001030305)	-43	NM_001030305	18857	Mm.371777	NM_001030305	ENSMUSG00000052468	Pmp2	P2	peripheral myelin protein 2	protein-coding
mm_34561.1	chr4	149647954	149647956	+	1	NA	3' UTR (NM_023051, exon 19 of 19)	3' UTR (NM_023051, exon 19 of 19)	7612	NR_105990	102465983		NR_105990	ENSMUSG00000098580	Mir7023	Gm27912|mmu-mir-7023	microRNA 7023	ncRNA
mm_134329.1	chr16	16367248	16367271	-	1	NA	Intergenic	ERVB7_2-LTR_MM|LTR|ERVK	-8228	NM_001276340	74006	Mm.218820	NM_152816	ENSMUSG00000022789	Dnm1l	6330417M19Rik|AI450666|Dlp1|Dnmlp1|Drp1|python	dynamin 1-like	protein-coding
mm_20987.1	chr2	152106041	152106056	-	1	NA	intron (NM_029688, intron 1 of 1)	intron (NM_029688, intron 1 of 1)	524	NM_029688	76650	Mm.218639	NM_029688	ENSMUSG00000032802	Srxn1	1700127B04Rik|AI854065|AW488194|Npn3|Srx|Srx1|TX01	sulfiredoxin 1 homolog (S. cerevisiae)	protein-coding
mm_30172.1	chr3	144202351	144202367	-	1	NA	promoter-TSS (NM_001161769)	promoter-TSS (NM_001161769)	-27	NM_001161770	16911	Mm.29187	NM_010723	ENSMUSG00000028266	Lmo4	A730077C12Rik|Crp3|Etohi4	LIM domain only 4	protein-coding
mm_91271.1	chr10	24445079	24445089	-	1	NA	Intergenic	Intergenic	-150358	NM_010217	14219	Mm.390287	NM_010217	ENSMUSG00000019997	Ctgf	Ccn2|Fisp12|Hcs24|fisp-12	connective tissue growth factor	protein-coding
mm_164093.1	chr15	10223750	10223767	+	1	NA	promoter-TSS (NM_001253781)	promoter-TSS (NM_001253781)	-148	NM_001253781	19116	Mm.10516	NM_011169	ENSMUSG00000005268	Prlr	AI987712|Pr-1|Pr-3|Prlr-rs1	prolactin receptor	protein-coding
mm_73160.1	chr8	94995751	94995761	+	1	NA	intron (NM_018882, intron 1 of 13)	intron (NM_018882, intron 1 of 13)	11357	NM_018882	14766	Mm.290834	NM_018882	ENSMUSG00000031785	Adgrg1	Cyt28|Gpr56|TM7LN4|TM7XN1	adhesion G protein-coupled receptor G1	protein-coding
mm_41252.1	chr5	88793934	88793936	+	1	NA	Intergenic	Intergenic	28922	NM_007832	13178	Mm.298892	NM_007832	ENSMUSG00000029366	Dck	-	deoxycytidine kinase	protein-coding
mm_93920.1	chr10	127070233	127070249	-	1	NA	promoter-TSS (NR_040660)	promoter-TSS (NR_040660)	20	NM_025982	67125	Mm.35650	NM_025982	ENSMUSG00000006736	Tspan31	2700085A14Rik|AW742554|Sas	tetraspanin 31	protein-coding
mm_346.1	chr1	30952590	30952594	+	1	NA	Intergenic	Intergenic	-2837	NM_011200	19243	Mm.491181	NM_011200	ENSMUSG00000026064	Ptp4a1	AA415290|AU019864|C130021B01|Prl-1	protein tyrosine phosphatase 4a1	protein-coding
mm_114564.1	chr13	74546549	74546582	+	1	NA	Intergenic	Intergenic	-52615	NM_146231	235956	Mm.296909	NM_146231	ENSMUSG00000069208	Zfp825	-	zinc finger protein 825	protein-coding
mm_81763.1	chr9	114390154	114390167	+	1	NA	exon (NM_019922, exon 1 of 7)	exon (NM_019922, exon 1 of 7)	552	NM_019922	56693	Mm.20904	NM_019922	ENSMUSG00000032431	Crtap	5730529N23Rik|CASP|Leprel3|P3h5	cartilage associated protein	protein-coding
mm_172228.1	chr6	67267226	67267245	+	1	NA	exon (NM_025814, exon 1 of 8)	exon (NM_025814, exon 1 of 8)	256	NM_025814	66870	Mm.240490	NM_025814	ENSMUSG00000036371	Serbp1	1200009K13Rik|9330147J08Rik|AL022786|Pairbp1	serpine1 mRNA binding protein 1	protein-coding
mm_162457.1	chr1	128417295	128417305	-	1	NA	5' UTR (NM_145507, exon 1 of 4)	5' UTR (NM_145507, exon 1 of 4)	116	NM_177445	226414	Mm.28693	NM_145507	ENSMUSG00000026356	Dars	5730439G15Rik	aspartyl-tRNA synthetase	protein-coding
mm_56754.1	chr6	116073038	116073077	-	1	NA	intron (NM_177412, intron 3 of 5)	intron (NM_177412, intron 3 of 5)	-78052	NM_026376	67784	Mm.3085	NM_026376	ENSMUSG00000030123	Plxnd1	6230425C21Rik|b2b1863Clo|b2b553Clo	plexin D1	protein-coding
mm_2242.1	chr1	91053552	91053562	+	1	NA	5' UTR (NM_008515, exon 1 of 23)	5' UTR (NM_008515, exon 1 of 23)	113	NM_008515	16978	Mm.45039	NM_008515	ENSMUSG00000026305	Lrrfip1	AU024550|Fliiap1	leucine rich repeat (in FLII) interacting protein 1	protein-coding
mm_161170.1	chr13	37888846	37888846	+	1	NA	promoter-TSS (NM_001177869)	promoter-TSS (NM_001177869)	-25	NM_001177869	68750	Mm.491109	NM_026830	ENSMUSG00000039087	Rreb1	1110037N09Rik|AA414966|B930013M22Rik	ras responsive element binding protein 1	protein-coding
mm_67923.1	chr7	99865321	99865337	-	1	NA	intron (NM_001164258, intron 2 of 18)	intron (NM_001164258, intron 2 of 18)	6111	NM_001164258	446101	Mm.440757	NM_001164258	ENSMUSG00000035211	Xrra1	AI449753	X-ray radiation resistance associated 1	protein-coding
mm_47230.1	chr5	121384851	121384854	-	1	NA	intron (NM_172275, intron 1 of 11)	ID_B1|SINE|B4	763	NM_001163470	231712	Mm.20488	NM_172275	ENSMUSG00000042726	Trafd1	1110008K06Rik|Fln29	TRAF type zinc finger domain containing 1	protein-coding
mm_3396.1	chr1	143640785	143640787	+	1	NA	promoter-TSS (NM_020025)	promoter-TSS (NM_020025)	89	NM_020025	26878	Mm.285580	NM_020025	ENSMUSG00000033849	B3galt2	-	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 2	protein-coding
mm_135214.1	chr16	36642788	36642806	-	1	NA	intron (NM_019388, intron 1 of 7)	intron (NM_019388, intron 1 of 7)	23280	NM_019388	12524	Mm.1452	NM_019388	ENSMUSG00000022901	Cd86	B7|B7-2|B7.2|B70|CLS1|Cd28l2|ETC-1|Ly-58|Ly58|MB7|MB7-2|TS/A-2	CD86 antigen	protein-coding
mm_104200.1	chr11	87987477	87987487	-	1	NA	promoter-TSS (NM_001168472)	promoter-TSS (NM_001168472)	51	NM_026556	68097	Mm.246436	NM_026556	ENSMUSG00000020483	Dynll2	1700064A15Rik|6720463E02Rik|C87222|DLC8|DLC8b|Dlc2	dynein light chain LC8-type 2	protein-coding
mm_119145.1	chr14	31336634	31336656	+	1	NA	promoter-TSS (NM_009796)	promoter-TSS (NM_009796)	-79	NM_009796	12339	Mm.201535	NM_009796	ENSMUSG00000021893	Capn7	AU022319|PalBH	calpain 7	protein-coding
mm_27564.1	chr3	58577699	58577726	-	1	NA	intron (NM_001040396, intron 1 of 5)	intron (NM_001040396, intron 1 of 5)	1054	NM_001040396	69227	Mm.270950	NM_001040396	ENSMUSG00000075700	Selenot	2810407C02Rik|5730408P04Rik|Selt	selenoprotein T	protein-coding
mm_10011.1	chr1	191872197	191872211	-	1	NA	Intergenic	Intergenic	-34577	NM_009579	22782	Mm.9024	NM_009579	ENSMUSG00000037434	Slc30a1	AI839647|C130040I11Rik|Znt1	solute carrier family 30 (zinc transporter), member 1	protein-coding
mm_114785.1	chr13	89051408	89051411	+	1	NA	intron (NM_010103, intron 3 of 9)	Lx6|LINE|L1	229937	NM_001037987	13612	Mm.125580	NM_010103	ENSMUSG00000034488	Edil3	Del-1|Del1	EGF-like repeats and discoidin I-like domains 3	protein-coding
mm_113750.1	chr13	44731282	44731292	+	1	NA	promoter-TSS (NM_001205043)	promoter-TSS (NM_001205043)	16	NM_001205043	16468	Mm.25059	NM_021878	ENSMUSG00000038518	Jarid2	Jmj|jumonji	jumonji, AT rich interactive domain 2	protein-coding
mm_82313.1	chr9	7872972	7872978	-	1	NA	5' UTR (NM_007464, exon 1 of 9)	5' UTR (NM_007464, exon 1 of 9)	195	NM_007464	11796	Mm.2026	NM_007464	ENSMUSG00000032000	Birc3	AW107670|Api1|Api2|Birc2|C-IAP2|HIAP2|IAP1|IAP2|MIAP1|MIAP2|MIHB|MIHC|RNF49|cIAP-1|cIAP-2|cIAP1|cIAP2	baculoviral IAP repeat-containing 3	protein-coding
mm_169215.1	chr13	66681065	66681084	+	1	NA	Intergenic	Intergenic	224276	NM_026219	67530	Mm.379136	NM_026219	ENSMUSG00000021520	Uqcrb	2210415M14Rik|QP-C|QPC|UQBC|UQBP|UQPC	ubiquinol-cytochrome c reductase binding protein	protein-coding
mm_91898.1	chr10	60003057	60003136	-	1	NA	promoter-TSS (NM_001199187)	promoter-TSS (NM_001199187)	39	NM_001347451	52717	Mm.21793	NM_025514	ENSMUSG00000020107	Anapc16	2310005G07Rik|APC16|D10Ertd641e	anaphase promoting complex subunit 16	protein-coding
mm_89058.1	chr10	82881859	82881874	+	1	NA	exon (NM_001042523, exon 8 of 15)	exon (NM_001042523, exon 8 of 15)	15240	NM_025499	66341	Mm.443284	NM_025499	ENSMUSG00000109864	Eid3	1700027M21Rik|NS4EB	EP300 interacting inhibitor of differentiation 3	protein-coding
mm_151306.1	chr19	55742772	55742784	+	1	NA	exon (NM_001142918, exon 2 of 15)	exon (NM_001142918, exon 2 of 15)	968	NM_001142923	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_28825.1	chr3	96292417	96292429	-	1	NA	exon (NM_010186, exon 3 of 6)	exon (NM_010186, exon 3 of 6)	1546	NM_010186	14129	Mm.150	NM_010186	ENSMUSG00000015947	Fcgr1	AI323638|AV092959|CD64|FcgammaRI|IGGHAFC	Fc receptor, IgG, high affinity I	protein-coding
mm_33636.1	chr4	132974094	132974096	+	1	NA	promoter-TSS (NM_010208)	promoter-TSS (NM_010208)	0	NM_010208	14191	Mm.271665	NM_010208	ENSMUSG00000028874	Fgr	-	FGR proto-oncogene, Src family tyrosine kinase	protein-coding
mm_116568.1	chr13	47043117	47043186	-	1	NA	promoter-TSS (NM_016785)	promoter-TSS (NM_016785)	66	NM_016785	22017	Mm.10169	NM_016785	ENSMUSG00000021376	Tpmt	AW106912	thiopurine methyltransferase	protein-coding
mm_148072.1	chr18	72350496	72350567	-	1	NA	5' UTR (NM_007831, exon 1 of 29)	5' UTR (NM_007831, exon 1 of 29)	538	NM_007831	13176	Mm.167882	NM_007831	ENSMUSG00000060534	Dcc	C030036D22Rik|Igdcc1	deleted in colorectal carcinoma	protein-coding
mm_160828.1	chr11	45980411	45980411	+	1	NA	exon (NM_173384, exon 1 of 5)	exon (NM_173384, exon 1 of 5)	101	NM_173384	214105	Mm.66708	NM_173384	ENSMUSG00000040489	Sox30	-	SRY (sex determining region Y)-box 30	protein-coding
mm_162500.1	chr1	139660973	139661006	-	1	NA	Intergenic	Intergenic	-100767	NM_015780	50702	Mm.220362	NM_015780	ENSMUSG00000057037	Cfhr1	AI194696|CFHRB|Cfhl1	complement factor H-related 1	protein-coding
mm_113082.1	chr13	23839446	23839470	+	1	NA	promoter-TSS (NM_001164743)	promoter-TSS (NM_001164743)	24	NM_134069	105355	Mm.27038	NM_134069	ENSMUSG00000036083	Slc17a3	AW261723|Npt4	solute carrier family 17 (sodium phosphate), member 3	protein-coding
mm_96365.1	chr11	67171096	67171112	+	1	NA	promoter-TSS (NM_001039545)	promoter-TSS (NM_001039545)	77	NM_001039545	17882	Mm.422801	NM_144961	ENSMUSG00000033196	Myh2	MHC2A|MyHC-IIa|Myh2a|Myhs-f|Myhs-f1|Myhsf1	myosin, heavy polypeptide 2, skeletal muscle, adult	protein-coding
mm_48785.1	chr5	148553994	148554025	-	1	NA	Intergenic	Intergenic	-1221	NM_011908	24109	Mm.21846	NM_011908	ENSMUSG00000001687	Ubl3	AW108023|HCG	ubiquitin-like 3	protein-coding
mm_63877.1	chr7	136894576	136894597	+	1	NA	promoter-TSS (NM_008598)	promoter-TSS (NM_008598)	-25	NM_008598	17314	Mm.440219	NM_008598	ENSMUSG00000054612	Mgmt	AGT|AI267024|Agat	O-6-methylguanine-DNA methyltransferase	protein-coding
mm_98566.1	chr11	95384886	95384918	+	1	NA	promoter-TSS (NM_016752)	promoter-TSS (NM_016752)	-20	NM_016752	110172	Mm.4593	NM_016752	ENSMUSG00000020873	Slc35b1	Ugalt2	solute carrier family 35, member B1	protein-coding
mm_71459.1	chr8	46527200	46527245	+	1	NA	exon (NM_007981, exon 14 of 21)	exon (NM_007981, exon 14 of 21)	-24847	NM_027973	71876	Mm.22108	NM_027973	ENSMUSG00000031629	Cenpu	1700029A22Rik|Mlf1ip	centromere protein U	protein-coding
mm_60036.1	chr7	31035229	31035268	+	1	NA	exon (NM_001111073, exon 7 of 8)	exon (NM_001111073, exon 7 of 8)	5069	NR_106017	102465635		NR_106017	ENSMUSG00000098783	Mir7050	Gm27578|mmu-mir-7050	microRNA 7050	ncRNA
mm_30643.1	chr4	8822810	8822818	+	1	NA	intron (NM_001277149, intron 8 of 37)	intron (NM_001277149, intron 8 of 37)	132408	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_1059.1	chr1	58973632	58973659	+	1	NA	promoter-TSS (NM_172406)	promoter-TSS (NM_172406)	74	NM_172656	227154	Mm.286006	NM_172656	ENSMUSG00000026027	Stradb	AA792893|Als2cr2|B830008M19|D1Ucla2|ILPIP|ILPIPA|PRO1038|Papk|Syradb	STE20-related kinase adaptor beta	protein-coding
mm_8552.1	chr1	155232577	155232589	-	1	NA	Intergenic	Intergenic	73880	NM_021433	58244	Mm.66264	NM_021433	ENSMUSG00000026470	Stx6	2310039E05Rik|2410005I16Rik|AA437559|AI415714|AI845861	syntaxin 6	protein-coding
mm_20448.1	chr2	129364800	129364807	-	1	NA	3' UTR (NM_008361, exon 7 of 7)	3' UTR (NM_008361, exon 7 of 7)	-5099	NR_015474	329514	Mm.207315	NM_177848	ENSMUSG00000074805	Il1bos	9430083I22|Gm14047|OTTMUSG00000015529	interleukin 1 beta, opposite strand	ncRNA
mm_58062.1	chr6	136872496	136872506	-	1	NA	TTS (NM_008597)	TTS (NM_008597)	3322	NM_008597	17313	Mm.243085	NM_008597	ENSMUSG00000030218	Mgp	Mglap	matrix Gla protein	protein-coding
mm_48472.1	chr5	140965256	140965280	-	1	NA	intron (NM_175362, intron 1 of 24)	B4|SINE|B4	35328	NM_175362	108723	Mm.46187	NM_175362	ENSMUSG00000036526	Card11	0610008L17Rik|2410011D02Rik|BIMP3|CARMA1	caspase recruitment domain family, member 11	protein-coding
mm_9545.1	chr1	173912991	173912999	-	1	NA	promoter-TSS (NM_001301745)	promoter-TSS (NM_001301745)	51	NM_001301745	381308	Mm.490248	NM_001033450	ENSMUSG00000026536	Ifi211	A730048F03|Ifi205b|Mnda|ifi-205-B	interferon activated gene 211	protein-coding
mm_21273.1	chr2	156881260	156881268	-	1	NA	intron (NM_029983, intron 2 of 7)	intron (NM_029983, intron 2 of 7)	5814	NM_029983	77799	Mm.29264	NM_029983	ENSMUSG00000027636	Sla2	A930009E21Rik|AI430952|SLAP-2|SLAP2	Src-like-adaptor 2	protein-coding
mm_2572.1	chr1	118481449	118481457	+	1	NA	intron (NM_001293300, intron 8 of 40)	intron (NM_001293300, intron 8 of 40)	-22188	NR_027901	68204	Mm.443536	NR_027901	ENSMUSG00000107722	2900060B14Rik	-	RIKEN cDNA 2900060B14 gene	ncRNA
mm_135782.1	chr16	56886094	56886125	-	1	NA	promoter-TSS (NM_019631)	promoter-TSS (NM_019631)	54	NM_019631	56277	Mm.262328	NM_019631	ENSMUSG00000022754	Tmem45a	C630002M10Rik|M32486|p19.5	transmembrane protein 45a	protein-coding
mm_62699.1	chr7	110221698	110221708	+	1	NA	promoter-TSS (NM_009302)	promoter-TSS (NM_009302)	0	NM_009302	20947	Mm.334144	NM_009302	ENSMUSG00000031015	Swap70	70kDa|AV235546	SWA-70 protein	protein-coding
mm_112195.1	chr12	113425709	113425732	-	1	NA	Intergenic	(CAGCT)n|Simple_repeat|Simple_repeat	-63845	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_134912.1	chr16	30283167	30283171	-	1	NA	promoter-TSS (NM_028973)	promoter-TSS (NM_028973)	85	NM_028973	74488	Mm.290677	NM_028973	ENSMUSG00000052316	Lrrc15	5430427N11Rik|LIB	leucine rich repeat containing 15	protein-coding
mm_151516.1	chr19	58738136	58738256	+	1	NA	exon (NM_018874, exon 10 of 13)	exon (NM_018874, exon 10 of 13)	9309	NM_018874	18946	Mm.10753	NM_018874	ENSMUSG00000042179	Pnliprp1	Plrp1	pancreatic lipase related protein 1	protein-coding
mm_93428.1	chr10	108902253	108902265	-	1	NA	5' UTR (NM_001252342, exon 2 of 11)	5' UTR (NM_001252342, exon 2 of 11)	108716	NM_009306	20979	Mm.289702	NM_009306	ENSMUSG00000035864	Syt1	AW124717|G630098F17Rik|SytI	synaptotagmin I	protein-coding
mm_121021.1	chr14	79587671	79587679	+	1	NA	promoter-TSS (NM_026474)	promoter-TSS (NM_026474)	-16	NM_026474	67955	Mm.18972	NM_026474	ENSMUSG00000022024	Sugt1	2410174K12Rik|SGT1	SGT1, suppressor of G2 allele of SKP1 (S. cerevisiae)	protein-coding
mm_169556.1	chr15	103655480	103655481	+	1	NA	Intergenic	Intergenic	-90399	NM_008134	14663	Mm.219621	NM_008134	ENSMUSG00000022491	Glycam1	MC26|Sgp50|glyCAM-1	glycosylation dependent cell adhesion molecule 1	protein-coding
mm_153504.1	chr19	41358616	41358620	-	1	NA	intron (NM_031376, intron 2 of 16)	intron (NM_031376, intron 2 of 16)	26452	NM_031376	83490	Mm.222266	NM_031376	ENSMUSG00000025017	Pik3ap1	1810044J04Rik|BCAP	phosphoinositide-3-kinase adaptor protein 1	protein-coding
mm_64033.1	chr7	140770048	140770060	+	1	NA	exon (NM_021282, exon 5 of 9)	exon (NM_021282, exon 5 of 9)	6222	NM_021282	13106	Mm.21758	NM_021282	ENSMUSG00000025479	Cyp2e1	Cyp2e	cytochrome P450, family 2, subfamily e, polypeptide 1	protein-coding
mm_15537.1	chr2	158383682	158383694	+	1	NA	3' UTR (NM_175692, exon 5 of 5)	3' UTR (NM_175692, exon 5 of 5)	8050	NM_175692	319317	Mm.294494	NM_175692	ENSMUSG00000044349	Snhg11	A930034L06Rik|AI854265|AL022637|AW319638|E130013N09Rik	small nucleolar RNA host gene 11	protein-coding
mm_142889.1	chr17	51832693	51832697	-	1	NA	promoter-TSS (NM_009122)	promoter-TSS (NM_009122)	-48	NM_009122	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_31423.1	chr4	48056567	48056573	+	1	NA	exon (NM_015743, exon 5 of 8)	exon (NM_015743, exon 5 of 8)	5324	NM_001307989	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_33318.1	chr4	129080508	129080521	+	1	NA	exon (NM_029219, exon 7 of 9)	exon (NM_029219, exon 7 of 9)	22243	NM_029219	75234	Mm.259672	NM_029219	ENSMUSG00000028793	Rnf19b	4930534K13Rik|4930555L03Rik|Ibrdc3	ring finger protein 19B	protein-coding
mm_146792.1	chr18	20114875	20114883	-	1	NA	promoter-TSS (NM_001291804)	promoter-TSS (NM_001291804)	-106	NM_013504	13505	Mm.33740	NM_013504	ENSMUSG00000044322	Dsc1	1110020A10Rik|AI507491	desmocollin 1	protein-coding
mm_83540.1	chr9	46234474	46234478	-	1	NA	exon (NM_001289755, exon 3 of 4)	exon (NM_001289755, exon 3 of 4)	823	NM_001289833	11814	Mm.390161	NM_023114	ENSMUSG00000032081	Apoc3	apo-CIII|apoC-III	apolipoprotein C-III	protein-coding
mm_162615.1	chr1	183345433	183345487	-	1	NA	intron (NM_177389, intron 6 of 26)	CpG	24105	NM_177389	338366	Mm.41152	NM_177389		Mia3	9130229H14Rik|A930039G15Rik|AU022327|B230399H06Rik|C80126|Gm1525|TANGO1|Tango	melanoma inhibitory activity 3	protein-coding
mm_127107.1	chr15	97854425	97854434	+	1	NA	TTS (NM_009504)	TTS (NM_009504)	-9927	NM_001204278	56233	Mm.384027	NM_019572	ENSMUSG00000022475	Hdac7	5830434K02Rik|HD7|HD7a|Hdac7a|mFLJ00062	histone deacetylase 7	protein-coding
mm_114673.1	chr13	80883396	80883398	+	1	NA	promoter-TSS (NM_001042591)	promoter-TSS (NM_001042591)	-25	NM_001042591	105171	Mm.423137	NM_001042591	ENSMUSG00000074794	Arrdc3	AI450344|mKIAA1376	arrestin domain containing 3	protein-coding
mm_107909.1	chr12	70974967	70975005	+	1	NA	intron (NM_001310596, intron 1 of 10)	CpG	363	NM_011184	19167	Mm.296338	NM_011184	ENSMUSG00000060073	Psma3	Lmpc8	proteasome (prosome, macropain) subunit, alpha type 3	protein-coding
mm_141379.1	chr17	29078954	29078972	-	1	NA	non-coding (NR_036469, exon 1 of 2)	non-coding (NR_036469, exon 1 of 2)	163	NR_036469	100504267	Mm.438550	NR_036469	ENSMUSG00000085912	Trp53cor1	Gm16197|OTTMUSG00000031656|linc-p21|lincRNA-p21	tumor protein p53 pathway corepressor 1	ncRNA
mm_53561.1	chr6	137136550	137136552	+	1	NA	intron (NM_181988, intron 2 of 4)	intron (NM_181988, intron 2 of 4)	33167	NM_001164214	232441	Mm.46233	NM_181988	ENSMUSG00000030222	Rerg	-	RAS-like, estrogen-regulated, growth-inhibitor	protein-coding
mm_57190.1	chr6	122849557	122849593	-	1	NA	3' UTR (NM_009779, exon 2 of 2)	3' UTR (NM_009779, exon 2 of 2)	6582	NM_009779	12267	Mm.2408	NM_009779	ENSMUSG00000040552	C3ar1	AZ3B|C3AR|HNFAG09	complement component 3a receptor 1	protein-coding
mm_167277.1	chr8	35061979	35061980	+	1	NA	Intergenic	MER21C|LTR|ERVL	-96289	NM_175091	21951	Mm.88364	NM_175091	ENSMUSG00000031529	Tnks	4930554K12Rik|AI662855|ARTD5|C86528|D130072O21Rik|TANK1|mTNKS1	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase	protein-coding
mm_9841.1	chr1	184478124	184478162	-	1	NA	Intergenic	Intergenic	79548	NR_040472	73590	Mm.82792	NR_040472	ENSMUSG00000101574	1700112H15Rik	-	RIKEN cDNA 1700112H15 gene	ncRNA
mm_77920.1	chr9	7352548	7352570	+	1	NA	intron (NM_001320077, intron 5 of 10)	L1MA6|LINE|L1	5185	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_138339.1	chr17	34903170	34903180	+	1	NA	intron (NM_147151, intron 5 of 26)	intron (NM_147151, intron 5 of 26)	4201	NM_145830	110147	Mm.35345	NM_145830	ENSMUSG00000013787	Ehmt2	Bat8|D17Ertd710e|G9a|KMT1C|NG36	euchromatic histone lysine N-methyltransferase 2	protein-coding
mm_142986.1	chr17	56287881	56287909	-	1	NA	intron (NM_025836, intron 1 of 7)	intron (NM_025836, intron 1 of 7)	2616	NM_025836	66905	Mm.311696	NM_025836	ENSMUSG00000024197	Plin3	1300012C15Rik|M6prbp1|Tip47	perilipin 3	protein-coding
mm_77909.1	chr9	7349721	7349731	+	1	NA	exon (NM_008605, exon 3 of 10)	exon (NM_008605, exon 3 of 10)	2352	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_39056.1	chr4	153975011	153975029	-	1	NA	promoter-TSS (NM_177673)	promoter-TSS (NM_177673)	61	NM_007859	13368	Mm.388918	NM_007859	ENSMUSG00000029027	Dffb	40kDa|5730477D02Rik|CAD|CPAN|DFF40|Didff	DNA fragmentation factor, beta subunit	protein-coding
mm_66311.1	chr7	39797741	39797746	-	1	NA	Intergenic	MTEa-int|LTR|ERVL-MaLR	279977	NM_001004139	70227	Mm.333800	NM_001004139	ENSMUSG00000068959	Zfp619	3000002G13Rik	zinc finger protein 619	protein-coding
mm_125942.1	chr15	76248106	76248142	+	1	NA	promoter-TSS (NR_105918)	promoter-TSS (NR_105918)	-67	NR_105918	102465575		NR_105918	ENSMUSG00000098625	Mir6953	Gm27738|mmu-mir-6953	microRNA 6953	ncRNA
mm_46502.1	chr5	105134615	105134617	-	1	NA	intron (NM_008620, intron 3 of 10)	intron (NM_008620, intron 3 of 10)	4936	NM_008620	17472	Mm.440525	NM_008620	ENSMUSG00000079363	Gbp4	AW228052|Mag-2|Mpa-2|Mpa2	guanylate binding protein 4	protein-coding
mm_76548.1	chr8	88180201	88180201	-	1	NA	Intergenic	RLTR1B|LTR|ERV1	-19012	NM_001164499	214627	Mm.491211	NM_001164497	ENSMUSG00000036779	Papd5	5730445M16Rik|5830428A09	PAP associated domain containing 5	protein-coding
mm_121217.1	chr14	103054853	103054859	+	1	NA	exon (NM_008392, exon 5 of 5)	exon (NM_008392, exon 5 of 5)	7844	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_133034.1	chr16	57353007	57353035	+	1	NA	promoter-TSS (NM_001040397)	promoter-TSS (NM_001040397)	-256	NM_001040397	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding
mm_253.1	chr1	19237602	19237612	+	1	NA	3' UTR (NM_009334, exon 7 of 7)	3' UTR (NM_009334, exon 7 of 7)	25553	NM_001025305	21419	Mm.137021	NM_009334	ENSMUSG00000025927	Tfap2b	AI606113|AP-2(beta)|E130018K07Rik|Tcfap2b	transcription factor AP-2 beta	protein-coding
mm_81311.1	chr9	108392896	108392902	+	1	NA	promoter-TSS (NM_053216)	promoter-TSS (NM_053216)	65	NM_053216	112418	Mm.78287	NM_053216	ENSMUSG00000032611	1700102P08Rik	AI593206	RIKEN cDNA 1700102P08 gene	protein-coding
mm_92144.1	chr10	67013274	67013290	-	1	NA	3' UTR (NM_001204915, exon 9 of 9)	3' UTR (NM_001204915, exon 9 of 9)	8207	NR_110511	102634101	Mm.445258	NR_110511		Gm31763	-	predicted gene, 31763	ncRNA
mm_66982.1	chr7	63938844	63938856	-	1	NA	promoter-TSS (NM_021366)	promoter-TSS (NM_021366)	65	NM_021366	50794	Mm.240473	NM_021366	ENSMUSG00000052040	Klf13	0610043C13Rik|9430029L20Rik|Bteb3|FKLF-2|FKLF2|NSLP1|RFLAT-1|RFLAT1	Kruppel-like factor 13	protein-coding
mm_150652.1	chr19	41917158	41917161	+	1	NA	intron (NM_023418, intron 3 of 3)	intron (NM_023418, intron 3 of 3)	5288	NM_023418	18648	Mm.16783	NM_023418	ENSMUSG00000011752	Pgam1	2310050F24Rik|Pgam-1	phosphoglycerate mutase 1	protein-coding
mm_155111.1	chrX	48519477	48519523	+	1	NA	5' UTR (NM_011228, exon 1 of 2)	5' UTR (NM_011228, exon 1 of 2)	215	NM_011228	19337	Mm.2015	NM_011228	ENSMUSG00000031104	Rab33a	Rabs10	RAB33A, member RAS oncogene family	protein-coding
mm_76725.1	chr8	94876325	94876335	-	1	NA	promoter-TSS (NM_053246)	promoter-TSS (NM_053246)	-18	NM_053246	114255	Mm.203949	NM_053246	ENSMUSG00000040631	Dok4	-	docking protein 4	protein-coding
mm_91878.1	chr10	59586112	59586114	-	1	NA	intron (NM_001033259, intron 1 of 7)	L1MB8|LINE|L1	30579	NM_001033259	215999	Mm.296470	NM_001033259	ENSMUSG00000009647	Mcu	2010012O16Rik|AV064928|C10orf42|Ccdc109a|D130073L02Rik|Gm64	mitochondrial calcium uniporter	protein-coding
mm_58882.1	chr7	17087935	17087961	+	1	NA	intron (NM_001310628, intron 1 of 5)	intron (NM_001310628, intron 1 of 5)	13908	NM_007676	26436	Mm.143686	NM_007676	ENSMUSG00000066760	Psg16	Cea11|PSG|bCEA	pregnancy specific glycoprotein 16	protein-coding
mm_132017.1	chr16	26062243	26062245	+	1	NA	intron (NM_173379, intron 1 of 14)	intron (NM_173379, intron 1 of 14)	43540	NM_173379	210530	Mm.326869	NM_173379	ENSMUSG00000038168	P3h2	4832416N06|AW553532|Leprel1|Mlat4	prolyl 3-hydroxylase 2	protein-coding
mm_41866.1	chr5	104440775	104440789	+	1	NA	3' UTR (NM_001204203, exon 7 of 7)	3' UTR (NM_001204203, exon 7 of 7)	4590	NM_001204233	20750	Mm.288474	NM_009263	ENSMUSG00000029304	Spp1	2AR|Apl-1|BNSP|BSPI|Bsp|ETA-1|Eta|OP|Opn|Opnl|Ric|Spp-1	secreted phosphoprotein 1	protein-coding
mm_84661.1	chr9	71771536	71771601	-	1	NA	promoter-TSS (NM_026599)	promoter-TSS (NM_026599)	34	NM_026599	68178	Mm.99961	NM_026599	ENSMUSG00000032232	Cgnl1	4933421H10Rik|9930020M10Rik|AI503810|Jacop	cingulin-like 1	protein-coding
mm_96963.1	chr11	70647313	70647323	+	1	NA	promoter-TSS (NM_024211)	promoter-TSS (NM_024211)	31	NM_027445	70510	Mm.261818	NM_027445	ENSMUSG00000040746	Rnf167	0610010G05Rik|5730408C10Rik|AU019305|AV328608	ring finger protein 167	protein-coding
mm_4553.1	chr1	177442536	177442547	+	1	NA	Intergenic	CpG	-2120	NM_001012330	30928	Mm.330700	NM_013915	ENSMUSG00000063659	Zbtb18	RP58|Zfp238|Znf238	zinc finger and BTB domain containing 18	protein-coding
mm_55819.1	chr6	83053779	83053828	-	1	NA	promoter-TSS (NR_125891)	promoter-TSS (NR_125891)	-718	NR_125891	11993	Mm.386752	NM_007517	ENSMUSG00000068328	Aup1	AA589454	ancient ubiquitous protein 1	protein-coding
mm_111039.1	chr12	79192214	79192242	-	1	NA	promoter-TSS (NM_021557)	promoter-TSS (NM_021557)	-409	NM_021557	17252	Mm.291799	NM_021557	ENSMUSG00000066441	Rdh11	2610319N22Rik|AI428145|AU045252|Arsdr1|C85936|CGI-82|HCBP12|M42C60|Mdt1|Psdr1|SCALD|UBE-1c1|Ube-1c	retinol dehydrogenase 11	protein-coding
mm_108366.1	chr12	80800589	80800593	+	1	NA	intron (NM_001242419, intron 1 of 6)	(TTTC)n|Simple_repeat|Simple_repeat	10059	NM_001242419	217684	Mm.341776	NM_178682	ENSMUSG00000021133	Susd6	4933426M11Rik|mKIAA0247	sushi domain containing 6	protein-coding
mm_147631.1	chr18	58210571	58210573	-	1	NA	promoter-TSS (NM_010181)	promoter-TSS (NM_010181)	-646	NM_010181	14119	Mm.20271	NM_010181	ENSMUSG00000024598	Fbn2	BC063774|Fib-2|mKIAA4226|sne|sy	fibrillin 2	protein-coding
mm_113720.1	chr13	43765506	43765530	+	1	NA	Intergenic	Intergenic	-19594	NM_009856	12522	Mm.57175	NM_009856	ENSMUSG00000015396	Cd83	-	CD83 antigen	protein-coding
mm_119950.1	chr14	55023551	55023557	+	1	NA	intron (NM_026890, intron 10 of 10)	(T)n|Simple_repeat|Simple_repeat	8100	NM_026890	68966	Mm.21214	NM_026890	ENSMUSG00000022204	Ngdn	1500001L15Rik|Ngd|neuroguidin	neuroguidin, EIF4E binding protein	protein-coding
mm_173103.1	chrX	152910183	152910192	-	1	NA	Intergenic	Lx3B|LINE|L1	-96282	NM_001137547	635253	Mm.426169	NM_001137547	ENSMUSG00000067215	Usp51	AV136873	ubiquitin specific protease 51	protein-coding
mm_155203.1	chrX	56731514	56731608	+	1	NA	promoter-TSS (NM_010211)	promoter-TSS (NM_010211)	-200	NM_010211	14199	Mm.3126	NM_010211	ENSMUSG00000023092	Fhl1	FHL-1|KyoT|RAM14-1|SLIM|SLIM-1	four and a half LIM domains 1	protein-coding
mm_6019.1	chr1	59094886	59094903	-	1	NA	promoter-TSS (NM_175200)	promoter-TSS (NM_175200)	6	NM_175200	73463	Mm.252811	NM_175200	ENSMUSG00000072295	Als2cr11	1700052H20Rik|4930408G06Rik	amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 11 (human)	protein-coding
mm_150222.1	chr19	33961196	33961210	+	1	NA	promoter-TSS (NM_026334)	promoter-TSS (NM_026334)	-45	NM_026334	67717	Mm.329816	NM_026334	ENSMUSG00000024768	Lipf	2310051B21Rik|AV082900	lipase, gastric	protein-coding
mm_120529.1	chr14	67159241	67159257	+	1	NA	Intergenic	MT2A|LTR|ERVL	-74043	NM_010095	13592	Mm.319947	NM_010095	ENSMUSG00000022053	Ebf2	D14Ggc1e|EBF-2|Mmot1|O/E-3|OE-3	early B cell factor 2	protein-coding
mm_147519.1	chr18	52528349	52528385	-	1	NA	exon (NM_010728, exon 2 of 7)	exon (NM_010728, exon 2 of 7)	1354	NM_001286181	16948	Mm.172	NM_010728	ENSMUSG00000024529	Lox	AI893619|TSC-160|rrg	lysyl oxidase	protein-coding
mm_91728.1	chr10	45289257	45289262	-	1	NA	promoter-TSS (NM_024286)	promoter-TSS (NM_024286)	-46	NM_024286	78977	Mm.24748	NM_024286	ENSMUSG00000019848	Popdc3	AA682104|Pop3	popeye domain containing 3	protein-coding
mm_86399.1	chr9	123968684	123968697	-	1	NA	promoter-TSS (NM_009912)	promoter-TSS (NM_009912)	2	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_43759.1	chr5	140607704	140607754	+	1	NA	exon (NM_008494, exon 1 of 8)	exon (NM_008494, exon 1 of 8)	388	NM_008494	16848	Mm.12834	NM_008494	ENSMUSG00000029570	Lfng	AW061165	LFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	protein-coding
mm_74909.1	chr8	25240851	25240861	-	1	NA	Intergenic	CpG	-39314	NM_177089	320165	Mm.308452	NM_177089	ENSMUSG00000065954	Tacc1	4833447E04Rik|AA960202|B230378H13Rik	transforming, acidic coiled-coil containing protein 1	protein-coding
mm_108370.1	chr12	80819406	80819451	+	1	NA	intron (NM_001242419, intron 1 of 6)	intron (NM_001242419, intron 1 of 6)	28896	NM_001242419	217684	Mm.341776	NM_178682	ENSMUSG00000021133	Susd6	4933426M11Rik|mKIAA0247	sushi domain containing 6	protein-coding
mm_153205.1	chr19	34640760	34640793	-	1	NA	promoter-TSS (NM_053217)	promoter-TSS (NM_053217)	-33	NM_053217	112419	Mm.440727	NM_053217	ENSMUSG00000067297	Ifit1bl2	2010002M12Rik|AW412491|Ifit1b	interferon induced protein with tetratricopeptide repeats 1B like 2	protein-coding
mm_116419.1	chr13	41607772	41607815	-	1	NA	intron (NM_001163572, intron 1 of 2)	intron (NM_001163572, intron 1 of 2)	1577	NM_001163572	621976	Mm.259830	NM_001163572	ENSMUSG00000087370	Tmem170b	EG621976	transmembrane protein 170B	protein-coding
mm_14249.1	chr2	128127559	128127572	+	1	NA	promoter-TSS (NM_001284410)	promoter-TSS (NM_001284410)	-10	NM_001284410	12125	Mm.141083	NM_009754	ENSMUSG00000027381	Bcl2l11	1500006F24Rik|Bim|Bod|bcl2-L-11	BCL2-like 11 (apoptosis facilitator)	protein-coding
mm_59753.1	chr7	28825203	28825215	+	1	NA	promoter-TSS (NM_016772)	promoter-TSS (NM_016772)	-129	NM_016772	51798	Mm.291776	NM_016772	ENSMUSG00000053898	Ech1	AA617331	enoyl coenzyme A hydratase 1, peroxisomal	protein-coding
mm_24636.1	chr3	94342140	94342144	+	1	NA	promoter-TSS (NM_025416)	promoter-TSS (NM_025416)	43	NM_025416	66198	Mm.180200	NM_025416	ENSMUSG00000028148	Them5	1110007B02Rik|1110038F21Rik	thioesterase superfamily member 5	protein-coding
mm_17127.1	chr2	24819037	24819061	-	1	NA	intron (NM_001012518, intron 16 of 26)	Lx9|LINE|L1	-55897	NM_007579	12287	Mm.4424	NM_007579	ENSMUSG00000004113	Cacna1b	AW050276|AW060892|AW822256|BIII|Cav2.2|Cchn1a|alpha(1B)	calcium channel, voltage-dependent, N type, alpha 1B subunit	protein-coding
mm_163639.1	chr13	60606964	60606968	+	1	NA	intron (NM_029653, intron 2 of 25)	intron (NM_029653, intron 2 of 25)	4755	NM_134062	69635	Mm.24103	NM_029653	ENSMUSG00000021559	Dapk1	D13Ucla1|DAP-Kinase	death associated protein kinase 1	protein-coding
mm_29105.1	chr3	104818323	104818333	-	1	NA	promoter-TSS (NM_008619)	promoter-TSS (NM_008619)	-23	NM_001163441	17454	Mm.1597	NM_008619	ENSMUSG00000002227	Mov10	C77703|Mov-10	Moloney leukemia virus 10	protein-coding
mm_162571.1	chr1	174191850	174191860	+	1	NA	intron (NM_011465, intron 12 of 51)	intron (NM_011465, intron 12 of 51)	19079	NM_011465	20739	Mm.200611	NM_011465	ENSMUSG00000026532	Spta1	AF093576|AI451697|Spna-1|Spna1|ha|ihj|nmf4|sph	spectrin alpha, erythrocytic 1	protein-coding
mm_107702.1	chr12	55465849	55465864	+	1	NA	intron (NR_035430, intron 1 of 3)	intron (NR_035430, intron 1 of 3)	26791	NM_010907	18035	Mm.170515	NM_010907	ENSMUSG00000021025	Nfkbia	AI462015|Nfkbi	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, alpha	protein-coding
mm_105898.1	chr11	114982727	114982747	-	1	NA	3' UTR (NM_145437, exon 4 of 4)	3' UTR (NM_145437, exon 4 of 4)	7149	NM_145437	217305	Mm.275986	NM_145437	ENSMUSG00000034641	Cd300ld	4732429D16Rik|CLM5|Cd300ld1|LMIR4|MAIR-IV|clm-5	CD300 molecule like family member d	protein-coding
mm_132227.1	chr16	32658905	32658949	+	1	NA	intron (NM_016788, intron 1 of 15)	intron (NM_016788, intron 1 of 15)	9270	NR_033493	675921	Mm.404316	NR_033493	ENSMUSG00000075265	Tnk2os	ENSMUSG00000075265|Gm10818	tyrosine kinase, non-receptor 2, opposite strand	ncRNA
mm_103422.1	chr11	75594764	75594764	-	1	NA	intron (NM_008850, intron 2 of 11)	intron (NM_008850, intron 2 of 11)	5467	NR_110477	654359	Mm.439961	NR_110477		Gm12338	OTTMUSG00000006216	cytochrome c oxidase, subunit VIIc pseudogene	pseudo
mm_64689.1	chr7	4518350	4518360	-	1	NA	TTS (NM_009406)	TTS (NM_009406)	-2380	NM_011618	21955	Mm.358643	NM_011618	ENSMUSG00000064179	Tnnt1	AW146156|Tnt|sTnT|ssTnT	troponin T1, skeletal, slow	protein-coding
mm_82159.1	chr9	123781404	123781420	+	1	NA	3' UTR (NM_001166625, exon 4 of 4)	3' UTR (NM_001166625, exon 4 of 4)	14201	NM_001166625	12769	Mm.440604	NM_009913	ENSMUSG00000029530	Ccr9	A130091K22Rik|Cmkbr10|GPR-9-6	chemokine (C-C motif) receptor 9	protein-coding
mm_80214.1	chr9	72531729	72531757	+	1	NA	promoter-TSS (NM_001033536)	promoter-TSS (NM_001033536)	115	NR_045735	75115	Mm.280755	NR_045735	ENSMUSG00000096986	4930509E16Rik	-	RIKEN cDNA 4930509E16 gene	ncRNA
mm_130118.1	chr15	89477440	89477450	-	1	NA	promoter-TSS (NM_009713)	promoter-TSS (NM_009713)	-21	NM_009713	11883	Mm.620	NM_009713	ENSMUSG00000022620	Arsa	AS-A|ASA|AW212749|As-2|As2|TISP73	arylsulfatase A	protein-coding
mm_170748.1	chr2	156180116	156180117	-	1	NA	promoter-TSS (NM_001291115)	promoter-TSS (NM_001291115)	122	NM_001291114	170791	Mm.392436	NM_133242	ENSMUSG00000027620	Rbm39	1500012C14Rik|2310040E03Rik|B330012G18Rik|C79248|R75070|Rnpc2|caper	RNA binding motif protein 39	protein-coding
mm_70739.1	chr8	19141430	19141440	+	1	NA	exon (NM_001034905, exon 2 of 2)	exon (NM_001034905, exon 2 of 2)	676	NM_001286493	546038	Mm.99206	NM_001034905	ENSMUSG00000059463	Spag11b	EG546038|Ep2c/h|Spag11c/h	sperm associated antigen 11B	protein-coding
mm_95427.1	chr11	50200442	50200460	+	1	NA	TTS (NM_026543)	TTS (NM_026543)	10369	NM_001290769	18412	Mm.40828	NM_011018	ENSMUSG00000015837	Sqstm1	A170|OSF-6|Osi|STAP|STONE14|p62	sequestosome 1	protein-coding
mm_5617.1	chr1	39739058	39739060	-	1	NA	Intergenic	Intergenic	-18070	NM_001145660	619289	Mm.334107	NM_001145660	ENSMUSG00000057173	Rfx8	4933400N17Rik	regulatory factor X 8	protein-coding
mm_101446.1	chr11	30197857	30197896	-	1	NA	5' UTR (NM_009260, exon 1 of 31)	5' UTR (NM_009260, exon 1 of 31)	381	NM_009260	20742	Mm.123110	NM_009260	ENSMUSG00000020315	Sptbn1	9930031C03Rik|AL033301|SPTB2|Spnb-2|Spnb2|elf1|elf3|mKIAA4049	spectrin beta, non-erythrocytic 1	protein-coding
mm_76236.1	chr8	83574781	83574785	-	1	NA	intron (NM_134118, intron 1 of 12)	intron (NM_134118, intron 1 of 12)	8025	NM_025843	66916	Mm.29683	NM_025843	ENSMUSG00000033938	Ndufb7	1110002H15Rik	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 7	protein-coding
mm_8951.1	chr1	164453775	164453820	-	1	NA	intron (NM_009721, intron 1 of 5)	intron (NM_009721, intron 1 of 5)	4558	NM_009721	11931	Mm.4550	NM_009721	ENSMUSG00000026576	Atp1b1	Atp4b|Atpb|Atpb-1|NKbeta1	ATPase, Na+/K+ transporting, beta 1 polypeptide	protein-coding
mm_1553.1	chr1	72942735	72942739	+	1	NA	Intergenic	Intergenic	-67872	NM_010518	16011	Mm.405761	NM_010518	ENSMUSG00000026185	Igfbp5	AI256729|AW208790|IGFBP-5|IGFBP-5P	insulin-like growth factor binding protein 5	protein-coding
mm_168814.1	chr12	21784497	21784514	-	1	NA	Intergenic	CpG	-367069	NM_011739	22630	Mm.289630	NM_011739	ENSMUSG00000076432	Ywhaq	2700028P07Rik|AA409740|AU021156|R74690	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide	protein-coding
mm_70474.1	chr8	12385770	12385780	+	1	NA	promoter-TSS (NR_027975)	promoter-TSS (NR_027975)	4	NR_027975	434280	Mm.447484	NM_001013812	ENSMUSG00000047935	Gm5607	EG434280	predicted gene 5607	ncRNA
mm_115069.1	chr13	101478952	101478953	+	1	NA	Intergenic	Intergenic	-81372	NR_046187	78136	Mm.399065	NR_046187		4922502H24Rik	-	RIKEN cDNA 4922502H24 gene	ncRNA
mm_96804.1	chr11	69981492	69981502	+	1	NA	promoter-TSS (NM_018740)	promoter-TSS (NM_018740)	-262	NM_018740	54351	Mm.13430	NM_018740	ENSMUSG00000018565	Elp5	Derp6|Rai12	elongator acetyltransferase complex subunit 5	protein-coding
mm_538.1	chr1	37998116	37998149	+	1	NA	promoter-TSS (NM_172054)	promoter-TSS (NM_172054)	122	NM_198303	226982	Mm.260943	NM_198303	ENSMUSG00000026083	Eif5b	A030003E17Rik|BC018347|IF2	eukaryotic translation initiation factor 5B	protein-coding
mm_149543.1	chr19	12573509	12573542	+	1	NA	promoter-TSS (NM_026640)	promoter-TSS (NM_026640)	0	NM_026640	107373	Mm.1643	NM_026640	ENSMUSG00000024691	Fam111a	4632417K18Rik|AW413625	family with sequence similarity 111, member A	protein-coding
mm_53796.1	chr6	146752341	146752359	+	1	NA	intron (NM_001346666, intron 1 of 11)	intron (NM_001346666, intron 1 of 11)	27420	NM_172734	232533	Mm.322121	NM_172734	ENSMUSG00000001630	Stk38l	4930473A22Rik|Ndr2|Ndr54	serine/threonine kinase 38 like	protein-coding
mm_30391.1	chr3	152247973	152248001	-	1	NA	exon (NM_199465, exon 7 of 13)	exon (NM_199465, exon 7 of 13)	18333	NM_199465	68810	Mm.200188	NM_199465	ENSMUSG00000039103	Nexn	1110046H09Rik|AA553326|NELIN	nexilin	protein-coding
mm_63972.1	chr7	139950388	139950424	+	1	NA	Intergenic	Intergenic	6550	NM_009482	22286	Mm.10205	NM_009482	ENSMUSG00000047751	Utf1	AI505934	undifferentiated embryonic cell transcription factor 1	protein-coding
mm_8660.1	chr1	156559348	156559357	-	1	NA	intron (NM_001136104, intron 1 of 12)	CpG	565	NM_001136104	11352	Mm.329515	NM_009595	ENSMUSG00000026596	Abl2	AA536808|Abll|Arg	v-abl Abelson murine leukemia viral oncogene 2 (arg, Abelson-related gene)	protein-coding
mm_7093.1	chr1	88699301	88699332	-	1	NA	3' UTR (NM_177305, exon 1 of 1)	3' UTR (NM_177305, exon 1 of 1)	2875	NM_177305	320982	Mm.27968	NM_177305	ENSMUSG00000049866	Arl4c	A630084M22Rik|Arl7|LAK	ADP-ribosylation factor-like 4C	protein-coding
mm_6059.1	chr1	60498509	60498529	-	1	NA	exon (NM_001045513, exon 10 of 14)	exon (NM_001045513, exon 10 of 14)	68246	NM_001045513	77300	Mm.440325	NM_001045513	ENSMUSG00000026014	Raph1	9430025M21Rik|C730009O10Rik|Lpd	Ras association (RalGDS/AF-6) and pleckstrin homology domains 1	protein-coding
mm_29496.1	chr3	115933705	115933707	-	1	NA	Intergenic	Intergenic	45523	NM_027193	69740	Mm.5915	NM_027193	ENSMUSG00000033554	Dph5	2410012M04Rik|AU045680|C80186	diphthamide biosynthesis 5	protein-coding
mm_128721.1	chr15	64058999	64059001	-	1	NA	intron (NM_144846, intron 1 of 11)	intron (NM_144846, intron 1 of 11)	1448	NM_144846	223601	Mm.246108	NM_144846	ENSMUSG00000022378	Fam49b	0910001A06Rik|AW122079	family with sequence similarity 49, member B	protein-coding
mm_34377.1	chr4	144895188	144895224	+	1	NA	intron (NM_011303, intron 1 of 5)	intron (NM_011303, intron 1 of 5)	2069	NM_011303	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding
mm_126780.1	chr15	86194823	86194854	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-8697	NM_145475	223753	Mm.222685	NM_145475	ENSMUSG00000035891	Cerk	AI848610|D330016D08Rik|mKIAA1646	ceramide kinase	protein-coding
mm_99784.1	chr11	107338010	107338027	+	1	NA	intron (NM_145823, intron 1 of 9)	intron (NM_145823, intron 1 of 9)	132702	NM_145823	71795	Mm.397413	NM_145823	ENSMUSG00000040430	Pitpnc1	1110020B03Rik|5830436L09Rik|AI662802|AI851387|C330017I21Rik|Dnr411|RDGBB|RDGBB1|rdgB-beta	phosphatidylinositol transfer protein, cytoplasmic 1	protein-coding
mm_55808.1	chr6	82939635	82939652	-	1	NA	5' UTR (NM_011350, exon 1 of 14)	5' UTR (NM_011350, exon 1 of 14)	126	NM_001308374	20355	Mm.270543	NM_011350	ENSMUSG00000000627	Sema4f	Sema W	sema domain, immunoglobulin domain (Ig), TM domain, and short cytoplasmic domain	protein-coding
mm_53281.1	chr6	128676620	128676624	+	1	NA	3' UTR (NM_053165, exon 5 of 5)	3' UTR (NM_053165, exon 5 of 5)	14237	NM_053165	94071	Mm.197689	NM_053165	ENSMUSG00000030364	Clec2h	Clrf|clr-f	C-type lectin domain family 2, member h	protein-coding
mm_35493.1	chr4	40948302	40948318	-	1	NA	promoter-TSS (NM_001171739)	promoter-TSS (NM_001171739)	-16	NM_001171739	12017	Mm.688	NM_009736	ENSMUSG00000028416	Bag1	BAG-1|Rap46	BCL2-associated athanogene 1	protein-coding
mm_140673.1	chr17	12960702	12960723	-	1	NA	promoter-TSS (NM_009338)	promoter-TSS (NM_009338)	13	NM_009338	110460	Mm.439711	NM_009338	ENSMUSG00000023832	Acat2	AW742799|Tcp-1x|Tcp1-rs1	acetyl-Coenzyme A acetyltransferase 2	protein-coding
mm_21130.1	chr2	154205462	154205475	-	1	NA	exon (NM_153418, exon 4 of 16)	exon (NM_153418, exon 4 of 16)	5088	NM_153418	228801	Mm.3783	NM_153418	ENSMUSG00000027485	Bpifb1	Lplunc1	BPI fold containing family B, member 1	protein-coding
mm_121014.1	chr14	79535763	79535773	+	1	NA	intron (NM_001286411, intron 1 of 8)	intron (NM_001286411, intron 1 of 8)	20094	NM_001286411	13709	Mm.20938	NM_007920	ENSMUSG00000036461	Elf1	Elf-1|Sts1|mElf-1|p70	E74-like factor 1	protein-coding
mm_45799.1	chr5	87568891	87568908	-	1	NA	5' UTR (NM_016771, exon 1 of 8)	5' UTR (NM_016771, exon 1 of 8)	107	NM_016771	53315	Mm.6824	NM_016771	ENSMUSG00000029273	Sult1d1	5033411P13Rik|AI987815|ST1d1|SULT-N|Sultn	sulfotransferase family 1D, member 1	protein-coding
mm_50175.1	chr6	41559661	41559676	+	1	NA	Intergenic	Intergenic	37892	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_28747.1	chr3	95754842	95754887	-	1	NA	5' UTR (NM_001163617, exon 1 of 17)	5' UTR (NM_001163617, exon 1 of 17)	113	NM_027931	71807	Mm.271754	NM_027931	ENSMUSG00000028107	Tars2	2610024N01Rik|AI429208|Tarsl1	threonyl-tRNA synthetase 2, mitochondrial (putative)	protein-coding
mm_91604.1	chr10	41303096	41303140	-	1	NA	5' UTR (NM_133999, exon 1 of 23)	5' UTR (NM_133999, exon 1 of 23)	123	NM_133999	103199	Mm.277242	NM_133999	ENSMUSG00000038417	Fig4	A530089I17Rik|AI326867|Sac3	FIG4 phosphoinositide 5-phosphatase	protein-coding
mm_102336.1	chr11	57831764	57831766	-	1	NA	exon (NM_008213, exon 1 of 2)	exon (NM_008213, exon 1 of 2)	382	NM_008213	15110	Mm.4746	NM_008213	ENSMUSG00000037335	Hand1	Ehand1|Hxt|Th1|Thing1|bHLHa27|eHAND	heart and neural crest derivatives expressed transcript 1	protein-coding
mm_122681.1	chr14	52014560	52014606	-	1	NA	promoter-TSS (NM_001253695)	promoter-TSS (NM_001253695)	-25	NM_001253695	69890	Mm.475652	NM_027248	ENSMUSG00000049295	Zfp219	2010302A17Rik	zinc finger protein 219	protein-coding
mm_88675.1	chr10	80019622	80019690	+	1	NA	promoter-TSS (NM_027521)	promoter-TSS (NM_027521)	-19	NM_027521	70719	Mm.243954	NM_027521	ENSMUSG00000035697	Hmha1	6330406L22Rik|AW539505|Ha-1	histocompatibility (minor) HA-1	protein-coding
mm_4891.1	chr1	188680588	188680599	+	1	NA	intron (NM_021408, intron 37 of 70)	B4A|SINE|B4	327247	NM_172650	226823	Mm.209880	NM_172650	ENSMUSG00000026608	Kctd3	4930438A20Rik|9330185B06|E330032J19Rik|NY-REN-45	potassium channel tetramerisation domain containing 3	protein-coding
mm_138539.1	chr17	35259347	35259359	+	1	NA	Intergenic	RMER15|LTR|ERVL	-3741	NM_010380	14964	Mm.439675	NM_010380	ENSMUSG00000073411	H2-D1	H-2D|H2-D	histocompatibility 2, D region locus 1	protein-coding
mm_111396.1	chr12	90738096	90738157	-	1	NA	exon (NM_010050, exon 1 of 2)	exon (NM_010050, exon 1 of 2)	911	NM_010050	13371	Mm.21389	NM_010050	ENSMUSG00000007682	Dio2	5DII|AI324267|DIOII	deiodinase, iodothyronine, type II	protein-coding
mm_18389.1	chr2	60125652	60125775	-	1	NA	promoter-TSS (NM_001001182)	promoter-TSS (NM_001001182)	27	NM_001001182	407823	Mm.228071	NM_001001182	ENSMUSG00000026987	Baz2b	5830435C13Rik|BC053917|D2Ertd794e	bromodomain adjacent to zinc finger domain, 2B	protein-coding
mm_106484.1	chr11	120231518	120231541	-	1	NA	Intergenic	CpG	-1418	NM_001347621	268515	Mm.309498	NM_198423	ENSMUSG00000039741	Bahcc1	B930044J06|BC060615	BAH domain and coiled-coil containing 1	protein-coding
mm_148138.1	chr18	76555223	76555231	-	1	NA	Intergenic	Intergenic	292782	NM_001311070	17126	Mm.152699	NM_010754	ENSMUSG00000024563	Smad2	7120426M23Rik|Madh2|Madr2|Smad-2|mMad2	SMAD family member 2	protein-coding
mm_60542.1	chr7	44480503	44480513	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-4009	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_172337.1	chr7	11005719	11005725	+	1	NA	promoter-TSS (NM_001013765)	promoter-TSS (NM_001013765)	-23	NM_001013765	245109	Mm.131747	NM_001013765	ENSMUSG00000054272	Zscan4c	Gm397|XM_142517|Zscan4d	zinc finger and SCAN domain containing 4C	protein-coding
mm_95997.1	chr11	59208795	59208799	+	1	NA	intron (NM_024210, intron 1 of 6)	intron (NM_024210, intron 1 of 6)	436	NM_024210	67862	Mm.358708	NM_024210	ENSMUSG00000020441	2310033P09Rik	Mmtag2	RIKEN cDNA 2310033P09 gene	protein-coding
mm_136275.1	chr16	91061587	91061601	-	1	NA	intron (NM_028905, intron 1 of 2)	MLT1J2|LTR|ERVL-MaLR	7551	NM_001163695	74387	Mm.236220	NM_028905	ENSMUSG00000039851	4932438H23Rik	4931406G06Rik|AI550392	RIKEN cDNA 4932438H23 gene	protein-coding
mm_82584.1	chr9	21224952	21224954	-	1	NA	intron (NR_106127, intron 1 of 3)	B1_Mur1|SINE|Alu	1328	NR_106127	102465769		NR_106127	ENSMUSG00000098764	Mir7667	Gm27756|mmu-mir-7667	microRNA 7667	ncRNA
mm_73380.1	chr8	105649320	105649323	+	1	NA	intron (NM_181322, intron 2 of 11)	AT_rich|Low_complexity|Low_complexity	12783	NM_181322	13018	Mm.269474	NM_181322	ENSMUSG00000005698	Ctcf	AW108038	CCCTC-binding factor	protein-coding
mm_93636.1	chr10	117282330	117282367	-	1	NA	promoter-TSS (NM_017372)	promoter-TSS (NM_017372)	-76	NM_017372	17105	Mm.45436	NM_017372	ENSMUSG00000069516	Lyz2	AI326280|Lys|Lysm|Lyzf2|Lyzs|Lzm|Lzm-s1|Lzp	lysozyme 2	protein-coding
mm_50194.1	chr6	41852843	41852855	+	1	NA	TTS (NM_008843)	TTS (NM_008843)	5300	NM_008843	18716	Mm.214755	NM_008843	ENSMUSG00000058499	Pip	GCDFP-15|GP17|mSMGP	prolactin induced protein	protein-coding
mm_98378.1	chr11	94076393	94076421	+	1	NA	intron (NM_001025430, intron 5 of 25)	B1_Mur4|SINE|Alu	32202	NM_001025429	70834	Mm.260737	NM_027569	ENSMUSG00000020859	Spag9	3110018C07Rik|4733401I23Rik|4831406C20Rik|AW552012|JLP|JSAP2|JSAP2a|Jip4|Mapk8ip4|syd1	sperm associated antigen 9	protein-coding
mm_155580.1	chrX	78125500	78125506	+	1	NA	promoter-TSS (NM_001085534)	promoter-TSS (NM_001085534)	36	NM_001085534	546335	Mm.476683	NM_001085534	ENSMUSG00000079521	Gm5938	EG546335|OBP6	predicted gene 5938	protein-coding
mm_156652.1	chrX	157702833	157702841	+	1	NA	intron (NR_045569, intron 1 of 6)	intron (NR_045569, intron 1 of 6)	3864	NR_103722	66106	Mm.140340	NM_025357	ENSMUSG00000041476	Smpx	1010001C09Rik|Csl	small muscle protein, X-linked	protein-coding
mm_76392.1	chr8	84844156	84844171	-	1	NA	exon (NM_007591, exon 7 of 9)	exon (NM_007591, exon 7 of 9)	2768	NM_007591	12317	Mm.1971	NM_007591	ENSMUSG00000003814	Calr	CRT|Calregulin	calreticulin	protein-coding
mm_56186.1	chr6	88508614	88508647	-	1	NA	exon (NM_016906, exon 8 of 12)	exon (NM_016906, exon 8 of 12)	10170	NM_016906	53421	Mm.28375	NM_016906	ENSMUSG00000030082	Sec61a1	AA408394|AA410007|Sec61a	Sec61 alpha 1 subunit (S. cerevisiae)	protein-coding
mm_89772.1	chr10	100485403	100485450	+	1	NA	intron (NM_001033332, intron 1 of 12)	intron (NM_001033332, intron 1 of 12)	1921	NM_001033332	237500	Mm.296805	NM_001033332	ENSMUSG00000036676	Tmtc3	9130014E20Rik|B130008E12Rik|mSmile	transmembrane and tetratricopeptide repeat containing 3	protein-coding
mm_107848.1	chr12	69372546	69372645	+	1	NA	5' UTR (NM_007481, exon 2 of 2)	5' UTR (NM_007481, exon 2 of 2)	445	NM_007481	11845	Mm.27308	NM_007481	ENSMUSG00000044147	Arf6	AI788669|AW496366	ADP-ribosylation factor 6	protein-coding
mm_95111.1	chr11	34075129	34075149	+	1	NA	intron (NM_010696, intron 9 of 20)	intron (NM_010696, intron 9 of 20)	27938	NM_010696	16822	Mm.265350	NM_010696	ENSMUSG00000002699	Lcp2	AI323664|BB161688|SLP-76|SLP76|m1Khoe|twm	lymphocyte cytosolic protein 2	protein-coding
mm_160257.1	chr7	108367461	108367461	+	1	NA	promoter-TSS (NM_146737)	promoter-TSS (NM_146737)	-31	NM_146737	258732	Mm.377662	NM_146737	ENSMUSG00000109631	Olfr494	MOR204-10	olfactory receptor 494	protein-coding
mm_151921.1	chr19	5799914	5799924	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	2753	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_152153.1	chr19	7240999	7241076	-	1	NA	5' UTR (NM_027643, exon 1 of 8)	5' UTR (NM_027643, exon 1 of 8)	185	NM_027643	70999	Mm.329605	NM_027643	ENSMUSG00000024764	Naa40	4931433E08Rik|AU023197|Nat11	N(alpha)-acetyltransferase 40, NatD catalytic subunit	protein-coding
mm_95843.1	chr11	57518242	57518249	+	1	NA	promoter-TSS (NM_145426)	promoter-TSS (NM_145426)	399	NM_001168667	67726	Mm.25632	NM_026342	ENSMUSG00000020523	Fam114a2	1810073G14Rik|9030624B09Rik	family with sequence similarity 114, member A2	protein-coding
mm_4348.1	chr1	171864592	171864611	+	1	NA	intron (NM_001289470, intron 3 of 8)	Lx6|LINE|L1	24904	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_122367.1	chr14	39392198	39392202	-	1	NA	intron (NM_001190187, intron 1 of 9)	intron (NM_001190187, intron 1 of 9)	-80229	NR_131973	432842	Mm.352566	NR_131973		LOC432842	-	uncharacterized LOC432842	ncRNA
mm_61863.1	chr7	88430300	88430320	+	1	NA	promoter-TSS (NM_028238)	promoter-TSS (NM_028238)	37	NM_028238	72433	Mm.276669	NM_028238	ENSMUSG00000030559	Rab38	2310011F14Rik|AU043391|cht	RAB38, member RAS oncogene family	protein-coding
mm_36705.1	chr4	97521517	97521519	-	1	NA	Intergenic	Intergenic	-60425	NM_001122952	18027	Mm.31274	NM_010905	ENSMUSG00000028565	Nfia	1110047K16Rik|9430022M17Rik|CTF|NF1-A|NF1A	nuclear factor I/A	protein-coding
mm_73679.1	chr8	111536834	111536853	+	1	NA	5' UTR (NM_133206, exon 1 of 4)	5' UTR (NM_133206, exon 1 of 4)	203	NM_001168621	170737	Mm.271578	NM_133206	ENSMUSG00000033545	Znrf1	B830022L21Rik|Rnf42|Zrfp1|nin283	zinc and ring finger 1	protein-coding
mm_61375.1	chr7	70365350	70365361	+	1	NA	promoter-TSS (NR_045850)	promoter-TSS (NR_045850)	-28	NR_045850	434198	Mm.389911	NR_045850	ENSMUSG00000100005	B130024G19Rik	-	RIKEN cDNA B130024G19 gene	ncRNA
mm_55904.1	chr6	83698082	83698103	-	1	NA	intron (NR_002871, intron 2 of 5)	MTE2a|LTR|ERVL-MaLR	12714	NR_075094	574519	Mm.487605	NR_002871	ENSMUSG00000085794	Vax2os	Vas2os|Vax2os1|Vax2os2	ventral anterior homeobox 2, opposite strand	ncRNA
mm_133683.1	chr16	92498086	92498094	+	1	NA	promoter-TSS (NM_172469)	promoter-TSS (NM_172469)	-57	NM_172469	209195	Mm.44747	NM_172469	ENSMUSG00000022949	Clic6	5730466J16Rik|AL022908|AW045520|CLIC1L	chloride intracellular channel 6	protein-coding
mm_81408.1	chr9	109051984	109051993	+	1	NA	intron (NM_025858, intron 3 of 5)	intron (NM_025858, intron 3 of 5)	-2878	NM_026381	66940	Mm.196533	NM_025858	ENSMUSG00000025647	Shisa5	2310008D10Rik|6430628I05Rik|Scotin|mShisa5	shisa family member 5	protein-coding
mm_91410.1	chr10	31445944	31445967	-	1	NA	promoter-TSS (NM_009413)	promoter-TSS (NM_009413)	-34	NM_009413	21987	Mm.439966	NM_009413	ENSMUSG00000000296	Tpd52l1	D53	tumor protein D52-like 1	protein-coding
mm_157225.1	chrX	13846509	13846591	-	1	NA	promoter-TSS (NM_001284505)	promoter-TSS (NM_001284505)	6	NM_001284505	12361	Mm.327591	NM_009806	ENSMUSG00000031012	Cask	DXPri1|DXRib1|LIN-2|Pals3|mLin-2	calcium/calmodulin-dependent serine protein kinase (MAGUK family)	protein-coding
mm_97652.1	chr11	79507538	79507568	+	1	NA	intron (NM_010897, intron 36 of 57)	B2_Mm1t|SINE|B2	-3471	NM_019409	18377	Mm.93335	NM_019409	ENSMUSG00000049612	Omg	-	oligodendrocyte myelin glycoprotein	protein-coding
mm_157976.1	chrX	93832702	93832713	-	1	NA	promoter-TSS (NM_145630)	promoter-TSS (NM_145630)	-612	NM_145630	236900	Mm.12775	NM_145630	ENSMUSG00000035232	Pdk3	2610001M10Rik|AI035637	pyruvate dehydrogenase kinase, isoenzyme 3	protein-coding
mm_41000.1	chr5	77387022	77387026	+	1	NA	intron (NM_008048, intron 1 of 4)	intron (NM_008048, intron 1 of 4)	21021	NM_001159518	29817	Mm.233470	NM_008048	ENSMUSG00000036256	Igfbp7	AGM|Fstl2|Mac25	insulin-like growth factor binding protein 7	protein-coding
mm_58814.1	chr7	16400305	16400331	+	1	NA	promoter-TSS (NM_198631)	promoter-TSS (NM_198631)	-878	NM_198631	330474	Mm.333594	NM_198631	ENSMUSG00000059273	Zc3h4	Bwq1|Gm768|Kiaa1064-hp|mKIAA1064	zinc finger CCCH-type containing 4	protein-coding
mm_101912.1	chr11	49712638	49712668	-	1	NA	promoter-TSS (NM_212484)	promoter-TSS (NM_212484)	69	NM_212484	104625	Mm.247113	NM_212484	ENSMUSG00000020362	Cnot6	CCR4	CCR4-NOT transcription complex, subunit 6	protein-coding
mm_115358.1	chr13	112800961	112800965	+	1	NA	5' UTR (NM_008903, exon 1 of 6)	5' UTR (NM_008903, exon 1 of 6)	186	NM_008247	19012	Mm.291029	NM_008247	ENSMUSG00000021759	Plpp1	Hic53|Hpic53|LPP-1|LPP1|PAP-2a|PAP2-alpha|PAP2a|Ppap2a|mPAP	phospholipid phosphatase 1	protein-coding
mm_166581.1	chr6	52866494	52866503	+	1	NA	intron (NM_173406, intron 2 of 4)	intron (NM_173406, intron 2 of 4)	43122	NM_001168277	231986	Mm.386865	NM_173406	ENSMUSG00000063568	Jazf1	AI591476|C820002C15|Jaz1|Tip27	JAZF zinc finger 1	protein-coding
mm_162388.1	chr1	75400973	75401020	+	1	NA	intron (NM_001173477, intron 1 of 4)	intron (NM_001173477, intron 1 of 4)	911	NM_001173477	11790	Mm.275397	NM_007463	ENSMUSG00000026207	Speg	AW125581|Apeg1|BPEG|D1Bwg1450e|SPEGalpha|SPEGbeta|mKIAA1297	SPEG complex locus	protein-coding
mm_131019.1	chr15	103563432	103563463	-	1	NA	exon (NM_008134, exon 3 of 4)	exon (NM_008134, exon 3 of 4)	1634	NM_001289587	14663	Mm.219621	NM_008134	ENSMUSG00000022491	Glycam1	MC26|Sgp50|glyCAM-1	glycosylation dependent cell adhesion molecule 1	protein-coding
mm_88281.1	chr10	75130568	75130631	+	1	NA	intron (NM_001081412, intron 2 of 22)	intron (NM_001081412, intron 2 of 22)	69703	NM_001081412	110279	Mm.333722	NM_001081412	ENSMUSG00000009681	Bcr	5133400C09Rik|AI561783|AI853148|mKIAA3017	breakpoint cluster region	protein-coding
mm_8536.1	chr1	155055180	155055185	-	1	NA	Intergenic	Intergenic	44454	NM_010500	15939	Mm.12246	NM_010500	ENSMUSG00000056708	Ier5	-	immediate early response 5	protein-coding
mm_12398.1	chr2	70142971	70142975	+	1	NA	intron (NM_177376, intron 8 of 34)	intron (NM_177376, intron 8 of 34)	103847	NM_177376	329421	Mm.99648	NM_177376	ENSMUSG00000042064	Myo3b	A430065P19Rik	myosin IIIB	protein-coding
mm_73176.1	chr8	95056670	95056678	+	1	NA	exon (NM_001042715, exon 3 of 18)	exon (NM_001042715, exon 3 of 18)	1571	NM_001042715	330830	Mm.277112	NM_001042715	ENSMUSG00000031786	Drc7	Ccdc135|Gm770|SRG-L|SRG-S	dynein regulatory complex subunit 7	protein-coding
mm_59880.1	chr7	30291917	30291939	+	1	NA	intron (NM_001081114, intron 1 of 13)	intron (NM_001081114, intron 1 of 13)	175	NM_001081114	76686	Mm.159258	NM_001081114	ENSMUSG00000013921	Clip3	1500005P14Rik|AI844915|Clipr-59	CAP-GLY domain containing linker protein 3	protein-coding
mm_62457.1	chr7	101451408	101451429	+	1	NA	exon (NM_001143849, exon 1 of 30)	exon (NM_001143849, exon 1 of 30)	166	NM_001243757	207728	Mm.247564	NM_001008548	ENSMUSG00000030653	Pde2a	CGS-PDE|cGSPDE	phosphodiesterase 2A, cGMP-stimulated	protein-coding
mm_111712.1	chr12	103701127	103701131	-	1	NA	Intergenic	Intergenic	-5600	NM_026687	68348	Mm.20149	NM_026687	ENSMUSG00000021081	Serpina1f	0610012A11Rik|AI327419|Serpina2|epserin	serine (or cysteine) peptidase inhibitor, clade A, member 1F	protein-coding
mm_170450.1	chr18	84659729	84659734	-	1	NA	Intergenic	Intergenic	-9636	NM_177450	338403	Mm.23278	NM_177450	ENSMUSG00000056162	Cndp1	AI746433|Cn1	carnosine dipeptidase 1 (metallopeptidase M20 family)	protein-coding
mm_60959.1	chr7	47516074	47516078	+	1	NA	Intergenic	Intergenic	-26494	NM_153101	235712	Mm.425459	NM_153101	ENSMUSG00000096719	Mrgpra2b	MrgA2|Mrgpra2|OTTMUSG00000028717	MAS-related GPR, member A2B	protein-coding
mm_13862.1	chr2	119742290	119742305	+	1	NA	promoter-TSS (NM_146125)	promoter-TSS (NM_146125)	-40	NM_146125	228550	Mm.65337	NM_146125	ENSMUSG00000027296	Itpka	-	inositol 1,4,5-trisphosphate 3-kinase A	protein-coding
mm_55363.1	chr6	57535411	57535421	-	1	NA	promoter-TSS (NM_175523)	promoter-TSS (NM_175523)	10	NM_175523	243382	Mm.396893	NM_175523	ENSMUSG00000037826	Ppm1k	2900063A19Rik|A930026L03Rik|PP2Cm	protein phosphatase 1K (PP2C domain containing)	protein-coding
mm_55105.1	chr6	50261744	50261788	-	1	NA	promoter-TSS (NM_018769)	promoter-TSS (NM_018769)	3	NM_018769	54722	Mm.248361	NM_018769	ENSMUSG00000029821	Dfna5	2310037D07Rik|4932441K13Rik|Dfna5h|EG14210|Fin15	deafness, autosomal dominant 5 (human)	protein-coding
mm_154687.1	chrX	7922415	7922428	+	1	NA	exon (NM_013892, exon 2 of 3)	exon (NM_013892, exon 2 of 3)	2599	NM_013892	30052	Mm.4881	NM_013892	ENSMUSG00000039278	Pcsk1n	AI848336|KEP|PEN|PEN19|PEN20|Pan3|SAAS|SAASCT|bLEN|lLEN|proSAAS	proprotein convertase subtilisin/kexin type 1 inhibitor	protein-coding
mm_72631.1	chr8	84664212	84664238	+	1	NA	Intergenic	CpG	-1373	NM_010499	15936	Mm.399	NM_010499	ENSMUSG00000053560	Ier2	AI317238|Ch1|Pip92	immediate early response 2	protein-coding
mm_170284.1	chr18	27599559	27599567	+	1	NA	Intergenic	RLTR19-int|LTR|ERVK	-960601	NR_045398	320624	Mm.50107	NR_045398		4930474G06Rik	-	RIKEN cDNA 4930474G06 gene	ncRNA
mm_66713.1	chr7	46030317	46030325	-	1	NA	promoter-TSS (NM_018795)	promoter-TSS (NM_018795)	-35	NM_018795	27421	Mm.63514	NM_018795	ENSMUSG00000030834	Abcc6	Abcc1b|DCC|Dyscalc1|Mrp6|dyscalc	ATP-binding cassette, sub-family C (CFTR/MRP), member 6	protein-coding
mm_77685.1	chr8	125898292	125898322	-	1	NA	promoter-TSS (NM_175561)	promoter-TSS (NM_175561)	10	NM_175561	270109	Mm.145535	NM_175561	ENSMUSG00000060212	Pcnx2	A830048P05|AU067631|E330039K12Rik|Pcnxl2|mKIAA0435	pecanex homolog 2	protein-coding
mm_29061.1	chr3	103778310	103778326	-	1	NA	intron (NM_001301304, intron 1 of 15)	intron (NM_001301304, intron 1 of 15)	12957	NM_001301306	15257	Mm.20827	NM_010432	ENSMUSG00000008730	Hipk1	1110062K04Rik|Myak	homeodomain interacting protein kinase 1	protein-coding
mm_87318.1	chr10	42860349	42860377	+	1	NA	promoter-TSS (NM_172938)	promoter-TSS (NM_172938)	-149	NM_172938	268297	Mm.98731	NM_172938	ENSMUSG00000044770	Scml4	9330161D17|mFLJ00197	sex comb on midleg-like 4 (Drosophila)	protein-coding
mm_5846.1	chr1	52963269	52963269	-	1	NA	Intergenic	Intergenic	-10429	NM_144953	67080	Mm.236287	NM_144953	ENSMUSG00000043629	1700019D03Rik	2410136C24Rik|AA410151|smAKAP	RIKEN cDNA 1700019D03 gene	protein-coding
mm_121430.1	chr14	120359436	120359452	+	1	NA	intron (NM_175341, intron 2 of 8)	B4A|SINE|B4	83775	NM_175341	105559	Mm.238266	NM_175341	ENSMUSG00000022139	Mbnl2	1110002M11Rik|AI047808|AI837313|AI849185|AL118326|MBLL|R75232|mKIAA4072	muscleblind-like 2	protein-coding
mm_107655.1	chr12	52773081	52773094	+	1	NA	intron (NM_198111, intron 1 of 13)	intron (NM_198111, intron 1 of 13)	73704	NM_198111	238161	Mm.310822	NM_198111	ENSMUSG00000061603	Akap6	AI482140|Akapalpha|Akapbeta|PRKA	A kinase (PRKA) anchor protein 6	protein-coding
mm_51837.1	chr6	90302067	90302081	+	1	NA	intron (NM_177738, intron 2 of 4)	intron (NM_177738, intron 2 of 4)	804	NM_177738	243535	Mm.233854	NM_177738	ENSMUSG00000049694	BC048671	-	cDNA sequence BC048671	protein-coding
mm_46559.1	chr5	106696820	106696839	-	1	NA	promoter-TSS (NM_026856)	promoter-TSS (NM_026856)	1	NM_026856	52397	Mm.249474	NM_026856	ENSMUSG00000049606	Zfp644	1110068L01Rik|AA408882|BM-005|D5Ertd689e|Zep-2	zinc finger protein 644	protein-coding
mm_141990.1	chr17	35172609	35172638	-	1	NA	5' UTR (NM_019467, exon 3 of 8)	5' UTR (NM_019467, exon 3 of 8)	3378	NM_019467	11629	Mm.10747	NM_019467	ENSMUSG00000024397	Aif1	AI607846|AIF-1|D17H6S50E|G1|Iba1	allograft inflammatory factor 1	protein-coding
mm_34504.1	chr4	148667177	148667199	+	1	NA	intron (NM_001085505, intron 7 of 10)	intron (NM_001085505, intron 7 of 10)	23871	NM_001085505	230909	Mm.332067	NM_001085505	ENSMUSG00000070577	Gm572	b2b1167Clo	predicted gene 572	protein-coding
mm_135205.1	chr16	36561787	36561799	-	1	NA	intron (NM_013803, intron 1 of 6)	intron (NM_013803, intron 1 of 6)	341	NM_013803	12374	Mm.103619	NM_013803	ENSMUSG00000051980	Casr	CaR|Gprc2a	calcium-sensing receptor	protein-coding
mm_59091.1	chr7	19696509	19696519	+	1	NA	exon (NM_009696, exon 4 of 4)	exon (NM_009696, exon 4 of 4)	1884	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_168513.1	chr1	156524061	156524068	+	1	NA	Intergenic	Intergenic	-34723	NM_009595	11352	Mm.329515	NM_009595	ENSMUSG00000026596	Abl2	AA536808|Abll|Arg	v-abl Abelson murine leukemia viral oncogene 2 (arg, Abelson-related gene)	protein-coding
mm_140475.1	chr17	94834889	94834924	+	1	NA	promoter-TSS (NR_045964)	promoter-TSS (NR_045964)	-107	NR_045963	100038746	Mm.456686	NR_045963	ENSMUSG00000066057	Gm1976	100038868	predicted gene 1976	ncRNA
mm_159099.1	chr2	36688076	36688076	+	1	NA	promoter-TSS (NM_146938)	promoter-TSS (NM_146938)	72	NM_146938	258940	Mm.223338	NM_146938	ENSMUSG00000094764	Olfr346	MOR136-11	olfactory receptor 346	protein-coding
mm_157899.1	chrX	77845046	77845088	-	1	NA	exon (NM_017471, exon 3 of 7)	exon (NM_017471, exon 3 of 7)	8433	NM_017471	54192	Mm.8034	NM_017471	ENSMUSG00000000003	Pbsn	PB|Prbs	probasin	protein-coding
mm_154503.1	chrM	11925	11936	-	1	NA	NA	Intergenic	NA	NA								
mm_117523.1	chr13	81633120	81633153	-	1	NA	promoter-TSS (NM_054053)	promoter-TSS (NM_054053)	8	NM_054053	110789	Mm.288694	NM_054053	ENSMUSG00000069170	Adgrv1	Frings|Gpr98|Mass1|Mgr1|VLGR1	adhesion G protein-coupled receptor V1	protein-coding
mm_166552.1	chr6	41312311	41312334	+	1	NA	exon (NM_001003405, exon 3 of 5)	exon (NM_001003405, exon 3 of 5)	2388	NM_001003405	103964	Mm.333022	NM_001003405	ENSMUSG00000036938	Try5	1810049H19Rik|Tc|Tesp4	trypsin 5	protein-coding
mm_63059.1	chr7	122067165	122067216	+	1	NA	promoter-TSS (NM_138589)	promoter-TSS (NM_138589)	-8	NM_138589	28018	Mm.282122	NM_138589	ENSMUSG00000030870	Ubfd1	AI467302|D7Wsu105e|D7Wsu128e|Ubph	ubiquitin family domain containing 1	protein-coding
mm_126369.1	chr15	80126554	80126559	+	1	NA	Intergenic	B1_Mur4|SINE|Alu	-6598	NM_025609	66513	Mm.288245	NM_025609	ENSMUSG00000022414	Tab1	2310012M03Rik|Map3k7ip1|b2b449Clo	TGF-beta activated kinase 1/MAP3K7 binding protein 1	protein-coding
mm_78337.1	chr9	25265408	25265433	+	1	NA	exon (NM_001205367, exon 2 of 13)	exon (NM_001205367, exon 2 of 13)	12981	NM_001205367	235072	Mm.270259	NM_009859	ENSMUSG00000001833	Sept7	Cdc10|E430034N22	septin 7	protein-coding
mm_39720.1	chr5	28165360	28165370	+	1	NA	promoter-TSS (NM_010134)	promoter-TSS (NM_010134)	-331	NM_010134	13799	Mm.4298	NM_010134	ENSMUSG00000039095	En2	BB131122|En-2	engrailed 2	protein-coding
mm_142058.1	chr17	35667547	35667618	-	1	NA	promoter-TSS (NM_175137)	promoter-TSS (NM_175137)	10	NM_175137	68915	Mm.32002	NM_175137	ENSMUSG00000038838	Vars2	1190004I24Rik|Vars2l|mKIAA1885	valyl-tRNA synthetase 2, mitochondrial	protein-coding
mm_109104.1	chr12	105336809	105336837	+	1	NA	promoter-TSS (NR_125773)	promoter-TSS (NR_125773)	-170	NR_125773	69952	Mm.158311	NR_045047	ENSMUSG00000097929	Tunar	2810011L19Rik|Tuna	Tcl1 upstream neural differentiation associated RNA	ncRNA
mm_139920.1	chr17	70974233	70974261	+	1	NA	3' UTR (NM_023402, exon 4 of 4)	3' UTR (NM_023402, exon 4 of 4)	16269	NM_023402	67938	Mm.261329	NM_023402	ENSMUSG00000034868	Myl12b	1500001M02Rik|C77744|Mylc2b|RLC-B	myosin, light chain 12B, regulatory	protein-coding
mm_93083.1	chr10	89533592	89533635	-	1	NA	promoter-TSS (NM_001163504)	promoter-TSS (NM_001163504)	9	NM_001163504	20186	Mm.3095	NM_009108	ENSMUSG00000047638	Nr1h4	AI957360|Fxr|HRR1|RIP14|Rxrip14	nuclear receptor subfamily 1, group H, member 4	protein-coding
mm_88905.1	chr10	81179151	81179205	+	1	NA	TTS (NR_028549)	TTS (NR_028549)	217	NR_028549	100217454		NR_028549	ENSMUSG00000064441	Snord37	MBII-376	small nucleolar RNA, C/D box 37	snoRNA
mm_82530.1	chr9	20668045	20668096	-	1	NA	TTS (NM_173777)	TTS (NM_173777)	15940	NM_023371	23988	Mm.7906	NM_023371	ENSMUSG00000032171	Pin1	0610025L01Rik|D9Bwg1161e	protein (peptidyl-prolyl cis/trans isomerase) NIMA-interacting 1	protein-coding
mm_22949.1	chr3	32364912	32364928	+	1	NA	promoter-TSS (NR_027966)	promoter-TSS (NR_027966)	-569	NR_027966	67576	Mm.435324	NR_027966		4930429B21Rik	-	RIKEN cDNA 4930429B21 gene	ncRNA
mm_86451.1	chr10	4334537	4334553	+	1	NA	intron (NM_031185, intron 2 of 3)	intron (NM_031185, intron 2 of 3)	53563	NM_001033466	381990	Mm.262466	NM_001033466	ENSMUSG00000075327	Zbtb2	Gm1103	zinc finger and BTB domain containing 2	protein-coding
mm_94973.1	chr11	30985456	30985459	+	1	NA	intron (NM_026527, intron 1 of 2)	intron (NM_026527, intron 1 of 2)	908	NM_026527	68044	Mm.32656	NM_026527	ENSMUSG00000020309	Chac2	-	ChaC, cation transport regulator 2	protein-coding
mm_11362.1	chr2	30952956	30953016	+	1	NA	promoter-TSS (NM_133673)	promoter-TSS (NM_133673)	-15	NM_133673	30934	Mm.249164	NM_133673	ENSMUSG00000026848	Tor1b	2610016F05Rik|DQ1|torsinB	torsin family 1, member B	protein-coding
mm_11098.1	chr2	28032088	28032098	+	1	NA	intron (NM_015734, intron 64 of 65)	intron (NM_015734, intron 64 of 65)	52785	NM_010190	14134	Mm.182935	NM_010190	ENSMUSG00000026835	Fcnb	Fcn2	ficolin B	protein-coding
mm_31430.1	chr4	48085552	48085556	+	1	NA	3' UTR (NM_015743, exon 8 of 8)	3' UTR (NM_015743, exon 8 of 8)	34308	NM_001307989	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_37371.1	chr4	120951665	120951697	-	1	NA	promoter-TSS (NM_001005788)	promoter-TSS (NM_001005788)	20	NM_001005788	381549	Mm.331840	NM_001005788	ENSMUSG00000064141	Zfp69	Gm1029|Krab2|Zfp63	zinc finger protein 69	protein-coding
mm_57765.1	chr6	129234020	129234027	-	1	NA	intron (NR_040265, intron 1 of 2)	intron (NR_040265, intron 1 of 2)	4022	NR_040265	76432	Mm.261738	NR_040265	ENSMUSG00000097354	2310001H17Rik	AI646108	RIKEN cDNA 2310001H17 gene	ncRNA
mm_162408.1	chr1	86504392	86504410	-	1	NA	Intergenic	CpG	-22335	NM_008972	19231	Mm.19187	NM_008972	ENSMUSG00000026238	Ptma	Thym	prothymosin alpha	protein-coding
mm_123728.1	chr14	70167993	70168004	-	1	NA	exon (NM_001253736, exon 7 of 10)	exon (NM_001253736, exon 7 of 10)	-8496	NM_001004155	268759	Mm.12148	NM_001004155	ENSMUSG00000044551	9930012K11Rik	-	RIKEN cDNA 9930012K11 gene	protein-coding
mm_116689.1	chr13	49308987	49309001	-	1	NA	intron (NM_015759, intron 1 of 17)	intron (NM_015759, intron 1 of 17)	214	NM_015759	30938	Mm.291089	NM_015759	ENSMUSG00000037946	Fgd3	5830461L01Rik|ZFYVE5	FYVE, RhoGEF and PH domain containing 3	protein-coding
mm_112211.1	chr12	113428535	113428547	-	1	NA	Intergenic	Intergenic	-61024	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_138049.1	chr17	33926166	33926191	+	1	NA	exon (NM_009318, exon 5 of 8)	exon (NM_009318, exon 5 of 8)	-3716	NM_009059	19732	Mm.43777	NM_009059	ENSMUSG00000041354	Rgl2	KE1.5|Rab2l|Rgt2|Rlf	ral guanine nucleotide dissociation stimulator-like 2	protein-coding
mm_166894.1	chr7	28302200	28302214	-	1	NA	promoter-TSS (NM_007866)	promoter-TSS (NM_007866)	-422	NM_007866	13389	Mm.12896	NM_007866	ENSMUSG00000003436	Dll3	pu|pudgy	delta-like 3 (Drosophila)	protein-coding
mm_49318.1	chr6	18848605	18848693	+	1	NA	promoter-TSS (NM_133939)	promoter-TSS (NM_133939)	14	NM_133939	76522	Mm.275158	NM_133939	ENSMUSG00000044155	Lsm8	2010003I05Rik|AW214405|Naa38	LSM8 homolog, U6 small nuclear RNA associated	protein-coding
mm_63895.1	chr7	138848477	138848490	+	1	NA	intron (NM_026391, intron 2 of 8)	intron (NM_026391, intron 2 of 8)	2097	NM_026391	52432	Mm.258739	NM_026391	ENSMUSG00000041769	Ppp2r2d	1300017E19Rik|D7Ertd753e|MDS026	protein phosphatase 2, regulatory subunit B, delta	protein-coding
mm_153032.1	chr19	31765028	31765079	-	1	NA	promoter-TSS (NM_001013833)	promoter-TSS (NM_001013833)	-20	NM_001013833	19091	Mm.381170	NM_011160	ENSMUSG00000052920	Prkg1	AW125416|CGKI|Gm19690|Prkg1b|Prkgr1b	protein kinase, cGMP-dependent, type I	protein-coding
mm_165565.1	chr3	16183614	16183618	-	1	NA	intron (NR_027375, intron 1 of 5)	CpG	433	NM_001145919	229096	Mm.23834	NM_172677	ENSMUSG00000047213	Ythdf3	9130022A11Rik	YTH domain family 3	protein-coding
mm_115632.1	chr13	12176864	12176871	-	1	NA	Intergenic	RLTR17|LTR|ERVK	9621	NR_045170	328186	Mm.188154	NM_183202		Gm10336	B330003H21|ENSMUSG00000071543	predicted gene 10336	ncRNA
mm_84452.1	chr9	66514568	66514597	-	1	NA	promoter-TSS (NM_175206)	promoter-TSS (NM_175206)	11	NM_175206	74165	Mm.297998	NM_175206	ENSMUSG00000050503	Fbxl22	1110004B15Rik	F-box and leucine-rich repeat protein 22	protein-coding
mm_41812.1	chr5	103783812	103783830	+	1	NA	exon (NM_133919, exon 3 of 20)	exon (NM_133919, exon 3 of 20)	29248	NM_001080798	17355	Mm.6949	NM_133919	ENSMUSG00000029313	Aff1	9630032B01Rik|AW319193|Af4|Mllt2h|Rob	AF4/FMR2 family, member 1	protein-coding
mm_31225.1	chr4	44032361	44032373	+	1	NA	intron (NM_001290470, intron 5 of 5)	intron (NM_001290470, intron 5 of 5)	19717	NM_001290470	12757	Mm.298875	NM_016760	ENSMUSG00000028478	Clta	AV026556|Lca	clathrin, light polypeptide (Lca)	protein-coding
mm_40187.1	chr5	36374875	36374883	+	1	NA	intron (NM_030889, intron 1 of 26)	L1MB5|LINE|L1	23260	NM_030889	81840	Mm.34113	NM_030889	ENSMUSG00000029093	Sorcs2	N28137|mKIAA1329	sortilin-related VPS10 domain containing receptor 2	protein-coding
mm_121775.1	chr14	19890400	19890416	-	1	NA	intron (NM_001038637, intron 4 of 4)	B4A|SINE|B4	51483	NR_105025	52512	Mm.483998	NR_105025		D14Ertd670e	-	DNA segment, Chr 14, ERATO Doi 670, expressed	ncRNA
mm_137875.1	chr17	31471043	31471047	+	1	NA	intron (NM_008804, intron 16 of 18)	intron (NM_008804, intron 16 of 18)	41442	NM_021322	57773	Mm.143771	NM_021322	ENSMUSG00000024037	Wdr4	AI415180|AI448349|D530049K22Rik	WD repeat domain 4	protein-coding
mm_91467.1	chr10	34178577	34178581	-	1	NA	intron (NM_172508, intron 2 of 5)	AT_rich|Low_complexity|Low_complexity	28972	NM_172508	212898	Mm.34557	NM_172508	ENSMUSG00000039497	Dse	6030499O08|AI480506|B130024B19Rik|DS-epi1|Sart2	dermatan sulfate epimerase	protein-coding
mm_10206.1	chr2	5137757	5137772	+	1	NA	promoter-TSS (NM_028804)	promoter-TSS (NM_028804)	-12	NM_028804	74186	Mm.274715	NM_028804	ENSMUSG00000026676	Ccdc3	2310045O21Rik	coiled-coil domain containing 3	protein-coding
mm_8158.1	chr1	136949433	136949461	-	1	NA	intron (NM_030676, intron 2 of 8)	intron (NM_030676, intron 2 of 8)	4183	NM_001159769	26424	Mm.16794	NM_030676	ENSMUSG00000026398	Nr5a2	AU020803|D1Ertd308e|Ftf|LRH-1|UF2-H3B	nuclear receptor subfamily 5, group A, member 2	protein-coding
mm_128862.1	chr15	72809946	72809960	-	1	NA	non-coding (NR_002864, exon 1 of 1)	non-coding (NR_002864, exon 1 of 1)	371	NR_002864	353342	Mm.440245	NR_002864	ENSMUSG00000106847	Peg13	-	paternally expressed 13	ncRNA
mm_128351.1	chr15	39943690	39943777	-	1	NA	promoter-TSS (NM_172814)	promoter-TSS (NM_172814)	24	NM_172814	239393	Mm.39874	NM_172814	ENSMUSG00000022305	Lrp12	AI848829|C820005L12Rik|LRP-12	low density lipoprotein-related protein 12	protein-coding
mm_23594.1	chr3	64977532	64977546	+	1	NA	Intergenic	Intergenic	-131829	NM_010597	16497	Mm.316402	NM_010597	ENSMUSG00000027827	Kcnab1	Akr8a8|Kvbeta1.1|mKv(beta)1	potassium voltage-gated channel, shaker-related subfamily, beta member 1	protein-coding
mm_50852.1	chr6	54889013	54889033	+	1	NA	3' UTR (NM_199143, exon 5 of 5)	3' UTR (NM_199143, exon 5 of 5)	72107	NM_199143	387524	Mm.286149	NM_199143	ENSMUSG00000058446	Znrf2	1190002C14Rik|AU044205|D6Ertd365e	zinc and ring finger 2	protein-coding
mm_36281.1	chr4	63860893	63860921	-	1	NA	exon (NM_009403, exon 1 of 4)	exon (NM_009403, exon 1 of 4)	377	NM_009403	21949	Mm.4664	NM_009403	ENSMUSG00000028362	Tnfsf8	CD153|CD30LG|Cd30l|Tnlg3a	tumor necrosis factor (ligand) superfamily, member 8	protein-coding
mm_44023.1	chr5	147418647	147418659	+	1	NA	promoter-TSS (NR_033625)	promoter-TSS (NR_033625)	33	NR_033625	100039805	Mm.394705	NR_033625	ENSMUSG00000106820	D5Ertd605e	Gm2433	DNA segment, Chr 5, ERATO Doi 605, expressed	ncRNA
mm_141404.1	chr17	29347754	29347792	-	1	NA	exon (NM_019880, exon 1 of 12)	exon (NM_019880, exon 1 of 12)	131	NM_019880	56462	Mm.285322	NM_019880	ENSMUSG00000024012	Mtch1	2310034O17Rik|AI255158|AU018396|C77849|PSAP	mitochondrial carrier 1	protein-coding
mm_145157.1	chr18	46525200	46525232	+	1	NA	intron (NM_173423, intron 1 of 2)	CpG	755	NM_173423	240263	Mm.38249	NM_173423	ENSMUSG00000033319	Fem1c	2610312A07Rik|3632443A22Rik|AI646567	fem-1 homolog c (C.elegans)	protein-coding
mm_135156.1	chr16	35858365	35858375	-	1	NA	exon (NM_001039530, exon 6 of 17)	exon (NM_001039530, exon 6 of 17)	13012	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_131493.1	chr16	17276663	17276680	+	1	NA	exon (NM_177473, exon 2 of 10)	exon (NM_177473, exon 2 of 10)	371	NM_177473	224019	Mm.246388	NM_177473	ENSMUSG00000055692	Tmem191c	4933405M22Rik|D16Bwg1494e|MNCb-4137	transmembrane protein 191C	protein-coding
mm_145731.1	chr18	64264870	64264881	+	1	NA	intron (NM_009182, intron 2 of 5)	intron (NM_009182, intron 2 of 5)	10516	NM_009182	20451	Mm.252110	NM_009182	ENSMUSG00000056812	St8sia3	AI847333|ST8SiaIII|Siat8c	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3	protein-coding
mm_165979.1	chr4	102986401	102986409	+	1	NA	promoter-TSS (NM_026100)	promoter-TSS (NM_026100)	26	NM_026100	67344	Mm.111346	NM_026100	ENSMUSG00000028523	Tctex1d1	1700055O19Rik	Tctex1 domain containing 1	protein-coding
mm_63800.1	chr7	132931352	132931363	+	1	NA	Intergenic	CpG	-18265	NM_207302	360216	Mm.389984	NM_207302	ENSMUSG00000030967	Zranb1	9330160G10Rik|D7Wsu87e|Gm1956|Trabid	zinc finger, RAN-binding domain containing 1	protein-coding
mm_160165.1	chr7	44748021	44748021	-	1	NA	promoter-TSS (NM_133945)	promoter-TSS (NM_133945)	328	NM_001289836	243963	Mm.382935	NM_178734	ENSMUSG00000048012	Zfp473	D030014N22Rik|Znf473|zfp-100	zinc finger protein 473	protein-coding
mm_104303.1	chr11	90638068	90638100	-	1	NA	promoter-TSS (NM_011505)	promoter-TSS (NM_011505)	24	NM_011505	20913	Mm.207203	NM_011505	ENSMUSG00000020546	Stxbp4	6030470M02Rik|Synip	syntaxin binding protein 4	protein-coding
mm_142041.1	chr17	35267185	35267221	-	1	NA	TTS (NM_001267808)	TTS (NM_001267808)	4080	NM_001267808	14980	Mm.439675	NM_001267808		H2-L	H-2L	histocompatibility 2, D region locus L	protein-coding
mm_156904.1	chrX	169036611	169036672	+	1	NA	promoter-TSS (NM_178754)	promoter-TSS (NM_178754)	30	NR_109847	11856	Mm.441810	NM_009707	ENSMUSG00000031355	Arhgap6	AI504284|RhoGAPX-1	Rho GTPase activating protein 6	protein-coding
mm_95647.1	chr11	53723939	53723955	+	1	NA	exon (NM_010558, exon 4 of 4)	exon (NM_010558, exon 4 of 4)	3153	NM_010558	16191	Mm.4461	NM_010558	ENSMUSG00000036117	Il5	Il-5	interleukin 5	protein-coding
mm_82346.1	chr9	13826543	13826554	-	1	NA	non-coding (NR_037622, exon 1 of 11)	non-coding (NR_037622, exon 1 of 11)	505	NR_037622	74360	Mm.157212	NM_026665	ENSMUSG00000031922	Cep57	3110002L15Rik|4921510P06Rik|4931428M20Rik|AI467480|Tsp57|mKIAA0092	centrosomal protein 57	protein-coding
mm_70183.1	chr7	143766986	143766996	-	1	NA	promoter-TSS (NM_203492)	promoter-TSS (NM_203492)	2	NM_203492	381974	Mm.297839	NM_203492	ENSMUSG00000050276	Mrgprg	Gm1098|Mrgg	MAS-related GPR, member G	protein-coding
mm_140820.1	chr17	23564118	23564161	-	1	NA	promoter-TSS (NM_001033496)	promoter-TSS (NM_001033496)	87	NM_001033496	449521	Mm.268582	NM_001033496	ENSMUSG00000071256	Zfp213	BC038178|D17Ertd197e	zinc finger protein 213	protein-coding
mm_49412.1	chr6	28645399	28645409	+	1	NA	intron (NM_019776, intron 11 of 23)	intron (NM_019776, intron 11 of 23)	165056	NM_019776	56463	Mm.439987	NM_019776	ENSMUSG00000001424	Snd1	AL033314|Tudor-SN	staphylococcal nuclease and tudor domain containing 1	protein-coding
mm_155617.1	chrX	83116796	83116806	+	1	NA	intron (NM_007868, intron 1 of 78)	intron (NM_007868, intron 1 of 78)	167931	NM_007868	13405	Mm.275608	NM_007868	ENSMUSG00000045103	Dmd	DXSmh7|DXSmh9|Dp427|Dp71|dys|mdx|pke	dystrophin, muscular dystrophy	protein-coding
mm_139975.1	chr17	71781276	71781284	+	1	NA	promoter-TSS (NM_030179)	promoter-TSS (NM_030179)	-19	NM_001271483	78785	Mm.196382	NM_030179	ENSMUSG00000024059	Clip4	1700024K14Rik|1700074B05Rik|4833417L20Rik|5830409B12Rik|Rsnl2	CAP-GLY domain containing linker protein family, member 4	protein-coding
mm_70482.1	chr8	12395875	12395885	+	1	NA	5' UTR (NM_009233, exon 1 of 1)	5' UTR (NM_009233, exon 1 of 1)	361	NM_009233	20664	Mm.39088	NM_009233	ENSMUSG00000096014	Sox1	BB176347|Sox-1	SRY (sex determining region Y)-box 1	protein-coding
mm_155836.1	chrX	100777274	100777296	+	1	NA	promoter-TSS (NM_001177780)	promoter-TSS (NM_001177780)	14	NM_001177780	53310	Mm.4615	NM_016747	ENSMUSG00000000881	Dlg3	Dlgh3|SAP102|mKIAA1232	discs, large homolog 3 (Drosophila)	protein-coding
mm_71334.1	chr8	45507503	45507522	+	1	NA	promoter-TSS (NM_001205219)	promoter-TSS (NM_001205219)	-276	NM_172752	234214	Mm.211096	NM_172752	ENSMUSG00000031626	Sorbs2	2010203O03Rik|9430041O17Rik|A530071H08|Argbp2|mKIAA0777|nArgBP2	sorbin and SH3 domain containing 2	protein-coding
mm_88671.1	chr10	80017861	80017905	+	1	NA	exon (NM_001142701, exon 2 of 23)	exon (NM_001142701, exon 2 of 23)	968	NM_001347074	70719	Mm.243954	NM_027521	ENSMUSG00000035697	Hmha1	6330406L22Rik|AW539505|Ha-1	histocompatibility (minor) HA-1	protein-coding
mm_72039.1	chr8	70841273	70841302	+	1	NA	TTS (NM_032397)	TTS (NM_032397)	-1567	NM_027560	70807	Mm.24215	NM_027560	ENSMUSG00000002910	Arrdc2	4632416I05Rik|Ilad1	arrestin domain containing 2	protein-coding
mm_35559.1	chr4	41569485	41569491	-	1	NA	promoter-TSS (NM_027993)	promoter-TSS (NM_027993)	39	NM_001159583	71901	Mm.39215	NM_027993	ENSMUSG00000028439	Fam219a	2310028H24Rik	family with sequence similarity 219, member A	protein-coding
mm_13443.1	chr2	105130965	105130981	+	1	NA	intron (NM_144783, intron 1 of 9)	CpG	4444	NM_144783	22431	Mm.389339	NM_144783	ENSMUSG00000016458	Wt1	D630046I19Rik|Wt-1	Wilms tumor 1 homolog	protein-coding
mm_93281.1	chr10	96163277	96163291	-	1	NA	Intergenic	Intergenic	-62923	NR_110448	74881	Mm.410819	NR_110448		4930459C07Rik	-	RIKEN cDNA 4930459C07 gene	ncRNA
mm_163811.1	chr14	19416273	19416290	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	186306	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_151200.1	chr19	53537675	53537680	+	1	NA	intron (NM_001085390, intron 3 of 3)	intron (NM_001085390, intron 3 of 3)	8359	NM_001085390	240672	Mm.482424	NM_001085390	ENSMUSG00000034765	Dusp5	Gm337	dual specificity phosphatase 5	protein-coding
mm_12367.1	chr2	69821677	69821696	+	1	NA	promoter-TSS (NM_177784)	promoter-TSS (NM_177784)	-684	NM_177784	277396	Mm.138073	NM_177784	ENSMUSG00000042155	Klhl23	C130068N17Rik	kelch-like 23	protein-coding
mm_171112.1	chr3	137600417	137600422	+	1	NA	Intergenic	Intergenic	-23253	NM_030143	73284	Mm.250841	NM_030143	ENSMUSG00000046818	Ddit4l	1700037B15Rik|1700108M02Rik|REDD2|RTP801L|Smhs1	DNA-damage-inducible transcript 4-like	protein-coding
mm_100507.1	chr11	120491963	120491971	+	1	NA	5' UTR (NM_013770, exon 1 of 11)	5' UTR (NM_013770, exon 1 of 11)	130	NM_013770	27376	Mm.3991	NM_013770	ENSMUSG00000025792	Slc25a10	Dic	solute carrier family 25 (mitochondrial carrier, dicarboxylate transporter), member 10	protein-coding
mm_163971.1	chr14	55510470	55510485	+	1	NA	promoter-TSS (NM_009947)	promoter-TSS (NM_009947)	29	NM_001136057	12891	Mm.5249	NM_009947	ENSMUSG00000022212	Cpne6	AU067659|BB076446	copine VI	protein-coding
mm_47374.1	chr5	122987402	122987447	-	1	NA	intron (NM_001003953, intron 2 of 22)	intron (NM_001003953, intron 2 of 22)	1675	NM_001003953	30841	Mm.86406	NM_013910	ENSMUSG00000029475	Kdm2b	Cxxc2|Fbl10|Fbxl10|Jhdm1b|PCCX2	lysine (K)-specific demethylase 2B	protein-coding
mm_170058.1	chr17	30624287	30624288	-	1	NA	non-coding (NR_045287, exon 3 of 4)	non-coding (NR_045287, exon 3 of 4)	2618	NR_045287	67522	Mm.254797	NR_045287	ENSMUSG00000099474	1700097N02Rik	-	RIKEN cDNA 1700097N02 gene	ncRNA
mm_22699.1	chr3	18054234	18054249	+	1	NA	promoter-TSS (NM_021560)	promoter-TSS (NM_021560)	-84	NM_021560	59058	Mm.149938	NM_021560	ENSMUSG00000025128	Bhlhe22	Beta3|Beta3a|Bhlhb5	basic helix-loop-helix family, member e22	protein-coding
mm_2979.1	chr1	133130085	133130106	+	1	NA	Intergenic	Intergenic	-1071	NM_133819	108954	Mm.293628	NM_133819	ENSMUSG00000046062	Ppp1r15b	1810033K10Rik|AI606441|C530022L24Rik|CReP	protein phosphatase 1, regulatory (inhibitor) subunit 15b	protein-coding
mm_33578.1	chr4	132515823	132515828	+	1	NA	Intergenic	ID_B1|SINE|B4	-5369	NM_144907	230784	Mm.23608	NM_144907	ENSMUSG00000028893	Sesn2	HI95|SEST2|Ses2	sestrin 2	protein-coding
mm_44368.1	chr5	17813045	17813089	-	1	NA	exon (NM_001159558, exon 8 of 16)	exon (NM_001159558, exon 8 of 16)	22829	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_124606.1	chr15	3279286	3279296	+	1	NA	exon (NM_009155, exon 5 of 5)	exon (NM_009155, exon 5 of 5)	8314	NM_009155	20363	Mm.392203	NM_009155	ENSMUSG00000064373	Selenop	AU018766|D15Ucla1|Se-P|Sepp1|selp	selenoprotein P	protein-coding
mm_113087.1	chr13	23880883	23880884	+	1	NA	intron (NM_001170638, intron 10 of 12)	L1MA8|LINE|L1	10610	NM_001170638	20504	Mm.2656	NM_009198	ENSMUSG00000021335	Slc17a1	NAPI-1|Napi1|Npt1	solute carrier family 17 (sodium phosphate), member 1	protein-coding
mm_57013.1	chr6	121173776	121173783	-	1	NA	Intergenic	Intergenic	-9888	NM_001304774	74043	Mm.491240	NM_028730	ENSMUSG00000067825	Pex26	4632428M11Rik	peroxisomal biogenesis factor 26	protein-coding
mm_87273.1	chr10	41810529	41810580	+	1	NA	promoter-TSS (NM_001162908)	promoter-TSS (NM_001162908)	-20	NM_001162908	140742	Mm.139418	NM_001013370	ENSMUSG00000038332	Sesn1	1110002G11Rik|AU044290|Pa26|Sest1	sestrin 1	protein-coding
mm_111231.1	chr12	84760855	84760873	-	1	NA	exon (NM_023409, exon 3 of 4)	exon (NM_023409, exon 3 of 4)	12248	NM_023409	67963	Mm.282556	NM_023409	ENSMUSG00000021242	Npc2	2700012J19Rik|AA408070|AU045843|HE1	Niemann-Pick type C2	protein-coding
mm_152435.1	chr19	10725302	10725311	-	1	NA	exon (NM_007650, exon 5 of 11)	exon (NM_007650, exon 5 of 11)	13668	NM_007650	12507	Mm.779	NM_007650	ENSMUSG00000024669	Cd5	Ly-1|Ly-12|Ly-A|Lyt-1	CD5 antigen	protein-coding
mm_121869.1	chr14	20734558	20734584	-	1	NA	promoter-TSS (NM_010811)	promoter-TSS (NM_010811)	-9	NM_010811	17423	Mm.4084	NM_010811	ENSMUSG00000039308	Ndst2	Mndns|NDST-2	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 2	protein-coding
mm_158701.1	chrX	162072419	162072423	-	1	NA	intron (NM_001081052, intron 1 of 7)	intron (NM_001081052, intron 1 of 7)	87020	NM_001081052	195727	Mm.336313	NM_001081052	ENSMUSG00000059493	Nhs	Gm389|Gm48|Nhs1|Xcat	Nance-Horan syndrome (human)	protein-coding
mm_34389.1	chr4	144927395	144927410	+	1	NA	3' UTR (NM_001172424, exon 7 of 7)	3' UTR (NM_001172424, exon 7 of 7)	34265	NM_011303	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding
mm_137928.1	chr17	32536577	32536615	+	1	NA	promoter-TSS (NM_024442)	promoter-TSS (NM_024442)	-33	NM_024442	70101	Mm.30504	NM_024442	ENSMUSG00000048440	Cyp4f16	2310021J05Rik|AI746515	cytochrome P450, family 4, subfamily f, polypeptide 16	protein-coding
mm_21037.1	chr2	152490201	152490212	-	1	NA	promoter-TSS (NM_001002791)	promoter-TSS (NM_001002791)	-68	NM_001002791	442835	Mm.99065	NM_001002791	ENSMUSG00000027468	Defb22	9230002F21Rik	defensin beta 22	protein-coding
mm_143927.1	chr17	85688253	85688275	-	1	NA	promoter-TSS (NM_011380)	promoter-TSS (NM_011380)	-10	NM_011380	20472	Mm.5039	NM_011380	ENSMUSG00000024134	Six2	-	sine oculis-related homeobox 2	protein-coding
mm_5175.1	chr1	10719899	10719939	-	1	NA	promoter-TSS (NM_001289497)	promoter-TSS (NM_001289497)	26	NM_001289497	329093	Mm.336423	NM_177834	ENSMUSG00000042501	Cpa6	9030616D13Rik	carboxypeptidase A6	protein-coding
mm_32094.1	chr4	98546663	98546689	+	1	NA	promoter-TSS (NM_007704)	promoter-TSS (NM_007704)	42	NM_001005787	12695	Mm.90218	NM_007704	ENSMUSG00000061859	Patj	Cipp|Inadl	PATJ, crumbs cell polarity complex component	protein-coding
mm_159681.1	chr5	3893925	3893925	-	1	NA	promoter-TSS (NM_172135)	promoter-TSS (NM_172135)	8	NM_001013023	545725	Mm.99593	NM_172135	ENSMUSG00000040429	Mterf1a	4931431L11Rik|9230106K09Rik|Mterf|Mterf1|mTERF1b	mitochondrial transcription termination factor 1a	protein-coding
mm_157631.1	chrX	56822309	56822346	-	1	NA	promoter-TSS (NM_177293)	promoter-TSS (NM_177293)	-2	NM_177293	320923	Mm.186745	NM_177293	ENSMUSG00000067878	Mtap7d3	4933424A10Rik|Map7d3	MAP7 domain containing 3	protein-coding
mm_112096.1	chr12	112785155	112785170	-	1	NA	Intergenic	Intergenic	-23813	NM_145450	217887	Mm.186678	NM_145450	ENSMUSG00000037594	BC022687	AW050009|C130001I08Rik|Flj20080	cDNA sequence BC022687	protein-coding
mm_24413.1	chr3	90509078	90509105	+	1	NA	intron (NM_001293777, intron 1 of 5)	C-rich|Low_complexity|Low_complexity	407	NM_001293776	66511	Mm.154136	NM_023215	ENSMUSG00000001017	Chtop	2500003M10Rik|Fop|Srag	chromatin target of PRMT1	protein-coding
mm_110407.1	chr12	45074458	45074488	-	1	NA	promoter-TSS (NM_144552)	promoter-TSS (NM_144552)	10	NM_144552	217517	Mm.285400	NM_144552	ENSMUSG00000046314	Stxbp6	BC024598|C85317	syntaxin binding protein 6 (amisyn)	protein-coding
mm_77657.1	chr8	124636999	124637013	-	1	NA	3' UTR (NM_175149, exon 4 of 4)	3' UTR (NM_175149, exon 4 of 4)	26363	NM_175149	69551	Mm.261920	NM_175149	ENSMUSG00000031983	2310022B05Rik	-	RIKEN cDNA 2310022B05 gene	protein-coding
mm_69766.1	chr7	141010661	141010685	-	1	NA	promoter-TSS (NM_025378)	promoter-TSS (NM_025378)	71	NM_025378	66141	Mm.141021	NM_025378	ENSMUSG00000025492	Ifitm3	1110004C05Rik|Cd225|Cdw217|DSPA2b|Fgls|IP15|mil-1	interferon induced transmembrane protein 3	protein-coding
mm_150493.1	chr19	39011723	39011727	+	1	NA	exon (NM_028089, exon 3 of 9)	exon (NM_028089, exon 3 of 9)	4706	NM_028089	72082	Mm.142581	NM_028089	ENSMUSG00000025002	Cyp2c55	2010318C06Rik	cytochrome P450, family 2, subfamily c, polypeptide 55	protein-coding
mm_90435.1	chr10	127634696	127634708	+	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-8284	NM_009284	20852	Mm.121721	NM_009284	ENSMUSG00000002147	Stat6	-	signal transducer and activator of transcription 6	protein-coding
mm_39201.1	chr4	156030693	156030701	-	1	NA	Intergenic	Intergenic	4355	NM_021985	21936	Mm.3180	NM_009400	ENSMUSG00000041954	Tnfrsf18	AITR|Gitr	tumor necrosis factor receptor superfamily, member 18	protein-coding
mm_88982.1	chr10	81561210	81561259	+	1	NA	exon (NM_010347, exon 2 of 7)	exon (NM_010347, exon 2 of 7)	1790	NM_001276288	14797	Mm.180013	NM_010347	ENSMUSG00000054452	Aes	AL024115|Esp1|Grg|Grg-5|Grg5|Tle5	amino-terminal enhancer of split	protein-coding
mm_142991.1	chr17	56290500	56290529	-	1	NA	promoter-TSS (NM_025836)	promoter-TSS (NM_025836)	-3	NM_025836	66905	Mm.311696	NM_025836	ENSMUSG00000024197	Plin3	1300012C15Rik|M6prbp1|Tip47	perilipin 3	protein-coding
mm_109576.1	chr12	112146228	112146257	+	1	NA	promoter-TSS (NM_001097621)	promoter-TSS (NM_001097621)	34	NM_001097621	668303	Mm.313104	NM_001097621	ENSMUSG00000021294	Kif26a	mKIAA1236	kinesin family member 26A	protein-coding
mm_116986.1	chr13	56357190	56357205	-	1	NA	Intergenic	Intergenic	-5703	NR_046061	100038494	Mm.370447	NR_046061		Gm10782	ENSMUSG00000074885	predicted gene 10782	ncRNA
mm_171294.1	chr3	90651920	90651926	-	1	NA	Intergenic	Intergenic	-2379	NM_199422	381493	Mm.291525	NM_199422	ENSMUSG00000063767	S100a7a	AY465109|Gm1020|S100A7L1|S100A7f|S100a15|S100a15a|S100a17l1	S100 calcium binding protein A7A	protein-coding
mm_55302.1	chr6	54867554	54867556	-	1	NA	intron (NM_199143, intron 2 of 4)	intron (NM_199143, intron 2 of 4)	50639	NM_199143	387524	Mm.286149	NM_199143	ENSMUSG00000058446	Znrf2	1190002C14Rik|AU044205|D6Ertd365e	zinc and ring finger 2	protein-coding
mm_128285.1	chr15	37007768	37007788	-	1	NA	promoter-TSS (NM_026521)	promoter-TSS (NM_026521)	-376	NM_026521	68036	Mm.371631	NM_026521	ENSMUSG00000062397	Zfp706	3110006P09Rik|AA793007|AW536850|C77232|Znf706	zinc finger protein 706	protein-coding
mm_36365.1	chr4	76358232	76358234	-	1	NA	intron (NM_011211, intron 10 of 39)	intron (NM_011211, intron 10 of 39)	-1079947	NM_025849	66928	Mm.24332	NM_025849	ENSMUSG00000028398	Tmem261	1700027K24Rik|3110001D03Rik	transmembrane protein 261	protein-coding
mm_96625.1	chr11	69156889	69156901	+	1	NA	promoter-TSS (NM_009659)	promoter-TSS (NM_009659)	-177	NM_009659	11686	Mm.340329	NM_009659	ENSMUSG00000032807	Alox12b	12R-LOX|Aloxe2|e-LOX2	arachidonate 12-lipoxygenase, 12R type	protein-coding
mm_39247.1	chr5	3479708	3479724	+	1	NA	intron (NM_009873, intron 5 of 7)	intron (NM_009873, intron 5 of 7)	-64117	NM_001042501	68152	Mm.240265	NM_026583	ENSMUSG00000058503	Fam133b	2900022K02Rik|5830415L20Rik	family with sequence similarity 133, member B	protein-coding
mm_28840.1	chr3	96582596	96582599	-	1	NA	intron (NM_027241, intron 1 of 7)	B1_Mus1|SINE|Alu	11584	NM_001293701	69870	Mm.292739	NM_027241	ENSMUSG00000028104	Polr3gl	2010003I19Rik	polymerase (RNA) III (DNA directed) polypeptide G like	protein-coding
mm_38537.1	chr4	141571612	141571634	-	1	NA	Intergenic	Intergenic	25461	NR_030695	320456	Mm.32859	NM_177163		B330016D10Rik	-	RIKEN cDNA B330016D10 gene	ncRNA
mm_95437.1	chr11	50225069	50225087	+	1	NA	promoter-TSS (NM_145926)	promoter-TSS (NM_145926)	-257	NM_145926	103534	Mm.86759	NM_145926	ENSMUSG00000036620	Mgat4b	AA407995|GnTIVb	mannoside acetylglucosaminyltransferase 4, isoenzyme B	protein-coding
mm_36764.1	chr4	101356732	101356750	-	1	NA	promoter-TSS (NR_040708)	promoter-TSS (NR_040708)	-493	NR_040708	77866	Mm.137053	NR_040708	ENSMUSG00000086782	E130102H24Rik	-	RIKEN cDNA E130102H24 gene	ncRNA
mm_49381.1	chr6	24603370	24603381	+	1	NA	exon (NM_053098, exon 2 of 3)	exon (NM_053098, exon 2 of 3)	5604	NM_053098	93677	Mm.332941	NM_053098	ENSMUSG00000029683	Lmod2	C-Lmod	leiomodin 2 (cardiac)	protein-coding
mm_122996.1	chr14	54992207	54992220	-	1	NA	intron (NM_080728, intron 5 of 40)	intron (NM_080728, intron 5 of 40)	2336	NM_080728	140781	Mm.457983	NM_080728	ENSMUSG00000053093	Myh7	B-MHC|MyHC-I|Myhc-b|Myhcb|beta-MHC	myosin, heavy polypeptide 7, cardiac muscle, beta	protein-coding
mm_113075.1	chr13	23807030	23807063	+	1	NA	promoter-TSS (NM_144836)	promoter-TSS (NM_144836)	19	NM_144836	218103	Mm.24030	NM_144836	ENSMUSG00000036110	Slc17a2	C730032N17Rik|NPT3	solute carrier family 17 (sodium phosphate), member 2	protein-coding
mm_53498.1	chr6	135362382	135362397	+	1	NA	promoter-TSS (NM_001288628)	promoter-TSS (NM_001288628)	-542	NM_010128	13730	Mm.182785	NM_010128	ENSMUSG00000030208	Emp1	I-8-09|TMP	epithelial membrane protein 1	protein-coding
mm_35861.1	chr4	49481099	49481108	-	1	NA	Intergenic	RLTR9C|LTR|ERVK	25455	NM_007519	12012	Mm.2859	NM_007519	ENSMUSG00000039653	Baat	AI118337|AI158864|BAT	bile acid-Coenzyme A: amino acid N-acyltransferase	protein-coding
mm_155591.1	chrX	81070743	81070753	+	1	NA	5' UTR (NM_138751, exon 1 of 3)	5' UTR (NM_138751, exon 1 of 3)	104	NM_138751	192216	Mm.490421	NM_138751	ENSMUSG00000025666	Tmem47	3010015F07Rik|AI115536|BCMP1|Tm4sf10	transmembrane protein 47	protein-coding
mm_145570.1	chr18	60911806	60911847	+	1	NA	promoter-TSS (NM_001038499)	promoter-TSS (NM_001038499)	-414	NM_001038499	545260	Mm.20147	NM_001038499	ENSMUSG00000036412	Arsi	BC020108	arylsulfatase i	protein-coding
mm_75986.1	chr8	72351002	72351005	-	1	NA	intron (NM_007944, intron 22 of 23)	intron (NM_007944, intron 22 of 23)	31941	NM_008452	16598	Mm.26938	NM_008452	ENSMUSG00000055148	Klf2	Lklf	Kruppel-like factor 2 (lung)	protein-coding
mm_160320.1	chr7	143742156	143742156	-	1	NA	promoter-TSS (NM_024289)	promoter-TSS (NM_024289)	-193	NM_024289	79196	Mm.21199	NM_024289	ENSMUSG00000037606	Osbpl5	1110006M06Rik|AI462538|ORP5|Obph1|Osbp2	oxysterol binding protein-like 5	protein-coding
mm_40261.1	chr5	38277168	38277190	+	1	NA	promoter-TSS (NM_172709)	promoter-TSS (NM_172709)	-225	NM_172709	21906	Mm.204765	NM_172709	ENSMUSG00000051596	Otop1	A530025J20Rik|Otp1|tlt	otopetrin 1	protein-coding
mm_42111.1	chr5	110597688	110597691	+	1	NA	intron (NM_198306, intron 5 of 10)	intron (NM_198306, intron 5 of 10)	-5816	NM_001122639	231605	Mm.275748	NM_198306	ENSMUSG00000033316	Galnt9	GalNAc-T9	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 9	protein-coding
mm_3517.1	chr1	150107466	150107487	+	1	NA	3' UTR (NM_011198, exon 10 of 10)	3' UTR (NM_011198, exon 10 of 10)	7445	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_70318.1	chr8	4248249	4248267	+	1	NA	promoter-TSS (NM_001195258)	promoter-TSS (NM_001195258)	44	NM_001195258	100044509	Mm.439193	NM_001195258	ENSMUSG00000089736	Tgfbr3l	Gm14378|OTTMUSG00000016477	transforming growth factor, beta receptor III-like	protein-coding
mm_59102.1	chr7	19697588	19697601	+	1	NA	exon (NM_009696, exon 3 of 4)	exon (NM_009696, exon 3 of 4)	804	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_89184.1	chr10	86346043	86346084	+	1	NA	3' UTR (NM_011595, exon 5 of 5)	3' UTR (NM_011595, exon 5 of 5)	45651	NM_011595	21859	Mm.4871	NM_011595	ENSMUSG00000020044	Timp3	Timp-3	tissue inhibitor of metalloproteinase 3	protein-coding
mm_99562.1	chr11	103697712	103697780	+	1	NA	promoter-TSS (NM_019650)	promoter-TSS (NM_019650)	22	NR_102396	399609	Mm.351922	NR_102388		C130046K22Rik	-	RIKEN cDNA C130046K22 gene	ncRNA
mm_104779.1	chr11	98546135	98546141	-	1	NA	promoter-TSS (NM_011771)	promoter-TSS (NM_011771)	-107	NM_011771	22780	Mm.133367	NM_011771	ENSMUSG00000018168	Ikzf3	5830411O07Rik|Aiolos|Zfpn1a3|Znfn1a3	IKAROS family zinc finger 3	protein-coding
mm_99696.1	chr11	106113738	106113743	+	1	NA	intron (NM_011947, intron 3 of 15)	intron (NM_011947, intron 3 of 15)	28838	NM_011947	26406	Mm.27041	NM_011947	ENSMUSG00000020700	Map3k3	AW548911|MAPKKK3|Mekk3|mKIAA4031	mitogen-activated protein kinase kinase kinase 3	protein-coding
mm_30666.1	chr4	10932678	10932688	+	1	NA	Intergenic	Intergenic	58185	NM_026005	67157	Mm.440552	NM_026005	ENSMUSG00000059482	2610301B20Rik	AI428449	RIKEN cDNA 2610301B20 gene	protein-coding
mm_164302.1	chr15	103897382	103897419	-	1	NA	exon (NM_009267, exon 3 of 4)	exon (NM_009267, exon 3 of 4)	1900	NM_009268	20771	Mm.30276	NM_009268		Mucl1	Spt-2|Spt2	mucin-like 1	protein-coding
mm_136534.1	chr16	97611073	97611088	-	1	NA	5' UTR (NM_015775, exon 1 of 14)	5' UTR (NM_015775, exon 1 of 14)	115	NM_015775	50528	Mm.276145	NM_015775	ENSMUSG00000000385	Tmprss2	D16Ertd61e	transmembrane protease, serine 2	protein-coding
mm_117616.1	chr13	91741867	91741880	-	1	NA	promoter-TSS (NR_028314)	promoter-TSS (NR_028314)	-1	NR_028313	373852	Mm.466817	NR_015501	ENSMUSG00000074782	4833422C13Rik	-	RIKEN cDNA 4833422C13 gene	ncRNA
mm_149780.1	chr19	23136088	23136097	+	1	NA	Intergenic	CpG	-5134	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_58530.1	chr7	4237700	4237712	+	1	NA	promoter-TSS (NM_001081239)	promoter-TSS (NM_001081239)	-48	NM_001081239	232801	Mm.258061	NM_001081239	ENSMUSG00000070873	Lilra5	E030017K20|EG232801|Gm4878|Lilrc1	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 5	protein-coding
mm_106965.1	chr12	8932388	8932401	+	1	NA	intron (NM_008640, intron 2 of 6)	intron (NM_008640, intron 2 of 6)	11087	NM_008640	17775	Mm.30071	NM_008640	ENSMUSG00000020585	Laptm4a	AA286466|LAPTM4|MTP|Mtrp|mKIAA0108	lysosomal-associated protein transmembrane 4A	protein-coding
mm_169501.1	chr14	77735598	77735617	-	1	NA	Intergenic	BGLII|LTR|ERVK	63361	NM_001033440	380920	Mm.297771	NM_001033440	ENSMUSG00000075512	Gm1587	-	predicted gene 1587	protein-coding
mm_16586.1	chr2	3726721	3726748	-	1	NA	intron (NM_025626, intron 1 of 3)	intron (NM_025626, intron 1 of 3)	13276	NM_025626	66540	Mm.277864	NM_025626	ENSMUSG00000026655	Fam107b	3110001A13Rik|AA589595|AA959793|AI132312	family with sequence similarity 107, member B	protein-coding
mm_80964.1	chr9	103111727	103111737	+	1	NA	promoter-TSS (NM_173781)	promoter-TSS (NM_173781)	-342	NM_173781	270192	Mm.490252	NM_173781	ENSMUSG00000032549	Rab6b	9630015C03|AI844641|C330006L04Rik|D9Bwg0185e	RAB6B, member RAS oncogene family	protein-coding
mm_95876.1	chr11	58059383	58059427	+	1	NA	3' UTR (NM_028451, exon 19 of 19)	3' UTR (NM_028451, exon 19 of 19)	-44748	NM_026949	69125	Mm.28910	NM_026949	ENSMUSG00000020515	Cnot8	1500015I04Rik|1810022F04Rik|AA536816|AU015770|AU043059	CCR4-NOT transcription complex, subunit 8	protein-coding
mm_159638.1	chr4	141088119	141088119	+	1	NA	promoter-TSS (NM_177867)	promoter-TSS (NM_177867)	-226	NM_177867	329972	Mm.247201	NM_177867	ENSMUSG00000045004	Spata21	4933414G08	spermatogenesis associated 21	protein-coding
mm_99913.1	chr11	110145594	110145604	+	1	NA	exon (NM_147220, exon 13 of 39)	exon (NM_147220, exon 13 of 39)	22554	NM_147220	217262	Mm.291459	NM_147220	ENSMUSG00000041797	Abca9	D630040K07Rik	ATP-binding cassette, sub-family A (ABC1), member 9	protein-coding
mm_69416.1	chr7	132589774	132589788	-	1	NA	Intergenic	Intergenic	9856	NM_009123	20231	Mm.334281	NM_009123	ENSMUSG00000048528	Nkx1-2	Nkx-1.1|Nkx-1.2|Sax1	NK1 transcription factor related, locus 2 (Drosophila)	protein-coding
mm_60867.1	chr7	45923202	45923235	+	1	NA	Intergenic	Intergenic	-1792	NM_010129	13732	Mm.20829	NM_010129	ENSMUSG00000040212	Emp3	H-4|H4|HNMP-1|MI-35|Ymp	epithelial membrane protein 3	protein-coding
mm_143570.1	chr17	74295095	74295121	-	1	NA	promoter-TSS (NM_133771)	promoter-TSS (NM_133771)	-245	NM_133771	76890	Mm.311874	NM_133771	ENSMUSG00000058704	Memo1	0610016J10Rik|D930048L02Rik	mediator of cell motility 1	protein-coding
mm_160406.1	chr8	71689299	71689299	+	1	NA	promoter-TSS (NM_013564)	promoter-TSS (NM_013564)	47	NM_013564	16336	Mm.476857	NM_013564	ENSMUSG00000079019	Insl3	Rlf|Rlnl	insulin-like 3	protein-coding
mm_101094.1	chr11	11889681	11889684	-	1	NA	intron (NM_001190448, intron 1 of 14)	(A)n|Simple_repeat|Simple_repeat	726	NM_016672	13195	Mm.12906	NM_016672	ENSMUSG00000020182	Ddc	Aadc	dopa decarboxylase	protein-coding
mm_153937.1	chr19	47464095	47464113	-	1	NA	exon (NM_008018, exon 1 of 15)	exon (NM_008018, exon 1 of 15)	307	NM_001164717	14218	Mm.127560	NM_008018	ENSMUSG00000053617	Sh3pxd2a	2310014D11Rik|AA589508|AI256723|AI413738|C230050L11|EG329070|Fish|Gm5098|Sh3md1|TSK5|Tks5	SH3 and PX domains 2A	protein-coding
mm_51596.1	chr6	84008338	84008357	+	1	NA	promoter-TSS (NM_001077694)	promoter-TSS (NM_001077694)	-251	NM_001077694	26903	Mm.220982	NM_021469	ENSMUSG00000033788	Dysf	2310004N10Rik|AI604795|D6Pas3	dysferlin	protein-coding
mm_121563.1	chr14	122484451	122484457	+	1	NA	Intergenic	Intergenic	9070	NM_009574	22772	Mm.308936	NM_009574	ENSMUSG00000061524	Zic2	HPE5|Ku	zinc finger protein of the cerebellum 2	protein-coding
mm_19863.1	chr2	113848624	113848638	-	1	NA	promoter-TSS (NM_181416)	promoter-TSS (NM_181416)	30	NM_181416	228482	Mm.45753	NM_181416	ENSMUSG00000041219	Arhgap11a	6530401L14Rik|mKIAA0013	Rho GTPase activating protein 11A	protein-coding
mm_102530.1	chr11	60935353	60935370	-	1	NA	intron (NM_008928, intron 1 of 11)	intron (NM_008928, intron 1 of 11)	3304	NM_008928	26397	Mm.18494	NM_008928	ENSMUSG00000018932	Map2k3	AW212142|MEK3|MKK3|Prkmk3|mMKK3b	mitogen-activated protein kinase kinase 3	protein-coding
mm_18951.1	chr2	76785829	76785838	-	1	NA	intron (NM_028004, intron 101 of 191)	intron (NM_028004, intron 101 of 191)	110518	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_7704.1	chr1	130448721	130448734	-	1	NA	intron (NM_010016, intron 7 of 9)	intron (NM_010016, intron 7 of 9)	14017	NM_010016	13136	Mm.101591	NM_010016	ENSMUSG00000026399	Cd55	Daf|Daf-GPI|Daf1|GPI-DAF	CD55 molecule, decay accelerating factor for complement	protein-coding
mm_32603.1	chr4	112006190	112006199	+	1	NA	promoter-TSS (NM_001102662)	promoter-TSS (NM_001102662)	-75	NM_001102662	639781	Mm.398873	NM_001102662	ENSMUSG00000089773	Skint1	OTTMUSG00000008542|Skint-1	selection and upkeep of intraepithelial T cells 1	protein-coding
mm_68519.1	chr7	111779964	111779993	-	1	NA	promoter-TSS (NM_173739)	promoter-TSS (NM_173739)	-1	NM_173739	233733	Mm.323322	NM_173739	ENSMUSG00000038296	Galnt18	2900011G21Rik|BC024988|Galntl4	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 18	protein-coding
mm_162455.1	chr1	127206586	127206623	+	1	NA	intron (NM_145128, intron 1 of 17)	intron (NM_145128, intron 1 of 17)	1618	NM_145128	107895	Mm.214682	NM_145128	ENSMUSG00000036155	Mgat5	4930471A21Rik|5330407H02Rik|AI480971|GlcNAc-TV	mannoside acetylglucosaminyltransferase 5	protein-coding
mm_16511.1	chr2	181365450	181365476	+	1	NA	promoter-TSS (NM_001165995)	promoter-TSS (NM_001165995)	40	NM_001048148	229007	Mm.87720	NM_144894	ENSMUSG00000027582	Zgpat	1500006I01Rik|BC021513	zinc finger, CCCH-type with G patch domain	protein-coding
mm_93582.1	chr10	116926080	116926102	-	1	NA	intron (NM_001003950, intron 3 of 9)	L1M2|LINE|L1	24289	NM_001003950	216363	Mm.336394	NM_001003950	ENSMUSG00000064181	Rab3ip	B230311A06|Gtpat12|Rabin3	RAB3A interacting protein	protein-coding
mm_21416.1	chr2	158127178	158127188	-	1	NA	exon (NM_009373, exon 9 of 13)	exon (NM_009373, exon 9 of 13)	19209	NM_009373	21817	Mm.330731	NM_009373	ENSMUSG00000037820	Tgm2	G[a]h|TG2|TGase2|tTG|tTGas	transglutaminase 2, C polypeptide	protein-coding
mm_54843.1	chr6	42586832	42586842	-	1	NA	TTS (NM_203396)	TTS (NM_203396)	10535	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_95099.1	chr11	34047116	34047242	+	1	NA	promoter-TSS (NM_010696)	promoter-TSS (NM_010696)	-22	NM_010696	16822	Mm.265350	NM_010696	ENSMUSG00000002699	Lcp2	AI323664|BB161688|SLP-76|SLP76|m1Khoe|twm	lymphocyte cytosolic protein 2	protein-coding
mm_166633.1	chr6	79096569	79096570	+	1	NA	Intergenic	RMER15|LTR|ERVL	64527	NR_040301	100504701	Mm.400420	NR_040301	ENSMUSG00000108072	Gm20362	-	predicted gene, 20362	ncRNA
mm_88462.1	chr10	77561123	77561152	+	1	NA	exon (NM_008404, exon 14 of 16)	exon (NM_008404, exon 14 of 16)	-20630	NM_145925	108705	Mm.28853	NM_145925	ENSMUSG00000009291	Pttg1ip	1810010L20Rik|AI314311|AU018448|C79540	pituitary tumor-transforming 1 interacting protein	protein-coding
mm_39589.1	chr5	23496109	23496137	+	1	NA	exon (NM_026984, exon 17 of 26)	exon (NM_026984, exon 17 of 26)	61694	NM_026984	69188	Mm.205190	NM_026984	ENSMUSG00000029004	Kmt2e	1810033J14Rik|9530077A04Rik|D230038D11Rik|Mll5|NKp44L	lysine (K)-specific methyltransferase 2E	protein-coding
mm_41258.1	chr5	88934332	88934345	+	1	NA	intron (NM_001197147, intron 1 of 25)	intron (NM_001197147, intron 1 of 25)	47078	NM_018760	54403	Mm.41044	NM_018760	ENSMUSG00000060961	Slc4a4	AI835705|NBC|NBC1	solute carrier family 4 (anion exchanger), member 4	protein-coding
mm_95531.1	chr11	52246188	52246208	+	1	NA	3' UTR (NM_011543, exon 6 of 6)	3' UTR (NM_011543, exon 6 of 6)	14203	NM_011543	21402	Mm.42944	NM_011543	ENSMUSG00000036309	Skp1a	15kDa|2610043E24Rik|2610206H23Rik|EMC19|OCP-II|OCP2|SKP1|Tceb1l|p19A|p19Skp1	S-phase kinase-associated protein 1A	protein-coding
mm_87107.1	chr10	33196016	33196026	+	1	NA	exon (NM_029726, exon 8 of 38)	exon (NM_029726, exon 8 of 38)	60336	NR_040657	442820	Mm.490725	NR_040657		D830005E20Rik	-	RIKEN cDNA D830005E20 gene	ncRNA
mm_121720.1	chr14	16575036	16575061	-	1	NA	5' UTR (NM_011243, exon 1 of 8)	5' UTR (NM_011243, exon 1 of 8)	428	NM_011243	218772	Mm.259318	NM_011243	ENSMUSG00000017491	Rarb	A830025K23|Hap|Nr1b2	retinoic acid receptor, beta	protein-coding
mm_123059.1	chr14	55660398	55660466	-	1	NA	promoter-TSS (NR_028316)	promoter-TSS (NR_028316)	76	NM_023397	67881	Mm.24601	NM_023397	ENSMUSG00000002329	Mdp1	1810034K20Rik|AI035604	magnesium-dependent phosphatase 1	protein-coding
mm_38903.1	chr4	149909720	149909744	-	1	NA	intron (NM_029035, intron 1 of 2)	intron (NM_029035, intron 1 of 2)	45274	NM_029035	74646	Mm.30	NM_029035	ENSMUSG00000039911	Spsb1	1110014L01Rik|4930422J18Rik|AI596360|AI854583|SSB-1|SSB1	splA/ryanodine receptor domain and SOCS box containing 1	protein-coding
mm_46208.1	chr5	98031472	98031487	-	1	NA	promoter-TSS (NM_133738)	promoter-TSS (NM_133738)	-517	NM_133738	71914	Mm.24842	NM_133738	ENSMUSG00000029338	Antxr2	2310046B19Rik|AW561899|CMG-2|CMG2|cI-35	anthrax toxin receptor 2	protein-coding
mm_134067.1	chr16	8637577	8637587	-	1	NA	promoter-TSS (NM_016881)	promoter-TSS (NM_016881)	119	NM_025708	66690	Mm.10068	NM_025708	ENSMUSG00000043140	Tmem186	2810440M13Rik|4432406C05Rik|AI648175|AW210586	transmembrane protein 186	protein-coding
mm_70322.1	chr8	4253068	4253128	+	1	NA	promoter-TSS (NM_133968)	promoter-TSS (NM_133968)	-4	NM_133968	102209	Mm.28452	NM_133968	ENSMUSG00000011837	Snapc2	0610007H10Rik|AU015675	small nuclear RNA activating complex, polypeptide 2	protein-coding
mm_169990.1	chr17	15053056	15053073	+	1	NA	promoter-TSS (NM_001034891)	promoter-TSS (NM_001034891)	5	NM_001034891	381062	Mm.393767	NM_183133	ENSMUSG00000036552	Ermard	2210404J11Rik|2410011O22Rik|AI448938	ER membrane associated RNA degradation	protein-coding
mm_135455.1	chr16	45724550	45724560	-	1	NA	promoter-TSS (NM_019754)	promoter-TSS (NM_019754)	-24	NM_019754	56370	Mm.24183	NM_019754	ENSMUSG00000022658	Tagln3	2700038H05Rik|2900005O10Rik|AI426007|Np25	transgelin 3	protein-coding
mm_139390.1	chr17	52217682	52217694	+	1	NA	Intergenic	Intergenic	334961	NR_045095	100504169	Mm.417731	NR_045095		Gm20098	-	predicted gene, 20098	ncRNA
mm_60684.1	chr7	45154385	45154406	+	1	NA	promoter-TSS (NM_029406)	promoter-TSS (NM_029406)	92	NM_001278207	68845	Mm.181689	NM_029406	ENSMUSG00000003423	Pih1d1	1110061L23Rik|4933413A04Rik|Nop17	PIH1 domain containing 1	protein-coding
mm_78889.1	chr9	44604665	44604700	+	1	NA	promoter-TSS (NM_001110826)	promoter-TSS (NM_001110826)	-210	NM_001110826	13209	Mm.267061	NM_007841	ENSMUSG00000032097	Ddx6	1110001P04Rik|E230023J21Rik|HLR2|mRCK/P54|p54|rck	DEAD (Asp-Glu-Ala-Asp) box polypeptide 6	protein-coding
mm_46134.1	chr5	92675254	92675287	-	1	NA	promoter-TSS (NM_177230)	promoter-TSS (NM_177230)	-143	NM_177230	320696	Mm.209991	NM_177230	ENSMUSG00000050050	Ccdc158	4932413O14Rik	coiled-coil domain containing 158	protein-coding
mm_53138.1	chr6	125218982	125218994	+	1	NA	exon (NM_001080557, exon 3 of 4)	exon (NM_001080557, exon 3 of 4)	3407	NM_001080557	22317	Mm.32321	NM_009496	ENSMUSG00000030337	Vamp1	Syb-1|Syb1|VAMP-1|lew	vesicle-associated membrane protein 1	protein-coding
mm_60910.1	chr7	46753495	46753508	+	1	NA	exon (NM_011314, exon 3 of 4)	exon (NM_011314, exon 3 of 4)	1668	NM_011314	20209	Mm.200941	NM_011314	ENSMUSG00000057465	Saa2	AW111173|Saa-2|Saa1	serum amyloid A 2	protein-coding
mm_124503.1	chr14	121879587	121879598	-	1	NA	promoter-TSS (NR_130999)	promoter-TSS (NR_130999)	-184	NR_130999	78312	Mm.188743	NR_130999	ENSMUSG00000102112	1810041H14Rik	-	RIKEN cDNA 1810041H14 gene	ncRNA
mm_31518.1	chr4	54945015	54945035	+	1	NA	Intergenic	Intergenic	-2920	NM_172867	242466	Mm.102904	NM_172867	ENSMUSG00000060206	Zfp462	6030417H05|9430078C22Rik|Gt4-2|Zfpip	zinc finger protein 462	protein-coding
mm_47292.1	chr5	122240918	122240940	-	1	NA	non-coding (NR_104441, exon 13 of 13)	non-coding (NR_104441, exon 13 of 13)	23531	NR_104441	654470	Mm.28804	NM_001039153	ENSMUSG00000038593	Tctn1	G730031O11Rik|Tect1	tectonic family member 1	protein-coding
mm_51068.1	chr6	66535393	66535412	+	1	NA	promoter-TSS (NM_019499)	promoter-TSS (NM_019499)	-66	NM_019499	56150	Mm.489653	NM_019499	ENSMUSG00000029910	Mad2l1	AA673185|MAD2	MAD2 mitotic arrest deficient-like 1	protein-coding
mm_68408.1	chr7	109628022	109628025	-	1	NA	Intergenic	PB1D10|SINE|Alu	-10876	NM_029811	76954	Mm.252009	NM_029811	ENSMUSG00000031024	St5	2010004M01Rik|2610305K15Rik	suppression of tumorigenicity 5	protein-coding
mm_101645.1	chr11	36498844	36498854	-	1	NA	intron (NM_011856, intron 2 of 28)	intron (NM_011856, intron 2 of 28)	445392	NM_001290702	23964	Mm.439889	NM_011856	ENSMUSG00000049336	Tenm2	Odz2|Odz3|Ten-2|Ten-m2	teneurin transmembrane protein 2	protein-coding
mm_13109.1	chr2	91526944	91526987	+	1	NA	Intergenic	CpG	-19357	NM_001165989	75786	Mm.168478	NM_029437	ENSMUSG00000040549	Ckap5	3110043H24Rik|4930432B04Rik|D730027C18Rik|T25636|mKIAA0097	cytoskeleton associated protein 5	protein-coding
mm_159838.1	chr5	134376994	134376994	-	1	NA	exon (NM_001081464, exon 21 of 30)	exon (NM_001081464, exon 21 of 30)	-62234	NM_010365	14886	Mm.261570	NM_010365	ENSMUSG00000060261	Gtf2i	6030441I21Rik|BAP-135|Diws1t|GtfII-I|Spin|TFII-I|WBSCR6	general transcription factor II I	protein-coding
mm_16246.1	chr2	173158485	173158495	+	1	NA	exon (NM_011044, exon 10 of 10)	exon (NM_011044, exon 10 of 10)	5417	NM_011044	18534	Mm.266867	NM_011044	ENSMUSG00000027513	Pck1	AI265463|PEPCK|Pck-1	phosphoenolpyruvate carboxykinase 1, cytosolic	protein-coding
mm_29816.1	chr3	127896272	127896337	-	1	NA	promoter-TSS (NM_027482)	promoter-TSS (NM_027482)	19	NM_027482	70617	Mm.317049	NM_027482	ENSMUSG00000050549	5730508B09Rik	2700063A17Rik|C80506	RIKEN cDNA 5730508B09 gene	protein-coding
mm_7441.1	chr1	120086788	120086809	-	1	NA	Intergenic	MTEa|LTR|ERVL-MaLR	-13018	NM_019432	170706	Mm.24750	NM_019432	ENSMUSG00000050777	Tmem37	AI173373|AW540203|Pr|Pr1	transmembrane protein 37	protein-coding
mm_104730.1	chr11	98326692	98326702	-	1	NA	3' UTR (NM_010895, exon 2 of 2)	3' UTR (NM_010895, exon 2 of 2)	2948	NM_010895	18013	Mm.4814	NM_010895	ENSMUSG00000038255	Neurod2	Ndrf|bHLHa1	neurogenic differentiation 2	protein-coding
mm_98200.1	chr11	87795856	87795874	+	1	NA	exon (NM_010824, exon 5 of 14)	exon (NM_010824, exon 5 of 14)	2081	NM_010824	17523	Mm.4668	NM_010824	ENSMUSG00000009350	Mpo	mKIAA4033	myeloperoxidase	protein-coding
mm_101477.1	chr11	30954081	30954143	-	1	NA	promoter-TSS (NM_023906)	promoter-TSS (NM_023906)	19	NM_025745	66753	Mm.294641	NM_025745	ENSMUSG00000020311	Erlec1	4933407N01Rik	endoplasmic reticulum lectin 1	protein-coding
mm_100107.1	chr11	115780661	115780688	+	1	NA	intron (NM_028014, intron 2 of 31)	intron (NM_028014, intron 2 of 31)	-15150	NR_049194	100885833		NR_049194	ENSMUSG00000093539	Mir5621	Gm22564|mir-5621|mmu-mir-5621	microRNA 5621	ncRNA
mm_101365.1	chr11	23746731	23746750	-	1	NA	intron (NM_009044, intron 5 of 9)	B4|SINE|B4	24230	NM_009044	19696	Mm.4869	NM_009044	ENSMUSG00000020275	Rel	c-Rel	reticuloendotheliosis oncogene	protein-coding
mm_7298.1	chr1	97949503	97949506	-	1	NA	intron (NM_013626, intron 3 of 25)	intron (NM_013626, intron 3 of 25)	98289	NR_037993	78603	Mm.442597	NR_037993	ENSMUSG00000089706	B230216N24Rik	-	RIKEN cDNA B230216N24 gene	ncRNA
mm_130977.1	chr15	103340131	103340141	-	1	NA	promoter-TSS (NM_013866)	promoter-TSS (NM_013866)	-50	NM_013866	29813	Mm.14099	NM_013866	ENSMUSG00000000552	Zfp385a	Hzf|Zfp385|Znf385a	zinc finger protein 385A	protein-coding
mm_150138.1	chr19	30963864	30963872	+	1	NA	intron (NM_011160, intron 4 of 17)	IAPLTR2a2_Mm|LTR|ERVK	-32906	NR_033643	625995	Mm.454508	NR_033643		Gm6642	EG625995	ubiquitin-like 5 pseudogene	pseudo
mm_163720.1	chr13	112800848	112800850	+	1	NA	promoter-TSS (NM_008903)	promoter-TSS (NM_008903)	72	NM_008247	19012	Mm.291029	NM_008247	ENSMUSG00000021759	Plpp1	Hic53|Hpic53|LPP-1|LPP1|PAP-2a|PAP2-alpha|PAP2a|Ppap2a|mPAP	phospholipid phosphatase 1	protein-coding
mm_127999.1	chr15	12739915	12739942	-	1	NA	Intergenic	CpG	84729	NM_029998	77877	Mm.207311	NM_029998	ENSMUSG00000022195	6030458C11Rik	-	RIKEN cDNA 6030458C11 gene	protein-coding
mm_52646.1	chr6	117179017	117179044	+	1	NA	3' UTR (NM_001012477, exon 4 of 4)	3' UTR (NM_001012477, exon 4 of 4)	10495	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_136291.1	chr16	91425123	91425151	-	1	NA	3' UTR (NM_008349, exon 7 of 7)	3' UTR (NM_008349, exon 7 of 7)	18902	NM_008349	16155	Mm.4154	NM_008349	ENSMUSG00000022969	Il10rb	6620401D04Rik|AI528744|CRF2-4|Crfb4|D16H21S58|D21S58h|IL-10R2|Il10r2	interleukin 10 receptor, beta	protein-coding
mm_141101.1	chr17	26019733	26019747	-	1	NA	intron (NM_001162869, intron 3 of 14)	Lx7|LINE|L1	2120	NM_153140	215445	Mm.41191	NM_153140	ENSMUSG00000037098	Rab11fip3	Cart1|D030060O14Rik|Rab11-FIP3|mKIAA0665	RAB11 family interacting protein 3 (class II)	protein-coding
mm_158334.1	chrX	133981708	133981719	-	1	NA	promoter-TSS (NM_001290718)	promoter-TSS (NM_001290718)	99	NM_001290718	27359	Mm.38674	NM_013757	ENSMUSG00000031255	Sytl4	Gph|Slp4	synaptotagmin-like 4	protein-coding
mm_26891.1	chr3	19043571	19043584	-	1	NA	Intergenic	(TAGA)n|Simple_repeat|Simple_repeat	119488	NM_028840	74252	Mm.200383	NM_028840	ENSMUSG00000027599	Armc1	2310016N05Rik|2900046P06Rik|3110009G21Rik|AA409258|AW048872|Arcp|C330014L16Rik	armadillo repeat containing 1	protein-coding
mm_12100.1	chr2	61530571	61530586	+	1	NA	Intergenic	Intergenic	-48008	NM_011529	21353	Mm.244393	NM_011529	ENSMUSG00000064289	Tank	C86182|E430026L09Rik|I-TRAF	TRAF family member-associated Nf-kappa B activator	protein-coding
mm_66232.1	chr7	35178291	35178292	-	1	NA	Intergenic	Intergenic	-8094	NM_017394	53896	Mm.35567	NM_017394	ENSMUSG00000030495	Slc7a10	AL024237|Asc-1|D7Bwg0847e	solute carrier family 7 (cationic amino acid transporter, y+ system), member 10	protein-coding
mm_168565.1	chr11	69662729	69662748	-	1	NA	promoter-TSS (NR_035455)	promoter-TSS (NR_035455)	-89	NM_011900	24070	Mm.89579	NM_011900	ENSMUSG00000018761	Mpdu1	LEC35|SL15|Supl15h	mannose-P-dolichol utilization defect 1	protein-coding
mm_131586.1	chr16	18498866	18498942	+	1	NA	promoter-TSS (NM_001285494)	promoter-TSS (NM_001285494)	33	NR_104347	13972	Mm.236139	NM_023120	ENSMUSG00000000884	Gnb1l	ESTM55|Gm16314|Me49f07|OTTMUSG00000033458|Wdr14|Wdvcf	guanine nucleotide binding protein (G protein), beta polypeptide 1-like	protein-coding
mm_141465.1	chr17	30593535	30593539	-	1	NA	3' UTR (NM_025374, exon 6 of 6)	3' UTR (NM_025374, exon 6 of 6)	-17250	NM_027060	224671	Mm.41220	NM_027060	ENSMUSG00000062202	Btbd9	1700023F20Rik|4930402L05|AI464421	BTB (POZ) domain containing 9	protein-coding
mm_100695.1	chr11	3530016	3530040	-	1	NA	exon (NM_001284429, exon 11 of 22)	exon (NM_001284429, exon 11 of 22)	9264	NM_013870	29856	Mm.188516	NM_013870	ENSMUSG00000020439	Smtn	smsmo	smoothelin	protein-coding
mm_152369.1	chr19	10121970	10121974	-	1	NA	Intergenic	Intergenic	-20469	NM_019699	56473	Mm.38901	NM_019699	ENSMUSG00000024665	Fads2	2900042M13Rik|Fadsd2	fatty acid desaturase 2	protein-coding
mm_40901.1	chr5	75180089	75180108	+	1	NA	intron (NM_001347718, intron 12 of 15)	intron (NM_001347718, intron 12 of 15)	3267	NR_105992	102465620		NR_105992	ENSMUSG00000099060	Mir7025	Gm27860|mmu-mir-7025	microRNA 7025	ncRNA
mm_139551.1	chr17	56831677	56831680	+	1	NA	promoter-TSS (NM_009056)	promoter-TSS (NM_009056)	-670	NM_027787	19725	Mm.102	NM_009056	ENSMUSG00000024206	Rfx2	5430432H19Rik	regulatory factor X, 2 (influences HLA class II expression)	protein-coding
mm_159283.1	chr2	168742085	168742085	-	1	NA	promoter-TSS (NM_015731)	promoter-TSS (NM_015731)	51	NM_001289446	11981	Mm.330819	NM_015731	ENSMUSG00000027546	Atp9a	IIa	ATPase, class II, type 9A	protein-coding
mm_168264.1	chr10	91225111	91225111	+	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	-53492	NM_001080130	21917	Mm.159684	NM_011605	ENSMUSG00000019961	Tmpo	5630400D24Rik|AI195756|AI606875|AW214352|AW547477|LAP2|TP	thymopoietin	protein-coding
mm_117691.1	chr13	94285994	94286020	-	1	NA	promoter-TSS (NM_029153)	promoter-TSS (NM_029153)	-176	NM_001346609	107767	Mm.201455	NM_029153	ENSMUSG00000021687	Scamp1	4930505M11Rik|AI415563|AW122395	secretory carrier membrane protein 1	protein-coding
mm_148585.1	chr19	5050808	5050858	+	1	NA	promoter-TSS (NM_145495)	promoter-TSS (NM_145495)	25	NM_145495	225870	Mm.271922	NM_145495	ENSMUSG00000024883	Rin1	-	Ras and Rab interactor 1	protein-coding
mm_50800.1	chr6	54269136	54269161	+	1	NA	promoter-TSS (NM_001311134)	promoter-TSS (NM_001311134)	-8	NM_001311134	69993	Mm.321147	NM_023543	ENSMUSG00000004633	Chn2	1700026N20Rik|4930557O16Rik|ARHGAP3|Bch	chimerin 2	protein-coding
mm_119776.1	chr14	54176272	54176285	+	1	NA	Intergenic	Intergenic	77651	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_59458.1	chr7	27195900	27195915	+	1	NA	promoter-TSS (NM_001046637)	promoter-TSS (NM_001046637)	126	NM_001243888	414069	Mm.379069	NM_001243888	ENSMUSG00000078786	BC024978	-	cDNA sequence BC024978	protein-coding
mm_103958.1	chr11	84129583	84129620	-	1	NA	promoter-TSS (NM_172562)	promoter-TSS (NM_172562)	-33	NM_172562	217031	Mm.45159	NM_172562	ENSMUSG00000018651	Tada2a	AV319371|D030022J10Rik|Tada2l	transcriptional adaptor 2A	protein-coding
mm_4547.1	chr1	177258509	177258528	+	1	NA	Intergenic	CpG	-9751	NM_011785	23797	Mm.235194	NM_011785	ENSMUSG00000019699	Akt3	AI851531|D930002M15Rik|Nmf350	thymoma viral proto-oncogene 3	protein-coding
mm_14145.1	chr2	126552758	126552768	+	1	NA	promoter-TSS (NM_011978)	promoter-TSS (NM_011978)	-261	NM_011978	26458	Mm.290044	NM_011978	ENSMUSG00000027359	Slc27a2	ACSVL1|FATP2|VLCS|Vlac|Vlacs	solute carrier family 27 (fatty acid transporter), member 2	protein-coding
mm_12153.1	chr2	61812945	61812960	+	1	NA	3' UTR (NM_009322, exon 6 of 6)	3' UTR (NM_009322, exon 6 of 6)	8499	NM_009322	21375	Mm.308525	NM_009322	ENSMUSG00000035033	Tbr1	-	T-box brain gene 1	protein-coding
mm_45868.1	chr5	88008077	88008080	-	1	NA	exon (NM_011422, exon 3 of 3)	exon (NM_011422, exon 3 of 3)	5553	NM_011422	20599	Mm.261199	NM_011422	ENSMUSG00000029280	Smr3a	AA589601|MSG1|MSG3|Smr1|Smr3	submaxillary gland androgen regulated protein 3A	protein-coding
mm_121538.1	chr14	122384070	122384074	+	1	NA	intron (NM_029556, intron 6 of 7)	intron (NM_029556, intron 6 of 7)	67043	NR_033325	328479	Mm.86095	NR_033325	ENSMUSG00000064052	Gm5089	6530402A20|C030005G22Rik|EG328479	predicted gene 5089	ncRNA
mm_51225.1	chr6	71373377	71373379	+	1	NA	promoter-TSS (NM_009857)	promoter-TSS (NM_009857)	-49	NM_009857	12525	Mm.1858	NM_009857	ENSMUSG00000053977	Cd8a	BB154331|Ly-2|Ly-35|Ly-B|Lyt-2	CD8 antigen, alpha chain	protein-coding
mm_66090.1	chr7	30973368	30973380	-	1	NA	promoter-TSS (NM_017405)	promoter-TSS (NM_017405)	95	NM_001164185	54135	Mm.4067	NM_017405	ENSMUSG00000001247	Lsr	ILDR3|Lisch7	lipolysis stimulated lipoprotein receptor	protein-coding
mm_128089.1	chr15	27785377	27785388	-	1	NA	intron (NM_001081302, intron 34 of 56)	intron (NM_001081302, intron 34 of 56)	-103840	NM_001242423	223433	Mm.266485	NM_198301	ENSMUSG00000056069	Fam105a	9830126M18	family with sequence similarity 105, member A	protein-coding
mm_3137.1	chr1	135132694	135132741	+	1	NA	promoter-TSS (NM_177081)	promoter-TSS (NM_177081)	-8	NM_177081	320139	Mm.258388	NM_177081	ENSMUSG00000031506	Ptpn7	BPTP-4|C920001D21Rik|HEPTP|LC-PTP|LPTP	protein tyrosine phosphatase, non-receptor type 7	protein-coding
mm_12018.1	chr2	58154005	58154014	+	1	NA	intron (NM_139200, intron 1 of 7)	intron (NM_139200, intron 1 of 7)	6113	NM_139200	227929	Mm.273905	NM_139200	ENSMUSG00000026832	Cytip	A130053M09Rik|AI462064|C80816|Cbp|Cybr|Pscdbp	cytohesin 1 interacting protein	protein-coding
mm_169270.1	chr13	86046765	86046765	-	1	NA	promoter-TSS (NM_007749)	promoter-TSS (NM_007749)	30	NM_007749	12867	Mm.378898	NM_007749	ENSMUSG00000017778	Cox7c	COXVIIc|Cox7c1	cytochrome c oxidase subunit VIIc	protein-coding
mm_113393.1	chr13	33041004	33041009	+	1	NA	TTS (NM_011452)	TTS (NM_011452)	13592	NM_011452	20706	Mm.45371	NM_011452	ENSMUSG00000021403	Serpinb9b	1600019A21Rik|R86|SPI-CI|Spi10|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 9b	protein-coding
mm_170558.1	chr19	43351200	43351211	+	1	NA	intron (NM_001081257, intron 2 of 11)	IAP1-MM_LTR|LTR|ERVK	37150	NM_001081257	545291	Mm.442200	NM_001081257	ENSMUSG00000074852	Hpse2	Gm968|Hpa2	heparanase 2	protein-coding
mm_11959.1	chr2	53107591	53107629	+	1	NA	exon (NM_172409, exon 14 of 27)	exon (NM_172409, exon 14 of 27)	83577	NM_018785	56194	Mm.257474	NM_018785	ENSMUSG00000061136	Prpf40a	2810012K09Rik|FBP-11|FBP11|Fnbp11|Fnbp3	pre-mRNA processing factor 40A	protein-coding
mm_167114.1	chr7	118129593	118129599	-	1	NA	promoter-TSS (NM_019419)	promoter-TSS (NM_019419)	29	NM_019419	54208	Mm.29924	NM_019419	ENSMUSG00000030654	Arl6ip1	AIP-6|AL022945|ARMER|AU042858|Aip-1|Arl6ip|C85138|mKIAA0069	ADP-ribosylation factor-like 6 interacting protein 1	protein-coding
mm_162206.1	chrX	135839105	135839105	+	1	NA	promoter-TSS (NM_001163017)	promoter-TSS (NM_001163017)	71	NM_001163017	245607	Mm.489763	NM_001163015	ENSMUSG00000072966	Gprasp2	5330440H13Rik|GASP-2|GASP2|Prpl5	G protein-coupled receptor associated sorting protein 2	protein-coding
mm_18098.1	chr2	44987721	44987793	-	1	NA	3' UTR (NM_015753, exon 10 of 10)	3' UTR (NM_015753, exon 10 of 10)	35420	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_171801.1	chr5	123826438	123826442	-	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	39076	NM_030701	80885	Mm.440567	NM_030701	ENSMUSG00000045502	Hcar2	Gpr109a|Gpr109b|HM74|Niacr1|PUMA-G|Pumag|mHM74b	hydroxycarboxylic acid receptor 2	protein-coding
mm_90970.1	chr10	13446109	13446134	-	1	NA	intron (NM_001195065, intron 1 of 12)	intron (NM_001195065, intron 1 of 12)	28275	NM_001195065	215789	Mm.283359	NM_001033257	ENSMUSG00000062866	Phactr2	AV158170|BC012871	phosphatase and actin regulator 2	protein-coding
mm_5668.1	chr1	42695280	42695290	-	1	NA	promoter-TSS (NR_027826)	promoter-TSS (NR_027826)	-460	NR_027826	66297	Mm.45203	NM_183252	ENSMUSG00000060424	Pantr1	2610017I09Rik|Pou3f3os|linc-Brn1a	POU domain, class 3, transcription factor 3 adjacent noncoding transcript 1	ncRNA
mm_104242.1	chr11	88718297	88718310	-	1	NA	promoter-TSS (NM_054043)	promoter-TSS (NM_054043)	-36	NM_001201341	76626	Mm.400451	NM_054043	ENSMUSG00000069769	Msi2	1700105C15Rik|AI451722|AI563628|AW489193|Msi2h	musashi RNA-binding protein 2	protein-coding
mm_90993.1	chr10	13966781	13966788	-	1	NA	intron (NM_010437, intron 1 of 8)	CpG-904	405	NM_010437	15273	Mm.42157	NM_010437	ENSMUSG00000015501	Hivep2	Gm20114|MIBP1|Schnurri-2|Shn-2	human immunodeficiency virus type I enhancer binding protein 2	protein-coding
mm_45227.1	chr5	53505505	53505523	-	1	NA	Intergenic	ORR1D2|LTR|ERVL-MaLR	-50265	NM_001080928	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_111301.1	chr12	85599182	85599243	-	1	NA	promoter-TSS (NM_001205053)	promoter-TSS (NM_001205053)	107	NM_001205052	81703	Mm.103560	NM_030887	ENSMUSG00000034271	Jdp2	Jundm2|Jundp2|TIF	Jun dimerization protein 2	protein-coding
mm_80459.1	chr9	77983518	77983547	+	1	NA	3' UTR (NM_134255, exon 8 of 8)	3' UTR (NM_134255, exon 8 of 8)	66167	NM_134255	68801	Mm.430736	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	ELOVL family member 5, elongation of long chain fatty acids (yeast)	protein-coding
mm_121529.1	chr14	122228349	122228368	+	1	NA	intron (NM_029556, intron 1 of 7)	(T)n|Simple_repeat|Simple_repeat	5280	NR_015532	68245	Mm.443285	NR_015532	ENSMUSG00000100585	1700108J01Rik	-	RIKEN cDNA 1700108J01 gene	ncRNA
mm_14993.1	chr2	152293980	152294002	+	1	NA	exon (NM_024196, exon 1 of 8)	exon (NM_024196, exon 1 of 8)	119	NM_024196	67231	Mm.288733	NM_024196	ENSMUSG00000027465	Tbc1d20	1110028I04Rik|2810442O16Rik|AI414693|bs	TBC1 domain family, member 20	protein-coding
mm_88604.1	chr10	79807263	79807277	+	1	NA	intron (NM_023128, intron 3 of 8)	intron (NM_023128, intron 3 of 8)	13698	NM_001161747	18483	Mm.34650	NM_023128	ENSMUSG00000035863	Palm	-	paralemmin	protein-coding
mm_133467.1	chr16	89211476	89211481	+	1	NA	Intergenic	Intergenic	5617	NM_001163615	622935	Mm.459837	NM_001163615	ENSMUSG00000091039	Krtap20-2	1190004K03Rik|EG622935|Gm6371	keratin associated protein 20-2	protein-coding
mm_112916.1	chr13	20923143	20923161	+	1	NA	intron (NM_012054, intron 11 of 20)	Lx8b|LINE|L1	129039	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_124084.1	chr14	78713657	78713657	-	1	NA	intron (NM_001081336, intron 1 of 28)	intron (NM_001081336, intron 1 of 28)	11432	NM_001081336	380921	Mm.89591	NM_001081336	ENSMUSG00000034731	Dgkh	5930402B05Rik|D130015C16|DGK	diacylglycerol kinase, eta	protein-coding
mm_172145.1	chr6	37686871	37686885	-	1	NA	Intergenic	Intergenic	156705	NM_145364	208665	Mm.262635	NM_145364	ENSMUSG00000038641	Akr1d1	-	aldo-keto reductase family 1, member D1	protein-coding
mm_84956.1	chr9	83434609	83434614	-	1	NA	intron (NR_102437, intron 1 of 2)	L2|LINE|L2	3064	NR_102437	100039186	Mm.212721	NR_102437	ENSMUSG00000099718	Gm2087	-	predicted gene 2087	ncRNA
mm_74908.1	chr8	25238198	25238202	-	1	NA	Intergenic	Intergenic	-36658	NM_177089	320165	Mm.308452	NM_177089	ENSMUSG00000065954	Tacc1	4833447E04Rik|AA960202|B230378H13Rik	transforming, acidic coiled-coil containing protein 1	protein-coding
mm_11888.1	chr2	49721826	49721856	+	1	NA	intron (NM_008449, intron 11 of 25)	intron (NM_008449, intron 11 of 25)	-65845	NM_027990	71897	Mm.41381	NM_027990	ENSMUSG00000026765	Lypd6b	2310010M24Rik|AW049525	LY6/PLAUR domain containing 6B	protein-coding
mm_117293.1	chr13	66932981	66932989	-	1	NA	promoter-TSS (NM_025547)	promoter-TSS (NM_025547)	87	NM_025547	66410	Mm.347939	NM_025547	ENSMUSG00000021519	Mterf3	2410017I18Rik|Mterfd1	mitochondrial transcription termination factor 3	protein-coding
mm_10191.1	chr2	4919005	4919038	+	1	NA	promoter-TSS (NM_010726)	promoter-TSS (NM_010726)	25	NM_010726	16922	Mm.391704	NM_010726	ENSMUSG00000026664	Phyh	AI256161|AI265699|Lnap1|PAHX	phytanoyl-CoA hydroxylase	protein-coding
mm_72610.1	chr8	84597870	84597890	+	1	NA	intron (NM_001252059, intron 30 of 45)	PB1D9|SINE|Alu	64972	NM_010499	15936	Mm.399	NM_010499	ENSMUSG00000053560	Ier2	AI317238|Ch1|Pip92	immediate early response 2	protein-coding
mm_22635.1	chr3	14862841	14862855	+	1	NA	promoter-TSS (NM_007606)	promoter-TSS (NM_007606)	-690	NM_007606	12350	Mm.300	NM_007606	ENSMUSG00000027559	Car3	BB219044|Ca3|Car-3	carbonic anhydrase 3	protein-coding
mm_90938.1	chr10	12923076	12923080	-	1	NA	promoter-TSS (NR_038028)	promoter-TSS (NR_038028)	49	NR_038027	320273	Mm.417706	NR_038027	ENSMUSG00000097378	B230208H11Rik	-	RIKEN cDNA B230208H11 gene	ncRNA
mm_92273.1	chr10	71159831	71159868	-	1	NA	promoter-TSS (NM_001347189)	promoter-TSS (NM_001347189)	-159	NM_001347189	83675	Mm.286834	NM_031397	ENSMUSG00000014329	Bicc1	Bic-C|bpk|jcpk	BicC family RNA binding protein 1	protein-coding
mm_25091.1	chr3	100921693	100921702	+	1	NA	promoter-TSS (NM_001165953)	promoter-TSS (NM_001165953)	-796	NM_001165952	229644	Mm.189351	NM_194343	ENSMUSG00000033233	Trim45	4921530N01Rik	tripartite motif-containing 45	protein-coding
mm_70803.1	chr8	22939343	22939357	+	1	NA	exon (NM_001081149, exon 18 of 18)	exon (NM_001081149, exon 18 of 18)	-35486	NM_001110783	11733	Mm.334444	NM_031158	ENSMUSG00000031543	Ank1	Ank-1|nb|pale	ankyrin 1, erythroid	protein-coding
mm_88400.1	chr10	76583893	76583900	+	1	NA	intron (NM_080845, intron 8 of 13)	intron (NM_080845, intron 8 of 13)	8248	NM_080845	14317	Mm.36278	NM_080845	ENSMUSG00000001155	Ftcd	-	formiminotransferase cyclodeaminase	protein-coding
mm_63551.1	chr7	128070657	128070679	+	1	NA	exon (NM_008401, exon 4 of 30)	exon (NM_008401, exon 4 of 30)	8028	NM_008401	16409	Mm.262106	NM_008401	ENSMUSG00000030786	Itgam	CD11b/CD18|CR3|CR3A|Cd11b|F730045J24Rik|Ly-40|MAC1|Mac-1|Mac-1a	integrin alpha M	protein-coding
mm_74378.1	chr8	128685747	128685782	+	1	NA	5' UTR (NM_010578, exon 1 of 16)	5' UTR (NM_010578, exon 1 of 16)	110	NM_010578	16412	Mm.263396	NM_010578	ENSMUSG00000025809	Itgb1	4633401G24Rik|AA409975|AA960159|CD29|ENSMUSG00000051907|Fnrb|Gm9863|gpIIa	integrin beta 1 (fibronectin receptor beta)	protein-coding
mm_111766.1	chr12	104013641	104013658	-	1	NA	promoter-TSS (NM_027997)	promoter-TSS (NM_027997)	3	NM_027997	71907	Mm.326723	NM_027997	ENSMUSG00000058260	Serpina9	2310014L03Rik|AW049635|Centerin	serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9	protein-coding
mm_126414.1	chr15	80287235	80287252	+	1	NA	promoter-TSS (NM_001044308)	promoter-TSS (NM_001044308)	5	NM_001044308	239556	Mm.291058	NM_001044308	ENSMUSG00000022416	Cacna1i	Ca(V)3.3	calcium channel, voltage-dependent, alpha 1I subunit	protein-coding
mm_1156.1	chr1	60887362	60887386	+	1	NA	Intergenic	Intergenic	-21651	NM_009843	12477	Mm.390	NM_009843	ENSMUSG00000026011	Ctla4	Cd152|Ctla-4|Ly-56	cytotoxic T-lymphocyte-associated protein 4	protein-coding
mm_70159.1	chr7	143548793	143548839	-	1	NA	promoter-TSS (NM_001285490)	promoter-TSS (NM_001285490)	12	NM_001285490	17955	Mm.294625	NM_008672	ENSMUSG00000059119	Nap1l4	2810410H14Rik|AI316776|D7Wsu30e|Nap2	nucleosome assembly protein 1-like 4	protein-coding
mm_136125.1	chr16	85900720	85900745	-	1	NA	5' UTR (NM_011782, exon 1 of 8)	5' UTR (NM_011782, exon 1 of 8)	393	NM_011782	23794	Mm.112933	NM_011782	ENSMUSG00000022894	Adamts5	9530092O11Rik|ADAM-TS5|ADAMTS1|ADAMTS11|ADMP-2|AI481094|ASMP-2	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)	protein-coding
mm_47489.1	chr5	123910494	123910537	-	1	NA	intron (NM_026603, intron 2 of 7)	intron (NM_026603, intron 2 of 7)	3240	NM_026603	68184	Mm.28549	NM_026603	ENSMUSG00000023106	Denr	1500003K04Rik	density-regulated protein	protein-coding
mm_136320.1	chr16	91931644	91931654	-	1	NA	promoter-TSS (NM_138597)	promoter-TSS (NM_138597)	-19	NM_138597	28080	Mm.41	NM_138597	ENSMUSG00000022956	Atp5o	ATPO|D12Wsu28e|OSCP	ATP synthase, H+ transporting, mitochondrial F1 complex, O subunit	protein-coding
mm_65495.1	chr7	25712559	25712569	-	1	NA	3' UTR (NM_028771, exon 5 of 5)	3' UTR (NM_028771, exon 5 of 5)	6489	NM_028771	52132	Mm.278798	NM_028771	ENSMUSG00000002608	Ccdc97	1200014H14Rik|2810446P04Rik|AA545218|D7Ertd462e	coiled-coil domain containing 97	protein-coding
mm_134441.1	chr16	18248612	18248692	-	1	NA	promoter-TSS (NM_011239)	promoter-TSS (NM_011239)	42	NM_011239	19385	Mm.235287	NM_011239	ENSMUSG00000005732	Ranbp1	Htf9a	RAN binding protein 1	protein-coding
mm_55913.1	chr6	83775583	83775597	-	1	NA	intron (NM_009357, intron 1 of 5)	CpG	222	NM_009357	21766	Mm.28371	NM_009357	ENSMUSG00000014748	Tex261	3110001O07Rik|AA409339|AI480706|AL033351|TEG-261	testis expressed gene 261	protein-coding
mm_35760.1	chr4	45826947	45826962	-	1	NA	promoter-TSS (NM_018741)	promoter-TSS (NM_018741)	-127	NM_018741	75426	Mm.3919	NM_018741	ENSMUSG00000035551	Igfbpl1	2810011G06Rik|2810453O06Rik|IGFBPL	insulin-like growth factor binding protein-like 1	protein-coding
mm_131014.1	chr15	103563295	103563298	-	1	NA	exon (NM_008134, exon 3 of 4)	exon (NM_008134, exon 3 of 4)	1785	NM_001289587	14663	Mm.219621	NM_008134	ENSMUSG00000022491	Glycam1	MC26|Sgp50|glyCAM-1	glycosylation dependent cell adhesion molecule 1	protein-coding
mm_15387.1	chr2	156613665	156613706	+	1	NA	promoter-TSS (NM_146128)	promoter-TSS (NM_146128)	-12	NM_146128	228836	Mm.22094	NM_146128	ENSMUSG00000061689	Dlgap4	AI225853|BC024558|DAP-4|DAP4|SAPAP-4|Sapap4|WBP16	discs, large homolog-associated protein 4 (Drosophila)	protein-coding
mm_64080.1	chr7	140941887	140941956	+	1	NA	intron (NM_145387, intron 1 of 13)	intron (NM_145387, intron 1 of 13)	340	NM_145387	212974	Mm.260139	NM_145387	ENSMUSG00000062031	Pgghg	5730511L01Rik|Athl1|BC023151	protein glucosylgalactosylhydroxylysine glucosidase	protein-coding
mm_162694.1	chr10	19939482	19939492	+	1	NA	intron (NM_008580, intron 1 of 29)	intron (NM_008580, intron 1 of 29)	4961	NM_008580	26408	Mm.6595	NM_008580	ENSMUSG00000071369	Map3k5	7420452D20Rik|ASK|ASK1|MAPKKK5|Mekk5	mitogen-activated protein kinase kinase kinase 5	protein-coding
mm_23503.1	chr3	60528470	60528495	+	1	NA	intron (NM_001253710, intron 1 of 7)	intron (NM_001253710, intron 1 of 7)	27303	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_129886.1	chr15	83489603	83489623	-	1	NA	exon (NM_178869, exon 11 of 12)	exon (NM_178869, exon 11 of 12)	21294	NM_178869	319953	Mm.235007	NM_178869	ENSMUSG00000022442	Ttll1	6330444E16Rik|AV014541	tubulin tyrosine ligase-like 1	protein-coding
mm_64799.1	chr7	6689497	6689507	-	1	NA	5' UTR (NM_011769, exon 3 of 8)	5' UTR (NM_011769, exon 3 of 8)	6930	NM_011769	22776	Mm.89976	NM_011769	ENSMUSG00000002266	Zim1	-	zinc finger, imprinted 1	protein-coding
mm_2007.1	chr1	87127409	87127419	+	1	NA	exon (NM_007432, exon 10 of 11)	exon (NM_007432, exon 10 of 11)	2406	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_110675.1	chr12	65213507	65213514	-	1	NA	Intergenic	Intergenic	-12007	NM_027614	70948	Mm.219475	NM_027614	ENSMUSG00000035560	Wdr20rt	4921538B03Rik|4930427E19Rik|Wdr20|Wdr20b	WD repeat domain 20, retrogene	protein-coding
mm_97584.1	chr11	78945634	78945656	+	1	NA	exon (NM_010927, exon 14 of 27)	exon (NM_010927, exon 14 of 27)	20354	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_168020.1	chrY	90737833	90737843	+	1	NA	Intergenic	RLTR31D_MM|LTR|ERVK	17212	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_91989.1	chr10	61979114	61979136	-	1	NA	promoter-TSS (NM_007731)	promoter-TSS (NM_007731)	-17	NM_007731	12817	Mm.300931	NM_007731	ENSMUSG00000058806	Col13a1	-	collagen, type XIII, alpha 1	protein-coding
mm_81609.1	chr9	110689443	110689463	+	1	NA	intron (NM_028312, intron 1 of 6)	intron (NM_028312, intron 1 of 6)	32950	NM_028312	72654	Mm.249115	NM_028312	ENSMUSG00000019659	Ccdc12	2700094L05Rik|C76605	coiled-coil domain containing 12	protein-coding
mm_53350.1	chr6	129350283	129350297	+	1	NA	promoter-TSS (NM_177686)	promoter-TSS (NM_177686)	46	NM_177686	232413	Mm.90241	NM_177686	ENSMUSG00000053063	Clec12a	CLL-1|D230024O04|KLRL1|Micl	C-type lectin domain family 12, member a	protein-coding
mm_35055.1	chr4	6355416	6355477	-	1	NA	Intergenic	Intergenic	-10234	NM_016807	53378	Mm.247473	NM_016807	ENSMUSG00000028249	Sdcbp	MDA-9|Sycl|syntenin-1	syndecan binding protein	protein-coding
mm_138292.1	chr17	34629411	34629449	+	1	NA	promoter-TSS (NM_030890)	promoter-TSS (NM_030890)	-256	NM_030890	260297	Mm.390965	NM_030890	ENSMUSG00000015476	Prrt1	Bat-4|Bat4|D17H6S54E|DSPD1|G5b|NG5|ORF31	proline-rich transmembrane protein 1	protein-coding
mm_107658.1	chr12	52790736	52790751	+	1	NA	intron (NM_198111, intron 1 of 13)	intron (NM_198111, intron 1 of 13)	91360	NM_198111	238161	Mm.310822	NM_198111	ENSMUSG00000061603	Akap6	AI482140|Akapalpha|Akapbeta|PRKA	A kinase (PRKA) anchor protein 6	protein-coding
mm_143079.1	chr17	57044537	57044551	-	1	NA	3' UTR (NM_025877, exon 10 of 10)	3' UTR (NM_025877, exon 10 of 10)	-2890	NM_175333	103775	Mm.33647	NM_175333	ENSMUSG00000011486	Slc25a41	4933406J04Rik|AI507137	solute carrier family 25, member 41	protein-coding
mm_54964.1	chr6	48718674	48718679	-	1	NA	promoter-TSS (NM_146167)	promoter-TSS (NM_146167)	55	NM_146167	231932	Mm.30479	NM_146167	ENSMUSG00000043931	Gimap7	IAN7|Ian3	GTPase, IMAP family member 7	protein-coding
mm_21325.1	chr2	157101231	157101270	-	1	NA	intron (NM_018851, intron 15 of 15)	intron (NM_018851, intron 15 of 15)	14195	NM_001177439	383766	Mm.480305	NM_001177439	ENSMUSG00000074628	Tldc2	Gm1332	TBC/LysM associated domain containing 2	protein-coding
mm_134027.1	chr16	5010071	5010125	-	1	NA	exon (NM_133185, exon 8 of 11)	exon (NM_133185, exon 8 of 11)	2782	NR_045596	432995	Mm.271618	NM_001253796	ENSMUSG00000096215	Smim22	EG432995|Gm5480	small integral membrane protein 22	protein-coding
mm_10175.1	chr2	4559932	4559943	+	1	NA	5' UTR (NM_001177844, exon 1 of 12)	5' UTR (NM_001177844, exon 1 of 12)	183	NM_001177844	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding
mm_133530.1	chr16	91011279	91011296	+	1	NA	promoter-TSS (NM_001045515)	promoter-TSS (NM_001045515)	21	NM_001164483	104015	Mm.187079	NM_001045515	ENSMUSG00000022973	Synj1	A930006D20Rik|AA675315|mKIAA0910	synaptojanin 1	protein-coding
mm_32477.1	chr4	107830959	107830967	+	1	NA	intron (NR_033496, intron 2 of 20)	intron (NR_033496, intron 2 of 20)	28704	NM_001080926	16975	Mm.442134	NM_053073	ENSMUSG00000028613	Lrp8	4932703M08Rik|AA921429|AI848122|ApoER2|Lr8b	low density lipoprotein receptor-related protein 8, apolipoprotein e receptor	protein-coding
mm_140121.1	chr17	79052232	79052267	+	1	NA	5' UTR (NM_001316729, exon 1 of 6)	5' UTR (NM_001316729, exon 1 of 6)	343	NM_001316729	70536	Mm.293870	NM_027455	ENSMUSG00000024084	Qpct	5730422A13Rik	glutaminyl-peptide cyclotransferase (glutaminyl cyclase)	protein-coding
mm_163567.1	chr13	28901859	28901861	+	1	NA	Intergenic	Intergenic	-16438	NR_045053	72518	Mm.37454	NR_045053		2610307P16Rik	AI666457	RIKEN cDNA 2610307P16 gene	ncRNA
mm_147987.1	chr18	67610823	67610852	-	1	NA	Intergenic	CpG	30499	NM_001081073	225659	Mm.111928	NM_001081073	ENSMUSG00000073542	Cep76	6230425F05Rik|9630013E05	centrosomal protein 76	protein-coding
mm_2680.1	chr1	127306297	127306314	+	1	NA	intron (NM_145128, intron 2 of 17)	intron (NM_145128, intron 2 of 17)	101319	NM_145128	107895	Mm.214682	NM_145128	ENSMUSG00000036155	Mgat5	4930471A21Rik|5330407H02Rik|AI480971|GlcNAc-TV	mannoside acetylglucosaminyltransferase 5	protein-coding
mm_31664.1	chr4	59964190	59964198	+	1	NA	Intergenic	RLTR9A3A|LTR|ERVK	-3529	NM_008648	17843	Mm.457982	NM_008648	ENSMUSG00000041333	Mup4	Mup-4|Mup1	major urinary protein 4	protein-coding
mm_139350.1	chr17	50509076	50509098	+	1	NA	promoter-TSS (NM_013880)	promoter-TSS (NM_013880)	-460	NM_013880	224860	Mm.217362	NM_013880	ENSMUSG00000038910	Plcl2	PLC-L2|PRIP-2|Plce2|mKIAA1092	phospholipase C-like 2	protein-coding
mm_39256.1	chr5	3527059	3527093	+	1	NA	3' UTR (NM_009873, exon 8 of 8)	3' UTR (NM_009873, exon 8 of 8)	-16757	NM_001042501	68152	Mm.240265	NM_026583	ENSMUSG00000058503	Fam133b	2900022K02Rik|5830415L20Rik	family with sequence similarity 133, member B	protein-coding
mm_116567.1	chr13	47014815	47014863	-	1	NA	promoter-TSS (NM_175340)	promoter-TSS (NM_175340)	11	NM_175340	105193	Mm.25593	NM_175340	ENSMUSG00000044231	Nhlrc1	AI505271|B230309E09Rik|EPM2B	NHL repeat containing 1	protein-coding
mm_127144.1	chr15	98481526	98481532	+	1	NA	intron (NM_010679, intron 3 of 3)	intron (NM_010679, intron 3 of 3)	1154	NM_010679	16770	Mm.5074	NM_010679	ENSMUSG00000022991	Lalba	AW208827|Lyzg	lactalbumin, alpha	protein-coding
mm_17224.1	chr2	25501744	25501759	-	1	NA	promoter-TSS (NM_001271777)	promoter-TSS (NM_001271777)	-32	NM_001271777	69379	Mm.24596	NM_027062	ENSMUSG00000015083	C8g	-	complement component 8, gamma polypeptide	protein-coding
mm_171327.1	chr3	96488725	96488726	+	1	NA	Intergenic	Intergenic	-36419	NM_001256180	329716	Mm.275223	NM_183223	ENSMUSG00000046317	BC107364	D730018G16	cDNA sequence BC107364	protein-coding
mm_97238.1	chr11	75656104	75656177	+	1	NA	5' UTR (NM_001080775, exon 1 of 32)	5' UTR (NM_001080775, exon 1 of 32)	125	NM_001080775	17913	Mm.234502	NM_008659	ENSMUSG00000017774	Myo1c	C80397|MMIb|MYO1E|NMI|mm1beta|myr2	myosin IC	protein-coding
mm_122767.1	chr14	54259136	54259158	-	1	NA	promoter-TSS (NM_134076)	promoter-TSS (NM_134076)	-85	NM_134076	105501	Mm.28771	NM_134076	ENSMUSG00000040997	Abhd4	1110035H23Rik|AI429574|Abh4	abhydrolase domain containing 4	protein-coding
mm_130000.1	chr15	86186314	86186354	-	1	NA	promoter-TSS (NM_145475)	promoter-TSS (NM_145475)	-193	NM_145475	223753	Mm.222685	NM_145475	ENSMUSG00000035891	Cerk	AI848610|D330016D08Rik|mKIAA1646	ceramide kinase	protein-coding
mm_31313.1	chr4	46106353	46106356	+	1	NA	intron (NM_021883, intron 8 of 9)	L1M4|LINE|L1	32121	NM_173033	272027	Mm.331588	NM_173033	ENSMUSG00000035495	Tstd2	3010020C06	thiosulfate sulfurtransferase (rhodanese)-like domain containing 2	protein-coding
mm_48860.1	chr5	149802549	149802574	-	1	NA	intron (NR_077242, intron 4 of 4)	RMER4B|LTR|ERVK	9190	NR_077242	100861794	Mm.402054	NR_077242	ENSMUSG00000106740	Gm21221	-	predicted gene, 21221	ncRNA
mm_17918.1	chr2	35432826	35432836	-	1	NA	intron (NM_001308300, intron 1 of 6)	intron (NM_001308300, intron 1 of 6)	28618	NM_001308299	14594	Mm.281124	NM_010283	ENSMUSG00000035778	Ggta1	AW108479|GALT|Gal|Ggta|Ggta-1|alpha Gal|alpha3GalT	glycoprotein galactosyltransferase alpha 1, 3	protein-coding
mm_50799.1	chr6	54267190	54267191	+	1	NA	intron (NM_001311133, intron 1 of 7)	intron (NM_001311133, intron 1 of 7)	-1966	NM_001311134	69993	Mm.321147	NM_023543	ENSMUSG00000004633	Chn2	1700026N20Rik|4930557O16Rik|ARHGAP3|Bch	chimerin 2	protein-coding
mm_77472.1	chr8	122432447	122432456	-	1	NA	intron (NM_001301284, intron 1 of 4)	intron (NM_001301284, intron 1 of 4)	489	NM_001301284	13057	Mm.271671	NM_007806	ENSMUSG00000006519	Cyba	b558|nmf333|p22-phox|p22phox	cytochrome b-245, alpha polypeptide	protein-coding
mm_155679.1	chrX	93094407	93094407	+	1	NA	Intergenic	MT2_Mm|LTR|ERVL	-61747	NR_105038	69357	Mm.443312	NM_183280	ENSMUSG00000096153	BC061195	-	cDNA sequence BC061195	pseudo
mm_6278.1	chr1	69683158	69683178	-	1	NA	intron (NM_011770, intron 3 of 7)	intron (NM_011770, intron 3 of 7)	2792	NM_011770	22779	Mm.106343	NM_011770	ENSMUSG00000025997	Ikzf2	A730095J18Rik|Helios|Zfpn1a2|Znfn1a2	IKAROS family zinc finger 2	protein-coding
mm_88752.1	chr10	80299171	80299173	+	1	NA	intron (NR_038088, intron 1 of 4)	intron (NR_038088, intron 1 of 4)	-2648	NM_011789	23805	Mm.57247	NM_011789	ENSMUSG00000020135	Apc2	AI852447|APCL|R75424	adenomatosis polyposis coli 2	protein-coding
mm_47597.1	chr5	124862467	124862483	-	1	NA	promoter-TSS (NM_001081750)	promoter-TSS (NM_001081750)	-230	NM_001081750	269704	Mm.138617	NM_001081750	ENSMUSG00000079215	Zfp664	AW060232|D930038J03Rik|ZFOC1|Znf664	zinc finger protein 664	protein-coding
mm_164509.1	chr16	94027636	94027636	+	1	NA	Intergenic	Intergenic	-18799	NM_019500	56173	Mm.328716	NM_019500	ENSMUSG00000047109	Cldn14	AI851731	claudin 14	protein-coding
mm_35606.1	chr4	43046163	43046173	-	1	NA	promoter-TSS (NM_172691)	promoter-TSS (NM_172691)	52	NR_045567	230088	Mm.260162	NM_172691	ENSMUSG00000036002	Fam214b	B230312A22Rik	family with sequence similarity 214, member B	protein-coding
mm_93180.1	chr10	93594104	93594140	-	1	NA	intron (NR_045810, intron 1 of 3)	intron (NR_045810, intron 1 of 3)	-4464	NM_027246	69878	Mm.259642	NM_027246	ENSMUSG00000020018	Snrpf	2010013O18Rik|SMF|sm-F|snRNP-F	small nuclear ribonucleoprotein polypeptide F	protein-coding
mm_42478.1	chr5	115468446	115468458	+	1	NA	intron (NM_011107, intron 1 of 3)	L2a|LINE|L2	2186	NM_011107	18778	Mm.20190	NM_011107	ENSMUSG00000029522	Pla2g1b	Pla2a|sPLA2IB	phospholipase A2, group IB, pancreas	protein-coding
mm_162597.1	chr1	183147465	183147487	-	1	NA	promoter-TSS (NM_001278220)	promoter-TSS (NM_001278220)	81	NM_001278220	68897	Mm.327216	NM_026866	ENSMUSG00000030768	Disp1	1190008H24Rik|DispA	dispatched RND transporter family member 1	protein-coding
mm_27998.1	chr3	82876509	82876527	-	1	NA	promoter-TSS (NM_001146328)	promoter-TSS (NM_001146328)	-35	NM_001146328	633285	Mm.265114	NM_001146328	ENSMUSG00000033882	Rbm46	EG633285|ENSMUSG00000033882|Gm761	RNA binding motif protein 46	protein-coding
mm_157918.1	chrX	78583784	78583796	-	1	NA	promoter-TSS (NM_001164275)	promoter-TSS (NM_001164275)	15	NM_001164275	546336	Mm.211712	NM_027322	ENSMUSG00000047996	Prrg1	2010007L08Rik	proline rich Gla (G-carboxyglutamic acid) 1	protein-coding
mm_141832.1	chr17	34628187	34628239	-	1	NA	promoter-TSS (NM_001302396)	promoter-TSS (NM_001302396)	66	NM_001302393	54397	Mm.373627	NM_019441	ENSMUSG00000015474	Ppt2	0610007M19Rik|AA672937	palmitoyl-protein thioesterase 2	protein-coding
mm_162129.1	chrX	73117089	73117089	+	1	NA	promoter-TSS (NM_001025384)	promoter-TSS (NM_001025384)	42	NM_001025384	574405	Mm.336093	NM_001025384	ENSMUSG00000071745	DXBay18	-	DNA segment, Chr X, Baylor 18	protein-coding
mm_63027.1	chr7	121036667	121036673	+	1	NA	intron (NM_021554, intron 1 of 4)	intron (NM_021554, intron 1 of 4)	2225	NM_021554	59052	Mm.29122	NM_021554	ENSMUSG00000030876	Mettl9	0610012D09Rik|AA517660|Drev|MNCb-5680	methyltransferase like 9	protein-coding
mm_86448.1	chr10	4268476	4268484	+	1	NA	intron (NM_031185, intron 1 of 3)	intron (NM_031185, intron 1 of 3)	2151	NM_031185	83397	Mm.27481	NM_031185	ENSMUSG00000038587	Akap12	AI317366|SSeCKS|Srcs5|Tsga12	A kinase (PRKA) anchor protein (gravin) 12	protein-coding
mm_11063.1	chr2	27540420	27540463	+	1	NA	Intergenic	CpG	25294	NM_080848	140858	Mm.28265	NM_080848	ENSMUSG00000026917	Wdr5	2410008O07Rik|AA408785|AA960360|Big|Big-3	WD repeat domain 5	protein-coding
mm_66752.1	chr7	46712620	46712626	-	1	NA	exon (NM_011315, exon 3 of 4)	exon (NM_011315, exon 3 of 4)	-1972	NM_030233	78935	Mm.289866	NM_030233	ENSMUSG00000006763	Saal1	5031425D22Rik|SPACIA1	serum amyloid A-like 1	protein-coding
mm_146644.1	chr18	10787685	10787699	-	1	NA	intron (NM_144860, intron 12 of 20)	intron (NM_144860, intron 12 of 20)	-2140	NR_029781	723959		NR_029781	ENSMUSG00000106348	Mir1a-2	Mir1-2|Mirn1-2|mir-1a-2|mmu-mir-1-2|mmu-mir-1a-2	microRNA 1a-2	ncRNA
mm_49950.1	chr6	40359906	40359940	+	1	NA	intron (NM_023538, intron 5 of 15)	L1_Mus3|LINE|L1	34445	NM_023538	69923	Mm.32840	NM_023538	ENSMUSG00000029916	Agk	2610037M15Rik|6720408I04Rik|AI465370|Mulk	acylglycerol kinase	protein-coding
mm_172381.1	chr7	130834551	130834557	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-31170	NM_001346515	101476	Mm.323554	NM_133942	ENSMUSG00000040268	Plekha1	AA960558|C920009D07Rik|TAPP1	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 1	protein-coding
mm_143516.1	chr17	73074718	73074758	-	1	NA	Intergenic	Intergenic	-33247	NM_001177968	225010	Mm.329194	NM_001081071	ENSMUSG00000054469	Lclat1	AI181996|Agpat8|Alcat1|Gm91|Lycat	lysocardiolipin acyltransferase 1	protein-coding
mm_114688.1	chr13	81754207	81754215	+	1	NA	TTS (NM_028372)	TTS (NM_028372)	-29081	NM_007684	12626	Mm.12481	NM_007684	ENSMUSG00000021537	Cetn3	MmCEN3	centrin 3	protein-coding
mm_25176.1	chr3	103171729	103171767	+	1	NA	promoter-TSS (NM_026602)	promoter-TSS (NM_026602)	37	NM_026602	68183	Mm.104919	NM_026602	ENSMUSG00000005687	Bcas2	6430539P16Rik|AI132645|C76366|C80030	breast carcinoma amplified sequence 2	protein-coding
mm_18977.1	chr2	76848898	76848908	-	1	NA	exon (NM_011652, exon 137 of 313)	exon (NM_011652, exon 137 of 313)	133644	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_36080.1	chr4	58206559	58206575	-	1	NA	promoter-TSS (NM_022814)	promoter-TSS (NM_022814)	29	NM_022814	64817	Mm.261024	NM_022814	ENSMUSG00000028369	Svep1	1110021D17Rik|4833413O10Rik|AA387071|D430029O09Rik|Polydom	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	protein-coding
mm_62947.1	chr7	119561700	119561726	+	1	NA	promoter-TSS (NM_146197)	promoter-TSS (NM_146197)	5	NM_001177978	233799	Mm.268448	NM_146197	ENSMUSG00000030945	Acsm2	AI315615|BC031140	acyl-CoA synthetase medium-chain family member 2	protein-coding
mm_119707.1	chr14	53806464	53806472	+	1	NA	Intergenic	Intergenic	447461	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_15671.1	chr2	163438540	163438546	+	1	NA	promoter-TSS (NM_144891)	promoter-TSS (NM_144891)	76	NM_144891	228858	Mm.102080	NM_144891	ENSMUSG00000017943	Gdap1l1	Gdap1l	ganglioside-induced differentiation-associated protein 1-like 1	protein-coding
mm_131659.1	chr16	20590147	20590174	+	1	NA	5' UTR (NM_182636, exon 2 of 15)	5' UTR (NM_182636, exon 2 of 15)	578	NM_001144953	328643	Mm.40539	NM_182636	ENSMUSG00000046613	Vwa5b2	BB182430|EG328644|Gm1738|Gm931	von Willebrand factor A domain containing 5B2	protein-coding
mm_61182.1	chr7	62348279	62348332	+	1	NA	promoter-TSS (NM_010882)	promoter-TSS (NM_010882)	28	NM_010882	17984	Mm.400253	NM_010882	ENSMUSG00000033585	Ndn	AI528698|Peg6	necdin	protein-coding
mm_132137.1	chr16	31933924	31933964	+	1	NA	promoter-TSS (NM_172822)	promoter-TSS (NM_172822)	93	NM_172822	239827	Mm.440388	NM_172822	ENSMUSG00000045625	Pigz	F630022B06Rik	phosphatidylinositol glycan anchor biosynthesis, class Z	protein-coding
mm_170429.1	chr18	7515773	7515783	-	1	NA	intron (NM_001081287, intron 2 of 16)	RLTR17|LTR|ERVK	111085	NM_001081287	75739	Mm.133293	NM_001081287	ENSMUSG00000057440	Mpp7	1110068J02Rik|2810038M04Rik|5430426E14Rik|AI415104|Gm955	membrane protein, palmitoylated 7 (MAGUK p55 subfamily member 7)	protein-coding
mm_98260.1	chr11	88864772	88864807	+	1	NA	promoter-TSS (NM_001042541)	promoter-TSS (NM_001042541)	-203	NM_001042541	11640	Mm.2969	NM_009648	ENSMUSG00000018428	Akap1	AKAP121|AKAP84|Akap|C76494|C81186|DAKAP1|S-AKAP84	A kinase (PRKA) anchor protein 1	protein-coding
mm_166802.1	chr7	4129297	4129305	+	1	NA	exon (NM_001109765, exon 6 of 14)	exon (NM_001109765, exon 6 of 14)	7625	NR_033548	100037396	Mm.447887	NR_033548	ENSMUSG00000085886	D030047H15Rik	Gm15924|OTTMUSG00000027889	RIKEN cDNA D030047H15 gene	ncRNA
mm_84089.1	chr9	58221091	58221113	-	1	NA	promoter-TSS (NR_105806)	promoter-TSS (NR_105806)	-48	NR_105806	102466639		NR_105806	ENSMUSG00000098886	Mir6385	Gm28021|mmu-mir-6385	microRNA 6385	ncRNA
mm_114978.1	chr13	97245976	97245987	+	1	NA	exon (NM_007930, exon 2 of 3)	exon (NM_007930, exon 2 of 3)	4876	NM_007930	13803	Mm.241073	NM_007930	ENSMUSG00000041773	Enc1	Nrpb|PIG10	ectodermal-neural cortex 1	protein-coding
mm_49504.1	chr6	29792134	29792136	+	1	NA	intron (NM_001171000, intron 1 of 16)	intron (NM_001171000, intron 1 of 16)	23692	NM_001171000	74340	Mm.210899	NM_021414	ENSMUSG00000029772	Ahcyl2	4631427C17Rik|AI227036|Adohcyase3|mKIAA0828	S-adenosylhomocysteine hydrolase-like 2	protein-coding
mm_112443.1	chr13	5861495	5861501	+	1	NA	promoter-TSS (NM_011803)	promoter-TSS (NM_011803)	9	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_135907.1	chr16	67518266	67518268	-	1	NA	intron (NM_178721, intron 1 of 9)	intron (NM_178721, intron 1 of 9)	102641	NM_001347247	239857	Mm.394300	NM_178721	ENSMUSG00000064115	Cadm2	2900078E11Rik|9330131D06|A830029E02Rik|Igdf4d|Igsf4d|NECL3|SynCAM 2|SynCAM2	cell adhesion molecule 2	protein-coding
mm_150949.1	chr19	46328180	46328205	+	1	NA	promoter-TSS (NM_133694)	promoter-TSS (NM_133694)	8	NM_133694	68431	Mm.19973	NM_133694	ENSMUSG00000025226	Fbxl15	0710008C12Rik|Fbxo37	F-box and leucine-rich repeat protein 15	protein-coding
mm_141653.1	chr17	33685413	33685423	-	1	NA	promoter-TSS (NM_001109913)	promoter-TSS (NM_001109913)	40	NM_001109913	76936	Mm.311439	NM_029804	ENSMUSG00000059208	Hnrnpm	2610023M21Rik|AA409009|Hnrpm|mKIAA4193	heterogeneous nuclear ribonucleoprotein M	protein-coding
mm_32361.1	chr4	105170539	105170544	+	1	NA	intron (NM_080555, intron 1 of 5)	intron (NM_080555, intron 1 of 5)	13194	NM_080555	67916	Mm.348326	NM_080555	ENSMUSG00000028517	Plpp3	1110003O22Rik|2610002D05Rik|AV025606|D4Bwg0538e|D4Bwg1535e|Lpp3|Ppab2b|Ppap2b	phospholipid phosphatase 3	protein-coding
mm_126236.1	chr15	78983049	78983120	+	1	NA	promoter-TSS (NM_001024716)	promoter-TSS (NM_001024716)	28	NM_001024716	110253	Mm.123714	NM_138579	ENSMUSG00000033088	Triobp	AI428493|EST478828|Tara|mKIAA1662	TRIO and F-actin binding protein	protein-coding
mm_153639.1	chr19	44107427	44107441	-	1	NA	promoter-TSS (NM_007700)	promoter-TSS (NM_007700)	43	NM_007700	12675	Mm.3996	NM_007700	ENSMUSG00000025199	Chuk	AI256658|Chuk1|Fbx24|Fbxo24|IKBKA|IKK1|Ikka|NFKBIKA	conserved helix-loop-helix ubiquitous kinase	protein-coding
mm_141897.1	chr17	34882005	34882080	-	1	NA	promoter-TSS (NM_013484)	promoter-TSS (NM_013484)	58	NM_013484	12263	Mm.283217	NM_013484	ENSMUSG00000024371	C2	-	complement component 2 (within H-2S)	protein-coding
mm_16882.1	chr2	13010900	13010919	-	1	NA	promoter-TSS (NM_153155)	promoter-TSS (NM_153155)	-45	NM_153155	227580	Mm.229322	NM_153155	ENSMUSG00000049630	C1ql3	1110065A22Rik|AI661623|C1ql|C1qtnf13|CTRP13|K100	C1q-like 3	protein-coding
mm_46189.1	chr5	97929815	97929833	-	1	NA	intron (NM_133738, intron 16 of 16)	Lx9|LINE|L1	101138	NM_133738	71914	Mm.24842	NM_133738	ENSMUSG00000029338	Antxr2	2310046B19Rik|AW561899|CMG-2|CMG2|cI-35	anthrax toxin receptor 2	protein-coding
mm_105115.1	chr11	101062861	101062876	-	1	NA	3' UTR (NM_001243049, exon 21 of 21)	3' UTR (NM_001243049, exon 21 of 21)	-7226	NM_013792	27419	Mm.95452	NM_013792	ENSMUSG00000001751	Naglu	-	alpha-N-acetylglucosaminidase (Sanfilippo disease IIIB)	protein-coding
mm_19722.1	chr2	104433638	104433659	-	1	NA	exon (NM_001145824, exon 12 of 16)	exon (NM_001145824, exon 12 of 16)	-4708	NR_035432	100316678		NR_035432	ENSMUSG00000084516	Mir1902	Mirn1902|mmu-mir-1902	microRNA 1902	ncRNA
mm_47643.1	chr5	125389151	125389170	-	1	NA	intron (NM_019639, intron 1 of 1)	intron (NM_019639, intron 1 of 1)	857	NM_019639	22190	Mm.331	NM_019639	ENSMUSG00000008348	Ubc	2700054O04Rik|AI194771|Rps27a|TI-225|Uba52|Ubb	ubiquitin C	protein-coding
mm_151364.1	chr19	55919503	55919518	+	1	NA	intron (NM_001142924, intron 6 of 11)	intron (NM_001142924, intron 6 of 11)	24189	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_13415.1	chr2	104122739	104122774	+	1	NA	promoter-TSS (NM_026634)	promoter-TSS (NM_026634)	-13	NM_026634	68243	Mm.158191	NM_026634	ENSMUSG00000032671	A930018P22Rik	-	RIKEN cDNA A930018P22 gene	protein-coding
mm_23622.1	chr3	65957489	65957537	+	1	NA	exon (NM_019937, exon 2 of 11)	exon (NM_019937, exon 2 of 11)	712	NM_019937	56706	Mm.175612	NM_019937	ENSMUSG00000027829	Ccnl1	2610030E23Rik|AU018493|Ccnl|ania-6a	cyclin L1	protein-coding
mm_29753.1	chr3	127124848	127124886	-	1	NA	intron (NM_001327938, intron 1 of 47)	intron (NM_001327938, intron 1 of 47)	-36438	NR_105030	100862268	Mm.444603	NR_105029	ENSMUSG00000097456	LOC100862268	-	uncharacterized LOC100862268	ncRNA
mm_69850.1	chr7	141427421	141427440	-	1	NA	3' UTR (NM_021316, exon 2 of 2)	3' UTR (NM_021316, exon 2 of 2)	1990	NM_021316	57754	Mm.87027	NM_021316	ENSMUSG00000060240	Cend1	1500001H12Rik|AI415214|BM88	cell cycle exit and neuronal differentiation 1	protein-coding
mm_22463.1	chr3	3512958	3512961	+	1	NA	intron (NM_013920, intron 1 of 9)	intron (NM_013920, intron 1 of 9)	4929	NM_013920	30942	Mm.330897	NM_013920	ENSMUSG00000017688	Hnf4g	NR2A2	hepatocyte nuclear factor 4, gamma	protein-coding
mm_4502.1	chr1	173729099	173729131	+	1	NA	exon (NM_001204910, exon 5 of 8)	exon (NM_001204910, exon 5 of 8)	12694	NM_001204910	226691	Mm.440876	NM_001204910	ENSMUSG00000073490	Ifi207	AI607873|Pyhin-A	interferon activated gene 207	protein-coding
mm_138000.1	chr17	33761068	33761072	+	1	NA	promoter-TSS (NM_008997)	promoter-TSS (NM_008997)	-584	NM_008997	19326	Mm.387587	NM_008997	ENSMUSG00000077450	Rab11b	A730055L17Rik	RAB11B, member RAS oncogene family	protein-coding
mm_14004.1	chr2	122028122	122028147	+	1	NA	promoter-TSS (NM_001256055)	promoter-TSS (NM_001256055)	-446	NM_144545	78655	Mm.458184	NM_144545	ENSMUSG00000027236	Eif3j1	1810016I04Rik|2700079K05Rik|AA409117|AA409446|C78575|Eif3j|Eif3j-1|Eif3j-2|Eif3j2|Eif3s1|eIF-3-alpha-A|eIF-3-alpha-B|eIF3-alpha|eIF3-p35|eIF3j-A|eIF3j-B	eukaryotic translation initiation factor 3, subunit J1	protein-coding
mm_140936.1	chr17	24440396	24440399	-	1	NA	TTS (NM_025718)	TTS (NM_025718)	2704	NM_025718	66705	Mm.29017	NM_025718	ENSMUSG00000024136	Dnase1l2	4733401H14Rik	deoxyribonuclease 1-like 2	protein-coding
mm_73012.1	chr8	93963268	93963279	+	1	NA	intron (NM_010308, intron 6 of 8)	intron (NM_010308, intron 6 of 8)	49367	NM_011787	23802	Mm.34641	NM_011787	ENSMUSG00000031751	Amfr	gp78	autocrine motility factor receptor	protein-coding
mm_67359.1	chr7	79838295	79838320	-	1	NA	exon (NM_008486, exon 9 of 20)	exon (NM_008486, exon 9 of 20)	4045	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_20719.1	chr2	135215611	135215622	-	1	NA	promoter-TSS (NR_040517)	promoter-TSS (NR_040517)	0	NR_040517	78805	Mm.78702	NR_040517	ENSMUSG00000085247	4930545L23Rik	-	RIKEN cDNA 4930545L23 gene	ncRNA
mm_79221.1	chr9	49518313	49518332	+	1	NA	promoter-TSS (NR_029465)	promoter-TSS (NR_029465)	34	NR_029465	100036537	Mm.437541	NR_029465	ENSMUSG00000079564	Gm11149	ENSMUSG00000060603|ENSMUSG00000079564	predicted gene 11149	ncRNA
mm_19151.1	chr2	80581069	80581181	-	1	NA	promoter-TSS (NM_001290745)	promoter-TSS (NM_001290745)	57	NM_001290745	50884	Mm.25203	NM_016965	ENSMUSG00000027002	Nckap1	C79304|H19|Hem-2|Hem2|Nap1|mKIAA0587|mh19|p125Nap1	NCK-associated protein 1	protein-coding
mm_2655.1	chr1	125677114	125677122	+	1	NA	5' UTR (NM_027677, exon 1 of 2)	5' UTR (NM_027677, exon 1 of 2)	122	NM_027677	71111	Mm.32727	NM_027677	ENSMUSG00000026343	Gpr39	4933415E13Rik	G protein-coupled receptor 39	protein-coding
mm_159233.1	chr2	137116315	137116315	-	1	NA	5' UTR (NM_013822, exon 1 of 26)	5' UTR (NM_013822, exon 1 of 26)	205	NM_013822	16449	Mm.22398	NM_013822	ENSMUSG00000027276	Jag1	ABE2|Gsfabe2|Htu|Ozz|Ser-1	jagged 1	protein-coding
mm_165413.1	chr2	145707271	145707272	+	1	NA	intron (NR_033220, intron 1 of 3)	ORR1F|LTR|ERVL-MaLR	6076	NR_033220	408057	Mm.486711	NR_033220	ENSMUSG00000087594	BC039771	-	cDNA sequence BC039771	ncRNA
mm_170016.1	chr17	18476765	18476777	-	1	NA	Intergenic	Intergenic	52667	NM_001102581	328759	Mm.469839	NM_001102581	ENSMUSG00000091631	Vmn2r95	-	vomeronasal 2, receptor 95	protein-coding
mm_144840.1	chr18	36560582	36560620	+	1	NA	promoter-TSS (NM_175375)	promoter-TSS (NM_175375)	-2	NM_175375	108857	Mm.482287	NM_175375	ENSMUSG00000024483	Ankhd1	1110004O12Rik|4933432B13Rik|9130019P20Rik|A530027J04Rik|A630021B20Rik|AA571404|Mask|mFLJ00246|mKIAA1085	ankyrin repeat and KH domain containing 1	protein-coding
mm_85447.1	chr9	104262961	104262971	-	1	NA	promoter-TSS (NM_001163026)	promoter-TSS (NM_001163026)	-36	NM_001163026	235567	Mm.217256	NM_001163026	ENSMUSG00000032560	Dnajc13	D030002L11Rik|Gm1124|RME-8|Rme8|mKIAA0678	DnaJ heat shock protein family (Hsp40) member C13	protein-coding
mm_153691.1	chr19	44397171	44397173	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	10537	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_17860.1	chr2	34807676	34807676	-	1	NA	intron (NM_001164768, intron 4 of 5)	intron (NM_001164768, intron 4 of 5)	-7764	NM_145522	227746	Mm.158705	NM_145522	ENSMUSG00000070953	Rabepk	8430412M01Rik|9530020D24Rik|AV073337|C87311|Rab9p40	Rab9 effector protein with kelch motifs	protein-coding
mm_12636.1	chr2	74705739	74705769	+	1	NA	exon (NM_001290730, exon 1 of 2)	exon (NM_001290730, exon 1 of 2)	265	NM_008276	15437	Mm.280673	NM_008276	ENSMUSG00000027102	Hoxd8	4921540P06Rik|AI047735|Hox-4.3|Hox-5.4	homeobox D8	protein-coding
mm_82183.1	chr9	123935722	123935724	+	1	NA	Intergenic	Intergenic	32969	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_62468.1	chr7	101763518	101763524	+	1	NA	intron (NM_009191, intron 6 of 15)	intron (NM_009191, intron 6 of 15)	-54792	NM_008887	11859	Mm.5028	NM_008887	ENSMUSG00000007946	Phox2a	Arix|Phox2|Pmx2|Pmx2a|Px2a	paired-like homeobox 2a	protein-coding
mm_141136.1	chr17	26244119	26244177	-	1	NA	promoter-TSS (NM_001206335)	promoter-TSS (NM_001206335)	94	NM_207217	106581	Mm.28844	NM_207217	ENSMUSG00000024187	Fam234a	Itfg3	family with sequence similarity 234, member A	protein-coding
mm_104476.1	chr11	95514696	95514707	-	1	NA	promoter-TSS (NM_130858)	promoter-TSS (NM_130858)	-136	NM_130858	104079	Mm.22970	NM_130858	ENSMUSG00000046719	Nxph3	-	neurexophilin 3	protein-coding
mm_5290.1	chr1	20869925	20869930	-	1	NA	Intergenic	Intergenic	20546	NR_040492	77741	Mm.159984	NR_040492	ENSMUSG00000097934	6720483E21Rik	-	RIKEN cDNA 6720483E21 gene	ncRNA
mm_154403.1	chrM	14139	14154	+	1	NA	NA	Intergenic	NA	NA								
mm_89153.1	chr10	86032963	86032976	+	1	NA	intron (NM_001347151, intron 4 of 8)	intron (NM_001347151, intron 4 of 8)	10815	NM_001347151	69754	Mm.44236	NM_153195	ENSMUSG00000001786	Fbxo7	2410015K21Rik|A230052G17Rik|AI117679|AW260462|C85118	F-box protein 7	protein-coding
mm_113410.1	chr13	33967102	33967108	+	1	NA	promoter-TSS (NM_001163242)	promoter-TSS (NM_001163242)	-48	NM_001163242	18105	Mm.264036	NM_020282	ENSMUSG00000046949	Nqo2	NMO2|Nmor2|Ox2	NAD(P)H dehydrogenase, quinone 2	protein-coding
mm_125468.1	chr15	53621650	53621659	+	1	NA	intron (NM_177225, intron 4 of 4)	intron (NM_177225, intron 4 of 4)	-275471	NM_010162	14042	Mm.309395	NM_010162	ENSMUSG00000061731	Ext1	AA409028	exostoses (multiple) 1	protein-coding
mm_137884.1	chr17	31594823	31594839	+	1	NA	intron (NR_027493, intron 6 of 11)	L1MD|LINE|L1	30058	NM_016670	18771	Mm.259295	NM_016670	ENSMUSG00000006705	Pknox1	D17Wsu76e|PREP1	Pbx/knotted 1 homeobox	protein-coding
mm_79873.1	chr9	65141430	65141444	+	1	NA	exon (NM_008988, exon 1 of 14)	exon (NM_008988, exon 1 of 14)	248	NM_008988	19289	Mm.41529	NM_008988	ENSMUSG00000032394	Igdcc3	2810401C09Rik|AI851425|Punc|WI-14920	immunoglobulin superfamily, DCC subclass, member 3	protein-coding
mm_105746.1	chr11	109425761	109425770	-	1	NA	promoter-TSS (NM_025275)	promoter-TSS (NM_025275)	-181	NM_025275	13929	Mm.211850	NM_025275	ENSMUSG00000020610	Amz2	AA408420|ESTM12|X83328	archaelysin family metallopeptidase 2	protein-coding
mm_169327.1	chr14	116901846	116901859	+	1	NA	Intergenic	L1VL1|LINE|L1	-23445	NM_001079844	23888	Mm.440025	NM_011821	ENSMUSG00000058571	Gpc6	-	glypican 6	protein-coding
mm_151986.1	chr19	5845783	5845840	-	1	NA	promoter-TSS (NR_003513)	promoter-TSS (NR_003513)	-331	NR_003513	66961	Mm.281895	NR_003513	ENSMUSG00000092274	Neat1	2310043N10Rik|VINC	nuclear paraspeckle assembly transcript 1 (non-protein coding)	ncRNA
mm_162378.1	chr1	72284273	72284279	-	1	NA	promoter-TSS (NM_175564)	promoter-TSS (NM_175564)	38	NM_023523	111175	Mm.281738	NM_023523	ENSMUSG00000026189	Pecr	2400003B18Rik|TERP	peroxisomal trans-2-enoyl-CoA reductase	protein-coding
mm_126970.1	chr15	93397999	93398012	+	1	NA	promoter-TSS (NM_001083114)	promoter-TSS (NM_001083114)	285	NM_026025	67197	Mm.293181	NM_026025	ENSMUSG00000022635	Zcrb1	2700088M22Rik|Madp-1	zinc finger CCHC-type and RNA binding motif 1	protein-coding
mm_169509.1	chr14	8286707	8286709	+	1	NA	Intergenic	Intergenic	23068	NM_183187	268709	Mm.256058	NM_183187	ENSMUSG00000021750	Fam107a	DRR1	family with sequence similarity 107, member A	protein-coding
mm_83525.1	chr9	46230085	46230089	-	1	NA	exon (NM_009692, exon 4 of 4)	exon (NM_009692, exon 4 of 4)	1457	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2|apo-AI|apoA-I	apolipoprotein A-I	protein-coding
mm_129566.1	chr15	79605087	79605114	-	1	NA	promoter-TSS (NM_001278226)	promoter-TSS (NM_001278226)	9	NR_103477	13404	Mm.2524	NM_010059	ENSMUSG00000022429	Dmc1	Dmc1h|Lim15|Mei11|sgdp	DNA meiotic recombinase 1	protein-coding
mm_150172.1	chr19	32543429	32543450	+	1	NA	Intergenic	RMER20B|LTR|ERVK	-52276	NM_001201470	23972	Mm.203916	NM_011864	ENSMUSG00000024899	Papss2	1810018P12Rik|AI159688|AtpsU2|Atpsk2|Sk2|bm	3'-phosphoadenosine 5'-phosphosulfate synthase 2	protein-coding
mm_156635.1	chrX	156491652	156491652	+	1	NA	Intergenic	RMER13A1|LTR|ERVK	-47831	NR_033598	74941	Mm.484588	NR_033598		4930503H13Rik	-	gem (nuclear organelle) associated protein 8 pseudogene	pseudo
mm_55205.1	chr6	52211668	52211712	-	1	NA	intron (NR_015611, intron 1 of 2)	CpG	1377	NM_010452	15400	Mm.71533	NM_010452	ENSMUSG00000079560	Hoxa3	Hox-1.5|Mo-10	homeobox A3	protein-coding
mm_115382.1	chr13	113101127	113101130	+	1	NA	promoter-TSS (NM_010370)	promoter-TSS (NM_010370)	-147	NM_010370	14938	Mm.15510	NM_010370	ENSMUSG00000023132	Gzma	AW494114|Ctla-3|Ctla3|Hf|Hf1|SE1|TSP-1|TSP1	granzyme A	protein-coding
mm_38439.1	chr4	139832921	139832952	-	1	NA	promoter-TSS (NM_011039)	promoter-TSS (NM_011039)	32	NM_011039	18509	Mm.218760	NM_011039	ENSMUSG00000028736	Pax7	Pax-7	paired box 7	protein-coding
mm_158266.1	chrX	109160737	109160763	-	1	NA	3' UTR (NM_019989, exon 4 of 4)	3' UTR (NM_019989, exon 4 of 4)	-36006	NM_001037917	622976	Mm.482747	NM_001037917	ENSMUSG00000048621	Gm6377	EG622976	predicted gene 6377	protein-coding
mm_54321.1	chr6	30304514	30304570	-	1	NA	promoter-TSS (NM_009459)	promoter-TSS (NM_009459)	-3	NM_001169576	22214	Mm.332967	NM_009459	ENSMUSG00000039159	Ube2h	1500009C23Rik|AI181839|AI326965|AI462483|AW227540|E2-20K|Gid3|N28148|Ubc8	ubiquitin-conjugating enzyme E2H	protein-coding
mm_58723.1	chr7	13024655	13024667	+	1	NA	5' UTR (NM_011588, exon 1 of 17)	5' UTR (NM_011588, exon 1 of 17)	509	NM_011588	21849	Mm.15701	NM_011588	ENSMUSG00000005566	Trim28	AA408787|KAP-1|KRIP-1|MommeD9|Tif1b|Tif1beta	tripartite motif-containing 28	protein-coding
mm_33096.1	chr4	124698213	124698243	+	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-2471	NM_010213	14201	Mm.331856	NM_010213	ENSMUSG00000032643	Fhl3	SLIM2	four and a half LIM domains 3	protein-coding
mm_116000.1	chr13	24415491	24415501	-	1	NA	intron (NM_007717, intron 1 of 15)	intron (NM_007717, intron 1 of 15)	374	NM_001284520	12763	Mm.8396	NM_007717	ENSMUSG00000016756	Cmah	-	cytidine monophospho-N-acetylneuraminic acid hydroxylase	protein-coding
mm_2950.1	chr1	132417378	132417402	+	1	NA	promoter-TSS (NM_172516)	promoter-TSS (NM_172516)	-63	NM_172516	213452	Mm.257120	NM_172516	ENSMUSG00000042046	Dstyk	A930019K20Rik|C430014H23Rik|C820013G01|Ripk5	dual serine/threonine and tyrosine protein kinase	protein-coding
mm_141222.1	chr17	27245067	27245076	-	1	NA	intron (NR_131118, intron 1 of 2)	intron (NR_131118, intron 1 of 2)	2995	NR_131118	319720	Mm.394996	NR_131118		9630028I04Rik	-	RIKEN cDNA 9630028I04 gene	ncRNA
mm_14651.1	chr2	136911393	136911403	+	1	NA	intron (NM_001038641, intron 2 of 7)	MER33|DNA|hAT-Charlie	12047	NM_001038641	74243	Mm.330612	NM_028201	ENSMUSG00000027281	Slx4ip	2210009G21Rik|2410004I22Rik|C85661|Slxip	SLX4 interacting protein	protein-coding
mm_12763.1	chr2	79256116	79256141	+	1	NA	intron (NM_010576, intron 1 of 27)	intron (NM_010576, intron 1 of 27)	702	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D|Itga4B	integrin alpha 4	protein-coding
mm_22335.1	chr2	180709120	180709149	-	1	NA	intron (NM_177852, intron 1 of 14)	intron (NM_177852, intron 1 of 14)	865	NM_177852	23856	Mm.253836	NM_011805	ENSMUSG00000038914	Dido1	6720461J16Rik|D130048F08Rik|DATF-1|DIO-1|Datf1|dido	death inducer-obliterator 1	protein-coding
mm_86751.1	chr10	19591953	19592087	+	1	NA	promoter-TSS (NM_010511)	promoter-TSS (NM_010511)	71	NM_010511	15979	Mm.549	NM_010511	ENSMUSG00000020009	Ifngr1	CD119|IFN-gammaR|Ifgr|Ifngr|Nktar	interferon gamma receptor 1	protein-coding
mm_107322.1	chr12	31418727	31418732	+	1	NA	Intergenic	Intergenic	-19490	NM_021353	13487	Mm.490454	NM_021353	ENSMUSG00000001225	Slc26a3	9030623B18Rik|9130013M11Rik|AV376035|Dra	solute carrier family 26, member 3	protein-coding
mm_1667.1	chr1	74771915	74771932	+	1	NA	promoter-TSS (NM_009526)	promoter-TSS (NM_009526)	31	NM_009526	22420	Mm.268282	NM_009526	ENSMUSG00000033227	Wnt6	AA409270|Wnt-6	wingless-type MMTV integration site family, member 6	protein-coding
mm_48830.1	chr5	149181938	149181945	-	1	NA	promoter-TSS (NR_015478)	promoter-TSS (NR_015478)	95	NR_015478	433966	Mm.207047	NR_015478	ENSMUSG00000097191	5730422E09Rik	-	RIKEN cDNA 5730422E09 gene	ncRNA
mm_3724.1	chr1	154205148	154205149	+	1	NA	exon (NM_001204908, exon 2 of 2)	exon (NM_001204908, exon 2 of 2)	3961	NM_001204908	100503355	Mm.484410	NM_001204908	ENSMUSG00000066797	Zfp648	ENSMUSG00000066797|Gm10178|Gm203	zinc finger protein 648	protein-coding
mm_108385.1	chr12	80945501	80945505	+	1	NA	promoter-TSS (NM_001079694)	promoter-TSS (NM_001079694)	4	NM_001347415	20384	Mm.43331	NM_009159	ENSMUSG00000021134	Srsf5	Sfrs5	serine/arginine-rich splicing factor 5	protein-coding
mm_53325.1	chr6	129229377	129229383	+	1	NA	Intergenic	Intergenic	8665	NR_040265	76432	Mm.261738	NR_040265	ENSMUSG00000097354	2310001H17Rik	AI646108	RIKEN cDNA 2310001H17 gene	ncRNA
mm_1748.1	chr1	75505630	75505675	+	1	NA	exon (NM_178884, exon 1 of 20)	exon (NM_178884, exon 1 of 20)	800	NM_178884	98733	Mm.236454	NM_178884	ENSMUSG00000026211	Obsl1	AW822216	obscurin-like 1	protein-coding
mm_23217.1	chr3	46673104	46673107	+	1	NA	Intergenic	L1_Mur3|LINE|L1	-225164	NM_001101479	241989	Mm.119234	NM_001101479	ENSMUSG00000090919	Pabpc4l	C330050A14Rik|EG241989	poly(A) binding protein, cytoplasmic 4-like	protein-coding
mm_163288.1	chr11	118145988	118146009	+	1	NA	Intergenic	Intergenic	-16779	NM_001167746	69926	Mm.473893	NM_001167746	ENSMUSG00000033987	Dnah17	2810003K23Rik|Dnahc17|Dnahcl1|Gm1178|mKIAA3028	dynein, axonemal, heavy chain 17	protein-coding
mm_93301.1	chr10	96664213	96664222	-	1	NA	Intergenic	Intergenic	47216	NM_007569	12226	Mm.23811	NM_007569	ENSMUSG00000036478	Btg1	AI426953|AW546738	B cell translocation gene 1, anti-proliferative	protein-coding
mm_108737.1	chr12	88360804	88360826	+	1	NA	promoter-TSS (NM_028105)	promoter-TSS (NM_028105)	33	NM_028105	72113	Mm.181387	NM_028105	ENSMUSG00000021044	Adck1	2610005A10Rik	aarF domain containing kinase 1	protein-coding
mm_157158.1	chrX	9463840	9463849	-	1	NA	intron (NM_007807, intron 3 of 12)	intron (NM_007807, intron 3 of 12)	5480	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_99565.1	chr11	103810198	103810204	+	1	NA	intron (NM_009521, intron 2 of 4)	CpG	36026	NM_009521	22415	Mm.159091	NM_009521	ENSMUSG00000000125	Wnt3	Int-4|Wnt-3	wingless-type MMTV integration site family, member 3	protein-coding
mm_140125.1	chr17	79615034	79615043	+	1	NA	intron (NM_201361, intron 1 of 10)	intron (NM_201361, intron 1 of 10)	138	NM_201361	381110	Mm.209801	NM_201361	ENSMUSG00000036368	Rmdn2	AW061290|Fam82a1|RMD-2|mRMD-2	regulator of microtubule dynamics 2	protein-coding
mm_168130.1	chr10	25382183	25382189	+	1	NA	intron (NM_001199265, intron 1 of 19)	ORR1F|LTR|ERVL-MaLR	22388	NM_001199265	13822	Mm.306026	NM_013511	ENSMUSG00000019978	Epb41l2	4.1G|AW555191|D10Ertd398e|Epb4.1l2|NBL2	erythrocyte membrane protein band 4.1 like 2	protein-coding
mm_141848.1	chr17	34801755	34801759	-	1	NA	3' UTR (NM_009995, exon 10 of 10)	3' UTR (NM_009995, exon 10 of 10)	2669	NM_009995	13079	Mm.440407	NM_009995	ENSMUSG00000024365	Cyp21a1	21-OH|21OH|21OHA|21OHB|CYP21OH-A|Cyp21|Cyp21-ps1|Cyp21B|Cyp21a2-ps|Cyp21a2ps|Oh21-1|Oh21-2	cytochrome P450, family 21, subfamily a, polypeptide 1	protein-coding
mm_96834.1	chr11	70017132	70017146	+	1	NA	Intergenic	Intergenic	-1466	NM_001109752	13385	Mm.27256	NM_007864	ENSMUSG00000020886	Dlg4	Dlgh4|PSD-95|PSD95|SAP90|SAP90A	discs, large homolog 4 (Drosophila)	protein-coding
mm_149037.1	chr19	8819967	8820034	+	1	NA	promoter-TSS (NM_027412)	promoter-TSS (NM_027412)	599	NM_001081196	68693	Mm.476519	NM_001081196	ENSMUSG00000071659	Hnrnpul2	1110031M08Rik|AI465155|Hnrpul2	heterogeneous nuclear ribonucleoprotein U-like 2	protein-coding
mm_127388.1	chr15	101041104	101041140	+	1	NA	3' UTR (NM_011323, exon 26 of 26)	3' UTR (NM_011323, exon 26 of 26)	13277	NM_001214911	668225	Mm.385011	NM_001214911	ENSMUSG00000095440	Fignl2	EG668225	fidgetin-like 2	protein-coding
mm_158206.1	chrX	105855909	105855922	-	1	NA	exon (NM_009530, exon 12 of 35)	exon (NM_009530, exon 12 of 35)	73457	NM_009530	22589	Mm.10141	NM_009530	ENSMUSG00000031229	Atrx	4833408C14Rik|AI447451|ATR2|DXHXS6677E|HP1-BP38|Hp1bp2|Hp1bp38|MRXS3|RAD54L|Rad54|XH2|Xnp|ZNF-HX	alpha thalassemia/mental retardation syndrome X-linked	protein-coding
mm_82210.1	chr9	124121535	124121584	+	1	NA	promoter-TSS (NM_009917)	promoter-TSS (NM_009917)	16	NM_009917	12774	Mm.14302	NM_009917	ENSMUSG00000079227	Ccr5	AM4-7|CD195|Cmkbr5	chemokine (C-C motif) receptor 5	protein-coding
mm_126751.1	chr15	85746880	85746899	+	1	NA	intron (NM_001113418, intron 2 of 7)	intron (NM_001113418, intron 2 of 7)	11113	NM_011144	19013	Mm.212789	NM_011144	ENSMUSG00000022383	Ppara	4933429D07Rik|AW742785|Nr1c1|PPAR-alpha|PPARalpha|Ppar	peroxisome proliferator activated receptor alpha	protein-coding
mm_19905.1	chr2	114157590	114157596	-	1	NA	exon (NM_009702, exon 7 of 35)	exon (NM_009702, exon 7 of 35)	-7023	NR_105968	102465982		NR_105968	ENSMUSG00000098464	Mir7002	Gm27429|mmu-mir-7002	microRNA 7002	ncRNA
mm_24921.1	chr3	96402125	96402136	+	1	NA	Intergenic	CpG	12703	NR_001579	21748		NR_001579	ENSMUSG00000064796	Terc	mTER|mTR	telomerase RNA component	ncRNA
mm_120886.1	chr14	75446668	75446671	+	1	NA	Intergenic	Intergenic	-9313	NM_001128093	380918	Mm.484360	NM_001128093	ENSMUSG00000091722	Siah3	Gm912	seven in absentia homolog 3 (Drosophila)	protein-coding
mm_130904.1	chr15	102510625	102510649	-	1	NA	intron (NM_001163643, intron 1 of 15)	CpG	6367	NM_001163643	26404	Mm.172897	NM_009582	ENSMUSG00000023050	Map3k12	DLK|MUK|Zpk	mitogen-activated protein kinase kinase kinase 12	protein-coding
mm_75650.1	chr8	65129375	65129383	-	1	NA	non-coding (NR_033217, exon 1 of 3)	non-coding (NR_033217, exon 1 of 3)	158	NR_033217	407795	Mm.387876	NR_033217	ENSMUSG00000074300	BC030870	-	cDNA sequence BC030870	ncRNA
mm_60306.1	chr7	44105569	44105578	+	1	NA	exon (NM_010642, exon 3 of 5)	exon (NM_010642, exon 3 of 5)	3281	NM_010642	16616	Mm.443292	NM_010642	ENSMUSG00000066516	Klk1b21	Klk21|mGk-21	kallikrein 1-related peptidase b21	protein-coding
mm_59386.1	chr7	26221915	26221918	+	1	NA	Intergenic	L1_Mus3|LINE|L1	-44915	NM_001167540	100312477	Mm.480246	NM_001167540	ENSMUSG00000046130	Vmn1r184	-	vomeronasal 1 receptor, 184	protein-coding
mm_140417.1	chr17	87650823	87650827	+	1	NA	3' UTR (NM_008532, exon 10 of 10)	3' UTR (NM_008532, exon 10 of 10)	14846	NM_008532	17075	Mm.4259	NM_008532	ENSMUSG00000045394	Epcam	CD326|EGP|EGP-2|Egp314|Ep-CAM|EpCAM1|GA733-2|Ly74|TROP1|Tacsd1|Tacstd1|gp40	epithelial cell adhesion molecule	protein-coding
mm_90009.1	chr10	114757762	114757789	+	1	NA	intron (NM_146241, intron 2 of 18)	intron (NM_146241, intron 2 of 18)	43595	NM_146241	237553	Mm.445550	NM_146241	ENSMUSG00000050663	Trhde	9330155P21Rik	TRH-degrading enzyme	protein-coding
mm_18512.1	chr2	62622152	62622156	-	1	NA	intron (NM_001164477, intron 3 of 14)	intron (NM_001164477, intron 3 of 14)	24101	NM_027835	71586	Mm.136224	NM_027835	ENSMUSG00000026896	Ifih1	9130009C22Rik|Helicard|Hlcd|MDA5|RLR-2	interferon induced with helicase C domain 1	protein-coding
mm_110978.1	chr12	77052851	77052867	-	1	NA	Intergenic	Intergenic	-90611	NM_001146176	17187	Mm.268548	NM_008558	ENSMUSG00000059436	Max	AA960152|AI875693|bHLHd4|bHLHd5|bHLHd6|bHLHd7|bHLHd8	Max protein	protein-coding
mm_98215.1	chr11	87801217	87801262	+	1	NA	exon (NM_010824, exon 10 of 14)	exon (NM_010824, exon 10 of 14)	7455	NM_010824	17523	Mm.4668	NM_010824	ENSMUSG00000009350	Mpo	mKIAA4033	myeloperoxidase	protein-coding
mm_164411.1	chr16	36642723	36642731	-	1	NA	intron (NM_019388, intron 1 of 7)	intron (NM_019388, intron 1 of 7)	23350	NM_019388	12524	Mm.1452	NM_019388	ENSMUSG00000022901	Cd86	B7|B7-2|B7.2|B70|CLS1|Cd28l2|ETC-1|Ly-58|Ly58|MB7|MB7-2|TS/A-2	CD86 antigen	protein-coding
mm_29613.1	chr3	121277129	121277142	-	1	NA	Intergenic	Intergenic	-13819	NM_178936	99887	Mm.26088	NM_178936	ENSMUSG00000028132	Tmem56	4930577M16Rik|AU018104|AW109744|C730036B01Rik	transmembrane protein 56	protein-coding
mm_102839.1	chr11	69332107	69332128	-	1	NA	exon (NM_010599, exon 14 of 14)	exon (NM_010599, exon 14 of 14)	5859	NM_010599	16499	Mm.232472	NM_010599	ENSMUSG00000018470	Kcnab3	C330022D06Rik|Kcnab4|mKv(beta)4	potassium voltage-gated channel, shaker-related subfamily, beta member 3	protein-coding
mm_150684.1	chr19	42090423	42090502	+	1	NA	promoter-TSS (NM_145501)	promoter-TSS (NM_145501)	27	NM_145501	84095	Mm.117037	NM_145501	ENSMUSG00000025178	Pi4k2a	Pi4k2	phosphatidylinositol 4-kinase type 2 alpha	protein-coding
mm_88148.1	chr10	69533804	69533848	+	1	NA	5' UTR (NM_170688, exon 1 of 43)	5' UTR (NM_170688, exon 1 of 43)	118	NM_146005	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_38169.1	chr4	135217136	135217150	-	1	NA	exon (NM_013885, exon 6 of 6)	exon (NM_013885, exon 6 of 6)	55617	NM_013885	29876	Mm.257765	NM_013885	ENSMUSG00000037242	Clic4	D0Jmb3|TU-74|mc3s5|mtCLIC	chloride intracellular channel 4 (mitochondrial)	protein-coding
mm_129827.1	chr15	83127593	83127640	-	1	NA	3' UTR (NM_178627, exon 9 of 9)	3' UTR (NM_178627, exon 9 of 9)	-4815	NM_029101	74778	Mm.30056	NM_029101	ENSMUSG00000018040	Rrp7a	1110014J01Rik|AA408146|Kheg1	ribosomal RNA processing 7 homolog A (S. cerevisiae)	protein-coding
mm_129830.1	chr15	83138183	83138215	-	1	NA	exon (NM_178627, exon 2 of 9)	exon (NM_178627, exon 2 of 9)	11137	NM_178627	73826	Mm.23758	NM_178627	ENSMUSG00000041815	Poldip3	1110008P04Rik|AA408269|AL022852|C77954|PDIP46|SKAR|mKIAA1649	polymerase (DNA-directed), delta interacting protein 3	protein-coding
mm_115903.1	chr13	23423767	23423775	-	1	NA	promoter-TSS (NM_013924)	promoter-TSS (NM_013924)	95	NM_013924	30946	Mm.292094	NM_013924	ENSMUSG00000036376	Abt1	-	activator of basal transcription 1	protein-coding
mm_273.1	chr1	21218826	21218858	+	1	NA	5' UTR (NM_001290679, exon 1 of 5)	5' UTR (NM_001290679, exon 1 of 5)	267	NM_029398	75712	Mm.304763	NM_029398	ENSMUSG00000025933	Tmem14a	5730496E24Rik|C85783|PTD011	transmembrane protein 14A	protein-coding
mm_2918.1	chr1	132017750	132017769	+	1	NA	exon (NM_007923, exon 3 of 5)	exon (NM_007923, exon 3 of 5)	10154	NM_007923	13714	Mm.254233	NM_007923	ENSMUSG00000026436	Elk4	2310011G17Rik|A130026I01Rik|BB162516|SAP-1|Sap1	ELK4, member of ETS oncogene family	protein-coding
mm_102426.1	chr11	59449942	59449950	-	1	NA	promoter-TSS (NM_178659)	promoter-TSS (NM_178659)	10	NM_144521	67826	Mm.26680	NM_144521	ENSMUSG00000009894	Snap47	1110031B06Rik|SNAP-47	synaptosomal-associated protein, 47	protein-coding
mm_89325.1	chr10	87931479	87931489	+	1	NA	3' UTR (NM_010512, exon 5 of 5)	3' UTR (NM_010512, exon 5 of 5)	-35187	NR_000040	22172	Mm.391420	NR_000040		Tyms-ps	-	thymidylate synthase, pseudogene	pseudo
mm_62111.1	chr7	96532719	96532739	+	1	NA	intron (NM_001310762, intron 4 of 32)	intron (NM_001310762, intron 4 of 32)	-190765	NR_046043	670727	Mm.421352	NR_046043	ENSMUSG00000085751	Gm15412	OTTMUSG00000021245	predicted gene 15412	ncRNA
mm_118199.1	chr13	107890060	107890073	-	1	NA	promoter-TSS (NM_145456)	promoter-TSS (NM_145456)	-2	NM_145456	67263	Mm.490418	NM_145456	ENSMUSG00000032846	Zswim6	2900036G02Rik|mKIAA1577	zinc finger SWIM-type containing 6	protein-coding
mm_135189.1	chr16	36334331	36334347	-	1	NA	promoter-TSS (NM_001001332)	promoter-TSS (NM_001001332)	-7	NM_001001332	100038854	Mm.383561	NM_001001332	ENSMUSG00000079594	BC117090	Gm1975	cDNA sequence BC1179090	protein-coding
mm_34179.1	chr4	140699987	140699998	+	1	NA	Intergenic	Intergenic	-1481	NM_173867	108911	Mm.253	NM_173867	ENSMUSG00000040945	Rcc2	2610510H01Rik|2610529N02Rik|AA536646|AA675016|Td60|mKIAA1470	regulator of chromosome condensation 2	protein-coding
mm_101956.1	chr11	50298164	50298212	-	1	NA	exon (NM_001110500, exon 12 of 15)	exon (NM_001110500, exon 12 of 15)	-5852	NM_175334	103806	Mm.51116	NM_175334	ENSMUSG00000050567	Maml1	AI644666|AW743257|D930008C07Rik|Mam-1|Mam1|mKIAA0200	mastermind like 1 (Drosophila)	protein-coding
mm_80979.1	chr9	103208876	103208903	+	1	NA	TTS (NM_133977)	TTS (NM_133977)	-6824	NM_009275	20818	Mm.273053	NM_009275	ENSMUSG00000032553	Srprb	AA409543	signal recognition particle receptor, B subunit	protein-coding
mm_45549.1	chr5	73024807	73024811	-	1	NA	intron (NM_028194, intron 60 of 62)	intron (NM_028194, intron 60 of 62)	17905	NM_173403	231290	Mm.491387	NM_173403	ENSMUSG00000029219	Slc10a4	E130304D01	solute carrier family 10 (sodium/bile acid cotransporter family), member 4	protein-coding
mm_47927.1	chr5	135013115	135013125	-	1	NA	promoter-TSS (NR_026688)	promoter-TSS (NR_026688)	37	NR_026688	69812	Mm.18422	NR_026688	ENSMUSG00000085042	Abhd11os	2010001M06Rik|AI462243|Wbscr26|Wnscr26	abhydrolase domain containing 11, opposite strand	ncRNA
mm_145581.1	chr18	60969657	60969680	+	1	NA	intron (NM_009792, intron 2 of 6)	intron (NM_009792, intron 2 of 6)	6114	NM_001286809	12322	Mm.131530	NM_009792	ENSMUSG00000024617	Camk2a	CaMKII|R74975|mKIAA0968	calcium/calmodulin-dependent protein kinase II alpha	protein-coding
mm_64269.1	chr7	141788962	141788979	+	1	NA	promoter-TSS (NM_010844)	promoter-TSS (NM_010844)	-41	NM_010844	17833	Mm.334332	NM_010844	ENSMUSG00000037974	Muc5ac	2210005L13Rik|MGM	mucin 5, subtypes A and C, tracheobronchial/gastric	protein-coding
mm_19744.1	chr2	104816743	104816792	-	1	NA	promoter-TSS (NM_001123327)	promoter-TSS (NM_001123327)	-71	NM_001123327	99003	Mm.274314	NM_001123327	ENSMUSG00000074994	Qser1	4732486I23Rik|AI502974	glutamine and serine rich 1	protein-coding
mm_69509.1	chr7	134413844	134413856	-	1	NA	Intergenic	Intergenic	-37022	NM_001081331	71007	Mm.334285	NM_001081331	ENSMUSG00000030994	D7Ertd443e	4933400E14Rik|FATS|Gm497	DNA segment, Chr 7, ERATO Doi 443, expressed	protein-coding
mm_149179.1	chr19	9283564	9283607	+	1	NA	Intergenic	Intergenic	-148019	NM_025610	66514	Mm.272847	NM_025610	ENSMUSG00000024654	Asrgl1	2410004D18Rik|ALP|ALP1|AU040643|AW060375	asparaginase like 1	protein-coding
mm_97453.1	chr11	78194697	78194707	+	1	NA	intron (NM_001045516, intron 1 of 3)	intron (NM_001045516, intron 1 of 3)	1310	NM_001045516	216974	Mm.50974	NM_001045516	ENSMUSG00000044122	Proca1	4933404M19Rik	protein interacting with cyclin A1	protein-coding
mm_86187.1	chr9	119339990	119340035	-	1	NA	promoter-TSS (NM_010851)	promoter-TSS (NM_010851)	28	NM_010851	17874	Mm.213003	NM_010851	ENSMUSG00000032508	Myd88	-	myeloid differentiation primary response gene 88	protein-coding
mm_43547.1	chr5	137564534	137564535	+	1	NA	exon (NM_031404, exon 6 of 14)	exon (NM_031404, exon 6 of 14)	-5306	NM_001289509	50765	Mm.21757	NM_015799	ENSMUSG00000029716	Tfr2	Trfr2	transferrin receptor 2	protein-coding
mm_98587.1	chr11	95763619	95763631	+	1	NA	exon (NM_201609, exon 5 of 5)	exon (NM_201609, exon 5 of 5)	14558	NM_201609	268469	Mm.389038	NM_201609	ENSMUSG00000075595	Zfp652	9530033F24Rik|ZNF652	zinc finger protein 652	protein-coding
mm_100157.1	chr11	116232712	116232728	+	1	NA	exon (NM_025276, exon 8 of 22)	exon (NM_025276, exon 8 of 22)	5371	NM_025276	14027	Mm.293683	NM_025276	ENSMUSG00000034282	Evpl	-	envoplakin	protein-coding
mm_68700.1	chr7	119631612	119631618	-	1	NA	intron (NM_054094, intron 2 of 13)	L1M4c|LINE|L1	13787	NM_054094	117147	Mm.427560	NM_054094	ENSMUSG00000033533	Acsm1	Acas3|Bucs1|Macs	acyl-CoA synthetase medium-chain family member 1	protein-coding
mm_60253.1	chr7	43782828	43782832	+	1	NA	exon (NM_133712, exon 3 of 6)	exon (NM_133712, exon 3 of 6)	1776	NM_133712	69540	Mm.46421	NM_133712	ENSMUSG00000030693	Klk10	2300002A13Rik|NES1|PRSSL1	kallikrein related-peptidase 10	protein-coding
mm_76306.1	chr8	84587603	84587621	-	1	NA	intron (NM_001252059, intron 28 of 45)	ZP3AR|Satellite|Satellite	75240	NM_010499	15936	Mm.399	NM_010499	ENSMUSG00000053560	Ier2	AI317238|Ch1|Pip92	immediate early response 2	protein-coding
mm_40684.1	chr5	65584780	65584791	+	1	NA	intron (NR_144566, intron 3 of 5)	B1_Mus2|SINE|Alu	47540	NM_001310619	53323	Mm.319512	NM_016786	ENSMUSG00000029203	Ube2k	AW492011|D5Ertd601e|E2-25k|HIP-2|Hip2|Hypg|Lig	ubiquitin-conjugating enzyme E2K	protein-coding
mm_40884.1	chr5	74581247	74581249	+	1	NA	intron (NM_001159574, intron 11 of 15)	intron (NM_001159574, intron 11 of 15)	45766	NM_001159574	66899	Mm.272468	NM_024183	ENSMUSG00000029227	Fip1l1	1300019H17Rik|Rje	FIP1 like 1 (S. cerevisiae)	protein-coding
mm_26233.1	chr3	139933308	139933325	+	1	NA	Intergenic	MLT1F2|LTR|ERVL-MaLR	-94933	NR_105798	102465198		NR_105798	ENSMUSG00000099169	Mir7j	Gm27716|Mirlet7j|mmu-let-7j	microRNA 7j	ncRNA
mm_58003.1	chr6	136415568	136415572	-	1	NA	promoter-TSS (NM_001201390)	promoter-TSS (NM_001201390)	-1	NM_001201390	100502936	Mm.21182	NM_001201390	ENSMUSG00000045291	E330021D16Rik	C85549	RIKEN cDNA E330021D16 gene	protein-coding
mm_32880.1	chr4	118741648	118741668	+	1	NA	Intergenic	RLTR9D|LTR|ERVK	7127	NM_146852	258851	Mm.377719	NM_146852	ENSMUSG00000070820	Olfr1339	MOR258-2	olfactory receptor 1339	protein-coding
mm_35335.1	chr4	31877531	31877542	-	1	NA	Intergenic	Intergenic	-86571	NM_009316	26409	Mm.258589	NM_009316	ENSMUSG00000028284	Map3k7	B430101B05|C87327|Tak1	mitogen-activated protein kinase kinase kinase 7	protein-coding
mm_123780.1	chr14	70331309	70331328	-	1	NA	5' UTR (NM_144808, exon 2 of 10)	5' UTR (NM_144808, exon 2 of 10)	17115	NM_001135152	213053	Mm.270647	NM_144808	ENSMUSG00000022094	Slc39a14	FAD-123|ZIP-14|Zip14|fad123	solute carrier family 39 (zinc transporter), member 14	protein-coding
mm_34591.1	chr4	150189199	150189205	+	1	NA	exon (NM_009802, exon 7 of 8)	exon (NM_009802, exon 7 of 8)	11933	NM_009802	12353	Mm.232523	NM_009802	ENSMUSG00000028972	Car6	Ca6|DOC1	carbonic anhydrase 6	protein-coding
mm_172054.1	chr6	128843286	128843303	+	1	NA	Intergenic	4.5SRNA|scRNA|scRNA	-16979	NM_030599	80782	Mm.6180	NM_030599	ENSMUSG00000079298	Klrb1b	Klrb1d|Ly55b|Ly55d|NKR-P1B|NKR-P1D|Nkrp1-b|Nkrp1d|ly-55b|ly-55d	killer cell lectin-like receptor subfamily B member 1B	protein-coding
mm_128560.1	chr15	55917061	55917079	-	1	NA	Intergenic	Intergenic	-10121	NM_016667	20649	Mm.309425	NM_016667	ENSMUSG00000060429	Sntb1	-	syntrophin, basic 1	protein-coding
mm_30663.1	chr4	9952980	9952981	+	1	NA	Intergenic	Intergenic	-35583	NR_004448	74662	Mm.483401	NR_004448	ENSMUSG00000082843	4930448K20Rik	1700009K09Rik	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_42348.1	chr5	114911354	114911363	+	1	NA	exon (NM_011854, exon 6 of 6)	exon (NM_011854, exon 6 of 6)	-11882	NM_145209	231655	Mm.95479	NM_145209	ENSMUSG00000041827	Oasl1	7530414C13Rik|oasl9	2'-5' oligoadenylate synthetase-like 1	protein-coding
mm_104175.1	chr11	87748809	87748837	-	1	NA	Intergenic	Intergenic	-8041	NR_029555	387160		NR_029555	ENSMUSG00000105196	Mir142	Mirn142|miR-142|mir-142a|mmu-mir-142|mmu-mir-142a	microRNA 142	ncRNA
mm_89387.1	chr10	89781170	89781185	+	1	NA	exon (NM_029166, exon 6 of 21)	exon (NM_029166, exon 6 of 21)	36186	NM_029166	75089	Mm.268922	NM_029166	ENSMUSG00000019951	Uhrf1bp1l	2010319N22Rik|4930506D01Rik|AA589495|C80672|E030041M21Rik|mKIAA0701	UHRF1 (ICBP90) binding protein 1-like	protein-coding
mm_124866.1	chr15	10177589	10177591	+	1	NA	5' UTR (NM_011169, exon 1 of 10)	5' UTR (NM_011169, exon 1 of 10)	352	NM_011169	19116	Mm.10516	NM_011169	ENSMUSG00000005268	Prlr	AI987712|Pr-1|Pr-3|Prlr-rs1	prolactin receptor	protein-coding
mm_111029.1	chr12	79165047	79165057	-	1	NA	exon (NM_016800, exon 3 of 6)	exon (NM_016800, exon 3 of 6)	7406	NM_016800	53612	Mm.265929	NM_016800	ENSMUSG00000021124	Vti1b	AU015348|GES30|MVti1b|SNARE|Vti1-rp1	vesicle transport through interaction with t-SNAREs 1B	protein-coding
mm_59441.1	chr7	27132559	27132570	+	1	NA	exon (NM_007817, exon 9 of 10)	exon (NM_007817, exon 9 of 10)	12609	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_97971.1	chr11	83852921	83852944	+	1	NA	promoter-TSS (NM_001291269)	promoter-TSS (NM_001291269)	-28	NM_001291269	21410	Mm.7226	NM_009330	ENSMUSG00000020679	Hnf1b	HNF-1-beta|HNF-1B|HNF-1Beta|Hnf1beta|LFB3|Tcf-2|Tcf2|vHNF1	HNF1 homeobox B	protein-coding
mm_172040.1	chr6	127128873	127128873	-	1	NA	3' UTR (NM_009829, exon 5 of 5)	3' UTR (NM_009829, exon 5 of 5)	-19321	NM_177003	319801	Mm.101836	NM_177003	ENSMUSG00000038028	Tigar	9630033F20Rik|AA793651|AI595337|C79710|C85509	Trp53 induced glycolysis repulatory phosphatase	protein-coding
mm_39398.1	chr5	14025594	14025604	+	1	NA	5' UTR (NM_011348, exon 1 of 17)	5' UTR (NM_011348, exon 1 of 17)	323	NM_011348	20349	Mm.134093	NM_011348	ENSMUSG00000063531	Sema3e	6430702L12|AA408817|Semah|mKIAA0331	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	protein-coding
mm_117036.1	chr13	58274834	58274851	-	1	NA	promoter-TSS (NM_019832)	promoter-TSS (NM_019832)	-654	NM_019832	56278	Mm.296625	NM_019832	ENSMUSG00000021552	Gkap1	42kDa|4933400B15Rik|D13Ertd340e|Gkap42	G kinase anchoring protein 1	protein-coding
mm_41458.1	chr5	90905947	90905956	+	1	NA	TTS (NM_009140)	TTS (NM_009140)	2052	NM_009140	20310	Mm.4979	NM_009140	ENSMUSG00000058427	Cxcl2	CINC-2a|GROb|Gro2|MIP-2|MIP-2a|Mgsa-b|Mip2|Scyb|Scyb2	chemokine (C-X-C motif) ligand 2	protein-coding
mm_133141.1	chr16	69863803	69863812	+	1	NA	promoter-TSS (NM_173069)	promoter-TSS (NM_173069)	-63	NM_173069	224318	Mm.212743	NM_173069	ENSMUSG00000063163	Speer2	SPEER-2	spermatogenesis associated glutamate (E)-rich protein 2	protein-coding
mm_42001.1	chr5	107900860	107900879	+	1	NA	intron (NM_016980, intron 1 of 7)	CpG	341	NM_016980	100503670	Mm.277897	NM_016980	ENSMUSG00000058558	Rpl5	U21RNA	ribosomal protein L5	protein-coding
mm_56476.1	chr6	99057296	99057331	-	1	NA	intron (NM_001347345, intron 6 of 19)	intron (NM_001347345, intron 6 of 19)	-29015	NM_001197322	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_67890.1	chr7	99382321	99382340	-	1	NA	intron (NM_201352, intron 1 of 17)	intron (NM_201352, intron 1 of 17)	781	NM_201352	233552	Mm.286317	NM_201352	ENSMUSG00000035314	Gdpd5	BC024955|Gde2	glycerophosphodiester phosphodiesterase domain containing 5	protein-coding
mm_114545.1	chr13	73937785	73937795	+	1	NA	promoter-TSS (NM_027182)	promoter-TSS (NM_027182)	-21	NM_001024508	105246	Mm.278509	NM_001024508	ENSMUSG00000057649	Brd9	AL022779	bromodomain containing 9	protein-coding
mm_66879.1	chr7	57768684	57768715	-	1	NA	intron (NM_008071, intron 4 of 8)	intron (NM_008071, intron 4 of 8)	177526	NM_008071	14402	Mm.8004	NM_008071	ENSMUSG00000033676	Gabrb3	A230092K12Rik|AW049585|Cp1|Gabrb-3|beta3	gamma-aminobutyric acid (GABA) A receptor, subunit beta 3	protein-coding
mm_149868.1	chr19	25148418	25148434	+	1	NA	intron (NM_028785, intron 25 of 47)	B3A|SINE|B2	-88776	NM_181404	107351	Mm.260722	NM_181404	ENSMUSG00000032702	Kank1	A930031B09Rik|AU015049|AW121052|Ankrd15|D330024H06Rik|mKIAA0172	KN motif and ankyrin repeat domains 1	protein-coding
mm_401.1	chr1	34160255	34160271	+	1	NA	promoter-TSS (NM_010081)	promoter-TSS (NM_010081)	-67	NM_010081	13518	Mm.336625	NM_010081	ENSMUSG00000026131	Dst	2310001O04Rik|A830042E19Rik|AW554249|BP230|BPAG1-n|Bpag|Bpag1|Macf2|ah|athetoid|dt|mKIAA0728|nmf203|nmf339	dystonin	protein-coding
mm_95302.1	chr11	46123617	46123620	+	1	NA	intron (NM_001291890, intron 10 of 22)	B1F2|SINE|Alu	-4286	NM_001311209	11492	Mm.89940	NM_009616	ENSMUSG00000011256	Adam19	AL024287|MADDAM|MTLNB|Mltnb	a disintegrin and metallopeptidase domain 19 (meltrin beta)	protein-coding
mm_113993.1	chr13	52583125	52583181	+	1	NA	promoter-TSS (NM_001198977)	promoter-TSS (NM_001198977)	-284	NM_001198977	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_75259.1	chr8	40595143	40595153	-	1	NA	intron (NM_001040699, intron 4 of 13)	intron (NM_001040699, intron 4 of 13)	39644	NM_001040699	54384	Mm.294871	NM_019433	ENSMUSG00000039431	Mtmr7	-	myotubularin related protein 7	protein-coding
mm_14523.1	chr2	132691969	132691975	+	1	NA	exon (NM_028637, exon 2 of 3)	exon (NM_028637, exon 2 of 3)	1689	NM_028637	73747	Mm.284114	NM_028637	ENSMUSG00000044991	1110034G24Rik	-	RIKEN cDNA 1110034G24 gene	protein-coding
mm_24518.1	chr3	92691003	92691008	+	1	NA	Intergenic	MER34B-int|LTR|ERV1	-3795	NM_027137	69611	Mm.176243	NM_027137	ENSMUSG00000103243	Lce1d	2310037L11Rik|AI415320|Sprrl7	late cornified envelope 1D	protein-coding
mm_112023.1	chr12	111445654	111445675	-	1	NA	exon (NM_009396, exon 3 of 12)	exon (NM_009396, exon 3 of 12)	3003	NM_009396	21928	Mm.255332	NM_009396	ENSMUSG00000021281	Tnfaip2	B94|Exoc3l3|M-sec|Tnfip2|tnfb94	tumor necrosis factor, alpha-induced protein 2	protein-coding
mm_3439.1	chr1	150102643	150102645	+	1	NA	exon (NM_011198, exon 5 of 10)	exon (NM_011198, exon 5 of 10)	2613	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_2492.1	chr1	105991516	105991569	+	1	NA	exon (NM_001122675, exon 1 of 13)	exon (NM_001122675, exon 1 of 13)	1136	NM_001122675	227449	Mm.210188	NM_001122675	ENSMUSG00000038866	Zcchc2	9930114B20Rik|AW212015	zinc finger, CCHC domain containing 2	protein-coding
mm_48389.1	chr5	139813995	139814014	-	1	NA	promoter-TSS (NM_144914)	promoter-TSS (NM_144914)	279	NM_001161548	231832	Mm.482655	NM_144914	ENSMUSG00000036687	Tmem184a	Sdmg1	transmembrane protein 184a	protein-coding
mm_73691.1	chr8	111562684	111562732	+	1	NA	intron (NM_001168623, intron 1 of 4)	intron (NM_001168623, intron 1 of 4)	24365	NM_001168623	170737	Mm.271578	NM_133206	ENSMUSG00000033545	Znrf1	B830022L21Rik|Rnf42|Zrfp1|nin283	zinc and ring finger 1	protein-coding
mm_40077.1	chr5	34352084	34352112	+	1	NA	3' UTR (NM_011278, exon 8 of 8)	3' UTR (NM_011278, exon 8 of 8)	15166	NM_001304270	19822	Mm.21281	NM_011278	ENSMUSG00000029110	Rnf4	AU018689|Gtrgeo8|SNURF	ring finger protein 4	protein-coding
mm_37433.1	chr4	122934028	122934039	-	1	NA	Intergenic	Intergenic	27155	NM_029662	76574	Mm.331842	NM_029662	ENSMUSG00000028655	Mfsd2a	1700018O18Rik|Mfsd2|NLS1	major facilitator superfamily domain containing 2A	protein-coding
mm_97217.1	chr11	75630949	75630959	+	1	NA	promoter-TSS (NM_008916)	promoter-TSS (NM_008916)	-66	NM_008916	19062	Mm.1458	NM_008916	ENSMUSG00000006127	Inpp5k	C62|Pps|SKIP	inositol polyphosphate 5-phosphatase K	protein-coding
mm_32101.1	chr4	98549679	98549717	+	1	NA	intron (NM_001005787, intron 1 of 15)	intron (NM_001005787, intron 1 of 15)	3064	NM_001005787	12695	Mm.90218	NM_007704	ENSMUSG00000061859	Patj	Cipp|Inadl	PATJ, crumbs cell polarity complex component	protein-coding
mm_127035.1	chr15	96461438	96461454	+	1	NA	promoter-TSS (NM_028148)	promoter-TSS (NM_028148)	-603	NM_028148	72193	Mm.324474	NM_028148	ENSMUSG00000033228	Scaf11	1110061H03Rik|2610510E10Rik|AI462454|CASP11|SIP1|SRRP129|Sfrs2ip|Srsf2ip|mKIAA3013	SR-related CTD-associated factor 11	protein-coding
mm_38051.1	chr4	134000831	134000850	-	1	NA	promoter-TSS (NM_026144)	promoter-TSS (NM_026144)	24	NM_026144	67422	Mm.100290	NM_026144	ENSMUSG00000012117	Dhdds	3222401G21Rik|CIT|DS|HDS|W91638	dehydrodolichyl diphosphate synthase	protein-coding
mm_48862.1	chr5	149819993	149819996	-	1	NA	Intergenic	Intergenic	-8243	NR_077242	100861794	Mm.402054	NR_077242	ENSMUSG00000106740	Gm21221	-	predicted gene, 21221	ncRNA
mm_51736.1	chr6	87093472	87093503	+	1	NA	Intergenic	Intergenic	-11259	NM_001167938	52372	Mm.282851	NM_001167937	ENSMUSG00000090891	D6Ertd527e	AU043841	DNA segment, Chr 6, ERATO Doi 527, expressed	protein-coding
mm_107016.1	chr12	12345313	12345320	+	1	NA	intron (NM_029758, intron 4 of 12)	(T)n|Simple_repeat|Simple_repeat	47159	NR_045829	70858	Mm.410838	NR_045829		4921511I17Rik	-	RIKEN cDNA 4921511I17 gene	ncRNA
mm_64812.1	chr7	6709980	6709990	-	1	NA	exon (NM_008817, exon 9 of 9)	exon (NM_008817, exon 9 of 9)	3225	NR_023846	100169889	Mm.491213	NR_023846		Peg3os	Apeg3|Peg3as	Peg3 opposite strand	ncRNA
mm_94472.1	chr11	6546876	6546898	+	1	NA	promoter-TSS (NM_001190343)	promoter-TSS (NM_001190343)	0	NM_146014	216527	Mm.221271	NM_146014	ENSMUSG00000000378	Ccm2	BC029157	cerebral cavernous malformation 2	protein-coding
mm_30729.1	chr4	13785022	13785071	+	1	NA	5' UTR (NM_009822, exon 1 of 11)	5' UTR (NM_009822, exon 1 of 11)	264	NM_009822	12395	Mm.4909	NM_009822	ENSMUSG00000006586	Runx1t1	Cbfa2t1h|ETO|MTG8	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	protein-coding
mm_42533.1	chr5	115859124	115859132	+	1	NA	intron (NM_007708, intron 2 of 46)	intron (NM_007708, intron 2 of 46)	13472	NM_007708	12704	Mm.8321	NM_007708	ENSMUSG00000029516	Cit	C030025P15Rik|CRIK|CRIK-SK|Cit-k	citron	protein-coding
mm_104402.1	chr11	94509814	94509825	-	1	NA	exon (NM_170671, exon 9 of 19)	exon (NM_170671, exon 9 of 19)	-9845	NM_027984	71889	Mm.248620	NM_027984	ENSMUSG00000010080	Epn3	2310022G12Rik	epsin 3	protein-coding
mm_36558.1	chr4	87073270	87073274	-	1	NA	exon (NM_001110240, exon 4 of 10)	exon (NM_001110240, exon 4 of 10)	154691	NM_001110240	76376	Mm.490487	NM_172426	ENSMUSG00000037996	Slc24a2	2810021B17Rik|6330417K15Rik|AI847460|Nckx2	solute carrier family 24 (sodium/potassium/calcium exchanger), member 2	protein-coding
mm_94427.1	chr11	6291608	6291655	+	1	NA	promoter-TSS (NM_001252282)	promoter-TSS (NM_001252282)	34	NM_001252283	18293	Mm.276348	NM_010956	ENSMUSG00000020456	Ogdh	2210403E04Rik|2210412K19Rik|AA409584|d1401|mKIAA4192	oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)	protein-coding
mm_155969.1	chrX	106085365	106085376	+	1	NA	exon (NM_009726, exon 3 of 23)	exon (NM_009726, exon 3 of 23)	-57905	NM_205820	279572	Mm.336203	NM_205820	ENSMUSG00000033777	Tlr13	AI666735|Gm713	toll-like receptor 13	protein-coding
mm_64871.1	chr7	14254885	14254890	-	1	NA	promoter-TSS (NM_001081325)	promoter-TSS (NM_001081325)	-17	NM_001081325	629219	Mm.439627	NM_001081325	ENSMUSG00000070810	Sult2a6	EG629219|Gm6957	sulfotransferase family 2A, dehydroepiandrosterone (DHEA)-preferring, member 6	protein-coding
mm_136153.1	chr16	87700057	87700066	-	1	NA	intron (NM_007520, intron 1 of 4)	intron (NM_007520, intron 1 of 4)	1107	NM_007520	12013	Mm.26147	NM_007520	ENSMUSG00000025612	Bach1	6230421P05Rik|AI323795	BTB and CNC homology 1, basic leucine zipper transcription factor 1	protein-coding
mm_43665.1	chr5	138754771	138754790	+	1	NA	promoter-TSS (NM_030565)	promoter-TSS (NM_030565)	-301	NM_030565	80752	Mm.320355	NM_030565	ENSMUSG00000025854	Fam20c	C76981|DMP-4|DMP4|GEF-CK|mKIAA4081	family with sequence similarity 20, member C	protein-coding
mm_137740.1	chr17	29360970	29360982	+	1	NA	promoter-TSS (NM_013710)	promoter-TSS (NM_013710)	62	NM_001159538	26382	Mm.279187	NM_013710	ENSMUSG00000024013	Fgd2	Tcd-2|Tcd2|ZFYVE4|tcs-2|tcs2	FYVE, RhoGEF and PH domain containing 2	protein-coding
mm_119481.1	chr14	47351675	47351680	+	1	NA	Intergenic	RLTR1B|LTR|ERV1	-22183	NM_010705	16854	Mm.248615	NM_010705	ENSMUSG00000050335	Lgals3	GBP|L-34|Mac-2|gal3	lectin, galactose binding, soluble 3	protein-coding
mm_31760.1	chr4	63381369	63381373	+	1	NA	intron (NM_001305432, intron 8 of 20)	intron (NM_001305432, intron 8 of 20)	16869	NM_001305432	100182	Mm.387725	NM_001045514	ENSMUSG00000039158	Akna	AI597013	AT-hook transcription factor	protein-coding
mm_39035.1	chr4	152305272	152305283	-	1	NA	non-coding (NR_037908, exon 6 of 6)	non-coding (NR_037908, exon 6 of 6)	8063	NM_133788	57295	Mm.277464	NM_133788	ENSMUSG00000039662	Icmt	1700008E11Rik|C80758|Gm13095|HSTE14|OTTMUSG00000010406|PPMT|STE14|pcCMT	isoprenylcysteine carboxyl methyltransferase	protein-coding
mm_99233.1	chr11	101063091	101063110	+	1	NA	3' UTR (NM_001243049, exon 21 of 21)	3' UTR (NM_001243049, exon 21 of 21)	-6994	NM_013792	27419	Mm.95452	NM_013792	ENSMUSG00000001751	Naglu	-	alpha-N-acetylglucosaminidase (Sanfilippo disease IIIB)	protein-coding
mm_153100.1	chr19	32712747	32712760	-	1	NA	promoter-TSS (NM_026487)	promoter-TSS (NM_026487)	-455	NM_026487	67979	Mm.27123	NM_026487	ENSMUSG00000013662	Atad1	4921525H23Rik|AW107648|Thorase	ATPase family, AAA domain containing 1	protein-coding
mm_131256.1	chr16	10772349	10772352	+	1	NA	Intergenic	Intergenic	13186	NM_009896	12703	Mm.130	NM_009896	ENSMUSG00000038037	Socs1	Cish1|Cish7|JAB|SOCS-1|SSI-1	suppressor of cytokine signaling 1	protein-coding
mm_144744.1	chr18	35598608	35598653	+	1	NA	promoter-TSS (NM_026420)	promoter-TSS (NM_026420)	-37	NM_026420	67869	Mm.126534	NM_026420	ENSMUSG00000037058	Paip2	2310050K10Rik|AU045972	polyadenylate-binding protein-interacting protein 2	protein-coding
mm_72057.1	chr8	71371776	71371822	+	1	NA	exon (NM_001293800, exon 1 of 3)	exon (NM_001293800, exon 1 of 3)	501	NM_001293800	77090	Mm.440170	NM_029865	ENSMUSG00000002396	Ocel1	9430098E02Rik|AI326022|AI593544	occludin/ELL domain containing 1	protein-coding
mm_55922.1	chr6	83888611	83888617	-	1	NA	Intergenic	RMER17C2|LTR|ERVK	-25739	NM_001166371	18139	Mm.132392	NM_008717	ENSMUSG00000030016	Zfp638	AI323587|Np220|Zfml|Znf638|mNP220	zinc finger protein 638	protein-coding
mm_123512.1	chr14	66242498	66242498	-	1	NA	intron (NM_001162365, intron 1 of 30)	intron (NM_001162365, intron 1 of 30)	-28946	NM_001162366	19229	Mm.21613	NM_172498	ENSMUSG00000059456	Ptk2b	CADTK|CAKB|CAKbeta|E430023O05Rik|FADK2|FAK2|PYK2|Raftk	PTK2 protein tyrosine kinase 2 beta	protein-coding
mm_2049.1	chr1	87362664	87362665	+	1	NA	intron (NM_146112, intron 3 of 28)	intron (NM_146112, intron 3 of 28)	32065	NM_001110227	100040591	Mm.443539	NM_001110227	ENSMUSG00000079436	Kcnj13	-	potassium inwardly-rectifying channel, subfamily J, member 13	protein-coding
mm_127313.1	chr15	100251679	100251703	+	1	NA	intron (NM_007497, intron 3 of 6)	intron (NM_007497, intron 3 of 6)	23832	NM_007497	11908	Mm.676	NM_007497	ENSMUSG00000023027	Atf1	-	activating transcription factor 1	protein-coding
mm_10184.1	chr2	4881757	4881772	+	1	NA	5' UTR (NM_175400, exon 1 of 9)	5' UTR (NM_175400, exon 1 of 9)	200	NM_175400	109079	Mm.34329	NM_175400	ENSMUSG00000026662	Sephs1	1110046B24Rik|AA589574|AI505014|AW111620|SELD|SPS|SPS1	selenophosphate synthetase 1	protein-coding
mm_33483.1	chr4	130818959	130818970	+	1	NA	exon (NM_011520, exon 3 of 5)	exon (NM_011520, exon 3 of 5)	26427	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_31060.1	chr4	41314322	41314359	+	1	NA	intron (NM_026893, intron 1 of 8)	CpG	561	NM_026893	68970	Mm.28891	NM_026893	ENSMUSG00000028436	Dcaf12	1500001L20Rik|5830424K06Rik|AA420338|AI851081|Wdr40a	DDB1 and CUL4 associated factor 12	protein-coding
mm_32084.1	chr4	98396379	98396408	+	1	NA	intron (NM_001005784, intron 1 of 19)	intron (NM_001005784, intron 1 of 19)	567	NM_172696	12695	Mm.90218	NM_007704	ENSMUSG00000061859	Patj	Cipp|Inadl	PATJ, crumbs cell polarity complex component	protein-coding
mm_75772.1	chr8	69989758	69989776	-	1	NA	intron (NM_145596, intron 1 of 12)	intron (NM_145596, intron 1 of 12)	6617	NM_001286450	234366	Mm.270044	NM_145596	ENSMUSG00000036180	Gatad2a	1110066C11Rik|BC031407|C80248	GATA zinc finger domain containing 2A	protein-coding
mm_146051.1	chr18	69593625	69593638	+	1	NA	intron (NM_013685, intron 8 of 19)	intron (NM_013685, intron 8 of 19)	247910	NM_001083967	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding
mm_28125.1	chr3	86998998	86999033	-	1	NA	intron (NM_007639, intron 1 of 5)	intron (NM_007639, intron 1 of 5)	325	NM_007639	12479	Mm.1894	NM_007639	ENSMUSG00000028076	Cd1d1	AI747460|CD1.1|Cd1a|Cd1d|Ly-38	CD1d1 antigen	protein-coding
mm_157806.1	chrX	73930736	73930750	-	1	NA	exon (NM_001164704, exon 1 of 11)	exon (NM_001164704, exon 1 of 11)	107	NM_023132	19703	Mm.236969	NM_023132	ENSMUSG00000031387	Renbp	Age|Rnbp	renin binding protein	protein-coding
mm_160362.1	chr8	21946708	21946708	+	1	NA	promoter-TSS (NM_139223)	promoter-TSS (NM_139223)	-54	NM_139223	246083	Mm.219548	NM_139223	ENSMUSG00000044222	Defb13	BD-13	defensin beta 13	protein-coding
mm_126105.1	chr15	78247439	78247456	+	1	NA	intron (NM_008677, intron 1 of 9)	intron (NM_008677, intron 1 of 9)	2636	NM_008677	17972	Mm.2068	NM_008677	ENSMUSG00000071715	Ncf4	AI451400|p40phox	neutrophil cytosolic factor 4	protein-coding
mm_121416.1	chr14	119719338	119719342	+	1	NA	intron (NM_015820, intron 1 of 1)	RMER1B|Other|Other	-29887	NR_045621	75432	Mm.443277	NR_045621	ENSMUSG00000100274	1700006F04Rik	-	RIKEN cDNA 1700006F04 gene	ncRNA
mm_162706.1	chr10	23237216	23237224	-	1	NA	intron (NM_010167, intron 2 of 18)	intron (NM_010167, intron 2 of 18)	112670	NM_001347372	14051	Mm.332128	NM_010167	ENSMUSG00000010461	Eya4	B130023L16Rik	EYA transcriptional coactivator and phosphatase 4	protein-coding
mm_140706.1	chr17	14694083	14694099	-	1	NA	5' UTR (NM_011581, exon 1 of 22)	5' UTR (NM_011581, exon 1 of 22)	171	NM_011581	21826	Mm.26688	NM_011581	ENSMUSG00000023885	Thbs2	TSP2|Thbs-2	thrombospondin 2	protein-coding
mm_20335.1	chr2	127541390	127541405	-	1	NA	promoter-TSS (NM_178047)	promoter-TSS (NM_178047)	20	NM_178047	192212	Mm.34171	NM_138750	ENSMUSG00000027376	Prom2	AI507243|Prom-rp	prominin 2	protein-coding
mm_4331.1	chr1	171854867	171854877	+	1	NA	3' UTR (NM_001252472, exon 3 of 3)	3' UTR (NM_001252472, exon 3 of 3)	15175	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_23777.1	chr3	77033710	77033710	+	1	NA	Intergenic	Intergenic	958127	NM_001253719	213262	Mm.379337	NM_178673	ENSMUSG00000034098	Fstl5	9130207J01Rik	follistatin-like 5	protein-coding
mm_51510.1	chr6	83137135	83137152	+	1	NA	promoter-TSS (NM_133641)	promoter-TSS (NM_133641)	59	NM_009106	20166	Mm.4139	NM_009106	ENSMUSG00000034930	Rtkn	-	rhotekin	protein-coding
mm_91780.1	chr10	52195358	52195377	-	1	NA	promoter-TSS (NM_011282)	promoter-TSS (NM_011282)	-123	NM_011282	19886	Mm.236163	NM_011282	ENSMUSG00000019893	Ros1	Ros-1|c-ros	Ros1 proto-oncogene	protein-coding
mm_171046.1	chr3	100131486	100131502	-	1	NA	intron (NM_028892, intron 48 of 48)	L1Md_T|LINE|L1	30909	NM_175552	269470	Mm.24591	NM_175552	ENSMUSG00000033285	Wdr3	AW546279|D030020G18Rik	WD repeat domain 3	protein-coding
mm_50510.1	chr6	49038097	49038140	+	1	NA	intron (NM_053110, intron 1 of 10)	intron (NM_053110, intron 1 of 10)	1600	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_83572.1	chr9	47474854	47474865	-	1	NA	Intergenic	Intergenic	-55311	NM_001310841	54725	Mm.234832	NM_018770	ENSMUSG00000032076	Cadm1	2900073G06Rik|3100001I08Rik|AI987920|Bl2|Igsf4|Igsf4a|Necl2|RA175|RA175A|RA175B|RA175C|RA175N|ST17|SgIGSF|SynCam|Tslc1	cell adhesion molecule 1	protein-coding
mm_126073.1	chr15	77618966	77618970	+	1	NA	Intergenic	Intergenic	-22843	NM_177820	328561	Mm.379486	NM_177820	ENSMUSG00000050014	Apol10b	9130218O11Rik	apolipoprotein L 10B	protein-coding
mm_58491.1	chr7	3694513	3694552	+	1	NA	promoter-TSS (NM_024168)	promoter-TSS (NM_024168)	24	NM_024168	66078	Mm.379100	NM_024168	ENSMUSG00000035585	Tsen34	0610027F08Rik|Leng5	tRNA splicing endonuclease subunit 34	protein-coding
mm_121465.1	chr14	120896880	120896897	+	1	NA	Intergenic	Intergenic	-14306	NM_023579	70572	Mm.221452	NM_023579	ENSMUSG00000030662	Ipo5	1110011C18Rik|5730478E03Rik|AA409333|C76941|IMB3|Kpnb3|Ranbp5	importin 5	protein-coding
mm_164098.1	chr15	14645190	14645193	+	1	NA	Intergenic	RMER6C|LTR|ERVK	-1471516	NM_007666	12563	Mm.57048	NM_007666	ENSMUSG00000039385	Cdh6	cad6	cadherin 6	protein-coding
mm_51572.1	chr6	83743041	83743065	+	1	NA	promoter-TSS (NM_134157)	promoter-TSS (NM_134157)	36	NM_134157	110935	Mm.220823	NM_134157	ENSMUSG00000006269	Atp6v1b1	AW208839|Atp6b1|D630003L15|D630030L16Rik|D630039P21Rik|Vpp-3|Vpp3	ATPase, H+ transporting, lysosomal V1 subunit B1	protein-coding
mm_146221.1	chr18	77057428	77057429	+	1	NA	Intergenic	ORR1D1|LTR|ERVL-MaLR	-7780	NM_008602	17344	Mm.6370	NM_008602	ENSMUSG00000025423	Pias2	6330408K17Rik|AI462206|ARIP3|AU018068|Dib|Miz1|PIASxalpha|PIASxb|PIASxbeta|SIZ2	protein inhibitor of activated STAT 2	protein-coding
mm_15540.1	chr2	158384618	158384629	+	1	NA	3' UTR (NM_175692, exon 5 of 5)	3' UTR (NM_175692, exon 5 of 5)	8985	NM_175692	319317	Mm.294494	NM_175692	ENSMUSG00000044349	Snhg11	A930034L06Rik|AI854265|AL022637|AW319638|E130013N09Rik	small nucleolar RNA host gene 11	protein-coding
mm_147830.1	chr18	62188866	62188901	-	1	NA	Intergenic	Intergenic	-8902	NM_007420	11555	Mm.5598	NM_007420	ENSMUSG00000045730	Adrb2	Adrb-2|Badm|Gpcr7	adrenergic receptor, beta 2	protein-coding
mm_75610.1	chr8	62123130	62123138	-	1	NA	promoter-TSS (NM_001136089)	promoter-TSS (NM_001136089)	59	NM_001136089	26359	Mm.42179	NM_011922	ENSMUSG00000031635	Anxa10	-	annexin A10	protein-coding
mm_160226.1	chr7	102065465	102065465	-	1	NA	promoter-TSS (NR_104582)	promoter-TSS (NR_104582)	-26	NR_104582	102443351	Mm.292904	NM_011644	ENSMUSG00000070425	Xntrpc	Xndr-trpc2	Xndc1-transient receptor potential cation channel, subfamily C, member 2 readthrough	protein-coding
mm_116972.1	chr13	56178823	56178833	-	1	NA	promoter-TSS (NM_001168615)	promoter-TSS (NM_001168615)	57	NM_145976	212937	Mm.116697	NM_145976	ENSMUSG00000049625	Tifab	-	TRAF-interacting protein with forkhead-associated domain, family member B	protein-coding
mm_164698.1	chr17	49117629	49117630	+	1	NA	Intergenic	B3A|SINE|B2	-4096	NR_038144	69311	Mm.46140	NR_038141	ENSMUSG00000101012	1700008K24Rik	-	RIKEN cDNA 1700008K24 gene	ncRNA
mm_15772.1	chr2	164332795	164332800	+	1	NA	promoter-TSS (NM_009301)	promoter-TSS (NM_009301)	32	NM_009301	20944	Mm.140154	NM_009301	ENSMUSG00000017004	Svs5	BB115186|Semg1|Svp-1|Svp1|Svp5	seminal vesicle secretory protein 5	protein-coding
mm_76979.1	chr8	106886331	106886359	-	1	NA	exon (NM_145412, exon 4 of 4)	exon (NM_145412, exon 4 of 4)	7248	NM_145412	214987	Mm.490308	NM_145412	ENSMUSG00000046691	Chtf8	5830457O10Rik|Ctf8|Derpc	CTF8, chromosome transmission fidelity factor 8	protein-coding
mm_63603.1	chr7	128148057	128148070	+	1	NA	exon (NM_021334, exon 25 of 30)	exon (NM_021334, exon 25 of 30)	18495	NM_021334	16411	Mm.22378	NM_021334	ENSMUSG00000030789	Itgax	AI449405|Cd11c|Cr4|N418	integrin alpha X	protein-coding
mm_97721.1	chr11	80300867	80300889	+	1	NA	promoter-TSS (NM_139228)	promoter-TSS (NM_139228)	-34	NM_139228	246104	Mm.194148	NM_139228	ENSMUSG00000017692	Rhbdl3	AI847581|Rhbdl4|Rhomr1|Vrho	rhomboid, veinlet-like 3 (Drosophila)	protein-coding
mm_104483.1	chr11	95581004	95581012	-	1	NA	exon (NM_033217, exon 2 of 6)	exon (NM_033217, exon 2 of 6)	6690	NM_033217	18053	Mm.283893	NM_033217	ENSMUSG00000000120	Ngfr	LNGFR|Tnfrsf16|p75|p75NGFR|p75NTR	nerve growth factor receptor (TNFR superfamily, member 16)	protein-coding
mm_135112.1	chr16	35770231	35770255	-	1	NA	promoter-TSS (NM_153550)	promoter-TSS (NM_153550)	-143	NM_175111	66667	Mm.45272	NM_175111	ENSMUSG00000022849	Hspbap1	3830421G21Rik	Hspb associated protein 1	protein-coding
mm_49470.1	chr6	29471458	29471497	+	1	NA	promoter-TSS (NM_001145360)	promoter-TSS (NM_001145360)	40	NM_001145360	668210	Mm.420607	NM_001145360	ENSMUSG00000090685	Gm9047	EG668210	predicted gene 9047	protein-coding
mm_65116.1	chr7	19359417	19359476	-	1	NA	promoter-TSS (NM_145822)	promoter-TSS (NM_145822)	37	NM_145822	70333	Mm.171370	NM_145822	ENSMUSG00000047649	Cd3eap	1190028F09|2610103M17Rik|ASE-1|Ase1|CAST|PAF49	CD3E antigen, epsilon polypeptide associated protein	protein-coding
mm_99775.1	chr11	107189432	107189442	+	1	NA	promoter-TSS (NM_001161329)	promoter-TSS (NM_001161329)	-56	NM_001161329	68979	Mm.294617	NM_133702	ENSMUSG00000018433	Nol11	1500002M01Rik|AU015220|AU019874	nucleolar protein 11	protein-coding
mm_70401.1	chr8	11312861	11312867	+	1	NA	promoter-TSS (NM_009932)	promoter-TSS (NM_009932)	-38	NM_009931	12826	Mm.738	NM_009931	ENSMUSG00000031502	Col4a1	Bru|Col4a-1|Raw|Svc	collagen, type IV, alpha 1	protein-coding
mm_156302.1	chrX	136837908	136837920	+	1	NA	3' UTR (NM_011123, exon 7 of 7)	3' UTR (NM_011123, exon 7 of 7)	15168	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_7408.1	chr1	119421154	119421163	-	1	NA	5' UTR (NM_008381, exon 1 of 2)	5' UTR (NM_008381, exon 1 of 2)	1090	NM_008381	16324	Mm.3092	NM_008381	ENSMUSG00000037035	Inhbb	-	inhibin beta-B	protein-coding
mm_79580.1	chr9	58135045	58135078	+	1	NA	intron (NM_001162479, intron 1 of 18)	intron (NM_001162479, intron 1 of 18)	396	NM_001162479	20897	Mm.10801	NM_009291	ENSMUSG00000032327	Stra6	AI891933	stimulated by retinoic acid gene 6	protein-coding
mm_55499.1	chr6	69751335	69751348	-	1	NA	Intergenic	Intergenic	-424167	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_24537.1	chr3	93279582	93279607	+	1	NA	Intergenic	Intergenic	-40155	NM_133698	68723	Mm.208047	NM_133698	ENSMUSG00000041991	Hrnr	1110033K19Rik|A530063N20Rik|S100a18	hornerin	protein-coding
mm_108109.1	chr12	75308440	75308450	+	1	NA	5' UTR (NM_023275, exon 1 of 5)	5' UTR (NM_023275, exon 1 of 5)	132	NM_023275	80837	Mm.27467	NM_023275	ENSMUSG00000046768	Rhoj	1110005O19Rik|AW210585|Arhj|TC10L|TCL	ras homolog family member J	protein-coding
mm_61641.1	chr7	80343092	80343146	+	1	NA	promoter-TSS (NM_026812)	promoter-TSS (NM_026812)	-18	NM_026812	68695	Mm.21171	NM_026812	ENSMUSG00000030532	Hddc3	1110033O09Rik|C86475|MESH1	HD domain containing 3	protein-coding
mm_148436.1	chr19	3944147	3944171	+	1	NA	exon (NM_019449, exon 9 of 11)	exon (NM_019449, exon 9 of 11)	8973	NM_001161428	54445	Mm.262094	NM_019449	ENSMUSG00000036908	Unc93b1	Unc-93B1|Unc93b	unc-93 homolog B1 (C. elegans)	protein-coding
mm_32650.1	chr4	115063372	115063385	+	1	NA	exon (NM_011527, exon 3 of 5)	exon (NM_011527, exon 3 of 5)	5567	NM_001287388	21349	Mm.239869	NM_011527	ENSMUSG00000028717	Tal1	Hpt|SCL/tal-1|Scl|bHLHa17|tal-1	T cell acute lymphocytic leukemia 1	protein-coding
mm_104857.1	chr11	99366100	99366115	-	1	NA	intron (NM_027574, intron 6 of 7)	B3A|SINE|B2	8796	NM_027574	70843	Mm.180256	NM_027574	ENSMUSG00000055937	Krt28	4733401L19Rik|Krt25d	keratin 28	protein-coding
mm_138030.1	chr17	33919487	33919498	+	1	NA	promoter-TSS (NM_009318)	promoter-TSS (NM_009318)	14	NM_009318	21356	Mm.154457	NM_009318	ENSMUSG00000024308	Tapbp	D17Wsu91e|TPN	TAP binding protein	protein-coding
mm_42108.1	chr5	110544376	110544400	+	1	NA	promoter-TSS (NM_198306)	promoter-TSS (NM_198306)	33	NM_198306	231605	Mm.275748	NM_198306	ENSMUSG00000033316	Galnt9	GalNAc-T9	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 9	protein-coding
mm_105476.1	chr11	105936905	105936914	-	1	NA	intron (NM_007805, intron 2 of 5)	intron (NM_007805, intron 2 of 5)	7238	NM_007805	13056	Mm.149403	NM_007805	ENSMUSG00000019590	Cyb561	-	cytochrome b-561	protein-coding
mm_56049.1	chr6	86741934	86741966	-	1	NA	exon (NM_001331120, exon 12 of 13)	exon (NM_001331120, exon 12 of 13)	-8572	NM_011818	23885	Mm.321452	NM_011818	ENSMUSG00000001157	Gmcl1	2810049L19Rik|Btbd13|DIP|Gcl|Gcl-1|glc-1|mglc-1	germ cell-less, spermatogenesis associated 1	protein-coding
mm_109326.1	chr12	109564665	109564676	+	1	NA	TTS (NR_030427)	TTS (NR_030427)	978	NR_030427	791079		NR_030427	ENSMUSG00000076451	Mir770	Mirn770|mir-770|mmu-mir-770	microRNA 770	ncRNA
mm_136957.1	chr17	15374627	15374637	+	1	NA	intron (NM_007865, intron 2 of 10)	intron (NM_007865, intron 2 of 10)	1191	NM_007865	13388	Mm.4875	NM_007865	ENSMUSG00000014773	Dll1	Delta1	delta-like 1 (Drosophila)	protein-coding
mm_158579.1	chrX	150657367	150657377	-	1	NA	promoter-TSS (NM_019548)	promoter-TSS (NM_019548)	64	NM_019548	56191	Mm.3597	NM_019548	ENSMUSG00000025272	Tro	AA409408|Maged3|Maged3l|Tnn|Trol|magphinin	trophinin	protein-coding
mm_139931.1	chr17	71064104	71064106	+	1	NA	intron (NM_010867, intron 11 of 37)	RSINE1|SINE|B4	44548	NM_001083934	17929	Mm.4103	NM_010867	ENSMUSG00000024049	Myom1	D430047A17Rik	myomesin 1	protein-coding
mm_118149.1	chr13	105242635	105242649	-	1	NA	intron (NM_027934, intron 5 of 7)	Lx9|LINE|L1	50372	NM_027934	71816	Mm.317015	NM_027934	ENSMUSG00000021720	Rnf180	3110001E11Rik|Rines	ring finger protein 180	protein-coding
mm_165879.1	chr4	41284356	41284356	+	1	NA	Intergenic	Intergenic	-9221	NM_026872	68926	Mm.41864	NM_026872	ENSMUSG00000028433	Ubap2	1190005K07Rik|AA408600|AU045235|UBAP-2|mKIAA1491	ubiquitin-associated protein 2	protein-coding
mm_103149.1	chr11	70322521	70322537	-	1	NA	promoter-TSS (NM_145684)	promoter-TSS (NM_145684)	-11	NM_145684	11685	Mm.274093	NM_145684	ENSMUSG00000018907	Alox12e	8-LOX|AW259591|Alox12-ps1|Alox12-ps2|Aloxe|e-LOX1	arachidonate lipoxygenase, epidermal	protein-coding
mm_83657.1	chr9	49517560	49517578	-	1	NA	promoter-TSS (NR_029465)	promoter-TSS (NR_029465)	-719	NR_029465	100036537	Mm.437541	NR_029465	ENSMUSG00000079564	Gm11149	ENSMUSG00000060603|ENSMUSG00000079564	predicted gene 11149	ncRNA
mm_19824.1	chr2	110950194	110950206	-	1	NA	promoter-TSS (NM_001128103)	promoter-TSS (NM_001128103)	44	NM_001128103	228432	Mm.483325	NM_001081556	ENSMUSG00000074968	Ano3	AI838058|B230324K02Rik|Tmem16c	anoctamin 3	protein-coding
mm_42777.1	chr5	121385475	121385479	+	1	NA	intron (NM_172275, intron 1 of 11)	CpG	138	NM_001163470	231712	Mm.20488	NM_172275	ENSMUSG00000042726	Trafd1	1110008K06Rik|Fln29	TRAF type zinc finger domain containing 1	protein-coding
mm_54255.1	chr6	28262467	28262492	-	1	NA	promoter-TSS (NM_001081678)	promoter-TSS (NM_001081678)	-878	NM_001081678	627049	Mm.84441	NM_001081678	ENSMUSG00000039841	Zfp800	AA407452|Znf800	zinc finger protein 800	protein-coding
mm_114199.1	chr13	55929299	55929310	+	1	NA	Intergenic	Intergenic	-97879	NM_011097	18740	Mm.135195	NM_011097	ENSMUSG00000021506	Pitx1	Bft|P-OTX|Potx|Ptx1	paired-like homeodomain transcription factor 1	protein-coding
mm_12128.1	chr2	61649830	61649848	+	1	NA	exon (NM_001164072, exon 7 of 8)	exon (NM_001164072, exon 7 of 8)	56742	NM_001164071	21353	Mm.244393	NM_011529	ENSMUSG00000064289	Tank	C86182|E430026L09Rik|I-TRAF	TRAF family member-associated Nf-kappa B activator	protein-coding
mm_35609.1	chr4	43340133	43340137	-	1	NA	intron (NM_177195, intron 13 of 28)	RLTR9A3|LTR|ERVK	-41847	NM_001037709	100213	Mm.235730	NM_199057	ENSMUSG00000035969	Rusc2	AI840675|mKIAA0375	RUN and SH3 domain containing 2	protein-coding
mm_51298.1	chr6	72307139	72307212	+	1	NA	exon (NM_001282071, exon 6 of 11)	exon (NM_001282071, exon 6 of 11)	2565	NM_147779	20388	Mm.46033	NM_147779	ENSMUSG00000056370	Sftpb	AI562151|SF-B|SP-B|Sftp-3|Sftp3	surfactant associated protein B	protein-coding
mm_78918.1	chr9	45039747	45039757	+	1	NA	Intergenic	Intergenic	-2592	NM_007962	14012	Mm.33240	NM_007962	ENSMUSG00000032092	Mpzl2	Eva|Eva1	myelin protein zero-like 2	protein-coding
mm_137409.1	chr17	26113287	26113363	+	1	NA	promoter-TSS (NM_021793)	promoter-TSS (NM_021793)	9	NM_021793	60455	Mm.304656	NM_021793	ENSMUSG00000024180	Tmem8	AW490096|M83|Tmem8a	transmembrane protein 8 (five membrane-spanning domains)	protein-coding
mm_76843.1	chr8	105289466	105289541	-	1	NA	promoter-TSS (NM_028888)	promoter-TSS (NM_028888)	25	NM_001166394	74356	Mm.204876	NM_028888	ENSMUSG00000014837	4931428F04Rik	AI426165|Kiaa0895l	RIKEN cDNA 4931428F04 gene	protein-coding
mm_6094.1	chr1	63214310	63214322	-	1	NA	promoter-TSS (NM_146250)	promoter-TSS (NM_146250)	-35	NM_146250	241070	Mm.103354	NM_146250	ENSMUSG00000046856	Gpr1	-	G protein-coupled receptor 1	protein-coding
mm_8533.1	chr1	155054751	155054761	-	1	NA	Intergenic	Intergenic	44880	NM_010500	15939	Mm.12246	NM_010500	ENSMUSG00000056708	Ier5	-	immediate early response 5	protein-coding
mm_133072.1	chr16	58677786	58677825	+	1	NA	intron (NM_007757, intron 5 of 6)	intron (NM_007757, intron 5 of 6)	7597	NM_007757	12892	Mm.291519	NM_007757	ENSMUSG00000022742	Cpox	CPX|Cpo|HCP|cac|nct	coproporphyrinogen oxidase	protein-coding
mm_89654.1	chr10	97480215	97480227	+	1	NA	intron (NM_001190451, intron 1 of 7)	intron (NM_001190451, intron 1 of 7)	721	NM_001190451	13179	Mm.56769	NM_007833	ENSMUSG00000019929	Dcn	DC|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding
mm_129633.1	chr15	80235316	80235328	-	1	NA	intron (NM_178719, intron 1 of 5)	intron (NM_178719, intron 1 of 5)	1242	NM_178719	239555	Mm.307163	NM_178719	ENSMUSG00000022412	Mief1	A230016E22|AI452372|Smcr7l	mitochondrial elongation factor 1	protein-coding
mm_141996.1	chr17	35188428	35188446	-	1	NA	promoter-TSS (NM_010734)	promoter-TSS (NM_010734)	3	NM_010734	16988	Mm.19379	NM_010734	ENSMUSG00000073412	Lst1	B144	leukocyte specific transcript 1	protein-coding
mm_77551.1	chr8	123254170	123254197	-	1	NA	promoter-TSS (NM_020497)	promoter-TSS (NM_020497)	-12	NM_020497	57247	Mm.379084	NM_020497	ENSMUSG00000001065	Zfp276	AW048709|D8Ertd370e|D8Ertd377e|Znf276	zinc finger protein (C2H2 type) 276	protein-coding
mm_52887.1	chr6	122571553	122571564	+	1	NA	Intergenic	MIR|SINE|MIR	17749	NM_009645	11628	Mm.391503	NM_009645	ENSMUSG00000040627	Aicda	Aid|Arp2	activation-induced cytidine deaminase	protein-coding
mm_149376.1	chr19	11375567	11375580	+	1	NA	promoter-TSS (NM_001310331)	promoter-TSS (NM_001310331)	85	NM_001310331	666907		NM_001310331	ENSMUSG00000101389	Ms4a4a	EG666907	membrane-spanning 4-domains, subfamily A, member 4A	protein-coding
mm_52307.1	chr6	108828550	108828558	+	1	NA	promoter-TSS (NM_138677)	promoter-TSS (NM_138677)	-87	NM_138677	192193	Mm.21596	NM_138677	ENSMUSG00000030104	Edem1	A130059K23Rik|EDEM|mKIAA0212	ER degradation enhancer, mannosidase alpha-like 1	protein-coding
mm_169644.1	chr15	50889111	50889113	-	1	NA	promoter-TSS (NR_035444)	promoter-TSS (NR_035444)	2	NR_035444	100316685		NR_035444	ENSMUSG00000084458	Mir1907	Mirn1907|mmu-mir-1907	microRNA 1907	ncRNA
mm_84210.1	chr9	61105381	61105392	-	1	NA	promoter-TSS (NR_105026)	promoter-TSS (NR_105026)	0	NR_105026	66785	Mm.158134	NR_105026	ENSMUSG00000111807	4933433G08Rik	-	RIKEN cDNA 4933433G08 gene	ncRNA
mm_110909.1	chr12	76177062	76177071	-	1	NA	non-coding (NR_104386, exon 1 of 8)	non-coding (NR_104386, exon 1 of 8)	193	NM_010157	13983	Mm.2561	NM_010157	ENSMUSG00000021055	Esr2	ER[b]|ERbeta|Estrb	estrogen receptor 2 (beta)	protein-coding
mm_153245.1	chr19	36119834	36119847	-	1	NA	promoter-TSS (NM_013468)	promoter-TSS (NM_013468)	4	NM_013468	107765	Mm.10279	NM_013468	ENSMUSG00000024803	Ankrd1	Alrp|CARP|Crap|MARP1	ankyrin repeat domain 1 (cardiac muscle)	protein-coding
mm_45448.1	chr5	67428060	67428095	-	1	NA	promoter-TSS (NM_001164806)	promoter-TSS (NM_001164806)	-278	NM_001164806	666938	Mm.101339	NM_001164806	ENSMUSG00000092060	Bend4	D330027G24Rik|EG666938	BEN domain containing 4	protein-coding
mm_136114.1	chr16	85550387	85550402	-	1	NA	promoter-TSS (NM_144853)	promoter-TSS (NM_144853)	-21	NM_144853	224405	Mm.213203	NM_144853	ENSMUSG00000041134	Cyyr1	-	cysteine and tyrosine-rich protein 1	protein-coding
mm_34186.1	chr4	140701467	140701509	+	1	NA	promoter-TSS (NM_173867)	promoter-TSS (NM_173867)	15	NM_173867	108911	Mm.253	NM_173867	ENSMUSG00000040945	Rcc2	2610510H01Rik|2610529N02Rik|AA536646|AA675016|Td60|mKIAA1470	regulator of chromosome condensation 2	protein-coding
mm_92867.1	chr10	81627535	81627586	-	1	NA	promoter-TSS (NM_027480)	promoter-TSS (NM_027480)	48	NM_181586	50721	Mm.25643	NM_181586	ENSMUSG00000034748	Sirt6	2810449N18Rik|AI043036|Sir2l6	sirtuin 6	protein-coding
mm_14670.1	chr2	139493955	139493972	+	1	NA	promoter-TSS (NM_175467)	promoter-TSS (NM_175467)	43	NM_175467	228677	Mm.100450	NM_175467	ENSMUSG00000039092	Sptlc3	C130053K05Rik	serine palmitoyltransferase, long chain base subunit 3	protein-coding
mm_73178.1	chr8	95056704	95056712	+	1	NA	exon (NM_001042715, exon 3 of 18)	exon (NM_001042715, exon 3 of 18)	1605	NM_001042715	330830	Mm.277112	NM_001042715	ENSMUSG00000031786	Drc7	Ccdc135|Gm770|SRG-L|SRG-S	dynein regulatory complex subunit 7	protein-coding
mm_103457.1	chr11	76304177	76304181	-	1	NA	intron (NM_008750, intron 1 of 7)	intron (NM_008750, intron 1 of 7)	60443	NM_183263	67390	Mm.24886	NM_183263	ENSMUSG00000038046	Rnmtl1	4833420N02Rik|AI255153|HC90|Mrm3	RNA methyltransferase like 1	protein-coding
mm_28394.1	chr3	90045036	90045044	-	1	NA	intron (NM_153489, intron 2 of 26)	intron (NM_153489, intron 2 of 26)	-6596	NM_001287087	99650	Mm.300083	NM_025762	ENSMUSG00000027942	4933434E20Rik	5730552F22Rik|AI462154|NICE-3|NS5ATP4	RIKEN cDNA 4933434E20 gene	protein-coding
mm_14737.1	chr2	144337437	144337445	+	1	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	-5361	NM_026924	107586	Mm.252750	NM_026924	ENSMUSG00000037279	Ovol2	1700108N11Rik|1810007D21Rik|M-OVO|M-OVO-A|M-OVO-B|MOVO|Ovo2|Zfp339|movo2	ovo like zinc finger 2	protein-coding
mm_21673.1	chr2	164425813	164425828	-	1	NA	3' UTR (NM_011521, exon 5 of 5)	3' UTR (NM_011521, exon 5 of 5)	17368	NM_011521	20971	Mm.3815	NM_011521	ENSMUSG00000017009	Sdc4	AA959608|AW108331|S4|Synd4|ryudocan|syndecan-4	syndecan 4	protein-coding
mm_60305.1	chr7	44102326	44102329	+	1	NA	promoter-TSS (NM_010642)	promoter-TSS (NM_010642)	35	NM_010642	16616	Mm.443292	NM_010642	ENSMUSG00000066516	Klk1b21	Klk21|mGk-21	kallikrein 1-related peptidase b21	protein-coding
mm_99854.1	chr11	109363065	109363076	+	1	NA	exon (NM_010303, exon 1 of 4)	exon (NM_010303, exon 1 of 4)	276	NM_010303	14674	Mm.193925	NM_010303	ENSMUSG00000020611	Gna13	AU024132|AU043124|Galpha13	guanine nucleotide binding protein, alpha 13	protein-coding
mm_144597.1	chr18	32377136	32377139	+	1	NA	promoter-TSS (NM_009668)	promoter-TSS (NM_009668)	-80	NM_001083334	30948	Mm.4383	NM_009668	ENSMUSG00000024381	Bin1	ALP-1|Amphl|BRAMP-2|SH3P9	bridging integrator 1	protein-coding
mm_156052.1	chrX	109095482	109095522	+	1	NA	promoter-TSS (NM_019989)	promoter-TSS (NM_019989)	95	NM_019989	56726	Mm.260760	NM_019989	ENSMUSG00000031246	Sh3bgrl	1190008F14Rik	SH3-binding domain glutamic acid-rich protein like	protein-coding
mm_17982.1	chr2	37801019	37801030	-	1	NA	exon (NM_146122, exon 22 of 22)	exon (NM_146122, exon 22 of 22)	24775	NM_001163566	241324	Mm.392369	NM_001163566	ENSMUSG00000035403	Crb2	5930402A21|BC043114	crumbs family member 2	protein-coding
mm_73010.1	chr8	93811323	93811348	+	1	NA	TTS (NR_026888)	TTS (NR_026888)	497	NM_001113384	14681	Mm.251445	NM_010308	ENSMUSG00000031748	Gnao1	AW050213|Galphao|Gnao|alphaO	guanine nucleotide binding protein, alpha O	protein-coding
mm_104316.1	chr11	93886092	93886140	-	1	NA	promoter-TSS (NM_134012)	promoter-TSS (NM_134012)	-91	NM_001346525	103537	Mm.210334	NM_134012	ENSMUSG00000059474	Mbtd1	AA408199|AI194990|hemp	mbt domain containing 1	protein-coding
mm_97838.1	chr11	83065129	83065151	+	1	NA	promoter-TSS (NM_011408)	promoter-TSS (NM_011408)	28	NM_011408	20556	Mm.278689	NM_011408	ENSMUSG00000072620	Slfn2	Shlf2	schlafen 2	protein-coding
mm_92295.1	chr10	73086706	73086731	-	1	NA	promoter-TSS (NR_040646)	promoter-TSS (NR_040646)	-13	NR_040646	327768	Mm.417745	NR_040646		A330049N07Rik	-	RIKEN cDNA A330049N07 gene	ncRNA
mm_135534.1	chr16	49769795	49769822	-	1	NA	Intergenic	Intergenic	70514	NM_028680	73916	Mm.241276	NM_028680	ENSMUSG00000032965	Ift57	4833420A15Rik|Esrrbl1|Hippi|MHS4R2	intraflagellar transport 57	protein-coding
mm_153529.1	chr19	41848077	41848111	-	1	NA	promoter-TSS (NM_177603)	promoter-TSS (NM_177603)	38	NM_177603	212398	Mm.222723	NM_177603	ENSMUSG00000047604	Frat2	-	frequently rearranged in advanced T cell lymphomas 2	protein-coding
mm_28743.1	chr3	95738261	95738308	-	1	NA	exon (NM_007899, exon 2 of 11)	exon (NM_007899, exon 2 of 11)	1285	NM_007899	13601	Mm.3433	NM_007899	ENSMUSG00000028108	Ecm1	AI663821|p85	extracellular matrix protein 1	protein-coding
mm_73834.1	chr8	117460796	117460812	+	1	NA	3' UTR (NM_001163262, exon 21 of 21)	3' UTR (NM_001163262, exon 21 of 21)	1539	NR_106046	102465653		NR_106046	ENSMUSG00000098483	Mir7078	Gm27386|mmu-mir-7078	microRNA 7078	ncRNA
mm_111096.1	chr12	80643800	80643857	-	1	NA	promoter-TSS (NM_026244)	promoter-TSS (NM_026244)	283	NM_007951	13877	Mm.246551	NM_007951	ENSMUSG00000021131	Erh	Mer|Prei1	enhancer of rudimentary homolog (Drosophila)	protein-coding
mm_140534.1	chr17	6756020	6756030	-	1	NA	intron (NM_009510, intron 2 of 12)	intron (NM_009510, intron 2 of 12)	26755	NM_009510	22350	Mm.277812	NM_009510	ENSMUSG00000052397	Ezr	AW146364|R75297|Vil2|p81	ezrin	protein-coding
mm_27267.1	chr3	39009701	39009708	-	1	NA	exon (NM_183221, exon 17 of 17)	exon (NM_183221, exon 17 of 17)	122764	NM_183221	329628	Mm.316210	NM_183221	ENSMUSG00000046743	Fat4	6030410K14Rik|9430004M15	FAT atypical cadherin 4	protein-coding
mm_48006.1	chr5	136161416	136161461	-	1	NA	intron (NM_178751, intron 2 of 2)	intron (NM_178751, intron 2 of 2)	9218	NM_178751	269717	Mm.308396	NM_178751	ENSMUSG00000039747	Orai2	A730041O15Rik|Tmem142b	ORAI calcium release-activated calcium modulator 2	protein-coding
mm_80576.1	chr9	84037846	84037863	+	1	NA	intron (NM_001305935, intron 8 of 10)	intron (NM_001305935, intron 8 of 10)	89073	NM_199195	12040	Mm.12819	NM_199195	ENSMUSG00000032263	Bckdhb	BCKDE1B|BCKDH E1-beta	branched chain ketoacid dehydrogenase E1, beta polypeptide	protein-coding
mm_801.1	chr1	45348608	45348624	+	1	NA	exon (NM_009930, exon 51 of 51)	exon (NM_009930, exon 51 of 51)	37078	NM_009930	12825	Mm.249555	NM_009930	ENSMUSG00000026043	Col3a1	AW550625|Col3a-1|Tsk-2|Tsk2	collagen, type III, alpha 1	protein-coding
mm_73892.1	chr8	119418984	119418987	+	1	NA	Intergenic	Intergenic	-18177	NM_027950	71839	Mm.272357	NM_027950	ENSMUSG00000074063	Osgin1	1700012B18Rik|Okl38	oxidative stress induced growth inhibitor 1	protein-coding
mm_156973.1	chrX	6083416	6083423	-	1	NA	promoter-TSS (NM_001166433)	promoter-TSS (NM_001166433)	1	NM_001166433	102991	Mm.199793	NM_001033211	ENSMUSG00000073294	AU022751	AU023811	expressed sequence AU022751	protein-coding
mm_75770.1	chr8	69984995	69984999	-	1	NA	intron (NM_145596, intron 1 of 12)	BC1_Mm|scRNA|scRNA	-10614	NM_001113346	234366	Mm.270044	NM_145596	ENSMUSG00000036180	Gatad2a	1110066C11Rik|BC031407|C80248	GATA zinc finger domain containing 2A	protein-coding
mm_87716.1	chr10	60105975	60105996	+	1	NA	promoter-TSS (NM_052994)	promoter-TSS (NM_052994)	-272	NM_052994	94214	Mm.153429	NM_052994	ENSMUSG00000058297	Spock2	AA407235|Gcap26|mKIAA0275	sparc/osteonectin, cwcv and kazal-like domains proteoglycan 2	protein-coding
mm_83634.1	chr9	49486167	49486189	-	1	NA	promoter-TSS (NM_172770)	promoter-TSS (NM_172770)	47	NM_172770	235330	Mm.177413	NM_172770	ENSMUSG00000040219	Ttc12	E330017O07Rik	tetratricopeptide repeat domain 12	protein-coding
mm_78995.1	chr9	45403254	45403268	+	1	NA	5' UTR (NM_052823, exon 1 of 6)	5' UTR (NM_052823, exon 1 of 6)	123	NM_052823	11936	Mm.22742	NM_007503	ENSMUSG00000059412	Fxyd2	Atp1g1	FXYD domain-containing ion transport regulator 2	protein-coding
mm_115107.1	chr13	103356402	103356410	+	1	NA	Intergenic	Intergenic	-21914	NM_175171	328329	Mm.202606	NM_175171	ENSMUSG00000034751	Mast4	4930420O11Rik|AI642422|mKIAA0303	microtubule associated serine/threonine kinase family member 4	protein-coding
mm_113786.1	chr13	45516980	45517025	+	1	NA	exon (NM_025508, exon 3 of 9)	exon (NM_025508, exon 3 of 9)	9558	NM_025508	66355	Mm.290802	NM_025508	ENSMUSG00000000253	Gmpr	2310004P21Rik|AV028449|GMPR 1	guanosine monophosphate reductase	protein-coding
mm_35205.1	chr4	19526587	19526588	-	1	NA	intron (NM_027769, intron 13 of 15)	intron (NM_027769, intron 13 of 15)	43517	NM_027769	70568	Mm.38390	NM_027769	ENSMUSG00000028228	Cpne3	5430428M23Rik|5730450C07Rik|C85108|CPN3	copine III	protein-coding
mm_27871.1	chr3	79162843	79162853	-	1	NA	Intergenic	B3|SINE|B2	-16973	NM_001099624	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_20443.1	chr2	129309172	129309176	-	1	NA	intron (NM_010554, intron 1 of 6)	intron (NM_010554, intron 1 of 6)	798	NM_010554	16175	Mm.15534	NM_010554	ENSMUSG00000027399	Il1a	Il-1a	interleukin 1 alpha	protein-coding
mm_32665.1	chr4	115332020	115332035	+	1	NA	3' UTR (NM_177406, exon 12 of 12)	3' UTR (NM_177406, exon 12 of 12)	32981	NM_177406	277753	Mm.276106	NM_177406	ENSMUSG00000066071	Cyp4a12a	BC025936|Cyp4a12	cytochrome P450, family 4, subfamily a, polypeptide 12a	protein-coding
mm_139246.1	chr17	47734203	47734235	+	1	NA	exon (NM_025973, exon 9 of 9)	exon (NM_025973, exon 9 of 9)	-2818	NM_001161722	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_95577.1	chr11	52407403	52407454	+	1	NA	3' UTR (NM_153117, exon 3 of 3)	3' UTR (NM_153117, exon 3 of 3)	11000	NM_153117	213673	Mm.291979	NM_153117	ENSMUSG00000036275	9530068E07Rik	C85061|Kct2	RIKEN cDNA 9530068E07 gene	protein-coding
mm_92487.1	chr10	78298136	78298146	-	1	NA	intron (NM_053014, intron 2 of 9)	intron (NM_053014, intron 2 of 9)	42066	NR_106119	102465765		NR_106119	ENSMUSG00000098885	Mir7659	Gm27433|mmu-mir-7659	microRNA 7659	ncRNA
mm_123893.1	chr14	72980452	72980466	-	1	NA	Intergenic	CpG	-45144	NR_027860	668489	Mm.158324	NR_027860		Gm9199	EG668489	glycine cleavage system protein H (aminomethyl carrier) pseudogene	pseudo
mm_94442.1	chr11	6320596	6320599	+	1	NA	intron (NM_001252287, intron 4 of 22)	ID_B1|SINE|B4	28039	NM_001252288	18293	Mm.276348	NM_010956	ENSMUSG00000020456	Ogdh	2210403E04Rik|2210412K19Rik|AA409584|d1401|mKIAA4192	oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)	protein-coding
mm_120677.1	chr14	70573844	70573847	+	1	NA	TTS (NM_021877)	TTS (NM_021877)	-4002	NM_153136	213484	Mm.34191	NM_153136	ENSMUSG00000045211	Nudt18	BC036718	nudix (nucleoside diphosphate linked moiety X)-type motif 18	protein-coding
mm_155314.1	chrX	61785367	61785368	+	1	NA	Intergenic	Intergenic	75751	NM_001018087	434784	Mm.23468	NM_001018087	ENSMUSG00000057615	Ldoc1	Gm366|Mar7|Mart7|Sirh7	leucine zipper, down-regulated in cancer 1	protein-coding
mm_16591.1	chr2	4593536	4593570	-	1	NA	intron (NM_001347086, intron 17 of 24)	ORR1E|LTR|ERVL-MaLR	33799	NM_001177844	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding
mm_137454.1	chr17	26560719	26560742	+	1	NA	promoter-TSS (NM_026170)	promoter-TSS (NM_026170)	-782	NM_026170	67458	Mm.30496	NM_026170	ENSMUSG00000001576	Ergic1	1200007D18Rik|maa-136	endoplasmic reticulum-golgi intermediate compartment (ERGIC) 1	protein-coding
mm_139612.1	chr17	57358683	57358723	+	1	NA	promoter-TSS (NM_010130)	promoter-TSS (NM_010130)	17	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_36351.1	chr4	73950815	73950833	-	1	NA	promoter-TSS (NM_027104)	promoter-TSS (NM_027104)	22	NM_027981	71886	Mm.158769	NM_027104	ENSMUSG00000028396	2310002L09Rik	2310003M01Rik|AV083437	RIKEN cDNA 2310002L09 gene	protein-coding
mm_105028.1	chr11	100476730	100476732	-	1	NA	3' UTR (NM_134037, exon 28 of 28)	3' UTR (NM_134037, exon 28 of 28)	1749	NR_130343	102465671		NR_130343	ENSMUSG00000104854	Mir7116	mmu-mir-7116	microRNA 7116	ncRNA
mm_130948.1	chr15	103253498	103253501	-	1	NA	promoter-TSS (NM_001302343)	promoter-TSS (NM_001302343)	-347	NM_001302343	18022	Mm.457989	NM_008685	ENSMUSG00000058794	Nfe2	NF-E2|NF-E2/P45|p45|p45NFE2|p45nf-e2	nuclear factor, erythroid derived 2	protein-coding
mm_146736.1	chr18	15402727	15402786	-	1	NA	5' UTR (NM_001308647, exon 1 of 5)	5' UTR (NM_001308647, exon 1 of 5)	243	NM_001308647	11829	Mm.250786	NM_009700	ENSMUSG00000024411	Aqp4	WCH4	aquaporin 4	protein-coding
mm_28284.1	chr3	88951120	88951133	-	1	NA	promoter-TSS (NM_022994)	promoter-TSS (NM_022994)	-844	NM_001164533	65111	Mm.29028	NM_022994	ENSMUSG00000068921	Dap3	4921514D13Rik|DAP-3|MRP-S29|S29mt	death associated protein 3	protein-coding
mm_3114.1	chr1	134575359	134575362	+	1	NA	intron (NM_152895, intron 1 of 26)	B1_Mus1|SINE|Alu	15182	NM_152895	75605	Mm.28995	NM_152895	ENSMUSG00000042207	Kdm5b	2010009J12Rik|2210016I17Rik|AW556288|D1Ertd202e|Jarid1b|PLU-1|PUT1|Plu1|RBBP2H1A|Rb-Bp2|mKIAA4034	lysine (K)-specific demethylase 5B	protein-coding
mm_70518.1	chr8	12949373	12949383	+	1	NA	promoter-TSS (NM_001159485)	promoter-TSS (NM_001159485)	-40	NM_001159486	17207	Mm.334413	NM_178076	ENSMUSG00000031442	Mcf2l	C130040G20Rik|Dbs|Ost|mKIAA0362	mcf.2 transforming sequence-like	protein-coding
mm_92421.1	chr10	77029540	77029554	-	1	NA	Intergenic	MTC|LTR|ERVL-MaLR	-3192	NM_001199271	20509	Mm.265060	NM_031196	ENSMUSG00000001436	Slc19a1	AI323572|RFC|RFC-1|RFC1	solute carrier family 19 (folate transporter), member 1	protein-coding
mm_147073.1	chr18	35343033	35343036	-	1	NA	intron (NM_030749, intron 4 of 9)	intron (NM_030749, intron 4 of 9)	-128010	NM_178005	107065	Mm.39900	NM_178005	ENSMUSG00000071862	Lrrtm2	AI851755|BB129880|C630011A14Rik|mKIAA0416	leucine rich repeat transmembrane neuronal 2	protein-coding
mm_75209.1	chr8	39605312	39605332	-	1	NA	3' UTR (NM_031195, exon 9 of 9)	3' UTR (NM_031195, exon 9 of 9)	37356	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_32290.1	chr4	103114463	103114475	+	1	NA	promoter-TSS (NM_027696)	promoter-TSS (NM_027696)	79	NM_001286222	71148	Mm.288721	NM_027696	ENSMUSG00000028522	Mier1	4933425I22Rik|5830411K19Rik|er1	MEIR1 treanscription regulator	protein-coding
mm_128963.1	chr15	74832094	74832101	-	1	NA	Intergenic	Intergenic	9546	NM_001033229	110115	Mm.322606	NM_001033229	ENSMUSG00000075604	Cyp11b1	AA389061|CPN1|Cyp11b|Cyp11b-1|FHI	cytochrome P450, family 11, subfamily b, polypeptide 1	protein-coding
mm_82398.1	chr9	14740692	14740696	-	1	NA	promoter-TSS (NM_177905)	promoter-TSS (NM_177905)	39	NM_177905	330890	Mm.334969	NM_177905	ENSMUSG00000036912	Piwil4	9230101H05Rik|Miwi2	piwi-like RNA-mediated gene silencing 4	protein-coding
mm_31432.1	chr4	48124945	48124955	+	1	NA	promoter-TSS (NM_026343)	promoter-TSS (NM_026343)	31	NM_026343	67727	Mm.171334	NM_026343	ENSMUSG00000061455	Stx17	4833418L03Rik|6330411F21Rik|9030425C21Rik|AW048351	syntaxin 17	protein-coding
mm_25635.1	chr3	120356592	120356593	+	1	NA	Intergenic	Intergenic	530140	NR_130170	320739	Mm.388474	NR_130170		6530403H02Rik	-	RIKEN cDNA 6530403H02 gene	ncRNA
mm_135332.1	chr16	38828746	38828754	-	1	NA	promoter-TSS (NM_029042)	promoter-TSS (NM_029042)	-1	NM_029042	74663	Mm.50263	NM_029042	ENSMUSG00000022798	4930435E12Rik	TSCPA	RIKEN cDNA 4930435E12 gene	protein-coding
mm_12137.1	chr2	61711788	61711812	+	1	NA	5' UTR (NM_021526, exon 1 of 12)	5' UTR (NM_021526, exon 1 of 12)	106	NM_021526	59029	Mm.218198	NM_021526	ENSMUSG00000026914	Psmd14	2610312C03Rik|3200001M20Rik|AA986732|Pad1|Poh1|rpm11	proteasome (prosome, macropain) 26S subunit, non-ATPase, 14	protein-coding
mm_73032.1	chr8	94180078	94180084	+	1	NA	intron (NM_013602, intron 2 of 2)	intron (NM_013602, intron 2 of 2)	992	NM_013602	17748	Mm.192991	NM_013602	ENSMUSG00000031765	Mt1	MT-I|Mt-1	metallothionein 1	protein-coding
mm_64658.1	chr7	4164248	4164266	-	1	NA	intron (NM_021454, intron 1 of 2)	intron (NM_021454, intron 1 of 2)	442	NM_021454	58804	Mm.34268	NM_021454	ENSMUSG00000063838	Cdc42ep5	1700027J19Rik|2010007O02Rik|Borg3|C85526|CEP5	CDC42 effector protein (Rho GTPase binding) 5	protein-coding
mm_52787.1	chr6	121257248	121257261	+	1	NA	intron (NM_011909, intron 4 of 10)	B1F2|SINE|Alu	11348	NM_011909	24110	Mm.326911	NM_011909	ENSMUSG00000030107	Usp18	1110058H21Rik|AW047653|UBP43|Ubp15	ubiquitin specific peptidase 18	protein-coding
mm_105928.1	chr11	115116633	115116674	-	1	NA	3' UTR (NM_001169153, exon 7 of 7)	3' UTR (NM_001169153, exon 7 of 7)	17339	NM_001347648	246746	Mm.277387	NM_145634	ENSMUSG00000047798	Cd300lf	CLIM1|CLM-1|CLM1|Digr2|F730004D16Rik|IREM1|IgSF13|LMIR3|Pigr3	CD300 molecule like family member F	protein-coding
mm_103978.1	chr11	84823669	84823695	-	1	NA	intron (NM_177564, intron 2 of 6)	intron (NM_177564, intron 2 of 6)	-4167	NM_145433	217038	Mm.280825	NM_145433	ENSMUSG00000018405	Mrm1	A530065E19Rik|ENSMUSG00000054212	mitochondrial rRNA methyltransferase 1	protein-coding
mm_50453.1	chr6	48906157	48906167	+	1	NA	exon (NM_001161622, exon 2 of 5)	exon (NM_001161622, exon 2 of 5)	1176	NM_001161621	76507	Mm.213898	NM_029638	ENSMUSG00000029811	Aoc1	1600012D06Rik|Abp1|DAO	amine oxidase, copper-containing 1	protein-coding
mm_130156.1	chr15	91191514	91191525	-	1	NA	exon (NM_011994, exon 1 of 10)	exon (NM_011994, exon 1 of 10)	288	NM_011994	26874	Mm.295456	NM_011994	ENSMUSG00000055782	Abcd2	ABC39|ALDL1|ALDR|ALDRP	ATP-binding cassette, sub-family D (ALD), member 2	protein-coding
mm_92654.1	chr10	80399553	80399563	-	1	NA	promoter-TSS (NM_013595)	promoter-TSS (NM_013595)	-27	NM_001306143	17192	Mm.7142	NM_013595	ENSMUSG00000035478	Mbd3	AI181826|AU019209	methyl-CpG binding domain protein 3	protein-coding
mm_159644.1	chr4	144190492	144190492	+	1	NA	promoter-TSS (NM_198661)	promoter-TSS (NM_198661)	-225	NM_198661	381570	Mm.332028	NM_198661	ENSMUSG00000066030	Oog2	C85069	oogenesin 2	protein-coding
mm_49234.1	chr6	17281192	17281204	+	1	NA	promoter-TSS (NM_001277756)	promoter-TSS (NM_001277756)	13	NM_016900	12390	Mm.396075	NM_016900	ENSMUSG00000000058	Cav2	AI447843	caveolin 2	protein-coding
mm_151996.1	chr19	5894071	5894097	-	1	NA	promoter-TSS (NM_198634)	promoter-TSS (NM_198634)	23	NM_198634	332359	Mm.329642	NM_198634	ENSMUSG00000044390	Tigd3	-	tigger transposable element derived 3	protein-coding
mm_133068.1	chr16	58670263	58670362	+	1	NA	5' UTR (NM_007757, exon 1 of 7)	5' UTR (NM_007757, exon 1 of 7)	104	NM_007757	12892	Mm.291519	NM_007757	ENSMUSG00000022742	Cpox	CPX|Cpo|HCP|cac|nct	coproporphyrinogen oxidase	protein-coding
mm_50823.1	chr6	54595168	54595243	+	1	NA	promoter-TSS (NM_001164361)	promoter-TSS (NM_001164361)	94	NM_001164361	231999	Mm.35416	NM_001001335	ENSMUSG00000005225	Plekha8	6330400G01|AA517676|BC052360|Fapp-2|Fapp2	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 8	protein-coding
mm_135989.1	chr16	75092975	75092997	-	1	NA	Intergenic	Intergenic	493075	NM_001252513	320355	Mm.99517	NM_177142	ENSMUSG00000032948	Lipi	D930038D03Rik|lpd1	lipase, member I	protein-coding
mm_140128.1	chr17	79615209	79615231	+	1	NA	intron (NM_201361, intron 1 of 10)	CpG	320	NM_201361	381110	Mm.209801	NM_201361	ENSMUSG00000036368	Rmdn2	AW061290|Fam82a1|RMD-2|mRMD-2	regulator of microtubule dynamics 2	protein-coding
mm_5370.1	chr1	29485935	29485939	-	1	NA	Intergenic	Intergenic	64449	NR_105760	102465174		NR_105760	ENSMUSG00000099257	Mir6342	Gm27268|mmu-mir-6342	microRNA 6342	ncRNA
mm_92736.1	chr10	80918068	80918078	-	1	NA	exon (NM_010722, exon 1 of 12)	exon (NM_010722, exon 1 of 12)	172	NM_010722	16907	Mm.7362	NM_010722	ENSMUSG00000062075	Lmnb2	-	lamin B2	protein-coding
mm_152663.1	chr19	14083437	14083440	-	1	NA	Intergenic	RLTR10C|LTR|ERVK	164416	NM_001011850	258151	Mm.377361	NM_001011850	ENSMUSG00000062314	Olfr1505	MOR211-4P	olfactory receptor 1505	protein-coding
mm_9505.1	chr1	173735217	173735226	-	1	NA	exon (NM_001204910, exon 3 of 8)	exon (NM_001204910, exon 3 of 8)	6588	NM_001204910	226691	Mm.440876	NM_001204910	ENSMUSG00000073490	Ifi207	AI607873|Pyhin-A	interferon activated gene 207	protein-coding
mm_155578.1	chrX	78070318	78070324	+	1	NA	Intergenic	L1VL4|LINE|L1	21053	NM_008754	18249	Mm.430771	NM_008754	ENSMUSG00000067684	Obp1a	OBP-1a|OBP5	odorant binding protein IA	protein-coding
mm_92022.1	chr10	62422399	62422409	-	1	NA	promoter-TSS (NM_145419)	promoter-TSS (NM_145419)	53	NM_145419	216019	Mm.213213	NM_145419	ENSMUSG00000020080	Hkdc1	BC016235	hexokinase domain containing 1	protein-coding
mm_149792.1	chr19	23141184	23141263	+	1	NA	promoter-TSS (NM_010638)	promoter-TSS (NM_010638)	-3	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_38902.1	chr4	149909681	149909694	-	1	NA	intron (NM_029035, intron 1 of 2)	intron (NM_029035, intron 1 of 2)	45319	NM_029035	74646	Mm.30	NM_029035	ENSMUSG00000039911	Spsb1	1110014L01Rik|4930422J18Rik|AI596360|AI854583|SSB-1|SSB1	splA/ryanodine receptor domain and SOCS box containing 1	protein-coding
mm_122616.1	chr14	51105414	51105427	-	1	NA	3' UTR (NM_201239, exon 2 of 2)	3' UTR (NM_201239, exon 2 of 2)	9420	NM_201239	58809	Mm.202665	NM_021472	ENSMUSG00000021876	Rnase4	C730049F20Rik|Rab1	ribonuclease, RNase A family 4	protein-coding
mm_112506.1	chr13	8885633	8885656	+	1	NA	promoter-TSS (NM_145360)	promoter-TSS (NM_145360)	38	NM_145360	319554	Mm.29847	NM_145360	ENSMUSG00000058258	Idi1	4832416K17Rik	isopentenyl-diphosphate delta isomerase	protein-coding
mm_139108.1	chr17	47325614	47325617	+	1	NA	intron (NM_001097623, intron 11 of 19)	intron (NM_001097623, intron 11 of 19)	-43272	NM_001146212	64657	Mm.216250	NM_183086	ENSMUSG00000034729	Mrps10	1110038B19Rik|AW743084|Rpms10	mitochondrial ribosomal protein S10	protein-coding
mm_129320.1	chr15	77765767	77765780	-	1	NA	exon (NM_022410, exon 35 of 41)	exon (NM_022410, exon 35 of 41)	-10544	NM_001081970	239552	Mm.125650	NM_001081970	ENSMUSG00000056656	Apol8	9830006J20Rik|APOL-II|Apol2	apolipoprotein L 8	protein-coding
mm_116363.1	chr13	40730751	40730762	-	1	NA	promoter-TSS (NM_001122948)	promoter-TSS (NM_001122948)	-299	NM_001122948	21418	Mm.85544	NM_011547	ENSMUSG00000021359	Tfap2a	AP-2|AP2alpha|Ap-2 (a)|Ap2|Ap2tf|Tcfap2a	transcription factor AP-2, alpha	protein-coding
mm_76935.1	chr8	105939780	105939787	-	1	NA	exon (NM_008490, exon 6 of 6)	exon (NM_008490, exon 6 of 6)	-1391	NM_013640	19171	Mm.787	NM_013640	ENSMUSG00000031897	Psmb10	Mecl-1|Mecl1	proteasome (prosome, macropain) subunit, beta type 10	protein-coding
mm_13057.1	chr2	91114259	91114283	+	1	NA	exon (NM_011355, exon 4 of 5)	exon (NM_011355, exon 4 of 5)	-3873	NM_008653	17868	Mm.10728	NM_008653	ENSMUSG00000002100	Mybpc3	-	myosin binding protein C, cardiac	protein-coding
mm_39559.1	chr5	22908334	22908359	+	1	NA	intron (NM_001081231, intron 1 of 3)	intron (NM_001081231, intron 1 of 3)	-161462	NR_027362	330052	Mm.459265	NR_027362	ENSMUSG00000105076	A930003O13Rik	-	RIKEN cDNA A930003O13 gene	ncRNA
mm_88958.1	chr10	81393044	81393058	+	1	NA	promoter-TSS (NM_001099917)	promoter-TSS (NM_001099917)	-13	NM_001099917	72273	Mm.253147	NM_001099917	ENSMUSG00000078439	Smim24	2210404O07Rik	small integral membrane protein 24	protein-coding
mm_126113.1	chr15	78260689	78260707	+	1	NA	exon (NM_008677, exon 8 of 10)	exon (NM_008677, exon 8 of 10)	15887	NM_008677	17972	Mm.2068	NM_008677	ENSMUSG00000071715	Ncf4	AI451400|p40phox	neutrophil cytosolic factor 4	protein-coding
mm_123246.1	chr14	60425328	60425329	-	1	NA	Intergenic	Intergenic	47042	NM_001164705	72125	Mm.275499	NM_028113	ENSMUSG00000021986	Amer2	2600011E07Rik|Fam123a	APC membrane recruitment 2	protein-coding
mm_91802.1	chr10	53751094	53751164	-	1	NA	promoter-TSS (NM_001081428)	promoter-TSS (NM_001081428)	-220	NM_001081428	75906	Mm.436785	NM_001081428	ENSMUSG00000019856	Fam184a	3110012E06Rik|4930438C08Rik|4930589M24Rik	family with sequence similarity 184, member A	protein-coding
mm_45611.1	chr5	75835242	75835256	-	1	NA	Intergenic	Intergenic	143179	NM_010612	16542	Mm.285	NM_010612	ENSMUSG00000062960	Kdr	6130401C07|Flk-1|Flk1|Krd-1|Ly73|VEGFR-2|VEGFR2|sVEGFR-2	kinase insert domain protein receptor	protein-coding
mm_168080.1	chr10	11609243	11609244	+	1	NA	promoter-TSS (NM_013898)	promoter-TSS (NM_013898)	19	NM_013898	30058	Mm.214504	NM_013898	ENSMUSG00000048007	Timm8a1	DXHXS1274E|Ddp1|Fci-12|Tim8a|Timm8a	translocase of inner mitochondrial membrane 8A1	protein-coding
mm_41888.1	chr5	105495541	105495546	+	1	NA	Intergenic	Intergenic	-23928	NM_133897	100604	Mm.319847	NM_133897	ENSMUSG00000054720	Lrrc8c	AD158|AI326115|E430036I04Rik|fad158	leucine rich repeat containing 8 family, member C	protein-coding
mm_65751.1	chr7	28561102	28561112	-	1	NA	promoter-TSS (NR_106016)	promoter-TSS (NR_106016)	-123	NR_106016	102466795		NR_106016	ENSMUSG00000098558	Mir7049	Gm27277|mmu-mir-7049	microRNA 7049	ncRNA
mm_73835.1	chr8	117460857	117460881	+	1	NA	3' UTR (NM_001163262, exon 21 of 21)	3' UTR (NM_001163262, exon 21 of 21)	1604	NR_106046	102465653		NR_106046	ENSMUSG00000098483	Mir7078	Gm27386|mmu-mir-7078	microRNA 7078	ncRNA
mm_7550.1	chr1	124564844	124564891	-	1	NA	Intergenic	Lx2|LINE|L1	-519308	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_20199.1	chr2	124711096	124711106	-	1	NA	Intergenic	Intergenic	57520	NM_199239	214968	Mm.330536	NM_172537	ENSMUSG00000027200	Sema6d	1110067B02Rik|AA409156|D330011G23|mKIAA1479	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	protein-coding
mm_165682.1	chr3	90692876	90692921	-	1	NA	exon (NM_001281852, exon 3 of 3)	exon (NM_001281852, exon 3 of 3)	2823	NM_001281852	20202	Mm.2128	NM_009114	ENSMUSG00000056071	S100a9	60B8Ag|AW546964|BEE22|Cagb|GAGB|L1Ag|MRP14|p14	S100 calcium binding protein A9 (calgranulin B)	protein-coding
mm_173105.1	chrX	15421535	15421540	+	1	NA	Intergenic	MT2_Mm|LTR|ERVL	-310048	NR_033171	67395	Mm.50369	NM_026128	ENSMUSG00000045217	Ppp1r2-ps9	4930403L05Rik	protein phosphatase 1, regulatory (inhibitor) subunit 2, pseudogene 9	pseudo
mm_102558.1	chr11	61453858	61453866	-	1	NA	5' UTR (NM_009548, exon 1 of 15)	5' UTR (NM_009548, exon 1 of 15)	130	NM_009548	22671	Mm.89201	NM_009548	ENSMUSG00000010086	Rnf112	ZNF179|Zfp179|bfp|neurolastin	ring finger protein 112	protein-coding
mm_124190.1	chr14	98068603	98068605	-	1	NA	intron (NM_007826, intron 1 of 11)	intron (NM_007826, intron 1 of 11)	101161	NM_001038610	13134	Mm.320593	NM_007826	ENSMUSG00000055639	Dach1	Dac|Dach	dachshund 1 (Drosophila)	protein-coding
mm_48295.1	chr5	138227381	138227418	-	1	NA	intron (NM_001013773, intron 1 of 5)	URR1B|DNA|hAT-Charlie	1495	NM_001013773	381680	Mm.156846	NM_001013773	ENSMUSG00000047592	Nxpe5	-	neurexophilin and PC-esterase domain family, member 5	protein-coding
mm_34620.1	chr4	150563508	150563510	+	1	NA	intron (NM_001085492, intron 11 of 22)	intron (NM_001085492, intron 11 of 22)	88665	NM_173774	242773	Mm.29280	NM_173774	ENSMUSG00000039838	Slc45a1	C230078B22|Dnb5	solute carrier family 45, member 1	protein-coding
mm_116493.1	chr13	44869661	44869671	-	1	NA	intron (NM_001205044, intron 4 of 18)	LSU-rRNA_Hsa|rRNA|rRNA	132430	NM_025772	94245	Mm.352311	NM_025772	ENSMUSG00000057531	Dtnbp1	5430437B18Rik|AW048963|Bloc1s8|dysbindin|sdy	dystrobrevin binding protein 1	protein-coding
mm_2634.1	chr1	121486950	121486961	+	1	NA	intron (NM_001025156, intron 18 of 23)	B3A|SINE|B2	41510	NM_010483	15564	Mm.4833	NM_010483	ENSMUSG00000050534	Htr5b	5-Ht5b	5-hydroxytryptamine (serotonin) receptor 5B	protein-coding
mm_171724.1	chr4	86856801	86856815	-	1	NA	exon (NM_009096, exon 2 of 5)	exon (NM_009096, exon 2 of 5)	559	NM_009096	20104	Mm.379007	NM_009096	ENSMUSG00000028495	Rps6	S6R	ribosomal protein S6	protein-coding
mm_98284.1	chr11	89065815	89065826	+	1	NA	intron (NR_110336, intron 1 of 3)	intron (NR_110336, intron 1 of 3)	5069	NR_110336	414094	Mm.124287	NM_001001497		Dgkeos	A930013B10Rik	diacylglycerol kinase, epsilon, opposite strand	ncRNA
mm_88205.1	chr10	70182082	70182092	+	1	NA	intron (NM_001111121, intron 6 of 8)	intron (NM_001111121, intron 6 of 8)	-22577	NM_001304739	69563	Mm.64672	NM_001304739	ENSMUSG00000019933	Mrln	2310015B20Rik|Mln	myoregulin	protein-coding
mm_28975.1	chr3	101097066	101097070	-	1	NA	intron (NM_011197, intron 1 of 8)	B1F2|SINE|Alu	13098	NM_011197	19221	Mm.24807	NM_011197	ENSMUSG00000027864	Ptgfrn	4833445A08Rik|AU042434|CD9P-1|FPRP|Trim45	prostaglandin F2 receptor negative regulator	protein-coding
mm_60734.1	chr7	45434936	45434973	+	1	NA	promoter-TSS (NM_011304)	promoter-TSS (NM_011304)	115	NM_030678	14936	Mm.275654	NM_030678	ENSMUSG00000003865	Gys1	Gys3|MGS	glycogen synthase 1, muscle	protein-coding
mm_92875.1	chr10	82492541	82492548	-	1	NA	promoter-TSS (NM_001255990)	promoter-TSS (NM_001255990)	74	NM_001255990	432480	Mm.280394	NM_001255990	ENSMUSG00000094186	Gm1553	Lcrn	predicted gene 1553	protein-coding
mm_41978.1	chr5	107497719	107497759	+	1	NA	promoter-TSS (NM_001007574)	promoter-TSS (NM_001007574)	-6	NM_001007574	231570	Mm.261891	NM_001007574	ENSMUSG00000044060	A830010M20Rik	AI849226|Kiaa1107|mKIAA1107	RIKEN cDNA A830010M20 gene	protein-coding
mm_54966.1	chr6	48725562	48725603	-	1	NA	TTS (NM_146167)	TTS (NM_146167)	6961	NM_146167	231932	Mm.30479	NM_146167	ENSMUSG00000043931	Gimap7	IAN7|Ian3	GTPase, IMAP family member 7	protein-coding
mm_160562.1	chr9	53946875	53946875	-	1	NA	5' UTR (NM_177769, exon 2 of 11)	5' UTR (NM_177769, exon 2 of 11)	28426	NM_177769	270162	Mm.259791	NM_177769	ENSMUSG00000041986	Elmod1	4831417L10|AI428506|AI834991	ELMO/CED-12 domain containing 1	protein-coding
mm_133724.1	chr16	93776710	93776723	+	1	NA	intron (NM_027293, intron 21 of 36)	intron (NM_027293, intron 21 of 36)	-55405	NM_001045529	338467	Mm.287329	NM_001045529	ENSMUSG00000039456	Morc3	1110051N18Rik|AI452146|BF318192|D16Jhu32e|NXP2|Zcwcc3	microrchidia 3	protein-coding
mm_13769.1	chr2	118598233	118598267	+	1	NA	promoter-TSS (NM_009773)	promoter-TSS (NM_009773)	39	NM_009773	12236	Mm.29133	NM_009773	ENSMUSG00000040084	Bub1b	AU045529|BUBR1	BUB1B, mitotic checkpoint serine/threonine kinase	protein-coding
mm_83168.1	chr9	40531104	40531127	-	1	NA	Intergenic	Intergenic	-75351	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_63675.1	chr7	130525747	130525763	+	1	NA	Intergenic	Intergenic	-5386	NM_001271343	11907	Mm.216321	NM_013799	ENSMUSG00000030850	Ate1	AI225793|AW547406	arginyltransferase 1	protein-coding
mm_63795.1	chr7	132931113	132931123	+	1	NA	Intergenic	CpG	-18504	NM_207302	360216	Mm.389984	NM_207302	ENSMUSG00000030967	Zranb1	9330160G10Rik|D7Wsu87e|Gm1956|Trabid	zinc finger, RAN-binding domain containing 1	protein-coding
mm_45553.1	chr5	73156371	73156390	-	1	NA	intron (NM_028194, intron 3 of 62)	Lx8|LINE|L1	100238	NM_028194	72313	Mm.260594	NM_028194	ENSMUSG00000070733	Fryl	2010313D22Rik|2310004H21Rik|2510002A14Rik|9030227G01Rik|mKIAA0826	FRY like transcription coactivator	protein-coding
mm_53565.1	chr6	137252367	137252388	+	1	NA	promoter-TSS (NM_011216)	promoter-TSS (NM_011216)	78	NM_011216	19277	Mm.186361	NM_011216	ENSMUSG00000030223	Ptpro	D28|GLEPP1|PTPBK|PTPROt|PTPU2|PTPoc|PTPphi|Ptpn15|R-PTP-O	protein tyrosine phosphatase, receptor type, O	protein-coding
mm_45304.1	chr5	65421582	65421590	-	1	NA	intron (NM_009466, intron 6 of 11)	ID4_|SINE|ID	14256	NM_009466	22235	Mm.344831	NM_009466	ENSMUSG00000029201	Ugdh	Udpgdh	UDP-glucose dehydrogenase	protein-coding
mm_70226.1	chr7	145283916	145283941	-	1	NA	promoter-TSS (NM_146206)	promoter-TSS (NM_146206)	83	NR_132644	233979	Mm.102235	NM_146206	ENSMUSG00000048677	Tpcn2	D830047E22Rik|Gm35086	two pore segment channel 2	protein-coding
mm_75483.1	chr8	48668711	48668731	-	1	NA	intron (NM_011857, intron 1 of 28)	intron (NM_011857, intron 1 of 28)	5969	NM_001145937	23965	Mm.42191	NM_011857	ENSMUSG00000031561	Tenm3	2610100B16Rik|Odz1|Odz3|Ten-m3|mKIAA1455	teneurin transmembrane protein 3	protein-coding
mm_91882.1	chr10	59800265	59800273	-	1	NA	intron (NM_001291443, intron 9 of 12)	intron (NM_001291443, intron 9 of 12)	-79322	NM_019965	56709	Mm.103610	NM_019965	ENSMUSG00000020109	Dnajb12	Dj10|mDj10	DnaJ heat shock protein family (Hsp40) member B12	protein-coding
mm_60820.1	chr7	45705331	45705349	+	1	NA	promoter-TSS (NM_016974)	promoter-TSS (NM_016974)	93	NM_016974	13170	Mm.24222	NM_016974	ENSMUSG00000059824	Dbp	-	D site albumin promoter binding protein	protein-coding
mm_145181.1	chr18	48045330	48045348	+	1	NA	promoter-TSS (NM_001025388)	promoter-TSS (NM_001025388)	4	NM_001025388	433182	Mm.70666	NM_001025388	ENSMUSG00000059040	Eno1b	EG433182|Eno1|Gm5506	enolase 1B, retrotransposed	protein-coding
mm_85272.1	chr9	99436630	99436641	-	1	NA	promoter-TSS (NM_008624)	promoter-TSS (NM_008624)	77	NM_008624	17532	Mm.2045	NM_008624	ENSMUSG00000032470	Mras	2900078C09Rik|AI326250	muscle and microspikes RAS	protein-coding
mm_127071.1	chr15	97374200	97374206	+	1	NA	intron (NM_172293, intron 5 of 5)	intron (NM_172293, intron 5 of 5)	-126916	NM_001164602	105827	Mm.24005	NM_178114	ENSMUSG00000048218	Amigo2	AI415330|AMIGO-2|AW208913|Ali1	adhesion molecule with Ig like domain 2	protein-coding
mm_136829.1	chr17	12615284	12615290	+	1	NA	exon (NM_013667, exon 9 of 11)	exon (NM_013667, exon 9 of 11)	31098	NM_013667	20518	Mm.17322	NM_013667	ENSMUSG00000040966	Slc22a2	Oct2|Orct2	solute carrier family 22 (organic cation transporter), member 2	protein-coding
mm_173208.1	chrX	71197083	71197094	+	1	NA	Intergenic	Intergenic	-13679	NM_001164190	17772	Mm.274981	NM_019926	ENSMUSG00000031337	Mtm1	AF073996|Mtm|mKIAA4176	X-linked myotubular myopathy gene 1	protein-coding
mm_47260.1	chr5	121821525	121821529	-	1	NA	intron (NM_001306126, intron 3 of 8)	ID_B1|SINE|B4	-2254	NR_105998	102465624		NR_105998	ENSMUSG00000099063	Mir7031	Gm27859|mmu-mir-7031	microRNA 7031	ncRNA
mm_6752.1	chr1	84036688	84036699	-	1	NA	3' UTR (NM_001003948, exon 3 of 3)	3' UTR (NM_001003948, exon 3 of 3)	182268	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_163445.1	chr12	86884071	86884081	-	1	NA	5' UTR (NM_145836, exon 1 of 1)	5' UTR (NM_145836, exon 1 of 1)	738	NM_145836	238330	Mm.248358	NM_145836	ENSMUSG00000034168	Irf2bpl	6430527G18Rik|Eap1	interferon regulatory factor 2 binding protein-like	protein-coding
mm_80273.1	chr9	72985411	72985424	+	1	NA	promoter-TSS (NM_001286546)	promoter-TSS (NM_001286546)	-41	NM_001198789	546143	Mm.260946	NM_001198789	ENSMUSG00000086158	Ccpg1os	EG546143|Gm5918	cell cycle progression 1, opposite strand	protein-coding
mm_86076.1	chr9	114779256	114779261	-	1	NA	intron (NM_001252479, intron 1 of 3)	RLTR25B|LTR|ERVK	2735	NM_133978	102545	Mm.35600	NM_133978	ENSMUSG00000032436	Cmtm7	AI481279|Cklfsf7|LNV	CKLF-like MARVEL transmembrane domain containing 7	protein-coding
mm_43436.1	chr5	136089838	136089851	+	1	NA	intron (NM_001039103, intron 2 of 19)	MIRb|SINE|MIR	5928	NM_001039103	54153	Mm.290655	NM_133914	ENSMUSG00000004952	Rasa4	AA793972|AW112107|BB079060|CAPRI|GAPL	RAS p21 protein activator 4	protein-coding
mm_83109.1	chr9	40346296	40346337	-	1	NA	intron (NM_172768, intron 2 of 19)	intron (NM_172768, intron 2 of 19)	12844	NR_040728	73558	Mm.398307	NR_040728		1700110K17Rik	-	RIKEN cDNA 1700110K17 gene	ncRNA
mm_164246.1	chr15	95803015	95803017	+	1	NA	intron (NM_175344, intron 1 of 19)	intron (NM_175344, intron 1 of 19)	12173	NM_001253813	105722	Mm.38087	NM_175344	ENSMUSG00000064210	Ano6	2900059G15Rik|AA407480|AW554778|F730003B03Rik|Tmem16f	anoctamin 6	protein-coding
mm_28784.1	chr3	95995641	95995659	-	1	NA	exon (NM_023320, exon 2 of 6)	exon (NM_023320, exon 2 of 6)	189	NM_023320	67220	Mm.458147	NM_023320	ENSMUSG00000015745	Plekho1	2810052M02Rik|CKIP-1|Ckip1|JZA-20|Jza2	pleckstrin homology domain containing, family O member 1	protein-coding
mm_19214.1	chr2	84637688	84637690	-	1	NA	intron (NM_007615, intron 1 of 19)	PB1D10|SINE|Alu	12821	NM_001085453	12388	Mm.35738	NM_007615	ENSMUSG00000034101	Ctnnd1	AA409437|AU019353|Catns|Ctnnd|P120|mKIAA0384	catenin (cadherin associated protein), delta 1	protein-coding
mm_5867.1	chr1	53776679	53776700	-	1	NA	intron (NM_133810, intron 1 of 7)	intron (NM_133810, intron 1 of 7)	8526	NM_133810	98267	Mm.25559	NM_133810	ENSMUSG00000026094	Stk17b	3110009A03Rik|AI120141|Drak2	serine/threonine kinase 17b (apoptosis-inducing)	protein-coding
mm_124526.1	chr14	122233552	122233556	-	1	NA	promoter-TSS (NR_015532)	promoter-TSS (NR_015532)	84	NR_015532	68245	Mm.443285	NR_015532	ENSMUSG00000100585	1700108J01Rik	-	RIKEN cDNA 1700108J01 gene	ncRNA
mm_119955.1	chr14	55062936	55062944	+	1	NA	exon (NM_001039198, exon 10 of 10)	exon (NM_001039198, exon 10 of 10)	-10151	NR_004444	432855	Mm.490799	NR_004444	ENSMUSG00000093452	Zfhx2os	Zfhx2as	zinc finger homeobox 2, opposite strand	ncRNA
mm_77400.1	chr8	120489429	120489453	-	1	NA	intron (NM_198671, intron 1 of 15)	CpG-14576	575	NM_198671	382034	Mm.334856	NM_198671	ENSMUSG00000031822	Gse1	2210013I18Rik|mKIAA0182	genetic suppressor element 1, coiled-coil protein	protein-coding
mm_12599.1	chr2	74675069	74675086	+	1	NA	promoter-TSS (NM_008274)	promoter-TSS (NM_008274)	64	NM_008274	15432	Mm.57124	NM_008274	ENSMUSG00000001823	Hoxd12	Hox-4.7|Hox-5.6	homeobox D12	protein-coding
mm_105213.1	chr11	102163602	102163632	-	1	NA	3' UTR (NM_172947, exon 5 of 5)	3' UTR (NM_172947, exon 5 of 5)	-7210	NM_029649	76547	Mm.46529	NM_029649	ENSMUSG00000020921	Tmem101	2610511E22Rik	transmembrane protein 101	protein-coding
mm_144217.1	chr18	9745540	9745583	+	1	NA	intron (NM_130449, intron 2 of 9)	L1_Mur2|LINE|L1	37913	NM_130449	140792	Mm.218571	NM_130449	ENSMUSG00000036103	Colec12	CL-P1|SRCL|Scara4	collectin sub-family member 12	protein-coding
mm_155263.1	chrX	58030623	58030636	+	1	NA	promoter-TSS (NM_009575)	promoter-TSS (NM_009575)	1	NM_009575	22773	Mm.255890	NM_009575	ENSMUSG00000067860	Zic3	Bn|Ka	zinc finger protein of the cerebellum 3	protein-coding
mm_40574.1	chr5	63840235	63840245	+	1	NA	intron (NM_029554, intron 1 of 3)	intron (NM_029554, intron 1 of 3)	27745	NM_029554	76261	Mm.38143	NM_029554	ENSMUSG00000060512	0610040J01Rik	AI662686	RIKEN cDNA 0610040J01 gene	protein-coding
mm_151158.1	chr19	53185816	53185826	+	1	NA	intron (NM_013758, intron 1 of 15)	intron (NM_013758, intron 1 of 15)	41824	NM_013758	27360	Mm.426080	NM_013758	ENSMUSG00000025026	Add3	AI463285|R75380	adducin 3 (gamma)	protein-coding
mm_98132.1	chr11	87471593	87471603	+	1	NA	intron (NM_001199293, intron 2 of 30)	intron (NM_001199293, intron 2 of 30)	44007	NM_001199293	83560	Mm.440758	NM_031386	ENSMUSG00000010342	Tex14	C85585	testis expressed gene 14	protein-coding
mm_98048.1	chr11	85739882	85739892	+	1	NA	intron (NM_138681, intron 24 of 25)	intron (NM_138681, intron 24 of 25)	-20143	NR_045875	71489	Mm.442482	NR_045875	ENSMUSG00000086199	Bcas3os1	8430403D17Rik	breast carcinoma amplified sequence 3, opposite strand 1	ncRNA
mm_143139.1	chr17	57218873	57218892	-	1	NA	exon (NM_009778, exon 20 of 41)	exon (NM_009778, exon 20 of 41)	-1654	NR_105944	102465591		NR_105944	ENSMUSG00000099066	Mir6978	Gm27858|mmu-mir-6978	microRNA 6978	ncRNA
mm_75766.1	chr8	69974319	69974333	-	1	NA	promoter-TSS (NM_001113346)	promoter-TSS (NM_001113346)	57	NM_001113346	234366	Mm.270044	NM_145596	ENSMUSG00000036180	Gatad2a	1110066C11Rik|BC031407|C80248	GATA zinc finger domain containing 2A	protein-coding
mm_65801.1	chr7	28949671	28949679	-	1	NA	intron (NM_021895, intron 1 of 20)	intron (NM_021895, intron 1 of 20)	12605	NM_021895	60595	Mm.81144	NM_021895	ENSMUSG00000054808	Actn4	C77391	actinin alpha 4	protein-coding
mm_168335.1	chr11	118308886	118308894	+	1	NA	intron (NM_011594, intron 4 of 4)	RLTR9D|LTR|ERVK	-18646	NM_001033528	72344	Mm.232293	NM_001033528	ENSMUSG00000033909	Usp36	2700002L06Rik|mKIAA1453	ubiquitin specific peptidase 36	protein-coding
mm_99778.1	chr11	107335486	107335500	+	1	NA	intron (NM_145823, intron 2 of 9)	L3|LINE|CR1	135227	NM_145823	71795	Mm.397413	NM_145823	ENSMUSG00000040430	Pitpnc1	1110020B03Rik|5830436L09Rik|AI662802|AI851387|C330017I21Rik|Dnr411|RDGBB|RDGBB1|rdgB-beta	phosphatidylinositol transfer protein, cytoplasmic 1	protein-coding
mm_102733.1	chr11	67249254	67249272	-	1	NA	exon (NM_010855, exon 17 of 40)	exon (NM_010855, exon 17 of 40)	11451	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_135430.1	chr16	45382776	45382790	-	1	NA	3' UTR (NM_010818, exon 6 of 6)	3' UTR (NM_010818, exon 6 of 6)	26270	NM_010818	17470	Mm.245851	NM_010818	ENSMUSG00000022661	Cd200	Mox2|OX2	CD200 antigen	protein-coding
mm_41479.1	chr5	91962923	91962942	+	1	NA	promoter-TSS (NR_028429)	promoter-TSS (NR_028429)	50	NR_028429	381650	Mm.159453	NR_028429	ENSMUSG00000102644	Thap6	4930534K21Rik|AI448650	THAP domain containing 6	pseudo
mm_126992.1	chr15	94629083	94629129	+	1	NA	promoter-TSS (NM_178789)	promoter-TSS (NM_178789)	-79	NM_178789	320709	Mm.74873	NM_178789	ENSMUSG00000063296	Tmem117	B930062P21Rik	transmembrane protein 117	protein-coding
mm_105625.1	chr11	106877897	106877899	-	1	NA	intron (NM_025481, intron 1 of 18)	B1_Mur3|SINE|Alu	42817	NM_025481	66313	Mm.340955	NM_025481	ENSMUSG00000018363	Smurf2	2810411E22Rik|AI558114|AI649275	SMAD specific E3 ubiquitin protein ligase 2	protein-coding
mm_95839.1	chr11	57011833	57011843	+	1	NA	5' UTR (NM_001113325, exon 1 of 16)	5' UTR (NM_001113325, exon 1 of 16)	220	NM_008165	14799	Mm.4920	NM_008165	ENSMUSG00000020524	Gria1	2900051M01Rik|Glr-1|Glr1|GluA1|GluR-A|GluRA|Glur-1|Glur1|HIPA1|gluR-K1	glutamate receptor, ionotropic, AMPA1 (alpha 1)	protein-coding
mm_168399.1	chr11	29438947	29438951	-	1	NA	intron (NM_176841, intron 7 of 31)	L1Md_T|LINE|L1	64777	NM_176841	108686	Mm.338284	NM_176841	ENSMUSG00000032740	Ccdc88a	A430106J12Rik|AI848406|Ape|C130096N06Rik|C330012F17Rik|D130005J21Rik|Girdin|Giv|Grdn|Hkrp1	coiled coil domain containing 88A	protein-coding
mm_131913.1	chr16	23307754	23307768	+	1	NA	intron (NM_001252506, intron 1 of 6)	intron (NM_001252506, intron 1 of 6)	17291	NM_001252506	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_144102.1	chr18	3507946	3507964	+	1	NA	promoter-TSS (NM_026505)	promoter-TSS (NM_026505)	-2	NM_026505	68010	Mm.284863	NM_026505	ENSMUSG00000024232	Bambi	2610003H06Rik	BMP and activin membrane-bound inhibitor	protein-coding
mm_46897.1	chr5	114091299	114091324	-	1	NA	promoter-TSS (NM_026805)	promoter-TSS (NM_026805)	69	NM_026805	68666	Mm.63584	NM_026805	ENSMUSG00000042078	Svop	1110030H18Rik|AI415691|msvop	SV2 related protein	protein-coding
mm_170681.1	chr2	126709560	126709575	-	1	NA	intron (NM_019729, intron 1 of 18)	intron (NM_019729, intron 1 of 18)	2239	NM_019729	84092	Mm.272629	NM_019729	ENSMUSG00000027363	Usp8	AI574262|AW557536|Ubpy|mKIAA0055	ubiquitin specific peptidase 8	protein-coding
mm_79537.1	chr9	57827285	57827296	+	1	NA	intron (NM_019689, intron 1 of 7)	intron (NM_019689, intron 1 of 7)	6944	NM_019689	56380	Mm.425588	NM_019689	ENSMUSG00000004661	Arid3b	Bdp|Dri2	AT rich interactive domain 3B (BRIGHT-like)	protein-coding
mm_119822.1	chr14	54232551	54232564	+	1	NA	Intergenic	Intergenic	21372	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_19338.1	chr2	90580564	90580574	-	1	NA	promoter-TSS (NM_008982)	promoter-TSS (NM_008982)	78	NM_008982	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_82965.1	chr9	35648194	35648208	-	1	NA	promoter-TSS (NM_001167592)	promoter-TSS (NM_001167592)	1	NM_001167592	100312956	Mm.475850	NM_001167592	ENSMUSG00000094995	Pate3	Gm17365|Pate-dj	prostate and testis expressed 3	protein-coding
mm_128359.1	chr15	40014631	40014636	-	1	NA	Intergenic	Intergenic	51984	NR_045719	105976	Mm.394885	NR_045719		AU022793	-	expressed sequence AU022793	ncRNA
mm_71585.1	chr8	54954810	54954820	+	1	NA	promoter-TSS (NM_153581)	promoter-TSS (NM_153581)	87	NM_001253756	234267	Mm.241700	NM_153581	ENSMUSG00000031517	Gpm6a	Gpm6|M6A	glycoprotein m6a	protein-coding
mm_98970.1	chr11	98685510	98685523	+	1	NA	exon (NM_009439, exon 2 of 12)	exon (NM_009439, exon 2 of 12)	2962	NM_009439	22123	Mm.12194	NM_009439	ENSMUSG00000017221	Psmd3	AI255837|AntP91a|D11Bwg1349e|Psd3|Tstap91a	proteasome (prosome, macropain) 26S subunit, non-ATPase, 3	protein-coding
mm_142907.1	chr17	52348643	52348658	-	1	NA	Intergenic	Intergenic	-254059	NM_001031811	211468	Mm.399068	NM_001031811	ENSMUSG00000035580	Kcnh8	C130090D05Rik|ELK|ELK1|ELK3|Kv12.1	potassium voltage-gated channel, subfamily H (eag-related), member 8	protein-coding
mm_115759.1	chr13	19193496	19193514	-	1	NA	Intergenic	Intergenic	202308	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_118785.1	chr14	24100287	24100293	+	1	NA	Intergenic	Intergenic	11413	NR_106069	102465697		NR_106069	ENSMUSG00000105723	Mir7210	mir-7210|mmu-mir-7210	microRNA 7210	ncRNA
mm_126537.1	chr15	82022777	82022801	+	1	NA	intron (NM_010247, intron 4 of 12)	intron (NM_010247, intron 4 of 12)	6420	NM_010247	14375	Mm.288809	NM_010247	ENSMUSG00000022471	Xrcc6	70kDa|G22p1|Ku70	X-ray repair complementing defective repair in Chinese hamster cells 6	protein-coding
mm_132083.1	chr16	30259797	30259814	+	1	NA	exon (NM_027904, exon 2 of 2)	exon (NM_027904, exon 2 of 2)	7727	NM_027904	71756	Mm.290614	NM_027904	ENSMUSG00000023176	Cpn2	1300018K11Rik	carboxypeptidase N, polypeptide 2	protein-coding
mm_38924.1	chr4	150009531	150009548	-	1	NA	promoter-TSS (NM_173371)	promoter-TSS (NM_173371)	-516	NM_173371	100198	Mm.22183	NM_173371	ENSMUSG00000028980	H6pd	AI785303|G6pd1|Gpd-1|Gpd1	hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase)	protein-coding
mm_61777.1	chr7	83641751	83641768	+	1	NA	3' UTR (NM_023377, exon 6 of 6)	3' UTR (NM_023377, exon 6 of 6)	9742	NM_023377	170460	Mm.357953	NM_023377	ENSMUSG00000046027	Stard5	2310058G22Rik|AI607880|D7Ertd152e	StAR-related lipid transfer (START) domain containing 5	protein-coding
mm_95627.1	chr11	53586832	53586843	+	1	NA	exon (NM_008443, exon 9 of 18)	exon (NM_008443, exon 9 of 18)	19468	NM_001290806	16568	Mm.88694	NM_008443	ENSMUSG00000018395	Kif3a	Kif3|Kifl|Kns3	kinesin family member 3A	protein-coding
mm_34891.1	chr4	155609515	155609547	+	1	NA	non-coding (NR_040441, exon 3 of 3)	non-coding (NR_040441, exon 3 of 3)	8115	NM_177186	320541	Mm.306018	NM_177186	ENSMUSG00000042202	Slc35e2	A530082C11Rik|AI957035	solute carrier family 35, member E2	protein-coding
mm_125702.1	chr15	67336506	67336506	+	1	NA	intron (NR_045140, intron 5 of 8)	intron (NR_045140, intron 5 of 8)	109737	NR_045140	69334	Mm.63770	NR_045140	ENSMUSG00000102069	1700012I11Rik	-	RIKEN cDNA 1700012I11 gene	ncRNA
mm_41370.1	chr5	90546289	90546289	+	1	NA	intron (NM_145146, intron 9 of 14)	intron (NM_145146, intron 9 of 14)	-14920	NM_001252661	622307	Mm.389654	NM_001252661	ENSMUSG00000070690	5830473C10Rik	Arg|Gm17754	RIKEN cDNA 5830473C10 gene	protein-coding
mm_33700.1	chr4	133622710	133622746	+	1	NA	intron (NM_001017968, intron 2 of 7)	intron (NM_001017968, intron 2 of 7)	10701	NM_001017968	503610	Mm.331948	NM_001017968	ENSMUSG00000037553	Zdhhc18	-	zinc finger, DHHC domain containing 18	protein-coding
mm_67524.1	chr7	80947766	80947777	-	1	NA	promoter-TSS (NM_019951)	promoter-TSS (NM_019951)	-221	NM_019951	56529	Mm.43760	NM_019951	ENSMUSG00000025724	Sec11a	1810012E07Rik|18kDa|Sec11l1|Sid2895p|Spc18|sid2895	SEC11 homolog A, signal peptidase complex subunit	protein-coding
mm_7665.1	chr1	128447273	128447284	-	1	NA	Intergenic	Intergenic	-29862	NM_145507	226414	Mm.28693	NM_145507	ENSMUSG00000026356	Dars	5730439G15Rik	aspartyl-tRNA synthetase	protein-coding
mm_152443.1	chr19	10772071	10772096	-	1	NA	intron (NR_027805, intron 1 of 3)	ID_B1|SINE|B4	31136	NR_027805	403202	Mm.34482	NM_207529	ENSMUSG00000067577	A430093F15Rik	Gm674	RIKEN cDNA A430093F15 gene	ncRNA
mm_58800.1	chr7	16295120	16295153	+	1	NA	Intergenic	Intergenic	-8341	NM_001136471	243846	Mm.482401	NM_172297	ENSMUSG00000041375	Ccdc9	2600011L02Rik	coiled-coil domain containing 9	protein-coding
mm_75728.1	chr8	69184178	69184240	-	1	NA	Intergenic	Intergenic	-24837	NM_001013379	234358	Mm.334577	NM_001013379	ENSMUSG00000059897	Zfp930	-	zinc finger protein 930	protein-coding
mm_139592.1	chr17	57226026	57226044	+	1	NA	exon (NM_009778, exon 4 of 41)	exon (NM_009778, exon 4 of 41)	2101	NM_009778	12266	Mm.19131	NM_009778	ENSMUSG00000024164	C3	AI255234|ASP|HSE-MSF|Plp	complement component 3	protein-coding
mm_98895.1	chr11	97884581	97884594	+	1	NA	promoter-TSS (NM_001081435)	promoter-TSS (NM_001081435)	-433	NM_001081435	72973	Mm.245939	NM_001081435	ENSMUSG00000070336	Fbxo47	2900052P03Rik|Gm1562	F-box protein 47	protein-coding
mm_117280.1	chr13	65122206	65122228	-	1	NA	Intergenic	Intergenic	-9235	NM_133680	66631	Mm.239196	NM_133680	ENSMUSG00000038212	Mfsd14b	5730414C17Rik|AU045608|AW539692|Hiatl1	major facilitator superfamily domain containing 14B	protein-coding
mm_25249.1	chr3	104220872	104220888	+	1	NA	promoter-TSS (NM_133853)	promoter-TSS (NM_133853)	-474	NM_001159354	99470	Mm.264849	NM_133853	ENSMUSG00000052539	Magi3	4732496O19Rik|6530407C02Rik|AA407180|AI120132|mKIAA1634	membrane associated guanylate kinase, WW and PDZ domain containing 3	protein-coding
mm_135204.1	chr16	36561750	36561763	-	1	NA	intron (NM_013803, intron 1 of 6)	intron (NM_013803, intron 1 of 6)	378	NM_013803	12374	Mm.103619	NM_013803	ENSMUSG00000051980	Casr	CaR|Gprc2a	calcium-sensing receptor	protein-coding
mm_160184.1	chr7	48027788	48027788	-	1	NA	promoter-TSS (NM_207540)	promoter-TSS (NM_207540)	-191	NM_207540	404242	Mm.354955	NM_207540	ENSMUSG00000070552	Mrgprx1	MrgC11|Mrgprc11	MAS-related GPR, member X1	protein-coding
mm_123571.1	chr14	66911078	66911093	-	1	NA	promoter-TSS (NM_175498)	promoter-TSS (NM_175498)	-123	NM_175498	239157	Mm.44358	NM_175498	ENSMUSG00000046204	Pnma2	A830049P17Rik|mKIAA0883	paraneoplastic antigen MA2	protein-coding
mm_19119.1	chr2	80038885	80038921	-	1	NA	intron (NM_001159582, intron 2 of 15)	intron (NM_001159582, intron 2 of 15)	90068	NM_016744	18573	Mm.40678	NM_016744	ENSMUSG00000059173	Pde1a	AI987702|AW125737	phosphodiesterase 1A, calmodulin-dependent	protein-coding
mm_58444.1	chr7	3299038	3299048	+	1	NA	3' UTR (NM_016969, exon 3 of 3)	3' UTR (NM_016969, exon 3 of 3)	-4489	NM_001291434	18752	Mm.7980	NM_011102	ENSMUSG00000078816	Prkcg	PKCgamma|Pkcc|Prkcc	protein kinase C, gamma	protein-coding
mm_131860.1	chr16	23107391	23107401	+	1	NA	promoter-TSS (NM_001123037)	promoter-TSS (NM_001123037)	-1	NM_001347179	13682	Mm.260084	NM_013506	ENSMUSG00000022884	Eif4a2	4833432N07Rik|BM-010|Ddx2b|Eif4|eIF-4A-II|eIF4A-II	eukaryotic translation initiation factor 4A2	protein-coding
mm_111903.1	chr12	108765786	108765795	-	1	NA	Intergenic	Intergenic	-27521	NM_009537	22632	Mm.3868	NM_009537	ENSMUSG00000021264	Yy1	AW488674|NF-E1	YY1 transcription factor	protein-coding
mm_125304.1	chr15	37233370	37233398	+	1	NA	5' UTR (NM_026496, exon 1 of 16)	5' UTR (NM_026496, exon 1 of 16)	348	NM_026496	252973	Mm.244612	NM_026496	ENSMUSG00000022286	Grhl2	0610015A08Rik|BOM|Tcfcp2l3|clft3	grainyhead-like 2 (Drosophila)	protein-coding
mm_9021.1	chr1	166238428	166238442	-	1	NA	intron (NM_175296, intron 1 of 11)	intron (NM_175296, intron 1 of 11)	309	NM_175296	98558	Mm.26189	NM_175296	ENSMUSG00000040629	Mael	4933405K18Rik|AU019877	maelstrom spermatogenic transposon silencer	protein-coding
mm_22016.1	chr2	167847824	167847834	-	1	NA	Intergenic	Intergenic	-84498	NM_011201	19246	Mm.277916	NM_011201	ENSMUSG00000027540	Ptpn1	PTP-1B|PTP-HA2|PTP1B	protein tyrosine phosphatase, non-receptor type 1	protein-coding
mm_90850.1	chr10	8762452	8762466	-	1	NA	intron (NM_175155, intron 8 of 19)	intron (NM_175155, intron 8 of 19)	123611	NM_175155	70097	Mm.338275	NM_175155	ENSMUSG00000015305	Sash1	1100001C18Rik|2500002E12Rik|A330076K04Rik|mKIAA0790	SAM and SH3 domain containing 1	protein-coding
mm_62243.1	chr7	98838996	98839010	+	1	NA	5' UTR (NM_009519, exon 1 of 5)	5' UTR (NM_009519, exon 1 of 5)	158	NM_001285795	22411	Mm.22182	NM_009519	ENSMUSG00000015957	Wnt11	-	wingless-type MMTV integration site family, member 11	protein-coding
mm_24792.1	chr3	95545460	95545471	+	1	NA	exon (NM_021281, exon 5 of 8)	exon (NM_021281, exon 5 of 8)	-14212	NM_026489	67981	Mm.179050	NM_026489	ENSMUSG00000028109	Hormad1	4921522K05Rik|Nohma	HORMA domain containing 1	protein-coding
mm_64000.1	chr7	140137560	140137593	+	1	NA	promoter-TSS (NM_199301)	promoter-TSS (NM_199301)	12	NM_199301	212508	Mm.296088	NM_199301	ENSMUSG00000039018	Mtg1	Gm169|Gtpbp7	mitochondrial ribosome-associated GTPase 1	protein-coding
mm_56304.1	chr6	91796242	91796249	-	1	NA	intron (NM_001159507, intron 1 of 23)	intron (NM_001159507, intron 1 of 23)	11148	NM_001159507	243547	Mm.333264	NM_001033353	ENSMUSG00000030098	Grip2	-	glutamate receptor interacting protein 2	protein-coding
mm_10130.1	chr2	3780924	3780929	+	1	NA	3' UTR (NM_025626, exon 4 of 4)	3' UTR (NM_025626, exon 4 of 4)	67468	NM_025626	66540	Mm.277864	NM_025626	ENSMUSG00000026655	Fam107b	3110001A13Rik|AA589595|AA959793|AI132312	family with sequence similarity 107, member B	protein-coding
mm_47804.1	chr5	132543164	132543235	-	1	NA	promoter-TSS (NM_177047)	promoter-TSS (NM_177047)	-856	NM_177047	319974	Mm.409595	NM_177047	ENSMUSG00000029673	Auts2	2700063G02Rik|A730011F23Rik|D830032G16Rik	autism susceptibility candidate 2	protein-coding
mm_102128.1	chr11	53430393	53430405	-	1	NA	intron (NM_001326614, intron 2 of 2)	intron (NM_001326614, intron 2 of 2)	432	NM_025352	22272	Mm.251621	NM_025352	ENSMUSG00000044894	Uqcrq	1100001F06Rik|1500040F11Rik|5830407L17Rik|9.5kDa|AA959903|QP-C|Qpc|Uqcrb|c1502	ubiquinol-cytochrome c reductase, complex III subunit VII	protein-coding
mm_34935.1	chr4	155841102	155841108	+	1	NA	exon (NM_024263, exon 3 of 10)	exon (NM_024263, exon 3 of 10)	1425	NM_024263	74761	Mm.159028	NM_024263	ENSMUSG00000029070	Mxra8	1200013A08Rik|1700095D18Rik|AI131686|Asp3|Dicam	matrix-remodelling associated 8	protein-coding
mm_94098.1	chr10	128551757	128551759	-	1	NA	Intergenic	MT2B1|LTR|ERVL	-2590	NM_018860	67945	Mm.290786	NM_018860	ENSMUSG00000093674	Rpl41	1810055P16Rik|2210411K19Rik	ribosomal protein L41	protein-coding
mm_159215.1	chr2	125724021	125724021	-	1	NA	5' UTR (NM_199022, exon 1 of 12)	5' UTR (NM_199022, exon 1 of 12)	127	NM_199022	271849	Mm.425101	NM_199022	ENSMUSG00000035109	Shc4	6230417E10Rik|9930029B02Rik|Gm685|RaLP	SHC (Src homology 2 domain containing) family, member 4	protein-coding
mm_129505.1	chr15	78927259	78927269	-	1	NA	intron (NM_008495, intron 1 of 3)	intron (NM_008495, intron 1 of 3)	539	NM_008495	16852	Mm.43831	NM_008495	ENSMUSG00000068220	Lgals1	AA410090|Gal-1|Galbp|L-14.5|L14|Lect14|galectin-1	lectin, galactose binding, soluble 1	protein-coding
mm_60594.1	chr7	44496608	44496677	+	1	NA	promoter-TSS (NM_197991)	promoter-TSS (NM_197991)	54	NM_028169	75538	Mm.258841	NM_028169	ENSMUSG00000051113	Fam71e1	0610007G24Rik|1700021N13Rik|1700021P22Rik|GARI-L5	family with sequence similarity 71, member E1	protein-coding
mm_59683.1	chr7	28437448	28437486	+	1	NA	promoter-TSS (NM_022024)	promoter-TSS (NM_022024)	20	NM_001290550	63986	Mm.194536	NM_022024	ENSMUSG00000060791	Gmfg	0610039G16Rik|2310057N07Rik|AI324845	glia maturation factor, gamma	protein-coding
mm_76781.1	chr8	99386714	99386717	-	1	NA	intron (NR_133570, intron 2 of 10)	intron (NR_133570, intron 2 of 10)	29756	NM_001285913	12564	Mm.441131	NM_007667	ENSMUSG00000036510	Cdh8	AI851472|cad8	cadherin 8	protein-coding
mm_29327.1	chr3	108081143	108081144	-	1	NA	intron (NM_001289719, intron 2 of 18)	intron (NM_001289719, intron 2 of 18)	4259	NM_001346665	109674	Mm.274335	NM_028779	ENSMUSG00000027889	Ampd2	1200014F01Rik|AI552571|Ampd-2|m4521Dajl	adenosine monophosphate deaminase 2	protein-coding
mm_50756.1	chr6	53446134	53446140	+	1	NA	intron (NM_001327821, intron 4 of 10)	intron (NM_001327821, intron 4 of 10)	-127237	NM_172728	231991	Mm.227444	NM_172728	ENSMUSG00000053007	Creb5	9430076C15Rik|CRE-BPa|Crebpa|D430026C09Rik	cAMP responsive element binding protein 5	protein-coding
mm_11235.1	chr2	29803651	29803660	+	1	NA	intron (NM_011989, intron 1 of 12)	intron (NM_011989, intron 1 of 12)	975	NM_011989	26569	Mm.330113	NM_011989	ENSMUSG00000059316	Slc27a4	BB144259|FATP4	solute carrier family 27 (fatty acid transporter), member 4	protein-coding
mm_163930.1	chr14	47380387	47380398	+	1	NA	exon (NM_010705, exon 3 of 6)	exon (NM_010705, exon 3 of 6)	6532	NM_001145953	16854	Mm.248615	NM_010705	ENSMUSG00000050335	Lgals3	GBP|L-34|Mac-2|gal3	lectin, galactose binding, soluble 3	protein-coding
mm_85832.1	chr9	110462423	110462431	-	1	NA	intron (NM_177771, intron 1 of 9)	intron (NM_177771, intron 1 of 9)	14267	NM_177771	270201	Mm.41744	NM_177771	ENSMUSG00000054792	Klhl18	A930041K15|AW545966	kelch-like 18	protein-coding
mm_17775.1	chr2	32847232	32847242	-	1	NA	promoter-TSS (NM_001113569)	promoter-TSS (NM_001113569)	0	NM_001113569	20910	Mm.278865	NM_009295	ENSMUSG00000026797	Stxbp1	AI317162|AI326233|MMS10-G|Ms10g|Munc-18a|Munc18-1|N-sec1|Rb-sec1|Sxtbp1|Unc18-1|Unc18h|nsec1	syntaxin binding protein 1	protein-coding
mm_140331.1	chr17	86754154	86754160	+	1	NA	5' UTR (NM_010137, exon 1 of 16)	5' UTR (NM_010137, exon 1 of 16)	293	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_21604.1	chr2	164238339	164238346	-	1	NA	promoter-TSS (NM_017390)	promoter-TSS (NM_017390)	-1	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_116817.1	chr13	54551908	54551939	-	1	NA	TTS (NM_176987)	TTS (NM_176987)	13459	NM_001252647	97820	Mm.24593	NM_133797	ENSMUSG00000025871	4833439L19Rik	4930558H15Rik|C81457|Kiaa1191|P33monox	RIKEN cDNA 4833439L19 gene	protein-coding
mm_127123.1	chr15	98108466	98108481	+	1	NA	promoter-TSS (NM_001163487)	promoter-TSS (NM_001163487)	2	NM_001163487	18642	Mm.272582	NM_021514	ENSMUSG00000033065	Pfkm	AI131669|ATP-PFK|PFK-A|PFK-M|Pfk-4|Pfk4|Pfka|Pfkx	phosphofructokinase, muscle	protein-coding
mm_63320.1	chr7	126941361	126941402	+	1	NA	exon (NM_172747, exon 3 of 6)	exon (NM_172747, exon 3 of 6)	8200	NM_001347657	233879	Mm.444143	NM_001039645	ENSMUSG00000046378	Asphd1	A830007L07Rik|Gm168	aspartate beta-hydroxylase domain containing 1	protein-coding
mm_33893.1	chr4	136189500	136189502	+	1	NA	intron (NM_001305399, intron 4 of 4)	B3|SINE|B2	8719	NM_001305399	242705	Mm.307932	NM_177733	ENSMUSG00000018983	E2f2	E2F-2	E2F transcription factor 2	protein-coding
mm_48457.1	chr5	140760534	140760553	-	1	NA	3' UTR (NM_010302, exon 4 of 4)	3' UTR (NM_010302, exon 4 of 4)	36416	NM_173405	231842	Mm.491298	NM_173405	ENSMUSG00000050022	Amz1	5330426I05|6530401C20Rik	archaelysin family metallopeptidase 1	protein-coding
mm_24246.1	chr3	89140214	89140230	+	1	NA	intron (NM_013631, intron 2 of 10)	intron (NM_013631, intron 2 of 10)	3599	NM_001099779	18770	Mm.383180	NM_013631	ENSMUSG00000041237	Pklr	Pk-1|Pk1|R-PK	pyruvate kinase liver and red blood cell	protein-coding
mm_142022.1	chr17	35204666	35204685	-	1	NA	promoter-TSS (NR_105940)	promoter-TSS (NR_105940)	-118	NR_105940	102466990		NR_105940	ENSMUSG00000099006	Mir6974	Gm27658|mmu-mir-6974	microRNA 6974	ncRNA
mm_52263.1	chr6	108257911	108257915	+	1	NA	intron (NM_010585, intron 4 of 61)	intron (NM_010585, intron 4 of 61)	44817	NM_010585	16438	Mm.227912	NM_010585	ENSMUSG00000030102	Itpr1	D6Pas2|ENSMUSG00000072853|Gm10429|IP3R 1|IP3R1|InsP3R|Ip3r|Itpr-1|P400|Pcp-1|Pcp1|insP3R1|opt|wblo	inositol 1,4,5-trisphosphate receptor 1	protein-coding
mm_107781.1	chr12	61523890	61523922	+	1	NA	5' UTR (NM_001310586, exon 1 of 6)	5' UTR (NM_001310586, exon 1 of 6)	739	NM_001310586	238205	Mm.28802	NM_178714	ENSMUSG00000035653	Lrfn5	AI427653|AI604817|C130061B21|mKIAA4208	leucine rich repeat and fibronectin type III domain containing 5	protein-coding
mm_146545.1	chr18	6135860	6135870	-	1	NA	5' UTR (NM_001039692, exon 1 of 19)	5' UTR (NM_001039692, exon 1 of 19)	233	NM_029277	75415	Mm.239675	NM_029277	ENSMUSG00000041225	Arhgap12	2810011M08Rik	Rho GTPase activating protein 12	protein-coding
mm_73366.1	chr8	105605042	105605056	+	1	NA	promoter-TSS (NM_001081241)	promoter-TSS (NM_001081241)	-180	NM_001081241	75687	Mm.41261	NM_001081241	ENSMUSG00000038604	Fam65a	2310066E14Rik|AI837433	family with sequence similarity 65, member A	protein-coding
mm_87253.1	chr10	41501277	41501325	+	1	NA	intron (NM_028430, intron 3 of 7)	intron (NM_028430, intron 3 of 7)	10862	NM_028430	73075	Mm.359762	NM_028430	ENSMUSG00000078451	Ppil6	2900084F20Rik	peptidylprolyl isomerase (cyclophilin)-like 6	protein-coding
mm_156827.1	chrX	164200813	164200837	+	1	NA	exon (NM_009759, exon 17 of 19)	exon (NM_009759, exon 17 of 19)	57368	NM_009759	12169	Mm.504	NM_009759	ENSMUSG00000031377	Bmx	Etk|Etk/Bmx|Tyro8	BMX non-receptor tyrosine kinase	protein-coding
mm_2260.1	chr1	91121735	91121747	+	1	NA	intron (NM_001310732, intron 21 of 24)	intron (NM_001310732, intron 21 of 24)	-23362	NM_001033408	329207	Mm.295940	NM_001033408	ENSMUSG00000070732	Rbm44	Gm817	RNA binding motif protein 44	protein-coding
mm_33120.1	chr4	124791412	124791417	+	1	NA	intron (NR_126474, intron 16 of 24)	intron (NR_126474, intron 16 of 24)	-11135	NM_008636	17764	Mm.272397	NM_008636	ENSMUSG00000028890	Mtf1	MTF-1|Thyls	metal response element binding transcription factor 1	protein-coding
mm_119115.1	chr14	31019440	31019506	+	1	NA	promoter-TSS (NM_153547)	promoter-TSS (NM_153547)	335	NM_001081251	66923	Mm.27913	NM_025847	ENSMUSG00000042323	Pbrm1	2610016F04Rik|AI507524|BAF180|Pb1	polybromo 1	protein-coding
mm_5816.1	chr1	52661002	52661043	-	1	NA	exon (NM_133829, exon 6 of 7)	exon (NM_133829, exon 6 of 7)	30317	NM_001142647	227094	Mm.83541	NM_172654	ENSMUSG00000043015	Nemp2	5330401P04Rik|9830163O08|Tmem194b	nuclear envelope integral membrane protein 2	protein-coding
mm_168365.1	chr1	116763002	116763003	-	1	NA	Intergenic	L1Md_F2|LINE|L1	1077865	NM_001077425	636808	Mm.101576	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding
mm_150252.1	chr19	34181445	34181453	+	1	NA	Intergenic	Intergenic	-10821	NM_029682	76630	Mm.130952	NM_029682	ENSMUSG00000024776	Stambpl1	1700095N21Rik|8230401J17Rik|ALMalpha|AMSH-FP	STAM binding protein like 1	protein-coding
mm_108467.1	chr12	83632209	83632325	+	1	NA	promoter-TSS (NM_027349)	promoter-TSS (NM_027349)	33	NM_027349	67039	Mm.46005	NM_027349	ENSMUSG00000010608	Rbm25	2600011C06Rik|2610015J01Rik|A130095G20Rik|AI159652|AL023075|AU043498|RNPC7	RNA binding motif protein 25	protein-coding
mm_28239.1	chr3	88459022	88459043	-	1	NA	promoter-TSS (NM_001163490)	promoter-TSS (NM_001163490)	69	NM_001163490	20351	Mm.439752	NM_013658	ENSMUSG00000028064	Sema4a	AI132332|SemB|Semab	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A	protein-coding
mm_62228.1	chr7	98531926	98531949	+	1	NA	Intergenic	Intergenic	37715	NM_001113379	434215	Mm.323057	NM_001113379	ENSMUSG00000090958	Lrrc32	AI426318|D11S833Eh|D7H11S833E|EG434215|Garp	leucine rich repeat containing 32	protein-coding
mm_52957.1	chr6	123123314	123123342	+	1	NA	promoter-TSS (NM_001170333)	promoter-TSS (NM_001170333)	12	NM_001170333	26888	Mm.47384	NM_011999	ENSMUSG00000030148	Clec4a2	Clec4a|Clecsf6|DCIR|Dcir1	C-type lectin domain family 4, member a2	protein-coding
mm_103175.1	chr11	70459859	70459869	-	1	NA	5' UTR (NM_001029929, exon 1 of 14)	5' UTR (NM_001029929, exon 1 of 14)	120	NM_023158	66102	Mm.425692	NM_023158	ENSMUSG00000018920	Cxcl16	0910001K24Rik|AV290116|BB024863|CXCL16v1|CXCL16v2|SR-PSOX|Zmynd15|b2b498Clo	chemokine (C-X-C motif) ligand 16	protein-coding
mm_154979.1	chrX	37827045	37827047	+	1	NA	promoter-TSS (NM_008955)	promoter-TSS (NM_008955)	-9	NM_008955	19202	Mm.10105	NM_008955	ENSMUSG00000006200	Rhox6	AV213605|AW548842|Psx1	reproductive homeobox 6	protein-coding
mm_136004.1	chr16	75683280	75683310	-	1	NA	Intergenic	RMER20B|LTR|ERVK	83523	NR_027492	110920	Mm.26704	NM_030201	ENSMUSG00000032932	Hspa13	1600002I10Rik|AV006182|B230217N24Rik|Stch	heat shock protein 70 family, member 13	protein-coding
mm_55794.1	chr6	82737281	82737304	-	1	NA	intron (NM_013820, intron 9 of 17)	intron (NM_013820, intron 9 of 17)	37162	NM_013820	15277	Mm.255848	NM_013820	ENSMUSG00000000628	Hk2	AI642394|HKII	hexokinase 2	protein-coding
mm_15697.1	chr2	163694016	163694058	+	1	NA	promoter-TSS (NM_011106)	promoter-TSS (NM_011106)	0	NM_011106	18769	Mm.10091	NM_011106	ENSMUSG00000035268	Pkig	PKIgamma	protein kinase inhibitor, gamma	protein-coding
mm_2161.1	chr1	88218429	88218456	+	1	NA	3' UTR (NM_201643, exon 5 of 5)	3' UTR (NM_201643, exon 5 of 5)	6483	NM_201645	394436	Mm.300095	NM_201645	ENSMUSG00000089960	Ugt1a1	Gnt1|UDPGT 1-1|UGT1A01|Udpgt-1a|UgtBr1	UDP glucuronosyltransferase 1 family, polypeptide A1	protein-coding
mm_124852.1	chr15	9528473	9528483	+	1	NA	intron (NM_008372, intron 1 of 7)	intron (NM_008372, intron 1 of 7)	1398	NM_008372	16197	Mm.389	NM_008372	ENSMUSG00000003882	Il7r	CD127|IL-7Ralpha	interleukin 7 receptor	protein-coding
mm_172549.1	chr8	102148584	102148589	-	1	NA	Intergenic	Intergenic	636525	NM_009866	12552	Mm.1571	NM_009866	ENSMUSG00000031673	Cdh11	Cad11|OSF-4	cadherin 11	protein-coding
mm_62902.1	chr7	116604053	116604053	+	1	NA	Intergenic	RMER17C2|LTR|ERVK	99684	NM_001130479	53322	Mm.9901	NM_016773	ENSMUSG00000030659	Nucb2	AI607786|Calnuc|Nefa|Nesfatin-1	nucleobindin 2	protein-coding
mm_143489.1	chr17	71310953	71310969	-	1	NA	promoter-TSS (NM_145158)	promoter-TSS (NM_145158)	4	NM_145158	246707	Mm.23462	NM_145158	ENSMUSG00000024053	Emilin2	FOAP-10	elastin microfibril interfacer 2	protein-coding
mm_90253.1	chr10	121739916	121739965	+	1	NA	promoter-TSS (NM_173022)	promoter-TSS (NM_173022)	3	NM_173022	270802	Mm.209172	NM_173022	ENSMUSG00000053684	BC048403	E030027L10	cDNA sequence BC048403	protein-coding
mm_54881.1	chr6	42710002	42710015	-	1	NA	Intergenic	Intergenic	-16949	NM_029930	77574	Mm.24652	NM_029930	ENSMUSG00000036667	Tcaf1	2810407D09Rik|3321401G04Rik|A230020K05Rik|AI848529|Fam115a	TRPM8 channel-associated factor 1	protein-coding
mm_32300.1	chr4	103119468	103119486	+	1	NA	promoter-TSS (NM_001039081)	promoter-TSS (NM_001039081)	87	NM_001039081	71148	Mm.288721	NM_027696	ENSMUSG00000028522	Mier1	4933425I22Rik|5830411K19Rik|er1	MEIR1 treanscription regulator	protein-coding
mm_135504.1	chr16	46496988	46497010	-	1	NA	promoter-TSS (NM_021495)	promoter-TSS (NM_021495)	-32	NM_021497	58998	Mm.40477	NM_021495	ENSMUSG00000022656	Nectin3	2610301B19Rik|3000002N23Rik|4921513D19Rik|AA407785|AU016832|AW538082|CD113|Pvrl3	nectin cell adhesion molecule 3	protein-coding
mm_38784.1	chr4	148084268	148084294	-	1	NA	intron (NM_001301281, intron 1 of 4)	intron (NM_001301281, intron 1 of 4)	3783	NM_009642	11610	Mm.46247	NM_009642	ENSMUSG00000029007	Agtrap	3300002E14Rik|AT1R|Atrap|D4Wsu124e	angiotensin II, type I receptor-associated protein	protein-coding
mm_160768.1	chr10	100366523	100366523	+	1	NA	promoter-TSS (NM_001166636).2	promoter-TSS (NM_001166636).2	24	NM_001166636	100043247	Mm.478257	NM_001166636	ENSMUSG00000096640	Gm4312	-	predicted gene 4312	protein-coding
mm_71573.1	chr8	54528026	54528031	+	1	NA	intron (NM_029701, intron 2 of 4)	intron (NM_029701, intron 2 of 4)	1970	NM_029701	76687	Mm.86437	NM_029701	ENSMUSG00000054408	Spcs3	1810011E08Rik|SPC22/23	signal peptidase complex subunit 3 homolog (S. cerevisiae)	protein-coding
mm_167218.1	chr8	10705636	10705636	-	1	NA	Intergenic	Intergenic	176818	NR_040705	320014	Mm.403203	NR_040705	ENSMUSG00000109473	B930025P03Rik	-	RIKEN cDNA B930025P03 gene	ncRNA
mm_97812.1	chr11	82962642	82962684	+	1	NA	3' UTR (NM_183201, exon 6 of 6)	3' UTR (NM_183201, exon 6 of 6)	-1982	NR_045932	76392	Mm.295205	NR_045932	ENSMUSG00000086327	Slfn5os	1700003F17Rik	schlafen 5, opposite strand	ncRNA
mm_54085.1	chr6	15793321	15793329	-	1	NA	intron (NM_175088, intron 4 of 4)	intron (NM_175088, intron 4 of 4)	72664	NM_175088	16543	Mm.1314	NM_175088	ENSMUSG00000041390	Mdfic	Kdt1|Mdfid	MyoD family inhibitor domain containing	protein-coding
mm_144883.1	chr18	36796061	36796073	+	1	NA	exon (NM_025594, exon 4 of 6)	exon (NM_025594, exon 4 of 6)	2144	NM_025594	66492	Mm.251155	NM_025594	ENSMUSG00000001383	Zmat2	2610510D14Rik|2900082I05Rik	zinc finger, matrin type 2	protein-coding
mm_111640.1	chr12	102653303	102653315	-	1	NA	intron (NM_172584, intron 2 of 9)	MIRc|SINE|MIR	31711	NR_035457	100316812		NR_035457	ENSMUSG00000089324	Mir1936	mir-1936|mmu-mir-1936	microRNA 1936	ncRNA
mm_116801.1	chr13	54055089	54055118	-	1	NA	promoter-TSS (NM_001291801)	promoter-TSS (NM_001291801)	-323	NM_001291801	13488	Mm.54161	NM_010076	ENSMUSG00000021478	Drd1	C030036C15Rik|Drd-1|Drd1a|Gpcr15	dopamine receptor D1	protein-coding
mm_121900.1	chr14	21848879	21848921	-	1	NA	promoter-TSS (NM_026965)	promoter-TSS (NM_026965)	10	NM_026965	69156	Mm.11827	NM_026965	ENSMUSG00000021773	Comtd1	1810030M08Rik|MT773	catechol-O-methyltransferase domain containing 1	protein-coding
mm_109690.1	chr12	113143511	113143547	+	1	NA	exon (NM_024223, exon 2 of 7)	exon (NM_024223, exon 2 of 7)	2924	NM_001347443	68337	Mm.133825	NM_024223	ENSMUSG00000006356	Crip2	0610010I23Rik|AW743261|C77570|CRP2|CRP4|Crp|ESP1|Hlp	cysteine rich protein 2	protein-coding
mm_147433.1	chr18	46447689	46447729	-	1	NA	Intergenic	Intergenic	18107	NR_045438	72076	Mm.82766	NM_028086		Mospd4	2010013H21Rik	motile sperm domain containing 4	pseudo
mm_27412.1	chr3	51396504	51396526	-	1	NA	promoter-TSS (NM_026358)	promoter-TSS (NM_026358)	32	NM_026358	67749	Mm.273339	NM_026358	ENSMUSG00000037161	Mgarp	4930583H14Rik|AI195347|CESP-1|HUMMR|Osap|Qsap	mitochondria localized glutamic acid rich protein	protein-coding
mm_95309.1	chr11	46235461	46235471	+	1	NA	promoter-TSS (NM_177075)	promoter-TSS (NM_177075)	-91	NM_177075	320116	Mm.39600	NM_177075	ENSMUSG00000048721	Fndc9	C030019I05Rik	fibronectin type III domain containing 9	protein-coding
mm_162471.1	chr1	132008548	132008584	+	1	NA	intron (NM_007923, intron 1 of 4)	intron (NM_007923, intron 1 of 4)	961	NM_007923	13714	Mm.254233	NM_007923	ENSMUSG00000026436	Elk4	2310011G17Rik|A130026I01Rik|BB162516|SAP-1|Sap1	ELK4, member of ETS oncogene family	protein-coding
mm_109456.1	chr12	111160217	111160227	+	1	NA	non-coding (NR_130987, exon 4 of 4)	non-coding (NR_130987, exon 4 of 4)	-6148	NM_001286122	22031	Mm.27431	NM_011632	ENSMUSG00000021277	Traf3	AI528849|CAP-1|CD40bp|CRAF1|LAP1|T-BAM|amn	TNF receptor-associated factor 3	protein-coding
mm_14691.1	chr2	140783690	140783702	+	1	NA	intron (NM_001013802, intron 3 of 18)	intron (NM_001013802, intron 3 of 18)	-112220	NM_178382	71436	Mm.426781	NM_178382	ENSMUSG00000051379	Flrt3	5530600M07Rik|C430047I10Rik|mKIAA1469	fibronectin leucine rich transmembrane protein 3	protein-coding
mm_143528.1	chr17	73902006	73902019	-	1	NA	intron (NM_011723, intron 24 of 35)	(TATG)n|Simple_repeat|Simple_repeat	48184	NM_011723	22436	Mm.11223	NM_011723	ENSMUSG00000024066	Xdh	XO|Xor|Xox-1|Xox1	xanthine dehydrogenase	protein-coding
mm_21260.1	chr2	156392995	156393003	-	1	NA	promoter-TSS (NR_024329)	promoter-TSS (NR_024329)	-20	NR_024329	347740	Mm.324242	NR_024329		2900097C17Rik	1810005K14Rik|4930563C06Rik	RIKEN cDNA 2900097C17 gene	ncRNA
mm_62141.1	chr7	97101170	97101180	+	1	NA	intron (NM_001162477, intron 1 of 9)	intron (NM_001162477, intron 1 of 9)	19424	NM_010248	14389	Mm.42033	NM_010248	ENSMUSG00000004508	Gab2	AI463667|D130058I17Rik|p97	growth factor receptor bound protein 2-associated protein 2	protein-coding
mm_166745.1	chr6	124917896	124917899	-	1	NA	promoter-TSS (NM_026988)	promoter-TSS (NM_026988)	49	NM_026988	69202	Mm.142187	NM_026988	ENSMUSG00000030122	Ptms	2610009E16Rik	parathymosin	protein-coding
mm_139524.1	chr17	56628158	56628171	+	1	NA	promoter-TSS (NM_175350)	promoter-TSS (NM_175350)	21	NM_175350	106757	Mm.23401	NM_175350	ENSMUSG00000040828	Catsperd	4921529N20Rik|4933402B14Rik|619718|AW045609|Gm6095|Tmem146	catsper channel auxiliary subunit delta	protein-coding
mm_146458.1	chr18	86601944	86601960	+	1	NA	Intergenic	Intergenic	-109158	NM_001302356	12405	Mm.70775	NM_172633	ENSMUSG00000024647	Cbln2	6330593N19Rik|A730004O05	cerebellin 2 precursor protein	protein-coding
mm_104472.1	chr11	95310187	95310213	-	1	NA	promoter-TSS (NM_001195004)	promoter-TSS (NM_001195004)	46	NM_001195004	217127	Mm.90213	NM_177619	ENSMUSG00000038909	Kat7	Hbo1|Hboa|Myst2	K(lysine) acetyltransferase 7	protein-coding
mm_99032.1	chr11	98944427	98944457	+	1	NA	intron (NM_001177303, intron 1 of 8)	intron (NM_001177303, intron 1 of 8)	4731	NM_001177303	19401	Mm.439744	NM_009024	ENSMUSG00000037992	Rara	Nr1b1|RAR|RARalpha1	retinoic acid receptor, alpha	protein-coding
mm_85890.1	chr9	111055005	111055016	-	1	NA	3' UTR (NM_017466, exon 2 of 2)	3' UTR (NM_017466, exon 2 of 2)	2234	NM_001302377	54199	Mm.7336	NM_017466	ENSMUSG00000043953	Ccrl2	1810047I05Rik|Ackr5|CCR11|Cmkbr1l2|E01|L-CCR	chemokine (C-C motif) receptor-like 2	protein-coding
mm_17081.1	chr2	22941900	22941949	-	1	NA	exon (NM_001077190, exon 11 of 11)	exon (NM_001077190, exon 11 of 11)	46402	NM_019501	56075	Mm.249752	NM_019501	ENSMUSG00000026784	Pdss1	2610203G20Rik|2700031G06Rik|TPT|TPT 1|Tprt|mDLP1|mSPS1	prenyl (solanesyl) diphosphate synthase, subunit 1	protein-coding
mm_145096.1	chr18	43207711	43207721	+	1	NA	promoter-TSS (NM_178749)	promoter-TSS (NM_178749)	19	NM_178749	269019	Mm.150401	NM_178749	ENSMUSG00000039954	Stk32a	A930015B13Rik|YANK1	serine/threonine kinase 32A	protein-coding
mm_4915.1	chr1	190596562	190596584	+	1	NA	Intergenic	Intergenic	315197	NM_178775	320119	Mm.220912	NM_178775	ENSMUSG00000089872	Rps6kc1	AA682037|B130003F20Rik|C80612|Rpk118	ribosomal protein S6 kinase polypeptide 1	protein-coding
mm_116204.1	chr13	32701708	32701726	-	1	NA	3' UTR (NM_001166030, exon 12 of 12)	3' UTR (NM_001166030, exon 12 of 12)	80062	NM_001166030	238564	Mm.60041	NM_001166030	ENSMUSG00000044951	Mylk4	EG238564	myosin light chain kinase family, member 4	protein-coding
mm_147315.1	chr18	41998974	41998976	-	1	NA	promoter-TSS (NM_001033426)	promoter-TSS (NM_001033426)	74	NM_001033426	332309	Mm.240520	NM_001033426	ENSMUSG00000073574	Grxcr2	Gm851	glutaredoxin, cysteine rich 2	protein-coding
mm_74944.1	chr8	25847622	25847676	-	1	NA	promoter-TSS (NM_001080793)	promoter-TSS (NM_001080793)	45	NM_001080793	23808	Mm.27706	NM_011791	ENSMUSG00000031575	Ash2l	-	ash2 (absent, small, or homeotic)-like (Drosophila)	protein-coding
mm_128601.1	chr15	58214838	58214848	-	1	NA	promoter-TSS (NM_026346)	promoter-TSS (NM_026346)	49	NM_026346	67731	Mm.25683	NM_026346	ENSMUSG00000022358	Fbxo32	4833442G10Rik|AI430017|ATROGIN1|Gm20361|MAFbx	F-box protein 32	protein-coding
mm_44900.1	chr5	35525568	35525617	-	1	NA	promoter-TSS (NM_153107)	promoter-TSS (NM_153107)	34	NM_153107	242939	Mm.108557	NM_153107	ENSMUSG00000036596	Cpz	AV136066	carboxypeptidase Z	protein-coding
mm_48572.1	chr5	143315361	143315396	-	1	NA	promoter-TSS (NM_172726)	promoter-TSS (NM_172726)	-18	NM_172726	231868	Mm.440105	NM_172726	ENSMUSG00000039244	E130309D02Rik	A630028N22	RIKEN cDNA E130309D02 gene	protein-coding
mm_139703.1	chr17	57451596	57451609	+	1	NA	intron (NM_010130, intron 17 of 21)	intron (NM_010130, intron 17 of 21)	92916	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_170559.1	chr19	43890260	43890276	-	1	NA	intron (NM_028029, intron 4 of 15)	intron (NM_028029, intron 4 of 15)	-10500	NM_001306088	71972	Mm.159024	NM_028029	ENSMUSG00000025195	Dnmbp	2410003L07Rik|2410003M15Rik|TUBA	dynamin binding protein	protein-coding
mm_64798.1	chr7	6685609	6685619	-	1	NA	intron (NM_011769, intron 5 of 7)	intron (NM_011769, intron 5 of 7)	10818	NM_011769	22776	Mm.89976	NM_011769	ENSMUSG00000002266	Zim1	-	zinc finger, imprinted 1	protein-coding
mm_170613.1	chr19	58900577	58900589	-	1	NA	intron (NM_001327998, intron 2 of 12)	RLTR10D2|LTR|ERVK	11176	NR_037247	100526480		NR_037247	ENSMUSG00000092813	Mir3086	mir-3086|mmu-mir-3086	microRNA 3086	ncRNA
mm_55579.1	chr6	71396951	71396975	-	1	NA	intron (NM_024288, intron 6 of 8)	intron (NM_024288, intron 6 of 8)	23536	NM_001081110	12525	Mm.1858	NM_009857	ENSMUSG00000053977	Cd8a	BB154331|Ly-2|Ly-35|Ly-B|Lyt-2	CD8 antigen, alpha chain	protein-coding
mm_102798.1	chr11	68853120	68853140	-	1	NA	promoter-TSS (NM_023668)	promoter-TSS (NM_023668)	1	NM_023668	83431	Mm.31979	NM_023668	ENSMUSG00000018736	Ndel1	2600006O07Rik|MITAP1|NUDEL|mNudel	nudE neurodevelopment protein 1 like 1	protein-coding
mm_137036.1	chr17	17890639	17890645	+	1	NA	intron (NM_008039, intron 1 of 1)	RMER15|LTR|ERVL	2818	NM_008039	14289	Mm.378918	NM_008039	ENSMUSG00000052270	Fpr2	E330010I07Rik|Fpr-rs2	formyl peptide receptor 2	protein-coding
mm_44568.1	chr5	24730612	24730622	-	1	NA	promoter-TSS (NM_001081441)	promoter-TSS (NM_001081441)	63	NM_001081441	269633	Mm.392539	NM_026621	ENSMUSG00000055235	Wdr86	2810046M22Rik|BC059069	WD repeat domain 86	protein-coding
mm_84892.1	chr9	79793291	79793372	-	1	NA	promoter-TSS (NR_040734)	promoter-TSS (NR_040734)	99	NM_133718	69981	Mm.486324	NM_133718	ENSMUSG00000032328	Tmem30a	2010200I23Rik|AW540225|Cdc50a|D9Wsu20e	transmembrane protein 30A	protein-coding
mm_98850.1	chr11	97661876	97661878	+	1	NA	Intergenic	Intergenic	-1535	NM_139311	246198	Mm.23685	NM_139311	ENSMUSG00000038437	Mllt6	AI315037|Af17	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 6	protein-coding
mm_101277.1	chr11	21557281	21557307	-	1	NA	3' UTR (NM_001316675, exon 9 of 9)	3' UTR (NM_001316675, exon 9 of 9)	14640	NM_008618	17449	Mm.212703	NM_008618	ENSMUSG00000020321	Mdh1	B230377B03Rik|D17921|MDH-s|MDHA|Mor-2|Mor2	malate dehydrogenase 1, NAD (soluble)	protein-coding
mm_5451.1	chr1	36244325	36244335	-	1	NA	promoter-TSS (NM_198899)	promoter-TSS (NM_198899)	-28	NM_198899	320011	Mm.261022	NM_198899	ENSMUSG00000037470	Uggt1	0910001L17Rik|A930007H10Rik|AA589501|AI414429|AI448372|C820010P03Rik|GT|UGT1|Ugcgl1	UDP-glucose glycoprotein glucosyltransferase 1	protein-coding
mm_38227.1	chr4	136005239	136005242	-	1	NA	3' UTR (NM_013736, exon 11 of 11)	3' UTR (NM_013736, exon 11 of 11)	16409	NM_013736	27224	Mm.27663	NM_013736	ENSMUSG00000028668	Eloa	110kDa|AA408125|Tceb3|Tceb3a	elongin A	protein-coding
mm_158160.1	chrX	103482551	103482577	-	1	NA	non-coding (NR_002844, exon 4 of 4)	non-coding (NR_002844, exon 4 of 4)	669	NR_001570	213742	Mm.274770	NR_001463	ENSMUSG00000086503	Xist	A430022B11|AI314753	inactive X specific transcripts	ncRNA
mm_122775.1	chr14	54409470	54409477	-	1	NA	promoter-TSS (NM_001253680)	promoter-TSS (NM_001253680)	-1	NM_001253680	20540	Mm.142455	NM_011405	ENSMUSG00000000958	Slc7a7	AI790233|my+lat1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 7	protein-coding
mm_31424.1	chr4	48083600	48083603	+	1	NA	3' UTR (NM_015743, exon 8 of 8)	3' UTR (NM_015743, exon 8 of 8)	32355	NM_001307989	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_19978.1	chr2	118373348	118373379	-	1	NA	promoter-TSS (NM_201367)	promoter-TSS (NM_201367)	56	NM_201367	381413	Mm.70979	NM_201367	ENSMUSG00000040133	Gpr176	Gm1012	G protein-coupled receptor 176	protein-coding
mm_50733.1	chr6	52713732	52713800	+	1	NA	promoter-TSS (NM_025816)	promoter-TSS (NM_025816)	37	NM_025816	52440	Mm.389757	NM_025816	ENSMUSG00000004535	Tax1bp1	1200003J11Rik|1700069J21Rik|AA930106|D6Ertd404e|D6Ertd772e|T6bp|TXBP151	Tax1 (human T cell leukemia virus type I) binding protein 1	protein-coding
mm_41139.1	chr5	87885005	87885018	+	1	NA	promoter-TSS (NM_027128)	promoter-TSS (NM_027128)	-684	NM_027128	69592	Mm.389652	NM_027128	ENSMUSG00000009580	Odam	2310011G06Rik|APIN	odontogenic, ameloblast asssociated	protein-coding
mm_127283.1	chr15	99972835	99972896	+	1	NA	promoter-TSS (NM_001284521)	promoter-TSS (NM_001284521)	85	NM_001284523	207214	Mm.28811	NM_001024526	ENSMUSG00000023025	Larp4	DXErtd793|DXErtd793e	La ribonucleoprotein domain family, member 4	protein-coding
mm_16222.1	chr2	173110849	173110855	+	1	NA	intron (NM_001081387, intron 5 of 10)	intron (NM_001081387, intron 5 of 10)	8673	NM_001081387	664799	Mm.389396	NM_001081387	ENSMUSG00000070495	Ctcfl	Boris|OTTMUSG00000016680	CCCTC-binding factor (zinc finger protein)-like	protein-coding
mm_84870.1	chr9	79639773	79639778	-	1	NA	exon (NM_001290308, exon 42 of 66)	exon (NM_001290308, exon 42 of 66)	78947	NM_001290308	12816	Mm.3819	NM_007730	ENSMUSG00000032332	Col12a1	-	collagen, type XII, alpha 1	protein-coding
mm_58108.1	chr6	138421380	138421405	-	1	NA	intron (NM_207222, intron 2 of 4)	intron (NM_207222, intron 2 of 4)	-1713	NR_126073	319702	Mm.403785	NR_126072	ENSMUSG00000089957	A830011K09Rik	-	RIKEN cDNA A830011K09 gene	ncRNA
mm_172468.1	chr7	43213998	43214002	+	1	NA	promoter-TSS (NM_001177525)	promoter-TSS (NM_001177525)	-39	NM_001177525	100170401		NM_001177525		EU599041	TU7	expressed sequence EU599041	protein-coding
mm_97926.1	chr11	83640466	83640476	+	1	NA	Intergenic	Intergenic	8907	NM_011337	20302	Mm.1282	NM_011337	ENSMUSG00000000982	Ccl3	AI323804|G0S19-1|LD78alpha|MIP-1alpha|MIP1-(a)|MIP1-alpha|Mip1a|Scya3	chemokine (C-C motif) ligand 3	protein-coding
mm_90368.1	chr10	127167670	127167684	+	1	NA	intron (NR_045166, intron 5 of 9)	intron (NR_045166, intron 5 of 9)	1846	NM_001244618	14421	Mm.386762	NM_008080	ENSMUSG00000006731	B4galnt1	4933429D13Rik|Gal-NAc-T|GalNAc-T|GalNAcT|Galgt1|Ggm-2|Ggm2	beta-1,4-N-acetyl-galactosaminyl transferase 1	protein-coding
mm_130939.1	chr15	103239798	103239806	-	1	NA	promoter-TSS (NM_010447)	promoter-TSS (NM_010447)	14	NM_001076789	12419	Mm.262059	NM_007626	ENSMUSG00000009575	Cbx5	2610029O15Rik|C75991|HP1|Hp1a|Hp1alpha	chromobox 5	protein-coding
mm_40865.1	chr5	73651845	73651892	+	1	NA	intron (NM_178387, intron 1 of 12)	intron (NM_178387, intron 1 of 12)	488	NM_178387	73472	Mm.87067	NM_178387	ENSMUSG00000029155	Spata18	1700067I02Rik	spermatogenesis associated 18	protein-coding
mm_156964.1	chrX	169990220	169990232	+	1	NA	3' UTR (NM_001290504, exon 10 of 10)	3' UTR (NM_001290504, exon 10 of 10)	-11309	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_112359.1	chr12	119070529	119070548	-	1	NA	Intergenic	Intergenic	-104117	NM_029961	77706	Mm.261496	NM_029961	ENSMUSG00000072791	Abcb5	9230106F14Rik	ATP-binding cassette, sub-family B (MDR/TAP), member 5	protein-coding
mm_57198.1	chr6	122850366	122850411	-	1	NA	exon (NM_009779, exon 2 of 2)	exon (NM_009779, exon 2 of 2)	5769	NM_009779	12267	Mm.2408	NM_009779	ENSMUSG00000040552	C3ar1	AZ3B|C3AR|HNFAG09	complement component 3a receptor 1	protein-coding
mm_117891.1	chr13	99422876	99422887	-	1	NA	3' UTR (NM_008634, exon 7 of 7)	3' UTR (NM_008634, exon 7 of 7)	-10055	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_140540.1	chr17	6782776	6782784	-	1	NA	promoter-TSS (NM_009510)	promoter-TSS (NM_009510)	0	NM_009510	22350	Mm.277812	NM_009510	ENSMUSG00000052397	Ezr	AW146364|R75297|Vil2|p81	ezrin	protein-coding
mm_67677.1	chr7	89189715	89189721	-	1	NA	intron (NM_028343, intron 6 of 14)	intron (NM_028343, intron 6 of 14)	149069	NM_028343	72759	Mm.208477	NM_028343	ENSMUSG00000039428	Tmem135	2810439K08Rik|AW319712|PMP52	transmembrane protein 135	protein-coding
mm_55626.1	chr6	72310768	72310780	-	1	NA	exon (NM_001282071, exon 8 of 11)	exon (NM_001282071, exon 8 of 11)	6164	NM_147779	20388	Mm.46033	NM_147779	ENSMUSG00000056370	Sftpb	AI562151|SF-B|SP-B|Sftp-3|Sftp3	surfactant associated protein B	protein-coding
mm_30416.1	chr3	152265823	152265850	-	1	NA	intron (NM_199465, intron 1 of 12)	CpG	484	NM_199465	68810	Mm.200188	NM_199465	ENSMUSG00000039103	Nexn	1110046H09Rik|AA553326|NELIN	nexilin	protein-coding
mm_146318.1	chr18	80555228	80555233	+	1	NA	Intergenic	Intergenic	-10684	NR_028424	100039348	Mm.254722	NR_028424		Gm2176	A430076E10Rik	glucosamine-6-phosphate deaminase 1 pseudogene	pseudo
mm_102156.1	chr11	53713082	53713086	-	1	NA	Intergenic	RMER1C|Other|Other	-5765	NM_009012	19360	Mm.4888	NM_009012	ENSMUSG00000020380	Rad50	Mrell|Rad50l	RAD50 double strand break repair protein	protein-coding
mm_68544.1	chr7	114117762	114117787	-	1	NA	promoter-TSS (NM_025846)	promoter-TSS (NM_025846)	7	NM_025846	66922	Mm.276572	NM_025846	ENSMUSG00000055723	Rras2	2610016H24Rik|C86394|TC21	related RAS viral (r-ras) oncogene 2	protein-coding
mm_75865.1	chr8	70760890	70760953	-	1	NA	promoter-TSS (NM_183170)	promoter-TSS (NM_183170)	0	NM_183170	234384	Mm.213010	NM_183170	ENSMUSG00000035559	Mpv17l2	Fksg24	MPV17 mitochondrial membrane protein-like 2	protein-coding
mm_145899.1	chr18	65631744	65631747	+	1	NA	intron (NM_207255, intron 3 of 5)	B1_Mur1|SINE|Alu	-12130	NR_105742	100526497		NR_105742	ENSMUSG00000077113	Mir466p	mmu-mir-466p	microRNA 466p	ncRNA
mm_115419.1	chr13	117050581	117050606	+	1	NA	Intergenic	Intergenic	-25077	NM_001081009	52552	Mm.274466	NM_027272	ENSMUSG00000021725	Parp8	2810430O08Rik|ARTD16|D13Ertd275e	poly (ADP-ribose) polymerase family, member 8	protein-coding
mm_133000.1	chr16	55966295	55966334	+	1	NA	promoter-TSS (NM_024218)	promoter-TSS (NM_024218)	39	NM_024218	68193	Mm.29221	NM_024218	ENSMUSG00000098274	Rpl24	0610008L05Rik|Bst	ribosomal protein L24	protein-coding
mm_50233.1	chr6	42351106	42351127	+	1	NA	exon (NM_001289618, exon 3 of 10)	exon (NM_001289618, exon 3 of 10)	1288	NM_001289619	22793	Mm.282303	NM_011777	ENSMUSG00000029860	Zyx	9530098H06Rik|R75157	zyxin	protein-coding
mm_4445.1	chr1	172550745	172550769	+	1	NA	promoter-TSS (NR_040558)	promoter-TSS (NR_040558)	49	NR_040558	71319	Mm.123774	NR_040558	ENSMUSG00000085184	4933439K11Rik	-	RIKEN cDNA 4933439K11 gene	ncRNA
mm_165883.1	chr4	42773988	42773995	-	1	NA	promoter-TSS (NM_011124)	promoter-TSS (NM_011124)	0	NM_011124	18829	Mm.220853	NM_011124	ENSMUSG00000094686	Ccl21a	6CKBAC2|6Ckine|ALP|AW987545|CKb9|SCYA21a|SLC|Scya21|Scya21b|Tca4|plt	chemokine (C-C motif) ligand 21A (serine)	protein-coding
mm_166645.1	chr6	85122730	85122731	-	1	NA	intron (NM_001034902, intron 1 of 2)	intron (NM_001034902, intron 1 of 2)	3364	NM_001034902	545861	Mm.321419	NM_001034902	ENSMUSG00000072952	Gm5878	EG545861	predicted gene 5878	protein-coding
mm_86669.1	chr10	18055521	18055595	+	1	NA	promoter-TSS (NM_001111065)	promoter-TSS (NM_001111065)	-382	NM_009048	19707	Mm.4479	NM_009048	ENSMUSG00000019854	Reps1	BB161292	RalBP1 associated Eps domain containing protein	protein-coding
mm_170847.1	chr2	177600329	177600347	+	1	NA	Intergenic	Intergenic	102112	NR_036450	433520	Mm.425117	NM_001024825		Gm14403	OTTMUSG00000016571	predicted gene 14403	ncRNA
mm_55704.1	chr6	72957827	72957839	-	1	NA	intron (NM_001190327, intron 3 of 3)	intron (NM_001190327, intron 3 of 3)	399	NM_001039392	19240	Mm.3532	NM_025284	ENSMUSG00000079523	Tmsb10	Ptmb10|Tb10	thymosin, beta 10	protein-coding
mm_69272.1	chr7	127930067	127930122	-	1	NA	promoter-TSS (NM_133351)	promoter-TSS (NM_133351)	19	NM_133351	76560	Mm.5875	NM_133351	ENSMUSG00000030800	Prss8	2410039E18Rik|AI313909|C79772|CAP1|fr|mCAP1	protease, serine 8 (prostasin)	protein-coding
mm_68826.1	chr7	126200120	126200168	-	1	NA	5' UTR (NM_028816, exon 1 of 24)	5' UTR (NM_028816, exon 1 of 24)	264	NM_028816	74204	Mm.235663	NM_028816	ENSMUSG00000000131	Xpo6	2610005L19Rik|AL022631|C230091E20Rik|R75304|Ranbp20|mKIAA0370	exportin 6	protein-coding
mm_111804.1	chr12	105010063	105010086	-	1	NA	promoter-TSS (NM_172500)	promoter-TSS (NM_172500)	-265	NM_172500	212073	Mm.212688	NM_172500	ENSMUSG00000054150	Syne3	nesprin-3	spectrin repeat containing, nuclear envelope family member 3	protein-coding
mm_144783.1	chr18	35854680	35854715	+	1	NA	intron (NM_133687, intron 1 of 2)	intron (NM_133687, intron 1 of 2)	24879	NM_133687	67393	Mm.94560	NM_133687	ENSMUSG00000046668	Cxxc5	4930415K17Rik	CXXC finger 5	protein-coding
mm_139853.1	chr17	69969076	69969086	+	1	NA	promoter-TSS (NM_001347412)	promoter-TSS (NM_001347412)	8	NM_001347411	224997	Mm.311840	NM_027712	ENSMUSG00000003279	Dlgap1	4933422O14Rik|9630002F18|AI845682|AI848168|BB075781|D17Bwg0511e|GKAP/SAPAP|GKPA/SAPAP|Gkap|Sapap1|mKIAA4162	discs, large (Drosophila) homolog-associated protein 1	protein-coding
mm_165561.1	chr3	14886525	14886569	+	1	NA	5' UTR (NM_009801, exon 1 of 7)	5' UTR (NM_009801, exon 1 of 7)	121	NM_009801	12349	Mm.1186	NM_009801	ENSMUSG00000027562	Car2	AI131712|CAII|Ca2|Car-2|Ltw-5|Lvtw-5	carbonic anhydrase 2	protein-coding
mm_74931.1	chr8	25754215	25754250	-	1	NA	promoter-TSS (NM_028102)	promoter-TSS (NM_028102)	48	NM_028102	72108	Mm.246875	NM_028102	ENSMUSG00000061313	Ddhd2	2010305K11Rik|SAMWD1|mKIAA0725	DDHD domain containing 2	protein-coding
mm_158034.1	chrX	98259744	98259773	-	1	NA	intron (NM_013476, intron 2 of 7)	intron (NM_013476, intron 2 of 7)	111001	NM_013476	11835	Mm.39005	NM_013476	ENSMUSG00000046532	Ar	AW320017|Tfm	androgen receptor	protein-coding
mm_102279.1	chr11	55395575	55395594	-	1	NA	3' UTR (NM_009242, exon 10 of 10)	3' UTR (NM_009242, exon 10 of 10)	24496	NM_009242	20692	Mm.291442	NM_009242	ENSMUSG00000018593	Sparc	BM-40|ON	secreted acidic cysteine rich glycoprotein	protein-coding
mm_94154.1	chr10	128744266	128744282	-	1	NA	promoter-TSS (NM_016811)	promoter-TSS (NM_016811)	-218	NM_016811	13139	Mm.291235	NM_016811	ENSMUSG00000025357	Dgka	80kDa|AW146112|Dagk1	diacylglycerol kinase, alpha	protein-coding
mm_118976.1	chr14	28030386	28030393	+	1	NA	intron (NM_001347497, intron 12 of 19)	intron (NM_001347497, intron 12 of 19)	407982	NM_177814	238988	Mm.318004	NM_177814	ENSMUSG00000040640	Erc2	6430531D06|CAST|CAST1/ERC2|D14Ertd171e|ELKS2alpha	ELKS/RAB6-interacting/CAST family member 2	protein-coding
mm_158633.1	chrX	153696196	153696258	-	1	NA	promoter-TSS (NM_175429)	promoter-TSS (NM_175429)	53	NM_175429	207474	Mm.271572	NM_175429	ENSMUSG00000041633	Kctd12b	9530071H11Rik|B430319H24Rik	potassium channel tetramerisation domain containing 12b	protein-coding
mm_40476.1	chr5	54045827	54045830	+	1	NA	intron (NM_001081103, intron 1 of 11)	intron (NM_001081103, intron 1 of 11)	47305	NM_001081103	116873	Mm.265985	NM_054083	ENSMUSG00000039156	Stim2	-	stromal interaction molecule 2	protein-coding
mm_54298.1	chr6	29397660	29397661	-	1	NA	intron (NM_001347071, intron 2 of 17)	intron (NM_001347071, intron 2 of 17)	1076	NM_001347073	232664	Mm.251303	NM_145574	ENSMUSG00000029769	Ccdc136	4921511K06Rik|BC006583	coiled-coil domain containing 136	protein-coding
mm_91187.1	chr10	21125438	21125450	-	1	NA	3' UTR (NM_001198914, exon 16 of 16)	3' UTR (NM_001198914, exon 16 of 16)	35540	NM_001198914	17863	Mm.52109	NM_010848	ENSMUSG00000019982	Myb	AI550390|M16449|c-myb	myeloblastosis oncogene	protein-coding
mm_140606.1	chr17	10320327	10320346	-	1	NA	promoter-TSS (NM_001159517)	promoter-TSS (NM_001159517)	417	NR_037588	100526796	Mm.384135	NR_037588		Cahm	B930003M22Rik	colon adenocarcinoma hypermethylated RNA	ncRNA
mm_32869.1	chr4	118431207	118431214	+	1	NA	intron (NM_001039176, intron 4 of 7)	intron (NM_001039176, intron 4 of 7)	1509	NM_001039176	54325	Mm.282096	NM_019422	ENSMUSG00000006390	Elovl1	AA407424|BB151133|Ssc1	elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 1	protein-coding
mm_71414.1	chr8	46474377	46474390	+	1	NA	intron (NM_007981, intron 1 of 20)	B3|SINE|B2	3346	NM_007981	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_49248.1	chr6	17307879	17307893	+	1	NA	exon (NM_007616, exon 2 of 3)	exon (NM_007616, exon 2 of 3)	246	NM_001243064	12389	Mm.28278	NM_007616	ENSMUSG00000007655	Cav1	Cav|Cav-1	caveolin 1, caveolae protein	protein-coding
mm_27649.1	chr3	63929377	63929413	-	1	NA	promoter-TSS (NM_177856)	promoter-TSS (NM_177856)	-10	NM_177856	329659	Mm.39342	NM_177856	ENSMUSG00000048581	E130311K13Rik	-	RIKEN cDNA E130311K13 gene	protein-coding
mm_40551.1	chr5	58132547	58132550	+	1	NA	3' UTR (NM_001310606, exon 3 of 3)	3' UTR (NM_001310606, exon 3 of 3)	320450	NR_046190	78163	Mm.243828	NR_046190	ENSMUSG00000105234	4930459L07Rik	-	RIKEN cDNA 4930459L07 gene	ncRNA
mm_155635.1	chrX	85048285	85048307	+	1	NA	promoter-TSS (NM_001314037)	promoter-TSS (NM_001314037)	1	NM_001314034	13405	Mm.275608	NM_007868	ENSMUSG00000045103	Dmd	DXSmh7|DXSmh9|Dp427|Dp71|dys|mdx|pke	dystrophin, muscular dystrophy	protein-coding
mm_94891.1	chr11	28763469	28763472	+	1	NA	promoter-TSS (NR_029828)	promoter-TSS (NR_029828)	-258	NR_029828	387213		NR_029828	ENSMUSG00000065415	Mir217	Mirn217|mir-217|mmu-mir-217	microRNA 217	ncRNA
mm_49004.1	chr6	4757020	4757034	+	1	NA	exon (NM_130877, exon 2 of 2)	exon (NM_130877, exon 2 of 2)	9721	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_124975.1	chr15	20449082	20449088	+	1	NA	Intergenic	Intergenic	217665	NM_022816	64833	Mm.352763	NM_022816	ENSMUSG00000047565	Acot10	Acate3|MT-ACT48|p48	acyl-CoA thioesterase 10	protein-coding
mm_11546.1	chr2	32657601	32657613	+	1	NA	exon (NM_001146350, exon 2 of 14)	exon (NM_001146350, exon 2 of 14)	11012	NM_001146348	13805	Mm.225297	NM_007932	ENSMUSG00000026814	Eng	AI528660|AI662476|CD105|Endo|S-endoglin	endoglin	protein-coding
mm_57572.1	chr6	127139222	127139251	-	1	NA	exon (NM_009829, exon 4 of 5)	exon (NM_009829, exon 4 of 5)	-10153	NR_040274	77558	Mm.358918	NR_040273	ENSMUSG00000097166	9330179D12Rik	-	RIKEN cDNA 9330179D12 gene	ncRNA
mm_99155.1	chr11	100580885	100580889	+	1	NA	3' UTR (NM_009923, exon 4 of 4)	3' UTR (NM_009923, exon 4 of 4)	4996	NM_001146318	12799	Mm.15711	NM_009923	ENSMUSG00000006782	Cnp	CNPase|Cnp-1|Cnp1	2',3'-cyclic nucleotide 3' phosphodiesterase	protein-coding
mm_57600.1	chr6	127796275	127796296	-	1	NA	Intergenic	Intergenic	-8142	NR_106092	102466996		NR_106092	ENSMUSG00000104804	Mir7233	mmu-mir-7233	microRNA 7233	ncRNA
mm_123347.1	chr14	63141797	63141821	-	1	NA	exon (NM_007798, exon 9 of 10)	exon (NM_007798, exon 9 of 10)	19347	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_73136.1	chr8	94977102	94977123	+	1	NA	promoter-TSS (NM_001198894)	promoter-TSS (NM_001198894)	3	NM_001198894	14766	Mm.290834	NM_018882	ENSMUSG00000031785	Adgrg1	Cyt28|Gpr56|TM7LN4|TM7XN1	adhesion G protein-coupled receptor G1	protein-coding
mm_66054.1	chr7	30737933	30737939	-	1	NA	exon (NM_001290631, exon 2 of 11)	exon (NM_001290631, exon 2 of 11)	1471	NM_008085	14447	Mm.436562	NM_008085	ENSMUSG00000061099	Gapdhs	Gapd-s|Gapds	glyceraldehyde-3-phosphate dehydrogenase, spermatogenic	protein-coding
mm_87299.1	chr10	42534860	42534875	+	1	NA	3' UTR (NM_017472, exon 4 of 4)	3' UTR (NM_017472, exon 4 of 4)	32813	NM_017472	54198	Mm.277870	NM_017472	ENSMUSG00000019804	Snx3	SDP3	sorting nexin 3	protein-coding
mm_30252.1	chr3	146596589	146596611	-	1	NA	promoter-TSS (NM_009474)	promoter-TSS (NM_009474)	-549	NM_009474	22262	Mm.10865	NM_009474	ENSMUSG00000028186	Uox	AI663847	urate oxidase	protein-coding
mm_152951.1	chr19	29047833	29047844	-	1	NA	promoter-TSS (NM_021299)	promoter-TSS (NM_021299)	64	NM_021299	56248	Mm.196067	NM_021299	ENSMUSG00000024782	Ak3	AA407498|AI506714|AK-3|Ak3l|Ak3l1|Akl3l	adenylate kinase 3	protein-coding
mm_49582.1	chr6	30642856	30642881	+	1	NA	exon (NM_025350, exon 8 of 10)	exon (NM_025350, exon 8 of 10)	3650	NM_025350	109697	Mm.25377	NM_025350	ENSMUSG00000054446	Cpa1	0910001L12Rik|Cpa	carboxypeptidase A1, pancreatic	protein-coding
mm_91040.1	chr10	18545794	18545806	-	1	NA	5' UTR (NM_019487, exon 1 of 4)	5' UTR (NM_019487, exon 1 of 4)	276	NM_019487	56016	Mm.35551	NM_019487	ENSMUSG00000019853	Hebp2	SOUL	heme binding protein 2	protein-coding
mm_85109.1	chr9	95404735	95404748	-	1	NA	exon (NM_018763, exon 2 of 2)	exon (NM_018763, exon 2 of 2)	2529	NM_018763	54371	Mm.212446	NM_018763	ENSMUSG00000033350	Chst2	AI428561|AW121776|C130041E03Rik|Chts2|GST-2|GlcNAc6ST|Gn6st	carbohydrate sulfotransferase 2	protein-coding
mm_11876.1	chr2	49451843	49451849	+	1	NA	exon (NM_172663, exon 1 of 14)	exon (NM_172663, exon 1 of 14)	360	NM_172663	227867	Mm.29167	NM_172663	ENSMUSG00000069495	Epc2	5830499L14|D2Ertd694e	enhancer of polycomb homolog 2 (Drosophila)	protein-coding
mm_121934.1	chr14	24003927	24003984	-	1	NA	exon (NM_001253365, exon 1 of 30)	exon (NM_001253365, exon 1 of 30)	250	NM_001253375	16531	Mm.343607	NM_010610	ENSMUSG00000063142	Kcnma1	5730414M22Rik|BKCa|MaxiK|Slo|Slo1|mSlo|mSlo1	potassium large conductance calcium-activated channel, subfamily M, alpha member 1	protein-coding
mm_28156.1	chr3	87748620	87748630	-	1	NA	promoter-TSS (NM_028971)	promoter-TSS (NM_028971)	-2	NM_028971	74485	Mm.474494	NM_028971	ENSMUSG00000023084	Lrrc71	4933430H15Rik	leucine rich repeat containing 71	protein-coding
mm_83024.1	chr9	37208032	37208034	-	1	NA	promoter-TSS (NM_025464)	promoter-TSS (NM_025464)	-190	NM_025464	66279	Mm.41451	NM_025464	ENSMUSG00000032121	Tmem218	1810021J13Rik|AV004931	transmembrane protein 218	protein-coding
mm_86236.1	chr9	120755617	120755644	-	1	NA	Intergenic	RLTR20A4|LTR|ERVK	159620	NR_040742	76402	Mm.436588	NR_040742	ENSMUSG00000100146	1700020M21Rik	-	RIKEN cDNA 1700020M21 gene	ncRNA
mm_160805.1	chr11	9048983	9048983	-	1	NA	promoter-TSS (NM_001290520)	promoter-TSS (NM_001290520)	8	NM_001290520	194974	Mm.79210	NM_177576	ENSMUSG00000040985	Sun3	Sunc1	Sad1 and UNC84 domain containing 3	protein-coding
mm_33580.1	chr4	132532675	132532701	+	1	NA	intron (NM_007512, intron 3 of 3)	intron (NM_007512, intron 3 of 3)	2726	NM_007512	11983	Mm.2171	NM_007512	ENSMUSG00000054428	Atpif1	Atpi|IF(1)|If1	ATPase inhibitory factor 1	protein-coding
mm_37947.1	chr4	133169639	133169643	-	1	NA	intron (NM_153423, intron 1 of 8)	intron (NM_153423, intron 1 of 8)	-26014	NR_105984	102466215		NR_105984	ENSMUSG00000099202	Mir7017	Gm27945|mmu-mir-7017	microRNA 7017	ncRNA
mm_127419.1	chr15	101261691	101261705	+	1	NA	Intergenic	Intergenic	-5148	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_83175.1	chr9	40783651	40783661	-	1	NA	3' UTR (NM_133733, exon 7 of 7)	3' UTR (NM_133733, exon 7 of 7)	-17617	NM_031165	15481	Mm.290774	NM_031165	ENSMUSG00000015656	Hspa8	2410008N15Rik|Hsc70|Hsc71|Hsc73|Hsp73|Hspa10	heat shock protein 8	protein-coding
mm_102350.1	chr11	58201558	58201574	-	1	NA	5' UTR (NM_018738, exon 2 of 3)	5' UTR (NM_018738, exon 2 of 3)	2010	NM_018738	16145	Mm.33902	NM_018738	ENSMUSG00000078853	Igtp	AW558444|Irgm3	interferon gamma induced GTPase	protein-coding
mm_92125.1	chr10	64055748	64055758	-	1	NA	intron (NM_178678, intron 2 of 2)	intron (NM_178678, intron 2 of 2)	34502	NM_178678	216028	Mm.431318	NM_178678	ENSMUSG00000042846	Lrrtm3	9630044H04Rik	leucine rich repeat transmembrane neuronal 3	protein-coding
mm_79171.1	chr9	47852556	47852572	+	1	NA	3' UTR (NM_018770, exon 10 of 10)	3' UTR (NM_018770, exon 10 of 10)	-34356	NR_046048	100038460	Mm.447649	NR_046048		Gm10677	ENSMUSG00000074363	predicted gene 10677	ncRNA
mm_66760.1	chr7	46728599	46728628	-	1	NA	3' UTR (NM_011316, exon 4 of 4)	3' UTR (NM_011316, exon 4 of 4)	3990	NM_011316	20211	Mm.3489	NM_011316	ENSMUSG00000040017	Saa4	Saa-4|Saa-5	serum amyloid A 4	protein-coding
mm_135634.1	chr16	52338508	52338542	-	1	NA	intron (NM_009655, intron 1 of 15)	L1_Mus3|LINE|L1	114556	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_130349.1	chr15	97749786	97749797	-	1	NA	intron (NM_144850, intron 21 of 27)	intron (NM_144850, intron 21 of 27)	17875	NM_001177810	223864	Mm.24028	NM_144850	ENSMUSG00000022469	Rapgef3	2310016P22Rik|9330170P05Rik|Epac|Epac1	Rap guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_150668.1	chr19	42045859	42045897	+	1	NA	promoter-TSS (NM_026152)	promoter-TSS (NM_026152)	27	NM_026152	67432	Mm.24196	NM_026152	ENSMUSG00000025176	Hoga1	0610010D20Rik|Dhdpsl|Npl2	4-hydroxy-2-oxoglutarate aldolase 1	protein-coding
mm_47653.1	chr5	125392259	125392275	-	1	NA	Intergenic	B1_Mur4|SINE|Alu	-2250	NM_019639	22190	Mm.331	NM_019639	ENSMUSG00000008348	Ubc	2700054O04Rik|AI194771|Rps27a|TI-225|Uba52|Ubb	ubiquitin C	protein-coding
mm_157424.1	chrX	38564636	38564671	-	1	NA	intron (NM_001110142, intron 3 of 22)	intron (NM_001110142, intron 3 of 22)	11543	NM_028288	72584	Mm.327675	NM_028288	ENSMUSG00000031095	Cul4b	2700050M05Rik|AA409770|CUL-4B|mKIAA0695	cullin 4B	protein-coding
mm_76850.1	chr8	105326282	105326301	-	1	NA	promoter-TSS (NM_177449)	promoter-TSS (NM_177449)	-15	NM_177449	234684	Mm.381717	NM_177449	ENSMUSG00000041679	Lrrc29	A630024J02Rik|FBL9|FBXL9	leucine rich repeat containing 29	protein-coding
mm_98866.1	chr11	97798996	97799021	+	1	NA	promoter-TSS (NM_010688)	promoter-TSS (NM_010688)	-664	NM_010688	16796	Mm.271967	NM_010688	ENSMUSG00000038366	Lasp1	AA408629|Def-4|SH3P6|Tg(Col1a1-lacZ)1Ngma	LIM and SH3 protein 1	protein-coding
mm_29219.1	chr3	107211318	107211326	-	1	NA	TTS (NM_001111143)	TTS (NM_001111143)	10410	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_99727.1	chr11	106300781	106300803	+	1	NA	exon (NM_008117, exon 4 of 5)	exon (NM_008117, exon 4 of 5)	1104	NM_008117	14599	Mm.343934	NM_008117	ENSMUSG00000020713	Gh	Gh1|Ghb1	growth hormone	protein-coding
mm_172103.1	chr6	31799484	31799499	-	1	NA	Intergenic	IAPLTR1_Mm|LTR|ERVK	-235554	NM_013723	27205	Mm.89918	NM_013723	ENSMUSG00000025608	Podxl	AW121214|Ly102|PC|PCLP-1|Pclp1	podocalyxin-like	protein-coding
mm_170421.1	chr18	7033716	7033718	+	1	NA	Intergenic	L1Md_F2|LINE|L1	-28938	NM_177595	210719	Mm.257186	NM_177595	ENSMUSG00000061013	Mkx	9430023B20Rik|Irxl1	mohawk homeobox	protein-coding
mm_19013.1	chr2	76905809	76905822	-	1	NA	intron (NM_011652, intron 46 of 312)	B1_Mur4|SINE|Alu	76732	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_26821.1	chr3	10335651	10335661	-	1	NA	promoter-TSS (NM_001010834)	promoter-TSS (NM_001010834)	0	NM_001010834	241877	Mm.442146	NM_001010834	ENSMUSG00000058921	Slc10a5	Gm405|mP5	solute carrier family 10 (sodium/bile acid cotransporter family), member 5	protein-coding
mm_67983.1	chr7	100662432	100662440	-	1	NA	promoter-TSS (NM_001163182)	promoter-TSS (NM_001163182)	-42	NM_001163182	27276	Mm.491216	NM_013746	ENSMUSG00000030701	Plekhb1	AI315628|PHR1|Phret1|evt-1	pleckstrin homology domain containing, family B (evectins) member 1	protein-coding
mm_140638.1	chr17	12652740	12652753	-	1	NA	intron (NM_009202, intron 8 of 10)	intron (NM_009202, intron 8 of 10)	23092	NM_009202	20517	Mm.594	NM_009202	ENSMUSG00000023829	Slc22a1	Lx1|Oct1|Orct|Orct1	solute carrier family 22 (organic cation transporter), member 1	protein-coding
mm_54505.1	chr6	35510751	35510764	-	1	NA	3' UTR (NM_008098, exon 4 of 4)	3' UTR (NM_008098, exon 4 of 4)	29131	NM_008098	14489	Mm.182746	NM_008098	ENSMUSG00000029840	Mtpn	5033418D15Rik|Gcdp|V1	myotrophin	protein-coding
mm_145283.1	chr18	53195190	53195192	+	1	NA	intron (NM_026386, intron 3 of 14)	intron (NM_026386, intron 3 of 14)	18826	NM_026386	67804	Mm.252171	NM_026386	ENSMUSG00000034484	Snx2	0610030A03Rik	sorting nexin 2	protein-coding
mm_17876.1	chr2	34958153	34958173	-	1	NA	intron (NM_009421, intron 4 of 10)	intron (NM_009421, intron 4 of 10)	3609	NM_009421	22029	Mm.239514	NM_009421	ENSMUSG00000026875	Traf1	4732496E14Rik	TNF receptor-associated factor 1	protein-coding
mm_57347.1	chr6	124756324	124756363	-	1	NA	5' UTR (NM_007881, exon 1 of 10)	5' UTR (NM_007881, exon 1 of 10)	144	NM_007881	13498	Mm.333380	NM_007881	ENSMUSG00000004263	Atn1	Atr1|Drpla|atrophin-1	atrophin 1	protein-coding
mm_13395.1	chr2	103970116	103970174	+	1	NA	promoter-TSS (NM_008505)	promoter-TSS (NM_008505)	-142	NM_008505	16909	Mm.29266	NM_008505	ENSMUSG00000032698	Lmo2	Rbtn-2|Rbtn2|Rhom-2|Ttg2	LIM domain only 2	protein-coding
mm_93295.1	chr10	96400773	96400777	-	1	NA	Intergenic	Intergenic	174568	NR_110448	74881	Mm.410819	NR_110448		4930459C07Rik	-	RIKEN cDNA 4930459C07 gene	ncRNA
mm_165790.1	chr3	135440263	135440276	-	1	NA	intron (NM_025356, intron 2 of 7)	intron (NM_025356, intron 2 of 7)	1510	NM_025356	66105	Mm.49884	NM_025356	ENSMUSG00000078578	Ube2d3	1100001F19Rik|9430029A22Rik|AA414951	ubiquitin-conjugating enzyme E2D 3	protein-coding
mm_37547.1	chr4	125127287	125127307	-	1	NA	intron (NM_153159, intron 1 of 5)	MIRb|SINE|MIR	584	NM_153159	230738	Mm.402	NM_153159	ENSMUSG00000042677	Zc3h12a	BC036563|MCPIP|MCPIP-1|Mcpip1|Reg1	zinc finger CCCH type containing 12A	protein-coding
mm_9402.1	chr1	172258411	172258438	-	1	NA	promoter-TSS (NM_013734)	promoter-TSS (NM_013734)	0	NM_013734	27222	Mm.482392	NM_013734	ENSMUSG00000007107	Atp1a4	-	ATPase, Na+/K+ transporting, alpha 4 polypeptide	protein-coding
mm_151487.1	chr19	58679525	58679537	+	1	NA	exon (NM_026925, exon 10 of 13)	exon (NM_026925, exon 10 of 13)	9166	NM_026925	69060	Mm.20407	NM_026925	ENSMUSG00000046008	Pnlip	1810007A24Rik|PL|PTL	pancreatic lipase	protein-coding
mm_14722.1	chr2	143989981	143990064	+	1	NA	exon (NM_133626, exon 2 of 3)	exon (NM_133626, exon 2 of 3)	21241	NM_133626	81910	Mm.13705	NM_024281	ENSMUSG00000027422	Rrbp1	1700087N07Rik|5730465C04Rik|ES/130|mKIAA1398|mRRp0|mRRp1.8|mRRp10|mRRp15a|mRRp15b|mRRp16.8|mRRp2|mRRp41|mRRp47|mRRp5.4|p180	ribosome binding protein 1	protein-coding
mm_165025.1	chr19	32472866	32472869	+	1	NA	Intergenic	L1M2|LINE|L1	-12902	NM_010799	17330	Mm.255116	NM_010799	ENSMUSG00000024896	Minpp1	AA408516	multiple inositol polyphosphate histidine phosphatase 1	protein-coding
mm_25813.1	chr3	127791039	127791049	+	1	NA	intron (NM_145133, intron 1 of 2)	intron (NM_145133, intron 1 of 2)	1131	NM_145133	211550	Mm.31852	NM_145133	ENSMUSG00000046688	Tifa	T2bp	TRAF-interacting protein with forkhead-associated domain	protein-coding
mm_73109.1	chr8	94666777	94666787	+	1	NA	promoter-TSS (NM_024269)	promoter-TSS (NM_024269)	182	NM_024191	107566	Mm.393247	NM_024191	ENSMUSG00000031776	Arl2bp	1700010P10Rik|1700027H16Rik|6330544B05Rik|AI482273|AI849834|BART|Bart1	ADP-ribosylation factor-like 2 binding protein	protein-coding
mm_119354.1	chr14	41114754	41114775	+	1	NA	exon (NM_133653, exon 6 of 10)	exon (NM_133653, exon 6 of 10)	9731	NM_133653	11720	Mm.14064	NM_133653	ENSMUSG00000037798	Mat1a	AI046368|AdoMet|Ams|MAT|MATA1|SAMS|SAMS1	methionine adenosyltransferase I, alpha	protein-coding
mm_82867.1	chr9	32344309	32344352	-	1	NA	promoter-TSS (NM_010605)	promoter-TSS (NM_010605)	-93	NM_010605	16521	Mm.69472	NM_010605	ENSMUSG00000032034	Kcnj5	GIRK4|Kir3.4	potassium inwardly-rectifying channel, subfamily J, member 5	protein-coding
mm_135135.1	chr16	35845357	35845367	-	1	NA	exon (NM_001039530, exon 10 of 17)	exon (NM_001039530, exon 10 of 17)	26020	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_143060.1	chr17	57011222	57011232	-	1	NA	promoter-TSS (NM_133801)	promoter-TSS (NM_133801)	61	NM_133801	98053	Mm.24632	NM_133801	ENSMUSG00000002658	Gtf2f1	2810405L04Rik|C76800|RAP74	general transcription factor IIF, polypeptide 1	protein-coding
mm_140270.1	chr17	84683160	84683185	+	1	NA	promoter-TSS (NM_031884)	promoter-TSS (NM_031884)	51	NM_026180	67470	Mm.26581	NM_026180	ENSMUSG00000024254	Abcg8	1300003C16Rik|AI114946|sterolin-2	ATP-binding cassette, sub-family G (WHITE), member 8	protein-coding
mm_75355.1	chr8	45261977	45261996	-	1	NA	promoter-TSS (NM_028066)	promoter-TSS (NM_028066)	45	NM_028066	109821	Mm.33326	NM_028066	ENSMUSG00000031645	F11	1600027G01Rik|AI503996|Cf11|FXI|PTA	coagulation factor XI	protein-coding
mm_134663.1	chr16	22246873	22246875	-	1	NA	intron (NM_009186, intron 8 of 8)	intron (NM_009186, intron 8 of 8)	19131	NM_001330554	20462	Mm.210352	NM_009186	ENSMUSG00000022858	Tra2b	5730405G21Rik|D16Ertd266e|SIG-41|Sfrs10|Silg41|TRA2beta	transformer 2 beta homolog (Drosophila)	protein-coding
mm_133810.1	chr16	95702399	95702435	+	1	NA	promoter-TSS (NM_011809)	promoter-TSS (NM_011809)	10	NM_011809	23872	Mm.290207	NM_011809	ENSMUSG00000022895	Ets2	AU022856|Ets-2	E26 avian leukemia oncogene 2, 3' domain	protein-coding
mm_7529.1	chr1	124240249	124240259	-	1	NA	Intergenic	Intergenic	-194695	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_73508.1	chr8	107368065	107368098	+	1	NA	exon (NM_018823, exon 13 of 15)	exon (NM_018823, exon 13 of 15)	35124	NM_008706	18104	Mm.252	NM_008706	ENSMUSG00000003849	Nqo1	AV001255|Dia4|Dtd|Nmo-1|Nmo1|Nmor1|Ox-1|Ox1|Qr1	NAD(P)H dehydrogenase, quinone 1	protein-coding
mm_6098.1	chr1	63686905	63686917	-	1	NA	promoter-TSS (NM_001081658)	promoter-TSS (NM_001081658)	16	NM_001081658	241073	Mm.297680	NM_001081658	ENSMUSG00000069085	Dytn	Gm215	dystrotelin	protein-coding
mm_163392.1	chr12	63387701	63387710	+	1	NA	Intergenic	(TTAG)n|Simple_repeat|Simple_repeat	699918	NR_131949	73309	Mm.276558	NR_131949		Spanxn4	1700047L15Rik	SPANX family, member N4	ncRNA
mm_72930.1	chr8	91313246	91313246	+	1	NA	promoter-TSS (NM_173431)	promoter-TSS (NM_173431)	-24	NM_173431	244585	Mm.324592	NM_173431	ENSMUSG00000033282	Rpgrip1l	1700047E16Rik|4931437C01|Ftm|Nphp8	Rpgrip1-like	protein-coding
mm_169376.1	chr14	37229308	37229308	-	1	NA	Intergenic	IAPLTR1_Mm|LTR|ERVK	-93986	NM_078478	66092	Mm.182912	NM_078478	ENSMUSG00000041028	Ghitm	1010001P14Rik|C77840|MICS1|PTD010|Tmbim5	growth hormone inducible transmembrane protein	protein-coding
mm_114470.1	chr13	67813778	67813831	+	1	NA	promoter-TSS (NM_198322)	promoter-TSS (NM_198322)	-12	NM_198322	212569	Mm.358842	NM_198322	ENSMUSG00000030446	Zfp273	6820416H06Rik|Rslcan1	zinc finger protein 273	protein-coding
mm_34354.1	chr4	144613668	144613683	+	1	NA	promoter-TSS (NM_001081248)	promoter-TSS (NM_001081248)	-32	NM_001081248	435815	Mm.439623	NM_001081248	ENSMUSG00000070609	Gm13177	OTTMUSG00000010747	predicted gene 13177	protein-coding
mm_124298.1	chr14	103055232	103055242	-	1	NA	exon (NM_008392, exon 5 of 5)	exon (NM_008392, exon 5 of 5)	8225	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_71464.1	chr8	46534575	46534600	+	1	NA	3' UTR (NM_007981, exon 21 of 21)	3' UTR (NM_007981, exon 21 of 21)	-17482	NM_027973	71876	Mm.22108	NM_027973	ENSMUSG00000031629	Cenpu	1700029A22Rik|Mlf1ip	centromere protein U	protein-coding
mm_118198.1	chr13	107885520	107885522	-	1	NA	intron (NM_145456, intron 2 of 14)	intron (NM_145456, intron 2 of 14)	4543	NM_145456	67263	Mm.490418	NM_145456	ENSMUSG00000032846	Zswim6	2900036G02Rik|mKIAA1577	zinc finger SWIM-type containing 6	protein-coding
mm_41411.1	chr5	90787570	90787579	+	1	NA	3' UTR (NM_203320, exon 4 of 4)	3' UTR (NM_203320, exon 4 of 4)	1473	NM_203320	330122	Mm.244289	NM_203320	ENSMUSG00000029379	Cxcl3	Dcip1|Gm1960	chemokine (C-X-C motif) ligand 3	protein-coding
mm_42064.1	chr5	109055716	109055720	+	1	NA	intron (NM_001104622, intron 1 of 5)	RLTR9A3B|LTR|ERVK	3734	NM_001104622	384219	Mm.469885	NM_001104622	ENSMUSG00000091450	Vmn2r11	EG384219	vomeronasal 2, receptor 11	protein-coding
mm_153454.1	chr19	41077064	41077078	-	1	NA	promoter-TSS (NM_153520)	promoter-TSS (NM_153520)	42	NM_153520	226115	Mm.54119	NM_153520	ENSMUSG00000050121	Opalin	Tmem10|Tmp10	oligodendrocytic myelin paranodal and inner loop protein	protein-coding
mm_146866.1	chr18	24603769	24603785	-	1	NA	promoter-TSS (NM_021448)	promoter-TSS (NM_021448)	40	NM_139143	106957	Mm.21688	NM_139143	ENSMUSG00000024270	Slc39a6	Ermelin	solute carrier family 39 (metal ion transporter), member 6	protein-coding
mm_7105.1	chr1	89563504	89563513	-	1	NA	intron (NM_001037136, intron 1 of 16)	intron (NM_001037136, intron 1 of 16)	108697	NM_001037136	347722	Mm.291135	NM_178119	ENSMUSG00000055013	Agap1	Centg2|Ggap1|R75364|mKIAA1099	ArfGAP with GTPase domain, ankyrin repeat and PH domain 1	protein-coding
mm_59149.1	chr7	24370008	24370016	+	1	NA	promoter-TSS (NM_001163510)	promoter-TSS (NM_001163510)	-251	NM_001163510	16534	Mm.9911	NM_008433	ENSMUSG00000054342	Kcnn4	IK1|IKCA1|KCA4|KCa3.1|SK4|SKCas|mIKCa1	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4	protein-coding
mm_61731.1	chr7	81862625	81862659	+	1	NA	promoter-TSS (NM_001291282)	promoter-TSS (NM_001291282)	-45	NM_001291282	107769	Mm.221412	NM_145375	ENSMUSG00000038623	Tm6sf1	AI428514|BC023123|C630016D09Rik	transmembrane 6 superfamily member 1	protein-coding
mm_52636.1	chr6	117174527	117174535	+	1	NA	3' UTR (NM_021704, exon 3 of 3)	3' UTR (NM_021704, exon 3 of 3)	5996	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_141638.1	chr17	33068036	33068043	-	1	NA	promoter-TSS (NM_001009544)	promoter-TSS (NM_001009544)	19	NM_001009544	74042	Mm.84774	NM_001009544	ENSMUSG00000023350	4921501E09Rik	PHF8	RIKEN cDNA 4921501E09 gene	protein-coding
mm_135875.1	chr16	62847009	62847041	-	1	NA	promoter-TSS (NM_026577)	promoter-TSS (NM_026577)	15	NM_026577	68146	Mm.96833	NM_026577	ENSMUSG00000022911	Arl13b	A530097K21Rik|A930014M17Rik|Arl2l1|C530009C10Rik|hnn	ADP-ribosylation factor-like 13B	protein-coding
mm_80314.1	chr9	74861858	74861864	+	1	NA	promoter-TSS (NM_008262)	promoter-TSS (NM_008262)	-60	NM_008262	15379	Mm.303355	NM_008262	ENSMUSG00000043013	Onecut1	D9Ertd423e|HNF-6|Hfh12|Hnf6|Hnf6b|OC-1|Oc1	one cut domain, family member 1	protein-coding
mm_145248.1	chr18	51235507	51235507	+	1	NA	intron (NM_001081224, intron 1 of 1)	MTD|LTR|ERVL-MaLR	117609	NM_001081224	71373	Mm.63546	NM_001081224	ENSMUSG00000073565	Prr16	5430406M13Rik|AI607429	proline rich 16	protein-coding
mm_34168.1	chr4	139923456	139923459	+	1	NA	Intergenic	Intergenic	9617	NR_045160	71235	Mm.61253	NR_045159	ENSMUSG00000085928	4933427I22Rik	-	RIKEN cDNA 4933427I22 gene	ncRNA
mm_154442.1	chrM	1412	1423	-	1	NA	NA	Intergenic	NA	NA								
mm_76082.1	chr8	79372647	79372669	-	1	NA	intron (NM_008539, intron 1 of 6)	MLT1B|LTR|ERVL-MaLR	26810	NM_008539	17125	Mm.223717	NM_008539	ENSMUSG00000031681	Smad1	AI528653|Madh1|Madr1|Mlp1|MusMLP	SMAD family member 1	protein-coding
mm_82625.1	chr9	21809920	21809930	-	1	NA	promoter-TSS (NR_106051)	promoter-TSS (NR_106051)	75	NR_106051	102465657		NR_106051	ENSMUSG00000098473	Mir7083	Gm27888|mmu-mir-7083	microRNA 7083	ncRNA
mm_118484.1	chr14	12189970	12190001	+	1	NA	promoter-TSS (NM_001347593)	promoter-TSS (NM_001347593)	42	NM_001347593	19270	Mm.431266	NM_008981	ENSMUSG00000021745	Ptprg	5430405N12Rik|AW046354|AW549872|RPTPgamma	protein tyrosine phosphatase, receptor type, G	protein-coding
mm_150514.1	chr19	39031260	39031270	+	1	NA	exon (NM_028089, exon 5 of 9)	exon (NM_028089, exon 5 of 9)	24246	NM_028089	72082	Mm.142581	NM_028089	ENSMUSG00000025002	Cyp2c55	2010318C06Rik	cytochrome P450, family 2, subfamily c, polypeptide 55	protein-coding
mm_18496.1	chr2	62606387	62606412	-	1	NA	exon (NM_027835, exon 10 of 16)	exon (NM_027835, exon 10 of 16)	-32378	NM_007986	14089	Mm.41816	NM_007986	ENSMUSG00000000392	Fap	SIMP	fibroblast activation protein	protein-coding
mm_14218.1	chr2	127337954	127337978	+	1	NA	promoter-TSS (NM_172539)	promoter-TSS (NM_172539)	-673	NM_172539	215095	Mm.31313	NM_172539	ENSMUSG00000050468	Astl	7420700F21|C87576|Sas1b	astacin-like metalloendopeptidase (M12 family)	protein-coding
mm_152472.1	chr19	10974665	10974710	-	1	NA	promoter-TSS (NM_023529)	promoter-TSS (NM_023529)	-17	NM_023529	69826	Mm.273404	NM_023529	ENSMUSG00000024731	Ms4a10	2010001N17Rik	membrane-spanning 4-domains, subfamily A, member 10	protein-coding
mm_71157.1	chr8	40385357	40385360	+	1	NA	3' UTR (NM_030110, exon 15 of 15)	3' UTR (NM_030110, exon 15 of 15)	-38457	NM_178395	70546	Mm.34326	NM_178395	ENSMUSG00000039470	Zdhhc2	5730415P04Rik|6430583A19Rik	zinc finger, DHHC domain containing 2	protein-coding
mm_356.1	chr1	33719864	33719901	+	1	NA	promoter-TSS (NM_008999)	promoter-TSS (NM_008999)	-14	NM_008999	19335	Mm.86744	NM_008999	ENSMUSG00000004768	Rab23	AW545388|opb|opb2	RAB23, member RAS oncogene family	protein-coding
mm_554.1	chr1	38019410	38019420	+	1	NA	exon (NM_198303, exon 4 of 24)	exon (NM_198303, exon 4 of 24)	21405	NM_198303	226982	Mm.260943	NM_198303	ENSMUSG00000026083	Eif5b	A030003E17Rik|BC018347|IF2	eukaryotic translation initiation factor 5B	protein-coding
mm_45652.1	chr5	77095151	77095161	-	1	NA	5' UTR (NM_001159901, exon 1 of 2)	5' UTR (NM_001159901, exon 1 of 2)	111	NM_001159901	74318	Mm.181852	NM_175606	ENSMUSG00000059325	Hopx	1110018K11Rik|1200015P04Rik|2300002F06Rik|AI848177|AW490897|Cameo|Hdop|Hod|Hop|Ob1|Obl|Toto	HOP homeobox	protein-coding
mm_157975.1	chrX	93832667	93832681	-	1	NA	promoter-TSS (NM_145630)	promoter-TSS (NM_145630)	-579	NM_145630	236900	Mm.12775	NM_145630	ENSMUSG00000035232	Pdk3	2610001M10Rik|AI035637	pyruvate dehydrogenase kinase, isoenzyme 3	protein-coding
mm_55353.1	chr6	56837348	56837362	-	1	NA	intron (NM_012056, intron 1 of 9)	RLTR17|LTR|ERVK	5296	NM_012056	27055	Mm.20943	NM_012056	ENSMUSG00000029781	Fkbp9	1810014L23|AW549641|FKBP-63|FKBP-9|FKBP60|FKBP63|FKBP65RS	FK506 binding protein 9	protein-coding
mm_148330.1	chr18	84086450	84086491	-	1	NA	promoter-TSS (NM_001081300)	promoter-TSS (NM_001081300)	92	NM_001081300	110796	Mm.102136	NM_001081300	ENSMUSG00000046982	Tshz1	5730407I04Rik|D18Bwg1409e|Mtsh1|NY-CO-33|Sdccag33|Tsh1|mKIAA4206|teashirt1	teashirt zinc finger family member 1	protein-coding
mm_104272.1	chr11	89092922	89092926	-	1	NA	3' UTR (NM_001033266, exon 4 of 4)	3' UTR (NM_001033266, exon 4 of 4)	19083	NM_001033266	217071	Mm.342127	NM_001033266	ENSMUSG00000072553	Gm525	-	predicted gene 525	protein-coding
mm_87563.1	chr10	56115393	56115423	+	1	NA	exon (NM_001163833, exon 2 of 2)	exon (NM_001163833, exon 2 of 2)	8491	NM_001163833	73390	Mm.181475	NM_133751	ENSMUSG00000047669	Msl3l2	1700060H10Rik	male-specific lethal 3-like 2 (Drosophila)	protein-coding
mm_153685.1	chr19	44396743	44396751	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	10962	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_116267.1	chr13	34649472	34649474	-	1	NA	intron (NM_025831, intron 1 of 4)	intron (NM_025831, intron 1 of 4)	3208	NM_025831	66895	Mm.28943	NM_025831	ENSMUSG00000021411	Pxdc1	1300014I06Rik	PX domain containing 1	protein-coding
mm_23161.1	chr3	40540752	40540790	+	1	NA	promoter-TSS (NM_175515)	promoter-TSS (NM_175515)	4	NM_175515	380614	Mm.105309	NM_175515	ENSMUSG00000060798	Intu	9230116I04Rik|9430087H23Rik|Pdzd6|Pdzk6|mKIAA1284	inturned planar cell polarity protein	protein-coding
mm_77294.1	chr8	116978883	116978906	-	1	NA	promoter-TSS (NM_027103)	promoter-TSS (NM_027103)	49	NM_027103	69528	Mm.272846	NM_027103	ENSMUSG00000031847	1700030J22Rik	-	RIKEN cDNA 1700030J22 gene	protein-coding
mm_171281.1	chr3	88835265	88835266	+	1	NA	promoter-TSS (NM_027389)	promoter-TSS (NM_027389)	34	NM_001242372	76022	Mm.126870	NM_027389	ENSMUSG00000054199	Gon4l	1500041I23Rik|2610100B20Rik|3632445O20Rik|5430404N14Rik|AA387005	gon-4-like (C.elegans)	protein-coding
mm_114093.1	chr13	54687873	54687887	+	1	NA	promoter-TSS (NM_001146025)	promoter-TSS (NM_001146025)	-72	NM_001146026	105239	Mm.25366	NM_134064	ENSMUSG00000034928	Rnf44	AI854545|mKIAA1100	ring finger protein 44	protein-coding
mm_15706.1	chr2	164006559	164006583	+	1	NA	intron (NM_018753, intron 1 of 5)	BC1_Mm|scRNA|scRNA	11374	NM_018753	54401	Mm.34319	NM_018753	ENSMUSG00000018326	Ywhab	1300003C17Rik|14-3-3b	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta polypeptide	protein-coding
mm_137841.1	chr17	31001937	31001942	+	1	NA	intron (NM_177465, intron 19 of 21)	MTC|LTR|ERVL-MaLR	47256	NM_177465	52020	Mm.25923	NM_177465	ENSMUSG00000054134	Umodl1	D17Ertd488e	uromodulin-like 1	protein-coding
mm_150925.1	chr19	46219734	46219734	+	1	NA	intron (NM_178930, intron 3 of 39)	B1_Mur1|SINE|Alu	67176	NM_178930	107338	Mm.271620	NM_178930	ENSMUSG00000025224	Gbf1	1700083E03Rik|AI035702|AW049900|mKIAA0248	golgi-specific brefeldin A-resistance factor 1	protein-coding
mm_40017.1	chr5	33148952	33148961	+	1	NA	exon (NM_019810, exon 10 of 15)	exon (NM_019810, exon 10 of 15)	44737	NM_019810	20537	Mm.25237	NM_019810	ENSMUSG00000011034	Slc5a1	Sglt1	solute carrier family 5 (sodium/glucose cotransporter), member 1	protein-coding
mm_124180.1	chr14	93876976	93876981	-	1	NA	intron (NM_001346722, intron 2 of 4)	AT_rich|Low_complexity|Low_complexity	11910	NM_001271800	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding
mm_29003.1	chr3	101592459	101592473	-	1	NA	exon (NM_144900, exon 4 of 23)	exon (NM_144900, exon 4 of 23)	12241	NM_144900	11928	Mm.193670	NM_144900	ENSMUSG00000033161	Atp1a1	Atpa-1|BC010319	ATPase, Na+/K+ transporting, alpha 1 polypeptide	protein-coding
mm_14605.1	chr2	136502047	136502047	+	1	NA	Intergenic	Intergenic	-30274	NM_175667	319196	Mm.477841	NM_175667	ENSMUSG00000074771	Ankef1	AV276460|Ankrd5	ankyrin repeat and EF-hand domain containing 1	protein-coding
mm_80243.1	chr9	72736867	72736887	+	1	NA	exon (NM_010890, exon 21 of 29)	exon (NM_010890, exon 21 of 29)	-70397	NM_175485	235472	Mm.31696	NM_175485	ENSMUSG00000036030	Prtg	A230098A12Rik|Igdcc5	protogenin	protein-coding
mm_46110.1	chr5	92361094	92361104	-	1	NA	exon (NM_019494, exon 3 of 4)	exon (NM_019494, exon 3 of 4)	2178	NM_019494	56066	Mm.131723	NM_019494	ENSMUSG00000060183	Cxcl11	Cxc11|H174|I-tac|Ip9|Itac|Scyb11|Scyb9b|b-R1|betaR1	chemokine (C-X-C motif) ligand 11	protein-coding
mm_83062.1	chr9	37546133	37546184	-	1	NA	exon (NM_022029, exon 2 of 4)	exon (NM_022029, exon 2 of 4)	6587	NM_022029	64011	Mm.335065	NM_022029	ENSMUSG00000053310	Nrgn	0710001B06Rik|AI838505|NG|NG/RC3|Pss1|R75334|RC3	neurogranin	protein-coding
mm_123760.1	chr14	70205874	70205886	-	1	NA	5' UTR (NM_001271407, exon 1 of 21)	5' UTR (NM_001271407, exon 1 of 21)	142	NM_001271407	20410	Mm.5068	NM_011366	ENSMUSG00000022091	Sorbs3	SCAM-1|SH3P3|Sh3d4|vinexin-g	sorbin and SH3 domain containing 3	protein-coding
mm_96984.1	chr11	70656727	70656743	+	1	NA	promoter-TSS (NM_007933)	promoter-TSS (NM_007933)	-441	NM_001136062	13808	Mm.251322	NM_007933	ENSMUSG00000060600	Eno3	Eno-3|MSE	enolase 3, beta muscle	protein-coding
mm_42365.1	chr5	114922502	114922521	+	1	NA	promoter-TSS (NM_145209)	promoter-TSS (NM_145209)	-729	NM_145209	231655	Mm.95479	NM_145209	ENSMUSG00000041827	Oasl1	7530414C13Rik|oasl9	2'-5' oligoadenylate synthetase-like 1	protein-coding
mm_146331.1	chr18	81130467	81130472	+	1	NA	Intergenic	Intergenic	-143891	NM_178280	20689	Mm.215917	NM_178280	ENSMUSG00000024565	Sall3	B130022O04Rik|Msal|Msal-1|Sal|Salt|Spalt	sal-like 3 (Drosophila)	protein-coding
mm_162407.1	chr1	86433974	86433978	+	1	NA	Intergenic	Intergenic	7647	NM_027966	71863	Mm.179627	NM_027966	ENSMUSG00000036574	1700019O17Rik	-	RIKEN cDNA 1700019O17 gene	protein-coding
mm_113443.1	chr13	34924439	34924455	+	1	NA	promoter-TSS (NM_025750)	promoter-TSS (NM_025750)	38	NM_025750	66761	Mm.157047	NM_025750	ENSMUSG00000021415	4933417A18Rik	-	RIKEN cDNA 4933417A18 gene	protein-coding
mm_20490.1	chr2	130179311	130179376	-	1	NA	promoter-TSS (NM_009225)	promoter-TSS (NM_009225)	21	NM_009225	20638	Mm.88216	NM_009225	ENSMUSG00000027404	Snrpb	AL024368|AU018828|SM-B|SM11|SMB|SNRNP-B	small nuclear ribonucleoprotein B	protein-coding
mm_77341.1	chr8	119570025	119570035	-	1	NA	intron (NM_175185, intron 1 of 4)	intron (NM_175185, intron 1 of 4)	5170	NM_175185	72552	Mm.36756	NM_175185	ENSMUSG00000034189	Hsdl1	2700067E09Rik	hydroxysteroid dehydrogenase like 1	protein-coding
mm_86981.1	chr10	25437008	25437032	+	1	NA	intron (NM_013511, intron 1 of 19)	intron (NM_013511, intron 1 of 19)	28652	NM_013511	13822	Mm.306026	NM_013511	ENSMUSG00000019978	Epb41l2	4.1G|AW555191|D10Ertd398e|Epb4.1l2|NBL2	erythrocyte membrane protein band 4.1 like 2	protein-coding
mm_134074.1	chr16	8671594	8671606	-	1	NA	intron (NM_025821, intron 1 of 3)	CpG	553	NM_025821	52502	Mm.142095	NM_025821	ENSMUSG00000008393	Carhsp1	1200011K09Rik|Crhsp-24|D16Ertd465e	calcium regulated heat stable protein 1	protein-coding
mm_173043.1	chrX	116287230	116287240	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-161709	NM_001033471	382239	Mm.336224	NM_001033471	ENSMUSG00000072995	Cpxcr1	Gm1143	CPX chromosome region, candidate 1	protein-coding
mm_116348.1	chr13	38960458	38960466	-	1	NA	promoter-TSS (NM_001170430)	promoter-TSS (NM_001170430)	75	NM_001170430	108652	Mm.255506	NM_134060	ENSMUSG00000021432	Slc35b3	4921526O06Rik|AI428480|CGI-19|PABST2|PAPST2	solute carrier family 35, member B3	protein-coding
mm_107271.1	chr12	29533352	29533364	+	1	NA	intron (NM_001093778, intron 1 of 24)	intron (NM_001093778, intron 1 of 24)	-1547	NM_001093776	17933	Mm.253067	NM_008666	ENSMUSG00000061911	Myt1l	2900046C06Rik|2900093J19Rik|C630034G21Rik|Nztf1|Pmng1|Png-1|mKIAA1106	myelin transcription factor 1-like	protein-coding
mm_150934.1	chr19	46305885	46305907	+	1	NA	promoter-TSS (NM_001177370)	promoter-TSS (NM_001177370)	-34	NM_001177370	18034	Mm.102365	NM_019408	ENSMUSG00000025225	Nfkb2	NF-kappaB2|lyt|p49|p49/p100|p50B|p52	nuclear factor of kappa light polypeptide gene enhancer in B cells 2, p49/p100	protein-coding
mm_1570.1	chr1	74245987	74245989	+	1	NA	intron (NM_029711, intron 1 of 9)	RSINE1|SINE|B4	9438	NM_029711	76709	Mm.337038	NM_029711	ENSMUSG00000006304	Arpc2	2210023N03Rik|34kDa|p34-Arc	actin related protein 2/3 complex, subunit 2	protein-coding
mm_113237.1	chr13	27259591	27259600	+	1	NA	5' UTR (NM_025896, exon 1 of 5)	5' UTR (NM_025896, exon 1 of 5)	106	NM_025896	67000	Mm.69279	NM_025896	ENSMUSG00000038883	Prl3a1	1600016E11Rik|Ghd9|PLP-H|PLP-I|Plpi|Prlpi	prolactin family 3, subfamily a, member 1	protein-coding
mm_18565.1	chr2	65239242	65239262	-	1	NA	promoter-TSS (NM_177025)	promoter-TSS (NM_177025)	-626	NM_027225	319876	Mm.34159	NM_027225	ENSMUSG00000034903	Cobll1	1810047P18Rik|Coblr1|D430044D16Rik	Cobl-like 1	protein-coding
mm_56589.1	chr6	108165010	108165021	-	1	NA	intron (NM_145937, intron 3 of 8)	B4|SINE|B4	20568	NM_145937	58911	Mm.439876	NM_145937	ENSMUSG00000030101	Sumf1	AA543204|AI463102|AI851573|FGE	sulfatase modifying factor 1	protein-coding
mm_7065.1	chr1	87621519	87621540	-	1	NA	intron (NM_010566, intron 1 of 26)	intron (NM_010566, intron 1 of 26)	1217	NM_001110193	16331	Mm.15105	NM_010566	ENSMUSG00000026288	Inpp5d	SHIP|SHIP-1|SHIP1|SIP-145|p150Ship|s-SHIP	inositol polyphosphate-5-phosphatase D	protein-coding
mm_52219.1	chr6	103510909	103510917	+	1	NA	promoter-TSS (NM_007697)	promoter-TSS (NM_007697)	37	NM_007697	12661	Mm.251288	NM_007697	ENSMUSG00000030077	Chl1	A530023M13Rik|AI465420|CALL|LICAM2	cell adhesion molecule L1-like	protein-coding
mm_20299.1	chr2	127133885	127133908	-	1	NA	promoter-TSS (NM_144818)	promoter-TSS (NM_144818)	58	NM_144818	215387	Mm.29786	NM_144818	ENSMUSG00000034906	Ncaph	A730011O11Rik|Brrn1|HCAP-H|mKIAA0074	non-SMC condensin I complex, subunit H	protein-coding
mm_31921.1	chr4	85388131	85388142	+	1	NA	3' UTR (NM_019535, exon 9 of 9)	3' UTR (NM_019535, exon 9 of 9)	182680	NM_019535	20404	Mm.143603	NM_019535	ENSMUSG00000028488	Sh3gl2	9530001L19Rik|AI120490|AW555077|B930049H17Rik|EEN-B1|SH3PA|Sh3d2a	SH3-domain GRB2-like 2	protein-coding
mm_19088.1	chr2	79254742	79254754	-	1	NA	promoter-TSS (NM_010576)	promoter-TSS (NM_010576)	-678	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D|Itga4B	integrin alpha 4	protein-coding
mm_74999.1	chr8	27228035	27228041	-	1	NA	exon (NM_013462, exon 2 of 4)	exon (NM_013462, exon 2 of 4)	1550	NM_013462	11556	Mm.278475	NM_013462	ENSMUSG00000031489	Adrb3	Adrb-3	adrenergic receptor, beta 3	protein-coding
mm_65441.1	chr7	25389013	25389030	-	1	NA	intron (NM_010719, intron 1 of 9)	intron (NM_010719, intron 1 of 9)	1091	NM_001039507	16890	Mm.158548	NM_010719	ENSMUSG00000003123	Lipe	4933403G17Rik|HSL	lipase, hormone sensitive	protein-coding
mm_138627.1	chr17	35841792	35841805	+	1	NA	intron (NM_001010833, intron 1 of 15)	intron (NM_001010833, intron 1 of 15)	300	NM_001010833	240087	Mm.218511	NM_001010833	ENSMUSG00000061607	Mdc1	6820401C03|AA413496|Nfbd1|mKIAA0170	mediator of DNA damage checkpoint 1	protein-coding
mm_147974.1	chr18	67304644	67304667	-	1	NA	intron (NM_053261, intron 2 of 7)	ORR1C1|LTR|ERVL-MaLR	15432	NM_053261	114663	Mm.34079	NM_053261	ENSMUSG00000024525	Impa2	2210415D20Rik|AI326924|AW259601	inositol (myo)-1(or 4)-monophosphatase 2	protein-coding
mm_108624.1	chr12	85599048	85599090	+	1	NA	promoter-TSS (NM_001205053)	promoter-TSS (NM_001205053)	-36	NM_001205052	81703	Mm.103560	NM_030887	ENSMUSG00000034271	Jdp2	Jundm2|Jundp2|TIF	Jun dimerization protein 2	protein-coding
mm_139083.1	chr17	46711460	46711497	+	1	NA	promoter-TSS (NM_145488)	promoter-TSS (NM_145488)	15	NM_145488	224824	Mm.299399	NM_145488	ENSMUSG00000002763	Pex6	AI132582|D130055I09Rik|mKIAA4177	peroxisomal biogenesis factor 6	protein-coding
mm_146619.1	chr18	10104456	10104478	-	1	NA	exon (NM_009071, exon 15 of 33)	exon (NM_009071, exon 15 of 33)	-74318	NM_001038589	59025	Mm.329277	NM_021522	ENSMUSG00000047879	Usp14	2610005K12Rik|2610037B11Rik|AW107924|C78769|ax|nmf375	ubiquitin specific peptidase 14	protein-coding
mm_81563.1	chr9	110415548	110415558	+	1	NA	Intergenic	Intergenic	-4255	NM_008694	18054	Mm.236225	NM_008694	ENSMUSG00000032484	Ngp	bectenecin	neutrophilic granule protein	protein-coding
mm_61491.1	chr7	75725963	75725974	+	1	NA	exon (NM_029332, exon 22 of 37)	exon (NM_029332, exon 22 of 37)	-122370	NM_001122780	207952	Mm.206223	NM_029652	ENSMUSG00000055652	Klhl25	2810402K13Rik|BC027373|Enc-1	kelch-like 25	protein-coding
mm_99743.1	chr11	106500909	106500925	+	1	NA	promoter-TSS (NR_030703)	promoter-TSS (NR_030703)	-74	NR_030703	100216537		NR_030703	ENSMUSG00000065126	Snord104	-	small nucleolar RNA, C/D box 104	snoRNA
mm_25275.1	chr3	105451850	105451937	+	1	NA	promoter-TSS (NM_001039347)	promoter-TSS (NM_001039347)	-437	NM_001039347	56543	Mm.44530	NM_019931	ENSMUSG00000040896	Kcnd3	AW045978|Kncd3|Kv4.3	potassium voltage-gated channel, Shal-related family, member 3	protein-coding
mm_34406.1	chr4	145236325	145236333	+	1	NA	intron (NM_011610, intron 1 of 9)	intron (NM_011610, intron 1 of 9)	10541	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_60081.1	chr7	34168606	34168628	+	1	NA	promoter-TSS (NM_016682)	promoter-TSS (NM_016682)	-88	NM_016682	50995	Mm.27560	NM_016682	ENSMUSG00000052997	Uba2	AA986091|Arx|Sae2|UBA1|Ubl1a2|Uble1b	ubiquitin-like modifier activating enzyme 2	protein-coding
mm_86674.1	chr10	18077552	18077575	+	1	NA	intron (NM_009048, intron 1 of 19)	intron (NM_009048, intron 1 of 19)	21623	NM_001111065	19707	Mm.4479	NM_009048	ENSMUSG00000019854	Reps1	BB161292	RalBP1 associated Eps domain containing protein	protein-coding
mm_138351.1	chr17	34959575	34959579	+	1	NA	promoter-TSS (NM_010478)	promoter-TSS (NM_010478)	-339	NM_010478	15511	Mm.372314	NM_010478	ENSMUSG00000090877	Hspa1b	Hsp70|Hsp70-1|Hsp70.1|hsp68	heat shock protein 1B	protein-coding
mm_83895.1	chr9	56136351	56136360	-	1	NA	3' UTR (NM_019793, exon 7 of 7)	3' UTR (NM_019793, exon 7 of 7)	24715	NM_019793	56434	Mm.28484	NM_019793	ENSMUSG00000032324	Tspan3	1700055K04Rik|TM4-A|Tm4sf8	tetraspanin 3	protein-coding
mm_70310.1	chr8	4226926	4226963	+	1	NA	5' UTR (NM_028175, exon 1 of 3)	5' UTR (NM_028175, exon 1 of 3)	117	NM_028175	72267	Mm.25479	NM_028175	ENSMUSG00000046589	Lrrc8e	1810049O03Rik|C87354	leucine rich repeat containing 8 family, member E	protein-coding
mm_90108.1	chr10	117247982	117247992	+	1	NA	Intergenic	Intergenic	-9306	NM_029906	77397	Mm.118350	NM_029906	ENSMUSG00000020177	9530003J23Rik	Lyzf1	RIKEN cDNA 9530003J23 gene	protein-coding
mm_135576.1	chr16	50429867	50429884	-	1	NA	intron (NM_001347240, intron 1 of 16)	intron (NM_001347240, intron 1 of 16)	2514	NM_027444	70508	Mm.28940	NM_027444	ENSMUSG00000022641	Bbx	5530401J07Rik|5730403O13Rik	bobby sox HMG box containing	protein-coding
mm_69181.1	chr7	127232749	127232752	-	1	NA	promoter-TSS (NM_146201)	promoter-TSS (NM_146201)	380	NR_030674	100043580	Mm.482209	NR_030674	ENSMUSG00000000486	Gm4532	-	predicted gene 4532	ncRNA
mm_125312.1	chr15	38079102	38079117	+	1	NA	promoter-TSS (NM_001081359)	promoter-TSS (NM_001081359)	-255	NM_001081359	70790	Mm.476840	NM_027553	ENSMUSG00000037487	Ubr5	Edd|Edd1	ubiquitin protein ligase E3 component n-recognin 5	protein-coding
mm_128654.1	chr15	59652845	59652856	-	1	NA	intron (NM_144549, intron 2 of 2)	intron (NM_144549, intron 2 of 2)	4196	NM_144549	211770	Mm.40298	NM_144549	ENSMUSG00000032501	Trib1	A530090O15Rik|TRB-1|Trb1	tribbles pseudokinase 1	protein-coding
mm_51122.1	chr6	68049958	68049964	+	1	NA	Intergenic	Intergenic	-484262	NR_003100	75070	Mm.463364	NR_003100		4930515G16Rik	-	myc induced nuclear antigen pseudogene	pseudo
mm_146010.1	chr18	69345823	69345840	+	1	NA	5' UTR (NM_001083967, exon 1 of 20)	5' UTR (NM_001083967, exon 1 of 20)	110	NM_001083967	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding
mm_105804.1	chr11	110251633	110251641	-	1	NA	5' UTR (NM_147218, exon 1 of 39)	5' UTR (NM_147218, exon 1 of 39)	139	NM_147218	76184	Mm.159704	NM_147218	ENSMUSG00000044749	Abca6	6330565N06Rik	ATP-binding cassette, sub-family A (ABC1), member 6	protein-coding
mm_150372.1	chr19	34908144	34908158	+	1	NA	Intergenic	RMER17A|LTR|ERVK	-14207	NM_183046	240641	Mm.278471	NM_183046	ENSMUSG00000024795	Kif20b	33cex|B130024C23|C330014J10Rik|Mphosph1|magoo	kinesin family member 20B	protein-coding
mm_76447.1	chr8	85072103	85072125	-	1	NA	intron (NM_001039514, intron 1 of 8)	CpG	357	NM_001039514	330817	Mm.193086	NM_201408	ENSMUSG00000060038	Dhps	Dhs	deoxyhypusine synthase	protein-coding
mm_23999.1	chr3	86783718	86783723	+	1	NA	Intergenic	Intergenic	137164	NM_001195496	70762	Mm.44490	NM_027539	ENSMUSG00000028078	Dclk2	6330415M09Rik|AU044875|CL2|CLICK2|Click-II|Dcamkl2	doublecortin-like kinase 2	protein-coding
mm_75843.1	chr8	70616716	70616741	-	1	NA	promoter-TSS (NM_153074)	promoter-TSS (NM_153074)	-116	NM_153074	211228	Mm.132939	NM_153074	ENSMUSG00000049988	Lrrc25	Mapa	leucine rich repeat containing 25	protein-coding
mm_131967.1	chr16	24681770	24681785	+	1	NA	exon (NM_178665, exon 7 of 13)	exon (NM_178665, exon 7 of 13)	-40078	NM_001145954	210126	Mm.209385	NM_178665	ENSMUSG00000033306	Lpp	9430020K16Rik|AA959454|AU024130|B130055L10Rik|C79715|D630048H16	LIM domain containing preferred translocation partner in lipoma	protein-coding
mm_166180.1	chr5	30960521	30960531	+	1	NA	promoter-TSS (NM_001294302)	promoter-TSS (NM_001294302)	-199	NM_016703	50907	Mm.272414	NM_016703	ENSMUSG00000045302	Preb	C85705	prolactin regulatory element binding	protein-coding
mm_65533.1	chr7	25803614	25803629	-	1	NA	exon (NM_028775, exon 9 of 9)	exon (NM_028775, exon 9 of 9)	12909	NM_028775	74134	Mm.275188	NM_028775	ENSMUSG00000040703	Cyp2s1	1200011C15Rik|AU041727|C79779	cytochrome P450, family 2, subfamily s, polypeptide 1	protein-coding
mm_130490.1	chr15	98778546	98778568	-	1	NA	promoter-TSS (NM_011718)	promoter-TSS (NM_011718)	-407	NM_011718	22410	Mm.4709	NM_011718	ENSMUSG00000022996	Wnt10b	Wnt12	wingless-type MMTV integration site family, member 10B	protein-coding
mm_166992.1	chr7	46240936	46240942	+	1	NA	promoter-TSS (NM_013624)	promoter-TSS (NM_013624)	-48	NM_013624	18419	Mm.8020	NM_013624	ENSMUSG00000009487	Otog	4932420K09|Otgn|twt	otogelin	protein-coding
mm_107052.1	chr12	16653476	16653486	+	1	NA	promoter-TSS (NM_008747)	promoter-TSS (NM_008747)	11	NM_008747	18217	Mm.281715	NM_008747	ENSMUSG00000020591	Ntsr2	NT2R|NTRL	neurotensin receptor 2	protein-coding
mm_18229.1	chr2	51933305	51933320	-	1	NA	intron (NM_030243, intron 1 of 4)	B1_Mur4|SINE|Alu	1332	NM_001141982	71684	Mm.28309	NM_030243	ENSMUSG00000036249	Rbm43	0610033I05Rik	RNA binding motif protein 43	protein-coding
mm_47938.1	chr5	135350043	135350049	-	1	NA	promoter-TSS (NM_001277893)	promoter-TSS (NM_001277893)	-2	NM_001277891	94244	Mm.26037	NM_033571	ENSMUSG00000040013	Fkbp6	1700008G22Rik|36kDa|AU017274|D5Ertd724e|FKBP-36|FKBP-6	FK506 binding protein 6	protein-coding
mm_84317.1	chr9	63745510	63745512	-	1	NA	intron (NM_016769, intron 1 of 8)	intron (NM_016769, intron 1 of 8)	12483	NM_016769	17127	Mm.7320	NM_016769	ENSMUSG00000032402	Smad3	AU022421|Madh3	SMAD family member 3	protein-coding
mm_159121.1	chr2	69712524	69712524	-	1	NA	promoter-TSS (NM_177244)	promoter-TSS (NM_177244)	82	NM_177244	320720	Mm.289566	NM_177244	ENSMUSG00000027086	Fastkd1	5330408N05Rik|mKIAA1800	FAST kinase domains 1	protein-coding
mm_85436.1	chr9	104063050	104063146	-	1	NA	promoter-TSS (NM_175324)	promoter-TSS (NM_175324)	23	NM_025692	66663	Mm.224935	NM_025692	ENSMUSG00000032557	Uba5	5730525G14Rik|AW240750|Ube1dc1	ubiquitin-like modifier activating enzyme 5	protein-coding
mm_27506.1	chr3	55780873	55780895	-	1	NA	intron (NM_030595, intron 41 of 57)	intron (NM_030595, intron 41 of 57)	-1626	NM_010750	17116	Mm.440209	NM_010750	ENSMUSG00000056947	Mab21l1	AW047968	mab-21-like 1 (C. elegans)	protein-coding
mm_162120.1	chrX	68761823	68761823	+	1	NA	promoter-TSS (NM_001166620)	promoter-TSS (NM_001166620)	-16	NM_174993	207854	Mm.284945	NM_174993	ENSMUSG00000062170	Fmr1nb	3830422N12Rik|NY-SAR-35|NYSAR35	fragile X mental retardation 1 neighbor	protein-coding
mm_98145.1	chr11	87582234	87582244	+	1	NA	intron (NM_001284392, intron 1 of 10)	intron (NM_001284392, intron 1 of 10)	1178	NM_001284392	18952	Mm.2214	NM_011129	ENSMUSG00000020486	Sept4	ARTS|Bh5|OTTMUSG00000001265|Pnutl2	septin 4	protein-coding
mm_9092.1	chr1	168675901	168675913	-	1	NA	Intergenic	Intergenic	185264	NR_105766	102465178		NR_105766	ENSMUSG00000098407	Mir6348	Gm27412|mmu-mir-6348	microRNA 6348	ncRNA
mm_114417.1	chr13	64367883	64367899	+	1	NA	exon (NM_009984, exon 4 of 8)	exon (NM_009984, exon 4 of 8)	2629	NM_009984	13039	Mm.930	NM_009984	ENSMUSG00000021477	Ctsl	1190035F06Rik|CatL|Ctsl1|MEP|fs|nkt	cathepsin L	protein-coding
mm_116766.1	chr13	52600227	52600244	-	1	NA	intron (NM_011518, intron 1 of 13)	intron (NM_011518, intron 1 of 13)	3353	NM_011518	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_82202.1	chr9	124101967	124101987	+	1	NA	promoter-TSS (NM_009915)	promoter-TSS (NM_009915)	-206	NM_009915	12772	Mm.6272	NM_009915	ENSMUSG00000049103	Ccr2	Cc-ckr-2|Ccr2a|Ccr2b|Ckr2|Ckr2a|Ckr2b|Cmkbr2|mJe-r	chemokine (C-C motif) receptor 2	protein-coding
mm_27810.1	chr3	78594410	78594419	-	1	NA	Intergenic	Intergenic	550473	NM_001310536	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_55799.1	chr6	82760823	82760845	-	1	NA	intron (NM_013820, intron 1 of 17)	intron (NM_013820, intron 1 of 17)	13620	NM_013820	15277	Mm.255848	NM_013820	ENSMUSG00000000628	Hk2	AI642394|HKII	hexokinase 2	protein-coding
mm_122913.1	chr14	54958493	54958530	-	1	NA	exon (NM_010856, exon 15 of 39)	exon (NM_010856, exon 15 of 39)	8096	NM_001164171	17888	Mm.290003	NM_010856	ENSMUSG00000040752	Myh6	A830009F23Rik|AA517445|Myhc-a|Myhca|alpha-MHC	myosin, heavy polypeptide 6, cardiac muscle, alpha	protein-coding
mm_112787.1	chr13	20184999	20185011	+	1	NA	intron (NM_080288, intron 1 of 21)	intron (NM_080288, intron 1 of 21)	94498	NM_080288	140580	Mm.342392	NM_080288	ENSMUSG00000041112	Elmo1	6330578D22Rik|C230095H21Rik|CED-12	engulfment and cell motility 1	protein-coding
mm_173174.1	chrX	50162364	50162365	-	1	NA	Intergenic	L1Md_A|LINE|L1	-152129	NM_146390	258385	Mm.377470	NM_146390	ENSMUSG00000050504	Olfr1323	MOR216-1	olfactory receptor 1323	protein-coding
mm_44706.1	chr5	30814646	30814655	-	1	NA	promoter-TSS (NM_133350)	promoter-TSS (NM_133350)	9	NM_133350	100732	Mm.332295	NM_133350	ENSMUSG00000029166	Mapre3	AI790651|EB2|EB3|EBF3|RP3	microtubule-associated protein, RP/EB family, member 3	protein-coding
mm_68003.1	chr7	100938283	100938291	-	1	NA	exon (NM_183168, exon 3 of 3)	exon (NM_183168, exon 3 of 3)	-6126	NM_001081116	207212	Mm.29954	NM_001081116	ENSMUSG00000032875	Arhgef17	8030463K16|AI428794|AW558066|BC035332|mKIAA0337	Rho guanine nucleotide exchange factor (GEF) 17	protein-coding
mm_67047.1	chr7	67290952	67290996	-	1	NA	intron (NM_001033713, intron 4 of 11)	intron (NM_001033713, intron 4 of 11)	68358	NM_001191051	75099	Mm.121691	NM_175215	ENSMUSG00000043831	Lysmd4	4930506D23Rik	LysM, putative peptidoglycan-binding, domain containing 4	protein-coding
mm_158571.1	chrX	150588074	150588153	-	1	NA	promoter-TSS (NM_029943)	promoter-TSS (NM_029943)	42	NM_029943	77622	Mm.440275	NM_029943	ENSMUSG00000025269	Apex2	C430040P13Rik|ape2	apurinic/apyrimidinic endonuclease 2	protein-coding
mm_71697.1	chr8	61609409	61609414	+	1	NA	intron (NM_001293772, intron 10 of 21)	intron (NM_001293772, intron 10 of 21)	-18242	NM_001293774	72333	Mm.29933	NM_001081390	ENSMUSG00000058056	Palld	2410003B16Rik|6030492A02	palladin, cytoskeletal associated protein	protein-coding
mm_65805.1	chr7	28962327	28962337	-	1	NA	promoter-TSS (NM_021895)	promoter-TSS (NM_021895)	-52	NM_021895	60595	Mm.81144	NM_021895	ENSMUSG00000054808	Actn4	C77391	actinin alpha 4	protein-coding
mm_125837.1	chr15	74958522	74958534	+	1	NA	exon (NM_001164036, exon 4 of 4)	exon (NM_001164036, exon 4 of 4)	3422	NM_001164040	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_97919.1	chr11	83535084	83535109	+	1	NA	Intergenic	Intergenic	-4578	NM_013653	20304	Mm.284248	NM_013653	ENSMUSG00000035042	Ccl5	MuRantes|RANTES|SISd|Scya5|TCP228	chemokine (C-C motif) ligand 5	protein-coding
mm_79183.1	chr9	48403794	48403833	+	1	NA	Intergenic	Intergenic	41772	NM_172921	244853	Mm.325522	NM_172921	ENSMUSG00000044229	Nxpe4	C130036J11|D930028F11Rik|Fam55d	neurexophilin and PC-esterase domain family, member 4	protein-coding
mm_47571.1	chr5	124478331	124478384	-	1	NA	promoter-TSS (NM_030259)	promoter-TSS (NM_030259)	-122	NM_030259	80291	Mm.425280	NM_030259	ENSMUSG00000029401	Rilpl2	-	Rab interacting lysosomal protein-like 2	protein-coding
mm_108618.1	chr12	85524832	85524841	+	1	NA	Intergenic	Intergenic	50935	NM_010234	14281	Mm.246513	NM_010234	ENSMUSG00000021250	Fos	D12Rfj1|c-fos|cFos	FBJ osteosarcoma oncogene	protein-coding
mm_166047.1	chr4	130932126	130932132	+	1	NA	intron (NM_010686, intron 7 of 7)	MIRb|SINE|MIR	-12256	NM_010769	17180	Mm.271796	NM_010769	ENSMUSG00000040533	Matn1	CMP|Crtm|Mat1|matrilin-1	matrilin 1, cartilage matrix protein	protein-coding
mm_42298.1	chr5	114567405	114567418	+	1	NA	promoter-TSS (NM_001004180)	promoter-TSS (NM_001004180)	-840	NM_001004180	433940	Mm.194212	NM_001004180	ENSMUSG00000041930	Fam222a	-	family with sequence similarity 222, member A	protein-coding
mm_142328.1	chr17	43502796	43502806	-	1	NA	promoter-TSS (NM_008585)	promoter-TSS (NM_008585)	-28	NM_008585	17287	Mm.5346	NM_008585	ENSMUSG00000023914	Mep1a	AI098089|AW107200|Mep-1|Mep-1a|Mep1	meprin 1 alpha	protein-coding
mm_60879.1	chr7	46102702	46102703	+	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-1938	NM_001204411	16514	Mm.333863	NM_010602	ENSMUSG00000096146	Kcnj11	Kir6.2|mBIR	potassium inwardly rectifying channel, subfamily J, member 11	protein-coding
mm_122958.1	chr14	54968153	54968161	-	1	NA	promoter-TSS (NR_033497)	promoter-TSS (NR_033497)	-630	NR_033497	791403	Mm.319176	NR_033497	ENSMUSG00000097652	Mhrt	D830015G02Rik|ENSMUSG00000053118|Myheart	myosin heavy chain associated RNA transcript	ncRNA
mm_85455.1	chr9	105145073	105145106	-	1	NA	promoter-TSS (NM_028562)	promoter-TSS (NM_028562)	-7	NM_028562	73532	Mm.23516	NM_028562	ENSMUSG00000032566	1700080E11Rik	AI429110|Tseg8	RIKEN cDNA 1700080E11 gene	protein-coding
mm_53474.1	chr6	134925304	134925308	+	1	NA	3' UTR (NM_009875, exon 3 of 3)	3' UTR (NM_009875, exon 3 of 3)	-3786	NR_037956	381822	Mm.5935	NR_037955	ENSMUSG00000098318	Lockd	1190002F15Rik|AI120476|Droc	lncRNA downstream of Cdkn1b	ncRNA
mm_158954.1	chr1	88134820	88134820	+	1	NA	promoter-TSS (NM_145079)	promoter-TSS (NM_145079)	11	NM_145079	94284	Mm.300095	NM_145079	ENSMUSG00000054545	Ugt1a6a	UDPGT|UDPGT 1-6|UGT1-06|UGT1.6|Ugt1a6|Ugt1a7	UDP glucuronosyltransferase 1 family, polypeptide A6A	protein-coding
mm_24800.1	chr3	95550102	95550119	+	1	NA	exon (NM_021281, exon 7 of 8)	exon (NM_021281, exon 7 of 8)	-9567	NM_026489	67981	Mm.179050	NM_026489	ENSMUSG00000028109	Hormad1	4921522K05Rik|Nohma	HORMA domain containing 1	protein-coding
mm_56179.1	chr6	88166162	88166172	-	1	NA	Intergenic	Intergenic	-32497	NM_008090	14461	Mm.491156	NM_008090	ENSMUSG00000015053	Gata2	Gata-2	GATA binding protein 2	protein-coding
mm_153539.1	chr19	41964602	41964604	-	1	NA	intron (NM_028152, intron 3 of 30)	intron (NM_028152, intron 3 of 30)	16533	NM_028152	72199	Mm.218940	NM_028152	ENSMUSG00000025159	Mms19	2410001K24Rik|2610042O15Rik|AI316855|C79368|C86341|Mms19l	MMS19 (MET18 S. cerevisiae)	protein-coding
mm_68152.1	chr7	102250324	102250334	-	1	NA	promoter-TSS (NM_019566)	promoter-TSS (NM_019566)	-211	NM_019566	56212	Mm.259795	NM_019566	ENSMUSG00000073982	Rhog	2810426G09Rik|Arhg|Sid10750	ras homolog family member G	protein-coding
mm_58500.1	chr7	3705716	3705739	+	1	NA	intron (NM_029767, intron 3 of 4)	intron (NM_029767, intron 3 of 4)	1686	NM_029767	76846	Mm.13944	NM_029767	ENSMUSG00000006333	Rps9	3010033P07Rik|AL022771|AL022885	ribosomal protein S9	protein-coding
mm_106621.1	chr11	120821199	120821209	-	1	NA	intron (NM_007988, intron 3 of 42)	intron (NM_007988, intron 3 of 42)	3343	NM_007988	14104	Mm.236443	NM_007988	ENSMUSG00000025153	Fasn	A630082H08Rik|FAS	fatty acid synthase	protein-coding
mm_98822.1	chr11	97362276	97362313	+	1	NA	promoter-TSS (NM_138657)	promoter-TSS (NM_138657)	-257	NM_138657	192157	Mm.34339	NM_138657	ENSMUSG00000038485	Socs7	2310063P06Rik|C85125|Nap4	suppressor of cytokine signaling 7	protein-coding
mm_134769.1	chr16	23520802	23520815	-	1	NA	promoter-TSS (NM_008555)	promoter-TSS (NM_008555)	-218	NM_008555	17174	Mm.1213	NM_008555	ENSMUSG00000022887	Masp1	AW048060|CCPII|Crarf|Masp1/3	mannan-binding lectin serine peptidase 1	protein-coding
mm_31024.1	chr4	40769532	40769533	+	1	NA	Intergenic	B3A|SINE|B2	-11647	NM_021535	74255	Mm.289929	NM_021535	ENSMUSG00000028409	Smu1	2600001O03Rik|2610203K23Rik|AB044414|AI845086|AW556129|Bwd	smu-1 suppressor of mec-8 and unc-52 homolog (C. elegans)	protein-coding
mm_151163.1	chr19	53194497	53194507	+	1	NA	intron (NM_013758, intron 1 of 15)	intron (NM_013758, intron 1 of 15)	50505	NM_013758	27360	Mm.426080	NM_013758	ENSMUSG00000025026	Add3	AI463285|R75380	adducin 3 (gamma)	protein-coding
mm_85434.1	chr9	103761821	103761847	-	1	NA	promoter-TSS (NM_178638)	promoter-TSS (NM_178638)	3	NM_178638	81907	Mm.384704	NM_178638	ENSMUSG00000042757	Tmem108	AI462967|B130017P16Rik|R74726	transmembrane protein 108	protein-coding
mm_151267.1	chr19	54045744	54045753	+	1	NA	5' UTR (NM_007417, exon 1 of 1)	5' UTR (NM_007417, exon 1 of 1)	566	NM_007417	11551	Mm.235195	NM_007417	ENSMUSG00000033717	Adra2a	AW122659|Adra-2|Adra-2a|alpha(2A)AR|alpha2-C10|alpha2A|alpha2A-AR	adrenergic receptor, alpha 2a	protein-coding
mm_154714.1	chrX	9104611	9104617	+	1	NA	promoter-TSS (NM_001270700)	promoter-TSS (NM_001270700)	52	NM_001270700	75775	Mm.50374	NM_001270700	ENSMUSG00000045797	4930402K13Rik	-	RIKEN cDNA 4930402K13 gene	protein-coding
mm_154559.1	chrX	4136296	4136316	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-60270	NM_001085543	627264	Mm.457960	NM_001085543	ENSMUSG00000094307	Btbd35f28	Gm14347|OTTMUSG00000016407	BTB domain containing 35, family member 28	protein-coding
mm_116052.1	chr13	27437073	27437080	-	1	NA	exon (NM_011167, exon 2 of 6)	exon (NM_011167, exon 2 of 6)	1612	NM_001271379	19112	Mm.142728	NM_011167	ENSMUSG00000021345	Prl8a6	Ghd13|PLP-C1|PLP-Ca|PLP-calpha|Prlpc|Prlpc1	prolactin family 8, subfamily a, member 6	protein-coding
mm_150248.1	chr19	34100956	34100983	+	1	NA	promoter-TSS (NM_023903)	promoter-TSS (NM_023903)	26	NM_023903	78753	Mm.195937	NM_023903	ENSMUSG00000056078	Lipm	4632427C23Rik|AW227514|Lipl3	lipase, family member M	protein-coding
mm_159967.1	chr6	92567375	92567375	-	1	NA	promoter-TSS (NM_001134461)	promoter-TSS (NM_001134461)	-9	NM_001134461	243548	Mm.248820	NM_001081146	ENSMUSG00000030020	Prickle2	6230400G14Rik|6720451F06Rik|mpk2	prickle planar cell polarity protein 2	protein-coding
mm_98330.1	chr11	90638213	90638223	+	1	NA	promoter-TSS (NM_011505)	promoter-TSS (NM_011505)	34	NM_199008	69802	Mm.151940	NM_199008	ENSMUSG00000020544	Cox11	2010004I09Rik	cytochrome c oxidase assembly protein 11	protein-coding
mm_32885.1	chr4	118961867	118961871	+	1	NA	promoter-TSS (NM_133892)	promoter-TSS (NM_133892)	-98	NM_133892	100470	Mm.26698	NM_133892	ENSMUSG00000024903	Lao1	AW990848	L-amino acid oxidase 1	protein-coding
mm_48390.1	chr5	139814026	139814062	-	1	NA	promoter-TSS (NM_144914)	promoter-TSS (NM_144914)	239	NM_001161548	231832	Mm.482655	NM_144914	ENSMUSG00000036687	Tmem184a	Sdmg1	transmembrane protein 184a	protein-coding
mm_50488.1	chr6	48988764	48988773	+	1	NA	exon (NM_172888, exon 1 of 5)	exon (NM_172888, exon 1 of 5)	1907	NM_172888	243377	Mm.446302	NM_172888	ENSMUSG00000039215	Svs1	9530003A11	seminal vesicle secretory protein 1	protein-coding
mm_16567.1	chr2	3366600	3366613	-	1	NA	promoter-TSS (NM_145921)	promoter-TSS (NM_145921)	-37	NM_145921	99035	Mm.13808	NM_145921	ENSMUSG00000026645	Olah	AI607300|E230009B14Rik|Thedc1	oleoyl-ACP hydrolase	protein-coding
mm_8700.1	chr1	158356325	158356344	-	1	NA	promoter-TSS (NM_207583)	promoter-TSS (NM_207583)	-74	NM_207583	240843	Mm.329579	NM_207583	ENSMUSG00000004031	Brinp2	6430517E21Rik|BB361039|Fam5b|mKIAA1747	bone morphogenic protein/retinoic acid inducible neural-specific 2	protein-coding
mm_143042.1	chr17	56794713	56794717	-	1	NA	intron (NM_009056, intron 5 of 16)	L1M4c|LINE|L1	24439	NM_001195673	100504446	Mm.46157	NM_001195673	ENSMUSG00000090273	Prr22	Gm546	proline rich 22	protein-coding
mm_59153.1	chr7	24370184	24370199	+	1	NA	promoter-TSS (NM_001163510)	promoter-TSS (NM_001163510)	-72	NM_001163510	16534	Mm.9911	NM_008433	ENSMUSG00000054342	Kcnn4	IK1|IKCA1|KCA4|KCa3.1|SK4|SKCas|mIKCa1	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4	protein-coding
mm_115707.1	chr13	14523097	14523165	-	1	NA	promoter-TSS (NM_001081348)	promoter-TSS (NM_001081348)	95	NM_001081348	94253	Mm.125298	NM_153130	ENSMUSG00000021301	Hecw1	9330116H24Rik|AV273951|E130207I19Rik|Nedl1	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	protein-coding
mm_9335.1	chr1	172004271	172004311	-	1	NA	3' UTR (NM_033509, exon 8 of 8)	3' UTR (NM_033509, exon 8 of 8)	23004	NM_033509	93840	Mm.36148	NM_033509	ENSMUSG00000026556	Vangl2	C530001F03Rik|Lootl|Lp|Lpp1|Ltap|Vang1l2|loop-tail|ska17|ska<m17Jus>|stbm|strabismus	vang-like 2 (van gogh, Drosophila)	protein-coding
mm_109879.1	chr12	4918187	4918196	-	1	NA	intron (NM_001099628, intron 1 of 30)	intron (NM_001099628, intron 1 of 30)	838	NM_001099628	320817	Mm.210966	NM_001099628	ENSMUSG00000052812	Atad2b	1110014E10Rik|BC032887|C79189|D530031C13Rik	ATPase family, AAA domain containing 2B	protein-coding
mm_130073.1	chr15	89355656	89355668	-	1	NA	promoter-TSS (NM_001271601)	promoter-TSS (NM_001271601)	-3	NM_178919	105847	Mm.34511	NM_178919	ENSMUSG00000022614	Lmf2	AI451006|Tmem112b|Tmem153	lipase maturation factor 2	protein-coding
mm_143982.1	chr17	87473796	87473808	-	1	NA	Intergenic	Intergenic	-26867	NM_007589	12314	Mm.329243	NM_007589	ENSMUSG00000036438	Calm2	1500001E21Rik|AL024017	calmodulin 2	protein-coding
mm_98580.1	chr11	95716260	95716272	+	1	NA	Intergenic	Intergenic	-3512	NR_045780	432396	Mm.426849	NR_045780	ENSMUSG00000086191	Zfp652os	1110035M17Rik	zinc finger protein 652, opposite strand	ncRNA
mm_153981.1	chr19	47900664	47900695	-	1	NA	intron (NM_001001738, intron 1 of 1)	intron (NM_001001738, intron 1 of 1)	18620	NM_001001738	414801	Mm.29457	NM_001001738	ENSMUSG00000044948	Itprip	4833424O12Rik|DANGER|mKIAA1754	inositol 1,4,5-triphosphate receptor interacting protein	protein-coding
mm_25323.1	chr3	106547823	106547888	+	1	NA	promoter-TSS (NM_026013)	promoter-TSS (NM_026013)	-53	NM_133869	99712	Mm.429443	NM_133869	ENSMUSG00000040774	Cept1	9930118K05Rik|mCEPT1	choline/ethanolaminephosphotransferase 1	protein-coding
mm_97632.1	chr11	78959888	78959900	+	1	NA	3' UTR (NM_010927, exon 27 of 27)	3' UTR (NM_010927, exon 27 of 27)	25030	NM_001159301	16859	Mm.341434	NM_010708	ENSMUSG00000001123	Lgals9	AA407335|AI194909|AI265545|LGALS35|Lgals5|gal-9|galectin-9	lectin, galactose binding, soluble 9	protein-coding
mm_158217.1	chrX	105928548	105928583	-	1	NA	intron (NM_009530, intron 1 of 34)	CpG	807	NM_009530	22589	Mm.10141	NM_009530	ENSMUSG00000031229	Atrx	4833408C14Rik|AI447451|ATR2|DXHXS6677E|HP1-BP38|Hp1bp2|Hp1bp38|MRXS3|RAD54L|Rad54|XH2|Xnp|ZNF-HX	alpha thalassemia/mental retardation syndrome X-linked	protein-coding
mm_80203.1	chr9	72437986	72438016	+	1	NA	promoter-TSS (NM_008613)	promoter-TSS (NM_008613)	-528	NM_008613	17427	Mm.387671	NM_008613	ENSMUSG00000032221	Mns1	AW546487	meiosis-specific nuclear structural protein 1	protein-coding
mm_22122.1	chr2	170194034	170194064	-	1	NA	Intergenic	Intergenic	-51374	NM_001159683	228913	Mm.22858	NM_001033299	ENSMUSG00000052056	Zfp217	4933431C08Rik|AW987152|Gm562|ZABC1|Znf217	zinc finger protein 217	protein-coding
mm_166816.1	chr7	17074051	17074089	+	1	NA	promoter-TSS (NM_007676)	promoter-TSS (NM_007676)	30	NM_007676	26436	Mm.143686	NM_007676	ENSMUSG00000066760	Psg16	Cea11|PSG|bCEA	pregnancy specific glycoprotein 16	protein-coding
mm_14688.1	chr2	140395447	140395465	+	1	NA	promoter-TSS (NM_028387)	promoter-TSS (NM_028387)	21	NM_028387	72899	Mm.229466	NM_028387	ENSMUSG00000068205	Macrod2	1110033L15Rik|2610107G07Rik|2900006F19Rik	MACRO domain containing 2	protein-coding
mm_146665.1	chr18	12190998	12191000	-	1	NA	exon (NM_008720, exon 25 of 25)	exon (NM_008720, exon 25 of 25)	22269	NM_029623	76482	Mm.196596	NM_029623	ENSMUSG00000024410	3110002H16Rik	2400010D15Rik|Mic-1|Mic1	RIKEN cDNA 3110002H16 gene	protein-coding
mm_104431.1	chr11	94951510	94951537	-	1	NA	exon (NM_007742, exon 51 of 51)	exon (NM_007742, exon 51 of 51)	15299	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_24714.1	chr3	95228756	95228832	+	1	NA	promoter-TSS (NM_019914)	promoter-TSS (NM_019914)	-117	NM_019914	56772	Mm.331208	NM_019914	ENSMUSG00000053192	Mllt11	AI839562|Af1q|Zfp692	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 11	protein-coding
mm_71205.1	chr8	40889526	40889539	+	1	NA	intron (NM_007514, intron 1 of 11)	intron (NM_007514, intron 1 of 11)	27165	NM_001044740	11988	Mm.4676	NM_007514	ENSMUSG00000031596	Slc7a2	20.5|AI158848|Atrc2|CAT-2|Cat2|Tea	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	protein-coding
mm_74935.1	chr8	25785224	25785230	-	1	NA	promoter-TSS (NM_026032)	promoter-TSS (NM_026032)	-18	NM_026121	67384	Mm.118400	NM_026121	ENSMUSG00000037316	Bag4	2410112I15Rik|SODD	BCL2-associated athanogene 4	protein-coding
mm_110784.1	chr12	71114078	71114100	-	1	NA	intron (NM_029227, intron 2 of 4)	intron (NM_029227, intron 2 of 4)	2661	NM_029227	75266	Mm.402075	NM_029227	ENSMUSG00000021078	Tomm20l	4930553D19Rik	translocase of outer mitochondrial membrane 20 homolog (yeast)-like	protein-coding
mm_85310.1	chr9	101071151	101071151	-	1	NA	Intergenic	Intergenic	-3611	NM_001100451	77853	Mm.326206	NM_001100451	ENSMUSG00000066415	Msl2	E130103E02Rik|Msl2l1|Rnf184	male-specific lethal 2 homolog (Drosophila)	protein-coding
mm_142630.1	chr17	47400586	47400599	-	1	NA	promoter-TSS (NM_008189)	promoter-TSS (NM_008189)	14	NM_008189	14913	Mm.16224	NM_008189	ENSMUSG00000023982	Guca1a	GC-A|Gcap1|Guca1|mGCAP1	guanylate cyclase activator 1a (retina)	protein-coding
mm_104270.1	chr11	89060698	89060799	-	1	NA	promoter-TSS (NM_019505)	promoter-TSS (NM_019505)	0	NM_019505	56077	Mm.153695	NM_019505	ENSMUSG00000000276	Dgke	C87606|DAGK6|DGK	diacylglycerol kinase, epsilon	protein-coding
mm_397.1	chr1	34121442	34121458	+	1	NA	intron (NM_001276764, intron 8 of 102)	intron (NM_001276764, intron 8 of 102)	4091	NR_105861	102466987		NR_105861	ENSMUSG00000105982	Mir6896	mmu-mir-6896	microRNA 6896	ncRNA
mm_149676.1	chr19	20405281	20405291	+	1	NA	promoter-TSS (NR_045817)	promoter-TSS (NR_045817)	-2	NR_045817	68994	Mm.261028	NM_183277	ENSMUSG00000094732	1500015L24Rik	-	RIKEN cDNA 1500015L24 gene	ncRNA
mm_123197.1	chr14	59178757	59178773	-	1	NA	promoter-TSS (NM_001004158)	promoter-TSS (NM_001004158)	-16	NM_001004158	380907	Mm.81009	NM_001004158	ENSMUSG00000053868	Gm5142	EG380907	predicted gene 5142	protein-coding
mm_110171.1	chr12	27336468	27336488	-	1	NA	3' UTR (NM_009234, exon 1 of 1)	3' UTR (NM_009234, exon 1 of 1)	6240	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding
mm_130837.1	chr15	101849119	101849132	-	1	NA	exon (NM_008473, exon 2 of 9)	exon (NM_008473, exon 2 of 9)	1661	NM_008473	16678	Mm.183137	NM_008473	ENSMUSG00000046834	Krt1	Krt-2.1|Krt2-1|Krt86	keratin 1	protein-coding
mm_100978.1	chr11	7207186	7207213	-	1	NA	3' UTR (NM_008343, exon 5 of 5)	3' UTR (NM_008343, exon 5 of 5)	6724	NM_008343	16009	Mm.29254	NM_008343	ENSMUSG00000020427	Igfbp3	AI649005|IGFBP-3|IGgfbp3	insulin-like growth factor binding protein 3	protein-coding
mm_58846.1	chr7	16843050	16843077	+	1	NA	promoter-TSS (NM_178900)	promoter-TSS (NM_178900)	-2	NM_178900	101540	Mm.1881	NM_178900	ENSMUSG00000041187	Prkd2	AI325941|PKD2	protein kinase D2	protein-coding
mm_55777.1	chr6	81841447	81841447	-	1	NA	Intergenic	Intergenic	54216	NR_106091	102465711		NR_106091	ENSMUSG00000106154	Mir7232	mmu-mir-7232	microRNA 7232	ncRNA
mm_130376.1	chr15	97831461	97831519	-	1	NA	5' UTR (NM_019572, exon 1 of 24)	5' UTR (NM_019572, exon 1 of 24)	277	NM_019572	56233	Mm.384027	NM_019572	ENSMUSG00000022475	Hdac7	5830434K02Rik|HD7|HD7a|Hdac7a|mFLJ00062	histone deacetylase 7	protein-coding
mm_44423.1	chr5	20882015	20882023	-	1	NA	promoter-TSS (NM_177601)	promoter-TSS (NM_177601)	105	NM_172992	68770	Mm.86410	NM_172992	ENSMUSG00000039987	Phtf2	1110054G21Rik|9530062N20Rik|AI447096|C77923	putative homeodomain transcription factor 2	protein-coding
mm_120072.1	chr14	57217209	57217218	+	1	NA	Intergenic	Intergenic	-83602	NM_001010937	14623	Mm.25652	NM_008128	ENSMUSG00000040055	Gjb6	AA958971|Cx30|D14Bwg0506e	gap junction protein, beta 6	protein-coding
mm_66677.1	chr7	45759528	45759538	-	1	NA	promoter-TSS (NM_017465)	promoter-TSS (NM_017465)	22	NM_017465	54200	Mm.271634	NM_017465	ENSMUSG00000003271	Sult2b1	AI326997|BB173635|ST2B1|SULT2B	sulfotransferase family, cytosolic, 2B, member 1	protein-coding
mm_121592.1	chr14	7967409	7967419	-	1	NA	3' UTR (NM_007870, exon 8 of 8)	3' UTR (NM_007870, exon 8 of 8)	26768	NM_007870	13421	Mm.272258	NM_007870	ENSMUSG00000025279	Dnase1l3	DNasegamma|Dhp2|Lsd	deoxyribonuclease 1-like 3	protein-coding
mm_98572.1	chr11	95480466	95480473	+	1	NA	intron (NM_025287, intron 6 of 10)	intron (NM_025287, intron 6 of 10)	34096	NM_130858	104079	Mm.22970	NM_130858	ENSMUSG00000046719	Nxph3	-	neurexophilin 3	protein-coding
mm_122679.1	chr14	52010849	52010863	-	1	NA	intron (NM_027248, intron 1 of 4)	intron (NM_027248, intron 1 of 4)	3702	NM_001253695	69890	Mm.475652	NM_027248	ENSMUSG00000049295	Zfp219	2010302A17Rik	zinc finger protein 219	protein-coding
mm_37698.1	chr4	129335244	129335264	-	1	NA	promoter-TSS (NM_025970)	promoter-TSS (NM_025970)	116	NM_009030	19646	Mm.12145	NM_009030	ENSMUSG00000057236	Rbbp4	RBAP48|mRbAp48	retinoblastoma binding protein 4	protein-coding
mm_46329.1	chr5	100846093	100846130	-	1	NA	promoter-TSS (NM_172715)	promoter-TSS (NM_172715)	-118	NM_172715	231510	Mm.271911	NM_172715	ENSMUSG00000029314	Agpat9	1-AGPAT|1-AGPAT 9|4933407I02Rik|4933408F15|A230097K15Rik|GPAT-3|Gpat3|mGPAT3	1-acylglycerol-3-phosphate O-acyltransferase 9	protein-coding
mm_106345.1	chr11	118393378	118393391	-	1	NA	exon (NM_011150, exon 6 of 6)	exon (NM_011150, exon 6 of 6)	8547	NM_011150	19039	Mm.3152	NM_011150	ENSMUSG00000033880	Lgals3bp	90K|CyCAP|MAC-2BP|Ppicap|Tango10b	lectin, galactoside-binding, soluble, 3 binding protein	protein-coding
mm_117504.1	chr13	78200351	78200362	-	1	NA	intron (NR_045195, intron 1 of 2)	intron (NR_045195, intron 1 of 2)	-1483	NM_010151	13865	Mm.439653	NM_010151	ENSMUSG00000069171	Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR-3|EAR3|Erbal3|SVP44|Tcfcoup1	nuclear receptor subfamily 2, group F, member 1	protein-coding
mm_65677.1	chr7	28318881	28318896	-	1	NA	intron (NM_013676, intron 19 of 29)	intron (NM_013676, intron 19 of 29)	-6842	NM_025616	66525	Mm.167913	NM_025616	ENSMUSG00000003438	Timm50	2810403L02Rik|AU015082|TIM50L	translocase of inner mitochondrial membrane 50	protein-coding
mm_3220.1	chr1	135846696	135846730	+	1	NA	intron (NM_001130174, intron 5 of 13)	intron (NM_001130174, intron 5 of 13)	5852	NM_001130176	21956	Mm.247470	NM_011619	ENSMUSG00000026414	Tnnt2	Tnt|cTnT	troponin T2, cardiac	protein-coding
mm_762.1	chr1	43983180	43983193	+	1	NA	exon (NM_009418, exon 22 of 30)	exon (NM_009418, exon 22 of 30)	36820	NM_001013799	433294	Mm.123621	NM_001013799	ENSMUSG00000047343	Mettl21c	A530098C11Rik	methyltransferase like 21C	protein-coding
mm_171341.1	chr4	102882604	102882610	-	1	NA	intron (NM_001285862, intron 6 of 19)	IAPLTR1_Mm|LTR|ERVK	-103772	NM_001163767	67344	Mm.111346	NM_026100	ENSMUSG00000028523	Tctex1d1	1700055O19Rik	Tctex1 domain containing 1	protein-coding
mm_93066.1	chr10	89257579	89257599	-	1	NA	non-coding (NR_102339, exon 1 of 27)	non-coding (NR_102339, exon 1 of 27)	201	NM_001277188	320091	Mm.236464	NM_178773	ENSMUSG00000035189	Ano4	A330096O15Rik|Gm65|Tmem16d	anoctamin 4	protein-coding
mm_138007.1	chr17	33824891	33824922	+	1	NA	promoter-TSS (NM_016844)	promoter-TSS (NM_016844)	261	NR_103514	66416	Mm.29513	NM_023202	ENSMUSG00000041881	Ndufa7	14.5kDa|2400007M02Rik|CI-B14.5a	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 7 (B14.5a)	protein-coding
mm_77179.1	chr8	111718598	111718601	-	1	NA	intron (NM_001198839, intron 2 of 6)	L1MEd|LINE|L1	13537	NM_001198839	12927	Mm.3758	NM_009954	ENSMUSG00000031955	Bcar1	AI385681|Cas|Crkas	breast cancer anti-estrogen resistance 1	protein-coding
mm_8151.1	chr1	136608483	136608487	-	1	NA	Intergenic	Intergenic	-16416	NM_177643	226442	Mm.62521	NM_177643	ENSMUSG00000041483	Zfp281	Znf281	zinc finger protein 281	protein-coding
mm_124154.1	chr14	93202226	93202236	-	1	NA	intron (NM_001346722, intron 4 of 4)	intron (NM_001346722, intron 4 of 4)	686657	NM_001271800	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding
mm_151815.1	chr19	5489078	5489091	-	1	NA	promoter-TSS (NM_027877)	promoter-TSS (NM_027877)	-748	NM_027877	71711	Mm.27697	NM_027877	ENSMUSG00000024906	Mus81	1200008A18Rik|AI182501|AW045863	MUS81 structure-specific endonuclease subunit	protein-coding
mm_82458.1	chr9	15627898	15627907	-	1	NA	promoter-TSS (NM_181816)	promoter-TSS (NM_181816)	31	NM_181816	234964	Mm.32237	NM_181816	ENSMUSG00000039977	Ccdc67	4933401K09Rik|Deup1	coiled-coil domain containing 67	protein-coding
mm_135271.1	chr16	38396202	38396222	-	1	NA	TTS (NM_134102)	TTS (NM_134102)	34022	NM_022318	64082	Mm.390856	NM_022318	ENSMUSG00000022803	Popdc2	AV006127|Pop2	popeye domain containing 2	protein-coding
mm_154842.1	chrX	20364556	20364616	+	1	NA	non-coding (NR_110966, exon 1 of 8)	non-coding (NR_110966, exon 1 of 8)	105	NR_110967	19889	Mm.288141	NM_133669	ENSMUSG00000060090	Rp2	AI662636|Rp2h	retinitis pigmentosa 2 homolog	protein-coding
mm_73877.1	chr8	119277430	119277440	+	1	NA	intron (NM_019707, intron 10 of 13)	intron (NM_019707, intron 10 of 13)	-67103	NM_024219	68196	Mm.358714	NM_024219	ENSMUSG00000031839	Hsbp1	0610007A03Rik|AA408769|Hsp25	heat shock factor binding protein 1	protein-coding
mm_126127.1	chr15	78334049	78334063	+	1	NA	intron (NM_007780, intron 1 of 13)	intron (NM_007780, intron 1 of 13)	8066	NM_007780	12983	Mm.235324	NM_007780	ENSMUSG00000071713	Csf2rb	AI848964|AIC2B|Bc|CDw131|Csf2rb1|Csfgmrb|Il3r|Il3rb|Il3rb1|Il5rb	colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage)	protein-coding
mm_65649.1	chr7	28115331	28115345	-	1	NA	intron (NM_001122603, intron 17 of 19)	intron (NM_001122603, intron 17 of 19)	-14128	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_158665.1	chrX	157492281	157492340	-	1	NA	promoter-TSS (NM_009214)	promoter-TSS (NM_009214)	-264	NM_009214	20603	Mm.18652	NM_009214	ENSMUSG00000071708	Sms	AI427066|Gy|SPMSY|SpmST|gyro	spermine synthase	protein-coding
mm_88548.1	chr10	78591665	78591692	+	1	NA	intron (NM_027875, intron 1 of 7)	intron (NM_027875, intron 1 of 7)	286	NM_027875	71709	Mm.86439	NM_027875	ENSMUSG00000032714	Syde1	1200008N06Rik|BB043000|mSYD1A	synapse defective 1, Rho GTPase, homolog 1 (C. elegans)	protein-coding
mm_96242.1	chr11	62554675	62554679	+	1	NA	Intergenic	B1_Mur3|SINE|Alu	2946	NM_001313984	22187	Mm.371592	NM_011664	ENSMUSG00000019505	Ubb	AL033289|Rps27a|Uba52|Ubb2|Ubc	ubiquitin B	protein-coding
mm_144770.1	chr18	35795516	35795519	+	1	NA	intron (NM_019912, intron 2 of 6)	intron (NM_019912, intron 2 of 6)	23958	NM_019912	56550	Mm.180052	NM_019912	ENSMUSG00000091896	Ube2d2a	1500034D03Rik|Ubc2e|Ube2d2|ubc4	ubiquitin-conjugating enzyme E2D 2A	protein-coding
mm_40931.1	chr5	76588664	76588742	+	1	NA	Intergenic	CpG	-3011	NM_199032	381644	Mm.332452	NM_199032	ENSMUSG00000036403	Cep135	BC062951|Cep4|Gm1044	centrosomal protein 135	protein-coding
mm_71797.1	chr8	67956546	67956558	+	1	NA	intron (NM_177698, intron 3 of 14)	intron (NM_177698, intron 3 of 14)	18022	NM_177698	234353	Mm.32525	NM_027626	ENSMUSG00000030465	Psd3	4931420C21Rik|AI661273|BC003498|D430018P08|EFA6D	pleckstrin and Sec7 domain containing 3	protein-coding
mm_129158.1	chr15	76242619	76242627	-	1	NA	exon (NM_001163575, exon 4 of 11)	exon (NM_001163575, exon 4 of 11)	817	NM_001163576	671535	Mm.373750	NM_001163575	ENSMUSG00000063268	Parp10	-	poly (ADP-ribose) polymerase family, member 10	protein-coding
mm_127474.1	chr15	101273140	101273157	+	1	NA	exon (NM_010444, exon 6 of 7)	exon (NM_010444, exon 6 of 7)	6302	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_141281.1	chr17	27907707	27907770	-	1	NA	promoter-TSS (NM_026836)	promoter-TSS (NM_026836)	-14	NM_026836	68776	Mm.267998	NM_026836	ENSMUSG00000024218	Taf11	1110038O14Rik|28kDa|AI115401|AL024207|AW552398|PRO214|TAF2I|TAFII28	TATA-box binding protein associated factor 11	protein-coding
mm_97113.1	chr11	74665351	74665365	+	1	NA	exon (NM_001081158, exon 16 of 26)	exon (NM_001081158, exon 16 of 26)	15863	NM_001081158	74148	Mm.214574	NM_001081158	ENSMUSG00000020741	Cluh	1300001I01Rik|Kiaa0664|mKIAA0664	clustered mitochondria (cluA/CLU1) homolog	protein-coding
mm_36388.1	chr4	77168823	77168836	-	1	NA	intron (NM_011211, intron 7 of 39)	RLTR16C_MM|LTR|ERVK	1043066	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding
mm_76241.1	chr8	83583370	83583391	-	1	NA	intron (NM_134118, intron 1 of 12)	intron (NM_134118, intron 1 of 12)	11111	NM_027179	106529	Mm.352239	NM_027179	ENSMUSG00000031708	Tecr	2410016D23Rik|A230102P12Rik|AI173355|D17Ertd178e|Gpsn2|SC2	trans-2,3-enoyl-CoA reductase	protein-coding
mm_153124.1	chr19	33966910	33966922	-	1	NA	exon (NM_026334, exon 5 of 10)	exon (NM_026334, exon 5 of 10)	5668	NM_026334	67717	Mm.329816	NM_026334	ENSMUSG00000024768	Lipf	2310051B21Rik|AV082900	lipase, gastric	protein-coding
mm_39803.1	chr5	30623194	30623206	+	1	NA	3' UTR (NM_010608, exon 2 of 2)	3' UTR (NM_010608, exon 2 of 2)	-24736	NR_049199	100885838		NR_049199	ENSMUSG00000093710	Mir5625	Gm23930|mmu-mir-5625	microRNA 5625	ncRNA
mm_98076.1	chr11	86484720	86484731	+	1	NA	promoter-TSS (NM_029788)	promoter-TSS (NM_029788)	68	NM_029788	76892	Mm.262707	NM_029788	ENSMUSG00000020521	Rnft1	0610013E23Rik|AV007605	ring finger protein, transmembrane 1	protein-coding
mm_129991.1	chr15	86160527	86160542	-	1	NA	intron (NM_145475, intron 3 of 12)	ID_B1|SINE|B4	25607	NM_145475	223753	Mm.222685	NM_145475	ENSMUSG00000035891	Cerk	AI848610|D330016D08Rik|mKIAA1646	ceramide kinase	protein-coding
mm_140461.1	chr17	90179295	90179296	+	1	NA	intron (NM_001346959, intron 3 of 6)	intron (NM_001346959, intron 3 of 6)	-90927	NM_001347419	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_33649.1	chr4	133039511	133039525	+	1	NA	intron (NM_146155, intron 2 of 6)	CpG	28012	NM_146155	230793	Mm.31816	NM_146155	ENSMUSG00000037692	Ahdc1	D030015G18Rik	AT hook, DNA binding motif, containing 1	protein-coding
mm_38502.1	chr4	141113670	141113686	-	1	NA	TTS (NM_177867)	TTS (NM_177867)	25333	NM_177867	329972	Mm.247201	NM_177867	ENSMUSG00000045004	Spata21	4933414G08	spermatogenesis associated 21	protein-coding
mm_70011.1	chr7	142443631	142443660	-	1	NA	exon (NM_009405, exon 4 of 6)	exon (NM_009405, exon 4 of 6)	1177	NM_009405	21953	Mm.39469	NM_009405	ENSMUSG00000031097	Tnni2	-	troponin I, skeletal, fast 2	protein-coding
mm_31818.1	chr4	66841835	66841853	+	1	NA	3' UTR (NM_021297, exon 3 of 3)	3' UTR (NM_021297, exon 3 of 3)	14293	NM_021297	21898	Mm.38049	NM_021297	ENSMUSG00000039005	Tlr4	Lps|Ly87|Ran/M1|Rasl2-8	toll-like receptor 4	protein-coding
mm_50861.1	chr6	55336114	55336129	+	1	NA	promoter-TSS (NM_007472)	promoter-TSS (NM_007472)	-178	NM_007472	11826	Mm.18625	NM_007472	ENSMUSG00000004655	Aqp1	CHIP28	aquaporin 1	protein-coding
mm_100706.1	chr11	3648984	3649028	-	1	NA	promoter-TSS (NM_001159288)	promoter-TSS (NM_001159288)	-192	NR_002321	544752	Mm.390314	NR_002321	ENSMUSG00000056579	Tug1	AI316828	taurine upregulated gene 1	ncRNA
mm_2638.1	chr1	121706512	121706527	+	1	NA	Intergenic	Intergenic	-138539	NM_025860	66942	Mm.44219	NM_025860	ENSMUSG00000001674	Ddx18	2310005B10Rik	DEAD (Asp-Glu-Ala-Asp) box polypeptide 18	protein-coding
mm_99465.1	chr11	102435705	102435727	+	1	NA	exon (NM_008175, exon 11 of 13)	exon (NM_008175, exon 11 of 13)	5394	NM_008175	14824	Mm.1568	NM_008175	ENSMUSG00000034708	Grn	Pgrn|epithelin	granulin	protein-coding
mm_157077.1	chrX	9256901	9256917	-	1	NA	intron (NM_173414, intron 3 of 4)	ID2|SINE|ID	-15875	NM_023500	22439	Mm.56468	NM_023500	ENSMUSG00000015342	Xk	1810038K19Rik|XRG1|Xkh	X-linked Kx blood group	protein-coding
mm_142724.1	chr17	48167188	48167218	-	1	NA	promoter-TSS (NM_178796)	promoter-TSS (NM_178796)	54	NM_001113556	328830	Mm.470939	NM_178796	ENSMUSG00000043939	A530064D06Rik	Trem4|pdctrem	RIKEN cDNA A530064D06 gene	protein-coding
mm_17432.1	chr2	27507637	27507647	-	1	NA	Intergenic	Intergenic	-7505	NM_080848	140858	Mm.28265	NM_080848	ENSMUSG00000026917	Wdr5	2410008O07Rik|AA408785|AA960360|Big|Big-3	WD repeat domain 5	protein-coding
mm_78607.1	chr9	37544996	37545006	+	1	NA	TTS (NM_020518)	TTS (NM_020518)	5746	NM_020518	57276	Mm.27478	NM_020518	ENSMUSG00000001943	Vsig2	1190004B15Rik|2210413P10Rik|AU040484|CTX|Ctm	V-set and immunoglobulin domain containing 2	protein-coding
mm_127437.1	chr15	101270299	101270310	+	1	NA	exon (NM_010444, exon 2 of 7)	exon (NM_010444, exon 2 of 7)	3458	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_49848.1	chr6	38354914	38354923	+	1	NA	promoter-TSS (NM_028421)	promoter-TSS (NM_028421)	-315	NM_028421	78781	Mm.25243	NM_028421	ENSMUSG00000029826	Zc3hav1	1200014N16Rik|2900058M19Rik|9130009D18Rik|9830115L13Rik|ARTD13|D6Bwg1452e|ZAP	zinc finger CCCH type, antiviral 1	protein-coding
mm_145552.1	chr18	60810384	60810395	+	1	NA	exon (NM_010545, exon 6 of 8)	exon (NM_010545, exon 6 of 8)	-1687	NR_039567	100628611		NR_039567	ENSMUSG00000093327	Mir5107	mir-5107|mmu-mir-5107|mu-mir-5107	microRNA 5107	ncRNA
mm_119014.1	chr14	29978424	29978434	+	1	NA	promoter-TSS (NM_027493)	promoter-TSS (NM_027493)	92	NM_027493	56249	Mm.215110	NM_027493	ENSMUSG00000015971	Actr8	5730542K05Rik|ARP8	ARP8 actin-related protein 8	protein-coding
mm_52726.1	chr6	120093371	120093381	+	1	NA	promoter-TSS (NM_016718)	promoter-TSS (NM_016718)	-4	NM_016718	29862	Mm.103668	NM_016718	ENSMUSG00000041377	Ninj2	-	ninjurin 2	protein-coding
mm_133183.1	chr16	72663032	72663044	+	1	NA	promoter-TSS (NM_019413)	promoter-TSS (NM_019413)	-111	NM_019413	19876	Mm.310772	NM_019413	ENSMUSG00000022883	Robo1	AW494633|AW742721|DUTT1|Gm310	roundabout guidance receptor 1	protein-coding
mm_165476.1	chr2	164333330	164333334	+	1	NA	exon (NM_009301, exon 2 of 3)	exon (NM_009301, exon 2 of 3)	567	NM_009301	20944	Mm.140154	NM_009301	ENSMUSG00000017004	Svs5	BB115186|Semg1|Svp-1|Svp1|Svp5	seminal vesicle secretory protein 5	protein-coding
mm_143418.1	chr17	70842098	70842100	-	1	NA	Intergenic	Intergenic	4678	NM_001164077	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_27352.1	chr3	50417159	50417171	-	1	NA	intron (NM_011990, intron 6 of 11)	intron (NM_011990, intron 6 of 11)	26448	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_173016.1	chrX	100294767	100294784	+	1	NA	intron (NM_001177941, intron 1 of 6)	L1Md_T|LINE|L1	-86322	NR_030525	751534		NR_030525	ENSMUSG00000076398	Mir676	Mirn676|mir-676|mmu-mir-676	microRNA 676	ncRNA
mm_28599.1	chr3	94572607	94572632	-	1	NA	intron (NM_001082484, intron 1 of 11)	intron (NM_001082484, intron 1 of 11)	10097	NM_001082484	76742	Mm.28160	NM_029721	ENSMUSG00000028136	Snx27	5730552M22Rik|ESTM45|ESTM47|R75405	sorting nexin family member 27	protein-coding
mm_46283.1	chr5	100159391	100159435	-	1	NA	intron (NM_182841, intron 1 of 7)	CpG	395	NM_182841	231503	Mm.99790	NM_182841	ENSMUSG00000050640	Tmem150c	-	transmembrane protein 150C	protein-coding
mm_168563.1	chr1	169174719	169174723	+	1	NA	Intergenic	Intergenic	356743	NM_023284	66977	Mm.151315	NM_023284	ENSMUSG00000026683	Nuf2	2410003C07Rik|AU044112|C85691|Cdca1|NUF2R	NUF2, NDC80 kinetochore complex component	protein-coding
mm_152582.1	chr19	11603198	11603296	-	1	NA	exon (NM_026835, exon 2 of 7)	exon (NM_026835, exon 2 of 7)	1557	NM_026835	68774	Mm.290390	NM_026835	ENSMUSG00000024679	Ms4a6d	1110058E16Rik|AI447446|Ms4a11	membrane-spanning 4-domains, subfamily A, member 6D	protein-coding
mm_17712.1	chr2	32385982	32386001	-	1	NA	exon (NM_008491, exon 3 of 6)	exon (NM_008491, exon 3 of 6)	1748	NM_008491	16819	Mm.9537	NM_008491	ENSMUSG00000026822	Lcn2	24p3|AW212229|NRL|Sip24	lipocalin 2	protein-coding
mm_51201.1	chr6	71322755	71322765	+	1	NA	promoter-TSS (NM_009858)	promoter-TSS (NM_009858)	-52	NM_009858	12526	Mm.333148	NM_009858	ENSMUSG00000053044	Cd8b1	Cd8b|Ly-3|Ly-C|Lyt-3	CD8 antigen, beta chain 1	protein-coding
mm_88401.1	chr10	76595966	76596010	+	1	NA	3' UTR (NM_146007, exon 28 of 28)	3' UTR (NM_146007, exon 28 of 28)	20340	NM_080845	14317	Mm.36278	NM_080845	ENSMUSG00000001155	Ftcd	-	formiminotransferase cyclodeaminase	protein-coding
mm_54175.1	chr6	23655143	23655168	-	1	NA	promoter-TSS (NM_027754)	promoter-TSS (NM_027754)	-19	NM_027754	71300	Mm.443309	NM_027754	ENSMUSG00000078179	Rnf148	4933432M07Rik|Greul3	ring finger protein 148	protein-coding
mm_3226.1	chr1	135848806	135848848	+	1	NA	exon (NM_001130176, exon 8 of 13)	exon (NM_001130176, exon 8 of 13)	7966	NM_001130176	21956	Mm.247470	NM_011619	ENSMUSG00000026414	Tnnt2	Tnt|cTnT	troponin T2, cardiac	protein-coding
mm_103392.1	chr11	75422588	75422609	-	1	NA	promoter-TSS (NM_011340)	promoter-TSS (NM_011340)	25	NM_011340	20317	Mm.2044	NM_011340	ENSMUSG00000000753	Serpinf1	AI195227|EPC-1|Pedf|Pedfl|Sdf3	serine (or cysteine) peptidase inhibitor, clade F, member 1	protein-coding
mm_106338.1	chr11	118393123	118393131	-	1	NA	exon (NM_011150, exon 6 of 6)	exon (NM_011150, exon 6 of 6)	8804	NM_011150	19039	Mm.3152	NM_011150	ENSMUSG00000033880	Lgals3bp	90K|CyCAP|MAC-2BP|Ppicap|Tango10b	lectin, galactoside-binding, soluble, 3 binding protein	protein-coding
mm_133990.1	chr16	4635414	4635453	-	1	NA	exon (NM_030205, exon 10 of 28)	exon (NM_030205, exon 10 of 28)	-4512	NM_139307	246154	Mm.482140	NM_139307	ENSMUSG00000039646	Vasn	2610528G05Rik|Atia|Slitl2	vasorin	protein-coding
mm_11175.1	chr2	28699788	28699818	+	1	NA	promoter-TSS (NM_027283)	promoter-TSS (NM_027283)	-152	NM_027283	69987	Mm.239376	NM_027283	ENSMUSG00000026809	Spaca9	1700026L06Rik|MAST	sperm acrosome associated 9	protein-coding
mm_134274.1	chr16	13986945	13986950	-	1	NA	promoter-TSS (NM_001270718)	promoter-TSS (NM_001270718)	-80	NM_001270718	74482	Mm.484026	NM_028968	ENSMUSG00000065968	Ifitm7	4933438K12Rik|Mil4	interferon induced transmembrane protein 7	protein-coding
mm_30543.1	chr4	3679183	3679191	+	1	NA	intron (NM_010747, intron 1 of 12)	intron (NM_010747, intron 1 of 12)	1066	NM_010747	17096	Mm.317331	NM_010747	ENSMUSG00000042228	Lyn	AA407514|Hck-2|p53Lyn|p56Lyn	LYN proto-oncogene, Src family tyrosine kinase	protein-coding
mm_95202.1	chr11	43474258	43474267	+	1	NA	promoter-TSS (NM_026979)	promoter-TSS (NM_026979)	-44	NM_026979	69183	Mm.390374	NM_026979	ENSMUSG00000046491	C1qtnf2	1810033K05Rik|CTRP2	C1q and tumor necrosis factor related protein 2	protein-coding
mm_156996.1	chrX	7429640	7429655	-	1	NA	Intergenic	Intergenic	-6659	NR_027924	68355	Mm.45111	NR_027924		2010204K13Rik	0610010M13Rik|Cip7	RIKEN cDNA 2010204K13 gene	ncRNA
mm_49407.1	chr6	28480338	28480370	+	1	NA	promoter-TSS (NM_019776)	promoter-TSS (NM_019776)	6	NM_019776	56463	Mm.439987	NM_019776	ENSMUSG00000001424	Snd1	AL033314|Tudor-SN	staphylococcal nuclease and tudor domain containing 1	protein-coding
mm_89716.1	chr10	98880355	98880379	+	1	NA	Intergenic	Intergenic	-34785	NM_026482	67972	Mm.166944	NM_026482	ENSMUSG00000019943	Atp2b1	2810442I22Rik|E130111D10Rik|Pmca1	ATPase, Ca++ transporting, plasma membrane 1	protein-coding
mm_39763.1	chr5	30013273	30013277	+	1	NA	intron (NM_001314054, intron 1 of 4)	intron (NM_001314054, intron 1 of 4)	161	NM_031168	16193	Mm.1019	NM_031168	ENSMUSG00000025746	Il6	Il-6	interleukin 6	protein-coding
mm_73611.1	chr8	110090026	110090045	+	1	NA	exon (NM_175480, exon 5 of 5)	exon (NM_175480, exon 5 of 5)	10301	NM_175480	234725	Mm.87487	NM_175480	ENSMUSG00000044676	Zfp612	B230354B21Rik	zinc finger protein 612	protein-coding
mm_28615.1	chr3	94886946	94886956	-	1	NA	promoter-TSS (NM_008945)	promoter-TSS (NM_008945)	7	NM_008945	19172	Mm.368	NM_008945	ENSMUSG00000005779	Psmb4	Pros-27	proteasome (prosome, macropain) subunit, beta type 4	protein-coding
mm_148296.1	chr18	82585507	82585515	-	1	NA	3' UTR (NM_010777, exon 7 of 7)	3' UTR (NM_010777, exon 7 of 7)	31003	NM_001025254	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_49637.1	chr6	30805067	30805080	+	1	NA	intron (NM_017478, intron 20 of 23)	intron (NM_017478, intron 20 of 23)	63774	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_77280.1	chr8	116711468	116711510	-	1	NA	intron (NM_029441, intron 1 of 6)	Lx9|LINE|L1	21502	NM_029441	75796	Mm.159575	NM_029441	ENSMUSG00000031758	Cdyl2	1700029M19Rik|4930453I21Rik|Gm20194	chromodomain protein, Y chromosome-like 2	protein-coding
mm_161929.1	chr18	80364307	80364307	-	1	NA	promoter-TSS (NM_001190373)	promoter-TSS (NM_001190373)	-53	NM_001190373	240444	Mm.279568	NM_001190373	ENSMUSG00000059852	Kcng2	AA591524	potassium voltage-gated channel, subfamily G, member 2	protein-coding
mm_127975.1	chr15	12321314	12321324	-	1	NA	promoter-TSS (NM_025673)	promoter-TSS (NM_025673)	-177	NM_025673	66629	Mm.157655	NM_025673	ENSMUSG00000022200	Golph3	4733401N08Rik|5730410D03Rik|AW413496	golgi phosphoprotein 3	protein-coding
mm_156283.1	chrX	136837231	136837246	+	1	NA	3' UTR (NM_011123, exon 7 of 7)	3' UTR (NM_011123, exon 7 of 7)	14492	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_163320.1	chr12	7977731	7977741	+	1	NA	promoter-TSS (NM_009693)	promoter-TSS (NM_009693)	59	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_140216.1	chr17	83827101	83827107	+	1	NA	Intergenic	Intergenic	19686	NM_025325	107766	Mm.30100	NM_025325	ENSMUSG00000000673	Haao	0610007K21Rik|0610012J07Rik|3-HAO|3-HAOxase|3HAO	3-hydroxyanthranilate 3,4-dioxygenase	protein-coding
mm_150871.1	chr19	45055295	45055308	+	1	NA	3' UTR (NM_053197, exon 11 of 11)	3' UTR (NM_053197, exon 11 of 11)	7725	NM_001178013	94280	Mm.36169	NM_053197	ENSMUSG00000025212	Sfxn3	-	sideroflexin 3	protein-coding
mm_21140.1	chr2	154216244	154216267	-	1	NA	exon (NM_153418, exon 13 of 16)	exon (NM_153418, exon 13 of 16)	-7487	NM_144890	228802	Mm.167411	NM_144890	ENSMUSG00000038572	Bpifb5	Lplunc5	BPI fold containing family B, member 5	protein-coding
mm_142865.1	chr17	51814292	51814303	-	1	NA	intron (NM_001163632, intron 1 of 10)	intron (NM_001163632, intron 1 of 10)	-2243	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_124433.1	chr14	118368566	118368568	-	1	NA	intron (NR_045624, intron 3 of 5)	RMER17C|LTR|ERVK	2689	NR_045624	73306	Mm.362328	NR_045624	ENSMUSG00000099911	1700044C05Rik	-	RIKEN cDNA 1700044C05 gene	ncRNA
mm_18668.1	chr2	70825579	70825618	-	1	NA	promoter-TSS (NM_172664)	promoter-TSS (NM_172664)	-118	NM_172664	228012	Mm.136511	NM_172664	ENSMUSG00000041997	Tlk1	4930545J15Rik	tousled-like kinase 1	protein-coding
mm_126289.1	chr15	79346609	79346617	+	1	NA	promoter-TSS (NM_001304830)	promoter-TSS (NM_001304830)	-8	NM_001304830	17133	Mm.86646	NM_010755	ENSMUSG00000042622	Maff	-	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein F (avian)	protein-coding
mm_59067.1	chr7	19489046	19489067	+	1	NA	Intergenic	Intergenic	19275	NM_177692	232946	Mm.64557	NM_177692	ENSMUSG00000057667	Bloc1s3	BC043666|Blos3|E230011O18|rp	biogenesis of lysosomal organelles complex-1, subunit 3	protein-coding
mm_93556.1	chr10	116473396	116473406	-	1	NA	exon (NM_021452, exon 1 of 3)	exon (NM_021452, exon 1 of 3)	122	NM_021452	58802	Mm.440652	NM_021452	ENSMUSG00000054934	Kcnmb4	1700058G18Rik|2900045G12Rik	potassium large conductance calcium-activated channel, subfamily M, beta member 4	protein-coding
mm_117175.1	chr13	63272658	63272664	-	1	NA	intron (NR_110520, intron 2 of 5)	intron (NR_110520, intron 2 of 5)	24486	NR_045794	100504114	Mm.437070	NR_045794	ENSMUSG00000097242	Gm16907	-	predicted gene, 16907	ncRNA
mm_101481.1	chr11	30986298	30986325	-	1	NA	promoter-TSS (NM_026527)	promoter-TSS (NM_026527)	54	NM_026527	68044	Mm.32656	NM_026527	ENSMUSG00000020309	Chac2	-	ChaC, cation transport regulator 2	protein-coding
mm_142175.1	chr17	36257858	36257871	-	1	NA	promoter-TSS (NM_026308)	promoter-TSS (NM_026308)	-18	NM_026308	67676	Mm.27131	NM_026308	ENSMUSG00000024446	Rpp21	0610037N01Rik	ribonuclease P 21 subunit	protein-coding
mm_152241.1	chr19	8713363	8713404	-	1	NA	exon (NM_008577, exon 1 of 9)	exon (NM_008577, exon 1 of 9)	514	NM_008577	17254	Mm.4114	NM_008577	ENSMUSG00000010095	Slc3a2	4F2|4F2HC|AI314110|Cd98|Ly-10|Ly-m10|Ly10|Mdu1|Mgp-2hc|NACAE	solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2	protein-coding
mm_48148.1	chr5	137150882	137150887	-	1	NA	Intergenic	(TGG)n|Simple_repeat|Simple_repeat	-34677	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_129928.1	chr15	84482844	84482865	-	1	NA	Intergenic	Intergenic	-35757	NM_001163145	72301	Mm.275387	NM_001163145	ENSMUSG00000062760	1810041L15Rik	Kiaa1644	RIKEN cDNA 1810041L15 gene	protein-coding
mm_17674.1	chr2	32236378	32236393	-	1	NA	promoter-TSS (NM_145145)	promoter-TSS (NM_145145)	-298	NM_145145	99011	Mm.31192	NM_145145	ENSMUSG00000039254	Pomt1	AI505244	protein-O-mannosyltransferase 1	protein-coding
mm_66776.1	chr7	46861181	46861187	-	1	NA	promoter-TSS (NM_013580)	promoter-TSS (NM_013580)	-79	NM_013580	16833	Mm.16563	NM_013580	ENSMUSG00000030851	Ldhc	LDH-C4|Ldh-3|Ldh-x|Ldh3|Ldhc4	lactate dehydrogenase C	protein-coding
mm_141421.1	chr17	29435447	29435460	-	1	NA	Intergenic	Intergenic	-55592	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_152252.1	chr19	8723167	8723287	-	1	NA	promoter-TSS (NR_002896)	promoter-TSS (NR_002896)	142	NM_001161413	17254	Mm.4114	NM_008577	ENSMUSG00000010095	Slc3a2	4F2|4F2HC|AI314110|Cd98|Ly-10|Ly-m10|Ly10|Mdu1|Mgp-2hc|NACAE	solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2	protein-coding
mm_4083.1	chr1	167000797	167000818	+	1	NA	promoter-TSS (NM_175461)	promoter-TSS (NM_175461)	-610	NM_175461	226610	Mm.389217	NM_175461	ENSMUSG00000060568	Fam78b	C030014K22Rik|C030020L09Rik	family with sequence similarity 78, member B	protein-coding
mm_162451.1	chr1	124279203	124279206	+	1	NA	Intergenic	L1_Mur2|LINE|L1	-233645	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_80982.1	chr9	103219839	103219862	+	1	NA	exon (NM_133977, exon 10 of 17)	exon (NM_133977, exon 10 of 17)	10436	NM_133977	22041	Mm.37214	NM_133977	ENSMUSG00000032554	Trf	AI266983|Cd176|HP|Tf|Tfn|hpx	transferrin	protein-coding
mm_70667.1	chr8	14888951	14888961	+	1	NA	5' UTR (NM_012000, exon 1 of 3)	5' UTR (NM_012000, exon 1 of 3)	420	NM_012000	26889	Mm.254027	NM_012000	ENSMUSG00000026317	Cln8	mnd	ceroid-lipofuscinosis, neuronal 8	protein-coding
mm_139328.1	chr17	48932369	48932399	+	1	NA	promoter-TSS (NM_027452)	promoter-TSS (NM_027452)	-198	NM_027452	70530	Mm.133607	NM_027452	ENSMUSG00000040490	Lrfn2	5730420O05Rik|SALM1|mKIAA1246	leucine rich repeat and fibronectin type III domain containing 2	protein-coding
mm_141471.1	chr17	30612559	30612577	-	1	NA	promoter-TSS (NM_001113560)	promoter-TSS (NM_001113560)	91	NM_025374	109801	Mm.261984	NM_025374	ENSMUSG00000024026	Glo1	0610009E22Rik|1110008E19Rik|2510049H23Rik|AW550643|GLY1|Glo-1|Glo-1r|Glo-1s|Glo1-r|Glo1-s|Qglo	glyoxalase 1	protein-coding
mm_75013.1	chr8	28829432	28829436	-	1	NA	intron (NM_001347498, intron 4 of 14)	intron (NM_001347498, intron 4 of 14)	390202	NM_001347499	210801	Mm.248433	NM_153135	ENSMUSG00000063626	Unc5d	D930029E11Rik|Unc5h4|mKIAA1777	unc-5 netrin receptor D	protein-coding
mm_16278.1	chr2	173737640	173737646	+	1	NA	promoter-TSS (NM_019806)	promoter-TSS (NM_019806)	72	NM_019806	56491	Mm.260456	NM_019806	ENSMUSG00000054455	Vapb	AI225786|AI840687|AI848259|D2Abb2e|R75548|VAP33b|Vamp33b	vesicle-associated membrane protein, associated protein B and C	protein-coding
mm_88003.1	chr10	67096342	67096361	+	1	NA	intron (NM_178606, intron 1 of 7)	CpG	637	NM_001204915	28193	Mm.41272	NM_178606	ENSMUSG00000019873	Reep3	D10Ucla1	receptor accessory protein 3	protein-coding
mm_109689.1	chr12	113142865	113142880	+	1	NA	intron (NM_001347443, intron 1 of 6)	intron (NM_001347443, intron 1 of 6)	2267	NM_001347443	68337	Mm.133825	NM_024223	ENSMUSG00000006356	Crip2	0610010I23Rik|AW743261|C77570|CRP2|CRP4|Crp|ESP1|Hlp	cysteine rich protein 2	protein-coding
mm_138271.1	chr17	34604820	34604856	+	1	NA	Intergenic	Intergenic	-1023	NM_001163379	55979	Mm.8684	NM_018862	ENSMUSG00000034254	Agpat1	1-AGP|1-AGPAT|AW047140	1-acylglycerol-3-phosphate O-acyltransferase 1 (lysophosphatidic acid acyltransferase, alpha)	protein-coding
mm_20061.1	chr2	120352986	120352996	-	1	NA	non-coding (NR_027618, exon 1 of 26)	non-coding (NR_027618, exon 1 of 26)	142	NM_178851	269338	Mm.246131	NM_147153	ENSMUSG00000027291	Vps39	A230065P22Rik|AW743070|Vam6|Vam6P|mVam6	VPS39 HOPS complex subunit	protein-coding
mm_162671.1	chr10	7458314	7458318	+	1	NA	intron (NM_029975, intron 1 of 5)	intron (NM_029975, intron 1 of 5)	15161	NM_029975	77777	Mm.442442	NM_029975	ENSMUSG00000079685	Ulbp1	A430108B07Rik|MULT1	UL16 binding protein 1	protein-coding
mm_11087.1	chr2	27886006	27886047	+	1	NA	promoter-TSS (NM_015734)	promoter-TSS (NM_015734)	-399	NM_015734	12831	Mm.7281	NM_015734	ENSMUSG00000026837	Col5a1	AI413331	collagen, type V, alpha 1	protein-coding
mm_85208.1	chr9	96787866	96787880	-	1	NA	Intergenic	Intergenic	22311	NR_102296	319707	Mm.392191	NR_102293	ENSMUSG00000101581	C430002N11Rik	-	RIKEN cDNA C430002N11 gene	ncRNA
mm_83257.1	chr9	42428182	42428197	-	1	NA	intron (NM_173038, intron 7 of 7)	L2a|LINE|L2	-28260	NM_001324548	21683	Mm.42209	NM_009347	ENSMUSG00000037705	Tecta	Tctna	tectorin alpha	protein-coding
mm_146804.1	chr18	20745719	20745739	-	1	NA	5' UTR (NM_019737, exon 1 of 9)	5' UTR (NM_019737, exon 1 of 9)	675	NM_019737	56386	Mm.393827	NM_019737	ENSMUSG00000056124	B4galt6	AA536803|AU022389	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 6	protein-coding
mm_158509.1	chrX	142966666	142966675	-	1	NA	promoter-TSS (NM_019496)	promoter-TSS (NM_019496)	58	NM_019496	56068	Mm.143724	NM_019496	ENSMUSG00000042225	Ammecr1	6230420G18Rik	Alport syndrome, mental retardation, midface hypoplasia and elliptocytosis chromosomal region gene 1	protein-coding
mm_40178.1	chr5	36003403	36003412	+	1	NA	3' UTR (NM_027373, exon 17 of 17)	3' UTR (NM_027373, exon 17 of 17)	110088	NM_027373	70292	Mm.125167	NM_027373	ENSMUSG00000029094	Afap1	2600003E23Rik|9630044L16Rik|AI848729|Afap|mKIAA3018	actin filament associated protein 1	protein-coding
mm_133162.1	chr16	70409855	70409858	+	1	NA	intron (NM_028803, intron 3 of 15)	intron (NM_028803, intron 3 of 15)	95907	NM_028803	74185	Mm.396102	NM_028803	ENSMUSG00000022707	Gbe1	2310045H19Rik|2810426P10Rik|D16Ertd536e	glucan (1,4-alpha-), branching enzyme 1	protein-coding
mm_59016.1	chr7	19256932	19256940	+	1	NA	TTS (NM_001282022)	TTS (NM_001282022)	14918	NM_001282021	22323	Mm.9684	NM_009499	ENSMUSG00000030403	Vasp	-	vasodilator-stimulated phosphoprotein	protein-coding
mm_12016.1	chr2	57372657	57372665	+	1	NA	Intergenic	Intergenic	134279	NM_010274	14571	Mm.3711	NM_010274	ENSMUSG00000026827	Gpd2	AA408484|AI448216|AU021455|AW494132|GPDH|Gdm1|Gpd-m|Gpdh-m|TISP38	glycerol phosphate dehydrogenase 2, mitochondrial	protein-coding
mm_82815.1	chr9	30922550	30922567	-	1	NA	promoter-TSS (NM_001024139)	promoter-TSS (NM_001024139)	-106	NM_001024139	235130	Mm.65867	NM_001024139	ENSMUSG00000033453	Adamts15	-	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 15	protein-coding
mm_59693.1	chr7	28540719	28540728	+	1	NA	promoter-TSS (NM_026716)	promoter-TSS (NM_026716)	-162	NM_026716	68416	Mm.25210	NM_026716	ENSMUSG00000084174	Sycn	0910001K16Rik|1810038B08Rik|SYL	syncollin	protein-coding
mm_65607.1	chr7	27446718	27446748	-	1	NA	promoter-TSS (NM_032610)	promoter-TSS (NM_032610)	-144	NM_032610	80297	Mm.459123	NM_032610	ENSMUSG00000011751	Sptbn4	1700022P15Rik|5830426A08Rik|ROSA62|SpbIV|Spnb4|dyn|lnd|nmf261|nmf379|qv	spectrin beta, non-erythrocytic 4	protein-coding
mm_147081.1	chr18	35627207	35627222	-	1	NA	promoter-TSS (NM_011397)	promoter-TSS (NM_011397)	13	NM_011397	20522	Mm.22702	NM_011397	ENSMUSG00000024354	Slc23a1	D18Ucla2|SVCT1|Slc23a2|YSPL3	solute carrier family 23 (nucleobase transporters), member 1	protein-coding
mm_161465.1	chr15	78119157	78119157	-	1	NA	5' UTR (NM_007583, exon 1 of 4)	5' UTR (NM_007583, exon 1 of 4)	123	NM_007583	12300	Mm.277338	NM_007583	ENSMUSG00000019146	Cacng2	AW060990|B230105C07Rik|B930041E13Rik|stargazer|stargazin|stg|wag|waggler	calcium channel, voltage-dependent, gamma subunit 2	protein-coding
mm_66141.1	chr7	31126717	31126725	-	1	NA	5' UTR (NM_011322, exon 1 of 6)	5' UTR (NM_011322, exon 1 of 6)	302	NM_011322	20266	Mm.1418	NM_011322	ENSMUSG00000019194	Scn1b	-	sodium channel, voltage-gated, type I, beta	protein-coding
mm_159824.1	chr5	123510619	123510619	+	1	NA	TTS (NM_023232)	TTS (NM_023232)	159	NM_198611	231727	Mm.484068	NM_198611	ENSMUSG00000029431	B3gnt4	1010001G17Rik|BGnT-4	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 4	protein-coding
mm_120658.1	chr14	70536205	70536228	+	1	NA	intron (NM_145219, intron 7 of 7)	intron (NM_145219, intron 7 of 7)	5395	NM_145219	213469	Mm.41708	NM_145219	ENSMUSG00000033595	Lgi3	AI841179|AW049851	leucine-rich repeat LGI family, member 3	protein-coding
mm_103920.1	chr11	83592553	83592570	-	1	NA	intron (NM_009139, intron 1 of 3)	intron (NM_009139, intron 1 of 3)	526	NM_009139	20305	Mm.137	NM_009139	ENSMUSG00000018927	Ccl6	MRP-1|Scya6|c10	chemokine (C-C motif) ligand 6	protein-coding
mm_140505.1	chr17	5406633	5406664	-	1	NA	Intergenic	Intergenic	12119	NM_175349	106557	Mm.432764	NM_175349	ENSMUSG00000101959	Ldhal6b	4933402O15Rik|AI326310|LDHL|Ldhal	lactate dehydrogenase A-like 6B	protein-coding
mm_133604.1	chr16	91485116	91485144	+	1	NA	promoter-TSS (NM_010508)	promoter-TSS (NM_010508)	-85	NM_010508	15975	Mm.502	NM_010508	ENSMUSG00000022967	Ifnar1	CD118|Ifar|Ifnar|Ifrc|Infar	interferon (alpha and beta) receptor 1	protein-coding
mm_38685.1	chr4	145103771	145103784	-	1	NA	intron (NM_001276502, intron 38 of 68)	intron (NM_001276502, intron 38 of 68)	86889	NM_001276502	230895	Mm.240310	NM_001033190	ENSMUSG00000020220	Vps13d	-	vacuolar protein sorting 13D	protein-coding
mm_4741.1	chr1	181860890	181860898	+	1	NA	Intergenic	Intergenic	-18493	NM_133815	98386	Mm.4538	NM_133815	ENSMUSG00000004880	Lbr	AI505894|ic	lamin B receptor	protein-coding
mm_116227.1	chr13	33034652	33034663	-	1	NA	intron (NM_011452, intron 4 of 6)	intron (NM_011452, intron 4 of 6)	7243	NM_011452	20706	Mm.45371	NM_011452	ENSMUSG00000021403	Serpinb9b	1600019A21Rik|R86|SPI-CI|Spi10|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 9b	protein-coding
mm_163706.1	chr13	108326560	108326567	+	1	NA	intron (NM_178683, intron 2 of 10)	intron (NM_178683, intron 2 of 10)	10226	NM_178683	218581	Mm.32318	NM_178683	ENSMUSG00000021697	Depdc1b	9830132O03|AW260467|XTP1	DEP domain containing 1B	protein-coding
mm_69955.1	chr7	142373734	142373771	-	1	NA	promoter-TSS (NM_001347541)	promoter-TSS (NM_001347541)	-6	NM_001347541	320802	Mm.154486	NM_177265	ENSMUSG00000045777	Ifitm10	6330512M04Rik|AI848576|DSPA3	interferon induced transmembrane protein 10	protein-coding
mm_102236.1	chr11	54962874	54962874	-	1	NA	promoter-TSS (NM_021327)	promoter-TSS (NM_021327)	66	NM_021327	57783	Mm.259671	NM_021327	ENSMUSG00000020400	Tnip1	ABIN|ABIN-1|ABIN1|AU018810|Naf1|Nef|VAN	TNFAIP3 interacting protein 1	protein-coding
mm_2132.1	chr1	88055515	88055519	+	1	NA	exon (NM_201641, exon 1 of 5)	exon (NM_201641, exon 1 of 5)	106	NM_201641	394430	Mm.300095	NM_201641	ENSMUSG00000090165	Ugt1a10	A13|Ugt1a13	UDP glycosyltransferase 1 family, polypeptide A10	protein-coding
mm_80882.1	chr9	99183554	99183598	+	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	-43365	NM_029094	74769	Mm.213128	NM_029094	ENSMUSG00000032462	Pik3cb	1110001J02Rik|AI447572|p110beta	phosphatidylinositol 3-kinase, catalytic, beta polypeptide	protein-coding
mm_135179.1	chr16	35939738	35939762	-	1	NA	promoter-TSS (NM_001013371)	promoter-TSS (NM_001013371)	-723	NM_001013371	209200	Mm.390852	NM_001013371	ENSMUSG00000049502	Dtx3l	AU042200|BC023741	deltex 3-like, E3 ubiquitin ligase	protein-coding
mm_146128.1	chr18	74531234	74531250	+	1	NA	promoter-TSS (NR_045368)	promoter-TSS (NR_045368)	-118	NR_045368	73606	Mm.444734	NR_045368		1700120E14Rik	-	RIKEN cDNA 1700120E14 gene	ncRNA
mm_119965.1	chr14	55478868	55478914	+	1	NA	5' UTR (NM_030686, exon 1 of 5)	5' UTR (NM_030686, exon 1 of 5)	133	NM_030686	28200	Mm.27427	NM_030686	ENSMUSG00000022210	Dhrs4	AI043103|AI790593|CR|D14Ucla2|NDRD|PHCR|PSCD|RRD|mouNRDR	dehydrogenase/reductase (SDR family) member 4	protein-coding
mm_26492.1	chr3	145292698	145292714	+	1	NA	5' UTR (NM_027770, exon 1 of 60)	5' UTR (NM_027770, exon 1 of 60)	234	NM_001317733	71355	Mm.235570	NM_027770	ENSMUSG00000028197	Col24a1	5430404K19Rik	collagen, type XXIV, alpha 1	protein-coding
mm_163636.1	chr13	59712283	59712285	+	1	NA	promoter-TSS (NM_001167593)	promoter-TSS (NM_001167593)	0	NM_001167593	238662	Mm.295939	NM_001167593	ENSMUSG00000091311	Spata31d1b	EG238662|Fam75d1b|Gm4934	spermatogenesis associated 31 subfamily D, member 1B	protein-coding
mm_21871.1	chr2	165982582	165982615	-	1	NA	Intergenic	Intergenic	-10039	NM_008679	17979	Mm.469663	NM_008679	ENSMUSG00000027678	Ncoa3	2010305B15Rik|AW321064|Actr|Aib1|KAT13B|Rac3|Src3|Tram-1|Tram1|bHLHe42|p/Cip|pCip	nuclear receptor coactivator 3	protein-coding
mm_163403.1	chr12	74968259	74968260	+	1	NA	intron (NM_172805, intron 9 of 10)	Lx9|LINE|L1	209073	NM_172805	238271	Mm.44465	NM_172805	ENSMUSG00000034402	Kcnh5	Eag2	potassium voltage-gated channel, subfamily H (eag-related), member 5	protein-coding
mm_90412.1	chr10	127420886	127420916	+	1	NA	promoter-TSS (NM_001168293)	promoter-TSS (NM_001168293)	34	NM_001168293	71750	Mm.29342	NM_027900	ENSMUSG00000025404	R3hdm2	1300003K24Rik|AU041262|mKIAA1002	R3H domain containing 2	protein-coding
mm_7755.1	chr1	131098109	131098128	-	1	NA	promoter-TSS (NM_008551)	promoter-TSS (NM_008551)	-275	NM_008551	17164	Mm.221235	NM_008551	ENSMUSG00000016528	Mapkapk2	AA960234|MAPKAP-K2|MK-2|MK2|Rps6kc1	MAP kinase-activated protein kinase 2	protein-coding
mm_1354.1	chr1	66321972	66321980	+	1	NA	5' UTR (NM_001310634, exon 1 of 15)	5' UTR (NM_001310634, exon 1 of 15)	252	NM_001310634	17756	Mm.256966	NM_008632	ENSMUSG00000015222	Map2	G1-397-34|MAP-2|Mtap-2|Mtap2|repro4	microtubule-associated protein 2	protein-coding
mm_132399.1	chr16	35001269	35001283	+	1	NA	3' UTR (NM_139300, exon 32 of 32)	3' UTR (NM_139300, exon 32 of 32)	-21145	NM_023587	70757	Mm.27286	NM_023587	ENSMUSG00000035376	Hacd2	6330408J20Rik|AI255777|AI481689|Hcad2|Ptplb	3-hydroxyacyl-CoA dehydratase 2	protein-coding
mm_60155.1	chr7	39517745	39517785	+	1	NA	promoter-TSS (NM_001004139)	promoter-TSS (NM_001004139)	-1	NM_001004139	70227	Mm.333800	NM_001004139	ENSMUSG00000068959	Zfp619	3000002G13Rik	zinc finger protein 619	protein-coding
mm_146181.1	chr18	75424680	75424687	+	1	NA	Intergenic	Intergenic	57318	NM_001042660	17131	Mm.34407	NM_008543	ENSMUSG00000025880	Smad7	Madh7	SMAD family member 7	protein-coding
mm_123158.1	chr14	57132535	57132551	-	1	NA	intron (NM_001010937, intron 1 of 2)	intron (NM_001010937, intron 1 of 2)	1068	NM_001271663	14623	Mm.25652	NM_008128	ENSMUSG00000040055	Gjb6	AA958971|Cx30|D14Bwg0506e	gap junction protein, beta 6	protein-coding
mm_120841.1	chr14	75194180	75194185	+	1	NA	intron (NM_008879, intron 2 of 16)	intron (NM_008879, intron 2 of 16)	-48105	NM_019775	56373	Mm.24242	NM_019775	ENSMUSG00000021999	Cpb2	1110032P04Rik|4930405E17Rik|AI255929|CPR|Cpu|TAFI	carboxypeptidase B2 (plasma)	protein-coding
mm_137986.1	chr17	33629079	33629114	+	1	NA	promoter-TSS (NM_026712)	promoter-TSS (NM_026712)	4	NM_026712	328801	Mm.181488	NM_026712	ENSMUSG00000073423	Zfp414	0610030H11Rik|Znf414	zinc finger protein 414	protein-coding
mm_57014.1	chr6	121226169	121226184	-	1	NA	TTS (NM_017379)	TTS (NM_017379)	15442	NM_017379	53857	Mm.32884	NM_017379	ENSMUSG00000030137	Tuba8	-	tubulin, alpha 8	protein-coding
mm_56896.1	chr6	119121156	119121174	-	1	NA	intron (NM_001255998, intron 1 of 47)	intron (NM_001255998, intron 1 of 47)	-12670	NM_001256002	12288	Mm.41628	NM_009781	ENSMUSG00000051331	Cacna1c	Cav1.2|Cchl1a1|D930026N18Rik|MBC|MELC-CC	calcium channel, voltage-dependent, L type, alpha 1C subunit	protein-coding
mm_102565.1	chr11	61488292	61488317	-	1	NA	TTS (NM_001291037)	TTS (NM_001291037)	2860	NM_029568	76293	Mm.272278	NM_029568	ENSMUSG00000042436	Mfap4	1110007F23Rik	microfibrillar-associated protein 4	protein-coding
mm_91903.1	chr10	60215322	60215328	-	1	NA	intron (NM_016803, intron 1 of 3)	intron (NM_016803, intron 1 of 3)	3935	NM_016803	53374	Mm.12866	NM_016803	ENSMUSG00000057337	Chst3	C6ST|C6ST-1|GST-0	carbohydrate (chondroitin 6/keratan) sulfotransferase 3	protein-coding
mm_41070.1	chr5	87667244	87667258	+	1	NA	exon (NM_007784, exon 2 of 34)	exon (NM_007784, exon 2 of 34)	1043	NM_001286016	12990	Mm.427467	NM_007784	ENSMUSG00000070702	Csn1s1	AA959832|AW212882|Csna	casein alpha s1	protein-coding
mm_92824.1	chr10	81461847	81461862	-	1	NA	3' UTR (NM_176954, exon 12 of 12)	3' UTR (NM_176954, exon 12 of 12)	11277	NM_001311127	319586	Mm.152689	NM_176954	ENSMUSG00000034818	Celf5	4930565A21Rik|Brunol5	CUGBP, Elav-like family member 5	protein-coding
mm_92549.1	chr10	79761051	79761085	-	1	NA	exon (NM_144528, exon 7 of 9)	exon (NM_144528, exon 7 of 9)	5884	NM_144528	70294	Mm.466670	NM_144528	ENSMUSG00000035890	Rnf126	2610010O19Rik	ring finger protein 126	protein-coding
mm_109215.1	chr12	108688128	108688153	+	1	NA	3' UTR (NM_007965, exon 13 of 13)	3' UTR (NM_007965, exon 13 of 13)	14166	NM_001171002	70059	Mm.207605	NM_027299	ENSMUSG00000021263	Degs2	2210008A03Rik|AI852933|DES2	delta(4)-desaturase, sphingolipid 2	protein-coding
mm_87560.1	chr10	56106946	56106959	+	1	NA	promoter-TSS (NM_001163833)	promoter-TSS (NM_001163833)	35	NM_001163833	73390	Mm.181475	NM_133751	ENSMUSG00000047669	Msl3l2	1700060H10Rik	male-specific lethal 3-like 2 (Drosophila)	protein-coding
mm_66932.1	chr7	61546184	61546194	-	1	NA	intron (NR_045727, intron 2 of 4)	intron (NR_045727, intron 2 of 4)	69138	NR_045727	319752	Mm.294476	NR_045727		B230209E15Rik	-	RIKEN cDNA B230209E15 gene	ncRNA
mm_47761.1	chr5	131472397	131472418	-	1	NA	exon (NM_177047, exon 9 of 19)	exon (NM_177047, exon 9 of 19)	-164885	NM_145218	212996	Mm.299204	NM_145218	ENSMUSG00000034040	Wbscr17	AA388321|E330012B09Rik	Williams-Beuren syndrome chromosome region 17 homolog (human)	protein-coding
mm_75251.1	chr8	40495862	40495880	-	1	NA	exon (NM_001271542, exon 6 of 7)	exon (NM_001271542, exon 6 of 7)	15883	NM_001271543	18983	Mm.272551	NM_011135	ENSMUSG00000031601	Cnot7	AU022737|CAF-1|Caf1|Pop2	CCR4-NOT transcription complex, subunit 7	protein-coding
mm_66980.1	chr7	63938365	63938378	-	1	NA	exon (NM_021366, exon 1 of 2)	exon (NM_021366, exon 1 of 2)	544	NM_021366	50794	Mm.240473	NM_021366	ENSMUSG00000052040	Klf13	0610043C13Rik|9430029L20Rik|Bteb3|FKLF-2|FKLF2|NSLP1|RFLAT-1|RFLAT1	Kruppel-like factor 13	protein-coding
mm_52536.1	chr6	115915787	115915845	+	1	NA	intron (NM_001167763, intron 20 of 28)	intron (NM_001167763, intron 20 of 28)	-16111	NM_145383	212541	Mm.2965	NM_145383	ENSMUSG00000030324	Rho	Noerg1|Opn2|Ops|RP4	rhodopsin	protein-coding
mm_20892.1	chr2	148872925	148872939	-	1	NA	intron (NM_009976, intron 1 of 2)	intron (NM_009976, intron 1 of 2)	2580	NM_009976	13010	Mm.4263	NM_009976	ENSMUSG00000027447	Cst3	CysC	cystatin C	protein-coding
mm_115410.1	chr13	114803322	114803334	+	1	NA	Intergenic	ORR1C1-int|LTR|ERVL-MaLR	-14909	NM_013826	17434	Mm.19027	NM_013826	ENSMUSG00000015536	Mocs2	AI415403	molybdenum cofactor synthesis 2	protein-coding
mm_20565.1	chr2	131081376	131081407	-	1	NA	exon (NM_011426, exon 6 of 21)	exon (NM_011426, exon 6 of 21)	5374	NM_011426	20612	Mm.1374	NM_011426	ENSMUSG00000027322	Siglec1	Cd169|Siglec-1|Sn	sialic acid binding Ig-like lectin 1, sialoadhesin	protein-coding
mm_56979.1	chr6	120357343	120357400	-	1	NA	promoter-TSS (NM_026028)	promoter-TSS (NM_026028)	98	NM_026028	67200	Mm.45767	NM_026028	ENSMUSG00000030177	Ccdc77	2400002C23Rik|2700091N06Rik|AV168274	coiled-coil domain containing 77	protein-coding
mm_84311.1	chr9	63706417	63706430	-	1	NA	intron (NM_016769, intron 1 of 8)	intron (NM_016769, intron 1 of 8)	51571	NM_016769	17127	Mm.7320	NM_016769	ENSMUSG00000032402	Smad3	AU022421|Madh3	SMAD family member 3	protein-coding
mm_96077.1	chr11	59948210	59948261	+	1	NA	promoter-TSS (NR_045273)	promoter-TSS (NR_045273)	21	NM_138675	192191	Mm.125288	NM_138675	ENSMUSG00000061650	Med9	BC019367|Med25	mediator complex subunit 9	protein-coding
mm_112101.1	chr12	112785367	112785389	-	1	NA	Intergenic	Intergenic	-23597	NM_145450	217887	Mm.186678	NM_145450	ENSMUSG00000037594	BC022687	AW050009|C130001I08Rik|Flj20080	cDNA sequence BC022687	protein-coding
mm_56934.1	chr6	119818315	119818344	-	1	NA	intron (NR_104484, intron 3 of 20)	RLTR10C|LTR|ERVK	29821	NM_053204	111173	Mm.288860	NM_053204	ENSMUSG00000030172	Erc1	4930404L01Rik|5033405M01Rik|9630025C19Rik|B430107L16Rik|CAST2|ELKS|Elks1|RAB6IP2A|RAB6IP2B|Rab6ip2|mKIAA1081	ELKS/RAB6-interacting/CAST family member 1	protein-coding
mm_159027.1	chr1	173868602	173868602	-	1	NA	intron (NM_001170853, intron 6 of 9)	MMERVK9C_I-int|LTR|ERVK	11585	NM_001170853	100040462	Mm.463437	NM_001170853	ENSMUSG00000090272	Mndal	Gm2785|Ifi212	myeloid nuclear differentiation antigen like	protein-coding
mm_135342.1	chr16	42875715	42875757	-	1	NA	promoter-TSS (NR_040522)	promoter-TSS (NR_040522)	26	NR_040522	75722	Mm.243747	NR_040521	ENSMUSG00000075070	4932412D23Rik	ENSMUSG00000075070|Gm10809	RIKEN cDNA 4932412D23 gene	ncRNA
mm_34480.1	chr4	148448565	148448598	+	1	NA	promoter-TSS (NM_020009)	promoter-TSS (NM_020009)	-1	NM_020009	56717	Mm.21158	NM_020009	ENSMUSG00000028991	Mtor	2610315D21Rik|AI327068|FRAP|FRAP2|Frap1|RAFT1|RAPT1|flat	mechanistic target of rapamycin (serine/threonine kinase)	protein-coding
mm_78769.1	chr9	43311149	43311159	+	1	NA	exon (NM_023655, exon 1 of 9)	exon (NM_023655, exon 1 of 9)	391	NM_023655	72169	Mm.273277	NM_023655	ENSMUSG00000032013	Trim29	1110047J21Rik|2810431N19Rik|4732461M22Rik|AI119726	tripartite motif-containing 29	protein-coding
mm_11946.1	chr2	52899387	52899389	+	1	NA	intron (NM_172409, intron 1 of 26)	intron (NM_172409, intron 1 of 26)	41520	NM_172409	71409	Mm.394427	NM_172409	ENSMUSG00000036053	Fmnl2	5430425K04Rik|Man	formin-like 2	protein-coding
mm_118896.1	chr14	26638121	26638151	+	1	NA	promoter-TSS (NM_007479)	promoter-TSS (NM_007479)	-61	NM_007479	11843	Mm.297768	NM_007479	ENSMUSG00000021877	Arf4	AA407803	ADP-ribosylation factor 4	protein-coding
mm_158349.1	chrX	134541667	134541672	-	1	NA	promoter-TSS (NM_013898).2	promoter-TSS (NM_013898).2	1	NM_013898	30058	Mm.214504	NM_013898	ENSMUSG00000048007	Timm8a1	DXHXS1274E|Ddp1|Fci-12|Tim8a|Timm8a	translocase of inner mitochondrial membrane 8A1	protein-coding
mm_75478.1	chr8	48555403	48555431	-	1	NA	intron (NM_011857, intron 2 of 28)	CpG	119273	NM_001145937	23965	Mm.42191	NM_011857	ENSMUSG00000031561	Tenm3	2610100B16Rik|Odz1|Odz3|Ten-m3|mKIAA1455	teneurin transmembrane protein 3	protein-coding
mm_13318.1	chr2	102675548	102675557	+	1	NA	intron (NM_001077514, intron 1 of 10)	intron (NM_001077514, intron 1 of 10)	16869	NM_001077514	20511	Mm.267547	NM_011393	ENSMUSG00000005089	Slc1a2	1700091C19Rik|2900019G14Rik|AI159670|Eaat2|GLT-1|GLT1|MGLT1	solute carrier family 1 (glial high affinity glutamate transporter), member 2	protein-coding
mm_112975.1	chr13	21287504	21287535	+	1	NA	exon (NM_010343, exon 5 of 5)	exon (NM_010343, exon 5 of 5)	5167	NM_010343	14780	Mm.1332	NM_010343	ENSMUSG00000004344	Gpx5	AV379049|Arep	glutathione peroxidase 5	protein-coding
mm_125859.1	chr15	75216245	75216254	+	1	NA	Intergenic	Intergenic	-52172	NM_008530	17071	Mm.377095	NM_008530	ENSMUSG00000022583	Ly6f	-	lymphocyte antigen 6 complex, locus F	protein-coding
mm_40342.1	chr5	45493450	45493466	+	1	NA	promoter-TSS (NM_024434)	promoter-TSS (NM_024434)	84	NM_024434	66988	Mm.286830	NM_024434	ENSMUSG00000039682	Lap3	2410015L10Rik|AA410100|LAP-3|Lap|Lapep|Pep-7|Pep-S|Pep7|Peps	leucine aminopeptidase 3	protein-coding
mm_163419.1	chr12	79758248	79758272	+	1	NA	intron (NM_009014, intron 8 of 10)	(T)n|Simple_repeat|Simple_repeat	166473	NR_131075	77290	Mm.395042	NR_131073		9430078K24Rik	-	RIKEN cDNA 9430078K24 gene	ncRNA
mm_82590.1	chr9	21238931	21238991	-	1	NA	5' UTR (NM_016679, exon 1 of 5)	5' UTR (NM_016679, exon 1 of 5)	371	NM_016679	50868	Mm.248266	NM_016679	ENSMUSG00000003308	Keap1	INRF2|mKIAA0132	kelch-like ECH-associated protein 1	protein-coding
mm_142574.1	chr17	46680750	46680756	-	1	NA	promoter-TSS (NM_010787)	promoter-TSS (NM_010787)	-30	NM_001277311	17256	Mm.329083	NM_010787	ENSMUSG00000002768	Mea1	Mea-1	male enhanced antigen 1	protein-coding
mm_47806.1	chr5	132756416	132756426	-	1	NA	Intergenic	Intergenic	-214078	NM_177047	319974	Mm.409595	NM_177047	ENSMUSG00000029673	Auts2	2700063G02Rik|A730011F23Rik|D830032G16Rik	autism susceptibility candidate 2	protein-coding
mm_107693.1	chr12	55384228	55384261	+	1	NA	promoter-TSS (NM_001310583)	promoter-TSS (NM_001310583)	22	NM_001310583	26443	Mm.30210	NM_011968	ENSMUSG00000021024	Psma6	IOTA	proteasome (prosome, macropain) subunit, alpha type 6	protein-coding
mm_17479.1	chr2	28561235	28561243	-	1	NA	exon (NM_009885, exon 2 of 11)	exon (NM_009885, exon 2 of 11)	2164	NM_009885	12613	Mm.236017	NM_009885	ENSMUSG00000026818	Cel	1810036E18Rik|BAL	carboxyl ester lipase	protein-coding
mm_38571.1	chr4	141793184	141793188	-	1	NA	promoter-TSS (NM_015733)	promoter-TSS (NM_015733)	-426	NM_015733	12371	Mm.88829	NM_015733	ENSMUSG00000028914	Casp9	AI115399|APAF-3|AW493809|CASP-9|Caspase-9|ICE-LAP6|Mch6	caspase 9	protein-coding
mm_46749.1	chr5	111761698	111761727	-	1	NA	promoter-TSS (NR_045834)	promoter-TSS (NR_045834)	16	NR_045834	269683	Mm.136946	NM_207252	ENSMUSG00000085271	E130006D01Rik	Gm16018|Gm681|OTTMUSG00000029083	RIKEN cDNA E130006D01 gene	ncRNA
mm_6576.1	chr1	75216517	75216546	-	1	NA	TTS (NM_011494)	TTS (NM_011494)	2763	NM_001313723	22145	Mm.1155	NM_009447	ENSMUSG00000026202	Tuba4a	M[a]4|Tuba4	tubulin, alpha 4A	protein-coding
mm_140539.1	chr17	6782747	6782762	-	1	NA	promoter-TSS (NM_009510)	promoter-TSS (NM_009510)	26	NM_009510	22350	Mm.277812	NM_009510	ENSMUSG00000052397	Ezr	AW146364|R75297|Vil2|p81	ezrin	protein-coding
mm_171382.1	chr4	119520951	119520956	+	1	NA	Intergenic	Intergenic	17816	NM_001004178	433752	Mm.425205	NM_001004178	ENSMUSG00000087385	AA415398	-	expressed sequence AA415398	protein-coding
mm_28854.1	chr3	96905274	96905292	-	1	NA	promoter-TSS (NM_026229)	promoter-TSS (NM_026229)	15	NM_026229	67549	Mm.46722	NM_026229	ENSMUSG00000028096	Gpr89	4933412D19Rik|Gpr89a|SH120	G protein-coupled receptor 89	protein-coding
mm_70503.1	chr8	12873794	12873826	+	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	-41891	NR_045775	100504249	Mm.441494	NR_045775	ENSMUSG00000084780	Gm15350	OTTMUSG00000020611	predicted gene 15350	ncRNA
mm_5445.1	chr1	36063136	36063150	-	1	NA	Intergenic	Intergenic	-5257	NM_015818	50785	Mm.213566	NM_015818	ENSMUSG00000045216	Hs6st1	6Ost1	heparan sulfate 6-O-sulfotransferase 1	protein-coding
mm_104638.1	chr11	97523921	97523934	-	1	NA	intron (NM_018873, intron 16 of 19)	intron (NM_018873, intron 16 of 19)	-23587	NM_001289118	100141474	Mm.482426	NM_001289118	ENSMUSG00000047988	4933428G20Rik	-	RIKEN cDNA 4933428G20 gene	protein-coding
mm_1687.1	chr1	74885773	74885775	+	1	NA	promoter-TSS (NM_153111)	promoter-TSS (NM_153111)	-366	NM_153111	260298	Mm.150496	NM_153111	ENSMUSG00000055197	Fev	Pet-1|Pet1|mPet-1	FEV (ETS oncogene family)	protein-coding
mm_31542.1	chr4	55477924	55477930	+	1	NA	Intergenic	Intergenic	54548	NM_010637	16600	Mm.4325	NM_010637	ENSMUSG00000003032	Klf4	EZF|Gklf|Zie	Kruppel-like factor 4 (gut)	protein-coding
mm_158519.1	chrX	143792499	143792501	-	1	NA	3' UTR (NM_001195047, exon 15 of 15)	3' UTR (NM_001195047, exon 15 of 15)	34912	NM_007603	12338	Mm.30290	NM_007603	ENSMUSG00000067276	Capn6	-	calpain 6	protein-coding
mm_52325.1	chr6	108836727	108836739	+	1	NA	intron (NM_138677, intron 1 of 11)	intron (NM_138677, intron 1 of 11)	8092	NM_138677	192193	Mm.21596	NM_138677	ENSMUSG00000030104	Edem1	A130059K23Rik|EDEM|mKIAA0212	ER degradation enhancer, mannosidase alpha-like 1	protein-coding
mm_6255.1	chr1	69041918	69041921	-	1	NA	intron (NM_010154, intron 1 of 26)	intron (NM_010154, intron 1 of 26)	66140	NM_010154	13869	Mm.442420	NM_010154	ENSMUSG00000062209	Erbb4	Her4|c-erbB-4	erb-b2 receptor tyrosine kinase 4	protein-coding
mm_55211.1	chr6	52221574	52221591	-	1	NA	Intergenic	CpG	-3009	NM_010455	15404	Mm.294826	NM_010455	ENSMUSG00000038236	Hoxa7	AV118143|Hox-1.1|M6	homeobox A7	protein-coding
mm_158269.1	chrX	109392167	109392194	-	1	NA	Intergenic	Intergenic	195424	NM_001037917	622976	Mm.482747	NM_001037917	ENSMUSG00000048621	Gm6377	EG622976	predicted gene 6377	protein-coding
mm_72394.1	chr8	81767793	81767806	+	1	NA	intron (NM_001297593, intron 4 of 23)	intron (NM_001297593, intron 4 of 23)	425237	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_71058.1	chr8	33732238	33732247	+	1	NA	promoter-TSS (NM_001167922)	promoter-TSS (NM_001167922)	-97	NM_001167922	68153	Mm.286104	NM_026584	ENSMUSG00000031585	Gtf2e2	34kDa|AI462509|C330006J08Rik	general transcription factor II E, polypeptide 2 (beta subunit)	protein-coding
mm_76639.1	chr8	92356123	92356143	-	1	NA	promoter-TSS (NR_033641)	promoter-TSS (NR_033641)	-13	NR_033641	71296	Mm.86664	NR_033641	ENSMUSG00000031736	Crnde	4933436C20Rik	colorectal neoplasia differentially expressed (non-protein coding)	ncRNA
mm_143470.1	chr17	71086568	71086571	-	1	NA	intron (NM_010867, intron 19 of 37)	PB1D10|SINE|Alu	67012	NM_001083934	17929	Mm.4103	NM_010867	ENSMUSG00000024049	Myom1	D430047A17Rik	myomesin 1	protein-coding
mm_90296.1	chr10	125388564	125388593	+	1	NA	Intergenic	Intergenic	-60043	NM_011391	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|Mct2	solute carrier family 16 (monocarboxylic acid transporters), member 7	protein-coding
mm_2066.1	chr1	87620307	87620323	+	1	NA	promoter-TSS (NM_001110192)	promoter-TSS (NM_001110192)	3	NM_001110193	16331	Mm.15105	NM_010566	ENSMUSG00000026288	Inpp5d	SHIP|SHIP-1|SHIP1|SIP-145|p150Ship|s-SHIP	inositol polyphosphate-5-phosphatase D	protein-coding
mm_171786.1	chr5	11064170	11064185	+	1	NA	Intergenic	L1Md_A|LINE|L1	62278	NR_126451	75330	Mm.326776	NR_126451	ENSMUSG00000106506	4930558F17Rik	-	RIKEN cDNA 4930558F17 gene	ncRNA
mm_158294.1	chrX	113099458	113099476	-	1	NA	intron (NM_018818, intron 8 of 14)	MIRb|SINE|MIR	-24574	NR_029849	723850		NR_029849	ENSMUSG00000065510	Mir361	Mirn361|mir-361|mmu-mir-361	microRNA 361	ncRNA
mm_164976.1	chr19	8831225	8831227	+	1	NA	exon (NM_001081196, exon 13 of 14)	exon (NM_001081196, exon 13 of 14)	-6241	NM_001136064	14705	Mm.345134	NM_008144	ENSMUSG00000071657	Bscl2	2900097C17Rik|AI046355|Gng3lg	Berardinelli-Seip congenital lipodystrophy 2 (seipin)	protein-coding
mm_83652.1	chr9	49506938	49506972	-	1	NA	exon (NM_001113204, exon 18 of 19)	exon (NM_001113204, exon 18 of 19)	-11333	NR_029465	100036537	Mm.437541	NR_029465	ENSMUSG00000079564	Gm11149	ENSMUSG00000060603|ENSMUSG00000079564	predicted gene 11149	ncRNA
mm_111434.1	chr12	91804372	91804376	-	1	NA	Intergenic	Intergenic	-17938	NM_175367	108800	Mm.23125	NM_175367	ENSMUSG00000020961	Ston2	4933401N24Rik|AI425999|AW544599	stonin 2	protein-coding
mm_100167.1	chr11	116531827	116531842	+	1	NA	promoter-TSS (NM_001172472)	promoter-TSS (NM_001172472)	-77	NM_001172475	20698	Mm.20944	NM_011451	ENSMUSG00000061878	Sphk1	1110006G24Rik|Sk1|Spk1	sphingosine kinase 1	protein-coding
mm_86188.1	chr9	119341391	119341420	-	1	NA	5' UTR (NM_130864, exon 1 of 12)	5' UTR (NM_130864, exon 1 of 12)	111	NM_130864	113868	Mm.205266	NM_130864	ENSMUSG00000036138	Acaa1a	Acaa|Acaa1|D9Ertd25e|PTL	acetyl-Coenzyme A acyltransferase 1A	protein-coding
mm_138746.1	chr17	37009886	37009900	+	1	NA	TTS (NM_010814)	TTS (NM_010814)	6227	NR_033137	22715	Mm.305561	NM_009559	ENSMUSG00000036036	Zfp57	G19|Zfp-57	zinc finger protein 57	protein-coding
mm_43548.1	chr5	137569825	137569845	+	1	NA	promoter-TSS (NM_001289507)	promoter-TSS (NM_001289507)	-5	NM_001289509	50765	Mm.21757	NM_015799	ENSMUSG00000029716	Tfr2	Trfr2	transferrin receptor 2	protein-coding
mm_60378.1	chr7	44468089	44468133	+	1	NA	TTS (NM_026690)	TTS (NM_026690)	131	NM_001205070	66124	Mm.358691	NM_025368	ENSMUSG00000038695	Josd2	1110007C05Rik	Josephin domain containing 2	protein-coding
mm_9123.1	chr1	170312997	170312999	-	1	NA	TTS (NM_001039593)	TTS (NM_001039593)	4137	NM_001039593	76925	Mm.33631	NM_001039593	ENSMUSG00000042800	1700015E13Rik	-	RIKEN cDNA 1700015E13 gene	protein-coding
mm_33324.1	chr4	129105533	129105622	+	1	NA	promoter-TSS (NM_001290706)	promoter-TSS (NM_001290706)	29	NM_001290706	66260	Mm.25295	NM_025452	ENSMUSG00000028786	Tmem54	1810017F10Rik|AI507302	transmembrane protein 54	protein-coding
mm_108924.1	chr12	100885873	100885881	+	1	NA	intron (NM_001177673, intron 2 of 2)	intron (NM_001177673, intron 2 of 2)	13647	NM_001177674	238377	Mm.32160	NM_175493	ENSMUSG00000047415	Gpr68	BB131428|Ogr1	G protein-coupled receptor 68	protein-coding
mm_122039.1	chr14	30008868	30008885	-	1	NA	promoter-TSS (NM_001136240)	promoter-TSS (NM_001136240)	20	NM_019583	50905	Mm.269363	NM_019583	ENSMUSG00000015966	Il17rb	Evi27|IL-17ER|IL-17Rh1|IL17RH1|Il17br	interleukin 17 receptor B	protein-coding
mm_125287.1	chr15	36726393	36726401	+	1	NA	Intergenic	Intergenic	64535	NM_001253807	22631	Mm.3360	NM_011740	ENSMUSG00000022285	Ywhaz	1110013I11Rik|14-3-3zeta|AI596267|AL022924|AU020854	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide	protein-coding
mm_141320.1	chr17	28365207	28365224	-	1	NA	promoter-TSS (NM_021478)	promoter-TSS (NM_021478)	-72	NM_021478	22157	Mm.42102	NM_021478	ENSMUSG00000037446	Tulp1	Tulp1l	tubby like protein 1	protein-coding
mm_95833.1	chr11	56072911	56072918	+	1	NA	Intergenic	Intergenic	-31927	NM_153079	216749	Mm.213205	NM_153079	ENSMUSG00000037393	Nmur2	Nmu2r	neuromedin U receptor 2	protein-coding
mm_169757.1	chr15	93234362	93234380	+	1	NA	Intergenic	7SK|RNA|RNA	40713	NM_001033275	223827	Mm.22819	NM_001033275	ENSMUSG00000036197	Gxylt1	Glt8d3|Gm1228|Gm87	glucoside xylosyltransferase 1	protein-coding
mm_15514.1	chr2	158285733	158285736	+	1	NA	Intergenic	Intergenic	-20759	NM_008489	16803	Mm.218846	NM_008489	ENSMUSG00000016024	Lbp	Bpifd2|Ly88	lipopolysaccharide binding protein	protein-coding
mm_86836.1	chr10	21394409	21394413	+	1	NA	intron (NM_178713, intron 6 of 6)	Lx8b|LINE|L1	17111	NM_178713	237320	Mm.90181	NM_178713	ENSMUSG00000037542	Aldh8a1	Raldh4	aldehyde dehydrogenase 8 family, member A1	protein-coding
mm_167331.1	chr8	70676185	70676222	+	1	NA	intron (NM_015816, intron 1 of 4)	intron (NM_015816, intron 1 of 4)	2972	NM_015816	50783	Mm.248188	NM_015816	ENSMUSG00000031848	Lsm4	-	LSM4 homolog, U6 small nuclear RNA and mRNA degradation associated	protein-coding
mm_105409.1	chr11	103621423	103621442	-	1	NA	Intergenic	Intergenic	-6693	NM_001033434	380730	Mm.380214	NM_001033434	ENSMUSG00000034239	Gm884	LRRC37	predicted gene 884	protein-coding
mm_137061.1	chr17	18958080	18958084	+	1	NA	Intergenic	RLTR50A|LTR|ERVK	43760	NM_001104549	627367	Mm.384131	NM_001104549	ENSMUSG00000091491	Vmn2r97	EG627367|Vn2r97	vomeronasal 2, receptor 97	protein-coding
mm_82359.1	chr9	14500304	14500319	-	1	NA	promoter-TSS (NM_023153)	promoter-TSS (NM_023153)	171	NM_173433	244694	Mm.240457	NM_173433	ENSMUSG00000053914	Kdm4d	4932416A15|Jmjd2d	lysine (K)-specific demethylase 4D	protein-coding
mm_85242.1	chr9	98957294	98957296	-	1	NA	3' UTR (NM_012020, exon 1 of 1)	3' UTR (NM_012020, exon 1 of 1)	1688	NM_012020	26927	Mm.151239	NM_012020	ENSMUSG00000050397	Foxl2	AU045128|BPES|PINTO|Pfrk	forkhead box L2	protein-coding
mm_159095.1	chr2	35151601	35151601	+	1	NA	intron (NM_012018, intron 22 of 43)	intron (NM_012018, intron 22 of 43)	19367	NM_001290635	26920	Mm.231332	NM_012018	ENSMUSG00000057110	Cntrl	6720467O09Rik|AA968343|Cep1|Cep110|IB3/5|Ma2a8|b2b1468.1Clo|b2b1468Clo	centriolin	protein-coding
mm_131996.1	chr16	25059906	25059950	+	1	NA	intron (NR_040374, intron 1 of 2)	intron (NR_040374, intron 1 of 2)	289	NR_040374	319487	Mm.137341	NR_040374	ENSMUSG00000096960	A230028O05Rik	-	RIKEN cDNA A230028O05 gene	ncRNA
mm_153901.1	chr19	47090611	47090655	-	1	NA	promoter-TSS (NM_011053)	promoter-TSS (NM_011053)	-8	NM_023211	66477	Mm.29722	NM_023211	ENSMUSG00000071528	Usmg5	2010301L15Rik	upregulated during skeletal muscle growth 5	protein-coding
mm_155011.1	chrX	41401477	41401565	+	1	NA	promoter-TSS (NM_001290451)	promoter-TSS (NM_001290451)	-8	NM_001290451	53623	Mm.327681	NM_016886	ENSMUSG00000001986	Gria3	2900064I19Rik|GluA3|GluR-C|GluR-K3|Glur-3|Glur3|Gluralpha3	glutamate receptor, ionotropic, AMPA3 (alpha 3)	protein-coding
mm_66497.1	chr7	45061720	45061740	-	1	NA	promoter-TSS (NM_025533)	promoter-TSS (NM_025533)	-78	NM_022999	65116	Mm.379098	NM_022999	ENSMUSG00000007837	Prrg2	1600014G02Rik|2510041M06Rik|N4WBP1	proline-rich Gla (G-carboxyglutamic acid) polypeptide 2	protein-coding
mm_152595.1	chr19	11640728	11640744	-	1	NA	5' UTR (NM_133246, exon 1 of 7)	5' UTR (NM_133246, exon 1 of 7)	115	NM_133246	170813	Mm.240438	NM_133246	ENSMUSG00000024681	Ms4a3	HTm4	membrane-spanning 4-domains, subfamily A, member 3	protein-coding
mm_6975.1	chr1	86351400	86351425	-	1	NA	promoter-TSS (NR_028478)	promoter-TSS (NR_028478)	-127	NR_028478	100303740	Mm.154378	NR_028478	ENSMUSG00000064837	Snora75	MBI-55	small nucleolar RNA, H/ACA box 75	snoRNA
mm_78013.1	chr9	13473864	13473867	+	1	NA	Intergenic	B1F|SINE|Alu	42504	NR_028271	18689	Mm.41972	NM_008835	ENSMUSG00000031802	Phxr4	Sp5	per-hexamer repeat gene 4	ncRNA
mm_23674.1	chr3	68584104	68584125	+	1	NA	intron (NM_013928, intron 1 of 6)	intron (NM_013928, intron 1 of 6)	11746	NM_013928	30953	Mm.331064	NM_013928	ENSMUSG00000027777	Schip1	Nf2ip|Schip-1	schwannomin interacting protein 1	protein-coding
mm_24848.1	chr3	95674487	95674502	+	1	NA	Intergenic	Intergenic	13423	NM_144899	229595	Mm.490574	NM_144899	ENSMUSG00000015850	Adamtsl4	ADAMTSL-4|Tsrc1	ADAMTS-like 4	protein-coding
mm_158875.1	chrY	1286624	1286635	-	1	NA	promoter-TSS (NM_012008)	promoter-TSS (NM_012008)	-16	NM_012008	26900	Mm.302938	NM_012008	ENSMUSG00000069045	Ddx3y	8030469F12Rik|D1Pas1-rs1|Dby	DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, Y-linked	protein-coding
mm_119077.1	chr14	30880443	30880453	+	1	NA	intron (NM_181390, intron 1 of 2)	intron (NM_181390, intron 1 of 2)	1191	NM_181390	66175	Mm.220895	NM_181390	ENSMUSG00000042485	Mustn1	1110028G01Rik|Mustang	musculoskeletal, embryonic nuclear protein 1	protein-coding
mm_66065.1	chr7	30821143	30821156	-	1	NA	promoter-TSS (NM_001168512)	promoter-TSS (NM_001168512)	-10	NM_001168511	233079	Mm.97338	NM_146187	ENSMUSG00000051314	Ffar2	GPCR43|Gpr43	free fatty acid receptor 2	protein-coding
mm_103545.1	chr11	77553832	77553835	-	1	NA	exon (NM_144825, exon 14 of 20)	exon (NM_144825, exon 14 of 20)	38716	NM_026185	67477	Mm.432526	NM_026185	ENSMUSG00000000686	Abhd15	1300007F04Rik	abhydrolase domain containing 15	protein-coding
mm_12533.1	chr2	72227926	72227949	+	1	NA	intron (NM_001204165, intron 22 of 30)	intron (NM_001204165, intron 22 of 30)	-57700	NM_023057	65964	Mm.304143	NM_023057	ENSMUSG00000004085	Map3k20	AV006891|B230120H23Rik|MLTK|MLTKalpha|MLTKbeta|Zak	mitogen-activated protein kinase kinase kinase 20	protein-coding
mm_117289.1	chr13	66698264	66698279	-	1	NA	Intergenic	Intergenic	207079	NM_026219	67530	Mm.379136	NM_026219	ENSMUSG00000021520	Uqcrb	2210415M14Rik|QP-C|QPC|UQBC|UQBP|UQPC	ubiquinol-cytochrome c reductase binding protein	protein-coding
mm_72811.1	chr8	87473408	87473418	+	1	NA	promoter-TSS (NM_019626)	promoter-TSS (NM_019626)	297	NR_125722	100040294	Mm.213632	NR_033430	ENSMUSG00000097248	Gm2694	C230036H16Rik|linc1582	predicted gene 2694	ncRNA
mm_169623.1	chr15	39835767	39835772	+	1	NA	intron (NM_022722, intron 4 of 9)	RLTRETN_Mm|LTR|ERVK	21701	NM_001164466	64705	Mm.275974	NM_022722	ENSMUSG00000022304	Dpys	1200017I10Rik|1300004I01Rik|DHP|DHPase	dihydropyrimidinase	protein-coding
mm_139750.1	chr17	63863120	63863143	+	1	NA	promoter-TSS (NM_001037997)	promoter-TSS (NM_001037997)	-850	NM_001037997	14158	Mm.23039	NM_008000	ENSMUSG00000000127	Fer	AV082135|C330004K01Rik|Fert|Fert2	fer (fms/fps related) protein kinase	protein-coding
mm_152057.1	chr19	6299580	6299619	-	1	NA	3' UTR (NM_010119, exon 5 of 5)	3' UTR (NM_010119, exon 5 of 5)	-6858	NM_001033342	240505	Mm.329622	NM_001033342	ENSMUSG00000024769	Cdc42bpg	BC046418|MRCKgamma	CDC42 binding protein kinase gamma (DMPK-like)	protein-coding
mm_84747.1	chr9	75409353	75409383	-	1	NA	promoter-TSS (NR_040719)	promoter-TSS (NR_040719)	-9	NM_027418	50772	Mm.480076	NM_015806	ENSMUSG00000042688	Mapk6	2610021I23Rik|D130053K17Rik|Erk3|Mapk4|Mapk63|Prkm4|Prkm6	mitogen-activated protein kinase 6	protein-coding
mm_123161.1	chr14	57133374	57133389	-	1	NA	5' UTR (NM_001271663, exon 1 of 3)	5' UTR (NM_001271663, exon 1 of 3)	230	NM_001271663	14623	Mm.25652	NM_008128	ENSMUSG00000040055	Gjb6	AA958971|Cx30|D14Bwg0506e	gap junction protein, beta 6	protein-coding
mm_78698.1	chr9	41206153	41206171	+	1	NA	promoter-TSS (NR_040392)	promoter-TSS (NR_040392)	7	NR_040392	78500	Mm.275715	NR_040392	ENSMUSG00000100837	1700063D05Rik	-	RIKEN cDNA 1700063D05 gene	ncRNA
mm_27452.1	chr3	52041319	52041323	-	1	NA	intron (NM_001004176, intron 1 of 4)	intron (NM_001004176, intron 1 of 4)	63685	NM_001004176	433586	Mm.234972	NM_001004176	ENSMUSG00000061143	Maml3	AV234550|BC049812|Mam-2|mKIAA1816	mastermind like 3 (Drosophila)	protein-coding
mm_53778.1	chr6	146501645	146501656	+	1	NA	intron (NM_010586, intron 1 of 55)	CpG	573	NM_010586	16439	Mm.7800	NM_010586	ENSMUSG00000030287	Itpr2	AI649341|InsP3R-2|InsP3R-5|Ip3r2|Itpr5|insP3R2	inositol 1,4,5-triphosphate receptor 2	protein-coding
mm_107270.1	chr12	29533293	29533315	+	1	NA	intron (NM_001093778, intron 1 of 24)	intron (NM_001093778, intron 1 of 24)	-1601	NM_001093776	17933	Mm.253067	NM_008666	ENSMUSG00000061911	Myt1l	2900046C06Rik|2900093J19Rik|C630034G21Rik|Nztf1|Pmng1|Png-1|mKIAA1106	myelin transcription factor 1-like	protein-coding
mm_86059.1	chr9	114640028	114640047	-	1	NA	5' UTR (NM_153585, exon 1 of 20)	5' UTR (NM_153585, exon 1 of 20)	163	NM_153585	78893	Mm.283708	NM_153585	ENSMUSG00000056167	Cnot10	2600001P13Rik	CCR4-NOT transcription complex, subunit 10	protein-coding
mm_43419.1	chr5	136038682	136038707	+	1	NA	5' UTR (NM_175309, exon 1 of 6)	5' UTR (NM_175309, exon 1 of 6)	198	NM_175309	100647	Mm.3089	NM_175309	ENSMUSG00000042985	Upk3b	AI447729|AI957187|P35|PMS2L14|UpIIIb	uroplakin 3B	protein-coding
mm_63775.1	chr7	131554290	131554299	+	1	NA	5' UTR (NM_145998, exon 1 of 2)	5' UTR (NM_145998, exon 1 of 2)	232	NM_145998	15372	Mm.303357	NM_145998	ENSMUSG00000050100	Hmx2	Nkx-5.2|Nkx5-2	H6 homeobox 2	protein-coding
mm_62384.1	chr7	100834005	100834019	+	1	NA	exon (NM_178764, exon 7 of 9)	exon (NM_178764, exon 7 of 9)	29401	NM_177073	320100	Mm.40336	NM_177073	ENSMUSG00000008318	Relt	E430021K24Rik|Tnfrsf19l	RELT tumor necrosis factor receptor	protein-coding
mm_93234.1	chr10	95324127	95324144	-	1	NA	promoter-TSS (NM_001330175)	promoter-TSS (NM_001330175)	2	NM_001330141	12905	Mm.473739	NM_009950	ENSMUSG00000045867	Cradd	RAIDD	CASP2 and RIPK1 domain containing adaptor with death domain	protein-coding
mm_84840.1	chr9	78378149	78378160	-	1	NA	exon (NM_026480, exon 2 of 3)	exon (NM_026480, exon 2 of 3)	434	NM_026480	67968	Mm.26883	NM_026480	ENSMUSG00000032346	Ooep	2410146L05Rik|Floped|Moep19|Sddr	oocyte expressed protein	protein-coding
mm_143305.1	chr17	65986553	65986580	-	1	NA	exon (NM_001025572, exon 9 of 13)	exon (NM_001025572, exon 9 of 13)	-35379	NM_023053	65960	Mm.10153	NM_023053	ENSMUSG00000024098	Twsg1	1810013J15Rik|9030422N06Rik|AW552143|D17Ertd403e|Tsg|Twg	twisted gastrulation BMP signaling modulator 1	protein-coding
mm_87525.1	chr10	53337699	53337724	+	1	NA	promoter-TSS (NM_001141927)	promoter-TSS (NM_001141927)	25	NM_001141927	18821	Mm.34145	NM_023129	ENSMUSG00000038583	Pln	Plb	phospholamban	protein-coding
mm_78106.1	chr9	20544609	20544651	+	1	NA	Intergenic	Intergenic	-23211	NM_001082485	77519	Mm.431849	NM_001082485	ENSMUSG00000060510	Zfp266	5330440G10Rik|5730601F06Rik|AW552317	zinc finger protein 266	protein-coding
mm_63036.1	chr7	121075296	121075329	+	1	NA	promoter-TSS (NM_030691)	promoter-TSS (NM_030691)	-782	NM_030691	80719	Mm.160384	NM_030691	ENSMUSG00000035004	Igsf6	-	immunoglobulin superfamily, member 6	protein-coding
mm_72415.1	chr8	81856379	81856399	+	1	NA	intron (NM_001297591, intron 7 of 24)	intron (NM_001297591, intron 7 of 24)	513827	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_107147.1	chr12	21587204	21587211	+	1	NA	Intergenic	MT2_Mm|LTR|ERVL	-169771	NM_011739	22630	Mm.289630	NM_011739	ENSMUSG00000076432	Ywhaq	2700028P07Rik|AA409740|AU021156|R74690	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide	protein-coding
mm_80079.1	chr9	70012541	70012592	+	1	NA	promoter-TSS (NM_001282084)	promoter-TSS (NM_001282084)	18	NM_001282083	235459	Mm.293117	NM_199151	ENSMUSG00000033543	Gtf2a2	TFIIA-gamma|TfIIg|Tfiia2	general transcription factor II A, 2	protein-coding
mm_89704.1	chr10	97647146	97647156	+	1	NA	intron (NM_007884, intron 1 of 7)	intron (NM_007884, intron 1 of 7)	3083	NM_007884	13516	Mm.148886	NM_007884	ENSMUSG00000019936	Epyc	Dspg3|PG-Lb|SLRR3B	epiphycan	protein-coding
mm_166245.1	chr5	76183805	76183829	-	1	NA	promoter-TSS (NM_011626)	promoter-TSS (NM_011626)	-63	NM_011626	21982	Mm.790	NM_011626	ENSMUSG00000029234	Tmem165	AV026557|Tpardl|Tparl|pFT27	transmembrane protein 165	protein-coding
mm_13263.1	chr2	98666465	98666475	+	1	NA	Intergenic	SYNREP_MM|Satellite|Satellite	1198813	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_141354.1	chr17	28689769	28689778	-	1	NA	5' UTR (NM_001290320, exon 1 of 20)	5' UTR (NM_001290320, exon 1 of 20)	214	NM_001290320	224661		NM_146076	ENSMUSG00000036196	Slc26a8	-	solute carrier family 26, member 8	protein-coding
mm_91474.1	chr10	34207575	34207589	-	1	NA	promoter-TSS (NM_172508)	promoter-TSS (NM_172508)	-31	NM_172508	212898	Mm.34557	NM_172508	ENSMUSG00000039497	Dse	6030499O08|AI480506|B130024B19Rik|DS-epi1|Sart2	dermatan sulfate epimerase	protein-coding
mm_114085.1	chr13	54589927	54589952	+	1	NA	promoter-TSS (NM_025933)	promoter-TSS (NM_025933)	135	NM_178605	28126	Mm.439993	NM_178605	ENSMUSG00000025869	Nop16	AA409471|D13Wsu177e	NOP16 nucleolar protein	protein-coding
mm_136193.1	chr16	89487946	89487957	-	1	NA	promoter-TSS (NM_010675)	promoter-TSS (NM_010675)	1	NM_010675	16703	Mm.13979	NM_010675	ENSMUSG00000059632	Krtap8-1	AI326176	keratin associated protein 8-1	protein-coding
mm_43325.1	chr5	134990037	134990042	+	1	NA	intron (NR_026907, intron 3 of 4)	intron (NR_026907, intron 3 of 4)	3825	NM_009902	12739	Mm.158662	NM_009902	ENSMUSG00000070473	Cldn3	AI182374|Cpetr2|mRVP1	claudin 3	protein-coding
mm_66039.1	chr7	30660237	30660248	-	1	NA	intron (NM_027999, intron 7 of 18)	intron (NM_027999, intron 7 of 18)	4752	NM_027999	71909	Mm.290410	NM_027999	ENSMUSG00000078762	Haus5	2310022K01Rik	HAUS augmin-like complex, subunit 5	protein-coding
mm_15590.1	chr2	160366255	160366284	+	1	NA	exon (NM_010658, exon 1 of 1)	exon (NM_010658, exon 1 of 1)	796	NM_010658	16658	Mm.330745	NM_010658	ENSMUSG00000074622	Mafb	Kreisler|Krml|Krml1|kr	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein B (avian)	protein-coding
mm_129506.1	chr15	78929735	78929748	-	1	NA	exon (NM_008495, exon 3 of 4)	exon (NM_008495, exon 3 of 4)	3016	NM_008495	16852	Mm.43831	NM_008495	ENSMUSG00000068220	Lgals1	AA410090|Gal-1|Galbp|L-14.5|L14|Lect14|galectin-1	lectin, galactose binding, soluble 1	protein-coding
mm_55299.1	chr6	54811741	54811759	-	1	NA	Intergenic	Intergenic	-5166	NM_199143	387524	Mm.286149	NM_199143	ENSMUSG00000058446	Znrf2	1190002C14Rik|AU044205|D6Ertd365e	zinc and ring finger 2	protein-coding
mm_34455.1	chr4	148044279	148044308	+	1	NA	intron (NM_010840, intron 3 of 11)	L2c|LINE|L2	3104	NM_001161798	17769	Mm.89959	NM_010840	ENSMUSG00000029009	Mthfr	AI323986	5,10-methylenetetrahydrofolate reductase	protein-coding
mm_74041.1	chr8	121950676	121950687	+	1	NA	intron (NM_016812, intron 1 of 13)	CpG	189	NM_001285983	53325	Mm.287163	NM_016812	ENSMUSG00000025316	Banp	AA408158|SMAR1	BTG3 associated nuclear protein	protein-coding
mm_126962.1	chr15	92344366	92344383	+	1	NA	Intergenic	RLTR16C_MM|LTR|ERVK	-52436	NM_001164593	239618	Mm.309826	NM_001164593	ENSMUSG00000036218	Pdzrn4	1110017D07Rik|LNX4|SAMCAP3L|mKIAA3027	PDZ domain containing RING finger 4	protein-coding
mm_57755.1	chr6	129229088	129229119	-	1	NA	Intergenic	Intergenic	8942	NR_040265	76432	Mm.261738	NR_040265	ENSMUSG00000097354	2310001H17Rik	AI646108	RIKEN cDNA 2310001H17 gene	ncRNA
mm_8656.1	chr1	156473162	156473172	-	1	NA	intron (NM_009230, intron 1 of 15)	intron (NM_009230, intron 1 of 15)	1161	NM_009230	20652	Mm.28099	NM_009230	ENSMUSG00000026600	Soat1	8430426K15Rik|ACAT-1|AW550831|Acact|ald|hid	sterol O-acyltransferase 1	protein-coding
mm_104366.1	chr11	94346133	94346157	-	1	NA	intron (NM_029600, intron 29 of 30)	intron (NM_029600, intron 29 of 30)	18144	NM_146024	71452	Mm.141054	NM_027799	ENSMUSG00000020864	Ankrd40	1110011C06Rik|5530600A18Rik|Gcap15	ankyrin repeat domain 40	protein-coding
mm_14628.1	chr2	136781128	136781164	+	1	NA	3' UTR (NM_001291056, exon 8 of 8)	3' UTR (NM_001291056, exon 8 of 8)	67696	NM_001291056	20614	Mm.45953	NM_011428	ENSMUSG00000027273	Snap25	Bdr|GENA70|SNAP-25|SUP|sp	synaptosomal-associated protein 25	protein-coding
mm_1679.1	chr1	74854911	74854945	+	1	NA	promoter-TSS (NM_009872)	promoter-TSS (NM_009872)	-101	NM_009872	12570	Mm.153833	NM_009872	ENSMUSG00000090071	Cdk5r2	B230310J22Rik|p39	cyclin-dependent kinase 5, regulatory subunit 2 (p39)	protein-coding
mm_120572.1	chr14	69158581	69158587	+	1	NA	Intergenic	Intergenic	-13218	NM_010920	18092	Mm.390691	NM_010920	ENSMUSG00000044186	Nkx2-6	AV044928|Nkx-2.6|Nkx2.6|Tix|tinman	NK2 homeobox 6	protein-coding
mm_62795.1	chr7	112742026	112742060	+	1	NA	intron (NM_009346, intron 1 of 12)	intron (NM_009346, intron 1 of 12)	-17341	NM_001166585	21676	Mm.24685	NM_009346	ENSMUSG00000055320	Tead1	2610024B07Rik|B230114H05Rik|Gtrgeo5|TEAD-1|TEF-1|Tcf13|mTEF-1	TEA domain family member 1	protein-coding
mm_94210.1	chr11	3124000	3124031	+	1	NA	promoter-TSS (NR_003517)	promoter-TSS (NR_003517)	-6	NR_003517	236604	Mm.247625	NM_001004146		Pisd-ps1	-	phosphatidylserine decarboxylase, pseudogene 1	pseudo
mm_94258.1	chr11	3452459	3452510	+	1	NA	promoter-TSS (NR_045276)	promoter-TSS (NR_045276)	1	NR_045276	71523	Mm.72795	NM_027820	ENSMUSG00000034587	8430429K09Rik	-	RIKEN cDNA 8430429K09 gene	ncRNA
mm_5007.1	chr1	191978285	191978291	+	1	NA	promoter-TSS (NM_001303132)	promoter-TSS (NM_001303132)	34	NM_001303132	74023	Mm.274393	NM_023727	ENSMUSG00000049353	Rd3	3322402L07Rik|rd-3|rd3	retinal degeneration 3	protein-coding
mm_64986.1	chr7	16916340	16916353	-	1	NA	3' UTR (NM_007590, exon 6 of 6)	3' UTR (NM_007590, exon 6 of 6)	7686	NM_007590	12315	Mm.288630	NM_007590	ENSMUSG00000019370	Calm3	CaMA|R75142	calmodulin 3	protein-coding
mm_116358.1	chr13	40726913	40726913	-	1	NA	promoter-TSS (NR_125899)	promoter-TSS (NR_125899)	-895	NR_125899	102633805		NR_125899	ENSMUSG00000097752	Gm26688	Tfap2a-as1	predicted gene, 26688	ncRNA
mm_155812.1	chrX	99975571	99975649	+	1	NA	promoter-TSS (NM_001177943)	promoter-TSS (NM_001177943)	4	NM_001177943	13607	Mm.328086	NM_010099	ENSMUSG00000059327	Eda	EDA1|Ed1|Eda-A1|Eda-A2|HED|Ta|Tnlg7c|XLHED|tabby	ectodysplasin-A	protein-coding
mm_167191.1	chr7	142558582	142558584	-	1	NA	promoter-TSS (NR_002452)	promoter-TSS (NR_002452)	15	NR_002452	330677	Mm.265130	NR_002452	ENSMUSG00000087090	Nctc1	9530074L01|Rhit1	non-coding transcript 1	ncRNA
mm_169915.1	chr16	57174565	57174579	-	1	NA	intron (NM_026254, intron 15 of 17)	BGLII|LTR|ERVK	-7240	NM_023175	52633	Mm.383203	NM_023175	ENSMUSG00000022751	Nit2	1190017B19Rik|D16Ertd502e	nitrilase family, member 2	protein-coding
mm_63056.1	chr7	121914298	121914303	+	1	NA	exon (NM_011325, exon 8 of 13)	exon (NM_011325, exon 8 of 13)	49262	NR_073548	20277	Mm.7709	NM_011325	ENSMUSG00000030873	Scnn1b	-	sodium channel, nonvoltage-gated 1 beta	protein-coding
mm_173346.1	chrY	90813052	90813053	+	1	NA	intron (NM_133362, intron 2 of 3)	(TTAGGG)n|Simple_repeat|Simple_repeat	26354	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_33807.1	chr4	135120924	135120934	+	1	NA	5' UTR (NM_019732, exon 1 of 6)	5' UTR (NM_019732, exon 1 of 6)	284	NM_019732	12399	Mm.378894	NM_019732	ENSMUSG00000070691	Runx3	AML2|Cbfa3|Pebp2a3	runt related transcription factor 3	protein-coding
mm_78308.1	chr9	22655147	22655159	+	1	NA	intron (NM_178415, intron 15 of 22)	intron (NM_178415, intron 15 of 22)	179438	NM_178415	319845	Mm.176725	NM_178415	ENSMUSG00000035919	Bbs9	E130103I17Rik	Bardet-Biedl syndrome 9 (human)	protein-coding
mm_117154.1	chr13	61541829	61541842	-	1	NA	promoter-TSS (NM_022326)	promoter-TSS (NM_022326)	4	NM_022326	64139	Mm.279933	NM_022326	ENSMUSG00000074871	Ctsm	1600027J17Rik|AI324100|Catm	cathepsin M	protein-coding
mm_79850.1	chr9	64848025	64848029	+	1	NA	intron (NM_001162917, intron 6 of 34)	MIR|SINE|MIR	37016	NM_001162917	102442	Mm.222473	NM_176935	ENSMUSG00000053641	Dennd4a	AI115600|AI851943|F730015K02Rik	DENN/MADD domain containing 4A	protein-coding
mm_69960.1	chr7	142376385	142376391	-	1	NA	3' UTR (NM_009983, exon 9 of 9)	3' UTR (NM_009983, exon 9 of 9)	-2642	NM_001347541	320802	Mm.154486	NM_177265	ENSMUSG00000045777	Ifitm10	6330512M04Rik|AI848576|DSPA3	interferon induced transmembrane protein 10	protein-coding
mm_124858.1	chr15	9554563	9554581	+	1	NA	Intergenic	Intergenic	-24696	NM_008372	16197	Mm.389	NM_008372	ENSMUSG00000003882	Il7r	CD127|IL-7Ralpha	interleukin 7 receptor	protein-coding
mm_28285.1	chr3	88951147	88951213	-	1	NA	promoter-TSS (NM_022994)	promoter-TSS (NM_022994)	-898	NM_001164533	65111	Mm.29028	NM_022994	ENSMUSG00000068921	Dap3	4921514D13Rik|DAP-3|MRP-S29|S29mt	death associated protein 3	protein-coding
mm_21033.1	chr2	152490128	152490146	-	1	NA	promoter-TSS (NM_001002791)	promoter-TSS (NM_001002791)	1	NM_001002791	442835	Mm.99065	NM_001002791	ENSMUSG00000027468	Defb22	9230002F21Rik	defensin beta 22	protein-coding
mm_124373.1	chr14	105922601	105922609	-	1	NA	Intergenic	Intergenic	-25786	NM_011897	24064	Mm.89982	NM_011897	ENSMUSG00000022114	Spry2	sprouty2	sprouty homolog 2 (Drosophila)	protein-coding
mm_75966.1	chr8	71725697	71725736	-	1	NA	promoter-TSS (NM_028715)	promoter-TSS (NM_028715)	-35	NM_028715	74015	Mm.22025	NM_028715	ENSMUSG00000070000	Fcho1	3322402E17Rik|N28152	FCH domain only 1	protein-coding
mm_8322.1	chr1	149449943	149449956	-	1	NA	Intergenic	Intergenic	472490	NM_001305632	18783	Mm.4186	NM_008869	ENSMUSG00000056220	Pla2g4a	Pla2g4|cPLA2|cPLA2-alpha|cPLA2alpha	phospholipase A2, group IVA (cytosolic, calcium-dependent)	protein-coding
mm_112953.1	chr13	21179434	21179440	+	1	NA	promoter-TSS (NM_009054)	promoter-TSS (NM_009054)	-494	NM_009054	19720	Mm.314056	NM_009054	ENSMUSG00000021326	Trim27	AW538890|Gm19403|Rfp	tripartite motif-containing 27	protein-coding
mm_43768.1	chr5	140767956	140767971	+	1	NA	intron (NM_010302, intron 2 of 3)	intron (NM_010302, intron 2 of 3)	43836	NM_173405	231842	Mm.491298	NM_173405	ENSMUSG00000050022	Amz1	5330426I05|6530401C20Rik	archaelysin family metallopeptidase 1	protein-coding
mm_128008.1	chr15	13148150	13148153	-	1	NA	intron (NM_007666, intron 1 of 11)	AT_rich|Low_complexity|Low_complexity	25524	NM_007666	12563	Mm.57048	NM_007666	ENSMUSG00000039385	Cdh6	cad6	cadherin 6	protein-coding
mm_158529.1	chrX	143861245	143861254	-	1	NA	3' UTR (NM_010025, exon 7 of 7)	3' UTR (NM_010025, exon 7 of 7)	-33837	NM_007603	12338	Mm.30290	NM_007603	ENSMUSG00000067276	Capn6	-	calpain 6	protein-coding
mm_91181.1	chr10	20907047	20907083	-	1	NA	Intergenic	Intergenic	-45482	NM_026203	52906	Mm.253280	NM_026203	ENSMUSG00000019986	Ahi1	1700015F03Rik|Ahi-1|D10Bwg0629e	Abelson helper integration site 1	protein-coding
mm_5582.1	chr1	39552193	39552220	-	1	NA	3' UTR (NM_001033135, exon 7 of 7)	3' UTR (NM_001033135, exon 7 of 7)	-3366	NR_028555	100217461		NR_028555	ENSMUSG00000077704	Snord89	MBII-289	small nucleolar RNA, C/D box 89	snoRNA
mm_143276.1	chr17	65675065	65675076	-	1	NA	intron (NM_133685, intron 5 of 6)	intron (NM_133685, intron 5 of 6)	-32866	NM_001146002	213272	Mm.255732	NM_153519	ENSMUSG00000050612	Txndc2	AU021712|Sptrx-1|Sptrx1|Trx4	thioredoxin domain containing 2 (spermatozoa)	protein-coding
mm_66314.1	chr7	39910965	39910975	-	1	NA	Intergenic	Intergenic	393204	NM_001004139	70227	Mm.333800	NM_001004139	ENSMUSG00000068959	Zfp619	3000002G13Rik	zinc finger protein 619	protein-coding
mm_43986.1	chr5	146385263	146385313	+	1	NA	5' UTR (NM_145155, exon 1 of 10)	5' UTR (NM_145155, exon 1 of 10)	282	NM_145155	245880	Mm.472750	NM_145155	ENSMUSG00000029636	Wasf3	Scar3|Wave3	WAS protein family, member 3	protein-coding
mm_111327.1	chr12	86478947	86478957	-	1	NA	intron (NM_001159500, intron 2 of 6)	intron (NM_001159500, intron 2 of 6)	57308	NM_011934	26380	Mm.235550	NM_011934	ENSMUSG00000021255	Esrrb	Err2|Errb|Estrrb|Nr3b2	estrogen related receptor, beta	protein-coding
mm_69719.1	chr7	140218220	140218230	-	1	NA	promoter-TSS (NM_172909)	promoter-TSS (NM_172909)	-42	NM_172909	244233	Mm.19283	NM_172909	ENSMUSG00000025461	Cd163l1	B430307C05|E430002D04Rik|Scart1	CD163 molecule-like 1	protein-coding
mm_159167.1	chr2	92320332	92320332	+	1	NA	exon (NM_001109690, exon 4 of 16)	exon (NM_001109690, exon 4 of 16)	50725	NM_001290774	228366	Mm.31158	NM_172670	ENSMUSG00000040434	Large2	5730485C17Rik|AI891893|Gyltl1b|Largel|mKIAA4105	LARGE xylosyl- and glucuronyltransferase 2	protein-coding
mm_14518.1	chr2	132597449	132597461	+	1	NA	promoter-TSS (NR_033469)	promoter-TSS (NR_033469)	-741	NR_033468	767814	Mm.371752	NR_033468	ENSMUSG00000074783	AU019990	-	expressed sequence AU019990	ncRNA
mm_78206.1	chr9	21469929	21469929	+	1	NA	intron (NM_007871, intron 4 of 19)	intron (NM_007871, intron 4 of 19)	26635	NR_029585	387194		NR_029585	ENSMUSG00000065547	Mir199a-1	Mirn199|Mirn199a-1|mir-199a-1	microRNA 199a-1	ncRNA
mm_26112.1	chr3	137624032	137624062	+	1	NA	intron (NM_030143, intron 1 of 2)	intron (NM_030143, intron 1 of 2)	375	NM_030143	73284	Mm.250841	NM_030143	ENSMUSG00000046818	Ddit4l	1700037B15Rik|1700108M02Rik|REDD2|RTP801L|Smhs1	DNA-damage-inducible transcript 4-like	protein-coding
mm_72197.1	chr8	72548460	72548470	+	1	NA	promoter-TSS (NM_027485)	promoter-TSS (NM_027485)	-155	NM_027485	70625	Mm.235885	NM_027485	ENSMUSG00000045248	Med26	5730493L18Rik|AI414941|AW495270|Crsp7	mediator complex subunit 26	protein-coding
mm_113289.1	chr13	30245621	30245625	+	1	NA	3' UTR (NM_153546, exon 13 of 13)	3' UTR (NM_153546, exon 13 of 13)	-90733	NM_177322	11607	Mm.35062	NM_177322	ENSMUSG00000049115	Agtr1a	1810074K20Rik|AG2S|AI551199|AT1|AT1a|AT2R1|AT2R1A|Agtr-1a|Agtr1|Angtr-1a	angiotensin II receptor, type 1a	protein-coding
mm_108838.1	chr12	96923047	96923062	+	1	NA	Intergenic	Intergenic	-875832	NR_103800	69423	Mm.46121	NM_027076		1700019M22Rik	-	NFX-like protein	pseudo
mm_109512.1	chr12	111454220	111454230	+	1	NA	3' UTR (NM_009396, exon 12 of 12)	3' UTR (NM_009396, exon 12 of 12)	11564	NM_009396	21928	Mm.255332	NM_009396	ENSMUSG00000021281	Tnfaip2	B94|Exoc3l3|M-sec|Tnfip2|tnfb94	tumor necrosis factor, alpha-induced protein 2	protein-coding
mm_46725.1	chr5	110770177	110770187	-	1	NA	intron (NM_173066, intron 1 of 50)	CpG	535	NM_029337	75560	Mm.270487	NM_029337	ENSMUSG00000029505	Ep400	1700020J09Rik|AU023439|mDomino|mKIAA1498|p400	E1A binding protein p400	protein-coding
mm_91503.1	chr10	37136193	37136219	-	1	NA	exon (NM_008538, exon 2 of 2)	exon (NM_008538, exon 2 of 2)	2720	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_107298.1	chr12	30910545	30910556	+	1	NA	intron (NM_001110239, intron 1 of 5)	intron (NM_001110239, intron 1 of 5)	1062	NM_021330	11431	Mm.359831	NM_021330	ENSMUSG00000044573	Acp1	4632432E04Rik|AI427468|Acp-1|LMW-PTP|Lmptp	acid phosphatase 1, soluble	protein-coding
mm_101440.1	chr11	30159547	30159557	-	1	NA	intron (NM_175836, intron 1 of 34)	intron (NM_175836, intron 1 of 34)	38705	NM_009260	20742	Mm.123110	NM_009260	ENSMUSG00000020315	Sptbn1	9930031C03Rik|AL033301|SPTB2|Spnb-2|Spnb2|elf1|elf3|mKIAA4049	spectrin beta, non-erythrocytic 1	protein-coding
mm_57720.1	chr6	128826278	128826330	-	1	NA	promoter-TSS (NM_030599)	promoter-TSS (NM_030599)	11	NM_030599	80782	Mm.6180	NM_030599	ENSMUSG00000079298	Klrb1b	Klrb1d|Ly55b|Ly55d|NKR-P1B|NKR-P1D|Nkrp1-b|Nkrp1d|ly-55b|ly-55d	killer cell lectin-like receptor subfamily B member 1B	protein-coding
mm_52614.1	chr6	117173897	117173901	+	1	NA	3' UTR (NM_021704, exon 3 of 3)	3' UTR (NM_021704, exon 3 of 3)	5364	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_19363.1	chr2	91098888	91098901	-	1	NA	intron (NM_011355, intron 1 of 4)	intron (NM_011355, intron 1 of 4)	2216	NM_011355	20375	Mm.1302	NM_011355	ENSMUSG00000002111	Spi1	Dis-1|Dis1|PU.1|Sfpi-1|Sfpi1|Spi-1|Tcfpu1|Tfpu.1	spleen focus forming virus (SFFV) proviral integration oncogene	protein-coding
mm_1836.1	chr1	82821713	82821716	+	1	NA	Intergenic	Intergenic	-17746	NM_001310713	15463	Mm.392569	NM_010472	ENSMUSG00000026159	Agfg1	AU045498|C130049H11Rik|C85612|D730048C23Rik|Hrb|RAB|Rip	ArfGAP with FG repeats 1	protein-coding
mm_75012.1	chr8	28651171	28651174	-	1	NA	3' UTR (NM_001347499, exon 17 of 17)	3' UTR (NM_001347499, exon 17 of 17)	-566319	NR_033590	666422	Mm.484413	NR_033590	ENSMUSG00000110372	Gm8096	EG666422	3-phosphoglycerate dehydrogenase pseudogene	pseudo
mm_115594.1	chr13	11827304	11827319	-	1	NA	intron (NM_023868, intron 15 of 104)	intron (NM_023868, intron 15 of 104)	279634	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding
mm_79248.1	chr9	50593226	50593265	+	1	NA	Intergenic	Intergenic	10604	NM_025848	66925	Mm.10406	NM_025848	ENSMUSG00000000171	Sdhd	3110001M13Rik|AVLL5809|C78570|PRO19626	succinate dehydrogenase complex, subunit D, integral membrane protein	protein-coding
mm_30727.1	chr4	13751538	13751557	+	1	NA	5' UTR (NM_001111027, exon 1 of 12)	5' UTR (NM_001111027, exon 1 of 12)	250	NM_001111027	12395	Mm.4909	NM_009822	ENSMUSG00000006586	Runx1t1	Cbfa2t1h|ETO|MTG8	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	protein-coding
mm_43488.1	chr5	136919339	136919381	+	1	NA	non-coding (NR_015555, exon 1 of 4)	non-coding (NR_015555, exon 1 of 4)	214	NR_015555	66752	Mm.135764	NR_015555	ENSMUSG00000097908	4933404O12Rik	AW494809	RIKEN cDNA 4933404O12 gene	ncRNA
mm_97339.1	chr11	77348273	77348292	+	1	NA	promoter-TSS (NM_001291190)	promoter-TSS (NM_001291190)	2	NM_001291190	237860	Mm.440381	NM_177710	ENSMUSG00000037926	Ssh2	SSH-2|SSH-2L|mSSH-2L	slingshot homolog 2 (Drosophila)	protein-coding
mm_108593.1	chr12	85374126	85374136	+	1	NA	intron (NM_026775, intron 1 of 4)	intron (NM_026775, intron 1 of 4)	586	NM_026775	68581	Mm.379159	NM_026775	ENSMUSG00000021248	Tmed10	1110014C03Rik|Tmp21|p23|p24delta1	transmembrane p24 trafficking protein 10	protein-coding
mm_54057.1	chr6	13839896	13839908	-	1	NA	promoter-TSS (NM_001330667)	promoter-TSS (NM_001330667)	40	NM_001330666	64450	Mm.167625	NM_145066	ENSMUSG00000048216	Gpr85	2900026B03Rik	G protein-coupled receptor 85	protein-coding
mm_165199.1	chr2	32608665	32608686	+	1	NA	intron (NM_001289549, intron 2 of 6)	intron (NM_001289549, intron 2 of 6)	1690	NR_110347	50935	Mm.88831	NM_016973	ENSMUSG00000026811	St6galnac6	ST6GalNAcVI|Siat7f	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 6	protein-coding
mm_116863.1	chr13	54930200	54930213	-	1	NA	Intergenic	Intergenic	-19205	NM_001311128	107448	Mm.23573	NM_153131	ENSMUSG00000025876	Unc5a	Unc5h1|mKIAA1976	unc-5 netrin receptor A	protein-coding
mm_12465.1	chr2	71389223	71389237	+	1	NA	promoter-TSS (NM_026115)	promoter-TSS (NM_026115)	-30	NM_026115	107435	Mm.272472	NM_026115	ENSMUSG00000027018	Hat1	2410071B14Rik|AA536933|Hat-1|KAT1	histone aminotransferase 1	protein-coding
mm_51025.1	chr6	65145167	65145199	+	1	NA	promoter-TSS (NM_019455)	promoter-TSS (NM_019455)	-453	NM_019455	54486	Mm.410688	NM_019455	ENSMUSG00000029919	Hpgds	H-PGDS|Ptgds2	hematopoietic prostaglandin D synthase	protein-coding
mm_36711.1	chr4	97751817	97751861	-	1	NA	intron (NM_001122952, intron 1 of 10)	CpG	-25787	NM_001122953	18027	Mm.31274	NM_010905	ENSMUSG00000028565	Nfia	1110047K16Rik|9430022M17Rik|CTF|NF1-A|NF1A	nuclear factor I/A	protein-coding
mm_33134.1	chr4	125030007	125030070	+	1	NA	promoter-TSS (NM_145552)	promoter-TSS (NM_145552)	24	NM_145552	230737	Mm.90760	NM_145552	ENSMUSG00000028869	Gnl2	BC003262|HUMAUANTIG|Ngp-1	guanine nucleotide binding protein-like 2 (nucleolar)	protein-coding
mm_122527.1	chr14	47380272	47380332	-	1	NA	exon (NM_010705, exon 3 of 6)	exon (NM_010705, exon 3 of 6)	6442	NM_001145953	16854	Mm.248615	NM_010705	ENSMUSG00000050335	Lgals3	GBP|L-34|Mac-2|gal3	lectin, galactose binding, soluble 3	protein-coding
mm_134468.1	chr16	18426603	18426619	-	1	NA	5' UTR (NM_001111062, exon 1 of 6)	5' UTR (NM_001111062, exon 1 of 6)	105	NM_007744	12846	Mm.100940	NM_007744	ENSMUSG00000000326	Comt	Comt1|D16Wsu103e|D330014B15Rik	catechol-O-methyltransferase	protein-coding
mm_133264.1	chr16	77351696	77351706	+	1	NA	intron (NR_015543, intron 1 of 4)	intron (NR_015543, intron 1 of 4)	22373	NR_015543	77994	Mm.394688	NR_015543	ENSMUSG00000090386	Mir99ahg	2810055G20Rik|D730043B02Rik	Mir99a and Mirlet7c-1 host gene (non-protein coding)	ncRNA
mm_172670.1	chr8	44233833	44233849	+	1	NA	Intergenic	Lx5c|LINE|L1	-534350	NM_001079931	384814	Mm.491652	NM_001079931		Gm5347	EG384814	predicted gene 5347	protein-coding
mm_7981.1	chr1	134099194	134099204	-	1	NA	Intergenic	Intergenic	-12043	NM_001284524	71884	Mm.328268	NM_027979	ENSMUSG00000026450	Chit1	2300002L19Rik	chitinase 1 (chitotriosidase)	protein-coding
mm_19022.1	chr2	76949051	76949063	-	1	NA	exon (NM_011652, exon 22 of 313)	exon (NM_011652, exon 22 of 313)	33490	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_14018.1	chr2	122150911	122150930	+	1	NA	exon (NM_009735, exon 2 of 4)	exon (NM_009735, exon 2 of 4)	3233	NM_009735	12010	Mm.163	NM_009735	ENSMUSG00000060802	B2m	Ly-m11|beta2-m|beta2m	beta-2 microglobulin	protein-coding
mm_68798.1	chr7	125349746	125349783	-	1	NA	promoter-TSS (NR_045804)	promoter-TSS (NR_045804)	22	NR_045804	71208	Mm.159465	NM_172408	ENSMUSG00000045928	4933440M02Rik	-	RIKEN cDNA 4933440M02 gene	ncRNA
mm_9720.1	chr1	179803829	179803846	-	1	NA	5' UTR (NM_026375, exon 1 of 36)	5' UTR (NM_026375, exon 1 of 36)	178	NM_026375	226747	Mm.128165	NM_026375	ENSMUSG00000026491	Ahctf1	6230412P20Rik|AV011447|Elys	AT hook containing transcription factor 1	protein-coding
mm_159011.1	chr1	164308048	164308048	+	1	NA	promoter-TSS (NM_001160209)	promoter-TSS (NM_001160209)	376	NM_178071	171567	Mm.219428	NM_138314	ENSMUSG00000026575	Nme7	D530024H21Rik|Nm23-M7|Nm23-r7	NME/NM23 family member 7	protein-coding
mm_141779.1	chr17	34293711	34293726	-	1	NA	Intergenic	Intergenic	-5947	NM_010378	14960	Mm.235338	NM_010378	ENSMUSG00000036594	H2-Aa	Aalpha|H-2Aa|H2Aa|I-Aalpha|IAalpha|Ia-1|Ia1	histocompatibility 2, class II antigen A, alpha	protein-coding
mm_136453.1	chr16	94997577	94997592	-	1	NA	5' UTR (NM_010606, exon 1 of 4)	5' UTR (NM_010606, exon 1 of 4)	112	NM_001025584	16522	Mm.328720	NM_010606	ENSMUSG00000043301	Kcnj6	BIR1|GIRK2|KATP2|KCNJ7|Kir3.2|weaver|wv	potassium inwardly-rectifying channel, subfamily J, member 6	protein-coding
mm_41556.1	chr5	93003796	93003810	+	1	NA	Intergenic	Intergenic	41219	NM_175270	78088	Mm.245085	NM_175270	ENSMUSG00000045314	Sowahb	5730467H21Rik|Ankrd56	sosondowah ankyrin repeat domain family member B	protein-coding
mm_30108.1	chr3	138982780	138982785	-	1	NA	intron (NM_145544, intron 4 of 13)	intron (NM_145544, intron 4 of 13)	92419	NM_145544	229877	Mm.28893	NM_145544	ENSMUSG00000028149	Rap1gds1	BC011279|GDS1	RAP1, GTP-GDP dissociation stimulator 1	protein-coding
mm_105999.1	chr11	115699258	115699268	-	1	NA	5' UTR (NM_008163, exon 2 of 6)	5' UTR (NM_008163, exon 2 of 6)	271	NM_001313937	14784	Mm.439649	NM_008163	ENSMUSG00000059923	Grb2	AA408164|Ash	growth factor receptor bound protein 2	protein-coding
mm_49433.1	chr6	29279588	29279599	+	1	NA	Intergenic	B4|SINE|B4	-1548	NM_001101486	245884	Mm.33683	NM_001101486	ENSMUSG00000079652	Fam71f2	AI507611|GARI	family with sequence similarity 71, member F2	protein-coding
mm_165754.1	chr3	110143407	110143410	+	1	NA	promoter-TSS (NM_001163350)	promoter-TSS (NM_001163350)	64	NM_001163348	80883	Mm.39262	NM_030699	ENSMUSG00000059857	Ntng1	A930010C08Rik|AI853992|Lmnt1	netrin G1	protein-coding
mm_44397.1	chr5	17835753	17835757	-	1	NA	5' UTR (NM_001159555, exon 1 of 15)	5' UTR (NM_001159555, exon 1 of 15)	141	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_171936.1	chr5	65300496	65300503	+	1	NA	intron (NM_001347358, intron 6 of 24)	intron (NM_001347358, intron 6 of 24)	35140	NM_011258	19687	Mm.148877	NM_011258	ENSMUSG00000029191	Rfc1	140kDa|Alp145|RFC140|Recc1	replication factor C (activator 1) 1	protein-coding
mm_167283.1	chr8	39622254	39622274	-	1	NA	intron (NM_001113326, intron 4 of 9)	(CTATT)n|Simple_repeat|Simple_repeat	20414	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_15497.1	chr2	157817959	157817983	+	1	NA	intron (NM_025680, intron 8 of 15)	intron (NM_025680, intron 8 of 15)	80570	NM_025680	66642	Mm.45193	NM_025680	ENSMUSG00000027649	Ctnnbl1	5730471K09Rik|NAP|NYD-SP19|P14L	catenin, beta like 1	protein-coding
mm_48228.1	chr5	137669572	137669575	-	1	NA	intron (NM_001303271, intron 1 of 12)	intron (NM_001303271, intron 1 of 12)	15180	NM_001303271	231801	Mm.260869	NM_145566	ENSMUSG00000029722	Agfg2	A630095P14Rik|Hrbl|RAB-R|RABR	ArfGAP with FG repeats 2	protein-coding
mm_161322.1	chr14	47308566	47308566	+	1	NA	intron (NM_178684, intron 1 of 3)	intron (NM_178684, intron 1 of 3)	10252	NM_178684	218975	Mm.212297	NM_178684	ENSMUSG00000021840	Mapk1ip1l	9130202B12|C130032J12Rik	mitogen-activated protein kinase 1 interacting protein 1-like	protein-coding
mm_165646.1	chr3	82358216	82358220	+	1	NA	5' UTR (NM_001081230, exon 1 of 14)	5' UTR (NM_001081230, exon 1 of 14)	146	NM_001081230	213582	Mm.271269	NM_001081230	ENSMUSG00000033900	Map9	5033421J10Rik|5330427D05Rik|ASAP|Mtap9	microtubule-associated protein 9	protein-coding
mm_16087.1	chr2	168766545	168766550	+	1	NA	intron (NM_201395, intron 1 of 3)	CpG	654	NM_201395	99377	Mm.434054	NM_175303	ENSMUSG00000027547	Sall4	5730441M18Rik|AA407717|AL022809|AW536104|C330011P20Rik|C78083|C78563|Tex20	sal-like 4 (Drosophila)	protein-coding
mm_147444.1	chr18	46525941	46525999	-	1	NA	promoter-TSS (NM_173423)	promoter-TSS (NM_173423)	1	NM_173423	240263	Mm.38249	NM_173423	ENSMUSG00000033319	Fem1c	2610312A07Rik|3632443A22Rik|AI646567	fem-1 homolog c (C.elegans)	protein-coding
mm_155212.1	chrX	56787046	56787049	+	1	NA	intron (NM_001287800, intron 1 of 5)	(T)n|Simple_repeat|Simple_repeat	520	NM_001287800	14199	Mm.3126	NM_010211	ENSMUSG00000023092	Fhl1	FHL-1|KyoT|RAM14-1|SLIM|SLIM-1	four and a half LIM domains 1	protein-coding
mm_157011.1	chrX	7652803	7652811	-	1	NA	3' UTR (NM_009305, exon 7 of 7)	3' UTR (NM_009305, exon 7 of 7)	-4572	NM_001290624	54630	Mm.232232	NM_175097	ENSMUSG00000031145	Prickle3	Lmo6|Sfc16	prickle planar cell polarity protein 3	protein-coding
mm_42354.1	chr5	114911645	114911660	+	1	NA	3' UTR (NM_011854, exon 6 of 6)	3' UTR (NM_011854, exon 6 of 6)	-11588	NM_145209	231655	Mm.95479	NM_145209	ENSMUSG00000041827	Oasl1	7530414C13Rik|oasl9	2'-5' oligoadenylate synthetase-like 1	protein-coding
mm_145486.1	chr18	60383661	60383666	+	1	NA	intron (NM_001146275, intron 2 of 2)	Lx8|LINE|L1	7634	NM_001146275	60440	Mm.261140	NM_021792	ENSMUSG00000054072	Iigp1	2900074L10Rik|AI046432|AW111922|Ifgga1|Iigp|Irga6	interferon inducible GTPase 1	protein-coding
mm_143538.1	chr17	73950606	73950615	-	1	NA	promoter-TSS (NM_011723)	promoter-TSS (NM_011723)	-414	NM_011723	22436	Mm.11223	NM_011723	ENSMUSG00000024066	Xdh	XO|Xor|Xox-1|Xox1	xanthine dehydrogenase	protein-coding
mm_163810.1	chr14	19416169	19416209	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	186398	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_4566.1	chr1	177448200	177448210	+	1	NA	exon (NM_013915, exon 1 of 1)	exon (NM_013915, exon 1 of 1)	2384	NM_013915	30928	Mm.330700	NM_013915	ENSMUSG00000063659	Zbtb18	RP58|Zfp238|Znf238	zinc finger and BTB domain containing 18	protein-coding
mm_72419.1	chr8	82041775	82041791	+	1	NA	intron (NM_001024617, intron 19 of 24)	intron (NM_001024617, intron 19 of 24)	360803	NM_001254747	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_96950.1	chr11	70562936	70562946	+	1	NA	promoter-TSS (NM_001045964)	promoter-TSS (NM_001045964)	60	NM_016713	50932	Mm.42967	NM_016713	ENSMUSG00000020827	Mink1	B55|MINK|Map4k6|Ysk2	misshapen-like kinase 1 (zebrafish)	protein-coding
mm_171233.1	chr3	67607850	67607854	-	1	NA	Intergenic	Intergenic	25084	NM_025813	66868	Mm.491153	NM_025813	ENSMUSG00000027775	Mfsd1	1200003O06Rik	major facilitator superfamily domain containing 1	protein-coding
mm_35987.1	chr4	55528132	55528140	-	1	NA	exon (NM_010637, exon 5 of 5)	exon (NM_010637, exon 5 of 5)	4339	NM_010637	16600	Mm.4325	NM_010637	ENSMUSG00000003032	Klf4	EZF|Gklf|Zie	Kruppel-like factor 4 (gut)	protein-coding
mm_148473.1	chr19	4097679	4097713	+	1	NA	intron (NM_026373, intron 1 of 3)	intron (NM_026373, intron 1 of 3)	345	NM_026373	52004	Mm.29609	NM_026373	ENSMUSG00000024856	Cdk2ap2	5830466O21Rik|D19Ertd144e|Doc-1r	CDK2-associated protein 2	protein-coding
mm_149235.1	chr19	10183008	10183036	+	1	NA	5' UTR (NM_146094, exon 1 of 12)	5' UTR (NM_146094, exon 1 of 12)	134	NM_146094	76267	Mm.30158	NM_146094	ENSMUSG00000010663	Fads1	0710001O03Rik|A930006B21Rik|AI317215|DSD	fatty acid desaturase 1	protein-coding
mm_69579.1	chr7	135701990	135702029	-	1	NA	exon (NM_001081117, exon 11 of 14)	exon (NM_001081117, exon 11 of 14)	14370	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_13384.1	chr2	103957948	103957973	+	1	NA	promoter-TSS (NM_001142337)	promoter-TSS (NM_001142337)	-35	NM_001142337	16909	Mm.29266	NM_008505	ENSMUSG00000032698	Lmo2	Rbtn-2|Rbtn2|Rhom-2|Ttg2	LIM domain only 2	protein-coding
mm_21295.1	chr2	157007040	157007082	-	1	NA	promoter-TSS (NM_025853)	promoter-TSS (NM_025853)	14	NM_025853	66934	Mm.25410	NM_025853	ENSMUSG00000027635	Dsn1	1700022L09Rik|AW552447	DSN1 homolog, MIS12 kinetochore complex component	protein-coding
mm_158100.1	chrX	101734201	101734211	-	1	NA	promoter-TSS (NM_009910)	promoter-TSS (NM_009910)	-59	NM_009910	12766	Mm.12876	NM_009910	ENSMUSG00000050232	Cxcr3	Cd183|Cmkar3	chemokine (C-X-C motif) receptor 3	protein-coding
mm_570.1	chr1	38049244	38049264	+	1	NA	exon (NM_198303, exon 21 of 24)	exon (NM_198303, exon 21 of 24)	51244	NM_198303	226982	Mm.260943	NM_198303	ENSMUSG00000026083	Eif5b	A030003E17Rik|BC018347|IF2	eukaryotic translation initiation factor 5B	protein-coding
mm_64866.1	chr7	13333273	13333280	-	1	NA	intron (NM_001004762, intron 3 of 15)	intron (NM_001004762, intron 3 of 15)	3954	NM_001004762	232889	Mm.223639	NM_001004762	ENSMUSG00000033847	Pla2g4c	D7Ertd445e	phospholipase A2, group IVC (cytosolic, calcium-independent)	protein-coding
mm_98711.1	chr11	96307132	96307155	+	1	NA	promoter-TSS (NR_131758)	promoter-TSS (NR_131758)	-233	NR_131758	75395	Mm.440014	NR_131758	ENSMUSG00000085645	Hoxb5os	0610040B09Rik|AV302770|Hoxb5/6as	homeobox B5 and homeobox B6, opposite strand	ncRNA
mm_130601.1	chr15	99780567	99780585	-	1	NA	exon (NM_001113545, exon 11 of 11)	exon (NM_001113545, exon 11 of 11)	-8061	NM_028015	71949	Mm.390821	NM_028015	ENSMUSG00000023021	Cers5	2310081H14Rik|AU045339|AW544927|Lass5|Trh4	ceramide synthase 5	protein-coding
mm_80008.1	chr9	67840364	67840372	+	1	NA	promoter-TSS (NM_177184)	promoter-TSS (NM_177184)	-28	NM_177184	320528	Mm.241454	NM_177184	ENSMUSG00000035284	Vps13c	AI552542|AV026040|C230055H22Rik|W51662|chorein	vacuolar protein sorting 13C	protein-coding
mm_51975.1	chr6	91758833	91758848	+	1	NA	3' UTR (NM_009320, exon 15 of 15)	3' UTR (NM_009320, exon 15 of 15)	48553	NM_001159507	243547	Mm.333264	NM_001033353	ENSMUSG00000030098	Grip2	-	glutamate receptor interacting protein 2	protein-coding
mm_70453.1	chr8	11797375	11797387	+	1	NA	intron (NM_001113517, intron 6 of 18)	intron (NM_001113517, intron 6 of 18)	39051	NM_001113518	54126	Mm.244068	NM_017402	ENSMUSG00000031511	Arhgef7	Cool|PIX|Pak3bp|betaPix|betaPix-b|betaPix-c|cool-1|mKIAA0142|p85Cool1|p85SPR	Rho guanine nucleotide exchange factor (GEF7)	protein-coding
mm_124937.1	chr15	12234328	12234328	+	1	NA	intron (NM_172958, intron 4 of 15)	PB1D10|SINE|Alu	29234	NM_172958	268783	Mm.54460	NM_172958	ENSMUSG00000039458	Mtmr12	3Pap|4932703C11|C730015A02Rik|Pip3ap|mKIAA1682	myotubularin related protein 12	protein-coding
mm_35517.1	chr4	41191230	41191240	-	1	NA	3' UTR (NM_026275, exon 5 of 5)	3' UTR (NM_026275, exon 5 of 5)	55214	NM_026275	67615	Mm.389540	NM_026275	ENSMUSG00000036241	Ube2r2	1200003M11Rik|Cdc34b|Ubc3b	ubiquitin-conjugating enzyme E2R 2	protein-coding
mm_34004.1	chr4	137920889	137920920	+	1	NA	intron (NM_199307, intron 3 of 19)	intron (NM_199307, intron 3 of 19)	58667	NM_199307	230857	Mm.401062	NM_199307	ENSMUSG00000057530	Ece1	AW322500|ECE-1|ECE-1a|ECE-1b|ECE-1d	endothelin converting enzyme 1	protein-coding
mm_160505.1	chr9	19712753	19712753	+	1	NA	promoter-TSS (NM_001012265)	promoter-TSS (NM_001012265)	-76	NM_001012265	257963	Mm.377317	NM_001012265	ENSMUSG00000094678	Olfr857	GA_x5J8B7TQMB7-1-306|MOR146-8P	olfactory receptor 857	protein-coding
mm_36256.1	chr4	63410684	63410702	-	1	NA	Intergenic	CpG	-7248	NM_001045514	100182	Mm.387725	NM_001045514	ENSMUSG00000039158	Akna	AI597013	AT-hook transcription factor	protein-coding
mm_5454.1	chr1	36273428	36273443	-	1	NA	promoter-TSS (NM_153408)	promoter-TSS (NM_153408)	-10	NM_153408	214854	Mm.389110	NM_153408	ENSMUSG00000047180	Neurl3	2010300P06Rik|Lincr	neuralized E3 ubiquitin protein ligase 3	protein-coding
mm_44015.1	chr5	147270147	147270168	+	1	NA	promoter-TSS (NM_008814)	promoter-TSS (NM_008814)	26	NM_008814	18609	Mm.389714	NM_008814	ENSMUSG00000029644	Pdx1	IDX-1|IPF-1|Ipf1|Mody4|STF-1|pdx-1	pancreatic and duodenal homeobox 1	protein-coding
mm_84561.1	chr9	67733799	67733803	-	1	NA	Intergenic	Intergenic	-4224	NR_106101	102465716		NR_106101	ENSMUSG00000098446	Mir7242	Gm27809|mmu-mir-7242	microRNA 7242	ncRNA
mm_74422.1	chr8	3645958	3645988	-	1	NA	Intergenic	MTC|LTR|ERVL-MaLR	-9797	NM_001204959	57264	Mm.1181	NM_022984	ENSMUSG00000012705	Retn	ADSF|Fizz3|Rstn|Xcp4	resistin	protein-coding
mm_41921.1	chr5	105609403	105609413	+	1	NA	TTS (NM_133897)	TTS (NM_133897)	89937	NM_133897	100604	Mm.319847	NM_133897	ENSMUSG00000054720	Lrrc8c	AD158|AI326115|E430036I04Rik|fad158	leucine rich repeat containing 8 family, member C	protein-coding
mm_166773.1	chr6	136645981	136645981	+	1	NA	intron (NM_025806, intron 2 of 10)	intron (NM_025806, intron 2 of 10)	15912	NM_025806	66857	Mm.3311	NM_025806	ENSMUSG00000030214	Plbd1	1100001H23Rik	phospholipase B domain containing 1	protein-coding
mm_100175.1	chr11	116533286	116533303	+	1	NA	promoter-TSS (NM_025367)	promoter-TSS (NM_025367)	56	NM_025367	20698	Mm.20944	NM_011451	ENSMUSG00000061878	Sphk1	1110006G24Rik|Sk1|Spk1	sphingosine kinase 1	protein-coding
mm_122152.1	chr14	31269499	31269560	-	1	NA	intron (NM_001033668, intron 58 of 77)	intron (NM_001033668, intron 58 of 77)	18040	NM_027088	104416	Mm.3779	NM_027088	ENSMUSG00000021901	Bap1	2300006C11Rik|AA989761|AW553466|mKIAA0272|uch-x4	Brca1 associated protein 1	protein-coding
mm_9455.1	chr1	172632932	172632943	-	1	NA	promoter-TSS (NM_026725)	promoter-TSS (NM_026725)	37	NM_026725	68440	Mm.33024	NM_026725	ENSMUSG00000026544	Dusp23	1300005N15Rik|LDP-3	dual specificity phosphatase 23	protein-coding
mm_115035.1	chr13	99344776	99344806	+	1	NA	promoter-TSS (NM_026873)	promoter-TSS (NM_026873)	5	NM_173757	218506	Mm.30208	NM_173757	ENSMUSG00000041632	Mrps27	2610028H14Rik	mitochondrial ribosomal protein S27	protein-coding
mm_7155.1	chr1	91456531	91456550	-	1	NA	intron (NM_011066, intron 1 of 22)	intron (NM_011066, intron 1 of 22)	2788	NM_011066	18627	Mm.482463	NM_011066	ENSMUSG00000055866	Per2	mKIAA0347|mPer2	period circadian clock 2	protein-coding
mm_163711.1	chr13	109342652	109342653	+	1	NA	intron (NM_011056, intron 3 of 16)	intron (NM_011056, intron 3 of 16)	17908	NR_030644	100124489		NR_030644	ENSMUSG00000076946	Mir582	Mirn582|mir-582|mmu-mir-582	microRNA 582	ncRNA
mm_82090.1	chr9	123051185	123051204	+	1	NA	exon (NM_177911, exon 7 of 14)	exon (NM_177911, exon 7 of 14)	16453	NM_177911	331046	Mm.195309	NM_177911	ENSMUSG00000025787	Tgm4	9530008N10Rik|Eapa1|TGP	transglutaminase 4 (prostate)	protein-coding
mm_14806.1	chr2	145903223	145903227	+	1	NA	promoter-TSS (NM_001141965)	promoter-TSS (NM_001141965)	-16	NM_026425	67877	Mm.151168	NM_026425	ENSMUSG00000002728	Naa20	1500004D14Rik|2900026I01Rik|AU041458|D2Ertd186e|Nat5	N(alpha)-acetyltransferase 20, NatB catalytic subunit	protein-coding
mm_467.1	chr1	36372188	36372192	+	1	NA	promoter-TSS (NM_001277076)	promoter-TSS (NM_001277076)	-101	NM_001277076	100534273	Mm.389112	NM_001277076	ENSMUSG00000037432	Fer1l5	4930533C12Rik	fer-1-like 5 (C. elegans)	protein-coding
mm_162641.1	chr1	191536576	191536578	-	1	NA	TTS (NM_001305233)	TTS (NM_001305233)	38967	NM_001305233	76843	Mm.189102	NM_029766	ENSMUSG00000037474	Dtl	2810047L02Rik|5730564G15Rik|L2dtl|Ramp	denticleless E3 ubiquitin protein ligase	protein-coding
mm_57495.1	chr6	125313797	125313805	-	1	NA	promoter-TSS (NM_010736)	promoter-TSS (NM_010736)	69	NM_010736	17000	Mm.3122	NM_010736	ENSMUSG00000030339	Ltbr	AI256028|CD18|LTbetaR|Ltar|TNF-R-III|TNFCR|TNFR-RP|TNFR2-RP|TNFRrp|Tnfbr|Tnfrsf3	lymphotoxin B receptor	protein-coding
mm_21051.1	chr2	152622126	152622136	-	1	NA	TTS (NM_001039122)	TTS (NM_001039122)	922	NM_001039122	654459	Mm.358531	NM_001039122	ENSMUSG00000074678	Defb25	BD-25|OTTMUSG00000015862|mBD-25	defensin beta 25	protein-coding
mm_63630.1	chr7	128376304	128376313	+	1	NA	intron (NM_026418, intron 4 of 4)	intron (NM_026418, intron 4 of 4)	41864	NM_026418	67865	Mm.18635	NM_026418	ENSMUSG00000030844	Rgs10	2310010N19Rik	regulator of G-protein signalling 10	protein-coding
mm_98589.1	chr11	95769754	95769757	+	1	NA	Intergenic	Intergenic	20688	NM_201609	268469	Mm.389038	NM_201609	ENSMUSG00000075595	Zfp652	9530033F24Rik|ZNF652	zinc finger protein 652	protein-coding
mm_156182.1	chrX	130524568	130524594	+	1	NA	Intergenic	Intergenic	774839	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diaph2	Dia3|Diap2|Drf2|E430022I22Rik	diaphanous related formin 2	protein-coding
mm_137373.1	chr17	25574421	25574425	+	1	NA	non-coding (NR_045176, exon 2 of 2)	non-coding (NR_045176, exon 2 of 2)	3612	NR_045176	72834	Mm.33042	NR_045176	ENSMUSG00000091475	2810468N07Rik	-	RIKEN cDNA 2810468N07 gene	ncRNA
mm_65800.1	chr7	28949654	28949660	-	1	NA	intron (NM_021895, intron 1 of 20)	intron (NM_021895, intron 1 of 20)	12623	NM_021895	60595	Mm.81144	NM_021895	ENSMUSG00000054808	Actn4	C77391	actinin alpha 4	protein-coding
mm_147862.1	chr18	64334845	64334848	-	1	NA	Intergenic	Intergenic	-5518	NM_194268	225631	Mm.234723	NM_194268	ENSMUSG00000045991	Onecut2	C730009D12|OC-2|Oc2	one cut domain, family member 2	protein-coding
mm_68807.1	chr7	125491587	125491595	-	1	NA	promoter-TSS (NM_026330)	promoter-TSS (NM_026330)	-49	NM_026330	67711	Mm.4467	NM_026330	ENSMUSG00000030750	Nsmce1	2510027N19Rik	NSE1 homolog, SMC5-SMC6 complex component	protein-coding
mm_2833.1	chr1	131525267	131525279	+	1	NA	5' UTR (NM_001081011, exon 2 of 23)	5' UTR (NM_001081011, exon 2 of 23)	2088	NM_001081011	14270	Mm.276259	NM_019520	ENSMUSG00000026425	Srgap2	9930124L22Rik|AI448945|FBP2|Fnbp2|srGAP3	SLIT-ROBO Rho GTPase activating protein 2	protein-coding
mm_163171.1	chr11	87687731	87687733	+	1	NA	intron (NM_172448, intron 2 of 9)	intron (NM_172448, intron 2 of 9)	-11792	NR_045139	68690	Mm.342009	NR_045139		1110028F11Rik	-	RIKEN cDNA 1110028F11 gene	ncRNA
mm_1027.1	chr1	58754916	58754926	+	1	NA	3' UTR (NM_207653, exon 10 of 10)	3' UTR (NM_207653, exon 10 of 10)	24369	NM_001293805	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_145441.1	chr18	59075589	59075599	+	1	NA	non-coding (NR_033765, exon 5 of 5)	non-coding (NR_033765, exon 5 of 5)	13213	NR_033765	225583	Mm.209711	NM_173759	ENSMUSG00000050875	A730017C20Rik	-	RIKEN cDNA A730017C20 gene	protein-coding
mm_81234.1	chr9	107906867	107906918	+	1	NA	promoter-TSS (NM_009074)	promoter-TSS (NM_009074)	3	NR_109782	19882	Mm.3901	NM_009074	ENSMUSG00000032584	Mst1r	CD136|CDw136|Fv-2|Fv2|PTK8|Ron|STK	macrophage stimulating 1 receptor (c-met-related tyrosine kinase)	protein-coding
mm_2575.1	chr1	118481695	118481716	+	1	NA	intron (NM_001293300, intron 8 of 40)	intron (NM_001293300, intron 8 of 40)	-22440	NR_027901	68204	Mm.443536	NR_027901	ENSMUSG00000107722	2900060B14Rik	-	RIKEN cDNA 2900060B14 gene	ncRNA
mm_37653.1	chr4	128806291	128806369	-	1	NA	promoter-TSS (NM_001081098)	promoter-TSS (NM_001081098)	-218	NM_001081098	230761	Mm.22616	NM_001081098	ENSMUSG00000028799	Zfp362	-	zinc finger protein 362	protein-coding
mm_101405.1	chr11	26594640	26594653	-	1	NA	promoter-TSS (NM_027260)	promoter-TSS (NM_027260)	-726	NM_001252447	69922	Mm.285351	NM_027260	ENSMUSG00000064090	Vrk2	2810003O05Rik|AI447698	vaccinia related kinase 2	protein-coding
mm_165148.1	chr2	19388891	19388904	-	1	NA	intron (NM_029619, intron 3 of 4)	intron (NM_029619, intron 3 of 4)	17261	NM_029619	76467	Mm.27166	NM_029619	ENSMUSG00000023094	Msrb2	2310050L06Rik|Mrsb|Msrb|Pilb	methionine sulfoxide reductase B2	protein-coding
mm_75939.1	chr8	71566605	71566612	-	1	NA	promoter-TSS (NM_145598)	promoter-TSS (NM_145598)	41	NM_145598	234404	Mm.213208	NM_145598	ENSMUSG00000034829	Nxnl1	A930031O08Rik|RdCVF|Txnl6	nucleoredoxin-like 1	protein-coding
mm_7674.1	chr1	128588977	128588986	-	1	NA	exon (NM_009911, exon 2 of 2)	exon (NM_009911, exon 2 of 2)	3318	NM_009911	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding
mm_16897.1	chr2	13271420	13271437	-	1	NA	promoter-TSS (NM_009105)	promoter-TSS (NM_009105)	-13	NM_009105	20163	Mm.905	NM_009105	ENSMUSG00000026727	Rsu1	RsuI|rsp-1	Ras suppressor protein 1	protein-coding
mm_113708.1	chr13	43398626	43398695	+	1	NA	intron (NM_023554, intron 1 of 7)	CpG	284	NM_023554	70078	Mm.439927	NM_023554	ENSMUSG00000063200	Nol7	2210008F15Rik|5730556I21Rik|NOP27|RARG-1	nucleolar protein 7	protein-coding
mm_54676.1	chr6	39377682	39377710	-	1	NA	promoter-TSS (NM_028123)	promoter-TSS (NM_028123)	11	NM_028123	72144	Mm.482167	NM_028123	ENSMUSG00000029924	Slc37a3	2610507O21Rik|AU044904	solute carrier family 37 (glycerol-3-phosphate transporter), member 3	protein-coding
mm_47295.1	chr5	122246482	122246485	-	1	NA	intron (NR_104441, intron 10 of 12)	intron (NR_104441, intron 10 of 12)	17977	NR_104441	654470	Mm.28804	NM_001039153	ENSMUSG00000038593	Tctn1	G730031O11Rik|Tect1	tectonic family member 1	protein-coding
mm_72588.1	chr8	84338639	84338658	+	1	NA	Intergenic	Intergenic	-68246	NM_026350	67736	Mm.30095	NM_026350	ENSMUSG00000004994	Ccdc130	4930527D15Rik|C77430	coiled-coil domain containing 130	protein-coding
mm_137009.1	chr17	17830621	17830634	+	1	NA	promoter-TSS (NR_029539)	promoter-TSS (NR_029539)	-185	NR_029539	387235		NR_029539	ENSMUSG00000065479	Mir125a	Mirn125a	microRNA 125a	ncRNA
mm_147018.1	chr18	34595877	34595913	-	1	NA	intron (NM_177773, intron 1 of 5)	G-rich|Low_complexity|Low_complexity	1573	NM_177773	271508	Mm.417609	NM_177773	ENSMUSG00000049357	4933408B17Rik	-	RIKEN cDNA 4933408B17 gene	protein-coding
mm_17717.1	chr2	32387082	32387105	-	1	NA	exon (NM_008491, exon 2 of 6)	exon (NM_008491, exon 2 of 6)	646	NM_008491	16819	Mm.9537	NM_008491	ENSMUSG00000026822	Lcn2	24p3|AW212229|NRL|Sip24	lipocalin 2	protein-coding
mm_87665.1	chr10	58595026	58595075	+	1	NA	Intergenic	Intergenic	80646	NM_010100	13608	Mm.174523	NM_010100	ENSMUSG00000003227	Edar	ED1R|ED3|ED5|EDA-A1R|EDA3|dl	ectodysplasin-A receptor	protein-coding
mm_104400.1	chr11	94508348	94508349	-	1	NA	intron (NM_170671, intron 10 of 18)	intron (NM_170671, intron 10 of 18)	-8374	NM_027984	71889	Mm.248620	NM_027984	ENSMUSG00000010080	Epn3	2310022G12Rik	epsin 3	protein-coding
mm_133237.1	chr16	77071689	77071708	+	1	NA	exon (NM_013918, exon 10 of 24)	exon (NM_013918, exon 10 of 24)	57629	NM_013918	30940	Mm.40986	NM_013918	ENSMUSG00000022867	Usp25	-	ubiquitin specific peptidase 25	protein-coding
mm_39617.1	chr5	24393641	24393664	+	1	NA	promoter-TSS (NM_029020)	promoter-TSS (NM_029020)	-504	NM_029020	74610	Mm.283914	NM_029020	ENSMUSG00000028973	Abcb8	4833412N02Rik|AA409895	ATP-binding cassette, sub-family B (MDR/TAP), member 8	protein-coding
mm_85211.1	chr9	96800516	96800537	-	1	NA	Intergenic	RLTR23|LTR|ERV1	34964	NR_102296	319707	Mm.392191	NR_102293	ENSMUSG00000101581	C430002N11Rik	-	RIKEN cDNA C430002N11 gene	ncRNA
mm_121742.1	chr14	18703930	18703933	-	1	NA	intron (NM_144839, intron 3 of 5)	intron (NM_144839, intron 3 of 5)	189696	NM_144839	218793	Mm.23551	NM_144839	ENSMUSG00000058317	Ube2e2	BC016265	ubiquitin-conjugating enzyme E2E 2	protein-coding
mm_76483.1	chr8	85555318	85555374	-	1	NA	promoter-TSS (NM_019794)	promoter-TSS (NM_019794)	-75	NM_019794	56445	Mm.475573	NM_019794	ENSMUSG00000031701	Dnaja2	1500017M13Rik|2010206B19Rik|DNAJ|DNJ3|Dnaj3|HIRIP4|PRO3015|mDj3	DnaJ heat shock protein family (Hsp40) member A2	protein-coding
mm_172206.1	chr6	5673523	5673533	+	1	NA	Intergenic	RLTR9E|LTR|ERVK	-52111	NM_001191023	13426	Mm.20893	NM_010063	ENSMUSG00000029757	Dync1i1	DH IC-1|DHIC-1|DIC|Dncic1|IC74	dynein cytoplasmic 1 intermediate chain 1	protein-coding
mm_73018.1	chr8	93969118	93969154	+	1	NA	3' UTR (NM_010308, exon 9 of 9)	3' UTR (NM_010308, exon 9 of 9)	43504	NM_011787	23802	Mm.34641	NM_011787	ENSMUSG00000031751	Amfr	gp78	autocrine motility factor receptor	protein-coding
mm_171468.1	chr4	145781445	145781446	+	1	NA	promoter-TSS (NM_001083918)	promoter-TSS (NM_001083918)	-98	NM_001083918	666532	Mm.392861	NM_001083918	ENSMUSG00000067916	Zfp991	Gm13139|OTTMUSG00000010657	zinc finger protein 991	protein-coding
mm_166268.1	chr5	89180818	89180821	+	1	NA	intron (NM_001197147, intron 16 of 25)	intron (NM_001197147, intron 16 of 25)	277079	NM_008096	14473	Mm.196595	NM_008096	ENSMUSG00000035540	Gc	DBP|VDB	group specific component	protein-coding
mm_105309.1	chr11	102819115	102819214	-	1	NA	promoter-TSS (NM_001159382)	promoter-TSS (NM_001159382)	-5	NM_001159382	14615	Mm.390369	NM_008122	ENSMUSG00000034520	Gjc1	C130009G16Rik|Cnx45|Cx45|Gja-7|Gja7	gap junction protein, gamma 1	protein-coding
mm_110419.1	chr12	46818079	46818096	-	1	NA	intron (NM_021361, intron 1 of 4)	intron (NM_021361, intron 1 of 4)	688	NM_021361	664883	Mm.247195	NM_021361	ENSMUSG00000021047	Nova1	9430099M15Rik|G630039L02|Nova-1	neuro-oncological ventral antigen 1	protein-coding
mm_95076.1	chr11	32642707	32642821	+	1	NA	5' UTR (NM_134015, exon 1 of 14)	5' UTR (NM_134015, exon 1 of 14)	209	NM_001271347	103583	Mm.28017	NM_134015	ENSMUSG00000020271	Fbxw11	2310065A07Rik|AA536858|BTRC2|BTRCP2|Fbxw1b|HOS	F-box and WD-40 domain protein 11	protein-coding
mm_9191.1	chr1	171150593	171150609	-	1	NA	promoter-TSS (NM_025321)	promoter-TSS (NM_025321)	2	NM_025321	66052	Mm.198138	NM_025321	ENSMUSG00000058076	Sdhc	0610010E03Rik|AI316496|AU019277	succinate dehydrogenase complex, subunit C, integral membrane protein	protein-coding
mm_119693.1	chr14	53590902	53590908	+	1	NA	Intergenic	Intergenic	663024	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_161903.1	chr18	60212060	60212060	+	1	NA	promoter-TSS (NM_001033767)	promoter-TSS (NM_001033767)	-17	NM_001033767	240327	Mm.357104	NM_001033767	ENSMUSG00000073555	Gm4951	EG240327|Ifgga2	predicted gene 4951	protein-coding
mm_38456.1	chr4	140581533	140581558	-	1	NA	intron (NM_001290803, intron 9 of 28)	intron (NM_001290803, intron 9 of 28)	67211	NM_001112723	72754	Mm.29329	NM_172415	ENSMUSG00000040964	Arhgef10l	2810441C07Rik	Rho guanine nucleotide exchange factor (GEF) 10-like	protein-coding
mm_66627.1	chr7	45493575	45493604	-	1	NA	3' UTR (NM_008749, exon 13 of 13)	3' UTR (NM_008749, exon 13 of 13)	-4793	NM_027903	71755	Mm.34208	NM_027903	ENSMUSG00000011382	Dhdh	1300018L09Rik|AA591799|Xld-1|Xld1	dihydrodiol dehydrogenase (dimeric)	protein-coding
mm_153193.1	chr19	34523438	34523545	-	1	NA	exon (NM_021460, exon 3 of 10)	exon (NM_021460, exon 3 of 10)	3983	NM_001111100	16889	Mm.157545	NM_021460	ENSMUSG00000024781	Lipa	AA960673|Lal|Lip-1|Lip1	lysosomal acid lipase A	protein-coding
mm_101056.1	chr11	8903718	8903727	-	1	NA	Intergenic	RMER17B|LTR|ERVK	107469	NM_001303610	15574	Mm.42201	NM_008316	ENSMUSG00000020413	Hus1	-	HUS1 checkpoint clamp component	protein-coding
mm_794.1	chr1	45345857	45345928	+	1	NA	exon (NM_009930, exon 48 of 51)	exon (NM_009930, exon 48 of 51)	34354	NM_009930	12825	Mm.249555	NM_009930	ENSMUSG00000026043	Col3a1	AW550625|Col3a-1|Tsk-2|Tsk2	collagen, type III, alpha 1	protein-coding
mm_15410.1	chr2	156775410	156775432	+	1	NA	promoter-TSS (NM_172118)	promoter-TSS (NM_172118)	-43	NM_172118	98932	Mm.271770	NM_172118	ENSMUSG00000067818	Myl9	AI327049|MLC20|Mylc2c|RLC-C	myosin, light polypeptide 9, regulatory	protein-coding
mm_171361.1	chr4	117189939	117189943	+	1	NA	Intergenic	Intergenic	-7317	NM_134471	73804	Mm.247651	NM_134471	ENSMUSG00000028678	Kif2c	4930402F02Rik|ESTM5|Knsl6|MCAK|X83316	kinesin family member 2C	protein-coding
mm_173228.1	chrX	77509481	77509490	+	1	NA	Intergenic	Intergenic	-1742	NM_020601	21372	Mm.258476	NM_020601	ENSMUSG00000025246	Tbl1x	5330429M20|Tbl1	transducin (beta)-like 1 X-linked	protein-coding
mm_101130.1	chr11	12412137	12412153	-	1	NA	promoter-TSS (NM_001282994)	promoter-TSS (NM_001282994)	-5	NM_001282994	12808	Mm.22847	NM_172496	ENSMUSG00000020173	Cobl	-	cordon-bleu WH2 repeat	protein-coding
mm_108448.1	chr12	82451206	82451225	+	1	NA	3' UTR (NM_001167983, exon 24 of 24)	3' UTR (NM_001167983, exon 24 of 24)	139866	NM_172579	217692	Mm.261333	NM_172579	ENSMUSG00000042700	Sipa1l1	4931426N11Rik|AW213287|Spar|mKIAA0440	signal-induced proliferation-associated 1 like 1	protein-coding
mm_28635.1	chr3	95217742	95217765	-	1	NA	TTS (NM_019914)	TTS (NM_019914)	189	NM_172512	213054	Mm.224820	NM_029885	ENSMUSG00000038766	Gabpb2	1810015F01Rik|5830427M07|9430006E19Rik|A430024B14Rik|AV050852|Gabpb2-1	GA repeat binding protein, beta 2	protein-coding
mm_148602.1	chr19	5298303	5298357	+	1	NA	promoter-TSS (NM_001024717)	promoter-TSS (NM_001024717)	-1	NM_001024717	545276	Mm.447174	NM_001024717	ENSMUSG00000047658	Gal3st3	-	galactose-3-O-sulfotransferase 3	protein-coding
mm_102049.1	chr11	52000749	52000775	-	1	NA	promoter-TSS (NM_009458)	promoter-TSS (NM_009458)	-296	NM_009458	22210	Mm.384918	NM_009458	ENSMUSG00000020390	Ube2b	2610301N02Rik|E2-14k|HR6B|Rad6b|mHR6B	ubiquitin-conjugating enzyme E2B	protein-coding
mm_119850.1	chr14	54440895	54440905	+	1	NA	3' UTR (NM_008608, exon 10 of 10)	3' UTR (NM_008608, exon 10 of 10)	9302	NM_008608	17387	Mm.280175	NM_008608	ENSMUSG00000000957	Mmp14	AI325305|MMP-X1|MT-MMP-1|MT1-MMP|sabe	matrix metallopeptidase 14 (membrane-inserted)	protein-coding
mm_1116.1	chr1	59875197	59875209	+	1	NA	3' UTR (NM_007561, exon 13 of 13)	3' UTR (NM_007561, exon 13 of 13)	-37803	NM_001037725	72750	Mm.258250	NM_001037725	ENSMUSG00000041040	Fam117b	2810425F24Rik|6330416D14Rik|Als2cr13	family with sequence similarity 117, member B	protein-coding
mm_90357.1	chr10	127165400	127165402	+	1	NA	promoter-TSS (NM_027739)	promoter-TSS (NM_027739)	245	NM_001244617	14421	Mm.386762	NM_008080	ENSMUSG00000006731	B4galnt1	4933429D13Rik|Gal-NAc-T|GalNAc-T|GalNAcT|Galgt1|Ggm-2|Ggm2	beta-1,4-N-acetyl-galactosaminyl transferase 1	protein-coding
mm_131508.1	chr16	17489640	17489683	+	1	NA	promoter-TSS (NM_175178)	promoter-TSS (NM_175178)	-16	NM_175178	72168	Mm.40038	NM_175178	ENSMUSG00000022763	Aifm3	2810401C16Rik|AI840249|Aifl	apoptosis-inducing factor, mitochondrion-associated 3	protein-coding
mm_121198.1	chr14	103051818	103051827	+	1	NA	intron (NM_008392, intron 4 of 4)	intron (NM_008392, intron 4 of 4)	4810	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_132755.1	chr16	44173272	44173294	+	1	NA	promoter-TSS (NM_001029889)	promoter-TSS (NM_001029889)	-114	NM_001029889	207806	Mm.310566	NM_001029889	ENSMUSG00000068284	Usf3	5530400K22Rik|Gm1779|Gm608|mKIAA2018	upstream transcription factor family member 3	protein-coding
mm_96857.1	chr11	70056855	70056895	+	1	NA	exon (NM_009714, exon 6 of 9)	exon (NM_009714, exon 6 of 9)	2520	NM_001291132	11889	Mm.6559	NM_009714	ENSMUSG00000020884	Asgr1	ASGPR1|Asgr|Asgr-1|HL-1	asialoglycoprotein receptor 1	protein-coding
mm_45020.1	chr5	38561555	38561622	-	1	NA	promoter-TSS (NM_011715)	promoter-TSS (NM_011715)	7	NM_011715	22388	Mm.2654	NM_011715	ENSMUSG00000005103	Wdr1	Aip1|D5Wsu185e|rede	WD repeat domain 1	protein-coding
mm_107990.1	chr12	73226916	73226916	+	1	NA	intron (NM_008612, intron 7 of 7)	intron (NM_008612, intron 7 of 7)	59795	NM_029580	76357	Mm.311344	NM_029580	ENSMUSG00000034442	Trmt5	2610027O18Rik|mKIAA1393	TRM5 tRNA methyltransferase 5	protein-coding
mm_161780.1	chr17	38554280	38554280	+	1	NA	promoter-TSS (NM_001177585)	promoter-TSS (NM_001177585)	88	NM_001177585	100126773	Mm.471587	NM_001177585	ENSMUSG00000092244	Esp34	Gm20410	exocrine gland secreted peptide 34	protein-coding
mm_127475.1	chr15	101273312	101273316	+	1	NA	intron (NM_010444, intron 6 of 6)	intron (NM_010444, intron 6 of 6)	6468	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_84349.1	chr9	64306808	64306811	-	1	NA	TTS (NM_001177784)	TTS (NM_001177784)	25224	NM_001324557	66131	Mm.196219	NM_025372	ENSMUSG00000032397	Tipin	1110005A05Rik|1110018P21Rik	timeless interacting protein	protein-coding
mm_41709.1	chr5	101765221	101765295	+	1	NA	5' UTR (NM_173370, exon 1 of 13)	5' UTR (NM_173370, exon 1 of 13)	128	NM_173370	74596	Mm.46764	NM_173370	ENSMUSG00000029330	Cds1	4833409J18Rik|AI314024|AW125888	CDP-diacylglycerol synthase 1	protein-coding
mm_142112.1	chr17	35836688	35836731	-	1	NA	exon (NM_011655, exon 2 of 4)	exon (NM_011655, exon 2 of 4)	1592	NM_011655	22154	Mm.273538	NM_011655	ENSMUSG00000001525	Tubb5	AA408537|AI596182|B130022C14Rik|M(beta)5	tubulin, beta 5 class I	protein-coding
mm_28231.1	chr3	88455174	88455192	-	1	NA	intron (NM_001163489, intron 1 of 14)	intron (NM_001163489, intron 1 of 14)	578	NM_013658	20351	Mm.439752	NM_013658	ENSMUSG00000028064	Sema4a	AI132332|SemB|Semab	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A	protein-coding
mm_12825.1	chr2	80318031	80318041	+	1	NA	intron (NM_024181, intron 2 of 22)	intron (NM_024181, intron 2 of 22)	2570	NM_024181	66861	Mm.21762	NM_024181	ENSMUSG00000027006	Dnajc10	1200006L06Rik|D2Ertd706e|ERdj5|JPDI	DnaJ heat shock protein family (Hsp40) member C10	protein-coding
mm_71919.1	chr8	70148678	70148682	+	1	NA	TTS (NM_001309841)	TTS (NM_001309841)	-4081	NM_001045484	17259	Mm.432505	NM_008578	ENSMUSG00000079033	Mef2b	AI451606	myocyte enhancer factor 2B	protein-coding
mm_64618.1	chr7	3616136	3616152	-	1	NA	promoter-TSS (NM_001290377)	promoter-TSS (NM_001290377)	13	NM_175632	232790	Mm.358882	NM_175632	ENSMUSG00000054594	Oscar	mOSCAR|mOSCAR-M1|mOSCAR-M2|mOSCAR-M3	osteoclast associated receptor	protein-coding
mm_160227.1	chr7	102075710	102075710	+	1	NA	intron (NM_001286689, intron 4 of 10)	intron (NM_001286689, intron 4 of 10)	4491	NM_011644	102443351	Mm.292904	NM_011644	ENSMUSG00000070425	Xntrpc	Xndr-trpc2	Xndc1-transient receptor potential cation channel, subfamily C, member 2 readthrough	protein-coding
mm_153615.1	chr19	43986136	43986223	-	1	NA	exon (NM_030703, exon 1 of 9)	exon (NM_030703, exon 1 of 9)	341	NM_030703	93721	Mm.206774	NM_030703	ENSMUSG00000025196	Cpn1	0610011F20Rik|CPN	carboxypeptidase N, polypeptide 1	protein-coding
mm_94982.1	chr11	31822736	31822740	+	1	NA	intron (NR_102310, intron 2 of 3)	intron (NR_102310, intron 2 of 3)	1809	NR_102310	414116	Mm.150222	NR_102310	ENSMUSG00000085772	D630024D03Rik	-	RIKEN cDNA D630024D03 gene	ncRNA
mm_99725.1	chr11	106300471	106300525	+	1	NA	exon (NM_008117, exon 5 of 5)	exon (NM_008117, exon 5 of 5)	1398	NM_008117	14599	Mm.343934	NM_008117	ENSMUSG00000020713	Gh	Gh1|Ghb1	growth hormone	protein-coding
mm_93177.1	chr10	93539972	93540014	-	1	NA	promoter-TSS (NM_027908)	promoter-TSS (NM_027908)	40	NM_027908	71761	Mm.244518	NM_027908	ENSMUSG00000015890	Amdhd1	1300019J08Rik	amidohydrolase domain containing 1	protein-coding
mm_60422.1	chr7	44476421	44476449	+	1	NA	Intergenic	L1MEd|LINE|L1	6088	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_104677.1	chr11	97690109	97690165	-	1	NA	exon (NM_009545, exon 13 of 13)	exon (NM_009545, exon 13 of 13)	4185	NM_001085500	217149	Mm.29659	NM_001085500	ENSMUSG00000078695	Cisd3	Mel-13|Mel13	CDGSH iron sulfur domain 3	protein-coding
mm_13527.1	chr2	110021969	110021992	+	1	NA	exon (NM_026613, exon 2 of 6)	exon (NM_026613, exon 2 of 6)	4163	NM_026613	68201	Mm.181767	NM_026613	ENSMUSG00000027160	Ccdc34	2810027O19Rik|4930522P10Rik|AI596202	coiled-coil domain containing 34	protein-coding
mm_120928.1	chr14	76479297	76479307	+	1	NA	intron (NM_001310646, intron 3 of 4)	intron (NM_001310646, intron 3 of 4)	-9134	NM_001177751	21807	Mm.153272	NM_009366	ENSMUSG00000022010	Tsc22d1	AA589566|AW105905|Egr5|TSC-22|Tgfb1i4|Tsc|Tsc22	TSC22 domain family, member 1	protein-coding
mm_78281.1	chr9	22101208	22101222	+	1	NA	exon (NM_009922, exon 2 of 7)	exon (NM_009922, exon 2 of 7)	1962	NM_009922	12797	Mm.4356	NM_009922	ENSMUSG00000001349	Cnn1	CN|CnnI	calponin 1	protein-coding
mm_136581.1	chr17	3558098	3558112	+	1	NA	promoter-TSS (NM_146074)	promoter-TSS (NM_146074)	281	NR_045302	68230	Mm.431352	NR_045302		1700102H20Rik	-	RIKEN cDNA 1700102H20 gene	ncRNA
mm_11453.1	chr2	32095703	32095717	+	1	NA	promoter-TSS (NM_145521)	promoter-TSS (NM_145521)	59	NM_145521	227721	Mm.257236	NM_145521	ENSMUSG00000051373	Plpp7	D830019K17Rik|NET39|Ppapdc3	phospholipid phosphatase 7 (inactive)	protein-coding
mm_54806.1	chr6	41704341	41704351	-	1	NA	promoter-TSS (NM_032540)	promoter-TSS (NM_032540)	-21	NM_032540	23925	Mm.19958	NM_032540	ENSMUSG00000029866	Kel	CD238|Ece3	Kell blood group	protein-coding
mm_107759.1	chr12	59071589	59071603	+	1	NA	exon (NM_008891, exon 9 of 9)	exon (NM_008891, exon 9 of 9)	4677	NM_008891	18949	Mm.22347	NM_008891	ENSMUSG00000020994	Pnn	AU045199|D12Ertd512e	pinin	protein-coding
mm_14893.1	chr2	149405011	149405028	+	1	NA	promoter-TSS (NM_021405)	promoter-TSS (NM_021405)	-230	NM_021405	58214	Mm.117117	NM_021405	ENSMUSG00000033156	Cst10	DD72	cystatin 10 (chondrocytes)	protein-coding
mm_119837.1	chr14	54427142	54427163	+	1	NA	intron (NM_026851, intron 2 of 4)	intron (NM_026851, intron 2 of 4)	243	NM_026851	68836	Mm.248163	NM_026851	ENSMUSG00000010406	Mrpl52	1110047B07Rik	mitochondrial ribosomal protein L52	protein-coding
mm_171378.1	chr4	119285114	119285131	-	1	NA	exon (NM_011732, exon 3 of 8)	exon (NM_011732, exon 3 of 8)	9391	NM_011732	22608	Mm.258204	NM_011732	ENSMUSG00000028639	Ybx1	1700102N10Rik|C79409|EF1A|MSY1|Nsep1|YB-1|dbpB|mYB-1a	Y box protein 1	protein-coding
mm_88603.1	chr10	79806013	79806031	+	1	NA	intron (NM_023128, intron 1 of 8)	intron (NM_023128, intron 1 of 8)	12450	NM_001161747	18483	Mm.34650	NM_023128	ENSMUSG00000035863	Palm	-	paralemmin	protein-coding
mm_1482.1	chr1	71578692	71578702	+	1	NA	3' UTR (NM_026195, exon 16 of 16)	3' UTR (NM_026195, exon 16 of 16)	21541	NM_026195	108147	Mm.38010	NM_026195	ENSMUSG00000026192	Atic	2610509C24Rik|AA536954|AW212393	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	protein-coding
mm_103783.1	chr11	82764773	82764786	-	1	NA	promoter-TSS (NM_001291242)	promoter-TSS (NM_001291242)	434	NM_025884	66983	Mm.29622	NM_025884	ENSMUSG00000046010	Zfp830	2410003C20Rik|AV301118|AW048207|Ccdc16|Omcg1|Znf830	zinc finger protein 830	protein-coding
mm_97344.1	chr11	77462559	77462565	+	1	NA	Intergenic	CpG	-1351	NM_139129	216961	Mm.33477	NM_139128	ENSMUSG00000020836	Coro6	-	coronin 6	protein-coding
mm_107291.1	chr12	29982143	29982153	+	1	NA	intron (NM_181395, intron 4 of 22)	intron (NM_181395, intron 4 of 22)	44112	NM_181395	69675	Mm.251774	NM_181395	ENSMUSG00000020674	Pxdn	2310075M15Rik|C85409|E330004E07|VPO1|mKIAA0230	peroxidasin	protein-coding
mm_130994.1	chr15	103430360	103430373	-	1	NA	promoter-TSS (NM_028797)	promoter-TSS (NM_028797)	61	NM_028797	74174	Mm.325325	NM_028797	ENSMUSG00000022487	Gtsf1	1700006H03Rik|Cue110	gametocyte specific factor 1	protein-coding
mm_46132.1	chr5	92675216	92675218	-	1	NA	promoter-TSS (NM_177230)	promoter-TSS (NM_177230)	-90	NM_177230	320696	Mm.209991	NM_177230	ENSMUSG00000050050	Ccdc158	4932413O14Rik	coiled-coil domain containing 158	protein-coding
mm_2666.1	chr1	126992787	126992791	+	1	NA	Intergenic	Intergenic	-162157	NM_176957	210356	Mm.377234	NM_172484	ENSMUSG00000049690	Nckap5	8430408F21|D130011D22Rik|E030049G20Rik|Erih1|Erih2|Gm1548|Nap5	NCK-associated protein 5	protein-coding
mm_672.1	chr1	40465704	40465729	+	1	NA	promoter-TSS (NM_001161843)	promoter-TSS (NM_001161843)	95	NM_001161843	16182	Mm.253664	NM_008365	ENSMUSG00000026070	Il18r1	Il18ralpha|Il1rrp	interleukin 18 receptor 1	protein-coding
mm_36032.1	chr4	57143579	57143624	-	1	NA	promoter-TSS (NM_019427)	promoter-TSS (NM_019427)	-445	NM_019427	54357	Mm.28217	NM_019427	ENSMUSG00000028434	Epb41l4b	6430543G08Rik|AA589614|AU021054|BB007528|D4Ertd346e|Ehm2|Epb4.1l4b|Lulu2	erythrocyte membrane protein band 4.1 like 4b	protein-coding
mm_33252.1	chr4	127168352	127168361	+	1	NA	promoter-TSS (NM_198618)	promoter-TSS (NM_198618)	-848	NM_198618	242667	Mm.331885	NM_198618	ENSMUSG00000042388	Dlgap3	BC058433|DAP-3|DAP3|Prpl8|Sapap3	discs, large (Drosophila) homolog-associated protein 3	protein-coding
mm_139782.1	chr17	65783407	65783468	+	1	NA	promoter-TSS (NM_001114131)	promoter-TSS (NM_001114131)	82	NR_104465	70351	Mm.48686	NM_146081	ENSMUSG00000061950	Ppp4r1	3110001J10Rik|Pp4r1	protein phosphatase 4, regulatory subunit 1	protein-coding
mm_116726.1	chr13	51703402	51703422	-	1	NA	exon (NM_001281880, exon 17 of 17)	exon (NM_001281880, exon 17 of 17)	51704	NM_029279	75420	Mm.275981	NM_029279	ENSMUSG00000035139	Secisbp2	2210413N07Rik|2810012K13Rik|SBP2	SECIS binding protein 2	protein-coding
mm_42563.1	chr5	117142118	117142128	+	1	NA	intron (NM_001081308, intron 1 of 19)	intron (NM_001081308, intron 1 of 19)	8535	NM_183306	330177	Mm.24343	NM_183306	ENSMUSG00000061288	Taok3	2900006A08Rik|A130052D22|A430105I05Rik	TAO kinase 3	protein-coding
mm_7800.1	chr1	131525522	131525538	-	1	NA	5' UTR (NM_001081011, exon 2 of 23)	5' UTR (NM_001081011, exon 2 of 23)	1831	NM_001081011	14270	Mm.276259	NM_019520	ENSMUSG00000026425	Srgap2	9930124L22Rik|AI448945|FBP2|Fnbp2|srGAP3	SLIT-ROBO Rho GTPase activating protein 2	protein-coding
mm_28053.1	chr3	84155763	84155796	-	1	NA	promoter-TSS (NM_029797)	promoter-TSS (NM_029797)	7	NM_029797	76915	Mm.274829	NM_029797	ENSMUSG00000033752	Mnd1	2610034E18Rik|AI591601|Gaj	meiotic nuclear divisions 1	protein-coding
mm_147589.1	chr18	56562262	56562283	-	1	NA	promoter-TSS (NM_138600)	promoter-TSS (NM_138600)	26	NM_138600	110695	Mm.30250	NM_138600	ENSMUSG00000053644	Aldh7a1	Atq1|D18Wsu181e	aldehyde dehydrogenase family 7, member A1	protein-coding
mm_20429.1	chr2	129305914	129305925	-	1	NA	intron (NR_040371, intron 3 of 4)	intron (NR_040371, intron 3 of 4)	4053	NM_010554	16175	Mm.15534	NM_010554	ENSMUSG00000027399	Il1a	Il-1a	interleukin 1 alpha	protein-coding
mm_14761.1	chr2	145167707	145167773	+	1	NA	Intergenic	CpG	-74871	NM_053195	94249	Mm.217171	NM_053195	ENSMUSG00000063873	Slc24a3	NCKX3	solute carrier family 24 (sodium/potassium/calcium exchanger), member 3	protein-coding
mm_71948.1	chr8	70439776	70439808	+	1	NA	promoter-TSS (NM_001004062)	promoter-TSS (NM_001004062)	-219	NM_001004062	382056	Mm.227767	NM_001004062	ENSMUSG00000003575	Crtc1	AI413414|Mect1|R74955|TORC1|mKIAA0616	CREB regulated transcription coactivator 1	protein-coding
mm_44650.1	chr5	28210048	28210055	-	1	NA	5' UTR (NM_001310511, exon 1 of 3)	5' UTR (NM_001310511, exon 1 of 3)	117	NM_001310511	269637	Mm.68286	NM_175651	ENSMUSG00000044681	Cnpy1	1500012D20Rik|9630008K15Rik|AI853839	canopy FGF signaling regulator 1	protein-coding
mm_122467.1	chr14	45530021	45530056	-	1	NA	promoter-TSS (NM_146054)	promoter-TSS (NM_146054)	27	NM_146054	218952	Mm.210018	NM_146054	ENSMUSG00000037712	Fermt2	AA960555|Kindlin-2|Mig2|Plekhc1	fermitin family member 2	protein-coding
mm_117416.1	chr13	74317214	74317233	-	1	NA	5' UTR (NM_011051, exon 1 of 6)	5' UTR (NM_011051, exon 1 of 6)	103	NM_011051	18570	Mm.24254	NM_011051	ENSMUSG00000021576	Pdcd6	AV299538|Alg2|MA-3|PS2|alg-2	programmed cell death 6	protein-coding
mm_171124.1	chr3	144596821	144596822	+	1	NA	intron (NM_053102, intron 4 of 4)	intron (NM_053102, intron 4 of 4)	26394	NM_053102	93684	Mm.29812	NM_053102	ENSMUSG00000037072	Selenof	9430015P09Rik|Sep15	selenoprotein F	protein-coding
mm_46963.1	chr5	115148007	115148039	-	1	NA	exon (NM_175403, exon 5 of 5)	exon (NM_175403, exon 5 of 5)	10153	NM_175403	109154	Mm.153963	NM_175403	ENSMUSG00000048578	Mlec	2410014A08Rik|AI850530|ESTM19|X83352|mKIAA0152	malectin	protein-coding
mm_123257.1	chr14	61046864	61046874	-	1	NA	promoter-TSS (NM_013869)	promoter-TSS (NM_013869)	-14	NM_013869	29820	Mm.281356	NM_013869	ENSMUSG00000060548	Tnfrsf19	AL023044|AW123854|TAJ|TAJ-ALPHA|TRADE|Troy	tumor necrosis factor receptor superfamily, member 19	protein-coding
mm_128505.1	chr15	53151924	53151927	-	1	NA	intron (NM_010162, intron 1 of 10)	intron (NM_010162, intron 1 of 10)	194258	NM_010162	14042	Mm.309395	NM_010162	ENSMUSG00000061731	Ext1	AA409028	exostoses (multiple) 1	protein-coding
mm_150469.1	chr19	38480999	38481013	+	1	NA	Intergenic	CpG	-43191	NM_019588	74055	Mm.34031	NM_019588	ENSMUSG00000024998	Plce1	4933403A21Rik|PLCepsilon|Plce|mKIAA1516	phospholipase C, epsilon 1	protein-coding
mm_38470.1	chr4	140653953	140653998	-	1	NA	intron (NM_001290803, intron 1 of 28)	intron (NM_001290803, intron 1 of 28)	-5219	NM_172415	72754	Mm.29329	NM_172415	ENSMUSG00000040964	Arhgef10l	2810441C07Rik	Rho guanine nucleotide exchange factor (GEF) 10-like	protein-coding
mm_68276.1	chr7	105598816	105598819	-	1	NA	intron (NM_017371, intron 4 of 9)	MLT1A1|LTR|ERVL-MaLR	1299	NM_017371	15458	Mm.3485	NM_017371	ENSMUSG00000030895	Hpx	Hpxn|hx	hemopexin	protein-coding
mm_74714.1	chr8	17333310	17333321	-	1	NA	intron (NM_053171, intron 1 of 69)	intron (NM_053171, intron 1 of 69)	202070	NM_053171	94109	Mm.436988	NM_053171	ENSMUSG00000060924	Csmd1	B930082H09|mKIAA1890	CUB and Sushi multiple domains 1	protein-coding
mm_102904.1	chr11	69554772	69554811	-	1	NA	3' UTR (NM_007911, exon 5 of 5)	3' UTR (NM_007911, exon 5 of 5)	5446	NM_007911	13643	Mm.249637	NM_007911	ENSMUSG00000003934	Efnb3	EFL-6|ELF-3|Elk-L3|Epl8|LERK-8|NLERK-2	ephrin B3	protein-coding
mm_114710.1	chr13	83572392	83572413	+	1	NA	intron (NM_001347566, intron 1 of 10)	intron (NM_001347566, intron 1 of 10)	-1205	NM_001347577	17260	Mm.24001	NM_025282	ENSMUSG00000005583	Mef2c	5430401D19Rik|9930028G15Rik|AV011172|Mef2	myocyte enhancer factor 2C	protein-coding
mm_16086.1	chr2	168766142	168766147	+	1	NA	intron (NM_201395, intron 1 of 3)	CpG	1057	NM_201395	99377	Mm.434054	NM_175303	ENSMUSG00000027547	Sall4	5730441M18Rik|AA407717|AL022809|AW536104|C330011P20Rik|C78083|C78563|Tex20	sal-like 4 (Drosophila)	protein-coding
mm_137615.1	chr17	28272115	28272131	+	1	NA	intron (NR_045427, intron 1 of 2)	intron (NR_045427, intron 1 of 2)	415	NR_045427	69050	Mm.486938	NR_045427	ENSMUSG00000002250	1810013A23Rik	-	RIKEN cDNA 1810013A23 gene	ncRNA
mm_100707.1	chr11	3649062	3649077	-	1	NA	promoter-TSS (NM_001159288)	promoter-TSS (NM_001159288)	-255	NR_002321	544752	Mm.390314	NR_002321	ENSMUSG00000056579	Tug1	AI316828	taurine upregulated gene 1	ncRNA
mm_28182.1	chr3	88027229	88027240	-	1	NA	intron (NM_022031, intron 1 of 6)	intron (NM_022031, intron 1 of 6)	277	NM_022031	73940	Mm.294467	NM_022031	ENSMUSG00000004894	Hapln2	4930401E20Rik|Bral1	hyaluronan and proteoglycan link protein 2	protein-coding
mm_116182.1	chr13	30974024	30974047	-	1	NA	promoter-TSS (NM_025588)	promoter-TSS (NM_025588)	12	NM_025588	66482	Mm.293510	NM_025588	ENSMUSG00000021357	Exoc2	2410030I24Rik|AI648199|Sec5|Sec5l1	exocyst complex component 2	protein-coding
mm_143751.1	chr17	81582137	81582153	-	1	NA	intron (NR_104580, intron 2 of 8)	intron (NR_104580, intron 2 of 8)	156242	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_168180.1	chr10	56497655	56497658	+	1	NA	Intergenic	Intergenic	120356	NM_010288	14609	Mm.378921	NM_010288	ENSMUSG00000050953	Gja1	AU042049|AW546267|Cnx43|Cx43|Cx43alpha1|Gja-1|Npm1|connexin43	gap junction protein, alpha 1	protein-coding
mm_125606.1	chr15	60822948	60822970	+	1	NA	promoter-TSS (NR_030696)	promoter-TSS (NR_030696)	-6	NR_030696	320469	Mm.230853	NM_177166		9930014A18Rik	-	RIKEN cDNA 9930014A18 gene	ncRNA
mm_100870.1	chr11	5915096	5915100	-	1	NA	promoter-TSS (NM_001287386)	promoter-TSS (NM_001287386)	37	NM_001287386	103988	Mm.220358	NM_010292	ENSMUSG00000041798	Gck	GLK|Gk|Gls006|HK4|HKIV|HXKP|Hlb62|MODY2	glucokinase	protein-coding
mm_10913.1	chr2	25373234	25373241	+	1	NA	intron (NM_001290407, intron 1 of 5)	intron (NM_001290407, intron 1 of 5)	1202	NM_001081085	72080	Mm.250293	NM_001081085	ENSMUSG00000026955	Sapcd2	2010317E24Rik|6030458L21Rik|AL033337|ang	suppressor APC domain containing 2	protein-coding
mm_86435.1	chr10	3872781	3872788	+	1	NA	intron (NM_001033253, intron 1 of 15)	intron (NM_001033253, intron 1 of 15)	117	NM_001033253	213783	Mm.150831	NM_001033253	ENSMUSG00000040624	Plekhg1	D10Ertd733e|Gm521|mKIAA1209	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	protein-coding
mm_150623.1	chr19	41264116	41264182	+	1	NA	promoter-TSS (NM_133352)	promoter-TSS (NM_133352)	-145	NM_133352	107358	Mm.246440	NM_133352	ENSMUSG00000025016	Tm9sf3	1810073M23Rik|2810031D16Rik|AI115521|AI413748|AW146116|AW549777|Smbp|mKIAA4036	transmembrane 9 superfamily member 3	protein-coding
mm_79719.1	chr9	61435756	61435759	+	1	NA	Intergenic	MTE2a|LTR|ERVL-MaLR	63391	NM_001083927	21887	Mm.24255	NM_009389	ENSMUSG00000032280	Tle3	2610103N05Rik|ESG|Grg3a|Grg3b|mKIAA1547	transducin-like enhancer of split 3	protein-coding
mm_73038.1	chr8	94227535	94227611	+	1	NA	intron (NM_172410, intron 2 of 22)	intron (NM_172410, intron 2 of 22)	12972	NM_172410	71805	Mm.458170	NM_172410	ENSMUSG00000032939	Nup93	2410008G02Rik	nucleoporin 93	protein-coding
mm_37704.1	chr4	129377848	129377924	-	1	NA	5' UTR (NM_028603, exon 1 of 5)	5' UTR (NM_028603, exon 1 of 5)	142	NM_028603	73680	Mm.32997	NM_028603	ENSMUSG00000028807	Zbtb8a	2410081M15Rik|AI480941	zinc finger and BTB domain containing 8a	protein-coding
mm_77047.1	chr8	109575943	109576000	-	1	NA	exon (NM_017370, exon 5 of 5)	exon (NM_017370, exon 5 of 5)	3201	NM_017370	15439	Mm.26730	NM_017370	ENSMUSG00000031722	Hp	HP-1|preHP2	haptoglobin	protein-coding
mm_140479.1	chr17	3082850	3082863	-	1	NA	intron (NR_003519, intron 1 of 7)	intron (NR_003519, intron 1 of 7)	1327	NR_003519	328734	Mm.335641	NR_003519		Pisd-ps2	D030013I16Rik	phosphatidylserine decarboxylase, pseudogene 2	pseudo
mm_19803.1	chr2	110305656	110305670	-	1	NA	promoter-TSS (NM_130452)	promoter-TSS (NM_130452)	62	NM_130452	170442	Mm.27335	NM_130452	ENSMUSG00000041660	Bbox1	AI874739	butyrobetaine (gamma), 2-oxoglutarate dioxygenase 1 (gamma-butyrobetaine hydroxylase)	protein-coding
mm_163214.1	chr11	100622862	100622868	+	1	NA	promoter-TSS (NM_028024)	promoter-TSS (NM_028024)	-90	NM_028024	71966	Mm.274734	NM_028024	ENSMUSG00000017837	Nkiras2	2410003M04Rik|4930527H08Rik|D630018G21Rik|KBRAS2	NFKB inhibitor interacting Ras-like protein 2	protein-coding
mm_103340.1	chr11	74705618	74705630	-	1	NA	intron (NM_013625, intron 1 of 10)	intron (NM_013625, intron 1 of 10)	18234	NR_037610	18472	Mm.397111	NM_013625	ENSMUSG00000020745	Pafah1b1	LIS-1|Lis1|MMS10-U|Mdsh|Ms10u|Pafaha	platelet-activating factor acetylhydrolase, isoform 1b, subunit 1	protein-coding
mm_143844.1	chr17	84128383	84128396	-	1	NA	Intergenic	Intergenic	49729	NR_045458	74473	Mm.399575	NR_045458		4933433H22Rik	-	RIKEN cDNA 4933433H22 gene	ncRNA
mm_48618.1	chr5	144761634	144761644	-	1	NA	promoter-TSS (NM_177735)	promoter-TSS (NM_177735)	-61	NM_177735	243339	Mm.126793	NM_177735	ENSMUSG00000043388	Tmem130	BC067004|C130036G08	transmembrane protein 130	protein-coding
mm_34950.1	chr4	155962293	155962337	+	1	NA	promoter-TSS (NM_026125)	promoter-TSS (NM_026125)	3	NM_026125	67389	Mm.29140	NM_026125	ENSMUSG00000023571	Fam132a	1110035L05Rik|C1qdc2|CTRP12|alipolin	family with sequence similarity 132, member A	protein-coding
mm_137405.1	chr17	25985826	25985834	+	1	NA	promoter-TSS (NM_001347334)	promoter-TSS (NM_001347334)	44	NM_001347334	50817	Mm.216072	NM_015830	ENSMUSG00000037326	Capn15	Solh	calpain 15	protein-coding
mm_110649.1	chr12	59011997	59012034	-	1	NA	promoter-TSS (NM_009147)	promoter-TSS (NM_009147)	2	NM_009147	20334	Mm.491137	NM_009147	ENSMUSG00000020986	Sec23a	Msec23|Sec23r	SEC23 homolog A, COPII coat complex component	protein-coding
mm_72700.1	chr8	84978017	84978026	+	1	NA	exon (NM_008416, exon 1 of 1)	exon (NM_008416, exon 1 of 1)	727	NM_008416	16477	Mm.1167	NM_008416	ENSMUSG00000052837	Junb	-	jun B proto-oncogene	protein-coding
mm_22377.1	chr2	181156743	181156757	-	1	NA	5' UTR (NM_007906, exon 1 of 8)	5' UTR (NM_007906, exon 1 of 8)	265	NM_007906	13628	Mm.2645	NM_007906	ENSMUSG00000016349	Eef1a2	Eef1a|S1|wasted|wst	eukaryotic translation elongation factor 1 alpha 2	protein-coding
mm_26854.1	chr3	14808359	14808373	-	1	NA	promoter-TSS (NM_009799)	promoter-TSS (NM_009799)	-1	NM_009799	12346	Mm.273195	NM_009799	ENSMUSG00000027556	Car1	AW555628|Ca1|Car-1	carbonic anhydrase 1	protein-coding
mm_39135.1	chr4	155197571	155197575	-	1	NA	intron (NM_011385, intron 1 of 6)	intron (NM_011385, intron 1 of 6)	24962	NM_011385	20481	Mm.28520	NM_011385	ENSMUSG00000029050	Ski	2310012I02Rik|2610001A11Rik|AA062172|AA589460|BC004088	ski sarcoma viral oncogene homolog (avian)	protein-coding
mm_41796.1	chr5	103753676	103753705	+	1	NA	promoter-TSS (NM_133919)	promoter-TSS (NM_133919)	-472	NM_133919	17355	Mm.6949	NM_133919	ENSMUSG00000029313	Aff1	9630032B01Rik|AW319193|Af4|Mllt2h|Rob	AF4/FMR2 family, member 1	protein-coding
mm_34309.1	chr4	141814983	141814987	+	1	NA	TTS (NM_007919)	TTS (NM_007919)	11020	NM_007919	13706	Mm.45316	NM_007919	ENSMUSG00000058579	Cela2a	Ela-2|Ela2|Ela2a	chymotrypsin-like elastase family, member 2A	protein-coding
mm_18405.1	chr2	60370342	60370344	-	1	NA	intron (NM_013825, intron 2 of 34)	intron (NM_013825, intron 2 of 34)	12888	NM_013825	17076	Mm.2074	NM_013825	ENSMUSG00000026980	Ly75	CD205|DEC-205|DEC205	lymphocyte antigen 75	protein-coding
mm_139048.1	chr17	46253982	46253986	+	1	NA	promoter-TSS (NM_001111142)	promoter-TSS (NM_001111142)	-181	NM_001111142	224813	Mm.70999	NM_001111142	ENSMUSG00000071073	Lrrc73	Gm88	leucine rich repeat containing 73	protein-coding
mm_75508.1	chr8	54412342	54412360	-	1	NA	Intergenic	Intergenic	117647	NM_029701	76687	Mm.86437	NM_029701	ENSMUSG00000054408	Spcs3	1810011E08Rik|SPC22/23	signal peptidase complex subunit 3 homolog (S. cerevisiae)	protein-coding
mm_135596.1	chr16	50732210	50732220	-	1	NA	intron (NR_028300, intron 1 of 1)	intron (NR_028300, intron 1 of 1)	558	NR_028300	68190	Mm.139089	NR_028300		Dubr	5330426P16Rik|Dum	Dppa2 upstream binding RNA	ncRNA
mm_36253.1	chr4	63410011	63410024	-	1	NA	Intergenic	Intergenic	-6572	NM_001045514	100182	Mm.387725	NM_001045514	ENSMUSG00000039158	Akna	AI597013	AT-hook transcription factor	protein-coding
mm_39473.1	chr5	19952657	19952659	+	1	NA	intron (NM_015823, intron 1 of 21)	intron (NM_015823, intron 1 of 21)	45140	NM_015823	50791	Mm.332231	NM_015823	ENSMUSG00000040003	Magi2	AIP-1|Acvri1|Acvrinp1|Acvrip1|Magi-2|S-SCAM|mKIAA0705	membrane associated guanylate kinase, WW and PDZ domain containing 2	protein-coding
mm_50443.1	chr6	48874182	48874192	+	1	NA	Intergenic	Intergenic	-21068	NM_029638	76507	Mm.213898	NM_029638	ENSMUSG00000029811	Aoc1	1600012D06Rik|Abp1|DAO	amine oxidase, copper-containing 1	protein-coding
mm_153428.1	chr19	40821493	40821512	-	1	NA	Intergenic	Intergenic	-9777	NM_172839	240665	Mm.309	NM_172839	ENSMUSG00000025010	Ccnj	D430039C20Rik	cyclin J	protein-coding
mm_106282.1	chr11	118148012	118148026	-	1	NA	Intergenic	RMER4B|LTR|ERVK	-18800	NM_001167746	69926	Mm.473893	NM_001167746	ENSMUSG00000033987	Dnah17	2810003K23Rik|Dnahc17|Dnahcl1|Gm1178|mKIAA3028	dynein, axonemal, heavy chain 17	protein-coding
mm_140832.1	chr17	23645265	23645309	-	1	NA	promoter-TSS (NM_001033339)	promoter-TSS (NM_001033339)	-18	NM_001320258	240047	Mm.235343	NM_001033339	ENSMUSG00000023903	Mmp25	F730048C11Rik|Leukolysin|MMP20|MT6-MMP	matrix metallopeptidase 25	protein-coding
mm_86548.1	chr10	10184592	10184614	+	1	NA	Intergenic	Intergenic	-283563	NM_001081344	78808	Mm.331751	NM_030191	ENSMUSG00000019790	Stxbp5	0710001E20Rik|4930565N16Rik|AW742610|LGL3|mKIAA1006	syntaxin binding protein 5 (tomosyn)	protein-coding
mm_96620.1	chr11	69126105	69126116	+	1	NA	promoter-TSS (NM_011786)	promoter-TSS (NM_011786)	-267	NM_011786	23801	Mm.41989	NM_011786	ENSMUSG00000020892	Aloxe3	e-LOX-3|eLOX-3	arachidonate lipoxygenase 3	protein-coding
mm_106456.1	chr11	120020144	120020150	-	1	NA	intron (NM_001198787, intron 2 of 13)	intron (NM_001198787, intron 2 of 13)	-5285	NR_029767	723844		NR_029767	ENSMUSG00000065600	Mir338	Mirn338|mir-338|mmu-mir-338	microRNA 338	ncRNA
mm_129968.1	chr15	85703983	85703984	-	1	NA	non-coding (NR_110483, exon 1 of 2)	non-coding (NR_110483, exon 1 of 2)	210	NR_110483	102800312	Mm.33117	NR_110483		Lncppara	Lincppara|Mirlet7bhg|linc-Ppara	long noncoding RNA near Ppara	ncRNA
mm_159656.1	chr4	147702565	147702565	-	1	NA	promoter-TSS (NM_001127188)	promoter-TSS (NM_001127188)	66	NM_001127188	100503584	Mm.276881	NM_001127188	ENSMUSG00000062518	Zfp534	Gm13159|OTTMUSG00000010681	zinc finger protein 534	protein-coding
mm_88336.1	chr10	75574201	75574225	+	1	NA	intron (NM_008116, intron 1 of 12)	intron (NM_008116, intron 1 of 12)	718	NM_008116	14598	Mm.4559	NM_008116	ENSMUSG00000006345	Ggt1	CD224|GGT|GGT 1|GGT-1|Ggtp|dwg	gamma-glutamyltransferase 1	protein-coding
mm_49200.1	chr6	15326874	15326922	+	1	NA	intron (NM_053242, intron 5 of 18)	intron (NM_053242, intron 5 of 18)	141392	NM_001286607	114142	Mm.332919	NM_053242	ENSMUSG00000029563	Foxp2	2810043D05Rik|AI449000|CAG-16|D0Kist7	forkhead box P2	protein-coding
mm_44476.1	chr5	23433867	23433880	-	1	NA	promoter-TSS (NM_026984)	promoter-TSS (NM_026984)	480	NR_040469	269630	Mm.425231	NR_040469	ENSMUSG00000073147	5031425E22Rik	-	RIKEN cDNA 5031425E22 gene	ncRNA
mm_84860.1	chr9	78585077	78585087	-	1	NA	intron (NM_001276452, intron 1 of 10)	RLTR18B|LTR|ERVK	2963	NM_172773	235504	Mm.46932	NM_172773	ENSMUSG00000049624	Slc17a5	4631416G20Rik|4732491M05|AST|ISSD|NSD|SD|SIALIN|SIASD|SLD	solute carrier family 17 (anion/sugar transporter), member 5	protein-coding
mm_123575.1	chr14	67000442	67000455	-	1	NA	intron (NM_009761, intron 1 of 5)	intron (NM_009761, intron 1 of 5)	8429	NM_009761	12177	Mm.29820	NM_009761	ENSMUSG00000022051	Bnip3l	C86132|D14Ertd719e|Nip3L|Nix	BCL2/adenovirus E1B interacting protein 3-like	protein-coding
mm_125259.1	chr15	35371110	35371138	+	1	NA	promoter-TSS (NM_177151)	promoter-TSS (NM_177151)	-422	NM_177151	666173	Mm.309250	NM_177151	ENSMUSG00000037646	Vps13b	1810042B05Rik|2310042E16Rik|4732488H20|C330002D13Rik|C87206|Coh1|D230005K13|mKIAA0532|mKIAA5032	vacuolar protein sorting 13B	protein-coding
mm_69867.1	chr7	141455371	141455380	-	1	NA	non-coding (NR_028142, exon 1 of 10)	non-coding (NR_028142, exon 1 of 10)	187	NM_001163689	66853	Mm.29998	NM_025802	ENSMUSG00000025509	Pnpla2	0610039C21Rik|1110001C14Rik|Atgl|TTS-2.2	patatin-like phospholipase domain containing 2	protein-coding
mm_135779.1	chr16	56885956	56885968	-	1	NA	5' UTR (NM_019631, exon 1 of 6)	5' UTR (NM_019631, exon 1 of 6)	201	NM_019631	56277	Mm.262328	NM_019631	ENSMUSG00000022754	Tmem45a	C630002M10Rik|M32486|p19.5	transmembrane protein 45a	protein-coding
mm_4620.1	chr1	178821041	178821041	+	1	NA	intron (NM_001161665, intron 4 of 14)	intron (NM_001161665, intron 4 of 14)	291916	NM_001161665	269152	Mm.129727	NM_177724	ENSMUSG00000026494	Kif26b	4832420M10|BC056349|D230039L06Rik	kinesin family member 26B	protein-coding
mm_159336.1	chr3	41744506	41744506	+	1	NA	intron (NM_001291048, intron 1 of 4)	intron (NM_001291048, intron 1 of 4)	1888	NM_027271	73852	Mm.29006	NM_027271	ENSMUSG00000025766	D3Ertd751e	2810009O15Rik|4930415G15Rik	DNA segment, Chr 3, ERATO Doi 751, expressed	protein-coding
mm_29724.1	chr3	125938523	125938536	-	1	NA	promoter-TSS (NM_011674)	promoter-TSS (NM_011674)	21	NM_011674	22239	Mm.306021	NM_011674	ENSMUSG00000032854	Ugt8a	AI850488|AW455908|Cgt|Ugt8|mCerGT	UDP galactosyltransferase 8A	protein-coding
mm_82397.1	chr9	14740667	14740677	-	1	NA	promoter-TSS (NM_177905)	promoter-TSS (NM_177905)	61	NM_177905	330890	Mm.334969	NM_177905	ENSMUSG00000036912	Piwil4	9230101H05Rik|Miwi2	piwi-like RNA-mediated gene silencing 4	protein-coding
mm_103696.1	chr11	79516319	79516329	-	1	NA	exon (NM_001077496, exon 2 of 2)	exon (NM_001077496, exon 2 of 2)	7438	NM_001077496	216984	Mm.439665	NM_001077496	ENSMUSG00000093938	Evi2b	Evi-2|Evi2	ecotropic viral integration site 2b	protein-coding
mm_30750.1	chr4	14914451	14914457	+	1	NA	3' UTR (NM_028264, exon 7 of 7)	3' UTR (NM_028264, exon 7 of 7)	-16187	NM_001243100	100038514	Mm.331495	NM_001243100		Gm11837	OTTMUSG00000004551	predicted gene 11837	protein-coding
mm_134068.1	chr16	8637663	8637703	-	1	NA	promoter-TSS (NM_025708)	promoter-TSS (NM_025708)	18	NM_025708	66690	Mm.10068	NM_025708	ENSMUSG00000043140	Tmem186	2810440M13Rik|4432406C05Rik|AI648175|AW210586	transmembrane protein 186	protein-coding
mm_150663.1	chr19	41981710	41981778	+	1	NA	promoter-TSS (NM_028152)	promoter-TSS (NM_028152)	-19	NM_145500	226122	Mm.22948	NM_145500	ENSMUSG00000025171	Ubtd1	BC016129	ubiquitin domain containing 1	protein-coding
mm_8177.1	chr1	138078560	138078575	-	1	NA	exon (NM_001268286, exon 22 of 29)	exon (NM_001268286, exon 22 of 29)	96559	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_145425.1	chr18	58612828	58612832	+	1	NA	TTS (NM_001081072)	TTS (NM_001081072)	-46652	NM_025478	66307	Mm.182574	NM_025478	ENSMUSG00000024601	Isoc1	2610034N03Rik	isochorismatase domain containing 1	protein-coding
mm_155676.1	chrX	91181445	91181446	+	1	NA	Intergenic	Intergenic	26277	NR_126535	101055749	Mm.300769	NR_126535	ENSMUSG00000059972	LOC101055749	-	Gm5941 pseudogene	pseudo
mm_48774.1	chr5	148509365	148509381	-	1	NA	intron (NM_011908, intron 2 of 4)	intron (NM_011908, intron 2 of 4)	43415	NM_011908	24109	Mm.21846	NM_011908	ENSMUSG00000001687	Ubl3	AW108023|HCG	ubiquitin-like 3	protein-coding
mm_152235.1	chr19	8709578	8709627	-	1	NA	exon (NM_008577, exon 5 of 9)	exon (NM_008577, exon 5 of 9)	4295	NM_008577	17254	Mm.4114	NM_008577	ENSMUSG00000010095	Slc3a2	4F2|4F2HC|AI314110|Cd98|Ly-10|Ly-m10|Ly10|Mdu1|Mgp-2hc|NACAE	solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2	protein-coding
mm_132993.1	chr16	55526262	55526266	+	1	NA	Intergenic	Intergenic	31533	NR_039578	100628589		NR_039578	ENSMUSG00000093292	Mir5118	mmu-mir-5118|mu-mir-5118	microRNA 5118	ncRNA
mm_122024.1	chr14	28969375	28969381	-	1	NA	intron (NM_009785, intron 30 of 37)	intron (NM_009785, intron 30 of 37)	-48830	NM_176920	319476	Mm.95780	NM_176920	ENSMUSG00000045776	Lrtm1	A930016D02Rik	leucine-rich repeats and transmembrane domains 1	protein-coding
mm_77736.1	chr8	126908232	126908244	-	1	NA	Intergenic	Intergenic	37683	NM_024214	67952	Mm.6932	NM_024214	ENSMUSG00000093904	Tomm20	1810060K07Rik|BB284719|Gm19268|MAS20|MOM19|TOM20|mKIAA0016	translocase of outer mitochondrial membrane 20 homolog (yeast)	protein-coding
mm_106959.1	chr12	8921708	8921710	+	1	NA	5' UTR (NM_008640, exon 1 of 7)	5' UTR (NM_008640, exon 1 of 7)	402	NM_008640	17775	Mm.30071	NM_008640	ENSMUSG00000020585	Laptm4a	AA286466|LAPTM4|MTP|Mtrp|mKIAA0108	lysosomal-associated protein transmembrane 4A	protein-coding
mm_107725.1	chr12	57230407	57230460	+	1	NA	promoter-TSS (NM_001164370)	promoter-TSS (NM_001164370)	8	NM_001164370	73490	Mm.268180	NM_001164370	ENSMUSG00000047022	Mipol1	1700081O04Rik|6030439O22Rik|AU021838|AW536152|D12Ertd19e	mirror-image polydactyly 1	protein-coding
mm_21927.1	chr2	166996222	166996256	-	1	NA	promoter-TSS (NM_011490)	promoter-TSS (NM_011490)	60	NM_011490	20853	Mm.73276	NM_011490	ENSMUSG00000039536	Stau1	5830401L18Rik|AW549911|C85792|Stau	staufen (RNA binding protein) homolog 1 (Drosophila)	protein-coding
mm_163824.1	chr14	19416874	19416884	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	185708	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_49276.1	chr6	17637020	17637055	+	1	NA	promoter-TSS (NM_007604)	promoter-TSS (NM_007604)	-61	NM_007604	12343	Mm.392504	NM_007604	ENSMUSG00000015733	Capza2	1110053K06Rik|AW208808|Cappa2	capping protein (actin filament) muscle Z-line, alpha 2	protein-coding
mm_152351.1	chr19	9992957	9992993	-	1	NA	exon (NM_011913, exon 4 of 12)	exon (NM_011913, exon 4 of 12)	8658	NM_011913	24115	Mm.31577	NM_011913	ENSMUSG00000037418	Best1	Bmd|Vmd2|mBest1	bestrophin 1	protein-coding
mm_68845.1	chr7	126364910	126364922	-	1	NA	intron (NM_010689, intron 8 of 11)	intron (NM_010689, intron 8 of 11)	3129	NR_106025	102466797		NR_106025	ENSMUSG00000099017	Mir7058	Gm27766|mmu-mir-7058	microRNA 7058	ncRNA
mm_49952.1	chr6	40480309	40480312	+	1	NA	intron (NM_212468, intron 6 of 6)	B1_Mur4|SINE|Alu	8842	NM_001286663	381760	Mm.276356	NM_028358	ENSMUSG00000029911	Ssbp1	2810480P10Rik|G630031O20Rik|MtSSB|mtDBP	single-stranded DNA binding protein 1	protein-coding
mm_6844.1	chr1	84236925	84236935	-	1	NA	intron (NM_001003948, intron 1 of 2)	intron (NM_001003948, intron 1 of 2)	-17969	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_51804.1	chr6	88724668	88724751	+	1	NA	promoter-TSS (NM_001166251)	promoter-TSS (NM_001166251)	5	NM_001166251	23945	Mm.272197	NM_011844	ENSMUSG00000033174	Mgll	AA589436|Magl|Mgl	monoglyceride lipase	protein-coding
mm_112373.1	chr12	119210256	119210257	-	1	NA	intron (NM_177290, intron 1 of 13)	intron (NM_177290, intron 1 of 13)	28020	NM_177290	320910	Mm.217000	NM_177290	ENSMUSG00000025321	Itgb8	4832412O06Rik	integrin beta 8	protein-coding
mm_69049.1	chr7	126861691	126861728	-	1	NA	promoter-TSS (NM_153580)	promoter-TSS (NM_153580)	-246	NM_153580	233875	Mm.486253	NM_153580	ENSMUSG00000030689	Ino80e	AI225782|AI854876|Ccdc85|Ccdc95	INO80 complex subunit E	protein-coding
mm_120656.1	chr14	70531702	70531712	+	1	NA	intron (NM_145219, intron 1 of 7)	intron (NM_145219, intron 1 of 7)	886	NM_145219	213469	Mm.41708	NM_145219	ENSMUSG00000033595	Lgi3	AI841179|AW049851	leucine-rich repeat LGI family, member 3	protein-coding
mm_58492.1	chr7	3694588	3694590	+	1	NA	promoter-TSS (NM_024168)	promoter-TSS (NM_024168)	81	NM_024168	66078	Mm.379100	NM_024168	ENSMUSG00000035585	Tsen34	0610027F08Rik|Leng5	tRNA splicing endonuclease subunit 34	protein-coding
mm_125055.1	chr15	25910068	25910076	+	1	NA	intron (NM_001034851, intron 3 of 8)	intron (NM_001034851, intron 3 of 8)	-23480	NM_001277318	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_152883.1	chr19	24555820	24555888	-	1	NA	promoter-TSS (NM_008846)	promoter-TSS (NM_008846)	-27	NM_008846	18719	Mm.217214	NM_008846	ENSMUSG00000024867	Pip5k1b	PI4P5K-I[b]|PIP5K1-beta|PIP5KIbeta|Pipk5b|STM7	phosphatidylinositol-4-phosphate 5-kinase, type 1 beta	protein-coding
mm_97428.1	chr11	78073225	78073237	+	1	NA	promoter-TSS (NR_105850)	promoter-TSS (NR_105850)	10	NR_105850	102466649		NR_105850	ENSMUSG00000104813	Mir451b	mmu-mir-451b	microRNA 451b	ncRNA
mm_39239.1	chr5	3270375	3270385	+	1	NA	Intergenic	Intergenic	-73513	NM_009873	12571	Mm.31672	NM_009873	ENSMUSG00000040274	Cdk6	AI504062|Crk2	cyclin-dependent kinase 6	protein-coding
mm_41030.1	chr5	85778284	85778287	+	1	NA	Intergenic	RMER19C|LTR|ERVK	287298	NM_001345902	12617	Mm.4649	NM_007683	ENSMUSG00000029253	Cenpc1	CENP-C|Cenpc	centromere protein C1	protein-coding
mm_124104.1	chr14	79301075	79301092	-	1	NA	intron (NM_025427, intron 1 of 4)	CpG	552	NM_025427	66214	Mm.29811	NM_025427	ENSMUSG00000022018	Rgcc	1190002H23Rik|Rgc-32|Rgc32	regulator of cell cycle	protein-coding
mm_12534.1	chr2	72285705	72285749	+	1	NA	promoter-TSS (NM_178084)	promoter-TSS (NM_178084)	26	NM_178084	65964	Mm.304143	NM_023057	ENSMUSG00000004085	Map3k20	AV006891|B230120H23Rik|MLTK|MLTKalpha|MLTKbeta|Zak	mitogen-activated protein kinase kinase kinase 20	protein-coding
mm_75057.1	chr8	33642366	33642403	-	1	NA	promoter-TSS (NM_178648)	promoter-TSS (NM_178648)	-408	NM_178648	108159	Mm.29301	NM_178648	ENSMUSG00000052906	Ubxn8	D0H8S2298E|Rep-8|Rep8h|Ubxd6	UBX domain protein 8	protein-coding
mm_65449.1	chr7	25412808	25412816	-	1	NA	promoter-TSS (NM_153576)	promoter-TSS (NM_153576)	74	NM_153576	232983	Mm.10545	NM_153576	ENSMUSG00000060188	Cxcl17	VCC-1|Vcc1	chemokine (C-X-C motif) ligand 17	protein-coding
mm_79432.1	chr9	56027515	56027532	+	1	NA	promoter-TSS (NR_033529)	promoter-TSS (NR_033529)	-113	NR_033529	665005	Mm.384788	NR_033529		Gm7444	EG665005	ring finger protein 19A pseudogene	pseudo
mm_152370.1	chr19	10183457	10183469	-	1	NA	intron (NM_146094, intron 1 of 11)	intron (NM_146094, intron 1 of 11)	575	NM_146094	76267	Mm.30158	NM_146094	ENSMUSG00000010663	Fads1	0710001O03Rik|A930006B21Rik|AI317215|DSD	fatty acid desaturase 1	protein-coding
mm_89221.1	chr10	86908717	86908726	+	1	NA	intron (NM_138673, intron 31 of 68)	intron (NM_138673, intron 31 of 68)	99221	NM_138673	192188	Mm.279611	NM_138673	ENSMUSG00000035459	Stab2	FEEL-2|FELL|MFEEL-2|STAB-2	stabilin 2	protein-coding
mm_155269.1	chrX	59179614	59179637	+	1	NA	intron (NM_001290414, intron 3 of 6)	intron (NM_001290414, intron 3 of 6)	-13537	NM_001290415	14168	Mm.7995	NM_010200	ENSMUSG00000031137	Fgf13	Fhf2	fibroblast growth factor 13	protein-coding
mm_74708.1	chr8	17115064	17115065	-	1	NA	intron (NM_053171, intron 2 of 69)	intron (NM_053171, intron 2 of 69)	420321	NM_053171	94109	Mm.436988	NM_053171	ENSMUSG00000060924	Csmd1	B930082H09|mKIAA1890	CUB and Sushi multiple domains 1	protein-coding
mm_72943.1	chr8	91759177	91759183	+	1	NA	Intergenic	Intergenic	42474	NM_001253822	16373	Mm.238044	NM_008393	ENSMUSG00000031734	Irx3	AI894186	Iroquois related homeobox 3	protein-coding
mm_99048.1	chr11	99041898	99041938	+	1	NA	intron (NM_010517, intron 1 of 3)	intron (NM_010517, intron 1 of 3)	658	NM_010517	16010	Mm.233799	NM_010517	ENSMUSG00000017493	Igfbp4	AI875747|Deb2|IGFBP-4	insulin-like growth factor binding protein 4	protein-coding
mm_118845.1	chr14	25663230	25663245	+	1	NA	3' UTR (NM_183208, exon 24 of 24)	3' UTR (NM_183208, exon 24 of 24)	-30933	NM_134084	105675	Mm.41656	NM_134084	ENSMUSG00000021868	Ppif	AW457192|CyP-D|CyP-F|CypD|PPIase	peptidylprolyl isomerase F (cyclophilin F)	protein-coding
mm_157455.1	chrX	43428948	43428956	-	1	NA	Intergenic	Intergenic	-154168	NM_011855	23963	Mm.327698	NM_011855	ENSMUSG00000016150	Tenm1	Odz1|Odz2|TCAP-1|Ten-m1|ten-1	teneurin transmembrane protein 1	protein-coding
mm_158878.1	chrY	4167829	4167868	-	1	NA	Intergenic	Intergenic	396175	NM_011253	19657	Mm.4711	NM_011253	ENSMUSG00000094658	Rbmy	RBM|Rbm1|Rbm1-rs1|Rbmy1a1|Rbmy1a1-rs1|Rbmy1b	RNA binding motif protein, Y chromosome	protein-coding
mm_100264.1	chr11	117333479	117333488	+	1	NA	intron (NM_001113488, intron 1 of 9)	intron (NM_001113488, intron 1 of 9)	1170	NM_001113488	53860	Mm.38450	NM_017380	ENSMUSG00000059248	Sept9	MSF1|Msf|PNUTL4|Sint1	septin 9	protein-coding
mm_11791.1	chr2	43128781	43128788	+	1	NA	Intergenic	RMER1B|Other|Other	-426541	NM_001289593	70789	Mm.105278	NM_027552	ENSMUSG00000026866	Kynu	4432411A05Rik	kynureninase (L-kynurenine hydrolase)	protein-coding
mm_137886.1	chr17	31677925	31677939	+	1	NA	promoter-TSS (NM_001278570)	promoter-TSS (NM_001278570)	1	NM_001278570	12954	Mm.1228	NM_013501	ENSMUSG00000024041	Cryaa	Acry-1|Crya-1|Crya1|DAcry-1|lop18	crystallin, alpha A	protein-coding
mm_71053.1	chr8	33697674	33697705	+	1	NA	3' UTR (NM_010344, exon 13 of 13)	3' UTR (NM_010344, exon 13 of 13)	-34225	NM_001167921	68153	Mm.286104	NM_026584	ENSMUSG00000031585	Gtf2e2	34kDa|AI462509|C330006J08Rik	general transcription factor II E, polypeptide 2 (beta subunit)	protein-coding
mm_57733.1	chr6	128970289	128970306	-	1	NA	promoter-TSS (NM_001316752)	promoter-TSS (NM_001316752)	-863	NM_001168224	70809	Mm.439891	NM_027562	ENSMUSG00000000248	Clec2g	4632413B12Rik|Clr-c|Clr-d|Clrc|Clrd|Clrx|Ddv10|Ocilrp1	C-type lectin domain family 2, member g	protein-coding
mm_114288.1	chr13	58806565	58806622	+	1	NA	promoter-TSS (NM_008745)	promoter-TSS (NM_008745)	24	NM_008745	18212	Mm.130054	NM_008745	ENSMUSG00000055254	Ntrk2	GP145-TrkB/GP95-TrkB|Tkrb|trk-B|trkB	neurotrophic tyrosine kinase, receptor, type 2	protein-coding
mm_39949.1	chr5	32001366	32001390	+	1	NA	exon (NM_181282, exon 8 of 12)	exon (NM_181282, exon 8 of 12)	-135094	NM_008037	14284	Mm.24684	NM_008037	ENSMUSG00000029135	Fosl2	Fra-2	fos-like antigen 2	protein-coding
mm_114852.1	chr13	93102977	93102988	+	1	NA	intron (NM_023821, intron 1 of 12)	ORR1B1|LTR|ERVL-MaLR	8149	NR_046182	408254	Mm.474857	NR_046182		A630019I02Rik	-	RIKEN cDNA A630019I02 gene	ncRNA
mm_23323.1	chr3	53463896	53463906	+	1	NA	promoter-TSS (NM_172501)	promoter-TSS (NM_172501)	84	NM_173382	212127	Mm.491292	NM_173382	ENSMUSG00000049504	Proser1	2810046L04Rik|9330161F11	proline and serine rich 1	protein-coding
mm_66229.1	chr7	35056563	35056586	-	1	NA	promoter-TSS (NM_009884)	promoter-TSS (NM_009884)	-8	NM_009884	12611	Mm.273090	NM_009884	ENSMUSG00000056216	Cebpg	C/EBP[g]|C/EBPgamma|GPE1-BP|Gpe1bp|Ig/EBP	CCAAT/enhancer binding protein (C/EBP), gamma	protein-coding
mm_172924.1	chr9	69453718	69453718	+	1	NA	promoter-TSS (NM_007585)	promoter-TSS (NM_007585)	35	NM_007585	12306	Mm.238343	NM_007585	ENSMUSG00000032231	Anxa2	AW215814|Cal1h	annexin A2	protein-coding
mm_29492.1	chr3	115888002	115888012	-	1	NA	promoter-TSS (NM_027193)	promoter-TSS (NM_027193)	52	NR_027894	68161	Mm.392043	NR_015487	ENSMUSG00000054426	A930005H10Rik	-	RIKEN cDNA A930005H10 gene	ncRNA
mm_100271.1	chr11	117665504	117665514	+	1	NA	intron (NM_198022, intron 1 of 21)	(T)n|Simple_repeat|Simple_repeat	11220	NM_198022	217351	Mm.40272	NM_198022	ENSMUSG00000025571	Tnrc6c	9930033H14Rik|mKIAA1582	trinucleotide repeat containing 6C	protein-coding
mm_135354.1	chr16	43861977	43861985	-	1	NA	3' UTR (NM_029128, exon 8 of 8)	3' UTR (NM_029128, exon 8 of 8)	27695	NM_029128	106248	Mm.275354	NM_029128	ENSMUSG00000022704	Qtrtd1	3110012M05Rik|4930470H18Rik|AI648807|Qtrt2	queuine tRNA-ribosyltransferase domain containing 1	protein-coding
mm_58873.1	chr7	16983174	16983183	+	1	NA	Intergenic	Intergenic	-11410	NM_001101535	434130	Mm.459162	NM_001101535	ENSMUSG00000041117	Ccdc8	ENSMUSG00000041117	coiled-coil domain containing 8	protein-coding
mm_83556.1	chr9	46242738	46242738	-	1	NA	exon (NM_007468, exon 3 of 3)	exon (NM_007468, exon 3 of 3)	1894	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_150198.1	chr19	32757577	32757587	+	1	NA	promoter-TSS (NM_008960)	promoter-TSS (NM_008960)	5	NM_008960	19211	Mm.245395	NM_008960	ENSMUSG00000013663	Pten	2310035O07Rik|A130070J02Rik|AI463227|B430203M17Rik|MMAC1|TEP1	phosphatase and tensin homolog	protein-coding
mm_51269.1	chr6	72104202	72104206	+	1	NA	intron (NM_011375, intron 1 of 6)	L2c|LINE|L2	6596	NM_011375	20454	Mm.38248	NM_011375	ENSMUSG00000056091	St3gal5	3S-T|Siat9|[a]2	ST3 beta-galactoside alpha-2,3-sialyltransferase 5	protein-coding
mm_72540.1	chr8	83997303	83997315	+	1	NA	promoter-TSS (NM_001081415)	promoter-TSS (NM_001081415)	-363	NM_001081415	666704	Mm.298091	NM_001081415	ENSMUSG00000079003	Samd1	AA589507	sterile alpha motif domain containing 1	protein-coding
mm_50356.1	chr6	48602002	48602043	+	1	NA	Intergenic	CpG	8139	NM_001079904	58887	Mm.219183	NM_175099	ENSMUSG00000052751	Repin1	AI425994|Ap4|E430037F08Rik|Zfp-464|Zfp464	replication initiator 1	protein-coding
mm_89930.1	chr10	111233704	111233716	+	1	NA	intron (NM_175489, intron 4 of 23)	intron (NM_175489, intron 4 of 23)	-64969	NM_027914	71769	Mm.45256	NM_027914	ENSMUSG00000035759	Bbs10	1300007O09Rik|AI452285	Bardet-Biedl syndrome 10 (human)	protein-coding
mm_170773.1	chr2	163645119	163645119	-	1	NA	promoter-TSS (NM_012032)	promoter-TSS (NM_012032)	24	NM_012032	26943	Mm.218473	NM_012032	ENSMUSG00000017707	Serinc3	AA959945|AA960047|AIGP1|DIFF33|TMS-1|Tde1	serine incorporator 3	protein-coding
mm_105827.1	chr11	113172952	113172958	-	1	NA	intron (NR_015556, intron 1 of 2)	intron (NR_015556, intron 1 of 2)	28883	NR_015556	72386	Mm.266961	NR_015556	ENSMUSG00000087259	2610035D17Rik	-	RIKEN cDNA 2610035D17 gene	ncRNA
mm_73607.1	chr8	110039450	110039478	+	1	NA	promoter-TSS (NM_011998)	promoter-TSS (NM_011998)	-130	NM_011998	26887	Mm.89207	NM_011998	ENSMUSG00000035930	Chst4	GST-3|Gn6st-2|HEC-GlcNAc6ST	carbohydrate (chondroitin 6/keratan) sulfotransferase 4	protein-coding
mm_51680.1	chr6	86443820	86443863	+	1	NA	5' UTR (NM_001243742, exon 2 of 10)	5' UTR (NM_001243742, exon 2 of 10)	5195	NM_001243741	232196	Mm.404040	NM_146170	ENSMUSG00000046679	C87436	-	expressed sequence C87436	protein-coding
mm_92061.1	chr10	62513540	62513549	-	1	NA	Intergenic	Intergenic	-5789	NM_011157	19073	Mm.338790	NM_011157	ENSMUSG00000020077	Srgn	Prg|Prg1|Sgc	serglycin	protein-coding
mm_112610.1	chr13	14630238	14630296	+	1	NA	promoter-TSS (NM_134067)	promoter-TSS (NM_134067)	9	NM_134067	105351	Mm.41450	NM_134067	ENSMUSG00000039182	AW209491	-	expressed sequence AW209491	protein-coding
mm_105590.1	chr11	106732545	106732557	-	1	NA	Intergenic	PB1D9|SINE|Alu	-17270	NM_001305157	18613	Mm.343951	NM_008816	ENSMUSG00000020717	Pecam1	C85791|Cd31|PECAM-1|Pecam	platelet/endothelial cell adhesion molecule 1	protein-coding
mm_69391.1	chr7	131410326	131410346	-	1	NA	promoter-TSS (NM_025826)	promoter-TSS (NM_025826)	142	NM_175115	67143	Mm.334273	NM_175115	ENSMUSG00000040167	Ikzf5	2610034F18Rik|PEGASUS|Zfpn1a5	IKAROS family zinc finger 5	protein-coding
mm_44535.1	chr5	24526734	24526739	-	1	NA	exon (NM_015739, exon 1 of 2)	exon (NM_015739, exon 1 of 2)	112	NM_015739	231044	Mm.246596	NM_015739	ENSMUSG00000067724	Gbx1	Gbx-1	gastrulation brain homeobox 1	protein-coding
mm_71553.1	chr8	48136132	48136168	+	1	NA	intron (NM_178788, intron 3 of 5)	intron (NM_178788, intron 3 of 5)	26137	NM_001161515	320685	Mm.121549	NM_178788	ENSMUSG00000031562	Dctd	6030466N05Rik	dCMP deaminase	protein-coding
mm_62130.1	chr7	97081557	97081565	+	1	NA	promoter-TSS (NM_010248)	promoter-TSS (NM_010248)	-190	NM_001162477	14389	Mm.42033	NM_010248	ENSMUSG00000004508	Gab2	AI463667|D130058I17Rik|p97	growth factor receptor bound protein 2-associated protein 2	protein-coding
mm_25209.1	chr3	103832742	103832840	+	1	NA	promoter-TSS (NM_001142960)	promoter-TSS (NM_001142960)	95	NM_001142960	229672	Mm.297245	NM_001142959	ENSMUSG00000044165	Bcl2l15	Bfk|Gm566	BCLl2-like 15	protein-coding
mm_23307.1	chr3	52739727	52739736	+	1	NA	promoter-TSS (NR_038079)	promoter-TSS (NR_038079)	7	NR_038079	329639	Mm.131245	NR_038079	ENSMUSG00000102785	Gm2447	100039832|A530017F20	predicted gene 2447	ncRNA
mm_119902.1	chr14	54948152	54948170	+	1	NA	TTS (NR_029724)	TTS (NR_029724)	981	NR_029724	387204		NR_029724	ENSMUSG00000065432	Mir208a	Mirn208|Mirn208a|mir-208|mir-208a|mmu-mir-208	microRNA 208a	ncRNA
mm_139867.1	chr17	70522150	70522169	+	1	NA	promoter-TSS (NM_001128180)	promoter-TSS (NM_001128180)	49	NM_001128180	224997	Mm.311840	NM_027712	ENSMUSG00000003279	Dlgap1	4933422O14Rik|9630002F18|AI845682|AI848168|BB075781|D17Bwg0511e|GKAP/SAPAP|GKPA/SAPAP|Gkap|Sapap1|mKIAA4162	discs, large (Drosophila) homolog-associated protein 1	protein-coding
mm_72460.1	chr8	83251287	83251303	+	1	NA	intron (NM_027758, intron 7 of 17)	intron (NM_027758, intron 7 of 17)	-39053	NM_009463	22227	Mm.4177	NM_009463	ENSMUSG00000031710	Ucp1	AI385626|Slc25a7|Ucp	uncoupling protein 1 (mitochondrial, proton carrier)	protein-coding
mm_8822.1	chr1	162274622	162274626	-	1	NA	intron (NM_001038619, intron 12 of 20)	intron (NM_001038619, intron 12 of 20)	51256	NR_029796	387210		NR_029796	ENSMUSG00000065516	Mir214	Mirn214|mir-214|mmu-mir-214	microRNA 214	ncRNA
mm_151330.1	chr19	55894448	55894461	+	1	NA	promoter-TSS (NM_001142924)	promoter-TSS (NM_001142924)	-867	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_158841.1	chrX	169187206	169187210	-	1	NA	promoter-TSS (NM_001081978)	promoter-TSS (NM_001081978)	1	NM_001290371	11704	Mm.391342	NM_009666	ENSMUSG00000031354	Amelx	ALGN|AMGL|AMGX|Amel|Amg|LRAP|Rgsc888	amelogenin, X-linked	protein-coding
mm_102301.1	chr11	55607820	55607822	-	1	NA	5' UTR (NM_020492, exon 1 of 9)	5' UTR (NM_020492, exon 1 of 9)	377	NM_001290821	14654	Mm.89320	NM_020492	ENSMUSG00000000263	Glra1	nmf11|oscillator|ot|spasmodic|spd	glycine receptor, alpha 1 subunit	protein-coding
mm_45408.1	chr5	66299925	66299932	-	1	NA	3' UTR (NM_009686, exon 18 of 18)	3' UTR (NM_009686, exon 18 of 18)	37737	NM_001201416	11787	Mm.5159	NM_009686	ENSMUSG00000029207	Apbb2	2310007D03Rik|FE65L1|Rirl1|TR2L|Zfra	amyloid beta (A4) precursor protein-binding, family B, member 2	protein-coding
mm_64702.1	chr7	4547461	4547506	-	1	NA	promoter-TSS (NM_016908)	promoter-TSS (NM_016908)	-916	NM_016908	53420	Mm.358663	NM_016908	ENSMUSG00000004961	Syt5	SytV	synaptotagmin V	protein-coding
mm_24826.1	chr3	95653751	95653763	+	1	NA	Intergenic	Intergenic	-4964	NM_008562	17210	Mm.1639	NM_008562	ENSMUSG00000038612	Mcl1	AW556805|Mcl-1	myeloid cell leukemia sequence 1	protein-coding
mm_134017.1	chr16	4879873	4879892	-	1	NA	promoter-TSS (NM_145359)	promoter-TSS (NM_145359)	-31	NM_145359	207740	Mm.268895	NM_145359	ENSMUSG00000039568	Ubald1	1500031H01Rik|BC013706|Fam100a	UBA-like domain containing 1	protein-coding
mm_87068.1	chr10	29144114	29144126	+	1	NA	5' UTR (NM_026138, exon 1 of 7)	5' UTR (NM_026138, exon 1 of 7)	124	NM_026138	67412	Mm.390264	NM_026138	ENSMUSG00000038916	Soga3	6330407J23Rik	SOGA family member 3	protein-coding
mm_115064.1	chr13	101060472	101060479	+	1	NA	Intergenic	B4A|SINE|B4	-171652	NR_046158	328324	Mm.402274	NR_046158		5930438M14Rik	5930438M14	RIKEN cDNA 5930438M14 gene	ncRNA
mm_155261.1	chrX	57920055	57920061	+	1	NA	Intergenic	Intergenic	-110570	NM_009575	22773	Mm.255890	NM_009575	ENSMUSG00000067860	Zic3	Bn|Ka	zinc finger protein of the cerebellum 3	protein-coding
mm_69939.1	chr7	142095311	142095315	-	1	NA	promoter-TSS (NM_008748)	promoter-TSS (NM_008748)	-29	NM_008748	18218	Mm.39725	NM_008748	ENSMUSG00000037887	Dusp8	5530400B01Rik|AI593498|Nttp1	dual specificity phosphatase 8	protein-coding
mm_129884.1	chr15	83489550	83489558	-	1	NA	exon (NM_178869, exon 11 of 12)	exon (NM_178869, exon 11 of 12)	21353	NM_178869	319953	Mm.235007	NM_178869	ENSMUSG00000022442	Ttll1	6330444E16Rik|AV014541	tubulin tyrosine ligase-like 1	protein-coding
mm_19199.1	chr2	84473995	84474008	-	1	NA	5' UTR (NM_011576, exon 1 of 9)	5' UTR (NM_011576, exon 1 of 9)	173	NM_011576	21788	Mm.124316	NM_011576	ENSMUSG00000027082	Tfpi	A630013F22Rik|AW552122|EPI|LACI	tissue factor pathway inhibitor	protein-coding
mm_41378.1	chr5	90722375	90722380	+	1	NA	Intergenic	Intergenic	-36921	NM_009141	20311	Mm.4660	NM_009141	ENSMUSG00000029371	Cxcl5	AMCF-II|Cxcl6|ENA-78|GCP-2|LIX|Scyb5|Scyb6	chemokine (C-X-C motif) ligand 5	protein-coding
mm_82192.1	chr9	123965026	123965035	+	1	NA	intron (NM_009912, intron 1 of 1)	intron (NM_009912, intron 1 of 1)	3662	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_17396.1	chr2	27142430	27142481	-	1	NA	promoter-TSS (NM_175427)	promoter-TSS (NM_175427)	22	NM_175427	109349	Mm.314080	NM_175427	ENSMUSG00000009216	Fam163b	C630035N08Rik	family with sequence similarity 163, member B	protein-coding
mm_457.1	chr1	36272791	36272792	+	1	NA	intron (NM_153408, intron 1 of 3)	intron (NM_153408, intron 1 of 3)	634	NM_153408	214854	Mm.389110	NM_153408	ENSMUSG00000047180	Neurl3	2010300P06Rik|Lincr	neuralized E3 ubiquitin protein ligase 3	protein-coding
mm_73288.1	chr8	104926293	104926303	+	1	NA	promoter-TSS (NM_001163756)	promoter-TSS (NM_001163756)	38	NM_172759	234673	Mm.441134	NM_172759	ENSMUSG00000031886	Ces2e	9030624L02Rik|Ces5	carboxylesterase 2E	protein-coding
mm_98397.1	chr11	94327985	94328029	+	1	NA	promoter-TSS (NM_027799)	promoter-TSS (NM_027799)	6	NM_146024	71452	Mm.141054	NM_027799	ENSMUSG00000020864	Ankrd40	1110011C06Rik|5530600A18Rik|Gcap15	ankyrin repeat domain 40	protein-coding
mm_106762.1	chr12	4507239	4507240	+	1	NA	Intergenic	Intergenic	-16874	NR_136891	102634330	Mm.402324	NR_136891		Gm31938	-	predicted gene, 31938	ncRNA
mm_70687.1	chr8	15011378	15011393	+	1	NA	intron (NM_029116, intron 1 of 1)	CpG	360	NM_029116	74901	Mm.46675	NM_029116	ENSMUSG00000055675	Kbtbd11	2900016B01Rik|4930465M17Rik|mKIAA0711	kelch repeat and BTB (POZ) domain containing 11	protein-coding
mm_103249.1	chr11	70969954	70969978	-	1	NA	promoter-TSS (NM_001276406)	promoter-TSS (NM_001276406)	7	NM_172394	19069	Mm.288962	NM_172394	ENSMUSG00000040667	Nup88	Nup84|Prei2	nucleoporin 88	protein-coding
mm_114079.1	chr13	54571021	54571069	+	1	NA	Intergenic	RLTR30|LTR|ERV1	-3968	NM_019968	56795	Mm.89484	NM_019968	ENSMUSG00000025870	Arl10	Arl10a|Arm1	ADP-ribosylation factor-like 10	protein-coding
mm_170694.1	chr2	132285928	132285943	+	1	NA	promoter-TSS (NM_001291039)	promoter-TSS (NM_001291039)	-4	NM_001291039	110911	Mm.284503	NM_138651	ENSMUSG00000058793	Cds2	5730450N06Rik|5730460C18Rik|AI854580|D2Wsu127e	CDP-diacylglycerol synthase (phosphatidate cytidylyltransferase) 2	protein-coding
mm_73919.1	chr8	119754210	119754240	+	1	NA	exon (NM_026922, exon 24 of 27)	exon (NM_026922, exon 24 of 27)	24191	NM_028883	74347	Mm.358759	NM_028883	ENSMUSG00000034105	Tldc1	4632415K11Rik|Kiaa1609	TBC/LysM associated domain containing 1	protein-coding
mm_100023.1	chr11	114903543	114903561	+	1	NA	3' UTR (NM_170758, exon 7 of 7)	3' UTR (NM_170758, exon 7 of 7)	13511	NM_170758	217303	Mm.294439	NM_170758	ENSMUSG00000034652	Cd300a	B230315M08Rik|Clm8|LMIR1|MAIR-I|MAIR-Ia|MMAC8|Pigr4|mcpir1	CD300A molecule	protein-coding
mm_104666.1	chr11	97629718	97629745	-	1	NA	promoter-TSS (NM_175332)	promoter-TSS (NM_175332)	-15	NM_175332	103551	Mm.24506	NM_175332	ENSMUSG00000043439	Epop	AA409164|AI413509|AW539173|E13|E130012A19Rik|esPRC2p48	elongin BC and polycomb repressive complex 2 associated protein	protein-coding
mm_61100.1	chr7	51880289	51880295	+	1	NA	intron (NM_008087, intron 1 of 7)	intron (NM_008087, intron 1 of 7)	1325	NM_001330607	14453	Mm.207360	NM_008087	ENSMUSG00000030498	Gas2	Gas-2	growth arrest specific 2	protein-coding
mm_152703.1	chr19	17339664	17339676	-	1	NA	promoter-TSS (NM_001136484)	promoter-TSS (NM_001136484)	-165	NM_001136484	14537	Mm.244825	NM_010265	ENSMUSG00000038843	Gcnt1	5630400D21Rik|B130048E03|C2 GlcNAcT|C2GNT|IGnT	glucosaminyl (N-acetyl) transferase 1, core 2	protein-coding
mm_70378.1	chr8	10153941	10153984	+	1	NA	promoter-TSS (NM_001319151)	promoter-TSS (NM_001319151)	51	NM_001319151	244281	Mm.422761	NM_001081397	ENSMUSG00000039057	Myo16	BM140241|C230040D10Rik|Gm1105|NYAP3|mKIAA0865	myosin XVI	protein-coding
mm_68481.1	chr7	110956882	110956892	-	1	NA	intron (NM_194464, intron 1 of 20)	ORR1E|LTR|ERVL-MaLR	-10700	NM_010826	17540	Mm.250023	NM_010826	ENSMUSG00000005611	Mrvi1	BB115629|Irag|Ris1	MRV integration site 1	protein-coding
mm_86727.1	chr10	19062808	19062816	+	1	NA	Intergenic	Intergenic	-47402	NM_009397	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_55369.1	chr6	57703857	57703903	-	1	NA	intron (NM_133737, intron 1 of 8)	Lx8|LINE|L1	1425	NM_133737	71835	Mm.274904	NM_133737	ENSMUSG00000062190	Lancl2	1700003F10Rik	LanC (bacterial lantibiotic synthetase component C)-like 2	protein-coding
mm_100675.1	chr11	3409117	3409159	-	1	NA	promoter-TSS (NM_010718)	promoter-TSS (NM_010718)	100	NM_010718	16886	Mm.124176	NM_010718	ENSMUSG00000020451	Limk2	Limk-2|whe	LIM motif-containing protein kinase 2	protein-coding
mm_77323.1	chr8	119417983	119417990	-	1	NA	Intergenic	Intergenic	-19176	NM_027950	71839	Mm.272357	NM_027950	ENSMUSG00000074063	Osgin1	1700012B18Rik|Okl38	oxidative stress induced growth inhibitor 1	protein-coding
mm_21427.1	chr2	158231170	158231173	-	1	NA	Intergenic	Intergenic	-1947	NM_177657	228846	Mm.187574	NM_177657	ENSMUSG00000037813	D630003M21Rik	-	RIKEN cDNA D630003M21 gene	protein-coding
mm_142700.1	chr17	47867844	47867862	-	1	NA	3' UTR (NM_028767, exon 17 of 17)	3' UTR (NM_028767, exon 17 of 17)	-33162	NM_001109973	17240	Mm.329100	NM_010783	ENSMUSG00000032717	Mdfi	I-mf|I-mfa	MyoD family inhibitor	protein-coding
mm_115024.1	chr13	99007082	99007086	+	1	NA	Intergenic	Intergenic	-22519	NM_027064	69382	Mm.45466	NM_027064	ENSMUSG00000045022	1700024P04Rik	H2bl1|Subh2bv	RIKEN cDNA 1700024P04 gene	protein-coding
mm_50147.1	chr6	41543626	41543642	+	1	NA	Intergenic	Intergenic	21858	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_15528.1	chr2	158382846	158382857	+	1	NA	3' UTR (NM_175692, exon 5 of 5)	3' UTR (NM_175692, exon 5 of 5)	7213	NM_175692	319317	Mm.294494	NM_175692	ENSMUSG00000044349	Snhg11	A930034L06Rik|AI854265|AL022637|AW319638|E130013N09Rik	small nucleolar RNA host gene 11	protein-coding
mm_32668.1	chr4	115563680	115563699	+	1	NA	promoter-TSS (NM_001252539)	promoter-TSS (NM_001252539)	40	NM_201640	666168	Mm.482086	NM_201640	ENSMUSG00000028712	Cyp4a31	-	cytochrome P450, family 4, subfamily a, polypeptide 31	protein-coding
mm_119131.1	chr14	31160682	31160692	+	1	NA	intron (NM_138672, intron 11 of 68)	intron (NM_138672, intron 11 of 68)	7954	NM_138672	192187	Mm.220821	NM_138672	ENSMUSG00000042286	Stab1	FEEL-1|FELE-1|MFEEL-1|MS-1|STAB-1|mKIAA0246	stabilin 1	protein-coding
mm_126346.1	chr15	79905841	79905846	+	1	NA	intron (NM_001347041, intron 5 of 7)	intron (NM_001347041, intron 5 of 7)	10820	NM_001347041	80287	Mm.284059	NM_030255	ENSMUSG00000009585	Apobec3	Apobec|Arp3|BC003314|Cem15|Rfv3	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 3	protein-coding
mm_141815.1	chr17	34605748	34605765	-	1	NA	promoter-TSS (NM_001163379)	promoter-TSS (NM_001163379)	-105	NM_001163379	55979	Mm.8684	NM_018862	ENSMUSG00000034254	Agpat1	1-AGP|1-AGPAT|AW047140	1-acylglycerol-3-phosphate O-acyltransferase 1 (lysophosphatidic acid acyltransferase, alpha)	protein-coding
mm_27176.1	chr3	34079061	34079069	-	1	NA	intron (NM_001026211, intron 4 of 5)	intron (NM_001026211, intron 4 of 5)	2289	NM_001286972	67713	Mm.274266	NM_026332	ENSMUSG00000027679	Dnajc19	1810055D05Rik|AA959924|Tim14	DnaJ heat shock protein family (Hsp40) member C19	protein-coding
mm_37904.1	chr4	132732566	132732586	-	1	NA	promoter-TSS (NM_201368)	promoter-TSS (NM_201368)	-30	NM_201368	381560	Mm.44558	NM_201368	ENSMUSG00000037752	Xkr8	4931440N07Rik|AI597014|Gm1031|XRG8|mXkr8	X-linked Kx blood group related 8	protein-coding
mm_157010.1	chrX	7605375	7605402	-	1	NA	promoter-TSS (NM_138603)	promoter-TSS (NM_138603)	32	NM_138603	54638	Mm.288192	NM_138603	ENSMUSG00000031143	Ccdc22	AI481216|DXImx40e|Ppp1r3f|Sfc22	coiled-coil domain containing 22	protein-coding
mm_75306.1	chr8	41133698	41133755	-	1	NA	promoter-TSS (NM_001005863)	promoter-TSS (NM_001005863)	0	NM_001005863	102103	Mm.149438	NM_001005863	ENSMUSG00000045636	Mtus1	AI481402|ATBP135|Atip1|B430010I23Rik|B430305I03Rik|C85752|Cctsg1-440|MD44|MTSG1|mKIAA1288	mitochondrial tumor suppressor 1	protein-coding
mm_109926.1	chr12	8674065	8674094	-	1	NA	promoter-TSS (NM_001160219)	promoter-TSS (NM_001160219)	-55	NM_001160221	80913	Mm.341243	NM_030723	ENSMUSG00000020594	Pum2	5730503J23Rik|Pumm2	pumilio RNA-binding family member 2	protein-coding
mm_74167.1	chr8	123420630	123420643	+	1	NA	exon (NM_023279, exon 4 of 4)	exon (NM_023279, exon 4 of 4)	9072	NM_023279	22152	Mm.40068	NM_023279	ENSMUSG00000062380	Tubb3	3200002H15Rik|M(beta)3|M(beta)6	tubulin, beta 3 class III	protein-coding
mm_2862.1	chr1	131712621	131712632	+	1	NA	3' UTR (NM_145509, exon 6 of 6)	3' UTR (NM_145509, exon 6 of 6)	23931	NM_001311096	226421	Mm.44508	NM_145509	ENSMUSG00000052688	Rab7b	5430435G22Rik	RAB7B, member RAS oncogene family	protein-coding
mm_142704.1	chr17	47878876	47878887	-	1	NA	intron (NM_001110824, intron 5 of 16)	intron (NM_001110824, intron 5 of 16)	-44190	NM_001109973	17240	Mm.329100	NM_010783	ENSMUSG00000032717	Mdfi	I-mf|I-mfa	MyoD family inhibitor	protein-coding
mm_40020.1	chr5	33335541	33335571	+	1	NA	promoter-TSS (NM_021500)	promoter-TSS (NM_021500)	-16	NM_021500	59003	Mm.138617	NM_021500	ENSMUSG00000079562	Maea	1110030D19Rik|EMP|Gid9	macrophage erythroblast attacher	protein-coding
mm_122221.1	chr14	32460902	32460916	-	1	NA	5' UTR (NM_009891, exon 2 of 16)	5' UTR (NM_009891, exon 2 of 16)	3941	NM_021712	20508	Mm.190503	NM_021712	ENSMUSG00000100241	Slc18a3	VAChT|VAT	solute carrier family 18 (vesicular monoamine), member 3	protein-coding
mm_42276.1	chr5	114146718	114146735	+	1	NA	Intergenic	Intergenic	15570	NM_011677	22256	Mm.1393	NM_011677	ENSMUSG00000029591	Ung	UNG1|UNG2	uracil DNA glycosylase	protein-coding
mm_100465.1	chr11	119913803	119913854	+	1	NA	promoter-TSS (NM_001085498)	promoter-TSS (NM_001085498)	18	NM_001085498	208092	Mm.306673	NM_001085498	ENSMUSG00000025371	Chmp6	2400004G01Rik	charged multivesicular body protein 6	protein-coding
mm_93231.1	chr10	95323551	95323610	-	1	NA	5' UTR (NM_001330138, exon 1 of 3)	5' UTR (NM_001330138, exon 1 of 3)	129	NM_001330138	12905	Mm.473739	NM_009950	ENSMUSG00000045867	Cradd	RAIDD	CASP2 and RIPK1 domain containing adaptor with death domain	protein-coding
mm_96942.1	chr11	70540491	70540508	+	1	NA	5' UTR (NM_001302476, exon 1 of 10)	5' UTR (NM_001302476, exon 1 of 10)	227	NM_001302476	18806	Mm.260177	NM_008876	ENSMUSG00000020828	Pld2	PLD1C	phospholipase D2	protein-coding
mm_146362.1	chr18	82584362	82584377	+	1	NA	3' UTR (NM_010777, exon 7 of 7)	3' UTR (NM_010777, exon 7 of 7)	29861	NM_001025254	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_41052.1	chr5	86804193	86804208	+	1	NA	promoter-TSS (NM_177680)	promoter-TSS (NM_177680)	-66	NM_001347375	231386	Mm.196325	NM_177680	ENSMUSG00000035851	Ythdc1	A730098D12Rik|C80342|mKIAA1966	YTH domain containing 1	protein-coding
mm_65287.1	chr7	24435564	24435580	-	1	NA	intron (NM_199013, intron 2 of 2)	intron (NM_199013, intron 2 of 2)	10110	NM_199013	210145	Mm.33811	NM_199013	ENSMUSG00000062028	Irgc1	F630044M05Rik|Gm1102|Gm474|Ifgge|Iigp5|Irgc	immunity-related GTPase family, cinema 1	protein-coding
mm_161958.1	chr19	7267356	7267356	+	1	NA	promoter-TSS (NM_054048)	promoter-TSS (NM_054048)	-38	NM_054048	104383	Mm.283859	NM_054048	ENSMUSG00000024968	Rcor2	1A13|AW122124|CoREST|Rcor|Rcor1	REST corepressor 2	protein-coding
mm_118624.1	chr14	21179657	21179659	+	1	NA	intron (NM_001243041, intron 4 of 10)	intron (NM_001243041, intron 4 of 10)	103506	NM_001243041	11534	Mm.188734	NM_134079	ENSMUSG00000039197	Adk	2310026J05Rik|5033405D03Rik|AI255373|AI987814|Ak	adenosine kinase	protein-coding
mm_134231.1	chr16	11456299	11456300	-	1	NA	intron (NM_001290148, intron 6 of 13)	intron (NM_001290148, intron 6 of 13)	50651	NM_001290148	74478	Mm.325831	NM_028964	ENSMUSG00000071669	Snx29	4933437K13Rik|ENSMUSG00000079738|Gm11170|Gm1737|Gm930|Rundc2a	sorting nexin 29	protein-coding
mm_81543.1	chr9	110245507	110245518	+	1	NA	5' UTR (NM_013884, exon 1 of 5)	5' UTR (NM_013884, exon 1 of 5)	1729	NM_001166273	29873	Mm.38496	NM_013884	ENSMUSG00000032482	Cspg5	Caleb|Ngc	chondroitin sulfate proteoglycan 5	protein-coding
mm_102034.1	chr11	51833521	51833547	-	1	NA	intron (NM_199299, intron 4 of 11)	intron (NM_199299, intron 4 of 11)	23947	NM_199299	76901	Mm.259996	NM_199299	ENSMUSG00000020387	Jade2	1200017K05Rik|AI480685|Phf15|mKIAA0239	jade family PHD finger 2	protein-coding
mm_163538.1	chr13	13538517	13538545	-	1	NA	Intergenic	Intergenic	-51878	NM_010748	17101	Mm.342337	NM_010748	ENSMUSG00000019726	Lyst	D13Sfk13|beige|bg	lysosomal trafficking regulator	protein-coding
mm_113640.1	chr13	42069663	42069666	+	1	NA	intron (NM_007772, intron 2 of 8)	intron (NM_007772, intron 2 of 8)	17643	NM_007772	110521	Mm.4808	NM_007772	ENSMUSG00000021366	Hivep1	Cryabp1	human immunodeficiency virus type I enhancer binding protein 1	protein-coding
mm_83896.1	chr9	56136372	56136390	-	1	NA	3' UTR (NM_019793, exon 7 of 7)	3' UTR (NM_019793, exon 7 of 7)	24689	NM_019793	56434	Mm.28484	NM_019793	ENSMUSG00000032324	Tspan3	1700055K04Rik|TM4-A|Tm4sf8	tetraspanin 3	protein-coding
mm_93004.1	chr10	87007923	87007950	-	1	NA	promoter-TSS (NM_138673)	promoter-TSS (NM_138673)	6	NM_138673	192188	Mm.279611	NM_138673	ENSMUSG00000035459	Stab2	FEEL-2|FELL|MFEEL-2|STAB-2	stabilin 2	protein-coding
mm_92812.1	chr10	81406137	81406165	-	1	NA	exon (NM_008688, exon 7 of 10)	exon (NM_008688, exon 7 of 10)	10146	NR_106141	102465778		NR_106141	ENSMUSG00000105379	Mir1191b	mmu-mir-1191b	microRNA 1191b	ncRNA
mm_138770.1	chr17	37130869	37130896	+	1	NA	Intergenic	Intergenic	-18902	NM_146456	258448	Mm.377508	NM_146456	ENSMUSG00000096477	Olfr92	MOR256-29|bM573K1.4	olfactory receptor 92	protein-coding
mm_23714.1	chr3	69005119	69005142	+	1	NA	promoter-TSS (NM_026641)	promoter-TSS (NM_026641)	158	NM_133786	70099	Mm.206841	NM_133786	ENSMUSG00000034349	Smc4	2500002A22Rik|C79747|SMC-4|Smc4l1	structural maintenance of chromosomes 4	protein-coding
mm_88892.1	chr10	81138005	81138021	+	1	NA	intron (NM_010731, intron 1 of 2)	CpG	1742	NM_010731	16969	Mm.20920	NM_010731	ENSMUSG00000035011	Zbtb7a	9030619K07Rik|9130006G12Rik|AI452336|FBI-1|Lrf|Pokemon|Zbtb7	zinc finger and BTB domain containing 7a	protein-coding
mm_170328.1	chr18	43171130	43171130	+	1	NA	Intergenic	Intergenic	-36567	NM_178749	269019	Mm.150401	NM_178749	ENSMUSG00000039954	Stk32a	A930015B13Rik|YANK1	serine/threonine kinase 32A	protein-coding
mm_67291.1	chr7	78835783	78835799	-	1	NA	intron (NM_029585, intron 3 of 4)	L2b|LINE|L2	11420	NM_029585	76375	Mm.250541	NM_029585	ENSMUSG00000030610	Det1	2610034H20Rik	de-etiolated homolog 1 (Arabidopsis)	protein-coding
mm_8123.1	chr1	136135157	136135169	-	1	NA	intron (NM_001039472, intron 1 of 34)	intron (NM_001039472, intron 1 of 34)	3762	NM_001039472	16565	Mm.276135	NM_019962	ENSMUSG00000041642	Kif21b	2610511N21Rik|mKIAA0449	kinesin family member 21B	protein-coding
mm_106793.1	chr12	4817546	4817578	+	1	NA	promoter-TSS (NM_025323)	promoter-TSS (NM_025323)	-46	NM_025323	66055	Mm.102627	NM_025323	ENSMUSG00000037361	Sf3b6	0610009D07Rik|6030419K15Rik|AV001342|Sf3b14	splicing factor 3B, subunit 6	protein-coding
mm_20651.1	chr2	132060781	132060792	-	1	NA	exon (NM_018824, exon 14 of 16)	exon (NM_018824, exon 14 of 16)	-30798	NM_175445	215653	Mm.204737	NM_175445	ENSMUSG00000027339	Rassf2	3830431H01Rik|9030412M04Rik|AI852669|AW495050	Ras association (RalGDS/AF-6) domain family member 2	protein-coding
mm_31365.1	chr4	47288063	47288076	+	1	NA	intron (NM_009928, intron 22 of 39)	intron (NM_009928, intron 22 of 39)	-65153	NM_001312868	21812	Mm.197552	NM_009370	ENSMUSG00000007613	Tgfbr1	ALK5|AU017191|Alk-5|ESK2|TGFR-1|TbetaR-I|TbetaRI	transforming growth factor, beta receptor I	protein-coding
mm_92619.1	chr10	80160908	80160921	-	1	NA	intron (NR_038088, intron 1 of 4)	intron (NR_038088, intron 1 of 4)	-6927	NM_007705	12696	Mm.17898	NM_007705	ENSMUSG00000045193	Cirbp	Cirp|R74941	cold inducible RNA binding protein	protein-coding
mm_140930.1	chr17	24316321	24316324	-	1	NA	intron (NM_001031621, intron 10 of 29)	Lx3B|LINE|L1	30930	NM_001031621	381072	Mm.328842	NM_001031621	ENSMUSG00000035435	Abca17	-	ATP-binding cassette, sub-family A (ABC1), member 17	protein-coding
mm_94654.1	chr11	17051927	17051974	+	1	NA	promoter-TSS (NM_029861)	promoter-TSS (NM_029861)	16	NM_029861	380686	Mm.425666	NM_029861	ENSMUSG00000044629	Cnrip1	1500041B16Rik|3110054C06Rik|5330437A18Rik|AI854501|C2orf32	cannabinoid receptor interacting protein 1	protein-coding
mm_43280.1	chr5	131494876	131494880	+	1	NA	intron (NM_177047, intron 6 of 18)	intron (NM_177047, intron 6 of 18)	-187356	NM_145218	212996	Mm.299204	NM_145218	ENSMUSG00000034040	Wbscr17	AA388321|E330012B09Rik	Williams-Beuren syndrome chromosome region 17 homolog (human)	protein-coding
mm_57318.1	chr6	124729981	124729991	-	1	NA	intron (NM_001077705, intron 3 of 15)	intron (NM_001077705, intron 3 of 15)	3168	NM_013545	15170	Mm.271799	NM_013545	ENSMUSG00000004266	Ptpn6	70Z-SHP|Hcph|PTPTY-42|Ptp1C|SH-PTP1|SHP-1|hcp|me	protein tyrosine phosphatase, non-receptor type 6	protein-coding
mm_98480.1	chr11	94950850	94950856	+	1	NA	exon (NM_007742, exon 49 of 51)	exon (NM_007742, exon 49 of 51)	14629	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_160199.1	chr7	79713973	79713973	-	1	NA	exon (NM_010626, exon 1 of 18)	exon (NM_010626, exon 1 of 18)	213	NM_010626	16576	Mm.101633	NM_010626	ENSMUSG00000050382	Kif7	-	kinesin family member 7	protein-coding
mm_103720.1	chr11	79530424	79530435	-	1	NA	5' UTR (NM_010161, exon 1 of 2)	5' UTR (NM_010161, exon 1 of 2)	180	NM_146023	101488212	Mm.439665	NM_146023	ENSMUSG00000070354	Gm21975	Evi2a-evi2b	predicted gene 21975	protein-coding
mm_54319.1	chr6	30254051	30254060	-	1	NA	intron (NM_009459, intron 3 of 6)	(TCCC)n|Simple_repeat|Simple_repeat	-10252	NM_001169577	22214	Mm.332967	NM_009459	ENSMUSG00000039159	Ube2h	1500009C23Rik|AI181839|AI326965|AI462483|AW227540|E2-20K|Gid3|N28148|Ubc8	ubiquitin-conjugating enzyme E2H	protein-coding
mm_80451.1	chr9	77979919	77979925	+	1	NA	exon (NM_134255, exon 6 of 8)	exon (NM_134255, exon 6 of 8)	62557	NM_134255	68801	Mm.430736	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	ELOVL family member 5, elongation of long chain fatty acids (yeast)	protein-coding
mm_36719.1	chr4	98702449	98702471	-	1	NA	intron (NM_172696, intron 42 of 43)	intron (NM_172696, intron 42 of 43)	-24294	NM_001081202	381591	Mm.34340	NM_001081202	ENSMUSG00000087166	L1td1	AA546746|AB211064|D76865|ECAT11	LINE-1 type transposase domain containing 1	protein-coding
mm_96271.1	chr11	62820472	62820489	+	1	NA	5' UTR (NM_053169, exon 1 of 6)	5' UTR (NM_053169, exon 1 of 6)	227	NM_053169	94092	Mm.117087	NM_053169	ENSMUSG00000047821	Trim16	9130006M08Rik|AI482483|EBBP	tripartite motif-containing 16	protein-coding
mm_170253.1	chr18	10271436	10271436	-	1	NA	Intergenic	LTRIS2|LTR|ERV1	-53743	NM_001083628	381157	Mm.261535	NM_001083628	ENSMUSG00000042942	Greb1l	mKIAA4095	growth regulation by estrogen in breast cancer-like	protein-coding
mm_72598.1	chr8	84414741	84414751	+	1	NA	promoter-TSS (NM_001252060)	promoter-TSS (NM_001252060)	-618	NM_001252060	12286	Mm.334658	NM_007578	ENSMUSG00000034656	Cacna1a	APCA|BI|Caca1a|Cacnl1a4|Cav2.1|Ccha1a|EA2|FHM|HPCA|MHP|MHP1|SCA6|alpha1A|la|nmf352|rkr|smrl|tg	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	protein-coding
mm_97221.1	chr11	75636818	75636848	+	1	NA	intron (NM_008916, intron 3 of 11)	intron (NM_008916, intron 3 of 11)	5813	NM_008916	19062	Mm.1458	NM_008916	ENSMUSG00000006127	Inpp5k	C62|Pps|SKIP	inositol polyphosphate 5-phosphatase K	protein-coding
mm_26219.1	chr3	138813519	138813543	+	1	NA	intron (NM_019571, intron 1 of 7)	intron (NM_019571, intron 1 of 7)	71323	NM_019571	56224	Mm.31927	NM_019571	ENSMUSG00000028152	Tspan5	2810455A09Rik|4930505M03Rik|NET-4|Tm4sf9	tetraspanin 5	protein-coding
mm_168454.1	chr11	41224166	41224174	+	1	NA	Intergenic	LTRIS2|LTR|ERV1	-468884	NM_009831	12450	Mm.2103	NM_009831	ENSMUSG00000020326	Ccng1	AI314029	cyclin G1	protein-coding
mm_46607.1	chr5	107869294	107869310	-	1	NA	intron (NM_007964, intron 1 of 17)	CpG	5805	NM_007964	14020	Mm.35796	NM_007964	ENSMUSG00000011831	Evi5	NB4S	ecotropic viral integration site 5	protein-coding
mm_122183.1	chr14	31591317	31591362	-	1	NA	Intergenic	Intergenic	-13956	NM_009937	382864	Mm.239821	NM_009937	ENSMUSG00000057606	Colq	A130034K24Rik	collagen-like tail subunit (single strand of homotrimer) of asymmetric acetylcholinesterase	protein-coding
mm_124921.1	chr15	12118033	12118074	+	1	NA	intron (NM_011767, intron 1 of 19)	CpG	202	NM_011767	22763	Mm.273496	NM_011767	ENSMUSG00000022201	Zfr	C920030H05Rik	zinc finger RNA binding protein	protein-coding
mm_62968.1	chr7	119861493	119861525	+	1	NA	intron (NM_001163703, intron 1 of 2)	intron (NM_001163703, intron 1 of 2)	33949	NM_173408	233805	Mm.31539	NM_173408	ENSMUSG00000048787	Dcun1d3	1700020A13Rik|BC030335	DCN1, defective in cullin neddylation 1, domain containing 3 (S. cerevisiae)	protein-coding
mm_162297.1	chr1	33899262	33899269	+	1	NA	intron (NM_177235, intron 1 of 6)	intron (NM_177235, intron 1 of 6)	8356	NM_177235	320705	Mm.336619	NM_177235	ENSMUSG00000042182	Bend6	B230209C24Rik	BEN domain containing 6	protein-coding
mm_152041.1	chr19	6128145	6128191	-	1	NA	promoter-TSS (NM_026912)	promoter-TSS (NM_026912)	47	NM_026912	69024	Mm.329629	NM_026912	ENSMUSG00000024787	Snx15	1500032B08Rik|E130013C21Rik	sorting nexin 15	protein-coding
mm_24948.1	chr3	96629888	96629913	+	1	NA	promoter-TSS (NR_003619)	promoter-TSS (NR_003619)	-28	NM_025875	60365	Mm.261972	NM_025875	ENSMUSG00000038374	Rbm8a	2310057C03Rik|AA673428|Rbm8	RNA binding motif protein 8a	protein-coding
mm_76973.1	chr8	106288827	106288831	-	1	NA	intron (NM_021491, intron 1 of 8)	RMER17C|LTR|ERVK	6600	NR_126090	75044	Mm.445896	NR_126090		4930506A18Rik	-	RIKEN cDNA 4930506A18 gene	ncRNA
mm_53024.1	chr6	124320528	124320537	+	1	NA	exon (NM_001170395, exon 11 of 17)	exon (NM_001170395, exon 11 of 17)	15881	NM_053094	93671	Mm.37426	NM_053094	ENSMUSG00000008845	Cd163	CD163v2|CD163v3	CD163 antigen	protein-coding
mm_72438.1	chr8	83153208	83153227	+	1	NA	Intergenic	Intergenic	-12135	NM_001111304	71310	Mm.24031	NM_027758	ENSMUSG00000031709	Tbc1d9	4933431N12Rik|AI847101|AW490653|C76116	TBC1 domain family, member 9	protein-coding
mm_6267.1	chr1	69548718	69548726	-	1	NA	exon (NM_011770, exon 6 of 8)	exon (NM_011770, exon 6 of 8)	137238	NM_011770	22779	Mm.106343	NM_011770	ENSMUSG00000025997	Ikzf2	A730095J18Rik|Helios|Zfpn1a2|Znfn1a2	IKAROS family zinc finger 2	protein-coding
mm_12204.1	chr2	65932071	65932100	+	1	NA	5' UTR (NM_001290665, exon 1 of 5)	5' UTR (NM_001290665, exon 1 of 5)	220	NM_001290665	77771	Mm.102025	NM_153409	ENSMUSG00000044647	Csrnp3	A330102K23Rik|CSRNP-3|Csnrp3|Mbu1|taip-2	cysteine-serine-rich nuclear protein 3	protein-coding
mm_79065.1	chr9	46233133	46233189	+	1	NA	3' UTR (NM_001289755, exon 4 of 4)	3' UTR (NM_001289755, exon 4 of 4)	2138	NM_001289833	11814	Mm.390161	NM_023114	ENSMUSG00000032081	Apoc3	apo-CIII|apoC-III	apolipoprotein C-III	protein-coding
mm_96885.1	chr11	70432628	70432707	+	1	NA	promoter-TSS (NM_001271358)	promoter-TSS (NM_001271358)	87	NM_001271358	216869	Mm.203747	NM_145429	ENSMUSG00000060216	Arrb2	AI326910|AW122872	arrestin, beta 2	protein-coding
mm_126340.1	chr15	79900296	79900311	+	1	NA	intron (NM_001160415, intron 5 of 8)	intron (NM_001160415, intron 5 of 8)	5280	NM_001347041	80287	Mm.284059	NM_030255	ENSMUSG00000009585	Apobec3	Apobec|Arp3|BC003314|Cem15|Rfv3	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 3	protein-coding
mm_32905.1	chr4	119108796	119108812	+	1	NA	promoter-TSS (NM_011400)	promoter-TSS (NM_011400)	59	NM_011400	20525	Mm.21002	NM_011400	ENSMUSG00000028645	Slc2a1	Glut-1|Glut1	solute carrier family 2 (facilitated glucose transporter), member 1	protein-coding
mm_148901.1	chr19	6910536	6910560	+	1	NA	promoter-TSS (NM_012021)	promoter-TSS (NM_012021)	850	NM_026306	67674	Mm.318804	NM_026306	ENSMUSG00000038812	Trmt112	0610038D11Rik|Trm112p	tRNA methyltransferase 11-2	protein-coding
mm_58173.1	chr6	142702325	142702372	-	1	NA	promoter-TSS (NM_011511)	promoter-TSS (NM_011511)	-74	NM_001310143	20928	Mm.35670	NM_011511	ENSMUSG00000030249	Abcc9	AI414027|AI449286|SUR2A|SUR2B|Sur2	ATP-binding cassette, sub-family C (CFTR/MRP), member 9	protein-coding
mm_15754.1	chr2	164254575	164254577	+	1	NA	3' UTR (NM_173377, exon 3 of 3)	3' UTR (NM_173377, exon 3 of 3)	2067	NM_173377	329557	Mm.118769	NM_173377	ENSMUSG00000050383	Svs3b	9530004A22Rik	seminal vesicle secretory protein 3B	protein-coding
mm_117889.1	chr13	99422693	99422704	-	1	NA	3' UTR (NM_008634, exon 7 of 7)	3' UTR (NM_008634, exon 7 of 7)	-9872	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_106837.1	chr12	8006618	8006629	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	28946	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_40112.1	chr5	34865745	34865766	+	1	NA	intron (NM_010414, intron 39 of 66)	intron (NM_010414, intron 39 of 66)	-50160	NM_207277	403174	Mm.291225	NM_207277	ENSMUSG00000051246	Msantd1	A930005I04Rik|Gm144	Myb/SANT-like DNA-binding domain containing 1	protein-coding
mm_167976.1	chrX	158043131	158043139	-	1	NA	promoter-TSS (NM_177751)	promoter-TSS (NM_177751)	62	NM_001310719	245684	Mm.197074	NM_177751	ENSMUSG00000025658	Cnksr2	Cnk2|Ksr2	connector enhancer of kinase suppressor of Ras 2	protein-coding
mm_81298.1	chr9	108339222	108339232	+	1	NA	5' UTR (NM_008160, exon 1 of 2)	5' UTR (NM_008160, exon 1 of 2)	147	NM_001329528	14775	Mm.1090	NM_008160	ENSMUSG00000063856	Gpx1	AI195024|AL033363|CGPx|GPx-1|GSHPx-1|Gpx	glutathione peroxidase 1	protein-coding
mm_13284.1	chr2	101627407	101627421	+	1	NA	intron (NM_009020, intron 1 of 2)	Lx8|LINE|L1	1572	NM_026592	68170	Mm.31263	NM_026592	ENSMUSG00000027165	B230118H07Rik	NWC	RIKEN cDNA B230118H07 gene	protein-coding
mm_70714.1	chr8	15064821	15064830	+	1	NA	intron (NM_008664, intron 2 of 36)	intron (NM_008664, intron 2 of 36)	7172	NM_008664	17930	Mm.272115	NM_008664	ENSMUSG00000031461	Myom2	AW146149	myomesin 2	protein-coding
mm_60131.1	chr7	37272509	37272513	+	1	NA	Intergenic	Intergenic	497241	NM_172385	243937	Mm.322505	NM_172385	ENSMUSG00000043456	Zfp536	9630010P11Rik|Znf536|mKIAA0390	zinc finger protein 536	protein-coding
mm_41057.1	chr5	86804361	86804367	+	1	NA	promoter-TSS (NM_177680)	promoter-TSS (NM_177680)	98	NM_001347376	231386	Mm.196325	NM_177680	ENSMUSG00000035851	Ythdc1	A730098D12Rik|C80342|mKIAA1966	YTH domain containing 1	protein-coding
mm_48233.1	chr5	137707072	137707082	-	1	NA	Intergenic	MLT1F|LTR|ERVL-MaLR	-22324	NM_001303266	231801	Mm.260869	NM_145566	ENSMUSG00000029722	Agfg2	A630095P14Rik|Hrbl|RAB-R|RABR	ArfGAP with FG repeats 2	protein-coding
mm_67349.1	chr7	79827633	79827655	-	1	NA	exon (NM_008486, exon 15 of 20)	exon (NM_008486, exon 15 of 20)	14708	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_166678.1	chr6	97854736	97854753	+	1	NA	intron (NM_001113198, intron 1 of 9)	intron (NM_001113198, intron 1 of 9)	47686	NM_001113198	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_124339.1	chr14	103844269	103844298	-	1	NA	promoter-TSS (NM_001276296)	promoter-TSS (NM_001276296)	193	NM_001136061	13618	Mm.229532	NM_007904	ENSMUSG00000022122	Ednrb	ET-B|ET-BR|ETR-b|ETb|Sox10m1	endothelin receptor type B	protein-coding
mm_20709.1	chr2	134488757	134488758	-	1	NA	Intergenic	Intergenic	65595	NM_010403	15112	Mm.26634	NM_010403	ENSMUSG00000027261	Hao1	GOX|Gox1|Hao-1	hydroxyacid oxidase 1, liver	protein-coding
mm_157590.1	chrX	53114510	53114524	-	1	NA	promoter-TSS (NM_019538)	promoter-TSS (NM_019538)	-112	NM_019538	56096	Mm.274842	NM_019538	ENSMUSG00000061082	Plac1	DXWsu72e|Epcs26|Oosp2l	placental specific protein 1	protein-coding
mm_129398.1	chr15	78283047	78283059	-	1	NA	3' UTR (NM_007781, exon 14 of 14)	3' UTR (NM_007781, exon 14 of 14)	1796	NR_106138	102466845		NR_106138	ENSMUSG00000099059	Mir7676-2	Gm27790|mmu-mir-7676-2	microRNA 7676-2	ncRNA
mm_166367.1	chr5	124637505	124637524	+	1	NA	exon (NM_011596, exon 4 of 20)	exon (NM_011596, exon 4 of 20)	8462	NM_011596	21871	Mm.1158	NM_011596	ENSMUSG00000038023	Atp6v0a2	8430408C20Rik|AI385560|ATP6a2|AW489264|Atp6n1d|Atp6n2|C76904|ISF|J6B7|SHIF|Stv1|TJ6M|TJ6s|Tj6|V-ATPase 116 kDa|V-ATPase a2	ATPase, H+ transporting, lysosomal V0 subunit A2	protein-coding
mm_172859.1	chr9	40802538	40802541	+	1	NA	exon (NM_031165, exon 3 of 9)	exon (NM_031165, exon 3 of 9)	1266	NM_031165	15481	Mm.290774	NM_031165	ENSMUSG00000015656	Hspa8	2410008N15Rik|Hsc70|Hsc71|Hsc73|Hsp73|Hspa10	heat shock protein 8	protein-coding
mm_58712.1	chr7	12978324	12978338	+	1	NA	intron (NM_001168561, intron 1 of 4)	intron (NM_001168561, intron 1 of 4)	483	NM_001168561	269870	Mm.62083	NM_175558	ENSMUSG00000033961	Zfp446	A630035I11Rik|A930031C22|AA120513|AV306632	zinc finger protein 446	protein-coding
mm_153730.1	chr19	44407884	44407901	-	1	NA	promoter-TSS (NM_009127)	promoter-TSS (NM_009127)	-183	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_119924.1	chr14	54968673	54968683	+	1	NA	promoter-TSS (NR_033497)	promoter-TSS (NR_033497)	-109	NR_033497	791403	Mm.319176	NR_033497	ENSMUSG00000097652	Mhrt	D830015G02Rik|ENSMUSG00000053118|Myheart	myosin heavy chain associated RNA transcript	ncRNA
mm_19241.1	chr2	84715295	84715305	-	1	NA	promoter-TSS (NM_144887)	promoter-TSS (NM_144887)	-136	NM_144887	228136	Mm.288508	NM_144887	ENSMUSG00000034075	Zdhhc5	1110032A17Rik|AI451382|Zisp	zinc finger, DHHC domain containing 5	protein-coding
mm_16040.1	chr2	167690750	167690769	+	1	NA	promoter-TSS (NR_015500)	promoter-TSS (NR_015500)	0	NR_110334	329562	Mm.123101	NM_177851	ENSMUSG00000006462	A530013C23Rik	-	RIKEN cDNA A530013C23 gene	ncRNA
mm_82500.1	chr9	20431246	20431249	-	1	NA	3' UTR (NM_011753, exon 10 of 10)	3' UTR (NM_011753, exon 10 of 10)	28913	NM_011753	22688	Mm.107441	NM_011753	ENSMUSG00000063108	Zfp26	5033428C05Rik|KRAB15|Zfp-26|Zfp70|Zfp81-rs1|mKIAA4196|mkr-3|mszf14|mszf52	zinc finger protein 26	protein-coding
mm_61615.1	chr7	80090592	80090618	+	1	NA	3' UTR (NM_175433, exon 5 of 5)	3' UTR (NM_175433, exon 5 of 5)	-15348	NR_045695	100859962	Mm.392575	NR_045695	ENSMUSG00000108714	Gm21057	-	predicted gene, 21057	ncRNA
mm_124995.1	chr15	23036398	23036408	+	1	NA	promoter-TSS (NM_001081299)	promoter-TSS (NM_001081299)	-60	NM_001081299	320865	Mm.241965	NM_001081299	ENSMUSG00000040420	Cdh18	B230220E17Rik|Cdh14l	cadherin 18	protein-coding
mm_133659.1	chr16	91835364	91835367	+	1	NA	intron (NM_001110275, intron 16 of 28)	intron (NM_001110275, intron 16 of 28)	96265	NM_138597	28080	Mm.41	NM_138597	ENSMUSG00000022956	Atp5o	ATPO|D12Wsu28e|OSCP	ATP synthase, H+ transporting, mitochondrial F1 complex, O subunit	protein-coding
mm_6526.1	chr1	74588213	74588230	-	1	NA	promoter-TSS (NM_025784)	promoter-TSS (NM_025784)	-68	NM_001305652	66821	Mm.358700	NM_025784	ENSMUSG00000026172	Bcs1l	9130022O19Rik	BCS1-like (yeast)	protein-coding
mm_129895.1	chr15	83595078	83595082	-	1	NA	promoter-TSS (NM_183017)	promoter-TSS (NM_183017)	77	NM_183017	223723	Mm.46778	NM_183017	ENSMUSG00000016757	Ttll12	BC055368|D430005B17	tubulin tyrosine ligase-like family, member 12	protein-coding
mm_103562.1	chr11	77764048	77764060	-	1	NA	Intergenic	Intergenic	-13181	NM_001291213	360013	Mm.341248	NM_011586	ENSMUSG00000000631	Myo18a	MAJN|MyoPDZ|MysPDZ|SP-R210	myosin XVIIIA	protein-coding
mm_72525.1	chr8	83977046	83977061	+	1	NA	5' UTR (NM_001277898, exon 1 of 10)	5' UTR (NM_001277898, exon 1 of 10)	170	NM_001277898	18747	Mm.19111	NM_008854	ENSMUSG00000005469	Prkaca	PKCD|Pkaca	protein kinase, cAMP dependent, catalytic, alpha	protein-coding
mm_28668.1	chr3	95281796	95281814	-	1	NA	5' UTR (NM_173347, exon 1 of 8)	5' UTR (NM_173347, exon 1 of 8)	271	NM_173347	229589	Mm.14155	NM_173347	ENSMUSG00000015711	Prune1	9230112O05Rik|C130058A12|DRES-17|HTCD37|PRUNEM1|Prune|Prune-M1	prune exopolyphosphatase	protein-coding
mm_115884.1	chr13	21810191	21810200	-	1	NA	promoter-TSS (NM_001110555).2	promoter-TSS (NM_001110555).2	4	NM_001313878	665622	Mm.471247	NM_001110555	ENSMUSG00000069303	Hist1h2br	Gm11277|OTTMUSG00000000449	histone cluster 1 H2br	protein-coding
mm_134865.1	chr16	28564865	28564886	-	1	NA	promoter-TSS (NM_001276419)	promoter-TSS (NM_001276419)	76	NM_001276419	14167	Mm.7996	NM_010199	ENSMUSG00000022523	Fgf12	AV114868|B230343J05Rik|FGF-12|FHF-1|Fhf1	fibroblast growth factor 12	protein-coding
mm_54338.1	chr6	30645259	30645289	-	1	NA	TTS (NM_025350)	TTS (NM_025350)	6056	NM_025350	109697	Mm.25377	NM_025350	ENSMUSG00000054446	Cpa1	0910001L12Rik|Cpa	carboxypeptidase A1, pancreatic	protein-coding
mm_168258.1	chr10	8762485	8762485	-	1	NA	intron (NM_175155, intron 8 of 19)	intron (NM_175155, intron 8 of 19)	123585	NM_175155	70097	Mm.338275	NM_175155	ENSMUSG00000015305	Sash1	1100001C18Rik|2500002E12Rik|A330076K04Rik|mKIAA0790	SAM and SH3 domain containing 1	protein-coding
mm_40760.1	chr5	66968533	66968546	+	1	NA	5' UTR (NM_001256122, exon 1 of 21)	5' UTR (NM_001256122, exon 1 of 21)	123	NM_001256122	77569	Mm.374778	NM_001001980	ENSMUSG00000037736	Limch1	3732412D22Rik|mKIAA1102	LIM and calponin homology domains 1	protein-coding
mm_162812.1	chr10	79681826	79681833	+	1	NA	promoter-TSS (NM_177613)	promoter-TSS (NM_177613)	-366	NM_177613	216150	Mm.21981	NM_177613	ENSMUSG00000020307	Cdc34	AI327276|UBE2R1	cell division cycle 34	protein-coding
mm_158337.1	chrX	134111767	134111788	-	1	NA	promoter-TSS (NM_172203)	promoter-TSS (NM_172203)	77	NM_172203	237038	Mm.67938	NM_172203	ENSMUSG00000031257	Nox1	GP91-2|MOX1|NOH-1|NOH1|NOX1a|NOX1alpha|Nox-1	NADPH oxidase 1	protein-coding
mm_126686.1	chr15	84906653	84906672	+	1	NA	Intergenic	LFSINE_Vert|SINE|tRNA	-16766	NM_016714	18141	Mm.28379	NM_016714	ENSMUSG00000016619	Nup50	1700030K07Rik|AI413123|Npap60	nucleoporin 50	protein-coding
mm_64334.1	chr7	142375912	142375924	+	1	NA	TTS (NM_009983)	TTS (NM_009983)	-2172	NM_001347541	320802	Mm.154486	NM_177265	ENSMUSG00000045777	Ifitm10	6330512M04Rik|AI848576|DSPA3	interferon induced transmembrane protein 10	protein-coding
mm_161018.1	chr11	120458032	120458032	-	1	NA	promoter-TSS (NM_025560)	promoter-TSS (NM_025560)	31	NM_025560	66431	Mm.45063	NM_025560	ENSMUSG00000039670	Oxld1	1810049H13Rik	oxidoreductase like domain containing 1	protein-coding
mm_110770.1	chr12	70280654	70280661	-	1	NA	exon (NM_001110203, exon 5 of 9)	exon (NM_001110203, exon 5 of 9)	-27848	NR_037248	100526482		NR_037248	ENSMUSG00000078026	Mir466o	Mir4660|mmu-mir-466o	microRNA 466o	ncRNA
mm_16678.1	chr2	6872508	6872534	-	1	NA	promoter-TSS (NM_001347094)	promoter-TSS (NM_001347094)	-486	NM_001347094	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_7569.1	chr1	124820496	124820532	-	1	NA	Intergenic	Lx8|LINE|L1	615213	NM_023735	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding
mm_103709.1	chr11	79516795	79516805	-	1	NA	intron (NM_146023, intron 3 of 3)	intron (NM_146023, intron 3 of 3)	6962	NM_001077496	216984	Mm.439665	NM_001077496	ENSMUSG00000093938	Evi2b	Evi-2|Evi2	ecotropic viral integration site 2b	protein-coding
mm_132111.1	chr16	31455141	31455160	+	1	NA	exon (NM_001122683, exon 6 of 7)	exon (NM_001122683, exon 6 of 7)	26397	NM_001122683	71911	Mm.293470	NM_175177	ENSMUSG00000046598	Bdh1	2310032J20Rik|AI327223|Bdh	3-hydroxybutyrate dehydrogenase, type 1	protein-coding
mm_12883.1	chr2	84734051	84734107	+	1	NA	promoter-TSS (NM_001005342)	promoter-TSS (NM_001005342)	-125	NM_001005342	241525	Mm.486398	NM_001005342	ENSMUSG00000034059	Ypel4	-	yippee-like 4 (Drosophila)	protein-coding
mm_106336.1	chr11	118393077	118393087	-	1	NA	exon (NM_011150, exon 6 of 6)	exon (NM_011150, exon 6 of 6)	8849	NM_011150	19039	Mm.3152	NM_011150	ENSMUSG00000033880	Lgals3bp	90K|CyCAP|MAC-2BP|Ppicap|Tango10b	lectin, galactoside-binding, soluble, 3 binding protein	protein-coding
mm_149867.1	chr19	25148136	25148140	+	1	NA	intron (NM_028785, intron 25 of 47)	B1_Mur2|SINE|Alu	-89064	NM_181404	107351	Mm.260722	NM_181404	ENSMUSG00000032702	Kank1	A930031B09Rik|AU015049|AW121052|Ankrd15|D330024H06Rik|mKIAA0172	KN motif and ankyrin repeat domains 1	protein-coding
mm_128559.1	chr15	55908085	55908101	-	1	NA	Intergenic	Intergenic	-1144	NM_016667	20649	Mm.309425	NM_016667	ENSMUSG00000060429	Sntb1	-	syntrophin, basic 1	protein-coding
mm_134395.1	chr16	17508865	17508899	-	1	NA	promoter-TSS (NM_001331226)	promoter-TSS (NM_001331226)	199	NM_025808	66863	Mm.161726	NM_025808	ENSMUSG00000022761	Lztr1	1200003E21Rik|AI591627|AW550890	leucine-zipper-like transcriptional regulator, 1	protein-coding
mm_54445.1	chr6	34599877	34599892	-	1	NA	intron (NM_001347100, intron 1 of 13)	intron (NM_001347100, intron 1 of 13)	1380	NM_001347100	109624	Mm.308134	NM_145575	ENSMUSG00000029761	Cald1	4833423D12Rik|AI195384|AV071549|AW536160|C920027I18Rik	caldesmon 1	protein-coding
mm_79821.1	chr9	64385676	64385698	+	1	NA	promoter-TSS (NM_001134399)	promoter-TSS (NM_001134399)	61	NM_001134399	214058	Mm.127721	NM_172522	ENSMUSG00000036466	Megf11	2410080H04Rik|D130061K05	multiple EGF-like-domains 11	protein-coding
mm_117990.1	chr13	100296415	100296418	-	1	NA	intron (NM_021545, intron 11 of 14)	intron (NM_021545, intron 11 of 14)	20200	NM_010871	17952	Mm.218759	NM_010871	ENSMUSG00000078942	Naip6	Birc1f|Naip-rs4|Naip-rs4A	NLR family, apoptosis inhibitory protein 6	protein-coding
mm_37090.1	chr4	116555897	116555957	-	1	NA	promoter-TSS (NM_177670)	promoter-TSS (NM_177670)	16	NM_177670	230657	Mm.291484	NM_177670	ENSMUSG00000055900	Tmem69	A630048M13Rik	transmembrane protein 69	protein-coding
mm_2401.1	chr1	93754900	93754932	+	1	NA	promoter-TSS (NM_025920)	promoter-TSS (NM_025920)	-78	NM_025920	67026	Mm.272356	NM_025920	ENSMUSG00000026279	Thap4	2010320B01Rik	THAP domain containing 4	protein-coding
mm_12631.1	chr2	74705047	74705078	+	1	NA	promoter-TSS (NM_001290730)	promoter-TSS (NM_001290730)	-427	NM_001290730	15437	Mm.280673	NM_008276	ENSMUSG00000027102	Hoxd8	4921540P06Rik|AI047735|Hox-4.3|Hox-5.4	homeobox D8	protein-coding
mm_84398.1	chr9	65552245	65552256	-	1	NA	TTS (NM_153119)	TTS (NM_153119)	27837	NM_153119	102595	Mm.247303	NM_153119	ENSMUSG00000050721	Plekho2	AI840980|Plekhq1	pleckstrin homology domain containing, family O member 2	protein-coding
mm_41758.1	chr5	102857337	102857340	+	1	NA	intron (NM_001346585, intron 1 of 6)	B1_Mus1|SINE|Alu	12331	NM_001346585	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding
mm_85571.1	chr9	107280681	107280700	-	1	NA	intron (NM_001316691, intron 1 of 7)	intron (NM_001316691, intron 1 of 7)	8706	NM_001316691	102626	Mm.222612	NM_178907	ENSMUSG00000032577	Mapkapk3	3PK|AI874665|MAPKAP-K3|MAPKAP3|MK-3|MK3|MapkKapk3	mitogen-activated protein kinase-activated protein kinase 3	protein-coding
mm_62354.1	chr7	100498887	100498899	+	1	NA	exon (NM_011671, exon 7 of 8)	exon (NM_011671, exon 7 of 8)	5535	NM_011671	22228	Mm.171378	NM_011671	ENSMUSG00000033685	Ucp2	Slc25a8	uncoupling protein 2 (mitochondrial, proton carrier)	protein-coding
mm_151511.1	chr19	58734660	58734733	+	1	NA	exon (NM_018874, exon 7 of 13)	exon (NM_018874, exon 7 of 13)	5809	NM_018874	18946	Mm.10753	NM_018874	ENSMUSG00000042179	Pnliprp1	Plrp1	pancreatic lipase related protein 1	protein-coding
mm_84612.1	chr9	70421492	70421529	-	1	NA	promoter-TSS (NM_007630)	promoter-TSS (NM_007630)	44	NM_007630	12442	Mm.22592	NM_007630	ENSMUSG00000032218	Ccnb2	CycB2	cyclin B2	protein-coding
mm_142.1	chr1	10993483	10993620	+	1	NA	promoter-TSS (NM_029525)	promoter-TSS (NM_029525)	86	NM_029525	109294	Mm.123247	NM_029525	ENSMUSG00000048960	Prex2	6230420N16Rik|AI316880|AI553603|C030045D06Rik|D430013K02|Depdc2|P-Rex2	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	protein-coding
mm_125698.1	chr15	66891540	66891546	+	1	NA	5' UTR (NM_018865, exon 1 of 5)	5' UTR (NM_018865, exon 1 of 5)	150	NM_018865	22402	Mm.10222	NM_018865	ENSMUSG00000005124	Wisp1	AW146261|CCN4|Elm1	WNT1 inducible signaling pathway protein 1	protein-coding
mm_75199.1	chr8	39118940	39118957	-	1	NA	intron (NM_030254, intron 6 of 7)	intron (NM_030254, intron 6 of 7)	113081	NM_030254	80286	Mm.272722	NM_030254	ENSMUSG00000039530	Tusc3	AU022242|BC003311|N33	tumor suppressor candidate 3	protein-coding
mm_160372.1	chr8	34807795	34807795	+	1	NA	exon (NM_176933, exon 1 of 4)	exon (NM_176933, exon 1 of 4)	185	NM_176933	319520	Mm.170276	NM_176933	ENSMUSG00000031530	Dusp4	2700078F24Rik|AI844617|BB104621|E130306H24Rik|MKP2	dual specificity phosphatase 4	protein-coding
mm_54617.1	chr6	38355534	38355551	-	1	NA	promoter-TSS (NM_028421)	promoter-TSS (NM_028421)	-939	NM_028421	78781	Mm.25243	NM_028421	ENSMUSG00000029826	Zc3hav1	1200014N16Rik|2900058M19Rik|9130009D18Rik|9830115L13Rik|ARTD13|D6Bwg1452e|ZAP	zinc finger CCCH type, antiviral 1	protein-coding
mm_172250.1	chr6	69576552	69576556	-	1	NA	Intergenic	Intergenic	-249380	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_99422.1	chr11	102361177	102361202	+	1	NA	exon (NM_011403, exon 3 of 20)	exon (NM_011403, exon 3 of 20)	4092	NM_011403	20533	Mm.7248	NM_011403	ENSMUSG00000006574	Slc4a1	Ae1|CD233|Empb3|l11Jus51	solute carrier family 4 (anion exchanger), member 1	protein-coding
mm_156382.1	chrX	139672270	139672296	+	1	NA	3' UTR (NM_023270, exon 7 of 7)	3' UTR (NM_023270, exon 7 of 7)	-12713	NM_001081499	245638	Mm.275869	NM_001081499	ENSMUSG00000042473	Tbc1d8b	4921505D17Rik|9030605E16Rik	TBC1 domain family, member 8B	protein-coding
mm_167804.1	chr9	123928291	123928308	+	1	NA	Intergenic	Intergenic	40393	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_21290.1	chr2	156991839	156991847	-	1	NA	intron (NM_013865, intron 1 of 15)	CpG	268	NM_013865	29812	Mm.279256	NM_013865	ENSMUSG00000027634	Ndrg3	4833415O14Rik|AI747193|Ndr3	N-myc downstream regulated gene 3	protein-coding
mm_155524.1	chrX	74260890	74260895	+	1	NA	Intergenic	Intergenic	6205	NM_007927	13726	Mm.18892	NM_007927	ENSMUSG00000001964	Emd	AW550900|Sta	emerin	protein-coding
mm_92771.1	chr10	81167711	81167754	-	1	NA	promoter-TSS (NM_021501)	promoter-TSS (NM_021501)	-12	NM_021501	59004	Mm.34428	NM_021501	ENSMUSG00000004934	Pias4	PIASY|Pias-gamma|Piasg	protein inhibitor of activated STAT 4	protein-coding
mm_964.1	chr1	58113167	58113184	+	1	NA	promoter-TSS (NM_023617)	promoter-TSS (NM_023617)	39	NM_023617	71724	Mm.20108	NM_023617	ENSMUSG00000064294	Aox3	1200011D03Rik|AI326299|Aoh1|Aoh2	aldehyde oxidase 3	protein-coding
mm_140008.1	chr17	73142696	73142709	+	1	NA	intron (NM_001081071, intron 1 of 5)	intron (NM_001081071, intron 1 of 5)	34717	NM_001177967	225010	Mm.329194	NM_001081071	ENSMUSG00000054469	Lclat1	AI181996|Agpat8|Alcat1|Gm91|Lycat	lysocardiolipin acyltransferase 1	protein-coding
mm_159555.1	chr4	106757256	106757256	-	1	NA	intron (NM_001347159, intron 8 of 15)	intron (NM_001347159, intron 8 of 15)	23341	NM_146149	230579	Mm.222956	NM_146149	ENSMUSG00000034871	Fam151a	2010309H15Rik	family with sequence simliarity 151, member A	protein-coding
mm_53896.1	chr6	3399452	3399464	-	1	NA	5' UTR (NM_010156, exon 1 of 2)	5' UTR (NM_010156, exon 1 of 2)	113	NM_010156	209086	Mm.196013	NM_010156	ENSMUSG00000047735	Samd9l	AA175286|ESTM25|mKIAA2005	sterile alpha motif domain containing 9-like	protein-coding
mm_102170.1	chr11	53891669	53891708	-	1	NA	promoter-TSS (NM_011396)	promoter-TSS (NM_011396)	15	NM_011396	20520	Mm.42253	NM_011396	ENSMUSG00000018900	Slc22a5	Lstpl|Octn2|jvs	solute carrier family 22 (organic cation transporter), member 5	protein-coding
mm_52607.1	chr6	117173659	117173673	+	1	NA	3' UTR (NM_021704, exon 3 of 3)	3' UTR (NM_021704, exon 3 of 3)	5131	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_57164.1	chr6	122801640	122801653	-	1	NA	Intergenic	CpG	-18538	NM_021899	60611	Mm.87142	NM_021899	ENSMUSG00000003154	Foxj2	Fhx	forkhead box J2	protein-coding
mm_137829.1	chr17	30678569	30678573	+	1	NA	intron (NM_013811, intron 18 of 92)	intron (NM_013811, intron 18 of 92)	51635	NM_013811	13417	Mm.426017	NM_013811	ENSMUSG00000033826	Dnah8	ATPase|Dnahc8|Hst6.7b|P1-Loop	dynein, axonemal, heavy chain 8	protein-coding
mm_47141.1	chr5	120557796	120557824	-	1	NA	exon (NM_145853, exon 4 of 28)	exon (NM_145853, exon 4 of 28)	30803	NM_145853	252972	Mm.114054	NM_145853	ENSMUSG00000032741	Tpcn1	5730403B01Rik|Tpc1|mKIAA1169	two pore channel 1	protein-coding
mm_155311.1	chrX	61709479	61709489	+	1	NA	promoter-TSS (NM_001018087)	promoter-TSS (NM_001018087)	-132	NM_001018087	434784	Mm.23468	NM_001018087	ENSMUSG00000057615	Ldoc1	Gm366|Mar7|Mart7|Sirh7	leucine zipper, down-regulated in cancer 1	protein-coding
mm_110415.1	chr12	46720837	46720844	-	1	NA	exon (NM_021361, exon 3 of 5)	exon (NM_021361, exon 3 of 5)	97935	NM_021361	664883	Mm.247195	NM_021361	ENSMUSG00000021047	Nova1	9430099M15Rik|G630039L02|Nova-1	neuro-oncological ventral antigen 1	protein-coding
mm_166441.1	chr5	137263595	137263602	-	1	NA	Intergenic	Intergenic	-24656	NM_009599	11423	Mm.255464	NM_009599	ENSMUSG00000023328	Ache	-	acetylcholinesterase	protein-coding
mm_161839.1	chr17	86168196	86168196	+	1	NA	5' UTR (NM_011104, exon 1 of 15)	5' UTR (NM_011104, exon 1 of 15)	411	NM_011104	18754	Mm.24614	NM_011104	ENSMUSG00000045038	Prkce	5830406C15Rik|PKC[e]|PKCepsilon|Pkce|R75156	protein kinase C, epsilon	protein-coding
mm_33940.1	chr4	136945680	136945694	+	1	NA	exon (NM_007939, exon 3 of 17)	exon (NM_007939, exon 3 of 17)	11129	NM_007939	13842	Mm.1390	NM_007939	ENSMUSG00000028661	Epha8	AW047546|Eek|Hek3|mKIAA1459	Eph receptor A8	protein-coding
mm_170717.1	chr2	14627332	14627346	-	1	NA	intron (NM_023116, intron 2 of 13)	CpG	23033	NM_023116	12296	Mm.313930	NM_023116	ENSMUSG00000057914	Cacnb2	AW060387|CAB2|Cavbeta2|Cchb2	calcium channel, voltage-dependent, beta 2 subunit	protein-coding
mm_86033.1	chr9	113708182	113708197	-	1	NA	promoter-TSS (NM_001164677)	promoter-TSS (NM_001164677)	70	NM_001164678	18571	Mm.29816	NM_011052	ENSMUSG00000032504	Pdcd6ip	AI480591|AW544830|Aip1|Alix|C76364|Eig2|mKIAA1375	programmed cell death 6 interacting protein	protein-coding
mm_56858.1	chr6	118197357	118197374	-	1	NA	5' UTR (NM_009050, exon 1 of 20)	5' UTR (NM_009050, exon 1 of 20)	379	NM_009050	19713	Mm.57199	NM_009050	ENSMUSG00000030110	Ret	PTC|RET51|RET9|c-Ret	ret proto-oncogene	protein-coding
mm_89266.1	chr10	87860063	87860086	+	1	NA	intron (NM_001314010, intron 2 of 4)	intron (NM_001314010, intron 2 of 4)	1022	NM_010512	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_145132.1	chr18	44811657	44811693	+	1	NA	intron (NM_001085373, intron 1 of 18)	intron (NM_001085373, intron 1 of 18)	507	NM_001085373	328949	Mm.312511	NM_001033406	ENSMUSG00000071856	Mcc	D18Ertd451e|E330037C19	mutated in colorectal cancers	protein-coding
mm_33026.1	chr4	122008141	122008172	+	1	NA	Intergenic	Intergenic	-386031	NM_001099309	666927	Mm.465133	NM_001099309	ENSMUSG00000078575	Gm12887	OTTMUSG00000008910	predicted gene 12887	protein-coding
mm_14212.1	chr2	127277684	127277687	+	1	NA	intron (NM_139308, intron 1 of 7)	PB1D10|SINE|Alu	7456	NM_139308	99138	Mm.41271	NM_139308	ENSMUSG00000027367	Stard7	AI852671|AL022671|AW544915	START domain containing 7	protein-coding
mm_150357.1	chr19	34649105	34649118	+	1	NA	3' UTR (NM_008331, exon 2 of 2)	3' UTR (NM_008331, exon 2 of 2)	8222	NM_008331	15957	Mm.439751	NM_008331	ENSMUSG00000034459	Ifit1	ISG56|Ifi56|P56	interferon-induced protein with tetratricopeptide repeats 1	protein-coding
mm_33029.1	chr4	122689254	122689258	+	1	NA	promoter-TSS (NM_023865)	promoter-TSS (NM_023865)	-3	NM_023865	77432	Mm.491436	NM_023865	ENSMUSG00000023263	9530002B09Rik	Aump|Vpp1|Vppl	RIKEN cDNA 9530002B09 gene	protein-coding
mm_47850.1	chr5	134520312	134520324	-	1	NA	intron (NM_009990, intron 3 of 16)	intron (NM_009990, intron 3 of 16)	32116	NM_001039162	269713	Mm.255138	NM_009990	ENSMUSG00000063146	Clip2	B230327O20|CLIP-115|Clip1|Cyln2|WSCR4|mKIAA0291|wbscr4	CAP-GLY domain containing linker protein 2	protein-coding
mm_53625.1	chr6	140491025	140491046	+	1	NA	intron (NM_144920, intron 3 of 30)	intron (NM_144920, intron 3 of 30)	66936	NM_144920	109135	Mm.247670	NM_144920	ENSMUSG00000030231	Plekha5	2810431N21Rik|AI428202|AK129423|AMH-Cre|Ayu21-9|Gt(pU21)9Imeg|Pepp2|Tg(AMH-cre)1Flor	pleckstrin homology domain containing, family A member 5	protein-coding
mm_74640.1	chr8	13254155	13254168	-	1	NA	promoter-TSS (NM_172750)	promoter-TSS (NM_172750)	1	NM_172750	234072	Mm.132785	NM_172750	ENSMUSG00000031448	Adprhl1	Arh2|D330008N11Rik	ADP-ribosylhydrolase like 1	protein-coding
mm_75163.1	chr8	36586736	36586738	-	1	NA	exon (NM_015802, exon 4 of 14)	exon (NM_015802, exon 4 of 14)	27206	NM_015802	50768	Mm.125155	NM_015802	ENSMUSG00000031523	Dlc1	A730069N07Rik|Arhgap7|HP|STARD12|dlc-1	deleted in liver cancer 1	protein-coding
mm_99280.1	chr11	101279158	101279188	+	1	NA	promoter-TSS (NM_026618)	promoter-TSS (NM_026618)	-30	NM_026562	68107	Mm.262369	NM_026562	ENSMUSG00000078653	Cntd1	1700051C09Rik|4921513J16Rik|5430417M23Rik|Cntd	cyclin N-terminal domain containing 1	protein-coding
mm_92307.1	chr10	75152863	75152868	-	1	NA	intron (NM_001081412, intron 8 of 22)	intron (NM_001081412, intron 8 of 22)	-59208	NM_153406	74392	Mm.27716	NM_153406	ENSMUSG00000033444	Specc1l	4930470P14Rik|4932439K10Rik|9530057A13Rik|AI317249|Cytsa|mKIAA0376	sperm antigen with calponin homology and coiled-coil domains 1-like	protein-coding
mm_10847.1	chr2	24976118	24976140	+	1	NA	promoter-TSS (NM_146251)	promoter-TSS (NM_146251)	96	NM_146251	241274	Mm.389243	NM_146251	ENSMUSG00000036833	Pnpla7	BC027342|E430013P11Rik|Nre	patatin-like phospholipase domain containing 7	protein-coding
mm_109568.1	chr12	112106693	112106705	+	1	NA	promoter-TSS (NM_001081169)	promoter-TSS (NM_001081169)	16	NM_001081169	104816	Mm.77133	NM_001081169	ENSMUSG00000037686	Aspg	A530050D06Rik|AI429460|Gm690	asparaginase	protein-coding
mm_142042.1	chr17	35380257	35380277	-	1	NA	intron (NM_001143689, intron 2 of 5)	CpG-6320	650	NM_001143689	15015	Mm.464284	NM_001143689	ENSMUSG00000035929	H2-Q4	H-2Q4|H2-Gs10|Qa-4|Qa4|Qat-4|Qb-1|Qb1	histocompatibility 2, Q region locus 4	protein-coding
mm_86403.1	chr9	123986649	123986653	-	1	NA	Intergenic	Intergenic	-8243	NM_007718	12770	Mm.423532	NM_007718	ENSMUSG00000064039	Ccr1l1	Cmkbr1l1	chemokine (C-C motif) receptor 1-like 1	protein-coding
mm_132338.1	chr16	33829682	33829706	+	1	NA	promoter-TSS (NM_001145884)	promoter-TSS (NM_001145884)	29	NM_001145884	16419	Mm.6424	NM_010580	ENSMUSG00000022817	Itgb5	AA475909|AI874634|ESTM23|[b]-5|[b]5|[b]5A|[b]5B|beta-5|beta5	integrin beta 5	protein-coding
mm_3515.1	chr1	150107423	150107439	+	1	NA	3' UTR (NM_011198, exon 10 of 10)	3' UTR (NM_011198, exon 10 of 10)	7400	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_19815.1	chr2	110363116	110363130	-	1	NA	promoter-TSS (NM_026271)	promoter-TSS (NM_026271)	-130	NM_026271	67606	Mm.291809	NM_026271	ENSMUSG00000074971	Fibin	1110018M03Rik	fin bud initiation factor homolog (zebrafish)	protein-coding
mm_167834.1	chr9	124424385	124424453	-	1	NA	non-coding (NR_015516, exon 1 of 1)	non-coding (NR_015516, exon 1 of 1)	632	NR_015516	75135	Mm.476814	NR_015516		4930526I15Rik	1600027J15Rik	RIKEN cDNA 4930526I15 gene	ncRNA
mm_120392.1	chr14	64590730	64590732	+	1	NA	promoter-TSS (NR_029813)	promoter-TSS (NR_029813)	74	NR_029813	387233		NR_029813	ENSMUSG00000065597	Mir124a-1	Mirn124a|Mirn124a-1	microRNA 124a-1	ncRNA
mm_72679.1	chr8	84946988	84947012	+	1	NA	promoter-TSS (NM_144929)	promoter-TSS (NM_144929)	9	NM_144929	234542	Mm.461701	NM_144929	ENSMUSG00000048617	Rtbdn	A330096I21Rik|BC022744|Rtbnd	retbindin	protein-coding
mm_39997.1	chr5	32611248	32611265	+	1	NA	promoter-TSS (NM_009535)	promoter-TSS (NM_009535)	85	NM_009535	22612	Mm.4558	NM_009535	ENSMUSG00000014932	Yes1	Yes|p61-Yes	YES proto-oncogene 1, Src family tyrosine kinase	protein-coding
mm_153340.1	chr19	38372507	38372520	-	1	NA	Intergenic	Intergenic	-23467	NM_175507	240660	Mm.262085	NM_175507	ENSMUSG00000044026	Slc35g1	AA590464|D330039I19Rik|Tmem20	solute carrier family 35, member G1	protein-coding
mm_1013.1	chr1	58728653	58728698	+	1	NA	intron (NM_001293804, intron 3 of 9)	intron (NM_001293804, intron 3 of 9)	-1877	NM_001293805	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_15266.1	chr2	155096024	155096034	+	1	NA	Intergenic	Intergenic	4050	NR_040634	100504268	Mm.410858	NR_040634	ENSMUSG00000087254	2310005A03Rik	-	RIKEN cDNA 2310005A03 gene	ncRNA
mm_73511.1	chr8	107368544	107368589	+	1	NA	exon (NM_018823, exon 13 of 15)	exon (NM_018823, exon 13 of 15)	34639	NM_008706	18104	Mm.252	NM_008706	ENSMUSG00000003849	Nqo1	AV001255|Dia4|Dtd|Nmo-1|Nmo1|Nmor1|Ox-1|Ox1|Qr1	NAD(P)H dehydrogenase, quinone 1	protein-coding
mm_164202.1	chr15	80193111	80193132	+	1	NA	intron (NM_010795, intron 1 of 1)	intron (NM_010795, intron 1 of 1)	19400	NM_010795	17309	Mm.299693	NM_010795	ENSMUSG00000042428	Mgat3	1110038J12Rik|AI848272|GnT-III	mannoside acetylglucosaminyltransferase 3	protein-coding
mm_160065.1	chr7	5067828	5067828	+	1	NA	intron (NM_133671, intron 4 of 11)	intron (NM_133671, intron 4 of 11)	5685	NM_001205231	22185	Mm.360389	NM_133671	ENSMUSG00000030435	U2af2	65kDa	U2 small nuclear ribonucleoprotein auxiliary factor (U2AF) 2	protein-coding
mm_31140.1	chr4	43382095	43382138	+	1	NA	5' UTR (NM_001037709, exon 1 of 12)	5' UTR (NM_001037709, exon 1 of 12)	134	NM_001037709	100213	Mm.235730	NM_199057	ENSMUSG00000035969	Rusc2	AI840675|mKIAA0375	RUN and SH3 domain containing 2	protein-coding
mm_128923.1	chr15	73830996	73831003	-	1	NA	intron (NM_001033365, intron 1 of 10)	intron (NM_001033365, intron 1 of 10)	8672	NM_001033365	268816	Mm.440635	NM_001033365	ENSMUSG00000072487	Mroh5	Gm628	maestro heat-like repeat family member 5	protein-coding
mm_18639.1	chr2	69414509	69414519	-	1	NA	Intergenic	Intergenic	34052	NM_175512	241452	Mm.211655	NM_175512	ENSMUSG00000027068	Dhrs9	C730025I08Rik|Rdh15	dehydrogenase/reductase (SDR family) member 9	protein-coding
mm_51028.1	chr6	65432871	65432898	+	1	NA	intron (NM_175524, intron 1 of 5)	intron (NM_175524, intron 1 of 5)	51590	NM_175524	243407	Mm.389758	NM_175524	ENSMUSG00000029917	C130060K24Rik	-	RIKEN cDNA C130060K24 gene	protein-coding
mm_118866.1	chr14	25854334	25854364	+	1	NA	intron (NM_013469, intron 1 of 14)	intron (NM_013469, intron 1 of 14)	12194	NM_013469	11744	Mm.294083	NM_013469	ENSMUSG00000021866	Anxa11	A830099O17Rik|Anx11	annexin A11	protein-coding
mm_13570.1	chr2	112283192	112283195	+	1	NA	intron (NM_133649, intron 1 of 24)	(T)n|Simple_repeat|Simple_repeat	-1495	NM_133648	107723	Mm.491155	NM_133648	ENSMUSG00000027130	Slc12a6	9530023I19Rik|KCC3|gaxp	solute carrier family 12, member 6	protein-coding
mm_84114.1	chr9	58370463	58370474	-	1	NA	promoter-TSS (NR_040727)	promoter-TSS (NR_040727)	-36	NR_040727	73529	Mm.490924	NR_040727	ENSMUSG00000100487	1700072B07Rik	-	RIKEN cDNA 1700072B07 gene	ncRNA
mm_147846.1	chr18	63545197	63545206	-	1	NA	Intergenic	Intergenic	147158	NM_016792	53382	Mm.19169	NM_016792	ENSMUSG00000024583	Txnl1	32kDa|TRP32|Txnl	thioredoxin-like 1	protein-coding
mm_97068.1	chr11	72961164	72961179	+	1	NA	promoter-TSS (NM_001163337)	promoter-TSS (NM_001163337)	2	NM_001163337	53313	Mm.6306	NM_016745	ENSMUSG00000020788	Atp2a3	SERCA3b|Serca3	ATPase, Ca++ transporting, ubiquitous	protein-coding
mm_136124.1	chr16	85900682	85900691	-	1	NA	5' UTR (NM_011782, exon 1 of 8)	5' UTR (NM_011782, exon 1 of 8)	439	NM_011782	23794	Mm.112933	NM_011782	ENSMUSG00000022894	Adamts5	9530092O11Rik|ADAM-TS5|ADAMTS1|ADAMTS11|ADMP-2|AI481094|ASMP-2	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)	protein-coding
mm_34691.1	chr4	152008937	152008948	+	1	NA	promoter-TSS (NM_001033352)	promoter-TSS (NM_001033352)	51	NM_001033352	242785	Mm.22306	NM_001033352	ENSMUSG00000073700	Klhl21	1810045K06Rik|D330008A20|mKIAA0469	kelch-like 21	protein-coding
mm_99339.1	chr11	101468334	101468354	+	1	NA	promoter-TSS (NM_009708)	promoter-TSS (NM_009708)	6	NM_009708	11858	Mm.378883	NM_009708	ENSMUSG00000001313	Rnd2	Arhn|Rohn	Rho family GTPase 2	protein-coding
mm_96207.1	chr11	62249063	62249073	+	1	NA	promoter-TSS (NM_007413)	promoter-TSS (NM_007413)	84	NM_007413	11541	Mm.40740	NM_007413	ENSMUSG00000018500	Adora2b	A2BAR|A2BR|A2b|AA2BR|AI480866|AI605384	adenosine A2b receptor	protein-coding
mm_11418.1	chr2	31688331	31688386	+	1	NA	promoter-TSS (NM_001283047)	promoter-TSS (NM_001283047)	-179	NM_001283047	11350	Mm.1318	NM_009594	ENSMUSG00000026842	Abl1	AI325092|Abl|E430008G22Rik|c-Abl	c-abl oncogene 1, non-receptor tyrosine kinase	protein-coding
mm_42900.1	chr5	122489237	122489250	+	1	NA	exon (NM_009722, exon 5 of 21)	exon (NM_009722, exon 5 of 21)	12982	NM_001110140	11938	Mm.227583	NM_009722	ENSMUSG00000029467	Atp2a2	9530097L16Rik|D5Wsu150e|SERCA2|SERCA2B|Serca2a|mKIAA4195	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	protein-coding
mm_42454.1	chr5	115435246	115435256	+	1	NA	intron (NM_008629, intron 5 of 14)	intron (NM_008629, intron 5 of 14)	5566	NM_008629	17690	Mm.5077	NM_008629	ENSMUSG00000054256	Msi1	Msi1h|Musahi1|m-Msi-1	musashi RNA-binding protein 1	protein-coding
mm_113067.1	chr13	23751108	23751118	+	1	NA	promoter-TSS (NM_175660)	promoter-TSS (NM_175660)	25	NM_175660	319172	Mm.423402	NM_175660	ENSMUSG00000061615	Hist1h2ab	H2A.1|H2a-53	histone cluster 1, H2ab	protein-coding
mm_21314.1	chr2	157098863	157098880	-	1	NA	3' UTR (NM_001139520, exon 17 of 17)	3' UTR (NM_001139520, exon 17 of 17)	11816	NM_001177439	383766	Mm.480305	NM_001177439	ENSMUSG00000074628	Tldc2	Gm1332	TBC/LysM associated domain containing 2	protein-coding
mm_128492.1	chr15	51865449	51865474	-	1	NA	promoter-TSS (NM_080635)	promoter-TSS (NM_080635)	0	NM_080635	68135	Mm.289800	NM_080635	ENSMUSG00000022312	Eif3h	1110008A16Rik|40kD|9430017H16Rik|EIF3-P40|EIF3-gamma|Eif3s3	eukaryotic translation initiation factor 3, subunit H	protein-coding
mm_33328.1	chr4	129106808	129106817	+	1	NA	intron (NM_025452, intron 1 of 5)	intron (NM_025452, intron 1 of 5)	1264	NM_001290706	66260	Mm.25295	NM_025452	ENSMUSG00000028786	Tmem54	1810017F10Rik|AI507302	transmembrane protein 54	protein-coding
mm_83586.1	chr9	48340877	48340893	-	1	NA	promoter-TSS (NM_030069)	promoter-TSS (NM_030069)	13	NM_030069	78252	Mm.31626	NM_030069	ENSMUSG00000032028	Nxpe2	4432416J03Rik|AI323362|Fam55b	neurexophilin and PC-esterase domain family, member 2	protein-coding
mm_35433.1	chr4	36856503	36856506	-	1	NA	intron (NM_001165999, intron 1 of 7)	intron (NM_001165999, intron 1 of 7)	95240	NM_001165999	242384	Mm.132507	NM_175516	ENSMUSG00000045083	Lingo2	B230217C06Rik|Lern3|Lrrn6c	leucine rich repeat and Ig domain containing 2	protein-coding
mm_164624.1	chr17	31277379	31277382	-	1	NA	promoter-TSS (NM_025290)	promoter-TSS (NM_025290)	-24	NM_025290	22092	Mm.12743	NM_025290	ENSMUSG00000024033	Rsph1	MCA|Tsga2	radial spoke head 1 homolog (Chlamydomonas)	protein-coding
mm_88949.1	chr10	81364027	81364038	+	1	NA	TTS (NM_028657)	TTS (NM_028657)	1788	NM_001014836	432479	Mm.440450	NM_001014836	ENSMUSG00000020234	4930404N11Rik	2210409H10Rik|5730551K18Rik|AI854616	RIKEN cDNA 4930404N11 gene	protein-coding
mm_102362.1	chr11	58330320	58330358	-	1	NA	promoter-TSS (NM_024480)	promoter-TSS (NM_024480)	0	NM_001256520	319475	Mm.72124	NM_178761	ENSMUSG00000049755	Zfp672	4930488P06Rik|4930511N19Rik|Znf672	zinc finger protein 672	protein-coding
mm_142768.1	chr17	49529104	49529124	-	1	NA	intron (NM_001008231, intron 1 of 25)	intron (NM_001008231, intron 1 of 25)	35223	NM_001008231	76441	Mm.211275	NM_001008231	ENSMUSG00000040260	Daam2	2310016D11Rik|AI843643|AW557870	dishevelled associated activator of morphogenesis 2	protein-coding
mm_112028.1	chr12	111485809	111485826	-	1	NA	promoter-TSS (NM_001033248)	promoter-TSS (NM_001033248)	6	NM_001033248	212539	Mm.81916	NM_001033248	ENSMUSG00000010529	Gm266	-	predicted gene 266	protein-coding
mm_30187.1	chr3	144691444	144691468	-	1	NA	exon (NM_019464, exon 9 of 9)	exon (NM_019464, exon 9 of 9)	28879	NM_001282042	54673	Mm.271775	NM_019464	ENSMUSG00000037062	Sh3glb1	AA409932|AI314629|AU015566|Bif-1|mKIAA0491	SH3-domain GRB2-like B1 (endophilin)	protein-coding
mm_62619.1	chr7	107370713	107370730	+	1	NA	promoter-TSS (NM_021889)	promoter-TSS (NM_021889)	-69	NM_021889	60510	Mm.302793	NM_021889	ENSMUSG00000062542	Syt9	-	synaptotagmin IX	protein-coding
mm_39015.1	chr4	152128859	152128898	-	1	NA	promoter-TSS (NM_019585)	promoter-TSS (NM_019585)	47	NM_019585	56226	Mm.264215	NM_019585	ENSMUSG00000028943	Espn	je	espin	protein-coding
mm_171148.1	chr3	155962572	155962575	-	1	NA	Intergenic	RLTR10D2|LTR|ERVK	-13781	NR_040553	329780	Mm.119000	NR_040553	ENSMUSG00000104553	9330178D15Rik	9330178D15	RIKEN cDNA 9330178D15 gene	ncRNA
mm_69267.1	chr7	127917708	127917723	-	1	NA	intron (NM_026370, intron 3 of 10)	MER3|DNA|hAT-Charlie	5198	NM_026370	67773	Mm.425492	NM_026370	ENSMUSG00000030801	Kat8	2010203C02Rik|5830450F21Rik|D7Ertd629e|MOF|Myst1	K(lysine) acetyltransferase 8	protein-coding
mm_122393.1	chr14	40966882	40966896	-	1	NA	promoter-TSS (NM_145928)	promoter-TSS (NM_145928)	7	NM_145928	52588	Mm.28876	NM_145928	ENSMUSG00000037824	Tspan14	AA958793|D14Ertd226e|Tm4sf14|tspan-14	tetraspanin 14	protein-coding
mm_163768.1	chr13	120018017	120018036	+	1	NA	Intergenic	Intergenic	34178	NM_001302966	100861753	Mm.165042	NM_001302966	ENSMUSG00000095609	Gm21188	-	predicted gene, 21188	protein-coding
mm_57378.1	chr6	124813096	124813111	-	1	NA	intron (NM_009415, intron 1 of 6)	intron (NM_009415, intron 1 of 6)	1193	NM_009415	21991	Mm.4222	NM_009415	ENSMUSG00000023456	Tpi1	AI255506|Tpi|Tpi-1	triosephosphate isomerase 1	protein-coding
mm_15340.1	chr2	155989308	155989331	+	1	NA	intron (NM_001130000, intron 26 of 32)	intron (NM_001130000, intron 26 of 32)	15108	NM_001145351	320095	Mm.442175	NM_001145351	ENSMUSG00000074646	6430550D23Rik	-	RIKEN cDNA 6430550D23 gene	protein-coding
mm_156171.1	chrX	130186771	130186807	+	1	NA	intron (NM_172493, intron 23 of 26)	Lx7|LINE|L1	437047	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diaph2	Dia3|Diap2|Drf2|E430022I22Rik	diaphanous related formin 2	protein-coding
mm_50097.1	chr6	41533039	41533047	+	1	NA	Intergenic	Intergenic	11267	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_100491.1	chr11	120444312	120444323	+	1	NA	exon (NM_145363, exon 2 of 3)	exon (NM_145363, exon 2 of 3)	1686	NM_145363	208634	Mm.209875	NM_145363	ENSMUSG00000039691	Tspan10	Ocsp	tetraspanin 10	protein-coding
mm_89222.1	chr10	87058044	87058067	+	1	NA	promoter-TSS (NM_029685)	promoter-TSS (NM_029685)	9	NM_029685	76640	Mm.78423	NM_029685	ENSMUSG00000047129	1700113H08Rik	-	RIKEN cDNA 1700113H08 gene	protein-coding
mm_170069.1	chr17	32113410	32113421	+	1	NA	Intergenic	Intergenic	-21992	NR_027316	435518	Mm.328944	NR_027316	ENSMUSG00000002791	Pdxk-ps	ENSMUSG00000002791|Gm9743	pyridoxal (pyridoxine, vitamin B6) kinase, pseudogene	pseudo
mm_41310.1	chr5	90468652	90468662	+	1	NA	exon (NM_009654, exon 8 of 15)	exon (NM_009654, exon 8 of 15)	7787	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_9476.1	chr1	173345804	173345810	-	1	NA	exon (NM_053199, exon 3 of 9)	exon (NM_053199, exon 3 of 9)	-12304	NM_010045	13349	Mm.6393	NM_010045	ENSMUSG00000037872	Ackr1	AA162249|CCBP1|CD234|Darc|Dfy|ESTM35|FY|GPD	atypical chemokine receptor 1 (Duffy blood group)	protein-coding
mm_129927.1	chr15	84447038	84447065	-	1	NA	promoter-TSS (NM_001163145)	promoter-TSS (NM_001163145)	46	NM_001163145	72301	Mm.275387	NM_001163145	ENSMUSG00000062760	1810041L15Rik	Kiaa1644	RIKEN cDNA 1810041L15 gene	protein-coding
mm_91682.1	chr10	43829201	43829215	-	1	NA	intron (NR_131055, intron 1 of 2)	ORR1D1|LTR|ERVL-MaLR	3301	NR_131055	71018	Mm.410796	NR_131055	ENSMUSG00000111342	4933404K13Rik	-	RIKEN cDNA 4933404K13 gene	ncRNA
mm_1910.1	chr1	85906417	85906432	+	1	NA	exon (NM_022417, exon 4 of 6)	exon (NM_022417, exon 4 of 6)	11914	NM_022417	64294	Mm.29870	NM_022417	ENSMUSG00000026223	Itm2c	3110038L02Rik|BRI3|Bricd2c|E25|E25C|ITM3	integral membrane protein 2C	protein-coding
mm_6960.1	chr1	86110767	86110775	-	1	NA	exon (NM_008311, exon 2 of 4)	exon (NM_008311, exon 2 of 4)	1199	NM_008311	15559	Mm.439747	NM_008311	ENSMUSG00000026228	Htr2b	5-HT2B|AJ012488|AV377389	5-hydroxytryptamine (serotonin) receptor 2B	protein-coding
mm_120722.1	chr14	73138739	73138750	+	1	NA	Intergenic	Intergenic	-3766	NM_001170694	105670	Mm.280068	NM_134083	ENSMUSG00000022106	Rcbtb2	2610028E02Rik|2810420M18Rik|AI448345|AW240694|Chc1l|RC/BTB2	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 2	protein-coding
mm_54967.1	chr6	48732670	48732683	-	1	NA	Intergenic	Intergenic	-6371	NM_175860	16205	Mm.252599	NM_008376	ENSMUSG00000090019	Gimap1	IAP38|Imap38|imap	GTPase, IMAP family member 1	protein-coding
mm_24849.1	chr3	95735908	95735938	+	1	NA	promoter-TSS (NR_105981)	promoter-TSS (NR_105981)	-950	NR_105981	102466787		NR_105981	ENSMUSG00000098737	Mir7014	Gm27837|mmu-mir-7014	microRNA 7014	ncRNA
mm_78798.1	chr9	44046905	44046916	+	1	NA	exon (NM_009382, exon 3 of 4)	exon (NM_009382, exon 3 of 4)	3526	NM_009382	21838	Mm.3951	NM_009382	ENSMUSG00000032011	Thy1	CD90|T25|Thy-1|Thy-1.2|Thy1.1|Thy1.2	thymus cell antigen 1, theta	protein-coding
mm_97144.1	chr11	75415640	75415657	+	1	NA	exon (NM_011340, exon 4 of 8)	exon (NM_011340, exon 4 of 8)	6975	NM_011340	20317	Mm.2044	NM_011340	ENSMUSG00000000753	Serpinf1	AI195227|EPC-1|Pedf|Pedfl|Sdf3	serine (or cysteine) peptidase inhibitor, clade F, member 1	protein-coding
mm_151752.1	chr19	5094598	5094624	-	1	NA	intron (NM_009920, intron 2 of 5)	intron (NM_009920, intron 2 of 5)	3910	NM_001302333	12794	Mm.299737	NM_009920	ENSMUSG00000024873	Cnih2	CNIH-2|Cnil	cornichon family AMPA receptor auxiliary protein 2	protein-coding
mm_74981.1	chr8	27141706	27141720	-	1	NA	3' UTR (NM_001080813, exon 6 of 6)	3' UTR (NM_001080813, exon 6 of 6)	-1197	NR_045840	71082	Mm.395259	NR_045840		4933416M07Rik	-	RIKEN cDNA 4933416M07 gene	ncRNA
mm_109594.1	chr12	112644842	112644855	+	1	NA	promoter-TSS (NM_001161737)	promoter-TSS (NM_001161737)	20	NM_013929	30954	Mm.289812	NM_013929	ENSMUSG00000064326	Siva1	CD27bp|Siva	SIVA1, apoptosis-inducing factor	protein-coding
mm_107892.1	chr12	70460523	70460547	+	1	NA	exon (NM_028339, exon 6 of 8)	exon (NM_028339, exon 6 of 8)	7381	NM_028339	72736	Mm.204670	NM_028339	ENSMUSG00000021072	Tmx1	2810425A04Rik|AI465319|Txndc1	thioredoxin-related transmembrane protein 1	protein-coding
mm_95620.1	chr11	53548744	53548748	+	1	NA	3' UTR (NM_001347496, exon 10 of 10)	3' UTR (NM_001347496, exon 10 of 10)	-18623	NM_008443	16568	Mm.88694	NM_008443	ENSMUSG00000018395	Kif3a	Kif3|Kifl|Kns3	kinesin family member 3A	protein-coding
mm_32017.1	chr4	94845749	94845752	+	1	NA	intron (NM_001290549, intron 12 of 22)	L1M2|LINE|L1	83093	NM_027089	67753	Mm.25097	NM_027089	ENSMUSG00000028575	Eqtn	1700028B15Rik|4930579C15Rik|Afaf|C81058|Eqtl|Eqts	equatorin, sperm acrosome associated	protein-coding
mm_61010.1	chr7	49364871	49364915	+	1	NA	intron (NM_175272, intron 2 of 37)	intron (NM_175272, intron 2 of 37)	118704	NM_175272	78286	Mm.333881	NM_175272	ENSMUSG00000052512	Nav2	5330421F07Rik|AU067780|BQ960892|HELAD1|POMFIL2|RAINB1|RAINB2|Unc53H2|mKIAA3015	neuron navigator 2	protein-coding
mm_83944.1	chr9	56852027	56852030	-	1	NA	promoter-TSS (NM_198673)	promoter-TSS (NM_198673)	-65	NM_198673	382075	Mm.335177	NM_198673	ENSMUSG00000045620	Odf3l1	BC049697|Gm1116	outer dense fiber of sperm tails 3-like 1	protein-coding
mm_64327.1	chr7	142201362	142201367	+	1	NA	promoter-TSS (NM_023860)	promoter-TSS (NM_023860)	0	NM_023860	77215	Mm.462993	NM_023860	ENSMUSG00000046248	Krtap5-3	A030007E19Rik	keratin associated protein 5-3	protein-coding
mm_142219.1	chr17	37185469	37185475	-	1	NA	Intergenic	Intergenic	-8420	NM_023137	24108	Mm.140210	NM_023137	ENSMUSG00000035186	Ubd	FAT10	ubiquitin D	protein-coding
mm_76713.1	chr8	94667129	94667137	-	1	NA	promoter-TSS (NM_024269)	promoter-TSS (NM_024269)	42	NM_024269	107566	Mm.393247	NM_024191	ENSMUSG00000031776	Arl2bp	1700010P10Rik|1700027H16Rik|6330544B05Rik|AI482273|AI849834|BART|Bart1	ADP-ribosylation factor-like 2 binding protein	protein-coding
mm_127734.1	chr15	103296726	103296759	+	1	NA	exon (NM_019817, exon 7 of 9)	exon (NM_019817, exon 7 of 9)	11617	NR_029766	724064		NR_029766	ENSMUSG00000065560	Mir148b	Mirn148b|mir-148b	microRNA 148b	ncRNA
mm_5170.1	chr1	10230772	10230775	-	1	NA	intron (NM_001102430, intron 1 of 37)	intron (NM_001102430, intron 1 of 37)	1897	NM_001102430	211673	Mm.229141	NM_001102430	ENSMUSG00000067851	Arfgef1	ARFGEP1|BIG1|D130059B05Rik|D730028O18Rik|P200	ADP-ribosylation factor guanine nucleotide-exchange factor 1(brefeldin A-inhibited)	protein-coding
mm_60479.1	chr7	44478361	44478373	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-6150	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_8984.1	chr1	165685522	165685525	-	1	NA	intron (NM_178593, intron 1 of 6)	intron (NM_178593, intron 1 of 6)	22571	NM_178593	226594	Mm.265552	NM_178593	ENSMUSG00000040723	Rcsd1	A430105K13Rik|BC025872|CapZIP	RCSD domain containing 1	protein-coding
mm_139808.1	chr17	66364592	66364622	+	1	NA	intron (NM_001114098, intron 8 of 14)	intron (NM_001114098, intron 8 of 14)	85143	NM_172963	68617	Mm.33421	NM_172963	ENSMUSG00000052105	Mtcl1	1110012J17Rik|Ccdc165|D130071O13|Kiaa0802|Soga2|mKIAA0802|t8219b25	microtubule crosslinking factor 1	protein-coding
mm_74850.1	chr8	24595635	24595671	-	1	NA	promoter-TSS (NM_001293690)	promoter-TSS (NM_001293690)	13	NM_001293690	15930	Mm.392	NM_008324	ENSMUSG00000031551	Ido1	Ido|Indo	indoleamine 2,3-dioxygenase 1	protein-coding
mm_151165.1	chr19	53195331	53195361	+	1	NA	intron (NM_013758, intron 1 of 15)	intron (NM_013758, intron 1 of 15)	51349	NM_013758	27360	Mm.426080	NM_013758	ENSMUSG00000025026	Add3	AI463285|R75380	adducin 3 (gamma)	protein-coding
mm_141506.1	chr17	31636632	31636652	-	1	NA	intron (NM_178224, intron 1 of 15)	CpG	563	NM_144855	12411	Mm.206417	NM_144855	ENSMUSG00000024039	Cbs	AI047524|AI303044|HIP4	cystathionine beta-synthase	protein-coding
mm_169888.1	chr16	46663738	46663745	-	1	NA	Intergenic	Intergenic	-166774	NM_021497	58998	Mm.40477	NM_021495	ENSMUSG00000022656	Nectin3	2610301B19Rik|3000002N23Rik|4921513D19Rik|AA407785|AU016832|AW538082|CD113|Pvrl3	nectin cell adhesion molecule 3	protein-coding
mm_50534.1	chr6	49045745	49045758	+	1	NA	intron (NM_053110, intron 4 of 10)	intron (NM_053110, intron 4 of 10)	9233	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_105024.1	chr11	100472726	100472759	-	1	NA	promoter-TSS (NM_172565)	promoter-TSS (NM_172565)	40	NM_172565	217194	Mm.183320	NM_172565	ENSMUSG00000048732	Klhl11	BC011167	kelch-like 11	protein-coding
mm_60156.1	chr7	39517793	39517802	+	1	NA	promoter-TSS (NM_001004139)	promoter-TSS (NM_001004139)	31	NM_001004139	70227	Mm.333800	NM_001004139	ENSMUSG00000068959	Zfp619	3000002G13Rik	zinc finger protein 619	protein-coding
mm_32543.1	chr4	109316844	109316852	+	1	NA	intron (NM_007943, intron 8 of 24)	B1_Mus1|SINE|Alu	-26208	NM_001159964	13858	Mm.318250	NM_007943	ENSMUSG00000028552	Eps15	2410112D09Rik	epidermal growth factor receptor pathway substrate 15	protein-coding
mm_2914.1	chr1	132008370	132008397	+	1	NA	intron (NM_007923, intron 1 of 4)	CpG	778	NM_007923	13714	Mm.254233	NM_007923	ENSMUSG00000026436	Elk4	2310011G17Rik|A130026I01Rik|BB162516|SAP-1|Sap1	ELK4, member of ETS oncogene family	protein-coding
mm_156550.1	chrX	151522353	151522384	+	1	NA	intron (NM_177201, intron 1 of 18)	intron (NM_177201, intron 1 of 18)	1696	NM_001113354	320595	Mm.17156	NM_177201	ENSMUSG00000041229	Phf8	9830141C09Rik|mKIAA1111	PHD finger protein 8	protein-coding
mm_6568.1	chr1	75190351	75190381	-	1	NA	non-coding (NR_109938, exon 3 of 16)	non-coding (NR_109938, exon 3 of 16)	1644	NM_001003917	245860	Mm.238266	NM_001003917	ENSMUSG00000033124	Atg9a	AU019532|Apg9l1|Atg9|Atg9l1	autophagy related 9A	protein-coding
mm_120678.1	chr14	70577811	70577838	+	1	NA	promoter-TSS (NM_153136)	promoter-TSS (NM_153136)	-23	NM_153136	213484	Mm.34191	NM_153136	ENSMUSG00000045211	Nudt18	BC036718	nudix (nucleoside diphosphate linked moiety X)-type motif 18	protein-coding
mm_53867.1	chr6	149328847	149328860	+	1	NA	exon (NM_001289662, exon 3 of 5)	exon (NM_001289662, exon 3 of 5)	19439	NM_001289662	67246	Mm.333515	NM_026054	ENSMUSG00000032712	2810474O19Rik	6720435I21Rik|AA536804|AU020969|GET|Kiaa1551	RIKEN cDNA 2810474O19 gene	protein-coding
mm_10003.1	chr1	191541360	191541366	-	1	NA	exon (NM_001305233, exon 15 of 16)	exon (NM_001305233, exon 15 of 16)	34181	NM_001305233	76843	Mm.189102	NM_029766	ENSMUSG00000037474	Dtl	2810047L02Rik|5730564G15Rik|L2dtl|Ramp	denticleless E3 ubiquitin protein ligase	protein-coding
mm_64540.1	chr7	144238719	144238730	+	1	NA	intron (NM_001113373, intron 4 of 15)	intron (NM_001113373, intron 4 of 15)	-45661	NM_001081370	210274	Mm.483624	NM_001081370	ENSMUSG00000037541	Shank2	ProSAP1|mKIAA1022	SH3/ankyrin domain gene 2	protein-coding
mm_126372.1	chr15	80135238	80135241	+	1	NA	intron (NM_025609, intron 1 of 10)	intron (NM_025609, intron 1 of 10)	2085	NM_025609	66513	Mm.288245	NM_025609	ENSMUSG00000022414	Tab1	2310012M03Rik|Map3k7ip1|b2b449Clo	TGF-beta activated kinase 1/MAP3K7 binding protein 1	protein-coding
mm_12039.1	chr2	58769764	58769772	+	1	NA	intron (NM_029692, intron 2 of 6)	intron (NM_029692, intron 2 of 6)	14584	NM_029692	76654	Mm.200370	NM_029692	ENSMUSG00000026839	Upp2	1700124F02Rik|AI266885|UDRPASE2|UP2|UPASE2	uridine phosphorylase 2	protein-coding
mm_29916.1	chr3	131489764	131489774	-	1	NA	Intergenic	Intergenic	-74999	NM_001289479	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_166855.1	chr7	19989457	19989459	+	1	NA	intron (NM_027839, intron 11 of 11)	B1_Mur4|SINE|Alu	-18565	NM_194058	243874	Mm.277114	NM_194058	ENSMUSG00000060508	Nlrp9b	Nalp-delta|Nalp9b|Nlrp9	NLR family, pyrin domain containing 9B	protein-coding
mm_69459.1	chr7	133123384	133123404	-	1	NA	promoter-TSS (NM_009980)	promoter-TSS (NM_009980)	89	NM_009980	13017	Mm.246240	NM_009980	ENSMUSG00000030970	Ctbp2	AA407280|D7Ertd45e|Gtrgeo6|Ribeye	C-terminal binding protein 2	protein-coding
mm_58654.1	chr7	6389651	6389688	+	1	NA	intron (NM_175247, intron 3 of 6)	intron (NM_175247, intron 3 of 6)	6351	NM_175247	22690	Mm.127014	NM_175247	ENSMUSG00000062861	Zfp28	2810438M17Rik|Zfp-28|mkr-5	zinc finger protein 28	protein-coding
mm_113265.1	chr13	28951521	28951541	+	1	NA	3' UTR (NM_009238, exon 1 of 1)	3' UTR (NM_009238, exon 1 of 1)	2151	NM_009238	20677	Mm.240627	NM_009238	ENSMUSG00000076431	Sox4	AA682046|Sox-4	SRY (sex determining region Y)-box 4	protein-coding
mm_78422.1	chr9	31071912	31071913	+	1	NA	3' UTR (NM_001115130, exon 6 of 6)	3' UTR (NM_001115130, exon 6 of 6)	41268	NM_172765	235132	Mm.239355	NM_172765	ENSMUSG00000047412	Zbtb44	6030404E16Rik|Btbd15|E230011F09	zinc finger and BTB domain containing 44	protein-coding
mm_38243.1	chr4	136593013	136593043	-	1	NA	exon (NM_133872, exon 2 of 19)	exon (NM_133872, exon 2 of 19)	9695	NM_133872	99982	Mm.28540	NM_133872	ENSMUSG00000036940	Kdm1a	1810043O07Rik|AA408884|Aof2|D4Ertd478e|Kdm1|Lsd1|mKIAA0601	lysine (K)-specific demethylase 1A	protein-coding
mm_114542.1	chr13	73770232	73770252	+	1	NA	intron (NM_011390, intron 1 of 23)	intron (NM_011390, intron 1 of 23)	6545	NM_011390	20499	Mm.275800	NM_011390	ENSMUSG00000017756	Slc12a7	AA408796|D13Ertd261e|Kcc4	solute carrier family 12, member 7	protein-coding
mm_122257.1	chr14	34201605	34201622	-	1	NA	promoter-TSS (NM_183209)	promoter-TSS (NM_183209)	20	NM_183209	432839	Mm.294643	NM_183209	ENSMUSG00000071531	Gprin2	C130040D06Rik|C230073P13|Gm286|mKIAA0514	G protein regulated inducer of neurite outgrowth 2	protein-coding
mm_93630.1	chr10	117280736	117280766	-	1	NA	exon (NM_017372, exon 2 of 4)	exon (NM_017372, exon 2 of 4)	1521	NM_017372	17105	Mm.45436	NM_017372	ENSMUSG00000069516	Lyz2	AI326280|Lys|Lysm|Lyzf2|Lyzs|Lzm|Lzm-s1|Lzp	lysozyme 2	protein-coding
mm_144403.1	chr18	20782588	20782617	+	1	NA	Intergenic	Intergenic	-36198	NM_019737	56386	Mm.393827	NM_019737	ENSMUSG00000056124	B4galt6	AA536803|AU022389	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 6	protein-coding
mm_31363.1	chr4	47285961	47285966	+	1	NA	intron (NM_009928, intron 21 of 39)	intron (NM_009928, intron 21 of 39)	-67259	NM_001312868	21812	Mm.197552	NM_009370	ENSMUSG00000007613	Tgfbr1	ALK5|AU017191|Alk-5|ESK2|TGFR-1|TbetaR-I|TbetaRI	transforming growth factor, beta receptor I	protein-coding
mm_9920.1	chr1	189402749	189402761	-	1	NA	promoter-TSS (NM_001281848)	promoter-TSS (NM_001281848)	-482	NM_001281848	16526	Mm.33304	NM_010607	ENSMUSG00000037624	Kcnk2	A430027H14Rik|AI848635|TREK-1	potassium channel, subfamily K, member 2	protein-coding
mm_82082.1	chr9	123021316	123021374	+	1	NA	promoter-TSS (NM_025339)	promoter-TSS (NM_025339)	19	NM_001164823	66079	Mm.482265	NM_025339	ENSMUSG00000066233	Tmem42	0610027O18Rik|4933429E06Rik|AV003444|D9Ertd662e	transmembrane protein 42	protein-coding
mm_142636.1	chr17	47421853	47421864	-	1	NA	promoter-TSS (NM_001347584)	promoter-TSS (NM_001347584)	22	NM_001347584	75462	Mm.46129	NM_029296	ENSMUSG00000047150	1700001C19Rik	-	RIKEN cDNA 1700001C19 gene	protein-coding
mm_26766.1	chr3	8863271	8863302	-	1	NA	intron (NM_025434, intron 2 of 2)	intron (NM_025434, intron 2 of 2)	60571	NM_025434	66230	Mm.38460	NM_025434	ENSMUSG00000040269	Mrps28	1500012D08Rik|AW061224	mitochondrial ribosomal protein S28	protein-coding
mm_21925.1	chr2	166996148	166996158	-	1	NA	5' UTR (NM_011490, exon 1 of 12)	5' UTR (NM_011490, exon 1 of 12)	146	NM_011490	20853	Mm.73276	NM_011490	ENSMUSG00000039536	Stau1	5830401L18Rik|AW549911|C85792|Stau	staufen (RNA binding protein) homolog 1 (Drosophila)	protein-coding
mm_36928.1	chr4	108301046	108301107	-	1	NA	promoter-TSS (NM_001033634)	promoter-TSS (NM_001033634)	14	NM_001033634	414872	Mm.426241	NM_001033634	ENSMUSG00000034636	Zyg11b	1110046I03Rik|2810482G21Rik|D4Mgi23|Gm431|mKIAA1730	zyg-ll family member B, cell cycle regulator	protein-coding
mm_39499.1	chr5	21186285	21186340	+	1	NA	promoter-TSS (NM_175437)	promoter-TSS (NM_175437)	45	NM_175437	212167	Mm.121705	NM_175437	ENSMUSG00000039934	Gsap	A530088I07Rik|Pion	gamma-secretase activating protein	protein-coding
mm_41867.1	chr5	104459540	104459580	+	1	NA	5' UTR (NM_008861, exon 1 of 15)	5' UTR (NM_008861, exon 1 of 15)	103	NM_008861	18764	Mm.6442	NM_008861	ENSMUSG00000034462	Pkd2	C030034P18Rik|PC2|TRPP2	polycystic kidney disease 2	protein-coding
mm_117533.1	chr13	83571990	83572010	-	1	NA	intron (NM_001347566, intron 1 of 10)	intron (NM_001347566, intron 1 of 10)	-1607	NM_001347577	17260	Mm.24001	NM_025282	ENSMUSG00000005583	Mef2c	5430401D19Rik|9930028G15Rik|AV011172|Mef2	myocyte enhancer factor 2C	protein-coding
mm_158713.1	chrX	162565607	162565617	-	1	NA	intron (NM_178256, intron 1 of 17)	intron (NM_178256, intron 1 of 17)	78046	NM_001290633	194590	Mm.442441	NM_178256	ENSMUSG00000040855	Reps2	POB1	RALBP1 associated Eps domain containing protein 2	protein-coding
mm_6973.1	chr1	86348015	86348018	-	1	NA	3' UTR (NM_010880, exon 14 of 14)	3' UTR (NM_010880, exon 14 of 14)	3269	NR_028478	100303740	Mm.154378	NR_028478	ENSMUSG00000064837	Snora75	MBI-55	small nucleolar RNA, H/ACA box 75	snoRNA
mm_132228.1	chr16	32661224	32661245	+	1	NA	intron (NM_016788, intron 1 of 15)	intron (NM_016788, intron 1 of 15)	6963	NR_033493	675921	Mm.404316	NR_033493	ENSMUSG00000075265	Tnk2os	ENSMUSG00000075265|Gm10818	tyrosine kinase, non-receptor 2, opposite strand	ncRNA
mm_17213.1	chr2	25493435	25493439	-	1	NA	intron (NM_029958, intron 1 of 5)	intron (NM_029958, intron 1 of 5)	474	NM_029958	77701	Mm.99123	NM_029958	ENSMUSG00000026943	Lcn12	9230102M18Rik	lipocalin 12	protein-coding
mm_8867.1	chr1	162834304	162834307	-	1	NA	intron (NM_010231, intron 6 of 8)	intron (NM_010231, intron 6 of 8)	-21756	NM_144878	226564	Mm.155164	NM_144878	ENSMUSG00000026692	Fmo4	D1Ertd532e	flavin containing monooxygenase 4	protein-coding
mm_80620.1	chr9	88549863	88549864	+	1	NA	intron (NM_001163061, intron 1 of 4)	intron (NM_001163061, intron 1 of 4)	1843	NM_001163061	71640	Mm.259988	NM_001142943	ENSMUSG00000032425	Zfp949	4930422I07Rik	zinc finger protein 949	protein-coding
mm_86164.1	chr9	118701861	118701869	-	1	NA	intron (NM_133721, intron 15 of 27)	intron (NM_133721, intron 15 of 27)	-9827	NM_001113514	104099	Mm.335520	NM_133721	ENSMUSG00000039115	Itga9	(alpha)9|2610002H11Rik|6720458D17Rik|AI461869|D130073C02|D9Ertd428e	integrin alpha 9	protein-coding
mm_10229.1	chr2	6341021	6341031	+	1	NA	intron (NM_001080548, intron 2 of 14)	intron (NM_001080548, intron 2 of 14)	-11710	NM_181399	98910	Mm.40673	NM_181399	ENSMUSG00000039046	Usp6nl	AI316785|RNTRE|TRE2NL|mKIAA0019	USP6 N-terminal like	protein-coding
mm_43524.1	chr5	137152436	137152443	+	1	NA	Intergenic	Intergenic	-36232	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_168975.1	chr12	88066644	88066648	+	1	NA	Intergenic	Intergenic	112166	NM_001270792	100039087	Mm.458830	NM_001270792	ENSMUSG00000096276	Gm2042	-	predicted gene 2042	protein-coding
mm_158915.1	chr1	52953071	52953071	-	1	NA	promoter-TSS (NM_144953)	promoter-TSS (NM_144953)	-231	NM_144953	67080	Mm.236287	NM_144953	ENSMUSG00000043629	1700019D03Rik	2410136C24Rik|AA410151|smAKAP	RIKEN cDNA 1700019D03 gene	protein-coding
mm_32291.1	chr4	103114713	103114759	+	1	NA	promoter-TSS (NM_146254)	promoter-TSS (NM_146254)	346	NM_001286222	71148	Mm.288721	NM_027696	ENSMUSG00000028522	Mier1	4933425I22Rik|5830411K19Rik|er1	MEIR1 treanscription regulator	protein-coding
mm_24845.1	chr3	95662183	95662197	+	1	NA	3' UTR (NM_008562, exon 3 of 3)	3' UTR (NM_008562, exon 3 of 3)	3469	NM_008562	17210	Mm.1639	NM_008562	ENSMUSG00000038612	Mcl1	AW556805|Mcl-1	myeloid cell leukemia sequence 1	protein-coding
mm_116691.1	chr13	49309218	49309257	-	1	NA	promoter-TSS (NM_015759)	promoter-TSS (NM_015759)	-29	NM_015759	30938	Mm.291089	NM_015759	ENSMUSG00000037946	Fgd3	5830461L01Rik|ZFYVE5	FYVE, RhoGEF and PH domain containing 3	protein-coding
mm_148977.1	chr19	7561729	7561746	+	1	NA	intron (NM_139269, intron 2 of 4)	intron (NM_139269, intron 2 of 4)	4278	NM_139269	225845	Mm.274810	NM_139269	ENSMUSG00000060675	Pla2g16	C78643|HRSL3|Hrasls3|Hrev107|MLP-3	phospholipase A2, group XVI	protein-coding
mm_161999.1	chr19	39886729	39886729	-	1	NA	promoter-TSS (NM_001104525)	promoter-TSS (NM_001104525)	40	NM_001104525	100043108	Mm.482331	NM_001104525	ENSMUSG00000092008	Cyp2c69	AI098658	cytochrome P450, family 2, subfamily c, polypeptide 69	protein-coding
mm_17598.1	chr2	30803626	30803673	-	1	NA	promoter-TSS (NR_028487)	promoter-TSS (NR_028487)	15	NR_028486	73598	Mm.34166	NM_198000	ENSMUSG00000044320	1700001O22Rik	1700113K14Rik|4930549G18Rik	RIKEN cDNA 1700001O22 gene	protein-coding
mm_164224.1	chr15	85580146	85580150	+	1	NA	promoter-TSS (NR_040433)	promoter-TSS (NR_040433)	581	NM_001163633	22422	Mm.306946	NM_009528	ENSMUSG00000022382	Wnt7b	Wnt-7b	wingless-type MMTV integration site family, member 7B	protein-coding
mm_132570.1	chr16	38132051	38132061	+	1	NA	intron (NM_001347232, intron 1 of 11)	intron (NM_001347232, intron 1 of 11)	-42796	NR_033221	414072	Mm.483602	NR_033221		BC031361	-	cDNA sequence BC031361	ncRNA
mm_26162.1	chr3	138277749	138277757	+	1	NA	intron (NM_007409, intron 1 of 8)	intron (NM_007409, intron 1 of 8)	108	NM_007409	11522	Mm.2409	NM_007409	ENSMUSG00000074207	Adh1	ADH-AA|AI194826|Adh-1|Adh-1-t|Adh-1e|Adh-1t|Adh-3e|Adh1-e|Adh1-t|Adh1tl|Adh3-e	alcohol dehydrogenase 1 (class I)	protein-coding
mm_32133.1	chr4	99194125	99194204	+	1	NA	promoter-TSS (NM_001145967)	promoter-TSS (NM_001145967)	17	NM_001145967	242557	Mm.241663	NM_175029	ENSMUSG00000028550	Atg4c	Apg4-C|Apg4c|Atg4cl|Autl1	autophagy related 4C, cysteine peptidase	protein-coding
mm_42426.1	chr5	115332722	115332793	+	1	NA	TTS (NM_029645)	TTS (NM_029645)	5580	NR_036616	108014	Mm.287826	NM_025573	ENSMUSG00000029538	Srsf9	25kDa|2610029M16Rik|SRp30c|Sfrs9	serine/arginine-rich splicing factor 9	protein-coding
mm_92620.1	chr10	80165070	80165108	-	1	NA	intron (NR_038088, intron 1 of 4)	intron (NR_038088, intron 1 of 4)	-2752	NM_007705	12696	Mm.17898	NM_007705	ENSMUSG00000045193	Cirbp	Cirp|R74941	cold inducible RNA binding protein	protein-coding
mm_102189.1	chr11	54249336	54249385	-	1	NA	exon (NM_009969, exon 2 of 4)	exon (NM_009969, exon 2 of 4)	539	NM_009969	12981	Mm.4922	NM_009969	ENSMUSG00000018916	Csf2	Csfgm|GMCSF|Gm-CSf|MGI-IGM	colony stimulating factor 2 (granulocyte-macrophage)	protein-coding
mm_132260.1	chr16	32755747	32755776	+	1	NA	exon (NM_080457, exon 4 of 27)	exon (NM_080457, exon 4 of 27)	19875	NM_080457	140474	Mm.214599	NM_080457	ENSMUSG00000079620	Muc4	4933405I11Rik|Asgp	mucin 4	protein-coding
mm_158133.1	chrX	103186476	103186486	-	1	NA	5' UTR (NM_008671, exon 1 of 1)	5' UTR (NM_008671, exon 1 of 1)	183	NM_008671	17954	Mm.388694	NM_008671	ENSMUSG00000082229	Nap1l2	Bpx	nucleosome assembly protein 1-like 2	protein-coding
mm_55838.1	chr6	83155838	83155849	-	1	NA	promoter-TSS (NM_027948)	promoter-TSS (NM_027948)	536	NM_023790	75659	Mm.130665	NM_023790	ENSMUSG00000030032	Wdr54	1700030E05Rik	WD repeat domain 54	protein-coding
mm_38639.1	chr4	143161330	143161337	-	1	NA	intron (NM_001256380, intron 6 of 7)	intron (NM_001256380, intron 6 of 7)	-25171	NR_105988	102465618		NR_105988	ENSMUSG00000106597	Mir7021	mmu-mir-7021	microRNA 7021	ncRNA
mm_80062.1	chr9	69403838	69403840	+	1	NA	intron (NM_145618, intron 3 of 15)	intron (NM_145618, intron 3 of 15)	5841	NM_145618	93697	Mm.35911	NM_145618	ENSMUSG00000032235	Ice2	B230343B06Rik|Narg2	interactor of little elongation complex ELL subunit 2	protein-coding
mm_61712.1	chr7	81296548	81296555	+	1	NA	intron (NM_008803, intron 6 of 21)	intron (NM_008803, intron 6 of 21)	48683	NM_009092	20068	Mm.42767	NM_009092	ENSMUSG00000061787	Rps17	-	ribosomal protein S17	protein-coding
mm_112277.1	chr12	114322845	114322860	-	1	NA	Intergenic	Intergenic	146614	NR_106062	102465663		NR_106062	ENSMUSG00000105438	Mir7094-1	mmu-mir-7094-1	microRNA 7094-1	ncRNA
mm_114786.1	chr13	89209710	89209714	+	1	NA	intron (NM_010103, intron 8 of 9)	intron (NM_010103, intron 8 of 9)	-330924	NM_013500	12950	Mm.266790	NM_013500	ENSMUSG00000021613	Hapln1	BB099155|CLP|Crtl1|Crtl1l|LP|LP-1	hyaluronan and proteoglycan link protein 1	protein-coding
mm_16295.1	chr2	174285274	174285284	+	1	NA	exon (NM_022000, exon 2 of 13)	exon (NM_022000, exon 2 of 13)	959	NM_022000	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_11597.1	chr2	33641055	33641068	+	1	NA	promoter-TSS (NM_010725)	promoter-TSS (NM_010725)	-132	NR_046275	100504399	Mm.72070	NM_177842		C130021I20Rik	-	Riken cDNA C130021I20 gene	ncRNA
mm_32416.1	chr4	107048145	107048182	+	1	NA	3' UTR (NM_198438, exon 17 of 17)	3' UTR (NM_198438, exon 17 of 17)	18703	NM_025500	56280	Mm.29517	NM_025500	ENSMUSG00000028622	Mrpl37	2300004O14Rik|AI132596|MRP-L2|Rpml2	mitochondrial ribosomal protein L37	protein-coding
mm_158382.1	chrX	136051208	136051218	-	1	NA	Intergenic	Intergenic	17023	NM_009749	12069	Mm.94160	NM_009749	ENSMUSG00000042750	Bex2	AL024066|Bex1	brain expressed X-linked 2	protein-coding
mm_57674.1	chr6	128494562	128494580	-	1	NA	intron (NM_007376, intron 21 of 35)	intron (NM_007376, intron 21 of 35)	32149	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_171898.1	chr5	41832632	41832636	-	1	NA	exon (NM_001081422, exon 4 of 27)	exon (NM_001081422, exon 4 of 27)	11681	NM_001310601	665775	Mm.158726	NM_001081422	ENSMUSG00000061755	Bod1l	A230054D04Rik|AI853319|FAM44A|mKIAA1327	biorientation of chromosomes in cell division 1-like	protein-coding
mm_101328.1	chr11	22972870	22972881	-	1	NA	5' UTR (NM_011663, exon 1 of 1)	5' UTR (NM_011663, exon 1 of 1)	870	NM_011663	22183	Mm.29542	NM_011663	ENSMUSG00000044068	Zrsr1	D11Ncvs75|Irlgs2|SP2|U2af1-rs1|U2afbp-rs	zinc finger (CCCH type), RNA binding motif and serine/arginine rich 1	protein-coding
mm_74012.1	chr8	121421209	121421218	+	1	NA	Intergenic	Intergenic	120741	NM_029597	76405	Mm.165697	NM_029597	ENSMUSG00000031809	1700018B08Rik	1700084O22Rik	RIKEN cDNA 1700018B08 gene	protein-coding
mm_81585.1	chr9	110422639	110422645	+	1	NA	3' UTR (NM_008694, exon 4 of 4)	3' UTR (NM_008694, exon 4 of 4)	2834	NM_008694	18054	Mm.236225	NM_008694	ENSMUSG00000032484	Ngp	bectenecin	neutrophilic granule protein	protein-coding
mm_69149.1	chr7	127122008	127122027	-	1	NA	promoter-TSS (NM_133686)	promoter-TSS (NM_133686)	12	NM_133686	67375	Mm.26928	NM_133686	ENSMUSG00000030674	Qprt	2410027J01Rik|AI647766|QPRTase	quinolinate phosphoribosyltransferase	protein-coding
mm_4610.1	chr1	178529114	178529134	+	1	NA	promoter-TSS (NM_001161665)	promoter-TSS (NM_001161665)	-1	NM_001161665	269152	Mm.129727	NM_177724	ENSMUSG00000026494	Kif26b	4832420M10|BC056349|D230039L06Rik	kinesin family member 26B	protein-coding
mm_124385.1	chr14	108913947	108913959	-	1	NA	5' UTR (NM_199065, exon 1 of 1)	5' UTR (NM_199065, exon 1 of 1)	286	NM_199065	76965	Mm.257268	NM_199065	ENSMUSG00000075478	Slitrk1	3200001I04Rik	SLIT and NTRK-like family, member 1	protein-coding
mm_36125.1	chr4	58981883	58981886	-	1	NA	intron (NM_025968, intron 3 of 9)	intron (NM_025968, intron 3 of 9)	5194	NM_025968	67103	Mm.34497	NM_025968	ENSMUSG00000028378	Ptgr1	2510002C21Rik|Ltb4dh|Zadh3	prostaglandin reductase 1	protein-coding
mm_31282.1	chr4	45848884	45848910	+	1	NA	promoter-TSS (NM_028788)	promoter-TSS (NM_028788)	-50	NM_028788	74152	Mm.63645	NM_028788	ENSMUSG00000028327	Stra6l	1300002K09Rik|Rbpr2	STRA6-like	protein-coding
mm_113868.1	chr13	48550809	48550845	+	1	NA	Intergenic	Intergenic	-12555	NR_029725	387244		NR_029725	ENSMUSG00000065421	Mirlet7a-1	Let-7a|Mirnlet7a|Mirnlet7a-1|let-7a-1	microRNA let7a-1	ncRNA
mm_152165.1	chr19	7295395	7295468	-	1	NA	promoter-TSS (NM_001080390)	promoter-TSS (NM_001080390)	16	NM_001080390	13728	Mm.258986	NM_007928	ENSMUSG00000024969	Mark2	EMK-1|Emk|Par-1|Par-1b	MAP/microtubule affinity regulating kinase 2	protein-coding
mm_43698.1	chr5	139211935	139211948	+	1	NA	intron (NM_001256115, intron 1 of 21)	intron (NM_001256115, intron 1 of 21)	-3217	NM_001256118	77053	Mm.210845	NM_024451	ENSMUSG00000036817	Sun1	4632417G13Rik|5730434D03Rik|Unc84a|mKIAA0810	Sad1 and UNC84 domain containing 1	protein-coding
mm_117013.1	chr13	58113622	58113655	-	1	NA	Intergenic	Intergenic	-11210	NM_001195075	100503085	Mm.379256	NM_001195075	ENSMUSG00000014164	Klhl3	7530408C15Rik|AI430941|EG627648	kelch-like 3	protein-coding
mm_82046.1	chr9	122351764	122351771	+	1	NA	5' UTR (NM_026179, exon 1 of 7)	5' UTR (NM_026179, exon 1 of 7)	151	NM_026179	67469	Mm.280254	NM_026179	ENSMUSG00000032540	Abhd5	1300003D03Rik|2010002J10Rik|CDS|CGI-58|IECN5|NCIE2	abhydrolase domain containing 5	protein-coding
mm_106298.1	chr11	118222755	118222792	-	1	NA	intron (NM_001112699, intron 1 of 12)	intron (NM_001112699, intron 1 of 12)	-10031	NM_001112700	19157	Mm.86413	NM_011180	ENSMUSG00000017132	Cyth1	CLM1|CTH-1|CYTIP|Pscd1	cytohesin 1	protein-coding
mm_132891.1	chr16	48842720	48842736	+	1	NA	intron (NM_020509, intron 1 of 3)	intron (NM_020509, intron 1 of 3)	176	NM_020509	57262	Mm.441868	NM_020509	ENSMUSG00000061100	Retnla	1810019L16Rik|Fizz-1|Fizz1|HIMF|RELM-alpha|RELMa|RELMalpha|Xcp2	resistin like alpha	protein-coding
mm_143303.1	chr17	65986012	65986024	-	1	NA	exon (NM_001025572, exon 9 of 13)	exon (NM_001025572, exon 9 of 13)	-34831	NM_023053	65960	Mm.10153	NM_023053	ENSMUSG00000024098	Twsg1	1810013J15Rik|9030422N06Rik|AW552143|D17Ertd403e|Tsg|Twg	twisted gastrulation BMP signaling modulator 1	protein-coding
mm_145946.1	chr18	67390701	67390724	+	1	NA	promoter-TSS (NM_026473)	promoter-TSS (NM_026473)	-19	NM_026473	67951	Mm.181860	NM_026473	ENSMUSG00000001473	Tubb6	2310057H16Rik|BB220206	tubulin, beta 6 class V	protein-coding
mm_119753.1	chr14	54158457	54158467	+	1	NA	Intergenic	Intergenic	95467	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_162423.1	chr1	92048750	92048755	+	1	NA	intron (NM_207225, intron 3 of 26)	intron (NM_207225, intron 3 of 26)	131589	NM_207225	208727	Mm.318567	NM_207225	ENSMUSG00000026313	Hdac4	4932408F19Rik|HD4	histone deacetylase 4	protein-coding
mm_111060.1	chr12	80110457	80110470	-	1	NA	exon (NM_007564, exon 2 of 2)	exon (NM_007564, exon 2 of 2)	2550	NM_007564	12192	Mm.235132	NM_007564	ENSMUSG00000021127	Zfp36l1	AW742437|AW743212|Berg36|Brf1|D530020L18Rik|ERF1|TIS11b|cMG1	zinc finger protein 36, C3H type-like 1	protein-coding
mm_136305.1	chr16	91618987	91619024	-	1	NA	promoter-TSS (NM_138664)	promoter-TSS (NM_138664)	-6	NM_138664	246738	Mm.101927	NM_138664	ENSMUSG00000039763	Dnajc28	BC020175|ORF28	DnaJ heat shock protein family (Hsp40) member C28	protein-coding
mm_14775.1	chr2	145822143	145822157	+	1	NA	intron (NM_028724, intron 2 of 12)	intron (NM_028724, intron 2 of 12)	36034	NM_028724	74030	Mm.228799	NM_028724	ENSMUSG00000001768	Rin2	2010003K16Rik|4632403N06Rik|AW821980|RASSF4	Ras and Rab interactor 2	protein-coding
mm_152772.1	chr19	21077875	21077880	-	1	NA	Intergenic	Intergenic	-26833	NR_126458	75354	Mm.243873	NR_126458		4930554I06Rik	-	RIKEN cDNA 4930554I06 gene	ncRNA
mm_146774.1	chr18	20059308	20059318	-	1	NA	5' UTR (NM_013505, exon 1 of 17)	5' UTR (NM_013505, exon 1 of 17)	241	NM_013505	13506	Mm.280547	NM_013505	ENSMUSG00000024331	Dsc2	AW228162	desmocollin 2	protein-coding
mm_63282.1	chr7	126770978	126771028	+	1	NA	exon (NM_024228, exon 8 of 10)	exon (NM_024228, exon 8 of 10)	4589	NM_024228	68616	Mm.246881	NM_024228	ENSMUSG00000030703	Gdpd3	1110015E22Rik	glycerophosphodiester phosphodiesterase domain containing 3	protein-coding
mm_165692.1	chr3	93443428	93443430	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	1099	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_39286.1	chr5	3995034	3995035	+	1	NA	intron (NM_194462, intron 15 of 47)	intron (NM_194462, intron 15 of 47)	66848	NM_194462	100986	Mm.46044	NM_194462	ENSMUSG00000040407	Akap9	5730481H23Rik|AKAP-9|AKAP450|AW545847|C79026|G1-448-15|PRKA9|mKIAA0803|mei2-5|repro12	A kinase (PRKA) anchor protein (yotiao) 9	protein-coding
mm_103178.1	chr11	70459958	70459984	-	1	NA	promoter-TSS (NM_023158)	promoter-TSS (NM_023158)	13	NM_023158	66102	Mm.425692	NM_023158	ENSMUSG00000018920	Cxcl16	0910001K24Rik|AV290116|BB024863|CXCL16v1|CXCL16v2|SR-PSOX|Zmynd15|b2b498Clo	chemokine (C-X-C motif) ligand 16	protein-coding
mm_2815.1	chr1	130878328	130878340	+	1	NA	exon (NM_026976, exon 6 of 8)	exon (NM_026976, exon 6 of 8)	9077	NM_053095	93672	Mm.196691	NM_053095	ENSMUSG00000026420	Il24	FISP|Mda-7|Mda7|St16	interleukin 24	protein-coding
mm_133161.1	chr16	70408453	70408457	+	1	NA	intron (NM_028803, intron 3 of 15)	intron (NM_028803, intron 3 of 15)	94506	NM_028803	74185	Mm.396102	NM_028803	ENSMUSG00000022707	Gbe1	2310045H19Rik|2810426P10Rik|D16Ertd536e	glucan (1,4-alpha-), branching enzyme 1	protein-coding
mm_138443.1	chr17	35128426	35128434	+	1	NA	TTS (NM_018816)	TTS (NM_018816)	2028	NM_033477	114585	Mm.42070	NM_033477	ENSMUSG00000043311	D17H6S53E	G4|NG34	DNA segment, Chr 17, human D6S53E	protein-coding
mm_132342.1	chr16	33829914	33829953	+	1	NA	5' UTR (NM_001145884, exon 1 of 15)	5' UTR (NM_001145884, exon 1 of 15)	268	NM_001145884	16419	Mm.6424	NM_010580	ENSMUSG00000022817	Itgb5	AA475909|AI874634|ESTM23|[b]-5|[b]5|[b]5A|[b]5B|beta-5|beta5	integrin beta 5	protein-coding
mm_97347.1	chr11	77469851	77469864	+	1	NA	TTS (NM_139129)	TTS (NM_139129)	5944	NM_139130	216961	Mm.33477	NM_139128	ENSMUSG00000020836	Coro6	-	coronin 6	protein-coding
mm_48124.1	chr5	137146759	137146766	-	1	NA	Intergenic	Intergenic	-30555	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_80380.1	chr9	75434344	75434354	+	1	NA	Intergenic	Intergenic	-7175	NM_001039522	235497	Mm.41508	NM_001006122	ENSMUSG00000042487	Leo1	Gm185	Leo1, Paf1/RNA polymerase II complex component	protein-coding
mm_51070.1	chr6	66537534	66537544	+	1	NA	intron (NM_019499, intron 2 of 4)	intron (NM_019499, intron 2 of 4)	2071	NM_019499	56150	Mm.489653	NM_019499	ENSMUSG00000029910	Mad2l1	AA673185|MAD2	MAD2 mitotic arrest deficient-like 1	protein-coding
mm_108906.1	chr12	100205609	100205661	+	1	NA	exon (NM_009790, exon 4 of 6)	exon (NM_009790, exon 4 of 6)	5491	NM_001313934	12313	Mm.285993	NM_009790	ENSMUSG00000001175	Calm1	AI256814|AI327027|AI461935|AL024000|CaM|Calm	calmodulin 1	protein-coding
mm_81900.1	chr9	119937655	119937705	+	1	NA	promoter-TSS (NM_028735)	promoter-TSS (NM_028735)	74	NM_028735	74052	Mm.189573	NM_028735	ENSMUSG00000032514	Ttc21a	4921538N17Rik|AA387572|Thm2	tetratricopeptide repeat domain 21A	protein-coding
mm_108945.1	chr12	102283088	102283096	+	1	NA	promoter-TSS (NM_001161365)	promoter-TSS (NM_001161365)	18	NM_177620	217835	Mm.24145	NM_177620	ENSMUSG00000044456	Rin3	6430500K07|C86933	Ras and Rab interactor 3	protein-coding
mm_77169.1	chr8	111689551	111689561	-	1	NA	TTS (NR_106044)	TTS (NR_106044)	118	NR_106044	102466993		NR_106044	ENSMUSG00000099129	Mir7076	Gm27318|mmu-mir-7076	microRNA 7076	ncRNA
mm_4825.1	chr1	185455053	185455088	+	1	NA	non-coding (NR_040305, exon 1 of 3)	non-coding (NR_040305, exon 1 of 3)	222	NM_001033286	226781	Mm.227117	NM_001033286	ENSMUSG00000026614	Slc30a10	E130106K10Rik|Gm212	solute carrier family 30, member 10	protein-coding
mm_6033.1	chr1	59551118	59551133	-	1	NA	intron (NM_001013771, intron 5 of 19)	intron (NM_001013771, intron 5 of 19)	34861	NM_001013771	381260	Mm.486706	NM_001013771	ENSMUSG00000047361	Gm973	AW554518	predicted gene 973	protein-coding
mm_27913.1	chr3	79531696	79531706	-	1	NA	intron (NM_001162999, intron 1 of 16)	intron (NM_001162999, intron 1 of 16)	35978	NM_001162999	329679	Mm.244005	NM_001162999	ENSMUSG00000061175	Fnip2	D630023B12Rik|mKIAA1450	folliculin interacting protein 2	protein-coding
mm_170349.1	chr18	51003025	51003035	+	1	NA	Intergenic	CpG	-114868	NM_001081224	71373	Mm.63546	NM_001081224	ENSMUSG00000073565	Prr16	5430406M13Rik|AI607429	proline rich 16	protein-coding
mm_51219.1	chr6	71369699	71369710	+	1	NA	Intergenic	Intergenic	-3723	NM_009857	12525	Mm.1858	NM_009857	ENSMUSG00000053977	Cd8a	BB154331|Ly-2|Ly-35|Ly-B|Lyt-2	CD8 antigen, alpha chain	protein-coding
mm_98785.1	chr11	96926151	96926156	+	1	NA	Intergenic	Intergenic	-3171	NM_146026	217138	Mm.342551	NM_146026	ENSMUSG00000047040	Prr15l	Atad4|BC022765|E230006A12Rik	proline rich 15-like	protein-coding
mm_43147.1	chr5	125475827	125475860	+	1	NA	promoter-TSS (NM_030210)	promoter-TSS (NM_030210)	-30	NM_030210	78894	Mm.431573	NM_030210	ENSMUSG00000029482	Aacs	2210408B16Rik|SUR5	acetoacetyl-CoA synthetase	protein-coding
mm_164524.1	chr17	3557835	3557838	-	1	NA	promoter-TSS (NR_045303)	promoter-TSS (NR_045303)	12	NR_045302	68230	Mm.431352	NR_045302		1700102H20Rik	-	RIKEN cDNA 1700102H20 gene	ncRNA
mm_94269.1	chr11	3531687	3531689	+	1	NA	intron (NM_001159284, intron 7 of 21)	intron (NM_001159284, intron 7 of 21)	7604	NM_013870	29856	Mm.188516	NM_013870	ENSMUSG00000020439	Smtn	smsmo	smoothelin	protein-coding
mm_74649.1	chr8	13389860	13389866	-	1	NA	exon (NM_009724, exon 4 of 7)	exon (NM_009724, exon 4 of 7)	6915	NM_009724	11945	Mm.154039	NM_009724	ENSMUSG00000031449	Atp4b	AV080843	ATPase, H+/K+ exchanging, beta polypeptide	protein-coding
mm_143446.1	chr17	70874810	70874822	-	1	NA	Intergenic	Intergenic	-21284	NM_001164074	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_160013.1	chr6	127015613	127015613	+	1	NA	promoter-TSS (NM_010204)	promoter-TSS (NM_010204)	71	NM_010204	14177	Mm.3403	NM_010204	ENSMUSG00000000183	Fgf6	Fgf-6|HSTF-2	fibroblast growth factor 6	protein-coding
mm_130236.1	chr15	96474723	96474734	-	1	NA	Intergenic	Intergenic	-13885	NM_028148	72193	Mm.324474	NM_028148	ENSMUSG00000033228	Scaf11	1110061H03Rik|2610510E10Rik|AI462454|CASP11|SIP1|SRRP129|Sfrs2ip|Srsf2ip|mKIAA3013	SR-related CTD-associated factor 11	protein-coding
mm_172557.1	chr8	106212600	106212603	+	1	NA	intron (NM_145404, intron 2 of 17)	intron (NM_145404, intron 2 of 17)	1547	NM_145404	214572	Mm.251804	NM_145404	ENSMUSG00000060098	Prmt7	4933402B05Rik|BC006705	protein arginine N-methyltransferase 7	protein-coding
mm_133457.1	chr16	89092096	89092105	+	1	NA	Intergenic	Intergenic	-28098	NM_001276278	68637	Mm.384089	NM_001276278	ENSMUSG00000068073	1110025L11Rik	-	RIKEN cDNA 1110025L11 gene	protein-coding
mm_74656.1	chr8	13501301	13501334	-	1	NA	Intergenic	RMER19C|LTR|ERVK	-6782	NM_019521	14456	Mm.3982	NM_019521	ENSMUSG00000031451	Gas6	Gas-6	growth arrest specific 6	protein-coding
mm_170382.1	chr1	85650065	85650065	+	1	NA	promoter-TSS (NM_013673)	promoter-TSS (NM_013673)	77	NM_001313714	20684	Mm.290906	NM_013673	ENSMUSG00000026222	Sp100	A430075G10Rik	nuclear antigen Sp100	protein-coding
mm_119312.1	chr14	36317071	36317074	+	1	NA	Intergenic	Intergenic	222107	NM_175008	218921	Mm.212464	NM_175008	ENSMUSG00000096405	4930474N05Rik	-	RIKEN cDNA 4930474N05 gene	protein-coding
mm_155638.1	chrX	85202669	85202685	+	1	NA	3' UTR (NM_007868, exon 79 of 79)	3' UTR (NM_007868, exon 79 of 79)	-47000	NM_028046	71996	Mm.20201	NM_028046	ENSMUSG00000035491	Fthl17a	1600014K23Rik|AI324104	ferritin, heavy polypeptide-like 17, member A	protein-coding
mm_115596.1	chr13	11827616	11827633	-	1	NA	exon (NM_023868, exon 15 of 105)	exon (NM_023868, exon 15 of 105)	279321	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding
mm_159748.1	chr5	76273997	76273997	-	1	NA	5' UTR (NM_001289826, exon 3 of 23)	5' UTR (NM_001289826, exon 3 of 23)	29505	NM_001305222	12753	Mm.3552	NM_007715	ENSMUSG00000029238	Clock	5330400M04Rik|KAT13D	circadian locomotor output cycles kaput	protein-coding
mm_149770.1	chr19	23061485	23061496	+	1	NA	Intergenic	Intergenic	-79736	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_71502.1	chr8	46806519	46806538	+	1	NA	exon (NM_008391, exon 3 of 9)	exon (NM_008391, exon 3 of 9)	66783	NM_008391	16363	Mm.1149	NM_008391	ENSMUSG00000031627	Irf2	9830146E22Rik|AI646973|Irf-2	interferon regulatory factor 2	protein-coding
mm_86437.1	chr10	3874660	3874668	+	1	NA	intron (NM_001033253, intron 2 of 15)	T-rich|Low_complexity|Low_complexity	1997	NM_001033253	213783	Mm.150831	NM_001033253	ENSMUSG00000040624	Plekhg1	D10Ertd733e|Gm521|mKIAA1209	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	protein-coding
mm_48291.1	chr5	138195546	138195552	-	1	NA	TTS (NM_177878)	TTS (NM_177878)	1235	NM_177878	330216	Mm.19719	NM_177878	ENSMUSG00000049285	Mblac1	-	metallo-beta-lactamase domain containing 1	protein-coding
mm_92901.1	chr10	83337400	83337414	-	1	NA	intron (NM_177388, intron 1 of 10)	CpG	410	NM_177388	338365	Mm.67073	NM_177388	ENSMUSG00000034591	Slc41a2	A230035L05Rik|SLC41A1-L1	solute carrier family 41, member 2	protein-coding
mm_58435.1	chr7	3297740	3297806	+	1	NA	3' UTR (NM_016969, exon 3 of 3)	3' UTR (NM_016969, exon 3 of 3)	4745	NM_001093766	50918	Mm.29874	NM_016969	ENSMUSG00000068566	Myadm	D7Wsu62e	myeloid-associated differentiation marker	protein-coding
mm_94457.1	chr11	6415804	6415813	+	1	NA	promoter-TSS (NM_008907)	promoter-TSS (NM_008907)	-62	NM_008907	268373	Mm.5246	NM_008907	ENSMUSG00000071866	Ppia	2700098C05|Cphn|CyP-18|CypA	peptidylprolyl isomerase A	protein-coding
mm_66266.1	chr7	35802969	35803007	-	1	NA	promoter-TSS (NM_177739)	promoter-TSS (NM_177739)	1	NM_177739	668501	Mm.286296	NM_177739	ENSMUSG00000044452	Zfp507	1810022O10Rik|A230056M16Rik|AL024009|AU021817|BB105092|Gm480|Znf507|mKIAA1084	zinc finger protein 507	protein-coding
mm_23677.1	chr3	68584213	68584292	+	1	NA	intron (NM_013928, intron 1 of 6)	intron (NM_013928, intron 1 of 6)	11884	NM_013928	30953	Mm.331064	NM_013928	ENSMUSG00000027777	Schip1	Nf2ip|Schip-1	schwannomin interacting protein 1	protein-coding
mm_112812.1	chr13	20794313	20794364	+	1	NA	5' UTR (NM_001281854, exon 1 of 5)	5' UTR (NM_001281854, exon 1 of 5)	225	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_72687.1	chr8	84968968	84968981	+	1	NA	promoter-TSS (NM_011563)	promoter-TSS (NM_011563)	-648	NM_001317385	21672	Mm.347009	NM_011563	ENSMUSG00000005161	Prdx2	AL022839|Band-8|NkefB|PRP|PrxII|TDX1|TPx|TPx-B|TR|TSA|Tdpx1|Torin	peroxiredoxin 2	protein-coding
mm_110680.1	chr12	67059898	67059923	-	1	NA	intron (NM_001193266, intron 1 of 16)	GSAT_MM|Satellite|Satellite	162639	NM_001193266	320772	Mm.227680	NM_207010	ENSMUSG00000034912	Mdga2	6720489L24Rik|9330209L04Rik|Adp|Mamdc1	MAM domain containing glycosylphosphatidylinositol anchor 2	protein-coding
mm_22685.1	chr3	16792798	16792800	+	1	NA	Intergenic	MMERGLN_LTR|LTR|ERV1	609616	NM_001145919	229096	Mm.23834	NM_172677	ENSMUSG00000047213	Ythdf3	9130022A11Rik	YTH domain family 3	protein-coding
mm_161798.1	chr17	52602657	52602657	+	1	NA	promoter-TSS (NM_001031811)	promoter-TSS (NM_001031811)	-52	NM_001031811	211468	Mm.399068	NM_001031811	ENSMUSG00000035580	Kcnh8	C130090D05Rik|ELK|ELK1|ELK3|Kv12.1	potassium voltage-gated channel, subfamily H (eag-related), member 8	protein-coding
mm_85375.1	chr9	103223610	103223642	-	1	NA	exon (NM_133977, exon 6 of 17)	exon (NM_133977, exon 6 of 17)	6660	NM_133977	22041	Mm.37214	NM_133977	ENSMUSG00000032554	Trf	AI266983|Cd176|HP|Tf|Tfn|hpx	transferrin	protein-coding
mm_82842.1	chr9	31168761	31168808	-	1	NA	exon (NM_009691, exon 6 of 16)	exon (NM_009691, exon 6 of 16)	-36985	NM_011176	19143	Mm.243926	NM_011176	ENSMUSG00000031995	St14	Epithin|MT-SP1|Prss14|Tmprss14|mCAP3|matriptase	suppression of tumorigenicity 14 (colon carcinoma)	protein-coding
mm_53322.1	chr6	129205501	129205506	+	1	NA	Intergenic	MLT1D|LTR|ERVL-MaLR	24888	NM_053109	93694	Mm.197536	NM_053109	ENSMUSG00000030157	Clec2d	Clr-b|Clrb|Ocil	C-type lectin domain family 2, member d	protein-coding
mm_37765.1	chr4	129696818	129696843	-	1	NA	promoter-TSS (NM_199305)	promoter-TSS (NM_199305)	8	NM_199305	230770	Mm.257157	NM_199305	ENSMUSG00000053730	Tmem39b	6330509E05Rik|BC037095	transmembrane protein 39b	protein-coding
mm_81780.1	chr9	114688852	114688865	+	1	NA	promoter-TSS (NM_146229)	promoter-TSS (NM_146229)	27	NM_146229	235661	Mm.128627	NM_146229	ENSMUSG00000032435	Dync1li1	1110053F02Rik|Dnclic1|LIC-1	dynein cytoplasmic 1 light intermediate chain 1	protein-coding
mm_136890.1	chr17	13010876	13010889	+	1	NA	intron (NM_013671, intron 3 of 4)	B2_Mm1t|SINE|B2	3043	NM_013671	20656	Mm.290876	NM_013671	ENSMUSG00000006818	Sod2	MnSOD|Sod-2	superoxide dismutase 2, mitochondrial	protein-coding
mm_84350.1	chr9	64340802	64340822	-	1	NA	promoter-TSS (NM_001177784)	promoter-TSS (NM_001177784)	-39	NM_001177784	213550	Mm.268341	NM_172519	ENSMUSG00000032396	Dis3l	AV340375	DIS3 like exosome 3'-5' exoribonuclease	protein-coding
mm_41710.1	chr5	101765331	101765344	+	1	NA	5' UTR (NM_173370, exon 1 of 13)	5' UTR (NM_173370, exon 1 of 13)	207	NM_173370	74596	Mm.46764	NM_173370	ENSMUSG00000029330	Cds1	4833409J18Rik|AI314024|AW125888	CDP-diacylglycerol synthase 1	protein-coding
mm_155865.1	chrX	101383766	101383777	+	1	NA	promoter-TSS (NM_001302497)	promoter-TSS (NM_001302497)	39	NM_001302497	14618	Mm.21198	NM_008124	ENSMUSG00000047797	Gjb1	Cnx32|Cx32|connexin-32	gap junction protein, beta 1	protein-coding
mm_20687.1	chr2	132670387	132670395	-	1	NA	Intergenic	L1_Rod|LINE|L1	-19892	NM_028637	73747	Mm.284114	NM_028637	ENSMUSG00000044991	1110034G24Rik	-	RIKEN cDNA 1110034G24 gene	protein-coding
mm_40774.1	chr5	67260726	67260741	+	1	NA	5' UTR (NM_030108, exon 1 of 9)	5' UTR (NM_030108, exon 1 of 9)	168	NM_030108	67878	Mm.23217	NM_028975	ENSMUSG00000037720	Tmem33	1110006G02Rik|1600019D15Rik|2410089A21Rik|2700052H22Rik|5430406L04Rik|AA388285|AI314185|AI426615|db83	transmembrane protein 33	protein-coding
mm_50936.1	chr6	57702928	57702940	+	1	NA	5' UTR (NM_133737, exon 1 of 9)	5' UTR (NM_133737, exon 1 of 9)	479	NM_133737	71835	Mm.274904	NM_133737	ENSMUSG00000062190	Lancl2	1700003F10Rik	LanC (bacterial lantibiotic synthetase component C)-like 2	protein-coding
mm_74105.1	chr8	122848442	122848461	+	1	NA	promoter-TSS (NM_007662)	promoter-TSS (NM_007662)	77	NM_007662	12555	Mm.1976	NM_007662	ENSMUSG00000031962	Cdh15	AI323380|Cdh14|Mcad	cadherin 15	protein-coding
mm_91192.1	chr10	21146404	21146412	-	1	NA	exon (NM_001198914, exon 9 of 16)	exon (NM_001198914, exon 9 of 16)	14576	NM_001198914	17863	Mm.52109	NM_010848	ENSMUSG00000019982	Myb	AI550390|M16449|c-myb	myeloblastosis oncogene	protein-coding
mm_60865.1	chr7	45916156	45916185	+	1	NA	exon (NM_144801, exon 7 of 8)	exon (NM_144801, exon 7 of 8)	4679	NM_001146346	13732	Mm.20829	NM_010129	ENSMUSG00000040212	Emp3	H-4|H4|HNMP-1|MI-35|Ymp	epithelial membrane protein 3	protein-coding
mm_76680.1	chr8	94012538	94012554	-	1	NA	promoter-TSS (NM_011787)	promoter-TSS (NM_011787)	94	NM_011787	23802	Mm.34641	NM_011787	ENSMUSG00000031751	Amfr	gp78	autocrine motility factor receptor	protein-coding
mm_11112.1	chr2	28193193	28193214	+	1	NA	5' UTR (NM_001038613, exon 1 of 6)	5' UTR (NM_001038613, exon 1 of 6)	110	NM_001038614	56177	Mm.43278	NM_019498	ENSMUSG00000026833	Olfm1	AMY|AW742568|Noe1|OlfA|Pancortin|Pancortin3	olfactomedin 1	protein-coding
mm_44674.1	chr5	29735929	29735945	-	1	NA	promoter-TSS (NM_001037941)	promoter-TSS (NM_001037941)	-1	NR_028426	332993	Mm.473746	NR_028426		Gm5129	EG332993|ENSMUSG00000053121	predicted gene 5129	ncRNA
mm_57901.1	chr6	131388346	131388365	-	1	NA	promoter-TSS (NM_011733)	promoter-TSS (NM_011733)	95	NM_139117	56449	Mm.458000	NM_011733	ENSMUSG00000030189	Ybx3	Csda|Dpba|MSY3|MSY4|Yb2|dbpA|oxyR	Y box protein 3	protein-coding
mm_151077.1	chr19	47579733	47579743	+	1	NA	promoter-TSS (NM_001164639)	promoter-TSS (NM_001164639)	-281	NM_009289	20874	Mm.281011	NM_009289	ENSMUSG00000025060	Slk	9A2|AV021402|AW411554|Etk4|SMAK|Stk2|mKIAA0204|mSLK	STE20-like kinase	protein-coding
mm_25016.1	chr3	98013484	98013502	+	1	NA	promoter-TSS (NM_010928)	promoter-TSS (NM_010928)	-45	NM_010928	18129	Mm.485843	NM_010928	ENSMUSG00000027878	Notch2	AI853703|N2	notch 2	protein-coding
mm_40068.1	chr5	34242836	34242847	+	1	NA	intron (NM_001015039, intron 2 of 12)	intron (NM_001015039, intron 2 of 12)	45483	NM_001015039	231125	Mm.113388	NM_001015039	ENSMUSG00000037224	Zfyve28	9630058O20Rik|Gm146|mKIAA1643	zinc finger, FYVE domain containing 28	protein-coding
mm_71262.1	chr8	40918496	40918506	+	1	NA	3' UTR (NM_001044740, exon 12 of 12)	3' UTR (NM_001044740, exon 12 of 12)	-7732	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_151225.1	chr19	53717846	53717857	+	1	NA	intron (NM_001170847, intron 1 of 13)	intron (NM_001170847, intron 1 of 13)	40545	NM_001170847	73713	Mm.313695	NM_001170847	ENSMUSG00000043639	Rbm20	1110018J23Rik|2010003H22Rik|AI646761	RNA binding motif protein 20	protein-coding
mm_61004.1	chr7	49347430	49347478	+	1	NA	intron (NM_175272, intron 1 of 37)	intron (NM_175272, intron 1 of 37)	101265	NM_175272	78286	Mm.333881	NM_175272	ENSMUSG00000052512	Nav2	5330421F07Rik|AU067780|BQ960892|HELAD1|POMFIL2|RAINB1|RAINB2|Unc53H2|mKIAA3015	neuron navigator 2	protein-coding
mm_135833.1	chr16	58523523	58523538	-	1	NA	promoter-TSS (NM_018784)	promoter-TSS (NM_018784)	-218	NM_018784	54613	Mm.212742	NM_018784	ENSMUSG00000022747	St3gal6	1700023B24Rik|AI930218|AW552396|Siat10|St3galVI	ST3 beta-galactoside alpha-2,3-sialyltransferase 6	protein-coding
mm_670.1	chr1	40462341	40462358	+	1	NA	3' UTR (NM_001025602, exon 11 of 11)	3' UTR (NM_001025602, exon 11 of 11)	-3203	NM_001161842	16182	Mm.253664	NM_008365	ENSMUSG00000026070	Il18r1	Il18ralpha|Il1rrp	interleukin 18 receptor 1	protein-coding
mm_150916.1	chr19	46075940	46075946	+	1	NA	promoter-TSS (NM_001039352)	promoter-TSS (NM_001039352)	96	NM_001039351	70769	Mm.402190	NM_053086	ENSMUSG00000015176	Nolc1	NOPP130|NOPP140|P130	nucleolar and coiled-body phosphoprotein 1	protein-coding
mm_17043.1	chr2	20870032	20870045	-	1	NA	intron (NM_001128084, intron 10 of 24)	(A)n|Simple_repeat|Simple_repeat	97683	NM_001081364	71435	Mm.28507	NM_001081364	ENSMUSG00000036591	Arhgap21	5530401C11Rik|AA416458|ARHGAP10	Rho GTPase activating protein 21	protein-coding
mm_75791.1	chr8	70095690	70095700	-	1	NA	3' UTR (NM_007789, exon 15 of 15)	3' UTR (NM_007789, exon 15 of 15)	6891	NR_106033	102465646		NR_106033	ENSMUSG00000099042	Mir7066	Gm27290|mmu-mir-7066	microRNA 7066	ncRNA
mm_57659.1	chr6	128486963	128486985	-	1	NA	exon (NM_007376, exon 32 of 36)	exon (NM_007376, exon 32 of 36)	39746	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_72168.1	chr8	72247415	72247432	+	1	NA	intron (NM_007456, intron 2 of 11)	RMER15-int|LTR|ERVL	7405	NM_007456	11767	Mm.290086	NM_007456	ENSMUSG00000003033	Ap1m1	AA408894|AP47|Adtm1A|Cltnm|mu1A	adaptor-related protein complex AP-1, mu subunit 1	protein-coding
mm_21452.1	chr2	160682723	160682780	-	1	NA	exon (NM_009408, exon 4 of 21)	exon (NM_009408, exon 4 of 21)	36854	NM_009408	21969	Mm.217233	NM_009408	ENSMUSG00000070544	Top1	AI467334|D130064I21Rik|Top-1	topoisomerase (DNA) I	protein-coding
mm_94827.1	chr11	23306500	23306602	+	1	NA	promoter-TSS (NM_001190401)	promoter-TSS (NM_001190401)	-344	NM_001190401	17847	Mm.119155	NM_001190401	ENSMUSG00000056342	Usp34	A530081C03Rik|Murr2	ubiquitin specific peptidase 34	protein-coding
mm_86565.1	chr10	11285005	11285008	+	1	NA	intron (NM_001168297, intron 1 of 2)	intron (NM_001168297, intron 1 of 2)	3419	NM_001168297	71865	Mm.276229	NM_027968	ENSMUSG00000047648	Fbxo30	1700026A16Rik|MUSA1	F-box protein 30	protein-coding
mm_38749.1	chr4	145300775	145300777	-	1	NA	intron (NM_009401, intron 2 of 12)	intron (NM_009401, intron 2 of 12)	14371	NM_009401	21941	Mm.12810	NM_009401	ENSMUSG00000028602	Tnfrsf8	Cd30|D1S166E|Ki|Ki-1	tumor necrosis factor receptor superfamily, member 8	protein-coding
mm_34849.1	chr4	155469124	155469142	+	1	NA	promoter-TSS (NM_027161)	promoter-TSS (NM_027161)	19	NM_027161	69671	Mm.45401	NM_027161	ENSMUSG00000023153	Tmem52	2310043I08Rik	transmembrane protein 52	protein-coding
mm_70861.1	chr8	24503087	24503087	+	1	NA	Intergenic	Intergenic	-18101	NR_035483	100316707		NR_035483	ENSMUSG00000088552	Mir1957a	Mir1957|mmu-mir-1957|mmu-mir-1957a	microRNA 1957a	ncRNA
mm_66192.1	chr7	34213433	34213448	-	1	NA	intron (NM_008155, intron 9 of 17)	intron (NM_008155, intron 9 of 17)	-16793	NM_026549	68079	Mm.38173	NM_026549	ENSMUSG00000002635	Pdcd2l	6030457N17Rik	programmed cell death 2-like	protein-coding
mm_148361.1	chr18	85698031	85698062	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-696906	NM_144946	246317	Mm.329578	NM_144946	ENSMUSG00000050321	Neto1	AI851453|Btcl1|C130005O10Rik	neuropilin (NRP) and tolloid (TLL)-like 1	protein-coding
mm_1072.1	chr1	59432173	59432176	+	1	NA	Intergenic	RLTR20C2_MM|LTR|ERVK	-49973	NM_008057	14369	Mm.297906	NM_008057	ENSMUSG00000041075	Fzd7	Fz7	frizzled class receptor 7	protein-coding
mm_59422.1	chr7	27124614	27124627	+	1	NA	intron (NM_007817, intron 3 of 9)	intron (NM_007817, intron 3 of 9)	4665	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_53765.1	chr6	145815391	145815423	+	1	NA	exon (NM_027760, exon 2 of 4)	exon (NM_027760, exon 2 of 4)	7024	NM_027760	71323	Mm.158669	NM_027760	ENSMUSG00000030259	Rassf8	5133400D11Rik|AA815821|AW123240|Hoj1|mHoj-1	Ras association (RalGDS/AF-6) domain family (N-terminal) member 8	protein-coding
mm_146872.1	chr18	25422028	25422029	-	1	NA	intron (NM_001033532, intron 10 of 10)	ID2|SINE|ID	253008	NM_001033532	225289	Mm.391081	NM_001033532	ENSMUSG00000033632	AW554918	4921538P22|AI461742|Kiaa1328|mKIAA1328	expressed sequence AW554918	protein-coding
mm_13777.1	chr2	118746986	118746989	+	1	NA	3' UTR (NM_001301269, exon 1 of 1)	3' UTR (NM_001301269, exon 1 of 1)	1229	NM_001301269	100043272	Mm.398072	NM_001301269	ENSMUSG00000074918	Inafm2	5430417L22Rik|ENSMUSG00000074918	InaF motif containing 2	protein-coding
mm_67019.1	chr7	65635995	65635998	-	1	NA	Intergenic	Intergenic	-8902	NM_172310	272396	Mm.35127	NM_172310	ENSMUSG00000030515	Tarsl2	A530046H20Rik	threonyl-tRNA synthetase-like 2	protein-coding
mm_126889.1	chr15	89497960	89497968	+	1	NA	Intergenic	Intergenic	-1893	NM_021423	58234	Mm.146855	NM_021423	ENSMUSG00000022623	Shank3	AI841104|SHANK3c-3|SHANK3c-4|Shank3b	SH3/ankyrin domain gene 3	protein-coding
mm_30545.1	chr4	3683713	3683724	+	1	NA	intron (NM_010747, intron 1 of 12)	intron (NM_010747, intron 1 of 12)	5597	NM_010747	17096	Mm.317331	NM_010747	ENSMUSG00000042228	Lyn	AA407514|Hck-2|p53Lyn|p56Lyn	LYN proto-oncogene, Src family tyrosine kinase	protein-coding
mm_103191.1	chr11	70615693	70615718	-	1	NA	promoter-TSS (NM_001145537)	promoter-TSS (NM_001145537)	-189	NM_001145537	668433	Mm.425687	NM_001145537	ENSMUSG00000087279	4930544D05Rik	-	RIKEN cDNA 4930544D05 gene	protein-coding
mm_120203.1	chr14	61681544	61681569	+	1	NA	intron (NR_028264, intron 1 of 6)	CpG	817	NR_028264	668253	Mm.32886	NR_028264	ENSMUSG00000097589	Dleu2	1810047A16Rik|4932411A06Rik|7730401J12Rik|AI197277|AI788824|Alt1|Gm9069|Leu2	deleted in lymphocytic leukemia, 2	ncRNA
mm_92651.1	chr10	80399431	80399476	-	1	NA	promoter-TSS (NM_013595)	promoter-TSS (NM_013595)	78	NM_013595	17192	Mm.7142	NM_013595	ENSMUSG00000035478	Mbd3	AI181826|AU019209	methyl-CpG binding domain protein 3	protein-coding
mm_120404.1	chr14	64953142	64953143	+	1	NA	intron (NM_001253731, intron 1 of 16)	intron (NM_001253731, intron 1 of 16)	3097	NM_001253731	210925	Mm.71332	NM_153414	ENSMUSG00000021975	Ints9	BC028953|D14Ertd231e	integrator complex subunit 9	protein-coding
mm_106768.1	chr12	4593137	4593147	+	1	NA	5' UTR (NM_001198969, exon 1 of 17)	5' UTR (NM_001198969, exon 1 of 17)	134	NM_001198968	20403	Mm.341204	NM_011365	ENSMUSG00000020640	Itsn2	AI327390|Ese2|Sh3d1B|Sh3p18|mKIAA1256	intersectin 2	protein-coding
mm_49610.1	chr6	30747247	30747262	+	1	NA	TTS (NM_017478)	TTS (NM_017478)	5955	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_77720.1	chr8	126804168	126804175	-	1	NA	Intergenic	Intergenic	141750	NM_024214	67952	Mm.6932	NM_024214	ENSMUSG00000093904	Tomm20	1810060K07Rik|BB284719|Gm19268|MAS20|MOM19|TOM20|mKIAA0016	translocase of outer mitochondrial membrane 20 homolog (yeast)	protein-coding
mm_102602.1	chr11	62392579	62392595	-	1	NA	exon (NM_001252313, exon 11 of 45)	exon (NM_001252313, exon 11 of 45)	45928	NM_001252313	20185	Mm.271814	NM_011308	ENSMUSG00000018501	Ncor1	5730405M06Rik|A230020K14Rik|N-CoR|RIP13|Rxrip13|mKIAA1047	nuclear receptor co-repressor 1	protein-coding
mm_65978.1	chr7	30444580	30444611	-	1	NA	intron (NM_007467, intron 1 of 16)	intron (NM_007467, intron 1 of 16)	987	NM_007467	11803	Mm.2381	NM_007467	ENSMUSG00000006651	Aplp1	-	amyloid beta (A4) precursor-like protein 1	protein-coding
mm_149219.1	chr19	10001719	10001732	+	1	NA	promoter-TSS (NM_011913)	promoter-TSS (NM_011913)	56	NM_001347429	74760	Mm.281969	NM_144538	ENSMUSG00000024663	Rab3il1	1200014K04Rik|AI115013|C76746|Rab3ail1	RAB3A interacting protein (rabin3)-like 1	protein-coding
mm_91485.1	chr10	36750192	36750196	-	1	NA	intron (NM_001253355, intron 4 of 5)	RMER17C|LTR|ERVK	-224350	NM_008229	15182	Mm.19806	NM_008229	ENSMUSG00000019777	Hdac2	D10Wsu179e|YAF1|Yy1bp|mRPD3	histone deacetylase 2	protein-coding
mm_92631.1	chr10	80323380	80323428	-	1	NA	intron (NM_008793, intron 11 of 14)	CpG	-2856	NM_025521	66374	Mm.383824	NM_025521	ENSMUSG00000020133	2310011J03Rik	AI452186|AW545358	RIKEN cDNA 2310011J03 gene	protein-coding
mm_94328.1	chr11	4266482	4266497	+	1	NA	promoter-TSS (NM_001039537)	promoter-TSS (NM_001039537)	-307	NM_001039537	16878	Mm.4964	NM_008501	ENSMUSG00000034394	Lif	-	leukemia inhibitory factor	protein-coding
mm_143969.1	chr17	87282794	87282821	-	1	NA	promoter-TSS (NM_028639)	promoter-TSS (NM_028639)	7	NR_015506	74597	Mm.63783	NR_015506	ENSMUSG00000085287	4833418N02Rik	-	RIKEN cDNA 4833418N02 gene	ncRNA
mm_48465.1	chr5	140830338	140830348	-	1	NA	promoter-TSS (NM_010302)	promoter-TSS (NM_010302)	88	NM_010302	14673	Mm.370185	NM_010302	ENSMUSG00000000149	Gna12	AI414047|AI504261|Galpha12	guanine nucleotide binding protein, alpha 12	protein-coding
mm_59259.1	chr7	24870991	24870996	+	1	NA	intron (NM_027732, intron 1 of 8)	intron (NM_027732, intron 1 of 8)	936	NM_027732	71241	Mm.66855	NM_027732	ENSMUSG00000011349	Dmrtc2	4933432E21Rik|Dmrt7	doublesex and mab-3 related transcription factor like family C2	protein-coding
mm_12833.1	chr2	80635276	80635282	+	1	NA	Intergenic	Intergenic	-3533	NM_027091	69482	Mm.29200	NM_027091	ENSMUSG00000026999	Nup35	2310006I24Rik|35kDa|5330402E05Rik|MP44|NO44	nucleoporin 35	protein-coding
mm_37153.1	chr4	117121256	117121285	-	1	NA	non-coding (NR_024078, exon 6 of 7)	non-coding (NR_024078, exon 6 of 7)	4455	NR_024078	78611	Mm.446227	NM_001033187		Btbd19	9530048O09Rik|BB115071	BTB (POZ) domain containing 19	ncRNA
mm_87108.1	chr10	33197363	33197369	+	1	NA	intron (NM_029726, intron 8 of 37)	intron (NM_029726, intron 8 of 37)	58991	NR_040657	442820	Mm.490725	NR_040657		D830005E20Rik	-	RIKEN cDNA D830005E20 gene	ncRNA
mm_111887.1	chr12	108274382	108274391	-	1	NA	exon (NM_001159910, exon 1 of 6)	exon (NM_001159910, exon 1 of 6)	1031	NM_001159910	668158	Mm.482792	NM_001159910	ENSMUSG00000084883	Ccdc85c	EG668158|Gm265|Gm9010	coiled-coil domain containing 85C	protein-coding
mm_147806.1	chr18	61665485	61665502	-	1	NA	promoter-TSS (NR_045402)	promoter-TSS (NR_045402)	45	NR_045402	328968	Mm.392305	NR_045402		Carmn	Carmen|E330013P06|Gm16908|Mir143hg	cardiac mesoderm enhancer-associated non-coding RNA	ncRNA
mm_78945.1	chr9	45138541	45138549	+	1	NA	promoter-TSS (NM_001013390)	promoter-TSS (NM_001013390)	-497	NM_001013390	399548	Mm.335112	NM_001013390	ENSMUSG00000046480	Scn4b	Gm1471	sodium channel, type IV, beta	protein-coding
mm_141730.1	chr17	34117008	34117026	-	1	NA	exon (NM_001204973, exon 3 of 13)	exon (NM_001204973, exon 3 of 13)	2883	NR_037970	14312	Mm.3444	NM_010238	ENSMUSG00000024335	Brd2	AW228947|D17H6S113E|Frg-1|Fsrg-1|Fsrg1|Nat|Ring3|Rnf3|mKIAA4005	bromodomain containing 2	protein-coding
mm_81992.1	chr9	121460281	121460305	+	1	NA	intron (NM_175114, intron 13 of 15)	intron (NM_175114, intron 13 of 15)	35401	NM_001284508	12424	Mm.2619	NM_031161	ENSMUSG00000032532	Cck	-	cholecystokinin	protein-coding
mm_105492.1	chr11	106159201	106159227	-	1	NA	intron (NM_172397, intron 2 of 4)	intron (NM_172397, intron 2 of 4)	928	NM_172397	67803	Mm.21687	NM_172397	ENSMUSG00000040699	Limd2	0610025L06Rik|AI413966	LIM domain containing 2	protein-coding
mm_56242.1	chr6	90716490	90716543	-	1	NA	promoter-TSS (NM_001134383)	promoter-TSS (NM_001134383)	13	NM_001134383	232227	Mm.196943	NM_182784	ENSMUSG00000034312	Iqsec1	AW561907|BC026481|BRAG2|D6Ertd349e|cI-43	IQ motif and Sec7 domain 1	protein-coding
mm_71712.1	chr8	61938191	61938212	+	1	NA	intron (NM_001293783, intron 1 of 37)	RMER6D|LTR|ERVK	10114	NM_001293783	234311	Mm.275233	NM_144928	ENSMUSG00000037921	Ddx60	9830118M07	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	protein-coding
mm_58932.1	chr7	17975588	17975598	+	1	NA	exon (NM_023289, exon 3 of 4)	exon (NM_023289, exon 3 of 4)	3426	NM_023289	66996	Mm.36666	NM_023289	ENSMUSG00000030368	Ceacam11	1600015D01Rik	carcinoembryonic antigen-related cell adhesion molecule 11	protein-coding
mm_66674.1	chr7	45742347	45742367	-	1	NA	intron (NM_017465, intron 1 of 6)	MIRb|SINE|MIR	-16541	NM_027055	69363	Mm.45607	NM_027055	ENSMUSG00000070563	Spaca4	1700008E09Rik|AV043694|Samp14	sperm acrosome associated 4	protein-coding
mm_112498.1	chr13	8202861	8202871	+	1	NA	promoter-TSS (NM_001289530)	promoter-TSS (NM_001289530)	0	NM_001289530	94191	Mm.425794	NM_052977	ENSMUSG00000052551	Adarb2	Adar3|RED2	adenosine deaminase, RNA-specific, B2	protein-coding
mm_123830.1	chr14	70627092	70627098	-	1	NA	promoter-TSS (NM_001252663)	promoter-TSS (NM_001252663)	-30	NM_001252663	13829	Mm.210863	NM_013514	ENSMUSG00000022099	Dmtn	AI325486|Epb4.9|Epb49|dematin	dematin actin binding protein	protein-coding
mm_137622.1	chr17	28300050	28300067	+	1	NA	3' UTR (NM_011145, exon 8 of 8)	3' UTR (NM_011145, exon 8 of 8)	-13472	NR_028297	72775	Mm.201859	NM_028348	ENSMUSG00000007570	Fance	2810451D06Rik|AI415634|AW209126	Fanconi anemia, complementation group E	protein-coding
mm_1778.1	chr1	78511806	78511816	+	1	NA	intron (NM_026713, intron 1 of 6)	intron (NM_026713, intron 1 of 6)	751	NM_026713	68393	Mm.41325	NM_026713	ENSMUSG00000012187	Mogat1	0610030A14Rik|1110064N14Rik|Dgat2l|Dgat2l1|MGAT1|WI1-2612I11.1|mDC2	monoacylglycerol O-acyltransferase 1	protein-coding
mm_3277.1	chr1	136574357	136574358	+	1	NA	Intergenic	(T)n|Simple_repeat|Simple_repeat	-50544	NM_177643	226442	Mm.62521	NM_177643	ENSMUSG00000041483	Zfp281	Znf281	zinc finger protein 281	protein-coding
mm_109716.1	chr12	116047714	116047807	+	1	NA	promoter-TSS (NM_019565)	promoter-TSS (NM_019565)	36	NM_019565	56220	Mm.254997	NM_019565	ENSMUSG00000042063	Zfp386	Kzf1|mKIAA4205	zinc finger protein 386 (Kruppel-like)	protein-coding
mm_92535.1	chr10	79587115	79587130	-	1	NA	promoter-TSS (NM_199226)	promoter-TSS (NM_199226)	14	NM_199226	21830	Mm.89197	NM_011583	ENSMUSG00000020317	Theg	-	testicular haploid expressed gene	protein-coding
mm_55221.1	chr6	52230556	52230574	-	1	NA	promoter-TSS (NR_029912)	promoter-TSS (NR_029912)	-400	NR_029912	723820		NR_029912	ENSMUSG00000065443	Mir196b	Mirn196b|mir-196b	microRNA 196b	ncRNA
mm_9001.1	chr1	165789998	165790006	-	1	NA	intron (NM_001113391, intron 1 of 7)	intron (NM_001113391, intron 1 of 7)	1321	NM_001113392	12503	Mm.217308	NM_031162	ENSMUSG00000005763	Cd247	4930549J05Rik|A430104F18Rik|AW552088|Cd3|Cd3-eta|Cd3-zeta|Cd3h|Cd3z|Cd3zeta|T3z|Tcrk|Tcrz	CD247 antigen	protein-coding
mm_24065.1	chr3	87915613	87915635	+	1	NA	3' UTR (NM_008231, exon 6 of 6)	3' UTR (NM_008231, exon 6 of 6)	-3920	NM_026591	67707	Mm.393802	NM_026591	ENSMUSG00000019710	Mrpl24	2010005E08Rik|2810470K06Rik|6720473G22Rik|AA407670	mitochondrial ribosomal protein L24	protein-coding
mm_68097.1	chr7	101934330	101934344	-	1	NA	promoter-TSS (NM_027053)	promoter-TSS (NM_027053)	-480	NM_001162973	69358	Mm.214841	NM_027053	ENSMUSG00000064307	Lrrc51	1700008D07Rik|Lrtomt	leucine rich repeat containing 51	protein-coding
mm_14583.1	chr2	135764911	135764935	+	1	NA	intron (NM_013829, intron 1 of 36)	intron (NM_013829, intron 1 of 36)	23093	NM_013829	18798	Mm.38009	NM_013829	ENSMUSG00000039943	Plcb4	A930039J07Rik|AI854601|C230058B11Rik	phospholipase C, beta 4	protein-coding
mm_129388.1	chr15	78201673	78201683	-	1	NA	intron (NM_013645, intron 3 of 4)	intron (NM_013645, intron 3 of 4)	2559	NM_001330686	19293	Mm.2766	NM_013645	ENSMUSG00000005716	Pvalb	PV|Parv|Pva	parvalbumin	protein-coding
mm_36457.1	chr4	82505371	82505386	-	1	NA	5' UTR (NM_001113209, exon 1 of 12)	5' UTR (NM_001113209, exon 1 of 12)	401	NM_001286127	18028	Mm.317947	NM_008687	ENSMUSG00000008575	Nfib	6720429L07Rik|CTF|E030026I10Rik|NF-I/B|NF1-B|NFI-B	nuclear factor I/B	protein-coding
mm_37927.1	chr4	132882438	132882441	-	1	NA	intron (NM_133887, intron 1 of 8)	intron (NM_133887, intron 1 of 8)	2019	NM_133887	100226	Mm.28237	NM_133887	ENSMUSG00000028879	Stx12	AI850350|AU041521|Stx13	syntaxin 12	protein-coding
mm_100929.1	chr11	6475993	6476102	-	1	NA	promoter-TSS (NM_011221)	promoter-TSS (NM_011221)	29	NM_011221	19291	Mm.296150	NM_011221	ENSMUSG00000094483	Purb	2310015K15Rik|AA114818|Cager-2|D11Bwg0414e	purine rich element binding protein B	protein-coding
mm_139613.1	chr17	57360434	57360462	+	1	NA	intron (NM_010130, intron 1 of 21)	Lx8|LINE|L1	1762	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_42358.1	chr5	114911783	114911793	+	1	NA	3' UTR (NM_011854, exon 6 of 6)	3' UTR (NM_011854, exon 6 of 6)	-11452	NM_145209	231655	Mm.95479	NM_145209	ENSMUSG00000041827	Oasl1	7530414C13Rik|oasl9	2'-5' oligoadenylate synthetase-like 1	protein-coding
mm_165514.1	chr2	173173660	173173672	+	1	NA	Intergenic	Intergenic	20593	NM_011044	18534	Mm.266867	NM_011044	ENSMUSG00000027513	Pck1	AI265463|PEPCK|Pck-1	phosphoenolpyruvate carboxykinase 1, cytosolic	protein-coding
mm_125577.1	chr15	59459776	59459814	+	1	NA	intron (NM_026746, intron 4 of 6)	ORR1E|LTR|ERVL-MaLR	85597	NM_001164604	68501	Mm.27762	NM_026746	ENSMUSG00000059586	Nsmce2	1110014D18Rik|AI661537	NSE2/MMS21 homolog, SMC5-SMC6 complex SUMO ligase	protein-coding
mm_113650.1	chr13	42301954	42301967	+	1	NA	intron (NM_010104, intron 1 of 4)	intron (NM_010104, intron 1 of 4)	484	NM_010104	13614	Mm.14543	NM_010104	ENSMUSG00000021367	Edn1	ET-1|PPET1|preproET	endothelin 1	protein-coding
mm_33056.1	chr4	123183723	123183738	+	1	NA	intron (NM_174998, intron 1 of 4)	intron (NM_174998, intron 1 of 4)	226	NM_174998	170638	Mm.270641	NM_174998	ENSMUSG00000046093	Hpcal4	AI846570|NVP-2	hippocalcin-like 4	protein-coding
mm_45578.1	chr5	73647721	73647754	-	1	NA	promoter-TSS (NM_011890)	promoter-TSS (NM_011890)	-6	NM_011890	24051	Mm.89310	NM_011890	ENSMUSG00000029156	Sgcb	43kDa|AI747103|AI844814|beta-SG	sarcoglycan, beta (dystrophin-associated glycoprotein)	protein-coding
mm_81874.1	chr9	119119626	119119658	+	1	NA	intron (NM_177117, intron 6 of 36)	intron (NM_177117, intron 6 of 36)	17164	NM_177117	320256	Mm.110648	NM_177117	ENSMUSG00000038060	Dlec1	D630005C06Rik	deleted in lung and esophageal cancer 1	protein-coding
mm_99860.1	chr11	109365175	109365191	+	1	NA	intron (NM_010303, intron 1 of 3)	intron (NM_010303, intron 1 of 3)	-1529	NR_038097	100036768	Mm.467767	NR_038097	ENSMUSG00000056687	Gm11696	OTTMUSG00000003456	predicted gene 11696	ncRNA
mm_143337.1	chr17	66494699	66494701	-	1	NA	3' UTR (NM_024448, exon 6 of 6)	3' UTR (NM_024448, exon 6 of 6)	24970	NM_024448	19328	Mm.248313	NM_024448	ENSMUSG00000023460	Rab12	2900054P15Rik|AW555448|C77700	RAB12, member RAS oncogene family	protein-coding
mm_44896.1	chr5	35391907	35391918	-	1	NA	exon (NM_010445, exon 2 of 2)	exon (NM_010445, exon 2 of 2)	2795	NM_010445	15371	Mm.358606	NM_010445	ENSMUSG00000067438	Hmx1	Nkx5-3	H6 homeobox 1	protein-coding
mm_134872.1	chr16	28753193	28753252	-	1	NA	promoter-TSS (NM_010199)	promoter-TSS (NM_010199)	21	NM_010199	14167	Mm.7996	NM_010199	ENSMUSG00000022523	Fgf12	AV114868|B230343J05Rik|FGF-12|FHF-1|Fhf1	fibroblast growth factor 12	protein-coding
mm_140515.1	chr17	5988192	5988201	-	1	NA	intron (NM_001113352, intron 3 of 25)	intron (NM_001113352, intron 3 of 25)	12610	NM_011523	20975	Mm.236068	NM_011523	ENSMUSG00000023805	Synj2	AI481647|SJ2|mKIAA0348	synaptojanin 2	protein-coding
mm_143706.1	chr17	80641243	80641243	-	1	NA	intron (NM_001290345, intron 12 of 33)	intron (NM_001290345, intron 12 of 33)	-77409	NM_001033443	381113	Mm.329216	NM_001033443	ENSMUSG00000033966	Cdkl4	AU067824|Gm942	cyclin-dependent kinase-like 4	protein-coding
mm_35827.1	chr4	47346571	47346616	-	1	NA	Intergenic	ORR1D1|LTR|ERVL-MaLR	-6629	NM_001312868	21812	Mm.197552	NM_009370	ENSMUSG00000007613	Tgfbr1	ALK5|AU017191|Alk-5|ESK2|TGFR-1|TbetaR-I|TbetaRI	transforming growth factor, beta receptor I	protein-coding
mm_67027.1	chr7	66388287	66388341	-	1	NA	promoter-TSS (NM_146191)	promoter-TSS (NM_146191)	27	NM_146191	233328	Mm.33284	NM_146191	ENSMUSG00000015133	Lrrk1	AW319595|C230002E15Rik|D130026O16Rik|mKIAA1790	leucine-rich repeat kinase 1	protein-coding
mm_126006.1	chr15	76538935	76538961	+	1	NA	promoter-TSS (NM_013909)	promoter-TSS (NM_013909)	5	NM_029643	52710	Mm.28597	NM_029643	ENSMUSG00000022560	Slc52a2	2010003P03Rik|D15Ertd747e|GPCR42|Gpr172b|PAR2|mRFT1	solute carrier protein 52, member 2	protein-coding
mm_93654.1	chr10	117413907	117413917	-	1	NA	Intergenic	Intergenic	-36939	NM_001310609	432508	Mm.478881	NM_001013391	ENSMUSG00000055531	Cpsf6	4733401N12Rik|AI256641|CFIM|CFIM68|HPBRII-4|HPBRII-7	cleavage and polyadenylation specific factor 6	protein-coding
mm_116687.1	chr13	49298679	49298697	-	1	NA	intron (NM_015759, intron 1 of 17)	intron (NM_015759, intron 1 of 17)	10520	NM_015759	30938	Mm.291089	NM_015759	ENSMUSG00000037946	Fgd3	5830461L01Rik|ZFYVE5	FYVE, RhoGEF and PH domain containing 3	protein-coding
mm_107303.1	chr12	30953626	30953629	+	1	NA	intron (NR_110343, intron 9 of 10)	Lx9|LINE|L1	41958	NM_013709	24057	Mm.218624	NM_013709	ENSMUSG00000020669	Sh3yl1	AI314953|Ray|YSC84	Sh3 domain YSC-like 1	protein-coding
mm_169238.1	chr13	72392849	72392865	-	1	NA	Intergenic	L1Md_T|LINE|L1	235707	NR_030701	328287	Mm.235072	NR_030701		Gm20554	D430050G20	predicted gene, 20554	ncRNA
mm_99702.1	chr11	106160215	106160225	+	1	NA	promoter-TSS (NM_172397)	promoter-TSS (NM_172397)	-78	NM_172397	67803	Mm.21687	NM_172397	ENSMUSG00000040699	Limd2	0610025L06Rik|AI413966	LIM domain containing 2	protein-coding
mm_105312.1	chr11	102862674	102862693	-	1	NA	exon (NM_001109995, exon 10 of 28)	exon (NM_001109995, exon 10 of 28)	18292	NM_011431	20624	Mm.873	NM_011431	ENSMUSG00000020929	Eftud2	116kDa|Snrp116|U5-116kD	elongation factor Tu GTP binding domain containing 2	protein-coding
mm_14911.1	chr2	150570497	150570505	+	1	NA	promoter-TSS (NM_009977)	promoter-TSS (NM_009977)	86	NM_009977	13011	Mm.12965	NM_009977	ENSMUSG00000068129	Cst7	Cmap	cystatin F (leukocystatin)	protein-coding
mm_54425.1	chr6	33060257	33060267	-	1	NA	promoter-TSS (NM_025336)	promoter-TSS (NM_025336)	-110	NM_025336	66075	Mm.21501	NM_025336	ENSMUSG00000053768	Chchd3	0610041L09Rik|1700039J09Rik|AW558177	coiled-coil-helix-coiled-coil-helix domain containing 3	protein-coding
mm_65588.1	chr7	27311194	27311204	-	1	NA	TTS (NM_001310678)	TTS (NM_001310678)	22449	NM_001113549	108075	Mm.272251	NM_175641	ENSMUSG00000040488	Ltbp4	2310046A13Rik	latent transforming growth factor beta binding protein 4	protein-coding
mm_50996.1	chr6	63331510	63331512	+	1	NA	intron (NM_008167, intron 1 of 15)	intron (NM_008167, intron 1 of 15)	74654	NM_008167	14804	Mm.439651	NM_008167	ENSMUSG00000071424	Grid2	B230104L07Rik|GluD2|GluRdelta2|Lc|Lc<J>|MMS10-AC|Ms10ac|cpr|ho|nmf408|tpr	glutamate receptor, ionotropic, delta 2	protein-coding
mm_96989.1	chr11	70657835	70657859	+	1	NA	5' UTR (NM_007933, exon 2 of 12)	5' UTR (NM_007933, exon 2 of 12)	671	NM_007933	13808	Mm.251322	NM_007933	ENSMUSG00000060600	Eno3	Eno-3|MSE	enolase 3, beta muscle	protein-coding
mm_76493.1	chr8	86527684	86527729	-	1	NA	intron (NM_172912, intron 19 of 28)	intron (NM_172912, intron 19 of 28)	38884	NM_172912	244562	Mm.67485	NM_172912	ENSMUSG00000036872	Abcc12	4930467B22Rik|MRP9	ATP-binding cassette, sub-family C (CFTR/MRP), member 12	protein-coding
mm_151831.1	chr19	5663702	5663710	-	1	NA	promoter-TSS (NM_001164482)	promoter-TSS (NM_001164482)	1	NM_001164482	20469	Mm.3072	NM_011379	ENSMUSG00000056917	Sipa1	Spa1	signal-induced proliferation associated gene 1	protein-coding
mm_5497.1	chr1	36958518	36958519	-	1	NA	Intergenic	Intergenic	-18991	NM_018872	56030	Mm.186943	NM_018872	ENSMUSG00000026116	Tmem131	2610524E03Rik|CC28|D1Bwg0491e|Neg|RW1|YR-23|mKIAA0257	transmembrane protein 131	protein-coding
mm_45237.1	chr5	53706514	53706525	-	1	NA	intron (NM_009827, intron 1 of 4)	intron (NM_009827, intron 1 of 4)	1185	NM_009827	12425	Mm.3521	NM_009827	ENSMUSG00000029193	Cckar	AW106902	cholecystokinin A receptor	protein-coding
mm_50684.1	chr6	51575871	51575892	+	1	NA	intron (NM_028035, intron 2 of 6)	intron (NM_028035, intron 2 of 6)	31358	NM_001127348	71982	Mm.294166	NM_028035	ENSMUSG00000038301	Snx10	2410004M09Rik	sorting nexin 10	protein-coding
mm_167358.1	chr8	84559031	84559039	+	1	NA	exon (NM_001252060, exon 19 of 48)	exon (NM_001252060, exon 19 of 48)	103817	NM_010499	15936	Mm.399	NM_010499	ENSMUSG00000053560	Ier2	AI317238|Ch1|Pip92	immediate early response 2	protein-coding
mm_144588.1	chr18	32067730	32067811	+	1	NA	promoter-TSS (NM_173441)	promoter-TSS (NM_173441)	36	NM_173441	73473	Mm.66853	NM_173441	ENSMUSG00000024384	Iws1	1700069O15Rik|3000008H23|AL117927|AW214353	IWS1, SUPT6 interacting protein	protein-coding
mm_100613.1	chr11	121487964	121488004	+	1	NA	intron (NM_029878, intron 7 of 38)	PB1D7|SINE|Alu	31358	NM_178763	319530	Mm.11395	NM_178763	ENSMUSG00000039238	Zfp750	A030007D23Rik|Znf750	zinc finger protein 750	protein-coding
mm_109203.1	chr12	108667259	108667264	+	1	NA	intron (NM_001163394, intron 3 of 13)	intron (NM_001163394, intron 3 of 13)	8641	NR_029771	723909		NR_029771	ENSMUSG00000065436	Mir342	Mirn342|mmu-mir-342	microRNA 342	ncRNA
mm_169091.1	chr13	38665201	38665209	+	1	NA	Intergenic	BGLII|LTR|ERVK	-6177	NM_025380	66143	Mm.490319	NM_025380	ENSMUSG00000001707	Eef1e1	1110003A02Rik	eukaryotic translation elongation factor 1 epsilon 1	protein-coding
mm_171886.1	chr5	35771183	35771191	-	1	NA	intron (NM_001177696, intron 1 of 21)	intron (NM_001177696, intron 1 of 21)	13307	NM_001177698	231148	Mm.254446	NM_177678	ENSMUSG00000029095	Ablim2	AI606905|C230091L11	actin-binding LIM protein 2	protein-coding
mm_3947.1	chr1	163994867	163994904	+	1	NA	promoter-TSS (NM_201364)	promoter-TSS (NM_201364)	-60	NM_027279	69962	Mm.27284	NM_027279	ENSMUSG00000041396	Mettl18	2810422O20Rik|C78571	methyltransferase like 18	protein-coding
mm_18664.1	chr2	70823412	70823415	-	1	NA	intron (NM_172664, intron 1 of 19)	intron (NM_172664, intron 1 of 19)	2067	NM_172664	228012	Mm.136511	NM_172664	ENSMUSG00000041997	Tlk1	4930545J15Rik	tousled-like kinase 1	protein-coding
mm_25672.1	chr3	121967823	121967838	+	1	NA	intron (NM_172525, intron 1 of 22)	intron (NM_172525, intron 1 of 22)	14504	NM_172525	214137	Mm.229287	NM_172525	ENSMUSG00000039831	Arhgap29	6720461J18Rik|A830014I19|AU040217|B130017I01Rik|C76601|Parg1	Rho GTPase activating protein 29	protein-coding
mm_36139.1	chr4	59438291	59438305	-	1	NA	exon (NM_001163288, exon 1 of 17)	exon (NM_001163288, exon 1 of 17)	335	NM_001163288	634731	Mm.483589	NM_001163288	ENSMUSG00000038578	Susd1	A530080P10|Gm12528|OTTMUSG00000007332	sushi domain containing 1	protein-coding
mm_106318.1	chr11	118303138	118303143	-	1	NA	3' UTR (NM_011594, exon 5 of 5)	3' UTR (NM_011594, exon 5 of 5)	-12896	NM_001033528	72344	Mm.232293	NM_001033528	ENSMUSG00000033909	Usp36	2700002L06Rik|mKIAA1453	ubiquitin specific peptidase 36	protein-coding
mm_51453.1	chr6	80809573	80809606	+	1	NA	3' UTR (NM_001134743, exon 3 of 3)	3' UTR (NM_001134743, exon 3 of 3)	789946	NM_178731	243499	Mm.483425	NM_178731	ENSMUSG00000052581	Lrrtm4	7530419J18Rik|A230052N11	leucine rich repeat transmembrane neuronal 4	protein-coding
mm_100031.1	chr11	114930048	114930064	+	1	NA	intron (NM_199221, intron 1 of 3)	intron (NM_199221, intron 1 of 3)	4330	NM_001347651	217304	Mm.185355	NM_199221	ENSMUSG00000063193	Cd300lb	CLM-7|Clm7|Gm253|LMIR5	CD300 molecule like family member B	protein-coding
mm_157585.1	chrX	53070465	53070490	-	1	NA	exon (NM_019538, exon 3 of 3)	exon (NM_019538, exon 3 of 3)	-13287	NR_038184	72575	Mm.59516	NR_038184		C430049B03Rik	2700063P19Rik|9430052C07Rik|mir-322|mir-351|mir-503	RIKEN cDNA C430049B03 gene	ncRNA
mm_135017.1	chr16	32487644	32487659	-	1	NA	5' UTR (NM_145932, exon 1 of 9)	5' UTR (NM_145932, exon 1 of 9)	228	NM_145932	106407	Mm.476915	NM_145932	ENSMUSG00000035699	Slc51a	AV001382|AW261577|D630035O19Rik|OSTalpha|Osta	solute carrier family 51, alpha subunit	protein-coding
mm_21652.1	chr2	164334294	164334309	-	1	NA	TTS (NM_009301)	TTS (NM_009301)	1536	NM_009301	20944	Mm.140154	NM_009301	ENSMUSG00000017004	Svs5	BB115186|Semg1|Svp-1|Svp1|Svp5	seminal vesicle secretory protein 5	protein-coding
mm_3494.1	chr1	150106593	150106599	+	1	NA	3' UTR (NM_011198, exon 10 of 10)	3' UTR (NM_011198, exon 10 of 10)	6565	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_141746.1	chr17	34187352	34187380	-	1	NA	promoter-TSS (NM_001161730)	promoter-TSS (NM_001161730)	-36	NM_013585	16912	Mm.390983	NM_013585	ENSMUSG00000096727	Psmb9	Lmp-2|Lmp2	proteasome (prosome, macropain) subunit, beta type 9 (large multifunctional peptidase 2)	protein-coding
mm_23331.1	chr3	54246134	54246144	+	1	NA	intron (NR_046161, intron 3 of 10)	intron (NR_046161, intron 3 of 10)	90082	NM_001253682	22066	Mm.10100	NM_016984	ENSMUSG00000027748	Trpc4	CCE1|STRPC4|Trp4|Trrp4	transient receptor potential cation channel, subfamily C, member 4	protein-coding
mm_9411.1	chr1	172289388	172289398	-	1	NA	exon (NM_178405, exon 7 of 23)	exon (NM_178405, exon 7 of 23)	8671	NM_178405	98660	Mm.207432	NM_178405	ENSMUSG00000007097	Atp1a2	AW060654|Atpa-3|mKIAA0778	ATPase, Na+/K+ transporting, alpha 2 polypeptide	protein-coding
mm_126122.1	chr15	78326006	78326025	+	1	NA	promoter-TSS (NM_007780)	promoter-TSS (NM_007780)	25	NM_007780	12983	Mm.235324	NM_007780	ENSMUSG00000071713	Csf2rb	AI848964|AIC2B|Bc|CDw131|Csf2rb1|Csfgmrb|Il3r|Il3rb|Il3rb1|Il5rb	colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage)	protein-coding
mm_68472.1	chr7	110773279	110773302	-	1	NA	intron (NM_009667, intron 1 of 14)	intron (NM_009667, intron 1 of 14)	686	NM_009667	11717	Mm.3238	NM_009667	ENSMUSG00000005686	Ampd3	-	adenosine monophosphate deaminase 3	protein-coding
mm_151692.1	chr19	4334017	4334031	-	1	NA	intron (NM_001001984, intron 12 of 20)	intron (NM_001001984, intron 12 of 20)	-27802	NM_001290818	110355	Mm.254144	NM_130863	ENSMUSG00000024858	Grk2	Adrbk-1|Adrbk1|Bark-1|beta ARK|betaARK1	G protein-coupled receptor kinase 2	protein-coding
mm_15109.1	chr2	153609821	153609833	+	1	NA	Intergenic	Intergenic	22954	NM_001195390	99311	Mm.294478	NM_133850	ENSMUSG00000056941	Commd7	2310010I22Rik|AW060956|mU3	COMM domain containing 7	protein-coding
mm_24353.1	chr3	90051538	90051565	+	1	NA	promoter-TSS (NM_001287087)	promoter-TSS (NM_001287087)	-85	NM_001287087	99650	Mm.300083	NM_025762	ENSMUSG00000027942	4933434E20Rik	5730552F22Rik|AI462154|NICE-3|NS5ATP4	RIKEN cDNA 4933434E20 gene	protein-coding
mm_78803.1	chr9	44047920	44047935	+	1	NA	3' UTR (NM_009382, exon 4 of 4)	3' UTR (NM_009382, exon 4 of 4)	4543	NM_009382	21838	Mm.3951	NM_009382	ENSMUSG00000032011	Thy1	CD90|T25|Thy-1|Thy-1.2|Thy1.1|Thy1.2	thymus cell antigen 1, theta	protein-coding
mm_10288.1	chr2	10365354	10365403	+	1	NA	Intergenic	RLTR11B|LTR|ERVK	-5073	NM_001198808	353282	Mm.329991	NM_177386	ENSMUSG00000061186	Sfmbt2	D2Wsu23e|D330030P06Rik	Scm-like with four mbt domains 2	protein-coding
mm_151624.1	chr19	3907964	3907984	-	1	NA	promoter-TSS (NM_001136091)	promoter-TSS (NM_001136091)	-841	NM_001136091	27060	Mm.271689	NM_016921	ENSMUSG00000001750	Tcirg1	ATP6N1C|ATP6a3|Atp6i|OC-116|OPTB1|Stv1|TIRC7|Vph1|oc	T cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 protein A3	protein-coding
mm_120877.1	chr14	75284328	75284336	+	1	NA	promoter-TSS (NM_026083)	promoter-TSS (NM_026083)	-41	NM_026083	67302	Mm.74704	NM_026083	ENSMUSG00000022000	Zc3h13	2600010B19Rik|3110050K21Rik|4930570G11Rik|C87618	zinc finger CCCH type containing 13	protein-coding
mm_173225.1	chrX	76707578	76707578	-	1	NA	Intergenic	MTC|LTR|ERVL-MaLR	-104654	NM_001201395	74987	Mm.107996	NM_001201395	ENSMUSG00000079525	Cldn34d	4930468A15Rik	claudin 34D	protein-coding
mm_163726.1	chr13	119597788	119597805	-	1	NA	intron (NM_001039244, intron 2 of 2)	intron (NM_001039244, intron 2 of 2)	-26023	NM_020279	56838	Mm.143745	NM_020279	ENSMUSG00000074715	Ccl28	CCK1|MEC|Scya28	chemokine (C-C motif) ligand 28	protein-coding
mm_130132.1	chr15	90679308	90679388	-	1	NA	promoter-TSS (NM_025815)	promoter-TSS (NM_025815)	40	NM_025815	66871	Mm.290991	NM_025815	ENSMUSG00000052560	Cpne8	1200003E11Rik|1500031E20Rik	copine VIII	protein-coding
mm_51109.1	chr6	67285332	67285335	+	1	NA	3' UTR (NM_025814, exon 8 of 8)	3' UTR (NM_025814, exon 8 of 8)	18354	NM_025814	66870	Mm.240490	NM_025814	ENSMUSG00000036371	Serbp1	1200009K13Rik|9330147J08Rik|AL022786|Pairbp1	serpine1 mRNA binding protein 1	protein-coding
mm_68676.1	chr7	118983752	118983759	-	1	NA	exon (NM_001195774, exon 2 of 4)	exon (NM_001195774, exon 2 of 4)	11456	NM_022420	64297	Mm.103439	NM_022420	ENSMUSG00000008734	Gprc5b	AW125761|Raig2	G protein-coupled receptor, family C, group 5, member B	protein-coding
mm_134158.1	chr16	10791480	10791483	-	1	NA	promoter-TSS (NM_013638)	promoter-TSS (NM_013638)	-567	NM_013638	19120	Mm.291887	NM_013638	ENSMUSG00000050058	Prm3	BC061127|PX|Pxg	protamine 3	protein-coding
mm_47184.1	chr5	120753938	120753949	-	1	NA	3' UTR (NM_145226, exon 16 of 16)	3' UTR (NM_145226, exon 16 of 16)	-4095	NM_001347448	246728	Mm.260926	NM_145227	ENSMUSG00000032690	Oas2	Oasl11	2'-5' oligoadenylate synthetase 2	protein-coding
mm_88412.1	chr10	77033241	77033258	+	1	NA	promoter-TSS (NM_031196)	promoter-TSS (NM_031196)	37	NM_031196	20509	Mm.265060	NM_031196	ENSMUSG00000001436	Slc19a1	AI323572|RFC|RFC-1|RFC1	solute carrier family 19 (folate transporter), member 1	protein-coding
mm_59899.1	chr7	30308742	30308758	+	1	NA	promoter-TSS (NM_198027)	promoter-TSS (NM_198027)	-3	NM_198027	233065	Mm.276277	NM_198027	ENSMUSG00000042831	Alkbh6	AI839550|Abh6|C130099A02	alkB homolog 6	protein-coding
mm_115028.1	chr13	99230272	99230275	+	1	NA	intron (NM_001004149, intron 2 of 4)	intron (NM_001004149, intron 2 of 4)	45450	NM_001004149	238803	Mm.343207	NM_001004149	ENSMUSG00000050919	Zfp366	DC-SCRIPT|Znf366	zinc finger protein 366	protein-coding
mm_160588.1	chr9	65576779	65576779	-	1	NA	intron (NM_153119, intron 1 of 5)	intron (NM_153119, intron 1 of 5)	3308	NM_153119	102595	Mm.247303	NM_153119	ENSMUSG00000050721	Plekho2	AI840980|Plekhq1	pleckstrin homology domain containing, family O member 2	protein-coding
mm_120241.1	chr14	62960681	62960708	+	1	NA	Intergenic	Intergenic	23816	NM_001037751	432867	Mm.99387	NM_001037751	ENSMUSG00000075574	Defb48	Defb42|EG432867	defensin beta 48	protein-coding
mm_22618.1	chr3	14603735	14603764	+	1	NA	exon (NM_007892, exon 6 of 8)	exon (NM_007892, exon 6 of 8)	7472	NM_001347206	69126	Mm.389020	NM_001099674	ENSMUSG00000078784	1810022K09Rik	AI746582|AL023036	RIKEN cDNA 1810022K09 gene	protein-coding
mm_65174.1	chr7	19692005	19692013	-	1	NA	exon (NM_001110009, exon 3 of 4)	exon (NM_001110009, exon 3 of 4)	650	NM_001110009	11812	Mm.182440	NM_007469	ENSMUSG00000040564	Apoc1	Apo-CIB|ApoC-IB|apo-CI|apoC-I	apolipoprotein C-I	protein-coding
mm_57641.1	chr6	128413687	128413728	-	1	NA	intron (NM_133927, intron 5 of 11)	intron (NM_133927, intron 5 of 11)	11203	NM_133927	101142	Mm.31345	NM_133927	ENSMUSG00000001518	Itfg2	2700050P07Rik|AI646725	integrin alpha FG-GAP repeat containing 2	protein-coding
mm_157815.1	chrX	74014904	74014917	-	1	NA	3' UTR (NM_001177975, exon 14 of 14)	3' UTR (NM_001177975, exon 14 of 14)	8688	NR_039594	100628601		NR_039594	ENSMUSG00000092907	Mir5132	mir-5132|mmu-mir-5132|mu-mir-5132	microRNA 5132	ncRNA
mm_88134.1	chr10	69398847	69398892	+	1	NA	Intergenic	CpG	-45957	NM_007659	12534	Mm.281367	NM_007659	ENSMUSG00000019942	Cdk1	Cdc2|Cdc2a|p34<CDC2>	cyclin-dependent kinase 1	protein-coding
mm_86837.1	chr10	21395931	21395958	+	1	NA	3' UTR (NM_178713, exon 7 of 7)	3' UTR (NM_178713, exon 7 of 7)	18644	NM_178713	237320	Mm.90181	NM_178713	ENSMUSG00000037542	Aldh8a1	Raldh4	aldehyde dehydrogenase 8 family, member A1	protein-coding
mm_20894.1	chr2	148875422	148875444	-	1	NA	promoter-TSS (NM_009976)	promoter-TSS (NM_009976)	79	NM_009976	13010	Mm.4263	NM_009976	ENSMUSG00000027447	Cst3	CysC	cystatin C	protein-coding
mm_8041.1	chr1	135271566	135271599	-	1	NA	exon (NM_145417, exon 5 of 11)	exon (NM_145417, exon 5 of 11)	12502	NM_145417	215615	Mm.291048	NM_145417	ENSMUSG00000041926	Rnpep	-	arginyl aminopeptidase (aminopeptidase B)	protein-coding
mm_53811.1	chr6	146933449	146933454	+	1	NA	intron (NM_026221, intron 1 of 26)	intron (NM_026221, intron 1 of 26)	20970	NM_001164236	73344	Mm.391543	NM_028509	ENSMUSG00000040163	1700034J05Rik	-	RIKEN cDNA 1700034J05 gene	protein-coding
mm_54802.1	chr6	41700727	41700729	-	1	NA	intron (NM_032540, intron 6 of 18)	intron (NM_032540, intron 6 of 18)	3597	NM_032540	23925	Mm.19958	NM_032540	ENSMUSG00000029866	Kel	CD238|Ece3	Kell blood group	protein-coding
mm_134006.1	chr16	4790221	4790300	-	1	NA	promoter-TSS (NM_025670)	promoter-TSS (NM_025670)	-325	NM_025670	66626	Mm.157648	NM_025670	ENSMUSG00000004071	Cdip1	2700048O17Rik|5730403B10Rik|AU018521|AW742692|CDIP	cell death inducing Trp53 target 1	protein-coding
mm_118006.1	chr13	100616690	100616711	-	1	NA	TTS (NM_001283011)	TTS (NM_001283011)	244	NM_178410	218518	Mm.25300	NM_178410	ENSMUSG00000021636	Marveld2	BC003296|MARVD2|Mrvldc2|Tric|Trica|Tricb|Tricc	MARVEL (membrane-associating) domain containing 2	protein-coding
mm_90884.1	chr10	9898324	9898328	-	1	NA	intron (NM_001081344, intron 2 of 25)	intron (NM_001081344, intron 2 of 25)	2714	NM_001081344	78808	Mm.331751	NM_030191	ENSMUSG00000019790	Stxbp5	0710001E20Rik|4930565N16Rik|AW742610|LGL3|mKIAA1006	syntaxin binding protein 5 (tomosyn)	protein-coding
mm_166103.1	chr4	146501989	146502002	+	1	NA	promoter-TSS (NM_001243138)	promoter-TSS (NM_001243138)	-5	NM_001243138	100041433	Mm.441741	NM_001243138	ENSMUSG00000056300	Zfp981	Gm13247|OTTMUSG00000011075	zinc finger protein 981	protein-coding
mm_64949.1	chr7	16387758	16387773	-	1	NA	5' UTR (NM_019748, exon 1 of 9)	5' UTR (NM_019748, exon 1 of 9)	131	NM_001285892	56459	Mm.258530	NM_019748	ENSMUSG00000052833	Sae1	2400010M20Rik|2610044L12Rik|AL033372|AOS1|AW743391|D7Ertd177e|HSPC140|Sua1|Uble1a	SUMO1 activating enzyme subunit 1	protein-coding
mm_102036.1	chr11	51857090	51857110	-	1	NA	intron (NM_199299, intron 1 of 11)	CpG	381	NM_199299	76901	Mm.259996	NM_199299	ENSMUSG00000020387	Jade2	1200017K05Rik|AI480685|Phf15|mKIAA0239	jade family PHD finger 2	protein-coding
mm_8469.1	chr1	153332961	153332967	-	1	NA	promoter-TSS (NM_010683)	promoter-TSS (NM_010683)	-178	NM_010683	226519	Mm.1249	NM_010683	ENSMUSG00000026478	Lamc1	Lamb2	laminin, gamma 1	protein-coding
mm_93088.1	chr10	89621264	89621275	-	1	NA	promoter-TSS (NM_182959)	promoter-TSS (NM_182959)	-20	NM_182959	216227	Mm.233921	NM_182959	ENSMUSG00000019935	Slc17a8	BC042593|Vglut3	solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 8	protein-coding
mm_46539.1	chr5	105718226	105718236	-	1	NA	intron (NM_178701, intron 1 of 2)	intron (NM_178701, intron 1 of 2)	17421	NM_178701	231549	Mm.23837	NM_178701	ENSMUSG00000046079	Lrrc8d	2810473G09Rik|4930525N13Rik|A930019F03|Lrrc5	leucine rich repeat containing 8D	protein-coding
mm_128384.1	chr15	43019123	43019131	-	1	NA	Intergenic	Intergenic	151691	NM_172815	239405	Mm.193274	NM_172815	ENSMUSG00000051920	Rspo2	2610028F08Rik|AA673245|D430027K22|ftls	R-spondin 2	protein-coding
mm_64970.1	chr7	16619873	16619873	-	1	NA	intron (NR_136929, intron 1 of 2)	ID_B1|SINE|B4	-4880	NM_172739	232906	Mm.28646	NM_172739	ENSMUSG00000058230	Arhgap35	6430596G11Rik|AI841135|Grlf1|mKIAA1722|p190A|p190RhoGAP	Rho GTPase activating protein 35	protein-coding
mm_17447.1	chr2	28539703	28539720	-	1	NA	intron (NM_001145836, intron 1 of 17)	intron (NM_001145836, intron 1 of 17)	6247	NM_001145836	19730	Mm.5236	NM_009058	ENSMUSG00000026821	Ralgds	Gnds|Rgds|mKIAA1308	ral guanine nucleotide dissociation stimulator	protein-coding
mm_64376.1	chr7	142460824	142460832	+	1	NA	promoter-TSS (NM_001271509)	promoter-TSS (NM_001271509)	16	NM_001136071	16985	Mm.234003	NM_019391	ENSMUSG00000018819	Lsp1	Lsp-1|WP34|p50|pp52	lymphocyte specific 1	protein-coding
mm_201.1	chr1	16105395	16105410	+	1	NA	promoter-TSS (NM_133832)	promoter-TSS (NM_133832)	-480	NM_133832	98711	Mm.274376	NM_133832	ENSMUSG00000025921	Rdh10	3110069K09Rik|4921506A21Rik|AI875664|AW549993|D1Ertd762e|m366Asp	retinol dehydrogenase 10 (all-trans)	protein-coding
mm_41547.1	chr5	92898142	92898166	+	1	NA	5' UTR (NM_001077596, exon 1 of 10)	5' UTR (NM_001077596, exon 1 of 10)	161	NM_001077596	27428	Mm.46014	NM_015756	ENSMUSG00000029381	Shroom3	AL022960|D5Ertd287e|Shrm|Shrm3	shroom family member 3	protein-coding
mm_74854.1	chr8	24725763	24725818	-	1	NA	promoter-TSS (NM_001324489)	promoter-TSS (NM_001324489)	62	NM_009619	11497	Mm.5168	NM_009619	ENSMUSG00000031553	Adam3	Cyrn1|Taz83|tMDC	a disintegrin and metallopeptidase domain 3 (cyritestin)	protein-coding
mm_41984.1	chr5	107597742	107597756	+	1	NA	promoter-TSS (NM_133248)	promoter-TSS (NM_133248)	53	NM_001289569	231571	Mm.482420	NM_144911	ENSMUSG00000033773	Rpap2	AW060207	RNA polymerase II associated protein 2	protein-coding
mm_160021.1	chr6	130067279	130067279	-	1	NA	promoter-TSS (NM_001252577)	promoter-TSS (NM_001252577)	-8	NM_001252577	16635	Mm.333431	NM_010649	ENSMUSG00000079852	Klra4	Chok|Klra32|Klra33|Ly-49d|Ly49d|ly49r<129>	killer cell lectin-like receptor, subfamily A, member 4	protein-coding
mm_74705.1	chr8	17065439	17065464	-	1	NA	intron (NM_053171, intron 2 of 69)	intron (NM_053171, intron 2 of 69)	469934	NM_053171	94109	Mm.436988	NM_053171	ENSMUSG00000060924	Csmd1	B930082H09|mKIAA1890	CUB and Sushi multiple domains 1	protein-coding
mm_155299.1	chrX	61185677	61185694	+	1	NA	promoter-TSS (NM_001166658)	promoter-TSS (NM_001166658)	-127	NM_001166658	631990	Mm.401324	NM_001166658	ENSMUSG00000090546	Cdr1	100039759|Cdr|Cdr34|EG631990|Gm2409|Gm7077	cerebellar degeneration related antigen 1	protein-coding
mm_34737.1	chr4	152199823	152199872	+	1	NA	promoter-TSS (NM_001146058)	promoter-TSS (NM_001146058)	3	NM_001146058	70025	Mm.296191	NM_133348	ENSMUSG00000028937	Acot7	2410041A17Rik|Ach1|Act|Bach|CTE-IIa|Cte-II|Lach1	acyl-CoA thioesterase 7	protein-coding
mm_125400.1	chr15	41447492	41447509	+	1	NA	promoter-TSS (NM_001130166)	promoter-TSS (NM_001130166)	18	NM_001130166	170719	Mm.254267	NM_130885	ENSMUSG00000022307	Oxr1	2210416C20Rik|C7|C7B	oxidation resistance 1	protein-coding
mm_19122.1	chr2	80065224	80065227	-	1	NA	intron (NM_001159582, intron 2 of 15)	RMER19C|LTR|ERVK	63746	NM_016744	18573	Mm.40678	NM_016744	ENSMUSG00000059173	Pde1a	AI987702|AW125737	phosphodiesterase 1A, calmodulin-dependent	protein-coding
mm_38910.1	chr4	149980940	149980956	-	1	NA	3' UTR (NM_173371, exon 5 of 5)	3' UTR (NM_173371, exon 5 of 5)	22288	NM_001291004	100198	Mm.22183	NM_173371	ENSMUSG00000028980	H6pd	AI785303|G6pd1|Gpd-1|Gpd1	hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase)	protein-coding
mm_68119.1	chr7	102116722	102116733	-	1	NA	promoter-TSS (NM_001081424)	promoter-TSS (NM_001081424)	-14	NM_001081424	504186	Mm.334074	NM_001081424	ENSMUSG00000066279	Chrna10	-	cholinergic receptor, nicotinic, alpha polypeptide 10	protein-coding
mm_28889.1	chr3	97868271	97868281	-	1	NA	intron (NM_001039376, intron 1 of 46)	CpG	20431	NM_001289702	83679	Mm.129840	NM_031401	ENSMUSG00000038170	Pde4dip	4732458A06Rik|9430063L05Rik|C87016|D130016K21Rik|D3Bwg1078e|Usmg4|mKIAA0454	phosphodiesterase 4D interacting protein (myomegalin)	protein-coding
mm_60238.1	chr7	43713188	43713194	+	1	NA	intron (NM_001039042, intron 1 of 5)	intron (NM_001039042, intron 1 of 5)	624	NM_001039042	626834	Mm.389891	NM_001039042	ENSMUSG00000054046	Klk13	Egfbp-2|mGk-13	kallikrein related-peptidase 13	protein-coding
mm_127286.1	chr15	100038636	100038669	+	1	NA	promoter-TSS (NM_001159361)	promoter-TSS (NM_001159361)	-12	NM_001159361	239667	Mm.243658	NM_172819	ENSMUSG00000023026	Dip2b	4932422C22|AI317237|AI854602|mKIAA1463	disco interacting protein 2 homolog B	protein-coding
mm_130595.1	chr15	99723781	99723811	-	1	NA	3' UTR (NM_010271, exon 8 of 8)	3' UTR (NM_010271, exon 8 of 8)	-1822	NM_183256	66379	Mm.5265	NM_183256	ENSMUSG00000023020	Cox14	2310016M24Rik|AA959804	cytochrome c oxidase assembly protein 14	protein-coding
mm_138750.1	chr17	37045964	37045975	+	1	NA	promoter-TSS (NM_019439)	promoter-TSS (NM_019439)	3	NM_019439	54393	Mm.32191	NM_019439	ENSMUSG00000024462	Gabbr1	GABAB1|GABAbR1|bM573K1.1	gamma-aminobutyric acid (GABA) B receptor, 1	protein-coding
mm_36468.1	chr4	82705624	82705637	-	1	NA	Intergenic	Intergenic	154031	NM_026647	68268	Mm.32047	NM_026647	ENSMUSG00000028403	Zdhhc21	9130404H11Rik|AL024349|D130004H04Rik|dep	zinc finger, DHHC domain containing 21	protein-coding
mm_66473.1	chr7	44986390	44986400	-	1	NA	promoter-TSS (NR_045266)	promoter-TSS (NR_045266)	25	NM_001252476	15469	Mm.27545	NM_019830	ENSMUSG00000109324	Prmt1	6720434D09Rik|AW214366|Hrmt1l2|Mrmt1	protein arginine N-methyltransferase 1	protein-coding
mm_161149.1	chr13	23136505	23136505	+	1	NA	promoter-TSS (NM_134222)	promoter-TSS (NM_134222)	20	NM_134222	171256	Mm.377210	NM_134222	ENSMUSG00000060490	Vmn1r218	V1ri5	vomeronasal 1 receptor 218	protein-coding
mm_173037.1	chrX	107175672	107175675	-	1	NA	Intergenic	RLTR27|LTR|ERVK	26058	NM_175442	213438	Mm.265244	NM_175442	ENSMUSG00000054293	A630033H20Rik	AI662791|P2ry10	RIKEN cDNA A630033H20 gene	protein-coding
mm_103416.1	chr11	75533025	75533035	-	1	NA	intron (NM_173388, intron 2 of 13)	intron (NM_173388, intron 2 of 13)	918	NM_001199283	215113	Mm.11186	NM_173388	ENSMUSG00000038178	Slc43a2	7630402D21Rik|BC042513|Lat4	solute carrier family 43, member 2	protein-coding
mm_19615.1	chr2	102811868	102811882	-	1	NA	3' UTR (NM_009851, exon 19 of 19)	3' UTR (NM_009851, exon 19 of 19)	89790	NM_001177785	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_18210.1	chr2	48946316	48946325	-	1	NA	intron (NR_033442, intron 1 of 13)	L1ME3B|LINE|L1	2947	NM_001177313	26428	Mm.291059	NM_011958	ENSMUSG00000026761	Orc4	Orc4P|Orc4l|mMmORC4	origin recognition complex, subunit 4	protein-coding
mm_70695.1	chr8	15027383	15027387	+	1	NA	5' UTR (NM_029116, exon 2 of 2)	5' UTR (NM_029116, exon 2 of 2)	16360	NM_029116	74901	Mm.46675	NM_029116	ENSMUSG00000055675	Kbtbd11	2900016B01Rik|4930465M17Rik|mKIAA0711	kelch repeat and BTB (POZ) domain containing 11	protein-coding
mm_101008.1	chr11	8503784	8503794	-	1	NA	intron (NM_001083587, intron 16 of 30)	intron (NM_001083587, intron 16 of 30)	160746	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_127506.1	chr15	101469397	101469411	+	1	NA	intron (NM_016879, intron 6 of 9)	intron (NM_016879, intron 6 of 9)	-4074	NM_010667	16679	Mm.383183	NM_010667	ENSMUSG00000067614	Krt86	5430421N21Rik|AI325212|Khb4|Krt2-10|Krt2-11|MHb4	keratin 86	protein-coding
mm_44925.1	chr5	36036959	36036974	-	1	NA	intron (NM_030889, intron 17 of 26)	intron (NM_030889, intron 17 of 26)	143647	NM_027373	70292	Mm.125167	NM_027373	ENSMUSG00000029094	Afap1	2600003E23Rik|9630044L16Rik|AI848729|Afap|mKIAA3018	actin filament associated protein 1	protein-coding
mm_104004.1	chr11	84916339	84916371	-	1	NA	promoter-TSS (NM_001005223)	promoter-TSS (NM_001005223)	1	NM_001005223	448850	Mm.379733	NM_001005223	ENSMUSG00000020526	Znhit3	Myohd1|Trip3	zinc finger, HIT type 3	protein-coding
mm_147524.1	chr18	52529693	52529709	-	1	NA	promoter-TSS (NM_001286181)	promoter-TSS (NM_001286181)	20	NM_001286181	16948	Mm.172	NM_010728	ENSMUSG00000024529	Lox	AI893619|TSC-160|rrg	lysyl oxidase	protein-coding
mm_57442.1	chr6	124965249	124965275	-	1	NA	intron (NM_001164089, intron 1 of 7)	CpG	135	NM_012003	26894	Mm.244536	NM_012003	ENSMUSG00000030127	Cops7a	D6Ertd35e	COP9 signalosome subunit 7A	protein-coding
mm_92849.1	chr10	81524131	81524139	-	1	NA	promoter-TSS (NM_010304)	promoter-TSS (NM_010304)	90	NM_010304	14676	Mm.1546	NM_010304	ENSMUSG00000034792	Gna15	G[a]15|Galpha15	guanine nucleotide binding protein, alpha 15	protein-coding
mm_135063.1	chr16	34095984	34096060	-	1	NA	intron (NM_177357, intron 34 of 59)	intron (NM_177357, intron 34 of 59)	-129019	NM_009471	22247	Mm.13145	NM_009471	ENSMUSG00000022814	Umps	1700095D23Rik|AA408257|AL033308|BB164745	uridine monophosphate synthetase	protein-coding
mm_90673.1	chr10	128900330	128900361	+	1	NA	Intergenic	Intergenic	-8574	NM_001042580	12512	Mm.371552	NM_007653	ENSMUSG00000025351	Cd63	C75951|ME491|Tspan30	CD63 antigen	protein-coding
mm_39519.1	chr5	21257923	21257932	+	1	NA	intron (NM_175437, intron 19 of 30)	intron (NM_175437, intron 19 of 30)	71660	NM_175437	212167	Mm.121705	NM_175437	ENSMUSG00000039934	Gsap	A530088I07Rik|Pion	gamma-secretase activating protein	protein-coding
mm_158932.1	chr1	66468318	66468318	+	1	NA	promoter-TSS (NM_175510)	promoter-TSS (NM_175510)	-129	NM_175510	329178	Mm.44798	NM_175510	ENSMUSG00000055567	Unc80	C030018G13Rik|C230061B10Rik|UNC-80	unc-80, NALCN activator	protein-coding
mm_116670.1	chr13	49208056	49208069	-	1	NA	exon (NM_026738, exon 2 of 6)	exon (NM_026738, exon 2 of 6)	7964	NM_026738	68480	Mm.3336	NM_026738	ENSMUSG00000037960	Card19	1110007C09Rik|AI851695|Bincard	caspase recruitment domain family, member 19	protein-coding
mm_125235.1	chr15	34143922	34143928	+	1	NA	Intergenic	Intergenic	61206	NM_026002	67154	Mm.130883	NM_026002	ENSMUSG00000022255	Mtdh	2610103J23Rik|3D3|3D3/Lyric|AEG-1|AV353288|D8Bwg1112e|Lyric	metadherin	protein-coding
mm_37279.1	chr4	118954825	118954838	-	1	NA	promoter-TSS (NR_137285)	promoter-TSS (NR_137285)	88	NR_137285	100038571	Mm.426714	NR_137285	ENSMUSG00000073765	Gm12863	OTTMUSG00000008822	predicted gene 12863	ncRNA
mm_104393.1	chr11	94491345	94491372	-	1	NA	exon (NM_027984, exon 10 of 10)	exon (NM_027984, exon 10 of 10)	-6048	NM_144827	217116	Mm.156123	NM_144827	ENSMUSG00000020867	Spata20	Tisp78	spermatogenesis associated 20	protein-coding
mm_13923.1	chr2	120692585	120692591	+	1	NA	Intergenic	Intergenic	38929	NM_026891	68968	Mm.2289	NM_026891	ENSMUSG00000027284	Cdan1	1500015A01Rik|AI448026|AW492297|CDA-I|CDA1|CDAI	congenital dyserythropoietic anemia, type I (human)	protein-coding
mm_115271.1	chr13	111686057	111686074	+	1	NA	promoter-TSS (NM_172593)	promoter-TSS (NM_172593)	-113	NM_172593	218613	Mm.31012	NM_172593	ENSMUSG00000032727	Mier3	5730509D14|AU015422|D130064H19Rik	MIER family member 3	protein-coding
mm_41998.1	chr5	107900501	107900509	+	1	NA	promoter-TSS (NM_016980)	promoter-TSS (NM_016980)	-23	NM_016980	100503670	Mm.277897	NM_016980	ENSMUSG00000058558	Rpl5	U21RNA	ribosomal protein L5	protein-coding
mm_144921.1	chr18	37668919	37668962	+	1	NA	promoter-TSS (NM_033585)	promoter-TSS (NM_033585)	-165	NM_033585	93710	Mm.247203	NM_033585	ENSMUSG00000103332	Pcdhga2	mKIAA0588	protocadherin gamma subfamily A, 2	protein-coding
mm_150290.1	chr19	34492841	34492855	+	1	NA	3' UTR (NM_021460, exon 10 of 10)	3' UTR (NM_021460, exon 10 of 10)	-17713	NM_009890	12642	Mm.30824	NM_009890	ENSMUSG00000050370	Ch25h	AI462618|m25OH	cholesterol 25-hydroxylase	protein-coding
mm_14797.1	chr2	145878828	145878839	+	1	NA	intron (NM_028724, intron 10 of 12)	intron (NM_028724, intron 10 of 12)	-24408	NM_026425	67877	Mm.151168	NM_026425	ENSMUSG00000002728	Naa20	1500004D14Rik|2900026I01Rik|AU041458|D2Ertd186e|Nat5	N(alpha)-acetyltransferase 20, NatB catalytic subunit	protein-coding
mm_23000.1	chr3	34046431	34046474	+	1	NA	exon (NM_001113188, exon 5 of 17)	exon (NM_001113188, exon 5 of 17)	26373	NM_001113188	14359	Mm.259021	NM_008053	ENSMUSG00000027680	Fxr1	1110050J02Rik|9530073J07Rik|AI851072|Fxr1h|Fxr1p	fragile X mental retardation gene 1, autosomal homolog	protein-coding
mm_80603.1	chr9	86571966	86572021	+	1	NA	promoter-TSS (NM_001145969)	promoter-TSS (NM_001145969)	5	NM_001145969	69519	Mm.272517	NM_027100	ENSMUSG00000032417	Rwdd2a	1700030C20Rik|AI848608|Rwdd2	RWD domain containing 2A	protein-coding
mm_4567.1	chr1	177448244	177448251	+	1	NA	exon (NM_013915, exon 1 of 1)	exon (NM_013915, exon 1 of 1)	2426	NM_013915	30928	Mm.330700	NM_013915	ENSMUSG00000063659	Zbtb18	RP58|Zfp238|Znf238	zinc finger and BTB domain containing 18	protein-coding
mm_164921.1	chr18	77177074	77177098	+	1	NA	Intergenic	Intergenic	-8761	NM_153124	225742	Mm.365178	NM_013666	ENSMUSG00000025425	St8sia5	ST8SiaV|Siat8e	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 5	protein-coding
mm_170023.1	chr17	21475063	21475070	+	1	NA	Intergenic	MMVL30-int|LTR|ERV1	-13922	NM_013843	24132	Mm.42140	NM_013843	ENSMUSG00000057409	Zfp53	D030067O06Rik|KRAZ1|Zfp-53|Zfp118|zfas8	zinc finger protein 53	protein-coding
mm_119045.1	chr14	30607912	30607923	+	1	NA	intron (NM_011103, intron 3 of 17)	intron (NM_011103, intron 3 of 17)	2393	NM_001310682	18753	Mm.2314	NM_011103	ENSMUSG00000021948	Prkcd	AI385711|D14Ertd420e|PKC[d]|PKCdelta|Pkcd	protein kinase C, delta	protein-coding
mm_114945.1	chr13	96543075	96543083	+	1	NA	promoter-TSS (NM_012048)	promoter-TSS (NM_012048)	344	NM_023420	68018	Mm.24125	NM_023420	ENSMUSG00000021669	Col4a3bp	2810404O15Rik|9230101K08Rik|AU016711|CERT|GPBP	collagen, type IV, alpha 3 (Goodpasture antigen) binding protein	protein-coding
mm_78170.1	chr9	21079732	21079735	+	1	NA	exon (NM_027911, exon 8 of 13)	exon (NM_027911, exon 8 of 13)	-4145	NR_106050	102465656		NR_106050	ENSMUSG00000098907	Mir7082	Gm27933|mmu-mir-7082	microRNA 7082	ncRNA
mm_71792.1	chr8	66889236	66889248	+	1	NA	exon (NM_001163564, exon 8 of 8)	exon (NM_001163564, exon 8 of 8)	29025	NM_001163564	234344	Mm.334561	NM_001163564	ENSMUSG00000014907	Naf1	Gm174	nuclear assembly factor 1 ribonucleoprotein	protein-coding
mm_91489.1	chr10	37135648	37135653	-	1	NA	3' UTR (NM_008538, exon 2 of 2)	3' UTR (NM_008538, exon 2 of 2)	3276	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_47770.1	chr5	131538738	131538749	-	1	NA	intron (NM_177047, intron 5 of 18)	CpG	-231221	NM_145218	212996	Mm.299204	NM_145218	ENSMUSG00000034040	Wbscr17	AA388321|E330012B09Rik	Williams-Beuren syndrome chromosome region 17 homolog (human)	protein-coding
mm_172817.1	chr9	123690275	123690275	-	1	NA	Intergenic	Intergenic	-11443	NM_139142	102680	Mm.440867	NM_139142	ENSMUSG00000036814	Slc6a20a	A730081N20Rik|AU022428|Xt3s1|Xtrp3s1	solute carrier family 6 (neurotransmitter transporter), member 20A	protein-coding
mm_171995.1	chr6	10146999	10147000	+	1	NA	Intergenic	Intergenic	827379	NR_033776	57866	Mm.4397	NR_033776		AA545190	-	EST AA545190	ncRNA
mm_5892.1	chr1	54438941	54438994	-	1	NA	promoter-TSS (NM_001033194)	promoter-TSS (NM_001033194)	59	NM_001033194	98488	Mm.25856	NM_001033194	ENSMUSG00000041303	Gtf3c3	TF3C-gamma|TFIIIC102	general transcription factor IIIC, polypeptide 3	protein-coding
mm_14183.1	chr2	127078921	127078925	+	1	NA	intron (NM_026678, intron 1 of 7)	B1_Mur4|SINE|Alu	8266	NM_026678	109778	Mm.22028	NM_026678	ENSMUSG00000001999	Blvra	0610006A11Rik|2500001N03Rik|Blvr	biliverdin reductase A	protein-coding
mm_80703.1	chr9	92249750	92249753	+	1	NA	promoter-TSS (NM_011636)	promoter-TSS (NM_011636)	-443	NM_011636	22038	Mm.421956	NM_011636	ENSMUSG00000032369	Plscr1	MmTRA1a|MmTRA1b|Nor1|Tra1|Tra1a|Tra1b|Tras1|Tras2	phospholipid scramblase 1	protein-coding
mm_137161.1	chr17	23803180	23803237	+	1	NA	promoter-TSS (NM_175229)	promoter-TSS (NM_175229)	21	NM_175229	75956	Mm.5222	NM_175229	ENSMUSG00000039218	Srrm2	5033413A03Rik|AA410130|SRm300|mKIAA0324	serine/arginine repetitive matrix 2	protein-coding
mm_154107.1	chr19	57118877	57118896	-	1	NA	5' UTR (NM_001103178, exon 1 of 20)	5' UTR (NM_001103178, exon 1 of 20)	138	NM_001347459	226251	Mm.217161	NM_178688	ENSMUSG00000025085	Ablim1	2210411C18Rik|2610209L21Rik|4833406P10Rik|9330196J19Rik|AV079770|AW060987|AW215784|Limab1|mKIAA0059	actin-binding LIM protein 1	protein-coding
mm_66873.1	chr7	57509398	57509410	-	1	NA	intron (NM_176942, intron 1 of 9)	CpG	605	NM_176942	110886	Mm.273114	NM_176942	ENSMUSG00000055078	Gabra5	A230018I05Rik	gamma-aminobutyric acid (GABA) A receptor, subunit alpha 5	protein-coding
mm_102182.1	chr11	54068951	54069017	-	1	NA	promoter-TSS (NM_019417)	promoter-TSS (NM_019417)	33	NM_019417	30794	Mm.21830	NM_019417	ENSMUSG00000020388	Pdlim4	Ril	PDZ and LIM domain 4	protein-coding
mm_112075.1	chr12	112629018	112629062	-	1	NA	intron (NM_007421, intron 2 of 12)	intron (NM_007421, intron 2 of 12)	8993	NM_007421	11565	Mm.3440	NM_007421	ENSMUSG00000011148	Adssl1	AI528595|Adss|Adss1	adenylosuccinate synthetase like 1	protein-coding
mm_140969.1	chr17	24689902	24689960	-	1	NA	promoter-TSS (NM_011522)	promoter-TSS (NM_011522)	18	NM_011522	20974	Mm.26032	NM_011522	ENSMUSG00000007021	Syngr3	-	synaptogyrin 3	protein-coding
mm_28064.1	chr3	84259737	84259787	-	1	NA	promoter-TSS (NM_001271727)	promoter-TSS (NM_001271727)	17	NM_001271727	80890	Mm.44876	NM_030706	ENSMUSG00000027993	Trim2	mKIAA0517|narf	tripartite motif-containing 2	protein-coding
mm_42868.1	chr5	122233413	122233436	+	1	NA	exon (NM_001042489, exon 4 of 8)	exon (NM_001042489, exon 4 of 8)	23137	NM_028752	74096	Mm.28804	NM_028752	ENSMUSG00000064267	Hvcn1	0610039P13Rik|AI450555|BTS|HV1|Vsop.|mVSOP	hydrogen voltage-gated channel 1	protein-coding
mm_54429.1	chr6	33992414	33992420	-	1	NA	Intergenic	Intergenic	-37031	NM_028886	74354	Mm.127952	NM_028886	ENSMUSG00000056215	Lrguk	4921528H16Rik	leucine-rich repeats and guanylate kinase domain containing	protein-coding
mm_51388.1	chr6	77244022	77244032	+	1	NA	exon (NM_028880, exon 2 of 2)	exon (NM_028880, exon 2 of 2)	1310	NM_028880	74342	Mm.292568	NM_028880	ENSMUSG00000060780	Lrrtm1	4632401D06Rik|AW125451	leucine rich repeat transmembrane neuronal 1	protein-coding
mm_57496.1	chr6	125313826	125313836	-	1	NA	promoter-TSS (NM_010736)	promoter-TSS (NM_010736)	39	NM_010736	17000	Mm.3122	NM_010736	ENSMUSG00000030339	Ltbr	AI256028|CD18|LTbetaR|Ltar|TNF-R-III|TNFCR|TNFR-RP|TNFR2-RP|TNFRrp|Tnfbr|Tnfrsf3	lymphotoxin B receptor	protein-coding
mm_84774.1	chr9	75683350	75683357	-	1	NA	intron (NM_009130, intron 1 of 11)	intron (NM_009130, intron 1 of 11)	703	NM_001164790	20255	Mm.2386	NM_009130	ENSMUSG00000032181	Scg3	1B1075|AI385542|Chgd|SgIII	secretogranin III	protein-coding
mm_14920.1	chr2	151127460	151127474	+	1	NA	Intergenic	Intergenic	29222	NM_001097977	433486	Mm.422661	NM_001097977	ENSMUSG00000079006	Gm14151	OTTMUSG00000015806	predicted gene 14151	protein-coding
mm_54845.1	chr6	42586923	42586937	-	1	NA	TTS (NM_203396)	TTS (NM_203396)	10442	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_1280.1	chr1	63528760	63528768	+	1	NA	exon (NM_011780, exon 5 of 26)	exon (NM_011780, exon 5 of 26)	82873	NM_011780	23792	Mm.124892	NM_011780	ENSMUSG00000025964	Adam23	AW046396|MDC3	a disintegrin and metallopeptidase domain 23	protein-coding
mm_27589.1	chr3	59130611	59130628	-	1	NA	5' UTR (NM_001287124, exon 1 of 2)	5' UTR (NM_001287124, exon 1 of 2)	143	NM_001008497	140795	Mm.439021	NM_133200	ENSMUSG00000036381	P2ry14	A330108O13Rik|Gpr105|P2Y14	purinergic receptor P2Y, G-protein coupled, 14	protein-coding
mm_99668.1	chr11	105967915	105967927	+	1	NA	promoter-TSS (NM_001281819)	promoter-TSS (NM_001281819)	-24	NM_001281819	11421	Mm.754	NM_009598	ENSMUSG00000020681	Ace	AW208573|CD143	angiotensin I converting enzyme (peptidyl-dipeptidase A) 1	protein-coding
mm_73088.1	chr8	94526815	94526818	+	1	NA	3' UTR (NM_001033207, exon 49 of 49)	3' UTR (NM_001033207, exon 49 of 49)	-6212	NM_153507	234577	Mm.291815	NM_153507	ENSMUSG00000034361	Cpne2	3322401K10Rik	copine II	protein-coding
mm_137505.1	chr17	27029363	27029366	+	1	NA	promoter-TSS (NM_007523)	promoter-TSS (NM_007523)	105	NM_027544	70772	Mm.440437	NM_027544	ENSMUSG00000048731	Ggnbp1	0610031G08Rik|mdf	gametogenetin binding protein 1	protein-coding
mm_126204.1	chr15	78882126	78882155	+	1	NA	exon (NM_145929, exon 3 of 17)	exon (NM_145929, exon 3 of 17)	4950	NM_145929	106039	Mm.251331	NM_145929	ENSMUSG00000033128	Gga1	4930406E12Rik|AU016030|AW209092	golgi associated, gamma adaptin ear containing, ARF binding protein 1	protein-coding
mm_99234.1	chr11	101063236	101063255	+	1	NA	3' UTR (NM_001243049, exon 21 of 21)	3' UTR (NM_001243049, exon 21 of 21)	-6849	NM_013792	27419	Mm.95452	NM_013792	ENSMUSG00000001751	Naglu	-	alpha-N-acetylglucosaminidase (Sanfilippo disease IIIB)	protein-coding
mm_119844.1	chr14	54437761	54437771	+	1	NA	intron (NM_008608, intron 5 of 9)	intron (NM_008608, intron 5 of 9)	6168	NM_008608	17387	Mm.280175	NM_008608	ENSMUSG00000000957	Mmp14	AI325305|MMP-X1|MT-MMP-1|MT1-MMP|sabe	matrix metallopeptidase 14 (membrane-inserted)	protein-coding
mm_13354.1	chr2	103411683	103411696	+	1	NA	promoter-TSS (NM_001145813)	promoter-TSS (NM_001145813)	-409	NM_001145813	13711	Mm.20888	NM_010125	ENSMUSG00000027186	Elf5	ESE-2|ESE-5|ESE-5.	E74-like factor 5	protein-coding
mm_132158.1	chr16	32179795	32179835	+	1	NA	promoter-TSS (NM_001033539)	promoter-TSS (NM_001033539)	15	NM_001033539	328660	Mm.441006	NM_001033539	ENSMUSG00000075269	Bex6	B020003O03Rik	brain expressed family member 6	protein-coding
mm_137937.1	chr17	32659067	32659079	+	1	NA	promoter-TSS (NM_001101588)	promoter-TSS (NM_001101588)	-410	NM_001101588	631304	Mm.328950	NM_001101588	ENSMUSG00000090700	Cyp4f40	EG631304	cytochrome P450, family 4, subfamily f, polypeptide 40	protein-coding
mm_161739.1	chr17	32621318	32621318	+	1	NA	promoter-TSS (NM_001100187)	promoter-TSS (NM_001100187)	-1	NM_001100187	677156	Mm.484117	NM_001100187	ENSMUSG00000062464	Cyp4f37	Gm9705	cytochrome P450, family 4, subfamily f, polypeptide 37	protein-coding
mm_140176.1	chr17	80762894	80762904	+	1	NA	Intergenic	Intergenic	-34874	NM_001290345	225028	Mm.311948	NM_001081357	ENSMUSG00000024242	Map4k3	4833416M01Rik|4833416M07Rik|9530052P13Rik|Glk|MAPKKKK3|MEKKK 3|MEKKK3|RAB8IPL1	mitogen-activated protein kinase kinase kinase kinase 3	protein-coding
mm_68090.1	chr7	101905680	101905701	-	1	NA	promoter-TSS (NM_025605)	promoter-TSS (NM_025605)	-147	NM_025605	66508	Mm.30003	NM_025605	ENSMUSG00000030842	Lamtor1	2400001E08Rik|Pdro|p18	late endosomal/lysosomal adaptor, MAPK and MTOR activator 1	protein-coding
mm_60467.1	chr7	44478032	44478044	+	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	-6479	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_121823.1	chr14	20473306	20473345	-	1	NA	exon (NM_001110794, exon 2 of 13)	exon (NM_001110794, exon 2 of 13)	6808	NM_001110794	11750	Mm.280231	NM_009674	ENSMUSG00000021814	Anxa7	AI265384|AI316497|Anx7|synexin	annexin A7	protein-coding
mm_48791.1	chr5	148678446	148678449	-	1	NA	Intergenic	RLTR10B2|LTR|ERVK	-63393	NR_028285	70138	Mm.417834	NR_028285	ENSMUSG00000086494	2210417A02Rik	AV081004	RIKEN cDNA 2210417A02 gene	ncRNA
mm_125331.1	chr15	38661986	38661999	+	1	NA	promoter-TSS (NM_025494)	promoter-TSS (NM_025494)	88	NM_025494	66335	Mm.276618	NM_025494	ENSMUSG00000022295	Atp6v1c1	1700025B18Rik|U13839	ATPase, H+ transporting, lysosomal V1 subunit C1	protein-coding
mm_36.1	chr1	6380273	6380282	+	1	NA	intron (NM_001195732, intron 1 of 4)	intron (NM_001195732, intron 1 of 4)	20946	NM_001195732	620393	Mm.388992	NM_001195732	ENSMUSG00000087247	Fam150a	EG620393	family with sequence similarity 150, member A	protein-coding
mm_78685.1	chr9	40799327	40799366	+	1	NA	Intergenic	Intergenic	-1927	NM_031165	15481	Mm.290774	NM_031165	ENSMUSG00000015656	Hspa8	2410008N15Rik|Hsc70|Hsc71|Hsc73|Hsp73|Hspa10	heat shock protein 8	protein-coding
mm_137910.1	chr17	32111217	32111232	+	1	NA	Intergenic	Intergenic	-19801	NR_027316	435518	Mm.328944	NR_027316	ENSMUSG00000002791	Pdxk-ps	ENSMUSG00000002791|Gm9743	pyridoxal (pyridoxine, vitamin B6) kinase, pseudogene	pseudo
mm_133906.1	chr16	97548791	97548816	+	1	NA	intron (NM_013606, intron 7 of 13)	L1_Mur3|LINE|L1	12720	NM_013606	17858	Mm.14157	NM_013606	ENSMUSG00000023341	Mx2	AI528743|Mx-2	MX dynamin-like GTPase 2	protein-coding
mm_153992.1	chr19	50455795	50455797	-	1	NA	intron (NM_001290356, intron 2 of 24)	intron (NM_001290356, intron 2 of 24)	222850	NM_001252501	58178	Mm.313672	NM_021377	ENSMUSG00000043531	Sorcs1	Sorcs|mSorCS	sortilin-related VPS10 domain containing receptor 1	protein-coding
mm_95319.1	chr11	46437066	46437088	+	1	NA	5' UTR (NM_025426, exon 1 of 3)	5' UTR (NM_025426, exon 1 of 3)	116	NM_025426	66213	Mm.24159	NM_025426	ENSMUSG00000020397	Med7	1110063B05Rik|Crsp33|Crsp9	mediator complex subunit 7	protein-coding
mm_164877.1	chr18	58209960	58209982	-	1	NA	promoter-TSS (NM_010181)	promoter-TSS (NM_010181)	-45	NM_010181	14119	Mm.20271	NM_010181	ENSMUSG00000024598	Fbn2	BC063774|Fib-2|mKIAA4226|sne|sy	fibrillin 2	protein-coding
mm_70096.1	chr7	142660865	142660865	-	1	NA	non-coding (NR_002855, exon 1 of 4)	non-coding (NR_002855, exon 1 of 4)	406	NM_001122736	16002	Mm.3862	NM_010514	ENSMUSG00000048583	Igf2	AL033362|Igf-2|Igf-II|M6pr|Mpr|Peg2	insulin-like growth factor 2	protein-coding
mm_2347.1	chr1	92910613	92910637	+	1	NA	promoter-TSS (NM_181405)	promoter-TSS (NM_181405)	64	NR_138577	75995	Mm.46179	NR_138577	ENSMUSG00000097251	5033417F24Rik	6330419D11Rik	RIKEN cDNA 5033417F24 gene	ncRNA
mm_144045.1	chr17	90422333	90422343	-	1	NA	intron (NM_001346957, intron 14 of 18)	intron (NM_001346957, intron 14 of 18)	33542	NM_001346958	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_96055.1	chr11	59566264	59566307	+	1	NA	3' UTR (NM_145827, exon 10 of 10)	3' UTR (NM_145827, exon 10 of 10)	5453	NM_001011789	257962	Mm.377316	NM_001011789	ENSMUSG00000059610	Olfr222	MOR256-45P	olfactory receptor 222	protein-coding
mm_98218.1	chr11	88047303	88047346	+	1	NA	promoter-TSS (NM_001078167)	promoter-TSS (NM_001078167)	-49	NM_001078167	110809	Mm.391719	NM_173374	ENSMUSG00000018379	Srsf1	1110054N12Rik|5730507C05Rik|6330415C05Rik|AI482334|AW491331|Asf|Sf2|Sfrs1	serine/arginine-rich splicing factor 1	protein-coding
mm_170749.1	chr2	156180213	156180213	-	1	NA	promoter-TSS (NM_001291114)	promoter-TSS (NM_001291114)	25	NM_001291114	170791	Mm.392436	NM_133242	ENSMUSG00000027620	Rbm39	1500012C14Rik|2310040E03Rik|B330012G18Rik|C79248|R75070|Rnpc2|caper	RNA binding motif protein 39	protein-coding
mm_79877.1	chr9	65195390	65195392	+	1	NA	Intergenic	Intergenic	-19299	NM_177460	214424	Mm.31129	NM_177460	ENSMUSG00000032392	Parp16	ARTD15|BC055447|C79952|PARP-16	poly (ADP-ribose) polymerase family, member 16	protein-coding
mm_126649.1	chr15	84127324	84127334	+	1	NA	Intergenic	(CCTA)n|Simple_repeat|Simple_repeat	-4154	NM_029427	75772	Mm.159565	NM_029427	ENSMUSG00000018868	Pnpla5	4833426H19Rik|GS2L	patatin-like phospholipase domain containing 5	protein-coding
mm_134600.1	chr16	20621256	20621304	-	1	NA	promoter-TSS (NM_028420)	promoter-TSS (NM_028420)	-2	NM_028420	73047	Mm.425977	NM_028420	ENSMUSG00000051146	Camk2n2	2900075A18Rik	calcium/calmodulin-dependent protein kinase II inhibitor 2	protein-coding
mm_103940.1	chr11	83832095	83832095	-	1	NA	Intergenic	Intergenic	-18774	NM_001291268	21410	Mm.7226	NM_009330	ENSMUSG00000020679	Hnf1b	HNF-1-beta|HNF-1B|HNF-1Beta|Hnf1beta|LFB3|Tcf-2|Tcf2|vHNF1	HNF1 homeobox B	protein-coding
mm_27306.1	chr3	49757258	49757308	-	1	NA	promoter-TSS (NM_130448)	promoter-TSS (NM_130448)	33	NM_130448	73173	Mm.87246	NM_130448	ENSMUSG00000037892	Pcdh18	3110038E07Rik|BB095589|PCDH68L	protocadherin 18	protein-coding
mm_32937.1	chr4	119257413	119257428	+	1	NA	intron (NM_001038590, intron 3 of 4)	intron (NM_001038590, intron 3 of 4)	1951	NM_001038590	242653	Mm.130701	NM_153105	ENSMUSG00000066058	Cldn19	-	claudin 19	protein-coding
mm_57686.1	chr6	128512378	128512388	-	1	NA	exon (NM_007376, exon 12 of 36)	exon (NM_007376, exon 12 of 36)	14337	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_9392.1	chr1	172218316	172218324	-	1	NA	intron (NM_009813, intron 1 of 10)	intron (NM_009813, intron 1 of 10)	1575	NM_009813	12372	Mm.12829	NM_009813	ENSMUSG00000007122	Casq1	CSQ|CSQ-1|CSQ1|sCSQ	calsequestrin 1	protein-coding
mm_21064.1	chr2	152787624	152787645	-	1	NA	intron (NM_001289717, intron 2 of 2)	intron (NM_001289717, intron 2 of 2)	33461	NM_053091	84682	Mm.196668	NM_053091	ENSMUSG00000009876	Cox4i2	Cox4b|CoxIV-2	cytochrome c oxidase subunit IV isoform 2	protein-coding
mm_35341.1	chr4	32239333	32239348	-	1	NA	Intergenic	CpG	-178095	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_52755.1	chr6	120773593	120773597	+	1	NA	promoter-TSS (NM_001081048)	promoter-TSS (NM_001081048)	-173	NM_001081048	71803	Mm.425340	NM_001081048	ENSMUSG00000004902	Slc25a18	1500015I14Rik|AW125787	solute carrier family 25 (mitochondrial carrier), member 18	protein-coding
mm_6334.1	chr1	71627348	71627362	-	1	NA	exon (NM_001276413, exon 18 of 44)	exon (NM_001276413, exon 18 of 44)	25879	NM_010233	14268	Mm.193099	NM_010233	ENSMUSG00000026193	Fn1	E330027I09|Fn|Fn-1	fibronectin 1	protein-coding
mm_24425.1	chr3	90537292	90537304	+	1	NA	Intergenic	Intergenic	-3925	NM_026416	67860	Mm.331185	NM_026416	ENSMUSG00000074457	S100a16	2300002L21Rik|AI325039|AI663996|DT1P1A7|S100F	S100 calcium binding protein A16	protein-coding
mm_29705.1	chr3	123385669	123385672	-	1	NA	intron (NM_201638, intron 1 of 10)	intron (NM_201638, intron 1 of 10)	320	NM_201638	210529	Mm.260039	NM_201638	ENSMUSG00000028114	Mettl14	G430022H21Rik|mKIAA1627	methyltransferase like 14	protein-coding
mm_37617.1	chr4	126968844	126968853	-	1	NA	promoter-TSS (NM_001114399)	promoter-TSS (NM_001114399)	-925	NM_001114399	67785	Mm.165401	NM_001114399	ENSMUSG00000042446	Zmym4	6330503C17Rik|AI480785|AW493829|CDIR|D630001M21|MYM|Zfp262|Znf262|mKIAA0425	zinc finger, MYM-type 4	protein-coding
mm_96361.1	chr11	67092074	67092088	+	1	NA	exon (NM_001099635, exon 22 of 41)	exon (NM_001099635, exon 22 of 41)	-7723	NR_105888	102466766		NR_105888	ENSMUSG00000098855	Mir6923	Gm27312|mmu-mir-6923	microRNA 6923	ncRNA
mm_87927.1	chr10	62598766	62598780	+	1	NA	exon (NM_019553, exon 2 of 15)	exon (NM_019553, exon 2 of 15)	3525	NM_019553	56200	Mm.413275	NM_019553	ENSMUSG00000020075	Ddx21	AI255159|AL022742|D10Ertd645e|D10Wsu42e	DEAD (Asp-Glu-Ala-Asp) box polypeptide 21	protein-coding
mm_93276.1	chr10	95842925	95842946	-	1	NA	Intergenic	Intergenic	-97728	NM_001001932	216238	Mm.210035	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding
mm_120087.1	chr14	57798700	57798708	+	1	NA	TTS (NR_037238)	TTS (NR_037238)	280	NR_037238	100526476		NR_037238	ENSMUSG00000092784	Mir3077	mir-3077|mmu-mir-3077	microRNA 3077	ncRNA
mm_99802.1	chr11	107793867	107793877	+	1	NA	intron (NM_019431, intron 1 of 3)	CpG	592	NM_019431	54377	Mm.103724	NM_019431	ENSMUSG00000020723	Cacng4	AI413107|AW491861	calcium channel, voltage-dependent, gamma subunit 4	protein-coding
mm_107395.1	chr12	33315413	33315447	+	1	NA	intron (NM_001033436, intron 1 of 7)	intron (NM_001033436, intron 1 of 7)	12915	NM_001033436	380753	Mm.41540	NM_028139	ENSMUSG00000020564	Atxn7l1	2810423G08Rik|Atxn7l4	ataxin 7-like 1	protein-coding
mm_48788.1	chr5	148652607	148652608	-	1	NA	Intergenic	Intergenic	-89233	NR_028285	70138	Mm.417834	NR_028285	ENSMUSG00000086494	2210417A02Rik	AV081004	RIKEN cDNA 2210417A02 gene	ncRNA
mm_154062.1	chr19	55195077	55195087	-	1	NA	3' UTR (NM_009348, exon 10 of 10)	3' UTR (NM_009348, exon 10 of 10)	2404	NR_106146	102465990		NR_106146	ENSMUSG00000098289	Mir6715	Gm27474|mmu-mir-6715	microRNA 6715	ncRNA
mm_19801.1	chr2	110305604	110305614	-	1	NA	exon (NM_130452, exon 1 of 7)	exon (NM_130452, exon 1 of 7)	116	NM_130452	170442	Mm.27335	NM_130452	ENSMUSG00000041660	Bbox1	AI874739	butyrobetaine (gamma), 2-oxoglutarate dioxygenase 1 (gamma-butyrobetaine hydroxylase)	protein-coding
mm_49631.1	chr6	30804879	30804887	+	1	NA	intron (NM_017478, intron 20 of 23)	intron (NM_017478, intron 20 of 23)	63584	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_94296.1	chr11	4077118	4077131	+	1	NA	3' UTR (NM_001029937, exon 12 of 12)	3' UTR (NM_001029937, exon 12 of 12)	12271	NM_001029937	380683	Mm.296806	NM_001029937	ENSMUSG00000054986	Sec14l3	1110069O07Rik	SEC14-like lipid binding 3	protein-coding
mm_137073.1	chr17	20961641	20961667	+	1	NA	exon (NM_016891, exon 12 of 15)	exon (NM_016891, exon 12 of 15)	16200	NM_016891	51792	Mm.294138	NM_016891	ENSMUSG00000007564	Ppp2r1a	6330556D22Rik|PP2A|PR65	protein phosphatase 2, regulatory subunit A, alpha	protein-coding
mm_82704.1	chr9	22468295	22468383	-	1	NA	promoter-TSS (NM_018739)	promoter-TSS (NM_018739)	17	NM_018739	55934	Mm.38235	NM_018739	ENSMUSG00000032239	Rp9	PAP-1|Rp9h	retinitis pigmentosa 9 (human)	protein-coding
mm_33583.1	chr4	132544657	132544676	+	1	NA	exon (NM_172400, exon 5 of 9)	exon (NM_172400, exon 5 of 9)	9107	NM_172400	68598	Mm.29685	NM_172400	ENSMUSG00000054405	Dnajc8	1110021D09Rik|2010009J04Rik|AL024084|AU019262|AU044514	DnaJ heat shock protein family (Hsp40) member C8	protein-coding
mm_53415.1	chr6	133106353	133106367	+	1	NA	3' UTR (NM_001163445, exon 1 of 1)	3' UTR (NM_001163445, exon 1 of 1)	1121	NR_073368	381820	Mm.291762	NM_001163445	ENSMUSG00000072704	Smim10l1	2700089E24Rik|AI662692	small integral membrane protein 10 like 1	protein-coding
mm_1541.1	chr1	72852101	72852104	+	1	NA	exon (NM_008342, exon 4 of 4)	exon (NM_008342, exon 4 of 4)	22763	NM_010518	16011	Mm.405761	NM_010518	ENSMUSG00000026185	Igfbp5	AI256729|AW208790|IGFBP-5|IGFBP-5P	insulin-like growth factor binding protein 5	protein-coding
mm_160913.1	chr11	83040150	83040150	-	1	NA	promoter-TSS (NR_073523)	promoter-TSS (NR_073523)	-108	NR_073523	237887	Mm.341645	NM_181542	ENSMUSG00000072621	Slfn10-ps	Slfn10|mFLJ00257	schlafen 10, pseudogene	pseudo
mm_62799.1	chr7	112816124	112816132	+	1	NA	intron (NM_009346, intron 2 of 12)	intron (NM_009346, intron 2 of 12)	56744	NM_001166585	21676	Mm.24685	NM_009346	ENSMUSG00000055320	Tead1	2610024B07Rik|B230114H05Rik|Gtrgeo5|TEAD-1|TEF-1|Tcf13|mTEF-1	TEA domain family member 1	protein-coding
mm_95164.1	chr11	40355385	40355393	+	1	NA	Intergenic	Intergenic	337293	NM_134017	108645	Mm.293771	NM_134017	ENSMUSG00000042032	Mat2b	1110064C04Rik|2410018D16Rik|AI182287|AU022853|MAT-II|MATIIbeta|TGR	methionine adenosyltransferase II, beta	protein-coding
mm_21434.1	chr2	158383202	158383218	-	1	NA	3' UTR (NM_175692, exon 5 of 5)	3' UTR (NM_175692, exon 5 of 5)	7572	NM_175692	319317	Mm.294494	NM_175692	ENSMUSG00000044349	Snhg11	A930034L06Rik|AI854265|AL022637|AW319638|E130013N09Rik	small nucleolar RNA host gene 11	protein-coding
mm_171944.1	chr5	72047409	72047430	+	1	NA	intron (NM_008069, intron 5 of 8)	intron (NM_008069, intron 5 of 8)	120764	NM_178599	27784	Mm.44223	NM_178599	ENSMUSG00000029213	Commd8	C77770|D5Buc26e	COMM domain containing 8	protein-coding
mm_103292.1	chr11	72411722	72411733	-	1	NA	promoter-TSS (NM_177776)	promoter-TSS (NM_177776)	-14	NM_177776	276829	Mm.46732	NM_177776	ENSMUSG00000045667	Smtnl2	D130058I21Rik	smoothelin-like 2	protein-coding
mm_111438.1	chr12	93444858	93444862	-	1	NA	promoter-TSS (NR_126436)	promoter-TSS (NR_126436)	-37	NR_126436	75295	Mm.243878	NR_126436		4930559C10Rik	-	RIKEN cDNA 4930559C10 gene	ncRNA
mm_67653.1	chr7	84689905	84689918	-	1	NA	intron (NR_038175, intron 1 of 4)	CpG	271	NR_038175	72495	Mm.382914	NR_038175	ENSMUSG00000085236	2610206C17Rik	-	RIKEN cDNA 2610206C17 gene	ncRNA
mm_16368.1	chr2	177074264	177074291	+	1	NA	Intergenic	Intergenic	-146464	NM_001305133	102639598	Mm.379980	NM_029813	ENSMUSG00000074527	Gm14296	-	predicted gene 14296	protein-coding
mm_70995.1	chr8	27471576	27471582	+	1	NA	intron (NM_027618, intron 9 of 13)	IAPLTR1_Mm|LTR|ERVK	23909	NM_027618	70952	Mm.158160	NM_026256	ENSMUSG00000063932	Poteg	4921537P18Rik|4930456F22Rik|Gsarp1|Gsarp2	POTE ankyrin domain family, member G	protein-coding
mm_100005.1	chr11	114851815	114851868	+	1	NA	promoter-TSS (NM_147217)	promoter-TSS (NM_147217)	-189	NM_147217	70355	Mm.242413	NM_147217	ENSMUSG00000051043	Gprc5c	1110028I06Rik|3200002M13Rik|Raig3	G protein-coupled receptor, family C, group 5, member C	protein-coding
mm_108391.1	chr12	80948586	80948638	+	1	NA	intron (NM_009159, intron 5 of 7)	intron (NM_009159, intron 5 of 7)	3113	NM_001347415	20384	Mm.43331	NM_009159	ENSMUSG00000021134	Srsf5	Sfrs5	serine/arginine-rich splicing factor 5	protein-coding
mm_115533.1	chr13	6595904	6595907	-	1	NA	intron (NM_001291071, intron 15 of 21)	intron (NM_001291071, intron 15 of 21)	47748	NM_145131	69617	Mm.41933	NM_145131	ENSMUSG00000021193	Pitrm1	2310012C15Rik|AA410010|MP-1|MP1|Ntup1|PreP|mKIAA1104	pitrilysin metallepetidase 1	protein-coding
mm_13974.1	chr2	121436356	121436364	+	1	NA	exon (NM_007952, exon 12 of 13)	exon (NM_007952, exon 12 of 13)	6241	NM_145973	269344	Mm.330522	NM_145973	ENSMUSG00000027246	Ell3	A930015D22Rik	elongation factor RNA polymerase II-like 3	protein-coding
mm_93876.1	chr10	124545255	124545274	-	1	NA	Intergenic	RLTR44-int|LTR|ERVK	76190	NR_028310	75030	Mm.159403	NR_028310		4930503E24Rik	-	eukaryotic translation initiation factor 3, subunit I pseudogene	pseudo
mm_8451.1	chr1	152903064	152903087	-	1	NA	promoter-TSS (NM_001160256)	promoter-TSS (NM_001160256)	-429	NM_001005507	226517	Mm.270775	NM_001005507	ENSMUSG00000042772	Smg7	9430023P16Rik|mKIAA0250	Smg-7 homolog, nonsense mediated mRNA decay factor (C. elegans)	protein-coding
mm_52972.1	chr6	123237097	123237121	+	1	NA	intron (NM_020001, intron 4 of 5)	Lx9|LINE|L1	7266	NM_001190321	56620	Mm.271782	NM_020001	ENSMUSG00000023349	Clec4n	Clec6a|Clecsf10|Nkcl	C-type lectin domain family 4, member n	protein-coding
mm_133026.1	chr16	57126498	57126501	+	1	NA	intron (NM_138599, intron 1 of 11)	PB1D9|SINE|Alu	4785	NM_138599	28185	Mm.196933	NM_138599	ENSMUSG00000022752	Tomm70a	2610044B22Rik|D16Ium22|D16Ium22e|D16Wsu109e|Tom70|Tomm70|mKIAA0719	translocase of outer mitochondrial membrane 70 homolog A (yeast)	protein-coding
mm_92459.1	chr10	77902468	77902529	-	1	NA	promoter-TSS (NM_145152)	promoter-TSS (NM_145152)	38	NM_145152	237387	Mm.133301	NM_145152	ENSMUSG00000051652	Lrrc3	1300011L04Rik|C21orf102	leucine rich repeat containing 3	protein-coding
mm_150660.1	chr19	41981471	41981481	+	1	NA	promoter-TSS (NM_028152)	promoter-TSS (NM_028152)	-287	NM_145500	226122	Mm.22948	NM_145500	ENSMUSG00000025171	Ubtd1	BC016129	ubiquitin domain containing 1	protein-coding
mm_40938.1	chr5	76677235	76677270	+	1	NA	Intergenic	Intergenic	85538	NM_199032	381644	Mm.332452	NM_199032	ENSMUSG00000036403	Cep135	BC062951|Cep4|Gm1044	centrosomal protein 135	protein-coding
mm_110277.1	chr12	32058361	32058375	-	1	NA	intron (NM_011158, intron 1 of 10)	intron (NM_011158, intron 1 of 10)	2911	NM_011158	19088	Mm.25594	NM_011158	ENSMUSG00000002997	Prkar2b	AI451071|AW061005|PKARIIbeta|Pkarb2|RII(beta)	protein kinase, cAMP dependent regulatory, type II beta	protein-coding
mm_43035.1	chr5	123974420	123974423	+	1	NA	intron (NM_145070, intron 1 of 31)	ID_B1|SINE|B4	793	NM_145070	29816	Mm.149954	NM_145070	ENSMUSG00000000915	Hip1r	AA410023|mKIAA0655	huntingtin interacting protein 1 related	protein-coding
mm_59525.1	chr7	27618082	27618100	+	1	NA	intron (NM_007434, intron 3 of 13)	intron (NM_007434, intron 3 of 13)	10755	NM_001331109	11652	Mm.177194	NM_007434	ENSMUSG00000004056	Akt2	2410016A19Rik|AW554154|PKB|PKBbeta	thymoma viral proto-oncogene 2	protein-coding
mm_57435.1	chr6	124915573	124915615	-	1	NA	intron (NM_026988, intron 1 of 4)	intron (NM_026988, intron 1 of 4)	2352	NM_026988	69202	Mm.142187	NM_026988	ENSMUSG00000030122	Ptms	2610009E16Rik	parathymosin	protein-coding
mm_52846.1	chr6	121838673	121838681	+	1	NA	exon (NM_008645, exon 1 of 36)	exon (NM_008645, exon 1 of 36)	136	NM_008645	17836	Mm.1311	NM_008645	ENSMUSG00000059908	Mug1	-	murinoglobulin 1	protein-coding
mm_15022.1	chr2	152685313	152685323	+	1	NA	TTS (NM_001159553)	TTS (NM_001159553)	-1830	NM_025543	66405	Mm.440291	NM_025543	ENSMUSG00000042814	Mcts2	2400002F11Rik|MCT-2	malignant T cell amplified sequence 2	protein-coding
mm_164048.1	chr14	99697782	99697784	+	1	NA	Intergenic	Intergenic	399092	NM_009769	12224	Mm.30262	NM_009769	ENSMUSG00000005148	Klf5	4930520J07Rik|Bteb2|CKLF|IKLF	Kruppel-like factor 5	protein-coding
mm_79870.1	chr9	65101454	65101528	+	1	NA	promoter-TSS (NM_020043)	promoter-TSS (NM_020043)	5	NM_020043	56741	Mm.209041	NM_020043	ENSMUSG00000032816	Igdcc4	DDM36|Nope	immunoglobulin superfamily, DCC subclass, member 4	protein-coding
mm_21951.1	chr2	167087769	167087775	-	1	NA	Intergenic	Intergenic	22479	NR_028540	100217443		NR_028540		Snord12	MBII-99	small nucleolar RNA, C/D box 12	snoRNA
mm_35976.1	chr4	53410888	53410900	-	1	NA	Intergenic	Intergenic	-29519	NM_001159633	100434	Mm.482207	NM_133891	ENSMUSG00000028412	Slc44a1	2210409B22Rik|4833416H08Rik|AW547365|CHTL1|CTL1|Cdw92	solute carrier family 44, member 1	protein-coding
mm_34210.1	chr4	140961302	140961312	+	1	NA	promoter-TSS (NM_023374)	promoter-TSS (NM_023374)	36	NM_023374	67680	Mm.246965	NM_023374	ENSMUSG00000009863	Sdhb	0710008N11Rik	succinate dehydrogenase complex, subunit B, iron sulfur (Ip)	protein-coding
mm_117668.1	chr13	93623604	93623610	-	1	NA	intron (NM_016668, intron 5 of 7)	L2a|LINE|L2	14151	NM_016668	12116	Mm.329582	NM_016668	ENSMUSG00000074768	Bhmt	-	betaine-homocysteine methyltransferase	protein-coding
mm_71984.1	chr8	70610700	70610718	+	1	NA	Intergenic	Intergenic	-2395	NM_133772	76900	Mm.6667	NM_133772	ENSMUSG00000070003	Ssbp4	1210002E11Rik|AW743380|Sspb4	single stranded DNA binding protein 4	protein-coding
mm_167320.1	chr8	67050752	67050757	+	1	NA	Intergenic	Intergenic	190537	NM_001163564	234344	Mm.334561	NM_001163564	ENSMUSG00000014907	Naf1	Gm174	nuclear assembly factor 1 ribonucleoprotein	protein-coding
mm_142841.1	chr17	51795636	51795642	-	1	NA	intron (NM_009122, intron 5 of 10)	A-rich|Low_complexity|Low_complexity	16415	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_148011.1	chr18	68268628	68268632	-	1	NA	3' UTR (NM_153794, exon 4 of 4)	3' UTR (NM_153794, exon 4 of 4)	-7657	NR_106078	102465702		NR_106078	ENSMUSG00000098253	Mir7219	Gm27613|mmu-mir-7219	microRNA 7219	ncRNA
mm_47795.1	chr5	132446845	132446849	-	1	NA	intron (NM_177047, intron 1 of 18)	intron (NM_177047, intron 1 of 18)	95496	NM_177047	319974	Mm.409595	NM_177047	ENSMUSG00000029673	Auts2	2700063G02Rik|A730011F23Rik|D830032G16Rik	autism susceptibility candidate 2	protein-coding
mm_94425.1	chr11	6242362	6242362	+	1	NA	Intergenic	Intergenic	-12117	NM_207242	237636	Mm.212492	NM_207242	ENSMUSG00000020447	Npc1l1	9130221N23Rik|Gm243	NPC1-like 1	protein-coding
mm_165880.1	chr4	41316731	41316733	-	1	NA	Intergenic	Intergenic	-1831	NM_026893	68970	Mm.28891	NM_026893	ENSMUSG00000028436	Dcaf12	1500001L20Rik|5830424K06Rik|AA420338|AI851081|Wdr40a	DDB1 and CUL4 associated factor 12	protein-coding
mm_40630.1	chr5	64822221	64822246	+	1	NA	exon (NM_008453, exon 3 of 6)	exon (NM_008453, exon 3 of 6)	18710	NM_008453	16599	Mm.392759	NM_008453	ENSMUSG00000029178	Klf3	9930027G08Rik|AL024007|Bklf|Tef-2	Kruppel-like factor 3 (basic)	protein-coding
mm_117789.1	chr13	97035301	97035309	-	1	NA	promoter-TSS (NM_001284205)	promoter-TSS (NM_001284205)	-51	NR_104276	66479	Mm.390629	NM_025585	ENSMUSG00000052075	1700029F12Rik	-	RIKEN cDNA 1700029F12 gene	protein-coding
mm_90740.1	chr10	5367725	5367770	-	1	NA	intron (NM_001347732, intron 14 of 145)	intron (NM_001347732, intron 14 of 145)	120567	NM_001347711	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_142187.1	chr17	36889665	36889675	-	1	NA	5' UTR (NM_001172168, exon 2 of 6)	5' UTR (NM_001172168, exon 2 of 6)	455	NM_001033235	195359	Mm.32606	NM_001033235	ENSMUSG00000073399	Trim40	Gm319|Gm35|Gm865	tripartite motif-containing 40	protein-coding
mm_142769.1	chr17	49550029	49550035	-	1	NA	intron (NM_001008231, intron 1 of 25)	intron (NM_001008231, intron 1 of 25)	14305	NM_001008231	76441	Mm.211275	NM_001008231	ENSMUSG00000040260	Daam2	2310016D11Rik|AI843643|AW557870	dishevelled associated activator of morphogenesis 2	protein-coding
mm_87837.1	chr10	60380647	60380658	+	1	NA	intron (NR_045556, intron 33 of 68)	intron (NR_045556, intron 33 of 68)	-19074	NM_001164374	100302688	Mm.444135	NM_001164374	ENSMUSG00000090439	Gm17455	-	predicted gene, 17455	protein-coding
mm_1651.1	chr1	74661715	74661789	+	1	NA	promoter-TSS (NM_001014974)	promoter-TSS (NM_001014974)	-2	NM_001014974	67534	Mm.260714	NM_001014974	ENSMUSG00000033257	Ttll4	4632407P03Rik|AI451681|mKIAA0173	tubulin tyrosine ligase-like family, member 4	protein-coding
mm_139400.1	chr17	52307707	52307717	+	1	NA	Intergenic	Intergenic	-294997	NM_001031811	211468	Mm.399068	NM_001031811	ENSMUSG00000035580	Kcnh8	C130090D05Rik|ELK|ELK1|ELK3|Kv12.1	potassium voltage-gated channel, subfamily H (eag-related), member 8	protein-coding
mm_62652.1	chr7	107693137	107693149	+	1	NA	intron (NM_001163557, intron 5 of 25)	intron (NM_001163557, intron 5 of 25)	64889	NM_001205227	320635	Mm.132828	NM_177216	ENSMUSG00000048065	Cyb5r2	D630003K02Rik|b5R.2	cytochrome b5 reductase 2	protein-coding
mm_128344.1	chr15	39780632	39780648	-	1	NA	intron (NM_022722, intron 9 of 9)	RLTR41C|LTR|ERV1	-16405	NR_045788	100503072	Mm.446661	NR_045788	ENSMUSG00000087695	Gm16291	OTTMUSG00000033244	predicted gene 16291	ncRNA
mm_105784.1	chr11	109797377	109797380	-	1	NA	exon (NM_001162428, exon 3 of 6)	exon (NM_001162428, exon 3 of 6)	30668	NM_027038	69324	Mm.31700	NM_027038	ENSMUSG00000020617	1700012B07Rik	1700069D21Rik	RIKEN cDNA 1700012B07 gene	protein-coding
mm_24977.1	chr3	96829428	96829435	+	1	NA	promoter-TSS (NM_001163497)	promoter-TSS (NM_001163497)	-80	NM_001163496	54215	Mm.34693	NM_018767	ENSMUSG00000038304	Cd160	AU045688|By55	CD160 antigen	protein-coding
mm_160360.1	chr8	21839846	21839846	+	1	NA	promoter-TSS (NM_010030)	promoter-TSS (NM_010030)	-80	NM_010030	13215	Mm.41981	NM_010030	ENSMUSG00000006570	Defb2	BD-2	defensin beta 2	protein-coding
mm_157265.1	chrX	19202577	19202617	-	1	NA	Intergenic	Intergenic	-55626	NR_029807	723828		NR_029807	ENSMUSG00000065471	Mir222	Mirn222|mir-222|mmu-mir-222	microRNA 222	ncRNA
mm_73423.1	chr8	106111543	106111553	+	1	NA	intron (NM_010901, intron 9 of 9)	B1_Mus2|SINE|Alu	-23852	NR_040345	69771	Mm.393274	NR_040344		1810019D21Rik	-	RIKEN cDNA 1810019D21 gene	ncRNA
mm_71386.1	chr8	45999318	45999324	+	1	NA	exon (NM_001039562, exon 2 of 5)	exon (NM_001039562, exon 2 of 5)	529	NM_001039562	654824	Mm.334517	NM_001039562	ENSMUSG00000050914	Ankrd37	-	ankyrin repeat domain 37	protein-coding
mm_111150.1	chr12	82478461	82478471	-	1	NA	Intergenic	Intergenic	-138459	NM_001310478	50779	Mm.126176	NM_015812	ENSMUSG00000021219	Rgs6	-	regulator of G-protein signaling 6	protein-coding
mm_92947.1	chr10	85102553	85102565	-	1	NA	promoter-TSS (NM_001013028)	promoter-TSS (NM_001013028)	-64	NM_010214	14202	Mm.46163	NM_010214	ENSMUSG00000050035	Fhl4	-	four and a half LIM domains 4	protein-coding
mm_120458.1	chr14	65970595	65970609	+	1	NA	intron (NM_013492, intron 1 of 8)	intron (NM_013492, intron 1 of 8)	2119	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_25094.1	chr3	100924929	100924946	+	1	NA	intron (NM_194343, intron 1 of 5)	intron (NM_194343, intron 1 of 5)	2444	NM_001165953	229644	Mm.189351	NM_194343	ENSMUSG00000033233	Trim45	4921530N01Rik	tripartite motif-containing 45	protein-coding
mm_65503.1	chr7	25726015	25726049	-	1	NA	exon (NM_144922, exon 12 of 15)	exon (NM_144922, exon 12 of 15)	-6979	NM_028771	52132	Mm.278798	NM_028771	ENSMUSG00000002608	Ccdc97	1200014H14Rik|2810446P04Rik|AA545218|D7Ertd462e	coiled-coil domain containing 97	protein-coding
mm_143273.1	chr17	65654310	65654325	-	1	NA	3' UTR (NM_133685, exon 7 of 7)	3' UTR (NM_133685, exon 7 of 7)	-12113	NM_001146002	213272	Mm.255732	NM_153519	ENSMUSG00000050612	Txndc2	AU021712|Sptrx-1|Sptrx1|Trx4	thioredoxin domain containing 2 (spermatozoa)	protein-coding
mm_121719.1	chr14	16491084	16491095	-	1	NA	intron (NM_011243, intron 3 of 7)	intron (NM_011243, intron 3 of 7)	84387	NM_011243	218772	Mm.259318	NM_011243	ENSMUSG00000017491	Rarb	A830025K23|Hap|Nr1b2	retinoic acid receptor, beta	protein-coding
mm_162256.1	chrX	168795248	168795248	+	1	NA	5' UTR (NM_009707, exon 1 of 13)	5' UTR (NM_009707, exon 1 of 13)	149	NM_009707	11856	Mm.441810	NM_009707	ENSMUSG00000031355	Arhgap6	AI504284|RhoGAPX-1	Rho GTPase activating protein 6	protein-coding
mm_93747.1	chr10	120160101	120160106	-	1	NA	intron (NM_028679, intron 8 of 11)	intron (NM_028679, intron 8 of 11)	41434	NM_028679	73914	Mm.146194	NM_028679	ENSMUSG00000020227	Irak3	4833428C18Rik|AI563835|IRAK-M	interleukin-1 receptor-associated kinase 3	protein-coding
mm_76970.1	chr8	106281061	106281073	-	1	NA	intron (NM_021491, intron 2 of 8)	intron (NM_021491, intron 2 of 8)	-1162	NR_126091	75044	Mm.445896	NR_126090		4930506A18Rik	-	RIKEN cDNA 4930506A18 gene	ncRNA
mm_35173.1	chr4	14826598	14826606	-	1	NA	promoter-TSS (NM_152812)	promoter-TSS (NM_152812)	-15	NM_152812	72201	Mm.387724	NM_152812	ENSMUSG00000040550	Otud6b	2600013N14Rik|AU015433	OTU domain containing 6B	protein-coding
mm_149177.1	chr19	9216339	9216345	+	1	NA	Intergenic	L1_Mus3|LINE|L1	-80776	NM_025610	66514	Mm.272847	NM_025610	ENSMUSG00000024654	Asrgl1	2410004D18Rik|ALP|ALP1|AU040643|AW060375	asparaginase like 1	protein-coding
mm_76492.1	chr8	85840878	85840957	-	1	NA	promoter-TSS (NM_199446)	promoter-TSS (NM_199446)	32	NM_028007	71927	Mm.61018	NM_028007	ENSMUSG00000031703	Itfg1	2310047C21Rik|AI314457|Cda08|D8Wsu49e	integrin alpha FG-GAP repeat containing 1	protein-coding
mm_107673.1	chr12	54135137	54135157	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	68727	NM_028133	112407	Mm.133037	NM_028133	ENSMUSG00000035105	Egln3	2610021G09Rik|AI505553|AI648162|Hif-p4h-3|Phd3|SM-20	egl-9 family hypoxia-inducible factor 3	protein-coding
mm_98904.1	chr11	98026696	98026744	+	1	NA	promoter-TSS (NM_001159483)	promoter-TSS (NM_001159483)	10	NM_001159483	19921	Mm.10247	NM_009078	ENSMUSG00000017404	Rpl19	-	ribosomal protein L19	protein-coding
mm_80285.1	chr9	73044887	73044908	+	1	NA	promoter-TSS (NM_023635)	promoter-TSS (NM_023635)	87	NM_001301230	11891	Mm.34867	NM_023635	ENSMUSG00000032202	Rab27a	2210402C08Rik|2410003M20Rik|4933437C11Rik|ash	RAB27A, member RAS oncogene family	protein-coding
mm_27421.1	chr3	51517934	51517945	-	1	NA	3' UTR (NM_080793, exon 8 of 8)	3' UTR (NM_080793, exon 8 of 8)	33973	NM_016858	19338	Mm.1664	NM_016858	ENSMUSG00000027739	Rab33b	-	RAB33B, member RAS oncogene family	protein-coding
mm_60602.1	chr7	44554099	44554118	+	1	NA	promoter-TSS (NM_009473)	promoter-TSS (NM_009473)	-143	NM_001285517	22260	Mm.968	NM_009473	ENSMUSG00000060601	Nr1h2	AI194859|LXR|LXRB|LXRBSV|LXRbeta|NER1|OR-1|RIP15|UR|Unr|Unr2	nuclear receptor subfamily 1, group H, member 2	protein-coding
mm_34033.1	chr4	138126498	138126510	+	1	NA	exon (NM_001256198, exon 12 of 33)	exon (NM_001256198, exon 12 of 33)	12014	NR_126429	73563	Mm.444294	NR_126429	ENSMUSG00000084804	1700095J12Rik	-	RIKEN cDNA 1700095J12 gene	ncRNA
mm_86764.1	chr10	19933688	19933698	+	1	NA	promoter-TSS (NM_008580)	promoter-TSS (NM_008580)	-833	NM_008580	26408	Mm.6595	NM_008580	ENSMUSG00000071369	Map3k5	7420452D20Rik|ASK|ASK1|MAPKKK5|Mekk5	mitogen-activated protein kinase kinase kinase 5	protein-coding
mm_44376.1	chr5	17814700	17814831	-	1	NA	exon (NM_001159558, exon 6 of 16)	exon (NM_001159558, exon 6 of 16)	21131	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_63518.1	chr7	127876956	127876971	+	1	NA	promoter-TSS (NM_146259)	promoter-TSS (NM_146259)	-140	NM_146259	244219	Mm.207872	NM_146259	ENSMUSG00000049728	Zfp668	BC030314|E130018B19Rik|Znf668	zinc finger protein 668	protein-coding
mm_142192.1	chr17	36951417	36951425	-	1	NA	intron (NM_029632, intron 1 of 2)	intron (NM_029632, intron 1 of 2)	371	NM_029632	76497	Mm.46176	NM_029632	ENSMUSG00000036398	Ppp1r11	1500041B02Rik|AV117883|Hcgv|Tcte5|Tctex-5|Tctex5	protein phosphatase 1, regulatory (inhibitor) subunit 11	protein-coding
mm_137410.1	chr17	26113679	26113706	+	1	NA	intron (NM_021793, intron 1 of 12)	CpG	376	NM_021793	60455	Mm.304656	NM_021793	ENSMUSG00000024180	Tmem8	AW490096|M83|Tmem8a	transmembrane protein 8 (five membrane-spanning domains)	protein-coding
mm_35358.1	chr4	32343818	32343829	-	1	NA	Intergenic	Intergenic	-73612	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_26929.1	chr3	20262105	20262106	-	1	NA	intron (NM_029706, intron 9 of 10)	intron (NM_029706, intron 9 of 10)	13628	NM_029706	76703	Mm.34692	NM_029706	ENSMUSG00000011463	Cpb1	0910001A18Rik|1810063F02Rik|2210008M23Rik|AI504870	carboxypeptidase B1 (tissue)	protein-coding
mm_88724.1	chr10	80172935	80172961	+	1	NA	promoter-TSS (NM_027207)	promoter-TSS (NM_027207)	4	NM_027207	69770	Mm.302754	NM_027207	ENSMUSG00000035595	1600002K03Rik	-	RIKEN cDNA 1600002K03 gene	protein-coding
mm_23870.1	chr3	83029078	83029097	+	1	NA	exon (NM_010196, exon 3 of 5)	exon (NM_010196, exon 3 of 5)	2934	NM_001111048	14161	Mm.88793	NM_010196	ENSMUSG00000028001	Fga	ENSMUSG00000059807|Fib	fibrinogen alpha chain	protein-coding
mm_157226.1	chrX	13846630	13846640	-	1	NA	promoter-TSS (NM_001284505)	promoter-TSS (NM_001284505)	-79	NM_009806	12361	Mm.327591	NM_009806	ENSMUSG00000031012	Cask	DXPri1|DXRib1|LIN-2|Pals3|mLin-2	calcium/calmodulin-dependent serine protein kinase (MAGUK family)	protein-coding
mm_104320.1	chr11	93955874	93955888	-	1	NA	promoter-TSS (NM_001077529)	promoter-TSS (NM_001077529)	-98	NM_001077529	18103	Mm.1260	NM_008705	ENSMUSG00000020857	Nme2	NM23-H2|NM23B|nm23-M2	NME/NM23 nucleoside diphosphate kinase 2	protein-coding
mm_101707.1	chr11	42000539	42000592	-	1	NA	5' UTR (NM_008073, exon 1 of 10)	5' UTR (NM_008073, exon 1 of 10)	149	NM_177408	14406	Mm.5309	NM_008073	ENSMUSG00000020436	Gabrg2	GABAA-R|Gabrg-2|gamma2	gamma-aminobutyric acid (GABA) A receptor, subunit gamma 2	protein-coding
mm_15048.1	chr2	152867243	152867264	+	1	NA	exon (NM_001141978, exon 3 of 18)	exon (NM_001141978, exon 3 of 18)	2186	NR_049195	100885834		NR_049195	ENSMUSG00000093746	Mir5622	Gm24421|mmu-mir-5622	microRNA 5622	ncRNA
mm_105822.1	chr11	112825096	112825139	-	1	NA	promoter-TSS (NR_130164)	promoter-TSS (NR_130164)	11	NR_130164	76393	Mm.86795	NR_130164		1700012H19Rik	-	RIKEN cDNA 1700012H19 gene	ncRNA
mm_95333.1	chr11	46752407	46752414	+	1	NA	exon (NM_001166632, exon 3 of 8)	exon (NM_001166632, exon 3 of 8)	1242	NM_134248	171283	Mm.17771	NM_134248	ENSMUSG00000040405	Havcr1	AI503787|KIM-1|TIM-1|Tim1|Timd1	hepatitis A virus cellular receptor 1	protein-coding
mm_56141.1	chr6	87790262	87790271	-	1	NA	non-coding (NR_104478, exon 3 of 3)	non-coding (NR_104478, exon 3 of 3)	12130	NM_018762	54368	Mm.12897	NM_018762	ENSMUSG00000030054	Gp9	Cd42|GPIX	glycoprotein 9 (platelet)	protein-coding
mm_161784.1	chr17	43952771	43952771	+	1	NA	promoter-TSS (NM_030598)	promoter-TSS (NM_030598)	-228	NM_001286654	53901	Mm.251242	NM_030598	ENSMUSG00000039601	Rcan2	Csp2|Dscr1l1|MCIP2|ZAKI-4	regulator of calcineurin 2	protein-coding
mm_73282.1	chr8	104831602	104831609	+	1	NA	promoter-TSS (NM_198171)	promoter-TSS (NM_198171)	-39	NM_198171	234669	Mm.443387	NM_198171	ENSMUSG00000050097	Ces2b	-	carboxyesterase 2B	protein-coding
mm_114508.1	chr13	71104563	71104569	+	1	NA	Intergenic	Intergenic	-2523	NR_130325	100316804		NR_130325	ENSMUSG00000080580	Mir466f-4	Mirn466f-4|mmu-mir-466f-4	microRNA 466f-4	ncRNA
mm_123552.1	chr14	66834518	66834528	-	1	NA	intron (NM_009955, intron 3 of 13)	intron (NM_009955, intron 3 of 13)	34077	NM_009955	12934	Mm.352648	NM_009955	ENSMUSG00000022048	Dpysl2	AI851130|Crmp2|DRP2|Musunc33|TOAD-64|Ulip2	dihydropyrimidinase-like 2	protein-coding
mm_5972.1	chr1	57396694	57396697	-	1	NA	intron (NM_001302962, intron 3 of 8)	intron (NM_001302962, intron 3 of 8)	-9853	NM_001081181	68115	Mm.275428	NM_001081181	ENSMUSG00000025971	Maip1	9430016H08Rik|AA409999|C78988	matrix AAA peptidase interacting protein 1	protein-coding
mm_164796.1	chr18	20669972	20669972	+	1	NA	intron (NM_013697, intron 2 of 3)	intron (NM_013697, intron 2 of 3)	4722	NM_013697	22139	Mm.2108	NM_013697	ENSMUSG00000061808	Ttr	AA408768|AI787086|D17860|prealbumin	transthyretin	protein-coding
mm_23388.1	chr3	57362242	57362252	+	1	NA	Intergenic	AT_rich|Low_complexity|Low_complexity	-60328	NM_008536	17112	Mm.856	NM_008536	ENSMUSG00000027800	Tm4sf1	L6|M3s1	transmembrane 4 superfamily member 1	protein-coding
mm_164011.1	chr14	70289406	70289412	-	1	NA	promoter-TSS (NM_001304992)	promoter-TSS (NM_001304992)	88	NM_008915	19057	Mm.439683	NM_008915	ENSMUSG00000022092	Ppp3cc	Calnc|PP2BA gamma	protein phosphatase 3, catalytic subunit, gamma isoform	protein-coding
mm_4282.1	chr1	171634872	171634906	+	1	NA	3' UTR (NM_144539, exon 8 of 8)	3' UTR (NM_144539, exon 8 of 8)	7011	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_171216.1	chr3	59344199	59344199	-	1	NA	promoter-TSS (NM_001162884)	promoter-TSS (NM_001162884)	57	NM_001162884	242050	Mm.228086	NM_001162884	ENSMUSG00000036334	Igsf10	6530405F15Rik|9030224D03|AA409708|AA536958|AI414626|Adlican2|CMF608	immunoglobulin superfamily, member 10	protein-coding
mm_112897.1	chr13	20886514	20886530	+	1	NA	intron (NM_012054, intron 4 of 20)	RSINE1|SINE|B4	92409	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_66290.1	chr7	38009018	38009023	-	1	NA	intron (NM_011274, intron 1 of 10)	intron (NM_011274, intron 1 of 10)	10532	NM_011274	19777	Mm.387220	NM_011274	ENSMUSG00000030421	Uri1	C80913|NNX3|Rmp	URI1, prefoldin-like chaperone	protein-coding
mm_94872.1	chr11	24080665	24080706	+	1	NA	promoter-TSS (NM_001159290)	promoter-TSS (NM_001159290)	-10	NM_001159290	14025	Mm.53687	NM_016707	ENSMUSG00000000861	Bcl11a	2810047E18Rik|BCL-11A|Ctip1|D930021L15Rik|Evi9|Evi9a|Evi9b|Evi9c|mKIAA1809	B cell CLL/lymphoma 11A (zinc finger protein)	protein-coding
mm_122712.1	chr14	52244452	52244523	-	1	NA	Intergenic	Intergenic	-6915	NM_201637	67772	Mm.289934	NM_201637	ENSMUSG00000053754	Chd8	5830451P18Rik|AU015341|Duplin|HELSNF1|mKIAA1564	chromodomain helicase DNA binding protein 8	protein-coding
mm_72165.1	chr8	72240053	72240181	+	1	NA	promoter-TSS (NM_007456)	promoter-TSS (NM_007456)	99	NM_007456	11767	Mm.290086	NM_007456	ENSMUSG00000003033	Ap1m1	AA408894|AP47|Adtm1A|Cltnm|mu1A	adaptor-related protein complex AP-1, mu subunit 1	protein-coding
mm_125099.1	chr15	27636478	27636481	+	1	NA	Intergenic	Charlie7|DNA|hAT-Charlie	-5786	NM_001013792	432940	Mm.309164	NM_001013792	ENSMUSG00000046034	Otulin	C79097|Fam105b|m3Sapc|m7-1Sapc	OTU deubiquitinase with linear linkage specificity	protein-coding
mm_153413.1	chr19	40588429	40588439	-	1	NA	promoter-TSS (NM_153554)	promoter-TSS (NM_153554)	29	NM_019698	56454	Mm.233117	NM_019698	ENSMUSG00000025007	Aldh18a1	2810433K04Rik|AI429789|Pycs	aldehyde dehydrogenase 18 family, member A1	protein-coding
mm_151410.1	chr19	56582848	56582864	+	1	NA	intron (NM_025811, intron 5 of 10)	intron (NM_025811, intron 5 of 10)	34595	NM_025811	66866	Mm.46346	NM_025811	ENSMUSG00000025078	Nhlrc2	1200003G01Rik|AI835049|AV002846|AW496455	NHL repeat containing 2	protein-coding
mm_60027.1	chr7	30957299	30957300	+	1	NA	promoter-TSS (NM_011680)	promoter-TSS (NM_011680)	-496	NM_011680	22282	Mm.322453	NM_011680	ENSMUSG00000058239	Usf2	Usf-2|bHLHb12	upstream transcription factor 2	protein-coding
mm_142801.1	chr17	50300359	50300364	-	1	NA	Intergenic	Intergenic	-6741	NM_001277863	13164	Mm.280641	NM_010021	ENSMUSG00000010592	Dazl	Daz-like|Dazh|Dazl1|Dazla|Tpx-2|Tpx2	deleted in azoospermia-like	protein-coding
mm_64996.1	chr7	16923902	16924026	-	1	NA	promoter-TSS (NM_007590)	promoter-TSS (NM_007590)	68	NM_007590	12315	Mm.288630	NM_007590	ENSMUSG00000019370	Calm3	CaMA|R75142	calmodulin 3	protein-coding
mm_26168.1	chr3	138282766	138282776	+	1	NA	exon (NM_007409, exon 5 of 9)	exon (NM_007409, exon 5 of 9)	5126	NM_007409	11522	Mm.2409	NM_007409	ENSMUSG00000074207	Adh1	ADH-AA|AI194826|Adh-1|Adh-1-t|Adh-1e|Adh-1t|Adh-3e|Adh1-e|Adh1-t|Adh1tl|Adh3-e	alcohol dehydrogenase 1 (class I)	protein-coding
mm_75261.1	chr8	40596211	40596216	-	1	NA	intron (NM_001040699, intron 4 of 13)	ID_B1|SINE|B4	38579	NM_001040699	54384	Mm.294871	NM_019433	ENSMUSG00000039431	Mtmr7	-	myotubularin related protein 7	protein-coding
mm_136117.1	chr16	85803107	85803121	-	1	NA	promoter-TSS (NM_009621)	promoter-TSS (NM_009621)	-1	NM_009621	11504	Mm.1421	NM_009621	ENSMUSG00000022893	Adamts1	ADAM-TS1|ADAMTS|ADAMTS-1|C3-C5|METH-1|METH1	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 1	protein-coding
mm_14444.1	chr2	130933130	130933146	+	1	NA	intron (NM_009730, intron 1 of 28)	RLTR31D_MM|LTR|ERVK	26643	NM_009730	11990	Mm.119936	NM_009730	ENSMUSG00000027312	Atrn	AW558010|Mgca|mg	attractin	protein-coding
mm_94895.1	chr11	29130734	29130757	+	1	NA	promoter-TSS (NM_027869)	promoter-TSS (NM_027869)	-6	NM_027869	71701	Mm.211131	NM_027869	ENSMUSG00000020464	Pnpt1	1200003F12Rik|Old35|PNPase|Pnptl1	polyribonucleotide nucleotidyltransferase 1	protein-coding
mm_137704.1	chr17	29098581	29098592	+	1	NA	exon (NM_007669, exon 2 of 3)	exon (NM_007669, exon 2 of 3)	4817	NM_007669	12575	Mm.195663	NM_007669	ENSMUSG00000023067	Cdkn1a	CAP20|CDKI|CIP1|Cdkn1|P21|SDI1|Waf1|mda6|p21Cip1|p21WAF	cyclin-dependent kinase inhibitor 1A (P21)	protein-coding
mm_80231.1	chr9	72670058	72670080	+	1	NA	exon (NM_010890, exon 2 of 29)	exon (NM_010890, exon 2 of 29)	7722	NM_010890	17999	Mm.279923	NM_010890	ENSMUSG00000032216	Nedd4	AA959633|AL023035|AU019897|E430025J12Rik|Nedd4-1|Nedd4a|mKIAA0093	neural precursor cell expressed, developmentally down-regulated 4	protein-coding
mm_60975.1	chr7	48881865	48881866	+	1	NA	promoter-TSS (NM_001013368)	promoter-TSS (NM_001013368)	-824	NM_001013368	108961	Mm.240566	NM_001013368	ENSMUSG00000046179	E2f8	4432406C08Rik|AA410048	E2F transcription factor 8	protein-coding
mm_152834.1	chr19	23273816	23273861	-	1	NA	promoter-TSS (NM_001252684)	promoter-TSS (NM_001252684)	59	NM_153808	226026	Mm.23267	NM_153808	ENSMUSG00000024943	Smc5	MLZ-453|SMC-5|Smc5l1|mKIAA0594|mSMC5	structural maintenance of chromosomes 5	protein-coding
mm_28857.1	chr3	96926057	96926067	-	1	NA	promoter-TSS (NM_008123)	promoter-TSS (NM_008123)	-11	NM_008123	14616	Mm.258183	NM_008123	ENSMUSG00000049908	Gja8	Aey5|Cnx50|Cx50|Lop10	gap junction protein, alpha 8	protein-coding
mm_63083.1	chr7	122288746	122288755	+	1	NA	promoter-TSS (NM_008855)	promoter-TSS (NM_008855)	-375	NM_001316672	18751	Mm.207496	NM_008855	ENSMUSG00000052889	Prkcb	PKC-B|PKC-Beta|Pkcb|Prkcb1|Prkcb2	protein kinase C, beta	protein-coding
mm_150016.1	chr19	29368839	29368857	+	1	NA	intron (NM_021893, intron 1 of 6)	intron (NM_021893, intron 1 of 6)	1410	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_20184.1	chr2	122600408	122600417	-	1	NA	exon (NM_025961, exon 6 of 9)	exon (NM_025961, exon 6 of 9)	10865	NM_025961	67092	Mm.29975	NM_025961	ENSMUSG00000027199	Gatm	1810003P21Rik|AI314789|AT	glycine amidinotransferase (L-arginine:glycine amidinotransferase)	protein-coding
mm_59187.1	chr7	24474292	24474304	+	1	NA	exon (NM_011113, exon 6 of 7)	exon (NM_011113, exon 6 of 7)	-7725	NM_153112	260299	Mm.178322	NM_153112	ENSMUSG00000054793	Cadm4	Igdf4c|Igsf4c|Tsll2	cell adhesion molecule 4	protein-coding
mm_94725.1	chr11	20647235	20647239	+	1	NA	intron (NM_001038625, intron 1 of 1)	intron (NM_001038625, intron 1 of 1)	15260	NM_001038625	58172	Mm.339676	NM_021372	ENSMUSG00000049800	Sertad2	AB041541|AU021878|Kiaa0127|MNCb-1504|SEI-2|Sei2|TRIP-Br2|mKIAA0127	SERTA domain containing 2	protein-coding
mm_134689.1	chr16	22469264	22469280	-	1	NA	exon (NM_138650, exon 25 of 25)	exon (NM_138650, exon 25 of 25)	-29702	NM_023794	104156	Mm.155708	NM_023794	ENSMUSG00000013089	Etv5	1110005E01Rik|8430401F14Rik|ERM	ets variant 5	protein-coding
mm_51372.1	chr6	72900077	72900093	+	1	NA	promoter-TSS (NM_019715)	promoter-TSS (NM_019715)	-106	NM_019715	74287	Mm.29194	NM_019715	ENSMUSG00000055239	Kcmf1	1700094M07Rik|Debt91|Pmcf	potassium channel modulatory factor 1	protein-coding
mm_91926.1	chr10	60351852	60351871	-	1	NA	intron (NM_028732, intron 1 of 6)	intron (NM_028732, intron 1 of 6)	5010	NM_028732	74048	Mm.273584	NM_028732	ENSMUSG00000020101	Vsir	4632428N05Rik|Dies1|PD-1H|VISTA	V-set immunoregulatory receptor	protein-coding
mm_158908.1	chr1	38939179	38939179	+	1	NA	promoter-TSS (NM_001311788)	promoter-TSS (NM_001311788)	30	NM_001011684	433292	Mm.333709	NM_001011684	ENSMUSG00000067604	Nms	AB164466	neuromedin S	protein-coding
mm_6635.1	chr1	78658291	78658309	-	1	NA	promoter-TSS (NM_001136226)	promoter-TSS (NM_001136226)	-140	NM_001136226	195434	Mm.276016	NM_001001981	ENSMUSG00000079470	Utp14b	4932411L21Rik|jsd	UTP14B small subunit processome component	protein-coding
mm_18841.1	chr2	75133755	75133767	-	1	NA	Intergenic	Intergenic	307949	NM_016804	53375	Mm.292613	NM_016804	ENSMUSG00000027099	Mtx2	1500012G02Rik	metaxin 2	protein-coding
mm_140894.1	chr17	24032330	24032342	-	1	NA	Intergenic	Intergenic	-5907	NM_175440	213171	Mm.133083	NM_175440	ENSMUSG00000050762	Prss27	CAPH2|Mpn|marapsin	protease, serine 27	protein-coding
mm_31561.1	chr4	57567709	57567718	+	1	NA	promoter-TSS (NM_172868)	promoter-TSS (NM_172868)	-535	NM_001304544	677884	Mm.331630	NM_001304544	ENSMUSG00000089945	Pakap	AF064781|Gm20459|Palm2-Akap2|Palm2Akap2|Palm2akap2	paralemmin A kinase anchor protein	protein-coding
mm_88813.1	chr10	80798032	80798110	+	1	NA	promoter-TSS (NM_013651)	promoter-TSS (NM_013651)	555	NM_023900	78670	Mm.41479	NM_023900	ENSMUSG00000035278	Plekhj1	9530063M10Rik	pleckstrin homology domain containing, family J member 1	protein-coding
mm_17781.1	chr2	32961595	32961620	-	1	NA	promoter-TSS (NM_009076)	promoter-TSS (NM_009076)	-105	NM_009076	269261	Mm.250030	NM_009076	ENSMUSG00000038900	Rpl12	E430018F03	ribosomal protein L12	protein-coding
mm_2380.1	chr1	93373875	93373899	+	1	NA	promoter-TSS (NM_207031)	promoter-TSS (NM_207031)	-9	NM_207031	404545	Mm.297411	NM_207031	ENSMUSG00000034107	Ano7	Ngep|Ngep-L|Pcanap5|Tmem16g	anoctamin 7	protein-coding
mm_164263.1	chr15	100675529	100675574	-	1	NA	intron (NM_033612, intron 6 of 7)	intron (NM_033612, intron 6 of 7)	-6051	NM_001270537	668218	Mm.451225	NM_001270537	ENSMUSG00000098112	Bin2	-	bridging integrator 2	protein-coding
mm_102016.1	chr11	51635723	51635784	-	1	NA	5' UTR (NM_025346, exon 1 of 10)	5' UTR (NM_025346, exon 1 of 10)	143	NM_025346	66089	Mm.288183	NM_025346	ENSMUSG00000001054	Rmnd5b	0610039K22Rik|Gid2	required for meiotic nuclear division 5 homolog B	protein-coding
mm_131022.1	chr15	103588394	103588401	-	1	NA	Intergenic	Intergenic	-23316	NM_008134	14663	Mm.219621	NM_008134	ENSMUSG00000022491	Glycam1	MC26|Sgp50|glyCAM-1	glycosylation dependent cell adhesion molecule 1	protein-coding
mm_98617.1	chr11	95843647	95843689	+	1	NA	intron (NM_001284397, intron 1 of 3)	intron (NM_001284397, intron 1 of 3)	423	NM_001284397	14710	Mm.46299	NM_023121	ENSMUSG00000038811	Gngt2	AV096488	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 2	protein-coding
mm_130179.1	chr15	93398264	93398343	-	1	NA	promoter-TSS (NM_026025)	promoter-TSS (NM_026025)	-13	NM_026025	67197	Mm.293181	NM_026025	ENSMUSG00000022635	Zcrb1	2700088M22Rik|Madp-1	zinc finger CCHC-type and RNA binding motif 1	protein-coding
mm_68706.1	chr7	119793946	119793956	-	1	NA	promoter-TSS (NM_028129)	promoter-TSS (NM_028129)	107	NM_027698	71151	Mm.274160	NM_027698	ENSMUSG00000030929	Eri2	4933424N09Rik|Exod1|mKIAA1504	exoribonuclease 2	protein-coding
mm_39143.1	chr4	155345641	155345649	-	1	NA	5' UTR (NM_001039079, exon 1 of 15)	5' UTR (NM_001039079, exon 1 of 15)	144	NM_001039079	18762	Mm.28561	NM_008860	ENSMUSG00000029053	Prkcz	AI098070|C80388|Pkcz|R74924|aPKCzeta|nPKC-zeta|zetaPKC	protein kinase C, zeta	protein-coding
mm_51738.1	chr6	87183486	87183491	+	1	NA	intron (NM_054041, intron 16 of 17)	intron (NM_054041, intron 16 of 17)	78742	NM_001167937	52372	Mm.282851	NM_001167937	ENSMUSG00000090891	D6Ertd527e	AU043841	DNA segment, Chr 6, ERATO Doi 527, expressed	protein-coding
mm_2283.1	chr1	91322118	91322128	+	1	NA	promoter-TSS (NM_001033292)	promoter-TSS (NM_001033292)	48	NM_001033292	227357	Mm.318167	NM_001033292	ENSMUSG00000049515	Espnl	Gm556	espin-like	protein-coding
mm_88992.1	chr10	81565863	81565878	+	1	NA	non-coding (NR_074087, exon 7 of 7)	non-coding (NR_074087, exon 7 of 7)	6426	NM_001276288	14797	Mm.180013	NM_010347	ENSMUSG00000054452	Aes	AL024115|Esp1|Grg|Grg-5|Grg5|Tle5	amino-terminal enhancer of split	protein-coding
mm_155701.1	chrX	94789677	94789686	+	1	NA	Intergenic	Intergenic	8608	NR_003292	668171	Mm.426134	NR_003292		Zxda	4933406P09Rik|AW413531	zinc finger, X-linked, duplicated A	pseudo
mm_67856.1	chr7	98931200	98931202	-	1	NA	intron (NM_178635, intron 13 of 14)	intron (NM_178635, intron 13 of 14)	92356	NM_001285795	22411	Mm.22182	NM_009519	ENSMUSG00000015957	Wnt11	-	wingless-type MMTV integration site family, member 11	protein-coding
mm_164977.1	chr19	8839017	8839054	-	1	NA	promoter-TSS (NM_008144)	promoter-TSS (NM_008144)	211	NM_010316	14704	Mm.329700	NM_010316	ENSMUSG00000071658	Gng3	-	guanine nucleotide binding protein (G protein), gamma 3	protein-coding
mm_171475.1	chr4	145781685	145781697	+	1	NA	intron (NM_001083918, intron 1 of 6)	intron (NM_001083918, intron 1 of 6)	148	NM_001083918	666532	Mm.392861	NM_001083918	ENSMUSG00000067916	Zfp991	Gm13139|OTTMUSG00000010657	zinc finger protein 991	protein-coding
mm_165172.1	chr2	26933629	26933637	+	1	NA	promoter-TSS (NM_011512)	promoter-TSS (NM_011512)	-122	NM_011512	20932	Mm.300594	NM_011512	ENSMUSG00000014867	Surf4	AL033340|AL033373|Surf-4	surfeit gene 4	protein-coding
mm_158054.1	chrX	100625902	100625954	-	1	NA	promoter-TSS (NM_008446)	promoter-TSS (NM_008446)	-21	NM_028303	72621	Mm.291607	NM_028303	ENSMUSG00000015668	Pdzd11	1810012H22Rik|2310079D11Rik|2700099C19Rik|AI854765|Pdzk11	PDZ domain containing 11	protein-coding
mm_25401.1	chr3	107278801	107278808	+	1	NA	promoter-TSS (NM_026774)	promoter-TSS (NM_026774)	-54	NM_026774	68576	Mm.290035	NM_026774	ENSMUSG00000087260	Lamtor5	1110003H18Rik|Hbxip|XIP	late endosomal/lysosomal adaptor, MAPK and MTOR activator 5	protein-coding
mm_61927.1	chr7	90163114	90163157	+	1	NA	intron (NM_001252520, intron 3 of 20)	intron (NM_001252520, intron 3 of 20)	32903	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_125243.1	chr15	34443297	34443370	+	1	NA	promoter-TSS (NR_028101)	promoter-TSS (NR_028101)	-57	NM_001163485	19946	Mm.358632	NM_009083	ENSMUSG00000058600	Rpl30	-	ribosomal protein L30	protein-coding
mm_172511.1	chr7	72649334	72649349	-	1	NA	Intergenic	Intergenic	-342746	NM_001024703	244049	Mm.217412	NM_001024703	ENSMUSG00000032776	Mctp2	Gm489	multiple C2 domains, transmembrane 2	protein-coding
mm_153310.1	chr19	38030648	38030651	-	1	NA	intron (NM_001302140, intron 1 of 53)	(CAA)n|Simple_repeat|Simple_repeat	12928	NM_001099634	226101	Mm.34674	NM_177035	ENSMUSG00000048612	Myof	2310004N10Rik|2310051D19Rik|E030042N20Rik|Fer1l3	myoferlin	protein-coding
mm_112144.1	chr12	113155191	113155201	-	1	NA	Intergenic	Intergenic	-1225	NM_134041	104732	Mm.87616	NM_134041	ENSMUSG00000037466	4930427A07Rik	AA536649|mFLJ00116	RIKEN cDNA 4930427A07 gene	protein-coding
mm_88735.1	chr10	80253685	80253720	+	1	NA	exon (NM_029272, exon 4 of 8)	exon (NM_029272, exon 4 of 8)	4250	NM_029272	75406	Mm.28712	NM_029272	ENSMUSG00000020153	Ndufs7	1010001M04Rik	NADH dehydrogenase (ubiquinone) Fe-S protein 7	protein-coding
mm_45963.1	chr5	90464925	90464945	-	1	NA	exon (NM_009654, exon 5 of 15)	exon (NM_009654, exon 5 of 15)	4065	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_101449.1	chr11	30198081	30198095	-	1	NA	5' UTR (NM_009260, exon 1 of 31)	5' UTR (NM_009260, exon 1 of 31)	169	NM_009260	20742	Mm.123110	NM_009260	ENSMUSG00000020315	Sptbn1	9930031C03Rik|AL033301|SPTB2|Spnb-2|Spnb2|elf1|elf3|mKIAA4049	spectrin beta, non-erythrocytic 1	protein-coding
mm_132253.1	chr16	32751689	32751703	+	1	NA	exon (NM_080457, exon 2 of 27)	exon (NM_080457, exon 2 of 27)	15810	NM_080457	140474	Mm.214599	NM_080457	ENSMUSG00000079620	Muc4	4933405I11Rik|Asgp	mucin 4	protein-coding
mm_29159.1	chr3	106032906	106032953	-	1	NA	promoter-TSS (NM_001080816)	promoter-TSS (NM_001080816)	-34	NM_001080816	229687	Mm.39224	NM_170594	ENSMUSG00000043873	Chil5	Bclp|Bclp1|Bclp2|Chi3l7	chitinase-like 5	protein-coding
mm_147551.1	chr18	54917958	54917961	-	1	NA	intron (NM_175751, intron 3 of 9)	intron (NM_175751, intron 3 of 9)	72221	NM_175751	269023	Mm.192984	NM_175751	ENSMUSG00000052713	Zfp608	4932417D18Rik|D430007A19Rik|Znf608	zinc finger protein 608	protein-coding
mm_88145.1	chr10	69533669	69533682	+	1	NA	promoter-TSS (NM_170688)	promoter-TSS (NM_170688)	-33	NM_170729	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_705.1	chr1	40681660	40681666	+	1	NA	promoter-TSS (NM_001033289)	promoter-TSS (NM_001033289)	-49	NM_001033289	226999	Mm.256414	NM_001033289	ENSMUSG00000026062	Slc9a2	2210416H12Rik|4932415O19Rik|AV333884|NHE2	solute carrier family 9 (sodium/hydrogen exchanger), member 2	protein-coding
mm_97829.1	chr11	83064384	83064409	+	1	NA	promoter-TSS (NM_011408)	promoter-TSS (NM_011408)	-716	NM_011408	20556	Mm.278689	NM_011408	ENSMUSG00000072620	Slfn2	Shlf2	schlafen 2	protein-coding
mm_122741.1	chr14	54138262	54138286	-	1	NA	Intergenic	Intergenic	115655	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_124281.1	chr14	103048409	103048421	-	1	NA	intron (NM_008392, intron 1 of 4)	intron (NM_008392, intron 1 of 4)	1403	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_18386.1	chr2	60118762	60118768	-	1	NA	intron (NM_001001182, intron 1 of 35)	intron (NM_001001182, intron 1 of 35)	6975	NM_001001182	407823	Mm.228071	NM_001001182	ENSMUSG00000026987	Baz2b	5830435C13Rik|BC053917|D2Ertd794e	bromodomain adjacent to zinc finger domain, 2B	protein-coding
mm_80971.1	chr9	103112064	103112068	+	1	NA	promoter-TSS (NM_173781)	promoter-TSS (NM_173781)	-8	NM_173781	270192	Mm.490252	NM_173781	ENSMUSG00000032549	Rab6b	9630015C03|AI844641|C330006L04Rik|D9Bwg0185e	RAB6B, member RAS oncogene family	protein-coding
mm_102298.1	chr11	55461167	55461177	-	1	NA	promoter-TSS (NM_009720)	promoter-TSS (NM_009720)	-34	NM_009720	11927	Mm.217759	NM_009720	ENSMUSG00000018585	Atox1	AI256639|Atx1	antioxidant 1 copper chaperone	protein-coding
mm_14268.1	chr2	128698904	128698924	+	1	NA	promoter-TSS (NM_008587)	promoter-TSS (NM_008587)	-83	NM_008587	17289	Mm.239655	NM_008587	ENSMUSG00000014361	Mertk	Eyk|Mer|Nyk|nmf12	c-mer proto-oncogene tyrosine kinase	protein-coding
mm_68718.1	chr7	120095652	120095674	-	1	NA	Intergenic	Intergenic	-6763	NM_145586	233806	Mm.257952	NM_145586	ENSMUSG00000030917	Tmem159	8430420C20Rik	transmembrane protein 159	protein-coding
mm_86618.1	chr10	13965852	13965871	+	1	NA	promoter-TSS (NM_010437)	promoter-TSS (NM_010437)	-518	NM_010437	15273	Mm.42157	NM_010437	ENSMUSG00000015501	Hivep2	Gm20114|MIBP1|Schnurri-2|Shn-2	human immunodeficiency virus type I enhancer binding protein 2	protein-coding
mm_61805.1	chr7	84750058	84750066	+	1	NA	intron (NR_038175, intron 2 of 4)	intron (NR_038175, intron 2 of 4)	60422	NR_038175	72495	Mm.382914	NR_038175	ENSMUSG00000085236	2610206C17Rik	-	RIKEN cDNA 2610206C17 gene	ncRNA
mm_147439.1	chr18	46525018	46525052	-	1	NA	intron (NM_173423, intron 1 of 2)	intron (NM_173423, intron 1 of 2)	936	NM_173423	240263	Mm.38249	NM_173423	ENSMUSG00000033319	Fem1c	2610312A07Rik|3632443A22Rik|AI646567	fem-1 homolog c (C.elegans)	protein-coding
mm_101966.1	chr11	50308817	50308831	-	1	NA	exon (NM_001110500, exon 5 of 15)	exon (NM_001110500, exon 5 of 15)	-16488	NM_175334	103806	Mm.51116	NM_175334	ENSMUSG00000050567	Maml1	AI644666|AW743257|D930008C07Rik|Mam-1|Mam1|mKIAA0200	mastermind like 1 (Drosophila)	protein-coding
mm_159374.1	chr3	89281179	89281179	-	1	NA	promoter-TSS (NM_001162425)	promoter-TSS (NM_001162425)	-228	NM_001162425	13636	Mm.15675	NM_010107	ENSMUSG00000027954	Efna1	AI325262|B61|Efl1|Epl1|Eplg1|Lerk1	ephrin A1	protein-coding
mm_148217.1	chr18	80236793	80236811	-	1	NA	5' UTR (NM_001136181, exon 2 of 5)	5' UTR (NM_001136181, exon 2 of 5)	10300	NM_001136181	66255	Mm.272341	NM_001136181	ENSMUSG00000078963	Hsbp1l1	1810005K13Rik	heat shock factor binding protein 1-like 1	protein-coding
mm_138775.1	chr17	37195510	37195518	+	1	NA	exon (NM_023137, exon 2 of 2)	exon (NM_023137, exon 2 of 2)	1622	NM_023137	24108	Mm.140210	NM_023137	ENSMUSG00000035186	Ubd	FAT10	ubiquitin D	protein-coding
mm_37168.1	chr4	117178714	117178718	-	1	NA	promoter-TSS (NM_001290662)	promoter-TSS (NM_001290662)	56	NM_001290662	73804	Mm.247651	NM_134471	ENSMUSG00000028678	Kif2c	4930402F02Rik|ESTM5|Knsl6|MCAK|X83316	kinesin family member 2C	protein-coding
mm_140170.1	chr17	80307397	80307413	+	1	NA	promoter-TSS (NM_001145452)	promoter-TSS (NM_001145452)	-2	NM_001145452	381112	Mm.360004	NM_001145452	ENSMUSG00000054901	Arhgef33	Gm941	Rho guanine nucleotide exchange factor (GEF) 33	protein-coding
mm_94375.1	chr11	5105178	5105187	+	1	NA	non-coding (NR_110961, exon 6 of 8)	non-coding (NR_110961, exon 6 of 8)	5017	NM_001290493	279766	Mm.260866	NM_177370	ENSMUSG00000034175	Rhbdd3	Ptag	rhomboid domain containing 3	protein-coding
mm_154335.1	chrM	3907	3926	+	1	NA	NA	Intergenic	NA	NA								
mm_131536.1	chr16	17759579	17759587	+	1	NA	promoter-TSS (NM_145479)	promoter-TSS (NM_145479)	-38	NM_145479	224023	Mm.282807	NM_145479	ENSMUSG00000022750	Klhl22	2610318I18Rik|Kelchl	kelch-like 22	protein-coding
mm_796.1	chr1	45346038	45346058	+	1	NA	exon (NM_009930, exon 48 of 51)	exon (NM_009930, exon 48 of 51)	34510	NM_009930	12825	Mm.249555	NM_009930	ENSMUSG00000026043	Col3a1	AW550625|Col3a-1|Tsk-2|Tsk2	collagen, type III, alpha 1	protein-coding
mm_71515.1	chr8	46846540	46846555	+	1	NA	3' UTR (NM_008391, exon 9 of 9)	3' UTR (NM_008391, exon 9 of 9)	106802	NM_008391	16363	Mm.1149	NM_008391	ENSMUSG00000031627	Irf2	9830146E22Rik|AI646973|Irf-2	interferon regulatory factor 2	protein-coding
mm_164970.1	chr19	7482982	7482984	-	1	NA	exon (NM_053076, exon 1 of 7)	exon (NM_053076, exon 1 of 7)	308	NM_001271486	20168	Mm.246990	NM_053076	ENSMUSG00000024758	Rtn3	RTN3-A1	reticulon 3	protein-coding
mm_70145.1	chr7	143458805	143458821	-	1	NA	3' UTR (NM_001161624, exon 4 of 4)	3' UTR (NM_001161624, exon 4 of 4)	2237	NM_009876	12577	Mm.168789	NM_009876	ENSMUSG00000037664	Cdkn1c	AL024410|CDKI|Kip2|p57(kip2)|p57Kip2	cyclin-dependent kinase inhibitor 1C (P57)	protein-coding
mm_19383.1	chr2	91236870	91236872	-	1	NA	promoter-TSS (NR_015464)	promoter-TSS (NR_015464)	195	NM_028119	107986	Mm.389334	NM_028119	ENSMUSG00000002109	Ddb2	2610043A19Rik	damage specific DNA binding protein 2	protein-coding
mm_97207.1	chr11	75612705	75612714	+	1	NA	intron (NM_008850, intron 7 of 11)	PB1D9|SINE|Alu	-12478	NR_110477	654359	Mm.439961	NR_110477		Gm12338	OTTMUSG00000006216	cytochrome c oxidase, subunit VIIc pseudogene	pseudo
mm_24727.1	chr3	95282898	95282942	+	1	NA	promoter-TSS (NM_133858)	promoter-TSS (NM_133858)	-15	NM_133858	75007	Mm.279287	NM_133858	ENSMUSG00000038712	Fam63a	1810005H09Rik|4930504E06Rik|AA562754|AA960384|AW561904|cI-40|mKIAA1390|ni	family with sequence similarity 63, member A	protein-coding
mm_71830.1	chr8	68896758	68896774	+	1	NA	exon (NM_008509, exon 6 of 10)	exon (NM_008509, exon 6 of 10)	16211	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_61701.1	chr7	81213288	81213322	+	1	NA	promoter-TSS (NM_008803)	promoter-TSS (NM_008803)	-499	NM_008803	18584	Mm.371577	NM_008803	ENSMUSG00000025584	Pde8a	AI551852|Pde8	phosphodiesterase 8A	protein-coding
mm_167868.1	chrX	33416472	33416506	+	1	NA	Intergenic	L1Md_F2|LINE|L1	103151	NM_001099333	100040606	Mm.460713	NM_001099333	ENSMUSG00000101500	Btbd35f12	Gm2863	BTB domain containing 35, family member 12	protein-coding
mm_73872.1	chr8	119062045	119062058	+	1	NA	intron (NM_019707, intron 6 of 13)	intron (NM_019707, intron 6 of 13)	-282487	NM_024219	68196	Mm.358714	NM_024219	ENSMUSG00000031839	Hsbp1	0610007A03Rik|AA408769|Hsp25	heat shock factor binding protein 1	protein-coding
mm_146915.1	chr18	31582251	31582259	-	1	NA	3' UTR (NM_026165, exon 8 of 8)	3' UTR (NM_026165, exon 8 of 8)	27647	NM_026165	67453	Mm.23896	NM_026165	ENSMUSG00000024259	Slc25a46	1200007B05Rik|AI325987	solute carrier family 25, member 46	protein-coding
mm_165635.1	chr3	69859856	69859864	-	1	NA	promoter-TSS (NM_133675)	promoter-TSS (NM_133675)	34	NM_001164210	66183	Mm.45481	NM_133675	ENSMUSG00000043461	Sptssb	1110032A04Rik|ADMP|Sssptb	serine palmitoyltransferase, small subunit B	protein-coding
mm_171205.1	chr3	54692846	54692846	+	1	NA	promoter-TSS (NM_019995)	promoter-TSS (NM_019995)	-259	NM_019995	56790	Mm.486375	NM_019995	ENSMUSG00000027751	Supt20	AA667204|AI450544|D3Ertd300e|Fam48a|Supt20h|p38IP	suppressor of Ty 20	protein-coding
mm_157785.1	chrX	73824436	73824452	-	1	NA	5' UTR (NM_001290540, exon 1 of 6)	5' UTR (NM_001290540, exon 1 of 6)	525	NM_001029868	245469	Mm.103782	NM_001029868	ENSMUSG00000002006	Pdzd4	B230341P03|D130075J17Rik|Kiaa1444-hp|LU1|PDZRN4L|Pdzk4|Pdzrnk4l|Xlu	PDZ domain containing 4	protein-coding
mm_83375.1	chr9	44526425	44526440	-	1	NA	promoter-TSS (NM_007551)	promoter-TSS (NM_007551)	-11	NM_007551	12145	Mm.6246	NM_007551	ENSMUSG00000047880	Cxcr5	Blr1|CXC-R5|CXCR-5|Gpcr6|MDR15	chemokine (C-X-C motif) receptor 5	protein-coding
mm_31600.1	chr4	57893929	57893940	+	1	NA	3' UTR (NM_001035533, exon 4 of 4)	3' UTR (NM_001035533, exon 4 of 4)	22330	NM_178727	242484	Mm.23214	NM_178727	ENSMUSG00000052117	D630039A03Rik	-	RIKEN cDNA D630039A03 gene	protein-coding
mm_140615.1	chr17	10840286	10840299	-	1	NA	promoter-TSS (NM_016694)	promoter-TSS (NM_016694)	-67	NM_001317726	50873	Mm.311110	NM_016694	ENSMUSG00000023826	Park2	PRKN	Parkinson disease (autosomal recessive, juvenile) 2, parkin	protein-coding
mm_119695.1	chr14	53621733	53621744	+	1	NA	Intergenic	Intergenic	632191	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_168069.1	chr10	105238418	105238437	+	1	NA	intron (NM_177368, intron 11 of 11)	LSU-rRNA_Hsa|rRNA|rRNA	336052	NM_177368	278279	Mm.25225	NM_177368	ENSMUSG00000036019	Tmtc2	8430438D04Rik|D330034A10Rik	transmembrane and tetratricopeptide repeat containing 2	protein-coding
mm_71379.1	chr8	45885480	45885494	+	1	NA	promoter-TSS (NM_016798)	promoter-TSS (NM_016798)	2	NM_016798	53318	Mm.282900	NM_016798	ENSMUSG00000031636	Pdlim3	AI463105|ALP|Actn2lp	PDZ and LIM domain 3	protein-coding
mm_62640.1	chr7	107664933	107664992	+	1	NA	intron (NM_001163557, intron 3 of 25)	intron (NM_001163557, intron 3 of 25)	58118	NM_001163557	19024	Mm.2817	NM_008905	ENSMUSG00000036528	Ppfibp2	Cclp1	PTPRF interacting protein, binding protein 2 (liprin beta 2)	protein-coding
mm_144845.1	chr18	36573581	36573585	+	1	NA	intron (NM_175375, intron 1 of 33)	intron (NM_175375, intron 1 of 33)	12980	NM_175375	108857	Mm.482287	NM_175375	ENSMUSG00000024483	Ankhd1	1110004O12Rik|4933432B13Rik|9130019P20Rik|A530027J04Rik|A630021B20Rik|AA571404|Mask|mFLJ00246|mKIAA1085	ankyrin repeat and KH domain containing 1	protein-coding
mm_67108.1	chr7	70354679	70354716	-	1	NA	exon (NM_183261, exon 3 of 3)	exon (NM_183261, exon 3 of 3)	5896	NM_009697	11819	Mm.158143	NM_009697	ENSMUSG00000030551	Nr2f2	2700033K02Rik|9430015G03Rik|ARP-1|Aporp1|COUP-TF2|COUP-TFII|COUPTFB|EAR3|SVP40|Tcfcoup2	nuclear receptor subfamily 2, group F, member 2	protein-coding
mm_60841.1	chr7	45742814	45742844	+	1	NA	intron (NM_017465, intron 1 of 6)	PB1D10|SINE|Alu	16726	NM_017465	54200	Mm.271634	NM_017465	ENSMUSG00000003271	Sult2b1	AI326997|BB173635|ST2B1|SULT2B	sulfotransferase family, cytosolic, 2B, member 1	protein-coding
mm_22834.1	chr3	27482494	27482504	+	1	NA	intron (NM_173182, intron 11 of 25)	intron (NM_173182, intron 11 of 25)	102496	NR_037275	100526525		NR_037275	ENSMUSG00000092695	Mir3092	mir-3092|mmu-mir-3092	microRNA 3092	ncRNA
mm_5873.1	chr1	53785215	53785229	-	1	NA	promoter-TSS (NM_133810)	promoter-TSS (NM_133810)	-7	NM_133810	98267	Mm.25559	NM_133810	ENSMUSG00000026094	Stk17b	3110009A03Rik|AI120141|Drak2	serine/threonine kinase 17b (apoptosis-inducing)	protein-coding
mm_72421.1	chr8	82084333	82084335	+	1	NA	intron (NM_001297593, intron 23 of 23)	intron (NM_001297593, intron 23 of 23)	318252	NM_001254747	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_75883.1	chr8	70796993	70797019	-	1	NA	Intergenic	CpG	-1129	NR_106099	102466823		NR_106099	ENSMUSG00000099031	Mir7240	Gm27487|mmu-mir-7240	microRNA 7240	ncRNA
mm_115121.1	chr13	104287034	104287062	+	1	NA	promoter-TSS (NM_001081020)	promoter-TSS (NM_001081020)	-787	NR_136938	108154	Mm.208125	NM_175496	ENSMUSG00000046169	Adamts6	A930019D11Rik|ADAM-TS6|b2b1879.1Clo|b2b2029Clo|b2b2182Clo|b2b2187.1Clo|b2b2228Clo	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 6	protein-coding
mm_120386.1	chr14	64590295	64590307	+	1	NA	promoter-TSS (NR_029813)	promoter-TSS (NR_029813)	-356	NR_029813	387233		NR_029813	ENSMUSG00000065597	Mir124a-1	Mirn124a|Mirn124a-1	microRNA 124a-1	ncRNA
mm_134827.1	chr16	26075108	26075111	-	1	NA	intron (NM_173379, intron 1 of 14)	intron (NM_173379, intron 1 of 14)	30675	NM_173379	210530	Mm.326869	NM_173379	ENSMUSG00000038168	P3h2	4832416N06|AW553532|Leprel1|Mlat4	prolyl 3-hydroxylase 2	protein-coding
mm_161582.1	chr16	31754445	31754445	+	1	NA	promoter-TSS (NM_001252436)	promoter-TSS (NM_001252436)	95	NM_001252436	13383	Mm.382	NM_007862	ENSMUSG00000022770	Dlg1	B130052P05Rik|Dlgh1|E-dlg/SAP97|SAP-97|SAP97|mKIAA4187	discs, large homolog 1 (Drosophila)	protein-coding
mm_23543.1	chr3	61364518	61364528	+	1	NA	promoter-TSS (NM_028712)	promoter-TSS (NM_028712)	16	NM_028712	74012	Mm.422674	NM_028712	ENSMUSG00000036894	Rap2b	4021402C18Rik|AA408554	RAP2B, member of RAS oncogene family	protein-coding
mm_39453.1	chr5	17574609	17574631	+	1	NA	promoter-TSS (NM_013657)	promoter-TSS (NM_013657)	-196	NM_013657	20348	Mm.5071	NM_013657	ENSMUSG00000028780	Sema3c	1110036B02Rik|SemE|Semae	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	protein-coding
mm_71993.1	chr8	70617798	70617829	+	1	NA	exon (NM_153074, exon 2 of 3)	exon (NM_153074, exon 2 of 3)	969	NM_153074	211228	Mm.132939	NM_153074	ENSMUSG00000049988	Lrrc25	Mapa	leucine rich repeat containing 25	protein-coding
mm_113498.1	chr13	37418843	37418860	+	1	NA	3' UTR (NM_010745, exon 5 of 5)	3' UTR (NM_010745, exon 5 of 5)	73506	NM_010745	17084	Mm.2639	NM_010745	ENSMUSG00000021423	Ly86	MD-1|MD1|ly86_tv2	lymphocyte antigen 86	protein-coding
mm_62081.1	chr7	92933068	92933096	+	1	NA	exon (NM_028243, exon 9 of 9)	exon (NM_028243, exon 9 of 9)	57829	NM_028243	72461	Mm.389969	NM_028243	ENSMUSG00000061119	Prcp	2510048K03Rik|2610104A14Rik|AI451719|HUMPCP|PCP	prolylcarboxypeptidase (angiotensinase C)	protein-coding
mm_166947.1	chr7	43826905	43826911	+	1	NA	exon (NM_011177, exon 3 of 6)	exon (NM_011177, exon 3 of 6)	1458	NM_011177	19144	Mm.3944	NM_011177	ENSMUSG00000050063	Klk6	AI849898|BSP|Bssp|Klk29|MSP|Prss18|Prss9|neurosin	kallikrein related-peptidase 6	protein-coding
mm_149034.1	chr19	8802842	8802850	+	1	NA	intron (NM_001098237, intron 1 of 1)	intron (NM_001098237, intron 1 of 1)	316	NM_001098237	75291	Mm.23423	NM_133759	ENSMUSG00000071661	Zbtb3	4930563M09Rik	zinc finger and BTB domain containing 3	protein-coding
mm_22068.1	chr2	168734237	168734286	-	1	NA	promoter-TSS (NM_001289445)	promoter-TSS (NM_001289445)	78	NM_001289445	11981	Mm.330819	NM_015731	ENSMUSG00000027546	Atp9a	IIa	ATPase, class II, type 9A	protein-coding
mm_72127.1	chr8	71757455	71757468	+	1	NA	Intergenic	(CTCA)n|Simple_repeat|Simple_repeat	-31780	NM_028715	74015	Mm.22025	NM_028715	ENSMUSG00000070000	Fcho1	3322402E17Rik|N28152	FCH domain only 1	protein-coding
mm_62753.1	chr7	112023434	112023444	+	1	NA	promoter-TSS (NM_177249)	promoter-TSS (NM_177249)	-67	NM_133758	74996	Mm.16974	NM_133758	ENSMUSG00000059263	Usp47	4930502N04Rik|A630020C16Rik	ubiquitin specific peptidase 47	protein-coding
mm_58013.1	chr6	136555587	136555593	-	1	NA	intron (NM_019426, intron 1 of 14)	intron (NM_019426, intron 1 of 14)	36739	NM_019426	54343	Mm.173271	NM_019426	ENSMUSG00000030213	Atf7ip	2610204M12Rik|AM|Mcaf1	activating transcription factor 7 interacting protein	protein-coding
mm_893.1	chr1	53297071	53297094	+	1	NA	promoter-TSS (NM_145517)	promoter-TSS (NM_145517)	-13	NM_145517	227102	Mm.212846	NM_145517	ENSMUSG00000026097	Ormdl1	C730042F17Rik	ORM1-like 1 (S. cerevisiae)	protein-coding
mm_75037.1	chr8	32477352	32477353	-	1	NA	Intergenic	Intergenic	325457	NR_046039	666589	Mm.367675	NR_046039		Gm8179	EG666589	predicted gene 8179	ncRNA
mm_92456.1	chr10	77827093	77827097	-	1	NA	promoter-TSS (NM_001135991)	promoter-TSS (NM_001135991)	-25	NM_001135991	100191037	Mm.432613	NM_001135991	ENSMUSG00000069582	Krtap10-4	675238|A030009A09Rik|AA589524	keratin associated protein 10-4	protein-coding
mm_122069.1	chr14	30573610	30573611	-	1	NA	3' UTR (NM_009388, exon 14 of 14)	3' UTR (NM_009388, exon 14 of 14)	1461	NR_037237	100526475		NR_037237	ENSMUSG00000093156	Mir3076	mir-3076|mmu-mir-3076	microRNA 3076	ncRNA
mm_15237.1	chr2	154650912	154650921	+	1	NA	Intergenic	RMER17C|LTR|ERVK	-6110	NM_029362	75608	Mm.262480	NM_029362	ENSMUSG00000038467	Chmp4b	2010012F05Rik|C76846|Snf7-2	charged multivesicular body protein 4B	protein-coding
mm_116316.1	chr13	37440069	37440089	-	1	NA	Intergenic	Intergenic	94734	NM_010745	17084	Mm.2639	NM_010745	ENSMUSG00000021423	Ly86	MD-1|MD1|ly86_tv2	lymphocyte antigen 86	protein-coding
mm_79381.1	chr9	54765630	54765640	+	1	NA	exon (NM_001284507, exon 2 of 3)	exon (NM_001284507, exon 2 of 3)	887	NM_013496	12903	Mm.34797	NM_013496	ENSMUSG00000032291	Crabp1	AI326249|CRABP-I|Crabp-1|CrabpI|Rbp-5	cellular retinoic acid binding protein I	protein-coding
mm_113743.1	chr13	44729640	44729697	+	1	NA	Intergenic	CpG	-1106	NM_021878	16468	Mm.25059	NM_021878	ENSMUSG00000038518	Jarid2	Jmj|jumonji	jumonji, AT rich interactive domain 2	protein-coding
mm_103561.1	chr11	77725282	77725294	-	1	NA	promoter-TSS (NM_009965)	promoter-TSS (NM_009965)	5	NM_001313933	12957	Mm.22830	NM_009965	ENSMUSG00000000724	Cryba1	BA3/A1|Cryb	crystallin, beta A1	protein-coding
mm_140471.1	chr17	93336166	93336170	+	1	NA	Intergenic	Intergenic	137000	NM_009625	11516	Mm.3407	NM_009625	ENSMUSG00000024256	Adcyap1	PACAP	adenylate cyclase activating polypeptide 1	protein-coding
mm_38355.1	chr4	137796309	137796325	-	1	NA	promoter-TSS (NM_007431)	promoter-TSS (NM_007431)	67	NM_007431	11647	Mm.288186	NM_007431	ENSMUSG00000028766	Alpl	ALP|APTNAP|Akp-2|Akp2|TNAP|TNSALP	alkaline phosphatase, liver/bone/kidney	protein-coding
mm_7237.1	chr1	93478330	93478391	-	1	NA	promoter-TSS (NM_010891)	promoter-TSS (NM_010891)	557	NM_133808	110611	Mm.30012	NM_133808	ENSMUSG00000034088	Hdlbp	1110005P14Rik|AA960365|AI118566|D1Ertd101e	high density lipoprotein (HDL) binding protein	protein-coding
mm_126945.1	chr15	92051256	92051262	+	1	NA	promoter-TSS (NM_001159648)	promoter-TSS (NM_001159648)	94	NM_001159648	12805	Mm.4911	NM_007727	ENSMUSG00000055022	Cntn1	AW495098|CNTN|F3cam|usl	contactin 1	protein-coding
mm_122532.1	chr14	47384690	47384728	-	1	NA	exon (NM_010705, exon 5 of 6)	exon (NM_010705, exon 5 of 6)	10849	NM_001145953	16854	Mm.248615	NM_010705	ENSMUSG00000050335	Lgals3	GBP|L-34|Mac-2|gal3	lectin, galactose binding, soluble 3	protein-coding
mm_163036.1	chr11	53315060	53315068	+	1	NA	Intergenic	Intergenic	-9625	NM_026479	67966	Mm.288072	NM_026479	ENSMUSG00000018239	Zcchc10	2410141K03Rik|AA675321|D11Ertd416e	zinc finger, CCHC domain containing 10	protein-coding
mm_25989.1	chr3	133666338	133666346	+	1	NA	Intergenic	Intergenic	-121952	NM_001040400	214133	Mm.347816	NM_145989	ENSMUSG00000040943	Tet2	Ayu17-449|E130014J05Rik|mKIAA1546	tet methylcytosine dioxygenase 2	protein-coding
mm_50423.1	chr6	48834029	48834060	+	1	NA	non-coding (NR_104575, exon 7 of 7)	non-coding (NR_104575, exon 7 of 7)	6944	NM_023056	65963	Mm.28385	NM_023056	ENSMUSG00000029810	Tmem176b	1810009M01Rik|Clast1|Lr8	transmembrane protein 176B	protein-coding
mm_83155.1	chr9	40457473	40457485	-	1	NA	Intergenic	Intergenic	-1715	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_60463.1	chr7	44477831	44477837	+	1	NA	Intergenic	Intergenic	-6683	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_110653.1	chr12	59050801	59050804	-	1	NA	intron (NM_030057, intron 2 of 5)	B1F|SINE|Alu	10670	NM_001306218	78232	Mm.290070	NM_030057	ENSMUSG00000020993	Trappc6b	5830498C14Rik|C79212	trafficking protein particle complex 6B	protein-coding
mm_99174.1	chr11	100850048	100850061	+	1	NA	intron (NM_001113563, intron 1 of 18)	intron (NM_001113563, intron 1 of 18)	531	NM_001113563	20851	Mm.34064	NM_011489	ENSMUSG00000020919	Stat5b	-	signal transducer and activator of transcription 5B	protein-coding
mm_41698.1	chr5	100846279	100846293	+	1	NA	promoter-TSS (NM_172715)	promoter-TSS (NM_172715)	57	NM_172715	231510	Mm.271911	NM_172715	ENSMUSG00000029314	Agpat9	1-AGPAT|1-AGPAT 9|4933407I02Rik|4933408F15|A230097K15Rik|GPAT-3|Gpat3|mGPAT3	1-acylglycerol-3-phosphate O-acyltransferase 9	protein-coding
mm_139765.1	chr17	64601368	64601386	+	1	NA	promoter-TSS (NM_008549)	promoter-TSS (NM_008549)	-272	NM_008549	17158	Mm.2433	NM_008549	ENSMUSG00000024085	Man2a1	Mana-2|Mana2|Map-2	mannosidase 2, alpha 1	protein-coding
mm_66475.1	chr7	44997529	44997534	-	1	NA	promoter-TSS (NM_016849)	promoter-TSS (NM_016849)	48	NM_029410	75736	Mm.261006	NM_029410	ENSMUSG00000003190	Bcl2l12	2810475P17Rik|5430429M05Rik|Bcl-L12|Bcl2-L12	BCL2-like 12 (proline rich)	protein-coding
mm_152213.1	chr19	7966010	7966037	-	1	NA	promoter-TSS (NM_134256)	promoter-TSS (NM_134256)	4	NM_134256	171405	Mm.326517	NM_134256	ENSMUSG00000067656	Slc22a27	Oat9|mOAT6-L|mOAT6-S	solute carrier family 22, member 27	protein-coding
mm_136991.1	chr17	17374616	17374624	+	1	NA	exon (NM_025934, exon 1 of 10)	exon (NM_025934, exon 1 of 10)	288	NM_025934	67045	Mm.35117	NM_025934	ENSMUSG00000023852	Riok2	2010110K24Rik|2410085M17Rik	RIO kinase 2 (yeast)	protein-coding
mm_28721.1	chr3	95674135	95674153	-	1	NA	Intergenic	Intergenic	13773	NM_144899	229595	Mm.490574	NM_144899	ENSMUSG00000015850	Adamtsl4	ADAMTSL-4|Tsrc1	ADAMTS-like 4	protein-coding
mm_3946.1	chr1	163930006	163930077	+	1	NA	5' UTR (NM_028776, exon 1 of 14)	5' UTR (NM_028776, exon 1 of 14)	276	NM_028776	240880	Mm.389213	NM_028776	ENSMUSG00000026584	Scyl3	1200016D23Rik|6030457O16|AW214499|Pace1	SCY1-like 3 (S. cerevisiae)	protein-coding
mm_25661.1	chr3	121723581	121723585	+	1	NA	promoter-TSS (NM_010171)	promoter-TSS (NM_010171)	46	NM_010171	14066	Mm.273188	NM_010171	ENSMUSG00000028128	F3	AA409063|CD142|Cf-3|Cf3|TF	coagulation factor III	protein-coding
mm_918.1	chr1	55087952	55087994	+	1	NA	promoter-TSS (NM_010477)	promoter-TSS (NM_010477)	-41	NM_010477	15510	Mm.1777	NM_010477	ENSMUSG00000025980	Hspd1	60kDa|Hsp60	heat shock protein 1 (chaperonin)	protein-coding
mm_1454.1	chr1	67230708	67230733	+	1	NA	3' UTR (NM_001080809, exon 38 of 38)	3' UTR (NM_001080809, exon 38 of 38)	107693	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_123786.1	chr14	70351315	70351330	-	1	NA	5' UTR (NM_144808, exon 1 of 10)	5' UTR (NM_144808, exon 1 of 10)	102	NM_144808	213053	Mm.270647	NM_144808	ENSMUSG00000022094	Slc39a14	FAD-123|ZIP-14|Zip14|fad123	solute carrier family 39 (zinc transporter), member 14	protein-coding
mm_137606.1	chr17	28227068	28227071	+	1	NA	intron (NM_027185, intron 9 of 10)	intron (NM_027185, intron 9 of 10)	-5685	NM_011145	19015	Mm.328914	NM_011145	ENSMUSG00000002250	Ppard	NUC-1|NUC1|Nr1c2|PPAR-beta|PPAR-delta|PPAR[b]|PPARdelta|Pparb|Pparb/d	peroxisome proliferator activator receptor delta	protein-coding
mm_74359.1	chr8	128359033	128359045	+	1	NA	promoter-TSS (NM_008737)	promoter-TSS (NM_008737)	-34	NM_008737	18186	Mm.271745	NM_008737	ENSMUSG00000025810	Nrp1	C530029I03|NP-1|NPN-1|Npn1|Nrp	neuropilin 1	protein-coding
mm_30339.1	chr3	151733886	151733888	-	1	NA	intron (NM_133871, intron 7 of 7)	Lx7|LINE|L1	16072	NM_133871	99899	Mm.30756	NM_133871	ENSMUSG00000028037	Ifi44	A430056A10Rik|AW261460|MTAP44|p44	interferon-induced protein 44	protein-coding
mm_97159.1	chr11	75468162	75468184	+	1	NA	5' UTR (NM_001291156, exon 1 of 5)	5' UTR (NM_001291156, exon 1 of 5)	123	NM_027249	380712	Mm.41393	NM_027249	ENSMUSG00000038217	Tlcd2	-	TLC domain containing 2	protein-coding
mm_16745.1	chr2	9594133	9594144	-	1	NA	Intergenic	Intergenic	284462	NM_008091	14462	Mm.313866	NM_008091	ENSMUSG00000015619	Gata3	Gata-3|jal	GATA binding protein 3	protein-coding
mm_127886.1	chr15	8710735	8710760	-	1	NA	promoter-TSS (NM_148938)	promoter-TSS (NM_148938)	60	NM_148938	20512	Mm.204834	NM_148938	ENSMUSG00000005360	Slc1a3	AI504299|B430115D02Rik|Eaat1|GLAST|GLAST-1|GLU-T|GluT-1|Gmt1|MGluT1	solute carrier family 1 (glial high affinity glutamate transporter), member 3	protein-coding
mm_145523.1	chr18	60560731	60560796	+	1	NA	promoter-TSS (NM_025776)	promoter-TSS (NM_025776)	-23	NM_025776	66810	Mm.275106	NM_025776	ENSMUSG00000024604	Rbm22	8430430L24Rik	RNA binding motif protein 22	protein-coding
mm_10049.1	chr1	193197951	193198031	-	1	NA	exon (NM_153137, exon 3 of 16)	exon (NM_153137, exon 3 of 16)	3555	NM_153137	215243	Mm.261259	NM_153137	ENSMUSG00000037318	Traf3ip3	6030423D04Rik|AI115021|T3jam	TRAF3 interacting protein 3	protein-coding
mm_65871.1	chr7	29505776	29505790	-	1	NA	promoter-TSS (NM_001081028)	promoter-TSS (NM_001081028)	-323	NM_001081028	74206	Mm.447042	NM_001081028	ENSMUSG00000030583	Sipa1l3	2610511M17Rik	signal-induced proliferation-associated 1 like 3	protein-coding
mm_158154.1	chrX	103478143	103478147	-	1	NA	non-coding (NR_001570, exon 1 of 8)	non-coding (NR_001570, exon 1 of 8)	5088	NR_001570	213742	Mm.274770	NR_001463	ENSMUSG00000086503	Xist	A430022B11|AI314753	inactive X specific transcripts	ncRNA
mm_124209.1	chr14	99099702	99099785	-	1	NA	promoter-TSS (NM_028315)	promoter-TSS (NM_028315)	27	NM_028315	72662	Mm.163339	NM_028315	ENSMUSG00000033166	Dis3	2810028N01Rik	DIS3 homolog, exosome endoribonuclease and 3'-5' exoribonuclease	protein-coding
mm_156458.1	chrX	142825699	142825716	+	1	NA	intron (NM_001199360, intron 5 of 6)	L2a|LINE|L2	86707	NR_030523	723976		NR_030523	ENSMUSG00000076011	Mir652	Mirn652|miRX|mmu-mir-652	microRNA 652	ncRNA
mm_25947.1	chr3	131564858	131564883	+	1	NA	5' UTR (NM_001289478, exon 1 of 13)	5' UTR (NM_001289478, exon 1 of 13)	102	NM_011863	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_7494.1	chr1	121346171	121346181	-	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-13587	NM_178082	72999	Mm.27136	NM_133748	ENSMUSG00000003721	Insig2	2900053I11Rik|C730043J18Rik|Insig-2	insulin induced gene 2	protein-coding
mm_107014.1	chr12	12262165	12262191	+	1	NA	promoter-TSS (NM_001146119)	promoter-TSS (NM_001146119)	39	NM_001146119	76820	Mm.440802	NM_029758	ENSMUSG00000020589	Fam49a	2410157M17Rik|9630047E15|D12Ertd553e	family with sequence similarity 49, member A	protein-coding
mm_470.1	chr1	36372232	36372241	+	1	NA	promoter-TSS (NM_001277076)	promoter-TSS (NM_001277076)	-55	NM_001277076	100534273	Mm.389112	NM_001277076	ENSMUSG00000037432	Fer1l5	4930533C12Rik	fer-1-like 5 (C. elegans)	protein-coding
mm_32750.1	chr4	116685860	116685872	+	1	NA	intron (NR_040442, intron 1 of 2)	CpG	156	NR_040442	100502959	Mm.395400	NR_040442		AV051173	-	expressed sequence AV051173	ncRNA
mm_7035.1	chr1	87100317	87100354	-	1	NA	intron (NM_001081082, intron 5 of 10)	intron (NM_001081082, intron 5 of 10)	1271	NM_001081082	76768	Mm.58068	NM_001081082	ENSMUSG00000079440	Alpi	2010001C14Rik|Akp6|gIAP	alkaline phosphatase, intestinal	protein-coding
mm_27856.1	chr3	79157271	79157282	-	1	NA	Intergenic	L1_Mur3|LINE|L1	-11401	NM_001099624	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_94611.1	chr11	16260586	16260607	+	1	NA	intron (NM_145967, intron 2 of 4)	intron (NM_145967, intron 2 of 4)	2872	NM_145967	211739	Mm.284015	NM_145967	ENSMUSG00000048834	Vstm2a	Vstm2	V-set and transmembrane domain containing 2A	protein-coding
mm_124978.1	chr15	20520511	20520511	+	1	NA	Intergenic	Intergenic	146239	NM_022816	64833	Mm.352763	NM_022816	ENSMUSG00000047565	Acot10	Acate3|MT-ACT48|p48	acyl-CoA thioesterase 10	protein-coding
mm_127280.1	chr15	99902937	99902957	+	1	NA	Intergenic	Intergenic	-27491	NM_001113545	65970	Mm.33207	NM_023063	ENSMUSG00000023022	Lima1	Eplin	LIM domain and actin binding 1	protein-coding
mm_68328.1	chr7	106504055	106504068	-	1	NA	Intergenic	Intergenic	-62988	NR_003967	209380	Mm.461779	NM_001001318		Gm4759	EG209380	GTPase, very large interferon inducible 1 pseudogene	pseudo
mm_83100.1	chr9	40321448	40321487	-	1	NA	intron (NM_172768, intron 4 of 19)	intron (NM_172768, intron 4 of 19)	-12005	NR_040728	73558	Mm.398307	NR_040728		1700110K17Rik	-	RIKEN cDNA 1700110K17 gene	ncRNA
mm_143071.1	chr17	57022462	57022509	-	1	NA	3' UTR (NM_010613, exon 18 of 18)	3' UTR (NM_010613, exon 18 of 18)	9022	NM_010613	16549	Mm.34296	NM_010613	ENSMUSG00000007670	Khsrp	6330409F21Rik|Fbp2|Fubp2|Ksrp	KH-type splicing regulatory protein	protein-coding
mm_72213.1	chr8	72646646	72646660	+	1	NA	promoter-TSS (NM_176940)	promoter-TSS (NM_176940)	-58	NM_176940	319555	Mm.212927	NM_176940	ENSMUSG00000048148	Nwd1	A230063L24Rik	NACHT and WD repeat domain containing 1	protein-coding
mm_72167.1	chr8	72240349	72240353	+	1	NA	intron (NM_007456, intron 1 of 11)	CpG	333	NM_007456	11767	Mm.290086	NM_007456	ENSMUSG00000003033	Ap1m1	AA408894|AP47|Adtm1A|Cltnm|mu1A	adaptor-related protein complex AP-1, mu subunit 1	protein-coding
mm_75573.1	chr8	60954793	60954803	-	1	NA	promoter-TSS (NM_173876)	promoter-TSS (NM_173876)	1	NM_173876	12725	Mm.25263	NM_007711	ENSMUSG00000004319	Clcn3	Clc3	chloride channel, voltage-sensitive 3	protein-coding
mm_18332.1	chr2	57297438	57297448	-	1	NA	intron (NM_001145820, intron 3 of 16)	intron (NM_001145820, intron 3 of 16)	59061	NM_010274	14571	Mm.3711	NM_010274	ENSMUSG00000026827	Gpd2	AA408484|AI448216|AU021455|AW494132|GPDH|Gdm1|Gpd-m|Gpdh-m|TISP38	glycerol phosphate dehydrogenase 2, mitochondrial	protein-coding
mm_5839.1	chr1	52952805	52952826	-	1	NA	promoter-TSS (NM_144953)	promoter-TSS (NM_144953)	25	NM_144953	67080	Mm.236287	NM_144953	ENSMUSG00000043629	1700019D03Rik	2410136C24Rik|AA410151|smAKAP	RIKEN cDNA 1700019D03 gene	protein-coding
mm_125672.1	chr15	66445560	66445597	+	1	NA	intron (NM_019457, intron 7 of 11)	L2|LINE|L2	55332	NM_019457	54562	Mm.244890	NM_019457	ENSMUSG00000022375	Lrrc6	LRTP	leucine rich repeat containing 6 (testis)	protein-coding
mm_30241.1	chr3	146495129	146495139	-	1	NA	intron (NM_027617, intron 1 of 14)	RLTR11C_MM|LTR|ERVK	4619	NM_001316756	70951	Mm.383235	NM_027617	ENSMUSG00000028188	Spata1	4921536I21Rik|AV266943|SP-2	spermatogenesis associated 1	protein-coding
mm_114889.1	chr13	94358944	94359055	+	1	NA	promoter-TSS (NM_009680)	promoter-TSS (NM_009680)	39	NM_009680	11774	Mm.21185	NM_009680	ENSMUSG00000021686	Ap3b1	AP-3|AU015684|C78395|Hps2|beta3A|pe|pearl|rim2	adaptor-related protein complex 3, beta 1 subunit	protein-coding
mm_38771.1	chr4	147932770	147932788	-	1	NA	exon (NM_011122, exon 2 of 19)	exon (NM_011122, exon 2 of 19)	3997	NM_011122	18822	Mm.23951	NM_011122	ENSMUSG00000019055	Plod1	2410042F05Rik|AI854890|AV007929|Lh1|Plod	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1	protein-coding
mm_81163.1	chr9	107298629	107298636	+	1	NA	intron (NM_001317354, intron 1 of 1)	intron (NM_001317354, intron 1 of 1)	1973	NM_009895	12700	Mm.4592	NM_009895	ENSMUSG00000032578	Cish	CIS-1|CIS1|Cis|F17|F23|SOCS	cytokine inducible SH2-containing protein	protein-coding
mm_64877.1	chr7	14446510	14446516	-	1	NA	promoter-TSS (NM_175250)	promoter-TSS (NM_175250)	74	NM_175250	76971	Mm.290727	NM_175250	ENSMUSG00000030378	Sult2a8	2810007J24Rik	sulfotransferase family 2A, dehydroepiandrosterone (DHEA)-preferring, member 8	protein-coding
mm_52217.1	chr6	103510836	103510867	+	1	NA	promoter-TSS (NM_007697)	promoter-TSS (NM_007697)	-25	NM_007697	12661	Mm.251288	NM_007697	ENSMUSG00000030077	Chl1	A530023M13Rik|AI465420|CALL|LICAM2	cell adhesion molecule L1-like	protein-coding
mm_153517.1	chr19	41665989	41666017	-	1	NA	intron (NM_015748, intron 4 of 36)	intron (NM_015748, intron 4 of 36)	77352	NR_106166	102465884		NR_106166	ENSMUSG00000098286	Mir8091	Gm27575|mmu-mir-8091	microRNA 8091	ncRNA
mm_126955.1	chr15	92161465	92161482	+	1	NA	5' UTR (NM_001159647, exon 1 of 24)	5' UTR (NM_001159647, exon 1 of 24)	116	NM_001159647	12805	Mm.4911	NM_007727	ENSMUSG00000055022	Cntn1	AW495098|CNTN|F3cam|usl	contactin 1	protein-coding
mm_40720.1	chr5	65955698	65955704	+	1	NA	Intergenic	Intergenic	-11423	NM_001081104	231252	Mm.140015	NM_001081104	ENSMUSG00000029205	Chrna9	2410015I05Rik|Acra9|EG666827|Gm8311	cholinergic receptor, nicotinic, alpha polypeptide 9	protein-coding
mm_94117.1	chr10	128626697	128626715	-	1	NA	promoter-TSS (NM_013765)	promoter-TSS (NM_013765)	-200	NM_013765	27370	Mm.32118	NM_013765	ENSMUSG00000025362	Rps26	-	ribosomal protein S26	protein-coding
mm_40216.1	chr5	37091075	37091085	+	1	NA	intron (NM_001347348, intron 1 of 20)	intron (NM_001347348, intron 1 of 20)	5844	NM_001347348	76071	Mm.85280	NM_178394	ENSMUSG00000063646	Jakmip1	5830437M04Rik|C330021K24Rik|Gababrbp|Marlin-1	janus kinase and microtubule interacting protein 1	protein-coding
mm_53816.1	chr6	147042756	147042797	+	1	NA	promoter-TSS (NM_145573)	promoter-TSS (NM_145573)	6	NM_145573	232536	Mm.46656	NM_145573	ENSMUSG00000040112	Mrps35	MDSO23|MRP-S28|MRPS28	mitochondrial ribosomal protein S35	protein-coding
mm_21993.1	chr2	167644172	167644184	-	1	NA	exon (NM_145538, exon 6 of 6)	exon (NM_145538, exon 6 of 6)	-12173	NM_023230	66589	Mm.278783	NM_023230	ENSMUSG00000078923	Ube2v1	0610011J09Rik|AI256840|CROC-1|CROC1|D7Bwg1382e|UEV-1	ubiquitin-conjugating enzyme E2 variant 1	protein-coding
mm_44532.1	chr5	24447776	24447830	-	1	NA	promoter-TSS (NM_022418)	promoter-TSS (NM_022418)	43	NM_022418	64295	Mm.150098	NM_022418	ENSMUSG00000028958	Tmub1	2010004O20Rik|AB030183|Hops	transmembrane and ubiquitin-like domain containing 1	protein-coding
mm_46428.1	chr5	104440422	104440448	-	1	NA	exon (NM_001204203, exon 7 of 7)	exon (NM_001204203, exon 7 of 7)	4243	NM_001204233	20750	Mm.288474	NM_009263	ENSMUSG00000029304	Spp1	2AR|Apl-1|BNSP|BSPI|Bsp|ETA-1|Eta|OP|Opn|Opnl|Ric|Spp-1	secreted phosphoprotein 1	protein-coding
mm_138184.1	chr17	34267968	34267974	+	1	NA	exon (NM_207105, exon 4 of 6)	exon (NM_207105, exon 4 of 6)	4744	NM_207105	14961	Mm.254067	NM_207105	ENSMUSG00000073421	H2-Ab1	AI845868|Abeta|H-2Ab|H2-Ab|I-Abeta|IAb|Ia-2|Ia2|Rmcs1	histocompatibility 2, class II antigen A, beta 1	protein-coding
mm_165380.1	chr2	128751902	128751934	+	1	NA	exon (NM_008587, exon 6 of 19)	exon (NM_008587, exon 6 of 19)	52921	NM_008587	17289	Mm.239655	NM_008587	ENSMUSG00000014361	Mertk	Eyk|Mer|Nyk|nmf12	c-mer proto-oncogene tyrosine kinase	protein-coding
mm_94736.1	chr11	21091136	21091156	+	1	NA	promoter-TSS (NM_023324)	promoter-TSS (NM_023324)	-178	NM_023324	67245	Mm.28957	NM_023324	ENSMUSG00000020134	Peli1	2810468L03Rik|A930031K15Rik|AA409794|AI586297|D11Ertd676e	pellino 1	protein-coding
mm_144441.1	chr18	21653322	21653331	+	1	NA	promoter-TSS (NM_001081403)	promoter-TSS (NM_001081403)	-958	NM_001081403	225266	Mm.436836	NM_001081403	ENSMUSG00000042514	Klhl14	6330403N15Rik|AI785250|printor	kelch-like 14	protein-coding
mm_17302.1	chr2	26300192	26300206	-	1	NA	Intergenic	Intergenic	-5642	NM_177841	329366	Mm.77712	NM_177841	ENSMUSG00000048038	Ccdc187	4932418E24Rik	coiled-coil domain containing 187	protein-coding
mm_62048.1	chr7	92393410	92393413	+	1	NA	intron (NM_011807, intron 16 of 22)	intron (NM_011807, intron 16 of 22)	158441	NM_001243047	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_49266.1	chr6	17491129	17491144	+	1	NA	intron (NM_008591, intron 2 of 21)	intron (NM_008591, intron 2 of 21)	27179	NM_008591	17295	Mm.86844	NM_008591	ENSMUSG00000009376	Met	AI838057|HGF|HGFR|Par4|c-Met	met proto-oncogene	protein-coding
mm_131805.1	chr16	22899414	22899421	+	1	NA	TTS (NM_001276450)	TTS (NM_001276450)	-5031	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_49994.1	chr6	41047498	41047507	+	1	NA	Intergenic	Intergenic	-11993	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_153938.1	chr19	47464116	47464154	-	1	NA	exon (NM_008018, exon 1 of 15)	exon (NM_008018, exon 1 of 15)	276	NM_001164717	14218	Mm.127560	NM_008018	ENSMUSG00000053617	Sh3pxd2a	2310014D11Rik|AA589508|AI256723|AI413738|C230050L11|EG329070|Fish|Gm5098|Sh3md1|TSK5|Tks5	SH3 and PX domains 2A	protein-coding
mm_47422.1	chr5	123141345	123141362	-	1	NA	promoter-TSS (NM_001040398)	promoter-TSS (NM_001040398)	-840	NM_001040398	208043	Mm.250391	NM_177581	ENSMUSG00000038384	Setd1b	AA516740|BC035291|KMT2G|mKIAA1076	SET domain containing 1B	protein-coding
mm_88204.1	chr10	70175014	70175020	+	1	NA	exon (NM_001111121, exon 6 of 9)	exon (NM_001111121, exon 6 of 9)	-29647	NM_001304739	69563	Mm.64672	NM_001304739	ENSMUSG00000019933	Mrln	2310015B20Rik|Mln	myoregulin	protein-coding
mm_35438.1	chr4	38855462	38855472	-	1	NA	Intergenic	RLTR6B_Mm|LTR|ERV1	-594826	NM_001081095	75471	Mm.23522	NM_001081095	ENSMUSG00000028287	1700009N14Rik	AI429145	RIKEN cDNA 1700009N14 gene	protein-coding
mm_130863.1	chr15	102196547	102196550	-	1	NA	Intergenic	B1F|SINE|Alu	-7097	NM_001289694	68744	Mm.352945	NM_153194	ENSMUSG00000046897	Zfp740	1110034O07Rik|AW548228|Znf740	zinc finger protein 740	protein-coding
mm_145497.1	chr18	60390632	60390641	+	1	NA	exon (NM_001146275, exon 3 of 3)	exon (NM_001146275, exon 3 of 3)	14607	NM_001146275	60440	Mm.261140	NM_021792	ENSMUSG00000054072	Iigp1	2900074L10Rik|AI046432|AW111922|Ifgga1|Iigp|Irga6	interferon inducible GTPase 1	protein-coding
mm_65972.1	chr7	30440320	30440336	-	1	NA	intron (NM_007467, intron 8 of 16)	intron (NM_007467, intron 8 of 16)	5254	NM_007467	11803	Mm.2381	NM_007467	ENSMUSG00000006651	Aplp1	-	amyloid beta (A4) precursor-like protein 1	protein-coding
mm_142305.1	chr17	42742126	42742137	-	1	NA	promoter-TSS (NM_001033493)	promoter-TSS (NM_001033493)	48	NM_001033493	435529	Mm.136350	NM_001033493	ENSMUSG00000057899	Adgrf2	Gpr111|PGR20	adhesion G protein-coupled receptor F2	protein-coding
mm_124553.1	chr14	122913041	122913058	-	1	NA	intron (NM_145466, intron 1 of 2)	CpG	116	NM_145466	223267	Mm.379358	NM_145466	ENSMUSG00000041625	Ggact	A2ld1	gamma-glutamylamine cyclotransferase	protein-coding
mm_24605.1	chr3	93445592	93445635	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	3283	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_80065.1	chr9	69458626	69458669	+	1	NA	intron (NM_007585, intron 1 of 12)	intron (NM_007585, intron 1 of 12)	1703	NR_037296	100526560		NR_037296	ENSMUSG00000093042	Mir3109	mir-3109|mmu-mir-3109	microRNA 3109	ncRNA
mm_150483.1	chr19	38931389	38931400	+	1	NA	5' UTR (NM_008234, exon 2 of 22)	5' UTR (NM_008234, exon 2 of 22)	404	NM_008234	15201	Mm.57223	NM_008234	ENSMUSG00000025001	Hells	AI323785|E130115I21Rik|LSH|Lysh|PASG|YFK8	helicase, lymphoid specific	protein-coding
mm_139722.1	chr17	57476153	57476213	+	1	NA	intron (NM_010130, intron 19 of 21)	B4A|SINE|B4	69131	NM_001104591	224916	Mm.469889	NM_001104591	ENSMUSG00000090655	Vmn2r120	EG224916	vomeronasal 2, receptor 120	protein-coding
mm_124194.1	chr14	98159781	98159795	-	1	NA	intron (NM_007826, intron 1 of 11)	intron (NM_007826, intron 1 of 11)	9977	NM_001038610	13134	Mm.320593	NM_007826	ENSMUSG00000055639	Dach1	Dac|Dach	dachshund 1 (Drosophila)	protein-coding
mm_163946.1	chr14	51923095	51923099	-	1	NA	promoter-TSS (NM_001011687)	promoter-TSS (NM_001011687)	-324	NM_001011687	497071	Mm.378602	NM_001011687	ENSMUSG00000068392	Rnase13	-	ribonuclease, RNase A family, 13 (non-active)	protein-coding
mm_102161.1	chr11	53763907	53763916	-	1	NA	promoter-TSS (NR_106131)	promoter-TSS (NR_106131)	-257	NR_106131	102465772		NR_106131	ENSMUSG00000099153	Mir7671	Gm27802|mmu-mir-7671	microRNA 7671	ncRNA
mm_94245.1	chr11	3330522	3330541	+	1	NA	promoter-TSS (NM_178149)	promoter-TSS (NM_178149)	-200	NM_178149	216505	Mm.390323	NM_178149	ENSMUSG00000034614	Pik3ip1	1500004A08Rik|5830455E04Rik|Crkd|Hgfl	phosphoinositide-3-kinase interacting protein 1	protein-coding
mm_148110.1	chr18	74215697	74215699	-	1	NA	promoter-TSS (NM_028868)	promoter-TSS (NM_028868)	-514	NM_028868	74322	Mm.17537	NM_028868	ENSMUSG00000024560	Cxxc1	2410002I16Rik|5830420C16Rik|AI426635|Cfp1|Cgbp|PHF18	CXXC finger 1 (PHD domain)	protein-coding
mm_131997.1	chr16	25286811	25286826	+	1	NA	promoter-TSS (NM_175165)	promoter-TSS (NM_175165)	1	NM_175165	71338	Mm.126851	NM_175165	ENSMUSG00000048399	Tprg	5430420C16Rik|Tprg1	transformation related protein 63 regulated	protein-coding
mm_18982.1	chr2	76851716	76851753	-	1	NA	exon (NM_011652, exon 132 of 313)	exon (NM_011652, exon 132 of 313)	130813	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_109340.1	chr12	109590901	109590918	+	1	NA	promoter-TSS (NR_029952)	promoter-TSS (NR_029952)	462	NR_029951	723866		NR_029951	ENSMUSG00000070080	Mir431	Mirn431|mir-431|mmu-mir-431	microRNA 431	ncRNA
mm_20367.1	chr2	128406637	128406640	-	1	NA	intron (NR_028591, intron 1 of 1)	RSINE1|SINE|B4	22713	NR_028591	100043424	Mm.297222	NR_028589		Gm14005	OTTMUSG00000015351	predicted gene 14005	ncRNA
mm_14377.1	chr2	129630588	129630600	+	1	NA	3' UTR (NM_001291022, exon 5 of 5)	3' UTR (NM_001291022, exon 5 of 5)	37425	NM_001291022	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_57538.1	chr6	126644576	126644591	-	1	NA	5' UTR (NM_010595, exon 1 of 2)	5' UTR (NM_010595, exon 1 of 2)	1218	NM_010595	16485	Mm.40424	NM_010595	ENSMUSG00000047976	Kcna1	AI840627|Kca1-1|Kv1.1|MBK1|Mk-1|Shak|mceph	potassium voltage-gated channel, shaker-related subfamily, member 1	protein-coding
mm_163093.1	chr11	69734799	69734826	-	1	NA	exon (NM_001291068, exon 29 of 29)	exon (NM_001291068, exon 29 of 29)	23821	NM_001291068	20020	Mm.16533	NM_009089	ENSMUSG00000005198	Polr2a	220kDa|Rpb1|Rpo2-1	polymerase (RNA) II (DNA directed) polypeptide A	protein-coding
mm_124129.1	chr14	82142531	82142572	-	1	NA	Intergenic	Intergenic	2142249	NM_001030294	380924	Mm.26456	NM_001030294	ENSMUSG00000022026	Olfm4	GC1|GW112|Gm296|Gm913|OlfD|pPD4	olfactomedin 4	protein-coding
mm_89314.1	chr10	87926397	87926405	+	1	NA	intron (NM_001111274, intron 4 of 4)	intron (NM_001111274, intron 4 of 4)	-40270	NR_000040	22172	Mm.391420	NR_000040		Tyms-ps	-	thymidylate synthase, pseudogene	pseudo
mm_163456.1	chr12	96047197	96047199	-	1	NA	promoter-TSS (NR_103800)	promoter-TSS (NR_103800)	24	NR_103800	69423	Mm.46121	NM_027076		1700019M22Rik	-	NFX-like protein	pseudo
mm_34266.1	chr4	141421842	141421882	+	1	NA	exon (NM_013868, exon 1 of 3)	exon (NM_013868, exon 1 of 3)	1083	NM_013868	29818	Mm.46181	NM_013868	ENSMUSG00000006221	Hspb7	27kDa|Hsp25-2|cvHsp	heat shock protein family, member 7 (cardiovascular)	protein-coding
mm_91828.1	chr10	56389551	56389580	-	1	NA	3' UTR (NM_010288, exon 2 of 2)	3' UTR (NM_010288, exon 2 of 2)	12265	NM_010288	14609	Mm.378921	NM_010288	ENSMUSG00000050953	Gja1	AU042049|AW546267|Cnx43|Cx43|Cx43alpha1|Gja-1|Npm1|connexin43	gap junction protein, alpha 1	protein-coding
mm_46941.1	chr5	114823462	114823475	-	1	NA	promoter-TSS (NM_181075)	promoter-TSS (NM_181075)	0	NM_181075	330173	Mm.482205	NM_181075	ENSMUSG00000092486	2610524H06Rik	-	RIKEN cDNA 2610524H06 gene	protein-coding
mm_72311.1	chr8	77723638	77723681	+	1	NA	intron (NM_010332, intron 1 of 7)	intron (NM_010332, intron 1 of 7)	793	NM_010332	13617	Mm.283168	NM_010332	ENSMUSG00000031616	Ednra	ET-AR|ETa|Gpcr10	endothelin receptor type A	protein-coding
mm_100862.1	chr11	5896665	5896691	-	1	NA	TTS (NM_022879)	TTS (NM_022879)	2104	NM_022879	17898	Mm.46514	NM_022879	ENSMUSG00000020469	Myl7	MLC-2alpha|MLC2a|MYL2A|Mylc2a|RLC-A	myosin, light polypeptide 7, regulatory	protein-coding
mm_78025.1	chr9	13765948	13765968	+	1	NA	intron (NR_024025, intron 1 of 15)	intron (NR_024025, intron 1 of 15)	16777	NR_024025	77116	Mm.210405	NM_023858	ENSMUSG00000031918	Mtmr2	6030445P13Rik	myotubularin related protein 2	protein-coding
mm_135415.1	chr16	45158274	45158286	-	1	NA	promoter-TSS (NM_026402)	promoter-TSS (NM_026402)	393	NM_028756	74102	Mm.264984	NM_028756	ENSMUSG00000022664	Slc35a5	1010001J06Rik|AU021179|BB097433|D16Ertd450e|D730043G07Rik	solute carrier family 35, member A5	protein-coding
mm_61096.1	chr7	51879007	51879024	+	1	NA	promoter-TSS (NM_001330607)	promoter-TSS (NM_001330607)	48	NM_001330607	14453	Mm.207360	NM_008087	ENSMUSG00000030498	Gas2	Gas-2	growth arrest specific 2	protein-coding
mm_60765.1	chr7	45549874	45549899	+	1	NA	exon (NM_148927, exon 17 of 20)	exon (NM_148927, exon 17 of 20)	-5042	NM_025330	66065	Mm.285710	NM_025330	ENSMUSG00000030825	Hsd17b14	0610039E24Rik|Dhrs10|retSDR3	hydroxysteroid (17-beta) dehydrogenase 14	protein-coding
mm_80785.1	chr9	95857945	95857951	+	1	NA	promoter-TSS (NM_001271569)	promoter-TSS (NM_001271569)	-66	NM_001271569	73410	Mm.443314	NM_028533	ENSMUSG00000096655	1700065D16Rik	-	RIKEN cDNA 1700065D16 gene	protein-coding
mm_44429.1	chr5	20951770	20951824	-	1	NA	promoter-TSS (NM_001080977)	promoter-TSS (NM_001080977)	25	NM_001080977	242860	Mm.254286	NM_001080977	ENSMUSG00000039968	Rsbn1l	8430412F05Rik|AI447441|C330002G24Rik	round spermatid basic protein 1-like	protein-coding
mm_156000.1	chrX	106187201	106187212	+	1	NA	5' UTR (NM_008828, exon 1 of 11)	5' UTR (NM_008828, exon 1 of 11)	106	NM_008828	18655	Mm.316355	NM_008828	ENSMUSG00000062070	Pgk1	Pgk-1	phosphoglycerate kinase 1	protein-coding
mm_11323.1	chr2	30416081	30416090	+	1	NA	promoter-TSS (NM_007760)	promoter-TSS (NM_007760)	35	NM_138748	110854	Mm.275393	NM_138748	ENSMUSG00000039515	Ptpa	2610042B21Rik|C77440|N28142|PR53|Ppp2r4	protein phosphatase 2 protein activator	protein-coding
mm_4701.1	chr1	180849221	180849228	+	1	NA	Intergenic	Intergenic	-1927	NM_145943	208768	Mm.272625	NM_145943	ENSMUSG00000038806	Sde2	-	SDE2 telomere maintenance homolog (S. pombe)	protein-coding
mm_146343.1	chr18	82475999	82476054	+	1	NA	intron (NM_001025245, intron 1 of 3)	intron (NM_001025245, intron 1 of 3)	903	NM_001025245	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_80716.1	chr9	92275773	92275785	+	1	NA	5' UTR (NM_001195084, exon 1 of 8)	5' UTR (NM_001195084, exon 1 of 8)	177	NM_001195084	18828	Mm.10306	NM_008880	ENSMUSG00000032372	Plscr2	-	phospholipid scramblase 2	protein-coding
mm_121952.1	chr14	24369782	24369793	-	1	NA	Intergenic	Intergenic	76423	NM_001033214	105418	Mm.2077	NM_001033214	ENSMUSG00000038925	E330034G19Rik	AA415275|Zpac	RIKEN cDNA E330034G19 gene	protein-coding
mm_135409.1	chr16	44774365	44774376	-	1	NA	intron (NM_021325, intron 1 of 6)	intron (NM_021325, intron 1 of 6)	8634	NM_021325	57781	Mm.416152	NM_021325	ENSMUSG00000022667	Cd200r1	CD200R|Mox2r|OX2R	CD200 receptor 1	protein-coding
mm_145719.1	chr18	63150836	63150841	+	1	NA	intron (NM_001039485, intron 5 of 53)	intron (NM_001039485, intron 5 of 53)	172922	NM_028017	108123	Mm.292687	NM_028017	ENSMUSG00000024581	Napg	2400003O04Rik|SNARE	N-ethylmaleimide sensitive fusion protein attachment protein gamma	protein-coding
mm_3672.1	chr1	153665588	153665595	+	1	NA	promoter-TSS (NM_001347115)	promoter-TSS (NM_001347115)	-82	NM_001347115	67792	Mm.379143	NM_026380	ENSMUSG00000042671	Rgs8	6530413N01Rik	regulator of G-protein signaling 8	protein-coding
mm_120668.1	chr14	70552240	70552252	+	1	NA	Intergenic	Intergenic	-1810	NM_021877	15460	Mm.7598	NM_021877	ENSMUSG00000022096	Hr	ALUNC|AU|N|ba|bldy|hr|rh|rh-bmh|rhino	hairless	protein-coding
mm_146518.1	chr18	4239249	4239254	-	1	NA	Intergenic	Intergenic	73419	NM_026092	67328	Mm.158148	NM_026092	ENSMUSG00000024233	Lyzl1	1700038F02Rik|Lyc2|Lyzd1	lysozyme-like 1	protein-coding
mm_145326.1	chr18	55042167	55042172	+	1	NA	Intergenic	RLTR20A4|LTR|ERVK	-51989	NM_175751	269023	Mm.192984	NM_175751	ENSMUSG00000052713	Zfp608	4932417D18Rik|D430007A19Rik|Znf608	zinc finger protein 608	protein-coding
mm_45200.1	chr5	52566221	52566262	-	1	NA	promoter-TSS (NM_144945)	promoter-TSS (NM_144945)	65	NM_001310604	246316	Mm.44721	NM_144945	ENSMUSG00000039252	Lgi2	mKIAA1916	leucine-rich repeat LGI family, member 2	protein-coding
mm_156797.1	chrX	162901695	162901733	+	1	NA	promoter-TSS (NR_033143)	promoter-TSS (NR_033143)	119	NM_018737	55936	Mm.2065	NM_018737	ENSMUSG00000031360	Ctps2	A830031M15Rik|AI326475|Ctpsh	cytidine 5'-triphosphate synthase 2	protein-coding
mm_97683.1	chr11	80012683	80012689	+	1	NA	intron (NM_199196, intron 6 of 15)	ID4_|SINE|ID	19580	NM_199196	52615	Mm.283410	NM_199196	ENSMUSG00000017548	Suz12	2610028O16Rik|AI195385|AU016842|AW536442|D11Ertd530e|mKIAA0160	suppressor of zeste 12 homolog (Drosophila)	protein-coding
mm_71332.1	chr8	45051557	45051657	+	1	NA	3' UTR (NM_001081286, exon 26 of 26)	3' UTR (NM_001081286, exon 26 of 26)	13811	NR_033588	434310	Mm.334512	NR_033588	ENSMUSG00000066158	AY512931	-	cDNA sequence AY512931	ncRNA
mm_137265.1	chr17	24669731	24669752	+	1	NA	promoter-TSS (NM_183149)	promoter-TSS (NM_183149)	-11	NM_183149	213753	Mm.219581	NM_183149	ENSMUSG00000041130	Zfp598	BC023040|Ntrap|Znf598	zinc finger protein 598	protein-coding
mm_101613.1	chr11	35833262	35833307	-	1	NA	exon (NM_025936, exon 2 of 15)	exon (NM_025936, exon 2 of 15)	1244	NM_025936	104458	Mm.284906	NM_025936	ENSMUSG00000018848	Rars	2610011N19Rik|2610037E21Rik|AL033339|AW985894	arginyl-tRNA synthetase	protein-coding
mm_73299.1	chr8	105083754	105083757	+	1	NA	promoter-TSS (NM_001159415)	promoter-TSS (NM_001159415)	0	NM_144511	13909	Mm.482444	NM_144511	ENSMUSG00000062181	Ces3b	Ces31L|Ces3L|EG13909|ES31L|Es31|Gm4738	carboxylesterase 3B	protein-coding
mm_20590.1	chr2	131164115	131164126	-	1	NA	intron (NR_037281, intron 2 of 2)	MLT2F|LTR|ERVL	-4039	NM_001311138	67326	Mm.27711	NM_026091	ENSMUSG00000027327	1700037H04Rik	-	RIKEN cDNA 1700037H04 gene	protein-coding
mm_47649.1	chr5	125390102	125390114	-	1	NA	promoter-TSS (NM_019639)	promoter-TSS (NM_019639)	-91	NM_019639	22190	Mm.331	NM_019639	ENSMUSG00000008348	Ubc	2700054O04Rik|AI194771|Rps27a|TI-225|Uba52|Ubb	ubiquitin C	protein-coding
mm_121615.1	chr14	8259263	8259283	-	1	NA	promoter-TSS (NM_053115)	promoter-TSS (NM_053115)	-254	NM_053115	93732	Mm.28700	NM_053115	ENSMUSG00000021751	Acox2	THCCox	acyl-Coenzyme A oxidase 2, branched chain	protein-coding
mm_101029.1	chr11	8579812	8579820	-	1	NA	intron (NM_001083587, intron 3 of 30)	intron (NM_001083587, intron 3 of 30)	84719	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_85566.1	chr9	106979959	106979961	-	1	NA	intron (NM_153413, intron 22 of 52)	intron (NM_153413, intron 22 of 52)	-88022	NM_029103	74840	Mm.29778	NM_029103	ENSMUSG00000032575	Manf	3230402M22Rik|AA407711|AA408789|AA673178|Armet|D17914|D18Mgi17	mesencephalic astrocyte-derived neurotrophic factor	protein-coding
mm_2433.1	chr1	96872226	96872253	+	1	NA	promoter-TSS (NM_172658)	promoter-TSS (NM_172658)	-68	NM_172658	227394	Mm.11662	NM_172658	ENSMUSG00000040693	Slco4c1	9530051F04|C330017E21Rik|OATP-H|OATP-M1|OATP4C1|OATPX|PRO2176|SLC21A20|oatp-R	solute carrier organic anion transporter family, member 4C1	protein-coding
mm_31686.1	chr4	62298216	62298235	+	1	NA	3' UTR (NM_025286, exon 4 of 4)	3' UTR (NM_025286, exon 4 of 4)	6678	NM_001290518	20530	Mm.292539	NM_025286	ENSMUSG00000066152	Slc31a2	AI604396|CTR2	solute carrier family 31, member 2	protein-coding
mm_82758.1	chr9	26861957	26861972	-	1	NA	Intergenic	Intergenic	-1141	NM_001113323	70893	Mm.78118	NM_001113323	ENSMUSG00000031966	Glb1l3	4921509F24Rik	galactosidase, beta 1 like 3	protein-coding
mm_130812.1	chr15	101734486	101734495	-	1	NA	3' UTR (NM_019956, exon 9 of 9)	3' UTR (NM_019956, exon 9 of 9)	8607	NM_019956	56735	Mm.358677	NM_019956	ENSMUSG00000051879	Krt71	AA589543|Ca|Cal4|Cu|Krt2-6g|mK6irs|mK6irs1	keratin 71	protein-coding
mm_110607.1	chr12	56536714	56536730	-	1	NA	5' UTR (NM_009385, exon 1 of 3)	5' UTR (NM_009385, exon 1 of 3)	186	NM_009385	21869	Mm.89972	NM_009385	ENSMUSG00000001496	Nkx2-1	AV026640|Nkx2.1|T/EBP|Titf1|Ttf-1	NK2 homeobox 1	protein-coding
mm_3260.1	chr1	136259433	136259462	+	1	NA	3' UTR (NM_001101516, exon 1 of 1)	3' UTR (NM_001101516, exon 1 of 1)	1426	NM_001101516	383563	Mm.40367	NM_001101516	ENSMUSG00000052759	Gpr25	Gm1300	G protein-coupled receptor 25	protein-coding
mm_39948.1	chr5	31912343	31912356	+	1	NA	intron (NM_144541, intron 7 of 11)	L1MC3|LINE|L1	214299	NM_144541	107976	Mm.482126	NM_144541	ENSMUSG00000052139	Bre	6030405P19Rik|AI429776|B830038C02Rik	brain and reproductive organ-expressed protein	protein-coding
mm_50035.1	chr6	41137329	41137352	+	1	NA	Intergenic	B4|SINE|B4	-101831	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_56671.1	chr6	113654919	113654924	-	1	NA	intron (NM_001113553, intron 2 of 11)	B1F|SINE|Alu	16454	NM_001113553	108960	Mm.152142	NM_172161	ENSMUSG00000060477	Irak2	6330415L08Rik|AI649099|IRAK-2	interleukin-1 receptor-associated kinase 2	protein-coding
mm_161867.1	chr18	35721565	35721565	-	1	NA	promoter-TSS (NM_001033141)	promoter-TSS (NM_001033141)	-74	NM_001033141	68545	Mm.329362	NM_001033141	ENSMUSG00000073599	Ecscr	1110006O17Rik|ARIA	endothelial cell surface expressed chemotaxis and apoptosis regulator	protein-coding
mm_170577.1	chr19	5490509	5490509	+	1	NA	promoter-TSS (NM_007687)	promoter-TSS (NM_007687)	54	NM_007687	12631	Mm.329655	NM_007687	ENSMUSG00000056201	Cfl1	AA959946|Cof	cofilin 1, non-muscle	protein-coding
mm_54304.1	chr6	29526533	29526554	-	1	NA	promoter-TSS (NM_012057)	promoter-TSS (NM_012057)	-82	NM_001311083	27056	Mm.6479	NM_012057	ENSMUSG00000029771	Irf5	AW491843|mirf5	interferon regulatory factor 5	protein-coding
mm_131489.1	chr16	17253116	17253134	+	1	NA	intron (NM_178922, intron 1 of 2)	intron (NM_178922, intron 1 of 2)	19538	NM_178922	58180	Mm.261602	NM_178922	ENSMUSG00000050240	Hic2	AA409108|HRG22|mKIAA1020	hypermethylated in cancer 2	protein-coding
mm_160889.1	chr11	70054828	70054828	+	1	NA	intron (NM_001291132, intron 1 of 7)	intron (NM_001291132, intron 1 of 7)	473	NM_001291132	11889	Mm.6559	NM_009714	ENSMUSG00000020884	Asgr1	ASGPR1|Asgr|Asgr-1|HL-1	asialoglycoprotein receptor 1	protein-coding
mm_4224.1	chr1	171331415	171331418	+	1	NA	intron (NM_001128609, intron 2 of 5)	intron (NM_001128609, intron 2 of 5)	2271	NM_011615	21945	Mm.270139	NM_011615	ENSMUSG00000013973	Dedd	CASP8IP1|DEFT|Dedpro1|FLDED1|KE05	death effector domain-containing	protein-coding
mm_42916.1	chr5	122707547	122707627	+	1	NA	promoter-TSS (NM_011026)	promoter-TSS (NM_011026)	43	NM_001310718	18438	Mm.290884	NM_011026	ENSMUSG00000029470	P2rx4	AI504491|AW555605|D5Ertd444e|P2X4	purinergic receptor P2X, ligand-gated ion channel 4	protein-coding
mm_84268.1	chr9	62666071	62666077	-	1	NA	Intergenic	Intergenic	-11781	NM_176922	319480	Mm.34883	NM_176922	ENSMUSG00000032243	Itga11	4732459H24Rik	integrin alpha 11	protein-coding
mm_161916.1	chr18	67549221	67549221	-	1	NA	promoter-TSS (NM_176832)	promoter-TSS (NM_176832)	-48	NM_176832	68166	Mm.208723	NM_176832	ENSMUSG00000024533	Spire1	6030430B19Rik|AI415299|AU022898|AW550622|Spir-1	spire homolog 1 (Drosophila)	protein-coding
mm_41628.1	chr5	96996021	96996033	+	1	NA	Intergenic	Intergenic	-1662	NM_080708	140780	Mm.281490	NM_080708	ENSMUSG00000034663	Bmp2k	4933417M22Rik|AA673486|AV128808|BIKE	BMP2 inducible kinase	protein-coding
mm_162915.1	chr10	119992912	119992912	+	1	NA	promoter-TSS (NM_001277295)	promoter-TSS (NM_001277295)	-10	NM_001277295	74053	Mm.196692	NM_028736	ENSMUSG00000034813	Grip1	4931400F03Rik|GRIP|eb	glutamate receptor interacting protein 1	protein-coding
mm_16925.1	chr2	13582633	13582686	-	1	NA	3' UTR (NM_011701, exon 9 of 9)	3' UTR (NM_011701, exon 9 of 9)	8348	NM_011701	22352	Mm.268000	NM_011701	ENSMUSG00000026728	Vim	-	vimentin	protein-coding
mm_121319.1	chr14	111675114	111675119	+	1	NA	promoter-TSS (NM_198865)	promoter-TSS (NM_198865)	1	NM_198865	75409	Mm.235097	NM_029273	ENSMUSG00000033214	Slitrk5	2610019D03Rik	SLIT and NTRK-like family, member 5	protein-coding
mm_58725.1	chr7	13025654	13025680	+	1	NA	exon (NM_011588, exon 3 of 17)	exon (NM_011588, exon 3 of 17)	1515	NM_011588	21849	Mm.15701	NM_011588	ENSMUSG00000005566	Trim28	AA408787|KAP-1|KRIP-1|MommeD9|Tif1b|Tif1beta	tripartite motif-containing 28	protein-coding
mm_159960.1	chr6	88724870	88724870	+	1	NA	5' UTR (NM_001166251, exon 1 of 8)	5' UTR (NM_001166251, exon 1 of 8)	166	NM_001166251	23945	Mm.272197	NM_011844	ENSMUSG00000033174	Mgll	AA589436|Magl|Mgl	monoglyceride lipase	protein-coding
mm_116495.1	chr13	44869719	44869729	-	1	NA	intron (NM_001205044, intron 4 of 18)	LSU-rRNA_Hsa|rRNA|rRNA	132372	NM_025772	94245	Mm.352311	NM_025772	ENSMUSG00000057531	Dtnbp1	5430437B18Rik|AW048963|Bloc1s8|dysbindin|sdy	dystrobrevin binding protein 1	protein-coding
mm_49611.1	chr6	30747320	30747333	+	1	NA	TTS (NM_017478)	TTS (NM_017478)	6027	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_112451.1	chr13	5862858	5862872	+	1	NA	intron (NM_011803, intron 1 of 3)	intron (NM_011803, intron 1 of 3)	1376	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_80744.1	chr9	94772825	94772829	+	1	NA	intron (NM_177909, intron 4 of 15)	intron (NM_177909, intron 4 of 15)	20998	NR_106116	102465763		NR_106116	ENSMUSG00000098251	Mir7656	Gm27614|mmu-mir-7656	microRNA 7656	ncRNA
mm_34430.1	chr4	145585190	145585211	+	1	NA	promoter-TSS (NM_001324416)	promoter-TSS (NM_001324416)	0	NM_001324416	433801	Mm.276881	NM_001013808	ENSMUSG00000078502	Gm13212	OTTMUSG00000010965	predicted gene 13212	protein-coding
mm_173233.1	chrX	80456684	80456697	+	1	NA	Intergenic	Intergenic	-613954	NM_138751	192216	Mm.490421	NM_138751	ENSMUSG00000025666	Tmem47	3010015F07Rik|AI115536|BCMP1|Tm4sf10	transmembrane protein 47	protein-coding
mm_60283.1	chr7	43975964	43975976	+	1	NA	promoter-TSS (NM_010116)	promoter-TSS (NM_010116)	-91	NM_010116	13648	Mm.440884	NM_010116	ENSMUSG00000059042	Klk1b9	EGF-BP C|Egfbp-3|Egfbp3|KAL|Klk9|kallikrein|mGk-9	kallikrein 1-related peptidase b9	protein-coding
mm_101291.1	chr11	22007433	22007452	-	1	NA	intron (NM_001252515, intron 23 of 24)	intron (NM_001252515, intron 23 of 24)	-5791	NM_011023	18423	Mm.129663	NM_011023	ENSMUSG00000005917	Otx1	A730044F23Rik|jv	orthodenticle homeobox 1	protein-coding
mm_142170.1	chr17	36190122	36190158	-	1	NA	promoter-TSS (NM_008208)	promoter-TSS (NM_008208)	11	NM_008208	15043	Mm.426002	NM_008208	ENSMUSG00000054128	H2-T3	H-2T3|H2-Tw3|MumuTL|TL	histocompatibility 2, T region locus 3	protein-coding
mm_145765.1	chr18	65008025	65008043	+	1	NA	intron (NM_001114386, intron 2 of 30)	intron (NM_001114386, intron 2 of 30)	-15493	NM_031881	83814	Mm.98668	NM_031881	ENSMUSG00000024589	Nedd4l	1300012C07Rik|Nedd4-2|Nedd4b	neural precursor cell expressed, developmentally down-regulated gene 4-like	protein-coding
mm_111342.1	chr12	86884757	86884806	-	1	NA	promoter-TSS (NM_145836)	promoter-TSS (NM_145836)	33	NM_145836	238330	Mm.248358	NM_145836	ENSMUSG00000034168	Irf2bpl	6430527G18Rik|Eap1	interferon regulatory factor 2 binding protein-like	protein-coding
mm_10586.1	chr2	18186771	18186805	+	1	NA	intron (NR_045539, intron 16 of 24)	B3A|SINE|B2	122203	NM_001252561	17354	Mm.209175	NM_010804	ENSMUSG00000026743	Mllt10	Af10|B130021D15Rik|D630001B22Rik|mKIAA4140	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 10	protein-coding
mm_124692.1	chr15	6435675	6435683	+	1	NA	exon (NM_001102400, exon 10 of 13)	exon (NM_001102400, exon 10 of 13)	-9654	NM_013485	12279	Mm.29095	NM_013485	ENSMUSG00000022149	C9	-	complement component 9	protein-coding
mm_31706.1	chr4	62615272	62615286	+	1	NA	intron (NM_019492, intron 7 of 19)	intron (NM_019492, intron 7 of 19)	-4393	NM_001081650	50780	Mm.286753	NM_019492	ENSMUSG00000059810	Rgs3	4930506N09Rik|C2PA-RGS3|C2pa|PDZ-RGS3|RGS3S	regulator of G-protein signaling 3	protein-coding
mm_12962.1	chr2	90579487	90579498	+	1	NA	intron (NM_008982, intron 1 of 23)	intron (NM_008982, intron 1 of 23)	1155	NM_008982	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_54722.1	chr6	40436090	40436101	-	1	NA	promoter-TSS (NM_175528)	promoter-TSS (NM_175528)	38	NM_175528	243780	Mm.333006	NM_175528	ENSMUSG00000037172	E330009J07Rik	AI841796|Lchn|mKIAA1147	RIKEN cDNA E330009J07 gene	protein-coding
mm_119508.1	chr14	47384592	47384613	+	1	NA	exon (NM_010705, exon 5 of 6)	exon (NM_010705, exon 5 of 6)	10742	NM_001145953	16854	Mm.248615	NM_010705	ENSMUSG00000050335	Lgals3	GBP|L-34|Mac-2|gal3	lectin, galactose binding, soluble 3	protein-coding
mm_131162.1	chr16	6996618	6996629	+	1	NA	intron (NM_021477, intron 5 of 16)	intron (NM_021477, intron 5 of 16)	-73212	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_148430.1	chr19	3941920	3941928	+	1	NA	exon (NM_019449, exon 5 of 11)	exon (NM_019449, exon 5 of 11)	6738	NM_001161428	54445	Mm.262094	NM_019449	ENSMUSG00000036908	Unc93b1	Unc-93B1|Unc93b	unc-93 homolog B1 (C. elegans)	protein-coding
mm_111242.1	chr12	84785488	84785518	-	1	NA	intron (NM_013589, intron 32 of 34)	intron (NM_013589, intron 32 of 34)	12233	NM_028863	74316	Mm.25719	NM_028863	ENSMUSG00000021241	Isca2	0710001C05Rik|5730594E03Rik|Hbld1	iron-sulfur cluster assembly 2	protein-coding
mm_75397.1	chr8	46163536	46163569	-	1	NA	Intergenic	CpG	-6004	NM_025747	66756	Mm.133623	NM_025747	ENSMUSG00000031631	Cfap97	1110068E21Rik|4933411K20Rik|AW049273|Kiaa1430|mKIAA1430	cilia and flagella associated protein 97	protein-coding
mm_163335.1	chr12	11436712	11436720	-	1	NA	promoter-TSS (NM_012038)	promoter-TSS (NM_012038)	-67	NM_012038	26950	Mm.27005	NM_012038	ENSMUSG00000054459	Vsnl1	VILIP|Vnsl1	visinin-like 1	protein-coding
mm_70735.1	chr8	18899613	18899617	+	1	NA	Intergenic	Intergenic	51256	NM_001286469	319581	Mm.111354	NM_176951	ENSMUSG00000039814	Xkr5	5430438H03Rik|XRG5	X-linked Kx blood group related 5	protein-coding
mm_91580.1	chr10	40135022	40135035	-	1	NA	intron (NM_001114332, intron 1 of 5)	ORR1F|LTR|ERVL-MaLR	7226	NM_028247	72472	Mm.186778	NM_028247	ENSMUSG00000019838	Slc16a10	2610103N14Rik|9830169E08|Mct10|PRO0813|TAT1	solute carrier family 16 (monocarboxylic acid transporters), member 10	protein-coding
mm_163356.1	chr12	26187734	26187740	+	1	NA	intron (NR_131149, intron 2 of 4)	intron (NR_131149, intron 2 of 4)	22768	NR_131149	629481	Mm.390460	NR_131149		Gm29687	-	predicted gene, 29687	ncRNA
mm_89281.1	chr10	87864723	87864861	+	1	NA	exon (NM_010512, exon 2 of 5)	exon (NM_010512, exon 2 of 5)	3681	NM_001111276	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_70883.1	chr8	25274502	25274518	+	1	NA	Intergenic	Intergenic	31760	NR_040352	74489	Mm.256468	NR_040352	ENSMUSG00000110140	5430421F17Rik	-	RIKEN cDNA 5430421F17 gene	ncRNA
mm_125522.1	chr15	57695218	57695221	+	1	NA	intron (NM_199449, intron 1 of 3)	CpG	552	NM_199449	387609	Mm.36557	NM_199449	ENSMUSG00000071757	Zhx2	Afr-1|Afr1|Raf|mKIAA0854	zinc fingers and homeoboxes 2	protein-coding
mm_28704.1	chr3	95550119	95550158	-	1	NA	exon (NM_021281, exon 7 of 8)	exon (NM_021281, exon 7 of 8)	-9539	NM_026489	67981	Mm.179050	NM_026489	ENSMUSG00000028109	Hormad1	4921522K05Rik|Nohma	HORMA domain containing 1	protein-coding
mm_43009.1	chr5	123714894	123714900	+	1	NA	intron (NM_027494, intron 3 of 13)	intron (NM_027494, intron 3 of 13)	6147	NM_027494	70650	Mm.279427	NM_027494	ENSMUSG00000029427	Zcchc8	5730565F05Rik	zinc finger, CCHC domain containing 8	protein-coding
mm_154628.1	chrX	7729874	7729896	+	1	NA	exon (NM_138602, exon 2 of 3)	exon (NM_138602, exon 2 of 3)	1314	NM_138602	54637	Mm.28850	NM_138602	ENSMUSG00000031149	Praf2	AA986329|C78013|DXImx39e|JM4|Sfc20	PRA1 domain family 2	protein-coding
mm_850.1	chr1	52008687	52008704	+	1	NA	5' UTR (NM_011487, exon 1 of 24)	5' UTR (NM_011487, exon 1 of 24)	455	NM_011487	20849	Mm.1550	NM_011487	ENSMUSG00000062939	Stat4	-	signal transducer and activator of transcription 4	protein-coding
mm_8753.1	chr1	160307466	160307482	-	1	NA	intron (NM_001038621, intron 2 of 8)	intron (NM_001038621, intron 2 of 8)	-11502	NR_035448	100316784		NR_035448	ENSMUSG00000089204	Mir1927	mmu-mir-1927	microRNA 1927	ncRNA
mm_50903.1	chr6	57581582	57581593	+	1	NA	intron (NM_025992, intron 1 of 22)	intron (NM_025992, intron 1 of 22)	595	NM_025992	67138	Mm.297393	NM_025992	ENSMUSG00000029798	Herc6	1700121D12Rik|2510038N07Rik|4930427L17Rik|AI451296|CEB1|Herc5	hect domain and RLD 6	protein-coding
mm_146956.1	chr18	32969833	32969852	-	1	NA	intron (NM_009793, intron 1 of 10)	intron (NM_009793, intron 1 of 10)	30801	NM_009793	12326	Mm.222329	NM_009793	ENSMUSG00000038128	Camk4	A430110E23Rik|AI666733|CaMKIV|CaMKIV/Gr|D18Bwg0362e	calcium/calmodulin-dependent protein kinase IV	protein-coding
mm_16646.1	chr2	6212974	6212977	-	1	NA	promoter-TSS (NM_024208)	promoter-TSS (NM_024208)	19	NM_024208	67856	Mm.38342	NM_024208	ENSMUSG00000039063	Echdc3	2310005D12Rik|AI662097	enoyl Coenzyme A hydratase domain containing 3	protein-coding
mm_157267.1	chrX	19219148	19219152	-	1	NA	Intergenic	Intergenic	-72179	NR_029807	723828		NR_029807	ENSMUSG00000065471	Mir222	Mirn222|mir-222|mmu-mir-222	microRNA 222	ncRNA
mm_76816.1	chr8	104443034	104443044	-	1	NA	promoter-TSS (NM_001013380)	promoter-TSS (NM_001013380)	8	NM_001013380	234663	Mm.289583	NM_001013380	ENSMUSG00000035770	Dync1li2	AA409702|C920003I06|Dncli2|Dnclic2|LIC2	dynein, cytoplasmic 1 light intermediate chain 2	protein-coding
mm_57525.1	chr6	126164949	126164965	-	1	NA	promoter-TSS (NM_001164035)	promoter-TSS (NM_001164035)	3	NM_001164035	18205	Mm.267570	NM_008742	ENSMUSG00000049107	Ntf3	AI316846|AI835689|HDNF|NGF-2|Nt3|Ntf-3	neurotrophin 3	protein-coding
mm_129454.1	chr15	78565945	78565957	-	1	NA	exon (NM_009008, exon 3 of 7)	exon (NM_009008, exon 3 of 7)	6832	NM_009008	19354	Mm.1972	NM_009008	ENSMUSG00000033220	Rac2	AI323801|AI452260	RAS-related C3 botulinum substrate 2	protein-coding
mm_36618.1	chr4	89310960	89311015	-	1	NA	promoter-TSS (NM_007670)	promoter-TSS (NM_007670)	45	NM_007670	12579	Mm.423094	NM_007670	ENSMUSG00000073802	Cdkn2b	AV083695|INK4b|MTS2|p15|p15(INK4b)|p15INK4b	cyclin-dependent kinase inhibitor 2B (p15, inhibits CDK4)	protein-coding
mm_134107.1	chr16	9995509	9995519	-	1	NA	Intergenic	CpG	-2981	NM_008170	14811	Mm.2953	NM_008170	ENSMUSG00000059003	Grin2a	GluN2A|NMDAR2A|NR2A	glutamate receptor, ionotropic, NMDA2A (epsilon 1)	protein-coding
mm_171187.1	chr3	42325121	42325130	-	1	NA	Intergenic	Intergenic	582507	NM_027271	73852	Mm.29006	NM_027271	ENSMUSG00000025766	D3Ertd751e	2810009O15Rik|4930415G15Rik	DNA segment, Chr 3, ERATO Doi 751, expressed	protein-coding
mm_42815.1	chr5	121848976	121848982	+	1	NA	promoter-TSS (NM_175474)	promoter-TSS (NM_175474)	-49	NM_175474	231717	Mm.12654	NM_175474	ENSMUSG00000044134	Fam109a	A230106M15Rik|AU017694|IPIP27A|Ses1	family with sequence similarity 109, member A	protein-coding
mm_73914.1	chr8	119666360	119666372	+	1	NA	promoter-TSS (NM_023395)	promoter-TSS (NM_023395)	1	NM_023395	67866	Mm.87599	NM_023395	ENSMUSG00000023336	Wfdc1	2310058A03Rik|ps20	WAP four-disulfide core domain 1	protein-coding
mm_14799.1	chr2	145886341	145886358	+	1	NA	3' UTR (NM_028724, exon 13 of 13)	3' UTR (NM_028724, exon 13 of 13)	-16892	NM_026425	67877	Mm.151168	NM_026425	ENSMUSG00000002728	Naa20	1500004D14Rik|2900026I01Rik|AU041458|D2Ertd186e|Nat5	N(alpha)-acetyltransferase 20, NatB catalytic subunit	protein-coding
mm_170124.1	chr17	39846956	39846962	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	3962	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_137290.1	chr17	24742326	24742356	+	1	NA	3' UTR (NM_001346668, exon 4 of 4)	3' UTR (NM_001346668, exon 4 of 4)	5748	NM_001346668	27361	Mm.28212	NM_013759	ENSMUSG00000075705	Msrb1	D17Wsu82e|SELX|SelR|Sepr|Sepx1	methionine sulfoxide reductase B1	protein-coding
mm_80087.1	chr9	70213212	70213214	+	1	NA	intron (NM_181072, intron 1 of 27)	B4|SINE|B4	5863	NM_181072	71602	Mm.249311	NM_181072	ENSMUSG00000032220	Myo1e	2310020N23Rik|9130023P14Rik|AA407778|myosin-1e|myr 3	myosin IE	protein-coding
mm_152476.1	chr19	11018027	11018040	-	1	NA	promoter-TSS (NM_001251849)	promoter-TSS (NM_001251849)	-70	NM_001251849	76002	Mm.139320	NM_001251849	ENSMUSG00000094584	Ms4a18	5033428B15Rik	membrane-spanning 4-domains, subfamily A, member 18	protein-coding
mm_101852.1	chr11	48866337	48866374	-	1	NA	exon (NM_008326, exon 3 of 3)	exon (NM_008326, exon 3 of 3)	4991	NM_008326	15944	Mm.29938	NM_008326	ENSMUSG00000046879	Irgm1	Ifggd3|Ifi1|Iigp3|Iipg3|Irgm|LRG-47	immunity-related GTPase family M member 1	protein-coding
mm_152849.1	chr19	24031239	24031251	-	1	NA	promoter-TSS (NM_001114174)	promoter-TSS (NM_001114174)	-226	NM_001114174	381217	Mm.426078	NM_001114174	ENSMUSG00000071604	Fam189a2	AI414343|AI666772|Gm967	family with sequence similarity 189, member A2	protein-coding
mm_80738.1	chr9	94696969	94696986	+	1	NA	intron (NM_177909, intron 2 of 15)	intron (NM_177909, intron 2 of 15)	27085	NM_177909	331004	Mm.326125	NM_177909	ENSMUSG00000031129	Slc9a9	5730527A11Rik|9930105B05|AI854429|Nhe9	solute carrier family 9 (sodium/hydrogen exchanger), member 9	protein-coding
mm_126761.1	chr15	85859657	85859679	+	1	NA	promoter-TSS (NM_013882)	promoter-TSS (NM_013882)	-39	NM_001168672	29870	Mm.20858	NM_013882	ENSMUSG00000022385	Gtse1	B99|Gtse-1	G two S phase expressed protein 1	protein-coding
mm_146259.1	chr18	77800189	77800196	+	1	NA	intron (NM_013831, intron 1 of 14)	T-rich|Low_complexity|Low_complexity	5642	NM_013831	19201	Mm.57174	NM_013831	ENSMUSG00000025429	Pstpip2	MAYP|cmo	proline-serine-threonine phosphatase-interacting protein 2	protein-coding
mm_129333.1	chr15	77815917	77815927	-	1	NA	intron (NM_022410, intron 1 of 40)	intron (NM_022410, intron 1 of 40)	26253	NM_022410	17886	Mm.29677	NM_022410	ENSMUSG00000022443	Myh9	Fltn|Myhn-1|Myhn1|NMHCIIA|NMMHC-A|NMMHC-IIA|TU72.6	myosin, heavy polypeptide 9, non-muscle	protein-coding
mm_118368.1	chr13	115529794	115529800	-	1	NA	Intergenic	Intergenic	-427833	NM_001033228	109700	Mm.317280	NM_001033228	ENSMUSG00000042284	Itga1	CD49A|E130012M19Rik|Vla1	integrin alpha 1	protein-coding
mm_95537.1	chr11	52261538	52261564	+	1	NA	exon (NM_009331, exon 3 of 10)	exon (NM_009331, exon 3 of 10)	21044	NM_009331	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_123612.1	chr14	68120489	68120499	-	1	NA	exon (NM_008691, exon 3 of 3)	exon (NM_008691, exon 3 of 3)	-3258	NR_045897	100043072	Mm.242832	NR_045897		A230070E04Rik	Gm4210	RIKEN cDNA A230070E04 gene	ncRNA
mm_166088.1	chr4	139198303	139198329	+	1	NA	intron (NM_001271405, intron 1 of 8)	intron (NM_001271405, intron 1 of 8)	4205	NM_001271405	12345	Mm.2945	NM_009798	ENSMUSG00000028745	Capzb	1700120C01Rik|AI325129|CPB1|CPB2|CPbeat2|CPbeta1|CPbeta2|Cappb1	capping protein (actin filament) muscle Z-line, beta	protein-coding
mm_89922.1	chr10	111226881	111226887	+	1	NA	intron (NM_175489, intron 3 of 23)	intron (NM_175489, intron 3 of 23)	62082	NM_175489	237542	Mm.220204	NM_175489	ENSMUSG00000020189	Osbpl8	AA536976|AA536995|C730029P18Rik|D330025H14Rik|ORP-8	oxysterol binding protein-like 8	protein-coding
mm_4966.1	chr1	191281415	191281417	+	1	NA	Intergenic	Intergenic	36702	NM_025424	66208	Mm.46444	NM_025424	ENSMUSG00000037499	Nenf	1110060M21Rik|SCIRP10|Spuf	neuron derived neurotrophic factor	protein-coding
mm_112084.1	chr12	112674076	112674086	-	1	NA	5' UTR (NM_001165894, exon 1 of 14)	5' UTR (NM_001165894, exon 1 of 14)	195	NM_001165894	11651	Mm.6645	NM_009652	ENSMUSG00000001729	Akt1	Akt|LTR-akt|PKB|PKB/Akt|PKBalpha|Rac	thymoma viral proto-oncogene 1	protein-coding
mm_138559.1	chr17	35267252	35267279	+	1	NA	TTS (NM_001267808)	TTS (NM_001267808)	4142	NM_001267808	14980	Mm.439675	NM_001267808		H2-L	H-2L	histocompatibility 2, D region locus L	protein-coding
mm_38350.1	chr4	137770031	137770040	-	1	NA	intron (NM_007431, intron 1 of 11)	intron (NM_007431, intron 1 of 11)	-3560	NM_001287172	11647	Mm.288186	NM_007431	ENSMUSG00000028766	Alpl	ALP|APTNAP|Akp-2|Akp2|TNAP|TNSALP	alkaline phosphatase, liver/bone/kidney	protein-coding
mm_92625.1	chr10	80261016	80261026	-	1	NA	promoter-TSS (NM_001347119)	promoter-TSS (NM_001347119)	-9	NM_010255	14431	Mm.7329	NM_010255	ENSMUSG00000020150	Gamt	AA571402|Spintz1	guanidinoacetate methyltransferase	protein-coding
mm_130930.1	chr15	103163295	103163336	-	1	NA	promoter-TSS (NM_027885)	promoter-TSS (NM_027885)	-31	NM_027885	71726	Mm.254820	NM_027885	ENSMUSG00000036061	Smug1	1200013B09Rik|A930006H09Rik|C85220	single-strand selective monofunctional uracil DNA glycosylase	protein-coding
mm_79022.1	chr9	45906926	45907013	+	1	NA	promoter-TSS (NM_178709)	promoter-TSS (NM_178709)	-58	NM_001310840	235315	Mm.3255	NM_178709	ENSMUSG00000042790	Rnf214	D130054N24Rik	ring finger protein 214	protein-coding
mm_138520.1	chr17	35238168	35238181	+	1	NA	3' UTR (NM_023179, exon 3 of 3)	3' UTR (NM_023179, exon 3 of 3)	1578	NM_023179	66237	Mm.396107	NM_023179	ENSMUSG00000024403	Atp6v1g2	1500002D01Rik|Atp6g2|NG38|VAG2	ATPase, H+ transporting, lysosomal V1 subunit G2	protein-coding
mm_155281.1	chrX	61128001	61128009	+	1	NA	intron (NR_030706, intron 5 of 7)	intron (NR_030706, intron 5 of 7)	11627	NR_030706	331424	Mm.127263	NM_177916	ENSMUSG00000071753	C230004F18Rik	-	RIKEN cDNA C230004F18 gene	ncRNA
mm_85189.1	chr9	96719405	96719479	-	1	NA	intron (NM_175537, intron 1 of 2)	intron (NM_175537, intron 1 of 2)	12233	NM_175537	245007	Mm.485954	NM_175537	ENSMUSG00000040433	Zbtb38	A930014K01Rik|CIBZ	zinc finger and BTB domain containing 38	protein-coding
mm_96902.1	chr11	70455186	70455196	+	1	NA	3' UTR (NM_023158, exon 5 of 5)	3' UTR (NM_023158, exon 5 of 5)	3260	NM_025397	66172	Mm.46424	NM_025397	ENSMUSG00000018923	Med11	1110030J09Rik|AI465144|AW545069	mediator complex subunit 11	protein-coding
mm_116299.1	chr13	36726427	36726445	-	1	NA	3' UTR (NM_153529, exon 3 of 3)	3' UTR (NM_153529, exon 3 of 3)	8041	NM_153529	68404	Mm.232930	NM_153529	ENSMUSG00000039114	Nrn1	0710008J23Rik|Cpg15|Nrn	neuritin 1	protein-coding
mm_99816.1	chr11	108587093	108587110	+	1	NA	intron (NM_029606, intron 19 of 27)	intron (NM_029606, intron 19 of 27)	-95508	NM_145688	76380	Mm.344071	NM_029586	ENSMUSG00000020728	Cep112	1700001M19Rik|1700029K01Rik|8430407H02Rik|AV043680|AV207351|Ccdc46|Macoco	centrosomal protein 112	protein-coding
mm_30638.1	chr4	8811364	8811377	+	1	NA	intron (NM_001277149, intron 6 of 37)	intron (NM_001277149, intron 6 of 37)	120964	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_44144.1	chr5	150259814	150259829	+	1	NA	promoter-TSS (NM_172887)	promoter-TSS (NM_172887)	-109	NM_172887	320365	Mm.216590	NM_172887	ENSMUSG00000056602	Fry	13CDNA73|9330186A19Rik|AF346502|AI462658|C87180|D930046M03|cg003|mKIAA4143	FRY microtubule binding protein	protein-coding
mm_98837.1	chr11	97440154	97440176	+	1	NA	Intergenic	CpG	-9995	NM_021493	58996	Mm.394118	NM_021493	ENSMUSG00000049807	Arhgap23	A330041B18Rik	Rho GTPase activating protein 23	protein-coding
mm_66265.1	chr7	35754395	35754434	-	1	NA	promoter-TSS (NM_178704)	promoter-TSS (NM_178704)	40	NM_178704	233115	Mm.257808	NM_178704	ENSMUSG00000043671	Dpy19l3	6030410G08|9330164H19Rik	dpy-19-like 3 (C. elegans)	protein-coding
mm_105400.1	chr11	103412655	103412666	-	1	NA	promoter-TSS (NM_183034)	promoter-TSS (NM_183034)	4	NM_183034	353047	Mm.18556	NM_183034	ENSMUSG00000034247	Plekhm1	AP162|B2|BC038943|D330036J23Rik	pleckstrin homology domain containing, family M (with RUN domain) member 1	protein-coding
mm_134960.1	chr16	31314587	31314605	-	1	NA	5' UTR (NM_007470, exon 1 of 6)	5' UTR (NM_007470, exon 1 of 6)	212	NM_001301353	11815	Mm.2082	NM_007470	ENSMUSG00000022548	Apod	-	apolipoprotein D	protein-coding
mm_150519.1	chr19	39035948	39035951	+	1	NA	intron (NM_028089, intron 7 of 8)	L1M2|LINE|L1	-25057	NM_028191	72303	Mm.482578	NM_028191	ENSMUSG00000067231	Cyp2c65	2210009K14Rik	cytochrome P450, family 2, subfamily c, polypeptide 65	protein-coding
mm_161421.1	chr15	37792676	37792676	-	1	NA	promoter-TSS (NM_134094)	promoter-TSS (NM_134094)	-248	NM_134094	52589	Mm.283370	NM_134094	ENSMUSG00000051359	Ncald	AI848120|D030020D09Rik|D15Ertd412e	neurocalcin delta	protein-coding
mm_70199.1	chr7	144569901	144569903	-	1	NA	Intergenic	RLTR14_RN|LTR|ERV1	12534	NM_010175	14082	Mm.5126	NM_010175	ENSMUSG00000031077	Fadd	Mort1/FADD	Fas (TNFRSF6)-associated via death domain	protein-coding
mm_71463.1	chr8	46534253	46534276	+	1	NA	intron (NM_001302163, intron 20 of 20)	intron (NM_001302163, intron 20 of 20)	-17805	NM_027973	71876	Mm.22108	NM_027973	ENSMUSG00000031629	Cenpu	1700029A22Rik|Mlf1ip	centromere protein U	protein-coding
mm_90860.1	chr10	8885662	8885698	-	1	NA	intron (NM_175155, intron 1 of 19)	intron (NM_175155, intron 1 of 19)	390	NM_175155	70097	Mm.338275	NM_175155	ENSMUSG00000015305	Sash1	1100001C18Rik|2500002E12Rik|A330076K04Rik|mKIAA0790	SAM and SH3 domain containing 1	protein-coding
mm_71926.1	chr8	70234642	70234655	+	1	NA	promoter-TSS (NM_133972)	promoter-TSS (NM_133972)	-226	NM_133972	76813	Mm.383251	NM_133972	ENSMUSG00000002343	Armc6	2410153K17Rik|AW554412	armadillo repeat containing 6	protein-coding
mm_158013.1	chrX	95658393	95658412	-	1	NA	5' UTR (NM_001003916, exon 1 of 5)	5' UTR (NM_001003916, exon 1 of 5)	107	NM_001289696	245522	Mm.336158	NM_001003916	ENSMUSG00000035062	Zc4h2	Gm372|mKIAA1166	zinc finger, C4H2 domain containing	protein-coding
mm_49052.1	chr6	5048244	5048255	+	1	NA	intron (NM_181595, intron 3 of 15)	intron (NM_181595, intron 3 of 15)	144929	NM_181595	243725	Mm.332901	NM_181595	ENSMUSG00000032827	Ppp1r9a	2810430P21Rik|4930518N04Rik|5330407E15|A230094E16Rik|BB181831|NRB|mKIAA1222|neurabin-I	protein phosphatase 1, regulatory (inhibitor) subunit 9A	protein-coding
mm_120940.1	chr14	76645658	76645668	+	1	NA	Intergenic	Intergenic	-31905	NR_015485	73272	Mm.116804	NR_015485	ENSMUSG00000101009	1700108F19Rik	1700020I02Rik|BB065030	RIKEN cDNA 1700108F19 gene	ncRNA
mm_171445.1	chr4	143562609	143562618	+	1	NA	Intergenic	MT2_Mm|LTR|ERVL	-4854	NM_001007579	329986	Mm.453523	NM_001007579	ENSMUSG00000070618	BC080695	-	cDNA sequence BC080695	protein-coding
mm_129064.1	chr15	75603922	75603922	-	1	NA	Intergenic	Intergenic	7255	NM_001347039	68453	Mm.46367	NM_026730	ENSMUSG00000022579	Gpihbp1	1110002J19Rik|GPI-HBP1	GPI-anchored HDL-binding protein 1	protein-coding
mm_12357.1	chr2	69749653	69749673	+	1	NA	exon (NM_001081086, exon 14 of 14)	exon (NM_001081086, exon 14 of 14)	26575	NM_001081086	228005	Mm.11815	NM_001081086	ENSMUSG00000042133	Ppig	AU019516|AU022200|B230312B02Rik|CYP|SRCyp	peptidyl-prolyl isomerase G (cyclophilin G)	protein-coding
mm_14969.1	chr2	152093489	152093498	+	1	NA	exon (NM_001160410, exon 2 of 2)	exon (NM_001160410, exon 2 of 2)	11964	NM_001160410	545474	Mm.214317	NM_001160410	ENSMUSG00000060257	Scrt2	AW060659	scratch family zinc finger 2	protein-coding
mm_66237.1	chr7	35396777	35396821	-	1	NA	promoter-TSS (NM_178643)	promoter-TSS (NM_178643)	-32	NM_178643	101831	Mm.389855	NM_178643	ENSMUSG00000030493	Faap24	AW124591|AW538696|C230052I12Rik	Fanconi anemia core complex associated protein 24	protein-coding
mm_56651.1	chr6	113419318	113419352	-	1	NA	promoter-TSS (NM_001033204)	promoter-TSS (NM_001033204)	5	NM_001033204	101122	Mm.31204	NM_001033204	ENSMUSG00000051169	Rpusd3	AI527266	RNA pseudouridylate synthase domain containing 3	protein-coding
mm_66433.1	chr7	44670821	44670862	-	1	NA	promoter-TSS (NM_001271540)	promoter-TSS (NM_001271540)	2	NM_001271540	71960	Mm.158289	NM_028021	ENSMUSG00000030739	Myh14	2400004E04Rik|II-C|NHMCII|NMHC II-C	myosin, heavy polypeptide 14	protein-coding
mm_122831.1	chr14	54712331	54712367	-	1	NA	promoter-TSS (NM_207131)	promoter-TSS (NM_207131)	-175	NM_207131	110794	Mm.236223	NM_207131	ENSMUSG00000052435	Cebpe	C/EBPe|CRP1|Gm294	CCAAT/enhancer binding protein (C/EBP), epsilon	protein-coding
mm_641.1	chr1	40404928	40404937	+	1	NA	Intergenic	Intergenic	-24638	NM_001294171	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_168655.1	chr11	87471363	87471383	+	1	NA	intron (NM_001199293, intron 2 of 30)	U3|snRNA|snRNA	43782	NM_001199293	83560	Mm.440758	NM_031386	ENSMUSG00000010342	Tex14	C85585	testis expressed gene 14	protein-coding
mm_162672.1	chr10	7473352	7473368	-	1	NA	5' UTR (NM_029975, exon 1 of 6)	5' UTR (NM_029975, exon 1 of 6)	117	NM_029975	77777	Mm.442442	NM_029975	ENSMUSG00000079685	Ulbp1	A430108B07Rik|MULT1	UL16 binding protein 1	protein-coding
mm_134387.1	chr16	17281513	17281516	-	1	NA	intron (NM_001001983, intron 52 of 54)	intron (NM_001001983, intron 52 of 54)	5214	NM_177473	224019	Mm.246388	NM_177473	ENSMUSG00000055692	Tmem191c	4933405M22Rik|D16Bwg1494e|MNCb-4137	transmembrane protein 191C	protein-coding
mm_18819.1	chr2	74579462	74579464	-	1	NA	promoter-TSS (NM_027133)	promoter-TSS (NM_027133)	-515	NM_027133	69605	Mm.156113	NM_027133	ENSMUSG00000009207	Lnpk	2310011O18Rik|4921514L11Rik|9530051D01Rik|AI666268|Lnp|Lnpk1|Ul|ulnaless	lunapark, ER junction formation factor	protein-coding
mm_50088.1	chr6	41523989	41524002	+	1	NA	exon (NM_009430, exon 3 of 5)	exon (NM_009430, exon 3 of 5)	2219	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_150318.1	chr19	34573743	34573791	+	1	NA	exon (NM_008332, exon 3 of 3)	exon (NM_008332, exon 3 of 3)	-9762	NM_010501	15959	Mm.426079	NM_010501	ENSMUSG00000074896	Ifit3	Ifi49|P49	interferon-induced protein with tetratricopeptide repeats 3	protein-coding
mm_19686.1	chr2	103456875	103456926	-	1	NA	exon (NM_009804, exon 11 of 13)	exon (NM_009804, exon 11 of 13)	28253	NM_009804	12359	Mm.4215	NM_009804	ENSMUSG00000027187	Cat	2210418N07|Cas-1|Cas1|Cs-1	catalase	protein-coding
mm_13835.1	chr2	119351259	119351270	+	1	NA	promoter-TSS (NM_026929)	promoter-TSS (NM_026929)	22	NM_026929	69065	Mm.35083	NM_026929	ENSMUSG00000027313	Chac1	1810008K03Rik	ChaC, cation transport regulator 1	protein-coding
mm_125924.1	chr15	76204352	76204367	+	1	NA	intron (NM_011117, intron 1 of 31)	intron (NM_011117, intron 1 of 31)	1962	NM_201389	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
mm_114863.1	chr13	93674404	93674452	+	1	NA	promoter-TSS (NM_022884)	promoter-TSS (NM_022884)	-8	NM_028772	74129	Mm.21789	NM_028772	ENSMUSG00000042102	Dmgdh	1200014D15Rik|AI787269	dimethylglycine dehydrogenase precursor	protein-coding
mm_95006.1	chr11	31910780	31910783	+	1	NA	intron (NM_001290676, intron 3 of 8)	intron (NM_001290676, intron 3 of 8)	39841	NM_026252	67579	Mm.339792	NM_026252	ENSMUSG00000020300	Cpeb4	Cpe-bp4|Cpeb-4|mCPEB-4	cytoplasmic polyadenylation element binding protein 4	protein-coding
mm_36885.1	chr4	107253389	107253406	-	1	NA	promoter-TSS (NM_028394)	promoter-TSS (NM_028394)	136	NM_029985	77809	Mm.29681	NM_029985	ENSMUSG00000028617	Lrrc42	A930011F22Rik|AA536996	leucine rich repeat containing 42	protein-coding
mm_11508.1	chr2	32570840	32570852	+	1	NA	promoter-TSS (NM_010073)	promoter-TSS (NM_010073)	-12	NM_010073	13481	Mm.22001	NM_010073	ENSMUSG00000026810	Dpm2	AW557993|R75484	dolichol-phosphate (beta-D) mannosyltransferase 2	protein-coding
mm_40457.1	chr5	53604183	53604209	+	1	NA	intron (NM_001277116, intron 3 of 12)	intron (NM_001277116, intron 3 of 12)	13710	NM_001080927	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_129691.1	chr15	81522941	81522960	-	1	NA	Intergenic	Intergenic	56634	NM_019712	56438	Mm.29405	NM_019712	ENSMUSG00000022400	Rbx1	1500002P15Rik|AA517855|ROC1	ring-box 1	protein-coding
mm_152701.1	chr19	17327787	17327789	-	1	NA	3' UTR (NM_001136484, exon 3 of 3)	3' UTR (NM_001136484, exon 3 of 3)	11717	NM_001136484	14537	Mm.244825	NM_010265	ENSMUSG00000038843	Gcnt1	5630400D21Rik|B130048E03|C2 GlcNAcT|C2GNT|IGnT	glucosaminyl (N-acetyl) transferase 1, core 2	protein-coding
mm_84407.1	chr9	65555531	65555544	-	1	NA	3' UTR (NM_153119, exon 6 of 6)	3' UTR (NM_153119, exon 6 of 6)	24550	NM_153119	102595	Mm.247303	NM_153119	ENSMUSG00000050721	Plekho2	AI840980|Plekhq1	pleckstrin homology domain containing, family O member 2	protein-coding
mm_109899.1	chr12	7901638	7901652	-	1	NA	Intergenic	Intergenic	-76032	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_15912.1	chr2	165062312	165062320	+	1	NA	non-coding (NR_027852, exon 2 of 8)	non-coding (NR_027852, exon 2 of 8)	6680	NM_011611	21939	Mm.271833	NM_011611	ENSMUSG00000017652	Cd40	AI326936|Bp50|GP39|HIGM1|IGM|IMD3|T-BAM|TRAP|Tnfrsf5|p50	CD40 antigen	protein-coding
mm_35979.1	chr4	53825884	53825893	-	1	NA	promoter-TSS (NM_028053)	promoter-TSS (NM_028053)	-157	NM_028053	52076	Mm.27184	NM_028053	ENSMUSG00000028420	Tmem38b	1600017F22Rik|AA437809|AV051057|D4Ertd89e|TRIC-B|mg33b	transmembrane protein 38B	protein-coding
mm_62091.1	chr7	94042685	94042698	+	1	NA	Intergenic	Intergenic	962812	NM_021427	58238	Mm.113787	NM_021427	ENSMUSG00000051515	Fam181b	A830059I20Rik|AB041569	family with sequence similarity 181, member B	protein-coding
mm_164110.1	chr15	28698043	28698044	+	1	NA	Intergenic	Intergenic	494277	NM_133365	110082	Mm.248464	NM_133365	ENSMUSG00000022262	Dnah5	AU022615|Dnahc5|Mdnah5|b2b1134Clo|b2b1154Clo|b2b1537Clo|b2b1565Clo|b2b601Clo|mKIAA1603	dynein, axonemal, heavy chain 5	protein-coding
mm_149518.1	chr19	12440348	12440361	+	1	NA	Intergenic	Intergenic	12449	NM_019540	56093	Mm.285849	NM_019540	ENSMUSG00000040065	Pfpl	Epcs5|Epcs50	pore forming protein-like	protein-coding
mm_30748.1	chr4	14864384	14864392	+	1	NA	exon (NM_028264, exon 1 of 7)	exon (NM_028264, exon 1 of 7)	169	NM_028264	72519	Mm.279158	NM_028264	ENSMUSG00000028221	Tmem55a	2610319K07Rik|AI315591|AV001360	transmembrane protein 55A	protein-coding
mm_119058.1	chr14	30715783	30715794	+	1	NA	5' UTR (NM_001166532, exon 1 of 21)	5' UTR (NM_001166532, exon 1 of 21)	173	NM_001166532	54650	Mm.294662	NM_019460	ENSMUSG00000006527	Sfmbt1	4930442N21Rik|9330180L21Rik|AA536974|Sfmbt|Smr	Scm-like with four mbt domains 1	protein-coding
mm_151429.1	chr19	56897869	56897875	+	1	NA	intron (NM_172840, intron 5 of 13)	intron (NM_172840, intron 5 of 13)	23456	NM_172840	240675	Mm.129534	NM_172840	ENSMUSG00000025082	Vwa2	Amaco	von Willebrand factor A domain containing 2	protein-coding
mm_11101.1	chr2	28095440	28095444	+	1	NA	Intergenic	Intergenic	-10564	NM_010190	14134	Mm.182935	NM_010190	ENSMUSG00000026835	Fcnb	Fcn2	ficolin B	protein-coding
mm_112930.1	chr13	20963884	20963901	+	1	NA	intron (NM_012054, intron 12 of 20)	intron (NM_012054, intron 12 of 20)	109407	NM_146535	258528	Mm.377554	NM_146535	ENSMUSG00000042869	Olfr1370	MOR256-14	olfactory receptor 1370	protein-coding
mm_85048.1	chr9	89738415	89738463	-	1	NA	promoter-TSS (NM_207260)	promoter-TSS (NM_207260)	36	NM_207260	330998	Mm.294417	NM_207260	ENSMUSG00000047606	Ankrd34c	B230218L05Rik|BB276295|Gm771	ankyrin repeat domain 34C	protein-coding
mm_72956.1	chr8	92549274	92549274	+	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-125015	NM_022428	64379	Mm.137247	NM_022428	ENSMUSG00000031738	Irx6	-	Iroquois related homeobox 6 (Drosophila)	protein-coding
mm_110239.1	chr12	30467392	30467401	-	1	NA	promoter-TSS (NR_045491)	promoter-TSS (NR_045491)	-38	NR_045491	69566	Mm.396405	NR_045491	ENSMUSG00000102098	2310016D03Rik	-	RIKEN cDNA 2310016D03 gene	ncRNA
mm_55087.1	chr6	49215413	49215470	-	1	NA	promoter-TSS (NM_023670)	promoter-TSS (NM_023670)	-487	NM_023670	140488	Mm.281018	NM_023670	ENSMUSG00000029814	Igf2bp3	2610101N11Rik|AA522010|AL022933|AU045931|IMP-3|IMP3|Koc13|Neilsen|mimp3	insulin-like growth factor 2 mRNA binding protein 3	protein-coding
mm_126082.1	chr15	77816355	77816401	+	1	NA	intron (NM_022410, intron 1 of 40)	intron (NM_022410, intron 1 of 40)	25797	NM_022410	17886	Mm.29677	NM_022410	ENSMUSG00000022443	Myh9	Fltn|Myhn-1|Myhn1|NMHCIIA|NMMHC-A|NMMHC-IIA|TU72.6	myosin, heavy polypeptide 9, non-muscle	protein-coding
mm_154768.1	chrX	12587865	12587877	+	1	NA	5' UTR (NM_027439, exon 1 of 9)	5' UTR (NM_027439, exon 1 of 9)	112	NM_027439	70495	Mm.25148	NM_027439	ENSMUSG00000031007	Atp6ap2	(P)RR|5730403E06Rik|APT6M8-9|ATP6M8-9|Atp6ip2|M8-9|PRR	ATPase, H+ transporting, lysosomal accessory protein 2	protein-coding
mm_10223.1	chr2	5957598	5957620	+	1	NA	exon (NM_001081132, exon 2 of 22)	exon (NM_001081132, exon 2 of 22)	6140	NM_001081132	326622	Mm.31102	NM_001081132	ENSMUSG00000043241	Upf2	-	UPF2 regulator of nonsense transcripts homolog (yeast)	protein-coding
mm_38984.1	chr4	151004622	151004625	-	1	NA	3' UTR (NM_001289878, exon 22 of 22)	3' UTR (NM_001289878, exon 22 of 22)	7526	NM_011910	24111	Mm.89984	NM_011910	ENSMUSG00000028963	Uts2	UII|Ucn2|prepro-UII	urotensin 2	protein-coding
mm_156046.1	chrX	108834651	108834712	+	1	NA	promoter-TSS (NM_001081477)	promoter-TSS (NM_001081477)	203	NR_015493	69964	Mm.160066	NR_015493	ENSMUSG00000086629	2810403D21Rik	1810022M18Rik|4632410B05Rik|AU017716	RIKEN cDNA 2810403D21 gene	ncRNA
mm_78459.1	chr9	32372510	32372520	+	1	NA	promoter-TSS (NM_019659)	promoter-TSS (NM_019659)	97	NM_019659	56379	Mm.390168	NM_019659	ENSMUSG00000041248	Kcnj1	Kir1.1|ROMK|Romk2	potassium inwardly-rectifying channel, subfamily J, member 1	protein-coding
mm_54941.1	chr6	48554675	48554687	-	1	NA	promoter-TSS (NM_177736)	promoter-TSS (NM_177736)	-118	NM_001110160	243371	Mm.290764	NM_177736	ENSMUSG00000073096	Lrrc61	BC027309	leucine rich repeat containing 61	protein-coding
mm_44020.1	chr5	147400449	147400473	+	1	NA	promoter-TSS (NM_010229)	promoter-TSS (NM_010229)	28	NM_010229	14255	Mm.194	NM_010229	ENSMUSG00000042817	Flt3	B230315G04|CD135|Flk-2|Flk2|Flt-3|Ly72|wmfl	FMS-like tyrosine kinase 3	protein-coding
mm_122654.1	chr14	51911281	51911315	-	1	NA	intron (NM_013864, intron 2 of 15)	intron (NM_013864, intron 2 of 15)	2190	NM_001145959	29811	Mm.26722	NM_013864	ENSMUSG00000004558	Ndrg2	AI182517|AU040374|Ndr2|SYLD	N-myc downstream regulated gene 2	protein-coding
mm_83643.1	chr9	49504964	49504980	-	1	NA	3' UTR (NM_001311065, exon 18 of 18)	3' UTR (NM_001311065, exon 18 of 18)	-13316	NR_029465	100036537	Mm.437541	NR_029465	ENSMUSG00000079564	Gm11149	ENSMUSG00000060603|ENSMUSG00000079564	predicted gene 11149	ncRNA
mm_75245.1	chr8	39642670	39642673	-	1	NA	promoter-TSS (NM_031195)	promoter-TSS (NM_031195)	7	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_107660.1	chr12	52818497	52818505	+	1	NA	intron (NM_198111, intron 2 of 13)	intron (NM_198111, intron 2 of 13)	119118	NM_198111	238161	Mm.310822	NM_198111	ENSMUSG00000061603	Akap6	AI482140|Akapalpha|Akapbeta|PRKA	A kinase (PRKA) anchor protein 6	protein-coding
mm_108479.1	chr12	83659555	83659568	+	1	NA	exon (NM_027349, exon 7 of 19)	exon (NM_027349, exon 7 of 19)	27327	NM_027349	67039	Mm.46005	NM_027349	ENSMUSG00000010608	Rbm25	2600011C06Rik|2610015J01Rik|A130095G20Rik|AI159652|AL023075|AU043498|RNPC7	RNA binding motif protein 25	protein-coding
mm_47241.1	chr5	121521574	121521599	-	1	NA	5' UTR (NM_172126, exon 1 of 1)	5' UTR (NM_172126, exon 1 of 1)	109	NM_172126	280668	Mm.1453	NM_172126	ENSMUSG00000072647	Adam1a	Adam1|Ftna	a disintegrin and metallopeptidase domain 1a	protein-coding
mm_53948.1	chr6	5220931	5220949	-	1	NA	TTS (NM_173006)	TTS (NM_173006)	-26994	NM_011134	18979	Mm.237657	NM_011134	ENSMUSG00000002588	Pon1	Pon	paraoxonase 1	protein-coding
mm_17528.1	chr2	29620528	29620546	-	1	NA	intron (NM_001039087, intron 1 of 25)	intron (NM_001039087, intron 1 of 25)	817	NM_001039086	107746	Mm.298274	NM_054050	ENSMUSG00000039844	Rapgef1	4932418O06Rik|C3G|Grf2	Rap guanine nucleotide exchange factor (GEF) 1	protein-coding
mm_141061.1	chr17	25754517	25754521	-	1	NA	promoter-TSS (NM_018857)	promoter-TSS (NM_018857)	-192	NM_018857	56047	Mm.17510	NM_018857	ENSMUSG00000063011	Msln	MPF	mesothelin	protein-coding
mm_47540.1	chr5	124249830	124249860	-	1	NA	promoter-TSS (NM_011256)	promoter-TSS (NM_011256)	-85	NM_011256	19679	Mm.44261	NM_011256	ENSMUSG00000029406	Pitpnm2	NIR3|RDGBA2|Rdgb2|mKIAA1457	phosphatidylinositol transfer protein, membrane-associated 2	protein-coding
mm_126926.1	chr15	91673131	91673141	+	1	NA	promoter-TSS (NM_025730)	promoter-TSS (NM_025730)	-88	NM_025730	66725	Mm.37558	NM_025730	ENSMUSG00000036273	Lrrk2	4921513O20Rik|9330188B09Rik|AW561911|D630001M17Rik|Gm927|cI-46	leucine-rich repeat kinase 2	protein-coding
mm_15100.1	chr2	153346155	153346168	+	1	NA	promoter-TSS (NM_001039939)	promoter-TSS (NM_001039939)	22	NM_001039939	228790	Mm.330677	NM_001039939	ENSMUSG00000042548	Asxl1	mKIAA0978	additional sex combs like 1	protein-coding
mm_168484.1	chr11	49198214	49198214	+	1	NA	Intergenic	RLTR10C|LTR|ERVK	-5286	NM_001024846	22720	Mm.16650	NM_009562	ENSMUSG00000046311	Zfp62	-	zinc finger protein 62	protein-coding
mm_39108.1	chr4	154928084	154928094	-	1	NA	promoter-TSS (NM_178931)	promoter-TSS (NM_178931)	-12	NM_178931	230979	Mm.215147	NM_178931	ENSMUSG00000042333	Tnfrsf14	Atar|HveA|Hvem|Tnfrs14	tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)	protein-coding
mm_28960.1	chr3	100684700	100684712	-	1	NA	exon (NM_010763, exon 1 of 13)	exon (NM_010763, exon 1 of 13)	767	NM_010763	17156	Mm.271617	NM_010763	ENSMUSG00000008763	Man1a2	AI428775|AI528764|AI854422|Man1b|PCR2	mannosidase, alpha, class 1A, member 2	protein-coding
mm_159675.1	chr4	155397926	155397926	-	1	NA	exon (NM_008072, exon 1 of 9)	exon (NM_008072, exon 1 of 9)	143	NM_008072	14403	Mm.388925	NM_008072	ENSMUSG00000029054	Gabrd	AI853201	gamma-aminobutyric acid (GABA) A receptor, subunit delta	protein-coding
mm_70210.1	chr7	144896900	144896939	-	1	NA	exon (NM_008003, exon 1 of 3)	exon (NM_008003, exon 1 of 3)	387	NM_008003	14170	Mm.3904	NM_008003	ENSMUSG00000031073	Fgf15	FGF19	fibroblast growth factor 15	protein-coding
mm_121077.1	chr14	99046377	99046381	+	1	NA	promoter-TSS (NM_175245)	promoter-TSS (NM_175245)	2	NM_175265	77744	Mm.23503	NM_175265	ENSMUSG00000022070	Bora	6720463M24Rik|AI317232	bora, aurora kinase A activator	protein-coding
mm_73362.1	chr8	105595135	105595156	+	1	NA	Intergenic	Intergenic	-10084	NM_001081241	75687	Mm.41261	NM_001081241	ENSMUSG00000038604	Fam65a	2310066E14Rik|AI837433	family with sequence similarity 65, member A	protein-coding
mm_50281.1	chr6	47244360	47244417	+	1	NA	promoter-TSS (NM_025771)	promoter-TSS (NM_025771)	-8	NM_025771	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding
mm_64335.1	chr7	142376318	142376358	+	1	NA	3' UTR (NM_009983, exon 9 of 9)	3' UTR (NM_009983, exon 9 of 9)	-2592	NM_001347541	320802	Mm.154486	NM_177265	ENSMUSG00000045777	Ifitm10	6330512M04Rik|AI848576|DSPA3	interferon induced transmembrane protein 10	protein-coding
mm_124225.1	chr14	100284948	100284992	-	1	NA	Intergenic	Intergenic	-135174	NM_010636	16597	Mm.396499	NM_010636	ENSMUSG00000072294	Klf12	2700063E05Rik|AI225908|AI315654|AP-2rep|B130052C06Rik|D530033K05Rik	Kruppel-like factor 12	protein-coding
mm_110505.1	chr12	54656497	54656517	-	1	NA	promoter-TSS (NM_134054)	promoter-TSS (NM_134054)	65	NM_134054	104725	Mm.485026	NM_134054	ENSMUSG00000044408	Sptssa	1110002B05Rik|AA407909|AA409588|AU041967|Ssspta	serine palmitoyltransferase, small subunit A	protein-coding
mm_68486.1	chr7	110990388	110990390	-	1	NA	Intergenic	RMER17C|LTR|ERVK	-7928	NM_194464	17540	Mm.250023	NM_010826	ENSMUSG00000005611	Mrvi1	BB115629|Irag|Ris1	MRV integration site 1	protein-coding
mm_89382.1	chr10	89444049	89444072	+	1	NA	promoter-TSS (NM_001284344)	promoter-TSS (NM_001284344)	-93	NM_001033331	237436	Mm.11982	NM_001033331	ENSMUSG00000074802	Gas2l3	8430435B07Rik|Gm240	growth arrest-specific 2 like 3	protein-coding
mm_31635.1	chr4	59434330	59434370	+	1	NA	intron (NM_001163288, intron 1 of 16)	intron (NM_001163288, intron 1 of 16)	4283	NM_001163288	634731	Mm.483589	NM_001163288	ENSMUSG00000038578	Susd1	A530080P10|Gm12528|OTTMUSG00000007332	sushi domain containing 1	protein-coding
mm_113005.1	chr13	21865843	21865851	+	1	NA	Intergenic	RLTR13B1|LTR|ERVK	31202	NR_035500	100316716		NR_035500	ENSMUSG00000088148	Mir1983	mmu-mir-1983	microRNA 1983	ncRNA
mm_149010.1	chr19	8725861	8725874	+	1	NA	promoter-TSS (NR_004445)	promoter-TSS (NR_004445)	1	NR_004445	100127111	Mm.292489	NR_004445	ENSMUSG00000065087	Snord22	Rnu22|U22	small nucleolar RNA, C/D box 22	snoRNA
mm_66581.1	chr7	45340751	45340777	-	1	NA	intron (NM_029741, intron 27 of 29)	intron (NM_029741, intron 27 of 29)	5495	NM_010473	15464	Mm.39968	NM_010473	ENSMUSG00000038239	Hrc	-	histidine rich calcium binding protein	protein-coding
mm_21549.1	chr2	164071050	164071052	-	1	NA	promoter-TSS (NM_025996)	promoter-TSS (NM_025996)	51	NM_025996	67145	Mm.23173	NM_025996	ENSMUSG00000018322	Tomm34	2610100K07Rik|TOM34	translocase of outer mitochondrial membrane 34	protein-coding
mm_70630.1	chr8	13757717	13757723	+	1	NA	promoter-TSS (NM_027276)	promoter-TSS (NM_027276)	30	NM_027276	69957	Mm.182412	NM_027276	ENSMUSG00000038416	Cdc16	2700071J12Rik|2810431D22Rik|APC6	CDC16 cell division cycle 16	protein-coding
mm_165258.1	chr2	72908565	72908601	-	1	NA	Intergenic	Intergenic	70698	NM_001098425	20687	Mm.124328	NM_011450	ENSMUSG00000027109	Sp3	D130027J01Rik	trans-acting transcription factor 3	protein-coding
mm_91048.1	chr10	18743673	18743684	-	1	NA	promoter-TSS (NM_001033258)	promoter-TSS (NM_001033258)	80	NM_001033258	215821	Mm.40491	NM_001033258	ENSMUSG00000019852	Arfgef3	9630004D11|B930094H20Rik|BIG3|D10Bwg1379e|mKIAA1244	ARFGEF family member 3	protein-coding
mm_113137.1	chr13	24636029	24636030	+	1	NA	intron (NM_178658, intron 1 of 13)	intron (NM_178658, intron 1 of 13)	-2619	NM_001080381	193385	Mm.217319	NM_029679	ENSMUSG00000036006	Fam65b	-	family with sequence similarity 65, member B	protein-coding
mm_18494.1	chr2	62606336	62606349	-	1	NA	exon (NM_027835, exon 10 of 16)	exon (NM_027835, exon 10 of 16)	-32321	NM_007986	14089	Mm.41816	NM_007986	ENSMUSG00000000392	Fap	SIMP	fibroblast activation protein	protein-coding
mm_116177.1	chr13	30820735	30820739	-	1	NA	intron (NM_025588, intron 25 of 27)	intron (NM_025588, intron 25 of 27)	71504	NM_013674	16364	Mm.4677	NM_013674	ENSMUSG00000021356	Irf4	AI385587|IRF-4|LSIRF|NF-EM5|Spip	interferon regulatory factor 4	protein-coding
mm_115651.1	chr13	12332197	12332214	-	1	NA	intron (NM_033268, intron 1 of 20)	RSINE1|SINE|B4	8527	NM_033268	11472	Mm.37638	NM_033268	ENSMUSG00000052374	Actn2	1110008F24Rik	actinin alpha 2	protein-coding
mm_54510.1	chr6	35511498	35511509	-	1	NA	3' UTR (NM_008098, exon 4 of 4)	3' UTR (NM_008098, exon 4 of 4)	28385	NM_008098	14489	Mm.182746	NM_008098	ENSMUSG00000029840	Mtpn	5033418D15Rik|Gcdp|V1	myotrophin	protein-coding
mm_167958.1	chrX	141980773	141980793	+	1	NA	Intergenic	Intergenic	216153	NM_001007576	245650	Mm.208511	NM_001007576	ENSMUSG00000042282	Gucy2f	A930002I06|GC-F|GC2	guanylate cyclase 2f	protein-coding
mm_167699.1	chr9	89199355	89199357	+	1	NA	promoter-TSS (NM_007534)	promoter-TSS (NM_007534)	83	NM_007534	12045	Mm.479217	NM_007534	ENSMUSG00000089929	Bcl2a1b	A1-b	B cell leukemia/lymphoma 2 related protein A1b	protein-coding
mm_10140.1	chr2	4152616	4152644	+	1	NA	promoter-TSS (NM_172475)	promoter-TSS (NM_172475)	-233	NM_172475	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding
mm_59639.1	chr7	28157782	28157789	+	1	NA	exon (NM_001164655, exon 16 of 20)	exon (NM_001164655, exon 16 of 20)	-11963	NM_007991	14113	Mm.4595	NM_007991	ENSMUSG00000046865	Fbl	AL022665|FIB|FLRN|RNU3IP1	fibrillarin	protein-coding
mm_147991.1	chr18	67641308	67641325	-	1	NA	promoter-TSS (NM_001081073)	promoter-TSS (NM_001081073)	20	NM_001081073	225659	Mm.111928	NM_001081073	ENSMUSG00000073542	Cep76	6230425F05Rik|9630013E05	centrosomal protein 76	protein-coding
mm_80250.1	chr9	72749302	72749314	+	1	NA	3' UTR (NM_010890, exon 29 of 29)	3' UTR (NM_010890, exon 29 of 29)	-57966	NM_175485	235472	Mm.31696	NM_175485	ENSMUSG00000036030	Prtg	A230098A12Rik|Igdcc5	protogenin	protein-coding
mm_17026.1	chr2	19431995	19432026	-	1	NA	Intergenic	CpG	-13653	NM_018809	19213	Mm.69647	NM_018809	ENSMUSG00000026735	Ptf1a	PTF1-p48|PTF1p48|bHLHa29	pancreas specific transcription factor, 1a	protein-coding
mm_77766.1	chr9	3004491	3004523	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	34236	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_103734.1	chr11	79974457	79974468	-	1	NA	Intergenic	CpG	-12075	NM_144826	216987	Mm.274961	NM_144826	ENSMUSG00000035575	Utp6	4732497O03Rik|HCA66	UTP6 small subunit processome component	protein-coding
mm_132419.1	chr16	35155531	35155545	+	1	NA	promoter-TSS (NM_001012765)	promoter-TSS (NM_001012765)	-98	NM_001012765	224129	Mm.41137	NM_001012765	ENSMUSG00000022840	Adcy5	AW121902|Ac5	adenylate cyclase 5	protein-coding
mm_144634.1	chr18	32958238	32958242	+	1	NA	intron (NM_009793, intron 1 of 10)	intron (NM_009793, intron 1 of 10)	19199	NM_009793	12326	Mm.222329	NM_009793	ENSMUSG00000038128	Camk4	A430110E23Rik|AI666733|CaMKIV|CaMKIV/Gr|D18Bwg0362e	calcium/calmodulin-dependent protein kinase IV	protein-coding
mm_48527.1	chr5	142903648	142903651	-	1	NA	3' UTR (NM_007393, exon 6 of 6)	3' UTR (NM_007393, exon 6 of 6)	3105	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_29149.1	chr3	105936268	105936272	-	1	NA	Intergenic	Intergenic	-3606	NM_001033780	433638	Mm.239081	NM_001033780	ENSMUSG00000074342	I830077J02Rik	-	RIKEN cDNA I830077J02 gene	protein-coding
mm_92998.1	chr10	86732419	86732429	-	1	NA	TTS (NM_153595)	TTS (NM_153595)	19659	NM_153595	103220	Mm.440762	NM_153595	ENSMUSG00000044937	Ttc41	AI449705|AU041509|Gnn	tetratricopeptide repeat domain 41	protein-coding
mm_87319.1	chr10	42860625	42860627	+	1	NA	5' UTR (NM_172938, exon 1 of 9)	5' UTR (NM_172938, exon 1 of 9)	114	NM_172938	268297	Mm.98731	NM_172938	ENSMUSG00000044770	Scml4	9330161D17|mFLJ00197	sex comb on midleg-like 4 (Drosophila)	protein-coding
mm_103995.1	chr11	84870032	84870107	-	1	NA	promoter-TSS (NR_131197)	promoter-TSS (NR_131197)	64	NR_131201	102635561	Mm.341797	NR_131197		Ggnbp2os	-	gametogenetin binding protein 2, opposite strand	ncRNA
mm_126849.1	chr15	89169783	89169793	+	1	NA	intron (NM_138749, intron 3 of 37)	intron (NM_138749, intron 3 of 37)	4163	NM_001159521	140570	Mm.267514	NM_138749	ENSMUSG00000036606	Plxnb2	Debt|plexin-B2	plexin B2	protein-coding
mm_132539.1	chr16	37878364	37878375	+	1	NA	exon (NM_177093, exon 3 of 4)	exon (NM_177093, exon 3 of 4)	9969	NM_177093	320184	Mm.390882	NM_177093	ENSMUSG00000034158	Lrrc58	1810012N18Rik|C330018J07Rik	leucine rich repeat containing 58	protein-coding
mm_85239.1	chr9	98954783	98954803	-	1	NA	promoter-TSS (NM_012020)	promoter-TSS (NM_012020)	517	NR_003248	768252	Mm.129645	NR_003248	ENSMUSG00000097072	Foxl2os	ENSMUSG00000074122	forkhead box L2, opposite strand	ncRNA
mm_14171.1	chr2	126675899	126675910	+	1	NA	promoter-TSS (NM_010249)	promoter-TSS (NM_010249)	-312	NR_073183	14391	Mm.293266	NM_010249	ENSMUSG00000027361	Gabpb1	BABPB2|E4TF1|E4TF1-47|E4TF1-53|E4Tf1B|GABPB|GABPB-1|GABPB-2|GABPB1-1|GABPB1-2|NRF2B1|NRF2B2	GA repeat binding protein, beta 1	protein-coding
mm_3973.1	chr1	164193368	164193377	+	1	NA	exon (NM_007976, exon 13 of 25)	exon (NM_007976, exon 13 of 25)	-41155	NR_037987	100503816	Mm.398579	NR_037987	ENSMUSG00000086593	Gm16548	-	predicted gene 16548	ncRNA
mm_109159.1	chr12	108179794	108179831	+	1	NA	promoter-TSS (NM_009832)	promoter-TSS (NM_009832)	74	NM_009832	12454	Mm.474441	NM_009832	ENSMUSG00000021258	Ccnk	AW123198|AW413594|CPR4|CycK	cyclin K	protein-coding
mm_121202.1	chr14	103052301	103052322	+	1	NA	intron (NM_008392, intron 4 of 4)	Lx8|LINE|L1	5299	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_49767.1	chr6	34863131	34863183	+	1	NA	promoter-TSS (NM_197986)	promoter-TSS (NM_197986)	11	NM_197986	68487	Mm.248440	NM_197986	ENSMUSG00000057137	Tmem140	1110007F12Rik	transmembrane protein 140	protein-coding
mm_14413.1	chr2	130405257	130405296	+	1	NA	promoter-TSS (NM_029375)	promoter-TSS (NM_029375)	17	NM_029375	75656	Mm.174788	NM_029375	ENSMUSG00000027409	1700020A23Rik	-	RIKEN cDNA 1700020A23 gene	protein-coding
mm_16021.1	chr2	167504128	167504139	+	1	NA	intron (NM_030743, intron 3 of 7)	CpG-8879	-11259	NM_170756	263876	Mm.34342	NM_170756	ENSMUSG00000047030	Spata2	AI504642|mKIAA0757	spermatogenesis associated 2	protein-coding
mm_89840.1	chr10	106879341	106879353	+	1	NA	intron (NM_001205341, intron 21 of 31)	intron (NM_001205341, intron 21 of 31)	244317	NM_001142804	380660	Mm.336072	NM_198636	ENSMUSG00000035948	Acss3	8430416H19Rik|Gm874	acyl-CoA synthetase short-chain family member 3	protein-coding
mm_150959.1	chr19	46396886	46396999	+	1	NA	promoter-TSS (NM_015752)	promoter-TSS (NM_015752)	46	NM_015752	24069	Mm.41210	NM_015752	ENSMUSG00000025231	Sufu	Su(fu)	suppressor of fused homolog (Drosophila)	protein-coding
mm_51635.1	chr6	85911855	85911865	+	1	NA	intron (NM_023160, intron 1 of 1)	intron (NM_023160, intron 1 of 1)	3817	NM_023160	66116	Mm.13036	NM_023160	ENSMUSG00000057103	Nat8f1	1110002I11Rik|AI266962|Cml1	N-acetyltransferase 8 (GCN5-related) family member 1	protein-coding
mm_29687.1	chr3	123034944	123034995	-	1	NA	promoter-TSS (NM_021503)	promoter-TSS (NM_021503)	18	NM_021503	59006	Mm.141157	NM_021503	ENSMUSG00000028116	Myoz2	1110012I24Rik|Fatz-2|Myozl2	myozenin 2	protein-coding
mm_57418.1	chr6	124911681	124911699	-	1	NA	promoter-TSS (NM_008479)	promoter-TSS (NM_008479)	15	NM_008479	16768	Mm.4528	NM_008479	ENSMUSG00000030124	Lag3	CD223|LAG-3|Ly66	lymphocyte-activation gene 3	protein-coding
mm_144892.1	chr18	36952622	36952660	+	1	NA	promoter-TSS (NM_001174154)	promoter-TSS (NM_001174154)	-7	NM_001174154	100384868	Mm.247203	NM_001174154	ENSMUSG00000103458	Gm37013	Pcdha4-g	predicted gene, 37013	protein-coding
mm_20961.1	chr2	151751430	151751462	-	1	NA	promoter-TSS (NR_138568)	promoter-TSS (NR_138568)	19	NR_138568	75283	Mm.195735	NM_029235		4930556L07Rik	1700020P01Rik|4930593I08Rik	RIKEN cDNA 4930556L07 gene	ncRNA
mm_86296.1	chr9	122294362	122294407	-	1	NA	promoter-TSS (NM_133979)	promoter-TSS (NM_133979)	39	NM_001271873	102566	Mm.87676	NM_133979	ENSMUSG00000037949	Ano10	AI604832|Tmem16k	anoctamin 10	protein-coding
mm_12092.1	chr2	60366483	60366494	+	1	NA	intron (NM_013825, intron 3 of 34)	intron (NM_013825, intron 3 of 34)	16743	NM_013825	17076	Mm.2074	NM_013825	ENSMUSG00000026980	Ly75	CD205|DEC-205|DEC205	lymphocyte antigen 75	protein-coding
mm_43656.1	chr5	138619283	138619295	+	1	NA	intron (NM_013844, intron 1 of 5)	intron (NM_013844, intron 1 of 5)	454	NM_001163797	24135	Mm.27575	NM_013844	ENSMUSG00000058291	Zfp68	KRAB3|KRAZ2|Zfp70|mszf22|mszf49	zinc finger protein 68	protein-coding
mm_108701.1	chr12	86952501	86952509	+	1	NA	intron (NM_001289432, intron 1 of 4)	intron (NM_001289432, intron 1 of 4)	5162	NM_001289432	217732	Mm.22337	NM_173735	ENSMUSG00000034157	Cipc	2310044G17Rik|AI842544|AI853744|Kiaa1737|mKIAA1737	CLOCK interacting protein, circadian	protein-coding
mm_165515.1	chr2	173218794	173218802	-	1	NA	5' UTR (NM_021394, exon 1 of 8)	5' UTR (NM_021394, exon 1 of 8)	124	NM_021394	58203	Mm.116687	NM_021394	ENSMUSG00000027514	Zbp1	2010010H03Rik|Dai|Dlm1|mZaDLM	Z-DNA binding protein 1	protein-coding
mm_42163.1	chr5	112259307	112259317	+	1	NA	exon (NM_001312894, exon 3 of 6)	exon (NM_001312894, exon 3 of 6)	3492	NM_001312893	12960	Mm.29488	NM_023695	ENSMUSG00000029343	Crybb1	3110006K12Rik|BB1CRY	crystallin, beta B1	protein-coding
mm_42075.1	chr5	110110268	110110298	+	1	NA	5' UTR (NM_001163996, exon 1 of 5)	5' UTR (NM_001163996, exon 1 of 5)	191	NM_001163996	675812	Mm.442122	NM_001163996	ENSMUSG00000023284	Zfp605	A830023I12Rik	zinc finger protein 605	protein-coding
mm_63162.1	chr7	123819946	123819947	+	1	NA	Intergenic	Lx8b|LINE|L1	-163235	NM_001252072	628779	Mm.40210	NM_001252072	ENSMUSG00000078591	Hs3st4	EG628779|Gm6915	heparan sulfate (glucosamine) 3-O-sulfotransferase 4	protein-coding
mm_27637.1	chr3	62506950	62506967	-	1	NA	promoter-TSS (NM_028136)	promoter-TSS (NM_028136)	30	NM_028136	72162	Mm.224233	NM_028136	ENSMUSG00000027770	Dhx36	2810407E23Rik|AI452301|AU022184|Ddx36|mKIAA1488	DEAH (Asp-Glu-Ala-His) box polypeptide 36	protein-coding
mm_172595.1	chr8	13896153	13896161	+	1	NA	Intergenic	Intergenic	-5886	NM_025556	66423	Mm.29063	NM_025556	ENSMUSG00000031458	Coprs	1700029I03Rik|2410022L05Rik|AA409325|AI256813|C85432|Copr5	coordinator of PRMT5, differentiation stimulator	protein-coding
mm_62176.1	chr7	97400126	97400136	+	1	NA	5' UTR (NM_024220, exon 1 of 3)	5' UTR (NM_024220, exon 1 of 3)	128	NM_024220	68197	Mm.334031	NM_024220	ENSMUSG00000030647	Ndufc2	1810004I06Rik|2010300P09Rik|G1|R75094	NADH dehydrogenase (ubiquinone) 1, subcomplex unknown, 2	protein-coding
mm_3362.1	chr1	138180368	138180382	+	1	NA	Intergenic	ORR1C2|LTR|ERVL-MaLR	-5070	NM_001268286	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_152656.1	chr19	12795367	12795377	-	1	NA	non-coding (NR_024093, exon 1 of 13)	non-coding (NR_024093, exon 1 of 13)	751	NR_024093	664779	Mm.290924	NM_001039718	ENSMUSG00000024695	Gm44505	Zfp91-Cntf|Zfp91Cntf	predicted readthrough transcript (NMD candidate), 44505	ncRNA
mm_12812.1	chr2	80315462	80315511	+	1	NA	promoter-TSS (NM_024181)	promoter-TSS (NM_024181)	20	NM_024181	66861	Mm.21762	NM_024181	ENSMUSG00000027006	Dnajc10	1200006L06Rik|D2Ertd706e|ERdj5|JPDI	DnaJ heat shock protein family (Hsp40) member C10	protein-coding
mm_119761.1	chr14	54171576	54171582	+	1	NA	Intergenic	Intergenic	82350	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_1674.1	chr1	74794638	74794650	+	1	NA	intron (NM_009518, intron 2 of 3)	intron (NM_009518, intron 2 of 3)	2625	NM_009518	22409	Mm.5130	NM_009518	ENSMUSG00000026167	Wnt10a	-	wingless-type MMTV integration site family, member 10A	protein-coding
mm_51720.1	chr6	86864928	86864931	+	1	NA	intron (NM_001040106, intron 1 of 20)	intron (NM_001040106, intron 1 of 20)	15412	NM_001040106	269774	Mm.221038	NM_177762	ENSMUSG00000057230	Aak1	5530400K14Rik|9630042K20|AU067724|AU067726|BC028270|C79663|D6Ertd245e|R75501|mKIAA1048	AP2 associated kinase 1	protein-coding
mm_151019.1	chr19	46772411	46772421	+	1	NA	intron (NM_033569, intron 1 of 7)	L1MB7|LINE|L1	10807	NM_001102471	94219	Mm.306903	NM_033569	ENSMUSG00000064105	Cnnm2	AU015877|AW048635|Acdp2|Clp2	cyclin M2	protein-coding
mm_39195.1	chr4	155999451	155999496	-	1	NA	exon (NM_011341, exon 3 of 7)	exon (NM_011341, exon 3 of 7)	6136	NM_001302468	20318	Mm.293517	NM_011341	ENSMUSG00000029076	Sdf4	Cab45	stromal cell derived factor 4	protein-coding
mm_133036.1	chr16	57353239	57353255	+	1	NA	promoter-TSS (NM_001040397)	promoter-TSS (NM_001040397)	-30	NM_001040397	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding
mm_77336.1	chr8	119558700	119558711	-	1	NA	promoter-TSS (NM_001167910)	promoter-TSS (NM_001167910)	56	NM_001167910	56453	Mm.206934	NM_019709	ENSMUSG00000031835	Mbtps1	0610038M03Rik|AV003995|S1P|SKI-1|Ski1|mKIAA0091	membrane-bound transcription factor peptidase, site 1	protein-coding
mm_15227.1	chr2	154548868	154548884	+	1	NA	promoter-TSS (NM_029305)	promoter-TSS (NM_029305)	-28	NM_029305	75480	Mm.440434	NM_029305	ENSMUSG00000038523	1700003F12Rik	-	RIKEN cDNA 1700003F12 gene	protein-coding
mm_2327.1	chr1	92752182	92752186	+	1	NA	Intergenic	Intergenic	-79502	NM_016696	14733	Mm.297976	NM_016696	ENSMUSG00000034220	Gpc1	AI462976	glypican 1	protein-coding
mm_35345.1	chr4	32248339	32248341	-	1	NA	Intergenic	Intergenic	-169095	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_91543.1	chr10	39638763	39638765	-	1	NA	intron (NM_134000, intron 3 of 8)	intron (NM_134000, intron 3 of 8)	25830	NM_134000	103213	Mm.436686	NM_134000	ENSMUSG00000019842	Traf3ip2	AI429613|Act1|CIKS	TRAF3 interacting protein 2	protein-coding
mm_54870.1	chr6	42598121	42598137	-	1	NA	promoter-TSS (NM_203396)	promoter-TSS (NM_203396)	-757	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_82812.1	chr9	30781389	30781396	-	1	NA	Intergenic	Intergenic	139558	NM_001329420	235130	Mm.65867	NM_001024139	ENSMUSG00000033453	Adamts15	-	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 15	protein-coding
mm_392.1	chr1	34099739	34099740	+	1	NA	intron (NM_001276764, intron 5 of 102)	intron (NM_001276764, intron 5 of 102)	-17620	NR_105861	102466987		NR_105861	ENSMUSG00000105982	Mir6896	mmu-mir-6896	microRNA 6896	ncRNA
mm_12104.1	chr2	61578991	61578999	+	1	NA	intron (NM_011529, intron 1 of 7)	intron (NM_011529, intron 1 of 7)	409	NM_011529	21353	Mm.244393	NM_011529	ENSMUSG00000064289	Tank	C86182|E430026L09Rik|I-TRAF	TRAF family member-associated Nf-kappa B activator	protein-coding
mm_12399.1	chr2	70215816	70215822	+	1	NA	intron (NM_177376, intron 9 of 34)	intron (NM_177376, intron 9 of 34)	176693	NM_177376	329421	Mm.99648	NM_177376	ENSMUSG00000042064	Myo3b	A430065P19Rik	myosin IIIB	protein-coding
mm_121103.1	chr14	100213184	100213194	+	1	NA	Intergenic	MTEa|LTR|ERVL-MaLR	-63393	NM_010636	16597	Mm.396499	NM_010636	ENSMUSG00000072294	Klf12	2700063E05Rik|AI225908|AI315654|AP-2rep|B130052C06Rik|D530033K05Rik	Kruppel-like factor 12	protein-coding
mm_108914.1	chr12	100207373	100207388	+	1	NA	3' UTR (NM_009790, exon 6 of 6)	3' UTR (NM_009790, exon 6 of 6)	7236	NM_001313934	12313	Mm.285993	NM_009790	ENSMUSG00000001175	Calm1	AI256814|AI327027|AI461935|AL024000|CaM|Calm	calmodulin 1	protein-coding
mm_39343.1	chr5	8893830	8893840	+	1	NA	5' UTR (NM_008830, exon 1 of 28)	5' UTR (NM_008830, exon 1 of 28)	114	NM_008830	18670	Mm.297825	NM_008830	ENSMUSG00000042476	Abcb4	Mdr2|Pgy-2|Pgy2|mdr-2	ATP-binding cassette, sub-family B (MDR/TAP), member 4	protein-coding
mm_111931.1	chr12	108888751	108888774	-	1	NA	intron (NM_001164314, intron 1 of 9)	intron (NM_001164314, intron 1 of 9)	4436	NM_001164488	22375	Mm.38433	NM_011710	ENSMUSG00000021266	Wars	TrpRS|WRS	tryptophanyl-tRNA synthetase	protein-coding
mm_172994.1	chrM	1412	1417	+	1	NA	NA	Intergenic	NA	NA								
mm_110235.1	chr12	30373303	30373315	-	1	NA	promoter-TSS (NM_172951)	promoter-TSS (NM_172951)	66	NM_172951	268534	Mm.279765	NM_172951	ENSMUSG00000020672	Sntg2	2210008K22Rik|9530013L23|BB121248|G2syn|Syn5	syntrophin, gamma 2	protein-coding
mm_117687.1	chr13	94279048	94279051	-	1	NA	intron (NM_001346609, intron 1 of 8)	intron (NM_001346609, intron 1 of 8)	6232	NM_029153	107767	Mm.201455	NM_029153	ENSMUSG00000021687	Scamp1	4930505M11Rik|AI415563|AW122395	secretory carrier membrane protein 1	protein-coding
mm_140999.1	chr17	24886384	24886394	-	1	NA	promoter-TSS (NM_001163750)	promoter-TSS (NM_001163750)	-39	NM_011956	26426	Mm.36718	NM_011956	ENSMUSG00000039183	Nubp2	D17Wsu11e	nucleotide binding protein 2	protein-coding
mm_31553.1	chr4	56745915	56745918	+	1	NA	TTS (NM_009611)	TTS (NM_009611)	2494	NM_009611	11470	Mm.30959	NM_009611	ENSMUSG00000070979	Actl7a	Tact2	actin-like 7a	protein-coding
mm_49455.1	chr6	29396666	29396666	+	1	NA	promoter-TSS (NM_001347073)	promoter-TSS (NM_001347073)	82	NM_001347073	232664	Mm.251303	NM_145574	ENSMUSG00000029769	Ccdc136	4921511K06Rik|BC006583	coiled-coil domain containing 136	protein-coding
mm_29128.1	chr3	105488034	105488064	-	1	NA	intron (NM_001039347, intron 2 of 6)	intron (NM_001039347, intron 2 of 6)	29233	NM_019931	56543	Mm.44530	NM_019931	ENSMUSG00000040896	Kcnd3	AW045978|Kncd3|Kv4.3	potassium voltage-gated channel, Shal-related family, member 3	protein-coding
mm_147689.1	chr18	60733460	60733481	-	1	NA	Intergenic	Intergenic	-20081	NM_008306	15531	Mm.181862	NM_008306	ENSMUSG00000054008	Ndst1	1200015G06Rik|HSNST|HSNST 1|Hsst|N-HSST|N-HSST 1|NDST-1|b2b2230Clo	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 1	protein-coding
mm_91426.1	chr10	32890081	32890172	-	1	NA	promoter-TSS (NM_001025286)	promoter-TSS (NM_001025286)	-211	NM_001025286	432450	Mm.49665	NM_001013411	ENSMUSG00000069670	Nkain2	6330571D19Rik|AW455467|Tcba1	Na+/K+ transporting ATPase interacting 2	protein-coding
mm_166147.1	chr5	3927534	3927544	+	1	NA	promoter-TSS (NM_194462)	promoter-TSS (NM_194462)	-647	NM_194462	100986	Mm.46044	NM_194462	ENSMUSG00000040407	Akap9	5730481H23Rik|AKAP-9|AKAP450|AW545847|C79026|G1-448-15|PRKA9|mKIAA0803|mei2-5|repro12	A kinase (PRKA) anchor protein (yotiao) 9	protein-coding
mm_58168.1	chr6	142589928	142589948	-	1	NA	3' UTR (NM_011511, exon 40 of 40)	3' UTR (NM_011511, exon 40 of 40)	-18324	NM_008428	16523	Mm.1482	NM_008428	ENSMUSG00000030247	Kcnj8	AI448900|Kir6.1|gnite|slmbr|sltr|uKATP-1	potassium inwardly-rectifying channel, subfamily J, member 8	protein-coding
mm_13039.1	chr2	91082217	91082252	+	1	NA	Intergenic	Intergenic	-11919	NM_001290765	68427	Mm.192375	NM_026721	ENSMUSG00000002105	Slc39a13	1100001L14Rik|AA387663|ZIP-13|ZIP13	solute carrier family 39 (metal ion transporter), member 13	protein-coding
mm_82492.1	chr9	18478261	18478304	-	1	NA	promoter-TSS (NM_028557)	promoter-TSS (NM_028557)	-113	NM_028557	73503	Mm.160088	NM_028557	ENSMUSG00000038691	Mbd3l1	1700070G05Rik|1700095H13Rik|Mbd3l	methyl-CpG binding domain protein 3-like 1	protein-coding
mm_8161.1	chr1	136949541	136949552	-	1	NA	intron (NM_030676, intron 2 of 8)	intron (NM_030676, intron 2 of 8)	4084	NM_001159769	26424	Mm.16794	NM_030676	ENSMUSG00000026398	Nr5a2	AU020803|D1Ertd308e|Ftf|LRH-1|UF2-H3B	nuclear receptor subfamily 5, group A, member 2	protein-coding
mm_103553.1	chr11	77718850	77718856	-	1	NA	TTS (NM_001024205)	TTS (NM_001024205)	6440	NM_001313933	12957	Mm.22830	NM_009965	ENSMUSG00000000724	Cryba1	BA3/A1|Cryb	crystallin, beta A1	protein-coding
mm_170652.1	chr2	101792032	101792032	+	1	NA	intron (NM_001110849, intron 2 of 9)	intron (NM_001110849, intron 2 of 9)	5675	NM_175181	72446	Mm.24138	NM_175181	ENSMUSG00000032841	Prr5l	2600010E01Rik|4833411O04Rik|Protor-2|Protor2	proline rich 5 like	protein-coding
mm_52664.1	chr6	117906721	117906726	+	1	NA	promoter-TSS (NM_001166431)	promoter-TSS (NM_001166431)	-59	NM_001166431	98758	Mm.422979	NM_133834	ENSMUSG00000042079	Hnrnpf	4833420I20Rik|AA407306|Hnrpf	heterogeneous nuclear ribonucleoprotein F	protein-coding
mm_77539.1	chr8	123042246	123042270	-	1	NA	promoter-TSS (NR_045268)	promoter-TSS (NR_045268)	26	NR_037865	77087	Mm.31567	NM_001081379	ENSMUSG00000035569	Ankrd11	2410104C19Rik|3010027A04Rik|6330578C09Rik|9530048I21Rik|AA930108|Gm176|Yod	ankyrin repeat domain 11	protein-coding
mm_17032.1	chr2	20341098	20341136	-	1	NA	intron (NM_001081006, intron 2 of 21)	intron (NM_001081006, intron 2 of 21)	51204	NM_001081006	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding
mm_124577.1	chr14	124594172	124594178	-	1	NA	intron (NM_207667, intron 1 of 4)	intron (NM_207667, intron 1 of 4)	82952	NM_207667	14169	Mm.206362	NM_010201	ENSMUSG00000025551	Fgf14	FHF-4|Fhf4|mFHF-4(1B)	fibroblast growth factor 14	protein-coding
mm_148832.1	chr19	6342550	6342560	+	1	NA	intron (NM_009006, intron 5 of 31)	intron (NM_009006, intron 5 of 31)	1395	NR_117093	26412	Mm.25860	NM_009006	ENSMUSG00000024948	Map4k2	AI385662|BL44|GCK|Rab8ip	mitogen-activated protein kinase kinase kinase kinase 2	protein-coding
mm_115561.1	chr13	9764372	9764421	-	1	NA	promoter-TSS (NM_001347480)	promoter-TSS (NM_001347480)	74	NM_001347470	66505	Mm.397307	NM_144516	ENSMUSG00000021156	Zmynd11	2210402G22Rik|BS69	zinc finger, MYND domain containing 11	protein-coding
mm_140641.1	chr17	12675729	12675739	-	1	NA	5' UTR (NM_009202, exon 1 of 11)	5' UTR (NM_009202, exon 1 of 11)	104	NM_009202	20517	Mm.594	NM_009202	ENSMUSG00000023829	Slc22a1	Lx1|Oct1|Orct|Orct1	solute carrier family 22 (organic cation transporter), member 1	protein-coding
mm_29864.1	chr3	130061020	130061030	-	1	NA	promoter-TSS (NM_207209)	promoter-TSS (NM_207209)	-118	NM_207209	99683	Mm.192303	NM_207209	ENSMUSG00000001052	Sec24b	AI605202|SEC24	Sec24 related gene family, member B (S. cerevisiae)	protein-coding
mm_10643.1	chr2	20548318	20548321	+	1	NA	intron (NM_029895, intron 3 of 18)	intron (NM_029895, intron 3 of 18)	28806	NM_001177631	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding
mm_84021.1	chr9	57681905	57681914	-	1	NA	exon (NM_009993, exon 2 of 7)	exon (NM_009993, exon 2 of 7)	1746	NM_009993	13077	Mm.15537	NM_009993	ENSMUSG00000032310	Cyp1a2	CP12|Cyp1a1|P450-3	cytochrome P450, family 1, subfamily a, polypeptide 2	protein-coding
mm_64245.1	chr7	141702647	141702748	+	1	NA	exon (NM_023566, exon 26 of 46)	exon (NM_023566, exon 26 of 46)	12357	NM_023566	17831	Mm.2041	NM_023566		Muc2	2010015E03Rik|MCM|wnn	mucin 2	protein-coding
mm_121949.1	chr14	24245655	24245693	-	1	NA	5' UTR (NM_027726, exon 1 of 31)	5' UTR (NM_027726, exon 1 of 31)	246	NM_001163513	71228	Mm.68971	NM_027726	ENSMUSG00000021782	Dlg5	4933429D20Rik|T25557|mKIAA0583	discs, large homolog 5 (Drosophila)	protein-coding
mm_104123.1	chr11	86757302	86757314	-	1	NA	5' UTR (NM_001003908, exon 1 of 32)	5' UTR (NM_001003908, exon 1 of 32)	184	NM_001003908	67300	Mm.254588	NM_001003908	ENSMUSG00000047126	Cltc	3110065L21Rik|CHC|R74732	clathrin, heavy polypeptide (Hc)	protein-coding
mm_114973.1	chr13	97241215	97241232	+	1	NA	5' UTR (NM_007930, exon 1 of 3)	5' UTR (NM_007930, exon 1 of 3)	118	NM_007930	13803	Mm.241073	NM_007930	ENSMUSG00000041773	Enc1	Nrpb|PIG10	ectodermal-neural cortex 1	protein-coding
mm_48461.1	chr5	140826731	140826735	-	1	NA	intron (NM_010302, intron 1 of 3)	AT_rich|Low_complexity|Low_complexity	3698	NM_010302	14673	Mm.370185	NM_010302	ENSMUSG00000000149	Gna12	AI414047|AI504261|Galpha12	guanine nucleotide binding protein, alpha 12	protein-coding
mm_167820.1	chr9	124316896	124316926	-	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	-4217	NM_001243119	630836	Mm.458553	NM_001243117	ENSMUSG00000074829	2010315B03Rik	BC029716	RIKEN cDNA 2010315B03 gene	protein-coding
mm_137250.1	chr17	24529108	24529108	+	1	NA	TTS (NR_045289)	TTS (NR_045289)	857	NR_045289	75614	Mm.440235	NR_045289	ENSMUSG00000093565	Rab26os	2610019E17Rik	RAB26, member RAS oncogene family, opposite strand	ncRNA
mm_119614.1	chr14	51114386	51114391	+	1	NA	Intergenic	Intergenic	-2165	NM_203508	219026	Mm.297297	NM_203508	ENSMUSG00000072575	Eddm3b	Fam12|Gm75	epididymal protein 3B	protein-coding
mm_56602.1	chr6	108938667	108938707	-	1	NA	Intergenic	Intergenic	110046	NM_138677	192193	Mm.21596	NM_138677	ENSMUSG00000030104	Edem1	A130059K23Rik|EDEM|mKIAA0212	ER degradation enhancer, mannosidase alpha-like 1	protein-coding
mm_37967.1	chr4	133432981	133433016	-	1	NA	Intergenic	MTEa|LTR|ERVL-MaLR	-47135	NM_175307	100342	Mm.204656	NM_175307	ENSMUSG00000046694	Fam46b	4732473B16Rik|AU045678|AU046069	family with sequence similarity 46, member B	protein-coding
mm_62478.1	chr7	101871541	101871551	+	1	NA	promoter-TSS (NM_008034)	promoter-TSS (NM_008034)	-758	NM_001252552	14275	Mm.2135	NM_008034	ENSMUSG00000001827	Folr1	FBP1|Folbp-1|Folbp1	folate receptor 1 (adult)	protein-coding
mm_165015.1	chr19	29068708	29068713	+	1	NA	intron (NR_045687, intron 1 of 1)	intron (NR_045687, intron 1 of 1)	1409	NR_045687	100503337	Mm.103412	NR_045687		Gm9895	ENSMUSG00000052976	predicted gene 9895	ncRNA
mm_19488.1	chr2	93203338	93203403	-	1	NA	3' UTR (NM_183180, exon 10 of 10)	3' UTR (NM_183180, exon 10 of 10)	15786	NM_001025246	277414	Mm.41033	NM_001025246	ENSMUSG00000068735	Trp53i11	Tp53i11	transformation related protein 53 inducible protein 11	protein-coding
mm_109735.1	chr12	117153859	117153872	+	1	NA	intron (NM_011215, intron 12 of 22)	intron (NM_011215, intron 12 of 22)	-2596	NR_033538	100038689	Mm.445351	NR_033538	ENSMUSG00000099907	Gm10421	ENSMUSG00000072792	predicted gene 10421	ncRNA
mm_27721.1	chr3	68990974	68990976	-	1	NA	intron (NM_026641, intron 2 of 19)	intron (NM_026641, intron 2 of 19)	13595	NM_026641	68259	Mm.389451	NM_026641	ENSMUSG00000027778	Ift80	4921524P20Rik|Wdr56|mKIAA1374	intraflagellar transport 80	protein-coding
mm_82779.1	chr9	27155419	27155425	-	1	NA	promoter-TSS (NM_023277)	promoter-TSS (NM_023277)	-1	NM_023277	83964	Mm.28770	NM_023277	ENSMUSG00000031990	Jam3	1110002N23Rik|JAM-3|JAM-C|Jcam3	junction adhesion molecule 3	protein-coding
mm_88342.1	chr10	75764444	75764477	+	1	NA	promoter-TSS (NM_172549)	promoter-TSS (NM_172549)	-103	NM_172549	104248	Mm.257404	NM_172549	ENSMUSG00000020196	Cabin1	A330070M20Rik|Cain|Ppp3in	calcineurin binding protein 1	protein-coding
mm_143900.1	chr17	84790518	84790585	-	1	NA	5' UTR (NM_028233, exon 1 of 38)	5' UTR (NM_028233, exon 1 of 38)	235	NM_028233	72416	Mm.217027	NM_028233	ENSMUSG00000024120	Lrpprc	3110001K13Rik|C76645|Gp130|Lrp130|Lsfc	leucine-rich PPR-motif containing	protein-coding
mm_65884.1	chr7	29853596	29853609	-	1	NA	promoter-TSS (NM_173738)	promoter-TSS (NM_173738)	46	NM_173738	233057	Mm.296864	NM_173738	ENSMUSG00000050855	Zfp940	-	zinc finger protein 940	protein-coding
mm_131451.1	chr16	16870728	16870736	+	1	NA	promoter-TSS (NM_011624)	promoter-TSS (NM_011624)	-4	NM_001326576	21976	Mm.326089	NM_011624	ENSMUSG00000022779	Top3b	-	topoisomerase (DNA) III beta	protein-coding
mm_33516.1	chr4	130928698	130928702	+	1	NA	exon (NM_010686, exon 4 of 8)	exon (NM_010686, exon 4 of 8)	15366	NM_010686	16792	Mm.271868	NM_010686	ENSMUSG00000028581	Laptm5	E3	lysosomal-associated protein transmembrane 5	protein-coding
mm_167553.1	chr9	35000442	35000446	+	1	NA	intron (NM_001190913, intron 5 of 13)	intron (NM_001190913, intron 5 of 13)	-116284	NR_029475	78934	Mm.391688	NR_029475	ENSMUSG00000070315	4930581F22Rik	-	RIKEN cDNA 4930581F22 gene	ncRNA
mm_163853.1	chr14	19418359	19418396	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	184210	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_126480.1	chr15	81585460	81585508	+	1	NA	promoter-TSS (NM_177821)	promoter-TSS (NM_177821)	-730	NM_177821	328572	Mm.258397	NM_177821	ENSMUSG00000055024	Ep300	A430090G16|A730011L11|KAT3B|p300|p300 HAT	E1A binding protein p300	protein-coding
mm_815.1	chr1	46066821	46066844	+	1	NA	promoter-TSS (NM_001160386)	promoter-TSS (NM_001160386)	94	NM_001160386	227058	Mm.296880	NM_001160386	ENSMUSG00000041144	Dnah7b	Dnahc7b|Gm107	dynein, axonemal, heavy chain 7B	protein-coding
mm_149655.1	chr19	18671191	18671201	+	1	NA	exon (NM_026120, exon 1 of 8)	exon (NM_026120, exon 1 of 8)	416	NM_026120	67383	Mm.306602	NM_026120	ENSMUSG00000024726	Carnmt1	2410127L17Rik	carnosine N-methyltransferase 1	protein-coding
mm_151276.1	chr19	55251953	55251963	+	1	NA	Intergenic	Intergenic	-1411	NM_027976	433256	Mm.292056	NM_027976	ENSMUSG00000024981	Acsl5	1700030F05Rik|ACS2|ACS5|Facl5	acyl-CoA synthetase long-chain family member 5	protein-coding
mm_49103.1	chr6	8209290	8209351	+	1	NA	promoter-TSS (NM_145374)	promoter-TSS (NM_145374)	93	NM_145374	252875	Mm.257151	NM_145374	ENSMUSG00000042447	Mios	C81488	missing oocyte, meiosis regulator, homolog (Drosophila)	protein-coding
mm_160214.1	chr7	98494066	98494066	+	1	NA	promoter-TSS (NM_001113379)	promoter-TSS (NM_001113379)	-156	NM_001113379	434215	Mm.323057	NM_001113379	ENSMUSG00000090958	Lrrc32	AI426318|D11S833Eh|D7H11S833E|EG434215|Garp	leucine rich repeat containing 32	protein-coding
mm_74379.1	chr8	128685787	128685818	+	1	NA	5' UTR (NM_010578, exon 1 of 16)	5' UTR (NM_010578, exon 1 of 16)	148	NM_010578	16412	Mm.263396	NM_010578	ENSMUSG00000025809	Itgb1	4633401G24Rik|AA409975|AA960159|CD29|ENSMUSG00000051907|Fnrb|Gm9863|gpIIa	integrin beta 1 (fibronectin receptor beta)	protein-coding
mm_48255.1	chr5	137831207	137831225	-	1	NA	exon (NM_153510, exon 3 of 7)	exon (NM_153510, exon 3 of 7)	5062	NM_153510	231805	Mm.379385	NM_153510	ENSMUSG00000046245	Pilra	AV021745|FDF03	paired immunoglobin-like type 2 receptor alpha	protein-coding
mm_101643.1	chr11	36477665	36477667	-	1	NA	intron (NM_011856, intron 2 of 28)	intron (NM_011856, intron 2 of 28)	466575	NM_001290702	23964	Mm.439889	NM_011856	ENSMUSG00000049336	Tenm2	Odz2|Odz3|Ten-2|Ten-m2	teneurin transmembrane protein 2	protein-coding
mm_123567.1	chr14	66910892	66910961	-	1	NA	promoter-TSS (NM_175498)	promoter-TSS (NM_175498)	-282	NM_175498	239157	Mm.44358	NM_175498	ENSMUSG00000046204	Pnma2	A830049P17Rik|mKIAA0883	paraneoplastic antigen MA2	protein-coding
mm_151426.1	chr19	56874042	56874058	+	1	NA	promoter-TSS (NM_172840)	promoter-TSS (NM_172840)	-366	NM_172840	240675	Mm.129534	NM_172840	ENSMUSG00000025082	Vwa2	Amaco	von Willebrand factor A domain containing 2	protein-coding
mm_16714.1	chr2	7125600	7125610	-	1	NA	intron (NM_001110231, intron 3 of 15)	intron (NM_001110231, intron 3 of 15)	-44303	NM_001160292	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_79740.1	chr9	62345447	62345453	+	1	NA	intron (NM_009672, intron 1 of 6)	intron (NM_009672, intron 1 of 6)	4107	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	protein-coding
mm_169796.1	chr16	16111322	16111324	+	1	NA	intron (NM_146068, intron 5 of 19)	intron (NM_146068, intron 5 of 19)	35528	NM_146068	224008	Mm.244703	NM_146068	ENSMUSG00000041974	Spidr	2310008H04Rik|Kiaa0146	scaffolding protein involved in DNA repair	protein-coding
mm_37404.1	chr4	121396577	121396585	-	1	NA	Intergenic	Intergenic	26518	NM_001144948	666921	Mm.477980	NM_001144948	ENSMUSG00000078576	Gm12886	OTTMUSG00000008908	predicted gene 12886	protein-coding
mm_155549.1	chrX	74424596	74424629	+	1	NA	promoter-TSS (NM_001161421)	promoter-TSS (NM_001161421)	0	NM_001161421	16151	Mm.12967	NM_010547	ENSMUSG00000004221	Ikbkg	1110037D23Rik|AI848108|AI851264|AW124339|IKK[g]|NEMO	inhibitor of kappaB kinase gamma	protein-coding
mm_170640.1	chr19	8989229	8989230	+	1	NA	promoter-TSS (NM_001286518)	promoter-TSS (NM_001286518)	-55	NR_104460	66395	Mm.203866	NM_009643	ENSMUSG00000069833	Ahnak	DY6	AHNAK nucleoprotein (desmoyokin)	protein-coding
mm_42105.1	chr5	110514935	110514949	+	1	NA	promoter-TSS (NR_102290)	promoter-TSS (NR_102290)	19	NR_102290	231603	Mm.22836	NM_173766	ENSMUSG00000048215	A630023P12Rik	-	RIKEN cDNA A630023P12 gene	ncRNA
mm_128460.1	chr15	50795405	50795415	-	1	NA	intron (NM_001310485, intron 5 of 7)	intron (NM_001310485, intron 5 of 7)	93639	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_29826.1	chr3	129683286	129683324	-	1	NA	exon (NM_010113, exon 22 of 24)	exon (NM_010113, exon 22 of 24)	41781	NM_001310737	13645	Mm.252481	NM_010113	ENSMUSG00000028017	Egf	AI790464	epidermal growth factor	protein-coding
mm_10047.1	chr1	193173399	193173418	-	1	NA	promoter-TSS (NM_181048)	promoter-TSS (NM_181048)	-61	NM_001160360	319266	Mm.482460	NM_181048	ENSMUSG00000079144	A130010J15Rik	-	RIKEN cDNA A130010J15 gene	protein-coding
mm_6307.1	chr1	71585559	71585590	-	1	NA	3' UTR (NM_001276413, exon 44 of 44)	3' UTR (NM_001276413, exon 44 of 44)	28418	NM_026195	108147	Mm.38010	NM_026195	ENSMUSG00000026192	Atic	2610509C24Rik|AA536954|AW212393	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	protein-coding
mm_28733.1	chr3	95736182	95736194	-	1	NA	exon (NM_007899, exon 8 of 11)	exon (NM_007899, exon 8 of 11)	-1215	NR_105981	102466787		NR_105981	ENSMUSG00000098737	Mir7014	Gm27837|mmu-mir-7014	microRNA 7014	ncRNA
mm_35328.1	chr4	26346636	26346678	-	1	NA	promoter-TSS (NM_172865)	promoter-TSS (NM_172865)	-5	NM_172865	242362	Mm.245602	NM_172865	ENSMUSG00000040520	Manea	4932703L02Rik	mannosidase, endo-alpha	protein-coding
mm_33701.1	chr4	133625988	133626009	+	1	NA	intron (NM_001017968, intron 2 of 7)	intron (NM_001017968, intron 2 of 7)	7431	NM_001017968	503610	Mm.331948	NM_001017968	ENSMUSG00000037553	Zdhhc18	-	zinc finger, DHHC domain containing 18	protein-coding
mm_76891.1	chr8	105701049	105701063	-	1	NA	promoter-TSS (NM_019695)	promoter-TSS (NM_019695)	39	NM_001012638	497652	Mm.12964	NM_001012638	ENSMUSG00000038000	Acd	-	adrenocortical dysplasia	protein-coding
mm_46125.1	chr5	92490425	92490428	-	1	NA	intron (NM_007644, intron 1 of 11)	intron (NM_007644, intron 1 of 11)	15231	NM_007644	12492	Mm.297964	NM_007644	ENSMUSG00000029426	Scarb2	9330185J12Rik|Cd36l2|LGP85|LIMP II|LIMP-2|MLGP85	scavenger receptor class B, member 2	protein-coding
mm_161959.1	chr19	7268611	7268611	+	1	NA	5' UTR (NM_001320554, exon 1 of 12)	5' UTR (NM_001320554, exon 1 of 12)	332	NM_001320554	104383	Mm.283859	NM_054048	ENSMUSG00000024968	Rcor2	1A13|AW122124|CoREST|Rcor|Rcor1	REST corepressor 2	protein-coding
mm_164890.1	chr18	61827052	61827056	-	1	NA	intron (NM_198649, intron 7 of 22)	intron (NM_198649, intron 7 of 22)	-40392	NM_178928	106877	Mm.26632	NM_178928	ENSMUSG00000033032	Afap1l1	AI173486	actin filament associated protein 1-like 1	protein-coding
mm_91173.1	chr10	20724966	20724995	-	1	NA	promoter-TSS (NM_013875)	promoter-TSS (NM_013875)	98	NM_013875	29863	Mm.425617	NM_013875	ENSMUSG00000019990	Pde7b	-	phosphodiesterase 7B	protein-coding
mm_13879.1	chr2	119972382	119972394	+	1	NA	promoter-TSS (NM_011941)	promoter-TSS (NM_011941)	-311	NM_011941	26390	Mm.330501	NM_011941	ENSMUSG00000033902	Mapkbp1	2810483F24Rik|AW123212|JNKBP-1|Jnkbp1|mKIAA0596	mitogen-activated protein kinase binding protein 1	protein-coding
mm_165356.1	chr2	121413928	121413930	+	1	NA	promoter-TSS (NM_007952)	promoter-TSS (NM_007952)	27	NM_007952	14827	Mm.263177	NM_007952	ENSMUSG00000027248	Pdia3	58kDa|ERp57|ERp60|ERp61|Erp|Grp58|PDI|PDI-Q2|PI-PLC|PLC[a]|Plca	protein disulfide isomerase associated 3	protein-coding
mm_75541.1	chr8	57487564	57487578	-	1	NA	promoter-TSS (NR_126555)	promoter-TSS (NR_126555)	289	NM_021788	60406	Mm.118	NM_021788	ENSMUSG00000031609	Sap30	30kDa	sin3 associated polypeptide	protein-coding
mm_111832.1	chr12	107735491	107735501	-	1	NA	promoter-TSS (NR_045973)	promoter-TSS (NR_045973)	-8	NR_045973	74968	Mm.359821	NR_045973	ENSMUSG00000085641	4930465M20Rik	4930431H15Rik	RIKEN cDNA 4930465M20 gene	ncRNA
mm_131034.1	chr16	3745795	3745849	+	1	NA	exon (NM_148924, exon 2 of 6)	exon (NM_148924, exon 2 of 6)	1723	NM_148924	74120	Mm.29081	NM_148924	ENSMUSG00000022529	Zfp263	1200014J04Rik|AI326880|AU020888|NT2|mFPM315	zinc finger protein 263	protein-coding
mm_154376.1	chrM	11121	11134	+	1	NA	NA	Intergenic	NA	NA								
mm_105124.1	chr11	101175441	101175444	-	1	NA	promoter-TSS (NM_016782)	promoter-TSS (NM_016782)	1	NM_007721	12777	Mm.8021	NM_007721	ENSMUSG00000044052	Ccr10	Cmkbr9|Gpr2	chemokine (C-C motif) receptor 10	protein-coding
mm_103132.1	chr11	70237606	70237633	-	1	NA	TTS (NM_173742)	TTS (NM_173742)	295	NM_001177601	104457	Mm.30016	NM_026757	ENSMUSG00000020831	0610010K14Rik	1110020A23Rik|AL033328|AU045833|Bap18	RIKEN cDNA 0610010K14 gene	protein-coding
mm_79589.1	chr9	58275541	58275556	+	1	NA	Intergenic	L1MD3|LINE|L1	22384	NM_026942	69106	Mm.216502	NM_026942	ENSMUSG00000032333	Stoml1	1810015E19Rik|AI847431|SLP1|STORP|UNC24|WPB72	stomatin-like 1	protein-coding
mm_55405.1	chr6	60829787	60829823	-	1	NA	promoter-TSS (NM_001042451)	promoter-TSS (NM_001042451)	50	NM_009221	20617	Mm.17484	NM_009221	ENSMUSG00000025889	Snca	NACP|alphaSYN	synuclein, alpha	protein-coding
mm_82004.1	chr9	121707999	121708001	+	1	NA	Intergenic	Intergenic	-2389	NM_026794	26901	Mm.24848	NM_026794	ENSMUSG00000032526	Ss18l2	1110020I04Rik|AI463209|Deb1	SS18, nBAF chromatin remodeling complex subunit like 2	protein-coding
mm_68012.1	chr7	100947531	100947557	-	1	NA	intron (NM_183168, intron 1 of 2)	RSINE1|SINE|B4	-15383	NM_001081116	207212	Mm.29954	NM_001081116	ENSMUSG00000032875	Arhgef17	8030463K16|AI428794|AW558066|BC035332|mKIAA0337	Rho guanine nucleotide exchange factor (GEF) 17	protein-coding
mm_161726.1	chr17	28350362	28350362	-	1	NA	promoter-TSS (NM_001204156)	promoter-TSS (NM_001204156)	-16	NM_001204156	21678	Mm.6655	NM_011566	ENSMUSG00000002249	Tead3	DTEF-1|ETFR-1|TEAD-3|TEF-5|Tcf13r2	TEA domain family member 3	protein-coding
mm_124827.1	chr15	9092225	9092234	+	1	NA	intron (NM_001040395, intron 5 of 12)	intron (NM_001040395, intron 5 of 12)	20969	NM_001040395	68646	Mm.244226	NM_001040395	ENSMUSG00000022253	Nadk2	MNADK|Nadkd1	NAD kinase 2, mitochondrial	protein-coding
mm_153949.1	chr19	47622300	47622316	-	1	NA	exon (NM_001164639, exon 10 of 18)	exon (NM_001164639, exon 10 of 18)	42289	NM_001164639	20874	Mm.281011	NM_009289	ENSMUSG00000025060	Slk	9A2|AV021402|AW411554|Etk4|SMAK|Stk2|mKIAA0204|mSLK	STE20-like kinase	protein-coding
mm_103922.1	chr11	83604694	83604702	-	1	NA	intron (NR_036453, intron 2 of 8)	LTR16E2|LTR|ERVL	-11611	NM_009139	20305	Mm.137	NM_009139	ENSMUSG00000018927	Ccl6	MRP-1|Scya6|c10	chemokine (C-C motif) ligand 6	protein-coding
mm_115496.1	chr13	3804308	3804337	-	1	NA	promoter-TSS (NM_027416)	promoter-TSS (NM_027416)	-4	NM_027416	70405	Mm.20079	NM_027416	ENSMUSG00000063130	Calml3	2310068O22Rik|AI326174	calmodulin-like 3	protein-coding
mm_103882.1	chr11	83530651	83530664	-	1	NA	promoter-TSS (NM_013653)	promoter-TSS (NM_013653)	-139	NM_013653	20304	Mm.284248	NM_013653	ENSMUSG00000035042	Ccl5	MuRantes|RANTES|SISd|Scya5|TCP228	chemokine (C-C motif) ligand 5	protein-coding
mm_91792.1	chr10	53371822	53371823	-	1	NA	intron (NM_001204983, intron 1 of 12)	MurERV4-int|LTR|ERVK	8029	NM_001204983	100038725	Mm.441403	NM_001204983	ENSMUSG00000038594	Cep85l	ENSMUSG00000038594|Gm9766	centrosomal protein 85-like	protein-coding
mm_111668.1	chr12	103336938	103336959	-	1	NA	intron (NM_023049, intron 3 of 9)	intron (NM_023049, intron 3 of 9)	19053	NM_023049	65256	Mm.27159	NM_023049	ENSMUSG00000021200	Asb2	1110008E15Rik	ankyrin repeat and SOCS box-containing 2	protein-coding
mm_51187.1	chr6	70956457	70956460	+	1	NA	promoter-TSS (NM_001101464)	promoter-TSS (NM_001101464)	-148	NM_001101464	232077	Mm.297656	NM_001101464	ENSMUSG00000055874	Foxi3	-	forkhead box I3	protein-coding
mm_168759.1	chr12	118178917	118178917	+	1	NA	intron (NM_010060, intron 7 of 81)	intron (NM_010060, intron 7 of 81)	20126	NM_010060	13411	Mm.390540	NM_010060	ENSMUSG00000018581	Dnah11	Dnahc11|b2b1203Clo|b2b1279Clo|b2b1289Clo|b2b1727Clo|b2b598Clo|iv|lrd	dynein, axonemal, heavy chain 11	protein-coding
mm_411.1	chr1	34215325	34215332	+	1	NA	intron (NM_001276764, intron 53 of 102)	intron (NM_001276764, intron 53 of 102)	54998	NM_010081	13518	Mm.336625	NM_010081	ENSMUSG00000026131	Dst	2310001O04Rik|A830042E19Rik|AW554249|BP230|BPAG1-n|Bpag|Bpag1|Macf2|ah|athetoid|dt|mKIAA0728|nmf203|nmf339	dystonin	protein-coding
mm_134123.1	chr16	10313941	10313953	-	1	NA	promoter-TSS (NM_007929)	promoter-TSS (NM_007929)	21	NM_007929	13731	Mm.246009	NM_007929	ENSMUSG00000022505	Emp2	XMP	epithelial membrane protein 2	protein-coding
mm_119586.1	chr14	50927216	50927219	+	1	NA	TTS (NM_009687)	TTS (NM_009687)	2268	NM_009687	11792	Mm.203	NM_009687	ENSMUSG00000035960	Apex1	APE|Apex|HAP1|Ref-1	apurinic/apyrimidinic endonuclease 1	protein-coding
mm_75627.1	chr8	64692949	64692979	-	1	NA	5' UTR (NM_013494, exon 1 of 9)	5' UTR (NM_013494, exon 1 of 9)	145	NM_013494	12876	Mm.31395	NM_013494	ENSMUSG00000037852	Cpe	CPH|Cph-1|Cph1|R74677|fat	carboxypeptidase E	protein-coding
mm_94797.1	chr11	22973201	22973260	+	1	NA	exon (NM_011663, exon 1 of 1)	exon (NM_011663, exon 1 of 1)	1225	NM_011663	22183	Mm.29542	NM_011663	ENSMUSG00000044068	Zrsr1	D11Ncvs75|Irlgs2|SP2|U2af1-rs1|U2afbp-rs	zinc finger (CCCH type), RNA binding motif and serine/arginine rich 1	protein-coding
mm_56037.1	chr6	86669111	86669125	-	1	NA	promoter-TSS (NM_010751)	promoter-TSS (NM_010751)	41	NM_010751	17119	Mm.279580	NM_010751	ENSMUSG00000001156	Mxd1	AW122478|Mad|Mad1	MAX dimerization protein 1	protein-coding
mm_142692.1	chr17	47768762	47768788	-	1	NA	intron (NM_001161723, intron 1 of 8)	intron (NM_001161723, intron 1 of 8)	-16969	NM_011549	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_33354.1	chr4	129458351	129458351	+	1	NA	Intergenic	U1|snRNA|snRNA	-3328	NM_133889	100383	Mm.17918	NM_133889	ENSMUSG00000040859	Bsdc1	1110063F24Rik|AW011758	BSD domain containing 1	protein-coding
mm_117483.1	chr13	77135498	77135514	-	1	NA	promoter-TSS (NM_134071)	promoter-TSS (NM_134071)	-30	NM_001081353	72371	Mm.81475	NM_028215	ENSMUSG00000071252	2210408I21Rik	-	RIKEN cDNA 2210408I21 gene	protein-coding
mm_145712.1	chr18	62950072	62950074	+	1	NA	exon (NM_133237, exon 4 of 5)	exon (NM_133237, exon 4 of 5)	27746	NM_133237	494504	Mm.391102	NM_133237	ENSMUSG00000071847	Apcdd1	AB023957|AU041258|Drapc1|EIG180	adenomatosis polyposis coli down-regulated 1	protein-coding
mm_172004.1	chr6	108565675	108565694	-	1	NA	Intergenic	Intergenic	57483	NR_040757	75394	Mm.395061	NR_040757	ENSMUSG00000087341	0610040F04Rik	-	RIKEN cDNA 0610040F04 gene	ncRNA
mm_130455.1	chr15	98567563	98567573	-	1	NA	promoter-TSS (NM_009833)	promoter-TSS (NM_009833)	68	NM_009833	12455	Mm.29941	NM_009833	ENSMUSG00000011960	Ccnt1	2810478G24Rik|AI115585|CycT1	cyclin T1	protein-coding
mm_164271.1	chr15	101469373	101469381	+	1	NA	intron (NM_016879, intron 6 of 9)	intron (NM_016879, intron 6 of 9)	-4101	NM_010667	16679	Mm.383183	NM_010667	ENSMUSG00000067614	Krt86	5430421N21Rik|AI325212|Khb4|Krt2-10|Krt2-11|MHb4	keratin 86	protein-coding
mm_124529.1	chr14	122233623	122233640	-	1	NA	promoter-TSS (NR_015532)	promoter-TSS (NR_015532)	7	NR_015532	68245	Mm.443285	NR_015532	ENSMUSG00000100585	1700108J01Rik	-	RIKEN cDNA 1700108J01 gene	ncRNA
mm_24557.1	chr3	93443570	93443573	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	1241	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_92766.1	chr10	81129049	81129085	-	1	NA	Intergenic	Intergenic	-7204	NM_010731	16969	Mm.20920	NM_010731	ENSMUSG00000035011	Zbtb7a	9030619K07Rik|9130006G12Rik|AI452336|FBI-1|Lrf|Pokemon|Zbtb7	zinc finger and BTB domain containing 7a	protein-coding
mm_142688.1	chr17	47734476	47734481	-	1	NA	TTS (NM_025973)	TTS (NM_025973)	-2559	NM_001161722	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_55809.1	chr6	82939677	82939760	-	1	NA	promoter-TSS (NM_011350)	promoter-TSS (NM_011350)	51	NM_001308374	20355	Mm.270543	NM_011350	ENSMUSG00000000627	Sema4f	Sema W	sema domain, immunoglobulin domain (Ig), TM domain, and short cytoplasmic domain	protein-coding
mm_132171.1	chr16	32312542	32312544	+	1	NA	Intergenic	RLTR41|LTR|ERV1	-19709	NM_177633	224111	Mm.31275	NM_177633	ENSMUSG00000053774	Ubxn7	A630090P18|AI196514|Ubxd7|mKIAA0794	UBX domain protein 7	protein-coding
mm_24315.1	chr3	89423386	89423397	+	1	NA	intron (NM_001113331, intron 2 of 11)	intron (NM_001113331, intron 2 of 11)	1770	NM_001113331	20416	Mm.86595	NM_011368	ENSMUSG00000042626	Shc1	Shc|ShcA|p66|p66shc	src homology 2 domain-containing transforming protein C1	protein-coding
mm_81685.1	chr9	111118243	111118264	+	1	NA	5' UTR (NM_001164838, exon 1 of 15)	5' UTR (NM_001164838, exon 1 of 15)	142	NM_001164838	71268	Mm.302287	NM_027742	ENSMUSG00000032497	Lrrfip2	5133400F20Rik|AI850587	leucine rich repeat (in FLII) interacting protein 2	protein-coding
mm_9427.1	chr1	172482119	172482131	-	1	NA	promoter-TSS (NM_001145800)	promoter-TSS (NM_001145800)	-88	NM_001145800	93842	Mm.214530	NM_033608	ENSMUSG00000037995	Igsf9	644ETD8|Dasm1|Kiaa1355-hp|NRT1|Ncaml|mKIAA1355	immunoglobulin superfamily, member 9	protein-coding
mm_62343.1	chr7	100498152	100498210	+	1	NA	exon (NM_011671, exon 5 of 8)	exon (NM_011671, exon 5 of 8)	4823	NM_011671	22228	Mm.171378	NM_011671	ENSMUSG00000033685	Ucp2	Slc25a8	uncoupling protein 2 (mitochondrial, proton carrier)	protein-coding
mm_153450.1	chr19	41031174	41031180	-	1	NA	intron (NM_009345, intron 1 of 11)	intron (NM_009345, intron 1 of 11)	1902	NM_009345	21673	Mm.25620	NM_009345	ENSMUSG00000025014	Dntt	Tdt	deoxynucleotidyltransferase, terminal	protein-coding
mm_100145.1	chr11	115993104	115993112	+	1	NA	exon (NM_133663, exon 24 of 39)	exon (NM_133663, exon 24 of 39)	18383	NM_133663	192897	Mm.213873	NM_133663	ENSMUSG00000020758	Itgb4	AA407042|C230078O20|CD104	integrin beta 4	protein-coding
mm_123844.1	chr14	70659800	70659811	-	1	NA	3' UTR (NM_023045, exon 28 of 28)	3' UTR (NM_023045, exon 28 of 28)	-6721	NM_181345	328440	Mm.347749	NM_181345	ENSMUSG00000047911	Npm2	-	nucleophosmin/nucleoplasmin 2	protein-coding
mm_2486.1	chr1	105990189	105990209	+	1	NA	promoter-TSS (NM_001122675)	promoter-TSS (NM_001122675)	-207	NM_001122676	227449	Mm.210188	NM_001122675	ENSMUSG00000038866	Zcchc2	9930114B20Rik|AW212015	zinc finger, CCHC domain containing 2	protein-coding
mm_95060.1	chr11	32455049	32455099	+	1	NA	promoter-TSS (NM_173784)	promoter-TSS (NM_173784)	-298	NM_173784	327900	Mm.260956	NM_173784	ENSMUSG00000044949	Ubtd2	4930571L24|9630054F20Rik|AI645720	ubiquitin domain containing 2	protein-coding
mm_164986.1	chr19	10555763	10555782	-	1	NA	promoter-TSS (NM_001277861)	promoter-TSS (NM_001277861)	-9	NM_001277860	68642	Mm.31236	NM_026798	ENSMUSG00000024667	Tmem216	1110017C22Rik|2810441K11Rik|4921533J23Rik|A930021F15Rik|AI482550	transmembrane protein 216	protein-coding
mm_172596.1	chr8	15034622	15034632	-	1	NA	Intergenic	RLTR11B|LTR|ERVK	11451	NR_037972	434285	Mm.334425	NM_001007591	ENSMUSG00000049008	BB014433	-	expressed sequence BB014433	ncRNA
mm_54622.1	chr6	38551993	38552027	-	1	NA	intron (NM_138680, intron 1 of 9)	CpG	676	NM_001170848	192196	Mm.276133	NM_138680	ENSMUSG00000029823	Luc7l2	4930471C18Rik|AA522013|AU015269|CGI59|Cgi74	LUC7-like 2 (S. cerevisiae)	protein-coding
mm_56282.1	chr6	91411321	91411331	-	1	NA	promoter-TSS (NM_009527)	promoter-TSS (NM_009527)	43	NM_009527	22421	Mm.56964	NM_009527	ENSMUSG00000030093	Wnt7a	AI849442|Wnt-7a|px|tw	wingless-type MMTV integration site family, member 7A	protein-coding
mm_14915.1	chr2	150786741	150786794	+	1	NA	promoter-TSS (NM_153781)	promoter-TSS (NM_153781)	-29	NM_153781	110078	Mm.222584	NM_153781	ENSMUSG00000033059	Pygb	-	brain glycogen phosphorylase	protein-coding
mm_285.1	chr1	21272367	21272401	+	1	NA	Intergenic	Intergenic	25928	NR_002858	241041	Mm.290634	NR_002858	ENSMUSG00000025936	Gm4956	EG241041	predicted gene 4956	pseudo
mm_31588.1	chr4	57845241	57845265	+	1	NA	promoter-TSS (NM_001035532)	promoter-TSS (NM_001035532)	5	NM_001035532	11641	Mm.467752	NM_009649	ENSMUSG00000038729	Akap2	AA959716|AI649048|Akap-2|Akap-kl|B230340M18Rik|Prka2	A kinase (PRKA) anchor protein 2	protein-coding
mm_1526.1	chr1	72832894	72832896	+	1	NA	intron (NM_001310659, intron 1 of 3)	intron (NM_001310659, intron 1 of 3)	7508	NM_001310659	16008	Mm.141936	NM_008342	ENSMUSG00000039323	Igfbp2	AI255832|IBP-2|Igfbp-2|mIGFBP-2	insulin-like growth factor binding protein 2	protein-coding
mm_5197.1	chr1	13373880	13373891	-	1	NA	intron (NM_008678, intron 1 of 22)	CpG	198	NM_008678	17978	Mm.2537	NM_008678	ENSMUSG00000005886	Ncoa2	D1Ertd433e|GRIP-1|Grip1|KAT13C|NCoA-2|SRC-2|TIF2|bHLHe75	nuclear receptor coactivator 2	protein-coding
mm_81503.1	chr9	110034599	110034618	+	1	NA	exon (NM_008633, exon 7 of 19)	exon (NM_008633, exon 7 of 19)	-17413	NM_001311163	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_78768.1	chr9	43311107	43311128	+	1	NA	exon (NM_023655, exon 1 of 9)	exon (NM_023655, exon 1 of 9)	354	NM_023655	72169	Mm.273277	NM_023655	ENSMUSG00000032013	Trim29	1110047J21Rik|2810431N19Rik|4732461M22Rik|AI119726	tripartite motif-containing 29	protein-coding
mm_168031.1	chrY	90738591	90738631	-	1	NA	Intergenic	IMPB_01|Satellite|Satellite	16439	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_133625.1	chr16	91563537	91563541	+	1	NA	3' UTR (NM_008338, exon 7 of 7)	3' UTR (NM_008338, exon 7 of 7)	16445	NM_008338	15980	Mm.249364	NM_008338	ENSMUSG00000022965	Ifngr2	Ifgr2|Ifgt	interferon gamma receptor 2	protein-coding
mm_38238.1	chr4	136180502	136180514	-	1	NA	promoter-TSS (NM_001305399)	promoter-TSS (NM_001305399)	-274	NM_001305399	242705	Mm.307932	NM_177733	ENSMUSG00000018983	E2f2	E2F-2	E2F transcription factor 2	protein-coding
mm_118474.1	chr14	11604057	11604060	+	1	NA	intron (NM_008981, intron 1 of 29)	intron (NM_008981, intron 1 of 29)	50505	NM_008981	19270	Mm.431266	NM_008981	ENSMUSG00000021745	Ptprg	5430405N12Rik|AW046354|AW549872|RPTPgamma	protein tyrosine phosphatase, receptor type, G	protein-coding
mm_135967.1	chr16	74867091	74867099	-	1	NA	Intergenic	Intergenic	-456183	NM_175549	268902	Mm.171736	NM_175549	ENSMUSG00000052516	Robo2	2600013A04Rik|9430089E08Rik|BB097918|D230004I22Rik|mKIAA1568	roundabout guidance receptor 2	protein-coding
mm_31941.1	chr4	86577104	86577116	+	1	NA	3' UTR (NM_178376, exon 1 of 1)	3' UTR (NM_178376, exon 1 of 1)	1437	NM_178376	68441	Mm.31178	NM_178376	ENSMUSG00000070934	Rraga	1300010C19Rik|AI255374|FIP-1|RAGA	Ras-related GTP binding A	protein-coding
mm_52123.1	chr6	97941196	97941209	+	1	NA	exon (NM_001178049, exon 2 of 10)	exon (NM_001178049, exon 2 of 10)	11385	NM_001178049	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_150763.1	chr19	44241894	44241908	+	1	NA	3' UTR (NM_024450, exon 6 of 6)	3' UTR (NM_024450, exon 6 of 6)	38613	NM_024450	30049	Mm.480594	NM_024450	ENSMUSG00000025202	Scd3	4930513N16Rik	stearoyl-coenzyme A desaturase 3	protein-coding
mm_142168.1	chr17	36168514	36168528	-	1	NA	promoter-TSS (NM_001081032)	promoter-TSS (NM_001081032)	16	NM_001081032	667977	Mm.441651	NM_001081032	ENSMUSG00000073402	Gm8909	EG667977|H2-Tw5l|H2-gs17	predicted gene 8909	protein-coding
mm_50394.1	chr6	48708359	48708368	+	1	NA	promoter-TSS (NM_153175)	promoter-TSS (NM_153175)	-119	NM_153175	231931	Mm.321047	NM_153175	ENSMUSG00000047867	Gimap6	4833419H03Rik|Ian6|mFLJ00102	GTPase, IMAP family member 6	protein-coding
mm_6583.1	chr1	75236262	75236283	-	1	NA	promoter-TSS (NM_001159883)	promoter-TSS (NM_001159883)	-151	NM_020266	56812	Mm.489660	NM_020266	ENSMUSG00000026203	Dnajb2	2700059H22Rik|Dnajb10|Hsj1|mDj8	DnaJ heat shock protein family (Hsp40) member B2	protein-coding
mm_144752.1	chr18	35703213	35703221	+	1	NA	promoter-TSS (NM_029669)	promoter-TSS (NM_029669)	-73	NM_029669	76594	Mm.108596	NM_029669	ENSMUSG00000024350	Dnajc18	2700075B01Rik|AU041129	DnaJ heat shock protein family (Hsp40) member C18	protein-coding
mm_65541.1	chr7	26939378	26939390	-	1	NA	promoter-TSS (NM_001101467)	promoter-TSS (NM_001101467)	2	NM_001101467	233005	Mm.291574	NM_001101467	ENSMUSG00000091867	Cyp2a22	EG233005	cytochrome P450, family 2, subfamily a, polypeptide 22	protein-coding
mm_77906.1	chr9	7349156	7349179	+	1	NA	intron (NM_001320077, intron 3 of 10)	B4A|SINE|B4	1793	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_8916.1	chr1	163313523	163313533	-	1	NA	5' UTR (NM_175686, exon 1 of 5)	5' UTR (NM_175686, exon 1 of 5)	122	NM_011127	18933	Mm.288642	NM_011127	ENSMUSG00000026586	Prrx1	A230024N07Rik|AA755424|AI385634|AI843499|K-2|Pmx|Pmx1|Prx1|mHox	paired related homeobox 1	protein-coding
mm_37191.1	chr4	117494978	117494996	-	1	NA	intron (NM_025739, intron 1 of 14)	CpG	2065	NM_025739	66743	Mm.318331	NM_025739	ENSMUSG00000028677	Rnf220	4732477A13|4931406I20Rik|5730503K05Rik|AV302541	ring finger protein 220	protein-coding
mm_66733.1	chr7	46667304	46667316	-	1	NA	promoter-TSS (NM_001276372)	promoter-TSS (NM_001276372)	67	NM_001136084	21990	Mm.248684	NM_009414	ENSMUSG00000040046	Tph1	Tph	tryptophan hydroxylase 1	protein-coding
mm_112516.1	chr13	9093960	9093970	+	1	NA	promoter-TSS (NM_172585)	promoter-TSS (NM_172585)	84	NM_172585	217980	Mm.234944	NM_172585	ENSMUSG00000033499	Larp4b	A630096F19|AI256361|D13Wsu64e|Larp5	La ribonucleoprotein domain family, member 4B	protein-coding
mm_27932.1	chr3	79567772	79567790	-	1	NA	promoter-TSS (NM_001162999)	promoter-TSS (NM_001162999)	-102	NM_001162999	329679	Mm.244005	NM_001162999	ENSMUSG00000061175	Fnip2	D630023B12Rik|mKIAA1450	folliculin interacting protein 2	protein-coding
mm_103989.1	chr11	84829124	84829132	-	1	NA	promoter-TSS (NR_046281)	promoter-TSS (NR_046281)	-50	NR_046281	74995	Mm.84413	NR_046281	ENSMUSG00000086799	4930502E09Rik	-	RIKEN cDNA 4930502E09 gene	ncRNA
mm_162307.1	chr1	36883296	36883300	+	1	NA	intron (NM_018872, intron 2 of 40)	ORR1B1|LTR|ERVL-MaLR	56229	NM_018872	56030	Mm.186943	NM_018872	ENSMUSG00000026116	Tmem131	2610524E03Rik|CC28|D1Bwg0491e|Neg|RW1|YR-23|mKIAA0257	transmembrane protein 131	protein-coding
mm_76210.1	chr8	83442522	83442543	-	1	NA	5' UTR (NM_019708, exon 1 of 4)	5' UTR (NM_019708, exon 1 of 4)	130	NM_001285992	56367	Mm.246911	NM_019708	ENSMUSG00000063253	Scoc	0610011C06Rik|2810002J11Rik|AA415030|SCOCO	short coiled-coil protein	protein-coding
mm_132047.1	chr16	29209708	29209726	+	1	NA	promoter-TSS (NM_013751)	promoter-TSS (NM_013751)	22	NM_013751	27281	Mm.103650	NM_013751	ENSMUSG00000022525	Hrasls	2810012B06Rik|A-C1|HRSL1|Hrasrs	HRAS-like suppressor	protein-coding
mm_88162.1	chr10	69706320	69706324	+	1	NA	intron (NM_170730, intron 1 of 17)	(TC)n|Simple_repeat|Simple_repeat	172614	NM_146005	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_51629.1	chr6	85464876	85464883	+	1	NA	exon (NM_007638, exon 7 of 12)	exon (NM_007638, exon 7 of 12)	-12909	NR_028081	73327	Mm.379221	NM_028505	ENSMUSG00000030008	Pradc1	1700040I03Rik|Pap21	protease-associated domain containing 1	protein-coding
mm_59104.1	chr7	19749905	19749941	+	1	NA	promoter-TSS (NM_001159724)	promoter-TSS (NM_001159724)	-350	NM_001159724	19294	Mm.4341	NM_008990	ENSMUSG00000062300	Nectin2	AI325026|AI987993|Cd112|MPH|Pvr|Pvrl2|Pvs|nectin-2	nectin cell adhesion molecule 2	protein-coding
mm_7648.1	chr1	128299954	128299987	-	1	NA	exon (NM_001081078, exon 8 of 17)	exon (NM_001081078, exon 8 of 17)	28348	NM_001081078	226413	Mm.26930	NM_001081078	ENSMUSG00000026354	Lct	Gm100|LAC|LPH|Lphl	lactase	protein-coding
mm_124971.1	chr15	18923338	18923341	+	1	NA	intron (NM_009865, intron 2 of 11)	intron (NM_009865, intron 2 of 11)	103010	NM_009865	320873	Mm.117794	NM_009865	ENSMUSG00000022321	Cdh10	A830016G23Rik|C030003B10Rik|C030011H18Rik	cadherin 10	protein-coding
mm_135723.1	chr16	55819624	55819637	-	1	NA	exon (NM_030612, exon 4 of 14)	exon (NM_030612, exon 4 of 14)	2508	NM_001159394	80859	Mm.247272	NM_030612	ENSMUSG00000035356	Nfkbiz	AA408868|INAP|Mail	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, zeta	protein-coding
mm_81433.1	chr9	109095399	109095411	+	1	NA	promoter-TSS (NM_172775)	promoter-TSS (NM_172775)	-31	NM_172775	235611	Mm.53862	NM_172775	ENSMUSG00000053646	Plxnb1	2900002G15Rik|AU042020|mKIAA0407	plexin B1	protein-coding
mm_24060.1	chr3	87915277	87915327	+	1	NA	3' UTR (NM_008231, exon 6 of 6)	3' UTR (NM_008231, exon 6 of 6)	-4242	NM_026591	67707	Mm.393802	NM_026591	ENSMUSG00000019710	Mrpl24	2010005E08Rik|2810470K06Rik|6720473G22Rik|AA407670	mitochondrial ribosomal protein L24	protein-coding
mm_16478.1	chr2	180825703	180825704	+	1	NA	Intergenic	Intergenic	-48803	NM_080641	140489	Mm.134062	NM_080641	ENSMUSG00000045493	Bhlhe23	A930001L02Rik|BETA4|Beta3b|Bhlhb4	basic helix-loop-helix family, member e23	protein-coding
mm_50791.1	chr6	54039747	54039761	+	1	NA	promoter-TSS (NM_001163640)	promoter-TSS (NM_001163640)	-178	NM_001163640	69993	Mm.321147	NM_023543	ENSMUSG00000004633	Chn2	1700026N20Rik|4930557O16Rik|ARHGAP3|Bch	chimerin 2	protein-coding
mm_64024.1	chr7	140763811	140763828	+	1	NA	promoter-TSS (NM_021282)	promoter-TSS (NM_021282)	-13	NM_021282	13106	Mm.21758	NM_021282	ENSMUSG00000025479	Cyp2e1	Cyp2e	cytochrome P450, family 2, subfamily e, polypeptide 1	protein-coding
mm_156014.1	chrX	107089387	107089409	+	1	NA	promoter-TSS (NM_172435)	promoter-TSS (NM_172435)	63	NM_172435	78826	Mm.74639	NM_172435	ENSMUSG00000050921	P2ry10	5830408N17Rik|Lypsr2|P2Y10	purinergic receptor P2Y, G-protein coupled 10	protein-coding
mm_172626.1	chr8	20398010	20398014	-	1	NA	intron (NR_028428, intron 5 of 5)	B3|SINE|B2	26802	NR_028428	381598	Mm.359054	NM_001024708	ENSMUSG00000071793	2610005L07Rik	2810038F24Rik|6720476A01Rik	cadherin 11 pseudogene	pseudo
mm_46016.1	chr5	90903115	90903143	-	1	NA	promoter-TSS (NM_009140)	promoter-TSS (NM_009140)	-770	NM_009140	20310	Mm.4979	NM_009140	ENSMUSG00000058427	Cxcl2	CINC-2a|GROb|Gro2|MIP-2|MIP-2a|Mgsa-b|Mip2|Scyb|Scyb2	chemokine (C-X-C motif) ligand 2	protein-coding
mm_6016.1	chr1	59014122	59014151	-	1	NA	Intergenic	Intergenic	40565	NM_172656	227154	Mm.286006	NM_172656	ENSMUSG00000026027	Stradb	AA792893|Als2cr2|B830008M19|D1Ucla2|ILPIP|ILPIPA|PRO1038|Papk|Syradb	STE20-related kinase adaptor beta	protein-coding
mm_109420.1	chr12	110497647	110497688	+	1	NA	intron (NM_012023, intron 1 of 13)	intron (NM_012023, intron 1 of 13)	11928	NM_012023	26931	Mm.240396	NM_012023	ENSMUSG00000017843	Ppp2r5c	2610043M05Rik|2700063L20Rik|AI060890|AW545884|C85228|D12Bwg0916e|mKIAA0044	protein phosphatase 2, regulatory subunit B', gamma	protein-coding
mm_18985.1	chr2	76856331	76856343	-	1	NA	exon (NM_011652, exon 124 of 313)	exon (NM_011652, exon 124 of 313)	126210	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_102723.1	chr11	67215947	67215957	-	1	NA	exon (NM_030679, exon 28 of 40)	exon (NM_030679, exon 28 of 40)	15838	NM_030679	17879	Mm.477065	NM_030679	ENSMUSG00000056328	Myh1	A530084A17Rik|IId|IId/x|MHC-2X/D|MHC2X/D|MYHC-IIX|MdMs|MyHC-IId/x|MyHC-IIx/d|Myhs-f|Myhs-f2|Myhsf2	myosin, heavy polypeptide 1, skeletal muscle, adult	protein-coding
mm_154370.1	chrM	9871	9885	+	1	NA	NA	Intergenic	NA	NA								
mm_126937.1	chr15	91838323	91838332	+	1	NA	promoter-TSS (NM_207243)	promoter-TSS (NM_207243)	1	NM_207243	239611	Mm.486225	NM_207243		Muc19	MUC-19|sld	mucin 19	protein-coding
mm_16576.1	chr2	3475028	3475086	-	1	NA	promoter-TSS (NM_022724)	promoter-TSS (NM_022724)	-71	NR_027509	64707	Mm.23483	NM_022724	ENSMUSG00000026646	Suv39h2	4930507K23Rik|AA536750|D030054H19Rik|D2Ertd544e|KMT1B	suppressor of variegation 3-9 homolog 2 (Drosophila)	protein-coding
mm_37456.1	chr4	123432237	123432245	-	1	NA	exon (NM_001199137, exon 52 of 93)	exon (NM_001199137, exon 52 of 93)	-20330	NM_001167918	442834	Mm.483803	NM_001167918		D830031N03Rik	Kiaa0754|mKIAA0754	RIKEN cDNA D830031N03 gene	protein-coding
mm_141294.1	chr17	28079800	28079809	-	1	NA	intron (NM_001085555, intron 2 of 9)	CpG	780	NM_013687	21463	Mm.29758	NM_013687	ENSMUSG00000062859	Tcp11	D17Ken1|Tcp-11	t-complex protein 11	protein-coding
mm_91729.1	chr10	45289691	45289700	-	1	NA	intron (NM_024286, intron 1 of 3)	CpG	390	NM_024286	78977	Mm.24748	NM_024286	ENSMUSG00000019848	Popdc3	AA682104|Pop3	popeye domain containing 3	protein-coding
mm_94513.1	chr11	8589808	8589822	+	1	NA	intron (NM_001083587, intron 3 of 30)	intron (NM_001083587, intron 3 of 30)	74720	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_74608.1	chr8	12466876	12466923	-	1	NA	Intergenic	Intergenic	71380	NM_009233	20664	Mm.39088	NM_009233	ENSMUSG00000096014	Sox1	BB176347|Sox-1	SRY (sex determining region Y)-box 1	protein-coding
mm_77912.1	chr9	7350031	7350054	+	1	NA	exon (NM_008605, exon 4 of 10)	exon (NM_008605, exon 4 of 10)	2668	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_102885.1	chr11	69411012	69411041	-	1	NA	intron (NM_001017426, intron 1 of 22)	CpG	2649	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_157198.1	chrX	12137138	12137161	-	1	NA	non-coding (NR_045434, exon 3 of 4)	non-coding (NR_045434, exon 3 of 4)	23197	NR_045434	71458	Mm.196328	NM_029510	ENSMUSG00000040363	Bcor	2900008C10Rik|5830466J11Rik|8430401K06Rik|BcorR|D930024N20Rik|mKIAA1575	BCL6 interacting corepressor	protein-coding
mm_136162.1	chr16	88563020	88563026	-	1	NA	exon (NM_018778, exon 1 of 1)	exon (NM_018778, exon 1 of 1)	160	NM_018778	54420	Mm.25836	NM_018778	ENSMUSG00000050520	Cldn8	AI648025	claudin 8	protein-coding
mm_57182.1	chr6	122848654	122848700	-	1	NA	3' UTR (NM_009779, exon 2 of 2)	3' UTR (NM_009779, exon 2 of 2)	7480	NM_009779	12267	Mm.2408	NM_009779	ENSMUSG00000040552	C3ar1	AZ3B|C3AR|HNFAG09	complement component 3a receptor 1	protein-coding
mm_12923.1	chr2	84988195	84988197	+	1	NA	promoter-TSS (NM_016914)	promoter-TSS (NM_016914)	-19	NM_016914	53856	Mm.19943	NM_016914	ENSMUSG00000027072	Prg3	MBP2|MBPH	proteoglycan 3	protein-coding
mm_142757.1	chr17	48963878	48963903	-	1	NA	intron (NM_027452, intron 1 of 2)	ORR1E|LTR|ERVL-MaLR	31308	NM_027452	70530	Mm.133607	NM_027452	ENSMUSG00000040490	Lrfn2	5730420O05Rik|SALM1|mKIAA1246	leucine rich repeat and fibronectin type III domain containing 2	protein-coding
mm_156735.1	chrX	159942890	159942902	+	1	NA	5' UTR (NM_001290664, exon 1 of 6)	5' UTR (NM_001290664, exon 1 of 6)	203	NM_001290664	58194	Mm.286495	NM_021389	ENSMUSG00000040990	Sh3kbp1	1200007H22Rik|1700125L08Rik|5830464D22Rik|AI447724|Cin85|IN85|Ruk|Seta	SH3-domain kinase binding protein 1	protein-coding
mm_139335.1	chr17	49449412	49449417	+	1	NA	intron (NM_028464, intron 5 of 10)	intron (NM_028464, intron 5 of 10)	21050	NM_020042	56738	Mm.22256	NM_020042	ENSMUSG00000064120	Mocs1	3110045D15Rik|AI043170|AW536397	molybdenum cofactor synthesis 1	protein-coding
mm_168937.1	chr12	69346351	69346362	-	1	NA	exon (NM_025441, exon 8 of 33)	exon (NM_025441, exon 8 of 33)	10820	NM_025441	66244	Mm.46705	NM_025441	ENSMUSG00000020982	Nemf	1500011I12Rik|4933405E14Rik|Sdccag1	nuclear export mediator factor	protein-coding
mm_62848.1	chr7	114317646	114317662	+	1	NA	intron (NR_029437, intron 3 of 3)	intron (NR_029437, intron 3 of 3)	-41538	NM_011965	26440	Mm.121265	NM_011965	ENSMUSG00000030751	Psma1	C2|HC2|Pros-30|alpha-type	proteasome (prosome, macropain) subunit, alpha type 1	protein-coding
mm_115144.1	chr13	104849605	104849615	+	1	NA	intron (NM_029984, intron 2 of 2)	MTD|LTR|ERVL-MaLR	14283	NM_029984	77803	Mm.159995	NM_029984	ENSMUSG00000042655	Fam159b	A930021C24Rik	family with sequence similarity 159, member B	protein-coding
mm_1119.1	chr1	59913077	59913092	+	1	NA	promoter-TSS (NM_001037725)	promoter-TSS (NM_001037725)	78	NM_001037725	72750	Mm.258250	NM_001037725	ENSMUSG00000041040	Fam117b	2810425F24Rik|6330416D14Rik|Als2cr13	family with sequence similarity 117, member B	protein-coding
mm_70939.1	chr8	25911671	25911688	+	1	NA	intron (NM_008432, intron 20 of 26)	intron (NM_008432, intron 20 of 26)	62056	NM_008432	16532	Mm.289679	NM_008432	ENSMUSG00000031576	Kcnu1	Kcnma3|Slo3|mSlo3	potassium channel, subfamily U, member 1	protein-coding
mm_40974.1	chr5	77015983	77015995	+	1	NA	promoter-TSS (NM_027970)	promoter-TSS (NM_027970)	-34	NM_027970	71868	Mm.151092	NM_027970	ENSMUSG00000029248	Thegl	1700023E05Rik	theg spermatid protein like	protein-coding
mm_62470.1	chr7	101818307	101818321	+	1	NA	promoter-TSS (NM_008887)	promoter-TSS (NM_008887)	1	NM_008887	11859	Mm.5028	NM_008887	ENSMUSG00000007946	Phox2a	Arix|Phox2|Pmx2|Pmx2a|Px2a	paired-like homeobox 2a	protein-coding
mm_54449.1	chr6	34746017	34746046	-	1	NA	intron (NM_001347100, intron 5 of 13)	intron (NM_001347100, intron 5 of 13)	-34401	NM_001289657	76223	Mm.150047	NM_178630	ENSMUSG00000038836	Agbl3	2900053G10Rik|4930431N21Rik|6530406M24Rik|CCP3	ATP/GTP binding protein-like 3	protein-coding
mm_66880.1	chr7	58740430	58740440	-	1	NA	intron (NM_009728, intron 2 of 20)	intron (NM_009728, intron 2 of 20)	82233	NM_009728	11982	Mm.135129	NM_009728	ENSMUSG00000025324	Atp10a	Atp10c|pfatp	ATPase, class V, type 10A	protein-coding
mm_81914.1	chr9	120110350	120110418	+	1	NA	promoter-TSS (NM_144793)	promoter-TSS (NM_144793)	-15	NM_144793	208638	Mm.236656	NM_144793	ENSMUSG00000032519	Slc25a38	AV019094|BC010801|appoptosin	solute carrier family 25, member 38	protein-coding
mm_90607.1	chr10	128322735	128322747	+	1	NA	5' UTR (NM_019953, exon 1 of 6)	5' UTR (NM_019953, exon 1 of 6)	282	NM_019953	56530	Mm.44220	NM_019953	ENSMUSG00000025381	Cnpy2	5330432A10Rik|AW229003|D10Bwg1546e|Tmem4|Zsig9	canopy FGF signaling regulator 2	protein-coding
mm_47723.1	chr5	130016828	130016833	-	1	NA	intron (NM_133768, intron 6 of 16)	ID_B1|SINE|B4	7501	NM_133768	109900	Mm.23869	NM_133768	ENSMUSG00000025533	Asl	2510006M18Rik	argininosuccinate lyase	protein-coding
mm_147577.1	chr18	56431825	56431854	-	1	NA	promoter-TSS (NM_026240)	promoter-TSS (NM_026240)	-293	NM_026240	107022	Mm.24356	NM_026240	ENSMUSG00000001700	Gramd3	9030613F08Rik|9130427A09Rik|AW061306|NS3TP2	GRAM domain containing 3	protein-coding
mm_39706.1	chr5	27262223	27262236	+	1	NA	5' UTR (NM_001136060, exon 1 of 26)	5' UTR (NM_001136060, exon 1 of 26)	294	NM_001136060	13483	Mm.42078	NM_010075	ENSMUSG00000061576	Dpp6	B930011P16Rik|D5Buc3|D5Buc4|D5Buc5|DPP VI|Dpp-6|Gm1377|In(5)6H-p|Peplb|Rw	dipeptidylpeptidase 6	protein-coding
mm_58270.1	chr6	145341875	145341909	-	1	NA	Intergenic	Intergenic	-45733	NR_003625	381827	Mm.179075	NM_001001987		1700073E17Rik	-	ribosomal protein L7 pseudogene	pseudo
mm_113507.1	chr13	37598720	37598728	+	1	NA	Intergenic	PB1D11|SINE|Alu	-227314	NM_026830	68750	Mm.491109	NM_026830	ENSMUSG00000039087	Rreb1	1110037N09Rik|AA414966|B930013M22Rik	ras responsive element binding protein 1	protein-coding
mm_18167.1	chr2	45102478	45102494	-	1	NA	intron (NM_001289521, intron 1 of 8)	intron (NM_001289521, intron 1 of 8)	7791	NM_001289521	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_144267.1	chr18	11053348	11053385	+	1	NA	promoter-TSS (NR_105023)	promoter-TSS (NR_105023)	-799	NR_105023	68434	Mm.57626	NR_105022	ENSMUSG00000097222	1010001N08Rik	Gata6as	RIKEN cDNA 1010001N08 gene	ncRNA
mm_39383.1	chr5	13125559	13125575	+	1	NA	Intergenic	Intergenic	-271217	NM_001243072	20346	Mm.372039	NM_009152	ENSMUSG00000028883	Sema3a	Hsema-I|SEMA1|SemD|Semad|coll-1	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	protein-coding
mm_171118.1	chr3	140235498	140235500	+	1	NA	Intergenic	MTA_Mm|LTR|ERVL-MaLR	207250	NR_105798	102465198		NR_105798	ENSMUSG00000099169	Mir7j	Gm27716|Mirlet7j|mmu-let-7j	microRNA 7j	ncRNA
mm_74091.1	chr8	122568002	122568020	+	1	NA	promoter-TSS (NM_026014)	promoter-TSS (NM_026014)	-4	NM_026014	67177	Mm.21873	NM_026014	ENSMUSG00000006585	Cdt1	2610318F11Rik|AW545653|C76791|Ris2	chromatin licensing and DNA replication factor 1	protein-coding
mm_60325.1	chr7	44228345	44228356	+	1	NA	intron (NM_001320332, intron 2 of 4)	intron (NM_001320332, intron 2 of 4)	2990	NM_001320331	16612	Mm.142722	NM_010639	ENSMUSG00000063903	Klk1	0610007D04Rik|KAL-B|Kal|Klk1b6|Klk6|mGk-6	kallikrein 1	protein-coding
mm_22125.1	chr2	170349242	170349243	-	1	NA	exon (NM_001164369, exon 11 of 12)	exon (NM_001164369, exon 11 of 12)	-7119	NR_040610	73303	Mm.443297	NR_040610	ENSMUSG00000086999	Bcas1os2	1700040N02Rik	breast carcinoma amplified sequence 1, opposite strand 2	ncRNA
mm_1365.1	chr1	66412953	66412971	+	1	NA	exon (NM_001310634, exon 7 of 15)	exon (NM_001310634, exon 7 of 15)	-55485	NM_175510	329178	Mm.44798	NM_175510	ENSMUSG00000055567	Unc80	C030018G13Rik|C230061B10Rik|UNC-80	unc-80, NALCN activator	protein-coding
mm_136040.1	chr16	78265950	78265980	-	1	NA	Intergenic	Intergenic	-10511	NR_045698	100503619	Mm.387531	NR_045698	ENSMUSG00000109841	E330011O21Rik	-	RIKEN cDNA E330011O21 gene	ncRNA
mm_582.1	chr1	39367875	39367885	+	1	NA	promoter-TSS (NM_053257)	promoter-TSS (NM_053257)	29	NM_001252218	114641	Mm.379302	NM_053257	ENSMUSG00000073702	Rpl31	Dts	ribosomal protein L31	protein-coding
mm_4017.1	chr1	165655271	165655286	+	1	NA	intron (NM_178593, intron 6 of 6)	intron (NM_178593, intron 6 of 6)	-20737	NM_001083897	68481	Mm.46438	NM_001001880	ENSMUSG00000026566	Mpzl1	1110007A10Rik|PZR	myelin protein zero-like 1	protein-coding
mm_99909.1	chr11	109803514	109803517	+	1	NA	intron (NM_027038, intron 2 of 4)	intron (NM_027038, intron 2 of 4)	24531	NM_027038	69324	Mm.31700	NM_027038	ENSMUSG00000020617	1700012B07Rik	1700069D21Rik	RIKEN cDNA 1700012B07 gene	protein-coding
mm_78212.1	chr9	21499499	21499514	+	1	NA	intron (NM_007871, intron 15 of 19)	intron (NM_007871, intron 15 of 19)	-2942	NR_029585	387194		NR_029585	ENSMUSG00000065547	Mir199a-1	Mirn199|Mirn199a-1|mir-199a-1	microRNA 199a-1	ncRNA
mm_105605.1	chr11	106781885	106781899	-	1	NA	TTS (NR_037224)	TTS (NR_037224)	867	NR_037224	100526469		NR_037224	ENSMUSG00000093273	Mir3064	mir-3064|mmu-mir-3064	microRNA 3064	ncRNA
mm_157307.1	chrX	20931464	20931481	-	1	NA	promoter-TSS (NM_008823)	promoter-TSS (NM_008823)	83	NM_008823	18636	Mm.3064	NM_008823	ENSMUSG00000001128	Cfp	BCFG|Pfc	complement factor properdin	protein-coding
mm_167864.1	chrX	20559431	20559441	-	1	NA	exon (NM_009060, exon 5 of 7)	exon (NM_009060, exon 5 of 7)	9618	NM_009060	19733	Mm.2118	NM_009060	ENSMUSG00000023070	Rgn	AI265316|GNL|SMP30	regucalcin	protein-coding
mm_160745.1	chr10	81098897	81098897	-	1	NA	promoter-TSS (NM_145365)	promoter-TSS (NM_145365)	-25	NM_145365	208677	Mm.294693	NM_145365	ENSMUSG00000035041	Creb3l3	BC010786|CREB-H|D10Bur1e	cAMP responsive element binding protein 3-like 3	protein-coding
mm_112785.1	chr13	20111505	20111515	+	1	NA	intron (NM_080288, intron 1 of 21)	ORR1F|LTR|ERVL-MaLR	21003	NM_080288	140580	Mm.342392	NM_080288	ENSMUSG00000041112	Elmo1	6330578D22Rik|C230095H21Rik|CED-12	engulfment and cell motility 1	protein-coding
mm_143068.1	chr17	57022025	57022049	-	1	NA	3' UTR (NM_010613, exon 18 of 18)	3' UTR (NM_010613, exon 18 of 18)	9470	NM_010613	16549	Mm.34296	NM_010613	ENSMUSG00000007670	Khsrp	6330409F21Rik|Fbp2|Fubp2|Ksrp	KH-type splicing regulatory protein	protein-coding
mm_163014.1	chr11	44735312	44735325	+	1	NA	intron (NM_007897, intron 6 of 15)	intron (NM_007897, intron 6 of 15)	117218	NM_001290710	13591	Mm.439662	NM_007897	ENSMUSG00000057098	Ebf1	Ebf|O/E-1|OE-1|Olf-1|Olf1	early B cell factor 1	protein-coding
mm_52596.1	chr6	117168567	117168584	+	1	NA	promoter-TSS (NM_021704)	promoter-TSS (NM_021704)	40	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_42738.1	chr5	120649337	120649347	+	1	NA	5' UTR (NM_001281999, exon 1 of 21)	5' UTR (NM_001281999, exon 1 of 21)	154	NM_001281999	19415	Mm.41209	NM_013832	ENSMUSG00000029602	Rasal1	MRASAL	RAS protein activator like 1 (GAP1 like)	protein-coding
mm_18729.1	chr2	72978989	72979066	-	1	NA	promoter-TSS (NR_045269)	promoter-TSS (NR_045269)	254	NM_001098425	20687	Mm.124328	NM_011450	ENSMUSG00000027109	Sp3	D130027J01Rik	trans-acting transcription factor 3	protein-coding
mm_132968.1	chr16	50783448	50783460	+	1	NA	promoter-TSS (NR_131006)	promoter-TSS (NR_131006)	45	NR_131005	78639	Mm.160109	NR_131005	ENSMUSG00000092276	1700116B05Rik	-	RIKEN cDNA 1700116B05 gene	ncRNA
mm_159344.1	chr3	62605121	62605121	-	1	NA	promoter-TSS (NM_177346)	promoter-TSS (NM_177346)	19	NM_177346	229357	Mm.95181	NM_177346	ENSMUSG00000043441	Gpr149	9630018L10Rik|Ieda|PGR10|R35	G protein-coupled receptor 149	protein-coding
mm_111883.1	chr12	108179238	108179339	-	1	NA	promoter-TSS (NM_009832)	promoter-TSS (NM_009832)	-4	NM_028262	52690	Mm.159185	NM_028262	ENSMUSG00000056770	Setd3	2610102I01Rik|2610305M23Rik|6030490B17Rik|D12Ertd771e	SET domain containing 3	protein-coding
mm_140919.1	chr17	24171868	24171909	-	1	NA	Intergenic	Intergenic	-2459	NM_009729	11984	Mm.30155	NM_009729	ENSMUSG00000024121	Atp6v0c	Atp6c|Atp6c2|Atp6l|Atpl|Atpl-rs1|PL16|VATL|Vma3	ATPase, H+ transporting, lysosomal V0 subunit C	protein-coding
mm_163606.1	chr13	49215837	49215847	-	1	NA	intron (NM_026738, intron 1 of 5)	CpG	184	NM_026738	68480	Mm.3336	NM_026738	ENSMUSG00000037960	Card19	1110007C09Rik|AI851695|Bincard	caspase recruitment domain family, member 19	protein-coding
mm_114881.1	chr13	94194314	94194320	+	1	NA	3' UTR (NM_172589, exon 4 of 4)	3' UTR (NM_172589, exon 4 of 4)	90964	NM_029153	107767	Mm.201455	NM_029153	ENSMUSG00000021687	Scamp1	4930505M11Rik|AI415563|AW122395	secretory carrier membrane protein 1	protein-coding
mm_30113.1	chr3	139075117	139075132	-	1	NA	promoter-TSS (NM_001286759)	promoter-TSS (NM_001286759)	77	NM_145544	229877	Mm.28893	NM_145544	ENSMUSG00000028149	Rap1gds1	BC011279|GDS1	RAP1, GTP-GDP dissociation stimulator 1	protein-coding
mm_110027.1	chr12	16800897	16800931	-	1	NA	promoter-TSS (NM_015764)	promoter-TSS (NM_015764)	-28	NM_015764	268527	Mm.428062	NM_015764	ENSMUSG00000036523	Greb1	5730583K22Rik|9130004E13|AF180470|AU023194|mKIAA0575	gene regulated by estrogen in breast cancer protein	protein-coding
mm_128047.1	chr15	25445634	25445643	-	1	NA	intron (NR_027376, intron 1 of 1)	intron (NR_027376, intron 1 of 1)	31446	NR_027376	432939	Mm.146555	NM_001013791		Gm5468	100040583|EG432939	predicted gene 5468	ncRNA
mm_141260.1	chr17	27623337	27623345	-	1	NA	promoter-TSS (NM_001291046)	promoter-TSS (NM_001291046)	111	NM_019837	56409	Mm.144699	NM_019837	ENSMUSG00000024213	Nudt3	1110011B09Rik|AA960325|Dipp|Dipp1	nudix (nucleotide diphosphate linked moiety X)-type motif 3	protein-coding
mm_160412.1	chr8	75033727	75033727	+	1	NA	promoter-TSS (NM_011622)	promoter-TSS (NM_011622)	41	NM_011622	21968	Mm.1967	NM_011622	ENSMUSG00000042870	Tom1	-	target of myb1 trafficking protein	protein-coding
mm_28863.1	chr3	97297853	97297916	-	1	NA	Intergenic	Intergenic	-11372	NR_105813	102465206		NR_105813	ENSMUSG00000099036	Mir378c	Gm27930|mmu-mir-378c	microRNA 378c	ncRNA
mm_64083.1	chr7	140943576	140943623	+	1	NA	exon (NM_145387, exon 4 of 14)	exon (NM_145387, exon 4 of 14)	2018	NM_145387	212974	Mm.260139	NM_145387	ENSMUSG00000062031	Pgghg	5730511L01Rik|Athl1|BC023151	protein glucosylgalactosylhydroxylysine glucosidase	protein-coding
mm_7362.1	chr1	106712360	106712384	-	1	NA	exon (NM_177410, exon 1 of 1)	exon (NM_177410, exon 1 of 1)	1918	NM_009741	12043	Mm.257460	NM_009741	ENSMUSG00000057329	Bcl2	AW986256|Bcl-2|C430015F12Rik|D630044D05Rik|D830018M01Rik	B cell leukemia/lymphoma 2	protein-coding
mm_147924.1	chr18	65935946	65935978	-	1	NA	intron (NM_013833, intron 2 of 2)	intron (NM_013833, intron 2 of 2)	3127	NM_013833	19434	Mm.431047	NM_013833	ENSMUSG00000024518	Rax	7530406A22Rik|E130303K03Rik|Rx|ey-1|ey1	retina and anterior neural fold homeobox	protein-coding
mm_162193.1	chrX	113297558	113297558	+	1	NA	promoter-TSS (NM_001142570)	promoter-TSS (NM_001142570)	48	NM_001289733	93837	Mm.79760	NM_033605	ENSMUSG00000025592	Dach2	9430028N04Rik	dachshund 2 (Drosophila)	protein-coding
mm_110311.1	chr12	33284545	33284549	-	1	NA	Intergenic	RLTR53_Mm|LTR|ERVK	-17968	NM_001033436	380753	Mm.41540	NM_028139	ENSMUSG00000020564	Atxn7l1	2810423G08Rik|Atxn7l4	ataxin 7-like 1	protein-coding
mm_143951.1	chr17	86811002	86811022	-	1	NA	intron (NM_010137, intron 6 of 15)	intron (NM_010137, intron 6 of 15)	57148	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_3106.1	chr1	134494737	134494763	+	1	NA	promoter-TSS (NM_145510)	promoter-TSS (NM_145510)	90	NM_145510	98710	Mm.198119	NM_145510	ENSMUSG00000042229	Rabif	AI842864|AW549708|E130318E12Rik|MSS4|RASGFR3	RAB interacting factor	protein-coding
mm_87062.1	chr10	28863563	28863603	+	1	NA	intron (NM_178666, intron 5 of 5)	intron (NM_178666, intron 5 of 5)	59924	NR_033601	114676	Mm.390292	NR_033601		4930519F09Rik	-	pyruvate dehydrogenase E1 alpha 1 pseudogene	pseudo
mm_130663.1	chr15	100667605	100667605	-	1	NA	intron (NM_001270537, intron 1 of 10)	intron (NM_001270537, intron 1 of 10)	1895	NM_001270537	668218	Mm.451225	NM_001270537	ENSMUSG00000098112	Bin2	-	bridging integrator 2	protein-coding
mm_12722.1	chr2	78304684	78304691	+	1	NA	Intergenic	ORR1D1|LTR|ERVL-MaLR	67140	NM_177843	329436	Mm.235448	NM_177843		Gm14461	A830093M07|OTTMUSG00000016703	predicted gene 14461	protein-coding
mm_33268.1	chr4	127522440	127522450	+	1	NA	Intergenic	Intergenic	-164281	NM_010291	14622	Mm.26859	NM_010291	ENSMUSG00000042357	Gjb5	Cnx31.1|Cx31.1|Gjb-5	gap junction protein, beta 5	protein-coding
mm_81457.1	chr9	109833164	109833201	+	1	NA	intron (NM_018757, intron 1 of 6)	intron (NM_018757, intron 1 of 6)	388	NM_018757	54369	Mm.12951	NM_018757	ENSMUSG00000032478	Nme6	nm23-M6	NME/NM23 nucleoside diphosphate kinase 6	protein-coding
mm_108976.1	chr12	102730702	102730717	+	1	NA	Intergenic	MLT1O|LTR|ERVL-MaLR	12952	NM_001142937	64113	Mm.291222	NM_022323	ENSMUSG00000096458	Moap1	AA987038|Map-1|Pnma4	modulator of apoptosis 1	protein-coding
mm_40632.1	chr5	64829880	64829900	+	1	NA	3' UTR (NM_008453, exon 6 of 6)	3' UTR (NM_008453, exon 6 of 6)	26367	NM_008453	16599	Mm.392759	NM_008453	ENSMUSG00000029178	Klf3	9930027G08Rik|AL024007|Bklf|Tef-2	Kruppel-like factor 3 (basic)	protein-coding
mm_97121.1	chr11	74839237	74839247	+	1	NA	intron (NM_010813, intron 4 of 5)	intron (NM_010813, intron 4 of 5)	8318	NM_010813	17428	Mm.3759	NM_010813	ENSMUSG00000000282	Mnt	Rox|bHLHd3	max binding protein	protein-coding
mm_85577.1	chr9	107289807	107289818	-	1	NA	promoter-TSS (NM_178907)	promoter-TSS (NM_178907)	65	NM_178907	102626	Mm.222612	NM_178907	ENSMUSG00000032577	Mapkapk3	3PK|AI874665|MAPKAP-K3|MAPKAP3|MK-3|MK3|MapkKapk3	mitogen-activated protein kinase-activated protein kinase 3	protein-coding
mm_136156.1	chr16	88167439	88167439	-	1	NA	intron (NM_146072, intron 1 of 16)	RLTR22_Mur|LTR|ERVK	122819	NM_146072	14805	Mm.5134	NM_010348	ENSMUSG00000022935	Grik1	A830007B11Rik|D16Ium24|D16Ium24e|GluK1|GluK5|Glur-5|Glur5|Glurbeta1	glutamate receptor, ionotropic, kainate 1	protein-coding
mm_9281.1	chr1	171634548	171634558	-	1	NA	3' UTR (NM_144539, exon 8 of 8)	3' UTR (NM_144539, exon 8 of 8)	7347	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_34782.1	chr4	154142364	154142383	+	1	NA	promoter-TSS (NM_021499)	promoter-TSS (NM_021499)	1	NM_021499	59002	Mm.46508	NM_021499	ENSMUSG00000029029	Wrap73	2610044M17Rik|5330425N03Rik|Dd57|Wdr8	WD repeat containing, antisense to Trp73	protein-coding
mm_20284.1	chr2	126897680	126897680	-	1	NA	intron (NM_023220, intron 14 of 14)	intron (NM_023220, intron 14 of 14)	4705	NR_106202	102466258		NR_106202	ENSMUSG00000098896	Mir3473g	Gm27751|mmu-mir-3473g	microRNA 3473g	ncRNA
mm_62229.1	chr7	98533287	98533315	+	1	NA	Intergenic	Intergenic	39079	NM_001113379	434215	Mm.323057	NM_001113379	ENSMUSG00000090958	Lrrc32	AI426318|D11S833Eh|D7H11S833E|EG434215|Garp	leucine rich repeat containing 32	protein-coding
mm_149932.1	chr19	26770927	26770956	+	1	NA	exon (NM_026003, exon 5 of 9)	exon (NM_026003, exon 5 of 9)	22538	NM_026003	67155	Mm.342988	NM_011416	ENSMUSG00000024921	Smarca2	2610209L14Rik|SNF2alpha|Snf2l2|brahma|brm	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	protein-coding
mm_19077.1	chr2	77817426	77817462	-	1	NA	promoter-TSS (NM_178723)	promoter-TSS (NM_178723)	-628	NM_178723	241494	Mm.490320	NM_178723	ENSMUSG00000027016	Zfp385b	B830010L13Rik|C130013B13Rik|Zfp533|Znf385b	zinc finger protein 385B	protein-coding
mm_85903.1	chr9	111056297	111056338	-	1	NA	exon (NM_017466, exon 2 of 2)	exon (NM_017466, exon 2 of 2)	927	NM_001302377	54199	Mm.7336	NM_017466	ENSMUSG00000043953	Ccrl2	1810047I05Rik|Ackr5|CCR11|Cmkbr1l2|E01|L-CCR	chemokine (C-C motif) receptor-like 2	protein-coding
mm_10974.1	chr2	25707122	25707124	+	1	NA	exon (NM_023326, exon 1 of 1)	exon (NM_023326, exon 1 of 1)	244	NM_023326	107771	Mm.330057	NM_023326	ENSMUSG00000049086	Bmyc	2900002K07Rik|AW060705|Mycb	brain expressed myelocytomatosis oncogene	protein-coding
mm_3757.1	chr1	156044252	156044252	+	1	NA	intron (NM_172843, intron 2 of 6)	intron (NM_172843, intron 2 of 6)	3391	NM_022329	240832	Mm.253335	NM_022329	ENSMUSG00000050565	Tor1aip2	1110020D10Rik|15kDa|A130072J07|AA103493|AW060462|AW610675|C77739|Ifrg15|Lull1	torsin A interacting protein 2	protein-coding
mm_24538.1	chr3	93279609	93279611	+	1	NA	Intergenic	Intergenic	-40139	NM_133698	68723	Mm.208047	NM_133698	ENSMUSG00000041991	Hrnr	1110033K19Rik|A530063N20Rik|S100a18	hornerin	protein-coding
mm_60101.1	chr7	35186410	35186432	+	1	NA	promoter-TSS (NM_017394)	promoter-TSS (NM_017394)	36	NM_017394	53896	Mm.35567	NM_017394	ENSMUSG00000030495	Slc7a10	AL024237|Asc-1|D7Bwg0847e	solute carrier family 7 (cationic amino acid transporter, y+ system), member 10	protein-coding
mm_146861.1	chr18	24530019	24530033	-	1	NA	exon (NM_144861, exon 1 of 7)	exon (NM_144861, exon 1 of 7)	178	NM_144861	225283	Mm.28427	NM_144861	ENSMUSG00000040446	Rprd1a	C77387|mKIAA4077	regulation of nuclear pre-mRNA domain containing 1A	protein-coding
mm_50017.1	chr6	41113583	41113593	+	1	NA	Intergenic	Intergenic	-78079	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_155632.1	chrX	84772763	84772770	+	1	NA	intron (NM_007868, intron 55 of 78)	intron (NM_007868, intron 55 of 78)	-275529	NM_001314038	13405	Mm.275608	NM_007868	ENSMUSG00000045103	Dmd	DXSmh7|DXSmh9|Dp427|Dp71|dys|mdx|pke	dystrophin, muscular dystrophy	protein-coding
mm_27384.1	chr3	50628378	50628390	-	1	NA	Intergenic	Intergenic	-184771	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_8644.1	chr1	156430451	156430498	-	1	NA	3' UTR (NM_009230, exon 16 of 16)	3' UTR (NM_009230, exon 16 of 16)	-9559	NM_001346967	77352	Mm.428709	NM_001033180	ENSMUSG00000026601	Axdnd1	9430070O13Rik|Gm979	axonemal dynein light chain domain containing 1	protein-coding
mm_115318.1	chr13	112367882	112367909	+	1	NA	exon (NM_029898, exon 9 of 11)	exon (NM_029898, exon 9 of 11)	79377	NM_001168404	77318	Mm.159895	NM_029898	ENSMUSG00000049985	Ankrd55	C030011J08Rik	ankyrin repeat domain 55	protein-coding
mm_27862.1	chr3	79158692	79158703	-	1	NA	Intergenic	L1_Mur3|LINE|L1	-12822	NM_001099624	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_89377.1	chr10	88885933	88885942	+	1	NA	promoter-TSS (NM_145423)	promoter-TSS (NM_145423)	-55	NM_145423	216225	Mm.77381	NM_145423	ENSMUSG00000020062	Slc5a8	Ait|SMCT	solute carrier family 5 (iodide transporter), member 8	protein-coding
mm_65778.1	chr7	28766446	28766468	-	1	NA	promoter-TSS (NM_001122766)	promoter-TSS (NM_001122766)	187	NM_001306222	18036	Mm.220333	NM_010908	ENSMUSG00000030595	Nfkbib	I(Kappa)B(beta)|I-kappa-B-beta|IKB-beta|IKappaBbeta|IkB|IkBb|NF-kappa-BIB|ikB-B	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, beta	protein-coding
mm_92698.1	chr10	80701812	80701878	-	1	NA	promoter-TSS (NM_027829)	promoter-TSS (NM_027829)	-25	NM_172457	208228	Mm.49309	NM_172457	ENSMUSG00000003348	Mob3a	5330417K06Rik|A630029F06|AV218468|Mobkl2a	MOB kinase activator 3A	protein-coding
mm_116274.1	chr13	34715489	34715492	-	1	NA	Intergenic	RMER15-int|LTR|ERVL	-24152	NM_138746	108161	Mm.41991	NM_138746	ENSMUSG00000038246	Fam50b	D0H6S2654E|X5L|XAP-5-like	family with sequence similarity 50, member B	protein-coding
mm_24012.1	chr3	87408438	87408446	+	1	NA	Intergenic	Intergenic	-27340	NM_183222	329693	Mm.331122	NM_183222	ENSMUSG00000048031	Fcrl5	Fcrh3|mBXMH2	Fc receptor-like 5	protein-coding
mm_163653.1	chr13	69611561	69611571	+	1	NA	promoter-TSS (NM_175283)	promoter-TSS (NM_175283)	-103	NM_175283	78925	Mm.451912	NM_175283	ENSMUSG00000021594	Srd5a1	0610031P22Rik|4930435F02Rik|S5AR 1|Srd5a-1	steroid 5 alpha-reductase 1	protein-coding
mm_26695.1	chr3	157534104	157534160	+	1	NA	promoter-TSS (NM_017381)	promoter-TSS (NM_017381)	-265	NM_017381	53861	Mm.259036	NM_017381	ENSMUSG00000028180	Zranb2	AI227013|Zfp265|Zis|Znf265	zinc finger, RAN-binding domain containing 2	protein-coding
mm_85751.1	chr9	108636458	108636494	-	1	NA	intron (NM_011790, intron 3 of 15)	intron (NM_011790, intron 3 of 15)	12904	NM_011790	23807	Mm.290447	NM_011790	ENSMUSG00000064145	Arih2	AI843547|ARI2|TRIAD1|UIP48	ariadne RBR E3 ubiquitin protein ligase 2	protein-coding
mm_4927.1	chr1	191036830	191036838	+	1	NA	promoter-TSS (NM_029336)	promoter-TSS (NM_029336)	12	NM_029336	75558	Mm.383398	NM_029336	ENSMUSG00000057072	Spata45	1700022P22Rik	spermatogenesis associated 45	protein-coding
mm_128889.1	chr15	73162228	73162233	-	1	NA	intron (NM_153178, intron 1 of 18)	Lx9|LINE|L1	22717	NM_153178	239528	Mm.23095	NM_153178	ENSMUSG00000036698	Ago2	1110029L17Rik|2310051F07Rik|AI225898|AL022874|AW546247|ENSMUSG00000072493|Eif2c2|Gerp95|Gm10365|mKIAA4215	argonaute RISC catalytic subunit 2	protein-coding
mm_38708.1	chr4	145215651	145215667	-	1	NA	3' UTR (NM_011610, exon 10 of 10)	3' UTR (NM_011610, exon 10 of 10)	-20654	NM_001276465	230895	Mm.240310	NM_001033190	ENSMUSG00000020220	Vps13d	-	vacuolar protein sorting 13D	protein-coding
mm_13695.1	chr2	117121166	117121177	+	1	NA	promoter-TSS (NM_001277256)	promoter-TSS (NM_001277256)	100	NM_033524	114715	Mm.245890	NM_033524	ENSMUSG00000027351	Spred1	5730461F13Rik|AL024345|AW047647	sprouty protein with EVH-1 domain 1, related sequence	protein-coding
mm_72278.1	chr8	75100240	75100252	+	1	NA	3' UTR (NM_010442, exon 5 of 5)	3' UTR (NM_010442, exon 5 of 5)	6628	NM_010442	15368	Mm.276389	NM_010442	ENSMUSG00000005413	Hmox1	D8Wsu38e|HO-1|HO1|Hemox|Hmox|Hsp32	heme oxygenase 1	protein-coding
mm_46942.1	chr5	114823479	114823489	-	1	NA	promoter-TSS (NM_181075)	promoter-TSS (NM_181075)	-16	NM_181075	330173	Mm.482205	NM_181075	ENSMUSG00000092486	2610524H06Rik	-	RIKEN cDNA 2610524H06 gene	protein-coding
mm_97436.1	chr11	78176736	78176761	+	1	NA	promoter-TSS (NM_080849)	promoter-TSS (NM_080849)	-82	NM_080849	140859	Mm.23788	NM_080849	ENSMUSG00000017405	Nek8	4632401F23Rik|b2b1449Clo|jck	NIMA (never in mitosis gene a)-related expressed kinase 8	protein-coding
mm_33377.1	chr4	129515806	129515844	+	1	NA	TTS (NM_008228)	TTS (NM_008228)	2244	NM_010807	17357	Mm.424974	NM_010807	ENSMUSG00000047945	Marcksl1	AL022768|AW215397|AW536807|D4Bc1|F52|MacMARCKS|Macs2|Macs3|Mlp|Mrp	MARCKS-like 1	protein-coding
mm_153978.1	chr19	47864640	47864658	-	1	NA	promoter-TSS (NM_030051)	promoter-TSS (NM_030051)	-896	NM_030051	68214	Mm.63791	NM_026619	ENSMUSG00000025069	Gsto2	1700020F09Rik|4930425C18Rik|GSTO 2-2	glutathione S-transferase omega 2	protein-coding
mm_79689.1	chr9	60482360	60482386	+	1	NA	intron (NM_001040426, intron 3 of 17)	intron (NM_001040426, intron 3 of 17)	28662	NM_001040426	207596	Mm.28791	NM_172444	ENSMUSG00000032289	Thsd4	ADAMTSL-6|ADAMTSL6|AI585901|Adamtsl4|B230114P05Rik	thrombospondin, type I, domain containing 4	protein-coding
mm_13828.1	chr2	119288726	119288771	+	1	NA	promoter-TSS (NM_172269)	promoter-TSS (NM_172269)	6	NM_172269	228545	Mm.294761	NM_172269	ENSMUSG00000034216	Vps18	9930024E13Rik	VPS18 CORVET/HOPS core subunit	protein-coding
mm_158763.1	chrX	166510425	166510475	-	1	NA	promoter-TSS (NM_001007577)	promoter-TSS (NM_001007577)	28	NM_001007577	245695	Mm.336318	NM_001007577	ENSMUSG00000051224	Tceanc	A630018P17Rik|Gm390	transcription elongation factor A (SII) N-terminal and central domain containing	protein-coding
mm_147386.1	chr18	43792874	43792881	-	1	NA	promoter-TSS (NM_001033280)	promoter-TSS (NM_001033280)	1	NM_001033280	225443	Mm.100304	NM_001033280	ENSMUSG00000071858	Gm94	-	predicted gene 94	protein-coding
mm_15674.1	chr2	163491710	163491722	+	1	NA	promoter-TSS (NM_001099331)	promoter-TSS (NM_001099331)	-602	NM_001099331	100043899	Mm.442535	NM_001099331	ENSMUSG00000078949	R3hdml	OTTMUSG00000001070	R3H domain containing-like	protein-coding
mm_79951.1	chr9	66061361	66061380	+	1	NA	intron (NM_011149, intron 1 of 4)	intron (NM_011149, intron 1 of 4)	1201	NM_011149	19035	Mm.335249	NM_011149	ENSMUSG00000032383	Ppib	AA408962|AA553318|AI844835|Cphn-2|Cphn2|CyP-20b	peptidylprolyl isomerase B	protein-coding
mm_134202.1	chr16	11134547	11134590	-	1	NA	promoter-TSS (NM_029582)	promoter-TSS (NM_029582)	-36	NM_029582	106200	Mm.291015	NM_029582	ENSMUSG00000022498	Txndc11	2810408E11Rik|AI427833|EFP1|Txdc11	thioredoxin domain containing 11	protein-coding
mm_43332.1	chr5	135009835	135009845	+	1	NA	non-coding (NR_033794, exon 1 of 5)	non-coding (NR_033794, exon 1 of 5)	384	NR_033794	68758	Mm.389700	NM_145215	ENSMUSG00000040532	Abhd11	1110054D16Rik|A630008N09Rik|Wbscr21	abhydrolase domain containing 11	protein-coding
mm_42012.1	chr5	108077950	108077968	+	1	NA	promoter-TSS (NM_001253878)	promoter-TSS (NM_001253878)	-206	NM_001253878	17765	Mm.257149	NM_013827	ENSMUSG00000029267	Mtf2	9230112N11Rik|AA537621|C76717|M96|Pcl2	metal response element binding transcription factor 2	protein-coding
mm_84586.1	chr9	70032445	70032448	-	1	NA	3' UTR (NM_028087, exon 3 of 3)	3' UTR (NM_028087, exon 3 of 3)	5642	NM_028087	72077	Mm.195555	NM_028087	ENSMUSG00000032226	Gcnt3	2010013H22Rik|2210021I22Rik|2210401J11Rik	glucosaminyl (N-acetyl) transferase 3, mucin type	protein-coding
mm_41946.1	chr5	105731892	105731909	+	1	NA	intron (NM_178701, intron 1 of 2)	intron (NM_178701, intron 1 of 2)	31090	NM_178701	231549	Mm.23837	NM_178701	ENSMUSG00000046079	Lrrc8d	2810473G09Rik|4930525N13Rik|A930019F03|Lrrc5	leucine rich repeat containing 8D	protein-coding
mm_87702.1	chr10	59879618	59879682	+	1	NA	promoter-TSS (NM_019965)	promoter-TSS (NM_019965)	59	NM_019965	56709	Mm.103610	NM_019965	ENSMUSG00000020109	Dnajb12	Dj10|mDj10	DnaJ heat shock protein family (Hsp40) member B12	protein-coding
mm_3764.1	chr1	156213135	156213164	+	1	NA	Intergenic	Intergenic	-8123	NM_177838	329274	Mm.150857	NM_177838	ENSMUSG00000015484	Fam163a	A230106N23Rik	family with sequence similarity 163, member A	protein-coding
mm_112413.1	chr13	3652778	3652783	+	1	NA	Intergenic	Intergenic	18748	NM_001267724	142688	Mm.253061	NM_178283	ENSMUSG00000033781	Asb13	2210015B19Rik|6430573K02Rik|Asb-13|C85285	ankyrin repeat and SOCS box-containing 13	protein-coding
mm_75159.1	chr8	36280842	36280844	-	1	NA	Intergenic	Intergenic	-31327	NM_001081150	244421	Mm.324032	NM_001081150	ENSMUSG00000039633	Lonrf1	-	LON peptidase N-terminal domain and ring finger 1	protein-coding
mm_74602.1	chr8	11678711	11678726	-	1	NA	promoter-TSS (NM_024271)	promoter-TSS (NM_024271)	32	NM_024271	76413	Mm.440041	NM_024271	ENSMUSG00000031509	1700016D06Rik	-	RIKEN cDNA 1700016D06 gene	protein-coding
mm_25460.1	chr3	108537524	108537583	+	1	NA	promoter-TSS (NM_029314)	promoter-TSS (NM_029314)	-31	NM_029314	75504	Mm.271255	NM_029314	ENSMUSG00000027886	1700013F07Rik	-	RIKEN cDNA 1700013F07 gene	protein-coding
mm_150071.1	chr19	29386659	29386708	+	1	NA	3' UTR (NM_021893, exon 7 of 7)	3' UTR (NM_021893, exon 7 of 7)	19245	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_151240.1	chr19	53832636	53832654	+	1	NA	intron (NM_001170847, intron 5 of 13)	intron (NM_001170847, intron 5 of 13)	-59586	NM_011050	18569	Mm.1605	NM_011050	ENSMUSG00000024975	Pdcd4	D19Ucla1|Ma3|Tis	programmed cell death 4	protein-coding
mm_60218.1	chr7	43546450	43546459	+	1	NA	Intergenic	Intergenic	-13283	NM_021293	12489	Mm.140157	NM_021293	ENSMUSG00000004609	Cd33	Siglec-3|gp67	CD33 antigen	protein-coding
mm_96971.1	chr11	70649907	70649927	+	1	NA	exon (NM_001316728, exon 7 of 10)	exon (NM_001316728, exon 7 of 10)	2630	NM_027445	70510	Mm.261818	NM_027445	ENSMUSG00000040746	Rnf167	0610010G05Rik|5730408C10Rik|AU019305|AV328608	ring finger protein 167	protein-coding
mm_16099.1	chr2	169006009	169006071	+	1	NA	Intergenic	RLTR20B3A_MM|LTR|ERVK	27771	NR_040326	75508	Mm.271256	NR_040326	ENSMUSG00000086348	1700017J07Rik	-	RIKEN cDNA 1700017J07 gene	ncRNA
mm_38915.1	chr4	150000283	150000289	-	1	NA	intron (NM_173371, intron 1 of 4)	ID4|SINE|ID	2950	NM_001291004	100198	Mm.22183	NM_173371	ENSMUSG00000028980	H6pd	AI785303|G6pd1|Gpd-1|Gpd1	hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase)	protein-coding
mm_30308.1	chr3	149445268	149445278	-	1	NA	Intergenic	Intergenic	170536	NR_040591	381482	Mm.393866	NR_040591		Gm1653	-	predicted gene 1653	ncRNA
mm_139150.1	chr17	47538640	47538653	+	1	NA	intron (NM_001081635, intron 1 of 6)	intron (NM_001081635, intron 1 of 6)	33595	NM_001081635	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_86698.1	chr10	18475835	18475838	+	1	NA	intron (NM_173390, intron 2 of 6)	intron (NM_173390, intron 2 of 6)	5855	NM_001163592	215819	Mm.297971	NM_173390	ENSMUSG00000039835	Nhsl1	5730409E15Rik|A630035H13Rik|A730096F01|BC013565|D10Bwg0940e|mKIAA1357	NHS-like 1	protein-coding
mm_117681.1	chr13	94203584	94203611	-	1	NA	3' UTR (NM_029153, exon 9 of 9)	3' UTR (NM_029153, exon 9 of 9)	81684	NM_029153	107767	Mm.201455	NM_029153	ENSMUSG00000021687	Scamp1	4930505M11Rik|AI415563|AW122395	secretory carrier membrane protein 1	protein-coding
mm_103751.1	chr11	80779800	80779841	-	1	NA	5' UTR (NM_177390, exon 1 of 22)	5' UTR (NM_177390, exon 1 of 22)	205	NM_177390	338367	Mm.151948	NM_177390	ENSMUSG00000035441	Myo1d	9930104H07Rik|AW544947|D11Ertd9e|myosin-1d	myosin ID	protein-coding
mm_144897.1	chr18	37143665	37143696	+	1	NA	promoter-TSS (NM_001003672)	promoter-TSS (NM_001003672)	-289	NM_001003672	353237	Mm.308500	NM_001003672	ENSMUSG00000102697	Pcdhac2	CNRc2	protocadherin alpha subfamily C, 2	protein-coding
mm_85995.1	chr9	112216545	112216563	-	1	NA	intron (NM_001177619, intron 1 of 10)	intron (NM_001177619, intron 1 of 10)	707	NM_001177617	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_49590.1	chr6	30643589	30643599	+	1	NA	exon (NM_025350, exon 9 of 10)	exon (NM_025350, exon 9 of 10)	4376	NM_025350	109697	Mm.25377	NM_025350	ENSMUSG00000054446	Cpa1	0910001L12Rik|Cpa	carboxypeptidase A1, pancreatic	protein-coding
mm_67496.1	chr7	80758030	80758034	-	1	NA	intron (NM_016721, intron 9 of 37)	intron (NM_016721, intron 9 of 37)	45299	NM_016721	29875	Mm.207619	NM_016721	ENSMUSG00000030536	Iqgap1	AA682088|D7Ertd237e|D7Ertd257e|mKIAA0051	IQ motif containing GTPase activating protein 1	protein-coding
mm_20856.1	chr2	148408107	148408127	-	1	NA	promoter-TSS (NM_009378)	promoter-TSS (NM_009378)	71	NM_009378	21824	Mm.24096	NM_009378	ENSMUSG00000074743	Thbd	AI385582|CD141|TM	thrombomodulin	protein-coding
mm_143292.1	chr17	65884793	65884888	-	1	NA	promoter-TSS (NM_001198949)	promoter-TSS (NM_001198949)	83	NM_001198949	19765	Mm.17009	NM_009067	ENSMUSG00000024096	Ralbp1	RLIP76|Rip1	ralA binding protein 1	protein-coding
mm_32176.1	chr4	100776665	100776692	+	1	NA	promoter-TSS (NM_198037)	promoter-TSS (NM_198037)	-1	NM_198037	320508	Mm.151962	NM_198037	ENSMUSG00000028532	Cachd1	1190007F10Rik|AI852726|B430218L07Rik|Vwcd1|mKIAA1573	cache domain containing 1	protein-coding
mm_159970.1	chr6	99162876	99162876	-	1	NA	exon (NM_053202, exon 4 of 19)	exon (NM_053202, exon 4 of 19)	103639	NM_001197321	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_23581.1	chr3	63439245	63439264	+	1	NA	Intergenic	MER102c|DNA|hAT-Charlie	143159	NM_001289463	17380	Mm.296022	NM_008604	ENSMUSG00000027820	Mme	6030454K05Rik|C85356|CALLA|CD10|NEP|SFE	membrane metallo endopeptidase	protein-coding
mm_53685.1	chr6	142387272	142387276	+	1	NA	promoter-TSS (NM_001204907)	promoter-TSS (NM_001204907)	31	NM_025872	66964	Mm.3676	NM_025872	ENSMUSG00000030245	Golt1b	2310061A22Rik|AA407874|AU024291|CGI-141	golgi transport 1B	protein-coding
mm_132643.1	chr16	40194726	40194726	+	1	NA	Intergenic	Intergenic	1292381	NM_170599	207683	Mm.245564	NM_170599	ENSMUSG00000022790	Igsf11	1700025L02Rik|BT-IgSF|Igsf13	immunoglobulin superfamily, member 11	protein-coding
mm_40871.1	chr5	74032265	74032273	+	1	NA	intron (NM_177561, intron 3 of 8)	intron (NM_177561, intron 3 of 8)	36142	NM_177561	69727	Mm.48795	NM_177561	ENSMUSG00000054814	Usp46	1190009E20Rik|2410018I08Rik|AI451644	ubiquitin specific peptidase 46	protein-coding
mm_170702.1	chr2	137369810	137369824	-	1	NA	Intergenic	L1Md_T|LINE|L1	-253297	NM_013822	16449	Mm.22398	NM_013822	ENSMUSG00000027276	Jag1	ABE2|Gsfabe2|Htu|Ozz|Ser-1	jagged 1	protein-coding
mm_26689.1	chr3	156646634	156646636	+	1	NA	intron (NM_177274, intron 1 of 6)	intron (NM_177274, intron 1 of 6)	84841	NM_001039094	320840	Mm.317293	NM_177274	ENSMUSG00000040037	Negr1	5330422G01Rik|KILON|Ntra	neuronal growth regulator 1	protein-coding
mm_34570.1	chr4	150048279	150048292	+	1	NA	Intergenic	Intergenic	-20169	NR_029751	723848		NR_029751	ENSMUSG00000065493	Mir34a	Mirn34a|mir-34a|mmu-mir-34a	microRNA 34a	ncRNA
mm_57975.1	chr6	135718689	135718720	-	1	NA	Intergenic	B2_Mm2|SINE|B2	59791	NR_126088	75024	Mm.399147	NR_126088	ENSMUSG00000107396	4930425L21Rik	4930473P14Rik	RIKEN cDNA 4930425L21 gene	ncRNA
mm_154571.1	chrX	6945248	6945261	+	1	NA	3' UTR (NM_177914, exon 27 of 27)	3' UTR (NM_177914, exon 27 of 27)	71770	NM_177914	331374	Mm.392752	NM_177914	ENSMUSG00000062393	Dgkk	Gm360	diacylglycerol kinase kappa	protein-coding
mm_69951.1	chr7	142372211	142372292	-	1	NA	promoter-TSS (NM_177265)	promoter-TSS (NM_177265)	8	NM_177265	320802	Mm.154486	NM_177265	ENSMUSG00000045777	Ifitm10	6330512M04Rik|AI848576|DSPA3	interferon induced transmembrane protein 10	protein-coding
mm_166847.1	chr7	19696628	19696645	+	1	NA	exon (NM_009696, exon 4 of 4)	exon (NM_009696, exon 4 of 4)	1762	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_139255.1	chr17	47737037	47737107	+	1	NA	promoter-TSS (NM_001161723)	promoter-TSS (NM_001161723)	35	NM_001161722	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_94387.1	chr11	5524790	5524804	+	1	NA	exon (NM_001271730, exon 6 of 6)	exon (NM_001271730, exon 6 of 6)	4156	NM_001271730	22433	Mm.469937	NM_013842	ENSMUSG00000020484	Xbp1	D11Ertd39e|TREB-5|TREB5|XBP-1	X-box binding protein 1	protein-coding
mm_95519.1	chr11	52120915	52120921	+	1	NA	intron (NM_019411, intron 5 of 6)	intron (NM_019411, intron 5 of 6)	-5828	NR_037221	100526467		NR_037221	ENSMUSG00000092870	Mir3061	mir-3061|mmu-mir-3061	microRNA 3061	ncRNA
mm_82909.1	chr9	32959606	32959613	-	1	NA	Intergenic	Intergenic	-30643	NR_131058	330917	Mm.488283	NR_131058		Gm27162	A430016B06	predicted gene 27162	ncRNA
mm_85552.1	chr9	106685809	106685824	-	1	NA	promoter-TSS (NM_011573)	promoter-TSS (NM_011573)	0	NM_011573	21767	Mm.22266	NM_011573	ENSMUSG00000040813	Tex264	TEG-264	testis expressed gene 264	protein-coding
mm_163251.1	chr11	108186824	108186837	+	1	NA	intron (NM_011101, intron 3 of 16)	RMER4B|LTR|ERVK	157058	NM_011101	18750	Mm.222178	NM_011101	ENSMUSG00000050965	Prkca	AI875142|Pkca	protein kinase C, alpha	protein-coding
mm_115808.1	chr13	19358613	19358624	-	1	NA	intron (NM_024270, intron 8 of 8)	intron (NM_024270, intron 8 of 8)	37195	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_127316.1	chr15	100271686	100271696	+	1	NA	Intergenic	MMERVK9C_I-int|LTR|ERVK	-9146	NM_183109	75002	Mm.261400	NM_183109	ENSMUSG00000045631	Tmprss12	4930478A21Rik	transmembrane (C-terminal) protease, serine 12	protein-coding
mm_49970.1	chr6	40768861	40768869	+	1	NA	3' UTR (NM_001171003, exon 48 of 48)	3' UTR (NM_001171003, exon 48 of 48)	118629	NM_139296	194357	Mm.207087	NM_139296	ENSMUSG00000029885	Moxd2	Dbhl1	monooxygenase, DBH-like 2	protein-coding
mm_108649.1	chr12	86060964	86060989	+	1	NA	intron (NM_009368, intron 5 of 6)	intron (NM_009368, intron 5 of 6)	18065	NM_009368	21809	Mm.3992	NM_009368	ENSMUSG00000021253	Tgfb3	TGF-beta-3|Tgfb-3	transforming growth factor, beta 3	protein-coding
mm_81767.1	chr9	114401478	114401495	+	1	NA	intron (NR_108101, intron 1 of 14)	CpG	391	NM_001200002	100504715	Mm.290516	NM_001200002	ENSMUSG00000079260	Tmppe	-	transmembrane protein with metallophosphoesterase domain	protein-coding
mm_135936.1	chr16	74279315	74279353	-	1	NA	intron (NM_175549, intron 2 of 27)	(TG)n|Simple_repeat|Simple_repeat	62733	NR_030464	751561		NR_030464	ENSMUSG00000104758	Mir691	Mirn691|mir-691|mmu-mir-691	microRNA 691	ncRNA
mm_144511.1	chr18	24709311	24709325	+	1	NA	5' UTR (NM_001289655, exon 1 of 26)	5' UTR (NM_001289655, exon 1 of 26)	695	NM_001289655	225288	Mm.329322	NM_175276	ENSMUSG00000034295	Fhod3	A930009H06Rik|FHOS2|mKIAA1695	formin homology 2 domain containing 3	protein-coding
mm_102953.1	chr11	69662626	69662636	-	1	NA	promoter-TSS (NR_035455)	promoter-TSS (NR_035455)	18	NR_125917	24070	Mm.89579	NM_011900	ENSMUSG00000018761	Mpdu1	LEC35|SL15|Supl15h	mannose-P-dolichol utilization defect 1	protein-coding
mm_38515.1	chr4	141398735	141398746	-	1	NA	promoter-TSS (NM_024412)	promoter-TSS (NM_024412)	-34	NM_024412	12733	Mm.167900	NM_024412	ENSMUSG00000033770	Clcnka	C75963|CLC-K1|Clcnk1	chloride channel, voltage-sensitive Ka	protein-coding
mm_142208.1	chr17	36988760	36988778	-	1	NA	exon (NM_001115075, exon 3 of 6)	exon (NM_001115075, exon 3 of 6)	735	NM_001115075	240095	Mm.246609	NM_001115075	ENSMUSG00000024459	H2-M5	CRW2|D130003B22Rik|H-2M5	histocompatibility 2, M region locus 5	protein-coding
mm_88792.1	chr10	80629647	80629655	+	1	NA	promoter-TSS (NM_001159591)	promoter-TSS (NM_001159591)	-5	NM_001159591	103236	Mm.29873	NM_134002	ENSMUSG00000003345	Csnk1g2	2810429I12Rik|AI463719	casein kinase 1, gamma 2	protein-coding
mm_80365.1	chr9	75314212	75314233	+	1	NA	non-coding (NR_073186, exon 1 of 12)	non-coding (NR_073186, exon 1 of 12)	154	NM_138719	14697	Mm.17604	NM_010313	ENSMUSG00000032192	Gnb5	GBS|Gbeta5|flr	guanine nucleotide binding protein (G protein), beta 5	protein-coding
mm_102880.1	chr11	69410441	69410453	-	1	NA	intron (NM_001017426, intron 1 of 22)	CpG	3228	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_11905.1	chr2	50394926	50394933	+	1	NA	intron (NR_040362, intron 1 of 2)	intron (NR_040362, intron 1 of 2)	98119	NR_040362	100502624	Mm.382825	NR_040361	ENSMUSG00000085862	Gm13483	OTTMUSG00000012382	predicted gene 13483	ncRNA
mm_31817.1	chr4	66841758	66841775	+	1	NA	3' UTR (NM_021297, exon 3 of 3)	3' UTR (NM_021297, exon 3 of 3)	14215	NM_021297	21898	Mm.38049	NM_021297	ENSMUSG00000039005	Tlr4	Lps|Ly87|Ran/M1|Rasl2-8	toll-like receptor 4	protein-coding
mm_30525.1	chr4	3089763	3089800	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	-82302	NM_001167534	100312470	Mm.480297	NM_001167534	ENSMUSG00000094798	Vmn1r2	Gm11776|OTTMUSG00000004179	vomeronasal 1 receptor 2	protein-coding
mm_126965.1	chr15	92597130	92597167	+	1	NA	promoter-TSS (NM_001164594)	promoter-TSS (NM_001164594)	39	NM_001164594	239618	Mm.309826	NM_001164593	ENSMUSG00000036218	Pdzrn4	1110017D07Rik|LNX4|SAMCAP3L|mKIAA3027	PDZ domain containing RING finger 4	protein-coding
mm_125008.1	chr15	25414176	25414197	+	1	NA	promoter-TSS (NM_027395)	promoter-TSS (NM_027395)	-6	NR_027376	432939	Mm.146555	NM_001013791		Gm5468	100040583|EG432939	predicted gene 5468	ncRNA
mm_16230.1	chr2	173156096	173156108	+	1	NA	intron (NM_011044, intron 6 of 9)	intron (NM_011044, intron 6 of 9)	3029	NM_011044	18534	Mm.266867	NM_011044	ENSMUSG00000027513	Pck1	AI265463|PEPCK|Pck-1	phosphoenolpyruvate carboxykinase 1, cytosolic	protein-coding
mm_23526.1	chr3	60618196	60618204	+	1	NA	intron (NM_001310514, intron 7 of 8)	intron (NM_001310514, intron 7 of 8)	117021	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_97337.1	chr11	77340058	77340061	+	1	NA	intron (NM_177710, intron 2 of 14)	B1_Mur1|SINE|Alu	-8221	NM_001291190	237860	Mm.440381	NM_177710	ENSMUSG00000037926	Ssh2	SSH-2|SSH-2L|mSSH-2L	slingshot homolog 2 (Drosophila)	protein-coding
mm_156677.1	chrX	159303313	159303340	+	1	NA	intron (NM_001346675, intron 4 of 23)	intron (NM_001346675, intron 4 of 23)	47544	NM_001346675	110651	Mm.328476	NM_148945	ENSMUSG00000031309	Rps6ka3	MAPKAPK-1b|MPK-9|Rsk2|S6K-alpha3|p90RSK3|pp90RSK2	ribosomal protein S6 kinase polypeptide 3	protein-coding
mm_149713.1	chr19	21653324	21653345	+	1	NA	promoter-TSS (NM_025423)	promoter-TSS (NM_025423)	25	NM_146096	226016	Mm.28796	NM_146096	ENSMUSG00000047368	Abhd17b	5730446C15Rik|Cgi67|Fam108b|Fam108b1	abhydrolase domain containing 17B	protein-coding
mm_69085.1	chr7	127016830	127016857	-	1	NA	TTS (NM_001102563)	TTS (NM_001102563)	509	NM_030240	67278	Mm.345385	NM_030240	ENSMUSG00000030680	Pagr1a	2900092E17Rik|C77040|PA1|PAGR1	PAXIP1 associated glutamate rich protein 1A	protein-coding
mm_136174.1	chr16	88707962	88707965	-	1	NA	promoter-TSS (NM_027155)	promoter-TSS (NM_027155)	-1	NM_027155	69661	Mm.58243	NM_027155	ENSMUSG00000050704	2310061N02Rik	-	RIKEN cDNA 2310061N02 gene	protein-coding
mm_855.1	chr1	52123110	52123233	+	1	NA	exon (NM_001205314, exon 4 of 25)	exon (NM_001205314, exon 4 of 25)	3549	NM_001205313	20846	Mm.277406	NM_009283	ENSMUSG00000026104	Stat1	2010005J02Rik|AA408197	signal transducer and activator of transcription 1	protein-coding
mm_28319.1	chr3	89322861	89322872	-	1	NA	promoter-TSS (NM_010108)	promoter-TSS (NM_010108)	13	NM_010108	13638	Mm.331159	NM_010108	ENSMUSG00000028039	Efna3	AW494418|EFL-2|Ehk1-L|Epl3|LERK-3	ephrin A3	protein-coding
mm_72510.1	chr8	83900448	83900488	+	1	NA	5' UTR (NM_181039, exon 1 of 23)	5' UTR (NM_181039, exon 1 of 23)	370	NM_181039	330814	Mm.260733	NM_181039	ENSMUSG00000013033	Adgrl1	2900070I05Rik|AI182398|CLIBA|Lec2|Lphn1|mKIAA0821	adhesion G protein-coupled receptor L1	protein-coding
mm_101444.1	chr11	30161000	30161004	-	1	NA	intron (NM_175836, intron 1 of 34)	intron (NM_175836, intron 1 of 34)	37255	NM_009260	20742	Mm.123110	NM_009260	ENSMUSG00000020315	Sptbn1	9930031C03Rik|AL033301|SPTB2|Spnb-2|Spnb2|elf1|elf3|mKIAA4049	spectrin beta, non-erythrocytic 1	protein-coding
mm_150072.1	chr19	29386733	29386753	+	1	NA	3' UTR (NM_021893, exon 7 of 7)	3' UTR (NM_021893, exon 7 of 7)	19305	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_122515.1	chr14	47177839	47177861	-	1	NA	intron (NM_008102, intron 1 of 5)	intron (NM_008102, intron 1 of 5)	11552	NM_008102	14528	Mm.10651	NM_008102	ENSMUSG00000037580	Gch1	GTP-CH|GTPCH|Gch	GTP cyclohydrolase 1	protein-coding
mm_42570.1	chr5	117209995	117210021	+	1	NA	intron (NM_001081308, intron 8 of 19)	intron (NM_001081308, intron 8 of 19)	76420	NM_183306	330177	Mm.24343	NM_183306	ENSMUSG00000061288	Taok3	2900006A08Rik|A130052D22|A430105I05Rik	TAO kinase 3	protein-coding
mm_169180.1	chr13	65817664	65817666	-	1	NA	Intergenic	Intergenic	-295788	NM_001177832	628709	Mm.390595	NM_001177832	ENSMUSG00000095909	Gm10324	ENSMUSG00000071302	predicted gene 10324	protein-coding
mm_93241.1	chr10	95415974	95416006	-	1	NA	promoter-TSS (NM_001168657)	promoter-TSS (NM_001168657)	222	NM_001168655	216233	Mm.474283	NM_007706	ENSMUSG00000020027	Socs2	8030460M17|AI527257|AW108012|CIS2|Cish2|D130043N08Rik|JAB|SOCS-2|SSI-2|hg	suppressor of cytokine signaling 2	protein-coding
mm_148312.1	chr18	83764940	83764985	-	1	NA	Intergenic	Intergenic	321600	NM_001081300	110796	Mm.102136	NM_001081300	ENSMUSG00000046982	Tshz1	5730407I04Rik|D18Bwg1409e|Mtsh1|NY-CO-33|Sdccag33|Tsh1|mKIAA4206|teashirt1	teashirt zinc finger family member 1	protein-coding
mm_17577.1	chr2	30415303	30415368	-	1	NA	promoter-TSS (NM_138748)	promoter-TSS (NM_138748)	413	NM_007760	12908	Mm.20396	NM_007760	ENSMUSG00000026853	Crat	AW107812|CARAT	carnitine acetyltransferase	protein-coding
mm_87093.1	chr10	33083158	33083197	+	1	NA	promoter-TSS (NM_029726)	promoter-TSS (NM_029726)	-306	NM_029726	76757	Mm.338508	NM_029726	ENSMUSG00000019787	Trdn	2310045H21Rik|EG432451|TDN	triadin	protein-coding
mm_125321.1	chr15	38300393	38300393	+	1	NA	intron (NM_001289471, intron 1 of 4)	CpG	318	NM_013692	21847	Mm.4292	NM_013692	ENSMUSG00000037465	Klf10	AI115143|EGR[a]|Egral|Gdnfif|TIEG-1|Tieg|Tieg1|mGIF	Kruppel-like factor 10	protein-coding
mm_86874.1	chr10	21996946	21996956	+	1	NA	intron (NM_001161848, intron 7 of 11)	intron (NM_001161848, intron 7 of 11)	2285	NM_011361	20393	Mm.28405	NM_011361	ENSMUSG00000019970	Sgk1	Sgk	serum/glucocorticoid regulated kinase 1	protein-coding
mm_2148.1	chr1	88134787	88134806	+	1	NA	promoter-TSS (NM_145079)	promoter-TSS (NM_145079)	-13	NM_145079	94284	Mm.300095	NM_145079	ENSMUSG00000054545	Ugt1a6a	UDPGT|UDPGT 1-6|UGT1-06|UGT1.6|Ugt1a6|Ugt1a7	UDP glucuronosyltransferase 1 family, polypeptide A6A	protein-coding
mm_171613.1	chr4	150247918	150247922	+	1	NA	exon (NM_001025388, exon 10 of 12)	exon (NM_001025388, exon 10 of 12)	10596	NM_001025388	433182	Mm.70666	NM_001025388	ENSMUSG00000059040	Eno1b	EG433182|Eno1|Gm5506	enolase 1B, retrotransposed	protein-coding
mm_146152.1	chr18	75000470	75000487	+	1	NA	promoter-TSS (NR_028552)	promoter-TSS (NR_028552)	1	NM_001002239	319195	Mm.276337	NM_001002239	ENSMUSG00000062328	Rpl17	-	ribosomal protein L17	protein-coding
mm_18082.1	chr2	44635238	44635252	-	1	NA	exon (NM_172662, exon 6 of 11)	exon (NM_172662, exon 6 of 11)	226377	NM_172662	227835	Mm.314312	NM_172662	ENSMUSG00000036890	Gtdc1	E330008O22Rik	glycosyltransferase-like domain containing 1	protein-coding
mm_102425.1	chr11	59430118	59430121	-	1	NA	intron (NM_144521, intron 2 of 4)	intron (NM_144521, intron 2 of 4)	19837	NM_144521	67826	Mm.26680	NM_144521	ENSMUSG00000009894	Snap47	1110031B06Rik|SNAP-47	synaptosomal-associated protein, 47	protein-coding
mm_123159.1	chr14	57133251	57133266	-	1	NA	5' UTR (NM_001271663, exon 1 of 3)	5' UTR (NM_001271663, exon 1 of 3)	353	NM_001271663	14623	Mm.25652	NM_008128	ENSMUSG00000040055	Gjb6	AA958971|Cx30|D14Bwg0506e	gap junction protein, beta 6	protein-coding
mm_157816.1	chrX	74023798	74023808	-	1	NA	promoter-TSS (NR_039594)	promoter-TSS (NR_039594)	115	NM_001177975	16179	Mm.38241	NM_008363	ENSMUSG00000031392	Irak1	AA408924|IRAK|IRAK-1|IRAK1-S|IRAK1b|Il1rak|Plpk|mPLK	interleukin-1 receptor-associated kinase 1	protein-coding
mm_134368.1	chr16	17121735	17121767	-	1	NA	intron (NM_183287, intron 2 of 7)	intron (NM_183287, intron 2 of 7)	2391	NR_029659	723816		NR_029659	ENSMUSG00000065572	Mir130b	Mirn130b|mir-130b	microRNA 130b	ncRNA
mm_150369.1	chr19	34651712	34651730	+	1	NA	Intergenic	B1_Mur4|SINE|Alu	10832	NM_008331	15957	Mm.439751	NM_008331	ENSMUSG00000034459	Ifit1	ISG56|Ifi56|P56	interferon-induced protein with tetratricopeptide repeats 1	protein-coding
mm_59028.1	chr7	19304083	19304092	+	1	NA	3' UTR (NM_008036, exon 4 of 4)	3' UTR (NM_008036, exon 4 of 4)	5958	NM_008036	14282	Mm.248335	NM_008036	ENSMUSG00000003545	Fosb	-	FBJ osteosarcoma oncogene B	protein-coding
mm_141926.1	chr17	35027649	35027657	-	1	NA	TTS (NR_130641)	TTS (NR_130641)	363	NR_028258	78376	Mm.390966	NM_023893	ENSMUSG00000036185	Sapcd1	2810436B06Rik|G7d|Ng23	suppressor APC domain containing 1	protein-coding
mm_75856.1	chr8	70699997	70700067	-	1	NA	exon (NM_001286944, exon 1 of 1)	exon (NM_001286944, exon 1 of 1)	2293	NM_001286944	16478	Mm.419851	NM_010592	ENSMUSG00000071076	Jund	Jund1	jun D proto-oncogene	protein-coding
mm_28939.1	chr3	98882284	98882294	-	1	NA	intron (NM_019545, intron 4 of 8)	intron (NM_019545, intron 4 of 8)	10941	NM_019545	56185	Mm.281874	NM_019545	ENSMUSG00000027870	Hao2	AI325478|Hao-2|Hao3|Haox3	hydroxyacid oxidase 2	protein-coding
mm_45177.1	chr5	51553897	51553905	-	1	NA	promoter-TSS (NR_027710)	promoter-TSS (NR_027710)	20	NR_027710	19017	Mm.259072	NM_008904	ENSMUSG00000029167	Ppargc1a	A830037N07Rik|ENSMUSG00000079510|Gm11133|PGC-1|PPARGC-1-alpha|Pgc-1alpha|Pgc1|Pgco1|Ppargc1	peroxisome proliferative activated receptor, gamma, coactivator 1 alpha	protein-coding
mm_75779.1	chr8	69996327	69996349	-	1	NA	promoter-TSS (NM_001286450)	promoter-TSS (NM_001286450)	46	NM_001286450	234366	Mm.270044	NM_145596	ENSMUSG00000036180	Gatad2a	1110066C11Rik|BC031407|C80248	GATA zinc finger domain containing 2A	protein-coding
mm_17713.1	chr2	32386021	32386042	-	1	NA	exon (NM_008491, exon 3 of 6)	exon (NM_008491, exon 3 of 6)	1708	NM_008491	16819	Mm.9537	NM_008491	ENSMUSG00000026822	Lcn2	24p3|AW212229|NRL|Sip24	lipocalin 2	protein-coding
mm_32595.1	chr4	111750619	111750632	+	1	NA	intron (NM_026470, intron 3 of 12)	intron (NM_026470, intron 3 of 12)	30615	NM_026470	67946	Mm.275526	NM_026470	ENSMUSG00000034401	Spata6	1700062C23Rik|AI790763|Hash|KRP|Mash	spermatogenesis associated 6	protein-coding
mm_103681.1	chr11	79273881	79273891	-	1	NA	Intergenic	Zaphod|DNA|hAT-Tip100	-19191	NM_019653	78889	Mm.307022	NM_019653	ENSMUSG00000017677	Wsb1	1110056B13Rik|2700038M07Rik	WD repeat and SOCS box-containing 1	protein-coding
mm_28172.1	chr3	88000149	88000180	-	1	NA	5' UTR (NM_001109758, exon 1 of 8)	5' UTR (NM_001109758, exon 1 of 8)	192	NM_007529	12032	Mm.4598	NM_007529	ENSMUSG00000004892	Bcan	Cspg7	brevican	protein-coding
mm_21366.1	chr2	157135086	157135110	-	1	NA	exon (NM_001139520, exon 1 of 17)	exon (NM_001139520, exon 1 of 17)	124	NM_001139520	56045	Mm.248478	NM_018851	ENSMUSG00000027639	Samhd1	E330031J07Rik|Mg11	SAM domain and HD domain, 1	protein-coding
mm_90179.1	chr10	119819494	119819541	+	1	NA	5' UTR (NM_130891, exon 1 of 22)	5' UTR (NM_130891, exon 1 of 22)	128	NM_028736	74053	Mm.196692	NM_028736	ENSMUSG00000034813	Grip1	4931400F03Rik|GRIP|eb	glutamate receptor interacting protein 1	protein-coding
mm_134117.1	chr16	10297144	10297148	-	1	NA	intron (NM_007929, intron 1 of 4)	intron (NM_007929, intron 1 of 4)	16822	NM_007929	13731	Mm.246009	NM_007929	ENSMUSG00000022505	Emp2	XMP	epithelial membrane protein 2	protein-coding
mm_11923.1	chr2	52072862	52072878	+	1	NA	promoter-TSS (NM_175238)	promoter-TSS (NM_175238)	33	NM_175238	51869	Mm.254530	NM_175238	ENSMUSG00000036202	Rif1	5730435J01Rik|6530403D07Rik|AU016181|AW549474|D2Ertd145e	replication timing regulatory factor 1	protein-coding
mm_73048.1	chr8	94355798	94355799	+	1	NA	intron (NM_019415, intron 21 of 24)	intron (NM_019415, intron 21 of 24)	26590	NM_001205311	20497	Mm.25804	NM_019415	ENSMUSG00000031766	Slc12a3	AI035291|NCC|NCCT|TSC	solute carrier family 12, member 3	protein-coding
mm_7898.1	chr1	133610243	133610245	-	1	NA	promoter-TSS (NM_009227)	promoter-TSS (NM_009227)	36	NM_009227	20643	Mm.249110	NM_009227	ENSMUSG00000090553	Snrpe	AL022645|C76690|SME	small nuclear ribonucleoprotein E	protein-coding
mm_48493.1	chr5	142629329	142629348	-	1	NA	promoter-TSS (NM_178398)	promoter-TSS (NM_178398)	-246	NM_178398	74781	Mm.29432	NM_178398	ENSMUSG00000029578	Wipi2	1110018O08Rik|2510001I10Rik	WD repeat domain, phosphoinositide interacting 2	protein-coding
mm_72831.1	chr8	88272285	88272298	+	1	NA	promoter-TSS (NM_007406)	promoter-TSS (NM_007406)	-112	NM_007406	11513	Mm.288206	NM_007406	ENSMUSG00000031659	Adcy7	AA407758	adenylate cyclase 7	protein-coding
mm_114667.1	chr13	78202637	78202661	+	1	NA	intron (NR_045195, intron 1 of 2)	intron (NR_045195, intron 1 of 2)	-3776	NM_010151	13865	Mm.439653	NM_010151	ENSMUSG00000069171	Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR-3|EAR3|Erbal3|SVP44|Tcfcoup1	nuclear receptor subfamily 2, group F, member 1	protein-coding
mm_103933.1	chr11	83648661	83648687	-	1	NA	exon (NM_011337, exon 2 of 3)	exon (NM_011337, exon 2 of 3)	704	NM_011337	20302	Mm.1282	NM_011337	ENSMUSG00000000982	Ccl3	AI323804|G0S19-1|LD78alpha|MIP-1alpha|MIP1-(a)|MIP1-alpha|Mip1a|Scya3	chemokine (C-C motif) ligand 3	protein-coding
mm_18722.1	chr2	72886613	72886614	-	1	NA	Intergenic	Intergenic	-72896	NR_102349	76218	Mm.75260	NR_102348	ENSMUSG00000085427	6430710C18Rik	5033406J01Rik	RIKEN cDNA 6430710C18 gene	ncRNA
mm_36373.1	chr4	76557038	76557040	-	1	NA	intron (NM_011211, intron 10 of 39)	Lx3_Mus|LINE|L1	-1278753	NM_025849	66928	Mm.24332	NM_025849	ENSMUSG00000028398	Tmem261	1700027K24Rik|3110001D03Rik	transmembrane protein 261	protein-coding
mm_65931.1	chr7	30322410	30322418	-	1	NA	promoter-TSS (NM_001033140)	promoter-TSS (NM_001033140)	-39	NM_001033140	68332	Mm.6844	NM_001033140	ENSMUSG00000074211	Sdhaf1	0610010E21Rik|AI430885|AW490662|Lyrm8	succinate dehydrogenase complex assembly factor 1	protein-coding
mm_124745.1	chr15	6607813	6607813	+	1	NA	intron (NM_011815, intron 1 of 17)	intron (NM_011815, intron 1 of 17)	27966	NM_011815	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_165307.1	chr2	98666901	98666909	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	1199248	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_36314.1	chr4	69926168	69926172	-	1	NA	Intergenic	Intergenic	484265	NM_001313762	214444	Mm.370777	NM_145990	ENSMUSG00000039298	Cdk5rap2	2900018K03Rik|an|mKIAA1633	CDK5 regulatory subunit associated protein 2	protein-coding
mm_80934.1	chr9	102690672	102690693	+	1	NA	Intergenic	Intergenic	-27122	NM_019764	56332	Mm.21145	NM_019764	ENSMUSG00000032531	Amotl2	AW549739|C79691|Lccp|MASCOT|mKIAA0989	angiomotin-like 2	protein-coding
mm_10774.1	chr2	24287079	24287084	+	1	NA	Intergenic	Intergenic	-4115	NM_153077	215274	Mm.218750	NM_153077	ENSMUSG00000046845	Il1f10	-	interleukin 1 family, member 10	protein-coding
mm_104792.1	chr11	98750507	98750528	-	1	NA	intron (NM_178060, intron 1 of 8)	intron (NM_178060, intron 1 of 8)	8732	NM_001313983	21833	Mm.265917	NM_178060	ENSMUSG00000058756	Thra	6430529J03Rik|AW259572|Erba|Nr1a1|Rvr|T3R[a]|T3Ralpha|Thra1|Thra2|c-erbA-1|c-erbA-alpha|c-erbAalpha	thyroid hormone receptor alpha	protein-coding
mm_89024.1	chr10	82585391	82585406	+	1	NA	Intergenic	Intergenic	37830	NM_001135569	544717	Mm.334867	NM_001135567	ENSMUSG00000063320	1190007I07Rik	-	RIKEN cDNA 1190007I07 gene	protein-coding
mm_130423.1	chr15	98093298	98093324	-	1	NA	5' UTR (NM_144851, exon 1 of 18)	5' UTR (NM_144851, exon 1 of 18)	258	NM_144851	223870	Mm.384023	NM_144851	ENSMUSG00000033075	Senp1	2310046A20Rik|D15Ertd528e|E330036L07Rik|suPr-2	SUMO1/sentrin specific peptidase 1	protein-coding
mm_170838.1	chr2	177249324	177249334	-	1	NA	Intergenic	Intergenic	-215413	NM_001177568	628308	Mm.460436	NM_001177568	ENSMUSG00000078866	Zfp970	Gm14420|OTTMUSG00000016588	zinc finger protein 970	protein-coding
mm_47984.1	chr5	135911571	135911583	-	1	NA	exon (NM_018871, exon 2 of 2)	exon (NM_018871, exon 2 of 2)	23064	NM_018871	22628	Mm.233813	NM_018871	ENSMUSG00000051391	Ywhag	14-3-3gamma|D7Bwg1348e	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, gamma polypeptide	protein-coding
mm_165892.1	chr4	44362270	44362270	+	1	NA	intron (NM_010790, intron 17 of 17)	intron (NM_010790, intron 17 of 17)	61353	NM_010790	17279	Mm.268668	NM_010790	ENSMUSG00000035683	Melk	AI327312|MPK38|mKIAA0175	maternal embryonic leucine zipper kinase	protein-coding
mm_137455.1	chr17	26561462	26561474	+	1	NA	promoter-TSS (NM_026170)	promoter-TSS (NM_026170)	-44	NM_026170	67458	Mm.30496	NM_026170	ENSMUSG00000001576	Ergic1	1200007D18Rik|maa-136	endoplasmic reticulum-golgi intermediate compartment (ERGIC) 1	protein-coding
mm_84488.1	chr9	66845844	66845884	-	1	NA	3' UTR (NM_173413, exon 8 of 8)	3' UTR (NM_173413, exon 8 of 8)	-11158	NM_026674	68318	Mm.284229	NM_026674	ENSMUSG00000053040	Aph1c	0610008A10Rik|APH-1b|Aph1b	aph1 homolog C, gamma secretase subunit	protein-coding
mm_41848.1	chr5	104437646	104437656	+	1	NA	intron (NM_001204233, intron 2 of 5)	intron (NM_001204233, intron 2 of 5)	1459	NM_001204233	20750	Mm.288474	NM_009263	ENSMUSG00000029304	Spp1	2AR|Apl-1|BNSP|BSPI|Bsp|ETA-1|Eta|OP|Opn|Opnl|Ric|Spp-1	secreted phosphoprotein 1	protein-coding
mm_48216.1	chr5	137611338	137611348	-	1	NA	promoter-TSS (NM_008788)	promoter-TSS (NM_008788)	61	NM_008788	18542	Mm.262345	NM_008788	ENSMUSG00000029718	Pcolce	Astt-2|Astt2|P14|PCPE-1	procollagen C-endopeptidase enhancer protein	protein-coding
mm_51507.1	chr6	83135893	83135903	+	1	NA	promoter-TSS (NM_001136227)	promoter-TSS (NM_001136227)	90	NM_001136227	20166	Mm.4139	NM_009106	ENSMUSG00000034930	Rtkn	-	rhotekin	protein-coding
mm_166463.1	chr5	140830266	140830273	-	1	NA	exon (NM_010302, exon 1 of 4)	exon (NM_010302, exon 1 of 4)	162	NM_010302	14673	Mm.370185	NM_010302	ENSMUSG00000000149	Gna12	AI414047|AI504261|Galpha12	guanine nucleotide binding protein, alpha 12	protein-coding
mm_40086.1	chr5	34531964	34531984	+	1	NA	intron (NM_011893, intron 1 of 12)	intron (NM_011893, intron 1 of 12)	6190	NM_011893	24055	Mm.5012	NM_011893	ENSMUSG00000054520	Sh3bp2	3BP2	SH3-domain binding protein 2	protein-coding
mm_66630.1	chr7	45510367	45510399	-	1	NA	promoter-TSS (NM_008749)	promoter-TSS (NM_008749)	25	NM_008749	18220	Mm.258923	NM_008749	ENSMUSG00000030824	Nucb1	B230337F23Rik|C77483|Calnuc|MTEST82|Nucb	nucleobindin 1	protein-coding
mm_16741.1	chr2	9520133	9520135	-	1	NA	Intergenic	Intergenic	330619	NR_038180	73438	Mm.23558	NR_038180	ENSMUSG00000085580	1700061F12Rik	-	RIKEN cDNA 1700061F12 gene	ncRNA
mm_38118.1	chr4	134548075	134548085	-	1	NA	exon (NM_029100, exon 3 of 12)	exon (NM_029100, exon 3 of 12)	4086	NM_029100	74777	Mm.29773	NM_029100	ENSMUSG00000050989	Selenon	1110019I12Rik|AI414492|SelN|Sepn1	selenoprotein N	protein-coding
mm_113731.1	chr13	43974922	43974928	+	1	NA	Intergenic	Intergenic	-146242	NR_045285	328235	Mm.188356	NR_045285	ENSMUSG00000089815	Gm5083	A730030A06	predicted gene 5083	ncRNA
mm_62939.1	chr7	118937077	118937083	+	1	NA	intron (NM_001081446, intron 7 of 8)	intron (NM_001081446, intron 7 of 8)	58131	NM_022420	64297	Mm.103439	NM_022420	ENSMUSG00000008734	Gprc5b	AW125761|Raig2	G protein-coupled receptor, family C, group 5, member B	protein-coding
mm_67147.1	chr7	73476104	73476107	-	1	NA	intron (NM_001081345, intron 20 of 38)	intron (NM_001081345, intron 20 of 38)	65641	NM_001081345	244059	Mm.34539	NM_001081345	ENSMUSG00000078671	Chd2	2810013C04Rik|2810040A01Rik|5630401D06Rik|AI851092|BC029703|CHD-2	chromodomain helicase DNA binding protein 2	protein-coding
mm_20507.1	chr2	130582570	130582574	-	1	NA	promoter-TSS (NM_009732)	promoter-TSS (NM_009732)	16	NM_009732	11998	Mm.6190	NM_009732	ENSMUSG00000037727	Avp	Vp|Vsp	arginine vasopressin	protein-coding
mm_172161.1	chr6	44792975	44792981	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-267083	NM_001004357	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding
mm_1321.1	chr1	65100535	65100542	+	1	NA	exon (NM_007774, exon 3 of 3)	exon (NM_007774, exon 3 of 3)	2825	NM_007774	12964	Mm.26904	NM_007774	ENSMUSG00000044429	Cryga	Cryg-4|DGcry-4	crystallin, gamma A	protein-coding
mm_97748.1	chr11	80477016	80477085	+	1	NA	promoter-TSS (NM_009871)	promoter-TSS (NM_009871)	4	NM_009871	12569	Mm.142275	NM_009871	ENSMUSG00000048895	Cdk5r1	Cdk5r|D11Bwg0379e|p25|p35	cyclin-dependent kinase 5, regulatory subunit 1 (p35)	protein-coding
mm_90879.1	chr10	9675800	9675819	-	1	NA	promoter-TSS (NM_177271)	promoter-TSS (NM_177271)	-601	NM_177271	320825	Mm.101115	NM_177271	ENSMUSG00000060487	Samd5	E130306M17Rik	sterile alpha motif domain containing 5	protein-coding
mm_124731.1	chr15	6580626	6580634	+	1	NA	exon (NM_001278269, exon 1 of 17)	exon (NM_001278269, exon 1 of 17)	783	NM_011815	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_36649.1	chr4	94569286	94569304	-	1	NA	3' UTR (NM_172695, exon 14 of 14)	3' UTR (NM_172695, exon 14 of 14)	-12499	NM_026368	67770	Mm.35170	NM_026368	ENSMUSG00000028578	Caap1	5830433M19Rik|AI536248|CAAP	caspase activity and apoptosis inhibitor 1	protein-coding
mm_28068.1	chr3	84270719	84270735	-	1	NA	promoter-TSS (NM_001271725)	promoter-TSS (NM_001271725)	56	NM_001271725	80890	Mm.44876	NM_030706	ENSMUSG00000027993	Trim2	mKIAA0517|narf	tripartite motif-containing 2	protein-coding
mm_125538.1	chr15	58140929	58140967	+	1	NA	promoter-TSS (NM_001326602)	promoter-TSS (NM_001326602)	-418	NM_001326602	76773	Mm.26771	NM_029734	ENSMUSG00000022359	Wdyhv1	2410187C16Rik|AU014961|AW550036|Ntaq1	WDYHV motif containing 1	protein-coding
mm_147250.1	chr18	38598974	38598976	-	1	NA	intron (NM_011898, intron 1 of 1)	intron (NM_011898, intron 1 of 1)	2293	NM_011898	24066	Mm.42038	NM_011898	ENSMUSG00000024427	Spry4	A030006O18Rik|sprouty4	sprouty homolog 4 (Drosophila)	protein-coding
mm_95398.1	chr11	49712922	49712962	+	1	NA	promoter-TSS (NM_212484)	promoter-TSS (NM_212484)	-220	NM_212484	104625	Mm.247113	NM_212484	ENSMUSG00000020362	Cnot6	CCR4	CCR4-NOT transcription complex, subunit 6	protein-coding
mm_118727.1	chr14	22225021	22225051	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	205324	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_19811.1	chr2	110362905	110362913	-	1	NA	promoter-TSS (NM_026271)	promoter-TSS (NM_026271)	84	NM_026271	67606	Mm.291809	NM_026271	ENSMUSG00000074971	Fibin	1110018M03Rik	fin bud initiation factor homolog (zebrafish)	protein-coding
mm_108714.1	chr12	87147786	87147792	+	1	NA	promoter-TSS (NM_001252556)	promoter-TSS (NM_001252556)	82	NM_010363	14874	Mm.29652	NM_010363	ENSMUSG00000021033	Gstz1	MAAI	glutathione transferase zeta 1 (maleylacetoacetate isomerase)	protein-coding
mm_120223.1	chr14	62838627	62838677	+	1	NA	TTS (NR_106174)	TTS (NR_106174)	931	NR_106174	102465889		NR_106174	ENSMUSG00000099245	Mir8098	Gm27462|mmu-mir-8098	microRNA 8098	ncRNA
mm_19096.1	chr2	79428959	79428990	-	1	NA	promoter-TSS (NM_001048176)	promoter-TSS (NM_001048176)	14	NM_001048176	228094	Mm.440704	NM_001033295	ENSMUSG00000075256	Cerkl	Gm1958|Rp26	ceramide kinase-like	protein-coding
mm_17625.1	chr2	31031768	31031779	-	1	NA	intron (NM_001038700, intron 14 of 14)	B1_Mus1|SINE|Alu	49494	NM_028846	74270	Mm.346654	NM_028846	ENSMUSG00000026854	Usp20	1700055M05Rik|AI467231|Vdu2	ubiquitin specific peptidase 20	protein-coding
mm_160209.1	chr7	92663622	92663622	-	1	NA	exon (NM_029078, exon 4 of 16)	exon (NM_029078, exon 4 of 16)	6290	NM_029078	74737	Mm.288645	NM_029078	ENSMUSG00000041328	Pcf11	2500001H09Rik|5730417B17Rik|C77803	PCF11 cleavage and polyadenylation factor subunit	protein-coding
mm_119456.1	chr14	47062871	47062874	+	1	NA	intron (NM_001037221, intron 4 of 12)	AT_rich|Low_complexity|Low_complexity	-6105	NM_001310544	74480	Mm.214454	NM_028966	ENSMUSG00000021838	Samd4	1700024G08Rik|1700111L17Rik|4933436G17Rik|Samd4a|Smaug|Smaug1|sunk	sterile alpha motif domain containing 4	protein-coding
mm_145559.1	chr18	60812269	60812277	+	1	NA	TTS (NR_039567)	TTS (NR_039567)	197	NR_039567	100628611		NR_039567	ENSMUSG00000093327	Mir5107	mir-5107|mmu-mir-5107|mu-mir-5107	microRNA 5107	ncRNA
mm_72974.1	chr8	92887450	92887457	+	1	NA	intron (NM_173014, intron 9 of 13)	Lx9|LINE|L1	-13942	NM_027112	69543	Mm.440514	NM_027112	ENSMUSG00000078144	Capns2	2310005G05Rik|30K-2	calpain, small subunit 2	protein-coding
mm_110780.1	chr12	71009257	71009259	-	1	NA	TTS (NR_045056)	TTS (NR_045056)	6565	NR_045056	73204	Mm.363770	NR_045055	ENSMUSG00000085622	3110056K07Rik	4921536K06Rik	RIKEN cDNA 3110056K07 gene	ncRNA
mm_147571.1	chr18	55336357	55336357	-	1	NA	Intergenic	Intergenic	-346177	NM_175751	269023	Mm.192984	NM_175751	ENSMUSG00000052713	Zfp608	4932417D18Rik|D430007A19Rik|Znf608	zinc finger protein 608	protein-coding
mm_126772.1	chr15	86067817	86067853	+	1	NA	intron (NM_001205353, intron 1 of 18)	intron (NM_001205353, intron 1 of 18)	9108	NM_001205353	223752	Mm.24442	NM_172611	ENSMUSG00000035900	Gramd4	9930016O13	GRAM domain containing 4	protein-coding
mm_116141.1	chr13	29654313	29654339	-	1	NA	intron (NR_131896, intron 8 of 16)	intron (NR_131896, intron 8 of 16)	201347	NR_131896	68916	Mm.212227	NM_144536	ENSMUSG00000006191	Cdkal1	1190005B03Rik|6620401C13Rik	CDK5 regulatory subunit associated protein 1-like 1	protein-coding
mm_25530.1	chr3	114904353	114904381	+	1	NA	promoter-TSS (NM_001286750)	promoter-TSS (NM_001286750)	-268	NM_001286750	229759	Mm.54183	NM_153157	ENSMUSG00000027965	Olfm3	B230206G02Rik	olfactomedin 3	protein-coding
mm_41782.1	chr5	103720007	103720025	+	1	NA	Intergenic	Intergenic	-34146	NM_133919	17355	Mm.6949	NM_133919	ENSMUSG00000029313	Aff1	9630032B01Rik|AW319193|Af4|Mllt2h|Rob	AF4/FMR2 family, member 1	protein-coding
mm_108779.1	chr12	89813577	89813617	+	1	NA	exon (NM_001252074, exon 1 of 7)	exon (NM_001252074, exon 1 of 7)	1114	NM_001252074	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding
mm_30143.1	chr3	142395628	142395653	-	1	NA	promoter-TSS (NM_001190853)	promoter-TSS (NM_001190853)	56	NM_001190853	56376	Mm.117709	NM_019808	ENSMUSG00000028273	Pdlim5	1110001A05Rik|AI987914|C87059|Enh|Enh1|Enh2|Enh3|LIM	PDZ and LIM domain 5	protein-coding
mm_73066.1	chr8	94393545	94393548	+	1	NA	intron (NM_022331, intron 6 of 7)	B1F|SINE|Alu	7046	NM_022331	64209	Mm.29151	NM_022331	ENSMUSG00000031770	Herpud1	Herp|Mifl|SUP	homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1	protein-coding
mm_83227.1	chr9	42338954	42338970	-	1	NA	exon (NM_001324548, exon 18 of 24)	exon (NM_001324548, exon 18 of 24)	60967	NM_009347	21683	Mm.42209	NM_009347	ENSMUSG00000037705	Tecta	Tctna	tectorin alpha	protein-coding
mm_10282.1	chr2	10080576	10080595	+	1	NA	promoter-TSS (NM_001112738)	promoter-TSS (NM_001112738)	-27	NM_025280	16588	Mm.35498	NM_025280	ENSMUSG00000037262	Kin	Kin17	Kin17 DNA and RNA binding protein	protein-coding
mm_71242.1	chr8	40910816	40910858	+	1	NA	intron (NM_007514, intron 7 of 11)	intron (NM_007514, intron 7 of 11)	-15396	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_60545.1	chr7	44480628	44480645	+	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	-3881	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_93596.1	chr10	117148482	117148510	-	1	NA	promoter-TSS (NM_177798)	promoter-TSS (NM_177798)	-22	NM_177798	327826	Mm.135965	NM_177798	ENSMUSG00000020170	Frs2	4732458E18|C330018A15Rik|Frs2alpha|SNT1	fibroblast growth factor receptor substrate 2	protein-coding
mm_165468.1	chr2	164237457	164237461	+	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	882	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_47581.1	chr5	124579024	124579044	-	1	NA	promoter-TSS (NM_145371)	promoter-TSS (NM_145371)	97	NM_145371	209354	Mm.28839	NM_145371	ENSMUSG00000029388	Eif2b1	D5Ertd406e|EIF2BA	eukaryotic translation initiation factor 2B, subunit 1 (alpha)	protein-coding
mm_3341.1	chr1	137969216	137969227	+	1	NA	Intergenic	Intergenic	2582	NR_029820	723890		NR_029820	ENSMUSG00000065458	Mir181b-1	Mirn181b-1|mir-181b-1	microRNA 181b-1	ncRNA
mm_113736.1	chr13	44439723	44439732	+	1	NA	promoter-TSS (NR_045489)	promoter-TSS (NR_045489)	0	NR_045489	69491	Mm.392410	NR_045489	ENSMUSG00000098144	1700029N11Rik	-	RIKEN cDNA 1700029N11 gene	ncRNA
mm_66315.1	chr7	40535040	40535042	-	1	NA	Intergenic	Intergenic	-139696	NR_045504	71029	Mm.399496	NR_045504	ENSMUSG00000102004	4933402C06Rik	-	RIKEN cDNA 4933402C06 gene	ncRNA
mm_150309.1	chr19	34571007	34571018	+	1	NA	intron (NM_008332, intron 2 of 2)	RMER17C|LTR|ERVK	-12517	NM_010501	15959	Mm.426079	NM_010501	ENSMUSG00000074896	Ifit3	Ifi49|P49	interferon-induced protein with tetratricopeptide repeats 3	protein-coding
mm_100108.1	chr11	115780699	115780718	+	1	NA	intron (NM_028014, intron 2 of 31)	intron (NM_028014, intron 2 of 31)	-15116	NR_049194	100885833		NR_049194	ENSMUSG00000093539	Mir5621	Gm22564|mir-5621|mmu-mir-5621	microRNA 5621	ncRNA
mm_61587.1	chr7	80024828	80024841	+	1	NA	promoter-TSS (NM_001146000)	promoter-TSS (NM_001146000)	20	NM_001146000	209225	Mm.290925	NM_175433	ENSMUSG00000048897	Zfp710	5430400N05Rik|9830165K13|AI324798|Znf710	zinc finger protein 710	protein-coding
mm_11877.1	chr2	49465930	49465931	+	1	NA	intron (NM_172663, intron 1 of 13)	intron (NM_172663, intron 1 of 13)	14444	NM_172663	227867	Mm.29167	NM_172663	ENSMUSG00000069495	Epc2	5830499L14|D2Ertd694e	enhancer of polycomb homolog 2 (Drosophila)	protein-coding
mm_50260.1	chr6	43265685	43265712	+	1	NA	promoter-TSS (NM_133674)	promoter-TSS (NM_133674)	54	NM_133674	54324	Mm.320978	NM_133674	ENSMUSG00000033542	Arhgef5	2210412D05Rik|AA717842|AW495314|Tim1	Rho guanine nucleotide exchange factor (GEF) 5	protein-coding
mm_165483.1	chr2	164333517	164333528	+	1	NA	exon (NM_009301, exon 2 of 3)	exon (NM_009301, exon 2 of 3)	757	NM_009301	20944	Mm.140154	NM_009301	ENSMUSG00000017004	Svs5	BB115186|Semg1|Svp-1|Svp1|Svp5	seminal vesicle secretory protein 5	protein-coding
mm_15103.1	chr2	153347396	153347398	+	1	NA	intron (NM_001039939, intron 1 of 11)	intron (NM_001039939, intron 1 of 11)	1258	NM_001039939	228790	Mm.330677	NM_001039939	ENSMUSG00000042548	Asxl1	mKIAA0978	additional sex combs like 1	protein-coding
mm_5084.1	chr1	4496373	4496389	-	1	NA	5' UTR (NM_001289467, exon 1 of 3)	5' UTR (NM_001289467, exon 1 of 3)	973	NM_001289464	20671	Mm.279103	NM_011441	ENSMUSG00000025902	Sox17	-	SRY (sex determining region Y)-box 17	protein-coding
mm_122063.1	chr14	30434099	30434115	-	1	NA	intron (NM_028981, intron 1 of 46)	LTR33A_|LTR|ERVL	-23929	NR_131095	77710	Mm.410773	NR_131095		4831407H17Rik	-	RIKEN cDNA 4831407H17 gene	ncRNA
mm_52462.1	chr6	113697248	113697258	+	1	NA	5' UTR (NM_001347356, exon 1 of 8)	5' UTR (NM_001347356, exon 1 of 8)	203	NM_001033463	381801	Mm.333322	NM_001033463	ENSMUSG00000056952	Tatdn2	AI646012|mKIAA0218	TatD DNase domain containing 2	protein-coding
mm_31476.1	chr4	51216649	51216683	+	1	NA	promoter-TSS (NM_001162865)	promoter-TSS (NM_001162865)	-12	NM_001162865	74914	Mm.159368	NM_001162865	ENSMUSG00000039555	Cylc2	4930488P18Rik	cylicin, basic protein of sperm head cytoskeleton 2	protein-coding
mm_157486.1	chrX	48208871	48208881	-	1	NA	promoter-TSS (NM_172465)	promoter-TSS (NM_172465)	-174	NM_172465	208884	Mm.207367	NM_172465	ENSMUSG00000036985	Zdhhc9	6430508G22|9530098M12Rik	zinc finger, DHHC domain containing 9	protein-coding
mm_58304.1	chr6	146116090	146116092	-	1	NA	intron (NM_010586, intron 54 of 55)	intron (NM_010586, intron 54 of 55)	181944	NM_010656	16651	Mm.49689	NM_010656	ENSMUSG00000030255	Sspn	Krag	sarcospan	protein-coding
mm_61055.1	chr7	49910308	49910314	+	1	NA	promoter-TSS (NM_001146013)	promoter-TSS (NM_001146013)	12	NM_001146013	104245	Mm.207053	NM_148931	ENSMUSG00000039728	Slc6a5	Glyt2|prestin	solute carrier family 6 (neurotransmitter transporter, glycine), member 5	protein-coding
mm_108292.1	chr12	79152006	79152025	+	1	NA	exon (NM_009705, exon 7 of 8)	exon (NM_009705, exon 7 of 8)	20443	NM_016800	53612	Mm.265929	NM_016800	ENSMUSG00000021124	Vti1b	AU015348|GES30|MVti1b|SNARE|Vti1-rp1	vesicle transport through interaction with t-SNAREs 1B	protein-coding
mm_22708.1	chr3	19187360	19187362	+	1	NA	promoter-TSS (NM_001253391)	promoter-TSS (NM_001253391)	32	NM_001253391	67472	Mm.45125	NM_026182	ENSMUSG00000027601	Mtfr1	1300002C08Rik|1700080D04Rik|2810026O10Rik|4930579E05Rik|Chppr|Fam54a2	mitochondrial fission regulator 1	protein-coding
mm_50179.1	chr6	41590158	41590160	+	1	NA	Intergenic	Intergenic	-15323	NM_001146351	13848	Mm.271976	NM_007680	ENSMUSG00000029869	Ephb6	Cekl|Mep	Eph receptor B6	protein-coding
mm_86300.1	chr9	122310922	122310936	-	1	NA	Intergenic	MLT1F1|LTR|ERVL-MaLR	-16506	NM_133979	102566	Mm.87676	NM_133979	ENSMUSG00000037949	Ano10	AI604832|Tmem16k	anoctamin 10	protein-coding
mm_7287.1	chr1	97761612	97761666	-	1	NA	5' UTR (NM_173760, exon 2 of 28)	5' UTR (NM_173760, exon 2 of 28)	8453	NM_173760	227399	Mm.220817	NM_173760	ENSMUSG00000040648	Ppip5k2	AW555814|Cfap160|D330021B20|Hisppd1|Vip2|mKIAA0433	diphosphoinositol pentakisphosphate kinase 2	protein-coding
mm_133130.1	chr16	65828617	65828625	+	1	NA	intron (NM_028572, intron 2 of 3)	intron (NM_028572, intron 2 of 3)	12988	NM_028572	73569	Mm.25670	NM_028572	ENSMUSG00000091243	Vgll3	1700110N18Rik|4832416J22|C80713|Vgl-3|Vito-2	vestigial like family member 3	protein-coding
mm_111080.1	chr12	80181973	80181977	-	1	NA	intron (NM_001346669, intron 10 of 20)	intron (NM_001346669, intron 10 of 20)	-49131	NR_033514	69548	Mm.269712	NR_033514	ENSMUSG00000097729	2310015A10Rik	5330419I17Rik	RIKEN cDNA 2310015A10 gene	ncRNA
mm_155122.1	chrX	48872001	48872007	+	1	NA	intron (NM_001085499, intron 8 of 20)	intron (NM_001085499, intron 8 of 20)	5709	NM_001085499	209005	Mm.336054	NM_001085499	ENSMUSG00000079606	Gm595	-	predicted gene 595	protein-coding
mm_150651.1	chr19	41912012	41912036	+	1	NA	5' UTR (NM_023418, exon 1 of 4)	5' UTR (NM_023418, exon 1 of 4)	153	NM_023418	18648	Mm.16783	NM_023418	ENSMUSG00000011752	Pgam1	2310050F24Rik|Pgam-1	phosphoglycerate mutase 1	protein-coding
mm_153997.1	chr19	50678713	50678733	-	1	NA	promoter-TSS (NM_021377)	promoter-TSS (NM_021377)	-77	NM_001290356	58178	Mm.313672	NM_021377	ENSMUSG00000043531	Sorcs1	Sorcs|mSorCS	sortilin-related VPS10 domain containing receptor 1	protein-coding
mm_6812.1	chr1	84157435	84157445	-	1	NA	intron (NM_001003948, intron 2 of 2)	intron (NM_001003948, intron 2 of 2)	61521	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_116754.1	chr13	52530458	52530522	-	1	NA	5' UTR (NM_001024474, exon 1 of 2)	5' UTR (NM_001024474, exon 1 of 2)	346	NM_001024474	68203	Mm.29362	NM_001024474	ENSMUSG00000047842	Diras2	2900052J15Rik|AI414999	DIRAS family, GTP-binding RAS-like 2	protein-coding
mm_18804.1	chr2	73910974	73910985	-	1	NA	exon (NM_175015, exon 2 of 5)	exon (NM_175015, exon 2 of 5)	347	NM_175015	228033	Mm.2966	NM_175015	ENSMUSG00000018770	Atp5g3	6030447M23	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit C3 (subunit 9)	protein-coding
mm_34528.1	chr4	149323969	149323977	+	1	NA	Intergenic	ID_B1|SINE|B4	-10666	NR_131918	74310	Mm.440455	NR_131918	ENSMUSG00000085286	Ube4bos3	1700121F15Rik	ubiquitination factor E4B, opposite strand 3	ncRNA
mm_55262.1	chr6	53710716	53710746	-	1	NA	Intergenic	Intergenic	110094	NM_025817	66873	Mm.422727	NM_025817	ENSMUSG00000043496	Tril	1200009O22Rik|AI316813|mKIAA0644	TLR4 interactor with leucine-rich repeats	protein-coding
mm_127489.1	chr15	101316098	101316110	+	1	NA	Intergenic	Intergenic	22892	NR_033803	77717	Mm.391998	NR_033803	ENSMUSG00000075408	6030408B16Rik	AI225877	RIKEN cDNA 6030408B16 gene	ncRNA
mm_32116.1	chr4	99030908	99030944	+	1	NA	promoter-TSS (NM_013913)	promoter-TSS (NM_013913)	-28	NM_013913	30924	Mm.28341	NM_013913	ENSMUSG00000028553	Angptl3	hypl	angiopoietin-like 3	protein-coding
mm_140978.1	chr17	24707608	24707610	-	1	NA	promoter-TSS (NM_145396)	promoter-TSS (NM_145396)	44	NM_145396	213773	Mm.100353	NM_145396	ENSMUSG00000040688	Tbl3	9430070M15Rik	transducin (beta)-like 3	protein-coding
mm_149472.1	chr19	11694988	11694999	+	1	NA	Intergenic	Intergenic	-2062	NM_001033283	225923	Mm.297596	NM_001033283	ENSMUSG00000055933	Oosp3	Gm97	oocyte secreted protein 3	protein-coding
mm_28525.1	chr3	92605942	92605944	-	1	NA	Intergenic	Intergenic	15717	NM_001166172	78382	Mm.235474	NM_001166172	ENSMUSG00000086848	Lce6a	2210420J11Rik	late cornified envelope 6A	protein-coding
mm_108879.1	chr12	99964514	99964524	+	1	NA	promoter-TSS (NM_001164426)	promoter-TSS (NM_001164426)	20	NM_001164427	217826	Mm.312335	NM_146037	ENSMUSG00000045404	Kcnk13	BB085247|F730021E22Rik|Gm1570|Gm1685	potassium channel, subfamily K, member 13	protein-coding
mm_11899.1	chr2	50066488	50066492	+	1	NA	promoter-TSS (NM_177139)	promoter-TSS (NM_177139)	61	NM_177139	320343	Mm.130607	NM_177139	ENSMUSG00000050447	Lypd6	E130115E03Rik	LY6/PLAUR domain containing 6	protein-coding
mm_47789.1	chr5	132212908	132212909	-	1	NA	intron (NM_177047, intron 2 of 18)	intron (NM_177047, intron 2 of 18)	329435	NM_177047	319974	Mm.409595	NM_177047	ENSMUSG00000029673	Auts2	2700063G02Rik|A730011F23Rik|D830032G16Rik	autism susceptibility candidate 2	protein-coding
mm_83606.1	chr9	48605074	48605084	-	1	NA	promoter-TSS (NM_001311062)	promoter-TSS (NM_001311062)	44	NM_001311062	18113	Mm.8362	NM_010924	ENSMUSG00000032271	Nnmt	-	nicotinamide N-methyltransferase	protein-coding
mm_59685.1	chr7	28440947	28441018	+	1	NA	promoter-TSS (NM_001039192)	promoter-TSS (NM_001039192)	45	NM_001039192	63986	Mm.194536	NM_022024	ENSMUSG00000060791	Gmfg	0610039G16Rik|2310057N07Rik|AI324845	glia maturation factor, gamma	protein-coding
mm_87063.1	chr10	28874022	28874024	+	1	NA	intron (NM_178666, intron 5 of 5)	intron (NM_178666, intron 5 of 5)	49484	NR_033601	114676	Mm.390292	NR_033601		4930519F09Rik	-	pyruvate dehydrogenase E1 alpha 1 pseudogene	pseudo
mm_4488.1	chr1	173631071	173631080	+	1	NA	5' UTR (NM_175026, exon 1 of 7)	5' UTR (NM_175026, exon 1 of 7)	216	NM_175026	236312	Mm.447	NM_175026	ENSMUSG00000043263	Ifi209	4930422C14|AI447904|Ifix|Pyhin-1|Pyhin1	interferon activated gene 209	protein-coding
mm_170136.1	chr17	39847836	39847838	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	4840	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_27332.1	chr3	50396246	50396250	-	1	NA	intron (NM_011990, intron 6 of 11)	MTD|LTR|ERVL-MaLR	47365	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_84855.1	chr9	78488117	78488147	-	1	NA	Intergenic	ORR1A0|LTR|ERVL-MaLR	-6408	NM_010106	13627	Mm.138471	NM_010106	ENSMUSG00000037742	Eef1a1	-	eukaryotic translation elongation factor 1 alpha 1	protein-coding
mm_60276.1	chr7	43945060	43945075	+	1	NA	promoter-TSS (NR_033120)	promoter-TSS (NR_033120)	55	NR_033120	16604	Mm.195787	NR_033120	ENSMUSG00000060161	Klk1b7-ps	1700127D06Rik|Klk-ps2|mGK-7	kallikrein 1-related peptidase b7, pseudogene	pseudo
mm_107132.1	chr12	21224287	21224323	+	1	NA	exon (NM_001098168, exon 13 of 28)	exon (NM_001098168, exon 13 of 28)	61932	NM_008403	16413	Mm.273333	NM_008403	ENSMUSG00000062352	Itgb1bp1	AI449260|AU019480|Icap1	integrin beta 1 binding protein 1	protein-coding
mm_72834.1	chr8	88275386	88275404	+	1	NA	intron (NM_007406, intron 1 of 27)	B1_Mus1|SINE|Alu	2992	NM_007406	11513	Mm.288206	NM_007406	ENSMUSG00000031659	Adcy7	AA407758	adenylate cyclase 7	protein-coding
mm_79802.1	chr9	64173365	64173388	+	1	NA	promoter-TSS (NM_026507)	promoter-TSS (NM_026507)	-11	NM_024212	67891	Mm.280083	NM_024212	ENSMUSG00000032399	Rpl4	2010004J23Rik	ribosomal protein L4	protein-coding
mm_68690.1	chr7	119479170	119479185	-	1	NA	promoter-TSS (NM_001278605)	promoter-TSS (NM_001278605)	85	NM_009470	22242	Mm.10826	NM_009470	ENSMUSG00000030963	Umod	THP|Urehd1|urehr4	uromodulin	protein-coding
mm_91025.1	chr10	17920094	17920096	-	1	NA	intron (NM_001033432, intron 1 of 3)	intron (NM_001033432, intron 1 of 3)	27972	NM_001033432	380629	Mm.276430	NM_001033432	ENSMUSG00000039879	Heca	Gm869|HDC|HDCL	hdc homolog, cell cycle regulator	protein-coding
mm_71378.1	chr8	45885365	45885387	+	1	NA	promoter-TSS (NM_016798)	promoter-TSS (NM_016798)	-109	NM_016798	53318	Mm.282900	NM_016798	ENSMUSG00000031636	Pdlim3	AI463105|ALP|Actn2lp	PDZ and LIM domain 3	protein-coding
mm_60033.1	chr7	30981899	30981924	+	1	NA	promoter-TSS (NM_001242647)	promoter-TSS (NM_001242647)	-10	NM_001242647	76415	Mm.259739	NM_175240	ENSMUSG00000046826	Fam187b	1700020B09Rik|Tmem162	family with sequence similarity 187, member B	protein-coding
mm_93868.1	chr10	123147343	123147360	-	1	NA	intron (NM_001301628, intron 6 of 20)	intron (NM_001301628, intron 6 of 20)	49668	NM_027604	14479	Mm.244209	NM_027604	ENSMUSG00000020124	Usp15	4921514G19Rik|AI327321|E430033I05Rik|Gcap18	ubiquitin specific peptidase 15	protein-coding
mm_77973.1	chr9	7837162	7837243	+	1	NA	promoter-TSS (NM_007465)	promoter-TSS (NM_007465)	-145	NM_007465	11797	Mm.335659	NM_007465	ENSMUSG00000057367	Birc2	AW146227|Api1|Api2|Birc3|C-IAP1|C330006D17Rik|HIAP1|HIAP2|IAP1|IAP2|MIAP1|MIAP2|MIHB|MIHC|RNF48|cIAP1|cIAP2|mcIAP1	baculoviral IAP repeat-containing 2	protein-coding
mm_69683.1	chr7	139988984	139989032	-	1	NA	exon (NM_001291066, exon 7 of 24)	exon (NM_001291066, exon 7 of 24)	-2134	NR_106029	102465643		NR_106029	ENSMUSG00000099092	Mir7062	Gm27339|mmu-mir-7062	microRNA 7062	ncRNA
mm_81229.1	chr9	107675781	107675794	+	1	NA	intron (NM_008140, intron 8 of 8)	intron (NM_008140, intron 8 of 8)	3805	NM_008140	14685	Mm.284853	NM_008140	ENSMUSG00000034837	Gnat1	Gnat-1|Ird1|Ird2|Tralpha|irdc|irdr|transducin	guanine nucleotide binding protein, alpha transducing 1	protein-coding
mm_31274.1	chr4	45640778	45640790	+	1	NA	Intergenic	Intergenic	-42805	NM_001033412	329839	Mm.331582	NM_001033412		Gm829	-	predicted gene 829	protein-coding
mm_164091.1	chr15	9567303	9567307	+	1	NA	Intergenic	Intergenic	-37429	NM_008372	16197	Mm.389	NM_008372	ENSMUSG00000003882	Il7r	CD127|IL-7Ralpha	interleukin 7 receptor	protein-coding
mm_41379.1	chr5	90723469	90723486	+	1	NA	Intergenic	Intergenic	-35821	NM_009141	20311	Mm.4660	NM_009141	ENSMUSG00000029371	Cxcl5	AMCF-II|Cxcl6|ENA-78|GCP-2|LIX|Scyb5|Scyb6	chemokine (C-X-C motif) ligand 5	protein-coding
mm_122938.1	chr14	54965285	54965296	-	1	NA	exon (NM_010856, exon 3 of 39)	exon (NM_010856, exon 3 of 39)	1317	NM_001164171	17888	Mm.290003	NM_010856	ENSMUSG00000040752	Myh6	A830009F23Rik|AA517445|Myhc-a|Myhca|alpha-MHC	myosin, heavy polypeptide 6, cardiac muscle, alpha	protein-coding
mm_135453.1	chr16	45724501	45724513	-	1	NA	promoter-TSS (NM_019754)	promoter-TSS (NM_019754)	24	NM_019754	56370	Mm.24183	NM_019754	ENSMUSG00000022658	Tagln3	2700038H05Rik|2900005O10Rik|AI426007|Np25	transgelin 3	protein-coding
mm_108303.1	chr12	79327100	79327131	+	1	NA	intron (NM_001252562, intron 6 of 7)	intron (NM_001252562, intron 6 of 7)	29764	NM_001252562	19363	Mm.341756	NM_009014	ENSMUSG00000059060	Rad51b	AI553500|R51H2|Rad51l1|mREC2	RAD51 paralog B	protein-coding
mm_40432.1	chr5	53589430	53589444	+	1	NA	promoter-TSS (NM_001277116)	promoter-TSS (NM_001277116)	-909	NM_009035	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_104140.1	chr11	86993716	86993771	-	1	NA	promoter-TSS (NM_001005341)	promoter-TSS (NM_001005341)	19	NM_001005341	77864	Mm.191894	NM_001005341	ENSMUSG00000018427	Ypel2	6430570G24|E130113K08Rik	yippee-like 2 (Drosophila)	protein-coding
mm_139823.1	chr17	67728558	67728561	+	1	NA	intron (NM_008480, intron 3 of 62)	L1MB3|LINE|L1	31294	NM_008480	16772	Mm.303386	NM_008480	ENSMUSG00000032796	Lama1	AA408497|Lama	laminin, alpha 1	protein-coding
mm_27520.1	chr3	57294911	57294921	-	1	NA	5' UTR (NM_008536, exon 3 of 7)	5' UTR (NM_008536, exon 3 of 7)	7003	NM_008536	17112	Mm.856	NM_008536	ENSMUSG00000027800	Tm4sf1	L6|M3s1	transmembrane 4 superfamily member 1	protein-coding
mm_87043.1	chr10	28784964	28784980	+	1	NA	intron (NM_001305663, intron 5 of 5)	MLT1D|LTR|ERVL-MaLR	116612	NM_178666	210757	Mm.123021	NM_178666	ENSMUSG00000049109	Themis	E430004N04Rik|Gasp|Spot|Tsepa|thylex	thymocyte selection associated	protein-coding
mm_3164.1	chr1	135324771	135324820	+	1	NA	promoter-TSS (NM_053106)	promoter-TSS (NM_053106)	-18	NM_053106	93689	Mm.180124	NM_053106	ENSMUSG00000048096	Lmod1	9530015K06Rik|SM-Lmod	leiomodin 1 (smooth muscle)	protein-coding
mm_15105.1	chr2	153357036	153357048	+	1	NA	intron (NM_001039939, intron 2 of 11)	intron (NM_001039939, intron 2 of 11)	10903	NM_001039939	228790	Mm.330677	NM_001039939	ENSMUSG00000042548	Asxl1	mKIAA0978	additional sex combs like 1	protein-coding
mm_47101.1	chr5	118244984	118245048	-	1	NA	promoter-TSS (NM_001081236)	promoter-TSS (NM_001081236)	9	NM_001109902	269695	Mm.320042	NM_172998	ENSMUSG00000032850	Rnft2	AW049082|B830028P19Rik|Tmem118	ring finger protein, transmembrane 2	protein-coding
mm_127234.1	chr15	99406569	99406631	+	1	NA	exon (NM_026669, exon 8 of 10)	exon (NM_026669, exon 8 of 10)	13381	NM_001171035	110213	Mm.16769	NM_026669	ENSMUSG00000023010	Tmbim6	5031406P05Rik|Bi1|Tegt	transmembrane BAX inhibitor motif containing 6	protein-coding
mm_151339.1	chr19	55895198	55895224	+	1	NA	promoter-TSS (NM_001142924)	promoter-TSS (NM_001142924)	-110	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_45014.1	chr5	38527281	38527297	-	1	NA	3' UTR (NM_011715, exon 15 of 15)	3' UTR (NM_011715, exon 15 of 15)	-25137	NM_145559	117591	Mm.260137	NM_145559	ENSMUSG00000005107	Slc2a9	Glut9|SLC2A9B|SLC2a9A	solute carrier family 2 (facilitated glucose transporter), member 9	protein-coding
mm_54173.1	chr6	23650299	23650309	-	1	NA	promoter-TSS (NM_198251)	promoter-TSS (NM_198251)	1	NM_198251	386611	Mm.436547	NM_198251	ENSMUSG00000051956	Rnf133	Greul2	ring finger protein 133	protein-coding
mm_124973.1	chr15	20418187	20418191	+	1	NA	Intergenic	Intergenic	248561	NM_022816	64833	Mm.352763	NM_022816	ENSMUSG00000047565	Acot10	Acate3|MT-ACT48|p48	acyl-CoA thioesterase 10	protein-coding
mm_126957.1	chr15	92161564	92161581	+	1	NA	5' UTR (NM_001159647, exon 1 of 24)	5' UTR (NM_001159647, exon 1 of 24)	215	NM_001159647	12805	Mm.4911	NM_007727	ENSMUSG00000055022	Cntn1	AW495098|CNTN|F3cam|usl	contactin 1	protein-coding
mm_55070.1	chr6	49051996	49052030	-	1	NA	exon (NM_053110, exon 9 of 11)	exon (NM_053110, exon 9 of 11)	15495	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_26366.1	chr3	142560194	142560214	+	1	NA	promoter-TSS (NM_001289493)	promoter-TSS (NM_001289493)	152	NM_001289492	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_170195.1	chr17	66449774	66449788	-	1	NA	promoter-TSS (NM_172963)	promoter-TSS (NM_172963)	-31	NM_001114098	68617	Mm.33421	NM_172963	ENSMUSG00000052105	Mtcl1	1110012J17Rik|Ccdc165|D130071O13|Kiaa0802|Soga2|mKIAA0802|t8219b25	microtubule crosslinking factor 1	protein-coding
mm_51350.1	chr6	72556081	72556118	+	1	NA	exon (NM_001042534, exon 5 of 10)	exon (NM_001042534, exon 5 of 10)	6452	NM_001271395	12332	Mm.18626	NM_007599	ENSMUSG00000056737	Capg	gCap39|mbh1	capping protein (actin filament), gelsolin-like	protein-coding
mm_19347.1	chr2	90917679	90917697	-	1	NA	exon (NM_025576, exon 2 of 5)	exon (NM_025576, exon 2 of 5)	362	NM_025576	66461	Mm.23926	NM_025576		Ptpmt1	1110001D10Rik|2810004N20Rik|PLIP	protein tyrosine phosphatase, mitochondrial 1	protein-coding
mm_25897.1	chr3	131110839	131110849	+	1	NA	5' UTR (NM_001276402, exon 1 of 10)	5' UTR (NM_001276402, exon 1 of 10)	547	NM_001276402	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_62512.1	chr7	102210500	102210553	+	1	NA	promoter-TSS (NM_001287167)	promoter-TSS (NM_001287167)	191	NM_001291358	233575	Mm.302013	NM_145583	ENSMUSG00000030990	Pgap2	1810006G21Rik|C76649|Frag1	post-GPI attachment to proteins 2	protein-coding
mm_62952.1	chr7	119606814	119606837	+	1	NA	Intergenic	Intergenic	-11003	NM_054094	117147	Mm.427560	NM_054094	ENSMUSG00000033533	Acsm1	Acas3|Bucs1|Macs	acyl-CoA synthetase medium-chain family member 1	protein-coding
mm_61334.1	chr7	68275971	68276025	+	1	NA	promoter-TSS (NR_040341)	promoter-TSS (NR_040341)	596	NR_040340	100504026	Mm.426764	NR_040340	ENSMUSG00000086628	Gm16157	OTTMUSG00000031023	predicted gene 16157	ncRNA
mm_25489.1	chr3	109340465	109340473	+	1	NA	promoter-TSS (NM_020505)	promoter-TSS (NM_020505)	-214	NM_020505	57257	Mm.282257	NM_020505	ENSMUSG00000033721	Vav3	A530094I06Rik|AA986410|Idd18.1	vav 3 oncogene	protein-coding
mm_76825.1	chr8	104624211	104624239	-	1	NA	5' UTR (NM_001252627, exon 1 of 17)	5' UTR (NM_001252627, exon 1 of 17)	171	NM_007663	12556	Mm.19423	NM_007663	ENSMUSG00000031881	Cdh16	-	cadherin 16	protein-coding
mm_112910.1	chr13	20910661	20910672	+	1	NA	intron (NM_012054, intron 7 of 20)	intron (NM_012054, intron 7 of 20)	116553	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_164133.1	chr15	45583508	45583510	+	1	NA	Intergenic	L1Md_T|LINE|L1	-468575	NM_026200	67498	Mm.300079	NM_026200	ENSMUSG00000022342	Kcnv1	2700023A03Rik|vibe	potassium channel, subfamily V, member 1	protein-coding
mm_169367.1	chr14	32267741	32267752	-	1	NA	intron (NM_011960, intron 13 of 17)	intron (NM_011960, intron 13 of 17)	-54273	NM_001081130	239017	Mm.318302	NM_001081130	ENSMUSG00000021913	Ogdhl	-	oxoglutarate dehydrogenase-like	protein-coding
mm_150118.1	chr19	29945742	29945752	+	1	NA	promoter-TSS (NM_001164724)	promoter-TSS (NM_001164724)	-43	NM_001164724	77125	Mm.182359	NM_133775	ENSMUSG00000024810	Il33	9230117N10Rik|Il-33|Il1f11|NF-HEV	interleukin 33	protein-coding
mm_90638.1	chr10	128499236	128499259	+	1	NA	promoter-TSS (NM_172259)	promoter-TSS (NM_172259)	0	NR_131150	654440	Mm.441262	NR_131150	ENSMUSG00000097353	A430046D13Rik	-	Riken cDNA A430046D13 gene	ncRNA
mm_26678.1	chr3	155093560	155093573	+	1	NA	promoter-TSS (NM_029330)	promoter-TSS (NM_029330)	132	NM_028938	74435	Mm.195711	NM_028938	ENSMUSG00000028182	Lrriq3	4930438B07Rik|4930511J15Rik|4933403H06Rik|BB020367|Lrrc44	leucine-rich repeats and IQ motif containing 3	protein-coding
mm_45709.1	chr5	84067103	84067112	-	1	NA	intron (NM_007937, intron 15 of 15)	intron (NM_007937, intron 15 of 15)	350275	NM_007937	13839	Mm.137991	NM_007937	ENSMUSG00000029245	Epha5	AI854630|AW125296|Cek7|Ehk1|Els1|Hek7|Rek7|bsk	Eph receptor A5	protein-coding
mm_126193.1	chr15	78687193	78687194	+	1	NA	intron (NM_183141, intron 1 of 1)	intron (NM_183141, intron 1 of 1)	30920	NM_183141	207393	Mm.323188	NM_183141	ENSMUSG00000043460	Elfn2	6330514E13|AW048948|BC094219|Lrrc62|Ppp1r29	leucine rich repeat and fibronectin type III, extracellular 2	protein-coding
mm_171714.1	chr4	81148932	81148932	-	1	NA	Intergenic	L1Md_T|LINE|L1	238246	NM_026821	52829	Mm.273986	NM_026821	ENSMUSG00000048706	Lurap1l	1110029A09Rik|AV077978|AV175137|D4Bwg0951e|WI-13707|bM350F23.1	leucine rich adaptor protein 1-like	protein-coding
mm_110381.1	chr12	40217180	40217190	-	1	NA	exon (NM_013562, exon 3 of 12)	exon (NM_013562, exon 3 of 12)	5626	NR_035459	100316693		NR_035459	ENSMUSG00000089371	Mir1938	mir-1938|mmu-mir-1938	microRNA 1938	ncRNA
mm_57751.1	chr6	129160208	129160215	-	1	NA	Intergenic	Intergenic	-20404	NM_053109	93694	Mm.197536	NM_053109	ENSMUSG00000030157	Clec2d	Clr-b|Clrb|Ocil	C-type lectin domain family 2, member d	protein-coding
mm_161599.1	chr16	36808677	36808677	-	1	NA	promoter-TSS (NM_001113405)	promoter-TSS (NM_001113405)	28	NM_001113405	106389	Mm.432078	NM_134111	ENSMUSG00000022838	Eaf2	AW048865|FESTA-L|FESTA-S|Festa|Traits|U19	ELL associated factor 2	protein-coding
mm_173235.1	chrX	80535280	80535284	-	1	NA	Intergenic	Intergenic	-535362	NM_138751	192216	Mm.490421	NM_138751	ENSMUSG00000025666	Tmem47	3010015F07Rik|AI115536|BCMP1|Tm4sf10	transmembrane protein 47	protein-coding
mm_26497.1	chr3	145652090	145652109	+	1	NA	Intergenic	Intergenic	-2114	NM_010516	16007	Mm.1231	NM_010516	ENSMUSG00000028195	Cyr61	AI325051|CCN1|Igfbp10	cysteine rich protein 61	protein-coding
mm_114568.1	chr13	74639867	74639878	+	1	NA	promoter-TSS (NM_030711)	promoter-TSS (NM_030711)	0	NM_030711	80898	Mm.83526	NM_030711	ENSMUSG00000021583	Erap1	Arts1|ERAAP|PILSA|PILSAP	endoplasmic reticulum aminopeptidase 1	protein-coding
mm_159328.1	chr3	32561502	32561502	+	1	NA	exon (NM_024200, exon 10 of 18)	exon (NM_024200, exon 10 of 18)	32020	NM_024200	67414	Mm.290414	NM_024200	ENSMUSG00000027668	Mfn1	2310002F04Rik|6330416C07Rik|D3Ertd265e|HR2|mKIAA4032	mitofusin 1	protein-coding
mm_127189.1	chr15	99030288	99030297	+	1	NA	5' UTR (NM_009448, exon 1 of 4)	5' UTR (NM_009448, exon 1 of 4)	401	NM_009448	22146	Mm.88212	NM_009448	ENSMUSG00000043091	Tuba1c	M[a]6|Tuba6	tubulin, alpha 1C	protein-coding
mm_89028.1	chr10	82699160	82699170	+	1	NA	exon (NM_001081218, exon 1 of 15)	exon (NM_001081218, exon 1 of 15)	158	NM_001081218	67933	Mm.127405	NM_026462	ENSMUSG00000020246	Hcfc2	1700129L13Rik|AU019838	host cell factor C2	protein-coding
mm_151612.1	chr19	3898849	3898854	-	1	NA	exon (NM_001136091, exon 12 of 20)	exon (NM_001136091, exon 12 of 20)	6379	NM_016921	27060	Mm.271689	NM_016921	ENSMUSG00000001750	Tcirg1	ATP6N1C|ATP6a3|Atp6i|OC-116|OPTB1|Stv1|TIRC7|Vph1|oc	T cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 protein A3	protein-coding
mm_154938.1	chrX	36112073	36112083	+	1	NA	promoter-TSS (NM_133990)	promoter-TSS (NM_133990)	-30	NM_133990	16164	Mm.24208	NM_133990	ENSMUSG00000017057	Il13ra1	AI882074|CD213a1|IL-13R-alpha-1|IL-13r[a]|Il13ra|NR4	interleukin 13 receptor, alpha 1	protein-coding
mm_43269.1	chr5	130384566	130384588	+	1	NA	promoter-TSS (NM_198665)	promoter-TSS (NM_198665)	54	NM_198665	381673	Mm.192133	NM_198665	ENSMUSG00000052014	A330070K13Rik	Gm1051	RIKEN cDNA A330070K13 gene	protein-coding
mm_106462.1	chr11	120047073	120047129	-	1	NA	promoter-TSS (NM_007377)	promoter-TSS (NM_007377)	44	NM_001198785	11302	Mm.6826	NM_007377	ENSMUSG00000025375	Aatk	AATYK|aatyk1|mKIAA0641	apoptosis-associated tyrosine kinase	protein-coding
mm_78934.1	chr9	45103895	45103920	+	1	NA	intron (NM_001005421, intron 9 of 10)	intron (NM_001005421, intron 9 of 10)	-13969	NM_001014761	72821	Mm.229373	NM_001014761	ENSMUSG00000070304	Scn2b	2810451E09Rik|AI840361|Gm183	sodium channel, voltage-gated, type II, beta	protein-coding
mm_115285.1	chr13	111867947	111867959	+	1	NA	promoter-TSS (NR_130345)	promoter-TSS (NR_130345)	17	NR_130345	102636620	Mm.402328	NR_130345	ENSMUSG00000086111	Gm15326	OTTMUSG00000020187	predicted gene 15326	ncRNA
mm_29519.1	chr3	116508036	116508070	-	1	NA	5' UTR (NM_025517, exon 1 of 11)	5' UTR (NM_025517, exon 1 of 11)	122	NM_025517	66368	Mm.251228	NM_025517	ENSMUSG00000000339	Rtca	2310009A18Rik|AI450277|RPC|Rtcd1	RNA 3'-terminal phosphate cyclase	protein-coding
mm_5334.1	chr1	23922284	23922366	-	1	NA	promoter-TSS (NM_028534)	promoter-TSS (NM_028534)	56	NM_028534	98366	Mm.329963	NM_028534	ENSMUSG00000026155	Smap1	1700056O10Rik|4921514B13Rik|4921525H11Rik|AI462175	small ArfGAP 1	protein-coding
mm_147954.1	chr18	67045933	67045944	-	1	NA	Intergenic	(A)n|Simple_repeat|Simple_repeat	-42360	NM_177137	14680	Mm.440746	NM_010307	ENSMUSG00000024524	Gnal	2610011C15Rik|9630020G10Rik|Galphaolf|Gna10|Golf	guanine nucleotide binding protein, alpha stimulating, olfactory type	protein-coding
mm_45384.1	chr5	66136079	66136091	-	1	NA	intron (NM_001127382, intron 2 of 7)	intron (NM_001127382, intron 2 of 7)	14893	NM_001291226	245945	Mm.36863	NM_139065	ENSMUSG00000070780	Rbm47	9530077J19Rik	RNA binding motif protein 47	protein-coding
mm_94993.1	chr11	31871561	31871598	+	1	NA	5' UTR (NM_026252, exon 1 of 10)	5' UTR (NM_026252, exon 1 of 10)	639	NM_026252	67579	Mm.339792	NM_026252	ENSMUSG00000020300	Cpeb4	Cpe-bp4|Cpeb-4|mCPEB-4	cytoplasmic polyadenylation element binding protein 4	protein-coding
mm_75495.1	chr8	50916172	50916204	-	1	NA	Intergenic	CpG	548076	NR_046067	100039954	Mm.400419	NR_046067	ENSMUSG00000110281	Gm2516	-	predicted gene 2516	ncRNA
mm_163495.1	chr12	110088808	110088808	+	1	NA	Intergenic	B4|SINE|B4	69265	NR_045466	67280	Mm.390495	NR_045466		3110009F21Rik	-	RIKEN cDNA 3110009F21 gene	ncRNA
mm_10495.1	chr2	14914243	14914251	+	1	NA	intron (NM_023116, intron 3 of 13)	intron (NM_023116, intron 3 of 13)	40591	NM_001309519	12296	Mm.313930	NM_023116	ENSMUSG00000057914	Cacnb2	AW060387|CAB2|Cavbeta2|Cchb2	calcium channel, voltage-dependent, beta 2 subunit	protein-coding
mm_5141.1	chr1	9745572	9745598	-	1	NA	exon (NM_173443, exon 1 of 3)	exon (NM_173443, exon 1 of 3)	-2063	NR_040462	73331	Mm.460470	NR_040462		1700034P13Rik	-	RIKEN cDNA 1700034P13 gene	ncRNA
mm_129466.1	chr15	78599188	78599223	-	1	NA	intron (NM_028195, intron 1 of 12)	intron (NM_028195, intron 1 of 12)	2158	NM_028195	72318	Mm.32911	NM_028195	ENSMUSG00000018008	Cyth4	2510004M07Rik|5830469K17Rik|AI467541|Pscd4|mFLJ00017	cytohesin 4	protein-coding
mm_108538.1	chr12	84243413	84243427	+	1	NA	Intergenic	Intergenic	-24539	NM_001163501	238317	Mm.31256	NM_001163501	ENSMUSG00000042507	Elmsan1	9430029N19Rik|C130039O16Rik|Gm260	ELM2 and Myb/SANT-like domain containing 1	protein-coding
mm_138562.1	chr17	35342300	35342330	+	1	NA	promoter-TSS (NM_010392)	promoter-TSS (NM_010392)	-18	NM_010392	15013	Mm.427969	NM_010392	ENSMUSG00000091705	H2-Q2	BE136769|ENSMUSG00000079507|Gm11132|H-2Q2|gs14-2	histocompatibility 2, Q region locus 2	protein-coding
mm_55547.1	chr6	71144364	71144381	-	1	NA	promoter-TSS (NM_001033929)	promoter-TSS (NM_001033929)	8	NM_001033929	232078	Mm.37547	NM_178413	ENSMUSG00000054474	Thnsl2	BC051244|TSH2	threonine synthase-like 2 (bacterial)	protein-coding
mm_72764.1	chr8	85555454	85555500	+	1	NA	promoter-TSS (NM_019794)	promoter-TSS (NM_019794)	-206	NM_019794	56445	Mm.475573	NM_019794	ENSMUSG00000031701	Dnaja2	1500017M13Rik|2010206B19Rik|DNAJ|DNJ3|Dnaj3|HIRIP4|PRO3015|mDj3	DnaJ heat shock protein family (Hsp40) member A2	protein-coding
mm_35948.1	chr4	53113468	53113491	-	1	NA	intron (NM_013454, intron 5 of 49)	intron (NM_013454, intron 5 of 49)	46416	NM_013454	11303	Mm.277376	NM_013454	ENSMUSG00000015243	Abca1	ABC-1|Abc1	ATP-binding cassette, sub-family A (ABC1), member 1	protein-coding
mm_135058.1	chr16	33967033	33967043	-	1	NA	promoter-TSS (NM_009471)	promoter-TSS (NM_009471)	-35	NM_009471	22247	Mm.13145	NM_009471	ENSMUSG00000022814	Umps	1700095D23Rik|AA408257|AL033308|BB164745	uridine monophosphate synthetase	protein-coding
mm_167027.1	chr7	68133833	68133842	+	1	NA	intron (NM_010513, intron 2 of 20)	intron (NM_010513, intron 2 of 20)	130396	NM_030101	78444	Mm.425468	NM_030101	ENSMUSG00000030553	Pgpep1l	C330024D12Rik	pyroglutamyl-peptidase I-like	protein-coding
mm_154009.1	chr19	53058081	53058099	-	1	NA	Intergenic	Intergenic	-18162	NR_045320	78457	Mm.76932	NR_045320	ENSMUSG00000099988	1700054A03Rik	-	RIKEN cDNA 1700054A03 gene	ncRNA
mm_45159.1	chr5	49524810	49524890	-	1	NA	Intergenic	CpG	-239191	NM_001199244	80334	Mm.160172	NM_030265	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding
mm_76418.1	chr8	84969491	84969527	-	1	NA	promoter-TSS (NM_011563)	promoter-TSS (NM_011563)	-113	NM_001317385	21672	Mm.347009	NM_011563	ENSMUSG00000005161	Prdx2	AL022839|Band-8|NkefB|PRP|PrxII|TDX1|TPx|TPx-B|TR|TSA|Tdpx1|Torin	peroxiredoxin 2	protein-coding
mm_13114.1	chr2	91586164	91586175	+	1	NA	intron (NM_029437, intron 24 of 42)	intron (NM_029437, intron 24 of 42)	-9912	NR_028553	100217458		NR_028553	ENSMUSG00000077221	Snord67	MBII-166	small nucleolar RNA, C/D box 67	snoRNA
mm_92565.1	chr10	79874542	79874561	-	1	NA	promoter-TSS (NM_001170935)	promoter-TSS (NM_001170935)	83	NM_181681	216152	Mm.29678	NM_181681	ENSMUSG00000035835	Plppr3	Lppr3|Prg2	phospholipid phosphatase related 3	protein-coding
mm_100606.1	chr11	121261197	121261200	+	1	NA	intron (NM_001080932, intron 1 of 8)	intron (NM_001080932, intron 1 of 8)	1211	NM_001080932	68837	Mm.209750	NM_001080932	ENSMUSG00000039275	Foxk2	1110054H05Rik|5730434B08Rik|6230415M23Rik|ILF|Ilf1	forkhead box K2	protein-coding
mm_133166.1	chr16	70504336	70504351	+	1	NA	intron (NM_028803, intron 12 of 15)	B1_Mur2|SINE|Alu	-112082	NR_040474	52645	Mm.188475	NR_040474		D16Ertd519e	-	DNA segment, Chr 16, ERATO Doi 519, expressed	ncRNA
mm_111353.1	chr12	86983089	86983108	-	1	NA	TTS (NM_001080943)	TTS (NM_001080943)	5578	NM_001080943	238331	Mm.185890	NM_001080943	ENSMUSG00000048483	Zdhhc22	Gm262	zinc finger, DHHC-type containing 22	protein-coding
mm_14312.1	chr2	129198794	129198811	+	1	NA	promoter-TSS (NM_015747)	promoter-TSS (NM_015747)	29	NM_001159593	20515	Mm.272675	NM_015747	ENSMUSG00000027397	Slc20a1	AI607883|Glvr-1|Glvr1	solute carrier family 20, member 1	protein-coding
mm_55427.1	chr6	65144983	65144999	-	1	NA	promoter-TSS (NM_019455)	promoter-TSS (NM_019455)	-261	NM_019455	54486	Mm.410688	NM_019455	ENSMUSG00000029919	Hpgds	H-PGDS|Ptgds2	hematopoietic prostaglandin D synthase	protein-coding
mm_155961.1	chrX	106015700	106015759	+	1	NA	promoter-TSS (NM_025379)	promoter-TSS (NM_025379)	29	NM_025379	66142	Mm.197728	NM_025379	ENSMUSG00000031231	Cox7b	1100001F07Rik|1110004F07Rik|C80563	cytochrome c oxidase subunit VIIb	protein-coding
mm_97542.1	chr11	78922218	78922306	+	1	NA	5' UTR (NM_010927, exon 2 of 27)	5' UTR (NM_010927, exon 2 of 27)	1475	NM_010927	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_44031.1	chr5	147430839	147430863	+	1	NA	exon (NM_028291, exon 1 of 19)	exon (NM_028291, exon 1 of 19)	271	NM_028291	72587	Mm.320469	NM_028291	ENSMUSG00000029647	Pan3	2700050F09Rik|A430027N15Rik|AU014670	PAN3 poly(A) specific ribonuclease subunit	protein-coding
mm_170682.1	chr2	126844428	126844431	-	1	NA	exon (NM_001164325, exon 8 of 39)	exon (NM_001164325, exon 8 of 39)	31832	NM_001164325	58800	Mm.244705	NM_021450	ENSMUSG00000027365	Trpm7	2310022G15Rik|4833414K03Rik|5033407O22Rik|CHAK|CHAK1|LTrpC-7|Ltpr7|Ltrpc7|TRPPLIK	transient receptor potential cation channel, subfamily M, member 7	protein-coding
mm_120038.1	chr14	56365005	56365016	+	1	NA	promoter-TSS (NM_138652)	promoter-TSS (NM_138652)	-58	NM_138652	192113	Mm.273271	NM_138652	ENSMUSG00000022229	Atp12a	Atp1al1|HKalpha2|cHKA	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	protein-coding
mm_26717.1	chr3	158038347	158038351	+	1	NA	intron (NM_001289525, intron 1 of 12)	intron (NM_001289525, intron 1 of 12)	1667	NM_001289524	67144	Mm.358704	NM_024194	ENSMUSG00000063052	Lrrc40	2610040E16Rik|AI837674	leucine rich repeat containing 40	protein-coding
mm_124216.1	chr14	100208813	100208816	-	1	NA	Intergenic	Intergenic	-59018	NM_010636	16597	Mm.396499	NM_010636	ENSMUSG00000072294	Klf12	2700063E05Rik|AI225908|AI315654|AP-2rep|B130052C06Rik|D530033K05Rik	Kruppel-like factor 12	protein-coding
mm_11316.1	chr2	30364263	30364304	+	1	NA	promoter-TSS (NM_001242407)	promoter-TSS (NM_001242407)	50	NM_001242407	108958	Mm.254974	NM_175392	ENSMUSG00000026858	Miga2	5730472N09Rik|AA408683|AI790341|C9orf54|Fam73b|R74766	mitoguardin 2	protein-coding
mm_107715.1	chr12	56253148	56253162	+	1	NA	promoter-TSS (NR_045048)	promoter-TSS (NR_045048)	-88	NR_045048	100503961	Mm.136732	NR_045048		Gm19990	-	predicted gene, 19990	ncRNA
mm_153634.1	chr19	44029202	44029214	-	1	NA	promoter-TSS (NM_001167905)	promoter-TSS (NM_001167905)	39	NM_001001446	226143	Mm.329866	NM_001001446	ENSMUSG00000025197	Cyp2c44	AW107714|BC034834|b2b386Clo	cytochrome P450, family 2, subfamily c, polypeptide 44	protein-coding
mm_153423.1	chr19	40699782	40699786	-	1	NA	intron (NM_009848, intron 1 of 9)	intron (NM_009848, intron 1 of 9)	40014	NM_009848	12495	Mm.2824	NM_009848	ENSMUSG00000048120	Entpd1	2610206B08Rik|AA408691|Cd39|NTPDase-1	ectonucleoside triphosphate diphosphohydrolase 1	protein-coding
mm_66894.1	chr7	59649305	59649310	-	1	NA	intron (NR_015351, intron 5 of 5)	PB1D9|SINE|Alu	26772	NR_002895	64243	Mm.423722	NR_002895	ENSMUSG00000096019	Snord116	MBII-85|Pwcr1	small nucleolar RNA, C/D box 116	snoRNA
mm_140970.1	chr17	24695988	24695996	-	1	NA	promoter-TSS (NM_027988)	promoter-TSS (NM_027988)	164	NM_023040	11692	Mm.28124	NM_023040	ENSMUSG00000040888	Gfer	Alr|ERV1	growth factor, erv1 (S. cerevisiae)-like (augmenter of liver regeneration)	protein-coding
mm_17171.1	chr2	25316857	25316867	-	1	NA	exon (NM_001177657, exon 2 of 19)	exon (NM_001177657, exon 2 of 19)	2325	NM_008169	14810	Mm.278672	NM_008169	ENSMUSG00000026959	Grin1	GluN1|GluRdelta1|GluRzeta1|M100174|NMD-R1|NMDAR1|NR1|Nmdar|Rgsc174	glutamate receptor, ionotropic, NMDA1 (zeta 1)	protein-coding
mm_50609.1	chr6	49481537	49481540	+	1	NA	Intergenic	(T)n|Simple_repeat|Simple_repeat	85934	NM_029916	77485	Mm.128054	NM_029916	ENSMUSG00000023403	Stk31	C330007K24Rik	serine threonine kinase 31	protein-coding
mm_18587.1	chr2	66440754	66440846	-	1	NA	promoter-TSS (NR_033495)	promoter-TSS (NR_033495)	37	NM_018733	20265	Mm.439704	NM_018733	ENSMUSG00000064329	Scn1a	B230332M13|Nav1.1	sodium channel, voltage-gated, type I, alpha	protein-coding
mm_45660.1	chr5	77115146	77115156	-	1	NA	promoter-TSS (NM_175606)	promoter-TSS (NM_175606)	-28	NM_175606	74318	Mm.181852	NM_175606	ENSMUSG00000059325	Hopx	1110018K11Rik|1200015P04Rik|2300002F06Rik|AI848177|AW490897|Cameo|Hdop|Hod|Hop|Ob1|Obl|Toto	HOP homeobox	protein-coding
mm_142014.1	chr17	35200472	35200486	-	1	NA	exon (NM_013693, exon 4 of 4)	exon (NM_013693, exon 4 of 4)	1528	NM_013693	21926	Mm.1293	NM_013693	ENSMUSG00000024401	Tnf	DIF|TNF-a|TNF-alpha|TNFSF2|TNFalpha|Tnfa|Tnfsf1a|Tnlg1f	tumor necrosis factor	protein-coding
mm_161981.1	chr19	22698659	22698659	+	1	NA	intron (NM_001035243, intron 2 of 23)	intron (NM_001035243, intron 2 of 23)	6040	NM_001035244	226025	Mm.131943	NM_177341	ENSMUSG00000052387	Trpm3	6330504P12Rik|9330180E14|AU018608|B930001P07Rik|LTRPC3|MLSN2	transient receptor potential cation channel, subfamily M, member 3	protein-coding
mm_55455.1	chr6	67376119	67376129	-	1	NA	promoter-TSS (NM_008354)	promoter-TSS (NM_008354)	13	NM_008354	16162	Mm.188337	NM_008354	ENSMUSG00000018341	Il12rb2	A930027I18Rik|IL-12RB2|Ifnm	interleukin 12 receptor, beta 2	protein-coding
mm_129405.1	chr15	78287947	78287968	-	1	NA	exon (NM_007781, exon 10 of 14)	exon (NM_007781, exon 10 of 14)	-3108	NR_106137	102465776		NR_106137	ENSMUSG00000098996	Mir7676-1	Gm27600|mmu-mir-7676-1	microRNA 7676-1	ncRNA
mm_42550.1	chr5	116406791	116406801	+	1	NA	Intergenic	Intergenic	16068	NM_030704	80888	Mm.21549	NM_030704	ENSMUSG00000041548	Hspb8	AU018630|AW413033|Cryac|D5Ucla4|E2IG1|H11|H11K|HSP20-like|HSP22	heat shock protein 8	protein-coding
mm_33804.1	chr4	134930947	134930997	+	1	NA	promoter-TSS (NM_026780)	promoter-TSS (NM_026780)	-8	NM_026780	68592	Mm.29989	NM_026780	ENSMUSG00000028821	Syf2	1110018L13Rik|Cbpin|D4Bwg1551e|Gcipip|Ntc31|mp29|p29	SYF2 homolog, RNA splicing factor (S. cerevisiae)	protein-coding
mm_145019.1	chr18	38869581	38869590	+	1	NA	intron (NM_010197, intron 1 of 3)	B1_Mur1|SINE|Alu	-22871	NM_001033789	545253	Mm.244585	NM_001033789	ENSMUSG00000036452	Gm5820	EG545253	predicted gene 5820	protein-coding
mm_109462.1	chr12	111198510	111198540	+	1	NA	intron (NM_001286122, intron 1 of 9)	B2_Mm2|SINE|B2	-14034	NR_130987	78062	Mm.427248	NR_130987	ENSMUSG00000083193	4930595D18Rik	-	RIKEN cDNA 4930595D18 gene	ncRNA
mm_119530.1	chr14	47649294	47649389	+	1	NA	promoter-TSS (NM_001293636)	promoter-TSS (NM_001293636)	30	NM_001347524	16709	Mm.3110	NM_008477	ENSMUSG00000021843	Ktn1	-	kinectin 1	protein-coding
mm_130845.1	chr15	101918801	101918819	-	1	NA	3' UTR (NM_008475, exon 9 of 9)	3' UTR (NM_008475, exon 9 of 9)	5925	NM_008475	16682	Mm.46425	NM_008475	ENSMUSG00000059668	Krt4	AW108092|K4|Krt-2.4|Krt2-4	keratin 4	protein-coding
mm_79487.1	chr9	56997527	56997530	+	1	NA	intron (NM_019651, intron 1 of 12)	B1_Mur4|SINE|Alu	2560	NM_019651	56294	Mm.325643	NM_019651	ENSMUSG00000032290	Ptpn9	MEG2	protein tyrosine phosphatase, non-receptor type 9	protein-coding
mm_167641.1	chr9	64790795	64790810	-	1	NA	Intergenic	MIRb|SINE|MIR	-20209	NM_001162917	102442	Mm.222473	NM_176935	ENSMUSG00000053641	Dennd4a	AI115600|AI851943|F730015K02Rik	DENN/MADD domain containing 4A	protein-coding
mm_119027.1	chr14	30022751	30022776	+	1	NA	5' UTR (NM_175343, exon 1 of 8)	5' UTR (NM_175343, exon 1 of 8)	130	NM_175343	218865	Mm.259916	NM_172264	ENSMUSG00000015970	Chdh	AU041472|D630034H06Rik	choline dehydrogenase	protein-coding
mm_161912.1	chr18	67343479	67343479	+	1	NA	promoter-TSS (NM_007702)	promoter-TSS (NM_007702)	-85	NM_007702	12683	Mm.449	NM_007702	ENSMUSG00000024526	Cidea	AW212747	cell death-inducing DNA fragmentation factor, alpha subunit-like effector A	protein-coding
mm_21973.1	chr2	167349112	167349122	-	1	NA	promoter-TSS (NM_019835)	promoter-TSS (NM_019835)	61	NM_019835	56336	Mm.200886	NM_019835	ENSMUSG00000017929	B4galt5	9430078I07Rik|AW049941|AW539721	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 5	protein-coding
mm_17526.1	chr2	29253002	29253013	-	1	NA	promoter-TSS (NR_029460)	promoter-TSS (NR_029460)	-14	NR_029460	76220	Mm.330108	NR_029460	ENSMUSG00000079499	6530402F18Rik	mKIAA1857	RIKEN cDNA 6530402F18 gene	ncRNA
mm_151465.1	chr19	58670351	58670355	+	1	NA	promoter-TSS (NM_026925)	promoter-TSS (NM_026925)	-12	NM_026925	69060	Mm.20407	NM_026925	ENSMUSG00000046008	Pnlip	1810007A24Rik|PL|PTL	pancreatic lipase	protein-coding
mm_159487.1	chr4	42168588	42168588	-	1	NA	promoter-TSS (NM_001099348).2	promoter-TSS (NM_001099348).2	15	NM_001099348	100042555	Mm.458019	NM_001099348	ENSMUSG00000073876	Gm13305	OTTMUSG00000011351	predicted gene 13305	protein-coding
mm_61444.1	chr7	75569628	75569639	+	1	NA	intron (NM_029332, intron 2 of 36)	intron (NM_029332, intron 2 of 36)	114099	NM_029332	75547	Mm.216107	NM_029332	ENSMUSG00000066406	Akap13	1700026G02Rik|5730522G15Rik|5830460E08Rik|AKAP-13|AKAP-Lbc|BRX|Ht31|LBC|PROTO-LB|PROTO-LBC	A kinase (PRKA) anchor protein 13	protein-coding
mm_639.1	chr1	40399835	40399845	+	1	NA	Intergenic	Intergenic	-29730	NM_001294171	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_165982.1	chr4	105165871	105165875	+	1	NA	intron (NM_080555, intron 1 of 5)	intron (NM_080555, intron 1 of 5)	8526	NM_080555	67916	Mm.348326	NM_080555	ENSMUSG00000028517	Plpp3	1110003O22Rik|2610002D05Rik|AV025606|D4Bwg0538e|D4Bwg1535e|Lpp3|Ppab2b|Ppap2b	phospholipid phosphatase 3	protein-coding
mm_119016.1	chr14	30008930	30008944	+	1	NA	promoter-TSS (NM_001136240)	promoter-TSS (NM_001136240)	-41	NM_019583	50905	Mm.269363	NM_019583	ENSMUSG00000015966	Il17rb	Evi27|IL-17ER|IL-17Rh1|IL17RH1|Il17br	interleukin 17 receptor B	protein-coding
mm_84542.1	chr9	67299298	67299308	-	1	NA	intron (NM_001081242, intron 36 of 57)	intron (NM_001081242, intron 36 of 57)	-62577	NR_029576	387185		NR_029576	ENSMUSG00000076379	Mir190a	Mir190|Mirn190|mir-190|mir-190a|mmu-mir-190|mmu-mir-190a	microRNA 190a	ncRNA
mm_171217.1	chr3	59563566	59563579	-	1	NA	Intergenic	RLTR9D|LTR|ERVK	-166214	NM_001101531	433597	Mm.297801	NM_001101531	ENSMUSG00000090527	Gm5538	-	predicted gene 5538	protein-coding
mm_41902.1	chr5	105560267	105560279	+	1	NA	intron (NM_133897, intron 2 of 3)	B1_Mus1|SINE|Alu	40802	NM_133897	100604	Mm.319847	NM_133897	ENSMUSG00000054720	Lrrc8c	AD158|AI326115|E430036I04Rik|fad158	leucine rich repeat containing 8 family, member C	protein-coding
mm_120896.1	chr14	75845900	75845943	+	1	NA	promoter-TSS (NR_045294)	promoter-TSS (NR_045294)	665	NM_009429	22070	Mm.297482	NM_009429	ENSMUSG00000060126	Tpt1	TCTP|Trt|p21|p23	tumor protein, translationally-controlled 1	protein-coding
mm_96213.1	chr11	62456645	62456662	+	1	NA	intron (NM_177229, intron 1 of 8)	intron (NM_177229, intron 1 of 8)	679	NM_177229	20185	Mm.271814	NM_011308	ENSMUSG00000018501	Ncor1	5730405M06Rik|A230020K14Rik|N-CoR|RIP13|Rxrip13|mKIAA1047	nuclear receptor co-repressor 1	protein-coding
mm_102436.1	chr11	59506446	59506456	-	1	NA	non-coding (NR_135273, exon 1 of 4)	non-coding (NR_135273, exon 1 of 4)	189	NM_001291014	268417	Mm.239793	NM_172941	ENSMUSG00000020472	Zkscan17	Nizp1|Zfp496|Znf496	zinc finger with KRAB and SCAN domains 17	protein-coding
mm_22525.1	chr3	7647074	7647091	+	1	NA	Intergenic	Intergenic	-33322	NM_001313888	16196	Mm.3825	NM_008371	ENSMUSG00000040329	Il7	A630026I06Rik|Il-7|hlb368	interleukin 7	protein-coding
mm_53110.1	chr6	125083253	125083263	+	1	NA	TTS (NM_001163269)	TTS (NM_001163269)	11981	NM_001163268	381810	Mm.333386	NM_001163268	ENSMUSG00000067714	Lpar5	GPR93|Gm1072|Gpr92|LPA5	lysophosphatidic acid receptor 5	protein-coding
mm_110553.1	chr12	55491180	55491197	-	1	NA	exon (NM_010907, exon 3 of 6)	exon (NM_010907, exon 3 of 6)	1459	NM_010907	18035	Mm.170515	NM_010907	ENSMUSG00000021025	Nfkbia	AI462015|Nfkbi	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, alpha	protein-coding
mm_76734.1	chr8	95056908	95056949	-	1	NA	intron (NM_001042715, intron 3 of 17)	intron (NM_001042715, intron 3 of 17)	1825	NM_001042715	330830	Mm.277112	NM_001042715	ENSMUSG00000031786	Drc7	Ccdc135|Gm770|SRG-L|SRG-S	dynein regulatory complex subunit 7	protein-coding
mm_59471.1	chr7	27311438	27311450	+	1	NA	TTS (NM_001310678)	TTS (NM_001310678)	22204	NM_001113549	108075	Mm.272251	NM_175641	ENSMUSG00000040488	Ltbp4	2310046A13Rik	latent transforming growth factor beta binding protein 4	protein-coding
mm_101186.1	chr11	17095693	17095703	-	1	NA	Intergenic	Intergenic	43764	NM_029861	380686	Mm.425666	NM_029861	ENSMUSG00000044629	Cnrip1	1500041B16Rik|3110054C06Rik|5330437A18Rik|AI854501|C2orf32	cannabinoid receptor interacting protein 1	protein-coding
mm_112898.1	chr13	20895555	20895576	+	1	NA	intron (NM_012054, intron 4 of 20)	RMER17A2|LTR|ERVK	101452	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_61663.1	chr7	80777279	80777311	+	1	NA	intron (NM_016721, intron 2 of 37)	intron (NM_016721, intron 2 of 37)	26036	NM_016721	29875	Mm.207619	NM_016721	ENSMUSG00000030536	Iqgap1	AA682088|D7Ertd237e|D7Ertd257e|mKIAA0051	IQ motif containing GTPase activating protein 1	protein-coding
mm_79861.1	chr9	65032471	65032491	+	1	NA	promoter-TSS (NM_028906)	promoter-TSS (NM_028906)	23	NM_028906	74388	Mm.202749	NM_028906	ENSMUSG00000032393	Dpp8	2310004I03Rik|4932434F09Rik|AI666706|DPP VIII	dipeptidylpeptidase 8	protein-coding
mm_15984.1	chr2	166825284	166825290	+	1	NA	intron (NM_001085495, intron 1 of 38)	intron (NM_001085495, intron 1 of 38)	19706	NM_001085495	99371	Mm.297192	NM_001085495	ENSMUSG00000074582	Arfgef2	AI463430|AW493672|BIG2|E230011G24Rik	ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited)	protein-coding
mm_31219.1	chr4	44012658	44012660	+	1	NA	promoter-TSS (NM_001080385)	promoter-TSS (NM_001080385)	9	NM_001290470	12757	Mm.298875	NM_016760	ENSMUSG00000028478	Clta	AV026556|Lca	clathrin, light polypeptide (Lca)	protein-coding
mm_35654.1	chr4	43555917	43555934	-	1	NA	exon (NM_011602, exon 4 of 57)	exon (NM_011602, exon 4 of 57)	6658	NM_011602	21894	Mm.208601	NM_011602	ENSMUSG00000028465	Tln1	Tln	talin 1	protein-coding
mm_40783.1	chr5	67315787	67315806	+	1	NA	exon (NM_178651, exon 2 of 18)	exon (NM_178651, exon 2 of 18)	8841	NM_001310629	109108	Mm.234455	NM_178651	ENSMUSG00000029221	Slc30a9	2310024J23Rik|AL024256|GAC63|HUEL|znT-9	solute carrier family 30 (zinc transporter), member 9	protein-coding
mm_115644.1	chr13	12275697	12275699	-	1	NA	intron (NM_033268, intron 17 of 20)	intron (NM_033268, intron 17 of 20)	-17585	NM_001081128	238505	Mm.40335	NM_001081128	ENSMUSG00000021311	Mtr	AI894170|D830038K18Rik|MS	5-methyltetrahydrofolate-homocysteine methyltransferase	protein-coding
mm_116943.1	chr13	56104460	56104472	-	1	NA	exon (NM_001159515, exon 4 of 9)	exon (NM_001159515, exon 4 of 9)	31084	NM_012015	26914	Mm.283802	NM_012015	ENSMUSG00000015937	H2afy	H2AF12M|mH2a1|macroH2A1	H2A histone family, member Y	protein-coding
mm_103704.1	chr11	79516586	79516597	-	1	NA	exon (NM_001077496, exon 2 of 2)	exon (NM_001077496, exon 2 of 2)	7171	NM_001077496	216984	Mm.439665	NM_001077496	ENSMUSG00000093938	Evi2b	Evi-2|Evi2	ecotropic viral integration site 2b	protein-coding
mm_48883.1	chr5	151190143	151190153	-	1	NA	promoter-TSS (NM_001163493)	promoter-TSS (NM_001163493)	45	NM_001163493	243362	Mm.209272	NM_146258	ENSMUSG00000016128	Stard13	DLC2|GT650	StAR-related lipid transfer (START) domain containing 13	protein-coding
mm_97918.1	chr11	83532469	83532471	+	1	NA	Intergenic	Intergenic	-1952	NM_013653	20304	Mm.284248	NM_013653	ENSMUSG00000035042	Ccl5	MuRantes|RANTES|SISd|Scya5|TCP228	chemokine (C-C motif) ligand 5	protein-coding
mm_132523.1	chr16	37777069	37777079	+	1	NA	promoter-TSS (NM_008047)	promoter-TSS (NM_008047)	19	NM_008047	14314	Mm.182434	NM_008047	ENSMUSG00000022816	Fstl1	AI316791|AW107808|Fstl|TSC-36	follistatin-like 1	protein-coding
mm_168637.1	chr1	183297254	183297255	-	1	NA	promoter-TSS (NM_027861)	promoter-TSS (NM_027861)	194	NM_181732	108909	Mm.290502	NM_145626	ENSMUSG00000042901	Aida	2610208M17Rik|BC004835	axin interactor, dorsalization associated	protein-coding
mm_102518.1	chr11	60811256	60811270	-	1	NA	promoter-TSS (NM_009171)	promoter-TSS (NM_009171)	2	NM_009171	20425	Mm.364956	NM_009171	ENSMUSG00000020534	Shmt1	AI324848|AI385541|C81125|Shmt|mshmt|mshmt1|mshmt2	serine hydroxymethyltransferase 1 (soluble)	protein-coding
mm_154812.1	chrX	13661332	13661343	+	1	NA	promoter-TSS (NM_175669)	promoter-TSS (NM_175669)	-26	NM_175669	319200	Mm.383294	NM_175669	ENSMUSG00000047678	Gpr82	-	G protein-coupled receptor 82	protein-coding
mm_171162.1	chr3	24968478	24968497	-	1	NA	Intergenic	L1Md_T|LINE|L1	-184481	NM_001326288	635702	Mm.448351	NM_001326288	ENSMUSG00000102758	Naaladl2	2810043G22Rik|EG635702|Gm1021	N-acetylated alpha-linked acidic dipeptidase-like 2	protein-coding
mm_123330.1	chr14	63037842	63037871	-	1	NA	promoter-TSS (NM_001039566)	promoter-TSS (NM_001039566)	-10	NM_001039566	73670	Mm.82875	NM_001039566	ENSMUSG00000075571	Defb30	2410125J01Rik|4930449O14Rik|BD-30|mBD-30	defensin beta 30	protein-coding
mm_4436.1	chr1	172506789	172506850	+	1	NA	3' UTR (NM_178598, exon 5 of 5)	3' UTR (NM_178598, exon 5 of 5)	6573	NM_178598	21346	Mm.271711	NM_178598	ENSMUSG00000026547	Tagln2	2700094C18Rik|SM22beta|Sm22B|Sm22a	transgelin 2	protein-coding
mm_95783.1	chr11	54909936	54909946	+	1	NA	TTS (NM_021327)	TTS (NM_021327)	7087	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_168867.1	chr12	34000541	34000541	-	1	NA	Intergenic	Intergenic	42870	NM_011658	22160	Mm.3280	NM_011658	ENSMUSG00000035799	Twist1	M-Twist|Pde|Ska10|Ska<m10Jus>|Twist|bHLHa38|pdt	twist basic helix-loop-helix transcription factor 1	protein-coding
mm_135824.1	chr16	58499820	58499841	-	1	NA	intron (NM_018784, intron 2 of 10)	intron (NM_018784, intron 2 of 10)	23482	NM_018784	54613	Mm.212742	NM_018784	ENSMUSG00000022747	St3gal6	1700023B24Rik|AI930218|AW552396|Siat10|St3galVI	ST3 beta-galactoside alpha-2,3-sialyltransferase 6	protein-coding
mm_8222.1	chr1	138165267	138165287	-	1	NA	intron (NM_001111316, intron 1 of 31)	B1_Mur2|SINE|Alu	9849	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_146837.1	chr18	22850781	22850795	-	1	NA	intron (NM_001347510, intron 5 of 9)	intron (NM_001347510, intron 5 of 9)	187875	NM_001161483	319211	Mm.209896	NM_199024	ENSMUSG00000041923	Nol4	1700013J13Rik|4930568N03Rik|Gm1262	nucleolar protein 4	protein-coding
mm_128993.1	chr15	74838595	74838619	-	1	NA	exon (NM_001033229, exon 5 of 9)	exon (NM_001033229, exon 5 of 9)	3036	NM_001033229	110115	Mm.322606	NM_001033229	ENSMUSG00000075604	Cyp11b1	AA389061|CPN1|Cyp11b|Cyp11b-1|FHI	cytochrome P450, family 11, subfamily b, polypeptide 1	protein-coding
mm_162967.1	chr11	9598078	9598078	+	1	NA	intron (NM_178259, intron 55 of 61)	intron (NM_178259, intron 55 of 61)	406136	NM_178259	268379	Mm.39270	NM_178259	ENSMUSG00000004668	Abca13	9830132L24|A930002G16Rik|AI956815	ATP-binding cassette, sub-family A (ABC1), member 13	protein-coding
mm_161813.1	chr17	65885776	65885776	-	1	NA	promoter-TSS (NM_001198949)	promoter-TSS (NM_001198949)	-21	NM_009067	19765	Mm.17009	NM_009067	ENSMUSG00000024096	Ralbp1	RLIP76|Rip1	ralA binding protein 1	protein-coding
mm_43213.1	chr5	129511180	129511182	+	1	NA	intron (NM_172276, intron 4 of 17)	intron (NM_172276, intron 4 of 17)	9950	NM_172276	231769	Mm.288714	NM_172276	ENSMUSG00000029439	Sfswap	1190005N23Rik|6330437E22Rik|AI197402|AW212079|SWAP|Sfrs8|Srsf8	splicing factor, suppressor of white-apricot homolog (Drosophila)	protein-coding
mm_71120.1	chr8	36181797	36181800	+	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	67718	NM_001081150	244421	Mm.324032	NM_001081150	ENSMUSG00000039633	Lonrf1	-	LON peptidase N-terminal domain and ring finger 1	protein-coding
mm_54792.1	chr6	41636373	41636384	-	1	NA	promoter-TSS (NM_022413)	promoter-TSS (NM_022413)	27	NM_022413	64177	Mm.296889	NM_022413	ENSMUSG00000029868	Trpv6	CAT|CaT1|Cac|Ecac2|Otrpc3	transient receptor potential cation channel, subfamily V, member 6	protein-coding
mm_445.1	chr1	34851833	34851862	+	1	NA	intron (NM_175421, intron 1 of 6)	intron (NM_175421, intron 1 of 6)	1888	NM_145516	226971	Mm.292751	NM_145516	ENSMUSG00000026123	Plekhb2	2310009M15Rik|AU018239|Evt2|Phdc|evt-2	pleckstrin homology domain containing, family B (evectins) member 2	protein-coding
mm_69591.1	chr7	135707460	135707470	-	1	NA	exon (NM_001081117, exon 6 of 14)	exon (NM_001081117, exon 6 of 14)	8914	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_103334.1	chr11	74590066	74590149	-	1	NA	promoter-TSS (NM_001015046)	promoter-TSS (NM_001015046)	51	NM_001015046	380711	Mm.425690	NM_001015046	ENSMUSG00000038807	Rap1gap2	AU067654|Garnl4|Gm1561|mKIAA1039	RAP1 GTPase activating protein 2	protein-coding
mm_10161.1	chr2	4401161	4401172	+	1	NA	5' UTR (NM_001177843, exon 1 of 24)	5' UTR (NM_001177843, exon 1 of 24)	190	NM_001177843	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding
mm_27870.1	chr3	79162669	79162675	-	1	NA	Intergenic	Intergenic	-16797	NM_001099624	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_49005.1	chr6	4757080	4757093	+	1	NA	exon (NM_130877, exon 2 of 2)	exon (NM_130877, exon 2 of 2)	9780	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_43858.1	chr5	143421319	143421319	+	1	NA	3' UTR (NM_025841, exon 5 of 5)	3' UTR (NM_025841, exon 5 of 5)	17499	NM_025841	66913	Mm.181880	NM_025841	ENSMUSG00000079111	Kdelr2	1110007A14Rik	KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 2	protein-coding
mm_95144.1	chr11	35544485	35544495	+	1	NA	intron (NM_011412, intron 5 of 35)	intron (NM_011412, intron 5 of 35)	-72326	NR_029799	723924		NR_029799	ENSMUSG00000065583	Mir218-2	Mirn218-2|mir-218-2	microRNA 218-2	ncRNA
mm_96819.1	chr11	69994540	69994556	+	1	NA	3' UTR (NM_019749, exon 4 of 4)	3' UTR (NM_019749, exon 4 of 4)	-1218	NM_001291125	78246	Mm.20805	NM_030064	ENSMUSG00000018572	Phf23	JUNE-1	PHD finger protein 23	protein-coding
mm_47719.1	chr5	130002839	130002893	-	1	NA	promoter-TSS (NM_010368)	promoter-TSS (NM_010368)	-38	NM_010368	110006	Mm.3317	NM_010368	ENSMUSG00000025534	Gusb	AI747421|Gur|Gus|Gus-r|Gus-s|Gus-t|Gus-u|Gut|asd|g	glucuronidase, beta	protein-coding
mm_6118.1	chr1	64121399	64121452	-	1	NA	promoter-TSS (NM_033563)	promoter-TSS (NM_033563)	-36	NM_033563	93691	Mm.29466	NM_033563	ENSMUSG00000025959	Klf7	9830124P08Rik	Kruppel-like factor 7 (ubiquitous)	protein-coding
mm_38234.1	chr4	136142215	136142228	-	1	NA	Intergenic	Intergenic	-1601	NM_008321	15903	Mm.110	NM_008321	ENSMUSG00000007872	Id3	Hlh462|Idb3|bHLHb25	inhibitor of DNA binding 3	protein-coding
mm_38566.1	chr4	141723298	141723308	-	1	NA	5' UTR (NM_001017966, exon 1 of 10)	5' UTR (NM_001017966, exon 1 of 10)	116	NM_001017966	68817	Mm.393721	NM_001017966	ENSMUSG00000078515	Ddi2	1110056G13Rik|1700027M01Rik|9130022E05Rik|AI604911|AU040698	DNA-damage inducible protein 2	protein-coding
mm_71858.1	chr8	68906460	68906470	+	1	NA	3' UTR (NM_008509, exon 10 of 10)	3' UTR (NM_008509, exon 10 of 10)	25910	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_68181.1	chr7	103883097	103883131	-	1	NA	promoter-TSS (NM_013618)	promoter-TSS (NM_013618)	-873	NM_013618	18367	Mm.445781	NM_013618	ENSMUSG00000058200	Olfr66	5'[b]1|5'beta1|MOR1-3|ORL532	olfactory receptor 66	protein-coding
mm_160628.1	chr9	105400774	105400774	+	1	NA	promoter-TSS (NM_001164828)	promoter-TSS (NM_001164828)	-14	NM_001164828	66595	Mm.84941	NM_025651	ENSMUSG00000032567	Aste1	1100001A21Rik|AV006403	asteroid homolog 1 (Drosophila)	protein-coding
mm_3476.1	chr1	150105425	150105436	+	1	NA	exon (NM_011198, exon 10 of 10)	exon (NM_011198, exon 10 of 10)	5399	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_128257.1	chr15	36771246	36771272	-	1	NA	3' UTR (NM_001253807, exon 5 of 5)	3' UTR (NM_001253807, exon 5 of 5)	19673	NM_001253807	22631	Mm.3360	NM_011740	ENSMUSG00000022285	Ywhaz	1110013I11Rik|14-3-3zeta|AI596267|AL022924|AU020854	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide	protein-coding
mm_145242.1	chr18	50715661	50715710	+	1	NA	Intergenic	Intergenic	-146986	NM_026108	67365	Mm.158150	NM_026108	ENSMUSG00000048875	Hdhd1a	1700121L12Rik|GS1|Hdhd1|Pudp	haloacid dehalogenase-like hydrolase domain containing 1A	protein-coding
mm_39717.1	chr5	28071357	28071372	+	1	NA	promoter-TSS (NM_153526)	promoter-TSS (NM_153526)	-48	NM_153526	231070	Mm.30221	NM_153526	ENSMUSG00000045294	Insig1	1810013C12Rik|Insig-1	insulin induced gene 1	protein-coding
mm_72334.1	chr8	79028630	79028654	+	1	NA	5' UTR (NM_178267, exon 1 of 15)	5' UTR (NM_178267, exon 1 of 15)	205	NM_178267	622675	Mm.48724	NM_178267	ENSMUSG00000071064	Zfp827	2810449M09Rik|D630040G17Rik|Znf827	zinc finger protein 827	protein-coding
mm_115330.1	chr13	112467469	112467475	+	1	NA	intron (NM_010560, intron 1 of 16)	B1_Mus2|SINE|Alu	3402	NM_010560	16195	Mm.4364	NM_010560	ENSMUSG00000021756	Il6st	5133400A03Rik|AA389424|BB405851|CD130|D13Ertd699e|gp130	interleukin 6 signal transducer	protein-coding
mm_86472.1	chr10	4611871	4611880	+	1	NA	promoter-TSS (NR_126357)	promoter-TSS (NR_126357)	-114	NM_001302532	13982	Mm.9213	NM_007956	ENSMUSG00000019768	Esr1	ER|ER-alpha|ERa|ERalpha|ESR|Estr|Estra|Nr3a1	estrogen receptor 1 (alpha)	protein-coding
mm_146990.1	chr18	34007449	34007484	-	1	NA	promoter-TSS (NM_013512)	promoter-TSS (NM_013512)	-260	NM_013512	13824	Mm.3465	NM_013512	ENSMUSG00000024376	Epb41l4a	Epb4.1l4|Epb4.1l4a|NBL4	erythrocyte membrane protein band 4.1 like 4a	protein-coding
mm_136470.1	chr16	95715036	95715059	-	1	NA	exon (NM_011809, exon 7 of 10)	exon (NM_011809, exon 7 of 10)	12640	NM_011809	23872	Mm.290207	NM_011809	ENSMUSG00000022895	Ets2	AU022856|Ets-2	E26 avian leukemia oncogene 2, 3' domain	protein-coding
mm_94327.1	chr11	4265245	4265264	+	1	NA	intron (NM_008501, intron 1 of 3)	intron (NM_008501, intron 1 of 3)	-1542	NM_001039537	16878	Mm.4964	NM_008501	ENSMUSG00000034394	Lif	-	leukemia inhibitory factor	protein-coding
mm_139472.1	chr17	55970647	55970660	+	1	NA	5' UTR (NM_009168, exon 1 of 7)	5' UTR (NM_009168, exon 1 of 7)	171	NM_009168	20420	Mm.20908	NM_009168	ENSMUSG00000039154	Shd	AI413439	src homology 2 domain-containing transforming protein D	protein-coding
mm_152267.1	chr19	8798572	8798593	-	1	NA	promoter-TSS (NM_026329)	promoter-TSS (NM_026329)	-25	NM_026329	67710	Mm.22117	NM_026329	ENSMUSG00000071662	Polr2g	2410046K11Rik|A230108L04Rik|C76415|RBP7|Rpo2-7l	polymerase (RNA) II (DNA directed) polypeptide G	protein-coding
mm_4183.1	chr1	171160285	171160306	+	1	NA	3' UTR (NM_008623, exon 8 of 8)	3' UTR (NM_008623, exon 8 of 8)	4777	NM_001315500	17528	Mm.9986	NM_008623	ENSMUSG00000056569	Mpz	Mpp|P-zero|P0	myelin protein zero	protein-coding
mm_8447.1	chr1	152882815	152882817	-	1	NA	intron (NM_001005507, intron 1 of 21)	MT2B|LTR|ERVL	-4648	NM_001160257	226517	Mm.270775	NM_001005507	ENSMUSG00000042772	Smg7	9430023P16Rik|mKIAA0250	Smg-7 homolog, nonsense mediated mRNA decay factor (C. elegans)	protein-coding
mm_87047.1	chr10	28793537	28793544	+	1	NA	intron (NM_001305663, intron 5 of 5)	intron (NM_001305663, intron 5 of 5)	125180	NM_178666	210757	Mm.123021	NM_178666	ENSMUSG00000049109	Themis	E430004N04Rik|Gasp|Spot|Tsepa|thylex	thymocyte selection associated	protein-coding
mm_100086.1	chr11	115475803	115475829	+	1	NA	5' UTR (NM_177778, exon 1 of 3)	5' UTR (NM_177778, exon 1 of 3)	139	NM_177778	276905	Mm.38019	NM_177778	ENSMUSG00000057219	Armc7	A630084C13|BC023126	armadillo repeat containing 7	protein-coding
mm_4888.1	chr1	188383101	188383112	+	1	NA	intron (NM_021408, intron 10 of 70)	MTD|LTR|ERVL-MaLR	120268	NM_021408	22283	Mm.331238	NM_021408	ENSMUSG00000026609	Ush2a	A930011D15Rik|A930037M10Rik|Gm676|Gm983|Mush2a|Usherin|Ushrn	Usher syndrome 2A	protein-coding
mm_141521.1	chr17	31692987	31693005	-	1	NA	Intergenic	Intergenic	15065	NM_001278570	12954	Mm.1228	NM_013501	ENSMUSG00000024041	Cryaa	Acry-1|Crya-1|Crya1|DAcry-1|lop18	crystallin, alpha A	protein-coding
mm_59129.1	chr7	19965429	19965433	+	1	NA	promoter-TSS (NM_027839)	promoter-TSS (NM_027839)	19	NM_027839	71601	Mm.98097	NM_027839	ENSMUSG00000070777	Ceacam20	9130012D09Rik	carcinoembryonic antigen-related cell adhesion molecule 20	protein-coding
mm_117207.1	chr13	64084636	64084644	-	1	NA	intron (NM_008291, intron 2 of 10)	RSINE1|SINE|B4	4561	NM_008291	15487	Mm.5109	NM_008291	ENSMUSG00000033122	Hsd17b3	-	hydroxysteroid (17-beta) dehydrogenase 3	protein-coding
mm_64129.1	chr7	141165955	141165961	+	1	NA	intron (NM_145135, intron 2 of 9)	intron (NM_145135, intron 2 of 9)	2728	NM_001172101	107702	Mm.197493	NM_145135	ENSMUSG00000038650	Rnh1	AW546468|C80305|RNH	ribonuclease/angiogenin inhibitor 1	protein-coding
mm_170615.1	chr19	61198649	61198668	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-22349	NM_001177513	633057	Mm.426097	NM_001177513	ENSMUSG00000094649	Gm7102	EG633057	predicted gene 7102	protein-coding
mm_18620.1	chr2	68472121	68472137	-	1	NA	promoter-TSS (NM_016866)	promoter-TSS (NM_016866)	-148	NM_016866	53416	Mm.198414	NM_016866	ENSMUSG00000027030	Stk39	AW227544|AW556857|DCHT|RF005|Rnl5|SPAK	serine/threonine kinase 39	protein-coding
mm_25539.1	chr3	115799535	115799545	+	1	NA	Intergenic	Intergenic	-84485	NM_007901	13609	Mm.982	NM_007901	ENSMUSG00000045092	S1pr1	AI849002|Edg1|Lpb1|S1p|S1p1	sphingosine-1-phosphate receptor 1	protein-coding
mm_81192.1	chr9	107551517	107551575	+	1	NA	promoter-TSS (NM_001243748)	promoter-TSS (NM_001243748)	-9	NM_001243748	56289	Mm.12091	NM_019713	ENSMUSG00000010067	Rassf1	123F2|AA536941|AU044980|NORE2A|RDA32|REH3P21|Rassf1A|Rassf1B|Rassf1C	Ras association (RalGDS/AF-6) domain family member 1	protein-coding
mm_79503.1	chr9	57296599	57296607	+	1	NA	Intergenic	RMER10A|LTR|ERVL	-34004	NM_028820	74211	Mm.428905	NM_028820	ENSMUSG00000032300	1700017B05Rik	AA682102|D9Ertd278e	RIKEN cDNA 1700017B05 gene	protein-coding
mm_54151.1	chr6	22356069	22356175	-	1	NA	promoter-TSS (NM_138587)	promoter-TSS (NM_138587)	-41	NM_138587	27999	Mm.490307	NM_138587	ENSMUSG00000029672	Fam3c	D6Wsu176e|Ilei	family with sequence similarity 3, member C	protein-coding
mm_132262.1	chr16	32776283	32776286	+	1	NA	intron (NM_080457, intron 21 of 26)	intron (NM_080457, intron 21 of 26)	21151	NM_146071	224116	Mm.153301	NM_146071	ENSMUSG00000035638	Muc20	BC026367	mucin 20	protein-coding
mm_157352.1	chrX	36991725	36991727	-	1	NA	Intergenic	Intergenic	-2031	NM_001177323	56526	Mm.260036	NM_019942	ENSMUSG00000050379	Sept6	2810035H17Rik|C920001C06Rik|Sep6|mKIAA0128	septin 6	protein-coding
mm_110957.1	chr12	76795317	76795355	-	1	NA	exon (NM_030677, exon 1 of 2)	exon (NM_030677, exon 1 of 2)	218	NM_030677	14776	Mm.441856	NM_030677	ENSMUSG00000042808	Gpx2	GI-GPx|GPx-GI|GSHPx-2|GSHPx-GI	glutathione peroxidase 2	protein-coding
mm_35378.1	chr4	33189411	33189455	-	1	NA	5' UTR (NM_001034867, exon 1 of 7)	5' UTR (NM_001034867, exon 1 of 7)	304	NM_001034867	242377	Mm.372465	NM_001034867	ENSMUSG00000054659	Pm20d2	Acy1l2|Gm424	peptidase M20 domain containing 2	protein-coding
mm_5532.1	chr1	37997220	37997280	-	1	NA	promoter-TSS (NM_172054)	promoter-TSS (NM_172054)	-42	NM_172054	98258	Mm.28438	NM_172054	ENSMUSG00000058407	Txndc9	AI098020|APACD	thioredoxin domain containing 9	protein-coding
mm_64967.1	chr7	16615055	16615067	-	1	NA	promoter-TSS (NM_172739)	promoter-TSS (NM_172739)	-68	NM_172739	232906	Mm.28646	NM_172739	ENSMUSG00000058230	Arhgap35	6430596G11Rik|AI841135|Grlf1|mKIAA1722|p190A|p190RhoGAP	Rho GTPase activating protein 35	protein-coding
mm_63853.1	chr7	135666848	135666860	+	1	NA	intron (NM_001316681, intron 7 of 17)	intron (NM_001316681, intron 7 of 17)	-14540	NR_015548	67765	Mm.445272	NR_015548	ENSMUSG00000097471	5830432E09Rik	-	RIKEN cDNA 5830432E09 gene	ncRNA
mm_9534.1	chr1	173871802	173871812	-	1	NA	intron (NM_001170853, intron 5 of 9)	ORR1C1|LTR|ERVL-MaLR	8380	NM_001170853	100040462	Mm.463437	NM_001170853	ENSMUSG00000090272	Mndal	Gm2785|Ifi212	myeloid nuclear differentiation antigen like	protein-coding
mm_136422.1	chr16	93982519	93982531	-	1	NA	intron (NM_019500, intron 1 of 2)	ORR1E|LTR|ERVL-MaLR	26312	NM_019500	56173	Mm.328716	NM_019500	ENSMUSG00000047109	Cldn14	AI851731	claudin 14	protein-coding
mm_6454.1	chr1	74016605	74016627	-	1	NA	intron (NM_027884, intron 3 of 34)	intron (NM_027884, intron 3 of 34)	107831	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_80835.1	chr9	97110610	97110652	+	1	NA	intron (NM_138756, intron 1 of 6)	CpG	410	NM_138756	192287	Mm.228067	NM_138756	ENSMUSG00000032449	Slc25a36	C330005L02Rik	solute carrier family 25, member 36	protein-coding
mm_55378.1	chr6	58906251	58906261	-	1	NA	3' UTR (NM_021432, exon 1 of 1)	3' UTR (NM_021432, exon 1 of 1)	870	NM_021432	58243	Mm.389747	NM_021432	ENSMUSG00000055430	Nap1l5	1110020M21Rik	nucleosome assembly protein 1-like 5	protein-coding
mm_138825.1	chr17	39847842	39847872	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	4860	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_134225.1	chr16	11254367	11254375	-	1	NA	promoter-TSS (NM_001130008)	promoter-TSS (NM_001130008)	-46	NM_146066	14852	Mm.325827	NM_146066	ENSMUSG00000062203	Gspt1	AI314175|AI326449|AV307676|C79774|G1st|Gst-1	G1 to S phase transition 1	protein-coding
mm_146810.1	chr18	20746335	20746394	-	1	NA	promoter-TSS (NM_019737)	promoter-TSS (NM_019737)	40	NM_019737	56386	Mm.393827	NM_019737	ENSMUSG00000056124	B4galt6	AA536803|AU022389	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 6	protein-coding
mm_100930.1	chr11	6519169	6519180	-	1	NA	exon (NM_178440, exon 2 of 22)	exon (NM_178440, exon 2 of 22)	1784	NM_178440	246177	Mm.239554	NM_178440	ENSMUSG00000020437	Myo1g	E430002D17Rik	myosin IG	protein-coding
mm_3194.1	chr1	135810889	135810893	+	1	NA	TTS (NM_021467)	TTS (NM_021467)	-7707	NM_133664	16763	Mm.36726	NM_133664	ENSMUSG00000041782	Lad1	-	ladinin	protein-coding
mm_29605.1	chr3	121232424	121232435	-	1	NA	intron (NM_178936, intron 3 of 7)	PB1D11|SINE|Alu	30887	NM_178936	99887	Mm.26088	NM_178936	ENSMUSG00000028132	Tmem56	4930577M16Rik|AU018104|AW109744|C730036B01Rik	transmembrane protein 56	protein-coding
mm_56946.1	chr6	119966040	119966042	-	1	NA	intron (NM_001199083, intron 8 of 27)	intron (NM_001199083, intron 8 of 27)	63343	NM_001166381	19365	Mm.149	NM_011236	ENSMUSG00000030166	Rad52	Rad52yh	RAD52 homolog, DNA repair protein	protein-coding
mm_99704.1	chr11	106160262	106160285	+	1	NA	promoter-TSS (NM_172397)	promoter-TSS (NM_172397)	-131	NM_172397	67803	Mm.21687	NM_172397	ENSMUSG00000040699	Limd2	0610025L06Rik|AI413966	LIM domain containing 2	protein-coding
mm_74634.1	chr8	13200577	13200636	-	1	NA	promoter-TSS (NM_025768)	promoter-TSS (NM_025768)	18	NM_025768	66790	Mm.34901	NM_025768	ENSMUSG00000038515	Grtp1	5430401C05Rik|C81211|Tbc1d6	GH regulated TBC protein 1	protein-coding
mm_26997.1	chr3	25832967	25832977	-	1	NA	intron (NM_001163387, intron 3 of 5)	intron (NM_001163387, intron 3 of 5)	320335	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_17701.1	chr2	32381800	32381810	-	1	NA	5' UTR (NM_198001, exon 1 of 2)	5' UTR (NM_198001, exon 1 of 2)	110	NM_198001	73737	Mm.27608	NM_198001	ENSMUSG00000039195	1110008P14Rik	C79326	RIKEN cDNA 1110008P14 gene	protein-coding
mm_43395.1	chr5	135778648	135778663	+	1	NA	promoter-TSS (NM_029659)	promoter-TSS (NM_029659)	6	NM_008617	17448	Mm.297096	NM_008617	ENSMUSG00000019179	Mdh2	MDH|Mdh-2|Mor-1|Mor1	malate dehydrogenase 2, NAD (mitochondrial)	protein-coding
mm_30240.1	chr3	146477377	146477381	-	1	NA	intron (NM_027617, intron 8 of 14)	intron (NM_027617, intron 8 of 14)	22374	NM_001316756	70951	Mm.383235	NM_027617	ENSMUSG00000028188	Spata1	4921536I21Rik|AV266943|SP-2	spermatogenesis associated 1	protein-coding
mm_58273.1	chr6	145434060	145434071	-	1	NA	intron (NM_028742, intron 1 of 9)	intron (NM_028742, intron 1 of 9)	860	NM_028742	74071	Mm.441497	NM_028742	ENSMUSG00000054966	Lmntd1	4933403M22Rik|AI482300|Ifltd1|Lmna-rs1|Lmna1|OTTMUSG00000022798	lamin tail domain containing 1	protein-coding
mm_139263.1	chr17	47767321	47767355	+	1	NA	intron (NM_001161723, intron 1 of 8)	intron (NM_001161723, intron 1 of 8)	-18406	NM_011549	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_136968.1	chr17	15731840	15731855	+	1	NA	intron (NM_007690, intron 7 of 35)	intron (NM_007690, intron 7 of 35)	26880	NM_007690	12648	Mm.8137	NM_007690	ENSMUSG00000023852	Chd1	4930525N21Rik|AI851787|AW555109	chromodomain helicase DNA binding protein 1	protein-coding
mm_153420.1	chr19	40661247	40661261	-	1	NA	intron (NM_009848, intron 1 of 9)	intron (NM_009848, intron 1 of 9)	1484	NM_009848	12495	Mm.2824	NM_009848	ENSMUSG00000048120	Entpd1	2610206B08Rik|AA408691|Cd39|NTPDase-1	ectonucleoside triphosphate diphosphohydrolase 1	protein-coding
mm_8358.1	chr1	150454556	150454588	-	1	NA	exon (NM_021400, exon 7 of 13)	exon (NM_021400, exon 7 of 13)	11593	NM_021400	96875	Mm.174256	NM_021400	ENSMUSG00000006014	Prg4	CACP|DOL54|JCAP|MSF|SZP|lubricin	proteoglycan 4 (megakaryocyte stimulating factor, articular superficial zone protein)	protein-coding
mm_9716.1	chr1	179803217	179803222	-	1	NA	intron (NM_026375, intron 1 of 35)	CpG	796	NM_026375	226747	Mm.128165	NM_026375	ENSMUSG00000026491	Ahctf1	6230412P20Rik|AV011447|Elys	AT hook containing transcription factor 1	protein-coding
mm_136698.1	chr17	7170102	7170132	+	1	NA	promoter-TSS (NM_011299)	promoter-TSS (NM_011299)	2	NM_011299	20112	Mm.268383	NM_011299	ENSMUSG00000023809	Rps6ka2	90kDa|D17Wsu134e|Rps6ka-rs1|Rsk3|p90rsk|pp90rsk	ribosomal protein S6 kinase, polypeptide 2	protein-coding
mm_172768.1	chr8	94179071	94179073	+	1	NA	promoter-TSS (NM_013602)	promoter-TSS (NM_013602)	-17	NM_013602	17748	Mm.192991	NM_013602	ENSMUSG00000031765	Mt1	MT-I|Mt-1	metallothionein 1	protein-coding
mm_135153.1	chr16	35857829	35857850	-	1	NA	exon (NM_001039530, exon 6 of 17)	exon (NM_001039530, exon 6 of 17)	13543	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_24187.1	chr3	88607128	88607199	+	1	NA	Intergenic	Intergenic	-9044	NM_001198911	16800	Mm.239329	NM_008487	ENSMUSG00000028059	Arhgef2	AA408978|GEF|GEF-H1|GEFH1|LFP40|Lbcl1|Lfc|P40|mKIAA0651	rho/rac guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_24967.1	chr3	96727614	96727620	+	1	NA	promoter-TSS (NM_026406)	promoter-TSS (NM_026406)	6	NM_026406	67845	Mm.386792	NM_026406	ENSMUSG00000028098	Rnf115	2610028E05Rik|AU042696|Zfp364	ring finger protein 115	protein-coding
mm_144156.1	chr18	5593883	5593900	+	1	NA	intron (NM_011546, intron 1 of 7)	intron (NM_011546, intron 1 of 7)	-1454	NR_033552	791318	Mm.84339	NR_033552	ENSMUSG00000063087	Gm10125	ENSMUSG00000063087|Zeb1os	predicted gene 10125	ncRNA
mm_37574.1	chr4	126249498	126249502	-	1	NA	intron (NM_001347198, intron 1 of 17)	intron (NM_001347198, intron 1 of 17)	6819	NM_144941	245877	Mm.266716	NM_144941	ENSMUSG00000028849	Map7d1	AV028413|BC019977|Mtap7d1|Parcc1|Rprc1|mKIAA1187	MAP7 domain containing 1	protein-coding
mm_3590.1	chr1	151360014	151360023	+	1	NA	exon (NM_001039512, exon 9 of 14)	exon (NM_001039512, exon 9 of 14)	15520	NM_001039511	117198	Mm.33764	NM_028582	ENSMUSG00000023150	Ivns1abp	1190004M08Rik|1700126I16Rik|AA960440|HSPC068|ND1|NS-1|NS1-BP|Nd1-L|Nd1-S|mKIAA0850	influenza virus NS1A binding protein	protein-coding
mm_36494.1	chr4	83285126	83285138	-	1	NA	intron (NM_027238, intron 2 of 19)	intron (NM_027238, intron 2 of 19)	39057	NM_027238	69863	Mm.5540	NM_025782	ENSMUSG00000038172	Ttc39b	1810054D07Rik|9130422G05Rik|AI450603|AV103077|AW215585	tetratricopeptide repeat domain 39B	protein-coding
mm_110881.1	chr12	74890091	74890111	-	1	NA	Intergenic	Intergenic	287231	NM_172805	238271	Mm.44465	NM_172805	ENSMUSG00000034402	Kcnh5	Eag2	potassium voltage-gated channel, subfamily H (eag-related), member 5	protein-coding
mm_20332.1	chr2	127521332	127521357	-	1	NA	promoter-TSS (NM_019789)	promoter-TSS (NM_019789)	48	NM_001291005	56461	Mm.315292	NM_019789	ENSMUSG00000079056	Kcnip3	4933407H12Rik|AI413860|Csen|DREAM|KChIP3|R74849	Kv channel interacting protein 3, calsenilin	protein-coding
mm_166223.1	chr5	64961330	64961337	-	1	NA	Intergenic	Intergenic	-1299	NM_011604	21899	Mm.42146	NM_011604	ENSMUSG00000051498	Tlr6	-	toll-like receptor 6	protein-coding
mm_122238.1	chr14	33247863	33247873	-	1	NA	intron (NM_153800, intron 2 of 10)	intron (NM_153800, intron 2 of 10)	31045	NM_153800	239027	Mm.318350	NM_153800	ENSMUSG00000063506	Arhgap22	B230341L19Rik|RHOGAP2|p68RacGAP	Rho GTPase activating protein 22	protein-coding
mm_171143.1	chr3	152213994	152213994	+	1	NA	exon (NM_057172, exon 2 of 20)	exon (NM_057172, exon 2 of 20)	3536	NM_057172	51886	Mm.278922	NM_057172	ENSMUSG00000028034	Fubp1	9530027K12Rik|D3Ertd330e|FBP|Fubp|Fubp4	far upstream element (FUSE) binding protein 1	protein-coding
mm_39712.1	chr5	27791759	27791791	+	1	NA	promoter-TSS (NM_018878)	promoter-TSS (NM_018878)	-225	NM_018878	55982	Mm.277190	NM_018878	ENSMUSG00000002221	Paxip1	D5Ertd149e|PTIP	PAX interacting (with transcription-activation domain) protein 1	protein-coding
mm_42106.1	chr5	110544298	110544314	+	1	NA	promoter-TSS (NM_198306)	promoter-TSS (NM_198306)	-49	NM_198306	231605	Mm.275748	NM_198306	ENSMUSG00000033316	Galnt9	GalNAc-T9	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 9	protein-coding
mm_82978.1	chr9	35849927	35849938	-	1	NA	promoter-TSS (NR_030730)	promoter-TSS (NR_030730)	-52	NR_030730	100041605	Mm.99350	NR_030730	ENSMUSG00000098705	Gm3428	-	predicted gene 3428	ncRNA
mm_64231.1	chr7	141694575	141694588	+	1	NA	exon (NM_023566, exon 9 of 46)	exon (NM_023566, exon 9 of 46)	4241	NM_023566	17831	Mm.2041	NM_023566		Muc2	2010015E03Rik|MCM|wnn	mucin 2	protein-coding
mm_161513.1	chr15	98777278	98777278	-	1	NA	intron (NM_011718, intron 1 of 4)	intron (NM_011718, intron 1 of 4)	872	NM_011718	22410	Mm.4709	NM_011718	ENSMUSG00000022996	Wnt10b	Wnt12	wingless-type MMTV integration site family, member 10B	protein-coding
mm_44725.1	chr5	31038263	31038276	-	1	NA	intron (NM_001177621, intron 13 of 17)	intron (NM_001177621, intron 13 of 17)	9810	NM_177870	330064	Mm.205463	NM_177870	ENSMUSG00000006641	Slc5a6	E430023I20	solute carrier family 5 (sodium-dependent vitamin transporter), member 6	protein-coding
mm_112656.1	chr13	16026777	16026783	+	1	NA	exon (NM_008380, exon 5 of 5)	exon (NM_008380, exon 5 of 5)	14929	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_123431.1	chr14	64440869	64440923	-	1	NA	5' UTR (NM_026322, exon 6 of 11)	5' UTR (NM_026322, exon 6 of 11)	130	NM_001253715	110265	Mm.26713	NM_026322	ENSMUSG00000054733	Msra	2310045J23Rik|6530413P12Rik|MSR-A	methionine sulfoxide reductase A	protein-coding
mm_111158.1	chr12	83487714	83487729	-	1	NA	promoter-TSS (NM_001267626)	promoter-TSS (NM_001267626)	15	NM_001267626	70127	Mm.151308	NM_058212	ENSMUSG00000021221	Dpf3	2810403B03Rik|6530402L11Rik|BAF45C|C78788|CERD4|cer-d4	D4, zinc and double PHD fingers, family 3	protein-coding
mm_74510.1	chr8	8661233	8661249	-	1	NA	promoter-TSS (NM_010111)	promoter-TSS (NM_010111)	-468	NM_010111	13642	Mm.209813	NM_010111	ENSMUSG00000001300	Efnb2	ELF-2|Epl5|Eplg5|Htk-L|LERK-5|Lerk5|NLERK-1	ephrin B2	protein-coding
mm_143680.1	chr17	80062076	80062086	-	1	NA	5' UTR (NM_144802, exon 1 of 13)	5' UTR (NM_144802, exon 1 of 13)	187	NM_144802	72692	Mm.64579	NM_144802	ENSMUSG00000024095	Hnrnpll	2510028H02Rik|2810036L13Rik|AI256697|AI852082|Hnrpll	heterogeneous nuclear ribonucleoprotein L-like	protein-coding
mm_15786.1	chr2	164405265	164405297	+	1	NA	promoter-TSS (NM_013592)	promoter-TSS (NM_013592)	-121	NM_001252563	17183	Mm.29428	NM_013592	ENSMUSG00000016995	Matn4	matrilin-4	matrilin 4	protein-coding
mm_116845.1	chr13	54749628	54749697	-	1	NA	5' UTR (NM_001316710, exon 1 of 2)	5' UTR (NM_001316710, exon 1 of 2)	212	NM_001316710	26913	Mm.41812	NM_012014	ENSMUSG00000069227	Gprin1	GRIN1|Z16	G protein-regulated inducer of neurite outgrowth 1	protein-coding
mm_28204.1	chr3	88296851	88296909	-	1	NA	promoter-TSS (NM_009836)	promoter-TSS (NM_009836)	-42	NM_029801	76927	Mm.273330	NM_029801	ENSMUSG00000010538	Tsacc	1700021C14Rik|SIP	TSSK6 activating co-chaperone	protein-coding
mm_42965.1	chr5	123135792	123135802	+	1	NA	Intergenic	Intergenic	-3168	NM_175092	23912	Mm.253876	NM_175092	ENSMUSG00000029449	Rhof	AI845056|AV026554|Arhf|Ifld1|Rif	ras homolog family member F (in filopodia)	protein-coding
mm_76535.1	chr8	87960486	87960501	-	1	NA	promoter-TSS (NM_033327)	promoter-TSS (NM_033327)	-898	NM_033327	94187	Mm.23452	NM_033327	ENSMUSG00000045333	Zfp423	Ebfaz|Roaz|Zfp104|Znf423|ataxia1|mKIAA0760|nur12	zinc finger protein 423	protein-coding
mm_5823.1	chr1	52734295	52734310	-	1	NA	Intergenic	MLT1A1|LTR|ERVL-MaLR	-6984	NM_133829	98682	Mm.491173	NM_133829	ENSMUSG00000041439	Mfsd6	2210010L05Rik|9630025I22Rik|AI836200|AW212394|MMR2	major facilitator superfamily domain containing 6	protein-coding
mm_21632.1	chr2	164277577	164277581	-	1	NA	intron (NM_009300, intron 1 of 2)	RLTR10C|LTR|ERVK	728	NM_009300	20941	Mm.1286	NM_009300	ENSMUSG00000016998	Svs4	SVS-IV|Svp-2|Svp-4|Svp2|Svp4	seminal vesicle secretory protein 4	protein-coding
mm_56287.1	chr6	91473505	91473552	-	1	NA	promoter-TSS (NM_133928)	promoter-TSS (NM_133928)	-105	NM_133928	72170	Mm.41622	NM_133928	ENSMUSG00000034203	Chchd4	2410012P20Rik|2810014D17Rik|AI838740	coiled-coil-helix-coiled-coil-helix domain containing 4	protein-coding
mm_155723.1	chrX	96152696	96152764	+	1	NA	exon (NM_010833, exon 4 of 13)	exon (NM_010833, exon 4 of 13)	56685	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_9206.1	chr1	171229798	171229807	-	1	NA	3' UTR (NM_010185, exon 5 of 5)	3' UTR (NM_010185, exon 5 of 5)	4547	NM_010185	14127	Mm.22673	NM_010185	ENSMUSG00000058715	Fcer1g	AI573376|CD23|FcR-gamma|FcR[g]|FcRgamma|Fce1g|FcepsilonRI|Ly-50	Fc receptor, IgE, high affinity I, gamma polypeptide	protein-coding
mm_121019.1	chr14	79549397	79549443	+	1	NA	intron (NM_001286411, intron 2 of 8)	intron (NM_001286411, intron 2 of 8)	33746	NM_001286411	13709	Mm.20938	NM_007920	ENSMUSG00000036461	Elf1	Elf-1|Sts1|mElf-1|p70	E74-like factor 1	protein-coding
mm_69581.1	chr7	135704192	135704217	-	1	NA	exon (NM_001081117, exon 10 of 14)	exon (NM_001081117, exon 10 of 14)	12175	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_134566.1	chr16	20356178	20356207	-	1	NA	intron (NM_013790, intron 25 of 29)	MERVL_2A-int|LTR|ERVL	-30788	NM_183158	224044	Mm.276400	NM_183158	ENSMUSG00000022818	Cyp2ab1	EG224044|F730023N20	cytochrome P450, family 2, subfamily ab, polypeptide 1	protein-coding
mm_77115.1	chr8	111082044	111082078	-	1	NA	promoter-TSS (NM_181549)	promoter-TSS (NM_181549)	-353	NM_181549	353287	Mm.135495	NM_181549	ENSMUSG00000033633	Clec18a	Mrcl	C-type lectin domain family 18, member A	protein-coding
mm_4717.1	chr1	181051233	181051242	+	1	NA	promoter-TSS (NM_001033819)	promoter-TSS (NM_001033819)	0	NM_001033819	619326	Mm.355174	NM_001033819	ENSMUSG00000038768	9130409I23Rik	-	RIKEN cDNA 9130409I23 gene	protein-coding
mm_166452.1	chr5	137533202	137533206	-	1	NA	promoter-TSS (NM_010312)	promoter-TSS (NM_010312)	25	NM_010312	14693	Mm.30141	NM_010312	ENSMUSG00000029713	Gnb2	Gnb-2	guanine nucleotide binding protein (G protein), beta 2	protein-coding
mm_129687.1	chr15	81421679	81421690	-	1	NA	intron (NM_001347075, intron 2 of 9)	intron (NM_001347075, intron 2 of 9)	-13411	NM_021317	57755	Mm.440590	NM_021317	ENSMUSG00000047108	Dnajb7	4933424H20Rik|Dj5|mDj5	DnaJ heat shock protein family (Hsp40) member B7	protein-coding
mm_140579.1	chr17	10211720	10211739	-	1	NA	3' UTR (NM_001159516, exon 7 of 7)	3' UTR (NM_001159516, exon 7 of 7)	107632	NM_021881	19317	Mm.130694	NM_021881	ENSMUSG00000062078	Qk	1110003F05Rik|1500005P18|QkI|l(17)-1Wis|l17Wis1	quaking	protein-coding
mm_55609.1	chr6	71908737	71908770	-	1	NA	promoter-TSS (NM_009088)	promoter-TSS (NM_009088)	9	NM_027275	69956	Mm.30256	NM_027275	ENSMUSG00000063884	Ptcd3	2610034F17Rik|2810422B04Rik|AA589622|AU045708|MRP-S39	pentatricopeptide repeat domain 3	protein-coding
mm_143465.1	chr17	71002127	71002285	-	1	NA	5' UTR (NM_026064, exon 1 of 4)	5' UTR (NM_026064, exon 1 of 4)	327	NM_026064	67268	Mm.489605	NM_026064	ENSMUSG00000024048	Myl12a	2900073G15Rik|AI838292|C80200	myosin, light chain 12A, regulatory, non-sarcomeric	protein-coding
mm_114554.1	chr13	74121406	74121421	+	1	NA	promoter-TSS (NM_001081060)	promoter-TSS (NM_001081060)	-102	NM_001081060	105243	Mm.261564	NM_001081060	ENSMUSG00000036123	Slc9a3	9030624O13Rik|AI930210|NHE-3|NHE3	solute carrier family 9 (sodium/hydrogen exchanger), member 3	protein-coding
mm_158130.1	chrX	103027260	103027267	-	1	NA	Intergenic	RMER17A|LTR|ERVK	-93040	NR_026596	331480	Mm.145294	NR_026596		Gm5126	EG331480	predicted pseudogene 5126	ncRNA
mm_7310.1	chr1	98047794	98047817	-	1	NA	promoter-TSS (NR_037993)	promoter-TSS (NR_037993)	-12	NR_037993	78603	Mm.442597	NR_037993	ENSMUSG00000089706	B230216N24Rik	-	RIKEN cDNA B230216N24 gene	ncRNA
mm_46115.1	chr5	92363284	92363295	-	1	NA	promoter-TSS (NM_019494)	promoter-TSS (NM_019494)	7	NR_038116	56066	Mm.131723	NM_019494	ENSMUSG00000060183	Cxcl11	Cxc11|H174|I-tac|Ip9|Itac|Scyb11|Scyb9b|b-R1|betaR1	chemokine (C-X-C motif) ligand 11	protein-coding
mm_16292.1	chr2	174120849	174120860	+	1	NA	intron (NM_213733, intron 9 of 11)	intron (NM_213733, intron 9 of 11)	10503	NM_213733	228961	Mm.295629	NM_213733	ENSMUSG00000039263	Npepl1	BC023239|C85514|mKIAA1974	aminopeptidase-like 1	protein-coding
mm_26970.1	chr3	24783562	24783607	-	1	NA	5' UTR (NM_001326288, exon 1 of 14)	5' UTR (NM_001326288, exon 1 of 14)	422	NM_001326288	635702	Mm.448351	NM_001326288	ENSMUSG00000102758	Naaladl2	2810043G22Rik|EG635702|Gm1021	N-acetylated alpha-linked acidic dipeptidase-like 2	protein-coding
mm_98168.1	chr11	87751192	87751216	+	1	NA	Intergenic	Intergenic	-5660	NR_029555	387160		NR_029555	ENSMUSG00000105196	Mir142	Mirn142|miR-142|mir-142a|mmu-mir-142|mmu-mir-142a	microRNA 142	ncRNA
mm_138894.1	chr17	43568291	43568303	+	1	NA	promoter-TSS (NM_013737)	promoter-TSS (NM_013737)	-154	NM_013737	27226	Mm.9277	NM_013737	ENSMUSG00000023913	Pla2g7	PAF-AH|R75400	phospholipase A2, group VII (platelet-activating factor acetylhydrolase, plasma)	protein-coding
mm_84971.1	chr9	85323176	85323184	-	1	NA	3' UTR (NM_001160378, exon 3 of 3)	3' UTR (NM_001160378, exon 3 of 3)	3944	NM_001160378	212943	Mm.74610	NM_001160378	ENSMUSG00000032265	Fam46a	BAP014|D930050G01Rik	family with sequence similarity 46, member A	protein-coding
mm_9478.1	chr1	173367639	173367656	-	1	NA	promoter-TSS (NM_053199)	promoter-TSS (NM_053199)	48	NM_053199	94332	Mm.330524	NM_053199	ENSMUSG00000005338	Cadm3	BIgR|Igsf4b|Necl-1|Necl1|SynCAM3|Tsll1	cell adhesion molecule 3	protein-coding
mm_114051.1	chr13	54304816	54304829	+	1	NA	Intergenic	Intergenic	-66527	NM_009946	12890	Mm.268902	NM_009946	ENSMUSG00000025867	Cplx2	921-L|AI413745|AW492120	complexin 2	protein-coding
mm_126814.1	chr15	87715593	87715614	+	1	NA	intron (NM_134096, intron 2 of 3)	intron (NM_134096, intron 2 of 3)	80340	NR_105817	102465209		NR_105817	ENSMUSG00000098938	Mir6393	Gm27424|mmu-mir-6393	microRNA 6393	ncRNA
mm_91725.1	chr10	44631662	44631686	-	1	NA	Intergenic	Intergenic	-172926	NM_007548	12142	Mm.4800	NM_007548	ENSMUSG00000038151	Prdm1	Blimp-1|Blimp1|PRDI-BF1|ZNFPR1A1|b2b1765Clo	PR domain containing 1, with ZNF domain	protein-coding
mm_115735.1	chr13	17789252	17789273	-	1	NA	intron (NM_027118, intron 1 of 13)	L1_Mur3|LINE|L1	15835	NM_001081058	69562	Mm.193924	NM_027118	ENSMUSG00000041297	Cdk13	2310015O17Rik|Cdc2l5	cyclin-dependent kinase 13	protein-coding
mm_167766.1	chr9	110680219	110680219	-	1	NA	intron (NM_028312, intron 1 of 6)	intron (NM_028312, intron 1 of 6)	23716	NM_028312	72654	Mm.249115	NM_028312	ENSMUSG00000019659	Ccdc12	2700094L05Rik|C76605	coiled-coil domain containing 12	protein-coding
mm_138639.1	chr17	35866122	35866144	+	1	NA	promoter-TSS (NM_001146710)	promoter-TSS (NM_001146710)	5	NM_001146710	76448	Mm.359982	NM_175242	ENSMUSG00000034595	Ppp1r18	2310014H01Rik|AA407849|AI450394	protein phosphatase 1, regulatory subunit 18	protein-coding
mm_161984.1	chr19	28964005	28964005	-	1	NA	promoter-TSS (NM_028922)	promoter-TSS (NM_028922)	85	NM_028922	74411	Mm.441887	NM_028922	ENSMUSG00000040105	Plpp6	4932443D16Rik|Ppapdc2	phospholipid phosphatase 6	protein-coding
mm_69712.1	chr7	140116439	140116449	-	1	NA	promoter-TSS (NM_053119)	promoter-TSS (NM_053119)	-21	NM_053119	93747	Mm.24452	NM_053119	ENSMUSG00000025465	Echs1	C80529	enoyl Coenzyme A hydratase, short chain, 1, mitochondrial	protein-coding
mm_144257.1	chr18	11047579	11047617	+	1	NA	non-coding (NR_105023, exon 4 of 6)	non-coding (NR_105023, exon 4 of 6)	-4912	NM_010258	14465	Mm.329287	NM_010258	ENSMUSG00000005836	Gata6	AA410133|GATA-6	GATA binding protein 6	protein-coding
mm_151859.1	chr19	5797179	5797188	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	-1202	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_61698.1	chr7	81141851	81141864	+	1	NA	intron (NM_001004184, intron 9 of 17)	intron (NM_001004184, intron 9 of 17)	27058	NM_001004184	434203	Mm.389909	NM_001004184	ENSMUSG00000025726	Slc28a1	Cnt1	solute carrier family 28 (sodium-coupled nucleoside transporter), member 1	protein-coding
mm_39291.1	chr5	4333449	4333452	+	1	NA	Intergenic	LTRIS2|LTR|ERV1	141083	NM_001042670	208595	Mm.129815	NM_001042670	ENSMUSG00000053178	Mterf1b	ENSMUSG00000053178|Gm9897	mitochondrial transcription termination factor 1b	protein-coding
mm_171817.1	chr5	138504762	138504763	+	1	NA	Intergenic	Intergenic	59932	NM_029693	76658	Mm.73235	NM_029693	ENSMUSG00000029526	1700123K08Rik	-	RIKEN cDNA 1700123K08 gene	protein-coding
mm_172182.1	chr6	49236609	49236610	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-21655	NM_023670	140488	Mm.281018	NM_023670	ENSMUSG00000029814	Igf2bp3	2610101N11Rik|AA522010|AL022933|AU045931|IMP-3|IMP3|Koc13|Neilsen|mimp3	insulin-like growth factor 2 mRNA binding protein 3	protein-coding
mm_155860.1	chrX	101376360	101376373	+	1	NA	promoter-TSS (NM_008124)	promoter-TSS (NM_008124)	-10	NM_001302496	14618	Mm.21198	NM_008124	ENSMUSG00000047797	Gjb1	Cnx32|Cx32|connexin-32	gap junction protein, beta 1	protein-coding
mm_98034.1	chr11	85312139	85312149	+	1	NA	intron (NM_016910, intron 1 of 5)	intron (NM_016910, intron 1 of 5)	890	NM_016910	53892	Mm.45609	NM_016910	ENSMUSG00000020525	Ppm1d	AV338790|Wip1	protein phosphatase 1D magnesium-dependent, delta isoform	protein-coding
mm_79771.1	chr9	62838613	62838630	+	1	NA	promoter-TSS (NM_001033175)	promoter-TSS (NM_001033175)	-166	NM_001033175	76524	Mm.283636	NM_001033175	ENSMUSG00000032245	Cln6	1810065L06Rik|AW743417|D9Bwg1455e|nclf	ceroid-lipofuscinosis, neuronal 6	protein-coding
mm_125813.1	chr15	74932111	74932157	+	1	NA	Intergenic	RLTR6-int|LTR|ERV1	-22917	NM_001164039	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_158834.1	chrX	168419659	168419663	-	1	NA	intron (NM_001033330, intron 3 of 19)	intron (NM_001033330, intron 3 of 19)	157572	NM_001033330	333605	Mm.426168	NM_001033330	ENSMUSG00000049176	Frmpd4	Gm196|PKAP1|Pdzd10|Pdzk10|Preso1|preso	FERM and PDZ domain containing 4	protein-coding
mm_56415.1	chr6	97252458	97252486	-	1	NA	exon (NM_001081157, exon 1 of 3)	exon (NM_001081157, exon 1 of 3)	308	NM_001081157	320502	Mm.68163	NM_001081157	ENSMUSG00000044086	Lmod3	5430424A14Rik	leiomodin 3 (fetal)	protein-coding
mm_58206.1	chr6	143909137	143909147	-	1	NA	intron (NM_011444, intron 8 of 14)	intron (NM_011444, intron 8 of 14)	37964	NM_001347506	20678	Mm.1752	NM_011444	ENSMUSG00000041540	Sox5	A730017D01Rik|AI528773	SRY (sex determining region Y)-box 5	protein-coding
mm_107747.1	chr12	59013380	59013398	+	1	NA	promoter-TSS (NM_025656)	promoter-TSS (NM_025656)	-2	NM_025656	66603	Mm.35353	NM_025656	ENSMUSG00000060121	Gemin2	Sip1|gemin-2	gem (nuclear organelle) associated protein 2	protein-coding
mm_26849.1	chr3	14769213	14769219	-	1	NA	intron (NM_009799, intron 6 of 7)	intron (NM_009799, intron 6 of 7)	9244	NM_001083957	12346	Mm.273195	NM_009799	ENSMUSG00000027556	Car1	AW555628|Ca1|Car-1	carbonic anhydrase 1	protein-coding
mm_68538.1	chr7	113564962	113564969	-	1	NA	promoter-TSS (NR_126544)	promoter-TSS (NR_126544)	22	NR_126544	69295	Mm.396150	NR_126544	ENSMUSG00000084984	Far1os	1700006P19Rik	fatty acyl CoA reductase 1, opposite strand	ncRNA
mm_85527.1	chr9	106465966	106465990	-	1	NA	promoter-TSS (NM_001159652)	promoter-TSS (NM_001159652)	-38	NM_001159652	436090	Mm.482905	NM_001159652	ENSMUSG00000091735	Gpr62	4933402E03Rik	G protein-coupled receptor 62	protein-coding
mm_144216.1	chr18	9745471	9745517	+	1	NA	intron (NM_130449, intron 2 of 9)	L1_Mur2|LINE|L1	37846	NM_130449	140792	Mm.218571	NM_130449	ENSMUSG00000036103	Colec12	CL-P1|SRCL|Scara4	collectin sub-family member 12	protein-coding
mm_73500.1	chr8	107205368	107205374	+	1	NA	Intergenic	Intergenic	-50793	NR_039557	100628577		NR_039557	ENSMUSG00000093061	Mir5098	mmu-mir-5098|mu-mir-5098	microRNA 5098	ncRNA
mm_127585.1	chr15	102328516	102328555	+	1	NA	exon (NM_027044, exon 4 of 6)	exon (NM_027044, exon 4 of 6)	2419	NM_027044	56612	Mm.158264	NM_020031	ENSMUSG00000001289	Pfdn5	1190001O17Rik|1700010A06Rik|D15Ertd697e|Eig1|MM-1	prefoldin 5	protein-coding
mm_77319.1	chr8	118309057	118309060	-	1	NA	intron (NM_019707, intron 1 of 13)	MER20|DNA|hAT-Charlie	25447	NM_019707	12554	Mm.334841	NM_019707	ENSMUSG00000031841	Cdh13	4932416G01Rik|Cdht|Tcad	cadherin 13	protein-coding
mm_19964.1	chr2	117965890	117965932	-	1	NA	intron (NR_126479, intron 8 of 9)	intron (NR_126479, intron 8 of 9)	143983	NR_040631	73938	Mm.399107	NR_040631	ENSMUSG00000086221	4930412B13Rik	-	RIKEN cDNA 4930412B13 gene	ncRNA
mm_31834.1	chr4	70625174	70625202	+	1	NA	Intergenic	RMER1C|Other|Other	-90260	NM_172694	230316	Mm.251188	NM_172694	ENSMUSG00000039270	Megf9	4933405H16Rik|9630025C07|Egfl5|mKIAA0818	multiple EGF-like-domains 9	protein-coding
mm_89315.1	chr10	87929096	87929145	+	1	NA	intron (NM_001111274, intron 4 of 4)	intron (NM_001111274, intron 4 of 4)	-37551	NR_000040	22172	Mm.391420	NR_000040		Tyms-ps	-	thymidylate synthase, pseudogene	pseudo
mm_138349.1	chr17	34934060	34934079	+	1	NA	exon (NM_010893, exon 4 of 6)	exon (NM_010893, exon 4 of 6)	2816	NM_010893	18010	Mm.8856	NM_010893	ENSMUSG00000007038	Neu1	AA407268|AA407316|Aglp|Apl|Bat-7|Bat7|G9|Map-2|Neu|Neu-1	neuraminidase 1	protein-coding
mm_145869.1	chr18	65464116	65464119	+	1	NA	intron (NM_172833, intron 11 of 15)	intron (NM_172833, intron 11 of 15)	33120	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_7205.1	chr1	93071013	93071021	-	1	NA	intron (NM_001294150, intron 9 of 46)	MTEa|LTR|ERVL-MaLR	11463	NM_001294150	16560	Mm.276408	NM_008440	ENSMUSG00000014602	Kif1a	ATSV|C630002N23Rik|Gm1626|Kns1	kinesin family member 1A	protein-coding
mm_146975.1	chr18	33464366	33464386	-	1	NA	promoter-TSS (NM_001267717)	promoter-TSS (NM_001267717)	213	NR_045415	433171	Mm.353332	NR_045415		Gm10549	ENSMUSG00000073610	predicted gene 10549	ncRNA
mm_71635.1	chr8	57488067	57488097	+	1	NA	promoter-TSS (NM_021788)	promoter-TSS (NM_021788)	119	NR_126555	78353	Mm.426240	NR_126553	ENSMUSG00000096917	2500002B13Rik	-	RIKEN cDNA 2500002B13 gene	ncRNA
mm_37175.1	chr4	117251774	117251807	-	1	NA	promoter-TSS (NM_001285816)	promoter-TSS (NM_001285816)	127	NM_001145637	381544	Mm.23504	NM_001033774	ENSMUSG00000060268	Gm1661	Gm1662|Ncrna00082	predicted gene 1661	protein-coding
mm_70868.1	chr8	25017253	25017305	+	1	NA	promoter-TSS (NM_007404)	promoter-TSS (NM_007404)	68	NM_027194	69742	Mm.28626	NM_027194	ENSMUSG00000031556	Tm2d2	2410018G23Rik|Blp1	TM2 domain containing 2	protein-coding
mm_119169.1	chr14	32085805	32085865	+	1	NA	promoter-TSS (NM_001284346)	promoter-TSS (NM_001284346)	107	NM_145460	218885	Mm.202257	NM_145460	ENSMUSG00000021906	Oxnad1	2410002F01Rik|AW492292|BC019806	oxidoreductase NAD-binding domain containing 1	protein-coding
mm_2711.1	chr1	128104135	128104151	+	1	NA	intron (NM_181750, intron 1 of 26)	intron (NM_181750, intron 1 of 26)	837	NM_181750	226412	Mm.221041	NM_181750	ENSMUSG00000056211	R3hdm1	R3hdm	R3H domain containing 1	protein-coding
mm_108876.1	chr12	99647207	99647208	+	1	NA	Intergenic	RLTR50A|LTR|ERVK	-19233	NR_045288	73457	Mm.383439	NR_045288	ENSMUSG00000100211	1700064M15Rik	-	RIKEN cDNA 1700064M15 gene	ncRNA
mm_152695.1	chr19	17125429	17125479	-	1	NA	exon (NM_181348, exon 9 of 20)	exon (NM_181348, exon 9 of 20)	169336	NM_181348	353211	Mm.257354	NM_181348	ENSMUSG00000039126	Prune2	6330414G02Rik|A230083H22Rik|A330102H22Rik|Bmcc1|mKIAA0367	prune homolog 2	protein-coding
mm_8755.1	chr1	160309159	160309178	-	1	NA	intron (NM_001038621, intron 2 of 8)	intron (NM_001038621, intron 2 of 8)	-13196	NR_035448	100316784		NR_035448	ENSMUSG00000089204	Mir1927	mmu-mir-1927	microRNA 1927	ncRNA
mm_12444.1	chr2	71084170	71084180	+	1	NA	TTS (NM_001165982)	TTS (NM_001165982)	28431	NM_001165980	75763	Mm.281668	NM_198005	ENSMUSG00000041966	Dcaf17	2810055O12Rik|4833418A01Rik|A030004A10Rik|A930009G19Rik|AI448937	DDB1 and CUL4 associated factor 17	protein-coding
mm_122727.1	chr14	52316202	52316253	-	1	NA	promoter-TSS (NM_001244916)	promoter-TSS (NM_001244916)	96	NM_001244916	50524	Mm.39487	NM_015772	ENSMUSG00000049532	Sall2	AI225809|AW559097|Msal-2|Sal-2|mKIAA0360|p150(Sal2)	sal-like 2 (Drosophila)	protein-coding
mm_172342.1	chr7	111028978	111028979	+	1	NA	promoter-TSS (NM_009431)	promoter-TSS (NM_009431)	27	NM_009431	22083	Mm.255858	NM_009431	ENSMUSG00000005609	Ctr9	AA409336|Sh2bp1|Tsbp|Tsp|mKIAA0155	CTR9 homolog, Paf1/RNA polymerase II complex component	protein-coding
mm_99517.1	chr11	103133172	103133180	+	1	NA	promoter-TSS (NM_027658)	promoter-TSS (NM_027658)	-163	NM_001130516	71059	Mm.273871	NM_027658	ENSMUSG00000043372	Hexim2	4933402L21Rik	hexamethylene bis-acetamide inducible 2	protein-coding
mm_63650.1	chr7	128695601	128695612	+	1	NA	TTS (NM_145955)	TTS (NM_145955)	6736	NM_001346517	101490	Mm.490344	NM_178641	ENSMUSG00000042105	Inpp5f	5830435P03Rik|AI115354|AW561896|SAC2|cI-27|hSAC2|mKIAA0966	inositol polyphosphate-5-phosphatase F	protein-coding
mm_43310.1	chr5	134858416	134858418	+	1	NA	Intergenic	Intergenic	48316	NM_029681	76629	Mm.159750	NM_029681	ENSMUSG00000040576	Wbscr28	1700111I05Rik	Williams-Beuren syndrome chromosome region 28 (human)	protein-coding
mm_30732.1	chr4	13797060	13797064	+	1	NA	intron (NM_009822, intron 1 of 10)	intron (NM_009822, intron 1 of 10)	12280	NM_009822	12395	Mm.4909	NM_009822	ENSMUSG00000006586	Runx1t1	Cbfa2t1h|ETO|MTG8	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	protein-coding
mm_150250.1	chr19	34101072	34101085	+	1	NA	intron (NM_023903, intron 1 of 9)	intron (NM_023903, intron 1 of 9)	135	NM_023903	78753	Mm.195937	NM_023903	ENSMUSG00000056078	Lipm	4632427C23Rik|AW227514|Lipl3	lipase, family member M	protein-coding
mm_42006.1	chr5	108001206	108001220	+	1	NA	Intergenic	Intergenic	-14136	NM_026062	67266	Mm.277897	NM_026062	ENSMUSG00000029270	Fam69a	2900024C23Rik|AI315274	family with sequence similarity 69, member A	protein-coding
mm_168811.1	chr12	21417086	21417103	-	1	NA	5' UTR (NM_011739, exon 1 of 5)	5' UTR (NM_011739, exon 1 of 5)	342	NM_011739	22630	Mm.289630	NM_011739	ENSMUSG00000076432	Ywhaq	2700028P07Rik|AA409740|AU021156|R74690	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide	protein-coding
mm_128820.1	chr15	67128896	67128896	-	1	NA	intron (NM_009177, intron 2 of 8)	intron (NM_009177, intron 2 of 8)	47986	NM_009177	20442	Mm.248334	NM_009177	ENSMUSG00000013846	St3gal1	5330418N22Rik|AI467004|ST3GalI|Siat4|Siat4a|St3gal-1	ST3 beta-galactoside alpha-2,3-sialyltransferase 1	protein-coding
mm_129131.1	chr15	76195692	76195706	-	1	NA	promoter-TSS (NM_201394)	promoter-TSS (NM_201394)	11	NM_201394	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
mm_149405.1	chr19	11392733	11392744	+	1	NA	exon (NM_001310331, exon 7 of 7)	exon (NM_001310331, exon 7 of 7)	-14923	NM_029499	64380	Mm.440715	NM_029499	ENSMUSG00000024675	Ms4a4c	5830413L19Rik|AI449185|Ms4a9	membrane-spanning 4-domains, subfamily A, member 4C	protein-coding
mm_21997.1	chr2	167698014	167698034	-	1	NA	TTS (NR_015500)	TTS (NR_015500)	6847	NR_015500	329562	Mm.123101	NM_177851	ENSMUSG00000006462	A530013C23Rik	-	RIKEN cDNA A530013C23 gene	ncRNA
mm_37757.1	chr4	129662443	129662485	-	1	NA	intron (NM_008468, intron 1 of 13)	intron (NM_008468, intron 1 of 13)	10303	NM_008468	16650	Mm.202358	NM_008468	ENSMUSG00000003731	Kpna6	IPOA7|Kpna5|NPI-2	karyopherin (importin) alpha 6	protein-coding
mm_75458.1	chr8	47714164	47714170	-	1	NA	promoter-TSS (NM_172407)	promoter-TSS (NM_172407)	-236	NM_172407	70925	Mm.393807	NM_172407	ENSMUSG00000038069	Cdkn2aip	4921511I16Rik|AW208986|CARF	CDKN2A interacting protein	protein-coding
mm_66308.1	chr7	39447224	39447225	-	1	NA	Intergenic	MT2B2|LTR|ERVL	-2294	NM_001243021	233147	Mm.148946	NM_001243021	ENSMUSG00000030424	Zfp939	9430025M13Rik	zinc finger protein 939	protein-coding
mm_74947.1	chr8	25976646	25976652	-	1	NA	promoter-TSS (NM_029884)	promoter-TSS (NM_029884)	95	NM_029884	52120	Mm.28326	NM_029884	ENSMUSG00000037260	Hgsnat	9430010M12Rik|AW208455|D8Ertd354e|Tmem76	heparan-alpha-glucosaminide N-acetyltransferase	protein-coding
mm_44744.1	chr5	31201933	31201948	-	1	NA	TTS (NM_008014)	TTS (NM_008014)	102	NM_001177901	101023	Mm.45033	NM_175311	ENSMUSG00000043059	Zfp513	AW990386|D430028M17Rik|Znf513	zinc finger protein 513	protein-coding
mm_75680.1	chr8	68061374	68061376	-	1	NA	Intergenic	Intergenic	-86801	NM_177698	234353	Mm.32525	NM_027626	ENSMUSG00000030465	Psd3	4931420C21Rik|AI661273|BC003498|D430018P08|EFA6D	pleckstrin and Sec7 domain containing 3	protein-coding
mm_140458.1	chr17	90036896	90036901	+	1	NA	3' UTR (NM_001347419, exon 3 of 3)	3' UTR (NM_001347419, exon 3 of 3)	51470	NM_001346962	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_12393.1	chr2	70039115	70039125	+	1	NA	promoter-TSS (NM_177376)	promoter-TSS (NM_177376)	-6	NM_177376	329421	Mm.99648	NM_177376	ENSMUSG00000042064	Myo3b	A430065P19Rik	myosin IIIB	protein-coding
mm_162085.1	chrX	35404218	35404218	+	1	NA	promoter-TSS (NM_001099325).6	promoter-TSS (NM_001099325).6	0	NM_001099325	100042109	Mm.432195	NM_001099325	ENSMUSG00000073257	Gm10488	ENSMUSG00000073257	predicted gene 10488	protein-coding
mm_132962.1	chr16	50526214	50526226	+	1	NA	promoter-TSS (NR_040380)	promoter-TSS (NR_040380)	-25	NR_040380	619312	Mm.427671	NR_040379		G730013B05Rik	linc-Cblb|linc1610	RIKEN cDNA G730013B05 gene	ncRNA
mm_143759.1	chr17	81620463	81620466	-	1	NA	intron (NR_104580, intron 2 of 8)	intron (NR_104580, intron 2 of 8)	117923	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_102949.1	chr11	69617880	69617926	-	1	NA	promoter-TSS (NM_011367)	promoter-TSS (NM_011367)	2	NM_011367	20415	Mm.1431	NM_011367	ENSMUSG00000005202	Shbg	ABP	sex hormone binding globulin	protein-coding
mm_142921.1	chr17	53824109	53824137	-	1	NA	Intergenic	Intergenic	21835	NM_026935	69083	Mm.19320	NM_026935	ENSMUSG00000023122	Sult1c2	1810008N17Rik|ST1C1|ST1C2|Sult1c1	sulfotransferase family, cytosolic, 1C, member 2	protein-coding
mm_148209.1	chr18	80151468	80151517	-	1	NA	promoter-TSS (NM_175028)	promoter-TSS (NM_175028)	-10	NM_175028	240442	Mm.26594	NM_175028	ENSMUSG00000053950	Adnp2	8430420L05Rik|BC024969|Kiaa0863|Zfp508|mKIAA0863	ADNP homeobox 2	protein-coding
mm_157256.1	chrX	19153648	19153660	-	1	NA	Intergenic	Intergenic	-6683	NR_029807	723828		NR_029807	ENSMUSG00000065471	Mir222	Mirn222|mir-222|mmu-mir-222	microRNA 222	ncRNA
mm_127794.1	chr15	3583192	3583241	-	1	NA	5' UTR (NM_010284, exon 1 of 11)	5' UTR (NM_010284, exon 1 of 11)	136	NM_001048178	14600	Mm.3986	NM_010284	ENSMUSG00000055737	Ghr	GHBP|GHR/BP	growth hormone receptor	protein-coding
mm_86595.1	chr10	13130317	13130337	+	1	NA	3' UTR (NM_009538, exon 6 of 6)	3' UTR (NM_009538, exon 6 of 6)	39482	NR_131912	338438		NR_131912		Hymai	-	hydatidiform mole associated and imprinted transcript	ncRNA
mm_115580.1	chr13	11615246	11615255	-	1	NA	intron (NM_023868, intron 84 of 104)	intron (NM_023868, intron 84 of 104)	93198	NR_027813	664793	Mm.410565	NR_027813		Zp4-ps	EG664793|Zp4|Zpb	zona pellucida glycoprotein 4, pseudogene	pseudo
mm_4025.1	chr1	165766109	165766151	+	1	NA	intron (NM_011804, intron 1 of 3)	intron (NM_011804, intron 1 of 3)	2350	NM_011804	433375	Mm.294885	NM_011804	ENSMUSG00000040713	Creg1	AA755314|Creg	cellular repressor of E1A-stimulated genes 1	protein-coding
mm_62647.1	chr7	107681680	107681691	+	1	NA	intron (NM_001163557, intron 3 of 25)	intron (NM_001163557, intron 3 of 25)	74841	NM_001163557	19024	Mm.2817	NM_008905	ENSMUSG00000036528	Ppfibp2	Cclp1	PTPRF interacting protein, binding protein 2 (liprin beta 2)	protein-coding
mm_145377.1	chr18	56746543	56746545	+	1	NA	intron (NM_010721, intron 8 of 10)	intron (NM_010721, intron 8 of 10)	38731	NM_010721	16906	Mm.4105	NM_010721	ENSMUSG00000024590	Lmnb1	-	lamin B1	protein-coding
mm_98443.1	chr11	94942380	94942410	+	1	NA	exon (NM_007742, exon 19 of 51)	exon (NM_007742, exon 19 of 51)	6171	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_126840.1	chr15	89059762	89059782	+	1	NA	promoter-TSS (NM_001002005)	promoter-TSS (NM_001002005)	46	NM_001002005	406218	Mm.483059	NM_001002005	ENSMUSG00000058441	Panx2	-	pannexin 2	protein-coding
mm_122548.1	chr14	48665099	48665115	-	1	NA	promoter-TSS (NM_001286483)	promoter-TSS (NM_001286483)	2	NM_001286483	18424	Mm.134516	NM_144841	ENSMUSG00000021848	Otx2	E130306E05Rik	orthodenticle homeobox 2	protein-coding
mm_82754.1	chr9	26860650	26860697	-	1	NA	5' UTR (NM_001113323, exon 1 of 20)	5' UTR (NM_001113323, exon 1 of 20)	150	NM_001113323	70893	Mm.78118	NM_001113323	ENSMUSG00000031966	Glb1l3	4921509F24Rik	galactosidase, beta 1 like 3	protein-coding
mm_76340.1	chr8	84721721	84721731	-	1	NA	exon (NM_010906, exon 7 of 9)	exon (NM_010906, exon 7 of 9)	20269	NM_008535	17095	Mm.4925	NM_008535	ENSMUSG00000034041	Lyl1	Lyl-1|bHLHa18	lymphoblastomic leukemia 1	protein-coding
mm_103226.1	chr11	70669962	70670002	-	1	NA	promoter-TSS (NM_001167669)	promoter-TSS (NM_001167669)	-566	NM_001167669	216873	Mm.432524	NM_172561	ENSMUSG00000018287	Spag7	5730443G10|ACRP|FSA-1|Fsa1l	sperm associated antigen 7	protein-coding
mm_9211.1	chr1	171229916	171229930	-	1	NA	exon (NM_010185, exon 5 of 5)	exon (NM_010185, exon 5 of 5)	4426	NM_010185	14127	Mm.22673	NM_010185	ENSMUSG00000058715	Fcer1g	AI573376|CD23|FcR-gamma|FcR[g]|FcRgamma|Fce1g|FcepsilonRI|Ly-50	Fc receptor, IgE, high affinity I, gamma polypeptide	protein-coding
mm_61705.1	chr7	81213568	81213632	+	1	NA	promoter-TSS (NM_008803)	promoter-TSS (NM_008803)	-204	NM_008803	18584	Mm.371577	NM_008803	ENSMUSG00000025584	Pde8a	AI551852|Pde8	phosphodiesterase 8A	protein-coding
mm_65685.1	chr7	28367661	28367665	-	1	NA	exon (NM_001083912, exon 9 of 19)	exon (NM_001083912, exon 9 of 19)	4999	NM_138752	101497	Mm.235700	NM_138752	ENSMUSG00000037552	Plekhg2	AI194308|Clg|Cslg	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	protein-coding
mm_114776.1	chr13	88821733	88821739	+	1	NA	5' UTR (NM_001037987, exon 1 of 11)	5' UTR (NM_001037987, exon 1 of 11)	264	NM_001037987	13612	Mm.125580	NM_010103	ENSMUSG00000034488	Edil3	Del-1|Del1	EGF-like repeats and discoidin I-like domains 3	protein-coding
mm_14770.1	chr2	145786123	145786152	+	1	NA	promoter-TSS (NM_028724)	promoter-TSS (NM_028724)	21	NM_028724	74030	Mm.228799	NM_028724	ENSMUSG00000001768	Rin2	2010003K16Rik|4632403N06Rik|AW821980|RASSF4	Ras and Rab interactor 2	protein-coding
mm_160636.1	chr9	107753244	107753244	-	1	NA	intron (NM_148930, intron 10 of 24)	(GAAA)n|Simple_repeat|Simple_repeat	17758	NM_148930	83486	Mm.259197	NM_148930	ENSMUSG00000032580	Rbm5	D030069N10Rik	RNA binding motif protein 5	protein-coding
mm_55750.1	chr6	78372891	78372905	-	1	NA	exon (NM_011036, exon 5 of 6)	exon (NM_011036, exon 5 of 6)	2013	NM_011036	18489	Mm.2553	NM_011036	ENSMUSG00000071356	Reg3b	HIP|PAP1|Pap|REG-III	regenerating islet-derived 3 beta	protein-coding
mm_117765.1	chr13	96435957	96435967	-	1	NA	exon (NM_001042714, exon 8 of 14)	exon (NM_001042714, exon 8 of 14)	35198	NM_001042714	271144	Mm.470057	NM_001042714	ENSMUSG00000047117	Ankdd1b	9330128J19Rik	ankyrin repeat and death domain containing 1B	protein-coding
mm_3554.1	chr1	150421712	150421722	+	1	NA	exon (NM_133780, exon 23 of 52)	exon (NM_133780, exon 23 of 52)	-28662	NM_145511	226499	Mm.222093	NM_145511	ENSMUSG00000006010	BC003331	1810053E15Rik|Odr4|odr-4	cDNA sequence BC003331	protein-coding
mm_19085.1	chr2	78973050	78973057	-	1	NA	Intergenic	Intergenic	104006	NM_009454	22193	Mm.1485	NM_009454	ENSMUSG00000027011	Ube2e3	Ubce4|ubcM2	ubiquitin-conjugating enzyme E2E 3	protein-coding
mm_64959.1	chr7	16614549	16614606	-	1	NA	5' UTR (NM_172739, exon 1 of 7)	5' UTR (NM_172739, exon 1 of 7)	416	NM_172739	232906	Mm.28646	NM_172739	ENSMUSG00000058230	Arhgap35	6430596G11Rik|AI841135|Grlf1|mKIAA1722|p190A|p190RhoGAP	Rho GTPase activating protein 35	protein-coding
mm_20226.1	chr2	125782816	125782826	-	1	NA	promoter-TSS (NM_177608)	promoter-TSS (NM_177608)	49	NM_177608	70354	Mm.138091	NM_133725	ENSMUSG00000035093	Secisbp2l	3110001I20Rik|AI504340|C630011I23	SECIS binding protein 2-like	protein-coding
mm_36480.1	chr4	82859831	82859855	-	1	NA	promoter-TSS (NM_026647)	promoter-TSS (NM_026647)	-182	NM_026647	68268	Mm.32047	NM_026647	ENSMUSG00000028403	Zdhhc21	9130404H11Rik|AL024349|D130004H04Rik|dep	zinc finger, DHHC domain containing 21	protein-coding
mm_95027.1	chr11	32024820	32024835	+	1	NA	intron (NM_001290680, intron 3 of 4)	intron (NM_001290680, intron 3 of 4)	23550	NM_001290681	18197	Mm.3304	NM_008741	ENSMUSG00000020297	Nsg2	-	neuron specific gene family member 2	protein-coding
mm_64922.1	chr7	16257526	16257528	-	1	NA	intron (NM_007577, intron 2 of 2)	B2_Mm2|SINE|B2	1811	NM_001173550	12273	Mm.247623	NM_007577	ENSMUSG00000049130	C5ar1	C5aR|C5r1|Cd88|D7Msu1	complement component 5a receptor 1	protein-coding
mm_160611.1	chr9	81632800	81632800	-	1	NA	promoter-TSS (NM_010482)	promoter-TSS (NM_010482)	-248	NM_010482	15551	Mm.445308	NM_010482	ENSMUSG00000049511	Htr1b	-	5-hydroxytryptamine (serotonin) receptor 1B	protein-coding
mm_157662.1	chrX	57503734	57503741	-	1	NA	promoter-TSS (NM_001033360)	promoter-TSS (NM_001033360)	20	NM_001033360	245424	Mm.336070	NM_001033360	ENSMUSG00000036357	Gpr101	GPCR6|Gm365	G protein-coupled receptor 101	protein-coding
mm_141754.1	chr17	34261631	34261644	-	1	NA	Intergenic	Intergenic	-1590	NM_207105	14961	Mm.254067	NM_207105	ENSMUSG00000073421	H2-Ab1	AI845868|Abeta|H-2Ab|H2-Ab|I-Abeta|IAb|Ia-2|Ia2|Rmcs1	histocompatibility 2, class II antigen A, beta 1	protein-coding
mm_142665.1	chr17	47728797	47728801	-	1	NA	exon (NM_025973, exon 2 of 9)	exon (NM_025973, exon 2 of 9)	1957	NM_025973	109820	Mm.22957	NM_025973	ENSMUSG00000023987	Pgc	2210410L06Rik|Upg-1|Upg1	progastricsin (pepsinogen C)	protein-coding
mm_124641.1	chr15	4727176	4727201	+	1	NA	promoter-TSS (NM_016704)	promoter-TSS (NM_016704)	-22	NM_016704	12274	Mm.20247	NM_016704	ENSMUSG00000022181	C6	AW111623	complement component 6	protein-coding
mm_36033.1	chr4	57143679	57143732	-	1	NA	promoter-TSS (NM_019427)	promoter-TSS (NM_019427)	-549	NM_019427	54357	Mm.28217	NM_019427	ENSMUSG00000028434	Epb41l4b	6430543G08Rik|AA589614|AU021054|BB007528|D4Ertd346e|Ehm2|Epb4.1l4b|Lulu2	erythrocyte membrane protein band 4.1 like 4b	protein-coding
mm_48958.1	chr6	4540908	4540922	+	1	NA	3' UTR (NM_007743, exon 52 of 52)	3' UTR (NM_007743, exon 52 of 52)	35297	NM_007743	12843	Mm.277792	NM_007743	ENSMUSG00000029661	Col1a2	AA960264|AI325291|Col1a-2|Cola-2|Cola2|oim	collagen, type I, alpha 2	protein-coding
mm_162000.1	chr19	39992424	39992424	+	1	NA	promoter-TSS (NM_010001)	promoter-TSS (NM_010001)	0	NM_010001	13096	Mm.38963	NM_010001	ENSMUSG00000042248	Cyp2c37	-	cytochrome P450, family 2. subfamily c, polypeptide 37	protein-coding
mm_154708.1	chrX	8276772	8276779	+	1	NA	exon (NM_172479, exon 10 of 16)	exon (NM_172479, exon 10 of 16)	5394	NM_172479	209837	Mm.6055	NM_172479	ENSMUSG00000031170	Slc38a5	C81234|E330031E14|JM24|SN2	solute carrier family 38, member 5	protein-coding
mm_74470.1	chr8	4258249	4258279	-	1	NA	3' UTR (NM_183315, exon 2 of 2)	3' UTR (NM_183315, exon 2 of 2)	1010	NM_183315	330695	Mm.34210	NM_183315	ENSMUSG00000048644	Ctxn1	BC028881|Ctxn	cortexin 1	protein-coding
mm_90087.1	chr10	116914149	116914181	+	1	NA	exon (NM_001003950, exon 7 of 10)	exon (NM_001003950, exon 7 of 10)	-17286	NM_001033333	237558	Mm.336386	NM_001033333	ENSMUSG00000034057	Myrfl	Gm239	myelin regulatory factor-like	protein-coding
mm_160183.1	chr7	47452141	47452141	-	1	NA	promoter-TSS (NM_001172588)	promoter-TSS (NM_001172588)	-2	NM_001172588	668727	Mm.431311	NM_001172588	ENSMUSG00000093973	Mrgpra2a	-	MAS-related GPR, member A2A	protein-coding
mm_29153.1	chr3	106001475	106001513	-	1	NA	promoter-TSS (NM_029604)	promoter-TSS (NM_029604)	3	NM_029604	100503311	Mm.386825	NM_029604	ENSMUSG00000010136	Pifo	1700027A23Rik	primary cilia formation	protein-coding
mm_108406.1	chr12	81663340	81663348	+	1	NA	intron (NM_001033149, intron 2 of 2)	intron (NM_001033149, intron 2 of 2)	32095	NM_001033149	69480	Mm.130002	NM_001033149	ENSMUSG00000042734	Ttc9	-	tetratricopeptide repeat domain 9	protein-coding
mm_58137.1	chr6	141778088	141778098	-	1	NA	Intergenic	Intergenic	78078	NM_030687	28250	Mm.255586	NM_030687	ENSMUSG00000030237	Slco1a4	AI785519|Oatp1a4|Oatp2|Slc21a5	solute carrier organic anion transporter family, member 1a4	protein-coding
mm_74410.1	chr8	3624570	3624577	-	1	NA	TTS (NM_001195244)	TTS (NM_001195244)	476	NM_001129804	18545	Mm.440882	NM_008790	ENSMUSG00000004630	Pcp2	L7|Pcp-2	Purkinje cell protein 2 (L7)	protein-coding
mm_119608.1	chr14	51104875	51104889	+	1	NA	exon (NM_201239, exon 2 of 2)	exon (NM_201239, exon 2 of 2)	8882	NM_201239	58809	Mm.202665	NM_021472	ENSMUSG00000021876	Rnase4	C730049F20Rik|Rab1	ribonuclease, RNase A family 4	protein-coding
mm_67982.1	chr7	100662377	100662395	-	1	NA	promoter-TSS (NM_001163182)	promoter-TSS (NM_001163182)	8	NM_013746	27276	Mm.491216	NM_013746	ENSMUSG00000030701	Plekhb1	AI315628|PHR1|Phret1|evt-1	pleckstrin homology domain containing, family B (evectins) member 1	protein-coding
mm_141241.1	chr17	27467514	27467524	-	1	NA	intron (NM_001013385, intron 2 of 8)	intron (NM_001013385, intron 2 of 8)	36014	NM_001013385	268934	Mm.358940	NM_001013385	ENSMUSG00000063239	Grm4	Gprc1d|mGluR4	glutamate receptor, metabotropic 4	protein-coding
mm_2824.1	chr1	131139948	131139962	+	1	NA	Intergenic	B3A|SINE|B2	-1721	NM_145508	226419	Mm.39299	NM_145508	ENSMUSG00000016526	Dyrk3	BC006704	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 3	protein-coding
mm_121107.1	chr14	101214429	101214430	+	1	NA	Intergenic	Intergenic	-14360	NM_029680	76627	Mm.31415	NM_029680	ENSMUSG00000042888	Prr30	1700110M21Rik	proline rich 30	protein-coding
mm_1710.1	chr1	75236528	75236548	+	1	NA	promoter-TSS (NM_001159885)	promoter-TSS (NM_001159885)	115	NM_001159883	56812	Mm.489660	NM_020266	ENSMUSG00000026203	Dnajb2	2700059H22Rik|Dnajb10|Hsj1|mDj8	DnaJ heat shock protein family (Hsp40) member B2	protein-coding
mm_21430.1	chr2	158360568	158360610	-	1	NA	non-coding (NR_015463, exon 3 of 6)	non-coding (NR_015463, exon 3 of 6)	920	NR_015463	68108	Mm.119198	NR_015463		Snhg17	9430008C03Rik	small nucleolar RNA host gene 17	ncRNA
mm_24993.1	chr3	97159011	97159037	+	1	NA	5' UTR (NM_019800, exon 1 of 10)	5' UTR (NM_019800, exon 1 of 10)	247	NM_019800	66659	Mm.101368	NM_019800	ENSMUSG00000028093	Acp6	5730559A09Rik|ACPL1|AU022842|mPACPL1	acid phosphatase 6, lysophosphatidic	protein-coding
mm_137850.1	chr17	31067350	31067358	+	1	NA	intron (NM_009593, intron 2 of 14)	intron (NM_009593, intron 2 of 14)	9660	NM_009593	11307	Mm.15691	NM_009593	ENSMUSG00000024030	Abcg1	AW413978|Abc8|White	ATP-binding cassette, sub-family G (WHITE), member 1	protein-coding
mm_59952.1	chr7	30427070	30427076	+	1	NA	exon (NM_172142, exon 9 of 11)	exon (NM_172142, exon 9 of 11)	3769	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_31021.1	chr4	40727102	40727105	+	1	NA	intron (NM_008298, intron 4 of 8)	AT_rich|Low_complexity|Low_complexity	4173	NM_001164672	15502	Mm.27897	NM_008298	ENSMUSG00000028410	Dnaja1	HSJ-2|Hsj2|Nedd7	DnaJ heat shock protein family (Hsp40) member A1	protein-coding
mm_46137.1	chr5	92964771	92964787	-	1	NA	3' UTR (NM_001077596, exon 10 of 10)	3' UTR (NM_001077596, exon 10 of 10)	66786	NM_001077596	27428	Mm.46014	NM_015756	ENSMUSG00000029381	Shroom3	AL022960|D5Ertd287e|Shrm|Shrm3	shroom family member 3	protein-coding
mm_147599.1	chr18	56733848	56733856	-	1	NA	intron (NM_010721, intron 5 of 10)	PB1D9|SINE|Alu	26039	NM_010721	16906	Mm.4105	NM_010721	ENSMUSG00000024590	Lmnb1	-	lamin B1	protein-coding
mm_119230.1	chr14	33317050	33317060	+	1	NA	intron (NM_153800, intron 4 of 10)	intron (NM_153800, intron 4 of 10)	93969	NM_001310452	26419	Mm.21495	NM_016700	ENSMUSG00000021936	Mapk8	AI849689|JNK|JNK1|Prkm8|SAPK1	mitogen-activated protein kinase 8	protein-coding
mm_135756.1	chr16	56021261	56021264	-	1	NA	intron (NM_001024622, intron 3 of 4)	AT_rich|Low_complexity|Low_complexity	8455	NM_001024622	76302	Mm.310642	NM_001024622	ENSMUSG00000071533	Pcnp	1110018D06Rik|AI647035	PEST proteolytic signal containing nuclear protein	protein-coding
mm_17823.1	chr2	33887384	33887400	-	1	NA	exon (NM_175184, exon 1 of 10)	exon (NM_175184, exon 1 of 10)	554	NM_175184	72543	Mm.254914	NM_175184	ENSMUSG00000038740	Mvb12b	2610200O14Rik|2610528K11Rik|AI414895|Fam125b	multivesicular body subunit 12B	protein-coding
mm_17303.1	chr2	26351988	26352053	-	1	NA	promoter-TSS (NM_001139504)	promoter-TSS (NM_001139504)	90	NM_026828	52838	Mm.31239	NM_026828	ENSMUSG00000075467	Dnlz	1110034G11Rik|D2Bwg1335e|HEP1	DNL-type zinc finger	protein-coding
mm_26069.1	chr3	136670077	136670186	+	1	NA	promoter-TSS (NM_001293622)	promoter-TSS (NM_001293622)	65	NM_001293622	19055	Mm.331389	NM_008913	ENSMUSG00000028161	Ppp3ca	2900074D19Rik|CN|Caln|Calna|CnA	protein phosphatase 3, catalytic subunit, alpha isoform	protein-coding
mm_132894.1	chr16	48843544	48843595	+	1	NA	exon (NM_020509, exon 3 of 4)	exon (NM_020509, exon 3 of 4)	1017	NM_020509	57262	Mm.441868	NM_020509	ENSMUSG00000061100	Retnla	1810019L16Rik|Fizz-1|Fizz1|HIMF|RELM-alpha|RELMa|RELMalpha|Xcp2	resistin like alpha	protein-coding
mm_120913.1	chr14	76312256	76312264	+	1	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	-102701	NM_001310646	21807	Mm.153272	NM_009366	ENSMUSG00000022010	Tsc22d1	AA589566|AW105905|Egr5|TSC-22|Tgfb1i4|Tsc|Tsc22	TSC22 domain family, member 1	protein-coding
mm_149112.1	chr19	8967000	8967019	+	1	NA	promoter-TSS (NM_026007)	promoter-TSS (NM_026007)	-32	NM_026007	67160	Mm.247762	NM_026007	ENSMUSG00000071644	Eef1g	2610301D06Rik|AA407312|EF1G	eukaryotic translation elongation factor 1 gamma	protein-coding
mm_153223.1	chr19	34877844	34877861	-	1	NA	promoter-TSS (NM_023792)	promoter-TSS (NM_023792)	65	NM_023792	75735	Mm.24742	NM_023792	ENSMUSG00000033610	Pank1	Pank|Pank1b	pantothenate kinase 1	protein-coding
mm_162265.1	chr1	5083522	5083530	+	1	NA	intron (NM_001310442, intron 1 of 12)	CpG	440	NM_001310442	108664	Mm.27082	NM_133826	ENSMUSG00000033793	Atp6v1h	0710001F19Rik|AU022349|CGI-11|SFD|SFDalpha|SFDbeta|VMA13	ATPase, H+ transporting, lysosomal V1 subunit H	protein-coding
mm_112298.1	chr12	114647055	114647057	-	1	NA	Intergenic	Intergenic	-133362	NR_106063	102465664		NR_106063	ENSMUSG00000098357	Mir7094-2	Gm27508|mmu-mir-7094-2	microRNA 7094-2	ncRNA
mm_30386.1	chr3	152247187	152247197	-	1	NA	exon (NM_199465, exon 8 of 13)	exon (NM_199465, exon 8 of 13)	19128	NM_199465	68810	Mm.200188	NM_199465	ENSMUSG00000039103	Nexn	1110046H09Rik|AA553326|NELIN	nexilin	protein-coding
mm_102514.1	chr11	60808844	60808875	-	1	NA	intron (NM_009171, intron 1 of 11)	intron (NM_009171, intron 1 of 11)	2406	NM_009171	20425	Mm.364956	NM_009171	ENSMUSG00000020534	Shmt1	AI324848|AI385541|C81125|Shmt|mshmt|mshmt1|mshmt2	serine hydroxymethyltransferase 1 (soluble)	protein-coding
mm_120786.1	chr14	74732303	74732374	+	1	NA	promoter-TSS (NM_016903)	promoter-TSS (NM_016903)	41	NM_016903	13885	Mm.38055	NM_016903	ENSMUSG00000021996	Esd	Es-10|Es10|FGH|sid478	esterase D/formylglutathione hydrolase	protein-coding
mm_46593.1	chr5	107725988	107726014	-	1	NA	promoter-TSS (NM_001267621)	promoter-TSS (NM_001267621)	-196	NM_001267621	14581	Mm.2078	NM_010278	ENSMUSG00000029275	Gfi1	AW495828|Gfi-1|Pal-1|Pal1	growth factor independent 1	protein-coding
mm_29391.1	chr3	108904195	108904208	-	1	NA	exon (NM_025845, exon 6 of 6)	exon (NM_025845, exon 6 of 6)	7503	NM_025845	66921	Mm.51049	NM_025845	ENSMUSG00000027881	Prpf38b	1110021E09Rik|AU018955	PRP38 pre-mRNA processing factor 38 (yeast) domain containing B	protein-coding
mm_3964.1	chr1	164151720	164151732	+	1	NA	promoter-TSS (NM_007976)	promoter-TSS (NM_007976)	-109	NM_007976	14067	Mm.12900	NM_007976	ENSMUSG00000026579	F5	AI173222|Cf-5|Cf5	coagulation factor V	protein-coding
mm_21867.1	chr2	165900893	165900902	-	1	NA	Intergenic	Intergenic	-16059	NM_001252587	228880	Mm.227598	NM_027230	ENSMUSG00000039671	Zmynd8	1110013E22Rik|2010005I16Rik|3632413B07Rik|AI316811|AL024039|Prkcbp1|RACK7	zinc finger, MYND-type containing 8	protein-coding
mm_171132.1	chr3	148151751	148151751	-	1	NA	Intergenic	L1Md_T|LINE|L1	802884	NM_001081298	99633	Mm.9776	NM_001081298	ENSMUSG00000028184	Adgrl2	AI450192|CIRL-2|Gm619|Lec1|Lphh1|Lphn2|mKIAA0786	adhesion G protein-coupled receptor L2	protein-coding
mm_22767.1	chr3	20105031	20105042	+	1	NA	intron (NM_009210, intron 18 of 24)	ORR1B2|LTR|ERVL-MaLR	46745	NR_105047	20585	Mm.209650	NM_009210	ENSMUSG00000002428	Hltf	AF010600|BC057116|P113|Smarca3|Snf2l3	helicase-like transcription factor	protein-coding
mm_3033.1	chr1	133914638	133914669	+	1	NA	exon (NM_054077, exon 2 of 3)	exon (NM_054077, exon 2 of 3)	-6654	NM_001160420	269120	Mm.59985	NM_054076	ENSMUSG00000010311	Optc	-	opticin	protein-coding
mm_134252.1	chr16	13672632	13672646	-	1	NA	intron (NM_025976, intron 1 of 7)	intron (NM_025976, intron 1 of 7)	781	NM_025653	67118	Mm.223689	NM_025653	ENSMUSG00000022684	Bfar	3010001A07Rik|3110001I22Rik|AI666707|AW107665|Bar|Rnf47	bifunctional apoptosis regulator	protein-coding
mm_79401.1	chr9	54951105	54951126	+	1	NA	promoter-TSS (NM_145229)	promoter-TSS (NM_145229)	-161	NM_145229	246735	Mm.473773	NM_145229	ENSMUSG00000044820	AY074887	Mcpr1	cDNA sequence AY074887	protein-coding
mm_148161.1	chr18	77713917	77713973	-	1	NA	promoter-TSS (NM_178670)	promoter-TSS (NM_178670)	65	NM_178670	212163	Mm.23293	NM_178670	ENSMUSG00000047466	8030462N17Rik	Akd2|Ark2N	RIKEN cDNA 8030462N17 gene	protein-coding
mm_110569.1	chr12	56275735	56275766	-	1	NA	Intergenic	Intergenic	22507	NR_045048	100503961	Mm.136732	NR_045048		Gm19990	-	predicted gene, 19990	ncRNA
mm_110952.1	chr12	76709998	76710026	-	1	NA	5' UTR (NM_013675, exon 1 of 36)	5' UTR (NM_013675, exon 1 of 36)	535	NM_013675	20741	Mm.32881	NM_013675	ENSMUSG00000021061	Sptb	AI842465|D330027P03Rik|Gm1301|Spnb-1|Spnb1|ja|jaundiced|mKIAA4219	spectrin beta, erythrocytic	protein-coding
mm_113985.1	chr13	52582722	52582735	+	1	NA	promoter-TSS (NM_001198977)	promoter-TSS (NM_001198977)	-709	NM_001198977	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_23704.1	chr3	68784353	68784392	+	1	NA	Intergenic	Intergenic	-85214	NM_001167996	68725	Mm.45741	NM_001167996	ENSMUSG00000046999	1110032F04Rik	AI115547	RIKEN cDNA 1110032F04 gene	protein-coding
mm_38996.1	chr4	151154463	151154473	-	1	NA	intron (NM_001081557, intron 7 of 23)	intron (NM_001081557, intron 7 of 23)	64898	NM_001308446	105704528	Mm.415128	NM_001308446	ENSMUSG00000078491	Gm13090	OTTMUSG00000010356	predicted gene 13090	protein-coding
mm_128748.1	chr15	64383024	64383035	-	1	NA	promoter-TSS (NM_001276467)	promoter-TSS (NM_001276467)	-110	NM_010026	13196	Mm.277236	NM_010026	ENSMUSG00000022377	Asap1	AV239055|DEF-1|Ddef1|PAP|mKIAA1249|s19	ArfGAP with SH3 domain, ankyrin repeat and PH domain1	protein-coding
mm_129201.1	chr15	76511961	76511974	-	1	NA	promoter-TSS (NM_010046)	promoter-TSS (NM_010046)	-149	NM_010046	13350	Mm.22633	NM_010046	ENSMUSG00000022555	Dgat1	ARAT|C75990|D15Ertd23e|Dgat	diacylglycerol O-acyltransferase 1	protein-coding
mm_133350.1	chr16	84371131	84371151	+	1	NA	promoter-TSS (NR_040567)	promoter-TSS (NR_040567)	-2	NR_040567	75247	Mm.417813	NR_040567		4930553E22Rik	-	RIKEN cDNA 4930553E22 gene	ncRNA
mm_85125.1	chr9	95511858	95511892	-	1	NA	5' UTR (NM_001114977, exon 1 of 28)	5' UTR (NM_001114977, exon 1 of 28)	121	NM_026476	67958	Mm.292742	NM_026476	ENSMUSG00000032407	U2surp	2610101N10Rik|AU023006|Sr140	U2 snRNP-associated SURP domain containing	protein-coding
mm_56011.1	chr6	86516255	86516276	-	1	NA	Intergenic	MIR3|SINE|MIR	9900	NM_011865	23983	Mm.274146	NM_011865	ENSMUSG00000051695	Pcbp1	WBP17|[a]CP-1|alphaCP-1|hnRNP E1	poly(rC) binding protein 1	protein-coding
mm_44587.1	chr5	24908764	24908777	-	1	NA	promoter-TSS (NM_001170556)	promoter-TSS (NM_001170556)	-261	NM_001170555	108099	Mm.33649	NM_145401	ENSMUSG00000028944	Prkag2	2410051C13Rik|AAKG|AAKG2|AI854673|H91620p|WPWS	protein kinase, AMP-activated, gamma 2 non-catalytic subunit	protein-coding
mm_160237.1	chr7	103882069	103882069	-	1	NA	exon (NM_013618, exon 1 of 1)	exon (NM_013618, exon 1 of 1)	172	NM_013618	18367	Mm.445781	NM_013618	ENSMUSG00000058200	Olfr66	5'[b]1|5'beta1|MOR1-3|ORL532	olfactory receptor 66	protein-coding
mm_105444.1	chr11	104441741	104441795	-	1	NA	5' UTR (NM_001081045, exon 1 of 14)	5' UTR (NM_001081045, exon 1 of 14)	523	NM_001081045	76719	Mm.136418	NM_001081045	ENSMUSG00000018412	Kansl1	1700081L11Rik|9430041J06Rik|mKIAA1267	KAT8 regulatory NSL complex subunit 1	protein-coding
mm_130040.1	chr15	88982769	88982775	-	1	NA	promoter-TSS (NM_031260)	promoter-TSS (NM_031260)	-222	NM_031260	83456	Mm.358791	NM_031260	ENSMUSG00000015365	Mov10l1	CHAMP|Csm	Moloney leukemia virus 10-like 1	protein-coding
mm_23289.1	chr3	52069970	52069970	+	1	NA	intron (NM_001004176, intron 1 of 4)	intron (NM_001004176, intron 1 of 4)	35036	NM_001004176	433586	Mm.234972	NM_001004176	ENSMUSG00000061143	Maml3	AV234550|BC049812|Mam-2|mKIAA1816	mastermind like 3 (Drosophila)	protein-coding
mm_140789.1	chr17	18969028	18969060	-	1	NA	Intergenic	IAPLTR4|LTR|ERVK	54722	NM_001104549	627367	Mm.384131	NM_001104549	ENSMUSG00000091491	Vmn2r97	EG627367|Vn2r97	vomeronasal 2, receptor 97	protein-coding
mm_83722.1	chr9	50765939	50765943	-	1	NA	promoter-TSS (NM_001311073)	promoter-TSS (NM_001311073)	-8	NM_001311073	68721	Mm.171374	NM_023483	ENSMUSG00000037971	1110032A03Rik	4930500N06Rik|c11orf1	RIKEN cDNA 1110032A03 gene	protein-coding
mm_74171.1	chr8	123428411	123428420	+	1	NA	Intergenic	MuLV-int|LTR|ERV1	-14541	NM_001253784	23854	Mm.275127	NM_054046	ENSMUSG00000001482	Def8	AI449518|D8Ertd713e|DEF-8	differentially expressed in FDCP 8	protein-coding
mm_164867.1	chr18	56505799	56505803	+	1	NA	Intergenic	Intergenic	-32338	NR_106160	102465790		NR_106160	ENSMUSG00000099196	Mir1258	Gm27371|mmu-mir-1258	microRNA 1258	ncRNA
mm_149767.1	chr19	22994209	22994212	+	1	NA	Intergenic	Intergenic	-147016	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_57468.1	chr6	125231140	125231173	-	1	NA	promoter-TSS (NR_015604)	promoter-TSS (NR_015604)	-120	NR_015604	78668	Mm.10626	NR_015604	ENSMUSG00000030337	E130112N10Rik	5830448L21Rik|9530059J11Rik	RIKEN cDNA E130112N10 gene	ncRNA
mm_169207.1	chr13	66441361	66441380	+	1	NA	promoter-TSS (NM_001290196)	promoter-TSS (NM_001290196)	-252	NM_001290196	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
mm_115403.1	chr13	113989751	113989753	+	1	NA	intron (NM_172595, intron 4 of 4)	intron (NM_172595, intron 4 of 4)	161840	NR_045836	319803	Mm.386896	NM_177004		A430090L17Rik	-	RIKEN cDNA A430090L17 gene	ncRNA
mm_86539.1	chr10	8751901	8751903	+	1	NA	intron (NM_175155, intron 9 of 19)	ID_B1|SINE|B4	134168	NM_175155	70097	Mm.338275	NM_175155	ENSMUSG00000015305	Sash1	1100001C18Rik|2500002E12Rik|A330076K04Rik|mKIAA0790	SAM and SH3 domain containing 1	protein-coding
mm_3174.1	chr1	135729214	135729234	+	1	NA	promoter-TSS (NM_007791)	promoter-TSS (NM_007791)	27	NM_007791	13007	Mm.196484	NM_007791	ENSMUSG00000026421	Csrp1	AA408841|AA959891|AW545626|CRP1|Csrp	cysteine and glycine-rich protein 1	protein-coding
mm_18746.1	chr2	73312560	73312585	-	1	NA	promoter-TSS (NM_025854)	promoter-TSS (NM_025854)	20	NM_025854	66935	Mm.292140	NM_025854	ENSMUSG00000041777	Cir1	1700023B02Rik|2810021A19Rik|Cicr|Cir	corepressor interacting with RBPJ, 1	protein-coding
mm_99041.1	chr11	98960780	98960790	+	1	NA	5' UTR (NM_001176528, exon 1 of 8)	5' UTR (NM_001176528, exon 1 of 8)	314	NM_001176528	19401	Mm.439744	NM_009024	ENSMUSG00000037992	Rara	Nr1b1|RAR|RARalpha1	retinoic acid receptor, alpha	protein-coding
mm_53521.1	chr6	136518787	136518810	+	1	NA	promoter-TSS (NM_019426)	promoter-TSS (NM_019426)	-53	NM_019426	54343	Mm.173271	NM_019426	ENSMUSG00000030213	Atf7ip	2610204M12Rik|AM|Mcaf1	activating transcription factor 7 interacting protein	protein-coding
mm_65414.1	chr7	25245468	25245481	-	1	NA	exon (NM_010155, exon 4 of 4)	exon (NM_010155, exon 4 of 4)	5284	NM_010155	13875	Mm.8068	NM_010155	ENSMUSG00000040857	Erf	-	Ets2 repressor factor	protein-coding
mm_157291.1	chrX	20862097	20862109	-	1	NA	intron (NM_013680, intron 12 of 12)	intron (NM_013680, intron 12 of 12)	1079	NR_049190	100885829		NR_049190	ENSMUSG00000093408	Mir5617	Gm25192|mir-5617|mmu-mir-5617	microRNA 5617	ncRNA
mm_123600.1	chr14	67886932	67886935	-	1	NA	intron (NM_177780, intron 1 of 51)	intron (NM_177780, intron 1 of 51)	-27188	NR_105857	102465310		NR_105857	ENSMUSG00000098866	Mir6539	Gm27464|mir-6539|mmu-mir-6539	microRNA 6539	ncRNA
mm_166034.1	chr4	128935907	128935912	-	1	NA	intron (NM_001301841, intron 7 of 8)	intron (NM_001301841, intron 7 of 8)	26546	NM_172875	242669	Mm.215814	NM_172875	ENSMUSG00000028789	Azin2	4933429I20Rik|Adc|Azi2|B930082O19|ODC-p|Odcp	antizyme inhibitor 2	protein-coding
mm_32576.1	chr4	110397689	110397708	+	1	NA	promoter-TSS (NM_001284190)	promoter-TSS (NM_001284190)	0	NM_001048189	78933	Mm.435620	NM_030231	ENSMUSG00000061298	Agbl4	4930578N11Rik|4931433A01Rik	ATP/GTP binding protein-like 4	protein-coding
mm_5057.1	chr1	194981144	194981148	+	1	NA	Intergenic	Intergenic	-4187	NR_033564	320400	Mm.417608	NR_033564	ENSMUSG00000097325	Gm16897	C030002c11rik	predicted gene, 16897	ncRNA
mm_138228.1	chr17	34355234	34355251	+	1	NA	intron (NM_079835, intron 1 of 8)	PB1D7|SINE|Alu	420	NM_079835	547431	Mm.441007	NM_079835	ENSMUSG00000024340	Btnl2	BTL-II|BTLN2|Btl2|Gm315|NG9	butyrophilin-like 2	protein-coding
mm_27214.1	chr3	35933052	35933077	-	1	NA	promoter-TSS (NM_001205362)	promoter-TSS (NM_001205362)	-98	NM_001205361	114893	Mm.374810	NM_033623	ENSMUSG00000027708	Dcun1d1	Rp42|SCCRO|Tes3|pTes3	DCN1, defective in cullin neddylation 1, domain containing 1 (S. cerevisiae)	protein-coding
mm_152838.1	chr19	23448191	23448201	-	1	NA	5' UTR (NM_174857, exon 1 of 14)	5' UTR (NM_174857, exon 1 of 14)	126	NM_174857	71738	Mm.50841	NM_174857	ENSMUSG00000033207	Mamdc2	1200015L10Rik|AI591564|mamcan	MAM domain containing 2	protein-coding
mm_156765.1	chrX	160529981	160530029	+	1	NA	intron (NM_172783, intron 5 of 32)	intron (NM_172783, intron 5 of 32)	27571	NM_001177878	110094	Mm.350712	NM_172783	ENSMUSG00000031295	Phka2	6330505C01Rik|D330034O08|Phk	phosphorylase kinase alpha 2	protein-coding
mm_109206.1	chr12	108676219	108676231	+	1	NA	intron (NM_001163394, intron 7 of 13)	intron (NM_001163394, intron 7 of 13)	17605	NR_029771	723909		NR_029771	ENSMUSG00000065436	Mir342	Mirn342|mmu-mir-342	microRNA 342	ncRNA
mm_170283.1	chr18	27599340	27599349	+	1	NA	Intergenic	(TGG)n|Simple_repeat|Simple_repeat	-960820	NR_045398	320624	Mm.50107	NR_045398		4930474G06Rik	-	RIKEN cDNA 4930474G06 gene	ncRNA
mm_133766.1	chr16	94569775	94569787	+	1	NA	promoter-TSS (NM_007890)	promoter-TSS (NM_007890)	-425	NM_007890	13548	Mm.310973	NM_007890	ENSMUSG00000022897	Dyrk1a	2310043O08Rik|D16Ertd272e|D16Ertd493e|Dyrk|ENSMUSG00000074897|Gm10783|Mnbh|Mp86|mmb	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1a	protein-coding
mm_58214.1	chr6	144204129	144204160	-	1	NA	intron (NM_001113559, intron 1 of 13)	intron (NM_001113559, intron 1 of 13)	5424	NM_001113559	20678	Mm.1752	NM_011444	ENSMUSG00000041540	Sox5	A730017D01Rik|AI528773	SRY (sex determining region Y)-box 5	protein-coding
mm_123473.1	chr14	65974929	65974943	-	1	NA	exon (NM_013492, exon 4 of 9)	exon (NM_013492, exon 4 of 9)	6453	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_82976.1	chr9	35844223	35844233	-	1	NA	promoter-TSS (NM_029863)	promoter-TSS (NM_029863)	-78	NM_029863	77080	Mm.159846	NM_029863	ENSMUSG00000047980	9230110F15Rik	Pate-A|Pate5|mANLP3	RIKEN cDNA 9230110F15 gene	protein-coding
mm_155496.1	chrX	73757070	73757111	+	1	NA	promoter-TSS (NM_019587)	promoter-TSS (NM_019587)	-13	NM_019587	140571	Mm.275600	NM_019587	ENSMUSG00000031385	Plxnb3	AI451018|Plxn6	plexin B3	protein-coding
mm_102902.1	chr11	69523225	69523228	-	1	NA	intron (NM_001081330, intron 5 of 85)	intron (NM_001081330, intron 5 of 85)	25882	NM_001081330	327954	Mm.247478	NM_177617	ENSMUSG00000005237	Dnah2	2900022L05Rik|4930564A01|D130094J20|D330014H01Rik|Dnahc2|Dnhd3	dynein, axonemal, heavy chain 2	protein-coding
mm_121572.1	chr14	122876807	122876817	+	1	NA	exon (NM_144844, exon 22 of 24)	exon (NM_144844, exon 22 of 24)	36353	NM_145466	223267	Mm.379358	NM_145466	ENSMUSG00000041625	Ggact	A2ld1	gamma-glutamylamine cyclotransferase	protein-coding
mm_20482.1	chr2	129699806	129699818	-	1	NA	5' UTR (NM_018863, exon 1 of 4)	5' UTR (NM_018863, exon 1 of 4)	126	NM_018863	18610	Mm.6239	NM_018863	ENSMUSG00000027400	Pdyn	Dyn	prodynorphin	protein-coding
mm_54741.1	chr6	41030916	41030926	-	1	NA	3' UTR (NM_023333, exon 5 of 5)	3' UTR (NM_023333, exon 5 of 5)	4588	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_15564.1	chr2	158610732	158610787	+	1	NA	promoter-TSS (NM_009508)	promoter-TSS (NM_009508)	1	NM_009508	22348	Mm.143404	NM_009508	ENSMUSG00000037771	Slc32a1	R75019|VGAT|Viaat	solute carrier family 32 (GABA vesicular transporter), member 1	protein-coding
mm_56575.1	chr6	106748064	106748077	-	1	NA	intron (NM_008370, intron 1 of 12)	intron (NM_008370, intron 1 of 12)	967	NM_008370	16192	Mm.3448	NM_008370	ENSMUSG00000005364	Il5ra	CD125|CDw125|Il5r	interleukin 5 receptor, alpha	protein-coding
mm_95565.1	chr11	52374295	52374320	+	1	NA	exon (NM_011694, exon 2 of 9)	exon (NM_011694, exon 2 of 9)	13445	NM_011694	22333	Mm.3555	NM_011694	ENSMUSG00000020402	Vdac1	AL033343|Vdac5|mVDAC1|mVDAC5	voltage-dependent anion channel 1	protein-coding
mm_88058.1	chr10	67548226	67548236	+	1	NA	exon (NM_001005419, exon 1 of 1)	exon (NM_001005419, exon 1 of 1)	724	NM_001005419	211488	Mm.297250	NM_001005419	ENSMUSG00000057134	Ado	Gm237	2-aminoethanethiol (cysteamine) dioxygenase	protein-coding
mm_134246.1	chr16	13468751	13468785	-	1	NA	Intergenic	Intergenic	2412	NR_105784	102466153		NR_105784	ENSMUSG00000099214	Mir6365	Gm27683|mmu-mir-6365	microRNA 6365	ncRNA
mm_52990.1	chr6	123266067	123266076	+	1	NA	intron (NM_001163161, intron 2 of 5)	L1ME3A|LINE|L1	3964	NM_010819	17474	Mm.441101	NM_010819	ENSMUSG00000030144	Clec4d	Clecsf8|Mpcl|mcl	C-type lectin domain family 4, member d	protein-coding
mm_17410.1	chr2	27246887	27246904	-	1	NA	5' UTR (NM_138665, exon 1 of 21)	5' UTR (NM_138665, exon 1 of 21)	408	NM_138665	192166	Mm.278467	NM_138665	ENSMUSG00000009614	Sardh	-	sarcosine dehydrogenase	protein-coding
mm_33776.1	chr4	134502237	134502250	+	1	NA	intron (NM_001285847, intron 2 of 2)	intron (NM_001285847, intron 2 of 2)	5202	NM_001285849	71904	Mm.142343	NM_027995	ENSMUSG00000037348	Paqr7	2310021M12Rik|AV001994|BB007237|Mpra|PGLP|mPR	progestin and adipoQ receptor family member VII	protein-coding
mm_96069.1	chr11	59810108	59810133	+	1	NA	promoter-TSS (NM_001271357)	promoter-TSS (NM_001271357)	40	NR_045686	100504104	Mm.391737	NR_045686	ENSMUSG00000087249	Gm16062	ENSMUSG00000072890|OTTMUSG00000029633	predicted gene 16062	ncRNA
mm_123886.1	chr14	72709951	72709961	-	1	NA	promoter-TSS (NM_207636)	promoter-TSS (NM_207636)	47	NM_207636	319448	Mm.205421	NM_207636	ENSMUSG00000033487	Fndc3a	1700094E19Rik|D14Ertd453e|F730017H24Rik|Fndc3|sys	fibronectin type III domain containing 3A	protein-coding
mm_52183.1	chr6	99521349	99521363	+	1	NA	promoter-TSS (NM_001347345)	promoter-TSS (NM_001347345)	-363	NM_001347345	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_9812.1	chr1	182014490	182014498	-	1	NA	intron (NM_001083121, intron 1 of 13)	intron (NM_001083121, intron 1 of 13)	5486	NM_008680	13800	Mm.87759	NM_008680	ENSMUSG00000022995	Enah	Mena|NDPP-1|Ndpp1|WBP8	enabled homolog (Drosophila)	protein-coding
mm_168552.1	chr1	164458492	164458498	+	1	NA	promoter-TSS (NM_009721)	promoter-TSS (NM_009721)	-140	NM_009721	11931	Mm.4550	NM_009721	ENSMUSG00000026576	Atp1b1	Atp4b|Atpb|Atpb-1|NKbeta1	ATPase, Na+/K+ transporting, beta 1 polypeptide	protein-coding
mm_132808.1	chr16	45159007	45159017	+	1	NA	promoter-TSS (NM_028756)	promoter-TSS (NM_028756)	183	NM_026402	67841	Mm.41775	NM_026402	ENSMUSG00000022663	Atg3	2610016C12Rik|APG3|Apg3l|Atg3l|PC3-96	autophagy related 3	protein-coding
mm_44135.1	chr5	150080597	150080618	+	1	NA	intron (NM_001289566, intron 16 of 16)	RMER17C|LTR|ERVK	61932	NM_001289566	140498	Mm.444643	NM_080468	ENSMUSG00000053368	Rxfp2	Gpr106|Great|Lgr8	relaxin/insulin-like family peptide receptor 2	protein-coding
mm_68200.1	chr7	104380553	104380587	-	1	NA	Intergenic	Intergenic	-21924	NM_175648	244183	Mm.347647	NM_175648	ENSMUSG00000052749	Trim30b	A530023O14Rik|Trim30-1	tripartite motif-containing 30B	protein-coding
mm_87788.1	chr10	60297401	60297417	+	1	NA	intron (NM_011179, intron 8 of 14)	intron (NM_011179, intron 8 of 14)	12948	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_7611.1	chr1	126492901	126492951	-	1	NA	promoter-TSS (NM_172484)	promoter-TSS (NM_172484)	1	NM_172484	210356	Mm.377234	NM_172484	ENSMUSG00000049690	Nckap5	8430408F21|D130011D22Rik|E030049G20Rik|Erih1|Erih2|Gm1548|Nap5	NCK-associated protein 5	protein-coding
mm_99976.1	chr11	114091430	114091443	+	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-25485	NM_172800	237979	Mm.130504	NM_172800	ENSMUSG00000041592	Sdk2	4632412F08Rik|5330435L01Rik|Sdk-2|mKIAA1514	sidekick cell adhesion molecule 2	protein-coding
mm_54351.1	chr6	30958794	30958815	-	1	NA	5' UTR (NM_001135093, exon 1 of 1)	5' UTR (NM_001135093, exon 1 of 1)	186	NM_001135093	619665	Mm.204671	NM_001135093	ENSMUSG00000073209	Klf14	5330411L03Rik|AL022736|BTEB5	Kruppel-like factor 14	protein-coding
mm_70065.1	chr7	142652360	142652374	-	1	NA	3' UTR (NM_010514, exon 4 of 4)	3' UTR (NM_010514, exon 4 of 4)	2629	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_6262.1	chr1	69131332	69131338	-	1	NA	Intergenic	Intergenic	-23276	NM_010154	13869	Mm.442420	NM_010154	ENSMUSG00000062209	Erbb4	Her4|c-erbB-4	erb-b2 receptor tyrosine kinase 4	protein-coding
mm_21455.1	chr2	160859602	160859630	-	1	NA	intron (NM_177263, intron 1 of 3)	intron (NM_177263, intron 1 of 3)	13374	NM_177263	320799	Mm.436734	NM_177263	ENSMUSG00000035877	Zhx3	1810059C13Rik|4932418O04Rik|9530010N21Rik|Tix1|mKIAA0395	zinc fingers and homeoboxes 3	protein-coding
mm_5042.1	chr1	194619816	194619833	+	1	NA	promoter-TSS (NM_008882)	promoter-TSS (NM_008882)	-5	NM_008882	18845	Mm.2251	NM_008882	ENSMUSG00000026640	Plxna2	2810428A13Rik|AA589422|AW457381|OCT|PlexA2|Plxn2|mKIAA0463	plexin A2	protein-coding
mm_92413.1	chr10	76725979	76726050	-	1	NA	promoter-TSS (NM_009933)	promoter-TSS (NM_009933)	30	NM_009933	12833	Mm.2509	NM_009933	ENSMUSG00000001119	Col6a1	AI747156|Col6a-1	collagen, type VI, alpha 1	protein-coding
mm_107129.1	chr12	21111779	21111809	+	1	NA	promoter-TSS (NM_001098168)	promoter-TSS (NM_001098168)	38	NM_001135192	211914	Mm.358946	NM_001004364	ENSMUSG00000052632	Asap2	6530401G17Rik|Ddef2|Gm1523|Gm592|PAG3|PAP	ArfGAP with SH3 domain, ankyrin repeat and PH domain 2	protein-coding
mm_121571.1	chr14	122876467	122876480	+	1	NA	intron (NM_144844, intron 21 of 23)	intron (NM_144844, intron 21 of 23)	36692	NM_145466	223267	Mm.379358	NM_145466	ENSMUSG00000041625	Ggact	A2ld1	gamma-glutamylamine cyclotransferase	protein-coding
mm_125539.1	chr15	58141343	58141394	+	1	NA	promoter-TSS (NM_001326602)	promoter-TSS (NM_001326602)	2	NM_001326599	76773	Mm.26771	NM_029734	ENSMUSG00000022359	Wdyhv1	2410187C16Rik|AU014961|AW550036|Ntaq1	WDYHV motif containing 1	protein-coding
mm_126966.1	chr15	92701426	92701438	+	1	NA	intron (NM_001164593, intron 5 of 9)	RMER17A|LTR|ERVK	104323	NM_001164594	239618	Mm.309826	NM_001164593	ENSMUSG00000036218	Pdzrn4	1110017D07Rik|LNX4|SAMCAP3L|mKIAA3027	PDZ domain containing RING finger 4	protein-coding
mm_157958.1	chrX	88115598	88115626	-	1	NA	promoter-TSS (NM_001160403)	promoter-TSS (NM_001160403)	11	NM_001160403	331461	Mm.121680	NM_001160403	ENSMUSG00000052372	Il1rapl1	6330532G10Rik|C030039N24|IL1R8|IL1RAPL|MRX34|OPHN4|TIGIRR-2	interleukin 1 receptor accessory protein-like 1	protein-coding
mm_157274.1	chrX	20291777	20291834	-	1	NA	promoter-TSS (NM_177353)	promoter-TSS (NM_177353)	-41	NM_177353	236727	Mm.132983	NM_177353	ENSMUSG00000037341	Slc9a7	A530087D17Rik|NHE7	solute carrier family 9 (sodium/hydrogen exchanger), member 7	protein-coding
mm_42978.1	chr5	123176098	123176134	+	1	NA	exon (NM_008277, exon 10 of 14)	exon (NM_008277, exon 10 of 14)	6570	NM_008277	15445	Mm.439709	NM_008277	ENSMUSG00000029445	Hpd	Fla|Flp|Hppd|Laf	4-hydroxyphenylpyruvic acid dioxygenase	protein-coding
mm_154917.1	chrX	21715095	21715103	+	1	NA	5' UTR (NM_020049, exon 1 of 14)	5' UTR (NM_020049, exon 1 of 14)	199	NM_020049	56774	Mm.253984	NM_020049	ENSMUSG00000031089	Slc6a14	1110007A17Rik|9030613J17Rik|ATB0plus|CATB0plus	solute carrier family 6 (neurotransmitter transporter), member 14	protein-coding
mm_168424.1	chr11	33395389	33395400	-	1	NA	intron (NM_023146, intron 14 of 27)	L1_Mus3|LINE|L1	118352	NR_110973	66011	Mm.383775	NM_023146	ENSMUSG00000040594	Ranbp17	-	RAN binding protein 17	protein-coding
mm_86621.1	chr10	13966175	13966201	+	1	NA	promoter-TSS (NM_010437)	promoter-TSS (NM_010437)	-191	NM_010437	15273	Mm.42157	NM_010437	ENSMUSG00000015501	Hivep2	Gm20114|MIBP1|Schnurri-2|Shn-2	human immunodeficiency virus type I enhancer binding protein 2	protein-coding
mm_79086.1	chr9	46242551	46242587	+	1	NA	exon (NM_007468, exon 3 of 3)	exon (NM_007468, exon 3 of 3)	1725	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_123678.1	chr14	69487576	69487630	-	1	NA	Intergenic	B4|SINE|B4	24946	NM_173420	239167	Mm.259889	NM_173420	ENSMUSG00000047977	Synb	D930020E02Rik|syncytin-B	syncytin b	protein-coding
mm_7738.1	chr1	130887409	130887421	-	1	NA	promoter-TSS (NM_053095)	promoter-TSS (NM_053095)	-4	NM_053095	93672	Mm.196691	NM_053095	ENSMUSG00000026420	Il24	FISP|Mda-7|Mda7|St16	interleukin 24	protein-coding
mm_142571.1	chr17	46678610	46678622	-	1	NA	intron (NM_001163729, intron 1 of 10)	intron (NM_001163729, intron 1 of 10)	-1837	NM_001277310	17256	Mm.329083	NM_010787	ENSMUSG00000002768	Mea1	Mea-1	male enhanced antigen 1	protein-coding
mm_25302.1	chr3	105974975	105974977	+	1	NA	exon (NM_007696, exon 3 of 11)	exon (NM_007696, exon 3 of 11)	1174	NM_007696	12659	Mm.431947	NM_007696	ENSMUSG00000074340	Ovgp1	120kDa|AU016433|AU019448|Chit5|MOGP|OGP|muc9	oviductal glycoprotein 1	protein-coding
mm_105384.1	chr11	103356325	103356385	-	1	NA	intron (NM_001205236, intron 3 of 17)	intron (NM_001205236, intron 3 of 17)	7337	NM_183288	544817	Mm.259113	NM_133715	ENSMUSG00000034255	Arhgap27	2310069I04Rik|5730442P18Rik|Gm21552|Sh3d20	Rho GTPase activating protein 27	protein-coding
mm_111312.1	chr12	85817921	85817933	-	1	NA	intron (NM_021446, intron 3 of 4)	intron (NM_021446, intron 3 of 4)	6618	NM_021446	58520	Mm.143795	NM_021446	ENSMUSG00000021252	0610007P14Rik	1190004E09Rik|AU019315|C77855|ORF11	RIKEN cDNA 0610007P14 gene	protein-coding
mm_7557.1	chr1	124708188	124708192	-	1	NA	Intergenic	Lx3_Mus|LINE|L1	-662631	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_128547.1	chr15	55090423	55090496	-	1	NA	promoter-TSS (NM_183089)	promoter-TSS (NM_183089)	19	NM_183089	72107	Mm.486550	NM_183089	ENSMUSG00000022422	Dscc1	2010006I05Rik|2600005O03Rik|Dcc1	DNA replication and sister chromatid cohesion 1	protein-coding
mm_48487.1	chr5	142530042	142530084	-	1	NA	promoter-TSS (NM_019943)	promoter-TSS (NM_019943)	13	NM_019943	56522	Mm.441372	NM_019943	ENSMUSG00000074817	Papolb	PAP|Paplob|Papola-ps|Papt|Plap-ps|Tpap	poly (A) polymerase beta (testis specific)	protein-coding
mm_63685.1	chr7	130569903	130569906	+	1	NA	Intergenic	Intergenic	-7580	NM_001004468	57752	Mm.86322	NM_021314	ENSMUSG00000030852	Tacc2	mKIAA4180	transforming, acidic coiled-coil containing protein 2	protein-coding
mm_1925.1	chr1	86053866	86053879	+	1	NA	3' UTR (NM_001144992, exon 3 of 3)	3' UTR (NM_001144992, exon 3 of 3)	8009	NM_001144992	72792	Mm.54981	NM_001144992	ENSMUSG00000026227	2810459M11Rik	-	RIKEN cDNA 2810459M11 gene	protein-coding
mm_99062.1	chr11	99155232	99155244	+	1	NA	promoter-TSS (NM_007719)	promoter-TSS (NM_007719)	-161	NM_007719	12775	Mm.2932	NM_007719	ENSMUSG00000037944	Ccr7	CC-CKR-7|CCR-7|CD197|Cdw197|Cmkbr7|EBI1|Ebi1h	chemokine (C-C motif) receptor 7	protein-coding
mm_72462.1	chr8	83259313	83259339	+	1	NA	exon (NM_001111304, exon 15 of 21)	exon (NM_001111304, exon 15 of 21)	-31022	NM_009463	22227	Mm.4177	NM_009463	ENSMUSG00000031710	Ucp1	AI385626|Slc25a7|Ucp	uncoupling protein 1 (mitochondrial, proton carrier)	protein-coding
mm_32812.1	chr4	117148913	117148914	+	1	NA	Intergenic	CpG	5661	NR_028524	100217424		NR_028524	ENSMUSG00000065680	Snord38a	MBII-329	small nucleolar RNA, C/D box 38A	snoRNA
mm_403.1	chr1	34184108	34184112	+	1	NA	TTS (NM_010081)	TTS (NM_010081)	23780	NM_010081	13518	Mm.336625	NM_010081	ENSMUSG00000026131	Dst	2310001O04Rik|A830042E19Rik|AW554249|BP230|BPAG1-n|Bpag|Bpag1|Macf2|ah|athetoid|dt|mKIAA0728|nmf203|nmf339	dystonin	protein-coding
mm_81190.1	chr9	107550771	107550798	+	1	NA	promoter-TSS (NM_001243748)	promoter-TSS (NM_001243748)	-771	NM_001243748	56289	Mm.12091	NM_019713	ENSMUSG00000010067	Rassf1	123F2|AA536941|AU044980|NORE2A|RDA32|REH3P21|Rassf1A|Rassf1B|Rassf1C	Ras association (RalGDS/AF-6) domain family member 1	protein-coding
mm_51824.1	chr6	89254393	89254396	+	1	NA	Intergenic	Intergenic	31331	NR_131021	75131	Mm.391482	NR_131021	ENSMUSG00000107622	4930512J16Rik	-	RIKEN cDNA 4930512J16 gene	ncRNA
mm_108335.1	chr12	80115850	80115936	+	1	NA	Intergenic	CpG	-2880	NM_007564	12192	Mm.235132	NM_007564	ENSMUSG00000021127	Zfp36l1	AW742437|AW743212|Berg36|Brf1|D530020L18Rik|ERF1|TIS11b|cMG1	zinc finger protein 36, C3H type-like 1	protein-coding
mm_160038.1	chr6	134471171	134471171	-	1	NA	intron (NM_008514, intron 12 of 22)	intron (NM_008514, intron 12 of 22)	74842	NM_025778	66813	Mm.474472	NM_025778	ENSMUSG00000030200	Bcl2l14	4930452K23Rik|4933405K19Rik|9030625M01Rik|AI429211|Bclg	BCL2-like 14 (apoptosis facilitator)	protein-coding
mm_152050.1	chr19	6235666	6235679	-	1	NA	5' UTR (NM_198168, exon 1 of 14)	5' UTR (NM_198168, exon 1 of 14)	168	NM_198168	225849	Mm.118076	NM_198168	ENSMUSG00000024777	Ppp2r5b	B'beta|BC026670	protein phosphatase 2, regulatory subunit B', beta	protein-coding
mm_16603.1	chr2	5063976	5063986	-	1	NA	promoter-TSS (NM_181848)	promoter-TSS (NM_181848)	-43	NM_181848	71648	Mm.116942	NM_181848	ENSMUSG00000026672	Optn	4930441O07Rik|FIP2|HYPL|NRP	optineurin	protein-coding
mm_134569.1	chr16	20362240	20362261	-	1	NA	exon (NM_013790, exon 24 of 30)	exon (NM_013790, exon 24 of 30)	-36846	NM_183158	224044	Mm.276400	NM_183158	ENSMUSG00000022818	Cyp2ab1	EG224044|F730023N20	cytochrome P450, family 2, subfamily ab, polypeptide 1	protein-coding
mm_68793.1	chr7	123500101	123500115	-	1	NA	5' UTR (NM_001081329, exon 1 of 7)	5' UTR (NM_001081329, exon 1 of 7)	341	NM_001081329	210162	Mm.135397	NM_175435	ENSMUSG00000030757	Zkscan2	9430065N20Rik|AW493225|Zfp694	zinc finger with KRAB and SCAN domains 2	protein-coding
mm_37247.1	chr4	118180044	118180054	-	1	NA	promoter-TSS (NM_001161823)	promoter-TSS (NM_001161823)	-6	NM_001161823	230674	Mm.234234	NM_172382	ENSMUSG00000033326	Kdm4a	D4Ertd222e|JHDM3A|Jmjd2|Jmjd2a|mKIAA0677	lysine (K)-specific demethylase 4A	protein-coding
mm_86021.1	chr9	112235855	112235865	-	1	NA	non-coding (NR_015468, exon 2 of 2)	non-coding (NR_015468, exon 2 of 2)	-1019	NM_001177619	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_76171.1	chr8	82392110	82392126	-	1	NA	intron (NM_001254747, intron 1 of 7)	Lx7|LINE|L1	10468	NM_001254747	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_10551.1	chr2	16675303	16675306	+	1	NA	intron (NM_026162, intron 9 of 13)	intron (NM_026162, intron 9 of 13)	319000	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding
mm_78263.1	chr9	21936987	21937070	+	1	NA	promoter-TSS (NM_001290299)	promoter-TSS (NM_001290299)	18	NM_001290299	235044	Mm.277521	NM_144935	ENSMUSG00000040563	Plppr2	Lppr2|PRG-4	phospholipid phosphatase related 2	protein-coding
mm_67558.1	chr7	81707083	81707098	-	1	NA	promoter-TSS (NM_001164086)	promoter-TSS (NM_001164086)	-165	NM_001164086	26557	Mm.228	NM_011983	ENSMUSG00000025813	Homer2	9330120H11Rik|AW539445|CPD|Vesl-2	homer scaffolding protein 2	protein-coding
mm_20918.1	chr2	150668199	150668257	-	1	NA	promoter-TSS (NM_080575)	promoter-TSS (NM_080575)	12	NM_080575	68738	Mm.7044	NM_080575	ENSMUSG00000027452	Acss1	1110032O15Rik|AI788978|Acas2|Acas2l|AceCS2	acyl-CoA synthetase short-chain family member 1	protein-coding
mm_753.1	chr1	43730789	43730799	+	1	NA	5' UTR (NM_024283, exon 1 of 4)	5' UTR (NM_024283, exon 1 of 4)	192	NM_024283	78896	Mm.50109	NM_024283	ENSMUSG00000026051	1500015O10Rik	Ecrg4	RIKEN cDNA 1500015O10 gene	protein-coding
mm_73882.1	chr8	119344750	119344761	+	1	NA	intron (NM_024219, intron 1 of 3)	CpG	217	NM_024219	68196	Mm.358714	NM_024219	ENSMUSG00000031839	Hsbp1	0610007A03Rik|AA408769|Hsp25	heat shock factor binding protein 1	protein-coding
mm_4480.1	chr1	173436102	173436116	+	1	NA	intron (NM_001013779, intron 2 of 8)	B4A|SINE|B4	15505	NM_001013779	383619	Mm.131453	NM_001013779	ENSMUSG00000037860	Aim2	Gm1313|Ifi210	absent in melanoma 2	protein-coding
mm_84621.1	chr9	70543161	70543174	-	1	NA	intron (NM_026337, intron 1 of 20)	CpG	297	NM_025690	66660	Mm.22379	NM_025690	ENSMUSG00000032212	Sltm	5730455C01Rik|5730555F13Rik|9130215G10Rik|Met	SAFB-like, transcription modulator	protein-coding
mm_61930.1	chr7	90166053	90166066	+	1	NA	intron (NM_001252520, intron 4 of 20)	PB1D9|SINE|Alu	35827	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_55879.1	chr6	83523220	83523240	-	1	NA	exon (NM_009610, exon 4 of 9)	exon (NM_009610, exon 4 of 9)	13021	NM_009610	11468	Mm.292865	NM_009610	ENSMUSG00000059430	Actg2	ACTA3|Act-4|Act4|SMGA	actin, gamma 2, smooth muscle, enteric	protein-coding
mm_131961.1	chr16	24567878	24567882	+	1	NA	intron (NM_001145952, intron 3 of 11)	intron (NM_001145952, intron 3 of 11)	38566	NR_038091	624582	Mm.439775	NR_038091		Morf4l1-ps1	A730098P11Rik	mortality factor 4 like 1, pseudogene 1	pseudo
mm_28482.1	chr3	92457194	92457203	-	1	NA	exon (NM_011478, exon 2 of 2)	exon (NM_011478, exon 2 of 2)	1522	NM_001204427	20766	Mm.57092	NM_011478	ENSMUSG00000045539	Sprr3	SPR3	small proline-rich protein 3	protein-coding
mm_93828.1	chr10	121555656	121555659	-	1	NA	intron (NM_019786, intron 13 of 20)	intron (NM_019786, intron 13 of 20)	31137	NM_019786	56480	Mm.34580	NM_019786	ENSMUSG00000020115	Tbk1	1200008B05Rik|AI462036|AW048562	TANK-binding kinase 1	protein-coding
mm_11536.1	chr2	32629827	32629850	+	1	NA	intron (NM_021515, intron 1 of 5)	intron (NM_021515, intron 1 of 5)	338	NM_021515	11636	Mm.29189	NM_021515	ENSMUSG00000026817	Ak1	Ak-1|B430205N08Rik	adenylate kinase 1	protein-coding
mm_58007.1	chr6	136497897	136497900	-	1	NA	Intergenic	Intergenic	-20953	NM_019426	54343	Mm.173271	NM_019426	ENSMUSG00000030213	Atf7ip	2610204M12Rik|AM|Mcaf1	activating transcription factor 7 interacting protein	protein-coding
mm_137395.1	chr17	25823627	25823637	+	1	NA	promoter-TSS (NM_173741)	promoter-TSS (NM_173741)	5	NM_173741	268933	Mm.95512	NM_173741	ENSMUSG00000025737	Wdr24	BC037651	WD repeat domain 24	protein-coding
mm_118513.1	chr14	14346582	14346615	+	1	NA	intron (NM_008369, intron 1 of 11)	intron (NM_008369, intron 1 of 11)	103	NM_008369	16188	Mm.425857	NM_008369	ENSMUSG00000068758	Il3ra	CD123|CDw123|SUT-1	interleukin 3 receptor, alpha chain	protein-coding
mm_4330.1	chr1	171854272	171854291	+	1	NA	3' UTR (NM_001252472, exon 3 of 3)	3' UTR (NM_001252472, exon 3 of 3)	14584	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_170119.1	chr17	39846764	39846765	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	3767	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_150219.1	chr19	33961150	33961154	+	1	NA	promoter-TSS (NM_026334)	promoter-TSS (NM_026334)	-96	NM_026334	67717	Mm.329816	NM_026334	ENSMUSG00000024768	Lipf	2310051B21Rik|AV082900	lipase, gastric	protein-coding
mm_79984.1	chr9	66946830	66946845	+	1	NA	exon (NM_026467, exon 2 of 4)	exon (NM_026467, exon 2 of 4)	761	NM_026467	67941	Mm.30120	NM_026467	ENSMUSG00000036781	Rps27l	1810034D23Rik	ribosomal protein S27-like	protein-coding
mm_31690.1	chr4	62360696	62360758	+	1	NA	promoter-TSS (NM_001045528)	promoter-TSS (NM_001045528)	26	NM_175090	20529	Mm.248637	NM_175090	ENSMUSG00000066150	Slc31a1	4930445G01Rik|AI787263|AU016967|Ctr1	solute carrier family 31, member 1	protein-coding
mm_84817.1	chr9	77544761	77544772	-	1	NA	promoter-TSS (NM_001146048)	promoter-TSS (NM_001146048)	86	NM_001146048	214345	Mm.28534	NM_172528	ENSMUSG00000032352	Lrrc1	A430093J20Rik|AU016091|D030059I21|mKIAA4018	leucine rich repeat containing 1	protein-coding
mm_99758.1	chr11	106752462	106752472	+	1	NA	intron (NM_001033435, intron 2 of 6)	B1F|SINE|Alu	1241	NM_001033435	380732	Mm.343952	NM_001033435	ENSMUSG00000040528	Milr1	Allergin-1|Gm885|Mca32	mast cell immunoglobulin like receptor 1	protein-coding
mm_168636.1	chr1	183205922	183205941	-	1	NA	intron (NM_026866, intron 1 of 9)	intron (NM_026866, intron 1 of 9)	15598	NM_001278218	68897	Mm.327216	NM_026866	ENSMUSG00000030768	Disp1	1190008H24Rik|DispA	dispatched RND transporter family member 1	protein-coding
mm_101772.1	chr11	44470443	44470459	-	1	NA	promoter-TSS (NM_024475)	promoter-TSS (NM_024475)	97	NM_024475	79560	Mm.338784	NM_024475	ENSMUSG00000041231	Ublcp1	4930527B16Rik|8430435I17Rik|BC002236	ubiquitin-like domain containing CTD phosphatase 1	protein-coding
mm_66588.1	chr7	45395673	45395719	-	1	NA	promoter-TSS (NR_126539)	promoter-TSS (NR_126539)	46	NM_009224	20637	Mm.216386	NM_009224	ENSMUSG00000063511	Snrnp70	2700022N21Rik|3200002N22Rik|AI325098|R74807|Rnu1p70|Rnulp70|Snrp70|Srnp70|U1-70|U1-70K	small nuclear ribonucleoprotein 70 (U1)	protein-coding
mm_4235.1	chr1	171370386	171370408	+	1	NA	5' UTR (NM_027893, exon 1 of 9)	5' UTR (NM_027893, exon 1 of 9)	224	NM_001122680	71740	Mm.263414	NM_027893	ENSMUSG00000006411	Nectin4	1200017F15Rik|Prr4|Pvrl4	nectin cell adhesion molecule 4	protein-coding
mm_99251.1	chr11	101119918	101119949	+	1	NA	promoter-TSS (NM_134024)	promoter-TSS (NM_134024)	-90	NM_028933	67998	Mm.33881	NM_026501	ENSMUSG00000017802	Fam134c	1300010M03Rik|4933404C01Rik|AI551748	family with sequence similarity 134, member C	protein-coding
mm_118978.1	chr14	28057391	28057393	+	1	NA	intron (NM_001347497, intron 14 of 19)	intron (NM_001347497, intron 14 of 19)	434985	NM_177814	238988	Mm.318004	NM_177814	ENSMUSG00000040640	Erc2	6430531D06|CAST|CAST1/ERC2|D14Ertd171e|ELKS2alpha	ELKS/RAB6-interacting/CAST family member 2	protein-coding
mm_29596.1	chr3	119783231	119783241	-	1	NA	5' UTR (NM_019550, exon 1 of 14)	5' UTR (NM_019550, exon 1 of 14)	152	NM_001310711	56195	Mm.29966	NM_019550	ENSMUSG00000028134	Ptbp2	Ptb2|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding
mm_79955.1	chr9	66126754	66126781	+	1	NA	5' UTR (NM_026635, exon 1 of 5)	5' UTR (NM_026635, exon 1 of 5)	156	NM_026635	68250	Mm.27107	NM_026635	ENSMUSG00000032381	Fam96a	5730536A07Rik	family with sequence similarity 96, member A	protein-coding
mm_93627.1	chr10	117278174	117278196	-	1	NA	exon (NM_017372, exon 4 of 4)	exon (NM_017372, exon 4 of 4)	4087	NM_017372	17105	Mm.45436	NM_017372	ENSMUSG00000069516	Lyz2	AI326280|Lys|Lysm|Lyzf2|Lyzs|Lzm|Lzm-s1|Lzp	lysozyme 2	protein-coding
mm_171353.1	chr4	110321511	110321524	-	1	NA	intron (NM_001163397, intron 1 of 5)	L1Md_T|LINE|L1	30394	NM_001163397	15572	Mm.3970	NM_010488	ENSMUSG00000028546	Elavl4	Elav|Hud|PNEM	ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4 (Hu antigen D)	protein-coding
mm_94132.1	chr10	128696184	128696190	-	1	NA	promoter-TSS (NM_177411)	promoter-TSS (NM_177411)	81	NM_177411	19344	Mm.12815	NM_011229	ENSMUSG00000000711	Rab5b	C030027M18Rik	RAB5B, member RAS oncogene family	protein-coding
mm_158652.1	chrX	155623526	155623561	-	1	NA	promoter-TSS (NM_001093750)	promoter-TSS (NM_001093750)	-216	NM_001093750	211612	Mm.218811	NM_001093750	ENSMUSG00000041552	Ptchd1	9630036J22Rik|AI848149|Gm387	patched domain containing 1	protein-coding
mm_122108.1	chr14	30923548	30923565	-	1	NA	promoter-TSS (NM_008407)	promoter-TSS (NM_008407)	31	NM_008407	16426	Mm.4517	NM_008407	ENSMUSG00000006522	Itih3	AW108094|ITI-HC3|Intin3|Itih-3	inter-alpha trypsin inhibitor, heavy chain 3	protein-coding
mm_106176.1	chr11	116680705	116680713	-	1	NA	intron (NM_009180, intron 6 of 8)	intron (NM_009180, intron 6 of 8)	6112	NR_028570	100216538		NR_028570	ENSMUSG00000065094	Snord1a	snR38	small nucleolar RNA, C/D box 1A	snoRNA
mm_15311.1	chr2	155561106	155561128	+	1	NA	exon (NM_019811, exon 16 of 18)	exon (NM_019811, exon 16 of 18)	-4187	NR_040613	74945	Mm.401956	NR_040613	ENSMUSG00000086529	Acss2os	4930471I20Rik	acyl-CoA synthetase short-chain family member 2, opposite strand	ncRNA
mm_27340.1	chr3	50414713	50414724	-	1	NA	intron (NM_011990, intron 6 of 11)	intron (NM_011990, intron 6 of 11)	28895	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_146672.1	chr18	12644360	12644376	-	1	NA	intron (NM_028341, intron 1 of 13)	CpG	835	NM_028341	72747	Mm.52526	NM_028341	ENSMUSG00000024424	Ttc39c	1700008N02Rik|2810439F02Rik	tetratricopeptide repeat domain 39C	protein-coding
mm_127673.1	chr15	102750413	102750436	+	1	NA	Intergenic	Intergenic	-3515	NR_104334	102216269		NR_104334		Gm38436	Cistr|Cistr-act	predicted gene, 38436	ncRNA
mm_10174.1	chr2	4559914	4559930	+	1	NA	5' UTR (NM_001177844, exon 1 of 12)	5' UTR (NM_001177844, exon 1 of 12)	168	NM_001177844	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding
mm_73785.1	chr8	117115841	117115844	+	1	NA	intron (NM_001163028, intron 6 of 11)	intron (NM_001163028, intron 6 of 11)	19977	NM_001163028	63857	Mm.174133	NM_021486	ENSMUSG00000031845	Bco1	Bcdo|Bcdo1|Bcmo1|CMO1|Cmoi|beta-CD|betaCMOOX	beta-carotene oxygenase 1	protein-coding
mm_67734.1	chr7	90131102	90131112	-	1	NA	intron (NM_001252520, intron 1 of 20)	intron (NM_001252520, intron 1 of 20)	875	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_105587.1	chr11	106715252	106715293	-	1	NA	promoter-TSS (NM_008816)	promoter-TSS (NM_008816)	9	NM_001305158	18613	Mm.343951	NM_008816	ENSMUSG00000020717	Pecam1	C85791|Cd31|PECAM-1|Pecam	platelet/endothelial cell adhesion molecule 1	protein-coding
mm_109069.1	chr12	104345362	104345372	+	1	NA	exon (NM_011458, exon 5 of 5)	exon (NM_011458, exon 5 of 5)	6881	NM_011458	20714	Mm.291569	NM_011458	ENSMUSG00000058207	Serpina3k	1300001I07Rik|D12Rp54|MMCM2|MMSpi2|RP54|Spi-2|Spi2|contrapsin	serine (or cysteine) peptidase inhibitor, clade A, member 3K	protein-coding
mm_137504.1	chr17	27018006	27018067	+	1	NA	promoter-TSS (NM_001251881)	promoter-TSS (NM_001251881)	1	NM_001251881	70772	Mm.440437	NM_027544	ENSMUSG00000048731	Ggnbp1	0610031G08Rik|mdf	gametogenetin binding protein 1	protein-coding
mm_947.1	chr1	57127306	57127340	+	1	NA	Intergenic	Intergenic	87673	NR_037990	407809	Mm.134505	NR_037990	ENSMUSG00000101429	BC055402	-	cDNA sequence BC055402	ncRNA
mm_93412.1	chr10	108445020	108445027	-	1	NA	Intergenic	Intergenic	112834	NM_054056	114774	Mm.391419	NM_054056	ENSMUSG00000035873	Pawr	2310001G03Rik|PAR4|Par-4	PRKC, apoptosis, WT1, regulator	protein-coding
mm_79522.1	chr9	57589443	57589482	+	1	NA	promoter-TSS (NM_027895)	promoter-TSS (NM_027895)	10	NM_027895	71742	Mm.155877	NM_027895	ENSMUSG00000032308	Ulk3	1200015E14Rik	unc-51-like kinase 3	protein-coding
mm_71787.1	chr8	66697445	66697461	+	1	NA	promoter-TSS (NM_010934)	promoter-TSS (NM_010934)	31	NM_010934	18166	Mm.5112	NM_010934	ENSMUSG00000036437	Npy1r	Npyr|Y1-R	neuropeptide Y receptor Y1	protein-coding
mm_103587.1	chr11	78190131	78190142	-	1	NA	exon (NM_001159482, exon 4 of 11)	exon (NM_001159482, exon 4 of 11)	1388	NM_033475	19376	Mm.275864	NM_033475	ENSMUSG00000002059	Rab34	AI326479|Narr|Rah|Rah1	RAB34, member RAS oncogene family	protein-coding
mm_4242.1	chr1	171389131	171389137	+	1	NA	TTS (NM_027893)	TTS (NM_027893)	174	NM_001005508	226652	Mm.251048	NM_001005508	ENSMUSG00000048865	Arhgap30	6030405P05Rik|Gm102|mFLJ00267	Rho GTPase activating protein 30	protein-coding
mm_147283.1	chr18	39487778	39487780	-	1	NA	promoter-TSS (NM_008173)	promoter-TSS (NM_008173)	-534	NM_008173	14815	Mm.129481	NM_008173	ENSMUSG00000024431	Nr3c1	GR|Grl-1|Grl1	nuclear receptor subfamily 3, group C, member 1	protein-coding
mm_96161.1	chr11	61487897	61487909	+	1	NA	TTS (NM_001291037)	TTS (NM_001291037)	2459	NM_029568	76293	Mm.272278	NM_029568	ENSMUSG00000042436	Mfap4	1110007F23Rik	microfibrillar-associated protein 4	protein-coding
mm_24971.1	chr3	96750931	96750938	+	1	NA	intron (NM_026406, intron 1 of 8)	ORR1B1|LTR|ERVL-MaLR	23323	NM_026406	67845	Mm.386792	NM_026406	ENSMUSG00000028098	Rnf115	2610028E05Rik|AU042696|Zfp364	ring finger protein 115	protein-coding
mm_43863.1	chr5	143471239	143471264	+	1	NA	intron (NM_144915, intron 2 of 14)	intron (NM_144915, intron 2 of 14)	6758	NM_144915	231871	Mm.469963	NM_144915	ENSMUSG00000039206	Daglb	E330036I19Rik	diacylglycerol lipase, beta	protein-coding
mm_169618.1	chr15	38243614	38243614	-	1	NA	Intergenic	Intergenic	24411	NM_008757	18285	Mm.252830	NM_008757	ENSMUSG00000061923	Odf1	-	outer dense fiber of sperm tails 1	protein-coding
mm_44986.1	chr5	37448446	37448452	-	1	NA	3' UTR (NM_022416, exon 12 of 12)	3' UTR (NM_022416, exon 12 of 12)	109971	NM_145920	68525	Mm.25506	NM_145920	ENSMUSG00000050248	Evc2	1110017L09Rik|Lbn|limbin	Ellis van Creveld syndrome 2	protein-coding
mm_155668.1	chrX	89651719	89651745	+	1	NA	Intergenic	Intergenic	-100536	NM_001085511	245509	Mm.297700	NM_001085511	ENSMUSG00000079513	4932429P05Rik	-	RIKEN cDNA 4932429P05 gene	protein-coding
mm_85783.1	chr9	109059217	109059259	-	1	NA	promoter-TSS (NM_001012236)	promoter-TSS (NM_001012236)	13	NM_001012236	22040	Mm.439964	NM_011637	ENSMUSG00000049734	Trex1	AU041952	three prime repair exonuclease 1	protein-coding
mm_22318.1	chr2	180456095	180456105	-	1	NA	Intergenic	Intergenic	-4878	NM_148933	108115	Mm.133687	NM_148933	ENSMUSG00000038963	Slco4a1	OATP-E|Slc21a12	solute carrier organic anion transporter family, member 4a1	protein-coding
mm_80092.1	chr9	70235163	70235206	+	1	NA	intron (NM_181072, intron 1 of 27)	MTD|LTR|ERVL-MaLR	27834	NM_181072	71602	Mm.249311	NM_181072	ENSMUSG00000032220	Myo1e	2310020N23Rik|9130023P14Rik|AA407778|myosin-1e|myr 3	myosin IE	protein-coding
mm_151503.1	chr19	58729972	58730091	+	1	NA	exon (NM_018874, exon 3 of 13)	exon (NM_018874, exon 3 of 13)	1144	NM_018874	18946	Mm.10753	NM_018874	ENSMUSG00000042179	Pnliprp1	Plrp1	pancreatic lipase related protein 1	protein-coding
mm_2317.1	chr1	92048710	92048720	+	1	NA	intron (NM_207225, intron 3 of 26)	intron (NM_207225, intron 3 of 26)	131626	NM_207225	208727	Mm.318567	NM_207225	ENSMUSG00000026313	Hdac4	4932408F19Rik|HD4	histone deacetylase 4	protein-coding
mm_16486.1	chr2	180967219	180967289	+	1	NA	promoter-TSS (NM_001177706)	promoter-TSS (NM_001177706)	29	NM_001177707	228998	Mm.33765	NM_145760	ENSMUSG00000027575	Arfgap1	AI115377|Arf1gap	ADP-ribosylation factor GTPase activating protein 1	protein-coding
mm_170417.1	chr18	68692242	68692255	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-47152	NR_105774	102465183		NR_105774	ENSMUSG00000099300	Mir6356	Gm27461|mmu-mir-6356	microRNA 6356	ncRNA
mm_90189.1	chr10	120172016	120172020	+	1	NA	intron (NM_028679, intron 5 of 11)	ORR1A3|LTR|ERVL-MaLR	29519	NM_028679	73914	Mm.146194	NM_028679	ENSMUSG00000020227	Irak3	4833428C18Rik|AI563835|IRAK-M	interleukin-1 receptor-associated kinase 3	protein-coding
mm_119300.1	chr14	34700729	34700736	+	1	NA	intron (NM_001004436, intron 4 of 18)	B1_Mur3|SINE|Alu	26804	NM_001301330	218914	Mm.27957	NM_001004436	ENSMUSG00000041408	Wapl	A530089A20Rik|BC037674|DIF-2|FOE|Wapal	WAPL cohesin release factor	protein-coding
mm_152986.1	chr19	29611606	29611624	-	1	NA	3' UTR (NM_001081213, exon 15 of 15)	3' UTR (NM_001081213, exon 15 of 15)	36805	NM_001081213	226090	Mm.267131	NM_146098	ENSMUSG00000046324	Ermp1	D19Ertd410e|D19Wsu12e|Fxna|mKIAA1815	endoplasmic reticulum metallopeptidase 1	protein-coding
mm_157402.1	chrX	38431018	38431049	-	1	NA	exon (NM_001017959, exon 6 of 9)	exon (NM_001017959, exon 6 of 9)	25427	NM_010685	16784	Mm.486	NM_010685	ENSMUSG00000016534	Lamp2	CD107b|LGP-B|Lamp II|Lamp-2|Lamp-2a|Lamp-2b|Lamp-2c|Mac3	lysosomal-associated membrane protein 2	protein-coding
mm_137441.1	chr17	26509702	26509708	+	1	NA	Intergenic	Intergenic	-1233	NM_013642	19252	Mm.239041	NM_013642	ENSMUSG00000024190	Dusp1	3CH134|MKP1|Ptpn16|U19515|erp|mkp-1	dual specificity phosphatase 1	protein-coding
mm_12572.1	chr2	73024069	73024097	+	1	NA	Intergenic	Intergenic	-43637	NM_001018042	20687	Mm.124328	NM_011450	ENSMUSG00000027109	Sp3	D130027J01Rik	trans-acting transcription factor 3	protein-coding
mm_21897.1	chr2	166155812	166155843	-	1	NA	promoter-TSS (NM_028072)	promoter-TSS (NM_028072)	-144	NM_028072	72043	Mm.1011	NM_028072	ENSMUSG00000006800	Sulf2	2010004N24Rik|AU020235|MSulf-2|mKIAA1247	sulfatase 2	protein-coding
mm_6065.1	chr1	60781687	60781735	-	1	NA	Intergenic	Lx9|LINE|L1	35323	NM_007642	12487	Mm.255003	NM_007642	ENSMUSG00000026012	Cd28	-	CD28 antigen	protein-coding
mm_112334.1	chr12	115953011	115953033	-	1	NA	Intergenic	Intergenic	-94702	NM_001004066	56220	Mm.254997	NM_019565	ENSMUSG00000042063	Zfp386	Kzf1|mKIAA4205	zinc finger protein 386 (Kruppel-like)	protein-coding
mm_16953.1	chr2	17390861	17390871	-	1	NA	intron (NM_028757, intron 4 of 6)	intron (NM_028757, intron 4 of 6)	-172648	NR_105847	102465964		NR_105847	ENSMUSG00000099161	Mir6419	Gm27713|mmu-mir-6419	microRNA 6419	ncRNA
mm_52997.1	chr6	123268096	123268113	+	1	NA	exon (NM_010819, exon 4 of 6)	exon (NM_010819, exon 4 of 6)	5997	NM_010819	17474	Mm.441101	NM_010819	ENSMUSG00000030144	Clec4d	Clecsf8|Mpcl|mcl	C-type lectin domain family 4, member d	protein-coding
mm_42417.1	chr5	115279729	115279739	+	1	NA	promoter-TSS (NM_026504)	promoter-TSS (NM_026504)	32	NM_026504	52064	Mm.290142	NM_026504	ENSMUSG00000041733	Coq5	1810014G04Rik|D5Ertd33e	coenzyme Q5 methyltransferase	protein-coding
mm_60891.1	chr7	46397163	46397201	+	1	NA	5' UTR (NM_001112739, exon 1 of 4)	5' UTR (NM_001112739, exon 1 of 4)	714	NM_001112739	16502	Mm.249386	NM_008421	ENSMUSG00000058975	Kcnc1	C230009H10Rik|KShIIIB|KV4|Kcr2-1|Kv3.1|NGK2|Shaw	potassium voltage gated channel, Shaw-related subfamily, member 1	protein-coding
mm_4974.1	chr1	191325920	191325984	+	1	NA	promoter-TSS (NM_025864)	promoter-TSS (NM_025864)	-13	NM_025864	66950	Mm.236300	NM_025864	ENSMUSG00000026627	Tmem206	2310028N02Rik|AI118576	transmembrane protein 206	protein-coding
mm_144578.1	chr18	31922270	31922272	+	1	NA	Intergenic	Intergenic	-9236	NM_144862	225341	Mm.24551	NM_144862	ENSMUSG00000024395	Lims2	PINCH2	LIM and senescent cell antigen like domains 2	protein-coding
mm_119553.1	chr14	48655282	48655295	+	1	NA	Intergenic	Intergenic	7584	NM_144841	18424	Mm.134516	NM_144841	ENSMUSG00000021848	Otx2	E130306E05Rik	orthodenticle homeobox 2	protein-coding
mm_30771.1	chr4	17853344	17853356	+	1	NA	promoter-TSS (NM_019724)	promoter-TSS (NM_019724)	-108	NM_019724	17389	Mm.187315	NM_019724	ENSMUSG00000028226	Mmp16	MT-MMP 3|MT3-MMP|Mt3mmp	matrix metallopeptidase 16	protein-coding
mm_148413.1	chr19	3935253	3935261	+	1	NA	promoter-TSS (NM_019449)	promoter-TSS (NM_019449)	71	NM_001161428	54445	Mm.262094	NM_019449	ENSMUSG00000036908	Unc93b1	Unc-93B1|Unc93b	unc-93 homolog B1 (C. elegans)	protein-coding
mm_171517.1	chr4	146514925	146514925	+	1	NA	promoter-TSS (NM_001243139)	promoter-TSS (NM_001243139)	5	NM_001243139	100041433	Mm.441741	NM_001243138	ENSMUSG00000056300	Zfp981	Gm13247|OTTMUSG00000011075	zinc finger protein 981	protein-coding
mm_96817.1	chr11	69994480	69994490	+	1	NA	exon (NM_019749, exon 4 of 4)	exon (NM_019749, exon 4 of 4)	-1281	NM_001291125	78246	Mm.20805	NM_030064	ENSMUSG00000018572	Phf23	JUNE-1	PHD finger protein 23	protein-coding
mm_47647.1	chr5	125389752	125389756	-	1	NA	intron (NM_019639, intron 1 of 1)	CpG	263	NM_019639	22190	Mm.331	NM_019639	ENSMUSG00000008348	Ubc	2700054O04Rik|AI194771|Rps27a|TI-225|Uba52|Ubb	ubiquitin C	protein-coding
mm_82945.1	chr9	35544702	35544705	-	1	NA	intron (NM_013932, intron 10 of 11)	MER3|DNA|hAT-Charlie	13767	NM_013932	30959	Mm.291723	NM_013932	ENSMUSG00000032101	Ddx25	AW047046|GRTH	DEAD (Asp-Glu-Ala-Asp) box polypeptide 25	protein-coding
mm_168312.1	chr11	109011961	109011966	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	91614	NM_015732	12006	Mm.71710	NM_015732	ENSMUSG00000000142	Axin2	Axi1|Axil|Conductin	axin 2	protein-coding
mm_8066.1	chr1	135441480	135441495	-	1	NA	3' UTR (NM_173437, exon 29 of 29)	3' UTR (NM_173437, exon 29 of 29)	-10996	NM_153774	226432	Mm.271642	NM_153774	ENSMUSG00000041879	Ipo9	0710008K06Rik|AI845704|C78347|Imp9|Ranbp9|mKIAA1192	importin 9	protein-coding
mm_151641.1	chr19	4036814	4036825	-	1	NA	intron (NM_013541, intron 4 of 6)	intron (NM_013541, intron 4 of 6)	1093	NM_013541	14870	Mm.299292	NM_013541	ENSMUSG00000060803	Gstp1	GstpiB	glutathione S-transferase, pi 1	protein-coding
mm_49254.1	chr6	17405901	17405903	+	1	NA	Intergenic	Intergenic	-58055	NM_008591	17295	Mm.86844	NM_008591	ENSMUSG00000009376	Met	AI838057|HGF|HGFR|Par4|c-Met	met proto-oncogene	protein-coding
mm_157913.1	chrX	78552759	78552762	-	1	NA	intron (NM_027322, intron 1 of 3)	RLTR14-int|LTR|ERV1	31045	NM_001164275	546336	Mm.211712	NM_027322	ENSMUSG00000047996	Prrg1	2010007L08Rik	proline rich Gla (G-carboxyglutamic acid) 1	protein-coding
mm_145011.1	chr18	38601606	38601619	+	1	NA	promoter-TSS (NM_011898)	promoter-TSS (NM_011898)	-344	NM_011898	24066	Mm.42038	NM_011898	ENSMUSG00000024427	Spry4	A030006O18Rik|sprouty4	sprouty homolog 4 (Drosophila)	protein-coding
mm_12960.1	chr2	90479229	90479238	+	1	NA	promoter-TSS (NM_001135657)	promoter-TSS (NM_001135657)	-59	NM_001135657	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_168459.1	chr1	143683643	143683653	+	1	NA	intron (NM_145991, intron 6 of 16)	intron (NM_145991, intron 6 of 16)	19245	NM_145991	214498	Mm.156727	NM_145991	ENSMUSG00000026361	Cdc73	8430414L16Rik|C130030P16Rik|C81219|Hrpt2	cell division cycle 73, Paf1/RNA polymerase II complex component	protein-coding
mm_38845.1	chr4	149214159	149214196	-	1	NA	intron (NM_207682, intron 26 of 46)	intron (NM_207682, intron 26 of 46)	-47470	NM_001081274	110208	Mm.252080	NM_025801	ENSMUSG00000028961	Pgd	0610042A05Rik|AU019875|C78335	phosphogluconate dehydrogenase	protein-coding
mm_87592.1	chr10	57486571	57486575	+	1	NA	promoter-TSS (NR_045353)	promoter-TSS (NR_045353)	188	NM_008297	15500	Mm.261395	NM_008297	ENSMUSG00000019878	Hsf2	AI661205	heat shock factor 2	protein-coding
mm_12281.1	chr2	69008399	69008418	+	1	NA	intron (NM_172856, intron 4 of 9)	intron (NM_172856, intron 4 of 9)	-127392	NM_181547	329416	Mm.90047	NM_181547	ENSMUSG00000034738	Nostrin	Daip2|mDaIP2	nitric oxide synthase trafficker	protein-coding
mm_166663.1	chr6	88802729	88802731	+	1	NA	intron (NM_011844, intron 3 of 7)	intron (NM_011844, intron 3 of 7)	39205	NM_030251	80283	Mm.166858	NM_030251	ENSMUSG00000030083	Abtb1	AI847549|BC003234|BPOZ|EF1ABP	ankyrin repeat and BTB (POZ) domain containing 1	protein-coding
mm_137540.1	chr17	27556707	27556717	+	1	NA	promoter-TSS (NM_001166477)	promoter-TSS (NM_001166477)	59	NM_001166477	111241	Mm.426212	NM_001166476	ENSMUSG00000078249	Hmga1-rs1	ENSMUSG00000041059|Hmgi-rs1	high mobility group AT-hook I, related sequence 1	protein-coding
mm_100662.1	chr11	3266378	3266423	-	1	NA	promoter-TSS (NM_007879)	promoter-TSS (NM_007879)	-14	NM_007879	13494	Mm.3250	NM_007879	ENSMUSG00000020457	Drg1	AA408859|AI132520|Nedd3	developmentally regulated GTP binding protein 1	protein-coding
mm_104782.1	chr11	98550969	98550977	-	1	NA	promoter-TSS (NM_001166494)	promoter-TSS (NM_001166494)	-124	NM_199419	69376	Mm.55996	NM_027061	ENSMUSG00000017195	Zpbp2	1700017D11Rik|2610022C02Rik|ZPBPL	zona pellucida binding protein 2	protein-coding
mm_85257.1	chr9	99358519	99358552	-	1	NA	promoter-TSS (NM_177775)	promoter-TSS (NM_177775)	-5	NM_177775	272636	Mm.490440	NM_177775	ENSMUSG00000037681	Esyt3	D930024E11|D9Ertd280e|Fam62c|mKIAA4186	extended synaptotagmin-like protein 3	protein-coding
mm_83578.1	chr9	48340624	48340634	-	1	NA	5' UTR (NM_030069, exon 1 of 6)	5' UTR (NM_030069, exon 1 of 6)	269	NM_030069	78252	Mm.31626	NM_030069	ENSMUSG00000032028	Nxpe2	4432416J03Rik|AI323362|Fam55b	neurexophilin and PC-esterase domain family, member 2	protein-coding
mm_154983.1	chrX	38179885	38179891	+	1	NA	Intergenic	Intergenic	-9905	NM_020256	56805	Mm.391248	NM_020256	ENSMUSG00000048047	Zbtb33	AW260253|E130014G12Rik|Kaiso|Znf-kaiso	zinc finger and BTB domain containing 33	protein-coding
mm_85559.1	chr9	106891367	106891373	-	1	NA	intron (NM_029103, intron 1 of 3)	intron (NM_029103, intron 1 of 3)	568	NM_029103	74840	Mm.29778	NM_029103	ENSMUSG00000032575	Manf	3230402M22Rik|AA407711|AA408789|AA673178|Armet|D17914|D18Mgi17	mesencephalic astrocyte-derived neurotrophic factor	protein-coding
mm_128759.1	chr15	65912286	65912292	-	1	NA	promoter-TSS (NM_010953)	promoter-TSS (NM_010953)	-2	NM_010953	18256	Mm.41776	NM_010953	ENSMUSG00000015001	Oc90	Ocn-95|PLA2L|Pla2ll|oc95	otoconin 90	protein-coding
mm_15936.1	chr2	165655238	165655317	+	1	NA	promoter-TSS (NM_010165)	promoter-TSS (NM_010165)	-21	NM_010165	14049	Mm.282719	NM_010165	ENSMUSG00000017897	Eya2	Eab1	EYA transcriptional coactivator and phosphatase 2	protein-coding
mm_99529.1	chr11	103171082	103171122	+	1	NA	promoter-TSS (NM_001077698)	promoter-TSS (NM_001077698)	-36	NM_001077698	57778	Mm.138913	NM_019679	ENSMUSG00000055805	Fmnl1	8030453N10Rik|AI553564|Fmnl|Fnrl|Frls	formin-like 1	protein-coding
mm_78644.1	chr9	40269474	40269496	+	1	NA	5' UTR (NM_001083917, exon 1 of 7)	5' UTR (NM_001083917, exon 1 of 7)	269	NM_178227	235281	Mm.290083	NM_153522	ENSMUSG00000049281	Scn3b	1110001K16Rik|4833414B02Rik|Scnb3	sodium channel, voltage-gated, type III, beta	protein-coding
mm_138748.1	chr17	37044907	37044913	+	1	NA	Intergenic	MER20B|DNA|hAT-Charlie	-1056	NM_019439	54393	Mm.32191	NM_019439	ENSMUSG00000024462	Gabbr1	GABAB1|GABAbR1|bM573K1.1	gamma-aminobutyric acid (GABA) B receptor, 1	protein-coding
mm_59733.1	chr7	28810887	28810918	+	1	NA	promoter-TSS (NM_177301)	promoter-TSS (NM_177301)	12	NM_177301	15388	Mm.9043	NM_177301	ENSMUSG00000015165	Hnrnpl	C79783|D830027H13Rik|Hnrpl	heterogeneous nuclear ribonucleoprotein L	protein-coding
mm_39062.1	chr4	154025907	154025919	-	1	NA	TTS (NM_001033455)	TTS (NM_001033455)	131	NM_001163722	68859	Mm.477488	NM_001033144	ENSMUSG00000078350	Smim1	0610011H04Rik|1190007F08Rik|2700009I11Rik	small integral membrane protein 1	protein-coding
mm_154726.1	chrX	9436655	9436709	+	1	NA	3' UTR (NM_007807, exon 13 of 13)	3' UTR (NM_007807, exon 13 of 13)	32642	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_118949.1	chr14	27361066	27361107	+	1	NA	promoter-TSS (NM_001289688)	promoter-TSS (NM_001289688)	-303	NM_001289688	71704	Mm.248606	NM_027871	ENSMUSG00000021895	Arhgef3	1200004I24Rik|9830169H03Rik|C76747|Xpln	Rho guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_14902.1	chr2	150181780	150181801	+	1	NA	promoter-TSS (NM_001145863)	promoter-TSS (NM_001145863)	35	NM_001145863	100271882		NM_001145863	ENSMUSG00000079009	Gm14139	OTTMUSG00000015769	predicted gene 14139	protein-coding
mm_66519.1	chr7	45120151	45120171	-	1	NA	Intergenic	Intergenic	-1596	NR_029560	387168		NR_029560	ENSMUSG00000065495	Mir150	Mirn150|mir-150|mmu-mir-150	microRNA 150	ncRNA
mm_80261.1	chr9	72856869	72856909	+	1	NA	exon (NM_175485, exon 10 of 20)	exon (NM_175485, exon 10 of 20)	49615	NM_175485	235472	Mm.31696	NM_175485	ENSMUSG00000036030	Prtg	A230098A12Rik|Igdcc5	protogenin	protein-coding
mm_67813.1	chr7	98162178	98162190	-	1	NA	intron (NM_007602, intron 1 of 12)	intron (NM_007602, intron 1 of 12)	158	NM_001301250	12337	Mm.326847	NM_007602	ENSMUSG00000035547	Capn5	nCL-3	calpain 5	protein-coding
mm_87611.1	chr10	57785504	57785521	+	1	NA	exon (NM_021272, exon 2 of 4)	exon (NM_021272, exon 2 of 4)	589	NM_021272	12140	Mm.3644	NM_021272	ENSMUSG00000019874	Fabp7	B-FABP|BFABP|Blbp|MRG	fatty acid binding protein 7, brain	protein-coding
mm_13194.1	chr2	93200294	93200307	+	1	NA	3' UTR (NM_001025246, exon 8 of 8)	3' UTR (NM_001025246, exon 8 of 8)	12716	NM_001025246	277414	Mm.41033	NM_001025246	ENSMUSG00000068735	Trp53i11	Tp53i11	transformation related protein 53 inducible protein 11	protein-coding
mm_61396.1	chr7	73375481	73375492	+	1	NA	promoter-TSS (NM_177740)	promoter-TSS (NM_177740)	-34	NM_177740	244058	Mm.333943	NM_177740	ENSMUSG00000070509	Rgma	BC059072|C230063O06	repulsive guidance molecule family member A	protein-coding
mm_132479.1	chr16	36784893	36784923	+	1	NA	promoter-TSS (NM_021301)	promoter-TSS (NM_021301)	54	NM_001145899	57738	Mm.281804	NM_021301	ENSMUSG00000022899	Slc15a2	8430408C16Rik|C78862|Pept2	solute carrier family 15 (H+/peptide transporter), member 2	protein-coding
mm_22830.1	chr3	27316897	27316927	+	1	NA	promoter-TSS (NM_009425)	promoter-TSS (NM_009425)	-165	NM_009425	22035	Mm.1062	NM_009425	ENSMUSG00000039304	Tnfsf10	A330042I21Rik|AI448571|APO-2L|Ly81|TL2|Tnlg6a|Trail	tumor necrosis factor (ligand) superfamily, member 10	protein-coding
mm_150394.1	chr19	36409834	36409856	+	1	NA	intron (NM_029508, intron 1 of 8)	CpG	30778	NM_029508	76073	Mm.259180	NM_029508	ENSMUSG00000024805	Pcgf5	0610009F02Rik|1110054A01Rik|5830406C17Rik|5830443C21Rik|9530023M17Rik|AI324127	polycomb group ring finger 5	protein-coding
mm_37436.1	chr4	122955511	122955533	-	1	NA	intron (NM_029662, intron 3 of 13)	intron (NM_029662, intron 3 of 13)	5666	NM_029662	76574	Mm.331842	NM_029662	ENSMUSG00000028655	Mfsd2a	1700018O18Rik|Mfsd2|NLS1	major facilitator superfamily domain containing 2A	protein-coding
mm_88588.1	chr10	79710891	79710900	+	1	NA	exon (NM_001077184, exon 5 of 7)	exon (NM_001077184, exon 5 of 7)	-5739	NM_008226	15166	Mm.12956	NM_008226	ENSMUSG00000020331	Hcn2	BCNG2|HAC1|trls	hyperpolarization-activated, cyclic nucleotide-gated K+ 2	protein-coding
mm_166039.1	chr4	129640968	129640978	-	1	NA	promoter-TSS (NM_001199695)	promoter-TSS (NM_001199695)	92	NM_001199695	109658	Mm.268863	NM_001005506	ENSMUSG00000053841	Txlna	2600010N21Rik|AI425952|AW209241|Il14|Txln	taxilin alpha	protein-coding
mm_149566.1	chr19	12798625	12798636	+	1	NA	promoter-TSS (NM_134152)	promoter-TSS (NM_134152)	21	NM_134152	107321	Mm.313136	NM_134152	ENSMUSG00000024696	Lpxn	4933402K05Rik|A530083L21Rik|AV278559|LDPL	leupaxin	protein-coding
mm_114716.1	chr13	83609430	83609441	+	1	NA	intron (NM_001347569, intron 3 of 10)	intron (NM_001347569, intron 3 of 10)	35828	NM_001347569	17260	Mm.24001	NM_025282	ENSMUSG00000005583	Mef2c	5430401D19Rik|9930028G15Rik|AV011172|Mef2	myocyte enhancer factor 2C	protein-coding
mm_30086.1	chr3	138143353	138143396	-	1	NA	promoter-TSS (NM_175389)	promoter-TSS (NM_175389)	14	NM_001163457	17777	Mm.2941	NM_008642	ENSMUSG00000028158	Mttp	1810043K16Rik|MTP	microsomal triglyceride transfer protein	protein-coding
mm_161864.1	chr18	33463956	33463956	-	1	NA	promoter-TSS (NM_001267717)	promoter-TSS (NM_001267717)	73	NM_001109988	27528	Mm.407415	NM_053078	ENSMUSG00000042834	Nrep	AI325076|D0H4S114|Harp|P311|PTZ17|SEZ17	neuronal regeneration related protein	protein-coding
mm_97192.1	chr11	75576891	75576909	+	1	NA	3' UTR (NM_001199283, exon 14 of 14)	3' UTR (NM_001199283, exon 14 of 14)	-11179	NM_008850	18738	Mm.3128	NM_008850	ENSMUSG00000017781	Pitpna	Pitpn|vb|vibrator	phosphatidylinositol transfer protein, alpha	protein-coding
mm_47861.1	chr5	134611859	134611876	-	1	NA	intron (NM_020044, intron 1 of 12)	intron (NM_020044, intron 1 of 12)	3158	NM_022964	56743	Mm.391375	NM_020044	ENSMUSG00000040751	Lat2	AW125574|LAB|NTAL|WSCR5|Wbscr15|Wbscr5	linker for activation of T cells family, member 2	protein-coding
mm_92449.1	chr10	77742679	77742683	-	1	NA	intron (NM_001287074, intron 1 of 11)	intron (NM_001287074, intron 1 of 11)	16195	NM_001205033	100502953	Mm.486157	NM_001205033	ENSMUSG00000096421	Gm10100	ENSMUSG00000061452	predicted gene 10100	protein-coding
mm_148759.1	chr19	6061268	6061288	+	1	NA	promoter-TSS (NM_013859)	promoter-TSS (NM_013859)	71	NM_013859	29805	Mm.2310	NM_013859	ENSMUSG00000075227	Znhit2	C11orf5|Fon|ORF6|Znhit2-ps	zinc finger, HIT domain containing 2	protein-coding
mm_6653.1	chr1	79762931	79762965	-	1	NA	Intergenic	RMER15|LTR|ERVL	-1179	NM_027057	69368	Mm.293273	NM_027057	ENSMUSG00000073643	Wdfy1	1700013B03Rik|1700120F24Rik|FENS-1|Jr1|WDF1|ZFYVE17|mKIAA1435	WD repeat and FYVE domain containing 1	protein-coding
mm_6725.1	chr1	82586857	82586863	-	1	NA	promoter-TSS (NM_007735)	promoter-TSS (NM_007735)	-11	NM_007735	12829	Mm.40253	NM_007735	ENSMUSG00000067158	Col4a4	E130010M05Rik|[a]4(IV)	collagen, type IV, alpha 4	protein-coding
mm_2061.1	chr1	87574017	87574032	+	1	NA	promoter-TSS (NM_001160164)	promoter-TSS (NM_001160164)	-3	NM_001160164	23956	Mm.143717	NM_015750	ENSMUSG00000079434	Neu2	MBS|MSS|MTS	neuraminidase 2	protein-coding
mm_109826.1	chr12	3872959	3872971	-	1	NA	intron (NM_007872, intron 5 of 22)	intron (NM_007872, intron 5 of 22)	-10721	NR_045884	100038522	Mm.417270	NR_045884	ENSMUSG00000073242	Dnmt3aos	ENSMUSG00000073242|Gm10485	DNA methyltransferase 3A, opposite strand	ncRNA
mm_72553.1	chr8	84066385	84066398	+	1	NA	promoter-TSS (NM_009055)	promoter-TSS (NM_009055)	-445	NM_009055	19724	Mm.7892	NM_009055	ENSMUSG00000031706	Rfx1	AI047719|AI385641	regulatory factor X, 1 (influences HLA class II expression)	protein-coding
mm_109651.1	chr12	112861090	112861101	+	1	NA	promoter-TSS (NM_019925)	promoter-TSS (NM_019925)	-179	NM_019925	56696	Mm.20455	NM_019925	ENSMUSG00000021298	Gpr132	G2a	G protein-coupled receptor 132	protein-coding
mm_142838.1	chr17	51793909	51793918	-	1	NA	intron (NM_009122, intron 5 of 10)	intron (NM_009122, intron 5 of 10)	18141	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_76402.1	chr8	84845954	84845962	-	1	NA	exon (NM_007591, exon 3 of 9)	exon (NM_007591, exon 3 of 9)	973	NM_007591	12317	Mm.1971	NM_007591	ENSMUSG00000003814	Calr	CRT|Calregulin	calreticulin	protein-coding
mm_45317.1	chr5	65436425	65436462	-	1	NA	promoter-TSS (NM_009466)	promoter-TSS (NM_009466)	-601	NM_009466	22235	Mm.344831	NM_009466	ENSMUSG00000029201	Ugdh	Udpgdh	UDP-glucose dehydrogenase	protein-coding
mm_5754.1	chr1	46853850	46853862	-	1	NA	promoter-TSS (NM_172653)	promoter-TSS (NM_172653)	-347	NM_172653	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|mKIAA1265	solute carrier family 39 (zinc transporter), member 10	protein-coding
mm_16500.1	chr2	181201178	181201179	+	1	NA	intron (NM_009184, intron 1 of 7)	intron (NM_009184, intron 1 of 7)	1611	NM_009184	20459	Mm.4497	NM_009184	ENSMUSG00000038751	Ptk6	BRK|Sik|Tksk|tks	PTK6 protein tyrosine kinase 6	protein-coding
mm_32666.1	chr4	115452572	115452578	+	1	NA	promoter-TSS (NM_001100185)	promoter-TSS (NM_001100185)	-29	NM_001100185	435802	Mm.466611	NM_001100185	ENSMUSG00000084346	Cyp4a30b	Cyp4a30b-ps|OTTMUSG00000008626	cytochrome P450, family 4, subfamily a, polypeptide 30b	protein-coding
mm_53815.1	chr6	147042746	147042750	+	1	NA	promoter-TSS (NM_145573)	promoter-TSS (NM_145573)	-22	NM_145573	232536	Mm.46656	NM_145573	ENSMUSG00000040112	Mrps35	MDSO23|MRP-S28|MRPS28	mitochondrial ribosomal protein S35	protein-coding
mm_128413.1	chr15	44748445	44748483	-	1	NA	5' UTR (NM_001285840, exon 1 of 7)	5' UTR (NM_001285840, exon 1 of 7)	208	NM_001285840	319613	Mm.207715	NM_176998	ENSMUSG00000022340	Sybu	Golsyn	syntabulin (syntaxin-interacting)	protein-coding
mm_66669.1	chr7	45725768	45725777	-	1	NA	promoter-TSS (NM_027055)	promoter-TSS (NM_027055)	44	NM_027055	69363	Mm.45607	NM_027055	ENSMUSG00000070563	Spaca4	1700008E09Rik|AV043694|Samp14	sperm acrosome associated 4	protein-coding
mm_105416.1	chr11	103652663	103652666	-	1	NA	Intergenic	Intergenic	3155	NM_001033212	104582	Mm.44618	NM_001033212	ENSMUSG00000046215	Rprml	AW049332	reprimo-like	protein-coding
mm_114818.1	chr13	91676783	91676793	+	1	NA	intron (NM_024272, intron 9 of 16)	(T)n|Simple_repeat|Simple_repeat	-64733	NM_028790	74156	Mm.275963	NM_028790	ENSMUSG00000021620	Acot12	1300004O04Rik|4930449F15Rik|AV027244|Cach|mCACH-1	acyl-CoA thioesterase 12	protein-coding
mm_76077.1	chr8	79248538	79248565	-	1	NA	promoter-TSS (NM_026315)	promoter-TSS (NM_026315)	32	NM_026315	67687	Mm.178707	NM_026315	ENSMUSG00000031682	1700011L22Rik	-	RIKEN cDNA 1700011L22 gene	protein-coding
mm_3482.1	chr1	150105591	150105600	+	1	NA	exon (NM_011198, exon 10 of 10)	exon (NM_011198, exon 10 of 10)	5564	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_154230.1	chr19	60224900	60224905	-	1	NA	intron (NM_029648, intron 1 of 7)	intron (NM_029648, intron 1 of 7)	1795	NM_029648	76539	Mm.290183	NM_029648	ENSMUSG00000057858	Fam204a	2310065H12Rik|2610015K05Rik|D19Ertd737e	family with sequence similarity 204, member A	protein-coding
mm_125856.1	chr15	75070783	75070796	+	1	NA	Intergenic	Intergenic	-21952	NM_001252056	17067	Mm.1583	NM_010741	ENSMUSG00000079018	Ly6c1	AA682074|AA959465|Ly-6C|Ly-6C1|Ly6c	lymphocyte antigen 6 complex, locus C1	protein-coding
mm_128405.1	chr15	44691691	44691695	-	1	NA	intron (NM_001032727, intron 2 of 5)	intron (NM_001032727, intron 2 of 5)	14795	NM_001285842	319613	Mm.207715	NM_176998	ENSMUSG00000022340	Sybu	Golsyn	syntabulin (syntaxin-interacting)	protein-coding
mm_33422.1	chr4	130006736	130006754	+	1	NA	intron (NM_001290714, intron 4 of 27)	CpG	14691	NM_001290715	230775	Mm.262241	NM_173071	ENSMUSG00000028782	Adgrb2	Bai2	adhesion G protein-coupled receptor B2	protein-coding
mm_10520.1	chr2	16361414	16361420	+	1	NA	intron (NM_026162, intron 1 of 13)	intron (NM_026162, intron 1 of 13)	5113	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding
mm_132388.1	chr16	34994879	34994944	+	1	NA	intron (NM_139300, intron 29 of 31)	intron (NM_139300, intron 29 of 31)	-27510	NM_023587	70757	Mm.27286	NM_023587	ENSMUSG00000035376	Hacd2	6330408J20Rik|AI255777|AI481689|Hcad2|Ptplb	3-hydroxyacyl-CoA dehydratase 2	protein-coding
mm_163141.1	chr11	80183908	80183918	+	1	NA	promoter-TSS (NM_028019)	promoter-TSS (NM_028019)	41	NM_028019	71956	Mm.22985	NM_028019	ENSMUSG00000020707	Rnf135	0610037N03Rik|2410006N06Rik	ring finger protein 135	protein-coding
mm_156564.1	chrX	151858205	151858208	+	1	NA	intron (NM_021523, intron 16 of 82)	intron (NM_021523, intron 16 of 82)	-1356	NR_130340	100526542		NR_130340	ENSMUSG00000093219	Mir3113	mmu-mir-3113	microRNA 3113	ncRNA
mm_143545.1	chr17	74017102	74017110	-	1	NA	TTS (NM_053188)	TTS (NM_053188)	30810	NM_053188	94224	Mm.38933	NM_053188	ENSMUSG00000038541	Srd5a2	5ART2|S5AR 2	steroid 5 alpha-reductase 2	protein-coding
mm_63460.1	chr7	127565478	127565480	+	1	NA	TTS (NM_001304267)	TTS (NM_001304267)	4256	NM_001304267	105180375	Mm.428042	NM_001304267	ENSMUSG00000106715	Tmem265	-	transmembrane protein 265	protein-coding
mm_98082.1	chr11	86545174	86545193	+	1	NA	promoter-TSS (NM_001114334)	promoter-TSS (NM_001114334)	192	NM_001199046	56427	Mm.383207	NM_019756	ENSMUSG00000020513	Tubd1	4930550G19Rik|Tubd	tubulin, delta 1	protein-coding
mm_87951.1	chr10	63060726	63060752	+	1	NA	promoter-TSS (NM_026701)	promoter-TSS (NM_026701)	-878	NM_026701	68371	Mm.261389	NM_026701	ENSMUSG00000020072	Pbld1	0610038K03Rik|Mawbp|Pbld	phenazine biosynthesis-like protein domain containing 1	protein-coding
mm_129189.1	chr15	76350647	76350657	-	1	NA	promoter-TSS (NM_026859)	promoter-TSS (NM_026859)	458	NM_025340	106025	Mm.41463	NM_025340	ENSMUSG00000022552	Sharpin	0610041B22Rik|AW121341|RBCKL1|SIPL1|cpdm	SHANK-associated RH domain interacting protein	protein-coding
mm_11164.1	chr2	28557604	28557627	+	1	NA	exon (NM_009885, exon 9 of 11)	exon (NM_009885, exon 9 of 11)	5788	NM_009885	12613	Mm.236017	NM_009885	ENSMUSG00000026818	Cel	1810036E18Rik|BAL	carboxyl ester lipase	protein-coding
mm_67510.1	chr7	80786851	80786864	-	1	NA	intron (NM_016721, intron 2 of 37)	intron (NM_016721, intron 2 of 37)	16474	NM_016721	29875	Mm.207619	NM_016721	ENSMUSG00000030536	Iqgap1	AA682088|D7Ertd237e|D7Ertd257e|mKIAA0051	IQ motif containing GTPase activating protein 1	protein-coding
mm_127645.1	chr15	102484196	102484204	+	1	NA	exon (NM_001174073, exon 8 of 13)	exon (NM_001174073, exon 8 of 13)	13568	NM_001174073	18521	Mm.236513	NM_011042	ENSMUSG00000056851	Pcbp2	AW412548|Hnrpx|alphaCP-2	poly(rC) binding protein 2	protein-coding
mm_53099.1	chr6	125049953	125049971	+	1	NA	promoter-TSS (NM_016845)	promoter-TSS (NM_016845)	35	NM_016845	54137	Mm.347910	NM_016845	ENSMUSG00000072770	Acrbp	OY-TES-1|sp32	proacrosin binding protein	protein-coding
mm_64770.1	chr7	4995389	4995414	-	1	NA	intron (NM_026741, intron 1 of 1)	intron (NM_026741, intron 1 of 1)	700	NM_026741	68490	Mm.76400	NM_026741	ENSMUSG00000051550	Zfp579	1110003A17Rik|Znf579	zinc finger protein 579	protein-coding
mm_107257.1	chr12	28675246	28675254	+	1	NA	promoter-TSS (NM_134052)	promoter-TSS (NM_134052)	43	NM_134052	104923	Mm.291504	NM_134052	ENSMUSG00000020629	Adi1	AL024210|Fe-ARD|MTCBP-1|Ni-ARD	acireductone dioxygenase 1	protein-coding
mm_84795.1	chr9	77223349	77223355	-	1	NA	intron (NM_027150, intron 2 of 7)	PB1D9|SINE|Alu	124518	NM_027150	69642	Mm.35008	NM_027150	ENSMUSG00000032355	Mlip	2310046A06Rik|AI931782|CIP	muscular LMNA-interacting protein	protein-coding
mm_172696.1	chr8	62162598	62162599	-	1	NA	Intergenic	L1Md_T|LINE|L1	-39405	NM_011922	26359	Mm.42179	NM_011922	ENSMUSG00000031635	Anxa10	-	annexin A10	protein-coding
mm_152265.1	chr19	8798466	8798470	-	1	NA	promoter-TSS (NM_026329)	promoter-TSS (NM_026329)	89	NM_026329	67710	Mm.22117	NM_026329	ENSMUSG00000071662	Polr2g	2410046K11Rik|A230108L04Rik|C76415|RBP7|Rpo2-7l	polymerase (RNA) II (DNA directed) polypeptide G	protein-coding
mm_42747.1	chr5	120753925	120753941	+	1	NA	3' UTR (NM_145226, exon 16 of 16)	3' UTR (NM_145226, exon 16 of 16)	-4085	NM_001347448	246728	Mm.260926	NM_145227	ENSMUSG00000032690	Oas2	Oasl11	2'-5' oligoadenylate synthetase 2	protein-coding
mm_33331.1	chr4	129136860	129136876	+	1	NA	promoter-TSS (NM_027402)	promoter-TSS (NM_027402)	-131	NM_027402	384061	Mm.44075	NM_027402	ENSMUSG00000001334	Fndc5	1500001L03Rik|AI836596|C87088|PeP|Pxp	fibronectin type III domain containing 5	protein-coding
mm_95965.1	chr11	58893704	58893710	+	1	NA	intron (NM_011758, intron 3 of 4)	(GGGA)n|Simple_repeat|Simple_repeat	10518	NM_011758	22698	Mm.127646	NM_011758	ENSMUSG00000037001	Zfp39	CTfin33|Zfp-39	zinc finger protein 39	protein-coding
mm_3179.1	chr1	135751171	135751210	+	1	NA	3' UTR (NM_007791, exon 6 of 6)	3' UTR (NM_007791, exon 6 of 6)	-14895	NM_013750	27280	Mm.34346	NM_013750	ENSMUSG00000041801	Phlda3	Tih1	pleckstrin homology like domain, family A, member 3	protein-coding
mm_123542.1	chr14	66824446	66824466	-	1	NA	exon (NM_009955, exon 8 of 14)	exon (NM_009955, exon 8 of 14)	44144	NM_009955	12934	Mm.352648	NM_009955	ENSMUSG00000022048	Dpysl2	AI851130|Crmp2|DRP2|Musunc33|TOAD-64|Ulip2	dihydropyrimidinase-like 2	protein-coding
mm_43834.1	chr5	142972416	142972433	+	1	NA	3' UTR (NM_007984, exon 5 of 5)	3' UTR (NM_007984, exon 5 of 5)	12069	NM_007984	14086	Mm.289707	NM_007984	ENSMUSG00000029581	Fscn1	AI663989|Fan1|fascin-1	fascin actin-bundling protein 1	protein-coding
mm_112250.1	chr12	113626024	113626037	-	1	NA	Intergenic	Intergenic	82122	NM_174885	238406	Mm.188683	NM_174885	ENSMUSG00000043945	Adam6a	Adam6|tMDCIV	a disintegrin and metallopeptidase domain 6A	protein-coding
mm_131756.1	chr16	22857917	22857927	+	1	NA	promoter-TSS (NM_001190805)	promoter-TSS (NM_001190805)	77	NM_001190804	67838	Mm.37516	NM_026400	ENSMUSG00000004460	Dnajb11	1810031F23Rik|ABBP-2|AL024055|Dj9|ERdj3|ERj3p	DnaJ heat shock protein family (Hsp40) member B11	protein-coding
mm_71478.1	chr8	46617384	46617385	+	1	NA	promoter-TSS (NM_009810)	promoter-TSS (NM_009810)	93	NM_009810	12367	Mm.34405	NM_009810	ENSMUSG00000031628	Casp3	A830040C14Rik|AC-3|CASP-3|CC3|CPP-32|CPP32|Caspase-3|Lice|SCA-1|Yama|mldy	caspase 3	protein-coding
mm_69017.1	chr7	126707833	126707864	-	1	NA	Intergenic	Intergenic	-3032	NM_009898	12721	Mm.290482	NM_009898	ENSMUSG00000030707	Coro1a	Clabp|Lmb3|TACO|p57	coronin, actin binding protein 1A	protein-coding
mm_2246.1	chr1	91056648	91056668	+	1	NA	intron (NM_001310732, intron 1 of 24)	intron (NM_001310732, intron 1 of 24)	3214	NM_008515	16978	Mm.45039	NM_008515	ENSMUSG00000026305	Lrrfip1	AU024550|Fliiap1	leucine rich repeat (in FLII) interacting protein 1	protein-coding
mm_54481.1	chr6	35112631	35112634	-	1	NA	intron (NM_016877, intron 1 of 10)	intron (NM_016877, intron 1 of 10)	21105	NM_001164412	53621	Mm.214525	NM_016877	ENSMUSG00000038784	Cnot4	Not4|Not4h|Not4hp	CCR4-NOT transcription complex, subunit 4	protein-coding
mm_35148.1	chr4	11965672	11965678	-	1	NA	promoter-TSS (NM_001098231)	promoter-TSS (NM_001098231)	38	NM_001098231	381511	Mm.331489	NM_001033453	ENSMUSG00000049225	Pdp1	Gm1024|Ppm2c	pyruvate dehyrogenase phosphatase catalytic subunit 1	protein-coding
mm_116492.1	chr13	44869609	44869623	-	1	NA	intron (NM_001205044, intron 4 of 18)	LSU-rRNA_Hsa|rRNA|rRNA	132480	NM_025772	94245	Mm.352311	NM_025772	ENSMUSG00000057531	Dtnbp1	5430437B18Rik|AW048963|Bloc1s8|dysbindin|sdy	dystrobrevin binding protein 1	protein-coding
mm_55206.1	chr6	52213321	52213343	-	1	NA	promoter-TSS (NM_010452)	promoter-TSS (NM_010452)	-265	NM_010452	15400	Mm.71533	NM_010452	ENSMUSG00000079560	Hoxa3	Hox-1.5|Mo-10	homeobox A3	protein-coding
mm_5511.1	chr1	37496123	37496156	-	1	NA	intron (NM_001290801, intron 2 of 14)	intron (NM_001290801, intron 2 of 14)	-7534	NR_024017	77633	Mm.483177	NR_024017	ENSMUSG00000103948	4930594C11Rik	-	G1 to S phase transition pseudogene	pseudo
mm_83853.1	chr9	54560139	54560225	-	1	NA	promoter-TSS (NM_019686)	promoter-TSS (NM_019686)	-103	NM_019686	56506	Mm.42192	NM_019686	ENSMUSG00000037493	Cib2	2810434I23Rik|AI449053	calcium and integrin binding family member 2	protein-coding
mm_66928.1	chr7	61529950	61529985	-	1	NA	non-coding (NR_045727, exon 5 of 5)	non-coding (NR_045727, exon 5 of 5)	85360	NR_045727	319752	Mm.294476	NR_045727		B230209E15Rik	-	RIKEN cDNA B230209E15 gene	ncRNA
mm_57477.1	chr6	125236839	125236854	-	1	NA	exon (NM_001042564, exon 1 of 4)	exon (NM_001042564, exon 1 of 4)	181	NM_001033126	21940	Mm.367714	NM_001033126	ENSMUSG00000030336	Cd27	S152|Tnfrsf7|Tp55	CD27 antigen	protein-coding
mm_19380.1	chr2	91195148	91195189	-	1	NA	promoter-TSS (NM_013839)	promoter-TSS (NM_013839)	-52	NM_001177730	22259	Mm.22690	NM_013839	ENSMUSG00000002108	Nr1h3	AU018371|LXR|RLD1|Unr1	nuclear receptor subfamily 1, group H, member 3	protein-coding
mm_156634.1	chrX	155912003	155912005	+	1	NA	Intergenic	Intergenic	-288677	NM_001093750	211612	Mm.218811	NM_001093750	ENSMUSG00000041552	Ptchd1	9630036J22Rik|AI848149|Gm387	patched domain containing 1	protein-coding
mm_138948.1	chr17	44125346	44125349	+	1	NA	Intergenic	URR1A|DNA|hAT-Charlie	-19539	NM_199016	224794	Mm.255971	NM_199016	ENSMUSG00000023961	Enpp4	4933413N07Rik|AA986363|AI195364|E-NPP 4|Gm90|mKIAA0879	ectonucleotide pyrophosphatase/phosphodiesterase 4	protein-coding
mm_43330.1	chr5	135009749	135009765	+	1	NA	exon (NM_145215, exon 1 of 6)	exon (NM_145215, exon 1 of 6)	301	NR_033794	68758	Mm.389700	NM_145215	ENSMUSG00000040532	Abhd11	1110054D16Rik|A630008N09Rik|Wbscr21	abhydrolase domain containing 11	protein-coding
mm_71042.1	chr8	33667810	33667826	+	1	NA	intron (NM_010344, intron 1 of 12)	intron (NM_010344, intron 1 of 12)	14580	NM_010344	14782	Mm.283573	NM_010344	ENSMUSG00000031584	Gsr	AI325518|D8Ertd238e|Gr-1|Gr1	glutathione reductase	protein-coding
mm_58648.1	chr7	6277441	6277454	+	1	NA	exon (NM_001177416, exon 10 of 12)	exon (NM_001177416, exon 10 of 12)	-9133	NM_001024928	384763	Mm.276279	NM_001024928	ENSMUSG00000054893	Zfp667	A830025F02Rik|Mip1|ZNF667	zinc finger protein 667	protein-coding
mm_143458.1	chr17	70990692	70990704	-	1	NA	promoter-TSS (NM_023402)	promoter-TSS (NM_023402)	-182	NM_023402	67938	Mm.261329	NM_023402	ENSMUSG00000034868	Myl12b	1500001M02Rik|C77744|Mylc2b|RLC-B	myosin, light chain 12B, regulatory	protein-coding
mm_49534.1	chr6	30175258	30175264	+	1	NA	Intergenic	Intergenic	-1136	NR_126541	101447999		NR_126540		Mirc35hg	-	microRNA cluster 35, host gene	ncRNA
mm_82267.1	chr9	7184441	7184518	-	1	NA	promoter-TSS (NM_029775)	promoter-TSS (NM_029775)	-87	NM_029775	76863	Mm.27293	NM_029775	ENSMUSG00000032002	Dcun1d5	3110001A18Rik|4833420K19Rik|AW060460|D430047L21Rik	DCN1, defective in cullin neddylation 1, domain containing 5 (S. cerevisiae)	protein-coding
mm_165165.1	chr2	25500142	25500147	-	1	NA	promoter-TSS (NM_013908)	promoter-TSS (NM_013908)	362	NM_027062	69379	Mm.24596	NM_027062	ENSMUSG00000015083	C8g	-	complement component 8, gamma polypeptide	protein-coding
mm_166691.1	chr6	113544100	113544109	+	1	NA	intron (NM_001347350, intron 8 of 42)	intron (NM_001347350, intron 8 of 42)	12422	NM_001347350	211651	Mm.160061	NM_001033244	ENSMUSG00000034023	Fancd2	2410150O07Rik|AU015151|BB137857|FA-D2|FA4|FACD|FAD|FANCD	Fanconi anemia, complementation group D2	protein-coding
mm_26066.1	chr3	135840324	135840345	+	1	NA	promoter-TSS (NR_040540)	promoter-TSS (NR_040540)	-65	NR_040540	71038	Mm.410798	NR_040540	ENSMUSG00000106306	4933401H06Rik	-	RIKEN cDNA 4933401H06 gene	ncRNA
mm_12898.1	chr2	84799445	84799469	+	1	NA	intron (NM_019949, intron 1 of 3)	intron (NM_019949, intron 1 of 3)	629	NM_019949	56791	Mm.38261	NM_019949	ENSMUSG00000027078	Ube2l6	2810489I21Rik|RIG-B|UBCH8|Ubce8|Ubcm8	ubiquitin-conjugating enzyme E2L 6	protein-coding
mm_61406.1	chr7	73418440	73418468	+	1	NA	3' UTR (NM_177740, exon 4 of 4)	3' UTR (NM_177740, exon 4 of 4)	-42680	NR_040324	319783	Mm.349813	NR_040324	ENSMUSG00000097756	A730056A06Rik	C76391	RIKEN cDNA A730056A06 gene	ncRNA
mm_19513.1	chr2	93984789	93984795	-	1	NA	intron (NM_026944, intron 8 of 9)	intron (NM_026944, intron 8 of 9)	4758	NR_045827	70852	Mm.437014	NR_045827	ENSMUSG00000027196	Alkbh3os1	4921507L20Rik	alkB homolog 3, opposite strand 1	ncRNA
mm_45648.1	chr5	77015930	77015940	-	1	NA	promoter-TSS (NM_027970)	promoter-TSS (NM_027970)	-88	NM_027970	71868	Mm.151092	NM_027970	ENSMUSG00000029248	Thegl	1700023E05Rik	theg spermatid protein like	protein-coding
mm_77463.1	chr8	122421088	122421110	-	1	NA	promoter-TSS (NM_145834)	promoter-TSS (NM_145834)	-986	NM_145834	234836	Mm.222808	NM_145834	ENSMUSG00000046108	Il17c	IL-17C	interleukin 17C	protein-coding
mm_52186.1	chr6	99522450	99522454	+	1	NA	Intergenic	CpG-12329	-1459	NM_001347345	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_94441.1	chr11	6301541	6301546	+	1	NA	intron (NM_001252287, intron 2 of 22)	B1_Mur1|SINE|Alu	8985	NM_001252288	18293	Mm.276348	NM_010956	ENSMUSG00000020456	Ogdh	2210403E04Rik|2210412K19Rik|AA409584|d1401|mKIAA4192	oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)	protein-coding
mm_150041.1	chr19	29377937	29377948	+	1	NA	intron (NM_021893, intron 3 of 6)	intron (NM_021893, intron 3 of 6)	10504	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_83582.1	chr9	48340775	48340791	-	1	NA	5' UTR (NM_030069, exon 1 of 6)	5' UTR (NM_030069, exon 1 of 6)	115	NM_030069	78252	Mm.31626	NM_030069	ENSMUSG00000032028	Nxpe2	4432416J03Rik|AI323362|Fam55b	neurexophilin and PC-esterase domain family, member 2	protein-coding
mm_145205.1	chr18	50017024	50017037	+	1	NA	intron (NM_001177759, intron 1 of 1)	intron (NM_001177759, intron 1 of 1)	-36252	NM_134131	106869	Mm.27740	NM_134131	ENSMUSG00000062210	Tnfaip8	AA987150|E130304C20Rik|ENSMUSG00000073567|Gg2-1|Gm10539|Nded|Ssc-2|Tipe	tumor necrosis factor, alpha-induced protein 8	protein-coding
mm_32579.1	chr4	110409563	110409566	+	1	NA	intron (NM_001048189, intron 1 of 12)	intron (NM_001048189, intron 1 of 12)	11866	NM_030231	78933	Mm.435620	NM_030231	ENSMUSG00000061298	Agbl4	4930578N11Rik|4931433A01Rik	ATP/GTP binding protein-like 4	protein-coding
mm_141401.1	chr17	29264116	29264146	-	1	NA	promoter-TSS (NM_026845)	promoter-TSS (NM_026845)	-160	NM_026845	68816	Mm.328928	NM_026845	ENSMUSG00000024007	Ppil1	1110060O10Rik|AI327391|Cypl1	peptidylprolyl isomerase (cyclophilin)-like 1	protein-coding
mm_99020.1	chr11	98918662	98918690	+	1	NA	intron (NM_001025779, intron 9 of 11)	intron (NM_001025779, intron 9 of 11)	10525	NM_011799	23834	Mm.20912	NM_011799	ENSMUSG00000017499	Cdc6	CDC18L	cell division cycle 6	protein-coding
mm_3032.1	chr1	133880943	133880947	+	1	NA	Intergenic	Intergenic	26228	NM_054076	269120	Mm.59985	NM_054076	ENSMUSG00000010311	Optc	-	opticin	protein-coding
mm_56646.1	chr6	113377511	113377548	-	1	NA	promoter-TSS (NM_026552)	promoter-TSS (NM_026552)	-9	NM_133932	101206	Mm.266811	NM_133932	ENSMUSG00000048930	Tada3	1110004B19Rik|ADA3|AI987856|Tada3l	transcriptional adaptor 3	protein-coding
mm_21070.1	chr2	152826174	152826181	-	1	NA	intron (NM_001289717, intron 2 of 2)	intron (NM_001289717, intron 2 of 2)	4540	NM_001289716	12048	Mm.238213	NM_009743	ENSMUSG00000007659	Bcl2l1	Bcl(X)L|Bcl-XL|Bcl2l|BclX|bcl-x|bcl2-L-1	BCL2-like 1	protein-coding
mm_85958.1	chr9	112124763	112124772	-	1	NA	exon (NM_033264, exon 16 of 19)	exon (NM_033264, exon 16 of 19)	-6056	NR_029823	723815		NR_029823	ENSMUSG00000065441	Mir128-2	Mirn128-2|Mirn128b|mir-128-2|mir-128b	microRNA 128-2	ncRNA
mm_141127.1	chr17	26201190	26201227	-	1	NA	5' UTR (NM_008113, exon 1 of 6)	5' UTR (NM_008113, exon 1 of 6)	142	NM_008113	14570	Mm.1383	NM_008113	ENSMUSG00000073433	Arhgdig	Gdi5|RIP2|Rho-GDI-3|Rho-GDI2	Rho GDP dissociation inhibitor (GDI) gamma	protein-coding
mm_71217.1	chr8	40898931	40898966	+	1	NA	5' UTR (NM_001044740, exon 2 of 12)	5' UTR (NM_001044740, exon 2 of 12)	-27285	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_146345.1	chr18	82537606	82537617	+	1	NA	intron (NM_001025245, intron 3 of 3)	B4A|SINE|B4	-16852	NM_001025256	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_71677.1	chr8	60870016	60870019	+	1	NA	Intergenic	Intergenic	-20434	NM_028299	72612	Mm.25263	NM_028299	ENSMUSG00000038005	Hpf1	2700029M09Rik|C230006B22Rik|C4orf27	histone PARylation factor 1	protein-coding
mm_2453.1	chr1	101231852	101231856	+	1	NA	Intergenic	Intergenic	76086	NR_037989	100504525	Mm.87065	NR_037989	ENSMUSG00000100684	Gm20268	-	predicted gene, 20268	ncRNA
mm_30182.1	chr3	144257327	144257372	-	1	NA	Intergenic	Intergenic	-52094	NM_010723	16911	Mm.29187	NM_010723	ENSMUSG00000028266	Lmo4	A730077C12Rik|Crp3|Etohi4	LIM domain only 4	protein-coding
mm_106464.1	chr11	120070547	120070552	-	1	NA	exon (NM_009734, exon 15 of 26)	exon (NM_009734, exon 15 of 26)	16278	NM_009734	12009	Mm.2556	NM_009734	ENSMUSG00000039781	Cep131	AZ1|Azi|Azi1	centrosomal protein 131	protein-coding
mm_27628.1	chr3	60501826	60501834	-	1	NA	intron (NM_001253710, intron 1 of 7)	intron (NM_001253710, intron 1 of 7)	651	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_26503.1	chr3	145758719	145758738	+	1	NA	promoter-TSS (NM_026993)	promoter-TSS (NM_026993)	36	NM_026993	69219	Mm.234247	NM_026993	ENSMUSG00000028194	Ddah1	2410006N07Rik|2510015N06Rik|AI987801|AW050362	dimethylarginine dimethylaminohydrolase 1	protein-coding
mm_138927.1	chr17	43801789	43801817	+	1	NA	promoter-TSS (NM_207649)	promoter-TSS (NM_207649)	-48	NM_207649	53901	Mm.251242	NM_030598	ENSMUSG00000039601	Rcan2	Csp2|Dscr1l1|MCIP2|ZAKI-4	regulator of calcineurin 2	protein-coding
mm_84904.1	chr9	79962019	79962031	-	1	NA	intron (NM_001081243, intron 1 of 5)	intron (NM_001081243, intron 1 of 5)	15857	NM_001081243	70598	Mm.23049	NM_001081243	ENSMUSG00000034898	Filip1	5730485H21Rik|AI843021	filamin A interacting protein 1	protein-coding
mm_83460.1	chr9	45262957	45263008	-	1	NA	intron (NR_136903, intron 4 of 5)	intron (NR_136903, intron 4 of 5)	3725	NR_106054	102466803		NR_106054	ENSMUSG00000098361	Mir7086	Gm27643|mmu-mir-7086	microRNA 7086	ncRNA
mm_51189.1	chr6	70968803	70968804	+	1	NA	Intergenic	B1F1|SINE|Alu	12197	NM_001101464	232077	Mm.297656	NM_001101464	ENSMUSG00000055874	Foxi3	-	forkhead box I3	protein-coding
mm_105704.1	chr11	108270516	108270587	-	1	NA	intron (NM_011101, intron 2 of 16)	intron (NM_011101, intron 2 of 16)	73337	NM_011101	18750	Mm.222178	NM_011101	ENSMUSG00000050965	Prkca	AI875142|Pkca	protein kinase C, alpha	protein-coding
mm_155407.1	chrX	73356435	73356445	+	1	NA	3' UTR (NM_031494, exon 6 of 6)	3' UTR (NM_031494, exon 6 of 6)	13819	NM_001160229	27081	Mm.26595	NM_031494	ENSMUSG00000031365	Zfp275	5430431L06Rik|AI593314|DXBay20|DXHXS52|DXPas8	zinc finger protein 275	protein-coding
mm_151378.1	chr19	56035095	56035097	+	1	NA	Intergenic	Intergenic	139775	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_110423.1	chr12	46818497	46818517	-	1	NA	intron (NM_021361, intron 1 of 4)	intron (NM_021361, intron 1 of 4)	268	NM_021361	664883	Mm.247195	NM_021361	ENSMUSG00000021047	Nova1	9430099M15Rik|G630039L02|Nova-1	neuro-oncological ventral antigen 1	protein-coding
mm_113735.1	chr13	44216192	44216226	+	1	NA	intron (NR_045088, intron 1 of 3)	intron (NR_045088, intron 1 of 3)	278	NR_045088	100503592	Mm.184925	NR_045088		A330076C08Rik	-	RIKEN cDNA A330076C08 gene	ncRNA
mm_157445.1	chrX	41822412	41822446	-	1	NA	exon (NM_001033422, exon 30 of 39)	exon (NM_001033422, exon 30 of 39)	89472	NM_001033422	331401	Mm.259498	NM_001033422	ENSMUSG00000037475	Thoc2	6330441O12Rik|D130005M13Rik|Gm1139|Gm1793|Tho2	THO complex 2	protein-coding
mm_140897.1	chr17	24073480	24073490	-	1	NA	promoter-TSS (NM_027008)	promoter-TSS (NM_027008)	0	NM_027008	69259	Mm.28171	NM_027008	ENSMUSG00000016946	Kctd5	2610030N08Rik|mKIAA0176	potassium channel tetramerisation domain containing 5	protein-coding
mm_38957.1	chr4	150678757	150678766	-	1	NA	Intergenic	RSINE1|SINE|B4	-26587	NM_173774	242773	Mm.29280	NM_173774	ENSMUSG00000039838	Slc45a1	C230078B22|Dnb5	solute carrier family 45, member 1	protein-coding
mm_40854.1	chr5	73502646	73502654	+	1	NA	intron (NM_001190733, intron 1 of 9)	intron (NM_001190733, intron 1 of 9)	11624	NM_178896	100737	Mm.220312	NM_178896	ENSMUSG00000051674	Dcun1d4	AI836376	DCN1, defective in cullin neddylation 1, domain containing 4 (S. cerevisiae)	protein-coding
mm_83760.1	chr9	51963405	51963425	-	1	NA	exon (NM_007996, exon 1 of 4)	exon (NM_007996, exon 1 of 4)	187	NM_007996	14148	Mm.1061	NM_007996	ENSMUSG00000032051	Fdx1	-	ferredoxin 1	protein-coding
mm_20174.1	chr2	122396216	122396217	-	1	NA	Intergenic	RMER1B|Other|Other	-27298	NM_001013829	435684	Mm.458215	NM_001013829	ENSMUSG00000033256	Shf	-	Src homology 2 domain containing F	protein-coding
mm_110622.1	chr12	57176089	57176091	-	1	NA	intron (NM_172577, intron 1 of 9)	intron (NM_172577, intron 1 of 9)	-15447	NM_001167976	217593	Mm.32835	NM_172577	ENSMUSG00000035472	Slc25a21	9930033G19Rik|A630030I10|BB158148	solute carrier family 25 (mitochondrial oxodicarboxylate carrier), member 21	protein-coding
mm_87411.1	chr10	45875305	45875309	+	1	NA	Intergenic	Intergenic	67603	NR_040624	320363	Mm.123343	NR_040624	ENSMUSG00000110874	D030045P18Rik	-	RIKEN cDNA D030045P18 gene	ncRNA
mm_148812.1	chr19	6294428	6294445	+	1	NA	exon (NM_010119, exon 3 of 5)	exon (NM_010119, exon 3 of 5)	-12021	NM_001033342	240505	Mm.329622	NM_001033342	ENSMUSG00000024769	Cdc42bpg	BC046418|MRCKgamma	CDC42 binding protein kinase gamma (DMPK-like)	protein-coding
mm_67821.1	chr7	98199506	98199521	-	1	NA	promoter-TSS (NM_001081167)	promoter-TSS (NM_001081167)	-38	NM_001081167	272411	Mm.98333	NM_001081167	ENSMUSG00000074004	B3gnt6	BC039789|Core-3|Core3	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 6 (core 3 synthase)	protein-coding
mm_96836.1	chr11	70018071	70018092	+	1	NA	promoter-TSS (NM_007864)	promoter-TSS (NM_007864)	-524	NM_001109752	13385	Mm.27256	NM_007864	ENSMUSG00000020886	Dlg4	Dlgh4|PSD-95|PSD95|SAP90|SAP90A	discs, large homolog 4 (Drosophila)	protein-coding
mm_135196.1	chr16	36455313	36455331	-	1	NA	promoter-TSS (NM_025288)	promoter-TSS (NM_025288)	70	NM_025288	20863	Mm.136573	NM_025288	ENSMUSG00000054905	Stfa3	Stf3	stefin A3	protein-coding
mm_101997.1	chr11	51262797	51262809	-	1	NA	promoter-TSS (NM_007714)	promoter-TSS (NM_007714)	148	NM_177567	193286	Mm.80975	NM_177567	ENSMUSG00000045942	BC049762	4930503F14	cDNA sequence BC049762	protein-coding
mm_59522.1	chr7	27607759	27607804	+	1	NA	intron (NM_001331109, intron 1 of 13)	intron (NM_001331109, intron 1 of 13)	445	NM_001331109	11652	Mm.177194	NM_007434	ENSMUSG00000004056	Akt2	2410016A19Rik|AW554154|PKB|PKBbeta	thymoma viral proto-oncogene 2	protein-coding
mm_114517.1	chr13	73260511	73260546	+	1	NA	promoter-TSS (NM_018885)	promoter-TSS (NM_018885)	31	NM_018885	50916	Mm.103784	NM_018885	ENSMUSG00000021604	Irx4	-	Iroquois related homeobox 4 (Drosophila)	protein-coding
mm_23770.1	chr3	75557531	75557561	+	1	NA	promoter-TSS (NM_009250)	promoter-TSS (NM_009250)	13	NM_009250	20713	Mm.41560	NM_009250	ENSMUSG00000027834	Serpini1	AI837402|Ns|PI-12|PI12|Spi17	serine (or cysteine) peptidase inhibitor, clade I, member 1	protein-coding
mm_41250.1	chr5	88793866	88793874	+	1	NA	Intergenic	Intergenic	28857	NM_007832	13178	Mm.298892	NM_007832	ENSMUSG00000029366	Dck	-	deoxycytidine kinase	protein-coding
mm_68908.1	chr7	126457153	126457170	-	1	NA	exon (NM_007504, exon 7 of 23)	exon (NM_007504, exon 7 of 23)	5912	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_135235.1	chr16	36957339	36957362	-	1	NA	exon (NM_008225, exon 10 of 14)	exon (NM_008225, exon 10 of 14)	21786	NM_001037321	207215	Mm.211899	NM_001037321	ENSMUSG00000047746	Fbxo40	9830003A13Rik|mKIAA1195	F-box protein 40	protein-coding
mm_102432.1	chr11	59506200	59506239	-	1	NA	non-coding (NR_135273, exon 1 of 4)	non-coding (NR_135273, exon 1 of 4)	421	NM_001291014	268417	Mm.239793	NM_172941	ENSMUSG00000020472	Zkscan17	Nizp1|Zfp496|Znf496	zinc finger with KRAB and SCAN domains 17	protein-coding
mm_58297.1	chr6	145865445	145865474	-	1	NA	promoter-TSS (NM_001271768)	promoter-TSS (NM_001271768)	-39	NM_024469	79362	Mm.154529	NM_024469	ENSMUSG00000030256	Bhlhe41	6430520M22Rik|Bhlhb2l|Bhlhb3|DEC2|Sharp1	basic helix-loop-helix family, member e41	protein-coding
mm_100759.1	chr11	4497526	4497532	-	1	NA	intron (NM_028860, intron 10 of 17)	intron (NM_028860, intron 10 of 17)	-56447	NM_029458	75828	Mm.159592	NM_029458	ENSMUSG00000020419	Hormad2	4930529M09Rik	HORMA domain containing 2	protein-coding
mm_126882.1	chr15	89453914	89453934	+	1	NA	promoter-TSS (NM_021921)	promoter-TSS (NM_021921)	13	NM_021921	60597	Mm.173337	NM_021921	ENSMUSG00000022619	Mapk8ip2	3230402N03Rik|AI847694|AW049958|IB2|Jip2|R75148	mitogen-activated protein kinase 8 interacting protein 2	protein-coding
mm_163829.1	chr14	19417500	19417543	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	185066	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_37467.1	chr4	123512143	123512154	-	1	NA	exon (NM_001199137, exon 9 of 93)	exon (NM_001199137, exon 9 of 93)	-100237	NM_001167918	442834	Mm.483803	NM_001167918		D830031N03Rik	Kiaa0754|mKIAA0754	RIKEN cDNA D830031N03 gene	protein-coding
mm_26454.1	chr3	142701068	142701105	+	1	NA	promoter-TSS (NM_001293560)	promoter-TSS (NM_001293560)	38	NM_001293560	229905	Mm.289643	NM_173763	ENSMUSG00000040213	Kyat3	Ccbl2|KATIII|Kat3	kynurenine aminotransferase 3	protein-coding
mm_44153.1	chr5	150445720	150445730	+	1	NA	intron (NM_172887, intron 46 of 60)	intron (NM_172887, intron 46 of 60)	56494	NR_024513	194292	Mm.300184	NR_024513		Gm5	Gm1812	predicted gene 5	ncRNA
mm_111842.1	chr12	107938647	107938662	-	1	NA	intron (NM_001286343, intron 1 of 1)	(TG)n|Simple_repeat|Simple_repeat	64760	NM_001079883	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_32122.1	chr4	99031418	99031437	+	1	NA	exon (NM_013913, exon 1 of 7)	exon (NM_013913, exon 1 of 7)	473	NM_013913	30924	Mm.28341	NM_013913	ENSMUSG00000028553	Angptl3	hypl	angiopoietin-like 3	protein-coding
mm_37718.1	chr4	129550797	129550801	-	1	NA	intron (NM_001162432, intron 12 of 12)	ID_B1|SINE|B4	7012	NR_106199	102465997		NR_106199	ENSMUSG00000099070	Mir8119	Gm27567|mmu-mir-8119	microRNA 8119	ncRNA
mm_23964.1	chr3	84952458	84952474	+	1	NA	exon (NM_080428, exon 1 of 11)	exon (NM_080428, exon 1 of 11)	255	NM_080428	50754	Mm.196475	NM_080428	ENSMUSG00000028086	Fbxw7	1110001A17Rik|AGO|Cdc4|Fbw7|Fbwd6|Fbx30|Fbxo30|Fbxw6|SEL-10	F-box and WD-40 domain protein 7	protein-coding
mm_147319.1	chr18	42216927	42216945	-	1	NA	exon (NM_134137, exon 27 of 32)	exon (NM_134137, exon 27 of 32)	-20227	NM_027072	69401	Mm.34841	NM_027072	ENSMUSG00000059455	Plac8l1	1700009N18Rik|1700015M15Rik	PLAC8-like 1	protein-coding
mm_123761.1	chr14	70205986	70205997	-	1	NA	promoter-TSS (NM_001271407)	promoter-TSS (NM_001271407)	31	NM_001271407	20410	Mm.5068	NM_011366	ENSMUSG00000022091	Sorbs3	SCAM-1|SH3P3|Sh3d4|vinexin-g	sorbin and SH3 domain containing 3	protein-coding
mm_47891.1	chr5	134714016	134714053	-	1	NA	exon (NM_007925, exon 24 of 37)	exon (NM_007925, exon 24 of 37)	-25444	NM_010717	16885	Mm.15409	NM_010717	ENSMUSG00000029674	Limk1	KIZ-1|LIMK-1|Limk	LIM-domain containing, protein kinase	protein-coding
mm_125692.1	chr15	66868801	66868805	+	1	NA	Intergenic	Intergenic	-22590	NM_018865	22402	Mm.10222	NM_018865	ENSMUSG00000005124	Wisp1	AW146261|CCN4|Elm1	WNT1 inducible signaling pathway protein 1	protein-coding
mm_66516.1	chr7	45103748	45103800	-	1	NA	promoter-TSS (NM_010189)	promoter-TSS (NM_010189)	48	NM_010189	14132	Mm.3303	NM_010189	ENSMUSG00000003420	Fcgrt	FcRn	Fc receptor, IgG, alpha chain transporter	protein-coding
mm_52164.1	chr6	98275487	98275505	+	1	NA	intron (NM_001128092, intron 2 of 3)	intron (NM_001128092, intron 2 of 3)	67258	NM_001128092	330390	Mm.484161	NM_001128092	ENSMUSG00000090667	Gm765	-	predicted gene 765	protein-coding
mm_172666.1	chr8	43180335	43180335	-	1	NA	Intergenic	Intergenic	-2787	NM_001160412	622117	Mm.390031	NM_001160412	ENSMUSG00000091490	Triml2	EG622117|Tu4	tripartite motif family-like 2	protein-coding
mm_115267.1	chr13	110943515	110943518	+	1	NA	Intergenic	Intergenic	-39670	NR_131194	102636142	Mm.417611	NR_131194		4930526H09Rik	-	RIKEN cDNA 4930526H09 gene	ncRNA
mm_137618.1	chr17	28280232	28280254	+	1	NA	intron (NM_011145, intron 2 of 7)	intron (NM_011145, intron 2 of 7)	-6621	NR_039557	100628577		NR_039557	ENSMUSG00000093061	Mir5098	mmu-mir-5098|mu-mir-5098	microRNA 5098	ncRNA
mm_21726.1	chr2	164674082	164674095	-	1	NA	promoter-TSS (NM_001161806)	promoter-TSS (NM_001161806)	-1	NM_001161806	629761	Mm.389336	NM_001161806	ENSMUSG00000078940	Wfdc11	-	WAP four-disulfide core domain 11	protein-coding
mm_115174.1	chr13	108211261	108211283	+	1	NA	Intergenic	Intergenic	-3132	NM_029001	74559	Mm.286127	NM_029001	ENSMUSG00000021696	Elovl7	9130013K24Rik|AI840082	ELOVL family member 7, elongation of long chain fatty acids (yeast)	protein-coding
mm_69244.1	chr7	127807246	127807268	-	1	NA	3' UTR (NM_024414, exon 10 of 10)	3' UTR (NM_024414, exon 10 of 10)	6648	NM_001040684	101502	Mm.157103	NM_133943	ENSMUSG00000042289	Hsd3b7	AI195443|BB098564	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 7	protein-coding
mm_17756.1	chr2	32775358	32775377	-	1	NA	promoter-TSS (NM_001290566)	promoter-TSS (NM_001290566)	-28	NM_001290566	338348	Mm.475130	NM_177384	ENSMUSG00000039021	Ttc16	1200002K10Rik	tetratricopeptide repeat domain 16	protein-coding
mm_68492.1	chr7	111075612	111075669	-	1	NA	exon (NM_013507, exon 15 of 22)	exon (NM_013507, exon 15 of 22)	7390	NM_001040131	13690	Mm.185453	NM_013507	ENSMUSG00000005610	Eif4g2	DAP-5|E130105L11Rik|Nat1|Natm1|p97	eukaryotic translation initiation factor 4, gamma 2	protein-coding
mm_103367.1	chr11	75169168	75169176	-	1	NA	exon (NM_010430, exon 1 of 2)	exon (NM_010430, exon 1 of 2)	-1020	NM_001098203	15248	Mm.57250	NM_010430	ENSMUSG00000043099	Hic1	AA408311|HIC-1	hypermethylated in cancer 1	protein-coding
mm_22413.1	chr2	181459365	181459439	-	1	NA	promoter-TSS (NM_028125)	promoter-TSS (NM_028125)	24	NM_028125	72147	Mm.486504	NM_027656	ENSMUSG00000027583	Zbtb46	2610019F01Rik|4933406L05Rik|BZEL|Btbd4	zinc finger and BTB domain containing 46	protein-coding
mm_93911.1	chr10	127060136	127060148	-	1	NA	promoter-TSS (NM_001033262)	promoter-TSS (NM_001033262)	42	NM_001033262	216438	Mm.37892	NM_001033262	ENSMUSG00000040502	March9	AI608492|BC019560	membrane-associated ring finger (C3HC4) 9	protein-coding
mm_57516.1	chr6	125483512	125483525	-	1	NA	intron (NM_007657, intron 1 of 7)	intron (NM_007657, intron 1 of 7)	11237	NM_007657	12527	Mm.210676	NM_007657	ENSMUSG00000030342	Cd9	Tspan29	CD9 antigen	protein-coding
mm_44793.1	chr5	32458801	32458822	-	1	NA	promoter-TSS (NM_172707)	promoter-TSS (NM_172707)	-159	NM_172707	19046	Mm.241931	NM_172707	ENSMUSG00000014956	Ppp1cb	1200010B19	protein phosphatase 1, catalytic subunit, beta isoform	protein-coding
mm_76752.1	chr8	95434787	95434830	-	1	NA	promoter-TSS (NM_008187)	promoter-TSS (NM_008187)	61	NM_008187	14894	Mm.2080	NM_008187	ENSMUSG00000031796	Cfap20	2600014O15Rik|AL024127|Gtl3|T10-2A2	cilia and flagella associated protein 20	protein-coding
mm_171421.1	chr4	13378113	13378113	+	1	NA	Intergenic	L1VL1|LINE|L1	-365189	NM_001111026	12395	Mm.4909	NM_009822	ENSMUSG00000006586	Runx1t1	Cbfa2t1h|ETO|MTG8	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	protein-coding
mm_101872.1	chr11	48892027	48892041	-	1	NA	intron (NM_001024230, intron 4 of 4)	intron (NM_001024230, intron 4 of 4)	10118	NM_001024230	432555	Mm.338931	NM_001024230	ENSMUSG00000058163	Gm5431	EG432555|Irgb9b8	predicted gene 5431	protein-coding
mm_125554.1	chr15	58823821	58823825	+	1	NA	promoter-TSS (NM_175212)	promoter-TSS (NM_175212)	-396	NM_175212	74868	Mm.293754	NM_175212	ENSMUSG00000062373	Tmem65	2610029O13Rik|4930438D12Rik	transmembrane protein 65	protein-coding
mm_13964.1	chr2	121422441	121422493	+	1	NA	exon (NM_007952, exon 2 of 13)	exon (NM_007952, exon 2 of 13)	8565	NM_007952	14827	Mm.263177	NM_007952	ENSMUSG00000027248	Pdia3	58kDa|ERp57|ERp60|ERp61|Erp|Grp58|PDI|PDI-Q2|PI-PLC|PLC[a]|Plca	protein disulfide isomerase associated 3	protein-coding
mm_6082.1	chr1	62832212	62832219	-	1	NA	Intergenic	ORR1D1|LTR|ERVL-MaLR	-37483	NR_040601	74992	Mm.401979	NR_040601		4930487H11Rik	-	RIKEN cDNA 4930487H11 gene	ncRNA
mm_128921.1	chr15	73765736	73765739	-	1	NA	Intergenic	ORR1D1|LTR|ERVL-MaLR	17711	NM_008975	19245	Mm.390807	NM_008975	ENSMUSG00000059895	Ptp4a3	AV088979|Prl-3|pPtp4a3	protein tyrosine phosphatase 4a3	protein-coding
mm_35767.1	chr4	46194326	46194328	-	1	NA	intron (NM_011728, intron 1 of 5)	intron (NM_011728, intron 1 of 5)	1984	NM_011728	22590	Mm.247036	NM_011728	ENSMUSG00000028329	Xpa	AI573865|Xpac	xeroderma pigmentosum, complementation group A	protein-coding
mm_29091.1	chr3	104638533	104638542	-	1	NA	promoter-TSS (NM_009196)	promoter-TSS (NM_009196)	-127	NM_009196	20501	Mm.9086	NM_009196	ENSMUSG00000032902	Slc16a1	AL022710|Mct1	solute carrier family 16 (monocarboxylic acid transporters), member 1	protein-coding
mm_82430.1	chr9	15007895	15007901	-	1	NA	exon (NM_019482, exon 4 of 5)	exon (NM_019482, exon 4 of 5)	37580	NM_019482	55991	Mm.142253	NM_019482	ENSMUSG00000031934	Panx1	AI847747	pannexin 1	protein-coding
mm_71105.1	chr8	35587781	35587825	+	1	NA	promoter-TSS (NM_001081279)	promoter-TSS (NM_001081279)	5	NM_001081279	52065	Mm.103246	NM_001081279	ENSMUSG00000070056	Mfhas1	2310066G09Rik|D8Ertd91e	malignant fibrous histiocytoma amplified sequence 1	protein-coding
mm_145046.1	chr18	39774834	39774870	+	1	NA	exon (NM_011033, exon 1 of 1)	exon (NM_011033, exon 1 of 1)	1355	NM_011033	18459	Mm.9493	NM_011033	ENSMUSG00000051732	Pabpc2	Pabp|Pabp+|Pabp2	poly(A) binding protein, cytoplasmic 2	protein-coding
mm_72592.1	chr8	84356776	84356787	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-58583	NM_001252060	12286	Mm.334658	NM_007578	ENSMUSG00000034656	Cacna1a	APCA|BI|Caca1a|Cacnl1a4|Cav2.1|Ccha1a|EA2|FHM|HPCA|MHP|MHP1|SCA6|alpha1A|la|nmf352|rkr|smrl|tg	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	protein-coding
mm_127795.1	chr15	3583392	3583411	-	1	NA	promoter-TSS (NM_010284)	promoter-TSS (NM_010284)	-49	NM_010284	14600	Mm.3986	NM_010284	ENSMUSG00000055737	Ghr	GHBP|GHR/BP	growth hormone receptor	protein-coding
mm_67852.1	chr7	98694223	98694233	-	1	NA	non-coding (NR_144495, exon 1 of 1)	non-coding (NR_144495, exon 1 of 1)	8700	NR_144495	100040769	Mm.126401	NR_144495		Gm15506	OTTMUSG00000023003	predicted gene 15506	ncRNA
mm_55435.1	chr6	66875750	66875766	-	1	NA	Intergenic	Intergenic	-20639	NM_001177557	14701	Mm.234342	NM_025278	ENSMUSG00000036402	Gng12	2010305F15Rik|AA536815|AI115529|AI314170|AI842738	guanine nucleotide binding protein (G protein), gamma 12	protein-coding
mm_163899.1	chr14	29309994	29309999	+	1	NA	intron (NM_009785, intron 9 of 37)	L1Md_T|LINE|L1	291788	NM_176920	319476	Mm.95780	NM_176920	ENSMUSG00000045776	Lrtm1	A930016D02Rik	leucine-rich repeats and transmembrane domains 1	protein-coding
mm_147828.1	chr18	62177861	62177862	-	1	NA	3' UTR (NM_007420, exon 1 of 1)	3' UTR (NM_007420, exon 1 of 1)	2120	NM_007420	11555	Mm.5598	NM_007420	ENSMUSG00000045730	Adrb2	Adrb-2|Badm|Gpcr7	adrenergic receptor, beta 2	protein-coding
mm_61801.1	chr7	84312734	84312739	+	1	NA	intron (NM_007488, intron 5 of 18)	RMER17A2|LTR|ERVK	97302	NM_007488	11864	Mm.38594	NM_007488	ENSMUSG00000015709	Arnt2	Hif-2b|bHLHe1|mKIAA0307	aryl hydrocarbon receptor nuclear translocator 2	protein-coding
mm_86791.1	chr10	20205296	20205323	+	1	NA	intron (NM_001198635, intron 1 of 17)	intron (NM_001198635, intron 1 of 17)	-3130	NM_001101561	621697	Mm.440587	NM_001101561		Rpl32l	EG621697|Gm6251	ribosomal protein L32-like	protein-coding
mm_160332.1	chr8	10272682	10272682	+	1	NA	exon (NM_001319151, exon 2 of 35)	exon (NM_001319151, exon 2 of 35)	118771	NM_001319151	244281	Mm.422761	NM_001081397	ENSMUSG00000039057	Myo16	BM140241|C230040D10Rik|Gm1105|NYAP3|mKIAA0865	myosin XVI	protein-coding
mm_65544.1	chr7	27129758	27129788	-	1	NA	exon (NM_007817, exon 6 of 10)	exon (NM_007817, exon 6 of 10)	9818	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_43904.1	chr5	144255245	144255284	+	1	NA	promoter-TSS (NM_018772)	promoter-TSS (NM_018772)	39	NM_018772	55950	Mm.38011	NM_018772	ENSMUSG00000047843	Bri3	I3	brain protein I3	protein-coding
mm_93544.1	chr10	115587740	115587768	-	1	NA	promoter-TSS (NM_010195)	promoter-TSS (NM_010195)	26	NM_010195	14160	Mm.42103	NM_010195	ENSMUSG00000020140	Lgr5	FEX|Gpr49	leucine rich repeat containing G protein coupled receptor 5	protein-coding
mm_88882.1	chr10	81128976	81128998	+	1	NA	Intergenic	Intergenic	-7284	NM_010731	16969	Mm.20920	NM_010731	ENSMUSG00000035011	Zbtb7a	9030619K07Rik|9130006G12Rik|AI452336|FBI-1|Lrf|Pokemon|Zbtb7	zinc finger and BTB domain containing 7a	protein-coding
mm_59990.1	chr7	30554872	30554884	+	1	NA	TTS (NM_001290569)	TTS (NM_001290569)	1576	NM_001012401	243912	Mm.34885	NM_001012401	ENSMUSG00000036854	Hspb6	AA387366|Gm479|Hsp20	heat shock protein, alpha-crystallin-related, B6	protein-coding
mm_35947.1	chr4	53113415	53113439	-	1	NA	intron (NM_013454, intron 5 of 49)	intron (NM_013454, intron 5 of 49)	46468	NM_013454	11303	Mm.277376	NM_013454	ENSMUSG00000015243	Abca1	ABC-1|Abc1	ATP-binding cassette, sub-family A (ABC1), member 1	protein-coding
mm_56991.1	chr6	120916765	120916780	-	1	NA	promoter-TSS (NM_007544)	promoter-TSS (NM_007544)	48	NM_007544	12122	Mm.235081	NM_007544	ENSMUSG00000004446	Bid	2700049M22Rik|AI875481|AU022477	BH3 interacting domain death agonist	protein-coding
mm_20455.1	chr2	129365112	129365160	-	1	NA	exon (NM_008361, exon 7 of 7)	exon (NM_008361, exon 7 of 7)	-4766	NR_015474	329514	Mm.207315	NM_177848	ENSMUSG00000074805	Il1bos	9430083I22|Gm14047|OTTMUSG00000015529	interleukin 1 beta, opposite strand	ncRNA
mm_69760.1	chr7	141009686	141009707	-	1	NA	3' UTR (NM_025378, exon 2 of 2)	3' UTR (NM_025378, exon 2 of 2)	1048	NM_025378	66141	Mm.141021	NM_025378	ENSMUSG00000025492	Ifitm3	1110004C05Rik|Cd225|Cdw217|DSPA2b|Fgls|IP15|mil-1	interferon induced transmembrane protein 3	protein-coding
mm_146612.1	chr18	10030018	10030146	-	1	NA	promoter-TSS (NM_021522)	promoter-TSS (NM_021522)	67	NM_021522	59025	Mm.329277	NM_021522	ENSMUSG00000047879	Usp14	2610005K12Rik|2610037B11Rik|AW107924|C78769|ax|nmf375	ubiquitin specific peptidase 14	protein-coding
mm_8725.1	chr1	160047735	160047748	-	1	NA	intron (NM_001162896, intron 1 of 2)	intron (NM_001162896, intron 1 of 2)	3361	NM_001162896	67647	Mm.171518	NM_001024470	ENSMUSG00000090394	4930523C07Rik	-	RIKEN cDNA 4930523C07 gene	protein-coding
mm_42443.1	chr5	115430318	115430336	+	1	NA	intron (NM_008629, intron 2 of 14)	CpG-11404	642	NM_008629	17690	Mm.5077	NM_008629	ENSMUSG00000054256	Msi1	Msi1h|Musahi1|m-Msi-1	musashi RNA-binding protein 1	protein-coding
mm_157190.1	chrX	12058624	12058636	-	1	NA	exon (NM_029510, exon 4 of 15)	exon (NM_029510, exon 4 of 15)	21923	NM_175045	71458	Mm.196328	NM_029510	ENSMUSG00000040363	Bcor	2900008C10Rik|5830466J11Rik|8430401K06Rik|BcorR|D930024N20Rik|mKIAA1575	BCL6 interacting corepressor	protein-coding
mm_8879.1	chr1	162866360	162866402	-	1	NA	5' UTR (NM_010231, exon 1 of 9)	5' UTR (NM_010231, exon 1 of 9)	229	NM_010231	14261	Mm.976	NM_010231	ENSMUSG00000040181	Fmo1	-	flavin containing monooxygenase 1	protein-coding
mm_124696.1	chr15	6439196	6439207	+	1	NA	3' UTR (NM_001102400, exon 13 of 13)	3' UTR (NM_001102400, exon 13 of 13)	-6132	NM_013485	12279	Mm.29095	NM_013485	ENSMUSG00000022149	C9	-	complement component 9	protein-coding
mm_17481.1	chr2	28561329	28561340	-	1	NA	intron (NM_009885, intron 1 of 10)	intron (NM_009885, intron 1 of 10)	2069	NM_009885	12613	Mm.236017	NM_009885	ENSMUSG00000026818	Cel	1810036E18Rik|BAL	carboxyl ester lipase	protein-coding
mm_58531.1	chr7	4274156	4274163	+	1	NA	promoter-TSS (NM_008848)	promoter-TSS (NM_008848)	16	NM_011093	18729	Mm.326531	NM_008848		Pira6	12M1|Pira10|p91B	paired-Ig-like receptor A6	protein-coding
mm_36666.1	chr4	95052189	95052207	-	1	NA	promoter-TSS (NM_010591)	promoter-TSS (NM_010591)	24	NM_010591	16476	Mm.275071	NM_010591	ENSMUSG00000052684	Jun	AP-1|Junc|c-jun	jun proto-oncogene	protein-coding
mm_1286.1	chr1	64121886	64121903	+	1	NA	promoter-TSS (NM_033563)	promoter-TSS (NM_033563)	-505	NM_033563	93691	Mm.29466	NM_033563	ENSMUSG00000025959	Klf7	9830124P08Rik	Kruppel-like factor 7 (ubiquitous)	protein-coding
mm_104928.1	chr11	100016205	100016216	-	1	NA	promoter-TSS (NM_027983)	promoter-TSS (NM_027983)	2	NM_027983	71888	Mm.440318	NM_027983	ENSMUSG00000035592	Krt33a	2310015J09Rik	keratin 33A	protein-coding
mm_104869.1	chr11	99389352	99389369	-	1	NA	promoter-TSS (NM_010660)	promoter-TSS (NM_010660)	4	NM_010660	16661	Mm.22662	NM_010660	ENSMUSG00000019761	Krt10	D130054E02Rik|K10|K1C1|Krt-1.10|Krt1-10	keratin 10	protein-coding
mm_119653.1	chr14	52016885	52016897	+	1	NA	promoter-TSS (NM_001033805)	promoter-TSS (NM_001033805)	26	NM_001033805	619301	Mm.475177	NM_001033805	ENSMUSG00000072571	Tmem253	G630016D24Rik	transmembrane protein 253	protein-coding
mm_150814.1	chr19	44397142	44397162	+	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	10557	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_132959.1	chr16	50046429	50046448	+	1	NA	intron (NR_045935, intron 1 of 3)	intron (NR_045935, intron 1 of 3)	26414	NR_045935	224180	Mm.146439	NM_175010		Gm4827	B130050K08|EG224180	predicted gene 4827	ncRNA
mm_74536.1	chr8	9758549	9758576	-	1	NA	intron (NM_001347127, intron 1 of 3)	intron (NM_001347127, intron 1 of 3)	12461	NM_173446	270028	Mm.268163	NM_173446	ENSMUSG00000079157	Fam155a	6430500D16|AW121567|Tmem28	family with sequence similarity 155, member A	protein-coding
mm_94289.1	chr11	4031771	4031833	+	1	NA	promoter-TSS (NM_146013)	promoter-TSS (NM_146013)	20	NM_146013	103655	Mm.337476	NM_146013	ENSMUSG00000019368	Sec14l4	AI256582|AW536553|SPF|TAP	SEC14-like lipid binding 4	protein-coding
mm_109443.1	chr12	110850274	110850302	+	1	NA	promoter-TSS (NM_028365)	promoter-TSS (NM_028365)	9	NM_028365	72805	Mm.443524	NM_028365	ENSMUSG00000021271	Zfp839	2810455K09Rik	zinc finger protein 839	protein-coding
mm_121917.1	chr14	22780533	22780535	-	1	NA	intron (NM_028275, intron 5 of 6)	intron (NM_028275, intron 5 of 6)	-237736	NR_046307	74896	Mm.444661	NR_046307		4930405A10Rik	4930456G20Rik	RIKEN cDNA 4930405A10 gene	ncRNA
mm_69767.1	chr7	141010693	141010746	-	1	NA	promoter-TSS (NM_025378)	promoter-TSS (NM_025378)	25	NM_025378	66141	Mm.141021	NM_025378	ENSMUSG00000025492	Ifitm3	1110004C05Rik|Cd225|Cdw217|DSPA2b|Fgls|IP15|mil-1	interferon induced transmembrane protein 3	protein-coding
mm_103199.1	chr11	70651870	70651873	-	1	NA	TTS (NM_011072)	TTS (NM_011072)	2779	NM_011072	18643	Mm.2647	NM_011072	ENSMUSG00000018293	Pfn1	Pfn	profilin 1	protein-coding
mm_125705.1	chr15	68258275	68258320	+	1	NA	intron (NM_001145888, intron 1 of 15)	intron (NM_001145888, intron 1 of 15)	559	NM_001145888	380993	Mm.309526	NM_198644	ENSMUSG00000022335	Zfat	Gm922|Zfat1|Zfp406	zinc finger and AT hook domain containing	protein-coding
mm_105748.1	chr11	109453073	109453082	-	1	NA	non-coding (NR_040680, exon 2 of 2)	non-coding (NR_040680, exon 2 of 2)	12999	NR_040680	100503496	Mm.265874	NR_040680		LOC100503496	-	uncharacterized LOC100503496	ncRNA
mm_86690.1	chr10	18431268	18431282	+	1	NA	intron (NM_173390, intron 1 of 6)	intron (NM_173390, intron 1 of 6)	23600	NM_173390	215819	Mm.297971	NM_173390	ENSMUSG00000039835	Nhsl1	5730409E15Rik|A630035H13Rik|A730096F01|BC013565|D10Bwg0940e|mKIAA1357	NHS-like 1	protein-coding
mm_132330.1	chr16	33818888	33818899	+	1	NA	3' UTR (NM_010739, exon 13 of 13)	3' UTR (NM_010739, exon 13 of 13)	-10772	NM_010580	16419	Mm.6424	NM_010580	ENSMUSG00000022817	Itgb5	AA475909|AI874634|ESTM23|[b]-5|[b]5|[b]5A|[b]5B|beta-5|beta5	integrin beta 5	protein-coding
mm_30405.1	chr3	152253696	152253714	-	1	NA	intron (NM_199465, intron 2 of 12)	intron (NM_199465, intron 2 of 12)	12615	NM_199465	68810	Mm.200188	NM_199465	ENSMUSG00000039103	Nexn	1110046H09Rik|AA553326|NELIN	nexilin	protein-coding
mm_112469.1	chr13	5868399	5868409	+	1	NA	3' UTR (NM_011803, exon 4 of 4)	3' UTR (NM_011803, exon 4 of 4)	6915	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_84759.1	chr9	75597675	75597712	-	1	NA	intron (NM_016711, intron 1 of 9)	intron (NM_016711, intron 1 of 9)	1440	NM_001038710	50876	Mm.291880	NM_016711	ENSMUSG00000032186	Tmod2	N-Tmod|NTMOD	tropomodulin 2	protein-coding
mm_111863.1	chr12	107974947	107974950	-	1	NA	intron (NM_001079883, intron 2 of 3)	intron (NM_001079883, intron 2 of 3)	28466	NM_001079883	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_133425.1	chr16	87454977	87454987	+	1	NA	promoter-TSS (NM_024258)	promoter-TSS (NM_024258)	-3	NM_024258	74112	Mm.152941	NM_024258	ENSMUSG00000025616	Usp16	1200004E02Rik|2810483I07Rik|6330514E22Rik|UBPM	ubiquitin specific peptidase 16	protein-coding
mm_85538.1	chr9	106656082	106656096	-	1	NA	promoter-TSS (NM_001160353)	promoter-TSS (NM_001160353)	20	NM_001160353	108068	Mm.410822	NM_001160353	ENSMUSG00000023192	Grm2	4930441L02Rik|Gprc1b|mGluR2|mGluR7	glutamate receptor, metabotropic 2	protein-coding
mm_70887.1	chr8	25518784	25518801	+	1	NA	promoter-TSS (NM_010206)	promoter-TSS (NM_010206)	33	NM_001079908	14182	Mm.265716	NM_010206	ENSMUSG00000031565	Fgfr1	AW208770|Eask|FGFR-I|FLG|Fgfr-1|Flt-2|Hspy|MFR|bFGF-R-1|c-fgr	fibroblast growth factor receptor 1	protein-coding
mm_68319.1	chr7	106441104	106441112	-	1	NA	promoter-TSS (NR_003967)	promoter-TSS (NR_003967)	-35	NR_003967	209380	Mm.461779	NM_001001318		Gm4759	EG209380	GTPase, very large interferon inducible 1 pseudogene	pseudo
mm_107968.1	chr12	72761218	72761265	+	1	NA	promoter-TSS (NM_008910)	promoter-TSS (NM_008910)	30	NM_008910	19042	Mm.261045	NM_008910	ENSMUSG00000021096	Ppm1a	2310003C21Rik|2900017D14Rik|AI427932|AU017636|MMPa-2|MPPa-1	protein phosphatase 1A, magnesium dependent, alpha isoform	protein-coding
mm_28932.1	chr3	98882019	98882036	-	1	NA	exon (NM_019545, exon 5 of 9)	exon (NM_019545, exon 5 of 9)	11203	NM_019545	56185	Mm.281874	NM_019545	ENSMUSG00000027870	Hao2	AI325478|Hao-2|Hao3|Haox3	hydroxyacid oxidase 2	protein-coding
mm_61523.1	chr7	78914011	78914021	+	1	NA	promoter-TSS (NM_001113527)	promoter-TSS (NM_001113527)	-219	NM_001113527	57444	Mm.322843	NM_020583	ENSMUSG00000039236	Isg20	1600023I01Rik|2010107M23Rik|20kDa|DnaQL|HEM45	interferon-stimulated protein	protein-coding
mm_117141.1	chr13	60941933	60941939	-	1	NA	promoter-TSS (NM_009411)	promoter-TSS (NM_009411)	-1	NM_009411	21984	Mm.2372	NM_009411	ENSMUSG00000033834	Tpbpa	AV033951|Tb-1|Tb1|Tpbp|b2b1247Clo	trophoblast specific protein alpha	protein-coding
mm_123841.1	chr14	70642301	70642323	-	1	NA	promoter-TSS (NM_008004)	promoter-TSS (NM_008004)	-44	NM_008004	14171	Mm.12814	NM_008004	ENSMUSG00000022101	Fgf17	-	fibroblast growth factor 17	protein-coding
mm_55229.1	chr6	52240469	52240501	-	1	NA	5' UTR (NM_001122950, exon 1 of 2)	5' UTR (NM_001122950, exon 1 of 2)	369	NM_001122950	15395	Mm.5	NM_008263	ENSMUSG00000000938	Hoxa10	Hox-1.8|Hoxa-10	homeobox A10	protein-coding
mm_13239.1	chr2	98662501	98662510	+	1	NA	Intergenic	SYNREP_MM|Satellite|Satellite	1194848	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_173196.1	chrX	62776366	62776367	-	1	NA	Intergenic	Intergenic	-249355	NR_045442	75545	Mm.391270	NR_045442	ENSMUSG00000085757	1700019B21Rik	-	RIKEN cDNA 1700019B21 gene	ncRNA
mm_49586.1	chr6	30642941	30642949	+	1	NA	exon (NM_025350, exon 8 of 10)	exon (NM_025350, exon 8 of 10)	3727	NM_025350	109697	Mm.25377	NM_025350	ENSMUSG00000054446	Cpa1	0910001L12Rik|Cpa	carboxypeptidase A1, pancreatic	protein-coding
mm_89432.1	chr10	91096695	91096697	+	1	NA	3' UTR (NM_026166, exon 3 of 3)	3' UTR (NM_026166, exon 3 of 3)	13657	NM_026166	67454	Mm.252843	NM_026166	ENSMUSG00000019975	Ikbip	1200009F10Rik|1700023M03Rik|D18354|Ikip	IKBKB interacting protein	protein-coding
mm_35061.1	chr4	6453664	6453678	-	1	NA	intron (NM_010945, intron 1 of 30)	CpG	600	NM_010945	18201	Mm.3059	NM_010945	ENSMUSG00000028245	Nsmaf	AA959567|C630007J05|Fan	neutral sphingomyelinase (N-SMase) activation associated factor	protein-coding
mm_166717.1	chr6	119196739	119196751	-	1	NA	promoter-TSS (NM_009781)	promoter-TSS (NM_009781)	-336	NM_001255999	12288	Mm.41628	NM_009781	ENSMUSG00000051331	Cacna1c	Cav1.2|Cchl1a1|D930026N18Rik|MBC|MELC-CC	calcium channel, voltage-dependent, L type, alpha 1C subunit	protein-coding
mm_124356.1	chr14	105116965	105116966	-	1	NA	intron (NM_134077, intron 20 of 20)	intron (NM_134077, intron 20 of 20)	-2289	NR_040628	100502987	Mm.124957	NR_040628		Gm17066	-	predicted gene 17066	ncRNA
mm_71972.1	chr8	70579859	70579861	+	1	NA	intron (NM_007924, intron 4 of 11)	intron (NM_007924, intron 4 of 11)	-14621	NM_023627	71780	Mm.29357	NM_023627	ENSMUSG00000019139	Isyna1	1300017C10Rik|AU018670	myo-inositol 1-phosphate synthase A1	protein-coding
mm_32046.1	chr4	95969951	95969959	+	1	NA	intron (NM_030014, intron 1 of 21)	Lx2B2|LINE|L1	-2300	NR_045776	319247	Mm.473527	NM_175680	ENSMUSG00000044125	9530080O11Rik	-	RIKEN cDNA 9530080O11 gene	ncRNA
mm_49688.1	chr6	33375243	33375257	+	1	NA	intron (NM_001347089, intron 7 of 9)	intron (NM_001347089, intron 7 of 9)	126100	NM_009148	20336	Mm.265512	NM_009148	ENSMUSG00000029763	Exoc4	C78892|Sec8|Sec8l1	exocyst complex component 4	protein-coding
mm_138283.1	chr17	34610934	34610948	+	1	NA	exon (NM_018862, exon 3 of 7)	exon (NM_018862, exon 3 of 7)	1927	NM_018862	55979	Mm.8684	NM_018862	ENSMUSG00000034254	Agpat1	1-AGP|1-AGPAT|AW047140	1-acylglycerol-3-phosphate O-acyltransferase 1 (lysophosphatidic acid acyltransferase, alpha)	protein-coding
mm_119094.1	chr14	30892674	30892691	+	1	NA	exon (NM_001289633, exon 11 of 22)	exon (NM_001289633, exon 11 of 22)	6206	NM_001289632	16427	Mm.34819	NM_018746	ENSMUSG00000021922	Itih4	ITI-HC4|Itih-4|PK-120	inter alpha-trypsin inhibitor, heavy chain 4	protein-coding
mm_145444.1	chr18	59175473	59175493	+	1	NA	5' UTR (NM_001081328, exon 1 of 3)	5' UTR (NM_001081328, exon 1 of 3)	143	NM_001081328	78923	Mm.84007	NM_001081328	ENSMUSG00000058152	Chsy3	4833446K15Rik|AI662215	chondroitin sulfate synthase 3	protein-coding
mm_32192.1	chr4	101292299	101292308	+	1	NA	Intergenic	CpG	-27021	NM_146145	16451	Mm.289657	NM_146145	ENSMUSG00000028530	Jak1	AA960307|BAP004|C130039L05Rik	Janus kinase 1	protein-coding
mm_88796.1	chr10	80677409	80677419	+	1	NA	Intergenic	Intergenic	-1121	NM_021462	17347	Mm.42126	NM_021462	ENSMUSG00000020190	Mknk2	2010016G11Rik|Gprk7|Mnk2	MAP kinase-interacting serine/threonine kinase 2	protein-coding
mm_135442.1	chr16	45454915	45454926	-	1	NA	intron (NM_001005854, intron 1 of 4)	intron (NM_001005854, intron 1 of 4)	38049	NM_001005854	208166	Mm.451852	NM_001005854	ENSMUSG00000053182	Gm609	Gm1749|isec1	predicted gene 609	protein-coding
mm_14473.1	chr2	131491959	131491969	+	1	NA	5' UTR (NM_001177840, exon 1 of 4)	5' UTR (NM_001177840, exon 1 of 4)	102	NM_001177838	228608	Mm.136586	NM_145533	ENSMUSG00000027333	Smox	B130066H01Rik|PAO|PAOh1|SMO	spermine oxidase	protein-coding
mm_149231.1	chr19	10182886	10182896	+	1	NA	promoter-TSS (NM_146094)	promoter-TSS (NM_146094)	3	NM_146094	76267	Mm.30158	NM_146094	ENSMUSG00000010663	Fads1	0710001O03Rik|A930006B21Rik|AI317215|DSD	fatty acid desaturase 1	protein-coding
mm_34401.1	chr4	145214282	145214299	+	1	NA	3' UTR (NM_011610, exon 10 of 10)	3' UTR (NM_011610, exon 10 of 10)	-19285	NM_001276465	230895	Mm.240310	NM_001033190	ENSMUSG00000020220	Vps13d	-	vacuolar protein sorting 13D	protein-coding
mm_72390.1	chr8	81767575	81767584	+	1	NA	intron (NM_001297593, intron 4 of 23)	intron (NM_001297593, intron 4 of 23)	425017	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_131731.1	chr16	21855146	21855166	+	1	NA	Intergenic	B4A|SINE|B4	-36813	NM_172821	71751	Mm.420837	NM_172821	ENSMUSG00000033618	Map3k13	C130026N12Rik|LZK	mitogen-activated protein kinase kinase kinase 13	protein-coding
mm_93591.1	chr10	117071790	117071806	-	1	NA	3' UTR (NM_177798, exon 10 of 10)	3' UTR (NM_177798, exon 10 of 10)	-7984	NM_007636	12461	Mm.247788	NM_007636	ENSMUSG00000034024	Cct2	Cctb	chaperonin containing Tcp1, subunit 2 (beta)	protein-coding
mm_57503.1	chr6	125460589	125460599	-	1	NA	3' UTR (NM_007657, exon 8 of 8)	3' UTR (NM_007657, exon 8 of 8)	34161	NM_007657	12527	Mm.210676	NM_007657	ENSMUSG00000030342	Cd9	Tspan29	CD9 antigen	protein-coding
mm_6917.1	chr1	84839745	84839752	-	1	NA	promoter-TSS (NM_025386)	promoter-TSS (NM_025386)	-93	NM_025386	66153	Mm.381192	NM_025386	ENSMUSG00000073633	Fbxo36	0610008D19Rik|1110020F21Rik|2410002G19Rik|D1Ertd757e	F-box protein 36	protein-coding
mm_77461.1	chr8	122094821	122094865	-	1	NA	Intergenic	Intergenic	116819	NR_106096	102466915		NR_106096	ENSMUSG00000099140	Mir7237	Gm27482|mmu-mir-7237	microRNA 7237	ncRNA
mm_128922.1	chr15	73830979	73830988	-	1	NA	intron (NM_001033365, intron 1 of 10)	intron (NM_001033365, intron 1 of 10)	8688	NM_001033365	268816	Mm.440635	NM_001033365	ENSMUSG00000072487	Mroh5	Gm628	maestro heat-like repeat family member 5	protein-coding
mm_158821.1	chrX	167382673	167382738	-	1	NA	promoter-TSS (NM_001313758)	promoter-TSS (NM_001313758)	44	NM_026662	110639	Mm.272955	NM_026662	ENSMUSG00000025742	Prps2	2610101M19Rik|AA589463|AI464149|Prps-2	phosphoribosyl pyrophosphate synthetase 2	protein-coding
mm_75978.1	chr8	72160806	72160869	-	1	NA	promoter-TSS (NM_023126)	promoter-TSS (NM_023126)	-363	NM_023126	17274	Mm.162811	NM_023126	ENSMUSG00000003037	Rab8a	AA409338|Mel	RAB8A, member RAS oncogene family	protein-coding
mm_118332.1	chr13	113794406	113794410	-	1	NA	promoter-TSS (NM_172595)	promoter-TSS (NM_172595)	-100	NM_172595	218639	Mm.79837	NM_172595	ENSMUSG00000042348	Arl15	A430036I03|Arfrp2|C230032K13Rik	ADP-ribosylation factor-like 15	protein-coding
mm_24614.1	chr3	93468752	93468756	+	1	NA	promoter-TSS (NM_027762)	promoter-TSS (NM_027762)	0	NM_027762	71325	Mm.68064	NM_027762	ENSMUSG00000027908	Tchhl1	5430400H23Rik|AA589420|S100a17|Thhl1	trichohyalin-like 1	protein-coding
mm_171926.1	chr5	60848178	60848180	-	1	NA	Intergenic	L1_Mur1|LINE|L1	-862177	NR_040682	71057	Mm.50817	NR_040682	ENSMUSG00000106013	4933402J10Rik	-	RIKEN cDNA 4933402J10 gene	ncRNA
mm_110191.1	chr12	27340258	27340268	-	1	NA	3' UTR (NM_009234, exon 1 of 1)	3' UTR (NM_009234, exon 1 of 1)	2455	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding
mm_143182.1	chr17	57290896	57290914	-	1	NA	intron (NM_001163816, intron 1 of 25)	intron (NM_001163816, intron 1 of 25)	11805	NM_001163815	22324	Mm.248172	NM_011691	ENSMUSG00000034116	Vav1	Vav|vav-T	vav 1 oncogene	protein-coding
mm_33780.1	chr4	134853579	134853614	+	1	NA	promoter-TSS (NM_025382)	promoter-TSS (NM_025382)	-251	NM_025382	66146	Mm.99793	NM_025382	ENSMUSG00000028826	Tmem57	1110007C24Rik|9230118A01Rik|AI317300|AI606104|C61	transmembrane protein 57	protein-coding
mm_48796.1	chr5	148928700	148928713	-	1	NA	promoter-TSS (NM_153572)	promoter-TSS (NM_153572)	-59	NM_153572	231912	Mm.397405	NM_153572	ENSMUSG00000041298	Katnal1	-	katanin p60 subunit A-like 1	protein-coding
mm_155491.1	chrX	73716940	73717064	+	1	NA	promoter-TSS (NM_012060)	promoter-TSS (NM_012060)	405	NM_007435	11666	Mm.365	NM_007435	ENSMUSG00000031378	Abcd1	ALDP|Ald|Aldgh	ATP-binding cassette, sub-family D (ALD), member 1	protein-coding
mm_102669.1	chr11	65162908	65162976	-	1	NA	promoter-TSS (NM_001099288)	promoter-TSS (NM_001099288)	19	NM_001099288	216831	Mm.134338	NM_175003	ENSMUSG00000033389	Arhgap44	6330543G20|AI840762|AU040829|AW493732|Rich2	Rho GTPase activating protein 44	protein-coding
mm_149420.1	chr19	11437148	11437150	+	1	NA	Intergenic	L1VL4|LINE|L1	-6409	NM_021718	60361	Mm.33957	NM_021718	ENSMUSG00000056290	Ms4a4b	AI463180|Chandra|Ly116	membrane-spanning 4-domains, subfamily A, member 4B	protein-coding
mm_45959.1	chr5	90464101	90464161	-	1	NA	exon (NM_009654, exon 4 of 15)	exon (NM_009654, exon 4 of 15)	3261	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_16767.1	chr2	9878468	9878481	-	1	NA	5' UTR (NM_008091, exon 1 of 6)	5' UTR (NM_008091, exon 1 of 6)	126	NM_008091	14462	Mm.313866	NM_008091	ENSMUSG00000015619	Gata3	Gata-3|jal	GATA binding protein 3	protein-coding
mm_148045.1	chr18	70528610	70528614	-	1	NA	intron (NM_011972, intron 2 of 9)	intron (NM_011972, intron 2 of 9)	1709	NM_001136090	26447	Mm.244352	NM_011972	ENSMUSG00000038425	Poli	Rad30b	polymerase (DNA directed), iota	protein-coding
mm_41292.1	chr5	90464066	90464078	+	1	NA	exon (NM_009654, exon 4 of 15)	exon (NM_009654, exon 4 of 15)	3202	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_154550.1	chrM	14984	15032	-	1	NA	NA	Intergenic	NA	NA								
mm_29016.1	chr3	101836228	101836237	-	1	NA	promoter-TSS (NM_172295)	promoter-TSS (NM_172295)	-9	NM_172295	242125	Mm.32900	NM_172295	ENSMUSG00000044313	Mab21l3	-	mab-21-like 3 (C. elegans)	protein-coding
mm_65797.1	chr7	28907376	28907392	-	1	NA	intron (NM_021895, intron 8 of 20)	intron (NM_021895, intron 8 of 20)	25728	NM_001110807	60594	Mm.476990	NM_021894	ENSMUSG00000054083	Capn12	CANP 12	calpain 12	protein-coding
mm_108576.1	chr12	84996470	84996480	+	1	NA	5' UTR (NM_001347421, exon 1 of 20)	5' UTR (NM_001347421, exon 1 of 20)	154	NM_178363	56531	Mm.153183	NM_178363	ENSMUSG00000021244	Ylpm1	A930013E17Rik|ZAP|Zap3	YLP motif containing 1	protein-coding
mm_41688.1	chr5	100553730	100553735	+	1	NA	TTS (NM_139198)	TTS (NM_139198)	18473	NM_139198	231507	Mm.34609	NM_139198	ENSMUSG00000029322	Plac8	C15|D5Wsu111e	placenta-specific 8	protein-coding
mm_57314.1	chr6	124727213	124727216	-	1	NA	intron (NM_001077705, intron 9 of 15)	RSINE1|SINE|B4	5940	NM_013545	15170	Mm.271799	NM_013545	ENSMUSG00000004266	Ptpn6	70Z-SHP|Hcph|PTPTY-42|Ptp1C|SH-PTP1|SHP-1|hcp|me	protein tyrosine phosphatase, non-receptor type 6	protein-coding
mm_159126.1	chr2	73312540	73312540	-	1	NA	promoter-TSS (NM_025854)	promoter-TSS (NM_025854)	52	NM_025854	66935	Mm.292140	NM_025854	ENSMUSG00000041777	Cir1	1700023B02Rik|2810021A19Rik|Cicr|Cir	corepressor interacting with RBPJ, 1	protein-coding
mm_88746.1	chr10	80285326	80285354	+	1	NA	exon (NM_133188, exon 11 of 12)	exon (NM_133188, exon 11 of 12)	-7091	NM_009091	20054	Mm.643	NM_009091	ENSMUSG00000063457	Rps15	rig	ribosomal protein S15	protein-coding
mm_93872.1	chr10	123196917	123196961	-	1	NA	promoter-TSS (NM_027604)	promoter-TSS (NM_027604)	80	NM_027604	14479	Mm.244209	NM_027604	ENSMUSG00000020124	Usp15	4921514G19Rik|AI327321|E430033I05Rik|Gcap18	ubiquitin specific peptidase 15	protein-coding
mm_152907.1	chr19	26260491	26260495	-	1	NA	Intergenic	U4|snRNA|snRNA	-344667	NM_011416	67155	Mm.342988	NM_011416	ENSMUSG00000024921	Smarca2	2610209L14Rik|SNF2alpha|Snf2l2|brahma|brm	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	protein-coding
mm_159120.1	chr2	69705521	69705521	-	1	NA	exon (NM_177244, exon 5 of 14)	exon (NM_177244, exon 5 of 14)	7085	NM_177244	320720	Mm.289566	NM_177244	ENSMUSG00000027086	Fastkd1	5330408N05Rik|mKIAA1800	FAST kinase domains 1	protein-coding
mm_58259.1	chr6	145210836	145210894	-	1	NA	promoter-TSS (NM_001163628)	promoter-TSS (NM_001163628)	105	NM_177222	320662	Mm.207779	NM_177222	ENSMUSG00000043541	Casc1	A230084G12Rik|Las1	cancer susceptibility candidate 1	protein-coding
mm_32643.1	chr4	115057353	115057407	+	1	NA	promoter-TSS (NM_001287388)	promoter-TSS (NM_001287388)	-431	NM_001287388	21349	Mm.239869	NM_011527	ENSMUSG00000028717	Tal1	Hpt|SCL/tal-1|Scl|bHLHa17|tal-1	T cell acute lymphocytic leukemia 1	protein-coding
mm_109928.1	chr12	8674833	8674846	-	1	NA	intron (NM_030723, intron 1 of 20)	CpG	158	NM_030723	80913	Mm.341243	NM_030723	ENSMUSG00000020594	Pum2	5730503J23Rik|Pumm2	pumilio RNA-binding family member 2	protein-coding
mm_21649.1	chr2	164333625	164333625	-	1	NA	3' UTR (NM_009301, exon 2 of 3)	3' UTR (NM_009301, exon 2 of 3)	860	NM_009301	20944	Mm.140154	NM_009301	ENSMUSG00000017004	Svs5	BB115186|Semg1|Svp-1|Svp1|Svp5	seminal vesicle secretory protein 5	protein-coding
mm_145506.1	chr18	60391568	60391578	+	1	NA	3' UTR (NM_001146275, exon 3 of 3)	3' UTR (NM_001146275, exon 3 of 3)	15544	NM_001146275	60440	Mm.261140	NM_021792	ENSMUSG00000054072	Iigp1	2900074L10Rik|AI046432|AW111922|Ifgga1|Iigp|Irga6	interferon inducible GTPase 1	protein-coding
mm_50158.1	chr6	41547345	41547378	+	1	NA	Intergenic	Intergenic	25585	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_90727.1	chr10	5194784	5194812	-	1	NA	promoter-TSS (NM_001079686)	promoter-TSS (NM_001079686)	-91	NM_001079686	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_127601.1	chr15	102401949	102401958	+	1	NA	Intergenic	Intergenic	-4363	NM_013672	20683	Mm.4618	NM_013672	ENSMUSG00000001280	Sp1	1110003E12Rik|AA450830|AI845540|Sp1-1	trans-acting transcription factor 1	protein-coding
mm_25157.1	chr3	103029106	103029130	+	1	NA	5' UTR (NM_001310693, exon 2 of 18)	5' UTR (NM_001310693, exon 2 of 18)	8572	NM_144901	229663	Mm.277713	NM_144901	ENSMUSG00000068823	Csde1	AA960392|BC016898|D3Jfr1|mKIAA0885|unr	cold shock domain containing E1, RNA binding	protein-coding
mm_125781.1	chr15	74716035	74716044	+	1	NA	exon (NM_028216, exon 2 of 3)	exon (NM_028216, exon 2 of 3)	1200	NM_028216	72373	Mm.46395	NM_028216	ENSMUSG00000022598	Psca	2210408B04Rik	prostate stem cell antigen	protein-coding
mm_99657.1	chr11	105731729	105731753	+	1	NA	intron (NM_181071, intron 4 of 25)	intron (NM_181071, intron 4 of 25)	141755	NM_181071	77097	Mm.22501	NM_175492	ENSMUSG00000053580	Tanc2	3526402J09Rik|5730590C14Rik	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2	protein-coding
mm_8218.1	chr1	138159074	138159085	-	1	NA	intron (NM_001111316, intron 1 of 31)	intron (NM_001111316, intron 1 of 31)	16047	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_126600.1	chr15	82379376	82379421	+	1	NA	intron (NM_019823, intron 1 of 9)	B1_Mur2|SINE|Alu	862	NM_019823	56448	Mm.474216	NM_019823	ENSMUSG00000061740	Cyp2d22	2D22	cytochrome P450, family 2, subfamily d, polypeptide 22	protein-coding
mm_90068.1	chr10	116325230	116325233	+	1	NA	intron (NM_029928, intron 7 of 31)	intron (NM_029928, intron 7 of 31)	23857	NM_029928	19263	Mm.37213	NM_029928	ENSMUSG00000020154	Ptprb	3230402H02Rik|C130094E24|Ptpz|Rptpb|VE-PTP|Veptp	protein tyrosine phosphatase, receptor type, B	protein-coding
mm_90060.1	chr10	116275537	116275576	+	1	NA	TTS (NM_001161837)	TTS (NM_001161837)	-25818	NM_029928	19263	Mm.37213	NM_029928	ENSMUSG00000020154	Ptprb	3230402H02Rik|C130094E24|Ptpz|Rptpb|VE-PTP|Veptp	protein tyrosine phosphatase, receptor type, B	protein-coding
mm_164835.1	chr18	39026684	39026686	+	1	NA	intron (NM_175164, intron 1 of 22)	intron (NM_175164, intron 1 of 22)	33540	NM_175164	71302	Mm.329396	NM_175164	ENSMUSG00000036452	Arhgap26	1810044B20Rik|2610010G17Rik|4933432P15Rik|AI853435|mKIAA0621	Rho GTPase activating protein 26	protein-coding
mm_2006.1	chr1	87127350	87127374	+	1	NA	exon (NM_007432, exon 10 of 11)	exon (NM_007432, exon 10 of 11)	2354	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_130444.1	chr15	98482732	98482742	-	1	NA	promoter-TSS (NM_010679)	promoter-TSS (NM_010679)	-54	NM_010679	16770	Mm.5074	NM_010679	ENSMUSG00000022991	Lalba	AW208827|Lyzg	lactalbumin, alpha	protein-coding
mm_130743.1	chr15	101256172	101256180	-	1	NA	Intergenic	Intergenic	-10670	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_87430.1	chr10	50894741	50894762	+	1	NA	promoter-TSS (NM_011376)	promoter-TSS (NM_011376)	-900	NM_011376	20464	Mm.4774	NM_011376	ENSMUSG00000019913	Sim1	bHLHe14|mSIM1	single-minded homolog 1 (Drosophila)	protein-coding
mm_147353.1	chr18	43360996	43360999	-	1	NA	exon (NM_001291455, exon 3 of 14)	exon (NM_001291455, exon 3 of 14)	12275	NM_001136086	22240	Mm.8180	NM_009468	ENSMUSG00000024501	Dpysl3	CRMP-4|DRP-3|TUC4|ULIP-1|Ulip|Ulip1	dihydropyrimidinase-like 3	protein-coding
mm_7062.1	chr1	87510549	87510584	-	1	NA	promoter-TSS (NM_019867)	promoter-TSS (NM_019867)	-204	NM_019867	53972	Mm.435439	NM_019867	ENSMUSG00000026259	Ngef	Tims2|ephexin	neuronal guanine nucleotide exchange factor	protein-coding
mm_155019.1	chrX	42059905	42059926	+	1	NA	Intergenic	Intergenic	-7921	NM_009688	11798	Mm.259879	NM_009688	ENSMUSG00000025860	Xiap	1110015C02Rik|Aipa|Api3|Birc4|IAP3|ILP-1|MIHA	X-linked inhibitor of apoptosis	protein-coding
mm_138229.1	chr17	34372272	34372278	+	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-4857	NM_001111094	100038862	Mm.440426	NM_201405	ENSMUSG00000062638	Btnl1	Btnl3|Gm316|Gm33	butyrophilin-like 1	protein-coding
mm_105523.1	chr11	106300441	106300443	-	1	NA	exon (NM_008117, exon 5 of 5)	exon (NM_008117, exon 5 of 5)	1454	NM_008117	14599	Mm.343934	NM_008117	ENSMUSG00000020713	Gh	Gh1|Ghb1	growth hormone	protein-coding
mm_154861.1	chrX	20659001	20659005	+	1	NA	intron (NM_001276317, intron 1 of 25)	intron (NM_001276317, intron 1 of 25)	499	NM_001276317	22201	Mm.1104	NM_009457	ENSMUSG00000001924	Uba1	A1S9|Sbx|Ube-1|Ube1x	ubiquitin-like modifier activating enzyme 1	protein-coding
mm_72224.1	chr8	72741725	72741737	+	1	NA	intron (NM_009188, intron 7 of 18)	intron (NM_009188, intron 7 of 18)	18461	NM_009188	20467	Mm.2137	NM_009188	ENSMUSG00000031622	Sin3b	2810430C10Rik	transcriptional regulator, SIN3B (yeast)	protein-coding
mm_122894.1	chr14	54949927	54949933	-	1	NA	promoter-TSS (NR_029724)	promoter-TSS (NR_029724)	-788	NR_029724	387204		NR_029724	ENSMUSG00000065432	Mir208a	Mirn208|Mirn208a|mir-208|mir-208a|mmu-mir-208	microRNA 208a	ncRNA
mm_48826.1	chr5	149053039	149053053	-	1	NA	promoter-TSS (NM_010439)	promoter-TSS (NM_010439)	11	NM_010439	15289	Mm.207047	NM_010439	ENSMUSG00000066551	Hmgb1	HMG-1|Hmg1|SBP-1|p30	high mobility group box 1	protein-coding
mm_46291.1	chr5	100383983	100383993	-	1	NA	intron (NM_026969, intron 16 of 27)	intron (NM_026969, intron 16 of 27)	32246	NM_026969	69162	Mm.18634	NM_026969	ENSMUSG00000035325	Sec31a	1810024J13Rik|ABP125|ABP130|AU042160|HSPC275|Sec31l1	Sec31 homolog A (S. cerevisiae)	protein-coding
mm_66468.1	chr7	44974445	44974455	-	1	NA	intron (NM_001252470, intron 1 of 18)	intron (NM_001252470, intron 1 of 18)	401	NM_153679	78070	Mm.231465	NM_153679	ENSMUSG00000007783	Cpt1c	6530437J22Rik|9630004I06Rik	carnitine palmitoyltransferase 1c	protein-coding
mm_100524.1	chr11	120576900	120576916	+	1	NA	TTS (NM_133796)	TTS (NM_133796)	-3972	NM_011032	18453	Mm.16660	NM_011032	ENSMUSG00000025130	P4hb	ERp59|PDI|Pdia1|Thbp	prolyl 4-hydroxylase, beta polypeptide	protein-coding
mm_147785.1	chr18	61632516	61632540	-	1	NA	Intergenic	Intergenic	-7125	NR_045420	545261	Mm.426593	NR_045420	ENSMUSG00000098098	Bvht	Braveheart|Gm20748	braveheart long non-coding RNA	ncRNA
mm_133865.1	chr16	96361729	96361740	+	1	NA	promoter-TSS (NM_028078)	promoter-TSS (NM_028078)	-23	NM_001177887	72058	Mm.119714	NM_028078	ENSMUSG00000000159	Igsf5	2010003D20Rik|JCAM|Jam4	immunoglobulin superfamily, member 5	protein-coding
mm_33173.1	chr4	126046904	126047023	+	1	NA	promoter-TSS (NM_025544)	promoter-TSS (NM_025544)	35	NM_025544	66407	Mm.195628	NM_025544	ENSMUSG00000028861	Mrps15	1500003E24Rik|2410002B11Rik|Mprs15	mitochondrial ribosomal protein S15	protein-coding
mm_169492.1	chr14	75292194	75292207	+	1	NA	exon (NM_026083, exon 3 of 19)	exon (NM_026083, exon 3 of 19)	7827	NM_026083	67302	Mm.74704	NM_026083	ENSMUSG00000022000	Zc3h13	2600010B19Rik|3110050K21Rik|4930570G11Rik|C87618	zinc finger CCCH type containing 13	protein-coding
mm_4828.1	chr1	185534381	185534413	+	1	NA	Intergenic	Intergenic	-2939	NR_030555	100124483		NR_030555	ENSMUSG00000076976	Mir297c	Mirn297c	microRNA 297c	ncRNA
mm_144872.1	chr18	36749241	36749259	+	1	NA	exon (NM_011879, exon 7 of 20)	exon (NM_011879, exon 7 of 20)	4594	NM_011879	24010	Mm.30234	NM_011879	ENSMUSG00000024474	Ik	MuRED	IK cytokine	protein-coding
mm_64178.1	chr7	141458853	141458862	+	1	NA	non-coding (NR_028142, exon 8 of 10)	non-coding (NR_028142, exon 8 of 10)	-2237	NM_001025103	213573	Mm.386851	NM_001025103	ENSMUSG00000048200	Cracr2b	6330520A15Rik|BC026645|Cracr2a|Efcab4|Efcab4a	calcium release activated channel regulator 2B	protein-coding
mm_98490.1	chr11	94951487	94951537	+	1	NA	exon (NM_007742, exon 51 of 51)	exon (NM_007742, exon 51 of 51)	15288	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_164170.1	chr15	74728039	74728043	-	1	NA	promoter-TSS (NM_020519)	promoter-TSS (NM_020519)	-15	NM_020519	57277	Mm.27630	NM_020519	ENSMUSG00000022596	Slurp1	1110021N19Rik|AI415082|ARS|ArsB|Slurp-1	secreted Ly6/Plaur domain containing 1	protein-coding
mm_129734.1	chr15	82147043	82147059	-	1	NA	promoter-TSS (NM_033218)	promoter-TSS (NM_033218)	-218	NM_033218	20788	Mm.9002	NM_033218	ENSMUSG00000022463	Srebf2	AI608257|SREBP-2|SREBP2|SREBP2gc|bHLHd2|lop13|nuc	sterol regulatory element binding factor 2	protein-coding
mm_138854.1	chr17	40937114	40937123	+	1	NA	exon (NM_008650, exon 2 of 13)	exon (NM_008650, exon 2 of 13)	2433	NM_008650	17850	Mm.259884	NM_008650	ENSMUSG00000023921	Mut	D230010K02Rik|Mcm	methylmalonyl-Coenzyme A mutase	protein-coding
mm_147913.1	chr18	65505491	65505537	-	1	NA	intron (NR_105742, intron 3 of 6)	intron (NR_105742, intron 3 of 6)	74517	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_17249.1	chr2	25627961	25627974	-	1	NA	promoter-TSS (NM_007995)	promoter-TSS (NM_007995)	7	NM_007995	14133	Mm.10510	NM_007995	ENSMUSG00000026938	Fcna	Fcn1	ficolin A	protein-coding
mm_65218.1	chr7	19698420	19698435	-	1	NA	promoter-TSS (NM_001305819)	promoter-TSS (NM_001305819)	-29	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_15206.1	chr2	154213016	154213025	+	1	NA	exon (NM_153418, exon 9 of 16)	exon (NM_153418, exon 9 of 16)	-10722	NM_144890	228802	Mm.167411	NM_144890	ENSMUSG00000038572	Bpifb5	Lplunc5	BPI fold containing family B, member 5	protein-coding
mm_41114.1	chr5	87779997	87780026	+	1	NA	exon (NM_001304768, exon 7 of 13)	exon (NM_001304768, exon 7 of 13)	5561	NM_007785	12993	Mm.4908	NM_007785	ENSMUSG00000061937	Csn1s2a	Csng|PP22	casein alpha s2-like A	protein-coding
mm_160476.1	chr8	120535913	120535913	+	1	NA	promoter-TSS (NM_001145897)	promoter-TSS (NM_001145897)	56	NM_001145897	382034	Mm.334856	NM_198671	ENSMUSG00000031822	Gse1	2210013I18Rik|mKIAA0182	genetic suppressor element 1, coiled-coil protein	protein-coding
mm_100583.1	chr11	120939037	120939069	+	1	NA	Intergenic	Intergenic	-6181	NM_027745	71276	Mm.275751	NM_027745	ENSMUSG00000048445	Ccdc57	4933434G05Rik	coiled-coil domain containing 57	protein-coding
mm_122448.1	chr14	45295964	45295976	-	1	NA	intron (NM_015774, intron 9 of 15)	intron (NM_015774, intron 9 of 15)	22602	NM_015774	50527	Mm.387108	NM_015774	ENSMUSG00000021831	Ero1l	ERO1-L|Ero1a	ERO1-like (S. cerevisiae)	protein-coding
mm_123704.1	chr14	69804115	69804142	-	1	NA	intron (NM_153514, intron 1 of 9)	intron (NM_153514, intron 1 of 9)	1417	NM_153514	246710	Mm.102367	NM_153514	ENSMUSG00000022075	Rhobtb2	Dbc2|E130206H14Rik|mKIAA0717	Rho-related BTB domain containing 2	protein-coding
mm_68712.1	chr7	119895447	119895462	-	1	NA	promoter-TSS (NM_001285961)	promoter-TSS (NM_001285961)	4	NM_173408	233805	Mm.31539	NM_173408	ENSMUSG00000048787	Dcun1d3	1700020A13Rik|BC030335	DCN1, defective in cullin neddylation 1, domain containing 3 (S. cerevisiae)	protein-coding
mm_40647.1	chr5	65024329	65024352	+	1	NA	intron (NM_026667, intron 8 of 13)	B4|SINE|B4	54022	NR_030577	100124451		NR_030577	ENSMUSG00000077042	Mir574	Mirn574|mir-574|mmu-mir-574	microRNA 574	ncRNA
mm_165306.1	chr2	98663756	98663758	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	1196100	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_23348.1	chr3	54755575	54755589	+	1	NA	promoter-TSS (NM_019483)	promoter-TSS (NM_019483)	0	NM_019483	55994	Mm.244353	NM_019483	ENSMUSG00000027796	Smad9	MADH6|Madh8|Madh9|Smad8	SMAD family member 9	protein-coding
mm_102088.1	chr11	52282565	52282579	-	1	NA	promoter-TSS (NM_009331)	promoter-TSS (NM_009331)	23	NM_009331	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_78498.1	chr9	32732148	32732165	+	1	NA	intron (NM_011808, intron 3 of 7)	intron (NM_011808, intron 3 of 7)	36114	NM_001038642	23871	Mm.292415	NM_011808	ENSMUSG00000032035	Ets1	AI196000|AI448617|D230050P06|Ets-1|Tpl1|vs	E26 avian leukemia oncogene 1, 5' domain	protein-coding
mm_5970.1	chr1	57377477	57377539	-	1	NA	promoter-TSS (NM_028546)	promoter-TSS (NM_028546)	36	NR_037999	75323	Mm.362968	NR_037999	ENSMUSG00000097519	4930558J18Rik	-	RIKEN cDNA 4930558J18 gene	ncRNA
mm_87248.1	chr10	41303969	41303975	+	1	NA	promoter-TSS (NM_133999)	promoter-TSS (NM_133999)	-731	NM_133999	103199	Mm.277242	NM_133999	ENSMUSG00000038417	Fig4	A530089I17Rik|AI326867|Sac3	FIG4 phosphoinositide 5-phosphatase	protein-coding
mm_88478.1	chr10	77613810	77613820	+	1	NA	intron (NR_125903, intron 1 of 2)	intron (NR_125903, intron 1 of 2)	106	NR_125903	20610	Mm.24433	NM_019929	ENSMUSG00000020265	Sumo3	2810014B19Rik|D10Ertd345e|SMT3A|SUMO-3|Smt3h1	small ubiquitin-like modifier 3	protein-coding
mm_83604.1	chr9	48604980	48605000	-	1	NA	5' UTR (NM_001311062, exon 1 of 4)	5' UTR (NM_001311062, exon 1 of 4)	133	NM_001311062	18113	Mm.8362	NM_010924	ENSMUSG00000032271	Nnmt	-	nicotinamide N-methyltransferase	protein-coding
mm_44436.1	chr5	21188500	21188515	-	1	NA	intron (NM_175437, intron 1 of 30)	intron (NM_175437, intron 1 of 30)	2240	NM_175437	212167	Mm.121705	NM_175437	ENSMUSG00000039934	Gsap	A530088I07Rik|Pion	gamma-secretase activating protein	protein-coding
mm_106872.1	chr12	8010486	8010501	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	32816	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_165432.1	chr2	153527966	153527979	+	1	NA	intron (NM_001134300, intron 1 of 10)	CpG	1999	NM_001134300	329540	Mm.50600	NM_001001986	ENSMUSG00000061411	Nol4l	4931410H15|8430427H17Rik|AI429157|Gm1636	nucleolar protein 4-like	protein-coding
mm_66608.1	chr7	45466273	45466298	-	1	NA	intron (NM_007527, intron 1 of 5)	intron (NM_007527, intron 1 of 5)	613	NM_007527	12028	Mm.19904	NM_007527	ENSMUSG00000003873	Bax	-	BCL2-associated X protein	protein-coding
mm_64868.1	chr7	13837411	13837411	-	1	NA	promoter-TSS (NM_001111296)	promoter-TSS (NM_001111296)	-1	NM_001111296	20859	Mm.260026	NM_001111296	ENSMUSG00000078798	Sult2a1	ST2A1|Std|Sth1|mSTa1	sulfotransferase family 2A, dehydroepiandrosterone (DHEA)-preferring, member 1	protein-coding
mm_93104.1	chr10	91007318	91007325	-	1	NA	intron (NM_009684, intron 22 of 26)	ID_B1|SINE|B4	75422	NM_001042558	11783	Mm.220289	NM_009684	ENSMUSG00000019979	Apaf1	6230400I06Rik|Apaf-1|Apaf1l|fog|mKIAA0413	apoptotic peptidase activating factor 1	protein-coding
mm_138585.1	chr17	35506029	35506049	+	1	NA	promoter-TSS (NM_013633)	promoter-TSS (NM_013633)	7	NM_013633	18999	Mm.17031	NM_013633	ENSMUSG00000024406	Pou5f1	NF-A3|Oct-3|Oct-3/4|Oct-4|Oct3|Oct3/4|Oct4|Otf-3|Otf-4|Otf3|Otf3-rs7|Otf3g|Otf4	POU domain, class 5, transcription factor 1	protein-coding
mm_141382.1	chr17	29079061	29079075	-	1	NA	promoter-TSS (NR_036469)	promoter-TSS (NR_036469)	58	NR_036469	100504267	Mm.438550	NR_036469	ENSMUSG00000085912	Trp53cor1	Gm16197|OTTMUSG00000031656|linc-p21|lincRNA-p21	tumor protein p53 pathway corepressor 1	ncRNA
mm_103445.1	chr11	76126701	76126704	-	1	NA	intron (NM_026664, intron 7 of 21)	ID_B1|SINE|B4	52928	NM_026664	68299	Mm.46397	NM_026664	ENSMUSG00000017288	Vps53	2010002A08Rik|2310040I21Rik|3100002B05Rik|Hccs1	VPS53 GARP complex subunit	protein-coding
mm_116194.1	chr13	31582500	31582518	-	1	NA	promoter-TSS (NR_029439)	promoter-TSS (NR_029439)	4	NR_029439	71307	Mm.376184	NR_029439	ENSMUSG00000038408	1700018A04Rik	4930551G20Rik|4933439J11Rik	RIKEN cDNA 1700018A04 gene	ncRNA
mm_108606.1	chr12	85474303	85474307	+	1	NA	intron (NM_010234, intron 1 of 3)	CpG	404	NM_010234	14281	Mm.246513	NM_010234	ENSMUSG00000021250	Fos	D12Rfj1|c-fos|cFos	FBJ osteosarcoma oncogene	protein-coding
mm_125731.1	chr15	73176139	73176142	+	1	NA	intron (NM_153178, intron 1 of 18)	RMER4B|LTR|ERVK	8807	NM_153178	239528	Mm.23095	NM_153178	ENSMUSG00000036698	Ago2	1110029L17Rik|2310051F07Rik|AI225898|AL022874|AW546247|ENSMUSG00000072493|Eif2c2|Gerp95|Gm10365|mKIAA4215	argonaute RISC catalytic subunit 2	protein-coding
mm_119882.1	chr14	54894134	54894153	+	1	NA	promoter-TSS (NM_019402)	promoter-TSS (NM_019402)	0	NM_019402	54196	Mm.7723	NM_019402	ENSMUSG00000022194	Pabpn1	PAB2|Pabp3|mPABII	poly(A) binding protein, nuclear 1	protein-coding
mm_56776.1	chr6	116629157	116629161	-	1	NA	promoter-TSS (NM_026057)	promoter-TSS (NM_026057)	-160	NM_026057	67255	Mm.18810	NM_026057	ENSMUSG00000059878	Zfp422	2900028O21Rik|AU041373|KOX15|Krox-25-2|Krox-26|Krox25|Krox26|Znf22	zinc finger protein 422	protein-coding
mm_51888.1	chr6	90604700	90604754	+	1	NA	promoter-TSS (NM_027868)	promoter-TSS (NM_027868)	-153	NM_027868	71699	Mm.272633	NM_027868	ENSMUSG00000030089	Slc41a3	1010001P06Rik|AI480742|SLC41A1-L2	solute carrier family 41, member 3	protein-coding
mm_96458.1	chr11	67586626	67586634	+	1	NA	5' UTR (NM_001109657, exon 1 of 14)	5' UTR (NM_001109657, exon 1 of 14)	130	NM_001109657	14457	Mm.40338	NM_008088	ENSMUSG00000033066	Gas7	AW124766|B230343A10Rik|Gas7-cb	growth arrest specific 7	protein-coding
mm_21623.1	chr2	164277087	164277093	-	1	NA	exon (NM_009300, exon 2 of 3)	exon (NM_009300, exon 2 of 3)	1217	NM_009300	20941	Mm.1286	NM_009300	ENSMUSG00000016998	Svs4	SVS-IV|Svp-2|Svp-4|Svp2|Svp4	seminal vesicle secretory protein 4	protein-coding
mm_83517.1	chr9	46154591	46154594	-	1	NA	intron (NM_027498, intron 3 of 24)	intron (NM_027498, intron 3 of 24)	-74038	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2|apo-AI|apoA-I	apolipoprotein A-I	protein-coding
mm_76866.1	chr8	105496976	105496982	-	1	NA	promoter-TSS (NM_175160)	promoter-TSS (NM_175160)	-109	NM_175160	70796	Mm.100917	NM_175160	ENSMUSG00000039199	Zdhhc1	4432412D04Rik	zinc finger, DHHC domain containing 1	protein-coding
mm_139163.1	chr17	47557605	47557620	+	1	NA	intron (NM_001081635, intron 1 of 6)	ID4|SINE|ID	-35855	NM_007632	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_124658.1	chr15	5496196	5496218	+	1	NA	promoter-TSS (NR_045274)	promoter-TSS (NR_045274)	-111	NR_045274	71432	Mm.291087	NR_045274		5430437J10Rik	-	RIKEN cDNA 5430437J10 gene	ncRNA
mm_16928.1	chr2	13793794	13793806	-	1	NA	promoter-TSS (NM_145838)	promoter-TSS (NM_145838)	-280	NM_145838	241230	Mm.330004	NM_145838	ENSMUSG00000003418	St8sia6	1700007J08Rik|AI314453|AI875066|ST8SiaVI|Siat8f	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 6	protein-coding
mm_37461.1	chr4	123472380	123472410	-	1	NA	exon (NM_001199136, exon 36 of 98)	exon (NM_001199136, exon 36 of 98)	-60484	NM_001167918	442834	Mm.483803	NM_001167918		D830031N03Rik	Kiaa0754|mKIAA0754	RIKEN cDNA D830031N03 gene	protein-coding
mm_128336.1	chr15	38473722	38473732	-	1	NA	Intergenic	CpG	16820	NR_105916	102465574		NR_105916	ENSMUSG00000099110	Mir6951	Gm27765|mmu-mir-6951	microRNA 6951	ncRNA
mm_126197.1	chr15	78850936	78850959	+	1	NA	TTS (NM_025622)	TTS (NM_025622)	4582	NM_025622	107753	Mm.390793	NM_025622	ENSMUSG00000043501	Lgals2	2200008F12Rik|AI324147	lectin, galactose-binding, soluble 2	protein-coding
mm_31411.1	chr4	48048113	48048119	+	1	NA	intron (NM_015743, intron 1 of 7)	intron (NM_015743, intron 1 of 7)	2811	NM_015743	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_132718.1	chr16	43510189	43510200	+	1	NA	intron (NM_181058, intron 3 of 6)	(T)n|Simple_repeat|Simple_repeat	-89998	NR_046026	626693	Mm.447083	NR_046026	ENSMUSG00000085499	Gm15713	OTTMUSG00000025617	predicted gene 15713	ncRNA
mm_44297.1	chr5	8622952	8622970	-	1	NA	promoter-TSS (NM_198620)	promoter-TSS (NM_198620)	-9	NM_198620	242819	Mm.332192	NM_198620	ENSMUSG00000040570	Rundc3b	Gm440	RUN domain containing 3B	protein-coding
mm_79058.1	chr9	46230105	46230196	+	1	NA	exon (NM_009692, exon 4 of 4)	exon (NM_009692, exon 4 of 4)	1520	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2|apo-AI|apoA-I	apolipoprotein A-I	protein-coding
mm_126210.1	chr15	78899409	78899422	+	1	NA	promoter-TSS (NM_009164)	promoter-TSS (NM_009164)	-353	NR_133564	20401	Mm.4462	NM_009164	ENSMUSG00000022436	Sh3bp1	3BP-1	SH3-domain binding protein 1	protein-coding
mm_91548.1	chr10	39731975	39732011	-	1	NA	promoter-TSS (NM_011264)	promoter-TSS (NM_011264)	14	NR_038037	327744	Mm.295265	NM_183198	ENSMUSG00000087177	E130307A14Rik	-	RIKEN cDNA E130307A14 gene	ncRNA
mm_6214.1	chr1	66838465	66838512	-	1	NA	intron (NM_007381, intron 8 of 10)	intron (NM_007381, intron 8 of 10)	-20893	NM_001122738	68691	Mm.240912	NM_177645	ENSMUSG00000026004	Kansl1l	1110028C15Rik|1190030G24|AI427598|C430010P07Rik|mKIAA4189	KAT8 regulatory NSL complex subunit 1-like	protein-coding
mm_118957.1	chr14	27403137	27403150	+	1	NA	3' UTR (NM_027871, exon 11 of 11)	3' UTR (NM_027871, exon 11 of 11)	-25704	NM_028945	218850	Mm.247767	NM_028945	ENSMUSG00000040651	Fam208a	4732418E12|4933409E02Rik|D14Abb1e|MommeD6	family with sequence similarity 208, member A	protein-coding
mm_58968.1	chr7	18992401	18992422	+	1	NA	exon (NM_145579, exon 2 of 3)	exon (NM_145579, exon 2 of 3)	1166	NM_145579	232934	Mm.440069	NM_145579	ENSMUSG00000048481	Mypop	Myodysa|P42pop	Myb-related transcription factor, partner of profilin	protein-coding
mm_987.1	chr1	58586382	58586401	+	1	NA	promoter-TSS (NM_172513)	promoter-TSS (NM_172513)	-6	NM_025597	66495	Mm.2033	NM_025597	ENSMUSG00000026032	Ndufb3	2700033I16Rik|CI-B12	NADH dehydrogenase (ubiquinone) 1 beta subcomplex 3	protein-coding
mm_171983.1	chr5	92140938	92140958	-	1	NA	intron (NM_019490, intron 1 of 23)	intron (NM_019490, intron 1 of 23)	3010	NM_019490	56041	Mm.15868	NM_019490	ENSMUSG00000029407	Uso1	115kDa|TAP|Vdp	USO1 vesicle docking factor	protein-coding
mm_166349.1	chr5	119670985	119670991	+	1	NA	promoter-TSS (NM_011535)	promoter-TSS (NM_011535)	126	NM_198052	21386	Mm.219139	NM_011535	ENSMUSG00000018604	Tbx3	D5Ertd189e	T-box 3	protein-coding
mm_145878.1	chr18	65476495	65476509	+	1	NA	3' UTR (NM_172833, exon 16 of 16)	3' UTR (NM_172833, exon 16 of 16)	45505	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_90425.1	chr10	127498854	127498888	+	1	NA	3' UTR (NM_001168293, exon 24 of 24)	3' UTR (NM_001168293, exon 24 of 24)	-2846	NM_177707	237611	Mm.32087	NM_177707	ENSMUSG00000040287	Stac3	9830125E18	SH3 and cysteine rich domain 3	protein-coding
mm_13365.1	chr2	103454342	103454366	+	1	NA	3' UTR (NM_009804, exon 13 of 13)	3' UTR (NM_009804, exon 13 of 13)	30286	NM_010125	13711	Mm.20888	NM_010125	ENSMUSG00000027186	Elf5	ESE-2|ESE-5|ESE-5.	E74-like factor 5	protein-coding
mm_132436.1	chr16	35923769	35923773	+	1	NA	Intergenic	MYSERV6-int|LTR|ERVK	-14699	NM_030253	80285	Mm.49074	NM_030253	ENSMUSG00000022906	Parp9	ARTD9|AW214463|BC003281|Bagl|Bal|PARP-9	poly (ADP-ribose) polymerase family, member 9	protein-coding
mm_61306.1	chr7	67952370	67952428	+	1	NA	5' UTR (NM_010513, exon 1 of 21)	5' UTR (NM_010513, exon 1 of 21)	142	NM_010513	16001	Mm.275742	NM_010513	ENSMUSG00000005533	Igf1r	A330103N21Rik|CD221|D930020L01|IGF-1R|hyft	insulin-like growth factor I receptor	protein-coding
mm_106303.1	chr11	118290071	118290166	-	1	NA	5' UTR (NM_001033528, exon 1 of 21)	5' UTR (NM_001033528, exon 1 of 21)	126	NM_001033528	72344	Mm.232293	NM_001033528	ENSMUSG00000033909	Usp36	2700002L06Rik|mKIAA1453	ubiquitin specific peptidase 36	protein-coding
mm_137627.1	chr17	28328577	28328591	+	1	NA	5' UTR (NM_011287, exon 1 of 6)	5' UTR (NM_011287, exon 1 of 6)	113	NM_011287	19896	Mm.336955	NM_011287	ENSMUSG00000037805	Rpl10a	CsA-19|Nedd6	ribosomal protein L10A	protein-coding
mm_65098.1	chr7	19272715	19272753	-	1	NA	promoter-TSS (NM_001282022)	promoter-TSS (NM_001282022)	-880	NM_001282022	22323	Mm.9684	NM_009499	ENSMUSG00000030403	Vasp	-	vasodilator-stimulated phosphoprotein	protein-coding
mm_39675.1	chr5	25516062	25516102	+	1	NA	promoter-TSS (NM_198621)	promoter-TSS (NM_198621)	15	NM_198621	242891	Mm.291521	NM_198621	ENSMUSG00000038044	Cct8l1	Gm443	chaperonin containing TCP1, subunit 8 (theta)-like 1	protein-coding
mm_6530.1	chr1	74748855	74748887	-	1	NA	promoter-TSS (NM_153744)	promoter-TSS (NM_153744)	84	NM_153744	241113	Mm.166501	NM_153744	ENSMUSG00000006542	Prkag3	AMPKg3L|AMPKg3S|Amkg3|Ampkg3	protein kinase, AMP-activated, gamma 3 non-catatlytic subunit	protein-coding
mm_164.1	chr1	12772135	12772137	+	1	NA	intron (NM_172294, intron 2 of 21)	intron (NM_172294, intron 2 of 21)	53591	NM_172294	240725	Mm.45563	NM_172294	ENSMUSG00000016918	Sulf1	AI467640|AW121680|mKIAA1077	sulfatase 1	protein-coding
mm_158816.1	chrX	167328613	167328623	-	1	NA	intron (NM_001290755, intron 2 of 4)	intron (NM_001290755, intron 2 of 4)	1953	NM_001290757	170743	Mm.23979	NM_133211	ENSMUSG00000044583	Tlr7	-	toll-like receptor 7	protein-coding
mm_131932.1	chr16	23611381	23611407	+	1	NA	intron (NM_023386, intron 1 of 1)	RMER10B|LTR|ERVL	1475	NM_023386	67775	Mm.475107	NM_023386	ENSMUSG00000033355	Rtp4	5830458K16Rik|Ifrg28	receptor transporter protein 4	protein-coding
mm_65764.1	chr7	28741717	28741731	-	1	NA	promoter-TSS (NM_023637)	promoter-TSS (NM_023637)	57	NM_011885	24030	Mm.358650	NM_011885	ENSMUSG00000045948	Mrps12	AI327385|Rpms12|rps12	mitochondrial ribosomal protein S12	protein-coding
mm_141472.1	chr17	30612614	30612663	-	1	NA	promoter-TSS (NM_001113560)	promoter-TSS (NM_001113560)	21	NM_025374	109801	Mm.261984	NM_025374	ENSMUSG00000024026	Glo1	0610009E22Rik|1110008E19Rik|2510049H23Rik|AW550643|GLY1|Glo-1|Glo-1r|Glo-1s|Glo1-r|Glo1-s|Qglo	glyoxalase 1	protein-coding
mm_76602.1	chr8	90347195	90347201	-	1	NA	intron (NM_172913, intron 1 of 6)	intron (NM_172913, intron 1 of 6)	1054	NM_172913	244579	Mm.302755	NM_172913	ENSMUSG00000043668	Tox3	500-9|BC052044|C230068E13|CAGF9|Tnrc9	TOX high mobility group box family member 3	protein-coding
mm_96717.1	chr11	69664368	69664388	+	1	NA	non-coding (NR_110993, exon 5 of 5)	non-coding (NR_110993, exon 5 of 5)	1335	NR_035455	100316840		NR_035455	ENSMUSG00000088752	Mir1934	mir-1934|mmu-mir-1934	microRNA 1934	ncRNA
mm_143215.1	chr17	62882664	62882692	-	1	NA	Intergenic	CpG-6536	-1361	NM_010109	13640	Mm.7978	NM_010109	ENSMUSG00000048915	Efna5	AL-1|AV158822|EFL-5|Ephrin-A5|Epl7|LERK-7|RAGS	ephrin A5	protein-coding
mm_79298.1	chr9	51765326	51765364	+	1	NA	promoter-TSS (NM_175535)	promoter-TSS (NM_175535)	-7	NM_175535	244867	Mm.400352	NM_175535	ENSMUSG00000053199	Arhgap20	6530403F17Rik|A530023E23Rik|RARhoGAP|mKIAA1391	Rho GTPase activating protein 20	protein-coding
mm_23593.1	chr3	64977484	64977496	+	1	NA	Intergenic	Intergenic	-131878	NM_010597	16497	Mm.316402	NM_010597	ENSMUSG00000027827	Kcnab1	Akr8a8|Kvbeta1.1|mKv(beta)1	potassium voltage-gated channel, shaker-related subfamily, beta member 1	protein-coding
mm_38231.1	chr4	136021723	136021736	-	1	NA	promoter-TSS (NM_013736)	promoter-TSS (NM_013736)	-80	NM_013736	27224	Mm.27663	NM_013736	ENSMUSG00000028668	Eloa	110kDa|AA408125|Tceb3|Tceb3a	elongin A	protein-coding
mm_74301.1	chr8	126298630	126298643	+	1	NA	promoter-TSS (NM_175434)	promoter-TSS (NM_175434)	57	NM_175434	210027	Mm.405238	NM_175434	ENSMUSG00000057060	Slc35f3	B230375D17Rik	solute carrier family 35, member F3	protein-coding
mm_132379.1	chr16	34921519	34921594	+	1	NA	intron (NM_139300, intron 15 of 31)	intron (NM_139300, intron 15 of 31)	17773	NR_040536	76649	Mm.420532	NR_040536	ENSMUSG00000100593	1700119H24Rik	-	RIKEN cDNA 1700119H24 gene	ncRNA
mm_109286.1	chr12	109558740	109558745	+	1	NA	non-coding (NR_003633, exon 5 of 5)	non-coding (NR_003633, exon 5 of 5)	-4950	NR_030427	791079		NR_030427	ENSMUSG00000076451	Mir770	Mirn770|mir-770|mmu-mir-770	microRNA 770	ncRNA
mm_87354.1	chr10	43610469	43610477	+	1	NA	intron (NR_033558, intron 2 of 2)	PB1D10|SINE|Alu	17046	NR_033558	414125	Mm.244305	NR_033558	ENSMUSG00000075184	F830002L21Rik	F930017D23Rik	RIKEN cDNA F830002L21 gene	ncRNA
mm_21441.1	chr2	158668754	158668759	-	1	NA	intron (NM_001159662, intron 1 of 10)	intron (NM_001159662, intron 1 of 10)	1621	NM_001159662	228852	Mm.150540	NM_153089	ENSMUSG00000037754	Ppp1r16b	ANKRD4|C130078N17Rik|TIMAP|Wdt4	protein phosphatase 1, regulatory (inhibitor) subunit 16B	protein-coding
mm_82910.1	chr9	34589280	34589294	-	1	NA	intron (NM_001190912, intron 1 of 15)	intron (NM_001190912, intron 1 of 15)	100556	NM_001190911	67703	Mm.220710	NM_026324	ENSMUSG00000032036	Kirrel3	1500010O20Rik|2900036G11Rik|NEPH2|SST4|mKIAA1867	kin of IRRE like 3 (Drosophila)	protein-coding
mm_94575.1	chr11	11690138	11690184	+	1	NA	promoter-TSS (NM_001301865)	promoter-TSS (NM_001301865)	-16	NM_001301865	22778	Mm.103545	NM_009578	ENSMUSG00000018654	Ikzf1	5832432G11Rik|Ikaros|LyF-1|Zfpn1a1|Znfn1a1|hlk-1|mKIAA4227	IKAROS family zinc finger 1	protein-coding
mm_76264.1	chr8	84023250	84023295	-	1	NA	intron (NM_028877, intron 1 of 6)	intron (NM_028877, intron 1 of 6)	1798	NM_028877	74337	Mm.250943	NM_028877	ENSMUSG00000047986	Palm3	4432412L15Rik|AL024300	paralemmin 3	protein-coding
mm_109672.1	chr12	113074476	113074524	+	1	NA	promoter-TSS (NM_029381)	promoter-TSS (NM_029381)	-2	NM_029381	75671	Mm.23377	NM_029381	ENSMUSG00000012211	Tex22	1700028O09Rik|AV210422|Tep22	testis expressed gene 22	protein-coding
mm_34182.1	chr4	140700488	140700529	+	1	NA	promoter-TSS (NM_173867)	promoter-TSS (NM_173867)	-965	NM_173867	108911	Mm.253	NM_173867	ENSMUSG00000040945	Rcc2	2610510H01Rik|2610529N02Rik|AA536646|AA675016|Td60|mKIAA1470	regulator of chromosome condensation 2	protein-coding
mm_150223.1	chr19	33961215	33961255	+	1	NA	promoter-TSS (NM_026334)	promoter-TSS (NM_026334)	-13	NM_026334	67717	Mm.329816	NM_026334	ENSMUSG00000024768	Lipf	2310051B21Rik|AV082900	lipase, gastric	protein-coding
mm_121129.1	chr14	101840875	101840884	+	1	NA	exon (NM_201529, exon 4 of 31)	exon (NM_201529, exon 4 of 31)	256	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_120540.1	chr14	67234796	67234837	+	1	NA	intron (NM_010095, intron 1 of 16)	intron (NM_010095, intron 1 of 16)	1524	NM_001276387	13592	Mm.319947	NM_010095	ENSMUSG00000022053	Ebf2	D14Ggc1e|EBF-2|Mmot1|O/E-3|OE-3	early B cell factor 2	protein-coding
mm_163311.1	chr12	4850723	4850726	+	1	NA	exon (NM_001170858, exon 2 of 4)	exon (NM_001170858, exon 2 of 4)	7421	NM_001170858	238037	Mm.146087	NM_173416	ENSMUSG00000051721	BC068281	A430092C04|Wdcp	cDNA sequence BC068281	protein-coding
mm_47485.1	chr5	123865492	123865518	-	1	NA	promoter-TSS (NM_030701)	promoter-TSS (NM_030701)	11	NM_030701	80885	Mm.440567	NM_030701	ENSMUSG00000045502	Hcar2	Gpr109a|Gpr109b|HM74|Niacr1|PUMA-G|Pumag|mHM74b	hydroxycarboxylic acid receptor 2	protein-coding
mm_90521.1	chr10	128059065	128059083	+	1	NA	promoter-TSS (NM_019766)	promoter-TSS (NM_019766)	92	NM_019766	56351	Mm.305816	NM_019766	ENSMUSG00000071072	Ptges3	5730442A20Rik|Ptges|Tebp|cPGES|p23|sid3177	prostaglandin E synthase 3 (cytosolic)	protein-coding
mm_4277.1	chr1	171607507	171607517	+	1	NA	promoter-TSS (NM_001277968)	promoter-TSS (NM_001277968)	-102	NM_008534	17085	Mm.560	NM_008534	ENSMUSG00000004707	Ly9	AI893573|CD229|Lgp100|Ly-9|SLAMF3|T100	lymphocyte antigen 9	protein-coding
mm_143898.1	chr17	84682933	84682944	-	1	NA	promoter-TSS (NM_031884)	promoter-TSS (NM_031884)	73	NM_031884	27409	Mm.289590	NM_031884	ENSMUSG00000040505	Abcg5	cmp|sterolin-1|trac	ATP-binding cassette, sub-family G (WHITE), member 5	protein-coding
mm_72750.1	chr8	85171524	85171526	+	1	NA	exon (NM_001037922, exon 2 of 2)	exon (NM_001037922, exon 2 of 2)	19601	NM_001037922	624855	Mm.390061	NM_001037922	ENSMUSG00000062687	Cks1brt	EG624855|Gm6531	CDC28 protein kinase 1b, retrogene	protein-coding
mm_28169.1	chr3	87885559	87885608	-	1	NA	promoter-TSS (NM_033573)	promoter-TSS (NM_033573)	-21	NM_033573	94315	Mm.35089	NM_033573	ENSMUSG00000004895	Prcc	-	papillary renal cell carcinoma (translocation-associated)	protein-coding
mm_162835.1	chr10	82986376	82986387	-	1	NA	intron (NM_021439, intron 1 of 2)	intron (NM_021439, intron 1 of 2)	884	NM_021439	58250	Mm.360747	NM_021439	ENSMUSG00000034612	Chst11	1110020P09Rik|C4ST|C4ST-1|C4ST1|C4s	carbohydrate sulfotransferase 11	protein-coding
mm_146139.1	chr18	74733736	74733824	+	1	NA	intron (NM_201600, intron 30 of 38)	intron (NM_201600, intron 30 of 38)	44675	NR_028560	100217466		NR_028560		Scarna17	MBII-119	small Cajal body-specific RNA 17	ncRNA
mm_153802.1	chr19	46040366	46040377	-	1	NA	promoter-TSS (NM_010697)	promoter-TSS (NM_010697)	-750	NM_010697	16825	Mm.327442	NM_010697	ENSMUSG00000025223	Ldb1	CLIM2|NLI	LIM domain binding 1	protein-coding
mm_3412.1	chr1	144317868	144317880	+	1	NA	Intergenic	Intergenic	-68770	NM_015811	50778	Mm.103701	NM_015811	ENSMUSG00000026358	Rgs1	BL34	regulator of G-protein signaling 1	protein-coding
mm_123037.1	chr14	55560341	55560395	-	1	NA	promoter-TSS (NM_001199009)	promoter-TSS (NM_001199009)	339	NM_133734	28199	Mm.11535	NM_133734	ENSMUSG00000022214	Dcaf11	0710008A13Rik|C76035|D14Ucla1|Dacf11|GLO14|Wdr23	DDB1 and CUL4 associated factor 11	protein-coding
mm_142258.1	chr17	39843484	39843543	-	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	516	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_25467.1	chr3	108653908	108653928	+	1	NA	promoter-TSS (NM_145543)	promoter-TSS (NM_145543)	5	NM_145543	229725	Mm.214545	NM_145543	ENSMUSG00000027884	Clcc1	Mclc	chloride channel CLIC-like 1	protein-coding
mm_86929.1	chr10	24150937	24150971	+	1	NA	intron (NM_016797, intron 1 of 9)	intron (NM_016797, intron 1 of 9)	1637	NM_016797	53331	Mm.248042	NM_016797	ENSMUSG00000019998	Stx7	AI315064|AI317144|AW107239|Syn7	syntaxin 7	protein-coding
mm_55505.1	chr6	69835270	69835274	-	1	NA	Intergenic	Intergenic	-508098	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_133089.1	chr16	62854300	62854310	+	1	NA	promoter-TSS (NM_011173)	promoter-TSS (NM_011173)	-2	NM_011173	19128	Mm.127156	NM_011173	ENSMUSG00000022912	Pros1	AW214361	protein S (alpha)	protein-coding
mm_93468.1	chr10	111131892	111131893	-	1	NA	Intergenic	ID2|SINE|ID	-32910	NM_001003717	237542	Mm.220204	NM_175489	ENSMUSG00000020189	Osbpl8	AA536976|AA536995|C730029P18Rik|D330025H14Rik|ORP-8	oxysterol binding protein-like 8	protein-coding
mm_4119.1	chr1	168502713	168502721	+	1	NA	Intergenic	LTR103b_Mam|LTR|ERV1?	12074	NR_105766	102465178		NR_105766	ENSMUSG00000098407	Mir6348	Gm27412|mmu-mir-6348	microRNA 6348	ncRNA
mm_128298.1	chr15	37458524	37458581	-	1	NA	intron (NM_001170867, intron 1 of 4)	intron (NM_001170867, intron 1 of 4)	830	NM_001170867	52589	Mm.283370	NM_134094	ENSMUSG00000051359	Ncald	AI848120|D030020D09Rik|D15Ertd412e	neurocalcin delta	protein-coding
mm_51815.1	chr6	88902416	88902428	+	1	NA	5' UTR (NM_011906, exon 1 of 12)	5' UTR (NM_011906, exon 1 of 12)	171	NM_011906	24100	Mm.284480	NM_011906	ENSMUSG00000002871	Tpra1	40kDa|Gpr175|Tpra40	transmembrane protein, adipocyte asscociated 1	protein-coding
mm_138098.1	chr17	34048434	34048438	+	1	NA	intron (NM_001317722, intron 7 of 64)	intron (NM_001317722, intron 7 of 64)	9298	NM_001317722	12815	Mm.20230	NM_009926	ENSMUSG00000024330	Col11a2	-	collagen, type XI, alpha 2	protein-coding
mm_55776.1	chr6	81033765	81033775	-	1	NA	Intergenic	RLTR10C|LTR|ERVK	861893	NR_106091	102465711		NR_106091	ENSMUSG00000106154	Mir7232	mmu-mir-7232	microRNA 7232	ncRNA
mm_109370.1	chr12	109646461	109646474	+	1	NA	non-coding (NR_028261, exon 11 of 21)	non-coding (NR_028261, exon 11 of 21)	-3150	NR_046304	100861570		NR_046304	ENSMUSG00000084549	DQ267100	-	snoRNA DQ267100	snoRNA
mm_131335.1	chr16	13358142	13358190	+	1	NA	promoter-TSS (NM_153588)	promoter-TSS (NM_153588)	-255	NM_153588	239719	Mm.270643	NM_153588	ENSMUSG00000009569	Mkl2	ENSMUSG00000075401|Gt4-1|MRTF-B|Mrtfb|mKIAA1243	MKL/myocardin-like 2	protein-coding
mm_34312.1	chr4	141817904	141817930	+	1	NA	exon (NM_007919, exon 7 of 8)	exon (NM_007919, exon 7 of 8)	8088	NM_007919	13706	Mm.45316	NM_007919	ENSMUSG00000058579	Cela2a	Ela-2|Ela2|Ela2a	chymotrypsin-like elastase family, member 2A	protein-coding
mm_164362.1	chr16	22895948	22895957	+	1	NA	intron (NR_075099, intron 3 of 5)	intron (NR_075099, intron 3 of 5)	-1566	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_141004.1	chr17	24943190	24943231	-	1	NA	3' UTR (NM_198937, exon 5 of 5)	3' UTR (NM_198937, exon 5 of 5)	-6233	NM_013931	30957	Mm.43081	NM_013931	ENSMUSG00000024163	Mapk8ip3	BB120594|D17Wsu15e|JIP-3|JSAP1|JSAP1a|JSAP1b|JSAP1c|JSAP1d|Jip3|Syd2|mKIAA1066	mitogen-activated protein kinase 8 interacting protein 3	protein-coding
mm_138590.1	chr17	35506405	35506415	+	1	NA	exon (NM_013633, exon 1 of 5)	exon (NM_013633, exon 1 of 5)	378	NM_013633	18999	Mm.17031	NM_013633	ENSMUSG00000024406	Pou5f1	NF-A3|Oct-3|Oct-3/4|Oct-4|Oct3|Oct3/4|Oct4|Otf-3|Otf-4|Otf3|Otf3-rs7|Otf3g|Otf4	POU domain, class 5, transcription factor 1	protein-coding
mm_76378.1	chr8	84838565	84838589	-	1	NA	exon (NM_001297607, exon 3 of 9)	exon (NM_001297607, exon 3 of 9)	2088	NM_001297607	19358	Mm.255539	NM_009010	ENSMUSG00000003813	Rad23a	2310040P19Rik|AL024030|HR23A|mHR23A	RAD23 homolog A, nucleotide excision repair protein	protein-coding
mm_114358.1	chr13	61003709	61003749	+	1	NA	exon (NM_012007, exon 4 of 8)	exon (NM_012007, exon 4 of 8)	2182	NM_012007	26898	Mm.31948	NM_012007	ENSMUSG00000055298	Ctsj	CATP|CatRLP|Ctsp	cathepsin J	protein-coding
mm_74283.1	chr8	125669829	125669875	+	1	NA	promoter-TSS (NM_028908)	promoter-TSS (NM_028908)	34	NM_028908	74393	Mm.41709	NM_028908	ENSMUSG00000050930	Map10	4933403G14Rik|AI835009|mKIAA1383	microtubule-associated protein 10	protein-coding
mm_35024.1	chr4	4016473	4016482	-	1	NA	intron (NM_181989, intron 1 of 6)	intron (NM_181989, intron 1 of 6)	3186	NM_181989	242285	Mm.98096	NM_181989	ENSMUSG00000028236	Sdr16c5	Rdhe2|Scdr9	short chain dehydrogenase/reductase family 16C, member 5	protein-coding
mm_18233.1	chr2	51972930	51972981	-	1	NA	5' UTR (NM_001141948, exon 1 of 8)	5' UTR (NM_001141948, exon 1 of 8)	253	NM_001141949	64685	Mm.7491	NM_019401	ENSMUSG00000026946	Nmi	-	N-myc (and STAT) interactor	protein-coding
mm_29133.1	chr3	105687745	105687772	-	1	NA	promoter-TSS (NM_017397)	promoter-TSS (NM_017397)	-187	NM_017397	53975	Mm.272826	NM_017397	ENSMUSG00000027905	Ddx20	GEMIN3|dp103	DEAD (Asp-Glu-Ala-Asp) box polypeptide 20	protein-coding
mm_39318.1	chr5	8067630	8067652	+	1	NA	3' UTR (NM_025618, exon 8 of 8)	3' UTR (NM_025618, exon 8 of 8)	11099	NM_001080974	109552	Mm.96211	NM_025618	ENSMUSG00000003161	Sri	2210417O06Rik|2900070H08Rik|Sor	sorcin	protein-coding
mm_166529.1	chr6	28929526	28929529	-	1	NA	Intergenic	RLTR10A|LTR|ERVK	-93092	NR_029567	387237		NR_029567	ENSMUSG00000065469	Mir129-1	Mirn129-1|Mirn129b|miR-129b|mir-129-1	microRNA 129-1	ncRNA
mm_81790.1	chr9	114978508	114978550	+	1	NA	Intergenic	CpG	-44542	NM_175380	333433	Mm.38198	NM_175380	ENSMUSG00000050627	Gpd1l	2210409H23Rik|D9Ertd660e	glycerol-3-phosphate dehydrogenase 1-like	protein-coding
mm_118629.1	chr14	21250607	21250623	+	1	NA	intron (NM_001243041, intron 6 of 10)	intron (NM_001243041, intron 6 of 10)	174463	NM_001243041	11534	Mm.188734	NM_134079	ENSMUSG00000039197	Adk	2310026J05Rik|5033405D03Rik|AI255373|AI987814|Ak	adenosine kinase	protein-coding
mm_158346.1	chrX	134276970	134276980	-	1	NA	promoter-TSS (NM_001167995)	promoter-TSS (NM_001167995)	9	NM_172540	215201	Mm.289368	NM_172540	ENSMUSG00000067369	Trmt2b	4732479N06Rik	TRM2 tRNA methyltransferase 2B	protein-coding
mm_140016.1	chr17	73804829	73804839	+	1	NA	promoter-TSS (NM_020578)	promoter-TSS (NM_020578)	-7	NM_020578	57440	Mm.18526	NM_020578	ENSMUSG00000024065	Ehd3	Ehd2	EH-domain containing 3	protein-coding
mm_135246.1	chr16	37539694	37539710	-	1	NA	promoter-TSS (NM_001042499)	promoter-TSS (NM_001042499)	67	NM_028812	74197	Mm.287795	NM_028812	ENSMUSG00000022828	Gtf2e1	2610024P03Rik|56kDa|AI303800|FE|TFIIE-A	general transcription factor II E, polypeptide 1 (alpha subunit)	protein-coding
mm_168727.1	chr12	110695633	110695642	-	1	NA	exon (NM_010480, exon 2 of 11)	exon (NM_010480, exon 2 of 11)	758	NM_010480	15519	Mm.1843	NM_010480	ENSMUSG00000021270	Hsp90aa1	86kDa|89kDa|AL024080|AL024147|Hsp86-1|Hsp89|Hsp90|Hspca|hsp4	heat shock protein 90, alpha (cytosolic), class A member 1	protein-coding
mm_26189.1	chr3	138432458	138432460	+	1	NA	Intergenic	Intergenic	-4741	NM_001288578	11532	Mm.3874	NM_007410	ENSMUSG00000028138	Adh5	Adh-5|Adh3|GSNOR	alcohol dehydrogenase 5 (class III), chi polypeptide	protein-coding
mm_40670.1	chr5	65423588	65423621	+	1	NA	exon (NM_009466, exon 4 of 12)	exon (NM_009466, exon 4 of 12)	12238	NM_009466	22235	Mm.344831	NM_009466	ENSMUSG00000029201	Ugdh	Udpgdh	UDP-glucose dehydrogenase	protein-coding
mm_26156.1	chr3	138217763	138217777	+	1	NA	promoter-TSS (NM_009626)	promoter-TSS (NM_009626)	-3	NM_009626	11529	Mm.8473	NM_009626	ENSMUSG00000055301	Adh7	AI325182|Adh-3|Adh-3e|Adh-3t|Adh3|Adh3-e|Adh3-t|Adh4|Adt-1	alcohol dehydrogenase 7 (class IV), mu or sigma polypeptide	protein-coding
mm_97336.1	chr11	77294036	77294081	+	1	NA	intron (NM_177710, intron 1 of 14)	intron (NM_177710, intron 1 of 14)	-54222	NM_001291190	237860	Mm.440381	NM_177710	ENSMUSG00000037926	Ssh2	SSH-2|SSH-2L|mSSH-2L	slingshot homolog 2 (Drosophila)	protein-coding
mm_94233.1	chr11	3291328	3291371	+	1	NA	exon (NM_001253691, exon 1 of 5)	exon (NM_001253691, exon 1 of 5)	892	NM_019574	56218	Mm.275563	NM_019574	ENSMUSG00000020453	Patz1	8430401L15Rik|AI447519|Mazr|Patz|Zfp278	POZ (BTB) and AT hook containing zinc finger 1	protein-coding
mm_8216.1	chr1	138155583	138155586	-	1	NA	intron (NM_001111316, intron 1 of 31)	L1MA6|LINE|L1	19542	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_1363.1	chr1	66386918	66386967	+	1	NA	intron (NM_001310634, intron 4 of 14)	intron (NM_001310634, intron 4 of 14)	65218	NM_001310634	17756	Mm.256966	NM_008632	ENSMUSG00000015222	Map2	G1-397-34|MAP-2|Mtap-2|Mtap2|repro4	microtubule-associated protein 2	protein-coding
mm_26133.1	chr3	137882814	137882820	+	1	NA	intron (NM_001033155, intron 1 of 7)	intron (NM_001033155, intron 1 of 7)	15142	NM_001033155	70604	Mm.256488	NM_001033155	ENSMUSG00000074212	Dnajb14	5730496F10Rik	DnaJ heat shock protein family (Hsp40) member B14	protein-coding
mm_123825.1	chr14	70619971	70619971	-	1	NA	intron (NM_001252664, intron 1 of 14)	intron (NM_001252664, intron 1 of 14)	-1402	NM_001252666	13829	Mm.210863	NM_013514	ENSMUSG00000022099	Dmtn	AI325486|Epb4.9|Epb49|dematin	dematin actin binding protein	protein-coding
mm_19343.1	chr2	90783153	90783163	-	1	NA	intron (NM_178755, intron 1 of 17)	CpG	414	NM_178755	271813	Mm.61146	NM_178755	ENSMUSG00000040812	Agbl2	4930524K04|A430081C19Rik|CCP2	ATP/GTP binding protein-like 2	protein-coding
mm_113702.1	chr13	43171519	43171530	+	1	NA	promoter-TSS (NM_025935)	promoter-TSS (NM_025935)	-23	NM_001252640	67046	Mm.269213	NM_025935	ENSMUSG00000021368	Tbc1d7	2610009C09Rik	TBC1 domain family, member 7	protein-coding
mm_101937.1	chr11	50207523	50207558	-	1	NA	exon (NM_011018, exon 3 of 8)	exon (NM_011018, exon 3 of 8)	3280	NM_001290769	18412	Mm.40828	NM_011018	ENSMUSG00000015837	Sqstm1	A170|OSF-6|Osi|STAP|STONE14|p62	sequestosome 1	protein-coding
mm_68858.1	chr7	126377402	126377438	-	1	NA	non-coding (NR_045537, exon 1 of 13)	non-coding (NR_045537, exon 1 of 13)	514	NM_023712	73658	Mm.11112	NM_023712	ENSMUSG00000030741	Spns1	2210013K02Rik|Spin1|Spinl	spinster homolog 1	protein-coding
mm_5357.1	chr1	25756828	25756831	-	1	NA	intron (NM_175642, intron 2 of 30)	intron (NM_175642, intron 2 of 30)	72878	NM_175642	210933	Mm.336569	NM_175642	ENSMUSG00000033569	Adgrb3	A830096D10Rik|Bai3	adhesion G protein-coupled receptor B3	protein-coding
mm_149994.1	chr19	29257962	29257962	+	1	NA	intron (NM_008413, intron 2 of 24)	intron (NM_008413, intron 2 of 24)	6159	NM_008413	16452	Mm.275839	NM_008413	ENSMUSG00000024789	Jak2	Fd17	Janus kinase 2	protein-coding
mm_59172.1	chr7	24403027	24403045	+	1	NA	intron (NM_028047, intron 1 of 13)	B3A|SINE|B2	3408	NM_028047	71997	Mm.150977	NM_028047	ENSMUSG00000002210	Smg9	1500002O20Rik|AI429693|N28092	smg-9 homolog, nonsense mediated mRNA decay factor (C. elegans)	protein-coding
mm_56498.1	chr6	99266382	99266401	-	1	NA	5' UTR (NM_001197321, exon 1 of 18)	5' UTR (NM_001197321, exon 1 of 18)	124	NM_001197321	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_39421.1	chr5	15934914	15934926	+	1	NA	5' UTR (NM_001110843, exon 1 of 39)	5' UTR (NM_001110843, exon 1 of 39)	229	NM_001110844	12293	Mm.159842	NM_009784	ENSMUSG00000040118	Cacna2d1	Ca(v)alpha2delta1|Cacna2|Cchl2a	calcium channel, voltage-dependent, alpha2/delta subunit 1	protein-coding
mm_105463.1	chr11	105181202	105181242	-	1	NA	promoter-TSS (NM_001112705)	promoter-TSS (NM_001112705)	211	NR_027956	73431	Mm.351426	NM_028539		1700052K11Rik	AI840954	RIKEN cDNA 1700052K11 gene	ncRNA
mm_44942.1	chr5	36530490	36530587	-	1	NA	promoter-TSS (NM_001113364)	promoter-TSS (NM_001113364)	85	NM_001113364	100855	Mm.486203	NM_133910	ENSMUSG00000029192	Tbc1d14	2810413P16Rik|AU043625|C86258|D5Ertd110e|mKIAA1322	TBC1 domain family, member 14	protein-coding
mm_37827.1	chr4	131967825	131967838	-	1	NA	exon (NM_001128607, exon 12 of 18)	exon (NM_001128607, exon 12 of 18)	46060	NM_001201367	623230	Mm.421179	NM_001201367	ENSMUSG00000070720	Tmem200b	EG623230	transmembrane protein 200B	protein-coding
mm_43476.1	chr5	136695216	136695231	+	1	NA	intron (NM_001085387, intron 1 of 4)	intron (NM_001085387, intron 1 of 4)	1046	NM_001085387	59310	Mm.5178	NM_021611	ENSMUSG00000005474	Myl10	1700027I08Rik|Mylc2pl|PLRLC	myosin, light chain 10, regulatory	protein-coding
mm_67282.1	chr7	78578963	78578987	-	1	NA	Intergenic	Intergenic	-1137	NM_182809	18213	Mm.33496	NM_008746	ENSMUSG00000059146	Ntrk3	AW125844|Ntrk3_tv3|TrkC	neurotrophic tyrosine kinase, receptor, type 3	protein-coding
mm_20642.1	chr2	132029162	132029184	-	1	NA	intron (NM_175445, intron 1 of 10)	CpG	815	NM_175445	215653	Mm.204737	NM_175445	ENSMUSG00000027339	Rassf2	3830431H01Rik|9030412M04Rik|AI852669|AW495050	Ras association (RalGDS/AF-6) domain family member 2	protein-coding
mm_157417.1	chrX	38564063	38564086	-	1	NA	exon (NM_028288, exon 4 of 23)	exon (NM_028288, exon 4 of 23)	12122	NM_028288	72584	Mm.327675	NM_028288	ENSMUSG00000031095	Cul4b	2700050M05Rik|AA409770|CUL-4B|mKIAA0695	cullin 4B	protein-coding
mm_170432.1	chr18	77789928	77789940	+	1	NA	Intergenic	RLTR31B_Mm|LTR|ERVK	-4616	NM_013831	19201	Mm.57174	NM_013831	ENSMUSG00000025429	Pstpip2	MAYP|cmo	proline-serine-threonine phosphatase-interacting protein 2	protein-coding
mm_55075.1	chr6	49111084	49111100	-	1	NA	intron (NM_023670, intron 6 of 14)	intron (NM_023670, intron 6 of 14)	37297	NM_029353	75593	Mm.439947	NM_029353	ENSMUSG00000029815	Malsu1	2410003K15Rik|Matsu1	mitochondrial assembly of ribosomal large subunit 1	protein-coding
mm_26221.1	chr3	138877338	138877345	+	1	NA	intron (NM_019571, intron 2 of 7)	intron (NM_019571, intron 2 of 7)	135133	NM_019571	56224	Mm.31927	NM_019571	ENSMUSG00000028152	Tspan5	2810455A09Rik|4930505M03Rik|NET-4|Tm4sf9	tetraspanin 5	protein-coding
mm_123391.1	chr14	63405252	63405262	-	1	NA	intron (NM_007549, intron 1 of 12)	intron (NM_007549, intron 1 of 12)	11930	NM_007549	12143	Mm.3962	NM_007549	ENSMUSG00000014453	Blk	-	B lymphoid kinase	protein-coding
mm_24750.1	chr3	95320148	95320165	+	1	NA	exon (NM_001320492, exon 2 of 11)	exon (NM_001320492, exon 2 of 11)	1326	NM_001320492	76893	Mm.181009	NM_029789	ENSMUSG00000015714	Cers2	0610013I17Rik|AI225939|Lass2|TRH3	ceramide synthase 2	protein-coding
mm_40245.1	chr5	38039305	38039322	+	1	NA	promoter-TSS (NM_026959)	promoter-TSS (NM_026959)	83	NM_026959	71116	Mm.18959	NM_026959	ENSMUSG00000029125	Stx18	1810035L21Rik|4933425D03Rik|AU041562	syntaxin 18	protein-coding
mm_145768.1	chr18	65023731	65023736	+	1	NA	5' UTR (NM_031881, exon 1 of 30)	5' UTR (NM_031881, exon 1 of 30)	206	NM_031881	83814	Mm.98668	NM_031881	ENSMUSG00000024589	Nedd4l	1300012C07Rik|Nedd4-2|Nedd4b	neural precursor cell expressed, developmentally down-regulated gene 4-like	protein-coding
mm_82973.1	chr9	35844095	35844106	-	1	NA	promoter-TSS (NM_029863)	promoter-TSS (NM_029863)	50	NM_029863	77080	Mm.159846	NM_029863	ENSMUSG00000047980	9230110F15Rik	Pate-A|Pate5|mANLP3	RIKEN cDNA 9230110F15 gene	protein-coding
mm_171427.1	chr4	134659128	134659129	+	1	NA	intron (NM_207237, intron 1 of 11)	RLTR10A|LTR|ERVK	45162	NM_207237	230815	Mm.18905	NM_207237	ENSMUSG00000037306	Man1c1	AI593348	mannosidase, alpha, class 1C, member 1	protein-coding
mm_35863.1	chr4	49481169	49481182	-	1	NA	Intergenic	Intergenic	25383	NM_007519	12012	Mm.2859	NM_007519	ENSMUSG00000039653	Baat	AI118337|AI158864|BAT	bile acid-Coenzyme A: amino acid N-acyltransferase	protein-coding
mm_85926.1	chr9	111977878	111977904	-	1	NA	Intergenic	Intergenic	140820	NR_029823	723815		NR_029823	ENSMUSG00000065441	Mir128-2	Mirn128-2|Mirn128b|mir-128-2|mir-128b	microRNA 128-2	ncRNA
mm_58908.1	chr7	17203494	17203502	+	1	NA	promoter-TSS (NM_054064)	promoter-TSS (NM_054064)	21	NM_054064	114872	Mm.322280	NM_054064	ENSMUSG00000023159	Psg29	AA102956|AA409969|cea17	pregnancy-specific glycoprotein 29	protein-coding
mm_87868.1	chr10	61309803	61309808	+	1	NA	Intergenic	Intergenic	11969	NM_011073	18646	Mm.240313	NM_011073	ENSMUSG00000037202	Prf1	Pfn|Pfp|Prf-1	perforin 1 (pore forming protein)	protein-coding
mm_10026.1	chr1	192092541	192092619	-	1	NA	promoter-TSS (NM_011633)	promoter-TSS (NM_011633)	19	NM_011633	22033	Mm.380491	NM_011633		Traf5	-	TNF receptor-associated factor 5	protein-coding
mm_74354.1	chr8	128166410	128166437	+	1	NA	Intergenic	Intergenic	111802	NR_105822	102465212		NR_105822	ENSMUSG00000099326	Mir21c	Gm28013|mmu-mir-21c	microRNA 21c	ncRNA
mm_53959.1	chr6	5495842	5495852	-	1	NA	intron (NM_013743, intron 1 of 10)	intron (NM_013743, intron 1 of 10)	431	NM_013743	27273	Mm.235547	NM_013743	ENSMUSG00000019577	Pdk4	AV005916	pyruvate dehydrogenase kinase, isoenzyme 4	protein-coding
mm_89271.1	chr10	87860438	87860464	+	1	NA	promoter-TSS (NM_001111276)	promoter-TSS (NM_001111276)	-660	NM_001111274	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_38680.1	chr4	145019510	145019516	-	1	NA	intron (NM_001276502, intron 65 of 68)	intron (NM_001276502, intron 65 of 68)	126376	NM_011303	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding
mm_118032.1	chr13	101690568	101690587	-	1	NA	exon (NM_001024955, exon 2 of 10)	exon (NM_001024955, exon 2 of 10)	2053	NM_001024955	18708	Mm.259333	NM_001024955	ENSMUSG00000041417	Pik3r1	PI3K|p50alpha|p55alpha|p85alpha	phosphatidylinositol 3-kinase, regulatory subunit, polypeptide 1 (p85 alpha)	protein-coding
mm_8517.1	chr1	154816907	154816926	-	1	NA	Intergenic	MIR|SINE|MIR	-90996	NM_009782	12290	Mm.267517	NM_009782	ENSMUSG00000004110	Cacna1e	A430040I15|BII|Cach6|Cacnl1a6|Cav2.3|Cchra1|alpha1E	calcium channel, voltage-dependent, R type, alpha 1E subunit	protein-coding
mm_91606.1	chr10	41450230	41450249	-	1	NA	promoter-TSS (NM_001277230)	promoter-TSS (NM_001277230)	-119	NM_001277229	268294	Mm.258475	NM_153398	ENSMUSG00000019826	Zbtb24	BC055367|Bif1|Bsg1|ZNF450	zinc finger and BTB domain containing 24	protein-coding
mm_15473.1	chr2	157500624	157500660	+	1	NA	Intergenic	Intergenic	-59436	NM_001291129	18111	Mm.34330	NM_010923	ENSMUSG00000067786	Nnat	5730414I02Rik|AW107673|Peg5	neuronatin	protein-coding
mm_35352.1	chr4	32263148	32263162	-	1	NA	Intergenic	Intergenic	-154280	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_50641.1	chr6	51432664	51432674	+	1	NA	promoter-TSS (NM_010903)	promoter-TSS (NM_010903)	-1	NM_010903	18025	Mm.42138	NM_010903	ENSMUSG00000029832	Nfe2l3	Nrf3	nuclear factor, erythroid derived 2, like 3	protein-coding
mm_119219.1	chr14	33216974	33216984	+	1	NA	5' UTR (NM_153800, exon 2 of 11)	5' UTR (NM_153800, exon 2 of 11)	156	NM_153800	239027	Mm.318350	NM_153800	ENSMUSG00000063506	Arhgap22	B230341L19Rik|RHOGAP2|p68RacGAP	Rho GTPase activating protein 22	protein-coding
mm_139627.1	chr17	57367201	57367232	+	1	NA	intron (NM_010130, intron 2 of 21)	intron (NM_010130, intron 2 of 21)	8530	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_133617.1	chr16	91560185	91560192	+	1	NA	intron (NM_008338, intron 4 of 6)	intron (NM_008338, intron 4 of 6)	13094	NM_008338	15980	Mm.249364	NM_008338	ENSMUSG00000022965	Ifngr2	Ifgr2|Ifgt	interferon gamma receptor 2	protein-coding
mm_127955.1	chr15	11399595	11399674	-	1	NA	promoter-TSS (NM_033074)	promoter-TSS (NM_033074)	24	NM_033074	110960	Mm.286061	NM_033074	ENSMUSG00000022241	Tars	D15Wsu59e|ThrRS	threonyl-tRNA synthetase	protein-coding
mm_59260.1	chr7	24884569	24884607	+	1	NA	promoter-TSS (NM_023133)	promoter-TSS (NM_023133)	-126	NM_023133	20085	Mm.300281	NM_023133	ENSMUSG00000040952	Rps19	Dsk3	ribosomal protein S19	protein-coding
mm_28581.1	chr3	93500323	93500334	-	1	NA	Intergenic	Intergenic	-20168	NM_016740	20195	Mm.280038	NM_016740	ENSMUSG00000027907	S100a11	EMAPI|Emap1|S100a14|S100c|cal	S100 calcium binding protein A11	protein-coding
mm_28807.1	chr3	96245307	96245318	-	1	NA	promoter-TSS (NM_178212).2	promoter-TSS (NM_178212).2	-145	NM_178212	319192	Mm.5220	NM_178212	ENSMUSG00000063954	Hist2h2aa2	H2a-614|H2a-615	histone cluster 2, H2aa2	protein-coding
mm_43887.1	chr5	143902243	143902268	+	1	NA	TTS (NM_146165)	TTS (NM_146165)	-7188	NM_001310772	66729	Mm.439817	NM_025732	ENSMUSG00000029607	Ankrd61	4921520G13Rik	ankyrin repeat domain 61	protein-coding
mm_142092.1	chr17	35834365	35834392	-	1	NA	3' UTR (NM_011655, exon 4 of 4)	3' UTR (NM_011655, exon 4 of 4)	3923	NM_011655	22154	Mm.273538	NM_011655	ENSMUSG00000001525	Tubb5	AA408537|AI596182|B130022C14Rik|M(beta)5	tubulin, beta 5 class I	protein-coding
mm_24004.1	chr3	87357875	87357890	+	1	NA	promoter-TSS (NM_009690)	promoter-TSS (NM_009690)	1	NM_009690	11801	Mm.6676	NM_009690	ENSMUSG00000015854	Cd5l	1/6|AAC-11|AI047839|Api6|CT2|Pdp|Sp-alpha|mAIM	CD5 antigen-like	protein-coding
mm_31503.1	chr4	53440517	53440548	+	1	NA	5' UTR (NM_001159633, exon 1 of 13)	5' UTR (NM_001159633, exon 1 of 13)	119	NM_133891	100434	Mm.482207	NM_133891	ENSMUSG00000028412	Slc44a1	2210409B22Rik|4833416H08Rik|AW547365|CHTL1|CTL1|Cdw92	solute carrier family 44, member 1	protein-coding
mm_15421.1	chr2	156863111	156863170	+	1	NA	promoter-TSS (NM_026124)	promoter-TSS (NM_026124)	18	NM_026124	67388	Mm.29264	NM_026124	ENSMUSG00000027637	1110008F13Rik	AI316789	RIKEN cDNA 1110008F13 gene	protein-coding
mm_150603.1	chr19	40748849	40748857	+	1	NA	Intergenic	Intergenic	-82426	NM_172839	240665	Mm.309	NM_172839	ENSMUSG00000025010	Ccnj	D430039C20Rik	cyclin J	protein-coding
mm_34238.1	chr4	141151012	141151050	+	1	NA	intron (NM_172518, intron 1 of 9)	B1_Mur2|SINE|Alu	3109	NM_172518	213499	Mm.28865	NM_172518	ENSMUSG00000028920	Fbxo42	6720460I06Rik|mKIAA1332	F-box protein 42	protein-coding
mm_58592.1	chr7	5015522	5015536	+	1	NA	promoter-TSS (NM_001110329)	promoter-TSS (NM_001110329)	21	NM_025324	66056	Mm.19974	NM_025324	ENSMUSG00000051184	Zfp524	0610012F07Rik|2300009P13Rik|Znf524	zinc finger protein 524	protein-coding
mm_37973.1	chr4	133545619	133545628	-	1	NA	intron (NM_010948, intron 1 of 7)	intron (NM_010948, intron 1 of 7)	404	NM_010948	18221	Mm.69	NM_010948	ENSMUSG00000028851	Nudc	SIG-92|Silg92	nudC nuclear distribution protein	protein-coding
mm_101892.1	chr11	49064203	49064206	-	1	NA	promoter-TSS (NM_001145164)	promoter-TSS (NM_001145164)	8	NM_001145164	100039796	Mm.482363	NM_001145164	ENSMUSG00000078921	Tgtp2	OTTMUSG00000005537|TGTP	T cell specific GTPase 2	protein-coding
mm_37659.1	chr4	129032702	129032730	-	1	NA	Intergenic	Intergenic	-25555	NM_029219	75234	Mm.259672	NM_029219	ENSMUSG00000028793	Rnf19b	4930534K13Rik|4930555L03Rik|Ibrdc3	ring finger protein 19B	protein-coding
mm_23711.1	chr3	68869647	68869659	+	1	NA	promoter-TSS (NM_001167996)	promoter-TSS (NM_001167996)	67	NM_001167996	68725	Mm.45741	NM_001167996	ENSMUSG00000046999	1110032F04Rik	AI115547	RIKEN cDNA 1110032F04 gene	protein-coding
mm_5732.1	chr1	45332176	45332210	-	1	NA	exon (NM_009930, exon 20 of 51)	exon (NM_009930, exon 20 of 51)	20655	NM_009930	12825	Mm.249555	NM_009930	ENSMUSG00000026043	Col3a1	AW550625|Col3a-1|Tsk-2|Tsk2	collagen, type III, alpha 1	protein-coding
mm_162221.1	chrX	143394217	143394217	-	1	NA	promoter-TSS (NM_031258)	promoter-TSS (NM_031258)	45	NM_031258	83453	Mm.157697	NM_031258	ENSMUSG00000031283	Chrdl1	CHL|CHL1|Nrln1|VOPT	chordin-like 1	protein-coding
mm_54820.1	chr6	42351528	42351566	-	1	NA	exon (NM_001289618, exon 4 of 10)	exon (NM_001289618, exon 4 of 10)	1719	NM_001289619	22793	Mm.282303	NM_011777	ENSMUSG00000029860	Zyx	9530098H06Rik|R75157	zyxin	protein-coding
mm_110728.1	chr12	69746336	69746345	-	1	NA	TTS (NM_183294)	TTS (NM_183294)	17604	NR_030450	751538		NR_030450	ENSMUSG00000076065	Mir681	Mirn681|mmu-mir-681	microRNA 681	ncRNA
mm_144533.1	chr18	25234286	25234295	+	1	NA	intron (NM_001033532, intron 5 of 10)	MLT1A|LTR|ERVL-MaLR	65270	NM_001033532	225289	Mm.391081	NM_001033532	ENSMUSG00000033632	AW554918	4921538P22|AI461742|Kiaa1328|mKIAA1328	expressed sequence AW554918	protein-coding
mm_4759.1	chr1	182409163	182409184	+	1	NA	promoter-TSS (NM_173378)	promoter-TSS (NM_173378)	6	NM_173378	209456	Mm.287450	NM_173378	ENSMUSG00000026510	Trp53bp2	53BP2|AI746547|ASPP2|PPP1R13A|Tp53bp2|X98550	transformation related protein 53 binding protein 2	protein-coding
mm_131167.1	chr16	7039600	7039616	+	1	NA	intron (NM_021477, intron 5 of 16)	intron (NM_021477, intron 5 of 16)	-30227	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_47979.1	chr5	135911305	135911322	-	1	NA	exon (NM_018871, exon 2 of 2)	exon (NM_018871, exon 2 of 2)	23328	NM_018871	22628	Mm.233813	NM_018871	ENSMUSG00000051391	Ywhag	14-3-3gamma|D7Bwg1348e	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, gamma polypeptide	protein-coding
mm_140506.1	chr17	5418665	5418742	-	1	NA	promoter-TSS (NM_175349)	promoter-TSS (NM_175349)	64	NM_175349	106557	Mm.432764	NM_175349	ENSMUSG00000101959	Ldhal6b	4933402O15Rik|AI326310|LDHL|Ldhal	lactate dehydrogenase A-like 6B	protein-coding
mm_136414.1	chr16	93912204	93912216	-	1	NA	Intergenic	Intergenic	17357	NM_001165925	56173	Mm.328716	NM_019500	ENSMUSG00000047109	Cldn14	AI851731	claudin 14	protein-coding
mm_29591.1	chr3	119720092	119720093	-	1	NA	3' UTR (NM_019550, exon 14 of 14)	3' UTR (NM_019550, exon 14 of 14)	63296	NM_001310711	56195	Mm.29966	NM_019550	ENSMUSG00000028134	Ptbp2	Ptb2|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding
mm_38413.1	chr4	139130235	139130277	-	1	NA	intron (NM_001163006, intron 1 of 3)	CpG	781	NR_033745	433771	Mm.305990	NM_001163006	ENSMUSG00000050608	Minos1	2310028O11Rik	mitochondrial inner membrane organizing system 1	protein-coding
mm_7885.1	chr1	133071754	133071773	-	1	NA	intron (NM_001099276, intron 5 of 32)	intron (NM_001099276, intron 5 of 32)	25751	NM_001099276	240752	Mm.387308	NM_001099276	ENSMUSG00000026447	Pik3c2b	C330011J12Rik|Gm199|PI3K-C2beta|PI3KC2beta	phosphoinositide-3-kinase, class 2, beta polypeptide	protein-coding
mm_23682.1	chr3	68620589	68620607	+	1	NA	intron (NM_001113419, intron 9 of 10)	B4|SINE|B4	48230	NM_013928	30953	Mm.331064	NM_013928	ENSMUSG00000027777	Schip1	Nf2ip|Schip-1	schwannomin interacting protein 1	protein-coding
mm_47816.1	chr5	134222100	134222119	-	1	NA	exon (NM_001286037, exon 10 of 11)	exon (NM_001286037, exon 10 of 11)	7516	NM_001286037	17969	Mm.425296	NM_010876	ENSMUSG00000015950	Ncf1	NCF-47K|NOXO2|Ncf-1|p47-phox|p47<phox>|p47phox	neutrophil cytosolic factor 1	protein-coding
mm_52598.1	chr6	117171477	117171487	+	1	NA	exon (NM_021704, exon 2 of 3)	exon (NM_021704, exon 2 of 3)	2947	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_30258.1	chr3	146683263	146683266	-	1	NA	Intergenic	Intergenic	-31947	NM_029144	75015	Mm.250432	NM_029144	ENSMUSG00000048652	4930503B20Rik	1700013A07Rik|1700095G21Rik|4930483N21Rik|Gm1652|Samd13	RIKEN cDNA 4930503B20 gene	protein-coding
mm_49870.1	chr6	38561230	38561236	+	1	NA	intron (NM_001331223, intron 2 of 12)	intron (NM_001331223, intron 2 of 12)	5510	NM_001331223	192196	Mm.276133	NM_138680	ENSMUSG00000029823	Luc7l2	4930471C18Rik|AA522013|AU015269|CGI59|Cgi74	LUC7-like 2 (S. cerevisiae)	protein-coding
mm_136493.1	chr16	96127690	96127736	-	1	NA	promoter-TSS (NM_008251)	promoter-TSS (NM_008251)	12	NM_008251	15312	Mm.2756	NM_008251	ENSMUSG00000040681	Hmgn1	HMG-14|Hmg14	high mobility group nucleosomal binding domain 1	protein-coding
mm_22171.1	chr2	173148123	173148152	-	1	NA	Intergenic	Intergenic	-4936	NM_011044	18534	Mm.266867	NM_011044	ENSMUSG00000027513	Pck1	AI265463|PEPCK|Pck-1	phosphoenolpyruvate carboxykinase 1, cytosolic	protein-coding
mm_127358.1	chr15	100665298	100665310	+	1	NA	intron (NM_001270537, intron 1 of 10)	intron (NM_001270537, intron 1 of 10)	4196	NM_001270537	668218	Mm.451225	NM_001270537	ENSMUSG00000098112	Bin2	-	bridging integrator 2	protein-coding
mm_40771.1	chr5	67205810	67205820	+	1	NA	Intergenic	Intergenic	-54750	NM_001285452	67878	Mm.23217	NM_028975	ENSMUSG00000037720	Tmem33	1110006G02Rik|1600019D15Rik|2410089A21Rik|2700052H22Rik|5430406L04Rik|AA388285|AI314185|AI426615|db83	transmembrane protein 33	protein-coding
mm_111586.1	chr12	101913117	101913161	-	1	NA	promoter-TSS (NM_028446)	promoter-TSS (NM_028446)	32	NM_028446	109181	Mm.208618	NM_028446	ENSMUSG00000021188	Trip11	2610511G22Rik|3110031G15Rik|6030460N08Rik|AI450776|GMAP-210|TRIP230	thyroid hormone receptor interactor 11	protein-coding
mm_19804.1	chr2	110305678	110305721	-	1	NA	promoter-TSS (NM_130452)	promoter-TSS (NM_130452)	26	NM_130452	170442	Mm.27335	NM_130452	ENSMUSG00000041660	Bbox1	AI874739	butyrobetaine (gamma), 2-oxoglutarate dioxygenase 1 (gamma-butyrobetaine hydroxylase)	protein-coding
mm_87136.1	chr10	34297563	34297577	+	1	NA	exon (NM_030203, exon 1 of 1)	exon (NM_030203, exon 1 of 1)	149	NM_030203	72480	Mm.21485	NM_030203	ENSMUSG00000039485	Tspyl4	2610102M01Rik|B230210I21Rik|D10Bwg0791e	TSPY-like 4	protein-coding
mm_74937.1	chr8	25797073	25797077	-	1	NA	intron (NM_026032, intron 3 of 3)	RMER19B|LTR|ERVK	-11399	NM_011485	20845	Mm.293314	NM_011485	ENSMUSG00000031574	Star	AV363654|D8Ertd419e|stARD1	steroidogenic acute regulatory protein	protein-coding
mm_162771.1	chr10	67713300	67713320	+	1	NA	Intergenic	Intergenic	-164355	NM_001005419	211488	Mm.297250	NM_001005419	ENSMUSG00000057134	Ado	Gm237	2-aminoethanethiol (cysteamine) dioxygenase	protein-coding
mm_117209.1	chr13	64089146	64089164	-	1	NA	promoter-TSS (NM_008291)	promoter-TSS (NM_008291)	46	NM_008291	15487	Mm.5109	NM_008291	ENSMUSG00000033122	Hsd17b3	-	hydroxysteroid (17-beta) dehydrogenase 3	protein-coding
mm_144508.1	chr18	24653903	24653913	+	1	NA	5' UTR (NM_026779, exon 1 of 15)	5' UTR (NM_026779, exon 1 of 15)	217	NM_026779	68591	Mm.28252	NM_026779	ENSMUSG00000039616	Mocos	1110018O12Rik|HMCS|MCS|MOS	molybdenum cofactor sulfurase	protein-coding
mm_123771.1	chr14	70212426	70212436	-	1	NA	Intergenic	Intergenic	-4760	NM_011366	20410	Mm.5068	NM_011366	ENSMUSG00000022091	Sorbs3	SCAM-1|SH3P3|Sh3d4|vinexin-g	sorbin and SH3 domain containing 3	protein-coding
mm_134012.1	chr16	4878335	4878352	-	1	NA	intron (NM_145359, intron 1 of 2)	intron (NM_145359, intron 1 of 2)	1508	NM_145359	207740	Mm.268895	NM_145359	ENSMUSG00000039568	Ubald1	1500031H01Rik|BC013706|Fam100a	UBA-like domain containing 1	protein-coding
mm_69911.1	chr7	141655390	141655395	-	1	NA	promoter-TSS (NM_001330001)	promoter-TSS (NM_001330001)	-73	NM_001330001	353328	Mm.246621	NM_181729	ENSMUSG00000048191	Muc6	-	mucin 6, gastric	protein-coding
mm_54829.1	chr6	42585861	42585881	-	1	NA	Intergenic	Intergenic	11501	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_62447.1	chr7	101384051	101384075	+	1	NA	intron (NM_001040112, intron 1 of 30)	intron (NM_001040112, intron 1 of 30)	-1463	NM_027180	69710	Mm.277687	NM_027180	ENSMUSG00000032812	Arap1	2410002L19Rik|Centd2|mKIAA0782	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	protein-coding
mm_18862.1	chr2	75704536	75704552	-	1	NA	non-coding (NR_132727, exon 1 of 2)	non-coding (NR_132727, exon 1 of 2)	119	NR_132727	18024	Mm.1025	NM_010902	ENSMUSG00000015839	Nfe2l2	Nrf2	nuclear factor, erythroid derived 2, like 2	protein-coding
mm_23001.1	chr3	34052272	34052275	+	1	NA	intron (NM_001113189, intron 9 of 16)	intron (NM_001113189, intron 9 of 16)	29081	NM_001286972	67713	Mm.274266	NM_026332	ENSMUSG00000027679	Dnajc19	1810055D05Rik|AA959924|Tim14	DnaJ heat shock protein family (Hsp40) member C19	protein-coding
mm_29303.1	chr3	107931861	107931885	-	1	NA	promoter-TSS (NM_026672)	promoter-TSS (NM_026672)	-128	NM_026672	68312	Mm.458189	NM_026672	ENSMUSG00000004035	Gstm7	0610005A07Rik|AI894236|Cd203c	glutathione S-transferase, mu 7	protein-coding
mm_122646.1	chr14	51877631	51877639	-	1	NA	Intergenic	Intergenic	-7207	NM_001029990	52535	Mm.5750	NM_001029990	ENSMUSG00000004561	Mettl17	2310032K15Rik|D14Ertd209e|Mett11d1	methyltransferase like 17	protein-coding
mm_119911.1	chr14	54952661	54952682	+	1	NA	exon (NM_010856, exon 24 of 39)	exon (NM_010856, exon 24 of 39)	-3529	NR_029724	387204		NR_029724	ENSMUSG00000065432	Mir208a	Mirn208|Mirn208a|mir-208|mir-208a|mmu-mir-208	microRNA 208a	ncRNA
mm_109552.1	chr12	111713256	111713303	+	1	NA	promoter-TSS (NM_026511)	promoter-TSS (NM_026511)	10	NM_026511	68020	Mm.425762	NM_026511	ENSMUSG00000037787	Apopt1	1700081D05Rik|2810002N01Rik|Apop-1|Apop1	apoptogenic, mitochondrial 1	protein-coding
mm_127382.1	chr15	100870979	100870989	+	1	NA	intron (NM_001077499, intron 1 of 26)	CpG	339	NM_001077499	20273	Mm.385012	NM_011323	ENSMUSG00000023033	Scn8a	AI853486|C630029C19Rik|NaCh6|Nav1.6|dmu|med|mnd-2|mnd2|nmf2|nmf335|nmf58|nur14|seal	sodium channel, voltage-gated, type VIII, alpha	protein-coding
mm_164007.1	chr14	67716136	67716228	+	1	NA	promoter-TSS (NM_001111028)	promoter-TSS (NM_001111028)	84	NM_001285933	105440	Mm.6720	NM_134073	ENSMUSG00000034327	Kctd9	-	potassium channel tetramerisation domain containing 9	protein-coding
mm_111172.1	chr12	83632506	83632531	-	1	NA	intron (NM_027349, intron 1 of 18)	CpG	284	NM_027349	67039	Mm.46005	NM_027349	ENSMUSG00000010608	Rbm25	2600011C06Rik|2610015J01Rik|A130095G20Rik|AI159652|AL023075|AU043498|RNPC7	RNA binding motif protein 25	protein-coding
mm_155172.1	chrX	53434990	53435015	+	1	NA	promoter-TSS (NR_034074)	promoter-TSS (NR_034074)	84	NR_034074	69501	Mm.63828	NM_175147	ENSMUSG00000060967	Etd	1700030K02Rik	embryonic testis differentiation	ncRNA
mm_82720.1	chr9	24765445	24765449	-	1	NA	intron (NM_194263, intron 4 of 7)	intron (NM_194263, intron 4 of 7)	8856	NM_020496	57246	Mm.31452	NM_020496	ENSMUSG00000031965	Tbx20	9430010M06Rik|AL022859|Tbx12	T-box 20	protein-coding
mm_131771.1	chr16	22894314	22894408	+	1	NA	promoter-TSS (NR_110508)	promoter-TSS (NR_110508)	25	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_71330.1	chr8	45050921	45050933	+	1	NA	exon (NM_001081286, exon 26 of 26)	exon (NM_001081286, exon 26 of 26)	14491	NR_033588	434310	Mm.334512	NR_033588	ENSMUSG00000066158	AY512931	-	cDNA sequence AY512931	ncRNA
mm_133283.1	chr16	77422916	77422948	+	1	NA	intron (NR_015543, intron 2 of 4)	intron (NR_015543, intron 2 of 4)	93604	NR_015543	77994	Mm.394688	NR_015543	ENSMUSG00000090386	Mir99ahg	2810055G20Rik|D730043B02Rik	Mir99a and Mirlet7c-1 host gene (non-protein coding)	ncRNA
mm_78114.1	chr9	20642914	20642942	+	1	NA	promoter-TSS (NM_013911)	promoter-TSS (NM_013911)	-122	NM_013911	30843	Mm.24608	NM_013911	ENSMUSG00000066892	Fbxl12	3110048D16Rik|Fbl12	F-box and leucine-rich repeat protein 12	protein-coding
mm_104542.1	chr11	96747406	96747416	-	1	NA	intron (NM_001177898, intron 10 of 10)	intron (NM_001177898, intron 10 of 10)	30144	NM_028965	74479	Mm.270781	NM_028965	ENSMUSG00000020876	Snx11	4933439F10Rik|A930041K09Rik|AI117694	sorting nexin 11	protein-coding
mm_14231.1	chr2	127587269	127587279	+	1	NA	promoter-TSS (NM_029963)	promoter-TSS (NM_029963)	-152	NM_029963	77721	Mm.274601	NM_029963	ENSMUSG00000027374	Mrps5	1620401I16Rik|AI850294	mitochondrial ribosomal protein S5	protein-coding
mm_34700.1	chr4	152076257	152076265	+	1	NA	Intergenic	Intergenic	-10602	NR_104381	269608	Mm.332102	NM_001004156	ENSMUSG00000039713	Plekhg5	BC023181|Syx	pleckstrin homology domain containing, family G (with RhoGef domain) member 5	protein-coding
mm_45243.1	chr5	54045636	54045648	-	1	NA	intron (NM_001081103, intron 1 of 11)	intron (NM_001081103, intron 1 of 11)	47119	NM_001081103	116873	Mm.265985	NM_054083	ENSMUSG00000039156	Stim2	-	stromal interaction molecule 2	protein-coding
mm_100909.1	chr11	6229084	6229102	-	1	NA	exon (NM_207242, exon 2 of 19)	exon (NM_207242, exon 2 of 19)	1152	NM_207242	237636	Mm.212492	NM_207242	ENSMUSG00000020447	Npc1l1	9130221N23Rik|Gm243	NPC1-like 1	protein-coding
mm_109221.1	chr12	108792998	108793014	+	1	NA	promoter-TSS (NM_009537)	promoter-TSS (NM_009537)	-305	NM_009537	22632	Mm.3868	NM_009537	ENSMUSG00000021264	Yy1	AW488674|NF-E1	YY1 transcription factor	protein-coding
mm_133818.1	chr16	95719851	95719867	+	1	NA	3' UTR (NM_011809, exon 10 of 10)	3' UTR (NM_011809, exon 10 of 10)	17452	NM_011809	23872	Mm.290207	NM_011809	ENSMUSG00000022895	Ets2	AU022856|Ets-2	E26 avian leukemia oncogene 2, 3' domain	protein-coding
mm_59410.1	chr7	27120807	27120840	+	1	NA	intron (NM_007817, intron 1 of 9)	intron (NM_007817, intron 1 of 9)	868	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_92179.1	chr10	67912399	67912460	-	1	NA	5' UTR (NM_178679, exon 1 of 5)	5' UTR (NM_178679, exon 1 of 5)	233	NM_178679	216049	Mm.268346	NM_178679	ENSMUSG00000037855	Zfp365	AI839779|AV340892|DBZ|Su48|Znf365|talanin	zinc finger protein 365	protein-coding
mm_25399.1	chr3	107241861	107241880	+	1	NA	Intergenic	Intergenic	-2163	NM_001044382	246691	Mm.490697	NM_001044382	ENSMUSG00000070368	Prok1	EG-VEGF	prokineticin 1	protein-coding
mm_31343.1	chr4	46489376	46489382	+	1	NA	promoter-TSS (NM_053179)	promoter-TSS (NM_053179)	50	NM_053179	94181	Mm.249349	NM_053179	ENSMUSG00000028334	Nans	4632418E04Rik|BB056474|Sas	N-acetylneuraminic acid synthase (sialic acid synthase)	protein-coding
mm_34553.1	chr4	149587283	149587296	+	1	NA	intron (NM_001290989, intron 1 of 17)	CpG	821	NM_023051	65945	Mm.38993	NM_023051	ENSMUSG00000039953	Clstn1	1810034E21Rik|Cst-1|Cstn1	calsyntenin 1	protein-coding
mm_118781.1	chr14	24082106	24082121	+	1	NA	Intergenic	Intergenic	-6764	NR_106069	102465697		NR_106069	ENSMUSG00000105723	Mir7210	mir-7210|mmu-mir-7210	microRNA 7210	ncRNA
mm_19420.1	chr2	91931452	91931534	-	1	NA	intron (NM_001291483, intron 1 of 3)	intron (NM_001291483, intron 1 of 3)	209	NM_001291481	17242	Mm.906	NM_010784	ENSMUSG00000027239	Mdk	MK|Mek	midkine	protein-coding
mm_119725.1	chr14	53960985	53960996	+	1	NA	Intergenic	Intergenic	292939	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_45204.1	chr5	52669678	52669728	-	1	NA	promoter-TSS (NM_172490)	promoter-TSS (NM_172490)	-2	NM_172490	211006	Mm.244719	NM_172490	ENSMUSG00000029173	Sepsecs	AA986712|D5Ertd135e|SLA|SecS	Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase	protein-coding
mm_80805.1	chr9	96288375	96288378	+	1	NA	intron (NM_001184711, intron 3 of 10)	B1_Mus1|SINE|Alu	29128	NM_001184710	211586	Mm.17977	NM_178667	ENSMUSG00000032411	Tfdp2	1110029I05Rik|A330080J22Rik|DP-3|DP3	transcription factor Dp 2	protein-coding
mm_138653.1	chr17	35867779	35867789	+	1	NA	exon (NM_001146711, exon 2 of 4)	exon (NM_001146711, exon 2 of 4)	1169	NM_175242	76448	Mm.359982	NM_175242	ENSMUSG00000034595	Ppp1r18	2310014H01Rik|AA407849|AI450394	protein phosphatase 1, regulatory subunit 18	protein-coding
mm_27806.1	chr3	75956788	75956869	-	1	NA	5' UTR (NM_175193, exon 1 of 15)	5' UTR (NM_175193, exon 1 of 15)	121	NM_175193	73124	Mm.249232	NM_175193	ENSMUSG00000034109	Golim4	3110027H23Rik|GIMPC|GPP130|Golph4|P138	golgi integral membrane protein 4	protein-coding
mm_129949.1	chr15	84988023	84988031	-	1	NA	promoter-TSS (NM_001033273)	promoter-TSS (NM_001033273)	-56	NM_001033273	223739	Mm.323925	NM_001033273	ENSMUSG00000036046	5031439G07Rik	AW554572|mKIAA0930	RIKEN cDNA 5031439G07 gene	protein-coding
mm_46177.1	chr5	97094112	97094113	-	1	NA	intron (NM_198422, intron 6 of 6)	B1_Mur2|SINE|Alu	17484	NM_198422	231474	Mm.332505	NM_198422	ENSMUSG00000055725	Paqr3	6330415A20Rik|AY424292|RKTG	progestin and adipoQ receptor family member III	protein-coding
mm_89455.1	chr10	93160979	93160989	+	1	NA	5' UTR (NM_146239, exon 1 of 17)	5' UTR (NM_146239, exon 1 of 17)	108	NM_146239	237459	Mm.217404	NM_146239	ENSMUSG00000020015	Cdk17	6430598J10Rik|Pctk2	cyclin-dependent kinase 17	protein-coding
mm_5412.1	chr1	33814517	33814573	-	1	NA	promoter-TSS (NM_001290700)	promoter-TSS (NM_001290700)	50	NM_133817	98403	Mm.289103	NM_133817	ENSMUSG00000042197	Zfp451	4930515K21Rik|4933435G09Rik|AI596398|COASTER|Kiaa0576-hp|Znf451|mKIAA1702	zinc finger protein 451	protein-coding
mm_40503.1	chr5	57728232	57728249	+	1	NA	3' UTR (NM_018764, exon 2 of 2)	3' UTR (NM_018764, exon 2 of 2)	10159	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_66155.1	chr7	31150982	31151070	-	1	NA	promoter-TSS (NM_027898)	promoter-TSS (NM_027898)	24	NM_027898	52857	Mm.27366	NM_027898	ENSMUSG00000001248	Gramd1a	1300003M23Rik|AI415002|AW547240|D7Bwg0611e	GRAM domain containing 1A	protein-coding
mm_42327.1	chr5	114901533	114901550	+	1	NA	intron (NM_011854, intron 3 of 5)	ID4_|SINE|ID	4607	NM_011854	23962	Mm.228363	NM_011854	ENSMUSG00000029561	Oasl2	M1204|Mmu-OASL|Oasl	2'-5' oligoadenylate synthetase-like 2	protein-coding
mm_73580.1	chr8	109830481	109830484	+	1	NA	intron (NM_009677, intron 7 of 23)	intron (NM_009677, intron 7 of 23)	-8830	NR_028532	100217432		NR_028532		Snord71	MBII-239	small nucleolar RNA, C/D box 71	snoRNA
mm_61294.1	chr7	67655415	67655442	+	1	NA	intron (NM_001168476, intron 1 of 9)	intron (NM_001168476, intron 1 of 9)	8018	NM_025905	67009	Mm.249356	NM_025905	ENSMUSG00000030555	Ttc23	1600012K10Rik	tetratricopeptide repeat domain 23	protein-coding
mm_13629.1	chr2	113641318	113641322	+	1	NA	intron (NM_001285458, intron 13 of 16)	intron (NM_001285458, intron 13 of 16)	-43770	NM_001287818	14260	Mm.4938	NM_010230	ENSMUSG00000044042	Fmn1	Fmn|formin-1|ld	formin 1	protein-coding
mm_9758.1	chr1	180848650	180848658	-	1	NA	Intergenic	Intergenic	-2497	NM_145943	208768	Mm.272625	NM_145943	ENSMUSG00000038806	Sde2	-	SDE2 telomere maintenance homolog (S. pombe)	protein-coding
mm_124558.1	chr14	122983186	122983209	-	1	NA	promoter-TSS (NM_028651)	promoter-TSS (NM_028651)	64	NM_028651	70551	Mm.271988	NM_028651	ENSMUSG00000041594	Tmtc4	4930403J22Rik|5730419O14Rik	transmembrane and tetratricopeptide repeat containing 4	protein-coding
mm_73628.1	chr8	110715119	110715129	+	1	NA	intron (NM_146216, intron 17 of 18)	intron (NM_146216, intron 17 of 18)	-6352	NM_198625	244654	Mm.490385	NM_198625	ENSMUSG00000033763	Mtss1l	ABBA	metastasis suppressor 1-like	protein-coding
mm_10560.1	chr2	18027735	18027748	+	1	NA	non-coding (NR_028376, exon 2 of 2)	non-coding (NR_028376, exon 2 of 2)	492	NR_028378	100034739	Mm.401643	NR_028378		Gm17762	-	predicted gene, 17762	ncRNA
mm_108314.1	chr12	79570228	79570232	+	1	NA	intron (NM_009014, intron 7 of 10)	L1_Mur3|LINE|L1	272879	NM_001252562	19363	Mm.341756	NM_009014	ENSMUSG00000059060	Rad51b	AI553500|R51H2|Rad51l1|mREC2	RAD51 paralog B	protein-coding
mm_141934.1	chr17	35046502	35046514	-	1	NA	non-coding (NR_130641, exon 1 of 24)	non-coding (NR_130641, exon 1 of 24)	114	NM_013600	17687	Mm.24192	NM_013600	ENSMUSG00000007035	Msh5	Mut5	mutS homolog 5	protein-coding
mm_154668.1	chrX	7882074	7882106	+	1	NA	exon (NM_138606, exon 5 of 6)	exon (NM_138606, exon 5 of 6)	-2154	NM_001083937	22232	Mm.214976	NM_078484	ENSMUSG00000031156	Slc35a2	AI327289|Had-1|Had1|Sfc8|UGT|Ugalt	solute carrier family 35 (UDP-galactose transporter), member A2	protein-coding
mm_36467.1	chr4	82687822	82687822	-	1	NA	Intergenic	Intergenic	171839	NM_026647	68268	Mm.32047	NM_026647	ENSMUSG00000028403	Zdhhc21	9130404H11Rik|AL024349|D130004H04Rik|dep	zinc finger, DHHC domain containing 21	protein-coding
mm_148362.1	chr18	85698108	85698138	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-696829	NM_144946	246317	Mm.329578	NM_144946	ENSMUSG00000050321	Neto1	AI851453|Btcl1|C130005O10Rik	neuropilin (NRP) and tolloid (TLL)-like 1	protein-coding
mm_79115.1	chr9	46273149	46273201	+	1	NA	5' UTR (NM_011752, exon 1 of 14)	5' UTR (NM_011752, exon 1 of 14)	111	NM_011752	22687	Mm.17519	NM_011752	ENSMUSG00000032078	Zpr1	AI303781|Zfp259|Znf259	ZPR1 zinc finger	protein-coding
mm_79815.1	chr9	64281576	64281630	+	1	NA	promoter-TSS (NM_025372)	promoter-TSS (NM_025372)	18	NM_001324557	66131	Mm.196219	NM_025372	ENSMUSG00000032397	Tipin	1110005A05Rik|1110018P21Rik	timeless interacting protein	protein-coding
mm_131356.1	chr16	13729795	13729803	+	1	NA	promoter-TSS (NR_040574)	promoter-TSS (NR_040574)	-37	NR_040574	76684	Mm.491043	NR_040574		Pla2g10os	1810007I06Rik	phospholipase A2, group X, opposite strand	ncRNA
mm_38677.1	chr4	144981266	144981279	-	1	NA	intron (NM_001276502, intron 67 of 68)	intron (NM_001276502, intron 67 of 68)	88135	NM_011303	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding
mm_122329.1	chr14	37102239	37102250	-	1	NA	3' UTR (NM_001206684, exon 3 of 3)	3' UTR (NM_001206684, exon 3 of 3)	-3933	NM_130878	170677	Mm.156506	NM_130878	ENSMUSG00000021803	Cdhr1	Pcdh21|Prcad|mKIAA1775	cadherin-related family member 1	protein-coding
mm_137720.1	chr17	29114143	29114202	+	1	NA	Intergenic	Intergenic	20403	NM_007669	12575	Mm.195663	NM_007669	ENSMUSG00000023067	Cdkn1a	CAP20|CDKI|CIP1|Cdkn1|P21|SDI1|Waf1|mda6|p21Cip1|p21WAF	cyclin-dependent kinase inhibitor 1A (P21)	protein-coding
mm_75242.1	chr8	39639200	39639224	-	1	NA	intron (NM_001113326, intron 1 of 9)	intron (NM_001113326, intron 1 of 9)	3466	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_83709.1	chr9	50728257	50728266	-	1	NA	promoter-TSS (NM_178118)	promoter-TSS (NM_178118)	-277	NM_178118	330938	Mm.82598	NM_178118	ENSMUSG00000032064	Dixdc1	4930563F16Rik|BC048182|Ccd1|Ccd1Aalpha1L|Ccd1Abeta1L|Ccd1BalphaL|Ccd1BbetaL|Ccd1CL|mKIAA1735	DIX domain containing 1	protein-coding
mm_162800.1	chr10	77008399	77008410	+	1	NA	Intergenic	Intergenic	-3591	NR_045882	100038479	Mm.387034	NR_045882	ENSMUSG00000074919	Gm10787	ENSMUSG00000074919	predicted gene 10787	ncRNA
mm_32007.1	chr4	94642418	94642421	+	1	NA	intron (NM_175305, intron 2 of 4)	intron (NM_175305, intron 2 of 4)	7725	NM_175305	100061	Mm.26760	NM_175305	ENSMUSG00000049799	Lrrc19	9130022A01Rik|AI314124|AL022954|AW261791	leucine rich repeat containing 19	protein-coding
mm_62956.1	chr7	119640298	119640305	+	1	NA	intron (NM_054094, intron 5 of 13)	intron (NM_054094, intron 5 of 13)	22473	NM_054094	117147	Mm.427560	NM_054094	ENSMUSG00000033533	Acsm1	Acas3|Bucs1|Macs	acyl-CoA synthetase medium-chain family member 1	protein-coding
mm_9189.1	chr1	171136064	171136075	-	1	NA	exon (NM_025321, exon 5 of 6)	exon (NM_025321, exon 5 of 6)	14408	NM_001081275	75472	Mm.32760	NM_029301	ENSMUSG00000026649	Cfap126	1700009P17Rik|AV282292|Flattop|Fltp	cilia and flagella associated protein 126	protein-coding
mm_4805.1	chr1	185283058	185283070	+	1	NA	intron (NM_001163754, intron 33 of 34)	L2a|LINE|L2	-30255	NR_029580	387189		NR_029580	ENSMUSG00000065581	Mir194-1	Mirn194|Mirn194-1|miR-194|mir-194-1	microRNA 194-1	ncRNA
mm_27379.1	chr3	50443579	50443592	-	1	NA	promoter-TSS (NM_011990)	promoter-TSS (NM_011990)	28	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_145821.1	chr18	65432070	65432082	+	1	NA	intron (NM_172833, intron 1 of 15)	Charlie1b|DNA|hAT-Charlie	1079	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_24081.1	chr3	87952533	87952555	+	1	NA	exon (NM_007759, exon 3 of 4)	exon (NM_007759, exon 3 of 4)	3851	NM_007759	12904	Mm.4757	NM_007759	ENSMUSG00000004885	Crabp2	AI893628|Crabp-2|CrabpII	cellular retinoic acid binding protein II	protein-coding
mm_10587.1	chr2	18192894	18192897	+	1	NA	intron (NR_045539, intron 16 of 24)	intron (NR_045539, intron 16 of 24)	128310	NM_001252561	17354	Mm.209175	NM_010804	ENSMUSG00000026743	Mllt10	Af10|B130021D15Rik|D630001B22Rik|mKIAA4140	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 10	protein-coding
mm_146297.1	chr18	80186223	80186231	+	1	NA	promoter-TSS (NR_131039)	promoter-TSS (NR_131039)	-12	NR_131039	105246506	Mm.392326	NR_131039		LOC105246506	-	uncharacterized LOC105246506	ncRNA
mm_14858.1	chr2	148750353	148750376	+	1	NA	promoter-TSS (NM_177655)	promoter-TSS (NM_177655)	3	NM_177655	228756	Mm.189390	NM_177655	ENSMUSG00000055177	Cstl1	RCET1|RCET2|RCET3	cystatin-like 1	protein-coding
mm_35710.1	chr4	44168482	44168501	-	1	NA	promoter-TSS (NM_175201)	promoter-TSS (NM_175201)	-208	NM_001038993	73469	Mm.262859	NM_175201	ENSMUSG00000035696	Rnf38	1700065B19Rik|2610202O07Rik|AA673263|Oip1	ring finger protein 38	protein-coding
mm_13320.1	chr2	102691329	102691329	+	1	NA	intron (NM_001077514, intron 1 of 10)	MTD|LTR|ERVL-MaLR	-15109	NM_011393	20511	Mm.267547	NM_011393	ENSMUSG00000005089	Slc1a2	1700091C19Rik|2900019G14Rik|AI159670|Eaat2|GLT-1|GLT1|MGLT1	solute carrier family 1 (glial high affinity glutamate transporter), member 2	protein-coding
mm_42704.1	chr5	120116481	120116525	+	1	NA	promoter-TSS (NM_028762)	promoter-TSS (NM_028762)	-10	NM_028762	74111	Mm.41022	NM_028762	ENSMUSG00000029594	Rbm19	1200009A02Rik|AV302714|NPO	RNA binding motif protein 19	protein-coding
mm_43214.1	chr5	129584174	129584232	+	1	NA	promoter-TSS (NM_011846)	promoter-TSS (NM_011846)	34	NM_011846	23948	Mm.42047	NM_011846	ENSMUSG00000029436	Mmp17	MT4-MMP|MT4MMP|MTMMP4	matrix metallopeptidase 17	protein-coding
mm_68269.1	chr7	105595621	105595629	-	1	NA	exon (NM_017371, exon 6 of 10)	exon (NM_017371, exon 6 of 10)	4491	NM_017371	15458	Mm.3485	NM_017371	ENSMUSG00000030895	Hpx	Hpxn|hx	hemopexin	protein-coding
mm_128874.1	chr15	73038639	73038658	-	1	NA	intron (NM_180662, intron 4 of 21)	intron (NM_180662, intron 4 of 21)	17164	NM_029640	76510	Mm.158902	NM_029640	ENSMUSG00000047921	Trappc9	1810044A24Rik|2900005P22Rik|4632408O18Rik|Ibp|Nibp|TRS130|mKIAA1882	trafficking protein particle complex 9	protein-coding
mm_68433.1	chr7	109865638	109865652	-	1	NA	promoter-TSS (NM_020052)	promoter-TSS (NM_020052)	34	NM_020052	56788	Mm.40447	NM_020052	ENSMUSG00000007279	Scube2	4932442O19Rik|Cegf1|Cegp1	signal peptide, CUB domain, EGF-like 2	protein-coding
mm_60749.1	chr7	45481753	45481766	+	1	NA	intron (NM_027903, intron 4 of 6)	intron (NM_027903, intron 4 of 6)	-4503	NM_001290996	56734	Mm.439742	NM_008807	ENSMUSG00000023467	Tulp2	Pdet	tubby-like protein 2	protein-coding
mm_116583.1	chr13	47106145	47106171	-	1	NA	promoter-TSS (NM_025900)	promoter-TSS (NM_025900)	63	NM_025900	110052	Mm.131150	NM_025900	ENSMUSG00000021377	Dek	1810019E15Rik|D13H6S231E	DEK oncogene (DNA binding)	protein-coding
mm_21916.1	chr2	166713759	166713827	-	1	NA	promoter-TSS (NM_177782)	promoter-TSS (NM_177782)	39	NM_177782	277360	Mm.34420	NM_177782	ENSMUSG00000039621	Prex1	G630042G04|P-REX1|Setd6	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	protein-coding
mm_57293.1	chr6	124433780	124433801	-	1	NA	intron (NM_001346656, intron 16 of 17)	intron (NM_001346656, intron 16 of 17)	-18723	NM_001277805	19305	Mm.22418	NM_008995	ENSMUSG00000005069	Pex5	AW212715|ESTM1|PTS1R|Pxr1|X83306	peroxisomal biogenesis factor 5	protein-coding
mm_130643.1	chr15	100591685	100591690	-	1	NA	intron (NM_001304965, intron 3 of 10)	B1_Mus1|SINE|Alu	-5322	NM_010127	19009	Mm.28825	NM_010127	ENSMUSG00000009739	Pou6f1	2310038G18Rik|C79593|Emb|cns-1	POU domain, class 6, transcription factor 1	protein-coding
mm_153815.1	chr19	46148250	46148255	-	1	NA	promoter-TSS (NM_008852)	promoter-TSS (NM_008852)	73	NM_008852	18742	Mm.6255	NM_008852	ENSMUSG00000025229	Pitx3	Ptx3|ak	paired-like homeodomain transcription factor 3	protein-coding
mm_25372.1	chr3	107183140	107183144	+	1	NA	promoter-TSS (NM_001081140)	promoter-TSS (NM_001081140)	-1	NM_001081140	242151	Mm.245155	NM_001081140	ENSMUSG00000042861	Kcna10	Gm1962|Kcna8|Kv1.8	potassium voltage-gated channel, shaker-related subfamily, member 10	protein-coding
mm_69798.1	chr7	141171161	141171181	-	1	NA	intron (NM_001172100, intron 1 of 9)	B1_Mur2|SINE|Alu	1680	NM_001172100	107702	Mm.197493	NM_145135	ENSMUSG00000038650	Rnh1	AW546468|C80305|RNH	ribonuclease/angiogenin inhibitor 1	protein-coding
mm_151188.1	chr19	53421620	53421647	+	1	NA	Intergenic	Intergenic	-31060	NM_172429	76479	Mm.313687	NM_172429	ENSMUSG00000025024	Smndc1	2410004J23Rik|4933440I19Rik	survival motor neuron domain containing 1	protein-coding
mm_34701.1	chr4	152086831	152086893	+	1	NA	promoter-TSS (NR_104381)	promoter-TSS (NR_104381)	-1	NR_104381	269608	Mm.332102	NM_001004156	ENSMUSG00000039713	Plekhg5	BC023181|Syx	pleckstrin homology domain containing, family G (with RhoGef domain) member 5	protein-coding
mm_41783.1	chr5	103722766	103722782	+	1	NA	Intergenic	B1_Mur1|SINE|Alu	-31388	NM_133919	17355	Mm.6949	NM_133919	ENSMUSG00000029313	Aff1	9630032B01Rik|AW319193|Af4|Mllt2h|Rob	AF4/FMR2 family, member 1	protein-coding
mm_120818.1	chr14	75132047	75132054	+	1	NA	intron (NM_001247984, intron 1 of 15)	intron (NM_001247984, intron 1 of 15)	927	NM_001247984	18826	Mm.153911	NM_008879	ENSMUSG00000021998	Lcp1	AW536232|D14Ertd310e|LCP-1|Pls2|pp65	lymphocyte cytosolic protein 1	protein-coding
mm_97892.1	chr11	83302642	83302803	+	1	NA	promoter-TSS (NM_001035854)	promoter-TSS (NM_001035854)	25	NM_001035854	71770	Mm.39053	NM_027915	ENSMUSG00000035152	Ap2b1	1300012O03Rik|AI788979	adaptor-related protein complex 2, beta 1 subunit	protein-coding
mm_74522.1	chr8	9394045	9394048	-	1	NA	intron (NM_001347127, intron 1 of 3)	intron (NM_001347127, intron 1 of 3)	249377	NR_073360	74688	Mm.159298	NR_073360	ENSMUSG00000109215	4930453L07Rik	-	RIKEN cDNA 4930453L07 gene	ncRNA
mm_3135.1	chr1	135131274	135131306	+	1	NA	intron (NM_007955, intron 1 of 37)	intron (NM_007955, intron 1 of 37)	1285	NM_007955	13924	Mm.4450	NM_007955		Ptprv	Esp|OST|OST-PTP|mOST-PTP	protein tyrosine phosphatase, receptor type, V	protein-coding
mm_172751.1	chr8	84854599	84854616	-	1	NA	Intergenic	Intergenic	-2379	NM_025648	66590	Mm.292517	NM_025648	ENSMUSG00000003808	Farsa	0610012A19Rik|Farsla	phenylalanyl-tRNA synthetase, alpha subunit	protein-coding
mm_138506.1	chr17	35235858	35235890	+	1	NA	promoter-TSS (NM_010909)	promoter-TSS (NM_010909)	-59	NM_010909	18038	Mm.300795	NM_010909	ENSMUSG00000042419	Nfkbil1	Def-7|IKBL	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor like 1	protein-coding
mm_149851.1	chr19	25061009	25061053	+	1	NA	intron (NM_028785, intron 2 of 47)	intron (NM_028785, intron 2 of 47)	61502	NM_028785	76088	Mm.102485	NM_028785	ENSMUSG00000052085	Dock8	1200017A24Rik|5830472H07Rik|A130095G14Rik|AI461977	dedicator of cytokinesis 8	protein-coding
mm_3169.1	chr1	135686907	135686929	+	1	NA	Intergenic	Intergenic	-42279	NM_007791	13007	Mm.196484	NM_007791	ENSMUSG00000026421	Csrp1	AA408841|AA959891|AW545626|CRP1|Csrp	cysteine and glycine-rich protein 1	protein-coding
mm_171961.1	chr5	83389729	83389731	-	1	NA	Intergenic	L1Md_T|LINE|L1	-34535	NM_153801	243078	Mm.126783	NM_153801	ENSMUSG00000049537	Tecrl	D330017N19Rik|Srd5a2l2	trans-2,3-enoyl-CoA reductase-like	protein-coding
mm_83969.1	chr9	57158272	57158285	-	1	NA	promoter-TSS (NM_025417)	promoter-TSS (NM_025417)	21	NM_025417	66199	Mm.41687	NM_025417	ENSMUSG00000032299	Commd4	1110039H05Rik	COMM domain containing 4	protein-coding
mm_3171.1	chr1	135687107	135687117	+	1	NA	Intergenic	Intergenic	-42085	NM_007791	13007	Mm.196484	NM_007791	ENSMUSG00000026421	Csrp1	AA408841|AA959891|AW545626|CRP1|Csrp	cysteine and glycine-rich protein 1	protein-coding
mm_141403.1	chr17	29342856	29342860	-	1	NA	exon (NM_019880, exon 2 of 12)	exon (NM_019880, exon 2 of 12)	5046	NM_019880	56462	Mm.285322	NM_019880	ENSMUSG00000024012	Mtch1	2310034O17Rik|AI255158|AU018396|C77849|PSAP	mitochondrial carrier 1	protein-coding
mm_32448.1	chr4	107347419	107347443	+	1	NA	intron (NM_145550, intron 8 of 9)	intron (NM_145550, intron 8 of 9)	-20353	NM_028355	72787	Mm.28478	NM_028355	ENSMUSG00000028614	Ndc1	2810475A17Rik|AI450313|Tmem48|sks	NDC1 transmembrane nucleoporin	protein-coding
mm_73787.1	chr8	117157973	117158035	+	1	NA	promoter-TSS (NM_001081151)	promoter-TSS (NM_001081151)	-131	NM_001081151	209239	Mm.132992	NM_001081151	ENSMUSG00000052557	Gan	A330045G18|gigaxonin	giant axonal neuropathy	protein-coding
mm_72854.1	chr8	88331057	88331060	+	1	NA	Intergenic	PB1D7|SINE|Alu	31133	NM_012047	26992	Mm.5400	NM_012047	ENSMUSG00000031660	Brd7	BP75|CELTIX1|Ptpn13ip	bromodomain containing 7	protein-coding
mm_151022.1	chr19	46863886	46863894	+	1	NA	intron (NM_033569, intron 4 of 7)	intron (NM_033569, intron 4 of 7)	98461	NM_029810	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_78275.1	chr9	22099272	22099287	+	1	NA	promoter-TSS (NM_009922)	promoter-TSS (NM_009922)	26	NM_009922	12797	Mm.4356	NM_009922	ENSMUSG00000001349	Cnn1	CN|CnnI	calponin 1	protein-coding
mm_98462.1	chr11	94948329	94948354	+	1	NA	exon (NM_007742, exon 41 of 51)	exon (NM_007742, exon 41 of 51)	12117	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_99673.1	chr11	105974663	105974681	+	1	NA	promoter-TSS (NM_009598)	promoter-TSS (NM_009598)	-536	NM_009598	11421	Mm.754	NM_009598	ENSMUSG00000020681	Ace	AW208573|CD143	angiotensin I converting enzyme (peptidyl-dipeptidase A) 1	protein-coding
mm_98616.1	chr11	95843635	95843644	+	1	NA	intron (NM_001284397, intron 1 of 3)	intron (NM_001284397, intron 1 of 3)	394	NM_001284397	14710	Mm.46299	NM_023121	ENSMUSG00000038811	Gngt2	AV096488	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 2	protein-coding
mm_144220.1	chr18	9781845	9781848	+	1	NA	intron (NM_130449, intron 2 of 9)	intron (NM_130449, intron 2 of 9)	74198	NM_130449	140792	Mm.218571	NM_130449	ENSMUSG00000036103	Colec12	CL-P1|SRCL|Scara4	collectin sub-family member 12	protein-coding
mm_22151.1	chr2	172401125	172401136	-	1	NA	intron (NM_001080820, intron 1 of 6)	intron (NM_001080820, intron 1 of 6)	7336	NM_001276423	320664	Mm.210195	NM_001033538	ENSMUSG00000074570	Cass4	F730031O20Rik	Cas scaffolding protein family member 4	protein-coding
mm_66577.1	chr7	45336441	45336468	-	1	NA	exon (NM_010473, exon 1 of 6)	exon (NM_010473, exon 1 of 6)	1185	NM_010473	15464	Mm.39968	NM_010473	ENSMUSG00000038239	Hrc	-	histidine rich calcium binding protein	protein-coding
mm_167223.1	chr8	12385807	12385809	+	1	NA	promoter-TSS (NR_027975)	promoter-TSS (NR_027975)	37	NR_027975	434280	Mm.447484	NM_001013812	ENSMUSG00000047935	Gm5607	EG434280	predicted gene 5607	ncRNA
mm_16211.1	chr2	173073172	173073175	+	1	NA	Intergenic	Intergenic	46352	NM_001081387	664799	Mm.389396	NM_001081387	ENSMUSG00000070495	Ctcfl	Boris|OTTMUSG00000016680	CCCTC-binding factor (zinc finger protein)-like	protein-coding
mm_70223.1	chr7	145208070	145208086	-	1	NA	promoter-TSS (NR_033626)	promoter-TSS (NR_033626)	41	NR_033626	100040049	Mm.102235	NR_033626	ENSMUSG00000109305	1810010D01Rik	Gm2572	RIKEN cDNA 1810010D01 gene	ncRNA
mm_32034.1	chr4	95637415	95637418	+	1	NA	intron (NM_001113412, intron 5 of 15)	intron (NM_001113412, intron 5 of 15)	57995	NM_029347	75578	Mm.276098	NM_029347	ENSMUSG00000028573	Fggy	2310009E04Rik	FGGY carbohydrate kinase domain containing	protein-coding
mm_19660.1	chr2	103073450	103073492	-	1	NA	promoter-TSS (NM_019735)	promoter-TSS (NM_019735)	42	NM_175094	27402	Mm.315011	NM_175094	ENSMUSG00000010914	Pdhx	AI481367|E3bp|Pdx1	pyruvate dehydrogenase complex, component X	protein-coding
mm_9965.1	chr1	191177134	191177145	-	1	NA	intron (NM_007498, intron 2 of 3)	intron (NM_007498, intron 2 of 3)	6194	NM_007498	11910	Mm.2706	NM_007498	ENSMUSG00000026628	Atf3	LRG-21	activating transcription factor 3	protein-coding
mm_135264.1	chr16	38294775	38294838	-	1	NA	promoter-TSS (NM_010936)	promoter-TSS (NM_010936)	18	NM_010936	18171	Mm.8509	NM_010936	ENSMUSG00000022809	Nr1i2	PXR|PXR.1|PXR.2|PXR1|SXR|mPXR	nuclear receptor subfamily 1, group I, member 2	protein-coding
mm_35677.1	chr4	43656438	43656471	-	1	NA	promoter-TSS (NM_026871)	promoter-TSS (NM_026871)	-9	NM_026871	68917	Mm.25285	NM_026871	ENSMUSG00000028470	Hint2	1190005L05Rik	histidine triad nucleotide binding protein 2	protein-coding
mm_105377.1	chr11	103267352	103267362	-	1	NA	promoter-TSS (NM_016896)	promoter-TSS (NM_016896)	44	NM_016896	53859	Mm.158981	NM_016896	ENSMUSG00000020941	Map3k14	Nik|aly	mitogen-activated protein kinase kinase kinase 14	protein-coding
mm_37253.1	chr4	118291341	118291404	-	1	NA	promoter-TSS (NM_011213)	promoter-TSS (NM_011213)	25	NM_011213	19268	Mm.29855	NM_011213	ENSMUSG00000033295	Ptprf	AA591035|LAR|LARS|RPTP-LAR	protein tyrosine phosphatase, receptor type, F	protein-coding
mm_100085.1	chr11	115475744	115475790	+	1	NA	promoter-TSS (NM_177778)	promoter-TSS (NM_177778)	90	NM_177778	276905	Mm.38019	NM_177778	ENSMUSG00000057219	Armc7	A630084C13|BC023126	armadillo repeat containing 7	protein-coding
mm_3611.1	chr1	151872093	151872094	+	1	NA	Intergenic	MT2_Mm|LTR|ERVL	116719	NM_001311166	66967	Mm.337691	NM_001039644	ENSMUSG00000043019	Edem3	2310050N11Rik	ER degradation enhancer, mannosidase alpha-like 3	protein-coding
mm_128052.1	chr15	25826460	25826467	-	1	NA	Intergenic	Intergenic	-16835	NM_001034851	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_33790.1	chr4	134924025	134924065	+	1	NA	exon (NM_023665, exon 2 of 5)	exon (NM_023665, exon 2 of 5)	420	NM_023665	27981	Mm.331964	NM_023665	ENSMUSG00000037266	Rsrp1	2700043I21Rik|D4Ucla2|D4Wsu53e	arginine/serine rich protein 1	protein-coding
mm_84470.1	chr9	66593123	66593131	-	1	NA	promoter-TSS (NM_144937)	promoter-TSS (NM_144937)	-12	NM_001302122	235441	Mm.32465	NM_144937	ENSMUSG00000032376	Usp3	AA409661|BC017156	ubiquitin specific peptidase 3	protein-coding
mm_41830.1	chr5	104114158	104114163	+	1	NA	promoter-TSS (NM_010097)	promoter-TSS (NM_010097)	-72	NM_010097	13602	Mm.29027	NM_010097	ENSMUSG00000029309	Sparcl1	Ecm2|Sc1|hevin|mast9	SPARC-like 1	protein-coding
mm_65592.1	chr7	27329474	27329489	-	1	NA	exon (NM_175641, exon 7 of 33)	exon (NM_175641, exon 7 of 33)	4167	NM_001113549	108075	Mm.272251	NM_175641	ENSMUSG00000040488	Ltbp4	2310046A13Rik	latent transforming growth factor beta binding protein 4	protein-coding
mm_168239.1	chr10	81818935	81818952	-	1	NA	intron (NM_001142963, intron 1 of 3).2	intron (NM_001142963, intron 1 of 3).2	6757	NM_001142963	100233208	Mm.327168	NM_001142963	ENSMUSG00000096856	Gm10778	ENSMUSG00000074860	predicted gene 10778	protein-coding
mm_151575.1	chr19	61050893	61050894	+	1	NA	intron (NM_018869, intron 4 of 15)	L1M4|LINE|L1	89947	NR_131956	414758	Mm.100056	NM_001001737	ENSMUSG00000074733	Zfp950	5830428H23Rik|AU016073|BC055757|Gm34518|Zfp826|mszf84	zinc finger protein 950	protein-coding
mm_15691.1	chr2	163658598	163658608	+	1	NA	5' UTR (NM_001164053, exon 1 of 4)	5' UTR (NM_001164053, exon 1 of 4)	145	NM_001164053	18769	Mm.10091	NM_011106	ENSMUSG00000035268	Pkig	PKIgamma	protein kinase inhibitor, gamma	protein-coding
mm_152292.1	chr19	9002948	9002967	-	1	NA	exon (NM_009643, exon 5 of 5)	exon (NM_009643, exon 5 of 5)	13673	NM_001286518	66395	Mm.203866	NM_009643	ENSMUSG00000069833	Ahnak	DY6	AHNAK nucleoprotein (desmoyokin)	protein-coding
mm_115342.1	chr13	112508191	112508204	+	1	NA	Intergenic	Intergenic	44127	NM_010560	16195	Mm.4364	NM_010560	ENSMUSG00000021756	Il6st	5133400A03Rik|AA389424|BB405851|CD130|D13Ertd699e|gp130	interleukin 6 signal transducer	protein-coding
mm_51130.1	chr6	68437418	68437452	+	1	NA	Intergenic	Intergenic	-871736	NR_003100	75070	Mm.463364	NR_003100		4930515G16Rik	-	myc induced nuclear antigen pseudogene	pseudo
mm_40297.1	chr5	43515922	43515930	+	1	NA	5' UTR (NM_001135172, exon 1 of 3)	5' UTR (NM_001135172, exon 1 of 3)	357	NM_001135172	109323	Mm.275553	NM_175425	ENSMUSG00000061535	C1qtnf7	5530401N20Rik|8430425G24Rik|Ctrp7	C1q and tumor necrosis factor related protein 7	protein-coding
mm_13561.1	chr2	112265784	112265794	+	1	NA	promoter-TSS (NM_133649)	promoter-TSS (NM_133649)	-525	NM_133649	107723	Mm.491155	NM_133648	ENSMUSG00000027130	Slc12a6	9530023I19Rik|KCC3|gaxp	solute carrier family 12, member 6	protein-coding
mm_127725.1	chr15	103240406	103240429	+	1	NA	promoter-TSS (NM_010447)	promoter-TSS (NM_010447)	-15	NR_002885	654467	Mm.432031	NR_002885		Gm10052	ENSMUSG00000058922|XM_001481145	heterogeneous nuclear ribonucleoprotein A1 pseudogene	pseudo
mm_168939.1	chr12	69370914	69370914	-	1	NA	Intergenic	B4A|SINE|B4	-1236	NM_007481	11845	Mm.27308	NM_007481	ENSMUSG00000044147	Arf6	AI788669|AW496366	ADP-ribosylation factor 6	protein-coding
mm_77737.1	chr8	126937351	126937358	-	1	NA	intron (NM_024214, intron 3 of 4)	intron (NM_024214, intron 3 of 4)	8567	NM_024214	67952	Mm.6932	NM_024214	ENSMUSG00000093904	Tomm20	1810060K07Rik|BB284719|Gm19268|MAS20|MOM19|TOM20|mKIAA0016	translocase of outer mitochondrial membrane 20 homolog (yeast)	protein-coding
mm_37909.1	chr4	132757108	132757152	-	1	NA	promoter-TSS (NM_133888)	promoter-TSS (NM_133888)	41	NM_133888	100340	Mm.287187	NM_133888	ENSMUSG00000028885	Smpdl3b	1110054A24Rik|AU045240|Asml3b	sphingomyelin phosphodiesterase, acid-like 3B	protein-coding
mm_32030.1	chr4	95557495	95557544	+	1	NA	promoter-TSS (NM_001113412)	promoter-TSS (NM_001113412)	12	NM_001113412	75578	Mm.276098	NM_029347	ENSMUSG00000028573	Fggy	2310009E04Rik	FGGY carbohydrate kinase domain containing	protein-coding
mm_86367.1	chr9	123792488	123792492	-	1	NA	3' UTR (NM_001110253, exon 18 of 18)	3' UTR (NM_001110253, exon 18 of 18)	-13987	NM_030712	80901	Mm.124289	NM_030712	ENSMUSG00000048521	Cxcr6	BB217514|BONZO|STRL33	chemokine (C-X-C motif) receptor 6	protein-coding
mm_43727.1	chr5	139547971	139547982	+	1	NA	3' UTR (NM_013702, exon 3 of 3)	3' UTR (NM_013702, exon 3 of 3)	4078	NM_013702	22255	Mm.42190	NM_013702	ENSMUSG00000029546	Uncx	Chx4|Uncx4.1	UNC homeobox	protein-coding
mm_96383.1	chr11	67243450	67243463	+	1	NA	exon (NM_010855, exon 11 of 40)	exon (NM_010855, exon 11 of 40)	5644	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_133399.1	chr16	84793561	84793574	+	1	NA	intron (NM_023844, intron 1 of 9)	intron (NM_023844, intron 1 of 9)	19444	NM_023844	67374	Mm.41758	NM_023844	ENSMUSG00000053062	Jam2	1110002N23Rik|2410030G21Rik|2410167M24Rik|JAM-2|JAM-B|Jcam2|VE-JAM	junction adhesion molecule 2	protein-coding
mm_150427.1	chr19	37436733	37436748	+	1	NA	intron (NM_008245, intron 1 of 3)	intron (NM_008245, intron 1 of 3)	1899	NM_008245	15242	Mm.33896	NM_008245	ENSMUSG00000024986	Hhex	Hex|Hex1|Hhex-rs2|Prh|Prhx	hematopoietically expressed homeobox	protein-coding
mm_45181.1	chr5	51772706	51772726	-	1	NA	Intergenic	B1F|SINE|Alu	-204991	NR_132764	19017	Mm.259072	NM_008904	ENSMUSG00000029167	Ppargc1a	A830037N07Rik|ENSMUSG00000079510|Gm11133|PGC-1|PPARGC-1-alpha|Pgc-1alpha|Pgc1|Pgco1|Ppargc1	peroxisome proliferative activated receptor, gamma, coactivator 1 alpha	protein-coding
mm_80272.1	chr9	72985392	72985406	+	1	NA	promoter-TSS (NM_001286546)	promoter-TSS (NM_001286546)	-23	NM_001198789	546143	Mm.260946	NM_001198789	ENSMUSG00000086158	Ccpg1os	EG546143|Gm5918	cell cycle progression 1, opposite strand	protein-coding
mm_161154.1	chr13	23842248	23842248	+	1	NA	intron (NM_001164743, intron 1 of 11)	(TCTCTG)n|Simple_repeat|Simple_repeat	2814	NM_134069	105355	Mm.27038	NM_134069	ENSMUSG00000036083	Slc17a3	AW261723|Npt4	solute carrier family 17 (sodium phosphate), member 3	protein-coding
mm_5558.1	chr1	38777585	38777591	-	1	NA	Intergenic	Intergenic	43627	NM_001029878	381338	Mm.487137	NM_028403	ENSMUSG00000048814	Lonrf2	2900060P06Rik|AI851349	LON peptidase N-terminal domain and ring finger 2	protein-coding
mm_53400.1	chr6	129591786	129591817	+	1	NA	promoter-TSS (NM_010654)	promoter-TSS (NM_010654)	-10	NM_010654	16643	Mm.391515	NM_010654	ENSMUSG00000030165	Klrd1	CD94	killer cell lectin-like receptor, subfamily D, member 1	protein-coding
mm_106736.1	chr12	3897385	3897396	+	1	NA	exon (NM_153743, exon 6 of 18)	exon (NM_153743, exon 6 of 18)	5646	NM_153743	13435	Mm.5001	NM_007872	ENSMUSG00000020661	Dnmt3a	MmuIIIA	DNA methyltransferase 3A	protein-coding
mm_108088.1	chr12	74284272	74284310	+	1	NA	promoter-TSS (NR_030735)	promoter-TSS (NR_030735)	15	NR_030735	74284	Mm.287421	NR_030733	ENSMUSG00000071265	1700086L19Rik	1700006L05Rik|AU016007	RIKEN cDNA 1700086L19 gene	ncRNA
mm_172936.1	chr9	78480855	78480856	-	1	NA	intron (NM_010106, intron 1 of 7)	intron (NM_010106, intron 1 of 7)	869	NM_010106	13627	Mm.138471	NM_010106	ENSMUSG00000037742	Eef1a1	-	eukaryotic translation elongation factor 1 alpha 1	protein-coding
mm_103678.1	chr11	79243457	79243468	-	1	NA	promoter-TSS (NM_001042565)	promoter-TSS (NM_001042565)	-438	NM_001042565	78889	Mm.307022	NM_019653	ENSMUSG00000017677	Wsb1	1110056B13Rik|2700038M07Rik	WD repeat and SOCS box-containing 1	protein-coding
mm_143803.1	chr17	83514291	83514305	-	1	NA	promoter-TSS (NM_001159529)	promoter-TSS (NM_001159529)	35	NM_009187	20463	Mm.30072	NM_009187	ENSMUSG00000024248	Cox7a2l	COX7AR|COX7RP|EB1|SIG-81|SIG81|Silg81	cytochrome c oxidase subunit VIIa polypeptide 2-like	protein-coding
mm_76437.1	chr8	84986147	84986219	-	1	NA	Intergenic	CpG	-4412	NM_133255	170833	Mm.247775	NM_133255	ENSMUSG00000052566	Hook2	A630054I03Rik	hook microtubule tethering protein 2	protein-coding
mm_47913.1	chr5	134966480	134966492	-	1	NA	Intergenic	Intergenic	-19552	NM_009903	12740	Mm.7339	NM_009903	ENSMUSG00000047501	Cldn4	Cep-r|Cpetr|Cpetr1	claudin 4	protein-coding
mm_76853.1	chr8	105349211	105349222	-	1	NA	5' UTR (NM_001081332, exon 1 of 16)	5' UTR (NM_001081332, exon 1 of 16)	958	NM_001081332	277973	Mm.334766	NM_001081332	ENSMUSG00000014786	Slc9a5	Gm696	solute carrier family 9 (sodium/hydrogen exchanger), member 5	protein-coding
mm_114384.1	chr13	63246839	63246847	+	1	NA	intron (NR_110520, intron 2 of 5)	intron (NR_110520, intron 2 of 5)	6814	NR_110521	72061	Mm.188105	NM_028079	ENSMUSG00000021458	2010111I01Rik	2300006M17Rik|AP-O|AW742919|Aopep|ApO|mir-23b|mir-24-1|mir-27b	RIKEN cDNA 2010111I01 gene	protein-coding
mm_153547.1	chr19	42086281	42086294	-	1	NA	promoter-TSS (NM_198108)	promoter-TSS (NM_198108)	83	NM_198108	226123	Mm.259441	NM_198108	ENSMUSG00000049670	Morn4	-	MORN repeat containing 4	protein-coding
mm_124266.1	chr14	102980517	102980523	-	1	NA	3' UTR (NM_177715, exon 1 of 1)	3' UTR (NM_177715, exon 1 of 1)	2112	NR_039592	100628599		NR_039592	ENSMUSG00000092901	Mir5130	mir-5130|mmu-mir-5130|mu-mir-5130	microRNA 5130	ncRNA
mm_79064.1	chr9	46230405	46230433	+	1	NA	TTS (NM_009692)	TTS (NM_009692)	1789	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2|apo-AI|apoA-I	apolipoprotein A-I	protein-coding
mm_97106.1	chr11	74619677	74619714	+	1	NA	promoter-TSS (NM_001013784)	promoter-TSS (NM_001013784)	90	NM_001013784	432582	Mm.274369	NM_001013784	ENSMUSG00000069814	Ccdc92b	E130309D14Rik	coiled-coil domain containing 92B	protein-coding
mm_140646.1	chr17	12688559	12688565	-	1	NA	intron (NM_010515, intron 43 of 47)	intron (NM_010515, intron 43 of 47)	-12724	NM_009202	20517	Mm.594	NM_009202	ENSMUSG00000023829	Slc22a1	Lx1|Oct1|Orct|Orct1	solute carrier family 22 (organic cation transporter), member 1	protein-coding
mm_110594.1	chr12	56535017	56535030	-	1	NA	exon (NM_009385, exon 2 of 3)	exon (NM_009385, exon 2 of 3)	1885	NM_009385	21869	Mm.89972	NM_009385	ENSMUSG00000001496	Nkx2-1	AV026640|Nkx2.1|T/EBP|Titf1|Ttf-1	NK2 homeobox 1	protein-coding
mm_56577.1	chr6	106748960	106748992	-	1	NA	promoter-TSS (NM_008370)	promoter-TSS (NM_008370)	61	NM_008370	16192	Mm.3448	NM_008370	ENSMUSG00000005364	Il5ra	CD125|CDw125|Il5r	interleukin 5 receptor, alpha	protein-coding
mm_109245.1	chr12	109452834	109452849	+	1	NA	promoter-TSS (NM_010052)	promoter-TSS (NM_010052)	18	NR_033813	13386	Mm.157069	NM_010052	ENSMUSG00000040856	Dlk1	AW742678|DLK-1|DlkI|FA1|Ly107|Peg9|SCP1|ZOG|pG2|pref-1	delta-like 1 homolog (Drosophila)	protein-coding
mm_42770.1	chr5	121283658	121283666	+	1	NA	intron (NM_181421, intron 11 of 75)	RLTR10B2|LTR|ERVK	63443	NM_181421	269700	Mm.184589	NM_181421	ENSMUSG00000042744	Gm15800	A130010L24|AU042671|BC019639|EG545802|OTTMUSG00000026283|mKIAA0614	predicted gene 15800	protein-coding
mm_170021.1	chr17	21474730	21474740	+	1	NA	Intergenic	MMVL30-int|LTR|ERV1	-14253	NM_013843	24132	Mm.42140	NM_013843	ENSMUSG00000057409	Zfp53	D030067O06Rik|KRAZ1|Zfp-53|Zfp118|zfas8	zinc finger protein 53	protein-coding
mm_43053.1	chr5	124175396	124175408	+	1	NA	intron (NM_011256, intron 2 of 24)	intron (NM_011256, intron 2 of 24)	11780	NM_001289472	19679	Mm.44261	NM_011256	ENSMUSG00000029406	Pitpnm2	NIR3|RDGBA2|Rdgb2|mKIAA1457	phosphatidylinositol transfer protein, membrane-associated 2	protein-coding
mm_162264.1	chrY	3771672	3771672	+	1	NA	promoter-TSS (NM_001166384).3	promoter-TSS (NM_001166384).3	-1	NM_001270516	100862398	Mm.4711	NM_001270516	ENSMUSG00000095948	Gm21708	-	predicted gene, 21708	protein-coding
mm_57239.1	chr6	123283039	123283049	-	1	NA	3' UTR (NM_019948, exon 6 of 6)	3' UTR (NM_019948, exon 6 of 6)	6827	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_53601.1	chr6	138147714	138147744	+	1	NA	exon (NM_019946, exon 2 of 4)	exon (NM_019946, exon 2 of 4)	6135	NM_001347489	56615	Mm.14796	NM_019946	ENSMUSG00000008540	Mgst1	1500002K10Rik|Gst	microsomal glutathione S-transferase 1	protein-coding
mm_100579.1	chr11	120784258	120784272	+	1	NA	promoter-TSS (NM_145370)	promoter-TSS (NM_145370)	-7	NM_001346709	209318	Mm.30195	NM_145370	ENSMUSG00000025156	Gps1	Cops1|Csn1|R75577|Sgn1	G protein pathway suppressor 1	protein-coding
mm_12965.1	chr2	90677209	90677236	+	1	NA	promoter-TSS (NM_021512)	promoter-TSS (NM_021512)	7	NM_021512	59015	Mm.24532	NM_021512	ENSMUSG00000051329	Nup160	160kDa|2810011M03Rik|AA414952|AU020188|Gtl-13|Gtl1-13|Gtl13|mKIAA0197	nucleoporin 160	protein-coding
mm_96166.1	chr11	61488147	61488164	+	1	NA	TTS (NM_001291037)	TTS (NM_001291037)	2711	NM_029568	76293	Mm.272278	NM_029568	ENSMUSG00000042436	Mfap4	1110007F23Rik	microfibrillar-associated protein 4	protein-coding
mm_14487.1	chr2	131856544	131856553	+	1	NA	5' UTR (NM_001166206, exon 2 of 2)	5' UTR (NM_001166206, exon 2 of 2)	3199	NM_001166206	71995	Mm.22	NM_028045	ENSMUSG00000037482	Erv3	1600014E20Rik|AA389086|AI426069|AI448024|D19349	endogenous retroviral sequence 3	protein-coding
mm_45220.1	chr5	53213419	53213444	-	1	NA	promoter-TSS (NM_172710)	promoter-TSS (NM_172710)	21	NM_172710	231238	Mm.235020	NM_172710	ENSMUSG00000029189	Sel1l3	2310045A20Rik|AI429585|mKIAA0746	sel-1 suppressor of lin-12-like 3 (C. elegans)	protein-coding
mm_143590.1	chr17	74459190	74459207	-	1	NA	promoter-TSS (NM_001033367)	promoter-TSS (NM_001033367)	-90	NM_001033367	268973	Mm.311884	NM_001033367	ENSMUSG00000039193	Nlrc4	9530011P19Rik|CLAN|CLAN1|CLANA|CLANB|CLANC|CLAND|Card12|IPAF	NLR family, CARD domain containing 4	protein-coding
mm_4509.1	chr1	174172889	174172916	+	1	NA	5' UTR (NM_011465, exon 1 of 52)	5' UTR (NM_011465, exon 1 of 52)	126	NM_011465	20739	Mm.200611	NM_011465	ENSMUSG00000026532	Spta1	AF093576|AI451697|Spna-1|Spna1|ha|ihj|nmf4|sph	spectrin alpha, erythrocytic 1	protein-coding
mm_3933.1	chr1	163762130	163762153	+	1	NA	Intergenic	Intergenic	-17442	NM_001305643	16579	Mm.4651	NM_010629	ENSMUSG00000026585	Kifap3	KAP-3|KAP3|SMAP	kinesin-associated protein 3	protein-coding
mm_156788.1	chrX	162566810	162566818	+	1	NA	intron (NM_178256, intron 1 of 17)	intron (NM_178256, intron 1 of 17)	76844	NM_001290633	194590	Mm.442441	NM_178256	ENSMUSG00000040855	Reps2	POB1	RALBP1 associated Eps domain containing protein 2	protein-coding
mm_128787.1	chr15	66804061	66804069	-	1	NA	intron (NM_001029841, intron 1 of 7)	intron (NM_001029841, intron 1 of 7)	27764	NM_001029841	20491	Mm.7601	NM_009192	ENSMUSG00000022372	Sla	Slap|Slap-1	src-like adaptor	protein-coding
mm_126141.1	chr15	78348281	78348291	+	1	NA	promoter-TSS (NR_106138)	promoter-TSS (NR_106138)	-313	NR_106137	102465776		NR_106137	ENSMUSG00000098996	Mir7676-1	Gm27600|mmu-mir-7676-1	microRNA 7676-1	ncRNA
mm_79316.1	chr9	52069746	52069755	+	1	NA	exon (NM_009041, exon 9 of 14)	exon (NM_009041, exon 9 of 14)	-21045	NR_023357	629557	Mm.422775	NR_023357		Gm6981	EG629557	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_49338.1	chr6	21344536	21344539	+	1	NA	intron (NM_019697, intron 1 of 5)	intron (NM_019697, intron 1 of 5)	128428	NM_019697	16508	Mm.425316	NM_019697	ENSMUSG00000060882	Kcnd2	AI839615|AW555701|Kv4.2|R75121|mKIAA1044	potassium voltage-gated channel, Shal-related family, member 2	protein-coding
mm_51126.1	chr6	68256377	68256384	+	1	NA	Intergenic	Intergenic	-690681	NR_003100	75070	Mm.463364	NR_003100		4930515G16Rik	-	myc induced nuclear antigen pseudogene	pseudo
mm_4393.1	chr1	172341354	172341370	+	1	NA	5' UTR (NM_001039484, exon 1 of 2)	5' UTR (NM_001039484, exon 1 of 2)	152	NM_001039484	16513	Mm.254563	NM_020269	ENSMUSG00000044708	Kcnj10	BIR10|BIRK-1|Kir1.2|Kir4.1	potassium inwardly-rectifying channel, subfamily J, member 10	protein-coding
mm_77614.1	chr8	123894745	123894760	-	1	NA	promoter-TSS (NM_009606)	promoter-TSS (NM_009606)	23	NM_001272041	11459	Mm.214950	NM_009606	ENSMUSG00000031972	Acta1	AA959943|Acta-2|Acts|Actsk-1	actin, alpha 1, skeletal muscle	protein-coding
mm_82228.1	chr9	3027476	3027488	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	11261	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_19508.1	chr2	93849922	93849980	-	1	NA	promoter-TSS (NM_183220)	promoter-TSS (NM_183220)	-8	NM_001290782	329470	Mm.486910	NM_183220	ENSMUSG00000040272	Accs	2610203E10Rik|Phacs	1-aminocyclopropane-1-carboxylate synthase (non-functional)	protein-coding
mm_146044.1	chr18	69593259	69593274	+	1	NA	intron (NM_013685, intron 8 of 19)	intron (NM_013685, intron 8 of 19)	247545	NM_001083967	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding
mm_43681.1	chr5	138804712	138804742	+	1	NA	intron (NM_030565, intron 5 of 9)	B4|SINE|B4	-15353	NM_001195128	384244	Mm.485002	NM_001195128	ENSMUSG00000094504	Gm5294	EG384244	predicted gene 5294	protein-coding
mm_72922.1	chr8	91082242	91082270	+	1	NA	intron (NM_001282000, intron 4 of 20)	intron (NM_001282000, intron 4 of 20)	12199	NM_001282000	19651	Mm.235580	NM_011250	ENSMUSG00000031666	Rbl2	PRB2|RBR-2|Rb2|p130	retinoblastoma-like 2	protein-coding
mm_55425.1	chr6	65144837	65144842	-	1	NA	promoter-TSS (NM_019455)	promoter-TSS (NM_019455)	-109	NM_019455	54486	Mm.410688	NM_019455	ENSMUSG00000029919	Hpgds	H-PGDS|Ptgds2	hematopoietic prostaglandin D synthase	protein-coding
mm_142448.1	chr17	45592570	45592581	-	1	NA	promoter-TSS (NM_022880)	promoter-TSS (NM_022880)	-182	NM_022880	63959	Mm.29744	NM_022880	ENSMUSG00000023942	Slc29a1	1200014D21Rik|AA407560|ENT1	solute carrier family 29 (nucleoside transporters), member 1	protein-coding
mm_147387.1	chr18	44088489	44088499	-	1	NA	Intergenic	Intergenic	-16029	NM_030061	78242	Mm.99782	NM_030061	ENSMUSG00000061144	Spink12	9230117E20Rik	serine peptidase inhibitor, Kazal type 12	protein-coding
mm_132528.1	chr16	37834555	37834571	+	1	NA	3' UTR (NM_008047, exon 11 of 11)	3' UTR (NM_008047, exon 11 of 11)	-33837	NM_177093	320184	Mm.390882	NM_177093	ENSMUSG00000034158	Lrrc58	1810012N18Rik|C330018J07Rik	leucine rich repeat containing 58	protein-coding
mm_13778.1	chr2	118747264	118747265	+	1	NA	3' UTR (NM_001301269, exon 1 of 1)	3' UTR (NM_001301269, exon 1 of 1)	1506	NM_001301269	100043272	Mm.398072	NM_001301269	ENSMUSG00000074918	Inafm2	5430417L22Rik|ENSMUSG00000074918	InaF motif containing 2	protein-coding
mm_24953.1	chr3	96635818	96635837	+	1	NA	promoter-TSS (NM_001162388)	promoter-TSS (NM_001162388)	-20	NM_001162388	18632	Mm.20901	NM_011069	ENSMUSG00000028102	Pex11b	PEX11beta|Pex11pbeta	peroxisomal biogenesis factor 11 beta	protein-coding
mm_64829.1	chr7	12807310	12807314	-	1	NA	3' UTR (NM_026046, exon 2 of 2)	3' UTR (NM_026046, exon 2 of 2)	11548	NM_026046	67230	Mm.333574	NM_026046	ENSMUSG00000057894	Zfp329	2810439M05Rik|4632409L22Rik|ZNF329	zinc finger protein 329	protein-coding
mm_13368.1	chr2	103566305	103566323	+	1	NA	promoter-TSS (NM_178890)	promoter-TSS (NM_178890)	4	NM_178890	99382	Mm.35850	NM_178890	ENSMUSG00000032724	Abtb2	AW539457|BPOZ-2	ankyrin repeat and BTB (POZ) domain containing 2	protein-coding
mm_26198.1	chr3	138526476	138526521	+	1	NA	promoter-TSS (NR_035481)	promoter-TSS (NR_035481)	77	NR_035481	100316706		NR_035481	ENSMUSG00000088373	Mir1956	mir-1956|mmu-mir-1956	microRNA 1956	ncRNA
mm_167385.1	chr8	94696179	94696200	-	1	NA	promoter-TSS (NM_026385)	promoter-TSS (NM_026385)	53	NM_026385	67801	Mm.279977	NM_026385	ENSMUSG00000031775	Pllp	0610010I06Rik|AV001002|Plapi|Tm4sf11	plasma membrane proteolipid	protein-coding
mm_122590.1	chr14	50897473	50897507	-	1	NA	Intergenic	Intergenic	-4235	NM_001166651	546611	Mm.390692	NM_001166651	ENSMUSG00000090799	Klhl33	EG546611	kelch-like 33	protein-coding
mm_148853.1	chr19	6389794	6389804	+	1	NA	exon (NM_011224, exon 11 of 20)	exon (NM_011224, exon 11 of 20)	5391	NM_011224	19309	Mm.27806	NM_011224	ENSMUSG00000032648	Pygm	AI115133|PG	muscle glycogen phosphorylase	protein-coding
mm_78040.1	chr9	14282371	14282373	+	1	NA	intron (NM_030261, intron 1 of 9)	Charlie1|DNA|hAT-Charlie	6071	NM_030261	75747	Mm.325126	NM_030261	ENSMUSG00000032009	Sesn3	5630400E15Rik|BC003348|SEST3	sestrin 3	protein-coding
mm_25361.1	chr3	107091431	107091442	+	1	NA	Intergenic	Intergenic	-10131	NM_008417	16490	Mm.39285	NM_008417	ENSMUSG00000040724	Kcna2	Akr6a4|ENSMUSG00000074335|Gm10672|Kca1-2|Kv1.2|Mk-2	potassium voltage-gated channel, shaker-related subfamily, member 2	protein-coding
mm_69523.1	chr7	135651807	135651868	-	1	NA	promoter-TSS (NM_001316681)	promoter-TSS (NM_001316681)	-62	NM_001316681	19267	Mm.945	NM_011212	ENSMUSG00000041836	Ptpre	PTPe|PTPepsilon|RPTPepsilon	protein tyrosine phosphatase, receptor type, E	protein-coding
mm_31020.1	chr4	40726826	40726831	+	1	NA	intron (NM_008298, intron 4 of 8)	(T)n|Simple_repeat|Simple_repeat	3898	NM_001164672	15502	Mm.27897	NM_008298	ENSMUSG00000028410	Dnaja1	HSJ-2|Hsj2|Nedd7	DnaJ heat shock protein family (Hsp40) member A1	protein-coding
mm_158748.1	chrX	164980280	164980309	-	1	NA	promoter-TSS (NM_175027)	promoter-TSS (NM_175027)	81	NM_001290523	76763	Mm.291758	NM_029730	ENSMUSG00000061778	Mospd2	2410013I23Rik	motile sperm domain containing 2	protein-coding
mm_149346.1	chr19	10859780	10859795	+	1	NA	intron (NM_133804, intron 9 of 10)	intron (NM_133804, intron 9 of 10)	9992	NM_133804	98170	Mm.490254	NM_133804	ENSMUSG00000024736	Tmem132a	6720481D13Rik|Hspa5bp1|Orai1|R74613	transmembrane protein 132A	protein-coding
mm_96116.1	chr11	60704681	60704716	+	1	NA	exon (NM_001159405, exon 3 of 22)	exon (NM_001159405, exon 3 of 22)	5008	NM_008502	16897	Mm.285453	NM_008502	ENSMUSG00000020536	Llgl1	AI325176|Lgl1|Llglh|Mgl1	lethal giant larvae homolog 1 (Drosophila)	protein-coding
mm_172233.1	chr6	67839765	67839773	+	1	NA	Intergenic	Intergenic	-274070	NR_003100	75070	Mm.463364	NR_003100		4930515G16Rik	-	myc induced nuclear antigen pseudogene	pseudo
mm_11825.1	chr2	44927436	44927446	+	1	NA	Intergenic	CpG	-65819	NM_172662	227835	Mm.314312	NM_172662	ENSMUSG00000036890	Gtdc1	E330008O22Rik	glycosyltransferase-like domain containing 1	protein-coding
mm_94627.1	chr11	16805638	16805647	+	1	NA	intron (NM_207655, intron 1 of 27)	Lx8|LINE|L1	53439	NM_007912	13649	Mm.8534	NM_007912	ENSMUSG00000020122	Egfr	9030024J15Rik|AI552599|Erbb|Errb1|Errp|Wa5|wa-2|wa2	epidermal growth factor receptor	protein-coding
mm_83335.1	chr9	44256926	44256942	-	1	NA	intron (NM_178420, intron 6 of 9)	intron (NM_178420, intron 6 of 9)	-5470	NM_133226	170761	Mm.29872	NM_133226	ENSMUSG00000032105	Pdzd3	NaPi-Cap2|Pdzk2	PDZ domain containing 3	protein-coding
mm_89229.1	chr10	87521955	87521977	+	1	NA	5' UTR (NM_008777, exon 1 of 13)	5' UTR (NM_008777, exon 1 of 13)	171	NM_008777	18478	Mm.263539	NM_008777	ENSMUSG00000020051	Pah	AW106920	phenylalanine hydroxylase	protein-coding
mm_160606.1	chr9	78313902	78313902	-	1	NA	5' UTR (NM_001111286, exon 1 of 3)	5' UTR (NM_001111286, exon 1 of 3)	146	NM_001111286	18379	Mm.335311	NM_001111286	ENSMUSG00000066463	Omt2a	OM2a	oocyte maturation, alpha	protein-coding
mm_473.1	chr1	36471591	36471606	+	1	NA	promoter-TSS (NM_033570)	promoter-TSS (NM_033570)	1	NM_033570	94220	Mm.422638	NM_033570	ENSMUSG00000037408	Cnnm4	5430430O18Rik|Acdp4	cyclin M4	protein-coding
mm_78943.1	chr9	45138458	45138462	+	1	NA	promoter-TSS (NM_001013390)	promoter-TSS (NM_001013390)	-582	NM_001013390	399548	Mm.335112	NM_001013390	ENSMUSG00000046480	Scn4b	Gm1471	sodium channel, type IV, beta	protein-coding
mm_29923.1	chr3	131490730	131490742	-	1	NA	Intergenic	CpG	-74032	NM_001289479	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_87456.1	chr10	51484310	51484316	+	1	NA	intron (NM_001291892, intron 6 of 8)	intron (NM_001291892, intron 6 of 8)	3701	NM_001291892	14727	Mm.439661	NM_008147	ENSMUSG00000062593	Lilr4b	Gp49a|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4B	protein-coding
mm_152928.1	chr19	28146351	28146351	-	1	NA	Intergenic	Intergenic	-135185	NM_011265	19726	Mm.313321	NM_011265	ENSMUSG00000040929	Rfx3	C230093O12Rik|MRFX3	regulatory factor X, 3 (influences HLA class II expression)	protein-coding
mm_105469.1	chr11	105455300	105455325	-	1	NA	intron (NM_172568, intron 1 of 11)	intron (NM_172568, intron 1 of 11)	1423	NM_172568	632687	Mm.121570	NM_172568	ENSMUSG00000078627	March10	4933417C16Rik|AV039223|OTTMUSG00000002847|Rnf190	membrane-associated ring finger (C3HC4) 10	protein-coding
mm_75341.1	chr8	43306957	43306965	-	1	NA	promoter-TSS (NM_009556)	promoter-TSS (NM_009556)	48	NM_009556	22702	Mm.285848	NM_009556	ENSMUSG00000051176	Zfp42	Rex-1|Rex1|Zfp-42	zinc finger protein 42	protein-coding
mm_94700.1	chr11	20201407	20201448	+	1	NA	promoter-TSS (NM_008996)	promoter-TSS (NM_008996)	-175	NM_008996	19324	Mm.271944	NM_008996	ENSMUSG00000020149	Rab1a	Gtbp|Rab-1|Rab1|Ypt1|mKIAA3012	RAB1A, member RAS oncogene family	protein-coding
mm_73911.1	chr8	119612702	119612732	+	1	NA	promoter-TSS (NM_029428)	promoter-TSS (NM_029428)	-30	NM_029428	75773	Mm.159566	NM_029428	ENSMUSG00000024266	Adad2	4930403J07Rik	adenosine deaminase domain containing 2	protein-coding
mm_82142.1	chr9	123769881	123769890	+	1	NA	intron (NM_009913, intron 1 of 2)	intron (NM_009913, intron 1 of 2)	2674	NM_001166625	12769	Mm.440604	NM_009913	ENSMUSG00000029530	Ccr9	A130091K22Rik|Cmkbr10|GPR-9-6	chemokine (C-C motif) receptor 9	protein-coding
mm_129865.1	chr15	83367240	83367250	-	1	NA	promoter-TSS (NR_027980)	promoter-TSS (NR_027980)	52	NR_027980	69291	Mm.66794	NM_001033147		1700001L05Rik	-	RIKEN cDNA 1700001L05 gene	ncRNA
mm_722.1	chr1	42701166	42701169	+	1	NA	TTS (NM_008900)	TTS (NM_008900)	831	NR_027891	73100	Mm.467885	NR_027891		2900092D14Rik	-	RIKEN cDNA 2900092D14 gene	ncRNA
mm_146948.1	chr18	32553658	32553673	-	1	NA	intron (NM_001048207, intron 1 of 2)	intron (NM_001048207, intron 1 of 2)	6369	NM_001347610	71683	Mm.292145	NM_027863	ENSMUSG00000090523	Gypc	0610037F22Rik|Cd236r	glycophorin C	protein-coding
mm_58455.1	chr7	3332135	3332168	+	1	NA	Intergenic	Intergenic	-4434	NM_133189	81904	Mm.214994	NM_133189	ENSMUSG00000069806	Cacng7	-	calcium channel, voltage-dependent, gamma subunit 7	protein-coding
mm_38410.1	chr4	139093011	139093021	-	1	NA	promoter-TSS (NM_008675)	promoter-TSS (NM_008675)	-46	NM_008675	17965	Mm.9404	NM_008675	ENSMUSG00000041120	Nbl1	D4H1S1733E|DAN|Dana|NO3	neuroblastoma, suppression of tumorigenicity 1	protein-coding
mm_153833.1	chr19	46324830	46324845	-	1	NA	exon (NM_001347454, exon 3 of 18)	exon (NM_001347454, exon 3 of 18)	2029	NM_001347454	73728	Mm.268532	NM_028627	ENSMUSG00000037126	Psd	1110007H17Rik|A930015K15|Efa6|Efa6a|Psdl|mKIAA2011	pleckstrin and Sec7 domain containing	protein-coding
mm_65477.1	chr7	25539846	25539858	-	1	NA	5' UTR (NM_001113369, exon 1 of 7)	5' UTR (NM_001113369, exon 1 of 7)	152	NM_001113368	26367	Mm.439731	NM_007543	ENSMUSG00000054385	Ceacam2	AI267129|Bgp2|Ceacam2-L	carcinoembryonic antigen-related cell adhesion molecule 2	protein-coding
mm_33815.1	chr4	135337768	135337770	+	1	NA	intron (NM_016799, intron 9 of 17)	intron (NM_016799, intron 9 of 17)	15445	NM_016799	51796	Mm.1963	NM_016799	ENSMUSG00000028809	Srrm1	AA407769|POP101|Srm160	serine/arginine repetitive matrix 1	protein-coding
mm_118575.1	chr14	19750904	19750925	+	1	NA	promoter-TSS (NM_008695)	promoter-TSS (NM_008695)	-343	NM_008695	18074	Mm.20348	NM_008695	ENSMUSG00000021806	Nid2	AW547149|Ly111|NID-2|entactin-2|nidogen-2	nidogen 2	protein-coding
mm_49923.1	chr6	39226466	39226499	+	1	NA	Intergenic	Intergenic	-19709	NM_001033430	338523	Mm.293175	NM_001033430	ENSMUSG00000042599	Kdm7a	A630082K20Rik|BB041802|ENSMUSG00000073143|Jhdm1d|mKIAA1718	lysine (K)-specific demethylase 7A	protein-coding
mm_142745.1	chr17	48432609	48432627	-	1	NA	5' UTR (NM_009694, exon 1 of 3)	5' UTR (NM_009694, exon 1 of 3)	110	NM_009694	11811	Mm.281793	NM_009694	ENSMUSG00000040694	Apobec2	Arp1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 2	protein-coding
mm_11649.1	chr2	34961703	34961717	+	1	NA	promoter-TSS (NM_001326601)	promoter-TSS (NM_001326601)	62	NM_009421	22029	Mm.239514	NM_009421	ENSMUSG00000026875	Traf1	4732496E14Rik	TNF receptor-associated factor 1	protein-coding
mm_4856.1	chr1	187609003	187609024	+	1	NA	promoter-TSS (NM_001243792)	promoter-TSS (NM_001243792)	7	NM_001243792	26381	Mm.89989	NM_011935	ENSMUSG00000026610	Esrrg	ERR3|Errg|NR3B3|mKIAA0832	estrogen-related receptor gamma	protein-coding
mm_169202.1	chr13	66349266	66349267	-	1	NA	Intergenic	Intergenic	91852	NM_183119	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
mm_15104.1	chr2	153354884	153354887	+	1	NA	intron (NM_001039939, intron 2 of 11)	intron (NM_001039939, intron 2 of 11)	8746	NM_001039939	228790	Mm.330677	NM_001039939	ENSMUSG00000042548	Asxl1	mKIAA0978	additional sex combs like 1	protein-coding
mm_122669.1	chr14	51923037	51923041	-	1	NA	promoter-TSS (NM_001011687)	promoter-TSS (NM_001011687)	-266	NM_001011687	497071	Mm.378602	NM_001011687	ENSMUSG00000068392	Rnase13	-	ribonuclease, RNase A family, 13 (non-active)	protein-coding
mm_135662.1	chr16	52407597	52407609	-	1	NA	intron (NM_009655, intron 1 of 15)	intron (NM_009655, intron 1 of 15)	45478	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_154733.1	chrX	9747756	9747779	+	1	NA	Intergenic	Intergenic	-84784	NM_025975	67117	Mm.29150	NM_025975	ENSMUSG00000031176	Dynlt3	2310075M16Rik|AU042796|Tcte1l	dynein light chain Tctex-type 3	protein-coding
mm_91874.1	chr10	59582996	59583007	-	1	NA	intron (NM_001033259, intron 1 of 7)	(TG)n|Simple_repeat|Simple_repeat	33691	NM_001033259	215999	Mm.296470	NM_001033259	ENSMUSG00000009647	Mcu	2010012O16Rik|AV064928|C10orf42|Ccdc109a|D130073L02Rik|Gm64	mitochondrial calcium uniporter	protein-coding
mm_97019.1	chr11	71749915	71749937	+	1	NA	promoter-TSS (NM_177618)	promoter-TSS (NM_177618)	-777	NM_177618	216881	Mm.48648	NM_177618	ENSMUSG00000020811	Wscd1	mKIAA0523	WSC domain containing 1	protein-coding
mm_127390.1	chr15	101115739	101115753	+	1	NA	promoter-TSS (NM_144790)	promoter-TSS (NM_144790)	-9	NM_144790	208258	Mm.152952	NM_144790	ENSMUSG00000047034	Ankrd33	A930021G21Rik|Panky|Panky-a	ankyrin repeat domain 33	protein-coding
mm_110037.1	chr12	17000331	17000354	-	1	NA	promoter-TSS (NM_001161111)	promoter-TSS (NM_001161111)	-224	NM_001161111	217430	Mm.379451	NM_172574	ENSMUSG00000045679	Pqlc3	C78076|E030024M05Rik	PQ loop repeat containing	protein-coding
mm_142683.1	chr17	47733087	47733110	-	1	NA	exon (NM_025973, exon 7 of 9)	exon (NM_025973, exon 7 of 9)	-3939	NM_001161722	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_47916.1	chr5	135000855	135000861	-	1	NA	non-coding (NR_026907, exon 1 of 5)	non-coding (NR_026907, exon 1 of 5)	492	NR_026907	71304	Mm.482317	NR_026907	ENSMUSG00000054909	Wbscr25	4933433J03Rik|4933439O14Rik	Williams Beuren syndrome chromosome region 25 (human)	ncRNA
mm_49078.1	chr6	6299440	6299453	+	1	NA	intron (NR_136905, intron 1 of 3)	intron (NR_136905, intron 1 of 3)	50787	NR_136905	101056138	Mm.389085	NR_136904	ENSMUSG00000093482	Gm20619	-	predicted gene 20619	ncRNA
mm_27669.1	chr3	65381397	65381400	-	1	NA	3' UTR (NM_026155, exon 5 of 5)	3' UTR (NM_026155, exon 5 of 5)	11155	NM_026155	67437	Mm.232728	NM_026155	ENSMUSG00000027828	Ssr3	0610038P07Rik|AL022999|AU022074|AW553833|TRAPG	signal sequence receptor, gamma	protein-coding
mm_121930.1	chr14	23962220	23962222	-	1	NA	intron (NM_001253366, intron 1 of 29)	L1MD3|LINE|L1	41984	NM_001253375	16531	Mm.343607	NM_010610	ENSMUSG00000063142	Kcnma1	5730414M22Rik|BKCa|MaxiK|Slo|Slo1|mSlo|mSlo1	potassium large conductance calcium-activated channel, subfamily M, alpha member 1	protein-coding
mm_139002.1	chr17	45563979	45563987	+	1	NA	promoter-TSS (NM_028662)	promoter-TSS (NM_028662)	-169	NM_028662	73836	Mm.289716	NM_028662	ENSMUSG00000037089	Slc35b2	1110003M08Rik|AA407792|AI842275|PAPST1|Slc35b1	solute carrier family 35, member B2	protein-coding
mm_7929.1	chr1	133906974	133907014	-	1	NA	exon (NM_001160422, exon 1 of 5)	exon (NM_001160422, exon 1 of 5)	179	NM_054076	269120	Mm.59985	NM_054076	ENSMUSG00000010311	Optc	-	opticin	protein-coding
mm_145981.1	chr18	68160187	68160194	+	1	NA	intron (NM_172631, intron 3 of 5)	Tigger6a|DNA|TcMar-Tigger	100783	NR_106078	102465702		NR_106078	ENSMUSG00000098253	Mir7219	Gm27613|mmu-mir-7219	microRNA 7219	ncRNA
mm_161045.1	chr12	37880260	37880260	+	1	NA	promoter-TSS (NM_178681)	promoter-TSS (NM_178681)	-445	NM_178681	217480	Mm.126525	NM_178681	ENSMUSG00000036095	Dgkb	6430574F24|90kda|C630029D13Rik|DAGK2|DGK|DGK-beta|mKIAA0718	diacylglycerol kinase, beta	protein-coding
mm_165531.1	chr2	178506162	178506168	-	1	NA	Intergenic	Intergenic	75650	NM_198656	381409	Mm.330860	NM_198656	ENSMUSG00000039155	Cdh26	Gm1010	cadherin-like 26	protein-coding
mm_50275.1	chr6	45545881	45545886	+	1	NA	intron (NM_001004357, intron 1 of 23)	ORR1B1|LTR|ERVL-MaLR	485822	NM_001004357	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding
mm_142875.1	chr17	51823529	51823530	-	1	NA	intron (NM_001163632, intron 1 of 10)	intron (NM_001163632, intron 1 of 10)	3059	NM_001163631	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_79137.1	chr9	47636802	47636812	+	1	NA	intron (NM_001025600, intron 1 of 8)	intron (NM_001025600, intron 1 of 8)	106455	NM_018770	54725	Mm.234832	NM_018770	ENSMUSG00000032076	Cadm1	2900073G06Rik|3100001I08Rik|AI987920|Bl2|Igsf4|Igsf4a|Necl2|RA175|RA175A|RA175B|RA175C|RA175N|ST17|SgIGSF|SynCam|Tslc1	cell adhesion molecule 1	protein-coding
mm_128408.1	chr15	44729016	44729020	-	1	NA	intron (NM_001032727, intron 1 of 5)	B1_Mur2|SINE|Alu	19654	NM_001285840	319613	Mm.207715	NM_176998	ENSMUSG00000022340	Sybu	Golsyn	syntabulin (syntaxin-interacting)	protein-coding
mm_86676.1	chr10	18105769	18105772	+	1	NA	intron (NM_001111065, intron 9 of 18)	intron (NM_001111065, intron 9 of 18)	49830	NM_001111065	19707	Mm.4479	NM_009048	ENSMUSG00000019854	Reps1	BB161292	RalBP1 associated Eps domain containing protein	protein-coding
mm_89767.1	chr10	100098137	100098154	+	1	NA	3' UTR (NM_013598, exon 10 of 10)	3' UTR (NM_013598, exon 10 of 10)	82324	NM_013598	17311	Mm.45124	NM_013598	ENSMUSG00000019966	Kitl	Clo|Con|Gb|Kitlg|Mgf|SCF|SF|SLF|Sl|blz|contrasted	kit ligand	protein-coding
mm_129643.1	chr15	80565124	80565128	-	1	NA	Intergenic	Intergenic	-4656	NM_001163189	383075	Mm.297626	NM_001163189	ENSMUSG00000050439	Enthd1	Gm1242|Gm86	ENTH domain containing 1	protein-coding
mm_77083.1	chr8	110522132	110522158	-	1	NA	intron (NM_172916, intron 42 of 86)	L2a|LINE|L2	-19789	NR_105058	100861869	Mm.84499	NR_105058		Gm21283	-	predicted gene, 21283	ncRNA
mm_113125.1	chr13	24597466	24597507	+	1	NA	TTS (NR_024599)	TTS (NR_024599)	7281	NR_024599	76024	Mm.440710	NR_024599		Gm11346	5830431A10Rik|AI447617|Gm11347|OTTMUSG00000000601|OTTMUSG00000000602	X-linked lymphocyte-regulated 5 pseudogene	pseudo
mm_62314.1	chr7	100264646	100264667	+	1	NA	non-coding (NR_033563, exon 1 of 1)	non-coding (NR_033563, exon 1 of 1)	112	NR_033563	14777	Mm.57225	NR_033563		Gpx2-ps1	AU041318	glutathione peroxidase 2, pseudogene 1	pseudo
mm_26694.1	chr3	156770883	156770916	+	1	NA	intron (NM_177274, intron 1 of 6)	intron (NM_177274, intron 1 of 6)	209105	NM_001039094	320840	Mm.317293	NM_177274	ENSMUSG00000040037	Negr1	5330422G01Rik|KILON|Ntra	neuronal growth regulator 1	protein-coding
mm_83781.1	chr9	52149352	52149372	-	1	NA	intron (NM_001162921, intron 1 of 5)	intron (NM_001162921, intron 1 of 5)	18749	NM_001162921	244871	Mm.295686	NM_001162921	ENSMUSG00000035164	Zc3h12c	A230108E06|C230027N18Rik|mKIAA1726	zinc finger CCCH type containing 12C	protein-coding
mm_65316.1	chr7	24892194	24892233	-	1	NA	Intergenic	B3|SINE|B2	-5298	NM_007655	12518	Mm.1355	NM_007655	ENSMUSG00000003379	Cd79a	Ig-alpha|Iga|Igalpha|Ly-54|Ly54|mb-1	CD79A antigen (immunoglobulin-associated alpha)	protein-coding
mm_87650.1	chr10	58421642	58421668	+	1	NA	3' UTR (NM_201242, exon 10 of 10)	3' UTR (NM_201242, exon 10 of 10)	-25197	NM_011240	19386	Mm.431695	NM_011240	ENSMUSG00000003226	Ranbp2	A430087B05Rik|AI256741|NUP358	RAN binding protein 2	protein-coding
mm_23113.1	chr3	37613912	37613927	+	1	NA	promoter-TSS (NR_130163)	promoter-TSS (NR_130163)	6	NR_130161	75947	Mm.109620	NR_130161	ENSMUSG00000085677	4930594O21Rik	-	RIKEN cDNA 4930594O21 gene	ncRNA
mm_18983.1	chr2	76853645	76853655	-	1	NA	exon (NM_011652, exon 128 of 313)	exon (NM_011652, exon 128 of 313)	128897	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_123451.1	chr14	65199996	65199999	-	1	NA	3' UTR (NM_021458, exon 7 of 7)	3' UTR (NM_021458, exon 7 of 7)	62466	NM_021458	14365	Mm.214687	NM_021458	ENSMUSG00000007989	Fzd3	AU020229|D930050A07Rik|Fz3	frizzled class receptor 3	protein-coding
mm_98952.1	chr11	98458004	98458009	+	1	NA	Intergenic	CpG	11172	NM_010346	14786	Mm.276702	NM_010346	ENSMUSG00000019312	Grb7	mKIAA4028	growth factor receptor bound protein 7	protein-coding
mm_93981.1	chr10	127351754	127351764	-	1	NA	promoter-TSS (NM_008382)	promoter-TSS (NM_008382)	89	NM_008382	16326	Mm.3510	NM_008382	ENSMUSG00000047492	Inhbe	-	inhibin beta-E	protein-coding
mm_154613.1	chrX	7652928	7652944	+	1	NA	3' UTR (NM_009305, exon 7 of 7)	3' UTR (NM_009305, exon 7 of 7)	-4443	NM_001290624	54630	Mm.232232	NM_175097	ENSMUSG00000031145	Prickle3	Lmo6|Sfc16	prickle planar cell polarity protein 3	protein-coding
mm_118940.1	chr14	27238049	27238063	+	1	NA	promoter-TSS (NM_027871)	promoter-TSS (NM_027871)	46	NM_027871	71704	Mm.248606	NM_027871	ENSMUSG00000021895	Arhgef3	1200004I24Rik|9830169H03Rik|C76747|Xpln	Rho guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_129240.1	chr15	76639899	76639952	-	1	NA	promoter-TSS (NM_183091)	promoter-TSS (NM_183091)	4	NM_183091	72749	Mm.358749	NM_183091	ENSMUSG00000059323	Tonsl	2810439M11Rik|Nfkbil2	tonsoku-like, DNA repair protein	protein-coding
mm_110267.1	chr12	31950214	31950246	-	1	NA	5' UTR (NM_153198, exon 1 of 11)	5' UTR (NM_153198, exon 1 of 11)	305	NM_177993	73389	Mm.390461	NM_153198	ENSMUSG00000002996	Hbp1	1700058O05Rik|BE629963|C330012F01Rik|C86454	high mobility group box transcription factor 1	protein-coding
mm_149126.1	chr19	8990645	8990658	+	1	NA	intron (NR_104460, intron 1 of 6)	intron (NR_104460, intron 1 of 6)	1367	NM_001286518	66395	Mm.203866	NM_009643	ENSMUSG00000069833	Ahnak	DY6	AHNAK nucleoprotein (desmoyokin)	protein-coding
mm_143255.1	chr17	65540786	65540792	-	1	NA	promoter-TSS (NM_001289485)	promoter-TSS (NM_001289485)	-7	NM_001289486	381107	Mm.141275	NM_001008973	ENSMUSG00000045036	Tmem232	E130009J12Rik|Gm940|Tes13-L|Tes13-S	transmembrane protein 232	protein-coding
mm_142075.1	chr17	35701938	35701946	-	1	NA	intron (NM_007584, intron 1 of 17)	intron (NM_007584, intron 1 of 17)	102	NM_001198831	12305	Mm.5021	NM_007584	ENSMUSG00000003534	Ddr1	6030432F18|AI323681|CD167a|Cak|Nep|PTK3A	discoidin domain receptor family, member 1	protein-coding
mm_76654.1	chr8	93195078	93195081	-	1	NA	exon (NM_053200, exon 2 of 14)	exon (NM_053200, exon 2 of 14)	2725	NM_053200	104158	Mm.292803	NM_053200	ENSMUSG00000056973	Ces1d	Ces3|TGH	carboxylesterase 1D	protein-coding
mm_111503.1	chr12	99434415	99434420	-	1	NA	intron (NM_183186, intron 1 of 5)	B4|SINE|B4	15657	NM_183186	71375	Mm.341972	NM_183186	ENSMUSG00000033713	Foxn3	5430426H20Rik|AA589593|AW556347|Ches1|Ches1l|HTLFL1	forkhead box N3	protein-coding
mm_164952.1	chr19	5406797	5406836	+	1	NA	promoter-TSS (NR_015545)	promoter-TSS (NR_015545)	1	NR_027938	74931	Mm.388511	NR_015545	ENSMUSG00000086938	4930481A15Rik	-	RIKEN cDNA 4930481A15 gene	ncRNA
mm_87687.1	chr10	59346324	59346340	+	1	NA	intron (NM_001316370, intron 5 of 13)	Lx7|LINE|L1	23036	NM_001316370	18451	Mm.2212	NM_011030	ENSMUSG00000019916	P4ha1	AL022634|P4ha	procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha 1 polypeptide	protein-coding
mm_53789.1	chr6	146640291	146640293	+	1	NA	Intergenic	RSINE1|SINE|B4	-2287	NM_025315	108098	Mm.26212	NM_025315	ENSMUSG00000030291	Med21	0610007L03Rik|AI449604|D19234|D6Ertd782e|Srb7|Surb7	mediator complex subunit 21	protein-coding
mm_6439.1	chr1	73998413	73998419	-	1	NA	intron (NM_027884, intron 6 of 34)	intron (NM_027884, intron 6 of 34)	126031	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_49363.1	chr6	22936478	22936479	+	1	NA	intron (NM_001081306, intron 2 of 29)	intron (NM_001081306, intron 2 of 29)	60976	NM_001081306	19283	Mm.41639	NM_011219	ENSMUSG00000068748	Ptprz1	AI850339|DSD-1-PG|PTPbeta|PTPzeta|Ptprz|Ptpz|R-PTP-zeta|RPTPz|Rptpbeta	protein tyrosine phosphatase, receptor type Z, polypeptide 1	protein-coding
mm_141924.1	chr17	35002579	35002590	-	1	NA	intron (NM_011690, intron 2 of 29)	intron (NM_011690, intron 2 of 29)	1677	NM_011690	22321	Mm.28420	NM_011690	ENSMUSG00000007029	Vars	Bat6|D17H6S56E|G7a|Vars2	valyl-tRNA synthetase	protein-coding
mm_107793.1	chr12	62065955	62065957	+	1	NA	Intergenic	Intergenic	542789	NM_001310586	238205	Mm.28802	NM_178714	ENSMUSG00000035653	Lrfn5	AI427653|AI604817|C130061B21|mKIAA4208	leucine rich repeat and fibronectin type III domain containing 5	protein-coding
mm_135127.1	chr16	35843850	35843861	-	1	NA	intron (NM_001039530, intron 12 of 16)	RLTR17B_Mm|LTR|ERVK	27527	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_79174.1	chr9	47852844	47852892	+	1	NA	3' UTR (NM_018770, exon 10 of 10)	3' UTR (NM_018770, exon 10 of 10)	-34660	NR_046048	100038460	Mm.447649	NR_046048		Gm10677	ENSMUSG00000074363	predicted gene 10677	ncRNA
mm_62165.1	chr7	97211503	97211513	+	1	NA	intron (NM_001162477, intron 1 of 9)	intron (NM_001162477, intron 1 of 9)	114456	NM_001177412	244144	Mm.297541	NM_001177412	ENSMUSG00000035713	Usp35	Gm1088|Gm493	ubiquitin specific peptidase 35	protein-coding
mm_68248.1	chr7	105565501	105565523	-	1	NA	intron (NM_001310600, intron 8 of 12)	intron (NM_001310600, intron 8 of 12)	3265	NM_001310600	11785	Mm.38469	NM_009685	ENSMUSG00000037032	Apbb1	Fe65|Rir	amyloid beta (A4) precursor protein-binding, family B, member 1	protein-coding
mm_34128.1	chr4	139268706	139268712	+	1	NA	intron (NM_001037761, intron 4 of 9)	intron (NM_001037761, intron 4 of 9)	41991	NM_145384	212555	Mm.45131	NM_145384	ENSMUSG00000028744	Pqlc2	BC019216	PQ loop repeat containing 2	protein-coding
mm_95028.1	chr11	32024849	32024866	+	1	NA	intron (NM_001290680, intron 3 of 4)	intron (NM_001290680, intron 3 of 4)	23580	NM_001290681	18197	Mm.3304	NM_008741	ENSMUSG00000020297	Nsg2	-	neuron specific gene family member 2	protein-coding
mm_96979.1	chr11	70655089	70655105	+	1	NA	promoter-TSS (NM_011072)	promoter-TSS (NM_011072)	-447	NM_011072	18643	Mm.2647	NM_011072	ENSMUSG00000018293	Pfn1	Pfn	profilin 1	protein-coding
mm_40308.1	chr5	43818940	43818954	+	1	NA	promoter-TSS (NM_009763)	promoter-TSS (NM_009763)	54	NM_009763	12182	Mm.246332	NM_009763	ENSMUSG00000029082	Bst1	114/A10|A530073F09|BP-3|Bp3|Bsta1|CD157|Ly65	bone marrow stromal cell antigen 1	protein-coding
mm_59904.1	chr7	30321778	30321822	+	1	NA	3' UTR (NM_001033140, exon 1 of 1)	3' UTR (NM_001033140, exon 1 of 1)	575	NM_001033140	68332	Mm.6844	NM_001033140	ENSMUSG00000074211	Sdhaf1	0610010E21Rik|AI430885|AW490662|Lyrm8	succinate dehydrogenase complex assembly factor 1	protein-coding
mm_55961.1	chr6	85451956	85451990	-	1	NA	promoter-TSS (NM_001163427)	promoter-TSS (NM_001163427)	-3	NR_028081	73327	Mm.379221	NM_028505	ENSMUSG00000030008	Pradc1	1700040I03Rik|Pap21	protease-associated domain containing 1	protein-coding
mm_81212.1	chr9	107580747	107580833	+	1	NA	promoter-TSS (NM_178020)	promoter-TSS (NM_178020)	121	NM_019750	56441	Mm.10305	NM_019750	ENSMUSG00000079334	Nat6	AI225910|Fus2	N-acetyltransferase 6	protein-coding
mm_4751.1	chr1	182255424	182255451	+	1	NA	Intergenic	Intergenic	27322	NM_007853	13244	Mm.29648	NM_007853	ENSMUSG00000038633	Degs1	AA536663|Degs|Des1|Mdes	delta(4)-desaturase, sphingolipid 1	protein-coding
mm_57825.1	chr6	129463087	129463117	-	1	NA	exon (NM_020008, exon 6 of 6)	exon (NM_020008, exon 6 of 6)	9677	NM_001309637	56644	Mm.239516	NM_020008	ENSMUSG00000079293	Clec7a	BGR|Clecsf12|beta-GR	C-type lectin domain family 7, member a	protein-coding
mm_8838.1	chr1	162675488	162675542	-	1	NA	intron (NM_001081290, intron 34 of 34)	intron (NM_001081290, intron 34 of 34)	-17296	NM_001177581	100038657	Mm.416999	NM_001177581	ENSMUSG00000091060	7420461P10Rik	ENSMUSG00000073516	RIKEN cDNA 7420461P10 gene	protein-coding
mm_50563.1	chr6	49047958	49047968	+	1	NA	exon (NM_053110, exon 6 of 11)	exon (NM_053110, exon 6 of 11)	11445	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_5256.1	chr1	16656844	16656897	-	1	NA	promoter-TSS (NM_026456)	promoter-TSS (NM_026456)	-5	NM_026456	67923	Mm.289248	NM_026456	ENSMUSG00000079658	Eloc	2610043E24Rik|2610301I15Rik|AA407206|AI987979|AW049146|Tceb1	elongin C	protein-coding
mm_111384.1	chr12	87443801	87443850	-	1	NA	promoter-TSS (NM_001102565)	promoter-TSS (NM_001102565)	14	NM_001102565	211064	Mm.486235	NM_001102565	ENSMUSG00000079036	Alkbh1	2700073G19Rik|Abh|Alkbh|alkB|hABH	alkB homolog 1, histone H2A dioxygenase	protein-coding
mm_11517.1	chr2	32606947	32606973	+	1	NA	promoter-TSS (NM_016973)	promoter-TSS (NM_016973)	-25	NM_001289547	50935	Mm.88831	NM_016973	ENSMUSG00000026811	St6galnac6	ST6GalNAcVI|Siat7f	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 6	protein-coding
mm_118187.1	chr13	107565323	107565336	-	1	NA	Intergenic	RMER19A|LTR|ERVK	95507	NR_045084	105120	Mm.417700	NR_045083		AI197445	-	expressed sequence AI197445	ncRNA
mm_56890.1	chr6	119086661	119086672	-	1	NA	intron (NM_001255998, intron 1 of 47)	intron (NM_001255998, intron 1 of 47)	21829	NM_001159534	12288	Mm.41628	NM_009781	ENSMUSG00000051331	Cacna1c	Cav1.2|Cchl1a1|D930026N18Rik|MBC|MELC-CC	calcium channel, voltage-dependent, L type, alpha 1C subunit	protein-coding
mm_498.1	chr1	36983992	36984006	+	1	NA	Intergenic	RMER10B|LTR|ERVL	-44472	NM_018872	56030	Mm.186943	NM_018872	ENSMUSG00000026116	Tmem131	2610524E03Rik|CC28|D1Bwg0491e|Neg|RW1|YR-23|mKIAA0257	transmembrane protein 131	protein-coding
mm_65554.1	chr7	27133468	27133495	-	1	NA	3' UTR (NM_007817, exon 10 of 10)	3' UTR (NM_007817, exon 10 of 10)	13526	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_124049.1	chr14	77856967	77856991	-	1	NA	exon (NM_025384, exon 2 of 6)	exon (NM_025384, exon 2 of 6)	17938	NM_025384	66148	Mm.248046	NM_025384	ENSMUSG00000022013	Dnajc15	1110003P16Rik|Dnajd1	DnaJ heat shock protein family (Hsp40) member C15	protein-coding
mm_103436.1	chr11	75906689	75906714	-	1	NA	intron (NM_029548, intron 2 of 7)	intron (NM_029548, intron 2 of 7)	4358	NM_029548	380714	Mm.425697	NM_029548	ENSMUSG00000020847	Rph3al	Gm1753|Noc2	rabphilin 3A-like (without C2 domains)	protein-coding
mm_28725.1	chr3	95687847	95687895	-	1	NA	promoter-TSS (NM_144899)	promoter-TSS (NM_144899)	46	NM_144899	229595	Mm.490574	NM_144899	ENSMUSG00000015850	Adamtsl4	ADAMTSL-4|Tsrc1	ADAMTS-like 4	protein-coding
mm_33132.1	chr4	124937078	124937108	+	1	NA	promoter-TSS (NM_177573)	promoter-TSS (NM_177573)	45	NM_177573	194268	Mm.266907	NM_177573		9930104L06Rik	-	RIKEN cDNA 9930104L06 gene	protein-coding
mm_3932.1	chr1	163762126	163762126	+	1	NA	Intergenic	Intergenic	-17457	NM_001305643	16579	Mm.4651	NM_010629	ENSMUSG00000026585	Kifap3	KAP-3|KAP3|SMAP	kinesin-associated protein 3	protein-coding
mm_43237.1	chr5	130029278	130029340	+	1	NA	promoter-TSS (NM_007761)	promoter-TSS (NM_007761)	3	NM_007761	12909	Mm.18072	NM_007761	ENSMUSG00000025532	Crcp	AL022669	calcitonin gene-related peptide-receptor component protein	protein-coding
mm_16079.1	chr2	168231262	168231267	+	1	NA	promoter-TSS (NM_010072)	promoter-TSS (NM_010072)	642	NM_001160330	69372	Mm.482182	NM_001160330	ENSMUSG00000074576	Mocs3	1700020H17Rik|Uba4	molybdenum cofactor synthesis 3	protein-coding
mm_75231.1	chr8	39625089	39625130	-	1	NA	intron (NM_001113326, intron 3 of 9)	intron (NM_001113326, intron 3 of 9)	17569	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_116718.1	chr13	51644895	51644899	-	1	NA	promoter-TSS (NM_025415)	promoter-TSS (NM_025415)	-335	NM_025415	66197	Mm.222228	NM_025415	ENSMUSG00000062248	Cks2	1110038L14Rik|CKSHS2	CDC28 protein kinase regulatory subunit 2	protein-coding
mm_68334.1	chr7	106504413	106504424	-	1	NA	Intergenic	Intergenic	-63345	NR_003967	209380	Mm.461779	NM_001001318		Gm4759	EG209380	GTPase, very large interferon inducible 1 pseudogene	pseudo
mm_102157.1	chr11	53724349	53724357	-	1	NA	3' UTR (NM_010558, exon 4 of 4)	3' UTR (NM_010558, exon 4 of 4)	3559	NM_010558	16191	Mm.4461	NM_010558	ENSMUSG00000036117	Il5	Il-5	interleukin 5	protein-coding
mm_125010.1	chr15	25622526	25622558	+	1	NA	promoter-TSS (NM_019472)	promoter-TSS (NM_019472)	-8	NM_019472	17909	Mm.60590	NM_019472	ENSMUSG00000022272	Myo10	AW048724|D15Ertd600e|mKIAA0799|myosin-X	myosin X	protein-coding
mm_165210.1	chr2	34976659	34976674	+	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	-14894	NM_001326601	22029	Mm.239514	NM_009421	ENSMUSG00000026875	Traf1	4732496E14Rik	TNF receptor-associated factor 1	protein-coding
mm_126922.1	chr15	91672233	91672250	+	1	NA	promoter-TSS (NM_025730)	promoter-TSS (NM_025730)	-983	NM_025730	66725	Mm.37558	NM_025730	ENSMUSG00000036273	Lrrk2	4921513O20Rik|9330188B09Rik|AW561911|D630001M17Rik|Gm927|cI-46	leucine-rich repeat kinase 2	protein-coding
mm_149064.1	chr19	8840566	8840577	+	1	NA	promoter-TSS (NM_001290823)	promoter-TSS (NM_001290823)	68	NM_001290823	14705	Mm.345134	NM_008144	ENSMUSG00000071657	Bscl2	2900097C17Rik|AI046355|Gng3lg	Berardinelli-Seip congenital lipodystrophy 2 (seipin)	protein-coding
mm_157749.1	chrX	73458991	73459044	-	1	NA	promoter-TSS (NM_028633)	promoter-TSS (NM_028633)	12	NM_028633	73738	Mm.264899	NM_028633	ENSMUSG00000031371	Haus7	1110020L19Rik|Uchl5ip|Uip1	HAUS augmin-like complex, subunit 7	protein-coding
mm_161074.1	chr12	80518379	80518379	+	1	NA	promoter-TSS (NM_001081421)	promoter-TSS (NM_001081421)	-611	NM_001081421	108760	Mm.308296	NM_001081421	ENSMUSG00000021130	Galnt16	5730405L21Rik|AI415388|Galntl1|mpp-GalNAc-T16	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 16	protein-coding
mm_171976.1	chr5	89209160	89209165	-	1	NA	intron (NM_001197147, intron 18 of 25)	ERVB7_1-LTR_MM|LTR|ERVK	248736	NM_008096	14473	Mm.196595	NM_008096	ENSMUSG00000035540	Gc	DBP|VDB	group specific component	protein-coding
mm_146574.1	chr18	7004718	7004733	-	1	NA	promoter-TSS (NM_177595)	promoter-TSS (NM_177595)	54	NM_177595	210719	Mm.257186	NM_177595	ENSMUSG00000061013	Mkx	9430023B20Rik|Irxl1	mohawk homeobox	protein-coding
mm_126453.1	chr15	80897194	80897198	+	1	NA	intron (NM_144812, intron 14 of 24)	intron (NM_144812, intron 14 of 24)	-42843	NR_039573	100628612		NR_039573	ENSMUSG00000092868	Mir5113	mir-5113|mmu-mir-5113|mu-mir-5113	microRNA 5113	ncRNA
mm_76243.1	chr8	83588504	83588527	-	1	NA	intron (NM_134118, intron 1 of 12)	intron (NM_134118, intron 1 of 12)	5976	NM_027179	106529	Mm.352239	NM_027179	ENSMUSG00000031708	Tecr	2410016D23Rik|A230102P12Rik|AI173355|D17Ertd178e|Gpsn2|SC2	trans-2,3-enoyl-CoA reductase	protein-coding
mm_2220.1	chr1	90005191	90005194	+	1	NA	intron (NM_139152, intron 1 of 5)	intron (NM_139152, intron 1 of 5)	9385	NM_139152	208372	Mm.215164	NM_139152	ENSMUSG00000067081	Asb18	Asb-18	ankyrin repeat and SOCS box-containing 18	protein-coding
mm_88417.1	chr10	77166620	77166646	+	1	NA	promoter-TSS (NM_009929)	promoter-TSS (NM_009929)	-103	NM_009929	12822	Mm.4352	NM_009929	ENSMUSG00000001435	Col18a1	-	collagen, type XVIII, alpha 1	protein-coding
mm_88040.1	chr10	67537862	67537877	+	1	NA	promoter-TSS (NM_010118)	promoter-TSS (NM_010118)	0	NM_010118	13654	Mm.290421	NM_010118	ENSMUSG00000037868	Egr2	Egr-2|Krox-20|Krox20|NGF1-B|Zfp-25|Zfp-6	early growth response 2	protein-coding
mm_155550.1	chrX	74424633	74424671	+	1	NA	promoter-TSS (NM_001161421)	promoter-TSS (NM_001161421)	40	NM_001136067	16151	Mm.12967	NM_010547	ENSMUSG00000004221	Ikbkg	1110037D23Rik|AI848108|AI851264|AW124339|IKK[g]|NEMO	inhibitor of kappaB kinase gamma	protein-coding
mm_25182.1	chr3	103321899	103321903	+	1	NA	intron (NM_001079830, intron 5 of 18)	B1_Mur4|SINE|Alu	42608	NM_001079830	94093	Mm.195036	NM_053170	ENSMUSG00000033014	Trim33	8030451N04Rik|AI413936|Ecto|Tif1g	tripartite motif-containing 33	protein-coding
mm_100804.1	chr11	5061994	5062034	-	1	NA	intron (NM_144560, intron 6 of 6)	CpG	3313	NM_144560	78926	Mm.44591	NM_030228	ENSMUSG00000034201	Gas2l1	4930500E24Rik|D0Jmb1|Gar22|TU-71.1	growth arrest-specific 2 like 1	protein-coding
mm_49871.1	chr6	38562264	38562297	+	1	NA	intron (NM_001331223, intron 2 of 12)	B1_Mus1|SINE|Alu	6557	NM_001331223	192196	Mm.276133	NM_138680	ENSMUSG00000029823	Luc7l2	4930471C18Rik|AA522013|AU015269|CGI59|Cgi74	LUC7-like 2 (S. cerevisiae)	protein-coding
mm_169312.1	chr14	104715980	104715985	-	1	NA	intron (NR_015593, intron 1 of 5)	LSU-rRNA_Hsa|rRNA|rRNA	76835	NR_015593	320249	Mm.320725	NR_015593		D130009I18Rik	-	RIKEN cDNA D130009I18 gene	ncRNA
mm_132800.1	chr16	45094119	45094137	+	1	NA	promoter-TSS (NM_026439)	promoter-TSS (NM_026439)	75	NM_026439	67896	Mm.181074	NM_026439	ENSMUSG00000022665	Ccdc80	2610001E17Rik|DRO1|Ssg1|Urb	coiled-coil domain containing 80	protein-coding
mm_141107.1	chr17	26021854	26021866	-	1	NA	promoter-TSS (NM_153140)	promoter-TSS (NM_153140)	0	NM_153140	215445	Mm.41191	NM_153140	ENSMUSG00000037098	Rab11fip3	Cart1|D030060O14Rik|Rab11-FIP3|mKIAA0665	RAB11 family interacting protein 3 (class II)	protein-coding
mm_12369.1	chr2	69821915	69821934	+	1	NA	promoter-TSS (NM_177784)	promoter-TSS (NM_177784)	-446	NM_177784	277396	Mm.138073	NM_177784	ENSMUSG00000042155	Klhl23	C130068N17Rik	kelch-like 23	protein-coding
mm_35381.1	chr4	33246457	33246484	-	1	NA	exon (NM_001033225, exon 2 of 2)	exon (NM_001033225, exon 2 of 2)	2317	NM_001033225	108767	Mm.27769	NM_001033225	ENSMUSG00000040128	Pnrc1	5730463C12Rik|B4-2|PRR2|Prol2	proline-rich nuclear receptor coactivator 1	protein-coding
mm_170160.1	chr17	51796243	51796248	-	1	NA	intron (NM_009122, intron 5 of 10)	intron (NM_009122, intron 5 of 10)	15809	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_129524.1	chr15	79254738	79254764	-	1	NA	promoter-TSS (NM_020516)	promoter-TSS (NM_020516)	-3	NM_020516	57274	Mm.441697	NM_020516	ENSMUSG00000032988	Slc16a8	Mct3	solute carrier family 16 (monocarboxylic acid transporters), member 8	protein-coding
mm_122487.1	chr14	46390477	46390491	-	1	NA	5' UTR (NM_007554, exon 1 of 4)	5' UTR (NM_007554, exon 1 of 4)	185	NM_001316360	12159	Mm.6813	NM_007554	ENSMUSG00000021835	Bmp4	Bmp-4|Bmp2b|Bmp2b-1|Bmp2b1	bone morphogenetic protein 4	protein-coding
mm_156915.1	chrX	169082741	169082758	+	1	NA	intron (NR_109847, intron 1 of 14)	intron (NR_109847, intron 1 of 14)	-30129	NM_001287530	11856	Mm.441810	NM_009707	ENSMUSG00000031355	Arhgap6	AI504284|RhoGAPX-1	Rho GTPase activating protein 6	protein-coding
mm_108171.1	chr12	76404405	76404426	+	1	NA	promoter-TSS (NM_008301)	promoter-TSS (NM_008301)	45	NM_008301	15512	Mm.296181	NM_008301	ENSMUSG00000059970	Hspa2	70kDa|HSP70.2|HSP70A2|Hsp70-2	heat shock protein 2	protein-coding
mm_25570.1	chr3	116661762	116661775	+	1	NA	intron (NM_008246, intron 1 of 11)	intron (NM_008246, intron 1 of 11)	909	NM_008246	15247	Mm.280077	NM_008246	ENSMUSG00000089911	Mfsd14a	Hiat1	major facilitator superfamily domain containing 14A	protein-coding
mm_129710.1	chr15	81858263	81858280	-	1	NA	promoter-TSS (NM_020507)	promoter-TSS (NM_020507)	55	NM_020507	57259	Mm.323595	NM_020507	ENSMUSG00000048546	Tob2	2900090N22Rik|4930545K18Rik|AV071822|mKIAA1663	transducer of ERBB2, 2	protein-coding
mm_46359.1	chr5	103211237	103211245	-	1	NA	promoter-TSS (NM_001081567)	promoter-TSS (NM_001081567)	93	NM_001081567	26414	Mm.39253	NM_009158	ENSMUSG00000046709	Mapk10	C230008H04Rik|JNK3|JNK3B1|JNK3B2|SAPK(beta)|Serk2|p493F12|p54bSAPK	mitogen-activated protein kinase 10	protein-coding
mm_160870.1	chr11	67238001	67238001	+	1	NA	intron (NM_010855, intron 1 of 39)	intron (NM_010855, intron 1 of 39)	189	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_146043.1	chr18	69593211	69593221	+	1	NA	intron (NM_013685, intron 8 of 19)	intron (NM_013685, intron 8 of 19)	247495	NM_001083967	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding
mm_171296.1	chr3	91127028	91127028	+	1	NA	Intergenic	L1Md_T|LINE|L1	-36223	NM_001101461	229550	Mm.98335	NM_001101461	ENSMUSG00000091175	9130204L05Rik	Gm127	RIKEN cDNA 9130204L05 gene	protein-coding
mm_80151.1	chr9	70928300	70928307	+	1	NA	intron (NM_001324473, intron 1 of 8)	intron (NM_001324473, intron 1 of 8)	6505	NM_008280	15450	Mm.390187	NM_008280	ENSMUSG00000032207	Lipc	AI256194|HL|Hpl	lipase, hepatic	protein-coding
mm_44321.1	chr5	9725254	9725265	-	1	NA	promoter-TSS (NM_181850)	promoter-TSS (NM_181850)	93	NM_181850	108069	Mm.318966	NM_181850	ENSMUSG00000003974	Grm3	0710001G23Rik|Gprc1c|mGlu3|mGluR3	glutamate receptor, metabotropic 3	protein-coding
mm_120196.1	chr14	61607416	61607426	+	1	NA	promoter-TSS (NM_001039105)	promoter-TSS (NM_001039105)	-36	NM_206974	328424	Mm.224464	NM_206974	ENSMUSG00000046168	Kcnrg	Clld4|E030012H22Rik|Gm745	potassium channel regulator	protein-coding
mm_120583.1	chr14	69775109	69775119	+	1	NA	exon (NM_020275, exon 4 of 8)	exon (NM_020275, exon 4 of 8)	7642	NM_020275	21933	Mm.193430	NM_020275	ENSMUSG00000022074	Tnfrsf10b	DR5|KILLER|Ly98|MK|TRAILR2|TRICK2A|TRICK2B|TRICKB	tumor necrosis factor receptor superfamily, member 10b	protein-coding
mm_23805.1	chr3	79885107	79885119	+	1	NA	promoter-TSS (NM_133187)	promoter-TSS (NM_133187)	-817	NM_133187	68659	Mm.427274	NM_133187	ENSMUSG00000027955	Fam198b	1110032E23Rik|2210419I08Rik|AV011458|Ened	family with sequence similarity 198, member B	protein-coding
mm_1590.1	chr1	74332650	74332692	+	1	NA	promoter-TSS (NM_019999)	promoter-TSS (NM_019999)	61	NM_019999	56695	Mm.384726	NM_019999	ENSMUSG00000026179	Pnkd	2210013N15Rik|2810403H05Rik|AI854243|Brp17|MNCb-5687|MR-1|Tahccp2	paroxysmal nonkinesiogenic dyskinesia	protein-coding
mm_32883.1	chr4	118961692	118961698	+	1	NA	promoter-TSS (NM_133892)	promoter-TSS (NM_133892)	-272	NM_133892	100470	Mm.26698	NM_133892	ENSMUSG00000024903	Lao1	AW990848	L-amino acid oxidase 1	protein-coding
mm_143687.1	chr17	80173809	80173815	-	1	NA	intron (NM_176963, intron 4 of 6)	RLTR31C_MM|LTR|ERVK	33493	NM_001195486	225027	Mm.292016	NM_146083	ENSMUSG00000024097	Srsf7	35kDa|9430065L19Rik|9G8|NX-96|Sfrs7	serine/arginine-rich splicing factor 7	protein-coding
mm_53971.1	chr6	6215351	6215362	-	1	NA	intron (NM_015829, intron 1 of 17)	intron (NM_015829, intron 1 of 17)	1817	NM_015829	50799	Mm.24513	NM_015829	ENSMUSG00000015112	Slc25a13	AI785475|Ctrn	solute carrier family 25 (mitochondrial carrier, adenine nucleotide translocator), member 13	protein-coding
mm_169406.1	chr14	51483161	51483178	-	1	NA	Intergenic	ERVB4_3-LTR_MM|LTR|ERVK	31207	NM_009486	22301	Mm.482572	NM_009486	ENSMUSG00000070448	Vmn2r89	V2r10|V2r11	vomeronasal 2, receptor 89	protein-coding
mm_139193.1	chr17	47611571	47611619	+	1	NA	promoter-TSS (NM_020048)	promoter-TSS (NM_020048)	-1	NM_020048	56771	Mm.59393	NM_020048	ENSMUSG00000092558	Med20	1110011O05Rik|2410115I17Rik|AU018348|Trfp	mediator complex subunit 20	protein-coding
mm_15722.1	chr2	164078108	164078146	+	1	NA	intron (NM_021420, intron 1 of 10)	intron (NM_021420, intron 1 of 10)	3949	NM_021420	58231	Mm.234472	NM_021420	ENSMUSG00000018209	Stk4	AI447339|AU020804|Kas-2|Mst1|Ysk3	serine/threonine kinase 4	protein-coding
mm_37071.1	chr4	116151360	116151366	-	1	NA	promoter-TSS (NM_001290658)	promoter-TSS (NM_001290658)	-68	NM_001290658	68273	Mm.196045	NM_026651	ENSMUSG00000028700	Pomgnt1	0610016I07Rik|4930467B06Rik	protein O-linked mannose beta 1,2-N-acetylglucosaminyltransferase	protein-coding
mm_2334.1	chr1	92831769	92831789	+	1	NA	promoter-TSS (NM_016696)	promoter-TSS (NM_016696)	93	NM_016696	14733	Mm.297976	NM_016696	ENSMUSG00000034220	Gpc1	AI462976	glypican 1	protein-coding
mm_134599.1	chr16	20621232	20621252	-	1	NA	promoter-TSS (NM_028420)	promoter-TSS (NM_028420)	36	NM_028420	73047	Mm.425977	NM_028420	ENSMUSG00000051146	Camk2n2	2900075A18Rik	calcium/calmodulin-dependent protein kinase II inhibitor 2	protein-coding
mm_109337.1	chr12	109583662	109583678	+	1	NA	Intergenic	Intergenic	-2119	NR_029765	723843		NR_029765	ENSMUSG00000065526	Mir337	Mirn337|mir-337|mmu-mir-337	microRNA 337	ncRNA
mm_108384.1	chr12	80885841	80885853	+	1	NA	Intergenic	Intergenic	38600	NR_033786	67340	Mm.386790	NR_033786	ENSMUSG00000101912	1700052I22Rik	-	RIKEN cDNA 1700052I22 gene	ncRNA
mm_163346.1	chr12	16853561	16853574	+	1	NA	Intergenic	Intergenic	-41411	NM_009072	19878	Mm.276024	NM_009072	ENSMUSG00000020580	Rock2	B230113H15Rik|ROKalpha|Rho-kinase|Rock-II|Rock2m|mKIAA0619	Rho-associated coiled-coil containing protein kinase 2	protein-coding
mm_117231.1	chr13	64272620	64272623	-	1	NA	intron (NM_172587, intron 1 of 13)	intron (NM_172587, intron 1 of 13)	2367	NM_172587	218294	Mm.25335	NM_172587	ENSMUSG00000033102	Cdc14b	2810432N10Rik|A530086E13Rik|AA472821|CDC14B3|Cdc14B1	CDC14 cell division cycle 14B	protein-coding
mm_164198.1	chr15	79739632	79739640	+	1	NA	intron (NM_001205346, intron 2 of 17)	intron (NM_001205346, intron 2 of 17)	2900	NM_194342	223697	Mm.202715	NM_194342	ENSMUSG00000042524	Sun2	B230369L08Rik|C030011B15|Unc84b	Sad1 and UNC84 domain containing 2	protein-coding
mm_67355.1	chr7	79836361	79836389	-	1	NA	exon (NM_008486, exon 10 of 20)	exon (NM_008486, exon 10 of 20)	5977	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_20715.1	chr2	134644080	134644109	-	1	NA	promoter-TSS (NM_029148)	promoter-TSS (NM_029148)	27	NM_029148	52837	Mm.264096	NM_029148	ENSMUSG00000034723	Tmx4	2810417D04Rik|4930500L08Rik|AI843224|AW046784|D2Bwg1356e|Txndc13|mKIAA1162	thioredoxin-related transmembrane protein 4	protein-coding
mm_118174.1	chr13	106936087	106936087	-	1	NA	intron (NM_029665, intron 1 of 29)	intron (NM_029665, intron 1 of 29)	828	NM_029665	76582	Mm.132208	NM_029665	ENSMUSG00000042590	Ipo11	1700081H05Rik|2510001A17Rik|AI314624|AW555235|E330021B14Rik|Ranbp11	importin 11	protein-coding
mm_61646.1	chr7	80388025	80388055	+	1	NA	promoter-TSS (NM_010194)	promoter-TSS (NM_010194)	-94	NM_010194	14159	Mm.48757	NM_010194	ENSMUSG00000053158	Fes	AI586313|BB137047|FPS|c-fes	feline sarcoma oncogene	protein-coding
mm_7770.1	chr1	131200182	131200188	-	1	NA	promoter-TSS (NM_001311094)	promoter-TSS (NM_001311094)	0	NM_001311094	54354	Mm.248291	NM_018750	ENSMUSG00000026430	Rassf5	1300019G20Rik|Maxp1|Nore1|Nore1A|Nore1B|Rapl	Ras association (RalGDS/AF-6) domain family member 5	protein-coding
mm_60640.1	chr7	44840196	44840209	+	1	NA	TTS (NM_001042655)	TTS (NM_001042655)	3914	NM_010215	14204	Mm.2565	NM_010215	ENSMUSG00000074141	Il4i1	Fig1|Fig1-ps|LAAO|LAO	interleukin 4 induced 1	protein-coding
mm_33952.1	chr4	137453254	137453316	+	1	NA	promoter-TSS (NM_027063)	promoter-TSS (NM_027063)	-11	NM_027063	69380	Mm.272519	NM_027063	ENSMUSG00000041399	1700013G24Rik	AI507018	RIKEN cDNA 1700013G24 gene	protein-coding
mm_79123.1	chr9	46913558	46913573	+	1	NA	promoter-TSS (NR_015605)	promoter-TSS (NR_015605)	-38	NR_015605	73040	Mm.265384	NR_015605	ENSMUSG00000099696	2900052N01Rik	AU067665	RIKEN cDNA 2900052N01 gene	ncRNA
mm_102295.1	chr11	55419860	55419874	-	1	NA	5' UTR (NM_009242, exon 1 of 10)	5' UTR (NM_009242, exon 1 of 10)	213	NM_009242	20692	Mm.291442	NM_009242	ENSMUSG00000018593	Sparc	BM-40|ON	secreted acidic cysteine rich glycoprotein	protein-coding
mm_143597.1	chr17	75505084	75505094	-	1	NA	intron (NM_001166493, intron 9 of 16)	intron (NM_001166493, intron 9 of 16)	39551	NM_207246	240168	Mm.329203	NM_207246	ENSMUSG00000071042	Rasgrp3	BC066069|Gm327	RAS, guanyl releasing protein 3	protein-coding
mm_5625.1	chr1	40382493	40382497	-	1	NA	Intergenic	Intergenic	-47075	NM_001294171	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_131447.1	chr16	16303019	16303029	+	1	NA	promoter-TSS (NM_198246)	promoter-TSS (NM_198246)	59	NM_198246	70120	Mm.37486	NM_198246	ENSMUSG00000022792	Yars2	2210023C10Rik|tyrRS	tyrosyl-tRNA synthetase 2 (mitochondrial)	protein-coding
mm_159452.1	chr3	144819486	144819486	-	1	NA	promoter-TSS (NM_030601)	promoter-TSS (NM_030601)	8	NM_030601	80797	Mm.20897	NM_030601	ENSMUSG00000028262	Clca3a2	Clca2	chloride channel accessory 3A2	protein-coding
mm_156665.1	chrX	158248774	158248774	+	1	NA	Intergenic	L1_Mus3|LINE|L1	-205577	NM_177751	245684	Mm.197074	NM_177751	ENSMUSG00000025658	Cnksr2	Cnk2|Ksr2	connector enhancer of kinase suppressor of Ras 2	protein-coding
mm_93475.1	chr10	111516963	111516982	-	1	NA	Intergenic	Intergenic	10686	NM_009344	21664	Mm.3117	NM_009344	ENSMUSG00000020205	Phlda1	DT1P1B11|TDAG51|Tdag	pleckstrin homology like domain, family A, member 1	protein-coding
mm_131666.1	chr16	20629985	20630006	+	1	NA	5' UTR (NM_139293, exon 1 of 19)	5' UTR (NM_139293, exon 1 of 19)	144	NM_139293	107522	Mm.263319	NM_025462	ENSMUSG00000022842	Ece2	1810009K13Rik|6330509A19Rik|9630025D12Rik|BB127715|Ece-2	endothelin converting enzyme 2	protein-coding
mm_42874.1	chr5	122240933	122241013	+	1	NA	non-coding (NR_104441, exon 13 of 13)	non-coding (NR_104441, exon 13 of 13)	23487	NR_104441	654470	Mm.28804	NM_001039153	ENSMUSG00000038593	Tctn1	G730031O11Rik|Tect1	tectonic family member 1	protein-coding
mm_124779.1	chr15	7216339	7216339	+	1	NA	intron (NM_001289496, intron 20 of 22)	U2|snRNA|snRNA	75797	NM_013584	16880	Mm.149720	NM_013584	ENSMUSG00000054263	Lifr	A230075M04Rik|AW061234|LIF	leukemia inhibitory factor receptor	protein-coding
mm_34382.1	chr4	144912686	144912702	+	1	NA	intron (NM_011303, intron 1 of 5)	(GA)n|Simple_repeat|Simple_repeat	19557	NM_011303	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding
mm_76239.1	chr8	83577962	83577967	-	1	NA	intron (NM_134118, intron 1 of 12)	ID_B1|SINE|B4	11206	NM_025843	66916	Mm.29683	NM_025843	ENSMUSG00000033938	Ndufb7	1110002H15Rik	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 7	protein-coding
mm_56002.1	chr6	86487937	86487948	-	1	NA	non-coding (NR_040292, exon 1 of 2)	non-coding (NR_040292, exon 1 of 2)	285	NR_040293	381792	Mm.333223	NR_040292	ENSMUSG00000101655	2310040G24Rik	-	RIKEN cDNA 2310040G24 gene	ncRNA
mm_63131.1	chr7	123001873	123001930	+	1	NA	exon (NM_011247, exon 18 of 18)	exon (NM_011247, exon 18 of 18)	31337	NM_175023	19647	Mm.4480	NM_011247	ENSMUSG00000030779	Rbbp6	4933422O15Rik|AI316869|BB233631|C030034J04Rik|C77662|P2P-R|PACT	retinoblastoma binding protein 6	protein-coding
mm_154838.1	chrX	19167484	19167494	+	1	NA	Intergenic	Intergenic	-20518	NR_029807	723828		NR_029807	ENSMUSG00000065471	Mir222	Mirn222|mir-222|mmu-mir-222	microRNA 222	ncRNA
mm_7347.1	chr1	105990244	105990275	-	1	NA	promoter-TSS (NM_001122675)	promoter-TSS (NM_001122675)	-147	NM_001122676	227449	Mm.210188	NM_001122675	ENSMUSG00000038866	Zcchc2	9930114B20Rik|AW212015	zinc finger, CCHC domain containing 2	protein-coding
mm_20266.1	chr2	126675462	126675509	-	1	NA	non-coding (NR_073183, exon 1 of 6)	non-coding (NR_073183, exon 1 of 6)	107	NM_001271469	14391	Mm.293266	NM_010249	ENSMUSG00000027361	Gabpb1	BABPB2|E4TF1|E4TF1-47|E4TF1-53|E4Tf1B|GABPB|GABPB-1|GABPB-2|GABPB1-1|GABPB1-2|NRF2B1|NRF2B2	GA repeat binding protein, beta 1	protein-coding
mm_163166.1	chr11	86600043	86600094	+	1	NA	intron (NM_029478, intron 10 of 11)	intron (NM_029478, intron 10 of 11)	-15910	NR_029738	387140		NR_029738	ENSMUSG00000065455	Mir21a	Mir21|Mirn21|mmu-mir-21|mmu-mir-21a	microRNA 21a	ncRNA
mm_113917.1	chr13	49544480	49544533	+	1	NA	promoter-TSS (NM_025711)	promoter-TSS (NM_025711)	63	NM_025711	66695	Mm.383216	NM_025711	ENSMUSG00000021388	Aspn	4631401G09Rik|AA986886|Plap1|Slrr1c	asporin	protein-coding
mm_114143.1	chr13	55316866	55316869	+	1	NA	3' UTR (NM_008739, exon 23 of 23)	3' UTR (NM_008739, exon 23 of 23)	5113	NM_009000	19336	Mm.220923	NM_009000	ENSMUSG00000034789	Rab24	6530406O07Rik	RAB24, member RAS oncogene family	protein-coding
mm_7342.1	chr1	105984146	105984158	-	1	NA	Intergenic	Intergenic	-6254	NM_001122676	227449	Mm.210188	NM_001122675	ENSMUSG00000038866	Zcchc2	9930114B20Rik|AW212015	zinc finger, CCHC domain containing 2	protein-coding
mm_98840.1	chr11	97450137	97450180	+	1	NA	promoter-TSS (NM_021493)	promoter-TSS (NM_021493)	-2	NM_021493	58996	Mm.394118	NM_021493	ENSMUSG00000049807	Arhgap23	A330041B18Rik	Rho GTPase activating protein 23	protein-coding
mm_96752.1	chr11	69901705	69901758	+	1	NA	promoter-TSS (NM_001291119)	promoter-TSS (NM_001291119)	-85	NM_001291118	216860	Mm.268347	NM_001013414	ENSMUSG00000047284	Neurl4	-	neuralized E3 ubiquitin protein ligase 4	protein-coding
mm_161785.1	chr17	44237148	44237148	+	1	NA	exon (NM_172621, exon 2 of 6)	exon (NM_172621, exon 2 of 6)	48576	NM_172621	224796	Mm.37666	NM_172621	ENSMUSG00000023959	Clic5	5730531E12Rik|B330005L24|Gm322|jbg	chloride intracellular channel 5	protein-coding
mm_98881.1	chr11	97815592	97815598	+	1	NA	intron (NM_010688, intron 2 of 6)	intron (NM_010688, intron 2 of 6)	15923	NM_010688	16796	Mm.271967	NM_010688	ENSMUSG00000038366	Lasp1	AA408629|Def-4|SH3P6|Tg(Col1a1-lacZ)1Ngma	LIM and SH3 protein 1	protein-coding
mm_120794.1	chr14	74733934	74733949	+	1	NA	intron (NM_001285423, intron 1 of 8)	intron (NM_001285423, intron 1 of 8)	1644	NM_016903	13885	Mm.38055	NM_016903	ENSMUSG00000021996	Esd	Es-10|Es10|FGH|sid478	esterase D/formylglutathione hydrolase	protein-coding
mm_64287.1	chr7	141856700	141856710	+	1	NA	exon (NM_028801, exon 30 of 49)	exon (NM_028801, exon 30 of 49)	17633	NM_028801	74180	Mm.200752	NM_028801	ENSMUSG00000066108	Muc5b	2300002I04Rik|A130042M24|AV085033|MUC5|MUC9|mucin 5b	mucin 5, subtype B, tracheobronchial	protein-coding
mm_41444.1	chr5	90905264	90905321	+	1	NA	3' UTR (NM_009140, exon 4 of 4)	3' UTR (NM_009140, exon 4 of 4)	1393	NM_009140	20310	Mm.4979	NM_009140	ENSMUSG00000058427	Cxcl2	CINC-2a|GROb|Gro2|MIP-2|MIP-2a|Mgsa-b|Mip2|Scyb|Scyb2	chemokine (C-X-C motif) ligand 2	protein-coding
mm_92733.1	chr10	80906411	80906416	-	1	NA	promoter-TSS (NM_001347140)	promoter-TSS (NM_001347140)	-1	NM_001347140	16907	Mm.7362	NM_010722	ENSMUSG00000062075	Lmnb2	-	lamin B2	protein-coding
mm_159415.1	chr3	105458803	105458803	+	1	NA	promoter-TSS (NM_019931)	promoter-TSS (NM_019931)	-13	NM_019931	56543	Mm.44530	NM_019931	ENSMUSG00000040896	Kcnd3	AW045978|Kncd3|Kv4.3	potassium voltage-gated channel, Shal-related family, member 3	protein-coding
mm_142968.1	chr17	56121995	56122001	-	1	NA	promoter-TSS (NM_029796)	promoter-TSS (NM_029796)	-52	NM_029796	76905	Mm.348025	NM_029796	ENSMUSG00000037095	Lrg1	1300008B03Rik|2310031E04Rik|Lrg|Lrhg	leucine-rich alpha-2-glycoprotein 1	protein-coding
mm_95358.1	chr11	48871639	48871662	+	1	NA	promoter-TSS (NM_008326)	promoter-TSS (NM_008326)	-304	NM_008326	15944	Mm.29938	NM_008326	ENSMUSG00000046879	Irgm1	Ifggd3|Ifi1|Iigp3|Iipg3|Irgm|LRG-47	immunity-related GTPase family M member 1	protein-coding
mm_8764.1	chr1	160792834	160792878	-	1	NA	promoter-TSS (NM_013862)	promoter-TSS (NM_013862)	82	NM_013862	29809	Mm.25833	NM_013862	ENSMUSG00000026721	Rabgap1l	5830411O09Rik|8430421H08Rik|9630005B12Rik|AW049894|HHL|Hh1|mKIAA0471	RAB GTPase activating protein 1-like	protein-coding
mm_120419.1	chr14	65358662	65358691	+	1	NA	promoter-TSS (NM_199029)	promoter-TSS (NM_199029)	0	NM_199029	380912	Mm.270087	NM_199029	ENSMUSG00000034522	Zfp395	BC053701|Gm910	zinc finger protein 395	protein-coding
mm_37169.1	chr4	117178727	117178754	-	1	NA	promoter-TSS (NM_001290662)	promoter-TSS (NM_001290662)	32	NM_001290662	73804	Mm.247651	NM_134471	ENSMUSG00000028678	Kif2c	4930402F02Rik|ESTM5|Knsl6|MCAK|X83316	kinesin family member 2C	protein-coding
mm_34894.1	chr4	155624932	155624940	+	1	NA	promoter-TSS (NM_007661)	promoter-TSS (NM_007661)	67	NM_007661	12537	Mm.267410	NM_007661	ENSMUSG00000029062	Cdk11b	AA989746|CDK11-p110|CDK11-p46|CDK11-p58|Cdc11b|Cdc2l1|Cdc2l2|Cdk11|p58	cyclin-dependent kinase 11B	protein-coding
mm_172802.1	chr9	118674992	118674996	-	1	NA	intron (NM_133721, intron 11 of 27)	LSU-rRNA_Hsa|rRNA|rRNA	-36698	NM_001113514	104099	Mm.335520	NM_133721	ENSMUSG00000039115	Itga9	(alpha)9|2610002H11Rik|6720458D17Rik|AI461869|D130073C02|D9Ertd428e	integrin alpha 9	protein-coding
mm_126001.1	chr15	76520905	76520919	+	1	NA	intron (NM_130893, intron 1 of 1)	intron (NM_130893, intron 1 of 1)	1217	NM_130893	170729	Mm.218747	NM_130893	ENSMUSG00000048385	Scrt1	-	scratch family zinc finger 1	protein-coding
mm_16132.1	chr2	170336705	170336741	+	1	NA	Intergenic	Intergenic	-19638	NR_040610	73303	Mm.443297	NR_040610	ENSMUSG00000086999	Bcas1os2	1700040N02Rik	breast carcinoma amplified sequence 1, opposite strand 2	ncRNA
mm_147.1	chr1	11089758	11089763	+	1	NA	exon (NM_029525, exon 6 of 40)	exon (NM_029525, exon 6 of 40)	96295	NM_029525	109294	Mm.123247	NM_029525	ENSMUSG00000048960	Prex2	6230420N16Rik|AI316880|AI553603|C030045D06Rik|D430013K02|Depdc2|P-Rex2	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	protein-coding
mm_109705.1	chr12	113421606	113421617	+	1	NA	Intergenic	Intergenic	-67954	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_132552.1	chr16	37883735	37883761	+	1	NA	3' UTR (NM_177093, exon 4 of 4)	3' UTR (NM_177093, exon 4 of 4)	15348	NM_177093	320184	Mm.390882	NM_177093	ENSMUSG00000034158	Lrrc58	1810012N18Rik|C330018J07Rik	leucine rich repeat containing 58	protein-coding
mm_129157.1	chr15	76241285	76241289	-	1	NA	intron (NM_001163576, intron 5 of 9)	intron (NM_001163576, intron 5 of 9)	2153	NM_001163576	671535	Mm.373750	NM_001163575	ENSMUSG00000063268	Parp10	-	poly (ADP-ribose) polymerase family, member 10	protein-coding
mm_134031.1	chr16	5012736	5012745	-	1	NA	intron (NM_133185, intron 2 of 10)	intron (NM_133185, intron 2 of 10)	813	NM_133185	66049	Mm.27792	NM_133185	ENSMUSG00000022540	Rogdi	0610011C19Rik|AU020118|C76152|Lzf	rogdi homolog	protein-coding
mm_150005.1	chr19	29289232	29289245	+	1	NA	intron (NM_001048177, intron 11 of 23)	intron (NM_001048177, intron 11 of 23)	36080	NM_013754	27356	Mm.306511	NM_013754	ENSMUSG00000050957	Insl6	RIF1	insulin-like 6	protein-coding
mm_91896.1	chr10	60002994	60003004	-	1	NA	promoter-TSS (NM_001199187)	promoter-TSS (NM_001199187)	136	NM_001347451	52717	Mm.21793	NM_025514	ENSMUSG00000020107	Anapc16	2310005G07Rik|APC16|D10Ertd641e	anaphase promoting complex subunit 16	protein-coding
mm_96815.1	chr11	69992576	69992640	+	1	NA	exon (NM_019749, exon 3 of 4)	exon (NM_019749, exon 3 of 4)	1238	NM_019749	56486	Mm.272460	NM_019749	ENSMUSG00000018567	Gabarap	-	gamma-aminobutyric acid receptor associated protein	protein-coding
mm_109009.1	chr12	103341523	103341554	+	1	NA	intron (NM_023049, intron 2 of 9)	intron (NM_023049, intron 2 of 9)	14463	NM_023049	65256	Mm.27159	NM_023049	ENSMUSG00000021200	Asb2	1110008E15Rik	ankyrin repeat and SOCS box-containing 2	protein-coding
mm_20595.1	chr2	131174822	131174837	-	1	NA	promoter-TSS (NM_027641)	promoter-TSS (NM_027641)	-19	NM_027641	70997	Mm.252722	NM_027641	ENSMUSG00000027329	Spef1	4931426K16Rik|Clamp	sperm flagellar 1	protein-coding
mm_136375.1	chr16	92825752	92825766	-	1	NA	intron (NM_001111022, intron 1 of 6)	intron (NM_001111022, intron 1 of 6)	315	NM_001111021	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_4347.1	chr1	171864384	171864411	+	1	NA	intron (NM_001289470, intron 3 of 8)	RLTRETN_Mm|LTR|ERVK	24700	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_162419.1	chr1	91437957	91437983	+	1	NA	intron (NM_011066, intron 9 of 22)	U2|snRNA|snRNA	21358	NM_011066	18627	Mm.482463	NM_011066	ENSMUSG00000055866	Per2	mKIAA0347|mPer2	period circadian clock 2	protein-coding
mm_53516.1	chr6	136417812	136417816	+	1	NA	Intergenic	U4|snRNA|snRNA	-2245	NM_001201390	100502936	Mm.21182	NM_001201390	ENSMUSG00000045291	E330021D16Rik	C85549	RIKEN cDNA E330021D16 gene	protein-coding
mm_11055.1	chr2	27442458	27442570	+	1	NA	Intergenic	CpG	8116	NR_106102	102466836		NR_106102	ENSMUSG00000098812	Mir7578	Gm27789|mmu-mir-7578	microRNA 7578	ncRNA
mm_46314.1	chr5	100593644	100593644	-	1	NA	Intergenic	RMER4B|LTR|ERVK	-21439	NM_139198	231507	Mm.34609	NM_139198	ENSMUSG00000029322	Plac8	C15|D5Wsu111e	placenta-specific 8	protein-coding
mm_125096.1	chr15	27571543	27571577	+	1	NA	promoter-TSS (NR_106065)	promoter-TSS (NR_106065)	66	NR_106065	102466808		NR_106065	ENSMUSG00000098416	Mir7117	Gm27729|mmu-mir-7117	microRNA 7117	ncRNA
mm_122382.1	chr14	40899256	40899263	-	1	NA	Intergenic	Intergenic	-6294	NM_177816	328381	Mm.235694	NM_177816	ENSMUSG00000037833	Sh2d4b	A430109M18Rik|D030001E08	SH2 domain containing 4B	protein-coding
mm_49356.1	chr6	22075894	22075896	+	1	NA	intron (NM_001081351, intron 4 of 21)	intron (NM_001081351, intron 4 of 21)	89985	NM_001081351	214642	Mm.221404	NM_001081351	ENSMUSG00000062980	Cped1	6720481P07|A430107O13Rik|AI552584	cadherin-like and PC-esterase domain containing 1	protein-coding
mm_36807.1	chr4	103173590	103173600	-	1	NA	3' UTR (NM_177732, exon 10 of 10)	3' UTR (NM_177732, exon 10 of 10)	41289	NM_177732	242585	Mm.281800	NM_177732	ENSMUSG00000028521	Slc35d1	AI834976|C330011J09|UGTREL7|mKIAA0260	solute carrier family 35 (UDP-glucuronic acid/UDP-N-acetylgalactosamine dual transporter), member D1	protein-coding
mm_115944.1	chr13	23706042	23706063	-	1	NA	exon (NM_001347493, exon 3 of 5)	exon (NM_001347493, exon 3 of 5)	4802	NM_001347493	15216	Mm.2681	NM_010424	ENSMUSG00000006611	Hfe	MR2	hemochromatosis	protein-coding
mm_169696.1	chr15	75049003	75049005	+	1	NA	promoter-TSS (NM_001252055)	promoter-TSS (NM_001252055)	-167	NM_001252056	17067	Mm.1583	NM_010741	ENSMUSG00000079018	Ly6c1	AA682074|AA959465|Ly-6C|Ly-6C1|Ly6c	lymphocyte antigen 6 complex, locus C1	protein-coding
mm_88486.1	chr10	77686598	77686608	+	1	NA	promoter-TSS (NM_001287074)	promoter-TSS (NM_001287074)	34	NM_001287074	252974	Mm.221237	NM_145855	ENSMUSG00000069581	Tspear	C330046G03Rik|ORF65|TSP-EAR|Tnep1	thrombospondin type laminin G domain and EAR repeats	protein-coding
mm_91634.1	chr10	42192020	42192038	-	1	NA	intron (NM_019740, intron 3 of 3)	intron (NM_019740, intron 3 of 3)	84713	NM_019740	56484	Mm.338613	NM_019740	ENSMUSG00000048756	Foxo3	1110048B16Rik|2010203A17Rik|C76856|FKHRL1|Fkhr2|Foxo3a	forkhead box O3	protein-coding
mm_33999.1	chr4	137913698	137913728	+	1	NA	intron (NM_199307, intron 2 of 19)	CpG	51476	NM_199307	230857	Mm.401062	NM_199307	ENSMUSG00000057530	Ece1	AW322500|ECE-1|ECE-1a|ECE-1b|ECE-1d	endothelin converting enzyme 1	protein-coding
mm_140810.1	chr17	22347906	22347912	-	1	NA	intron (NM_176962, intron 3 of 5)	RLTR25B|LTR|ERVK	13491	NM_176962	319615	Mm.442162	NM_176962	ENSMUSG00000033972	Zfp944	6330416L07Rik	zinc finger protein 944	protein-coding
mm_38503.1	chr4	141115274	141115291	-	1	NA	non-coding (NR_102344, exon 3 of 3)	non-coding (NR_102344, exon 3 of 3)	24514	NR_102344	213491	Mm.332006	NM_174996	ENSMUSG00000040842	Szrd1	1110022I03|D4Ertd22e	SUZ RNA binding domain containing 1	protein-coding
mm_65604.1	chr7	27366535	27366564	-	1	NA	intron (NM_001199235, intron 10 of 17)	intron (NM_001199235, intron 10 of 17)	-10541	NM_138676	192192	Mm.21297	NM_138676	ENSMUSG00000089832	Shkbp1	B930062H15Rik|Sb1	Sh3kbp1 binding protein 1	protein-coding
mm_138740.1	chr17	37002488	37002499	+	1	NA	promoter-TSS (NM_001013745)	promoter-TSS (NM_001013745)	11	NM_001168501	22715	Mm.305561	NM_009559	ENSMUSG00000036036	Zfp57	G19|Zfp-57	zinc finger protein 57	protein-coding
mm_166202.1	chr5	38480262	38480270	-	1	NA	promoter-TSS (NM_001102415)	promoter-TSS (NM_001102415)	40	NM_001102414	117591	Mm.260137	NM_145559	ENSMUSG00000005107	Slc2a9	Glut9|SLC2A9B|SLC2a9A	solute carrier family 2 (facilitated glucose transporter), member 9	protein-coding
mm_1339.1	chr1	66175189	66175199	+	1	NA	promoter-TSS (NM_008632)	promoter-TSS (NM_008632)	-135	NM_008632	17756	Mm.256966	NM_008632	ENSMUSG00000015222	Map2	G1-397-34|MAP-2|Mtap-2|Mtap2|repro4	microtubule-associated protein 2	protein-coding
mm_160156.1	chr7	43995869	43995869	+	1	NA	promoter-TSS (NM_010640)	promoter-TSS (NM_010640)	-8	NM_010640	16613	Mm.443378	NM_010640	ENSMUSG00000044485	Klk1b11	Klk11|mGK-11	kallikrein 1-related peptidase b11	protein-coding
mm_95589.1	chr11	53330575	53330609	+	1	NA	intron (NM_026479, intron 2 of 3)	intron (NM_026479, intron 2 of 3)	5903	NM_026479	67966	Mm.288072	NM_026479	ENSMUSG00000018239	Zcchc10	2410141K03Rik|AA675321|D11Ertd416e	zinc finger, CCHC domain containing 10	protein-coding
mm_16762.1	chr2	9877885	9877887	-	1	NA	5' UTR (NM_008091, exon 2 of 6)	5' UTR (NM_008091, exon 2 of 6)	714	NM_008091	14462	Mm.313866	NM_008091	ENSMUSG00000015619	Gata3	Gata-3|jal	GATA binding protein 3	protein-coding
mm_170700.1	chr2	135512355	135512373	+	1	NA	Intergenic	L1Md_T|LINE|L1	70856	NR_015544	320684	Mm.421433	NR_015544	ENSMUSG00000085631	9630028H03Rik	-	RIKEN cDNA 9630028H03 gene	ncRNA
mm_154271.1	chr19	60773929	60773952	-	1	NA	TTS (NR_105743)	TTS (NR_105743)	445	NR_034047	100217439		NR_034047		Snora19	MBI-51	small nucleolar RNA, H/ACA box 19	snoRNA
mm_31762.1	chr4	63386011	63386028	+	1	NA	intron (NM_001305432, intron 5 of 20)	intron (NM_001305432, intron 5 of 20)	12221	NM_001305432	100182	Mm.387725	NM_001045514	ENSMUSG00000039158	Akna	AI597013	AT-hook transcription factor	protein-coding
mm_85192.1	chr9	96719898	96719982	-	1	NA	intron (NM_175537, intron 1 of 2)	CpG	11735	NM_175537	245007	Mm.485954	NM_175537	ENSMUSG00000040433	Zbtb38	A930014K01Rik|CIBZ	zinc finger and BTB domain containing 38	protein-coding
mm_66552.1	chr7	45211891	45211904	-	1	NA	promoter-TSS (NM_015789)	promoter-TSS (NM_015789)	-14	NM_015789	50722	Mm.27287	NM_015789	ENSMUSG00000030792	Dkkl1	AI414495|SGY|SGY-1|SGY1|Soggy|mSgy	dickkopf-like 1	protein-coding
mm_144644.1	chr18	33181988	33181995	+	1	NA	intron (NM_009793, intron 9 of 10)	intron (NM_009793, intron 9 of 10)	31871	NM_001347624	170459	Mm.127058	NM_133774	ENSMUSG00000024378	Stard4	4632419C16Rik|9030213J02Rik	StAR-related lipid transfer (START) domain containing 4	protein-coding
mm_25671.1	chr3	121953327	121953345	+	1	NA	promoter-TSS (NM_172525)	promoter-TSS (NM_172525)	10	NM_172525	214137	Mm.229287	NM_172525	ENSMUSG00000039831	Arhgap29	6720461J18Rik|A830014I19|AU040217|B130017I01Rik|C76601|Parg1	Rho GTPase activating protein 29	protein-coding
mm_157479.1	chrX	48161561	48161564	-	1	NA	TTS (NM_028773)	TTS (NM_028773)	15126	NM_028773	74131	Mm.276131	NM_028773	ENSMUSG00000031101	Sash3	1200013B08Rik|AW413946|SLY1	SAM and SH3 domain containing 3	protein-coding
mm_12120.1	chr2	61616981	61617003	+	1	NA	intron (NM_001164072, intron 2 of 7)	ORR1C2|LTR|ERVL-MaLR	23895	NM_001164071	21353	Mm.244393	NM_011529	ENSMUSG00000064289	Tank	C86182|E430026L09Rik|I-TRAF	TRAF family member-associated Nf-kappa B activator	protein-coding
mm_143443.1	chr17	70853552	70853560	-	1	NA	promoter-TSS (NM_001164074)	promoter-TSS (NM_001164074)	-24	NM_001164074	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_55005.1	chr6	48836284	48836301	-	1	NA	exon (NM_001164209, exon 4 of 8)	exon (NM_001164209, exon 4 of 8)	4696	NM_023056	65963	Mm.28385	NM_023056	ENSMUSG00000029810	Tmem176b	1810009M01Rik|Clast1|Lr8	transmembrane protein 176B	protein-coding
mm_36912.1	chr4	108069965	108069968	-	1	NA	intron (NM_011327, intron 12 of 15)	intron (NM_011327, intron 12 of 15)	-17391	NR_105823	102465213		NR_105823	ENSMUSG00000098980	Mir6397	Gm28004|mmu-mir-6397	microRNA 6397	ncRNA
mm_84985.1	chr9	86359599	86359602	-	1	NA	intron (NM_027394, intron 9 of 9)	intron (NM_027394, intron 9 of 9)	105316	NM_027394	70348	Mm.53469	NM_027394	ENSMUSG00000032415	Ube2cbp	2610018I03Rik|Ube3d	ubiquitin-conjugating enzyme E2C binding protein	protein-coding
mm_5383.1	chr1	30950088	30950133	-	1	NA	promoter-TSS (NR_002688)	promoter-TSS (NR_002688)	-355	NM_011200	19243	Mm.491181	NM_011200	ENSMUSG00000026064	Ptp4a1	AA415290|AU019864|C130021B01|Prl-1	protein tyrosine phosphatase 4a1	protein-coding
mm_137736.1	chr17	29348017	29348030	+	1	NA	promoter-TSS (NM_019880)	promoter-TSS (NM_019880)	-91	NM_001347335	56462	Mm.285322	NM_019880	ENSMUSG00000024012	Mtch1	2310034O17Rik|AI255158|AU018396|C77849|PSAP	mitochondrial carrier 1	protein-coding
mm_137460.1	chr17	26602223	26602236	+	1	NA	intron (NM_026170, intron 1 of 9)	intron (NM_026170, intron 1 of 9)	40717	NM_026170	67458	Mm.30496	NM_026170	ENSMUSG00000001576	Ergic1	1200007D18Rik|maa-136	endoplasmic reticulum-golgi intermediate compartment (ERGIC) 1	protein-coding
mm_37785.1	chr4	130275524	130275537	-	1	NA	promoter-TSS (NM_001253386)	promoter-TSS (NM_001253386)	56	NM_172702	230779	Mm.45132	NM_172702	ENSMUSG00000023232	Serinc2	2310004K20Rik|AW121759|FKSG84|TDE2|Tde2l	serine incorporator 2	protein-coding
mm_146022.1	chr18	69519781	69519791	+	1	NA	intron (NM_013685, intron 5 of 19)	intron (NM_013685, intron 5 of 19)	174065	NM_001083967	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding
mm_110826.1	chr12	72628852	72628866	-	1	NA	Intergenic	Intergenic	35969	NM_025522	66375	Mm.289653	NM_025522	ENSMUSG00000021094	Dhrs7	2310016E22Rik|5730564L20Rik|AW061210|Retdsr4|Retsdr4	dehydrogenase/reductase (SDR family) member 7	protein-coding
mm_162928.1	chr10	122678965	122678994	-	1	NA	promoter-TSS (NR_106182)	promoter-TSS (NR_106182)	217	NM_001110218	319468	Mm.489703	NM_176919	ENSMUSG00000034613	Ppm1h	A430075L18Rik|ARHCL1|C030002B11Rik	protein phosphatase 1H (PP2C domain containing)	protein-coding
mm_171121.1	chr3	142632050	142632059	+	1	NA	exon (NM_010260, exon 7 of 11)	exon (NM_010260, exon 7 of 11)	-8108	NR_105802	102465200		NR_105802	ENSMUSG00000098871	Mir6381	Gm27963|mmu-mir-6381	microRNA 6381	ncRNA
mm_108959.1	chr12	102377164	102377164	+	1	NA	intron (NM_177620, intron 7 of 9)	intron (NM_177620, intron 7 of 9)	62649	NM_011175	19141	Mm.17185	NM_011175	ENSMUSG00000021190	Lgmn	AEP|AI746452|AU022324|Prsc1	legumain	protein-coding
mm_162757.1	chr10	61352007	61352008	+	1	NA	intron (NM_013753, intron 3 of 19)	intron (NM_013753, intron 3 of 19)	31516	NM_013753	27355	Mm.269699	NM_013753	ENSMUSG00000020092	Pald1	MMPAL|Pald|mKIAA1274	phosphatase domain containing, paladin 1	protein-coding
mm_161057.1	chr12	58211761	58211761	+	1	NA	promoter-TSS (NM_009216)	promoter-TSS (NM_009216)	-43	NM_009216	20605	Mm.278336	NM_009216	ENSMUSG00000035431	Sstr1	SRIF-2|SS-1-R|SS1-R|SS1R|Smstr-1|Smstr1|sst1	somatostatin receptor 1	protein-coding
mm_158523.1	chrX	143860397	143860408	-	1	NA	3' UTR (NM_010025, exon 7 of 7)	3' UTR (NM_010025, exon 7 of 7)	-32990	NM_007603	12338	Mm.30290	NM_007603	ENSMUSG00000067276	Capn6	-	calpain 6	protein-coding
mm_35856.1	chr4	49447173	49447176	-	1	NA	3' UTR (NM_001164565, exon 3 of 3)	3' UTR (NM_001164565, exon 3 of 3)	3935	NM_001164565	230161	Mm.30101	NM_001164565	ENSMUSG00000070985	Acnat1	AI132189	acyl-coenzyme A amino acid N-acyltransferase 1	protein-coding
mm_155195.1	chrX	56455460	56455474	+	1	NA	exon (NM_172779, exon 2 of 17)	exon (NM_172779, exon 2 of 17)	628	NM_172779	236790	Mm.474772	NM_172779	ENSMUSG00000035967	Ints6l	4930535D10Rik|6330505F04Rik|D130066O12|Ddx26b	integrator complex subunit 6 like	protein-coding
mm_137940.1	chr17	32685611	32685615	+	1	NA	promoter-TSS (NM_134127)	promoter-TSS (NM_134127)	-18	NM_001346538	106648	Mm.26539	NM_134127	ENSMUSG00000073424	Cyp4f15	AI787289|Cyp4f-15	cytochrome P450, family 4, subfamily f, polypeptide 15	protein-coding
mm_65369.1	chr7	25072687	25072797	-	1	NA	promoter-TSS (NM_008168)	promoter-TSS (NM_008168)	-373	NM_008168	14809	Mm.2879	NM_008168	ENSMUSG00000003378	Grik5	GluK5|GluRgamma2|KA2	glutamate receptor, ionotropic, kainate 5 (gamma 2)	protein-coding
mm_64814.1	chr7	7121434	7121469	-	1	NA	promoter-TSS (NM_172738)	promoter-TSS (NM_172738)	25	NM_172738	232853	Mm.23838	NM_172738	ENSMUSG00000062116	Zfp954	5730403M16Rik|8030437F07|AA123315	zinc finger protein 954	protein-coding
mm_150382.1	chr19	36348286	36348313	+	1	NA	Intergenic	Intergenic	-30768	NM_029508	76073	Mm.259180	NM_029508	ENSMUSG00000024805	Pcgf5	0610009F02Rik|1110054A01Rik|5830406C17Rik|5830443C21Rik|9530023M17Rik|AI324127	polycomb group ring finger 5	protein-coding
mm_10634.1	chr2	20209654	20209674	+	1	NA	Intergenic	RLTR17|LTR|ERVK	-80249	NM_001081006	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding
mm_28044.1	chr3	83980897	83980901	-	1	NA	intron (NM_172681, intron 3 of 34)	intron (NM_172681, intron 3 of 34)	59262	NM_172681	229473	Mm.28838	NM_172681	ENSMUSG00000033767	D930015E06Rik	Kiaa0922|mKIAA0922	RIKEN cDNA D930015E06 gene	protein-coding
mm_53247.1	chr6	127577964	127577979	+	1	NA	promoter-TSS (NM_001033464)	promoter-TSS (NM_001033464)	-4	NM_001033464	381812	Mm.296093	NM_001033464	ENSMUSG00000061414	Cracr2a	Efcab4b|Gm1073|Gm462	calcium release activated channel regulator 2A	protein-coding
mm_143352.1	chr17	67125952	67125954	-	1	NA	intron (NM_008984, intron 2 of 30)	intron (NM_008984, intron 2 of 30)	-99718	NR_049205	100885844		NR_049205	ENSMUSG00000093508	Mir5709	Gm22041|mir-5709|mmu-mir-5709	microRNA 5709	ncRNA
mm_157213.1	chrX	12954718	12954722	-	1	NA	Intergenic	Intergenic	17847	NM_001272033	245350	Mm.302695	NM_001272033		AA414768	OTTMUSG00000017000	expressed sequence AA414768	protein-coding
mm_110227.1	chr12	28750426	28750474	-	1	NA	promoter-TSS (NM_001161411)	promoter-TSS (NM_001161411)	3	NM_001161411	217449	Mm.132006	NM_178811	ENSMUSG00000020628	Trappc12	CGI-87|D930014A20Rik|Ttc15	trafficking protein particle complex 12	protein-coding
mm_34992.1	chr4	156029753	156029763	+	1	NA	TTS (NM_009400)	TTS (NM_009400)	3416	NM_021985	21936	Mm.3180	NM_009400	ENSMUSG00000041954	Tnfrsf18	AITR|Gitr	tumor necrosis factor receptor superfamily, member 18	protein-coding
mm_117850.1	chr13	98695561	98695578	-	1	NA	promoter-TSS (NM_001025606)	promoter-TSS (NM_001025606)	-738	NM_001025606	380863	Mm.28264	NM_001025606	ENSMUSG00000052485	Tmem171	Gm905	transmembrane protein 171	protein-coding
mm_132542.1	chr16	37882505	37882533	+	1	NA	3' UTR (NM_177093, exon 4 of 4)	3' UTR (NM_177093, exon 4 of 4)	14119	NM_177093	320184	Mm.390882	NM_177093	ENSMUSG00000034158	Lrrc58	1810012N18Rik|C330018J07Rik	leucine rich repeat containing 58	protein-coding
mm_48230.1	chr5	137684666	137684729	-	1	NA	promoter-TSS (NM_178162)	promoter-TSS (NM_178162)	56	NM_001303271	231801	Mm.260869	NM_145566	ENSMUSG00000029722	Agfg2	A630095P14Rik|Hrbl|RAB-R|RABR	ArfGAP with FG repeats 2	protein-coding
mm_139658.1	chr17	57402857	57402872	+	1	NA	intron (NM_010130, intron 5 of 21)	intron (NM_010130, intron 5 of 21)	44178	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_145213.1	chr18	50031297	50031324	+	1	NA	intron (NM_001177759, intron 1 of 1)	intron (NM_001177759, intron 1 of 1)	-21972	NM_134131	106869	Mm.27740	NM_134131	ENSMUSG00000062210	Tnfaip8	AA987150|E130304C20Rik|ENSMUSG00000073567|Gg2-1|Gm10539|Nded|Ssc-2|Tipe	tumor necrosis factor, alpha-induced protein 8	protein-coding
mm_121653.1	chr14	10453409	10453430	-	1	NA	promoter-TSS (NM_001308286)	promoter-TSS (NM_001308286)	39	NM_001308286	14198	Mm.397619	NM_010210	ENSMUSG00000060579	Fhit	AW045638|Fra14A2	fragile histidine triad gene	protein-coding
mm_17728.1	chr2	32451369	32451379	-	1	NA	promoter-TSS (NM_001164357)	promoter-TSS (NM_001164357)	96	NM_001164357	227731	Mm.37395	NM_146118	ENSMUSG00000026819	Slc25a25	1110030N17Rik|MCSC|mKIAA1896	solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 25	protein-coding
mm_19038.1	chr2	76977152	76977185	-	1	NA	exon (NM_011652, exon 3 of 313)	exon (NM_011652, exon 3 of 313)	5379	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_87829.1	chr10	60358483	60358485	+	1	NA	intron (NM_028732, intron 2 of 6)	intron (NM_028732, intron 2 of 6)	11633	NM_028732	74048	Mm.273584	NM_028732	ENSMUSG00000020101	Vsir	4632428N05Rik|Dies1|PD-1H|VISTA	V-set immunoregulatory receptor	protein-coding
mm_70612.1	chr8	13425470	13425503	+	1	NA	Intergenic	Intergenic	-9973	NM_001143671	272465	Mm.250502	NM_001143671	ENSMUSG00000038457	Tmem255b	Fam70b|Gm687	transmembrane protein 255B	protein-coding
mm_12515.1	chr2	72054934	72054965	+	1	NA	5' UTR (NM_001204166, exon 1 of 28)	5' UTR (NM_001204166, exon 1 of 28)	332	NM_001204166	56508	Mm.196153	NM_019688	ENSMUSG00000049044	Rapgef4	1300003D15Rik|5730402K07Rik|6330581N18Rik|EPAC 2|Epac-2|Epac2|mKIAA4040	Rap guanine nucleotide exchange factor (GEF) 4	protein-coding
mm_26653.1	chr3	154596675	154596688	+	1	NA	promoter-TSS (NM_009968)	promoter-TSS (NM_009968)	-30	NM_009968	12972	Mm.374855	NM_009968	ENSMUSG00000028199	Cryz	Sez9	crystallin, zeta	protein-coding
mm_142489.1	chr17	45757950	45757959	-	1	NA	Intergenic	MER117|DNA|hAT-Charlie	-24110	NM_028164	72240	Mm.482897	NM_028164	ENSMUSG00000094690	1600014C23Rik	-	RIKEN cDNA 1600014C23 gene	protein-coding
mm_9031.1	chr1	166506192	166506195	-	1	NA	Intergenic	Intergenic	-8605	NM_001164306	226601	Mm.475593	NM_001164306	ENSMUSG00000086056	Gm4846	EG226601|Fmo13	predicted gene 4846	protein-coding
mm_91402.1	chr10	30837893	30837911	-	1	NA	intron (NM_013904, intron 3 of 4)	B3A|SINE|B2	4881	NM_013904	15214	Mm.103573	NM_013904	ENSMUSG00000019789	Hey2	CHF1|Herp1|Hrt2|bHLHb32|hesr2	hairy/enhancer-of-split related with YRPW motif 2	protein-coding
mm_96170.1	chr11	61488449	61488460	+	1	NA	TTS (NM_001291037)	TTS (NM_001291037)	3010	NM_029568	76293	Mm.272278	NM_029568	ENSMUSG00000042436	Mfap4	1110007F23Rik	microfibrillar-associated protein 4	protein-coding
mm_108637.1	chr12	85746575	85746604	+	1	NA	promoter-TSS (NM_145447)	promoter-TSS (NM_145447)	50	NM_145447	217721	Mm.301076	NM_145447	ENSMUSG00000034258	Mfsd7c	CCT|Flvcr2	major facilitator superfamily domain containing 7C	protein-coding
mm_70613.1	chr8	13435135	13435159	+	1	NA	promoter-TSS (NM_001143672)	promoter-TSS (NM_001143672)	-312	NM_001143671	272465	Mm.250502	NM_001143671	ENSMUSG00000038457	Tmem255b	Fam70b|Gm687	transmembrane protein 255B	protein-coding
mm_92040.1	chr10	62494840	62494863	-	1	NA	3' UTR (NM_011157, exon 3 of 3)	3' UTR (NM_011157, exon 3 of 3)	-8046	NM_133672	30930	Mm.260703	NM_133672	ENSMUSG00000020078	Vps26a	AA407240|HB58|Vps26	VPS26 retromer complex component A	protein-coding
mm_73973.1	chr8	120522464	120522489	+	1	NA	intron (NM_198671, intron 1 of 15)	B1_Mur4|SINE|Alu	-13381	NM_001145897	382034	Mm.334856	NM_198671	ENSMUSG00000031822	Gse1	2210013I18Rik|mKIAA0182	genetic suppressor element 1, coiled-coil protein	protein-coding
mm_65655.1	chr7	28137109	28137120	-	1	NA	exon (NM_001164655, exon 4 of 20)	exon (NM_001164655, exon 4 of 20)	7648	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_120295.1	chr14	63138387	63138410	+	1	NA	exon (NM_007798, exon 7 of 10)	exon (NM_007798, exon 7 of 10)	15936	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_37633.1	chr4	127358125	127358187	-	1	NA	promoter-TSS (NM_010291)	promoter-TSS (NM_010291)	8	NM_010291	14622	Mm.26859	NM_010291	ENSMUSG00000042357	Gjb5	Cnx31.1|Cx31.1|Gjb-5	gap junction protein, beta 5	protein-coding
mm_110864.1	chr12	73546376	73546380	-	1	NA	promoter-TSS (NM_178715)	promoter-TSS (NM_178715)	17	NM_178715	238257	Mm.251196	NM_178715	ENSMUSG00000034435	Tmem30b	9130011B11Rik	transmembrane protein 30B	protein-coding
mm_11029.1	chr2	26912532	26912533	+	1	NA	TTS (NM_013677)	TTS (NM_013677)	1725	NM_013721	27176	Mm.328601	NM_013721	ENSMUSG00000062647	Rpl7a	Surf3	ribosomal protein L7A	protein-coding
mm_96072.1	chr11	59839399	59839409	+	1	NA	intron (NM_011991, intron 1 of 11)	CpG	363	NM_011991	26572	Mm.40	NM_011991	ENSMUSG00000019373	Cops3	Csn3|Sgn3	COP9 signalosome subunit 3	protein-coding
mm_90666.1	chr10	128821785	128821800	+	1	NA	promoter-TSS (NM_024180)	promoter-TSS (NM_024180)	21	NM_025364	66118	Mm.235562	NM_025364	ENSMUSG00000078427	Sarnp	1110005A23Rik|Cip29	SAP domain containing ribonucleoprotein	protein-coding
mm_4475.1	chr1	173420557	173420564	+	1	NA	promoter-TSS (NM_001013779)	promoter-TSS (NM_001013779)	-44	NM_001013779	383619	Mm.131453	NM_001013779	ENSMUSG00000037860	Aim2	Gm1313|Ifi210	absent in melanoma 2	protein-coding
mm_63889.1	chr7	138555223	138555225	+	1	NA	non-coding (NR_131022, exon 2 of 5)	non-coding (NR_131022, exon 2 of 5)	982	NR_131022	75187	Mm.410810	NR_131022	ENSMUSG00000110037	4930543N07Rik	-	RIKEN cDNA 4930543N07 gene	ncRNA
mm_34901.1	chr4	155638544	155638555	+	1	NA	exon (NM_007661, exon 7 of 20)	exon (NM_007661, exon 7 of 20)	13680	NM_007661	12537	Mm.267410	NM_007661	ENSMUSG00000029062	Cdk11b	AA989746|CDK11-p110|CDK11-p46|CDK11-p58|Cdc11b|Cdc2l1|Cdc2l2|Cdk11|p58	cyclin-dependent kinase 11B	protein-coding
mm_163186.1	chr11	94317671	94317686	-	1	NA	intron (NM_026313, intron 1 of 10)	intron (NM_026313, intron 1 of 10)	4233	NM_026313	67684	Mm.30927	NM_026313	ENSMUSG00000020863	Luc7l3	3300001P08Rik|Luc7a	LUC7-like 3 (S. cerevisiae)	protein-coding
mm_21797.1	chr2	164859808	164859813	-	1	NA	Intergenic	Lx5c|LINE|L1	-2102	NM_011125	18830	Mm.6105	NM_011125	ENSMUSG00000017754	Pltp	Bpife|OD107	phospholipid transfer protein	protein-coding
mm_83632.1	chr9	49410835	49410853	-	1	NA	Intergenic	Intergenic	16177	NM_172922	244859	Mm.119994	NM_172922	ENSMUSG00000032257	Ankk1	9930020N01Rik	ankyrin repeat and kinase domain containing 1	protein-coding
mm_51473.1	chr6	82998830	82998830	+	1	NA	intron (NM_033079, intron 4 of 9)	intron (NM_033079, intron 4 of 9)	34641	NM_010070	13448	Mm.156	NM_010070	ENSMUSG00000068335	Dok1	AW557123|p62DOK	docking protein 1	protein-coding
mm_59198.1	chr7	24507058	24507095	+	1	NA	promoter-TSS (NM_001290461)	promoter-TSS (NM_001290461)	-11	NM_001290461	232969	Mm.181332	NM_146183	ENSMUSG00000064264	Zfp428	2410005H09Rik|AV271806|AW047854|Znf428	zinc finger protein 428	protein-coding
mm_5026.1	chr1	193187258	193187307	+	1	NA	intron (NM_153137, intron 8 of 15)	intron (NM_153137, intron 8 of 15)	13705	NM_181048	319266	Mm.482460	NM_181048	ENSMUSG00000079144	A130010J15Rik	-	RIKEN cDNA A130010J15 gene	protein-coding
mm_88249.1	chr10	72673978	72674015	+	1	NA	3' UTR (NM_001293683, exon 8 of 8)	3' UTR (NM_001293683, exon 8 of 8)	19150	NM_001293683	52696	Mm.62876	NM_025635	ENSMUSG00000019923	Zwint	2010007E07Rik|2600001N01Rik|D10Ertd749e|Zwint-1	ZW10 interactor	protein-coding
mm_139760.1	chr17	64600741	64600764	+	1	NA	promoter-TSS (NM_008549)	promoter-TSS (NM_008549)	-897	NM_008549	17158	Mm.2433	NM_008549	ENSMUSG00000024085	Man2a1	Mana-2|Mana2|Map-2	mannosidase 2, alpha 1	protein-coding
mm_136403.1	chr16	93604041	93604077	-	1	NA	promoter-TSS (NM_145482)	promoter-TSS (NM_145482)	-244	NM_145482	224440	Mm.10628	NM_145482	ENSMUSG00000022948	Setd4	AY037804|C21orf18|ORF21	SET domain containing 4	protein-coding
mm_59265.1	chr7	24897490	24897516	+	1	NA	promoter-TSS (NM_007655)	promoter-TSS (NM_007655)	-8	NM_007655	12518	Mm.1355	NM_007655	ENSMUSG00000003379	Cd79a	Ig-alpha|Iga|Igalpha|Ly-54|Ly54|mb-1	CD79A antigen (immunoglobulin-associated alpha)	protein-coding
mm_83.1	chr1	6916535	6916536	+	1	NA	Intergenic	Intergenic	-172385	NM_183028	319263	Mm.21539	NM_183028	ENSMUSG00000051285	Pcmtd1	8430411F12Rik|A030012M09Rik	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding
mm_25674.1	chr3	122000159	122000171	+	1	NA	intron (NM_172525, intron 12 of 22)	Lx8|LINE|L1	-44295	NM_007378	11304	Mm.3918	NM_007378	ENSMUSG00000028125	Abca4	AW050280|Abc10|Abcr|D430003I15Rik|RmP	ATP-binding cassette, sub-family A (ABC1), member 4	protein-coding
mm_57710.1	chr6	128622832	128622847	-	1	NA	promoter-TSS (NM_001159902)	promoter-TSS (NM_001159902)	95	NM_001159902	17057	Mm.16729	NM_010737	ENSMUSG00000030361	Klrb1a	Ly55a|NKR-P1.7|NKR-P1A|NKRP12|Nkrp1-a|Nkrp1a|ly-55A	killer cell lectin-like receptor subfamily B member 1A	protein-coding
mm_148434.1	chr19	3943502	3943517	+	1	NA	intron (NM_001161428, intron 7 of 9)	intron (NM_001161428, intron 7 of 9)	8323	NM_001161428	54445	Mm.262094	NM_019449	ENSMUSG00000036908	Unc93b1	Unc-93B1|Unc93b	unc-93 homolog B1 (C. elegans)	protein-coding
mm_138989.1	chr17	45519373	45519397	+	1	NA	intron (NM_198608, intron 19 of 21)	intron (NM_198608, intron 19 of 21)	-4049	NM_013688	21645	Mm.491193	NM_013688	ENSMUSG00000023949	Tcte1	D17Sil1|Tcte-1	t-complex-associated testis expressed 1	protein-coding
mm_4397.1	chr1	172370685	172370701	+	1	NA	3' UTR (NM_001039484, exon 2 of 2)	3' UTR (NM_001039484, exon 2 of 2)	-5838	NM_026234	67556	Mm.26612	NM_026234	ENSMUSG00000050229	Pigm	4933437L05Rik|AI644422|AV302080|C920011G20Rik	phosphatidylinositol glycan anchor biosynthesis, class M	protein-coding
mm_167808.1	chr9	123928930	123928939	+	1	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	39758	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_116155.1	chr13	30532536	30532566	-	1	NA	Intergenic	Lx5b|LINE|L1	12765	NM_025710	66694	Mm.181933	NM_025710	ENSMUSG00000038462	Uqcrfs1	4430402G14Rik|AI875505	ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1	protein-coding
mm_77306.1	chr8	117480167	117480169	-	1	NA	Intergenic	RMER19C|LTR|ERVK	-18107	NM_172285	234779	Mm.192699	NM_172285	ENSMUSG00000034330	Plcg2	PLC-gamma-2|PLCgamma2|Plcg-2	phospholipase C, gamma 2	protein-coding
mm_66764.1	chr7	46728823	46728831	-	1	NA	3' UTR (NM_011316, exon 4 of 4)	3' UTR (NM_011316, exon 4 of 4)	3776	NM_011316	20211	Mm.3489	NM_011316	ENSMUSG00000040017	Saa4	Saa-4|Saa-5	serum amyloid A 4	protein-coding
mm_122363.1	chr14	39244109	39244110	-	1	NA	intron (NM_001190187, intron 1 of 9)	Lx2|LINE|L1	-228320	NR_131973	432842	Mm.352566	NR_131973		LOC432842	-	uncharacterized LOC432842	ncRNA
mm_116301.1	chr13	36726525	36726535	-	1	NA	3' UTR (NM_153529, exon 3 of 3)	3' UTR (NM_153529, exon 3 of 3)	7947	NM_153529	68404	Mm.232930	NM_153529	ENSMUSG00000039114	Nrn1	0710008J23Rik|Cpg15|Nrn	neuritin 1	protein-coding
mm_35748.1	chr4	45489248	45489258	-	1	NA	intron (NM_001033306, intron 1 of 5)	intron (NM_001033306, intron 1 of 5)	41575	NM_001033306	230126	Mm.251716	NM_001033306	ENSMUSG00000044813	Shb	BC028832	src homology 2 domain-containing transforming protein B	protein-coding
mm_63712.1	chr7	130692674	130692742	+	1	NA	5' UTR (NM_021314, exon 1 of 18)	5' UTR (NM_021314, exon 1 of 18)	152	NM_021314	57752	Mm.86322	NM_021314	ENSMUSG00000030852	Tacc2	mKIAA4180	transforming, acidic coiled-coil containing protein 2	protein-coding
mm_127303.1	chr15	100227836	100227856	+	1	NA	promoter-TSS (NM_007497)	promoter-TSS (NM_007497)	-13	NM_007497	11908	Mm.676	NM_007497	ENSMUSG00000023027	Atf1	-	activating transcription factor 1	protein-coding
mm_172966.1	chr9	88858798	88858811	-	1	NA	promoter-TSS (NR_037983)	promoter-TSS (NR_037983)	-3	NR_037982	319673	Mm.149040	NR_037982	ENSMUSG00000097177	9330159M07Rik	1700096K11Rik|mU50hg-a	RIKEN cDNA 9330159M07 gene	ncRNA
mm_132878.1	chr16	48786603	48786613	+	1	NA	Intergenic	Intergenic	-14652	NM_198297	77647	Mm.167298	NM_198297	ENSMUSG00000030775	Trat1	C030046M14Rik|Tcrim|Trim	T cell receptor associated transmembrane adaptor 1	protein-coding
mm_171109.1	chr3	135769678	135769680	-	1	NA	Intergenic	ERVB7_1-LTR_MM|LTR|ERVK	-55600	NM_026228	67547	Mm.30239	NM_026228	ENSMUSG00000053897	Slc39a8	4933419D20Rik|AA986696|BIGM103|ZIP-8|Zip8	solute carrier family 39 (metal ion transporter), member 8	protein-coding
mm_124583.1	chr14	124677500	124677540	-	1	NA	promoter-TSS (NM_207667)	promoter-TSS (NM_207667)	-393	NM_207667	14169	Mm.206362	NM_010201	ENSMUSG00000025551	Fgf14	FHF-4|Fhf4|mFHF-4(1B)	fibroblast growth factor 14	protein-coding
mm_65753.1	chr7	28576657	28576689	-	1	NA	intron (NM_027470, intron 1 of 9)	intron (NM_027470, intron 1 of 9)	-15689	NR_106016	102466795		NR_106016	ENSMUSG00000098558	Mir7049	Gm27277|mmu-mir-7049	microRNA 7049	ncRNA
mm_101947.1	chr11	50224633	50224641	-	1	NA	promoter-TSS (NM_145926)	promoter-TSS (NM_145926)	-698	NM_145926	103534	Mm.86759	NM_145926	ENSMUSG00000036620	Mgat4b	AA407995|GnTIVb	mannoside acetylglucosaminyltransferase 4, isoenzyme B	protein-coding
mm_75614.1	chr8	62547854	62547873	-	1	NA	Intergenic	(GAA)n|Simple_repeat|Simple_repeat	-403369	NM_001252620	72902	Mm.334552	NM_023689	ENSMUSG00000054162	Spock3	2900045C01Rik|AI428471|mKIAA4039	sparc/osteonectin, cwcv and kazal-like domains proteoglycan 3	protein-coding
mm_40405.1	chr5	53049147	53049156	+	1	NA	promoter-TSS (NM_011402)	promoter-TSS (NM_011402)	-202	NM_011402	20531	Mm.284891	NM_011402	ENSMUSG00000029188	Slc34a2	AA536683|D5Ertd227e|NaPi-2b|Npt2b	solute carrier family 34 (sodium phosphate), member 2	protein-coding
mm_155116.1	chrX	48623801	48623811	+	1	NA	exon (NM_001290705, exon 1 of 10)	exon (NM_001290705, exon 1 of 10)	132	NM_001166450	20523	Mm.34953	NM_011398	ENSMUSG00000031105	Slc25a14	BMCP1|UCP5|UCP5L|UCP5S	solute carrier family 25 (mitochondrial carrier, brain), member 14	protein-coding
mm_36060.1	chr4	57689443	57689451	-	1	NA	intron (NM_001304544, intron 4 of 8)	intron (NM_001304544, intron 4 of 8)	121199	NM_172868	242481	Mm.331630	NM_172868	ENSMUSG00000090053	Palm2	53-H12|B130066I24|R75368|pEN70	paralemmin 2	protein-coding
mm_61053.1	chr7	49910233	49910242	+	1	NA	promoter-TSS (NM_001146013)	promoter-TSS (NM_001146013)	-62	NM_001146013	104245	Mm.207053	NM_148931	ENSMUSG00000039728	Slc6a5	Glyt2|prestin	solute carrier family 6 (neurotransmitter transporter, glycine), member 5	protein-coding
mm_100857.1	chr11	5863968	5864003	-	1	NA	exon (NM_009636, exon 2 of 21)	exon (NM_009636, exon 2 of 21)	2119	NM_001291857	11568	Mm.3317	NM_009636	ENSMUSG00000020473	Aebp1	ACLP	AE binding protein 1	protein-coding
mm_93735.1	chr10	120112947	120112959	-	1	NA	promoter-TSS (NM_080446)	promoter-TSS (NM_080446)	12	NM_080446	117599	Mm.214703	NM_080446	ENSMUSG00000020228	Helb	AI447783|D10Ertd664e	helicase (DNA) B	protein-coding
mm_143322.1	chr17	66346551	66346565	-	1	NA	intron (NM_001114098, intron 11 of 14)	intron (NM_001114098, intron 11 of 14)	103192	NM_172963	68617	Mm.33421	NM_172963	ENSMUSG00000052105	Mtcl1	1110012J17Rik|Ccdc165|D130071O13|Kiaa0802|Soga2|mKIAA0802|t8219b25	microtubule crosslinking factor 1	protein-coding
mm_97896.1	chr11	83355256	83355259	+	1	NA	intron (NM_027915, intron 14 of 20)	intron (NM_027915, intron 14 of 20)	52560	NM_001035854	71770	Mm.39053	NM_027915	ENSMUSG00000035152	Ap2b1	1300012O03Rik|AI788979	adaptor-related protein complex 2, beta 1 subunit	protein-coding
mm_34857.1	chr4	155536798	155536801	+	1	NA	intron (NM_001160016, intron 5 of 11)	AT_rich|Low_complexity|Low_complexity	-25593	NM_138671	192185	Mm.28347	NM_138671	ENSMUSG00000029063	Nadk	4432404C02Rik|BC004012	NAD kinase	protein-coding
mm_23571.1	chr3	63296177	63296194	+	1	NA	promoter-TSS (NM_001289463)	promoter-TSS (NM_001289463)	90	NM_001289463	17380	Mm.296022	NM_008604	ENSMUSG00000027820	Mme	6030454K05Rik|C85356|CALLA|CD10|NEP|SFE	membrane metallo endopeptidase	protein-coding
mm_34980.1	chr4	156014308	156014318	+	1	NA	TTS (NM_011341)	TTS (NM_011341)	618	NM_011659	22163	Mm.13885	NM_011659	ENSMUSG00000029075	Tnfrsf4	ACT35|CD134|Ly-70|Ox40|TXGP1L|Txgp1	tumor necrosis factor receptor superfamily, member 4	protein-coding
mm_8433.1	chr1	152625077	152625085	-	1	NA	5' UTR (NM_016846, exon 1 of 18)	5' UTR (NM_016846, exon 1 of 18)	136	NM_016846	19731	Mm.245270	NM_016846	ENSMUSG00000026482	Rgl1	Rgl|mKIAA0959	ral guanine nucleotide dissociation stimulator,-like 1	protein-coding
mm_42401.1	chr5	114968790	114968808	+	1	NA	intron (NM_009327, intron 1 of 9)	intron (NM_009327, intron 1 of 9)	2263	NM_009327	21405	Mm.332607	NM_009327	ENSMUSG00000029556	Hnf1a	AI323641|HNF1|HNF1-alpha|HNF1[a]|Hnf-1|Hnf1alpha|LFB1|Tcf-1|Tcf1	HNF1 homeobox A	protein-coding
mm_111911.1	chr12	108794175	108794218	-	1	NA	intron (NM_009537, intron 1 of 4)	CpG-3499	885	NM_009537	22632	Mm.3868	NM_009537	ENSMUSG00000021264	Yy1	AW488674|NF-E1	YY1 transcription factor	protein-coding
mm_82139.1	chr9	123767218	123767241	+	1	NA	promoter-TSS (NM_001166625)	promoter-TSS (NM_001166625)	18	NM_001166625	12769	Mm.440604	NM_009913	ENSMUSG00000029530	Ccr9	A130091K22Rik|Cmkbr10|GPR-9-6	chemokine (C-C motif) receptor 9	protein-coding
mm_70775.1	chr8	22192801	22192856	+	1	NA	promoter-TSS (NM_027338)	promoter-TSS (NM_027338)	-32	NM_027338	70160	Mm.41453	NM_027338	ENSMUSG00000031479	Vps36	1700010A24Rik|2210415M20Rik|2810408E15Rik|Eap45	vacuolar protein sorting 36	protein-coding
mm_121169.1	chr14	103014500	103014519	+	1	NA	intron (NR_045657, intron 2 of 2)	RMER1B|Other|Other	19294	NR_045657	71264	Mm.399572	NR_045657		4933432I03Rik	-	RIKEN cDNA 4933432I03 gene	ncRNA
mm_68741.1	chr7	121064245	121064254	-	1	NA	3' UTR (NM_030691, exon 6 of 6)	3' UTR (NM_030691, exon 6 of 6)	10281	NM_030691	80719	Mm.160384	NM_030691	ENSMUSG00000035004	Igsf6	-	immunoglobulin superfamily, member 6	protein-coding
mm_106360.1	chr11	118393856	118393866	-	1	NA	exon (NM_011150, exon 6 of 6)	exon (NM_011150, exon 6 of 6)	8070	NM_011150	19039	Mm.3152	NM_011150	ENSMUSG00000033880	Lgals3bp	90K|CyCAP|MAC-2BP|Ppicap|Tango10b	lectin, galactoside-binding, soluble, 3 binding protein	protein-coding
mm_23138.1	chr3	38885711	38885728	+	1	NA	Intergenic	CpG	-1221	NM_183221	329628	Mm.316210	NM_183221	ENSMUSG00000046743	Fat4	6030410K14Rik|9430004M15	FAT atypical cadherin 4	protein-coding
mm_132256.1	chr16	32752593	32752619	+	1	NA	exon (NM_080457, exon 2 of 27)	exon (NM_080457, exon 2 of 27)	16720	NM_080457	140474	Mm.214599	NM_080457	ENSMUSG00000079620	Muc4	4933405I11Rik|Asgp	mucin 4	protein-coding
mm_152890.1	chr19	24861802	24861824	-	1	NA	promoter-TSS (NM_175013)	promoter-TSS (NM_175013)	29	NM_175013	226041	Mm.105222	NM_175013	ENSMUSG00000041731	Pgm5	4833423B07|9530034F03Rik|D830025G17|aciculin	phosphoglucomutase 5	protein-coding
mm_34145.1	chr4	139338283	139338301	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	14284	NM_001290810	69902	Mm.27871	NM_023536	ENSMUSG00000028741	Mrto4	2610012O22Rik|Mg684|Mrt4	mRNA turnover 4, ribosome maturation factor	protein-coding
mm_74865.1	chr8	24950841	24950844	-	1	NA	3' UTR (NM_007404, exon 23 of 23)	3' UTR (NM_007404, exon 23 of 23)	-2038	NM_153397	353188	Mm.269223	NM_153397	ENSMUSG00000037437	Adam32	-	a disintegrin and metallopeptidase domain 32	protein-coding
mm_111121.1	chr12	80968788	80968799	-	1	NA	promoter-TSS (NM_001177561)	promoter-TSS (NM_001177561)	-714	NM_001177561	20493	Mm.486361	NM_011387	ENSMUSG00000021135	Slc10a1	Ntcp	solute carrier family 10 (sodium/bile acid cotransporter family), member 1	protein-coding
mm_104474.1	chr11	95356795	95356838	-	1	NA	intron (NM_172543, intron 1 of 7)	intron (NM_172543, intron 1 of 7)	19798	NM_172543	215512	Mm.262113	NM_172543	ENSMUSG00000038893	Fam117a	5730593F17Rik|AW548096	family with sequence similarity 117, member A	protein-coding
mm_136441.1	chr16	94570777	94570802	-	1	NA	promoter-TSS (NM_001113389)	promoter-TSS (NM_001113389)	-118	NM_001113389	13548	Mm.310973	NM_007890	ENSMUSG00000022897	Dyrk1a	2310043O08Rik|D16Ertd272e|D16Ertd493e|Dyrk|ENSMUSG00000074897|Gm10783|Mnbh|Mp86|mmb	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1a	protein-coding
mm_88557.1	chr10	79496940	79496981	+	1	NA	Intergenic	RLTR9E|LTR|ERVK	28002	NM_001104537	625029	Mm.469865	NM_001104537	ENSMUSG00000091381	Vmn2r83	EG625029	vomeronasal 2, receptor 83	protein-coding
mm_89287.1	chr10	87892415	87892416	+	1	NA	intron (NM_001314010, intron 3 of 4)	B4A|SINE|B4	31304	NM_001111276	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_30860.1	chr4	30664588	30664599	+	1	NA	promoter-TSS (NR_040655)	promoter-TSS (NR_040655)	-3	NR_040655	75332	Mm.108636	NR_040655		4930556G01Rik	-	RIKEN cDNA 4930556G01 gene	ncRNA
mm_139919.1	chr17	70974185	70974197	+	1	NA	3' UTR (NM_023402, exon 4 of 4)	3' UTR (NM_023402, exon 4 of 4)	16325	NM_023402	67938	Mm.261329	NM_023402	ENSMUSG00000034868	Myl12b	1500001M02Rik|C77744|Mylc2b|RLC-B	myosin, light chain 12B, regulatory	protein-coding
mm_76938.1	chr8	105940061	105940097	-	1	NA	exon (NM_008490, exon 6 of 6)	exon (NM_008490, exon 6 of 6)	-1687	NM_013640	19171	Mm.787	NM_013640	ENSMUSG00000031897	Psmb10	Mecl-1|Mecl1	proteasome (prosome, macropain) subunit, beta type 10	protein-coding
mm_31973.1	chr4	88209783	88209822	+	1	NA	intron (NM_001081184, intron 11 of 43)	intron (NM_001081184, intron 11 of 43)	87762	NR_030478	735282		NR_030478	ENSMUSG00000070077	Mir491	Mirn491|mir-491|mmu-mir-491	microRNA 491	ncRNA
mm_108144.1	chr12	76255349	76255369	+	1	NA	5' UTR (NM_138745, exon 1 of 28)	5' UTR (NM_138745, exon 1 of 28)	127	NM_138745	108156	Mm.29584	NM_138745	ENSMUSG00000021048	Mthfd1	Dcs|E430024A07Rik|Mthfd	methylenetetrahydrofolate dehydrogenase (NADP+ dependent), methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthase	protein-coding
mm_121148.1	chr14	101900162	101900183	+	1	NA	exon (NM_201529, exon 14 of 31)	exon (NM_201529, exon 14 of 31)	59549	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_108001.1	chr12	73445105	73445128	+	1	NA	Intergenic	Intergenic	-35553	NR_046013	380765	Mm.490476	NR_046013		D830013O20Rik	Gm891	RIKEN cDNA D830013O20 gene	ncRNA
mm_140950.1	chr17	24527938	24527951	-	1	NA	promoter-TSS (NR_045289)	promoter-TSS (NR_045289)	-6	NM_001172114	224619	Mm.275150	NM_153792	ENSMUSG00000052752	Traf7	RFWD1	TNF receptor-associated factor 7	protein-coding
mm_69966.1	chr7	142376682	142376700	-	1	NA	exon (NM_009983, exon 9 of 9)	exon (NM_009983, exon 9 of 9)	-2945	NM_001347541	320802	Mm.154486	NM_177265	ENSMUSG00000045777	Ifitm10	6330512M04Rik|AI848576|DSPA3	interferon induced transmembrane protein 10	protein-coding
mm_35973.1	chr4	53159886	53159900	-	1	NA	promoter-TSS (NM_013454)	promoter-TSS (NM_013454)	2	NM_013454	11303	Mm.277376	NM_013454	ENSMUSG00000015243	Abca1	ABC-1|Abc1	ATP-binding cassette, sub-family A (ABC1), member 1	protein-coding
mm_146402.1	chr18	82914639	82914664	+	1	NA	promoter-TSS (NM_001177464)	promoter-TSS (NM_001177464)	19	NM_001177464	329003	Mm.326526	NM_183033	ENSMUSG00000058881	Zfp516	C330029B10Rik|D230016L03|Zfp26l|Znf516|mKIAA0222	zinc finger protein 516	protein-coding
mm_59084.1	chr7	19689584	19689604	+	1	NA	exon (NM_001110009, exon 4 of 4)	exon (NM_001110009, exon 4 of 4)	3065	NM_001110009	11812	Mm.182440	NM_007469	ENSMUSG00000040564	Apoc1	Apo-CIB|ApoC-IB|apo-CI|apoC-I	apolipoprotein C-I	protein-coding
mm_91840.1	chr10	57528922	57528923	-	1	NA	intron (NM_019760, intron 1 of 8)	HAL1b|LINE|L1	3607	NM_019760	56442	Mm.29344	NM_019760	ENSMUSG00000019877	Serinc1	1500011D18Rik|AI315070|AIGP-2|TMS-2|Tde1l|Tde2|Tms2|mKIAA1253	serine incorporator 1	protein-coding
mm_77252.1	chr8	115705987	115705997	-	1	NA	exon (NM_001025577, exon 1 of 1)	exon (NM_001025577, exon 1 of 1)	902	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_24292.1	chr3	89266558	89266590	+	1	NA	5' UTR (NM_026767, exon 1 of 2)	5' UTR (NM_026767, exon 1 of 2)	113	NM_026767	68563	Mm.272927	NM_026767	ENSMUSG00000042737	Dpm3	1110001H19Rik|AV117483	dolichyl-phosphate mannosyltransferase polypeptide 3	protein-coding
mm_157804.1	chrX	73930521	73930532	-	1	NA	intron (NM_023132, intron 1 of 10)	intron (NM_023132, intron 1 of 10)	324	NM_023132	19703	Mm.236969	NM_023132	ENSMUSG00000031387	Renbp	Age|Rnbp	renin binding protein	protein-coding
mm_110633.1	chr12	57545988	57546016	-	1	NA	5' UTR (NM_008259, exon 1 of 2)	5' UTR (NM_008259, exon 1 of 2)	119	NM_008259	15375	Mm.4578	NM_008259	ENSMUSG00000035451	Foxa1	Hnf-3a|Hnf3a|Tcf-3a|Tcf3a	forkhead box A1	protein-coding
mm_138487.1	chr17	35200284	35200304	+	1	NA	exon (NM_013693, exon 4 of 4)	exon (NM_013693, exon 4 of 4)	1713	NM_013693	21926	Mm.1293	NM_013693	ENSMUSG00000024401	Tnf	DIF|TNF-a|TNF-alpha|TNFSF2|TNFalpha|Tnfa|Tnfsf1a|Tnlg1f	tumor necrosis factor	protein-coding
mm_101269.1	chr11	21365884	21365892	-	1	NA	intron (NM_001290634, intron 1 of 9)	intron (NM_001290634, intron 1 of 9)	4741	NM_139297	216558	Mm.28877	NM_139297	ENSMUSG00000001891	Ugp2	UDPGP|UGPase	UDP-glucose pyrophosphorylase 2	protein-coding
mm_169766.1	chr15	99802163	99802173	-	1	NA	exon (NM_001113545, exon 7 of 11)	exon (NM_001113545, exon 7 of 11)	17981	NM_023063	65970	Mm.33207	NM_023063	ENSMUSG00000023022	Lima1	Eplin	LIM domain and actin binding 1	protein-coding
mm_52578.1	chr6	116440087	116440091	+	1	NA	intron (NM_009662, intron 3 of 13)	intron (NM_009662, intron 3 of 13)	21089	NM_009662	11689	Mm.41072	NM_009662	ENSMUSG00000025701	Alox5	5-LO|5-LOX|5LO|5LX|AI850497|F730011J02	arachidonate 5-lipoxygenase	protein-coding
mm_89907.1	chr10	111165764	111165777	+	1	NA	intron (NM_175489, intron 1 of 23)	intron (NM_175489, intron 1 of 23)	968	NM_175489	237542	Mm.220204	NM_175489	ENSMUSG00000020189	Osbpl8	AA536976|AA536995|C730029P18Rik|D330025H14Rik|ORP-8	oxysterol binding protein-like 8	protein-coding
mm_5662.1	chr1	42693101	42693111	-	1	NA	intron (NR_027826, intron 1 of 3)	intron (NR_027826, intron 1 of 3)	1719	NR_027826	66297	Mm.45203	NM_183252	ENSMUSG00000060424	Pantr1	2610017I09Rik|Pou3f3os|linc-Brn1a	POU domain, class 3, transcription factor 3 adjacent noncoding transcript 1	ncRNA
mm_8283.1	chr1	140105445	140105464	-	1	NA	exon (NM_009888, exon 15 of 22)	exon (NM_009888, exon 15 of 22)	77957	NM_009888	12628	Mm.8655	NM_009888	ENSMUSG00000026365	Cfh	Mud-1|NOM|Sas-1|Sas1	complement component factor h	protein-coding
mm_8869.1	chr1	162859685	162859735	-	1	NA	intron (NM_010231, intron 1 of 8)	intron (NM_010231, intron 1 of 8)	290	NM_001330291	14261	Mm.976	NM_010231	ENSMUSG00000040181	Fmo1	-	flavin containing monooxygenase 1	protein-coding
mm_90802.1	chr10	7663570	7663613	-	1	NA	promoter-TSS (NM_008786)	promoter-TSS (NM_008786)	-7	NM_008786	18537	Mm.258431	NM_008786	ENSMUSG00000019795	Pcmt1	C79501|PIMT	protein-L-isoaspartate (D-aspartate) O-methyltransferase 1	protein-coding
mm_126029.1	chr15	76710611	76710665	+	1	NA	promoter-TSS (NM_058214)	promoter-TSS (NM_058214)	-79	NM_058214	79456	Mm.18373	NM_058214	ENSMUSG00000033762	Recql4	RecQ4	RecQ protein-like 4	protein-coding
mm_43789.1	chr5	142656017	142656021	+	1	NA	intron (NM_178398, intron 3 of 11)	intron (NM_178398, intron 3 of 11)	26435	NM_178398	74781	Mm.29432	NM_178398	ENSMUSG00000029578	Wipi2	1110018O08Rik|2510001I10Rik	WD repeat domain, phosphoinositide interacting 2	protein-coding
mm_21843.1	chr2	165841797	165841841	-	1	NA	intron (NM_027230, intron 6 of 23)	intron (NM_027230, intron 6 of 23)	16354	NM_001252585	228880	Mm.227598	NM_027230	ENSMUSG00000039671	Zmynd8	1110013E22Rik|2010005I16Rik|3632413B07Rik|AI316811|AL024039|Prkcbp1|RACK7	zinc finger, MYND-type containing 8	protein-coding
mm_745.1	chr1	43532373	43532387	+	1	NA	intron (NM_010879, intron 2 of 4)	intron (NM_010879, intron 2 of 4)	86629	NM_010879	17974	Mm.389903	NM_010879	ENSMUSG00000066877	Nck2	4833426I10Rik|Grb4|NCKbeta|Nck-2	non-catalytic region of tyrosine kinase adaptor protein 2	protein-coding
mm_39246.1	chr5	3474944	3474956	+	1	NA	intron (NM_009873, intron 5 of 7)	intron (NM_009873, intron 5 of 7)	-68883	NM_001042501	68152	Mm.240265	NM_026583	ENSMUSG00000058503	Fam133b	2900022K02Rik|5830415L20Rik	family with sequence similarity 133, member B	protein-coding
mm_17421.1	chr2	27426600	27426613	-	1	NA	non-coding (NR_133905, exon 1 of 30)	non-coding (NR_133905, exon 1 of 30)	1002	NR_133905	22325	Mm.179011	NM_009500	ENSMUSG00000009621	Vav2	2810040F13Rik|AI847175|Vav-2	vav 2 oncogene	protein-coding
mm_159055.1	chr1	190924909	190924909	+	1	NA	promoter-TSS (NM_001199020)	promoter-TSS (NM_001199020)	-199	NM_001199020	52477	Mm.289914	NM_021421	ENSMUSG00000026634	Angel2	2610307I21Rik|5730410O10Rik|AI845692|D1Ertd396e|D1Ertd654e	angel homolog 2	protein-coding
mm_112438.1	chr13	5789610	5789612	+	1	NA	Intergenic	Intergenic	68481	NR_045891	71867	Mm.179181	NR_045891	ENSMUSG00000100625	1700016G22Rik	-	RIKEN cDNA 1700016G22 gene	ncRNA
mm_75558.1	chr8	57796575	57796596	-	1	NA	intron (NM_175032, intron 10 of 11)	intron (NM_175032, intron 10 of 11)	-143530	NM_144731	108150	Mm.62886	NM_144731	ENSMUSG00000031608	Galnt7	AI225872	UDP-N-acetyl-alpha-D-galactosamine: polypeptide N-acetylgalactosaminyltransferase 7	protein-coding
mm_23350.1	chr3	54766484	54766486	+	1	NA	intron (NM_019483, intron 1 of 5)	intron (NM_019483, intron 1 of 5)	10903	NM_019483	55994	Mm.244353	NM_019483	ENSMUSG00000027796	Smad9	MADH6|Madh8|Madh9|Smad8	SMAD family member 9	protein-coding
mm_63234.1	chr7	126487345	126487390	+	1	NA	promoter-TSS (NM_001163713)	promoter-TSS (NM_001163713)	12	NM_001163713	233870	Mm.197829	NM_172745	ENSMUSG00000073838	Tufm	2300002G02Rik|C76308|C76389|EF-TuMT|EFTU	Tu translation elongation factor, mitochondrial	protein-coding
mm_118604.1	chr14	20794256	20794275	+	1	NA	promoter-TSS (NM_178597)	promoter-TSS (NM_178597)	-177	NM_178597	12325	Mm.235182	NM_178597	ENSMUSG00000021820	Camk2g	Camkg	calcium/calmodulin-dependent protein kinase II gamma	protein-coding
mm_82863.1	chr9	31913467	31913483	-	1	NA	promoter-TSS (NM_013800)	promoter-TSS (NM_013800)	-190	NM_013800	12023	Mm.261044	NM_013800	ENSMUSG00000032033	Barx2	2310006E12Rik|Barx2b	BarH-like homeobox 2	protein-coding
mm_88672.1	chr10	80017943	80017953	+	1	NA	exon (NM_001142701, exon 2 of 23)	exon (NM_001142701, exon 2 of 23)	1033	NM_001347074	70719	Mm.243954	NM_027521	ENSMUSG00000035697	Hmha1	6330406L22Rik|AW539505|Ha-1	histocompatibility (minor) HA-1	protein-coding
mm_163248.1	chr11	106751105	106751120	-	1	NA	promoter-TSS (NM_001271373)	promoter-TSS (NM_001271373)	-114	NM_001271375	380732	Mm.343952	NM_001033435	ENSMUSG00000040528	Milr1	Allergin-1|Gm885|Mca32	mast cell immunoglobulin like receptor 1	protein-coding
mm_40794.1	chr5	67607998	67608008	+	1	NA	5' UTR (NM_001033415, exon 1 of 2)	5' UTR (NM_001033415, exon 1 of 2)	120	NM_001033415	330096	Mm.442747	NM_001033415	ENSMUSG00000050010	Shisa3	D830007B15Rik	shisa family member 3	protein-coding
mm_70087.1	chr7	142655685	142655712	-	1	NA	promoter-TSS (NR_030251)	promoter-TSS (NR_030251)	-702	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_147105.1	chr18	35662130	35662175	-	1	NA	promoter-TSS (NM_027733)	promoter-TSS (NM_027733)	34	NM_029485	71242	Mm.151498	NM_027733	ENSMUSG00000024352	Spata24	2700012K08Rik|4930583E11Rik|5133400G04Rik|AU016220|TIPT|TIPT2	spermatogenesis associated 24	protein-coding
mm_150888.1	chr19	45235606	45235610	+	1	NA	promoter-TSS (NM_010691)	promoter-TSS (NM_010691)	-372	NM_010691	16814	Mm.116815	NM_010691	ENSMUSG00000025216	Lbx1	Lbx1h	ladybird homeobox homolog 1 (Drosophila)	protein-coding
mm_108394.1	chr12	80948752	80948755	+	1	NA	intron (NM_009159, intron 5 of 7)	AT_rich|Low_complexity|Low_complexity	3254	NM_001347415	20384	Mm.43331	NM_009159	ENSMUSG00000021134	Srsf5	Sfrs5	serine/arginine-rich splicing factor 5	protein-coding
mm_118303.1	chr13	113098340	113098353	-	1	NA	exon (NM_010370, exon 2 of 5)	exon (NM_010370, exon 2 of 5)	2635	NM_010370	14938	Mm.15510	NM_010370	ENSMUSG00000023132	Gzma	AW494114|Ctla-3|Ctla3|Hf|Hf1|SE1|TSP-1|TSP1	granzyme A	protein-coding
mm_153714.1	chr19	44400273	44400308	-	1	NA	exon (NM_009127, exon 5 of 6)	exon (NM_009127, exon 5 of 6)	7419	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_28997.1	chr3	101538941	101538941	-	1	NA	Intergenic	Intergenic	65766	NM_144900	11928	Mm.193670	NM_144900	ENSMUSG00000033161	Atp1a1	Atpa-1|BC010319	ATPase, Na+/K+ transporting, alpha 1 polypeptide	protein-coding
mm_123042.1	chr14	55589986	55590003	-	1	NA	intron (NM_001029855, intron 3 of 10)	intron (NM_001029855, intron 3 of 10)	1027	NM_011190	19188	Mm.371573	NM_011190	ENSMUSG00000079197	Psme2	AA589371|AI788882|PA28b	proteasome (prosome, macropain) activator subunit 2 (PA28 beta)	protein-coding
mm_146460.1	chr18	86601990	86601998	+	1	NA	Intergenic	Intergenic	-109116	NM_001302356	12405	Mm.70775	NM_172633	ENSMUSG00000024647	Cbln2	6330593N19Rik|A730004O05	cerebellin 2 precursor protein	protein-coding
mm_91974.1	chr10	61452419	61452434	-	1	NA	exon (NM_010124, exon 1 of 3)	exon (NM_010124, exon 1 of 3)	243	NM_010124	13688	Mm.259516	NM_010124	ENSMUSG00000020091	Eif4ebp2	2810011I19Rik|4E-BP2|AA792569|BC010348|PHAS-II	eukaryotic translation initiation factor 4E binding protein 2	protein-coding
mm_42169.1	chr5	112261643	112261653	+	1	NA	intron (NM_023695, intron 3 of 5)	intron (NM_023695, intron 3 of 5)	5828	NM_001312893	12960	Mm.29488	NM_023695	ENSMUSG00000029343	Crybb1	3110006K12Rik|BB1CRY	crystallin, beta B1	protein-coding
mm_98891.1	chr11	97838413	97838425	+	1	NA	3' UTR (NM_010688, exon 7 of 7)	3' UTR (NM_010688, exon 7 of 7)	-2361	NM_001080935	68127	Mm.110270	NM_001080935	ENSMUSG00000050538	B230217C12Rik	AI840637	RIKEN cDNA B230217C12 gene	protein-coding
mm_61456.1	chr7	75586420	75586448	+	1	NA	intron (NM_029332, intron 5 of 36)	intron (NM_029332, intron 5 of 36)	130900	NM_029332	75547	Mm.216107	NM_029332	ENSMUSG00000066406	Akap13	1700026G02Rik|5730522G15Rik|5830460E08Rik|AKAP-13|AKAP-Lbc|BRX|Ht31|LBC|PROTO-LB|PROTO-LBC	A kinase (PRKA) anchor protein 13	protein-coding
mm_75509.1	chr8	54523155	54523161	-	1	NA	3' UTR (NM_029701, exon 5 of 5)	3' UTR (NM_029701, exon 5 of 5)	6840	NM_029701	76687	Mm.86437	NM_029701	ENSMUSG00000054408	Spcs3	1810011E08Rik|SPC22/23	signal peptidase complex subunit 3 homolog (S. cerevisiae)	protein-coding
mm_4810.1	chr1	185356644	185356659	+	1	NA	3' UTR (NM_011794, exon 9 of 9)	3' UTR (NM_011794, exon 9 of 9)	-6444	NM_029735	107508	Mm.154511	NM_029735	ENSMUSG00000026615	Eprs	2410081F06Rik|3010002K18Rik|C79379|Qprs	glutamyl-prolyl-tRNA synthetase	protein-coding
mm_75713.1	chr8	68905719	68905731	-	1	NA	3' UTR (NM_008509, exon 10 of 10)	3' UTR (NM_008509, exon 10 of 10)	25170	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_37230.1	chr4	117964745	117964770	-	1	NA	intron (NM_009176, intron 5 of 11)	intron (NM_009176, intron 5 of 11)	-34994	NM_001284192	11876	Mm.56897	NM_009711	ENSMUSG00000028539	Artn	neublastin	artemin	protein-coding
mm_153970.1	chr19	47858035	47858064	-	1	NA	exon (NM_010362, exon 3 of 6)	exon (NM_010362, exon 3 of 6)	3076	NM_010362	14873	Mm.378931	NM_010362	ENSMUSG00000025068	Gsto1	AA407097|AI194287|AU018802|Gsto-1|Gstx|Spg-r|p28	glutathione S-transferase omega 1	protein-coding
mm_98266.1	chr11	88973929	88973961	+	1	NA	promoter-TSS (NM_016706)	promoter-TSS (NM_016706)	10	NM_016706	12812	Mm.268004	NM_016706	ENSMUSG00000033983	Coil	C79982|Cln80|p80|p80-coilin	coilin	protein-coding
mm_165536.1	chr2	180381187	180381192	-	1	NA	intron (NR_040745, intron 4 of 6)	intron (NR_040745, intron 4 of 6)	-4415	NR_045331	622283	Mm.447602	NR_045331		Mir1a-1hg	EG622283|Gm6307	Mir1a-1 and Mir133a-2 host gene	ncRNA
mm_69395.1	chr7	132154666	132154712	-	1	NA	promoter-TSS (NM_018867)	promoter-TSS (NM_018867)	52	NM_018867	55987	Mm.471654	NM_018867	ENSMUSG00000030862	Cpxm2	4632435C11Rik|CPX-2|Cpx2	carboxypeptidase X 2 (M14 family)	protein-coding
mm_115917.1	chr13	23530948	23530966	-	1	NA	promoter-TSS (NM_153173)	promoter-TSS (NM_153173)	-87	NM_153173	69386	Mm.158272	NM_153173	ENSMUSG00000060981	Hist1h4h	1700024H08Rik	histone cluster 1, H4h	protein-coding
mm_124422.1	chr14	118132734	118132761	-	1	NA	promoter-TSS (NM_029578)	promoter-TSS (NM_029578)	18	NM_029578	76355	Mm.251537	NM_029578	ENSMUSG00000022130	Tgds	2610017J16Rik|2610025M23Rik|AI648925	TDP-glucose 4,6-dehydratase	protein-coding
mm_97118.1	chr11	74830908	74830920	+	1	NA	promoter-TSS (NM_010813)	promoter-TSS (NM_010813)	-10	NM_010813	17428	Mm.3759	NM_010813	ENSMUSG00000000282	Mnt	Rox|bHLHd3	max binding protein	protein-coding
mm_57010.1	chr6	121131051	121131065	-	1	NA	promoter-TSS (NM_001270475)	promoter-TSS (NM_001270475)	-36	NM_001270475	194401	Mm.122399	NM_153396	ENSMUSG00000051586	Mical3	C130040D16Rik|Mical-3|mKIAA1364	microtubule associated monooxygenase, calponin and LIM domain containing 3	protein-coding
mm_126443.1	chr15	80671830	80671861	+	1	NA	promoter-TSS (NM_145986)	promoter-TSS (NM_145986)	-2	NM_145986	213956	Mm.132439	NM_145986	ENSMUSG00000022408	Fam83f	AW544981	family with sequence similarity 83, member F	protein-coding
mm_74073.1	chr8	122438231	122438243	+	1	NA	intron (NR_028354, intron 5 of 10)	intron (NR_028354, intron 5 of 10)	5185	NM_138656	192156	Mm.28146	NM_138656	ENSMUSG00000006517	Mvd	C78718|Mpd	mevalonate (diphospho) decarboxylase	protein-coding
mm_2697.1	chr1	127783585	127783594	+	1	NA	intron (NM_028399, intron 2 of 8)	AT_rich|Low_complexity|Low_complexity	9425	NM_028399	72949	Mm.268672	NM_028399	ENSMUSG00000026349	Ccnt2	2900041I18Rik|C81304|CycT2|CycT2a|CycT2b	cyclin T2	protein-coding
mm_113739.1	chr13	44678555	44678562	+	1	NA	Intergenic	B4A|SINE|B4	-52216	NM_021878	16468	Mm.25059	NM_021878	ENSMUSG00000038518	Jarid2	Jmj|jumonji	jumonji, AT rich interactive domain 2	protein-coding
mm_140749.1	chr17	16669764	16669789	-	1	NA	Intergenic	Intergenic	-394327	NM_001005358	449000	Mm.483718	NM_001005358	ENSMUSG00000096696	Zfp960	-	zinc finger protein 960	protein-coding
mm_123265.1	chr14	61325894	61325894	-	1	NA	Intergenic	RLTR24|LTR|ERV1	16141	NM_177337	219144	Mm.206566	NM_177337	ENSMUSG00000043157	Arl11	ARLTS1|C730007L20Rik	ADP-ribosylation factor-like 11	protein-coding
mm_153723.1	chr19	44407490	44407498	-	1	NA	5' UTR (NM_009127, exon 1 of 6)	5' UTR (NM_009127, exon 1 of 6)	215	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_90708.1	chr10	3267719	3267742	-	1	NA	promoter-TSS (NM_001204916)	promoter-TSS (NM_001204916)	41	NM_001204916	670558	Mm.398582	NM_001204916	ENSMUSG00000091618	H60c	4632413I24Rik|Gm9491	histocompatibility 60c	protein-coding
mm_62999.1	chr7	120740006	120740036	+	1	NA	intron (NM_177697, intron 1 of 33)	intron (NM_177697, intron 1 of 33)	464	NM_177697	233813	Mm.389939	NM_177697	ENSMUSG00000030889	Vwa3a	E030013G06Rik	von Willebrand factor A domain containing 3A	protein-coding
mm_33008.1	chr4	120666936	120666943	+	1	NA	exon (NM_019563, exon 1 of 1)	exon (NM_019563, exon 1 of 1)	376	NM_019563	56222	Mm.272646	NM_019563	ENSMUSG00000070803	Cited4	MRG-2|Mrg2	Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 4	protein-coding
mm_9962.1	chr1	191111960	191111971	-	1	NA	Intergenic	Intergenic	13551	NM_030060	381319	Mm.6922	NM_030060	ENSMUSG00000026630	Batf3	9130211I03Rik|Snft	basic leucine zipper transcription factor, ATF-like 3	protein-coding
mm_24078.1	chr3	87930517	87930600	+	1	NA	promoter-TSS (NM_153562)	promoter-TSS (NM_153562)	244	NM_177663	229504	Mm.45744	NM_177663	ENSMUSG00000048039	Isg20l2	4930429N24|C80587	interferon stimulated exonuclease gene 20-like 2	protein-coding
mm_138808.1	chr17	39846348	39846361	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	3357	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_103221.1	chr11	70656468	70656506	-	1	NA	promoter-TSS (NM_007933)	promoter-TSS (NM_007933)	-689	NM_001136062	13808	Mm.251322	NM_007933	ENSMUSG00000060600	Eno3	Eno-3|MSE	enolase 3, beta muscle	protein-coding
mm_82576.1	chr9	21131227	21131248	-	1	NA	promoter-TSS (NM_018793)	promoter-TSS (NM_018793)	38	NM_018793	54721	Mm.20249	NM_018793	ENSMUSG00000032175	Tyk2	JTK1	tyrosine kinase 2	protein-coding
mm_128864.1	chr15	72810027	72810037	-	1	NA	non-coding (NR_002864, exon 1 of 1)	non-coding (NR_002864, exon 1 of 1)	292	NR_002864	353342	Mm.440245	NR_002864	ENSMUSG00000106847	Peg13	-	paternally expressed 13	ncRNA
mm_31131.1	chr4	43209225	43209275	+	1	NA	intron (NM_001310758, intron 10 of 38)	intron (NM_001310758, intron 10 of 38)	-57909	NM_177195	320571	Mm.74465	NM_177195	ENSMUSG00000028457	Atp8b5	4930417M19Rik|Feta	ATPase, class I, type 8B, member 5	protein-coding
mm_28594.1	chr3	94472862	94472866	-	1	NA	exon (NM_025506, exon 3 of 7)	exon (NM_025506, exon 3 of 7)	727	NM_025506	66353	Mm.46405	NM_025506	ENSMUSG00000028139	Riiad1	2310007A19Rik|Ncrna00166	regulatory subunit of type II PKA R-subunit (RIIa) domain containing 1	protein-coding
mm_150981.1	chr19	46511155	46511158	+	1	NA	intron (NM_053100, intron 1 of 5)	PB1D10|SINE|Alu	9508	NM_053100	93679	Mm.392177	NM_053100	ENSMUSG00000025034	Trim8	AA408830|BB006755|GERP|Rnf27	tripartite motif-containing 8	protein-coding
mm_62665.1	chr7	108938068	108938091	+	1	NA	exon (NM_025344, exon 3 of 8)	exon (NM_025344, exon 3 of 8)	3664	NM_025344	66085	Mm.182962	NM_025344	ENSMUSG00000031029	Eif3f	0610037M02Rik|AA409853|Eif3s5	eukaryotic translation initiation factor 3, subunit F	protein-coding
mm_126450.1	chr15	80798628	80798652	+	1	NA	promoter-TSS (NM_177124)	promoter-TSS (NM_177124)	30	NM_177124	213988	Mm.131328	NM_144812	ENSMUSG00000047888	Tnrc6b	2700090M07Rik|A730065C02Rik|AI848765|D230019K20Rik	trinucleotide repeat containing 6b	protein-coding
mm_72907.1	chr8	90908600	90908619	+	1	NA	intron (NM_177224, intron 2 of 39)	CpG	-23640	NM_001310530	109151	Mm.100615	NM_177224	ENSMUSG00000056608	Chd9	1810014J18Rik|9030205D12Rik|A330063D19Rik|AD013|PRIC320|mKIAA0308	chromodomain helicase DNA binding protein 9	protein-coding
mm_19209.1	chr2	84531361	84531389	-	1	NA	Intergenic	MTEa|LTR|ERVL-MaLR	-24502	NR_046046	672763	Mm.491046	NR_046046	ENSMUSG00000087362	Gm13710	OTTMUSG00000013441	predicted gene 13710	ncRNA
mm_65089.1	chr7	19264470	19264483	-	1	NA	exon (NM_001282022, exon 3 of 13)	exon (NM_001282022, exon 3 of 13)	7378	NM_001282021	22323	Mm.9684	NM_009499	ENSMUSG00000030403	Vasp	-	vasodilator-stimulated phosphoprotein	protein-coding
mm_45429.1	chr5	67099046	67099063	-	1	NA	promoter-TSS (NM_008888)	promoter-TSS (NM_008888)	72	NM_008888	18935	Mm.62505	NM_008888	ENSMUSG00000012520	Phox2b	Dilp1|NBPhox|Pmx2b|Px2b	paired-like homeobox 2b	protein-coding
mm_68951.1	chr7	126564459	126564484	-	1	NA	exon (NM_146200, exon 4 of 21)	exon (NM_146200, exon 4 of 21)	1895	NM_146200	56347	Mm.22776	NM_146200	ENSMUSG00000030738	Eif3c	110kDa|3230401O13Rik|Eif3s8|NIPIL(A3)|NipilA3|Xs|Xsl	eukaryotic translation initiation factor 3, subunit C	protein-coding
mm_22916.1	chr3	31094720	31094729	+	1	NA	promoter-TSS (NM_001039090)	promoter-TSS (NM_001039090)	-334	NM_011386	20482	Mm.15406	NM_011386	ENSMUSG00000027660	Skil	Skir|SnoN|sno	SKI-like	protein-coding
mm_106577.1	chr11	120727227	120727292	-	1	NA	promoter-TSS (NM_026428)	promoter-TSS (NM_026428)	22	NM_026428	67880	Mm.231091	NM_026428	ENSMUSG00000039450	Dcxr	0610038K04Rik|1810027P18Rik|XR	dicarbonyl L-xylulose reductase	protein-coding
mm_27927.1	chr3	79552159	79552207	-	1	NA	intron (NM_001162999, intron 1 of 16)	RMER15|LTR|ERVL	15496	NM_001162999	329679	Mm.244005	NM_001162999	ENSMUSG00000061175	Fnip2	D630023B12Rik|mKIAA1450	folliculin interacting protein 2	protein-coding
mm_23912.1	chr3	83043402	83043438	+	1	NA	exon (NM_181849, exon 7 of 8)	exon (NM_181849, exon 7 of 8)	6443	NM_181849	110135	Mm.30063	NM_181849	ENSMUSG00000033831	Fgb	2510049G14Rik	fibrinogen beta chain	protein-coding
mm_92910.1	chr10	83543841	83543883	-	1	NA	promoter-TSS (NM_001033375)	promoter-TSS (NM_001033375)	-79	NM_001033375	319277	Mm.491194	NM_001033375	ENSMUSG00000034560	Washc4	A230046K03Rik|AA589518|Kiaa1033|mKIAA1033	WASH complex subunit 4	protein-coding
mm_153851.1	chr19	46350247	46350279	-	1	NA	Intergenic	Intergenic	-1275	NR_040418	75579	Mm.436708	NR_040418		2310034G01Rik	-	RIKEN cDNA 2310034G01 gene	ncRNA
mm_60432.1	chr7	44476838	44476846	+	1	NA	Intergenic	L1MEd|LINE|L1	6495	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_56510.1	chr6	99376022	99376036	-	1	NA	intron (NM_001347345, intron 2 of 19)	intron (NM_001347345, intron 2 of 19)	59316	NM_053202	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_84180.1	chr9	60024561	60024596	-	1	NA	intron (NM_001040426, intron 8 of 17)	intron (NM_001040426, intron 8 of 17)	73284	NM_001101600	665389	Mm.335214	NM_001101600		Gm7616	EG665389	predicted gene 7616	protein-coding
mm_88344.1	chr10	75835972	75835980	+	1	NA	Intergenic	Intergenic	-1095	NM_010361	14872	Mm.24118	NM_010361	ENSMUSG00000033318	Gstt2	AI266894|Yrs|mGSTT2	glutathione S-transferase, theta 2	protein-coding
mm_86589.1	chr10	13109391	13109393	+	1	NA	intron (NM_009538, intron 2 of 5)	intron (NM_009538, intron 2 of 5)	18547	NR_131912	338438		NR_131912		Hymai	-	hydatidiform mole associated and imprinted transcript	ncRNA
mm_102945.1	chr11	69616975	69616985	-	1	NA	intron (NM_011367, intron 3 of 7)	MIRb|SINE|MIR	925	NM_011367	20415	Mm.1431	NM_011367	ENSMUSG00000005202	Shbg	ABP	sex hormone binding globulin	protein-coding
mm_134113.1	chr16	10128535	10128554	-	1	NA	Intergenic	Intergenic	-41684	NM_026594	68172	Mm.23690	NM_026594	ENSMUSG00000039209	Rpl39l	4930517K11Rik	ribosomal protein L39-like	protein-coding
mm_40180.1	chr5	36164041	36164044	+	1	NA	intron (NM_030889, intron 2 of 26)	intron (NM_030889, intron 2 of 26)	-39979	NM_175249	76943	Mm.44242	NM_175249	ENSMUSG00000043430	Psapl1	2310020A21Rik	prosaposin-like 1	protein-coding
mm_156106.1	chrX	114284604	114284614	+	1	NA	Intergenic	Intergenic	-189724	NM_001290478	237010	Mm.132583	NM_172781	ENSMUSG00000025597	Klhl4	B130014A11|C130018J01Rik	kelch-like 4	protein-coding
mm_151495.1	chr19	58698916	58698917	+	1	NA	promoter-TSS (NR_038140)	promoter-TSS (NR_038140)	-1	NR_038140	69166	Mm.491059	NR_038140	ENSMUSG00000101088	1810018F18Rik	1810031L05Rik|1810047O18Rik	RIKEN cDNA 1810018F18 gene	ncRNA
mm_32769.1	chr4	116693948	116693960	+	1	NA	intron (NM_011034, intron 5 of 5)	intron (NM_011034, intron 5 of 5)	-7932	NR_040442	100502959	Mm.395400	NR_040442		AV051173	-	expressed sequence AV051173	ncRNA
mm_114088.1	chr13	54590754	54590769	+	1	NA	promoter-TSS (NM_178605)	promoter-TSS (NM_178605)	530	NM_025933	67044	Mm.29353	NM_025933	ENSMUSG00000025868	Higd2a	2010110M21Rik|AA690237	HIG1 domain family, member 2A	protein-coding
mm_8390.1	chr1	151345209	151345222	-	1	NA	intron (NM_001039511, intron 1 of 7)	CpG	717	NM_001039511	117198	Mm.33764	NM_028582	ENSMUSG00000023150	Ivns1abp	1190004M08Rik|1700126I16Rik|AA960440|HSPC068|ND1|NS-1|NS1-BP|Nd1-L|Nd1-S|mKIAA0850	influenza virus NS1A binding protein	protein-coding
mm_109691.1	chr12	113144025	113144037	+	1	NA	exon (NM_024223, exon 3 of 7)	exon (NM_024223, exon 3 of 7)	3426	NM_001347443	68337	Mm.133825	NM_024223	ENSMUSG00000006356	Crip2	0610010I23Rik|AW743261|C77570|CRP2|CRP4|Crp|ESP1|Hlp	cysteine rich protein 2	protein-coding
mm_141762.1	chr17	34269323	34269337	-	1	NA	TTS (NM_207105)	TTS (NM_207105)	6103	NM_207105	14961	Mm.254067	NM_207105	ENSMUSG00000073421	H2-Ab1	AI845868|Abeta|H-2Ab|H2-Ab|I-Abeta|IAb|Ia-2|Ia2|Rmcs1	histocompatibility 2, class II antigen A, beta 1	protein-coding
mm_49738.1	chr6	34745780	34745789	+	1	NA	exon (NM_145575, exon 3 of 12)	exon (NM_145575, exon 3 of 12)	-34648	NM_001289657	76223	Mm.150047	NM_178630	ENSMUSG00000038836	Agbl3	2900053G10Rik|4930431N21Rik|6530406M24Rik|CCP3	ATP/GTP binding protein-like 3	protein-coding
mm_64252.1	chr7	141704535	141704573	+	1	NA	intron (NM_023566, intron 27 of 45)	intron (NM_023566, intron 27 of 45)	14214	NM_023566	17831	Mm.2041	NM_023566		Muc2	2010015E03Rik|MCM|wnn	mucin 2	protein-coding
mm_67024.1	chr7	66337616	66337655	-	1	NA	intron (NM_146191, intron 3 of 33)	L1MDa|LINE|L1	44089	NR_106024	102465640		NR_106024	ENSMUSG00000098353	Mir7057	Gm27550|mmu-mir-7057	microRNA 7057	ncRNA
mm_131149.1	chr16	6680720	6680760	+	1	NA	intron (NM_021477, intron 4 of 16)	intron (NM_021477, intron 4 of 16)	-389095	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_104541.1	chr11	96713411	96713423	-	1	NA	intron (NM_001177898, intron 9 of 10)	intron (NM_001177898, intron 9 of 10)	64138	NM_028965	74479	Mm.270781	NM_028965	ENSMUSG00000020876	Snx11	4933439F10Rik|A930041K09Rik|AI117694	sorting nexin 11	protein-coding
mm_33538.1	chr4	130934458	130934468	+	1	NA	exon (NM_010686, exon 8 of 8)	exon (NM_010686, exon 8 of 8)	-9922	NM_010769	17180	Mm.271796	NM_010769	ENSMUSG00000040533	Matn1	CMP|Crtm|Mat1|matrilin-1	matrilin 1, cartilage matrix protein	protein-coding
mm_144606.1	chr18	32400253	32400281	+	1	NA	intron (NM_001083334, intron 1 of 14)	intron (NM_001083334, intron 1 of 14)	-21983	NR_045403	402767	Mm.385109	NR_045403	ENSMUSG00000097413	A830052D11Rik	-	RIKEN cDNA A830052D11 gene	ncRNA
mm_10025.1	chr1	192092459	192092469	-	1	NA	5' UTR (NM_011633, exon 1 of 10)	5' UTR (NM_011633, exon 1 of 10)	135	NM_011633	22033	Mm.380491	NM_011633		Traf5	-	TNF receptor-associated factor 5	protein-coding
mm_24182.1	chr3	88586889	88586901	+	1	NA	exon (NM_025448, exon 4 of 5)	exon (NM_025448, exon 4 of 5)	7224	NM_025448	66256	Mm.7091	NM_025448	ENSMUSG00000041355	Ssr2	1500032E05Rik|AI315033|AU020133|TLAP|TRAPB|TRAPbeta	signal sequence receptor, beta	protein-coding
mm_10181.1	chr2	4718192	4718205	+	1	NA	5' UTR (NM_001190400, exon 1 of 9)	5' UTR (NM_001190400, exon 1 of 9)	367	NM_178663	209645	Mm.149539	NM_178663	ENSMUSG00000048186	Bend7	1110017O21Rik|E130319B15Rik	BEN domain containing 7	protein-coding
mm_132492.1	chr16	36934977	36935013	+	1	NA	promoter-TSS (NM_008225)	promoter-TSS (NM_008225)	12	NM_008225	15163	Mm.4091	NM_008225	ENSMUSG00000022831	Hcls1	AW213261|HS1	hematopoietic cell specific Lyn substrate 1	protein-coding
mm_65642.1	chr7	27979135	27979154	-	1	NA	promoter-TSS (NM_001081021)	promoter-TSS (NM_001081021)	13	NM_001081021	338354	Mm.389873	NM_001081021	ENSMUSG00000063047	Zfp780b	B230208L21Rik	zinc finger protein 780B	protein-coding
mm_42324.1	chr5	114899931	114899975	+	1	NA	exon (NM_011854, exon 2 of 6)	exon (NM_011854, exon 2 of 6)	3019	NM_011854	23962	Mm.228363	NM_011854	ENSMUSG00000029561	Oasl2	M1204|Mmu-OASL|Oasl	2'-5' oligoadenylate synthetase-like 2	protein-coding
mm_71542.1	chr8	47533640	47533709	+	1	NA	promoter-TSS (NM_203507)	promoter-TSS (NM_203507)	29	NM_203507	192174	Mm.273081	NM_203507	ENSMUSG00000031568	Rwdd4a	BC016198|Gm1942|Rwdd4	RWD domain containing 4A	protein-coding
mm_139686.1	chr17	57420407	57420419	+	1	NA	exon (NM_010130, exon 12 of 22)	exon (NM_010130, exon 12 of 22)	61727	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_55312.1	chr6	54992883	54992907	-	1	NA	promoter-TSS (NM_026637)	promoter-TSS (NM_026637)	-28	NM_026637	110175	Mm.294708	NM_026637	ENSMUSG00000002797	Ggct	A030007L17Rik|AA673177|Gctg|Ggc	gamma-glutamyl cyclotransferase	protein-coding
mm_52097.1	chr6	97850978	97850986	+	1	NA	intron (NM_001113198, intron 1 of 9)	RMER17C|LTR|ERVK	43924	NM_001113198	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_134306.1	chr16	15862924	15862951	-	1	NA	5' UTR (NM_029354, exon 1 of 3)	5' UTR (NM_029354, exon 1 of 3)	385	NM_029354	72083	Mm.22351	NM_029354	ENSMUSG00000022671	Mzt2	2410018G20Rik|2610001E06Rik|Fam128|Fam128b	mitotic spindle organizing protein 2	protein-coding
mm_172806.1	chr9	120791773	120791787	-	1	NA	Intergenic	7SK|RNA|RNA	123470	NR_040742	76402	Mm.436588	NR_040742	ENSMUSG00000100146	1700020M21Rik	-	RIKEN cDNA 1700020M21 gene	ncRNA
mm_66286.1	chr7	37773556	37773592	-	1	NA	Intergenic	CpG	-3822	NM_172385	243937	Mm.322505	NM_172385	ENSMUSG00000043456	Zfp536	9630010P11Rik|Znf536|mKIAA0390	zinc finger protein 536	protein-coding
mm_173240.1	chrX	86898751	86898754	-	1	NA	intron (NM_001160403, intron 6 of 10)	L1Md_T|LINE|L1	-543758	NR_036689	245502	Mm.490821	NR_036689		Gm41	-	melanoma antigen, family B, 4 pseudogene	pseudo
mm_85425.1	chr9	103499222	103499260	-	1	NA	exon (NM_178638, exon 4 of 6)	exon (NM_178638, exon 4 of 6)	-18913	NM_001002896	107993	Mm.335403	NM_001002896	ENSMUSG00000032556	Bfsp2	AI448593|CP49	beaded filament structural protein 2, phakinin	protein-coding
mm_149918.1	chr19	26607183	26607226	+	1	NA	intron (NM_011416, intron 1 of 32)	CpG	2044	NM_011416	67155	Mm.342988	NM_011416	ENSMUSG00000024921	Smarca2	2610209L14Rik|SNF2alpha|Snf2l2|brahma|brm	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	protein-coding
mm_7007.1	chr1	86487377	86487396	-	1	NA	Intergenic	CpG	-39350	NM_008972	19231	Mm.19187	NM_008972	ENSMUSG00000026238	Ptma	Thym	prothymosin alpha	protein-coding
mm_7517.1	chr1	124045284	124045294	-	1	NA	intron (NM_199021, intron 1 of 25)	intron (NM_199021, intron 1 of 25)	270	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_154957.1	chrX	36795622	36795640	+	1	NA	promoter-TSS (NM_007451)	promoter-TSS (NM_007451)	34	NM_007451	11740	Mm.371544	NM_007451	ENSMUSG00000016319	Slc25a5	Ant2	solute carrier family 25 (mitochondrial carrier, adenine nucleotide translocator), member 5	protein-coding
mm_101875.1	chr11	48893380	48893401	-	1	NA	intron (NM_001024230, intron 4 of 4)	L1M2|LINE|L1	8762	NM_001024230	432555	Mm.338931	NM_001024230	ENSMUSG00000058163	Gm5431	EG432555|Irgb9b8	predicted gene 5431	protein-coding
mm_120933.1	chr14	76504507	76504521	+	1	NA	promoter-TSS (NM_009366)	promoter-TSS (NM_009366)	4	NM_009366	21807	Mm.153272	NM_009366	ENSMUSG00000022010	Tsc22d1	AA589566|AW105905|Egr5|TSC-22|Tgfb1i4|Tsc|Tsc22	TSC22 domain family, member 1	protein-coding
mm_61560.1	chr7	79505337	79505347	+	1	NA	promoter-TSS (NR_029818)	promoter-TSS (NR_029818)	78	NR_029818	723968		NR_029818	ENSMUSG00000093238	Mir9-3	Mirn9-3|mir-9-3|mmu-mir-9-3	microRNA 9-3	ncRNA
mm_51437.1	chr6	80018958	80018997	+	1	NA	promoter-TSS (NM_178731)	promoter-TSS (NM_178731)	100	NM_001134743	243499	Mm.483425	NM_178731	ENSMUSG00000052581	Lrrtm4	7530419J18Rik|A230052N11	leucine rich repeat transmembrane neuronal 4	protein-coding
mm_109682.1	chr12	113140199	113140257	+	1	NA	promoter-TSS (NM_024223)	promoter-TSS (NM_024223)	-8	NM_024223	68337	Mm.133825	NM_024223	ENSMUSG00000006356	Crip2	0610010I23Rik|AW743261|C77570|CRP2|CRP4|Crp|ESP1|Hlp	cysteine rich protein 2	protein-coding
mm_46728.1	chr5	110770711	110770723	-	1	NA	promoter-TSS (NM_029337)	promoter-TSS (NM_029337)	0	NM_029337	75560	Mm.270487	NM_029337	ENSMUSG00000029505	Ep400	1700020J09Rik|AU023439|mDomino|mKIAA1498|p400	E1A binding protein p400	protein-coding
mm_35380.1	chr4	33246167	33246213	-	1	NA	exon (NM_001033225, exon 2 of 2)	exon (NM_001033225, exon 2 of 2)	2597	NM_001033225	108767	Mm.27769	NM_001033225	ENSMUSG00000040128	Pnrc1	5730463C12Rik|B4-2|PRR2|Prol2	proline-rich nuclear receptor coactivator 1	protein-coding
mm_160540.1	chr9	40984346	40984346	-	1	NA	exon (NM_019465, exon 6 of 10)	exon (NM_019465, exon 6 of 10)	-20234	NM_001081121	70989	Mm.335087	NM_001081121	ENSMUSG00000032023	Jhy	4931429I11Rik|BB239335	juvenile hydrocephalus	protein-coding
mm_126370.1	chr15	80133115	80133155	+	1	NA	promoter-TSS (NM_025609)	promoter-TSS (NM_025609)	-19	NM_025609	66513	Mm.288245	NM_025609	ENSMUSG00000022414	Tab1	2310012M03Rik|Map3k7ip1|b2b449Clo	TGF-beta activated kinase 1/MAP3K7 binding protein 1	protein-coding
mm_132378.1	chr16	34921505	34921517	+	1	NA	intron (NM_139300, intron 15 of 31)	intron (NM_139300, intron 15 of 31)	17818	NR_040536	76649	Mm.420532	NR_040536	ENSMUSG00000100593	1700119H24Rik	-	RIKEN cDNA 1700119H24 gene	ncRNA
mm_2750.1	chr1	128705744	128705758	+	1	NA	Intergenic	Intergenic	-113452	NM_009911	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding
mm_70266.1	chr8	3587611	3587637	+	1	NA	5' UTR (NM_027171, exon 1 of 17)	5' UTR (NM_027171, exon 1 of 17)	174	NM_001347111	69697	Mm.390010	NM_027171	ENSMUSG00000044433	Camsap3	2310057J16Rik|Kiaa1543|Nezha	calmodulin regulated spectrin-associated protein family, member 3	protein-coding
mm_83310.1	chr9	44046853	44046895	-	1	NA	exon (NM_009382, exon 3 of 4)	exon (NM_009382, exon 3 of 4)	3490	NM_009382	21838	Mm.3951	NM_009382	ENSMUSG00000032011	Thy1	CD90|T25|Thy-1|Thy-1.2|Thy1.1|Thy1.2	thymus cell antigen 1, theta	protein-coding
mm_144781.1	chr18	35830301	35830363	+	1	NA	intron (NM_133687, intron 1 of 2)	CpG	514	NM_133687	67393	Mm.94560	NM_133687	ENSMUSG00000046668	Cxxc5	4930415K17Rik	CXXC finger 5	protein-coding
mm_107501.1	chr12	38868025	38868039	+	1	NA	3' UTR (NM_001163154, exon 10 of 10)	3' UTR (NM_001163154, exon 10 of 10)	84321	NM_001163154	14009	Mm.4866	NM_007960	ENSMUSG00000004151	Etv1	ER81|Etsrp81	ets variant 1	protein-coding
mm_141940.1	chr17	35048497	35048507	-	1	NA	Intergenic	Intergenic	-1741	NM_033444	114584	Mm.29524	NM_033444	ENSMUSG00000007041	Clic1	Clcp|G6	chloride intracellular channel 1	protein-coding
mm_151924.1	chr19	5800030	5800043	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	2636	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_28639.1	chr3	95219731	95219741	-	1	NA	3' UTR (NM_019914, exon 2 of 2)	3' UTR (NM_019914, exon 2 of 2)	-1794	NM_029885	213054	Mm.224820	NM_029885	ENSMUSG00000038766	Gabpb2	1810015F01Rik|5830427M07|9430006E19Rik|A430024B14Rik|AV050852|Gabpb2-1	GA repeat binding protein, beta 2	protein-coding
mm_105588.1	chr11	106724422	106724434	-	1	NA	Intergenic	RLTR11B|LTR|ERVK	-9147	NM_001305157	18613	Mm.343951	NM_008816	ENSMUSG00000020717	Pecam1	C85791|Cd31|PECAM-1|Pecam	platelet/endothelial cell adhesion molecule 1	protein-coding
mm_55771.1	chr6	78467842	78467876	-	1	NA	exon (NM_011260, exon 3 of 6)	exon (NM_011260, exon 3 of 6)	1015	NM_011260	19695	Mm.252385	NM_011260	ENSMUSG00000030017	Reg3g	AI449515|REG-3-gamma|reg III-gamma	regenerating islet-derived 3 gamma	protein-coding
mm_37679.1	chr4	129189601	129189631	-	1	NA	promoter-TSS (NM_029036)	promoter-TSS (NM_029036)	111	NM_001347203	74648	Mm.172064	NM_029036	ENSMUSG00000040928	S100pbp	4930429A08Rik|AI851343|S100pbpr	S100P binding protein	protein-coding
mm_13381.1	chr2	103904459	103904494	+	1	NA	non-coding (NR_131913, exon 2 of 7)	non-coding (NR_131913, exon 2 of 7)	3525	NR_131913	100996933	Mm.394449	NR_131913		Lincred1	-	long intergenic non-protein coding RNA of erythroid differentiation 1	ncRNA
mm_77563.1	chr8	123427838	123427848	-	1	NA	Intergenic	MuLV-int|LTR|ERV1	-15113	NM_001253784	23854	Mm.275127	NM_054046	ENSMUSG00000001482	Def8	AI449518|D8Ertd713e|DEF-8	differentially expressed in FDCP 8	protein-coding
mm_115387.1	chr13	113209945	113209959	+	1	NA	exon (NM_023612, exon 1 of 3)	exon (NM_023612, exon 1 of 3)	293	NM_023612	71690	Mm.38929	NM_023612	ENSMUSG00000042379	Esm1	0610042H23Rik|AV004503|ESM-1	endothelial cell-specific molecule 1	protein-coding
mm_165464.1	chr2	162253177	162253177	+	1	NA	intron (NM_001291151, intron 5 of 30)	intron (NM_001291151, intron 5 of 30)	-137636	NR_040617	77645	Mm.447752	NR_040617	ENSMUSG00000084919	Ptprtos	C330008G21Rik	protein tyrosine phosphatase, receptor type T, opposite strand	ncRNA
mm_168768.1	chr12	13997390	13997396	-	1	NA	Intergenic	L1Md_T|LINE|L1	154645	NM_029007	105005	Mm.227253	NM_029007	ENSMUSG00000020607	Fam84a	2310003N02Rik|4731402F03Rik|AW125753|Nse1	family with sequence similarity 84, member A	protein-coding
mm_29587.1	chr3	117826090	117826094	-	1	NA	intron (NM_029655, intron 7 of 8)	intron (NM_029655, intron 7 of 8)	42844	NM_001190156	76561	Mm.33824	NM_029655	ENSMUSG00000028007	Snx7	2510028H01Rik	sorting nexin 7	protein-coding
mm_93184.1	chr10	93875072	93875077	-	1	NA	intron (NM_019648, intron 5 of 11)	intron (NM_019648, intron 5 of 11)	16128	NM_019648	56307	Mm.289329	NM_019648	ENSMUSG00000036112	Metap2	4930584B20Rik|A930035J23Rik|AI047573|AL024412|AU014659|Amp2|Mnpep|p67|p67eIF2	methionine aminopeptidase 2	protein-coding
mm_135295.1	chr16	38600050	38600061	-	1	NA	3' UTR (NM_020260, exon 12 of 12)	3' UTR (NM_020260, exon 12 of 12)	37241	NM_026407	67846	Mm.310476	NM_026407	ENSMUSG00000002845	Tmem39a	2610033C09Rik	transmembrane protein 39a	protein-coding
mm_69356.1	chr7	130463831	130463845	-	1	NA	intron (NM_001029895, intron 10 of 11)	intron (NM_001029895, intron 10 of 11)	55742	NM_001136054	11907	Mm.216321	NM_013799	ENSMUSG00000030850	Ate1	AI225793|AW547406	arginyltransferase 1	protein-coding
mm_1562.1	chr1	74154083	74154085	+	1	NA	promoter-TSS (NM_009909)	promoter-TSS (NM_009909)	90	NM_009909	12765	Mm.234466	NM_009909	ENSMUSG00000026180	Cxcr2	CD128|CDw128|Cmkar2|Gpcr16|IL-8Rh|IL-8rb|IL8RA|Il8rb|mIL-8RH	chemokine (C-X-C motif) receptor 2	protein-coding
mm_149221.1	chr19	10018221	10018237	+	1	NA	promoter-TSS (NM_144538)	promoter-TSS (NM_144538)	1	NM_144538	74760	Mm.281969	NM_144538	ENSMUSG00000024663	Rab3il1	1200014K04Rik|AI115013|C76746|Rab3ail1	RAB3A interacting protein (rabin3)-like 1	protein-coding
mm_153864.1	chr19	46619972	46620001	-	1	NA	intron (NM_001177812, intron 2 of 4)	intron (NM_001177812, intron 2 of 4)	-3415	NM_001177813	226178	Mm.329895	NM_146099	ENSMUSG00000047731	Wbp1l	D19Wsu162e|Opal1	WW domain binding protein 1 like	protein-coding
mm_32782.1	chr4	116708625	116708635	+	1	NA	promoter-TSS (NM_026714)	promoter-TSS (NM_026714)	-245	NM_025962	67096	Mm.252785	NM_025962	ENSMUSG00000028690	Mmachc	1810037K07Rik|CblC	methylmalonic aciduria cblC type, with homocystinuria	protein-coding
mm_21605.1	chr2	164238438	164238443	-	1	NA	promoter-TSS (NM_017390)	promoter-TSS (NM_017390)	-99	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_164683.1	chr17	47518883	47518922	+	1	NA	intron (NM_001081635, intron 1 of 6)	B1_Mus2|SINE|Alu	13851	NM_001081635	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_172205.1	chr6	5476871	5476877	+	1	NA	Intergenic	RLTR10C|LTR|ERVK	19404	NM_013743	27273	Mm.235547	NM_013743	ENSMUSG00000019577	Pdk4	AV005916	pyruvate dehydrogenase kinase, isoenzyme 4	protein-coding
mm_121970.1	chr14	25587669	25587680	-	1	NA	non-coding (NR_033492, exon 1 of 1)	non-coding (NR_033492, exon 1 of 1)	870	NR_033492	77592	Mm.444871	NM_175264		4931406H21Rik	-	RIKEN cDNA 4931406H21 gene	ncRNA
mm_10738.1	chr2	23069118	23069144	+	1	NA	promoter-TSS (NM_001102438)	promoter-TSS (NM_001102438)	59	NM_001102438	74159	Mm.181973	NM_028793	ENSMUSG00000026781	Acbd5	1300014E15Rik	acyl-Coenzyme A binding domain containing 5	protein-coding
mm_129292.1	chr15	77203764	77203776	-	1	NA	intron (NM_053104, intron 2 of 13)	intron (NM_053104, intron 2 of 13)	-49958	NM_001286418	93686	Mm.202774	NM_053104	ENSMUSG00000033565	Rbfox2	Fbm2|Fxh|Hrnbp2|Rbm9	RNA binding protein, fox-1 homolog (C. elegans) 2	protein-coding
mm_29379.1	chr3	108825890	108825897	-	1	NA	intron (NM_011504, intron 4 of 18)	intron (NM_011504, intron 4 of 18)	14609	NM_011504	20912	Mm.316894	NM_011504	ENSMUSG00000027882	Stxbp3	Munc-18c|Stxbp3a|Sxtbp3|Unc18-3	syntaxin binding protein 3	protein-coding
mm_80685.1	chr9	91369042	91369073	+	1	NA	promoter-TSS (NM_009576)	promoter-TSS (NM_009576)	85	NM_009576	22774	Mm.8062	NM_009576	ENSMUSG00000036972	Zic4	-	zinc finger protein of the cerebellum 4	protein-coding
mm_41077.1	chr5	87674048	87674065	+	1	NA	exon (NM_007784, exon 11 of 34)	exon (NM_007784, exon 11 of 34)	7848	NM_001286016	12990	Mm.427467	NM_007784	ENSMUSG00000070702	Csn1s1	AA959832|AW212882|Csna	casein alpha s1	protein-coding
mm_133044.1	chr16	57549206	57549217	+	1	NA	promoter-TSS (NM_001177871)	promoter-TSS (NM_001177871)	-31	NM_001177871	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding
mm_53291.1	chr6	129014107	129014114	+	1	NA	promoter-TSS (NM_001277202)	promoter-TSS (NM_001277202)	-2	NM_001277202	435921	Mm.489572	NM_001277202		Clec2f	Clec2f-ps|Clr-c|Clrc|Clrz	C-type lectin domain family 2, member f	protein-coding
mm_81531.1	chr9	110064354	110064367	+	1	NA	exon (NM_008633, exon 10 of 19)	exon (NM_008633, exon 10 of 19)	12339	NM_001311164	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_103884.1	chr11	83574050	83574065	-	1	NA	3' UTR (NM_011338, exon 4 of 4)	3' UTR (NM_011338, exon 4 of 4)	4579	NM_011338	20308	Mm.416125	NM_011338	ENSMUSG00000019122	Ccl9	CCF18|MRP-2|Scya10|Scya9	chemokine (C-C motif) ligand 9	protein-coding
mm_131741.1	chr16	22053665	22053702	+	1	NA	Intergenic	Intergenic	44199	NR_027488	75826	Mm.297431	NM_029457	ENSMUSG00000022855	Senp2	2310007L05Rik|4930538C18Rik|AI646780|AW554757|Smt3ip2|SuPr-1|mKIAA1331	SUMO/sentrin specific peptidase 2	protein-coding
mm_78086.1	chr9	17556472	17556493	+	1	NA	Intergenic	Lx9|LINE|L1	-735785	NM_025844	66917	Mm.103534	NM_025844	ENSMUSG00000001774	Chordc1	1110001O09Rik|AA409036|Chp-1|morgana	cysteine and histidine-rich domain (CHORD)-containing, zinc-binding protein 1	protein-coding
mm_166676.1	chr6	97312043	97312043	-	1	NA	intron (NM_001346639, intron 11 of 22)	intron (NM_001346639, intron 11 of 22)	-59263	NM_001081157	320502	Mm.68163	NM_001081157	ENSMUSG00000044086	Lmod3	5430424A14Rik	leiomodin 3 (fetal)	protein-coding
mm_3231.1	chr1	135849746	135849756	+	1	NA	intron (NM_001130174, intron 10 of 13)	intron (NM_001130174, intron 10 of 13)	8890	NM_001130176	21956	Mm.247470	NM_011619	ENSMUSG00000026414	Tnnt2	Tnt|cTnT	troponin T2, cardiac	protein-coding
mm_75464.1	chr8	47941559	47941562	-	1	NA	intron (NM_133791, intron 1 of 22)	intron (NM_133791, intron 1 of 22)	48991	NM_133791	52357	Mm.235074	NM_133791	ENSMUSG00000031563	Wwc2	5330431C14Rik|AU022508|C85457|D8Ertd594e	WW, C2 and coiled-coil domain containing 2	protein-coding
mm_54980.1	chr6	48740765	48740774	-	1	NA	intron (NM_175860, intron 1 of 2)	intron (NM_175860, intron 1 of 2)	1722	NM_008376	16205	Mm.252599	NM_008376	ENSMUSG00000090019	Gimap1	IAP38|Imap38|imap	GTPase, IMAP family member 1	protein-coding
mm_158787.1	chrX	167207972	167208063	-	1	NA	exon (NM_021278, exon 2 of 3)	exon (NM_021278, exon 2 of 3)	1201	NM_021278	19241	Mm.142729	NM_021278	ENSMUSG00000049775	Tmsb4x	Ptmb4|Tb4	thymosin, beta 4, X chromosome	protein-coding
mm_62746.1	chr7	111083211	111083227	+	1	NA	promoter-TSS (NM_013507)	promoter-TSS (NM_013507)	-189	NM_013507	13690	Mm.185453	NM_013507	ENSMUSG00000005610	Eif4g2	DAP-5|E130105L11Rik|Nat1|Natm1|p97	eukaryotic translation initiation factor 4, gamma 2	protein-coding
mm_63482.1	chr7	127746567	127746581	+	1	NA	promoter-TSS (NM_172748)	promoter-TSS (NM_172748)	-201	NM_172748	233902	Mm.259353	NM_172748	ENSMUSG00000030811	Fbxl19	6030430O11|BC059812|Fbl19	F-box and leucine-rich repeat protein 19	protein-coding
mm_17558.1	chr2	30133662	30133690	-	1	NA	promoter-TSS (NM_146252)	promoter-TSS (NM_146252)	-70	NM_146252	70296	Mm.19172	NM_146252	ENSMUSG00000039678	Tbc1d13	2600014A06Rik|BC025586	TBC1 domain family, member 13	protein-coding
mm_19228.1	chr2	84670660	84670726	-	1	NA	promoter-TSS (NM_001033166)	promoter-TSS (NM_001033166)	15	NM_001033166	72657	Mm.259293	NM_001033166	ENSMUSG00000076437	Selenoh	2700094K13Rik|Selh	selenoprotein H	protein-coding
mm_26398.1	chr3	142601305	142601313	+	1	NA	intron (NM_010259, intron 4 of 10)	intron (NM_010259, intron 4 of 10)	6462	NM_010259	14468	Mm.457978	NM_010259	ENSMUSG00000040264	Gbp2b	Gbp-1|Gbp1|Mag-1|Mpa-1|Mpa1	guanylate binding protein 2b	protein-coding
mm_2518.1	chr1	106318701	106318707	+	1	NA	intron (NM_133821, intron 3 of 16)	intron (NM_133821, intron 3 of 16)	146835	NM_133821	98432	Mm.24115	NM_133821	ENSMUSG00000044340	Phlpp1	AI836256|Phlpp|Plekhe1|SCOP|mKIAA0606	PH domain and leucine rich repeat protein phosphatase 1	protein-coding
mm_148661.1	chr19	5568069	5568089	+	1	NA	promoter-TSS (NM_001033448)	promoter-TSS (NM_001033448)	5	NM_001033448	381201	Mm.441906	NM_001033448	ENSMUSG00000049562	Ap5b1	Gm962	adaptor-related protein complex 5, beta 1 subunit	protein-coding
mm_9472.1	chr1	173334918	173334938	-	1	NA	3' UTR (NM_053199, exon 9 of 9)	3' UTR (NM_053199, exon 9 of 9)	-1425	NM_010045	13349	Mm.6393	NM_010045	ENSMUSG00000037872	Ackr1	AA162249|CCBP1|CD234|Darc|Dfy|ESTM35|FY|GPD	atypical chemokine receptor 1 (Duffy blood group)	protein-coding
mm_97083.1	chr11	73090555	73090603	+	1	NA	promoter-TSS (NM_008399)	promoter-TSS (NM_008399)	-16	NM_172944	16407	Mm.96	NM_008399	ENSMUSG00000005947	Itgae	A530055J10|CD103|aM290|alpha-E1|alpha-M290	integrin alpha E, epithelial-associated	protein-coding
mm_20339.1	chr2	127656158	127656166	-	1	NA	5' UTR (NM_001171187, exon 1 of 3)	5' UTR (NM_001171187, exon 1 of 3)	533	NM_010762	17153	Mm.39040	NM_010762	ENSMUSG00000027375	Mal	Mpv17|Vip17	myelin and lymphocyte protein, T cell differentiation protein	protein-coding
mm_16970.1	chr2	17731089	17731120	-	1	NA	promoter-TSS (NM_028757)	promoter-TSS (NM_028757)	-36	NM_028757	74103	Mm.120298	NM_028757	ENSMUSG00000053702	Nebl	1200007O21Rik|A630080F05Rik|BB140644|D830029A09Rik|Lnebl	nebulette	protein-coding
mm_28645.1	chr3	95228263	95228273	-	1	NA	promoter-TSS (NM_172395)	promoter-TSS (NM_172395)	-156	NM_172395	57912	Mm.28189	NM_172395	ENSMUSG00000046722	Cdc42se1	1300002M12Rik|AW558204|Cdcse1|SCIP1|Spec1	CDC42 small effector 1	protein-coding
mm_98878.1	chr11	97806599	97806620	+	1	NA	intron (NM_010688, intron 1 of 6)	intron (NM_010688, intron 1 of 6)	6937	NM_010688	16796	Mm.271967	NM_010688	ENSMUSG00000038366	Lasp1	AA408629|Def-4|SH3P6|Tg(Col1a1-lacZ)1Ngma	LIM and SH3 protein 1	protein-coding
mm_18513.1	chr2	62626140	62626174	-	1	NA	intron (NM_001164477, intron 2 of 14)	intron (NM_001164477, intron 2 of 14)	20098	NM_027835	71586	Mm.136224	NM_027835	ENSMUSG00000026896	Ifih1	9130009C22Rik|Helicard|Hlcd|MDA5|RLR-2	interferon induced with helicase C domain 1	protein-coding
mm_1751.1	chr1	75507191	75507201	+	1	NA	promoter-TSS (NM_178884)	promoter-TSS (NM_178884)	119	NM_010564	16322	Mm.1100	NM_010564	ENSMUSG00000032968	Inha	AW555078	inhibin alpha	protein-coding
mm_126155.1	chr15	78409911	78409922	+	1	NA	intron (NM_138670, intron 1 of 2)	intron (NM_138670, intron 1 of 2)	2812	NM_138670	246221	Mm.294215	NM_138670	ENSMUSG00000071711	Mpst	Mst	mercaptopyruvate sulfurtransferase	protein-coding
mm_167389.1	chr8	94976982	94976986	-	1	NA	promoter-TSS (NM_001198894)	promoter-TSS (NM_001198894)	-125	NM_001198894	14766	Mm.290834	NM_018882	ENSMUSG00000031785	Adgrg1	Cyt28|Gpr56|TM7LN4|TM7XN1	adhesion G protein-coupled receptor G1	protein-coding
mm_4465.1	chr1	173350130	173350137	+	1	NA	intron (NM_053199, intron 1 of 8)	intron (NM_053199, intron 1 of 8)	-16630	NM_010045	13349	Mm.6393	NM_010045	ENSMUSG00000037872	Ackr1	AA162249|CCBP1|CD234|Darc|Dfy|ESTM35|FY|GPD	atypical chemokine receptor 1 (Duffy blood group)	protein-coding
mm_11949.1	chr2	52938641	52938670	+	1	NA	intron (NM_172409, intron 1 of 26)	intron (NM_172409, intron 1 of 26)	80787	NM_172409	71409	Mm.394427	NM_172409	ENSMUSG00000036053	Fmnl2	5430425K04Rik|Man	formin-like 2	protein-coding
mm_59287.1	chr7	24978346	24978359	+	1	NA	3' UTR (NM_001290469, exon 23 of 23)	3' UTR (NM_001290469, exon 23 of 23)	-5624	NM_010261	14470	Mm.22473	NM_010261	ENSMUSG00000003380	Rabac1	2310040I06Rik|Gbpap1|PRA1|prenylin	Rab acceptor 1 (prenylated)	protein-coding
mm_101116.1	chr11	11970541	11970554	-	1	NA	exon (NM_010345, exon 3 of 17)	exon (NM_010345, exon 3 of 17)	57424	NM_001177629	14783	Mm.273117	NM_010345	ENSMUSG00000020176	Grb10	5730571D09Rik|AI325020|Meg1|mKIAA0207	growth factor receptor bound protein 10	protein-coding
mm_125207.1	chr15	33282140	33282152	+	1	NA	intron (NM_176073, intron 3 of 7)	intron (NM_176073, intron 3 of 7)	123793	NR_033608	73486	Mm.483393	NM_028551	ENSMUSG00000058101	1700084J12Rik	-	ribosomal protein L7-like 1 pseudogene	pseudo
mm_137258.1	chr17	24550104	24550116	+	1	NA	5' UTR (NM_013630, exon 1 of 46)	5' UTR (NM_013630, exon 1 of 46)	160	NM_013630	18763	Mm.30435	NM_013630	ENSMUSG00000032855	Pkd1	PC1|mFLJ00285	polycystic kidney disease 1 homolog	protein-coding
mm_147537.1	chr18	53498686	53498689	-	1	NA	intron (NM_001033281, intron 2 of 6)	intron (NM_001033281, intron 2 of 6)	34141	NM_001033281	225518	Mm.297645	NM_001033281	ENSMUSG00000069378	Prdm6	Gm92|PRISM	PR domain containing 6	protein-coding
mm_61104.1	chr7	51887947	51887960	+	1	NA	exon (NM_001330607, exon 2 of 8)	exon (NM_001330607, exon 2 of 8)	8986	NM_001330607	14453	Mm.207360	NM_008087	ENSMUSG00000030498	Gas2	Gas-2	growth arrest specific 2	protein-coding
mm_39515.1	chr5	21256909	21256920	+	1	NA	intron (NM_175437, intron 18 of 30)	intron (NM_175437, intron 18 of 30)	70647	NM_175437	212167	Mm.121705	NM_175437	ENSMUSG00000039934	Gsap	A530088I07Rik|Pion	gamma-secretase activating protein	protein-coding
mm_120789.1	chr14	74732976	74732986	+	1	NA	intron (NM_001285423, intron 1 of 8)	intron (NM_001285423, intron 1 of 8)	684	NM_016903	13885	Mm.38055	NM_016903	ENSMUSG00000021996	Esd	Es-10|Es10|FGH|sid478	esterase D/formylglutathione hydrolase	protein-coding
mm_124033.1	chr14	77031790	77031809	-	1	NA	intron (NM_172488, intron 5 of 7)	B1_Mus1|SINE|Alu	4818	NM_172488	210808	Mm.89278	NM_172488	ENSMUSG00000044350	Lacc1	9030625A04Rik	laccase (multicopper oxidoreductase) domain containing 1	protein-coding
mm_166220.1	chr5	64423168	64423171	-	1	NA	Intergenic	Intergenic	44773	NR_040681	69999	Mm.261413	NR_040681	ENSMUSG00000100911	1700027F09Rik	-	RIKEN cDNA 1700027F09 gene	ncRNA
mm_93821.1	chr10	121476236	121476246	-	1	NA	promoter-TSS (NM_138956)	promoter-TSS (NM_138956)	9	NM_138956	192678	Mm.41265	NM_138956	ENSMUSG00000025795	Rassf3	AW212023|AW322379	Ras association (RalGDS/AF-6) domain family member 3	protein-coding
mm_120565.1	chr14	68594295	68594298	+	1	NA	Intergenic	Intergenic	-12224	NM_021475	58860	Mm.36742	NM_021475	ENSMUSG00000022057	Adamdec1	2210414L24Rik|AI574231|Dcsn	ADAM-like, decysin 1	protein-coding
mm_127125.1	chr15	98108535	98108575	+	1	NA	promoter-TSS (NM_001163487)	promoter-TSS (NM_001163487)	84	NM_001163487	18642	Mm.272582	NM_021514	ENSMUSG00000033065	Pfkm	AI131669|ATP-PFK|PFK-A|PFK-M|Pfk-4|Pfk4|Pfka|Pfkx	phosphofructokinase, muscle	protein-coding
mm_21369.1	chr2	157204445	157204462	-	1	NA	promoter-TSS (NM_001139516)	promoter-TSS (NM_001139516)	81	NM_011249	19650	Mm.244671	NM_011249	ENSMUSG00000027641	Rbl1	AW547426|PRB1|p107	retinoblastoma-like 1 (p107)	protein-coding
mm_34873.1	chr4	155562349	155562413	+	1	NA	promoter-TSS (NM_138671)	promoter-TSS (NM_138671)	-11	NM_138671	192185	Mm.28347	NM_138671	ENSMUSG00000029063	Nadk	4432404C02Rik|BC004012	NAD kinase	protein-coding
mm_143555.1	chr17	74173852	74173862	-	1	NA	Intergenic	Intergenic	121006	NM_133771	76890	Mm.311874	NM_133771	ENSMUSG00000058704	Memo1	0610016J10Rik|D930048L02Rik	mediator of cell motility 1	protein-coding
mm_59822.1	chr7	29238511	29238557	+	1	NA	intron (NM_029887, intron 1 of 7)	CpG	211	NM_029887	77254	Mm.36699	NM_029887	ENSMUSG00000030588	Yif1b	9430029K10Rik|Yip1b	Yip1 interacting factor homolog B (S. cerevisiae)	protein-coding
mm_25077.1	chr3	99981317	99981338	+	1	NA	intron (NM_028892, intron 4 of 48)	GSAT_MM|Satellite|Satellite	95910	NM_028892	74362	Mm.55847	NM_028892	ENSMUSG00000027867	Spag17	4931427F14Rik|PF6|Spag17-ps	sperm associated antigen 17	protein-coding
mm_113962.1	chr13	51203209	51203213	+	1	NA	promoter-TSS (NR_132443)	promoter-TSS (NR_132443)	-145	NR_132443	667728		NR_132443		Hist1h2al	EG667728	histone cluster 1, H2al	pseudo
mm_142444.1	chr17	45592371	45592411	-	1	NA	promoter-TSS (NM_022880)	promoter-TSS (NM_022880)	2	NM_022880	63959	Mm.29744	NM_022880	ENSMUSG00000023942	Slc29a1	1200014D21Rik|AA407560|ENT1	solute carrier family 29 (nucleoside transporters), member 1	protein-coding
mm_40943.1	chr5	76810013	76810057	+	1	NA	Intergenic	Intergenic	-30564	NM_001163793	320827	Mm.101504	NM_001163793	ENSMUSG00000036377	C530008M17Rik	2810489J07Rik|4930529A19Rik|4931405B09Rik|Kiaa1211|mKIAA1211	RIKEN cDNA C530008M17 gene	protein-coding
mm_49715.1	chr6	34476287	34476362	+	1	NA	promoter-TSS (NM_007563)	promoter-TSS (NM_007563)	-32	NM_007563	12183	Mm.282863	NM_007563	ENSMUSG00000038871	Bpgm	AI323730|AL022789|C86192	2,3-bisphosphoglycerate mutase	protein-coding
mm_32762.1	chr4	116690061	116690070	+	1	NA	intron (NM_011034, intron 2 of 5)	intron (NM_011034, intron 2 of 5)	-4043	NR_040442	100502959	Mm.395400	NR_040442		AV051173	-	expressed sequence AV051173	ncRNA
mm_101167.1	chr11	16974025	16974097	-	1	NA	3' UTR (NM_019549, exon 10 of 10)	3' UTR (NM_019549, exon 10 of 10)	22651	NM_176982	319701	Mm.120672	NM_176982	ENSMUSG00000044966	Fbxo48	A630050E13Rik	F-box protein 48	protein-coding
mm_172771.1	chr8	94179194	94179194	+	1	NA	5' UTR (NM_013602, exon 1 of 3)	5' UTR (NM_013602, exon 1 of 3)	105	NM_013602	17748	Mm.192991	NM_013602	ENSMUSG00000031765	Mt1	MT-I|Mt-1	metallothionein 1	protein-coding
mm_62943.1	chr7	119526203	119526218	+	1	NA	promoter-TSS (NM_178758)	promoter-TSS (NM_178758)	-55	NM_178758	272428	Mm.185183	NM_178758	ENSMUSG00000030972	Acsm5	C730019D22|C730027J19Rik	acyl-CoA synthetase medium-chain family member 5	protein-coding
mm_91342.1	chr10	26343510	26343510	-	1	NA	intron (NM_001347467, intron 3 of 20)	intron (NM_001347467, intron 3 of 20)	30524	NM_001347467	237339	Mm.338439	NM_172787	ENSMUSG00000039089	L3mbtl3	AI481284|MBT-1	l(3)mbt-like 3 (Drosophila)	protein-coding
mm_91353.1	chr10	27616896	27616904	-	1	NA	promoter-TSS (NM_008481)	promoter-TSS (NM_008481)	42	NM_008481	16773	Mm.256087	NM_008481	ENSMUSG00000019899	Lama2	5830440B04|dy|mKIAA4087|mer|merosin	laminin, alpha 2	protein-coding
mm_112718.1	chr13	19190702	19190714	+	1	NA	Intergenic	Intergenic	205105	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_152819.1	chr19	23136172	23136176	-	1	NA	Intergenic	CpG	-5052	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_156247.1	chrX	136271360	136271394	+	1	NA	exon (NM_009750, exon 3 of 3)	exon (NM_009750, exon 3 of 3)	1124	NM_001110234	12070	Mm.90787	NM_009750	ENSMUSG00000046432	Bex3	AL033356|DXWsu67e|Gcap27|Nade|Ngfrap1	brain expressed X-linked 3	protein-coding
mm_150963.1	chr19	46500043	46500056	+	1	NA	Intergenic	CpG	-1599	NM_053100	93679	Mm.392177	NM_053100	ENSMUSG00000025034	Trim8	AA408830|BB006755|GERP|Rnf27	tripartite motif-containing 8	protein-coding
mm_14036.1	chr2	122160684	122160693	+	1	NA	promoter-TSS (NM_080510)	promoter-TSS (NM_080510)	-12	NM_080510	70928	Mm.379188	NM_080510	ENSMUSG00000033368	Trim69	4921519C19Rik|Rnf36|Trif|Trimless	tripartite motif-containing 69	protein-coding
mm_55969.1	chr6	85821002	85821007	-	1	NA	promoter-TSS (NM_023493)	promoter-TSS (NM_023493)	-32	NM_023493	69049	Mm.441449	NM_023493	ENSMUSG00000079494	Nat8f5	1810018F03Rik|Cml5	N-acetyltransferase 8 (GCN5-related) family member 5	protein-coding
mm_123092.1	chr14	55784008	55784019	-	1	NA	promoter-TSS (NM_080435)	promoter-TSS (NM_080435)	6	NM_080435	104110	Mm.287010	NM_080435	ENSMUSG00000022220	Adcy4	mKIAA4004	adenylate cyclase 4	protein-coding
mm_83546.1	chr9	46235757	46235789	-	1	NA	promoter-TSS (NM_001289755)	promoter-TSS (NM_001289755)	-137	NM_001289756	11814	Mm.390161	NM_023114	ENSMUSG00000032081	Apoc3	apo-CIII|apoC-III	apolipoprotein C-III	protein-coding
mm_60592.1	chr7	44496565	44496587	+	1	NA	promoter-TSS (NM_197991)	promoter-TSS (NM_197991)	-12	NM_028169	75538	Mm.258841	NM_028169	ENSMUSG00000051113	Fam71e1	0610007G24Rik|1700021N13Rik|1700021P22Rik|GARI-L5	family with sequence similarity 71, member E1	protein-coding
mm_4444.1	chr1	172548731	172548763	+	1	NA	intron (NR_040558, intron 1 of 2)	intron (NR_040558, intron 1 of 2)	2059	NR_040558	71319	Mm.123774	NR_040558	ENSMUSG00000085184	4933439K11Rik	-	RIKEN cDNA 4933439K11 gene	ncRNA
mm_170144.1	chr17	42876344	42876352	-	1	NA	promoter-TSS (NM_009847)	promoter-TSS (NM_009847)	76	NM_009847	12488	Mm.218637	NM_009847	ENSMUSG00000061665	Cd2ap	AL024079|C78928|METS-1|Mets1	CD2-associated protein	protein-coding
mm_23573.1	chr3	63298006	63298054	+	1	NA	intron (NM_001289463, intron 1 of 22)	intron (NM_001289463, intron 1 of 22)	1935	NM_001289463	17380	Mm.296022	NM_008604	ENSMUSG00000027820	Mme	6030454K05Rik|C85356|CALLA|CD10|NEP|SFE	membrane metallo endopeptidase	protein-coding
mm_108694.1	chr12	86902700	86902711	+	1	NA	Intergenic	B1_Mur2|SINE|Alu	-17891	NM_145836	238330	Mm.248358	NM_145836	ENSMUSG00000034168	Irf2bpl	6430527G18Rik|Eap1	interferon regulatory factor 2 binding protein-like	protein-coding
mm_50514.1	chr6	49039611	49039613	+	1	NA	intron (NM_053110, intron 1 of 10)	B3A|SINE|B2	3094	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_3898.1	chr1	161704824	161704834	+	1	NA	Intergenic	Intergenic	83666	NM_001205243	14103	Mm.3355	NM_010177	ENSMUSG00000000817	Fasl	APT1LG1|CD178|CD95-L|CD95L|Fas-L|Faslg|Tnfsf6|Tnlg1a|gld	Fas ligand (TNF superfamily, member 6)	protein-coding
mm_82020.1	chr9	121748048	121748068	+	1	NA	exon (NM_010918, exon 13 of 17)	exon (NM_010918, exon 13 of 17)	11885	NR_033503	320301	Mm.373883	NR_033503		E530011L22Rik	-	RIKEN cDNA E530011L22 gene	ncRNA
mm_56124.1	chr6	87532977	87532998	-	1	NA	5' UTR (NM_001286610, exon 1 of 10)	5' UTR (NM_001286610, exon 1 of 10)	272	NM_001037727	232201	Mm.119564	NM_175476	ENSMUSG00000030047	Arhgap25	A130039I20Rik	Rho GTPase activating protein 25	protein-coding
mm_1131.1	chr1	60409613	60409648	+	1	NA	promoter-TSS (NM_001198570)	promoter-TSS (NM_001198570)	11	NM_001198570	329165	Mm.212066	NM_198127	ENSMUSG00000026782	Abi2	8430425M24Rik|AI839867|C130078H13	abl-interactor 2	protein-coding
mm_33444.1	chr4	130520731	130520749	+	1	NA	Intergenic	Intergenic	53296	NM_025998	67149	Mm.423029	NM_025998	ENSMUSG00000078532	Nkain1	2610200G18Rik|2810426C15Rik	Na+/K+ transporting ATPase interacting 1	protein-coding
mm_25803.1	chr3	127789272	127789287	+	1	NA	promoter-TSS (NM_145133)	promoter-TSS (NM_145133)	-634	NM_145133	211550	Mm.31852	NM_145133	ENSMUSG00000046688	Tifa	T2bp	TRAF-interacting protein with forkhead-associated domain	protein-coding
mm_120302.1	chr14	63140467	63140480	+	1	NA	intron (NM_007798, intron 8 of 9)	intron (NM_007798, intron 8 of 9)	18011	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_35236.1	chr4	19877130	19877142	-	1	NA	3' UTR (NM_175406, exon 8 of 8)	3' UTR (NM_175406, exon 8 of 8)	45430	NM_175406	242341	Mm.19298	NM_175406	ENSMUSG00000028238	Atp6v0d2	1620401A02Rik|AI324824|V-ATPase	ATPase, H+ transporting, lysosomal V0 subunit D2	protein-coding
mm_110125.1	chr12	26444202	26444208	-	1	NA	3' UTR (NM_021384, exon 6 of 6)	3' UTR (NM_021384, exon 6 of 6)	12247	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_138824.1	chr17	39847820	39847829	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	4827	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_8595.1	chr1	156029770	156029793	-	1	NA	intron (NM_001160018, intron 4 of 9)	B1_Mm|SINE|Alu	5036	NM_001160019	208263	Mm.211654	NM_144791	ENSMUSG00000026466	Tor1aip1	LAP1|Lap1B	torsin A interacting protein 1	protein-coding
mm_158573.1	chrX	150589848	150589861	-	1	NA	promoter-TSS (NM_008824)	promoter-TSS (NM_008824)	-67	NM_008824	18639	Mm.249131	NM_008824	ENSMUSG00000025271	Pfkfb1	PFK/FBPase 1	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1	protein-coding
mm_52293.1	chr6	108668559	108668590	+	1	NA	Intergenic	CpG	-7640	NR_104577	75394	Mm.395061	NR_040757	ENSMUSG00000087341	0610040F04Rik	-	RIKEN cDNA 0610040F04 gene	ncRNA
mm_82174.1	chr9	123851249	123851283	+	1	NA	intron (NM_148925, intron 1 of 18)	intron (NM_148925, intron 1 of 18)	395	NM_148925	17281	Mm.252941	NM_148925	ENSMUSG00000025241	Fyco1	2810409M01Rik|Mem2|RUFY3|ZFYVE7	FYVE and coiled-coil domain containing 1	protein-coding
mm_167464.1	chr8	124585328	124585329	+	1	NA	intron (NM_023709, intron 1 of 19)	intron (NM_023709, intron 1 of 19)	9217	NM_023709	73647	Mm.6209	NM_023709	ENSMUSG00000031981	Capn9	2200003B16Rik|GC36|nCL-4|nCL4	calpain 9	protein-coding
mm_156323.1	chrX	137570781	137570784	+	1	NA	promoter-TSS (NM_030688)	promoter-TSS (NM_030688)	28	NM_030688	60367	Mm.328321	NM_030688	ENSMUSG00000059203	Il1rapl2	-	interleukin 1 receptor accessory protein-like 2	protein-coding
mm_59468.1	chr7	27266749	27266767	+	1	NA	exon (NM_010950, exon 5 of 10)	exon (NM_010950, exon 5 of 10)	7997	NM_010950	18223	Mm.458153	NM_010950	ENSMUSG00000063160	Numbl	nbl	numb-like	protein-coding
mm_131672.1	chr16	20672908	20672918	+	1	NA	intron (NM_001304432, intron 1 of 31)	CpG	186	NM_001304432	208643	Mm.260256	NM_145941	ENSMUSG00000045983	Eif4g1	E030015G23Rik|eIF-4-gamma 1|eIF-4G 1|eIF-4G1|eIF4GI	eukaryotic translation initiation factor 4, gamma 1	protein-coding
mm_77078.1	chr8	110489815	110489817	-	1	NA	exon (NM_172916, exon 27 of 87)	exon (NM_172916, exon 27 of 87)	12540	NR_105058	100861869	Mm.84499	NR_105058		Gm21283	-	predicted gene, 21283	ncRNA
mm_56743.1	chr6	115838204	115838223	-	1	NA	5' UTR (NM_001110506, exon 1 of 9)	5' UTR (NM_001110506, exon 1 of 9)	199	NM_001110506	212516	Mm.333333	NM_198603	ENSMUSG00000030321	Efcab12	BB124106	EF-hand calcium binding domain 12	protein-coding
mm_105795.1	chr11	109995776	109995800	-	1	NA	promoter-TSS (NM_013851)	promoter-TSS (NM_013851)	28	NM_013851	27404	Mm.341004	NM_013851	ENSMUSG00000020620	Abca8b	Abca8	ATP-binding cassette, sub-family A (ABC1), member 8b	protein-coding
mm_168104.1	chr10	13894277	13894289	+	1	NA	Intergenic	L1Md_Gf|LINE|L1	-25326	NM_001347362	66253	Mm.45755	NM_025446	ENSMUSG00000019806	Aig1	1500031O19Rik|AV064870|AW413422|CGI-103	androgen-induced 1	protein-coding
mm_144495.1	chr18	24205938	24206002	+	1	NA	promoter-TSS (NM_001160404)	promoter-TSS (NM_001160404)	-24	NM_001160404	14423	Mm.30249	NM_013814	ENSMUSG00000000420	Galnt1	-	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 1	protein-coding
mm_37143.1	chr4	116993625	116993634	-	1	NA	exon (NM_009478, exon 2 of 10)	exon (NM_009478, exon 2 of 10)	784	NM_009478	22275	Mm.46484	NM_009478	ENSMUSG00000028684	Urod	AI323803|UPD|Uro-d	uroporphyrinogen decarboxylase	protein-coding
mm_27945.1	chr3	79737872	79737895	-	1	NA	promoter-TSS (NM_212452)	promoter-TSS (NM_212452)	-89	NM_212452	381489	Mm.331086	NM_212452	ENSMUSG00000034009	Rxfp1	Gm1018|Lgr7	relaxin/insulin-like family peptide receptor 1	protein-coding
mm_54543.1	chr6	36809939	36809974	-	1	NA	5' UTR (NM_008973, exon 1 of 5)	5' UTR (NM_008973, exon 1 of 5)	1405	NM_008973	19242	Mm.279690	NM_008973	ENSMUSG00000029838	Ptn	HARP|HB-GAM|HBBN|HBGF-8|HBNF|OSF|Osf-1|Osf1	pleiotrophin	protein-coding
mm_69539.1	chr7	135695552	135695574	-	1	NA	exon (NM_001081117, exon 12 of 14)	exon (NM_001081117, exon 12 of 14)	20816	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_96474.1	chr11	67652643	67652653	+	1	NA	intron (NM_001109657, intron 4 of 13)	intron (NM_001109657, intron 4 of 13)	-42678	NM_009038	19674	Mm.439726	NM_009038	ENSMUSG00000020907	Rcvrn	CAR|S-modulin	recoverin	protein-coding
mm_56379.1	chr6	94283576	94283602	-	1	NA	5' UTR (NM_010367, exon 1 of 22)	5' UTR (NM_010367, exon 1 of 22)	328	NM_001286786	14924	Mm.217216	NM_010367	ENSMUSG00000045095	Magi1	AIP3|BAP1|Baiap1|Gukmi1|MAGI1c|Magi-1|TNRC19|WWP3|mKIAA4129	membrane associated guanylate kinase, WW and PDZ domain containing 1	protein-coding
mm_48150.1	chr5	137151096	137151103	-	1	NA	Intergenic	Intergenic	-34892	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_113349.1	chr13	31806899	31806916	+	1	NA	5' UTR (NM_008592, exon 1 of 1)	5' UTR (NM_008592, exon 1 of 1)	261	NM_008592	17300	Mm.12949	NM_008592	ENSMUSG00000050295	Foxc1	FREAC3|Fkh1|Mf1|Mf4|ch|fkh-1|frkhda	forkhead box C1	protein-coding
mm_136639.1	chr17	5799598	5799614	+	1	NA	non-coding (NR_045079, exon 1 of 3)	non-coding (NR_045079, exon 1 of 3)	116	NR_045080	78512	Mm.23696	NR_045079	ENSMUSG00000096965	3300005D01Rik	-	RIKEN cDNA 3300005D01 gene	ncRNA
mm_164032.1	chr14	77539748	77539791	+	1	NA	intron (NM_001253759, intron 7 of 19)	intron (NM_001253759, intron 7 of 19)	-32901	NR_033141	629678	Mm.390721	NM_001037935	ENSMUSG00000067973	Gm6994	EG629678	predicted gene 6994	ncRNA
mm_55700.1	chr6	72899900	72899951	-	1	NA	promoter-TSS (NM_019715)	promoter-TSS (NM_019715)	54	NM_019715	74287	Mm.29194	NM_019715	ENSMUSG00000055239	Kcmf1	1700094M07Rik|Debt91|Pmcf	potassium channel modulatory factor 1	protein-coding
mm_61163.1	chr7	59228785	59228824	+	1	NA	promoter-TSS (NM_001033962)	promoter-TSS (NM_001033962)	52	NM_011668	22215	Mm.9002	NM_011668	ENSMUSG00000025326	Ube3a	4732496B02|5830462N02Rik|A130086L21Rik|Hpve6a|mKIAA4216	ubiquitin protein ligase E3A	protein-coding
mm_32789.1	chr4	116807715	116807726	+	1	NA	promoter-TSS (NM_026654)	promoter-TSS (NM_026654)	-14	NM_133250	70603	Mm.180333	NM_133250	ENSMUSG00000028687	Mutyh	5730495A01Rik|Mutyha|Mutyhalpha|Mutyhb|Mutyhbeta|Mutyhc|Myh	mutY DNA glycosylase	protein-coding
mm_96680.1	chr11	69443644	69443648	+	1	NA	intron (NM_001081330, intron 63 of 85)	intron (NM_001081330, intron 63 of 85)	-29971	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_6437.1	chr1	73998034	73998038	-	1	NA	intron (NM_027884, intron 6 of 34)	intron (NM_027884, intron 6 of 34)	126411	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_131017.1	chr15	103563382	103563393	-	1	NA	exon (NM_008134, exon 3 of 4)	exon (NM_008134, exon 3 of 4)	1694	NM_001289587	14663	Mm.219621	NM_008134	ENSMUSG00000022491	Glycam1	MC26|Sgp50|glyCAM-1	glycosylation dependent cell adhesion molecule 1	protein-coding
mm_164545.1	chr17	9669726	9669729	-	1	NA	promoter-TSS (NM_001163836)	promoter-TSS (NM_001163836)	-23	NM_001163836	67543	Mm.26987	NM_026226	ENSMUSG00000046173	Pabpc6	4932702K14Rik|AI428050|Pabpc3	poly(A) binding protein, cytoplasmic 6	protein-coding
mm_124570.1	chr14	124192589	124192599	-	1	NA	promoter-TSS (NM_010201)	promoter-TSS (NM_010201)	-48	NM_010201	14169	Mm.206362	NM_010201	ENSMUSG00000025551	Fgf14	FHF-4|Fhf4|mFHF-4(1B)	fibroblast growth factor 14	protein-coding
mm_18511.1	chr2	62617349	62617361	-	1	NA	exon (NM_027835, exon 5 of 16)	exon (NM_027835, exon 5 of 16)	28900	NM_027835	71586	Mm.136224	NM_027835	ENSMUSG00000026896	Ifih1	9130009C22Rik|Helicard|Hlcd|MDA5|RLR-2	interferon induced with helicase C domain 1	protein-coding
mm_139656.1	chr17	57402757	57402822	+	1	NA	exon (NM_010130, exon 5 of 22)	exon (NM_010130, exon 5 of 22)	44103	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_45947.1	chr5	90337689	90337693	-	1	NA	intron (NM_198010, intron 1 of 32)	intron (NM_198010, intron 1 of 32)	28494	NM_030886	81702	Mm.245522	NM_030886	ENSMUSG00000055204	Ankrd17	4933425K22Rik|A130069E23Rik|A930008M01|AA407558|AA516750|AU040470|Foe|Gtar|Mask|mKIAA0697	ankyrin repeat domain 17	protein-coding
mm_43155.1	chr5	125555438	125555439	+	1	NA	intron (NM_001190352, intron 1 of 8)	B1_Mur2|SINE|Alu	23020	NM_001190352	208151	Mm.40397	NM_001190352	ENSMUSG00000070498	Tmem132b	AK220418|mKIAA1786	transmembrane protein 132B	protein-coding
mm_73841.1	chr8	117498252	117498264	+	1	NA	promoter-TSS (NM_172285)	promoter-TSS (NM_172285)	-17	NM_172285	234779	Mm.192699	NM_172285	ENSMUSG00000034330	Plcg2	PLC-gamma-2|PLCgamma2|Plcg-2	phospholipase C, gamma 2	protein-coding
mm_53526.1	chr6	136532925	136532939	+	1	NA	intron (NM_019426, intron 1 of 14)	intron (NM_019426, intron 1 of 14)	14081	NM_019426	54343	Mm.173271	NM_019426	ENSMUSG00000030213	Atf7ip	2610204M12Rik|AM|Mcaf1	activating transcription factor 7 interacting protein	protein-coding
mm_3610.1	chr1	151755453	151755463	+	1	NA	promoter-TSS (NM_001039644)	promoter-TSS (NM_001039644)	84	NM_001311166	66967	Mm.337691	NM_001039644	ENSMUSG00000043019	Edem3	2310050N11Rik	ER degradation enhancer, mannosidase alpha-like 3	protein-coding
mm_134187.1	chr16	10966462	10966491	-	1	NA	exon (NM_019980, exon 2 of 4)	exon (NM_019980, exon 2 of 4)	26645	NM_019980	56722	Mm.294753	NM_019980	ENSMUSG00000022500	Litaf	3222402J11Rik|C85531|N4WBP3|TBX1	LPS-induced TN factor	protein-coding
mm_20984.1	chr2	151980136	151980182	-	1	NA	promoter-TSS (NM_146127)	promoter-TSS (NM_146127)	60	NM_146127	73847	Mm.272444	NM_028666	ENSMUSG00000027459	Fam110a	1700008J10Rik|5430432M24Rik|AI747080	family with sequence similarity 110, member A	protein-coding
mm_93755.1	chr10	120174316	120174318	-	1	NA	intron (NM_028679, intron 5 of 11)	intron (NM_028679, intron 5 of 11)	27220	NM_028679	73914	Mm.146194	NM_028679	ENSMUSG00000020227	Irak3	4833428C18Rik|AI563835|IRAK-M	interleukin-1 receptor-associated kinase 3	protein-coding
mm_118042.1	chr13	101694514	101694612	-	1	NA	intron (NM_001077495, intron 7 of 15)	CpG	-1933	NM_001024955	18708	Mm.259333	NM_001024955	ENSMUSG00000041417	Pik3r1	PI3K|p50alpha|p55alpha|p85alpha	phosphatidylinositol 3-kinase, regulatory subunit, polypeptide 1 (p85 alpha)	protein-coding
mm_121264.1	chr14	103074318	103074330	+	1	NA	intron (NM_001033242, intron 3 of 3)	intron (NM_001033242, intron 3 of 3)	4108	NM_001033242	211286	Mm.295289	NM_001033242	ENSMUSG00000022125	Cln5	A730075N08Rik	ceroid-lipofuscinosis, neuronal 5	protein-coding
mm_58519.1	chr7	4139496	4139505	+	1	NA	exon (NM_172736, exon 3 of 15)	exon (NM_172736, exon 3 of 15)	2444	NM_172736	232798	Mm.22831	NM_172736	ENSMUSG00000035545	Leng8	AW049671	leukocyte receptor cluster (LRC) member 8	protein-coding
mm_72463.1	chr8	83290343	83290358	+	1	NA	promoter-TSS (NM_009463)	promoter-TSS (NM_009463)	2	NM_009463	22227	Mm.4177	NM_009463	ENSMUSG00000031710	Ucp1	AI385626|Slc25a7|Ucp	uncoupling protein 1 (mitochondrial, proton carrier)	protein-coding
mm_22157.1	chr2	172869439	172869478	-	1	NA	3' UTR (NM_007557, exon 7 of 7)	3' UTR (NM_007557, exon 7 of 7)	70863	NM_007557	12162	Mm.595	NM_007557	ENSMUSG00000008999	Bmp7	OP1	bone morphogenetic protein 7	protein-coding
mm_24676.1	chr3	94837534	94837564	+	1	NA	promoter-TSS (NM_172683)	promoter-TSS (NM_172683)	-18	NM_001165948	229584	Mm.274787	NM_172683	ENSMUSG00000038902	Pogz	9530006B08Rik	pogo transposable element with ZNF domain	protein-coding
mm_127282.1	chr15	99972811	99972821	+	1	NA	promoter-TSS (NM_001284521)	promoter-TSS (NM_001284521)	36	NM_001284523	207214	Mm.28811	NM_001024526	ENSMUSG00000023025	Larp4	DXErtd793|DXErtd793e	La ribonucleoprotein domain family, member 4	protein-coding
mm_141491.1	chr17	31296624	31296646	-	1	NA	5' UTR (NM_001242427, exon 1 of 20)	5' UTR (NM_001242427, exon 1 of 20)	411	NM_001242427	224674	Mm.311395	NM_153062	ENSMUSG00000024036	Slc37a1	G3PP	solute carrier family 37 (glycerol-3-phosphate transporter), member 1	protein-coding
mm_88276.1	chr10	75037292	75037332	+	1	NA	5' UTR (NM_029781, exon 1 of 11)	5' UTR (NM_029781, exon 1 of 11)	223	NM_029781	76877	Mm.133593	NM_029781	ENSMUSG00000020175	Rab36	6330593L16Rik|AW047545	RAB36, member RAS oncogene family	protein-coding
mm_67980.1	chr7	100658395	100658451	-	1	NA	promoter-TSS (NM_001291336)	promoter-TSS (NM_001291336)	33	NM_001163185	27276	Mm.491216	NM_013746	ENSMUSG00000030701	Plekhb1	AI315628|PHR1|Phret1|evt-1	pleckstrin homology domain containing, family B (evectins) member 1	protein-coding
mm_68201.1	chr7	104380666	104380696	-	1	NA	Intergenic	Intergenic	-22035	NM_175648	244183	Mm.347647	NM_175648	ENSMUSG00000052749	Trim30b	A530023O14Rik|Trim30-1	tripartite motif-containing 30B	protein-coding
mm_141239.1	chr17	27437081	27437093	-	1	NA	intron (NM_001013385, intron 7 of 8)	intron (NM_001013385, intron 7 of 8)	66446	NM_001013385	268934	Mm.358940	NM_001013385	ENSMUSG00000063239	Grm4	Gprc1d|mGluR4	glutamate receptor, metabotropic 4	protein-coding
mm_5200.1	chr1	13374122	13374182	-	1	NA	promoter-TSS (NM_008678)	promoter-TSS (NM_008678)	-69	NM_008678	17978	Mm.2537	NM_008678	ENSMUSG00000005886	Ncoa2	D1Ertd433e|GRIP-1|Grip1|KAT13C|NCoA-2|SRC-2|TIF2|bHLHe75	nuclear receptor coactivator 2	protein-coding
mm_82196.1	chr9	124021966	124021977	+	1	NA	promoter-TSS (NM_009914)	promoter-TSS (NM_009914)	0	NM_009914	12771	Mm.57050	NM_009914	ENSMUSG00000035448	Ccr3	CC-CKR3|CKR3|Cmkbr1l2|Cmkbr3	chemokine (C-C motif) receptor 3	protein-coding
mm_148467.1	chr19	4096881	4096945	+	1	NA	promoter-TSS (NM_026373)	promoter-TSS (NM_026373)	-438	NM_026373	52004	Mm.29609	NM_026373	ENSMUSG00000024856	Cdk2ap2	5830466O21Rik|D19Ertd144e|Doc-1r	CDK2-associated protein 2	protein-coding
mm_151742.1	chr19	5001772	5001783	-	1	NA	Intergenic	CpG	-11806	NM_153553	225872	Mm.287867	NM_153553	ENSMUSG00000045903	Npas4	LE-PAS|Nxf	neuronal PAS domain protein 4	protein-coding
mm_73509.1	chr8	107368196	107368206	+	1	NA	exon (NM_018823, exon 13 of 15)	exon (NM_018823, exon 13 of 15)	35004	NM_008706	18104	Mm.252	NM_008706	ENSMUSG00000003849	Nqo1	AV001255|Dia4|Dtd|Nmo-1|Nmo1|Nmor1|Ox-1|Ox1|Qr1	NAD(P)H dehydrogenase, quinone 1	protein-coding
mm_46930.1	chr5	114730355	114730378	-	1	NA	exon (NM_019834, exon 19 of 19)	exon (NM_019834, exon 19 of 19)	10851	NR_105995	102465622		NR_105995	ENSMUSG00000098656	Mir7028	Gm27674|mmu-mir-7028	microRNA 7028	ncRNA
mm_165174.1	chr2	27037720	27037720	+	1	NA	Intergenic	Intergenic	-9722	NM_001177627	227659	Mm.41203	NM_172659	ENSMUSG00000036067	Slc2a6	A330096C23|F630103L12Rik|Glut6|Glut9	solute carrier family 2 (facilitated glucose transporter), member 6	protein-coding
mm_53595.1	chr6	138140345	138140360	+	1	NA	promoter-TSS (NM_019946)	promoter-TSS (NM_019946)	-185	NM_019946	56615	Mm.14796	NM_019946	ENSMUSG00000008540	Mgst1	1500002K10Rik|Gst	microsomal glutathione S-transferase 1	protein-coding
mm_148156.1	chr18	77565308	77565349	-	1	NA	promoter-TSS (NM_001164504)	promoter-TSS (NM_001164504)	-192	NM_001164504	225743	Mm.23293	NM_001164504	ENSMUSG00000025427	Rnf165	2900024M11Rik|AI427432|Akd2|Ark2c|G630064H08Rik|Gm96	ring finger protein 165	protein-coding
mm_165960.1	chr4	88722522	88722529	-	1	NA	promoter-TSS (NM_172871)	promoter-TSS (NM_172871)	-17	NM_172871	242521	Mm.260601	NM_172871	ENSMUSG00000070923	Klhl9	8030469P05|C530050O22Rik|ENSMUSG00000070923|mKIAA1354	kelch-like 9	protein-coding
mm_62973.1	chr7	120098567	120098570	+	1	NA	Intergenic	B3|SINE|B2	-3858	NM_145586	233806	Mm.257952	NM_145586	ENSMUSG00000030917	Tmem159	8430420C20Rik	transmembrane protein 159	protein-coding
mm_1277.1	chr1	63446007	63446020	+	1	NA	5' UTR (NM_011780, exon 1 of 26)	5' UTR (NM_011780, exon 1 of 26)	122	NM_011780	23792	Mm.124892	NM_011780	ENSMUSG00000025964	Adam23	AW046396|MDC3	a disintegrin and metallopeptidase domain 23	protein-coding
mm_113740.1	chr13	44705903	44705918	+	1	NA	Intergenic	Intergenic	-24864	NM_021878	16468	Mm.25059	NM_021878	ENSMUSG00000038518	Jarid2	Jmj|jumonji	jumonji, AT rich interactive domain 2	protein-coding
mm_42685.1	chr5	119832683	119832692	+	1	NA	Intergenic	Intergenic	-1976	NM_011537	21388	Mm.103636	NM_011537	ENSMUSG00000018263	Tbx5	-	T-box 5	protein-coding
mm_8535.1	chr1	155054858	155054864	-	1	NA	Intergenic	Intergenic	44775	NM_010500	15939	Mm.12246	NM_010500	ENSMUSG00000056708	Ier5	-	immediate early response 5	protein-coding
mm_130719.1	chr15	101054326	101054344	-	1	NA	promoter-TSS (NM_001214911)	promoter-TSS (NM_001214911)	64	NM_001214911	668225	Mm.385011	NM_001214911	ENSMUSG00000095440	Fignl2	EG668225	fidgetin-like 2	protein-coding
mm_96796.1	chr11	69980831	69980841	+	1	NA	promoter-TSS (NM_026017)	promoter-TSS (NM_026017)	-332	NM_026017	67181	Mm.41678	NM_026017	ENSMUSG00000018559	Ctdnep1	2610507E10Rik|Dullard	CTD nuclear envelope phosphatase 1	protein-coding
mm_129371.1	chr15	78119581	78119624	-	1	NA	promoter-TSS (NM_007583)	promoter-TSS (NM_007583)	-322	NM_007583	12300	Mm.277338	NM_007583	ENSMUSG00000019146	Cacng2	AW060990|B230105C07Rik|B930041E13Rik|stargazer|stargazin|stg|wag|waggler	calcium channel, voltage-dependent, gamma subunit 2	protein-coding
mm_123561.1	chr14	66868573	66868684	-	1	NA	promoter-TSS (NM_001034881)	promoter-TSS (NM_001034881)	-28	NM_009955	12934	Mm.352648	NM_009955	ENSMUSG00000022048	Dpysl2	AI851130|Crmp2|DRP2|Musunc33|TOAD-64|Ulip2	dihydropyrimidinase-like 2	protein-coding
mm_60035.1	chr7	31032854	31032923	+	1	NA	3' UTR (NM_001111073, exon 8 of 8)	3' UTR (NM_001111073, exon 8 of 8)	7429	NR_106017	102465635		NR_106017	ENSMUSG00000098783	Mir7050	Gm27578|mmu-mir-7050	microRNA 7050	ncRNA
mm_60855.1	chr7	45833621	45833638	+	1	NA	exon (NM_008172, exon 12 of 12)	exon (NM_008172, exon 12 of 12)	-2840	NM_153419	101612	Mm.274847	NM_153419	ENSMUSG00000053801	Grwd1	A301|AI504353|Grwd|Wdr28	glutamate-rich WD repeat containing 1	protein-coding
mm_71550.1	chr8	48109950	48110002	+	1	NA	promoter-TSS (NR_027759)	promoter-TSS (NR_027759)	18	NM_178788	320685	Mm.121549	NM_178788	ENSMUSG00000031562	Dctd	6030466N05Rik	dCMP deaminase	protein-coding
mm_46905.1	chr5	114273834	114273838	-	1	NA	promoter-TSS (NM_148935)	promoter-TSS (NM_148935)	-75	NM_148935	116810	Mm.17709	NM_148935	ENSMUSG00000042002	Foxn4	-	forkhead box N4	protein-coding
mm_128124.1	chr15	31325316	31325336	-	1	NA	intron (NM_027496, intron 1 of 3)	intron (NM_027496, intron 1 of 3)	42433	NM_001164441	67434	Mm.102470	NM_026153	ENSMUSG00000022237	Ankrd33b	0610012A05Rik|3021401C12Rik|5730557B15Rik	ankyrin repeat domain 33B	protein-coding
mm_155432.1	chrX	73493237	73493265	+	1	NA	exon (NM_007542, exon 7 of 8)	exon (NM_007542, exon 7 of 8)	9650	NM_007542	12111	Mm.2608	NM_007542	ENSMUSG00000031375	Bgn	BG|DSPG1|PG-S1|PGI|SLRR1A	biglycan	protein-coding
mm_74225.1	chr8	124066790	124066796	+	1	NA	Intergenic	Intergenic	43320	NM_001029876	382038	Mm.334891	NM_001029876	ENSMUSG00000031976	Urb2	C77575|mKIAA0133	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	protein-coding
mm_122493.1	chr14	46634428	46634432	-	1	NA	intron (NR_046460, intron 1 of 4)	intron (NR_046460, intron 1 of 4)	2993	NR_046460	74458	Mm.390708	NR_046460		4933425B07Rik	-	RIKEN cDNA 4933425B07 gene	ncRNA
mm_7627.1	chr1	127577834	127577834	-	1	NA	intron (NM_028135, intron 2 of 7)	intron (NM_028135, intron 2 of 7)	100187	NM_028135	72160	Mm.281287	NM_028135	ENSMUSG00000026347	Tmem163	2610024A01Rik|SV31	transmembrane protein 163	protein-coding
mm_64352.1	chr7	142385491	142385510	+	1	NA	exon (NM_009983, exon 2 of 9)	exon (NM_009983, exon 2 of 9)	2370	NM_009983	13033	Mm.231395	NM_009983	ENSMUSG00000007891	Ctsd	CD|CatD	cathepsin D	protein-coding
mm_38950.1	chr4	150568701	150568733	-	1	NA	intron (NM_001085492, intron 11 of 22)	intron (NM_001085492, intron 11 of 22)	83457	NM_173774	242773	Mm.29280	NM_173774	ENSMUSG00000039838	Slc45a1	C230078B22|Dnb5	solute carrier family 45, member 1	protein-coding
mm_48345.1	chr5	139325374	139325405	-	1	NA	promoter-TSS (NM_172723)	promoter-TSS (NM_172723)	75	NM_172723	231821	Mm.297819	NM_172723	ENSMUSG00000056413	Adap1	4930431P11Rik|Centa1|GC1L|p42IP4	ArfGAP with dual PH domains 1	protein-coding
mm_42432.1	chr5	115404166	115404169	+	1	NA	Intergenic	Intergenic	-25518	NM_008629	17690	Mm.5077	NM_008629	ENSMUSG00000054256	Msi1	Msi1h|Musahi1|m-Msi-1	musashi RNA-binding protein 1	protein-coding
mm_170676.1	chr2	121807057	121807073	-	1	NA	promoter-TSS (NM_172673)	promoter-TSS (NM_172673)	-8	NM_172673	228564	Mm.121514	NM_172673	ENSMUSG00000027238	Frmd5	1500032A09Rik|5830442F04|A930004K21Rik|R75430	FERM domain containing 5	protein-coding
mm_169878.1	chr16	37815779	37815786	+	1	NA	exon (NM_008047, exon 3 of 11)	exon (NM_008047, exon 3 of 11)	38727	NM_008047	14314	Mm.182434	NM_008047	ENSMUSG00000022816	Fstl1	AI316791|AW107808|Fstl|TSC-36	follistatin-like 1	protein-coding
mm_106919.1	chr12	8287054	8287058	+	1	NA	Intergenic	Intergenic	14898	NM_001312876	238057	Mm.271308	NM_013527	ENSMUSG00000037660	Gdf7	BMP12	growth differentiation factor 7	protein-coding
mm_81622.1	chr9	110834622	110834637	+	1	NA	promoter-TSS (NM_153172)	promoter-TSS (NM_153172)	41	NM_153172	260408	Mm.79114	NM_153172	ENSMUSG00000047257	Prss45	Tespl|Tessp5	protease, serine 45	protein-coding
mm_121193.1	chr14	103051074	103051089	+	1	NA	intron (NM_008392, intron 3 of 4)	Lx7|LINE|L1	4069	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_71914.1	chr8	70131328	70131392	+	1	NA	promoter-TSS (NM_001025587)	promoter-TSS (NM_001025587)	33	NM_001025587	75692	Mm.161167	NM_001025586	ENSMUSG00000071078	Nr2c2ap	2310073E15Rik	nuclear receptor 2C2-associated protein	protein-coding
mm_102692.1	chr11	65745828	65745844	-	1	NA	intron (NM_009157, intron 2 of 10)	L3|LINE|CR1	-11004	NR_030417	791070		NR_030417	ENSMUSG00000076460	Mir744	Mirn744|mir-744|mmu-mir-744	microRNA 744	ncRNA
mm_27907.1	chr3	79516330	79516345	-	1	NA	intron (NM_001162999, intron 2 of 16)	intron (NM_001162999, intron 2 of 16)	51342	NM_001162999	329679	Mm.244005	NM_001162999	ENSMUSG00000061175	Fnip2	D630023B12Rik|mKIAA1450	folliculin interacting protein 2	protein-coding
mm_46063.1	chr5	92278140	92278150	-	1	NA	promoter-TSS (NM_001163687)	promoter-TSS (NM_001163687)	36	NM_001163687	67111	Mm.28890	NM_025972	ENSMUSG00000029413	Naaa	2210023K21Rik|3830414F09Rik|Asahl	N-acylethanolamine acid amidase	protein-coding
mm_60563.1	chr7	44481367	44481371	+	1	NA	Intergenic	Intergenic	-3148	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_68183.1	chr7	104129793	104129819	-	1	NA	promoter-TSS (NM_027634)	promoter-TSS (NM_027634)	17	NM_027634	70980	Mm.158518	NM_027634	ENSMUSG00000055643	4931431F19Rik	-	RIKEN cDNA 4931431F19 gene	protein-coding
mm_64691.1	chr7	4522428	4522449	-	1	NA	promoter-TSS (NM_009406)	promoter-TSS (NM_009406)	5	NM_009406	21954	Mm.27674	NM_009406	ENSMUSG00000035458	Tnni3	Tn1|cTnI	troponin I, cardiac 3	protein-coding
mm_135219.1	chr16	36666068	36666086	-	1	NA	promoter-TSS (NM_019388)	promoter-TSS (NM_019388)	0	NM_019388	12524	Mm.1452	NM_019388	ENSMUSG00000022901	Cd86	B7|B7-2|B7.2|B70|CLS1|Cd28l2|ETC-1|Ly-58|Ly58|MB7|MB7-2|TS/A-2	CD86 antigen	protein-coding
mm_31243.1	chr4	44824086	44824089	+	1	NA	intron (NM_138590, intron 2 of 8)	intron (NM_138590, intron 2 of 8)	67528	NM_138590	319885	Mm.331576	NM_138590	ENSMUSG00000035649	Zcchc7	4930572I07Rik|D4Wsu132e	zinc finger, CCHC domain containing 7	protein-coding
mm_152902.1	chr19	25347224	25347224	-	1	NA	intron (NM_181404, intron 3 of 13)	intron (NM_181404, intron 3 of 13)	110022	NM_181404	107351	Mm.260722	NM_181404	ENSMUSG00000032702	Kank1	A930031B09Rik|AU015049|AW121052|Ankrd15|D330024H06Rik|mKIAA0172	KN motif and ankyrin repeat domains 1	protein-coding
mm_163080.1	chr11	68872099	68872107	+	1	NA	Intergenic	Intergenic	-16450	NM_177060	320040	Mm.305696	NM_177060	ENSMUSG00000046490	Rnf222	9930039A11Rik	ring finger protein 222	protein-coding
mm_3088.1	chr1	134406335	134406357	+	1	NA	exon (NM_028057, exon 2 of 9)	exon (NM_028057, exon 2 of 9)	356	NM_028057	72017	Mm.280230	NM_028057	ENSMUSG00000026456	Cyb5r1	1500005G05Rik|B5R.1|C80155|Nqo3a2	cytochrome b5 reductase 1	protein-coding
mm_81665.1	chr9	111022391	111022401	+	1	NA	exon (NM_008522, exon 4 of 17)	exon (NM_008522, exon 4 of 17)	3104	NM_008522	17002	Mm.282359	NM_008522	ENSMUSG00000032496	Ltf	Csp82|Lf|MMS10R|Ms10r	lactotransferrin	protein-coding
mm_162333.1	chr1	43310920	43310920	-	1	NA	Intergenic	Intergenic	-114159	NM_001289533	14200	Mm.6799	NM_010212	ENSMUSG00000008136	Fhl2	FHL-2|SLIM-3|SLIM3	four and a half LIM domains 2	protein-coding
mm_43811.1	chr5	142904514	142904547	+	1	NA	exon (NM_007393, exon 4 of 6)	exon (NM_007393, exon 4 of 6)	2224	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_38531.1	chr4	141559420	141559427	-	1	NA	Intergenic	Intergenic	13261	NR_030695	320456	Mm.32859	NM_177163		B330016D10Rik	-	RIKEN cDNA B330016D10 gene	ncRNA
mm_146479.1	chr18	89197454	89197459	+	1	NA	promoter-TSS (NM_178687)	promoter-TSS (NM_178687)	29	NM_001039149	225825	Mm.139293	NM_178687	ENSMUSG00000034028	Cd226	BC051526|DNAM-1|DNAM1|Pta1|TLiSA1	CD226 antigen	protein-coding
mm_118852.1	chr14	25694171	25694233	+	1	NA	promoter-TSS (NM_134084)	promoter-TSS (NM_134084)	32	NM_134084	105675	Mm.41656	NM_134084	ENSMUSG00000021868	Ppif	AW457192|CyP-D|CyP-F|CypD|PPIase	peptidylprolyl isomerase F (cyclophilin F)	protein-coding
mm_30621.1	chr4	8690538	8690583	+	1	NA	5' UTR (NM_001277149, exon 1 of 38)	5' UTR (NM_001277149, exon 1 of 38)	154	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_169468.1	chr14	66757243	66757244	-	1	NA	intron (NM_001271761, intron 2 of 2)	intron (NM_001271761, intron 2 of 2)	111357	NM_009955	12934	Mm.352648	NM_009955	ENSMUSG00000022048	Dpysl2	AI851130|Crmp2|DRP2|Musunc33|TOAD-64|Ulip2	dihydropyrimidinase-like 2	protein-coding
mm_66666.1	chr7	45717920	45717950	-	1	NA	promoter-TSS (NM_001172561)	promoter-TSS (NM_001172561)	67	NM_203280	56632	Mm.24222	NM_020011	ENSMUSG00000057342	Sphk2	C76851	sphingosine kinase 2	protein-coding
mm_151882.1	chr19	5798536	5798544	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	-2559	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_124480.1	chr14	121597507	121597509	-	1	NA	intron (NM_001347596, intron 35 of 52)	intron (NM_001347596, intron 35 of 52)	-92254	NM_053079	56643	Mm.155618	NM_053079	ENSMUSG00000025557	Slc15a1	D630032F02|PECT1|PEPT1	solute carrier family 15 (oligopeptide transporter), member 1	protein-coding
mm_145456.1	chr18	60231153	60231171	+	1	NA	intron (NM_001033767, intron 2 of 2)	B4A|SINE|B4	19085	NM_001033767	240327	Mm.357104	NM_001033767	ENSMUSG00000073555	Gm4951	EG240327|Ifgga2	predicted gene 4951	protein-coding
mm_5778.1	chr1	51513032	51513033	-	1	NA	Intergenic	Intergenic	-34633	NM_001310549	109019	Mm.196290	NM_028696	ENSMUSG00000026107	Nabp1	4930434H03Rik|4930442A21Rik|4930488J04Rik|4933440J18Rik|5830411E10Rik|AI852561|Nbp1|Obfc2a|Ssb2	nucleic acid binding protein 1	protein-coding
mm_153999.1	chr19	51142679	51142695	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-464041	NM_001290356	58178	Mm.313672	NM_021377	ENSMUSG00000043531	Sorcs1	Sorcs|mSorCS	sortilin-related VPS10 domain containing receptor 1	protein-coding
mm_54497.1	chr6	35510287	35510327	-	1	NA	3' UTR (NM_008098, exon 4 of 4)	3' UTR (NM_008098, exon 4 of 4)	29581	NM_008098	14489	Mm.182746	NM_008098	ENSMUSG00000029840	Mtpn	5033418D15Rik|Gcdp|V1	myotrophin	protein-coding
mm_16193.1	chr2	172977909	172977922	+	1	NA	Intergenic	Intergenic	-1927	NM_012046	26972	Mm.23495	NM_012046	ENSMUSG00000005883	Spo11	AI449549|Spo11a|Spo11b	SPO11 meiotic protein covalently bound to DSB	protein-coding
mm_29930.1	chr3	131491400	131491409	-	1	NA	Intergenic	Intergenic	-73364	NM_001289479	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_8178.1	chr1	138078589	138078604	-	1	NA	intron (NM_001111316, intron 24 of 31)	intron (NM_001111316, intron 24 of 31)	96530	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_127453.1	chr15	101270864	101270874	+	1	NA	exon (NM_010444, exon 2 of 7)	exon (NM_010444, exon 2 of 7)	4023	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_149797.1	chr19	23619326	23619327	+	1	NA	intron (NM_026188, intron 1 of 5)	L1_Mm|LINE|L1	33486	NM_026188	67483	Mm.443287	NM_026188	ENSMUSG00000033053	1700028P14Rik	AV209940	RIKEN cDNA 1700028P14 gene	protein-coding
mm_166234.1	chr5	67473924	67473926	+	1	NA	non-coding (NR_110363, exon 6 of 8)	non-coding (NR_110363, exon 6 of 8)	10027	NR_015582	320479	Mm.387187	NR_015582	ENSMUSG00000107385	C330024D21Rik	-	RIKEN cDNA C330024D21 gene	ncRNA
mm_120512.1	chr14	66635191	66635208	+	1	NA	promoter-TSS (NM_001271761)	promoter-TSS (NM_001271761)	-52	NM_001271759	11549	Mm.57064	NM_013461	ENSMUSG00000045875	Adra1a	Adra1c	adrenergic receptor, alpha 1a	protein-coding
mm_155764.1	chrX	96168393	96168405	+	1	NA	3' UTR (NM_010833, exon 13 of 13)	3' UTR (NM_010833, exon 13 of 13)	-71527	NR_030718	100038363	Mm.30815	NR_030718	ENSMUSG00000078122	F630028O10Rik	ENSMUSG00000065522|Gm14924|OTTMUSG00000018496|mir-223	RIKEN cDNA F630028O10 gene	ncRNA
mm_131952.1	chr16	24433647	24433669	+	1	NA	intron (NM_178665, intron 1 of 12)	intron (NM_178665, intron 1 of 12)	-14433	NM_001145952	210126	Mm.209385	NM_178665	ENSMUSG00000033306	Lpp	9430020K16Rik|AA959454|AU024130|B130055L10Rik|C79715|D630048H16	LIM domain containing preferred translocation partner in lipoma	protein-coding
mm_55228.1	chr6	52234903	52234960	-	1	NA	promoter-TSS (NM_008263)	promoter-TSS (NM_008263)	8	NM_008263	15395	Mm.5	NM_008263	ENSMUSG00000000938	Hoxa10	Hox-1.8|Hoxa-10	homeobox A10	protein-coding
mm_144945.1	chr18	37806390	37806453	+	1	NA	promoter-TSS (NM_033581)	promoter-TSS (NM_033581)	11	NM_033581	93706	Mm.247203	NM_033581	ENSMUSG00000102918	Pcdhgc3	PC43|Pcdh2	protocadherin gamma subfamily C, 3	protein-coding
mm_138113.1	chr17	34135685	34135729	+	1	NA	exon (NM_010386, exon 2 of 6)	exon (NM_010386, exon 2 of 6)	-9709	NM_010388	15000	Mm.195060	NM_010388	ENSMUSG00000037548	H2-DMb2	H-2Mb2|H2-Mb2	histocompatibility 2, class II, locus Mb2	protein-coding
mm_153968.1	chr19	47857888	47857896	-	1	NA	exon (NM_010362, exon 3 of 6)	exon (NM_010362, exon 3 of 6)	2919	NM_010362	14873	Mm.378931	NM_010362	ENSMUSG00000025068	Gsto1	AA407097|AI194287|AU018802|Gsto-1|Gstx|Spg-r|p28	glutathione S-transferase omega 1	protein-coding
mm_57091.1	chr6	122587492	122587543	-	1	NA	intron (NM_001134391, intron 5 of 7)	intron (NM_001134391, intron 5 of 7)	14927	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_89138.1	chr10	85598727	85598755	+	1	NA	exon (NM_028709, exon 4 of 17)	exon (NM_028709, exon 4 of 17)	330	NM_001017525	74007	Mm.36544	NM_028709	ENSMUSG00000020042	Btbd11	6330404E16Rik	BTB (POZ) domain containing 11	protein-coding
mm_151604.1	chr19	3575709	3575756	-	1	NA	promoter-TSS (NM_028999)	promoter-TSS (NM_028999)	17	NM_001164159	52036	Mm.284686	NM_028999	ENSMUSG00000024908	Ppp6r3	4930528G08Rik|9130026N02Rik|D19Bwg1430e|D19Ertd703e|Pp6r3|Ppcs3|Pptcs3|Sapl|Saps3|mKIAA1558	protein phosphatase 6, regulatory subunit 3	protein-coding
mm_94922.1	chr11	29507693	29507703	+	1	NA	3' UTR (NM_176841, exon 32 of 32)	3' UTR (NM_176841, exon 32 of 32)	7335	NM_026465	67939	Mm.251087	NM_026465	ENSMUSG00000032673	Prorsd1	2010316F05Rik|Ncrna00117|Prdxdd1	prolyl-tRNA synthetase domain containing 1	protein-coding
mm_153214.1	chr19	34747224	34747251	-	1	NA	promoter-TSS (NM_172838)	promoter-TSS (NM_172838)	-126	NM_172838	240638	Mm.74636	NM_172838	ENSMUSG00000009378	Slc16a12	3230401A21|AW210596	solute carrier family 16 (monocarboxylic acid transporters), member 12	protein-coding
mm_116022.1	chr13	24831589	24831639	-	1	NA	promoter-TSS (NM_019551)	promoter-TSS (NM_019551)	-45	NM_019551	56196	Mm.427162	NM_019551	ENSMUSG00000035958	Tdp2	D13Ertd656e|Ttrap	tyrosyl-DNA phosphodiesterase 2	protein-coding
mm_145702.1	chr18	62657286	62657303	+	1	NA	intron (NM_177829, intron 5 of 8)	intron (NM_177829, intron 5 of 8)	-61030	NM_001001803	408198	Mm.478742	NM_001001803	ENSMUSG00000060201	Spink7	EG408198|Ecg2	serine peptidase inhibitor, Kazal type 7 (putative)	protein-coding
mm_137756.1	chr17	29467809	29467824	+	1	NA	Intergenic	Intergenic	-23229	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_93120.1	chr10	91170589	91170598	-	1	NA	promoter-TSS (NM_001283048)	promoter-TSS (NM_001283048)	-43	NM_001283048	21917	Mm.159684	NM_011605	ENSMUSG00000019961	Tmpo	5630400D24Rik|AI195756|AI606875|AW214352|AW547477|LAP2|TP	thymopoietin	protein-coding
mm_152438.1	chr19	10738870	10738935	-	1	NA	promoter-TSS (NM_007650)	promoter-TSS (NM_007650)	72	NM_007650	12507	Mm.779	NM_007650	ENSMUSG00000024669	Cd5	Ly-1|Ly-12|Ly-A|Lyt-1	CD5 antigen	protein-coding
mm_161037.1	chr12	29999882	29999882	+	1	NA	intron (NM_181395, intron 15 of 22)	intron (NM_181395, intron 15 of 22)	61846	NM_181395	69675	Mm.251774	NM_181395	ENSMUSG00000020674	Pxdn	2310075M15Rik|C85409|E330004E07|VPO1|mKIAA0230	peroxidasin	protein-coding
mm_34733.1	chr4	152186180	152186206	+	1	NA	promoter-TSS (NM_001146057)	promoter-TSS (NM_001146057)	59	NM_001146057	70025	Mm.296191	NM_133348	ENSMUSG00000028937	Acot7	2410041A17Rik|Ach1|Act|Bach|CTE-IIa|Cte-II|Lach1	acyl-CoA thioesterase 7	protein-coding
mm_121737.1	chr14	18331769	18331836	-	1	NA	promoter-TSS (NM_009455)	promoter-TSS (NM_009455)	42	NM_009455	22194	Mm.4429	NM_009455	ENSMUSG00000021774	Ube2e1	UbcM3|Ubce5|ubcM2	ubiquitin-conjugating enzyme E2E 1	protein-coding
mm_120446.1	chr14	65968545	65968558	+	1	NA	promoter-TSS (NM_013492)	promoter-TSS (NM_013492)	68	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_166273.1	chr5	90490698	90490711	+	1	NA	promoter-TSS (NM_007423)	promoter-TSS (NM_007423)	-10	NM_007423	11576	Mm.358570	NM_007423	ENSMUSG00000054932	Afp	-	alpha fetoprotein	protein-coding
mm_65189.1	chr7	19696567	19696579	-	1	NA	exon (NM_009696, exon 4 of 4)	exon (NM_009696, exon 4 of 4)	1825	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_157005.1	chrX	7584051	7584059	-	1	NA	intron (NM_001199348, intron 1 of 12)	intron (NM_001199348, intron 1 of 12)	3572	NM_001199348	20371	Mm.182291	NM_054039	ENSMUSG00000039521	Foxp3	JM2|scurfin|sf	forkhead box P3	protein-coding
mm_108982.1	chr12	102743993	102744008	+	1	NA	promoter-TSS (NM_001142937)	promoter-TSS (NM_001142937)	240	NM_177140	320351	Mm.86546	NM_177140	ENSMUSG00000046675	Tmem251	D230037D09Rik	transmembrane protein 251	protein-coding
mm_31468.1	chr4	49559980	49559983	+	1	NA	Intergenic	Intergenic	-10435	NM_144903	230163	Mm.482116	NM_144903	ENSMUSG00000028307	Aldob	Aldo-2|Aldo2|BC016435	aldolase B, fructose-bisphosphate	protein-coding
mm_16039.1	chr2	167690718	167690737	+	1	NA	promoter-TSS (NR_015500)	promoter-TSS (NR_015500)	-32	NR_110334	329562	Mm.123101	NM_177851	ENSMUSG00000006462	A530013C23Rik	-	RIKEN cDNA A530013C23 gene	ncRNA
mm_26474.1	chr3	144570557	144570571	+	1	NA	promoter-TSS (NM_011828)	promoter-TSS (NM_011828)	137	NM_053102	93684	Mm.29812	NM_053102	ENSMUSG00000037072	Selenof	9430015P09Rik|Sep15	selenoprotein F	protein-coding
mm_144474.1	chr18	23883576	23883591	+	1	NA	exon (NM_001162942, exon 7 of 8)	exon (NM_001162942, exon 7 of 8)	-71105	NM_027007	69256	Mm.218343	NM_027007	ENSMUSG00000024276	Zfp397	2810411K16Rik|6720480F11Rik|AI461664	zinc finger protein 397	protein-coding
mm_40032.1	chr5	33658124	33658160	+	1	NA	promoter-TSS (NM_026698)	promoter-TSS (NM_026698)	14	NM_001040435	21335	Mm.379024	NM_011524	ENSMUSG00000037313	Tacc3	Aint|C86661|Eric1	transforming, acidic coiled-coil containing protein 3	protein-coding
mm_32560.1	chr4	109484875	109484886	+	1	NA	Intergenic	Intergenic	-8375	NM_013876	29864	Mm.392580	NM_013876	ENSMUSG00000028557	Rnf11	-	ring finger protein 11	protein-coding
mm_90646.1	chr10	128744794	128744822	+	1	NA	promoter-TSS (NM_016811)	promoter-TSS (NM_016811)	-752	NM_016811	13139	Mm.291235	NM_016811	ENSMUSG00000025357	Dgka	80kDa|AW146112|Dagk1	diacylglycerol kinase, alpha	protein-coding
mm_67582.1	chr7	82971386	82971396	-	1	NA	promoter-TSS (NR_045855)	promoter-TSS (NR_045855)	0	NR_045855	71285	Mm.76818	NR_045855	ENSMUSG00000109106	4933430H16Rik	-	RIKEN cDNA 4933430H16 gene	ncRNA
mm_20942.1	chr2	151432393	151432403	-	1	NA	promoter-TSS (NR_131976)	promoter-TSS (NR_131976)	51	NR_131976	100125594	Mm.381283	NR_131976	ENSMUSG00000087495	LOC100125594	-	uncharacterized LOC100125594	ncRNA
mm_143773.1	chr17	81697687	81697690	-	1	NA	intron (NR_104580, intron 1 of 8)	intron (NR_104580, intron 1 of 8)	40699	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_64125.1	chr7	141132459	141132476	+	1	NA	intron (NM_013782, intron 1 of 11)	intron (NM_013782, intron 1 of 11)	1181	NM_013782	27388	Mm.293591	NM_013782	ENSMUSG00000025495	Ptdss2	AI481134|AI988017|PSS2	phosphatidylserine synthase 2	protein-coding
mm_79896.1	chr9	65346067	65346077	+	1	NA	promoter-TSS (NM_016688)	promoter-TSS (NM_016688)	4	NM_016688	50996	Mm.29193	NM_016688	ENSMUSG00000041837	Pdcd7	C80112|ES18	programmed cell death 7	protein-coding
mm_140477.1	chr17	94864929	94864933	+	1	NA	promoter-TSS (NM_001024731)	promoter-TSS (NM_001024731)	13	NM_001024731	100044193		NM_001024731	ENSMUSG00000095193	Gm20939	-	predicted gene, 20939	protein-coding
mm_148789.1	chr19	6164434	6164446	+	1	NA	promoter-TSS (NM_028967)	promoter-TSS (NM_028967)	-18	NM_028967	74481	Mm.159219	NM_028967	ENSMUSG00000039699	Batf2	4933430F08Rik	basic leucine zipper transcription factor, ATF-like 2	protein-coding
mm_24815.1	chr3	95623893	95623900	+	1	NA	Intergenic	RMER17C|LTR|ERVK	-1084	NM_019561	56205	Mm.241365	NM_019561	ENSMUSG00000038619	Ensa	1700020C18Rik|2610007F17Rik|AI451924	endosulfine alpha	protein-coding
mm_135329.1	chr16	38800327	38800337	-	1	NA	promoter-TSS (NM_178924)	promoter-TSS (NM_178924)	-129	NM_178924	22268	Mm.130793	NM_178924	ENSMUSG00000049436	Upk1b	AI413235|Tspan20|UPIb|Upk1	uroplakin 1B	protein-coding
mm_113372.1	chr13	33003457	33003471	+	1	NA	Intergenic	Intergenic	-1077	NM_009256	20723	Mm.245041	NM_009256	ENSMUSG00000045827	Serpinb9	BB283241|CAP-3|CAP3|PI-9|PI9|Spi6|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 9	protein-coding
mm_101925.1	chr11	50202468	50202481	-	1	NA	exon (NM_011018, exon 7 of 8)	exon (NM_011018, exon 7 of 8)	8346	NM_001290769	18412	Mm.40828	NM_011018	ENSMUSG00000015837	Sqstm1	A170|OSF-6|Osi|STAP|STONE14|p62	sequestosome 1	protein-coding
mm_152287.1	chr19	8942367	8942411	-	1	NA	TTS (NM_144872)	TTS (NM_144872)	469	NM_011842	23942	Mm.25339	NM_011842	ENSMUSG00000071646	Mta2	AW550797|Mata1l1|Mta1l1|mmta2	metastasis-associated gene family, member 2	protein-coding
mm_127798.1	chr15	3979433	3979562	-	1	NA	promoter-TSS (NM_134099)	promoter-TSS (NM_134099)	76	NM_134099	106052	Mm.234191	NM_134099	ENSMUSG00000022184	Fbxo4	1700096C12Rik|AI851261|AW494535|Fbx4	F-box protein 4	protein-coding
mm_33948.1	chr4	137320936	137320959	+	1	NA	TTS (NM_001243769)	TTS (NM_001243769)	36812	NM_009861	12540	Mm.1022	NM_009861	ENSMUSG00000006699	Cdc42	AI747189|AU018915	cell division cycle 42	protein-coding
mm_90658.1	chr10	128805012	128805032	+	1	NA	promoter-TSS (NM_178066)	promoter-TSS (NM_178066)	-652	NM_178066	73827	Mm.24630	NM_178066	ENSMUSG00000047090	Tmem198b	1110012D08Rik	transmembrane protein 198b	protein-coding
mm_74016.1	chr8	121542110	121542135	+	1	NA	promoter-TSS (NM_029597)	promoter-TSS (NM_029597)	-168	NM_029597	76405	Mm.165697	NM_029597	ENSMUSG00000031809	1700018B08Rik	1700084O22Rik	RIKEN cDNA 1700018B08 gene	protein-coding
mm_9532.1	chr1	173846465	173846469	-	1	NA	Intergenic	Intergenic	33720	NM_001170853	100040462	Mm.463437	NM_001170853	ENSMUSG00000090272	Mndal	Gm2785|Ifi212	myeloid nuclear differentiation antigen like	protein-coding
mm_171409.1	chr4	129312427	129312428	+	1	NA	intron (NM_009030, intron 11 of 11)	RLTR10B2|LTR|ERVK	22943	NM_009030	19646	Mm.12145	NM_009030	ENSMUSG00000057236	Rbbp4	RBAP48|mRbAp48	retinoblastoma binding protein 4	protein-coding
mm_173125.1	chrX	170001468	170001481	-	1	NA	Intergenic	Intergenic	-22557	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_127214.1	chr15	99249590	99249608	+	1	NA	intron (NM_001164156, intron 2 of 13)	intron (NM_001164156, intron 2 of 13)	-2189	NR_045627	73600	Mm.475134	NR_045627	ENSMUSG00000100599	1700120C14Rik	-	RIKEN cDNA 1700120C14 gene	ncRNA
mm_39010.1	chr4	152038435	152038445	-	1	NA	promoter-TSS (NM_028727)	promoter-TSS (NM_028727)	50	NM_031867	110326	Mm.29232	NM_031867	ENSMUSG00000028950	Tas1r1	Gpr70|T1r1|TR1	taste receptor, type 1, member 1	protein-coding
mm_156114.1	chrX	114474601	114474614	+	1	NA	exon (NM_001290478, exon 1 of 11)	exon (NM_001290478, exon 1 of 11)	274	NM_001290477	237010	Mm.132583	NM_172781	ENSMUSG00000025597	Klhl4	B130014A11|C130018J01Rik	kelch-like 4	protein-coding
mm_39306.1	chr5	7960446	7960464	+	1	NA	promoter-TSS (NM_054098)	promoter-TSS (NM_054098)	-17	NM_054098	117167	Mm.31403	NM_054098	ENSMUSG00000012428	Steap4	1110021O17Rik|AI481214|Tiarp|Tnfaip9	STEAP family member 4	protein-coding
mm_31652.1	chr4	59805004	59805012	+	1	NA	promoter-TSS (NM_172468)	promoter-TSS (NM_172468)	-642	NM_172468	209131	Mm.259705	NM_172468	ENSMUSG00000028385	Snx30	4732481H14Rik|C030041J06Rik	sorting nexin family member 30	protein-coding
mm_14860.1	chr2	148782087	148782108	+	1	NA	promoter-TSS (NM_030135)	promoter-TSS (NM_030135)	88	NM_030135	78609	Mm.160102	NM_030135	ENSMUSG00000027444	8030411F24Rik	Cst14	RIKEN cDNA 8030411F24 gene	protein-coding
mm_48833.1	chr5	149184938	149184952	-	1	NA	intron (NM_001115150, intron 1 of 7)	CpG	385	NM_001115149	231915	Mm.29402	NM_001013378	ENSMUSG00000041264	Uspl1	E430026A01Rik	ubiquitin specific peptidase like 1	protein-coding
mm_46366.1	chr5	103425721	103425729	-	1	NA	intron (NM_011204, intron 1 of 47)	CpG	533	NM_011204	19249	Mm.3414	NM_011204	ENSMUSG00000034573	Ptpn13	AI324989|PTP-BL|PTPL1|Ptpri|RIP	protein tyrosine phosphatase, non-receptor type 13	protein-coding
mm_107705.1	chr12	55490405	55490453	+	1	NA	exon (NM_010907, exon 5 of 6)	exon (NM_010907, exon 5 of 6)	2218	NM_010907	18035	Mm.170515	NM_010907	ENSMUSG00000021025	Nfkbia	AI462015|Nfkbi	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, alpha	protein-coding
mm_116613.1	chr13	48871037	48871071	-	1	NA	promoter-TSS (NM_011078)	promoter-TSS (NM_011078)	-169	NM_011078	18676	Mm.486213	NM_011078	ENSMUSG00000038025	Phf2	GRC5	PHD finger protein 2	protein-coding
mm_95622.1	chr11	53582221	53582226	+	1	NA	intron (NM_001290805, intron 5 of 16)	intron (NM_001290805, intron 5 of 16)	14854	NM_001290806	16568	Mm.88694	NM_008443	ENSMUSG00000018395	Kif3a	Kif3|Kifl|Kns3	kinesin family member 3A	protein-coding
mm_108246.1	chr12	78226430	78226440	+	1	NA	promoter-TSS (NM_172952)	promoter-TSS (NM_172952)	-220	NM_172952	268566	Mm.341742	NM_145965	ENSMUSG00000047454	Gphn	5730552E08Rik|AI662856|BC027112|C230040D23|GPH|GPHRYN|geph	gephyrin	protein-coding
mm_133027.1	chr16	57175751	57175784	+	1	NA	intron (NM_026254, intron 15 of 17)	B4|SINE|B4	-8435	NM_023175	52633	Mm.383203	NM_023175	ENSMUSG00000022751	Nit2	1190017B19Rik|D16Ertd502e	nitrilase family, member 2	protein-coding
mm_171935.1	chr5	64544971	64544971	-	1	NA	Intergenic	L1Md_A|LINE|L1	65728	NR_045078	100042198	Mm.25191	NR_045078	ENSMUSG00000105402	Gm3716	Gm1683	predicted gene 3716	ncRNA
mm_118375.1	chr13	117014803	117014809	-	1	NA	intron (NM_001081009, intron 3 of 26)	B1F|SINE|Alu	10710	NM_001081009	52552	Mm.274466	NM_027272	ENSMUSG00000021725	Parp8	2810430O08Rik|ARTD16|D13Ertd275e	poly (ADP-ribose) polymerase family, member 8	protein-coding
mm_58057.1	chr6	136857630	136857646	-	1	NA	promoter-TSS (NM_026639)	promoter-TSS (NM_026639)	-38	NM_026639	109978	Mm.31840	NM_026639	ENSMUSG00000030217	Art4	4432404K01Rik|ARTC4|DO|DOK1	ADP-ribosyltransferase 4	protein-coding
mm_63458.1	chr7	127543196	127543225	+	1	NA	intron (NM_001304266, intron 25 of 33)	intron (NM_001304266, intron 25 of 33)	15313	NR_034045	100217442	Mm.451113	NR_034045	ENSMUSG00000065259	Snora30	MBI-26	small nucleolar RNA, H/ACA box 30	snoRNA
mm_35842.1	chr4	48049098	48049107	-	1	NA	5' UTR (NM_015743, exon 2 of 8)	5' UTR (NM_015743, exon 2 of 8)	-2144	NM_001307989	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_119333.1	chr14	39655649	39655675	+	1	NA	promoter-TSS (NR_045936)	promoter-TSS (NR_045936)	-1	NR_045936	73591	Mm.65499	NR_045936	ENSMUSG00000101261	1700109I08Rik	-	RIKEN cDNA 1700109I08 gene	ncRNA
mm_170947.1	chr2	52742448	52742466	+	1	NA	promoter-TSS (NM_019667)	promoter-TSS (NM_019667)	-308	NM_019667	56324	Mm.263639	NM_019667	ENSMUSG00000055371	Stam2	1200004O12Rik|5730456G07Rik|BB145015|Hbp	signal transducing adaptor molecule (SH3 domain and ITAM motif) 2	protein-coding
mm_37050.1	chr4	116018024	116018034	-	1	NA	promoter-TSS (NM_010173)	promoter-TSS (NM_010173)	-127	NM_010173	14073	Mm.256025	NM_010173	ENSMUSG00000034171	Faah	AW412498	fatty acid amide hydrolase	protein-coding
mm_59978.1	chr7	30465296	30465318	+	1	NA	intron (NM_019459, intron 11 of 29)	intron (NM_019459, intron 11 of 29)	284	NR_004443	445267	Mm.398140	NR_004443	ENSMUSG00000087009	Nphs1os	Nphs1as	nephrosis 1 homolog, nephrin, opposite strand	ncRNA
mm_64201.1	chr7	141469172	141469212	+	1	NA	intron (NM_001111050, intron 1 of 6)	intron (NM_001111050, intron 1 of 6)	403	NM_001111050	12476	Mm.30246	NM_009842	ENSMUSG00000025510	Cd151	PETA-3|SFA-1|Tspan24	CD151 antigen	protein-coding
mm_96826.1	chr11	69995875	69995897	+	1	NA	TTS (NM_019749)	TTS (NM_019749)	120	NM_030064	78246	Mm.20805	NM_030064	ENSMUSG00000018572	Phf23	JUNE-1	PHD finger protein 23	protein-coding
mm_7518.1	chr1	124045488	124045522	-	1	NA	promoter-TSS (NM_199021)	promoter-TSS (NM_199021)	54	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_22257.1	chr2	177398311	177398340	-	1	NA	Intergenic	Intergenic	-66417	NM_001177568	628308	Mm.460436	NM_001177568	ENSMUSG00000078866	Zfp970	Gm14420|OTTMUSG00000016588	zinc finger protein 970	protein-coding
mm_152.1	chr1	11414185	11414248	+	1	NA	5' UTR (NM_001160369, exon 1 of 14)	5' UTR (NM_001160369, exon 1 of 14)	111	NM_001160371	320492	Mm.52021	NM_177173	ENSMUSG00000057715	A830018L16Rik	-	RIKEN cDNA A830018L16 gene	protein-coding
mm_47396.1	chr5	123036004	123036007	-	1	NA	Intergenic	Intergenic	10815	NM_029112	74890	Mm.141383	NM_029112	ENSMUSG00000029477	Morn3	4930438O03Rik	MORN repeat containing 3	protein-coding
mm_56975.1	chr6	120286680	120286684	-	1	NA	intron (NM_198884, intron 1 of 19)	intron (NM_198884, intron 1 of 19)	7877	NM_198884	330406	Mm.321840	NM_198884	ENSMUSG00000041372	B4galnt3	AB114826|B4GalNAcT3|C330047A21	beta-1,4-N-acetyl-galactosaminyl transferase 3	protein-coding
mm_96259.1	chr11	62603448	62603457	+	1	NA	promoter-TSS (NR_028550)	promoter-TSS (NR_028550)	-8	NR_028550	100217455		NR_028550	ENSMUSG00000065734	Snord49a	MBII-243	small nucleolar RNA, C/D box 49A	snoRNA
mm_5342.1	chr1	24587434	24587448	-	1	NA	promoter-TSS (NM_007733)	promoter-TSS (NM_007733)	-4	NM_007733	12823	Mm.329196	NM_007733	ENSMUSG00000026141	Col19a1	-	collagen, type XIX, alpha 1	protein-coding
mm_169103.1	chr1	34476214	34476219	-	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	16470	NM_011206	19253	Mm.361	NM_011206	ENSMUSG00000026126	Ptpn18	FLP1|HSCF|PTP-HSCF|PTP-K1|Ptpk1	protein tyrosine phosphatase, non-receptor type 18	protein-coding
mm_85689.1	chr9	108061989	108062007	-	1	NA	intron (NM_001311152, intron 25 of 38)	intron (NM_001311152, intron 25 of 38)	8839	NM_177275	320844	Mm.449806	NM_177275	ENSMUSG00000032593	Amigo3	E430002N15Rik|ali3|mKIAA1851	adhesion molecule with Ig like domain 3	protein-coding
mm_15957.1	chr2	165992716	165992726	+	1	NA	promoter-TSS (NM_008679)	promoter-TSS (NM_008679)	84	NM_008679	17979	Mm.469663	NM_008679	ENSMUSG00000027678	Ncoa3	2010305B15Rik|AW321064|Actr|Aib1|KAT13B|Rac3|Src3|Tram-1|Tram1|bHLHe42|p/Cip|pCip	nuclear receptor coactivator 3	protein-coding
mm_154472.1	chrM	3828	3873	-	1	NA	NA	Intergenic	NA	NA								
mm_137151.1	chr17	23679738	23679755	+	1	NA	intron (NM_018777, intron 1 of 2)	CpG	381	NM_018777	54419	Mm.86421	NM_018777	ENSMUSG00000023906	Cldn6	AL024037	claudin 6	protein-coding
mm_156672.1	chrX	159255852	159255899	+	1	NA	promoter-TSS (NM_148945)	promoter-TSS (NM_148945)	93	NM_001346675	110651	Mm.328476	NM_148945	ENSMUSG00000031309	Rps6ka3	MAPKAPK-1b|MPK-9|Rsk2|S6K-alpha3|p90RSK3|pp90RSK2	ribosomal protein S6 kinase polypeptide 3	protein-coding
mm_118998.1	chr14	28511345	28511381	+	1	NA	promoter-TSS (NM_001256224)	promoter-TSS (NM_001256224)	-42	NM_001256224	22418	Mm.287544	NM_009524	ENSMUSG00000021994	Wnt5a	8030457G12Rik|Wnt-5a	wingless-type MMTV integration site family, member 5A	protein-coding
mm_127879.1	chr15	8635268	8635278	-	1	NA	3' UTR (NM_148938, exon 10 of 10)	3' UTR (NM_148938, exon 10 of 10)	75534	NM_148938	20512	Mm.204834	NM_148938	ENSMUSG00000005360	Slc1a3	AI504299|B430115D02Rik|Eaat1|GLAST|GLAST-1|GLU-T|GluT-1|Gmt1|MGluT1	solute carrier family 1 (glial high affinity glutamate transporter), member 3	protein-coding
mm_134741.1	chr16	23029116	23029138	-	1	NA	promoter-TSS (NM_201375)	promoter-TSS (NM_201375)	-26	NM_001102410	385643	Mm.440414	NM_201375	ENSMUSG00000060459	Kng2	-	kininogen 2	protein-coding
mm_138156.1	chr17	34238915	34238964	+	1	NA	promoter-TSS (NM_010389)	promoter-TSS (NM_010389)	34	NM_010389	15002	Mm.327358	NM_010389	ENSMUSG00000041538	H2-Ob	A-beta-2|A-beta2|H-2Ab|H-2I|H-2Ob|H2-Ab|H2-Ab2|H2-IAb2|Ob	histocompatibility 2, O region beta locus	protein-coding
mm_96689.1	chr11	69590661	69590668	+	1	NA	exon (NM_011640, exon 10 of 11)	exon (NM_011640, exon 10 of 11)	10305	NM_001127233	22059	Mm.222	NM_011640	ENSMUSG00000059552	Trp53	Tp53|bbl|bfy|bhy|p44|p53	transformation related protein 53	protein-coding
mm_73108.1	chr8	94666723	94666769	+	1	NA	promoter-TSS (NM_024269)	promoter-TSS (NM_024269)	146	NM_024191	107566	Mm.393247	NM_024191	ENSMUSG00000031776	Arl2bp	1700010P10Rik|1700027H16Rik|6330544B05Rik|AI482273|AI849834|BART|Bart1	ADP-ribosylation factor-like 2 binding protein	protein-coding
mm_67545.1	chr7	81493700	81493719	-	1	NA	TTS (NM_183143)	TTS (NM_183143)	216	NM_021492	11775	Mm.322894	NM_021492	ENSMUSG00000062444	Ap3b2	AI549966|AU042881|Naptb|[b]-NAP|beta-NAP|beta3B	adaptor-related protein complex 3, beta 2 subunit	protein-coding
mm_18164.1	chr2	45099574	45099588	-	1	NA	intron (NM_001289521, intron 1 of 8)	intron (NM_001289521, intron 1 of 8)	10696	NM_001289521	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_20905.1	chr2	150306775	150306780	-	1	NA	Intergenic	Intergenic	49260	NM_001142410	100216455	Mm.484816	NM_001142410	ENSMUSG00000079008	Gm14124	EG640962|ENSMUSG00000074735|Gm10749|OTTMUSG00000015734	predicted gene 14124	protein-coding
mm_171685.1	chr4	58224803	58224803	+	1	NA	Intergenic	Intergenic	-18207	NM_022814	64817	Mm.261024	NM_022814	ENSMUSG00000028369	Svep1	1110021D17Rik|4833413O10Rik|AA387071|D430029O09Rik|Polydom	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	protein-coding
mm_63037.1	chr7	121075813	121075823	+	1	NA	intron (NM_021554, intron 4 of 4)	intron (NM_021554, intron 4 of 4)	-1288	NM_030691	80719	Mm.160384	NM_030691	ENSMUSG00000035004	Igsf6	-	immunoglobulin superfamily, member 6	protein-coding
mm_160177.1	chr7	45556125	45556125	+	1	NA	intron (NM_025330, intron 2 of 8)	intron (NM_025330, intron 2 of 8)	1197	NM_025330	66065	Mm.285710	NM_025330	ENSMUSG00000030825	Hsd17b14	0610039E24Rik|Dhrs10|retSDR3	hydroxysteroid (17-beta) dehydrogenase 14	protein-coding
mm_97890.1	chr11	83299006	83299046	+	1	NA	promoter-TSS (NM_134025)	promoter-TSS (NM_134025)	-49	NM_134025	103737	Mm.102205	NM_134025	ENSMUSG00000018733	Pex12	AI451906	peroxisomal biogenesis factor 12	protein-coding
mm_143809.1	chr17	83654670	83654681	-	1	NA	Intergenic	Intergenic	-22780	NM_153512	225030	Mm.223506	NM_153512	ENSMUSG00000045053	Kcng3	KV6.3|Kv10.1a|Kv10.1b	potassium voltage-gated channel, subfamily G, member 3	protein-coding
mm_133786.1	chr16	95257647	95257685	+	1	NA	non-coding (NR_073406, exon 1 of 6)	non-coding (NR_073406, exon 1 of 6)	108	NM_001271690	16516	Mm.272239	NM_019664	ENSMUSG00000062609	Kcnj15	4930414N08Rik|AI182284|AI267127|IRKK|Kir4.2	potassium inwardly-rectifying channel, subfamily J, member 15	protein-coding
mm_18991.1	chr2	76867192	76867208	-	1	NA	exon (NM_011652, exon 108 of 313)	exon (NM_011652, exon 108 of 313)	115347	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_47165.1	chr5	120743557	120743604	-	1	NA	intron (NM_001347448, intron 3 of 11)	RLTR17B_Mm|LTR|ERVK	6268	NM_145227	246728	Mm.260926	NM_145227	ENSMUSG00000032690	Oas2	Oasl11	2'-5' oligoadenylate synthetase 2	protein-coding
mm_30846.1	chr4	24894874	24894877	+	1	NA	Intergenic	MTEa|LTR|ERVL-MaLR	-3208	NM_026742	68493	Mm.204831	NM_026742	ENSMUSG00000028261	Ndufaf4	1110007M04Rik|3000003G13Rik|AW214064	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, assembly factor 4	protein-coding
mm_77289.1	chr8	116921409	116921451	-	1	NA	promoter-TSS (NM_028131)	promoter-TSS (NM_028131)	6	NM_026844	66531	Mm.4011	NM_026844	ENSMUSG00000014633	Cmc2	1110046L09Rik|2310061C15Rik|DC13	COX assembly mitochondrial protein 2	protein-coding
mm_144525.1	chr18	25045041	25045046	+	1	NA	intron (NM_175276, intron 13 of 26)	L1M3|LINE|L1	120922	NM_001142697	66648	Mm.263189	NM_001004361	ENSMUSG00000024269	Tpgs2	5730437P09Rik|5730494M16Rik|AI666318|Pgs2	tubulin polyglutamylase complex subunit 2	protein-coding
mm_105763.1	chr11	109603805	109603844	-	1	NA	exon (NM_145940, exon 3 of 13)	exon (NM_145940, exon 3 of 13)	7565	NM_145940	52639	Mm.35817	NM_145940	ENSMUSG00000041895	Wipi1	4930533H01Rik|AW411817|D11Ertd498e	WD repeat domain, phosphoinositide interacting 1	protein-coding
mm_93901.1	chr10	125488394	125488430	-	1	NA	Intergenic	Lx9|LINE|L1	-159877	NM_011391	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|Mct2	solute carrier family 16 (monocarboxylic acid transporters), member 7	protein-coding
mm_29053.1	chr3	103737996	103738006	-	1	NA	promoter-TSS (NM_133859)	promoter-TSS (NM_133859)	0	NM_133859	99543	Mm.211535	NM_133859	ENSMUSG00000027848	Olfml3	2810002E22Rik|AI115209|AW550633|HNOEL-iso|ONT3|mONT3	olfactomedin-like 3	protein-coding
mm_105772.1	chr11	109716741	109716743	-	1	NA	intron (NM_153782, intron 1 of 10)	intron (NM_153782, intron 1 of 10)	5514	NM_153782	208659	Mm.208662	NM_153782	ENSMUSG00000020614	Fam20a	AI606893	family with sequence similarity 20, member A	protein-coding
mm_62747.1	chr7	111083325	111083344	+	1	NA	promoter-TSS (NM_013507)	promoter-TSS (NM_013507)	-304	NM_013507	13690	Mm.185453	NM_013507	ENSMUSG00000005610	Eif4g2	DAP-5|E130105L11Rik|Nat1|Natm1|p97	eukaryotic translation initiation factor 4, gamma 2	protein-coding
mm_152014.1	chr19	5989271	5989311	-	1	NA	3' UTR (NM_007600, exon 22 of 22)	3' UTR (NM_007600, exon 22 of 22)	-3148	NM_198650	381203	Mm.329638	NM_198650	ENSMUSG00000037451	Slc22a20	Gm963|OAT1-L|mOAT6	solute carrier family 22 (organic anion transporter), member 20	protein-coding
mm_9621.1	chr1	176754378	176754407	-	1	NA	intron (NM_001099637, intron 13 of 19)	intron (NM_001099637, intron 13 of 19)	18031	NR_029775	723921		NR_029775	ENSMUSG00000065573	Mir350	Mirn350|mir-350|mmu-mir-350	microRNA 350	ncRNA
mm_21398.1	chr2	157571305	157571316	-	1	NA	Intergenic	ORR1B2|LTR|ERVL-MaLR	-4949	NM_016916	53619	Mm.480461	NM_016916	ENSMUSG00000067787	Blcap	AI462828|Bc10	bladder cancer associated protein	protein-coding
mm_67539.1	chr7	81455387	81455397	-	1	NA	promoter-TSS (NM_001252526)	promoter-TSS (NM_001252526)	-634	NM_001252526	12877	Mm.273122	NM_007755	ENSMUSG00000025586	Cpeb1	AU024112|Cpeb|mCPEB	cytoplasmic polyadenylation element binding protein 1	protein-coding
mm_108223.1	chr12	77189387	77189423	+	1	NA	Intergenic	Intergenic	-48699	NM_001252614	53618	Mm.35628	NM_016893	ENSMUSG00000021065	Fut8	-	fucosyltransferase 8	protein-coding
mm_37613.1	chr4	126968125	126968154	-	1	NA	promoter-TSS (NM_001114399)	promoter-TSS (NM_001114399)	-216	NM_001114399	67785	Mm.165401	NM_001114399	ENSMUSG00000042446	Zmym4	6330503C17Rik|AI480785|AW493829|CDIR|D630001M21|MYM|Zfp262|Znf262|mKIAA0425	zinc finger, MYM-type 4	protein-coding
mm_81973.1	chr9	121297497	121297552	+	1	NA	Intergenic	(CGGGG)n|Simple_repeat|Simple_repeat	-20352	NM_177589	209012	Mm.371804	NM_177589	ENSMUSG00000040936	Ulk4	4932415A06Rik|A730098P15	unc-51-like kinase 4	protein-coding
mm_11428.1	chr2	31950329	31950338	+	1	NA	promoter-TSS (NM_145144)	promoter-TSS (NM_145144)	30	NM_145144	108897	Mm.24838	NM_145144	ENSMUSG00000001864	Aif1l	2810003C17Rik|AI043124|C87647|Iba2	allograft inflammatory factor 1-like	protein-coding
mm_72577.1	chr8	84197405	84197416	+	1	NA	Intergenic	CpG	-11108	NR_029740	387216		NR_029740	ENSMUSG00000065611	Mir23a	Mirn23a|mir-23a|mmu-mir-23a	microRNA 23a	ncRNA
mm_16806.1	chr2	10130576	10130586	-	1	NA	5' UTR (NM_010582, exon 1 of 21)	5' UTR (NM_010582, exon 1 of 21)	102	NM_010582	16425	Mm.182043	NM_010582	ENSMUSG00000037254	Itih2	AI747202|Intin2|Itih-2	inter-alpha trypsin inhibitor, heavy chain 2	protein-coding
mm_48818.1	chr5	149015965	149015983	-	1	NA	Intergenic	Intergenic	9012	NR_040429	100503307	Mm.188008	NR_040429	ENSMUSG00000086610	Gm15408	OTTMUSG00000021225	predicted gene 15408	ncRNA
mm_81290.1	chr9	108320715	108320718	+	1	NA	intron (NM_001313962, intron 2 of 5)	intron (NM_001313962, intron 2 of 5)	13919	NM_001313962	11848	Mm.757	NM_016802	ENSMUSG00000007815	Rhoa	Arha|Arha1|Arha2	ras homolog family member A	protein-coding
mm_72509.1	chr8	83900115	83900165	+	1	NA	promoter-TSS (NM_181039)	promoter-TSS (NM_181039)	42	NM_181039	330814	Mm.260733	NM_181039	ENSMUSG00000013033	Adgrl1	2900070I05Rik|AI182398|CLIBA|Lec2|Lphn1|mKIAA0821	adhesion G protein-coupled receptor L1	protein-coding
mm_52528.1	chr6	115676715	115676754	+	1	NA	promoter-TSS (NM_029780)	promoter-TSS (NM_029780)	-99	NM_029780	110157	Mm.184163	NM_029780	ENSMUSG00000000441	Raf1	6430402F14Rik|AA990557|BB129353|Craf1|D830050J10Rik|Raf-1|c-Raf|v-Raf	v-raf-leukemia viral oncogene 1	protein-coding
mm_92227.1	chr10	68541843	68541908	-	1	NA	promoter-TSS (NM_028491)	promoter-TSS (NM_028491)	0	NM_028491	73287	Mm.141830	NM_028491	ENSMUSG00000019945	1700040L02Rik	-	RIKEN cDNA 1700040L02 gene	protein-coding
mm_91627.1	chr10	41809881	41809915	-	1	NA	promoter-TSS (NM_001162908)	promoter-TSS (NM_001162908)	-30	NM_026643	103268	Mm.338605	NM_026643	ENSMUSG00000019813	Cep57l1	2410017P07Rik|4930484D11Rik|AI607327|cep57R	centrosomal protein 57-like 1	protein-coding
mm_1608.1	chr1	74382368	74382380	+	1	NA	intron (NM_013612, intron 9 of 14)	intron (NM_013612, intron 9 of 14)	7171	NM_013612	18173	Mm.2913	NM_013612	ENSMUSG00000026177	Slc11a1	Bcg|Ity|Ity1|Lsh|Nramp|Nramp1|ity	solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1	protein-coding
mm_84011.1	chr9	57645433	57645443	-	1	NA	5' UTR (NM_007783, exon 1 of 13)	5' UTR (NM_007783, exon 1 of 13)	215	NM_007783	12988	Mm.21974	NM_007783	ENSMUSG00000032312	Csk	AW212630|p50CSK	c-src tyrosine kinase	protein-coding
mm_134034.1	chr16	5013561	5013569	-	1	NA	promoter-TSS (NM_133185)	promoter-TSS (NM_133185)	-12	NM_133185	66049	Mm.27792	NM_133185	ENSMUSG00000022540	Rogdi	0610011C19Rik|AU020118|C76152|Lzf	rogdi homolog	protein-coding
mm_128633.1	chr15	59082027	59082090	-	1	NA	promoter-TSS (NM_144800)	promoter-TSS (NM_144800)	-32	NM_144800	211401	Mm.215481	NM_144800	ENSMUSG00000022353	Mtss1	2310003N14Rik|BC024131|D130001D01Rik|Mim|mKIAA0429	metastasis suppressor 1	protein-coding
mm_31896.1	chr4	83342248	83342264	+	1	NA	Intergenic	Intergenic	-18067	NM_027238	69863	Mm.5540	NM_025782	ENSMUSG00000038172	Ttc39b	1810054D07Rik|9130422G05Rik|AI450603|AV103077|AW215585	tetratricopeptide repeat domain 39B	protein-coding
mm_86909.1	chr10	22731458	22731548	+	1	NA	promoter-TSS (NM_011603)	promoter-TSS (NM_011603)	-56	NM_011603	237336	Mm.86670	NM_011603	ENSMUSG00000071359	Tbpl1	4732475G08|AW011832|AW491032|D18347|STD|TLF|TRF2|TRP|Tlp	TATA box binding protein-like 1	protein-coding
mm_41251.1	chr5	88793887	88793897	+	1	NA	Intergenic	Intergenic	28879	NM_007832	13178	Mm.298892	NM_007832	ENSMUSG00000029366	Dck	-	deoxycytidine kinase	protein-coding
mm_68293.1	chr7	105736491	105736534	-	1	NA	promoter-TSS (NM_025897)	promoter-TSS (NM_025897)	72	NM_025897	101867	Mm.231400	NM_025897	ENSMUSG00000030888	Rrp8	1500003O22Rik|2900001K19Rik|AW538116	ribosomal RNA processing 8, methyltransferase, homolog (yeast)	protein-coding
mm_135699.1	chr16	52452959	52452983	-	1	NA	5' UTR (NM_001331110, exon 1 of 15)	5' UTR (NM_001331110, exon 1 of 15)	110	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_93357.1	chr10	103029044	103029053	-	1	NA	promoter-TSS (NM_172553)	promoter-TSS (NM_172553)	-271	NM_172553	216285	Mm.19287	NM_172553	ENSMUSG00000036602	Alx1	AI314867|C130005I02|Cart1	ALX homeobox 1	protein-coding
mm_123.1	chr1	9836049	9836052	+	1	NA	intron (NM_133220, intron 2 of 17)	MLT1B|LTR|ERVL-MaLR	-12231	NM_001037759	170755	Mm.336410	NM_133220	ENSMUSG00000025915	Sgk3	2510015P22Rik|A330005P07Rik|Cisk|fy|fz	serum/glucocorticoid regulated kinase 3	protein-coding
mm_44718.1	chr5	30957978	30958000	-	1	NA	exon (NM_001294302, exon 6 of 8)	exon (NM_001294302, exon 6 of 8)	2338	NM_001294302	50907	Mm.272414	NM_016703	ENSMUSG00000045302	Preb	C85705	prolactin regulatory element binding	protein-coding
mm_5813.1	chr1	52504300	52504300	-	1	NA	Intergenic	Intergenic	-3852	NM_008667	17936	Mm.25903	NM_008667	ENSMUSG00000002881	Nab1	-	Ngfi-A binding protein 1	protein-coding
mm_69637.1	chr7	138397705	138397786	-	1	NA	promoter-TSS (NM_183289)	promoter-TSS (NM_183289)	-15	NM_183289	70571	Mm.334297	NM_183289	ENSMUSG00000091002	Tcerg1l	5730476P14Rik	transcription elongation regulator 1-like	protein-coding
mm_60474.1	chr7	44478194	44478200	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-6320	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_117101.1	chr13	60174870	60174888	-	1	NA	3' UTR (NM_008086, exon 1 of 1)	3' UTR (NM_008086, exon 1 of 1)	2656	NM_008086	14451	Mm.22701	NM_008086	ENSMUSG00000052957	Gas1	AW554192|Gas-1	growth arrest specific 1	protein-coding
mm_40238.1	chr5	37486999	37487003	+	1	NA	intron (NM_022416, intron 6 of 11)	ORR1D1|LTR|ERVL-MaLR	148523	NM_145920	68525	Mm.25506	NM_145920	ENSMUSG00000050248	Evc2	1110017L09Rik|Lbn|limbin	Ellis van Creveld syndrome 2	protein-coding
mm_115642.1	chr13	12274117	12274126	-	1	NA	intron (NM_033268, intron 18 of 20)	B1F2|SINE|Alu	-16008	NM_001081128	238505	Mm.40335	NM_001081128	ENSMUSG00000021311	Mtr	AI894170|D830038K18Rik|MS	5-methyltetrahydrofolate-homocysteine methyltransferase	protein-coding
mm_68832.1	chr7	126200416	126200468	-	1	NA	promoter-TSS (NM_028816)	promoter-TSS (NM_028816)	-34	NM_028816	74204	Mm.235663	NM_028816	ENSMUSG00000000131	Xpo6	2610005L19Rik|AL022631|C230091E20Rik|R75304|Ranbp20|mKIAA0370	exportin 6	protein-coding
mm_101139.1	chr11	14147705	14147712	-	1	NA	intron (NR_131011, intron 1 of 3)	RLTR50A|LTR|ERVK	31333	NR_131011	75280	Mm.108492	NR_131011	ENSMUSG00000085452	4930554G24Rik	-	RIKEN cDNA 4930554G24 gene	ncRNA
mm_126331.1	chr15	79892437	79892482	+	1	NA	promoter-TSS (NM_001160415)	promoter-TSS (NM_001160415)	51	NM_030255	80287	Mm.284059	NM_030255	ENSMUSG00000009585	Apobec3	Apobec|Arp3|BC003314|Cem15|Rfv3	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 3	protein-coding
mm_142533.1	chr17	46487642	46487682	-	1	NA	promoter-TSS (NM_001162864)	promoter-TSS (NM_001162864)	13	NM_001162864	106763	Mm.297613	NM_175351	ENSMUSG00000015599	Ttbk1	AU017937|AW048023|C330008L01Rik	tau tubulin kinase 1	protein-coding
mm_35672.1	chr4	43578652	43578667	-	1	NA	promoter-TSS (NM_172866)	promoter-TSS (NM_172866)	-76	NM_172866	242406	Mm.259311	NM_172866	ENSMUSG00000028468	Rgp1	1110029E03Rik|AI527196|F730001J03|mKIAA0258	RAB6A GEF compex partner 1	protein-coding
mm_18119.1	chr2	44997020	44997031	-	1	NA	exon (NM_015753, exon 8 of 10)	exon (NM_015753, exon 8 of 10)	26152	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_118655.1	chr14	21757771	21757774	+	1	NA	intron (NM_026283, intron 1 of 5)	intron (NM_026283, intron 1 of 5)	7241	NM_026283	67630	Mm.102765	NM_026283	ENSMUSG00000021770	Samd8	1110053F04Rik|1700010P07Rik|SMSr	sterile alpha motif domain containing 8	protein-coding
mm_120473.1	chr14	65974254	65974262	+	1	NA	intron (NM_013492, intron 3 of 8)	intron (NM_013492, intron 3 of 8)	5775	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_92243.1	chr10	70288148	70288150	-	1	NA	Intergenic	Intergenic	42873	NM_025807	66859	Mm.19325	NM_025807	ENSMUSG00000037762	Slc16a9	1200003C15Rik|4930425B13Rik|AI552636	solute carrier family 16 (monocarboxylic acid transporters), member 9	protein-coding
mm_11937.1	chr2	52857802	52857826	+	1	NA	promoter-TSS (NM_172409)	promoter-TSS (NM_172409)	-54	NM_172409	71409	Mm.394427	NM_172409	ENSMUSG00000036053	Fmnl2	5430425K04Rik|Man	formin-like 2	protein-coding
mm_84997.1	chr9	86792031	86792041	-	1	NA	intron (NR_102729, intron 20 of 30)	intron (NR_102729, intron 20 of 30)	48403	NM_178738	244954	Mm.257629	NM_178738	ENSMUSG00000033491	Prss35	6030424L22Rik|P3D9	protease, serine 35	protein-coding
mm_122033.1	chr14	29722580	29722598	-	1	NA	promoter-TSS (NM_009785)	promoter-TSS (NM_009785)	-725	NM_009785	12294	Mm.386754	NM_009785	ENSMUSG00000021991	Cacna2d3	Cacnad3|alapha2delta3	calcium channel, voltage-dependent, alpha2/delta subunit 3	protein-coding
mm_58776.1	chr7	16061781	16061793	+	1	NA	Intergenic	CpG	-10058	NM_001347559	666528	Mm.290718	NM_001099277	ENSMUSG00000078796	Zfp541	EG666528|Znf541	zinc finger protein 541	protein-coding
mm_151031.1	chr19	47015205	47015216	+	1	NA	promoter-TSS (NM_001164363)	promoter-TSS (NM_001164363)	-21	NM_001164363	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_49900.1	chr6	38941318	38941328	+	1	NA	intron (NM_011539, intron 1 of 12)	intron (NM_011539, intron 1 of 12)	22337	NM_011539	21391	Mm.4054	NM_011539	ENSMUSG00000029925	Tbxas1	CYP5|CYP5A1|THAS|TS|TXAS|TXS	thromboxane A synthase 1, platelet	protein-coding
mm_139340.1	chr17	49615105	49615151	+	1	NA	promoter-TSS (NM_177052)	promoter-TSS (NM_177052)	-44	NM_177052	319991	Mm.441340	NM_177052	ENSMUSG00000023999	Kif6	D130004B10Rik|D130084M03Rik	kinesin family member 6	protein-coding
mm_139695.1	chr17	57445024	57445035	+	1	NA	exon (NM_010130, exon 15 of 22)	exon (NM_010130, exon 15 of 22)	86343	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_153303.1	chr19	37989697	37989727	-	1	NA	intron (NM_001302140, intron 5 of 53)	intron (NM_001302140, intron 5 of 53)	53865	NM_001099634	226101	Mm.34674	NM_177035	ENSMUSG00000048612	Myof	2310004N10Rik|2310051D19Rik|E030042N20Rik|Fer1l3	myoferlin	protein-coding
mm_57584.1	chr6	127152459	127152474	-	1	NA	intron (NR_040275, intron 1 of 1)	intron (NR_040275, intron 1 of 1)	-1418	NM_009829	12444	Mm.333406	NM_009829	ENSMUSG00000000184	Ccnd2	2600016F06Rik|AI256817|BF642806|C86853|Vin-1|Vin1|cD2	cyclin D2	protein-coding
mm_143806.1	chr17	83582255	83582258	-	1	NA	Intergenic	PB1D7|SINE|Alu	49639	NM_153512	225030	Mm.223506	NM_153512	ENSMUSG00000045053	Kcng3	KV6.3|Kv10.1a|Kv10.1b	potassium voltage-gated channel, subfamily G, member 3	protein-coding
mm_65005.1	chr7	17056670	17056696	-	1	NA	promoter-TSS (NM_016868)	promoter-TSS (NM_016868)	-4	NM_016868	53417	Mm.135110	NM_016868	ENSMUSG00000004328	Hif3a	Ipas|MOP7|NEPAS|bHLHe17	hypoxia inducible factor 3, alpha subunit	protein-coding
mm_437.1	chr1	34678177	34678213	+	1	NA	Intergenic	CpG	-41985	NR_033627	241051	Mm.282827	NR_033627		AA619741	-	PHD finger protein 19 pseudogene	pseudo
mm_2185.1	chr1	89016084	89016103	+	1	NA	promoter-TSS (NR_040471)	promoter-TSS (NR_040471)	-20	NR_040471	73475	Mm.491040	NR_040471	ENSMUSG00000099378	1700067G17Rik	-	RIKEN cDNA 1700067G17 gene	ncRNA
mm_29766.1	chr3	127225895	127225915	-	1	NA	intron (NM_001327938, intron 1 of 47)	intron (NM_001327938, intron 1 of 47)	64600	NR_105029	100862268	Mm.444603	NR_105029	ENSMUSG00000097456	LOC100862268	-	uncharacterized LOC100862268	ncRNA
mm_48262.1	chr5	137871740	137871768	-	1	NA	promoter-TSS (NM_001024932)	promoter-TSS (NM_001024932)	4	NM_001024932	545812	Mm.332769	NM_001024932	ENSMUSG00000066682	Pilrb2	EG545812	paired immunoglobin-like type 2 receptor beta 2	protein-coding
mm_147032.1	chr18	34746890	34746890	-	1	NA	intron (NM_009860, intron 7 of 14)	intron (NM_009860, intron 7 of 14)	4643	NM_009860	12532	Mm.286602	NM_009860	ENSMUSG00000044201	Cdc25c	Cdc25	cell division cycle 25C	protein-coding
mm_129226.1	chr15	76612924	76612962	-	1	NA	intron (NM_028064, intron 10 of 11)	intron (NM_028064, intron 10 of 11)	3909	NM_028064	72027	Mm.276829	NM_028064	ENSMUSG00000063354	Slc39a4	1600025H15Rik|AU041686|AWMS2|ZIP4	solute carrier family 39 (zinc transporter), member 4	protein-coding
mm_26073.1	chr3	136670281	136670307	+	1	NA	5' UTR (NM_001293622, exon 1 of 13)	5' UTR (NM_001293622, exon 1 of 13)	228	NM_001293622	19055	Mm.331389	NM_008913	ENSMUSG00000028161	Ppp3ca	2900074D19Rik|CN|Caln|Calna|CnA	protein phosphatase 3, catalytic subunit, alpha isoform	protein-coding
mm_16366.1	chr2	174760782	174760796	+	1	NA	5' UTR (NM_007903, exon 1 of 5)	5' UTR (NM_007903, exon 1 of 5)	170	NM_007903	13616	Mm.9478	NM_007903	ENSMUSG00000027524	Edn3	ET-3|PPET3|ls|tmgc48	endothelin 3	protein-coding
mm_136986.1	chr17	17234892	17234942	+	1	NA	Intergenic	Intergenic	-59526	NM_001324550	100862203	Mm.484235	NM_001324550		Gm6712	EG626854	predicted gene 6712	protein-coding
mm_80004.1	chr9	67733961	67733972	+	1	NA	Intergenic	Intergenic	-4389	NR_106101	102465716		NR_106101	ENSMUSG00000098446	Mir7242	Gm27809|mmu-mir-7242	microRNA 7242	ncRNA
mm_103137.1	chr11	70238306	70238322	-	1	NA	promoter-TSS (NM_001177601)	promoter-TSS (NM_001177601)	-400	NM_145758	104457	Mm.30016	NM_026757	ENSMUSG00000020831	0610010K14Rik	1110020A23Rik|AL033328|AU045833|Bap18	RIKEN cDNA 0610010K14 gene	protein-coding
mm_107823.1	chr12	69129830	69129860	+	1	NA	Intergenic	Intergenic	29341	NM_009093	20090	Mm.379006	NM_009093	ENSMUSG00000034892	Rps29	-	ribosomal protein S29	protein-coding
mm_108677.1	chr12	86679451	86679461	+	1	NA	5' UTR (NM_177354, exon 1 of 7)	5' UTR (NM_177354, exon 1 of 7)	756	NM_177354	238328	Mm.216101	NM_177354	ENSMUSG00000021256	Vash1	AI834978|D930046M13Rik|G630009D10Rik	vasohibin 1	protein-coding
mm_21349.1	chr2	157114278	157114326	-	1	NA	exon (NM_001139520, exon 8 of 17)	exon (NM_001139520, exon 8 of 17)	20920	NM_001139520	56045	Mm.248478	NM_018851	ENSMUSG00000027639	Samhd1	E330031J07Rik|Mg11	SAM domain and HD domain, 1	protein-coding
mm_23956.1	chr3	84925456	84925472	+	1	NA	intron (NM_001177773, intron 4 of 13)	intron (NM_001177773, intron 4 of 13)	-26747	NM_080428	50754	Mm.196475	NM_080428	ENSMUSG00000028086	Fbxw7	1110001A17Rik|AGO|Cdc4|Fbw7|Fbwd6|Fbx30|Fbxo30|Fbxw6|SEL-10	F-box and WD-40 domain protein 7	protein-coding
mm_44988.1	chr5	37717123	37717178	-	1	NA	promoter-TSS (NM_022416)	promoter-TSS (NM_022416)	3	NM_022416	64293	Mm.103714	NM_022416	ENSMUSG00000029123	Stk32b	2510009F08Rik|STKG6|Stk32|YANK2	serine/threonine kinase 32B	protein-coding
mm_74902.1	chr8	25201786	25201794	-	1	NA	promoter-TSS (NM_177089)	promoter-TSS (NM_177089)	-248	NM_177089	320165	Mm.308452	NM_177089	ENSMUSG00000065954	Tacc1	4833447E04Rik|AA960202|B230378H13Rik	transforming, acidic coiled-coil containing protein 1	protein-coding
mm_70540.1	chr8	13039370	13039397	+	1	NA	intron (NM_001242368, intron 2 of 8)	MTEa|LTR|ERVL-MaLR	2075	NM_001242368	14058	Mm.262589	NM_007972	ENSMUSG00000031444	F10	Cf10|fX	coagulation factor X	protein-coding
mm_166024.1	chr4	124397635	124397641	+	1	NA	Intergenic	Intergenic	88321	NR_040774	78460	Mm.452060	NR_040774		1700057H15Rik	-	RIKEN cDNA 1700057H15 gene	ncRNA
mm_39541.1	chr5	21543486	21543496	+	1	NA	promoter-TSS (NM_028977)	promoter-TSS (NM_028977)	-36	NM_028977	74511	Mm.439963	NM_028977	ENSMUSG00000039883	Lrrc17	37kDa|4833425M04Rik|6130400C22Rik|P37nb	leucine rich repeat containing 17	protein-coding
mm_79754.1	chr9	62373548	62373571	+	1	NA	exon (NM_009672, exon 4 of 7)	exon (NM_009672, exon 4 of 7)	32216	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	protein-coding
mm_6277.1	chr1	69683145	69683149	-	1	NA	intron (NM_011770, intron 3 of 7)	intron (NM_011770, intron 3 of 7)	2813	NM_011770	22779	Mm.106343	NM_011770	ENSMUSG00000025997	Ikzf2	A730095J18Rik|Helios|Zfpn1a2|Znfn1a2	IKAROS family zinc finger 2	protein-coding
mm_16458.1	chr2	180582781	180582798	+	1	NA	5' UTR (NM_028479, exon 2 of 6)	5' UTR (NM_028479, exon 2 of 6)	1485	NM_028479	73247	Mm.426558	NM_028479	ENSMUSG00000027569	Mrgbp	1600027N09Rik|AW060503|C80444	MRG/MORF4L binding protein	protein-coding
mm_36200.1	chr4	62360330	62360334	-	1	NA	promoter-TSS (NM_175090)	promoter-TSS (NM_175090)	216	NM_001045528	338355	Mm.357792	NM_001045528	ENSMUSG00000066151	Fkbp15	BB131447|C430014M02Rik|FKBO133|FKBP-133|FKBP-15|FKBP133|mKIAA0674	FK506 binding protein 15	protein-coding
mm_60117.1	chr7	35605678	35605680	+	1	NA	intron (NM_145633, intron 9 of 28)	intron (NM_145633, intron 9 of 28)	19432	NM_178263	245886	Mm.272620	NM_145633	ENSMUSG00000034867	Ankrd27	AA408090|BC016493|D330003H11Rik|Varp	ankyrin repeat domain 27 (VPS9 domain)	protein-coding
mm_108590.1	chr12	85339697	85339701	+	1	NA	promoter-TSS (NM_145138)	promoter-TSS (NM_145138)	-337	NM_145138	217718	Mm.29071	NM_145138	ENSMUSG00000034290	Nek9	C130021H08Rik	NIMA (never in mitosis gene a)-related expressed kinase 9	protein-coding
mm_159948.1	chr6	85762489	85762489	-	1	NA	5' UTR (NM_001037842, exon 2 of 3)	5' UTR (NM_001037842, exon 2 of 3)	3255	NM_001037842	93674	Mm.440772	NM_053097	ENSMUSG00000051262	Nat8f3	4833414A14Rik|4930583K21Rik|Cml3	N-acetyltransferase 8 (GCN5-related) family member 3	protein-coding
mm_66535.1	chr7	45154177	45154186	-	1	NA	promoter-TSS (NM_029406)	promoter-TSS (NM_029406)	-122	NM_029406	68845	Mm.181689	NM_029406	ENSMUSG00000003423	Pih1d1	1110061L23Rik|4933413A04Rik|Nop17	PIH1 domain containing 1	protein-coding
mm_7771.1	chr1	131200205	131200215	-	1	NA	promoter-TSS (NM_001311094)	promoter-TSS (NM_001311094)	-25	NM_001311094	54354	Mm.248291	NM_018750	ENSMUSG00000026430	Rassf5	1300019G20Rik|Maxp1|Nore1|Nore1A|Nore1B|Rapl	Ras association (RalGDS/AF-6) domain family member 5	protein-coding
mm_95423.1	chr11	50134400	50134421	+	1	NA	intron (NM_001290760, intron 1 of 21)	intron (NM_001290760, intron 1 of 21)	3050	NM_029745	76795	Mm.290975	NM_029745	ENSMUSG00000036644	Tbc1d9b	-	TBC1 domain family, member 9B	protein-coding
mm_114575.1	chr13	75089900	75089918	+	1	NA	promoter-TSS (NM_013628)	promoter-TSS (NM_013628)	-78	NM_013628	18548	Mm.1333	NM_013628	ENSMUSG00000021587	Pcsk1	Nec-1|Nec1|PC1|PC3|Phpp-1|SPC3	proprotein convertase subtilisin/kexin type 1	protein-coding
mm_162147.1	chrX	74740785	74740785	+	1	NA	promoter-TSS (NM_001099306)	promoter-TSS (NM_001099306)	-142	NM_001099306	628518	Mm.465110	NM_001099306	ENSMUSG00000079532	Gm6890	EG628518	predicted gene 6890	protein-coding
mm_169725.1	chr15	79847021	79847035	+	1	NA	Intergenic	BGLII|LTR|ERVK	-12695	NM_001013362	504193	Mm.38438	NM_029079	ENSMUSG00000089837	Npcd	Cbx6-Nptxr	neuronal pentraxin chromo domain	protein-coding
mm_91076.1	chr10	19011801	19011811	-	1	NA	exon (NM_001166402, exon 1 of 8)	exon (NM_001166402, exon 1 of 8)	157	NM_001166402	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_141581.1	chr17	32388999	32389047	-	1	NA	promoter-TSS (NM_011717)	promoter-TSS (NM_011717)	-73	NM_011717	22404	Mm.274948	NM_011717	ENSMUSG00000024050	Wiz	-	widely-interspaced zinc finger motifs	protein-coding
mm_43958.1	chr5	145236928	145236936	+	1	NA	intron (NM_001083958, intron 4 of 4)	intron (NM_001083958, intron 4 of 4)	5173	NM_028298	72611	Mm.206555	NM_028298	ENSMUSG00000007812	Zfp655	2700038I16Rik|9030409O18Rik|mKIAA4222	zinc finger protein 655	protein-coding
mm_126243.1	chr15	79002320	79002331	+	1	NA	TTS (NR_105921)	TTS (NR_105921)	102	NR_105921	102465577		NR_105921	ENSMUSG00000099180	Mir6956	Gm27880|mmu-mir-6956	microRNA 6956	ncRNA
mm_1157.1	chr1	60893537	60893551	+	1	NA	Intergenic	Intergenic	-15481	NM_009843	12477	Mm.390	NM_009843	ENSMUSG00000026011	Ctla4	Cd152|Ctla-4|Ly-56	cytotoxic T-lymphocyte-associated protein 4	protein-coding
mm_107243.1	chr12	26479199	26479214	+	1	NA	3' UTR (NM_020557, exon 5 of 5)	3' UTR (NM_020557, exon 5 of 5)	9991	NM_020557	22169	Mm.271839	NM_020557	ENSMUSG00000020638	Cmpk2	1200004E04Rik|TDKI|Tyki	cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial	protein-coding
mm_131793.1	chr16	22899004	22899014	+	1	NA	exon (NM_001276450, exon 7 of 7)	exon (NM_001276450, exon 7 of 7)	-4623	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_45898.1	chr5	88675614	88675655	-	1	NA	promoter-TSS (NM_001098476)	promoter-TSS (NM_001098476)	-54	NM_001098476	231413	Mm.332474	NM_178700	ENSMUSG00000044221	Grsf1	BB232551|C80280|D5Wsu31e	G-rich RNA sequence binding factor 1	protein-coding
mm_52756.1	chr6	120773612	120773624	+	1	NA	promoter-TSS (NM_001081048)	promoter-TSS (NM_001081048)	-150	NM_001081048	71803	Mm.425340	NM_001081048	ENSMUSG00000004902	Slc25a18	1500015I14Rik|AW125787	solute carrier family 25 (mitochondrial carrier), member 18	protein-coding
mm_1245.1	chr1	62798276	62798297	+	1	NA	intron (NM_010939, intron 15 of 15)	intron (NM_010939, intron 15 of 15)	-3554	NR_040601	74992	Mm.401979	NR_040601		4930487H11Rik	-	RIKEN cDNA 4930487H11 gene	ncRNA
mm_3433.1	chr1	150101205	150101273	+	1	NA	exon (NM_011198, exon 3 of 10)	exon (NM_011198, exon 3 of 10)	1208	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_164010.1	chr14	70145966	70145966	-	1	NA	intron (NM_146055, intron 7 of 20)	intron (NM_146055, intron 7 of 20)	7825	NM_146055	219158	Mm.218284	NM_146055	ENSMUSG00000033712	Ccar2	2610301G19Rik|Dbc1|mKIAA1967	cell cycle activator and apoptosis regulator 2	protein-coding
mm_42934.1	chr5	122949512	122949554	+	1	NA	intron (NM_001003953, intron 6 of 22)	intron (NM_001003953, intron 6 of 22)	39566	NM_001003953	30841	Mm.86406	NM_013910	ENSMUSG00000029475	Kdm2b	Cxxc2|Fbl10|Fbxl10|Jhdm1b|PCCX2	lysine (K)-specific demethylase 2B	protein-coding
mm_126087.1	chr15	77857923	77857940	+	1	NA	Intergenic	CpG	-15756	NM_022410	17886	Mm.29677	NM_022410	ENSMUSG00000022443	Myh9	Fltn|Myhn-1|Myhn1|NMHCIIA|NMMHC-A|NMMHC-IIA|TU72.6	myosin, heavy polypeptide 9, non-muscle	protein-coding
mm_8484.1	chr1	153549819	153549828	-	1	NA	promoter-TSS (NM_028749)	promoter-TSS (NM_028749)	-109	NM_028749	74091	Mm.24887	NM_028749	ENSMUSG00000042684	Npl	0610033B02Rik	N-acetylneuraminate pyruvate lyase	protein-coding
mm_73673.1	chr8	111522336	111522349	+	1	NA	promoter-TSS (NM_176923)	promoter-TSS (NM_176923)	-235	NM_176923	319481	Mm.247294	NM_176923	ENSMUSG00000031959	Wdr59	5430401O09Rik|Cdw12	WD repeat domain 59	protein-coding
mm_92380.1	chr10	76442650	76442672	-	1	NA	5' UTR (NM_001282992, exon 1 of 42)	5' UTR (NM_001282992, exon 1 of 42)	251	NM_008787	18541	Mm.251794	NM_008787	ENSMUSG00000001151	Pcnt	AW476095|C86676|KEN|Pcnt2|kendrin|m239Asp|m275Asp	pericentrin (kendrin)	protein-coding
mm_113668.1	chr13	42709483	42709538	+	1	NA	promoter-TSS (NM_001005740)	promoter-TSS (NM_001005740)	-71	NM_001005740	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding
mm_21905.1	chr2	166398239	166398275	-	1	NA	Intergenic	Intergenic	-49194	NR_015558	319684	Mm.399746	NR_015558		5031425F14Rik	-	RIKEN cDNA 5031425F14 gene	ncRNA
mm_93108.1	chr10	91082684	91082700	-	1	NA	promoter-TSS (NM_026166)	promoter-TSS (NM_026166)	51	NM_001042558	11783	Mm.220289	NM_009684	ENSMUSG00000019979	Apaf1	6230400I06Rik|Apaf-1|Apaf1l|fog|mKIAA0413	apoptotic peptidase activating factor 1	protein-coding
mm_129002.1	chr15	74856228	74856236	-	1	NA	promoter-TSS (NM_009991)	promoter-TSS (NM_009991)	86	NM_009991	13072	Mm.377079	NM_009991	ENSMUSG00000022589	Cyp11b2	Cpn2|Cyp11b|Cyp11b-2	cytochrome P450, family 11, subfamily b, polypeptide 2	protein-coding
mm_154750.1	chrX	10585550	10585572	+	1	NA	exon (NM_019634, exon 5 of 8)	exon (NM_019634, exon 5 of 8)	100445	NM_019634	21912	Mm.18590	NM_019634	ENSMUSG00000058254	Tspan7	1200014P11Rik|A15|AI323365|Cd231|Mxs1|PE31|R74651|TALLA|Tm4sf2	tetraspanin 7	protein-coding
mm_109507.1	chr12	111452303	111452328	+	1	NA	intron (NM_009396, intron 11 of 11)	(TCCA)n|Simple_repeat|Simple_repeat	9654	NM_009396	21928	Mm.255332	NM_009396	ENSMUSG00000021281	Tnfaip2	B94|Exoc3l3|M-sec|Tnfip2|tnfb94	tumor necrosis factor, alpha-induced protein 2	protein-coding
mm_99655.1	chr11	105655549	105655579	+	1	NA	intron (NM_181071, intron 2 of 25)	intron (NM_181071, intron 2 of 25)	65578	NM_181071	77097	Mm.22501	NM_175492	ENSMUSG00000053580	Tanc2	3526402J09Rik|5730590C14Rik	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2	protein-coding
mm_166042.1	chr4	130295433	130295436	-	1	NA	Intergenic	Intergenic	-13344	NM_010174	14077	Mm.388886	NM_010174	ENSMUSG00000028773	Fabp3	Fabph-1|Fabph-4|Fabph1|Fabph4|H-FABP|Mdgi	fatty acid binding protein 3, muscle and heart	protein-coding
mm_21655.1	chr2	164356285	164356298	-	1	NA	5' UTR (NM_011414, exon 1 of 4)	5' UTR (NM_011414, exon 1 of 4)	216	NM_011414	20568	Mm.371583	NM_011414	ENSMUSG00000017002	Slpi	-	secretory leukocyte peptidase inhibitor	protein-coding
mm_96538.1	chr11	68691947	68691979	+	1	NA	promoter-TSS (NM_175260)	promoter-TSS (NM_175260)	48	NM_175260	77579	Mm.218233	NM_175260	ENSMUSG00000020900	Myh10	5730504C04Rik|9330167F11Rik|Fltn|Myhn-2|Myhn2|NMHC II-B|NMHC-B|NMHCII-B|NMMHC II-b|NMMHC-B|NMMHC-IIB|SMemb|mKIAA3005	myosin, heavy polypeptide 10, non-muscle	protein-coding
mm_129144.1	chr15	76202229	76202246	-	1	NA	intron (NM_011117, intron 1 of 31)	intron (NM_011117, intron 1 of 31)	-1630	NM_201390	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
mm_115412.1	chr13	114824633	114824646	+	1	NA	exon (NM_001113375, exon 3 of 6)	exon (NM_001113375, exon 3 of 6)	6402	NM_001113374	17434	Mm.19027	NM_013826	ENSMUSG00000015536	Mocs2	AI415403	molybdenum cofactor synthesis 2	protein-coding
mm_83153.1	chr9	40456341	40456366	-	1	NA	promoter-TSS (NM_172768)	promoter-TSS (NM_172768)	-589	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_149638.1	chr19	17394791	17394840	+	1	NA	intron (NM_019437, intron 1 of 3)	intron (NM_019437, intron 1 of 3)	772	NM_019437	54391	Mm.7013	NM_019437	ENSMUSG00000024712	Rfk	0610038L10Rik|AF031381|KOI-4	riboflavin kinase	protein-coding
mm_79939.1	chr9	65908968	65909019	+	1	NA	promoter-TSS (NM_019797)	promoter-TSS (NM_019797)	-17	NM_173185	214897	Mm.325816	NM_173185	ENSMUSG00000032384	Csnk1g1	9130020E21Rik	casein kinase 1, gamma 1	protein-coding
mm_110719.1	chr12	69584547	69584580	-	1	NA	3' UTR (NM_001135559, exon 23 of 23)	3' UTR (NM_001135559, exon 23 of 23)	-1535	NM_001033236	207965	Mm.102487	NM_001033236	ENSMUSG00000049882	Vcpkmt	Gm71|Mettl21d|Mettl221d|VCP-KMT	valosin containing protein lysine (K) methyltransferase	protein-coding
mm_27374.1	chr3	50443417	50443423	-	1	NA	5' UTR (NM_011990, exon 1 of 12)	5' UTR (NM_011990, exon 1 of 12)	193	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_101881.1	chr11	48927178	48927182	-	1	NA	promoter-TSS (NM_001045540)	promoter-TSS (NM_001045540)	2	NM_001045540	620913	Mm.452174	NM_001045540	ENSMUSG00000048852	Gm12185	Irgb2b1|OTTMUSG00000005523	predicted gene 12185	protein-coding
mm_6308.1	chr1	71586225	71586233	-	1	NA	exon (NM_001276413, exon 44 of 44)	exon (NM_001276413, exon 44 of 44)	29073	NM_026195	108147	Mm.38010	NM_026195	ENSMUSG00000026192	Atic	2610509C24Rik|AA536954|AW212393	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	protein-coding
mm_146003.1	chr18	68692051	68692062	+	1	NA	Intergenic	MT-int|LTR|ERVL-MaLR	-47344	NR_105774	102465183		NR_105774	ENSMUSG00000099300	Mir6356	Gm27461|mmu-mir-6356	microRNA 6356	ncRNA
mm_30849.1	chr4	24972465	24972469	+	1	NA	promoter-TSS (NM_030733)	promoter-TSS (NM_030733)	-952	NM_030733	81006	Mm.160412	NM_030733	ENSMUSG00000040372	Gpr63	PSP24beta|Psp24-2	G protein-coupled receptor 63	protein-coding
mm_127686.1	chr15	102966858	102966871	+	1	NA	promoter-TSS (NM_010462)	promoter-TSS (NM_010462)	68	NM_010462	209448	Mm.31665	NM_010462	ENSMUSG00000022484	Hoxc10	AI506621|Hox-3.6	homeobox C10	protein-coding
mm_11700.1	chr2	35979388	35979404	+	1	NA	exon (NM_029774, exon 1 of 10)	exon (NM_029774, exon 1 of 10)	228	NM_029774	74410	Mm.21591	NM_028921	ENSMUSG00000026885	Ttll11	4932702F08Rik|4933424A20Rik|AU043211|D2Ertd624e	tubulin tyrosine ligase-like family, member 11	protein-coding
mm_59684.1	chr7	28440932	28440945	+	1	NA	promoter-TSS (NM_001039192)	promoter-TSS (NM_001039192)	1	NM_001039192	63986	Mm.194536	NM_022024	ENSMUSG00000060791	Gmfg	0610039G16Rik|2310057N07Rik|AI324845	glia maturation factor, gamma	protein-coding
mm_36442.1	chr4	82362217	82362219	-	1	NA	intron (NM_001113210, intron 3 of 11)	intron (NM_001113210, intron 3 of 11)	143561	NM_001286127	18028	Mm.317947	NM_008687	ENSMUSG00000008575	Nfib	6720429L07Rik|CTF|E030026I10Rik|NF-I/B|NF1-B|NFI-B	nuclear factor I/B	protein-coding
mm_58823.1	chr7	16714852	16714855	+	1	NA	Intergenic	Intergenic	-7076	NM_011927	26368	Mm.27096	NM_011927	ENSMUSG00000007209	Ceacam9	AA410097|AW545709|Cea-5|Cea5|mmCGM8	carcinoembryonic antigen-related cell adhesion molecule 9	protein-coding
mm_83835.1	chr9	54223794	54223796	-	1	NA	Intergenic	Intergenic	-30353	NM_007810	13075	Mm.5199	NM_007810	ENSMUSG00000032274	Cyp19a1	Ar|ArKO|Cyp19|Int-5|Int5|p450arom	cytochrome P450, family 19, subfamily a, polypeptide 1	protein-coding
mm_160857.1	chr11	58597526	58597526	+	1	NA	exon (NM_001011743, exon 1 of 1)	exon (NM_001011743, exon 1 of 1)	181	NM_001011743	257892	Mm.377288	NM_001011743	ENSMUSG00000056564	Olfr324	MOR102-2	olfactory receptor 324	protein-coding
mm_117435.1	chr13	74617290	74617326	-	1	NA	Intergenic	Intergenic	-22564	NM_030711	80898	Mm.83526	NM_030711	ENSMUSG00000021583	Erap1	Arts1|ERAAP|PILSA|PILSAP	endoplasmic reticulum aminopeptidase 1	protein-coding
mm_160603.1	chr9	78257144	78257144	+	1	NA	promoter-TSS (NM_001243092)	promoter-TSS (NM_001243092)	15	NM_001243092	100042295	Mm.197422	NM_001243092	ENSMUSG00000111709	Gm3776	-	predicted gene 3776	protein-coding
mm_55730.1	chr6	77227681	77227686	-	1	NA	intron (NM_001109764, intron 8 of 19)	intron (NM_001109764, intron 8 of 19)	-15034	NM_028880	74342	Mm.292568	NM_028880	ENSMUSG00000060780	Lrrtm1	4632401D06Rik|AW125451	leucine rich repeat transmembrane neuronal 1	protein-coding
mm_115704.1	chr13	14522408	14522439	-	1	NA	intron (NM_001081348, intron 1 of 28)	intron (NM_001081348, intron 1 of 28)	803	NM_001081348	94253	Mm.125298	NM_153130	ENSMUSG00000021301	Hecw1	9330116H24Rik|AV273951|E130207I19Rik|Nedl1	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	protein-coding
mm_72670.1	chr8	84908681	84908696	+	1	NA	promoter-TSS (NM_010062)	promoter-TSS (NM_010062)	64	NM_010062	13423	Mm.350831	NM_010062	ENSMUSG00000003812	Dnase2a	Dnase2	deoxyribonuclease II alpha	protein-coding
mm_130548.1	chr15	98955460	98955486	-	1	NA	Intergenic	Intergenic	-1972	NM_011653	22142	Mm.405359	NM_011653	ENSMUSG00000072235	Tuba1a	Tuba-1|Tuba1	tubulin, alpha 1A	protein-coding
mm_70749.1	chr8	19517033	19517041	+	1	NA	Intergenic	Intergenic	21940	NM_139220	246080	Mm.207067	NM_139220	ENSMUSG00000037790	Defb7	BD-7|Defb15	defensin beta 7	protein-coding
mm_630.1	chr1	40266579	40266659	+	1	NA	promoter-TSS (NM_001123382)	promoter-TSS (NM_001123382)	33	NM_001123382	16177	Mm.896	NM_008362	ENSMUSG00000026072	Il1r1	CD121a|CD121b|IL-1R1|IL-iR|Il1r-1	interleukin 1 receptor, type I	protein-coding
mm_82840.1	chr9	31167620	31167658	-	1	NA	exon (NM_001102455, exon 7 of 17)	exon (NM_001102455, exon 7 of 17)	-35840	NM_011176	19143	Mm.243926	NM_011176	ENSMUSG00000031995	St14	Epithin|MT-SP1|Prss14|Tmprss14|mCAP3|matriptase	suppression of tumorigenicity 14 (colon carcinoma)	protein-coding
mm_54587.1	chr6	38147370	38147379	-	1	NA	intron (NM_194061, intron 14 of 19)	intron (NM_194061, intron 14 of 19)	-22788	NM_080467	140494	Mm.462308	NM_080467	ENSMUSG00000038600	Atp6v0a4	Atp6n1b|a4	ATPase, H+ transporting, lysosomal V0 subunit A4	protein-coding
mm_62778.1	chr7	112391250	112391269	+	1	NA	intron (NM_027587, intron 4 of 9)	intron (NM_027587, intron 4 of 9)	22951	NM_027587	100504195	Mm.291129	NM_027587	ENSMUSG00000030771	Micalcl	4921517J23Rik	MICAL C-terminal like	protein-coding
mm_68216.1	chr7	104410015	104410027	-	1	NA	3' UTR (NM_009099, exon 8 of 8)	3' UTR (NM_009099, exon 8 of 8)	-51375	NM_175648	244183	Mm.347647	NM_175648	ENSMUSG00000052749	Trim30b	A530023O14Rik|Trim30-1	tripartite motif-containing 30B	protein-coding
mm_56638.1	chr6	113195381	113195387	-	1	NA	promoter-TSS (NM_177763)	promoter-TSS (NM_177763)	0	NM_177763	269788	Mm.37943	NM_177763	ENSMUSG00000042873	Lhfpl4	1190004M23Rik|AI604880|B230384L07|mKIAA4027	lipoma HMGIC fusion partner-like protein 4	protein-coding
mm_94048.1	chr10	128180017	128180024	-	1	NA	5' UTR (NM_001039080, exon 1 of 14)	5' UTR (NM_001039080, exon 1 of 14)	277	NM_001039080	56516	Mm.42247	NM_019711	ENSMUSG00000040043	Rbms2	2610315E04Rik|Scr3	RNA binding motif, single stranded interacting protein 2	protein-coding
mm_69113.1	chr7	127025147	127025157	-	1	NA	intron (NM_010772, intron 2 of 4)	intron (NM_010772, intron 2 of 4)	1327	NM_010772	17188	Mm.378964	NM_010772	ENSMUSG00000030678	Maz	MAZI|PUR1|Pur-1|SAF-1|SAF-2	MYC-associated zinc finger protein (purine-binding transcription factor)	protein-coding
mm_162302.1	chr1	36340875	36340876	-	1	NA	intron (NM_001310513, intron 21 of 21)	intron (NM_001310513, intron 21 of 21)	7883	NR_105863	102465541		NR_105863	ENSMUSG00000098680	Mir6898	Gm27816|mmu-mir-6898	microRNA 6898	ncRNA
mm_108634.1	chr12	85715257	85715258	+	1	NA	Intergenic	MLT1J|LTR|ERVL-MaLR	28537	NM_016767	53314	Mm.6672	NM_016767	ENSMUSG00000034266	Batf	B-ATF|SFA-2	basic leucine zipper transcription factor, ATF-like	protein-coding
mm_63049.1	chr7	121865032	121865043	+	1	NA	promoter-TSS (NM_011325)	promoter-TSS (NM_011325)	-1	NM_001272023	20277	Mm.7709	NM_011325	ENSMUSG00000030873	Scnn1b	-	sodium channel, nonvoltage-gated 1 beta	protein-coding
mm_91907.1	chr10	60220046	60220073	-	1	NA	promoter-TSS (NM_016803)	promoter-TSS (NM_016803)	-799	NM_016803	53374	Mm.12866	NM_016803	ENSMUSG00000057337	Chst3	C6ST|C6ST-1|GST-0	carbohydrate (chondroitin 6/keratan) sulfotransferase 3	protein-coding
mm_126641.1	chr15	83779976	83779988	+	1	NA	promoter-TSS (NM_172610)	promoter-TSS (NM_172610)	-41	NM_172610	223726	Mm.36395	NM_172610	ENSMUSG00000041708	Mpped1	6230403M19|AW456965|D15Bwg0669e	metallophosphoesterase domain containing 1	protein-coding
mm_165897.1	chr4	46403951	46403955	-	1	NA	exon (NM_053149, exon 1 of 4)	exon (NM_053149, exon 1 of 4)	230	NM_053149	93966	Mm.25793	NM_053149	ENSMUSG00000028332	Hemgn	4921524M03Rik|AI317176|EDAG|Hgn|mNDR	hemogen	protein-coding
mm_146991.1	chr18	34139346	34139351	-	1	NA	Intergenic	ORR1A3|LTR|ERVL-MaLR	-81636	NM_007462	11789	Mm.384171	NM_007462	ENSMUSG00000005871	Apc	AI047805|AU020952|AW124434|CC1|Min|mAPC	adenomatosis polyposis coli	protein-coding
mm_64279.1	chr7	141813051	141813058	+	1	NA	exon (NM_010844, exon 37 of 50)	exon (NM_010844, exon 37 of 50)	24043	NM_010844	17833	Mm.334332	NM_010844	ENSMUSG00000037974	Muc5ac	2210005L13Rik|MGM	mucin 5, subtypes A and C, tracheobronchial/gastric	protein-coding
mm_62030.1	chr7	91672638	91672657	+	1	NA	intron (NM_011807, intron 2 of 22)	intron (NM_011807, intron 2 of 22)	-389747	NM_001243046	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_119064.1	chr14	30819173	30819197	+	1	NA	3' UTR (NM_019460, exon 21 of 21)	3' UTR (NM_019460, exon 21 of 21)	-6409	NM_028839	69179	Mm.143025	NM_028839	ENSMUSG00000006526	Tmem110	1810038N08Rik|2310014H19Rik|AW554125|STIMATE	transmembrane protein 110	protein-coding
mm_4822.1	chr1	185454804	185454817	+	1	NA	promoter-TSS (NM_001033286)	promoter-TSS (NM_001033286)	-38	NM_001033286	226781	Mm.227117	NM_001033286	ENSMUSG00000026614	Slc30a10	E130106K10Rik|Gm212	solute carrier family 30, member 10	protein-coding
mm_9192.1	chr1	171173714	171173717	-	1	NA	3' UTR (NM_025557, exon 3 of 3)	3' UTR (NM_025557, exon 3 of 3)	18197	NM_001315500	17528	Mm.9986	NM_008623	ENSMUSG00000056569	Mpz	Mpp|P-zero|P0	myelin protein zero	protein-coding
mm_21934.1	chr2	167056792	167056811	-	1	NA	exon (NM_001033196, exon 3 of 14)	exon (NM_001033196, exon 3 of 14)	-6133	NR_138563	68949	Mm.391959	NM_001081005		Zfas1	1500012F01Rik|Zfos1	zinc finger, NFX1-type containing 1, antisense RNA 1	ncRNA
mm_71493.1	chr8	46755959	46755992	+	1	NA	intron (NM_008391, intron 1 of 8)	intron (NM_008391, intron 1 of 8)	16230	NM_008391	16363	Mm.1149	NM_008391	ENSMUSG00000031627	Irf2	9830146E22Rik|AI646973|Irf-2	interferon regulatory factor 2	protein-coding
mm_114108.1	chr13	54789985	54789989	+	1	NA	intron (NM_028841, intron 1 of 7)	CpG	582	NM_028841	74257	Mm.32883	NM_028841	ENSMUSG00000025875	Tspan17	2210021G21Rik|AI047581|Fbxo23|Tm4sf17	tetraspanin 17	protein-coding
mm_139639.1	chr17	57377235	57377245	+	1	NA	intron (NM_010130, intron 2 of 21)	Lx5b|LINE|L1	18554	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_165593.1	chr3	35937475	35937479	-	1	NA	Intergenic	Intergenic	-4511	NM_001205361	114893	Mm.374810	NM_033623	ENSMUSG00000027708	Dcun1d1	Rp42|SCCRO|Tes3|pTes3	DCN1, defective in cullin neddylation 1, domain containing 1 (S. cerevisiae)	protein-coding
mm_167785.1	chr9	120120708	120120714	+	1	NA	exon (NM_144793, exon 5 of 7)	exon (NM_144793, exon 5 of 7)	-7055	NM_011029	16785	Mm.4071	NM_011029	ENSMUSG00000032518	Rpsa	67kDa|67lr|AL022858|Lamr|Lamr1|Lamrl1|MLR|P40|P40-3|P40-8	ribosomal protein SA	protein-coding
mm_114368.1	chr13	62778597	62778604	+	1	NA	intron (NM_001256065, intron 1 of 3)	intron (NM_001256065, intron 1 of 3)	7208	NM_001256065	380850	Mm.439823	NM_001256065	ENSMUSG00000091183	Gm5141	-	predicted gene 5141	protein-coding
mm_96142.1	chr11	61022124	61022161	+	1	NA	promoter-TSS (NM_001267593)	promoter-TSS (NM_001267593)	-422	NM_001267593	16515	Mm.4970	NM_010603	ENSMUSG00000042529	Kcnj12	IRK-2|IRK2|Kir2.2|MB-IRK2	potassium inwardly-rectifying channel, subfamily J, member 12	protein-coding
mm_124838.1	chr15	9335566	9335623	+	1	NA	promoter-TSS (NM_144845)	promoter-TSS (NM_144845)	-4	NM_144845	223337	Mm.422853	NM_144845	ENSMUSG00000049152	Ugt3a2	AI313915	UDP glycosyltransferases 3 family, polypeptide A2	protein-coding
mm_128977.1	chr15	74833469	74833476	-	1	NA	Intergenic	B3|SINE|B2	8171	NM_001033229	110115	Mm.322606	NM_001033229	ENSMUSG00000075604	Cyp11b1	AA389061|CPN1|Cyp11b|Cyp11b-1|FHI	cytochrome P450, family 11, subfamily b, polypeptide 1	protein-coding
mm_106988.1	chr12	10390869	10390884	+	1	NA	promoter-TSS (NM_023697)	promoter-TSS (NM_023697)	96	NM_023697	105014	Mm.119343	NM_023697	ENSMUSG00000020621	Rdh14	3110030G19Rik|AW215439|PAN2	retinol dehydrogenase 14 (all-trans and 9-cis)	protein-coding
mm_126364.1	chr15	80097867	80097873	+	1	NA	intron (NM_207708, intron 1 of 3)	intron (NM_207708, intron 1 of 3)	6536	NM_207708	20972	Mm.230301	NM_009303	ENSMUSG00000022415	Syngr1	R75468|Syngr1b|p29	synaptogyrin 1	protein-coding
mm_63870.1	chr7	135716783	135716787	+	1	NA	promoter-TSS (NM_001081117)	promoter-TSS (NM_001081117)	-406	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_18957.1	chr2	76791231	76791242	-	1	NA	exon (NM_011652, exon 211 of 313)	exon (NM_011652, exon 211 of 313)	115921	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_110501.1	chr12	54289749	54289751	-	1	NA	Intergenic	IAPLTR1_Mm|LTR|ERVK	56135	NR_108033	73592	Mm.416874	NR_108033		1700104L18Rik	-	RIKEN cDNA 1700104L18 gene	ncRNA
mm_147264.1	chr18	38867082	38867092	-	1	NA	intron (NM_010197, intron 1 of 3)	L2b|LINE|L2	-25369	NM_001033789	545253	Mm.244585	NM_001033789	ENSMUSG00000036452	Gm5820	EG545253	predicted gene 5820	protein-coding
mm_146190.1	chr18	76059508	76059522	+	1	NA	intron (NM_145356, intron 3 of 4)	CpG	38956	NR_045365	73009	Mm.443541	NR_045365		2900057B20Rik	-	RIKEN cDNA 2900057B20 gene	ncRNA
mm_80847.1	chr9	98296591	98296647	+	1	NA	promoter-TSS (NM_144533)	promoter-TSS (NM_144533)	36	NM_144533	74080	Mm.294082	NM_144533	ENSMUSG00000032456	Nmnat3	4933408N02Rik|PNAT3	nicotinamide nucleotide adenylyltransferase 3	protein-coding
mm_31632.1	chr4	59331996	59332009	+	1	NA	intron (NM_001163288, intron 13 of 16)	intron (NM_001163288, intron 13 of 16)	71951	NR_105031	101055769	Mm.421401	NR_105031		Gm12596	OTTMUSG00000007649	predicted gene 12596	ncRNA
mm_49602.1	chr6	30740716	30740756	+	1	NA	promoter-TSS (NR_029900)	promoter-TSS (NR_029900)	-563	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_147542.1	chr18	53744729	53744743	-	1	NA	promoter-TSS (NM_178686)	promoter-TSS (NM_178686)	-189	NM_178686	225523	Mm.193678	NM_178686	ENSMUSG00000048799	Cep120	A230075C01|AU016693|Ccdc100	centrosomal protein 120	protein-coding
mm_81200.1	chr9	107563247	107563285	+	1	NA	promoter-TSS (NM_019742)	promoter-TSS (NM_019742)	11	NM_019742	80385	Mm.21739	NM_019742	ENSMUSG00000010054	Tusc2	1190001E22Rik|AA407686|Fus1|Lgcc|PAP|Pdap2	tumor suppressor candidate 2	protein-coding
mm_12526.1	chr2	72179988	72180049	+	1	NA	exon (NM_001204166, exon 7 of 28)	exon (NM_001204166, exon 7 of 28)	-105619	NM_023057	65964	Mm.304143	NM_023057	ENSMUSG00000004085	Map3k20	AV006891|B230120H23Rik|MLTK|MLTKalpha|MLTKbeta|Zak	mitogen-activated protein kinase kinase kinase 20	protein-coding
mm_68743.1	chr7	121064327	121064340	-	1	NA	3' UTR (NM_030691, exon 6 of 6)	3' UTR (NM_030691, exon 6 of 6)	10197	NM_030691	80719	Mm.160384	NM_030691	ENSMUSG00000035004	Igsf6	-	immunoglobulin superfamily, member 6	protein-coding
mm_102485.1	chr11	60220538	60220548	-	1	NA	promoter-TSS (NM_011480)	promoter-TSS (NM_011480)	84	NM_011480	20787	Mm.278701	NM_011480	ENSMUSG00000020538	Srebf1	ADD1|SREBP-1a|SREBP1|SREBP1c|bHLHd1	sterol regulatory element binding transcription factor 1	protein-coding
mm_78699.1	chr9	41210688	41210709	+	1	NA	intron (NR_040392, intron 1 of 4)	intron (NR_040392, intron 1 of 4)	4543	NR_040392	78500	Mm.275715	NR_040392	ENSMUSG00000100837	1700063D05Rik	-	RIKEN cDNA 1700063D05 gene	ncRNA
mm_67926.1	chr7	99889327	99889368	-	1	NA	intron (NM_001164258, intron 8 of 18)	L1M4c|LINE|L1	30129	NM_001164258	446101	Mm.440757	NM_001164258	ENSMUSG00000035211	Xrra1	AI449753	X-ray radiation resistance associated 1	protein-coding
mm_11371.1	chr2	30995732	30995750	+	1	NA	intron (NM_028846, intron 1 of 24)	intron (NM_028846, intron 1 of 24)	13462	NM_028846	74270	Mm.346654	NM_028846	ENSMUSG00000026854	Usp20	1700055M05Rik|AI467231|Vdu2	ubiquitin specific peptidase 20	protein-coding
mm_66268.1	chr7	36687768	36687771	-	1	NA	Intergenic	BC1_Mm|scRNA|scRNA	-10349	NM_172298	243931	Mm.44141	NM_172298	ENSMUSG00000021217	Tshz3	A630038G13Rik|Tsh3|Zfp537|mKIAA1474|teashirt3	teashirt zinc finger family member 3	protein-coding
mm_172437.1	chr7	29877892	29877897	+	1	NA	TTS (NM_172740)	TTS (NM_172740)	17915	NM_172740	233058	Mm.297657	NM_172740	ENSMUSG00000058402	Zfp420	B230119D13|B230312I18Rik|mszf59-1|mszf70	zinc finger protein 420	protein-coding
mm_47055.1	chr5	116381600	116381604	-	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	41262	NM_030704	80888	Mm.21549	NM_030704	ENSMUSG00000041548	Hspb8	AU018630|AW413033|Cryac|D5Ucla4|E2IG1|H11|H11K|HSP20-like|HSP22	heat shock protein 8	protein-coding
mm_97529.1	chr11	78512229	78512237	+	1	NA	promoter-TSS (NM_026389)	promoter-TSS (NM_026389)	-63	NM_026389	67811	Mm.197493	NM_026389	ENSMUSG00000001100	Poldip2	1300003F06Rik|Pdip38	polymerase (DNA-directed), delta interacting protein 2	protein-coding
mm_56135.1	chr6	87722762	87722780	-	1	NA	Intergenic	Intergenic	-8098	NM_001159697	58229	Mm.333229	NM_021418	ENSMUSG00000068263	Efcc1	Ccdc48	EF hand and coiled-coil domain containing 1	protein-coding
mm_53752.1	chr6	145341015	145341035	+	1	NA	Intergenic	B1F1|SINE|Alu	-46600	NR_003625	381827	Mm.179075	NM_001001987		1700073E17Rik	-	ribosomal protein L7 pseudogene	pseudo
mm_56079.1	chr6	87228819	87228833	-	1	NA	intron (NM_054041, intron 12 of 17)	intron (NM_054041, intron 12 of 17)	106949	NM_054041	69538	Mm.232525	NM_054041	ENSMUSG00000033420	Antxr1	2310008J16Rik|2810405N18Rik|Antrx1|Tem8	anthrax toxin receptor 1	protein-coding
mm_62636.1	chr7	107664679	107664693	+	1	NA	intron (NM_001163557, intron 3 of 25)	intron (NM_001163557, intron 3 of 25)	57842	NM_001163557	19024	Mm.2817	NM_008905	ENSMUSG00000036528	Ppfibp2	Cclp1	PTPRF interacting protein, binding protein 2 (liprin beta 2)	protein-coding
mm_158088.1	chrX	101273946	101273959	-	1	NA	promoter-TSS (NM_021521)	promoter-TSS (NM_021521)	-139	NM_021521	59024	Mm.20873	NM_021521	ENSMUSG00000079487	Med12	230kDa|Mopa|OPA-1|Tnrc11|Trap230	mediator complex subunit 12	protein-coding
mm_38481.1	chr4	140703667	140703675	-	1	NA	intron (NM_173867, intron 2 of 12)	RMER10A|LTR|ERVL	2198	NM_173867	108911	Mm.253	NM_173867	ENSMUSG00000040945	Rcc2	2610510H01Rik|2610529N02Rik|AA536646|AA675016|Td60|mKIAA1470	regulator of chromosome condensation 2	protein-coding
mm_54520.1	chr6	35539748	35539760	-	1	NA	5' UTR (NM_008098, exon 1 of 4)	5' UTR (NM_008098, exon 1 of 4)	134	NM_008098	14489	Mm.182746	NM_008098	ENSMUSG00000029840	Mtpn	5033418D15Rik|Gcdp|V1	myotrophin	protein-coding
mm_75634.1	chr8	64733535	64733554	-	1	NA	promoter-TSS (NM_025436)	promoter-TSS (NM_025436)	34	NM_025436	66234	Mm.30119	NM_025436	ENSMUSG00000031604	Msmo1	1500001G16Rik|C78600|DESP4|ERG25|Sc4mol	methylsterol monoxygenase 1	protein-coding
mm_60093.1	chr7	35040505	35040516	+	1	NA	intron (NM_008820, intron 12 of 14)	intron (NM_008820, intron 12 of 14)	16056	NM_009884	12611	Mm.273090	NM_009884	ENSMUSG00000056216	Cebpg	C/EBP[g]|C/EBPgamma|GPE1-BP|Gpe1bp|Ig/EBP	CCAAT/enhancer binding protein (C/EBP), gamma	protein-coding
mm_14968.1	chr2	152093457	152093475	+	1	NA	exon (NM_001160410, exon 2 of 2)	exon (NM_001160410, exon 2 of 2)	11937	NM_001160410	545474	Mm.214317	NM_001160410	ENSMUSG00000060257	Scrt2	AW060659	scratch family zinc finger 2	protein-coding
mm_84052.1	chr9	58158466	58158478	-	1	NA	promoter-TSS (NM_001195431)	promoter-TSS (NM_001195431)	82	NM_001195431	26968	Mm.367887	NM_012043	ENSMUSG00000037206	Islr	AW553146|Meflin	immunoglobulin superfamily containing leucine-rich repeat	protein-coding
mm_108341.1	chr12	80211142	80211148	+	1	NA	intron (NM_001346669, intron 1 of 20)	intron (NM_001346669, intron 1 of 20)	49226	NM_134156	109711	Mm.253564	NM_134156	ENSMUSG00000015143	Actn1	3110023F10Rik|Actn1a	actinin, alpha 1	protein-coding
mm_156374.1	chrX	139671773	139671787	+	1	NA	exon (NM_023270, exon 7 of 7)	exon (NM_023270, exon 7 of 7)	-13216	NM_001081499	245638	Mm.275869	NM_001081499	ENSMUSG00000042473	Tbc1d8b	4921505D17Rik|9030605E16Rik	TBC1 domain family, member 8B	protein-coding
mm_65802.1	chr7	28958179	28958182	-	1	NA	intron (NM_021895, intron 1 of 20)	intron (NM_021895, intron 1 of 20)	4100	NM_021895	60595	Mm.81144	NM_021895	ENSMUSG00000054808	Actn4	C77391	actinin alpha 4	protein-coding
mm_110232.1	chr12	29531108	29531143	-	1	NA	intron (NM_001093778, intron 1 of 24)	intron (NM_001093778, intron 1 of 24)	2741	NM_008666	17933	Mm.253067	NM_008666	ENSMUSG00000061911	Myt1l	2900046C06Rik|2900093J19Rik|C630034G21Rik|Nztf1|Pmng1|Png-1|mKIAA1106	myelin transcription factor 1-like	protein-coding
mm_4818.1	chr1	185431932	185431946	+	1	NA	non-coding (NR_038006, exon 2 of 2)	non-coding (NR_038006, exon 2 of 2)	9880	NR_038006	319562	Mm.184335	NM_176943	ENSMUSG00000051295	9630028B13Rik	-	RIKEN cDNA 9630028B13 gene	ncRNA
mm_144968.1	chr18	37825004	37825056	+	1	NA	exon (NM_033593, exon 2 of 4)	exon (NM_033593, exon 2 of 4)	5484	NM_033583	93708	Mm.247203	NM_033583	ENSMUSG00000102543	Pcdhgc5	-	protocadherin gamma subfamily C, 5	protein-coding
mm_125808.1	chr15	74931015	74931031	+	1	NA	Intergenic	MurERV4-int|LTR|ERVK	-24028	NM_001164039	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_131532.1	chr16	17704585	17704600	+	1	NA	intron (NM_001285886, intron 2 of 16)	intron (NM_001285886, intron 2 of 16)	18308	NM_001285886	94112	Mm.208970	NM_033609	ENSMUSG00000012114	Med15	A230074L19Rik|AW536074|Pcqap|mPcqap	mediator complex subunit 15	protein-coding
mm_46561.1	chr5	106925840	106925864	-	1	NA	promoter-TSS (NM_177873)	promoter-TSS (NM_177873)	38	NM_177873	330149	Mm.121664	NM_177873	ENSMUSG00000043410	Hfm1	A330009G12Rik|Gm1046|Mer3|Sec63d1	HFM1, ATP-dependent DNA helicase homolog	protein-coding
mm_131121.1	chr16	5431389	5431417	+	1	NA	Intergenic	Intergenic	-175447	NM_027446	70511	Mm.45780	NM_027446	ENSMUSG00000022544	Eef2kmt	5730409G15Rik|Fam86|Fam86a|eEF2-KMT	eukaryotic elongation factor 2 lysine methyltransferase	protein-coding
mm_109752.1	chr12	117688747	117688764	+	1	NA	intron (NM_175930, intron 12 of 27)	C-rich|Low_complexity|Low_complexity	-155106	NM_146040	217946	Mm.281149	NM_146040	ENSMUSG00000021175	Cdca7l	BC006933|JPO2	cell division cycle associated 7 like	protein-coding
mm_155907.1	chrX	101706009	101706011	+	1	NA	Intergenic	B1_Mus1|SINE|Alu	28137	NM_009910	12766	Mm.12876	NM_009910	ENSMUSG00000050232	Cxcr3	Cd183|Cmkar3	chemokine (C-X-C motif) receptor 3	protein-coding
mm_112948.1	chr13	21008581	21008594	+	1	NA	intron (NM_012054, intron 19 of 20)	B4A|SINE|B4	64712	NM_146535	258528	Mm.377554	NM_146535	ENSMUSG00000042869	Olfr1370	MOR256-14	olfactory receptor 1370	protein-coding
mm_9079.1	chr1	168431600	168431638	-	1	NA	5' UTR (NM_001291509, exon 1 of 7)	5' UTR (NM_001291509, exon 1 of 7)	550	NM_001291508	18514	Mm.43358	NM_008783	ENSMUSG00000052534	Pbx1	2310056B04Rik|D230003C07Rik|Pbx-1	pre B cell leukemia homeobox 1	protein-coding
mm_83437.1	chr9	44999259	44999282	-	1	NA	3' UTR (NM_007648, exon 8 of 8)	3' UTR (NM_007648, exon 8 of 8)	10320	NM_007648	12501	Mm.210361	NM_007648	ENSMUSG00000032093	Cd3e	AI504783|CD3|CD3epsilon|T3e	CD3 antigen, epsilon polypeptide	protein-coding
mm_161249.1	chr13	100786510	100786510	-	1	NA	promoter-TSS (NM_172301)	promoter-TSS (NM_172301)	-24	NM_172301	268697	Mm.260114	NM_172301	ENSMUSG00000041431	Ccnb1	Ccnb1-rs1|Ccnb1-rs13|CycB1|Cycb-4|Cycb-5|Cycb1-rs1	cyclin B1	protein-coding
mm_15499.1	chr2	157901449	157901477	+	1	NA	Intergenic	Intergenic	-13190	NM_198627	277432	Mm.441156	NM_198627	ENSMUSG00000037843	Vstm2l	Gm691	V-set and transmembrane domain containing 2-like	protein-coding
mm_4131.1	chr1	170309334	170309343	+	1	NA	intron (NM_001039593, intron 1 of 1)	RMER4B|LTR|ERVK	477	NM_001039593	76925	Mm.33631	NM_001039593	ENSMUSG00000042800	1700015E13Rik	-	RIKEN cDNA 1700015E13 gene	protein-coding
mm_140949.1	chr17	24527926	24527935	-	1	NA	promoter-TSS (NR_045289)	promoter-TSS (NR_045289)	8	NM_153792	224619	Mm.275150	NM_153792	ENSMUSG00000052752	Traf7	RFWD1	TNF receptor-associated factor 7	protein-coding
mm_42754.1	chr5	120813715	120813728	+	1	NA	intron (NM_001083925, intron 1 of 5)	intron (NM_001083925, intron 1 of 5)	1083	NM_001083925	23961	Mm.233471	NM_001083925	ENSMUSG00000029605	Oas1b	Flv|L1|Mmu-L1|Oas1|Oias-2|Oias2|Wnv	2'-5' oligoadenylate synthetase 1B	protein-coding
mm_140597.1	chr17	10294529	10294531	-	1	NA	intron (NM_021881, intron 1 of 6)	intron (NM_021881, intron 1 of 6)	24831	NM_021881	19317	Mm.130694	NM_021881	ENSMUSG00000062078	Qk	1110003F05Rik|1500005P18|QkI|l(17)-1Wis|l17Wis1	quaking	protein-coding
mm_87503.1	chr10	52276799	52276842	+	1	NA	intron (NM_025705, intron 2 of 10)	intron (NM_025705, intron 2 of 10)	43201	NM_025705	66686	Mm.62982	NM_025705	ENSMUSG00000019891	Dcbld1	4631413K11Rik	discoidin, CUB and LCCL domain containing 1	protein-coding
mm_57224.1	chr6	123265896	123265906	-	1	NA	intron (NM_001163161, intron 2 of 5)	intron (NM_001163161, intron 2 of 5)	3794	NM_010819	17474	Mm.441101	NM_010819	ENSMUSG00000030144	Clec4d	Clecsf8|Mpcl|mcl	C-type lectin domain family 4, member d	protein-coding
mm_13422.1	chr2	104559179	104559188	+	1	NA	promoter-TSS (NR_040323)	promoter-TSS (NR_040323)	-1	NR_040322	74959	Mm.417819	NR_040322	ENSMUSG00000086454	Platr14	4930500J02Rik	pluripotency associated transcript 14	ncRNA
mm_160950.1	chr11	97149766	97149766	-	1	NA	promoter-TSS (NM_198100)	promoter-TSS (NM_198100)	-54	NM_198100	73174	Mm.27882	NM_198100	ENSMUSG00000038517	Tbkbp1	3110043L15Rik|ProSAPiP2|SINTBAD	TBK1 binding protein 1	protein-coding
mm_156826.1	chrX	164162213	164162224	+	1	NA	intron (NM_001130513, intron 6 of 18)	intron (NM_001130513, intron 6 of 18)	21738	NM_027286	70008	Mm.13451	NM_027286	ENSMUSG00000015405	Ace2	2010305L05Rik	angiotensin I converting enzyme (peptidyl-dipeptidase A) 2	protein-coding
mm_104167.1	chr11	87404381	87404424	-	1	NA	promoter-TSS (NM_053269)	promoter-TSS (NM_053269)	93	NM_053269	114714	Mm.37376	NM_053269	ENSMUSG00000007646	Rad51c	R51H3|Rad51l2	RAD51 paralog C	protein-coding
mm_75489.1	chr8	48843881	48843894	-	1	NA	Intergenic	Intergenic	-169197	NM_011857	23965	Mm.42191	NM_011857	ENSMUSG00000031561	Tenm3	2610100B16Rik|Odz1|Odz3|Ten-m3|mKIAA1455	teneurin transmembrane protein 3	protein-coding
mm_155689.1	chrX	94023813	94023822	+	1	NA	Intergenic	Intergenic	55161	NR_028320	385493	Mm.328014	NM_001033480	ENSMUSG00000081044	AU015836	-	expressed sequence AU015836	ncRNA
mm_166144.1	chr5	3501700	3501710	-	1	NA	intron (NM_009873, intron 5 of 7)	intron (NM_009873, intron 5 of 7)	-42128	NM_001042501	68152	Mm.240265	NM_026583	ENSMUSG00000058503	Fam133b	2900022K02Rik|5830415L20Rik	family with sequence similarity 133, member B	protein-coding
mm_95017.1	chr11	32000453	32000470	+	1	NA	promoter-TSS (NM_008741)	promoter-TSS (NM_008741)	42	NM_008741	18197	Mm.3304	NM_008741	ENSMUSG00000020297	Nsg2	-	neuron specific gene family member 2	protein-coding
mm_19263.1	chr2	84822527	84822542	-	1	NA	5' UTR (NM_024230, exon 1 of 8)	5' UTR (NM_024230, exon 1 of 8)	118	NM_024230	68678	Mm.33452	NM_024230	ENSMUSG00000027077	Smtnl1	1110030K22Rik|CHASM	smoothelin-like 1	protein-coding
mm_38710.1	chr4	145215833	145215845	-	1	NA	exon (NM_011610, exon 10 of 10)	exon (NM_011610, exon 10 of 10)	-20834	NM_001276465	230895	Mm.240310	NM_001033190	ENSMUSG00000020220	Vps13d	-	vacuolar protein sorting 13D	protein-coding
mm_140843.1	chr17	23675060	23675104	-	1	NA	TTS (NM_013749)	TTS (NM_013749)	-1312	NM_001008425	386612	Mm.328831	NM_001008425	ENSMUSG00000041319	Thoc6	F830014G06Rik|Wdr58	THO complex 6	protein-coding
mm_142749.1	chr17	48450781	48450796	-	1	NA	intron (NM_027292, intron 2 of 4)	intron (NM_027292, intron 2 of 4)	713	NM_027292	70026	Mm.22613	NM_027292	ENSMUSG00000023995	Tspo2	2510027D20Rik|Bzrpl1	translocator protein 2	protein-coding
mm_164862.1	chr18	53862393	53862403	+	1	NA	5' UTR (NM_152809, exon 1 of 13)	5' UTR (NM_152809, exon 1 of 13)	285	NM_152809	70425	Mm.368668	NM_152809	ENSMUSG00000073563	Csnk1g3	3300002K07Rik|C330049O21Rik	casein kinase 1, gamma 3	protein-coding
mm_10489.1	chr2	14824063	14824072	+	1	NA	promoter-TSS (NM_001252533)	promoter-TSS (NM_001252533)	-25	NM_001252533	12296	Mm.313930	NM_023116	ENSMUSG00000057914	Cacnb2	AW060387|CAB2|Cavbeta2|Cchb2	calcium channel, voltage-dependent, beta 2 subunit	protein-coding
mm_130539.1	chr15	98951258	98951278	-	1	NA	exon (NM_011653, exon 3 of 4)	exon (NM_011653, exon 3 of 4)	2233	NM_011653	22142	Mm.405359	NM_011653	ENSMUSG00000072235	Tuba1a	Tuba-1|Tuba1	tubulin, alpha 1A	protein-coding
mm_91482.1	chr10	34713525	34713526	-	1	NA	Intergenic	Intergenic	230125	NM_010237	14302	Mm.332432	NM_010237	ENSMUSG00000019779	Frk	BSK|BSK/IYK|C85044|GTK|RAK	fyn-related kinase	protein-coding
mm_34101.1	chr4	138973242	138973255	+	1	NA	5' UTR (NM_029857, exon 1 of 17)	5' UTR (NM_029857, exon 1 of 17)	343	NM_029857	77056	Mm.122336	NM_029857	ENSMUSG00000041143	Tmco4	4632413C14Rik|AI430825	transmembrane and coiled-coil domains 4	protein-coding
mm_92675.1	chr10	80548714	80548725	-	1	NA	intron (NM_025852, intron 2 of 14)	intron (NM_025852, intron 2 of 14)	-9595	NM_026094	67331	Mm.52511	NM_026094	ENSMUSG00000003341	Atp8b3	1700042F02Rik|1700056N23Rik|ATPIK|SAPLT	ATPase, class I, type 8B, member 3	protein-coding
mm_74805.1	chr8	22593818	22593828	-	1	NA	promoter-TSS (NM_001198998)	promoter-TSS (NM_001198998)	-10	NM_011696	22335	Mm.227704	NM_011696	ENSMUSG00000008892	Vdac3	-	voltage-dependent anion channel 3	protein-coding
mm_131035.1	chr16	3847207	3847307	+	1	NA	promoter-TSS (NM_001081217)	promoter-TSS (NM_001081217)	34	NM_001081217	385674	Mm.244261	NM_001081217	ENSMUSG00000054939	Zfp174	Gm1754	zinc finger protein 174	protein-coding
mm_62857.1	chr7	114536791	114536810	+	1	NA	3' UTR (NM_011055, exon 16 of 16)	3' UTR (NM_011055, exon 16 of 16)	26172	NR_110407	244209	Mm.108037	NM_177382	ENSMUSG00000030670	Cyp2r1	-	cytochrome P450, family 2, subfamily r, polypeptide 1	protein-coding
mm_89564.1	chr10	95415592	95415627	+	1	NA	promoter-TSS (NM_001168657)	promoter-TSS (NM_001168657)	-125	NM_001168656	216233	Mm.474283	NM_007706	ENSMUSG00000020027	Socs2	8030460M17|AI527257|AW108012|CIS2|Cish2|D130043N08Rik|JAB|SOCS-2|SSI-2|hg	suppressor of cytokine signaling 2	protein-coding
mm_103067.1	chr11	69858688	69858713	-	1	NA	promoter-TSS (NM_031880)	promoter-TSS (NM_031880)	30	NM_031880	83813	Mm.28874	NM_031880	ENSMUSG00000001583	Tnk1	Kos1|Tnk1a|Tnk1b	tyrosine kinase, non-receptor, 1	protein-coding
mm_108892.1	chr12	100044609	100044615	+	1	NA	intron (NM_146037, intron 2 of 2)	intron (NM_146037, intron 2 of 2)	-67719	NM_008947	19179	Mm.157105	NM_008947	ENSMUSG00000021178	Psmc1	AI325227|P26s4|Rpt2/S4|S4|rpt2	protease (prosome, macropain) 26S subunit, ATPase 1	protein-coding
mm_68782.1	chr7	123286684	123286727	-	1	NA	exon (NM_001122643, exon 18 of 20)	exon (NM_001122643, exon 18 of 20)	71839	NM_146198	233836	Mm.211838	NM_146198	ENSMUSG00000030769	Slc5a11	2010013B02Rik|Kst1|RKST2|SMIT2|Slc5a10	solute carrier family 5 (sodium/glucose cotransporter), member 11	protein-coding
mm_56554.1	chr6	100671127	100671178	-	1	NA	promoter-TSS (NM_181590)	promoter-TSS (NM_181590)	5	NM_181590	72171	Mm.256022	NM_181590	ENSMUSG00000035378	Shq1	2810403P18Rik|Grim-1	SHQ1 homolog (S. cerevisiae)	protein-coding
mm_119204.1	chr14	32856783	32856808	+	1	NA	promoter-TSS (NM_178791)	promoter-TSS (NM_178791)	39	NM_178791	320736	Mm.187910	NM_178791	ENSMUSG00000050666	Vstm4	E130203B14Rik	V-set and transmembrane domain containing 4	protein-coding
mm_11751.1	chr2	38472153	38472169	+	1	NA	Intergenic	Intergenic	-39536	NM_021606	59126	Mm.143818	NM_021606	ENSMUSG00000026749	Nek6	1300007C09Rik	NIMA (never in mitosis gene a)-related expressed kinase 6	protein-coding
mm_57773.1	chr6	129237784	129237830	-	1	NA	non-coding (NR_040268, exon 2 of 4)	non-coding (NR_040268, exon 2 of 4)	238	NR_040265	76432	Mm.261738	NR_040265	ENSMUSG00000097354	2310001H17Rik	AI646108	RIKEN cDNA 2310001H17 gene	ncRNA
mm_107028.1	chr12	13102656	13102674	+	1	NA	Intergenic	Intergenic	146509	NM_134040	104721	Mm.251255	NM_134040	ENSMUSG00000037149	Ddx1	AA409185|DBP-RB	DEAD (Asp-Glu-Ala-Asp) box polypeptide 1	protein-coding
mm_21818.1	chr2	165283769	165283789	-	1	NA	intron (NM_144893, intron 1 of 9)	L2|LINE|L2	4008	NM_001252574	228875	Mm.21184	NM_144893	ENSMUSG00000017664	Slc35c2	C85957|CGI-15|D2Wsu58e|Ovcov1	solute carrier family 35, member C2	protein-coding
mm_137412.1	chr17	26113789	26113807	+	1	NA	intron (NM_021793, intron 1 of 12)	CpG	482	NM_021793	60455	Mm.304656	NM_021793	ENSMUSG00000024180	Tmem8	AW490096|M83|Tmem8a	transmembrane protein 8 (five membrane-spanning domains)	protein-coding
mm_89684.1	chr10	97518008	97518041	+	1	NA	3' UTR (NM_007833, exon 8 of 8)	3' UTR (NM_007833, exon 8 of 8)	35693	NM_007833	13179	Mm.56769	NM_007833	ENSMUSG00000019929	Dcn	DC|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding
mm_125332.1	chr15	38673893	38673931	+	1	NA	exon (NM_025494, exon 3 of 13)	exon (NM_025494, exon 3 of 13)	12008	NM_025494	66335	Mm.276618	NM_025494	ENSMUSG00000022295	Atp6v1c1	1700025B18Rik|U13839	ATPase, H+ transporting, lysosomal V1 subunit C1	protein-coding
mm_128105.1	chr15	27984780	27984783	-	1	NA	intron (NM_001081302, intron 1 of 56)	intron (NM_001081302, intron 1 of 56)	41067	NM_001081302	223435	Mm.485422	NM_001081302	ENSMUSG00000022263	Trio	6720464I07Rik|AA408740|Solo	triple functional domain (PTPRF interacting)	protein-coding
mm_99437.1	chr11	102432851	102432864	+	1	NA	intron (NM_008175, intron 1 of 12)	intron (NM_008175, intron 1 of 12)	2535	NM_008175	14824	Mm.1568	NM_008175	ENSMUSG00000034708	Grn	Pgrn|epithelin	granulin	protein-coding
mm_7250.1	chr1	93731900	93731929	-	1	NA	promoter-TSS (NM_001310761)	promoter-TSS (NM_001310761)	12	NM_001310761	67026	Mm.272356	NM_025920	ENSMUSG00000026279	Thap4	2010320B01Rik	THAP domain containing 4	protein-coding
mm_46161.1	chr5	96162483	96162576	-	1	NA	promoter-TSS (NM_178854)	promoter-TSS (NM_178854)	-539	NM_144910	231464	Mm.28374	NM_144910	ENSMUSG00000034724	Cnot6l	4932442K20Rik	CCR4-NOT transcription complex, subunit 6-like	protein-coding
mm_45772.1	chr5	87091985	87091987	-	1	NA	exon (NM_001029867, exon 1 of 6)	exon (NM_001029867, exon 1 of 6)	569	NM_001029867	231396	Mm.439851	NM_001029867	ENSMUSG00000070704	Ugt2b36	-	UDP glucuronosyltransferase 2 family, polypeptide B36	protein-coding
mm_63610.1	chr7	128203422	128203431	+	1	NA	promoter-TSS (NR_045183)	promoter-TSS (NR_045183)	-98	NR_045183	70973	Mm.441564	NR_045183	ENSMUSG00000108354	4931431B13Rik	1700108I23Rik|AA536668	RIKEN cDNA 4931431B13 gene	ncRNA
mm_130965.1	chr15	103316536	103316540	-	1	NA	intron (NM_013866, intron 4 of 7)	intron (NM_013866, intron 4 of 7)	-6100	NM_030720	80910	Mm.160369	NM_030720	ENSMUSG00000063234	Gpr84	EX33	G protein-coupled receptor 84	protein-coding
mm_169210.1	chr13	66519650	66519653	+	1	NA	Intergenic	Intergenic	-78533	NM_001290196	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
mm_17354.1	chr2	26608620	26608634	-	1	NA	Intergenic	MTE2b|LTR|ERVL-MaLR	-4210	NM_026212	67512	Mm.24244	NM_026212	ENSMUSG00000026922	Agpat2	2510002J07Rik|AV000834|BSCL|BSCL1|LPAAB|LPAAT-beta	1-acylglycerol-3-phosphate O-acyltransferase 2 (lysophosphatidic acid acyltransferase, beta)	protein-coding
mm_40580.1	chr5	64102888	64102903	+	1	NA	exon (NM_025700, exon 4 of 14)	exon (NM_025700, exon 4 of 14)	9945	NM_025700	66681	Mm.2325	NM_025700	ENSMUSG00000029171	Pgm1	3230402E02Rik|Pgm-1|Pgm2	phosphoglucomutase 1	protein-coding
mm_44774.1	chr5	32031049	32031059	-	1	NA	intron (NM_144541, intron 10 of 11)	intron (NM_144541, intron 10 of 11)	-105418	NM_008037	14284	Mm.24684	NM_008037	ENSMUSG00000029135	Fosl2	Fra-2	fos-like antigen 2	protein-coding
mm_74118.1	chr8	123102360	123102420	+	1	NA	promoter-TSS (NM_016738)	promoter-TSS (NM_016738)	40	NM_016738	270106	Mm.319719	NM_016738	ENSMUSG00000000740	Rpl13	A52|L13	ribosomal protein L13	protein-coding
mm_131315.1	chr16	11656118	11656137	+	1	NA	intron (NM_001290148, intron 9 of 13)	intron (NM_001290148, intron 9 of 13)	-123575	NR_126430	73761	Mm.39183	NR_126430		4833415N18Rik	-	RIKEN cDNA 4833415N18 gene	ncRNA
mm_131872.1	chr16	23175426	23175434	+	1	NA	Intergenic	Intergenic	28894	NM_009605	11450	Mm.3969	NM_009605	ENSMUSG00000022878	Adipoq	30kDa|APN|Acdc|Acrp30|Ad|GBP28|adipo|apM1	adiponectin, C1Q and collagen domain containing	protein-coding
mm_154452.1	chrM	2168	2182	-	1	NA	NA	LSU-rRNA_Hsa|rRNA|rRNA	NA	NA								
mm_20042.1	chr2	120137468	120137493	-	1	NA	intron (NM_133838, intron 1 of 5)	intron (NM_133838, intron 1 of 5)	17095	NM_133838	98878	Mm.132226	NM_133838	ENSMUSG00000027293	Ehd4	2210022F10Rik|AI197390|AI846352|AV006278|Past2	EH-domain containing 4	protein-coding
mm_162543.1	chr1	170111071	170111086	-	1	NA	Intergenic	Intergenic	-22134	NM_022563	18214	Mm.229249	NM_022563	ENSMUSG00000026674	Ddr2	AW495251|Ntrkr3|tyro10	discoidin domain receptor family, member 2	protein-coding
mm_123755.1	chr14	70196046	70196099	-	1	NA	intron (NM_001271408, intron 5 of 20)	intron (NM_001271408, intron 5 of 20)	-3826	NM_001271409	20410	Mm.5068	NM_011366	ENSMUSG00000022091	Sorbs3	SCAM-1|SH3P3|Sh3d4|vinexin-g	sorbin and SH3 domain containing 3	protein-coding
mm_162851.1	chr10	88459592	88459615	+	1	NA	promoter-TSS (NM_011517)	promoter-TSS (NM_011517)	16	NM_011517	20962	Mm.297977	NM_011517	ENSMUSG00000020059	Sycp3	Cor1|Scp3	synaptonemal complex protein 3	protein-coding
mm_12493.1	chr2	71787058	71787083	+	1	NA	5' UTR (NM_008397, exon 1 of 26)	5' UTR (NM_008397, exon 1 of 26)	131	NM_001277970	16403	Mm.225096	NM_008397	ENSMUSG00000027111	Itga6	5033401O05Rik|AI115430|Cd49f|VLA-6	integrin alpha 6	protein-coding
mm_154846.1	chrX	20425360	20425378	+	1	NA	promoter-TSS (NM_001289684)	promoter-TSS (NM_001289684)	-319	NM_199317	382207	Mm.281517	NM_199317	ENSMUSG00000037315	Jade3	5730598B06|AI851988|AW544806|Phf16|mKIAA0215	jade family PHD finger 3	protein-coding
mm_4049.1	chr1	165788685	165788728	+	1	NA	promoter-TSS (NM_031162)	promoter-TSS (NM_031162)	25	NM_001113392	12503	Mm.217308	NM_031162	ENSMUSG00000005763	Cd247	4930549J05Rik|A430104F18Rik|AW552088|Cd3|Cd3-eta|Cd3-zeta|Cd3h|Cd3z|Cd3zeta|T3z|Tcrk|Tcrz	CD247 antigen	protein-coding
mm_124478.1	chr14	121460510	121460522	-	1	NA	3' UTR (NM_053079, exon 23 of 23)	3' UTR (NM_053079, exon 23 of 23)	44738	NM_053079	56643	Mm.155618	NM_053079	ENSMUSG00000025557	Slc15a1	D630032F02|PECT1|PEPT1	solute carrier family 15 (oligopeptide transporter), member 1	protein-coding
mm_101207.1	chr11	19925498	19925512	-	1	NA	intron (NM_033523, intron 1 of 5)	CpG	1063	NM_033523	114716	Mm.266627	NM_033523	ENSMUSG00000045671	Spred2	C79158	sprouty-related, EVH1 domain containing 2	protein-coding
mm_14139.1	chr2	126232045	126232049	+	1	NA	Intergenic	Lx5|LINE|L1	79906	NM_026981	69185	Mm.29019	NM_026981	ENSMUSG00000023330	Dtwd1	1810033A06Rik	DTW domain containing 1	protein-coding
mm_120981.1	chr14	78732920	78732932	+	1	NA	Intergenic	CpG	-7837	NM_001081336	380921	Mm.89591	NM_001081336	ENSMUSG00000034731	Dgkh	5930402B05Rik|D130015C16|DGK	diacylglycerol kinase, eta	protein-coding
mm_86361.1	chr9	123769506	123769514	-	1	NA	intron (NM_009913, intron 1 of 2)	intron (NM_009913, intron 1 of 2)	2299	NM_001166625	12769	Mm.440604	NM_009913	ENSMUSG00000029530	Ccr9	A130091K22Rik|Cmkbr10|GPR-9-6	chemokine (C-C motif) receptor 9	protein-coding
mm_43721.1	chr5	139479404	139479423	+	1	NA	intron (NM_133349, intron 3 of 6)	intron (NM_133349, intron 3 of 6)	5078	NM_133349	100494	Mm.24521	NM_133349	ENSMUSG00000053581	Zfand2a	AA407930|AU016206|Airap	zinc finger, AN1-type domain 2A	protein-coding
mm_65278.1	chr7	24333976	24333982	-	1	NA	promoter-TSS (NM_001163810)	promoter-TSS (NM_001163810)	-14	NM_001163810	69301	Mm.144202	NM_027028	ENSMUSG00000055826	Tescl	1700008P20Rik	tescalcin-like	protein-coding
mm_15967.1	chr2	166068750	166068753	+	1	NA	intron (NM_008679, intron 20 of 22)	intron (NM_008679, intron 20 of 22)	76114	NM_008679	17979	Mm.469663	NM_008679	ENSMUSG00000027678	Ncoa3	2010305B15Rik|AW321064|Actr|Aib1|KAT13B|Rac3|Src3|Tram-1|Tram1|bHLHe42|p/Cip|pCip	nuclear receptor coactivator 3	protein-coding
mm_13531.1	chr2	110597322	110597353	+	1	NA	promoter-TSS (NM_001003915)	promoter-TSS (NM_001003915)	38	NM_001177624	241612	Mm.277148	NM_001003915	ENSMUSG00000041644	Slc5a12	AI315119|D630015G19|SMCT2	solute carrier family 5 (sodium/glucose cotransporter), member 12	protein-coding
mm_5926.1	chr1	55226743	55226764	-	1	NA	promoter-TSS (NM_028713)	promoter-TSS (NM_028713)	29	NM_028713	74013	Mm.292050	NM_028713	ENSMUSG00000025978	Rftn2	2700010E02Rik|3222401M22Rik	raftlin family member 2	protein-coding
mm_30019.1	chr3	135665344	135665354	-	1	NA	intron (NM_008689, intron 3 of 24)	intron (NM_008689, intron 3 of 24)	26198	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_87110.1	chr10	33197770	33197783	+	1	NA	intron (NM_029726, intron 8 of 37)	intron (NM_029726, intron 8 of 37)	58581	NR_040657	442820	Mm.490725	NR_040657		D830005E20Rik	-	RIKEN cDNA D830005E20 gene	ncRNA
mm_7510.1	chr1	123718588	123718589	-	1	NA	intron (NM_199021, intron 3 of 25)	intron (NM_199021, intron 3 of 25)	326971	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_6808.1	chr1	84157232	84157237	-	1	NA	intron (NM_001003948, intron 2 of 2)	AT_rich|Low_complexity|Low_complexity	61727	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_91922.1	chr10	60300178	60300257	-	1	NA	exon (NM_011179, exon 12 of 15)	exon (NM_011179, exon 12 of 15)	15756	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_133500.1	chr16	90497205	90497213	+	1	NA	3' UTR (NM_015755, exon 11 of 11)	3' UTR (NM_015755, exon 11 of 11)	110812	NM_015755	26559	Mm.125874	NM_015755	ENSMUSG00000053414	Hunk	Bstk1|Mak-v	hormonally upregulated Neu-associated kinase	protein-coding
mm_143941.1	chr17	86353853	86353867	-	1	NA	intron (NM_011104, intron 2 of 14)	intron (NM_011104, intron 2 of 14)	-66682	NR_045435	72104	Mm.443401	NR_045435	ENSMUSG00000100738	2010106C02Rik	-	RIKEN cDNA 2010106C02 gene	ncRNA
mm_55129.1	chr6	50596625	50596639	-	1	NA	promoter-TSS (NM_027564)	promoter-TSS (NM_027564)	-42	NM_027564	70821	Mm.157323	NM_027564	ENSMUSG00000029828	4921507P07Rik	TISP74	RIKEN cDNA 4921507P07 gene	protein-coding
mm_79944.1	chr9	65924208	65924216	+	1	NA	intron (NM_173185, intron 1 of 13)	intron (NM_173185, intron 1 of 13)	15202	NM_173185	214897	Mm.325816	NM_173185	ENSMUSG00000032384	Csnk1g1	9130020E21Rik	casein kinase 1, gamma 1	protein-coding
mm_163287.1	chr11	118100373	118100373	-	1	NA	intron (NM_001167746, intron 23 of 80)	intron (NM_001167746, intron 23 of 80)	28846	NM_001167746	69926	Mm.473893	NM_001167746	ENSMUSG00000033987	Dnah17	2810003K23Rik|Dnahc17|Dnahcl1|Gm1178|mKIAA3028	dynein, axonemal, heavy chain 17	protein-coding
mm_10818.1	chr2	24350450	24350460	+	1	NA	3' UTR (NM_031167, exon 5 of 5)	3' UTR (NM_031167, exon 5 of 5)	5084	NM_001039701	16181	Mm.882	NM_031167	ENSMUSG00000026981	Il1rn	F630041P17Rik|IL-1ra	interleukin 1 receptor antagonist	protein-coding
mm_99573.1	chr11	104132811	104132828	+	1	NA	promoter-TSS (NM_007762)	promoter-TSS (NM_007762)	38	NM_001313929	12921	Mm.1892	NM_007762	ENSMUSG00000018634	Crhr1	CRF1R|CRFR1|Crhr	corticotropin releasing hormone receptor 1	protein-coding
mm_144052.1	chr17	90599336	90599339	-	1	NA	intron (NM_001346957, intron 9 of 18)	intron (NM_001346957, intron 9 of 18)	-143457	NM_001346959	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_89726.1	chr10	98920578	98920583	+	1	NA	intron (NM_026482, intron 1 of 20)	T-rich|Low_complexity|Low_complexity	5428	NM_026482	67972	Mm.166944	NM_026482	ENSMUSG00000019943	Atp2b1	2810442I22Rik|E130111D10Rik|Pmca1	ATPase, Ca++ transporting, plasma membrane 1	protein-coding
mm_7407.1	chr1	119421110	119421144	-	1	NA	5' UTR (NM_008381, exon 1 of 2)	5' UTR (NM_008381, exon 1 of 2)	1121	NM_008381	16324	Mm.3092	NM_008381	ENSMUSG00000037035	Inhbb	-	inhibin beta-B	protein-coding
mm_43130.1	chr5	125305868	125305878	+	1	NA	intron (NM_001205083, intron 1 of 10)	intron (NM_001205083, intron 1 of 10)	35221	NM_016741	20778	Mm.282242	NM_016741	ENSMUSG00000037936	Scarb1	AI120173|CD36|Cd36l1|Chohd1|Cla-1|Cla1|D5Ertd460e|Hdlq1|Hlb398|SR-B1|SR-BI|SRBI|Srb1|mSR-BI	scavenger receptor class B, member 1	protein-coding
mm_36916.1	chr4	108080768	108080809	-	1	NA	intron (NM_011327, intron 10 of 15)	PB1D10|SINE|Alu	-6569	NR_105823	102465213		NR_105823	ENSMUSG00000098980	Mir6397	Gm28004|mmu-mir-6397	microRNA 6397	ncRNA
mm_109252.1	chr12	109458069	109458104	+	1	NA	exon (NM_010052, exon 4 of 5)	exon (NM_010052, exon 4 of 5)	4631	NM_010052	13386	Mm.157069	NM_010052	ENSMUSG00000040856	Dlk1	AW742678|DLK-1|DlkI|FA1|Ly107|Peg9|SCP1|ZOG|pG2|pref-1	delta-like 1 homolog (Drosophila)	protein-coding
mm_76596.1	chr8	89053007	89053037	-	1	NA	Intergenic	RLTR20B3|LTR|ERVK	-8860	NM_021390	58198	Mm.214361	NM_021390	ENSMUSG00000031665	Sall1	Msal-3	sal-like 1 (Drosophila)	protein-coding
mm_33724.1	chr4	134065898	134065926	+	1	NA	Intergenic	Intergenic	-2540	NM_001162970	230806	Mm.240080	NM_001162970	ENSMUSG00000012123	Aim1l	-	absent in melanoma 1-like	protein-coding
mm_108494.1	chr12	83682974	83682997	+	1	NA	3' UTR (NM_027349, exon 19 of 19)	3' UTR (NM_027349, exon 19 of 19)	-5578	NM_008943	19164	Mm.998	NM_008943	ENSMUSG00000019969	Psen1	Ad3h|PS-1|PS1|S182	presenilin 1	protein-coding
mm_54466.1	chr6	34907855	34907892	-	1	NA	intron (NM_001013366, intron 3 of 14)	intron (NM_001013366, intron 3 of 14)	2958	NM_001013366	101240	Mm.152120	NM_001013366	ENSMUSG00000058486	Wdr91	9530020G05Rik|AI987683|AU018665	WD repeat domain 91	protein-coding
mm_112266.1	chr12	114109461	114109493	-	1	NA	Intergenic	Intergenic	359989	NR_106062	102465663		NR_106062	ENSMUSG00000105438	Mir7094-1	mmu-mir-7094-1	microRNA 7094-1	ncRNA
mm_171374.1	chr4	119282788	119282789	-	1	NA	exon (NM_011732, exon 4 of 8)	exon (NM_011732, exon 4 of 8)	11725	NM_011732	22608	Mm.258204	NM_011732	ENSMUSG00000028639	Ybx1	1700102N10Rik|C79409|EF1A|MSY1|Nsep1|YB-1|dbpB|mYB-1a	Y box protein 1	protein-coding
mm_12908.1	chr2	84840348	84840364	+	1	NA	promoter-TSS (NM_001083809)	promoter-TSS (NM_001083809)	33	NM_024497	72401	Mm.22716	NM_024497	ENSMUSG00000027075	Slc43a1	2610016F07Rik|AA986141|Lat3|PB39|Pov1|R00504	solute carrier family 43, member 1	protein-coding
mm_101757.1	chr11	43424831	43424856	-	1	NA	exon (NM_001131054, exon 3 of 6)	exon (NM_001131054, exon 3 of 6)	1138	NM_013917	30939	Mm.6856	NM_013917	ENSMUSG00000020415	Pttg1	AW555095|C87862|Pttg|Pttg3	pituitary tumor-transforming gene 1	protein-coding
mm_137693.1	chr17	28952413	28952423	+	1	NA	promoter-TSS (NM_025888)	promoter-TSS (NM_025888)	-798	NM_025888	66989	Mm.435	NM_025888	ENSMUSG00000005936	Kctd20	2410004N11Rik|AI451943|AW541186|D17Ertd562e	potassium channel tetramerisation domain containing 20	protein-coding
mm_11635.1	chr2	34776270	34776277	+	1	NA	3' UTR (NM_001163434, exon 9 of 9)	3' UTR (NM_001163434, exon 9 of 9)	4183	NM_022310	14828	Mm.330160	NM_022310	ENSMUSG00000026864	Hspa5	AL022860|AU019543|Bip|D2Wsu141e|D2Wsu17e|Grp78|Hsce70|SEZ-7|Sez7|baffled|mBiP	heat shock protein 5	protein-coding
mm_86537.1	chr10	7868874	7868878	+	1	NA	3' UTR (NM_172785, exon 6 of 6)	3' UTR (NM_172785, exon 6 of 6)	32495	NR_039563	100628581		NR_039563	ENSMUSG00000093060	Mir5104	mir-5104|mmu-mir-5104|mu-mir-5104	microRNA 5104	ncRNA
mm_107099.1	chr12	17727274	17727274	+	1	NA	intron (NM_016677, intron 1 of 3)	intron (NM_016677, intron 1 of 3)	36460	NM_016677	53602	Mm.313619	NM_016677	ENSMUSG00000071379	Hpcal1	NVP-3|Nvp3|VILIP3|Vnsl3|Vsnl3	hippocalcin-like 1	protein-coding
mm_151925.1	chr19	5800084	5800092	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	2584	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_115490.1	chr13	3611065	3611118	-	1	NA	promoter-TSS (NM_134063)	promoter-TSS (NM_134063)	17	NM_134063	105203	Mm.221609	NM_134063	ENSMUSG00000033799	Fam208b	AI645998|Pap20|mKIAA2006	family with sequence similarity 208, member B	protein-coding
mm_9050.1	chr1	167285111	167285122	-	1	NA	promoter-TSS (NM_030724)	promoter-TSS (NM_030724)	11	NM_030724	80914	Mm.280895	NM_030724	ENSMUSG00000026558	Uck2	AA407809|AI481316|AU018180|AU020720|TSA903|UK|UMK|Umpk	uridine-cytidine kinase 2	protein-coding
mm_109351.1	chr12	109608774	109608793	+	1	NA	intron (NR_028261, intron 2 of 20)	intron (NR_028261, intron 2 of 20)	-2717	NR_029770	723846		NR_029770	ENSMUSG00000070101	Mir341	Mirn341|mmu-mir-341	microRNA 341	ncRNA
mm_161874.1	chr18	37090015	37090015	+	1	NA	promoter-TSS (NM_001003671)	promoter-TSS (NM_001003671)	-121	NM_001003671	353236	Mm.308500	NM_001003671	ENSMUSG00000103255	Pcdhac1	CNRc1	protocadherin alpha subfamily C, 1	protein-coding
mm_74959.1	chr8	26089874	26089883	-	1	NA	intron (NR_110583, intron 3 of 4)	HAL1ME|LINE|L1	7269	NR_110583	76604	Mm.437190	NR_110583	ENSMUSG00000085437	1700047A11Rik	4930554C15Rik	RIKEN cDNA 1700047A11 gene	ncRNA
mm_77368.1	chr8	119810264	119810281	-	1	NA	exon (NM_028071, exon 4 of 4)	exon (NM_028071, exon 4 of 4)	30307	NM_028071	72042	Mm.393405	NM_028071	ENSMUSG00000031827	Cotl1	1810074P22Rik|2010004C08Rik|Clp	coactosin-like 1 (Dictyostelium)	protein-coding
mm_131768.1	chr16	22893165	22893171	+	1	NA	intron (NR_075099, intron 1 of 5)	B1_Mur4|SINE|Alu	1153	NM_001276449	11625	Mm.197554	NM_013465	ENSMUSG00000022868	Ahsg	-	alpha-2-HS-glycoprotein	protein-coding
mm_145948.1	chr18	67401732	67401748	+	1	NA	exon (NM_026473, exon 4 of 4)	exon (NM_026473, exon 4 of 4)	11009	NM_026473	67951	Mm.181860	NM_026473	ENSMUSG00000001473	Tubb6	2310057H16Rik|BB220206	tubulin, beta 6 class V	protein-coding
mm_112370.1	chr12	119182289	119182309	-	1	NA	intron (NM_177290, intron 6 of 13)	intron (NM_177290, intron 6 of 13)	55977	NM_177290	320910	Mm.217000	NM_177290	ENSMUSG00000025321	Itgb8	4832412O06Rik	integrin beta 8	protein-coding
mm_22155.1	chr2	172806671	172806677	-	1	NA	Intergenic	Intergenic	133647	NM_007557	12162	Mm.595	NM_007557	ENSMUSG00000008999	Bmp7	OP1	bone morphogenetic protein 7	protein-coding
mm_115344.1	chr13	112509073	112509111	+	1	NA	Intergenic	Intergenic	45022	NM_010560	16195	Mm.4364	NM_010560	ENSMUSG00000021756	Il6st	5133400A03Rik|AA389424|BB405851|CD130|D13Ertd699e|gp130	interleukin 6 signal transducer	protein-coding
mm_26639.1	chr3	153675361	153675371	+	1	NA	intron (NM_011372, intron 1 of 4)	intron (NM_011372, intron 1 of 4)	49767	NM_011372	20447	Mm.296453	NM_011372	ENSMUSG00000052544	St6galnac3	Siat7c	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 3	protein-coding
mm_146899.1	chr18	30459595	30459600	-	1	NA	Intergenic	Intergenic	186701	NM_181414	225326	Mm.194127	NM_181414	ENSMUSG00000033628	Pik3c3	5330434F23Rik|Vps34	phosphoinositide-3-kinase, class 3	protein-coding
mm_97935.1	chr11	83648581	83648591	+	1	NA	exon (NM_011337, exon 2 of 3)	exon (NM_011337, exon 2 of 3)	792	NM_011337	20302	Mm.1282	NM_011337	ENSMUSG00000000982	Ccl3	AI323804|G0S19-1|LD78alpha|MIP-1alpha|MIP1-(a)|MIP1-alpha|Mip1a|Scya3	chemokine (C-C motif) ligand 3	protein-coding
mm_109066.1	chr12	104345290	104345311	+	1	NA	exon (NM_011458, exon 5 of 5)	exon (NM_011458, exon 5 of 5)	6814	NM_011458	20714	Mm.291569	NM_011458	ENSMUSG00000058207	Serpina3k	1300001I07Rik|D12Rp54|MMCM2|MMSpi2|RP54|Spi-2|Spi2|contrapsin	serine (or cysteine) peptidase inhibitor, clade A, member 3K	protein-coding
mm_130461.1	chr15	98607612	98607638	-	1	NA	promoter-TSS (NM_007405)	promoter-TSS (NM_007405)	8	NM_007405	11512	Mm.157091	NM_007405	ENSMUSG00000022994	Adcy6	AC6|mKIAA0422	adenylate cyclase 6	protein-coding
mm_80622.1	chr9	88731993	88732001	+	1	NA	promoter-TSS (NM_007536)	promoter-TSS (NM_007536)	-147	NM_007536	12047	Mm.378888	NM_007536	ENSMUSG00000099974	Bcl2a1d	A1-d	B cell leukemia/lymphoma 2 related protein A1d	protein-coding
mm_105884.1	chr11	114930624	114930640	-	1	NA	intron (NM_199221, intron 1 of 3)	intron (NM_199221, intron 1 of 3)	3754	NM_001347651	217304	Mm.185355	NM_199221	ENSMUSG00000063193	Cd300lb	CLM-7|Clm7|Gm253|LMIR5	CD300 molecule like family member B	protein-coding
mm_131675.1	chr16	20673196	20673245	+	1	NA	intron (NM_001304432, intron 1 of 31)	CpG	493	NM_001304432	208643	Mm.260256	NM_145941	ENSMUSG00000045983	Eif4g1	E030015G23Rik|eIF-4-gamma 1|eIF-4G 1|eIF-4G1|eIF4GI	eukaryotic translation initiation factor 4, gamma 1	protein-coding
mm_145265.1	chr18	52693668	52693670	+	1	NA	promoter-TSS (NM_010293)	promoter-TSS (NM_010293)	-10	NM_010293	14625	Mm.32242	NM_010293	ENSMUSG00000053624	Gykl1	AI449806|Gk-rs1	glycerol kinase-like 1	protein-coding
mm_70317.1	chr8	4248224	4248241	+	1	NA	promoter-TSS (NM_001195258)	promoter-TSS (NM_001195258)	18	NM_001195258	100044509	Mm.439193	NM_001195258	ENSMUSG00000089736	Tgfbr3l	Gm14378|OTTMUSG00000016477	transforming growth factor, beta receptor III-like	protein-coding
mm_31999.1	chr4	93334833	93334845	+	1	NA	exon (NM_026954, exon 1 of 1)	exon (NM_026954, exon 1 of 1)	672	NM_026954	69136	Mm.171558	NM_026954	ENSMUSG00000054000	Tusc1	2200001D17Rik|TSG-9	tumor suppressor candidate 1	protein-coding
mm_121890.1	chr14	21742871	21742893	-	1	NA	promoter-TSS (NM_013849)	promoter-TSS (NM_013849)	-3	NM_013849	27389	Mm.390674	NM_013849	ENSMUSG00000021768	Dusp13	DUSP13A|DUSP13B|Gm1203|LMW-DSP6|MDSP|TMDP|TS-DSP6	dual specificity phosphatase 13	protein-coding
mm_55251.1	chr6	52909560	52909574	-	1	NA	promoter-TSS (NM_001168277)	promoter-TSS (NM_001168277)	53	NM_001168277	231986	Mm.386865	NM_173406	ENSMUSG00000063568	Jazf1	AI591476|C820002C15|Jaz1|Tip27	JAZF zinc finger 1	protein-coding
mm_155586.1	chrX	78954018	78954020	+	1	NA	Intergenic	MMERVK9C_I-int|LTR|ERVK	216256	NM_001164739	70864	Mm.66681	NM_001164739	ENSMUSG00000078315	Fam47c	4921509A18Rik|Fam47a|Fam47a-ps	family with sequence similarity 47, member C	protein-coding
mm_49599.1	chr6	30723523	30723534	+	1	NA	Intergenic	Intergenic	-9978	NM_001252293	17294	Mm.335639	NM_008590	ENSMUSG00000051855	Mest	AA408879|AI256745|Peg1	mesoderm specific transcript	protein-coding
mm_36162.1	chr4	60421949	60421955	-	1	NA	promoter-TSS (NM_001281979)	promoter-TSS (NM_001281979)	0	NM_001281979	100038948	Mm.482231	NM_001126319	ENSMUSG00000078686	Mup9	Gm14076|Mup2|Mup6|OTTMUSG00000015595	major urinary protein 9	protein-coding
mm_78254.1	chr9	21748430	21748448	+	1	NA	3' UTR (NM_001252659, exon 18 of 18)	3' UTR (NM_001252659, exon 18 of 18)	11847	NM_026282	67629	Mm.295642	NM_026282	ENSMUSG00000074476	Spc24	2410030K01Rik|AV109292|Spbc24	SPC24, NDC80 kinetochore complex component, homolog (S. cerevisiae)	protein-coding
mm_157524.1	chrX	50942803	50942809	-	1	NA	promoter-TSS (NM_001190332)	promoter-TSS (NM_001190332)	-96	NM_001190332	385354	Mm.393050	NM_001190332	ENSMUSG00000036131	Frmd7	EG665849|Gm1533	FERM domain containing 7	protein-coding
mm_83132.1	chr9	40435146	40435153	-	1	NA	intron (NM_172768, intron 1 of 19)	intron (NM_172768, intron 1 of 19)	20615	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_170381.1	chr1	85601079	85601079	+	1	NA	5' UTR (NM_001013817, exon 1 of 17)	5' UTR (NM_001013817, exon 1 of 17)	376	NM_001013817	434484	Mm.445821	NM_001013817	ENSMUSG00000070031	Sp140	-	Sp140 nuclear body protein	protein-coding
mm_172804.1	chr9	120129777	120129779	+	1	NA	promoter-TSS (NR_002902)	promoter-TSS (NR_002902)	-656	NR_002902	104433	Mm.453530	NR_002902	ENSMUSG00000064925	Snora62	E2|MBI-13|MBI-136|Rnu108	small nucleolar RNA, H/ACA box 62	snoRNA
mm_145280.1	chr18	53176346	53176376	+	1	NA	promoter-TSS (NM_026386)	promoter-TSS (NM_026386)	-4	NM_026386	67804	Mm.252171	NM_026386	ENSMUSG00000034484	Snx2	0610030A03Rik	sorting nexin 2	protein-coding
mm_35755.1	chr4	45815550	45815561	-	1	NA	exon (NM_018741, exon 3 of 5)	exon (NM_018741, exon 3 of 5)	11272	NM_018741	75426	Mm.3919	NM_018741	ENSMUSG00000035551	Igfbpl1	2810011G06Rik|2810453O06Rik|IGFBPL	insulin-like growth factor binding protein-like 1	protein-coding
mm_87685.1	chr10	59323358	59323374	+	1	NA	promoter-TSS (NM_011030)	promoter-TSS (NM_011030)	70	NM_001316370	18451	Mm.2212	NM_011030	ENSMUSG00000019916	P4ha1	AL022634|P4ha	procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha 1 polypeptide	protein-coding
mm_84647.1	chr9	71485894	71485975	-	1	NA	promoter-TSS (NM_001164793)	promoter-TSS (NM_001164793)	49	NM_178602	28015	Mm.21094	NM_178602	ENSMUSG00000032199	Polr2m	AA407243|AA408799|AI303746|AW553238|D9Wsu138e|Grinl1a|mKIAA4185	polymerase (RNA) II (DNA directed) polypeptide M	protein-coding
mm_83644.1	chr9	49505155	49505175	-	1	NA	3' UTR (NM_001311065, exon 18 of 18)	3' UTR (NM_001311065, exon 18 of 18)	-13123	NR_029465	100036537	Mm.437541	NR_029465	ENSMUSG00000079564	Gm11149	ENSMUSG00000060603|ENSMUSG00000079564	predicted gene 11149	ncRNA
mm_126619.1	chr15	83148264	83148266	+	1	NA	intron (NM_001347082, intron 1 of 7)	intron (NM_001347082, intron 1 of 7)	1071	NM_178627	73826	Mm.23758	NM_178627	ENSMUSG00000041815	Poldip3	1110008P04Rik|AA408269|AL022852|C77954|PDIP46|SKAR|mKIAA1649	polymerase (DNA-directed), delta interacting protein 3	protein-coding
mm_79253.1	chr9	50739686	50739688	+	1	NA	TTS (NM_025865)	TTS (NM_025865)	-1952	NM_001311069	330938	Mm.82598	NM_178118	ENSMUSG00000032064	Dixdc1	4930563F16Rik|BC048182|Ccd1|Ccd1Aalpha1L|Ccd1Abeta1L|Ccd1BalphaL|Ccd1BbetaL|Ccd1CL|mKIAA1735	DIX domain containing 1	protein-coding
mm_115726.1	chr13	16261326	16261348	-	1	NA	Intergenic	Intergenic	249486	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_117700.1	chr13	94789268	94789269	-	1	NA	intron (NM_009321, intron 1 of 3)	CpG	325	NM_009321	21371	Mm.379025	NM_009321	ENSMUSG00000042043	Tbca	Tbca13	tubulin cofactor A	protein-coding
mm_35875.1	chr4	49536790	49536800	-	1	NA	exon (NM_144903, exon 9 of 9)	exon (NM_144903, exon 9 of 9)	12751	NM_144903	230163	Mm.482116	NM_144903	ENSMUSG00000028307	Aldob	Aldo-2|Aldo2|BC016435	aldolase B, fructose-bisphosphate	protein-coding
mm_23078.1	chr3	36475987	36476021	+	1	NA	promoter-TSS (NR_105976)	promoter-TSS (NR_105976)	67	NM_028183	72282	Mm.55317	NM_028183	ENSMUSG00000027713	1810062G17Rik	-	RIKEN cDNA 1810062G17 gene	protein-coding
mm_46166.1	chr5	96164120	96164142	-	1	NA	Intergenic	Intergenic	-2141	NM_144910	231464	Mm.28374	NM_144910	ENSMUSG00000034724	Cnot6l	4932442K20Rik	CCR4-NOT transcription complex, subunit 6-like	protein-coding
mm_8371.1	chr1	150971257	150971268	-	1	NA	intron (NM_001024720, intron 1 of 106)	intron (NM_001024720, intron 1 of 106)	22173	NM_001024720	545370	Mm.379425	NM_001024720	ENSMUSG00000066842	Hmcn1	EG545370|FIBL-6|Gm201	hemicentin 1	protein-coding
mm_120373.1	chr14	64587385	64587434	+	1	NA	promoter-TSS (NR_040709)	promoter-TSS (NR_040709)	-706	NR_040709	268755	Mm.194050	NR_040709	ENSMUSG00000097545	Mir124a-1hg	A930011O12Rik|Rncr3|mir-124-1|mir-3078	Mir124-1 host gene (non-protein coding)	ncRNA
mm_171447.1	chr4	144742231	144742231	+	1	NA	Intergenic	L1Md_A|LINE|L1	-20827	NM_001085536	546849	Mm.457885	NM_001085536	ENSMUSG00000041735	Gm13178	Gm437|OTTMUSG00000010750	predicted gene 13178	protein-coding
mm_84478.1	chr9	66834660	66834677	-	1	NA	promoter-TSS (NM_026674)	promoter-TSS (NM_026674)	38	NM_026674	68318	Mm.284229	NM_026674	ENSMUSG00000053040	Aph1c	0610008A10Rik|APH-1b|Aph1b	aph1 homolog C, gamma secretase subunit	protein-coding
mm_2571.1	chr1	118469810	118469820	+	1	NA	intron (NM_001293300, intron 7 of 40)	intron (NM_001293300, intron 7 of 40)	-10550	NR_027901	68204	Mm.443536	NR_027901	ENSMUSG00000107722	2900060B14Rik	-	RIKEN cDNA 2900060B14 gene	ncRNA
mm_20203.1	chr2	125123582	125123617	-	1	NA	promoter-TSS (NM_001162417)	promoter-TSS (NM_001162417)	61	NM_001162417	17876	Mm.18535	NM_010852	ENSMUSG00000027201	Myef2	9430071B01|mKIAA1341	myelin basic protein expression factor 2, repressor	protein-coding
mm_41838.1	chr5	104325361	104325368	+	1	NA	promoter-TSS (NM_053172)	promoter-TSS (NM_053172)	35	NM_053172	94111	Mm.196672	NM_053172	ENSMUSG00000053863	Mepe	Of45	matrix extracellular phosphoglycoprotein with ASARM motif (bone)	protein-coding
mm_56742.1	chr6	115838184	115838199	-	1	NA	5' UTR (NM_001110506, exon 1 of 9)	5' UTR (NM_001110506, exon 1 of 9)	221	NM_001110506	212516	Mm.333333	NM_198603	ENSMUSG00000030321	Efcab12	BB124106	EF-hand calcium binding domain 12	protein-coding
mm_132368.1	chr16	34807200	34807217	+	1	NA	intron (NM_139300, intron 1 of 31)	intron (NM_139300, intron 1 of 31)	22258	NM_139300	107589	Mm.33360	NM_139300	ENSMUSG00000022836	Mylk	9530072E15Rik|A930019C19Rik|AW489456|KRP|MLCK108|MLCK210|Mlck|nmMlck|smMLCK	myosin, light polypeptide kinase	protein-coding
mm_22189.1	chr2	173269440	173269447	-	1	NA	intron (NM_022995, intron 1 of 3)	intron (NM_022995, intron 1 of 3)	7090	NM_022995	65112	Mm.73682	NM_022995	ENSMUSG00000038400	Pmepa1	2210418I02Rik|AW455466|Erg1.2|N4wbp4|Stag1|Tmepai	prostate transmembrane protein, androgen induced 1	protein-coding
mm_124628.1	chr15	3637449	3637458	+	1	NA	Intergenic	Intergenic	-54101	NM_010284	14600	Mm.3986	NM_010284	ENSMUSG00000055737	Ghr	GHBP|GHR/BP	growth hormone receptor	protein-coding
mm_58067.1	chr6	136922170	136922198	-	1	NA	promoter-TSS (NM_026983)	promoter-TSS (NM_026983)	-4	NM_026983	69187	Mm.33692	NM_026983	ENSMUSG00000030219	Erp27	1810033M07Rik|1810047B09Rik	endoplasmic reticulum protein 27	protein-coding
mm_117508.1	chr13	78200516	78200550	-	1	NA	intron (NR_045195, intron 1 of 2)	intron (NR_045195, intron 1 of 2)	-1660	NM_010151	13865	Mm.439653	NM_010151	ENSMUSG00000069171	Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR-3|EAR3|Erbal3|SVP44|Tcfcoup1	nuclear receptor subfamily 2, group F, member 1	protein-coding
mm_162575.1	chr1	177258950	177258958	-	1	NA	Intergenic	CpG	-10187	NM_011785	23797	Mm.235194	NM_011785	ENSMUSG00000019699	Akt3	AI851531|D930002M15Rik|Nmf350	thymoma viral proto-oncogene 3	protein-coding
mm_145431.1	chr18	58836153	58836182	+	1	NA	promoter-TSS (NM_175506)	promoter-TSS (NM_175506)	-196	NM_175506	240322	Mm.71963	NM_175506	ENSMUSG00000053441	Adamts19	4831407I23Rik|AU015154|D230034E10Rik	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 19	protein-coding
mm_151826.1	chr19	5654263	5654304	-	1	NA	intron (NM_001164568, intron 8 of 15)	CpG-7241	9424	NM_001164482	20469	Mm.3072	NM_011379	ENSMUSG00000056917	Sipa1	Spa1	signal-induced proliferation associated gene 1	protein-coding
mm_84466.1	chr9	66593030	66593041	-	1	NA	promoter-TSS (NM_144937)	promoter-TSS (NM_144937)	80	NM_144937	235441	Mm.32465	NM_144937	ENSMUSG00000032376	Usp3	AA409661|BC017156	ubiquitin specific peptidase 3	protein-coding
mm_41826.1	chr5	104046919	104046975	+	1	NA	promoter-TSS (NM_028794)	promoter-TSS (NM_028794)	83	NM_028794	74167	Mm.241484	NM_028794	ENSMUSG00000029310	Nudt9	1190002C07Rik|ADPR-PPase|AI462474	nudix (nucleoside diphosphate linked moiety X)-type motif 9	protein-coding
mm_172483.1	chr7	5124123	5124123	-	1	NA	TTS (NM_009028)	TTS (NM_009028)	1827	NM_009028	19428	Mm.322186	NM_009028	ENSMUSG00000083649	Rasl2-9	M2|Ran|Ran/M2|Rasl2-9-ps	RAS-like, family 2, locus 9	protein-coding
mm_168775.1	chr12	17464620	17464627	-	1	NA	Intergenic	RLTR9D|LTR|ERVK	-80250	NM_013614	18263	Mm.34102	NM_013614	ENSMUSG00000011179	Odc1	ODC	ornithine decarboxylase, structural 1	protein-coding
mm_123188.1	chr14	57890185	57890239	-	1	NA	promoter-TSS (NM_029492)	promoter-TSS (NM_029492)	50	NM_029492	75965	Mm.29044	NM_029492	ENSMUSG00000021969	Zdhhc20	4930542A17Rik|5033406L14Rik|AI448102|B230110O18Rik|ENSMUSG00000055956|HK11	zinc finger, DHHC domain containing 20	protein-coding
mm_140178.1	chr17	80896844	80896854	+	1	NA	promoter-TSS (NR_131128)	promoter-TSS (NR_131128)	56	NR_131127	320784	Mm.474182	NR_131127		C230072F16Rik	-	RIKEN cDNA C230072F16 gene	ncRNA
mm_68001.1	chr7	100932535	100932570	-	1	NA	promoter-TSS (NM_001081116)	promoter-TSS (NM_001081116)	-391	NM_001081116	207212	Mm.29954	NM_001081116	ENSMUSG00000032875	Arhgef17	8030463K16|AI428794|AW558066|BC035332|mKIAA0337	Rho guanine nucleotide exchange factor (GEF) 17	protein-coding
mm_135639.1	chr16	52355887	52355925	-	1	NA	intron (NM_009655, intron 1 of 15)	intron (NM_009655, intron 1 of 15)	97175	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_33325.1	chr4	129105628	129105641	+	1	NA	promoter-TSS (NM_001290706)	promoter-TSS (NM_001290706)	86	NM_001290706	66260	Mm.25295	NM_025452	ENSMUSG00000028786	Tmem54	1810017F10Rik|AI507302	transmembrane protein 54	protein-coding
mm_6200.1	chr1	65186415	65186426	-	1	NA	promoter-TSS (NM_001310624)	promoter-TSS (NM_001310624)	59	NM_001111320	15926	Mm.9925	NM_010497	ENSMUSG00000025950	Idh1	AI314845|AI788952|E030024J03Rik|Id-1|Idh-1|Idpc	isocitrate dehydrogenase 1 (NADP+), soluble	protein-coding
mm_168744.1	chr12	115359622	115359627	-	1	NA	Intergenic	Intergenic	336170	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
mm_112482.1	chr13	5869457	5869477	+	1	NA	3' UTR (NM_011803, exon 4 of 4)	3' UTR (NM_011803, exon 4 of 4)	7978	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_67552.1	chr7	81567001	81567011	-	1	NA	promoter-TSS (NM_172904)	promoter-TSS (NM_172904)	-25	NM_172904	244091	Mm.38773	NM_172904	ENSMUSG00000038663	Fsd2	9830160G03Rik|Spryd1	fibronectin type III and SPRY domain containing 2	protein-coding
mm_20912.1	chr2	150600398	150600413	-	1	NA	intron (NM_027977, intron 1 of 8)	intron (NM_027977, intron 1 of 8)	8118	NM_027977	71881	Mm.26599	NM_027977	ENSMUSG00000033096	Apmap	2310001A20Rik|AI314817	adipocyte plasma membrane associated protein	protein-coding
mm_34780.1	chr4	154026195	154026212	+	1	NA	promoter-TSS (NM_001163722)	promoter-TSS (NM_001163722)	-159	NM_001163721	68859	Mm.477488	NM_001033144	ENSMUSG00000078350	Smim1	0610011H04Rik|1190007F08Rik|2700009I11Rik	small integral membrane protein 1	protein-coding
mm_62515.1	chr7	102223022	102223076	+	1	NA	promoter-TSS (NM_145583)	promoter-TSS (NM_145583)	21	NR_111937	233575	Mm.302013	NM_145583	ENSMUSG00000030990	Pgap2	1810006G21Rik|C76649|Frag1	post-GPI attachment to proteins 2	protein-coding
mm_117299.1	chr13	67081504	67081555	-	1	NA	promoter-TSS (NM_001292066)	promoter-TSS (NM_001292066)	16	NM_001012448	432769	Mm.458849	NM_001012325	ENSMUSG00000058883	Zfp708	Rslcan11	zinc finger protein 708	protein-coding
mm_24217.1	chr3	88646915	88646926	+	1	NA	3' UTR (NM_001198913, exon 22 of 22)	3' UTR (NM_001198913, exon 22 of 22)	6222	NM_181817	242093	Mm.269130	NM_181817	ENSMUSG00000049741	Rxfp4	GPCR142|Gpr100|Rln3r2|SALPR	relaxin family peptide receptor 4	protein-coding
mm_11646.1	chr2	34961003	34961028	+	1	NA	intron (NM_009421, intron 1 of 10)	intron (NM_009421, intron 1 of 10)	757	NM_009421	22029	Mm.239514	NM_009421	ENSMUSG00000026875	Traf1	4732496E14Rik	TNF receptor-associated factor 1	protein-coding
mm_78663.1	chr9	40685989	40685999	+	1	NA	promoter-TSS (NM_133733)	promoter-TSS (NM_133733)	30	NM_133733	71566	Mm.280560	NM_133733	ENSMUSG00000032024	Clmp	9030425E11Rik|ACAM|ASP5|AW557819	CXADR-like membrane protein	protein-coding
mm_122093.1	chr14	30626197	30626220	-	1	NA	promoter-TSS (NM_011103)	promoter-TSS (NM_011103)	0	NM_011103	18753	Mm.2314	NM_011103	ENSMUSG00000021948	Prkcd	AI385711|D14Ertd420e|PKC[d]|PKCdelta|Pkcd	protein kinase C, delta	protein-coding
mm_79926.1	chr9	65630730	65630736	+	1	NA	5' UTR (NM_028030, exon 1 of 8)	5' UTR (NM_028030, exon 1 of 8)	151	NM_028030	71973	Mm.29148	NM_028030	ENSMUSG00000032387	Rbpms2	2400008B06Rik|AI316523	RNA binding protein with multiple splicing 2	protein-coding
mm_63499.1	chr7	127800624	127800696	+	1	NA	promoter-TSS (NM_133943)	promoter-TSS (NM_133943)	51	NM_001040684	101502	Mm.157103	NM_133943	ENSMUSG00000042289	Hsd3b7	AI195443|BB098564	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 7	protein-coding
mm_132585.1	chr16	38362206	38362230	+	1	NA	promoter-TSS (NM_022318)	promoter-TSS (NM_022318)	28	NM_022318	64082	Mm.390856	NM_022318	ENSMUSG00000022803	Popdc2	AV006127|Pop2	popeye domain containing 2	protein-coding
mm_143937.1	chr17	86230349	86230361	-	1	NA	intron (NM_011104, intron 1 of 14)	intron (NM_011104, intron 1 of 14)	56823	NR_045435	72104	Mm.443401	NR_045435	ENSMUSG00000100738	2010106C02Rik	-	RIKEN cDNA 2010106C02 gene	ncRNA
mm_158924.1	chr1	59516229	59516229	+	1	NA	promoter-TSS (NM_001013771)	promoter-TSS (NM_001013771)	-35	NM_001013771	381260	Mm.486706	NM_001013771	ENSMUSG00000047361	Gm973	AW554518	predicted gene 973	protein-coding
mm_137430.1	chr17	26272957	26272962	+	1	NA	intron (NR_037906, intron 5 of 8)	MTC|LTR|ERVL-MaLR	20049	NR_037905	66978	Mm.440216	NM_025881	ENSMUSG00000024188	Luc7l	1810045C04Rik|2410018D03Rik	Luc7-like	protein-coding
mm_108493.1	chr12	83682919	83682929	+	1	NA	3' UTR (NM_027349, exon 19 of 19)	3' UTR (NM_027349, exon 19 of 19)	-5639	NM_008943	19164	Mm.998	NM_008943	ENSMUSG00000019969	Psen1	Ad3h|PS-1|PS1|S182	presenilin 1	protein-coding
mm_150607.1	chr19	40831297	40831313	+	1	NA	promoter-TSS (NM_172839)	promoter-TSS (NM_172839)	26	NM_172839	240665	Mm.309	NM_172839	ENSMUSG00000025010	Ccnj	D430039C20Rik	cyclin J	protein-coding
mm_77177.1	chr8	111691003	111691019	-	1	NA	promoter-TSS (NM_025583)	promoter-TSS (NM_025583)	-1	NM_025583	66473	Mm.34374	NM_025583	ENSMUSG00000031957	Ctrb1	2200008D09Rik|AI504462|Ctrb|Prt-2	chymotrypsinogen B1	protein-coding
mm_69109.1	chr7	127021584	127021595	-	1	NA	promoter-TSS (NM_001102563)	promoter-TSS (NM_001102563)	-378	NM_001102563	69017	Mm.392047	NM_001102563	ENSMUSG00000045114	Prrt2	1500031I19Rik|AI195361|DSPB3	proline-rich transmembrane protein 2	protein-coding
mm_111174.1	chr12	83668474	83668509	-	1	NA	exon (NM_027349, exon 12 of 19)	exon (NM_027349, exon 12 of 19)	-20072	NM_008943	19164	Mm.998	NM_008943	ENSMUSG00000019969	Psen1	Ad3h|PS-1|PS1|S182	presenilin 1	protein-coding
mm_134845.1	chr16	26526827	26526837	-	1	NA	promoter-TSS (NM_001101640)	promoter-TSS (NM_001101640)	-61	NM_001101640	100043057	Mm.295917	NM_001101640	ENSMUSG00000091972	Tmem207	Gm540	transmembrane protein 207	protein-coding
mm_132710.1	chr16	43503305	43503323	+	1	NA	intron (NM_181058, intron 3 of 6)	CT-rich|Low_complexity|Low_complexity	-83118	NR_046026	626693	Mm.447083	NR_046026	ENSMUSG00000085499	Gm15713	OTTMUSG00000025617	predicted gene 15713	ncRNA
mm_167140.1	chr7	127730913	127730914	+	1	NA	Intergenic	Intergenic	-5297	NM_198858	244218	Mm.249829	NM_198858	ENSMUSG00000060034	Ctf2	Gm494|NP	cardiotrophin 2	protein-coding
mm_59234.1	chr7	24778135	24778138	+	1	NA	exon (NM_007675, exon 2 of 4)	exon (NM_007675, exon 2 of 4)	932	NM_007675	26366	Mm.30300	NM_007675	ENSMUSG00000054169	Ceacam10	Bgp3|Cea10	carcinoembryonic antigen-related cell adhesion molecule 10	protein-coding
mm_133325.1	chr16	78301674	78301760	+	1	NA	promoter-TSS (NM_009988)	promoter-TSS (NM_009988)	46	NM_001276263	13052	Mm.66222	NM_009988	ENSMUSG00000022865	Cxadr	2610206D03Rik|AU016810|AW553441|CAR|MCAR|MCVADR	coxsackie virus and adenovirus receptor	protein-coding
mm_25612.1	chr3	118430300	118430368	+	1	NA	Intergenic	Intergenic	-3523	NR_029551	387155		NR_029551	ENSMUSG00000065569	Mir137	Mirn137|mir-137|mmu-mir-137	microRNA 137	ncRNA
mm_6716.1	chr1	82317588	82317596	-	1	NA	intron (NM_029777, intron 1 of 6)	intron (NM_029777, intron 1 of 6)	1013	NM_029777	76867	Mm.226994	NM_029777	ENSMUSG00000026142	Rhbdd1	4930418P06Rik|RRP4|mRHBDD1	rhomboid domain containing 1	protein-coding
mm_2052.1	chr1	87404978	87404982	+	1	NA	intron (NM_001110212, intron 9 of 28)	intron (NM_001110212, intron 9 of 28)	-10251	NM_001110227	100040591	Mm.443539	NM_001110227	ENSMUSG00000079436	Kcnj13	-	potassium inwardly-rectifying channel, subfamily J, member 13	protein-coding
mm_141898.1	chr17	34882095	34882114	-	1	NA	promoter-TSS (NM_013484)	promoter-TSS (NM_013484)	-4	NM_013484	12263	Mm.283217	NM_013484	ENSMUSG00000024371	C2	-	complement component 2 (within H-2S)	protein-coding
mm_133605.1	chr16	91485234	91485294	+	1	NA	promoter-TSS (NM_010508)	promoter-TSS (NM_010508)	49	NM_010508	15975	Mm.502	NM_010508	ENSMUSG00000022967	Ifnar1	CD118|Ifar|Ifnar|Ifrc|Infar	interferon (alpha and beta) receptor 1	protein-coding
mm_52467.1	chr6	114131230	114131246	+	1	NA	promoter-TSS (NM_172890)	promoter-TSS (NM_172890)	-3	NM_172890	243616	Mm.44683	NM_172890	ENSMUSG00000030307	Slc6a11	D930045G19Rik|E130202I16Rik|GAT4|Gabt4|Gat3	solute carrier family 6 (neurotransmitter transporter, GABA), member 11	protein-coding
mm_5946.1	chr1	56782392	56782399	-	1	NA	Intergenic	MTB|LTR|ERVL-MaLR	-144944	NM_027661	71066	Mm.152656	NM_027661	ENSMUSG00000045336	Hsfy2	4933413G11Rik|Hspy2l	heat shock transcription factor, Y-linked 2	protein-coding
mm_129306.1	chr15	77533313	77533317	-	1	NA	promoter-TSS (NM_175391)	promoter-TSS (NM_175391)	0	NM_175391	108956	Mm.86391	NM_175391	ENSMUSG00000044309	Apol7c	2210421G13Rik	apolipoprotein L 7c	protein-coding
mm_22547.1	chr3	9250013	9250024	+	1	NA	promoter-TSS (NM_177660)	promoter-TSS (NM_177660)	-549	NM_177660	229055	Mm.103262	NM_177660	ENSMUSG00000069114	Zbtb10	4832414A18|AU021107|RINZF	zinc finger and BTB domain containing 10	protein-coding
mm_89975.1	chr10	111595078	111595092	+	1	NA	promoter-TSS (NR_045344)	promoter-TSS (NR_045344)	-812	NR_045344	71321	Mm.410785	NR_045344	ENSMUSG00000097082	4933440J02Rik	-	RIKEN cDNA 4933440J02 gene	ncRNA
mm_61559.1	chr7	79504942	79504954	+	1	NA	promoter-TSS (NR_029818)	promoter-TSS (NR_029818)	-316	NR_029818	723968		NR_029818	ENSMUSG00000093238	Mir9-3	Mirn9-3|mir-9-3|mmu-mir-9-3	microRNA 9-3	ncRNA
mm_12798.1	chr2	79644527	79644551	+	1	NA	exon (NM_080558, exon 8 of 18)	exon (NM_080558, exon 8 of 18)	9114	NM_080558	70599	Mm.272881	NM_080558	ENSMUSG00000027007	Ssfa2	5730488C15Rik|CS-1|CS1|KRAP|SPAG13|mKIAA1927	sperm specific antigen 2	protein-coding
mm_150913.1	chr19	46064156	46064174	+	1	NA	exon (NM_001081214, exon 5 of 14)	exon (NM_001081214, exon 5 of 14)	7626	NM_001081214	226169	Mm.2415	NM_145504	ENSMUSG00000055491	Pprc1	A930018M19|BC013720|PRC|mKIAA0595	peroxisome proliferative activated receptor, gamma, coactivator-related 1	protein-coding
mm_53378.1	chr6	129512539	129512562	+	1	NA	promoter-TSS (NM_001081186)	promoter-TSS (NM_001081186)	-7	NM_001081186	330428	Mm.44237	NM_001081186	ENSMUSG00000030160	Tmem52b	D630042F21Rik	transmembrane protein 52B	protein-coding
mm_25386.1	chr3	107216007	107216015	+	1	NA	exon (NM_001111143, exon 5 of 9)	exon (NM_001111143, exon 5 of 9)	5721	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_117270.1	chr13	64624783	64624807	-	1	NA	Intergenic	Intergenic	-127003	NM_001195435	68880	Mm.390594	NM_001195435	ENSMUSG00000096537	1190003K10Rik	-	RIKEN cDNA 1190003K10 gene	protein-coding
mm_126971.1	chr15	93398345	93398423	+	1	NA	promoter-TSS (NM_026025)	promoter-TSS (NM_026025)	34	NM_175363	223828	Mm.74208	NM_146062	ENSMUSG00000036167	Pphln1	CR|HSPC206|HSPC232	periphilin 1	protein-coding
mm_102275.1	chr11	55395494	55395504	-	1	NA	3' UTR (NM_009242, exon 10 of 10)	3' UTR (NM_009242, exon 10 of 10)	24581	NM_009242	20692	Mm.291442	NM_009242	ENSMUSG00000018593	Sparc	BM-40|ON	secreted acidic cysteine rich glycoprotein	protein-coding
mm_18215.1	chr2	49710785	49710837	-	1	NA	exon (NM_008449, exon 11 of 26)	exon (NM_008449, exon 11 of 26)	-76875	NM_027990	71897	Mm.41381	NM_027990	ENSMUSG00000026765	Lypd6b	2310010M24Rik|AW049525	LY6/PLAUR domain containing 6B	protein-coding
mm_171812.1	chr5	134463214	134463233	+	1	NA	Intergenic	Intergenic	-6507	NM_001081464	57080	Mm.332735	NM_020331	ENSMUSG00000023079	Gtf2ird1	1700012P16Rik|BEN|Cream1|ESTM9|GTF3|Gtf2il|MusTRD1|Tg(Alb1-Myc)166.8Sst|WBSCR11|X83320	general transcription factor II I repeat domain-containing 1	protein-coding
mm_55927.1	chr6	84587645	84587654	-	1	NA	intron (NM_001177713, intron 2 of 6)	CpG	6161	NM_175475	232174	Mm.255246	NM_175475	ENSMUSG00000063415	Cyp26b1	CP26|P450RAI-2	cytochrome P450, family 26, subfamily b, polypeptide 1	protein-coding
mm_25774.1	chr3	126596409	126596419	+	1	NA	promoter-TSS (NM_001293663)	promoter-TSS (NM_001293663)	-537	NM_001293663	108058	Mm.255822	NM_023813	ENSMUSG00000053819	Camk2d	2810011D23Rik|8030469K03Rik|CaMK II|[d]-CaMKII	calcium/calmodulin-dependent protein kinase II, delta	protein-coding
mm_126730.1	chr15	85634907	85634920	+	1	NA	Intergenic	CpG	-53092	NM_009528	22422	Mm.306946	NM_009528	ENSMUSG00000022382	Wnt7b	Wnt-7b	wingless-type MMTV integration site family, member 7B	protein-coding
mm_54463.1	chr6	34893576	34893599	-	1	NA	intron (NM_001013366, intron 7 of 14)	MTC-int|LTR|ERVL-MaLR	-15522	NM_001135611	78412	Mm.248440	NM_199145	ENSMUSG00000046806	3110062M04Rik	AL023049|Mri	RIKEN cDNA 3110062M04 gene	protein-coding
mm_85406.1	chr9	103365732	103365739	-	1	NA	promoter-TSS (NM_001134427)	promoter-TSS (NM_001134427)	45	NM_175833	321022	Mm.261025	NM_175565	ENSMUSG00000032803	Cdv3	2510010F10Rik|C230084J24Rik|C79446|TPP36	carnitine deficiency-associated gene expressed in ventricle 3	protein-coding
mm_167134.1	chr7	127050263	127050275	+	1	NA	3' UTR (NM_026918, exon 3 of 3)	3' UTR (NM_026918, exon 3 of 3)	1708	NM_026918	69036	Mm.21835	NM_026918	ENSMUSG00000049350	Zg16	1810010M01Rik|AI593689|ZG16p	zymogen granule protein 16	protein-coding
mm_75781.1	chr8	70011023	70011062	-	1	NA	Intergenic	Intergenic	-14658	NM_145596	234366	Mm.270044	NM_145596	ENSMUSG00000036180	Gatad2a	1110066C11Rik|BC031407|C80248	GATA zinc finger domain containing 2A	protein-coding
mm_63168.1	chr7	124140522	124140525	+	1	NA	intron (NM_001252072, intron 1 of 1)	intron (NM_001252072, intron 1 of 1)	157342	NM_001252072	628779	Mm.40210	NM_001252072	ENSMUSG00000078591	Hs3st4	EG628779|Gm6915	heparan sulfate (glucosamine) 3-O-sulfotransferase 4	protein-coding
mm_3024.1	chr1	133661032	133661054	+	1	NA	promoter-TSS (NM_001166552)	promoter-TSS (NM_001166552)	-158	NM_001166552	667118	Mm.245357	NM_001166552	ENSMUSG00000094410	Zbed6	Gm8466|MGR	zinc finger, BED type containing 6	protein-coding
mm_165440.1	chr2	154202634	154202639	+	1	NA	exon (NM_153418, exon 2 of 16)	exon (NM_153418, exon 2 of 16)	2256	NM_153418	228801	Mm.3783	NM_153418	ENSMUSG00000027485	Bpifb1	Lplunc1	BPI fold containing family B, member 1	protein-coding
mm_16746.1	chr2	9594169	9594179	-	1	NA	Intergenic	Intergenic	284426	NM_008091	14462	Mm.313866	NM_008091	ENSMUSG00000015619	Gata3	Gata-3|jal	GATA binding protein 3	protein-coding
mm_128796.1	chr15	66812686	66812710	-	1	NA	5' UTR (NM_009192, exon 2 of 9)	5' UTR (NM_009192, exon 2 of 9)	19131	NM_001029841	20491	Mm.7601	NM_009192	ENSMUSG00000022372	Sla	Slap|Slap-1	src-like adaptor	protein-coding
mm_156272.1	chrX	136834152	136834202	+	1	NA	exon (NM_011123, exon 5 of 7)	exon (NM_011123, exon 5 of 7)	11431	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_140299.1	chr17	85621129	85621164	+	1	NA	5' UTR (NM_011381, exon 1 of 2)	5' UTR (NM_011381, exon 1 of 2)	312	NM_011381	20473	Mm.370208	NM_011381	ENSMUSG00000038805	Six3	E130112M24Rik|Six3a|Six3alpha|Six3b|Six3beta	sine oculis-related homeobox 3	protein-coding
mm_55619.1	chr6	72234472	72234543	-	1	NA	exon (NM_153778, exon 1 of 3)	exon (NM_153778, exon 1 of 3)	1070	NM_153778	71093	Mm.87449	NM_153778	ENSMUSG00000037621	Atoh8	4933425C05Rik|Hath6|Math6|bHLHa21|okadin	atonal bHLH transcription factor 8	protein-coding
mm_94635.1	chr11	16871018	16871024	+	1	NA	exon (NM_007912, exon 8 of 16)	exon (NM_007912, exon 8 of 16)	80261	NR_110421	72735	Mm.268598	NR_015469		Eldr	2810442I21Rik|4930500E12Rik|Fabl	Egfr long non-coding downstream RNA	ncRNA
mm_91581.1	chr10	40142248	40142260	-	1	NA	promoter-TSS (NM_028247)	promoter-TSS (NM_028247)	0	NM_028247	72472	Mm.186778	NM_028247	ENSMUSG00000019838	Slc16a10	2610103N14Rik|9830169E08|Mct10|PRO0813|TAT1	solute carrier family 16 (monocarboxylic acid transporters), member 10	protein-coding
mm_92275.1	chr10	71235318	71235339	-	1	NA	intron (NM_009360, intron 3 of 6)	intron (NM_009360, intron 3 of 6)	2716	NM_009360	21780	Mm.229292	NM_009360	ENSMUSG00000003923	Tfam	AI661103|Hmgts|mtTFA|tsHMG	transcription factor A, mitochondrial	protein-coding
mm_109881.1	chr12	4918274	4918284	-	1	NA	intron (NM_001099628, intron 1 of 30)	intron (NM_001099628, intron 1 of 30)	926	NM_001099628	320817	Mm.210966	NM_001099628	ENSMUSG00000052812	Atad2b	1110014E10Rik|BC032887|C79189|D530031C13Rik	ATPase family, AAA domain containing 2B	protein-coding
mm_144911.1	chr18	37447642	37447674	+	1	NA	promoter-TSS (NM_053139)	promoter-TSS (NM_053139)	1	NM_053139	93885	Mm.196699	NM_053139	ENSMUSG00000044043	Pcdhb14	2210006M07Rik|Pcdhb17|PcdhbN	protocadherin beta 14	protein-coding
mm_36422.1	chr4	81442744	81442754	-	1	NA	promoter-TSS (NM_001305286)	promoter-TSS (NM_001305286)	66	NM_010820	17475	Mm.153039	NM_010820	ENSMUSG00000028402	Mpdz	AI225843|B930003D11Rik|MUPP1	multiple PDZ domain protein	protein-coding
mm_113352.1	chr13	31808834	31808848	+	1	NA	exon (NM_008592, exon 1 of 1)	exon (NM_008592, exon 1 of 1)	2195	NM_008592	17300	Mm.12949	NM_008592	ENSMUSG00000050295	Foxc1	FREAC3|Fkh1|Mf1|Mf4|ch|fkh-1|frkhda	forkhead box C1	protein-coding
mm_54365.1	chr6	31126495	31126503	-	1	NA	intron (NR_110471, intron 3 of 3)	intron (NR_110471, intron 3 of 3)	-63406	NR_029532	387223		NR_029532	ENSMUSG00000065604	Mir29b-1	Mirn29b|Mirn29b-1|mir-29b-1	microRNA 29b-1	ncRNA
mm_77589.1	chr8	123883082	123883112	-	1	NA	Intergenic	Intergenic	11678	NM_001272041	11459	Mm.214950	NM_009606	ENSMUSG00000031972	Acta1	AA959943|Acta-2|Acts|Actsk-1	actin, alpha 1, skeletal muscle	protein-coding
mm_112087.1	chr12	112674375	112674385	-	1	NA	promoter-TSS (NM_001165894)	promoter-TSS (NM_001165894)	-104	NM_009652	11651	Mm.6645	NM_009652	ENSMUSG00000001729	Akt1	Akt|LTR-akt|PKB|PKB/Akt|PKBalpha|Rac	thymoma viral proto-oncogene 1	protein-coding
mm_73342.1	chr8	105345340	105345342	+	1	NA	intron (NM_177699, intron 1 of 21)	intron (NM_177699, intron 1 of 21)	2629	NM_177699	234686	Mm.87724	NM_177699	ENSMUSG00000014778	Fhod1	BC017144|FHOS|FHOS1	formin homology 2 domain containing 1	protein-coding
mm_137137.1	chr17	23604672	23604683	+	1	NA	intron (NM_001289482, intron 1 of 3)	ID_B1|SINE|B4	3851	NM_001289482	332221	Mm.270315	NM_001033425	ENSMUSG00000023902	Zscan10	BC068284|Zfp206|Zkscan10|Znf206	zinc finger and SCAN domain containing 10	protein-coding
mm_89905.1	chr10	111164870	111164882	+	1	NA	promoter-TSS (NM_001003717)	promoter-TSS (NM_001003717)	74	NM_175489	237542	Mm.220204	NM_175489	ENSMUSG00000020189	Osbpl8	AA536976|AA536995|C730029P18Rik|D330025H14Rik|ORP-8	oxysterol binding protein-like 8	protein-coding
mm_61949.1	chr7	90195453	90195463	+	1	NA	intron (NM_001252520, intron 18 of 20)	intron (NM_001252520, intron 18 of 20)	65226	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_100475.1	chr11	120145129	120145130	+	1	NA	intron (NM_024249, intron 2 of 16)	intron (NM_024249, intron 2 of 16)	6222	NM_001164799	72055	Mm.253403	NM_024249	ENSMUSG00000061306	Slc38a10	1810073N04Rik	solute carrier family 38, member 10	protein-coding
mm_126091.1	chr15	77906035	77906041	+	1	NA	Intergenic	B1_Mur3|SINE|Alu	22956	NM_019913	56551	Mm.291917	NM_019913	ENSMUSG00000005354	Txn2	2510006J11Rik|AI788873|Trx2	thioredoxin 2	protein-coding
mm_7279.1	chr1	97661022	97661033	-	1	NA	intron (NM_133825, intron 1 of 2)	CpG	991	NM_133825	52392	Mm.12309	NM_133825	ENSMUSG00000044768	D1Ertd622e	AI987691|AW047450	DNA segment, Chr 1, ERATO Doi 622, expressed	protein-coding
mm_123914.1	chr14	73362689	73362743	-	1	NA	3' UTR (NM_008410, exon 6 of 6)	3' UTR (NM_008410, exon 6 of 6)	22555	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_123072.1	chr14	55713483	55713503	-	1	NA	promoter-TSS (NM_001161715)	promoter-TSS (NM_001161715)	-1	NM_001161715	21816	Mm.41964	NM_019984	ENSMUSG00000022218	Tgm1	2310004J08Rik|Tgase1	transglutaminase 1, K polypeptide	protein-coding
mm_78966.1	chr9	45281095	45281134	+	1	NA	Intergenic	Intergenic	-11965	NM_001324486	16154	Mm.379327	NM_008348	ENSMUSG00000032089	Il10ra	AW553859|CDw210|CDw210a|IL-10R1|IL-10RA|Il10r|mIL-10R	interleukin 10 receptor, alpha	protein-coding
mm_59027.1	chr7	19304026	19304043	+	1	NA	3' UTR (NM_008036, exon 4 of 4)	3' UTR (NM_008036, exon 4 of 4)	6011	NM_008036	14282	Mm.248335	NM_008036	ENSMUSG00000003545	Fosb	-	FBJ osteosarcoma oncogene B	protein-coding
mm_129382.1	chr15	78174091	78174109	-	1	NA	promoter-TSS (NM_025931)	promoter-TSS (NM_025931)	8	NM_025931	67042	Mm.30191	NM_025931	ENSMUSG00000016637	Ift27	2600013G09Rik|Rabl4	intraflagellar transport 27	protein-coding
mm_67727.1	chr7	90129649	90129651	-	1	NA	promoter-TSS (NM_001252521)	promoter-TSS (NM_001252521)	-176	NR_046006	78329	Mm.389940	NR_046006	ENSMUSG00000097162	2310010J17Rik	-	RIKEN cDNA 2310010J17 gene	ncRNA
mm_117339.1	chr13	69534422	69534467	-	1	NA	promoter-TSS (NM_198600)	promoter-TSS (NM_198600)	-580	NM_001169131	210106	Mm.315959	NM_198600	ENSMUSG00000034575	Papd7	LAK-1|POLK|Pols|TRF4|TRF4-1	PAP associated domain containing 7	protein-coding
mm_128406.1	chr15	44706444	44706469	-	1	NA	promoter-TSS (NM_001285844)	promoter-TSS (NM_001285844)	32	NM_001285842	319613	Mm.207715	NM_176998	ENSMUSG00000022340	Sybu	Golsyn	syntabulin (syntaxin-interacting)	protein-coding
mm_18625.1	chr2	68565404	68565417	-	1	NA	Intergenic	RMER21B|LTR|ERV1	-17003	NM_177651	227998	Mm.67562	NM_177651	ENSMUSG00000053896	4933409G03Rik	-	RIKEN cDNA 4933409G03 gene	protein-coding
mm_93396.1	chr10	107547090	107547093	-	1	NA	intron (NM_001081432, intron 35 of 44)	intron (NM_001081432, intron 35 of 44)	-52362	NM_008657	17878	Mm.11	NM_008657	ENSMUSG00000035923	Myf6	MRF4|bHLHc4|herculin	myogenic factor 6	protein-coding
mm_21136.1	chr2	154213008	154213031	-	1	NA	exon (NM_153418, exon 9 of 16)	exon (NM_153418, exon 9 of 16)	-10723	NM_144890	228802	Mm.167411	NM_144890	ENSMUSG00000038572	Bpifb5	Lplunc5	BPI fold containing family B, member 5	protein-coding
mm_103251.1	chr11	70970763	70970781	-	1	NA	promoter-TSS (NM_001276406)	promoter-TSS (NM_001276406)	572	NM_001252415	69723	Mm.275691	NM_027186	ENSMUSG00000018449	Rpain	2400006N03Rik|Rip	RPA interacting protein	protein-coding
mm_12497.1	chr2	71814247	71814256	+	1	NA	intron (NM_001277970, intron 1 of 24)	intron (NM_001277970, intron 1 of 24)	27312	NM_001277970	16403	Mm.225096	NM_008397	ENSMUSG00000027111	Itga6	5033401O05Rik|AI115430|Cd49f|VLA-6	integrin alpha 6	protein-coding
mm_158836.1	chrX	168672529	168672564	-	1	NA	intron (NM_010832, intron 1 of 11)	intron (NM_010832, intron 1 of 11)	1356	NM_010832	17692	Mm.24248	NM_010832	ENSMUSG00000031358	Msl3	AU018931|Msl31|Msl3l1	male-specific lethal 3 homolog (Drosophila)	protein-coding
mm_148786.1	chr19	6114851	6114862	+	1	NA	exon (NM_001009546, exon 16 of 18)	exon (NM_001009546, exon 16 of 18)	3730	NM_133678	66406	Mm.303924	NM_133678	ENSMUSG00000024790	Sac3d1	2410004C24Rik|AU015683|shd1	SAC3 domain containing 1	protein-coding
mm_39490.1	chr5	20950957	20950972	+	1	NA	promoter-TSS (NR_030699)	promoter-TSS (NR_030699)	-25	NR_030699	320770	Mm.491217	NR_030699	ENSMUSG00000101013	A630072M18Rik	Aptr	RIKEN cDNA A630072M18 gene	ncRNA
mm_67703.1	chr7	89527536	89527548	-	1	NA	Intergenic	Intergenic	-9956	NM_029614	76453	Mm.250438	NM_029614	ENSMUSG00000039405	Prss23	2310046G15Rik|4930479H08Rik|AI790574|Spuve	protease, serine 23	protein-coding
mm_143574.1	chr17	74316127	74316137	-	1	NA	promoter-TSS (NM_001146224)	promoter-TSS (NM_001146224)	79	NM_001146224	66310	Mm.28536	NM_024428	ENSMUSG00000024067	Dpy30	2810410M20Rik|C87842	dpy-30, histone methyltransferase complex regulatory subunit	protein-coding
mm_36295.1	chr4	66346158	66346160	-	1	NA	intron (NM_019514, intron 1 of 21)	intron (NM_019514, intron 1 of 21)	58324	NM_019514	56079	Mm.445312	NM_019514	ENSMUSG00000028373	Astn2	1d8|Astnl|bM452J22.1	astrotactin 2	protein-coding
mm_73306.1	chr8	105170697	105170719	+	1	NA	promoter-TSS (NM_001161458)	promoter-TSS (NM_001161458)	34	NM_001161458	12400	Mm.2018	NM_022309	ENSMUSG00000031885	Cbfb	AI893578|PEA2|PEBP2b|Pebp2|Pebpb2	core binding factor beta	protein-coding
mm_105368.1	chr11	103201764	103201786	-	1	NA	intron (NM_001254724, intron 1 of 9)	intron (NM_001254724, intron 1 of 9)	6773	NM_001254724	69441	Mm.380648	NM_027082	ENSMUSG00000020940	1700023F06Rik	-	RIKEN cDNA 1700023F06 gene	protein-coding
mm_39443.1	chr5	17142231	17142269	+	1	NA	Intergenic	Intergenic	-333872	NM_027609	70935	Mm.332225	NM_027609	ENSMUSG00000058643	Speer4f1	4922502J04Rik|SPEER-4F|Speer4f	spermatogenesis associated glutamate (E)-rich protein 4F1	protein-coding
mm_56016.1	chr6	86525991	86526001	-	1	NA	5' UTR (NM_011865, exon 1 of 1)	5' UTR (NM_011865, exon 1 of 1)	169	NM_011865	23983	Mm.274146	NM_011865	ENSMUSG00000051695	Pcbp1	WBP17|[a]CP-1|alphaCP-1|hnRNP E1	poly(rC) binding protein 1	protein-coding
mm_94372.1	chr11	5099407	5099518	+	1	NA	promoter-TSS (NM_007968)	promoter-TSS (NM_007968)	189	NM_177370	279766	Mm.260866	NM_177370	ENSMUSG00000034175	Rhbdd3	Ptag	rhomboid domain containing 3	protein-coding
mm_87114.1	chr10	33256513	33256522	+	1	NA	promoter-TSS (NR_040657)	promoter-TSS (NR_040657)	-160	NR_040657	442820	Mm.490725	NR_040657		D830005E20Rik	-	RIKEN cDNA D830005E20 gene	ncRNA
mm_156262.1	chrX	136831103	136831121	+	1	NA	exon (NM_011123, exon 2 of 7)	exon (NM_011123, exon 2 of 7)	8366	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_153729.1	chr19	44407832	44407877	-	1	NA	promoter-TSS (NM_009127)	promoter-TSS (NM_009127)	-145	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_139.1	chr1	10993308	10993331	+	1	NA	promoter-TSS (NM_029525)	promoter-TSS (NM_029525)	-146	NM_029525	109294	Mm.123247	NM_029525	ENSMUSG00000048960	Prex2	6230420N16Rik|AI316880|AI553603|C030045D06Rik|D430013K02|Depdc2|P-Rex2	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	protein-coding
mm_87301.1	chr10	42534991	42535019	+	1	NA	3' UTR (NM_017472, exon 4 of 4)	3' UTR (NM_017472, exon 4 of 4)	32951	NM_017472	54198	Mm.277870	NM_017472	ENSMUSG00000019804	Snx3	SDP3	sorting nexin 3	protein-coding
mm_110219.1	chr12	28623457	28623463	-	1	NA	promoter-TSS (NM_027866)	promoter-TSS (NM_027866)	-130	NM_027866	71693	Mm.30724	NM_027866	ENSMUSG00000036655	Colec11	CL-K1	collectin sub-family member 11	protein-coding
mm_111012.1	chr12	78980744	78980754	-	1	NA	intron (NM_178745, intron 1 of 2)	intron (NM_178745, intron 1 of 2)	2729	NM_001170401	268567	Mm.341747	NM_178745	ENSMUSG00000046157	Tmem229b	6330442E10Rik|9830138K24|AU019070	transmembrane protein 229B	protein-coding
mm_171221.1	chr3	59767297	59767301	+	1	NA	Intergenic	L1Md_F3|LINE|L1	37513	NM_001101531	433597	Mm.297801	NM_001101531	ENSMUSG00000090527	Gm5538	-	predicted gene 5538	protein-coding
mm_163109.1	chr11	70214983	70214992	+	1	NA	exon (NM_153081, exon 3 of 5)	exon (NM_153081, exon 3 of 5)	1077	NM_153081	216867	Mm.289238	NM_153081	ENSMUSG00000040938	Slc16a11	AB041591|MCT 11|MNCb-2717	solute carrier family 16 (monocarboxylic acid transporters), member 11	protein-coding
mm_137026.1	chr17	17882875	17882912	+	1	NA	intron (NM_013521, intron 1 of 1)	intron (NM_013521, intron 1 of 1)	1046	NM_013521	14293	Mm.56951	NM_013521	ENSMUSG00000045551	Fpr1	FPR|LXA4R|fMLF-R	formyl peptide receptor 1	protein-coding
mm_61527.1	chr7	78916655	78916688	+	1	NA	exon (NM_020583, exon 3 of 4)	exon (NM_020583, exon 3 of 4)	2436	NM_001113527	57444	Mm.322843	NM_020583	ENSMUSG00000039236	Isg20	1600023I01Rik|2010107M23Rik|20kDa|DnaQL|HEM45	interferon-stimulated protein	protein-coding
mm_61383.1	chr7	72326481	72326504	+	1	NA	Intergenic	Intergenic	-19897	NM_001024703	244049	Mm.217412	NM_001024703	ENSMUSG00000032776	Mctp2	Gm489	multiple C2 domains, transmembrane 2	protein-coding
mm_145134.1	chr18	44828472	44828536	+	1	NA	promoter-TSS (NM_001163013)	promoter-TSS (NM_001163013)	-161	NM_001163013	240255	Mm.244482	NM_001163013	ENSMUSG00000034653	Ythdc2	3010002F02Rik|BC037178	YTH domain containing 2	protein-coding
mm_90374.1	chr10	127181913	127181922	+	1	NA	TTS (NM_028027)	TTS (NM_028027)	-1272	NM_177615	216441	Mm.248373	NM_177615	ENSMUSG00000040441	Slc26a10	C78409|D630010I07	solute carrier family 26, member 10	protein-coding
mm_61054.1	chr7	49910260	49910281	+	1	NA	promoter-TSS (NM_001146013)	promoter-TSS (NM_001146013)	-29	NM_001146013	104245	Mm.207053	NM_148931	ENSMUSG00000039728	Slc6a5	Glyt2|prestin	solute carrier family 6 (neurotransmitter transporter, glycine), member 5	protein-coding
mm_76519.1	chr8	87470669	87470677	-	1	NA	intron (NM_019626, intron 2 of 2)	CpG	1919	NM_019626	12404	Mm.4880	NM_019626	ENSMUSG00000031654	Cbln1	AI323299	cerebellin 1 precursor protein	protein-coding
mm_95594.1	chr11	53332468	53332481	+	1	NA	exon (NM_026479, exon 4 of 4)	exon (NM_026479, exon 4 of 4)	7785	NM_026479	67966	Mm.288072	NM_026479	ENSMUSG00000018239	Zcchc10	2410141K03Rik|AA675321|D11Ertd416e	zinc finger, CCHC domain containing 10	protein-coding
mm_44728.1	chr5	31047999	31048009	-	1	NA	promoter-TSS (NM_177870)	promoter-TSS (NM_177870)	75	NM_177870	330064	Mm.205463	NM_177870	ENSMUSG00000006641	Slc5a6	E430023I20	solute carrier family 5 (sodium-dependent vitamin transporter), member 6	protein-coding
mm_937.1	chr1	55892070	55892107	+	1	NA	Intergenic	Intergenic	-39153	NR_045837	329159	Mm.98697	NR_045837	ENSMUSG00000099950	9130227L01Rik	-	RIKEN cDNA 9130227L01 gene	ncRNA
mm_153562.1	chr19	42298077	42298093	-	1	NA	intron (NM_145123, intron 10 of 14)	intron (NM_145123, intron 10 of 14)	-17915	NR_037246	100526549		NR_037246	ENSMUSG00000093234	Mir3085	mir-3085|mmu-mir-3085	microRNA 3085	ncRNA
mm_7995.1	chr1	134326948	134326956	-	1	NA	exon (NM_001144855, exon 7 of 29)	exon (NM_001144855, exon 7 of 29)	5976	NM_001144855	68507	Mm.295105	NM_001144855	ENSMUSG00000026458	Ppfia4	100042382|1110008G13Rik|AI448359|AI852265|C81506|Gm3812	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 4	protein-coding
mm_107038.1	chr12	13564133	13564136	+	1	NA	intron (NM_027706, intron 50 of 51)	intron (NM_027706, intron 50 of 51)	63512	NR_136761	102639399	Mm.122052	NR_136761		Gm35725	-	predicted gene, 35725	ncRNA
mm_19178.1	chr2	84389699	84389707	-	1	NA	intron (NM_018782, intron 2 of 15)	intron (NM_018782, intron 2 of 15)	35563	NM_018782	54598	Mm.75467	NM_018782	ENSMUSG00000059588	Calcrl	AV071593|CRLR	calcitonin receptor-like	protein-coding
mm_110493.1	chr12	53309837	53309865	-	1	NA	intron (NM_013780, intron 1 of 11)	intron (NM_013780, intron 1 of 11)	61174	NM_013780	27386	Mm.247044	NM_013780	ENSMUSG00000021010	Npas3	4930423H22Rik|bHLHe12	neuronal PAS domain protein 3	protein-coding
mm_78484.1	chr9	32697928	32697939	+	1	NA	intron (NM_011808, intron 1 of 7)	intron (NM_011808, intron 1 of 7)	1891	NM_001038642	23871	Mm.292415	NM_011808	ENSMUSG00000032035	Ets1	AI196000|AI448617|D230050P06|Ets-1|Tpl1|vs	E26 avian leukemia oncogene 1, 5' domain	protein-coding
mm_148197.1	chr18	79109291	79109320	-	1	NA	promoter-TSS (NM_053099)	promoter-TSS (NM_053099)	86	NM_053099	240427	Mm.312871	NM_053099	ENSMUSG00000024548	Setbp1	C130092E12|Seb|mKIAA0437	SET binding protein 1	protein-coding
mm_168088.1	chr10	127620944	127620945	-	1	NA	5' UTR (NM_008512, exon 1 of 89)	5' UTR (NM_008512, exon 1 of 89)	204	NM_008512	16971	Mm.271854	NM_008512	ENSMUSG00000040249	Lrp1	A2mr|AI316852|CD91|Lrp|b2b1554Clo	low density lipoprotein receptor-related protein 1	protein-coding
mm_152644.1	chr19	12527560	12527577	-	1	NA	Intergenic	L1MC3|LINE|L1	-25572	NM_172442	207521	Mm.247695	NM_172442	ENSMUSG00000039982	Dtx4	AI449438|BC044798|D930042H13|RNF155	deltex 4, E3 ubiquitin ligase	protein-coding
mm_65821.1	chr7	29156173	29156210	-	1	NA	promoter-TSS (NM_001146023)	promoter-TSS (NM_001146023)	19	NM_001146023	73833	Mm.260890	NM_028661	ENSMUSG00000030590	Fam98c	1110006G06Rik|AI836081|AV026483|B230110F21Rik	family with sequence similarity 98, member C	protein-coding
mm_10156.1	chr2	4389616	4389639	+	1	NA	intron (NM_172475, intron 1 of 22)	intron (NM_172475, intron 1 of 22)	-11349	NM_001177843	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding
mm_94405.1	chr11	5793710	5793726	+	1	NA	exon (NM_001146309, exon 3 of 13)	exon (NM_001146309, exon 3 of 13)	5235	NM_013810	13169	Mm.256925	NM_013810	ENSMUSG00000020476	Dbnl	Abp1|SH3P7|mAbp1	drebrin-like	protein-coding
mm_88715.1	chr10	80156863	80156876	+	1	NA	3' UTR (NM_001305798, exon 8 of 8)	3' UTR (NM_001305798, exon 8 of 8)	7187	NM_001305799	59090	Mm.143813	NM_021565	ENSMUSG00000035621	Midn	3000003C15Rik	midnolin	protein-coding
mm_125430.1	chr15	44427401	44427413	+	1	NA	promoter-TSS (NM_175009)	promoter-TSS (NM_175009)	-704	NM_175009	223527	Mm.291828	NM_175009	ENSMUSG00000022338	Eny2	1810057B09Rik|6720481I12|DC6|Ey2	enhancer of yellow 2 homolog (Drosophila)	protein-coding
mm_120996.1	chr14	79426592	79426603	+	1	NA	promoter-TSS (NM_001024135)	promoter-TSS (NM_001024135)	86	NM_001024135	211255	Mm.284526	NM_001024135	ENSMUSG00000043881	Kbtbd7	1110008P08Rik|AU045792|Gm295	kelch repeat and BTB (POZ) domain containing 7	protein-coding
mm_146251.1	chr18	77779847	77779897	+	1	NA	exon (NM_007505, exon 7 of 12)	exon (NM_007505, exon 7 of 12)	6104	NM_007505	11946	Mm.276137	NM_007505	ENSMUSG00000025428	Atp5a1	AI035633|AL022851|AL023067|Atpm|D18Ertd206e|Mom2	ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1	protein-coding
mm_83151.1	chr9	40456231	40456241	-	1	NA	promoter-TSS (NM_172768)	promoter-TSS (NM_172768)	-472	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_133993.1	chr16	4679704	4679747	-	1	NA	promoter-TSS (NM_030205)	promoter-TSS (NM_030205)	-5	NM_030205	78885	Mm.325512	NM_030205	ENSMUSG00000039637	Coro7	0610011B16Rik|AW048373|AW556392	coronin 7	protein-coding
mm_77595.1	chr8	123892262	123892270	-	1	NA	exon (NM_009606, exon 6 of 7)	exon (NM_009606, exon 6 of 7)	2509	NM_001272041	11459	Mm.214950	NM_009606	ENSMUSG00000031972	Acta1	AA959943|Acta-2|Acts|Actsk-1	actin, alpha 1, skeletal muscle	protein-coding
mm_79106.1	chr9	46268690	46268703	+	1	NA	promoter-TSS (NM_080434)	promoter-TSS (NM_080434)	88	NM_080434	66113	Mm.29738	NM_080434	ENSMUSG00000032079	Apoa5	1300007O05Rik|Apoav|RAP3	apolipoprotein A-V	protein-coding
mm_68584.1	chr7	116031093	116031122	-	1	NA	promoter-TSS (NM_001025560)	promoter-TSS (NM_001025560)	-60	NM_001025560	20679	Mm.323365	NM_011445	ENSMUSG00000051910	Sox6	AI987981|SOX-LZ	SRY (sex determining region Y)-box 6	protein-coding
mm_29246.1	chr3	107218194	107218195	-	1	NA	exon (NM_001111143, exon 4 of 9)	exon (NM_001111143, exon 4 of 9)	3538	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_45701.1	chr5	83354925	83354944	-	1	NA	exon (NM_153801, exon 1 of 12)	exon (NM_153801, exon 1 of 12)	261	NM_153801	243078	Mm.126783	NM_153801	ENSMUSG00000049537	Tecrl	D330017N19Rik|Srd5a2l2	trans-2,3-enoyl-CoA reductase-like	protein-coding
mm_128539.1	chr15	54920116	54920138	-	1	NA	promoter-TSS (NM_001285995)	promoter-TSS (NM_001285995)	19	NM_015744	18606	Mm.250256	NM_015744	ENSMUSG00000022425	Enpp2	ATX|E-NPP 2|Npps2|PD-Ialpha|Pdnp2|lysoPLD	ectonucleotide pyrophosphatase/phosphodiesterase 2	protein-coding
mm_99167.1	chr11	100715266	100715273	+	1	NA	TTS (NM_029307)	TTS (NM_029307)	1419	NM_029307	75482	Mm.46175	NM_029307	ENSMUSG00000017832	Hspb9	1700007H20Rik	heat shock protein, alpha-crystallin-related, B9	protein-coding
mm_151018.1	chr19	46763428	46763431	+	1	NA	intron (NM_033569, intron 1 of 7)	intron (NM_033569, intron 1 of 7)	1820	NM_001102471	94219	Mm.306903	NM_033569	ENSMUSG00000064105	Cnnm2	AU015877|AW048635|Acdp2|Clp2	cyclin M2	protein-coding
mm_165261.1	chr2	73038450	73038460	-	1	NA	Intergenic	Intergenic	-58009	NM_001018042	20687	Mm.124328	NM_011450	ENSMUSG00000027109	Sp3	D130027J01Rik	trans-acting transcription factor 3	protein-coding
mm_90200.1	chr10	120230360	120230363	+	1	NA	intron (NM_025431, intron 2 of 2)	HAL1|LINE|L1	3301	NM_025431	66225	Mm.291755	NM_025431	ENSMUSG00000020224	Llph	1190005P17Rik	LLP homolog, long-term synaptic facilitation (Aplysia)	protein-coding
mm_156704.1	chrX	159627040	159627076	+	1	NA	promoter-TSS (NM_001135727)	promoter-TSS (NM_001135727)	-214	NM_001135727	58194	Mm.286495	NM_021389	ENSMUSG00000040990	Sh3kbp1	1200007H22Rik|1700125L08Rik|5830464D22Rik|AI447724|Cin85|IN85|Ruk|Seta	SH3-domain kinase binding protein 1	protein-coding
mm_131287.1	chr16	11254493	11254519	+	1	NA	promoter-TSS (NM_001130008)	promoter-TSS (NM_001130008)	-61	NR_035466	100316833		NR_035466	ENSMUSG00000088544	Mir1945	mir-1945|mmu-mir-1945	microRNA 1945	ncRNA
mm_12741.1	chr2	79065559	79065569	+	1	NA	Intergenic	Intergenic	-189862	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D|Itga4B	integrin alpha 4	protein-coding
mm_64688.1	chr7	4515968	4515982	-	1	NA	promoter-TSS (NM_001277904)	promoter-TSS (NM_001277904)	0	NM_001277903	21955	Mm.358643	NM_011618	ENSMUSG00000064179	Tnnt1	AW146156|Tnt|sTnT|ssTnT	troponin T1, skeletal, slow	protein-coding
mm_105662.1	chr11	107348196	107348213	-	1	NA	intron (NM_145823, intron 1 of 9)	intron (NM_145823, intron 1 of 9)	122516	NM_145823	71795	Mm.397413	NM_145823	ENSMUSG00000040430	Pitpnc1	1110020B03Rik|5830436L09Rik|AI662802|AI851387|C330017I21Rik|Dnr411|RDGBB|RDGBB1|rdgB-beta	phosphatidylinositol transfer protein, cytoplasmic 1	protein-coding
mm_108069.1	chr12	73941791	73941809	+	1	NA	exon (NM_010431, exon 11 of 15)	exon (NM_010431, exon 11 of 15)	-22730	NM_178392	75627	Mm.25937	NM_178392	ENSMUSG00000021113	Snapc1	2700033G17Rik|AU015787	small nuclear RNA activating complex, polypeptide 1	protein-coding
mm_16634.1	chr2	5760701	5760713	-	1	NA	Intergenic	RLTR16B_MM|LTR|ERVK	-45945	NM_177343	227541	Mm.191949	NM_177343	ENSMUSG00000039145	Camk1d	A630059D12Rik|CKLiK|CaMKIdelta|E030025C11Rik|mCKLiK	calcium/calmodulin-dependent protein kinase ID	protein-coding
mm_41107.1	chr5	87775785	87775802	+	1	NA	exon (NM_001304768, exon 2 of 13)	exon (NM_001304768, exon 2 of 13)	1343	NM_007785	12993	Mm.4908	NM_007785	ENSMUSG00000061937	Csn1s2a	Csng|PP22	casein alpha s2-like A	protein-coding
mm_135108.1	chr16	35769329	35769348	-	1	NA	promoter-TSS (NM_153550)	promoter-TSS (NM_153550)	18	NM_153550	224132	Mm.24094	NM_153550	ENSMUSG00000022848	Dirc2	RCC4	disrupted in renal carcinoma 2 (human)	protein-coding
mm_34451.1	chr4	148039036	148039087	+	1	NA	promoter-TSS (NM_010840)	promoter-TSS (NM_010840)	-16	NM_010840	17769	Mm.89959	NM_010840	ENSMUSG00000029009	Mthfr	AI323986	5,10-methylenetetrahydrofolate reductase	protein-coding
mm_29571.1	chr3	116968773	116968789	-	1	NA	5' UTR (NM_023245, exon 1 of 8)	5' UTR (NM_023245, exon 1 of 8)	171	NM_023245	114301	Mm.253736	NM_023245	ENSMUSG00000033377	Palmd	4631423C22Rik|PALML	palmdelphin	protein-coding
mm_37178.1	chr4	117251880	117251891	-	1	NA	promoter-TSS (NM_001033774)	promoter-TSS (NM_001033774)	32	NM_001145637	381544	Mm.23504	NM_001033774	ENSMUSG00000060268	Gm1661	Gm1662|Ncrna00082	predicted gene 1661	protein-coding
mm_14.1	chr1	4857761	4857796	+	1	NA	promoter-TSS (NM_011541)	promoter-TSS (NM_011541)	84	NM_011541	21399	Mm.207263	NM_011541	ENSMUSG00000033813	Tcea1	S-II	transcription elongation factor A (SII) 1	protein-coding
mm_66882.1	chr7	58740536	58740547	-	1	NA	intron (NM_009728, intron 2 of 20)	intron (NM_009728, intron 2 of 20)	82339	NM_009728	11982	Mm.135129	NM_009728	ENSMUSG00000025324	Atp10a	Atp10c|pfatp	ATPase, class V, type 10A	protein-coding
mm_114226.1	chr13	56505889	56505919	+	1	NA	Intergenic	Intergenic	-16568	NM_001346732	213311	Mm.233904	NM_178674	ENSMUSG00000035509	Fbxl21	D630045D17Rik|FBL3B|FBXL3B|Psttm	F-box and leucine-rich repeat protein 21	protein-coding
mm_112729.1	chr13	19194063	19194108	+	1	NA	Intergenic	Intergenic	201728	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_137196.1	chr17	23853520	23853541	+	1	NA	promoter-TSS (NM_027220)	promoter-TSS (NM_027220)	-242	NM_027220	69814	Mm.244143	NM_027220	ENSMUSG00000048992	Prss32	2010001P08Rik|mT5|tryptase-5	protease, serine 32	protein-coding
mm_80672.1	chr9	90198689	90198722	+	1	NA	intron (NM_001326294, intron 22 of 22)	intron (NM_001326294, intron 22 of 22)	35727	NM_001311115	108153	Mm.102141	NM_001003911	ENSMUSG00000032363	Adamts7	ADAM-TS7|ADAMTS7B	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 7	protein-coding
mm_156242.1	chrX	136245066	136245102	+	1	NA	promoter-TSS (NM_011712)	promoter-TSS (NM_011712)	4	NM_011712	22381	Mm.512	NM_011712	ENSMUSG00000042712	Wbp5	AL024233|Tceal9	WW domain binding protein 5	protein-coding
mm_143762.1	chr17	81627736	81627756	-	1	NA	intron (NR_104580, intron 2 of 8)	intron (NR_104580, intron 2 of 8)	110641	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_113651.1	chr13	42305028	42305038	+	1	NA	exon (NM_010104, exon 3 of 5)	exon (NM_010104, exon 3 of 5)	3557	NM_010104	13614	Mm.14543	NM_010104	ENSMUSG00000021367	Edn1	ET-1|PPET1|preproET	endothelin 1	protein-coding
mm_114487.1	chr13	69772777	69772784	+	1	NA	Intergenic	RMER17C2|LTR|ERVK	-32883	NM_001145162	76980	Mm.23960	NM_001145162	ENSMUSG00000052981	Ube2ql1	3110006E14Rik	ubiquitin-conjugating enzyme E2Q family-like 1	protein-coding
mm_50064.1	chr6	41188313	41188334	+	1	NA	Intergenic	Intergenic	-113949	NM_011646	22074	Mm.383263	NM_011646	ENSMUSG00000054106	Try4	0910001B19Rik|Td	trypsin 4	protein-coding
mm_152879.1	chr19	24518730	24518754	-	1	NA	intron (NM_008846, intron 1 of 14)	intron (NM_008846, intron 1 of 14)	37085	NM_008846	18719	Mm.217214	NM_008846	ENSMUSG00000024867	Pip5k1b	PI4P5K-I[b]|PIP5K1-beta|PIP5KIbeta|Pipk5b|STM7	phosphatidylinositol-4-phosphate 5-kinase, type 1 beta	protein-coding
mm_136084.1	chr16	84835558	84835617	-	1	NA	promoter-TSS (NM_016755)	promoter-TSS (NM_016755)	38	NM_016755	11957	Mm.353	NM_016755	ENSMUSG00000022890	Atp5j	CF6	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit F	protein-coding
mm_12777.1	chr2	79328770	79328787	+	1	NA	3' UTR (NM_010576, exon 28 of 28)	3' UTR (NM_010576, exon 28 of 28)	73352	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D|Itga4B	integrin alpha 4	protein-coding
mm_26598.1	chr3	151731527	151731538	+	1	NA	3' UTR (NM_133871, exon 8 of 8)	3' UTR (NM_133871, exon 8 of 8)	18427	NM_133871	99899	Mm.30756	NM_133871	ENSMUSG00000028037	Ifi44	A430056A10Rik|AW261460|MTAP44|p44	interferon-induced protein 44	protein-coding
mm_142113.1	chr17	35837032	35837078	-	1	NA	intron (NM_011655, intron 1 of 3)	intron (NM_011655, intron 1 of 3)	1246	NM_011655	22154	Mm.273538	NM_011655	ENSMUSG00000001525	Tubb5	AA408537|AI596182|B130022C14Rik|M(beta)5	tubulin, beta 5 class I	protein-coding
mm_120779.1	chr14	74641354	74641376	+	1	NA	5' UTR (NM_172812, exon 1 of 3)	5' UTR (NM_172812, exon 1 of 3)	525	NM_172812	15558	Mm.214351	NM_172812	ENSMUSG00000034997	Htr2a	E030013E04|Htr-2|Htr2	5-hydroxytryptamine (serotonin) receptor 2A	protein-coding
mm_51342.1	chr6	72549164	72549191	+	1	NA	promoter-TSS (NM_001042534)	promoter-TSS (NM_001042534)	-96	NM_001042534	12332	Mm.18626	NM_007599	ENSMUSG00000056737	Capg	gCap39|mbh1	capping protein (actin filament), gelsolin-like	protein-coding
mm_131087.1	chr16	4880675	4880710	+	1	NA	promoter-TSS (NM_145359)	promoter-TSS (NM_145359)	-841	NM_145359	207740	Mm.268895	NM_145359	ENSMUSG00000039568	Ubald1	1500031H01Rik|BC013706|Fam100a	UBA-like domain containing 1	protein-coding
mm_51132.1	chr6	68474580	68474585	+	1	NA	Intergenic	Intergenic	852592	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_31203.1	chr4	43727246	43727262	+	1	NA	promoter-TSS (NM_027511)	promoter-TSS (NM_027511)	56	NM_027511	100039781	Mm.18796	NM_027511	ENSMUSG00000071001	Hrct1	3830408D24Rik	histidine rich carboxyl terminus 1	protein-coding
mm_145010.1	chr18	38601499	38601525	+	1	NA	promoter-TSS (NM_011898)	promoter-TSS (NM_011898)	-244	NM_011898	24066	Mm.42038	NM_011898	ENSMUSG00000024427	Spry4	A030006O18Rik|sprouty4	sprouty homolog 4 (Drosophila)	protein-coding
mm_92407.1	chr10	76711653	76711663	-	1	NA	exon (NM_009933, exon 31 of 35)	exon (NM_009933, exon 31 of 35)	14386	NM_009933	12833	Mm.2509	NM_009933	ENSMUSG00000001119	Col6a1	AI747156|Col6a-1	collagen, type VI, alpha 1	protein-coding
mm_168108.1	chr10	14746172	14746191	-	1	NA	intron (NR_045824, intron 3 of 5)	intron (NR_045824, intron 3 of 5)	-14108	NM_008703	18101	Mm.487342	NM_008703	ENSMUSG00000019865	Nmbr	BB182387	neuromedin B receptor	protein-coding
mm_132010.1	chr16	25861190	25861197	+	1	NA	intron (NM_001127259, intron 4 of 13)	intron (NM_001127259, intron 4 of 13)	59277	NM_001127264	22061	Mm.20894	NM_011641	ENSMUSG00000022510	Trp63	AI462811|Ket|P51/P63|P63|P73l|Tp63|Trp53rp1	transformation related protein 63	protein-coding
mm_54693.1	chr6	39447575	39447581	-	1	NA	Intergenic	B3|SINE|B2	-27209	NM_018810	54484	Mm.270484	NM_018810	ENSMUSG00000029922	Mkrn1	RFP	makorin, ring finger protein, 1	protein-coding
mm_74958.1	chr8	26059376	26059381	-	1	NA	exon (NM_207659, exon 15 of 22)	exon (NM_207659, exon 15 of 22)	-23231	NR_110583	76604	Mm.437190	NR_110583	ENSMUSG00000085437	1700047A11Rik	4930554C15Rik	RIKEN cDNA 1700047A11 gene	ncRNA
mm_142548.1	chr17	46590468	46590484	-	1	NA	intron (NM_175168, intron 3 of 19)	intron (NM_175168, intron 3 of 19)	-34314	NM_020493	20807	Mm.45044	NM_020493	ENSMUSG00000015605	Srf	AW049942|AW240594	serum response factor	protein-coding
mm_18348.1	chr2	58160115	58160128	-	1	NA	promoter-TSS (NM_139200)	promoter-TSS (NM_139200)	1	NM_139200	227929	Mm.273905	NM_139200	ENSMUSG00000026832	Cytip	A130053M09Rik|AI462064|C80816|Cbp|Cybr|Pscdbp	cytohesin 1 interacting protein	protein-coding
mm_107643.1	chr12	52504064	52504093	+	1	NA	Intergenic	CpG	-11999	NM_009706	11855	Mm.35059	NM_009706	ENSMUSG00000035133	Arhgap5	p190-B|p190B	Rho GTPase activating protein 5	protein-coding
mm_153735.1	chr19	44446253	44446259	-	1	NA	Intergenic	L4_C_Mam|LINE|RTE-X	-38547	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_162279.1	chr1	17097750	17097753	-	1	NA	5' UTR (NM_020604, exon 1 of 5)	5' UTR (NM_020604, exon 1 of 5)	138	NM_020604	57339	Mm.143761	NM_020604	ENSMUSG00000042686	Jph1	ENSMUSG00000054314|JP-1|Jp1	junctophilin 1	protein-coding
mm_153468.1	chr19	41264326	41264338	-	1	NA	promoter-TSS (NM_133352)	promoter-TSS (NM_133352)	-328	NM_133352	107358	Mm.246440	NM_133352	ENSMUSG00000025016	Tm9sf3	1810073M23Rik|2810031D16Rik|AI115521|AI413748|AW146116|AW549777|Smbp|mKIAA4036	transmembrane 9 superfamily member 3	protein-coding
mm_129523.1	chr15	79164478	79164496	-	1	NA	promoter-TSS (NM_011437)	promoter-TSS (NM_011437)	3	NM_011437	20665	Mm.276739	NM_011437	ENSMUSG00000033006	Sox10	Dom|Sox21|gt	SRY (sex determining region Y)-box 10	protein-coding
mm_69644.1	chr7	138909449	138909491	-	1	NA	promoter-TSS (NM_009760)	promoter-TSS (NM_009760)	36	NM_009760	12176	Mm.378890	NM_009760	ENSMUSG00000078566	Bnip3	Nip3	BCL2/adenovirus E1B interacting protein 3	protein-coding
mm_130023.1	chr15	88861994	88862008	-	1	NA	promoter-TSS (NM_145478)	promoter-TSS (NM_145478)	-193	NM_145478	223775	Mm.400129	NM_145478	ENSMUSG00000035828	Pim3	BC026639|Kid1	proviral integration site 3	protein-coding
mm_14336.1	chr2	129592923	129592940	+	1	NA	promoter-TSS (NM_001291022)	promoter-TSS (NM_001291022)	92	NM_001291020	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_169913.1	chr16	55819768	55819772	-	1	NA	intron (NM_001159395, intron 2 of 12)	intron (NM_001159395, intron 2 of 12)	2368	NM_001159394	80859	Mm.247272	NM_030612	ENSMUSG00000035356	Nfkbiz	AA408868|INAP|Mail	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, zeta	protein-coding
mm_71772.1	chr8	66469028	66469032	+	1	NA	3' UTR (NM_001293784, exon 9 of 9)	3' UTR (NM_001293784, exon 9 of 9)	17477	NM_025465	66282	Mm.294985	NM_025465	ENSMUSG00000025591	Tma16	1810029B16Rik	translation machinery associated 16	protein-coding
mm_3373.1	chr1	138963718	138963808	+	1	NA	promoter-TSS (NM_001166501)	promoter-TSS (NM_001166501)	54	NM_001166501	329260	Mm.337604	NM_181347	ENSMUSG00000056268	Dennd1b	4632404N19Rik|4930467M19Rik|6820401H01Rik|F730008N07Rik	DENN/MADD domain containing 1B	protein-coding
mm_128676.1	chr15	60744916	60744918	-	1	NA	Intergenic	Intergenic	-78048	NR_030696	320469	Mm.230853	NM_177166		9930014A18Rik	-	RIKEN cDNA 9930014A18 gene	ncRNA
mm_29909.1	chr3	131474560	131474570	-	1	NA	Intergenic	Intergenic	-90203	NM_001289479	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_83862.1	chr9	54734469	54734523	-	1	NA	promoter-TSS (NM_001025376)	promoter-TSS (NM_001025376)	53	NM_023191	66317	Mm.28437	NM_023191	ENSMUSG00000061559	Wdr61	2700038L12Rik|2810418I05Rik|REC14	WD repeat domain 61	protein-coding
mm_155752.1	chrX	96167369	96167379	+	1	NA	3' UTR (NM_010833, exon 13 of 13)	3' UTR (NM_010833, exon 13 of 13)	71329	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_56649.1	chr6	113377788	113377855	-	1	NA	promoter-TSS (NM_026552)	promoter-TSS (NM_026552)	-292	NM_026552	68089	Mm.289306	NM_026552	ENSMUSG00000079426	Arpc4	20kDa|5330419I20Rik|AI327076|p20-Arc	actin related protein 2/3 complex, subunit 4	protein-coding
mm_173058.1	chrX	125936996	125936997	+	1	NA	Intergenic	Intergenic	897008	NM_177705	237029	Mm.60998	NM_177705	ENSMUSG00000058670	4932411N23Rik	-	RIKEN cDNA 4932411N23 gene	protein-coding
mm_104217.1	chr11	88349197	88349200	-	1	NA	intron (NM_054043, intron 11 of 13)	(A)n|Simple_repeat|Simple_repeat	-3575	NR_039545	100628571		NR_039545	ENSMUSG00000092985	Mir378b	mir-378b|mmu-mir-378b	microRNA 378b	ncRNA
mm_88638.1	chr10	79927040	79927088	+	1	NA	promoter-TSS (NM_001288626)	promoter-TSS (NM_001288626)	21	NM_007880	13496	Mm.301282	NM_007880	ENSMUSG00000019564	Arid3a	Bright|Dri1|Dril1	AT rich interactive domain 3A (BRIGHT-like)	protein-coding
mm_66198.1	chr7	34230254	34230276	-	1	NA	promoter-TSS (NM_008155)	promoter-TSS (NM_008155)	71	NM_008155	14751	Mm.589	NM_008155	ENSMUSG00000036427	Gpi1	Amf|Gpi|Gpi-1|Gpi-1r|Gpi-1s|Gpi-1t|Gpi1-r|Gpi1-s|Gpi1-t|Gpi1s|MF|NK|NK/GPI|Nlk|Org|Pgi|Phi	glucose phosphate isomerase 1	protein-coding
mm_57759.1	chr6	129232934	129232955	-	1	NA	non-coding (NR_040268, exon 4 of 4)	non-coding (NR_040268, exon 4 of 4)	5101	NR_040265	76432	Mm.261738	NR_040265	ENSMUSG00000097354	2310001H17Rik	AI646108	RIKEN cDNA 2310001H17 gene	ncRNA
mm_56368.1	chr6	93913539	93913562	-	1	NA	promoter-TSS (NR_104594)	promoter-TSS (NR_104594)	140	NM_001286788	14924	Mm.217216	NM_010367	ENSMUSG00000045095	Magi1	AIP3|BAP1|Baiap1|Gukmi1|MAGI1c|Magi-1|TNRC19|WWP3|mKIAA4129	membrane associated guanylate kinase, WW and PDZ domain containing 1	protein-coding
mm_124168.1	chr14	93718037	93718050	-	1	NA	intron (NM_001346722, intron 2 of 4)	A-rich|Low_complexity|Low_complexity	170845	NM_001271800	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding
mm_130035.1	chr15	88978568	88978597	-	1	NA	promoter-TSS (NM_133241)	promoter-TSS (NM_133241)	-29	NM_133241	170790	Mm.32780	NM_133241	ENSMUSG00000035805	Mlc1	AW048630|BB074274|Kiaa0027-hp|LVM|MLC|VL|WKL1|mKIAA0027	megalencephalic leukoencephalopathy with subcortical cysts 1 homolog (human)	protein-coding
mm_44578.1	chr5	24842510	24842520	-	1	NA	promoter-TSS (NM_053075)	promoter-TSS (NM_053075)	-154	NM_053075	19744	Mm.319175	NM_053075	ENSMUSG00000028945	Rheb	Rheb1	Ras homolog enriched in brain	protein-coding
mm_163121.1	chr11	75765485	75765499	+	1	NA	3' UTR (NM_009536, exon 6 of 6)	3' UTR (NM_009536, exon 6 of 6)	-30317	NR_136933	102641247	Mm.411386	NR_136932		Gm12339	OTTMUSG00000006218	predicted gene 12339	ncRNA
mm_171225.1	chr3	61744577	61744583	-	1	NA	Intergenic	L1Md_A|LINE|L1	380073	NM_028712	74012	Mm.422674	NM_028712	ENSMUSG00000036894	Rap2b	4021402C18Rik|AA408554	RAP2B, member of RAS oncogene family	protein-coding
mm_38603.1	chr4	141859717	141859742	-	1	NA	3' UTR (NM_025994, exon 4 of 4)	3' UTR (NM_025994, exon 4 of 4)	-13370	NM_001033875	76701	Mm.489680	NM_001033875	ENSMUSG00000062478	Ctrc	1810044E12Rik	chymotrypsin C (caldecrin)	protein-coding
mm_40443.1	chr5	53591401	53591407	+	1	NA	intron (NM_001080927, intron 1 of 10)	intron (NM_001080927, intron 1 of 10)	918	NM_001080927	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_4298.1	chr1	171787980	171787985	+	1	NA	exon (NM_013730, exon 4 of 7)	exon (NM_013730, exon 4 of 7)	20850	NM_013730	27218	Mm.103648	NM_013730	ENSMUSG00000015316	Slamf1	4933415F16|AA177906|CD150|CDw150|ESTM51|IPO-3|Slam	signaling lymphocytic activation molecule family member 1	protein-coding
mm_90678.1	chr10	128909405	128909429	+	1	NA	promoter-TSS (NM_007653)	promoter-TSS (NM_007653)	72	NM_001282966	12512	Mm.371552	NM_007653	ENSMUSG00000025351	Cd63	C75951|ME491|Tspan30	CD63 antigen	protein-coding
mm_115968.1	chr13	23967156	23967179	-	1	NA	intron (NM_145399, intron 6 of 10)	intron (NM_145399, intron 6 of 10)	24047	NM_145399	214189	Mm.255667	NM_145399	ENSMUSG00000021337	Scgn	-	secretagogin, EF-hand calcium binding protein	protein-coding
mm_122546.1	chr14	47993798	47993805	-	1	NA	Intergenic	RMER17B2|LTR|ERVK	94937	NR_045959	73961	Mm.390702	NR_045959		4930447J18Rik	4930425M13Rik	RIKEN cDNA 4930447J18 gene	ncRNA
mm_93038.1	chr10	88354422	88354427	-	1	NA	intron (NM_027878, intron 1 of 6)	ID|SINE|ID	2651	NM_027878	71712	Mm.35450	NM_027878	ENSMUSG00000020057	Dram1	1200002N14Rik|Dram	DNA-damage regulated autophagy modulator 1	protein-coding
mm_95444.1	chr11	50236888	50236917	+	1	NA	intron (NR_132732, intron 4 of 4)	CpG	1630	NM_001313968	17001	Mm.245151	NM_008521	ENSMUSG00000020377	Ltc4s	-	leukotriene C4 synthase	protein-coding
mm_31993.1	chr4	89688095	89688110	+	1	NA	promoter-TSS (NM_175647)	promoter-TSS (NM_175647)	-96	NM_175647	242523	Mm.130167	NM_175647	ENSMUSG00000043753	Dmrta1	Dmrt4	doublesex and mab-3 related transcription factor like family A1	protein-coding
mm_33758.1	chr4	134343599	134343608	+	1	NA	intron (NM_001346578, intron 1 of 7)	intron (NM_001346578, intron 1 of 7)	137	NM_001346578	230810	Mm.358876	NM_001039677	ENSMUSG00000028836	Slc30a2	ZnT-2|Znt2	solute carrier family 30 (zinc transporter), member 2	protein-coding
mm_124434.1	chr14	118370406	118370413	-	1	NA	intron (NR_045624, intron 3 of 5)	RMER17C|LTR|ERVK	4531	NR_045624	73306	Mm.362328	NR_045624	ENSMUSG00000099911	1700044C05Rik	-	RIKEN cDNA 1700044C05 gene	ncRNA
mm_86216.1	chr9	120056323	120056327	-	1	NA	intron (NM_009987, intron 1 of 1)	intron (NM_009987, intron 1 of 1)	11971	NM_009987	13051	Mm.44065	NM_009987	ENSMUSG00000052336	Cx3cr1	-	chemokine (C-X3-C motif) receptor 1	protein-coding
mm_18818.1	chr2	74579421	74579450	-	1	NA	promoter-TSS (NM_027133)	promoter-TSS (NM_027133)	-487	NM_027133	69605	Mm.156113	NM_027133	ENSMUSG00000009207	Lnpk	2310011O18Rik|4921514L11Rik|9530051D01Rik|AI666268|Lnp|Lnpk1|Ul|ulnaless	lunapark, ER junction formation factor	protein-coding
mm_146738.1	chr18	15403617	15403635	-	1	NA	promoter-TSS (NM_001308647)	promoter-TSS (NM_001308647)	132	NM_001317729	11829	Mm.250786	NM_009700	ENSMUSG00000024411	Aqp4	WCH4	aquaporin 4	protein-coding
mm_124219.1	chr14	100284454	100284498	-	1	NA	Intergenic	Intergenic	-134680	NM_010636	16597	Mm.396499	NM_010636	ENSMUSG00000072294	Klf12	2700063E05Rik|AI225908|AI315654|AP-2rep|B130052C06Rik|D530033K05Rik	Kruppel-like factor 12	protein-coding
mm_7303.1	chr1	97977211	97977227	-	1	NA	5' UTR (NM_013626, exon 2 of 26)	5' UTR (NM_013626, exon 2 of 26)	70574	NR_037993	78603	Mm.442597	NR_037993	ENSMUSG00000089706	B230216N24Rik	-	RIKEN cDNA B230216N24 gene	ncRNA
mm_163223.1	chr11	102097362	102097372	-	1	NA	Intergenic	Intergenic	3933	NM_008918	19064	Mm.1269	NM_008918	ENSMUSG00000017316	Ppy	AV061413|IGSPP|PP	pancreatic polypeptide	protein-coding
mm_167157.1	chr7	132317246	132317256	-	1	NA	promoter-TSS (NM_029935)	promoter-TSS (NM_029935)	-96	NM_029935	77590	Mm.213582	NM_029935	ENSMUSG00000030930	Chst15	4631426J05Rik|BRAG|GalNAcS-6ST|MAd5|mKIAA0598	carbohydrate (N-acetylgalactosamine 4-sulfate 6-O) sulfotransferase 15	protein-coding
mm_147042.1	chr18	34887335	34887339	-	1	NA	Intergenic	Intergenic	26130	NM_007913	13653	Mm.181959	NM_007913	ENSMUSG00000038418	Egr1	A530045N19Rik|ETR103|Egr-1|Krox-1|Krox-24|Krox24|NGF1-A|NGFI-A|NGFIA|TIS8|Zenk|Zfp-6|Zif268|egr	early growth response 1	protein-coding
mm_48518.1	chr5	142901398	142901399	-	1	NA	Intergenic	Intergenic	5356	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_7179.1	chr1	92473802	92473808	-	1	NA	promoter-TSS (NM_024197)	promoter-TSS (NM_024197)	-47	NM_024197	67273	Mm.248778	NM_024197	ENSMUSG00000026260	Ndufa10	2900053E13Rik	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex 10	protein-coding
mm_13850.1	chr2	119604752	119604773	+	1	NA	Intergenic	Intergenic	10466	NR_015473	66602	Mm.379181	NR_015473	ENSMUSG00000085438	1700020I14Rik	1190006L01Rik|4933437I03Rik|AI451541|AI585852|AW538376|AW558897|Cyrano	RIKEN cDNA 1700020I14 gene	ncRNA
mm_147472.1	chr18	46741513	46741524	-	1	NA	promoter-TSS (NM_026217)	promoter-TSS (NM_026217)	61	NM_026217	67526	Mm.9852	NM_026217	ENSMUSG00000032905	Atg12	4931423H11Rik|A330058M13Rik|Apg12l|Atg12l	autophagy related 12	protein-coding
mm_71085.1	chr8	34805459	34805473	+	1	NA	Intergenic	Intergenic	-2144	NM_176933	319520	Mm.170276	NM_176933	ENSMUSG00000031530	Dusp4	2700078F24Rik|AI844617|BB104621|E130306H24Rik|MKP2	dual specificity phosphatase 4	protein-coding
mm_62308.1	chr7	100227463	100227504	+	1	NA	promoter-TSS (NM_027629)	promoter-TSS (NM_027629)	-124	NM_027629	70974	Mm.440524	NM_027629	ENSMUSG00000030729	Pgm2l1	4931406N15Rik|AI553438|BM32A	phosphoglucomutase 2-like 1	protein-coding
mm_75962.1	chr8	71722031	71722034	-	1	NA	intron (NR_131256, intron 1 of 25)	intron (NR_131256, intron 1 of 25)	3649	NR_131256	74015	Mm.22025	NM_028715	ENSMUSG00000070000	Fcho1	3322402E17Rik|N28152	FCH domain only 1	protein-coding
mm_119267.1	chr14	34053159	34053176	+	1	NA	promoter-TSS (NM_172808)	promoter-TSS (NM_172808)	-303	NM_172808	239029	Mm.477093	NM_172808	ENSMUSG00000047441	Antxrl	1700112N15Rik|4933430J11	anthrax toxin receptor-like	protein-coding
mm_21572.1	chr2	164237066	164237083	-	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	1267	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_108595.1	chr12	85385994	85386032	+	1	NA	Intergenic	Intergenic	-11296	NM_026775	68581	Mm.379159	NM_026775	ENSMUSG00000021248	Tmed10	1110014C03Rik|Tmp21|p23|p24delta1	transmembrane p24 trafficking protein 10	protein-coding
mm_149117.1	chr19	8967176	8967208	+	1	NA	TTS (NM_197993)	TTS (NM_197993)	151	NM_026007	67160	Mm.247762	NM_026007	ENSMUSG00000071644	Eef1g	2610301D06Rik|AA407312|EF1G	eukaryotic translation elongation factor 1 gamma	protein-coding
mm_7117.1	chr1	90153397	90153406	-	1	NA	promoter-TSS (NM_029122)	promoter-TSS (NM_029122)	0	NM_029122	74918	Mm.317517	NM_029122	ENSMUSG00000026301	Iqca	4930465P12Rik|4930585L22Rik|BB288505|Iqca1	IQ motif containing with AAA domain	protein-coding
mm_17680.1	chr2	32288023	32288042	-	1	NA	promoter-TSS (NM_133852)	promoter-TSS (NM_133852)	37	NR_110965	72931	Mm.27344	NM_175190	ENSMUSG00000044627	Swi5	1500019F05Rik|2900010J23Rik|AI046671	SWI5 recombination repair homolog (yeast)	protein-coding
mm_86760.1	chr10	19679992	19679993	+	1	NA	Intergenic	Intergenic	-32595	NM_172786	237313	Mm.234667	NM_172786	ENSMUSG00000020007	Il20ra	E230031K19	interleukin 20 receptor, alpha	protein-coding
mm_76976.1	chr8	106337998	106338009	-	1	NA	promoter-TSS (NM_021491)	promoter-TSS (NM_021491)	-15	NM_021491	58994	Mm.23298	NM_021491	ENSMUSG00000031906	Smpd3	4631433G07Rik|AI427456|AW537966|fro|nSMase2	sphingomyelin phosphodiesterase 3, neutral	protein-coding
mm_54679.1	chr6	39419692	39419698	-	1	NA	promoter-TSS (NM_001311109)	promoter-TSS (NM_001311109)	81	NM_001311109	54484	Mm.270484	NM_018810	ENSMUSG00000029922	Mkrn1	RFP	makorin, ring finger protein, 1	protein-coding
mm_11218.1	chr2	29643789	29643805	+	1	NA	intron (NM_001039087, intron 1 of 25)	intron (NM_001039087, intron 1 of 25)	24077	NM_001039086	107746	Mm.298274	NM_054050	ENSMUSG00000039844	Rapgef1	4932418O06Rik|C3G|Grf2	Rap guanine nucleotide exchange factor (GEF) 1	protein-coding
mm_13673.1	chr2	116067214	116067250	+	1	NA	5' UTR (NM_001346047, exon 1 of 14)	5' UTR (NM_001346047, exon 1 of 14)	212	NM_001346047	17536	Mm.247566	NM_010825	ENSMUSG00000027210	Meis2	A430109D20Rik|Mrg1|Stra10	Meis homeobox 2	protein-coding
mm_170061.1	chr17	30624407	30624408	+	1	NA	non-coding (NR_045287, exon 3 of 4)	non-coding (NR_045287, exon 3 of 4)	2498	NR_045287	67522	Mm.254797	NR_045287	ENSMUSG00000099474	1700097N02Rik	-	RIKEN cDNA 1700097N02 gene	ncRNA
mm_71234.1	chr8	40906706	40906715	+	1	NA	intron (NM_007514, intron 6 of 11)	intron (NM_007514, intron 6 of 11)	-19523	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_42696.1	chr5	119871488	119871500	+	1	NA	intron (NM_011537, intron 8 of 8)	intron (NM_011537, intron 8 of 8)	36831	NM_011537	21388	Mm.103636	NM_011537	ENSMUSG00000018263	Tbx5	-	T-box 5	protein-coding
mm_101478.1	chr11	30954326	30954393	-	1	NA	promoter-TSS (NM_023906)	promoter-TSS (NM_023906)	-39	NM_023906	65257	Mm.440539	NM_023906	ENSMUSG00000020305	Asb3	2400011J03Rik|Asb-3	ankyrin repeat and SOCS box-containing 3	protein-coding
mm_113695.1	chr13	43125860	43125866	+	1	NA	intron (NM_001005740, intron 9 of 12)	intron (NM_001005740, intron 9 of 12)	3024	NM_001005748	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding
mm_148609.1	chr19	5335620	5335630	+	1	NA	promoter-TSS (NM_139301)	promoter-TSS (NM_139301)	-116	NM_139301	225865	Mm.87321	NM_139301	ENSMUSG00000038498	Catsper1	Catsper|KSper	cation channel, sperm associated 1	protein-coding
mm_91444.1	chr10	33933202	33933222	-	1	NA	intron (NM_028287, intron 6 of 9)	B1_Mus1|SINE|Alu	18000	NM_028287	72580	Mm.248081	NM_028287	ENSMUSG00000039531	Zufsp	2700019D07Rik	zinc finger with UFM1-specific peptidase domain	protein-coding
mm_72471.1	chr8	83389881	83389889	+	1	NA	promoter-TSS (NM_001329627)	promoter-TSS (NM_001329627)	43	NM_001329680	12745	Mm.358581	NM_009904	ENSMUSG00000002190	Clgn	4930459O04Rik|A2/6|AI528775|Cln	calmegin	protein-coding
mm_43092.1	chr5	124451150	124451167	+	1	NA	intron (NM_001310725, intron 3 of 6)	intron (NM_001310725, intron 3 of 6)	4454	NM_001310727	67956	Mm.137966	NM_030241	ENSMUSG00000049327	Kmt5a	2410195B05Rik|AA617402|AW536475|PR-SET7|PR/SET07|Setd8	lysine methyltransferase 5A	protein-coding
mm_23250.1	chr3	51224870	51224882	+	1	NA	5' UTR (NM_009834, exon 1 of 3)	5' UTR (NM_009834, exon 1 of 3)	429	NM_009834	12457	Mm.86541	NM_009834	ENSMUSG00000023087	Noct	AU043840|Ccr4|Ccrn4l	nocturnin	protein-coding
mm_27627.1	chr3	60501729	60501761	-	1	NA	intron (NM_001253710, intron 1 of 7)	intron (NM_001253710, intron 1 of 7)	566	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_48428.1	chr5	140596584	140596603	-	1	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	-10748	NM_008494	16848	Mm.12834	NM_008494	ENSMUSG00000029570	Lfng	AW061165	LFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	protein-coding
mm_118827.1	chr14	25597610	25597612	+	1	NA	intron (NM_001310666, intron 6 of 23)	intron (NM_001310666, intron 6 of 23)	-5902	NM_001309430	100188919	Mm.473810	NM_001309430		Israa	-	immune system released activating agent	protein-coding
mm_25457.1	chr3	108444275	108444297	+	1	NA	intron (NM_001204979, intron 1 of 10)	intron (NM_001204979, intron 1 of 10)	973	NM_011319	20226	Mm.28688	NM_011319	ENSMUSG00000068739	Sars	Sars1|Strs|serRS	seryl-aminoacyl-tRNA synthetase	protein-coding
mm_111451.1	chr12	98385828	98385834	-	1	NA	Intergenic	Intergenic	117196	NM_008152	14744	Mm.378924	NM_008152	ENSMUSG00000021886	Gpr65	Dig1|Gpcr25|TDAG8	G-protein coupled receptor 65	protein-coding
mm_24628.1	chr3	93560937	93560945	+	1	NA	intron (NM_009112, intron 1 of 2)	intron (NM_009112, intron 1 of 2)	5824	NM_009112	20194	Mm.1	NM_009112	ENSMUSG00000041959	S100a10	42C|AA409961|AL024248|CAL12|CLP11|Cal1l|p10|p11	S100 calcium binding protein A10 (calpactin)	protein-coding
mm_83507.1	chr9	45984520	45984524	-	1	NA	intron (NM_008775, intron 1 of 5)	CpG	349	NM_008775	18475	Mm.200859	NM_008775	ENSMUSG00000003131	Pafah1b2	AI747451|AU021353|Pafahb|mus[b]	platelet-activating factor acetylhydrolase, isoform 1b, subunit 2	protein-coding
mm_84340.1	chr9	64178396	64178449	-	1	NA	promoter-TSS (NM_183316)	promoter-TSS (NM_183316)	-875	NM_183316	330959	Mm.24082	NM_183316	ENSMUSG00000032398	Snapc5	2010103A03Rik	small nuclear RNA activating complex, polypeptide 5	protein-coding
mm_41700.1	chr5	100846451	100846508	+	1	NA	intron (NM_172715, intron 1 of 12)	CpG	250	NM_172715	231510	Mm.271911	NM_172715	ENSMUSG00000029314	Agpat9	1-AGPAT|1-AGPAT 9|4933407I02Rik|4933408F15|A230097K15Rik|GPAT-3|Gpat3|mGPAT3	1-acylglycerol-3-phosphate O-acyltransferase 9	protein-coding
mm_125281.1	chr15	36439075	36439087	+	1	NA	Intergenic	Intergenic	57710	NM_175134	68839	Mm.396537	NM_175134	ENSMUSG00000048307	Ankrd46	1110054N06Rik|AI314978|AI987733	ankyrin repeat domain 46	protein-coding
mm_155612.1	chrX	83043427	83043431	+	1	NA	intron (NM_007868, intron 1 of 78)	intron (NM_007868, intron 1 of 78)	94559	NM_007868	13405	Mm.275608	NM_007868	ENSMUSG00000045103	Dmd	DXSmh7|DXSmh9|Dp427|Dp71|dys|mdx|pke	dystrophin, muscular dystrophy	protein-coding
mm_161508.1	chr15	98341162	98341162	-	1	NA	promoter-TSS (NM_146281)	promoter-TSS (NM_146281)	-223	NM_146281	258278	Mm.377409	NM_146281	ENSMUSG00000051793	Olfr284	MOR160-4	olfactory receptor 284	protein-coding
mm_124896.1	chr15	10358557	10358598	+	1	NA	promoter-TSS (NM_001310735)	promoter-TSS (NM_001310735)	-2	NM_001031851	268782	Mm.482244	NM_001031851	ENSMUSG00000089678	Agxt2	AI303810|AI663818	alanine-glyoxylate aminotransferase 2	protein-coding
mm_2407.1	chr1	93803946	93803998	+	1	NA	promoter-TSS (NM_025454)	promoter-TSS (NM_025454)	7	NM_025454	66262	Mm.64065	NM_025454	ENSMUSG00000026283	Ing5	1700001C14Rik|1700027H23Rik|1810018M11Rik|AI225768	inhibitor of growth family, member 5	protein-coding
mm_138471.1	chr17	35194143	35194155	+	1	NA	promoter-TSS (NM_008518)	promoter-TSS (NM_008518)	-358	NM_008518	16994	Mm.1715	NM_008518	ENSMUSG00000024399	Ltb	AI662801|LTbeta|Tnfc|Tnfsf3|Tnlg1c|p33	lymphotoxin B	protein-coding
mm_1206.1	chr1	62726312	62726322	+	1	NA	intron (NM_001077405, intron 2 of 15)	intron (NM_001077405, intron 2 of 15)	23000	NM_001077405	18187	Mm.266341	NM_010939	ENSMUSG00000025969	Nrp2	1110048P06Rik|Np-2|Np2|Npn-2|Npn2	neuropilin 2	protein-coding
mm_81527.1	chr9	110062792	110062803	+	1	NA	intron (NM_001311163, intron 1 of 10)	intron (NM_001311163, intron 1 of 10)	10776	NM_001311164	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_27960.1	chr3	79886797	79886822	-	1	NA	exon (NM_133187, exon 1 of 4)	exon (NM_133187, exon 1 of 4)	879	NM_133187	68659	Mm.427274	NM_133187	ENSMUSG00000027955	Fam198b	1110032E23Rik|2210419I08Rik|AV011458|Ened	family with sequence similarity 198, member B	protein-coding
mm_115462.1	chr13	119428562	119428575	+	1	NA	promoter-TSS (NM_001079849)	promoter-TSS (NM_001079849)	-32	NM_001079849	218693	Mm.490243	NM_145457	ENSMUSG00000025451	Paip1	PAIP-1	polyadenylate binding protein-interacting protein 1	protein-coding
mm_128788.1	chr15	66804079	66804093	-	1	NA	intron (NM_001029841, intron 1 of 7)	intron (NM_001029841, intron 1 of 7)	27743	NM_001029841	20491	Mm.7601	NM_009192	ENSMUSG00000022372	Sla	Slap|Slap-1	src-like adaptor	protein-coding
mm_152683.1	chr19	16036096	16036118	-	1	NA	Intergenic	RLTR11A|LTR|ERVK	51032	NR_045355	100502653	Mm.149980	NR_045355	ENSMUSG00000097557	C130060C02Rik	-	RIKEN cDNA C130060C02 gene	ncRNA
mm_88353.1	chr10	75933320	75933353	+	1	NA	promoter-TSS (NM_008606)	promoter-TSS (NM_008606)	-834	NM_008606	17385	Mm.4561	NM_008606	ENSMUSG00000000901	Mmp11	MMP-11|SL-3|ST3|Stmy3	matrix metallopeptidase 11	protein-coding
mm_73290.1	chr8	104947340	104947344	+	1	NA	promoter-TSS (NM_001079865)	promoter-TSS (NM_001079865)	-14	NM_001079865	71903	Mm.442371	NM_001079865	ENSMUSG00000062826	Ces2f	2310038E17Rik|A430088E12	carboxylesterase 2F	protein-coding
mm_2000.1	chr1	87126992	87126995	+	1	NA	exon (NM_007432, exon 9 of 11)	exon (NM_007432, exon 9 of 11)	1985	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_112262.1	chr12	113994941	113994949	-	1	NA	Intergenic	Intergenic	451037	NM_174885	238406	Mm.188683	NM_174885	ENSMUSG00000043945	Adam6a	Adam6|tMDCIV	a disintegrin and metallopeptidase domain 6A	protein-coding
mm_158928.1	chr1	62010336	62010336	+	1	NA	exon (NM_001081050, exon 3 of 23)	exon (NM_001081050, exon 3 of 23)	371512	NM_001081050	72823	Mm.35153	NM_001081050	ENSMUSG00000052062	Pard3b	1810008K04Rik|2010002N16Rik|2810455B10Rik|Als2cr19|PAR3B|PAR3L|PAR3beta	par-3 family cell polarity regulator beta	protein-coding
mm_17214.1	chr2	25493444	25493464	-	1	NA	intron (NM_029958, intron 1 of 5)	intron (NM_029958, intron 1 of 5)	457	NM_029958	77701	Mm.99123	NM_029958	ENSMUSG00000026943	Lcn12	9230102M18Rik	lipocalin 12	protein-coding
mm_13985.1	chr2	121509857	121509862	+	1	NA	intron (NM_001290987, intron 1 of 11)	intron (NM_001290987, intron 1 of 11)	3136	NM_001290986	241627	Mm.293284	NM_030234	ENSMUSG00000027242	Wdr76	5830411K18Rik|6030457D09|AA517836	WD repeat domain 76	protein-coding
mm_69544.1	chr7	135695789	135695804	-	1	NA	exon (NM_001081117, exon 12 of 14)	exon (NM_001081117, exon 12 of 14)	20583	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_134939.1	chr16	31171567	31171569	-	1	NA	intron (NM_030138, intron 1 of 22)	B1_Mus2|SINE|Alu	29670	NM_030138	78618	Mm.274646	NM_030138	ENSMUSG00000049076	Acap2	4832442G16|9530039J15Rik|CNT-B2|Centb2|mKIAA0041	ArfGAP with coiled-coil, ankyrin repeat and PH domains 2	protein-coding
mm_116094.1	chr13	28772177	28772181	-	1	NA	intron (NR_045053, intron 3 of 8)	intron (NR_045053, intron 3 of 8)	-61306	NR_105787	102466635		NR_105787	ENSMUSG00000099158	Mir6368	Gm27800|mmu-mir-6368	microRNA 6368	ncRNA
mm_155438.1	chrX	73494724	73494736	+	1	NA	exon (NM_007542, exon 8 of 8)	exon (NM_007542, exon 8 of 8)	-8356	NM_001310537	320707	Mm.210095	NM_177236	ENSMUSG00000031376	Atp2b3	6430519O13Rik|Pmca3	ATPase, Ca++ transporting, plasma membrane 3	protein-coding
mm_114953.1	chr13	96924675	96924694	+	1	NA	promoter-TSS (NM_001166065)	promoter-TSS (NM_001166065)	-5	NM_001166065	218476	Mm.483490	NM_001166065	ENSMUSG00000091387	Gcnt4	C2gnt3|Gm279|Gm73	glucosaminyl (N-acetyl) transferase 4, core 2 (beta-1,6-N-acetylglucosaminyltransferase)	protein-coding
mm_73216.1	chr8	96452967	96452972	+	1	NA	Intergenic	B4A|SINE|B4	93004	NR_039538	100628567		NR_039538	ENSMUSG00000104794	Mir28c	mmu-mir-28c	microRNA 28c	ncRNA
mm_166828.1	chr7	18607039	18607057	-	1	NA	exon (NM_020261, exon 5 of 5)	exon (NM_020261, exon 5 of 5)	9453	NM_020261	56868	Mm.333617	NM_020261	ENSMUSG00000074359	Psg23	1620401C02Rik|cea11	pregnancy-specific glycoprotein 23	protein-coding
mm_66567.1	chr7	45239393	45239410	-	1	NA	promoter-TSS (NM_007645)	promoter-TSS (NM_007645)	-286	NM_001290804	12493	Mm.3689	NM_007645	ENSMUSG00000030798	Cd37	Tspan26	CD37 antigen	protein-coding
mm_128829.1	chr15	67176801	67176807	-	1	NA	promoter-TSS (NM_009177)	promoter-TSS (NM_009177)	78	NM_009177	20442	Mm.248334	NM_009177	ENSMUSG00000013846	St3gal1	5330418N22Rik|AI467004|ST3GalI|Siat4|Siat4a|St3gal-1	ST3 beta-galactoside alpha-2,3-sialyltransferase 1	protein-coding
mm_23562.1	chr3	63241469	63241469	+	1	NA	Intergenic	RLTR41|LTR|ERV1	-53966	NM_001289462	17380	Mm.296022	NM_008604	ENSMUSG00000027820	Mme	6030454K05Rik|C85356|CALLA|CD10|NEP|SFE	membrane metallo endopeptidase	protein-coding
mm_129161.1	chr15	76243133	76243166	-	1	NA	exon (NM_001163575, exon 2 of 11)	exon (NM_001163575, exon 2 of 11)	291	NM_001163576	671535	Mm.373750	NM_001163575	ENSMUSG00000063268	Parp10	-	poly (ADP-ribose) polymerase family, member 10	protein-coding
mm_121629.1	chr14	8318034	8318054	-	1	NA	Intergenic	Intergenic	-8268	NM_183187	268709	Mm.256058	NM_183187	ENSMUSG00000021750	Fam107a	DRR1	family with sequence similarity 107, member A	protein-coding
mm_126617.1	chr15	83121800	83121811	+	1	NA	intron (NM_029101, intron 2 of 6)	intron (NM_029101, intron 2 of 6)	996	NM_029101	74778	Mm.30056	NM_029101	ENSMUSG00000018040	Rrp7a	1110014J01Rik|AA408146|Kheg1	ribosomal RNA processing 7 homolog A (S. cerevisiae)	protein-coding
mm_89707.1	chr10	97674742	97674750	+	1	NA	exon (NM_007884, exon 5 of 8)	exon (NM_007884, exon 5 of 8)	-18313	NM_025724	66716	Mm.56430	NM_025724	ENSMUSG00000047025	Ccer1	4921510H08Rik|AV259683	coiled-coil glutamate-rich protein 1	protein-coding
mm_162440.1	chr1	112059191	112059192	+	1	NA	Intergenic	(GA)n|Simple_repeat|Simple_repeat	-194273	NM_001081316	319901	Mm.103468	NM_001081316	ENSMUSG00000038702	Dsel	9330132E09Rik|DS-epi2	dermatan sulfate epimerase-like	protein-coding
mm_143889.1	chr17	84419469	84419482	-	1	NA	intron (NM_183021, intron 21 of 37)	intron (NM_183021, intron 21 of 37)	46733	NM_183021	240174	Mm.246767	NM_177826	ENSMUSG00000024251	Thada	6530405K19|A930021O22|AU019899|BC052885|GITA	thyroid adenoma associated	protein-coding
mm_70851.1	chr8	23448522	23448523	+	1	NA	3' UTR (NM_013834, exon 3 of 3)	3' UTR (NM_013834, exon 3 of 3)	37020	NM_013834	20377	Mm.281691	NM_013834	ENSMUSG00000031548	Sfrp1	2210415K03Rik|AW011917|AW107218|AW742929|sFRP-1	secreted frizzled-related protein 1	protein-coding
mm_55858.1	chr6	83455475	83455512	-	1	NA	intron (NM_001347313, intron 1 of 11)	intron (NM_001347313, intron 1 of 11)	899	NM_001347313	194388	Mm.211030	NM_183138	ENSMUSG00000034832	Tet3	B430006D22Rik|BC037432|D230004J03Rik	tet methylcytosine dioxygenase 3	protein-coding
mm_167720.1	chr9	100546252	100546321	+	1	NA	promoter-TSS (NM_010878)	promoter-TSS (NM_010878)	-152	NM_010878	17973	Mm.181485	NM_010878	ENSMUSG00000032475	Nck1	6330586M15Rik|D230010O13Rik|Nck|Nck-1	non-catalytic region of tyrosine kinase adaptor protein 1	protein-coding
mm_102114.1	chr11	53300178	53300179	-	1	NA	5' UTR (NM_008300, exon 1 of 19)	5' UTR (NM_008300, exon 1 of 19)	301	NM_008300	15525	Mm.239865	NM_008300	ENSMUSG00000020361	Hspa4	70kDa|AI317151|APG-2|Hsp110|Hsp70RY|mKIAA4025	heat shock protein 4	protein-coding
mm_100051.1	chr11	115170911	115170919	+	1	NA	intron (NM_012030, intron 1 of 5)	intron (NM_012030, intron 1 of 5)	7574	NM_012030	26941	Mm.27842	NM_012030	ENSMUSG00000020733	Slc9a3r1	EBP-50|NHE-RF|NHERF-1|NHERF1	solute carrier family 9 (sodium/hydrogen exchanger), member 3 regulator 1	protein-coding
mm_70411.1	chr8	11431091	11431101	+	1	NA	intron (NM_009932, intron 29 of 47)	intron (NM_009932, intron 29 of 47)	-46833	NR_126558	102132	Mm.37632	NR_126558	ENSMUSG00000096957	E230013L22Rik	AI645545	RIKEN cDNA E230013L22 gene	ncRNA
mm_163338.1	chr12	13501233	13501237	+	1	NA	intron (NM_027706, intron 44 of 51)	intron (NM_027706, intron 44 of 51)	126411	NR_136761	102639399	Mm.122052	NR_136761		Gm35725	-	predicted gene, 35725	ncRNA
mm_35951.1	chr4	53117967	53117983	-	1	NA	intron (NM_013454, intron 5 of 49)	intron (NM_013454, intron 5 of 49)	41920	NM_013454	11303	Mm.277376	NM_013454	ENSMUSG00000015243	Abca1	ABC-1|Abc1	ATP-binding cassette, sub-family A (ABC1), member 1	protein-coding
mm_68656.1	chr7	118584670	118584741	-	1	NA	promoter-TSS (NM_172476)	promoter-TSS (NM_172476)	-19	NM_172476	209760	Mm.69380	NM_172476	ENSMUSG00000042246	Tmc7	1700030H01Rik|C230064B05|C630024K23Rik	transmembrane channel-like gene family 7	protein-coding
mm_128018.1	chr15	24306917	24306918	-	1	NA	Intergenic	Intergenic	1106847	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	brain abundant, membrane attached signal protein 1	protein-coding
mm_117590.1	chr13	89742273	89742277	-	1	NA	5' UTR (NM_001134474, exon 1 of 14)	5' UTR (NM_001134474, exon 1 of 14)	237	NM_001081249	13003	Mm.158700	NM_019389	ENSMUSG00000021614	Vcan	5430420N07Rik|9430051N09|Cspg2|DPEAAE|NG2|PG-M|PG-M(V0)|PG-M(V1)|hdf	versican	protein-coding
mm_101572.1	chr11	34228692	34228711	-	1	NA	exon (NM_033374, exon 51 of 52)	exon (NM_033374, exon 51 of 52)	-20612	NM_023907	14233	Mm.32926	NM_023907	ENSMUSG00000047861	Foxi1	5830401E05Rik|FREAC6|Fkh10|HFH-3|Hfh3	forkhead box I1	protein-coding
mm_157135.1	chrX	9455170	9455287	-	1	NA	exon (NM_007807, exon 5 of 13)	exon (NM_007807, exon 5 of 13)	14096	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_99896.1	chr11	109650509	109650529	+	1	NA	promoter-TSS (NM_021880)	promoter-TSS (NM_021880)	-402	NM_021880	19084	Mm.30039	NM_021880	ENSMUSG00000020612	Prkar1a	1300018C22Rik|RIalpha|Tse-1|Tse1	protein kinase, cAMP dependent regulatory, type I, alpha	protein-coding
mm_126916.1	chr15	91199477	91199497	+	1	NA	Intergenic	CpG	-7680	NM_011994	26874	Mm.295456	NM_011994	ENSMUSG00000055782	Abcd2	ABC39|ALDL1|ALDR|ALDRP	ATP-binding cassette, sub-family D (ALD), member 2	protein-coding
mm_134575.1	chr16	20402275	20402288	-	1	NA	3' UTR (NM_176839, exon 6 of 7)	3' UTR (NM_176839, exon 6 of 7)	24113	NM_013790	27416	Mm.20845	NM_013790	ENSMUSG00000022822	Abcc5	2900011L11Rik|AI132311|Abcc5a|Abcc5b|Mrp5	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	protein-coding
mm_132089.1	chr16	30944366	30944399	+	1	NA	intron (NR_035427, intron 1 of 2)	intron (NR_035427, intron 1 of 2)	137050	NM_198626	268880	Mm.286693	NM_198626	ENSMUSG00000047434	Xxylt1	AI480653	xyloside xylosyltransferase 1	protein-coding
mm_125882.1	chr15	75642535	75642545	+	1	NA	Intergenic	Intergenic	25856	NM_011759	22701	Mm.87210	NM_011759	ENSMUSG00000047003	Zfp41	CTfin92|Zfp-41	zinc finger protein 41	protein-coding
mm_84331.1	chr9	64022028	64022042	-	1	NA	promoter-TSS (NM_008542)	promoter-TSS (NM_008542)	24	NM_008542	17130	Mm.325757	NM_008542	ENSMUSG00000036867	Smad6	Madh6|b2b390Clo	SMAD family member 6	protein-coding
mm_146980.1	chr18	33832802	33832829	-	1	NA	intron (NM_013512, intron 13 of 23)	B4|SINE|B4	37923	NR_038151	69749	Mm.248787	NR_038151	ENSMUSG00000087590	Epb41l4aos	2410004N09Rik|Epb4.1l4aos	erythrocyte membrane protein band 4.1 like 4a, opposite strand	ncRNA
mm_9524.1	chr1	173766987	173766997	-	1	NA	promoter-TSS (NM_008329)	promoter-TSS (NM_008329)	-73	NM_008329	15951	Mm.261270	NM_008329	ENSMUSG00000073489	Ifi204	Ifi16|p204	interferon activated gene 204	protein-coding
mm_34489.1	chr4	148589920	148589939	+	1	NA	Intergenic	RMER17C|LTR|ERVK	-1584	NM_009272	20810	Mm.10	NM_009272	ENSMUSG00000006442	Srm	AA407669|SpdST|SpdSy	spermidine synthase	protein-coding
mm_172882.1	chr9	49325602	49325604	+	1	NA	Intergenic	RLTR18-int|LTR|ERVK	-15059	NM_010077	13489	Mm.41970	NM_010077	ENSMUSG00000032259	Drd2	D2R|Drd-2	dopamine receptor D2	protein-coding
mm_131066.1	chr16	4594854	4594884	+	1	NA	5' UTR (NM_031184, exon 1 of 7)	5' UTR (NM_031184, exon 1 of 7)	156	NM_031184	83396	Mm.134072	NM_031184	ENSMUSG00000014303	Glis2	Gli5|Klf16|Nkl	GLIS family zinc finger 2	protein-coding
mm_23867.1	chr3	83028542	83028548	+	1	NA	exon (NM_010196, exon 2 of 5)	exon (NM_010196, exon 2 of 5)	2392	NM_001111048	14161	Mm.88793	NM_010196	ENSMUSG00000028001	Fga	ENSMUSG00000059807|Fib	fibrinogen alpha chain	protein-coding
mm_44055.1	chr5	148138111	148138111	+	1	NA	intron (NM_029920, intron 4 of 14)	RLTR31C_MM|LTR|ERVK	180791	NM_029920	77521	Mm.244177	NM_029920	ENSMUSG00000029651	Mtus2	5730592G18Rik|A730013O20Rik|AU067634|C130038G02Rik|Cazip|Gm763|mKIAA0774	microtubule associated tumor suppressor candidate 2	protein-coding
mm_113579.1	chr13	40859928	40859989	+	1	NA	5' UTR (NM_023887, exon 1 of 3)	5' UTR (NM_023887, exon 1 of 3)	190	NM_023887	14538	Mm.314757	NM_008105	ENSMUSG00000021360	Gcnt2	5330430K10Rik|IGnT|IGnTA|IGnTB|IGnTC	glucosaminyl (N-acetyl) transferase 2, I-branching enzyme	protein-coding
mm_141006.1	chr17	24960599	24960614	-	1	NA	promoter-TSS (NM_198937)	promoter-TSS (NM_198937)	17	NM_198937	52009	Mm.371601	NM_198937	ENSMUSG00000024165	Hn1l	2810430B18Rik|AL022629|C16orf34|D17Ertd441e	hematological and neurological expressed 1-like	protein-coding
mm_134183.1	chr16	10961046	10961052	-	1	NA	exon (NM_019980, exon 4 of 4)	exon (NM_019980, exon 4 of 4)	32072	NM_019980	56722	Mm.294753	NM_019980	ENSMUSG00000022500	Litaf	3222402J11Rik|C85531|N4WBP3|TBX1	LPS-induced TN factor	protein-coding
mm_97564.1	chr11	78936400	78936423	+	1	NA	exon (NM_010927, exon 7 of 27)	exon (NM_010927, exon 7 of 27)	11120	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_141976.1	chr17	35159394	35159410	-	1	NA	exon (NM_020027, exon 12 of 31)	exon (NM_020027, exon 12 of 31)	5475	NM_001199044	53761	Mm.272462	NM_020027	ENSMUSG00000024393	Prrc2a	3110039B05Rik|Bat-2|Bat2|D17H6S51E|G2|Wbp12|mKIAA4178	proline-rich coiled-coil 2A	protein-coding
mm_93784.1	chr10	120476899	120476916	-	1	NA	promoter-TSS (NM_010441)	promoter-TSS (NM_010441)	-438	NM_010441	15364	Mm.157190	NM_010441	ENSMUSG00000056758	Hmga2	9430083A20Rik|HMGI-C|Hmgic|pg|pygmy	high mobility group AT-hook 2	protein-coding
mm_172911.1	chr9	61914508	61914510	-	1	NA	promoter-TSS (NM_018853)	promoter-TSS (NM_018853)	1	NM_018853	56040	Mm.3158	NM_018853	ENSMUSG00000007892	Rplp1	2410042H16Rik|Arpp1|C430017H15Rik	ribosomal protein, large, P1	protein-coding
mm_54484.1	chr6	35253092	35253104	-	1	NA	intron (NR_027875, intron 1 of 2)	intron (NR_027875, intron 1 of 2)	366	NR_027875	67705	Mm.228046	NR_015608	ENSMUSG00000073155	1810058I24Rik	AI414869|AI848234	RIKEN cDNA 1810058I24 gene	ncRNA
mm_37199.1	chr4	117825692	117825696	-	1	NA	Intergenic	Intergenic	-9564	NM_008135	14664	Mm.244549	NM_008135	ENSMUSG00000028542	Slc6a9	Glyt-1|Glyt1	solute carrier family 6 (neurotransmitter transporter, glycine), member 9	protein-coding
mm_143153.1	chr17	57223184	57223199	-	1	NA	exon (NM_009778, exon 12 of 41)	exon (NM_009778, exon 12 of 41)	4945	NM_009778	12266	Mm.19131	NM_009778	ENSMUSG00000024164	C3	AI255234|ASP|HSE-MSF|Plp	complement component 3	protein-coding
mm_76275.1	chr8	84147859	84147942	-	1	NA	promoter-TSS (NM_029045)	promoter-TSS (NM_029045)	-138	NM_001163752	74666	Mm.33625	NM_029045	ENSMUSG00000008129	4930432K21Rik	-	RIKEN cDNA 4930432K21 gene	protein-coding
mm_81571.1	chr9	110420912	110420918	+	1	NA	intron (NM_008694, intron 2 of 3)	intron (NM_008694, intron 2 of 3)	1107	NM_008694	18054	Mm.236225	NM_008694	ENSMUSG00000032484	Ngp	bectenecin	neutrophilic granule protein	protein-coding
mm_152998.1	chr19	30030318	30030346	-	1	NA	promoter-TSS (NM_144873)	promoter-TSS (NM_144873)	-181	NM_144873	109113	Mm.313364	NM_144873	ENSMUSG00000024817	Uhrf2	2310065A22Rik|AI426270|AW214556|D130071B19Rik|Nirf	ubiquitin-like, containing PHD and RING finger domains 2	protein-coding
mm_106708.1	chr12	3806963	3806973	+	1	NA	promoter-TSS (NM_001271753)	promoter-TSS (NM_001271753)	-12	NM_007872	13435	Mm.5001	NM_007872	ENSMUSG00000020661	Dnmt3a	MmuIIIA	DNA methyltransferase 3A	protein-coding
mm_3774.1	chr1	156470767	156470774	+	1	NA	intron (NM_009230, intron 1 of 15)	intron (NM_009230, intron 1 of 15)	3558	NM_009230	20652	Mm.28099	NM_009230	ENSMUSG00000026600	Soat1	8430426K15Rik|ACAT-1|AW550831|Acact|ald|hid	sterol O-acyltransferase 1	protein-coding
mm_161445.1	chr15	73748054	73748054	+	1	NA	promoter-TSS (NM_008975)	promoter-TSS (NM_008975)	28	NM_008975	19245	Mm.390807	NM_008975	ENSMUSG00000059895	Ptp4a3	AV088979|Prl-3|pPtp4a3	protein tyrosine phosphatase 4a3	protein-coding
mm_135581.1	chr16	50432355	50432409	-	1	NA	promoter-TSS (NM_027444)	promoter-TSS (NM_027444)	7	NM_027444	70508	Mm.28940	NM_027444	ENSMUSG00000022641	Bbx	5530401J07Rik|5730403O13Rik	bobby sox HMG box containing	protein-coding
mm_11427.1	chr2	31950308	31950315	+	1	NA	promoter-TSS (NM_145144)	promoter-TSS (NM_145144)	8	NM_145144	108897	Mm.24838	NM_145144	ENSMUSG00000001864	Aif1l	2810003C17Rik|AI043124|C87647|Iba2	allograft inflammatory factor 1-like	protein-coding
mm_50656.1	chr6	51470511	51470528	+	1	NA	promoter-TSS (NM_007624)	promoter-TSS (NM_007624)	-97	NM_007624	12417	Mm.280968	NM_007624	ENSMUSG00000029836	Cbx3	HP1g|M32	chromobox 3	protein-coding
mm_61067.1	chr7	51457947	51457956	+	1	NA	Intergenic	Intergenic	-53078	NR_073508	233246	Mm.254431	NM_177694	ENSMUSG00000055489	Ano5	9330162L24|Gdd1|Tmem16e	anoctamin 5	protein-coding
mm_70478.1	chr8	12395604	12395621	+	1	NA	promoter-TSS (NM_009233)	promoter-TSS (NM_009233)	93	NM_009233	20664	Mm.39088	NM_009233	ENSMUSG00000096014	Sox1	BB176347|Sox-1	SRY (sex determining region Y)-box 1	protein-coding
mm_86572.1	chr10	12608919	12608925	+	1	NA	intron (NM_011682, intron 50 of 73)	B1F|SINE|Alu	252813	NM_011682	22288	Mm.331784	NM_011682	ENSMUSG00000019820	Utrn	AA589569|DRP|Dmdl	utrophin	protein-coding
mm_136329.1	chr16	92359425	92359428	-	1	NA	promoter-TSS (NM_008424)	promoter-TSS (NM_008424)	42	NM_008424	16509	Mm.299425	NM_008424	ENSMUSG00000039639	Kcne1	Isk|MinK|nmf190	potassium voltage-gated channel, Isk-related subfamily, member 1	protein-coding
mm_142462.1	chr17	45596709	45596720	-	1	NA	promoter-TSS (NM_001199114)	promoter-TSS (NM_001199114)	-812	NM_001199114	63959	Mm.29744	NM_022880	ENSMUSG00000023942	Slc29a1	1200014D21Rik|AA407560|ENT1	solute carrier family 29 (nucleoside transporters), member 1	protein-coding
mm_823.1	chr1	47091159	47091164	+	1	NA	Intergenic	ORR1B2|LTR|ERVL-MaLR	-237652	NM_172653	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|mKIAA1265	solute carrier family 39 (zinc transporter), member 10	protein-coding
mm_118930.1	chr14	27067389	27067401	+	1	NA	intron (NM_134437, intron 1 of 12)	intron (NM_134437, intron 1 of 12)	28394	NM_134437	171463	Mm.206726	NM_027265	ENSMUSG00000040717	Il17rd	2810004A10Rik|AI428510|Sef|Sef-S	interleukin 17 receptor D	protein-coding
mm_55510.1	chr6	69943689	69943700	-	1	NA	Intergenic	Intergenic	-616520	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_96976.1	chr11	70652808	70652838	+	1	NA	exon (NM_011072, exon 2 of 3)	exon (NM_011072, exon 2 of 3)	1827	NM_011072	18643	Mm.2647	NM_011072	ENSMUSG00000018293	Pfn1	Pfn	profilin 1	protein-coding
mm_21842.1	chr2	165828032	165828032	-	1	NA	3' UTR (NM_001252587, exon 12 of 12)	3' UTR (NM_001252587, exon 12 of 12)	30141	NM_001252585	228880	Mm.227598	NM_027230	ENSMUSG00000039671	Zmynd8	1110013E22Rik|2010005I16Rik|3632413B07Rik|AI316811|AL024039|Prkcbp1|RACK7	zinc finger, MYND-type containing 8	protein-coding
mm_121591.1	chr14	7858510	7858540	-	1	NA	intron (NM_134080, intron 1 of 45)	intron (NM_134080, intron 1 of 45)	40568	NM_134080	286940	Mm.489652	NM_134080	ENSMUSG00000025278	Flnb	AL024016|Fln-b	filamin, beta	protein-coding
mm_172244.1	chr6	69268449	69268468	-	1	NA	Intergenic	Intergenic	58716	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_14534.1	chr2	132781637	132781650	+	1	NA	5' UTR (NM_007694, exon 1 of 5)	5' UTR (NM_007694, exon 1 of 5)	365	NM_007694	12653	Mm.255241	NM_007694	ENSMUSG00000027350	Chgb	Scg-1	chromogranin B	protein-coding
mm_44078.1	chr5	149053196	149053209	+	1	NA	promoter-TSS (NM_010439)	promoter-TSS (NM_010439)	-145	NM_010439	15289	Mm.207047	NM_010439	ENSMUSG00000066551	Hmgb1	HMG-1|Hmg1|SBP-1|p30	high mobility group box 1	protein-coding
mm_62187.1	chr7	97494068	97494072	+	1	NA	intron (NM_027256, intron 4 of 22)	B1F1|SINE|Alu	13114	NM_027256	101861	Mm.27383	NM_027256	ENSMUSG00000025133	Ints4	2610034N24Rik|AA692684|AW493223	integrator complex subunit 4	protein-coding
mm_160971.1	chr11	99879187	99879187	+	1	NA	promoter-TSS (NM_001101613)	promoter-TSS (NM_001101613)	0	NM_001101613	670533	Mm.459090	NM_001101613	ENSMUSG00000059845	Gm11567	OTTMUSG00000002206	predicted gene 11567	protein-coding
mm_14237.1	chr2	127691894	127691906	+	1	NA	Intergenic	B1F|SINE|Alu	-35205	NM_001171187	17153	Mm.39040	NM_010762	ENSMUSG00000027375	Mal	Mpv17|Vip17	myelin and lymphocyte protein, T cell differentiation protein	protein-coding
mm_145542.1	chr18	60807943	60807991	+	1	NA	exon (NM_010545, exon 2 of 8)	exon (NM_010545, exon 2 of 8)	-4109	NR_039567	100628611		NR_039567	ENSMUSG00000093327	Mir5107	mir-5107|mmu-mir-5107|mu-mir-5107	microRNA 5107	ncRNA
mm_78596.1	chr9	37402067	37402077	+	1	NA	exon (NM_028783, exon 1 of 18)	exon (NM_028783, exon 1 of 18)	175	NM_001309390	74144	Mm.485070	NM_028783	ENSMUSG00000032125	Robo4	1200012D01Rik|AI593217	roundabout guidance receptor 4	protein-coding
mm_45231.1	chr5	53590573	53590589	-	1	NA	promoter-TSS (NM_001080927)	promoter-TSS (NM_001080927)	95	NM_001080927	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_99450.1	chr11	102434142	102434154	+	1	NA	exon (NM_008175, exon 6 of 13)	exon (NM_008175, exon 6 of 13)	3826	NM_008175	14824	Mm.1568	NM_008175	ENSMUSG00000034708	Grn	Pgrn|epithelin	granulin	protein-coding
mm_170931.1	chr2	40556003	40556017	-	1	NA	Intergenic	Intergenic	-1329672	NM_024209	67857	Mm.389242	NM_024209	ENSMUSG00000026753	Ppp6c	2310003C10Rik	protein phosphatase 6, catalytic subunit	protein-coding
mm_134166.1	chr16	10796128	10796152	-	1	NA	TTS (NM_013637)	TTS (NM_013637)	683	NM_013637	19118	Mm.42733	NM_013637	ENSMUSG00000022501	Prm1	Prm-1	protamine 1	protein-coding
mm_119580.1	chr14	50896422	50896434	+	1	NA	Intergenic	Intergenic	-3173	NM_001166651	546611	Mm.390692	NM_001166651	ENSMUSG00000090799	Klhl33	EG546611	kelch-like 33	protein-coding
mm_36296.1	chr4	66404435	66404456	-	1	NA	promoter-TSS (NM_207109)	promoter-TSS (NM_207109)	38	NM_019514	56079	Mm.445312	NM_019514	ENSMUSG00000028373	Astn2	1d8|Astnl|bM452J22.1	astrotactin 2	protein-coding
mm_45795.1	chr5	87538203	87538213	-	1	NA	promoter-TSS (NM_019878)	promoter-TSS (NM_019878)	-13	NM_019878	56362	Mm.23502	NM_019878	ENSMUSG00000029269	Sult1b1	ST1B1|St2b2	sulfotransferase family 1B, member 1	protein-coding
mm_97878.1	chr11	83195531	83195543	+	1	NA	intron (NM_011409, intron 1 of 2)	RMER17C-int|LTR|ERVK	4207	NM_011409	20557	Mm.290922	NM_011409	ENSMUSG00000018986	Slfn3	-	schlafen 3	protein-coding
mm_130946.1	chr15	103252769	103252784	-	1	NA	promoter-TSS (NM_001302339)	promoter-TSS (NM_001302339)	34	NM_001302339	18022	Mm.457989	NM_008685	ENSMUSG00000058794	Nfe2	NF-E2|NF-E2/P45|p45|p45NFE2|p45nf-e2	nuclear factor, erythroid derived 2	protein-coding
mm_55275.1	chr6	54151033	54151052	-	1	NA	intron (NM_001163640, intron 1 of 12)	intron (NM_001163640, intron 1 of 12)	111110	NM_001163640	69993	Mm.321147	NM_023543	ENSMUSG00000004633	Chn2	1700026N20Rik|4930557O16Rik|ARHGAP3|Bch	chimerin 2	protein-coding
mm_120738.1	chr14	73173620	73173641	+	1	NA	intron (NR_033185, intron 11 of 15)	intron (NR_033185, intron 11 of 15)	30845	NR_033185	105670	Mm.280068	NM_134083	ENSMUSG00000022106	Rcbtb2	2610028E02Rik|2810420M18Rik|AI448345|AW240694|Chc1l|RC/BTB2	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 2	protein-coding
mm_158703.1	chrX	162122662	162122663	-	1	NA	intron (NM_001081052, intron 1 of 7)	Lx7|LINE|L1	36779	NM_001081052	195727	Mm.336313	NM_001081052	ENSMUSG00000059493	Nhs	Gm389|Gm48|Nhs1|Xcat	Nance-Horan syndrome (human)	protein-coding
mm_101680.1	chr11	40680159	40680168	-	1	NA	exon (NM_001199274, exon 7 of 7)	exon (NM_001199274, exon 7 of 7)	12519	NM_134017	108645	Mm.293771	NM_134017	ENSMUSG00000042032	Mat2b	1110064C04Rik|2410018D16Rik|AI182287|AU022853|MAT-II|MATIIbeta|TGR	methionine adenosyltransferase II, beta	protein-coding
mm_31849.1	chr4	74360085	74360086	+	1	NA	intron (NM_001172095, intron 17 of 21)	intron (NM_001172095, intron 17 of 21)	108206	NM_144787	76804	Mm.209059	NM_144787	ENSMUSG00000028397	Kdm4c	2410141F18Rik|AA517467|Gasc1|Jmjd2c	lysine (K)-specific demethylase 4C	protein-coding
mm_76757.1	chr8	95490022	95490058	-	1	NA	Intergenic	Intergenic	-1220	NM_009974	13000	Mm.51136	NM_009974	ENSMUSG00000046707	Csnk2a2	1110035J23Rik|C77789|CK2	casein kinase 2, alpha prime polypeptide	protein-coding
mm_168872.1	chr12	37080295	37080313	+	1	NA	Intergenic	RLTR9D|LTR|ERVK	-28242	NM_008584	17286	Mm.341398	NM_008584	ENSMUSG00000036144	Meox2	AI528662|Gax|Mox-2|Mox2	mesenchyme homeobox 2	protein-coding
mm_91609.1	chr10	41488887	41488917	-	1	NA	intron (NM_009213, intron 4 of 9)	intron (NM_009213, intron 4 of 9)	1438	NM_009213	20598	Mm.953	NM_009213	ENSMUSG00000019822	Smpd2	AW108287|nSMase|nSMase1	sphingomyelin phosphodiesterase 2, neutral	protein-coding
mm_161514.1	chr15	98778126	98778126	-	1	NA	promoter-TSS (NM_011718)	promoter-TSS (NM_011718)	24	NM_011718	22410	Mm.4709	NM_011718	ENSMUSG00000022996	Wnt10b	Wnt12	wingless-type MMTV integration site family, member 10B	protein-coding
mm_93051.1	chr10	88537289	88537290	-	1	NA	intron (NM_175418, intron 20 of 28)	intron (NM_175418, intron 20 of 28)	-33319	NM_001146690	212862	Mm.288897	NM_144807	ENSMUSG00000060002	Chpt1	-	choline phosphotransferase 1	protein-coding
mm_4508.1	chr1	174172811	174172857	+	1	NA	promoter-TSS (NM_011465)	promoter-TSS (NM_011465)	58	NM_011465	20739	Mm.200611	NM_011465	ENSMUSG00000026532	Spta1	AF093576|AI451697|Spna-1|Spna1|ha|ihj|nmf4|sph	spectrin alpha, erythrocytic 1	protein-coding
mm_88369.1	chr10	75954522	75954548	+	1	NA	promoter-TSS (NM_198635)	promoter-TSS (NM_198635)	21	NM_198635	333669	Mm.31077	NM_198635	ENSMUSG00000033255	Gm5134	EG333669	predicted gene 5134	protein-coding
mm_35910.1	chr4	49845731	49845774	-	1	NA	promoter-TSS (NM_001276355)	promoter-TSS (NM_001276355)	17	NM_001033351	242443	Mm.440095	NM_001033351	ENSMUSG00000039579	Grin3a	6430537F04|A830097C19Rik|NMDAR-L|NR3A|mKIAA1973	glutamate receptor ionotropic, NMDA3A	protein-coding
mm_21212.1	chr2	155692318	155692339	-	1	NA	promoter-TSS (NM_001163452)	promoter-TSS (NM_001163452)	56	NM_019828	56407	Mm.234944	NM_019828	ENSMUSG00000038324	Trpc4ap	4833429F06Rik|D2Ertd113e|Trrp4ap|mFLJ00177|truss	transient receptor potential cation channel, subfamily C, member 4 associated protein	protein-coding
mm_112033.1	chr12	111515732	111515733	-	1	NA	Intergenic	Intergenic	-22369	NM_178041	217869	Mm.271222	NM_173363	ENSMUSG00000021282	Eif5	2810011H21Rik|D12Ertd549e	eukaryotic translation initiation factor 5	protein-coding
mm_146951.1	chr18	32559840	32559855	-	1	NA	5' UTR (NM_001048207, exon 1 of 3)	5' UTR (NM_001048207, exon 1 of 3)	187	NM_001347610	71683	Mm.292145	NM_027863	ENSMUSG00000090523	Gypc	0610037F22Rik|Cd236r	glycophorin C	protein-coding
mm_59739.1	chr7	28814026	28814043	+	1	NA	exon (NM_177301, exon 3 of 13)	exon (NM_177301, exon 3 of 13)	3144	NM_177301	15388	Mm.9043	NM_177301	ENSMUSG00000015165	Hnrnpl	C79783|D830027H13Rik|Hnrpl	heterogeneous nuclear ribonucleoprotein L	protein-coding
mm_146296.1	chr18	80173098	80173120	+	1	NA	Intergenic	RLTR33|LTR|ERVK	-13130	NR_131039	105246506	Mm.392326	NR_131039		LOC105246506	-	uncharacterized LOC105246506	ncRNA
mm_136339.1	chr16	92603050	92603094	-	1	NA	3' UTR (NM_001111021, exon 8 of 8)	3' UTR (NM_001111021, exon 8 of 8)	94257	NM_001111023	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_43998.1	chr5	146833107	146833210	+	1	NA	5' UTR (NM_019647, exon 1 of 6)	5' UTR (NM_019647, exon 1 of 6)	268	NM_019647	19933	Mm.316592	NM_019647	ENSMUSG00000041453	Rpl21	8430440E03Rik|L21	ribosomal protein L21	protein-coding
mm_88806.1	chr10	80755241	80755251	+	1	NA	promoter-TSS (NM_199322)	promoter-TSS (NM_199322)	40	NM_199322	208266	Mm.152371	NM_199322	ENSMUSG00000061589	Dot1l	A630076O07|AW907654|Dot1|KMT4|mDot1	DOT1-like, histone H3 methyltransferase (S. cerevisiae)	protein-coding
mm_119720.1	chr14	53945993	53945998	+	1	NA	Intergenic	Intergenic	307934	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_9991.1	chr1	191370748	191370762	-	1	NA	intron (NM_144880, intron 2 of 12)	intron (NM_144880, intron 2 of 12)	26286	NM_144880	226849	Mm.205569	NM_144880	ENSMUSG00000026626	Ppp2r5a	PR61alpha	protein phosphatase 2, regulatory subunit B', alpha	protein-coding
mm_84378.1	chr9	65175746	65175747	-	1	NA	intron (NM_008988, intron 2 of 13)	intron (NM_008988, intron 2 of 13)	34557	NM_008988	19289	Mm.41529	NM_008988	ENSMUSG00000032394	Igdcc3	2810401C09Rik|AI851425|Punc|WI-14920	immunoglobulin superfamily, DCC subclass, member 3	protein-coding
mm_53725.1	chr6	145048539	145048548	+	1	NA	intron (NM_007532, intron 1 of 10)	CpG	269	NM_001024468	12035	Mm.4606	NM_007532	ENSMUSG00000030268	Bcat1	BCATc|Eca39	branched chain aminotransferase 1, cytosolic	protein-coding
mm_41738.1	chr5	102724972	102724993	+	1	NA	intron (NM_146161, intron 2 of 8)	intron (NM_146161, intron 2 of 8)	-43828	NM_001286468	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding
mm_110060.1	chr12	21286288	21286298	-	1	NA	promoter-TSS (NM_008403)	promoter-TSS (NM_008403)	-4	NM_018813	54451	Mm.356778	NM_018813	ENSMUSG00000054309	Cpsf3	-	cleavage and polyadenylation specificity factor 3	protein-coding
mm_1025.1	chr1	58754803	58754821	+	1	NA	3' UTR (NM_207653, exon 10 of 10)	3' UTR (NM_207653, exon 10 of 10)	24260	NM_001293805	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_107008.1	chr12	11438192	11438238	+	1	NA	promoter-TSS (NR_045966)	promoter-TSS (NR_045966)	-18	NR_045966	74712	Mm.399246	NR_045966	ENSMUSG00000097841	4930511A02Rik	-	RIKEN cDNA 4930511A02 gene	ncRNA
mm_148419.1	chr19	3936254	3936353	+	1	NA	exon (NM_019449, exon 3 of 11)	exon (NM_019449, exon 3 of 11)	1117	NM_001161428	54445	Mm.262094	NM_019449	ENSMUSG00000036908	Unc93b1	Unc-93B1|Unc93b	unc-93 homolog B1 (C. elegans)	protein-coding
mm_72135.1	chr8	71908678	71908687	+	1	NA	promoter-TSS (NM_001166645)	promoter-TSS (NM_001166645)	76	NM_001166645	382019	Mm.251482	NM_001166645	ENSMUSG00000089857	Zfp882	ENSMUSG00000052439|Gm15468|OTTMUSG00000022410	zinc finger protein 882	protein-coding
mm_146151.1	chr18	75000449	75000460	+	1	NA	promoter-TSS (NR_028552)	promoter-TSS (NR_028552)	-23	NM_001002239	319195	Mm.276337	NM_001002239	ENSMUSG00000062328	Rpl17	-	ribosomal protein L17	protein-coding
mm_32269.1	chr4	102625148	102625162	+	1	NA	Intergenic	Intergenic	35312	NM_001177981	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_67343.1	chr7	79822309	79822346	-	1	NA	exon (NM_008486, exon 20 of 20)	exon (NM_008486, exon 20 of 20)	11600	NM_008589	17293	Mm.31472	NM_008589	ENSMUSG00000030543	Mesp2	bHLHc6	mesoderm posterior 2	protein-coding
mm_58116.1	chr6	138426736	138426747	-	1	NA	intron (NR_126072, intron 2 of 3)	intron (NR_126072, intron 2 of 3)	3636	NR_126072	319702	Mm.403785	NR_126072	ENSMUSG00000089957	A830011K09Rik	-	RIKEN cDNA A830011K09 gene	ncRNA
mm_20703.1	chr2	132945761	132945772	-	1	NA	5' UTR (NM_198029, exon 1 of 15)	5' UTR (NM_198029, exon 1 of 15)	270	NM_198029	241639	Mm.209784	NM_198029	ENSMUSG00000027356	Fermt1	5830467P10Rik|Kindlin-1	fermitin family member 1	protein-coding
mm_94084.1	chr10	128493835	128493908	-	1	NA	promoter-TSS (NM_001317220)	promoter-TSS (NM_001317220)	15	NM_001317218	17904	Mm.337074	NM_010860	ENSMUSG00000090841	Myl6	ESMLC|LC17|LC17-GI|MLC-3|MLC1SM|Myln	myosin, light polypeptide 6, alkali, smooth muscle and non-muscle	protein-coding
mm_48822.1	chr5	149051394	149051455	-	1	NA	5' UTR (NM_001313894, exon 1 of 5)	5' UTR (NM_001313894, exon 1 of 5)	192	NM_001313894	15289	Mm.207047	NM_010439	ENSMUSG00000066551	Hmgb1	HMG-1|Hmg1|SBP-1|p30	high mobility group box 1	protein-coding
mm_5166.1	chr1	10057922	10057945	-	1	NA	intron (NM_026493, intron 3 of 29)	intron (NM_026493, intron 3 of 29)	19715	NM_026493	211660	Mm.244046	NM_026493	ENSMUSG00000056763	Cspp1	2310020J12Rik|4930413O22Rik|AA387550|BC055915|Cspp2|Cspp3	centrosome and spindle pole associated protein 1	protein-coding
mm_139838.1	chr17	69159966	69159991	+	1	NA	intron (NM_013813, intron 1 of 21)	intron (NM_013813, intron 1 of 21)	3168	NM_013813	13823	Mm.131135	NM_013813	ENSMUSG00000024044	Epb41l3	4.1B|DAL1P|Dal1|Epb4.1l3|NBL3	erythrocyte membrane protein band 4.1 like 3	protein-coding
mm_76629.1	chr8	91801901	91801914	-	1	NA	promoter-TSS (NM_001253822)	promoter-TSS (NM_001253822)	-253	NM_008393	16373	Mm.238044	NM_008393	ENSMUSG00000031734	Irx3	AI894186	Iroquois related homeobox 3	protein-coding
mm_167585.1	chr9	46053417	46053427	+	1	NA	intron (NM_027498, intron 1 of 24)	intron (NM_027498, intron 1 of 24)	40602	NM_027498	70661	Mm.219459	NM_027498	ENSMUSG00000034135	Sik3	5730525O22Rik|9030204A07Rik|AI447252|AI846254|AI849445|Qsk|SIK-3|mKIAA0999	SIK family kinase 3	protein-coding
mm_25608.1	chr3	117634241	117634243	+	1	NA	intron (NM_001305451, intron 3 of 5)	intron (NM_001305451, intron 3 of 5)	59015	NM_001305451	75769	Mm.72187	NM_029425	ENSMUSG00000033342	Plppr5	4833424O15Rik|Lppr5|PRG-5|Pap2d	phospholipid phosphatase related 5	protein-coding
mm_137019.1	chr17	17838458	17838475	+	1	NA	exon (NM_001162909, exon 8 of 9)	exon (NM_001162909, exon 8 of 9)	7491	NM_001162909	75202	Mm.227456	NM_029205	ENSMUSG00000080316	Spaca6	4930546H06Rik|9530079D04Rik|B230206P06Rik|Ncrna00085|SPACA6A|let-7e|mir-125a|mir-99b	sperm acrosome associated 6	protein-coding
mm_67927.1	chr7	99906207	99906217	-	1	NA	intron (NM_001164258, intron 11 of 18)	intron (NM_001164258, intron 11 of 18)	46994	NM_001164258	446101	Mm.440757	NM_001164258	ENSMUSG00000035211	Xrra1	AI449753	X-ray radiation resistance associated 1	protein-coding
mm_80494.1	chr9	78479652	78479653	+	1	NA	exon (NM_010106, exon 5 of 8)	exon (NM_010106, exon 5 of 8)	2072	NM_010106	13627	Mm.138471	NM_010106	ENSMUSG00000037742	Eef1a1	-	eukaryotic translation elongation factor 1 alpha 1	protein-coding
mm_66550.1	chr7	45211813	45211874	-	1	NA	promoter-TSS (NM_015789)	promoter-TSS (NM_015789)	40	NM_015789	50722	Mm.27287	NM_015789	ENSMUSG00000030792	Dkkl1	AI414495|SGY|SGY-1|SGY1|Soggy|mSgy	dickkopf-like 1	protein-coding
mm_146977.1	chr18	33825770	33825790	-	1	NA	intron (NM_013512, intron 16 of 23)	intron (NM_013512, intron 16 of 23)	30888	NR_038151	69749	Mm.248787	NR_038151	ENSMUSG00000087590	Epb41l4aos	2410004N09Rik|Epb4.1l4aos	erythrocyte membrane protein band 4.1 like 4a, opposite strand	ncRNA
mm_92314.1	chr10	75434448	75434471	-	1	NA	intron (NM_133995, intron 6 of 9)	intron (NM_133995, intron 6 of 9)	-15051	NR_045841	71125	Mm.399516	NR_045841		4933407G14Rik	-	RIKEN cDNA 4933407G14 gene	ncRNA
mm_113472.1	chr13	36486141	36486146	+	1	NA	intron (NM_001039189, intron 5 of 5)	(T)n|Simple_repeat|Simple_repeat	248334	NM_153529	68404	Mm.232930	NM_153529	ENSMUSG00000039114	Nrn1	0710008J23Rik|Cpg15|Nrn	neuritin 1	protein-coding
mm_172889.1	chr9	54593663	54593666	-	1	NA	intron (NM_029573, intron 3 of 10)	RLTR16B_MM|LTR|ERVK	7153	NM_029573	67834	Mm.279195	NM_029573	ENSMUSG00000032279	Idh3a	1110003P10Rik|1500012E04Rik|AA407078|AI316514	isocitrate dehydrogenase 3 (NAD+) alpha	protein-coding
mm_145984.1	chr18	68227988	68228002	+	1	NA	intron (NM_172631, intron 3 of 5)	intron (NM_172631, intron 3 of 5)	32978	NR_106078	102465702		NR_106078	ENSMUSG00000098253	Mir7219	Gm27613|mmu-mir-7219	microRNA 7219	ncRNA
mm_3303.1	chr1	137289773	137289777	+	1	NA	Intergenic	RMER19C|LTR|ERVK	-329327	NM_030676	26424	Mm.16794	NM_030676	ENSMUSG00000026398	Nr5a2	AU020803|D1Ertd308e|Ftf|LRH-1|UF2-H3B	nuclear receptor subfamily 5, group A, member 2	protein-coding
mm_129587.1	chr15	79774409	79774474	-	1	NA	promoter-TSS (NM_017470)	promoter-TSS (NM_017470)	26	NM_017470	54152	Mm.288159	NM_017470	ENSMUSG00000022420	Dnal4	D15Ertd424e|Dnalc4	dynein, axonemal, light chain 4	protein-coding
mm_119171.1	chr14	32142022	32142025	+	1	NA	promoter-TSS (NM_020597)	promoter-TSS (NM_020597)	0	NM_020597	17695	Mm.2540	NM_020597	ENSMUSG00000021907	Msmb	PIP|PSP94|beta-MSP	beta-microseminoprotein	protein-coding
mm_171861.1	chr5	22563782	22563802	+	1	NA	Intergenic	Intergenic	13379	NR_102315	320719	Mm.459265	NR_102315	ENSMUSG00000097207	6030443J06Rik	1700030G06Rik	RIKEN cDNA 6030443J06 gene	ncRNA
mm_166980.1	chr7	45277374	45277378	+	1	NA	Intergenic	CpG	-5497	NM_001033176	76713	Mm.425445	NM_001033176	ENSMUSG00000070568	Slc6a21	1700039E15Rik|Gm19188	solute carrier family 6 member 21	protein-coding
mm_130606.1	chr15	99820028	99820032	-	1	NA	5' UTR (NM_023063, exon 1 of 8)	5' UTR (NM_023063, exon 1 of 8)	119	NM_023063	65970	Mm.33207	NM_023063	ENSMUSG00000023022	Lima1	Eplin	LIM domain and actin binding 1	protein-coding
mm_139805.1	chr17	66206806	66206833	+	1	NA	Intergenic	Intergenic	83299	NM_001003919	320209	Mm.259605	NM_001003919	ENSMUSG00000035842	Ddx11	4732462I11Rik|CHL1|CHLR1|KRG2|essa15a	DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11	protein-coding
mm_138320.1	chr17	34837173	34837192	+	1	NA	promoter-TSS (NM_019442)	promoter-TSS (NM_019442)	163	NM_001163770	112403	Mm.275309	NM_033613	ENSMUSG00000040482	Dxo	Dom3z|NG6	decapping exoribonuclease	protein-coding
mm_71125.1	chr8	36458096	36458108	+	1	NA	Intergenic	CpG	-31089	NM_176952	319582	Mm.180924	NM_176952	ENSMUSG00000039620	6430573F11Rik	Kiaa1456|TRM9L	RIKEN cDNA 6430573F11 gene	protein-coding
mm_50168.1	chr6	41554722	41554742	+	1	NA	Intergenic	Intergenic	32956	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_71765.1	chr8	66420365	66420376	+	1	NA	intron (NM_175188, intron 6 of 7)	intron (NM_175188, intron 6 of 7)	34069	NM_001166375	72925	Mm.380457	NM_175188	ENSMUSG00000036469	March1	2900024D24Rik|BB085186	membrane-associated ring finger (C3HC4) 1	protein-coding
mm_6708.1	chr1	82286841	82286874	-	1	NA	exon (NM_010570, exon 1 of 2)	exon (NM_010570, exon 1 of 2)	4582	NM_010570	16367	Mm.4952	NM_010570	ENSMUSG00000055980	Irs1	G972R|IRS-1	insulin receptor substrate 1	protein-coding
mm_55084.1	chr6	49214848	49214856	-	1	NA	5' UTR (NM_023670, exon 1 of 15)	5' UTR (NM_023670, exon 1 of 15)	102	NM_023670	140488	Mm.281018	NM_023670	ENSMUSG00000029814	Igf2bp3	2610101N11Rik|AA522010|AL022933|AU045931|IMP-3|IMP3|Koc13|Neilsen|mimp3	insulin-like growth factor 2 mRNA binding protein 3	protein-coding
mm_171642.1	chr4	31885814	31885814	+	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	-78293	NM_009316	26409	Mm.258589	NM_009316	ENSMUSG00000028284	Map3k7	B430101B05|C87327|Tak1	mitogen-activated protein kinase kinase kinase 7	protein-coding
mm_62724.1	chr7	110773851	110773862	+	1	NA	intron (NM_009667, intron 1 of 14)	intron (NM_009667, intron 1 of 14)	1252	NM_009667	11717	Mm.3238	NM_009667	ENSMUSG00000005686	Ampd3	-	adenosine monophosphate deaminase 3	protein-coding
mm_162897.1	chr10	112837705	112837714	+	1	NA	Intergenic	Intergenic	91317	NM_001033474	382423	Mm.431239	NM_001033474	ENSMUSG00000074748	Atxn7l3b	4921506J03Rik|6230409E21Rik|AI315132|ENSMUSG00000074747	ataxin 7-like 3B	protein-coding
mm_15810.1	chr2	164497519	164497560	+	1	NA	promoter-TSS (NM_133779)	promoter-TSS (NM_133779)	14	NM_133779	78928	Mm.28228	NM_133779	ENSMUSG00000017721	Pigt	2510012P17Rik|4930534E15Rik|CGI-06|NDAP|Ndap7	phosphatidylinositol glycan anchor biosynthesis, class T	protein-coding
mm_129550.1	chr15	79429855	79429859	-	1	NA	exon (NM_013767, exon 4 of 11)	exon (NM_013767, exon 4 of 11)	11961	NM_001289899	27373	Mm.30199	NM_013767	ENSMUSG00000022433	Csnk1e	AI426939|AI551861|AW457082|CK1epsilon|CKIe|KC1epsilon|tau	casein kinase 1, epsilon	protein-coding
mm_139297.1	chr17	48319230	48319241	+	1	NA	intron (NM_177083, intron 3 of 5)	intron (NM_177083, intron 3 of 5)	3073	NM_177083	320148	Mm.123455	NM_177083	ENSMUSG00000043740	B430306N03Rik	Treml6	RIKEN cDNA B430306N03 gene	protein-coding
mm_161605.1	chr16	43906905	43906905	+	1	NA	exon (NM_027801, exon 4 of 16)	exon (NM_027801, exon 4 of 16)	17003	NM_027801	212153	Mm.209835	NM_027801	ENSMUSG00000022701	Ccdc191	2610015P09Rik|8430422M09Rik|AU040712	coiled-coil domain containing 191	protein-coding
mm_19936.1	chr2	116065786	116065796	-	1	NA	promoter-TSS (NM_010825)	promoter-TSS (NM_010825)	-733	NM_010825	17536	Mm.247566	NM_010825	ENSMUSG00000027210	Meis2	A430109D20Rik|Mrg1|Stra10	Meis homeobox 2	protein-coding
mm_103781.1	chr11	82764288	82764297	-	1	NA	promoter-TSS (NM_025884)	promoter-TSS (NM_025884)	29	NM_009839	12467	Mm.4126	NM_009839	ENSMUSG00000020698	Cct6b	CCT-zeta-2|CCTzeta-2|Cctz-2|TCP-1-zeta-2	chaperonin containing Tcp1, subunit 6b (zeta)	protein-coding
mm_106746.1	chr12	3913395	3913414	+	1	NA	3' UTR (NM_153743, exon 18 of 18)	3' UTR (NM_153743, exon 18 of 18)	21660	NM_153743	13435	Mm.5001	NM_007872	ENSMUSG00000020661	Dnmt3a	MmuIIIA	DNA methyltransferase 3A	protein-coding
mm_86128.1	chr9	116175441	116175451	-	1	NA	promoter-TSS (NM_029575)	promoter-TSS (NM_029575)	-83	NM_009371	21813	Mm.172346	NM_009371	ENSMUSG00000032440	Tgfbr2	1110020H15Rik|AU042018|DNIIR|RIIDN|TBR-II|TbetaR-II|TbetaRII	transforming growth factor, beta receptor II	protein-coding
mm_89611.1	chr10	96028428	96028439	+	1	NA	exon (NM_001001932, exon 21 of 29)	exon (NM_001001932, exon 21 of 29)	87770	NM_001001932	216238	Mm.210035	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding
mm_137964.1	chr17	33432284	33432290	+	1	NA	promoter-TSS (NM_183282)	promoter-TSS (NM_183282)	-612	NM_183282	69481	Mm.154333	NM_183282	ENSMUSG00000092519	Actl9	1700029I08Rik|AV259599	actin-like 9	protein-coding
mm_72018.1	chr8	70724045	70724059	+	1	NA	promoter-TSS (NM_201607)	promoter-TSS (NM_201607)	-12	NM_001310465	110385	Mm.255180	NM_201607	ENSMUSG00000031842	Pde4c	Dpde1|E130301F19Rik|dunce	phosphodiesterase 4C, cAMP specific	protein-coding
mm_35348.1	chr4	32250732	32250743	-	1	NA	Intergenic	Intergenic	-166698	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_26040.1	chr3	135548579	135548592	+	1	NA	intron (NM_027288, intron 10 of 16)	L2|LINE|L2	62974	NM_027288	110173	Mm.280536	NM_027288	ENSMUSG00000028164	Manba	2410030O07Rik|B930014J03Rik|Bmn	mannosidase, beta A, lysosomal	protein-coding
mm_144625.1	chr18	32938892	32938894	+	1	NA	promoter-TSS (NM_009793)	promoter-TSS (NM_009793)	-148	NM_009793	12326	Mm.222329	NM_009793	ENSMUSG00000038128	Camk4	A430110E23Rik|AI666733|CaMKIV|CaMKIV/Gr|D18Bwg0362e	calcium/calmodulin-dependent protein kinase IV	protein-coding
mm_10666.1	chr2	20967349	20967365	+	1	NA	exon (NM_001081364, exon 1 of 24)	exon (NM_001081364, exon 1 of 24)	364	NM_001081364	71435	Mm.28507	NM_001081364	ENSMUSG00000036591	Arhgap21	5530401C11Rik|AA416458|ARHGAP10	Rho GTPase activating protein 21	protein-coding
mm_33964.1	chr4	137560725	137560738	+	1	NA	intron (NM_008305, intron 81 of 96)	intron (NM_008305, intron 81 of 96)	14449	NM_001033979	435811	Mm.359646	NM_001033979	ENSMUSG00000094035	Ldlrad2	-	low density lipoprotein receptor A domain containing 2	protein-coding
mm_92340.1	chr10	75834436	75834494	-	1	NA	5' UTR (NM_010361, exon 1 of 5)	5' UTR (NM_010361, exon 1 of 5)	416	NM_010361	14872	Mm.24118	NM_010361	ENSMUSG00000033318	Gstt2	AI266894|Yrs|mGSTT2	glutathione S-transferase, theta 2	protein-coding
mm_142667.1	chr17	47728857	47728865	-	1	NA	exon (NM_025973, exon 2 of 9)	exon (NM_025973, exon 2 of 9)	2019	NM_025973	109820	Mm.22957	NM_025973	ENSMUSG00000023987	Pgc	2210410L06Rik|Upg-1|Upg1	progastricsin (pepsinogen C)	protein-coding
mm_28348.1	chr3	89455283	89455307	-	1	NA	intron (NM_001310640, intron 1 of 3)	intron (NM_001310640, intron 1 of 3)	754	NM_001310640	68603	Mm.34242	NM_026784	ENSMUSG00000027952	Pmvk	1110011E12Rik|2900002L22Rik|AV001327|PMK|PMKA|PMKASE	phosphomevalonate kinase	protein-coding
mm_116179.1	chr13	30833557	30833567	-	1	NA	intron (NM_025588, intron 23 of 27)	intron (NM_025588, intron 23 of 27)	84329	NM_013674	16364	Mm.4677	NM_013674	ENSMUSG00000021356	Irf4	AI385587|IRF-4|LSIRF|NF-EM5|Spip	interferon regulatory factor 4	protein-coding
mm_162165.1	chrX	96356997	96356997	-	1	NA	intron (NM_001310755, intron 2 of 10)	intron (NM_001310755, intron 2 of 10)	10922	NM_001310754	245525	Mm.166749	NM_172931	ENSMUSG00000045802	Hsf3	B230358A15Rik|HSF 3|HSTF 3	heat shock transcription factor 3	protein-coding
mm_70195.1	chr7	144470715	144470770	-	1	NA	5' UTR (NM_001252572, exon 1 of 17)	5' UTR (NM_001252572, exon 1 of 17)	193	NM_007803	13043	Mm.205601	NM_007803	ENSMUSG00000031078	Cttn	1110020L01Rik|Ems1	cortactin	protein-coding
mm_56804.1	chr6	116657361	116657409	-	1	NA	intron (NM_178045, intron 3 of 10)	intron (NM_178045, intron 3 of 10)	6701	NM_001166580	213393	Mm.38231	NM_145980	ENSMUSG00000048489	8430408G22Rik	Depp|Fseg	RIKEN cDNA 8430408G22 gene	protein-coding
mm_47915.1	chr5	135000758	135000762	-	1	NA	non-coding (NR_026907, exon 1 of 5)	non-coding (NR_026907, exon 1 of 5)	590	NR_026907	71304	Mm.482317	NR_026907	ENSMUSG00000054909	Wbscr25	4933433J03Rik|4933439O14Rik	Williams Beuren syndrome chromosome region 25 (human)	ncRNA
mm_120505.1	chr14	66296548	66296551	+	1	NA	promoter-TSS (NM_029979)	promoter-TSS (NM_029979)	-476	NM_029979	66854	Mm.43871	NM_029979	ENSMUSG00000022043	Trim35	0710005M05Rik|A430106H13Rik|AW046487|HLS5|Mair|NC8|mKIAA1098	tripartite motif-containing 35	protein-coding
mm_85154.1	chr9	96333132	96333155	-	1	NA	3' UTR (NM_007502, exon 7 of 7)	3' UTR (NM_007502, exon 7 of 7)	31156	NM_007502	11933	Mm.424	NM_007502	ENSMUSG00000032412	Atp1b3	AA409958|AI664000|AW212096	ATPase, Na+/K+ transporting, beta 3 polypeptide	protein-coding
mm_23353.1	chr3	55112081	55112171	+	1	NA	promoter-TSS (NM_001144988)	promoter-TSS (NM_001144988)	18	NM_144895	229285	Mm.235523	NM_144895	ENSMUSG00000036580	Spg20	AI840044|C79168|SPARTIN|TAHCCP1|mKIAA0610	spastic paraplegia 20, spartin (Troyer syndrome) homolog (human)	protein-coding
mm_128075.1	chr15	27663494	27663518	-	1	NA	intron (NM_001242423, intron 4 of 7)	intron (NM_001242423, intron 4 of 7)	18036	NM_001242424	223433	Mm.266485	NM_198301	ENSMUSG00000056069	Fam105a	9830126M18	family with sequence similarity 105, member A	protein-coding
mm_161817.1	chr17	70424995	70424995	+	1	NA	intron (NM_001347411, intron 4 of 14)	intron (NM_001347411, intron 4 of 14)	203	NM_027712	224997	Mm.311840	NM_027712	ENSMUSG00000003279	Dlgap1	4933422O14Rik|9630002F18|AI845682|AI848168|BB075781|D17Bwg0511e|GKAP/SAPAP|GKPA/SAPAP|Gkap|Sapap1|mKIAA4162	discs, large (Drosophila) homolog-associated protein 1	protein-coding
mm_131645.1	chr16	20531595	20531606	+	1	NA	3' UTR (NM_007889, exon 15 of 15)	3' UTR (NM_007889, exon 15 of 15)	-3880	NM_001302970	11773	Mm.18946	NM_009679	ENSMUSG00000022841	Ap2m1	-	adaptor-related protein complex 2, mu 1 subunit	protein-coding
mm_149203.1	chr19	9980547	9980564	+	1	NA	promoter-TSS (NR_073181)	promoter-TSS (NR_073181)	-45	NR_073181	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
mm_65121.1	chr7	19414968	19414974	-	1	NA	exon (NM_007710, exon 3 of 8)	exon (NM_007710, exon 3 of 8)	3877	NM_007710	12715	Mm.2375	NM_007710	ENSMUSG00000030399	Ckm	Ckmm|M-CK|MCK	creatine kinase, muscle	protein-coding
mm_57214.1	chr6	122856152	122856163	-	1	NA	promoter-TSS (NM_009779)	promoter-TSS (NM_009779)	0	NM_009779	12267	Mm.2408	NM_009779	ENSMUSG00000040552	C3ar1	AZ3B|C3AR|HNFAG09	complement component 3a receptor 1	protein-coding
mm_61116.1	chr7	54835693	54835703	+	1	NA	5' UTR (NM_178705, exon 1 of 12)	5' UTR (NM_178705, exon 1 of 12)	453	NM_178705	233271	Mm.387344	NM_178705	ENSMUSG00000063297	Luzp2	9330154K17Rik|D130073E01	leucine zipper protein 2	protein-coding
mm_108722.1	chr12	87163858	87163869	+	1	NA	3' UTR (NM_001252556, exon 8 of 8)	3' UTR (NM_001252556, exon 8 of 8)	-8378	NR_136901	625237	Mm.390529	NR_136901		Gm6566	EG625237	predicted gene 6566	ncRNA
mm_52472.1	chr6	114248346	114248361	+	1	NA	3' UTR (NM_172890, exon 14 of 14)	3' UTR (NM_172890, exon 14 of 14)	-34282	NM_178703	232333	Mm.5260	NM_178703	ENSMUSG00000030310	Slc6a1	A730043E01|GABATHG|GABATR|GAT-1|Gabt|Gabt1|Gat1|XT-1|Xtrp1	solute carrier family 6 (neurotransmitter transporter, GABA), member 1	protein-coding
mm_3799.1	chr1	157506778	157506811	+	1	NA	promoter-TSS (NM_033354)	promoter-TSS (NM_033354)	-2	NM_033354	89867	Mm.87114	NM_033354	ENSMUSG00000026589	Sec16b	Lztr2|Rgpr|Rgpr-p117	SEC16 homolog B (S. cerevisiae)	protein-coding
mm_9719.1	chr1	179803704	179803714	-	1	NA	5' UTR (NM_026375, exon 1 of 36)	5' UTR (NM_026375, exon 1 of 36)	306	NM_026375	226747	Mm.128165	NM_026375	ENSMUSG00000026491	Ahctf1	6230412P20Rik|AV011447|Elys	AT hook containing transcription factor 1	protein-coding
mm_150864.1	chr19	45018052	45018063	+	1	NA	promoter-TSS (NM_001130526)	promoter-TSS (NM_001130526)	-78	NM_001130526	226154	Mm.28204	NM_145503	ENSMUSG00000035342	Lzts2	BC014695|LAPSER1|mKIAA1813	leucine zipper, putative tumor suppressor 2	protein-coding
mm_39329.1	chr5	8660041	8660047	+	1	NA	promoter-TSS (NM_011076)	promoter-TSS (NM_011076)	-48	NM_011076	18671	Mm.207354	NM_011076	ENSMUSG00000040584	Abcb1a	Abcb4|Evi32|Mdr1a|Mdr3|P-gp|Pgp|Pgy-3|Pgy3|mdr-3	ATP-binding cassette, sub-family B (MDR/TAP), member 1A	protein-coding
mm_124054.1	chr14	77874888	77874941	-	1	NA	promoter-TSS (NM_025384)	promoter-TSS (NM_025384)	3	NM_025384	66148	Mm.248046	NM_025384	ENSMUSG00000022013	Dnajc15	1110003P16Rik|Dnajd1	DnaJ heat shock protein family (Hsp40) member C15	protein-coding
mm_118310.1	chr13	113101914	113101925	-	1	NA	promoter-TSS (NM_010370)	promoter-TSS (NM_010370)	-938	NM_010370	14938	Mm.15510	NM_010370	ENSMUSG00000023132	Gzma	AW494114|Ctla-3|Ctla3|Hf|Hf1|SE1|TSP-1|TSP1	granzyme A	protein-coding
mm_77544.1	chr8	123158308	123158325	-	1	NA	promoter-TSS (NM_020564)	promoter-TSS (NM_020564)	-36	NM_020564	57429	Mm.6562	NM_020564	ENSMUSG00000000739	Sult5a1	Sult-x1|Sultx1	sulfotransferase family 5A, member 1	protein-coding
mm_24961.1	chr3	96697077	96697090	+	1	NA	promoter-TSS (NM_001165949)	promoter-TSS (NM_001165949)	7	NM_018812	229615	Mm.1635	NM_018812	ENSMUSG00000028101	Pias3	Pias3l	protein inhibitor of activated STAT 3	protein-coding
mm_46432.1	chr5	104460256	104460279	-	1	NA	intron (NM_008861, intron 1 of 14)	CpG	810	NM_008861	18764	Mm.6442	NM_008861	ENSMUSG00000034462	Pkd2	C030034P18Rik|PC2|TRPP2	polycystic kidney disease 2	protein-coding
mm_110503.1	chr12	54459473	54459478	-	1	NA	Intergenic	LTR33|LTR|ERVL	-68157	NR_033689	665239	Mm.26856	NR_033689		Gm7550	EG665239|Gm666	predicted gene 7550	ncRNA
mm_109302.1	chr12	109560588	109560607	+	1	NA	non-coding (NR_003633, exon 5 of 5)	non-coding (NR_003633, exon 5 of 5)	-3095	NR_030427	791079		NR_030427	ENSMUSG00000076451	Mir770	Mirn770|mir-770|mmu-mir-770	microRNA 770	ncRNA
mm_119689.1	chr14	53544883	53544917	+	1	NA	Intergenic	Intergenic	709029	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_30854.1	chr4	28812813	28812821	+	1	NA	promoter-TSS (NM_010141)	promoter-TSS (NM_010141)	-314	NM_001290434	13841	Mm.257266	NM_010141	ENSMUSG00000028289	Epha7	Cek11|Ebk|Ehk3|Hek11|Mdk1	Eph receptor A7	protein-coding
mm_88195.1	chr10	70096961	70096965	+	1	NA	promoter-TSS (NM_001111121)	promoter-TSS (NM_001111121)	-158	NM_001111121	76551	Mm.281741	NM_001111121	ENSMUSG00000048701	Ccdc6	2810012H18Rik|AA536681|AA960498|AW061011	coiled-coil domain containing 6	protein-coding
mm_148184.1	chr18	78206409	78206419	-	1	NA	promoter-TSS (NM_001110274)	promoter-TSS (NM_001110274)	26	NM_001110274	27411	Mm.44158	NM_030683	ENSMUSG00000024552	Slc14a2	UT-A1|UT-A3	solute carrier family 14 (urea transporter), member 2	protein-coding
mm_485.1	chr1	36761848	36761897	+	1	NA	promoter-TSS (NM_009539)	promoter-TSS (NM_009539)	74	NM_009539	22637	Mm.8038	NM_009539	ENSMUSG00000026117	Zap70	Srk|ZAP-70|mrtle|mur	zeta-chain (TCR) associated protein kinase	protein-coding
mm_89927.1	chr10	111232404	111232414	+	1	NA	intron (NM_175489, intron 3 of 23)	RMER17C2|LTR|ERVK	-66270	NM_027914	71769	Mm.45256	NM_027914	ENSMUSG00000035759	Bbs10	1300007O09Rik|AI452285	Bardet-Biedl syndrome 10 (human)	protein-coding
mm_70365.1	chr8	8683857	8683938	+	1	NA	exon (NM_176849, exon 2 of 4)	exon (NM_176849, exon 2 of 4)	6265	NR_106114	102465762		NR_106114	ENSMUSG00000098917	Mir7654	Gm27748|mmu-mir-7654	microRNA 7654	ncRNA
mm_3725.1	chr1	154256983	154256984	+	1	NA	promoter-TSS (NR_040629)	promoter-TSS (NR_040629)	-77	NR_040629	78112	Mm.401935	NR_040629	ENSMUSG00000099933	4930452N14Rik	-	RIKEN cDNA 4930452N14 gene	ncRNA
mm_151685.1	chr19	4283086	4283142	-	1	NA	promoter-TSS (NM_026720)	promoter-TSS (NM_026720)	23	NM_026720	68423	Mm.23642	NM_026720	ENSMUSG00000005986	Ankrd13d	0710001P18Rik|AI430801	ankyrin repeat domain 13 family, member D	protein-coding
mm_54572.1	chr6	38096933	38096946	-	1	NA	intron (NM_080467, intron 1 of 20)	intron (NM_080467, intron 1 of 20)	-12414	NM_029921	77522	Mm.387207	NM_029921	ENSMUSG00000029829	Tmem213	D630002J15Rik	transmembrane protein 213	protein-coding
mm_2439.1	chr1	98060308	98060309	+	1	NA	intron (NM_013626, intron 1 of 25)	intron (NM_013626, intron 1 of 25)	-12515	NR_037993	78603	Mm.442597	NR_037993	ENSMUSG00000089706	B230216N24Rik	-	RIKEN cDNA B230216N24 gene	ncRNA
mm_111357.1	chr12	86990504	86990521	-	1	NA	Intergenic	CpG	-1836	NM_001080943	238331	Mm.185890	NM_001080943	ENSMUSG00000048483	Zdhhc22	Gm262	zinc finger, DHHC-type containing 22	protein-coding
mm_119893.1	chr14	54937820	54937828	+	1	NA	intron (NM_029390, intron 1 of 3)	intron (NM_029390, intron 1 of 3)	1327	NM_029390	67272	Mm.41614	NM_026066	ENSMUSG00000040759	Cmtm5	1500005P16Rik|2900052H21Rik|Cklfsf5	CKLF-like MARVEL transmembrane domain containing 5	protein-coding
mm_138359.1	chr17	34982100	34982151	+	1	NA	promoter-TSS (NM_030597)	promoter-TSS (NM_030597)	-5	NM_001204273	27756	Mm.165735	NM_030597	ENSMUSG00000007050	Lsm2	D17H6S56E-2|D17H6S56E2|Dmapl|Dmpkap|G7b|Sm-X5|SmX5|snRNP	LSM2 homolog, U6 small nuclear RNA and mRNA degradation associated	protein-coding
mm_63835.1	chr7	135537815	135537830	+	1	NA	promoter-TSS (NM_011212)	promoter-TSS (NM_011212)	-2	NM_011212	19267	Mm.945	NM_011212	ENSMUSG00000041836	Ptpre	PTPe|PTPepsilon|RPTPepsilon	protein tyrosine phosphatase, receptor type, E	protein-coding
mm_21780.1	chr2	164848006	164848016	-	1	NA	intron (NM_011125, intron 8 of 15)	intron (NM_011125, intron 8 of 15)	9697	NM_011125	18830	Mm.6105	NM_011125	ENSMUSG00000017754	Pltp	Bpife|OD107	phospholipid transfer protein	protein-coding
mm_37841.1	chr4	132075418	132075430	-	1	NA	promoter-TSS (NM_001128607)	promoter-TSS (NM_001128607)	-111	NM_001128607	269587	Mm.30038	NM_183428	ENSMUSG00000028906	Epb41	4.1R|AI415518|D4Ertd442e|Elp-1|Elp1|Epb4.1|mKIAA4056	erythrocyte membrane protein band 4.1	protein-coding
mm_44230.1	chr5	5215865	5215868	-	1	NA	intron (NM_011074, intron 4 of 14)	intron (NM_011074, intron 4 of 14)	50202	NM_001310448	18647	Mm.389061	NM_011074	ENSMUSG00000028926	Cdk14	Pftk1|mKIAA0834	cyclin-dependent kinase 14	protein-coding
mm_111907.1	chr12	108765991	108765995	-	1	NA	Intergenic	Intergenic	-27318	NM_009537	22632	Mm.3868	NM_009537	ENSMUSG00000021264	Yy1	AW488674|NF-E1	YY1 transcription factor	protein-coding
mm_73208.1	chr8	95713348	95713364	+	1	NA	3' UTR (NM_145602, exon 14 of 14)	3' UTR (NM_145602, exon 14 of 14)	-2557	NM_001035123	66083	Mm.261321	NM_001035123	ENSMUSG00000031671	Setd6	0610039J04Rik|3110004G14Rik|AI413388|C76402	SET domain containing 6	protein-coding
mm_92846.1	chr10	81509281	81509287	-	1	NA	intron (NM_010304, intron 5 of 6)	intron (NM_010304, intron 5 of 6)	-9147	NM_010102	13611	Mm.33065	NM_010102	ENSMUSG00000044199	S1pr4	Edg6|Lpc1|S1p4	sphingosine-1-phosphate receptor 4	protein-coding
mm_129915.1	chr15	84185065	84185105	-	1	NA	intron (NM_054088, intron 7 of 7)	intron (NM_054088, intron 7 of 7)	-7148	NM_178614	68653	Mm.290725	NM_178614	ENSMUSG00000022437	Samm50	1110030L07Rik	SAMM50 sorting and assembly machinery component	protein-coding
mm_138805.1	chr17	39106972	39106978	+	1	NA	Intergenic	IAPLTR3|LTR|ERVK	-29938	NM_001177582	100126779	Mm.471589	NM_001177582	ENSMUSG00000096697	Esp23	Gm20581	exocrine gland secreted peptide 23	protein-coding
mm_139924.1	chr17	71019334	71019345	+	1	NA	promoter-TSS (NM_001083934)	promoter-TSS (NM_001083934)	-218	NM_010867	17929	Mm.4103	NM_010867	ENSMUSG00000024049	Myom1	D430047A17Rik	myomesin 1	protein-coding
mm_60706.1	chr7	45220466	45220478	+	1	NA	exon (NM_001285498, exon 5 of 12)	exon (NM_001285498, exon 5 of 12)	4719	NM_001285498	21677	Mm.3019	NM_011565	ENSMUSG00000030796	Tead2	ETF|Etdf|TEAD-2|TEF-4|TEF4	TEA domain family member 2	protein-coding
mm_142129.1	chr17	35901436	35901452	-	1	NA	exon (NM_028476, exon 9 of 10)	exon (NM_028476, exon 9 of 10)	-4066	NM_001033630	69662	Mm.260159	NM_001033630	ENSMUSG00000050705	2310061I04Rik	-	RIKEN cDNA 2310061I04 gene	protein-coding
mm_14910.1	chr2	150570428	150570483	+	1	NA	promoter-TSS (NM_009977)	promoter-TSS (NM_009977)	40	NM_009977	13011	Mm.12965	NM_009977	ENSMUSG00000068129	Cst7	Cmap	cystatin F (leukocystatin)	protein-coding
mm_157707.1	chrX	64275930	64275938	-	1	NA	intron (NM_178740, intron 1 of 2)	CpG	1062	NM_178740	245446	Mm.101707	NM_178740	ENSMUSG00000046699	Slitrk4	6430513G13|D930039I09Rik	SLIT and NTRK-like family, member 4	protein-coding
mm_119377.1	chr14	41132297	41132304	+	1	NA	intron (NM_023134, intron 2 of 5)	intron (NM_023134, intron 2 of 5)	512	NM_023134	20387	Mm.46062	NM_023134	ENSMUSG00000021789	Sftpa1	SP-A|Sftp-1|Sftp1	surfactant associated protein A1	protein-coding
mm_57893.1	chr6	131368543	131368567	-	1	NA	exon (NM_011733, exon 7 of 9)	exon (NM_011733, exon 7 of 9)	19895	NM_139117	56449	Mm.458000	NM_011733	ENSMUSG00000030189	Ybx3	Csda|Dpba|MSY3|MSY4|Yb2|dbpA|oxyR	Y box protein 3	protein-coding
mm_83253.1	chr9	42401599	42401620	-	1	NA	Intergenic	Intergenic	-1680	NM_001324548	21683	Mm.42209	NM_009347	ENSMUSG00000037705	Tecta	Tctna	tectorin alpha	protein-coding
mm_82410.1	chr9	14780362	14780383	-	1	NA	3' UTR (NM_019683, exon 2 of 2)	3' UTR (NM_019683, exon 2 of 2)	2592	NM_019683	56503	Mm.395005	NM_019683	ENSMUSG00000031931	Ankrd49	AW060934|C86108|Gbif	ankyrin repeat domain 49	protein-coding
mm_72833.1	chr8	88272582	88272585	+	1	NA	5' UTR (NM_007406, exon 1 of 28)	5' UTR (NM_007406, exon 1 of 28)	180	NM_007406	11513	Mm.288206	NM_007406	ENSMUSG00000031659	Adcy7	AA407758	adenylate cyclase 7	protein-coding
mm_146800.1	chr18	20703279	20703286	-	1	NA	intron (NM_019737, intron 4 of 8)	RLTR15|LTR|ERVK	38032	NM_013697	22139	Mm.2108	NM_013697	ENSMUSG00000061808	Ttr	AA408768|AI787086|D17860|prealbumin	transthyretin	protein-coding
mm_33015.1	chr4	120951818	120951840	+	1	NA	promoter-TSS (NM_001005788)	promoter-TSS (NM_001005788)	-128	NM_001005788	381549	Mm.331840	NM_001005788	ENSMUSG00000064141	Zfp69	Gm1029|Krab2|Zfp63	zinc finger protein 69	protein-coding
mm_159694.1	chr5	24413632	24413632	+	1	NA	5' UTR (NM_183000, exon 1 of 11)	5' UTR (NM_183000, exon 1 of 11)	181	NM_001310474	171209	Mm.299636	NM_183000	ENSMUSG00000038276	Asic3	AW742291|Accn3|DRASIC|SLNAC1|TNAC1	acid-sensing (proton-gated) ion channel 3	protein-coding
mm_141707.1	chr17	33999966	34000003	-	1	NA	exon (NM_001001892, exon 2 of 8)	exon (NM_001001892, exon 2 of 8)	349	NM_001001892	14972	Mm.422886	NM_001001892	ENSMUSG00000061232	H2-K1	H-2K|H-2K(d)|H2-K|K-f	histocompatibility 2, K1, K region	protein-coding
mm_31933.1	chr4	86558431	86558448	+	1	NA	promoter-TSS (NM_001081096)	promoter-TSS (NM_001081096)	-5	NR_131920	74888		NR_131920	ENSMUSG00000085108	Saxo1os	4930457A20Rik|Fam154aos	stabilizer of axonemal microtubules 1, opposite strand	ncRNA
mm_14978.1	chr2	152109064	152109079	+	1	NA	exon (NM_029688, exon 2 of 2)	exon (NM_029688, exon 2 of 2)	3547	NM_029688	76650	Mm.218639	NM_029688	ENSMUSG00000032802	Srxn1	1700127B04Rik|AI854065|AW488194|Npn3|Srx|Srx1|TX01	sulfiredoxin 1 homolog (S. cerevisiae)	protein-coding
mm_155814.1	chrX	100494335	100494366	+	1	NA	promoter-TSS (NM_008784)	promoter-TSS (NM_008784)	59	NM_008784	18518	Mm.7454	NM_008784	ENSMUSG00000031221	Igbp1	AI115586|AI662457|AW208785|C81413|Pc52|Tap42|p52	immunoglobulin (CD79A) binding protein 1	protein-coding
mm_5666.1	chr1	42694949	42695014	-	1	NA	promoter-TSS (NR_027826)	promoter-TSS (NR_027826)	-156	NR_027826	66297	Mm.45203	NM_183252	ENSMUSG00000060424	Pantr1	2610017I09Rik|Pou3f3os|linc-Brn1a	POU domain, class 3, transcription factor 3 adjacent noncoding transcript 1	ncRNA
mm_166148.1	chr5	5420268	5420320	-	1	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	-40043	NM_011074	18647	Mm.389061	NM_011074	ENSMUSG00000028926	Cdk14	Pftk1|mKIAA0834	cyclin-dependent kinase 14	protein-coding
mm_2297.1	chr1	91494632	91494698	+	1	NA	promoter-TSS (NM_028718)	promoter-TSS (NM_028718)	-3	NM_028718	74019	Mm.318430	NM_028718	ENSMUSG00000034292	Traf3ip1	3930402D05Rik|AU041749|MIP-T3	TRAF3 interacting protein 1	protein-coding
mm_41369.1	chr5	90524814	90524839	+	1	NA	exon (NM_145146, exon 5 of 15)	exon (NM_145146, exon 5 of 15)	5877	NM_145146	280662	Mm.348786	NM_145146	ENSMUSG00000029369	Afm	Alf|alpha-Alb	afamin	protein-coding
mm_93599.1	chr10	117190262	117190278	-	1	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	34237	NM_026570	64050	Mm.233529	NM_026570	ENSMUSG00000020171	Yeats4	4930573H17Rik|B230215M10Rik|GAS41|NuBI-1	YEATS domain containing 4	protein-coding
mm_94591.1	chr11	11769184	11769185	+	1	NA	exon (NM_009578, exon 7 of 7)	exon (NM_009578, exon 7 of 7)	39778	NM_021891	60530	Mm.236114	NM_021891	ENSMUSG00000035455	Fignl1	-	fidgetin-like 1	protein-coding
mm_56086.1	chr6	87335700	87335706	-	1	NA	promoter-TSS (NM_054041)	promoter-TSS (NM_054041)	72	NM_054041	69538	Mm.232525	NM_054041	ENSMUSG00000033420	Antxr1	2310008J16Rik|2810405N18Rik|Antrx1|Tem8	anthrax toxin receptor 1	protein-coding
mm_125086.1	chr15	27466598	27466608	+	1	NA	promoter-TSS (NM_020332)	promoter-TSS (NM_020332)	-74	NM_020332	11732	Mm.265264	NM_020332	ENSMUSG00000022265	Ank	Ankh|D15Ertd221e|ank|mKIAA1581	progressive ankylosis	protein-coding
mm_146689.1	chr18	12862859	12862865	-	1	NA	promoter-TSS (NM_001252492)	promoter-TSS (NM_001252492)	-149	NM_001252491	64291	Mm.259470	NM_020573	ENSMUSG00000044252	Osbpl1a	G430090F17Rik|Gm753|ORP-1|Osbpl1b	oxysterol binding protein-like 1A	protein-coding
mm_14173.1	chr2	126707320	126707411	+	1	NA	promoter-TSS (NM_001252580)	promoter-TSS (NM_001252580)	37	NM_019729	84092	Mm.272629	NM_019729	ENSMUSG00000027363	Usp8	AI574262|AW557536|Ubpy|mKIAA0055	ubiquitin specific peptidase 8	protein-coding
mm_45015.1	chr5	38527682	38527693	-	1	NA	3' UTR (NM_011715, exon 15 of 15)	3' UTR (NM_011715, exon 15 of 15)	-25535	NM_145559	117591	Mm.260137	NM_145559	ENSMUSG00000005107	Slc2a9	Glut9|SLC2A9B|SLC2a9A	solute carrier family 2 (facilitated glucose transporter), member 9	protein-coding
mm_993.1	chr1	58712062	58712089	+	1	NA	intron (NM_001289704, intron 1 of 9)	intron (NM_001289704, intron 1 of 9)	584	NM_001293804	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_157714.1	chrX	67921431	67921438	-	1	NA	promoter-TSS (NM_025763)	promoter-TSS (NM_025763)	16	NM_025763	66780	Mm.79193	NM_025763	ENSMUSG00000025288	4933436I01Rik	-	RIKEN cDNA 4933436I01 gene	protein-coding
mm_111323.1	chr12	86469979	86469989	-	1	NA	intron (NM_011934, intron 1 of 6)	intron (NM_011934, intron 1 of 6)	48340	NM_011934	26380	Mm.235550	NM_011934	ENSMUSG00000021255	Esrrb	Err2|Errb|Estrrb|Nr3b2	estrogen related receptor, beta	protein-coding
mm_35639.1	chr4	43518460	43518473	-	1	NA	intron (NM_001277876, intron 6 of 8)	intron (NM_001277876, intron 6 of 8)	5088	NM_009416	22004	Mm.646	NM_009416	ENSMUSG00000028464	Tpm2	Tpm-2|Trop-2	tropomyosin 2, beta	protein-coding
mm_32843.1	chr4	117849310	117849334	+	1	NA	intron (NM_008135, intron 2 of 13)	intron (NM_008135, intron 2 of 13)	14064	NM_008135	14664	Mm.244549	NM_008135	ENSMUSG00000028542	Slc6a9	Glyt-1|Glyt1	solute carrier family 6 (neurotransmitter transporter, glycine), member 9	protein-coding
mm_167106.1	chr7	112681051	112681069	-	1	NA	intron (NM_009346, intron 1 of 12)	intron (NM_009346, intron 1 of 12)	1740	NM_009346	21676	Mm.24685	NM_009346	ENSMUSG00000055320	Tead1	2610024B07Rik|B230114H05Rik|Gtrgeo5|TEAD-1|TEF-1|Tcf13|mTEF-1	TEA domain family member 1	protein-coding
mm_120868.1	chr14	75230025	75230051	+	1	NA	3' UTR (NM_001247984, exon 16 of 16)	3' UTR (NM_001247984, exon 16 of 16)	-12249	NM_019775	56373	Mm.24242	NM_019775	ENSMUSG00000021999	Cpb2	1110032P04Rik|4930405E17Rik|AI255929|CPR|Cpu|TAFI	carboxypeptidase B2 (plasma)	protein-coding
mm_169841.1	chr16	3113490	3113498	-	1	NA	Intergenic	B1_Mur4|SINE|Alu	-478904	NM_146860	258859	Mm.377723	NM_146860	ENSMUSG00000051003	Olfr161	MOR131-1|OR912-47M6	olfactory receptor 161	protein-coding
mm_127268.1	chr15	99719141	99719164	+	1	NA	exon (NM_010271, exon 3 of 8)	exon (NM_010271, exon 3 of 8)	1559	NM_010271	14555	Mm.252391	NM_010271	ENSMUSG00000023019	Gpd1	AI747587|Gdc-1|Gdc1|mKIAA4010	glycerol-3-phosphate dehydrogenase 1 (soluble)	protein-coding
mm_64521.1	chr7	143841240	143841254	+	1	NA	exon (NM_007856, exon 6 of 9)	exon (NM_007856, exon 6 of 9)	18080	NM_007856	13360	Mm.249342	NM_007856	ENSMUSG00000058454	Dhcr7	AA409147	7-dehydrocholesterol reductase	protein-coding
mm_611.1	chr1	40009817	40009831	+	1	NA	exon (NM_001252202, exon 20 of 30)	exon (NM_001252202, exon 20 of 30)	-74944	NM_010555	16178	Mm.1349	NM_010555	ENSMUSG00000026073	Il1r2	CD121b|Il1r-2	interleukin 1 receptor, type II	protein-coding
mm_139281.1	chr17	48247846	48247855	+	1	NA	TTS (NM_021406)	TTS (NM_021406)	121	NM_021407	58218	Mm.302438	NM_021407	ENSMUSG00000041754	Trem3	BB134760	triggering receptor expressed on myeloid cells 3	protein-coding
mm_28401.1	chr3	90238826	90238845	-	1	NA	intron (NM_030080, intron 5 of 9)	intron (NM_030080, intron 5 of 9)	3715	NM_001307935	78284	Mm.299952	NM_030080	ENSMUSG00000027938	Creb3l4	1700012K17Rik|5330432F22Rik|AIBZIP|AV040530|AV258827|CREB4|JAL|TISP40|acre1	cAMP responsive element binding protein 3-like 4	protein-coding
mm_43264.1	chr5	130369248	130369289	+	1	NA	promoter-TSS (NM_181045)	promoter-TSS (NM_181045)	-190	NM_181045	140904	Mm.40875	NM_021371	ENSMUSG00000060371	Caln1	9630012C17Rik|Cabp8|MNCb-0849	calneuron 1	protein-coding
mm_5517.1	chr1	37665695	37665715	-	1	NA	intron (NM_028096, intron 1 of 9)	intron (NM_028096, intron 1 of 9)	54106	NM_028096	72097	Mm.142607	NM_028096	ENSMUSG00000026090	2010300C02Rik	-	RIKEN cDNA 2010300C02 gene	protein-coding
mm_16354.1	chr2	174426291	174426295	+	1	NA	intron (NM_020580, intron 11 of 14)	intron (NM_020580, intron 11 of 14)	10489	NM_020580	57314	Mm.271709	NM_020580	ENSMUSG00000016253	Nelfcd	2410003I03Rik|C77797|Th1|Th1l	negative elongation factor complex member C/D, Th1l	protein-coding
mm_46452.1	chr5	105116849	105116856	-	1	NA	3' UTR (NM_001256005, exon 11 of 11)	3' UTR (NM_001256005, exon 11 of 11)	-6560	NM_172777	236573	Mm.425261	NM_172777	ENSMUSG00000029298	Gbp9	-	guanylate-binding protein 9	protein-coding
mm_171284.1	chr3	89957394	89957395	-	1	NA	intron (NM_001081182, intron 7 of 27)	intron (NM_001081182, intron 7 of 27)	5938	NM_001081182	54667	Mm.30455	NM_001081182	ENSMUSG00000060671	Atp8b2	Id	ATPase, class I, type 8B, member 2	protein-coding
mm_48754.1	chr5	148184364	148184387	-	1	NA	intron (NM_029920, intron 4 of 14)	intron (NM_029920, intron 4 of 14)	208440	NM_001301424	11987	Mm.275489	NM_007513	ENSMUSG00000041313	Slc7a1	4831426K01Rik|AI447493|Atrc-1|Atrc1|Cat1|Rec-1|Rev-1|mCAT-1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 1	protein-coding
mm_158756.1	chrX	166469840	166469851	-	1	NA	intron (NM_019773, intron 1 of 2)	intron (NM_019773, intron 1 of 2)	10022	NM_019773	56382	Mm.25306	NM_019773	ENSMUSG00000079316	Rab9	2410064E05Rik|AI195561|Rab9a|Sid6061p	RAB9, member RAS oncogene family	protein-coding
mm_151348.1	chr19	55896416	55896420	+	1	NA	intron (NM_001142924, intron 1 of 11)	intron (NM_001142924, intron 1 of 11)	1097	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_120401.1	chr14	64950105	64950115	+	1	NA	promoter-TSS (NM_001253731)	promoter-TSS (NM_001253731)	65	NM_001253731	210925	Mm.71332	NM_153414	ENSMUSG00000021975	Ints9	BC028953|D14Ertd231e	integrator complex subunit 9	protein-coding
mm_107813.1	chr12	65182563	65182572	+	1	NA	Intergenic	L1_Mus3|LINE|L1	-9987	NM_172578	217653	Mm.21144	NM_172578	ENSMUSG00000047534	Mis18bp1	6720403H11|C79407|Knl2|mKIAA1903	MIS18 binding protein 1	protein-coding
mm_39669.1	chr5	25247386	25247409	+	1	NA	intron (NM_144908, intron 1 of 11)	intron (NM_144908, intron 1 of 11)	24504	NM_144908	231050	Mm.21814	NM_144908	ENSMUSG00000038072	Galnt11	A430075I06Rik|AI648252|E430002F06Rik	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 11	protein-coding
mm_74887.1	chr8	25102180	25102194	-	1	NA	promoter-TSS (NM_031257)	promoter-TSS (NM_031257)	-376	NM_031257	83436	Mm.261122	NM_031257	ENSMUSG00000031557	Plekha2	6430512N22Rik|AI851530|AU041791|TAPP2|W91773	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 2	protein-coding
mm_66479.1	chr7	45013511	45013535	-	1	NA	exon (NM_001008422, exon 2 of 11)	exon (NM_001008422, exon 2 of 11)	-1036	NR_106021	102466218		NR_106021	ENSMUSG00000098839	Mir7054	Gm27557|mmu-mir-7054	microRNA 7054	ncRNA
mm_172141.1	chr6	36810025	36810025	-	1	NA	5' UTR (NM_008973, exon 1 of 5)	5' UTR (NM_008973, exon 1 of 5)	1336	NM_008973	19242	Mm.279690	NM_008973	ENSMUSG00000029838	Ptn	HARP|HB-GAM|HBBN|HBGF-8|HBNF|OSF|Osf-1|Osf1	pleiotrophin	protein-coding
mm_82199.1	chr9	124073545	124073555	+	1	NA	Intergenic	RMER19C|LTR|ERVK	-28633	NM_009915	12772	Mm.6272	NM_009915	ENSMUSG00000049103	Ccr2	Cc-ckr-2|Ccr2a|Ccr2b|Ckr2|Ckr2a|Ckr2b|Cmkbr2|mJe-r	chemokine (C-C motif) receptor 2	protein-coding
mm_36657.1	chr4	94928821	94928848	-	1	NA	promoter-TSS (NM_001290623)	promoter-TSS (NM_001290623)	9	NM_027089	67753	Mm.25097	NM_027089	ENSMUSG00000028575	Eqtn	1700028B15Rik|4930579C15Rik|Afaf|C81058|Eqtl|Eqts	equatorin, sperm acrosome associated	protein-coding
mm_103555.1	chr11	77719511	77719522	-	1	NA	exon (NM_009965, exon 5 of 6)	exon (NM_009965, exon 5 of 6)	5777	NM_001313933	12957	Mm.22830	NM_009965	ENSMUSG00000000724	Cryba1	BA3/A1|Cryb	crystallin, beta A1	protein-coding
mm_78253.1	chr9	21743999	21744013	+	1	NA	exon (NM_001252659, exon 13 of 18)	exon (NM_001252659, exon 13 of 18)	16280	NM_026282	67629	Mm.295642	NM_026282	ENSMUSG00000074476	Spc24	2410030K01Rik|AV109292|Spbc24	SPC24, NDC80 kinetochore complex component, homolog (S. cerevisiae)	protein-coding
mm_62438.1	chr7	101373272	101373284	+	1	NA	exon (NM_001040111, exon 3 of 34)	exon (NM_001040111, exon 3 of 34)	-4844	NM_001040112	69710	Mm.277687	NM_027180	ENSMUSG00000032812	Arap1	2410002L19Rik|Centd2|mKIAA0782	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	protein-coding
mm_21981.1	chr2	167483320	167483347	-	1	NA	3' UTR (NM_170756, exon 3 of 3)	3' UTR (NM_170756, exon 3 of 3)	-9312	NM_030743	81018	Mm.22225	NM_030743	ENSMUSG00000006418	Rnf114	1110008J21Rik|AI225886|AW549494|Zfp228|Zfp313|Znf228	ring finger protein 114	protein-coding
mm_131310.1	chr16	11500706	11500712	+	1	NA	intron (NM_001290148, intron 6 of 13)	B4A|SINE|B4	95061	NM_001290148	74478	Mm.325831	NM_028964	ENSMUSG00000071669	Snx29	4933437K13Rik|ENSMUSG00000079738|Gm11170|Gm1737|Gm930|Rundc2a	sorting nexin 29	protein-coding
mm_19913.1	chr2	114654944	114654969	-	1	NA	promoter-TSS (NM_025675)	promoter-TSS (NM_025675)	-28	NM_025675	66632	Mm.117809	NM_025675	ENSMUSG00000057147	Dph6	5730421E18Rik|Atpbd4	diphthamine biosynthesis 6	protein-coding
mm_62597.1	chr7	105650814	105650833	+	1	NA	Intergenic	Intergenic	10283	NM_019502	14356	Mm.220330	NM_019502	ENSMUSG00000089847	Timm10b	Fxc1|Tim10b|Tim9b	translocase of inner mitochondrial membrane 10B	protein-coding
mm_89621.1	chr10	96181808	96181811	+	1	NA	Intergenic	Intergenic	-44398	NR_110448	74881	Mm.410819	NR_110448		4930459C07Rik	-	RIKEN cDNA 4930459C07 gene	ncRNA
mm_30142.1	chr3	142385006	142385012	-	1	NA	intron (NM_022554, intron 1 of 8)	intron (NM_022554, intron 1 of 8)	6841	NM_022554	56376	Mm.117709	NM_019808	ENSMUSG00000028273	Pdlim5	1110001A05Rik|AI987914|C87059|Enh|Enh1|Enh2|Enh3|LIM	PDZ and LIM domain 5	protein-coding
mm_19621.1	chr2	102812665	102812711	-	1	NA	3' UTR (NM_009851, exon 19 of 19)	3' UTR (NM_009851, exon 19 of 19)	88977	NM_001177785	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_16109.1	chr2	169633518	169633529	+	1	NA	promoter-TSS (NM_080455)	promoter-TSS (NM_080455)	-123	NM_080455	228911	Mm.315789	NM_080455	ENSMUSG00000047907	Tshz2	2900073F20Rik|B830045G17|Mtsh2|Sdccag33l|Tsh2|Zfp218|mKIAA4248|teashirt2	teashirt zinc finger family member 2	protein-coding
mm_59825.1	chr7	29289279	29289285	+	1	NA	promoter-TSS (NM_026731)	promoter-TSS (NM_026731)	-38	NM_026731	68458	Mm.2343	NM_026731	ENSMUSG00000037166	Ppp1r14a	1110001M11Rik|Cpi17	protein phosphatase 1, regulatory (inhibitor) subunit 14A	protein-coding
mm_84435.1	chr9	66069744	66069772	-	1	NA	promoter-TSS (NM_001025612)	promoter-TSS (NM_001025612)	-27	NM_001025612	382083	Mm.477103	NM_001025612	ENSMUSG00000039452	Snx22	Gm1120	sorting nexin 22	protein-coding
mm_80058.1	chr9	69397898	69397928	+	1	NA	promoter-TSS (NM_145618)	promoter-TSS (NM_145618)	-85	NM_145618	93697	Mm.35911	NM_145618	ENSMUSG00000032235	Ice2	B230343B06Rik|Narg2	interactor of little elongation complex ELL subunit 2	protein-coding
mm_165887.1	chr4	43522850	43522903	-	1	NA	intron (NM_001277875, intron 1 of 8)	intron (NM_001277875, intron 1 of 8)	678	NM_009416	22004	Mm.646	NM_009416	ENSMUSG00000028464	Tpm2	Tpm-2|Trop-2	tropomyosin 2, beta	protein-coding
mm_171067.1	chr3	113565648	113565649	+	1	NA	intron (NM_001110505, intron 3 of 10)	RLTR9D|LTR|ERVK	9114	NM_007446	11722	Mm.439727	NM_007446	ENSMUSG00000074264	Amy1	Amy-1|Amy1a|C030014B17Rik	amylase 1, salivary	protein-coding
mm_74558.1	chr8	10947807	10947820	-	1	NA	Intergenic	Intergenic	-19356	NR_135302	665306	Mm.358758	NR_030715	ENSMUSG00000038917	3930402G23Rik	-	RIKEN cDNA 3930402G23 gene	ncRNA
mm_94137.1	chr10	128704948	128704975	-	1	NA	promoter-TSS (NM_016756)	promoter-TSS (NM_016756)	90	NM_183417	12566	Mm.111326	NM_016756	ENSMUSG00000025358	Cdk2	A630093N05Rik	cyclin-dependent kinase 2	protein-coding
mm_106871.1	chr12	8010477	8010481	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	32802	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_149337.1	chr19	10850290	10850310	+	1	NA	intron (NM_023044, intron 2 of 7)	MTD|LTR|ERVL-MaLR	7756	NM_023044	65221	Mm.27387	NM_023044	ENSMUSG00000024737	Slc15a3	Ci1|cI-1	solute carrier family 15, member 3	protein-coding
mm_1278.1	chr1	63446086	63446090	+	1	NA	5' UTR (NM_011780, exon 1 of 26)	5' UTR (NM_011780, exon 1 of 26)	197	NM_011780	23792	Mm.124892	NM_011780	ENSMUSG00000025964	Adam23	AW046396|MDC3	a disintegrin and metallopeptidase domain 23	protein-coding
mm_164671.1	chr17	45569283	45569294	-	1	NA	exon (NM_008302, exon 8 of 11)	exon (NM_008302, exon 8 of 11)	3973	NM_008302	15516	Mm.2180	NM_008302	ENSMUSG00000023944	Hsp90ab1	90kDa|AL022974|C81438|Hsp84|Hsp84-1|Hsp90|Hspcb	heat shock protein 90 alpha (cytosolic), class B member 1	protein-coding
mm_64030.1	chr7	140769206	140769214	+	1	NA	exon (NM_021282, exon 3 of 9)	exon (NM_021282, exon 3 of 9)	5378	NM_021282	13106	Mm.21758	NM_021282	ENSMUSG00000025479	Cyp2e1	Cyp2e	cytochrome P450, family 2, subfamily e, polypeptide 1	protein-coding
mm_125407.1	chr15	41710655	41710661	+	1	NA	intron (NM_001130166, intron 3 of 16)	intron (NM_001130166, intron 3 of 16)	-78376	NM_001130165	170719	Mm.254267	NM_130885	ENSMUSG00000022307	Oxr1	2210416C20Rik|C7|C7B	oxidation resistance 1	protein-coding
mm_49137.1	chr6	8949671	8949686	+	1	NA	promoter-TSS (NM_008751)	promoter-TSS (NM_008751)	-341	NM_008751	18231	Mm.46954	NM_008751	ENSMUSG00000046178	Nxph1	C130005L03Rik	neurexophilin 1	protein-coding
mm_150262.1	chr19	34206394	34206394	+	1	NA	intron (NM_029682, intron 1 of 10)	intron (NM_029682, intron 1 of 10)	14124	NM_029682	76630	Mm.130952	NM_029682	ENSMUSG00000024776	Stambpl1	1700095N21Rik|8230401J17Rik|ALMalpha|AMSH-FP	STAM binding protein like 1	protein-coding
mm_26363.1	chr3	142560065	142560105	+	1	NA	promoter-TSS (NM_018734)	promoter-TSS (NM_018734)	33	NM_001289492	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_1038.1	chr1	58758380	58758403	+	1	NA	3' UTR (NM_207653, exon 10 of 10)	3' UTR (NM_207653, exon 10 of 10)	27839	NM_001293805	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_56686.1	chr6	113910579	113910585	-	1	NA	intron (NM_001347365, intron 2 of 23)	intron (NM_001347365, intron 2 of 23)	-19043	NM_001036684	11941	Mm.321755	NM_009723	ENSMUSG00000030302	Atp2b2	D6Abb2e|Gena300|PMCA2|Tmy|dfw|jog|wms|wri	ATPase, Ca++ transporting, plasma membrane 2	protein-coding
mm_17967.1	chr2	37577573	37577588	-	1	NA	3' UTR (NM_009261, exon 17 of 17)	3' UTR (NM_009261, exon 17 of 17)	60954	NM_177383	338346	Mm.445325	NM_177383	ENSMUSG00000053164	Gpr21	C230004C13Rik	G protein-coupled receptor 21	protein-coding
mm_44700.1	chr5	30545837	30545852	-	1	NA	promoter-TSS (NM_028483)	promoter-TSS (NM_028483)	-8	NM_028483	73259	Mm.443299	NM_028483	ENSMUSG00000053194	Cib4	1700041E20Rik	calcium and integrin binding family member 4	protein-coding
mm_132121.1	chr16	31713446	31713462	+	1	NA	intron (NR_045516, intron 4 of 24)	(TGG)n|Simple_repeat|Simple_repeat	-40896	NM_001252436	13383	Mm.382	NM_007862	ENSMUSG00000022770	Dlg1	B130052P05Rik|Dlgh1|E-dlg/SAP97|SAP-97|SAP97|mKIAA4187	discs, large homolog 1 (Drosophila)	protein-coding
mm_63937.1	chr7	139719357	139719359	+	1	NA	Intergenic	Intergenic	-35543	NM_001302546	212124	Mm.425507	NM_177212	ENSMUSG00000049571	Cfap46	9330101J02Rik|E030019B06Rik|Gm170|Ttc40	cilia and flagella associated protein 46	protein-coding
mm_115032.1	chr13	99247829	99247882	+	1	NA	TTS (NM_001004149)	TTS (NM_001004149)	63032	NM_001004149	238803	Mm.343207	NM_001004149	ENSMUSG00000050919	Zfp366	DC-SCRIPT|Znf366	zinc finger protein 366	protein-coding
mm_80007.1	chr9	67840332	67840358	+	1	NA	promoter-TSS (NM_177184)	promoter-TSS (NM_177184)	-51	NM_177184	320528	Mm.241454	NM_177184	ENSMUSG00000035284	Vps13c	AI552542|AV026040|C230055H22Rik|W51662|chorein	vacuolar protein sorting 13C	protein-coding
mm_95600.1	chr11	53350993	53350999	+	1	NA	5' UTR (NM_033565, exon 1 of 21)	5' UTR (NM_033565, exon 1 of 21)	229	NM_033565	93736	Mm.395281	NM_033565	ENSMUSG00000049470	Aff4	AF5Q31|Alf4|Laf4l|MCEF	AF4/FMR2 family, member 4	protein-coding
mm_152395.1	chr19	10525202	10525214	-	1	NA	promoter-TSS (NM_025333)	promoter-TSS (NM_025333)	1	NM_025333	66072	Mm.180063	NM_025333	ENSMUSG00000024668	Sdhaf2	0610038F07Rik|AA407634|AW049997	succinate dehydrogenase complex assembly factor 2	protein-coding
mm_45162.1	chr5	50024009	50024011	-	1	NA	intron (NM_133911, intron 2 of 18)	intron (NM_133911, intron 2 of 18)	34986	NM_133911	70693	Mm.272974	NM_133911	ENSMUSG00000029090	Adgra3	3830613O22Rik|AU044632|Gpr125|Tem5-like	adhesion G protein-coupled receptor A3	protein-coding
mm_3196.1	chr1	135818594	135818602	+	1	NA	promoter-TSS (NM_133664)	promoter-TSS (NM_133664)	0	NM_133664	16763	Mm.36726	NM_133664	ENSMUSG00000041782	Lad1	-	ladinin	protein-coding
mm_23440.1	chr3	59432007	59432022	+	1	NA	Intergenic	Intergenic	-87758	NM_001162884	242050	Mm.228086	NM_001162884	ENSMUSG00000036334	Igsf10	6530405F15Rik|9030224D03|AA409708|AA536958|AI414626|Adlican2|CMF608	immunoglobulin superfamily, member 10	protein-coding
mm_10131.1	chr2	3810196	3810210	+	1	NA	Intergenic	Intergenic	96745	NM_025626	66540	Mm.277864	NM_025626	ENSMUSG00000026655	Fam107b	3110001A13Rik|AA589595|AA959793|AI132312	family with sequence similarity 107, member B	protein-coding
mm_24245.1	chr3	89136609	89136629	+	1	NA	promoter-TSS (NM_001099779)	promoter-TSS (NM_001099779)	-4	NM_001099779	18770	Mm.383180	NM_013631	ENSMUSG00000041237	Pklr	Pk-1|Pk1|R-PK	pyruvate kinase liver and red blood cell	protein-coding
mm_82795.1	chr9	29412252	29412277	-	1	NA	intron (NM_172290, intron 1 of 7)	CpG	550865	NM_172290	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding
mm_57406.1	chr6	124865543	124865551	-	1	NA	3' UTR (NM_013488, exon 10 of 10)	3' UTR (NM_013488, exon 10 of 10)	-1630	NM_013533	14788	Mm.2514	NM_013533	ENSMUSG00000038390	Gpr162	A-2|BC031437|Grca	G protein-coupled receptor 162	protein-coding
mm_18285.1	chr2	52558540	52558571	-	1	NA	promoter-TSS (NM_146123)	promoter-TSS (NM_146123)	56	NM_146123	12298	Mm.330223	NM_146123	ENSMUSG00000017412	Cacnb4	3110038O15Rik|Cchb4|lh	calcium channel, voltage-dependent, beta 4 subunit	protein-coding
mm_44621.1	chr5	25665750	25665752	-	1	NA	Intergenic	Intergenic	40046	NM_020570	57434	Mm.143767	NM_020570	ENSMUSG00000028933	Xrcc2	4921524O04Rik|8030409M04Rik|RAD51|RecA	X-ray repair complementing defective repair in Chinese hamster cells 2	protein-coding
mm_103257.1	chr11	71004388	71004501	-	1	NA	promoter-TSS (NM_178367)	promoter-TSS (NM_178367)	-12	NM_178367	216877	Mm.35399	NM_178367	ENSMUSG00000040620	Dhx33	3110057P17Rik|9430096J02Rik|Ddx33	DEAH (Asp-Glu-Ala-His) box polypeptide 33	protein-coding
mm_50896.1	chr6	57366113	57366141	+	1	NA	Intergenic	RMER19C|LTR|ERVK	-4749	NM_134171	171189	Mm.377169	NM_134171	ENSMUSG00000093411	Vmn1r17	V1rc16	vomeronasal 1 receptor 17	protein-coding
mm_58790.1	chr7	16130272	16130283	+	1	NA	5' UTR (NM_148946, exon 1 of 10)	5' UTR (NM_148946, exon 1 of 10)	451	NM_148946	110891	Mm.241147	NM_148946	ENSMUSG00000030376	Slc8a2	Ncx2	solute carrier family 8 (sodium/calcium exchanger), member 2	protein-coding
mm_32281.1	chr4	102978692	102978713	+	1	NA	intron (NR_040444, intron 2 of 3)	intron (NR_040444, intron 2 of 3)	-7677	NM_001163767	67344	Mm.111346	NM_026100	ENSMUSG00000028523	Tctex1d1	1700055O19Rik	Tctex1 domain containing 1	protein-coding
mm_148227.1	chr18	80353764	80353767	-	1	NA	intron (NM_001190373, intron 1 of 3)	L1_Mur3|LINE|L1	10489	NM_001190373	240444	Mm.279568	NM_001190373	ENSMUSG00000059852	Kcng2	AA591524	potassium voltage-gated channel, subfamily G, member 2	protein-coding
mm_77747.1	chr8	127440269	127440285	-	1	NA	intron (NM_001309391, intron 20 of 24)	intron (NM_001309391, intron 20 of 24)	140625	NM_001013580	93742	Mm.299254	NM_033620	ENSMUSG00000025812	Pard3	AA960621|AI256638|Asip|D8Ertd580e|Par-3|Par3|Pard-3|Pard3a|Phip	par-3 family cell polarity regulator	protein-coding
mm_147224.1	chr18	38203799	38203828	-	1	NA	intron (NM_029357, intron 1 of 2)	intron (NM_029357, intron 1 of 2)	5949	NM_029357	75599	Mm.36560	NM_029357	ENSMUSG00000051375	Pcdh1	2010005A06Rik|AI585920	protocadherin 1	protein-coding
mm_122295.1	chr14	34588627	34588637	-	1	NA	promoter-TSS (NM_001039071)	promoter-TSS (NM_001039071)	-25	NM_001039074	24131	Mm.29733	NM_011918	ENSMUSG00000021798	Ldb3	AW742271|PDLIM6|ZASP	LIM domain binding 3	protein-coding
mm_1731.1	chr1	75383586	75383588	+	1	NA	intron (NM_001085371, intron 2 of 10)	intron (NM_001085371, intron 2 of 10)	1473	NM_001085371	11790	Mm.275397	NM_007463	ENSMUSG00000026207	Speg	AW125581|Apeg1|BPEG|D1Bwg1450e|SPEGalpha|SPEGbeta|mKIAA1297	SPEG complex locus	protein-coding
mm_40398.1	chr5	52834115	52834167	+	1	NA	promoter-TSS (NM_024213)	promoter-TSS (NM_024213)	6	NM_024213	52206	Mm.272568	NM_024213	ENSMUSG00000029176	Anapc4	2610306D21Rik|APC4|D5Ertd249e	anaphase promoting complex subunit 4	protein-coding
mm_72486.1	chr8	83666708	83666717	+	1	NA	promoter-TSS (NM_013641)	promoter-TSS (NM_013641)	72	NM_013641	19216	Mm.213000	NM_013641	ENSMUSG00000019464	Ptger1	42kDa|EP1|Ptgerep1	prostaglandin E receptor 1 (subtype EP1)	protein-coding
mm_56972.1	chr6	120227164	120227200	-	1	NA	intron (NM_198884, intron 3 of 19)	intron (NM_198884, intron 3 of 19)	33359	NM_001347432	29862	Mm.103668	NM_016718	ENSMUSG00000041377	Ninj2	-	ninjurin 2	protein-coding
mm_88430.1	chr10	77458000	77458038	+	1	NA	Intergenic	Intergenic	39643	NR_027377	100045653	Mm.363175	NR_027377		Gm17769	-	predicted gene, 17769	ncRNA
mm_74692.1	chr8	15018892	15018906	-	1	NA	intron (NM_029116, intron 1 of 1)	intron (NM_029116, intron 1 of 1)	7874	NM_029116	74901	Mm.46675	NM_029116	ENSMUSG00000055675	Kbtbd11	2900016B01Rik|4930465M17Rik|mKIAA0711	kelch repeat and BTB (POZ) domain containing 11	protein-coding
mm_77188.1	chr8	111864038	111864040	-	1	NA	TTS (NM_025781)	TTS (NM_025781)	-9729	NM_011801	23837	Mm.279437	NM_011801	ENSMUSG00000031954	Cfdp1	AA408409|Bcnt|Bucentaur|Cfdp|cp27	craniofacial development protein 1	protein-coding
mm_141247.1	chr17	27513388	27513405	-	1	NA	Intergenic	CpG	-9863	NM_001291045	268934	Mm.358940	NM_001013385	ENSMUSG00000063239	Grm4	Gprc1d|mGluR4	glutamate receptor, metabotropic 4	protein-coding
mm_122233.1	chr14	33185175	33185188	-	1	NA	promoter-TSS (NM_001146022)	promoter-TSS (NM_001146022)	-115	NM_001146022	545030	Mm.318345	NM_001146022	ENSMUSG00000051506	Wdfy4	Gm18810	WD repeat and FYVE domain containing 4	protein-coding
mm_33044.1	chr4	122971491	122971493	+	1	NA	Intergenic	Intergenic	-10304	NM_029662	76574	Mm.331842	NM_029662	ENSMUSG00000028655	Mfsd2a	1700018O18Rik|Mfsd2|NLS1	major facilitator superfamily domain containing 2A	protein-coding
mm_149899.1	chr19	25505783	25505815	+	1	NA	promoter-TSS (NM_015826)	promoter-TSS (NM_015826)	93	NM_015826	50796	Mm.391208	NM_015826	ENSMUSG00000024837	Dmrt1	-	doublesex and mab-3 related transcription factor 1	protein-coding
mm_138806.1	chr17	39406406	39406431	+	1	NA	promoter-TSS (NM_001244763)	promoter-TSS (NM_001244763)	59	NM_001244763	100126774	Mm.350534	NM_001244763	ENSMUSG00000094024	Esp18	Gm20579	exocrine gland secreted peptide 18	protein-coding
mm_53944.1	chr6	5188749	5188768	-	1	NA	intron (NM_011134, intron 1 of 8)	intron (NM_011134, intron 1 of 8)	5188	NM_011134	18979	Mm.237657	NM_011134	ENSMUSG00000002588	Pon1	Pon	paraoxonase 1	protein-coding
mm_77704.1	chr8	126591493	126591520	-	1	NA	exon (NM_001164598, exon 2 of 2)	exon (NM_001164598, exon 2 of 2)	1930	NM_001164598	270110	Mm.334918	NM_001164598	ENSMUSG00000051495	Irf2bp2	E130305N23Rik|IRF-2BP2	interferon regulatory factor 2 binding protein 2	protein-coding
mm_3461.1	chr1	150104038	150104082	+	1	NA	exon (NM_011198, exon 7 of 10)	exon (NM_011198, exon 7 of 10)	4029	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_133511.1	chr16	90738441	90738458	+	1	NA	5' UTR (NM_029844, exon 1 of 3)	5' UTR (NM_029844, exon 1 of 3)	125	NM_029844	77037	Mm.22455	NM_029844	ENSMUSG00000039956	Mrap	1110025G12Rik|Falp|ORF61	melanocortin 2 receptor accessory protein	protein-coding
mm_137011.1	chr17	17831048	17831069	+	1	NA	promoter-TSS (NM_001162909)	promoter-TSS (NM_001162909)	83	NM_001162909	75202	Mm.227456	NM_029205	ENSMUSG00000080316	Spaca6	4930546H06Rik|9530079D04Rik|B230206P06Rik|Ncrna00085|SPACA6A|let-7e|mir-125a|mir-99b	sperm acrosome associated 6	protein-coding
mm_128374.1	chr15	42676490	42676522	-	1	NA	5' UTR (NM_001286062, exon 1 of 9)	5' UTR (NM_001286062, exon 1 of 9)	471	NM_001286062	11600	Mm.309336	NM_009640	ENSMUSG00000022309	Angpt1	1110046O21Rik|Ang-1|Ang1	angiopoietin 1	protein-coding
mm_36712.1	chr4	97778043	97778071	-	1	NA	intron (NM_010905, intron 1 of 10)	CpG	431	NM_010905	18027	Mm.31274	NM_010905	ENSMUSG00000028565	Nfia	1110047K16Rik|9430022M17Rik|CTF|NF1-A|NF1A	nuclear factor I/A	protein-coding
mm_116247.1	chr13	33935834	33935861	-	1	NA	promoter-TSS (NR_040707)	promoter-TSS (NR_040707)	-185	NR_040707	68808	Mm.443347	NR_040707	ENSMUSG00000085457	1110046J04Rik	-	RIKEN cDNA 1110046J04 gene	ncRNA
mm_11187.1	chr2	29099879	29099890	+	1	NA	Intergenic	RLTR34D_MM|LTR|ERVK	-25108	NM_198033	269254	Mm.41867	NM_198033	ENSMUSG00000043535	Setx	A130090N03|A930037J23Rik|AOA2|AW060766|Als4|SCAR1|Sen1|mKIAA0625	senataxin	protein-coding
mm_139446.1	chr17	55445705	55445730	+	1	NA	promoter-TSS (NM_172829)	promoter-TSS (NM_172829)	0	NM_172829	240119	Mm.311687	NM_172829	ENSMUSG00000024172	St6gal2	C230064G14Rik|St6galII|mKIAA1877	beta galactoside alpha 2,6 sialyltransferase 2	protein-coding
mm_32050.1	chr4	97581917	97581958	+	1	NA	promoter-TSS (NM_001122952)	promoter-TSS (NM_001122952)	-6	NM_001122952	18027	Mm.31274	NM_010905	ENSMUSG00000028565	Nfia	1110047K16Rik|9430022M17Rik|CTF|NF1-A|NF1A	nuclear factor I/A	protein-coding
mm_123663.1	chr14	69244458	69244474	-	1	NA	3' UTR (NM_026331, exon 4 of 4)	3' UTR (NM_026331, exon 4 of 4)	40637	NM_026331	67712	Mm.293635	NM_026331	ENSMUSG00000034248	Slc25a37	1700020E22Rik|4930513O14Rik|4930526G11Rik|AI848481|C330015G08Rik|Mfrn|Mfrn1|Mscp|frascati|mitoferrin	solute carrier family 25, member 37	protein-coding
mm_164722.1	chr17	57031439	57031443	-	1	NA	promoter-TSS (NM_010613)	promoter-TSS (NM_010613)	66	NM_010613	16549	Mm.34296	NM_010613	ENSMUSG00000007670	Khsrp	6330409F21Rik|Fbp2|Fubp2|Ksrp	KH-type splicing regulatory protein	protein-coding
mm_140513.1	chr17	5803336	5803362	-	1	NA	TTS (NR_045081)	TTS (NR_045081)	3859	NR_045080	78512	Mm.23696	NR_045079	ENSMUSG00000096965	3300005D01Rik	-	RIKEN cDNA 3300005D01 gene	ncRNA
mm_12855.1	chr2	83724159	83724169	+	1	NA	promoter-TSS (NM_008402)	promoter-TSS (NM_008402)	-233	NM_008402	16410	Mm.227	NM_008402	ENSMUSG00000027087	Itgav	1110004F14Rik|2610028E01Rik|CD51|D430040G12Rik	integrin alpha V	protein-coding
mm_23699.1	chr3	68694096	68694104	+	1	NA	intron (NM_001159424, intron 3 of 7)	intron (NM_001159424, intron 3 of 7)	2676	NM_008351	16159	Mm.103783	NM_008351	ENSMUSG00000027776	Il12a	IL-12p35|Il-12a|Ll12a|p35	interleukin 12a	protein-coding
mm_57252.1	chr6	123283533	123283539	-	1	NA	3' UTR (NM_019948, exon 6 of 6)	3' UTR (NM_019948, exon 6 of 6)	6335	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_142825.1	chr17	51761802	51761804	-	1	NA	intron (NM_009122, intron 9 of 10)	intron (NM_009122, intron 9 of 10)	50251	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_31659.1	chr4	59905124	59905135	+	1	NA	TTS (NM_172468)	TTS (NM_172468)	9927	NM_021053	30936	Mm.284433	NM_021053	ENSMUSG00000028386	Slc46a2	5430429N04Rik|Ly110|TSO-1C12|Tscot	solute carrier family 46, member 2	protein-coding
mm_45165.1	chr5	50543589	50543591	-	1	NA	Intergenic	Intergenic	290828	NR_106197	102465903		NR_106197	ENSMUSG00000099124	Mir8117	Gm27323|mmu-mir-8117	microRNA 8117	ncRNA
mm_77620.1	chr8	123949202	123949287	-	1	NA	promoter-TSS (NM_172288)	promoter-TSS (NM_172288)	21	NM_172288	234865	Mm.267812	NM_172288	ENSMUSG00000039509	Nup133	mermaid	nucleoporin 133	protein-coding
mm_156989.1	chrX	7412775	7412788	-	1	NA	intron (NR_027924, intron 1 of 1)	intron (NR_027924, intron 1 of 1)	8266	NR_027925	68355	Mm.45111	NR_027924		2010204K13Rik	0610010M13Rik|Cip7	RIKEN cDNA 2010204K13 gene	ncRNA
mm_138084.1	chr17	33996394	33996419	+	1	NA	3' UTR (NM_001001892, exon 8 of 8)	3' UTR (NM_001001892, exon 8 of 8)	3927	NM_001001892	14972	Mm.422886	NM_001001892	ENSMUSG00000061232	H2-K1	H-2K|H-2K(d)|H2-K|K-f	histocompatibility 2, K1, K region	protein-coding
mm_66001.1	chr7	30559829	30559842	-	1	NA	promoter-TSS (NM_001290569)	promoter-TSS (NM_001290569)	-189	NM_001290569	75660	Mm.379242	NM_029377	ENSMUSG00000036845	Lin37	1810054G18Rik	lin-37 homolog (C. elegans)	protein-coding
mm_121696.1	chr14	13961860	13961887	-	1	NA	promoter-TSS (NM_025435)	promoter-TSS (NM_025435)	-560	NM_025435	66231	Mm.295875	NM_025435	ENSMUSG00000053453	Thoc7	Nif3l1bp1	THO complex 7	protein-coding
mm_18954.1	chr2	76787182	76787197	-	1	NA	exon (NM_011652, exon 220 of 313)	exon (NM_011652, exon 220 of 313)	111874	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_11518.1	chr2	32606980	32607057	+	1	NA	promoter-TSS (NM_016973)	promoter-TSS (NM_016973)	33	NR_110347	50935	Mm.88831	NM_016973	ENSMUSG00000026811	St6galnac6	ST6GalNAcVI|Siat7f	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 6	protein-coding
mm_137767.1	chr17	29490753	29490767	+	1	NA	promoter-TSS (NM_008842)	promoter-TSS (NM_008842)	-285	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_34962.1	chr4	156008579	156008603	+	1	NA	intron (NM_001302468, intron 4 of 6)	intron (NM_001302468, intron 4 of 6)	-5104	NM_011659	22163	Mm.13885	NM_011659	ENSMUSG00000029075	Tnfrsf4	ACT35|CD134|Ly-70|Ox40|TXGP1L|Txgp1	tumor necrosis factor receptor superfamily, member 4	protein-coding
mm_158850.1	chrX	169986127	169986141	-	1	NA	intron (NM_001290512, intron 8 of 9)	intron (NM_001290512, intron 8 of 9)	-7217	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_58957.1	chr7	18844446	18844448	+	1	NA	intron (NM_153761, intron 2 of 5)	RMER10A|LTR|ERVL	4481	NM_153760	243864	Mm.233503	NM_153760	ENSMUSG00000040987	Mill2	Micb	MHC I like leukocyte 2	protein-coding
mm_88254.1	chr10	73201957	73201988	+	1	NA	Intergenic	Intergenic	-115267	NR_040646	327768	Mm.417745	NR_040646		A330049N07Rik	-	RIKEN cDNA A330049N07 gene	ncRNA
mm_160180.1	chr7	45866781	45866781	-	1	NA	promoter-TSS (NM_008172)	promoter-TSS (NM_008172)	-100	NM_008172	14814	Mm.322594	NM_008172	ENSMUSG00000002771	Grin2d	GluN2D|NMDAR2D|NR2D	glutamate receptor, ionotropic, NMDA2D (epsilon 4)	protein-coding
mm_126278.1	chr15	79209244	79209263	+	1	NA	intron (NR_029470, intron 2 of 4)	intron (NR_029470, intron 2 of 4)	-19920	NM_008837	18693	Mm.259464	NM_008837	ENSMUSG00000068206	Pick1	Prkcabp	protein interacting with C kinase 1	protein-coding
mm_152159.1	chr19	7267432	7267449	-	1	NA	promoter-TSS (NM_054048)	promoter-TSS (NM_054048)	46	NM_054048	104383	Mm.283859	NM_054048	ENSMUSG00000024968	Rcor2	1A13|AW122124|CoREST|Rcor|Rcor1	REST corepressor 2	protein-coding
mm_111229.1	chr12	84760758	84760774	-	1	NA	exon (NM_023409, exon 3 of 4)	exon (NM_023409, exon 3 of 4)	12346	NM_023409	67963	Mm.282556	NM_023409	ENSMUSG00000021242	Npc2	2700012J19Rik|AA408070|AU045843|HE1	Niemann-Pick type C2	protein-coding
mm_79128.1	chr9	47539468	47539471	+	1	NA	intron (NM_001025600, intron 1 of 8)	intron (NM_001025600, intron 1 of 8)	9117	NM_018770	54725	Mm.234832	NM_018770	ENSMUSG00000032076	Cadm1	2900073G06Rik|3100001I08Rik|AI987920|Bl2|Igsf4|Igsf4a|Necl2|RA175|RA175A|RA175B|RA175C|RA175N|ST17|SgIGSF|SynCam|Tslc1	cell adhesion molecule 1	protein-coding
mm_146484.1	chr18	90510185	90510224	+	1	NA	promoter-TSS (NM_198295)	promoter-TSS (NM_198295)	50	NM_198295	67988	Mm.268041	NM_198295	ENSMUSG00000024614	Tmx3	6430411B10Rik|A730024F05Rik|AV259382|Txndc10|mKIAA1830	thioredoxin-related transmembrane protein 3	protein-coding
mm_92379.1	chr10	76425452	76425454	-	1	NA	intron (NM_008787, intron 10 of 41)	intron (NM_008787, intron 10 of 41)	17459	NM_008787	18541	Mm.251794	NM_008787	ENSMUSG00000001151	Pcnt	AW476095|C86676|KEN|Pcnt2|kendrin|m239Asp|m275Asp	pericentrin (kendrin)	protein-coding
mm_129568.1	chr15	79658790	79658798	-	1	NA	promoter-TSS (NM_028634)	promoter-TSS (NM_028634)	162	NM_029407	75729	Mm.78946	NM_029407	ENSMUSG00000042564	Fam227a	4933432B09Rik	family with sequence similarity 227, member A	protein-coding
mm_48169.1	chr5	137153125	137153137	-	1	NA	Intergenic	Intergenic	-36924	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_60793.1	chr7	45570495	45570519	+	1	NA	promoter-TSS (NM_001243052)	promoter-TSS (NM_001243052)	354	NM_009737	12036	Mm.24210	NM_009737	ENSMUSG00000030826	Bcat2	Bcat-2|Eca40	branched chain aminotransferase 2, mitochondrial	protein-coding
mm_59248.1	chr7	24818754	24818764	+	1	NA	promoter-TSS (NR_045096)	promoter-TSS (NR_045096)	-36	NR_045096	545936	Mm.376228	NR_045096	ENSMUSG00000011350	Gm5893	EG545936|Gm477	predicted gene 5893	pseudo
mm_115236.1	chr13	109903434	109903441	+	1	NA	promoter-TSS (NR_035442)	promoter-TSS (NR_035442)	-372	NR_035442	100316683		NR_035442	ENSMUSG00000084651	Mir1904	Mirn1904|mmu-mir-1904	microRNA 1904	ncRNA
mm_46643.1	chr5	108549935	108550002	-	1	NA	promoter-TSS (NM_007756)	promoter-TSS (NM_007756)	59	NM_007756	12889	Mm.5195	NM_007756	ENSMUSG00000033615	Cplx1	921-S	complexin 1	protein-coding
mm_40343.1	chr5	45493482	45493498	+	1	NA	exon (NM_024434, exon 1 of 13)	exon (NM_024434, exon 1 of 13)	116	NM_024434	66988	Mm.286830	NM_024434	ENSMUSG00000039682	Lap3	2410015L10Rik|AA410100|LAP-3|Lap|Lapep|Pep-7|Pep-S|Pep7|Peps	leucine aminopeptidase 3	protein-coding
mm_109189.1	chr12	108554671	108554689	+	1	NA	promoter-TSS (NM_007965)	promoter-TSS (NM_007965)	-40	NM_001163394	14026	Mm.238841	NM_007965	ENSMUSG00000021262	Evl	AI528774	Ena-vasodilator stimulated phosphoprotein	protein-coding
mm_136245.1	chr16	90934866	90934885	-	1	NA	promoter-TSS (NM_026502)	promoter-TSS (NM_026502)	-26	NM_026502	68001	Mm.45374	NM_026502	ENSMUSG00000022972	1110004E09Rik	-	RIKEN cDNA 1110004E09 gene	protein-coding
mm_63286.1	chr7	126780288	126780301	+	1	NA	3' UTR (NM_026875, exon 5 of 5)	3' UTR (NM_026875, exon 5 of 5)	-1189	NM_011538	21389	Mm.727	NM_011538	ENSMUSG00000030699	Tbx6	rv	T-box 6	protein-coding
mm_90461.1	chr10	127759735	127759746	+	1	NA	promoter-TSS (NM_080436)	promoter-TSS (NM_080436)	-23	NM_080436	107605	Mm.484271	NM_080436	ENSMUSG00000089789	Rdh1	-	retinol dehydrogenase 1 (all trans)	protein-coding
mm_47354.1	chr5	122763999	122764013	-	1	NA	exon (NM_001199676, exon 2 of 17)	exon (NM_001199676, exon 2 of 17)	15404	NM_001199676	207565	Mm.289237	NM_145358	ENSMUSG00000029471	Camkk2	6330570N16Rik|AW061083|mKIAA0787	calcium/calmodulin-dependent protein kinase kinase 2, beta	protein-coding
mm_158182.1	chrX	103981243	103981287	-	1	NA	promoter-TSS (NM_011276)	promoter-TSS (NM_011276)	19	NM_011276	19820	Mm.427762	NM_011276	ENSMUSG00000056537	Rlim	AL022832|AW743871|Ha1r|Rlim1|Rnf12	ring finger protein, LIM domain interacting	protein-coding
mm_115517.1	chr13	5845726	5845738	-	1	NA	Intergenic	Intergenic	12360	NR_045891	71867	Mm.179181	NR_045891	ENSMUSG00000100625	1700016G22Rik	-	RIKEN cDNA 1700016G22 gene	ncRNA
mm_132374.1	chr16	34887612	34887615	+	1	NA	intron (NM_139300, intron 9 of 31)	intron (NM_139300, intron 9 of 31)	51716	NR_040536	76649	Mm.420532	NR_040536	ENSMUSG00000100593	1700119H24Rik	-	RIKEN cDNA 1700119H24 gene	ncRNA
mm_73161.1	chr8	95002410	95002451	+	1	NA	intron (NM_018882, intron 1 of 13)	intron (NM_018882, intron 1 of 13)	-15262	NM_173036	54672	Mm.27995	NM_173036	ENSMUSG00000060470	Adgrg3	A030001G24Rik|AW214383|Gpr97|Pb1|Pb99	adhesion G protein-coupled receptor G3	protein-coding
mm_88959.1	chr10	81393611	81393688	+	1	NA	intron (NM_001099917, intron 1 of 3)	intron (NM_001099917, intron 1 of 3)	585	NM_001099917	72273	Mm.253147	NM_001099917	ENSMUSG00000078439	Smim24	2210404O07Rik	small integral membrane protein 24	protein-coding
mm_72243.1	chr8	75033642	75033663	+	1	NA	promoter-TSS (NM_011622)	promoter-TSS (NM_011622)	-34	NM_001136259	21968	Mm.1967	NM_011622	ENSMUSG00000042870	Tom1	-	target of myb1 trafficking protein	protein-coding
mm_153207.1	chr19	34662395	34662433	-	1	NA	Intergenic	Intergenic	21525	NM_008331	15957	Mm.439751	NM_008331	ENSMUSG00000034459	Ifit1	ISG56|Ifi56|P56	interferon-induced protein with tetratricopeptide repeats 1	protein-coding
mm_46149.1	chr5	93306427	93306432	-	1	NA	Intergenic	Intergenic	38856	NM_007635	12452	Mm.3527	NM_007635	ENSMUSG00000029385	Ccng2	-	cyclin G2	protein-coding
mm_112556.1	chr13	12565927	12565940	+	1	NA	promoter-TSS (NM_026184)	promoter-TSS (NM_026184)	50	NM_026184	67475	Mm.358706	NM_026184	ENSMUSG00000057069	Ero1lb	1300013B24Rik|1700065B09Rik|AI447560|Ero1b|ero1-beta	ERO1-like beta (S. cerevisiae)	protein-coding
mm_37676.1	chr4	129122065	129122095	-	1	NA	promoter-TSS (NM_010471)	promoter-TSS (NM_010471)	-155	NM_001286081	15444	Mm.384452	NM_010471	ENSMUSG00000028785	Hpca	-	hippocalcin	protein-coding
mm_9700.1	chr1	178590359	178590373	-	1	NA	intron (NM_001161665, intron 2 of 14)	intron (NM_001161665, intron 2 of 14)	61241	NM_001161665	269152	Mm.129727	NM_177724	ENSMUSG00000026494	Kif26b	4832420M10|BC056349|D230039L06Rik	kinesin family member 26B	protein-coding
mm_27406.1	chr3	51340525	51340534	-	1	NA	5' UTR (NM_001291059, exon 1 of 10)	5' UTR (NM_001291059, exon 1 of 10)	115	NM_001291059	69257	Mm.131038	NM_023502	ENSMUSG00000037174	Elf2	2610036A20Rik|A230104O07Rik|AW111824|BB183398|EU32|NERF|NERF-1A|NERF-1B|NERF-2	E74-like factor 2	protein-coding
mm_73535.1	chr8	108703619	108703650	+	1	NA	Intergenic	Intergenic	-11010	NM_007496	11906	Mm.416972	NM_007496	ENSMUSG00000038872	Zfhx3	A230102L03Rik|Atbf1|Sci|WBP9|mKIAA4228	zinc finger homeobox 3	protein-coding
mm_12566.1	chr2	72979147	72979157	+	1	NA	promoter-TSS (NR_045269)	promoter-TSS (NR_045269)	129	NM_001098425	20687	Mm.124328	NM_011450	ENSMUSG00000027109	Sp3	D130027J01Rik	trans-acting transcription factor 3	protein-coding
mm_100671.1	chr11	3355364	3355384	-	1	NA	exon (NM_010718, exon 7 of 16)	exon (NM_010718, exon 7 of 16)	767	NM_001034030	16886	Mm.124176	NM_010718	ENSMUSG00000020451	Limk2	Limk-2|whe	LIM motif-containing protein kinase 2	protein-coding
mm_78168.1	chr9	21032055	21032085	+	1	NA	promoter-TSS (NM_008319)	promoter-TSS (NM_008319)	32	NM_008319	15898	Mm.4629	NM_008319	ENSMUSG00000032174	Icam5	CD50|ICAM-3|Icam3|TLN|Tlcn	intercellular adhesion molecule 5, telencephalin	protein-coding
mm_169034.1	chr13	13232890	13232907	-	1	NA	Intergenic	CpG	50182	NM_001311129	107849	Mm.392548	NM_181852	ENSMUSG00000055360	Prl2c5	Ghd3|MRP-4|Mrpplf4|PLF-4	prolactin family 2, subfamily c, member 5	protein-coding
mm_132467.1	chr16	36693957	36693965	+	1	NA	promoter-TSS (NM_134109)	promoter-TSS (NM_134109)	-17	NM_001285788	106347	Mm.17807	NM_134109	ENSMUSG00000022900	Ildr1	AU041483|AU044638	immunoglobulin-like domain containing receptor 1	protein-coding
mm_133066.1	chr16	58670051	58670090	+	1	NA	promoter-TSS (NM_007757)	promoter-TSS (NM_007757)	-138	NM_007757	12892	Mm.291519	NM_007757	ENSMUSG00000022742	Cpox	CPX|Cpo|HCP|cac|nct	coproporphyrinogen oxidase	protein-coding
mm_50743.1	chr6	52729413	52729445	+	1	NA	exon (NM_025816, exon 4 of 18)	exon (NM_025816, exon 4 of 18)	15700	NM_025816	52440	Mm.389757	NM_025816	ENSMUSG00000004535	Tax1bp1	1200003J11Rik|1700069J21Rik|AA930106|D6Ertd404e|D6Ertd772e|T6bp|TXBP151	Tax1 (human T cell leukemia virus type I) binding protein 1	protein-coding
mm_139442.1	chr17	54859280	54859287	+	1	NA	Intergenic	RMER17A|LTR|ERVK	-489209	NR_045825	69418	Mm.391004	NR_045825	ENSMUSG00000099747	1700025K24Rik	-	RIKEN cDNA 1700025K24 gene	ncRNA
mm_120782.1	chr14	74641524	74641558	+	1	NA	5' UTR (NM_172812, exon 1 of 3)	5' UTR (NM_172812, exon 1 of 3)	701	NM_172812	15558	Mm.214351	NM_172812	ENSMUSG00000034997	Htr2a	E030013E04|Htr-2|Htr2	5-hydroxytryptamine (serotonin) receptor 2A	protein-coding
mm_165188.1	chr2	29890111	29890114	+	1	NA	promoter-TSS (NM_013615)	promoter-TSS (NM_013615)	49	NM_013615	18286	Mm.330116	NM_013615	ENSMUSG00000026790	Odf2	AI848335|MMTEST29	outer dense fiber of sperm tails 2	protein-coding
mm_134270.1	chr16	13903086	13903149	-	1	NA	promoter-TSS (NM_053181)	promoter-TSS (NM_053181)	28	NM_001039533	94184	Mm.171484	NM_053181	ENSMUSG00000022680	Pdxdc1	2210010A19Rik|AA415817|Kiaa0251-hp	pyridoxal-dependent decarboxylase domain containing 1	protein-coding
mm_9251.1	chr1	171437289	171437323	-	1	NA	promoter-TSS (NM_172647)	promoter-TSS (NM_172647)	-255	NM_172647	16456	Mm.294882	NM_172647	ENSMUSG00000038235	F11r	9130004G24|AA638916|ESTM33|JAM|JAM-1|JAM-A|Jcam|Jcam1|Ly106	F11 receptor	protein-coding
mm_130173.1	chr15	93336792	93336798	-	1	NA	non-coding (NR_028315, exon 1 of 5)	non-coding (NR_028315, exon 1 of 5)	140	NR_028315	67057	Mm.4714	NM_024189	ENSMUSG00000022634	Yaf2	2810021M11Rik	YY1 associated factor 2	protein-coding
mm_54477.1	chr6	35065017	35065022	-	1	NA	exon (NM_001164412, exon 7 of 11)	exon (NM_001164412, exon 7 of 11)	68718	NM_001164412	53621	Mm.214525	NM_016877	ENSMUSG00000038784	Cnot4	Not4|Not4h|Not4hp	CCR4-NOT transcription complex, subunit 4	protein-coding
mm_87392.1	chr10	45289169	45289202	+	1	NA	promoter-TSS (NM_024286)	promoter-TSS (NM_024286)	-120	NM_024286	78977	Mm.24748	NM_024286	ENSMUSG00000019848	Popdc3	AA682104|Pop3	popeye domain containing 3	protein-coding
mm_19469.1	chr2	92459268	92459313	-	1	NA	5' UTR (NM_211358, exon 1 of 2)	5' UTR (NM_211358, exon 1 of 2)	504	NM_211358	228368	Mm.273990	NM_145832	ENSMUSG00000049922	Slc35c1	E430007K15Rik|fuct1	solute carrier family 35, member C1	protein-coding
mm_27681.1	chr3	65958175	65958189	-	1	NA	promoter-TSS (NM_019937)	promoter-TSS (NM_019937)	43	NM_019937	56706	Mm.175612	NM_019937	ENSMUSG00000027829	Ccnl1	2610030E23Rik|AU018493|Ccnl|ania-6a	cyclin L1	protein-coding
mm_168357.1	chr1	114229815	114229831	-	1	NA	Intergenic	L1Md_T|LINE|L1	-1455314	NM_001077425	636808	Mm.101576	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding
mm_161304.1	chr14	32465794	32465794	-	1	NA	promoter-TSS (NM_021712)	promoter-TSS (NM_021712)	115	NM_009891	12647	Mm.442817	NM_009891	ENSMUSG00000021919	Chat	B230380D24Rik	choline acetyltransferase	protein-coding
mm_138099.1	chr17	34048445	34048456	+	1	NA	intron (NM_001317722, intron 7 of 64)	intron (NM_001317722, intron 7 of 64)	9312	NM_001317722	12815	Mm.20230	NM_009926	ENSMUSG00000024330	Col11a2	-	collagen, type XI, alpha 2	protein-coding
mm_165628.1	chr3	65613494	65613494	+	1	NA	Intergenic	Intergenic	-45794	NR_106200	102465905		NR_106200	ENSMUSG00000098944	Mir8120	Gm27637|mmu-mir-8120	microRNA 8120	ncRNA
mm_155349.1	chrX	68678785	68678801	+	1	NA	promoter-TSS (NR_033481)	promoter-TSS (NR_033481)	252	NM_001290424	14265	Mm.3451	NM_008031	ENSMUSG00000000838	Fmr1	FMRP|Fmr-1	fragile X mental retardation syndrome 1	protein-coding
mm_74743.1	chr8	18978192	18978201	-	1	NA	promoter-TSS (NM_183039)	promoter-TSS (NM_183039)	-80	NM_183039	360217	Mm.271560	NM_183039	ENSMUSG00000053678	Defb40	BD-40	defensin beta 40	protein-coding
mm_107597.1	chr12	49382653	49382667	+	1	NA	promoter-TSS (NM_008241)	promoter-TSS (NM_008241)	-223	NM_001160112	15228	Mm.4704	NM_008241	ENSMUSG00000020950	Foxg1	2900064B05Rik|BF-1|Bf1|Hfh9|Hfhbf1	forkhead box G1	protein-coding
mm_48011.1	chr5	136165228	136165232	-	1	NA	intron (NM_178751, intron 1 of 2)	B3A|SINE|B2	5426	NM_178751	269717	Mm.308396	NM_178751	ENSMUSG00000039747	Orai2	A730041O15Rik|Tmem142b	ORAI calcium release-activated calcium modulator 2	protein-coding
mm_124107.1	chr14	79390640	79390653	-	1	NA	promoter-TSS (NM_025832)	promoter-TSS (NM_025832)	22	NM_025832	66897	Mm.24425	NM_025832	ENSMUSG00000022020	Naa16	1300019C06Rik|Narg1l	N(alpha)-acetyltransferase 16, NatA auxiliary subunit	protein-coding
mm_27959.1	chr3	79886182	79886238	-	1	NA	5' UTR (NM_133187, exon 1 of 4)	5' UTR (NM_133187, exon 1 of 4)	280	NM_133187	68659	Mm.427274	NM_133187	ENSMUSG00000027955	Fam198b	1110032E23Rik|2210419I08Rik|AV011458|Ened	family with sequence similarity 198, member B	protein-coding
mm_54260.1	chr6	28397970	28397992	-	1	NA	Intergenic	CpG	23743	NM_028900	74375	Mm.332950	NM_028900	ENSMUSG00000029708	Gcc1	4932417P04Rik	golgi coiled coil 1	protein-coding
mm_63788.1	chr7	132559417	132559418	+	1	NA	intron (NM_016978, intron 9 of 9)	intron (NM_016978, intron 9 of 9)	16981	NM_016978	18242	Mm.13694	NM_016978	ENSMUSG00000030934	Oat	AI194874|rhg	ornithine aminotransferase	protein-coding
mm_57960.1	chr6	135247885	135247896	-	1	NA	promoter-TSS (NM_001080552)	promoter-TSS (NM_001080552)	-6	NM_001080552	14840	Mm.272306	NM_010352	ENSMUSG00000030206	Gsg1	-	germ cell associated 1	protein-coding
mm_166345.1	chr5	117988331	117988332	+	1	NA	intron (NM_145564, intron 4 of 11)	intron (NM_145564, intron 4 of 11)	11561	NM_001346588	231670	Mm.21912	NM_145564	ENSMUSG00000032898	Fbxo21	2810425J22Rik|AU016673	F-box protein 21	protein-coding
mm_63871.1	chr7	135854103	135854122	+	1	NA	Intergenic	Intergenic	-137733	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_46220.1	chr5	98943764	98943773	-	1	NA	intron (NM_008926, intron 15 of 18)	(TG)n|Simple_repeat|Simple_repeat	89353	NM_001310677	110075	Mm.136461	NM_173404	ENSMUSG00000029335	Bmp3	9530029I04Rik	bone morphogenetic protein 3	protein-coding
mm_168626.1	chr1	180579248	180579257	+	1	NA	exon (NM_007415, exon 4 of 23)	exon (NM_007415, exon 4 of 23)	-7949	NR_105869	102466761		NR_105869	ENSMUSG00000098926	Mir6904	Gm27426|mmu-mir-6904	microRNA 6904	ncRNA
mm_153567.1	chr19	42599950	42599959	-	1	NA	exon (NM_053083, exon 11 of 15)	exon (NM_053083, exon 11 of 15)	12852	NM_001164311	67573	Mm.178767	NM_053083	ENSMUSG00000025185	Loxl4	4833426I20Rik|Loxc	lysyl oxidase-like 4	protein-coding
mm_60981.1	chr7	48978282	48978294	+	1	NA	intron (NM_001111016, intron 2 of 38)	intron (NM_001111016, intron 2 of 38)	19215	NM_001111016	78286	Mm.333881	NM_175272	ENSMUSG00000052512	Nav2	5330421F07Rik|AU067780|BQ960892|HELAD1|POMFIL2|RAINB1|RAINB2|Unc53H2|mKIAA3015	neuron navigator 2	protein-coding
mm_111371.1	chr12	87238704	87238752	-	1	NA	promoter-TSS (NM_027744)	promoter-TSS (NM_027744)	-127	NM_027744	71275	Mm.79198	NM_027744	ENSMUSG00000072919	Noxred1	4933437F05Rik	NADP+ dependent oxidoreductase domain containing 1	protein-coding
mm_133388.1	chr16	84774137	84774145	+	1	NA	promoter-TSS (NM_023844)	promoter-TSS (NM_023844)	18	NM_023844	67374	Mm.41758	NM_023844	ENSMUSG00000053062	Jam2	1110002N23Rik|2410030G21Rik|2410167M24Rik|JAM-2|JAM-B|Jcam2|VE-JAM	junction adhesion molecule 2	protein-coding
mm_100350.1	chr11	118428274	118428284	+	1	NA	promoter-TSS (NM_001204129)	promoter-TSS (NM_001204129)	-178	NM_001204129	56745	Mm.23845	NM_019959	ENSMUSG00000017446	C1qtnf1	1600017K21Rik|CTRP1|Zsig37	C1q and tumor necrosis factor related protein 1	protein-coding
mm_4754.1	chr1	182288012	182288027	+	1	NA	Intergenic	LTR33A_|LTR|ERVL	-5260	NM_007853	13244	Mm.29648	NM_007853	ENSMUSG00000038633	Degs1	AA536663|Degs|Des1|Mdes	delta(4)-desaturase, sphingolipid 1	protein-coding
mm_147204.1	chr18	37894202	37894214	-	1	NA	exon (NM_001305981, exon 14 of 29)	exon (NM_001305981, exon 14 of 29)	-39548	NR_105945	102465592		NR_105945	ENSMUSG00000098706	Mir6979	Gm27524|mmu-mir-6979	microRNA 6979	ncRNA
mm_97108.1	chr11	74649527	74649550	+	1	NA	promoter-TSS (NM_001081158)	promoter-TSS (NM_001081158)	43	NM_001081158	74148	Mm.214574	NM_001081158	ENSMUSG00000020741	Cluh	1300001I01Rik|Kiaa0664|mKIAA0664	clustered mitochondria (cluA/CLU1) homolog	protein-coding
mm_39330.1	chr5	8660060	8660099	+	1	NA	promoter-TSS (NM_011076)	promoter-TSS (NM_011076)	-13	NM_011076	18671	Mm.207354	NM_011076	ENSMUSG00000040584	Abcb1a	Abcb4|Evi32|Mdr1a|Mdr3|P-gp|Pgp|Pgy-3|Pgy3|mdr-3	ATP-binding cassette, sub-family B (MDR/TAP), member 1A	protein-coding
mm_169088.1	chr13	38204898	38204898	+	1	NA	promoter-TSS (NM_026382)	promoter-TSS (NM_026382)	-41	NM_026382	67797	Mm.250783	NM_026382	ENSMUSG00000021431	Snrnp48	1110050F08Rik|6530403A03Rik|C6orf151	small nuclear ribonucleoprotein 48 (U11/U12)	protein-coding
mm_133200.1	chr16	73045777	73045788	+	1	NA	3' UTR (NM_019413, exon 29 of 29)	3' UTR (NM_019413, exon 29 of 29)	382633	NM_019413	19876	Mm.310772	NM_019413	ENSMUSG00000022883	Robo1	AW494633|AW742721|DUTT1|Gm310	roundabout guidance receptor 1	protein-coding
mm_47757.1	chr5	131307701	131307726	-	1	NA	promoter-TSS (NM_145218)	promoter-TSS (NM_145218)	-191	NM_145218	212996	Mm.299204	NM_145218	ENSMUSG00000034040	Wbscr17	AA388321|E330012B09Rik	Williams-Beuren syndrome chromosome region 17 homolog (human)	protein-coding
mm_132637.1	chr16	39984309	39984343	+	1	NA	Intergenic	Intergenic	1081981	NM_170599	207683	Mm.245564	NM_170599	ENSMUSG00000022790	Igsf11	1700025L02Rik|BT-IgSF|Igsf13	immunoglobulin superfamily, member 11	protein-coding
mm_43349.1	chr5	135168383	135168442	+	1	NA	promoter-TSS (NM_009745)	promoter-TSS (NM_009745)	40	NM_009745	12054	Mm.405834	NM_009745	ENSMUSG00000029681	Bcl7b	-	B cell CLL/lymphoma 7B	protein-coding
mm_145268.1	chr18	52767792	52767805	+	1	NA	promoter-TSS (NM_001199153)	promoter-TSS (NM_001199153)	-13	NM_026408	67847	Mm.292168	NM_026408	ENSMUSG00000024534	Sncaip	2810407O15Rik|4933427B05Rik|BB104594|SYPH1	synuclein, alpha interacting protein (synphilin)	protein-coding
mm_145485.1	chr18	60383449	60383451	+	1	NA	intron (NM_001146275, intron 2 of 2)	Lx8|LINE|L1	7421	NM_001146275	60440	Mm.261140	NM_021792	ENSMUSG00000054072	Iigp1	2900074L10Rik|AI046432|AW111922|Ifgga1|Iigp|Irga6	interferon inducible GTPase 1	protein-coding
mm_43133.1	chr5	125389285	125389327	+	1	NA	intron (NM_019639, intron 1 of 1)	CpG	711	NM_019639	22190	Mm.331	NM_019639	ENSMUSG00000008348	Ubc	2700054O04Rik|AI194771|Rps27a|TI-225|Uba52|Ubb	ubiquitin C	protein-coding
mm_57834.1	chr6	129465150	129465158	-	1	NA	intron (NR_132130, intron 5 of 5)	intron (NR_132130, intron 5 of 5)	7625	NM_001309637	56644	Mm.239516	NM_020008	ENSMUSG00000079293	Clec7a	BGR|Clecsf12|beta-GR	C-type lectin domain family 7, member a	protein-coding
mm_63831.1	chr7	135268580	135268581	+	1	NA	promoter-TSS (NM_001163611)	promoter-TSS (NM_001163611)	-39	NM_001163611	100043254	Mm.192092	NM_001163611	ENSMUSG00000073804	Nps	ENSMUSG00000073804	neuropeptide S	protein-coding
mm_950.1	chr1	57406729	57406774	+	1	NA	promoter-TSS (NM_001037742)	promoter-TSS (NM_001037742)	-77	NM_001302963	68736	Mm.288490	NM_001037742	ENSMUSG00000048495	Tyw5	1110034B05Rik	tRNA-yW synthesizing protein 5	protein-coding
mm_2686.1	chr1	127306707	127306752	+	1	NA	5' UTR (NM_145128, exon 3 of 18)	5' UTR (NM_145128, exon 3 of 18)	101743	NM_145128	107895	Mm.214682	NM_145128	ENSMUSG00000036155	Mgat5	4930471A21Rik|5330407H02Rik|AI480971|GlcNAc-TV	mannoside acetylglucosaminyltransferase 5	protein-coding
mm_26368.1	chr3	142560539	142560569	+	1	NA	promoter-TSS (NM_001289493)	promoter-TSS (NM_001289493)	58	NM_001289493	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_127758.1	chr15	103503262	103503288	+	1	NA	5' UTR (NM_008800, exon 1 of 16)	5' UTR (NM_008800, exon 1 of 16)	241	NM_008800	18574	Mm.390792	NM_008800	ENSMUSG00000022489	Pde1b	Pde1b1	phosphodiesterase 1B, Ca2+-calmodulin dependent	protein-coding
mm_94659.1	chr11	17159410	17159427	+	1	NA	5' UTR (NM_024459, exon 1 of 6)	5' UTR (NM_024459, exon 1 of 6)	120	NM_024459	19058	Mm.41840	NM_024459	ENSMUSG00000033953	Ppp3r1	CaNB1|Cnb1|MCIP1	protein phosphatase 3, regulatory subunit B, alpha isoform (calcineurin B, type I)	protein-coding
mm_166476.1	chr5	144026644	144026646	-	1	NA	intron (NM_033039, intron 1 of 4)	intron (NM_033039, intron 1 of 4)	-11792	NM_177682	231874	Mm.320432	NM_177682	ENSMUSG00000029617	Ccz1	AU022870	CCZ1 vacuolar protein trafficking and biogenesis associated	protein-coding
mm_64625.1	chr7	3677510	3677529	-	1	NA	promoter-TSS (NM_181820)	promoter-TSS (NM_181820)	34	NM_181820	353499	Mm.360398	NM_181820	ENSMUSG00000019734	Tmc4	-	transmembrane channel-like gene family 4	protein-coding
mm_134997.1	chr16	32165455	32165494	-	1	NA	promoter-TSS (NM_146069)	promoter-TSS (NM_146069)	2	NM_146069	224109	Mm.33498	NM_146069	ENSMUSG00000052384	Nrros	E430025L02Rik|Lrcc33|Lrrc33	negative regulator of reactive oxygen species	protein-coding
mm_135904.1	chr16	67182835	67182838	-	1	NA	intron (NM_178721, intron 1 of 9)	intron (NM_178721, intron 1 of 9)	438072	NM_001347247	239857	Mm.394300	NM_178721	ENSMUSG00000064115	Cadm2	2900078E11Rik|9330131D06|A830029E02Rik|Igdf4d|Igsf4d|NECL3|SynCAM 2|SynCAM2	cell adhesion molecule 2	protein-coding
mm_25992.1	chr3	134236332	134236373	+	1	NA	promoter-TSS (NM_001004367)	promoter-TSS (NM_001004367)	-143	NM_001004367	319478	Mm.224814	NM_001004367	ENSMUSG00000044365	Cxxc4	9330210J02Rik|C030003J12Rik|Idax	CXXC finger 4	protein-coding
mm_138199.1	chr17	34291868	34291872	+	1	NA	Intergenic	Intergenic	-4099	NM_010378	14960	Mm.235338	NM_010378	ENSMUSG00000036594	H2-Aa	Aalpha|H-2Aa|H2Aa|I-Aalpha|IAalpha|Ia-1|Ia1	histocompatibility 2, class II antigen A, alpha	protein-coding
mm_15715.1	chr2	164042369	164042375	+	1	NA	exon (NM_001114079, exon 8 of 14)	exon (NM_001114079, exon 8 of 14)	17148	NM_001114079	381404	Mm.82301	NM_001114079	ENSMUSG00000054582	Pabpc1l	1810053B01Rik|Epab	poly(A) binding protein, cytoplasmic 1-like	protein-coding
mm_5811.1	chr1	52500237	52500276	-	1	NA	5' UTR (NM_008667, exon 1 of 8)	5' UTR (NM_008667, exon 1 of 8)	192	NM_008667	17936	Mm.25903	NM_008667	ENSMUSG00000002881	Nab1	-	Ngfi-A binding protein 1	protein-coding
mm_11496.1	chr2	32493665	32493673	+	1	NA	Intergenic	Intergenic	-41690	NM_153560	98952	Mm.4065	NM_153560	ENSMUSG00000039157	Fam102a	AI426465|C230093N12Rik|Eeig1	family with sequence similarity 102, member A	protein-coding
mm_121177.1	chr14	103047008	103047020	+	1	NA	promoter-TSS (NM_008392)	promoter-TSS (NM_008392)	2	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_50845.1	chr6	54833472	54833490	+	1	NA	intron (NM_199143, intron 1 of 4)	intron (NM_199143, intron 1 of 4)	16565	NM_199143	387524	Mm.286149	NM_199143	ENSMUSG00000058446	Znrf2	1190002C14Rik|AU044205|D6Ertd365e	zinc and ring finger 2	protein-coding
mm_1099.1	chr1	59763385	59763395	+	1	NA	promoter-TSS (NM_007561)	promoter-TSS (NM_007561)	-889	NM_007561	12168	Mm.7106	NM_007561	ENSMUSG00000067336	Bmpr2	2610024H22Rik|AL117858|AW546137|BB189135|BMP-2|BMPR-2|BMPR-II|BMPRII|BRK-3|Gm20272	bone morphogenetic protein receptor, type II (serine/threonine kinase)	protein-coding
mm_91805.1	chr10	53906422	53906438	-	1	NA	3' UTR (NM_008548, exon 13 of 13)	3' UTR (NM_008548, exon 13 of 13)	-155521	NM_001081428	75906	Mm.436785	NM_001081428	ENSMUSG00000019856	Fam184a	3110012E06Rik|4930438C08Rik|4930589M24Rik	family with sequence similarity 184, member A	protein-coding
mm_147615.1	chr18	57418229	57418235	-	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-50254	NM_001134697	629147	Mm.57415	NM_001134697	ENSMUSG00000069372	Ctxn3	ENSMUSG00000069372	cortexin 3	protein-coding
mm_143172.1	chr17	57226814	57226853	-	1	NA	exon (NM_009778, exon 2 of 41)	exon (NM_009778, exon 2 of 41)	1303	NM_009778	12266	Mm.19131	NM_009778	ENSMUSG00000024164	C3	AI255234|ASP|HSE-MSF|Plp	complement component 3	protein-coding
mm_138214.1	chr17	34306664	34306672	+	1	NA	intron (NM_010382, intron 1 of 5)	intron (NM_010382, intron 1 of 5)	801	NM_010382	14969	Mm.22564	NM_010382	ENSMUSG00000060586	H2-Eb1	Eb|H-2Eb|H2Eb|Ia-4|Ia4	histocompatibility 2, class II antigen E beta	protein-coding
mm_49797.1	chr6	35266109	35266113	+	1	NA	Intergenic	Intergenic	13379	NR_027875	67705	Mm.228046	NR_015608	ENSMUSG00000073155	1810058I24Rik	AI414869|AI848234	RIKEN cDNA 1810058I24 gene	ncRNA
mm_21586.1	chr2	164237348	164237389	-	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	973	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_87943.1	chr10	62920649	62920682	+	1	NA	promoter-TSS (NM_175194)	promoter-TSS (NM_175194)	32	NM_175194	73132	Mm.37457	NM_175194	ENSMUSG00000071253	Slc25a16	3110021G18Rik|GDA|GDC|HGT.1|ML7	solute carrier family 25 (mitochondrial carrier, Graves disease autoantigen), member 16	protein-coding
mm_127031.1	chr15	96342571	96342574	+	1	NA	intron (NM_175251, intron 3 of 20)	B3A|SINE|B2	55050	NM_175251	77044	Mm.17166	NM_175251	ENSMUSG00000033237	Arid2	1700124K17Rik|4432409D24Rik|zipzap/p200	AT rich interactive domain 2 (ARID, RFX-like)	protein-coding
mm_75020.1	chr8	31163097	31163106	-	1	NA	exon (NM_026453, exon 7 of 10)	exon (NM_026453, exon 7 of 10)	5623	NM_026453	67920	Mm.289818	NM_026453	ENSMUSG00000031578	Mak16	2600016B03Rik|AI314911|Rbm13	MAK16 homolog	protein-coding
mm_134337.1	chr16	16527301	16527322	-	1	NA	promoter-TSS (NM_001301818)	promoter-TSS (NM_001301818)	100	NM_001301818	224014	Mm.256131	NM_139232	ENSMUSG00000022788	Fgd4	9030023J02Rik|9330209B17Rik|Frabp|ZFYVE6	FYVE, RhoGEF and PH domain containing 4	protein-coding
mm_66815.1	chr7	48167530	48167547	-	1	NA	TTS (NM_207538)	TTS (NM_207538)	1447	NM_207538	404239	Mm.377927	NM_207538	ENSMUSG00000070551	Mrgprb5	Mgrg11|MrgB5	MAS-related GPR, member B5	protein-coding
mm_75520.1	chr8	55906964	55906977	-	1	NA	promoter-TSS (NM_175939)	promoter-TSS (NM_175939)	-6	NM_175939	244486	Mm.67684	NM_175939	ENSMUSG00000046258	Adam29	-	a disintegrin and metallopeptidase domain 29	protein-coding
mm_170467.1	chr18	9916839	9916851	+	1	NA	Intergenic	Intergenic	-41335	NM_153552	225160	Mm.219648	NM_153552	ENSMUSG00000024287	Thoc1	3110002N20Rik|AW107452|NMP-84	THO complex 1	protein-coding
mm_31105.1	chr4	42880727	42880743	+	1	NA	Intergenic	RMER15|LTR|ERVL	-6532	NM_177785	277773	Mm.212727	NM_177785	ENSMUSG00000050141	Fam205c	4931430D02|FAM205CP	family with sequence similarity 205, member C	protein-coding
mm_108979.1	chr12	102743751	102743776	+	1	NA	promoter-TSS (NM_177140)	promoter-TSS (NM_177140)	3	NM_177140	320351	Mm.86546	NM_177140	ENSMUSG00000046675	Tmem251	D230037D09Rik	transmembrane protein 251	protein-coding
mm_171024.1	chr2	84510262	84510270	+	1	NA	Intergenic	IAPLTR1_Mm|LTR|ERVK	-3393	NR_046046	672763	Mm.491046	NR_046046	ENSMUSG00000087362	Gm13710	OTTMUSG00000013441	predicted gene 13710	ncRNA
mm_56880.1	chr6	119014358	119014386	-	1	NA	intron (NM_001256002, intron 3 of 47)	Lx7|LINE|L1	94123	NM_001159534	12288	Mm.41628	NM_009781	ENSMUSG00000051331	Cacna1c	Cav1.2|Cchl1a1|D930026N18Rik|MBC|MELC-CC	calcium channel, voltage-dependent, L type, alpha 1C subunit	protein-coding
mm_25596.1	chr3	116899875	116899938	+	1	NA	intron (NM_009146, intron 12 of 16)	Lx9|LINE|L1	38226	NM_009146	20321	Mm.66293	NM_009146	ENSMUSG00000033386	Frrs1	AI131732|Sdfr2	ferric-chelate reductase 1	protein-coding
mm_134205.1	chr16	11150134	11150137	-	1	NA	intron (NM_145931, intron 13 of 22)	intron (NM_145931, intron 13 of 22)	-15603	NM_029582	106200	Mm.291015	NM_029582	ENSMUSG00000022498	Txndc11	2810408E11Rik|AI427833|EFP1|Txdc11	thioredoxin domain containing 11	protein-coding
mm_105618.1	chr11	106788902	106788913	-	1	NA	promoter-TSS (NM_177088)	promoter-TSS (NM_177088)	-345	NM_177088	320162	Mm.30524	NM_177088	ENSMUSG00000018372	Cep95	4732496G21Rik|AI118346|AI448335|Ccdc45|D330027A14Rik|F630025I20Rik	centrosomal protein 95	protein-coding
mm_113124.1	chr13	24575574	24575585	+	1	NA	Intergenic	Intergenic	-6610	NM_001286100	193385	Mm.217319	NM_029679	ENSMUSG00000036006	Fam65b	-	family with sequence similarity 65, member B	protein-coding
mm_150391.1	chr19	36409670	36409691	+	1	NA	intron (NM_029508, intron 1 of 8)	CpG	30613	NM_029508	76073	Mm.259180	NM_029508	ENSMUSG00000024805	Pcgf5	0610009F02Rik|1110054A01Rik|5830406C17Rik|5830443C21Rik|9530023M17Rik|AI324127	polycomb group ring finger 5	protein-coding
mm_166669.1	chr6	91233543	91233552	+	1	NA	exon (NM_001081437, exon 2 of 17)	exon (NM_001081437, exon 2 of 17)	20783	NM_007992	14115	Mm.249146	NM_007992	ENSMUSG00000064080	Fbln2	5730577E14Rik|FIBL-2	fibulin 2	protein-coding
mm_168564.1	chr11	69416055	69416058	-	1	NA	Intergenic	Intergenic	-2381	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_76860.1	chr8	105471329	105471343	-	1	NA	promoter-TSS (NM_026481)	promoter-TSS (NM_026481)	86	NM_026481	67971	Mm.29358	NM_026481	ENSMUSG00000014846	Tppp3	2700055K07Rik|CGI-38|Ceacam9|mmCGM8	tubulin polymerization-promoting protein family member 3	protein-coding
mm_139375.1	chr17	51833008	51833017	+	1	NA	promoter-TSS (NM_009122)	promoter-TSS (NM_009122)	278	NM_001163632	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_154902.1	chrX	20961668	20961674	+	1	NA	promoter-TSS (NR_027446)	promoter-TSS (NR_027446)	-5	NR_027445	320742	Mm.391227	NR_027445		A230072C01Rik	-	RIKEN cDNA A230072C01 gene	ncRNA
mm_93507.1	chr10	114802236	114802245	-	1	NA	promoter-TSS (NM_146241)	promoter-TSS (NM_146241)	-870	NM_146241	237553	Mm.445550	NM_146241	ENSMUSG00000050663	Trhde	9330155P21Rik	TRH-degrading enzyme	protein-coding
mm_109446.1	chr12	110898078	110898081	+	1	NA	intron (NM_175336, intron 3 of 20)	intron (NM_175336, intron 3 of 20)	8815	NM_001081057	104859	Mm.35583	NM_175336	ENSMUSG00000021275	Tecpr2	4930573I19Rik|AI604920|mKIAA0297	tectonin beta-propeller repeat containing 2	protein-coding
mm_105955.1	chr11	115367671	115367679	-	1	NA	promoter-TSS (NM_175454)	promoter-TSS (NM_175454)	44	NM_175454	217310	Mm.205707	NM_175454	ENSMUSG00000034586	Hid1	C630004H02Rik	HID1 domain containing	protein-coding
mm_143221.1	chr17	63265052	63265054	-	1	NA	intron (NM_015794, intron 6 of 8)	intron (NM_015794, intron 6 of 8)	47920	NR_130176	414079	Mm.444282	NR_130176	ENSMUSG00000090565	4930405O22Rik	-	RIKEN cDNA 4930405O22 gene	ncRNA
mm_84233.1	chr9	62122597	62122617	-	1	NA	promoter-TSS (NR_039595)	promoter-TSS (NR_039595)	-13	NR_039595	100628602		NR_039595	ENSMUSG00000092696	Mir5133	mir-5133|mmu-mir-5133|mu-mir-5133	microRNA 5133	ncRNA
mm_172086.1	chr6	148946383	148946399	-	1	NA	promoter-TSS (NM_019643)	promoter-TSS (NM_019643)	41	NM_019643	56306	Mm.18637	NM_019643	ENSMUSG00000039985	Fam60a	Ppcs1|Pptcs1|Tera	family with sequence similarity 60, member A	protein-coding
mm_112388.1	chr12	119238327	119238337	-	1	NA	promoter-TSS (NM_177290)	promoter-TSS (NM_177290)	-56	NM_177290	320910	Mm.217000	NM_177290	ENSMUSG00000025321	Itgb8	4832412O06Rik	integrin beta 8	protein-coding
mm_157878.1	chrX	75842251	75842256	-	1	NA	intron (NM_001346519, intron 1 of 16)	intron (NM_001346519, intron 1 of 16)	768	NM_001166454	102866	Mm.28777	NM_145629	ENSMUSG00000016382	Pls3	AI115446|AL024105	plastin 3 (T-isoform)	protein-coding
mm_62106.1	chr7	96406812	96406827	+	1	NA	intron (NM_001310760, intron 2 of 32)	intron (NM_001310760, intron 2 of 32)	-64855	NR_046043	670727	Mm.421352	NR_046043	ENSMUSG00000085751	Gm15412	OTTMUSG00000021245	predicted gene 15412	ncRNA
mm_110644.1	chr12	58269163	58269187	-	1	NA	promoter-TSS (NM_025809)	promoter-TSS (NM_025809)	83	NM_025809	66864	Mm.280563	NM_025809	ENSMUSG00000045930	Clec14a	1200003C23Rik|AI642649	C-type lectin domain family 14, member a	protein-coding
mm_77431.1	chr8	121541963	121541974	-	1	NA	promoter-TSS (NM_029597)	promoter-TSS (NM_029597)	-14	NM_029597	76405	Mm.165697	NM_029597	ENSMUSG00000031809	1700018B08Rik	1700084O22Rik	RIKEN cDNA 1700018B08 gene	protein-coding
mm_39961.1	chr5	32136627	32136631	+	1	NA	5' UTR (NM_008037, exon 1 of 4)	5' UTR (NM_008037, exon 1 of 4)	157	NM_008037	14284	Mm.24684	NM_008037	ENSMUSG00000029135	Fosl2	Fra-2	fos-like antigen 2	protein-coding
mm_79772.1	chr9	62838643	62838682	+	1	NA	promoter-TSS (NM_001033175)	promoter-TSS (NM_001033175)	-125	NM_001033175	76524	Mm.283636	NM_001033175	ENSMUSG00000032245	Cln6	1810065L06Rik|AW743417|D9Bwg1455e|nclf	ceroid-lipofuscinosis, neuronal 6	protein-coding
mm_71528.1	chr8	46868458	46868496	+	1	NA	Intergenic	MTE-int|LTR|ERVL-MaLR	-118410	NM_177304	320981	Mm.211429	NM_177304	ENSMUSG00000038173	Enpp6	4833421B01Rik|B830047L21Rik|D8Ertd514e|E-NPP 6|GPC-Cpde|Npp6	ectonucleotide pyrophosphatase/phosphodiesterase 6	protein-coding
mm_65627.1	chr7	27541954	27541993	-	1	NA	exon (NM_011116, exon 5 of 14)	exon (NM_011116, exon 5 of 14)	11245	NM_011116	18807	Mm.6483	NM_011116	ENSMUSG00000003363	Pld3	Sam-9	phospholipase D family, member 3	protein-coding
mm_10017.1	chr1	192064612	192064641	-	1	NA	intron (NM_011633, intron 3 of 9)	MTD|LTR|ERVL-MaLR	27973	NM_011633	22033	Mm.380491	NM_011633		Traf5	-	TNF receptor-associated factor 5	protein-coding
mm_72701.1	chr8	84978168	84978171	+	1	NA	exon (NM_008416, exon 1 of 1)	exon (NM_008416, exon 1 of 1)	579	NM_008416	16477	Mm.1167	NM_008416	ENSMUSG00000052837	Junb	-	jun B proto-oncogene	protein-coding
mm_48344.1	chr5	139316327	139316344	-	1	NA	intron (NM_172723, intron 1 of 10)	B4A|SINE|B4	9129	NM_172723	231821	Mm.297819	NM_172723	ENSMUSG00000056413	Adap1	4930431P11Rik|Centa1|GC1L|p42IP4	ArfGAP with dual PH domains 1	protein-coding
mm_39907.1	chr5	31291353	31291365	+	1	NA	promoter-TSS (NM_026298)	promoter-TSS (NM_026298)	-245	NM_026298	67661	Mm.293023	NM_026298	ENSMUSG00000038564	Ift172	4930553F24Rik|Slb|avc1|wim	intraflagellar transport 172	protein-coding
mm_60775.1	chr7	45559357	45559369	+	1	NA	intron (NM_025330, intron 4 of 8)	intron (NM_025330, intron 4 of 8)	4435	NM_025330	66065	Mm.285710	NM_025330	ENSMUSG00000030825	Hsd17b14	0610039E24Rik|Dhrs10|retSDR3	hydroxysteroid (17-beta) dehydrogenase 14	protein-coding
mm_163188.1	chr11	94939103	94939127	+	1	NA	intron (NM_007742, intron 5 of 50)	L1MC4|LINE|L1	2891	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_114313.1	chr13	59829288	59829294	+	1	NA	Intergenic	RLTR17|LTR|ERVK	-6144	NM_153538	214290	Mm.233082	NM_153538	ENSMUSG00000035248	Zcchc6	6030448M23Rik|AA420405	zinc finger, CCHC domain containing 6	protein-coding
mm_126115.1	chr15	78261270	78261308	+	1	NA	intron (NM_008677, intron 9 of 9)	intron (NM_008677, intron 9 of 9)	16478	NM_008677	17972	Mm.2068	NM_008677	ENSMUSG00000071715	Ncf4	AI451400|p40phox	neutrophil cytosolic factor 4	protein-coding
mm_99446.1	chr11	102433519	102433534	+	1	NA	exon (NM_008175, exon 4 of 13)	exon (NM_008175, exon 4 of 13)	3204	NM_008175	14824	Mm.1568	NM_008175	ENSMUSG00000034708	Grn	Pgrn|epithelin	granulin	protein-coding
mm_164281.1	chr15	102406375	102406398	+	1	NA	promoter-TSS (NM_013672)	promoter-TSS (NM_013672)	70	NM_013672	20683	Mm.4618	NM_013672	ENSMUSG00000001280	Sp1	1110003E12Rik|AA450830|AI845540|Sp1-1	trans-acting transcription factor 1	protein-coding
mm_100500.1	chr11	120484636	120484646	+	1	NA	promoter-TSS (NM_027204)	promoter-TSS (NM_027204)	-28	NM_027204	56282	Mm.133851	NM_027204	ENSMUSG00000039640	Mrpl12	0610034O11Rik|1500031N16Rik|MRP-L12|Rpml12	mitochondrial ribosomal protein L12	protein-coding
mm_150571.1	chr19	40113665	40113676	+	1	NA	3' UTR (NM_001167875, exon 8 of 8)	3' UTR (NM_001167875, exon 8 of 8)	23991	NM_001167875	107141	Mm.474575	NM_134144	ENSMUSG00000054827	Cyp2c50	AI266900	cytochrome P450, family 2, subfamily c, polypeptide 50	protein-coding
mm_79857.1	chr9	65018818	65018827	+	1	NA	intron (NM_021345, intron 1 of 10)	intron (NM_021345, intron 1 of 10)	2895	NM_021345	57874	Mm.308180	NM_021345	ENSMUSG00000033629	Hacd3	4930523M17Rik|AW742319|B-ind1|Hcad3|Hspc121|Ptplad1	3-hydroxyacyl-CoA dehydratase 3	protein-coding
mm_130752.1	chr15	101270422	101270431	-	1	NA	exon (NM_010444, exon 2 of 7)	exon (NM_010444, exon 2 of 7)	3580	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_49804.1	chr6	36387968	36388027	+	1	NA	promoter-TSS (NM_203491)	promoter-TSS (NM_203491)	-87	NM_203491	243764	Mm.448632	NM_203491	ENSMUSG00000045613	Chrm2	AChR-M2|Chrm-2|M2	cholinergic receptor, muscarinic 2, cardiac	protein-coding
mm_23753.1	chr3	69722090	69722101	+	1	NA	promoter-TSS (NM_133787)	promoter-TSS (NM_133787)	40	NM_133787	97112	Mm.21062	NM_133787	ENSMUSG00000027787	Nmd3	C87860	NMD3 ribosome export adaptor	protein-coding
mm_98192.1	chr11	87794060	87794071	+	1	NA	5' UTR (NM_010824, exon 1 of 14)	5' UTR (NM_010824, exon 1 of 14)	281	NM_010824	17523	Mm.4668	NM_010824	ENSMUSG00000009350	Mpo	mKIAA4033	myeloperoxidase	protein-coding
mm_22494.1	chr3	6107533	6107554	+	1	NA	Intergenic	Intergenic	512900	NM_027048	69347	Mm.45822	NM_027048	ENSMUSG00000069118	1700008P02Rik	-	RIKEN cDNA 1700008P02 gene	protein-coding
mm_10656.1	chr2	20722307	20722311	+	1	NA	intron (NM_029895, intron 6 of 18)	intron (NM_029895, intron 6 of 18)	202796	NM_001177631	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding
mm_147401.1	chr18	44574659	44574670	-	1	NA	intron (NM_001085373, intron 3 of 18)	intron (NM_001085373, intron 3 of 18)	-87001	NR_026853	626275	Mm.427116	NR_026853	ENSMUSG00000097610	A930012L18Rik	-	RIKEN cDNA A930012L18 gene	ncRNA
mm_151952.1	chr19	5801300	5801301	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	1372	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_51841.1	chr6	90302514	90302516	+	1	NA	intron (NM_177738, intron 2 of 4)	intron (NM_177738, intron 2 of 4)	1245	NM_177738	243535	Mm.233854	NM_177738	ENSMUSG00000049694	BC048671	-	cDNA sequence BC048671	protein-coding
mm_23095.1	chr3	37063675	37063697	+	1	NA	promoter-TSS (NM_009350)	promoter-TSS (NM_009350)	30	NM_009350	21744	Mm.8122	NM_009350	ENSMUSG00000027719	Adad1	Tenr	adenosine deaminase domain containing 1 (testis specific)	protein-coding
mm_83619.1	chr9	48808217	48808225	-	1	NA	intron (NM_001033324, intron 2 of 6)	intron (NM_001033324, intron 2 of 6)	27724	NM_001033324	235320	Mm.457803	NM_001033324	ENSMUSG00000066687	Zbtb16	AI467657|PLZF|Zfp145|lu	zinc finger and BTB domain containing 16	protein-coding
mm_147864.1	chr18	64342343	64342379	-	1	NA	intron (NM_194268, intron 1 of 1)	intron (NM_194268, intron 1 of 1)	1997	NM_194268	225631	Mm.234723	NM_194268	ENSMUSG00000045991	Onecut2	C730009D12|OC-2|Oc2	one cut domain, family member 2	protein-coding
mm_45079.1	chr5	43948314	43948327	-	1	NA	Intergenic	Intergenic	33479	NM_008009	14181	Mm.46053	NM_008009	ENSMUSG00000048373	Fgfbp1	FGF-BP|FGF-BP1|FGFBP-1	fibroblast growth factor binding protein 1	protein-coding
mm_7695.1	chr1	129550315	129550340	-	1	NA	intron (NM_172485, intron 2 of 27)	intron (NM_172485, intron 2 of 27)	277023	NM_172485	210417	Mm.380518	NM_172485	ENSMUSG00000042581	Thsd7b	1700074E13Rik|B930082A18|D130067I03Rik	thrombospondin, type I, domain containing 7B	protein-coding
mm_119148.1	chr14	31435222	31435249	+	1	NA	intron (NM_011894, intron 1 of 8)	intron (NM_011894, intron 1 of 8)	865	NM_011894	24056	Mm.383198	NM_011894	ENSMUSG00000021892	Sh3bp5	AI606498|SH3BP-5|Sab	SH3-domain binding protein 5 (BTK-associated)	protein-coding
mm_167188.1	chr7	142472002	142472012	+	1	NA	5' UTR (NM_019391, exon 1 of 11)	5' UTR (NM_019391, exon 1 of 11)	164	NM_019391	16985	Mm.234003	NM_019391	ENSMUSG00000018819	Lsp1	Lsp-1|WP34|p50|pp52	lymphocyte specific 1	protein-coding
mm_63206.1	chr7	126248343	126248358	+	1	NA	promoter-TSS (NR_131046)	promoter-TSS (NR_131046)	-112	NR_131046	76728	Mm.76920	NR_131046	ENSMUSG00000108676	1700123J17Rik	-	RIKEN cDNA 1700123J17 gene	ncRNA
mm_52551.1	chr6	115989288	115989308	+	1	NA	intron (NM_026376, intron 1 of 35)	intron (NM_026376, intron 1 of 35)	5707	NM_026376	67784	Mm.3085	NM_026376	ENSMUSG00000030123	Plxnd1	6230425C21Rik|b2b1863Clo|b2b553Clo	plexin D1	protein-coding
mm_37828.1	chr4	131982727	131982730	-	1	NA	intron (NM_001128606, intron 7 of 17)	intron (NM_001128606, intron 7 of 17)	60957	NM_001201367	623230	Mm.421179	NM_001201367	ENSMUSG00000070720	Tmem200b	EG623230	transmembrane protein 200B	protein-coding
mm_61300.1	chr7	67937140	67937149	+	1	NA	Intergenic	Intergenic	-15113	NM_010513	16001	Mm.275742	NM_010513	ENSMUSG00000005533	Igf1r	A330103N21Rik|CD221|D930020L01|IGF-1R|hyft	insulin-like growth factor I receptor	protein-coding
mm_91196.1	chr10	21152948	21152969	-	1	NA	exon (NM_001198914, exon 4 of 16)	exon (NM_001198914, exon 4 of 16)	8026	NM_001198914	17863	Mm.52109	NM_010848	ENSMUSG00000019982	Myb	AI550390|M16449|c-myb	myeloblastosis oncogene	protein-coding
mm_26702.1	chr3	157566941	157566952	+	1	NA	promoter-TSS (NM_011196)	promoter-TSS (NM_011196)	54	NM_011196	19218	Mm.30424	NM_011196	ENSMUSG00000040016	Ptger3	EP3|Pgerep3|Ptgerep3	prostaglandin E receptor 3 (subtype EP3)	protein-coding
mm_117768.1	chr13	96542323	96542333	-	1	NA	promoter-TSS (NM_001164222)	promoter-TSS (NM_001164222)	251	NM_012048	27015	Mm.89926	NM_012048	ENSMUSG00000021668	Polk	DINP|Dinb1	polymerase (DNA directed), kappa	protein-coding
mm_143784.1	chr17	81731116	81731126	-	1	NA	intron (NR_104580, intron 1 of 8)	B4|SINE|B4	7266	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_50511.1	chr6	49038168	49038207	+	1	NA	intron (NM_053110, intron 1 of 10)	intron (NM_053110, intron 1 of 10)	1669	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_16337.1	chr2	174330112	174330126	+	1	NA	promoter-TSS (NM_001077510)	promoter-TSS (NM_001077510)	30	NM_001077510	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_87653.1	chr10	58446825	58446835	+	1	NA	promoter-TSS (NM_011240)	promoter-TSS (NM_011240)	-22	NM_011240	19386	Mm.431695	NM_011240	ENSMUSG00000003226	Ranbp2	A430087B05Rik|AI256741|NUP358	RAN binding protein 2	protein-coding
mm_166835.1	chr7	19271697	19271700	-	1	NA	non-coding (NR_104069, exon 1 of 11)	non-coding (NR_104069, exon 1 of 11)	156	NM_001282021	22323	Mm.9684	NM_009499	ENSMUSG00000030403	Vasp	-	vasodilator-stimulated phosphoprotein	protein-coding
mm_70765.1	chr8	21823534	21823548	+	1	NA	promoter-TSS (NM_199067)	promoter-TSS (NM_199067)	2	NM_199067	387334	Mm.346928	NM_199067	ENSMUSG00000058568	Defb50	AY387658|BD-50|Defb37|Pbd1|mBD-50	defensin beta 50	protein-coding
mm_5531.1	chr1	37996962	37996976	-	1	NA	intron (NM_172054, intron 1 of 4)	CpG	239	NM_172054	98258	Mm.28438	NM_172054	ENSMUSG00000058407	Txndc9	AI098020|APACD	thioredoxin domain containing 9	protein-coding
mm_109999.1	chr12	15816139	15816149	-	1	NA	5' UTR (NM_144551, exon 1 of 3)	5' UTR (NM_144551, exon 1 of 3)	641	NM_144551	217410	Mm.491136	NM_144551	ENSMUSG00000020601	Trib2	AW319517|TRB-2|TRB2	tribbles pseudokinase 2	protein-coding
mm_133791.1	chr16	95258311	95258333	+	1	NA	non-coding (NR_073406, exon 2 of 6)	non-coding (NR_073406, exon 2 of 6)	764	NM_001271690	16516	Mm.272239	NM_019664	ENSMUSG00000062609	Kcnj15	4930414N08Rik|AI182284|AI267127|IRKK|Kir4.2	potassium inwardly-rectifying channel, subfamily J, member 15	protein-coding
mm_152488.1	chr19	11050501	11050531	-	1	NA	promoter-TSS (NR_102366)	promoter-TSS (NR_102366)	50	NR_102366	107350	Mm.6381	NM_001177351	ENSMUSG00000075010	AW112010	-	expressed sequence AW112010	ncRNA
mm_104159.1	chr11	87293913	87293937	-	1	NA	intron (NR_106195, intron 6 of 8)	intron (NR_106195, intron 6 of 8)	65069	NM_177167	320472	Mm.341988	NM_177167	ENSMUSG00000046442	Ppm1e	AW049266|B930008A12Rik|POPX1|PP2CH|mKIAA1072	protein phosphatase 1E (PP2C domain containing)	protein-coding
mm_46730.1	chr5	110772846	110772847	-	1	NA	TTS (NM_019700)	TTS (NM_019700)	-2129	NM_173066	75560	Mm.270487	NM_029337	ENSMUSG00000029505	Ep400	1700020J09Rik|AU023439|mDomino|mKIAA1498|p400	E1A binding protein p400	protein-coding
mm_43056.1	chr5	124187133	124187137	+	1	NA	promoter-TSS (NM_001289472)	promoter-TSS (NM_001289472)	47	NM_001289472	19679	Mm.44261	NM_011256	ENSMUSG00000029406	Pitpnm2	NIR3|RDGBA2|Rdgb2|mKIAA1457	phosphatidylinositol transfer protein, membrane-associated 2	protein-coding
mm_66624.1	chr7	45484497	45484523	-	1	NA	intron (NM_027903, intron 3 of 6)	B1_Mus1|SINE|Alu	-1752	NM_001290996	56734	Mm.439742	NM_008807	ENSMUSG00000023467	Tulp2	Pdet	tubby-like protein 2	protein-coding
mm_128970.1	chr15	74832242	74832253	-	1	NA	Intergenic	B3|SINE|B2	9396	NM_001033229	110115	Mm.322606	NM_001033229	ENSMUSG00000075604	Cyp11b1	AA389061|CPN1|Cyp11b|Cyp11b-1|FHI	cytochrome P450, family 11, subfamily b, polypeptide 1	protein-coding
mm_109336.1	chr12	109581870	109581917	+	1	NA	Intergenic	Intergenic	1660	NR_030573	100124466		NR_030573	ENSMUSG00000077025	Mir493	Mirn493|mmu-mir-493	microRNA 493	ncRNA
mm_111458.1	chr12	98386876	98386879	-	1	NA	Intergenic	Zaphod|DNA|hAT-Tip100	118242	NM_008152	14744	Mm.378924	NM_008152	ENSMUSG00000021886	Gpr65	Dig1|Gpcr25|TDAG8	G-protein coupled receptor 65	protein-coding
mm_119841.1	chr14	54431697	54431707	+	1	NA	5' UTR (NM_008608, exon 1 of 10)	5' UTR (NM_008608, exon 1 of 10)	104	NM_008608	17387	Mm.280175	NM_008608	ENSMUSG00000000957	Mmp14	AI325305|MMP-X1|MT-MMP-1|MT1-MMP|sabe	matrix metallopeptidase 14 (membrane-inserted)	protein-coding
mm_149194.1	chr19	9954754	9954781	+	1	NA	Intergenic	Intergenic	-25833	NR_073181	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
mm_58497.1	chr7	3704557	3704586	+	1	NA	intron (NM_029767, intron 2 of 4)	CpG-12606	530	NM_029767	76846	Mm.13944	NM_029767	ENSMUSG00000006333	Rps9	3010033P07Rik|AL022771|AL022885	ribosomal protein S9	protein-coding
mm_50826.1	chr6	54596715	54596722	+	1	NA	intron (NM_001164361, intron 1 of 13)	intron (NM_001164361, intron 1 of 13)	1607	NM_001164361	231999	Mm.35416	NM_001001335	ENSMUSG00000005225	Plekha8	6330400G01|AA517676|BC052360|Fapp-2|Fapp2	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 8	protein-coding
mm_80029.1	chr9	68653762	68653785	+	1	NA	promoter-TSS (NM_001289917)	promoter-TSS (NM_001289917)	-13	NM_001289917	19883	Mm.378450	NM_013646	ENSMUSG00000032238	Rora	9530021D13Rik|Nr1f1|ROR1|ROR2|ROR3|nmf267|sg|staggerer|tmgc26	RAR-related orphan receptor alpha	protein-coding
mm_15296.1	chr2	155383049	155383066	+	1	NA	intron (NM_178111, intron 1 of 3)	intron (NM_178111, intron 1 of 3)	1201	NM_178111	68728	Mm.293605	NM_178111	ENSMUSG00000038375	Trp53inp2	1110029F20Rik|Tp53inp2	transformation related protein 53 inducible nuclear protein 2	protein-coding
mm_18537.1	chr2	64393809	64393812	-	1	NA	Intergenic	Intergenic	-295772	NM_001267847	60344	Mm.130769	NM_021716	ENSMUSG00000075324	Fign	fi|fidget	fidgetin	protein-coding
mm_101797.1	chr11	46221426	46221439	-	1	NA	exon (NM_001252459, exon 26 of 31)	exon (NM_001252459, exon 26 of 31)	-10703	NR_105955	102465598		NR_105955	ENSMUSG00000099230	Mir6989	Gm27885|mmu-mir-6989	microRNA 6989	ncRNA
mm_64196.1	chr7	141467387	141467427	+	1	NA	promoter-TSS (NM_001111049)	promoter-TSS (NM_001111049)	45	NM_001111049	12476	Mm.30246	NM_009842	ENSMUSG00000025510	Cd151	PETA-3|SFA-1|Tspan24	CD151 antigen	protein-coding
mm_25683.1	chr3	122243104	122243129	+	1	NA	Intergenic	Intergenic	-2441	NM_008129	14630	Mm.292676	NM_008129	ENSMUSG00000028124	Gclm	AI649393|Gcmc|Glclr	glutamate-cysteine ligase, modifier subunit	protein-coding
mm_13894.1	chr2	120406105	120406120	+	1	NA	intron (NM_172672, intron 1 of 23)	intron (NM_172672, intron 1 of 23)	-1996	NM_001110496	211499	Mm.260712	NM_173734	ENSMUSG00000033808	Tmem87a	A930025J12Rik	transmembrane protein 87A	protein-coding
mm_73386.1	chr8	105686274	105686293	+	1	NA	Intergenic	Intergenic	-4623	NM_001033320	234695	Mm.471640	NM_001033320	ENSMUSG00000050357	Carmil2	CG1399-PB|D130029J02Rik|Gm585|Rltpr	capping protein regulator and myosin 1 linker 2	protein-coding
mm_98921.1	chr11	98348467	98348473	+	1	NA	promoter-TSS (NM_144828)	promoter-TSS (NM_144828)	64	NM_144828	19049	Mm.45372	NM_144828	ENSMUSG00000061718	Ppp1r1b	AU040756|DARPP-32|Darpp32	protein phosphatase 1, regulatory (inhibitor) subunit 1B	protein-coding
mm_163153.1	chr11	83604830	83604836	-	1	NA	intron (NR_036453, intron 2 of 8)	intron (NR_036453, intron 2 of 8)	-11746	NM_009139	20305	Mm.137	NM_009139	ENSMUSG00000018927	Ccl6	MRP-1|Scya6|c10	chemokine (C-C motif) ligand 6	protein-coding
mm_138473.1	chr17	35194406	35194421	+	1	NA	promoter-TSS (NM_008518)	promoter-TSS (NM_008518)	-94	NM_008518	16994	Mm.1715	NM_008518	ENSMUSG00000024399	Ltb	AI662801|LTbeta|Tnfc|Tnfsf3|Tnlg1c|p33	lymphotoxin B	protein-coding
mm_111710.1	chr12	103695528	103695536	-	1	NA	promoter-TSS (NM_001164742)	promoter-TSS (NM_001164742)	-3	NM_026687	68348	Mm.20149	NM_026687	ENSMUSG00000021081	Serpina1f	0610012A11Rik|AI327419|Serpina2|epserin	serine (or cysteine) peptidase inhibitor, clade A, member 1F	protein-coding
mm_15487.1	chr2	157562156	157562218	+	1	NA	3' UTR (NM_010923, exon 3 of 3)	3' UTR (NM_010923, exon 3 of 3)	2109	NM_180960	18111	Mm.34330	NM_010923	ENSMUSG00000067786	Nnat	5730414I02Rik|AW107673|Peg5	neuronatin	protein-coding
mm_66524.1	chr7	45126663	45126685	-	1	NA	promoter-TSS (NR_000003)	promoter-TSS (NR_000003)	-6	NR_002455	27210		NR_002455	ENSMUSG00000065878	Snord34	Rnu34|U34	small nucleolar RNA, C/D box 34	snoRNA
mm_20416.1	chr2	129300731	129300766	-	1	NA	exon (NM_010554, exon 7 of 7)	exon (NM_010554, exon 7 of 7)	3378	NR_040371	100503468	Mm.446943	NR_040371	ENSMUSG00000085498	Gm14023	OTTMUSG00000015408	predicted gene 14023	ncRNA
mm_1331.1	chr1	65247181	65247190	+	1	NA	exon (NM_001310624, exon 20 of 42)	exon (NM_001310624, exon 20 of 42)	60500	NM_001310624	18711	Mm.38370	NM_011086	ENSMUSG00000025949	Pikfyve	5230400C17Rik|Pip5k|Pip5k3|Pipk5k3|PipkIII|p235	phosphoinositide kinase, FYVE finger containing	protein-coding
mm_126566.1	chr15	82171207	82171245	+	1	NA	exon (NM_033218, exon 3 of 19)	exon (NM_033218, exon 3 of 19)	23957	NM_033218	20788	Mm.9002	NM_033218	ENSMUSG00000022463	Srebf2	AI608257|SREBP-2|SREBP2|SREBP2gc|bHLHd2|lop13|nuc	sterol regulatory element binding factor 2	protein-coding
mm_55629.1	chr6	72314664	72314699	-	1	NA	TTS (NM_001282071)	TTS (NM_001282071)	10071	NM_147779	20388	Mm.46033	NM_147779	ENSMUSG00000056370	Sftpb	AI562151|SF-B|SP-B|Sftp-3|Sftp3	surfactant associated protein B	protein-coding
mm_128911.1	chr15	73487336	73487342	-	1	NA	Intergenic	Intergenic	-25221	NM_001081066	105841	Mm.322557	NM_001081066	ENSMUSG00000036661	Dennd3	AI447457|E030003N15Rik	DENN/MADD domain containing 3	protein-coding
mm_46486.1	chr5	105132112	105132128	-	1	NA	intron (NM_008620, intron 3 of 10)	intron (NM_008620, intron 3 of 10)	7432	NM_008620	17472	Mm.440525	NM_008620	ENSMUSG00000079363	Gbp4	AW228052|Mag-2|Mpa-2|Mpa2	guanylate binding protein 4	protein-coding
mm_92105.1	chr10	63023777	63023784	-	1	NA	promoter-TSS (NM_001079824)	promoter-TSS (NM_001079824)	69	NM_001079824	432467	Mm.274784	NM_001079824	ENSMUSG00000020069	Hnrnph3	AA693301|AI666703|Hnrph3	heterogeneous nuclear ribonucleoprotein H3	protein-coding
mm_65718.1	chr7	28378481	28378514	-	1	NA	intron (NM_011756, intron 1 of 1)	CpG	731	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_34506.1	chr4	148667231	148667256	+	1	NA	intron (NM_001085505, intron 7 of 10)	intron (NM_001085505, intron 7 of 10)	23926	NM_001085505	230909	Mm.332067	NM_001085505	ENSMUSG00000070577	Gm572	b2b1167Clo	predicted gene 572	protein-coding
mm_100299.1	chr11	117832287	117832299	+	1	NA	intron (NM_027827, intron 2 of 10)	intron (NM_027827, intron 2 of 10)	-6279	NM_009387	21877	Mm.2661	NM_009387	ENSMUSG00000025574	Tk1	D530002A18Rik|Tk-1|Tk1a|Tk1b	thymidine kinase 1	protein-coding
mm_151668.1	chr19	4181920	4181930	-	1	NA	Intergenic	B1_Mur1|SINE|Alu	-6446	NM_134148	107239	Mm.482310	NM_134148	ENSMUSG00000075289	Carns1	AI790298|Atpgd1|mKIAA1394	carnosine synthase 1	protein-coding
mm_159672.1	chr4	154871530	154871530	+	1	NA	5' UTR (NM_013783, exon 2 of 24)	5' UTR (NM_013783, exon 2 of 24)	1945	NM_013783	27390	Mm.116944	NM_013783	ENSMUSG00000058183	Mmel1	Mell1|NEP2|NEPII|Nl1|SEP	membrane metallo-endopeptidase-like 1	protein-coding
mm_140118.1	chr17	78937125	78937183	+	1	NA	promoter-TSS (NM_028611)	promoter-TSS (NM_028611)	19	NM_028611	73694	Mm.104959	NM_028611	ENSMUSG00000024082	Ndufaf7	2410091C18Rik|AL033374|PRO1853	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex assembly factor 7	protein-coding
mm_16183.1	chr2	172949736	172949742	+	1	NA	Intergenic	U2|snRNA|snRNA	-9418	NM_007557	12162	Mm.595	NM_007557	ENSMUSG00000008999	Bmp7	OP1	bone morphogenetic protein 7	protein-coding
mm_65040.1	chr7	18567192	18567197	-	1	NA	5' UTR (NM_001037168, exon 1 of 5)	5' UTR (NM_001037168, exon 1 of 5)	111	NM_001037168	545925	Mm.440302	NM_001037168	ENSMUSG00000070797	Psg27	EG545925|cea15	pregnancy-specific glycoprotein 27	protein-coding
mm_159136.1	chr2	77946183	77946183	-	1	NA	5' UTR (NM_001290740, exon 1 of 20)	5' UTR (NM_001290740, exon 1 of 20)	173	NM_001290740	80744	Mm.288151	NM_030560	ENSMUSG00000027014	Cwc22	AA684037|AI173004|AL022752|B230213M24|mKIAA1604	CWC22 spliceosome-associated protein	protein-coding
mm_104744.1	chr11	98443962	98443966	-	1	NA	Intergenic	PB1D11|SINE|Alu	-2870	NM_010346	14786	Mm.276702	NM_010346	ENSMUSG00000019312	Grb7	mKIAA4028	growth factor receptor bound protein 7	protein-coding
mm_137174.1	chr17	23815288	23815305	+	1	NA	exon (NM_175229, exon 10 of 14)	exon (NM_175229, exon 10 of 14)	12109	NM_175229	75956	Mm.5222	NM_175229	ENSMUSG00000039218	Srrm2	5033413A03Rik|AA410130|SRm300|mKIAA0324	serine/arginine repetitive matrix 2	protein-coding
mm_146304.1	chr18	80255284	80255300	+	1	NA	promoter-TSS (NM_001164424)	promoter-TSS (NM_001164424)	47	NM_001164420	66943	Mm.29247	NM_025861	ENSMUSG00000034006	Pqlc1	2310009N05Rik|4933425L21Rik|5730564E11Rik|C78974	PQ loop repeat containing 1	protein-coding
mm_38974.1	chr4	150907362	150907375	-	1	NA	intron (NM_020569, intron 2 of 6)	intron (NM_020569, intron 2 of 6)	2553	NM_020569	57320	Mm.277349	NM_020569	ENSMUSG00000028964	Park7	DJ-1|Dj1	Parkinson disease (autosomal recessive, early onset) 7	protein-coding
mm_5093.1	chr1	4785672	4785744	-	1	NA	promoter-TSS (NM_001177658)	promoter-TSS (NM_001177658)	18	NR_033530	27395	Mm.182927	NM_025300	ENSMUSG00000033845	Mrpl15	HSPC145|MRP-L7|Rpml7	mitochondrial ribosomal protein L15	protein-coding
mm_122622.1	chr14	51145574	51145583	-	1	NA	exon (NM_011271, exon 2 of 2)	exon (NM_011271, exon 2 of 2)	1189	NM_011271	19752	Mm.235538	NM_011271	ENSMUSG00000035896	Rnase1	AI574248|Rib-1|Rib1	ribonuclease, RNase A family, 1 (pancreatic)	protein-coding
mm_97465.1	chr11	78263398	78263418	+	1	NA	intron (NM_001002004, intron 2 of 38)	intron (NM_001002004, intron 2 of 38)	1654	NM_001002004	72503	Mm.237103	NM_001002004	ENSMUSG00000010277	2610507B11Rik	AU022687|D11Bhm178e|D11Bhm179e|E1|Kiaa0100|mKIAA0100	RIKEN cDNA 2610507B11 gene	protein-coding
mm_158170.1	chrX	103623705	103623762	-	1	NA	promoter-TSS (NR_028381)	promoter-TSS (NR_028381)	21	NR_028381	78878	Mm.259724	NR_028380	ENSMUSG00000086370	Ftx	B230206F22Rik|BB219131|NCRNA00182|Thcytx	Ftx transcript, Xist regulator (non-protein coding)	ncRNA
mm_112395.1	chr12	119238642	119238659	-	1	NA	promoter-TSS (NM_177290)	promoter-TSS (NM_177290)	-374	NM_177290	320910	Mm.217000	NM_177290	ENSMUSG00000025321	Itgb8	4832412O06Rik	integrin beta 8	protein-coding
mm_116418.1	chr13	41606410	41606435	-	1	NA	intron (NM_001163572, intron 1 of 2)	CpG	206	NM_001163572	621976	Mm.259830	NM_001163572	ENSMUSG00000087370	Tmem170b	EG621976	transmembrane protein 170B	protein-coding
mm_84639.1	chr9	71165205	71165222	-	1	NA	Intergenic	Intergenic	-1924	NM_022026	64008	Mm.449427	NM_022026	ENSMUSG00000032204	Aqp9	1700020I22Rik|AI266899|AQP-9	aquaporin 9	protein-coding
mm_88674.1	chr10	80019357	80019359	+	1	NA	promoter-TSS (NM_027521)	promoter-TSS (NM_027521)	-317	NM_027521	70719	Mm.243954	NM_027521	ENSMUSG00000035697	Hmha1	6330406L22Rik|AW539505|Ha-1	histocompatibility (minor) HA-1	protein-coding
mm_119055.1	chr14	30715600	30715641	+	1	NA	promoter-TSS (NM_001166532)	promoter-TSS (NM_001166532)	5	NM_001166532	54650	Mm.294662	NM_019460	ENSMUSG00000006527	Sfmbt1	4930442N21Rik|9330180L21Rik|AA536974|Sfmbt|Smr	Scm-like with four mbt domains 1	protein-coding
mm_133753.1	chr16	94425084	94425107	+	1	NA	exon (NM_009441, exon 23 of 46)	exon (NM_009441, exon 23 of 46)	-54080	NM_001159617	56176	Mm.474449	NM_019543	ENSMUSG00000022940	Pigp	Dcrc|Dscr5	phosphatidylinositol glycan anchor biosynthesis, class P	protein-coding
mm_115600.1	chr13	11887552	11887556	-	1	NA	intron (NM_023868, intron 5 of 104)	intron (NM_023868, intron 5 of 104)	219391	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding
mm_161505.1	chr15	97789766	97789766	+	1	NA	intron (NM_026353, intron 1 of 2)	intron (NM_026353, intron 1 of 2)	5401	NM_026353	67739	Mm.28955	NM_026353	ENSMUSG00000081534	Slc48a1	4930570C03Rik	solute carrier family 48 (heme transporter), member 1	protein-coding
mm_111298.1	chr12	85485929	85485939	-	1	NA	Intergenic	Intergenic	12033	NM_010234	14281	Mm.246513	NM_010234	ENSMUSG00000021250	Fos	D12Rfj1|c-fos|cFos	FBJ osteosarcoma oncogene	protein-coding
mm_143695.1	chr17	80450632	80450641	-	1	NA	intron (NM_009231, intron 5 of 21)	B3|SINE|B2	29817	NM_009231	20662	Mm.60975	NM_009231	ENSMUSG00000024241	Sos1	4430401P03Rik|9630010N06|AI449023	son of sevenless homolog 1 (Drosophila)	protein-coding
mm_134834.1	chr16	26164266	26164275	-	1	NA	Intergenic	Intergenic	-58486	NM_173379	210530	Mm.326869	NM_173379	ENSMUSG00000038168	P3h2	4832416N06|AW553532|Leprel1|Mlat4	prolyl 3-hydroxylase 2	protein-coding
mm_162787.1	chr10	72957948	72957949	+	1	NA	Intergenic	Intergenic	128757	NR_040646	327768	Mm.417745	NR_040646		A330049N07Rik	-	RIKEN cDNA A330049N07 gene	ncRNA
mm_166252.1	chr5	82701949	82701951	+	1	NA	Intergenic	Lx6|LINE|L1	97115	NR_035415	100316803		NR_035415	ENSMUSG00000080586	Mir1187	Mirn1187|mir-1187|mmu-mir-1187	microRNA 1187	ncRNA
mm_44565.1	chr5	24685353	24685389	-	1	NA	promoter-TSS (NM_001305264)	promoter-TSS (NM_001305264)	-444	NM_016736	53312	Mm.5856	NM_016736	ENSMUSG00000028954	Nub1	4931404D21Rik|6330412F12Rik|BS4|NY-REN-18	negative regulator of ubiquitin-like proteins 1	protein-coding
mm_162675.1	chr10	8762386	8762396	-	1	NA	intron (NM_175155, intron 8 of 19)	intron (NM_175155, intron 8 of 19)	123679	NM_175155	70097	Mm.338275	NM_175155	ENSMUSG00000015305	Sash1	1100001C18Rik|2500002E12Rik|A330076K04Rik|mKIAA0790	SAM and SH3 domain containing 1	protein-coding
mm_131056.1	chr16	4213371	4213419	+	1	NA	promoter-TSS (NM_001025432)	promoter-TSS (NM_001025432)	9	NM_001025432	12914	Mm.132238	NM_001025432	ENSMUSG00000022521	Crebbp	AW558298|CBP|CBP/p300|KAT3A|p300/CBP	CREB binding protein	protein-coding
mm_44926.1	chr5	36036975	36036994	-	1	NA	intron (NM_030889, intron 17 of 26)	intron (NM_030889, intron 17 of 26)	143665	NM_027373	70292	Mm.125167	NM_027373	ENSMUSG00000029094	Afap1	2600003E23Rik|9630044L16Rik|AI848729|Afap|mKIAA3018	actin filament associated protein 1	protein-coding
mm_38448.1	chr4	140037730	140037741	-	1	NA	intron (NM_198610, intron 4 of 9)	intron (NM_198610, intron 4 of 9)	-69709	NM_173427	242721	Mm.60400	NM_173427	ENSMUSG00000078234	Klhdc7a	B230308G19Rik	kelch domain containing 7A	protein-coding
mm_103014.1	chr11	69734791	69734793	-	1	NA	exon (NM_001291068, exon 29 of 29)	exon (NM_001291068, exon 29 of 29)	23841	NM_001291068	20020	Mm.16533	NM_009089	ENSMUSG00000005198	Polr2a	220kDa|Rpb1|Rpo2-1	polymerase (RNA) II (DNA directed) polypeptide A	protein-coding
mm_120682.1	chr14	70636111	70636123	+	1	NA	promoter-TSS (NM_001252664)	promoter-TSS (NM_001252664)	-69	NM_001252664	13829	Mm.210863	NM_013514	ENSMUSG00000022099	Dmtn	AI325486|Epb4.9|Epb49|dematin	dematin actin binding protein	protein-coding
mm_99130.1	chr11	100319872	100319878	+	1	NA	promoter-TSS (NM_011508)	promoter-TSS (NM_011508)	-74	NM_011508	20918	Mm.13886	NM_011508	ENSMUSG00000035530	Eif1	Sui1-rs1	eukaryotic translation initiation factor 1	protein-coding
mm_130860.1	chr15	102188984	102188996	-	1	NA	promoter-TSS (NM_144942)	promoter-TSS (NM_144942)	53	NM_144942	246277	Mm.296382	NM_144942	ENSMUSG00000023044	Csad	Csd	cysteine sulfinic acid decarboxylase	protein-coding
mm_99863.1	chr11	109394228	109394234	+	1	NA	intron (NM_010303, intron 3 of 3)	ID_B1|SINE|B4	-30577	NR_038097	100036768	Mm.467767	NR_038097	ENSMUSG00000056687	Gm11696	OTTMUSG00000003456	predicted gene 11696	ncRNA
mm_78773.1	chr9	43743947	43743968	+	1	NA	promoter-TSS (NM_021424)	promoter-TSS (NM_021424)	-619	NM_021424	58235	Mm.335096	NM_021424	ENSMUSG00000032012	Nectin1	AI835281|AW549174|Cd111|HIgR|HveC|PRR|PRR1|Pvrl1|nectin-1	nectin cell adhesion molecule 1	protein-coding
mm_80550.1	chr9	82830442	82830476	+	1	NA	intron (NM_001168240, intron 1 of 2)	intron (NM_001168240, intron 1 of 2)	653	NM_022986	65099	Mm.41415	NM_022986	ENSMUSG00000032251	Irak1bp1	4921528N06Rik|AI851240|Aabp3|Aip70|Simpl	interleukin-1 receptor-associated kinase 1 binding protein 1	protein-coding
mm_23339.1	chr3	54692850	54692868	+	1	NA	promoter-TSS (NM_019995)	promoter-TSS (NM_019995)	-246	NM_019995	56790	Mm.486375	NM_019995	ENSMUSG00000027751	Supt20	AA667204|AI450544|D3Ertd300e|Fam48a|Supt20h|p38IP	suppressor of Ty 20	protein-coding
mm_66687.1	chr7	45830777	45830816	-	1	NA	promoter-TSS (NM_153419)	promoter-TSS (NM_153419)	-7	NM_153419	101612	Mm.274847	NM_153419	ENSMUSG00000053801	Grwd1	A301|AI504353|Grwd|Wdr28	glutamate-rich WD repeat containing 1	protein-coding
mm_96284.1	chr11	63051327	63051341	+	1	NA	intron (NR_105772, intron 5 of 6)	intron (NR_105772, intron 5 of 6)	-10325	NM_027660	71062	Mm.23534	NM_027660	ENSMUSG00000042189	Tekt3	4933407G07Rik	tektin 3	protein-coding
mm_73095.1	chr8	94562374	94562376	+	1	NA	intron (NM_153507, intron 12 of 15)	intron (NM_153507, intron 12 of 15)	29347	NM_153507	234577	Mm.291815	NM_153507	ENSMUSG00000034361	Cpne2	3322401K10Rik	copine II	protein-coding
mm_128190.1	chr15	34878823	34878832	-	1	NA	intron (NM_019635, intron 10 of 10)	RLTR51A_Mm|LTR|ERVK?	40778	NM_001271704	16539	Mm.71045	NM_181317	ENSMUSG00000050963	Kcns2	E130006J24Rik|Kv9.2	K+ voltage-gated channel, subfamily S, 2	protein-coding
mm_110412.1	chr12	46626706	46626706	-	1	NA	Intergenic	MT2B|LTR|ERVL	192069	NM_021361	664883	Mm.247195	NM_021361	ENSMUSG00000021047	Nova1	9430099M15Rik|G630039L02|Nova-1	neuro-oncological ventral antigen 1	protein-coding
mm_25866.1	chr3	129881150	129881188	+	1	NA	promoter-TSS (NM_183423)	promoter-TSS (NM_183423)	-15	NM_183423	66350	Mm.151951	NM_023196	ENSMUSG00000027999	Pla2g12a	2310004B05Rik|GXII|GXII-1|GXII-1-PLA2|Pla2g12|Rossy|mGXII-1	phospholipase A2, group XIIA	protein-coding
mm_53820.1	chr6	147099553	147099578	+	1	NA	intron (NM_001081237, intron 1 of 2)	intron (NM_001081237, intron 1 of 2)	8490	NM_001081237	232539	Mm.491206	NM_001081237	ENSMUSG00000040102	Klhl42	A330079N23Rik|AI450355|C230080I20Rik|Ctb9|Klhdc5|mKIAA1340	kelch-like 42	protein-coding
mm_51908.1	chr6	91157374	91157391	+	1	NA	intron (NM_144919, intron 1 of 9)	intron (NM_144919, intron 1 of 9)	567	NM_144919	232232	Mm.206218	NM_144919	ENSMUSG00000034245	Hdac11	-	histone deacetylase 11	protein-coding
mm_79976.1	chr9	66754401	66754406	+	1	NA	intron (NM_001306148, intron 8 of 9)	intron (NM_001306148, intron 8 of 9)	40717	NM_001306148	76459	Mm.277921	NM_178396	ENSMUSG00000032373	Car12	2310047E01Rik|AI314958|CA-XII|Ca12	carbonic anhydrase 12	protein-coding
mm_160932.1	chr11	90663190	90663190	-	1	NA	intron (NM_028011, intron 7 of 15)	MER58B|DNA|hAT-Charlie	24411	NM_028011	71943	Mm.167868	NM_028011	ENSMUSG00000020541	Tom1l1	2310045L10Rik|C80573|Srcasm	target of myb1-like 1 (chicken)	protein-coding
mm_18088.1	chr2	44983903	44983906	-	1	NA	3' UTR (NM_015753, exon 10 of 10)	3' UTR (NM_015753, exon 10 of 10)	39273	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_169836.1	chr16	25855510	25855510	-	1	NA	intron (NM_001127259, intron 4 of 13)	intron (NM_001127259, intron 4 of 13)	53594	NM_001127264	22061	Mm.20894	NM_011641	ENSMUSG00000022510	Trp63	AI462811|Ket|P51/P63|P63|P73l|Tp63|Trp53rp1	transformation related protein 63	protein-coding
mm_106232.1	chr11	117360554	117360566	-	1	NA	3' UTR (NM_001113486, exon 12 of 12)	3' UTR (NM_001113486, exon 12 of 12)	28247	NM_001113488	53860	Mm.38450	NM_017380	ENSMUSG00000059248	Sept9	MSF1|Msf|PNUTL4|Sint1	septin 9	protein-coding
mm_87490.1	chr10	51495057	51495116	+	1	NA	intron (NM_001291894, intron 7 of 8)	(CCA)n|Simple_repeat|Simple_repeat	4188	NM_013532	14728	Mm.34408	NM_013532	ENSMUSG00000062593	Lilrb4a	CD85K|Gp49b|HM18|ILT3|LIR-5|Lilrb4|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4A	protein-coding
mm_22913.1	chr3	31094018	31094050	+	1	NA	Intergenic	Intergenic	-1024	NM_011386	20482	Mm.15406	NM_011386	ENSMUSG00000027660	Skil	Skir|SnoN|sno	SKI-like	protein-coding
mm_1198.1	chr1	62708801	62708829	+	1	NA	intron (NM_001077405, intron 1 of 15)	intron (NM_001077405, intron 1 of 15)	5498	NM_001077405	18187	Mm.266341	NM_010939	ENSMUSG00000025969	Nrp2	1110048P06Rik|Np-2|Np2|Npn-2|Npn2	neuropilin 2	protein-coding
mm_71580.1	chr8	54582630	54582632	+	1	NA	intron (NM_029569, intron 2 of 6)	intron (NM_029569, intron 2 of 6)	-18150	NM_133711	69281	Mm.45833	NM_133711	ENSMUSG00000031518	Spata4	1700001N01Rik|Srg2|TSARG2	spermatogenesis associated 4	protein-coding
mm_3592.1	chr1	151428613	151428718	+	1	NA	promoter-TSS (NM_025819)	promoter-TSS (NM_025819)	17	NM_026876	98685	Mm.289373	NM_026876	ENSMUSG00000053286	Trmt1l	1190005F20Rik|AW226554|C1orf25|Trm1-like|Trm1l	tRNA methyltransferase 1 like	protein-coding
mm_3625.1	chr1	152766592	152766687	+	1	NA	promoter-TSS (NM_026369)	promoter-TSS (NM_026369)	97	NM_026369	67771	Mm.288974	NM_026369	ENSMUSG00000008475	Arpc5	5830443F10Rik|p16-Arc	actin related protein 2/3 complex, subunit 5	protein-coding
mm_22112.1	chr2	170133543	170133565	-	1	NA	intron (NM_001159683, intron 1 of 6)	CpG	-2334	NM_001033299	228913	Mm.22858	NM_001033299	ENSMUSG00000052056	Zfp217	4933431C08Rik|AW987152|Gm562|ZABC1|Znf217	zinc finger protein 217	protein-coding
mm_30635.1	chr4	8811324	8811339	+	1	NA	intron (NM_001277149, intron 6 of 37)	intron (NM_001277149, intron 6 of 37)	120925	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_135839.1	chr16	58524188	58524198	-	1	NA	promoter-TSS (NM_018784)	promoter-TSS (NM_018784)	-881	NM_018784	54613	Mm.212742	NM_018784	ENSMUSG00000022747	St3gal6	1700023B24Rik|AI930218|AW552396|Siat10|St3galVI	ST3 beta-galactoside alpha-2,3-sialyltransferase 6	protein-coding
mm_131083.1	chr16	4756880	4756881	+	1	NA	intron (NM_010443, intron 1 of 5)	C-rich|Low_complexity|Low_complexity	15267	NM_010443	15369	Mm.272866	NM_010443	ENSMUSG00000004070	Hmox2	HO-2|HO2	heme oxygenase 2	protein-coding
mm_135285.1	chr16	38448430	38448436	-	1	NA	intron (NM_007414, intron 2 of 3)	intron (NM_007414, intron 2 of 3)	4256	NM_007414	11544	Mm.20047	NM_007414	ENSMUSG00000002844	Adprh	Arh1	ADP-ribosylarginine hydrolase	protein-coding
mm_1045.1	chr1	58795693	58795710	+	1	NA	5' UTR (NM_009812, exon 1 of 9)	5' UTR (NM_009812, exon 1 of 9)	327	NM_009812	12370	Mm.336851	NM_009812	ENSMUSG00000026029	Casp8	CASP-8|FLICE|MACH|Mch5	caspase 8	protein-coding
mm_168678.1	chr1	195240775	195240787	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-64066	NM_007758	12902	Mm.235387	NM_007758	ENSMUSG00000026616	Cr2	C3DR|CD21|CD35|Cr-1|Cr-2|Cr1	complement receptor 2	protein-coding
mm_104521.1	chr11	96065334	96065344	-	1	NA	promoter-TSS (NM_172300)	promoter-TSS (NM_172300)	25	NM_172300	268470	Mm.38802	NM_172300	ENSMUSG00000014349	Ube2z	AW049199|C030047H17Rik|D11Moh35	ubiquitin-conjugating enzyme E2Z	protein-coding
mm_139347.1	chr17	50470670	50470706	+	1	NA	Intergenic	Intergenic	-38859	NM_013880	224860	Mm.217362	NM_013880	ENSMUSG00000038910	Plcl2	PLC-L2|PRIP-2|Plce2|mKIAA1092	phospholipase C-like 2	protein-coding
mm_173044.1	chrX	116287369	116287378	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-161571	NM_001033471	382239	Mm.336224	NM_001033471	ENSMUSG00000072995	Cpxcr1	Gm1143	CPX chromosome region, candidate 1	protein-coding
mm_106431.1	chr11	119391083	119391101	-	1	NA	TTS (NR_035453)	TTS (NR_035453)	620	NR_035453	100316690		NR_035453	ENSMUSG00000088015	Mir1932	mir-1932|mmu-mir-1932	microRNA 1932	ncRNA
mm_71736.1	chr8	62017135	62017155	+	1	NA	exon (NM_001293783, exon 31 of 38)	exon (NM_001293783, exon 31 of 38)	89058	NM_001293783	234311	Mm.275233	NM_144928	ENSMUSG00000037921	Ddx60	9830118M07	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	protein-coding
mm_140678.1	chr17	12992228	12992249	-	1	NA	promoter-TSS (NM_001113533)	promoter-TSS (NM_001113533)	21	NM_001113533	60532	Mm.275521	NM_175394	ENSMUSG00000060475	Wtap	2810408K05Rik|9430038B09Rik	Wilms tumour 1-associating protein	protein-coding
mm_147302.1	chr18	39519325	39519333	-	1	NA	Intergenic	Intergenic	-32084	NM_008173	14815	Mm.129481	NM_008173	ENSMUSG00000024431	Nr3c1	GR|Grl-1|Grl1	nuclear receptor subfamily 3, group C, member 1	protein-coding
mm_83858.1	chr9	54647224	54647226	-	1	NA	intron (NM_053178, intron 1 of 13)	intron (NM_053178, intron 1 of 13)	14660	NM_053178	94180	Mm.20592	NM_053178	ENSMUSG00000032281	Acsbg1	BG1|Bgm|E230019G03Rik|GR-LACS|Lpd|R75185	acyl-CoA synthetase bubblegum family member 1	protein-coding
mm_137284.1	chr17	24730889	24730903	+	1	NA	exon (NM_001163945, exon 3 of 10)	exon (NM_001163945, exon 3 of 10)	-1789	NM_025425	66211	Mm.46198	NM_025425	ENSMUSG00000002500	Rpl3l	1110057H16Rik	ribosomal protein L3-like	protein-coding
mm_142903.1	chr17	52285502	52285508	-	1	NA	Intergenic	Intergenic	-317204	NM_001031811	211468	Mm.399068	NM_001031811	ENSMUSG00000035580	Kcnh8	C130090D05Rik|ELK|ELK1|ELK3|Kv12.1	potassium voltage-gated channel, subfamily H (eag-related), member 8	protein-coding
mm_33031.1	chr4	122689292	122689320	+	1	NA	promoter-TSS (NM_023865)	promoter-TSS (NM_023865)	47	NM_023865	77432	Mm.491436	NM_023865	ENSMUSG00000023263	9530002B09Rik	Aump|Vpp1|Vppl	RIKEN cDNA 9530002B09 gene	protein-coding
mm_96632.1	chr11	69324056	69324065	+	1	NA	promoter-TSS (NM_001024206)	promoter-TSS (NM_001024206)	74	NM_001024206	245828	Mm.28073	NM_001024206	ENSMUSG00000049299	Trappc1	BET5|D11Ertd172e|MUM2	trafficking protein particle complex 1	protein-coding
mm_126533.1	chr15	82017109	82017115	+	1	NA	promoter-TSS (NM_134095)	promoter-TSS (NM_134095)	743	NM_010247	14375	Mm.288809	NM_010247	ENSMUSG00000022471	Xrcc6	70kDa|G22p1|Ku70	X-ray repair complementing defective repair in Chinese hamster cells 6	protein-coding
mm_2838.1	chr1	131528362	131528376	+	1	NA	5' UTR (NM_175382, exon 1 of 4)	5' UTR (NM_175382, exon 1 of 4)	466	NM_175382	108900	Mm.31278	NM_175382	ENSMUSG00000055184	Fam72a	2700049P18Rik|P17	family with sequence similarity 72, member A	protein-coding
mm_69141.1	chr7	127051666	127051686	-	1	NA	exon (NM_026918, exon 2 of 3)	exon (NM_026918, exon 2 of 3)	301	NM_026918	69036	Mm.21835	NM_026918	ENSMUSG00000049350	Zg16	1810010M01Rik|AI593689|ZG16p	zymogen granule protein 16	protein-coding
mm_30901.1	chr4	32336040	32336046	+	1	NA	Intergenic	Intergenic	-81392	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_103058.1	chr11	69834666	69834675	-	1	NA	5' UTR (NM_198862, exon 1 of 7)	5' UTR (NM_198862, exon 1 of 7)	179	NM_198862	216856	Mm.151293	NM_198862	ENSMUSG00000051790	Nlgn2	NL2	neuroligin 2	protein-coding
mm_86898.1	chr10	22303058	22303059	+	1	NA	intron (NM_009018, intron 5 of 5)	intron (NM_009018, intron 5 of 5)	-3662	NR_015465	606736	Mm.387042	NR_015465	ENSMUSG00000097352	C920009B18Rik	-	RIKEN cDNA C920009B18 gene	ncRNA
mm_121983.1	chr14	25861873	25861890	-	1	NA	intron (NM_013469, intron 1 of 14)	intron (NM_013469, intron 1 of 14)	19726	NM_013469	11744	Mm.294083	NM_013469	ENSMUSG00000021866	Anxa11	A830099O17Rik|Anx11	annexin A11	protein-coding
mm_128011.1	chr15	13173651	13173658	-	1	NA	promoter-TSS (NM_007666)	promoter-TSS (NM_007666)	21	NM_007666	12563	Mm.57048	NM_007666	ENSMUSG00000039385	Cdh6	cad6	cadherin 6	protein-coding
mm_27875.1	chr3	79169807	79169817	-	1	NA	Intergenic	Intergenic	-23937	NM_001099624	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_1986.1	chr1	87099701	87099721	+	1	NA	exon (NM_001081082, exon 8 of 11)	exon (NM_001081082, exon 8 of 11)	1895	NM_001081082	76768	Mm.58068	NM_001081082	ENSMUSG00000079440	Alpi	2010001C14Rik|Akp6|gIAP	alkaline phosphatase, intestinal	protein-coding
mm_143756.1	chr17	81601216	81601219	-	1	NA	intron (NR_104580, intron 2 of 8)	intron (NR_104580, intron 2 of 8)	137170	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_125089.1	chr15	27466782	27466798	+	1	NA	5' UTR (NM_020332, exon 1 of 12)	5' UTR (NM_020332, exon 1 of 12)	113	NM_020332	11732	Mm.265264	NM_020332	ENSMUSG00000022265	Ank	Ankh|D15Ertd221e|ank|mKIAA1581	progressive ankylosis	protein-coding
mm_80806.1	chr9	96322151	96322155	+	1	NA	3' UTR (NM_001184710, exon 10 of 10)	3' UTR (NM_001184710, exon 10 of 10)	42146	NM_007502	11933	Mm.424	NM_007502	ENSMUSG00000032412	Atp1b3	AA409958|AI664000|AW212096	ATPase, Na+/K+ transporting, beta 3 polypeptide	protein-coding
mm_68829.1	chr7	126200346	126200354	-	1	NA	promoter-TSS (NM_028816)	promoter-TSS (NM_028816)	58	NM_028816	74204	Mm.235663	NM_028816	ENSMUSG00000000131	Xpo6	2610005L19Rik|AL022631|C230091E20Rik|R75304|Ranbp20|mKIAA0370	exportin 6	protein-coding
mm_18672.1	chr2	71044974	71044981	-	1	NA	intron (NM_145524, intron 1 of 9)	intron (NM_145524, intron 1 of 9)	10629	NM_145524	228019	Mm.490343	NM_145524	ENSMUSG00000041975	Mettl8	BC004636|Tip	methyltransferase like 8	protein-coding
mm_12019.1	chr2	58154023	58154032	+	1	NA	intron (NM_139200, intron 1 of 7)	intron (NM_139200, intron 1 of 7)	6095	NM_139200	227929	Mm.273905	NM_139200	ENSMUSG00000026832	Cytip	A130053M09Rik|AI462064|C80816|Cbp|Cybr|Pscdbp	cytohesin 1 interacting protein	protein-coding
mm_125307.1	chr15	37337678	37337687	+	1	NA	intron (NM_026496, intron 11 of 15)	intron (NM_026496, intron 11 of 15)	-87872	NM_029113	74892	Mm.107630	NM_029113	ENSMUSG00000022288	4930447A16Rik	-	RIKEN cDNA 4930447A16 gene	protein-coding
mm_130099.1	chr15	89425857	89425872	-	1	NA	promoter-TSS (NM_009948)	promoter-TSS (NM_009948)	-2	NM_009948	12895	Mm.227738	NM_009948	ENSMUSG00000078937	Cpt1b	Cpt1|Cpt1-m|Cpti|Cpti-m|M-cpti	carnitine palmitoyltransferase 1b, muscle	protein-coding
mm_10293.1	chr2	10372337	10372347	+	1	NA	promoter-TSS (NM_177386)	promoter-TSS (NM_177386)	-94	NM_001198809	353282	Mm.329991	NM_177386	ENSMUSG00000061186	Sfmbt2	D2Wsu23e|D330030P06Rik	Scm-like with four mbt domains 2	protein-coding
mm_4266.1	chr1	171503411	171503456	+	1	NA	promoter-TSS (NM_019484)	promoter-TSS (NM_019484)	-45	NM_019484	56009	Mm.389208	NM_019484	ENSMUSG00000060244	Alyref2	C130042O11Rik|REF2|Refbp2	Aly/REF export factor 2	protein-coding
mm_155813.1	chrX	100428907	100428912	+	1	NA	promoter-TSS (NM_001163191)	promoter-TSS (NM_001163191)	-104	NM_001163191	408193	Mm.469910	NM_001163191	ENSMUSG00000051582	Otud6a	EG408193|Hshin6	OTU domain containing 6A	protein-coding
mm_131817.1	chr16	22920366	22920376	+	1	NA	5' UTR (NM_021564, exon 1 of 8)	5' UTR (NM_021564, exon 1 of 8)	149	NM_001083904	59083	Mm.28461	NM_021564	ENSMUSG00000022871	Fetub	2310011O17Rik|AI255764|D17980|Gugu	fetuin beta	protein-coding
mm_100336.1	chr11	118342608	118342619	+	1	NA	promoter-TSS (NM_021440)	promoter-TSS (NM_021440)	-79	NM_021440	58251	Mm.439815	NM_021440	ENSMUSG00000076433	BC100451	Cep295nl|Ddc8|FS39|Kiaa1731nl	cDNA sequence BC100451	protein-coding
mm_77744.1	chr8	126979459	126979471	-	1	NA	Intergenic	Intergenic	-8386	NM_172762	52202	Mm.28199	NM_172762	ENSMUSG00000033931	Rbm34	4930547K05Rik|6330444B11|D8Ertd233e	RNA binding motif protein 34	protein-coding
mm_72003.1	chr8	70673739	70673759	+	1	NA	intron (NM_015816, intron 1 of 4)	intron (NM_015816, intron 1 of 4)	518	NM_015816	50783	Mm.248188	NM_015816	ENSMUSG00000031848	Lsm4	-	LSM4 homolog, U6 small nuclear RNA and mRNA degradation associated	protein-coding
mm_37763.1	chr4	129696735	129696743	-	1	NA	promoter-TSS (NM_199305)	promoter-TSS (NM_199305)	99	NM_199305	230770	Mm.257157	NM_199305	ENSMUSG00000053730	Tmem39b	6330509E05Rik|BC037095	transmembrane protein 39b	protein-coding
mm_153827.1	chr19	46317958	46317960	-	1	NA	intron (NM_028627, intron 11 of 17)	CpG	8907	NM_001347454	73728	Mm.268532	NM_028627	ENSMUSG00000037126	Psd	1110007H17Rik|A930015K15|Efa6|Efa6a|Psdl|mKIAA2011	pleckstrin and Sec7 domain containing	protein-coding
mm_15075.1	chr2	153120364	153120398	+	1	NA	intron (NM_001172117, intron 1 of 12)	L1MA4|LINE|L1	11913	NM_010407	15162	Mm.715	NM_010407	ENSMUSG00000003283	Hck	AI849071|Bmk	hemopoietic cell kinase	protein-coding
mm_23309.1	chr3	53041631	53041635	+	1	NA	promoter-TSS (NM_175386)	promoter-TSS (NM_175386)	86	NM_175386	108927	Mm.118617	NM_175386	ENSMUSG00000048332	Lhfp	2810489O06Rik|AI194968	lipoma HMGIC fusion partner	protein-coding
mm_56710.1	chr6	115252064	115252072	-	1	NA	promoter-TSS (NM_080639)	promoter-TSS (NM_080639)	-219	NM_080639	110595	Mm.255607	NM_080639	ENSMUSG00000030317	Timp4	TIMP-4	tissue inhibitor of metalloproteinase 4	protein-coding
mm_128348.1	chr15	39857420	39857426	-	1	NA	promoter-TSS (NM_001164466)	promoter-TSS (NM_001164466)	47	NM_001164466	64705	Mm.275974	NM_022722	ENSMUSG00000022304	Dpys	1200017I10Rik|1300004I01Rik|DHP|DHPase	dihydropyrimidinase	protein-coding
mm_15622.1	chr2	162045299	162045299	+	1	NA	intron (NM_001291151, intron 7 of 30)	intron (NM_001291151, intron 7 of 30)	-345514	NR_040617	77645	Mm.447752	NR_040617	ENSMUSG00000084919	Ptprtos	C330008G21Rik	protein tyrosine phosphatase, receptor type T, opposite strand	ncRNA
mm_45115.1	chr5	45639369	45639408	-	1	NA	non-coding (NR_102378, exon 1 of 4)	non-coding (NR_102378, exon 1 of 4)	113	NR_102378	319251	Mm.402857	NR_102378	ENSMUSG00000097825	9630001P10Rik	-	RIKEN cDNA 9630001P10 gene	ncRNA
mm_8014.1	chr1	134866568	134866577	-	1	NA	intron (NM_001081307, intron 12 of 23)	intron (NM_001081307, intron 12 of 23)	-62851	NR_015606	329251	Mm.188709	NM_001081307	ENSMUSG00000073557	Ppp1r12b	1810037O03Rik|9530009M10Rik|AI132431|Mypt2	protein phosphatase 1, regulatory (inhibitor) subunit 12B	protein-coding
mm_122723.1	chr14	52314776	52314784	-	1	NA	exon (NM_001244916, exon 2 of 2)	exon (NM_001244916, exon 2 of 2)	1543	NM_001244916	50524	Mm.39487	NM_015772	ENSMUSG00000049532	Sall2	AI225809|AW559097|Msal-2|Sal-2|mKIAA0360|p150(Sal2)	sal-like 2 (Drosophila)	protein-coding
mm_32360.1	chr4	105157629	105157635	+	1	NA	5' UTR (NM_080555, exon 1 of 6)	5' UTR (NM_080555, exon 1 of 6)	285	NM_080555	67916	Mm.348326	NM_080555	ENSMUSG00000028517	Plpp3	1110003O22Rik|2610002D05Rik|AV025606|D4Bwg0538e|D4Bwg1535e|Lpp3|Ppab2b|Ppap2b	phospholipid phosphatase 3	protein-coding
mm_124115.1	chr14	79481416	79481449	-	1	NA	promoter-TSS (NM_018765)	promoter-TSS (NM_018765)	-164	NM_018765	22380	Mm.476813	NM_018765	ENSMUSG00000022023	Wbp4	AW545037|BB101031|FBP21	WW domain binding protein 4	protein-coding
mm_77369.1	chr8	119810331	119810347	-	1	NA	exon (NM_028071, exon 4 of 4)	exon (NM_028071, exon 4 of 4)	30240	NM_028071	72042	Mm.393405	NM_028071	ENSMUSG00000031827	Cotl1	1810074P22Rik|2010004C08Rik|Clp	coactosin-like 1 (Dictyostelium)	protein-coding
mm_36745.1	chr4	100042097	100042107	-	1	NA	Intergenic	Intergenic	-53689	NM_013845	26563	Mm.57252	NM_013845	ENSMUSG00000035305	Ror1	2810404D04Rik|Ntrkr1	receptor tyrosine kinase-like orphan receptor 1	protein-coding
mm_172466.1	chr7	42853463	42853467	+	1	NA	intron (NR_046214, intron 1 of 3)	MT2_Mm|LTR|ERVL	13769	NR_046214	100039706	Mm.260936	NR_046214	ENSMUSG00000092225	Gm2381	-	zinc finger protein 936 pseudogene	pseudo
mm_9440.1	chr1	172558148	172558162	-	1	NA	intron (NM_177723, intron 1 of 6)	intron (NM_177723, intron 1 of 6)	-1751	NR_027644	240916	Mm.71940	NM_177723	ENSMUSG00000049598	Vsig8	A030011M19|EG240916	V-set and immunoglobulin domain containing 8	protein-coding
mm_41275.1	chr5	89441192	89441224	+	1	NA	exon (NM_008096, exon 6 of 13)	exon (NM_008096, exon 6 of 13)	16690	NM_008096	14473	Mm.196595	NM_008096	ENSMUSG00000035540	Gc	DBP|VDB	group specific component	protein-coding
mm_34045.1	chr4	138217121	138217203	+	1	NA	promoter-TSS (NM_001122897)	promoter-TSS (NM_001122897)	35	NM_001122897	15441	Mm.348429	NM_010470	ENSMUSG00000028759	Hp1bp3	Hp1bp74	heterochromatin protein 1, binding protein 3	protein-coding
mm_74061.1	chr8	122376663	122376673	+	1	NA	promoter-TSS (NM_001310650)	promoter-TSS (NM_001310650)	52	NM_001029993	76014	Mm.241489	NM_001029993	ENSMUSG00000017478	Zc3h18	1190001B23Rik|5830416A07Rik|Nhn1	zinc finger CCCH-type containing 18	protein-coding
mm_26059.1	chr3	135826129	135826173	+	1	NA	intron (NM_001135150, intron 1 of 8)	intron (NM_001135150, intron 1 of 8)	361	NM_001135150	67547	Mm.30239	NM_026228	ENSMUSG00000053897	Slc39a8	4933419D20Rik|AA986696|BIGM103|ZIP-8|Zip8	solute carrier family 39 (metal ion transporter), member 8	protein-coding
mm_158413.1	chrX	137038266	137038309	-	1	NA	promoter-TSS (NM_001082412)	promoter-TSS (NM_001082412)	15	NM_001082412	67062	Mm.276518	NM_001082412	ENSMUSG00000044348	Slc25a53	2310046F18Rik|2810402A17Rik|AI448995|AI841128|Mcart6	solute carrier family 25, member 53	protein-coding
mm_29784.1	chr3	127499077	127499093	-	1	NA	promoter-TSS (NM_001327938)	promoter-TSS (NM_001327938)	30	NM_001327938	109676	Mm.220242	NM_178655	ENSMUSG00000032826	Ank2	100043364|AI835472|AW491075|Ank-2|Gm4392	ankyrin 2, brain	protein-coding
mm_45942.1	chr5	90244355	90244366	-	1	NA	exon (NM_030886, exon 29 of 34)	exon (NM_030886, exon 29 of 34)	-20364	NM_001163456	231430	Mm.319697	NM_001033310	ENSMUSG00000035505	Cox18	BC038311	cytochrome c oxidase assembly protein 18	protein-coding
mm_64587.1	chr7	3155548	3155552	-	1	NA	3' UTR (NM_001004153, exon 12 of 12)	3' UTR (NM_001004153, exon 12 of 12)	13653	NM_001004153	245128	Mm.268551	NM_001004153	ENSMUSG00000054753	AU018091	-	expressed sequence AU018091	protein-coding
mm_95079.1	chr11	32682948	32682952	+	1	NA	intron (NM_001271347, intron 2 of 12)	intron (NM_001271347, intron 2 of 12)	40395	NM_001271347	103583	Mm.28017	NM_134015	ENSMUSG00000020271	Fbxw11	2310065A07Rik|AA536858|BTRC2|BTRCP2|Fbxw1b|HOS	F-box and WD-40 domain protein 11	protein-coding
mm_125927.1	chr15	76246817	76246831	+	1	NA	promoter-TSS (NM_023168)	promoter-TSS (NM_023168)	17	NM_023168	66168	Mm.41665	NM_023168	ENSMUSG00000022564	Grina	1110025J15Rik|Lag|Tmbim3	glutamate receptor, ionotropic, N-methyl D-aspartate-associated protein 1 (glutamate binding)	protein-coding
mm_136254.1	chr16	90961952	90961955	-	1	NA	intron (NM_001164483, intron 18 of 31)	intron (NM_001164483, intron 18 of 31)	-27104	NM_026502	68001	Mm.45374	NM_026502	ENSMUSG00000022972	1110004E09Rik	-	RIKEN cDNA 1110004E09 gene	protein-coding
mm_159789.1	chr5	107597868	107597868	-	1	NA	promoter-TSS (NM_133248)	promoter-TSS (NM_133248)	20	NM_001161738	170823	Mm.41417	NM_133248	ENSMUSG00000029276	Glmn	9330160J16Rik|AW227515|Fap48|Fap68	glomulin, FKBP associated protein	protein-coding
mm_125405.1	chr15	41612577	41612587	+	1	NA	intron (NM_001130166, intron 2 of 16)	intron (NM_001130166, intron 2 of 16)	165100	NM_001130166	170719	Mm.254267	NM_130885	ENSMUSG00000022307	Oxr1	2210416C20Rik|C7|C7B	oxidation resistance 1	protein-coding
mm_105554.1	chr11	106411744	106411756	-	1	NA	exon (NM_023913, exon 12 of 22)	exon (NM_023913, exon 12 of 22)	-28969	NM_010494	15896	Mm.394	NM_010494	ENSMUSG00000001029	Icam2	CD102|Icam-2|Ly-60	intercellular adhesion molecule 2	protein-coding
mm_17569.1	chr2	30286313	30286349	-	1	NA	promoter-TSS (NM_177648)	promoter-TSS (NM_177648)	23	NM_177648	227697	Mm.26690	NM_177648	ENSMUSG00000075419	Dolk	BC026973|Tmem15|mKIAA1094	dolichol kinase	protein-coding
mm_95237.1	chr11	44617355	44617361	+	1	NA	promoter-TSS (NM_001290711)	promoter-TSS (NM_001290711)	-742	NM_001290711	13591	Mm.439662	NM_007897	ENSMUSG00000057098	Ebf1	Ebf|O/E-1|OE-1|Olf-1|Olf1	early B cell factor 1	protein-coding
mm_33784.1	chr4	134915090	134915119	+	1	NA	promoter-TSS (NM_027935)	promoter-TSS (NM_027935)	-188	NM_027935	71817	Mm.88349	NM_027935	ENSMUSG00000028822	Tmem50a	3200001F09Rik|CAM|Smp1	transmembrane protein 50A	protein-coding
mm_158393.1	chrX	136733200	136733204	-	1	NA	3' UTR (NM_019768, exon 4 of 4)	3' UTR (NM_019768, exon 4 of 4)	7953	NM_001168225	56397	Mm.27218	NM_019768	ENSMUSG00000031422	Morf4l2	2410017O14Rik|Mrgx|Sid393p|mKIAA0026	mortality factor 4 like 2	protein-coding
mm_93352.1	chr10	102490426	102490440	-	1	NA	promoter-TSS (NM_024435)	promoter-TSS (NM_024435)	-15	NM_024435	67405	Mm.64201	NM_024435	ENSMUSG00000019890	Nts	5033428E16Rik|NMN-125|NN|NT|NT/N|NTS1	neurotensin	protein-coding
mm_11404.1	chr2	31510933	31510937	+	1	NA	intron (NR_002687, intron 13 of 15)	MER58B|DNA|hAT-Charlie	40627	NR_002687	432466	Mm.333323	NR_002687	ENSMUSG00000046687	Gm5424	EG432466	argininosuccinate synthase pseudogene	pseudo
mm_132726.1	chr16	43619044	43619058	+	1	NA	TTS (NM_019778)	TTS (NM_019778)	-21604	NR_030576	100124467		NR_030576	ENSMUSG00000076372	Mir568	Mirn568|mmu-mir-568	microRNA 568	ncRNA
mm_148522.1	chr19	4302520	4302546	+	1	NA	intron (NM_001290818, intron 1 of 20)	intron (NM_001290818, intron 1 of 20)	3689	NM_130863	110355	Mm.254144	NM_130863	ENSMUSG00000024858	Grk2	Adrbk-1|Adrbk1|Bark-1|beta ARK|betaARK1	G protein-coupled receptor kinase 2	protein-coding
mm_63052.1	chr7	121898338	121898359	+	1	NA	intron (NR_073548, intron 1 of 12)	intron (NR_073548, intron 1 of 12)	33310	NR_073548	20277	Mm.7709	NM_011325	ENSMUSG00000030873	Scnn1b	-	sodium channel, nonvoltage-gated 1 beta	protein-coding
mm_122780.1	chr14	54410165	54410179	-	1	NA	promoter-TSS (NM_001253680)	promoter-TSS (NM_001253680)	-700	NM_001253680	20540	Mm.142455	NM_011405	ENSMUSG00000000958	Slc7a7	AI790233|my+lat1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 7	protein-coding
mm_114351.1	chr13	60939560	60939584	+	1	NA	3' UTR (NM_009411, exon 5 of 5)	3' UTR (NM_009411, exon 5 of 5)	2363	NM_009411	21984	Mm.2372	NM_009411	ENSMUSG00000033834	Tpbpa	AV033951|Tb-1|Tb1|Tpbp|b2b1247Clo	trophoblast specific protein alpha	protein-coding
mm_105670.1	chr11	107462063	107462067	-	1	NA	intron (NM_145823, intron 1 of 9)	intron (NM_145823, intron 1 of 9)	8655	NM_145823	71795	Mm.397413	NM_145823	ENSMUSG00000040430	Pitpnc1	1110020B03Rik|5830436L09Rik|AI662802|AI851387|C330017I21Rik|Dnr411|RDGBB|RDGBB1|rdgB-beta	phosphatidylinositol transfer protein, cytoplasmic 1	protein-coding
mm_24711.1	chr3	95218071	95218082	+	1	NA	promoter-TSS (NM_172512)	promoter-TSS (NM_172512)	-134	NM_029885	213054	Mm.224820	NM_029885	ENSMUSG00000038766	Gabpb2	1810015F01Rik|5830427M07|9430006E19Rik|A430024B14Rik|AV050852|Gabpb2-1	GA repeat binding protein, beta 2	protein-coding
mm_59682.1	chr7	28436395	28436401	+	1	NA	promoter-TSS (NM_175021)	promoter-TSS (NM_175021)	-207	NM_175021	233033	Mm.54120	NM_175021	ENSMUSG00000109336	Samd4b	BC042901	sterile alpha motif domain containing 4B	protein-coding
mm_30791.1	chr4	19650301	19650323	+	1	NA	exon (NM_177327, exon 9 of 25)	exon (NM_177327, exon 9 of 25)	58692	NM_177327	107568	Mm.78312	NM_177327	ENSMUSG00000041058	Wwp1	8030445B08Rik|AIP5|SDRP1|Tiul1	WW domain containing E3 ubiquitin protein ligase 1	protein-coding
mm_147273.1	chr18	38929463	38929480	-	1	NA	intron (NM_001033789, intron 3 of 4)	intron (NM_001033789, intron 3 of 4)	-10772	NM_010197	14164	Mm.241282	NM_010197	ENSMUSG00000036585	Fgf1	Dffrx|Fam|Fgf-1|Fgfa	fibroblast growth factor 1	protein-coding
mm_3199.1	chr1	135818713	135818723	+	1	NA	5' UTR (NM_133664, exon 1 of 10)	5' UTR (NM_133664, exon 1 of 10)	120	NM_133664	16763	Mm.36726	NM_133664	ENSMUSG00000041782	Lad1	-	ladinin	protein-coding
mm_57761.1	chr6	129233183	129233187	-	1	NA	intron (NR_040265, intron 1 of 2)	intron (NR_040265, intron 1 of 2)	4860	NR_040265	76432	Mm.261738	NR_040265	ENSMUSG00000097354	2310001H17Rik	AI646108	RIKEN cDNA 2310001H17 gene	ncRNA
mm_55601.1	chr6	71823709	71823713	-	1	NA	promoter-TSS (NM_025430)	promoter-TSS (NM_025430)	73	NM_025430	66223	Mm.28579	NM_025430	ENSMUSG00000052962	Mrpl35	1110066C01Rik	mitochondrial ribosomal protein L35	protein-coding
mm_151608.1	chr19	3744375	3744392	-	1	NA	Intergenic	L1M4c|LINE|L1	-23038	NM_001167889	225888	Mm.278578	NM_144871	ENSMUSG00000045098	Kmt5b	AA117471|C630029K18Rik|Suv4-20h1|Suv420h1	lysine methyltransferase 5B	protein-coding
mm_168401.1	chr11	29547900	29547900	-	1	NA	promoter-TSS (NM_028504)	promoter-TSS (NM_028504)	-50	NM_028504	73324	Mm.69388	NM_028504	ENSMUSG00000020461	Clhc1	1700034F02Rik	clathrin heavy chain linker domain containing 1	protein-coding
mm_96023.1	chr11	59548510	59548523	+	1	NA	exon (NM_145827, exon 4 of 10)	exon (NM_145827, exon 4 of 10)	5830	NM_145827	216799	Mm.54174	NM_145827	ENSMUSG00000032691	Nlrp3	AGTAVPRL|AII/AVP|Cias1|FCAS|FCU|MWS|Mmig1|NALP3|Pypaf1	NLR family, pyrin domain containing 3	protein-coding
mm_41329.1	chr5	90490730	90490744	+	1	NA	promoter-TSS (NM_007423)	promoter-TSS (NM_007423)	23	NM_007423	11576	Mm.358570	NM_007423	ENSMUSG00000054932	Afp	-	alpha fetoprotein	protein-coding
mm_24204.1	chr3	88621103	88621130	+	1	NA	promoter-TSS (NM_001198913)	promoter-TSS (NM_001198913)	10	NM_008487	16800	Mm.239329	NM_008487	ENSMUSG00000028059	Arhgef2	AA408978|GEF|GEF-H1|GEFH1|LFP40|Lbcl1|Lfc|P40|mKIAA0651	rho/rac guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_168769.1	chr12	14455949	14455952	-	1	NA	Intergenic	L1Md_T|LINE|L1	194416	NR_045003	791361	Mm.217963	NR_045003		Gm16497	ENSMUSG00000066623	predicted gene 16497	ncRNA
mm_56044.1	chr6	86737243	86737254	-	1	NA	3' UTR (NM_001331120, exon 13 of 13)	3' UTR (NM_001331120, exon 13 of 13)	-3870	NM_011818	23885	Mm.321452	NM_011818	ENSMUSG00000001157	Gmcl1	2810049L19Rik|Btbd13|DIP|Gcl|Gcl-1|glc-1|mglc-1	germ cell-less, spermatogenesis associated 1	protein-coding
mm_34679.1	chr4	150997082	150997088	+	1	NA	promoter-TSS (NM_011910)	promoter-TSS (NM_011910)	-12	NM_011910	24111	Mm.89984	NM_011910	ENSMUSG00000028963	Uts2	UII|Ucn2|prepro-UII	urotensin 2	protein-coding
mm_800.1	chr1	45347770	45347787	+	1	NA	exon (NM_009930, exon 50 of 51)	exon (NM_009930, exon 50 of 51)	36240	NM_009930	12825	Mm.249555	NM_009930	ENSMUSG00000026043	Col3a1	AW550625|Col3a-1|Tsk-2|Tsk2	collagen, type III, alpha 1	protein-coding
mm_51813.1	chr6	88902294	88902351	+	1	NA	promoter-TSS (NM_011906)	promoter-TSS (NM_011906)	71	NM_011906	24100	Mm.284480	NM_011906	ENSMUSG00000002871	Tpra1	40kDa|Gpr175|Tpra40	transmembrane protein, adipocyte asscociated 1	protein-coding
mm_55743.1	chr6	77758422	77758445	-	1	NA	exon (NM_145732, exon 4 of 19)	exon (NM_145732, exon 4 of 19)	221234	NM_145732	12386	Mm.34637	NM_009819	ENSMUSG00000063063	Ctnna2	AI481747|Catna|Catna2|cdf|chp	catenin (cadherin associated protein), alpha 2	protein-coding
mm_12551.1	chr2	72406283	72406286	+	1	NA	3' UTR (NM_001164791, exon 12 of 12)	3' UTR (NM_001164791, exon 12 of 12)	-69935	NM_025866	66953	Mm.270676	NM_025866	ENSMUSG00000055612	Cdca7	2310021G01Rik|AU044109|JPO1	cell division cycle associated 7	protein-coding
mm_58217.1	chr6	144209361	144209369	-	1	NA	exon (NM_011444, exon 1 of 15)	exon (NM_011444, exon 1 of 15)	203	NM_001113559	20678	Mm.1752	NM_011444	ENSMUSG00000041540	Sox5	A730017D01Rik|AI528773	SRY (sex determining region Y)-box 5	protein-coding
mm_12804.1	chr2	80292469	80292509	+	1	NA	promoter-TSS (NM_177256)	promoter-TSS (NM_177256)	19	NM_177256	320769	Mm.60992	NM_177256	ENSMUSG00000050114	Prdx6b	1-cysPrx-P1|4930414C22Rik|Aop2-rs1|Prdx5-rs1|Prdx6-ps1|Prdx6-rs1|Prdx6-rs1-ps	peroxiredoxin 6B	protein-coding
mm_16556.1	chr2	181846640	181846643	+	1	NA	intron (NM_153594, intron 5 of 6)	intron (NM_153594, intron 5 of 6)	8787	NM_001291211	245867	Mm.491085	NM_153594	ENSMUSG00000027589	Pcmtd2	5330414D10Rik|AI314201	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 2	protein-coding
mm_108235.1	chr12	77239349	77239365	+	1	NA	intron (NR_045554, intron 1 of 11)	CpG	618	NR_045554	53618	Mm.35628	NM_016893	ENSMUSG00000021065	Fut8	-	fucosyltransferase 8	protein-coding
mm_109160.1	chr12	108179909	108179923	+	1	NA	promoter-TSS (NM_028262)	promoter-TSS (NM_028262)	178	NM_009832	12454	Mm.474441	NM_009832	ENSMUSG00000021258	Ccnk	AW123198|AW413594|CPR4|CycK	cyclin K	protein-coding
mm_54998.1	chr6	48834000	48834014	-	1	NA	non-coding (NR_104575, exon 7 of 7)	non-coding (NR_104575, exon 7 of 7)	6981	NM_023056	65963	Mm.28385	NM_023056	ENSMUSG00000029810	Tmem176b	1810009M01Rik|Clast1|Lr8	transmembrane protein 176B	protein-coding
mm_118869.1	chr14	25855608	25855638	+	1	NA	intron (NM_013469, intron 1 of 14)	intron (NM_013469, intron 1 of 14)	13468	NM_013469	11744	Mm.294083	NM_013469	ENSMUSG00000021866	Anxa11	A830099O17Rik|Anx11	annexin A11	protein-coding
mm_66855.1	chr7	52005793	52005872	-	1	NA	promoter-TSS (NR_027704)	promoter-TSS (NR_027704)	-118	NR_027704	75744	Mm.386823	NM_001160345	ENSMUSG00000074093	Svip	1700006C13Rik|6620401M08Rik	small VCP/p97-interacting protein	protein-coding
mm_91886.1	chr10	59899653	59899679	-	1	NA	Intergenic	Intergenic	20075	NM_019965	56709	Mm.103610	NM_019965	ENSMUSG00000020109	Dnajb12	Dj10|mDj10	DnaJ heat shock protein family (Hsp40) member B12	protein-coding
mm_119825.1	chr14	54254125	54254247	+	1	NA	promoter-TSS (NM_001205181)	promoter-TSS (NM_001205181)	57	NM_001205181	105501	Mm.28771	NM_134076	ENSMUSG00000040997	Abhd4	1110035H23Rik|AI429574|Abh4	abhydrolase domain containing 4	protein-coding
mm_17168.1	chr2	25291780	25291790	-	1	NA	TTS (NM_146117)	TTS (NM_146117)	565	NM_001242940	320354	Mm.445875	NM_001242940		Grin1os	E130003G02Rik	glutamate receptor, ionotropic, NMDA1 (zeta 1), opposite strand	protein-coding
mm_71921.1	chr8	70158752	70158768	+	1	NA	intron (NM_001045484, intron 1 of 8)	intron (NM_001045484, intron 1 of 8)	5999	NM_001045484	17259	Mm.432505	NM_008578	ENSMUSG00000079033	Mef2b	AI451606	myocyte enhancer factor 2B	protein-coding
mm_70838.1	chr8	23314690	23314691	+	1	NA	Intergenic	Intergenic	-57610	NM_001042484	57437	Mm.196269	NM_020585	ENSMUSG00000015341	Golga7	AB041568|C130038N16Rik|GCP16|GOLGA3AP1|HSPC041|R75586	golgi autoantigen, golgin subfamily a, 7	protein-coding
mm_2340.1	chr1	92855967	92855985	+	1	NA	exon (NM_016696, exon 4 of 9)	exon (NM_016696, exon 4 of 9)	5598	NR_029559	387167		NR_029559	ENSMUSG00000065470	Mir149	Mirn149|mir-149|mmu-mir-149	microRNA 149	ncRNA
mm_163329.1	chr12	8480562	8480562	-	1	NA	Intergenic	Intergenic	19423	NM_007483	11852	Mm.687	NM_007483	ENSMUSG00000054364	Rhob	AA017882|Arh6|Arhb	ras homolog family member B	protein-coding
mm_56117.1	chr6	87532114	87532135	-	1	NA	intron (NM_001037727, intron 1 of 10)	B1_Mur1|SINE|Alu	1135	NM_001037727	232201	Mm.119564	NM_175476	ENSMUSG00000030047	Arhgap25	A130039I20Rik	Rho GTPase activating protein 25	protein-coding
mm_91639.1	chr10	42275625	42275652	-	1	NA	intron (NM_019740, intron 1 of 3)	CpG-1005	1104	NM_019740	56484	Mm.338613	NM_019740	ENSMUSG00000048756	Foxo3	1110048B16Rik|2010203A17Rik|C76856|FKHRL1|Fkhr2|Foxo3a	forkhead box O3	protein-coding
mm_113945.1	chr13	49818591	49818594	+	1	NA	Intergenic	Lx8|LINE|L1	136462	NM_172015	105148	Mm.21118	NM_172015	ENSMUSG00000037851	Iars	2510016L12Rik|AI327140|AU044614|E430001P04Rik|ILRS	isoleucine-tRNA synthetase	protein-coding
mm_153806.1	chr19	46045195	46045222	-	1	NA	promoter-TSS (NM_001113408)	promoter-TSS (NM_001113408)	3	NM_001113408	16825	Mm.327442	NM_010697	ENSMUSG00000025223	Ldb1	CLIM2|NLI	LIM domain binding 1	protein-coding
mm_21590.1	chr2	164237496	164237520	-	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	833	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_85565.1	chr9	106891966	106891970	-	1	NA	promoter-TSS (NM_029103)	promoter-TSS (NM_029103)	-30	NM_029103	74840	Mm.29778	NM_029103	ENSMUSG00000032575	Manf	3230402M22Rik|AA407711|AA408789|AA673178|Armet|D17914|D18Mgi17	mesencephalic astrocyte-derived neurotrophic factor	protein-coding
mm_133198.1	chr16	73011608	73011621	+	1	NA	intron (NM_019413, intron 23 of 28)	intron (NM_019413, intron 23 of 28)	348465	NM_019413	19876	Mm.310772	NM_019413	ENSMUSG00000022883	Robo1	AW494633|AW742721|DUTT1|Gm310	roundabout guidance receptor 1	protein-coding
mm_139640.1	chr17	57377436	57377446	+	1	NA	intron (NM_010130, intron 2 of 21)	Lx5b|LINE|L1	18755	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_8239.1	chr1	138484888	138484904	-	1	NA	3' UTR (NM_021605, exon 10 of 10)	3' UTR (NM_021605, exon 10 of 10)	134861	NM_021605	59125	Mm.143817	NM_021605	ENSMUSG00000026393	Nek7	2810460C19Rik|AU020186	NIMA (never in mitosis gene a)-related expressed kinase 7	protein-coding
mm_74734.1	chr8	18741366	18741378	-	1	NA	5' UTR (NM_007426, exon 1 of 9)	5' UTR (NM_007426, exon 1 of 9)	190	NM_007426	11601	Mm.439874	NM_007426	ENSMUSG00000031465	Angpt2	Agpt2|Ang-2|Ang2	angiopoietin 2	protein-coding
mm_108916.1	chr12	100208225	100208239	+	1	NA	3' UTR (NM_009790, exon 6 of 6)	3' UTR (NM_009790, exon 6 of 6)	8088	NM_001313934	12313	Mm.285993	NM_009790	ENSMUSG00000001175	Calm1	AI256814|AI327027|AI461935|AL024000|CaM|Calm	calmodulin 1	protein-coding
mm_134406.1	chr16	17655554	17655580	-	1	NA	exon (NM_001040683, exon 10 of 17)	exon (NM_001040683, exon 10 of 17)	9097	NM_001166164	72315	Mm.297777	NM_001166164	ENSMUSG00000041617	Ccdc74a	2310015A05Rik	coiled-coil domain containing 74A	protein-coding
mm_9409.1	chr1	172274723	172274731	-	1	NA	exon (NM_178405, exon 23 of 23)	exon (NM_178405, exon 23 of 23)	-16303	NM_013734	27222	Mm.482392	NM_013734	ENSMUSG00000007107	Atp1a4	-	ATPase, Na+/K+ transporting, alpha 4 polypeptide	protein-coding
mm_147512.1	chr18	52488343	52488345	-	1	NA	exon (NM_026040, exon 6 of 8)	exon (NM_026040, exon 6 of 8)	22651	NM_026040	67222	Mm.100617	NM_026040	ENSMUSG00000024528	Srfbp1	2810036K01Rik|p49/STRAP	serum response factor binding protein 1	protein-coding
mm_21446.1	chr2	160367058	160367073	-	1	NA	promoter-TSS (NM_010658)	promoter-TSS (NM_010658)	0	NM_010658	16658	Mm.330745	NM_010658	ENSMUSG00000074622	Mafb	Kreisler|Krml|Krml1|kr	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein B (avian)	protein-coding
mm_167226.1	chr8	12756791	12756833	-	1	NA	promoter-TSS (NM_001293667)	promoter-TSS (NM_001293667)	-204	NM_015804	50770	Mm.257837	NM_015804	ENSMUSG00000031441	Atp11a	4930558F19Rik|AU040868|Atpc1h|Ih	ATPase, class VI, type 11A	protein-coding
mm_130252.1	chr15	96641620	96641631	-	1	NA	5' UTR (NM_134086, exon 1 of 16)	5' UTR (NM_134086, exon 1 of 16)	337	NM_134086	105727	Mm.103568	NM_134086	ENSMUSG00000023169	Slc38a1	AA408026|AA409865|AL022800|AU015942|NAT2	solute carrier family 38, member 1	protein-coding
mm_155820.1	chrX	100605536	100605548	+	1	NA	promoter-TSS (NM_133205)	promoter-TSS (NM_133205)	45	NM_133205	170735	Mm.95518	NM_133205	ENSMUSG00000060890	Arr3	Arr4|Car|Carfl|Carr	arrestin 3, retinal	protein-coding
mm_121846.1	chr14	20631356	20631368	-	1	NA	Intergenic	Intergenic	-13008	NM_030180	78787	Mm.301173	NM_030180	ENSMUSG00000034235	Usp54	4930429G18Rik|AI115571|C030002J06Rik	ubiquitin specific peptidase 54	protein-coding
mm_11979.1	chr2	55292347	55292379	+	1	NA	Intergenic	Intergenic	-143607	NM_001304810	16519	Mm.5127	NM_008426	ENSMUSG00000026824	Kcnj3	GIRK-1|GIRK1|Kcnf3|Kir3.1	potassium inwardly-rectifying channel, subfamily J, member 3	protein-coding
mm_172770.1	chr8	94179103	94179106	+	1	NA	promoter-TSS (NM_013602)	promoter-TSS (NM_013602)	15	NM_013602	17748	Mm.192991	NM_013602	ENSMUSG00000031765	Mt1	MT-I|Mt-1	metallothionein 1	protein-coding
mm_61380.1	chr7	70951315	70951321	+	1	NA	Intergenic	Intergenic	-584572	NM_183261	11819	Mm.158143	NM_009697	ENSMUSG00000030551	Nr2f2	2700033K02Rik|9430015G03Rik|ARP-1|Aporp1|COUP-TF2|COUP-TFII|COUPTFB|EAR3|SVP40|Tcfcoup2	nuclear receptor subfamily 2, group F, member 2	protein-coding
mm_102372.1	chr11	58612090	58612103	-	1	NA	exon (NM_144544, exon 4 of 6)	exon (NM_144544, exon 4 of 6)	1396	NM_144544	78354	Mm.58038	NM_144544	ENSMUSG00000037145	2210407C18Rik	Ep1	RIKEN cDNA 2210407C18 gene	protein-coding
mm_58619.1	chr7	5069006	5069024	+	1	NA	intron (NM_133671, intron 5 of 11)	C-rich|Low_complexity|Low_complexity	6872	NM_001205231	22185	Mm.360389	NM_133671	ENSMUSG00000030435	U2af2	65kDa	U2 small nuclear ribonucleoprotein auxiliary factor (U2AF) 2	protein-coding
mm_94854.1	chr11	23894797	23894803	+	1	NA	intron (NM_172555, intron 1 of 21)	CpG	470	NM_172555	216578	Mm.470599	NM_172555	ENSMUSG00000020273	Papolg	9630006B20Rik	poly(A) polymerase gamma	protein-coding
mm_163011.1	chr11	44620818	44620838	+	1	NA	intron (NM_007897, intron 2 of 15)	intron (NM_007897, intron 2 of 15)	2728	NM_001290710	13591	Mm.439662	NM_007897	ENSMUSG00000057098	Ebf1	Ebf|O/E-1|OE-1|Olf-1|Olf1	early B cell factor 1	protein-coding
mm_50465.1	chr6	48974934	48974960	+	1	NA	promoter-TSS (NM_001029987)	promoter-TSS (NM_001029987)	-196	NM_001029987	243376	Mm.244112	NM_001029987	ENSMUSG00000068536	Doxl2	-	diamine oxidase-like protein 2	protein-coding
mm_78190.1	chr9	21330195	21330220	+	1	NA	intron (NM_001199186, intron 1 of 21)	PB1D11|SINE|Alu	-7621	NM_152808	68682	Mm.148425	NM_152808	ENSMUSG00000057193	Slc44a2	1110028E10Rik|CTL2	solute carrier family 44, member 2	protein-coding
mm_52609.1	chr6	117173708	117173720	+	1	NA	3' UTR (NM_021704, exon 3 of 3)	3' UTR (NM_021704, exon 3 of 3)	5179	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_141111.1	chr17	26069476	26069550	-	1	NA	promoter-TSS (NM_001162868)	promoter-TSS (NM_001162868)	-336	NM_001162869	215445	Mm.41191	NM_153140	ENSMUSG00000037098	Rab11fip3	Cart1|D030060O14Rik|Rab11-FIP3|mKIAA0665	RAB11 family interacting protein 3 (class II)	protein-coding
mm_93515.1	chr10	115251408	115251464	-	1	NA	promoter-TSS (NM_025706)	promoter-TSS (NM_025706)	57	NM_025706	66687	Mm.22252	NM_025706	ENSMUSG00000020130	Tbc1d15	4432405K22Rik|AU022358|AU023730|AW557774|Ly6dl|Rab7-GAP	TBC1 domain family, member 15	protein-coding
mm_70869.1	chr8	25017307	25017320	+	1	NA	promoter-TSS (NM_007404)	promoter-TSS (NM_007404)	102	NM_027194	69742	Mm.28626	NM_027194	ENSMUSG00000031556	Tm2d2	2410018G23Rik|Blp1	TM2 domain containing 2	protein-coding
mm_18485.1	chr2	62601469	62601481	-	1	NA	exon (NM_027835, exon 13 of 16)	exon (NM_027835, exon 13 of 16)	-27454	NM_007986	14089	Mm.41816	NM_007986	ENSMUSG00000000392	Fap	SIMP	fibroblast activation protein	protein-coding
mm_101924.1	chr11	50202426	50202439	-	1	NA	exon (NM_011018, exon 7 of 8)	exon (NM_011018, exon 7 of 8)	8388	NM_001290769	18412	Mm.40828	NM_011018	ENSMUSG00000015837	Sqstm1	A170|OSF-6|Osi|STAP|STONE14|p62	sequestosome 1	protein-coding
mm_17910.1	chr2	35336970	35336983	-	1	NA	promoter-TSS (NM_013515)	promoter-TSS (NM_013515)	33	NM_013515	13830	Mm.295284	NM_013515	ENSMUSG00000026880	Stom	Epb7.2	stomatin	protein-coding
mm_48225.1	chr5	137645696	137645720	-	1	NA	promoter-TSS (NM_010571)	promoter-TSS (NM_010571)	6	NM_010571	16369	Mm.24486	NM_010571	ENSMUSG00000047182	Irs3	AA408304	insulin receptor substrate 3	protein-coding
mm_84076.1	chr9	58201962	58201974	-	1	NA	promoter-TSS (NM_001161540)	promoter-TSS (NM_001161540)	-169	NM_001161540	320563	Mm.186499	NM_177193	ENSMUSG00000051243	Islr2	B930052A04Rik|Linx|Mbu-3|mKIAA1465	immunoglobulin superfamily containing leucine-rich repeat 2	protein-coding
mm_15341.1	chr2	156008069	156008085	+	1	NA	promoter-TSS (NM_001145352)	promoter-TSS (NM_001145352)	-48	NM_025516	66366	Mm.141276	NM_025516	ENSMUSG00000005881	Ergic3	2310015B14Rik|AV318804|CGI-54|D2Ucla1|NY-BR-84|Sdbcag84	ERGIC and golgi 3	protein-coding
mm_40019.1	chr5	33288060	33288063	+	1	NA	Intergenic	RLTR13D3A|LTR|ERVK	-13057	NM_001198860	13016	Mm.7286	NM_013502	ENSMUSG00000037373	Ctbp1	BARS|CtBP3/BARS|D4S115h|D5H4S115|D5H4S115E	C-terminal binding protein 1	protein-coding
mm_54837.1	chr6	42586314	42586322	-	1	NA	TTS (NM_203396)	TTS (NM_203396)	11054	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_40838.1	chr5	73256774	73256792	+	1	NA	promoter-TSS (NM_028194)	promoter-TSS (NM_028194)	-165	NM_028194	72313	Mm.260594	NM_028194	ENSMUSG00000070733	Fryl	2010313D22Rik|2310004H21Rik|2510002A14Rik|9030227G01Rik|mKIAA0826	FRY like transcription coactivator	protein-coding
mm_52248.1	chr6	106769132	106769234	+	1	NA	promoter-TSS (NM_001242358)	promoter-TSS (NM_001242358)	45	NM_001242358	70047	Mm.196332	NM_027296	ENSMUSG00000013736	Trnt1	2410043H24Rik|2610044E04Rik|9830143O18Rik|AA408384|C76540|CGI-47|mt-Trat	tRNA nucleotidyl transferase, CCA-adding, 1	protein-coding
mm_111934.1	chr12	108893199	108893215	-	1	NA	promoter-TSS (NM_001164488)	promoter-TSS (NM_001164488)	4	NM_011710	22375	Mm.38433	NM_011710	ENSMUSG00000021266	Wars	TrpRS|WRS	tryptophanyl-tRNA synthetase	protein-coding
mm_15853.1	chr2	164777743	164777781	+	1	NA	exon (NM_009394, exon 4 of 6)	exon (NM_009394, exon 4 of 6)	1972	NM_009394	21925	Mm.1716	NM_009394	ENSMUSG00000017300	Tnnc2	Tncs	troponin C2, fast	protein-coding
mm_4925.1	chr1	190992796	190992835	+	1	NA	Intergenic	Intergenic	-13519	NR_027352	226841	Mm.22856	NM_144879	ENSMUSG00000037568	Vash2	B130052G07Rik	vasohibin 2	protein-coding
mm_7661.1	chr1	128417236	128417246	-	1	NA	5' UTR (NM_145507, exon 1 of 4)	5' UTR (NM_145507, exon 1 of 4)	175	NM_177445	226414	Mm.28693	NM_145507	ENSMUSG00000026356	Dars	5730439G15Rik	aspartyl-tRNA synthetase	protein-coding
mm_110885.1	chr12	75400225	75400234	-	1	NA	exon (NM_023275, exon 5 of 5)	exon (NM_023275, exon 5 of 5)	16552	NM_175644	217674	Mm.252250	NM_175644	ENSMUSG00000048982	Gphb5	OGH|Zlut1	glycoprotein hormone beta 5	protein-coding
mm_95815.1	chr11	55136992	55137019	+	1	NA	intron (NM_172258, intron 6 of 10)	intron (NM_172258, intron 6 of 10)	14701	NM_172258	215332	Mm.87054	NM_172258	ENSMUSG00000049491	Slc36a3	PAT3|TRAMD2|tramdorin2	solute carrier family 36 (proton/amino acid symporter), member 3	protein-coding
mm_120673.1	chr14	70554524	70554528	+	1	NA	5' UTR (NM_021877, exon 2 of 20)	5' UTR (NM_021877, exon 2 of 20)	470	NM_021877	15460	Mm.7598	NM_021877	ENSMUSG00000022096	Hr	ALUNC|AU|N|ba|bldy|hr|rh|rh-bmh|rhino	hairless	protein-coding
mm_66047.1	chr7	30671627	30671629	-	1	NA	promoter-TSS (NR_027849)	promoter-TSS (NR_027849)	-23	NR_027848	74927	Mm.87326	NM_183108	ENSMUSG00000049761	Pmis2	1700071L20Rik|4930479M11Rik	Pmis2, sperm specific protein	ncRNA
mm_155113.1	chrX	48519541	48519558	+	1	NA	5' UTR (NM_011228, exon 1 of 2)	5' UTR (NM_011228, exon 1 of 2)	264	NM_011228	19337	Mm.2015	NM_011228	ENSMUSG00000031104	Rab33a	Rabs10	RAB33A, member RAS oncogene family	protein-coding
mm_96897.1	chr11	70438678	70438695	+	1	NA	TTS (NR_106064)	TTS (NR_106064)	431	NR_106064	102465670		NR_106064	ENSMUSG00000099109	Mir7115	Gm27902|mmu-mir-7115	microRNA 7115	ncRNA
mm_158134.1	chrX	103186503	103186523	-	1	NA	5' UTR (NM_008671, exon 1 of 1)	5' UTR (NM_008671, exon 1 of 1)	151	NM_008671	17954	Mm.388694	NM_008671	ENSMUSG00000082229	Nap1l2	Bpx	nucleosome assembly protein 1-like 2	protein-coding
mm_34773.1	chr4	153957285	153957295	+	1	NA	promoter-TSS (NM_001163019)	promoter-TSS (NM_001163019)	53	NM_001163019	97159	Mm.7066	NM_175287	ENSMUSG00000047613	A430005L14Rik	C79672	RIKEN cDNA A430005L14 gene	protein-coding
mm_86639.1	chr10	14088744	14088756	+	1	NA	intron (NM_010437, intron 2 of 8)	intron (NM_010437, intron 2 of 8)	122371	NM_010437	15273	Mm.42157	NM_010437	ENSMUSG00000015501	Hivep2	Gm20114|MIBP1|Schnurri-2|Shn-2	human immunodeficiency virus type I enhancer binding protein 2	protein-coding
mm_42872.1	chr5	122240726	122240757	+	1	NA	non-coding (NR_104441, exon 13 of 13)	non-coding (NR_104441, exon 13 of 13)	23719	NR_104441	654470	Mm.28804	NM_001039153	ENSMUSG00000038593	Tctn1	G730031O11Rik|Tect1	tectonic family member 1	protein-coding
mm_87804.1	chr10	60300587	60300593	+	1	NA	exon (NM_011179, exon 13 of 15)	exon (NM_011179, exon 13 of 15)	16129	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_90026.1	chr10	115408863	115408874	+	1	NA	intron (NM_001033261, intron 10 of 34)	AT_rich|Low_complexity|Low_complexity	23909	NM_001033261	216345	Mm.207621	NM_001033261	ENSMUSG00000034163	Zfc3h1	BC033596|Ccdc131|Psrc2	zinc finger, C3H1-type containing	protein-coding
mm_164451.1	chr16	50513540	50513542	-	1	NA	Intergenic	Intergenic	-12704	NR_040380	619312	Mm.427671	NR_040379		G730013B05Rik	linc-Cblb|linc1610	RIKEN cDNA G730013B05 gene	ncRNA
mm_66901.1	chr7	59977611	59977614	-	1	NA	Intergenic	Intergenic	1244	NR_028529	100217429		NR_028529		Snord64	MBII-13	small nucleolar RNA, C/D box 64	snoRNA
mm_2992.1	chr1	133172949	133172951	+	1	NA	Intergenic	MTC|LTR|ERVL-MaLR	41784	NM_133819	108954	Mm.293628	NM_133819	ENSMUSG00000046062	Ppp1r15b	1810033K10Rik|AI606441|C530022L24Rik|CReP	protein phosphatase 1, regulatory (inhibitor) subunit 15b	protein-coding
mm_20893.1	chr2	148873044	148873070	-	1	NA	intron (NM_009976, intron 1 of 2)	intron (NM_009976, intron 1 of 2)	2455	NM_009976	13010	Mm.4263	NM_009976	ENSMUSG00000027447	Cst3	CysC	cystatin C	protein-coding
mm_40971.1	chr5	77001511	77001518	+	1	NA	Intergenic	Intergenic	-2541	NM_206935	384185	Mm.451858	NM_206935	ENSMUSG00000063820	Arl9	1700110A09Rik	ADP-ribosylation factor-like 9	protein-coding
mm_156684.1	chrX	159372176	159372290	+	1	NA	promoter-TSS (NM_025437)	promoter-TSS (NM_025437)	38	NM_025437	66235	Mm.294623	NM_025437	ENSMUSG00000067194	Eif1ax	1500010B24Rik|AI426898|Eif1ay	eukaryotic translation initiation factor 1A, X-linked	protein-coding
mm_119468.1	chr14	47291954	47291966	+	1	NA	TTS (NM_080843)	TTS (NM_080843)	-6354	NM_178684	218975	Mm.212297	NM_178684	ENSMUSG00000021840	Mapk1ip1l	9130202B12|C130032J12Rik	mitogen-activated protein kinase 1 interacting protein 1-like	protein-coding
mm_97190.1	chr11	75572813	75572824	+	1	NA	3' UTR (NM_001199283, exon 14 of 14)	3' UTR (NM_001199283, exon 14 of 14)	-15261	NM_008850	18738	Mm.3128	NM_008850	ENSMUSG00000017781	Pitpna	Pitpn|vb|vibrator	phosphatidylinositol transfer protein, alpha	protein-coding
mm_115939.1	chr13	23622549	23622563	-	1	NA	promoter-TSS (NM_015787)	promoter-TSS (NM_015787)	2	NM_015787	50709	Mm.170587	NM_015787	ENSMUSG00000051627	Hist1h1e	H1-4|H1.4|H1e|H1f4|H1s-4|H1var2	histone cluster 1, H1e	protein-coding
mm_16341.1	chr2	174343228	174343265	+	1	NA	non-coding (NR_003258, exon 7 of 13)	non-coding (NR_003258, exon 7 of 13)	13157	NM_001077510	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_156589.1	chrX	152179053	152179064	+	1	NA	promoter-TSS (NM_001005475)	promoter-TSS (NM_001005475)	49	NM_001005475	245666	Mm.33027	NM_001005475	ENSMUSG00000041115	Iqsec2	Brag1	IQ motif and Sec7 domain 2	protein-coding
mm_102274.1	chr11	55395453	55395486	-	1	NA	3' UTR (NM_009242, exon 10 of 10)	3' UTR (NM_009242, exon 10 of 10)	24611	NM_009242	20692	Mm.291442	NM_009242	ENSMUSG00000018593	Sparc	BM-40|ON	secreted acidic cysteine rich glycoprotein	protein-coding
mm_112072.1	chr12	112571203	112571247	-	1	NA	Intergenic	Intergenic	-17559	NM_198411	70435	Mm.250193	NM_198411	ENSMUSG00000037679	Inf2	2610204M08Rik|AA589465|AW125550|EG629699	inverted formin, FH2 and WH2 domain containing	protein-coding
mm_161838.1	chr17	86040412	86040412	-	1	NA	intron (NM_030133, intron 16 of 20)	intron (NM_030133, intron 16 of 20)	104763	NM_030133	78586	Mm.146236	NM_030133	ENSMUSG00000024135	Srbd1	AI461933|C85414|D530025C17Rik	S1 RNA binding domain 1	protein-coding
mm_104293.1	chr11	90389631	90389668	-	1	NA	intron (NM_172563, intron 1 of 3)	CpG	1268	NM_172563	217082	Mm.158903	NM_172563	ENSMUSG00000003949	Hlf	E230015K02Rik	hepatic leukemia factor	protein-coding
mm_159364.1	chr3	88287179	88287179	-	1	NA	exon (NM_029801, exon 3 of 4)	exon (NM_029801, exon 3 of 4)	9659	NM_029801	76927	Mm.273330	NM_029801	ENSMUSG00000010538	Tsacc	1700021C14Rik|SIP	TSSK6 activating co-chaperone	protein-coding
mm_165643.1	chr3	79795523	79795527	+	1	NA	Intergenic	Intergenic	47137	NM_027495	70652	Mm.46635	NM_027495	ENSMUSG00000027956	Tmem144	1110057I03Rik|5730537D05Rik	transmembrane protein 144	protein-coding
mm_70309.1	chr8	4226904	4226922	+	1	NA	promoter-TSS (NM_028175)	promoter-TSS (NM_028175)	86	NM_028175	72267	Mm.25479	NM_028175	ENSMUSG00000046589	Lrrc8e	1810049O03Rik|C87354	leucine rich repeat containing 8 family, member E	protein-coding
mm_122082.1	chr14	30609146	30609177	-	1	NA	exon (NM_001310682, exon 2 of 17)	exon (NM_001310682, exon 2 of 17)	1149	NM_001310682	18753	Mm.2314	NM_011103	ENSMUSG00000021948	Prkcd	AI385711|D14Ertd420e|PKC[d]|PKCdelta|Pkcd	protein kinase C, delta	protein-coding
mm_72293.1	chr8	75213431	75213461	+	1	NA	promoter-TSS (NM_029182)	promoter-TSS (NM_029182)	-498	NM_029182	75141	Mm.179267	NM_029182	ENSMUSG00000034472	Rasd2	4930526B11Rik|AU045414|Rhes|TEM-2|TEM2	RASD family, member 2	protein-coding
mm_159561.1	chr4	108723848	108723848	-	1	NA	promoter-TSS (NM_183300)	promoter-TSS (NM_183300)	28	NM_183300	230597	Mm.196776	NM_183300	ENSMUSG00000034557	Zfyve9	Madhip|NSP|SARA|SMADIP	zinc finger, FYVE domain containing 9	protein-coding
mm_60332.1	chr7	44310214	44310242	+	1	NA	promoter-TSS (NM_001034115)	promoter-TSS (NM_001034115)	-36	NM_001034115	243961	Mm.360368	NM_001034115	ENSMUSG00000038738	Shank1	-	SH3/ankyrin domain gene 1	protein-coding
mm_107459.1	chr12	37241634	37241654	+	1	NA	promoter-TSS (NM_178767)	promoter-TSS (NM_178767)	5	NM_178767	319660	Mm.485540	NM_178767	ENSMUSG00000050103	Agmo	A530016O06Rik|AI790538|Tmem195	alkylglycerol monooxygenase	protein-coding
mm_62215.1	chr7	98104940	98104986	+	1	NA	intron (NM_001256081, intron 3 of 48)	intron (NM_001256081, intron 3 of 48)	4285	NM_001256082	17921	Mm.1403	NM_008663	ENSMUSG00000030761	Myo7a	Hdb|Myo7|USH1B|nmf371|polka|sh-1|sh1	myosin VIIA	protein-coding
mm_134402.1	chr16	17576170	17576183	-	1	NA	intron (NM_144852, intron 1 of 4)	intron (NM_144852, intron 1 of 4)	495	NM_144852	224022	Mm.298878	NM_144852	ENSMUSG00000022756	Slc7a4	AI853530	solute carrier family 7 (cationic amino acid transporter, y+ system), member 4	protein-coding
mm_27772.1	chr3	72962133	72962137	-	1	NA	intron (NM_001081137, intron 2 of 46)	intron (NM_001081137, intron 2 of 46)	4731	NM_001081137	69983	Mm.261054	NM_001081137	ENSMUSG00000027790	Sis	2010204N08Rik|SI|Si-s	sucrase isomaltase (alpha-glucosidase)	protein-coding
mm_64234.1	chr7	141696643	141696653	+	1	NA	exon (NM_023566, exon 15 of 46)	exon (NM_023566, exon 15 of 46)	6308	NM_023566	17831	Mm.2041	NM_023566		Muc2	2010015E03Rik|MCM|wnn	mucin 2	protein-coding
mm_168594.1	chr1	173942178	173942182	-	1	NA	intron (NM_001302649, intron 2 of 9)	intron (NM_001302649, intron 2 of 9)	312	NM_001302649	15950	Mm.463437	NM_008328	ENSMUSG00000039997	Ifi203	Mndal	interferon activated gene 203	protein-coding
mm_80181.1	chr9	72289641	72289646	+	1	NA	intron (NM_001311105, intron 1 of 20)	intron (NM_001311105, intron 1 of 20)	14755	NM_001311105	235469	Mm.242791	NM_146224	ENSMUSG00000038535	Zfp280d	A930005F02Rik|BC027163|Suhw4|ZNF634|Znf280d	zinc finger protein 280D	protein-coding
mm_73907.1	chr8	119466433	119466450	+	1	NA	intron (NM_054095, intron 8 of 12)	intron (NM_054095, intron 8 of 12)	19722	NM_054095	117148	Mm.356184	NM_054095	ENSMUSG00000031837	Necab2	Efcbp2	N-terminal EF-hand calcium binding protein 2	protein-coding
mm_36636.1	chr4	93335426	93335436	-	1	NA	promoter-TSS (NM_026954)	promoter-TSS (NM_026954)	80	NM_026954	69136	Mm.171558	NM_026954	ENSMUSG00000054000	Tusc1	2200001D17Rik|TSG-9	tumor suppressor candidate 1	protein-coding
mm_67085.1	chr7	68282719	68282733	-	1	NA	intron (NM_001013811, intron 1 of 8)	intron (NM_001013811, intron 1 of 8)	-6132	NR_040340	100504026	Mm.426764	NR_040340	ENSMUSG00000086628	Gm16157	OTTMUSG00000031023	predicted gene 16157	ncRNA
mm_137669.1	chr17	28747602	28747613	+	1	NA	3' UTR (NM_011951, exon 12 of 12)	3' UTR (NM_011951, exon 12 of 12)	-21710	NM_011950	26415	Mm.27970	NM_011950	ENSMUSG00000004864	Mapk13	SAPK4|Serk4	mitogen-activated protein kinase 13	protein-coding
mm_44606.1	chr5	25270072	25270075	-	1	NA	Intergenic	Intergenic	47180	NM_144908	231050	Mm.21814	NM_144908	ENSMUSG00000038072	Galnt11	A430075I06Rik|AI648252|E430002F06Rik	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 11	protein-coding
mm_13097.1	chr2	91257324	91257371	+	1	NA	promoter-TSS (NM_028733)	promoter-TSS (NM_028733)	18	NM_028733	80708	Mm.236650	NM_028733	ENSMUSG00000027257	Pacsin3	4921507A02Rik|6330413E15Rik|AW413130	protein kinase C and casein kinase substrate in neurons 3	protein-coding
mm_24593.1	chr3	93445193	93445208	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	2870	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_70292.1	chr8	3665774	3665784	+	1	NA	promoter-TSS (NM_026985)	promoter-TSS (NM_026985)	17	NM_026985	69189	Mm.175176	NM_026985	ENSMUSG00000013974	Mcemp1	1810033B17Rik	mast cell expressed membrane protein 1	protein-coding
mm_89932.1	chr10	111244293	111244324	+	1	NA	intron (NM_175489, intron 4 of 23)	intron (NM_175489, intron 4 of 23)	-54371	NM_027914	71769	Mm.45256	NM_027914	ENSMUSG00000035759	Bbs10	1300007O09Rik|AI452285	Bardet-Biedl syndrome 10 (human)	protein-coding
mm_16600.1	chr2	5012717	5012766	-	1	NA	promoter-TSS (NM_027290)	promoter-TSS (NM_027290)	50	NM_027290	70024	Mm.23828	NM_027290	ENSMUSG00000026669	Mcm10	2410041F14Rik|AU018508|C330019M07Rik|C79164	minichromosome maintenance 10 replication initiation factor	protein-coding
mm_108228.1	chr12	77238802	77238831	+	1	NA	promoter-TSS (NR_045554)	promoter-TSS (NR_045554)	77	NR_045554	53618	Mm.35628	NM_016893	ENSMUSG00000021065	Fut8	-	fucosyltransferase 8	protein-coding
mm_117272.1	chr13	65052391	65052400	-	1	NA	Intergenic	Intergenic	19337	NM_001083890	238683	Mm.295543	NM_001083890	ENSMUSG00000074849	Spata31d1c	4932441B19Rik|Fam75d1c	spermatogenesis associated 31 subfamily D, member 1C	protein-coding
mm_73720.1	chr8	112011454	112011467	+	1	NA	promoter-TSS (NM_001286384)	promoter-TSS (NM_001286384)	101	NM_020584	57321	Mm.213064	NM_020584	ENSMUSG00000033430	Terf2ip	Rap1	telomeric repeat binding factor 2, interacting protein	protein-coding
mm_57629.1	chr6	128300440	128300444	-	1	NA	5' UTR (NM_001080979, exon 1 of 11)	5' UTR (NM_001080979, exon 1 of 11)	371	NM_001080979	21679	Mm.14774	NM_011567	ENSMUSG00000030353	Tead4	ETFR-2|Etfr2|FR-19|Rtef1|TEAD-4|TEF-3|Tcf13r1|Tef3|Tefr|Tefr1|Tefr1a	TEA domain family member 4	protein-coding
mm_7773.1	chr1	131245168	131245185	-	1	NA	promoter-TSS (NM_018750)	promoter-TSS (NM_018750)	2	NM_018750	54354	Mm.248291	NM_018750	ENSMUSG00000026430	Rassf5	1300019G20Rik|Maxp1|Nore1|Nore1A|Nore1B|Rapl	Ras association (RalGDS/AF-6) domain family member 5	protein-coding
mm_9779.1	chr1	181174556	181174566	-	1	NA	3' UTR (NM_145514, exon 14 of 14)	3' UTR (NM_145514, exon 14 of 14)	23630	NM_030131	98417	Mm.38229	NM_030131	ENSMUSG00000062169	Cnih4	AI647760|AW050376|CNIH-4|D530030D03Rik|E430023H19Rik|HSPC163	cornichon family AMPA receptor auxiliary protein 4	protein-coding
mm_46568.1	chr5	107176193	107176194	-	1	NA	intron (NM_011578, intron 4 of 16)	MTC|LTR|ERVL-MaLR	113402	NM_011578	21814	Mm.200775	NM_011578	ENSMUSG00000029287	Tgfbr3	1110036H20Rik|AU015626|AW215636|TBRIII	transforming growth factor, beta receptor III	protein-coding
mm_70440.1	chr8	11727818	11727831	+	1	NA	promoter-TSS (NM_001113517)	promoter-TSS (NM_001113517)	-281	NM_001113517	54126	Mm.244068	NM_017402	ENSMUSG00000031511	Arhgef7	Cool|PIX|Pak3bp|betaPix|betaPix-b|betaPix-c|cool-1|mKIAA0142|p85Cool1|p85SPR	Rho guanine nucleotide exchange factor (GEF7)	protein-coding
mm_107382.1	chr12	33146996	33147004	+	1	NA	promoter-TSS (NM_028139)	promoter-TSS (NM_028139)	586	NR_015602	320046	Mm.208337	NR_015602	ENSMUSG00000052125	F730043M19Rik	-	RIKEN cDNA F730043M19 gene	ncRNA
mm_97915.1	chr11	83525956	83525980	+	1	NA	3' UTR (NM_013653, exon 3 of 3)	3' UTR (NM_013653, exon 3 of 3)	-3869	NM_001045543	629303	Mm.390417	NM_001045543	ENSMUSG00000018925	Heatr9	Gm11435|OTTMUSG00000000990	HEAT repeat containing 9	protein-coding
mm_53437.1	chr6	134144660	134144660	+	1	NA	intron (NM_001303102, intron 3 of 8)	intron (NM_001303102, intron 3 of 8)	108960	NM_007961	14011	Mm.269995	NM_007961	ENSMUSG00000030199	Etv6	AW123102|AW557856|Tel	ets variant 6	protein-coding
mm_47462.1	chr5	123666714	123666726	-	1	NA	intron (NM_001347468, intron 1 of 24)	intron (NM_001347468, intron 1 of 24)	17641	NM_019765	56430	Mm.241109	NM_019765	ENSMUSG00000049550	Clip1	1110007I12Rik|4631429H07Rik|AV017631|C81039|CLIP-170|CLIP170|CYLN1|Clip50|Rsn|mKIAA4046|restin	CAP-GLY domain containing linker protein 1	protein-coding
mm_58892.1	chr7	17093674	17093686	+	1	NA	exon (NM_007676, exon 3 of 5)	exon (NM_007676, exon 3 of 5)	19640	NM_007676	26436	Mm.143686	NM_007676	ENSMUSG00000066760	Psg16	Cea11|PSG|bCEA	pregnancy specific glycoprotein 16	protein-coding
mm_118456.1	chr14	8610333	8610366	+	1	NA	intron (NM_028934, intron 4 of 15)	intron (NM_028934, intron 4 of 15)	55941	NM_028934	74430	Mm.271901	NM_028934	ENSMUSG00000021747	4930452B06Rik	4933406L09Rik|AI854000	RIKEN cDNA 4930452B06 gene	protein-coding
mm_128449.1	chr15	50772180	50772190	-	1	NA	intron (NM_001310485, intron 5 of 7)	intron (NM_001310485, intron 5 of 7)	116864	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_99926.1	chr11	110973036	110973039	+	1	NA	intron (NM_010604, intron 1 of 1)	intron (NM_010604, intron 1 of 1)	5004	NM_001252207	16517	Mm.30176	NM_010604	ENSMUSG00000051497	Kcnj16	6430410F18Rik|AI132396|Kir5.1	potassium inwardly-rectifying channel, subfamily J, member 16	protein-coding
mm_94152.1	chr10	128744092	128744109	-	1	NA	promoter-TSS (NM_016811)	promoter-TSS (NM_016811)	-44	NM_016811	13139	Mm.291235	NM_016811	ENSMUSG00000025357	Dgka	80kDa|AW146112|Dagk1	diacylglycerol kinase, alpha	protein-coding
mm_116159.1	chr13	30551728	30551731	-	1	NA	Intergenic	Intergenic	-6413	NM_025710	66694	Mm.181933	NM_025710	ENSMUSG00000038462	Uqcrfs1	4430402G14Rik|AI875505	ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1	protein-coding
mm_32696.1	chr4	116053568	116053592	+	1	NA	intron (NM_028142, intron 1 of 5)	intron (NM_028142, intron 1 of 5)	296	NM_028142	72181	Mm.282560	NM_028142	ENSMUSG00000028706	Nsun4	2310010O12Rik|2810405F18Rik|AI507900|Shtap	NOL1/NOP2/Sun domain family, member 4	protein-coding
mm_137134.1	chr17	23600888	23600929	+	1	NA	promoter-TSS (NM_001033425)	promoter-TSS (NM_001033425)	82	NM_001289482	332221	Mm.270315	NM_001033425	ENSMUSG00000023902	Zscan10	BC068284|Zfp206|Zkscan10|Znf206	zinc finger and SCAN domain containing 10	protein-coding
mm_55540.1	chr6	70792021	70792030	-	1	NA	exon (NM_009075, exon 1 of 9)	exon (NM_009075, exon 1 of 9)	150	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_119128.1	chr14	31138359	31138375	+	1	NA	TTS (NM_138672)	TTS (NM_138672)	3514	NM_027289	70021	Mm.261681	NM_027289	ENSMUSG00000071547	Nt5dc2	2510015F01Rik	5'-nucleotidase domain containing 2	protein-coding
mm_171653.1	chr4	40723835	40723837	+	1	NA	promoter-TSS (NR_077226)	promoter-TSS (NR_077226)	906	NM_001164672	15502	Mm.27897	NM_008298	ENSMUSG00000028410	Dnaja1	HSJ-2|Hsj2|Nedd7	DnaJ heat shock protein family (Hsp40) member A1	protein-coding
mm_48290.1	chr5	138187418	138187463	-	1	NA	promoter-TSS (NM_178612)	promoter-TSS (NM_178612)	-95	NM_178612	66455	Mm.24592	NM_178612	ENSMUSG00000036968	Cnpy4	2610019P18Rik	canopy FGF signaling regulator 4	protein-coding
mm_69552.1	chr7	135698008	135698025	-	1	NA	exon (NM_001081117, exon 12 of 14)	exon (NM_001081117, exon 12 of 14)	18363	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_37843.1	chr4	132144520	132144531	-	1	NA	promoter-TSS (NM_013622)	promoter-TSS (NM_013622)	-39	NM_013622	18386	Mm.5243	NM_013622	ENSMUSG00000050511	Oprd1	DOR|DOR-1|Nbor|mDOR	opioid receptor, delta 1	protein-coding
mm_101322.1	chr11	22859685	22859713	-	1	NA	promoter-TSS (NM_016888)	promoter-TSS (NM_016888)	36	NM_016888	53625	Mm.395495	NM_016888	ENSMUSG00000051650	B3gnt2	AA408337|AA409404|AW260308|B3Galt6|B3gnt1|BGnT-1|BGnT-2|BGnT1|BGnT2|Beta3gnt	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 2	protein-coding
mm_142663.1	chr17	47701974	47702008	-	1	NA	promoter-TSS (NR_045913)	promoter-TSS (NR_045913)	5	NR_045912	100126242	Mm.392746	NR_045912	ENSMUSG00000086930	Frs3os	4930417B13Rik|Gm14873|OTTMUSG00000018358	fibroblast growth factor receptor substrate 3, opposite strand	ncRNA
mm_45779.1	chr5	87140330	87140352	-	1	NA	promoter-TSS (NM_009467)	promoter-TSS (NM_009467)	-1	NM_009467	22238	Mm.291575	NM_009467	ENSMUSG00000054630	Ugt2b5	AI118071|M-1|Udpgt-3|Udpgt2b5|Ugt2b17	UDP glucuronosyltransferase 2 family, polypeptide B5	protein-coding
mm_8489.1	chr1	153790802	153790812	-	1	NA	intron (NM_001243223, intron 17 of 20)	intron (NM_001243223, intron 17 of 20)	41381	NM_011882	24014	Mm.259254	NM_011882	ENSMUSG00000066800	Rnasel	E230029I04Rik	ribonuclease L (2', 5'-oligoisoadenylate synthetase-dependent)	protein-coding
mm_34402.1	chr4	145220640	145220640	+	1	NA	intron (NM_011610, intron 8 of 9)	intron (NM_011610, intron 8 of 9)	-25635	NM_001276465	230895	Mm.240310	NM_001033190	ENSMUSG00000020220	Vps13d	-	vacuolar protein sorting 13D	protein-coding
mm_120848.1	chr14	75206196	75206210	+	1	NA	exon (NM_001247984, exon 7 of 16)	exon (NM_001247984, exon 7 of 16)	-36084	NM_019775	56373	Mm.24242	NM_019775	ENSMUSG00000021999	Cpb2	1110032P04Rik|4930405E17Rik|AI255929|CPR|Cpu|TAFI	carboxypeptidase B2 (plasma)	protein-coding
mm_13950.1	chr2	121300634	121300642	+	1	NA	exon (NM_001173506, exon 4 of 6)	exon (NM_001173506, exon 4 of 6)	5184	NM_001173506	17754	Mm.36501	NM_032393	ENSMUSG00000027254	Map1a	6330416M19Rik|AI853608|Mtap-1|Mtap1|Mtap1a|moth1	microtubule-associated protein 1 A	protein-coding
mm_2200.1	chr1	89482063	89482065	+	1	NA	intron (NM_001037136, intron 1 of 16)	ID_B1|SINE|B4	27253	NM_001037136	347722	Mm.291135	NM_178119	ENSMUSG00000055013	Agap1	Centg2|Ggap1|R75364|mKIAA1099	ArfGAP with GTPase domain, ankyrin repeat and PH domain 1	protein-coding
mm_77877.1	chr9	6238031	6238038	+	1	NA	intron (NM_027924, intron 1 of 6)	ORR1C1|LTR|ERVL-MaLR	28513	NM_027942	71829	Mm.141452	NM_027942	ENSMUSG00000047619	Ddi1	1700011N24Rik	DNA-damage inducible 1	protein-coding
mm_121838.1	chr14	20546483	20546485	-	1	NA	promoter-TSS (NM_008914)	promoter-TSS (NM_008914)	89	NM_001310426	19056	Mm.274432	NM_008914	ENSMUSG00000021816	Ppp3cb	1110063J16Rik|Calnb|CnAbeta|Cnab	protein phosphatase 3, catalytic subunit, beta isoform	protein-coding
mm_168676.1	chr11	94301510	94301531	-	1	NA	exon (NM_026313, exon 5 of 11)	exon (NM_026313, exon 5 of 11)	20391	NM_026313	67684	Mm.30927	NM_026313	ENSMUSG00000020863	Luc7l3	3300001P08Rik|Luc7a	LUC7-like 3 (S. cerevisiae)	protein-coding
mm_90459.1	chr10	127739612	127739623	+	1	NA	promoter-TSS (NM_198035)	promoter-TSS (NM_198035)	79	NM_198035	320080	Mm.27258	NM_198035	ENSMUSG00000044617	Zbtb39	7030401O21Rik|mKIAA0352	zinc finger and BTB domain containing 39	protein-coding
mm_44096.1	chr5	149265078	149265088	+	1	NA	promoter-TSS (NM_009663)	promoter-TSS (NM_009663)	79	NM_009663	11690	Mm.19844	NM_009663	ENSMUSG00000060063	Alox5ap	Flap	arachidonate 5-lipoxygenase activating protein	protein-coding
mm_134994.1	chr16	32163499	32163542	-	1	NA	intron (NM_146069, intron 1 of 3)	intron (NM_146069, intron 1 of 3)	1956	NM_146069	224109	Mm.33498	NM_146069	ENSMUSG00000052384	Nrros	E430025L02Rik|Lrcc33|Lrrc33	negative regulator of reactive oxygen species	protein-coding
mm_25356.1	chr3	107090843	107090851	+	1	NA	Intergenic	Intergenic	-10720	NM_008417	16490	Mm.39285	NM_008417	ENSMUSG00000040724	Kcna2	Akr6a4|ENSMUSG00000074335|Gm10672|Kca1-2|Kv1.2|Mk-2	potassium voltage-gated channel, shaker-related subfamily, member 2	protein-coding
mm_108880.1	chr12	99964527	99964539	+	1	NA	promoter-TSS (NM_001164426)	promoter-TSS (NM_001164426)	34	NM_001164427	217826	Mm.312335	NM_146037	ENSMUSG00000045404	Kcnk13	BB085247|F730021E22Rik|Gm1570|Gm1685	potassium channel, subfamily K, member 13	protein-coding
mm_84938.1	chr9	82974283	82974318	-	1	NA	intron (NM_001081216, intron 4 of 39)	intron (NM_001081216, intron 4 of 39)	1189	NM_001081216	83946	Mm.221688	NM_031879	ENSMUSG00000032253	Phip	2810004D21Rik|4632404O06Rik|Ndrp|Wdr11	pleckstrin homology domain interacting protein	protein-coding
mm_79963.1	chr9	66350466	66350515	+	1	NA	promoter-TSS (NM_145617)	promoter-TSS (NM_145617)	40	NM_145617	235439	Mm.244179	NM_145617	ENSMUSG00000038664	Herc1	2810449H11Rik|B230218H07|D130015N03Rik|tbl	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	protein-coding
mm_107179.1	chr12	24974915	24974948	+	1	NA	promoter-TSS (NM_001081378)	promoter-TSS (NM_001081378)	-1	NM_001081378	77480	Mm.250641	NM_001081378	ENSMUSG00000036333	Kidins220	3110039L19Rik|AI194387|AI316525|C330002I19Rik|mKIAA1250	kinase D-interacting substrate 220	protein-coding
mm_84322.1	chr9	63941775	63941787	-	1	NA	Intergenic	Intergenic	80278	NM_008542	17130	Mm.325757	NM_008542	ENSMUSG00000036867	Smad6	Madh6|b2b390Clo	SMAD family member 6	protein-coding
mm_105961.1	chr11	115462804	115462825	-	1	NA	intron (NM_001080934, intron 1 of 3)	intron (NM_001080934, intron 1 of 3)	341	NM_001080934	217316	Mm.25773	NM_001080934	ENSMUSG00000045775	Slc16a5	A130015N09Rik|MCT 5|MCT 6|MCT5	solute carrier family 16 (monocarboxylic acid transporters), member 5	protein-coding
mm_45378.1	chr5	66081804	66081816	-	1	NA	intron (NM_178446, intron 2 of 6)	intron (NM_178446, intron 2 of 6)	16369	NM_139065	245945	Mm.36863	NM_139065	ENSMUSG00000070780	Rbm47	9530077J19Rik	RNA binding motif protein 47	protein-coding
mm_69443.1	chr7	132988222	132988258	-	1	NA	exon (NM_001170744, exon 9 of 9)	exon (NM_001170744, exon 9 of 9)	27007	NM_001170744	13017	Mm.246240	NM_009980	ENSMUSG00000030970	Ctbp2	AA407280|D7Ertd45e|Gtrgeo6|Ribeye	C-terminal binding protein 2	protein-coding
mm_12125.1	chr2	61634111	61634116	+	1	NA	intron (NM_011529, intron 4 of 7)	MTD|LTR|ERVL-MaLR	41016	NM_001164071	21353	Mm.244393	NM_011529	ENSMUSG00000064289	Tank	C86182|E430026L09Rik|I-TRAF	TRAF family member-associated Nf-kappa B activator	protein-coding
mm_118726.1	chr14	22224608	22224619	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	204901	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_129499.1	chr15	78851380	78851404	-	1	NA	TTS (NM_027219)	TTS (NM_027219)	4137	NM_025622	107753	Mm.390793	NM_025622	ENSMUSG00000043501	Lgals2	2200008F12Rik|AI324147	lectin, galactose-binding, soluble 2	protein-coding
mm_44016.1	chr5	147304945	147304946	+	1	NA	intron (NM_007673, intron 1 of 2)	CpG	2304	NM_007673	12591	Mm.20358	NM_007673	ENSMUSG00000029646	Cdx2	Cdx-2	caudal type homeobox 2	protein-coding
mm_154245.1	chr19	60766464	60766516	-	1	NA	exon (NM_010123, exon 19 of 22)	exon (NM_010123, exon 19 of 22)	7895	NR_034047	100217439		NR_034047		Snora19	MBI-51	small nucleolar RNA, H/ACA box 19	snoRNA
mm_152615.1	chr19	11966165	11966193	-	1	NA	exon (NM_001033174, exon 1 of 14)	exon (NM_001033174, exon 1 of 14)	335	NM_001033174	76303	Mm.291279	NM_001033174	ENSMUSG00000024687	Osbp	1110018F06Rik|AW559088|mKIAA4220	oxysterol binding protein	protein-coding
mm_53660.1	chr6	141406780	141406790	+	1	NA	intron (NM_018779, intron 2 of 15)	B3A|SINE|B2	66232	NR_033555	100093700	Mm.483778	NR_033555	ENSMUSG00000107456	Gm10400	ENSMUSG00000072690	predicted gene 10400	ncRNA
mm_143543.1	chr17	74017041	74017041	-	1	NA	TTS (NM_053188)	TTS (NM_053188)	30875	NM_053188	94224	Mm.38933	NM_053188	ENSMUSG00000038541	Srd5a2	5ART2|S5AR 2	steroid 5 alpha-reductase 2	protein-coding
mm_15879.1	chr2	164837369	164837404	+	1	NA	exon (NM_008906, exon 11 of 15)	exon (NM_008906, exon 11 of 15)	3613	NM_008906	19025	Mm.359633	NM_008906	ENSMUSG00000017760	Ctsa	AU019505|PPCA|Ppgb	cathepsin A	protein-coding
mm_41983.1	chr5	107597697	107597731	+	1	NA	promoter-TSS (NM_133248)	promoter-TSS (NM_133248)	18	NM_001289569	231571	Mm.482420	NM_144911	ENSMUSG00000033773	Rpap2	AW060207	RNA polymerase II associated protein 2	protein-coding
mm_122026.1	chr14	29018318	29018321	-	1	NA	5' UTR (NM_176920, exon 1 of 3)	5' UTR (NM_176920, exon 1 of 3)	111	NM_176920	319476	Mm.95780	NM_176920	ENSMUSG00000045776	Lrtm1	A930016D02Rik	leucine-rich repeats and transmembrane domains 1	protein-coding
mm_41773.1	chr5	103557910	103557927	+	1	NA	exon (NM_011204, exon 26 of 48)	exon (NM_011204, exon 26 of 48)	71485	NM_029415	75750	Mm.7446	NM_029415	ENSMUSG00000029321	Slc10a6	8430417G17Rik|C78479|Soat	solute carrier family 10 (sodium/bile acid cotransporter family), member 6	protein-coding
mm_21386.1	chr2	157540883	157540904	-	1	NA	Intergenic	L1ME3G|LINE|L1	-19185	NM_001291129	18111	Mm.34330	NM_010923	ENSMUSG00000067786	Nnat	5730414I02Rik|AW107673|Peg5	neuronatin	protein-coding
mm_106180.1	chr11	116694780	116694800	-	1	NA	promoter-TSS (NM_009180)	promoter-TSS (NM_009180)	-130	NM_009180	20446	Mm.3947	NM_009180	ENSMUSG00000057286	St6galnac2	II|ST6GalNAc|Siat7|Siat7b	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2	protein-coding
mm_67599.1	chr7	83735441	83735463	-	1	NA	promoter-TSS (NM_010551)	promoter-TSS (NM_010551)	38	NM_010551	16170	Mm.10137	NM_010551	ENSMUSG00000001741	Il16	mKIAA4048	interleukin 16	protein-coding
mm_150799.1	chr19	44304598	44304617	+	1	NA	3' UTR (NM_009128, exon 6 of 6)	3' UTR (NM_009128, exon 6 of 6)	1436	NR_039574	100628619		NR_039574	ENSMUSG00000093315	Mir5114	mmu-mir-5114|mu-mir-5114	microRNA 5114	ncRNA
mm_20959.1	chr2	151744207	151744211	-	1	NA	Intergenic	MTA_Mm|LTR|ERVL-MaLR	-2899	NM_001305244	228769	Mm.146984	NM_144889	ENSMUSG00000032869	Psmf1	AW048666|BC012260|PI31	proteasome (prosome, macropain) inhibitor subunit 1	protein-coding
mm_86615.1	chr10	13965291	13965312	+	1	NA	Intergenic	CpG	-1078	NM_010437	15273	Mm.42157	NM_010437	ENSMUSG00000015501	Hivep2	Gm20114|MIBP1|Schnurri-2|Shn-2	human immunodeficiency virus type I enhancer binding protein 2	protein-coding
mm_80944.1	chr9	102720089	102720099	+	1	NA	5' UTR (NM_019764, exon 2 of 10)	5' UTR (NM_019764, exon 2 of 10)	2290	NM_019764	56332	Mm.21145	NM_019764	ENSMUSG00000032531	Amotl2	AW549739|C79691|Lccp|MASCOT|mKIAA0989	angiomotin-like 2	protein-coding
mm_101089.1	chr11	11853552	11853563	-	1	NA	intron (NM_001190448, intron 6 of 14)	MER2B|DNA|TcMar-Tigger	-14566	NR_045178	73321	Mm.443306	NR_045178	ENSMUSG00000086391	1700042O10Rik	-	RIKEN cDNA 1700042O10 gene	ncRNA
mm_95300.1	chr11	46086687	46086696	+	1	NA	intron (NM_001291890, intron 3 of 22)	intron (NM_001291890, intron 3 of 22)	-15579	NR_106177	102465996		NR_106177	ENSMUSG00000098942	Mir8100	Gm27638|mmu-mir-8100	microRNA 8100	ncRNA
mm_6979.1	chr1	86356180	86356198	-	1	NA	TTS (NR_002851)	TTS (NR_002851)	138	NR_002851	80828		NR_002851	ENSMUSG00000064823	Snord82	Rnu82|U82|Z25	small nucleolar RNA, C/D box 82	snoRNA
mm_129011.1	chr15	74914524	74914533	-	1	NA	Intergenic	Intergenic	-32824	NM_025929	67038	Mm.154566	NM_025929	ENSMUSG00000063522	2010109I03Rik	Ly6m	RIKEN cDNA 2010109I03 gene	protein-coding
mm_85645.1	chr9	107656150	107656165	-	1	NA	exon (NM_001199218, exon 10 of 16)	exon (NM_001199218, exon 10 of 16)	11242	NM_023805	76257	Mm.296560	NM_023805	ENSMUSG00000010064	Slc38a3	0610012J02Rik|D9Ucla2|Nat1|Slc38-3|Sn1|Snat3|mNAT	solute carrier family 38, member 3	protein-coding
mm_70368.1	chr8	9417991	9417993	+	1	NA	intron (NM_001347127, intron 1 of 3)	L1MC1|LINE|L1	273323	NR_073360	74688	Mm.159298	NR_073360	ENSMUSG00000109215	4930453L07Rik	-	RIKEN cDNA 4930453L07 gene	ncRNA
mm_133324.1	chr16	78301459	78301481	+	1	NA	promoter-TSS (NM_009988)	promoter-TSS (NM_009988)	-201	NM_009988	13052	Mm.66222	NM_009988	ENSMUSG00000022865	Cxadr	2610206D03Rik|AU016810|AW553441|CAR|MCAR|MCVADR	coxsackie virus and adenovirus receptor	protein-coding
mm_128225.1	chr15	36555314	36555348	-	1	NA	exon (NM_025712, exon 2 of 14)	exon (NM_025712, exon 2 of 14)	237	NM_001347022	66696	Mm.253627	NM_025712	ENSMUSG00000013611	Snx31	4631426E05Rik	sorting nexin 31	protein-coding
mm_163339.1	chr12	13536467	13536490	+	1	NA	intron (NM_027706, intron 48 of 51)	intron (NM_027706, intron 48 of 51)	91168	NR_136761	102639399	Mm.122052	NR_136761		Gm35725	-	predicted gene, 35725	ncRNA
mm_152603.1	chr19	11803435	11803452	-	1	NA	intron (NM_001025307, intron 2 of 10)	(CAAAAA)n|Simple_repeat|Simple_repeat	15960	NM_001286543	20908	Mm.272264	NM_011502	ENSMUSG00000041488	Stx3	Syn-3	syntaxin 3	protein-coding
mm_104356.1	chr11	94302481	94302483	-	1	NA	intron (NM_026313, intron 4 of 10)	PB1D10|SINE|Alu	19429	NM_026313	67684	Mm.30927	NM_026313	ENSMUSG00000020863	Luc7l3	3300001P08Rik|Luc7a	LUC7-like 3 (S. cerevisiae)	protein-coding
mm_109748.1	chr12	117658024	117658045	+	1	NA	intron (NM_175930, intron 10 of 27)	intron (NM_175930, intron 10 of 27)	141555	NM_175930	217944	Mm.227642	NM_175930	ENSMUSG00000041992	Rapgef5	4932413M22|C86120|D030051B22Rik|GFR|Mrgef|mKIAA0277|mmr-gef	Rap guanine nucleotide exchange factor (GEF) 5	protein-coding
mm_117028.1	chr13	58271922	58271925	-	1	NA	intron (NM_019832, intron 1 of 11)	PB1D10|SINE|Alu	2265	NM_019832	56278	Mm.296625	NM_019832	ENSMUSG00000021552	Gkap1	42kDa|4933400B15Rik|D13Ertd340e|Gkap42	G kinase anchoring protein 1	protein-coding
mm_128390.1	chr15	43167086	43167090	-	1	NA	intron (NM_172815, intron 2 of 5)	intron (NM_172815, intron 2 of 5)	3730	NM_172815	239405	Mm.193274	NM_172815	ENSMUSG00000051920	Rspo2	2610028F08Rik|AA673245|D430027K22|ftls	R-spondin 2	protein-coding
mm_169147.1	chr13	62510708	62510709	-	1	NA	Intergenic	Intergenic	-43896	NM_001136496	71508	Mm.442497	NM_178875	ENSMUSG00000055228	Zfp935	8430426H19Rik|Es113	zinc finger protein 935	protein-coding
mm_133900.1	chr16	97547533	97547540	+	1	NA	non-coding (NR_003508, exon 7 of 14)	non-coding (NR_003508, exon 7 of 14)	11453	NM_013606	17858	Mm.14157	NM_013606	ENSMUSG00000023341	Mx2	AI528743|Mx-2	MX dynamin-like GTPase 2	protein-coding
mm_75717.1	chr8	68993219	68993226	-	1	NA	Intergenic	Intergenic	-95514	NM_007509	11966	Mm.249096	NM_007509	ENSMUSG00000006273	Atp6v1b2	AI194269|AI790362|Atp6b2|HO57|R74844	ATPase, H+ transporting, lysosomal V1 subunit B2	protein-coding
mm_95813.1	chr11	55123927	55123949	+	1	NA	TTS (NM_172258)	TTS (NM_172258)	25953	NM_010299	14667	Mm.287807	NM_010299	ENSMUSG00000000594	Gm2a	AA408702|AW215435|GM2-AP|SAP-3	GM2 ganglioside activator protein	protein-coding
mm_86429.1	chr10	3859737	3859774	+	1	NA	intron (NM_001159942, intron 2 of 16)	intron (NM_001159942, intron 2 of 16)	-12912	NM_001033253	213783	Mm.150831	NM_001033253	ENSMUSG00000040624	Plekhg1	D10Ertd733e|Gm521|mKIAA1209	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	protein-coding
mm_81352.1	chr9	108648721	108648733	+	1	NA	intron (NM_011790, intron 1 of 15)	CpG	653	NM_011790	23807	Mm.290447	NM_011790	ENSMUSG00000064145	Arih2	AI843547|ARI2|TRIAD1|UIP48	ariadne RBR E3 ubiquitin protein ligase 2	protein-coding
mm_89480.1	chr10	93578572	93578586	+	1	NA	intron (NM_175488, intron 13 of 15)	intron (NM_175488, intron 13 of 15)	-10834	NR_045810	74454	Mm.410794	NR_045810	ENSMUSG00000097407	4933408J17Rik	-	RIKEN cDNA 4933408J17 gene	ncRNA
mm_27513.1	chr3	56174263	56174266	-	1	NA	intron (NM_030595, intron 1 of 57)	Lx6|LINE|L1	9437	NM_030595	26422	Mm.384353	NM_030595	ENSMUSG00000027799	Nbea	Lyst2|mKIAA1544	neurobeachin	protein-coding
mm_156842.1	chrX	164382362	164382373	+	1	NA	intron (NM_001308489, intron 1 of 5)	intron (NM_001308489, intron 1 of 5)	8845	NM_010216	14205	Mm.297978	NM_010216	ENSMUSG00000031380	Vegfd	AI325264|Figf|VEGF-D	vascular endothelial growth factor D	protein-coding
mm_101417.1	chr11	29346006	29346011	-	1	NA	Intergenic	RMER19B|LTR|ERVK	-28164	NM_176841	108686	Mm.338284	NM_176841	ENSMUSG00000032740	Ccdc88a	A430106J12Rik|AI848406|Ape|C130096N06Rik|C330012F17Rik|D130005J21Rik|Girdin|Giv|Grdn|Hkrp1	coiled coil domain containing 88A	protein-coding
mm_11128.1	chr2	28230026	28230032	+	1	NA	3' UTR (NM_001038613, exon 6 of 6)	3' UTR (NM_001038613, exon 6 of 6)	24340	NM_019498	56177	Mm.43278	NM_019498	ENSMUSG00000026833	Olfm1	AMY|AW742568|Noe1|OlfA|Pancortin|Pancortin3	olfactomedin 1	protein-coding
mm_36543.1	chr4	86669451	86669461	-	1	NA	intron (NM_007408, intron 1 of 7)	intron (NM_007408, intron 1 of 7)	603	NM_007408	11520	Mm.381	NM_007408	ENSMUSG00000028494	Plin2	AA407157|ADPH|Adfp|Adrp	perilipin 2	protein-coding
mm_74306.1	chr8	126566280	126566318	+	1	NA	Intergenic	Intergenic	27137	NM_001164598	270110	Mm.334918	NM_001164598	ENSMUSG00000051495	Irf2bp2	E130305N23Rik|IRF-2BP2	interferon regulatory factor 2 binding protein 2	protein-coding
mm_165212.1	chr2	35496201	35496212	+	1	NA	Intergenic	Intergenic	-34757	NM_001145821	14594	Mm.281124	NM_010283	ENSMUSG00000035778	Ggta1	AW108479|GALT|Gal|Ggta|Ggta-1|alpha Gal|alpha3GalT	glycoprotein galactosyltransferase alpha 1, 3	protein-coding
mm_106553.1	chr11	120617795	120617804	-	1	NA	promoter-TSS (NM_024229)	promoter-TSS (NM_024229)	91	NM_024229	68671	Mm.21439	NM_024229	ENSMUSG00000025137	Pcyt2	1110033E03Rik|ET	phosphate cytidylyltransferase 2, ethanolamine	protein-coding
mm_95932.1	chr11	58380542	58380552	+	1	NA	promoter-TSS (NM_001330197)	promoter-TSS (NM_001330197)	-99	NM_001330197	70163	Mm.24119	NM_027339	ENSMUSG00000013643	Lypd8	2210415F13Rik	LY6/PLAUR domain containing 8	protein-coding
mm_1462.1	chr1	69600558	69600559	+	1	NA	intron (NM_011770, intron 3 of 7)	intron (NM_011770, intron 3 of 7)	85402	NM_011770	22779	Mm.106343	NM_011770	ENSMUSG00000025997	Ikzf2	A730095J18Rik|Helios|Zfpn1a2|Znfn1a2	IKAROS family zinc finger 2	protein-coding
mm_10466.1	chr2	14316181	14316193	+	1	NA	intron (NM_008625, intron 22 of 29)	intron (NM_008625, intron 22 of 29)	55184	NR_030609	100124488		NR_030609	ENSMUSG00000077897	Mir511	Mirn511|mir-511|mmu-mir-511	microRNA 511	ncRNA
mm_157476.1	chrX	48143631	48143639	-	1	NA	Intergenic	Intergenic	-2801	NM_001313749	74131	Mm.276131	NM_028773	ENSMUSG00000031101	Sash3	1200013B08Rik|AW413946|SLY1	SAM and SH3 domain containing 3	protein-coding
mm_82338.1	chr9	10904698	10904708	-	1	NA	promoter-TSS (NM_001170787)	promoter-TSS (NM_001170787)	23	NM_001033359	244682	Mm.187021	NM_001033359	ENSMUSG00000039488	Cntn5	6720426O10Rik|A830025P08Rik|Gm507|NB-2	contactin 5	protein-coding
mm_143266.1	chr17	65639808	65639817	-	1	NA	promoter-TSS (NM_153519)	promoter-TSS (NM_153519)	-56	NM_153519	213272	Mm.255732	NM_153519	ENSMUSG00000050612	Txndc2	AU021712|Sptrx-1|Sptrx1|Trx4	thioredoxin domain containing 2 (spermatozoa)	protein-coding
mm_9039.1	chr1	167243189	167243189	-	1	NA	intron (NM_030724, intron 1 of 6)	intron (NM_030724, intron 1 of 6)	41938	NM_030724	80914	Mm.280895	NM_030724	ENSMUSG00000026558	Uck2	AA407809|AI481316|AU018180|AU020720|TSA903|UK|UMK|Umpk	uridine-cytidine kinase 2	protein-coding
mm_125870.1	chr15	75596625	75596643	+	1	NA	promoter-TSS (NM_026730)	promoter-TSS (NM_026730)	-24	NM_026730	68453	Mm.46367	NM_026730	ENSMUSG00000022579	Gpihbp1	1110002J19Rik|GPI-HBP1	GPI-anchored HDL-binding protein 1	protein-coding
mm_33820.1	chr4	135398314	135398335	+	1	NA	promoter-TSS (NM_001243306)	promoter-TSS (NM_001243306)	-97	NM_145555	230822	Mm.35548	NM_145555	ENSMUSG00000043924	Ncmap	A330049M08Rik|AA545175|Mp11	noncompact myelin associated protein	protein-coding
mm_86905.1	chr10	22343444	22343466	+	1	NA	intron (NM_009018, intron 5 of 5)	intron (NM_009018, intron 5 of 5)	-18439	NM_020030	56554	Mm.458004	NM_020030	ENSMUSG00000078452	Raet1d	RAE-1delta	retinoic acid early transcript delta	protein-coding
mm_143181.1	chr17	57290719	57290729	-	1	NA	intron (NM_001163816, intron 1 of 25)	intron (NM_001163816, intron 1 of 25)	11624	NM_001163815	22324	Mm.248172	NM_011691	ENSMUSG00000034116	Vav1	Vav|vav-T	vav 1 oncogene	protein-coding
mm_100442.1	chr11	119486480	119486490	+	1	NA	Intergenic	Intergenic	-4862	NM_001164636	338371	Mm.271946	NM_177394	ENSMUSG00000039850	Endov	A730011L01Rik	endonuclease V	protein-coding
mm_75840.1	chr8	70599725	70599746	-	1	NA	exon (NM_133772, exon 7 of 17)	exon (NM_133772, exon 7 of 17)	5254	NM_023627	71780	Mm.29357	NM_023627	ENSMUSG00000019139	Isyna1	1300017C10Rik|AU018670	myo-inositol 1-phosphate synthase A1	protein-coding
mm_12265.1	chr2	68961131	68961150	+	1	NA	intron (NM_172856, intron 3 of 9)	intron (NM_172856, intron 3 of 9)	99699	NM_001347161	241447	Mm.222222	NM_172856	ENSMUSG00000027035	Cers6	4732462C07Rik|AW544719|Lass6|T1L	ceramide synthase 6	protein-coding
mm_138355.1	chr17	34981899	34981940	+	1	NA	promoter-TSS (NM_001110101)	promoter-TSS (NM_001110101)	65	NM_001204274	27756	Mm.165735	NM_030597	ENSMUSG00000007050	Lsm2	D17H6S56E-2|D17H6S56E2|Dmapl|Dmpkap|G7b|Sm-X5|SmX5|snRNP	LSM2 homolog, U6 small nuclear RNA and mRNA degradation associated	protein-coding
mm_4144.1	chr1	170979766	170979770	+	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	-3697	NM_010187	14130	Mm.425062	NM_010187	ENSMUSG00000026656	Fcgr2b	AI528646|CD32|F630109E10Rik|Fc[g]RII|FcgRII|Fcgr2|Fcgr2a|Fcr-2|Fcr-3|Ly-17|Ly-m20|LyM-1|Lym-1|fcRII	Fc receptor, IgG, low affinity IIb	protein-coding
mm_34586.1	chr4	150187417	150187419	+	1	NA	exon (NM_009802, exon 8 of 8)	exon (NM_009802, exon 8 of 8)	13717	NM_009802	12353	Mm.232523	NM_009802	ENSMUSG00000028972	Car6	Ca6|DOC1	carbonic anhydrase 6	protein-coding
mm_163125.1	chr11	77078569	77078580	+	1	NA	promoter-TSS (NR_030756)	promoter-TSS (NR_030756)	-137	NM_001012309	237859	Mm.156195	NM_001012309	ENSMUSG00000037958	Nsrp1	8030451K07|AI851076|AL022898|Ccdc55|NSpr70|NSrp70	nuclear speckle regulatory protein 1	protein-coding
mm_29317.1	chr3	108012736	108012776	-	1	NA	exon (NM_010358, exon 8 of 8)	exon (NM_010358, exon 8 of 8)	5217	NM_010358	14862	Mm.37199	NM_010358	ENSMUSG00000058135	Gstm1	Gstb-1|Gstb1	glutathione S-transferase, mu 1	protein-coding
mm_89541.1	chr10	94568129	94568144	+	1	NA	intron (NM_172051, intron 1 of 3)	intron (NM_172051, intron 1 of 3)	-7121	NM_001168684	319880	Mm.23047	NM_172051	ENSMUSG00000020023	Tmcc3	AW488095|C630016B22Rik|C88213|Tmcc1	transmembrane and coiled coil domains 3	protein-coding
mm_161589.1	chr16	33400416	33400416	+	1	NA	intron (NM_011749, intron 1 of 8)	intron (NM_011749, intron 1 of 8)	19641	NM_011749	22661	Mm.392667	NM_011749	ENSMUSG00000022811	Zfp148	2210405J08Rik|AI480666|AW045217|BERF-1|BFCOL1|ZBP-89|Znf148	zinc finger protein 148	protein-coding
mm_61075.1	chr7	51621793	51621815	+	1	NA	promoter-TSS (NM_080853)	promoter-TSS (NM_080853)	-26	NM_080853	140919	Mm.256618	NM_080853	ENSMUSG00000030500	Slc17a6	2900073D12Rik|DNPI|VGLUT2	solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 6	protein-coding
mm_40685.1	chr5	65763311	65763349	+	1	NA	promoter-TSS (NM_001024917)	promoter-TSS (NM_001024917)	-191	NM_001024917	333789	Mm.332398	NM_001024917	ENSMUSG00000037795	N4bp2	B3bp|E430014I16|Gm1791|Gm868	NEDD4 binding protein 2	protein-coding
mm_18911.1	chr2	76735259	76735266	-	1	NA	exon (NM_011652, exon 276 of 313)	exon (NM_011652, exon 276 of 313)	59947	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_54751.1	chr6	41033191	41033195	-	1	NA	exon (NM_023333, exon 3 of 5)	exon (NM_023333, exon 3 of 5)	2316	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_167212.1	chr8	3664520	3664569	-	1	NA	Intergenic	Intergenic	-1218	NM_026985	69189	Mm.175176	NM_026985	ENSMUSG00000013974	Mcemp1	1810033B17Rik	mast cell expressed membrane protein 1	protein-coding
mm_93296.1	chr10	96523964	96523992	-	1	NA	Intergenic	Intergenic	-93023	NM_007569	12226	Mm.23811	NM_007569	ENSMUSG00000036478	Btg1	AI426953|AW546738	B cell translocation gene 1, anti-proliferative	protein-coding
mm_4848.1	chr1	187125129	187125147	+	1	NA	promoter-TSS (NR_040554)	promoter-TSS (NR_040554)	0	NR_040554	69308	Mm.490882	NR_040554	ENSMUSG00000089730	1700007P06Rik	-	RIKEN cDNA 1700007P06 gene	ncRNA
mm_173038.1	chrX	108893243	108893262	+	1	NA	Intergenic	Intergenic	58774	NR_015493	69964	Mm.160066	NR_015493	ENSMUSG00000086629	2810403D21Rik	1810022M18Rik|4632410B05Rik|AU017716	RIKEN cDNA 2810403D21 gene	ncRNA
mm_138785.1	chr17	37270921	37270941	+	1	NA	intron (NM_013819, intron 2 of 7)	intron (NM_013819, intron 2 of 7)	697	NM_013819	14991	Mm.14437	NM_013819	ENSMUSG00000016206	H2-M3	H-2M3|Hmt|M3a|MuprM3|MuprM301|MuprM302|R4B2	histocompatibility 2, M region locus 3	protein-coding
mm_75482.1	chr8	48668608	48668629	-	1	NA	intron (NM_011857, intron 1 of 28)	intron (NM_011857, intron 1 of 28)	6072	NM_001145937	23965	Mm.42191	NM_011857	ENSMUSG00000031561	Tenm3	2610100B16Rik|Odz1|Odz3|Ten-m3|mKIAA1455	teneurin transmembrane protein 3	protein-coding
mm_43874.1	chr5	143622556	143622571	+	1	NA	5' UTR (NM_011182, exon 1 of 13)	5' UTR (NM_011182, exon 1 of 13)	116	NM_011182	19159	Mm.281003	NM_011182	ENSMUSG00000018001	Cyth3	AI648983|ARNO3|CLM3|Grp1|Pscd3	cytohesin 3	protein-coding
mm_102690.1	chr11	65649796	65649814	-	1	NA	Intergenic	Intergenic	85027	NR_030417	791070		NR_030417	ENSMUSG00000076460	Mir744	Mirn744|mir-744|mmu-mir-744	microRNA 744	ncRNA
mm_164539.1	chr17	7079246	7079272	+	1	NA	intron (NM_001033442, intron 2 of 3)	intron (NM_001033442, intron 2 of 3)	53716	NM_001033442	381059	Mm.490353	NM_001033442	ENSMUSG00000095720	Gm1604b	ENSMUSG00000073470|Gm1604	predicted gene 1604b	protein-coding
mm_143116.1	chr17	57207439	57207446	-	1	NA	intron (NM_009778, intron 34 of 40)	intron (NM_009778, intron 34 of 40)	9786	NR_105944	102465591		NR_105944	ENSMUSG00000099066	Mir6978	Gm27858|mmu-mir-6978	microRNA 6978	ncRNA
mm_113963.1	chr13	51408757	51408781	+	1	NA	5' UTR (NM_010101, exon 1 of 2)	5' UTR (NM_010101, exon 1 of 2)	151	NM_010101	13610	Mm.136736	NM_010101	ENSMUSG00000067586	S1pr3	AI132464|Edg3|Lpb3|S1p3	sphingosine-1-phosphate receptor 3	protein-coding
mm_103503.1	chr11	76578026	76578048	-	1	NA	promoter-TSS (NM_198894)	promoter-TSS (NM_198894)	-298	NM_198894	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_4267.1	chr1	171503626	171503649	+	1	NA	5' UTR (NM_019484, exon 1 of 1)	5' UTR (NM_019484, exon 1 of 1)	159	NM_019484	56009	Mm.389208	NM_019484	ENSMUSG00000060244	Alyref2	C130042O11Rik|REF2|Refbp2	Aly/REF export factor 2	protein-coding
mm_50101.1	chr6	41533175	41533189	+	1	NA	Intergenic	Intergenic	11406	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_140139.1	chr17	79918902	79918920	+	1	NA	Intergenic	Intergenic	-22788	NM_001286647	56298	Mm.175403	NM_019717	ENSMUSG00000059811	Atl2	2010110I21Rik|AA407293|AV334690|Aip-2|Arl6ip2	atlastin GTPase 2	protein-coding
mm_15888.1	chr2	164857770	164857803	+	1	NA	promoter-TSS (NM_011125)	promoter-TSS (NM_011125)	-78	NM_011125	18830	Mm.6105	NM_011125	ENSMUSG00000017754	Pltp	Bpife|OD107	phospholipid transfer protein	protein-coding
mm_45355.1	chr5	65926824	65926826	-	1	NA	Intergenic	Intergenic	-40299	NM_001081104	231252	Mm.140015	NM_001081104	ENSMUSG00000029205	Chrna9	2410015I05Rik|Acra9|EG666827|Gm8311	cholinergic receptor, nicotinic, alpha polypeptide 9	protein-coding
mm_44073.1	chr5	148959264	148959268	+	1	NA	Intergenic	Intergenic	9016	NR_040686	71473	Mm.90306	NR_040686	ENSMUSG00000079069	8430423G03Rik	-	RIKEN cDNA 8430423G03 gene	ncRNA
mm_65747.1	chr7	28544442	28544452	-	1	NA	exon (NM_001081115, exon 5 of 6)	exon (NM_001081115, exon 5 of 6)	2807	NM_001081115	233038	Mm.224815	NM_001081115	ENSMUSG00000047586	Nccrp1	1190020J12Rik|Gm163|NCCRP-1	non-specific cytotoxic cell receptor protein 1 homolog (zebrafish)	protein-coding
mm_35458.1	chr4	40703189	40703203	-	1	NA	promoter-TSS (NM_025545)	promoter-TSS (NM_025545)	-2	NM_001025445	66408	Mm.430710	NM_025545	ENSMUSG00000028411	Aptx	2410016G21Rik|AA388047|FHA-HIT	aprataxin	protein-coding
mm_151208.1	chr19	53600450	53600478	+	1	NA	promoter-TSS (NM_007790)	promoter-TSS (NM_007790)	68	NM_007790	13006	Mm.14910	NM_007790	ENSMUSG00000024974	Smc3	Bamacan|Cspg6|HCAP|Mmip1|SMC-3|SmcD	structural maintenance of chromosomes 3	protein-coding
mm_49017.1	chr6	4758730	4758740	+	1	NA	3' UTR (NM_130877, exon 2 of 2)	3' UTR (NM_130877, exon 2 of 2)	11429	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_67385.1	chr7	79842408	79842419	-	1	NA	promoter-TSS (NM_008486)	promoter-TSS (NM_008486)	-61	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_18344.1	chr2	58157047	58157052	-	1	NA	intron (NM_139200, intron 1 of 7)	intron (NM_139200, intron 1 of 7)	3073	NM_139200	227929	Mm.273905	NM_139200	ENSMUSG00000026832	Cytip	A130053M09Rik|AI462064|C80816|Cbp|Cybr|Pscdbp	cytohesin 1 interacting protein	protein-coding
mm_20745.1	chr2	140042140	140042170	-	1	NA	exon (NM_175225, exon 4 of 14)	exon (NM_175225, exon 4 of 14)	24650	NM_001159640	75812	Mm.293449	NM_175225	ENSMUSG00000039033	Tasp1	4930485D02Rik|AW986064	taspase, threonine aspartase 1	protein-coding
mm_98427.1	chr11	94654005	94654027	+	1	NA	promoter-TSS (NM_177752)	promoter-TSS (NM_177752)	225	NM_053161	94064	Mm.34951	NM_053161	ENSMUSG00000024414	Mrpl27	A630055F16Rik|D11Moh47|D18Ertd643e	mitochondrial ribosomal protein L27	protein-coding
mm_157861.1	chrX	75114666	75114675	-	1	NA	intron (NM_008621, intron 7 of 11)	intron (NM_008621, intron 7 of 11)	16346	NM_008621	17524	Mm.391267	NM_008621	ENSMUSG00000031402	Mpp1	55kDa|C130070C03Rik|p55	membrane protein, palmitoylated	protein-coding
mm_118890.1	chr14	26608542	26608577	+	1	NA	exon (NM_001285466, exon 9 of 18)	exon (NM_001285466, exon 9 of 18)	29009	NM_145969	211922	Mm.260512	NM_145969	ENSMUSG00000040818	Dennd6a	Fam116a	DENN/MADD domain containing 6A	protein-coding
mm_8379.1	chr1	151250788	151250801	-	1	NA	Intergenic	MLT1H|LTR|ERVL-MaLR	-93704	NM_001039512	117198	Mm.33764	NM_028582	ENSMUSG00000023150	Ivns1abp	1190004M08Rik|1700126I16Rik|AA960440|HSPC068|ND1|NS-1|NS1-BP|Nd1-L|Nd1-S|mKIAA0850	influenza virus NS1A binding protein	protein-coding
mm_133212.1	chr16	75592939	75592965	+	1	NA	promoter-TSS (NM_198302)	promoter-TSS (NM_198302)	61	NM_198302	224344	Mm.273214	NM_198302	ENSMUSG00000032940	Rbm11	A330018F01	RNA binding motif protein 11	protein-coding
mm_71475.1	chr8	46535678	46535689	+	1	NA	3' UTR (NM_007981, exon 21 of 21)	3' UTR (NM_007981, exon 21 of 21)	-16386	NM_027973	71876	Mm.22108	NM_027973	ENSMUSG00000031629	Cenpu	1700029A22Rik|Mlf1ip	centromere protein U	protein-coding
mm_97236.1	chr11	75655980	75656000	+	1	NA	promoter-TSS (NM_001080775)	promoter-TSS (NM_001080775)	-25	NM_001080775	17913	Mm.234502	NM_008659	ENSMUSG00000017774	Myo1c	C80397|MMIb|MYO1E|NMI|mm1beta|myr2	myosin IC	protein-coding
mm_79215.1	chr9	49108663	49108665	+	1	NA	intron (NM_030709, intron 4 of 12)	intron (NM_030709, intron 4 of 12)	5885	NM_030709	80893	Mm.72799	NM_030709	ENSMUSG00000032268	Tmprss5	spinesin	transmembrane protease, serine 5 (spinesin)	protein-coding
mm_78986.1	chr9	45395086	45395121	+	1	NA	3' UTR (NM_022004, exon 8 of 8)	3' UTR (NM_022004, exon 8 of 8)	-4606	NR_028499	11936	Mm.22742	NM_007503	ENSMUSG00000059412	Fxyd2	Atp1g1	FXYD domain-containing ion transport regulator 2	protein-coding
mm_59431.1	chr7	27129809	27129815	+	1	NA	exon (NM_007817, exon 6 of 10)	exon (NM_007817, exon 6 of 10)	9857	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_166170.1	chr5	23586795	23586832	+	1	NA	intron (NM_009274, intron 1 of 14)	Lx8|LINE|L1	29758	NM_009274	20817	Mm.288728	NM_009274	ENSMUSG00000062604	Srpk2	AW226533|AW492537|AW547358|Wbp6|mSRPK2	serine/arginine-rich protein specific kinase 2	protein-coding
mm_160511.1	chr9	21143084	21143084	-	1	NA	exon (NM_016742, exon 2 of 8)	exon (NM_016742, exon 2 of 8)	6822	NM_016742	12539	Mm.32331	NM_016742	ENSMUSG00000019471	Cdc37	p50|p50Cdc37	cell division cycle 37	protein-coding
mm_126411.1	chr15	80256905	80256920	+	1	NA	exon (NM_009716, exon 3 of 3)	exon (NM_009716, exon 3 of 3)	1728	NM_009716	11911	Mm.641	NM_009716	ENSMUSG00000042406	Atf4	Atf-4|C/ATF|CREB2|TAXREB67	activating transcription factor 4	protein-coding
mm_5261.1	chr1	16770150	16770159	-	1	NA	Intergenic	Intergenic	81698	NM_016923	17087	Mm.116844	NM_016923	ENSMUSG00000025779	Ly96	ESOP-1|MD-2|MD2	lymphocyte antigen 96	protein-coding
mm_133157.1	chr16	70400712	70400730	+	1	NA	intron (NM_028803, intron 2 of 15)	(T)n|Simple_repeat|Simple_repeat	86772	NM_028803	74185	Mm.396102	NM_028803	ENSMUSG00000022707	Gbe1	2310045H19Rik|2810426P10Rik|D16Ertd536e	glucan (1,4-alpha-), branching enzyme 1	protein-coding
mm_15640.1	chr2	163054683	163054693	+	1	NA	promoter-TSS (NM_008652)	promoter-TSS (NM_008652)	53	NM_008652	17865	Mm.4594	NM_008652	ENSMUSG00000017861	Mybl2	B-Myb|Bmyb	myeloblastosis oncogene-like 2	protein-coding
mm_122169.1	chr14	31436194	31436204	-	1	NA	promoter-TSS (NM_011894)	promoter-TSS (NM_011894)	-99	NM_011894	24056	Mm.383198	NM_011894	ENSMUSG00000021892	Sh3bp5	AI606498|SH3BP-5|Sab	SH3-domain binding protein 5 (BTK-associated)	protein-coding
mm_133869.1	chr16	96372659	96372672	+	1	NA	intron (NM_001177886, intron 2 of 8)	intron (NM_001177886, intron 2 of 8)	10901	NM_028078	72058	Mm.119714	NM_028078	ENSMUSG00000000159	Igsf5	2010003D20Rik|JCAM|Jam4	immunoglobulin superfamily, member 5	protein-coding
mm_137006.1	chr17	17625465	17625503	+	1	NA	promoter-TSS (NM_172827)	promoter-TSS (NM_172827)	-995	NM_172827	240028	Mm.328807	NM_172827	ENSMUSG00000023845	Lnpep	2010309L07Rik|4732490P18Rik|CAP|IRAP|PLAP|gp160|vp165	leucyl/cystinyl aminopeptidase	protein-coding
mm_81586.1	chr9	110422852	110422862	+	1	NA	3' UTR (NM_008694, exon 4 of 4)	3' UTR (NM_008694, exon 4 of 4)	3049	NM_008694	18054	Mm.236225	NM_008694	ENSMUSG00000032484	Ngp	bectenecin	neutrophilic granule protein	protein-coding
mm_66613.1	chr7	45466780	45466790	-	1	NA	5' UTR (NM_007527, exon 1 of 6)	5' UTR (NM_007527, exon 1 of 6)	113	NM_007527	12028	Mm.19904	NM_007527	ENSMUSG00000003873	Bax	-	BCL2-associated X protein	protein-coding
mm_92309.1	chr10	75185188	75185203	-	1	NA	TTS (NM_001081412)	TTS (NM_001081412)	-26878	NM_153406	74392	Mm.27716	NM_153406	ENSMUSG00000033444	Specc1l	4930470P14Rik|4932439K10Rik|9530057A13Rik|AI317249|Cytsa|mKIAA0376	sperm antigen with calponin homology and coiled-coil domains 1-like	protein-coding
mm_157409.1	chrX	38440218	38440237	-	1	NA	exon (NM_001017959, exon 3 of 9)	exon (NM_001017959, exon 3 of 9)	16233	NM_010685	16784	Mm.486	NM_010685	ENSMUSG00000016534	Lamp2	CD107b|LGP-B|Lamp II|Lamp-2|Lamp-2a|Lamp-2b|Lamp-2c|Mac3	lysosomal-associated membrane protein 2	protein-coding
mm_126867.1	chr15	89355731	89355741	+	1	NA	promoter-TSS (NM_001271601)	promoter-TSS (NM_001271601)	17	NM_001271601	52683	Mm.143167	NM_001115132	ENSMUSG00000008690	Ncaph2	-	non-SMC condensin II complex, subunit H2	protein-coding
mm_4668.1	chr1	180382352	180382363	+	1	NA	intron (NM_001081175, intron 2 of 7)	intron (NM_001081175, intron 2 of 7)	-51808	NR_003623	277333	Mm.389223	NM_199472		Gm5069	EG277333	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_10580.1	chr2	18155981	18155995	+	1	NA	intron (NR_045539, intron 11 of 24)	intron (NR_045539, intron 11 of 24)	91403	NM_001252561	17354	Mm.209175	NM_010804	ENSMUSG00000026743	Mllt10	Af10|B130021D15Rik|D630001B22Rik|mKIAA4140	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 10	protein-coding
mm_57563.1	chr6	127125631	127125641	-	1	NA	TTS (NM_009829)	TTS (NM_009829)	-16084	NM_177003	319801	Mm.101836	NM_177003	ENSMUSG00000038028	Tigar	9630033F20Rik|AA793651|AI595337|C79710|C85509	Trp53 induced glycolysis repulatory phosphatase	protein-coding
mm_164334.1	chr16	10797035	10797064	+	1	NA	promoter-TSS (NM_013637)	promoter-TSS (NM_013637)	-226	NM_013637	19118	Mm.42733	NM_013637	ENSMUSG00000022501	Prm1	Prm-1	protamine 1	protein-coding
mm_118130.1	chr13	104623319	104623332	-	1	NA	Intergenic	Intergenic	193628	NM_026072	67285	Mm.235398	NM_026072	ENSMUSG00000021715	Cwc27	3110009E13Rik|NY-CO-10|Sdccag10	CWC27 spliceosome-associated protein	protein-coding
mm_33151.1	chr4	125445356	125445358	+	1	NA	Intergenic	Intergenic	-45474	NM_001081097	14807	Mm.40896	NM_001081097	ENSMUSG00000001985	Grik3	9630027E11|GluK3|GluR7-3|Glur-7|Glur7	glutamate receptor, ionotropic, kainate 3	protein-coding
mm_19983.1	chr2	118545163	118545169	-	1	NA	promoter-TSS (NR_138603)	promoter-TSS (NR_138603)	-579	NR_138603	171543	Mm.210125	NM_138313	ENSMUSG00000040093	Bmf	AW260063|AW411872	BCL2 modifying factor	protein-coding
mm_167054.1	chr7	87650180	87650180	+	1	NA	intron (NM_001143834, intron 3 of 10)	intron (NM_001143834, intron 3 of 10)	66012	NM_001143834	108071	Mm.235018	NM_001033224	ENSMUSG00000049583	Grm5	6430542K11Rik|AI850523|Glu5R|Gprc1e|mGluR5|mGluR5b	glutamate receptor, metabotropic 5	protein-coding
mm_17108.1	chr2	24049409	24049419	-	1	NA	promoter-TSS (NM_080462)	promoter-TSS (NM_080462)	-35	NM_080462	140483	Mm.33120	NM_080462	ENSMUSG00000026986	Hnmt	1500031F01Rik|AI788969	histamine N-methyltransferase	protein-coding
mm_34683.1	chr4	151685852	151685894	+	1	NA	intron (NM_001081557, intron 3 of 23)	Lx8|LINE|L1	175895	NM_001081557	100072	Mm.318846	NM_001081557	ENSMUSG00000014592	Camta1	1810059M14Rik|2310058O09Rik|AI316882|AW987475|mKIAA0833	calmodulin binding transcription activator 1	protein-coding
mm_105535.1	chr11	106301427	106301427	-	1	NA	exon (NM_008117, exon 2 of 5)	exon (NM_008117, exon 2 of 5)	469	NM_008117	14599	Mm.343934	NM_008117	ENSMUSG00000020713	Gh	Gh1|Ghb1	growth hormone	protein-coding
mm_62869.1	chr7	114722782	114722795	+	1	NA	intron (NM_054084, intron 4 of 4)	intron (NM_054084, intron 4 of 4)	4145	NM_054084	116903	Mm.273838	NM_054084	ENSMUSG00000030666	Calcb	CGRP2|Calc2	calcitonin-related polypeptide, beta	protein-coding
mm_80155.1	chr9	70934274	70934276	+	1	NA	intron (NM_001324473, intron 1 of 8)	intron (NM_001324473, intron 1 of 8)	533	NM_008280	15450	Mm.390187	NM_008280	ENSMUSG00000032207	Lipc	AI256194|HL|Hpl	lipase, hepatic	protein-coding
mm_128506.1	chr15	53189099	53189101	-	1	NA	intron (NM_010162, intron 1 of 10)	MTC|LTR|ERVL-MaLR	157083	NM_010162	14042	Mm.309395	NM_010162	ENSMUSG00000061731	Ext1	AA409028	exostoses (multiple) 1	protein-coding
mm_39731.1	chr5	28914033	28914034	+	1	NA	Intergenic	Intergenic	-281960	NM_001289757	56874	Mm.87352	NM_021470	ENSMUSG00000029130	Rnf32	1700009J01Rik|2700025B22Rik|4930542N22Rik|Lmbr2	ring finger protein 32	protein-coding
mm_36370.1	chr4	76450591	76450615	-	1	NA	intron (NM_011211, intron 10 of 39)	intron (NM_011211, intron 10 of 39)	-1172317	NM_025849	66928	Mm.24332	NM_025849	ENSMUSG00000028398	Tmem261	1700027K24Rik|3110001D03Rik	transmembrane protein 261	protein-coding
mm_61917.1	chr7	90151507	90151516	+	1	NA	intron (NM_001252520, intron 1 of 20)	intron (NM_001252520, intron 1 of 20)	21279	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_107343.1	chr12	32724712	32724721	+	1	NA	Intergenic	Intergenic	-95619	NM_021524	59027	Mm.202727	NM_021524	ENSMUSG00000020572	Nampt	1110035O14Rik|AI314458|AI480535|NAmPRTase|Pbef|Pbef1|Visfatin	nicotinamide phosphoribosyltransferase	protein-coding
mm_26339.1	chr3	142547172	142547182	+	1	NA	3' UTR (NM_001083312, exon 11 of 11)	3' UTR (NM_001083312, exon 11 of 11)	-12875	NM_018734	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_108420.1	chr12	82169420	82169443	+	1	NA	promoter-TSS (NM_001167983)	promoter-TSS (NM_001167983)	-585	NM_001167983	217692	Mm.261333	NM_172579	ENSMUSG00000042700	Sipa1l1	4931426N11Rik|AW213287|Spar|mKIAA0440	signal-induced proliferation-associated 1 like 1	protein-coding
mm_46.1	chr1	6507836	6507838	+	1	NA	intron (NM_001244693, intron 2 of 22)	ORR1B2-int|LTR|ERVL-MaLR	20606	NM_001244692	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding
mm_107153.1	chr12	24572250	24572266	+	1	NA	promoter-TSS (NM_001161406)	promoter-TSS (NM_001161406)	-29	NM_001161406	195733	Mm.263068	NM_145890	ENSMUSG00000020656	Grhl1	LBP-32|MGR|Tcfcp2l2	grainyhead-like 1 (Drosophila)	protein-coding
mm_160791.1	chr11	3157781	3157781	-	1	NA	intron (NM_030207, intron 11 of 32)	intron (NM_030207, intron 11 of 32)	33760	NR_003517	236604	Mm.247625	NM_001004146		Pisd-ps1	-	phosphatidylserine decarboxylase, pseudogene 1	pseudo
mm_168016.1	chrY	90734521	90734530	+	1	NA	Intergenic	Intergenic	20525	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_17344.1	chr2	26604236	26604252	-	1	NA	5' UTR (NM_026212, exon 1 of 6)	5' UTR (NM_026212, exon 1 of 6)	173	NM_026212	67512	Mm.24244	NM_026212	ENSMUSG00000026922	Agpat2	2510002J07Rik|AV000834|BSCL|BSCL1|LPAAB|LPAAT-beta	1-acylglycerol-3-phosphate O-acyltransferase 2 (lysophosphatidic acid acyltransferase, beta)	protein-coding
mm_169981.1	chr17	15010155	15010162	-	1	NA	promoter-TSS (NM_001123367)	promoter-TSS (NM_001123367)	26	NM_001123368	100041586	Mm.440445	NM_001123368	ENSMUSG00000079710	Gm3417	-	predicted gene 3417	protein-coding
mm_71733.1	chr8	61995840	61995843	+	1	NA	intron (NM_001293783, intron 26 of 37)	intron (NM_001293783, intron 26 of 37)	67754	NM_001293783	234311	Mm.275233	NM_144928	ENSMUSG00000037921	Ddx60	9830118M07	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	protein-coding
mm_21379.1	chr2	157425161	157425197	-	1	NA	intron (NM_009271, intron 1 of 14)	intron (NM_009271, intron 1 of 14)	886	NM_001025395	20779	Mm.22845	NM_009271	ENSMUSG00000027646	Src	AW259666|pp60c-src	Rous sarcoma oncogene	protein-coding
mm_49169.1	chr6	14901251	14901277	+	1	NA	promoter-TSS (NM_053242)	promoter-TSS (NM_053242)	-85	NM_053242	114142	Mm.332919	NM_053242	ENSMUSG00000029563	Foxp2	2810043D05Rik|AI449000|CAG-16|D0Kist7	forkhead box P2	protein-coding
mm_51935.1	chr6	91684178	91684191	+	1	NA	5' UTR (NM_009320, exon 1 of 15)	5' UTR (NM_009320, exon 1 of 15)	117	NM_009320	21366	Mm.395650	NM_009320	ENSMUSG00000030096	Slc6a6	AA589629|C80501|Taut	solute carrier family 6 (neurotransmitter transporter, taurine), member 6	protein-coding
mm_114557.1	chr13	74208735	74208757	+	1	NA	promoter-TSS (NM_177333)	promoter-TSS (NM_177333)	-46	NM_177333	211446	Mm.261859	NM_177333	ENSMUSG00000034152	Exoc3	2810050O03Rik|E430013E20Rik|Sec6|Sec6l1	exocyst complex component 3	protein-coding
mm_133765.1	chr16	94569717	94569769	+	1	NA	promoter-TSS (NM_007890)	promoter-TSS (NM_007890)	-463	NM_007890	13548	Mm.310973	NM_007890	ENSMUSG00000022897	Dyrk1a	2310043O08Rik|D16Ertd272e|D16Ertd493e|Dyrk|ENSMUSG00000074897|Gm10783|Mnbh|Mp86|mmb	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1a	protein-coding
mm_163913.1	chr14	33890337	33890338	+	1	NA	Intergenic	Intergenic	-33250	NM_145741	14560	Mm.432071	NM_145741	ENSMUSG00000021943	Gdf10	Bmp3b	growth differentiation factor 10	protein-coding
mm_90543.1	chr10	128091597	128091624	+	1	NA	Intergenic	Intergenic	-1173	NM_054078	116848	Mm.252213	NM_054078	ENSMUSG00000040054	Baz2a	AA415431|C030005G16Rik|C78388|Tip5|Walp3|mKIAA0314	bromodomain adjacent to zinc finger domain, 2A	protein-coding
mm_40925.1	chr5	76140299	76140317	+	1	NA	promoter-TSS (NM_020611)	promoter-TSS (NM_020611)	35	NM_020611	57357	Mm.289446	NM_020611	ENSMUSG00000029233	Srd5a3	1110025P14Rik|A430076C09|AV364670|AW987574|D730040M03Rik|H5ar|S5AR 3|Srd5a2l	steroid 5 alpha-reductase 3	protein-coding
mm_85901.1	chr9	111056070	111056099	-	1	NA	exon (NM_017466, exon 2 of 2)	exon (NM_017466, exon 2 of 2)	1160	NM_001302377	54199	Mm.7336	NM_017466	ENSMUSG00000043953	Ccrl2	1810047I05Rik|Ackr5|CCR11|Cmkbr1l2|E01|L-CCR	chemokine (C-C motif) receptor-like 2	protein-coding
mm_172692.1	chr8	6045218	6045222	+	1	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	-939933	NM_011388	20494	Mm.3500	NM_011388	ENSMUSG00000023073	Slc10a2	9130221J18Rik|AI605518|ASBT|IBAT|ISBT	solute carrier family 10, member 2	protein-coding
mm_159041.1	chr1	180935094	180935094	+	1	NA	promoter-TSS (NM_010094)	promoter-TSS (NM_010094)	72	NM_010094	13590	Mm.378911	NM_010094	ENSMUSG00000038793	Lefty1	AI450052|Ebaf|Leftb|Stra3|Tgfb4|lefty|lefty-1	left right determination factor 1	protein-coding
mm_149754.1	chr19	22692775	22692827	+	1	NA	5' UTR (NM_001035246, exon 1 of 8)	5' UTR (NM_001035246, exon 1 of 8)	182	NM_001035244	226025	Mm.131943	NM_177341	ENSMUSG00000052387	Trpm3	6330504P12Rik|9330180E14|AU018608|B930001P07Rik|LTRPC3|MLSN2	transient receptor potential cation channel, subfamily M, member 3	protein-coding
mm_134194.1	chr16	10993071	10993094	-	1	NA	promoter-TSS (NM_019980)	promoter-TSS (NM_019980)	39	NM_019980	56722	Mm.294753	NM_019980	ENSMUSG00000022500	Litaf	3222402J11Rik|C85531|N4WBP3|TBX1	LPS-induced TN factor	protein-coding
mm_74840.1	chr8	23257044	23257086	-	1	NA	promoter-TSS (NM_020585)	promoter-TSS (NM_020585)	15	NM_020585	57437	Mm.196269	NM_020585	ENSMUSG00000015341	Golga7	AB041568|C130038N16Rik|GCP16|GOLGA3AP1|HSPC041|R75586	golgi autoantigen, golgin subfamily a, 7	protein-coding
mm_124402.1	chr14	114948978	114949012	-	1	NA	Intergenic	Intergenic	-3047	NR_126548	74982		NR_126548		1700100I10Rik	1700085D13Rik|4930481K08Rik	RIKEN cDNA 1700100I10 gene	ncRNA
mm_96707.1	chr11	69655618	69655630	+	1	NA	exon (NM_009235, exon 1 of 2)	exon (NM_009235, exon 1 of 2)	587	NM_009235	20670	Mm.347499	NM_009235	ENSMUSG00000041287	Sox15	-	SRY (sex determining region Y)-box 15	protein-coding
mm_75064.1	chr8	33747725	33747781	-	1	NA	promoter-TSS (NM_001206849)	promoter-TSS (NM_001206849)	17	NM_001206849	72632	Mm.443483	NM_001206849	ENSMUSG00000094500	Smim18	2700090O03Rik|AI835723	small integral membrane protein 18	protein-coding
mm_217.1	chr1	16691732	16691748	+	1	NA	exon (NM_001159711, exon 2 of 5)	exon (NM_001159711, exon 2 of 5)	3284	NM_016923	17087	Mm.116844	NM_016923	ENSMUSG00000025779	Ly96	ESOP-1|MD-2|MD2	lymphocyte antigen 96	protein-coding
mm_94742.1	chr11	21095732	21095748	+	1	NA	intron (NM_023324, intron 1 of 6)	L1MC5|LINE|L1	4416	NM_023324	67245	Mm.28957	NM_023324	ENSMUSG00000020134	Peli1	2810468L03Rik|A930031K15Rik|AA409794|AI586297|D11Ertd676e	pellino 1	protein-coding
mm_43793.1	chr5	142702092	142702153	+	1	NA	promoter-TSS (NM_146257)	promoter-TSS (NM_146257)	21	NM_146257	243328	Mm.125942	NM_146257	ENSMUSG00000050822	Slc29a4	ENT4|mPMAT	solute carrier family 29 (nucleoside transporters), member 4	protein-coding
mm_34606.1	chr4	150240921	150240924	+	1	NA	intron (NM_023119, intron 2 of 11)	PB1D10|SINE|Alu	3598	NM_001025388	433182	Mm.70666	NM_001025388	ENSMUSG00000059040	Eno1b	EG433182|Eno1|Gm5506	enolase 1B, retrotransposed	protein-coding
mm_72235.1	chr8	74873594	74873615	+	1	NA	5' UTR (NM_027837, exon 1 of 4)	5' UTR (NM_027837, exon 1 of 4)	430	NM_001294278	71597	Mm.158735	NM_027837	ENSMUSG00000031621	Isx	9130012O13Rik|Pix-1	intestine specific homeobox	protein-coding
mm_77235.1	chr8	115704845	115704847	-	1	NA	3' UTR (NM_001025577, exon 1 of 1)	3' UTR (NM_001025577, exon 1 of 1)	2048	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_83567.1	chr9	46315951	46315965	-	1	NA	5' UTR (NM_183104, exon 3 of 13)	5' UTR (NM_183104, exon 3 of 13)	4028	NM_183104	74361	Mm.159169	NM_183104	ENSMUSG00000056617	4931429L15Rik	-	RIKEN cDNA 4931429L15 gene	protein-coding
mm_10243.1	chr2	8946957	8946967	+	1	NA	Intergenic	Intergenic	-242553	NR_038180	73438	Mm.23558	NR_038180	ENSMUSG00000085580	1700061F12Rik	-	RIKEN cDNA 1700061F12 gene	ncRNA
mm_169924.1	chr16	57391420	57391421	-	1	NA	intron (NM_001040397, intron 1 of 4)	LSU-rRNA_Hsa|rRNA|rRNA	38143	NM_001040397	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding
mm_6643.1	chr1	79440040	79440080	-	1	NA	promoter-TSS (NM_009129)	promoter-TSS (NM_009129)	30	NM_009129	20254	Mm.5038	NM_009129	ENSMUSG00000050711	Scg2	Chgc|SgII	secretogranin II	protein-coding
mm_27251.1	chr3	37125774	37125848	-	1	NA	exon (NM_008366, exon 1 of 4)	exon (NM_008366, exon 1 of 4)	143	NM_008366	16183	Mm.14190	NM_008366	ENSMUSG00000027720	Il2	Il-2	interleukin 2	protein-coding
mm_84974.1	chr9	85323961	85323974	-	1	NA	3' UTR (NM_001160378, exon 3 of 3)	3' UTR (NM_001160378, exon 3 of 3)	3157	NM_001160378	212943	Mm.74610	NM_001160378	ENSMUSG00000032265	Fam46a	BAP014|D930050G01Rik	family with sequence similarity 46, member A	protein-coding
mm_57254.1	chr6	123283584	123283594	-	1	NA	exon (NM_019948, exon 6 of 6)	exon (NM_019948, exon 6 of 6)	6282	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_85891.1	chr9	111055138	111055154	-	1	NA	3' UTR (NM_017466, exon 2 of 2)	3' UTR (NM_017466, exon 2 of 2)	2098	NM_001302377	54199	Mm.7336	NM_017466	ENSMUSG00000043953	Ccrl2	1810047I05Rik|Ackr5|CCR11|Cmkbr1l2|E01|L-CCR	chemokine (C-C motif) receptor-like 2	protein-coding
mm_52184.1	chr6	99521372	99521399	+	1	NA	promoter-TSS (NM_001347345)	promoter-TSS (NM_001347345)	-392	NM_001347345	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_92932.1	chr10	84527588	84527609	-	1	NA	exon (NM_175451, exon 2 of 2)	exon (NM_175451, exon 2 of 2)	6290	NM_175451	216197	Mm.334999	NM_175451	ENSMUSG00000046841	Ckap4	5630400A09Rik|CLIMP-63|P63	cytoskeleton-associated protein 4	protein-coding
mm_170202.1	chr17	6948357	6948375	-	1	NA	promoter-TSS (NM_001083945)	promoter-TSS (NM_001083945)	-10	NM_001083945	100037282	Mm.29830	NM_001083945	ENSMUSG00000023806	Rsph3b	Rshl2b	radial spoke 3B homolog (Chlamydomonas)	protein-coding
mm_70010.1	chr7	142443615	142443627	-	1	NA	exon (NM_009405, exon 4 of 6)	exon (NM_009405, exon 4 of 6)	1153	NM_009405	21953	Mm.39469	NM_009405	ENSMUSG00000031097	Tnni2	-	troponin I, skeletal, fast 2	protein-coding
mm_63160.1	chr7	123462319	123462329	+	1	NA	promoter-TSS (NM_007474)	promoter-TSS (NM_007474)	30	NM_001109045	11833	Mm.273175	NM_007474	ENSMUSG00000030762	Aqp8	AI255744|AQP-8	aquaporin 8	protein-coding
mm_141537.1	chr17	31855815	31855827	-	1	NA	promoter-TSS (NM_010831)	promoter-TSS (NM_010831)	-29	NM_010831	17691	Mm.290941	NM_010831	ENSMUSG00000024042	Sik1	Msk|Sik|Snf1lk	salt inducible kinase 1	protein-coding
mm_14259.1	chr2	128204259	128204265	+	1	NA	Intergenic	Intergenic	76687	NM_001284410	12125	Mm.141083	NM_009754	ENSMUSG00000027381	Bcl2l11	1500006F24Rik|Bim|Bod|bcl2-L-11	BCL2-like 11 (apoptosis facilitator)	protein-coding
mm_57571.1	chr6	127130281	127130311	-	1	NA	3' UTR (NM_009829, exon 5 of 5)	3' UTR (NM_009829, exon 5 of 5)	-19093	NR_040274	77558	Mm.358918	NR_040273	ENSMUSG00000097166	9330179D12Rik	-	RIKEN cDNA 9330179D12 gene	ncRNA
mm_100743.1	chr11	4118724	4118769	-	1	NA	promoter-TSS (NM_144520)	promoter-TSS (NM_144520)	-17	NM_144520	67815	Mm.253922	NM_144520	ENSMUSG00000003585	Sec14l2	1300013M05Rik|Spf|TAP	SEC14-like lipid binding 2	protein-coding
mm_86879.1	chr10	21997137	21997158	+	1	NA	intron (NM_001161848, intron 8 of 11)	intron (NM_001161848, intron 8 of 11)	2481	NM_011361	20393	Mm.28405	NM_011361	ENSMUSG00000019970	Sgk1	Sgk	serum/glucocorticoid regulated kinase 1	protein-coding
mm_64526.1	chr7	143978318	143978331	+	1	NA	intron (NR_037302, intron 5 of 5)	CpG	-30930	NR_037292	100526562		NR_037292	ENSMUSG00000093221	Mir3105	mmu-mir-3105	microRNA 3105	ncRNA
mm_108586.1	chr12	85219476	85219546	+	1	NA	promoter-TSS (NM_145445)	promoter-TSS (NM_145445)	30	NM_145445	217715	Mm.29041	NM_145445	ENSMUSG00000004788	Eif2b2	EIF-2Bbeta|EIF2B	eukaryotic translation initiation factor 2B, subunit 2 beta	protein-coding
mm_105441.1	chr11	104402858	104402862	-	1	NA	intron (NM_001081045, intron 2 of 13)	intron (NM_001081045, intron 2 of 13)	39431	NM_001081045	76719	Mm.136418	NM_001081045	ENSMUSG00000018412	Kansl1	1700081L11Rik|9430041J06Rik|mKIAA1267	KAT8 regulatory NSL complex subunit 1	protein-coding
mm_99170.1	chr11	100824217	100824239	+	1	NA	intron (NM_001113563, intron 1 of 18)	intron (NM_001113563, intron 1 of 18)	-1658	NM_011489	20851	Mm.34064	NM_011489	ENSMUSG00000020919	Stat5b	-	signal transducer and activator of transcription 5B	protein-coding
mm_97869.1	chr11	83175190	83175204	+	1	NA	promoter-TSS (NM_011410)	promoter-TSS (NM_011410)	11	NM_001302559	20558	Mm.38192	NM_011410	ENSMUSG00000000204	Slfn4	AI450778	schlafen 4	protein-coding
mm_163012.1	chr11	44621611	44621614	+	1	NA	intron (NM_001290711, intron 3 of 15)	intron (NM_001290711, intron 3 of 15)	3512	NM_001290710	13591	Mm.439662	NM_007897	ENSMUSG00000057098	Ebf1	Ebf|O/E-1|OE-1|Olf-1|Olf1	early B cell factor 1	protein-coding
mm_131289.1	chr16	11322916	11322930	+	1	NA	promoter-TSS (NM_028964)	promoter-TSS (NM_028964)	19	NM_028964	74478	Mm.325831	NM_028964	ENSMUSG00000071669	Snx29	4933437K13Rik|ENSMUSG00000079738|Gm11170|Gm1737|Gm930|Rundc2a	sorting nexin 29	protein-coding
mm_128127.1	chr15	31338087	31338093	-	1	NA	intron (NM_027496, intron 1 of 3)	intron (NM_027496, intron 1 of 3)	29669	NM_001164441	67434	Mm.102470	NM_026153	ENSMUSG00000022237	Ankrd33b	0610012A05Rik|3021401C12Rik|5730557B15Rik	ankyrin repeat domain 33B	protein-coding
mm_131439.1	chr16	16072756	16072773	+	1	NA	intron (NM_146068, intron 5 of 19)	intron (NM_146068, intron 5 of 19)	74087	NM_146068	224008	Mm.244703	NM_146068	ENSMUSG00000041974	Spidr	2310008H04Rik|Kiaa0146	scaffolding protein involved in DNA repair	protein-coding
mm_103285.1	chr11	72215178	72215218	-	1	NA	promoter-TSS (NM_001163728)	promoter-TSS (NM_001163728)	60	NM_001163728	75304	Mm.340776	NM_001163728		4930563E22Rik	-	RIKEN cDNA 4930563E22 gene	protein-coding
mm_46974.1	chr5	115194246	115194257	-	1	NA	5' UTR (NM_001310712, exon 1 of 6)	5' UTR (NM_001310712, exon 1 of 6)	130	NM_001310712	29867	Mm.38551	NM_013879	ENSMUSG00000029544	Cabp1	caldendrin	calcium binding protein 1	protein-coding
mm_84644.1	chr9	71481412	71481435	-	1	NA	exon (NM_001164793, exon 3 of 4)	exon (NM_001164793, exon 3 of 4)	3535	NM_001164793	28015	Mm.21094	NM_178602	ENSMUSG00000032199	Polr2m	AA407243|AA408799|AI303746|AW553238|D9Wsu138e|Grinl1a|mKIAA4185	polymerase (RNA) II (DNA directed) polypeptide M	protein-coding
mm_159998.1	chr6	119108182	119108182	-	1	NA	5' UTR (NM_001159534, exon 1 of 47)	5' UTR (NM_001159534, exon 1 of 47)	313	NM_001159534	12288	Mm.41628	NM_009781	ENSMUSG00000051331	Cacna1c	Cav1.2|Cchl1a1|D930026N18Rik|MBC|MELC-CC	calcium channel, voltage-dependent, L type, alpha 1C subunit	protein-coding
mm_49944.1	chr6	39872209	39872219	+	1	NA	Intergenic	CpG	-61278	NM_001010930	14548	Mm.377071	NM_010270	ENSMUSG00000029918	Mrps33	AI841153|CGI-139|Gdap3|MRP-S33|PTD003	mitochondrial ribosomal protein S33	protein-coding
mm_155145.1	chrX	52788337	52788348	+	1	NA	Intergenic	L2a|LINE|L2	-2858	NM_001034059	434778	Mm.23411	NM_001034059	ENSMUSG00000073207	Ccdc160	6330534C20Rik	coiled-coil domain containing 160	protein-coding
mm_108132.1	chr12	76079567	76079569	+	1	NA	intron (NM_001005510, intron 99 of 115)	intron (NM_001005510, intron 99 of 115)	97691	NM_010157	13983	Mm.2561	NM_010157	ENSMUSG00000021055	Esr2	ER[b]|ERbeta|Estrb	estrogen receptor 2 (beta)	protein-coding
mm_38596.1	chr4	141825998	141826012	-	1	NA	promoter-TSS (NM_007919)	promoter-TSS (NM_007919)	0	NM_007919	13706	Mm.45316	NM_007919	ENSMUSG00000058579	Cela2a	Ela-2|Ela2|Ela2a	chymotrypsin-like elastase family, member 2A	protein-coding
mm_81772.1	chr9	114440855	114440865	+	1	NA	intron (NR_108101, intron 8 of 14)	intron (NR_108101, intron 8 of 14)	39765	NM_001200002	100504715	Mm.290516	NM_001200002	ENSMUSG00000079260	Tmppe	-	transmembrane protein with metallophosphoesterase domain	protein-coding
mm_60744.1	chr7	45448980	45449001	+	1	NA	intron (NM_030678, intron 12 of 15)	ID_B1|SINE|B4	10896	NM_010240	14325	Mm.30357	NM_010240	ENSMUSG00000050708	Ftl1	Ftl|Ftl-1|L-ferritin	ferritin light polypeptide 1	protein-coding
mm_47.1	chr1	6518505	6518516	+	1	NA	intron (NM_001244693, intron 2 of 22)	intron (NM_001244693, intron 2 of 22)	31279	NM_001244692	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding
mm_120579.1	chr14	69555378	69555481	+	1	NA	promoter-TSS (NM_026174)	promoter-TSS (NM_026174)	28	NM_026174	67464	Mm.489765	NM_026174	ENSMUSG00000095463	Entpd4	1200014F22Rik|4930513O14Rik|A430102M06Rik|AI414893|Lysal1|mKIAA0392	ectonucleoside triphosphate diphosphohydrolase 4	protein-coding
mm_84227.1	chr9	61961618	61961651	-	1	NA	exon (NM_028748, exon 7 of 8)	exon (NM_028748, exon 7 of 8)	-14835	NM_024245	71819	Mm.259374	NM_024245	ENSMUSG00000032254	Kif23	3110001D19Rik|C87313|CHO1|Knsl5|MKLP-1|MKLP1	kinesin family member 23	protein-coding
mm_12872.1	chr2	84515552	84515590	+	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	-8698	NR_046046	672763	Mm.491046	NR_046046	ENSMUSG00000087362	Gm13710	OTTMUSG00000013441	predicted gene 13710	ncRNA
mm_85076.1	chr9	91361736	91361746	-	1	NA	exon (NM_009573, exon 3 of 3)	exon (NM_009573, exon 3 of 3)	4058	NM_009573	22771	Mm.335350	NM_009573	ENSMUSG00000032368	Zic1	ZIC|ZNF201	zinc finger protein of the cerebellum 1	protein-coding
mm_10311.1	chr2	11172289	11172302	+	1	NA	promoter-TSS (NM_008859)	promoter-TSS (NM_008859)	-87	NM_008859	18761	Mm.329993	NM_008859	ENSMUSG00000026778	Prkcq	A130035A12Rik|AW494342|PKC-0|PKC-theta|PKCtheta|Pkcq	protein kinase C, theta	protein-coding
mm_98474.1	chr11	94950439	94950462	+	1	NA	exon (NM_007742, exon 48 of 51)	exon (NM_007742, exon 48 of 51)	14226	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_52732.1	chr6	120382039	120382043	+	1	NA	intron (NM_145997, intron 5 of 27)	intron (NM_145997, intron 5 of 27)	-17672	NR_045558	67200	Mm.45767	NM_026028	ENSMUSG00000030177	Ccdc77	2400002C23Rik|2700091N06Rik|AV168274	coiled-coil domain containing 77	protein-coding
mm_161010.1	chr11	118482521	118482521	+	1	NA	intron (NM_172573, intron 5 of 13)	intron (NM_172573, intron 5 of 13)	5561	NM_172573	217364	Mm.473963	NM_172573	ENSMUSG00000033857	Engase	C130099A03|D230014K01Rik	endo-beta-N-acetylglucosaminidase	protein-coding
mm_142262.1	chr17	39844718	39844758	-	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	1741	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_113135.1	chr13	24633583	24633604	+	1	NA	intron (NM_178658, intron 1 of 13)	intron (NM_178658, intron 1 of 13)	-5055	NM_001080381	193385	Mm.217319	NM_029679	ENSMUSG00000036006	Fam65b	-	family with sequence similarity 65, member B	protein-coding
mm_167962.1	chrX	145505231	145505232	-	1	NA	Intergenic	Intergenic	-17592	NM_153319	27494	Mm.100068	NM_153319	ENSMUSG00000041688	Amot	CAG-2|D0Kist1|Sii6	angiomotin	protein-coding
mm_79644.1	chr9	59561022	59561035	+	1	NA	exon (NM_010421, exon 8 of 14)	exon (NM_010421, exon 8 of 14)	-17309	NM_175235	76183	Mm.265415	NM_175235	ENSMUSG00000032297	Celf6	6330569O16Rik|Brunol6	CUGBP, Elav-like family member 6	protein-coding
mm_17844.1	chr2	34372140	34372154	-	1	NA	promoter-TSS (NM_001290576)	promoter-TSS (NM_001290576)	-102	NM_016768	18516	Mm.239941	NM_016768	ENSMUSG00000038718	Pbx3	-	pre B cell leukemia homeobox 3	protein-coding
mm_65519.1	chr7	25756122	25756138	-	1	NA	TTS (NM_001190974)	TTS (NM_001190974)	-1410	NM_144922	232989	Mm.254223	NM_144922	ENSMUSG00000040725	Hnrnpul1	E130317O14Rik|E1B-AP5|E1BAP5|Hnrnpul|Hnrpul1	heterogeneous nuclear ribonucleoprotein U-like 1	protein-coding
mm_96628.1	chr11	69157054	69157061	+	1	NA	promoter-TSS (NM_009659)	promoter-TSS (NM_009659)	-15	NM_009659	11686	Mm.340329	NM_009659	ENSMUSG00000032807	Alox12b	12R-LOX|Aloxe2|e-LOX2	arachidonate 12-lipoxygenase, 12R type	protein-coding
mm_88202.1	chr10	70111966	70111972	+	1	NA	intron (NM_001111121, intron 1 of 8)	intron (NM_001111121, intron 1 of 8)	14848	NM_001111121	76551	Mm.281741	NM_001111121	ENSMUSG00000048701	Ccdc6	2810012H18Rik|AA536681|AA960498|AW061011	coiled-coil domain containing 6	protein-coding
mm_52334.1	chr6	110109215	110109215	+	1	NA	Intergenic	Intergenic	-536297	NM_001346640	108073	Mm.240881	NM_177328	ENSMUSG00000056755	Grm7	6330570A01Rik|BB176677|C030018L03|E130018M02Rik|Gpr1g|Gprc1g|SMN2|Tg(SMN2)89Ahmb|mGluR7	glutamate receptor, metabotropic 7	protein-coding
mm_135038.1	chr16	32877610	32877635	-	1	NA	promoter-TSS (NM_001159349)	promoter-TSS (NM_001159349)	-162	NM_027226	69823	Mm.12831	NM_027226	ENSMUSG00000022800	Fyttd1	2010005M05Rik|3830411L18Rik|3830421F13Rik|4933423A17Rik|AI098218|AW539567|C85190	forty-two-three domain containing 1	protein-coding
mm_18102.1	chr2	44988434	44988454	-	1	NA	3' UTR (NM_015753, exon 10 of 10)	3' UTR (NM_015753, exon 10 of 10)	34733	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_18858.1	chr2	75685505	75685523	-	1	NA	intron (NM_010902, intron 1 of 4)	intron (NM_010902, intron 1 of 4)	19149	NR_132727	18024	Mm.1025	NM_010902	ENSMUSG00000015839	Nfe2l2	Nrf2	nuclear factor, erythroid derived 2, like 2	protein-coding
mm_39018.1	chr4	152131427	152131447	-	1	NA	intron (NM_207688, intron 3 of 10)	CpG-10714	-2512	NM_019585	56226	Mm.264215	NM_019585	ENSMUSG00000028943	Espn	je	espin	protein-coding
mm_137443.1	chr17	26512728	26512760	+	1	NA	Intergenic	Intergenic	-4272	NM_013642	19252	Mm.239041	NM_013642	ENSMUSG00000024190	Dusp1	3CH134|MKP1|Ptpn16|U19515|erp|mkp-1	dual specificity phosphatase 1	protein-coding
mm_73090.1	chr8	94532992	94532996	+	1	NA	promoter-TSS (NM_153507)	promoter-TSS (NM_153507)	-34	NM_153507	234577	Mm.291815	NM_153507	ENSMUSG00000034361	Cpne2	3322401K10Rik	copine II	protein-coding
mm_146340.1	chr18	82475206	82475232	+	1	NA	promoter-TSS (NM_010777)	promoter-TSS (NM_010777)	96	NM_001025245	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_142278.1	chr17	39848638	39848660	-	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	5652	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_143207.1	chr17	62858365	62858380	-	1	NA	intron (NM_010109, intron 1 of 3)	intron (NM_010109, intron 1 of 3)	22945	NM_207654	13640	Mm.7978	NM_010109	ENSMUSG00000048915	Efna5	AL-1|AV158822|EFL-5|Ephrin-A5|Epl7|LERK-7|RAGS	ephrin A5	protein-coding
mm_16204.1	chr2	173034073	173034094	+	1	NA	3' UTR (NM_019547, exon 4 of 4)	3' UTR (NM_019547, exon 4 of 4)	12181	NM_019547	56190	Mm.485782	NM_019547	ENSMUSG00000027510	Rbm38	Rnpc1|Seb4|Seb4l	RNA binding motif protein 38	protein-coding
mm_49990.1	chr6	41047325	41047350	+	1	NA	Intergenic	Intergenic	-11828	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_55407.1	chr6	60993835	60993839	-	1	NA	Intergenic	Intergenic	49520	NM_001163507	70945	Mm.389770	NM_027613	ENSMUSG00000054641	Mmrn1	4921530G03Rik|Emilin4|Mmrn	multimerin 1	protein-coding
mm_44862.1	chr5	34288408	34288469	-	1	NA	promoter-TSS (NM_001015039)	promoter-TSS (NM_001015039)	-114	NM_001015039	231125	Mm.113388	NM_001015039	ENSMUSG00000037224	Zfyve28	9630058O20Rik|Gm146|mKIAA1643	zinc finger, FYVE domain containing 28	protein-coding
mm_134791.1	chr16	24090060	24090100	-	1	NA	Intergenic	Intergenic	-101468	NM_009744	12053	Mm.347398	NM_009744	ENSMUSG00000022508	Bcl6	Bcl5	B cell leukemia/lymphoma 6	protein-coding
mm_171239.1	chr3	70059738	70059739	+	1	NA	Intergenic	Intergenic	52125	NM_001018031	229389	Mm.331071	NM_001018031	ENSMUSG00000027788	Otol1	Gm414	otolin 1	protein-coding
mm_123284.1	chr14	61438332	61438334	-	1	NA	intron (NM_008466, intron 1 of 16)	intron (NM_008466, intron 1 of 16)	1614	NM_008466	16648	Mm.25548	NM_008466	ENSMUSG00000021929	Kpna3	IPOA4	karyopherin (importin) alpha 3	protein-coding
mm_77701.1	chr8	126590450	126590469	-	1	NA	3' UTR (NM_001164598, exon 2 of 2)	3' UTR (NM_001164598, exon 2 of 2)	2977	NM_001164598	270110	Mm.334918	NM_001164598	ENSMUSG00000051495	Irf2bp2	E130305N23Rik|IRF-2BP2	interferon regulatory factor 2 binding protein 2	protein-coding
mm_57763.1	chr6	129233970	129233979	-	1	NA	intron (NR_040265, intron 1 of 2)	intron (NR_040265, intron 1 of 2)	4071	NR_040265	76432	Mm.261738	NR_040265	ENSMUSG00000097354	2310001H17Rik	AI646108	RIKEN cDNA 2310001H17 gene	ncRNA
mm_136198.1	chr16	89701441	89701445	-	1	NA	Intergenic	RMER17C|LTR|ERVK	116909	NM_001145887	21844	Mm.310902	NM_009384	ENSMUSG00000002489	Tiam1	AI847750|D16Ium10|D16Ium10e	T cell lymphoma invasion and metastasis 1	protein-coding
mm_79206.1	chr9	48987429	48987436	+	1	NA	intron (NM_175482, intron 1 of 23)	intron (NM_175482, intron 1 of 23)	2047	NM_175482	235323	Mm.21630	NM_175482	ENSMUSG00000032267	Usp28	9830148O20Rik|AU022237|mKIAA1515	ubiquitin specific peptidase 28	protein-coding
mm_129190.1	chr15	76350675	76350745	-	1	NA	promoter-TSS (NM_026859)	promoter-TSS (NM_026859)	400	NM_025340	106025	Mm.41463	NM_025340	ENSMUSG00000022552	Sharpin	0610041B22Rik|AW121341|RBCKL1|SIPL1|cpdm	SHANK-associated RH domain interacting protein	protein-coding
mm_66177.1	chr7	34013944	34013947	-	1	NA	promoter-TSS (NM_001276475)	promoter-TSS (NM_001276475)	-3	NM_001100464	233099	Mm.110829	NM_001100464	ENSMUSG00000066584	Scgb2b27	Abpbg27|Abpbg5|Scgb2b5	secretoglobin, family 2B, member 27	protein-coding
mm_104576.1	chr11	96953733	96953744	-	1	NA	3' UTR (NM_030220, exon 7 of 7)	3' UTR (NM_030220, exon 7 of 7)	9592	NR_003293	319371	Mm.436865	NR_003293	ENSMUSG00000078700	D030028A08Rik	-	RIKEN cDNA D030028A08 gene	ncRNA
mm_21013.1	chr2	152396611	152396629	-	1	NA	3' UTR (NM_011438, exon 1 of 1)	3' UTR (NM_011438, exon 1 of 1)	1426	NM_011438	20667	Mm.28424	NM_011438	ENSMUSG00000051817	Sox12	2010205A02Rik	SRY (sex determining region Y)-box 12	protein-coding
mm_126824.1	chr15	88854702	88854715	+	1	NA	Intergenic	Intergenic	-7486	NM_145478	223775	Mm.400129	NM_145478	ENSMUSG00000035828	Pim3	BC026639|Kid1	proviral integration site 3	protein-coding
mm_130692.1	chr15	100682833	100682848	-	1	NA	intron (NM_033612, intron 5 of 7)	(TGGGGG)n|Simple_repeat|Simple_repeat	5080	NM_033612	109901	Mm.2131	NM_033612	ENSMUSG00000023031	Cela1	1810009A17Rik|1810062B19Rik|Ela-1|Ela1|PC-TsF	chymotrypsin-like elastase family, member 1	protein-coding
mm_127560.1	chr15	102203178	102203218	+	1	NA	promoter-TSS (NM_001289691)	promoter-TSS (NM_001289691)	-447	NM_001289694	68744	Mm.352945	NM_153194	ENSMUSG00000046897	Zfp740	1110034O07Rik|AW548228|Znf740	zinc finger protein 740	protein-coding
mm_152552.1	chr19	11484515	11484519	-	1	NA	Intergenic	Intergenic	-7521	NM_001164202	666926	Mm.486382	NM_001164202	ENSMUSG00000058470	Gm8369	EG666926	predicted gene 8369	protein-coding
mm_72574.1	chr8	84148305	84148321	+	1	NA	promoter-TSS (NM_145970)	promoter-TSS (NM_145970)	275	NM_029045	74666	Mm.33625	NM_029045	ENSMUSG00000008129	4930432K21Rik	-	RIKEN cDNA 4930432K21 gene	protein-coding
mm_31709.1	chr4	62619683	62619719	+	1	NA	promoter-TSS (NM_001081650)	promoter-TSS (NM_001081650)	29	NM_134257	50780	Mm.286753	NM_019492	ENSMUSG00000059810	Rgs3	4930506N09Rik|C2PA-RGS3|C2pa|PDZ-RGS3|RGS3S	regulator of G-protein signaling 3	protein-coding
mm_111609.1	chr12	102400169	102400213	-	1	NA	exon (NM_011175, exon 9 of 14)	exon (NM_011175, exon 9 of 14)	39622	NM_011175	19141	Mm.17185	NM_011175	ENSMUSG00000021190	Lgmn	AEP|AI746452|AU022324|Prsc1	legumain	protein-coding
mm_151992.1	chr19	5856748	5856775	-	1	NA	exon (NM_026169, exon 10 of 11)	exon (NM_026169, exon 10 of 11)	-11281	NR_003513	66961	Mm.281895	NR_003513	ENSMUSG00000092274	Neat1	2310043N10Rik|VINC	nuclear paraspeckle assembly transcript 1 (non-protein coding)	ncRNA
mm_2191.1	chr1	89070476	89070489	+	1	NA	promoter-TSS (NM_133816)	promoter-TSS (NM_133816)	20	NM_133816	98402	Mm.170983	NM_133816	ENSMUSG00000036206	Sh3bp4	AI594717|AW227605|BOG25	SH3-domain binding protein 4	protein-coding
mm_137317.1	chr17	24886879	24886898	+	1	NA	promoter-TSS (NM_011956)	promoter-TSS (NM_011956)	214	NM_001163751	79043	Mm.274794	NM_027141	ENSMUSG00000024160	Spsb3	2310012N15Rik|3300001M01Rik|SSB3|Tce1|mKIAA4204	splA/ryanodine receptor domain and SOCS box containing 3	protein-coding
mm_155295.1	chrX	61183940	61183950	+	1	NA	3' UTR (NM_001166658, exon 1 of 1)	3' UTR (NM_001166658, exon 1 of 1)	1613	NM_001166658	631990	Mm.401324	NM_001166658	ENSMUSG00000090546	Cdr1	100039759|Cdr|Cdr34|EG631990|Gm2409|Gm7077	cerebellar degeneration related antigen 1	protein-coding
mm_144118.1	chr18	4563124	4563130	+	1	NA	Intergenic	Intergenic	-71802	NM_001081963	240185	Mm.33179	NM_001081963	ENSMUSG00000033960	9430020K01Rik	1110056P05Rik|Gm328|Jcad|mKIAA1462	RIKEN cDNA 9430020K01 gene	protein-coding
mm_71727.1	chr8	61976991	61977002	+	1	NA	intron (NM_001293783, intron 17 of 37)	intron (NM_001293783, intron 17 of 37)	48909	NM_001293783	234311	Mm.275233	NM_144928	ENSMUSG00000037921	Ddx60	9830118M07	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	protein-coding
mm_71320.1	chr8	44935367	44935375	+	1	NA	Intergenic	CpG	-14837	NM_001081286	14107	Mm.27365	NM_001081286	ENSMUSG00000070047	Fat1	2310038E12Rik|AU023433|Fath|mFat1	FAT atypical cadherin 1	protein-coding
mm_25272.1	chr3	104865063	104865099	+	1	NA	promoter-TSS (NM_009797)	promoter-TSS (NM_009797)	575	NM_153091	229681	Mm.206379	NM_153091	ENSMUSG00000045576	St7l	St7r	suppression of tumorigenicity 7-like	protein-coding
mm_113185.1	chr13	24937145	24937166	+	1	NA	promoter-TSS (NR_102323)	promoter-TSS (NR_102323)	-246	NR_102323	493800	Mm.458692	NR_102323		9330162012Rik	-	cDNA RIKEN 9330162012 gene	ncRNA
mm_138470.1	chr17	35190357	35190377	+	1	NA	Intergenic	Intergenic	-1927	NM_010734	16988	Mm.19379	NM_010734	ENSMUSG00000073412	Lst1	B144	leukocyte specific transcript 1	protein-coding
mm_22072.1	chr2	168741977	168741993	-	1	NA	promoter-TSS (NM_015731)	promoter-TSS (NM_015731)	151	NM_001289446	11981	Mm.330819	NM_015731	ENSMUSG00000027546	Atp9a	IIa	ATPase, class II, type 9A	protein-coding
mm_26370.1	chr3	142560606	142560616	+	1	NA	5' UTR (NM_001289493, exon 1 of 11)	5' UTR (NM_001289493, exon 1 of 11)	115	NM_001289493	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_171142.1	chr3	151678972	151678976	+	1	NA	Intergenic	L1Md_T|LINE|L1	70985	NM_133871	99899	Mm.30756	NM_133871	ENSMUSG00000028037	Ifi44	A430056A10Rik|AW261460|MTAP44|p44	interferon-induced protein 44	protein-coding
mm_51173.1	chr6	70726637	70726647	+	1	NA	Intergenic	Intergenic	65533	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_162449.1	chr1	121307364	121307364	+	1	NA	intron (NM_001271532, intron 2 of 4)	intron (NM_001271532, intron 2 of 4)	20314	NM_001271531	72999	Mm.27136	NM_133748	ENSMUSG00000003721	Insig2	2900053I11Rik|C730043J18Rik|Insig-2	insulin induced gene 2	protein-coding
mm_89917.1	chr10	111186691	111186715	+	1	NA	intron (NM_175489, intron 1 of 23)	intron (NM_175489, intron 1 of 23)	21901	NM_175489	237542	Mm.220204	NM_175489	ENSMUSG00000020189	Osbpl8	AA536976|AA536995|C730029P18Rik|D330025H14Rik|ORP-8	oxysterol binding protein-like 8	protein-coding
mm_90135.1	chr10	117792956	117793004	+	1	NA	promoter-TSS (NM_134010)	promoter-TSS (NM_134010)	-275	NM_134010	103468	Mm.12568	NM_134010	ENSMUSG00000052798	Nup107	AW541137|C76801	nucleoporin 107	protein-coding
mm_28917.1	chr3	98856067	98856081	-	1	NA	exon (NM_001304800, exon 3 of 4)	exon (NM_001304800, exon 3 of 4)	3720	NM_001304800	15492	Mm.140811	NM_008293	ENSMUSG00000027871	Hsd3b1	3-beta-HSD I|D3Ertd383e	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1	protein-coding
mm_96229.1	chr11	62550571	62550600	+	1	NA	promoter-TSS (NR_002875).2	promoter-TSS (NR_002875).2	-586	NM_011664	22187	Mm.371592	NM_011664	ENSMUSG00000019505	Ubb	AL033289|Rps27a|Uba52|Ubb2|Ubc	ubiquitin B	protein-coding
mm_45473.1	chr5	69542590	69542620	-	1	NA	promoter-TSS (NM_023784)	promoter-TSS (NM_023784)	42	NM_023784	75581	Mm.154776	NM_023784	ENSMUSG00000029158	Yipf7	2310016N21Rik|Yip1b	Yip1 domain family, member 7	protein-coding
mm_21569.1	chr2	164236149	164236163	-	1	NA	3' UTR (NM_017390, exon 3 of 3)	3' UTR (NM_017390, exon 3 of 3)	2185	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_36503.1	chr4	83467210	83467218	-	1	NA	intron (NM_001347143, intron 7 of 10)	(A)n|Simple_repeat|Simple_repeat	19234	NM_001290527	101739	Mm.105331	NM_133948	ENSMUSG00000028484	Psip1	AA408851|AU015605|Dfs70|Ledgfa|Ledgfb|Psip2	PC4 and SFRS1 interacting protein 1	protein-coding
mm_152407.1	chr19	10604317	10604337	-	1	NA	promoter-TSS (NM_145496)	promoter-TSS (NM_145496)	-69	NM_145496	225913	Mm.374868	NM_145496	ENSMUSG00000034371	Tkfc	BC021917|Dak	triokinase, FMN cyclase	protein-coding
mm_159890.1	chr6	28831985	28831985	-	1	NA	promoter-TSS (NM_138682)	promoter-TSS (NM_138682)	-238	NM_138682	192198	Mm.443660	NM_138682	ENSMUSG00000049939	Lrrc4	MBAG1|NGL-2|NGL2|NLG-2|Nag14	leucine rich repeat containing 4	protein-coding
mm_32161.1	chr4	99983913	99983922	+	1	NA	intron (NM_028132, intron 9 of 10)	intron (NM_028132, intron 9 of 10)	54466	NM_028132	72157	Mm.217764	NM_028132	ENSMUSG00000025791	Pgm2	2610020G18Rik|AA407108|AI098105|Pgm-2|Pgm1	phosphoglucomutase 2	protein-coding
mm_59879.1	chr7	30291804	30291807	+	1	NA	promoter-TSS (NM_001081114)	promoter-TSS (NM_001081114)	52	NM_001081114	76686	Mm.159258	NM_001081114	ENSMUSG00000013921	Clip3	1500005P14Rik|AI844915|Clipr-59	CAP-GLY domain containing linker protein 3	protein-coding
mm_19603.1	chr2	102451761	102451774	-	1	NA	promoter-TSS (NM_010218)	promoter-TSS (NM_010218)	25	NM_010218	14221	Mm.29730	NM_010218	ENSMUSG00000075012	Fjx1	-	four jointed box 1 (Drosophila)	protein-coding
mm_36815.1	chr4	104625459	104625479	-	1	NA	intron (NM_010014, intron 4 of 6)	intron (NM_010014, intron 4 of 6)	-140848	NM_133882	110382	Mm.87072	NM_133882	ENSMUSG00000029656	C8b	4930439B20Rik|AI595927	complement component 8, beta polypeptide	protein-coding
mm_148460.1	chr19	4047064	4047070	+	1	NA	Intergenic	Intergenic	-4846	NM_181796	14869	Mm.441542	NM_181796	ENSMUSG00000038155	Gstp2	GSTpiA|Gst-3|Gst3	glutathione S-transferase, pi 2	protein-coding
mm_643.1	chr1	40404960	40404974	+	1	NA	Intergenic	Intergenic	-24603	NM_001294171	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_130572.1	chr15	99458143	99458156	-	1	NA	promoter-TSS (NM_001001884)	promoter-TSS (NM_001001884)	-401	NM_001001884	380969	Mm.22915	NM_001001884	ENSMUSG00000023009	Nckap5l	C230021P08Rik|Cep169	NCK-associated protein 5-like	protein-coding
mm_170367.1	chr1	85327312	85327329	-	1	NA	Intergenic	Intergenic	-56754	NM_001037909	620078	Mm.386456	NM_175219	ENSMUSG00000052477	C130026I21Rik	4930565N07Rik|OTTMUSG00000029174	RIKEN cDNA C130026I21 gene	protein-coding
mm_37048.1	chr4	116017657	116017764	-	1	NA	5' UTR (NM_010173, exon 1 of 15)	5' UTR (NM_010173, exon 1 of 15)	192	NM_010173	14073	Mm.256025	NM_010173	ENSMUSG00000034171	Faah	AW412498	fatty acid amide hydrolase	protein-coding
mm_100972.1	chr11	6720017	6720063	-	1	NA	promoter-TSS (NR_046025)	promoter-TSS (NR_046025)	-3	NR_046025	626419	Mm.390334	NR_046025	ENSMUSG00000086808	Gm11981	OTTMUSG00000005129	predicted gene 11981	ncRNA
mm_26707.1	chr3	157947048	157947066	+	1	NA	promoter-TSS (NM_001013806)	promoter-TSS (NM_001013806)	-409	NM_001013806	433667	Mm.265806	NM_001013806	ENSMUSG00000039988	Ankrd13c	AI505652|AU022220	ankyrin repeat domain 13c	protein-coding
mm_152785.1	chr19	21446362	21446366	-	1	NA	intron (NM_010266, intron 1 of 13)	intron (NM_010266, intron 1 of 13)	26297	NM_010266	14544	Mm.45054	NM_010266	ENSMUSG00000058624	Gda	AU015411|AW047581|GAH	guanine deaminase	protein-coding
mm_23737.1	chr3	69155024	69155032	+	1	NA	intron (NR_126533, intron 2 of 2)	B1_Mur2|SINE|Alu	23795	NR_126533	381452	Mm.331067	NM_001243000	ENSMUSG00000094763	Gm1647	-	predicted gene 1647	ncRNA
mm_91788.1	chr10	53348630	53348638	-	1	NA	exon (NM_001204983, exon 3 of 13)	exon (NM_001204983, exon 3 of 13)	10948	NM_001141927	18821	Mm.34145	NM_023129	ENSMUSG00000038583	Pln	Plb	phospholamban	protein-coding
mm_68484.1	chr7	110982444	110982468	-	1	NA	promoter-TSS (NM_194464)	promoter-TSS (NM_194464)	5	NM_194464	17540	Mm.250023	NM_010826	ENSMUSG00000005611	Mrvi1	BB115629|Irag|Ris1	MRV integration site 1	protein-coding
mm_91836.1	chr10	57516961	57516973	-	1	NA	3' UTR (NM_019760, exon 9 of 9)	3' UTR (NM_019760, exon 9 of 9)	15562	NM_019760	56442	Mm.29344	NM_019760	ENSMUSG00000019877	Serinc1	1500011D18Rik|AI315070|AIGP-2|TMS-2|Tde1l|Tde2|Tms2|mKIAA1253	serine incorporator 1	protein-coding
mm_31032.1	chr4	40948402	40948412	+	1	NA	promoter-TSS (NM_001171739)	promoter-TSS (NM_001171739)	-113	NM_001171739	12017	Mm.688	NM_009736	ENSMUSG00000028416	Bag1	BAG-1|Rap46	BCL2-associated athanogene 1	protein-coding
mm_157864.1	chrX	75130915	75130994	-	1	NA	promoter-TSS (NM_008621)	promoter-TSS (NM_008621)	62	NM_008621	17524	Mm.391267	NM_008621	ENSMUSG00000031402	Mpp1	55kDa|C130070C03Rik|p55	membrane protein, palmitoylated	protein-coding
mm_171962.1	chr5	84583690	84583695	-	1	NA	Intergenic	RLTR9D|LTR|ERVK	-166310	NM_007937	13839	Mm.137991	NM_007937	ENSMUSG00000029245	Epha5	AI854630|AW125296|Cek7|Ehk1|Els1|Hek7|Rek7|bsk	Eph receptor A5	protein-coding
mm_124233.1	chr14	101463083	101463110	-	1	NA	intron (NM_001081278, intron 11 of 18)	intron (NM_001081278, intron 11 of 18)	146095	NM_001081278	210789	Mm.320639	NM_173380	ENSMUSG00000033083	Tbc1d4	5930406J04Rik|A930035N22|AV295684|As160	TBC1 domain family, member 4	protein-coding
mm_96109.1	chr11	60553747	60553777	+	1	NA	exon (NM_172943, exon 3 of 4)	exon (NM_172943, exon 3 of 4)	16079	NM_172943	268420	Mm.262056	NM_172943	ENSMUSG00000042650	Alkbh5	AW050020|AW215868|Abh5|E130207K11|Ofoxd	alkB homolog 5, RNA demethylase	protein-coding
mm_84752.1	chr9	75559584	75559594	-	1	NA	promoter-TSS (NM_016963)	promoter-TSS (NM_016963)	68	NM_016963	50875	Mm.38445	NM_016963	ENSMUSG00000058587	Tmod3	U-Tmod|UTMOD	tropomodulin 3	protein-coding
mm_103953.1	chr11	84069125	84069135	-	1	NA	promoter-TSS (NM_019819)	promoter-TSS (NM_019819)	-773	NM_019819	56405	Mm.240885	NM_019819	ENSMUSG00000018648	Dusp14	1110014C10Rik|2310042C07Rik|D11Ertd395e|MKP-L|Mkp6	dual specificity phosphatase 14	protein-coding
mm_14114.1	chr2	125866225	125866282	+	1	NA	promoter-TSS (NM_001291002)	promoter-TSS (NM_001291002)	30	NM_001291002	69976	Mm.20216	NM_175154	ENSMUSG00000027207	Galk2	2810017M24Rik|AI327030|Gk2	galactokinase 2	protein-coding
mm_80865.1	chr9	98509664	98509683	+	1	NA	TTS (NM_009034)	TTS (NM_009034)	19136	NM_009034	19660	Mm.12825	NM_009034	ENSMUSG00000032454	Rbp2	Crbp-2|CrbpII|Rbp-2	retinol binding protein 2, cellular	protein-coding
mm_58193.1	chr6	143075832	143075846	-	1	NA	intron (NM_001109688, intron 7 of 24)	PB1D11|SINE|Alu	24313	NM_001286578	74741	Mm.130260	NM_029081	ENSMUSG00000030279	C2cd5	5730419I09Rik|C030008B15Rik|CDP138	C2 calcium-dependent domain containing 5	protein-coding
mm_98177.1	chr11	87756926	87756929	+	1	NA	promoter-TSS (NR_106176)	promoter-TSS (NR_106176)	28	NR_106176	102466883		NR_106176	ENSMUSG00000065420	Mir142b	Gm27750|mmu-mir-142b	microRNA 142b	ncRNA
mm_117935.1	chr13	99434481	99434542	-	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-21685	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_73237.1	chr8	104142843	104142862	+	1	NA	exon (NM_009868, exon 12 of 12)	exon (NM_009868, exon 12 of 12)	-27661	NM_001141924	65115	Mm.41849	NM_001141922	ENSMUSG00000031872	Bean1	Bean	brain expressed, associated with Nedd4, 1	protein-coding
mm_88000.1	chr10	67002865	67002894	+	1	NA	Intergenic	Intergenic	-2196	NR_110511	102634101	Mm.445258	NR_110511		Gm31763	-	predicted gene, 31763	ncRNA
mm_129951.1	chr15	85036924	85036944	-	1	NA	promoter-TSS (NM_133750)	promoter-TSS (NM_133750)	-128	NM_133750	73225	Mm.247535	NM_133750	ENSMUSG00000022434	Fam118a	-	family with sequence similarity 118, member A	protein-coding
mm_129379.1	chr15	78173927	78173947	-	1	NA	5' UTR (NM_025931, exon 1 of 7)	5' UTR (NM_025931, exon 1 of 7)	171	NM_025931	67042	Mm.30191	NM_025931	ENSMUSG00000016637	Ift27	2600013G09Rik|Rabl4	intraflagellar transport 27	protein-coding
mm_140381.1	chr17	87107686	87107702	+	1	NA	promoter-TSS (NM_019654)	promoter-TSS (NM_019654)	15	NM_019654	56468	Mm.126885	NM_019654	ENSMUSG00000037104	Socs5	1810018L08Rik|Cish5|mKIAA0671	suppressor of cytokine signaling 5	protein-coding
mm_59932.1	chr7	30423608	30423610	+	1	NA	intron (NM_172142, intron 1 of 10)	intron (NM_172142, intron 1 of 10)	305	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_22278.1	chr2	179963874	179963884	-	1	NA	intron (NM_001081092, intron 1 of 14)	intron (NM_001081092, intron 1 of 14)	12767	NM_001081092	228980	Mm.235542	NM_001081092	ENSMUSG00000039117	Taf4	135kDa|AI450312|TAFII130|TAFII135|Taf2c1|Taf4a	TATA-box binding protein associated factor 4	protein-coding
mm_86919.1	chr10	23851496	23851507	+	1	NA	promoter-TSS (NM_011979)	promoter-TSS (NM_011979)	39	NM_011979	26464	Mm.27334	NM_011979	ENSMUSG00000020010	Vnn3	-	vanin 3	protein-coding
mm_108414.1	chr12	81928157	81928172	+	1	NA	intron (NM_018814, intron 6 of 35)	intron (NM_018814, intron 6 of 35)	68134	NM_018814	54604	Mm.86584	NM_018814	ENSMUSG00000021140	Pcnx	2900024E21Rik|3526401J03Rik|AF096286|AI327143|AI413187|Pcnx1|Pcnxl1	pecanex homolog (Drosophila)	protein-coding
mm_42178.1	chr5	112261899	112261907	+	1	NA	intron (NM_023695, intron 3 of 5)	(TCCA)n|Simple_repeat|Simple_repeat	6083	NM_001312893	12960	Mm.29488	NM_023695	ENSMUSG00000029343	Crybb1	3110006K12Rik|BB1CRY	crystallin, beta B1	protein-coding
mm_21785.1	chr2	164854974	164855061	-	1	NA	exon (NM_011125, exon 4 of 16)	exon (NM_011125, exon 4 of 16)	2691	NM_011125	18830	Mm.6105	NM_011125	ENSMUSG00000017754	Pltp	Bpife|OD107	phospholipid transfer protein	protein-coding
mm_17715.1	chr2	32386085	32386093	-	1	NA	intron (NM_008491, intron 2 of 5)	intron (NM_008491, intron 2 of 5)	1650	NM_008491	16819	Mm.9537	NM_008491	ENSMUSG00000026822	Lcn2	24p3|AW212229|NRL|Sip24	lipocalin 2	protein-coding
mm_105549.1	chr11	106382555	106382612	-	1	NA	5' UTR (NM_010494, exon 1 of 4)	5' UTR (NM_010494, exon 1 of 4)	198	NM_010494	15896	Mm.394	NM_010494	ENSMUSG00000001029	Icam2	CD102|Icam-2|Ly-60	intercellular adhesion molecule 2	protein-coding
mm_50635.1	chr6	51329796	51329804	+	1	NA	Intergenic	MER20|DNA|hAT-Charlie	-49910	NR_110455	625167	Mm.389772	NR_110455	ENSMUSG00000107660	Gm6559	EG625167	predicted gene 6559	ncRNA
mm_21280.1	chr2	156943424	156943426	-	1	NA	intron (NM_013865, intron 8 of 15)	intron (NM_013865, intron 8 of 15)	48686	NM_013865	29812	Mm.279256	NM_013865	ENSMUSG00000027634	Ndrg3	4833415O14Rik|AI747193|Ndr3	N-myc downstream regulated gene 3	protein-coding
mm_49167.1	chr6	14608424	14608432	+	1	NA	Intergenic	LTR40a|LTR|ERVL	146846	NM_080464	140491	Mm.209429	NM_080464	ENSMUSG00000042717	Ppp1r3a	GM|RG1|RGL	protein phosphatase 1, regulatory (inhibitor) subunit 3A	protein-coding
mm_47419.1	chr5	123140712	123140731	-	1	NA	Intergenic	Intergenic	-1472	NM_001040398	208043	Mm.250391	NM_177581	ENSMUSG00000038384	Setd1b	AA516740|BC035291|KMT2G|mKIAA1076	SET domain containing 1B	protein-coding
mm_77804.1	chr9	3035720	3035737	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	3015	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_126352.1	chr15	79927840	79927894	+	1	NA	intron (NM_144811, intron 2 of 6)	CpG	4779	NM_144811	52609	Mm.323442	NM_144811	ENSMUSG00000053411	Cbx7	1600014J01Rik|AI851678|D15Ertd417e	chromobox 7	protein-coding
mm_128119.1	chr15	30173492	30173496	-	1	NA	intron (NM_008729, intron 1 of 22)	CpG	901	NM_008729	18163	Mm.321648	NM_008729	ENSMUSG00000022240	Ctnnd2	Catnd2|Nprap|neurojugin	catenin (cadherin associated protein), delta 2	protein-coding
mm_38818.1	chr4	148626732	148626746	-	1	NA	non-coding (NR_131120, exon 1 of 8)	non-coding (NR_131120, exon 1 of 8)	257	NR_027864	230908	Mm.22453	NM_145556	ENSMUSG00000041459	Tardbp	1190002A23Rik|C85084|TDP-43|Tdp43	TAR DNA binding protein	protein-coding
mm_22054.1	chr2	168515262	168515273	-	1	NA	intron (NM_001291174, intron 6 of 10)	ID_B1|SINE|B4	75098	NM_001291178	18019	Mm.116802	NM_010899	ENSMUSG00000027544	Nfatc2	AI607462|NF-ATc2|NF-ATp|NFAT1|NFAT1-D|Nfatp	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 2	protein-coding
mm_79623.1	chr9	59288844	59288844	+	1	NA	Intergenic	Intergenic	-2728	NM_028121	72141	Mm.22456	NM_028121	ENSMUSG00000025236	Adpgk	2610017G09Rik|Adp-gk|C77577	ADP-dependent glucokinase	protein-coding
mm_74771.1	chr8	21327016	21327020	-	1	NA	promoter-TSS (NM_007844)	promoter-TSS (NM_007844)	2	NM_007844	13218	Mm.304264	NM_007844	ENSMUSG00000074437	Defa29	2010300L12Rik|2010319H24Rik|CRS1C|CRS1C-2|CRS1C-4|CRS1C-5|Defa-rs1|Defcr-rs1	defensin, alpha, 29	protein-coding
mm_109246.1	chr12	109453195	109453212	+	1	NA	promoter-TSS (NM_010052)	promoter-TSS (NM_010052)	-252	NM_001190704	13386	Mm.157069	NM_010052	ENSMUSG00000040856	Dlk1	AW742678|DLK-1|DlkI|FA1|Ly107|Peg9|SCP1|ZOG|pG2|pref-1	delta-like 1 homolog (Drosophila)	protein-coding
mm_74893.1	chr8	25104792	25104806	-	1	NA	Intergenic	Intergenic	-2988	NM_031257	83436	Mm.261122	NM_031257	ENSMUSG00000031557	Plekha2	6430512N22Rik|AI851530|AU041791|TAPP2|W91773	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 2	protein-coding
mm_143287.1	chr17	65864720	65864735	-	1	NA	exon (NM_001198949, exon 3 of 10)	exon (NM_001198949, exon 3 of 10)	20196	NM_001198949	19765	Mm.17009	NM_009067	ENSMUSG00000024096	Ralbp1	RLIP76|Rip1	ralA binding protein 1	protein-coding
mm_62586.1	chr7	105569380	105569393	+	1	NA	promoter-TSS (NM_001253887)	promoter-TSS (NM_001253887)	-68	NM_001253887	11785	Mm.38469	NM_009685	ENSMUSG00000037032	Apbb1	Fe65|Rir	amyloid beta (A4) precursor protein-binding, family B, member 1	protein-coding
mm_98916.1	chr11	98248316	98248321	+	1	NA	intron (NM_001109628, intron 13 of 13)	B1_Mur4|SINE|Alu	-14288	NR_039579	100628613		NR_039579	ENSMUSG00000093176	Mir5119	mmu-mir-5119|mu-mir-5119	microRNA 5119	ncRNA
mm_158496.1	chrX	142366509	142366512	-	1	NA	intron (NM_019477, intron 1 of 15)	B1_Mur3|SINE|Alu	24025	NM_001033600	50790	Mm.391337	NM_019477	ENSMUSG00000031278	Acsl4	9430020A05Rik|ACS4|AU018108|Facl4|Lacs4	acyl-CoA synthetase long-chain family member 4	protein-coding
mm_31630.1	chr4	59287399	59287414	+	1	NA	Intergenic	Intergenic	27355	NR_105031	101055769	Mm.421401	NR_105031		Gm12596	OTTMUSG00000007649	predicted gene 12596	ncRNA
mm_65568.1	chr7	27178913	27178923	-	1	NA	promoter-TSS (NM_029391)	promoter-TSS (NM_029391)	-35	NM_029391	19342	Mm.482114	NM_029391	ENSMUSG00000053291	Rab4b	1500031G17Rik	RAB4B, member RAS oncogene family	protein-coding
mm_55617.1	chr6	72140484	72140509	-	1	NA	intron (NM_001035228, intron 3 of 6)	intron (NM_001035228, intron 3 of 6)	-17299	NR_045165	71265	Mm.442035	NR_045163	ENSMUSG00000108709	4933431G14Rik	4930565C19Rik	RIKEN cDNA 4933431G14 gene	ncRNA
mm_94217.1	chr11	3193491	3193510	+	1	NA	promoter-TSS (NM_030207)	promoter-TSS (NM_030207)	-37	NM_030207	78887	Mm.394071	NM_030207	ENSMUSG00000023764	Sfi1	-	Sfi1 homolog, spindle assembly associated (yeast)	protein-coding
mm_164788.1	chr18	12183865	12183874	+	1	NA	intron (NM_029623, intron 10 of 19)	intron (NM_029623, intron 10 of 19)	15139	NM_029623	76482	Mm.196596	NM_029623	ENSMUSG00000024410	3110002H16Rik	2400010D15Rik|Mic-1|Mic1	RIKEN cDNA 3110002H16 gene	protein-coding
mm_81076.1	chr9	106223523	106223544	+	1	NA	exon (NM_031178, exon 2 of 2)	exon (NM_031178, exon 2 of 2)	935	NM_031178	81897	Mm.44889	NM_031178	ENSMUSG00000045322	Tlr9	-	toll-like receptor 9	protein-coding
mm_128459.1	chr15	50795312	50795320	-	1	NA	intron (NM_001310485, intron 5 of 7)	intron (NM_001310485, intron 5 of 7)	93733	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_160572.1	chr9	57628680	57628680	-	1	NA	exon (NM_007783, exon 9 of 13)	exon (NM_007783, exon 9 of 13)	-7906	NM_199222	235416	Mm.295630	NM_199222	ENSMUSG00000056271	Lman1l	BC020188|slamp	lectin, mannose-binding 1 like	protein-coding
mm_78240.1	chr9	21625984	21625994	+	1	NA	intron (NM_001174079, intron 1 of 33)	intron (NM_001174079, intron 1 of 33)	9820	NM_001174078	20586	Mm.286593	NM_011417	ENSMUSG00000032187	Smarca4	Brg1|HP1-BP72|SNF2beta|SW1/SNF|b2b508.1Clo|b2b692Clo	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	protein-coding
mm_125474.1	chr15	54410809	54410821	+	1	NA	promoter-TSS (NM_173422)	promoter-TSS (NM_173422)	41	NM_173422	239447	Mm.82400	NM_173422	ENSMUSG00000038591	Colec10	CL-L1	collectin sub-family member 10	protein-coding
mm_103732.1	chr11	79962375	79962398	-	1	NA	promoter-TSS (NM_144826)	promoter-TSS (NM_144826)	1	NM_144826	216987	Mm.274961	NM_144826	ENSMUSG00000035575	Utp6	4732497O03Rik|HCA66	UTP6 small subunit processome component	protein-coding
mm_79780.1	chr9	62858086	62858138	+	1	NA	promoter-TSS (NM_138304)	promoter-TSS (NM_138304)	8	NM_138304	75600	Mm.440576	NM_138304	ENSMUSG00000032246	Calml4	2010002G05Rik	calmodulin-like 4	protein-coding
mm_102381.1	chr11	58889714	58889726	-	1	NA	3' UTR (NM_011758, exon 5 of 5)	3' UTR (NM_011758, exon 5 of 5)	14505	NM_011758	22698	Mm.127646	NM_011758	ENSMUSG00000037001	Zfp39	CTfin33|Zfp-39	zinc finger protein 39	protein-coding
mm_132009.1	chr16	25842559	25842561	+	1	NA	intron (NM_001127259, intron 4 of 13)	intron (NM_001127259, intron 4 of 13)	40644	NM_001127264	22061	Mm.20894	NM_011641	ENSMUSG00000022510	Trp63	AI462811|Ket|P51/P63|P63|P73l|Tp63|Trp53rp1	transformation related protein 63	protein-coding
mm_130685.1	chr15	100681885	100681919	-	1	NA	intron (NM_033612, intron 5 of 7)	B1_Mur2|SINE|Alu	6018	NM_033612	109901	Mm.2131	NM_033612	ENSMUSG00000023031	Cela1	1810009A17Rik|1810062B19Rik|Ela-1|Ela1|PC-TsF	chymotrypsin-like elastase family, member 1	protein-coding
mm_113454.1	chr13	35853557	35853568	+	1	NA	intron (NM_001123386, intron 2 of 6)	RLTR12E|LTR|ERVK	52785	NM_145938	208366	Mm.35545	NM_145938	ENSMUSG00000021418	Rpp40	D8Bwg1265e|Rnasep1	ribonuclease P 40 subunit	protein-coding
mm_80414.1	chr9	77784654	77784656	+	1	NA	intron (NM_010295, intron 6 of 15)	intron (NM_010295, intron 6 of 15)	30120	NM_010295	14629	Mm.89888	NM_010295	ENSMUSG00000032350	Gclc	D9Wsu168e|GLCL-H|Ggcs-hs|Glclc	glutamate-cysteine ligase, catalytic subunit	protein-coding
mm_50442.1	chr6	48872944	48872954	+	1	NA	Intergenic	Intergenic	-22306	NM_029638	76507	Mm.213898	NM_029638	ENSMUSG00000029811	Aoc1	1600012D06Rik|Abp1|DAO	amine oxidase, copper-containing 1	protein-coding
mm_108678.1	chr12	86680010	86680036	+	1	NA	exon (NM_177354, exon 1 of 7)	exon (NM_177354, exon 1 of 7)	1323	NM_177354	238328	Mm.216101	NM_177354	ENSMUSG00000021256	Vash1	AI834978|D930046M13Rik|G630009D10Rik	vasohibin 1	protein-coding
mm_110420.1	chr12	46818109	46818129	-	1	NA	intron (NM_021361, intron 1 of 4)	intron (NM_021361, intron 1 of 4)	656	NM_021361	664883	Mm.247195	NM_021361	ENSMUSG00000021047	Nova1	9430099M15Rik|G630039L02|Nova-1	neuro-oncological ventral antigen 1	protein-coding
mm_20697.1	chr2	132880848	132880907	-	1	NA	promoter-TSS (NM_177303)	promoter-TSS (NM_177303)	-15	NM_177303	320974	Mm.357342	NM_177303	ENSMUSG00000043110	Lrrn4	B430119L13Rik|Nlrr4	leucine rich repeat neuronal 4	protein-coding
mm_165700.1	chr3	95137924	95137946	+	1	NA	exon (NM_153121, exon 2 of 3)	exon (NM_153121, exon 2 of 3)	1251	NR_106201	102466888		NR_106201	ENSMUSG00000098931	Mir8099-2	Gm27692|mmu-mir-8099-2	microRNA 8099-2	ncRNA
mm_80538.1	chr9	80308195	80308197	+	1	NA	3' UTR (NM_001039546, exon 33 of 33)	3' UTR (NM_001039546, exon 33 of 33)	143162	NM_001039546	17920	Mm.4040	NM_008662	ENSMUSG00000033577	Myo6	BC029719|Tlc|sv	myosin VI	protein-coding
mm_30074.1	chr3	137981524	137981542	-	1	NA	promoter-TSS (NM_001310753)	promoter-TSS (NM_001310753)	16	NM_011932	26377	Mm.254835	NM_011932	ENSMUSG00000028159	Dapp1	Bam32	dual adaptor for phosphotyrosine and 3-phosphoinositides 1	protein-coding
mm_114467.1	chr13	67779684	67779768	+	1	NA	promoter-TSS (NM_028402)	promoter-TSS (NM_028402)	33	NM_028402	72958	Mm.53849	NM_028402	ENSMUSG00000090659	Zfp493	2900054J07Rik|Rslcan12	zinc finger protein 493	protein-coding
mm_98873.1	chr11	97799662	97799709	+	1	NA	promoter-TSS (NM_010688)	promoter-TSS (NM_010688)	13	NM_010688	16796	Mm.271967	NM_010688	ENSMUSG00000038366	Lasp1	AA408629|Def-4|SH3P6|Tg(Col1a1-lacZ)1Ngma	LIM and SH3 protein 1	protein-coding
mm_145346.1	chr18	56471050	56471065	+	1	NA	intron (NM_026240, intron 2 of 13)	intron (NM_026240, intron 2 of 13)	38925	NM_026240	107022	Mm.24356	NM_026240	ENSMUSG00000001700	Gramd3	9030613F08Rik|9130427A09Rik|AW061306|NS3TP2	GRAM domain containing 3	protein-coding
mm_146386.1	chr18	82692552	82692567	+	1	NA	intron (NM_177832, intron 1 of 29)	C-rich|Low_complexity|Low_complexity	175	NM_177832	329002	Mm.34438	NM_177832	ENSMUSG00000041258	Zfp236	AI447957|Gm335	zinc finger protein 236	protein-coding
mm_129914.1	chr15	84183059	84183074	-	1	NA	intron (NM_054088, intron 7 of 7)	intron (NM_054088, intron 7 of 7)	-9167	NM_178614	68653	Mm.290725	NM_178614	ENSMUSG00000022437	Samm50	1110030L07Rik	SAMM50 sorting and assembly machinery component	protein-coding
mm_90800.1	chr10	7663246	7663309	-	1	NA	promoter-TSS (NR_030698)	promoter-TSS (NR_030698)	-94	NR_030698	320642	Mm.398806	NR_030698		A630066F11Rik	-	RIKEN cDNA A630066F11 gene	ncRNA
mm_148740.1	chr19	5952630	5952640	+	1	NA	intron (NM_001164057, intron 7 of 17)	intron (NM_001164057, intron 7 of 17)	11571	NM_001164057	18969	Mm.209931	NM_008893	ENSMUSG00000024833	Pola2	AI573378	polymerase (DNA directed), alpha 2	protein-coding
mm_118392.1	chr13	118658738	118658757	-	1	NA	promoter-TSS (NR_131153)	promoter-TSS (NR_131153)	-4	NR_131153	100038690	Mm.384983	NR_131153		Gm10732	ENSMUSG00000074638	predicted gene 10732	ncRNA
mm_164930.1	chr18	81117806	81117820	+	1	NA	Intergenic	Intergenic	-131235	NM_178280	20689	Mm.215917	NM_178280	ENSMUSG00000024565	Sall3	B130022O04Rik|Msal|Msal-1|Sal|Salt|Spalt	sal-like 3 (Drosophila)	protein-coding
mm_80054.1	chr9	69340226	69340235	+	1	NA	intron (NM_001289916, intron 1 of 9)	intron (NM_001289916, intron 1 of 9)	24017	NR_136934	102642202	Mm.415363	NR_136934	ENSMUSG00000086648	Gm15511	OTTMUSG00000023029	predicted gene 15511	ncRNA
mm_148095.1	chr18	73816504	73816543	-	1	NA	Intergenic	Intergenic	-1131	NM_145494	107029	Mm.36817	NM_145494	ENSMUSG00000024556	Me2	AW120568|D030040L20Rik|NAD-ME	malic enzyme 2, NAD(+)-dependent, mitochondrial	protein-coding
mm_26090.1	chr3	136722296	136722301	+	1	NA	intron (NM_008913, intron 1 of 13)	intron (NM_008913, intron 1 of 13)	52232	NM_001293622	19055	Mm.331389	NM_008913	ENSMUSG00000028161	Ppp3ca	2900074D19Rik|CN|Caln|Calna|CnA	protein phosphatase 3, catalytic subunit, alpha isoform	protein-coding
mm_68838.1	chr7	126351550	126351560	-	1	NA	Intergenic	Intergenic	16490	NR_106025	102466797		NR_106025	ENSMUSG00000099017	Mir7058	Gm27766|mmu-mir-7058	microRNA 7058	ncRNA
mm_111245.1	chr12	84830074	84830090	-	1	NA	exon (NM_013589, exon 6 of 35)	exon (NM_013589, exon 6 of 35)	-45720	NR_028577	100303738	Mm.479389	NR_028577		D030025P21Rik	-	RIKEN cDNA D030025P21 gene	ncRNA
mm_16191.1	chr2	172977853	172977863	+	1	NA	Intergenic	Intergenic	-1984	NM_012046	26972	Mm.23495	NM_012046	ENSMUSG00000005883	Spo11	AI449549|Spo11a|Spo11b	SPO11 meiotic protein covalently bound to DSB	protein-coding
mm_26741.1	chr3	6785486	6785487	-	1	NA	Intergenic	(A)n|Simple_repeat|Simple_repeat	-165043	NM_027048	69347	Mm.45822	NM_027048	ENSMUSG00000069118	1700008P02Rik	-	RIKEN cDNA 1700008P02 gene	protein-coding
mm_138373.1	chr17	35001569	35001582	+	1	NA	promoter-TSS (NM_033075)	promoter-TSS (NM_033075)	668	NM_011690	22321	Mm.28420	NM_011690	ENSMUSG00000007029	Vars	Bat6|D17H6S56E|G7a|Vars2	valyl-tRNA synthetase	protein-coding
mm_54111.1	chr6	17171580	17171621	-	1	NA	Intergenic	Intergenic	-26151	NR_102305	319682	Mm.136046	NR_102304	ENSMUSG00000085171	D830026I12Rik	-	RIKEN cDNA D830026I12 gene	ncRNA
mm_61190.1	chr7	63896380	63896392	+	1	NA	intron (NM_021366, intron 1 of 1)	intron (NM_021366, intron 1 of 1)	-20471	NM_001256311	381994	Mm.425466	NM_001256311	ENSMUSG00000095061	E030018B13Rik	Gm1697	RIKEN cDNA E030018B13 gene	protein-coding
mm_53509.1	chr6	135382055	135382071	+	1	NA	3' UTR (NM_001288627, exon 5 of 5)	3' UTR (NM_001288627, exon 5 of 5)	14570	NM_001288627	13730	Mm.182785	NM_010128	ENSMUSG00000030208	Emp1	I-8-09|TMP	epithelial membrane protein 1	protein-coding
mm_15345.1	chr2	156065730	156065736	+	1	NA	intron (NM_139151, intron 1 of 11)	CpG	520	NM_139151	245865	Mm.330713	NM_139151	ENSMUSG00000038180	Spag4	1700041K21Rik|MNCb-0953|Sun4|mKIAA4118	sperm associated antigen 4	protein-coding
mm_126048.1	chr15	76905867	76905880	+	1	NA	exon (NM_012053, exon 5 of 6)	exon (NM_012053, exon 5 of 6)	1802	NM_012053	26961	Mm.30066	NM_012053	ENSMUSG00000003970	Rpl8	-	ribosomal protein L8	protein-coding
mm_15989.1	chr2	167015284	167015336	+	1	NA	promoter-TSS (NM_153065)	promoter-TSS (NM_153065)	-3	NM_153065	228889	Mm.295031	NM_153065	ENSMUSG00000017999	Ddx27	C86129	DEAD (Asp-Glu-Ala-Asp) box polypeptide 27	protein-coding
mm_58636.1	chr7	5097585	5097595	+	1	NA	exon (NM_001252454, exon 11 of 11)	exon (NM_001252454, exon 11 of 11)	17355	NM_001252454	13854	Mm.3091	NM_010147	ENSMUSG00000035203	Epn1	AA269831|Ibp1	epsin 1	protein-coding
mm_61369.1	chr7	69909757	69909768	+	1	NA	Intergenic	Intergenic	413668	NR_045940	73796	Mm.410832	NR_045940	ENSMUSG00000108885	4930402F11Rik	-	RIKEN cDNA 4930402F11 gene	ncRNA
mm_51747.1	chr6	87379286	87379292	+	1	NA	exon (NM_025467, exon 6 of 6)	exon (NM_025467, exon 6 of 6)	5924	NM_025467	66284	Mm.46446	NM_025467	ENSMUSG00000030049	Gkn2	1810036H07Rik|Bricd1b	gastrokine 2	protein-coding
mm_114800.1	chr13	90101823	90101827	+	1	NA	intron (NM_025335, intron 3 of 3)	intron (NM_025335, intron 3 of 3)	12158	NM_025335	66074	Mm.241387	NM_025335	ENSMUSG00000012422	Tmem167	0610041E09Rik|5730424F14Rik|AU041184|AW537806|ENSMUSG00000060669|Gm10085|Tmem167a	transmembrane protein 167	protein-coding
mm_140904.1	chr17	24150911	24150928	-	1	NA	promoter-TSS (NM_001286662)	promoter-TSS (NM_001286662)	3	NM_001286662	18607	Mm.10504	NM_011062	ENSMUSG00000024122	Pdpk1	Pdk1	3-phosphoinositide dependent protein kinase 1	protein-coding
mm_98602.1	chr11	95831362	95831373	+	1	NA	3' UTR (NM_001163464, exon 8 of 8)	3' UTR (NM_001163464, exon 8 of 8)	6867	NM_153104	237928	Mm.133075	NM_153104	ENSMUSG00000050860	Phospho1	D11Moh36|Phospo1	phosphatase, orphan 1	protein-coding
mm_168363.1	chr1	11624678	11624697	-	1	NA	intron (NM_001310451, intron 7 of 12)	ERVB7_1-LTR_MM|LTR|ERVK	210582	NM_001160371	320492	Mm.52021	NM_177173	ENSMUSG00000057715	A830018L16Rik	-	RIKEN cDNA A830018L16 gene	protein-coding
mm_42281.1	chr5	114212045	114212049	+	1	NA	intron (NM_133904, intron 20 of 51)	intron (NM_133904, intron 20 of 51)	46529	NM_133904	100705	Mm.81793	NM_133904	ENSMUSG00000042010	Acacb	AI597064|AW743042|Acc2|Accb	acetyl-Coenzyme A carboxylase beta	protein-coding
mm_73551.1	chr8	108957286	108957287	+	1	NA	3' UTR (NM_007496, exon 10 of 10)	3' UTR (NM_007496, exon 10 of 10)	20426	NR_037295	100526511		NR_037295	ENSMUSG00000093241	Mir3108	mir-3108|mmu-mir-3108	microRNA 3108	ncRNA
mm_132734.1	chr16	43807398	43807400	+	1	NA	exon (NM_007877, exon 3 of 7)	exon (NM_007877, exon 3 of 7)	45178	NM_007877	13490	Mm.439735	NM_007877	ENSMUSG00000022705	Drd3	D3R	dopamine receptor D3	protein-coding
mm_109504.1	chr12	111452136	111452209	+	1	NA	intron (NM_009396, intron 11 of 11)	(TCTA)n|Simple_repeat|Simple_repeat	9511	NM_009396	21928	Mm.255332	NM_009396	ENSMUSG00000021281	Tnfaip2	B94|Exoc3l3|M-sec|Tnfip2|tnfb94	tumor necrosis factor, alpha-induced protein 2	protein-coding
mm_112681.1	chr13	16028838	16028856	+	1	NA	3' UTR (NM_008380, exon 5 of 5)	3' UTR (NM_008380, exon 5 of 5)	16996	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_113162.1	chr13	24803702	24803713	+	1	NA	intron (NM_024473, intron 1 of 4)	intron (NM_024473, intron 1 of 4)	2050	NM_024473	79555	Mm.266668	NM_024473	ENSMUSG00000019132	BC005537	8030460C05Rik|C78201	cDNA sequence BC005537	protein-coding
mm_100653.1	chr11	3156342	3156344	-	1	NA	intron (NM_030207, intron 12 of 32)	intron (NM_030207, intron 12 of 32)	32322	NR_003517	236604	Mm.247625	NM_001004146		Pisd-ps1	-	phosphatidylserine decarboxylase, pseudogene 1	pseudo
mm_136556.1	chr17	3115005	3115013	+	1	NA	promoter-TSS (NM_134123)	promoter-TSS (NM_134123)	37	NM_134123	106583	Mm.124373	NM_134123	ENSMUSG00000046201	Scaf8	A630086M08Rik|A930036P18Rik|AA408306|AI447644|AI448652|AU015035|Rbm16|mKIAA1116	SR-related CTD-associated factor 8	protein-coding
mm_31239.1	chr4	44756554	44756601	+	1	NA	promoter-TSS (NM_138590)	promoter-TSS (NM_138590)	18	NM_138590	319885	Mm.331576	NM_138590	ENSMUSG00000035649	Zcchc7	4930572I07Rik|D4Wsu132e	zinc finger, CCHC domain containing 7	protein-coding
mm_144109.1	chr18	4322669	4322671	+	1	NA	Intergenic	L1_Mus3|LINE|L1	30283	NM_007746	26410	Mm.3275	NM_007746	ENSMUSG00000024235	Map3k8	Cot|Cot/Tpl2|Est|Estf|Tpl-2|Tpl2|c-COT	mitogen-activated protein kinase kinase kinase 8	protein-coding
mm_98135.1	chr11	87566671	87566673	+	1	NA	Intergenic	Intergenic	-11717	NM_001284398	18952	Mm.2214	NM_011129	ENSMUSG00000020486	Sept4	ARTS|Bh5|OTTMUSG00000001265|Pnutl2	septin 4	protein-coding
mm_143310.1	chr17	66076813	66076840	-	1	NA	intron (NM_001025572, intron 1 of 12)	CpG	220	NM_001025572	106585	Mm.34706	NM_001025572	ENSMUSG00000034647	Ankrd12	2900001A12Rik|AI447928|ANCO-2|AV347965|GAC-1|mKIAA0874	ankyrin repeat domain 12	protein-coding
mm_31353.1	chr4	47011239	47011268	+	1	NA	Intergenic	MIRc|SINE|MIR	-19539	NM_001081141	242425	Mm.101909	NM_001081141	ENSMUSG00000039809	Gabbr2	GABABR2|Gb2|Gm425|Gpr51	gamma-aminobutyric acid (GABA) B receptor, 2	protein-coding
mm_11282.1	chr2	30066420	30066461	+	1	NA	promoter-TSS (NM_001204875)	promoter-TSS (NM_001204875)	-34	NM_001204875	56086	Mm.326055	NM_023871	ENSMUSG00000054766	Set	2610030F17Rik|5730420M11Rik|AA407739|I-2PP2A|StF-IT-1|TAF-I	SET nuclear oncogene	protein-coding
mm_50669.1	chr6	51537438	51537475	+	1	NA	intron (NM_001127349, intron 1 of 6)	B2_Mm2|SINE|B2	-7067	NM_028035	71982	Mm.294166	NM_028035	ENSMUSG00000038301	Snx10	2410004M09Rik	sorting nexin 10	protein-coding
mm_95235.1	chr11	44617287	44617302	+	1	NA	promoter-TSS (NM_001290711)	promoter-TSS (NM_001290711)	-806	NM_001290711	13591	Mm.439662	NM_007897	ENSMUSG00000057098	Ebf1	Ebf|O/E-1|OE-1|Olf-1|Olf1	early B cell factor 1	protein-coding
mm_149704.1	chr19	21419322	21419325	+	1	NA	intron (NM_010266, intron 6 of 13)	intron (NM_010266, intron 6 of 13)	53338	NM_010266	14544	Mm.45054	NM_010266	ENSMUSG00000058624	Gda	AU015411|AW047581|GAH	guanine deaminase	protein-coding
mm_166675.1	chr6	97148442	97148442	+	1	NA	intron (NM_175313, intron 1 of 17)	intron (NM_175313, intron 1 of 17)	441	NM_175313	101351	Mm.116802	NM_175313	ENSMUSG00000035245	Eogt	A130022J15Rik|AI447490|AW214473|AW259391|Aer61	EGF domain-specific O-linked N-acetylglucosamine (GlcNAc) transferase	protein-coding
mm_60016.1	chr7	30764790	30764802	+	1	NA	exon (NM_001166174, exon 3 of 18)	exon (NM_001166174, exon 3 of 18)	1040	NM_001166174	73712	Mm.30138	NM_028618	ENSMUSG00000060962	Dmkn	1110014F24Rik|AW561900|C130074A08|SK30|SK89|cI-36	dermokine	protein-coding
mm_114026.1	chr13	52635960	52635970	+	1	NA	intron (NM_001198977, intron 9 of 13)	intron (NM_001198977, intron 9 of 13)	39083	NM_011518	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_151726.1	chr19	4867989	4867998	-	1	NA	exon (NM_013456, exon 10 of 21)	exon (NM_013456, exon 10 of 21)	9916	NM_013456	11474	Mm.5316	NM_013456	ENSMUSG00000006457	Actn3	-	actinin alpha 3	protein-coding
mm_87441.1	chr10	51481133	51481144	+	1	NA	intron (NM_001291893, intron 2 of 7)	intron (NM_001291893, intron 2 of 7)	526	NM_001291892	14727	Mm.439661	NM_008147	ENSMUSG00000062593	Lilr4b	Gp49a|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4B	protein-coding
mm_16094.1	chr2	168978242	168978242	+	1	NA	promoter-TSS (NR_040326)	promoter-TSS (NR_040326)	-27	NR_040326	75508	Mm.271256	NR_040326	ENSMUSG00000086348	1700017J07Rik	-	RIKEN cDNA 1700017J07 gene	ncRNA
mm_69858.1	chr7	141434471	141434486	-	1	NA	intron (NM_026646, intron 1 of 9)	intron (NM_026646, intron 1 of 9)	116	NM_001177576	68267	Mm.33729	NM_026646	ENSMUSG00000019082	Slc25a22	1300006L01Rik|AI060884|Gc1	solute carrier family 25 (mitochondrial carrier, glutamate), member 22	protein-coding
mm_140061.1	chr17	74670326	74670336	+	1	NA	exon (NM_007566, exon 64 of 73)	exon (NM_007566, exon 64 of 73)	-47419	NM_152817	74196	Mm.209503	NM_152817	ENSMUSG00000024078	Ttc27	2610511O17Rik	tetratricopeptide repeat domain 27	protein-coding
mm_169397.1	chr14	45713330	45713346	-	1	NA	Intergenic	Intergenic	-55195	NM_001042719	114874	Mm.121918	NM_176845	ENSMUSG00000037697	Ddhd1	Mir5131|PA-PLA1	DDHD domain containing 1	protein-coding
mm_71991.1	chr8	70616976	70616986	+	1	NA	5' UTR (NM_153074, exon 1 of 3)	5' UTR (NM_153074, exon 1 of 3)	137	NM_153074	211228	Mm.132939	NM_153074	ENSMUSG00000049988	Lrrc25	Mapa	leucine rich repeat containing 25	protein-coding
mm_94213.1	chr11	3147563	3147573	+	1	NA	intron (NM_030207, intron 14 of 32)	RMER4B|LTR|ERVK	23547	NR_003517	236604	Mm.247625	NM_001004146		Pisd-ps1	-	phosphatidylserine decarboxylase, pseudogene 1	pseudo
mm_123249.1	chr14	60784575	60784586	-	1	NA	promoter-TSS (NM_027436)	promoter-TSS (NM_027436)	14	NR_040642	70478	Mm.274650	NM_027436	ENSMUSG00000021993	Mipep	5730405E07Rik|MIP	mitochondrial intermediate peptidase	protein-coding
mm_59800.1	chr7	29071598	29071613	+	1	NA	exon (NM_009109, exon 49 of 106)	exon (NM_009109, exon 49 of 106)	12089	NR_035489	100316710		NR_035489	ENSMUSG00000089219	Mir1963	mir-1963|mmu-mir-1963	microRNA 1963	ncRNA
mm_88769.1	chr10	80335943	80335958	+	1	NA	3' UTR (NM_139292, exon 6 of 6)	3' UTR (NM_139292, exon 6 of 6)	5805	NM_139292	70335	Mm.28147	NM_139292	ENSMUSG00000035504	Reep6	0610011M24Rik|Dp1l1	receptor accessory protein 6	protein-coding
mm_1764.1	chr1	75546641	75546654	+	1	NA	intron (NM_009208, intron 1 of 22)	CpG	381	NM_009208	20536	Mm.5053	NM_009208	ENSMUSG00000006576	Slc4a3	A930038D23Rik|Ae3	solute carrier family 4 (anion exchanger), member 3	protein-coding
mm_110616.1	chr12	56692914	56692921	-	1	NA	Intergenic	Intergenic	-2554	NM_011041	18511	Mm.5035	NM_011041	ENSMUSG00000001497	Pax9	Pax-9	paired box 9	protein-coding
mm_84271.1	chr9	62794917	62794955	-	1	NA	3' UTR (NM_010193, exon 2 of 2)	3' UTR (NM_010193, exon 2 of 2)	16712	NM_010193	14155	Mm.24069	NM_010193	ENSMUSG00000032244	Fem1b	mKIAA0396	feminization 1 homolog b (C. elegans)	protein-coding
mm_41631.1	chr5	97048799	97048806	+	1	NA	intron (NM_080708, intron 7 of 15)	intron (NM_080708, intron 7 of 15)	51113	NM_080708	140780	Mm.281490	NM_080708	ENSMUSG00000034663	Bmp2k	4933417M22Rik|AA673486|AV128808|BIKE	BMP2 inducible kinase	protein-coding
mm_33347.1	chr4	129335594	129335645	+	1	NA	promoter-TSS (NM_009030)	promoter-TSS (NM_009030)	-249	NM_009030	19646	Mm.12145	NM_009030	ENSMUSG00000057236	Rbbp4	RBAP48|mRbAp48	retinoblastoma binding protein 4	protein-coding
mm_7886.1	chr1	133118281	133118320	-	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-12866	NM_133819	108954	Mm.293628	NM_133819	ENSMUSG00000046062	Ppp1r15b	1810033K10Rik|AI606441|C530022L24Rik|CReP	protein phosphatase 1, regulatory (inhibitor) subunit 15b	protein-coding
mm_151578.1	chr19	61166974	61166979	+	1	NA	Intergenic	Intergenic	9333	NM_001177513	633057	Mm.426097	NM_001177513	ENSMUSG00000094649	Gm7102	EG633057	predicted gene 7102	protein-coding
mm_123873.1	chr14	72602946	72603003	-	1	NA	intron (NM_207636, intron 3 of 25)	intron (NM_207636, intron 3 of 25)	107029	NM_207636	319448	Mm.205421	NM_207636	ENSMUSG00000033487	Fndc3a	1700094E19Rik|D14Ertd453e|F730017H24Rik|Fndc3|sys	fibronectin type III domain containing 3A	protein-coding
mm_139981.1	chr17	72836657	72836659	+	1	NA	promoter-TSS (NM_027166)	promoter-TSS (NM_027166)	-46	NM_027166	383295	Mm.277533	NM_027166	ENSMUSG00000039770	Ypel5	2310076K21Rik|CGI-127	yippee-like 5 (Drosophila)	protein-coding
mm_36379.1	chr4	76854484	76854485	-	1	NA	intron (NM_011211, intron 8 of 39)	Lx3B|LINE|L1	1357411	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding
mm_135381.1	chr16	44139683	44139720	-	1	NA	promoter-TSS (NM_007508)	promoter-TSS (NM_007508)	-90	NM_001347239	72117	Mm.278726	NM_028108	ENSMUSG00000022698	Naa50	2600005K24Rik|2810441M03Rik|AW112078|Mak3|Mak3p|Nat13|Nat5|San	N(alpha)-acetyltransferase 50, NatE catalytic subunit	protein-coding
mm_87280.1	chr10	41959127	41959130	+	1	NA	intron (NM_001034858, intron 10 of 17)	intron (NM_001034858, intron 10 of 17)	59254	NM_001034858	213402	Mm.211320	NM_001034858	ENSMUSG00000071324	Armc2	2610018I05Rik	armadillo repeat containing 2	protein-coding
mm_62811.1	chr7	113218434	113218438	+	1	NA	intron (NM_001243048, intron 1 of 16)	(T)n|Simple_repeat|Simple_repeat	10971	NM_007489	11865	Mm.33970	NM_007489	ENSMUSG00000055116	Arntl	Arnt3|BMAL1b|Bmal1|MOP3|bHLHe5|bmal1b'	aryl hydrocarbon receptor nuclear translocator-like	protein-coding
mm_104207.1	chr11	88049068	88049080	-	1	NA	exon (NM_001078167, exon 3 of 3)	exon (NM_001078167, exon 3 of 3)	1701	NM_173374	110809	Mm.391719	NM_173374	ENSMUSG00000018379	Srsf1	1110054N12Rik|5730507C05Rik|6330415C05Rik|AI482334|AW491331|Asf|Sf2|Sfrs1	serine/arginine-rich splicing factor 1	protein-coding
mm_71152.1	chr8	39636193	39636205	+	1	NA	intron (NM_001113326, intron 1 of 9)	intron (NM_001113326, intron 1 of 9)	6479	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_54200.1	chr6	24664922	24664957	-	1	NA	promoter-TSS (NM_028459)	promoter-TSS (NM_028459)	56	NM_001167745	73178	Mm.1574	NM_028459	ENSMUSG00000029684	Wasl	2900021I12Rik|3110031I02Rik|N-WASP	Wiskott-Aldrich syndrome-like (human)	protein-coding
mm_54647.1	chr6	38876164	38876234	-	1	NA	promoter-TSS (NM_010433)	promoter-TSS (NM_010433)	-9	NM_001294143	15258	Mm.23790	NM_010433	ENSMUSG00000061436	Hipk2	1110014O20Rik|B230339E18Rik|Stank	homeodomain interacting protein kinase 2	protein-coding
mm_101093.1	chr11	11882293	11882295	-	1	NA	intron (NM_001190448, intron 1 of 14)	MLT2B3|LTR|ERVL	8114	NM_016672	13195	Mm.12906	NM_016672	ENSMUSG00000020182	Ddc	Aadc	dopa decarboxylase	protein-coding
mm_85789.1	chr9	109095776	109095804	-	1	NA	intron (NM_172775, intron 1 of 37)	CpG	354	NM_172775	235611	Mm.53862	NM_172775	ENSMUSG00000053646	Plxnb1	2900002G15Rik|AU042020|mKIAA0407	plexin B1	protein-coding
mm_108345.1	chr12	80463166	80463179	+	1	NA	promoter-TSS (NM_133798)	promoter-TSS (NM_133798)	77	NM_133798	97827	Mm.206631	NM_133798	ENSMUSG00000032705	Exd2	4930539P14Rik|C85658|Exdl2	exonuclease 3'-5' domain containing 2	protein-coding
mm_117081.1	chr13	59640180	59640189	-	1	NA	exon (NM_001035122, exon 8 of 10)	exon (NM_001035122, exon 8 of 10)	35600	NM_001035122	105348	Mm.171335	NM_027307	ENSMUSG00000021556	Golm1	2310001L02Rik|AW125446|D030064E01Rik|GP73|Golph2|PSEC0257	golgi membrane protein 1	protein-coding
mm_27084.1	chr3	30013233	30013246	-	1	NA	promoter-TSS (NM_007963)	promoter-TSS (NM_007963)	-35	NM_007963	14013	Mm.56965	NM_007963	ENSMUSG00000027684	Mecom	D630039M04Rik|Evi-1|Evi1|Jbo|Mds|Mds1|Mds1-Evi1|Prdm3|Znfpr1b1	MDS1 and EVI1 complex locus	protein-coding
mm_21224.1	chr2	155834846	155834861	-	1	NA	promoter-TSS (NM_027788)	promoter-TSS (NM_027788)	1	NM_027788	71405	Mm.260918	NM_027788	ENSMUSG00000074647	Fam83c	5530400B04Rik	family with sequence similarity 83, member C	protein-coding
mm_161049.1	chr12	49385313	49385313	+	1	NA	exon (NM_008241, exon 2 of 2)	exon (NM_008241, exon 2 of 2)	2306	NM_008241	15228	Mm.4704	NM_008241	ENSMUSG00000020950	Foxg1	2900064B05Rik|BF-1|Bf1|Hfh9|Hfhbf1	forkhead box G1	protein-coding
mm_108862.1	chr12	98920568	98920619	+	1	NA	promoter-TSS (NM_198311)	promoter-TSS (NM_198311)	19	NM_029553	76260	Mm.282660	NM_029553	ENSMUSG00000021013	Ttc8	0610012F22Rik|AV001447|BBS8	tetratricopeptide repeat domain 8	protein-coding
mm_104798.1	chr11	98774016	98774026	-	1	NA	intron (NM_145434, intron 1 of 7)	CpG	1356	NM_145434	217166	Mm.390397	NM_145434	ENSMUSG00000020889	Nr1d1	A530070C09Rik|R75201	nuclear receptor subfamily 1, group D, member 1	protein-coding
mm_63778.1	chr7	131560426	131560428	+	1	NA	promoter-TSS (NM_009774)	promoter-TSS (NM_009774)	57	NM_009774	12237	Mm.927	NM_009774	ENSMUSG00000066979	Bub3	AU019800|AU021329|AU043350|AW146323|C78067	BUB3 mitotic checkpoint protein	protein-coding
mm_47740.1	chr5	130254249	130254252	-	1	NA	intron (NM_023248, intron 1 of 4)	B1F2|SINE|Alu	1280	NM_023248	66711	Mm.280484	NM_023248	ENSMUSG00000025337	Sbds	4733401P19Rik|AI836084|CGI-97|SDS	Shwachman-Bodian-Diamond syndrome homolog (human)	protein-coding
mm_154337.1	chrM	4229	4239	+	1	NA	NA	Intergenic	NA	NA								
mm_119853.1	chr14	54441157	54441191	+	1	NA	3' UTR (NM_008608, exon 10 of 10)	3' UTR (NM_008608, exon 10 of 10)	9576	NM_008608	17387	Mm.280175	NM_008608	ENSMUSG00000000957	Mmp14	AI325305|MMP-X1|MT-MMP-1|MT1-MMP|sabe	matrix metallopeptidase 14 (membrane-inserted)	protein-coding
mm_148675.1	chr19	5638224	5638226	+	1	NA	intron (NM_009045, intron 1 of 10)	intron (NM_009045, intron 1 of 10)	735	NM_009045	19697	Mm.249966	NM_009045	ENSMUSG00000024927	Rela	p65	v-rel reticuloendotheliosis viral oncogene homolog A (avian)	protein-coding
mm_26012.1	chr3	135348007	135348026	+	1	NA	promoter-TSS (NM_028946)	promoter-TSS (NM_028946)	-21	NM_028946	74446	Mm.85000	NM_028946	ENSMUSG00000050150	Slc9b1	1700094G20Rik|4933424B12Rik|4933425K02Rik|Nhedc1|mtsNHE	solute carrier family 9, subfamily B (NHA1, cation proton antiporter 1), member 1	protein-coding
mm_43163.1	chr5	127030824	127030834	+	1	NA	promoter-TSS (NR_040685)	promoter-TSS (NR_040685)	40	NR_040685	71247	Mm.399586	NR_040685	ENSMUSG00000105490	4933438B17Rik	-	RIKEN cDNA 4933438B17 gene	ncRNA
mm_78187.1	chr9	21243388	21243388	+	1	NA	3' UTR (NM_053190, exon 3 of 3)	3' UTR (NM_053190, exon 3 of 3)	-4056	NM_001110307	50868	Mm.248266	NM_016679	ENSMUSG00000003308	Keap1	INRF2|mKIAA0132	kelch-like ECH-associated protein 1	protein-coding
mm_61793.1	chr7	83892132	83892157	+	1	NA	5' UTR (NM_023403, exon 1 of 3)	5' UTR (NM_023403, exon 1 of 3)	144	NM_023403	67943	Mm.117365	NM_023403	ENSMUSG00000038503	Mesdc2	2210015O11Rik|AW537813|mKIAA0081|mesd|msd	mesoderm development candidate 2	protein-coding
mm_118163.1	chr13	105294350	105294358	-	1	NA	Intergenic	CpG	-1340	NM_027934	71816	Mm.317015	NM_027934	ENSMUSG00000021720	Rnf180	3110001E11Rik|Rines	ring finger protein 180	protein-coding
mm_11560.1	chr2	32775809	32775829	+	1	NA	promoter-TSS (NM_001290563)	promoter-TSS (NM_001290563)	-2	NM_178595	329384	Mm.268037	NM_178595	ENSMUSG00000053746	Ptrh1	2210013M04Rik|AW046744	peptidyl-tRNA hydrolase 1 homolog	protein-coding
mm_104126.1	chr11	86757453	86757463	-	1	NA	promoter-TSS (NM_001003908)	promoter-TSS (NM_001003908)	34	NM_001003908	67300	Mm.254588	NM_001003908	ENSMUSG00000047126	Cltc	3110065L21Rik|CHC|R74732	clathrin, heavy polypeptide (Hc)	protein-coding
mm_140356.1	chr17	86831430	86831438	+	1	NA	3' UTR (NM_010137, exon 16 of 16)	3' UTR (NM_010137, exon 16 of 16)	77570	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_96886.1	chr11	70435707	70435717	+	1	NA	intron (NM_001271359, intron 2 of 15)	intron (NM_001271359, intron 2 of 15)	-2543	NR_106064	102465670		NR_106064	ENSMUSG00000099109	Mir7115	Gm27902|mmu-mir-7115	microRNA 7115	ncRNA
mm_143155.1	chr17	57223291	57223339	-	1	NA	exon (NM_009778, exon 12 of 41)	exon (NM_009778, exon 12 of 41)	4821	NM_009778	12266	Mm.19131	NM_009778	ENSMUSG00000024164	C3	AI255234|ASP|HSE-MSF|Plp	complement component 3	protein-coding
mm_114932.1	chr13	95765326	95765364	+	1	NA	intron (NM_027711, intron 2 of 35)	intron (NM_027711, intron 2 of 35)	68425	NM_010170	14064	Mm.440952	NM_010170	ENSMUSG00000021675	F2rl2	F730031A08|PAR3	coagulation factor II (thrombin) receptor-like 2	protein-coding
mm_18698.1	chr2	71546485	71546498	-	1	NA	5' UTR (NM_010054, exon 1 of 3)	5' UTR (NM_010054, exon 1 of 3)	263	NM_010054	13392	Mm.3896	NM_010054	ENSMUSG00000023391	Dlx2	AW121999|Dlx-2|Tes-1	distal-less homeobox 2	protein-coding
mm_169301.1	chr14	102143893	102143909	+	1	NA	Intergenic	L1Md_A|LINE|L1	303278	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_86391.1	chr9	123957803	123957809	-	1	NA	Intergenic	RLTR30D_MM|LTR|ERV1	10886	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_43751.1	chr5	140419409	140419443	+	1	NA	exon (NM_133916, exon 1 of 19)	exon (NM_133916, exon 1 of 19)	121	NM_133916	27979	Mm.21671	NM_133916	ENSMUSG00000056076	Eif3b	AL033316|AL033334|AL033369|AW208965|D5Wsu45e|EIF3-ETA|EIF3-P110|EIF3-P116|Eif3s9|PRT1	eukaryotic translation initiation factor 3, subunit B	protein-coding
mm_80995.1	chr9	103423120	103423131	+	1	NA	promoter-TSS (NR_040466)	promoter-TSS (NR_040466)	-453	NR_040466	100529079	Mm.437003	NR_040466	ENSMUSG00000086236	5830418P13Rik	-	RIKEN cDNA 5830418P13 gene	ncRNA
mm_45756.1	chr5	86803994	86804006	-	1	NA	promoter-TSS (NM_177680)	promoter-TSS (NM_177680)	-266	NM_001347375	231386	Mm.196325	NM_177680	ENSMUSG00000035851	Ythdc1	A730098D12Rik|C80342|mKIAA1966	YTH domain containing 1	protein-coding
mm_68630.1	chr7	118146996	118147000	-	1	NA	intron (NM_001031814, intron 51 of 62)	intron (NM_001031814, intron 51 of 62)	-17373	NM_019419	54208	Mm.29924	NM_019419	ENSMUSG00000030654	Arl6ip1	AIP-6|AL022945|ARMER|AU042858|Aip-1|Arl6ip|C85138|mKIAA0069	ADP-ribosylation factor-like 6 interacting protein 1	protein-coding
mm_61752.1	chr7	82771211	82771235	+	1	NA	intron (NM_175317, intron 18 of 19)	C-rich|Low_complexity|Low_complexity	-15579	NR_046004	77800	Mm.444811	NR_046004	ENSMUSG00000086690	4933406J10Rik	A930009F24Rik	RIKEN cDNA 4933406J10 gene	ncRNA
mm_2582.1	chr1	118627944	118627951	+	1	NA	promoter-TSS (NM_023755)	promoter-TSS (NM_023755)	2	NM_023755	81879	Mm.24621	NM_023755	ENSMUSG00000026380	Tfcp2l1	1810030F05Rik|4932442M07Rik|AA575098|Cp2l1|Crtr-1|D930018N21Rik|LBP-9|Tcfcp2l1	transcription factor CP2-like 1	protein-coding
mm_52605.1	chr6	117173595	117173606	+	1	NA	3' UTR (NM_021704, exon 3 of 3)	3' UTR (NM_021704, exon 3 of 3)	5065	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_88386.1	chr10	76452912	76452914	+	1	NA	exon (NM_029816, exon 4 of 8)	exon (NM_029816, exon 4 of 8)	3832	NM_029816	76964	Mm.472489	NM_029816	ENSMUSG00000009114	2610028H24Rik	ORF67	RIKEN cDNA 2610028H24 gene	protein-coding
mm_33711.1	chr4	133816249	133816254	+	1	NA	Intergenic	Intergenic	58480	NM_001285506	20111	Mm.301827	NM_009097	ENSMUSG00000003644	Rps6ka1	Mapkapk-1a|Rsk|Rsk-1|Rsk1|S6K-alpha-1|p90-Rsk1|p90Rsk1|p90S6K|p90rsk	ribosomal protein S6 kinase polypeptide 1	protein-coding
mm_159952.1	chr6	86085890	86085890	+	1	NA	exon (NM_001271860, exon 3 of 13)	exon (NM_001271860, exon 3 of 13)	7842	NM_001271859	11519	Mm.104155	NM_013458	ENSMUSG00000030000	Add2	2900072M03Rik|add97	adducin 2 (beta)	protein-coding
mm_2399.1	chr1	93693721	93693735	+	1	NA	intron (NM_016778, intron 3 of 4)	intron (NM_016778, intron 3 of 4)	8153	NM_016778	51800	Mm.3295	NM_016778	ENSMUSG00000026278	Bok	matador|mtd	BCL2-related ovarian killer	protein-coding
mm_26570.1	chr3	146602389	146602398	+	1	NA	intron (NM_009474, intron 1 of 7)	intron (NM_009474, intron 1 of 7)	5244	NM_009474	22262	Mm.10865	NM_009474	ENSMUSG00000028186	Uox	AI663847	urate oxidase	protein-coding
mm_112039.1	chr12	111670627	111670637	-	1	NA	intron (NM_021273, intron 5 of 7)	CpG	1706	NM_021273	12709	Mm.16831	NM_021273	ENSMUSG00000001270	Ckb	B-CK|Bck|Ck-3|Ck3|Ckbb	creatine kinase, brain	protein-coding
mm_66934.1	chr7	61576791	61576801	-	1	NA	intron (NR_045727, intron 2 of 4)	intron (NR_045727, intron 2 of 4)	38531	NR_045727	319752	Mm.294476	NR_045727		B230209E15Rik	-	RIKEN cDNA B230209E15 gene	ncRNA
mm_86417.1	chr10	3540233	3540246	+	1	NA	promoter-TSS (NM_027391)	promoter-TSS (NM_027391)	-40	NM_027391	70337	Mm.24153	NM_027391	ENSMUSG00000019762	Iyd	0610009A07Rik|AI265638|Dehal1	iodotyrosine deiodinase	protein-coding
mm_116649.1	chr13	49183929	49183957	-	1	NA	Intergenic	Intergenic	-3604	NM_013610	18081	Mm.18503	NM_013610	ENSMUSG00000037966	Ninj1	AU024536	ninjurin 1	protein-coding
mm_23684.1	chr3	68633810	68633832	+	1	NA	Intergenic	Intergenic	-56823	NM_001159424	16159	Mm.103783	NM_008351	ENSMUSG00000027776	Il12a	IL-12p35|Il-12a|Ll12a|p35	interleukin 12a	protein-coding
mm_64781.1	chr7	5038428	5038450	-	1	NA	promoter-TSS (NM_001039532)	promoter-TSS (NM_001039532)	7	NM_001039532	654801	Mm.333548	NM_001039532	ENSMUSG00000043290	Zfp784	C730049F21Rik|Znf784	zinc finger protein 784	protein-coding
mm_120808.1	chr14	75016015	75016023	+	1	NA	promoter-TSS (NM_198642)	promoter-TSS (NM_198642)	-8	NM_198642	271221	Mm.320280	NM_198642	ENSMUSG00000034959	Rubcnl	5031414D18Rik|Gm744|Gm911|Kiaa0226l	RUN and cysteine rich domain containing beclin 1 interacting protein like	protein-coding
mm_1128.1	chr1	60343298	60343362	+	1	NA	promoter-TSS (NM_030013)	promoter-TSS (NM_030013)	30	NM_001313721	77951	Mm.197640	NM_030013	ENSMUSG00000049439	Cyp20a1	A930011N14Rik|Cypm	cytochrome P450, family 20, subfamily a, polypeptide 1	protein-coding
mm_78287.1	chr9	22188138	22188149	+	1	NA	promoter-TSS (NM_001033813)	promoter-TSS (NM_001033813)	-23	NM_001033813	619310	Mm.335016	NM_001033813	ENSMUSG00000074472	Zfp872	9530015I07Rik	zinc finger protein 872	protein-coding
mm_128125.1	chr15	31336720	31336730	-	1	NA	intron (NM_027496, intron 1 of 3)	intron (NM_027496, intron 1 of 3)	31034	NM_001164441	67434	Mm.102470	NM_026153	ENSMUSG00000022237	Ankrd33b	0610012A05Rik|3021401C12Rik|5730557B15Rik	ankyrin repeat domain 33B	protein-coding
mm_130297.1	chr15	97013682	97013687	-	1	NA	intron (NM_027052, intron 4 of 15)	intron (NM_027052, intron 4 of 15)	42272	NM_027052	69354	Mm.250980	NM_027052	ENSMUSG00000022464	Slc38a4	1110012E16Rik|1700012A18Rik|Ata3|mATA3|mNAT3	solute carrier family 38, member 4	protein-coding
mm_82241.1	chr9	4309433	4309504	-	1	NA	promoter-TSS (NM_026962)	promoter-TSS (NM_026962)	26	NR_136941	67618	Mm.33970	NM_026276	ENSMUSG00000025894	Aasdhppt	2010309J24Rik|2810407B07Rik|AASD-PPT|CGI-80|LYS2|LYS5	aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase	protein-coding
mm_2676.1	chr1	127273625	127273635	+	1	NA	intron (NM_145128, intron 2 of 17)	intron (NM_145128, intron 2 of 17)	68644	NM_145128	107895	Mm.214682	NM_145128	ENSMUSG00000036155	Mgat5	4930471A21Rik|5330407H02Rik|AI480971|GlcNAc-TV	mannoside acetylglucosaminyltransferase 5	protein-coding
mm_6589.1	chr1	75264196	75264219	-	1	NA	promoter-TSS (NM_008985)	promoter-TSS (NM_008985)	1	NM_008985	19275	Mm.2902	NM_008985	ENSMUSG00000026204	Ptprn	IA-2|mIA-A|mKIAA4064	protein tyrosine phosphatase, receptor type, N	protein-coding
mm_119867.1	chr14	54554045	54554061	+	1	NA	intron (NM_145462, intron 1 of 9)	CpG	308	NM_145462	219072	Mm.202152	NM_145462	ENSMUSG00000022177	Haus4	9430093H08Rik|AU016300|D14Ertd500e	HAUS augmin-like complex, subunit 4	protein-coding
mm_128076.1	chr15	27663554	27663564	-	1	NA	intron (NM_001242423, intron 4 of 7)	intron (NM_001242423, intron 4 of 7)	17983	NM_001242424	223433	Mm.266485	NM_198301	ENSMUSG00000056069	Fam105a	9830126M18	family with sequence similarity 105, member A	protein-coding
mm_71632.1	chr8	57456041	57456084	+	1	NA	5' UTR (NM_009136, exon 1 of 3)	5' UTR (NM_009136, exon 1 of 3)	139	NM_009136	20284	Mm.12886	NM_009136	ENSMUSG00000031610	Scrg1	AW124307	scrapie responsive gene 1	protein-coding
mm_137182.1	chr17	23816301	23816318	+	1	NA	exon (NM_175229, exon 10 of 14)	exon (NM_175229, exon 10 of 14)	12800	NM_026305	67673	Mm.153758	NM_026305	ENSMUSG00000055839	Elob	0610040H15Rik|Tceb2	elongin B	protein-coding
mm_153924.1	chr19	47314791	47314807	-	1	NA	intron (NM_001164717, intron 7 of 13)	intron (NM_001164717, intron 7 of 13)	-41210	NR_105961	102466782		NR_105961	ENSMUSG00000098786	Mir6995	Gm27576|mmu-mir-6995	microRNA 6995	ncRNA
mm_3018.1	chr1	133363826	133363840	+	1	NA	exon (NM_175443, exon 1 of 8)	exon (NM_175443, exon 1 of 8)	261	NM_175443	214253	Mm.52111	NM_175443	ENSMUSG00000070644	Etnk2	4933417N20Rik|AI197444|EKI 2|Eki2|Tuc1	ethanolamine kinase 2	protein-coding
mm_117569.1	chr13	85289083	85289136	-	1	NA	5' UTR (NM_145452, exon 1 of 25)	5' UTR (NM_145452, exon 1 of 25)	377	NM_145452	218397	Mm.259653	NM_145452	ENSMUSG00000021549	Rasa1	Gap|RasGAP|Rasa	RAS p21 protein activator 1	protein-coding
mm_53717.1	chr6	143404630	143404668	+	1	NA	Intergenic	MTE-int|LTR|ERVL-MaLR	158761	NR_027803	52285	Mm.354898	NM_001033129		D6Ertd474e	1700001I24Rik|AU023129	DNA segment, Chr 6, ERATO Doi 474, expressed	ncRNA
mm_144673.1	chr18	34624956	34625000	+	1	NA	promoter-TSS (NM_009004)	promoter-TSS (NM_009004)	42	NM_009004	19348	Mm.258846	NM_009004	ENSMUSG00000003779	Kif20a	AA415432|Rab6kifl	kinesin family member 20A	protein-coding
mm_156164.1	chrX	130033516	130033530	+	1	NA	intron (NM_172493, intron 17 of 26)	intron (NM_172493, intron 17 of 26)	283781	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diaph2	Dia3|Diap2|Drf2|E430022I22Rik	diaphanous related formin 2	protein-coding
mm_155876.1	chrX	101447992	101448001	+	1	NA	3' UTR (NM_001252518, exon 12 of 12)	3' UTR (NM_001252518, exon 12 of 12)	-1113	NM_013712	26549	Mm.46232	NM_013712	ENSMUSG00000031312	Itgb1bp2	Chordc3	integrin beta 1 binding protein 2	protein-coding
mm_164629.1	chr17	32811592	32811593	+	1	NA	Intergenic	Intergenic	-1661	NM_183177	240063	Mm.30675	NM_183177	ENSMUSG00000055202	Zfp811	BC052046	zinc finger protein 811	protein-coding
mm_52745.1	chr6	120473772	120473790	+	1	NA	exon (NM_008359, exon 4 of 13)	exon (NM_008359, exon 4 of 13)	10584	NM_008359	16172	Mm.4481	NM_008359	ENSMUSG00000002897	Il17ra	AW538159|Cdw217|Il17r|VDw217	interleukin 17 receptor A	protein-coding
mm_109259.1	chr12	109459986	109460030	+	1	NA	exon (NM_010052, exon 5 of 5)	exon (NM_010052, exon 5 of 5)	6553	NM_010052	13386	Mm.157069	NM_010052	ENSMUSG00000040856	Dlk1	AW742678|DLK-1|DlkI|FA1|Ly107|Peg9|SCP1|ZOG|pG2|pref-1	delta-like 1 homolog (Drosophila)	protein-coding
mm_121784.1	chr14	19976975	19977038	-	1	NA	promoter-TSS (NM_001285911)	promoter-TSS (NM_001285911)	243	NM_001038637	14702	Mm.41737	NM_010315	ENSMUSG00000043004	Gng2	-	guanine nucleotide binding protein (G protein), gamma 2	protein-coding
mm_40890.1	chr5	75151381	75151400	+	1	NA	promoter-TSS (NM_011058)	promoter-TSS (NM_011058)	-861	NR_144636	18595	Mm.221403	NM_011058	ENSMUSG00000029231	Pdgfra	AI115593|CD140a|Pdgfr-2	platelet derived growth factor receptor, alpha polypeptide	protein-coding
mm_139584.1	chr17	57223113	57223135	+	1	NA	exon (NM_009778, exon 12 of 41)	exon (NM_009778, exon 12 of 41)	5012	NM_009778	12266	Mm.19131	NM_009778	ENSMUSG00000024164	C3	AI255234|ASP|HSE-MSF|Plp	complement component 3	protein-coding
mm_110833.1	chr12	72667947	72667947	-	1	NA	Intergenic	Intergenic	-3119	NM_025522	66375	Mm.289653	NM_025522	ENSMUSG00000021094	Dhrs7	2310016E22Rik|5730564L20Rik|AW061210|Retdsr4|Retsdr4	dehydrogenase/reductase (SDR family) member 7	protein-coding
mm_44444.1	chr5	21664889	21664919	-	1	NA	3' UTR (NM_178728, exon 5 of 5)	3' UTR (NM_178728, exon 5 of 5)	18920	NM_026034	67211	Mm.260782	NM_026034	ENSMUSG00000038525	Armc10	2810037C14Rik|Svh	armadillo repeat containing 10	protein-coding
mm_102100.1	chr11	52360964	52361013	-	1	NA	5' UTR (NM_011694, exon 1 of 9)	5' UTR (NM_011694, exon 1 of 9)	126	NM_011694	22333	Mm.3555	NM_011694	ENSMUSG00000020402	Vdac1	AL033343|Vdac5|mVDAC1|mVDAC5	voltage-dependent anion channel 1	protein-coding
mm_129878.1	chr15	83447917	83447942	-	1	NA	intron (NM_001159509, intron 1 of 10)	intron (NM_001159509, intron 1 of 10)	-15079	NM_001159510	23970	Mm.23978	NM_011862	ENSMUSG00000016664	Pacsin2	AI197433	protein kinase C and casein kinase substrate in neurons 2	protein-coding
mm_102164.1	chr11	53805150	53805159	-	1	NA	intron (NR_033332, intron 3 of 3)	B3A|SINE|B2	34681	NM_001159396	16362	Mm.105218	NM_008390	ENSMUSG00000018899	Irf1	AU020929|Irf-1	interferon regulatory factor 1	protein-coding
mm_136992.1	chr17	17402684	17402771	+	1	NA	promoter-TSS (NM_025681)	promoter-TSS (NM_025681)	41	NM_025681	66643	Mm.268018	NM_025681	ENSMUSG00000047786	Lix1	5730466L18Rik	limb and CNS expressed 1	protein-coding
mm_171524.1	chr4	146610984	146610991	+	1	NA	Intergenic	Intergenic	-64114	NR_045468	67524	Mm.444300	NR_045468	ENSMUSG00000086046	1700095A21Rik	-	RIKEN cDNA 1700095A21 gene	ncRNA
mm_156004.1	chrX	106703867	106703897	+	1	NA	intron (NM_001033541, intron 3 of 3)	intron (NM_001033541, intron 3 of 3)	-100203	NM_001281859	58861	Mm.287166	NM_021476	ENSMUSG00000052821	Cysltr1	BB147369|CysLT1R|Cyslt1	cysteinyl leukotriene receptor 1	protein-coding
mm_84948.1	chr9	83141180	83141185	-	1	NA	intron (NM_175074, intron 1 of 5)	RMER4B|LTR|ERVK	5425	NM_175074	94353	Mm.244426	NM_026122	ENSMUSG00000066456	Hmgn3	1110002A15Rik|6330514M13Rik|BB071015|TRIP7	high mobility group nucleosomal binding domain 3	protein-coding
mm_83794.1	chr9	52676796	52676808	-	1	NA	3' UTR (NM_178906, exon 2 of 2)	3' UTR (NM_178906, exon 2 of 2)	2635	NM_178906	330941	Mm.335160	NM_177907	ENSMUSG00000078307	AI593442	E130102D23	expressed sequence AI593442	protein-coding
mm_32015.1	chr4	94751584	94751586	+	1	NA	intron (NM_001290549, intron 1 of 22)	intron (NM_001290549, intron 1 of 22)	12296	NM_001290551	21687	Mm.14313	NM_013690	ENSMUSG00000006386	Tek	AA517024|Cd202b|Hyk|STK1|Tie-2|Tie2	endothelial-specific receptor tyrosine kinase	protein-coding
mm_69528.1	chr7	135652260	135652268	-	1	NA	promoter-TSS (NR_015548)	promoter-TSS (NR_015548)	50	NR_015548	67765	Mm.445272	NR_015548	ENSMUSG00000097471	5830432E09Rik	-	RIKEN cDNA 5830432E09 gene	ncRNA
mm_134730.1	chr16	22899053	22899075	-	1	NA	exon (NM_001276450, exon 7 of 7)	exon (NM_001276450, exon 7 of 7)	-4678	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_25054.1	chr3	98427773	98427793	+	1	NA	exon (NM_172863, exon 3 of 3)	exon (NM_172863, exon 3 of 3)	29248	NM_001111336	15495	Mm.14309	NM_008294	ENSMUSG00000095143	Hsd3b4	-	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 4	protein-coding
mm_82800.1	chr9	29412636	29412678	-	1	NA	intron (NM_172290, intron 1 of 7)	CpG	550472	NM_172290	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding
mm_21642.1	chr2	164333424	164333428	-	1	NA	exon (NM_009301, exon 2 of 3)	exon (NM_009301, exon 2 of 3)	661	NM_009301	20944	Mm.140154	NM_009301	ENSMUSG00000017004	Svs5	BB115186|Semg1|Svp-1|Svp1|Svp5	seminal vesicle secretory protein 5	protein-coding
mm_4851.1	chr1	187215715	187215728	+	1	NA	promoter-TSS (NM_029067)	promoter-TSS (NM_029067)	210	NM_026367	67769	Mm.138321	NM_026367	ENSMUSG00000039210	Gpatch2	5830433G22Rik|5830436K05Rik|AI427714|AI447508|AW107440|AW491060|Gpatc2	G patch domain containing 2	protein-coding
mm_99642.1	chr11	105292638	105292669	+	1	NA	promoter-TSS (NM_008626)	promoter-TSS (NM_008626)	7	NM_008626	17534	Mm.235616	NM_008626	ENSMUSG00000020695	Mrc2	Endo180|mKIAA0709|uPARAP	mannose receptor, C type 2	protein-coding
mm_110358.1	chr12	40037625	40037630	-	1	NA	promoter-TSS (NM_007487)	promoter-TSS (NM_007487)	-251	NM_007487	11861	Mm.12723	NM_007487	ENSMUSG00000047446	Arl4a	AI467555|Arl4	ADP-ribosylation factor-like 4A	protein-coding
mm_142180.1	chr17	36271830	36271857	-	1	NA	promoter-TSS (NM_178281)	promoter-TSS (NM_178281)	161	NM_024468	79263	Mm.40624	NM_024468	ENSMUSG00000045409	Trim39	1100001D15Rik|E130103K13Rik|RBCC-B30.2|Rnf23|mKIAA4179|tfp	tripartite motif-containing 39	protein-coding
mm_23779.1	chr3	79028437	79028442	+	1	NA	Intergenic	Intergenic	116448	NM_001310536	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_98312.1	chr11	90035929	90035939	+	1	NA	3' UTR (NM_026433, exon 3 of 3)	3' UTR (NM_026433, exon 3 of 3)	5586	NM_026433	67888	Mm.212428	NM_026433	ENSMUSG00000069763	Tmem100	1810057C19Rik|AV011897	transmembrane protein 100	protein-coding
mm_64573.1	chr7	144915113	144915121	+	1	NA	promoter-TSS (NM_028184)	promoter-TSS (NM_028184)	17	NM_001347537	72284	Mm.273049	NM_028184	ENSMUSG00000031072	Oraov1	2210010N10Rik|TAOS1	oral cancer overexpressed 1	protein-coding
mm_56768.1	chr6	116264044	116264057	-	1	NA	promoter-TSS (NM_001290338)	promoter-TSS (NM_001290338)	-169	NM_001309446	67492	Mm.272772	NM_001081317	ENSMUSG00000042213	Zfand4	Anubl1	zinc finger, AN1-type domain 4	protein-coding
mm_139214.1	chr17	47728831	47728845	+	1	NA	exon (NM_025973, exon 2 of 9)	exon (NM_025973, exon 2 of 9)	1996	NM_025973	109820	Mm.22957	NM_025973	ENSMUSG00000023987	Pgc	2210410L06Rik|Upg-1|Upg1	progastricsin (pepsinogen C)	protein-coding
mm_73838.1	chr8	117461102	117461127	+	1	NA	3' UTR (NM_001163262, exon 21 of 21)	3' UTR (NM_001163262, exon 21 of 21)	1849	NR_106046	102465653		NR_106046	ENSMUSG00000098483	Mir7078	Gm27386|mmu-mir-7078	microRNA 7078	ncRNA
mm_7148.1	chr1	91398769	91398837	-	1	NA	promoter-TSS (NM_023343)	promoter-TSS (NM_023343)	-20	NM_023343	67444	Mm.337240	NM_023343	ENSMUSG00000026309	Ilkap	0710007A14Rik|1600009O09Rik|PP2C-DELTA	integrin-linked kinase-associated serine/threonine phosphatase 2C	protein-coding
mm_160077.1	chr7	10446880	10446880	+	1	NA	promoter-TSS (NM_134229)	promoter-TSS (NM_134229)	91	NM_134229	171263	Mm.377216	NM_134229	ENSMUSG00000046716	Vmn1r67	V1re10	vomeronasal 1 receptor 67	protein-coding
mm_42165.1	chr5	112259482	112259499	+	1	NA	intron (NM_023695, intron 3 of 5)	intron (NM_023695, intron 3 of 5)	3670	NM_001312893	12960	Mm.29488	NM_023695	ENSMUSG00000029343	Crybb1	3110006K12Rik|BB1CRY	crystallin, beta B1	protein-coding
mm_90389.1	chr10	127321908	127321912	+	1	NA	promoter-TSS (NM_001285785)	promoter-TSS (NM_001285785)	-54	NM_001285785	216445	Mm.227198	NM_146011	ENSMUSG00000040345	Arhgap9	AU043488	Rho GTPase activating protein 9	protein-coding
mm_102069.1	chr11	52258889	52258899	-	1	NA	exon (NM_009331, exon 5 of 10)	exon (NM_009331, exon 5 of 10)	23701	NM_009331	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_120406.1	chr14	65100698	65100709	+	1	NA	Intergenic	Intergenic	-2597	NM_018788	54616	Mm.103748	NM_018788	ENSMUSG00000021978	Extl3	2900009G18Rik|AU040105|Ext1l|mKIAA0519	exostoses (multiple)-like 3	protein-coding
mm_73713.1	chr8	111701812	111701818	+	1	NA	Intergenic	Intergenic	-10805	NM_025583	66473	Mm.34374	NM_025583	ENSMUSG00000031957	Ctrb1	2200008D09Rik|AI504462|Ctrb|Prt-2	chymotrypsinogen B1	protein-coding
mm_3184.1	chr1	135766242	135766257	+	1	NA	5' UTR (NM_013750, exon 1 of 2)	5' UTR (NM_013750, exon 1 of 2)	164	NM_013750	27280	Mm.34346	NM_013750	ENSMUSG00000041801	Phlda3	Tih1	pleckstrin homology like domain, family A, member 3	protein-coding
mm_5744.1	chr1	45925571	45925588	-	1	NA	promoter-TSS (NM_016917)	promoter-TSS (NM_016917)	15	NM_016917	53945	Mm.28756	NM_016917	ENSMUSG00000025993	Slc40a1	Dusg|Fpn1|IREG1|MTP|MTP1|Ol5|Pcm|Slc11a3|Slc39a1	solute carrier family 40 (iron-regulated transporter), member 1	protein-coding
mm_6840.1	chr1	84233389	84233390	-	1	NA	intron (NM_001003948, intron 1 of 2)	intron (NM_001003948, intron 1 of 2)	-14428	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_97990.1	chr11	83964370	83964390	+	1	NA	promoter-TSS (NM_194341)	promoter-TSS (NM_194341)	-51	NM_194341	217030	Mm.82680	NM_194341	ENSMUSG00000034940	Synrg	Ap1gbp1|SYNG	synergin, gamma	protein-coding
mm_163546.1	chr13	19337251	19337271	+	1	NA	Intergenic	Intergenic	58552	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_100338.1	chr11	118393258	118393349	+	1	NA	exon (NM_011150, exon 6 of 6)	exon (NM_011150, exon 6 of 6)	8628	NM_011150	19039	Mm.3152	NM_011150	ENSMUSG00000033880	Lgals3bp	90K|CyCAP|MAC-2BP|Ppicap|Tango10b	lectin, galactoside-binding, soluble, 3 binding protein	protein-coding
mm_163473.1	chr12	103958863	103958869	-	1	NA	Intergenic	Intergenic	-1969	NM_009247	20704	Mm.312593	NM_009247	ENSMUSG00000072849	Serpina1e	Dom5|PI5|Spi1-5	serine (or cysteine) peptidase inhibitor, clade A, member 1E	protein-coding
mm_143452.1	chr17	70924959	70925003	-	1	NA	Intergenic	Intergenic	65535	NM_023402	67938	Mm.261329	NM_023402	ENSMUSG00000034868	Myl12b	1500001M02Rik|C77744|Mylc2b|RLC-B	myosin, light chain 12B, regulatory	protein-coding
mm_6913.1	chr1	84839452	84839462	-	1	NA	promoter-TSS (NM_025386)	promoter-TSS (NM_025386)	-153	NM_133975	14897	Mm.209265	NM_133975	ENSMUSG00000026219	Trip12	1110036I07Rik|6720416K24Rik|AA410158|Gtl6|TRIP-12	thyroid hormone receptor interactor 12	protein-coding
mm_135500.1	chr16	46496325	46496338	-	1	NA	intron (NM_021496, intron 1 of 8)	CpG	636	NM_021496	58998	Mm.40477	NM_021495	ENSMUSG00000022656	Nectin3	2610301B19Rik|3000002N23Rik|4921513D19Rik|AA407785|AU016832|AW538082|CD113|Pvrl3	nectin cell adhesion molecule 3	protein-coding
mm_137320.1	chr17	24895520	24895542	+	1	NA	promoter-TSS (NM_001163102)	promoter-TSS (NM_001163102)	411	NM_023260	79044	Mm.328851	NM_023260	ENSMUSG00000038880	Mrps34	0610007F04Rik|5330430D13Rik|AV001970|Tce2	mitochondrial ribosomal protein S34	protein-coding
mm_22137.1	chr2	170497142	170497147	-	1	NA	promoter-TSS (NM_009996)	promoter-TSS (NM_009996)	1	NM_009996	13081	Mm.6575	NM_009996	ENSMUSG00000038567	Cyp24a1	24-OHase|CP24|Cyp24	cytochrome P450, family 24, subfamily a, polypeptide 1	protein-coding
mm_27135.1	chr3	32398218	32398226	-	1	NA	Intergenic	Intergenic	-32557	NM_009517	22401	Mm.35705	NM_009517	ENSMUSG00000027663	Zmat3	Wig1	zinc finger matrin type 3	protein-coding
mm_158025.1	chrX	96166891	96166921	-	1	NA	3' UTR (NM_010833, exon 13 of 13)	3' UTR (NM_010833, exon 13 of 13)	70861	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_65391.1	chr7	25092579	25092597	-	1	NA	3' UTR (NM_001163556, exon 14 of 14)	3' UTR (NM_001163556, exon 14 of 14)	4587	NR_105855	102465968		NR_105855	ENSMUSG00000098441	Mir6537	Gm27808|mmu-mir-6537	microRNA 6537	ncRNA
mm_140852.1	chr17	23684020	23684032	-	1	NA	promoter-TSS (NM_020293)	promoter-TSS (NM_020293)	0	NM_020293	56863	Mm.491368	NM_020293	ENSMUSG00000066720	Cldn9	nmf329	claudin 9	protein-coding
mm_143681.1	chr17	80062118	80062143	-	1	NA	5' UTR (NM_144802, exon 1 of 13)	5' UTR (NM_144802, exon 1 of 13)	138	NM_144802	72692	Mm.64579	NM_144802	ENSMUSG00000024095	Hnrnpll	2510028H02Rik|2810036L13Rik|AI256697|AI852082|Hnrpll	heterogeneous nuclear ribonucleoprotein L-like	protein-coding
mm_48106.1	chr5	137072262	137072277	-	1	NA	promoter-TSS (NM_008871)	promoter-TSS (NM_008871)	3	NM_008871	18787	Mm.250422	NM_008871	ENSMUSG00000037411	Serpine1	PAI-1|PAI1|Planh1	serine (or cysteine) peptidase inhibitor, clade E, member 1	protein-coding
mm_57299.1	chr6	124464773	124464783	-	1	NA	promoter-TSS (NM_153508)	promoter-TSS (NM_153508)	6	NM_153508	232370	Mm.193701	NM_153508	ENSMUSG00000008153	Clstn3	CSTN3|Cs3|Cst-3|alc-beta	calsyntenin 3	protein-coding
mm_58820.1	chr7	16453025	16453031	+	1	NA	exon (NM_026938, exon 1 of 3)	exon (NM_026938, exon 1 of 3)	249	NM_026938	69094	Mm.29633	NM_026938	ENSMUSG00000019158	Tmem160	1810008O21Rik	transmembrane protein 160	protein-coding
mm_6796.1	chr1	84150191	84150205	-	1	NA	intron (NM_001003948, intron 2 of 2)	intron (NM_001003948, intron 2 of 2)	68763	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_121405.1	chr14	119298958	119298978	+	1	NA	intron (NM_015820, intron 1 of 1)	B4A|SINE|B4	160703	NM_015820	50787	Mm.445777	NM_015820	ENSMUSG00000053465	Hs6st3	6OST3|HS6ST-3	heparan sulfate 6-O-sulfotransferase 3	protein-coding
mm_134024.1	chr16	4964169	4964220	-	1	NA	promoter-TSS (NM_001271586)	promoter-TSS (NM_001271586)	43	NM_028301	72615	Mm.290628	NM_028301	ENSMUSG00000022515	Anks3	2700067D09Rik|C81345|mKIAA1977	ankyrin repeat and sterile alpha motif domain containing 3	protein-coding
mm_164717.1	chr17	56121925	56121942	-	1	NA	promoter-TSS (NM_029796)	promoter-TSS (NM_029796)	13	NM_029796	76905	Mm.348025	NM_029796	ENSMUSG00000037095	Lrg1	1300008B03Rik|2310031E04Rik|Lrg|Lrhg	leucine-rich alpha-2-glycoprotein 1	protein-coding
mm_59255.1	chr7	24862429	24862437	+	1	NA	Intergenic	(CACCC)n|Simple_repeat|Simple_repeat	7258	NM_182785	232973	Mm.189648	NM_182785	ENSMUSG00000062732	Lypd4	4933400F01Rik	Ly6/Plaur domain containing 4	protein-coding
mm_25455.1	chr3	108384006	108384017	+	1	NA	promoter-TSS (NR_040560)	promoter-TSS (NR_040560)	173	NM_019976	56742	Mm.389499	NM_019976	ENSMUSG00000068744	Psrc1	5430413I02Rik|AL033312|Dda3	proline/serine-rich coiled-coil 1	protein-coding
mm_7012.1	chr1	86503427	86503448	-	1	NA	Intergenic	Intergenic	-23299	NM_008972	19231	Mm.19187	NM_008972	ENSMUSG00000026238	Ptma	Thym	prothymosin alpha	protein-coding
mm_48844.1	chr5	149367132	149367160	-	1	NA	Intergenic	Intergenic	-44660	NM_027519	70717	Mm.252139	NM_027519	ENSMUSG00000029659	Medag	6330406I15Rik|Awms3|MEDA-4|Meda4|mAWMS3	mesenteric estrogen dependent adipogenesis	protein-coding
mm_86968.1	chr10	25375239	25375249	+	1	NA	intron (NM_001199265, intron 1 of 19)	intron (NM_001199265, intron 1 of 19)	15446	NM_001199265	13822	Mm.306026	NM_013511	ENSMUSG00000019978	Epb41l2	4.1G|AW555191|D10Ertd398e|Epb4.1l2|NBL2	erythrocyte membrane protein band 4.1 like 2	protein-coding
mm_140039.1	chr17	74395647	74395655	+	1	NA	promoter-TSS (NM_144798)	promoter-TSS (NM_144798)	43	NM_144798	210148	Mm.243943	NM_144798	ENSMUSG00000024069	Slc30a6	9530029F08Rik|ZnT6	solute carrier family 30 (zinc transporter), member 6	protein-coding
mm_115434.1	chr13	117272039	117272076	+	1	NA	exon (NM_010330, exon 8 of 9)	exon (NM_010330, exon 8 of 9)	51484	NM_010330	13723	Mm.274926	NM_010330	ENSMUSG00000021728	Emb	AL022799|Gp70	embigin	protein-coding
mm_129055.1	chr15	75566609	75566658	-	1	NA	promoter-TSS (NM_001135689)	promoter-TSS (NM_001135689)	15	NM_001135689	23934	Mm.22154	NM_011837	ENSMUSG00000022577	Ly6h	-	lymphocyte antigen 6 complex, locus H	protein-coding
mm_133.1	chr1	10056923	10056926	+	1	NA	intron (NM_026493, intron 3 of 29)	intron (NM_026493, intron 3 of 29)	18706	NM_026493	211660	Mm.244046	NM_026493	ENSMUSG00000056763	Cspp1	2310020J12Rik|4930413O22Rik|AA387550|BC055915|Cspp2|Cspp3	centrosome and spindle pole associated protein 1	protein-coding
mm_134867.1	chr16	28641058	28641066	-	1	NA	intron (NM_010199, intron 2 of 5)	Lx5b|LINE|L1	-41019	NR_030463	751543		NR_030463	ENSMUSG00000076064	Mir690	Mirn690|mir-690|mmu-mir-690	microRNA 690	ncRNA
mm_76266.1	chr8	84042541	84042599	-	1	NA	promoter-TSS (NM_016671)	promoter-TSS (NM_016671)	5	NM_016671	50931	Mm.38386	NM_016671	ENSMUSG00000005465	Il27ra	CRL1|IL-27R|Tccr|WSX-1|Wsx1|zcytor1	interleukin 27 receptor, alpha	protein-coding
mm_27694.1	chr3	66296708	66296762	-	1	NA	5' UTR (NM_145820, exon 1 of 14)	5' UTR (NM_145820, exon 1 of 14)	102	NM_145820	72789	Mm.443526	NM_028357	ENSMUSG00000027831	Veph1	2810471M23Rik|Veph	ventricular zone expressed PH domain-containing 1	protein-coding
mm_69884.1	chr7	141637037	141637045	-	1	NA	intron (NM_001330001, intron 31 of 33)	intron (NM_001330001, intron 31 of 33)	16340	NR_106030	102466798		NR_106030	ENSMUSG00000098759	Mir7063	Gm27654|mmu-mir-7063	microRNA 7063	ncRNA
mm_136956.1	chr17	15327148	15327148	+	1	NA	Intergenic	Intergenic	27313	NR_033511	100038481	Mm.387544	NR_033511		Gm10510	ENSMUSG00000073453	predicted gene 10510	ncRNA
mm_116338.1	chr13	38179081	38179093	-	1	NA	exon (NM_023842, exon 11 of 24)	exon (NM_023842, exon 11 of 24)	-25852	NM_026382	67797	Mm.250783	NM_026382	ENSMUSG00000021431	Snrnp48	1110050F08Rik|6530403A03Rik|C6orf151	small nuclear ribonucleoprotein 48 (U11/U12)	protein-coding
mm_31717.1	chr4	62652459	62652477	+	1	NA	intron (NM_134257, intron 9 of 15)	intron (NM_134257, intron 9 of 15)	-21506	NM_001310706	50780	Mm.286753	NM_019492	ENSMUSG00000059810	Rgs3	4930506N09Rik|C2PA-RGS3|C2pa|PDZ-RGS3|RGS3S	regulator of G-protein signaling 3	protein-coding
mm_8042.1	chr1	135277943	135277946	-	1	NA	intron (NM_001159624, intron 2 of 9)	B1F2|SINE|Alu	6140	NM_145417	215615	Mm.291048	NM_145417	ENSMUSG00000041926	Rnpep	-	arginyl aminopeptidase (aminopeptidase B)	protein-coding
mm_21166.1	chr2	154613426	154613444	-	1	NA	promoter-TSS (NM_199304)	promoter-TSS (NM_199304)	67	NM_199304	228807	Mm.103555	NM_199304	ENSMUSG00000059842	Zfp341	Znf341	zinc finger protein 341	protein-coding
mm_91381.1	chr10	30618437	30618473	-	1	NA	promoter-TSS (NM_025798)	promoter-TSS (NM_025798)	-89	NM_025798	66847	Mm.46218	NM_025798	ENSMUSG00000019791	Hint3	0610010I17Rik|AV009015|HINT-3|HINT-4|HINT4	histidine triad nucleotide binding protein 3	protein-coding
mm_15738.1	chr2	164237264	164237272	+	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	1073	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_7021.1	chr1	86670566	86670579	-	1	NA	promoter-TSS (NM_010933)	promoter-TSS (NM_010933)	1	NM_010933	18159	Mm.12802	NM_010933	ENSMUSG00000026241	Nppc	CNP|lbab	natriuretic peptide type C	protein-coding
mm_20088.1	chr2	120850370	120850387	-	1	NA	promoter-TSS (NM_001024856)	promoter-TSS (NM_001024856)	40	NM_001024857	140810	Mm.275698	NM_080788	ENSMUSG00000090100	Ttbk2	2610507N02Rik|AI326283|B930008N24Rik|TTK|Ttbk|Ttbk1|mKIAA0847	tau tubulin kinase 2	protein-coding
mm_40039.1	chr5	33820375	33820441	+	1	NA	Intergenic	CpG	-22704	NM_175231	107823	Mm.19892	NM_175231	ENSMUSG00000057406	Whsc1	5830445G22Rik|9430010A17Rik|AW555663|C130020C13Rik|D030027O06Rik|D930023B08Rik|MMSET|NSD2|Whsc1l|mKIAA1090	Wolf-Hirschhorn syndrome candidate 1 (human)	protein-coding
mm_16532.1	chr2	181579316	181579339	+	1	NA	promoter-TSS (NR_027290)	promoter-TSS (NR_027290)	-205	NR_027290	100271841	Mm.438007	NR_027289	ENSMUSG00000010492	Uckl1os	Gm16119|OTTMUSG00000030649	uridine-cytidine kinase 1-like 1, opposite strand	ncRNA
mm_59506.1	chr7	27560499	27560516	+	1	NA	promoter-TSS (NM_001122767)	promoter-TSS (NM_001122767)	31	NM_001122767	66367	Mm.29831	NM_175107	ENSMUSG00000049643	2310022A10Rik	-	RIKEN cDNA 2310022A10 gene	protein-coding
mm_129289.1	chr15	77163337	77163339	-	1	NA	intron (NM_053104, intron 2 of 13)	intron (NM_053104, intron 2 of 13)	-9526	NM_001286418	93686	Mm.202774	NM_053104	ENSMUSG00000033565	Rbfox2	Fbm2|Fxh|Hrnbp2|Rbm9	RNA binding protein, fox-1 homolog (C. elegans) 2	protein-coding
mm_73009.1	chr8	93811284	93811320	+	1	NA	TTS (NR_026888)	TTS (NR_026888)	464	NM_001113384	14681	Mm.251445	NM_010308	ENSMUSG00000031748	Gnao1	AW050213|Galphao|Gnao|alphaO	guanine nucleotide binding protein, alpha O	protein-coding
mm_62328.1	chr7	100473017	100473024	+	1	NA	promoter-TSS (NM_009464)	promoter-TSS (NM_009464)	29	NM_009464	22229	Mm.6254	NM_009464	ENSMUSG00000032942	Ucp3	AI645527|Slc25a9|UCP-3	uncoupling protein 3 (mitochondrial, proton carrier)	protein-coding
mm_131196.1	chr16	8470764	8470807	+	1	NA	promoter-TSS (NM_146247)	promoter-TSS (NM_146247)	-28	NM_146247	239706	Mm.214953	NM_146247	ENSMUSG00000039345	Mettl22	-	methyltransferase like 22	protein-coding
mm_153326.1	chr19	38124330	38124354	-	1	NA	exon (NM_011255, exon 3 of 6)	exon (NM_011255, exon 3 of 6)	469	NM_011255	19662	Mm.2605	NM_011255	ENSMUSG00000024990	Rbp4	Rbp-4	retinol binding protein 4, plasma	protein-coding
mm_83563.1	chr9	46303076	46303089	-	1	NA	TTS (NM_183104)	TTS (NM_183104)	16904	NM_183104	74361	Mm.159169	NM_183104	ENSMUSG00000056617	4931429L15Rik	-	RIKEN cDNA 4931429L15 gene	protein-coding
mm_45347.1	chr5	65858187	65858214	-	1	NA	Intergenic	Intergenic	-5369	NM_001081105	74734	Mm.20323	NM_001081105	ENSMUSG00000029204	Rhoh	5830400A04Rik|AU019774|Arhh	ras homolog family member H	protein-coding
mm_55762.1	chr6	78466391	78466410	-	1	NA	3' UTR (NM_011260, exon 6 of 6)	3' UTR (NM_011260, exon 6 of 6)	2474	NM_011260	19695	Mm.252385	NM_011260	ENSMUSG00000030017	Reg3g	AI449515|REG-3-gamma|reg III-gamma	regenerating islet-derived 3 gamma	protein-coding
mm_116608.1	chr13	48819717	48819738	-	1	NA	intron (NM_011078, intron 9 of 21)	intron (NM_011078, intron 9 of 21)	51158	NM_011078	18676	Mm.486213	NM_011078	ENSMUSG00000038025	Phf2	GRC5	PHD finger protein 2	protein-coding
mm_95706.1	chr11	54446965	54446973	+	1	NA	intron (NM_173753, intron 1 of 17)	intron (NM_173753, intron 1 of 17)	8790	NM_173753	216742	Mm.34087	NM_173753	ENSMUSG00000035992	Fnip1	A730024A03Rik|AI838773|AW557298	folliculin interacting protein 1	protein-coding
mm_41464.1	chr5	91027458	91027492	+	1	NA	promoter-TSS (NM_053087)	promoter-TSS (NM_053087)	-42	NM_053087	71920	Mm.197319	NM_053087	ENSMUSG00000035020	Epgn	2310069M11Rik|epigen	epithelial mitogen	protein-coding
mm_67128.1	chr7	70366518	70366564	-	1	NA	5' UTR (NM_183261, exon 1 of 3)	5' UTR (NM_183261, exon 1 of 3)	205	NM_183261	11819	Mm.158143	NM_009697	ENSMUSG00000030551	Nr2f2	2700033K02Rik|9430015G03Rik|ARP-1|Aporp1|COUP-TF2|COUP-TFII|COUPTFB|EAR3|SVP40|Tcfcoup2	nuclear receptor subfamily 2, group F, member 2	protein-coding
mm_73900.1	chr8	119441398	119441418	+	1	NA	5' UTR (NM_027950, exon 2 of 6)	5' UTR (NM_027950, exon 2 of 6)	4246	NM_027950	71839	Mm.272357	NM_027950	ENSMUSG00000074063	Osgin1	1700012B18Rik|Okl38	oxidative stress induced growth inhibitor 1	protein-coding
mm_93119.1	chr10	91170501	91170528	-	1	NA	promoter-TSS (NM_001283048)	promoter-TSS (NM_001283048)	36	NM_001283048	21917	Mm.159684	NM_011605	ENSMUSG00000019961	Tmpo	5630400D24Rik|AI195756|AI606875|AW214352|AW547477|LAP2|TP	thymopoietin	protein-coding
mm_32150.1	chr4	99909794	99909799	+	1	NA	intron (NM_145549, intron 10 of 11)	intron (NM_145549, intron 10 of 11)	-19655	NM_028132	72157	Mm.217764	NM_028132	ENSMUSG00000025791	Pgm2	2610020G18Rik|AA407108|AI098105|Pgm-2|Pgm1	phosphoglucomutase 2	protein-coding
mm_121330.1	chr14	114949044	114949084	+	1	NA	Intergenic	Intergenic	-3116	NR_126548	74982		NR_126548		1700100I10Rik	1700085D13Rik|4930481K08Rik	RIKEN cDNA 1700100I10 gene	ncRNA
mm_45905.1	chr5	89209110	89209121	-	1	NA	intron (NM_001197147, intron 18 of 25)	ERVB7_1-LTR_MM|LTR|ERVK	248783	NM_008096	14473	Mm.196595	NM_008096	ENSMUSG00000035540	Gc	DBP|VDB	group specific component	protein-coding
mm_157676.1	chrX	59431827	59431830	-	1	NA	intron (NM_001290414, intron 2 of 6)	intron (NM_001290414, intron 2 of 6)	153744	NM_001290414	14168	Mm.7995	NM_010200	ENSMUSG00000031137	Fgf13	Fhf2	fibroblast growth factor 13	protein-coding
mm_162801.1	chr10	77215665	77215665	+	1	NA	Intergenic	Intergenic	43558	NR_026944	100169878	Mm.420901	NR_026944	ENSMUSG00000078444	Gm10941	ENSMUSG00000078444	predicted gene 10941	ncRNA
mm_134750.1	chr16	23157202	23157220	-	1	NA	exon (NM_009605, exon 3 of 3)	exon (NM_009605, exon 3 of 3)	10675	NM_009605	11450	Mm.3969	NM_009605	ENSMUSG00000022878	Adipoq	30kDa|APN|Acdc|Acrp30|Ad|GBP28|adipo|apM1	adiponectin, C1Q and collagen domain containing	protein-coding
mm_121042.1	chr14	80021423	80021430	+	1	NA	exon (NM_001030294, exon 7 of 7)	exon (NM_001030294, exon 7 of 7)	21124	NM_001030294	380924	Mm.26456	NM_001030294	ENSMUSG00000022026	Olfm4	GC1|GW112|Gm296|Gm913|OlfD|pPD4	olfactomedin 4	protein-coding
mm_140228.1	chr17	83998540	83998554	+	1	NA	promoter-TSS (NR_130994)	promoter-TSS (NR_130994)	-5	NR_130994	78148	Mm.243918	NR_130994		8430430B14Rik	-	RIKEN cDNA 8430430B14 gene	ncRNA
mm_148182.1	chr18	78205922	78205977	-	1	NA	intron (NM_030683, intron 5 of 11)	intron (NM_030683, intron 5 of 11)	491	NM_001110274	27411	Mm.44158	NM_030683	ENSMUSG00000024552	Slc14a2	UT-A1|UT-A3	solute carrier family 14 (urea transporter), member 2	protein-coding
mm_171436.1	chr4	141053742	141053743	-	1	NA	promoter-TSS (NM_172122)	promoter-TSS (NM_172122)	-81	NM_172122	230872	Mm.80685	NM_172122	ENSMUSG00000040860	Crocc	-	ciliary rootlet coiled-coil, rootletin	protein-coding
mm_159743.1	chr5	72581091	72581091	-	1	NA	promoter-TSS (NM_174877)	promoter-TSS (NM_174877)	-7	NM_174877	317755	Mm.11934	NM_174877	ENSMUSG00000063935	Zar1	-	zygote arrest 1	protein-coding
mm_132065.1	chr16	30055628	30055636	+	1	NA	Intergenic	Intergenic	-9725	NM_008235	15205	Mm.390859	NM_008235	ENSMUSG00000022528	Hes1	Hry|bHLHb39	hairy and enhancer of split 1 (Drosophila)	protein-coding
mm_167232.1	chr8	13507449	13507461	+	1	NA	Intergenic	Intergenic	-12920	NM_019521	14456	Mm.3982	NM_019521	ENSMUSG00000031451	Gas6	Gas-6	growth arrest specific 6	protein-coding
mm_2288.1	chr1	91366446	91366468	+	1	NA	promoter-TSS (NM_173395)	promoter-TSS (NM_173395)	27	NM_173395	227358	Mm.389157	NM_173395	ENSMUSG00000047443	Erfe	4832406C22|Fam132b|myonectin	erythroferrone	protein-coding
mm_104916.1	chr11	99764154	99764157	-	1	NA	Intergenic	Intergenic	8758	NM_001126322	100040276	Mm.475095	NM_001126322	ENSMUSG00000078668	Gm11595	OTTMUSG00000002543	predicted gene 11595	protein-coding
mm_93023.1	chr10	87930701	87930723	-	1	NA	exon (NM_001111276, exon 4 of 4)	exon (NM_001111276, exon 4 of 4)	-35959	NR_000040	22172	Mm.391420	NR_000040		Tyms-ps	-	thymidylate synthase, pseudogene	pseudo
mm_64929.1	chr7	16285455	16285479	-	1	NA	promoter-TSS (NM_172297)	promoter-TSS (NM_172297)	-808	NM_172297	243846	Mm.482401	NM_172297	ENSMUSG00000041375	Ccdc9	2600011L02Rik	coiled-coil domain containing 9	protein-coding
mm_79362.1	chr9	54467736	54467738	+	1	NA	intron (NM_172771, intron 6 of 43)	L2a|LINE|L2	33889	NM_172771	235380	Mm.93636	NM_172771	ENSMUSG00000041268	Dmxl2	6330586A12|6430411K14Rik|E130119P06Rik|mKIAA0856	Dmx-like 2	protein-coding
mm_105339.1	chr11	102994880	102994915	-	1	NA	exon (NM_026551, exon 5 of 5)	exon (NM_026551, exon 5 of 5)	5024	NR_105896	102466988		NR_105896	ENSMUSG00000098613	Mir6931	Gm27303|mmu-mir-6931	microRNA 6931	ncRNA
mm_164522.1	chr17	3155806	3155810	+	1	NA	intron (NM_134123, intron 3 of 19)	intron (NM_134123, intron 3 of 19)	40836	NM_134123	106583	Mm.124373	NM_134123	ENSMUSG00000046201	Scaf8	A630086M08Rik|A930036P18Rik|AA408306|AI447644|AI448652|AU015035|Rbm16|mKIAA1116	SR-related CTD-associated factor 8	protein-coding
mm_166006.1	chr4	117134135	117134158	+	1	NA	promoter-TSS (NM_013807)	promoter-TSS (NM_013807)	-183	NM_001313916	12795	Mm.259022	NM_013807	ENSMUSG00000028680	Plk3	Cnk|Fnk|PLK-3|PRK	polo-like kinase 3	protein-coding
mm_154124.1	chr19	57230396	57230449	-	1	NA	Intergenic	Intergenic	-14390	NM_178688	226251	Mm.217161	NM_178688	ENSMUSG00000025085	Ablim1	2210411C18Rik|2610209L21Rik|4833406P10Rik|9330196J19Rik|AV079770|AW060987|AW215784|Limab1|mKIAA0059	actin-binding LIM protein 1	protein-coding
mm_69543.1	chr7	135695747	135695784	-	1	NA	exon (NM_001081117, exon 12 of 14)	exon (NM_001081117, exon 12 of 14)	20614	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_158474.1	chrX	141473854	141473858	-	1	NA	5' UTR (NM_053185, exon 1 of 45)	5' UTR (NM_053185, exon 1 of 45)	220	NM_053185	94216	Mm.155586	NM_053185	ENSMUSG00000031273	Col4a6	BB116301	collagen, type IV, alpha 6	protein-coding
mm_61542.1	chr7	79299837	79299863	+	1	NA	intron (NM_018811, intron 3 of 10)	intron (NM_018811, intron 3 of 10)	26584	NM_018811	54608	Mm.365490	NM_018811	ENSMUSG00000039202	Abhd2	2210009N18Rik|LABH2|Labh-2	abhydrolase domain containing 2	protein-coding
mm_17799.1	chr2	33260932	33260957	-	1	NA	intron (NM_001290572, intron 7 of 17)	intron (NM_001290572, intron 7 of 17)	44983	NM_011923	26360	Mm.208919	NM_011923	ENSMUSG00000004105	Angptl2	AI593246|AW260363|Arp2	angiopoietin-like 2	protein-coding
mm_101940.1	chr11	50207607	50207637	-	1	NA	exon (NM_011018, exon 3 of 8)	exon (NM_011018, exon 3 of 8)	3198	NM_001290769	18412	Mm.40828	NM_011018	ENSMUSG00000015837	Sqstm1	A170|OSF-6|Osi|STAP|STONE14|p62	sequestosome 1	protein-coding
mm_161051.1	chr12	52795822	52795822	+	1	NA	intron (NM_198111, intron 1 of 13)	intron (NM_198111, intron 1 of 13)	96439	NM_198111	238161	Mm.310822	NM_198111	ENSMUSG00000061603	Akap6	AI482140|Akapalpha|Akapbeta|PRKA	A kinase (PRKA) anchor protein 6	protein-coding
mm_32946.1	chr4	119539717	119539727	+	1	NA	promoter-TSS (NM_001290696)	promoter-TSS (NM_001290696)	61	NM_172699	230700	Mm.259227	NM_172699	ENSMUSG00000032998	Foxj3	C330039G02Rik|Fhd6	forkhead box J3	protein-coding
mm_156527.1	chrX	151046132	151046143	+	1	NA	Intergenic	Intergenic	-1033	NM_008001	14163	Mm.8142	NM_008001	ENSMUSG00000025265	Fgd1	ZFYVE3	FYVE, RhoGEF and PH domain containing 1	protein-coding
mm_52454.1	chr6	113690723	113690743	+	1	NA	intron (NM_001113553, intron 10 of 11)	intron (NM_001113553, intron 10 of 11)	-6317	NM_001347356	381801	Mm.333322	NM_001033463	ENSMUSG00000056952	Tatdn2	AI646012|mKIAA0218	TatD DNase domain containing 2	protein-coding
mm_160239.1	chr7	104068865	104068865	-	1	NA	exon (NM_147121, exon 1 of 1)	exon (NM_147121, exon 1 of 1)	164	NM_147121	259125	Mm.377862	NM_147121	ENSMUSG00000110012	Olfr644	MOR13-1	olfactory receptor 644	protein-coding
mm_132671.1	chr16	42875883	42875903	+	1	NA	promoter-TSS (NR_040522)	promoter-TSS (NR_040522)	-131	NR_040522	75722	Mm.243747	NR_040521	ENSMUSG00000075070	4932412D23Rik	ENSMUSG00000075070|Gm10809	RIKEN cDNA 4932412D23 gene	ncRNA
mm_148341.1	chr18	84589492	84589527	-	1	NA	promoter-TSS (NM_001033341)	promoter-TSS (NM_001033341)	-5	NM_001033341	240476	Mm.329575	NM_001033341	ENSMUSG00000048410	Zfp407	6430585N13Rik|Gm333|Gm334|Gm948|ZNF407	zinc finger protein 407	protein-coding
mm_28101.1	chr3	86546644	86546655	-	1	NA	exon (NM_011839, exon 1 of 1)	exon (NM_011839, exon 1 of 1)	1634	NM_011839	23937	Mm.389466	NM_011839	ENSMUSG00000057777	Mab21l2	-	mab-21-like 2 (C. elegans)	protein-coding
mm_137775.1	chr17	29491788	29491798	+	1	NA	exon (NM_008842, exon 4 of 6)	exon (NM_008842, exon 4 of 6)	748	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_123190.1	chr14	57916610	57916618	-	1	NA	3' UTR (NM_028643, exon 12 of 12)	3' UTR (NM_028643, exon 12 of 12)	-26352	NM_029492	75965	Mm.29044	NM_029492	ENSMUSG00000021969	Zdhhc20	4930542A17Rik|5033406L14Rik|AI448102|B230110O18Rik|ENSMUSG00000055956|HK11	zinc finger, DHHC domain containing 20	protein-coding
mm_10001.1	chr1	191519832	191519842	-	1	NA	Intergenic	MTE2b|LTR|ERVL-MaLR	55707	NM_001305233	76843	Mm.189102	NM_029766	ENSMUSG00000037474	Dtl	2810047L02Rik|5730564G15Rik|L2dtl|Ramp	denticleless E3 ubiquitin protein ligase	protein-coding
mm_90120.1	chr10	117280635	117280667	+	1	NA	exon (NM_017372, exon 2 of 4)	exon (NM_017372, exon 2 of 4)	1621	NM_017372	17105	Mm.45436	NM_017372	ENSMUSG00000069516	Lyz2	AI326280|Lys|Lysm|Lyzf2|Lyzs|Lzm|Lzm-s1|Lzp	lysozyme 2	protein-coding
mm_101623.1	chr11	35915594	35915604	-	1	NA	intron (NM_170779, intron 1 of 22)	intron (NM_170779, intron 1 of 22)	64490	NM_170779	211652	Mm.31267	NM_170779	ENSMUSG00000018849	Wwc1	AA408228|AU017197|BC037006|Kibra|mKIAA0869	WW, C2 and coiled-coil domain containing 1	protein-coding
mm_166080.1	chr4	137510972	137510992	+	1	NA	exon (NM_008305, exon 8 of 97)	exon (NM_008305, exon 8 of 97)	-27304	NR_105985	102465616		NR_105985	ENSMUSG00000099134	Mir7018	Gm27606|mmu-mir-7018	microRNA 7018	ncRNA
mm_89141.1	chr10	85871404	85871407	+	1	NA	promoter-TSS (NM_133993)	promoter-TSS (NM_133993)	-426	NM_133993	103136	Mm.18834	NM_133993	ENSMUSG00000001785	Pwp1	2310058A11Rik|2610205J09Rik|AI098170|AL022879|AV083409|AW550690	PWP1 homolog, endonuclein	protein-coding
mm_112797.1	chr13	20429100	20429109	+	1	NA	intron (NM_080288, intron 15 of 21)	Lx6|LINE|L1	-43886	NM_198093	140580	Mm.342392	NM_080288	ENSMUSG00000041112	Elmo1	6330578D22Rik|C230095H21Rik|CED-12	engulfment and cell motility 1	protein-coding
mm_118864.1	chr14	25842584	25842626	+	1	NA	intron (NM_013469, intron 1 of 14)	intron (NM_013469, intron 1 of 14)	450	NM_013469	11744	Mm.294083	NM_013469	ENSMUSG00000021866	Anxa11	A830099O17Rik|Anx11	annexin A11	protein-coding
mm_66539.1	chr7	45179540	45179567	-	1	NA	promoter-TSS (NM_001195255)	promoter-TSS (NM_001195255)	44	NM_001195255	100039953	Mm.300663	NM_001195255	ENSMUSG00000095276	Gfy	Gm2515|Gm581|Goofy	golgi-associated olfactory signaling regulator	protein-coding
mm_125608.1	chr15	60823944	60823956	+	1	NA	non-coding (NR_030696, exon 1 of 3)	non-coding (NR_030696, exon 1 of 3)	985	NR_030696	320469	Mm.230853	NM_177166		9930014A18Rik	-	RIKEN cDNA 9930014A18 gene	ncRNA
mm_140745.1	chr17	15830831	15830849	-	1	NA	Intergenic	CpG	-4254	NM_178615	68799	Mm.293466	NM_178615	ENSMUSG00000048027	Rgmb	1110059F19Rik|DRAGON	repulsive guidance molecule family member B	protein-coding
mm_113986.1	chr13	52582741	52582759	+	1	NA	promoter-TSS (NM_001198977)	promoter-TSS (NM_001198977)	-687	NM_001198977	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_146627.1	chr18	10182035	10182053	-	1	NA	promoter-TSS (NM_009071)	promoter-TSS (NM_009071)	-252	NM_009071	19877	Mm.6710	NM_009071	ENSMUSG00000024290	Rock1	1110055K06Rik|Rock-I	Rho-associated coiled-coil containing protein kinase 1	protein-coding
mm_60807.1	chr7	45639965	45640012	+	1	NA	promoter-TSS (NM_172418)	promoter-TSS (NM_172418)	11	NM_172418	74490	Mm.107442	NM_172418	ENSMUSG00000042918	Mamstr	2810022D01Rik|5430432N15Rik|AW743872|Mastr	MEF2 activating motif and SAP domain containing transcriptional regulator	protein-coding
mm_8774.1	chr1	161070614	161070674	-	1	NA	promoter-TSS (NR_131028)	promoter-TSS (NR_131028)	16	NM_172644	226539	Mm.28125	NM_172644	ENSMUSG00000026709	Dars2	5830468K18Rik|aspRS	aspartyl-tRNA synthetase 2 (mitochondrial)	protein-coding
mm_106989.1	chr12	10391051	10391071	+	1	NA	TTS (NM_001310582)	TTS (NM_001310582)	281	NM_023697	105014	Mm.119343	NM_023697	ENSMUSG00000020621	Rdh14	3110030G19Rik|AW215439|PAN2	retinol dehydrogenase 14 (all-trans and 9-cis)	protein-coding
mm_83694.1	chr9	50603793	50603824	-	1	NA	promoter-TSS (NM_013897)	promoter-TSS (NM_013897)	41	NM_025848	66925	Mm.10406	NM_025848	ENSMUSG00000000171	Sdhd	3110001M13Rik|AVLL5809|C78570|PRO19626	succinate dehydrogenase complex, subunit D, integral membrane protein	protein-coding
mm_79163.1	chr9	47818721	47818751	+	1	NA	promoter-TSS (NR_046048)	promoter-TSS (NR_046048)	-528	NR_046048	100038460	Mm.447649	NR_046048		Gm10677	ENSMUSG00000074363	predicted gene 10677	ncRNA
mm_37888.1	chr4	132530703	132530757	-	1	NA	exon (NM_007512, exon 4 of 4)	exon (NM_007512, exon 4 of 4)	4684	NM_007512	11983	Mm.2171	NM_007512	ENSMUSG00000054428	Atpif1	Atpi|IF(1)|If1	ATPase inhibitory factor 1	protein-coding
mm_62312.1	chr7	100227784	100227788	+	1	NA	5' UTR (NM_027629, exon 1 of 14)	5' UTR (NM_027629, exon 1 of 14)	179	NM_027629	70974	Mm.440524	NM_027629	ENSMUSG00000030729	Pgm2l1	4931406N15Rik|AI553438|BM32A	phosphoglucomutase 2-like 1	protein-coding
mm_79349.1	chr9	53771322	53771324	+	1	NA	promoter-TSS (NM_028060)	promoter-TSS (NM_028060)	-212	NM_028060	72022	Mm.26159	NM_028060	ENSMUSG00000042195	Slc35f2	1500009K05Rik|AU019213	solute carrier family 35, member F2	protein-coding
mm_37978.1	chr4	133601823	133601838	-	1	NA	5' UTR (NM_018754, exon 1 of 1)	5' UTR (NM_018754, exon 1 of 1)	338	NM_018754	55948	Mm.44482	NM_018754	ENSMUSG00000047281	Sfn	Er|Mme1|Ywhas	stratifin	protein-coding
mm_38746.1	chr4	145270247	145270265	-	1	NA	intron (NM_009401, intron 12 of 12)	intron (NM_009401, intron 12 of 12)	-23386	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_145912.1	chr18	66470843	66470847	+	1	NA	Intergenic	Intergenic	12241	NM_021451	58801	Mm.271878	NM_021451	ENSMUSG00000024521	Pmaip1	Noxa	phorbol-12-myristate-13-acetate-induced protein 1	protein-coding
mm_49283.1	chr6	17641605	17641607	+	1	NA	intron (NM_007604, intron 1 of 9)	intron (NM_007604, intron 1 of 9)	4508	NM_007604	12343	Mm.392504	NM_007604	ENSMUSG00000015733	Capza2	1110053K06Rik|AW208808|Cappa2	capping protein (actin filament) muscle Z-line, alpha 2	protein-coding
mm_63929.1	chr7	139410296	139410299	+	1	NA	intron (NM_183144, intron 1 of 15)	intron (NM_183144, intron 1 of 15)	21188	NM_001127363	212111	Mm.28308	NM_183144	ENSMUSG00000025477	Inpp5a	-	inositol polyphosphate-5-phosphatase A	protein-coding
mm_5401.1	chr1	33720258	33720270	-	1	NA	promoter-TSS (NM_001159729)	promoter-TSS (NM_001159729)	-155	NM_001159729	19335	Mm.86744	NM_008999	ENSMUSG00000004768	Rab23	AW545388|opb|opb2	RAB23, member RAS oncogene family	protein-coding
mm_118707.1	chr14	22164972	22165003	+	1	NA	intron (NM_028275, intron 2 of 6)	Lx8b|LINE|L1	145275	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_84832.1	chr9	78342583	78342599	-	1	NA	intron (NM_008182, intron 1 of 6)	MTB|LTR|ERVL-MaLR	4554	NM_008182	14858	Mm.422778	NM_008182	ENSMUSG00000057933	Gsta2	Gst2-2|Gstc-2|Gstc2	glutathione S-transferase, alpha 2 (Yc2)	protein-coding
mm_91996.1	chr10	62143918	62143924	-	1	NA	Intergenic	Intergenic	10831	NM_009719	11925	Mm.57236	NM_009719	ENSMUSG00000044312	Neurog3	Atoh5|Math4B|bHLHa7|ngn3	neurogenin 3	protein-coding
mm_21176.1	chr2	154872067	154872077	-	1	NA	3' UTR (NM_026030, exon 9 of 9)	3' UTR (NM_026030, exon 9 of 9)	20834	NM_026030	67204	Mm.377134	NM_026030	ENSMUSG00000074656	Eif2s2	2810026E11Rik|38kDa|AA408636|AA571381|AA986487|AW822225|D2Ertd303e|EIF2|EIF2B	eukaryotic translation initiation factor 2, subunit 2 (beta)	protein-coding
mm_39342.1	chr5	8893678	8893745	+	1	NA	promoter-TSS (NM_008830)	promoter-TSS (NM_008830)	-10	NM_008830	18670	Mm.297825	NM_008830	ENSMUSG00000042476	Abcb4	Mdr2|Pgy-2|Pgy2|mdr-2	ATP-binding cassette, sub-family B (MDR/TAP), member 4	protein-coding
mm_23355.1	chr3	55112378	55112405	+	1	NA	5' UTR (NM_001144987, exon 1 of 9)	5' UTR (NM_001144987, exon 1 of 9)	225	NM_001144987	229285	Mm.235523	NM_144895	ENSMUSG00000036580	Spg20	AI840044|C79168|SPARTIN|TAHCCP1|mKIAA0610	spastic paraplegia 20, spartin (Troyer syndrome) homolog (human)	protein-coding
mm_130256.1	chr15	96642282	96642310	-	1	NA	promoter-TSS (NM_001166456)	promoter-TSS (NM_001166456)	47	NM_001166456	105727	Mm.103568	NM_134086	ENSMUSG00000023169	Slc38a1	AA408026|AA409865|AL022800|AU015942|NAT2	solute carrier family 38, member 1	protein-coding
mm_134418.1	chr16	17838127	17838149	-	1	NA	promoter-TSS (NM_030558)	promoter-TSS (NM_030558)	48	NM_030558	80733	Mm.390864	NM_030558	ENSMUSG00000090236	Car15	AI315043|Ca15|Cals2	carbonic anhydrase 15	protein-coding
mm_132676.1	chr16	42921791	42921795	+	1	NA	intron (NM_001285805, intron 1 of 10)	intron (NM_001285805, intron 1 of 10)	-9723	NR_040402	100503040	Mm.490721	NR_040402		Gm19522	-	predicted gene, 19522	ncRNA
mm_83769.1	chr9	52048749	52048759	-	1	NA	promoter-TSS (NR_023357)	promoter-TSS (NR_023357)	-49	NR_023357	629557	Mm.422775	NR_023357		Gm6981	EG629557	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_39881.1	chr5	31077600	31077608	+	1	NA	exon (NM_001289522, exon 41 of 43)	exon (NM_001289522, exon 41 of 43)	15923	NM_011773	22784	Mm.1396	NM_011773	ENSMUSG00000029151	Slc30a3	Znt3	solute carrier family 30 (zinc transporter), member 3	protein-coding
mm_117018.1	chr13	58127613	58127631	-	1	NA	exon (NM_029872, exon 1 of 1)	exon (NM_029872, exon 1 of 1)	934	NM_029872	77134	Mm.490274	NM_029872	ENSMUSG00000007836	Hnrnpa0	1110055B05Rik|3010025E17Rik|Hnrpa0|hnRNP A0	heterogeneous nuclear ribonucleoprotein A0	protein-coding
mm_5661.1	chr1	42681433	42681435	-	1	NA	intron (NR_027826, intron 1 of 3)	intron (NR_027826, intron 1 of 3)	13391	NR_027826	66297	Mm.45203	NM_183252	ENSMUSG00000060424	Pantr1	2610017I09Rik|Pou3f3os|linc-Brn1a	POU domain, class 3, transcription factor 3 adjacent noncoding transcript 1	ncRNA
mm_161303.1	chr14	32201883	32201883	-	1	NA	promoter-TSS (NM_011960)	promoter-TSS (NM_011960)	8	NM_016897	53600	Mm.303703	NM_016897	ENSMUSG00000013701	Timm23	Tim23	translocase of inner mitochondrial membrane 23	protein-coding
mm_17089.1	chr2	23021627	23021629	-	1	NA	intron (NM_001331043, intron 1 of 10)	RMER19B|LTR|ERVK	18613	NM_001077192	11308	Mm.205647	NM_007380	ENSMUSG00000058835	Abi1	E3B1|NAP1|Ssh3bp1|abi-1	abl-interactor 1	protein-coding
mm_165627.1	chr3	65515500	65515501	+	1	NA	Intergenic	B3|SINE|B2	-12947	NM_178892	99929	Mm.246398	NM_178892	ENSMUSG00000034640	Tiparp	ARTD14|AW558171|PARP7	TCDD-inducible poly(ADP-ribose) polymerase	protein-coding
mm_7768.1	chr1	131200090	131200145	-	1	NA	promoter-TSS (NM_001311094)	promoter-TSS (NM_001311094)	68	NM_001311094	54354	Mm.248291	NM_018750	ENSMUSG00000026430	Rassf5	1300019G20Rik|Maxp1|Nore1|Nore1A|Nore1B|Rapl	Ras association (RalGDS/AF-6) domain family member 5	protein-coding
mm_91263.1	chr10	23350809	23350832	-	1	NA	promoter-TSS (NM_001347372)	promoter-TSS (NM_001347372)	-877	NM_010167	14051	Mm.332128	NM_010167	ENSMUSG00000010461	Eya4	B130023L16Rik	EYA transcriptional coactivator and phosphatase 4	protein-coding
mm_135322.1	chr16	38783721	38783736	-	1	NA	intron (NM_178924, intron 5 of 7)	intron (NM_178924, intron 5 of 7)	16475	NM_178924	22268	Mm.130793	NM_178924	ENSMUSG00000049436	Upk1b	AI413235|Tspan20|UPIb|Upk1	uroplakin 1B	protein-coding
mm_7329.1	chr1	105157854	105157860	-	1	NA	Intergenic	Intergenic	198853	NM_178779	320311	Mm.389162	NM_178779	ENSMUSG00000047496	Rnf152	A930029B02Rik	ring finger protein 152	protein-coding
mm_7187.1	chr1	92880219	92880231	-	1	NA	intron (NM_001347091, intron 11 of 17)	intron (NM_001347091, intron 11 of 17)	22681	NM_172850	241158	Mm.108280	NM_172850	ENSMUSG00000034212	Ankmy1	4930483I10Rik|ZMYND13	ankyrin repeat and MYND domain containing 1	protein-coding
mm_121.1	chr1	9799173	9799220	+	1	NA	intron (NM_177547, intron 1 of 16)	intron (NM_177547, intron 1 of 16)	1066	NM_177547	170755	Mm.336410	NM_133220	ENSMUSG00000025915	Sgk3	2510015P22Rik|A330005P07Rik|Cisk|fy|fz	serum/glucocorticoid regulated kinase 3	protein-coding
mm_95211.1	chr11	43632805	43632819	+	1	NA	Intergenic	Intergenic	-31250	NM_008375	16204	Mm.142716	NM_008375	ENSMUSG00000020405	Fabp6	GT|I-15P|I-BABP|ILBP|ILBP3|Illbp	fatty acid binding protein 6, ileal (gastrotropin)	protein-coding
mm_21285.1	chr2	156970406	156970418	-	1	NA	intron (NM_013865, intron 1 of 15)	MLT1F2|LTR|ERVL-MaLR	21699	NM_013865	29812	Mm.279256	NM_013865	ENSMUSG00000027634	Ndrg3	4833415O14Rik|AI747193|Ndr3	N-myc downstream regulated gene 3	protein-coding
mm_119444.1	chr14	46832153	46832166	+	1	NA	promoter-TSS (NM_026832)	promoter-TSS (NM_026832)	-85	NM_026832	68755	Mm.343809	NM_026832	ENSMUSG00000055128	Cgrrf1	1110038G02Rik|1810009H17Rik|CGR19	cell growth regulator with ring finger domain 1	protein-coding
mm_4378.1	chr1	172148099	172148103	+	1	NA	promoter-TSS (NM_153555)	promoter-TSS (NM_153555)	86	NM_153555	98193	Mm.159915	NM_153555	ENSMUSG00000026554	Dcaf8	AA408877|AA433120|AA792214|AU018973|C76055|D1Dau35e|D1Ucla4|H326|Wdr42a	DDB1 and CUL4 associated factor 8	protein-coding
mm_91665.1	chr10	43002692	43002715	-	1	NA	3' UTR (NM_175407, exon 7 of 7)	3' UTR (NM_175407, exon 7 of 7)	142191	NM_172938	268297	Mm.98731	NM_172938	ENSMUSG00000044770	Scml4	9330161D17|mFLJ00197	sex comb on midleg-like 4 (Drosophila)	protein-coding
mm_63371.1	chr7	127092461	127092467	+	1	NA	exon (NM_178901, exon 2 of 2)	exon (NM_178901, exon 2 of 2)	1028	NM_178901	101602	Mm.490357	NM_178901	ENSMUSG00000045165	AI467606	-	expressed sequence AI467606	protein-coding
mm_113332.1	chr13	31558317	31558332	+	1	NA	5' UTR (NM_008239, exon 1 of 1)	5' UTR (NM_008239, exon 1 of 1)	154	NM_008239	15220	Mm.44235	NM_008239	ENSMUSG00000038415	Foxq1	HFH-1|Hfh1|Hfh1l|sa	forkhead box Q1	protein-coding
mm_132625.1	chr16	38902254	38902297	+	1	NA	promoter-TSS (NM_170599)	promoter-TSS (NM_170599)	-70	NM_170599	207683	Mm.245564	NM_170599	ENSMUSG00000022790	Igsf11	1700025L02Rik|BT-IgSF|Igsf13	immunoglobulin superfamily, member 11	protein-coding
mm_109134.1	chr12	106010205	106010225	+	1	NA	promoter-TSS (NM_011705)	promoter-TSS (NM_011705)	-48	NM_011705	22367	Mm.2981	NM_011705	ENSMUSG00000021115	Vrk1	51PK	vaccinia related kinase 1	protein-coding
mm_155866.1	chrX	101383782	101383802	+	1	NA	promoter-TSS (NM_001302497)	promoter-TSS (NM_001302497)	60	NM_001302497	14618	Mm.21198	NM_008124	ENSMUSG00000047797	Gjb1	Cnx32|Cx32|connexin-32	gap junction protein, beta 1	protein-coding
mm_20573.1	chr2	131085654	131085665	-	1	NA	exon (NM_011426, exon 2 of 21)	exon (NM_011426, exon 2 of 21)	1106	NM_011426	20612	Mm.1374	NM_011426	ENSMUSG00000027322	Siglec1	Cd169|Siglec-1|Sn	sialic acid binding Ig-like lectin 1, sialoadhesin	protein-coding
mm_42666.1	chr5	119671083	119671091	+	1	NA	promoter-TSS (NM_011535)	promoter-TSS (NM_011535)	-146	NM_011535	21386	Mm.219139	NM_011535	ENSMUSG00000018604	Tbx3	D5Ertd189e	T-box 3	protein-coding
mm_137957.1	chr17	32993170	32993178	+	1	NA	promoter-TSS (NM_001045559)	promoter-TSS (NM_001045559)	35	NM_001045559	240067	Mm.246667	NM_199020	ENSMUSG00000053390	Zfp952	BC057593|C920016K16Rik	zinc finger protein 952	protein-coding
mm_146571.1	chr18	6516090	6516106	-	1	NA	promoter-TSS (NM_007935)	promoter-TSS (NM_007935)	10	NM_007935	13831	Mm.312133	NM_007935	ENSMUSG00000024240	Epc1	2400007E14Rik|5730566F07Rik|A930032N02Rik|mir-1893	enhancer of polycomb homolog 1 (Drosophila)	protein-coding
mm_45469.1	chr5	69341574	69341582	-	1	NA	5' UTR (NM_175519, exon 1 of 2)	5' UTR (NM_175519, exon 1 of 2)	131	NM_175519	243043	Mm.234821	NM_175519	ENSMUSG00000037653	Kctd8	A730087N02Rik	potassium channel tetramerisation domain containing 8	protein-coding
mm_152289.1	chr19	8999692	8999737	-	1	NA	non-coding (NR_104460, exon 2 of 7)	non-coding (NR_104460, exon 2 of 7)	10430	NM_001286518	66395	Mm.203866	NM_009643	ENSMUSG00000069833	Ahnak	DY6	AHNAK nucleoprotein (desmoyokin)	protein-coding
mm_93550.1	chr10	116113953	116113957	-	1	NA	promoter-TSS (NM_001161855)	promoter-TSS (NM_001161855)	-38	NM_001161855	619332	Mm.391427	NM_001033821	ENSMUSG00000074734	4933416C03Rik	-	RIKEN cDNA 4933416C03 gene	protein-coding
mm_50249.1	chr6	42358305	42358320	+	1	NA	TTS (NM_023580)	TTS (NM_023580)	8484	NM_001289619	22793	Mm.282303	NM_011777	ENSMUSG00000029860	Zyx	9530098H06Rik|R75157	zyxin	protein-coding
mm_20157.1	chr2	122118365	122118397	-	1	NA	promoter-TSS (NM_145531)	promoter-TSS (NM_145531)	5	NM_145531	214585	Mm.222303	NM_145531	ENSMUSG00000033396	Spg11	6030465E24Rik|A330015I11|C530005A01Rik	spastic paraplegia 11	protein-coding
mm_125895.1	chr15	75890659	75890672	+	1	NA	TTS (NM_172607)	TTS (NM_172607)	-1942	NM_001282443	223645		NM_001282443	ENSMUSG00000098678	Mroh6	Gm19570	maestro heat-like repeat family member 6	protein-coding
mm_131524.1	chr16	17619504	17619514	+	1	NA	intron (NM_001164609, intron 1 of 19)	CpG	155	NM_001164609	77626	Mm.34659	NM_029945	ENSMUSG00000005899	Smpd4	4122402O22Rik|mKIAA1418	sphingomyelin phosphodiesterase 4	protein-coding
mm_49385.1	chr6	24791176	24791206	+	1	NA	promoter-TSS (NM_001079875)	promoter-TSS (NM_001079875)	3	NM_001079875	20690	Mm.4688	NM_009241	ENSMUSG00000029682	Spam1	AV039194|Ph-20	sperm adhesion molecule 1	protein-coding
mm_42717.1	chr5	120511174	120511211	+	1	NA	promoter-TSS (NM_133221)	promoter-TSS (NM_133221)	0	NM_001177595	170756	Mm.291070	NM_133221	ENSMUSG00000032754	Slc8b1	AF261233|NCKX6|NCLX|Slc24a6	solute carrier family 8 (sodium/lithium/calcium exchanger), member B1	protein-coding
mm_168222.1	chr10	78465363	78465377	-	1	NA	promoter-TSS (NM_172134)	promoter-TSS (NM_172134)	-422	NM_172134	216134	Mm.206159	NM_172134	ENSMUSG00000032788	Pdxk	2310036D04Rik|AA119688|C77999	pyridoxal (pyridoxine, vitamin B6) kinase	protein-coding
mm_76869.1	chr8	105525358	105525371	-	1	NA	exon (NM_013477, exon 6 of 8)	exon (NM_013477, exon 6 of 8)	6618	NM_008289	15484	Mm.5079	NM_008289	ENSMUSG00000031891	Hsd11b2	11HSD2	hydroxysteroid 11-beta dehydrogenase 2	protein-coding
mm_29738.1	chr3	126922826	126922847	-	1	NA	3' UTR (NM_178655, exon 25 of 25)	3' UTR (NM_178655, exon 25 of 25)	20550	NM_001034168	109676	Mm.220242	NM_178655	ENSMUSG00000032826	Ank2	100043364|AI835472|AW491075|Ank-2|Gm4392	ankyrin 2, brain	protein-coding
mm_33704.1	chr4	133632340	133632363	+	1	NA	intron (NM_001017968, intron 1 of 7)	intron (NM_001017968, intron 1 of 7)	1078	NM_001017968	503610	Mm.331948	NM_001017968	ENSMUSG00000037553	Zdhhc18	-	zinc finger, DHHC domain containing 18	protein-coding
mm_53401.1	chr6	131365284	131365333	+	1	NA	3' UTR (NM_011733, exon 9 of 9)	3' UTR (NM_011733, exon 9 of 9)	23142	NM_139117	56449	Mm.458000	NM_011733	ENSMUSG00000030189	Ybx3	Csda|Dpba|MSY3|MSY4|Yb2|dbpA|oxyR	Y box protein 3	protein-coding
mm_164917.1	chr18	75767162	75767169	+	1	NA	Intergenic	Intergenic	-53013	NM_145356	207259	Mm.159332	NM_145356	ENSMUSG00000044646	Zbtb7c	B230208J24Rik|Kr-pok|Zbtb36	zinc finger and BTB domain containing 7C	protein-coding
mm_68865.1	chr7	126414900	126414922	-	1	NA	promoter-TSS (NM_009844)	promoter-TSS (NM_009844)	-41	NM_009844	12478	Mm.4360	NM_009844	ENSMUSG00000030724	Cd19	AW495831	CD19 antigen	protein-coding
mm_113711.1	chr13	43508501	43508508	+	1	NA	Intergenic	Intergenic	-27531	NM_019930	56705	Mm.148781	NM_019930	ENSMUSG00000038546	Ranbp9	IBAP-1|Ibap1|RanBPM	RAN binding protein 9	protein-coding
mm_73451.1	chr8	106329242	106329247	+	1	NA	intron (NR_126090, intron 2 of 3)	intron (NR_126090, intron 2 of 3)	8744	NM_021491	58994	Mm.23298	NM_021491	ENSMUSG00000031906	Smpd3	4631433G07Rik|AI427456|AW537966|fro|nSMase2	sphingomyelin phosphodiesterase 3, neutral	protein-coding
mm_123253.1	chr14	61046231	61046241	-	1	NA	5' UTR (NM_013869, exon 1 of 10)	5' UTR (NM_013869, exon 1 of 10)	619	NM_013869	29820	Mm.281356	NM_013869	ENSMUSG00000060548	Tnfrsf19	AL023044|AW123854|TAJ|TAJ-ALPHA|TRADE|Troy	tumor necrosis factor receptor superfamily, member 19	protein-coding
mm_26236.1	chr3	141449196	141449198	+	1	NA	Intergenic	Intergenic	-16367	NM_009472	22253	Mm.24430	NM_009472	ENSMUSG00000059921	Unc5c	B130051O18Rik|Unc5h3|rcm	unc-5 netrin receptor C	protein-coding
mm_25753.1	chr3	123293759	123293806	+	1	NA	exon (NM_027135, exon 5 of 23)	exon (NM_027135, exon 5 of 23)	26286	NM_027135	69608	Mm.29293	NM_027135	ENSMUSG00000039234	Sec24d	2310020L09Rik|Gm1349	Sec24 related gene family, member D (S. cerevisiae)	protein-coding
mm_148552.1	chr19	4711996	4712008	+	1	NA	intron (NM_021287, intron 1 of 36)	CpG	779	NM_021287	20743	Mm.329668	NM_021287	ENSMUSG00000067889	Sptbn2	Spnb3|mKIAA0302	spectrin beta, non-erythrocytic 2	protein-coding
mm_36046.1	chr4	57290060	57290071	-	1	NA	intron (NM_011207, intron 1 of 25)	intron (NM_011207, intron 1 of 25)	11772	NM_011207	545622	Mm.246552	NM_011207	ENSMUSG00000038764	Ptpn3	9530011I20Rik|PTP-H1|PTPCL	protein tyrosine phosphatase, non-receptor type 3	protein-coding
mm_5472.1	chr1	36558351	36558366	-	1	NA	promoter-TSS (NM_001126047)	promoter-TSS (NM_001126047)	23	NM_001126047	20353	Mm.29558	NM_001126047	ENSMUSG00000026121	Sema4c	AI426163|M-Sema F|Semacl1|Semaf|Semai|sema I	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4C	protein-coding
mm_77879.1	chr9	7272521	7272537	+	1	NA	promoter-TSS (NM_008607)	promoter-TSS (NM_008607)	15	NM_008607	17386	Mm.5022	NM_008607	ENSMUSG00000050578	Mmp13	Clg|MMP-13|Mmp1	matrix metallopeptidase 13	protein-coding
mm_97315.1	chr11	76891133	76891152	+	1	NA	Intergenic	Intergenic	-13403	NM_025655	66601	Mm.25138	NM_025655	ENSMUSG00000020839	Tmigd1	2010002A20Rik|Tmigd	transmembrane and immunoglobulin domain containing 1	protein-coding
mm_149372.1	chr19	11372696	11372713	+	1	NA	Intergenic	Intergenic	-2784	NM_001310331	666907		NM_001310331	ENSMUSG00000101389	Ms4a4a	EG666907	membrane-spanning 4-domains, subfamily A, member 4A	protein-coding
mm_113803.1	chr13	46501860	46501885	+	1	NA	promoter-TSS (NM_026056)	promoter-TSS (NM_026056)	-31	NM_026056	67252	Mm.44529	NM_026056	ENSMUSG00000021373	Cap2	2810452G09Rik|AV045235	CAP, adenylate cyclase-associated protein, 2 (yeast)	protein-coding
mm_122733.1	chr14	52369686	52369731	-	1	NA	Intergenic	Intergenic	3343	NM_146432	258424	Mm.377493	NM_146432	ENSMUSG00000094140	Olfr1512	MOR223-5	olfactory receptor 1512	protein-coding
mm_116711.1	chr13	51567781	51567836	-	1	NA	promoter-TSS (NM_009167)	promoter-TSS (NM_009167)	-724	NM_009167	20418	Mm.131870	NM_009167	ENSMUSG00000021448	Shc3	N-Shc|Rai|ShcC	src homology 2 domain-containing transforming protein C3	protein-coding
mm_22418.1	chr2	181578907	181578946	-	1	NA	promoter-TSS (NR_027290)	promoter-TSS (NR_027290)	446	NR_027289	100271841	Mm.438007	NR_027289	ENSMUSG00000010492	Uckl1os	Gm16119|OTTMUSG00000030649	uridine-cytidine kinase 1-like 1, opposite strand	ncRNA
mm_43002.1	chr5	123445798	123445812	+	1	NA	exon (NM_177582, exon 9 of 9)	exon (NM_177582, exon 9 of 9)	36296	NM_029594	76399	Mm.75049	NM_029594	ENSMUSG00000029437	Il31	1700013B14Rik	interleukin 31	protein-coding
mm_67300.1	chr7	79300915	79300926	-	1	NA	intron (NM_018811, intron 3 of 10)	intron (NM_018811, intron 3 of 10)	27654	NM_018811	54608	Mm.365490	NM_018811	ENSMUSG00000039202	Abhd2	2210009N18Rik|LABH2|Labh-2	abhydrolase domain containing 2	protein-coding
mm_85652.1	chr9	107658672	107658683	-	1	NA	exon (NM_001199218, exon 4 of 16)	exon (NM_001199218, exon 4 of 16)	8722	NM_023805	76257	Mm.296560	NM_023805	ENSMUSG00000010064	Slc38a3	0610012J02Rik|D9Ucla2|Nat1|Slc38-3|Sn1|Snat3|mNAT	solute carrier family 38, member 3	protein-coding
mm_77868.1	chr9	5345415	5345435	+	1	NA	promoter-TSS (NM_009808)	promoter-TSS (NM_009808)	-51	NM_009808	12364	Mm.42163	NM_009808	ENSMUSG00000025887	Casp12	-	caspase 12	protein-coding
mm_30782.1	chr4	19491948	19491959	+	1	NA	intron (NM_013927, intron 15 of 17)	intron (NM_013927, intron 15 of 17)	78151	NM_027769	70568	Mm.38390	NM_027769	ENSMUSG00000028228	Cpne3	5430428M23Rik|5730450C07Rik|C85108|CPN3	copine III	protein-coding
mm_22854.1	chr3	28263433	28263437	+	1	NA	5' UTR (NM_001163009, exon 1 of 31)	5' UTR (NM_001163009, exon 1 of 31)	221	NM_001163009	665113	Mm.126193	NM_026910	ENSMUSG00000027692	Tnik	1500031A17Rik|4831440I19Rik|AI451411|C530008O15Rik|C630040K21Rik	TRAF2 and NCK interacting kinase	protein-coding
mm_131925.1	chr16	23375224	23375255	+	1	NA	Intergenic	Intergenic	-53894	NM_001004151	239766	Mm.208751	NM_001004151	ENSMUSG00000033383	Rtp1	Gm1766|Gm604	receptor transporter protein 1	protein-coding
mm_9217.1	chr1	171231930	171231950	-	1	NA	intron (NM_010185, intron 1 of 4)	intron (NM_010185, intron 1 of 4)	2409	NM_010185	14127	Mm.22673	NM_010185	ENSMUSG00000058715	Fcer1g	AI573376|CD23|FcR-gamma|FcR[g]|FcRgamma|Fce1g|FcepsilonRI|Ly-50	Fc receptor, IgE, high affinity I, gamma polypeptide	protein-coding
mm_26818.1	chr3	10331285	10331286	-	1	NA	TTS (NM_001010834)	TTS (NM_001010834)	154	NM_018864	55980	Mm.183042	NM_018864	ENSMUSG00000027531	Impa1	2610002K09Rik|2900059K10Rik|AI325909	inositol (myo)-1(or 4)-monophosphatase 1	protein-coding
mm_105288.1	chr11	102447613	102447642	-	1	NA	promoter-TSS (NM_199200)	promoter-TSS (NM_199200)	36	NM_199200	217219	Mm.259924	NM_199200	ENSMUSG00000034685	Fam171a2	-	family with sequence similarity 171, member A2	protein-coding
mm_8353.1	chr1	150362189	150362219	-	1	NA	3' UTR (NM_145511, exon 14 of 14)	3' UTR (NM_145511, exon 14 of 14)	-15433	NR_040603	75584	Mm.47709	NR_040603	ENSMUSG00000099447	2310030A07Rik	-	RIKEN cDNA 2310030A07 gene	ncRNA
mm_132476.1	chr16	36712036	36712044	+	1	NA	intron (NM_001285791, intron 3 of 6)	intron (NM_001285791, intron 3 of 6)	18062	NM_001285791	106347	Mm.17807	NM_134109	ENSMUSG00000022900	Ildr1	AU041483|AU044638	immunoglobulin-like domain containing receptor 1	protein-coding
mm_11983.1	chr2	55435789	55435801	+	1	NA	promoter-TSS (NM_001304810)	promoter-TSS (NM_001304810)	-175	NM_001304810	16519	Mm.5127	NM_008426	ENSMUSG00000026824	Kcnj3	GIRK-1|GIRK1|Kcnf3|Kir3.1	potassium inwardly-rectifying channel, subfamily J, member 3	protein-coding
mm_129115.1	chr15	76080895	76080921	-	1	NA	promoter-TSS (NM_028364)	promoter-TSS (NM_028364)	-38	NM_001164600	67959	Mm.29965	NM_028364	ENSMUSG00000002524	Puf60	2410104I19Rik|2810454F19Rik|SIAHBP1	poly-U binding splicing factor 60	protein-coding
mm_29504.1	chr3	116129450	116129464	-	1	NA	5' UTR (NM_011693, exon 1 of 9)	5' UTR (NM_011693, exon 1 of 9)	231	NM_011693	22329	Mm.76649	NM_011693	ENSMUSG00000027962	Vcam1	CD106|Vcam-1	vascular cell adhesion molecule 1	protein-coding
mm_156724.1	chrX	159840545	159840574	+	1	NA	promoter-TSS (NM_001135728)	promoter-TSS (NM_001135728)	91	NM_001135728	58194	Mm.286495	NM_021389	ENSMUSG00000040990	Sh3kbp1	1200007H22Rik|1700125L08Rik|5830464D22Rik|AI447724|Cin85|IN85|Ruk|Seta	SH3-domain kinase binding protein 1	protein-coding
mm_130734.1	chr15	101250267	101250275	-	1	NA	Intergenic	RMER15-int|LTR|ERVL	-16575	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_160343.1	chr8	19293570	19293570	+	1	NA	intron (NM_013756, intron 1 of 1)	(TCTCTG)n|Simple_repeat|Simple_repeat	209	NM_013756	27358	Mm.103651	NM_013756	ENSMUSG00000039775	Defb3	BD-3	defensin beta 3	protein-coding
mm_70532.1	chr8	13037340	13037352	+	1	NA	promoter-TSS (NM_007972)	promoter-TSS (NM_007972)	38	NM_001242368	14058	Mm.262589	NM_007972	ENSMUSG00000031444	F10	Cf10|fX	coagulation factor X	protein-coding
mm_90031.1	chr10	115430907	115430921	+	1	NA	intron (NM_001033261, intron 32 of 34)	intron (NM_001033261, intron 32 of 34)	45955	NM_001033261	216345	Mm.207621	NM_001033261	ENSMUSG00000034163	Zfc3h1	BC033596|Ccdc131|Psrc2	zinc finger, C3H1-type containing	protein-coding
mm_67570.1	chr7	81934317	81934463	-	1	NA	promoter-TSS (NM_013886)	promoter-TSS (NM_013886)	69	NM_013886	29877	Mm.392934	NM_013886	ENSMUSG00000025104	Hdgfrp3	2700022B06Rik|HRP-3	hepatoma-derived growth factor, related protein 3	protein-coding
mm_20930.1	chr2	150856000	150856030	-	1	NA	intron (NM_024465, intron 2 of 12)	B4A|SINE|B4	48716	NM_024465	76192	Mm.112632	NM_024465	ENSMUSG00000032046	Abhd12	1500011G07Rik|6330583M11Rik|AI431047|AW547313	abhydrolase domain containing 12	protein-coding
mm_167154.1	chr7	131322438	131322444	-	1	NA	promoter-TSS (NM_008411)	promoter-TSS (NM_008411)	-149	NM_008411	16433	Mm.142717	NM_008411	ENSMUSG00000040205	Cuzd1	Erg-1|Itmap1|Uo-44|Usg|Utczp	CUB and zona pellucida-like domains 1	protein-coding
mm_13722.1	chr2	117342392	117342395	+	1	NA	intron (NM_011246, intron 1 of 16)	intron (NM_011246, intron 1 of 16)	484	NM_011246	19419	Mm.42150	NM_011246	ENSMUSG00000027347	Rasgrp1	Rasgrp	RAS guanyl releasing protein 1	protein-coding
mm_142072.1	chr17	35698007	35698031	-	1	NA	intron (NM_007584, intron 1 of 17)	intron (NM_007584, intron 1 of 17)	2571	NM_001198833	12305	Mm.5021	NM_007584	ENSMUSG00000003534	Ddr1	6030432F18|AI323681|CD167a|Cak|Nep|PTK3A	discoidin domain receptor family, member 1	protein-coding
mm_105619.1	chr11	106788917	106788929	-	1	NA	promoter-TSS (NM_177088)	promoter-TSS (NM_177088)	-329	NM_177088	320162	Mm.30524	NM_177088	ENSMUSG00000018372	Cep95	4732496G21Rik|AI118346|AI448335|Ccdc45|D330027A14Rik|F630025I20Rik	centrosomal protein 95	protein-coding
mm_99404.1	chr11	102245378	102245415	+	1	NA	Intergenic	(CACG)n|Simple_repeat|Simple_repeat	-3486	NM_153544	217216	Mm.247335	NM_153544	ENSMUSG00000034773	BC030867	-	cDNA sequence BC030867	protein-coding
mm_114745.1	chr13	84063109	84063111	+	1	NA	intron (NR_131220, intron 1 of 1)	intron (NR_131220, intron 1 of 1)	1664	NR_131220	553095	Mm.39702	NR_131220	ENSMUSG00000098087	Gm17750	-	predicted gene, 17750	ncRNA
mm_122489.1	chr14	46390577	46390606	-	1	NA	promoter-TSS (NM_007554)	promoter-TSS (NM_007554)	78	NM_001316360	12159	Mm.6813	NM_007554	ENSMUSG00000021835	Bmp4	Bmp-4|Bmp2b|Bmp2b-1|Bmp2b1	bone morphogenetic protein 4	protein-coding
mm_125706.1	chr15	68258592	68258604	+	1	NA	intron (NM_001145888, intron 1 of 15)	CpG	258	NM_001145888	380993	Mm.309526	NM_198644	ENSMUSG00000022335	Zfat	Gm922|Zfat1|Zfp406	zinc finger and AT hook domain containing	protein-coding
mm_132327.1	chr16	33798968	33798989	+	1	NA	exon (NM_010739, exon 3 of 13)	exon (NM_010739, exon 3 of 13)	4941	NM_010739	17063	Mm.3177	NM_010739	ENSMUSG00000022824	Muc13	114/A10|14/A10|AI159736|Lrrp|Ly64|NJ-1	mucin 13, epithelial transmembrane	protein-coding
mm_78821.1	chr9	44089095	44089135	+	1	NA	intron (NM_198091, intron 1 of 11)	intron (NM_198091, intron 1 of 11)	4195	NM_198091	53376	Mm.272770	NM_016808	ENSMUSG00000032010	Usp2	B930035K21Rik|Ubp41	ubiquitin specific peptidase 2	protein-coding
mm_92768.1	chr10	81134378	81134419	-	1	NA	Intergenic	Intergenic	-1873	NM_010731	16969	Mm.20920	NM_010731	ENSMUSG00000035011	Zbtb7a	9030619K07Rik|9130006G12Rik|AI452336|FBI-1|Lrf|Pokemon|Zbtb7	zinc finger and BTB domain containing 7a	protein-coding
mm_160129.1	chr7	29168443	29168443	-	1	NA	intron (NM_182927, intron 1 of 5)	intron (NM_182927, intron 1 of 5)	204	NM_182927	101809	Mm.377262	NM_182927	ENSMUSG00000037239	Spred3	AW047143|D130060H24Rik|Spred-3	sprouty-related, EVH1 domain containing 3	protein-coding
mm_59317.1	chr7	25291195	25291209	+	1	NA	exon (NM_027882, exon 14 of 20)	exon (NM_027882, exon 14 of 20)	6753	NM_008776	18476	Mm.597	NM_008776	ENSMUSG00000005447	Pafah1b3	Pafahg|mus[g]	platelet-activating factor acetylhydrolase, isoform 1b, subunit 3	protein-coding
mm_65817.1	chr7	29155623	29155631	-	1	NA	intron (NM_001146023, intron 3 of 7)	CpG	583	NM_001146023	73833	Mm.260890	NM_028661	ENSMUSG00000030590	Fam98c	1110006G06Rik|AI836081|AV026483|B230110F21Rik	family with sequence similarity 98, member C	protein-coding
mm_149444.1	chr19	11484168	11484178	+	1	NA	Intergenic	Intergenic	-7865	NM_001164202	666926	Mm.486382	NM_001164202	ENSMUSG00000058470	Gm8369	EG666926	predicted gene 8369	protein-coding
mm_78312.1	chr9	23223510	23223601	+	1	NA	5' UTR (NM_028472, exon 1 of 15)	5' UTR (NM_028472, exon 1 of 15)	479	NM_028472	73230	Mm.335020	NM_028472	ENSMUSG00000031963	Bmper	3110056H04Rik|CV-2|Crim3|Cv2	BMP-binding endothelial regulator	protein-coding
mm_1966.1	chr1	86489046	86489059	+	1	NA	Intergenic	B1_Mm|SINE|Alu	-37684	NM_008972	19231	Mm.19187	NM_008972	ENSMUSG00000026238	Ptma	Thym	prothymosin alpha	protein-coding
mm_117659.1	chr13	93192376	93192424	-	1	NA	promoter-TSS (NM_133905)	promoter-TSS (NM_133905)	-117	NM_133905	100715	Mm.242865	NM_133905	ENSMUSG00000042167	Papd4	8030446C20Rik|AI649009|GLD-2|Gld2	PAP associated domain containing 4	protein-coding
mm_153377.1	chr19	40365164	40365193	-	1	NA	intron (NM_001034963, intron 6 of 22)	intron (NM_001034963, intron 6 of 22)	37132	NM_001034964	20411	Mm.210815	NM_009166	ENSMUSG00000025006	Sorbs1	2310065E01Rik|9530001P15Rik|CAP|SH3P12|Sh3d5|mKIAA1296	sorbin and SH3 domain containing 1	protein-coding
mm_159025.1	chr1	173344357	173344357	-	1	NA	exon (NM_053199, exon 5 of 9)	exon (NM_053199, exon 5 of 9)	-10854	NM_010045	13349	Mm.6393	NM_010045	ENSMUSG00000037872	Ackr1	AA162249|CCBP1|CD234|Darc|Dfy|ESTM35|FY|GPD	atypical chemokine receptor 1 (Duffy blood group)	protein-coding
mm_115215.1	chr13	109478817	109478844	+	1	NA	intron (NM_011056, intron 3 of 16)	intron (NM_011056, intron 3 of 16)	154086	NR_030644	100124489		NR_030644	ENSMUSG00000076946	Mir582	Mirn582|mir-582|mmu-mir-582	microRNA 582	ncRNA
mm_128999.1	chr15	74842583	74842590	-	1	NA	promoter-TSS (NM_001033229)	promoter-TSS (NM_001033229)	-943	NM_001033229	110115	Mm.322606	NM_001033229	ENSMUSG00000075604	Cyp11b1	AA389061|CPN1|Cyp11b|Cyp11b-1|FHI	cytochrome P450, family 11, subfamily b, polypeptide 1	protein-coding
mm_3987.1	chr1	164307683	164307737	+	1	NA	promoter-TSS (NM_001160209)	promoter-TSS (NM_001160209)	38	NM_178071	171567	Mm.219428	NM_138314	ENSMUSG00000026575	Nme7	D530024H21Rik|Nm23-M7|Nm23-r7	NME/NM23 family member 7	protein-coding
mm_136812.1	chr17	12391819	12391829	+	1	NA	exon (NM_008877, exon 6 of 19)	exon (NM_008877, exon 6 of 19)	13215	NM_008877	18815	Mm.971	NM_008877	ENSMUSG00000059481	Plg	AI649309|Pg	plasminogen	protein-coding
mm_142025.1	chr17	35205484	35205510	-	1	NA	promoter-TSS (NM_010735)	promoter-TSS (NM_010735)	-146	NM_010735	16992	Mm.87787	NM_010735	ENSMUSG00000024402	Lta	LT|LT-[a]|LT-alpha|LT[a]|LTalpha|Ltx|TNF-beta|TNFSF1|Tnfb|Tnfsf1b|Tnlg1e|hlb382	lymphotoxin A	protein-coding
mm_10375.1	chr2	11725115	11725130	+	1	NA	intron (NR_073191, intron 4 of 5)	B3A|SINE|B2	19410	NM_001271500	16169	Mm.200196	NM_008358	ENSMUSG00000023206	Il15ra	AA690181|IL-15RA	interleukin 15 receptor, alpha chain	protein-coding
mm_2624.1	chr1	120621605	120621634	+	1	NA	Intergenic	Intergenic	19132	NM_010133	13798	Mm.2657	NM_010133	ENSMUSG00000058665	En1	En-1|Mo-en.1|engrailed-1	engrailed 1	protein-coding
mm_44437.1	chr5	21330691	21330703	-	1	NA	exon (NM_029195, exon 4 of 19)	exon (NM_029195, exon 4 of 19)	-41976	NM_008013	14190	Mm.292100	NM_008013	ENSMUSG00000039899	Fgl2	AI385601|musfiblp	fibrinogen-like protein 2	protein-coding
mm_80778.1	chr9	95637413	95637424	+	1	NA	promoter-TSS (NM_029620)	promoter-TSS (NM_029620)	-210	NM_029620	76477	Mm.46016	NM_029620	ENSMUSG00000015354	Pcolce2	2400001O18Rik|Pcpe2	procollagen C-endopeptidase enhancer 2	protein-coding
mm_74471.1	chr8	4258298	4258313	-	1	NA	3' UTR (NM_183315, exon 2 of 2)	3' UTR (NM_183315, exon 2 of 2)	969	NM_183315	330695	Mm.34210	NM_183315	ENSMUSG00000048644	Ctxn1	BC028881|Ctxn	cortexin 1	protein-coding
mm_149073.1	chr19	8871637	8871686	+	1	NA	intron (NM_146093, intron 1 of 9)	CpG	102	NM_146093	225896	Mm.27839	NM_146093	ENSMUSG00000071655	Ubxn1	2B28|4930455J02Rik|D19Ertd721e|T25529	UBX domain protein 1	protein-coding
mm_7386.1	chr1	110977324	110977332	-	1	NA	promoter-TSS (NM_001081386)	promoter-TSS (NM_001081386)	44	NM_001081386	227485	Mm.322070	NM_001081386	ENSMUSG00000047216	Cdh19	-	cadherin 19, type 2	protein-coding
mm_99999.1	chr11	114851143	114851158	+	1	NA	promoter-TSS (NM_147217)	promoter-TSS (NM_147217)	-382	NM_001110337	70355	Mm.242413	NM_147217	ENSMUSG00000051043	Gprc5c	1110028I06Rik|3200002M13Rik|Raig3	G protein-coupled receptor, family C, group 5, member C	protein-coding
mm_24149.1	chr3	88337844	88337853	+	1	NA	intron (NM_178246, intron 1 of 21)	intron (NM_178246, intron 1 of 21)	1588	NM_178246	229512	Mm.439830	NM_173188	ENSMUSG00000001415	Smg5	BC024683|mKIAA1089	Smg-5 homolog, nonsense mediated mRNA decay factor (C. elegans)	protein-coding
mm_62163.1	chr7	97210325	97210327	+	1	NA	intron (NM_001162477, intron 1 of 9)	intron (NM_001162477, intron 1 of 9)	115638	NM_001177412	244144	Mm.297541	NM_001177412	ENSMUSG00000035713	Usp35	Gm1088|Gm493	ubiquitin specific peptidase 35	protein-coding
mm_60419.1	chr7	44476334	44476340	+	1	NA	Intergenic	L1MEd|LINE|L1	5990	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_28160.1	chr3	87769060	87769068	-	1	NA	promoter-TSS (NM_001289601)	promoter-TSS (NM_001289601)	-111	NM_001032414	73182	Mm.158962	NM_028460	ENSMUSG00000028073	Pear1	3110045G13Rik|Jedi-1|Megf12	platelet endothelial aggregation receptor 1	protein-coding
mm_121772.1	chr14	19875285	19875326	-	1	NA	3' UTR (NM_001285911, exon 4 of 4)	3' UTR (NM_001285911, exon 4 of 4)	36380	NR_105025	52512	Mm.483998	NR_105025		D14Ertd670e	-	DNA segment, Chr 14, ERATO Doi 670, expressed	ncRNA
mm_96156.1	chr11	61485748	61485776	+	1	NA	exon (NM_029568, exon 2 of 6)	exon (NM_029568, exon 2 of 6)	318	NM_029568	76293	Mm.272278	NM_029568	ENSMUSG00000042436	Mfap4	1110007F23Rik	microfibrillar-associated protein 4	protein-coding
mm_101057.1	chr11	9011112	9011164	-	1	NA	promoter-TSS (NM_008316)	promoter-TSS (NM_008316)	53	NM_001303610	15574	Mm.42201	NM_008316	ENSMUSG00000020413	Hus1	-	HUS1 checkpoint clamp component	protein-coding
mm_117566.1	chr13	85285760	85285776	-	1	NA	intron (NM_145452, intron 1 of 24)	(CA)n|Simple_repeat|Simple_repeat	3718	NM_145452	218397	Mm.259653	NM_145452	ENSMUSG00000021549	Rasa1	Gap|RasGAP|Rasa	RAS p21 protein activator 1	protein-coding
mm_61127.1	chr7	55842335	55842352	+	1	NA	intron (NM_011370, intron 1 of 30)	CpG	272	NM_001164661	20430	Mm.37249	NM_011370	ENSMUSG00000030447	Cyfip1	E030028J09Rik|P140SRA-1|P140sra1|Shyc|Sra-1|Sra1|l(7)1Rl|l71Rl|l7Rl1|mKIAA0068|pl-1	cytoplasmic FMR1 interacting protein 1	protein-coding
mm_150657.1	chr19	41981228	41981246	+	1	NA	promoter-TSS (NM_028152)	promoter-TSS (NM_028152)	-101	NM_028152	72199	Mm.218940	NM_028152	ENSMUSG00000025159	Mms19	2410001K24Rik|2610042O15Rik|AI316855|C79368|C86341|Mms19l	MMS19 (MET18 S. cerevisiae)	protein-coding
mm_122946.1	chr14	54965827	54965894	-	1	NA	5' UTR (NM_001164171, exon 2 of 39)	5' UTR (NM_001164171, exon 2 of 39)	747	NM_001164171	17888	Mm.290003	NM_010856	ENSMUSG00000040752	Myh6	A830009F23Rik|AA517445|Myhc-a|Myhca|alpha-MHC	myosin, heavy polypeptide 6, cardiac muscle, alpha	protein-coding
mm_165509.1	chr2	172100540	172100549	+	1	NA	Intergenic	Intergenic	-57078	NM_175631	228942	Mm.40555	NM_175631	ENSMUSG00000067578	Cbln4	AI848962	cerebellin 4 precursor protein	protein-coding
mm_138224.1	chr17	34341953	34341959	+	1	NA	TTS (NM_010381)	TTS (NM_010381)	2689	NM_010381	100504404	Mm.15680	NM_010381		H2-Ea-ps	AI323765|E-alpha-f|H-2Ea|H2-Ea|I-Ealpha|Ia-3|Ia3|MHC-H2-Ea	histocompatibility 2, class II antigen E alpha, pseudogene	protein-coding
mm_43069.1	chr5	124445462	124445532	+	1	NA	promoter-TSS (NM_001310723)	promoter-TSS (NM_001310723)	-2	NM_001310723	67956	Mm.137966	NM_030241	ENSMUSG00000049327	Kmt5a	2410195B05Rik|AA617402|AW536475|PR-SET7|PR/SET07|Setd8	lysine methyltransferase 5A	protein-coding
mm_6788.1	chr1	84140541	84140554	-	1	NA	intron (NM_001003948, intron 2 of 2)	L1_Mur3|LINE|L1	78414	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_162176.1	chrX	102157211	102157211	-	1	NA	promoter-TSS (NM_146235)	promoter-TSS (NM_146235)	-120	NM_146235	236930	Mm.31911	NM_146235	ENSMUSG00000051220	Ercc6l	BC004701|D330021P09Rik	excision repair cross-complementing rodent repair deficiency complementation group 6 like	protein-coding
mm_100760.1	chr11	4497550	4497554	-	1	NA	intron (NM_028860, intron 10 of 17)	intron (NM_028860, intron 10 of 17)	-56470	NM_029458	75828	Mm.159592	NM_029458	ENSMUSG00000020419	Hormad2	4930529M09Rik	HORMA domain containing 2	protein-coding
mm_22578.1	chr3	10366968	10366987	+	1	NA	promoter-TSS (NM_025519)	promoter-TSS (NM_025519)	4	NM_025519	66371	Mm.366147	NM_025519	ENSMUSG00000027536	Chmp4c	2010012P02Rik|2210015K02Rik|2310010I16Rik|Shax3|Snf7-3	charged multivesicular body protein 4C	protein-coding
mm_145004.1	chr18	38418947	38418985	+	1	NA	promoter-TSS (NM_022996)	promoter-TSS (NM_022996)	-9	NM_022996	65113	Mm.102496	NM_022996	ENSMUSG00000024425	Ndfip1	0610010M22Rik|N4wbp5	Nedd4 family interacting protein 1	protein-coding
mm_91748.1	chr10	49723053	49723064	-	1	NA	intron (NM_001111268, intron 2 of 16)	intron (NM_001111268, intron 2 of 16)	65696	NM_010349	14806	Mm.332838	NM_010349	ENSMUSG00000056073	Grik2	AW124492|GluK2|Glur-6|Glur6|Glurbeta2	glutamate receptor, ionotropic, kainate 2 (beta 2)	protein-coding
mm_168067.1	chr10	104545850	104545868	-	1	NA	Intergenic	L1Md_T|LINE|L1	258590	NR_105838	102465222		NR_105838	ENSMUSG00000099264	Mir6411	Gm27767|mmu-mir-6411	microRNA 6411	ncRNA
mm_15192.1	chr2	154204721	154204730	+	1	NA	exon (NM_153418, exon 3 of 16)	exon (NM_153418, exon 3 of 16)	4345	NM_153418	228801	Mm.3783	NM_153418	ENSMUSG00000027485	Bpifb1	Lplunc1	BPI fold containing family B, member 1	protein-coding
mm_25994.1	chr3	134236534	134236542	+	1	NA	promoter-TSS (NM_001004367)	promoter-TSS (NM_001004367)	43	NM_001004367	319478	Mm.224814	NM_001004367	ENSMUSG00000044365	Cxxc4	9330210J02Rik|C030003J12Rik|Idax	CXXC finger 4	protein-coding
mm_70882.1	chr8	25274478	25274483	+	1	NA	Intergenic	Intergenic	31790	NR_040352	74489	Mm.256468	NR_040352	ENSMUSG00000110140	5430421F17Rik	-	RIKEN cDNA 5430421F17 gene	ncRNA
mm_108280.1	chr12	79029197	79029218	+	1	NA	promoter-TSS (NM_181073)	promoter-TSS (NM_181073)	44	NM_181073	211945	Mm.478321	NM_181073	ENSMUSG00000060716	Plekhh1	AV308913|C77772|D630024D12Rik|mKIAA1200	pleckstrin homology domain containing, family H (with MyTH4 domain) member 1	protein-coding
mm_152607.1	chr19	11868923	11868943	-	1	NA	Intergenic	CpG	2281	NM_001011775	257938	Mm.377309	NM_001011775	ENSMUSG00000067545	Olfr1419	MOR266-10	olfactory receptor 1419	protein-coding
mm_47483.1	chr5	123865463	123865473	-	1	NA	promoter-TSS (NM_030701)	promoter-TSS (NM_030701)	48	NM_030701	80885	Mm.440567	NM_030701	ENSMUSG00000045502	Hcar2	Gpr109a|Gpr109b|HM74|Niacr1|PUMA-G|Pumag|mHM74b	hydroxycarboxylic acid receptor 2	protein-coding
mm_84001.1	chr9	57552723	57552757	-	1	NA	promoter-TSS (NM_025837)	promoter-TSS (NM_025837)	12	NM_025837	110119	Mm.247218	NM_025837	ENSMUSG00000032306	Mpi	1110002E17Rik|AI315153|Mpi-1|Mpi1	mannose phosphate isomerase	protein-coding
mm_37046.1	chr4	115939924	115939928	-	1	NA	promoter-TSS (NM_130865)	promoter-TSS (NM_130865)	0	NM_001025567	140477	Mm.213206	NM_130865	ENSMUSG00000028707	Dmbx1	Atx|Cdmx|Mbx|Otx3	diencephalon/mesencephalon homeobox 1	protein-coding
mm_155510.1	chrX	74027340	74027340	+	1	NA	3' UTR (NM_010788, exon 4 of 4)	3' UTR (NM_010788, exon 4 of 4)	-3404	NR_030758	751533		NR_030758	ENSMUSG00000076127	Mir718	Mirn718|mir-718|mmu-mir-718	microRNA 718	ncRNA
mm_126420.1	chr15	80320258	80320304	+	1	NA	intron (NM_001044308, intron 2 of 36)	intron (NM_001044308, intron 2 of 36)	33043	NM_001044308	239556	Mm.291058	NM_001044308	ENSMUSG00000022416	Cacna1i	Ca(V)3.3	calcium channel, voltage-dependent, alpha 1I subunit	protein-coding
mm_138494.1	chr17	35200527	35200543	+	1	NA	exon (NM_013693, exon 4 of 4)	exon (NM_013693, exon 4 of 4)	1472	NM_013693	21926	Mm.1293	NM_013693	ENSMUSG00000024401	Tnf	DIF|TNF-a|TNF-alpha|TNFSF2|TNFalpha|Tnfa|Tnfsf1a|Tnlg1f	tumor necrosis factor	protein-coding
mm_76342.1	chr8	84722899	84722921	-	1	NA	intron (NM_001297601, intron 6 of 8)	intron (NM_001297601, intron 6 of 8)	21453	NM_008535	17095	Mm.4925	NM_008535	ENSMUSG00000034041	Lyl1	Lyl-1|bHLHa18	lymphoblastomic leukemia 1	protein-coding
mm_158675.1	chrX	158043207	158043260	-	1	NA	promoter-TSS (NM_177751)	promoter-TSS (NM_177751)	-36	NM_177751	245684	Mm.197074	NM_177751	ENSMUSG00000025658	Cnksr2	Cnk2|Ksr2	connector enhancer of kinase suppressor of Ras 2	protein-coding
mm_96837.1	chr11	70018397	70018399	+	1	NA	promoter-TSS (NM_007864)	promoter-TSS (NM_007864)	-207	NM_001109752	13385	Mm.27256	NM_007864	ENSMUSG00000020886	Dlg4	Dlgh4|PSD-95|PSD95|SAP90|SAP90A	discs, large homolog 4 (Drosophila)	protein-coding
mm_31782.1	chr4	63560717	63560740	+	1	NA	intron (NM_144905, intron 1 of 9)	intron (NM_144905, intron 1 of 9)	368	NM_144905	230279	Mm.41523	NM_144905	ENSMUSG00000045917	Tmem268	6330416G13Rik|AW492431|bM230C2.2	transmembrane protein 268	protein-coding
mm_164704.1	chr17	51766606	51766616	-	1	NA	intron (NM_009122, intron 9 of 10)	intron (NM_009122, intron 9 of 10)	45443	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_122408.1	chr14	41008280	41008286	-	1	NA	promoter-TSS (NM_001316740)	promoter-TSS (NM_001316740)	-17	NM_001316740	70564	Mm.27227	NM_027464	ENSMUSG00000021792	Fam213a	5730469M10Rik|AU040822|Adrx|Pamm	family with sequence similarity 213, member A	protein-coding
mm_83290.1	chr9	43116669	43116678	-	1	NA	promoter-TSS (NM_001034863)	promoter-TSS (NM_001034863)	-103	NM_001034863	235300	Mm.261326	NM_001034863	ENSMUSG00000048503	Tmem136	AA396355|Gm184	transmembrane protein 136	protein-coding
mm_150018.1	chr19	29370227	29370258	+	1	NA	intron (NM_021893, intron 1 of 6)	intron (NM_021893, intron 1 of 6)	2804	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_167861.1	chrX	19149036	19149048	-	1	NA	Intergenic	Lx6|LINE|L1	-2071	NR_029807	723828		NR_029807	ENSMUSG00000065471	Mir222	Mirn222|mir-222|mmu-mir-222	microRNA 222	ncRNA
mm_49841.1	chr6	38346052	38346052	+	1	NA	intron (NM_001347122, intron 1 of 12)	intron (NM_001347122, intron 1 of 12)	8551	NM_028864	78781	Mm.25243	NM_028421	ENSMUSG00000029826	Zc3hav1	1200014N16Rik|2900058M19Rik|9130009D18Rik|9830115L13Rik|ARTD13|D6Bwg1452e|ZAP	zinc finger CCCH type, antiviral 1	protein-coding
mm_140551.1	chr17	7169818	7169828	-	1	NA	promoter-TSS (NM_011299)	promoter-TSS (NM_011299)	-292	NM_011299	20112	Mm.268383	NM_011299	ENSMUSG00000023809	Rps6ka2	90kDa|D17Wsu134e|Rps6ka-rs1|Rsk3|p90rsk|pp90rsk	ribosomal protein S6 kinase, polypeptide 2	protein-coding
mm_73891.1	chr8	119418953	119418957	+	1	NA	Intergenic	Intergenic	-18207	NM_027950	71839	Mm.272357	NM_027950	ENSMUSG00000074063	Osgin1	1700012B18Rik|Okl38	oxidative stress induced growth inhibitor 1	protein-coding
mm_77564.1	chr8	123428103	123428112	-	1	NA	Intergenic	MuLV-int|LTR|ERV1	-14849	NM_001253784	23854	Mm.275127	NM_054046	ENSMUSG00000001482	Def8	AI449518|D8Ertd713e|DEF-8	differentially expressed in FDCP 8	protein-coding
mm_33272.1	chr4	128221117	128221120	+	1	NA	intron (NM_001281955, intron 5 of 70)	intron (NM_001281955, intron 5 of 70)	39777	NM_027036	69317	Mm.331893	NM_027036	ENSMUSG00000048686	Hmgb4	1700001F22Rik|AI326135	high-mobility group box 4	protein-coding
mm_103930.1	chr11	83648400	83648445	-	1	NA	intron (NM_011337, intron 2 of 2)	intron (NM_011337, intron 2 of 2)	956	NM_011337	20302	Mm.1282	NM_011337	ENSMUSG00000000982	Ccl3	AI323804|G0S19-1|LD78alpha|MIP-1alpha|MIP1-(a)|MIP1-alpha|Mip1a|Scya3	chemokine (C-C motif) ligand 3	protein-coding
mm_24165.1	chr3	88537331	88537338	+	1	NA	promoter-TSS (NR_035434)	promoter-TSS (NR_035434)	-952	NR_035434	100316808		NR_035434	ENSMUSG00000084728	Mir1905	Mirn1905|mmu-mir-1905	microRNA 1905	ncRNA
mm_140955.1	chr17	24614500	24614510	-	1	NA	intron (NM_001286718, intron 18 of 39)	intron (NM_001286718, intron 18 of 39)	18122	NM_011647	22084	Mm.30435	NM_011647	ENSMUSG00000002496	Tsc2	Nafld|Tcs2	tuberous sclerosis 2	protein-coding
mm_94194.1	chr10	130280253	130280263	-	1	NA	promoter-TSS (NM_001329490)	promoter-TSS (NM_001329490)	-4	NM_007501	11923	Mm.10695	NM_007501	ENSMUSG00000048015	Neurod4	AI846749|ATH-3|Atoh3|MATH-3|Math3|bHLHa4	neurogenic differentiation 4	protein-coding
mm_89413.1	chr10	90829781	90829791	+	1	NA	promoter-TSS (NM_001347053)	promoter-TSS (NM_001347053)	-57	NM_001347053	77531	Mm.440605	NM_181398	ENSMUSG00000058589	Anks1b	AIDA-1b|C030032C09Rik|E530015N03Rik|ENSMUSG00000078431|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding
mm_712.1	chr1	42259804	42259810	+	1	NA	Intergenic	Intergenic	435018	NR_027826	66297	Mm.45203	NM_183252	ENSMUSG00000060424	Pantr1	2610017I09Rik|Pou3f3os|linc-Brn1a	POU domain, class 3, transcription factor 3 adjacent noncoding transcript 1	ncRNA
mm_70825.1	chr8	23140037	23140041	+	1	NA	intron (NM_001282148, intron 5 of 5)	intron (NM_001282148, intron 5 of 5)	1009	NM_001310437	11733	Mm.334444	NM_031158	ENSMUSG00000031543	Ank1	Ank-1|nb|pale	ankyrin 1, erythroid	protein-coding
mm_78145.1	chr9	21002746	21002790	+	1	NA	promoter-TSS (NM_023167)	promoter-TSS (NM_023167)	31	NM_023167	66163	Mm.427576	NM_023167	ENSMUSG00000003299	Mrpl4	1110017G11Rik	mitochondrial ribosomal protein L4	protein-coding
mm_65780.1	chr7	28766977	28766986	-	1	NA	promoter-TSS (NM_010908)	promoter-TSS (NM_010908)	229	NM_001122766	64383	Mm.272443	NM_022432	ENSMUSG00000015149	Sirt2	5730427M03Rik|SIR2L2|Sir2l	sirtuin 2	protein-coding
mm_90101.1	chr10	116966287	116966295	+	1	NA	promoter-TSS (NR_027846)	promoter-TSS (NR_027846)	17	NR_027846	103175	Mm.27138	NR_027846	ENSMUSG00000031294	D630029K05Rik	AI314111|AI875589	RIKEN cDNA D630029K05 gene	ncRNA
mm_95574.1	chr11	52403442	52403481	+	1	NA	exon (NM_153117, exon 2 of 3)	exon (NM_153117, exon 2 of 3)	7033	NM_153117	213673	Mm.291979	NM_153117	ENSMUSG00000036275	9530068E07Rik	C85061|Kct2	RIKEN cDNA 9530068E07 gene	protein-coding
mm_172236.1	chr6	68243137	68243152	+	1	NA	Intergenic	RLTR3_Mm|LTR|ERVK	-677445	NR_003100	75070	Mm.463364	NR_003100		4930515G16Rik	-	myc induced nuclear antigen pseudogene	pseudo
mm_111595.1	chr12	101976205	101976248	-	1	NA	intron (NM_016856, intron 1 of 14)	CpG	252	NM_016856	51786	Mm.716	NM_016856	ENSMUSG00000041781	Cpsf2	100kDa|2610024B04Rik|AI662483|Cpsf|MCPSF|mKIAA1367	cleavage and polyadenylation specific factor 2	protein-coding
mm_146909.1	chr18	31317139	31317149	-	1	NA	promoter-TSS (NM_009065)	promoter-TSS (NM_009065)	-16	NM_009065	19762	Mm.5163	NM_009065	ENSMUSG00000057455	Rit2	RIBA|Rin|Roc2	Ras-like without CAAX 2	protein-coding
mm_22207.1	chr2	173659668	173659677	-	1	NA	promoter-TSS (NM_024436)	promoter-TSS (NM_024436)	-133	NR_027957	100043911	Mm.260590	NM_001033179	ENSMUSG00000055897	Ppp4r1l-ps	1700007P14Rik|5830403E09Rik|C030010B13Rik|Ppp4r1l	protein phosphatase 4, regulatory subunit 1-like, pseudogene	pseudo
mm_38132.1	chr4	134703582	134703649	-	1	NA	5' UTR (NM_207237, exon 1 of 12)	5' UTR (NM_207237, exon 1 of 12)	675	NM_207237	230815	Mm.18905	NM_207237	ENSMUSG00000037306	Man1c1	AI593348	mannosidase, alpha, class 1C, member 1	protein-coding
mm_127021.1	chr15	96286757	96286767	+	1	NA	promoter-TSS (NM_175251)	promoter-TSS (NM_175251)	-760	NM_175251	77044	Mm.17166	NM_175251	ENSMUSG00000033237	Arid2	1700124K17Rik|4432409D24Rik|zipzap/p200	AT rich interactive domain 2 (ARID, RFX-like)	protein-coding
mm_40850.1	chr5	73481021	73481035	+	1	NA	promoter-TSS (NM_001190734)	promoter-TSS (NM_001190734)	-27	NM_001190734	100737	Mm.220312	NM_178896	ENSMUSG00000051674	Dcun1d4	AI836376	DCN1, defective in cullin neddylation 1, domain containing 4 (S. cerevisiae)	protein-coding
mm_92521.1	chr10	78591888	78591934	-	1	NA	promoter-TSS (NM_027875)	promoter-TSS (NM_027875)	53	NM_027875	71709	Mm.86439	NM_027875	ENSMUSG00000032714	Syde1	1200008N06Rik|BB043000|mSYD1A	synapse defective 1, Rho GTPase, homolog 1 (C. elegans)	protein-coding
mm_87891.1	chr10	61845755	61845764	+	1	NA	intron (NM_001304757, intron 35 of 37)	intron (NM_001304757, intron 35 of 37)	-61895	NM_207000	404634	Mm.272870	NM_207000	ENSMUSG00000020086	H2afy2	macroH2A2	H2A histone family, member Y2	protein-coding
mm_46370.1	chr5	103647471	103647479	-	1	NA	Intergenic	B1_Mur2|SINE|Alu	8249	NM_028824	74218	Mm.159141	NM_028824	ENSMUSG00000029320	1700016H13Rik	-	RIKEN cDNA 1700016H13 gene	protein-coding
mm_155874.1	chrX	101447889	101447906	+	1	NA	3' UTR (NM_001252518, exon 12 of 12)	3' UTR (NM_001252518, exon 12 of 12)	-1212	NM_013712	26549	Mm.46232	NM_013712	ENSMUSG00000031312	Itgb1bp2	Chordc3	integrin beta 1 binding protein 2	protein-coding
mm_23231.1	chr3	50436693	50436697	+	1	NA	intron (NM_011990, intron 2 of 11)	intron (NM_011990, intron 2 of 11)	6918	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_76015.1	chr8	73305722	73305741	-	1	NA	intron (NM_010687, intron 1 of 14)	intron (NM_010687, intron 1 of 14)	47809	NM_001317391	16795	Mm.324371	NM_010687	ENSMUSG00000004383	Large1	BPFD#36|Gyltl1a|Large|Mbp-1|Mbp1|enr|fg|froggy|myd	LARGE xylosyl- and glucuronyltransferase 1	protein-coding
mm_8564.1	chr1	155417262	155417272	-	1	NA	5' UTR (NM_011273, exon 1 of 15)	5' UTR (NM_011273, exon 1 of 15)	177	NM_011273	19775	Mm.266215	NM_011273	ENSMUSG00000026469	Xpr1	Rmc-1|Rmc1|Sxv|Syg1|XR	xenotropic and polytropic retrovirus receptor 1	protein-coding
mm_63830.1	chr7	135172759	135172762	+	1	NA	3' UTR (NM_001033420, exon 52 of 52)	3' UTR (NM_001033420, exon 52 of 52)	23242	NR_046050	74314	Mm.415339	NR_046050	ENSMUSG00000100717	1700120G07Rik	-	RIKEN cDNA 1700120G07 gene	ncRNA
mm_47454.1	chr5	123603676	123603706	-	1	NA	exon (NM_019765, exon 18 of 24)	exon (NM_019765, exon 18 of 24)	-30676	NM_029929	77573	Mm.41372	NM_029929	ENSMUSG00000029434	Vps33a	3830421M04Rik|AI503300|AW048546|AW554476|bf	VPS33A CORVET/HOPS core subunit	protein-coding
mm_65934.1	chr7	30353336	30353344	-	1	NA	Intergenic	Intergenic	9432	NM_175478	233067	Mm.23157	NM_175478	ENSMUSG00000036957	Lrfn3	A530045B06Rik|SALM4	leucine rich repeat and fibronectin type III domain containing 3	protein-coding
mm_114837.1	chr13	92568926	92568928	+	1	NA	Intergenic	RMER13A2|LTR|ERVK	7305	NM_030237	79401	Mm.23520	NM_030237	ENSMUSG00000046957	Spz1	1700027M20Rik|AI429130	spermatogenic leucine zipper 1	protein-coding
mm_10726.1	chr2	22869378	22869381	+	1	NA	intron (NM_019456, intron 12 of 13)	Lx8|LINE|L1	-26143	NM_019501	56075	Mm.249752	NM_019501	ENSMUSG00000026784	Pdss1	2610203G20Rik|2700031G06Rik|TPT|TPT 1|Tprt|mDLP1|mSPS1	prenyl (solanesyl) diphosphate synthase, subunit 1	protein-coding
mm_115853.1	chr13	21288802	21288809	-	1	NA	intron (NM_010343, intron 3 of 4)	intron (NM_010343, intron 3 of 4)	3881	NM_010343	14780	Mm.1332	NM_010343	ENSMUSG00000004344	Gpx5	AV379049|Arep	glutathione peroxidase 5	protein-coding
mm_164233.1	chr15	90610977	90610979	+	1	NA	intron (NM_025815, intron 5 of 19)	intron (NM_025815, intron 5 of 19)	68410	NM_025815	66871	Mm.290991	NM_025815	ENSMUSG00000052560	Cpne8	1200003E11Rik|1500031E20Rik	copine VIII	protein-coding
mm_143728.1	chr17	81379109	81379122	-	1	NA	non-coding (NR_104580, exon 9 of 9)	non-coding (NR_104580, exon 9 of 9)	-314030	NM_028138	72167	Mm.273257	NM_028138	ENSMUSG00000024246	Thumpd2	2810025A12Rik	THUMP domain containing 2	protein-coding
mm_91365.1	chr10	29052237	29052240	-	1	NA	Intergenic	RMER13B|LTR|ERVK	-65932	NM_026336	67719	Mm.440480	NM_026336	ENSMUSG00000015519	2310057J18Rik	2210414P04Rik|Leg1	RIKEN cDNA 2310057J18 gene	protein-coding
mm_100256.1	chr11	117331720	117331739	+	1	NA	promoter-TSS (NM_017380)	promoter-TSS (NM_017380)	14	NM_017380	53860	Mm.38450	NM_017380	ENSMUSG00000059248	Sept9	MSF1|Msf|PNUTL4|Sint1	septin 9	protein-coding
mm_26374.1	chr3	142564569	142564576	+	1	NA	intron (NM_001289493, intron 3 of 10)	intron (NM_001289493, intron 3 of 10)	4076	NM_001289493	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_147595.1	chr18	56707390	56707420	-	1	NA	promoter-TSS (NM_010721)	promoter-TSS (NM_010721)	-408	NM_010721	16906	Mm.4105	NM_010721	ENSMUSG00000024590	Lmnb1	-	lamin B1	protein-coding
mm_140768.1	chr17	17625032	17625067	-	1	NA	promoter-TSS (NM_172827)	promoter-TSS (NM_172827)	-560	NM_172827	240028	Mm.328807	NM_172827	ENSMUSG00000023845	Lnpep	2010309L07Rik|4732490P18Rik|CAP|IRAP|PLAP|gp160|vp165	leucyl/cystinyl aminopeptidase	protein-coding
mm_103085.1	chr11	69917243	69917272	-	1	NA	TTS (NM_019726)	TTS (NM_019726)	3065	NM_019726	56310	Mm.477738	NM_019726	ENSMUSG00000023170	Gps2	AI505953	G protein pathway suppressor 2	protein-coding
mm_124982.1	chr15	20861361	20861361	+	1	NA	Intergenic	Intergenic	-194611	NM_022816	64833	Mm.352763	NM_022816	ENSMUSG00000047565	Acot10	Acate3|MT-ACT48|p48	acyl-CoA thioesterase 10	protein-coding
mm_11679.1	chr2	35503518	35503536	+	1	NA	Intergenic	Intergenic	-42078	NM_001145821	14594	Mm.281124	NM_010283	ENSMUSG00000035778	Ggta1	AW108479|GALT|Gal|Ggta|Ggta-1|alpha Gal|alpha3GalT	glycoprotein galactosyltransferase alpha 1, 3	protein-coding
mm_161136.1	chr13	9765294	9765294	-	1	NA	promoter-TSS (NM_001347480)	promoter-TSS (NM_001347480)	27	NM_001347474	66505	Mm.397307	NM_144516	ENSMUSG00000021156	Zmynd11	2210402G22Rik|BS69	zinc finger, MYND domain containing 11	protein-coding
mm_119072.1	chr14	30870663	30870668	+	1	NA	intron (NM_028839, intron 4 of 7)	intron (NM_028839, intron 4 of 7)	-8592	NM_181390	66175	Mm.220895	NM_181390	ENSMUSG00000042485	Mustn1	1110028G01Rik|Mustang	musculoskeletal, embryonic nuclear protein 1	protein-coding
mm_63819.1	chr7	134031212	134031213	+	1	NA	intron (NM_007400, intron 3 of 22)	intron (NM_007400, intron 3 of 22)	193885	NM_007400	11489	Mm.439714	NM_007400	ENSMUSG00000054555	Adam12	Mltna	a disintegrin and metallopeptidase domain 12 (meltrin alpha)	protein-coding
mm_97983.1	chr11	83885870	83885879	+	1	NA	intron (NM_001291269, intron 5 of 8)	intron (NM_001291269, intron 5 of 8)	32914	NM_001291269	21410	Mm.7226	NM_009330	ENSMUSG00000020679	Hnf1b	HNF-1-beta|HNF-1B|HNF-1Beta|Hnf1beta|LFB3|Tcf-2|Tcf2|vHNF1	HNF1 homeobox B	protein-coding
mm_146452.1	chr18	86394953	86394968	+	1	NA	promoter-TSS (NM_144946)	promoter-TSS (NM_144946)	8	NM_144946	246317	Mm.329578	NM_144946	ENSMUSG00000050321	Neto1	AI851453|Btcl1|C130005O10Rik	neuropilin (NRP) and tolloid (TLL)-like 1	protein-coding
mm_63511.1	chr7	127848879	127848917	+	1	NA	TTS (NM_009294)	TTS (NM_009294)	7090	NM_009294	20909	Mm.24867	NM_009294	ENSMUSG00000030805	Stx4a	Stx4|Syn-4|Syn4	syntaxin 4A (placental)	protein-coding
mm_123386.1	chr14	63321565	63321569	-	1	NA	Intergenic	Intergenic	-76296	NM_001310610	14463	Mm.247669	NM_008092	ENSMUSG00000021944	Gata4	Gata-4	GATA binding protein 4	protein-coding
mm_166652.1	chr6	86615606	86615651	+	1	NA	Intergenic	Intergenic	-12546	NM_026414	67855	Mm.183043	NM_026414	ENSMUSG00000033508	Asprv1	2300003P22Rik|AA986851|SASP|SASPase|Taps	aspartic peptidase, retroviral-like 1	protein-coding
mm_106931.1	chr12	8521930	8521939	+	1	NA	Intergenic	Intergenic	17632	NM_001038660	328059	Mm.46326	NM_177802	ENSMUSG00000020600	Slc7a15	Arpat	solute carrier family 7 (cationic amino acid transporter, y+ system), member 15	protein-coding
mm_37885.1	chr4	132510485	132510491	-	1	NA	promoter-TSS (NM_144907)	promoter-TSS (NM_144907)	-32	NM_144907	230784	Mm.23608	NM_144907	ENSMUSG00000028893	Sesn2	HI95|SEST2|Ses2	sestrin 2	protein-coding
mm_148502.1	chr19	4195029	4195057	+	1	NA	TTS (NM_011237)	TTS (NM_011237)	2869	NM_031868	19045	Mm.1970	NM_031868	ENSMUSG00000040385	Ppp1ca	Ppp1c|dism2	protein phosphatase 1, catalytic subunit, alpha isoform	protein-coding
mm_167980.1	chrX	161717642	161717657	+	1	NA	promoter-TSS (NM_198409)	promoter-TSS (NM_198409)	96	NM_198409	24004	Mm.328503	NM_198409	ENSMUSG00000043518	Rai2	3f8	retinoic acid induced 2	protein-coding
mm_146690.1	chr18	12863372	12863389	-	1	NA	promoter-TSS (NM_001252492)	promoter-TSS (NM_001252492)	0	NM_001252490	64291	Mm.259470	NM_020573	ENSMUSG00000044252	Osbpl1a	G430090F17Rik|Gm753|ORP-1|Osbpl1b	oxysterol binding protein-like 1A	protein-coding
mm_115950.1	chr13	23746417	23746431	-	1	NA	promoter-TSS (NM_175664)	promoter-TSS (NM_175664)	-310	NM_175664	319178	Mm.390567	NM_175664	ENSMUSG00000075031	Hist1h2bb	H2b-143	histone cluster 1, H2bb	protein-coding
mm_134926.1	chr16	30587538	30587597	-	1	NA	promoter-TSS (NM_178069)	promoter-TSS (NM_178069)	22	NM_178069	224092	Mm.567	NM_178069	ENSMUSG00000022538	Lsg1	5830465I20|AA409273|D16Bwg1547e	large 60S subunit nuclear export GTPase 1	protein-coding
mm_102231.1	chr11	54917889	54917900	-	1	NA	exon (NM_021327, exon 14 of 18)	exon (NM_021327, exon 14 of 18)	15040	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_130515.1	chr15	98863989	98864007	-	1	NA	exon (NM_001033276, exon 11 of 55)	exon (NM_001033276, exon 11 of 55)	7207	NM_001033276	381022	Mm.264889	NM_001033276	ENSMUSG00000048154	Kmt2d	ALR|BC032281|BC058659|C430014K11Rik|KMT2B|Mll2|Mll4	lysine (K)-specific methyltransferase 2D	protein-coding
mm_4664.1	chr1	180368133	180368154	+	1	NA	intron (NM_001081175, intron 2 of 7)	intron (NM_001081175, intron 2 of 7)	-37594	NR_003623	277333	Mm.389223	NM_199472		Gm5069	EG277333	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_138732.1	chr17	36958656	36958751	+	1	NA	promoter-TSS (NM_023162)	promoter-TSS (NM_023162)	111	NM_029602	76416	Mm.26684	NM_029602	ENSMUSG00000036214	Znrd1as	1700022C21Rik|AI746295|Znrd1-as	zinc ribbon domain containing 1, antisense	protein-coding
mm_139803.1	chr17	66123584	66123594	+	1	NA	promoter-TSS (NM_001003919)	promoter-TSS (NM_001003919)	69	NM_001003919	320209	Mm.259605	NM_001003919	ENSMUSG00000035842	Ddx11	4732462I11Rik|CHL1|CHLR1|KRG2|essa15a	DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11	protein-coding
mm_17478.1	chr2	28561205	28561227	-	1	NA	exon (NM_009885, exon 2 of 11)	exon (NM_009885, exon 2 of 11)	2187	NM_009885	12613	Mm.236017	NM_009885	ENSMUSG00000026818	Cel	1810036E18Rik|BAL	carboxyl ester lipase	protein-coding
mm_121735.1	chr14	18331100	18331113	-	1	NA	5' UTR (NM_009455, exon 2 of 6)	5' UTR (NM_009455, exon 2 of 6)	738	NM_009455	22194	Mm.4429	NM_009455	ENSMUSG00000021774	Ube2e1	UbcM3|Ubce5|ubcM2	ubiquitin-conjugating enzyme E2E 1	protein-coding
mm_76750.1	chr8	95434669	95434679	-	1	NA	5' UTR (NM_008187, exon 1 of 6)	5' UTR (NM_008187, exon 1 of 6)	195	NM_008187	14894	Mm.2080	NM_008187	ENSMUSG00000031796	Cfap20	2600014O15Rik|AL024127|Gtl3|T10-2A2	cilia and flagella associated protein 20	protein-coding
mm_939.1	chr1	56019875	56019879	+	1	NA	non-coding (NR_126076, exon 2 of 2)	non-coding (NR_126076, exon 2 of 2)	899	NR_126076	69356	Mm.393775	NR_126075	ENSMUSG00000100372	1700003I22Rik	-	RIKEN cDNA 1700003I22 gene	ncRNA
mm_105830.1	chr11	113201835	113201847	-	1	NA	promoter-TSS (NR_015556)	promoter-TSS (NR_015556)	-3	NR_015556	72386	Mm.266961	NR_015556	ENSMUSG00000087259	2610035D17Rik	-	RIKEN cDNA 2610035D17 gene	ncRNA
mm_156425.1	chrX	140953872	140953906	+	1	NA	exon (NM_001164177, exon 2 of 5)	exon (NM_001164177, exon 2 of 5)	2822	NM_016883	53380	Mm.17640	NM_016883	ENSMUSG00000031429	Psmd10	AW554874	proteasome (prosome, macropain) 26S subunit, non-ATPase, 10	protein-coding
mm_11386.1	chr2	31314279	31314287	+	1	NA	Intergenic	CpG	68360	NM_019681	14299	Mm.249318	NM_019681	ENSMUSG00000062661	Ncs1	9430075O15Rik|A730032G13Rik|AI836659|Freq|Mfreq|NCS-1	neuronal calcium sensor 1	protein-coding
mm_87369.1	chr10	44211377	44211380	+	1	NA	intron (NR_001582, intron 3 of 6)	intron (NR_001582, intron 3 of 6)	-4047	NR_027506	70365	Mm.87073	NR_001582	ENSMUSG00000091358	Speer5-ps1	1700007C10Rik|SPEER-5|Speer5-ps	spermatogenesis associated glutamate (E)-rich protein 5, pseudogene 1	pseudo
mm_45127.1	chr5	48599988	48600000	-	1	NA	promoter-TSS (NM_001199245)	promoter-TSS (NM_001199245)	-312	NM_001199245	80334	Mm.160172	NM_030265	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding
mm_36958.1	chr4	109156708	109156762	-	1	NA	intron (NM_001346502, intron 2 of 23)	intron (NM_001346502, intron 2 of 23)	-38699	NM_001134791	100273	Mm.366315	NM_133885	ENSMUSG00000028559	Osbpl9	2600011I06Rik|AU015843|Orp-9	oxysterol binding protein-like 9	protein-coding
mm_110808.1	chr12	72216796	72216830	-	1	NA	exon (NM_001286448, exon 6 of 7)	exon (NM_001286448, exon 6 of 7)	18933	NR_104446	104001	Mm.221275	NM_153457	ENSMUSG00000021087	Rtn1	Nsp	reticulon 1	protein-coding
mm_144839.1	chr18	36559973	36560003	+	1	NA	promoter-TSS (NM_175375)	promoter-TSS (NM_175375)	-615	NM_175375	108857	Mm.482287	NM_175375	ENSMUSG00000024483	Ankhd1	1110004O12Rik|4933432B13Rik|9130019P20Rik|A530027J04Rik|A630021B20Rik|AA571404|Mask|mFLJ00246|mKIAA1085	ankyrin repeat and KH domain containing 1	protein-coding
mm_69774.1	chr7	141016899	141016915	-	1	NA	promoter-TSS (NM_001033632)	promoter-TSS (NM_001033632)	-15	NM_001033632	213002	Mm.276440	NM_001033632	ENSMUSG00000059108	Ifitm6	A330075D07|Dspa2f|Fgls5|fragilis5	interferon induced transmembrane protein 6	protein-coding
mm_110873.1	chr12	73781440	73781462	-	1	NA	Intergenic	Intergenic	-119873	NM_001313920	15251	Mm.3879	NM_010431	ENSMUSG00000021109	Hif1a	AA959795|HIF-1-alpha|HIF1-alpha|HIF1alpha|MOP1|bHLHe78	hypoxia inducible factor 1, alpha subunit	protein-coding
mm_116752.1	chr13	51848290	51848319	-	1	NA	3' UTR (NM_011817, exon 4 of 4)	3' UTR (NM_011817, exon 4 of 4)	1629	NM_011817	23882	Mm.281298	NM_011817	ENSMUSG00000021453	Gadd45g	AI327420|C86281|CR6|DDIT2|OIG37	growth arrest and DNA-damage-inducible 45 gamma	protein-coding
mm_137754.1	chr17	29464466	29464471	+	1	NA	Intergenic	Intergenic	-26577	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_66794.1	chr7	47132421	47132436	-	1	NA	5' UTR (NM_001163565, exon 1 of 14)	5' UTR (NM_001163565, exon 1 of 14)	170	NM_001163565	19259	Mm.4654	NM_013643	ENSMUSG00000030854	Ptpn5	Step	protein tyrosine phosphatase, non-receptor type 5	protein-coding
mm_166326.1	chr5	112292177	112292183	+	1	NA	intron (NM_001326590, intron 1 of 5)	intron (NM_001326590, intron 1 of 5)	15489	NM_009419	22022	Mm.250631	NM_009419	ENSMUSG00000029344	Tpst2	AI448750|D5Ucla3|Tango13b|grm|grt	protein-tyrosine sulfotransferase 2	protein-coding
mm_63893.1	chr7	138846580	138846623	+	1	NA	promoter-TSS (NM_027115)	promoter-TSS (NM_027115)	215	NM_026391	52432	Mm.258739	NM_026391	ENSMUSG00000041769	Ppp2r2d	1300017E19Rik|D7Ertd753e|MDS026	protein phosphatase 2, regulatory subunit B, delta	protein-coding
mm_138155.1	chr17	34238897	34238911	+	1	NA	promoter-TSS (NM_010389)	promoter-TSS (NM_010389)	-1	NM_010389	15002	Mm.327358	NM_010389	ENSMUSG00000041538	H2-Ob	A-beta-2|A-beta2|H-2Ab|H-2I|H-2Ob|H2-Ab|H2-Ab2|H2-IAb2|Ob	histocompatibility 2, O region beta locus	protein-coding
mm_48505.1	chr5	142817584	142817641	-	1	NA	promoter-TSS (NM_001122730)	promoter-TSS (NM_001122730)	-225	NM_001122730	231861	Mm.354649	NM_178242	ENSMUSG00000039477	Tnrc18	BC025631|EG381742|Zfp469	trinucleotide repeat containing 18	protein-coding
mm_70505.1	chr8	12915678	12915690	+	1	NA	promoter-TSS (NM_178076)	promoter-TSS (NM_178076)	-209	NM_178076	17207	Mm.334413	NM_178076	ENSMUSG00000031442	Mcf2l	C130040G20Rik|Dbs|Ost|mKIAA0362	mcf.2 transforming sequence-like	protein-coding
mm_160123.1	chr7	27927473	27927473	-	1	NA	intron (NM_028538, intron 1 of 3)	intron (NM_028538, intron 1 of 3)	1957	NM_028538	73430	Mm.379224	NM_028538	ENSMUSG00000070709	Zfp974	1700049G17Rik|AV321011|BB026409	zinc finger protein 974	protein-coding
mm_103071.1	chr11	69880867	69880937	-	1	NA	promoter-TSS (NM_153143)	promoter-TSS (NM_153143)	83	NM_153143	216858	Mm.239498	NM_153143	ENSMUSG00000046731	Kctd11	AF465352|Ren	potassium channel tetramerisation domain containing 11	protein-coding
mm_151887.1	chr19	5798691	5798696	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	-2712	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_44966.1	chr5	36748640	36748694	-	1	NA	promoter-TSS (NM_133724)	promoter-TSS (NM_133724)	12	NM_133724	117197	Mm.46744	NM_133724	ENSMUSG00000060708	Bloc1s4	2610101N07Rik|Blos4|Cno	biogenesis of lysosomal organelles complex-1, subunit 4, cappuccino	protein-coding
mm_3680.1	chr1	153695496	153695523	+	1	NA	3' UTR (NM_026380, exon 7 of 7)	3' UTR (NM_026380, exon 7 of 7)	29836	NM_001347115	67792	Mm.379143	NM_026380	ENSMUSG00000042671	Rgs8	6530413N01Rik	regulator of G-protein signaling 8	protein-coding
mm_96663.1	chr11	69409282	69409304	+	1	NA	intron (NM_001017426, intron 1 of 22)	intron (NM_001017426, intron 1 of 22)	4382	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_172116.1	chr6	3201030	3201051	+	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	-87479	NR_036696	667335	Mm.380219	NR_036696	ENSMUSG00000106779	Gm8579	EG667335	spermatogenesis associated glutamate (E)-rich protein 4a pseudogene	pseudo
mm_75748.1	chr8	69893980	69893984	-	1	NA	TTS (NM_023312)	TTS (NM_023312)	-6590	NM_026818	68709	Mm.334584	NM_026818	ENSMUSG00000044006	Cilp2	1110031K21Rik|AA407300|CLIP-2	cartilage intermediate layer protein 2	protein-coding
mm_156950.1	chrX	169986606	169986638	+	1	NA	intron (NM_001290512, intron 8 of 9)	intron (NM_001290512, intron 8 of 9)	-7705	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_166009.1	chr4	117649957	117649959	+	1	NA	intron (NM_001285901, intron 7 of 7)	intron (NM_001285901, intron 7 of 7)	32267	NM_023178	66233	Mm.29142	NM_023178	ENSMUSG00000009640	Dmap1	1500016M21Rik|DNMAP1|DNMTAP1|Dmtap1|mKIAA1425	DNA methyltransferase 1-associated protein 1	protein-coding
mm_18878.1	chr2	76360401	76360414	-	1	NA	promoter-TSS (NM_009989)	promoter-TSS (NM_009989)	46	NM_009989	13067	Mm.4872	NM_009989	ENSMUSG00000056436	Cyct	T-Cc	cytochrome c, testis	protein-coding
mm_33811.1	chr4	135176106	135176127	+	1	NA	3' UTR (NM_019732, exon 6 of 6)	3' UTR (NM_019732, exon 6 of 6)	55471	NM_019732	12399	Mm.378894	NM_019732	ENSMUSG00000070691	Runx3	AML2|Cbfa3|Pebp2a3	runt related transcription factor 3	protein-coding
mm_40909.1	chr5	75590326	75590334	+	1	NA	intron (NM_021099, intron 1 of 20)	intron (NM_021099, intron 1 of 20)	15339	NM_021099	16590	Mm.247073	NM_021099	ENSMUSG00000005672	Kit	Bs|CD117|Fdc|Gsfsco1|Gsfsco5|Gsfsow3|SCO1|SCO5|SOW3|Ssm|Tr-kit|W|c-KIT	KIT proto-oncogene receptor tyrosine kinase	protein-coding
mm_140649.1	chr17	12691997	12692012	-	1	NA	exon (NM_010515, exon 40 of 48)	exon (NM_010515, exon 40 of 48)	-16166	NM_009202	20517	Mm.594	NM_009202	ENSMUSG00000023829	Slc22a1	Lx1|Oct1|Orct|Orct1	solute carrier family 22 (organic cation transporter), member 1	protein-coding
mm_150585.1	chr19	40660485	40660498	+	1	NA	intron (NM_009848, intron 1 of 9)	intron (NM_009848, intron 1 of 9)	721	NM_009848	12495	Mm.2824	NM_009848	ENSMUSG00000048120	Entpd1	2610206B08Rik|AA408691|Cd39|NTPDase-1	ectonucleoside triphosphate diphosphohydrolase 1	protein-coding
mm_54948.1	chr6	48613750	48613782	-	1	NA	intron (NM_173429, intron 1 of 1)	intron (NM_173429, intron 1 of 1)	586	NM_173429	243372	Mm.435190	NM_173429	ENSMUSG00000007216	Zfp775	C130032F08Rik|Znf775	zinc finger protein 775	protein-coding
mm_73923.1	chr8	119811340	119811344	+	1	NA	intron (NM_028071, intron 3 of 3)	B1F1|SINE|Alu	29237	NM_028071	72042	Mm.393405	NM_028071	ENSMUSG00000031827	Cotl1	1810074P22Rik|2010004C08Rik|Clp	coactosin-like 1 (Dictyostelium)	protein-coding
mm_25744.1	chr3	123016552	123016578	+	1	NA	exon (NM_021503, exon 4 of 6)	exon (NM_021503, exon 4 of 6)	18422	NM_021503	59006	Mm.141157	NM_021503	ENSMUSG00000028116	Myoz2	1110012I24Rik|Fatz-2|Myozl2	myozenin 2	protein-coding
mm_106594.1	chr11	120730641	120730676	-	1	NA	exon (NM_007621, exon 4 of 8)	exon (NM_007621, exon 4 of 8)	1363	NM_007621	12409	Mm.21454	NM_007621	ENSMUSG00000025150	Cbr2	MLCR	carbonyl reductase 2	protein-coding
mm_37468.1	chr4	123527683	123527712	-	1	NA	intron (NM_001199136, intron 5 of 97)	intron (NM_001199136, intron 5 of 97)	-88723	NR_105824	102465214		NR_105824	ENSMUSG00000099005	Mir6398	Gm27657|mmu-mir-6398	microRNA 6398	ncRNA
mm_152059.1	chr19	6363214	6363230	-	1	NA	promoter-TSS (NR_122118)	promoter-TSS (NR_122118)	-468	NM_011750	22668	Mm.256422	NM_011750	ENSMUSG00000024949	Sf1	BBP|MZFM|WBP4|Zfp162	splicing factor 1	protein-coding
mm_7173.1	chr1	92180188	92180263	-	1	NA	intron (NM_207225, intron 1 of 26)	CpG	116	NM_207225	208727	Mm.318567	NM_207225	ENSMUSG00000026313	Hdac4	4932408F19Rik|HD4	histone deacetylase 4	protein-coding
mm_49215.1	chr6	15749549	15749565	+	1	NA	intron (NM_175088, intron 3 of 4)	intron (NM_175088, intron 3 of 4)	28896	NM_175088	16543	Mm.1314	NM_175088	ENSMUSG00000041390	Mdfic	Kdt1|Mdfid	MyoD family inhibitor domain containing	protein-coding
mm_81788.1	chr9	114978434	114978461	+	1	NA	Intergenic	CpG	-44460	NM_175380	333433	Mm.38198	NM_175380	ENSMUSG00000050627	Gpd1l	2210409H23Rik|D9Ertd660e	glycerol-3-phosphate dehydrogenase 1-like	protein-coding
mm_92216.1	chr10	68249247	68249251	-	1	NA	intron (NM_023598, intron 2 of 9)	intron (NM_023598, intron 2 of 9)	29477	NM_023598	71371	Mm.440357	NM_023598	ENSMUSG00000019947	Arid5b	4930580B11|5430435G07Rik|AI467247|Desrt|Mrf2|Mrf2alpha|Mrf2beta	AT rich interactive domain 5B (MRF1-like)	protein-coding
mm_4516.1	chr1	174501851	174501887	+	1	NA	promoter-TSS (NM_019445)	promoter-TSS (NM_019445)	44	NM_019445	54418	Mm.330620	NM_019445	ENSMUSG00000028354	Fmn2	AU024104	formin 2	protein-coding
mm_23168.1	chr3	40745333	40745345	+	1	NA	promoter-TSS (NM_011020)	promoter-TSS (NM_011020)	-274	NM_011020	18415	Mm.39330	NM_011020	ENSMUSG00000025757	Hspa4l	94kDa|AI461691|APG-1|Osp94	heat shock protein 4 like	protein-coding
mm_27162.1	chr3	33143125	33143159	-	1	NA	promoter-TSS (NM_001163516)	promoter-TSS (NM_001163516)	49	NM_001163516	58869	Mm.151332	NM_021483	ENSMUSG00000027674	Pex5l	1700016J08Rik|PXR2|Pex2|TRIP8b|pex5Rp	peroxisomal biogenesis factor 5-like	protein-coding
mm_18040.1	chr2	38926397	38926454	-	1	NA	promoter-TSS (NM_010264)	promoter-TSS (NM_010264)	36	NM_010264	14536	Mm.439703	NM_010264	ENSMUSG00000063972	Nr6a1	1700113M01Rik|Gcnf|NCNF|RTR	nuclear receptor subfamily 6, group A, member 1	protein-coding
mm_55141.1	chr6	51463484	51463499	-	1	NA	exon (NM_182650, exon 9 of 10)	exon (NM_182650, exon 9 of 10)	6403	NM_182650	53379	Mm.155896	NM_016806	ENSMUSG00000004980	Hnrnpa2b1	9130414A06Rik|Hnrpa2|Hnrpa2b1|hnrnp-A	heterogeneous nuclear ribonucleoprotein A2/B1	protein-coding
mm_36331.1	chr4	72137117	72137129	-	1	NA	exon (NM_011599, exon 14 of 20)	exon (NM_011599, exon 14 of 20)	63770	NM_011599	21885	Mm.278444	NM_011599	ENSMUSG00000008305	Tle1	C230057C06Rik|Estm14|Grg-1|Grg1|Tle4l	transducin-like enhancer of split 1	protein-coding
mm_140679.1	chr17	12992488	12992554	-	1	NA	promoter-TSS (NM_175394)	promoter-TSS (NM_175394)	18	NM_175394	60532	Mm.275521	NM_175394	ENSMUSG00000060475	Wtap	2810408K05Rik|9430038B09Rik	Wilms tumour 1-associating protein	protein-coding
mm_40246.1	chr5	38076498	38076508	+	1	NA	intron (NM_001289536, intron 1 of 9)	intron (NM_001289536, intron 1 of 9)	37273	NM_026959	71116	Mm.18959	NM_026959	ENSMUSG00000029125	Stx18	1810035L21Rik|4933425D03Rik|AU041562	syntaxin 18	protein-coding
mm_147798.1	chr18	61657978	61658007	-	1	NA	intron (NR_045402, intron 1 of 4)	(TG)n|Simple_repeat|Simple_repeat	7546	NR_045402	328968	Mm.392305	NR_045402		Carmn	Carmen|E330013P06|Gm16908|Mir143hg	cardiac mesoderm enhancer-associated non-coding RNA	ncRNA
mm_166971.1	chr7	44595264	44595273	+	1	NA	exon (NM_001290682, exon 2 of 5)	exon (NM_001290682, exon 2 of 5)	4382	NM_001290682	16504	Mm.40312	NM_008422	ENSMUSG00000062785	Kcnc3	KShIIID|Kcr2-3|Kv3.3	potassium voltage gated channel, Shaw-related subfamily, member 3	protein-coding
mm_100705.1	chr11	3648742	3648807	-	1	NA	promoter-TSS (NM_001159288)	promoter-TSS (NM_001159288)	40	NR_002321	544752	Mm.390314	NR_002321	ENSMUSG00000056579	Tug1	AI316828	taurine upregulated gene 1	ncRNA
mm_153465.1	chr19	41264287	41264289	-	1	NA	promoter-TSS (NM_133352)	promoter-TSS (NM_133352)	-284	NM_133352	107358	Mm.246440	NM_133352	ENSMUSG00000025016	Tm9sf3	1810073M23Rik|2810031D16Rik|AI115521|AI413748|AW146116|AW549777|Smbp|mKIAA4036	transmembrane 9 superfamily member 3	protein-coding
mm_122604.1	chr14	51050666	51050671	-	1	NA	promoter-TSS (NM_001011877)	promoter-TSS (NM_001011877)	-505	NM_001011877	497113	Mm.379741	NM_001011877	ENSMUSG00000059648	Rnase11	Raj1	ribonuclease, RNase A family, 11 (non-active)	protein-coding
mm_130912.1	chr15	102553833	102553854	-	1	NA	exon (NM_001310070, exon 5 of 12)	exon (NM_001310070, exon 5 of 12)	-29222	NM_018787	54615	Mm.445915	NM_018787	ENSMUSG00000023052	Npff	-	neuropeptide FF-amide peptide precursor	protein-coding
mm_126228.1	chr15	78935178	78935221	+	1	NA	intron (NM_133800, intron 1 of 5)	CpG	266	NM_133800	97961	Mm.157216	NM_133800	ENSMUSG00000033099	Nol12	C78541|Nop25	nucleolar protein 12	protein-coding
mm_43192.1	chr5	128736243	128736247	+	1	NA	promoter-TSS (NM_021311)	promoter-TSS (NM_021311)	-1	NM_021311	57749	Mm.272720	NM_021311	ENSMUSG00000029423	Piwil1	MIWI	piwi-like RNA-mediated gene silencing 1	protein-coding
mm_171001.1	chr2	76955496	76955501	+	1	NA	intron (NM_028004, intron 12 of 191)	L1Md_Gf|LINE|L1	27049	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_112368.1	chr12	119182094	119182105	-	1	NA	intron (NM_177290, intron 6 of 13)	ID4_|SINE|ID	56177	NM_177290	320910	Mm.217000	NM_177290	ENSMUSG00000025321	Itgb8	4832412O06Rik	integrin beta 8	protein-coding
mm_142318.1	chr17	43113195	43113203	-	1	NA	Intergenic	Intergenic	45092	NR_045155	545207	Mm.329050	NR_045153		E130008D07Rik	-	RIKEN cDNA E130008D07 gene	ncRNA
mm_61028.1	chr7	49522767	49522810	+	1	NA	intron (NM_175272, intron 11 of 37)	intron (NM_175272, intron 11 of 37)	114047	NM_001005232	13172	Mm.307176	NM_001005232	ENSMUSG00000030507	Dbx1	AI426026|Dbx	developing brain homeobox 1	protein-coding
mm_57316.1	chr6	124728446	124728454	-	1	NA	exon (NM_013545, exon 6 of 16)	exon (NM_013545, exon 6 of 16)	4704	NM_013545	15170	Mm.271799	NM_013545	ENSMUSG00000004266	Ptpn6	70Z-SHP|Hcph|PTPTY-42|Ptp1C|SH-PTP1|SHP-1|hcp|me	protein tyrosine phosphatase, non-receptor type 6	protein-coding
mm_4528.1	chr1	175632156	175632160	+	1	NA	promoter-TSS (NM_133809)	promoter-TSS (NM_133809)	-35	NM_133809	98256	Mm.27217	NM_133809	ENSMUSG00000039783	Kmo	AI046660	kynurenine 3-monooxygenase (kynurenine 3-hydroxylase)	protein-coding
mm_157348.1	chrX	36989483	36989507	-	1	NA	5' UTR (NM_001253706, exon 1 of 11)	5' UTR (NM_001253706, exon 1 of 11)	200	NM_001177324	56526	Mm.260036	NM_019942	ENSMUSG00000050379	Sept6	2810035H17Rik|C920001C06Rik|Sep6|mKIAA0128	septin 6	protein-coding
mm_6969.1	chr1	86226558	86226598	-	1	NA	intron (NM_030184, intron 19 of 24)	intron (NM_030184, intron 19 of 24)	71798	NM_001310702	78795	Mm.379264	NM_027456	ENSMUSG00000062590	Armc9	3830422A13Rik|4831423D23Rik|4930438O05Rik|5730415N24Rik	armadillo repeat containing 9	protein-coding
mm_110444.1	chr12	51030142	51030146	-	1	NA	intron (NR_126468, intron 2 of 4)	L1MEj|LINE|L1	24988	NR_126468	75494	Mm.416848	NR_126468		1700008C04Rik	-	RIKEN cDNA 1700008C04 gene	ncRNA
mm_140463.1	chr17	91088853	91088885	+	1	NA	5' UTR (NM_020252, exon 2 of 23)	5' UTR (NM_020252, exon 2 of 23)	736	NM_001346957	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_51917.1	chr6	91234019	91234027	+	1	NA	exon (NM_001081437, exon 2 of 17)	exon (NM_001081437, exon 2 of 17)	21259	NM_007992	14115	Mm.249146	NM_007992	ENSMUSG00000064080	Fbln2	5730577E14Rik|FIBL-2	fibulin 2	protein-coding
mm_109447.1	chr12	110954194	110954197	+	1	NA	intron (NM_175336, intron 17 of 20)	intron (NM_175336, intron 17 of 20)	24826	NM_175207	74251	Mm.250989	NM_175207	ENSMUSG00000037904	Ankrd9	2500003O20Rik	ankyrin repeat domain 9	protein-coding
mm_23943.1	chr3	84593548	84593563	+	1	NA	promoter-TSS (NM_207278)	promoter-TSS (NM_207278)	-19	NM_207278	403175	Mm.83086	NM_207278	ENSMUSG00000047819	Tigd4	C130063O11Rik|Gm418	tigger transposable element derived 4	protein-coding
mm_31038.1	chr4	41000989	41000992	+	1	NA	intron (NM_001290448, intron 11 of 15)	B2_Mm2|SINE|B2	7295	NR_037277	100526501		NR_037277	ENSMUSG00000092862	Mir3094	mir-3094|mmu-mir-3094	microRNA 3094	ncRNA
mm_29218.1	chr3	107092913	107092919	-	1	NA	Intergenic	Intergenic	-8651	NM_008417	16490	Mm.39285	NM_008417	ENSMUSG00000040724	Kcna2	Akr6a4|ENSMUSG00000074335|Gm10672|Kca1-2|Kv1.2|Mk-2	potassium voltage-gated channel, shaker-related subfamily, member 2	protein-coding
mm_149289.1	chr19	10669352	10669380	+	1	NA	exon (NM_021453, exon 8 of 9)	exon (NM_021453, exon 8 of 9)	8705	NM_021453	58803	Mm.34037	NM_021453	ENSMUSG00000024738	Pga5	1110035E17Rik|Pepf	pepsinogen 5, group I	protein-coding
mm_160969.1	chr11	99809892	99809892	-	1	NA	promoter-TSS (NM_001099313)	promoter-TSS (NM_001099313)	0	NM_001099313	670482	Mm.386956	NM_001099313	ENSMUSG00000078259	Gm11554	OTTMUSG00000002180	predicted gene 11554	protein-coding
mm_114421.1	chr13	64410778	64410781	+	1	NA	Intergenic	Intergenic	-21774	NM_053180	105278	Mm.74982	NM_053180	ENSMUSG00000021483	Cdk20	4932702G04Rik|AU019450|AW558027|CDCH|Ccrk|PNQLARE|p42	cyclin-dependent kinase 20	protein-coding
mm_109092.1	chr12	104819235	104819258	+	1	NA	intron (NM_001040682, intron 1 of 12)	intron (NM_001040682, intron 1 of 12)	45830	NR_104436	94040	Mm.244078	NM_053155	ENSMUSG00000021097	Clmn	9330188N17Rik|AI428889|AI788815|mKIAA1188	calmin	protein-coding
mm_28911.1	chr3	98760553	98760573	-	1	NA	intron (NM_001161742, intron 2 of 4)	RMER6A|LTR|ERVK	1847	NM_001161745	15494	Mm.158717	NM_001012306	ENSMUSG00000062410	Hsd3b3	9030618K22Rik|AI790201	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 3	protein-coding
mm_3992.1	chr1	164443265	164443293	+	1	NA	exon (NM_009721, exon 3 of 6)	exon (NM_009721, exon 3 of 6)	15076	NM_009721	11931	Mm.4550	NM_009721	ENSMUSG00000026576	Atp1b1	Atp4b|Atpb|Atpb-1|NKbeta1	ATPase, Na+/K+ transporting, beta 1 polypeptide	protein-coding
mm_104298.1	chr11	90390795	90390820	-	1	NA	5' UTR (NM_172563, exon 1 of 4)	5' UTR (NM_172563, exon 1 of 4)	110	NM_172563	217082	Mm.158903	NM_172563	ENSMUSG00000003949	Hlf	E230015K02Rik	hepatic leukemia factor	protein-coding
mm_81882.1	chr9	119341420	119341486	+	1	NA	5' UTR (NM_130864, exon 1 of 12)	5' UTR (NM_130864, exon 1 of 12)	159	NM_130864	113868	Mm.205266	NM_130864	ENSMUSG00000036138	Acaa1a	Acaa|Acaa1|D9Ertd25e|PTL	acetyl-Coenzyme A acyltransferase 1A	protein-coding
mm_79230.1	chr9	50494234	50494272	+	1	NA	promoter-TSS (NM_029639)	promoter-TSS (NM_029639)	-272	NM_029639	76509	Mm.29959	NM_029639	ENSMUSG00000032068	Plet1	0610037B23Rik|1600029D21Rik|AA407923|AU043048	placenta expressed transcript 1	protein-coding
mm_53085.1	chr6	124997048	124997059	+	1	NA	intron (NM_175696, intron 1 of 5)	intron (NM_175696, intron 1 of 5)	333	NM_175696	319352	Mm.295327	NM_175696	ENSMUSG00000030329	Pianp	AI255183|AU067746|C530028O21Rik|Panp	PILR alpha associated neural protein	protein-coding
mm_69991.1	chr7	142383470	142383495	-	1	NA	exon (NM_009983, exon 3 of 9)	exon (NM_009983, exon 3 of 9)	4388	NM_009983	13033	Mm.231395	NM_009983	ENSMUSG00000007891	Ctsd	CD|CatD	cathepsin D	protein-coding
mm_160474.1	chr8	119612600	119612600	+	1	NA	promoter-TSS (NM_029428)	promoter-TSS (NM_029428)	-147	NM_029428	75773	Mm.159566	NM_029428	ENSMUSG00000024266	Adad2	4930403J07Rik	adenosine deaminase domain containing 2	protein-coding
mm_32082.1	chr4	98395818	98395888	+	1	NA	promoter-TSS (NM_172696)	promoter-TSS (NM_172696)	27	NM_172696	12695	Mm.90218	NM_007704	ENSMUSG00000061859	Patj	Cipp|Inadl	PATJ, crumbs cell polarity complex component	protein-coding
mm_42184.1	chr5	112267519	112267525	+	1	NA	intron (NM_023695, intron 5 of 5)	intron (NM_023695, intron 5 of 5)	-9169	NM_001326590	22022	Mm.250631	NM_009419	ENSMUSG00000029344	Tpst2	AI448750|D5Ucla3|Tango13b|grm|grt	protein-tyrosine sulfotransferase 2	protein-coding
mm_86839.1	chr10	21396154	21396164	+	1	NA	3' UTR (NM_178713, exon 7 of 7)	3' UTR (NM_178713, exon 7 of 7)	18859	NM_178713	237320	Mm.90181	NM_178713	ENSMUSG00000037542	Aldh8a1	Raldh4	aldehyde dehydrogenase 8 family, member A1	protein-coding
mm_119616.1	chr14	51114424	51114446	+	1	NA	Intergenic	B1_Mus2|SINE|Alu	-2118	NM_203508	219026	Mm.297297	NM_203508	ENSMUSG00000072575	Eddm3b	Fam12|Gm75	epididymal protein 3B	protein-coding
mm_112429.1	chr13	4249706	4249709	+	1	NA	TTS (NR_028405)	TTS (NR_028405)	972	NR_028405	111002	Mm.482672	NR_028405		Marcksl1-ps4	Gm16264|Mlp-rs4|Mrp-rs4|OTTMUSG00000032901	MARCKS-like 1, pseudogene 4	pseudo
mm_138730.1	chr17	36958572	36958611	+	1	NA	promoter-TSS (NM_029602)	promoter-TSS (NM_029602)	-1	NM_029602	76416	Mm.26684	NM_029602	ENSMUSG00000036214	Znrd1as	1700022C21Rik|AI746295|Znrd1-as	zinc ribbon domain containing 1, antisense	protein-coding
mm_144551.1	chr18	31324470	31324476	+	1	NA	Intergenic	PB1|SINE|Alu	-7345	NM_009065	19762	Mm.5163	NM_009065	ENSMUSG00000057455	Rit2	RIBA|Rin|Roc2	Ras-like without CAAX 2	protein-coding
mm_30682.1	chr4	11202411	11202413	+	1	NA	TTS (NM_001159595)	TTS (NM_001159595)	10703	NM_001282943	12448	Mm.35867	NM_009830	ENSMUSG00000028212	Ccne2	-	cyclin E2	protein-coding
mm_108251.1	chr12	78226713	78226773	+	1	NA	promoter-TSS (NM_172952)	promoter-TSS (NM_172952)	88	NM_145965	268566	Mm.341742	NM_145965	ENSMUSG00000047454	Gphn	5730552E08Rik|AI662856|BC027112|C230040D23|GPH|GPHRYN|geph	gephyrin	protein-coding
mm_122815.1	chr14	54605910	54605935	-	1	NA	promoter-TSS (NM_028890)	promoter-TSS (NM_028890)	-14	NM_028890	74359	Mm.79815	NM_028890	ENSMUSG00000022179	4931414P19Rik	-	RIKEN cDNA 4931414P19 gene	protein-coding
mm_104633.1	chr11	97500351	97500368	-	1	NA	promoter-TSS (NM_001289118)	promoter-TSS (NM_001289118)	-19	NM_001289118	100141474	Mm.482426	NM_001289118	ENSMUSG00000047988	4933428G20Rik	-	RIKEN cDNA 4933428G20 gene	protein-coding
mm_41993.1	chr5	107755098	107755100	+	1	NA	intron (NM_007964, intron 17 of 17)	intron (NM_007964, intron 17 of 17)	-29294	NM_001267621	14581	Mm.2078	NM_010278	ENSMUSG00000029275	Gfi1	AW495828|Gfi-1|Pal-1|Pal1	growth factor independent 1	protein-coding
mm_59354.1	chr7	25670444	25670448	+	1	NA	intron (NM_177102, intron 3 of 3)	intron (NM_177102, intron 3 of 3)	4720	NM_001290497	320208	Mm.207484	NM_177102	ENSMUSG00000061702	Tmem91	A830041P22Rik|DSPC3	transmembrane protein 91	protein-coding
mm_139001.1	chr17	45563929	45563973	+	1	NA	promoter-TSS (NM_028662)	promoter-TSS (NM_028662)	-201	NM_028662	73836	Mm.289716	NM_028662	ENSMUSG00000037089	Slc35b2	1110003M08Rik|AA407792|AI842275|PAPST1|Slc35b1	solute carrier family 35, member B2	protein-coding
mm_165957.1	chr4	87230098	87230110	-	1	NA	intron (NM_172426, intron 1 of 10)	intron (NM_172426, intron 1 of 10)	436	NM_172426	76376	Mm.490487	NM_172426	ENSMUSG00000037996	Slc24a2	2810021B17Rik|6330417K15Rik|AI847460|Nckx2	solute carrier family 24 (sodium/potassium/calcium exchanger), member 2	protein-coding
mm_118822.1	chr14	25564270	25564296	+	1	NA	intron (NM_001310666, intron 3 of 23)	ORR1A2|LTR|ERVL-MaLR	-22521	NR_033492	77592	Mm.444871	NM_175264		4931406H21Rik	-	RIKEN cDNA 4931406H21 gene	ncRNA
mm_109417.1	chr12	110485790	110485806	+	1	NA	promoter-TSS (NM_001081458)	promoter-TSS (NM_001081458)	59	NM_012023	26931	Mm.240396	NM_012023	ENSMUSG00000017843	Ppp2r5c	2610043M05Rik|2700063L20Rik|AI060890|AW545884|C85228|D12Bwg0916e|mKIAA0044	protein phosphatase 2, regulatory subunit B', gamma	protein-coding
mm_102937.1	chr11	69601170	69601189	-	1	NA	3' UTR (NM_013415, exon 7 of 7)	3' UTR (NM_013415, exon 7 of 7)	4781	NM_013415	11932	Mm.235204	NM_013415	ENSMUSG00000041329	Atp1b2	Amog|Atpb-2	ATPase, Na+/K+ transporting, beta 2 polypeptide	protein-coding
mm_136474.1	chr16	95769121	95769123	-	1	NA	Intergenic	Intergenic	66715	NM_011809	23872	Mm.290207	NM_011809	ENSMUSG00000022895	Ets2	AU022856|Ets-2	E26 avian leukemia oncogene 2, 3' domain	protein-coding
mm_20315.1	chr2	127302022	127302051	-	1	NA	Intergenic	Intergenic	31807	NM_139308	99138	Mm.41271	NM_139308	ENSMUSG00000027367	Stard7	AI852671|AL022671|AW544915	START domain containing 7	protein-coding
mm_153535.1	chr19	41911812	41911820	-	1	NA	promoter-TSS (NM_023418)	promoter-TSS (NM_023418)	-55	NM_023418	18648	Mm.16783	NM_023418	ENSMUSG00000011752	Pgam1	2310050F24Rik|Pgam-1	phosphoglycerate mutase 1	protein-coding
mm_157234.1	chrX	16911676	16911691	-	1	NA	promoter-TSS (NM_010883)	promoter-TSS (NM_010883)	91	NM_010883	17986	Mm.5014	NM_010883	ENSMUSG00000040138	Ndp	ND|Ndph	Norrie disease (pseudoglioma) (human)	protein-coding
mm_76805.1	chr8	104310110	104310110	-	1	NA	promoter-TSS (NM_181990)	promoter-TSS (NM_181990)	35	NM_181990	100504164	Mm.443302	NM_181990	ENSMUSG00000110430	Cmtm1	CHLFH1a|CKLFH|CKLFH1|Cklfsf1	CKLF-like MARVEL transmembrane domain containing 1	protein-coding
mm_135565.1	chr16	50168959	50168960	-	1	NA	Intergenic	B4A|SINE|B4	-96107	NR_045935	224180	Mm.146439	NM_175010		Gm4827	B130050K08|EG224180	predicted gene 4827	ncRNA
mm_134245.1	chr16	13423723	13423743	-	1	NA	Intergenic	L1M2|LINE|L1	-25790	NR_030549	100124432		NR_030549	ENSMUSG00000076972	Mir193b	Mir193|Mirn193b|mir-193b	microRNA 193b	ncRNA
mm_38247.1	chr4	136602642	136602760	-	1	NA	promoter-TSS (NM_133872)	promoter-TSS (NM_133872)	22	NM_133872	99982	Mm.28540	NM_133872	ENSMUSG00000036940	Kdm1a	1810043O07Rik|AA408884|Aof2|D4Ertd478e|Kdm1|Lsd1|mKIAA0601	lysine (K)-specific demethylase 1A	protein-coding
mm_805.1	chr1	45348892	45348936	+	1	NA	3' UTR (NM_009930, exon 51 of 51)	3' UTR (NM_009930, exon 51 of 51)	37376	NM_009930	12825	Mm.249555	NM_009930	ENSMUSG00000026043	Col3a1	AW550625|Col3a-1|Tsk-2|Tsk2	collagen, type III, alpha 1	protein-coding
mm_163388.1	chr12	55961507	55961511	-	1	NA	Intergenic	L2c|LINE|L2	125143	NM_001037756	52592	Mm.24761	NM_027867	ENSMUSG00000012076	Brms1l	0710008O11Rik|AI159718|BRMS1|D12Ertd407e	breast cancer metastasis-suppressor 1-like	protein-coding
mm_24104.1	chr3	88141161	88141164	+	1	NA	Intergenic	Intergenic	-1210	NM_001310587	17261	Mm.28184	NM_133665	ENSMUSG00000001419	Mef2d	C80750	myocyte enhancer factor 2D	protein-coding
mm_48275.1	chr5	137963088	137963109	-	1	NA	promoter-TSS (NM_080450)	promoter-TSS (NM_080450)	-139	NM_080450	118446	Mm.332771	NM_080450	ENSMUSG00000056966	Gjc3	Cx29|Gje1	gap junction protein, gamma 3	protein-coding
mm_96744.1	chr11	69846666	69846681	+	1	NA	promoter-TSS (NM_023564)	promoter-TSS (NM_023564)	29	NR_033133	70310	Mm.28874	NM_023564	ENSMUSG00000019461	Plscr3	2210403O21Rik|2610037N06Rik|ESTM3|X83310	phospholipid scramblase 3	protein-coding
mm_160283.1	chr7	123169674	123169674	+	1	NA	exon (NM_144925, exon 6 of 24)	exon (NM_144925, exon 6 of 24)	-45192	NM_146198	233836	Mm.211838	NM_146198	ENSMUSG00000030769	Slc5a11	2010013B02Rik|Kst1|RKST2|SMIT2|Slc5a10	solute carrier family 5 (sodium/glucose cotransporter), member 11	protein-coding
mm_107824.1	chr12	69159282	69159296	+	1	NA	promoter-TSS (NM_009093)	promoter-TSS (NM_009093)	-103	NM_009093	20090	Mm.379006	NM_009093	ENSMUSG00000034892	Rps29	-	ribosomal protein S29	protein-coding
mm_136526.1	chr16	97460482	97460491	-	1	NA	intron (NR_003520, intron 2 of 8)	intron (NR_003520, intron 2 of 8)	2419	NM_010846	17857	Mm.33996	NM_010846	ENSMUSG00000000386	Mx1	AI893580|Mx|Mx-1	MX dynamin-like GTPase 1	protein-coding
mm_16069.1	chr2	168081104	168081122	+	1	NA	5' UTR (NM_021409, exon 1 of 3)	5' UTR (NM_021409, exon 1 of 3)	109	NM_021409	58220	Mm.292834	NM_021409	ENSMUSG00000044641	Pard6b	AV025615|Par6b	par-6 family cell polarity regulator beta	protein-coding
mm_144810.1	chr18	36287076	36287161	+	1	NA	5' UTR (NM_008989, exon 2 of 2)	5' UTR (NM_008989, exon 2 of 2)	5956	NM_008989	19290	Mm.231802	NM_008989	ENSMUSG00000043991	Pura	CAGER-1|Pur-alpha|ssCRE-BP	purine rich element binding protein A	protein-coding
mm_150090.1	chr19	29454247	29454279	+	1	NA	intron (NM_021396, intron 4 of 5)	intron (NM_021396, intron 4 of 5)	43344	NM_021396	58205	Mm.116737	NM_021396	ENSMUSG00000016498	Pdcd1lg2	B7-DC|Btdc|F730015O22Rik|PD-L2	programmed cell death 1 ligand 2	protein-coding
mm_140707.1	chr17	14694224	14694242	-	1	NA	promoter-TSS (NM_011581)	promoter-TSS (NM_011581)	29	NM_011581	21826	Mm.26688	NM_011581	ENSMUSG00000023885	Thbs2	TSP2|Thbs-2	thrombospondin 2	protein-coding
mm_19134.1	chr2	80300961	80300967	-	1	NA	Intergenic	Intergenic	8494	NM_177256	320769	Mm.60992	NM_177256	ENSMUSG00000050114	Prdx6b	1-cysPrx-P1|4930414C22Rik|Aop2-rs1|Prdx5-rs1|Prdx6-ps1|Prdx6-rs1|Prdx6-rs1-ps	peroxiredoxin 6B	protein-coding
mm_25184.1	chr3	103329106	103329131	+	1	NA	exon (NM_053170, exon 9 of 20)	exon (NM_053170, exon 9 of 20)	49825	NM_001079830	94093	Mm.195036	NM_053170	ENSMUSG00000033014	Trim33	8030451N04Rik|AI413936|Ecto|Tif1g	tripartite motif-containing 33	protein-coding
mm_54863.1	chr6	42597549	42597559	-	1	NA	promoter-TSS (NM_203396)	promoter-TSS (NM_203396)	-182	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_104266.1	chr11	88995730	88995760	-	1	NA	Intergenic	Intergenic	-3658	NM_009546	217069	Mm.248445	NM_009546	ENSMUSG00000000275	Trim25	AA960166|AL022677|EFP|Zfp147	tripartite motif-containing 25	protein-coding
mm_83976.1	chr9	57262564	57262580	-	1	NA	promoter-TSS (NM_028820)	promoter-TSS (NM_028820)	27	NM_028820	74211	Mm.428905	NM_028820	ENSMUSG00000032300	1700017B05Rik	AA682102|D9Ertd278e	RIKEN cDNA 1700017B05 gene	protein-coding
mm_102999.1	chr11	69687287	69687300	-	1	NA	exon (NM_001159503, exon 6 of 13)	exon (NM_001159503, exon 6 of 13)	-1739	NM_023517	69583	Mm.8983	NM_023517	ENSMUSG00000089669	Tnfsf13	2310026N09Rik|April|Tall2|Tnlg7b|Trdl1	tumor necrosis factor (ligand) superfamily, member 13	protein-coding
mm_165512.1	chr2	172972504	172972504	+	1	NA	Intergenic	Intergenic	-7338	NM_012046	26972	Mm.23495	NM_012046	ENSMUSG00000005883	Spo11	AI449549|Spo11a|Spo11b	SPO11 meiotic protein covalently bound to DSB	protein-coding
mm_74447.1	chr8	4213453	4213463	-	1	NA	exon (NM_207203, exon 6 of 7)	exon (NM_207203, exon 6 of 7)	3854	NM_207203	73072	Mm.477379	NM_207203	ENSMUSG00000064125	Prr36	-	proline rich 36	protein-coding
mm_167068.1	chr7	99353224	99353234	-	1	NA	promoter-TSS (NM_009825)	promoter-TSS (NM_009825)	10	NM_009825	12406	Mm.22708	NM_009825	ENSMUSG00000070436	Serpinh1	BERF-1|Cbp1|Cbp2|Hsp47|J6|Serpinh2|gp46	serine (or cysteine) peptidase inhibitor, clade H, member 1	protein-coding
mm_120797.1	chr14	74735690	74735694	+	1	NA	intron (NM_001285423, intron 1 of 8)	intron (NM_001285423, intron 1 of 8)	3395	NM_016903	13885	Mm.38055	NM_016903	ENSMUSG00000021996	Esd	Es-10|Es10|FGH|sid478	esterase D/formylglutathione hydrolase	protein-coding
mm_31998.1	chr4	92147301	92147306	+	1	NA	promoter-TSS (NM_027034)	promoter-TSS (NM_027034)	-82	NM_027034	69314	Mm.55891	NM_027034	ENSMUSG00000028533	Izumo3	1700011H22Rik	IZUMO family member 3	protein-coding
mm_80485.1	chr9	78257121	78257126	+	1	NA	promoter-TSS (NM_001243092)	promoter-TSS (NM_001243092)	-6	NM_001243092	100042295	Mm.197422	NM_001243092	ENSMUSG00000111709	Gm3776	-	predicted gene 3776	protein-coding
mm_79569.1	chr9	58134265	58134271	+	1	NA	promoter-TSS (NM_001162479)	promoter-TSS (NM_001162479)	193	NM_001162476	20897	Mm.10801	NM_009291	ENSMUSG00000032327	Stra6	AI891933	stimulated by retinoic acid gene 6	protein-coding
mm_107578.1	chr12	44525607	44525622	+	1	NA	intron (NM_001146031, intron 3 of 27)	intron (NM_001146031, intron 3 of 27)	196729	NM_001146031	319504	Mm.208439	NM_176930	ENSMUSG00000020598	Nrcam	Bravo|C030017F07Rik|C130076O07Rik|mKIAA0343	neuronal cell adhesion molecule	protein-coding
mm_170327.1	chr18	42913967	42913980	+	1	NA	intron (NM_028392, intron 1 of 8)	(TTAGGG)n|Simple_repeat|Simple_repeat	-14467	NR_073583	72930	Mm.26134	NM_027531	ENSMUSG00000024500	Ppp2r2b	2900026H06Rik|6330404L05Rik|E130009M08Rik|PP2A-PR55B|PR55-BETA|SCA12	protein phosphatase 2, regulatory subunit B, beta	protein-coding
mm_100112.1	chr11	115814733	115814778	+	1	NA	promoter-TSS (NM_029557)	promoter-TSS (NM_029557)	16	NM_029557	76265	Mm.275438	NM_029557	ENSMUSG00000020781	Tsen54	0610034P02Rik	tRNA splicing endonuclease subunit 54	protein-coding
mm_119958.1	chr14	55222006	55222009	+	1	NA	promoter-TSS (NM_027790)	promoter-TSS (NM_027790)	0	NM_027790	71412	Mm.85484	NM_027790	ENSMUSG00000022209	Dhrs2	5430405K24Rik|Hep27	dehydrogenase/reductase member 2	protein-coding
mm_166994.1	chr7	46715258	46715277	-	1	NA	intron (NM_011315, intron 1 of 3)	intron (NM_011315, intron 1 of 3)	409	NM_011315	20210	Mm.14277	NM_011315	ENSMUSG00000040026	Saa3	AV098916|Saa-3|l7R3	serum amyloid A 3	protein-coding
mm_143189.1	chr17	58991391	58991395	-	1	NA	promoter-TSS (NM_027001)	promoter-TSS (NM_027001)	-18	NM_027001	69239	Mm.246732	NM_027001	ENSMUSG00000024227	Pdzph1	2610034M16Rik|AV114557	PDZ and pleckstrin homology domains 1	protein-coding
mm_81114.1	chr9	106453935	106453945	+	1	NA	5' UTR (NM_021567, exon 1 of 13)	5' UTR (NM_021567, exon 1 of 13)	102	NM_021567	59092	Mm.286394	NM_021567	ENSMUSG00000023495	Pcbp4	1200003L19Rik|AlphaCP-4	poly(rC) binding protein 4	protein-coding
mm_84282.1	chr9	62812806	62812842	-	1	NA	Intergenic	L2|LINE|L2	-1176	NM_010193	14155	Mm.24069	NM_010193	ENSMUSG00000032244	Fem1b	mKIAA0396	feminization 1 homolog b (C. elegans)	protein-coding
mm_41642.1	chr5	98031265	98031289	+	1	NA	promoter-TSS (NM_133738)	promoter-TSS (NM_133738)	-315	NM_133738	71914	Mm.24842	NM_133738	ENSMUSG00000029338	Antxr2	2310046B19Rik|AW561899|CMG-2|CMG2|cI-35	anthrax toxin receptor 2	protein-coding
mm_156076.1	chrX	109161857	109161868	+	1	NA	3' UTR (NM_019989, exon 4 of 4)	3' UTR (NM_019989, exon 4 of 4)	-34894	NM_001037917	622976	Mm.482747	NM_001037917	ENSMUSG00000048621	Gm6377	EG622976	predicted gene 6377	protein-coding
mm_129202.1	chr15	76511998	76512008	-	1	NA	promoter-TSS (NM_010046)	promoter-TSS (NM_010046)	-185	NM_010046	13350	Mm.22633	NM_010046	ENSMUSG00000022555	Dgat1	ARAT|C75990|D15Ertd23e|Dgat	diacylglycerol O-acyltransferase 1	protein-coding
mm_137725.1	chr17	29268892	29268902	+	1	NA	5' UTR (NM_030561, exon 1 of 9)	5' UTR (NM_030561, exon 1 of 9)	109	NM_030561	80748	Mm.290116	NM_030561	ENSMUSG00000052712	BC004004	2400006G15Rik	cDNA sequence BC004004	protein-coding
mm_39526.1	chr5	21266273	21266318	+	1	NA	intron (NM_175437, intron 19 of 30)	intron (NM_175437, intron 19 of 30)	80028	NM_175437	212167	Mm.121705	NM_175437	ENSMUSG00000039934	Gsap	A530088I07Rik|Pion	gamma-secretase activating protein	protein-coding
mm_97152.1	chr11	75463672	75463683	+	1	NA	promoter-TSS (NR_029739)	promoter-TSS (NR_029739)	-39	NR_029739	387141		NR_029739	ENSMUSG00000065529	Mir22	Mirn22|mmu-mir-22	microRNA 22	ncRNA
mm_132355.1	chr16	34649921	34649944	+	1	NA	Intergenic	Intergenic	-1279	NM_030744	76378	Mm.23515	NM_030744	ENSMUSG00000022832	Ropn1	1700008N21Rik|ODF6|RHPNAP1|Rppn|ropporin	ropporin, rhophilin associated protein 1	protein-coding
mm_63118.1	chr7	122671469	122671482	+	1	NA	promoter-TSS (NM_019430)	promoter-TSS (NM_019430)	-269	NM_019430	54376	Mm.444212	NM_019430	ENSMUSG00000066189	Cacng3	-	calcium channel, voltage-dependent, gamma subunit 3	protein-coding
mm_124127.1	chr14	79704029	79704073	-	1	NA	intron (NR_045060, intron 1 of 3)	intron (NR_045060, intron 1 of 3)	1131	NR_045060	73989	Mm.107775	NR_045060		4930452G13Rik	-	RIKEN cDNA 4930452G13 gene	ncRNA
mm_137158.1	chr17	23749320	23749353	+	1	NA	promoter-TSS (NR_015472)	promoter-TSS (NR_015472)	100	NR_015472	638247	Mm.382600	NR_015472	ENSMUSG00000097006	9530082P21Rik	E030034P13Rik	RIKEN cDNA 9530082P21 gene	ncRNA
mm_130961.1	chr15	103314958	103314983	-	1	NA	3' UTR (NM_013866, exon 8 of 8)	3' UTR (NM_013866, exon 8 of 8)	-4532	NM_030720	80910	Mm.160369	NM_030720	ENSMUSG00000063234	Gpr84	EX33	G protein-coupled receptor 84	protein-coding
mm_46503.1	chr5	105134693	105134706	-	1	NA	intron (NM_008620, intron 3 of 10)	intron (NM_008620, intron 3 of 10)	4853	NM_008620	17472	Mm.440525	NM_008620	ENSMUSG00000079363	Gbp4	AW228052|Mag-2|Mpa-2|Mpa2	guanylate binding protein 4	protein-coding
mm_148537.1	chr19	4603091	4603102	+	1	NA	exon (NM_001162946, exon 8 of 21)	exon (NM_001162946, exon 8 of 21)	8777	NM_008797	18563	Mm.1845	NM_008797	ENSMUSG00000024892	Pcx	Pc|Pcb	pyruvate carboxylase	protein-coding
mm_106076.1	chr11	116174425	116174445	-	1	NA	exon (NM_015729, exon 13 of 14)	exon (NM_015729, exon 13 of 14)	-6257	NM_172571	217335	Mm.35241	NM_172571	ENSMUSG00000020776	Fbf1	1110033G01Rik|5930413D20|mKIAA1863	Fas (TNFRSF6) binding factor 1	protein-coding
mm_6357.1	chr1	71896446	71896452	-	1	NA	Intergenic	Intergenic	8337	NR_027659	667931	Mm.214128	NR_027658	ENSMUSG00000099707	Gm8883	EG667931|Gm554	predicted gene 8883	ncRNA
mm_133568.1	chr16	91406146	91406159	+	1	NA	promoter-TSS (NM_008349)	promoter-TSS (NM_008349)	-83	NM_008349	16155	Mm.4154	NM_008349	ENSMUSG00000022969	Il10rb	6620401D04Rik|AI528744|CRF2-4|Crfb4|D16H21S58|D21S58h|IL-10R2|Il10r2	interleukin 10 receptor, beta	protein-coding
mm_115065.1	chr13	101397667	101397673	+	1	NA	promoter-TSS (NR_046187)	promoter-TSS (NR_046187)	-90	NR_046187	78136	Mm.399065	NR_046187		4922502H24Rik	-	RIKEN cDNA 4922502H24 gene	ncRNA
mm_110659.1	chr12	59070237	59070264	-	1	NA	exon (NM_008891, exon 7 of 9)	exon (NM_008891, exon 7 of 9)	3331	NM_008891	18949	Mm.22347	NM_008891	ENSMUSG00000020994	Pnn	AU045199|D12Ertd512e	pinin	protein-coding
mm_152447.1	chr19	10829581	10829591	-	1	NA	intron (NM_001037801, intron 1 of 11)	intron (NM_001037801, intron 1 of 11)	472	NM_001037801	12511	Mm.290897	NM_009852	ENSMUSG00000024670	Cd6	-	CD6 antigen	protein-coding
mm_4087.1	chr1	167001433	167001448	+	1	NA	promoter-TSS (NM_175461)	promoter-TSS (NM_175461)	23	NM_001160261	226610	Mm.389217	NM_175461	ENSMUSG00000060568	Fam78b	C030014K22Rik|C030020L09Rik	family with sequence similarity 78, member B	protein-coding
mm_9177.1	chr1	171058039	171058060	-	1	NA	intron (NM_010188, intron 2 of 4)	intron (NM_010188, intron 2 of 4)	1354	NM_010188	14131	Mm.22119	NM_010188	ENSMUSG00000059498	Fcgr3	CD16	Fc receptor, IgG, low affinity III	protein-coding
mm_44414.1	chr5	17888742	17888837	-	1	NA	5' UTR (NM_001159558, exon 1 of 16)	5' UTR (NM_001159558, exon 1 of 16)	170	NM_001159558	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_97910.1	chr11	83473141	83473157	+	1	NA	promoter-TSS (NM_027427)	promoter-TSS (NM_027427)	41	NM_027427	70439	Mm.181050	NM_027427	ENSMUSG00000020680	Taf15	2610111C21Rik|68kDa|TAFII68|Taf2n	TATA-box binding protein associated factor 15	protein-coding
mm_97766.1	chr11	82036189	82036190	+	1	NA	intron (NM_011333, intron 1 of 2)	intron (NM_011333, intron 1 of 2)	612	NM_011333	20296	Mm.290320	NM_011333	ENSMUSG00000035385	Ccl2	AI323594|HC11|JE|MCAF|MCP-1|MCP1|SMC-CF|Scya2|Sigje	chemokine (C-C motif) ligand 2	protein-coding
mm_157844.1	chrX	74392776	74392806	-	1	NA	promoter-TSS (NM_001161424)	promoter-TSS (NM_001161424)	483	NM_025473	66294	Mm.166485	NM_025473	ENSMUSG00000031399	Fam3a	1810037C20Rik	family with sequence similarity 3, member A	protein-coding
mm_57063.1	chr6	122545345	122545386	-	1	NA	Intergenic	Intergenic	-8444	NM_009645	11628	Mm.391503	NM_009645	ENSMUSG00000040627	Aicda	Aid|Arp2	activation-induced cytidine deaminase	protein-coding
mm_25202.1	chr3	103791155	103791165	+	1	NA	5' UTR (NM_010432, exon 1 of 16)	5' UTR (NM_010432, exon 1 of 16)	115	NM_001301306	15257	Mm.20827	NM_010432	ENSMUSG00000008730	Hipk1	1110062K04Rik|Myak	homeodomain interacting protein kinase 1	protein-coding
mm_88453.1	chr10	77555379	77555414	+	1	NA	intron (NM_008404, intron 8 of 15)	B1_Mur4|SINE|Alu	25048	NM_008404	16414	Mm.1137	NM_008404	ENSMUSG00000000290	Itgb2	2E6|AI528527|Cd18|LAD|LCAMB|Lfa1|MF17	integrin beta 2	protein-coding
mm_35060.1	chr4	6453618	6453661	-	1	NA	intron (NM_010945, intron 1 of 30)	CpG	632	NM_010945	18201	Mm.3059	NM_010945	ENSMUSG00000028245	Nsmaf	AA959567|C630007J05|Fan	neutral sphingomyelinase (N-SMase) activation associated factor	protein-coding
mm_53065.1	chr6	124914147	124914163	+	1	NA	3' UTR (NM_026988, exon 5 of 5)	3' UTR (NM_026988, exon 5 of 5)	-2450	NM_008479	16768	Mm.4528	NM_008479	ENSMUSG00000030124	Lag3	CD223|LAG-3|Ly66	lymphocyte-activation gene 3	protein-coding
mm_90422.1	chr10	127481691	127481699	+	1	NA	exon (NM_001168293, exon 14 of 24)	exon (NM_001168293, exon 14 of 24)	-20022	NM_177707	237611	Mm.32087	NM_177707	ENSMUSG00000040287	Stac3	9830125E18	SH3 and cysteine rich domain 3	protein-coding
mm_150363.1	chr19	34649287	34649328	+	1	NA	3' UTR (NM_008331, exon 2 of 2)	3' UTR (NM_008331, exon 2 of 2)	8418	NM_008331	15957	Mm.439751	NM_008331	ENSMUSG00000034459	Ifit1	ISG56|Ifi56|P56	interferon-induced protein with tetratricopeptide repeats 1	protein-coding
mm_48439.1	chr5	140627265	140627280	-	1	NA	exon (NM_175274, exon 12 of 14)	exon (NM_175274, exon 12 of 14)	19931	NM_008494	16848	Mm.12834	NM_008494	ENSMUSG00000029570	Lfng	AW061165	LFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	protein-coding
mm_126329.1	chr15	79892380	79892390	+	1	NA	promoter-TSS (NM_001160415)	promoter-TSS (NM_001160415)	-23	NM_001160415	80287	Mm.284059	NM_030255	ENSMUSG00000009585	Apobec3	Apobec|Arp3|BC003314|Cem15|Rfv3	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 3	protein-coding
mm_124452.1	chr14	118925463	118925479	-	1	NA	promoter-TSS (NM_025943)	promoter-TSS (NM_025943)	-1	NM_025943	66573	Mm.87456	NM_025943	ENSMUSG00000042156	Dzip1	2510025K24Rik|2810422M04Rik	DAZ interacting protein 1	protein-coding
mm_37370.1	chr4	120924951	120925032	-	1	NA	promoter-TSS (NM_001160043)	promoter-TSS (NM_001160043)	14	NM_028457	73172	Mm.151436	NM_028457	ENSMUSG00000028629	Exo5	3110037I16Rik|AV297100|Dem1|Exo V|mExo5	exonuclease 5	protein-coding
mm_52842.1	chr6	121838451	121838470	+	1	NA	promoter-TSS (NM_008645)	promoter-TSS (NM_008645)	-81	NM_008645	17836	Mm.1311	NM_008645	ENSMUSG00000059908	Mug1	-	murinoglobulin 1	protein-coding
mm_53639.1	chr6	140622608	140622627	+	1	NA	promoter-TSS (NM_178803)	promoter-TSS (NM_178803)	-46	NM_178803	11569	Mm.86453	NM_009637	ENSMUSG00000030232	Aebp2	AU023766|B230313N05Rik	AE binding protein 2	protein-coding
mm_44214.1	chr5	4757798	4757806	-	1	NA	5' UTR (NM_021457, exon 1 of 1)	5' UTR (NM_021457, exon 1 of 1)	414	NM_021457	14362	Mm.246003	NM_021457	ENSMUSG00000044674	Fzd1	AW227548|FZ-1|Fz1	frizzled class receptor 1	protein-coding
mm_93122.1	chr10	91171513	91171523	-	1	NA	promoter-TSS (NM_001283048)	promoter-TSS (NM_001283048)	101	NM_001080132	21917	Mm.159684	NM_011605	ENSMUSG00000019961	Tmpo	5630400D24Rik|AI195756|AI606875|AW214352|AW547477|LAP2|TP	thymopoietin	protein-coding
mm_109110.1	chr12	105453832	105453919	+	1	NA	promoter-TSS (NM_001252508)	promoter-TSS (NM_001252508)	19	NM_001252508	268595	Mm.2388	NM_001252508	ENSMUSG00000094910	D430019H16Rik	AI852661	RIKEN cDNA D430019H16 gene	protein-coding
mm_24429.1	chr3	90539676	90539691	+	1	NA	Intergenic	Intergenic	-1540	NM_026416	67860	Mm.331185	NM_026416	ENSMUSG00000074457	S100a16	2300002L21Rik|AI325039|AI663996|DT1P1A7|S100F	S100 calcium binding protein A16	protein-coding
mm_110054.1	chr12	20815752	20815775	-	1	NA	promoter-TSS (NR_015521)	promoter-TSS (NR_015521)	16	NR_015521	69513	Mm.273972	NR_015521	ENSMUSG00000099759	1700030C10Rik	-	RIKEN cDNA 1700030C10 gene	ncRNA
mm_148685.1	chr19	5700771	5700795	+	1	NA	exon (NM_022012, exon 11 of 12)	exon (NM_022012, exon 11 of 12)	-3688	NM_010609	16530	Mm.440033	NM_010609	ENSMUSG00000024936	Kcnk7	2310014G03Rik|Kcnk6|Kcnk8|Knot|Mlk3	potassium channel, subfamily K, member 7	protein-coding
mm_14358.1	chr2	129615694	129615700	+	1	NA	exon (NM_007547, exon 3 of 8)	exon (NM_007547, exon 3 of 8)	22528	NM_001291022	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_110203.1	chr12	27341147	27341161	-	1	NA	3' UTR (NM_009234, exon 1 of 1)	3' UTR (NM_009234, exon 1 of 1)	1564	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding
mm_138358.1	chr17	34982023	34982034	+	1	NA	promoter-TSS (NM_030597)	promoter-TSS (NM_030597)	-102	NM_001204273	27756	Mm.165735	NM_030597	ENSMUSG00000007050	Lsm2	D17H6S56E-2|D17H6S56E2|Dmapl|Dmpkap|G7b|Sm-X5|SmX5|snRNP	LSM2 homolog, U6 small nuclear RNA and mRNA degradation associated	protein-coding
mm_29654.1	chr3	122391994	122391998	-	1	NA	Intergenic	Intergenic	-27784	NM_013867	29815	Mm.45815	NM_013867	ENSMUSG00000028121	Bcar3	AI131758|AND-34	breast cancer anti-estrogen resistance 3	protein-coding
mm_157845.1	chrX	74393017	74393072	-	1	NA	promoter-TSS (NM_001161424)	promoter-TSS (NM_001161424)	230	NM_025473	66294	Mm.166485	NM_025473	ENSMUSG00000031399	Fam3a	1810037C20Rik	family with sequence similarity 3, member A	protein-coding
mm_112646.1	chr13	16017284	16017298	+	1	NA	5' UTR (NM_008380, exon 4 of 5)	5' UTR (NM_008380, exon 4 of 5)	5440	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_127267.1	chr15	99719124	99719138	+	1	NA	intron (NM_010271, intron 2 of 7)	intron (NM_010271, intron 2 of 7)	1538	NM_010271	14555	Mm.252391	NM_010271	ENSMUSG00000023019	Gpd1	AI747587|Gdc-1|Gdc1|mKIAA4010	glycerol-3-phosphate dehydrogenase 1 (soluble)	protein-coding
mm_102648.1	chr11	62951096	62951110	-	1	NA	promoter-TSS (NM_025496)	promoter-TSS (NM_025496)	-90	NM_025496	66338	Mm.46166	NM_025496	ENSMUSG00000042200	Cdrt4	1700019I23Rik	CMT1A duplicated region transcript 4	protein-coding
mm_129300.1	chr15	77307006	77307032	-	1	NA	promoter-TSS (NM_175387)	promoter-TSS (NM_175387)	34	NM_001110827	93686	Mm.202774	NM_053104	ENSMUSG00000033565	Rbfox2	Fbm2|Fxh|Hrnbp2|Rbm9	RNA binding protein, fox-1 homolog (C. elegans) 2	protein-coding
mm_99342.1	chr11	101552136	101552184	+	1	NA	promoter-TSS (NM_001252222)	promoter-TSS (NM_001252222)	53	NM_001252220	17966	Mm.784	NM_008676	ENSMUSG00000017119	Nbr1	mKIAA0049	neighbor of Brca1 gene 1	protein-coding
mm_119808.1	chr14	54222365	54222374	+	1	NA	Intergenic	Intergenic	31560	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_105365.1	chr11	103199442	103199465	-	1	NA	TTS (NM_001077698)	TTS (NM_001077698)	9095	NM_001254724	69441	Mm.380648	NM_027082	ENSMUSG00000020940	1700023F06Rik	-	RIKEN cDNA 1700023F06 gene	protein-coding
mm_50436.1	chr6	48846105	48846115	+	1	NA	TTS (NM_025326)	TTS (NM_025326)	4454	NM_001098271	66058	Mm.27061	NM_025326	ENSMUSG00000023367	Tmem176a	0610011I04Rik|AU040201|AU041743|Keg2	transmembrane protein 176A	protein-coding
mm_102216.1	chr11	54909062	54909071	-	1	NA	exon (NM_008161, exon 4 of 5)	exon (NM_008161, exon 4 of 5)	6212	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_36715.1	chr4	98383233	98383280	-	1	NA	promoter-TSS (NM_053157)	promoter-TSS (NM_053157)	9	NM_053157	94043	Mm.331719	NM_053157	ENSMUSG00000028563	Tm2d1	2310026L18Rik|AA990549|Bbp	TM2 domain containing 1	protein-coding
mm_52419.1	chr6	113442629	113442635	+	1	NA	promoter-TSS (NM_001243739)	promoter-TSS (NM_001243739)	63	NM_001243739	67767	Mm.2053	NM_026365	ENSMUSG00000051256	Jagn1	5830427H10Rik	jagunal homolog 1	protein-coding
mm_63065.1	chr7	122131054	122131065	+	1	NA	intron (NM_001289843, intron 1 of 10)	intron (NM_001289843, intron 1 of 10)	1887	NM_001289844	233826	Mm.38348	NM_172744	ENSMUSG00000044702	Palb2	BC066140	partner and localizer of BRCA2	protein-coding
mm_119210.1	chr14	32991393	32991403	+	1	NA	promoter-TSS (NM_001146021)	promoter-TSS (NM_001146021)	16	NM_026253	67580	Mm.46115	NM_026253	ENSMUSG00000041673	Lrrc18	4930442L21Rik|MTLR1	leucine rich repeat containing 18	protein-coding
mm_107707.1	chr12	55507835	55507860	+	1	NA	Intergenic	Intergenic	-15200	NM_010907	18035	Mm.170515	NM_010907	ENSMUSG00000021025	Nfkbia	AI462015|Nfkbi	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, alpha	protein-coding
mm_147282.1	chr18	39487097	39487119	-	1	NA	exon (NM_008173, exon 1 of 8)	exon (NM_008173, exon 1 of 8)	137	NM_008173	14815	Mm.129481	NM_008173	ENSMUSG00000024431	Nr3c1	GR|Grl-1|Grl1	nuclear receptor subfamily 3, group C, member 1	protein-coding
mm_156843.1	chrX	164385686	164385690	+	1	NA	intron (NM_001308489, intron 1 of 5)	intron (NM_001308489, intron 1 of 5)	12166	NM_010216	14205	Mm.297978	NM_010216	ENSMUSG00000031380	Vegfd	AI325264|Figf|VEGF-D	vascular endothelial growth factor D	protein-coding
mm_114397.1	chr13	63279112	63279137	+	1	NA	intron (NR_110520, intron 2 of 5)	intron (NR_110520, intron 2 of 5)	18023	NR_045794	100504114	Mm.437070	NR_045794	ENSMUSG00000097242	Gm16907	-	predicted gene, 16907	ncRNA
mm_70277.1	chr8	3598643	3598671	+	1	NA	intron (NM_001347112, intron 2 of 17)	intron (NM_001347112, intron 2 of 17)	11207	NM_001347111	69697	Mm.390010	NM_027171	ENSMUSG00000044433	Camsap3	2310057J16Rik|Kiaa1543|Nezha	calmodulin regulated spectrin-associated protein family, member 3	protein-coding
mm_33911.1	chr4	136347310	136347312	+	1	NA	Intergenic	B1F2|SINE|Alu	36369	NM_001277123	74326	Mm.31051	NM_028871	ENSMUSG00000066037	Hnrnpr	2610003J05Rik|2610528B01Rik|Hnrpr	heterogeneous nuclear ribonucleoprotein R	protein-coding
mm_48891.1	chr5	151368494	151368505	-	1	NA	promoter-TSS (NR_045700)	promoter-TSS (NR_045700)	-176	NR_045700	625175	Mm.443286	NR_045699	ENSMUSG00000097321	1700028E10Rik	A630054D14|Gm6561	RIKEN cDNA 1700028E10 gene	ncRNA
mm_84496.1	chr9	66882457	66882466	-	1	NA	intron (NM_173413, intron 1 of 7)	intron (NM_173413, intron 1 of 7)	37244	NM_173413	235442	Mm.260376	NM_173413	ENSMUSG00000036943	Rab8b	5930437D16|D330025I23Rik	RAB8B, member RAS oncogene family	protein-coding
mm_41856.1	chr5	104440336	104440387	+	1	NA	exon (NM_001204203, exon 7 of 7)	exon (NM_001204203, exon 7 of 7)	4169	NM_001204233	20750	Mm.288474	NM_009263	ENSMUSG00000029304	Spp1	2AR|Apl-1|BNSP|BSPI|Bsp|ETA-1|Eta|OP|Opn|Opnl|Ric|Spp-1	secreted phosphoprotein 1	protein-coding
mm_135964.1	chr16	74826735	74826750	-	1	NA	Intergenic	B4|SINE|B4	-415830	NM_175549	268902	Mm.171736	NM_175549	ENSMUSG00000052516	Robo2	2600013A04Rik|9430089E08Rik|BB097918|D230004I22Rik|mKIAA1568	roundabout guidance receptor 2	protein-coding
mm_101608.1	chr11	34871543	34871545	-	1	NA	Intergenic	RMER19B|LTR|ERVK	-37903	NM_027411	70385	Mm.194368	NM_027411	ENSMUSG00000069910	Spdl1	1700018I02Rik|2600001J17Rik|2810049B11Rik|AA409762|Ccdc99	spindle apparatus coiled-coil protein 1	protein-coding
mm_130881.1	chr15	102248038	102248061	-	1	NA	intron (NM_011244, intron 3 of 9)	intron (NM_011244, intron 3 of 9)	-1549	NM_001042727	19411	Mm.1273	NM_011244	ENSMUSG00000001288	Rarg	Nr1b3|RAR-gamma|RARD|RARgamma2	retinoic acid receptor, gamma	protein-coding
mm_127638.1	chr15	102473497	102473501	+	1	NA	intron (NM_001103165, intron 2 of 14)	intron (NM_001103165, intron 2 of 14)	2867	NM_001174073	18521	Mm.236513	NM_011042	ENSMUSG00000056851	Pcbp2	AW412548|Hnrpx|alphaCP-2	poly(rC) binding protein 2	protein-coding
mm_93953.1	chr10	127263103	127263133	-	1	NA	5' UTR (NM_001039000, exon 1 of 29)	5' UTR (NM_001039000, exon 1 of 29)	245	NM_008447	16572	Mm.30355	NM_008447	ENSMUSG00000074657	Kif5a	D10Bwg0738e|Khc|Kif5|Kns|mKIAA4086	kinesin family member 5A	protein-coding
mm_53056.1	chr6	124829495	124829513	+	1	NA	promoter-TSS (NM_013538)	promoter-TSS (NM_013538)	-20	NM_013700	22225	Mm.3571	NM_013700	ENSMUSG00000038429	Usp5	AA407472|ISOT|ISOT-1|Ucht	ubiquitin specific peptidase 5 (isopeptidase T)	protein-coding
mm_111419.1	chr12	91588349	91588374	-	1	NA	intron (NM_175335, intron 1 of 8)	CpG	1288	NM_031391	83602	Mm.275728	NM_031391	ENSMUSG00000020962	Gtf2a1	6330549H03Rik|AA536742|AA959775|AW060250|TfIIAa/b|Tfiia1	general transcription factor II A, 1	protein-coding
mm_93075.1	chr10	89434649	89434659	-	1	NA	intron (NM_001079876, intron 2 of 10)	intron (NM_001079876, intron 2 of 10)	9313	NM_001284344	237436	Mm.11982	NM_001033331	ENSMUSG00000074802	Gas2l3	8430435B07Rik|Gm240	growth arrest-specific 2 like 3	protein-coding
mm_119705.1	chr14	53800798	53800813	+	1	NA	Intergenic	Intergenic	453124	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_33164.1	chr4	126023421	126023431	+	1	NA	Intergenic	MT2A|LTR|ERVL	-1233	NR_045561	12986	Mm.271701	NM_007782	ENSMUSG00000028859	Csf3r	Cd114|Csfgr|G-CSF-R|G-CSFR	colony stimulating factor 3 receptor (granulocyte)	protein-coding
mm_19711.1	chr2	103819666	103819670	-	1	NA	Intergenic	Intergenic	-9046	NR_040514	78031	Mm.243867	NR_040514	ENSMUSG00000086687	4930547E08Rik	-	RIKEN cDNA 4930547E08 gene	ncRNA
mm_127954.1	chr15	11399581	11399593	-	1	NA	promoter-TSS (NM_033074)	promoter-TSS (NM_033074)	71	NM_033074	110960	Mm.286061	NM_033074	ENSMUSG00000022241	Tars	D15Wsu59e|ThrRS	threonyl-tRNA synthetase	protein-coding
mm_147630.1	chr18	58210440	58210457	-	1	NA	promoter-TSS (NM_010181)	promoter-TSS (NM_010181)	-522	NM_010181	14119	Mm.20271	NM_010181	ENSMUSG00000024598	Fbn2	BC063774|Fib-2|mKIAA4226|sne|sy	fibrillin 2	protein-coding
mm_171808.1	chr5	129887335	129887337	-	1	NA	5' UTR (NM_024166, exon 1 of 4)	5' UTR (NM_024166, exon 1 of 4)	134	NM_024166	14004	Mm.30133	NM_024166	ENSMUSG00000070493	Chchd2	AL033347|Etohi6	coiled-coil-helix-coiled-coil-helix domain containing 2	protein-coding
mm_12588.1	chr2	73561069	73561090	+	1	NA	Intergenic	Intergenic	19259	NM_007389	11435	Mm.4583	NM_007389	ENSMUSG00000027107	Chrna1	AI385656|AI608266|Achr-1|Acra	cholinergic receptor, nicotinic, alpha polypeptide 1 (muscle)	protein-coding
mm_103582.1	chr11	78176965	78176978	-	1	NA	promoter-TSS (NM_080849)	promoter-TSS (NM_080849)	-305	NM_080849	140859	Mm.23788	NM_080849	ENSMUSG00000017405	Nek8	4632401F23Rik|b2b1449Clo|jck	NIMA (never in mitosis gene a)-related expressed kinase 8	protein-coding
mm_100177.1	chr11	116534038	116534054	+	1	NA	promoter-TSS (NM_011451)	promoter-TSS (NM_011451)	-694	NM_011451	20698	Mm.20944	NM_011451	ENSMUSG00000061878	Sphk1	1110006G24Rik|Sk1|Spk1	sphingosine kinase 1	protein-coding
mm_41102.1	chr5	87694962	87694964	+	1	NA	exon (NM_001286023, exon 5 of 7)	exon (NM_001286023, exon 5 of 7)	4462	NM_001286020	12991	Mm.268737	NM_009972	ENSMUSG00000063157	Csn2	Csnb	casein beta	protein-coding
mm_127262.1	chr15	99710754	99710775	+	1	NA	intron (NM_031842, intron 10 of 12)	intron (NM_031842, intron 10 of 12)	-6829	NM_010271	14555	Mm.252391	NM_010271	ENSMUSG00000023019	Gpd1	AI747587|Gdc-1|Gdc1|mKIAA4010	glycerol-3-phosphate dehydrogenase 1 (soluble)	protein-coding
mm_73832.1	chr8	117460600	117460647	+	1	NA	3' UTR (NM_001163262, exon 21 of 21)	3' UTR (NM_001163262, exon 21 of 21)	1358	NR_106046	102465653		NR_106046	ENSMUSG00000098483	Mir7078	Gm27386|mmu-mir-7078	microRNA 7078	ncRNA
mm_162428.1	chr1	93445804	93445808	+	1	NA	promoter-TSS (NM_001301364)	promoter-TSS (NM_001301364)	-105	NM_001301364	110611	Mm.30012	NM_133808	ENSMUSG00000034088	Hdlbp	1110005P14Rik|AA960365|AI118566|D1Ertd101e	high density lipoprotein (HDL) binding protein	protein-coding
mm_22376.1	chr2	181156238	181156251	-	1	NA	intron (NM_007906, intron 1 of 7)	intron (NM_007906, intron 1 of 7)	771	NM_007906	13628	Mm.2645	NM_007906	ENSMUSG00000016349	Eef1a2	Eef1a|S1|wasted|wst	eukaryotic translation elongation factor 1 alpha 2	protein-coding
mm_19008.1	chr2	76891471	76891478	-	1	NA	exon (NM_011652, exon 69 of 313)	exon (NM_011652, exon 69 of 313)	91073	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_110160.1	chr12	26474079	26474096	-	1	NA	exon (NM_020557, exon 3 of 5)	exon (NM_020557, exon 3 of 5)	4872	NM_020557	22169	Mm.271839	NM_020557	ENSMUSG00000020638	Cmpk2	1200004E04Rik|TDKI|Tyki	cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial	protein-coding
mm_63008.1	chr7	120917770	120917815	+	1	NA	promoter-TSS (NM_001164096)	promoter-TSS (NM_001164096)	48	NM_001164096	26939	Mm.193632	NM_025298	ENSMUSG00000030880	Polr3e	RPC5|Sin	polymerase (RNA) III (DNA directed) polypeptide E	protein-coding
mm_137889.1	chr17	31679640	31679655	+	1	NA	exon (NM_001278570, exon 2 of 3)	exon (NM_001278570, exon 2 of 3)	1716	NM_001278570	12954	Mm.1228	NM_013501	ENSMUSG00000024041	Cryaa	Acry-1|Crya-1|Crya1|DAcry-1|lop18	crystallin, alpha A	protein-coding
mm_66307.1	chr7	39264465	39264474	-	1	NA	Intergenic	Intergenic	148691	NM_177890	330513	Mm.67238	NM_177890	ENSMUSG00000053742	Gm5114	4921507A12|EG330513	predicted gene 5114	protein-coding
mm_82099.1	chr9	123061641	123061641	+	1	NA	exon (NM_177911, exon 11 of 14)	exon (NM_177911, exon 11 of 14)	26900	NM_177911	331046	Mm.195309	NM_177911	ENSMUSG00000025787	Tgm4	9530008N10Rik|Eapa1|TGP	transglutaminase 4 (prostate)	protein-coding
mm_62097.1	chr7	96210185	96210200	+	1	NA	promoter-TSS (NM_011858)	promoter-TSS (NM_011858)	-445	NM_011858	23966	Mm.254610	NM_011858	ENSMUSG00000048078	Tenm4	Doc4|ELM2|Odz4|R75022|Ten-m4|l(7)-3Rn|l7Rn3|mKIAA1302	teneurin transmembrane protein 4	protein-coding
mm_172453.1	chr7	3483722	3483732	+	1	NA	Intergenic	RLTR9D|LTR|ERVK	18825	NM_177363	245126	Mm.245747	NM_177363	ENSMUSG00000053338	Tarm1	9930022N03Rik|ENSMUSG00000053338|Gm9904|OLT-2	T cell-interacting, activating receptor on myeloid cells 1	protein-coding
mm_132548.1	chr16	37883379	37883392	+	1	NA	3' UTR (NM_177093, exon 4 of 4)	3' UTR (NM_177093, exon 4 of 4)	14985	NM_177093	320184	Mm.390882	NM_177093	ENSMUSG00000034158	Lrrc58	1810012N18Rik|C330018J07Rik	leucine rich repeat containing 58	protein-coding
mm_153746.1	chr19	44750802	44750809	-	1	NA	Intergenic	Intergenic	-6589	NM_011037	18504	Mm.192158	NM_011037	ENSMUSG00000004231	Pax2	Opdc|Pax-2	paired box 2	protein-coding
mm_165748.1	chr3	107852841	107852848	-	1	NA	Intergenic	Intergenic	-24386	NM_133867	99662	Mm.108491	NM_133867	ENSMUSG00000040600	Eps8l3	AI504489|Eps8r3	EPS8-like 3	protein-coding
mm_42097.1	chr5	110344700	110344710	+	1	NA	promoter-TSS (NM_001310709)	promoter-TSS (NM_001310709)	-25	NR_132326	381667	Mm.332572	NM_001033459	ENSMUSG00000072754	Lrcol1	Clpsl3|Gm1679	leucine rich colipase-like 1	protein-coding
mm_5325.1	chr1	23102244	23102266	-	1	NA	promoter-TSS (NM_025746)	promoter-TSS (NM_025746)	-2	NM_025746	66755	Mm.431297	NM_025746	ENSMUSG00000073730	4933415F23Rik	-	RIKEN cDNA 4933415F23 gene	protein-coding
mm_111477.1	chr12	98683727	98683746	-	1	NA	intron (NM_011877, intron 13 of 18)	intron (NM_011877, intron 13 of 18)	50909	NM_011877	24000	Mm.4420	NM_011877	ENSMUSG00000021009	Ptpn21	PTPD1|PTPRL10	protein tyrosine phosphatase, non-receptor type 21	protein-coding
mm_109167.1	chr12	108306381	108306402	+	1	NA	5' UTR (NM_001044380, exon 1 of 9)	5' UTR (NM_001044380, exon 1 of 9)	121	NM_001044380	214305	Mm.36423	NM_001044380	ENSMUSG00000021260	Hhipl1	1600002O04Rik|AK129450|mKIAA1822	hedgehog interacting protein-like 1	protein-coding
mm_150120.1	chr19	29951766	29951779	+	1	NA	intron (NM_133775, intron 2 of 7)	MTEa|LTR|ERVL-MaLR	5982	NM_001164724	77125	Mm.182359	NM_133775	ENSMUSG00000024810	Il33	9230117N10Rik|Il-33|Il1f11|NF-HEV	interleukin 33	protein-coding
mm_9101.1	chr1	169974990	169975003	-	1	NA	3' UTR (NM_022563, exon 17 of 17)	3' UTR (NM_022563, exon 17 of 17)	5587	NR_040438	67303	Mm.396611	NR_040438	ENSMUSG00000097503	3110045C21Rik	AI838577	RIKEN cDNA 3110045C21 gene	ncRNA
mm_73762.1	chr8	115251475	115251477	+	1	NA	intron (NM_019573, intron 8 of 8)	intron (NM_019573, intron 8 of 8)	455418	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_146559.1	chr18	6241165	6241214	-	1	NA	5' UTR (NM_008448, exon 1 of 26)	5' UTR (NM_008448, exon 1 of 26)	335	NM_008448	16573	Mm.223744	NM_008448	ENSMUSG00000006740	Kif5b	AL022807|Khc|Khcs|Kns1|Ukhc	kinesin family member 5B	protein-coding
mm_78079.1	chr9	15729352	15729360	+	1	NA	intron (NM_172289, intron 8 of 10)	intron (NM_172289, intron 8 of 10)	19587	NM_172289	234967	Mm.138815	NM_172289	ENSMUSG00000043885	Slc36a4	6330573I15Rik|PAT4	solute carrier family 36 (proton/amino acid symporter), member 4	protein-coding
mm_41183.1	chr5	88318567	88318571	+	1	NA	exon (NM_008644, exon 2 of 3)	exon (NM_008644, exon 2 of 3)	1257	NM_008644	17830	Mm.200411	NM_008644	ENSMUSG00000064156	Prol1	Muc10	proline rich, lacrimal 1	protein-coding
mm_53076.1	chr6	124935371	124935394	+	1	NA	exon (NM_001170341, exon 8 of 9)	exon (NM_001170341, exon 8 of 9)	3994	NM_001170341	30853	Mm.29737	NM_145385	ENSMUSG00000030120	Mlf2	AI256856|AU018944|C77284	myeloid leukemia factor 2	protein-coding
mm_138602.1	chr17	35556321	35556355	+	1	NA	3' UTR (NM_001008424, exon 2 of 2)	3' UTR (NM_001008424, exon 2 of 2)	4210	NM_001008424	386463	Mm.426664	NM_001008424	ENSMUSG00000039518	Cdsn	AI747712	corneodesmosin	protein-coding
mm_10575.1	chr2	18064793	18064816	+	1	NA	non-coding (NR_045538, exon 1 of 23)	non-coding (NR_045538, exon 1 of 23)	219	NM_001252561	17354	Mm.209175	NM_010804	ENSMUSG00000026743	Mllt10	Af10|B130021D15Rik|D630001B22Rik|mKIAA4140	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 10	protein-coding
mm_131052.1	chr16	4037137	4037152	+	1	NA	promoter-TSS (NM_010061)	promoter-TSS (NM_010061)	-1	NM_010061	13419	Mm.291048	NM_010061	ENSMUSG00000005980	Dnase1	AI788650|DNaseI|Dnl1	deoxyribonuclease I	protein-coding
mm_172400.1	chr7	142306308	142306329	-	1	NA	Intergenic	Intergenic	2816	NM_015809	50775	Mm.389990	NM_015809	ENSMUSG00000045236	Krtap5-4	-	keratin associated protein 5-4	protein-coding
mm_66068.1	chr7	30823822	30823834	-	1	NA	promoter-TSS (NM_146187)	promoter-TSS (NM_146187)	-53	NM_146187	233079	Mm.97338	NM_146187	ENSMUSG00000051314	Ffar2	GPCR43|Gpr43	free fatty acid receptor 2	protein-coding
mm_76644.1	chr8	93079966	93079974	-	1	NA	promoter-TSS (NM_001081372)	promoter-TSS (NM_001081372)	47	NM_001081372	382044	Mm.482549	NM_001081372	ENSMUSG00000078964	Ces1b	Gm5158	carboxylesterase 1B	protein-coding
mm_72607.1	chr8	84533411	84533442	+	1	NA	exon (NM_001252060, exon 7 of 48)	exon (NM_001252060, exon 7 of 48)	118062	NM_001252061	12286	Mm.334658	NM_007578	ENSMUSG00000034656	Cacna1a	APCA|BI|Caca1a|Cacnl1a4|Cav2.1|Ccha1a|EA2|FHM|HPCA|MHP|MHP1|SCA6|alpha1A|la|nmf352|rkr|smrl|tg	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	protein-coding
mm_149146.1	chr19	9005903	9005935	+	1	NA	exon (NM_009643, exon 5 of 5)	exon (NM_009643, exon 5 of 5)	-11985	NR_105786	102465190		NR_105786	ENSMUSG00000099308	Mir6367	Gm27467|mmu-mir-6367	microRNA 6367	ncRNA
mm_30904.1	chr4	32363945	32363954	+	1	NA	Intergenic	Intergenic	-53486	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_87666.1	chr10	58609107	58609134	+	1	NA	intron (NM_010100, intron 9 of 11)	intron (NM_010100, intron 9 of 11)	66576	NM_010100	13608	Mm.174523	NM_010100	ENSMUSG00000003227	Edar	ED1R|ED3|ED5|EDA-A1R|EDA3|dl	ectodysplasin-A receptor	protein-coding
mm_98162.1	chr11	87737531	87737566	+	1	NA	promoter-TSS (NM_009296)	promoter-TSS (NM_009296)	-17	NM_009296	20922	Mm.622	NM_009296	ENSMUSG00000020485	Supt4a	AL022777|Supt4h|Supt4h1|Supt4h1a	suppressor of Ty 4A	protein-coding
mm_121489.1	chr14	121239739	121239748	+	1	NA	intron (NM_134082, intron 10 of 26)	intron (NM_134082, intron 10 of 26)	139487	NM_145465	223255	Mm.390756	NM_145465	ENSMUSG00000063410	Stk24	1810013H02Rik|C76483|MST-3|Mst3|STE20	serine/threonine kinase 24	protein-coding
mm_138196.1	chr17	34288020	34288025	+	1	NA	promoter-TSS (NM_010378)	promoter-TSS (NM_010378)	-251	NM_010378	14960	Mm.235338	NM_010378	ENSMUSG00000036594	H2-Aa	Aalpha|H-2Aa|H2Aa|I-Aalpha|IAalpha|Ia-1|Ia1	histocompatibility 2, class II antigen A, alpha	protein-coding
mm_149607.1	chr19	16384291	16384302	+	1	NA	3' UTR (NM_008139, exon 7 of 7)	3' UTR (NM_008139, exon 7 of 7)	-51371	NM_008137	14675	Mm.313181	NM_008137	ENSMUSG00000024697	Gna14	AU023208	guanine nucleotide binding protein, alpha 14	protein-coding
mm_65386.1	chr7	25091299	25091328	-	1	NA	3' UTR (NM_001163556, exon 14 of 14)	3' UTR (NM_001163556, exon 14 of 14)	5862	NR_105855	102465968		NR_105855	ENSMUSG00000098441	Mir6537	Gm27808|mmu-mir-6537	microRNA 6537	ncRNA
mm_77057.1	chr8	109608376	109608409	-	1	NA	5' UTR (NM_020046, exon 1 of 9)	5' UTR (NM_020046, exon 1 of 9)	281	NM_020046	56749	Mm.23894	NM_020046	ENSMUSG00000031730	Dhodh	2810417D19Rik|AI834883	dihydroorotate dehydrogenase	protein-coding
mm_58746.1	chr7	13278779	13278874	+	1	NA	promoter-TSS (NM_010715)	promoter-TSS (NM_010715)	0	NM_010715	16881	Mm.288179	NM_010715	ENSMUSG00000056394	Lig1	AL033288|LigI	ligase I, DNA, ATP-dependent	protein-coding
mm_163779.1	chr13	120044298	120044338	-	1	NA	intron (NM_001302966, intron 4 of 5)	intron (NM_001302966, intron 4 of 5)	7886	NM_001302966	100861753	Mm.165042	NM_001302966	ENSMUSG00000095609	Gm21188	-	predicted gene, 21188	protein-coding
mm_172515.1	chr7	78847160	78847172	-	1	NA	promoter-TSS (NM_029585)	promoter-TSS (NM_029585)	45	NM_029585	76375	Mm.250541	NM_029585	ENSMUSG00000030610	Det1	2610034H20Rik	de-etiolated homolog 1 (Arabidopsis)	protein-coding
mm_109713.1	chr12	114323026	114323037	+	1	NA	Intergenic	Intergenic	146435	NR_106062	102465663		NR_106062	ENSMUSG00000105438	Mir7094-1	mmu-mir-7094-1	microRNA 7094-1	ncRNA
mm_169324.1	chr14	115280298	115280298	-	1	NA	intron (NM_175500, intron 2 of 7)	L1_Mm|LINE|L1	129254	NR_045761	75088	Mm.444706	NR_045761	ENSMUSG00000093551	4930505G20Rik	-	RIKEN cDNA 4930505G20 gene	ncRNA
mm_144621.1	chr18	32934941	32934978	+	1	NA	Intergenic	MLT1F|LTR|ERVL-MaLR	-4082	NM_009793	12326	Mm.222329	NM_009793	ENSMUSG00000038128	Camk4	A430110E23Rik|AI666733|CaMKIV|CaMKIV/Gr|D18Bwg0362e	calcium/calmodulin-dependent protein kinase IV	protein-coding
mm_158619.1	chrX	152657504	152657509	-	1	NA	exon (NM_172441, exon 5 of 10)	exon (NM_172441, exon 5 of 10)	-12958	NM_001290685	110380	Mm.40796	NM_172441	ENSMUSG00000045180	Shroom2	4832440C16|Apxl|C630003H05Rik|Shrm2	shroom family member 2	protein-coding
mm_69473.1	chr7	133730829	133730835	-	1	NA	intron (NM_133941, intron 7 of 11)	intron (NM_133941, intron 7 of 11)	21499	NM_025392	66165	Mm.389983	NM_025392	ENSMUSG00000030983	Bccip	1110013J05Rik|TOK-1	BRCA2 and CDKN1A interacting protein	protein-coding
mm_124711.1	chr15	6569522	6569553	+	1	NA	Intergenic	Intergenic	-10310	NM_001278269	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_31996.1	chr4	89818702	89818703	+	1	NA	Intergenic	Lx8|LINE|L1	130504	NM_175647	242523	Mm.130167	NM_175647	ENSMUSG00000043753	Dmrta1	Dmrt4	doublesex and mab-3 related transcription factor like family A1	protein-coding
mm_46100.1	chr5	92347377	92347386	-	1	NA	exon (NM_021274, exon 4 of 4)	exon (NM_021274, exon 4 of 4)	1508	NM_021274	15945	Mm.877	NM_021274	ENSMUSG00000034855	Cxcl10	C7|CRG-2|INP10|IP-10|IP10|Ifi10|Scyb10|gIP-10|mob-1	chemokine (C-X-C motif) ligand 10	protein-coding
mm_26872.1	chr3	17327907	17327926	-	1	NA	Intergenic	Intergenic	-462005	NR_033490	70441	Mm.458192	NR_033490	ENSMUSG00000100252	Mir124-2hg	100040120|2610100L16Rik|6430547I21Rik|A930005K07Rik|AW125202|Gm2612	Mir124-2 host gene (non-protein coding)	ncRNA
mm_10752.1	chr2	23196452	23196463	+	1	NA	intron (NM_013771, intron 18 of 18)	intron (NM_013771, intron 18 of 18)	-11019	NM_027635	70981	Mm.314026	NM_027635	ENSMUSG00000026774	4931423N10Rik	-	RIKEN cDNA 4931423N10 gene	protein-coding
mm_31684.1	chr4	62298133	62298144	+	1	NA	3' UTR (NM_025286, exon 4 of 4)	3' UTR (NM_025286, exon 4 of 4)	6591	NM_001290518	20530	Mm.292539	NM_025286	ENSMUSG00000066152	Slc31a2	AI604396|CTR2	solute carrier family 31, member 2	protein-coding
mm_87041.1	chr10	28744478	28744481	+	1	NA	intron (NM_001305663, intron 3 of 5)	Lx3A|LINE|L1	76119	NM_178666	210757	Mm.123021	NM_178666	ENSMUSG00000049109	Themis	E430004N04Rik|Gasp|Spot|Tsepa|thylex	thymocyte selection associated	protein-coding
mm_169741.1	chr15	85679436	85679442	+	1	NA	Intergenic	Intergenic	-24334	NR_110483	102800312	Mm.33117	NR_110483		Lncppara	Lincppara|Mirlet7bhg|linc-Ppara	long noncoding RNA near Ppara	ncRNA
mm_162749.1	chr10	58446678	58446726	-	1	NA	promoter-TSS (NM_011240)	promoter-TSS (NM_011240)	-150	NM_011240	19386	Mm.431695	NM_011240	ENSMUSG00000003226	Ranbp2	A430087B05Rik|AI256741|NUP358	RAN binding protein 2	protein-coding
mm_147597.1	chr18	56708306	56708323	-	1	NA	exon (NM_010721, exon 1 of 11)	exon (NM_010721, exon 1 of 11)	501	NM_010721	16906	Mm.4105	NM_010721	ENSMUSG00000024590	Lmnb1	-	lamin B1	protein-coding
mm_56740.1	chr6	115808737	115808754	-	1	NA	promoter-TSS (NR_028546)	promoter-TSS (NR_028546)	-2	NM_172086	19951	Mm.104368	NM_172086	ENSMUSG00000057841	Rpl32	AU020185|rpL32-3A	ribosomal protein L32	protein-coding
mm_71522.1	chr8	46851895	46851921	+	1	NA	Intergenic	Intergenic	112163	NM_008391	16363	Mm.1149	NM_008391	ENSMUSG00000031627	Irf2	9830146E22Rik|AI646973|Irf-2	interferon regulatory factor 2	protein-coding
mm_101424.1	chr11	29547907	29547917	-	1	NA	promoter-TSS (NM_028504)	promoter-TSS (NM_028504)	-38	NM_028504	73324	Mm.69388	NM_028504	ENSMUSG00000020461	Clhc1	1700034F02Rik	clathrin heavy chain linker domain containing 1	protein-coding
mm_37447.1	chr4	123379970	123379973	-	1	NA	intron (NM_001199136, intron 78 of 97)	intron (NM_001199136, intron 78 of 97)	31940	NM_001167918	442834	Mm.483803	NM_001167918		D830031N03Rik	Kiaa0754|mKIAA0754	RIKEN cDNA D830031N03 gene	protein-coding
mm_27697.1	chr3	66973781	66973827	-	1	NA	exon (NM_013665, exon 5 of 5)	exon (NM_013665, exon 5 of 5)	5007	NM_001302358	20429	Mm.39093	NM_013665	ENSMUSG00000027833	Shox2	6330543G17Rik|OG12|Og12x|Prx3|SHOT	short stature homeobox 2	protein-coding
mm_71698.1	chr8	61687364	61687376	+	1	NA	exon (NM_001293773, exon 8 of 20)	exon (NM_001293773, exon 8 of 20)	72728	NM_001293773	72333	Mm.29933	NM_001081390	ENSMUSG00000058056	Palld	2410003B16Rik|6030492A02	palladin, cytoskeletal associated protein	protein-coding
mm_147329.1	chr18	42579794	42579805	-	1	NA	promoter-TSS (NM_181543)	promoter-TSS (NM_181543)	-147	NM_181543	240239	Mm.186779	NM_181543	ENSMUSG00000042816	Gpr151	C130082O03Rik|GalRL|PGR7|nGPCR-2037	G protein-coupled receptor 151	protein-coding
mm_135213.1	chr16	36642743	36642753	-	1	NA	intron (NM_019388, intron 1 of 7)	intron (NM_019388, intron 1 of 7)	23329	NM_019388	12524	Mm.1452	NM_019388	ENSMUSG00000022901	Cd86	B7|B7-2|B7.2|B70|CLS1|Cd28l2|ETC-1|Ly-58|Ly58|MB7|MB7-2|TS/A-2	CD86 antigen	protein-coding
mm_31500.1	chr4	53340118	53340128	+	1	NA	Intergenic	Intergenic	-69891	NR_033139	381524	Mm.23351	NM_001033454	ENSMUSG00000086712	AI427809	Gm1659	expressed sequence AI427809	ncRNA
mm_75415.1	chr8	46551728	46551742	-	1	NA	promoter-TSS (NM_027973)	promoter-TSS (NM_027973)	-334	NM_027973	71876	Mm.22108	NM_027973	ENSMUSG00000031629	Cenpu	1700029A22Rik|Mlf1ip	centromere protein U	protein-coding
mm_126733.1	chr15	85653551	85653604	+	1	NA	Intergenic	Intergenic	-50196	NR_110483	102800312	Mm.33117	NR_110483		Lncppara	Lincppara|Mirlet7bhg|linc-Ppara	long noncoding RNA near Ppara	ncRNA
mm_11580.1	chr2	32961702	32961714	+	1	NA	promoter-TSS (NM_009076)	promoter-TSS (NM_009076)	-4	NM_009076	269261	Mm.250030	NM_009076	ENSMUSG00000038900	Rpl12	E430018F03	ribosomal protein L12	protein-coding
mm_119427.1	chr14	45391680	45391687	+	1	NA	Intergenic	RLTR13B2|LTR|ERVK	-2887	NM_019425	54342	Mm.312945	NM_019425	ENSMUSG00000037722	Gnpnat1	AU017428|AU040593|EMeg32|Gpnat1|Gsnpat	glucosamine-phosphate N-acetyltransferase 1	protein-coding
mm_54724.1	chr6	40519470	40519490	-	1	NA	promoter-TSS (NM_026317)	promoter-TSS (NM_026317)	28	NM_026317	67690	Mm.52550	NM_026317	ENSMUSG00000029909	Prss37	1700016G05Rik|Tryx2	protease, serine 37	protein-coding
mm_101490.1	chr11	31671805	31671856	-	1	NA	promoter-TSS (NM_001024919)	promoter-TSS (NM_001024919)	32	NM_001024919	69556	Mm.34183	NM_001024919	ENSMUSG00000044502	Bod1	2310022M17Rik|BOD2.1|Fam44b	biorientation of chromosomes in cell division 1	protein-coding
mm_110469.1	chr12	51829563	51829589	-	1	NA	promoter-TSS (NM_144788)	promoter-TSS (NM_144788)	-40	NM_144788	207304	Mm.249391	NM_144788	ENSMUSG00000035247	Hectd1	A630086P08Rik|AI844876|b2b327Clo|opm	HECT domain containing 1	protein-coding
mm_112239.1	chr12	113482422	113482432	-	1	NA	Intergenic	Intergenic	-7138	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_34853.1	chr4	155510523	155510525	+	1	NA	intron (NM_001160017, intron 1 of 10)	intron (NM_001160017, intron 1 of 10)	19163	NM_001160016	14688	Mm.2344	NM_008142	ENSMUSG00000029064	Gnb1	AA409223|C77571|Gnb-1	guanine nucleotide binding protein (G protein), beta 1	protein-coding
mm_81078.1	chr9	106223810	106223834	+	1	NA	exon (NM_031178, exon 2 of 2)	exon (NM_031178, exon 2 of 2)	1224	NM_031178	81897	Mm.44889	NM_031178	ENSMUSG00000045322	Tlr9	-	toll-like receptor 9	protein-coding
mm_122725.1	chr14	52316157	52316167	-	1	NA	5' UTR (NM_001244916, exon 1 of 2)	5' UTR (NM_001244916, exon 1 of 2)	161	NM_001244916	50524	Mm.39487	NM_015772	ENSMUSG00000049532	Sall2	AI225809|AW559097|Msal-2|Sal-2|mKIAA0360|p150(Sal2)	sal-like 2 (Drosophila)	protein-coding
mm_108843.1	chr12	98259581	98259589	+	1	NA	promoter-TSS (NM_008079)	promoter-TSS (NM_008079)	-126	NM_008079	14420	Mm.5120	NM_008079	ENSMUSG00000021003	Galc	2310068B06Rik|A930008M05Rik|AW212969|AW413532|Gacy|twi|twitcher	galactosylceramidase	protein-coding
mm_380.1	chr1	34022757	34022770	+	1	NA	intron (NM_133833, intron 1 of 92)	PB1D10|SINE|Alu	10938	NM_134448	13518	Mm.336625	NM_010081	ENSMUSG00000026131	Dst	2310001O04Rik|A830042E19Rik|AW554249|BP230|BPAG1-n|Bpag|Bpag1|Macf2|ah|athetoid|dt|mKIAA0728|nmf203|nmf339	dystonin	protein-coding
mm_49.1	chr1	6527813	6527860	+	1	NA	intron (NM_001244693, intron 2 of 22)	intron (NM_001244693, intron 2 of 22)	40605	NM_001244692	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding
mm_81182.1	chr9	107400044	107400064	+	1	NA	5' UTR (NM_001174049, exon 1 of 38)	5' UTR (NM_001174049, exon 1 of 38)	174	NM_020263	56808	Mm.273084	NM_020263	ENSMUSG00000010066	Cacna2d2	Cacna2d|a2d2|du|mKIAA0558|td|torpid	calcium channel, voltage-dependent, alpha 2/delta subunit 2	protein-coding
mm_103418.1	chr11	75533092	75533108	-	1	NA	intron (NM_173388, intron 2 of 13)	intron (NM_173388, intron 2 of 13)	988	NM_001199283	215113	Mm.11186	NM_173388	ENSMUSG00000038178	Slc43a2	7630402D21Rik|BC042513|Lat4	solute carrier family 43, member 2	protein-coding
mm_156424.1	chrX	140953833	140953862	+	1	NA	exon (NM_001164177, exon 2 of 5)	exon (NM_001164177, exon 2 of 5)	2864	NM_016883	53380	Mm.17640	NM_016883	ENSMUSG00000031429	Psmd10	AW554874	proteasome (prosome, macropain) 26S subunit, non-ATPase, 10	protein-coding
mm_168525.1	chr11	6006263	6006270	+	1	NA	intron (NM_007595, intron 3 of 20)	RLTR4_Mm|LTR|ERV1	50508	NM_019661	56418	Mm.294821	NM_019661	ENSMUSG00000002741	Ykt6	0610042I15Rik|1810013M05Rik|AW105923	YKT6 v-SNARE homolog (S. cerevisiae)	protein-coding
mm_4399.1	chr1	172376529	172376599	+	1	NA	promoter-TSS (NM_026234)	promoter-TSS (NM_026234)	33	NM_026234	67556	Mm.26612	NM_026234	ENSMUSG00000050229	Pigm	4933437L05Rik|AI644422|AV302080|C920011G20Rik	phosphatidylinositol glycan anchor biosynthesis, class M	protein-coding
mm_162007.1	chr19	40994726	40994726	-	1	NA	promoter-TSS (NM_008528)	promoter-TSS (NM_008528)	-191	NM_008528	17060	Mm.9749	NM_008528	ENSMUSG00000061132	Blnk	BASH|Bca|Ly-57|Ly57|Lyw-57|SLP-65	B cell linker	protein-coding
mm_88886.1	chr10	81136224	81136267	+	1	NA	promoter-TSS (NM_010731)	promoter-TSS (NM_010731)	-26	NM_010731	16969	Mm.20920	NM_010731	ENSMUSG00000035011	Zbtb7a	9030619K07Rik|9130006G12Rik|AI452336|FBI-1|Lrf|Pokemon|Zbtb7	zinc finger and BTB domain containing 7a	protein-coding
mm_117852.1	chr13	98725704	98725733	-	1	NA	3' UTR (NM_172591, exon 26 of 26)	3' UTR (NM_172591, exon 26 of 26)	-30887	NM_001025606	380863	Mm.28264	NM_001025606	ENSMUSG00000052485	Tmem171	Gm905	transmembrane protein 171	protein-coding
mm_54015.1	chr6	8364311	8364321	-	1	NA	intron (NM_001302353, intron 2 of 4)	intron (NM_001302353, intron 2 of 4)	105028	NM_001302353	100036521	Mm.446106	NM_001302353	ENSMUSG00000089862	Umad1	Gm16039|OTTMUSG00000029336	UMAP1-MVP12 associated (UMA) domain containing 1	protein-coding
mm_151725.1	chr19	4864021	4864062	-	1	NA	exon (NM_013456, exon 15 of 21)	exon (NM_013456, exon 15 of 21)	8912	NM_019861	56464	Mm.29561	NM_019861	ENSMUSG00000083282	Ctsf	AI481912	cathepsin F	protein-coding
mm_143381.1	chr17	67955708	67955721	-	1	NA	intron (NM_172964, intron 1 of 17)	intron (NM_172964, intron 1 of 17)	-4774	NM_001347410	268970	Mm.9935	NM_172964	ENSMUSG00000024043	Arhgap28	AU044757|AW550892|E130310N06	Rho GTPase activating protein 28	protein-coding
mm_23099.1	chr3	37281506	37281515	+	1	NA	Intergenic	Intergenic	30936	NM_145825	207175	Mm.344708	NM_145825	ENSMUSG00000045031	Cetn4	-	centrin 4	protein-coding
mm_34951.1	chr4	155962343	155962392	+	1	NA	promoter-TSS (NM_026125)	promoter-TSS (NM_026125)	55	NM_026125	67389	Mm.29140	NM_026125	ENSMUSG00000023571	Fam132a	1110035L05Rik|C1qdc2|CTRP12|alipolin	family with sequence similarity 132, member A	protein-coding
mm_3728.1	chr1	155059945	155059946	+	1	NA	Intergenic	Intergenic	39691	NM_010500	15939	Mm.12246	NM_010500	ENSMUSG00000056708	Ier5	-	immediate early response 5	protein-coding
mm_150374.1	chr19	34922410	34922418	+	1	NA	promoter-TSS (NM_183046)	promoter-TSS (NM_183046)	56	NM_183046	240641	Mm.278471	NM_183046	ENSMUSG00000024795	Kif20b	33cex|B130024C23|C330014J10Rik|Mphosph1|magoo	kinesin family member 20B	protein-coding
mm_154153.1	chr19	58455416	58455458	-	1	NA	promoter-TSS (NM_010279)	promoter-TSS (NM_010279)	-39	NM_010279	14585	Mm.88367	NM_010279	ENSMUSG00000025089	Gfra1	AU042498	glial cell line derived neurotrophic factor family receptor alpha 1	protein-coding
mm_88071.1	chr10	67909220	67909245	+	1	NA	exon (NM_178679, exon 2 of 5)	exon (NM_178679, exon 2 of 5)	3430	NM_178679	216049	Mm.268346	NM_178679	ENSMUSG00000037855	Zfp365	AI839779|AV340892|DBZ|Su48|Znf365|talanin	zinc finger protein 365	protein-coding
mm_58434.1	chr7	3297680	3297711	+	1	NA	3' UTR (NM_016969, exon 3 of 3)	3' UTR (NM_016969, exon 3 of 3)	4667	NM_001093766	50918	Mm.29874	NM_016969	ENSMUSG00000068566	Myadm	D7Wsu62e	myeloid-associated differentiation marker	protein-coding
mm_97573.1	chr11	78940249	78940262	+	1	NA	exon (NM_010927, exon 11 of 27)	exon (NM_010927, exon 11 of 27)	14964	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_33792.1	chr4	134924205	134924221	+	1	NA	exon (NM_023665, exon 2 of 5)	exon (NM_023665, exon 2 of 5)	588	NM_023665	27981	Mm.331964	NM_023665	ENSMUSG00000037266	Rsrp1	2700043I21Rik|D4Ucla2|D4Wsu53e	arginine/serine rich protein 1	protein-coding
mm_160163.1	chr7	44552729	44552729	-	1	NA	exon (NM_009473, exon 3 of 10)	exon (NM_009473, exon 3 of 10)	1236	NM_009473	22260	Mm.968	NM_009473	ENSMUSG00000060601	Nr1h2	AI194859|LXR|LXRB|LXRBSV|LXRbeta|NER1|OR-1|RIP15|UR|Unr|Unr2	nuclear receptor subfamily 1, group H, member 2	protein-coding
mm_108937.1	chr12	101975966	101976004	+	1	NA	promoter-TSS (NM_016856)	promoter-TSS (NM_016856)	11	NM_016856	51786	Mm.716	NM_016856	ENSMUSG00000041781	Cpsf2	100kDa|2610024B04Rik|AI662483|Cpsf|MCPSF|mKIAA1367	cleavage and polyadenylation specific factor 2	protein-coding
mm_21987.1	chr2	167590518	167590527	-	1	NA	Intergenic	Intergenic	41483	NM_001311146	66589	Mm.278783	NM_023230	ENSMUSG00000078923	Ube2v1	0610011J09Rik|AI256840|CROC-1|CROC1|D7Bwg1382e|UEV-1	ubiquitin-conjugating enzyme E2 variant 1	protein-coding
mm_60529.1	chr7	44480202	44480206	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-4313	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_126298.1	chr15	79348422	79348432	+	1	NA	promoter-TSS (NM_001304832)	promoter-TSS (NM_001304832)	25	NM_001304832	17133	Mm.86646	NM_010755	ENSMUSG00000042622	Maff	-	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein F (avian)	protein-coding
mm_14137.1	chr2	126152132	126152146	+	1	NA	promoter-TSS (NM_026981)	promoter-TSS (NM_026981)	-2	NM_026981	69185	Mm.29019	NM_026981	ENSMUSG00000023330	Dtwd1	1810033A06Rik	DTW domain containing 1	protein-coding
mm_26726.1	chr3	159927878	159927880	+	1	NA	intron (NM_026582, intron 11 of 11)	intron (NM_026582, intron 11 of 11)	88184	NM_026582	68151	Mm.6766	NM_026582	ENSMUSG00000028173	Wls	5031439A09Rik|AI173978|AI987742|Gpr177	wntless homolog (Drosophila)	protein-coding
mm_49398.1	chr6	28424573	28424589	+	1	NA	intron (NM_007480, intron 2 of 5)	intron (NM_007480, intron 2 of 5)	941	NM_007480	11844	Mm.389075	NM_007480	ENSMUSG00000020440	Arf5	-	ADP-ribosylation factor 5	protein-coding
mm_147694.1	chr18	60748609	60748694	-	1	NA	Intergenic	CpG	-25945	NM_020600	20044	Mm.43778	NM_020600	ENSMUSG00000024608	Rps14	2600014J02Rik|AL023078	ribosomal protein S14	protein-coding
mm_14720.1	chr2	143938546	143938589	+	1	NA	exon (NM_019771, exon 2 of 4)	exon (NM_019771, exon 2 of 4)	23236	NM_019771	56431	Mm.28919	NM_019771	ENSMUSG00000015932	Dstn	2610043P17Rik|ADF|AU042046|Dsn|corn1|sid23p	destrin	protein-coding
mm_45138.1	chr5	48935466	48935483	-	1	NA	intron (NM_001199244, intron 1 of 7)	intron (NM_001199244, intron 1 of 7)	-45917	NM_030265	80334	Mm.160172	NM_030265	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding
mm_10197.1	chr2	4927485	4927497	+	1	NA	exon (NM_010726, exon 4 of 9)	exon (NM_010726, exon 4 of 9)	8495	NM_010726	16922	Mm.391704	NM_010726	ENSMUSG00000026664	Phyh	AI256161|AI265699|Lnap1|PAHX	phytanoyl-CoA hydroxylase	protein-coding
mm_129554.1	chr15	79442111	79442124	-	1	NA	promoter-TSS (NM_013767)	promoter-TSS (NM_013767)	-60	NM_013767	27373	Mm.30199	NM_013767	ENSMUSG00000022433	Csnk1e	AI426939|AI551861|AW457082|CK1epsilon|CKIe|KC1epsilon|tau	casein kinase 1, epsilon	protein-coding
mm_27019.1	chr3	26046036	26046051	-	1	NA	intron (NM_138666, intron 3 of 7)	intron (NM_138666, intron 3 of 7)	107264	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_102186.1	chr11	54248506	54248516	-	1	NA	exon (NM_009969, exon 3 of 4)	exon (NM_009969, exon 3 of 4)	1388	NM_009969	12981	Mm.4922	NM_009969	ENSMUSG00000018916	Csf2	Csfgm|GMCSF|Gm-CSf|MGI-IGM	colony stimulating factor 2 (granulocyte-macrophage)	protein-coding
mm_113830.1	chr13	47066449	47066463	+	1	NA	intron (NM_172262, intron 11 of 20)	intron (NM_172262, intron 11 of 20)	22957	NM_172262	218214	Mm.31259	NM_172262	ENSMUSG00000038080	Kdm1b	4632428N09Rik|AI482520|Aof1	lysine (K)-specific demethylase 1B	protein-coding
mm_26433.1	chr3	142620597	142620627	+	1	NA	promoter-TSS (NM_010260)	promoter-TSS (NM_010260)	-51	NM_010260	14469	Mm.24038	NM_010260	ENSMUSG00000028270	Gbp2	-	guanylate binding protein 2	protein-coding
mm_53898.1	chr6	3487372	3487419	-	1	NA	intron (NM_178899, intron 1 of 9)	intron (NM_178899, intron 1 of 9)	7103	NM_178899	101202	Mm.206911	NM_178899	ENSMUSG00000044156	Hepacam2	AI987662	HEPACAM family member 2	protein-coding
mm_57027.1	chr6	122282911	122282921	-	1	NA	promoter-TSS (NM_016970)	promoter-TSS (NM_016970)	-83	NM_016970	50928	Mm.20434	NM_016970	ENSMUSG00000030114	Klrg1	2F1-Ag|MAFA|MAFA-L	killer cell lectin-like receptor subfamily G, member 1	protein-coding
mm_100296.1	chr11	117829491	117829510	+	1	NA	intron (NM_027827, intron 2 of 10)	B3A|SINE|B2	-3486	NM_009387	21877	Mm.2661	NM_009387	ENSMUSG00000025574	Tk1	D530002A18Rik|Tk-1|Tk1a|Tk1b	thymidine kinase 1	protein-coding
mm_113670.1	chr13	42717433	42717444	+	1	NA	intron (NM_001005740, intron 1 of 12)	MIR|SINE|MIR	7857	NM_001005740	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding
mm_144359.1	chr18	20221632	20221635	+	1	NA	Intergenic	Intergenic	-25707	NM_181680	211924	Mm.391118	NM_181680	ENSMUSG00000034774	Dsg1c	Dsg1gamma|Dsg6|dsg1g	desmoglein 1 gamma	protein-coding
mm_89227.1	chr10	87521894	87521917	+	1	NA	5' UTR (NM_008777, exon 1 of 13)	5' UTR (NM_008777, exon 1 of 13)	110	NM_008777	18478	Mm.263539	NM_008777	ENSMUSG00000020051	Pah	AW106920	phenylalanine hydroxylase	protein-coding
mm_46825.1	chr5	113211952	113211956	-	1	NA	Intergenic	Intergenic	-14955	NM_001033428	333048	Mm.332586	NM_001033428	ENSMUSG00000066964	Tmem211	Gm854	transmembrane protein 211	protein-coding
mm_157854.1	chrX	74494966	74494980	-	1	NA	Intergenic	Intergenic	-13574	NM_001099305	628456	Mm.455664	NM_001099305	ENSMUSG00000079536	Gm6880	EG628456	predicted gene 6880	protein-coding
mm_27359.1	chr3	50419142	50419145	-	1	NA	intron (NM_011990, intron 5 of 11)	intron (NM_011990, intron 5 of 11)	24470	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_35844.1	chr4	48279545	48279613	-	1	NA	promoter-TSS (NM_029572)	promoter-TSS (NM_029572)	10	NM_029572	76299	Mm.317701	NM_029572	ENSMUSG00000028343	Erp44	1110001E24Rik|AI849526|AL033348|Txndc4	endoplasmic reticulum protein 44	protein-coding
mm_121222.1	chr14	103055337	103055356	+	1	NA	exon (NM_008392, exon 5 of 5)	exon (NM_008392, exon 5 of 5)	8334	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_42005.1	chr5	107941488	107941513	+	1	NA	intron (NM_026062, intron 1 of 4)	intron (NM_026062, intron 1 of 4)	40972	NM_016980	100503670	Mm.277897	NM_016980	ENSMUSG00000058558	Rpl5	U21RNA	ribosomal protein L5	protein-coding
mm_70860.1	chr8	24480063	24480108	+	1	NA	Intergenic	Intergenic	4901	NR_035483	100316707		NR_035483	ENSMUSG00000088552	Mir1957a	Mir1957|mmu-mir-1957|mmu-mir-1957a	microRNA 1957a	ncRNA
mm_106948.1	chr12	8771406	8771425	+	1	NA	promoter-TSS (NM_011519)	promoter-TSS (NM_011519)	19	NM_011519	20969	Mm.2580	NM_011519	ENSMUSG00000020592	Sdc1	AA408134|AA409076|CD138|Sstn|Synd|Synd1|syn-1	syndecan 1	protein-coding
mm_22251.1	chr2	174853245	174853251	-	1	NA	Intergenic	Intergenic	92629	NM_007903	13616	Mm.9478	NM_007903	ENSMUSG00000027524	Edn3	ET-3|PPET3|ls|tmgc48	endothelin 3	protein-coding
mm_144234.1	chr18	10617769	10617845	+	1	NA	promoter-TSS (NM_009226)	promoter-TSS (NM_009226)	11	NM_009226	20641	Mm.603	NM_009226	ENSMUSG00000002477	Snrpd1	AA407109|AL023031|SMD1	small nuclear ribonucleoprotein D1	protein-coding
mm_153702.1	chr19	44397752	44397761	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	9953	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_119936.1	chr14	54975971	54976000	+	1	NA	promoter-TSS (NR_030607)	promoter-TSS (NR_030607)	-209	NR_030607	100124433		NR_030607	ENSMUSG00000077928	Mir208b	Mirn208b|mir-208b	microRNA 208b	ncRNA
mm_146968.1	chr18	33463451	33463473	-	1	NA	promoter-TSS (NR_045415)	promoter-TSS (NR_045415)	172	NM_001267717	27528	Mm.407415	NM_053078	ENSMUSG00000042834	Nrep	AI325076|D0H4S114|Harp|P311|PTZ17|SEZ17	neuronal regeneration related protein	protein-coding
mm_10407.1	chr2	13578766	13578778	+	1	NA	intron (NM_011701, intron 4 of 8)	intron (NM_011701, intron 4 of 8)	4461	NM_011701	22352	Mm.268000	NM_011701	ENSMUSG00000026728	Vim	-	vimentin	protein-coding
mm_82854.1	chr9	31434743	31434771	-	1	NA	intron (NM_144936, intron 1 of 5)	intron (NM_144936, intron 1 of 5)	29481	NM_144936	235135	Mm.390134	NM_144936	ENSMUSG00000041737	Tmem45b	BC018222	transmembrane protein 45b	protein-coding
mm_45163.1	chr5	50058909	50059010	-	1	NA	promoter-TSS (NM_133911)	promoter-TSS (NM_133911)	37	NM_133911	70693	Mm.272974	NM_133911	ENSMUSG00000029090	Adgra3	3830613O22Rik|AU044632|Gpr125|Tem5-like	adhesion G protein-coupled receptor A3	protein-coding
mm_127212.1	chr15	99249243	99249259	+	1	NA	intron (NM_001164156, intron 3 of 13)	intron (NM_001164156, intron 3 of 13)	-2537	NR_045627	73600	Mm.475134	NR_045627	ENSMUSG00000100599	1700120C14Rik	-	RIKEN cDNA 1700120C14 gene	ncRNA
mm_33674.1	chr4	133220859	133220906	+	1	NA	promoter-TSS (NM_027152)	promoter-TSS (NM_027152)	73	NM_027152	69655	Mm.285685	NM_027152	ENSMUSG00000028865	Cd164l2	2310047N01Rik	CD164 sialomucin-like 2	protein-coding
mm_73956.1	chr8	120369155	120369176	+	1	NA	Intergenic	Intergenic	-119701	NM_198671	382034	Mm.334856	NM_198671	ENSMUSG00000031822	Gse1	2210013I18Rik|mKIAA0182	genetic suppressor element 1, coiled-coil protein	protein-coding
mm_141115.1	chr17	26090067	26090100	-	1	NA	promoter-TSS (NM_011933)	promoter-TSS (NM_011933)	81	NM_011933	26378	Mm.292869	NM_011933	ENSMUSG00000036775	Decr2	-	2-4-dienoyl-Coenzyme A reductase 2, peroxisomal	protein-coding
mm_110585.1	chr12	56529411	56529437	-	1	NA	promoter-TSS (NR_045082)	promoter-TSS (NR_045082)	-4	NR_045082	104798	Mm.310950	NR_045082		E030019B13Rik	AI413669	RIKEN cDNA E030019B13 gene	ncRNA
mm_96614.1	chr11	69098916	69098936	+	1	NA	promoter-TSS (NM_011065)	promoter-TSS (NM_011065)	-30	NM_011065	18626	Mm.7373	NM_011065	ENSMUSG00000020893	Per1	Hftm|Per|m-rigui|mPer1	period circadian clock 1	protein-coding
mm_2831.1	chr1	131245324	131245334	+	1	NA	promoter-TSS (NM_018750)	promoter-TSS (NM_018750)	-151	NM_001313731	54354	Mm.248291	NM_018750	ENSMUSG00000026430	Rassf5	1300019G20Rik|Maxp1|Nore1|Nore1A|Nore1B|Rapl	Ras association (RalGDS/AF-6) domain family member 5	protein-coding
mm_169831.1	chr1	62534172	62534191	-	1	NA	intron (NM_001081050, intron 21 of 22)	IAPLTR1_Mm|LTR|ERVK	-169136	NM_001077406	18187	Mm.266341	NM_010939	ENSMUSG00000025969	Nrp2	1110048P06Rik|Np-2|Np2|Npn-2|Npn2	neuropilin 2	protein-coding
mm_148699.1	chr19	5742081	5742085	+	1	NA	5' UTR (NM_008520, exon 2 of 28)	5' UTR (NM_008520, exon 2 of 28)	1179	NM_008520	16998	Mm.182396	NM_008520	ENSMUSG00000024940	Ltbp3	Ltbp2|mFLJ00070	latent transforming growth factor beta binding protein 3	protein-coding
mm_158336.1	chrX	133981766	133981812	-	1	NA	promoter-TSS (NM_001290718)	promoter-TSS (NM_001290718)	23	NM_001290718	27359	Mm.38674	NM_013757	ENSMUSG00000031255	Sytl4	Gph|Slp4	synaptotagmin-like 4	protein-coding
mm_5878.1	chr1	53824994	53825003	-	1	NA	intron (NM_001001883, intron 28 of 28)	intron (NM_001001883, intron 28 of 28)	-24426	NR_106149	102465783		NR_106149	ENSMUSG00000098443	Mir7681	Gm27806|mmu-mir-7681	microRNA 7681	ncRNA
mm_145588.1	chr18	60985881	60985897	+	1	NA	3' UTR (NM_001286809, exon 6 of 6)	3' UTR (NM_001286809, exon 6 of 6)	22335	NM_001286809	12322	Mm.131530	NM_009792	ENSMUSG00000024617	Camk2a	CaMKII|R74975|mKIAA0968	calcium/calmodulin-dependent protein kinase II alpha	protein-coding
mm_75655.1	chr8	65129555	65129572	-	1	NA	promoter-TSS (NR_033217)	promoter-TSS (NR_033217)	-26	NR_033217	407795	Mm.387876	NR_033217	ENSMUSG00000074300	BC030870	-	cDNA sequence BC030870	ncRNA
mm_64489.1	chr7	143107235	143107250	+	1	NA	promoter-TSS (NM_008434)	promoter-TSS (NM_008434)	-12	NM_008434	16535	Mm.439769	NM_008434	ENSMUSG00000009545	Kcnq1	AW559127|KVLQT1|Kcna9	potassium voltage-gated channel, subfamily Q, member 1	protein-coding
mm_123747.1	chr14	70192665	70192712	-	1	NA	promoter-TSS (NM_001271409)	promoter-TSS (NM_001271409)	-442	NM_001271409	20410	Mm.5068	NM_011366	ENSMUSG00000022091	Sorbs3	SCAM-1|SH3P3|Sh3d4|vinexin-g	sorbin and SH3 domain containing 3	protein-coding
mm_140985.1	chr17	24724334	24724344	-	1	NA	promoter-TSS (NM_026684)	promoter-TSS (NM_026684)	49	NM_026684	68342	Mm.1129	NM_026684	ENSMUSG00000040048	Ndufb10	0610011B04Rik|22kDa|PDSW	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 10	protein-coding
mm_121992.1	chr14	26463613	26463629	-	1	NA	exon (NM_032008, exon 8 of 23)	exon (NM_032008, exon 8 of 23)	71003	NM_032008	83997	Mm.36769	NM_032008	ENSMUSG00000021870	Slmap	D330001L02Rik|Miranda|Slap|mKIAA1601	sarcolemma associated protein	protein-coding
mm_119784.1	chr14	54181631	54181633	+	1	NA	Intergenic	Intergenic	72297	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_41763.1	chr5	103425182	103425197	+	1	NA	promoter-TSS (NM_011204)	promoter-TSS (NM_011204)	-3	NM_011204	19249	Mm.3414	NM_011204	ENSMUSG00000034573	Ptpn13	AI324989|PTP-BL|PTPL1|Ptpri|RIP	protein tyrosine phosphatase, non-receptor type 13	protein-coding
mm_150463.1	chr19	38348732	38348743	+	1	NA	Intergenic	Intergenic	-47243	NM_175507	240660	Mm.262085	NM_175507	ENSMUSG00000044026	Slc35g1	AA590464|D330039I19Rik|Tmem20	solute carrier family 35, member G1	protein-coding
mm_117646.1	chr13	92706526	92706548	-	1	NA	intron (NM_172588, intron 11 of 11)	intron (NM_172588, intron 11 of 11)	88281	NM_011582	21828	Mm.20865	NM_011582	ENSMUSG00000021702	Thbs4	TSP4	thrombospondin 4	protein-coding
mm_33933.1	chr4	136890324	136890355	+	1	NA	exon (NM_007574, exon 3 of 3)	exon (NM_007574, exon 3 of 3)	2575	NM_007574	12262	Mm.439732	NM_007574	ENSMUSG00000036896	C1qc	AI385742|C1qg|Ciqc	complement component 1, q subcomponent, C chain	protein-coding
mm_53875.1	chr6	149531927	149531930	+	1	NA	intron (NM_001112796, intron 7 of 7)	B3|SINE|B2	122944	NM_009753	12121	Mm.177181	NM_009753	ENSMUSG00000003452	Bicd1	B830009D06Rik|bic-D 1	bicaudal D homolog 1 (Drosophila)	protein-coding
mm_120003.1	chr14	55643629	55643666	+	1	NA	5' UTR (NM_028780, exon 1 of 6)	5' UTR (NM_028780, exon 1 of 6)	159	NM_028780	74140	Mm.132857	NM_028780	ENSMUSG00000002320	Tm9sf1	1200014D02Rik|AI893436|MP70	transmembrane 9 superfamily member 1	protein-coding
mm_82318.1	chr9	7984116	7984121	-	1	NA	intron (NM_009534, intron 2 of 7)	PB1D7|SINE|Alu	20478	NM_001171147	22601	Mm.221992	NM_009534	ENSMUSG00000053110	Yap1	AI325207|Yap|Yap65|Yki|Yorkie	yes-associated protein 1	protein-coding
mm_154581.1	chrX	7572640	7572650	+	1	NA	promoter-TSS (NR_029473)	promoter-TSS (NR_029473)	-955	NR_029473	78185	Mm.160055	NR_029473	ENSMUSG00000039545	Ppp1r3fos	4930524L23Rik	protein phosphatase 1, regulatory subunit 3F, opposite strand	ncRNA
mm_79382.1	chr9	54768442	54768451	+	1	NA	exon (NM_013496, exon 3 of 4)	exon (NM_013496, exon 3 of 4)	3698	NM_013496	12903	Mm.34797	NM_013496	ENSMUSG00000032291	Crabp1	AI326249|CRABP-I|Crabp-1|CrabpI|Rbp-5	cellular retinoic acid binding protein I	protein-coding
mm_57097.1	chr6	122590427	122590463	-	1	NA	intron (NM_001134391, intron 4 of 7)	B3A|SINE|B2	11999	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_159008.1	chr1	163929140	163929140	+	1	NA	promoter-TSS (NM_028776)	promoter-TSS (NM_028776)	40	NM_001286002	240880	Mm.389213	NM_028776	ENSMUSG00000026584	Scyl3	1200016D23Rik|6030457O16|AW214499|Pace1	SCY1-like 3 (S. cerevisiae)	protein-coding
mm_90584.1	chr10	128269174	128269194	+	1	NA	exon (NM_133997, exon 2 of 2)	exon (NM_133997, exon 2 of 2)	1187	NM_133997	103161	Mm.26513	NM_133997	ENSMUSG00000047631	Apof	AI255964	apolipoprotein F	protein-coding
mm_107434.1	chr12	35992901	35992917	+	1	NA	promoter-TSS (NM_011783)	promoter-TSS (NM_011783)	-16	NM_011783	23795	Mm.7244	NM_011783	ENSMUSG00000020581	Agr2	Agr2h|Gob-4|HAG-2|XAG-2|mAG-2	anterior gradient 2	protein-coding
mm_129360.1	chr15	77956449	77956469	-	1	NA	intron (NM_001017983, intron 1 of 8)	CpG	263	NM_001168260	239554	Mm.295605	NM_001017983	ENSMUSG00000016552	Foxred2	A430097D04Rik|D15Bwg0759e|Gm304	FAD-dependent oxidoreductase domain containing 2	protein-coding
mm_74460.1	chr8	4214778	4214790	-	1	NA	exon (NM_207203, exon 6 of 7)	exon (NM_207203, exon 6 of 7)	2528	NM_207203	73072	Mm.477379	NM_207203	ENSMUSG00000064125	Prr36	-	proline rich 36	protein-coding
mm_83873.1	chr9	55044001	55044017	-	1	NA	intron (NM_148944, intron 1 of 5)	intron (NM_148944, intron 1 of 5)	4535	NM_148944	108015	Mm.32694	NM_148944	ENSMUSG00000035200	Chrnb4	Acrb-4|Acrb4	cholinergic receptor, nicotinic, beta polypeptide 4	protein-coding
mm_92443.1	chr10	77530158	77530204	-	1	NA	promoter-TSS (NM_008404)	promoter-TSS (NM_008404)	-167	NM_008404	16414	Mm.1137	NM_008404	ENSMUSG00000000290	Itgb2	2E6|AI528527|Cd18|LAD|LCAMB|Lfa1|MF17	integrin beta 2	protein-coding
mm_156750.1	chrX	160390473	160390494	+	1	NA	promoter-TSS (NM_178712)	promoter-TSS (NM_178712)	-207	NM_001079847	237175	Mm.213016	NM_178712	ENSMUSG00000031298	Adgrg2	AW212196|B830041D06Rik|Gpr64|Me6	adhesion G protein-coupled receptor G2	protein-coding
mm_10976.1	chr2	25765532	25765535	+	1	NA	promoter-TSS (NM_010694)	promoter-TSS (NM_010694)	-36	NM_010694	16820	Mm.4632	NM_010694	ENSMUSG00000026936	Lcn3	Vnsp1	lipocalin 3	protein-coding
mm_70633.1	chr8	13785621	13785661	+	1	NA	promoter-TSS (NM_025924)	promoter-TSS (NM_025924)	26	NM_025924	67031	Mm.44858	NM_025924	ENSMUSG00000038398	Upf3a	2600001C03Rik|4930546M19Rik|RENT3A|UPF3	UPF3 regulator of nonsense transcripts homolog A (yeast)	protein-coding
mm_55662.1	chr6	72394587	72394603	-	1	NA	Intergenic	Intergenic	-3928	NM_016794	22320	Mm.1838	NM_016794	ENSMUSG00000050732	Vamp8	AU041171|Edb|endobrevin	vesicle-associated membrane protein 8	protein-coding
mm_2365.1	chr1	93135311	93135326	+	1	NA	promoter-TSS (NM_016702)	promoter-TSS (NM_016702)	78	NM_001276710	11611	Mm.7457	NM_016702	ENSMUSG00000026272	Agxt	AGT|Agt1|Agxt1|SPT	alanine-glyoxylate aminotransferase	protein-coding
mm_150076.1	chr19	29386895	29386909	+	1	NA	3' UTR (NM_021893, exon 7 of 7)	3' UTR (NM_021893, exon 7 of 7)	19464	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_79541.1	chr9	57910975	57911023	+	1	NA	promoter-TSS (NM_027086)	promoter-TSS (NM_027086)	13	NM_001122873	69459	Mm.41735	NM_027086	ENSMUSG00000055720	Ubl7	2300004C15Rik	ubiquitin-like 7 (bone marrow stromal cell-derived)	protein-coding
mm_157318.1	chrX	21221654	21221666	-	1	NA	promoter-TSS (NM_001252013)	promoter-TSS (NM_001252013)	5	NM_001252013	100503481	Mm.272069	NM_001252013		4930453H23Rik	-	RIKEN cDNA 4930453H23 gene	protein-coding
mm_106406.1	chr11	118910037	118910058	-	1	NA	promoter-TSS (NM_001039167)	promoter-TSS (NM_001039167)	-475	NM_001039167	52897	Mm.341103	NM_001024931	ENSMUSG00000025576	Rbfox3	Fox-3|Hrnbp3|NeuN|Neuna60	RNA binding protein, fox-1 homolog (C. elegans) 3	protein-coding
mm_120769.1	chr14	73524972	73524989	+	1	NA	intron (NM_172527, intron 3 of 4)	CpG	14931	NM_026119	67381	Mm.282888	NM_026119	ENSMUSG00000022109	Med4	2410046H15Rik|DRIP36|HSPC126|TRAP36|Vdirp|Vdrip	mediator complex subunit 4	protein-coding
mm_13377.1	chr2	103761478	103761485	+	1	NA	promoter-TSS (NM_153126)	promoter-TSS (NM_153126)	-231	NM_153126	98956	Mm.288005	NM_153126	ENSMUSG00000027185	Nat10	AI429152	N-acetyltransferase 10	protein-coding
mm_35541.1	chr4	41422620	41422623	-	1	NA	intron (NM_024241, intron 3 of 12)	B1F2|SINE|Alu	42227	NM_024241	109242	Mm.370288	NM_024241	ENSMUSG00000028438	Kif24	4933425J19Rik|9430029L23Rik	kinesin family member 24	protein-coding
mm_39964.1	chr5	32137041	32137045	+	1	NA	intron (NM_008037, intron 1 of 3)	intron (NM_008037, intron 1 of 3)	571	NM_008037	14284	Mm.24684	NM_008037	ENSMUSG00000029135	Fosl2	Fra-2	fos-like antigen 2	protein-coding
mm_84836.1	chr9	78355744	78355776	-	1	NA	Intergenic	Intergenic	-8615	NM_008182	14858	Mm.422778	NM_008182	ENSMUSG00000057933	Gsta2	Gst2-2|Gstc-2|Gstc2	glutathione S-transferase, alpha 2 (Yc2)	protein-coding
mm_1504.1	chr1	72284368	72284419	+	1	NA	promoter-TSS (NM_175564)	promoter-TSS (NM_175564)	20	NM_175564	271711	Mm.80318	NM_175564	ENSMUSG00000026188	Tmem169	A830020B06Rik	transmembrane protein 169	protein-coding
mm_62133.1	chr7	97081712	97081778	+	1	NA	promoter-TSS (NM_010248)	promoter-TSS (NM_010248)	-6	NM_001162477	14389	Mm.42033	NM_010248	ENSMUSG00000004508	Gab2	AI463667|D130058I17Rik|p97	growth factor receptor bound protein 2-associated protein 2	protein-coding
mm_95637.1	chr11	53707753	53707762	+	1	NA	promoter-TSS (NM_009012)	promoter-TSS (NM_009012)	-438	NM_009012	19360	Mm.4888	NM_009012	ENSMUSG00000020380	Rad50	Mrell|Rad50l	RAD50 double strand break repair protein	protein-coding
mm_74285.1	chr8	125730006	125730026	+	1	NA	Intergenic	MTEa|LTR|ERVL-MaLR	-4187	NM_025636	66566	Mm.25296	NM_025636	ENSMUSG00000031851	Ntpcr	2310079N02Rik|AI449709	nucleoside-triphosphatase, cancer-related	protein-coding
mm_104165.1	chr11	87359012	87359081	-	1	NA	promoter-TSS (NM_177167)	promoter-TSS (NM_177167)	-52	NM_177167	320472	Mm.341988	NM_177167	ENSMUSG00000046442	Ppm1e	AW049266|B930008A12Rik|POPX1|PP2CH|mKIAA1072	protein phosphatase 1E (PP2C domain containing)	protein-coding
mm_25659.1	chr3	121723516	121723534	+	1	NA	promoter-TSS (NM_010171)	promoter-TSS (NM_010171)	-12	NM_010171	14066	Mm.273188	NM_010171	ENSMUSG00000028128	F3	AA409063|CD142|Cf-3|Cf3|TF	coagulation factor III	protein-coding
mm_153942.1	chr19	47507874	47507893	-	1	NA	intron (NM_175360, intron 8 of 9)	intron (NM_175360, intron 8 of 9)	-5099	NR_045322	100503104	Mm.442735	NR_045322	ENSMUSG00000097990	Gm19557	-	predicted gene, 19557	ncRNA
mm_8827.1	chr1	162548485	162548545	-	1	NA	promoter-TSS (NM_144877)	promoter-TSS (NM_144877)	-170	NM_144877	71449	Mm.270569	NM_144877	ENSMUSG00000026694	Mettl13	5630401D24Rik	methyltransferase like 13	protein-coding
mm_100159.1	chr11	116330476	116330490	+	1	NA	TTS (NM_008240)	TTS (NM_008240)	4871	NM_008240	15223	Mm.378938	NM_008240	ENSMUSG00000034227	Foxj1	FKHL-13|HFH-4|Hfh4	forkhead box J1	protein-coding
mm_172620.1	chr8	20136657	20136662	+	1	NA	Intergenic	Intergenic	160773	NR_030708	547150	Mm.359054	NR_030708	ENSMUSG00000071796	6820431F20Rik	-	cadherin 11 pseudogene	pseudo
mm_87857.1	chr10	61175311	61175318	+	1	NA	promoter-TSS (NM_001017407)	promoter-TSS (NM_001017407)	52	NM_023064	65971	Mm.30227	NM_023064	ENSMUSG00000020096	Tbata	1700021K02Rik|AI428928|Spatial|Titest	thymus, brain and testes associated	protein-coding
mm_151579.1	chr19	61176099	61176122	+	1	NA	5' UTR (NM_001177513, exon 1 of 1)	5' UTR (NM_001177513, exon 1 of 1)	199	NM_001177513	633057	Mm.426097	NM_001177513	ENSMUSG00000094649	Gm7102	EG633057	predicted gene 7102	protein-coding
mm_10167.1	chr2	4431947	4431997	+	1	NA	intron (NM_001347086, intron 3 of 24)	intron (NM_001347086, intron 3 of 24)	30996	NM_001177843	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding
mm_39911.1	chr5	31297795	31297797	+	1	NA	intron (NM_144909, intron 1 of 18)	ID_B1|SINE|B4	215	NM_144909	231103	Mm.100043	NM_144909	ENSMUSG00000059434	Gckr	GKRP	glucokinase regulatory protein	protein-coding
mm_52292.1	chr6	108666128	108666151	+	1	NA	3' UTR (NM_011498, exon 5 of 5)	3' UTR (NM_011498, exon 5 of 5)	-5205	NR_104577	75394	Mm.395061	NR_040757	ENSMUSG00000087341	0610040F04Rik	-	RIKEN cDNA 0610040F04 gene	ncRNA
mm_3956.1	chr1	164115291	164115300	+	1	NA	promoter-TSS (NM_011347)	promoter-TSS (NM_011347)	31	NM_011347	20344	Mm.3337	NM_011347	ENSMUSG00000026580	Selp	CD62P|GMP-140|Grmp|LECAM3|PADGEM	selectin, platelet	protein-coding
mm_147794.1	chr18	61652420	61652440	-	1	NA	intron (NR_045402, intron 2 of 4)	intron (NR_045402, intron 2 of 4)	-3172	NR_029601	387161		NR_029601	ENSMUSG00000065445	Mir143	Mirn143|mir-143|mmu-mir-143	microRNA 143	ncRNA
mm_10248.1	chr2	9187838	9187848	+	1	NA	Intergenic	Intergenic	-1672	NR_038180	73438	Mm.23558	NR_038180	ENSMUSG00000085580	1700061F12Rik	-	RIKEN cDNA 1700061F12 gene	ncRNA
mm_108911.1	chr12	100206540	100206578	+	1	NA	3' UTR (NM_009790, exon 6 of 6)	3' UTR (NM_009790, exon 6 of 6)	6415	NM_001313934	12313	Mm.285993	NM_009790	ENSMUSG00000001175	Calm1	AI256814|AI327027|AI461935|AL024000|CaM|Calm	calmodulin 1	protein-coding
mm_18158.1	chr2	45095915	45095954	-	1	NA	intron (NM_001289521, intron 1 of 8)	intron (NM_001289521, intron 1 of 8)	14343	NM_001289521	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_132988.1	chr16	52453339	52453415	+	1	NA	promoter-TSS (NM_001331110)	promoter-TSS (NM_001331110)	-296	NM_001331110	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_70126.1	chr7	143087209	143087219	-	1	NA	intron (NM_020277, intron 4 of 24)	intron (NM_020277, intron 4 of 24)	7428	NM_020277	56843	Mm.286668	NM_020277	ENSMUSG00000009246	Trpm5	9430099A16Rik|LTrpC-5|Ltrpc5|Mtr1	transient receptor potential cation channel, subfamily M, member 5	protein-coding
mm_115756.1	chr13	19192760	19192771	-	1	NA	Intergenic	Intergenic	203048	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_139770.1	chr17	64717054	64717058	+	1	NA	intron (NM_008549, intron 16 of 21)	intron (NM_008549, intron 16 of 21)	-50055	NR_105051	101202683	Mm.393309	NR_105051		Dreh	-	down-regulated in hepatocellular carcinoma	ncRNA
mm_73763.1	chr8	115707427	115707509	+	1	NA	promoter-TSS (NM_001025577)	promoter-TSS (NM_001025577)	-574	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_168788.1	chr12	19118902	19118912	+	1	NA	Intergenic	MMVL30-int|LTR|ERV1	604397	NM_001201330	236366	Mm.352227	NM_001033157	ENSMUSG00000073197	5730507C01Rik	-	RIKEN cDNA 5730507C01 gene	protein-coding
mm_154743.1	chrX	10416641	10416662	+	1	NA	Intergenic	Intergenic	-68465	NM_019634	21912	Mm.18590	NM_019634	ENSMUSG00000058254	Tspan7	1200014P11Rik|A15|AI323365|Cd231|Mxs1|PE31|R74651|TALLA|Tm4sf2	tetraspanin 7	protein-coding
mm_136906.1	chr17	13016541	13016550	+	1	NA	3' UTR (NM_013671, exon 5 of 5)	3' UTR (NM_013671, exon 5 of 5)	8706	NM_013671	20656	Mm.290876	NM_013671	ENSMUSG00000006818	Sod2	MnSOD|Sod-2	superoxide dismutase 2, mitochondrial	protein-coding
mm_73663.1	chr8	111036886	111036899	+	1	NA	intron (NM_146217, intron 1 of 20)	intron (NM_146217, intron 1 of 20)	3050	NM_146217	234734	Mm.24174	NM_146217	ENSMUSG00000031960	Aars	AI316495|C76919|sti	alanyl-tRNA synthetase	protein-coding
mm_40376.1	chr5	52363957	52363980	+	1	NA	5' UTR (NM_011435, exon 1 of 2)	5' UTR (NM_011435, exon 1 of 2)	164	NM_011435	20657	Mm.2407	NM_011435	ENSMUSG00000072941	Sod3	AI314465|EC-SOD	superoxide dismutase 3, extracellular	protein-coding
mm_68013.1	chr7	100947609	100947642	-	1	NA	intron (NM_183168, intron 1 of 2)	intron (NM_183168, intron 1 of 2)	-15464	NM_001081116	207212	Mm.29954	NM_001081116	ENSMUSG00000032875	Arhgef17	8030463K16|AI428794|AW558066|BC035332|mKIAA0337	Rho guanine nucleotide exchange factor (GEF) 17	protein-coding
mm_155258.1	chrX	57224149	57224162	+	1	NA	TTS (NM_011616)	TTS (NM_011616)	12012	NM_011616	21947	Mm.4861	NM_011616	ENSMUSG00000031132	Cd40lg	CD154|CD40-L|Cd40l|HIGM1|IGM|IMD3|Ly-62|Ly62|T-BAM|TRAP|Tnfsf5|Tnlg8b|gp39	CD40 ligand	protein-coding
mm_113110.1	chr13	24416742	24416750	+	1	NA	intron (NM_007717, intron 1 of 15)	intron (NM_007717, intron 1 of 15)	1624	NM_001284520	12763	Mm.8396	NM_007717	ENSMUSG00000016756	Cmah	-	cytidine monophospho-N-acetylneuraminic acid hydroxylase	protein-coding
mm_1353.1	chr1	66321826	66321861	+	1	NA	5' UTR (NM_001310634, exon 1 of 15)	5' UTR (NM_001310634, exon 1 of 15)	119	NM_001310634	17756	Mm.256966	NM_008632	ENSMUSG00000015222	Map2	G1-397-34|MAP-2|Mtap-2|Mtap2|repro4	microtubule-associated protein 2	protein-coding
mm_38938.1	chr4	150197356	150197360	-	1	NA	exon (NM_009802, exon 3 of 8)	exon (NM_009802, exon 3 of 8)	3777	NM_009802	12353	Mm.232523	NM_009802	ENSMUSG00000028972	Car6	Ca6|DOC1	carbonic anhydrase 6	protein-coding
mm_106646.1	chr11	121054876	121054910	-	1	NA	exon (NM_026907, exon 5 of 5)	exon (NM_026907, exon 5 of 5)	8676	NM_026907	58210	Mm.116986	NM_026907	ENSMUSG00000039364	Sectm1b	1810003C24Rik|K12|Sectm1	secreted and transmembrane 1B	protein-coding
mm_81528.1	chr9	110062813	110062819	+	1	NA	intron (NM_001311163, intron 1 of 10)	intron (NM_001311163, intron 1 of 10)	10795	NM_001311164	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_77117.1	chr8	111253878	111253908	-	1	NA	intron (NM_009149, intron 1 of 25)	intron (NM_009149, intron 1 of 25)	5309	NM_009149	20340	Mm.276271	NM_009149	ENSMUSG00000003316	Glg1	AI593353|AW537898|CFR|CFR-1|ESL-1|MG-160|MG160|Selel	golgi apparatus protein 1	protein-coding
mm_62114.1	chr7	96619095	96619099	+	1	NA	intron (NM_011858, intron 5 of 32)	intron (NM_011858, intron 5 of 32)	182452	NR_045874	791381	Mm.402112	NR_045874	ENSMUSG00000053049	Gm15413	ENSMUSG00000053049|OTTMUSG00000021246	predicted gene 15413	ncRNA
mm_163006.1	chr11	36053021	36053021	+	1	NA	intron (NM_011856, intron 20 of 28)	intron (NM_011856, intron 20 of 28)	-72932	NM_170779	211652	Mm.31267	NM_170779	ENSMUSG00000018849	Wwc1	AA408228|AU017197|BC037006|Kibra|mKIAA0869	WW, C2 and coiled-coil domain containing 1	protein-coding
mm_33076.1	chr4	123904837	123904851	+	1	NA	promoter-TSS (NM_019660)	promoter-TSS (NM_019660)	-169	NM_019660	56309	Mm.446553	NM_019660	ENSMUSG00000028647	Mycbp	5730488M09Rik|AW552132|AW742590|Amy-1	MYC binding protein	protein-coding
mm_171929.1	chr5	61313963	61313963	-	1	NA	Intergenic	Intergenic	-494880	NM_019468	14380	Mm.347430	NM_019468	ENSMUSG00000089992	G6pd2	G6pdx-ps1|Gpd-2|Gpd2	glucose-6-phosphate dehydrogenase 2	protein-coding
mm_44318.1	chr5	9485642	9485645	-	1	NA	3' UTR (NM_181850, exon 6 of 6)	3' UTR (NM_181850, exon 6 of 6)	109939	NR_030537	100124492		NR_030537	ENSMUSG00000077896	Mir879	Mirn879|mir-879|mmu-mir-879	microRNA 879	ncRNA
mm_44625.1	chr5	25740515	25740551	-	1	NA	Intergenic	MLTR12|LTR|ERV1	-19440	NM_001310504	242894	Mm.150319	NM_001004365	ENSMUSG00000056367	Actr3b	9630005C02|ARP11|AW047569|Arp3b|Arp3beta	ARP3 actin-related protein 3B	protein-coding
mm_7637.1	chr1	127896965	127896969	-	1	NA	intron (NM_178690, intron 5 of 23)	IAPLTR1_Mm|LTR|ERVK	28194	NM_178690	226407	Mm.489713	NM_178690	ENSMUSG00000036104	Rab3gap1	1700003B17Rik|4732493F09Rik|AL117896|Rab3gap|p130	RAB3 GTPase activating protein subunit 1	protein-coding
mm_84505.1	chr9	67023247	67023261	-	1	NA	TTS (NM_001164256)	TTS (NM_001164256)	20617	NM_001164252	22003	Mm.121878	NM_024427	ENSMUSG00000032366	Tpm1	AA986836|AI854628|TM2|Tm3|Tmpa|Tpm-1|alpha-TM	tropomyosin 1, alpha	protein-coding
mm_102112.1	chr11	53269777	53269815	-	1	NA	exon (NM_008300, exon 12 of 19)	exon (NM_008300, exon 12 of 19)	30683	NM_008300	15525	Mm.239865	NM_008300	ENSMUSG00000020361	Hspa4	70kDa|AI317151|APG-2|Hsp110|Hsp70RY|mKIAA4025	heat shock protein 4	protein-coding
mm_20131.1	chr2	121355067	121355084	-	1	NA	Intergenic	CpG	-3566	NM_009897	12716	Mm.252145	NM_009897	ENSMUSG00000000308	Ckmt1	Mt-CK|ScCKmit|UbCKmit|mi-CK	creatine kinase, mitochondrial 1, ubiquitous	protein-coding
mm_54279.1	chr6	29201158	29201169	-	1	NA	3' UTR (NM_011829, exon 14 of 14)	3' UTR (NM_011829, exon 14 of 14)	11134	NM_011829	23917	Mm.260707	NM_011829	ENSMUSG00000003500	Impdh1	B930086D20Rik|IMPDH-I	inosine 5'-phosphate dehydrogenase 1	protein-coding
mm_79446.1	chr9	56095553	56095583	+	1	NA	intron (NM_011193, intron 1 of 14)	intron (NM_011193, intron 1 of 14)	5592	NM_011193	19200	Mm.2534	NM_011193	ENSMUSG00000032322	Pstpip1	CD2BP1|def-2	proline-serine-threonine phosphatase-interacting protein 1	protein-coding
mm_40700.1	chr5	65860939	65860976	+	1	NA	Intergenic	Intergenic	-2612	NM_001081105	74734	Mm.20323	NM_001081105	ENSMUSG00000029204	Rhoh	5830400A04Rik|AU019774|Arhh	ras homolog family member H	protein-coding
mm_50753.1	chr6	53287330	53287342	+	1	NA	promoter-TSS (NM_001327821)	promoter-TSS (NM_001327821)	33	NM_001327821	231991	Mm.227444	NM_172728	ENSMUSG00000053007	Creb5	9430076C15Rik|CRE-BPa|Crebpa|D430026C09Rik	cAMP responsive element binding protein 5	protein-coding
mm_84018.1	chr9	57677141	57677145	-	1	NA	3' UTR (NM_009993, exon 7 of 7)	3' UTR (NM_009993, exon 7 of 7)	6512	NM_009993	13077	Mm.15537	NM_009993	ENSMUSG00000032310	Cyp1a2	CP12|Cyp1a1|P450-3	cytochrome P450, family 1, subfamily a, polypeptide 2	protein-coding
mm_28762.1	chr3	95882233	95882244	-	1	NA	promoter-TSS (NM_001033302)	promoter-TSS (NM_001033302)	-10	NM_001033302	229599	Mm.331218	NM_001033302	ENSMUSG00000038550	Ciart	Chrono|Gm129	circadian associated repressor of transcription	protein-coding
mm_88472.1	chr10	77606218	77606240	+	1	NA	promoter-TSS (NM_001301671)	promoter-TSS (NM_001301671)	132	NM_019929	20610	Mm.24433	NM_019929	ENSMUSG00000020265	Sumo3	2810014B19Rik|D10Ertd345e|SMT3A|SUMO-3|Smt3h1	small ubiquitin-like modifier 3	protein-coding
mm_9579.1	chr1	174028271	174028279	-	1	NA	exon (NM_172648, exon 2 of 7)	exon (NM_172648, exon 2 of 7)	3480	NM_172648	226695	Mm.425061	NM_172648	ENSMUSG00000054203	Ifi205	D3|D3cDNA|Ifi205a	interferon activated gene 205	protein-coding
mm_32376.1	chr4	106316050	106316070	+	1	NA	promoter-TSS (NM_183225)	promoter-TSS (NM_183225)	-153	NM_183225	329908	Mm.234544	NM_183225	ENSMUSG00000028514	Usp24	2700066K03Rik|2810030C21Rik|AI414051|B130021E18|C79851	ubiquitin specific peptidase 24	protein-coding
mm_63809.1	chr7	133709336	133709348	+	1	NA	promoter-TSS (NM_025392)	promoter-TSS (NM_025392)	9	NM_025392	66165	Mm.389983	NM_025392	ENSMUSG00000030983	Bccip	1110013J05Rik|TOK-1	BRCA2 and CDKN1A interacting protein	protein-coding
mm_163905.1	chr14	30607770	30607774	-	1	NA	intron (NM_011103, intron 3 of 17)	intron (NM_011103, intron 3 of 17)	2538	NM_001310682	18753	Mm.2314	NM_011103	ENSMUSG00000021948	Prkcd	AI385711|D14Ertd420e|PKC[d]|PKCdelta|Pkcd	protein kinase C, delta	protein-coding
mm_28993.1	chr3	101300198	101300206	-	1	NA	Intergenic	Intergenic	-12263	NM_013486	12481	Mm.22842	NM_013486	ENSMUSG00000027863	Cd2	LFA-2|Ly-37|Ly37	CD2 antigen	protein-coding
mm_112162.1	chr12	113330503	113330514	-	1	NA	Intergenic	Intergenic	144605	NM_153776	69195	Mm.313244	NM_153776	ENSMUSG00000049036	Tmem121	2410008J05Rik|Hole	transmembrane protein 121	protein-coding
mm_44612.1	chr5	25496370	25496373	-	1	NA	intron (NM_001081383, intron 1 of 58)	intron (NM_001081383, intron 1 of 58)	2412	NM_001081383	231051	Mm.332268	NM_001081383	ENSMUSG00000038056	Kmt2c	E330008K23Rik|HALR|Mll3|mKIAA1506	lysine (K)-specific methyltransferase 2C	protein-coding
mm_15010.1	chr2	152563242	152563247	+	1	NA	Intergenic	Intergenic	-9500	NM_207276	403172	Mm.84518	NM_207276	ENSMUSG00000056544	Defb21	4930525K10Rik|Gm121	defensin beta 21	protein-coding
mm_93017.1	chr10	87809441	87809452	-	1	NA	Intergenic	Lx5c|LINE|L1	-48819	NM_001314010	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_143141.1	chr17	57221042	57221052	-	1	NA	exon (NM_009778, exon 17 of 41)	exon (NM_009778, exon 17 of 41)	-3819	NR_105944	102465591		NR_105944	ENSMUSG00000099066	Mir6978	Gm27858|mmu-mir-6978	microRNA 6978	ncRNA
mm_156878.1	chrX	166238798	166238811	+	1	NA	promoter-TSS (NM_001177961)	promoter-TSS (NM_001177961)	-139	NM_001177961	14758	Mm.222320	NM_023122	ENSMUSG00000031342	Gpm6b	AI593561|Gpm6|M6B	glycoprotein m6b	protein-coding
mm_97195.1	chr11	75577091	75577124	+	1	NA	3' UTR (NM_001199283, exon 14 of 14)	3' UTR (NM_001199283, exon 14 of 14)	-10972	NM_008850	18738	Mm.3128	NM_008850	ENSMUSG00000017781	Pitpna	Pitpn|vb|vibrator	phosphatidylinositol transfer protein, alpha	protein-coding
mm_125884.1	chr15	75822206	75822213	+	1	NA	intron (NM_172121, intron 3 of 11)	intron (NM_172121, intron 3 of 11)	19699	NM_172121	223642	Mm.209800	NM_172121	ENSMUSG00000075600	Zc3h3	BC049953|Kiaa0150|Smicl|Zc3hdc3	zinc finger CCCH type containing 3	protein-coding
mm_34614.1	chr4	150371936	150371956	+	1	NA	intron (NM_001085492, intron 1 of 22)	CpG	90030	NM_001085492	68703	Mm.291274	NM_001085492	ENSMUSG00000039852	Rere	1110033A15Rik|AI414665|ARG|ARP|ATN1L|AW742570|Atr2|DNB1|eye<m03Jus>|eyes3|mKIAA0458	arginine glutamic acid dipeptide (RE) repeats	protein-coding
mm_46405.1	chr5	104093114	104093140	-	1	NA	exon (NM_010097, exon 4 of 11)	exon (NM_010097, exon 4 of 11)	-15519	NM_001163772	100271704	Mm.366664	NM_001163772	ENSMUSG00000091034	Gm17660	Scpppq1	predicted gene, 17660	protein-coding
mm_128606.1	chr15	58352844	58352860	-	1	NA	exon (NM_027211, exon 4 of 9)	exon (NM_027211, exon 4 of 9)	-28683	NM_177755	268807	Mm.124498	NM_177755	ENSMUSG00000022357	Klhl38	8230402K04Rik	kelch-like 38	protein-coding
mm_22835.1	chr3	27482512	27482522	+	1	NA	intron (NM_173182, intron 11 of 25)	intron (NM_173182, intron 11 of 25)	102478	NR_037275	100526525		NR_037275	ENSMUSG00000092695	Mir3092	mir-3092|mmu-mir-3092	microRNA 3092	ncRNA
mm_148838.1	chr19	6363897	6363941	+	1	NA	non-coding (NR_122118, exon 1 of 12)	non-coding (NR_122118, exon 1 of 12)	229	NR_122118	22668	Mm.256422	NM_011750	ENSMUSG00000024949	Sf1	BBP|MZFM|WBP4|Zfp162	splicing factor 1	protein-coding
mm_116066.1	chr13	27610581	27610583	-	1	NA	promoter-TSS (NM_029355)	promoter-TSS (NM_029355)	0	NM_029355	75596	Mm.46087	NM_029355	ENSMUSG00000021347	Prl7b1	1600014J19Rik|Ghd17|PLP-N|Prlpn	prolactin family 7, subfamily b, member 1	protein-coding
mm_146284.1	chr18	78030029	78030047	+	1	NA	exon (NM_001195633, exon 42 of 44)	exon (NM_001195633, exon 42 of 44)	27230	NM_001101038	620235	Mm.35607	NM_001101038	ENSMUSG00000091055	Siglec15	Cd33l3|EG620235|SIGLEC-I	sialic acid binding Ig-like lectin 15	protein-coding
mm_139901.1	chr17	70853744	70853760	+	1	NA	promoter-TSS (NM_001164074)	promoter-TSS (NM_001164074)	-220	NM_001164074	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_120557.1	chr14	68086709	68086720	+	1	NA	exon (NM_010910, exon 3 of 4)	exon (NM_010910, exon 3 of 4)	2830	NM_010910	18039	Mm.1956	NM_010910	ENSMUSG00000022055	Nefl	AI847934|CMT2E|NF-L|NF68|Nfl	neurofilament, light polypeptide	protein-coding
mm_163232.1	chr11	103363645	103363659	-	1	NA	promoter-TSS (NM_183288)	promoter-TSS (NM_183288)	40	NM_183288	544817	Mm.259113	NM_133715	ENSMUSG00000034255	Arhgap27	2310069I04Rik|5730442P18Rik|Gm21552|Sh3d20	Rho GTPase activating protein 27	protein-coding
mm_131858.1	chr16	23079728	23079731	+	1	NA	exon (NM_001102411, exon 10 of 10)	exon (NM_001102411, exon 10 of 10)	21429	NM_001102412	16644	Mm.2160	NM_023125	ENSMUSG00000022875	Kng1	Kng	kininogen 1	protein-coding
mm_74163.1	chr8	123407094	123407114	+	1	NA	promoter-TSS (NM_008559)	promoter-TSS (NM_008559)	22	NM_008559	17199	Mm.324942	NM_008559	ENSMUSG00000074037	Mc1r	Mcr1|Mshra|Tob|e	melanocortin 1 receptor	protein-coding
mm_17739.1	chr2	32704145	32704157	-	1	NA	Intergenic	Intergenic	8633	NM_130860	107951	Mm.27557	NM_130860	ENSMUSG00000009555	Cdk9	PITALRE	cyclin-dependent kinase 9 (CDC2-related kinase)	protein-coding
mm_102215.1	chr11	54908641	54908651	-	1	NA	exon (NM_008161, exon 3 of 5)	exon (NM_008161, exon 3 of 5)	5792	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_64568.1	chr7	144897048	144897056	+	1	NA	intron (NM_008003, intron 1 of 2)	CpG	520	NM_008003	14170	Mm.3904	NM_008003	ENSMUSG00000031073	Fgf15	FGF19	fibroblast growth factor 15	protein-coding
mm_51593.1	chr6	83914355	83914411	+	1	NA	promoter-TSS (NM_001166371)	promoter-TSS (NM_001166371)	30	NM_008717	18139	Mm.132392	NM_008717	ENSMUSG00000030016	Zfp638	AI323587|Np220|Zfml|Znf638|mNP220	zinc finger protein 638	protein-coding
mm_149678.1	chr19	20492266	20492272	+	1	NA	promoter-TSS (NR_015502)	promoter-TSS (NR_015502)	-446	NR_015502	320092	Mm.482524	NR_015502		E030003E18Rik	1700127G21Rik	RIKEN cDNA E030003E18 gene	ncRNA
mm_2944.1	chr1	132342016	132342042	+	1	NA	Intergenic	Intergenic	25904	NM_001195025	74137	Mm.100666	NM_028778	ENSMUSG00000009772	Nuak2	1200013B22Rik|Omphk2|Snark|mKIAA0537	NUAK family, SNF1-like kinase, 2	protein-coding
mm_150043.1	chr19	29378183	29378251	+	1	NA	intron (NM_021893, intron 3 of 6)	intron (NM_021893, intron 3 of 6)	10779	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_78513.1	chr9	32913060	32913066	+	1	NA	intron (NR_131058, intron 1 of 3)	intron (NR_131058, intron 1 of 3)	15903	NR_131058	330917	Mm.488283	NR_131058		Gm27162	A430016B06	predicted gene 27162	ncRNA
mm_168808.1	chr12	20624098	20624098	-	1	NA	Intergenic	Intergenic	191681	NR_015521	69513	Mm.273972	NR_015521	ENSMUSG00000099759	1700030C10Rik	-	RIKEN cDNA 1700030C10 gene	ncRNA
mm_115692.1	chr13	14039577	14039589	-	1	NA	promoter-TSS (NM_178337)	promoter-TSS (NM_178337)	55	NR_130788	70430	Mm.260209	NM_178337	ENSMUSG00000039233	Tbce	2610206D02Rik|C530005D02Rik|pmn	tubulin-specific chaperone E	protein-coding
mm_79119.1	chr9	46480350	46480359	+	1	NA	Intergenic	Intergenic	-160368	NM_183104	74361	Mm.159169	NM_183104	ENSMUSG00000056617	4931429L15Rik	-	RIKEN cDNA 4931429L15 gene	protein-coding
mm_85055.1	chr9	90114813	90114821	-	1	NA	promoter-TSS (NM_024431)	promoter-TSS (NM_024431)	3	NM_001039147	21761	Mm.426209	NM_024431	ENSMUSG00000062270	Morf4l1	MORFRG15|MRG15|TEG-189|Tex189|mKIAA4002	mortality factor 4 like 1	protein-coding
mm_85064.1	chr9	90270713	90270799	-	1	NA	promoter-TSS (NM_194334)	promoter-TSS (NM_194334)	13	NM_194334	67016	Mm.335347	NM_194334	ENSMUSG00000037410	Tbc1d2b	1810061M12Rik|AI480956|AV021536|AV023399|AW491493|mKIAA1055	TBC1 domain family, member 2B	protein-coding
mm_28454.1	chr3	90659442	90659448	-	1	NA	Intergenic	Intergenic	5143	NM_199422	381493	Mm.291525	NM_199422	ENSMUSG00000063767	S100a7a	AY465109|Gm1020|S100A7L1|S100A7f|S100a15|S100a15a|S100a17l1	S100 calcium binding protein A7A	protein-coding
mm_110581.1	chr12	56522186	56522198	-	1	NA	intron (NR_045082, intron 1 of 6)	intron (NR_045082, intron 1 of 6)	7228	NR_045082	104798	Mm.310950	NR_045082		E030019B13Rik	AI413669	RIKEN cDNA E030019B13 gene	ncRNA
mm_150322.1	chr19	34574079	34574095	+	1	NA	exon (NM_008332, exon 3 of 3)	exon (NM_008332, exon 3 of 3)	-9442	NM_010501	15959	Mm.426079	NM_010501	ENSMUSG00000074896	Ifit3	Ifi49|P49	interferon-induced protein with tetratricopeptide repeats 3	protein-coding
mm_59959.1	chr7	30427483	30427503	+	1	NA	exon (NM_172142, exon 10 of 11)	exon (NM_172142, exon 10 of 11)	4189	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_19525.1	chr2	94157882	94157915	-	1	NA	promoter-TSS (NM_019657)	promoter-TSS (NM_019657)	11	NM_019657	56348	Mm.22505	NM_019657	ENSMUSG00000027195	Hsd17b12	2610510O05Rik|AI172963|KIK-I|Kik1	hydroxysteroid (17-beta) dehydrogenase 12	protein-coding
mm_76708.1	chr8	94601543	94601556	-	1	NA	promoter-TSS (NM_026274)	promoter-TSS (NM_026274)	177	NM_028221	102122	Mm.250425	NM_028221	ENSMUSG00000031774	Fam192a	1700001O11Rik|2310065K24Rik|AI596259|Nip30	family with sequence similarity 192, member A	protein-coding
mm_720.1	chr1	42699642	42699652	+	1	NA	promoter-TSS (NR_027891)	promoter-TSS (NR_027891)	-689	NR_027891	73100	Mm.467885	NR_027891		2900092D14Rik	-	RIKEN cDNA 2900092D14 gene	ncRNA
mm_65195.1	chr7	19696795	19696805	-	1	NA	exon (NM_009696, exon 4 of 4)	exon (NM_009696, exon 4 of 4)	1598	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_66728.1	chr7	46238517	46238538	-	1	NA	promoter-TSS (NM_153677)	promoter-TSS (NM_153677)	-37	NM_153677	72088	Mm.119709	NM_023649	ENSMUSG00000030838	Ush1c	2010016F01Rik|harmonin	Usher syndrome 1C	protein-coding
mm_9765.1	chr1	180947584	180947584	-	1	NA	intron (NM_144794, intron 2 of 22)	MT2C_Mm|LTR|ERVL	5066	NM_144794	208795	Mm.185518	NM_144794	ENSMUSG00000026519	Tmem63a	BC014795|Tmem64a	transmembrane protein 63a	protein-coding
mm_87641.1	chr10	58371594	58371604	+	1	NA	exon (NM_201242, exon 1 of 10)	exon (NM_201242, exon 1 of 10)	145	NM_201242	110829	Mm.57734	NM_026148	ENSMUSG00000019920	Lims1	2310016J22Rik|4921524A02Rik|AI507642|AU021743|AW551584|C430041B13Rik|Lims1l|PINCH|PINCH1	LIM and senescent cell antigen-like domains 1	protein-coding
mm_168528.1	chr11	60352908	60352908	-	1	NA	promoter-TSS (NM_001039093)	promoter-TSS (NM_001039093)	-3	NM_001039092	216810	Mm.218875	NM_153080	ENSMUSG00000000538	Tom1l2	2900016I08Rik|A730055F12Rik|AU042072|Srebf1	target of myb1-like 2 (chicken)	protein-coding
mm_158714.1	chrX	162643464	162643474	-	1	NA	exon (NM_001290633, exon 1 of 18)	exon (NM_001290633, exon 1 of 18)	189	NM_001290633	194590	Mm.442441	NM_178256	ENSMUSG00000040855	Reps2	POB1	RALBP1 associated Eps domain containing protein 2	protein-coding
mm_125225.1	chr15	34123713	34123728	+	1	NA	exon (NM_026002, exon 7 of 12)	exon (NM_026002, exon 7 of 12)	41001	NM_026002	67154	Mm.130883	NM_026002	ENSMUSG00000022255	Mtdh	2610103J23Rik|3D3|3D3/Lyric|AEG-1|AV353288|D8Bwg1112e|Lyric	metadherin	protein-coding
mm_116661.1	chr13	49195993	49196007	-	1	NA	3' UTR (NM_013610, exon 4 of 4)	3' UTR (NM_013610, exon 4 of 4)	8453	NM_013610	18081	Mm.18503	NM_013610	ENSMUSG00000037966	Ninj1	AU024536	ninjurin 1	protein-coding
mm_27134.1	chr3	32365893	32365913	-	1	NA	promoter-TSS (NM_009517)	promoter-TSS (NM_009517)	-238	NM_009517	22401	Mm.35705	NM_009517	ENSMUSG00000027663	Zmat3	Wig1	zinc finger matrin type 3	protein-coding
mm_48407.1	chr5	140261562	140261570	-	1	NA	exon (NM_010752, exon 10 of 18)	exon (NM_010752, exon 10 of 18)	59986	NM_010752	17120	Mm.27250	NM_010752	ENSMUSG00000029554	Mad1l1	AI173502|AW550425|Mad1	MAD1 mitotic arrest deficient 1-like 1	protein-coding
mm_105964.1	chr11	115463672	115463702	-	1	NA	intron (NM_001080934, intron 1 of 3)	intron (NM_001080934, intron 1 of 3)	1214	NM_001080934	217316	Mm.25773	NM_001080934	ENSMUSG00000045775	Slc16a5	A130015N09Rik|MCT 5|MCT 6|MCT5	solute carrier family 16 (monocarboxylic acid transporters), member 5	protein-coding
mm_83706.1	chr9	50727922	50728008	-	1	NA	promoter-TSS (NM_178118)	promoter-TSS (NM_178118)	19	NM_178118	330938	Mm.82598	NM_178118	ENSMUSG00000032064	Dixdc1	4930563F16Rik|BC048182|Ccd1|Ccd1Aalpha1L|Ccd1Abeta1L|Ccd1BalphaL|Ccd1BbetaL|Ccd1CL|mKIAA1735	DIX domain containing 1	protein-coding
mm_81215.1	chr9	107587674	107587680	+	1	NA	promoter-TSS (NM_025903)	promoter-TSS (NM_025903)	-41	NM_025903	15983	Mm.215335	NM_025903	ENSMUSG00000010048	Ifrd2	1810034A24Rik|AA470234|AI838527|SKMc15	interferon-related developmental regulator 2	protein-coding
mm_171501.1	chr4	146270287	146270288	+	1	NA	promoter-TSS (NM_001083918).2	promoter-TSS (NM_001083918).2	-98	NM_001083918	666532	Mm.392861	NM_001083918	ENSMUSG00000067916	Zfp991	Gm13139|OTTMUSG00000010657	zinc finger protein 991	protein-coding
mm_7508.1	chr1	123470652	123470655	-	1	NA	intron (NM_199021, intron 7 of 25)	L1_Mur3|LINE|L1	574906	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_15001.1	chr2	152477004	152477006	+	1	NA	promoter-TSS (NM_176950)	promoter-TSS (NM_176950)	-58	NM_176950	319579	Mm.190454	NM_176950	ENSMUSG00000049560	Defb20	9230107O10Rik|BD-20|mBD-20	defensin beta 20	protein-coding
mm_84963.1	chr9	83806160	83806170	-	1	NA	5' UTR (NM_148941, exon 1 of 6)	5' UTR (NM_148941, exon 1 of 6)	140	NM_148941	83603	Mm.83949	NM_148941	ENSMUSG00000032262	Elovl4	-	elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 4	protein-coding
mm_109812.1	chr12	3426677	3426691	-	1	NA	promoter-TSS (NM_172421)	promoter-TSS (NM_172421)	63	NR_030694	100043040	Mm.415417	NR_030694	ENSMUSG00000071456	1110002L01Rik	-	RIKEN cDNA 1110002L01 gene	ncRNA
mm_1385.1	chr1	66944850	66944890	+	1	NA	exon (NM_021285, exon 1 of 7)	exon (NM_021285, exon 1 of 7)	186	NM_021285	17901	Mm.1000	NM_021285	ENSMUSG00000061816	Myl1	AI325107|MLC1f|MLC3f|Mylf	myosin, light polypeptide 1	protein-coding
mm_123432.1	chr14	64440935	64440955	-	1	NA	promoter-TSS (NM_001253715)	promoter-TSS (NM_001253715)	81	NM_001253715	110265	Mm.26713	NM_026322	ENSMUSG00000054733	Msra	2310045J23Rik|6530413P12Rik|MSR-A	methionine sulfoxide reductase A	protein-coding
mm_125560.1	chr15	58889209	58889231	+	1	NA	promoter-TSS (NM_175226)	promoter-TSS (NM_175226)	-9	NM_175226	75841	Mm.4537	NM_175226	ENSMUSG00000037075	Rnf139	4930555P18Rik	ring finger protein 139	protein-coding
mm_115926.1	chr13	23571117	23571125	-	1	NA	promoter-TSS (NM_178196)	promoter-TSS (NM_178196)	99	NM_178187	319166	Mm.261665	NM_178187	ENSMUSG00000069272	Hist1h2ae	1190022L06	histone cluster 1, H2ae	protein-coding
mm_90096.1	chr10	116964735	116964745	+	1	NA	promoter-TSS (NR_027847)	promoter-TSS (NR_027847)	0	NR_027847	103175	Mm.27138	NR_027846	ENSMUSG00000031294	D630029K05Rik	AI314111|AI875589	RIKEN cDNA D630029K05 gene	ncRNA
mm_124719.1	chr15	6579927	6579937	+	1	NA	promoter-TSS (NM_001278269)	promoter-TSS (NM_001278269)	85	NM_011815	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_145710.1	chr18	62922482	62922494	+	1	NA	5' UTR (NM_133237, exon 1 of 5)	5' UTR (NM_133237, exon 1 of 5)	161	NM_133237	494504	Mm.391102	NM_133237	ENSMUSG00000071847	Apcdd1	AB023957|AU041258|Drapc1|EIG180	adenomatosis polyposis coli down-regulated 1	protein-coding
mm_166327.1	chr5	112292198	112292200	+	1	NA	intron (NM_001326590, intron 1 of 5)	intron (NM_001326590, intron 1 of 5)	15508	NM_009419	22022	Mm.250631	NM_009419	ENSMUSG00000029344	Tpst2	AI448750|D5Ucla3|Tango13b|grm|grt	protein-tyrosine sulfotransferase 2	protein-coding
mm_102958.1	chr11	69664779	69664930	-	1	NA	non-coding (NR_110993, exon 4 of 5)	non-coding (NR_110993, exon 4 of 5)	1316	NM_001291058	12514	Mm.15819	NM_009853	ENSMUSG00000018774	Cd68	Lamp4|Scard1|gp110	CD68 antigen	protein-coding
mm_58312.1	chr6	146289412	146289424	-	1	NA	intron (NM_010586, intron 36 of 55)	B3|SINE|B2	212805	NM_010586	16439	Mm.7800	NM_010586	ENSMUSG00000030287	Itpr2	AI649341|InsP3R-2|InsP3R-5|Ip3r2|Itpr5|insP3R2	inositol 1,4,5-triphosphate receptor 2	protein-coding
mm_162361.1	chr1	62938388	62938393	+	1	NA	Intergenic	Intergenic	-143658	NR_040601	74992	Mm.401979	NR_040601		4930487H11Rik	-	RIKEN cDNA 4930487H11 gene	ncRNA
mm_42713.1	chr5	120433200	120433215	+	1	NA	intron (NM_008499, intron 1 of 4)	(T)n|Simple_repeat|Simple_repeat	1321	NM_008499	16873	Mm.5151	NM_008499	ENSMUSG00000029595	Lhx5	Lim2	LIM homeobox protein 5	protein-coding
mm_141405.1	chr17	29347801	29347811	-	1	NA	promoter-TSS (NM_019880)	promoter-TSS (NM_019880)	98	NM_019880	56462	Mm.285322	NM_019880	ENSMUSG00000024012	Mtch1	2310034O17Rik|AI255158|AU018396|C77849|PSAP	mitochondrial carrier 1	protein-coding
mm_151128.1	chr19	48205478	48205511	+	1	NA	promoter-TSS (NM_025696)	promoter-TSS (NM_025696)	-531	NM_025696	66673	Mm.70980	NM_025696	ENSMUSG00000063434	Sorcs3	6330404A12Rik|AW045579	sortilin-related VPS10 domain containing receptor 3	protein-coding
mm_32423.1	chr4	107126673	107126689	+	1	NA	Intergenic	Intergenic	29790	NM_172873	242603	Mm.257231	NM_172873	ENSMUSG00000047636	Cdcp2	D030010E02Rik	CUB domain containing protein 2	protein-coding
mm_45505.1	chr5	72503383	72503393	-	1	NA	intron (NM_001122756, intron 1 of 21)	intron (NM_001122756, intron 1 of 21)	820	NM_016869	53419	Mm.332425	NM_016869	ENSMUSG00000005220	Corin	AV273130|Lrp4	corin	protein-coding
mm_121188.1	chr14	103049638	103049666	+	1	NA	exon (NM_008392, exon 3 of 5)	exon (NM_008392, exon 3 of 5)	2640	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_81303.1	chr9	108339777	108339920	+	1	NA	exon (NM_008160, exon 2 of 2)	exon (NM_008160, exon 2 of 2)	768	NM_001329528	14775	Mm.1090	NM_008160	ENSMUSG00000063856	Gpx1	AI195024|AL033363|CGPx|GPx-1|GSHPx-1|Gpx	glutathione peroxidase 1	protein-coding
mm_128448.1	chr15	50772025	50772031	-	1	NA	intron (NM_001310485, intron 5 of 7)	intron (NM_001310485, intron 5 of 7)	117021	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_37688.1	chr4	129230811	129230830	-	1	NA	intron (NM_001285867, intron 1 of 6)	ID_B1|SINE|B4	-2909	NM_001285866	97130	Mm.331907	NM_001033189	ENSMUSG00000050390	C77080	Kiaa1522|mKIAA1522	expressed sequence C77080	protein-coding
mm_72456.1	chr8	83200857	83200874	+	1	NA	intron (NM_027758, intron 1 of 17)	intron (NM_027758, intron 1 of 17)	35513	NM_027758	71310	Mm.24031	NM_027758	ENSMUSG00000031709	Tbc1d9	4933431N12Rik|AI847101|AW490653|C76116	TBC1 domain family, member 9	protein-coding
mm_53311.1	chr6	129182679	129182689	+	1	NA	intron (NM_053109, intron 1 of 4)	B3A|SINE|B2	2069	NM_053109	93694	Mm.197536	NM_053109	ENSMUSG00000030157	Clec2d	Clr-b|Clrb|Ocil	C-type lectin domain family 2, member d	protein-coding
mm_58084.1	chr6	136941888	136941911	-	1	NA	promoter-TSS (NM_007486)	promoter-TSS (NM_007486)	0	NM_001301301	11857	Mm.2241	NM_007486	ENSMUSG00000030220	Arhgdib	D4|Gdid4|Ly-GDI	Rho, GDP dissociation inhibitor (GDI) beta	protein-coding
mm_135743.1	chr16	55895185	55895214	-	1	NA	promoter-TSS (NM_001134457)	promoter-TSS (NM_001134457)	80	NM_001134457	385658	Mm.310635	NM_001134457	ENSMUSG00000075033	Nxpe3	Fam55c|Gm1752|Gm611	neurexophilin and PC-esterase domain family, member 3	protein-coding
mm_84593.1	chr9	70036811	70036817	-	1	NA	5' UTR (NM_028087, exon 2 of 3)	5' UTR (NM_028087, exon 2 of 3)	1274	NM_028087	72077	Mm.195555	NM_028087	ENSMUSG00000032226	Gcnt3	2010013H22Rik|2210021I22Rik|2210401J11Rik	glucosaminyl (N-acetyl) transferase 3, mucin type	protein-coding
mm_99230.1	chr11	101062501	101062517	+	1	NA	3' UTR (NM_001243049, exon 21 of 21)	3' UTR (NM_001243049, exon 21 of 21)	-7585	NM_013792	27419	Mm.95452	NM_013792	ENSMUSG00000001751	Naglu	-	alpha-N-acetylglucosaminidase (Sanfilippo disease IIIB)	protein-coding
mm_41953.1	chr5	105767283	105767326	+	1	NA	intron (NM_001122768, intron 2 of 2)	intron (NM_001122768, intron 2 of 2)	66494	NM_178701	231549	Mm.23837	NM_178701	ENSMUSG00000046079	Lrrc8d	2810473G09Rik|4930525N13Rik|A930019F03|Lrrc5	leucine rich repeat containing 8D	protein-coding
mm_140831.1	chr17	23645233	23645261	-	1	NA	promoter-TSS (NM_001033339)	promoter-TSS (NM_001033339)	22	NM_001033339	240047	Mm.235343	NM_001033339	ENSMUSG00000023903	Mmp25	F730048C11Rik|Leukolysin|MMP20|MT6-MMP	matrix metallopeptidase 25	protein-coding
mm_66719.1	chr7	46100628	46100670	-	1	NA	promoter-TSS (NM_010602)	promoter-TSS (NM_010602)	115	NM_001204411	16514	Mm.333863	NM_010602	ENSMUSG00000096146	Kcnj11	Kir6.2|mBIR	potassium inwardly rectifying channel, subfamily J, member 11	protein-coding
mm_148476.1	chr19	4100937	4100987	+	1	NA	5' UTR (NM_008851, exon 1 of 23)	5' UTR (NM_008851, exon 1 of 23)	340	NM_008851	18739	Mm.1860	NM_008851	ENSMUSG00000024851	Pitpnm1	DRES9|Mpt-1|Nir-2|PITPnm 1|Pitpnm|R75447|Rd9|RdgB|RdgB1	phosphatidylinositol transfer protein, membrane-associated 1	protein-coding
mm_129341.1	chr15	77842048	77842058	-	1	NA	5' UTR (NM_022410, exon 1 of 41)	5' UTR (NM_022410, exon 1 of 41)	122	NM_022410	17886	Mm.29677	NM_022410	ENSMUSG00000022443	Myh9	Fltn|Myhn-1|Myhn1|NMHCIIA|NMMHC-A|NMMHC-IIA|TU72.6	myosin, heavy polypeptide 9, non-muscle	protein-coding
mm_166122.1	chr4	152199890	152199899	+	1	NA	promoter-TSS (NM_001146058)	promoter-TSS (NM_001146058)	50	NM_001146058	70025	Mm.296191	NM_133348	ENSMUSG00000028937	Acot7	2410041A17Rik|Ach1|Act|Bach|CTE-IIa|Cte-II|Lach1	acyl-CoA thioesterase 7	protein-coding
mm_59333.1	chr7	25431730	25431734	+	1	NA	intron (NR_015569, intron 4 of 6)	intron (NR_015569, intron 4 of 6)	-18846	NM_153576	232983	Mm.10545	NM_153576	ENSMUSG00000060188	Cxcl17	VCC-1|Vcc1	chemokine (C-X-C motif) ligand 17	protein-coding
mm_26875.1	chr3	17694613	17694614	-	1	NA	Intergenic	Lx6|LINE|L1	-95308	NR_033490	70441	Mm.458192	NR_033490	ENSMUSG00000100252	Mir124-2hg	100040120|2610100L16Rik|6430547I21Rik|A930005K07Rik|AW125202|Gm2612	Mir124-2 host gene (non-protein coding)	ncRNA
mm_157293.1	chrX	20862298	20862308	-	1	NA	TTS (NR_049190)	TTS (NR_049190)	879	NR_049190	100885829		NR_049190	ENSMUSG00000093408	Mir5617	Gm25192|mir-5617|mmu-mir-5617	microRNA 5617	ncRNA
mm_265.1	chr1	20917857	20917859	+	1	NA	intron (NM_028829, intron 1 of 2)	intron (NM_028829, intron 1 of 2)	27236	NM_028829	74229	Mm.40780	NM_028829	ENSMUSG00000025931	Paqr8	1700019B16Rik|3110001D06Rik	progestin and adipoQ receptor family member VIII	protein-coding
mm_57282.1	chr6	124357068	124357078	-	1	NA	promoter-TSS (NM_001177502)	promoter-TSS (NM_001177502)	13	NM_001177502	76921	Mm.425335	NM_001177502	ENSMUSG00000079346	1700013D24Rik	-	RIKEN cDNA 1700013D24 gene	protein-coding
mm_160755.1	chr10	81930521	81930521	-	1	NA	promoter-TSS (NM_199062).2	promoter-TSS (NM_199062).2	-9	NM_001346707	100040944		NM_001346707		Gm3055	-	predicted gene 3055	protein-coding
mm_125735.1	chr15	73487835	73487860	+	1	NA	Intergenic	Intergenic	-24713	NM_001081066	105841	Mm.322557	NM_001081066	ENSMUSG00000036661	Dennd3	AI447457|E030003N15Rik	DENN/MADD domain containing 3	protein-coding
mm_69273.1	chr7	127935452	127935525	-	1	NA	intron (NM_001319147, intron 10 of 14)	CpG	-5375	NM_133351	76560	Mm.5875	NM_133351	ENSMUSG00000030800	Prss8	2410039E18Rik|AI313909|C79772|CAP1|fr|mCAP1	protease, serine 8 (prostasin)	protein-coding
mm_170113.1	chr17	39845505	39845505	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	2508	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_29202.1	chr3	106766782	106766811	-	1	NA	intron (NM_007651, intron 5 of 7)	intron (NM_007651, intron 5 of 7)	23353	NM_007651	12508	Mm.316861	NM_007651	ENSMUSG00000040747	Cd53	AI323659|Ox-44|Tspan25	CD53 antigen	protein-coding
mm_37706.1	chr4	129378997	129379006	-	1	NA	promoter-TSS (NM_028603)	promoter-TSS (NM_028603)	-973	NM_028603	73680	Mm.32997	NM_028603	ENSMUSG00000028807	Zbtb8a	2410081M15Rik|AI480941	zinc finger and BTB domain containing 8a	protein-coding
mm_173267.1	chrX	95956776	95956776	-	1	NA	exon (NM_152822, exon 1 of 13)	exon (NM_152822, exon 1 of 13)	198	NM_152822	76130	Mm.274318	NM_152822	ENSMUSG00000057421	Las1l	1810030A06Rik|5830482G23Rik	LAS1-like (S. cerevisiae)	protein-coding
mm_145579.1	chr18	60963776	60963836	+	1	NA	5' UTR (NM_001286809, exon 1 of 6)	5' UTR (NM_001286809, exon 1 of 6)	252	NM_001286809	12322	Mm.131530	NM_009792	ENSMUSG00000024617	Camk2a	CaMKII|R74975|mKIAA0968	calcium/calmodulin-dependent protein kinase II alpha	protein-coding
mm_173241.1	chrX	88759653	88759664	-	1	NA	promoter-TSS (NR_035440)	promoter-TSS (NR_035440)	-105	NR_037313	100499530		NR_037313	ENSMUSG00000084559	Mir1906-2	mmu-mir-1906-2	microRNA 1906-2	ncRNA
mm_8424.1	chr1	152469387	152469389	-	1	NA	intron (NM_177756, intron 2 of 11)	MLT2B3|LTR|ERVL	69521	NM_177756	269132	Mm.23782	NM_177756	ENSMUSG00000032649	Colgalt2	AI427652|D730024P12|Glt25d2	collagen beta(1-O)galactosyltransferase 2	protein-coding
mm_4160.1	chr1	171029344	171029356	+	1	NA	3' UTR (NM_144559, exon 5 of 5)	3' UTR (NM_144559, exon 5 of 5)	10424	NM_144559	246256	Mm.251254	NM_144559	ENSMUSG00000059089	Fcgr4	4833442P21Rik|CD16-2|FcgRIV|FcgammaRIV|Fcgr3a|Fcrl3	Fc receptor, IgG, low affinity IV	protein-coding
mm_140828.1	chr17	23645000	23645037	-	1	NA	5' UTR (NM_001033339, exon 1 of 10)	5' UTR (NM_001033339, exon 1 of 10)	251	NM_001033339	240047	Mm.235343	NM_001033339	ENSMUSG00000023903	Mmp25	F730048C11Rik|Leukolysin|MMP20|MT6-MMP	matrix metallopeptidase 25	protein-coding
mm_68025.1	chr7	100979233	100979264	-	1	NA	Intergenic	Intergenic	-14882	NM_183168	233571	Mm.235193	NM_183168	ENSMUSG00000048779	P2ry6	2010204J23Rik|P2Y6	pyrimidinergic receptor P2Y, G-protein coupled, 6	protein-coding
mm_43908.1	chr5	144255825	144255842	+	1	NA	exon (NM_001163709, exon 2 of 3)	exon (NM_001163709, exon 2 of 3)	608	NM_018772	55950	Mm.38011	NM_018772	ENSMUSG00000047843	Bri3	I3	brain protein I3	protein-coding
mm_49909.1	chr6	39004036	39004050	+	1	NA	intron (NM_011539, intron 5 of 12)	CR1_Mam|LINE|CR1	63543	NR_040523	69986	Mm.490941	NR_040523	ENSMUSG00000100121	1700025N23Rik	-	RIKEN cDNA 1700025N23 gene	ncRNA
mm_58999.1	chr7	19176514	19176537	+	1	NA	5' UTR (NM_001347582, exon 1 of 22)	5' UTR (NM_001347582, exon 1 of 22)	104	NM_001347582	72205	Mm.154121	NM_028153	ENSMUSG00000040811	Eml2	1600029N02Rik|EMAP-2	echinoderm microtubule associated protein like 2	protein-coding
mm_106738.1	chr12	3904189	3904200	+	1	NA	exon (NM_153743, exon 15 of 18)	exon (NM_153743, exon 15 of 18)	12450	NM_153743	13435	Mm.5001	NM_007872	ENSMUSG00000020661	Dnmt3a	MmuIIIA	DNA methyltransferase 3A	protein-coding
mm_14820.1	chr2	146855862	146855926	+	1	NA	promoter-TSS (NM_001033298)	promoter-TSS (NM_001033298)	5	NM_001033298	228730	Mm.292352	NM_001033298	ENSMUSG00000074749	Kiz	Gm114|Ncrna00153|Plk1s1	kizuna centrosomal protein	protein-coding
mm_58412.1	chr7	3289262	3289301	+	1	NA	5' UTR (NM_001093764, exon 1 of 3)	5' UTR (NM_001093764, exon 1 of 3)	243	NM_001093764	50918	Mm.29874	NM_016969	ENSMUSG00000068566	Myadm	D7Wsu62e	myeloid-associated differentiation marker	protein-coding
mm_90867.1	chr10	8886202	8886216	-	1	NA	promoter-TSS (NM_175155)	promoter-TSS (NM_175155)	-139	NM_175155	70097	Mm.338275	NM_175155	ENSMUSG00000015305	Sash1	1100001C18Rik|2500002E12Rik|A330076K04Rik|mKIAA0790	SAM and SH3 domain containing 1	protein-coding
mm_95583.1	chr11	53187607	53187611	+	1	NA	TTS (NM_177059)	TTS (NM_177059)	-67553	NR_046047	790909	Mm.404626	NR_046047	ENSMUSG00000087668	Gm11186	OTTMUSG00000000039	predicted gene 11186	ncRNA
mm_101235.1	chr11	20631722	20631725	-	1	NA	promoter-TSS (NM_001038625)	promoter-TSS (NM_001038625)	-254	NM_001038625	58172	Mm.339676	NM_021372	ENSMUSG00000049800	Sertad2	AB041541|AU021878|Kiaa0127|MNCb-1504|SEI-2|Sei2|TRIP-Br2|mKIAA0127	SERTA domain containing 2	protein-coding
mm_101101.1	chr11	11931698	11931710	-	1	NA	3' UTR (NM_010345, exon 17 of 17)	3' UTR (NM_010345, exon 17 of 17)	-33560	NM_001190448	13195	Mm.12906	NM_016672	ENSMUSG00000020182	Ddc	Aadc	dopa decarboxylase	protein-coding
mm_168893.1	chr12	48559964	48559982	-	1	NA	Intergenic	Intergenic	-258511	NR_039586	100628593		NR_039586	ENSMUSG00000092981	Mir5125	mmu-mir-5125|mu-mir-5125	microRNA 5125	ncRNA
mm_151183.1	chr19	53390774	53390820	+	1	NA	promoter-TSS (NM_172429)	promoter-TSS (NM_172429)	-224	NM_172429	76479	Mm.313687	NM_172429	ENSMUSG00000025024	Smndc1	2410004J23Rik|4933440I19Rik	survival motor neuron domain containing 1	protein-coding
mm_114284.1	chr13	58402547	58402578	+	1	NA	promoter-TSS (NM_025279)	promoter-TSS (NM_025279)	-35	NM_028904	74386	Mm.85289	NM_028904	ENSMUSG00000035367	Rmi1	4932432N11Rik|C79893	RecQ mediated genome instability 1	protein-coding
mm_171790.1	chr5	115359078	115359095	+	1	NA	Intergenic	Intergenic	-10131	NM_007748	12861	Mm.43415	NM_007748	ENSMUSG00000041697	Cox6a1	VIaL	cytochrome c oxidase subunit VIa polypeptide 1	protein-coding
mm_44350.1	chr5	17788278	17788289	-	1	NA	exon (NM_001159558, exon 13 of 16)	exon (NM_001159558, exon 13 of 16)	47613	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_41669.1	chr5	99385614	99385616	+	1	NA	intron (NR_030692, intron 2 of 3)	intron (NR_030692, intron 2 of 3)	-132688	NM_145839	320292	Mm.259074	NM_145839	ENSMUSG00000089809	Rasgef1b	4732452O09Rik|GPIgamma4|Gpig4	RasGEF domain family, member 1B	protein-coding
mm_245.1	chr1	19209156	19209177	+	1	NA	5' UTR (NM_009334, exon 1 of 7)	5' UTR (NM_009334, exon 1 of 7)	252	NM_001286340	21419	Mm.137021	NM_009334	ENSMUSG00000025927	Tfap2b	AI606113|AP-2(beta)|E130018K07Rik|Tcfap2b	transcription factor AP-2 beta	protein-coding
mm_122351.1	chr14	38833406	38833417	-	1	NA	intron (NM_001190187, intron 2 of 9)	Lx5c|LINE|L1	-64891	NR_045713	75170	Mm.372967	NR_045713	ENSMUSG00000093528	Nrg3os	4930529F24Rik	neuregulin 3, opposite strand	ncRNA
mm_36142.1	chr4	59472824	59472850	-	1	NA	3' UTR (NM_144904, exon 15 of 15)	3' UTR (NM_144904, exon 15 of 15)	-34204	NM_001163288	634731	Mm.483589	NM_001163288	ENSMUSG00000038578	Susd1	A530080P10|Gm12528|OTTMUSG00000007332	sushi domain containing 1	protein-coding
mm_50086.1	chr6	41523898	41523923	+	1	NA	exon (NM_009430, exon 3 of 5)	exon (NM_009430, exon 3 of 5)	2134	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_5045.1	chr1	194619918	194619932	+	1	NA	promoter-TSS (NM_008882)	promoter-TSS (NM_008882)	96	NM_008882	18845	Mm.2251	NM_008882	ENSMUSG00000026640	Plxna2	2810428A13Rik|AA589422|AW457381|OCT|PlexA2|Plxn2|mKIAA0463	plexin A2	protein-coding
mm_127715.1	chr15	103018965	103018973	+	1	NA	Intergenic	Intergenic	4059	NR_030526	751557		NR_030526	ENSMUSG00000076010	Mir615	Mir|Mirn615|mir-615|mmu-mir-615	microRNA 615	ncRNA
mm_77342.1	chr8	119570080	119570091	-	1	NA	intron (NM_175185, intron 1 of 4)	intron (NM_175185, intron 1 of 4)	5115	NM_175185	72552	Mm.36756	NM_175185	ENSMUSG00000034189	Hsdl1	2700067E09Rik	hydroxysteroid dehydrogenase like 1	protein-coding
mm_66738.1	chr7	46672500	46672506	-	1	NA	promoter-TSS (NM_009414)	promoter-TSS (NM_009414)	34	NM_009414	21990	Mm.248684	NM_009414	ENSMUSG00000040046	Tph1	Tph	tryptophan hydroxylase 1	protein-coding
mm_25736.1	chr3	122885279	122885286	+	1	NA	intron (NR_046036, intron 5 of 5)	intron (NR_046036, intron 5 of 5)	-9790	NM_007980	14079	Mm.28398	NM_007980	ENSMUSG00000023057	Fabp2	Fabpi|I-FABP	fatty acid binding protein 2, intestinal	protein-coding
mm_99768.1	chr11	107012902	107012905	+	1	NA	Intergenic	tRNA-Arg-AGG|tRNA|tRNA	-13378	NM_010655	16647	Mm.12508	NM_010655	ENSMUSG00000018362	Kpna2	2410044B12Rik|IPOA1|PTAC58|Rch1	karyopherin (importin) alpha 2	protein-coding
mm_132760.1	chr16	44531254	44531264	+	1	NA	intron (NM_172506, intron 1 of 18)	T-rich|Low_complexity|Low_complexity	26870	NR_037242	100526478		NR_037242	ENSMUSG00000093046	Mir3081	mir-3081|mmu-mir-3081	microRNA 3081	ncRNA
mm_84506.1	chr9	67023315	67023345	-	1	NA	TTS (NM_001164256)	TTS (NM_001164256)	20541	NM_001164252	22003	Mm.121878	NM_024427	ENSMUSG00000032366	Tpm1	AA986836|AI854628|TM2|Tm3|Tmpa|Tpm-1|alpha-TM	tropomyosin 1, alpha	protein-coding
mm_81423.1	chr9	109056384	109056420	+	1	NA	exon (NM_026381, exon 3 of 4)	exon (NM_026381, exon 3 of 4)	1536	NM_026381	66940	Mm.196533	NM_025858	ENSMUSG00000025647	Shisa5	2310008D10Rik|6430628I05Rik|Scotin|mShisa5	shisa family member 5	protein-coding
mm_136337.1	chr16	92596114	92596126	-	1	NA	Intergenic	L2a|LINE|L2	97973	NM_172469	209195	Mm.44747	NM_172469	ENSMUSG00000022949	Clic6	5730466J16Rik|AL022908|AW045520|CLIC1L	chloride intracellular channel 6	protein-coding
mm_162558.1	chr1	172206629	172206633	-	1	NA	5' UTR (NM_001329871, exon 1 of 4)	5' UTR (NM_001329871, exon 1 of 4)	173	NM_001329871	18611	Mm.544	NM_011063	ENSMUSG00000013698	Pea15a	Mat1|PEA-15|Pea15|Pkcs15	phosphoprotein enriched in astrocytes 15A	protein-coding
mm_12119.1	chr2	61608955	61608957	+	1	NA	intron (NM_001164071, intron 2 of 8)	intron (NM_001164071, intron 2 of 8)	15859	NM_001164071	21353	Mm.244393	NM_011529	ENSMUSG00000064289	Tank	C86182|E430026L09Rik|I-TRAF	TRAF family member-associated Nf-kappa B activator	protein-coding
mm_154070.1	chr19	56377947	56377963	-	1	NA	intron (NM_008733, intron 11 of 41)	intron (NM_008733, intron 11 of 41)	12083	NM_198059	18175	Mm.386769	NM_008733	ENSMUSG00000049134	Nrap	-	nebulin-related anchoring protein	protein-coding
mm_36005.1	chr4	56757347	56757363	-	1	NA	intron (NM_026079, intron 34 of 36)	intron (NM_026079, intron 34 of 36)	13933	NM_009611	11470	Mm.30959	NM_009611	ENSMUSG00000070979	Actl7a	Tact2	actin-like 7a	protein-coding
mm_107697.1	chr12	55399790	55399839	+	1	NA	intron (NM_011968, intron 1 of 6)	intron (NM_011968, intron 1 of 6)	989	NM_011968	26443	Mm.30210	NM_011968	ENSMUSG00000021024	Psma6	IOTA	proteasome (prosome, macropain) subunit, alpha type 6	protein-coding
mm_150039.1	chr19	29377791	29377811	+	1	NA	intron (NM_021893, intron 3 of 6)	intron (NM_021893, intron 3 of 6)	10363	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_112135.1	chr12	113000244	113000269	-	1	NA	exon (NM_028193, exon 1 of 18)	exon (NM_028193, exon 1 of 18)	365	NM_028193	72308	Mm.196721	NM_028193	ENSMUSG00000011158	Brf1	2510002F24Rik|GTF3B|TAF3C|TAFIII90|TFIIIB90|mTFIIIB90	BRF1, RNA polymerase III transcription initiation factor 90 kDa subunit	protein-coding
mm_136008.1	chr16	75876478	75876489	-	1	NA	exon (NM_023380, exon 5 of 8)	exon (NM_023380, exon 5 of 8)	32783	NM_023380	67742	Mm.131406	NM_023380	ENSMUSG00000022876	Samsn1	4930571B16Rik|930571B16Rik|Hacs1|SLy2	SAM domain, SH3 domain and nuclear localization signals, 1	protein-coding
mm_100073.1	chr11	115440541	115440554	+	1	NA	promoter-TSS (NM_001033775)	promoter-TSS (NM_001033775)	2	NM_001033775	432613	Mm.308822	NM_001033775	ENSMUSG00000070332	Trim80	4933422H20Rik|Trim47l	tripartite motif-containing 80	protein-coding
mm_144087.1	chr17	94834744	94834759	-	1	NA	promoter-TSS (NR_045964)	promoter-TSS (NR_045964)	48	NR_045964	100038746	Mm.456686	NR_045963	ENSMUSG00000066057	Gm1976	100038868	predicted gene 1976	ncRNA
mm_105089.1	chr11	100882146	100882173	-	1	NA	exon (NM_011488, exon 19 of 20)	exon (NM_011488, exon 19 of 20)	21675	NM_001164062	20850	Mm.277403	NM_011488	ENSMUSG00000004043	Stat5a	AA959963|STAT5	signal transducer and activator of transcription 5A	protein-coding
mm_49289.1	chr6	17666261	17666279	+	1	NA	3' UTR (NM_007604, exon 10 of 10)	3' UTR (NM_007604, exon 10 of 10)	-27724	NM_001289624	64213	Mm.12051	NM_022332	ENSMUSG00000029534	St7	9430001H04Rik|Fam4a2|HELG|RAY1|SEN4|TSG7	suppression of tumorigenicity 7	protein-coding
mm_62075.1	chr7	92819893	92819915	+	1	NA	intron (NM_029494, intron 1 of 4)	intron (NM_029494, intron 1 of 4)	54328	NM_001080995	74041	Mm.26468	NM_028729	ENSMUSG00000030641	Ddias	4632434I11Rik|noxin	DNA damage-induced apoptosis suppressor	protein-coding
mm_3222.1	chr1	135847974	135847988	+	1	NA	exon (NM_001130176, exon 7 of 13)	exon (NM_001130176, exon 7 of 13)	7120	NM_001130176	21956	Mm.247470	NM_011619	ENSMUSG00000026414	Tnnt2	Tnt|cTnT	troponin T2, cardiac	protein-coding
mm_134918.1	chr16	30321640	30321643	-	1	NA	intron (NM_001128094, intron 32 of 32)	intron (NM_001128094, intron 32 of 32)	-10860	NM_008148	14729	Mm.3519	NM_008148	ENSMUSG00000047953	Gp5	GPV	glycoprotein 5 (platelet)	protein-coding
mm_98139.1	chr11	87578478	87578492	+	1	NA	promoter-TSS (NM_001284398)	promoter-TSS (NM_001284398)	96	NM_001284398	18952	Mm.2214	NM_011129	ENSMUSG00000020486	Sept4	ARTS|Bh5|OTTMUSG00000001265|Pnutl2	septin 4	protein-coding
mm_100688.1	chr11	3505463	3505471	-	1	NA	promoter-TSS (NM_172439)	promoter-TSS (NM_172439)	-646	NM_172439	170835	Mm.24313	NM_172439	ENSMUSG00000034570	Inpp5j	Pib5pa|Pipp	inositol polyphosphate 5-phosphatase J	protein-coding
mm_35521.1	chr4	41207027	41207037	-	1	NA	exon (NM_026872, exon 14 of 29)	exon (NM_026872, exon 14 of 29)	68103	NM_026872	68926	Mm.41864	NM_026872	ENSMUSG00000028433	Ubap2	1190005K07Rik|AA408600|AU045235|UBAP-2|mKIAA1491	ubiquitin-associated protein 2	protein-coding
mm_85687.1	chr9	108002385	108002437	-	1	NA	promoter-TSS (NM_013785)	promoter-TSS (NM_013785)	-237	NM_013785	27399	Mm.276155	NM_013785	ENSMUSG00000032594	Ip6k1	1200016D08Rik|AU022776|Ihpk1|InsP6|InsP6k1|Itpk6	inositol hexaphosphate kinase 1	protein-coding
mm_43991.1	chr5	146781929	146781950	+	1	NA	intron (NM_011669, intron 1 of 8)	intron (NM_011669, intron 1 of 8)	13017	NM_011669	22217	Mm.167971	NM_011669	ENSMUSG00000029640	Usp12	Ubh1	ubiquitin specific peptidase 12	protein-coding
mm_66148.1	chr7	31137307	31137319	-	1	NA	intron (NM_027898, intron 11 of 18)	B3A|SINE|B2	-10290	NM_011322	20266	Mm.1418	NM_011322	ENSMUSG00000019194	Scn1b	-	sodium channel, voltage-gated, type I, beta	protein-coding
mm_137655.1	chr17	28575753	28575772	+	1	NA	promoter-TSS (NM_026571)	promoter-TSS (NM_026571)	43	NM_026571	328789	Mm.284760	NM_026571	ENSMUSG00000062252	Lhfpl5	9330179O15Rik|Tmhs|hscy	lipoma HMGIC fusion partner-like 5	protein-coding
mm_62802.1	chr7	112856617	112856625	+	1	NA	intron (NM_009346, intron 5 of 12)	intron (NM_009346, intron 5 of 12)	97237	NM_001166585	21676	Mm.24685	NM_009346	ENSMUSG00000055320	Tead1	2610024B07Rik|B230114H05Rik|Gtrgeo5|TEAD-1|TEF-1|Tcf13|mTEF-1	TEA domain family member 1	protein-coding
mm_79848.1	chr9	64817942	64817958	+	1	NA	intron (NM_001162917, intron 2 of 34)	intron (NM_001162917, intron 2 of 34)	6939	NM_001162917	102442	Mm.222473	NM_176935	ENSMUSG00000053641	Dennd4a	AI115600|AI851943|F730015K02Rik	DENN/MADD domain containing 4A	protein-coding
mm_134435.1	chr16	18089154	18089170	-	1	NA	promoter-TSS (NM_011172)	promoter-TSS (NM_011172)	28	NM_011172	19125	Mm.28456	NM_011172	ENSMUSG00000003526	Prodh	Pro-1|Pro1|Ym24d07	proline dehydrogenase	protein-coding
mm_158615.1	chrX	152644432	152644470	-	1	NA	promoter-TSS (NM_001290687)	promoter-TSS (NM_001290687)	97	NM_001290686	110380	Mm.40796	NM_172441	ENSMUSG00000045180	Shroom2	4832440C16|Apxl|C630003H05Rik|Shrm2	shroom family member 2	protein-coding
mm_6039.1	chr1	59670777	59670810	-	1	NA	promoter-TSS (NM_009460)	promoter-TSS (NM_009460)	41	NM_009460	22218	Mm.362118	NM_009460	ENSMUSG00000026021	Sumo1	GMP1|PIC1|SENTRIN|SMT3|SMT3H3|SMTP3|SUMO-1|Smt3C|Ubl1	small ubiquitin-like modifier 1	protein-coding
mm_69817.1	chr7	141264254	141264274	-	1	NA	exon (NM_001252601, exon 7 of 10)	exon (NM_001252601, exon 7 of 10)	2160	NM_001252601	54123	Mm.3233	NM_016850	ENSMUSG00000025498	Irf7	-	interferon regulatory factor 7	protein-coding
mm_40752.1	chr5	66857458	66857475	+	1	NA	intron (NM_001001980, intron 1 of 25)	intron (NM_001001980, intron 1 of 25)	-110950	NM_001256122	77569	Mm.374778	NM_001001980	ENSMUSG00000037736	Limch1	3732412D22Rik|mKIAA1102	LIM and calponin homology domains 1	protein-coding
mm_49143.1	chr6	10883677	10883691	+	1	NA	Intergenic	Intergenic	90694	NR_033776	57866	Mm.4397	NR_033776		AA545190	-	EST AA545190	ncRNA
mm_93922.1	chr10	127121126	127121149	-	1	NA	promoter-TSS (NM_001171026)	promoter-TSS (NM_001171026)	23	NM_177614	216440	Mm.295246	NM_177614	ENSMUSG00000040462	Os9	4632413K17Rik|AU022351	amplified in osteosarcoma	protein-coding
mm_86823.1	chr10	20959695	20959710	+	1	NA	5' UTR (NM_026203, exon 2 of 24)	5' UTR (NM_026203, exon 2 of 24)	7155	NM_026203	52906	Mm.253280	NM_026203	ENSMUSG00000019986	Ahi1	1700015F03Rik|Ahi-1|D10Bwg0629e	Abelson helper integration site 1	protein-coding
mm_56586.1	chr6	107103602	107103604	-	1	NA	Intergenic	Intergenic	-303516	NM_175357	58799	Mm.290085	NM_021449	ENSMUSG00000005362	Crbn	2610203G15Rik|2900045O07Rik|AF229032|AW108261|piL	cereblon	protein-coding
mm_13049.1	chr2	91099576	91099587	+	1	NA	intron (NM_011355, intron 2 of 4)	intron (NM_011355, intron 2 of 4)	2903	NM_011355	20375	Mm.1302	NM_011355	ENSMUSG00000002111	Spi1	Dis-1|Dis1|PU.1|Sfpi-1|Sfpi1|Spi-1|Tcfpu1|Tfpu.1	spleen focus forming virus (SFFV) proviral integration oncogene	protein-coding
mm_43205.1	chr5	129114999	129115014	+	1	NA	intron (NM_001081342, intron 4 of 25)	intron (NM_001081342, intron 4 of 25)	18256	NM_001347486	243277	Mm.440501	NM_177734	ENSMUSG00000044017	Adgrd1	E230012M21Rik|Gpr133	adhesion G protein-coupled receptor D1	protein-coding
mm_145647.1	chr18	61127752	61127817	+	1	NA	intron (NM_001037859, intron 15 of 21)	intron (NM_001037859, intron 15 of 21)	10316	NR_105949	102466212		NR_105949	ENSMUSG00000098389	Mir6983	Gm27496|mmu-mir-6983	microRNA 6983	ncRNA
mm_171425.1	chr4	134159786	134159799	+	1	NA	intron (NM_144527, intron 3 of 13)	RLTR4_Mm|LTR|ERV1	27293	NM_144527	70012	Mm.26542	NM_144527	ENSMUSG00000037443	Cep85	2410030J07Rik|AI173272|AI173504|Ccdc21	centrosomal protein 85	protein-coding
mm_71093.1	chr8	34821462	34821481	+	1	NA	Intergenic	Intergenic	13861	NM_176933	319520	Mm.170276	NM_176933	ENSMUSG00000031530	Dusp4	2700078F24Rik|AI844617|BB104621|E130306H24Rik|MKP2	dual specificity phosphatase 4	protein-coding
mm_63645.1	chr7	128688030	128688047	+	1	NA	promoter-TSS (NM_001346517)	promoter-TSS (NM_001346517)	-832	NM_001346517	101490	Mm.490344	NM_178641	ENSMUSG00000042105	Inpp5f	5830435P03Rik|AI115354|AW561896|SAC2|cI-27|hSAC2|mKIAA0966	inositol polyphosphate-5-phosphatase F	protein-coding
mm_116438.1	chr13	42538217	42538223	-	1	NA	Intergenic	Intergenic	-142579	NM_001302635	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding
mm_121820.1	chr14	20456284	20456292	-	1	NA	3' UTR (NM_001110794, exon 13 of 13)	3' UTR (NM_001110794, exon 13 of 13)	-4063	NM_001163639	76670	Mm.159759	NM_029698	ENSMUSG00000039543	Cfap70	Ttc18	cilia and flagella associated protein 70	protein-coding
mm_140306.1	chr17	85691142	85691162	+	1	NA	Intergenic	Intergenic	-2898	NM_011380	20472	Mm.5039	NM_011380	ENSMUSG00000024134	Six2	-	sine oculis-related homeobox 2	protein-coding
mm_93194.1	chr10	94036724	94036749	-	1	NA	promoter-TSS (NM_001304720)	promoter-TSS (NM_001304720)	735	NM_053072	13998	Mm.269596	NM_053072	ENSMUSG00000020021	Fgd6	AA123052|Etohd4|ZFYVE24	FYVE, RhoGEF and PH domain containing 6	protein-coding
mm_39818.1	chr5	30746111	30746116	+	1	NA	intron (NM_023047, intron 2 of 12)	PB1D7|SINE|Alu	34218	NM_023047	65254	Mm.27732	NM_023047	ENSMUSG00000029168	Dpysl5	CRAM|CRMP-5|Crmp5	dihydropyrimidinase-like 5	protein-coding
mm_155456.1	chrX	73502778	73502818	+	1	NA	promoter-TSS (NM_177236)	promoter-TSS (NM_177236)	-288	NM_001310537	320707	Mm.210095	NM_177236	ENSMUSG00000031376	Atp2b3	6430519O13Rik|Pmca3	ATPase, Ca++ transporting, plasma membrane 3	protein-coding
mm_92078.1	chr10	62726087	62726102	-	1	NA	promoter-TSS (NM_001033260)	promoter-TSS (NM_001033260)	5	NM_001033260	216021	Mm.39821	NM_001033260	ENSMUSG00000036923	Stox1	4732470K04Rik|Gm63	storkhead box 1	protein-coding
mm_19820.1	chr2	110840022	110840040	-	1	NA	intron (NM_001128103, intron 4 of 26)	intron (NM_001128103, intron 4 of 26)	110213	NM_001128103	228432	Mm.483325	NM_001081556	ENSMUSG00000074968	Ano3	AI838058|B230324K02Rik|Tmem16c	anoctamin 3	protein-coding
mm_30485.1	chr3	155055316	155055322	-	1	NA	promoter-TSS (NM_177066)	promoter-TSS (NM_177066)	88	NM_177066	435766	Mm.210428	NM_177066	ENSMUSG00000040086	Tnni3k	Cark|D830019J24Rik	TNNI3 interacting kinase	protein-coding
mm_45344.1	chr5	65858089	65858124	-	1	NA	Intergenic	Intergenic	-5463	NM_001081105	74734	Mm.20323	NM_001081105	ENSMUSG00000029204	Rhoh	5830400A04Rik|AU019774|Arhh	ras homolog family member H	protein-coding
mm_105860.1	chr11	113771514	113771516	-	1	NA	Intergenic	Intergenic	-19700	NM_001163346	56699	Mm.293378	NM_020006	ENSMUSG00000041598	Cdc42ep4	1500041M20Rik|Borg4|CEP4	CDC42 effector protein (Rho GTPase binding) 4	protein-coding
mm_78302.1	chr9	22475814	22475858	+	1	NA	5' UTR (NM_181316, exon 1 of 22)	5' UTR (NM_181316, exon 1 of 22)	121	NM_178415	319845	Mm.176725	NM_178415	ENSMUSG00000035919	Bbs9	E130103I17Rik	Bardet-Biedl syndrome 9 (human)	protein-coding
mm_75367.1	chr8	45306147	45306155	-	1	NA	3' UTR (NM_133969, exon 11 of 11)	3' UTR (NM_133969, exon 11 of 11)	-11316	NM_008455	16621	Mm.482691	NM_008455	ENSMUSG00000109764	Klkb1	APS|Kal-3|Kal3|Klk3|PSA	kallikrein B, plasma 1	protein-coding
mm_141636.1	chr17	33033368	33033411	-	1	NA	promoter-TSS (NM_028543)	promoter-TSS (NM_028543)	-8	NM_028543	73451	Mm.129453	NM_028543	ENSMUSG00000067430	Zfp763	1700065O13Rik|AI839635	zinc finger protein 763	protein-coding
mm_66816.1	chr7	48167576	48167579	-	1	NA	TTS (NM_207538)	TTS (NM_207538)	1408	NM_207538	404239	Mm.377927	NM_207538	ENSMUSG00000070551	Mrgprb5	Mgrg11|MrgB5	MAS-related GPR, member B5	protein-coding
mm_66294.1	chr7	38019491	38019504	-	1	NA	promoter-TSS (NM_011274)	promoter-TSS (NM_011274)	55	NM_011274	19777	Mm.387220	NM_011274	ENSMUSG00000030421	Uri1	C80913|NNX3|Rmp	URI1, prefoldin-like chaperone	protein-coding
mm_15291.1	chr2	155277081	155277106	+	1	NA	intron (NM_025735, intron 2 of 3)	CpG-8721	729	NR_046364	66734	Mm.196239	NM_025735	ENSMUSG00000027602	Map1lc3a	1010001H21Rik|4922501H04Rik|LC3|LC3a	microtubule-associated protein 1 light chain 3 alpha	protein-coding
mm_116467.1	chr13	43481045	43481049	-	1	NA	promoter-TSS (NM_019930)	promoter-TSS (NM_019930)	-74	NM_019930	56705	Mm.148781	NM_019930	ENSMUSG00000038546	Ranbp9	IBAP-1|Ibap1|RanBPM	RAN binding protein 9	protein-coding
mm_16042.1	chr2	167698128	167698153	+	1	NA	TTS (NR_015500)	TTS (NR_015500)	6963	NR_015500	329562	Mm.123101	NM_177851	ENSMUSG00000006462	A530013C23Rik	-	RIKEN cDNA A530013C23 gene	ncRNA
mm_134935.1	chr16	31142116	31142129	-	1	NA	intron (NM_030138, intron 4 of 22)	intron (NM_030138, intron 4 of 22)	59116	NM_030138	78618	Mm.274646	NM_030138	ENSMUSG00000049076	Acap2	4832442G16|9530039J15Rik|CNT-B2|Centb2|mKIAA0041	ArfGAP with coiled-coil, ankyrin repeat and PH domains 2	protein-coding
mm_123104.1	chr14	55882749	55882763	-	1	NA	3' UTR (NM_019820, exon 3 of 3)	3' UTR (NM_019820, exon 3 of 3)	1500	NM_019820	56410	Mm.97163	NM_019820	ENSMUSG00000040380	Cbln3	-	cerebellin 3 precursor protein	protein-coding
mm_127988.1	chr15	12549347	12549361	-	1	NA	intron (NM_001081064, intron 1 of 23)	intron (NM_001081064, intron 1 of 23)	43202	NM_001081064	68070	Mm.423205	NM_001081064	ENSMUSG00000022197	Pdzd2	4930537L06Rik|A930022H17Rik|Gm21706|Gm82|Pdzk3|mKIAA0300	PDZ domain containing 2	protein-coding
mm_35326.1	chr4	25895632	25895639	-	1	NA	Intergenic	RMER12B|LTR|ERVK	-95632	NM_010243	14348	Mm.39101	NM_010243	ENSMUSG00000055373	Fut9	AI746471|AU067636|mFUT9|mFuc-TIX	fucosyltransferase 9	protein-coding
mm_139903.1	chr17	70865115	70865115	+	1	NA	Intergenic	Intergenic	-11583	NM_001164074	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_76419.1	chr8	84969532	84969559	-	1	NA	promoter-TSS (NM_011563)	promoter-TSS (NM_011563)	-77	NM_001317385	21672	Mm.347009	NM_011563	ENSMUSG00000005161	Prdx2	AL022839|Band-8|NkefB|PRP|PrxII|TDX1|TPx|TPx-B|TR|TSA|Tdpx1|Torin	peroxiredoxin 2	protein-coding
mm_168235.1	chr10	81694180	81694197	-	1	NA	Intergenic	Intergenic	-10637	NM_001243067	73610	Mm.490466	NM_001243067	ENSMUSG00000096795	Zfp433	1700123A16Rik	zinc finger protein 433	protein-coding
mm_4813.1	chr1	185363036	185363064	+	1	NA	promoter-TSS (NM_029735)	promoter-TSS (NM_029735)	-45	NM_029735	107508	Mm.154511	NM_029735	ENSMUSG00000026615	Eprs	2410081F06Rik|3010002K18Rik|C79379|Qprs	glutamyl-prolyl-tRNA synthetase	protein-coding
mm_171466.1	chr4	145730357	145730371	-	1	NA	Intergenic	Intergenic	-51179	NM_001083918	666532	Mm.392861	NM_001083918	ENSMUSG00000067916	Zfp991	Gm13139|OTTMUSG00000010657	zinc finger protein 991	protein-coding
mm_106546.1	chr11	120579316	120579332	-	1	NA	exon (NM_133796, exon 6 of 6)	exon (NM_133796, exon 6 of 6)	2296	NM_133796	192662	Mm.30016	NM_133796	ENSMUSG00000025132	Arhgdia	5330430M07Rik|Gdi-1|Rho-GDI|RhoDGI|RhoGDI-1	Rho GDP dissociation inhibitor (GDI) alpha	protein-coding
mm_26267.1	chr3	142501674	142501681	+	1	NA	intron (NM_153564, intron 3 of 10)	RMER17C|LTR|ERVK	4743	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_55971.1	chr6	85832220	85832232	-	1	NA	promoter-TSS (NM_023455)	promoter-TSS (NM_023455)	-336	NM_023455	68396	Mm.154782	NM_023455	ENSMUSG00000030004	Nat8	0610037O16Rik|CCNAT|Cml4	N-acetyltransferase 8 (GCN5-related)	protein-coding
mm_150236.1	chr19	34008324	34008338	+	1	NA	promoter-TSS (NM_172837)	promoter-TSS (NM_172837)	77	NM_001205349	240633	Mm.58924	NM_172837	ENSMUSG00000024771	Lipk	9930115F20|BC055815|Lipl2	lipase, family member K	protein-coding
mm_170913.1	chr2	35340334	35340335	+	1	NA	Intergenic	Intergenic	-3325	NM_013515	13830	Mm.295284	NM_013515	ENSMUSG00000026880	Stom	Epb7.2	stomatin	protein-coding
mm_159257.1	chr2	154257854	154257854	+	1	NA	promoter-TSS (NM_175167)	promoter-TSS (NM_175167)	-25	NM_175167	71425	Mm.389341	NM_175167	ENSMUSG00000067998	Bpifb9a	4833413D08Rik|AI413838	BPI fold containing family B, member 9A	protein-coding
mm_92525.1	chr10	78718271	78718304	-	1	NA	promoter-TSS (NM_009809)	promoter-TSS (NM_009809)	6	NM_009809	12365	Mm.20940	NM_009809	ENSMUSG00000005355	Casp14	MICE|mini-ICE	caspase 14	protein-coding
mm_117623.1	chr13	91861355	91861371	-	1	NA	intron (NM_198415, intron 4 of 9)	intron (NM_198415, intron 4 of 9)	15522	NM_198415	76722	Mm.316438	NM_198415	ENSMUSG00000021622	Ckmt2	2300008A19Rik|ScCKmit	creatine kinase, mitochondrial 2	protein-coding
mm_69127.1	chr7	127026568	127026608	-	1	NA	promoter-TSS (NM_010772)	promoter-TSS (NM_010772)	-109	NM_010772	17188	Mm.378964	NM_010772	ENSMUSG00000030678	Maz	MAZI|PUR1|Pur-1|SAF-1|SAF-2	MYC-associated zinc finger protein (purine-binding transcription factor)	protein-coding
mm_113113.1	chr13	24417655	24417677	+	1	NA	intron (NM_007717, intron 3 of 15)	intron (NM_007717, intron 3 of 15)	2544	NM_001284520	12763	Mm.8396	NM_007717	ENSMUSG00000016756	Cmah	-	cytidine monophospho-N-acetylneuraminic acid hydroxylase	protein-coding
mm_148898.1	chr19	6909812	6909822	+	1	NA	promoter-TSS (NM_012021)	promoter-TSS (NM_012021)	119	NM_026306	67674	Mm.318804	NM_026306	ENSMUSG00000038812	Trmt112	0610038D11Rik|Trm112p	tRNA methyltransferase 11-2	protein-coding
mm_12078.1	chr2	59779728	59779743	+	1	NA	intron (NM_198294, intron 7 of 26)	intron (NM_198294, intron 7 of 26)	102871	NM_001159636	72137	Mm.288734	NM_028118	ENSMUSG00000026988	Wdsub1	1700048E19Rik|2610014F08Rik	WD repeat, SAM and U-box domain containing 1	protein-coding
mm_115311.1	chr13	112318448	112318458	+	1	NA	exon (NM_029898, exon 2 of 11)	exon (NM_029898, exon 2 of 11)	29935	NM_001168404	77318	Mm.159895	NM_029898	ENSMUSG00000049985	Ankrd55	C030011J08Rik	ankyrin repeat domain 55	protein-coding
mm_67072.1	chr7	68149832	68149850	-	1	NA	intron (NM_010513, intron 2 of 20)	intron (NM_010513, intron 2 of 20)	114392	NM_030101	78444	Mm.425468	NM_030101	ENSMUSG00000030553	Pgpep1l	C330024D12Rik	pyroglutamyl-peptidase I-like	protein-coding
mm_19531.1	chr2	94264965	94264981	-	1	NA	Intergenic	Intergenic	-3574	NR_030431	735259		NR_030431	ENSMUSG00000076335	Mir670	Mirn670|mir-670|mmu-mir-670	microRNA 670	ncRNA
mm_106266.1	chr11	117969177	117969192	-	1	NA	5' UTR (NM_007707, exon 1 of 2)	5' UTR (NM_007707, exon 1 of 2)	182	NM_007707	12702	Mm.3468	NM_007707	ENSMUSG00000053113	Socs3	Cis3|Cish3|EF-10|Ef10|SSI-3|Ssi3	suppressor of cytokine signaling 3	protein-coding
mm_158814.1	chrX	167308158	167308173	-	1	NA	exon (NM_001290758, exon 4 of 4)	exon (NM_001290758, exon 4 of 4)	22406	NM_001290757	170743	Mm.23979	NM_133211	ENSMUSG00000044583	Tlr7	-	toll-like receptor 7	protein-coding
mm_150755.1	chr19	43921067	43921077	+	1	NA	intron (NM_028029, intron 1 of 15)	intron (NM_028029, intron 1 of 15)	19126	NM_028029	71972	Mm.159024	NM_028029	ENSMUSG00000025195	Dnmbp	2410003L07Rik|2410003M15Rik|TUBA	dynamin binding protein	protein-coding
mm_110652.1	chr12	59046122	59046128	-	1	NA	intron (NM_030057, intron 4 of 5)	(A)n|Simple_repeat|Simple_repeat	15347	NM_001306218	78232	Mm.290070	NM_030057	ENSMUSG00000020993	Trappc6b	5830498C14Rik|C79212	trafficking protein particle complex 6B	protein-coding
mm_40444.1	chr5	53591467	53591478	+	1	NA	intron (NM_001080927, intron 1 of 10)	intron (NM_001080927, intron 1 of 10)	986	NM_001080927	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_160121.1	chr7	27674651	27674651	+	1	NA	promoter-TSS (NM_198417)	promoter-TSS (NM_198417)	-10	NM_198417	112415	Mm.145362	NM_198417	ENSMUSG00000057093	Zfp607b	C030039L03Rik	zinc finger protein 607B	protein-coding
mm_17326.1	chr2	26503633	26503641	-	1	NA	promoter-TSS (NR_132655)	promoter-TSS (NR_132655)	185	NM_008714	18128	Mm.290610	NM_008714	ENSMUSG00000026923	Notch1	9930111A19Rik|Mis6|N1|Tan1|lin-12	notch 1	protein-coding
mm_71990.1	chr8	70616938	70616948	+	1	NA	promoter-TSS (NM_153074)	promoter-TSS (NM_153074)	99	NM_153074	211228	Mm.132939	NM_153074	ENSMUSG00000049988	Lrrc25	Mapa	leucine rich repeat containing 25	protein-coding
mm_64014.1	chr7	140218354	140218369	+	1	NA	promoter-TSS (NM_172909)	promoter-TSS (NM_172909)	94	NM_172909	244233	Mm.19283	NM_172909	ENSMUSG00000025461	Cd163l1	B430307C05|E430002D04Rik|Scart1	CD163 molecule-like 1	protein-coding
mm_18070.1	chr2	42288927	42288928	-	1	NA	intron (NM_053011, intron 2 of 90)	intron (NM_053011, intron 2 of 90)	158641	NR_105754	102465171		NR_105754	ENSMUSG00000098660	Mir6336	Gm27584|mmu-mir-6336	microRNA 6336	ncRNA
mm_28691.1	chr3	95521139	95521163	-	1	NA	Intergenic	Intergenic	-5635	NM_021281	13040	Mm.3619	NM_021281	ENSMUSG00000038642	Ctss	Cats	cathepsin S	protein-coding
mm_30550.1	chr4	3687911	3687928	+	1	NA	intron (NM_010747, intron 1 of 12)	B1_Mus1|SINE|Alu	9798	NM_010747	17096	Mm.317331	NM_010747	ENSMUSG00000042228	Lyn	AA407514|Hck-2|p53Lyn|p56Lyn	LYN proto-oncogene, Src family tyrosine kinase	protein-coding
mm_27293.1	chr3	45376013	45376016	-	1	NA	intron (NR_045172, intron 1 of 8)	intron (NR_045172, intron 1 of 8)	2246	NR_045172	72511	Mm.140700	NR_045172	ENSMUSG00000097040	2610316D01Rik	-	RIKEN cDNA 2610316D01 gene	ncRNA
mm_42405.1	chr5	115011112	115011208	+	1	NA	promoter-TSS (NM_029012)	promoter-TSS (NM_029012)	-364	NM_029012	74585	Mm.355894	NM_029012	ENSMUSG00000029550	Sppl3	4833416I09Rik|Psl4|Usmg3	signal peptide peptidase 3	protein-coding
mm_126120.1	chr15	78325817	78325837	+	1	NA	promoter-TSS (NM_007780)	promoter-TSS (NM_007780)	-163	NM_007780	12983	Mm.235324	NM_007780	ENSMUSG00000071713	Csf2rb	AI848964|AIC2B|Bc|CDw131|Csf2rb1|Csfgmrb|Il3r|Il3rb|Il3rb1|Il5rb	colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage)	protein-coding
mm_10826.1	chr2	24385314	24385352	+	1	NA	promoter-TSS (NM_177611)	promoter-TSS (NM_177611)	-64	NM_177611	215632	Mm.490434	NM_177611	ENSMUSG00000026979	Psd4	BC046518|EFA6B	pleckstrin and Sec7 domain containing 4	protein-coding
mm_10279.1	chr2	9884523	9884533	+	1	NA	non-coding (NR_024257, exon 5 of 5)	non-coding (NR_024257, exon 5 of 5)	3282	NR_024257	381347	Mm.441450	NR_024257		4930412O13Rik	ENSMUSG00000075535|Gm10853	RIKEN cDNA 4930412O13 gene	ncRNA
mm_51964.1	chr6	91758111	91758122	+	1	NA	3' UTR (NM_009320, exon 15 of 15)	3' UTR (NM_009320, exon 15 of 15)	49277	NM_001159507	243547	Mm.333264	NM_001033353	ENSMUSG00000030098	Grip2	-	glutamate receptor interacting protein 2	protein-coding
mm_19400.1	chr2	91635881	91635904	-	1	NA	exon (NM_010168, exon 2 of 14)	exon (NM_010168, exon 2 of 14)	565	NM_010168	14061	Mm.89048	NM_010168	ENSMUSG00000027249	F2	Cf-2|Cf2|FII	coagulation factor II	protein-coding
mm_53147.1	chr6	125241901	125241921	+	1	NA	Intergenic	Intergenic	-4884	NM_001286753	21940	Mm.367714	NM_001033126	ENSMUSG00000030336	Cd27	S152|Tnfrsf7|Tp55	CD27 antigen	protein-coding
mm_53947.1	chr6	5220488	5220501	-	1	NA	TTS (NM_173006)	TTS (NM_173006)	-26548	NM_011134	18979	Mm.237657	NM_011134	ENSMUSG00000002588	Pon1	Pon	paraoxonase 1	protein-coding
mm_47730.1	chr5	130171725	130171748	-	1	NA	promoter-TSS (NM_001199059)	promoter-TSS (NM_001199059)	-83	NM_001199059	56715	Mm.288639	NM_019983	ENSMUSG00000025340	Rabgef1	Rab5ef|Rabex5|Rin2	RAB guanine nucleotide exchange factor (GEF) 1	protein-coding
mm_19914.1	chr2	115344277	115344283	-	1	NA	promoter-TSS (NR_040516)	promoter-TSS (NR_040516)	0	NR_040516	78193	Mm.189508	NR_040516	ENSMUSG00000087309	4930528P14Rik	-	RIKEN cDNA 4930528P14 gene	ncRNA
mm_97036.1	chr11	72267275	72267300	+	1	NA	promoter-TSS (NM_001004148)	promoter-TSS (NM_001004148)	443	NR_045922	73366	Mm.396157	NR_045922	ENSMUSG00000086951	1700051A21Rik	-	RIKEN cDNA 1700051A21 gene	ncRNA
mm_50398.1	chr6	48718758	48718765	+	1	NA	intron (NM_146167, intron 1 of 1)	intron (NM_146167, intron 1 of 1)	140	NM_146167	231932	Mm.30479	NM_146167	ENSMUSG00000043931	Gimap7	IAN7|Ian3	GTPase, IMAP family member 7	protein-coding
mm_33262.1	chr4	127208292	127208303	+	1	NA	intron (NM_001302081, intron 5 of 11)	L1M4a2|LINE|L1	35417	NM_001302081	242667	Mm.331885	NM_198618	ENSMUSG00000042388	Dlgap3	BC058433|DAP-3|DAP3|Prpl8|Sapap3	discs, large (Drosophila) homolog-associated protein 3	protein-coding
mm_40407.1	chr5	53057726	53057733	+	1	NA	intron (NM_011402, intron 1 of 12)	intron (NM_011402, intron 1 of 12)	8376	NM_011402	20531	Mm.284891	NM_011402	ENSMUSG00000029188	Slc34a2	AA536683|D5Ertd227e|NaPi-2b|Npt2b	solute carrier family 34 (sodium phosphate), member 2	protein-coding
mm_158410.1	chrX	136976834	136976857	-	1	NA	promoter-TSS (NM_001081983)	promoter-TSS (NM_001081983)	29	NM_001081983	666244	Mm.381904	NM_001081983	ENSMUSG00000089768	Tmsb15b1	Tm15b	thymosin beta 15b1	protein-coding
mm_110070.1	chr12	21417220	21417270	-	1	NA	5' UTR (NM_011739, exon 1 of 5)	5' UTR (NM_011739, exon 1 of 5)	191	NM_011739	22630	Mm.289630	NM_011739	ENSMUSG00000076432	Ywhaq	2700028P07Rik|AA409740|AU021156|R74690	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide	protein-coding
mm_26686.1	chr3	156562672	156562690	+	1	NA	promoter-TSS (NR_040400)	promoter-TSS (NR_040400)	887	NM_001039094	320840	Mm.317293	NM_177274	ENSMUSG00000040037	Negr1	5330422G01Rik|KILON|Ntra	neuronal growth regulator 1	protein-coding
mm_54203.1	chr6	24956072	24956105	-	1	NA	promoter-TSS (NM_177013)	promoter-TSS (NM_177013)	37	NM_177013	319832	Mm.127446	NM_177013	ENSMUSG00000048022	Tmem229a	6332401O19Rik	transmembrane protein 229A	protein-coding
mm_562.1	chr1	38032271	38032289	+	1	NA	exon (NM_198303, exon 7 of 24)	exon (NM_198303, exon 7 of 24)	34270	NM_198303	226982	Mm.260943	NM_198303	ENSMUSG00000026083	Eif5b	A030003E17Rik|BC018347|IF2	eukaryotic translation initiation factor 5B	protein-coding
mm_43822.1	chr5	142961001	142961020	+	1	NA	exon (NM_007984, exon 1 of 5)	exon (NM_007984, exon 1 of 5)	655	NM_007984	14086	Mm.289707	NM_007984	ENSMUSG00000029581	Fscn1	AI663989|Fan1|fascin-1	fascin actin-bundling protein 1	protein-coding
mm_144755.1	chr18	35727020	35727039	+	1	NA	promoter-TSS (NM_001033168)	promoter-TSS (NM_001033168)	40	NM_001033168	73449	Mm.379225	NM_001033168	ENSMUSG00000073598	1700066B19Rik	-	RIKEN cDNA 1700066B19 gene	protein-coding
mm_98465.1	chr11	94948714	94948733	+	1	NA	exon (NM_007742, exon 43 of 51)	exon (NM_007742, exon 43 of 51)	12499	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_152813.1	chr19	23092879	23092885	-	1	NA	Intergenic	Intergenic	-48344	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_72494.1	chr8	83715505	83715524	+	1	NA	intron (NM_197982, intron 1 of 10)	CpG	337	NM_197982	68278	Mm.28222	NM_197982	ENSMUSG00000005481	Ddx39	2610307C23Rik|BAT1|DDXL|Ddx39a|URH49	DEAD (Asp-Glu-Ala-Asp) box polypeptide 39	protein-coding
mm_52540.1	chr6	115931939	115931963	+	1	NA	promoter-TSS (NM_145383)	promoter-TSS (NM_145383)	24	NM_145383	212541	Mm.2965	NM_145383	ENSMUSG00000030324	Rho	Noerg1|Opn2|Ops|RP4	rhodopsin	protein-coding
mm_16730.1	chr2	9141477	9141519	-	1	NA	Intergenic	MER44B|DNA|TcMar-Tigger	-48017	NR_038180	73438	Mm.23558	NR_038180	ENSMUSG00000085580	1700061F12Rik	-	RIKEN cDNA 1700061F12 gene	ncRNA
mm_6361.1	chr1	72186504	72186507	-	1	NA	intron (NM_001005423, intron 2 of 4)	intron (NM_001005423, intron 2 of 4)	25802	NM_001005423	381269	Mm.422636	NM_001005423	ENSMUSG00000039395	Mreg	Gm974|Wdt2|dsu	melanoregulin	protein-coding
mm_7114.1	chr1	89968719	89968729	-	1	NA	intron (NM_139152, intron 3 of 5)	CpG	-37548	NM_010262	14472	Mm.204730	NM_010262	ENSMUSG00000034486	Gbx2	D130058E05Rik|Gbx-2|MMoxA|Stra7	gastrulation brain homeobox 2	protein-coding
mm_127018.1	chr15	96063213	96063218	+	1	NA	intron (NR_126493, intron 3 of 3)	intron (NR_126493, intron 3 of 3)	16338	NR_126493	402773	Mm.210567	NM_001033483	ENSMUSG00000078925	D030018L15Rik	-	nuclear receptor coactivator 2 pseudogene	pseudo
mm_76173.1	chr8	82392461	82392524	-	1	NA	intron (NM_001254747, intron 1 of 7)	Lx7|LINE|L1	10094	NM_001254747	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_109130.1	chr12	105837413	105837461	+	1	NA	3' UTR (NM_001347440, exon 21 of 21)	3' UTR (NM_001347440, exon 21 of 21)	52740	NM_001347440	18789	Mm.255877	NM_011112	ENSMUSG00000021111	Papola	Pap|PapIII|Plap	poly (A) polymerase alpha	protein-coding
mm_122292.1	chr14	34561738	34561751	-	1	NA	3' UTR (NM_001039076, exon 8 of 8)	3' UTR (NM_001039076, exon 8 of 8)	26863	NM_001039074	24131	Mm.29733	NM_011918	ENSMUSG00000021798	Ldb3	AW742271|PDLIM6|ZASP	LIM domain binding 3	protein-coding
mm_134189.1	chr16	10966580	10966613	-	1	NA	exon (NM_019980, exon 2 of 4)	exon (NM_019980, exon 2 of 4)	26525	NM_019980	56722	Mm.294753	NM_019980	ENSMUSG00000022500	Litaf	3222402J11Rik|C85531|N4WBP3|TBX1	LPS-induced TN factor	protein-coding
mm_81516.1	chr9	110036810	110036825	+	1	NA	exon (NM_008633, exon 8 of 19)	exon (NM_008633, exon 8 of 19)	-15204	NM_001311163	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_58008.1	chr6	136499717	136499720	-	1	NA	Intergenic	PB1|SINE|Alu	-19133	NM_019426	54343	Mm.173271	NM_019426	ENSMUSG00000030213	Atf7ip	2610204M12Rik|AM|Mcaf1	activating transcription factor 7 interacting protein	protein-coding
mm_107505.1	chr12	40038071	40038091	+	1	NA	promoter-TSS (NM_007487)	promoter-TSS (NM_007487)	-94	NM_001039515	11861	Mm.12723	NM_007487	ENSMUSG00000047446	Arl4a	AI467555|Arl4	ADP-ribosylation factor-like 4A	protein-coding
mm_13939.1	chr2	121170667	121170691	+	1	NA	promoter-TSS (NR_110985)	promoter-TSS (NR_110985)	446	NM_001290819	99334	Mm.188422	NM_178889	ENSMUSG00000050619	Zscan29	AW125441|Zfp690	zinc finger SCAN domains 29	protein-coding
mm_137049.1	chr17	17917831	17917839	+	1	NA	Intergenic	Intergenic	30011	NM_008039	14289	Mm.378918	NM_008039	ENSMUSG00000052270	Fpr2	E330010I07Rik|Fpr-rs2	formyl peptide receptor 2	protein-coding
mm_57739.1	chr6	128996407	128996409	-	1	NA	intron (NR_015455, intron 1 of 2)	intron (NR_015455, intron 1 of 2)	3447	NR_015455	408064	Mm.172429	NR_015455		BC064078	-	cDNA sequence BC064078	ncRNA
mm_127587.1	chr15	102331921	102331953	+	1	NA	TTS (NM_027044)	TTS (NM_027044)	228	NM_021713	60315	Mm.251638	NM_021713	ENSMUSG00000001285	Myg1	0610023A07Rik|2810433J21Rik|5830429P19Rik|AI325965|Gamm1	melanocyte proliferating gene 1	protein-coding
mm_7098.1	chr1	88702094	88702104	-	1	NA	promoter-TSS (NM_177305)	promoter-TSS (NM_177305)	92	NM_177305	320982	Mm.27968	NM_177305	ENSMUSG00000049866	Arl4c	A630084M22Rik|Arl7|LAK	ADP-ribosylation factor-like 4C	protein-coding
mm_154749.1	chrX	10582146	10582154	+	1	NA	intron (NM_019634, intron 2 of 7)	intron (NM_019634, intron 2 of 7)	97034	NM_019634	21912	Mm.18590	NM_019634	ENSMUSG00000058254	Tspan7	1200014P11Rik|A15|AI323365|Cd231|Mxs1|PE31|R74651|TALLA|Tm4sf2	tetraspanin 7	protein-coding
mm_30691.1	chr4	11546069	11546095	+	1	NA	exon (NM_001347055, exon 22 of 24)	exon (NM_001347055, exon 22 of 24)	-12838	NM_001039556	623474	Mm.491200	NM_177285	ENSMUSG00000078773	Rad54b	E130016E03Rik	RAD54 homolog B (S. cerevisiae)	protein-coding
mm_116659.1	chr13	49191695	49191718	-	1	NA	intron (NM_013610, intron 1 of 3)	intron (NM_013610, intron 1 of 3)	4159	NM_013610	18081	Mm.18503	NM_013610	ENSMUSG00000037966	Ninj1	AU024536	ninjurin 1	protein-coding
mm_34699.1	chr4	152076202	152076209	+	1	NA	Intergenic	Intergenic	-10658	NR_104381	269608	Mm.332102	NM_001004156	ENSMUSG00000039713	Plekhg5	BC023181|Syx	pleckstrin homology domain containing, family G (with RhoGef domain) member 5	protein-coding
mm_64347.1	chr7	142380894	142380913	+	1	NA	exon (NM_009983, exon 5 of 9)	exon (NM_009983, exon 5 of 9)	6967	NM_009983	13033	Mm.231395	NM_009983	ENSMUSG00000007891	Ctsd	CD|CatD	cathepsin D	protein-coding
mm_69463.1	chr7	133602111	133602165	-	1	NA	promoter-TSS (NM_028654)	promoter-TSS (NM_028654)	-23	NM_028654	73808	Mm.159067	NM_028654	ENSMUSG00000030976	Tex36	4930404H21Rik	testis expressed 36	protein-coding
mm_46104.1	chr5	92347801	92347807	-	1	NA	intron (NM_021274, intron 3 of 3)	intron (NM_021274, intron 3 of 3)	1085	NM_021274	15945	Mm.877	NM_021274	ENSMUSG00000034855	Cxcl10	C7|CRG-2|INP10|IP-10|IP10|Ifi10|Scyb10|gIP-10|mob-1	chemokine (C-X-C motif) ligand 10	protein-coding
mm_164417.1	chr16	38712996	38712997	-	1	NA	promoter-TSS (NM_020260)	promoter-TSS (NM_020260)	39	NM_020260	12549	Mm.370848	NM_020260	ENSMUSG00000022799	Arhgap31	5830477L08Rik|AU041750|Cdgap|D330026I07Rik	Rho GTPase activating protein 31	protein-coding
mm_154630.1	chrX	7762653	7762689	+	1	NA	promoter-TSS (NM_001271489)	promoter-TSS (NM_001271489)	10	NM_172472	209446	Mm.249142	NM_172472	ENSMUSG00000000134	Tfe3	F830016E06Rik|Tcfe3|Tfe-3|bHLHe33	transcription factor E3	protein-coding
mm_110670.1	chr12	65071100	65071102	-	1	NA	intron (NM_013902, intron 1 of 6)	RSINE1|SINE|B4	2837	NM_013902	30795	Mm.28480	NM_013902	ENSMUSG00000020949	Fkbp3	25kDa|FKBP-3|FKBP25	FK506 binding protein 3	protein-coding
mm_27405.1	chr3	51340515	51340521	-	1	NA	5' UTR (NM_001291059, exon 1 of 10)	5' UTR (NM_001291059, exon 1 of 10)	126	NM_001291059	69257	Mm.131038	NM_023502	ENSMUSG00000037174	Elf2	2610036A20Rik|A230104O07Rik|AW111824|BB183398|EU32|NERF|NERF-1A|NERF-1B|NERF-2	E74-like factor 2	protein-coding
mm_97941.1	chr11	83662580	83662594	+	1	NA	promoter-TSS (NM_013652)	promoter-TSS (NM_013652)	3	NM_013652	20303	Mm.244263	NM_013652	ENSMUSG00000018930	Ccl4	AT744.1|Act-2|MIP-1B|Mip1b|Scya4	chemokine (C-C motif) ligand 4	protein-coding
mm_4457.1	chr1	172699191	172699200	+	1	NA	3' UTR (NM_007768, exon 2 of 2)	3' UTR (NM_007768, exon 2 of 2)	1139	NM_007768	12944	Mm.28767	NM_007768	ENSMUSG00000037942	Crp	AI255847	C-reactive protein, pentraxin-related	protein-coding
mm_29779.1	chr3	127408987	127409008	-	1	NA	promoter-TSS (NM_001327939)	promoter-TSS (NM_001327939)	61	NM_001327939	109676	Mm.220242	NM_178655	ENSMUSG00000032826	Ank2	100043364|AI835472|AW491075|Ank-2|Gm4392	ankyrin 2, brain	protein-coding
mm_17324.1	chr2	26502202	26502220	-	1	NA	intron (NM_008714, intron 1 of 33)	intron (NM_008714, intron 1 of 33)	1611	NM_008714	18128	Mm.290610	NM_008714	ENSMUSG00000026923	Notch1	9930111A19Rik|Mis6|N1|Tan1|lin-12	notch 1	protein-coding
mm_34846.1	chr4	155414978	155414986	+	1	NA	intron (NR_102283, intron 1 of 4)	RSINE1|SINE|B4	5792	NM_001166029	544678	Mm.472798	NM_177674	ENSMUSG00000078490	Cfap74	2010015L04Rik|A530045M11	cilia and flagella associated protein 74	protein-coding
mm_147868.1	chr18	64476615	64476618	-	1	NA	intron (NM_007998, intron 3 of 10)	B1_Mur4|SINE|Alu	12450	NM_007998	14151	Mm.1070	NM_007998	ENSMUSG00000024588	Fech	AI894116|Fcl|fch	ferrochelatase	protein-coding
mm_123551.1	chr14	66834303	66834321	-	1	NA	exon (NM_009955, exon 4 of 14)	exon (NM_009955, exon 4 of 14)	34288	NM_009955	12934	Mm.352648	NM_009955	ENSMUSG00000022048	Dpysl2	AI851130|Crmp2|DRP2|Musunc33|TOAD-64|Ulip2	dihydropyrimidinase-like 2	protein-coding
mm_77097.1	chr8	110902443	110902467	-	1	NA	promoter-TSS (NR_052009)	promoter-TSS (NR_052009)	33	NM_172283	234730	Mm.102591	NM_172283	ENSMUSG00000033703	Fuk	1110046B12Rik|AI303278	fucokinase	protein-coding
mm_101810.1	chr11	46378331	46378348	-	1	NA	intron (NM_010583, intron 1 of 16)	RSINE1|SINE|B4	11176	NM_001281968	16428	Mm.339927	NM_010583	ENSMUSG00000020395	Itk	Emt|Tcsk|Tsk	IL2 inducible T cell kinase	protein-coding
mm_56773.1	chr6	116628922	116628934	-	1	NA	promoter-TSS (NM_026057)	promoter-TSS (NM_026057)	0	NM_001302439	67255	Mm.18810	NM_026057	ENSMUSG00000059878	Zfp422	2900028O21Rik|AU041373|KOX15|Krox-25-2|Krox-26|Krox25|Krox26|Znf22	zinc finger protein 422	protein-coding
mm_160172.1	chr7	45282488	45282488	+	1	NA	promoter-TSS (NM_001033176)	promoter-TSS (NM_001033176)	-385	NM_001033176	76713	Mm.425445	NM_001033176	ENSMUSG00000070568	Slc6a21	1700039E15Rik|Gm19188	solute carrier family 6 member 21	protein-coding
mm_146231.1	chr18	77119810	77119827	+	1	NA	intron (NM_008602, intron 3 of 13)	intron (NM_008602, intron 3 of 13)	54138	NM_001164168	17344	Mm.6370	NM_008602	ENSMUSG00000025423	Pias2	6330408K17Rik|AI462206|ARIP3|AU018068|Dib|Miz1|PIASxalpha|PIASxb|PIASxbeta|SIZ2	protein inhibitor of activated STAT 2	protein-coding
mm_105985.1	chr11	115612941	115612975	-	1	NA	promoter-TSS (NM_027162)	promoter-TSS (NM_027162)	11	NM_001243584	69674	Mm.390387	NM_027162	ENSMUSG00000020743	Mif4gd	1110014L05Rik|2310075G12Rik	MIF4G domain containing	protein-coding
mm_78285.1	chr9	22156883	22156896	+	1	NA	promoter-TSS (NM_001082532)	promoter-TSS (NM_001082532)	43	NM_001082532	66268	Mm.28924	NM_025457	ENSMUSG00000010607	Pigyl	1810008A14Rik|PIG-Y|Pigy	phosphatidylinositol glycan anchor biosynthesis, class Y-like	protein-coding
mm_128929.1	chr15	74636293	74636330	-	1	NA	promoter-TSS (NM_001177437)	promoter-TSS (NM_001177437)	7	NM_001177437	69439	Mm.263708	NM_001177437	ENSMUSG00000022603	Mroh4	1700016M24Rik	maestro heat-like repeat family member 4	protein-coding
mm_157126.1	chrX	9446728	9446759	-	1	NA	exon (NM_007807, exon 9 of 13)	exon (NM_007807, exon 9 of 13)	22581	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_104251.1	chr11	88864535	88864591	-	1	NA	promoter-TSS (NM_001042541)	promoter-TSS (NM_001042541)	23	NM_001042541	11640	Mm.2969	NM_009648	ENSMUSG00000018428	Akap1	AKAP121|AKAP84|Akap|C76494|C81186|DAKAP1|S-AKAP84	A kinase (PRKA) anchor protein 1	protein-coding
mm_43219.1	chr5	129755682	129755715	+	1	NA	intron (NM_008095, intron 9 of 9)	T-rich|Low_complexity|Low_complexity	30623	NM_008095	14467	Mm.12468	NM_008095	ENSMUSG00000029432	Gbas	AV006093|Nipsnap2	glioblastoma amplified sequence	protein-coding
mm_146373.1	chr18	82584782	82584802	+	1	NA	3' UTR (NM_010777, exon 7 of 7)	3' UTR (NM_010777, exon 7 of 7)	30284	NM_001025254	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_81931.1	chr9	120179904	120179914	+	1	NA	Intergenic	L1ME3Cz|LINE|L1	30167	NM_001039364	17433	Mm.486167	NM_008614	ENSMUSG00000032517	Mobp	AI835053|AI839848|MOBP155|MOBP170|MOBP69|MOBP73|MOBP81|R74645	myelin-associated oligodendrocytic basic protein	protein-coding
mm_94644.1	chr11	16915357	16915359	+	1	NA	Intergenic	Intergenic	35924	NR_110421	72735	Mm.268598	NR_015469		Eldr	2810442I21Rik|4930500E12Rik|Fabl	Egfr long non-coding downstream RNA	ncRNA
mm_48932.1	chr6	4537774	4537798	+	1	NA	exon (NM_007743, exon 49 of 52)	exon (NM_007743, exon 49 of 52)	32168	NM_007743	12843	Mm.277792	NM_007743	ENSMUSG00000029661	Col1a2	AA960264|AI325291|Col1a-2|Cola-2|Cola2|oim	collagen, type I, alpha 2	protein-coding
mm_82466.1	chr9	15914417	15914423	-	1	NA	3' UTR (NM_001080814, exon 25 of 25)	3' UTR (NM_001080814, exon 25 of 25)	-39864	NM_145712	244701	Mm.222631	NM_145712	ENSMUSG00000050901	Mtnr1b	Mel-1B-R|Mel1b|Mt2	melatonin receptor 1B	protein-coding
mm_120348.1	chr14	63860291	63860361	+	1	NA	promoter-TSS (NM_028228)	promoter-TSS (NM_028228)	14	NM_028228	72400	Mm.379214	NM_028228	ENSMUSG00000021958	Pinx1	2210403I16Rik|2610028A01Rik|67-11-3|AU024023|LPTS|LPTS1	PIN2/TERF1 interacting, telomerase inhibitor 1	protein-coding
mm_7055.1	chr1	87128369	87128378	-	1	NA	TTS (NM_007432)	TTS (NM_007432)	3365	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_169617.1	chr15	38078431	38078438	-	1	NA	5' UTR (NM_001081359, exon 1 of 59)	5' UTR (NM_001081359, exon 1 of 59)	420	NM_001112721	70790	Mm.476840	NM_027553	ENSMUSG00000037487	Ubr5	Edd|Edd1	ubiquitin protein ligase E3 component n-recognin 5	protein-coding
mm_158005.1	chrX	95196605	95196694	-	1	NA	Intergenic	Intergenic	-30110	NM_001033329	236915	Mm.44841	NM_001033329	ENSMUSG00000025656	Arhgef9	9630036L12Rik	CDC42 guanine nucleotide exchange factor (GEF) 9	protein-coding
mm_123015.1	chr14	55106548	55106594	-	1	NA	promoter-TSS (NM_007455)	promoter-TSS (NM_007455)	22	NM_001303502	11766	Mm.238879	NM_007455	ENSMUSG00000040701	Ap1g2	Adtg2|G2ad	adaptor protein complex AP-1, gamma 2 subunit	protein-coding
mm_52902.1	chr6	122761231	122761241	+	1	NA	Intergenic	Intergenic	-18491	NM_011401	20527	Mm.395108	NM_011401	ENSMUSG00000003153	Slc2a3	AA408729|AL023014|AL024341|AU040424|C78366|Glut-3|Glut3	solute carrier family 2 (facilitated glucose transporter), member 3	protein-coding
mm_61064.1	chr7	50599173	50599179	+	1	NA	promoter-TSS (NM_172901)	promoter-TSS (NM_172901)	-14	NM_172901	243996	Mm.443270	NM_172901	ENSMUSG00000084234	4933405O20Rik	-	RIKEN cDNA 4933405O20 gene	protein-coding
mm_25565.1	chr3	116563065	116563088	+	1	NA	5' UTR (NM_175413, exon 1 of 9)	5' UTR (NM_175413, exon 1 of 9)	103	NM_175413	109245	Mm.216027	NM_027321	ENSMUSG00000027961	Lrrc39	2010005E21Rik|9430028I06Rik|Myomasp	leucine rich repeat containing 39	protein-coding
mm_88367.1	chr10	75948293	75948333	+	1	NA	promoter-TSS (NM_009514)	promoter-TSS (NM_009514)	1	NM_009514	22364	Mm.333851	NM_009514	ENSMUSG00000000903	Vpreb3	8HS-20|AI528709|Vpreb-3	pre-B lymphocyte gene 3	protein-coding
mm_103376.1	chr11	75348262	75348323	-	1	NA	promoter-TSS (NM_026653)	promoter-TSS (NM_026653)	91	NM_001164223	68275	Mm.102574	NM_026653	ENSMUSG00000000751	Rpa1	5031405K23Rik|70kDa|AA589576|AW557552|RF-A|RP-A|Rpa	replication protein A1	protein-coding
mm_153125.1	chr19	34008357	34008367	-	1	NA	5' UTR (NM_172837, exon 1 of 10)	5' UTR (NM_172837, exon 1 of 10)	108	NM_001205349	240633	Mm.58924	NM_172837	ENSMUSG00000024771	Lipk	9930115F20|BC055815|Lipl2	lipase, family member K	protein-coding
mm_8464.1	chr1	153332700	153332722	-	1	NA	promoter-TSS (NM_010683)	promoter-TSS (NM_010683)	75	NM_010683	226519	Mm.1249	NM_010683	ENSMUSG00000026478	Lamc1	Lamb2	laminin, gamma 1	protein-coding
mm_20883.1	chr2	148850900	148850954	-	1	NA	promoter-TSS (NM_029960)	promoter-TSS (NM_029960)	7	NM_029960	77705	Mm.159975	NM_029960	ENSMUSG00000027446	9230104L09Rik	mCST E2	RIKEN cDNA 9230104L09 gene	protein-coding
mm_78683.1	chr9	40794539	40794562	+	1	NA	Intergenic	PB1D7|SINE|Alu	-6723	NM_031165	15481	Mm.290774	NM_031165	ENSMUSG00000015656	Hspa8	2410008N15Rik|Hsc70|Hsc71|Hsc73|Hsp73|Hspa10	heat shock protein 8	protein-coding
mm_153483.1	chr19	41277022	41277061	-	1	NA	intron (NM_031376, intron 16 of 16)	intron (NM_031376, intron 16 of 16)	-13037	NM_133352	107358	Mm.246440	NM_133352	ENSMUSG00000025016	Tm9sf3	1810073M23Rik|2810031D16Rik|AI115521|AI413748|AW146116|AW549777|Smbp|mKIAA4036	transmembrane 9 superfamily member 3	protein-coding
mm_2116.1	chr1	87878163	87878183	+	1	NA	intron (NM_177646, intron 1 of 29)	intron (NM_177646, intron 1 of 29)	-23874	NR_136921	100503175	Mm.426422	NR_136921	ENSMUSG00000101942	Gm19582	-	predicted gene, 19582	ncRNA
mm_152088.1	chr19	6907703	6907712	-	1	NA	intron (NM_012021, intron 2 of 5)	intron (NM_012021, intron 2 of 5)	1938	NM_012021	54683	Mm.279782	NM_012021	ENSMUSG00000024953	Prdx5	AOEB166|AOPP|Pmp20|Prdx6|PrxV	peroxiredoxin 5	protein-coding
mm_135774.1	chr16	56831867	56831875	-	1	NA	intron (NM_019631, intron 1 of 5)	intron (NM_019631, intron 1 of 5)	-36013	NM_172825	239853	Mm.258979	NM_172825	ENSMUSG00000022755	Adgrg7	9130020O16Rik|Gpr128	adhesion G protein-coupled receptor G7	protein-coding
mm_62641.1	chr7	107665002	107665015	+	1	NA	intron (NM_001163557, intron 3 of 25)	intron (NM_001163557, intron 3 of 25)	58164	NM_001163557	19024	Mm.2817	NM_008905	ENSMUSG00000036528	Ppfibp2	Cclp1	PTPRF interacting protein, binding protein 2 (liprin beta 2)	protein-coding
mm_120281.1	chr14	63132492	63132504	+	1	NA	intron (NM_007798, intron 1 of 9)	intron (NM_007798, intron 1 of 9)	10036	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_150187.1	chr19	32665517	32665595	+	1	NA	exon (NM_011864, exon 13 of 13)	exon (NM_011864, exon 13 of 13)	45551	NM_011864	23972	Mm.203916	NM_011864	ENSMUSG00000024899	Papss2	1810018P12Rik|AI159688|AtpsU2|Atpsk2|Sk2|bm	3'-phosphoadenosine 5'-phosphosulfate synthase 2	protein-coding
mm_153859.1	chr19	46503677	46503696	-	1	NA	intron (NM_053100, intron 1 of 5)	intron (NM_053100, intron 1 of 5)	2038	NM_053100	93679	Mm.392177	NM_053100	ENSMUSG00000025034	Trim8	AA408830|BB006755|GERP|Rnf27	tripartite motif-containing 8	protein-coding
mm_74239.1	chr8	124614182	124614219	+	1	NA	intron (NM_023709, intron 16 of 19)	ID_B1|SINE|B4	38089	NM_023709	73647	Mm.6209	NM_023709	ENSMUSG00000031981	Capn9	2200003B16Rik|GC36|nCL-4|nCL4	calpain 9	protein-coding
mm_6927.1	chr1	84868230	84868233	-	1	NA	intron (NM_025386, intron 1 of 3)	ID4_|SINE|ID	28390	NM_025386	66153	Mm.381192	NM_025386	ENSMUSG00000073633	Fbxo36	0610008D19Rik|1110020F21Rik|2410002G19Rik|D1Ertd757e	F-box protein 36	protein-coding
mm_28012.1	chr3	83043461	83043477	-	1	NA	exon (NM_181849, exon 7 of 8)	exon (NM_181849, exon 7 of 8)	6394	NM_181849	110135	Mm.30063	NM_181849	ENSMUSG00000033831	Fgb	2510049G14Rik	fibrinogen beta chain	protein-coding
mm_161756.1	chr17	35141472	35141472	+	1	NA	exon (NM_001252469, exon 8 of 24)	exon (NM_001252469, exon 8 of 24)	5758	NM_001252469	224727	Mm.203962	NM_057171	ENSMUSG00000024392	Bag6	2410045D21Rik|AA408914|BAG-6|Bat3|D17H6S52E|G3|Scythe	BCL2-associated athanogene 6	protein-coding
mm_46255.1	chr5	99327094	99327113	-	1	NA	intron (NR_030692, intron 3 of 3)	B4A|SINE|B4	-74176	NM_145839	320292	Mm.259074	NM_145839	ENSMUSG00000089809	Rasgef1b	4732452O09Rik|GPIgamma4|Gpig4	RasGEF domain family, member 1B	protein-coding
mm_148493.1	chr19	4154641	4154668	+	1	NA	promoter-TSS (NM_016933)	promoter-TSS (NM_016933)	8	NM_016933	19265	Mm.271937	NM_016933	ENSMUSG00000045826	Ptprcap	AI605264|CD-45-AP|LPAP|LSM-1	protein tyrosine phosphatase, receptor type, C polypeptide-associated protein	protein-coding
mm_100402.1	chr11	119393392	119393425	+	1	NA	Intergenic	Intergenic	2936	NR_035453	100316690		NR_035453	ENSMUSG00000088015	Mir1932	mir-1932|mmu-mir-1932	microRNA 1932	ncRNA
mm_69210.1	chr7	127449110	127449166	-	1	NA	promoter-TSS (NM_175163)	promoter-TSS (NM_175163)	20	NM_175163	71131	Mm.474533	NM_175163	ENSMUSG00000048921	Zfp689	4933416E05Rik|Znf689	zinc finger protein 689	protein-coding
mm_151011.1	chr19	46707722	46707732	+	1	NA	intron (NM_020577, intron 1 of 10)	intron (NM_020577, intron 1 of 10)	284	NM_020577	57344	Mm.28566	NM_020577	ENSMUSG00000003559	As3mt	2310045H08Rik|Cyt19	arsenic (+3 oxidation state) methyltransferase	protein-coding
mm_13986.1	chr2	121544440	121544444	+	1	NA	3' UTR (NM_030234, exon 13 of 13)	3' UTR (NM_030234, exon 13 of 13)	37719	NM_001290986	241627	Mm.293284	NM_030234	ENSMUSG00000027242	Wdr76	5830411K18Rik|6030457D09|AA517836	WD repeat domain 76	protein-coding
mm_137723.1	chr17	29142322	29142323	+	1	NA	intron (NM_001002786, intron 3 of 7)	ORR1A2|LTR|ERVL-MaLR	7266	NM_001002786	442827	Mm.440341	NM_001002786	ENSMUSG00000064147	Rab44	9830134C10Rik	RAB44, member RAS oncogene family	protein-coding
mm_136649.1	chr17	5850787	5850800	+	1	NA	intron (NM_025664, intron 1 of 17)	MTE2a|LTR|ERVL-MaLR	9413	NM_025664	66616	Mm.89515	NM_025664	ENSMUSG00000002365	Snx9	2700073N08Rik|SDP1|SH3PX1	sorting nexin 9	protein-coding
mm_71960.1	chr8	70527830	70527840	+	1	NA	promoter-TSS (NM_001199631)	promoter-TSS (NM_001199631)	-11	NM_001199631	14232	Mm.141864	NM_010223	ENSMUSG00000019428	Fkbp8	38kDa|FKBP-38|FKBP-8|Fkbp38	FK506 binding protein 8	protein-coding
mm_74979.1	chr8	27141565	27141584	-	1	NA	3' UTR (NM_001080813, exon 6 of 6)	3' UTR (NM_001080813, exon 6 of 6)	-1336	NR_045840	71082	Mm.395259	NR_045840		4933416M07Rik	-	RIKEN cDNA 4933416M07 gene	ncRNA
mm_104456.1	chr11	95041392	95041407	-	1	NA	promoter-TSS (NM_133667)	promoter-TSS (NM_133667)	-28	NM_133667	18604	Mm.29768	NM_133667	ENSMUSG00000038967	Pdk2	-	pyruvate dehydrogenase kinase, isoenzyme 2	protein-coding
mm_171364.1	chr4	117367483	117367494	+	1	NA	intron (NM_025739, intron 2 of 14)	intron (NM_025739, intron 2 of 14)	7973	NM_001310729	66743	Mm.318331	NM_025739	ENSMUSG00000028677	Rnf220	4732477A13|4931406I20Rik|5730503K05Rik|AV302541	ring finger protein 220	protein-coding
mm_155262.1	chrX	58019587	58019604	+	1	NA	Intergenic	Intergenic	-11033	NM_009575	22773	Mm.255890	NM_009575	ENSMUSG00000067860	Zic3	Bn|Ka	zinc finger protein of the cerebellum 3	protein-coding
mm_51779.1	chr6	88193577	88193596	+	1	NA	Intergenic	CpG	-5078	NM_008090	14461	Mm.491156	NM_008090	ENSMUSG00000015053	Gata2	Gata-2	GATA binding protein 2	protein-coding
mm_17851.1	chr2	34754342	34754355	-	1	NA	5' UTR (NM_025709, exon 2 of 27)	5' UTR (NM_025709, exon 2 of 27)	884	NM_025709	66691	Mm.156452	NM_025709	ENSMUSG00000026867	Gapvd1	2010005B09Rik|4432404J10Rik|AW108497|Gapex-5|RAP6|RME-6|mKIAA1521	GTPase activating protein and VPS9 domains 1	protein-coding
mm_170280.1	chr18	27599225	27599229	+	1	NA	Intergenic	Intergenic	-960937	NR_045398	320624	Mm.50107	NR_045398		4930474G06Rik	-	RIKEN cDNA 4930474G06 gene	ncRNA
mm_74364.1	chr8	128359359	128359369	+	1	NA	TTS (NR_035436)	TTS (NR_035436)	123	NR_035436	100316680		NR_035436	ENSMUSG00000084523	Mir1903	Mirn1903|mmu-mir-1903	microRNA 1903	ncRNA
mm_159322.1	chr3	15848443	15848443	-	1	NA	promoter-TSS (NM_001173459)	promoter-TSS (NM_001173459)	44	NM_001173459	100038947	Mm.330924	NM_001173459	ENSMUSG00000074677	LOC100038947	-	signal-regulatory protein beta 1-like	protein-coding
mm_122435.1	chr14	45219247	45219257	-	1	NA	promoter-TSS (NM_027518)	promoter-TSS (NM_027518)	173	NM_172597	70561	Mm.28129	NM_172597	ENSMUSG00000021830	Txndc16	5730420B22Rik|C77647	thioredoxin domain containing 16	protein-coding
mm_27339.1	chr3	50412287	50412296	-	1	NA	intron (NM_011990, intron 6 of 11)	(A)n|Simple_repeat|Simple_repeat	31322	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_115352.1	chr13	112763979	112763984	+	1	NA	Intergenic	Intergenic	-36796	NM_008903	19012	Mm.291029	NM_008247	ENSMUSG00000021759	Plpp1	Hic53|Hpic53|LPP-1|LPP1|PAP-2a|PAP2-alpha|PAP2a|Ppap2a|mPAP	phospholipid phosphatase 1	protein-coding
mm_79495.1	chr9	57095363	57095379	+	1	NA	exon (NM_011378, exon 6 of 22)	exon (NM_011378, exon 6 of 22)	18995	NM_011378	20466	Mm.15755	NM_011378	ENSMUSG00000042557	Sin3a	AW553200|Sin3|mKIAA4126|mSin3A	transcriptional regulator, SIN3A (yeast)	protein-coding
mm_25334.1	chr3	106573973	106573989	+	1	NA	3' UTR (NM_026013, exon 9 of 9)	3' UTR (NM_026013, exon 9 of 9)	-26179	NM_133869	99712	Mm.429443	NM_133869	ENSMUSG00000040774	Cept1	9930118K05Rik|mCEPT1	choline/ethanolaminephosphotransferase 1	protein-coding
mm_127007.1	chr15	95801458	95801484	+	1	NA	intron (NM_175344, intron 1 of 19)	intron (NM_175344, intron 1 of 19)	10628	NM_001253813	105722	Mm.38087	NM_175344	ENSMUSG00000064210	Ano6	2900059G15Rik|AA407480|AW554778|F730003B03Rik|Tmem16f	anoctamin 6	protein-coding
mm_19747.1	chr2	104849466	104849483	-	1	NA	intron (NM_178695, intron 1 of 5)	CpG	376	NM_178695	228413	Mm.259609	NM_178695	ENSMUSG00000027171	Prrg4	9930111I18Rik|TMG4	proline rich Gla (G-carboxyglutamic acid) 4 (transmembrane)	protein-coding
mm_55802.1	chr6	82805068	82805077	-	1	NA	Intergenic	MER45B|DNA|hAT-Tip100	-30618	NM_013820	15277	Mm.255848	NM_013820	ENSMUSG00000000628	Hk2	AI642394|HKII	hexokinase 2	protein-coding
mm_121219.1	chr14	103054886	103054896	+	1	NA	exon (NM_008392, exon 5 of 5)	exon (NM_008392, exon 5 of 5)	7879	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_116087.1	chr13	28650141	28650146	-	1	NA	intron (NR_045053, intron 5 of 8)	intron (NR_045053, intron 5 of 8)	60730	NR_105787	102466635		NR_105787	ENSMUSG00000099158	Mir6368	Gm27800|mmu-mir-6368	microRNA 6368	ncRNA
mm_115753.1	chr13	19188610	19188615	-	1	NA	Intergenic	Intergenic	207201	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_33397.1	chr4	129820703	129820709	+	1	NA	promoter-TSS (NM_001164745)	promoter-TSS (NM_001164745)	-2	NM_001164745	19244	Mm.193688	NM_008974	ENSMUSG00000028788	Ptp4a2	Prl-2	protein tyrosine phosphatase 4a2	protein-coding
mm_119048.1	chr14	30626647	30626653	+	1	NA	promoter-TSS (NM_011103)	promoter-TSS (NM_011103)	-442	NM_011103	18753	Mm.2314	NM_011103	ENSMUSG00000021948	Prkcd	AI385711|D14Ertd420e|PKC[d]|PKCdelta|Pkcd	protein kinase C, delta	protein-coding
mm_15995.1	chr2	167062816	167062854	+	1	NA	promoter-TSS (NR_138563)	promoter-TSS (NR_138563)	-99	NR_138563	68949	Mm.391959	NM_001081005		Zfas1	1500012F01Rik|Zfos1	zinc finger, NFX1-type containing 1, antisense RNA 1	ncRNA
mm_68399.1	chr7	109602626	109602637	-	1	NA	intron (NM_001001326, intron 1 of 19)	intron (NM_001001326, intron 1 of 19)	13937	NR_037617	76954	Mm.252009	NM_029811	ENSMUSG00000031024	St5	2010004M01Rik|2610305K15Rik	suppression of tumorigenicity 5	protein-coding
mm_142245.1	chr17	37483000	37483042	-	1	NA	exon (NM_008204, exon 2 of 4)	exon (NM_008204, exon 2 of 4)	508	NM_008204	14990	Mm.329041	NM_008204	ENSMUSG00000016283	H2-M2	H-2M2|Thy19.4	histocompatibility 2, M region locus 2	protein-coding
mm_156295.1	chrX	136837570	136837576	+	1	NA	3' UTR (NM_011123, exon 7 of 7)	3' UTR (NM_011123, exon 7 of 7)	14827	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_149371.1	chr19	11372658	11372672	+	1	NA	Intergenic	Intergenic	-2823	NM_001310331	666907		NM_001310331	ENSMUSG00000101389	Ms4a4a	EG666907	membrane-spanning 4-domains, subfamily A, member 4A	protein-coding
mm_130097.1	chr15	89425601	89425631	-	1	NA	TTS (NM_007692)	TTS (NM_007692)	246	NM_009948	12895	Mm.227738	NM_009948	ENSMUSG00000078937	Cpt1b	Cpt1|Cpt1-m|Cpti|Cpti-m|M-cpti	carnitine palmitoyltransferase 1b, muscle	protein-coding
mm_124063.1	chr14	78332046	78332057	-	1	NA	Intergenic	L2c|LINE|L2	-24008	NM_011613	21943	Mm.249221	NM_011613	ENSMUSG00000022015	Tnfsf11	Ly109l|ODF|OPGL|RANKL|Trance	tumor necrosis factor (ligand) superfamily, member 11	protein-coding
mm_93217.1	chr10	94961477	94961481	-	1	NA	Intergenic	MLT1L|LTR|ERVL-MaLR	-16901	NM_018797	54712	Mm.256712	NM_018797	ENSMUSG00000074785	Plxnc1	2510048K12Rik|AW742158|CD232|Vespr	plexin C1	protein-coding
mm_48753.1	chr5	148012314	148012332	-	1	NA	intron (NM_029920, intron 1 of 14)	ORR1B1|LTR|ERVL-MaLR	55003	NM_029920	77521	Mm.244177	NM_029920	ENSMUSG00000029651	Mtus2	5730592G18Rik|A730013O20Rik|AU067634|C130038G02Rik|Cazip|Gm763|mKIAA0774	microtubule associated tumor suppressor candidate 2	protein-coding
mm_166183.1	chr5	31713253	31713286	-	1	NA	intron (NM_181281, intron 2 of 10)	intron (NM_181281, intron 2 of 10)	15219	NM_144541	107976	Mm.482126	NM_144541	ENSMUSG00000052139	Bre	6030405P19Rik|AI429776|B830038C02Rik	brain and reproductive organ-expressed protein	protein-coding
mm_58023.1	chr6	136661791	136661809	-	1	NA	promoter-TSS (NM_025806)	promoter-TSS (NM_025806)	93	NM_025806	66857	Mm.3311	NM_025806	ENSMUSG00000030214	Plbd1	1100001H23Rik	phospholipase B domain containing 1	protein-coding
mm_135522.1	chr16	48872969	48872996	-	1	NA	exon (NM_181596, exon 2 of 4)	exon (NM_181596, exon 2 of 4)	374	NM_181596	245195	Mm.231288	NM_181596	ENSMUSG00000022651	Retnlg	Fizz3|Relmg|Xcp1	resistin like gamma	protein-coding
mm_146862.1	chr18	24530053	24530129	-	1	NA	5' UTR (NM_144861, exon 1 of 7)	5' UTR (NM_144861, exon 1 of 7)	113	NM_144861	225283	Mm.28427	NM_144861	ENSMUSG00000040446	Rprd1a	C77387|mKIAA4077	regulation of nuclear pre-mRNA domain containing 1A	protein-coding
mm_39777.1	chr5	30144226	30144249	+	1	NA	exon (NM_178878, exon 5 of 20)	exon (NM_178878, exon 5 of 20)	10743	NM_178878	97212	Mm.200497	NM_178878	ENSMUSG00000025745	Hadha	C77020|Mtpa	hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), alpha subunit	protein-coding
mm_77218.1	chr8	115411900	115411940	-	1	NA	Intergenic	Intergenic	294974	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_44613.1	chr5	25498723	25498744	-	1	NA	promoter-TSS (NM_001081383)	promoter-TSS (NM_001081383)	50	NM_001081383	231051	Mm.332268	NM_001081383	ENSMUSG00000038056	Kmt2c	E330008K23Rik|HALR|Mll3|mKIAA1506	lysine (K)-specific methyltransferase 2C	protein-coding
mm_167312.1	chr8	61902737	61902741	-	1	NA	promoter-TSS (NM_001293772)	promoter-TSS (NM_001293772)	-45	NM_001293772	72333	Mm.29933	NM_001081390	ENSMUSG00000058056	Palld	2410003B16Rik|6030492A02	palladin, cytoskeletal associated protein	protein-coding
mm_103088.1	chr11	69920521	69920535	-	1	NA	5' UTR (NM_001166590, exon 1 of 6)	5' UTR (NM_001166590, exon 1 of 6)	102	NM_001166590	276770	Mm.18026	NM_181582	ENSMUSG00000078812	Eif5a	AA410058|D19Wsu54e|Eif4d|Eif5a1|eIF-4D|eIF-5A|eIF-5A-1|eIF-5A1	eukaryotic translation initiation factor 5A	protein-coding
mm_109966.1	chr12	12788668	12788681	-	1	NA	Intergenic	Intergenic	-118757	NR_136889	102637952	Mm.421393	NR_136889		Gm34637	-	predicted gene, 34637	ncRNA
mm_133131.1	chr16	65828647	65828670	+	1	NA	intron (NM_028572, intron 2 of 3)	intron (NM_028572, intron 2 of 3)	13025	NM_028572	73569	Mm.25670	NM_028572	ENSMUSG00000091243	Vgll3	1700110N18Rik|4832416J22|C80713|Vgl-3|Vito-2	vestigial like family member 3	protein-coding
mm_19358.1	chr2	91082983	91082999	-	1	NA	Intergenic	Intergenic	-12676	NM_001290765	68427	Mm.192375	NM_026721	ENSMUSG00000002105	Slc39a13	1100001L14Rik|AA387663|ZIP-13|ZIP13	solute carrier family 39 (metal ion transporter), member 13	protein-coding
mm_25932.1	chr3	131368971	131368979	+	1	NA	Intergenic	URR1A|DNA|hAT-Charlie	-24052	NM_028943	74442	Mm.273360	NM_028943	ENSMUSG00000050931	Sgms2	4933405A16Rik|5133401H06Rik|AI854299	sphingomyelin synthase 2	protein-coding
mm_106452.1	chr11	120017059	120017160	-	1	NA	intron (NM_001198787, intron 3 of 13)	intron (NM_001198787, intron 3 of 13)	-2247	NR_029767	723844		NR_029767	ENSMUSG00000065600	Mir338	Mirn338|mir-338|mmu-mir-338	microRNA 338	ncRNA
mm_173.1	chr1	13436491	13436494	+	1	NA	Intergenic	Intergenic	-62409	NM_008678	17978	Mm.2537	NM_008678	ENSMUSG00000005886	Ncoa2	D1Ertd433e|GRIP-1|Grip1|KAT13C|NCoA-2|SRC-2|TIF2|bHLHe75	nuclear receptor coactivator 2	protein-coding
mm_149476.1	chr19	11748454	11748480	+	1	NA	exon (NM_008118, exon 2 of 9)	exon (NM_008118, exon 2 of 9)	908	NM_008118	14603	Mm.456	NM_008118	ENSMUSG00000024682	Gif	AV073125	gastric intrinsic factor	protein-coding
mm_45503.1	chr5	72417718	72417728	-	1	NA	intron (NM_016869, intron 5 of 21)	intron (NM_016869, intron 5 of 21)	86485	NM_016869	53419	Mm.332425	NM_016869	ENSMUSG00000005220	Corin	AV273130|Lrp4	corin	protein-coding
mm_50287.1	chr6	47453955	47453992	+	1	NA	promoter-TSS (NM_012042)	promoter-TSS (NM_012042)	-351	NM_012042	26965	Mm.87611	NM_012042	ENSMUSG00000029686	Cul1	-	cullin 1	protein-coding
mm_2.1	chr1	3873211	3873235	+	1	NA	Intergenic	Lx2B2|LINE|L1	-201725	NM_001011874	497097	Mm.454496	NM_001011874	ENSMUSG00000051951	Xkr4	AY534250|Gm210|XRG4|mKIAA1889	X-linked Kx blood group related 4	protein-coding
mm_19950.1	chr2	117319611	117319616	-	1	NA	intron (NM_011246, intron 2 of 16)	intron (NM_011246, intron 2 of 16)	23264	NM_011246	19419	Mm.42150	NM_011246	ENSMUSG00000027347	Rasgrp1	Rasgrp	RAS guanyl releasing protein 1	protein-coding
mm_81494.1	chr9	110027743	110027753	+	1	NA	exon (NM_008633, exon 5 of 19)	exon (NM_008633, exon 5 of 19)	-24273	NM_001311163	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_32000.1	chr4	94603262	94603281	+	1	NA	promoter-TSS (NM_172695)	promoter-TSS (NM_172695)	-24	NM_172695	18786	Mm.490101	NM_172695	ENSMUSG00000028577	Plaa	2410007N06|AI536418|AU018445|AW208417|D4Ertd618e|PLA2P|PLAP|Ufd3	phospholipase A2, activating protein	protein-coding
mm_151289.1	chr19	55315674	55315677	+	1	NA	promoter-TSS (NM_016862)	promoter-TSS (NM_016862)	357	NM_025883	66980	Mm.386789	NM_025883	ENSMUSG00000024982	Zdhhc6	2400007G07Rik|5930409M18Rik|AI462345|C77369	zinc finger, DHHC domain containing 6	protein-coding
mm_40667.1	chr5	65391578	65391588	+	1	NA	promoter-TSS (NM_024471)	promoter-TSS (NM_024471)	86	NM_001310612	79464	Mm.195776	NM_024471	ENSMUSG00000029199	Lias	2900022L22Rik|4933425M12Rik|7a5ex|C77512|LS|lip-syn	lipoic acid synthetase	protein-coding
mm_155411.1	chrX	73483581	73483588	+	1	NA	promoter-TSS (NM_007542)	promoter-TSS (NM_007542)	-17	NM_007542	12111	Mm.2608	NM_007542	ENSMUSG00000031375	Bgn	BG|DSPG1|PG-S1|PGI|SLRR1A	biglycan	protein-coding
mm_30573.1	chr4	3834468	3834475	+	1	NA	3' UTR (NM_026147, exon 4 of 4)	3' UTR (NM_026147, exon 4 of 4)	1184	NM_026147	67427	Mm.21938	NM_026147	ENSMUSG00000028234	Rps20	4632426K06Rik|Dsk4	ribosomal protein S20	protein-coding
mm_42742.1	chr5	120711777	120711787	+	1	NA	promoter-TSS (NM_008052)	promoter-TSS (NM_008052)	-113	NM_008052	14357	Mm.1645	NM_008052	ENSMUSG00000029603	Dtx1	Fxit1|mKIAA4160	deltex 1, E3 ubiquitin ligase	protein-coding
mm_107735.1	chr12	57564112	57564150	+	1	NA	promoter-TSS (NM_001312644)	promoter-TSS (NM_001312644)	16	NM_001312644	70846	Mm.84118	NM_001037743	ENSMUSG00000046782	Ttc6	4921506M07Rik|EG639426|ENSMUSG00000046782|Gm69|Gm9813	tetratricopeptide repeat domain 6	protein-coding
mm_28376.1	chr3	89960541	89960557	-	1	NA	intron (NM_001081182, intron 2 of 27)	CpG	2783	NM_001081182	54667	Mm.30455	NM_001081182	ENSMUSG00000060671	Atp8b2	Id	ATPase, class I, type 8B, member 2	protein-coding
mm_56906.1	chr6	119196619	119196625	-	1	NA	promoter-TSS (NM_009781)	promoter-TSS (NM_009781)	-213	NM_001255999	12288	Mm.41628	NM_009781	ENSMUSG00000051331	Cacna1c	Cav1.2|Cchl1a1|D930026N18Rik|MBC|MELC-CC	calcium channel, voltage-dependent, L type, alpha 1C subunit	protein-coding
mm_137099.1	chr17	21567057	21567067	+	1	NA	promoter-TSS (NM_001002008)	promoter-TSS (NM_001002008)	16	NM_001002008	381066	Mm.441097	NM_001002008	ENSMUSG00000067931	Zfp948	-	zinc finger protein 948	protein-coding
mm_116699.1	chr13	49904628	49904630	-	1	NA	Intergenic	Intergenic	222499	NM_172015	105148	Mm.21118	NM_172015	ENSMUSG00000037851	Iars	2510016L12Rik|AI327140|AU044614|E430001P04Rik|ILRS	isoleucine-tRNA synthetase	protein-coding
mm_121541.1	chr14	122474415	122474417	+	1	NA	promoter-TSS (NM_009574)	promoter-TSS (NM_009574)	783	NR_045046	69248	Mm.235369	NR_045046	ENSMUSG00000085555	2610035F20Rik	-	RIKEN cDNA 2610035F20 gene	ncRNA
mm_161937.1	chr19	3389587	3389587	+	1	NA	5' UTR (NM_001286558, exon 1 of 9)	5' UTR (NM_001286558, exon 1 of 9)	209	NM_001286558	17771	Mm.209941	NM_010841	ENSMUSG00000024905	Mtl5	tesmin	metallothionein-like 5, testis-specific (tesmin)	protein-coding
mm_98979.1	chr11	98740596	98740608	+	1	NA	Intergenic	Intergenic	-1183	NM_178060	21833	Mm.265917	NM_178060	ENSMUSG00000058756	Thra	6430529J03Rik|AW259572|Erba|Nr1a1|Rvr|T3R[a]|T3Ralpha|Thra1|Thra2|c-erbA-1|c-erbA-alpha|c-erbAalpha	thyroid hormone receptor alpha	protein-coding
mm_19202.1	chr2	84499525	84499570	-	1	NA	Intergenic	ORR1A4-int|LTR|ERVL-MaLR	7326	NR_046046	672763	Mm.491046	NR_046046	ENSMUSG00000087362	Gm13710	OTTMUSG00000013441	predicted gene 13710	ncRNA
mm_26271.1	chr3	142503845	142503876	+	1	NA	exon (NM_153564, exon 5 of 11)	exon (NM_153564, exon 5 of 11)	6926	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_14388.1	chr2	129800452	129800526	+	1	NA	promoter-TSS (NM_183262)	promoter-TSS (NM_183262)	-28	NM_183262	67333	Mm.389329	NM_183262	ENSMUSG00000037885	Stk35	1700054C12Rik|CLIK1|Stk35l1	serine/threonine kinase 35	protein-coding
mm_159332.1	chr3	40855288	40855288	-	1	NA	promoter-TSS (NR_045392)	promoter-TSS (NR_045392)	-3	NR_045392	100039043	Mm.460823	NM_001129886		Gm10731	ENSMUSG00000074620	FUN14 domain containing 2 pseudogene	pseudo
mm_99046.1	chr11	99041238	99041254	+	1	NA	promoter-TSS (NM_010517)	promoter-TSS (NM_010517)	-14	NM_010517	16010	Mm.233799	NM_010517	ENSMUSG00000017493	Igfbp4	AI875747|Deb2|IGFBP-4	insulin-like growth factor binding protein 4	protein-coding
mm_168388.1	chr1	125435412	125435431	-	1	NA	5' UTR (NM_023735, exon 1 of 12)	5' UTR (NM_023735, exon 1 of 12)	306	NM_023735	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding
mm_47308.1	chr5	122456930	122456959	-	1	NA	non-coding (NR_027838, exon 20 of 21)	non-coding (NR_027838, exon 20 of 21)	34500	NM_019805	56317	Mm.37341	NM_019805	ENSMUSG00000029466	Anapc7	APC7|AW545589	anaphase promoting complex subunit 7	protein-coding
mm_81799.1	chr9	115908473	115908497	+	1	NA	promoter-TSS (NM_028638)	promoter-TSS (NM_028638)	-970	NM_028638	73748	Mm.485018	NM_028638	ENSMUSG00000056880	Gadl1	1110027M19Rik|ADC|CSADC	glutamate decarboxylase-like 1	protein-coding
mm_70490.1	chr8	12457241	12457265	+	1	NA	Intergenic	Intergenic	61734	NM_009233	20664	Mm.39088	NM_009233	ENSMUSG00000096014	Sox1	BB176347|Sox-1	SRY (sex determining region Y)-box 1	protein-coding
mm_106294.1	chr11	118212833	118212841	-	1	NA	promoter-TSS (NM_001112700)	promoter-TSS (NM_001112700)	-95	NM_001112700	19157	Mm.86413	NM_011180	ENSMUSG00000017132	Cyth1	CLM1|CTH-1|CYTIP|Pscd1	cytohesin 1	protein-coding
mm_139118.1	chr17	47436602	47436608	+	1	NA	promoter-TSS (NM_145489)	promoter-TSS (NM_145489)	-34	NM_145489	224833	Mm.218444	NM_145489	ENSMUSG00000034382	AI661453	-	expressed sequence AI661453	protein-coding
mm_69746.1	chr7	140955697	140955715	-	1	NA	exon (NM_030694, exon 1 of 2)	exon (NM_030694, exon 1 of 2)	255	NM_030694	80876	Mm.379266	NM_030694	ENSMUSG00000060591	Ifitm2	DSPA2c|Ifitm3l|fragilis3|mil-3	interferon induced transmembrane protein 2	protein-coding
mm_52042.1	chr6	96377811	96377814	+	1	NA	intron (NM_182808, intron 2 of 4)	intron (NM_182808, intron 2 of 4)	-211607	NR_003643	78482	Mm.391486	NM_030107	ENSMUSG00000072878	1700123L14Rik	-	nucleoporin 50 pseudogene	pseudo
mm_89500.1	chr10	94036045	94036055	+	1	NA	promoter-TSS (NM_053072)	promoter-TSS (NM_053072)	49	NM_053072	13998	Mm.269596	NM_053072	ENSMUSG00000020021	Fgd6	AA123052|Etohd4|ZFYVE24	FYVE, RhoGEF and PH domain containing 6	protein-coding
mm_31027.1	chr4	40853371	40853379	+	1	NA	intron (NM_022305, intron 1 of 5)	intron (NM_022305, intron 1 of 5)	1162	NM_022305	14595	Mm.15622	NM_022305	ENSMUSG00000028413	B4galt1	B-1,4-GalT|B-1,4-GalT1|GalT|Ggtb|Ggtb2|b4Gal-T1|beta-1,4-GalT|beta-1,4-GalT1|beta4Gal-T1	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1	protein-coding
mm_92217.1	chr10	68250441	68250444	-	1	NA	intron (NM_023598, intron 2 of 9)	intron (NM_023598, intron 2 of 9)	28284	NM_023598	71371	Mm.440357	NM_023598	ENSMUSG00000019947	Arid5b	4930580B11|5430435G07Rik|AI467247|Desrt|Mrf2|Mrf2alpha|Mrf2beta	AT rich interactive domain 5B (MRF1-like)	protein-coding
mm_147746.1	chr18	61176977	61176987	-	1	NA	promoter-TSS (NM_178277)	promoter-TSS (NM_178277)	67	NM_178277	106894	Mm.22574	NM_134134	ENSMUSG00000024622	Hmgxb3	2510002C16Rik|A630042L21Rik|AI413166|mKIAA0194	HMG box domain containing 3	protein-coding
mm_47808.1	chr5	133790795	133790806	-	1	NA	Intergenic	Intergenic	-308948	NM_030719	80909	Mm.45218	NM_030719	ENSMUSG00000015944	Gatsl2	7530428J21Rik|AW742413|Gats|Gatsl1	GATS protein-like 2	protein-coding
mm_48076.1	chr5	136696192	136696223	-	1	NA	intron (NM_001085387, intron 2 of 4)	intron (NM_001085387, intron 2 of 4)	2030	NM_001085387	59310	Mm.5178	NM_021611	ENSMUSG00000005474	Myl10	1700027I08Rik|Mylc2pl|PLRLC	myosin, light chain 10, regulatory	protein-coding
mm_117986.1	chr13	100202111	100202128	-	1	NA	promoter-TSS (NM_001126182)	promoter-TSS (NM_001126182)	3	NM_001126182	17948	Mm.89961	NM_010872	ENSMUSG00000078945	Naip2	Birc1b|Naip-rs6	NLR family, apoptosis inhibitory protein 2	protein-coding
mm_159112.1	chr2	54436911	54436911	+	1	NA	intron (NM_173030, intron 1 of 12)	CpG	524	NM_173030	271786	Mm.330227	NM_173030	ENSMUSG00000060988	Galnt13	A230002A12|A230020F20|BB182356	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13	protein-coding
mm_7838.1	chr1	132226151	132226190	-	1	NA	promoter-TSS (NM_001311102)	promoter-TSS (NM_001311102)	-144	NM_001311102	213409	Mm.426321	NM_001033250	ENSMUSG00000079330	Lemd1	4930540I23Rik|6430514M23Rik|AI428128|LEMP-1	LEM domain containing 1	protein-coding
mm_173221.1	chrX	74726341	74726345	+	1	NA	Intergenic	Intergenic	-14584	NM_001099306	628518	Mm.465110	NM_001099306	ENSMUSG00000079532	Gm6890	EG628518	predicted gene 6890	protein-coding
mm_94788.1	chr11	22608022	22608031	+	1	NA	Intergenic	RLTR17|LTR|ERVK	95743	NM_153596	103765	Mm.221274	NM_153596	ENSMUSG00000049904	Tmem17	AI503894|AW049890	transmembrane protein 17	protein-coding
mm_90160.1	chr10	118869962	118869976	+	1	NA	Intergenic	Intergenic	-1066	NM_001014390	69181	Mm.45565	NM_001014390	ENSMUSG00000028630	Dyrk2	1810038L18Rik	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 2	protein-coding
mm_155869.1	chrX	101384491	101384508	+	1	NA	exon (NM_008124, exon 2 of 2)	exon (NM_008124, exon 2 of 2)	767	NM_001302497	14618	Mm.21198	NM_008124	ENSMUSG00000047797	Gjb1	Cnx32|Cx32|connexin-32	gap junction protein, beta 1	protein-coding
mm_136091.1	chr16	85024888	85024931	-	1	NA	exon (NM_001198823, exon 11 of 18)	exon (NM_001198823, exon 11 of 18)	52698	NR_045889	100038614	Mm.441351	NR_045889		Gm10791	ENSMUSG00000074933	predicted gene 10791	ncRNA
mm_128812.1	chr15	67102024	67102041	-	1	NA	TTS (NM_009177)	TTS (NM_009177)	74850	NM_009177	20442	Mm.248334	NM_009177	ENSMUSG00000013846	St3gal1	5330418N22Rik|AI467004|ST3GalI|Siat4|Siat4a|St3gal-1	ST3 beta-galactoside alpha-2,3-sialyltransferase 1	protein-coding
mm_94677.1	chr11	17913679	17913685	+	1	NA	Intergenic	Intergenic	40193	NM_026576	68145	Mm.178684	NM_026576	ENSMUSG00000016984	Etaa1	5730466H23Rik|AA672646	Ewing tumor-associated antigen 1	protein-coding
mm_47492.1	chr5	124006472	124006494	-	1	NA	exon (NM_177876, exon 4 of 4)	exon (NM_177876, exon 4 of 4)	9631	NR_105999	102465625		NR_105999	ENSMUSG00000098454	Mir7032	Gm27309|mmu-mir-7032	microRNA 7032	ncRNA
mm_87129.1	chr10	34282180	34282193	+	1	NA	promoter-TSS (NM_009433)	promoter-TSS (NM_009433)	-4	NM_009433	22110	Mm.20445	NM_009433	ENSMUSG00000047514	Tspyl1	Tspyl	testis-specific protein, Y-encoded-like 1	protein-coding
mm_163402.1	chr12	74093326	74093330	+	1	NA	intron (NM_172804, intron 1 of 6)	intron (NM_172804, intron 1 of 6)	95567	NM_172804	238266	Mm.311393	NM_172804	ENSMUSG00000044912	Syt16	6430703N11|Strep14|Syt14l|syt14r	synaptotagmin XVI	protein-coding
mm_109233.1	chr12	108851123	108851129	+	1	NA	promoter-TSS (NM_001012310)	promoter-TSS (NM_001012310)	-3	NM_001012310	104910	Mm.202653	NM_001012310	ENSMUSG00000048856	Slc25a47	AI132487|AI876593|HDMCP	solute carrier family 25, member 47	protein-coding
mm_171246.1	chr3	77615367	77615378	-	1	NA	Intergenic	L1_Mus3|LINE|L1	1529515	NM_001310536	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_124598.1	chr15	3275594	3275665	+	1	NA	exon (NM_009155, exon 3 of 5)	exon (NM_009155, exon 3 of 5)	4652	NM_009155	20363	Mm.392203	NM_009155	ENSMUSG00000064373	Selenop	AU018766|D15Ucla1|Se-P|Sepp1|selp	selenoprotein P	protein-coding
mm_158980.1	chr1	125911128	125911128	-	1	NA	intron (NM_001311089, intron 1 of 2)	intron (NM_001311089, intron 1 of 2)	259	NM_001311090	72585	Mm.490405	NM_145100	ENSMUSG00000026344	Lypd1	2700050C12Rik|AI853408|C530008O16Rik|Lynx2|Lypdc1	Ly6/Plaur domain containing 1	protein-coding
mm_101873.1	chr11	48892129	48892131	-	1	NA	intron (NM_001024230, intron 4 of 4)	intron (NM_001024230, intron 4 of 4)	10022	NM_001024230	432555	Mm.338931	NM_001024230	ENSMUSG00000058163	Gm5431	EG432555|Irgb9b8	predicted gene 5431	protein-coding
mm_28532.1	chr3	92670315	92670316	-	1	NA	promoter-TSS (NM_028625)	promoter-TSS (NM_028625)	0	NM_028625	73722	Mm.279773	NM_028625	ENSMUSG00000068890	Lce1a2	1110004E04Rik|Sprrl2	late cornified envelope 1A2	protein-coding
mm_98501.1	chr11	94952004	94952017	+	1	NA	3' UTR (NM_007742, exon 51 of 51)	3' UTR (NM_007742, exon 51 of 51)	-15583	NM_018792	54388	Mm.30482	NM_018792	ENSMUSG00000038994	Hils1	H1.9|TISP64	histone H1-like protein in spermatids 1	protein-coding
mm_90871.1	chr10	8945236	8945269	-	1	NA	Intergenic	Intergenic	-59182	NM_175155	70097	Mm.338275	NM_175155	ENSMUSG00000015305	Sash1	1100001C18Rik|2500002E12Rik|A330076K04Rik|mKIAA0790	SAM and SH3 domain containing 1	protein-coding
mm_42071.1	chr5	110100415	110100425	+	1	NA	promoter-TSS (NM_001281812)	promoter-TSS (NM_001281812)	-139	NM_001281812	403178	Mm.297057	NM_207279	ENSMUSG00000064247	Plcxd1	A330045H12Rik|Gm576	phosphatidylinositol-specific phospholipase C, X domain containing 1	protein-coding
mm_57581.1	chr6	127150997	127151014	-	1	NA	promoter-TSS (NM_009829)	promoter-TSS (NM_009829)	43	NM_009829	12444	Mm.333406	NM_009829	ENSMUSG00000000184	Ccnd2	2600016F06Rik|AI256817|BF642806|C86853|Vin-1|Vin1|cD2	cyclin D2	protein-coding
mm_68683.1	chr7	119184528	119184546	-	1	NA	promoter-TSS (NM_001024138)	promoter-TSS (NM_001024138)	-163	NM_001024138	209776	Mm.300632	NM_001024138	ENSMUSG00000066197	Gpr139	GPRg1|Gm495|PGR3	G protein-coupled receptor 139	protein-coding
mm_7709.1	chr1	130452519	130452530	-	1	NA	exon (NM_010016, exon 6 of 10)	exon (NM_010016, exon 6 of 10)	10220	NM_010016	13136	Mm.101591	NM_010016	ENSMUSG00000026399	Cd55	Daf|Daf-GPI|Daf1|GPI-DAF	CD55 molecule, decay accelerating factor for complement	protein-coding
mm_8525.1	chr1	154884376	154884390	-	1	NA	Intergenic	Intergenic	-158463	NM_009782	12290	Mm.267517	NM_009782	ENSMUSG00000004110	Cacna1e	A430040I15|BII|Cach6|Cacnl1a6|Cav2.3|Cchra1|alpha1E	calcium channel, voltage-dependent, R type, alpha 1E subunit	protein-coding
mm_26676.1	chr3	155093415	155093475	+	1	NA	promoter-TSS (NM_028938)	promoter-TSS (NM_028938)	11	NM_028938	74435	Mm.195711	NM_028938	ENSMUSG00000028182	Lrriq3	4930438B07Rik|4930511J15Rik|4933403H06Rik|BB020367|Lrrc44	leucine-rich repeats and IQ motif containing 3	protein-coding
mm_125655.1	chr15	63476201	63476204	+	1	NA	intron (NR_045279, intron 1 of 5)	intron (NR_045279, intron 1 of 5)	3406	NR_045279	432958	Mm.255105	NR_045279		Gm20740	-	predicted gene, 20740	ncRNA
mm_51820.1	chr6	89096104	89096115	+	1	NA	promoter-TSS (NR_134977)	promoter-TSS (NR_134977)	-1	NR_134978	232217	Mm.281744	NM_175017	ENSMUSG00000055403	4933427D06Rik	-	RIKEN cDNA 4933427D06 gene	ncRNA
mm_151162.1	chr19	53194359	53194415	+	1	NA	intron (NM_013758, intron 1 of 15)	intron (NM_013758, intron 1 of 15)	50390	NM_013758	27360	Mm.426080	NM_013758	ENSMUSG00000025026	Add3	AI463285|R75380	adducin 3 (gamma)	protein-coding
mm_47589.1	chr5	124861983	124861993	-	1	NA	promoter-TSS (NM_001081750)	promoter-TSS (NM_001081750)	233	NM_144819	215707	Mm.389693	NM_144819	ENSMUSG00000037979	Ccdc92	AW050178|D5Bwg0834e	coiled-coil domain containing 92	protein-coding
mm_141936.1	chr17	35046738	35046763	-	1	NA	promoter-TSS (NR_130641)	promoter-TSS (NR_130641)	-5	NM_001146215	17687	Mm.24192	NM_013600	ENSMUSG00000007035	Msh5	Mut5	mutS homolog 5	protein-coding
mm_145279.1	chr18	53176300	53176310	+	1	NA	promoter-TSS (NM_026386)	promoter-TSS (NM_026386)	-60	NM_026386	67804	Mm.252171	NM_026386	ENSMUSG00000034484	Snx2	0610030A03Rik	sorting nexin 2	protein-coding
mm_167893.1	chrX	69853632	69853633	+	1	NA	intron (NM_008032, intron 15 of 19)	Lx5|LINE|L1	-91649	NM_029316	75509	Mm.233475	NM_029316	ENSMUSG00000059690	1700020N15Rik	-	RIKEN cDNA 1700020N15 gene	protein-coding
mm_128869.1	chr15	72925628	72925636	-	1	NA	exon (NM_001164642, exon 15 of 17)	exon (NM_001164642, exon 15 of 17)	-115308	NR_002864	353342	Mm.440245	NR_002864	ENSMUSG00000106847	Peg13	-	paternally expressed 13	ncRNA
mm_10553.1	chr2	16751198	16751208	+	1	NA	exon (NM_026162, exon 14 of 14)	exon (NM_026162, exon 14 of 14)	262523	NR_040632	75069	Mm.50378	NR_040632		4930515L03Rik	-	RIKEN cDNA 4930515L03 gene	ncRNA
mm_33690.1	chr4	133443317	133443335	+	1	NA	Intergenic	Intergenic	-36807	NM_175307	100342	Mm.204656	NM_175307	ENSMUSG00000046694	Fam46b	4732473B16Rik|AU045678|AU046069	family with sequence similarity 46, member B	protein-coding
mm_91028.1	chr10	17944350	17944354	-	1	NA	intron (NM_001033432, intron 1 of 3)	intron (NM_001033432, intron 1 of 3)	3715	NM_001033432	380629	Mm.276430	NM_001033432	ENSMUSG00000039879	Heca	Gm869|HDC|HDCL	hdc homolog, cell cycle regulator	protein-coding
mm_118843.1	chr14	25656916	25656933	+	1	NA	exon (NM_183208, exon 21 of 24)	exon (NM_183208, exon 21 of 24)	-37246	NM_134084	105675	Mm.41656	NM_134084	ENSMUSG00000021868	Ppif	AW457192|CyP-D|CyP-F|CypD|PPIase	peptidylprolyl isomerase F (cyclophilin F)	protein-coding
mm_133781.1	chr16	94984452	94984464	+	1	NA	intron (NM_001025584, intron 1 of 4)	intron (NM_001025584, intron 1 of 4)	13238	NM_001025584	16522	Mm.328720	NM_010606	ENSMUSG00000043301	Kcnj6	BIR1|GIRK2|KATP2|KCNJ7|Kir3.2|weaver|wv	potassium inwardly-rectifying channel, subfamily J, member 6	protein-coding
mm_47860.1	chr5	134607315	134607319	-	1	NA	intron (NM_020044, intron 3 of 12)	intron (NM_020044, intron 3 of 12)	7708	NM_022964	56743	Mm.391375	NM_020044	ENSMUSG00000040751	Lat2	AW125574|LAB|NTAL|WSCR5|Wbscr15|Wbscr5	linker for activation of T cells family, member 2	protein-coding
mm_2752.1	chr1	128747681	128747700	+	1	NA	Intergenic	Intergenic	-155391	NM_009911	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding
mm_10315.1	chr2	11172389	11172419	+	1	NA	promoter-TSS (NM_008859)	promoter-TSS (NM_008859)	22	NM_008859	18761	Mm.329993	NM_008859	ENSMUSG00000026778	Prkcq	A130035A12Rik|AW494342|PKC-0|PKC-theta|PKCtheta|Pkcq	protein kinase C, theta	protein-coding
mm_64745.1	chr7	4771332	4771338	-	1	NA	promoter-TSS (NM_172895)	promoter-TSS (NM_172895)	-65	NM_172895	243822	Mm.333542	NM_172895	ENSMUSG00000092518	Fam71e2	4930401F20Rik	family with sequence similarity 71, member E2	protein-coding
mm_158730.1	chrX	163958591	163958597	-	1	NA	promoter-TSS (NM_009453)	promoter-TSS (NM_009453)	72	NM_009453	22184	Mm.426178	NM_009453	ENSMUSG00000031370	Zrsr2	35kDa|5031411E02Rik|A230052C13Rik|C77286|U2af1-rs2|URP	zinc finger (CCCH type), RNA binding motif and serine/arginine rich 2	protein-coding
mm_110906.1	chr12	75745776	75745782	-	1	NA	Intergenic	MER34A|LTR|ERV1	-10050	NM_030750	81535	Mm.280199	NM_030750	ENSMUSG00000021054	Sgpp1	AI463453|SPP|SPP1|Spph1	sphingosine-1-phosphate phosphatase 1	protein-coding
mm_151651.1	chr19	4069226	4069239	-	1	NA	Intergenic	RLTR19-int|LTR|ERVK	-9938	NM_144869	225884	Mm.440201	NM_144869	ENSMUSG00000058216	Gstp3	-	glutathione S-transferase pi 3	protein-coding
mm_135979.1	chr16	75052191	75052196	-	1	NA	Intergenic	Intergenic	533868	NM_001252513	320355	Mm.99517	NM_177142	ENSMUSG00000032948	Lipi	D930038D03Rik|lpd1	lipase, member I	protein-coding
mm_56987.1	chr6	120531290	120531328	-	1	NA	promoter-TSS (NM_144815)	promoter-TSS (NM_144815)	-10	NM_144815	214932	Mm.255322	NM_144815	ENSMUSG00000058979	Cecr5	A930002G03Rik	cat eye syndrome chromosome region, candidate 5	protein-coding
mm_129462.1	chr15	78573215	78573229	-	1	NA	promoter-TSS (NM_009008)	promoter-TSS (NM_009008)	-439	NM_009008	19354	Mm.1972	NM_009008	ENSMUSG00000033220	Rac2	AI323801|AI452260	RAS-related C3 botulinum substrate 2	protein-coding
mm_21496.1	chr2	163417093	163417097	-	1	NA	intron (NM_025699, intron 1 of 3)	intron (NM_025699, intron 1 of 3)	2375	NM_025699	66680	Mm.25119	NM_025699	ENSMUSG00000035399	Oser1	3230401D17Rik|AI256769|Perit1	oxidative stress responsive serine rich 1	protein-coding
mm_125261.1	chr15	35371254	35371260	+	1	NA	promoter-TSS (NM_177151)	promoter-TSS (NM_177151)	-289	NM_177151	666173	Mm.309250	NM_177151	ENSMUSG00000037646	Vps13b	1810042B05Rik|2310042E16Rik|4732488H20|C330002D13Rik|C87206|Coh1|D230005K13|mKIAA0532|mKIAA5032	vacuolar protein sorting 13B	protein-coding
mm_158653.1	chrX	155623806	155623821	-	1	NA	promoter-TSS (NM_001093750)	promoter-TSS (NM_001093750)	-486	NM_001093750	211612	Mm.218811	NM_001093750	ENSMUSG00000041552	Ptchd1	9630036J22Rik|AI848149|Gm387	patched domain containing 1	protein-coding
mm_36144.1	chr4	59474793	59474803	-	1	NA	3' UTR (NM_144904, exon 15 of 15)	3' UTR (NM_144904, exon 15 of 15)	-36165	NM_001163288	634731	Mm.483589	NM_001163288	ENSMUSG00000038578	Susd1	A530080P10|Gm12528|OTTMUSG00000007332	sushi domain containing 1	protein-coding
mm_95477.1	chr11	51220561	51220586	+	1	NA	promoter-TSS (NR_110444)	promoter-TSS (NR_110444)	-155	NR_110444	71297	Mm.390420	NR_110444	ENSMUSG00000086646	Platr20	5133400J02Rik	pluripotency associated transcript 20	ncRNA
mm_34181.1	chr4	140700472	140700485	+	1	NA	promoter-TSS (NM_173867)	promoter-TSS (NM_173867)	-995	NM_173867	108911	Mm.253	NM_173867	ENSMUSG00000040945	Rcc2	2610510H01Rik|2610529N02Rik|AA536646|AA675016|Td60|mKIAA1470	regulator of chromosome condensation 2	protein-coding
mm_154409.1	chrM	14711	14722	+	1	NA	NA	Intergenic	NA	NA								
mm_64507.1	chr7	143626376	143626388	+	1	NA	intron (NM_175649, intron 1 of 7)	intron (NM_175649, intron 1 of 7)	1463	NM_175649	244237	Mm.247498	NM_175649	ENSMUSG00000045362	Tnfrsf26	Tnfrh3|Tnfrsf24	tumor necrosis factor receptor superfamily, member 26	protein-coding
mm_26017.1	chr3	135438281	135438303	+	1	NA	promoter-TSS (NM_025356)	promoter-TSS (NM_025356)	373	NR_030689	319587	Mm.358971	NR_030689	ENSMUSG00000097032	4930539J05Rik	8030475D13Rik	RIKEN cDNA 4930539J05 gene	ncRNA
mm_6500.1	chr1	74284637	74284712	-	1	NA	promoter-TSS (NM_025580)	promoter-TSS (NM_025580)	64	NM_146110	227290	Mm.379371	NM_146110	ENSMUSG00000006299	Aamp	AU040907|Aamp-rs	angio-associated migratory protein	protein-coding
mm_155581.1	chrX	78369637	78369671	+	1	NA	promoter-TSS (NM_001177966)	promoter-TSS (NM_001177966)	11	NM_001177966	74910	Mm.159364	NM_001177966	ENSMUSG00000035651	4930480E11Rik	-	RIKEN cDNA 4930480E11 gene	protein-coding
mm_123831.1	chr14	70627226	70627236	-	1	NA	promoter-TSS (NM_001252663)	promoter-TSS (NM_001252663)	-166	NM_001252663	13829	Mm.210863	NM_013514	ENSMUSG00000022099	Dmtn	AI325486|Epb4.9|Epb49|dematin	dematin actin binding protein	protein-coding
mm_131704.1	chr16	20718108	20718151	+	1	NA	intron (NM_145632, intron 1 of 4)	intron (NM_145632, intron 1 of 4)	303	NM_145632	245841	Mm.288730	NM_145632	ENSMUSG00000021018	Polr2h	-	polymerase (RNA) II (DNA directed) polypeptide H	protein-coding
mm_156293.1	chrX	136837519	136837529	+	1	NA	3' UTR (NM_011123, exon 7 of 7)	3' UTR (NM_011123, exon 7 of 7)	14778	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_90940.1	chr10	12929869	12929873	-	1	NA	Intergenic	Intergenic	-6744	NR_038028	320273	Mm.417706	NR_038027	ENSMUSG00000097378	B230208H11Rik	-	RIKEN cDNA B230208H11 gene	ncRNA
mm_79957.1	chr9	66145023	66145028	+	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	-13201	NM_010019	13143	Mm.304472	NM_010019	ENSMUSG00000032380	Dapk2	-	death-associated protein kinase 2	protein-coding
mm_159151.1	chr2	88391472	88391472	+	1	NA	exon (NM_001011868, exon 1 of 1)	exon (NM_001011868, exon 1 of 1)	223	NM_001011868	258203	Mm.376126	NM_001011868	ENSMUSG00000056995	Olfr1178	MOR225-6P	olfactory receptor 1178	protein-coding
mm_166382.1	chr5	131095771	131095812	-	1	NA	intron (NM_145218, intron 3 of 10)	MTE2a|LTR|ERVL-MaLR	211731	NM_145218	212996	Mm.299204	NM_145218	ENSMUSG00000034040	Wbscr17	AA388321|E330012B09Rik	Williams-Beuren syndrome chromosome region 17 homolog (human)	protein-coding
mm_168110.1	chr10	14746435	14746436	-	1	NA	intron (NR_045824, intron 3 of 5)	intron (NR_045824, intron 3 of 5)	-13854	NM_008703	18101	Mm.487342	NM_008703	ENSMUSG00000019865	Nmbr	BB182387	neuromedin B receptor	protein-coding
mm_24981.1	chr3	96830124	96830139	+	1	NA	promoter-TSS (NM_001163497)	promoter-TSS (NM_001163497)	66	NM_021517	59020	Mm.489677	NM_021517	ENSMUSG00000038298	Pdzk1	1700023D20Rik|2610507N21Rik|4921513F16Rik|AI267131|AI314638|AL022680|D3Ertd537e|Pdzd1|mPDZK1	PDZ domain containing 1	protein-coding
mm_157689.1	chrX	60179141	60179181	-	1	NA	promoter-TSS (NM_001289731)	promoter-TSS (NM_001289731)	-72	NM_001289731	109904	Mm.93796	NM_133197	ENSMUSG00000031139	Mcf2	B230117G22Rik|Dbl|Mcf-2	mcf.2 transforming sequence	protein-coding
mm_144694.1	chr18	34861201	34861215	+	1	NA	promoter-TSS (NM_007913)	promoter-TSS (NM_007913)	1	NM_007913	13653	Mm.181959	NM_007913	ENSMUSG00000038418	Egr1	A530045N19Rik|ETR103|Egr-1|Krox-1|Krox-24|Krox24|NGF1-A|NGFI-A|NGFIA|TIS8|Zenk|Zfp-6|Zif268|egr	early growth response 1	protein-coding
mm_148279.1	chr18	82332345	82332353	-	1	NA	Intergenic	(TTGG)n|Simple_repeat|Simple_repeat	74428	NM_008082	14427	Mm.6219	NM_008082	ENSMUSG00000024553	Galr1	Galnr1	galanin receptor 1	protein-coding
mm_142536.1	chr17	46546276	46546333	-	1	NA	promoter-TSS (NM_001081335)	promoter-TSS (NM_001081335)	84	NM_001081335	78309	Mm.329076	NM_001081335	ENSMUSG00000040327	Cul9	1810035I07Rik|Cul-9|Parc|mKIAA0708	cullin 9	protein-coding
mm_105011.1	chr11	100411887	100411895	-	1	NA	intron (NM_176830, intron 4 of 7)	intron (NM_176830, intron 4 of 7)	2928	NM_176830	66180	Mm.4940	NM_176830	ENSMUSG00000006931	P3h4	1110036O03Rik|AI413214|Leprel4|Sc65	prolyl 3-hydroxylase family member 4 (non-enzymatic)	protein-coding
mm_30136.1	chr3	142249553	142249561	-	1	NA	intron (NM_001190852, intron 12 of 15)	intron (NM_001190852, intron 12 of 15)	-80329	NM_001277216	12167	Mm.39089	NM_007560	ENSMUSG00000052430	Bmpr1b	AI385617|ALK-6|AV355320|Acvrlk6|Alk6|BMPR-1B|BMPR-IB|CFK-43a|SKR6	bone morphogenetic protein receptor, type 1B	protein-coding
mm_109608.1	chr12	112722164	112722239	+	1	NA	promoter-TSS (NM_001024602)	promoter-TSS (NM_001024602)	27	NM_001024602	217882	Mm.23689	NM_001024602	ENSMUSG00000072825	Cep170b	AI466840|AW555464|Kiaa0284|mKIAA0284	centrosomal protein 170B	protein-coding
mm_172815.1	chr9	123689754	123689758	-	1	NA	Intergenic	Intergenic	-10924	NM_139142	102680	Mm.440867	NM_139142	ENSMUSG00000036814	Slc6a20a	A730081N20Rik|AU022428|Xt3s1|Xtrp3s1	solute carrier family 6 (neurotransmitter transporter), member 20A	protein-coding
mm_132604.1	chr16	38562822	38562861	+	1	NA	promoter-TSS (NM_026407)	promoter-TSS (NM_026407)	27	NM_026407	67846	Mm.310476	NM_026407	ENSMUSG00000002845	Tmem39a	2610033C09Rik	transmembrane protein 39a	protein-coding
mm_77010.1	chr8	107581191	107581226	-	1	NA	exon (NM_010817, exon 7 of 7)	exon (NM_010817, exon 7 of 7)	7274	NM_010817	17463	Mm.18347	NM_010817	ENSMUSG00000039067	Psmd7	AW107203|Mov-34|Mov34	proteasome (prosome, macropain) 26S subunit, non-ATPase, 7	protein-coding
mm_156669.1	chrX	159210479	159210494	+	1	NA	Intergenic	Intergenic	-45296	NM_148945	110651	Mm.328476	NM_148945	ENSMUSG00000031309	Rps6ka3	MAPKAPK-1b|MPK-9|Rsk2|S6K-alpha3|p90RSK3|pp90RSK2	ribosomal protein S6 kinase polypeptide 3	protein-coding
mm_61516.1	chr7	78913437	78913448	+	1	NA	promoter-TSS (NM_020583)	promoter-TSS (NM_020583)	18	NM_001291220	57444	Mm.322843	NM_020583	ENSMUSG00000039236	Isg20	1600023I01Rik|2010107M23Rik|20kDa|DnaQL|HEM45	interferon-stimulated protein	protein-coding
mm_135169.1	chr16	35931022	35931036	-	1	NA	intron (NM_001013371, intron 4 of 4)	MTC|LTR|ERVL-MaLR	-7441	NM_030253	80285	Mm.49074	NM_030253	ENSMUSG00000022906	Parp9	ARTD9|AW214463|BC003281|Bagl|Bal|PARP-9	poly (ADP-ribose) polymerase family, member 9	protein-coding
mm_139450.1	chr17	55749979	55749992	+	1	NA	promoter-TSS (NM_139138)	promoter-TSS (NM_139138)	1	NM_139138	52614	Mm.210497	NM_139138	ENSMUSG00000032915	Adgre4	D17Ertd479e|Egf-tm7|Emr4|Fire|Gpr127	adhesion G protein-coupled receptor E4	protein-coding
mm_160255.1	chr7	107902786	107902786	+	1	NA	promoter-TSS (NM_146774)	promoter-TSS (NM_146774)	67	NM_146774	258770	Mm.389960	NM_146774	ENSMUSG00000073893	Olfr472	MOR204-5	olfactory receptor 472	protein-coding
mm_161768.1	chr17	36368228	36368228	-	1	NA	intron (NM_201608, intron 1 of 5)	intron (NM_201608, intron 1 of 5)	189	NM_201608	110696	Mm.303091	NM_201608	ENSMUSG00000058124	H2-M10.3	5.3H	histocompatibility 2, M region locus 10.3	protein-coding
mm_167147.1	chr7	128694244	128694247	+	1	NA	exon (NM_178641, exon 20 of 20)	exon (NM_178641, exon 20 of 20)	5375	NM_001346517	101490	Mm.490344	NM_178641	ENSMUSG00000042105	Inpp5f	5830435P03Rik|AI115354|AW561896|SAC2|cI-27|hSAC2|mKIAA0966	inositol polyphosphate-5-phosphatase F	protein-coding
mm_17893.1	chr2	35061432	35061447	-	1	NA	promoter-TSS (NM_010406)	promoter-TSS (NM_010406)	2	NM_010406	15139	Mm.2168	NM_010406	ENSMUSG00000026874	Hc	C5|C5a|He	hemolytic complement	protein-coding
mm_66271.1	chr7	37320042	37320046	-	1	NA	Intergenic	Intergenic	449708	NM_172385	243937	Mm.322505	NM_172385	ENSMUSG00000043456	Zfp536	9630010P11Rik|Znf536|mKIAA0390	zinc finger protein 536	protein-coding
mm_152030.1	chr19	6084680	6084690	-	1	NA	promoter-TSS (NM_026410)	promoter-TSS (NM_026410)	206	NM_024231	81909	Mm.289471	NM_024231	ENSMUSG00000024792	Zfpl1	1500015B20Rik	zinc finger like protein 1	protein-coding
mm_82899.1	chr9	32706329	32706350	-	1	NA	intron (NM_011808, intron 1 of 7)	intron (NM_011808, intron 1 of 7)	10297	NM_001038642	23871	Mm.292415	NM_011808	ENSMUSG00000032035	Ets1	AI196000|AI448617|D230050P06|Ets-1|Tpl1|vs	E26 avian leukemia oncogene 1, 5' domain	protein-coding
mm_90630.1	chr10	128469279	128469288	+	1	NA	exon (NM_001114096, exon 10 of 29)	exon (NM_001114096, exon 10 of 29)	10047	NM_001114097	68094	Mm.417338	NM_198160	ENSMUSG00000025369	Smarcc2	5930405J04Rik	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2	protein-coding
mm_3785.1	chr1	156838904	156838912	+	1	NA	promoter-TSS (NM_028333)	promoter-TSS (NM_028333)	-115	NM_028333	72713	Mm.389206	NM_028333	ENSMUSG00000033544	Angptl1	2810039D03Rik|ANG3|ANGPT3|ANGY|ARP1	angiopoietin-like 1	protein-coding
mm_56924.1	chr6	119417600	119417623	-	1	NA	promoter-TSS (NM_197985)	promoter-TSS (NM_197985)	-128	NM_197985	68465	Mm.291826	NM_197985	ENSMUSG00000030168	Adipor2	1110001I14Rik|ADCR2|AI115388|AW554121|D6Ucla1e|Paqr2	adiponectin receptor 2	protein-coding
mm_67279.1	chr7	78577772	78577828	-	1	NA	promoter-TSS (NM_182809)	promoter-TSS (NM_182809)	38	NM_008746	18213	Mm.33496	NM_008746	ENSMUSG00000059146	Ntrk3	AW125844|Ntrk3_tv3|TrkC	neurotrophic tyrosine kinase, receptor, type 3	protein-coding
mm_20639.1	chr2	132021136	132021178	-	1	NA	intron (NM_175445, intron 1 of 10)	intron (NM_175445, intron 1 of 10)	8831	NM_175445	215653	Mm.204737	NM_175445	ENSMUSG00000027339	Rassf2	3830431H01Rik|9030412M04Rik|AI852669|AW495050	Ras association (RalGDS/AF-6) domain family member 2	protein-coding
mm_140009.1	chr17	73157406	73157410	+	1	NA	intron (NM_001081071, intron 1 of 5)	intron (NM_001081071, intron 1 of 5)	49423	NM_001177967	225010	Mm.329194	NM_001081071	ENSMUSG00000054469	Lclat1	AI181996|Agpat8|Alcat1|Gm91|Lycat	lysocardiolipin acyltransferase 1	protein-coding
mm_143904.1	chr17	84879170	84879193	-	1	NA	Intergenic	Intergenic	-77560	NM_001159497	19043	Mm.249695	NM_011151	ENSMUSG00000061130	Ppm1b	PP2CB	protein phosphatase 1B, magnesium dependent, beta isoform	protein-coding
mm_67207.1	chr7	74303261	74303284	-	1	NA	exon (NM_023908, exon 8 of 10)	exon (NM_023908, exon 8 of 10)	251508	NM_023908	108116	Mm.425467	NM_023908	ENSMUSG00000025790	Slco3a1	5830414C08Rik|Anr1|MJAM|OATP-D|R75096|Slc21a11	solute carrier organic anion transporter family, member 3a1	protein-coding
mm_62006.1	chr7	91262310	91262338	+	1	NA	intron (NM_011807, intron 1 of 22)	intron (NM_011807, intron 1 of 22)	171538	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_94041.1	chr10	128146477	128146493	-	1	NA	intron (NM_001039080, intron 4 of 13)	intron (NM_001039080, intron 4 of 13)	30083	NM_019711	56516	Mm.42247	NM_019711	ENSMUSG00000040043	Rbms2	2610315E04Rik|Scr3	RNA binding motif, single stranded interacting protein 2	protein-coding
mm_33421.1	chr4	129985099	129985154	+	1	NA	promoter-TSS (NM_173071)	promoter-TSS (NM_173071)	48	NM_173071	230775	Mm.262241	NM_173071	ENSMUSG00000028782	Adgrb2	Bai2	adhesion G protein-coupled receptor B2	protein-coding
mm_43597.1	chr5	137787770	137787807	+	1	NA	promoter-TSS (NM_001005426)	promoter-TSS (NM_001005426)	-14	NM_001005426	381678	Mm.332765	NM_001005426	ENSMUSG00000037108	Zcwpw1	Gm1053	zinc finger, CW type with PWWP domain 1	protein-coding
mm_36512.1	chr4	83525281	83525322	-	1	NA	promoter-TSS (NM_001081012)	promoter-TSS (NM_001081012)	-244	NM_001081012	320226	Mm.180032	NM_029117	ENSMUSG00000052407	Ccdc171	4930418J05Rik|4930473A06Rik|A330015D16Rik	coiled-coil domain containing 171	protein-coding
mm_81103.1	chr9	106447754	106447780	+	1	NA	promoter-TSS (NM_145919)	promoter-TSS (NM_145919)	-89	NM_001110272	68644	Mm.268925	NM_145919	ENSMUSG00000042210	Abhd14a	1110013B16Rik|AW558221|Dorz1	abhydrolase domain containing 14A	protein-coding
mm_141724.1	chr17	34115500	34115572	-	1	NA	exon (NM_001204973, exon 6 of 13)	exon (NM_001204973, exon 6 of 13)	4364	NR_037970	14312	Mm.3444	NM_010238	ENSMUSG00000024335	Brd2	AW228947|D17H6S113E|Frg-1|Fsrg-1|Fsrg1|Nat|Ring3|Rnf3|mKIAA4005	bromodomain containing 2	protein-coding
mm_135132.1	chr16	35844236	35844244	-	1	NA	intron (NM_001039530, intron 12 of 16)	intron (NM_001039530, intron 12 of 16)	27142	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_137475.1	chr17	26766548	26766593	+	1	NA	intron (NM_029870, intron 8 of 8)	intron (NM_029870, intron 8 of 8)	-14509	NM_172149	224630	Mm.21795	NM_172149	ENSMUSG00000024191	Bnip1	2010005M06Rik|5930429G21Rik|Sec20	BCL2/adenovirus E1B interacting protein 1	protein-coding
mm_133979.1	chr16	4541765	4541779	-	1	NA	Intergenic	CpG	17948	NM_031182	83383	Mm.273210	NM_031182	ENSMUSG00000005718	Tfap4	AI642933|AP-4|D930048N17Rik|Tcfap4|bHLHc41	transcription factor AP4	protein-coding
mm_19419.1	chr2	91930920	91930938	-	1	NA	exon (NM_010784, exon 4 of 5)	exon (NM_010784, exon 4 of 5)	773	NM_001291481	17242	Mm.906	NM_010784	ENSMUSG00000027239	Mdk	MK|Mek	midkine	protein-coding
mm_34671.1	chr4	150927307	150927328	+	1	NA	promoter-TSS (NM_001077509)	promoter-TSS (NM_001077509)	-682	NM_001077509	21942	Mm.244187	NM_011612	ENSMUSG00000028965	Tnfrsf9	4-1BB|A930040I11Rik|AA408498|AI325004|CDw137|Cd137|ILA|Ly63	tumor necrosis factor receptor superfamily, member 9	protein-coding
mm_118489.1	chr14	12284243	12284271	+	1	NA	promoter-TSS (NM_146051)	promoter-TSS (NM_146051)	54	NM_001284386	218734	Mm.44068	NM_146051	ENSMUSG00000033111	3830406C13Rik	-	RIKEN cDNA 3830406C13 gene	protein-coding
mm_48265.1	chr5	137897956	137897960	-	1	NA	intron (NM_007819, intron 11 of 12)	intron (NM_007819, intron 11 of 12)	23661	NM_007819	13113	Mm.289886	NM_007819	ENSMUSG00000029727	Cyp3a13	IIIAm2	cytochrome P450, family 3, subfamily a, polypeptide 13	protein-coding
mm_98025.1	chr11	85171098	85171104	+	1	NA	promoter-TSS (NM_028589)	promoter-TSS (NM_028589)	5	NM_028589	73634	Mm.48850	NM_028589	ENSMUSG00000018479	1700125H20Rik	-	RIKEN cDNA 1700125H20 gene	protein-coding
mm_153692.1	chr19	44397178	44397187	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	10527	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_16309.1	chr2	174295613	174295631	+	1	NA	promoter-TSS (NR_002846)	promoter-TSS (NR_002846)	-186	NR_002846	56802	Mm.125770	NR_002846	ENSMUSG00000086537	Nespas	Gnas-as|Nespos	neuroendocrine secretory protein antisense	ncRNA
mm_70340.1	chr8	4613132	4613142	+	1	NA	promoter-TSS (NM_145591)	promoter-TSS (NM_145591)	-33	NM_145591	233987	Mm.102799	NM_145591	ENSMUSG00000058748	Zfp958	-	zinc finger protein 958	protein-coding
mm_51879.1	chr6	90570835	90570866	+	1	NA	exon (NM_027406, exon 11 of 23)	exon (NM_027406, exon 11 of 23)	20002	NM_027406	107747	Mm.30035	NM_027406	ENSMUSG00000030088	Aldh1l1	1810048F20Rik|FDH|Fthfd|Neut2	aldehyde dehydrogenase 1 family, member L1	protein-coding
mm_5916.1	chr1	55052599	55052622	-	1	NA	promoter-TSS (NM_001039710)	promoter-TSS (NM_001039710)	-160	NM_026424	67876	Mm.281019	NM_026424	ENSMUSG00000025981	Coq10b	1500041J02Rik|1700030I21Rik|9530077A17Rik|AV002237|AW742641	coenzyme Q10B	protein-coding
mm_162496.1	chr1	137966797	137966799	+	1	NA	TTS (NR_029820)	TTS (NR_029820)	159	NR_029820	723890		NR_029820	ENSMUSG00000065458	Mir181b-1	Mirn181b-1|mir-181b-1	microRNA 181b-1	ncRNA
mm_91302.1	chr10	24916411	24916441	-	1	NA	exon (NM_007482, exon 6 of 8)	exon (NM_007482, exon 6 of 8)	5762	NR_105870	102465545		NR_105870	ENSMUSG00000099181	Mir6905	Gm27879|mmu-mir-6905	microRNA 6905	ncRNA
mm_107928.1	chr12	71137158	71137160	+	1	NA	promoter-TSS (NM_001286203)	promoter-TSS (NM_001286203)	311	NM_001163378	76967	Mm.87290	NM_029818	ENSMUSG00000034601	2700049A03Rik	Ta3|Talpid3|mKIAA0586	RIKEN cDNA 2700049A03 gene	protein-coding
mm_2980.1	chr1	133130882	133130885	+	1	NA	promoter-TSS (NM_133819)	promoter-TSS (NM_133819)	-283	NM_133819	108954	Mm.293628	NM_133819	ENSMUSG00000046062	Ppp1r15b	1810033K10Rik|AI606441|C530022L24Rik|CReP	protein phosphatase 1, regulatory (inhibitor) subunit 15b	protein-coding
mm_116573.1	chr13	47100220	47100253	-	1	NA	exon (NM_025900, exon 5 of 11)	exon (NM_025900, exon 5 of 11)	5985	NM_025900	110052	Mm.131150	NM_025900	ENSMUSG00000021377	Dek	1810019E15Rik|D13H6S231E	DEK oncogene (DNA binding)	protein-coding
mm_157525.1	chrX	50943604	50943622	-	1	NA	promoter-TSS (NM_001190332)	promoter-TSS (NM_001190332)	-903	NM_001190332	385354	Mm.393050	NM_001190332	ENSMUSG00000036131	Frmd7	EG665849|Gm1533	FERM domain containing 7	protein-coding
mm_79302.1	chr9	51914440	51914467	+	1	NA	promoter-TSS (NR_040731)	promoter-TSS (NR_040731)	24	NR_040731	74072	Mm.84915	NR_040731	ENSMUSG00000111836	4933407I05Rik	-	RIKEN cDNA 4933407I05 gene	ncRNA
mm_140917.1	chr17	24170782	24170802	-	1	NA	Intergenic	Intergenic	-1363	NM_009729	11984	Mm.30155	NM_009729	ENSMUSG00000024121	Atp6v0c	Atp6c|Atp6c2|Atp6l|Atpl|Atpl-rs1|PL16|VATL|Vma3	ATPase, H+ transporting, lysosomal V0 subunit C	protein-coding
mm_145313.1	chr18	53922092	53922107	+	1	NA	intron (NM_152809, intron 6 of 12)	CT-rich|Low_complexity|Low_complexity	59986	NM_152809	70425	Mm.368668	NM_152809	ENSMUSG00000073563	Csnk1g3	3300002K07Rik|C330049O21Rik	casein kinase 1, gamma 3	protein-coding
mm_115948.1	chr13	23729068	23729088	-	1	NA	Intergenic	Intergenic	-9729	NM_015786	50708	Mm.193539	NM_015786	ENSMUSG00000036181	Hist1h1c	0610008C09Rik|H1.2|H1c|H1f2|H1var1|His1a	histone cluster 1, H1c	protein-coding
mm_43598.1	chr5	137787814	137787843	+	1	NA	promoter-TSS (NM_001005426)	promoter-TSS (NM_001005426)	26	NM_001005426	381678	Mm.332765	NM_001005426	ENSMUSG00000037108	Zcwpw1	Gm1053	zinc finger, CW type with PWWP domain 1	protein-coding
mm_149301.1	chr19	10712925	10712944	+	1	NA	exon (NM_181403, exon 5 of 5)	exon (NM_181403, exon 5 of 5)	24119	NM_181403	107305	Mm.19091	NM_181403	ENSMUSG00000048832	Vps37c	5730409F24Rik|AU042646	vacuolar protein sorting 37C	protein-coding
mm_23035.1	chr3	34684317	34684320	+	1	NA	Intergenic	Lx9|LINE|L1	32344	NR_038347	100041108	Mm.24764	NR_038347	ENSMUSG00000105153	Gm3143	-	predicted gene 3143	ncRNA
mm_162108.1	chrX	49886262	49886262	-	1	NA	exon (NM_001011794, exon 1 of 1)	exon (NM_001011794, exon 1 of 1)	139	NM_001011794	257978	Mm.377321	NM_001011794	ENSMUSG00000056281	Olfr1322	MOR264-16P	olfactory receptor 1322	protein-coding
mm_168193.1	chr10	62980307	62980315	+	1	NA	promoter-TSS (NM_027425)	promoter-TSS (NM_027425)	88	NM_027425	70432	Mm.234587	NM_027425	ENSMUSG00000020070	Rufy2	2610111M19Rik|AI844453|Denn|LZ-FYVE|ZFYVE13	RUN and FYVE domain-containing 2	protein-coding
mm_150863.1	chr19	45017690	45017702	+	1	NA	promoter-TSS (NM_001130526)	promoter-TSS (NM_001130526)	-439	NM_001130526	226154	Mm.28204	NM_145503	ENSMUSG00000035342	Lzts2	BC014695|LAPSER1|mKIAA1813	leucine zipper, putative tumor suppressor 2	protein-coding
mm_129842.1	chr15	83154672	83154680	-	1	NA	exon (NM_029787, exon 9 of 9)	exon (NM_029787, exon 9 of 9)	5031	NR_004432	104307	Mm.471434	NR_004432	ENSMUSG00000065176	Rnu12	-	RNA U12, small nuclear	snRNA
mm_24531.1	chr3	93277664	93277679	+	1	NA	Intergenic	Intergenic	-42078	NM_133698	68723	Mm.208047	NM_133698	ENSMUSG00000041991	Hrnr	1110033K19Rik|A530063N20Rik|S100a18	hornerin	protein-coding
mm_147313.1	chr18	41951188	41951232	-	1	NA	promoter-TSS (NM_029942)	promoter-TSS (NM_029942)	-16	NM_029942	77619	Mm.30649	NM_029942	ENSMUSG00000056671	Prelid2	1700003A01Rik|C330008K14Rik	PRELI domain containing 2	protein-coding
mm_168606.1	chr11	75348352	75348353	-	1	NA	promoter-TSS (NM_026653)	promoter-TSS (NM_026653)	31	NM_001164223	68275	Mm.102574	NM_026653	ENSMUSG00000000751	Rpa1	5031405K23Rik|70kDa|AA589576|AW557552|RF-A|RP-A|Rpa	replication protein A1	protein-coding
mm_147973.1	chr18	67288936	67288957	-	1	NA	promoter-TSS (NM_053261)	promoter-TSS (NM_053261)	-277	NM_053261	114663	Mm.34079	NM_053261	ENSMUSG00000024525	Impa2	2210415D20Rik|AI326924|AW259601	inositol (myo)-1(or 4)-monophosphatase 2	protein-coding
mm_23247.1	chr3	51224516	51224528	+	1	NA	promoter-TSS (NM_009834)	promoter-TSS (NM_009834)	75	NM_009834	12457	Mm.86541	NM_009834	ENSMUSG00000023087	Noct	AU043840|Ccr4|Ccrn4l	nocturnin	protein-coding
mm_155939.1	chrX	104017407	104017410	+	1	NA	Intergenic	Intergenic	-36124	NM_011276	19820	Mm.427762	NM_011276	ENSMUSG00000056537	Rlim	AL022832|AW743871|Ha1r|Rlim1|Rnf12	ring finger protein, LIM domain interacting	protein-coding
mm_138720.1	chr17	36869547	36869565	+	1	NA	promoter-TSS (NM_011280)	promoter-TSS (NM_011280)	-18	NM_011280	19824	Mm.299155	NM_011280	ENSMUSG00000073400	Trim10	AI324236|BB139825|Herf1|Rnf9	tripartite motif-containing 10	protein-coding
mm_89944.1	chr10	111280343	111280358	+	1	NA	exon (NM_001003717, exon 15 of 23)	exon (NM_001003717, exon 15 of 23)	-18329	NM_027914	71769	Mm.45256	NM_027914	ENSMUSG00000035759	Bbs10	1300007O09Rik|AI452285	Bardet-Biedl syndrome 10 (human)	protein-coding
mm_128143.1	chr15	31530977	31530992	-	1	NA	promoter-TSS (NM_172606)	promoter-TSS (NM_172606)	53	NM_172606	223455	Mm.272185	NM_172606	ENSMUSG00000039100	March6	3830408G03|F830029L24Rik|mKIAA0597	membrane-associated ring finger (C3HC4) 6	protein-coding
mm_81268.1	chr9	108080424	108080430	+	1	NA	promoter-TSS (NM_008243)	promoter-TSS (NM_008243)	-9	NM_008243	15235	Mm.8369	NM_008243	ENSMUSG00000032591	Mst1	D3F15S2h|D9H3F15S2|DNF15S2h|Hgfl	macrophage stimulating 1 (hepatocyte growth factor-like)	protein-coding
mm_95073.1	chr11	32614749	32614783	+	1	NA	intron (NM_009288, intron 16 of 18)	(CGTG)n|Simple_repeat|Simple_repeat	-27789	NM_001271348	103583	Mm.28017	NM_134015	ENSMUSG00000020271	Fbxw11	2310065A07Rik|AA536858|BTRC2|BTRCP2|Fbxw1b|HOS	F-box and WD-40 domain protein 11	protein-coding
mm_25814.1	chr3	127791107	127791145	+	1	NA	intron (NM_145133, intron 1 of 2)	intron (NM_145133, intron 1 of 2)	1213	NM_145133	211550	Mm.31852	NM_145133	ENSMUSG00000046688	Tifa	T2bp	TRAF-interacting protein with forkhead-associated domain	protein-coding
mm_128466.1	chr15	50816872	50816875	-	1	NA	intron (NM_001310485, intron 5 of 7)	intron (NM_001310485, intron 5 of 7)	72176	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_143798.1	chr17	83057971	83057981	-	1	NA	intron (NR_045094, intron 2 of 3)	intron (NR_045094, intron 2 of 3)	20249	NR_045094	100503434	Mm.187281	NR_045094		Gm19689	-	predicted gene, 19689	ncRNA
mm_69772.1	chr7	141016818	141016831	-	1	NA	promoter-TSS (NM_001033632)	promoter-TSS (NM_001033632)	68	NM_001033632	213002	Mm.276440	NM_001033632	ENSMUSG00000059108	Ifitm6	A330075D07|Dspa2f|Fgls5|fragilis5	interferon induced transmembrane protein 6	protein-coding
mm_88997.1	chr10	81575278	81575301	+	1	NA	promoter-TSS (NM_019725)	promoter-TSS (NM_019725)	2	NM_001252401	21886	Mm.38608	NM_019725	ENSMUSG00000034771	Tle2	Grg2|mKIAA4188	transducin-like enhancer of split 2	protein-coding
mm_77633.1	chr8	124080841	124080845	-	1	NA	Intergenic	Intergenic	57370	NM_001029876	382038	Mm.334891	NM_001029876	ENSMUSG00000031976	Urb2	C77575|mKIAA0133	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	protein-coding
mm_141322.1	chr17	28438051	28438061	-	1	NA	exon (NM_010220, exon 3 of 11)	exon (NM_010220, exon 3 of 11)	48093	NM_010220	14229	Mm.276405	NM_010220	ENSMUSG00000024222	Fkbp5	D17Ertd592e|Dit1|FKBP-5|FKBP51	FK506 binding protein 5	protein-coding
mm_23565.1	chr3	63295441	63295506	+	1	NA	promoter-TSS (NM_008604)	promoter-TSS (NM_008604)	38	NM_001289462	17380	Mm.296022	NM_008604	ENSMUSG00000027820	Mme	6030454K05Rik|C85356|CALLA|CD10|NEP|SFE	membrane metallo endopeptidase	protein-coding
mm_151491.1	chr19	58680735	58680762	+	1	NA	exon (NM_026925, exon 12 of 13)	exon (NM_026925, exon 12 of 13)	10383	NM_026925	69060	Mm.20407	NM_026925	ENSMUSG00000046008	Pnlip	1810007A24Rik|PL|PTL	pancreatic lipase	protein-coding
mm_35772.1	chr4	46396862	46396873	-	1	NA	exon (NM_053149, exon 3 of 4)	exon (NM_053149, exon 3 of 4)	7316	NM_053149	93966	Mm.25793	NM_053149	ENSMUSG00000028332	Hemgn	4921524M03Rik|AI317176|EDAG|Hgn|mNDR	hemogen	protein-coding
mm_127685.1	chr15	102966795	102966812	+	1	NA	promoter-TSS (NM_010462)	promoter-TSS (NM_010462)	7	NM_010462	209448	Mm.31665	NM_010462	ENSMUSG00000022484	Hoxc10	AI506621|Hox-3.6	homeobox C10	protein-coding
mm_131257.1	chr16	10785621	10785649	+	1	NA	promoter-TSS (NM_001271603)	promoter-TSS (NM_001271603)	-99	NM_001271603	12703	Mm.130	NM_009896	ENSMUSG00000038037	Socs1	Cish1|Cish7|JAB|SOCS-1|SSI-1	suppressor of cytokine signaling 1	protein-coding
mm_131303.1	chr16	11420694	11420724	+	1	NA	exon (NM_028964, exon 11 of 21)	exon (NM_028964, exon 11 of 21)	15061	NM_001290148	74478	Mm.325831	NM_028964	ENSMUSG00000071669	Snx29	4933437K13Rik|ENSMUSG00000079738|Gm11170|Gm1737|Gm930|Rundc2a	sorting nexin 29	protein-coding
mm_65068.1	chr7	18925777	18925786	-	1	NA	promoter-TSS (NM_001029877)	promoter-TSS (NM_001029877)	-107	NM_001029877	384569	Mm.262724	NM_001029877	ENSMUSG00000030411	Nova2	Gm1424	neuro-oncological ventral antigen 2	protein-coding
mm_52476.1	chr6	114302592	114302605	+	1	NA	exon (NM_178703, exon 4 of 16)	exon (NM_178703, exon 4 of 16)	19963	NM_178703	232333	Mm.5260	NM_178703	ENSMUSG00000030310	Slc6a1	A730043E01|GABATHG|GABATR|GAT-1|Gabt|Gabt1|Gat1|XT-1|Xtrp1	solute carrier family 6 (neurotransmitter transporter, GABA), member 1	protein-coding
mm_164204.1	chr15	81522094	81522104	-	1	NA	Intergenic	Intergenic	55783	NM_019712	56438	Mm.29405	NM_019712	ENSMUSG00000022400	Rbx1	1500002P15Rik|AA517855|ROC1	ring-box 1	protein-coding
mm_154068.1	chr19	55743194	55743220	-	1	NA	intron (NR_138565, intron 3 of 15)	CpG-7657	1397	NM_001142923	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_81965.1	chr9	120950163	120950193	+	1	NA	5' UTR (NM_007614, exon 2 of 15)	5' UTR (NM_007614, exon 2 of 15)	-4908	NR_106058	102465661		NR_106058	ENSMUSG00000106193	Mir7090	mmu-mir-7090	microRNA 7090	ncRNA
mm_16224.1	chr2	173153061	173153080	+	1	NA	promoter-TSS (NM_011044)	promoter-TSS (NM_011044)	-3	NM_011044	18534	Mm.266867	NM_011044	ENSMUSG00000027513	Pck1	AI265463|PEPCK|Pck-1	phosphoenolpyruvate carboxykinase 1, cytosolic	protein-coding
mm_137713.1	chr17	29099747	29099771	+	1	NA	3' UTR (NM_007669, exon 3 of 3)	3' UTR (NM_007669, exon 3 of 3)	5990	NM_007669	12575	Mm.195663	NM_007669	ENSMUSG00000023067	Cdkn1a	CAP20|CDKI|CIP1|Cdkn1|P21|SDI1|Waf1|mda6|p21Cip1|p21WAF	cyclin-dependent kinase inhibitor 1A (P21)	protein-coding
mm_13557.1	chr2	112265550	112265557	+	1	NA	promoter-TSS (NM_133649)	promoter-TSS (NM_133649)	-761	NM_133649	107723	Mm.491155	NM_133648	ENSMUSG00000027130	Slc12a6	9530023I19Rik|KCC3|gaxp	solute carrier family 12, member 6	protein-coding
mm_144629.1	chr18	32939142	32939205	+	1	NA	5' UTR (NM_009793, exon 1 of 11)	5' UTR (NM_009793, exon 1 of 11)	132	NM_009793	12326	Mm.222329	NM_009793	ENSMUSG00000038128	Camk4	A430110E23Rik|AI666733|CaMKIV|CaMKIV/Gr|D18Bwg0362e	calcium/calmodulin-dependent protein kinase IV	protein-coding
mm_157391.1	chrX	38406660	38406679	-	1	NA	intron (NM_001017959, intron 8 of 8)	intron (NM_001017959, intron 8 of 8)	49791	NM_010685	16784	Mm.486	NM_010685	ENSMUSG00000016534	Lamp2	CD107b|LGP-B|Lamp II|Lamp-2|Lamp-2a|Lamp-2b|Lamp-2c|Mac3	lysosomal-associated membrane protein 2	protein-coding
mm_92153.1	chr10	67535333	67535350	-	1	NA	Intergenic	CpG	-2528	NM_010118	13654	Mm.290421	NM_010118	ENSMUSG00000037868	Egr2	Egr-2|Krox-20|Krox20|NGF1-B|Zfp-25|Zfp-6	early growth response 2	protein-coding
mm_132812.1	chr16	45163243	45163288	+	1	NA	intron (NM_026402, intron 2 of 11)	CT-rich|Low_complexity|Low_complexity	4436	NM_026402	67841	Mm.41775	NM_026402	ENSMUSG00000022663	Atg3	2610016C12Rik|APG3|Apg3l|Atg3l|PC3-96	autophagy related 3	protein-coding
mm_169977.1	chr17	14978864	14978883	+	1	NA	promoter-TSS (NM_001123370)	promoter-TSS (NM_001123370)	9	NM_001123370	100041574	Mm.393767	NM_001123370	ENSMUSG00000036552	9030025P20Rik	D17Zt9e	RIKEN cDNA 9030025P20 gene	protein-coding
mm_134517.1	chr16	19218419	19218427	-	1	NA	Intergenic	L1_Rod|LINE|L1	68318	NM_146451	258443	Mm.377506	NM_146451	ENSMUSG00000050742	Olfr164	MOR279-2	olfactory receptor 164	protein-coding
mm_32934.1	chr4	119255428	119255456	+	1	NA	promoter-TSS (NM_153105)	promoter-TSS (NM_153105)	1	NM_153105	242653	Mm.130701	NM_153105	ENSMUSG00000066058	Cldn19	-	claudin 19	protein-coding
mm_93238.1	chr10	95415286	95415297	-	1	NA	promoter-TSS (NM_001168657)	promoter-TSS (NM_001168657)	-8	NM_001168657	216233	Mm.474283	NM_007706	ENSMUSG00000020027	Socs2	8030460M17|AI527257|AW108012|CIS2|Cish2|D130043N08Rik|JAB|SOCS-2|SSI-2|hg	suppressor of cytokine signaling 2	protein-coding
mm_70031.1	chr7	142576669	142576688	-	1	NA	TTS (NR_030416)	TTS (NR_030416)	469	NR_030416	735280		NR_030416	ENSMUSG00000076275	Mir675	Mirn675|mir-675|mmu-mir-675	microRNA 675	ncRNA
mm_8739.1	chr1	160232728	160232733	-	1	NA	intron (NM_001038621, intron 6 of 8)	B3|SINE|B2	-19838	NM_009786	12301	Mm.10702	NM_009786	ENSMUSG00000014226	Cacybp	SIP	calcyclin binding protein	protein-coding
mm_26124.1	chr3	137867759	137867797	+	1	NA	TTS (NM_016750)	TTS (NM_016750)	103	NM_001033155	70604	Mm.256488	NM_001033155	ENSMUSG00000074212	Dnajb14	5730496F10Rik	DnaJ heat shock protein family (Hsp40) member B14	protein-coding
mm_67709.1	chr7	89941221	89941223	-	1	NA	promoter-TSS (NM_001291289)	promoter-TSS (NM_001291289)	-18	NM_001291288	67669	Mm.28679	NM_026304	ENSMUSG00000062797	Hikeshi	0610007P06Rik|1110002N09Rik|l(7)6Rn|l7Rn6	heat shock protein nuclear import factor	protein-coding
mm_158356.1	chrX	134600254	134600301	-	1	NA	promoter-TSS (NM_001313716)	promoter-TSS (NM_001313716)	728	NM_013463	11605	Mm.1114	NM_013463	ENSMUSG00000031266	Gla	Ags	galactosidase, alpha	protein-coding
mm_10729.1	chr2	22895560	22895568	+	1	NA	promoter-TSS (NM_019501)	promoter-TSS (NM_019501)	42	NM_019501	56075	Mm.249752	NM_019501	ENSMUSG00000026784	Pdss1	2610203G20Rik|2700031G06Rik|TPT|TPT 1|Tprt|mDLP1|mSPS1	prenyl (solanesyl) diphosphate synthase, subunit 1	protein-coding
mm_50074.1	chr6	41339782	41339788	+	1	NA	Intergenic	Intergenic	-14320	NM_001038996	436522	Mm.443385	NM_001038996	ENSMUSG00000071521	Try10	-	trypsin 10	protein-coding
mm_71855.1	chr8	68906204	68906210	+	1	NA	3' UTR (NM_008509, exon 10 of 10)	3' UTR (NM_008509, exon 10 of 10)	25652	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_105984.1	chr11	115612914	115612937	-	1	NA	promoter-TSS (NM_027162)	promoter-TSS (NM_027162)	44	NM_001243584	69674	Mm.390387	NM_027162	ENSMUSG00000020743	Mif4gd	1110014L05Rik|2310075G12Rik	MIF4G domain containing	protein-coding
mm_140049.1	chr17	74528397	74528401	+	1	NA	5' UTR (NM_007566, exon 1 of 73)	5' UTR (NM_007566, exon 1 of 73)	104	NM_007566	12211	Mm.442564	NM_007566	ENSMUSG00000024073	Birc6	A430032G04Rik|A430040A19Rik|AA501170|Bruce|D630005A10Rik|mKIAA1289	baculoviral IAP repeat-containing 6	protein-coding
mm_123410.1	chr14	63987740	63987767	-	1	NA	promoter-TSS (NM_026359)	promoter-TSS (NM_026359)	27	NM_026359	67750	Mm.33864	NM_026359	ENSMUSG00000021961	4930578I06Rik	AI429111	RIKEN cDNA 4930578I06 gene	protein-coding
mm_37325.1	chr4	119415495	119415522	-	1	NA	promoter-TSS (NM_001270435)	promoter-TSS (NM_001270435)	13	NM_001270435	73332	Mm.425204	NM_028506	ENSMUSG00000028637	Ccdc30	1700001O02Rik|1700041C02Rik|1700111D19Rik|4930445I03Rik	coiled-coil domain containing 30	protein-coding
mm_106654.1	chr11	121118257	121118258	-	1	NA	5' UTR (NM_027622, exon 1 of 3)	5' UTR (NM_027622, exon 1 of 3)	420	NM_027622	70956	Mm.158506	NM_027622	ENSMUSG00000039337	Tex19.2	4921530G04Rik|Tex19b	testis expressed gene 19.2	protein-coding
mm_160716.1	chr10	62879812	62879812	-	1	NA	exon (NM_001253857, exon 1 of 12)	exon (NM_001253857, exon 1 of 12)	202	NM_027384	52463	Mm.17774	NM_027384	ENSMUSG00000047146	Tet1	2510010B09Rik|AA517754|BB001228|Cxxc6|D10Ertd17e|LCX|mKIAA1676	tet methylcytosine dioxygenase 1	protein-coding
mm_92370.1	chr10	76097569	76097571	-	1	NA	intron (NM_023219, intron 5 of 14)	Lx6|LINE|L1	13448	NM_023219	64454	Mm.155678	NM_023219	ENSMUSG00000020226	Slc5a4b	2010104G07Rik|SAAT1|SGLT3-b|SGLT3b|pSGLT2	solute carrier family 5 (neutral amino acid transporters, system A), member 4b	protein-coding
mm_146031.1	chr18	69521575	69521583	+	1	NA	intron (NM_013685, intron 6 of 19)	intron (NM_013685, intron 6 of 19)	175858	NM_001083967	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding
mm_61911.1	chr7	90143213	90143215	+	1	NA	intron (NM_001252520, intron 1 of 20)	PB1D11|SINE|Alu	12982	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_12278.1	chr2	69000365	69000371	+	1	NA	intron (NM_172856, intron 3 of 9)	intron (NM_172856, intron 3 of 9)	-135432	NM_181547	329416	Mm.90047	NM_181547	ENSMUSG00000034738	Nostrin	Daip2|mDaIP2	nitric oxide synthase trafficker	protein-coding
mm_148082.1	chr18	73251808	73251814	-	1	NA	Intergenic	RMER19B|LTR|ERVK	-320894	NM_001039214	240396	Mm.24131	NM_001039214	ENSMUSG00000037253	Mex3c	A130001D14Rik|BC035207|BM-013|Rkhd2	mex3 RNA binding family member C	protein-coding
mm_100762.1	chr11	4497588	4497592	-	1	NA	intron (NM_028860, intron 10 of 17)	intron (NM_028860, intron 10 of 17)	-56508	NM_029458	75828	Mm.159592	NM_029458	ENSMUSG00000020419	Hormad2	4930529M09Rik	HORMA domain containing 2	protein-coding
mm_9899.1	chr1	186706062	186706097	-	1	NA	promoter-TSS (NM_009367)	promoter-TSS (NM_009367)	-90	NM_001329107	21808	Mm.18213	NM_009367	ENSMUSG00000039239	Tgfb2	BB105277|Tgf-beta2|Tgfb-2	transforming growth factor, beta 2	protein-coding
mm_70281.1	chr8	3621480	3621493	+	1	NA	promoter-TSS (NM_026156)	promoter-TSS (NM_026156)	-65	NM_001195244	100503890	Mm.254898	NM_001195244	ENSMUSG00000087687	Pet100	2900053A13Rik	PET100 homolog	protein-coding
mm_26860.1	chr3	14872520	14872537	-	1	NA	TTS (NM_007606)	TTS (NM_007606)	8990	NM_007606	12350	Mm.300	NM_007606	ENSMUSG00000027559	Car3	BB219044|Ca3|Car-3	carbonic anhydrase 3	protein-coding
mm_112114.1	chr12	112797722	112797742	-	1	NA	Intergenic	Intergenic	-11243	NM_145450	217887	Mm.186678	NM_145450	ENSMUSG00000037594	BC022687	AW050009|C130001I08Rik|Flj20080	cDNA sequence BC022687	protein-coding
mm_116078.1	chr13	28413097	28413100	-	1	NA	Intergenic	B2_Mm2|SINE|B2	270614	NM_023746	28078	Mm.155058	NM_023746	ENSMUSG00000017064	Prl5a1	1600013P04Rik|D13Wsu14e|Ghd24|PLP-L|Prlpl	prolactin family 5, subfamily a, member 1	protein-coding
mm_40374.1	chr5	52363913	52363923	+	1	NA	5' UTR (NM_011435, exon 1 of 2)	5' UTR (NM_011435, exon 1 of 2)	114	NM_011435	20657	Mm.2407	NM_011435	ENSMUSG00000072941	Sod3	AI314465|EC-SOD	superoxide dismutase 3, extracellular	protein-coding
mm_140592.1	chr17	10265494	10265502	-	1	NA	intron (NM_021881, intron 3 of 6)	intron (NM_021881, intron 3 of 6)	53863	NM_021881	19317	Mm.130694	NM_021881	ENSMUSG00000062078	Qk	1110003F05Rik|1500005P18|QkI|l(17)-1Wis|l17Wis1	quaking	protein-coding
mm_61992.1	chr7	91108796	91108805	+	1	NA	intron (NM_011807, intron 1 of 22)	intron (NM_011807, intron 1 of 22)	18014	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_139973.1	chr17	71781216	71781221	+	1	NA	promoter-TSS (NM_030179)	promoter-TSS (NM_030179)	-81	NM_001271483	78785	Mm.196382	NM_030179	ENSMUSG00000024059	Clip4	1700024K14Rik|1700074B05Rik|4833417L20Rik|5830409B12Rik|Rsnl2	CAP-GLY domain containing linker protein family, member 4	protein-coding
mm_137848.1	chr17	31067274	31067291	+	1	NA	intron (NM_009593, intron 2 of 14)	intron (NM_009593, intron 2 of 14)	9588	NM_009593	11307	Mm.15691	NM_009593	ENSMUSG00000024030	Abcg1	AW413978|Abc8|White	ATP-binding cassette, sub-family G (WHITE), member 1	protein-coding
mm_90553.1	chr10	128104065	128104068	+	1	NA	intron (NM_054078, intron 2 of 29)	B2_Mm2|SINE|B2	11283	NM_054078	116848	Mm.252213	NM_054078	ENSMUSG00000040054	Baz2a	AA415431|C030005G16Rik|C78388|Tip5|Walp3|mKIAA0314	bromodomain adjacent to zinc finger domain, 2A	protein-coding
mm_115890.1	chr13	22006426	22006447	-	1	NA	intron (NM_019429, intron 7 of 11)	intron (NM_019429, intron 7 of 11)	3305	NM_019429	54373	Mm.32043	NM_019429	ENSMUSG00000006179	Prss16	AI448615|TSSP	protease, serine 16 (thymus)	protein-coding
mm_73068.1	chr8	94415458	94415488	+	1	NA	Intergenic	Intergenic	19630	NR_015514	320377	Mm.486022	NR_015514		9330175E14Rik	A630085K21	RIKEN cDNA 9330175E14 gene	ncRNA
mm_92931.1	chr10	84527344	84527367	-	1	NA	3' UTR (NM_175451, exon 2 of 2)	3' UTR (NM_175451, exon 2 of 2)	6533	NM_175451	216197	Mm.334999	NM_175451	ENSMUSG00000046841	Ckap4	5630400A09Rik|CLIMP-63|P63	cytoskeleton-associated protein 4	protein-coding
mm_72099.1	chr8	71592159	71592221	+	1	NA	promoter-TSS (NM_025396)	promoter-TSS (NM_025396)	6	NM_001294269	66171	Mm.282284	NM_025396	ENSMUSG00000031807	Pgls	1110030K05Rik|AI447866|Plgs	6-phosphogluconolactonase	protein-coding
mm_101576.1	chr11	34317776	34317780	-	1	NA	intron (NM_001025382, intron 1 of 3)	MIR|SINE|MIR	2956	NM_001025382	574403	Mm.444796	NM_001025382	ENSMUSG00000069911	Fam196b	EG574403|Gm6041	family with sequence similarity 196, member B	protein-coding
mm_156647.1	chrX	157699207	157699217	+	1	NA	non-coding (NR_103722, exon 1 of 6)	non-coding (NR_103722, exon 1 of 6)	239	NR_103722	66106	Mm.140340	NM_025357	ENSMUSG00000041476	Smpx	1010001C09Rik|Csl	small muscle protein, X-linked	protein-coding
mm_106001.1	chr11	115699332	115699404	-	1	NA	5' UTR (NM_001313937, exon 1 of 5)	5' UTR (NM_001313937, exon 1 of 5)	166	NM_001313937	14784	Mm.439649	NM_008163	ENSMUSG00000059923	Grb2	AA408164|Ash	growth factor receptor bound protein 2	protein-coding
mm_3726.1	chr1	155054973	155055015	+	1	NA	Intergenic	Intergenic	44642	NM_010500	15939	Mm.12246	NM_010500	ENSMUSG00000056708	Ier5	-	immediate early response 5	protein-coding
mm_157231.1	chrX	16817340	16817373	-	1	NA	promoter-TSS (NM_172778)	promoter-TSS (NM_172778)	10	NM_172778	109731	Mm.241656	NM_172778	ENSMUSG00000040147	Maob	6330414K01Rik|MAO-B	monoamine oxidase B	protein-coding
mm_113582.1	chr13	40860203	40860235	+	1	NA	5' UTR (NM_023887, exon 1 of 3)	5' UTR (NM_023887, exon 1 of 3)	451	NM_023887	14538	Mm.314757	NM_008105	ENSMUSG00000021360	Gcnt2	5330430K10Rik|IGnT|IGnTA|IGnTB|IGnTC	glucosaminyl (N-acetyl) transferase 2, I-branching enzyme	protein-coding
mm_130529.1	chr15	98918015	98918103	-	1	NA	promoter-TSS (NM_029098)	promoter-TSS (NM_029098)	39	NM_029098	74775	Mm.385020	NM_029098	ENSMUSG00000022999	Lmbr1l	1110013E13Rik|AA415653|D15Ertd735e|Limr	limb region 1 like	protein-coding
mm_55399.1	chr6	60813559	60813566	-	1	NA	intron (NM_009221, intron 4 of 5)	intron (NM_009221, intron 4 of 5)	15442	NM_001042451	20617	Mm.17484	NM_009221	ENSMUSG00000025889	Snca	NACP|alphaSYN	synuclein, alpha	protein-coding
mm_69172.1	chr7	127215380	127215443	-	1	NA	exon (NM_017461, exon 9 of 11)	exon (NM_017461, exon 9 of 11)	3034	NM_017461	54204	Mm.18	NM_017461	ENSMUSG00000000486	Sept1	Diff6|Pnutl3	septin 1	protein-coding
mm_48665.1	chr5	145981301	145981313	-	1	NA	intron (NR_030782, intron 11 of 11)	intron (NR_030782, intron 11 of 11)	28310	NM_019792	56388	Mm.301900	NM_019792	ENSMUSG00000029630	Cyp3a25	AI327008	cytochrome P450, family 3, subfamily a, polypeptide 25	protein-coding
mm_18205.1	chr2	46442900	46442914	-	1	NA	Intergenic	Intergenic	746302	NR_040497	69405	Mm.396184	NR_040497	ENSMUSG00000086202	1700019E08Rik	-	RIKEN cDNA 1700019E08 gene	ncRNA
mm_128848.1	chr15	71727886	71727909	-	1	NA	promoter-TSS (NM_177819)	promoter-TSS (NM_177819)	-59	NM_177819	70363	Mm.126450	NM_177819	ENSMUSG00000036800	Fam135b	1700010C24Rik|A830008O07Rik	family with sequence similarity 135, member B	protein-coding
mm_76557.1	chr8	88362109	88362122	-	1	NA	promoter-TSS (NM_012047)	promoter-TSS (NM_012047)	76	NM_012047	26992	Mm.5400	NM_012047	ENSMUSG00000031660	Brd7	BP75|CELTIX1|Ptpn13ip	bromodomain containing 7	protein-coding
mm_166203.1	chr5	41035652	41035662	+	1	NA	Intergenic	L1_Mur3|LINE|L1	672034	NM_001310592	100972	Mm.41555	NM_027295	ENSMUSG00000029128	Rab28	2700023P08Rik|AW496496	RAB28, member RAS oncogene family	protein-coding
mm_171340.1	chr4	102882595	102882595	-	1	NA	intron (NM_001285862, intron 6 of 19)	IAPLTR1_Mm|LTR|ERVK	-103784	NM_001163767	67344	Mm.111346	NM_026100	ENSMUSG00000028523	Tctex1d1	1700055O19Rik	Tctex1 domain containing 1	protein-coding
mm_159736.1	chr5	65763444	65763444	+	1	NA	promoter-TSS (NM_001024917)	promoter-TSS (NM_001024917)	-77	NM_001024917	333789	Mm.332398	NM_001024917	ENSMUSG00000037795	N4bp2	B3bp|E430014I16|Gm1791|Gm868	NEDD4 binding protein 2	protein-coding
mm_74940.1	chr8	25813164	25813180	-	1	NA	3' UTR (NM_011485, exon 7 of 7)	3' UTR (NM_011485, exon 7 of 7)	4698	NM_011485	20845	Mm.293314	NM_011485	ENSMUSG00000031574	Star	AV363654|D8Ertd419e|stARD1	steroidogenic acute regulatory protein	protein-coding
mm_118637.1	chr14	21426684	21426684	+	1	NA	intron (NM_001243041, intron 10 of 10)	intron (NM_001243041, intron 10 of 10)	-73086	NM_001205241	54169	Mm.248967	NM_017479	ENSMUSG00000021767	Kat6b	AI507552|B130044K16Rik|MYST-4|Morf|Myst4|mKIAA0383|qkf|querkopf	K(lysine) acetyltransferase 6B	protein-coding
mm_13060.1	chr2	91115196	91115213	+	1	NA	exon (NM_011355, exon 5 of 5)	exon (NM_011355, exon 5 of 5)	-2940	NM_008653	17868	Mm.10728	NM_008653	ENSMUSG00000002100	Mybpc3	-	myosin binding protein C, cardiac	protein-coding
mm_63290.1	chr7	126797615	126797639	+	1	NA	intron (NM_007438, intron 2 of 8)	intron (NM_007438, intron 2 of 8)	1551	NM_001177307	11674	Mm.275831	NM_007438	ENSMUSG00000030695	Aldoa	Aldo-1|Aldo1	aldolase A, fructose-bisphosphate	protein-coding
mm_34231.1	chr4	141088339	141088350	+	1	NA	promoter-TSS (NM_177867)	promoter-TSS (NM_177867)	-1	NM_177867	329972	Mm.247201	NM_177867	ENSMUSG00000045004	Spata21	4933414G08	spermatogenesis associated 21	protein-coding
mm_158468.1	chrX	140956676	140956717	-	1	NA	promoter-TSS (NM_001164177)	promoter-TSS (NM_001164177)	15	NM_016883	53380	Mm.17640	NM_016883	ENSMUSG00000031429	Psmd10	AW554874	proteasome (prosome, macropain) 26S subunit, non-ATPase, 10	protein-coding
mm_123545.1	chr14	66829977	66829982	-	1	NA	exon (NM_009955, exon 5 of 14)	exon (NM_009955, exon 5 of 14)	38621	NM_009955	12934	Mm.352648	NM_009955	ENSMUSG00000022048	Dpysl2	AI851130|Crmp2|DRP2|Musunc33|TOAD-64|Ulip2	dihydropyrimidinase-like 2	protein-coding
mm_156892.1	chrX	166663428	166663446	+	1	NA	intron (NR_046015, intron 2 of 8)	intron (NR_046015, intron 2 of 8)	1412	NR_046015	382255	Mm.336320	NR_046015	ENSMUSG00000086860	Gm1720	-	predicted gene 1720	ncRNA
mm_15779.1	chr2	164333435	164333441	+	1	NA	exon (NM_009301, exon 2 of 3)	exon (NM_009301, exon 2 of 3)	673	NM_009301	20944	Mm.140154	NM_009301	ENSMUSG00000017004	Svs5	BB115186|Semg1|Svp-1|Svp1|Svp5	seminal vesicle secretory protein 5	protein-coding
mm_157121.1	chrX	9444646	9444714	-	1	NA	exon (NM_007807, exon 10 of 13)	exon (NM_007807, exon 10 of 13)	24644	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_103656.1	chr11	78973432	78973435	-	1	NA	intron (NM_001159301, intron 2 of 9)	intron (NM_001159301, intron 2 of 9)	11491	NM_001159301	16859	Mm.341434	NM_010708	ENSMUSG00000001123	Lgals9	AA407335|AI194909|AI265545|LGALS35|Lgals5|gal-9|galectin-9	lectin, galactose binding, soluble 9	protein-coding
mm_13132.1	chr2	91811632	91811655	+	1	NA	intron (NM_172669, intron 9 of 17)	intron (NM_172669, intron 9 of 17)	81505	NM_001080754	228361	Mm.436667	NM_172669	ENSMUSG00000040506	Ambra1	2310079H06Rik|A130023A14|AA474864|AV021921|D030051N19Rik|mKIAA1736	autophagy/beclin 1 regulator 1	protein-coding
mm_13874.1	chr2	119872841	119872862	+	1	NA	Intergenic	CpG	-24377	NM_001164274	29808	Mm.87532	NM_013720	ENSMUSG00000033943	Mga	AV312082|C130042M01Rik|C80739|D030062C11Rik|Mad5	MAX gene associated	protein-coding
mm_127956.1	chr15	11399677	11399683	-	1	NA	promoter-TSS (NM_033074)	promoter-TSS (NM_033074)	-22	NM_033074	110960	Mm.286061	NM_033074	ENSMUSG00000022241	Tars	D15Wsu59e|ThrRS	threonyl-tRNA synthetase	protein-coding
mm_40615.1	chr5	64803471	64803477	+	1	NA	promoter-TSS (NM_008453)	promoter-TSS (NM_008453)	-49	NM_008453	16599	Mm.392759	NM_008453	ENSMUSG00000029178	Klf3	9930027G08Rik|AL024007|Bklf|Tef-2	Kruppel-like factor 3 (basic)	protein-coding
mm_170639.1	chr19	8989150	8989154	+	1	NA	promoter-TSS (NM_001286518)	promoter-TSS (NM_001286518)	-132	NR_104460	66395	Mm.203866	NM_009643	ENSMUSG00000069833	Ahnak	DY6	AHNAK nucleoprotein (desmoyokin)	protein-coding
mm_163605.1	chr13	48968277	48968286	-	1	NA	promoter-TSS (NM_001033268)	promoter-TSS (NM_001033268)	169	NR_015601	68128	Mm.426304	NR_015601		Fam120aos	C030044B11Rik	family with sequence similarity 120A, opposite strand	ncRNA
mm_164725.1	chr17	57087660	57087669	-	1	NA	5' UTR (NM_009451, exon 1 of 4)	5' UTR (NM_009451, exon 1 of 4)	118	NM_009451	22153	Mm.7420	NM_009451	ENSMUSG00000062591	Tubb4a	AI325297|M(beta)4|Tubb|Tubb4	tubulin, beta 4A class IVA	protein-coding
mm_14698.1	chr2	142217617	142217623	+	1	NA	exon (NM_001013802, exon 11 of 19)	exon (NM_001013802, exon 11 of 19)	683844	NM_001081133	16558	Mm.251934	NM_001081133	ENSMUSG00000038844	Kif16b	8430434E15Rik|AA623607|AI789011|C80253|C80902|mKIAA1590	kinesin family member 16B	protein-coding
mm_21538.1	chr2	163692106	163692108	-	1	NA	intron (NM_001039390, intron 2 of 4)	intron (NM_001039390, intron 2 of 4)	-1930	NM_011106	18769	Mm.10091	NM_011106	ENSMUSG00000035268	Pkig	PKIgamma	protein kinase inhibitor, gamma	protein-coding
mm_56263.1	chr6	90904300	90904307	-	1	NA	Intergenic	Intergenic	-94180	NM_001134384	232227	Mm.196943	NM_182784	ENSMUSG00000034312	Iqsec1	AW561907|BC026481|BRAG2|D6Ertd349e|cI-43	IQ motif and Sec7 domain 1	protein-coding
mm_27566.1	chr3	58621212	58621214	-	1	NA	exon (NM_001081262, exon 12 of 14)	exon (NM_001081262, exon 12 of 14)	15994	NM_001081262	545527	Mm.357722	NM_001081262	ENSMUSG00000070471	Erich6	4932431H17Rik|Fam194a	glutamate rich 6	protein-coding
mm_112255.1	chr12	113827188	113827204	-	1	NA	Intergenic	Intergenic	283288	NM_174885	238406	Mm.188683	NM_174885	ENSMUSG00000043945	Adam6a	Adam6|tMDCIV	a disintegrin and metallopeptidase domain 6A	protein-coding
mm_891.1	chr1	52845116	52845123	+	1	NA	promoter-TSS (NM_146108)	promoter-TSS (NM_146108)	81	NM_146108	227095	Mm.222063	NM_146108	ENSMUSG00000041426	Hibch	2610509I15Rik|HIBYL-COA-H	3-hydroxyisobutyryl-Coenzyme A hydrolase	protein-coding
mm_148252.1	chr18	80738302	80738311	-	1	NA	intron (NM_001201569, intron 28 of 29)	intron (NM_001201569, intron 28 of 29)	-25235	NM_001164109	18018	Mm.329560	NM_016791	ENSMUSG00000033016	Nfatc1	2210017P03Rik|AI449492|AV076380|NF-ATc|NFAT2|NFATc|Nfatcb	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 1	protein-coding
mm_2124.1	chr1	87901244	87901263	+	1	NA	intron (NM_177646, intron 3 of 29)	intron (NM_177646, intron 3 of 29)	-46954	NR_136921	100503175	Mm.426422	NR_136921	ENSMUSG00000101942	Gm19582	-	predicted gene, 19582	ncRNA
mm_162958.1	chr11	4261569	4261599	+	1	NA	intron (NM_008501, intron 1 of 3)	intron (NM_008501, intron 1 of 3)	4016	NM_008501	16878	Mm.4964	NM_008501	ENSMUSG00000034394	Lif	-	leukemia inhibitory factor	protein-coding
mm_61320.1	chr7	68148962	68148965	+	1	NA	intron (NM_010513, intron 2 of 20)	intron (NM_010513, intron 2 of 20)	115270	NM_030101	78444	Mm.425468	NM_030101	ENSMUSG00000030553	Pgpep1l	C330024D12Rik	pyroglutamyl-peptidase I-like	protein-coding
mm_90916.1	chr10	12548731	12548775	-	1	NA	intron (NM_011682, intron 50 of 73)	intron (NM_011682, intron 50 of 73)	312982	NM_011682	22288	Mm.331784	NM_011682	ENSMUSG00000019820	Utrn	AA589569|DRP|Dmdl	utrophin	protein-coding
mm_134729.1	chr16	22898992	22898996	-	1	NA	exon (NM_001276450, exon 7 of 7)	exon (NM_001276450, exon 7 of 7)	-4608	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_25649.1	chr3	121449681	121449694	+	1	NA	intron (NM_028044, intron 1 of 6)	intron (NM_028044, intron 1 of 6)	23146	NM_028044	71994	Mm.275555	NM_028044	ENSMUSG00000053931	Cnn3	1600014M03Rik|C85854|Calpo3	calponin 3, acidic	protein-coding
mm_62246.1	chr7	99164384	99164389	+	1	NA	intron (NM_026384, intron 4 of 7)	intron (NM_026384, intron 4 of 7)	18327	NM_026384	67800	Mm.180189	NM_026384	ENSMUSG00000030747	Dgat2	0610010B06Rik|ARAT|DGAT-2	diacylglycerol O-acyltransferase 2	protein-coding
mm_90927.1	chr10	12826931	12826976	-	1	NA	intron (NM_011682, intron 1 of 73)	intron (NM_011682, intron 1 of 73)	34782	NM_011682	22288	Mm.331784	NM_011682	ENSMUSG00000019820	Utrn	AA589569|DRP|Dmdl	utrophin	protein-coding
mm_75515.1	chr8	54644697	54644702	-	1	NA	intron (NM_001172152, intron 23 of 29)	RLTR20C1_MM|LTR|ERVK	43918	NM_133711	69281	Mm.45833	NM_133711	ENSMUSG00000031518	Spata4	1700001N01Rik|Srg2|TSARG2	spermatogenesis associated 4	protein-coding
mm_9301.1	chr1	171639018	171639044	-	1	NA	exon (NM_144539, exon 4 of 8)	exon (NM_144539, exon 4 of 8)	2869	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_145683.1	chr18	61632711	61632725	+	1	NA	Intergenic	Intergenic	-6935	NR_045420	545261	Mm.426593	NR_045420	ENSMUSG00000098098	Bvht	Braveheart|Gm20748	braveheart long non-coding RNA	ncRNA
mm_147320.1	chr18	42229864	42229872	-	1	NA	intron (NM_134137, intron 16 of 31)	intron (NM_134137, intron 16 of 31)	32203	NM_134137	107045	Mm.312170	NM_134137	ENSMUSG00000024493	Lars	2310045K21Rik|3110009L02Rik|AW536573|mKIAA1352	leucyl-tRNA synthetase	protein-coding
mm_87513.1	chr10	52423762	52423766	+	1	NA	intron (NM_030250, intron 1 of 4)	intron (NM_030250, intron 1 of 4)	6217	NM_030250	52014	Mm.199964	NM_030250	ENSMUSG00000023068	Nus1	1600027K07Rik|AU019165|AW538011|BC003223|D10Ertd438e	NUS1 dehydrodolichyl diphosphate synthase subunit	protein-coding
mm_19407.1	chr2	91650020	91650036	-	1	NA	promoter-TSS (NM_001145902)	promoter-TSS (NM_001145902)	-90	NR_027372	228359	Mm.22413	NM_146124	ENSMUSG00000027247	Arhgap1	B230365D05Rik|C76222|Cdc42GAP|p50rhoGAP	Rho GTPase activating protein 1	protein-coding
mm_125634.1	chr15	62039217	62039262	+	1	NA	promoter-TSS (NR_132746)	promoter-TSS (NR_132746)	-18	NR_132746	19296	Mm.4608	NM_011222	ENSMUSG00000097039	Pvt1	Ayu21-84Imeg|Gt(pU21)84Imeg|Mis-1|Mlvi-1|Pvt-1	plasmacytoma variant translocation 1	ncRNA
mm_144017.1	chr17	88792008	88792022	-	1	NA	promoter-TSS (NM_013582)	promoter-TSS (NM_013582)	-39	NM_013582	16867	Mm.1644	NM_013582	ENSMUSG00000024107	Lhcgr	Gpcr19-rs1|LH-R|Lhr	luteinizing hormone/choriogonadotropin receptor	protein-coding
mm_101825.1	chr11	46707098	46707112	-	1	NA	promoter-TSS (NM_134249)	promoter-TSS (NM_134249)	-1	NM_134249	171284	Mm.234654	NM_134249	ENSMUSG00000040413	Timd2	AA816106|AU019358|AU019662|C78111|G9D3|TIM-2|Tim2	T cell immunoglobulin and mucin domain containing 2	protein-coding
mm_80589.1	chr9	85842532	85842542	+	1	NA	promoter-TSS (NM_001164792)	promoter-TSS (NM_001164792)	157	NM_011627	21983	Mm.20864	NM_011627	ENSMUSG00000035274	Tpbg	5T4|AW495680|WAIF1	trophoblast glycoprotein	protein-coding
mm_106354.1	chr11	118393603	118393618	-	1	NA	exon (NM_011150, exon 6 of 6)	exon (NM_011150, exon 6 of 6)	8321	NM_011150	19039	Mm.3152	NM_011150	ENSMUSG00000033880	Lgals3bp	90K|CyCAP|MAC-2BP|Ppicap|Tango10b	lectin, galactoside-binding, soluble, 3 binding protein	protein-coding
mm_78101.1	chr9	19622244	19622264	+	1	NA	5' UTR (NM_172918, exon 1 of 9)	5' UTR (NM_172918, exon 1 of 9)	163	NM_172918	244713	Mm.67366	NM_172918	ENSMUSG00000057551	Zfp317	4932416G03|D230022C05Rik|KRAB9|Zfp67|Zfp75|mszf40	zinc finger protein 317	protein-coding
mm_99598.1	chr11	104442475	104442490	+	1	NA	promoter-TSS (NM_001081045)	promoter-TSS (NM_001081045)	-191	NM_001081045	76719	Mm.136418	NM_001081045	ENSMUSG00000018412	Kansl1	1700081L11Rik|9430041J06Rik|mKIAA1267	KAT8 regulatory NSL complex subunit 1	protein-coding
mm_40127.1	chr5	34999071	34999086	+	1	NA	promoter-TSS (NM_001163512)	promoter-TSS (NM_001163512)	0	NM_001163512	71729	Mm.196208	NM_173402	ENSMUSG00000029101	Rgs12	1200016K18Rik|4632412M04Rik|AI481290|E130309H11	regulator of G-protein signaling 12	protein-coding
mm_103658.1	chr11	78984835	78984923	-	1	NA	promoter-TSS (NM_010708)	promoter-TSS (NM_010708)	45	NM_001159301	16859	Mm.341434	NM_010708	ENSMUSG00000001123	Lgals9	AA407335|AI194909|AI265545|LGALS35|Lgals5|gal-9|galectin-9	lectin, galactose binding, soluble 9	protein-coding
mm_84055.1	chr9	58159049	58159078	-	1	NA	promoter-TSS (NM_001195431)	promoter-TSS (NM_001195431)	158	NM_012043	26968	Mm.367887	NM_012043	ENSMUSG00000037206	Islr	AW553146|Meflin	immunoglobulin superfamily containing leucine-rich repeat	protein-coding
mm_76281.1	chr8	84192665	84192680	-	1	NA	Intergenic	CpG	-13711	NR_029821	723819		NR_029821	ENSMUSG00000065483	Mir181c	Mirn181c|mir-181c	microRNA 181c	ncRNA
mm_25544.1	chr3	115885806	115885815	+	1	NA	intron (NR_015487, intron 1 of 1)	intron (NR_015487, intron 1 of 1)	2249	NR_027894	68161	Mm.392043	NR_015487	ENSMUSG00000054426	A930005H10Rik	-	RIKEN cDNA A930005H10 gene	ncRNA
mm_42490.1	chr5	115474505	115474515	+	1	NA	exon (NM_011107, exon 4 of 4)	exon (NM_011107, exon 4 of 4)	8244	NM_011107	18778	Mm.20190	NM_011107	ENSMUSG00000029522	Pla2g1b	Pla2a|sPLA2IB	phospholipase A2, group IB, pancreas	protein-coding
mm_28631.1	chr3	95142364	95142374	-	1	NA	promoter-TSS (NM_027206)	promoter-TSS (NM_027206)	-9	NM_027206	69769	Mm.34368	NM_027206	ENSMUSG00000013707	Tnfaip8l2	1810019A08Rik|AW610835|TIPE2	tumor necrosis factor, alpha-induced protein 8-like 2	protein-coding
mm_124077.1	chr14	78632746	78632767	-	1	NA	intron (NR_104044, intron 1 of 27)	intron (NR_104044, intron 1 of 27)	-3466	NM_001281794	380921	Mm.89591	NM_001081336	ENSMUSG00000034731	Dgkh	5930402B05Rik|D130015C16|DGK	diacylglycerol kinase, eta	protein-coding
mm_14250.1	chr2	128127588	128127643	+	1	NA	promoter-TSS (NM_001284410)	promoter-TSS (NM_001284410)	40	NM_001284410	12125	Mm.141083	NM_009754	ENSMUSG00000027381	Bcl2l11	1500006F24Rik|Bim|Bod|bcl2-L-11	BCL2-like 11 (apoptosis facilitator)	protein-coding
mm_97037.1	chr11	72267303	72267320	+	1	NA	promoter-TSS (NM_001004148)	promoter-TSS (NM_001004148)	467	NR_045922	73366	Mm.396157	NR_045922	ENSMUSG00000086951	1700051A21Rik	-	RIKEN cDNA 1700051A21 gene	ncRNA
mm_91090.1	chr10	19015869	19015872	-	1	NA	promoter-TSS (NM_009397)	promoter-TSS (NM_009397)	-460	NM_009397	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_96279.1	chr11	62951156	62951159	+	1	NA	promoter-TSS (NM_025496)	promoter-TSS (NM_025496)	-36	NM_025496	66338	Mm.46166	NM_025496	ENSMUSG00000042200	Cdrt4	1700019I23Rik	CMT1A duplicated region transcript 4	protein-coding
mm_130051.1	chr15	89167403	89167446	-	1	NA	exon (NM_001284506, exon 3 of 37)	exon (NM_001284506, exon 3 of 37)	-4516	NR_106066	102465672		NR_106066	ENSMUSG00000106328	Mir7118	mmu-mir-7118	microRNA 7118	ncRNA
mm_21520.1	chr2	163632176	163632192	-	1	NA	exon (NM_012032, exon 5 of 10)	exon (NM_012032, exon 5 of 10)	-12666	NR_028113	68386	Mm.410649	NR_028113	ENSMUSG00000058812	0610039K10Rik	-	RIKEN cDNA 0610039K10 gene	ncRNA
mm_54356.1	chr6	31088350	31088357	-	1	NA	Intergenic	Intergenic	-25260	NR_029532	387223		NR_029532	ENSMUSG00000065604	Mir29b-1	Mirn29b|Mirn29b-1|mir-29b-1	microRNA 29b-1	ncRNA
mm_158149.1	chrX	103469696	103469707	-	1	NA	non-coding (NR_001570, exon 4 of 8)	non-coding (NR_001570, exon 4 of 8)	13532	NR_001570	213742	Mm.274770	NR_001463	ENSMUSG00000086503	Xist	A430022B11|AI314753	inactive X specific transcripts	ncRNA
mm_64701.1	chr7	4547443	4547451	-	1	NA	promoter-TSS (NM_016908)	promoter-TSS (NM_016908)	-880	NM_016908	53420	Mm.358663	NM_016908	ENSMUSG00000004961	Syt5	SytV	synaptotagmin V	protein-coding
mm_18296.1	chr2	52742143	52742156	-	1	NA	promoter-TSS (NM_019667)	promoter-TSS (NM_019667)	0	NM_019667	56324	Mm.263639	NM_019667	ENSMUSG00000055371	Stam2	1200004O12Rik|5730456G07Rik|BB145015|Hbp	signal transducing adaptor molecule (SH3 domain and ITAM motif) 2	protein-coding
mm_43680.1	chr5	138799702	138799721	+	1	NA	intron (NM_030565, intron 5 of 9)	B4|SINE|B4	-20369	NM_001195128	384244	Mm.485002	NM_001195128	ENSMUSG00000094504	Gm5294	EG384244	predicted gene 5294	protein-coding
mm_169694.1	chr15	74997902	74997917	-	1	NA	5' UTR (NM_001271446, exon 1 of 4)	5' UTR (NM_001271446, exon 1 of 4)	122	NM_001271417	110454	Mm.425949	NM_010738	ENSMUSG00000075602	Ly6a	Ly-6A.2|Ly-6A/E|Ly-6E.1|Sca-1|Sca1|TAP	lymphocyte antigen 6 complex, locus A	protein-coding
mm_3913.1	chr1	161969285	161969313	+	1	NA	promoter-TSS (NM_001204905)	promoter-TSS (NM_001204905)	111	NM_026078	67292	Mm.45106	NM_026078	ENSMUSG00000026698	Pigc	3110030E07Rik|AW212108	phosphatidylinositol glycan anchor biosynthesis, class C	protein-coding
mm_43774.1	chr5	141241630	141241643	+	1	NA	5' UTR (NM_177879, exon 1 of 45)	5' UTR (NM_177879, exon 1 of 45)	102	NM_177879	330222	Mm.151931	NM_177879	ENSMUSG00000039683	Sdk1	5330440E10|6720466O15Rik	sidekick cell adhesion molecule 1	protein-coding
mm_120316.1	chr14	63142760	63142785	+	1	NA	3' UTR (NM_007798, exon 10 of 10)	3' UTR (NM_007798, exon 10 of 10)	20310	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_46908.1	chr5	114372278	114372289	-	1	NA	intron (NM_026145, intron 2 of 6)	intron (NM_026145, intron 2 of 6)	8222	NM_001159941	330171	Mm.238285	NM_026145	ENSMUSG00000001098	Kctd10	AW536343|C87062|mBACURD3	potassium channel tetramerisation domain containing 10	protein-coding
mm_87188.1	chr10	39369934	39369945	+	1	NA	5' UTR (NM_008054, exon 1 of 14)	5' UTR (NM_008054, exon 1 of 14)	140	NM_001122893	14360	Mm.4848	NM_008054	ENSMUSG00000019843	Fyn	AI448320|AW552119	Fyn proto-oncogene	protein-coding
mm_56173.1	chr6	88019972	88019972	-	1	NA	promoter-TSS (NM_001293655)	promoter-TSS (NM_001293655)	-177	NM_001293655	19349	Mm.333233	NM_009005	ENSMUSG00000079477	Rab7	Rab7a	RAB7, member RAS oncogene family	protein-coding
mm_71103.1	chr8	35439348	35439353	+	1	NA	Intergenic	Intergenic	56183	NM_026067	67276	Mm.207534	NM_026067	ENSMUSG00000031527	Eri1	3'hexo|3110010F15Rik|Thex1|eri-1	exoribonuclease 1	protein-coding
mm_143110.1	chr17	57194080	57194108	-	1	NA	promoter-TSS (NM_019418)	promoter-TSS (NM_019418)	87	NM_019418	50930	Mm.483369	NM_019418	ENSMUSG00000005824	Tnfsf14	HVEM-L|HVEML|LIGHT|LTg|Ly113|Tnlg1d	tumor necrosis factor (ligand) superfamily, member 14	protein-coding
mm_68950.1	chr7	126563686	126563711	-	1	NA	exon (NM_146200, exon 5 of 21)	exon (NM_146200, exon 5 of 21)	2668	NM_146200	56347	Mm.22776	NM_146200	ENSMUSG00000030738	Eif3c	110kDa|3230401O13Rik|Eif3s8|NIPIL(A3)|NipilA3|Xs|Xsl	eukaryotic translation initiation factor 3, subunit C	protein-coding
mm_11953.1	chr2	52967705	52967715	+	1	NA	intron (NM_172409, intron 1 of 26)	intron (NM_172409, intron 1 of 26)	109842	NM_172409	71409	Mm.394427	NM_172409	ENSMUSG00000036053	Fmnl2	5430425K04Rik|Man	formin-like 2	protein-coding
mm_54035.1	chr6	12749085	12749095	-	1	NA	5' UTR (NM_001164805, exon 1 of 27)	5' UTR (NM_001164805, exon 1 of 27)	163	NM_001164805	330267	Mm.11989	NM_001164805	ENSMUSG00000032625	Thsd7a	Gm837	thrombospondin, type I, domain containing 7A	protein-coding
mm_61814.1	chr7	87304250	87304263	+	1	NA	intron (NM_015760, intron 4 of 17)	intron (NM_015760, intron 4 of 17)	57607	NM_001285833	50490	Mm.31748	NM_015760	ENSMUSG00000030562	Nox4	AI648021	NADPH oxidase 4	protein-coding
mm_162625.1	chr1	183420651	183420659	+	1	NA	intron (NM_001308052, intron 1 of 8)	intron (NM_001308052, intron 1 of 8)	1407	NM_001308052	78772	Mm.29003	NM_030175	ENSMUSG00000053461	Hhipl2	4930507C10Rik|AW208802|Hhip3	hedgehog interacting protein-like 2	protein-coding
mm_80213.1	chr9	72492042	72492067	+	1	NA	promoter-TSS (NM_009359)	promoter-TSS (NM_009359)	-95	NM_009359	21778	Mm.14485	NM_009359	ENSMUSG00000090626	Tex9	Gm19407|tsec-1	testis expressed gene 9	protein-coding
mm_39374.1	chr5	12383326	12383336	+	1	NA	5' UTR (NM_028882, exon 1 of 18)	5' UTR (NM_028882, exon 1 of 18)	165	NM_028882	108151	Mm.89313	NM_028882	ENSMUSG00000040254	Sema3d	4631426B19Rik	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D	protein-coding
mm_122987.1	chr14	54985125	54985142	-	1	NA	exon (NM_080728, exon 22 of 41)	exon (NM_080728, exon 22 of 41)	-9357	NR_030607	100124433		NR_030607	ENSMUSG00000077928	Mir208b	Mirn208b|mir-208b	microRNA 208b	ncRNA
mm_144209.1	chr18	9707640	9707661	+	1	NA	promoter-TSS (NM_130449)	promoter-TSS (NM_130449)	2	NM_130449	140792	Mm.218571	NM_130449	ENSMUSG00000036103	Colec12	CL-P1|SRCL|Scara4	collectin sub-family member 12	protein-coding
mm_71560.1	chr8	49819100	49819113	+	1	NA	Intergenic	Lx8b|LINE|L1	-549006	NR_046067	100039954	Mm.400419	NR_046067	ENSMUSG00000110281	Gm2516	-	predicted gene 2516	ncRNA
mm_167370.1	chr8	89427220	89427246	+	1	NA	Intergenic	Intergenic	-383071	NM_021390	58198	Mm.214361	NM_021390	ENSMUSG00000031665	Sall1	Msal-3	sal-like 1 (Drosophila)	protein-coding
mm_76497.1	chr8	86686750	86686763	-	1	NA	intron (NM_001168591, intron 5 of 8)	intron (NM_001168591, intron 5 of 8)	35187	NM_001168591	66887	Mm.324550	NM_025827	ENSMUSG00000047866	Lonp2	1300002A08Rik|AU015403|Lonp	lon peptidase 2, peroxisomal	protein-coding
mm_5881.1	chr1	53887737	53887746	-	1	NA	intron (NM_001001883, intron 15 of 28)	intron (NM_001001883, intron 15 of 28)	38317	NR_106149	102465783		NR_106149	ENSMUSG00000098443	Mir7681	Gm27806|mmu-mir-7681	microRNA 7681	ncRNA
mm_153522.1	chr19	41747603	41747606	-	1	NA	non-coding (NR_040320, exon 2 of 3)	non-coding (NR_040320, exon 2 of 3)	643	NR_040320	100502871	Mm.394485	NR_040320		Gm19424	-	predicted gene, 19424	ncRNA
mm_17429.1	chr2	27475623	27475698	-	1	NA	promoter-TSS (NM_001113574)	promoter-TSS (NM_001113574)	13	NM_001113573	67382	Mm.28721	NM_023336	ENSMUSG00000026918	Brd3	2410084F24Rik|AW060456|Fsrg2|ORFX|RINGL3	bromodomain containing 3	protein-coding
mm_48692.1	chr5	146794789	146794834	-	1	NA	5' UTR (NM_011669, exon 1 of 9)	5' UTR (NM_011669, exon 1 of 9)	145	NM_011669	22217	Mm.167971	NM_011669	ENSMUSG00000029640	Usp12	Ubh1	ubiquitin specific peptidase 12	protein-coding
mm_58810.1	chr7	16400031	16400061	+	1	NA	Intergenic	CpG	-1150	NM_198631	330474	Mm.333594	NM_198631	ENSMUSG00000059273	Zc3h4	Bwq1|Gm768|Kiaa1064-hp|mKIAA1064	zinc finger CCCH-type containing 4	protein-coding
mm_6899.1	chr1	84750538	84750540	-	1	NA	intron (NM_133975, intron 22 of 40)	intron (NM_133975, intron 22 of 40)	-54318	NM_152915	227325	Mm.292560	NM_152915	ENSMUSG00000036766	Dner	A930026D19Rik|BET|Bret	delta/notch-like EGF repeat containing	protein-coding
mm_104548.1	chr11	96777479	96777479	-	1	NA	promoter-TSS (NM_028965)	promoter-TSS (NM_028965)	76	NM_028965	74479	Mm.270781	NM_028965	ENSMUSG00000020876	Snx11	4933439F10Rik|A930041K09Rik|AI117694	sorting nexin 11	protein-coding
mm_147852.1	chr18	63692310	63692338	-	1	NA	promoter-TSS (NM_016792)	promoter-TSS (NM_016792)	35	NM_016792	53382	Mm.19169	NM_016792	ENSMUSG00000024583	Txnl1	32kDa|TRP32|Txnl	thioredoxin-like 1	protein-coding
mm_8701.1	chr1	158712864	158712871	-	1	NA	3' UTR (NM_001085376, exon 22 of 22)	3' UTR (NM_001085376, exon 22 of 22)	207242	NR_030441	735253		NR_030441	ENSMUSG00000070103	Mir488	Mirn488|mir-488|mmu-mir-488	microRNA 488	ncRNA
mm_87016.1	chr10	26917296	26917306	+	1	NA	3' UTR (NM_176837, exon 15 of 15)	3' UTR (NM_176837, exon 15 of 15)	144789	NM_176837	73910	Mm.356496	NM_176837	ENSMUSG00000039031	Arhgap18	4833419J07Rik|AI314906|AI843501	Rho GTPase activating protein 18	protein-coding
mm_162194.1	chrX	113639899	113639899	+	1	NA	exon (NM_001142570, exon 3 of 12)	exon (NM_001142570, exon 3 of 12)	341643	NM_001142570	93837	Mm.79760	NM_033605	ENSMUSG00000025592	Dach2	9430028N04Rik	dachshund 2 (Drosophila)	protein-coding
mm_150399.1	chr19	36554691	36554714	+	1	NA	promoter-TSS (NM_001163471)	promoter-TSS (NM_001163471)	63	NM_172637	226098	Mm.61107	NM_172637	ENSMUSG00000041180	Hectd2	4921524L07|A630025O09Rik|AW212605	HECT domain containing 2	protein-coding
mm_21682.1	chr2	164428922	164428977	-	1	NA	exon (NM_011521, exon 4 of 5)	exon (NM_011521, exon 4 of 5)	14239	NM_011521	20971	Mm.3815	NM_011521	ENSMUSG00000017009	Sdc4	AA959608|AW108331|S4|Synd4|ryudocan|syndecan-4	syndecan 4	protein-coding
mm_99484.1	chr11	102606899	102606905	+	1	NA	3' UTR (NM_020510, exon 1 of 1)	3' UTR (NM_020510, exon 1 of 1)	2471	NM_020510	57265	Mm.36416	NM_020510	ENSMUSG00000050288	Fzd2	AL033370|AW456835|Fz10|Fzd10|Mfz10|Mfz10a	frizzled class receptor 2	protein-coding
mm_144919.1	chr18	37655892	37655915	+	1	NA	intron (NM_001301259, intron 1 of 3)	intron (NM_001301259, intron 1 of 3)	-6042	NM_033584	93709	Mm.247203	NM_033584	ENSMUSG00000103144	Pcdhga1	-	protocadherin gamma subfamily A, 1	protein-coding
mm_51662.1	chr6	86195414	86195422	+	1	NA	5' UTR (NM_031199, exon 1 of 6)	5' UTR (NM_031199, exon 1 of 6)	191	NM_031199	21802	Mm.137222	NM_031199	ENSMUSG00000029999	Tgfa	wa-1|wa1	transforming growth factor alpha	protein-coding
mm_167002.1	chr7	49553906	49553937	+	1	NA	intron (NM_175272, intron 16 of 37)	intron (NM_175272, intron 16 of 37)	82914	NM_001005232	13172	Mm.307176	NM_001005232	ENSMUSG00000030507	Dbx1	AI426026|Dbx	developing brain homeobox 1	protein-coding
mm_86440.1	chr10	3973188	3973208	+	1	NA	5' UTR (NM_001170785, exon 1 of 28)	5' UTR (NM_001170785, exon 1 of 28)	123	NM_172308	270685	Mm.184752	NM_172308	ENSMUSG00000040675	Mthfd1l	2410004L15Rik|AI647056|Fthfsdc1	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1-like	protein-coding
mm_162996.1	chr11	29862507	29862512	+	1	NA	intron (NM_146016, intron 7 of 41)	MIRc|SINE|MIR	-36841	NM_176829	216622	Mm.443260	NM_176829	ENSMUSG00000078157	4931440F15Rik	Fem1ab	RIKEN cDNA 4931440F15 gene	protein-coding
mm_54626.1	chr6	38688109	38688132	-	1	NA	Intergenic	Intergenic	25051	NM_001101507	665180	Mm.349066	NM_001101507	ENSMUSG00000079598	Clec2l	AI414054|AW122724|Gm1064	C-type lectin domain family 2, member L	protein-coding
mm_112085.1	chr12	112674194	112674275	-	1	NA	promoter-TSS (NM_001165894)	promoter-TSS (NM_001165894)	42	NM_001165894	11651	Mm.6645	NM_009652	ENSMUSG00000001729	Akt1	Akt|LTR-akt|PKB|PKB/Akt|PKBalpha|Rac	thymoma viral proto-oncogene 1	protein-coding
mm_132839.1	chr16	45610457	45610467	+	1	NA	promoter-TSS (NM_008099)	promoter-TSS (NM_008099)	22	NM_001159297	14525	Mm.4799	NM_008099	ENSMUSG00000022659	Gcsam	Gcet|Gcet2|M17|M17-L	germinal center associated, signaling and motility	protein-coding
mm_15327.1	chr2	155754946	155754957	+	1	NA	3' UTR (NM_011171, exon 4 of 4)	3' UTR (NM_011171, exon 4 of 4)	3734	NM_011171	19124	Mm.3243	NM_011171	ENSMUSG00000027611	Procr	AI325044|Ccca|Ccd41|Epcr	protein C receptor, endothelial	protein-coding
mm_81570.1	chr9	110420835	110420884	+	1	NA	exon (NM_008694, exon 2 of 4)	exon (NM_008694, exon 2 of 4)	1051	NM_008694	18054	Mm.236225	NM_008694	ENSMUSG00000032484	Ngp	bectenecin	neutrophilic granule protein	protein-coding
mm_153640.1	chr19	44107448	44107492	-	1	NA	promoter-TSS (NM_007700)	promoter-TSS (NM_007700)	7	NM_007700	12675	Mm.3996	NM_007700	ENSMUSG00000025199	Chuk	AI256658|Chuk1|Fbx24|Fbxo24|IKBKA|IKK1|Ikka|NFKBIKA	conserved helix-loop-helix ubiquitous kinase	protein-coding
mm_27630.1	chr3	61363086	61363096	-	1	NA	Intergenic	Intergenic	-1416	NM_028712	74012	Mm.422674	NM_028712	ENSMUSG00000036894	Rap2b	4021402C18Rik|AA408554	RAP2B, member of RAS oncogene family	protein-coding
mm_134009.1	chr16	4875736	4875753	-	1	NA	exon (NM_145359, exon 3 of 3)	exon (NM_145359, exon 3 of 3)	4107	NM_145359	207740	Mm.268895	NM_145359	ENSMUSG00000039568	Ubald1	1500031H01Rik|BC013706|Fam100a	UBA-like domain containing 1	protein-coding
mm_52452.1	chr6	113682042	113682057	+	1	NA	intron (NM_001113553, intron 8 of 11)	PB1D10|SINE|Alu	-15001	NM_001347356	381801	Mm.333322	NM_001033463	ENSMUSG00000056952	Tatdn2	AI646012|mKIAA0218	TatD DNase domain containing 2	protein-coding
mm_10256.1	chr2	9352482	9352499	+	1	NA	Intergenic	Intergenic	162975	NR_038180	73438	Mm.23558	NR_038180	ENSMUSG00000085580	1700061F12Rik	-	RIKEN cDNA 1700061F12 gene	ncRNA
mm_143490.1	chr17	71310976	71310995	-	1	NA	promoter-TSS (NM_145158)	promoter-TSS (NM_145158)	-20	NM_145158	246707	Mm.23462	NM_145158	ENSMUSG00000024053	Emilin2	FOAP-10	elastin microfibril interfacer 2	protein-coding
mm_54323.1	chr6	30477549	30477552	-	1	NA	Intergenic	Intergenic	16565	NR_131049	69337	Mm.396168	NR_131049	ENSMUSG00000085470	1700012C14Rik	-	RIKEN cDNA 1700012C14 gene	ncRNA
mm_118628.1	chr14	21243473	21243482	+	1	NA	intron (NM_001243041, intron 6 of 10)	L1MEc|LINE|L1	167325	NM_001243041	11534	Mm.188734	NM_134079	ENSMUSG00000039197	Adk	2310026J05Rik|5033405D03Rik|AI255373|AI987814|Ak	adenosine kinase	protein-coding
mm_39739.1	chr5	29434670	29434745	+	1	NA	promoter-TSS (NM_001033457)	promoter-TSS (NM_001033457)	40	NM_001033457	433864	Mm.262815	NM_001033457	ENSMUSG00000001569	Nom1	D5Kng1|Gm1040	nucleolar protein with MIF4G domain 1	protein-coding
mm_5081.1	chr1	4409248	4409275	-	1	NA	promoter-TSS (NM_001195662)	promoter-TSS (NM_001195662)	-20	NM_001195662	19888	Mm.294263	NM_011283	ENSMUSG00000025900	Rp1	Dcdc3|Orp1|Rp1h|mG145	retinitis pigmentosa 1 (human)	protein-coding
mm_17150.1	chr2	25211368	25211436	-	1	NA	promoter-TSS (NM_021393)	promoter-TSS (NM_021393)	87	NM_021393	58202	Mm.116418	NM_021393	ENSMUSG00000013465	Nelfb	A730008L03Rik|AB041607|AI663983|Cobra1|Nelf-b	negative elongation factor complex member B	protein-coding
mm_158649.1	chrX	155572437	155572437	-	1	NA	3' UTR (NM_001093750, exon 3 of 3)	3' UTR (NM_001093750, exon 3 of 3)	50890	NM_001093750	211612	Mm.218811	NM_001093750	ENSMUSG00000041552	Ptchd1	9630036J22Rik|AI848149|Gm387	patched domain containing 1	protein-coding
mm_142650.1	chr17	47535831	47535846	-	1	NA	intron (NM_001081635, intron 1 of 6)	intron (NM_001081635, intron 1 of 6)	30787	NM_001081635	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_19186.1	chr2	84412641	84412687	-	1	NA	intron (NM_018782, intron 1 of 15)	intron (NM_018782, intron 1 of 15)	12602	NM_018782	54598	Mm.75467	NM_018782	ENSMUSG00000059588	Calcrl	AV071593|CRLR	calcitonin receptor-like	protein-coding
mm_69142.1	chr7	127051689	127051716	-	1	NA	exon (NM_026918, exon 2 of 3)	exon (NM_026918, exon 2 of 3)	275	NM_026918	69036	Mm.21835	NM_026918	ENSMUSG00000049350	Zg16	1810010M01Rik|AI593689|ZG16p	zymogen granule protein 16	protein-coding
mm_118043.1	chr13	101694680	101694707	-	1	NA	intron (NM_001077495, intron 7 of 15)	CpG	-2063	NM_001024955	18708	Mm.259333	NM_001024955	ENSMUSG00000041417	Pik3r1	PI3K|p50alpha|p55alpha|p85alpha	phosphatidylinositol 3-kinase, regulatory subunit, polypeptide 1 (p85 alpha)	protein-coding
mm_137526.1	chr17	27398136	27398183	+	1	NA	Intergenic	Intergenic	40062	NR_106077	102466228		NR_106077	ENSMUSG00000106215	Mir7218	mmu-mir-7218	microRNA 7218	ncRNA
mm_29551.1	chr3	116807764	116807779	-	1	NA	intron (NM_001081326, intron 1 of 33)	intron (NM_001081326, intron 1 of 33)	395	NM_001081326	77559	Mm.237099	NM_001081326	ENSMUSG00000033400	Agl	1110061O17Rik|9430004C13Rik|9630046L06Rik|AI850929|C77197	amylo-1,6-glucosidase, 4-alpha-glucanotransferase	protein-coding
mm_73979.1	chr8	120537424	120537445	+	1	NA	promoter-TSS (NM_001145896)	promoter-TSS (NM_001145896)	25	NM_001145896	382034	Mm.334856	NM_198671	ENSMUSG00000031822	Gse1	2210013I18Rik|mKIAA0182	genetic suppressor element 1, coiled-coil protein	protein-coding
mm_86600.1	chr10	13501033	13501043	+	1	NA	promoter-TSS (NM_001330198)	promoter-TSS (NM_001330198)	10	NM_025799	66848	Mm.26625	NM_025799	ENSMUSG00000019810	Fuca2	0610025O11Rik|5530401P20Rik	fucosidase, alpha-L- 2, plasma	protein-coding
mm_59380.1	chr7	25913938	25913946	+	1	NA	exon (NM_009999, exon 4 of 9)	exon (NM_009999, exon 4 of 9)	16284	NM_009999	13088	Mm.218749	NM_009999	ENSMUSG00000030483	Cyp2b10	Cyp2b|Cyp2b20|p16	cytochrome P450, family 2, subfamily b, polypeptide 10	protein-coding
mm_76962.1	chr8	106134946	106134960	-	1	NA	promoter-TSS (NR_040346)	promoter-TSS (NR_040346)	-447	NR_040345	69771	Mm.393274	NR_040344		1810019D21Rik	-	RIKEN cDNA 1810019D21 gene	ncRNA
mm_62752.1	chr7	112023252	112023317	+	1	NA	promoter-TSS (NM_177249)	promoter-TSS (NM_177249)	-222	NM_133758	74996	Mm.16974	NM_133758	ENSMUSG00000059263	Usp47	4930502N04Rik|A630020C16Rik	ubiquitin specific peptidase 47	protein-coding
mm_59285.1	chr7	24918789	24918799	+	1	NA	intron (NM_001130150, intron 14 of 30)	intron (NM_001130150, intron 14 of 30)	14448	NM_001130152	16801	Mm.3181	NM_008488	ENSMUSG00000040940	Arhgef1	Lbcl2|Lsc	Rho guanine nucleotide exchange factor (GEF) 1	protein-coding
mm_137858.1	chr17	31115026	31115057	+	1	NA	3' UTR (NM_009593, exon 15 of 15)	3' UTR (NM_009593, exon 15 of 15)	14570	NM_011575	21786	Mm.4641	NM_011575	ENSMUSG00000024029	Tff3	ITF|mITF	trefoil factor 3, intestinal	protein-coding
mm_168612.1	chr1	176717801	176717804	-	1	NA	Intergenic	BGLII|LTR|ERVK	54621	NR_029775	723921		NR_029775	ENSMUSG00000065573	Mir350	Mirn350|mir-350|mmu-mir-350	microRNA 350	ncRNA
mm_124249.1	chr14	101640435	101640477	-	1	NA	promoter-TSS (NM_001168592)	promoter-TSS (NM_001168592)	15	NM_001033132	66200	Mm.250474	NM_001033132	ENSMUSG00000075486	Commd6	1110059J08Rik|1700063H17Rik	COMM domain containing 6	protein-coding
mm_85536.1	chr9	106561618	106561636	-	1	NA	promoter-TSS (NM_026645)	promoter-TSS (NM_026645)	-2	NM_026645	68265	Mm.141451	NM_026645	ENSMUSG00000023577	Iqcf3	1700012F17Rik|AV040440	IQ motif containing F3	protein-coding
mm_130130.1	chr15	90545138	90545139	-	1	NA	intron (NM_025815, intron 11 of 19)	intron (NM_025815, intron 11 of 19)	134250	NM_025815	66871	Mm.290991	NM_025815	ENSMUSG00000052560	Cpne8	1200003E11Rik|1500031E20Rik	copine VIII	protein-coding
mm_131205.1	chr16	8637713	8637776	+	1	NA	promoter-TSS (NM_025708)	promoter-TSS (NM_025708)	37	NM_016881	54128	Mm.9699	NM_016881	ENSMUSG00000022711	Pmm2	AI585868|C86848	phosphomannomutase 2	protein-coding
mm_168310.1	chr11	109011805	109011806	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	91456	NM_015732	12006	Mm.71710	NM_015732	ENSMUSG00000000142	Axin2	Axi1|Axil|Conductin	axin 2	protein-coding
mm_1250.1	chr1	62816300	62816320	+	1	NA	3' UTR (NM_010939, exon 16 of 16)	3' UTR (NM_010939, exon 16 of 16)	-21578	NR_040601	74992	Mm.401979	NR_040601		4930487H11Rik	-	RIKEN cDNA 4930487H11 gene	ncRNA
mm_32194.1	chr4	101355861	101355883	+	1	NA	intron (NR_040640, intron 1 of 3)	intron (NR_040640, intron 1 of 3)	376	NR_040708	77866	Mm.137053	NR_040708	ENSMUSG00000086782	E130102H24Rik	-	RIKEN cDNA E130102H24 gene	ncRNA
mm_27043.1	chr3	27153845	27153855	-	1	NA	promoter-TSS (NM_001177626)	promoter-TSS (NM_001177626)	4	NM_007900	13605	Mm.261453	NM_007900	ENSMUSG00000027699	Ect2	AI528536|mKIAA4037	ect2 oncogene	protein-coding
mm_66606.1	chr7	45460961	45460977	-	1	NA	TTS (NM_007527)	TTS (NM_007527)	-1083	NM_010240	14325	Mm.30357	NM_010240	ENSMUSG00000050708	Ftl1	Ftl|Ftl-1|L-ferritin	ferritin light polypeptide 1	protein-coding
mm_136158.1	chr16	88290187	88290197	-	1	NA	promoter-TSS (NM_001346964)	promoter-TSS (NM_001346964)	66	NM_146072	14805	Mm.5134	NM_010348	ENSMUSG00000022935	Grik1	A830007B11Rik|D16Ium24|D16Ium24e|GluK1|GluK5|Glur-5|Glur5|Glurbeta1	glutamate receptor, ionotropic, kainate 1	protein-coding
mm_15126.1	chr2	153826051	153826065	+	1	NA	Intergenic	Intergenic	45026	NM_001305048	76407	Mm.33629	NM_029599	ENSMUSG00000027480	Sun5	1700021O15Rik|SPAG4L-2|SRG4|Spag4l	Sad1 and UNC84 domain containing 5	protein-coding
mm_58515.1	chr7	4133158	4133169	+	1	NA	exon (NM_001109765, exon 11 of 14)	exon (NM_001109765, exon 11 of 14)	3763	NR_033548	100037396	Mm.447887	NR_033548	ENSMUSG00000085886	D030047H15Rik	Gm15924|OTTMUSG00000027889	RIKEN cDNA D030047H15 gene	ncRNA
mm_57355.1	chr6	124757021	124757031	-	1	NA	promoter-TSS (NM_007881)	promoter-TSS (NM_007881)	-539	NM_007881	13498	Mm.333380	NM_007881	ENSMUSG00000004263	Atn1	Atr1|Drpla|atrophin-1	atrophin 1	protein-coding
mm_15056.1	chr2	152911386	152911396	+	1	NA	promoter-TSS (NM_001081044)	promoter-TSS (NM_001081044)	39	NM_001081044	228785	Mm.250604	NM_001081044	ENSMUSG00000027470	Mylk2	9830004H17Rik|BB138278	myosin, light polypeptide kinase 2, skeletal muscle	protein-coding
mm_26351.1	chr3	142548761	142548775	+	1	NA	3' UTR (NM_001083312, exon 11 of 11)	3' UTR (NM_001083312, exon 11 of 11)	-11284	NM_018734	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_112448.1	chr13	5861663	5861673	+	1	NA	exon (NM_011803, exon 1 of 4)	exon (NM_011803, exon 1 of 4)	179	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_105340.1	chr11	102994950	102994966	-	1	NA	exon (NM_026551, exon 5 of 5)	exon (NM_026551, exon 5 of 5)	4963	NR_105896	102466988		NR_105896	ENSMUSG00000098613	Mir6931	Gm27303|mmu-mir-6931	microRNA 6931	ncRNA
mm_66625.1	chr7	45488775	45488802	-	1	NA	promoter-TSS (NM_027903)	promoter-TSS (NM_027903)	8	NM_027903	71755	Mm.34208	NM_027903	ENSMUSG00000011382	Dhdh	1300018L09Rik|AA591799|Xld-1|Xld1	dihydrodiol dehydrogenase (dimeric)	protein-coding
mm_6631.1	chr1	78422695	78422711	-	1	NA	intron (NM_001278075, intron 17 of 17)	intron (NM_001278075, intron 17 of 17)	66194	NR_102758	23874	Mm.17898	NM_011811	ENSMUSG00000026245	Farsb	C76708|Farsa|Farsl|Farslb|Frsb	phenylalanyl-tRNA synthetase, beta subunit	protein-coding
mm_146939.1	chr18	32138176	32138199	-	1	NA	promoter-TSS (NM_001042768)	promoter-TSS (NM_001042768)	18	NM_008934	19123	Mm.2786	NM_008934	ENSMUSG00000024386	Proc	PC	protein C	protein-coding
mm_28701.1	chr3	95545389	95545418	-	1	NA	exon (NM_021281, exon 5 of 8)	exon (NM_021281, exon 5 of 8)	-14274	NM_026489	67981	Mm.179050	NM_026489	ENSMUSG00000028109	Hormad1	4921522K05Rik|Nohma	HORMA domain containing 1	protein-coding
mm_100331.1	chr11	118245342	118245349	+	1	NA	intron (NM_001112699, intron 1 of 12)	intron (NM_001112699, intron 1 of 12)	3247	NM_001112699	19157	Mm.86413	NM_011180	ENSMUSG00000017132	Cyth1	CLM1|CTH-1|CYTIP|Pscd1	cytohesin 1	protein-coding
mm_139422.1	chr17	53479474	53479494	+	1	NA	5' UTR (NM_025887, exon 1 of 6)	5' UTR (NM_025887, exon 1 of 6)	250	NM_025887	271457	Mm.329123	NM_025887	ENSMUSG00000017831	Rab5a	2410015H04Rik|AI663973|AU021172|nnyRab5a	RAB5A, member RAS oncogene family	protein-coding
mm_143734.1	chr17	81465636	81465638	-	1	NA	intron (NR_104580, intron 2 of 8)	intron (NR_104580, intron 2 of 8)	272750	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_69869.1	chr7	141458916	141458927	-	1	NA	non-coding (NR_028142, exon 8 of 10)	non-coding (NR_028142, exon 8 of 10)	-2173	NM_001025103	213573	Mm.386851	NM_001025103	ENSMUSG00000048200	Cracr2b	6330520A15Rik|BC026645|Cracr2a|Efcab4|Efcab4a	calcium release activated channel regulator 2B	protein-coding
mm_5828.1	chr1	52800389	52800405	-	1	NA	intron (NM_008384, intron 1 of 5)	MT2B|LTR|ERVL	17291	NM_008384	16329	Mm.917	NM_008384	ENSMUSG00000026102	Inpp1	2300002C06Rik|AV137389	inositol polyphosphate-1-phosphatase	protein-coding
mm_130959.1	chr15	103314742	103314754	-	1	NA	3' UTR (NM_013866, exon 8 of 8)	3' UTR (NM_013866, exon 8 of 8)	-4310	NM_030720	80910	Mm.160369	NM_030720	ENSMUSG00000063234	Gpr84	EX33	G protein-coupled receptor 84	protein-coding
mm_43939.1	chr5	145123694	145123729	+	1	NA	exon (NM_023142, exon 4 of 10)	exon (NM_023142, exon 4 of 10)	9455	NM_023142	11867	Mm.30010	NM_023142	ENSMUSG00000029622	Arpc1b	41kDa|AA408064|AA408534|AA571392|AF007010|AW208418|L72|SOP2Hs|p41-ARC	actin related protein 2/3 complex, subunit 1B	protein-coding
mm_29699.1	chr3	123117165	123117169	-	1	NA	exon (NM_080451, exon 3 of 5)	exon (NM_080451, exon 3 of 5)	-82180	NM_021503	59006	Mm.141157	NM_021503	ENSMUSG00000028116	Myoz2	1110012I24Rik|Fatz-2|Myozl2	myozenin 2	protein-coding
mm_62909.1	chr7	117411435	117411467	+	1	NA	intron (NM_175645, intron 1 of 11)	intron (NM_175645, intron 1 of 11)	30472	NM_175645	233781	Mm.461427	NM_175645	ENSMUSG00000030657	Xylt1	8030490L12	xylosyltransferase 1	protein-coding
mm_66810.1	chr7	47252954	47252962	-	1	NA	promoter-TSS (NM_001288801)	promoter-TSS (NM_001288801)	-110	NM_001288801	668725	Mm.436563	NM_001177566	ENSMUSG00000074111	Mrgpra9	EG668725|MrgA9	MAS-related GPR, member A9	protein-coding
mm_126143.1	chr15	78348974	78348984	+	1	NA	TTS (NR_106138)	TTS (NR_106138)	380	NR_106138	102466845		NR_106138	ENSMUSG00000099059	Mir7676-2	Gm27790|mmu-mir-7676-2	microRNA 7676-2	ncRNA
mm_83044.1	chr9	37433139	37433167	-	1	NA	promoter-TSS (NM_001164767)	promoter-TSS (NM_001164767)	22	NM_001164767	19649	Mm.212826	NM_011248	ENSMUSG00000032128	Robo3	Rbig1|Rig-1|Rig1|Robo3a|Robo3b	roundabout guidance receptor 3	protein-coding
mm_110439.1	chr12	49841823	49841824	-	1	NA	Intergenic	Intergenic	-360961	NR_045472	69054	Mm.417838	NR_045472	ENSMUSG00000100844	1810007C17Rik	-	RIKEN cDNA 1810007C17 gene	ncRNA
mm_120809.1	chr14	75016029	75016045	+	1	NA	promoter-TSS (NM_198642)	promoter-TSS (NM_198642)	10	NM_198642	271221	Mm.320280	NM_198642	ENSMUSG00000034959	Rubcnl	5031414D18Rik|Gm744|Gm911|Kiaa0226l	RUN and cysteine rich domain containing beclin 1 interacting protein like	protein-coding
mm_149975.1	chr19	29067342	29067353	+	1	NA	promoter-TSS (NR_045687)	promoter-TSS (NR_045687)	46	NR_045687	100503337	Mm.103412	NR_045687		Gm9895	ENSMUSG00000052976	predicted gene 9895	ncRNA
mm_78507.1	chr9	32754458	32754461	+	1	NA	3' UTR (NM_001038642, exon 7 of 7)	3' UTR (NM_001038642, exon 7 of 7)	58417	NM_001038642	23871	Mm.292415	NM_011808	ENSMUSG00000032035	Ets1	AI196000|AI448617|D230050P06|Ets-1|Tpl1|vs	E26 avian leukemia oncogene 1, 5' domain	protein-coding
mm_54930.1	chr6	48086531	48086658	-	1	NA	promoter-TSS (NM_001163475)	promoter-TSS (NM_001163475)	-1	NM_001163475	69228	Mm.207555	NM_001163475	ENSMUSG00000057691	Zfp746	2810407L07Rik|AI317225|Znf746	zinc finger protein 746	protein-coding
mm_94287.1	chr11	4031458	4031498	+	1	NA	promoter-TSS (NM_146013)	promoter-TSS (NM_146013)	-304	NM_146013	103655	Mm.337476	NM_146013	ENSMUSG00000019368	Sec14l4	AI256582|AW536553|SPF|TAP	SEC14-like lipid binding 4	protein-coding
mm_55731.1	chr6	77292236	77292236	-	1	NA	intron (NM_001109764, intron 8 of 19)	intron (NM_001109764, intron 8 of 19)	49519	NM_028880	74342	Mm.292568	NM_028880	ENSMUSG00000060780	Lrrtm1	4632401D06Rik|AW125451	leucine rich repeat transmembrane neuronal 1	protein-coding
mm_110613.1	chr12	56613234	56613247	-	1	NA	promoter-TSS (NM_008701)	promoter-TSS (NM_008701)	44	NM_008701	18094	Mm.129420	NM_008701	ENSMUSG00000058669	Nkx2-9	Nkx-2.9|Nkx2-8|Nkx2.9|tinman	NK2 homeobox 9	protein-coding
mm_129311.1	chr15	77755219	77755265	-	1	NA	promoter-TSS (NM_001081970)	promoter-TSS (NM_001081970)	-13	NM_001081970	239552	Mm.125650	NM_001081970	ENSMUSG00000056656	Apol8	9830006J20Rik|APOL-II|Apol2	apolipoprotein L 8	protein-coding
mm_89301.1	chr10	87913767	87913769	+	1	NA	exon (NM_010512, exon 3 of 5)	exon (NM_010512, exon 3 of 5)	52657	NM_001111276	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_173168.1	chrX	42633037	42633042	+	1	NA	intron (NM_011855, intron 23 of 32)	L1Md_T|LINE|L1	127717	NM_001313691	20400	Mm.441197	NM_011364	ENSMUSG00000005696	Sh2d1a	Gm686|SAP	SH2 domain containing 1A	protein-coding
mm_153273.1	chr19	37176038	37176054	-	1	NA	promoter-TSS (NM_001290826)	promoter-TSS (NM_001290826)	17	NM_001290826	208922	Mm.391176	NM_198300	ENSMUSG00000039652	Cpeb3	4831444O18Rik|CPE-BP3|mKIAA0940	cytoplasmic polyadenylation element binding protein 3	protein-coding
mm_86168.1	chr9	119088208	119088280	-	1	NA	promoter-TSS (NM_001293648)	promoter-TSS (NM_001293648)	17	NM_001293648	18799	Mm.23963	NM_019676	ENSMUSG00000010660	Plcd1	AW212592|C79986	phospholipase C, delta 1	protein-coding
mm_99740.1	chr11	106387220	106387240	+	1	NA	Intergenic	RLTR15|LTR|ERVK	-4449	NM_010494	15896	Mm.394	NM_010494	ENSMUSG00000001029	Icam2	CD102|Icam-2|Ly-60	intercellular adhesion molecule 2	protein-coding
mm_121146.1	chr14	101898587	101898603	+	1	NA	exon (NM_201529, exon 13 of 31)	exon (NM_201529, exon 13 of 31)	57972	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_153655.1	chr19	44394844	44394857	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	12859	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_43528.1	chr5	137288274	137288292	+	1	NA	promoter-TSS (NM_009599)	promoter-TSS (NM_009599)	29	NM_001290010	11423	Mm.255464	NM_009599	ENSMUSG00000023328	Ache	-	acetylcholinesterase	protein-coding
mm_101442.1	chr11	30159662	30159672	-	1	NA	intron (NM_175836, intron 1 of 34)	intron (NM_175836, intron 1 of 34)	38590	NM_009260	20742	Mm.123110	NM_009260	ENSMUSG00000020315	Sptbn1	9930031C03Rik|AL033301|SPTB2|Spnb-2|Spnb2|elf1|elf3|mKIAA4049	spectrin beta, non-erythrocytic 1	protein-coding
mm_167396.1	chr8	95306588	95306598	-	1	NA	promoter-TSS (NM_145601)	promoter-TSS (NM_145601)	-8	NM_001195413	333329	Mm.484049	NM_145601	ENSMUSG00000031789	Cngb1	Cngb1b|Garp2|Gm1959	cyclic nucleotide gated channel beta 1	protein-coding
mm_56023.1	chr6	86585966	86585970	-	1	NA	Intergenic	RMER10B|LTR|ERVL	-42206	NM_026414	67855	Mm.183043	NM_026414	ENSMUSG00000033508	Asprv1	2300003P22Rik|AA986851|SASP|SASPase|Taps	aspartic peptidase, retroviral-like 1	protein-coding
mm_143763.1	chr17	81627878	81627888	-	1	NA	intron (NR_104580, intron 2 of 8)	MIR|SINE|MIR	110504	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_132673.1	chr16	42907544	42907562	+	1	NA	promoter-TSS (NM_001285805)	promoter-TSS (NM_001285805)	-92	NM_001285805	56490	Mm.136238	NM_019778	ENSMUSG00000022708	Zbtb20	1300017A20Rik|7330412A13Rik|A930017C21Rik|D16Wsu73e|DPZF|HOF|ODA-8S|Oda8|Zfp288	zinc finger and BTB domain containing 20	protein-coding
mm_141243.1	chr17	27467800	27467824	-	1	NA	intron (NM_001013385, intron 2 of 8)	intron (NM_001013385, intron 2 of 8)	35721	NM_001013385	268934	Mm.358940	NM_001013385	ENSMUSG00000063239	Grm4	Gprc1d|mGluR4	glutamate receptor, metabotropic 4	protein-coding
mm_52675.1	chr6	117908771	117908774	+	1	NA	intron (NM_001166428, intron 1 of 3)	intron (NM_001166428, intron 1 of 3)	968	NM_001166429	98758	Mm.422979	NM_133834	ENSMUSG00000042079	Hnrnpf	4833420I20Rik|AA407306|Hnrpf	heterogeneous nuclear ribonucleoprotein F	protein-coding
mm_159685.1	chr5	13398982	13398982	+	1	NA	promoter-TSS (NM_009152)	promoter-TSS (NM_009152)	-15	NM_001243073	20346	Mm.372039	NM_009152	ENSMUSG00000028883	Sema3a	Hsema-I|SEMA1|SemD|Semad|coll-1	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	protein-coding
mm_172367.1	chr7	12289185	12289198	-	1	NA	Intergenic	L1Md_T|LINE|L1	-15614	NM_134234	171268	Mm.377220	NM_134234	ENSMUSG00000058132	Vmn1r82	V1rg12	vomeronasal 1 receptor 82	protein-coding
mm_17139.1	chr2	25080209	25080239	-	1	NA	promoter-TSS (NM_028093)	promoter-TSS (NM_028093)	-99	NM_028093	72090	Mm.33403	NM_028093	ENSMUSG00000036813	Entpd8	-	ectonucleoside triphosphate diphosphohydrolase 8	protein-coding
mm_158612.1	chrX	152644092	152644123	-	1	NA	promoter-TSS (NM_001290687)	promoter-TSS (NM_001290687)	42	NM_001290687	110380	Mm.40796	NM_172441	ENSMUSG00000045180	Shroom2	4832440C16|Apxl|C630003H05Rik|Shrm2	shroom family member 2	protein-coding
mm_73062.1	chr8	94386487	94386509	+	1	NA	promoter-TSS (NM_022331)	promoter-TSS (NM_022331)	-2	NM_022331	64209	Mm.29151	NM_022331	ENSMUSG00000031770	Herpud1	Herp|Mifl|SUP	homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1	protein-coding
mm_16379.1	chr2	178295339	178295343	+	1	NA	intron (NM_001007154, intron 7 of 12)	intron (NM_001007154, intron 7 of 12)	102257	NM_001007154	74189	Mm.44413	NM_028806	ENSMUSG00000027525	Phactr3	1500003N10Rik|4930415A02Rik|H17739|Scapin1|Scapinin|mKIAA4224	phosphatase and actin regulator 3	protein-coding
mm_2445.1	chr1	99772395	99772408	+	1	NA	promoter-TSS (NM_172851)	promoter-TSS (NM_172851)	-364	NM_172851	241175	Mm.251301	NM_172851	ENSMUSG00000067028	Cntnap5b	C230078M14Rik|Caspr5-2	contactin associated protein-like 5B	protein-coding
mm_86291.1	chr9	121995963	121996041	-	1	NA	promoter-TSS (NM_153540)	promoter-TSS (NM_153540)	24	NM_001289559	215494	Mm.402151	NM_153540	ENSMUSG00000066235	Pomgnt2	Ago61|C85492|Gtdc2	protein O-linked mannose beta 1,4-N-acetylglucosaminyltransferase 2	protein-coding
mm_125975.1	chr15	76295229	76295292	+	1	NA	exon (NM_001195537, exon 1 of 7)	exon (NM_001195537, exon 1 of 7)	826	NM_001195537	100503915	Mm.393455	NM_001195537	ENSMUSG00000071724	Smpd5	ENSMUSG00000071724|Gm10345|MA-nSMase	sphingomyelin phosphodiesterase 5	protein-coding
mm_38462.1	chr4	140587934	140587949	-	1	NA	intron (NM_001290803, intron 7 of 28)	MER63B|DNA|hAT-Blackjack	60815	NM_001112723	72754	Mm.29329	NM_172415	ENSMUSG00000040964	Arhgef10l	2810441C07Rik	Rho guanine nucleotide exchange factor (GEF) 10-like	protein-coding
mm_43651.1	chr5	138280539	138280563	+	1	NA	promoter-TSS (NM_016964)	promoter-TSS (NM_016964)	42	NM_016964	50878	Mm.285609	NM_016964	ENSMUSG00000036928	Stag3	SA-2	stromal antigen 3	protein-coding
mm_56390.1	chr6	94700155	94700176	-	1	NA	promoter-TSS (NM_008377)	promoter-TSS (NM_008377)	-20	NM_008377	16206	Mm.245210	NM_008377	ENSMUSG00000030029	Lrig1	D6Bwg0781e|Img|LIG-1	leucine-rich repeats and immunoglobulin-like domains 1	protein-coding
mm_70106.1	chr7	142661859	142661880	-	1	NA	promoter-TSS (NM_001122736)	promoter-TSS (NM_001122736)	-598	NM_001122736	16002	Mm.3862	NM_010514	ENSMUSG00000048583	Igf2	AL033362|Igf-2|Igf-II|M6pr|Mpr|Peg2	insulin-like growth factor 2	protein-coding
mm_48519.1	chr5	142903141	142903169	-	1	NA	TTS (NM_007393)	TTS (NM_007393)	3599	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_81139.1	chr9	106814126	106814133	+	1	NA	Intergenic	Intergenic	-7847	NM_001015507	321006	Mm.440089	NM_001015507	ENSMUSG00000040325	Vprbp	AI447437|B930007L02Rik|mKIAA0800	Vpr (HIV-1) binding protein	protein-coding
mm_84353.1	chr9	64341146	64341228	-	1	NA	promoter-TSS (NM_001177784)	promoter-TSS (NM_001177784)	70	NM_001001295	213550	Mm.268341	NM_172519	ENSMUSG00000032396	Dis3l	AV340375	DIS3 like exosome 3'-5' exoribonuclease	protein-coding
mm_108054.1	chr12	73919347	73919356	+	1	NA	intron (NM_010431, intron 1 of 14)	intron (NM_010431, intron 1 of 14)	11484	NM_001313919	15251	Mm.3879	NM_010431	ENSMUSG00000021109	Hif1a	AA959795|HIF-1-alpha|HIF1-alpha|HIF1alpha|MOP1|bHLHe78	hypoxia inducible factor 1, alpha subunit	protein-coding
mm_17903.1	chr2	35200924	35201069	-	1	NA	5' UTR (NM_026697, exon 1 of 8)	5' UTR (NM_026697, exon 1 of 8)	124	NM_026697	68365	Mm.198264	NM_026697	ENSMUSG00000026878	Rab14	0610030G24Rik|2810475J17Rik|A830021G03Rik|AI314285|AI649155|D030017L14Rik	RAB14, member RAS oncogene family	protein-coding
mm_41713.1	chr5	101888221	101888231	+	1	NA	exon (NM_172882, exon 39 of 67)	exon (NM_172882, exon 39 of 67)	123096	NM_173370	74596	Mm.46764	NM_173370	ENSMUSG00000029330	Cds1	4833409J18Rik|AI314024|AW125888	CDP-diacylglycerol synthase 1	protein-coding
mm_102666.1	chr11	65031724	65031730	-	1	NA	exon (NM_001099288, exon 12 of 20)	exon (NM_001099288, exon 12 of 20)	52692	NM_023479	68626	Mm.157711	NM_023479	ENSMUSG00000020549	Elac2	1110017O07Rik|D11Wsu80e|Hpc2	elaC ribonuclease Z 2	protein-coding
mm_158895.1	chr1	22805850	22805850	-	1	NA	promoter-TSS (NM_001012625)	promoter-TSS (NM_001012625)	-126	NM_001012624	116837	Mm.60061	NM_053270	ENSMUSG00000041670	Rims1	C030033M19Rik|RIM1|RIM1a|RIM1alpha|Rab3ip1|Rim|Serg1|mKIAA0340	regulating synaptic membrane exocytosis 1	protein-coding
mm_107791.1	chr12	61698961	61698964	+	1	NA	intron (NM_178714, intron 2 of 3)	L1Md_T|LINE|L1	175795	NM_001310586	238205	Mm.28802	NM_178714	ENSMUSG00000035653	Lrfn5	AI427653|AI604817|C130061B21|mKIAA4208	leucine rich repeat and fibronectin type III domain containing 5	protein-coding
mm_22361.1	chr2	181039196	181039228	-	1	NA	promoter-TSS (NM_015730)	promoter-TSS (NM_015730)	-35	NM_015730	11438	Mm.252369	NM_015730	ENSMUSG00000027577	Chrna4	Acra-4|Acra4|EBN1|ENFL1	cholinergic receptor, nicotinic, alpha polypeptide 4	protein-coding
mm_104989.1	chr11	100269898	100269901	-	1	NA	promoter-TSS (NM_212483)	promoter-TSS (NM_212483)	-28	NM_212483	68239	Mm.158190	NM_212483	ENSMUSG00000053654	Krt42	2410039E07Rik|K17n|Ka22|ecat6	keratin 42	protein-coding
mm_41337.1	chr5	90497187	90497206	+	1	NA	intron (NM_007423, intron 4 of 14)	intron (NM_007423, intron 4 of 14)	6482	NM_007423	11576	Mm.358570	NM_007423	ENSMUSG00000054932	Afp	-	alpha fetoprotein	protein-coding
mm_106414.1	chr11	119111401	119111439	-	1	NA	Intergenic	Intergenic	-25183	NM_007625	12418	Mm.268070	NM_007625	ENSMUSG00000039989	Cbx4	MPc2|PC2	chromobox 4	protein-coding
mm_118960.1	chr14	27428879	27428890	+	1	NA	promoter-TSS (NM_001114879)	promoter-TSS (NM_001114879)	37	NM_001114879	218850	Mm.247767	NM_028945	ENSMUSG00000040651	Fam208a	4732418E12|4933409E02Rik|D14Abb1e|MommeD6	family with sequence similarity 208, member A	protein-coding
mm_5415.1	chr1	33887596	33887598	-	1	NA	intron (NM_177235, intron 1 of 6)	L1_Mur3|LINE|L1	20024	NM_177235	320705	Mm.336619	NM_177235	ENSMUSG00000042182	Bend6	B230209C24Rik	BEN domain containing 6	protein-coding
mm_46507.1	chr5	105136160	105136166	-	1	NA	intron (NM_008620, intron 2 of 10)	intron (NM_008620, intron 2 of 10)	3389	NM_008620	17472	Mm.440525	NM_008620	ENSMUSG00000079363	Gbp4	AW228052|Mag-2|Mpa-2|Mpa2	guanylate binding protein 4	protein-coding
mm_116645.1	chr13	49168274	49168316	-	1	NA	Intergenic	Intergenic	-19252	NM_013610	18081	Mm.18503	NM_013610	ENSMUSG00000037966	Ninj1	AU024536	ninjurin 1	protein-coding
mm_100050.1	chr11	115163439	115163449	+	1	NA	5' UTR (NM_012030, exon 1 of 6)	5' UTR (NM_012030, exon 1 of 6)	103	NM_012030	26941	Mm.27842	NM_012030	ENSMUSG00000020733	Slc9a3r1	EBP-50|NHE-RF|NHERF-1|NHERF1	solute carrier family 9 (sodium/hydrogen exchanger), member 3 regulator 1	protein-coding
mm_113949.1	chr13	50422610	50422616	+	1	NA	intron (NM_175401, intron 2 of 9)	(T)n|Simple_repeat|Simple_repeat	4736	NM_175401	109082	Mm.18638	NM_175401	ENSMUSG00000037816	Fbxw17	1110064L07Rik|C85886	F-box and WD-40 domain protein 17	protein-coding
mm_78609.1	chr9	37545062	37545066	+	1	NA	TTS (NM_020518)	TTS (NM_020518)	5809	NM_020518	57276	Mm.27478	NM_020518	ENSMUSG00000001943	Vsig2	1190004B15Rik|2210413P10Rik|AU040484|CTX|Ctm	V-set and immunoglobulin domain containing 2	protein-coding
mm_59488.1	chr7	27486947	27486960	+	1	NA	promoter-TSS (NM_018820)	promoter-TSS (NM_018820)	0	NM_018820	55942	Mm.153684	NM_018820	ENSMUSG00000008384	Sertad1	1110032C13Rik|AV000455|AW456625|Sei-1|Sei1|TRIP-Br1	SERTA domain containing 1	protein-coding
mm_96295.1	chr11	63133093	63133129	+	1	NA	intron (NM_001302260, intron 1 of 4)	CpG	308	NM_001302260	18858	Mm.1237	NM_008885	ENSMUSG00000018217	Pmp22	22kDa|Gas-3|HNPP|Tr|trembler	peripheral myelin protein 22	protein-coding
mm_147334.1	chr18	42899007	42899044	-	1	NA	non-coding (NR_073583, exon 1 of 9)	non-coding (NR_073583, exon 1 of 9)	481	NR_073583	72930	Mm.26134	NM_027531	ENSMUSG00000024500	Ppp2r2b	2900026H06Rik|6330404L05Rik|E130009M08Rik|PP2A-PR55B|PR55-BETA|SCA12	protein phosphatase 2, regulatory subunit B, beta	protein-coding
mm_147529.1	chr18	52530065	52530078	-	1	NA	promoter-TSS (NM_010728)	promoter-TSS (NM_010728)	-204	NM_001286182	16948	Mm.172	NM_010728	ENSMUSG00000024529	Lox	AI893619|TSC-160|rrg	lysyl oxidase	protein-coding
mm_25224.1	chr3	103859430	103859460	+	1	NA	promoter-TSS (NM_008979)	promoter-TSS (NM_008979)	-350	NR_104070	19260	Mm.395	NM_008979	ENSMUSG00000027843	Ptpn22	70zpep|PEP|Ptpn8	protein tyrosine phosphatase, non-receptor type 22 (lymphoid)	protein-coding
mm_130958.1	chr15	103310449	103310476	-	1	NA	promoter-TSS (NM_030720)	promoter-TSS (NM_030720)	-24	NM_030720	80910	Mm.160369	NM_030720	ENSMUSG00000063234	Gpr84	EX33	G protein-coupled receptor 84	protein-coding
mm_123611.1	chr14	68120421	68120431	-	1	NA	exon (NM_008691, exon 3 of 3)	exon (NM_008691, exon 3 of 3)	-3326	NR_045897	100043072	Mm.242832	NR_045897		A230070E04Rik	Gm4210	RIKEN cDNA A230070E04 gene	ncRNA
mm_148058.1	chr18	72159091	72159100	-	1	NA	intron (NM_007831, intron 1 of 28)	intron (NM_007831, intron 1 of 28)	191974	NM_007831	13176	Mm.167882	NM_007831	ENSMUSG00000060534	Dcc	C030036D22Rik|Igdcc1	deleted in colorectal carcinoma	protein-coding
mm_119759.1	chr14	54168643	54168653	+	1	NA	Intergenic	Intergenic	85281	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_613.1	chr1	40010046	40010063	+	1	NA	intron (NM_001252200, intron 22 of 31)	(CA)n|Simple_repeat|Simple_repeat	-74714	NM_010555	16178	Mm.1349	NM_010555	ENSMUSG00000026073	Il1r2	CD121b|Il1r-2	interleukin 1 receptor, type II	protein-coding
mm_154387.1	chrM	11735	11757	+	1	NA	NA	Intergenic	NA	NA								
mm_36268.1	chr4	63622415	63622417	-	1	NA	promoter-TSS (NM_029324)	promoter-TSS (NM_029324)	13	NM_029324	75524	Mm.38543	NM_029324	ENSMUSG00000058935	1700018C11Rik	bM230C2.3	RIKEN cDNA 1700018C11 gene	protein-coding
mm_95880.1	chr11	58102783	58102814	+	1	NA	Intergenic	Intergenic	-1355	NM_026949	69125	Mm.28910	NM_026949	ENSMUSG00000020515	Cnot8	1500015I04Rik|1810022F04Rik|AA536816|AU015770|AU043059	CCR4-NOT transcription complex, subunit 8	protein-coding
mm_94974.1	chr11	31545801	31545806	+	1	NA	Intergenic	RLTR10D2|LTR|ERVK	126059	NM_001024919	69556	Mm.34183	NM_001024919	ENSMUSG00000044502	Bod1	2310022M17Rik|BOD2.1|Fam44b	biorientation of chromosomes in cell division 1	protein-coding
mm_12117.1	chr2	61595882	61595885	+	1	NA	intron (NM_001164071, intron 2 of 8)	intron (NM_001164071, intron 2 of 8)	2786	NM_001164071	21353	Mm.244393	NM_011529	ENSMUSG00000064289	Tank	C86182|E430026L09Rik|I-TRAF	TRAF family member-associated Nf-kappa B activator	protein-coding
mm_171741.1	chr4	96185015	96185017	+	1	NA	Intergenic	RLTR9D|LTR|ERVK	-43864	NM_001100182	242546	Mm.302562	NM_001100182	ENSMUSG00000081225	Cyp2j12	BB197342|Cyp2j12-ps|OTTMUSG00000007939	cytochrome P450, family 2, subfamily j, polypeptide 12	protein-coding
mm_52711.1	chr6	119479746	119479795	+	1	NA	5' UTR (NM_133940, exon 1 of 1)	5' UTR (NM_133940, exon 1 of 1)	102	NM_133940	101358	Mm.125477	NM_133940	ENSMUSG00000030019	Fbxl14	AW322056|Fbx14l	F-box and leucine-rich repeat protein 14	protein-coding
mm_112748.1	chr13	19341881	19341905	+	1	NA	Intergenic	Intergenic	53920	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_86243.1	chr9	121277677	121277687	-	1	NA	promoter-TSS (NM_177589)	promoter-TSS (NM_177589)	-510	NM_177589	209012	Mm.371804	NM_177589	ENSMUSG00000040936	Ulk4	4932415A06Rik|A730098P15	unc-51-like kinase 4	protein-coding
mm_43603.1	chr5	137883101	137883123	+	1	NA	Intergenic	Intergenic	-11354	NM_001024932	545812	Mm.332769	NM_001024932	ENSMUSG00000066682	Pilrb2	EG545812	paired immunoglobin-like type 2 receptor beta 2	protein-coding
mm_77583.1	chr8	123793919	123793922	-	1	NA	Intergenic	Intergenic	-12076	NM_009003	19341	Mm.9221	NM_009003	ENSMUSG00000019478	Rab4a	AI848268|Rab4	RAB4A, member RAS oncogene family	protein-coding
mm_21371.1	chr2	157279513	157279518	-	1	NA	promoter-TSS (NM_001039557)	promoter-TSS (NM_001039557)	34	NM_001039557	629499	Mm.384235	NM_001039557	ENSMUSG00000074627	Mroh8	4922505G16Rik	maestro heat-like repeat family member 8	protein-coding
mm_39621.1	chr5	24423806	24423848	+	1	NA	promoter-TSS (NM_007668)	promoter-TSS (NM_007668)	-297	NM_007668	12568	Mm.298798	NM_007668	ENSMUSG00000028969	Cdk5	AW048668|Crk6	cyclin-dependent kinase 5	protein-coding
mm_32449.1	chr4	107356669	107356685	+	1	NA	intron (NM_145550, intron 9 of 9)	intron (NM_145550, intron 9 of 9)	-11107	NM_028355	72787	Mm.28478	NM_028355	ENSMUSG00000028614	Ndc1	2810475A17Rik|AI450313|Tmem48|sks	NDC1 transmembrane nucleoporin	protein-coding
mm_139068.1	chr17	46646226	46646272	+	1	NA	promoter-TSS (NM_001316742)	promoter-TSS (NM_001316742)	20	NM_025302	27398	Mm.391007	NM_025302	ENSMUSG00000002767	Mrpl2	CGI-22|L2mt|MRP-L14|MRP-L2|Rpml14	mitochondrial ribosomal protein L2	protein-coding
mm_61008.1	chr7	49364690	49364717	+	1	NA	intron (NM_175272, intron 2 of 37)	B4A|SINE|B4	118514	NM_175272	78286	Mm.333881	NM_175272	ENSMUSG00000052512	Nav2	5330421F07Rik|AU067780|BQ960892|HELAD1|POMFIL2|RAINB1|RAINB2|Unc53H2|mKIAA3015	neuron navigator 2	protein-coding
mm_27618.1	chr3	59343982	59343991	-	1	NA	5' UTR (NM_001162884, exon 1 of 7)	5' UTR (NM_001162884, exon 1 of 7)	270	NM_001162884	242050	Mm.228086	NM_001162884	ENSMUSG00000036334	Igsf10	6530405F15Rik|9030224D03|AA409708|AA536958|AI414626|Adlican2|CMF608	immunoglobulin superfamily, member 10	protein-coding
mm_135358.1	chr16	43889670	43889685	-	1	NA	promoter-TSS (NM_029128)	promoter-TSS (NM_029128)	-1	NM_029128	106248	Mm.275354	NM_029128	ENSMUSG00000022704	Qtrtd1	3110012M05Rik|4930470H18Rik|AI648807|Qtrt2	queuine tRNA-ribosyltransferase domain containing 1	protein-coding
mm_105367.1	chr11	103199713	103199747	-	1	NA	TTS (NM_001077698)	TTS (NM_001077698)	8818	NM_001254724	69441	Mm.380648	NM_027082	ENSMUSG00000020940	1700023F06Rik	-	RIKEN cDNA 1700023F06 gene	protein-coding
mm_11594.1	chr2	33431381	33431408	+	1	NA	promoter-TSS (NM_001085507)	promoter-TSS (NM_001085507)	-70	NM_001276332	241311	Mm.296512	NM_001085507	ENSMUSG00000068966	Zbtb34	Gm349|mKIAA1993	zinc finger and BTB domain containing 34	protein-coding
mm_136666.1	chr17	6106565	6106600	+	1	NA	promoter-TSS (NM_001103181)	promoter-TSS (NM_001103181)	-248	NM_001103181	68842	Mm.449307	NM_054040	ENSMUSG00000034377	Tulp4	1110057P05Rik|2210038L17Rik|Tusp	tubby like protein 4	protein-coding
mm_96514.1	chr11	68475402	68475415	+	1	NA	exon (NM_177320, exon 3 of 19)	exon (NM_177320, exon 3 of 19)	-27611	NM_001004435	104709	Mm.234573	NM_001004435	ENSMUSG00000046207	Pik3r6	BB220380|p84|p84 PIKAP|p87(PIKAP)|p87PIKAP	phosphoinositide-3-kinase, regulatory subunit 6	protein-coding
mm_89614.1	chr10	96039573	96039583	+	1	NA	exon (NM_001001932, exon 26 of 29)	exon (NM_001001932, exon 26 of 29)	98915	NM_001001932	216238	Mm.210035	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding
mm_26381.1	chr3	142568472	142568480	+	1	NA	intron (NM_001289493, intron 7 of 10)	intron (NM_001289493, intron 7 of 10)	7980	NM_001289493	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_41460.1	chr5	90930823	90930833	+	1	NA	promoter-TSS (NM_026788)	promoter-TSS (NM_026788)	-368	NM_026788	665563	Mm.153030	NM_026788	ENSMUSG00000029376	Mthfd2l	1110019K23Rik|C630010D07Rik	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2-like	protein-coding
mm_123936.1	chr14	73368352	73368399	-	1	NA	exon (NM_008410, exon 2 of 6)	exon (NM_008410, exon 2 of 6)	16896	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_106680.1	chr12	3110016	3110040	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	-125763	NR_015551	74173	Mm.309774	NM_028796	ENSMUSG00000079179	Rab10os	1700012B15Rik|1810036A22Rik	RAB10, member RAS oncogene family, opposite strand	ncRNA
mm_170079.1	chr17	34263266	34263266	+	1	NA	promoter-TSS (NM_207105)	promoter-TSS (NM_207105)	39	NM_207105	14961	Mm.254067	NM_207105	ENSMUSG00000073421	H2-Ab1	AI845868|Abeta|H-2Ab|H2-Ab|I-Abeta|IAb|Ia-2|Ia2|Rmcs1	histocompatibility 2, class II antigen A, beta 1	protein-coding
mm_106400.1	chr11	118869120	118869158	-	1	NA	intron (NM_001285437, intron 1 of 13)	(TGG)n|Simple_repeat|Simple_repeat	40433	NM_001024931	52897	Mm.341103	NM_001024931	ENSMUSG00000025576	Rbfox3	Fox-3|Hrnbp3|NeuN|Neuna60	RNA binding protein, fox-1 homolog (C. elegans) 3	protein-coding
mm_60495.1	chr7	44478781	44478828	+	1	NA	Intergenic	Intergenic	-5713	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_124336.1	chr14	103844209	103844221	-	1	NA	promoter-TSS (NM_001276296)	promoter-TSS (NM_001276296)	261	NM_001136061	13618	Mm.229532	NM_007904	ENSMUSG00000022122	Ednrb	ET-B|ET-BR|ETR-b|ETb|Sox10m1	endothelin receptor type B	protein-coding
mm_59786.1	chr7	28895220	28895228	+	1	NA	intron (NM_021895, intron 19 of 20)	intron (NM_021895, intron 19 of 20)	13568	NM_001110807	60594	Mm.476990	NM_021894	ENSMUSG00000054083	Capn12	CANP 12	calpain 12	protein-coding
mm_158315.1	chrX	127736562	127736570	-	1	NA	promoter-TSS (NM_001281537)	promoter-TSS (NM_001281537)	-12	NM_001281537	73934	Mm.159093	NM_001281537	ENSMUSG00000043569	Cldn34c4	4930412D23Rik	claudin 34C4	protein-coding
mm_128064.1	chr15	26761571	26761575	-	1	NA	intron (NM_176959, intron 2 of 3)	intron (NM_176959, intron 2 of 3)	133991	NM_176959	448987	Mm.253378	NM_176959	ENSMUSG00000043556	Fbxl7	AL023057|D230018M15Rik|FBL7|Fbl6	F-box and leucine-rich repeat protein 7	protein-coding
mm_28333.1	chr3	89382983	89382990	-	1	NA	intron (NM_009565, intron 1 of 2)	MIRb|SINE|MIR	-8878	NR_040403	545539	Mm.393389	NR_040403	ENSMUSG00000074466	Gm15417	ENSMUSG00000074466|OTTMUSG00000021274	predicted gene 15417	ncRNA
mm_111265.1	chr12	85187847	85187862	-	1	NA	Intergenic	Intergenic	-10541	NM_008827	18654	Mm.4809	NM_008827	ENSMUSG00000004791	Pgf	AI854365|PIGF|Plgf	placental growth factor	protein-coding
mm_77828.1	chr9	4250955	4250958	+	1	NA	Intergenic	L1Md_F|LINE|L1	58538	NR_136941	67618	Mm.33970	NM_026276	ENSMUSG00000025894	Aasdhppt	2010309J24Rik|2810407B07Rik|AASD-PPT|CGI-80|LYS2|LYS5	aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase	protein-coding
mm_59758.1	chr7	28827632	28827632	+	1	NA	intron (NM_016772, intron 3 of 9)	intron (NM_016772, intron 3 of 9)	2294	NM_016772	51798	Mm.291776	NM_016772	ENSMUSG00000053898	Ech1	AA617331	enoyl coenzyme A hydratase 1, peroxisomal	protein-coding
mm_113931.1	chr13	49622902	49622913	+	1	NA	exon (NM_008760, exon 7 of 7)	exon (NM_008760, exon 7 of 7)	14836	NM_008760	18295	Mm.4258	NM_008760	ENSMUSG00000021390	Ogn	3110079A16Rik|OG|OIF|SLRR3A|mimecan|mimican	osteoglycin	protein-coding
mm_118240.1	chr13	111777267	111777269	-	1	NA	intron (NM_011945, intron 1 of 19)	intron (NM_011945, intron 1 of 19)	31715	NM_011945	26401	Mm.15918	NM_011945	ENSMUSG00000021754	Map3k1	MAPKKK1|MEKK1|Mekk	mitogen-activated protein kinase kinase kinase 1	protein-coding
mm_131130.1	chr16	5885580	5885592	+	1	NA	5' UTR (NM_021477, exon 1 of 17)	5' UTR (NM_021477, exon 1 of 17)	793	NM_021477	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_126854.1	chr15	89211608	89211620	+	1	NA	promoter-TSS (NM_026813)	promoter-TSS (NM_026813)	55	NM_027805	71474	Mm.184055	NM_026813	ENSMUSG00000036561	Ppp6r2	1110033O10Rik|8430411H09Rik|B230107H12Rik|Pp6r2|Saps2	protein phosphatase 6, regulatory subunit 2	protein-coding
mm_35489.1	chr4	40948103	40948113	-	1	NA	promoter-TSS (NM_029814)	promoter-TSS (NM_029814)	186	NM_009736	12017	Mm.688	NM_009736	ENSMUSG00000028416	Bag1	BAG-1|Rap46	BCL2-associated athanogene 1	protein-coding
mm_23614.1	chr3	65531247	65531260	+	1	NA	5' UTR (NM_178892, exon 2 of 6)	5' UTR (NM_178892, exon 2 of 6)	-1839	NR_027955	71004	Mm.475465	NM_001033527	ENSMUSG00000074580	4931440P22Rik	-	RIKEN cDNA 4931440P22 gene	ncRNA
mm_50512.1	chr6	49038216	49038232	+	1	NA	intron (NM_053110, intron 1 of 10)	intron (NM_053110, intron 1 of 10)	1706	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_57324.1	chr6	124738580	124738591	-	1	NA	TTS (NM_013535)	TTS (NM_013535)	124	NM_001077705	15170	Mm.271799	NM_013545	ENSMUSG00000004266	Ptpn6	70Z-SHP|Hcph|PTPTY-42|Ptp1C|SH-PTP1|SHP-1|hcp|me	protein tyrosine phosphatase, non-receptor type 6	protein-coding
mm_97157.1	chr11	75468041	75468096	+	1	NA	promoter-TSS (NM_001291156)	promoter-TSS (NM_001291156)	18	NM_027249	380712	Mm.41393	NM_027249	ENSMUSG00000038217	Tlcd2	-	TLC domain containing 2	protein-coding
mm_6636.1	chr1	78680687	78680720	-	1	NA	intron (NM_028817, intron 2 of 15)	Lx9|LINE|L1	22263	NM_001136226	195434	Mm.276016	NM_001001981	ENSMUSG00000079470	Utp14b	4932411L21Rik|jsd	UTP14B small subunit processome component	protein-coding
mm_156556.1	chrX	151801145	151801161	+	1	NA	Intergenic	Intergenic	-2129	NM_021523	59026	Mm.27372	NM_021523	ENSMUSG00000025261	Huwe1	5430439H10Rik|AU041296|Arf-bp1|C430014N20Rik|C80292|Gm1718|Ib772|LASU1|Mule|Ureb1	HECT, UBA and WWE domain containing 1	protein-coding
mm_10809.1	chr2	24349917	24349927	+	1	NA	3' UTR (NM_031167, exon 5 of 5)	3' UTR (NM_031167, exon 5 of 5)	4551	NM_001039701	16181	Mm.882	NM_031167	ENSMUSG00000026981	Il1rn	F630041P17Rik|IL-1ra	interleukin 1 receptor antagonist	protein-coding
mm_33922.1	chr4	136622613	136622621	+	1	NA	promoter-TSS (NM_001243262)	promoter-TSS (NM_001243262)	-4	NM_001243262	242707	Mm.448979	NM_001243262	ENSMUSG00000070683	Lactbl1	-	lactamase, beta-like 1	protein-coding
mm_145995.1	chr18	68344404	68344418	+	1	NA	Intergenic	MTC-int|LTR|ERVL-MaLR	6808	NM_013596	17203	Mm.8003	NM_013596	ENSMUSG00000007480	Mc5r	-	melanocortin 5 receptor	protein-coding
mm_122747.1	chr14	54168017	54168019	-	1	NA	Intergenic	Intergenic	85911	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_55887.1	chr6	83528969	83528973	-	1	NA	intron (NM_009610, intron 1 of 8)	intron (NM_009610, intron 1 of 8)	7280	NM_009610	11468	Mm.292865	NM_009610	ENSMUSG00000059430	Actg2	ACTA3|Act-4|Act4|SMGA	actin, gamma 2, smooth muscle, enteric	protein-coding
mm_795.1	chr1	45345944	45345985	+	1	NA	exon (NM_009930, exon 48 of 51)	exon (NM_009930, exon 48 of 51)	34426	NM_009930	12825	Mm.249555	NM_009930	ENSMUSG00000026043	Col3a1	AW550625|Col3a-1|Tsk-2|Tsk2	collagen, type III, alpha 1	protein-coding
mm_106592.1	chr11	120730477	120730487	-	1	NA	exon (NM_007621, exon 5 of 8)	exon (NM_007621, exon 5 of 8)	1539	NM_007621	12409	Mm.21454	NM_007621	ENSMUSG00000025150	Cbr2	MLCR	carbonyl reductase 2	protein-coding
mm_124070.1	chr14	78565618	78565635	-	1	NA	Intergenic	Intergenic	-28766	NM_001164503	219181	Mm.89413	NM_001164503	ENSMUSG00000022016	Akap11	6330501D17Rik|AKAP220|Gm80|PRKA11|mKIAA0629	A kinase (PRKA) anchor protein 11	protein-coding
mm_139434.1	chr17	53584105	53584118	+	1	NA	promoter-TSS (NM_001190846)	promoter-TSS (NM_001190846)	-15	NM_001190846	18519	Mm.255025	NM_020005	ENSMUSG00000000708	Kat2b	A930006P13Rik|AI461839|AW536563|Pcaf|p/CAF	K(lysine) acetyltransferase 2B	protein-coding
mm_60992.1	chr7	49246209	49246215	+	1	NA	promoter-TSS (NM_175272)	promoter-TSS (NM_175272)	23	NM_175272	78286	Mm.333881	NM_175272	ENSMUSG00000052512	Nav2	5330421F07Rik|AU067780|BQ960892|HELAD1|POMFIL2|RAINB1|RAINB2|Unc53H2|mKIAA3015	neuron navigator 2	protein-coding
mm_146708.1	chr18	13972537	13972553	-	1	NA	5' UTR (NM_145492, exon 1 of 8)	5' UTR (NM_145492, exon 1 of 8)	188	NM_145492	225207	Mm.40325	NM_145492	ENSMUSG00000024420	Zfp521	B930086A16Rik|Evi3|Znf521	zinc finger protein 521	protein-coding
mm_171373.1	chr4	119282436	119282448	-	1	NA	exon (NM_011732, exon 5 of 8)	exon (NM_011732, exon 5 of 8)	12071	NM_011732	22608	Mm.258204	NM_011732	ENSMUSG00000028639	Ybx1	1700102N10Rik|C79409|EF1A|MSY1|Nsep1|YB-1|dbpB|mYB-1a	Y box protein 1	protein-coding
mm_7080.1	chr1	88277471	88277509	-	1	NA	promoter-TSS (NM_172505)	promoter-TSS (NM_172505)	67	NM_172505	212427	Mm.384762	NM_172505		A730008H23Rik	mFleg1	RIKEN cDNA A730008H23 gene	protein-coding
mm_116886.1	chr13	55211544	55211554	-	1	NA	intron (NM_008739, intron 1 of 22)	CpG	1767	NM_008739	18193	Mm.12964	NM_008739	ENSMUSG00000021488	Nsd1	AI528500|KMT3B	nuclear receptor-binding SET-domain protein 1	protein-coding
mm_80254.1	chr9	72807133	72807151	+	1	NA	promoter-TSS (NM_175485)	promoter-TSS (NM_175485)	-132	NM_175485	235472	Mm.31696	NM_175485	ENSMUSG00000036030	Prtg	A230098A12Rik|Igdcc5	protogenin	protein-coding
mm_113563.1	chr13	38192548	38192560	+	1	NA	exon (NM_023842, exon 23 of 24)	exon (NM_023842, exon 23 of 24)	-12385	NM_026382	67797	Mm.250783	NM_026382	ENSMUSG00000021431	Snrnp48	1110050F08Rik|6530403A03Rik|C6orf151	small nuclear ribonucleoprotein 48 (U11/U12)	protein-coding
mm_26668.1	chr3	154711140	154711144	+	1	NA	promoter-TSS (NM_175176)	promoter-TSS (NM_175176)	9	NM_175176	209601	Mm.331454	NM_175176	ENSMUSG00000078161	Erich3	1700013E18Rik|4922501L14Rik|5031409G23Rik|AI596448|Gm133	glutamate rich 3	protein-coding
mm_128951.1	chr15	74763575	74763588	-	1	NA	promoter-TSS (NM_010742)	promoter-TSS (NM_010742)	-14	NM_010742	17068	Mm.878	NM_010742	ENSMUSG00000034634	Ly6d	Ly-61|Ly61|Thb	lymphocyte antigen 6 complex, locus D	protein-coding
mm_43319.1	chr5	134986170	134986172	+	1	NA	promoter-TSS (NM_009902)	promoter-TSS (NM_009902)	-43	NM_009902	12739	Mm.158662	NM_009902	ENSMUSG00000070473	Cldn3	AI182374|Cpetr2|mRVP1	claudin 3	protein-coding
mm_108897.1	chr12	100187106	100187123	+	1	NA	promoter-TSS (NR_045282)	promoter-TSS (NR_045282)	-854	NR_045282	100038378	Mm.387075	NR_045282	ENSMUSG00000072884	Gm10433	ENSMUSG00000072884	predicted gene 10433	ncRNA
mm_138119.1	chr17	34145200	34145215	+	1	NA	promoter-TSS (NM_010388)	promoter-TSS (NM_010388)	-209	NM_010388	15000	Mm.195060	NM_010388	ENSMUSG00000037548	H2-DMb2	H-2Mb2|H2-Mb2	histocompatibility 2, class II, locus Mb2	protein-coding
mm_131351.1	chr16	13702477	13702504	+	1	NA	3' UTR (NM_001177552, exon 6 of 6)	3' UTR (NM_001177552, exon 6 of 6)	-27346	NR_040574	76684	Mm.491043	NR_040574		Pla2g10os	1810007I06Rik	phospholipase A2, group X, opposite strand	ncRNA
mm_70308.1	chr8	4181944	4181955	+	1	NA	intron (NM_001346730, intron 1 of 19)	intron (NM_001346730, intron 1 of 19)	15382	NM_001346730	213027	Mm.437106	NM_153536	ENSMUSG00000011832	Evi5l	1700084G18Rik|2310039H16Rik|3110007G05Rik|B130050I23Rik	ecotropic viral integration site 5 like	protein-coding
mm_128275.1	chr15	36794476	36794490	-	1	NA	promoter-TSS (NM_011740)	promoter-TSS (NM_011740)	55	NM_011740	22631	Mm.3360	NM_011740	ENSMUSG00000022285	Ywhaz	1110013I11Rik|14-3-3zeta|AI596267|AL022924|AU020854	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide	protein-coding
mm_136137.1	chr16	87128418	87128467	-	1	NA	Intergenic	Intergenic	-225743	NM_001159331	67768	Mm.296532	NM_026366	ENSMUSG00000044442	N6amt1	5830445C04Rik|Hemk2|Pred28	N-6 adenine-specific DNA methyltransferase 1 (putative)	protein-coding
mm_97283.1	chr11	76133986	76133996	+	1	NA	intron (NM_026664, intron 7 of 21)	MLT1G1|LTR|ERVL-MaLR	45639	NM_026664	68299	Mm.46397	NM_026664	ENSMUSG00000017288	Vps53	2010002A08Rik|2310040I21Rik|3100002B05Rik|Hccs1	VPS53 GARP complex subunit	protein-coding
mm_144145.1	chr18	4994904	4994943	+	1	NA	Intergenic	Intergenic	-51666	NM_153153	225115	Mm.136791	NM_153153	ENSMUSG00000024236	Svil	AU024053|B430302E16Rik	supervillin	protein-coding
mm_10561.1	chr2	18027949	18027983	+	1	NA	non-coding (NR_028376, exon 2 of 2)	non-coding (NR_028376, exon 2 of 2)	717	NR_028378	100034739	Mm.401643	NR_028378		Gm17762	-	predicted gene, 17762	ncRNA
mm_81067.1	chr9	106179746	106179757	+	1	NA	TTS (NR_029526)	TTS (NR_029526)	911	NR_029526	387249		NR_029526	ENSMUSG00000065440	Mirlet7g	Mirnlet7g|let-7g|mmu-let-7g	microRNA let7g	ncRNA
mm_77631.1	chr8	124080778	124080801	-	1	NA	Intergenic	Intergenic	57316	NM_001029876	382038	Mm.334891	NM_001029876	ENSMUSG00000031976	Urb2	C77575|mKIAA0133	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	protein-coding
mm_7130.1	chr1	91052817	91052828	-	1	NA	promoter-TSS (NM_008515)	promoter-TSS (NM_008515)	-622	NM_001310732	16978	Mm.45039	NM_008515	ENSMUSG00000026305	Lrrfip1	AU024550|Fliiap1	leucine rich repeat (in FLII) interacting protein 1	protein-coding
mm_17225.1	chr2	25535117	25535121	-	1	NA	intron (NM_009422, intron 4 of 10)	intron (NM_009422, intron 4 of 10)	11821	NM_001290413	22030	Mm.3399	NM_009422	ENSMUSG00000026942	Traf2	AI325259	TNF receptor-associated factor 2	protein-coding
mm_29906.1	chr3	131472971	131473003	-	1	NA	Intergenic	Intergenic	-91781	NM_001289479	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_117738.1	chr13	95671472	95671535	-	1	NA	intron (NM_027711, intron 20 of 35)	intron (NM_027711, intron 20 of 35)	-25417	NM_010170	14064	Mm.440952	NM_010170	ENSMUSG00000021675	F2rl2	F730031A08|PAR3	coagulation factor II (thrombin) receptor-like 2	protein-coding
mm_81635.1	chr9	110880250	110880264	+	1	NA	promoter-TSS (NM_001146059)	promoter-TSS (NM_001146059)	-65	NM_001146060	235633	Mm.86338	NM_146228	ENSMUSG00000044037	Als2cl	79H19D|79H19E|BC022645|D930044G19Rik|mRn.49018	ALS2 C-terminal like	protein-coding
mm_67083.1	chr7	68277060	68277102	-	1	NA	promoter-TSS (NR_040340)	promoter-TSS (NR_040340)	-487	NR_040340	100504026	Mm.426764	NR_040340	ENSMUSG00000086628	Gm16157	OTTMUSG00000031023	predicted gene 16157	ncRNA
mm_148501.1	chr19	4194623	4194647	+	1	NA	TTS (NM_011237)	TTS (NM_011237)	2461	NM_031868	19045	Mm.1970	NM_031868	ENSMUSG00000040385	Ppp1ca	Ppp1c|dism2	protein phosphatase 1, catalytic subunit, alpha isoform	protein-coding
mm_29068.1	chr3	103792574	103792590	-	1	NA	Intergenic	Intergenic	-1019	NM_001301304	15257	Mm.20827	NM_010432	ENSMUSG00000008730	Hipk1	1110062K04Rik|Myak	homeodomain interacting protein kinase 1	protein-coding
mm_47652.1	chr5	125391732	125391750	-	1	NA	Intergenic	Intergenic	-1724	NM_019639	22190	Mm.331	NM_019639	ENSMUSG00000008348	Ubc	2700054O04Rik|AI194771|Rps27a|TI-225|Uba52|Ubb	ubiquitin C	protein-coding
mm_104863.1	chr11	99386101	99386160	-	1	NA	exon (NM_010660, exon 7 of 8)	exon (NM_010660, exon 7 of 8)	3234	NM_010660	16661	Mm.22662	NM_010660	ENSMUSG00000019761	Krt10	D130054E02Rik|K10|K1C1|Krt-1.10|Krt1-10	keratin 10	protein-coding
mm_124730.1	chr15	6580576	6580586	+	1	NA	exon (NM_001278269, exon 1 of 17)	exon (NM_001278269, exon 1 of 17)	734	NM_011815	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_170065.1	chr17	3084034	3084053	-	1	NA	non-coding (NR_003519, exon 1 of 8)	non-coding (NR_003519, exon 1 of 8)	140	NR_003519	328734	Mm.335641	NR_003519		Pisd-ps2	D030013I16Rik	phosphatidylserine decarboxylase, pseudogene 2	pseudo
mm_74872.1	chr8	25017036	25017053	-	1	NA	promoter-TSS (NM_007404)	promoter-TSS (NM_007404)	-122	NM_007404	11502	Mm.28908	NM_007404	ENSMUSG00000031555	Adam9	AU020942|MDC9|Mltng|mKIAA0021	a disintegrin and metallopeptidase domain 9 (meltrin gamma)	protein-coding
mm_87254.1	chr10	41519437	41519447	+	1	NA	promoter-TSS (NM_016898)	promoter-TSS (NM_016898)	-58	NM_016898	53599	Mm.269815	NM_016898	ENSMUSG00000019818	Cd164	A115|A24|AA589639|AW540279|MGC-24|MSSP	CD164 antigen	protein-coding
mm_10263.1	chr2	9681794	9681804	+	1	NA	Intergenic	Intergenic	196801	NM_008091	14462	Mm.313866	NM_008091	ENSMUSG00000015619	Gata3	Gata-3|jal	GATA binding protein 3	protein-coding
mm_164950.1	chr19	4927970	4927997	-	1	NA	intron (NM_133803, intron 1 of 17)	intron (NM_133803, intron 1 of 17)	304	NM_133803	75221	Mm.234769	NM_133803	ENSMUSG00000063904	Dpp3	4930533O14Rik|C86324	dipeptidylpeptidase 3	protein-coding
mm_24203.1	chr3	88620433	88620440	+	1	NA	promoter-TSS (NM_001198913)	promoter-TSS (NM_001198913)	-670	NM_008487	16800	Mm.239329	NM_008487	ENSMUSG00000028059	Arhgef2	AA408978|GEF|GEF-H1|GEFH1|LFP40|Lbcl1|Lfc|P40|mKIAA0651	rho/rac guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_113453.1	chr13	35834838	35834841	+	1	NA	intron (NM_001123386, intron 2 of 6)	intron (NM_001123386, intron 2 of 6)	71508	NM_145938	208366	Mm.35545	NM_145938	ENSMUSG00000021418	Rpp40	D8Bwg1265e|Rnasep1	ribonuclease P 40 subunit	protein-coding
mm_67612.1	chr7	83884214	83884253	-	1	NA	5' UTR (NM_030705, exon 1 of 1)	5' UTR (NM_030705, exon 1 of 1)	108	NM_030705	80889	Mm.272998	NM_030705	ENSMUSG00000070462	Mesdc1	AW061151	mesoderm development candidate 1	protein-coding
mm_97785.1	chr11	82781145	82781224	+	1	NA	promoter-TSS (NM_010716)	promoter-TSS (NM_010716)	75	NM_010716	16882	Mm.277136	NM_010716	ENSMUSG00000020697	Lig3	D11Wsu78e	ligase III, DNA, ATP-dependent	protein-coding
mm_75225.1	chr8	39617460	39617472	-	1	NA	intron (NM_001113326, intron 5 of 9)	intron (NM_001113326, intron 5 of 9)	25212	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_142306.1	chr17	42742146	42742162	-	1	NA	promoter-TSS (NM_001033493)	promoter-TSS (NM_001033493)	25	NM_001033493	435529	Mm.136350	NM_001033493	ENSMUSG00000057899	Adgrf2	Gpr111|PGR20	adhesion G protein-coupled receptor F2	protein-coding
mm_145353.1	chr18	56573003	56573039	+	1	NA	promoter-TSS (NM_001127338)	promoter-TSS (NM_001127338)	-82	NM_001127338	110695	Mm.30250	NM_138600	ENSMUSG00000053644	Aldh7a1	Atq1|D18Wsu181e	aldehyde dehydrogenase family 7, member A1	protein-coding
mm_144097.1	chr18	3383224	3383263	+	1	NA	promoter-TSS (NM_029402)	promoter-TSS (NM_029402)	18	NM_029402	71745	Mm.291707	NM_029402	ENSMUSG00000024231	Cul2	1300003D18Rik|4932411N15Rik|AI327301|mKIAA4106	cullin 2	protein-coding
mm_107474.1	chr12	37880307	37880341	+	1	NA	promoter-TSS (NM_178681)	promoter-TSS (NM_178681)	-381	NM_178681	217480	Mm.126525	NM_178681	ENSMUSG00000036095	Dgkb	6430574F24|90kda|C630029D13Rik|DAGK2|DGK|DGK-beta|mKIAA0718	diacylglycerol kinase, beta	protein-coding
mm_48995.1	chr6	4756593	4756605	+	1	NA	exon (NM_130877, exon 2 of 2)	exon (NM_130877, exon 2 of 2)	9293	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_29395.1	chr3	108904498	108904508	-	1	NA	exon (NM_025845, exon 6 of 6)	exon (NM_025845, exon 6 of 6)	7201	NM_025845	66921	Mm.51049	NM_025845	ENSMUSG00000027881	Prpf38b	1110021E09Rik|AU018955	PRP38 pre-mRNA processing factor 38 (yeast) domain containing B	protein-coding
mm_61953.1	chr7	90207742	90207762	+	1	NA	3' UTR (NM_001252521, exon 20 of 20)	3' UTR (NM_001252521, exon 20 of 20)	57680	NM_029256	75338	Mm.487222	NM_029256	ENSMUSG00000030617	Ccdc83	4930549K11Rik|4930554C01Rik|4932423M01Rik	coiled-coil domain containing 83	protein-coding
mm_98337.1	chr11	90883322	90883325	+	1	NA	intron (NR_045956, intron 2 of 2)	intron (NR_045956, intron 2 of 2)	78632	NR_045956	73922	Mm.233289	NR_045956	ENSMUSG00000085940	4930405D11Rik	-	RIKEN cDNA 4930405D11 gene	ncRNA
mm_50591.1	chr6	49062087	49062119	+	1	NA	Intergenic	Intergenic	-11692	NM_029353	75593	Mm.439947	NM_029353	ENSMUSG00000029815	Malsu1	2410003K15Rik|Matsu1	mitochondrial assembly of ribosomal large subunit 1	protein-coding
mm_7382.1	chr1	107387428	107387429	-	1	NA	Intergenic	Intergenic	25114	NM_025867	66957	Mm.12638	NM_025867	ENSMUSG00000026327	Serpinb11	2310046M08Rik|AU015399	serine (or cysteine) peptidase inhibitor, clade B (ovalbumin), member 11	protein-coding
mm_48980.1	chr6	4755369	4755384	+	1	NA	exon (NM_130877, exon 2 of 2)	exon (NM_130877, exon 2 of 2)	8070	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_52443.1	chr6	113638484	113638544	+	1	NA	promoter-TSS (NM_172161)	promoter-TSS (NM_172161)	47	NM_001113553	108960	Mm.152142	NM_172161	ENSMUSG00000060477	Irak2	6330415L08Rik|AI649099|IRAK-2	interleukin-1 receptor-associated kinase 2	protein-coding
mm_36070.1	chr4	57951862	57951894	-	1	NA	exon (NM_011660, exon 2 of 5)	exon (NM_011660, exon 2 of 5)	4533	NM_011660	22166	Mm.260618	NM_011660	ENSMUSG00000028367	Txn1	ADF|AW550880|Trx1|Txn	thioredoxin 1	protein-coding
mm_152972.1	chr19	29386854	29386871	-	1	NA	3' UTR (NM_021893, exon 7 of 7)	3' UTR (NM_021893, exon 7 of 7)	19424	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_100329.1	chr11	118212247	118212260	+	1	NA	intron (NM_001112699, intron 1 of 12)	intron (NM_001112699, intron 1 of 12)	489	NM_001112700	19157	Mm.86413	NM_011180	ENSMUSG00000017132	Cyth1	CLM1|CTH-1|CYTIP|Pscd1	cytohesin 1	protein-coding
mm_133255.1	chr16	77329358	77329377	+	1	NA	promoter-TSS (NR_015543)	promoter-TSS (NR_015543)	39	NR_015543	77994	Mm.394688	NR_015543	ENSMUSG00000090386	Mir99ahg	2810055G20Rik|D730043B02Rik	Mir99a and Mirlet7c-1 host gene (non-protein coding)	ncRNA
mm_51329.1	chr6	72356105	72356127	+	1	NA	intron (NM_144916, intron 1 of 7)	intron (NM_144916, intron 1 of 7)	633	NM_144916	232086	Mm.491165	NM_144916	ENSMUSG00000055912	Tmem150a	BC014685|Tmem150	transmembrane protein 150A	protein-coding
mm_38953.1	chr4	150570077	150570097	-	1	NA	intron (NM_001085492, intron 11 of 22)	intron (NM_001085492, intron 11 of 22)	82087	NM_173774	242773	Mm.29280	NM_173774	ENSMUSG00000039838	Slc45a1	C230078B22|Dnb5	solute carrier family 45, member 1	protein-coding
mm_148951.1	chr19	7270136	7270155	+	1	NA	exon (NM_054048, exon 4 of 13)	exon (NM_054048, exon 4 of 13)	1866	NM_001320554	104383	Mm.283859	NM_054048	ENSMUSG00000024968	Rcor2	1A13|AW122124|CoREST|Rcor|Rcor1	REST corepressor 2	protein-coding
mm_57882.1	chr6	131316047	131316049	-	1	NA	Intergenic	B1_Mur4|SINE|Alu	-2221	NM_172891	243659	Mm.20114	NM_172891	ENSMUSG00000032899	Styk1	9130025L13|AI326477|Nok	serine/threonine/tyrosine kinase 1	protein-coding
mm_97865.1	chr11	83117004	83117021	+	1	NA	5' UTR (NM_011407, exon 1 of 2)	5' UTR (NM_011407, exon 1 of 2)	167	NM_011407	20555	Mm.10948	NM_011407	ENSMUSG00000078763	Slfn1	AV316259	schlafen 1	protein-coding
mm_47498.1	chr5	124034529	124034539	-	1	NA	Intergenic	Intergenic	-2274	NM_177876	330192	Mm.4079	NM_177876	ENSMUSG00000066278	Vps37b	2300007F24Rik|AI415429|BC026744	vacuolar protein sorting 37B	protein-coding
mm_87112.1	chr10	33233846	33233877	+	1	NA	exon (NM_029726, exon 10 of 38)	exon (NM_029726, exon 10 of 38)	22496	NR_040657	442820	Mm.490725	NR_040657		D830005E20Rik	-	RIKEN cDNA D830005E20 gene	ncRNA
mm_136341.1	chr16	92603187	92603199	-	1	NA	3' UTR (NM_001111021, exon 8 of 8)	3' UTR (NM_001111021, exon 8 of 8)	94136	NM_001111023	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_148735.1	chr19	5884747	5884792	+	1	NA	exon (NM_134154, exon 6 of 6)	exon (NM_134154, exon 6 of 6)	6303	NM_134154	107375	Mm.5323	NM_134154	ENSMUSG00000024818	Slc25a45	AW491445	solute carrier family 25, member 45	protein-coding
mm_159459.1	chr3	153973605	153973605	+	1	NA	5' UTR (NM_001081263, exon 1 of 22)	5' UTR (NM_001081263, exon 1 of 22)	169	NM_001081263	242259	Mm.239962	NM_001081263	ENSMUSG00000028360	Slc44a5	AA117069|Gm422	solute carrier family 44, member 5	protein-coding
mm_160319.1	chr7	143094562	143094562	-	1	NA	promoter-TSS (NM_020277)	promoter-TSS (NM_020277)	80	NM_020277	56843	Mm.286668	NM_020277	ENSMUSG00000009246	Trpm5	9430099A16Rik|LTrpC-5|Ltrpc5|Mtr1	transient receptor potential cation channel, subfamily M, member 5	protein-coding
mm_135374.1	chr16	44106195	44106196	-	1	NA	intron (NM_007508, intron 8 of 14)	intron (NM_007508, intron 8 of 14)	32824	NM_007508	11964	Mm.217787	NM_007508	ENSMUSG00000052459	Atp6v1a	AI647066|Atp6a1|Atp6a2|Atp6v1a1|VA68|VPP2	ATPase, H+ transporting, lysosomal V1 subunit A	protein-coding
mm_48591.1	chr5	143895079	143895091	-	1	NA	promoter-TSS (NM_001310772)	promoter-TSS (NM_001310772)	-18	NM_001310772	66729	Mm.439817	NM_025732	ENSMUSG00000029607	Ankrd61	4921520G13Rik	ankyrin repeat domain 61	protein-coding
mm_27722.1	chr3	69004366	69004378	-	1	NA	promoter-TSS (NM_133786)	promoter-TSS (NM_133786)	198	NM_026641	68259	Mm.389451	NM_026641	ENSMUSG00000027778	Ift80	4921524P20Rik|Wdr56|mKIAA1374	intraflagellar transport 80	protein-coding
mm_34877.1	chr4	155563799	155563865	+	1	NA	promoter-TSS (NM_001159637)	promoter-TSS (NM_001159637)	17	NM_001159637	192185	Mm.28347	NM_138671	ENSMUSG00000029063	Nadk	4432404C02Rik|BC004012	NAD kinase	protein-coding
mm_75875.1	chr8	70764980	70764995	-	1	NA	exon (NM_023065, exon 2 of 8)	exon (NM_023065, exon 2 of 8)	1676	NM_023065	65972	Mm.30241	NM_023065	ENSMUSG00000031838	Ifi30	GILT|IP30	interferon gamma inducible protein 30	protein-coding
mm_48179.1	chr5	137331070	137331077	-	1	NA	exon (NM_031406, exon 4 of 14)	exon (NM_031406, exon 4 of 14)	2509	NM_031406	83704	Mm.235625	NM_031406	ENSMUSG00000037344	Slc12a9	CIP1	solute carrier family 12 (potassium/chloride transporters), member 9	protein-coding
mm_95162.1	chr11	36962390	36962390	+	1	NA	Intergenic	Intergenic	-18149	NM_011856	23964	Mm.439889	NM_011856	ENSMUSG00000049336	Tenm2	Odz2|Odz3|Ten-2|Ten-m2	teneurin transmembrane protein 2	protein-coding
mm_115790.1	chr13	19337328	19337336	-	1	NA	Intergenic	Intergenic	58481	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_35252.1	chr4	19877808	19877822	-	1	NA	3' UTR (NM_175406, exon 8 of 8)	3' UTR (NM_175406, exon 8 of 8)	44751	NM_175406	242341	Mm.19298	NM_175406	ENSMUSG00000028238	Atp6v0d2	1620401A02Rik|AI324824|V-ATPase	ATPase, H+ transporting, lysosomal V0 subunit D2	protein-coding
mm_29756.1	chr3	127162047	127162093	-	1	NA	intron (NR_105029, intron 2 of 3)	intron (NR_105029, intron 2 of 3)	765	NR_105029	100862268	Mm.444603	NR_105029	ENSMUSG00000097456	LOC100862268	-	uncharacterized LOC100862268	ncRNA
mm_31112.1	chr4	42922254	42922260	+	1	NA	intron (NM_001346526, intron 1 of 8)	intron (NM_001346526, intron 1 of 8)	5006	NM_172690	230085	Mm.240965	NM_172690	ENSMUSG00000036062	Phf24	GINIP|N28178	PHD finger protein 24	protein-coding
mm_112624.1	chr13	15807242	15807243	+	1	NA	promoter-TSS (NR_046131)	promoter-TSS (NR_046131)	-1	NR_046131	328190	Mm.446957	NR_046131		A530046M15Rik	A530046M15	RIKEN cDNA A530046M15 gene	ncRNA
mm_1688.1	chr1	75028655	75028659	+	1	NA	intron (NM_029342, intron 2 of 4)	RLTR1B|LTR|ERV1	17982	NM_029342	75570	Mm.442409	NM_029342	ENSMUSG00000026162	Nhej1	1700029B21Rik|XLF|cernunnos	nonhomologous end-joining factor 1	protein-coding
mm_76316.1	chr8	84663922	84663955	-	1	NA	Intergenic	Intergenic	-1086	NM_010499	15936	Mm.399	NM_010499	ENSMUSG00000053560	Ier2	AI317238|Ch1|Pip92	immediate early response 2	protein-coding
mm_114507.1	chr13	70872402	70872404	+	1	NA	Intergenic	Intergenic	-10545	NM_029873	77166	Mm.159859	NM_029873	ENSMUSG00000021600	8030423J24Rik	-	RIKEN cDNA 8030423J24 gene	protein-coding
mm_35539.1	chr4	41316710	41316716	-	1	NA	Intergenic	Intergenic	-1812	NM_026893	68970	Mm.28891	NM_026893	ENSMUSG00000028436	Dcaf12	1500001L20Rik|5830424K06Rik|AA420338|AI851081|Wdr40a	DDB1 and CUL4 associated factor 12	protein-coding
mm_119568.1	chr14	49724621	49724642	+	1	NA	intron (NM_026142, intron 5 of 7)	intron (NM_026142, intron 5 of 7)	58736	NM_026142	67419	Mm.318710	NM_026142	ENSMUSG00000036242	3632451O06Rik	AU067705	RIKEN cDNA 3632451O06 gene	protein-coding
mm_134377.1	chr16	17147576	17147592	-	1	NA	promoter-TSS (NM_001306169)	promoter-TSS (NM_001306169)	-355	NM_001306169	76872	Mm.101656	NM_029779	ENSMUSG00000022768	Ccdc116	4930432J16Rik	coiled-coil domain containing 116	protein-coding
mm_82042.1	chr9	122151294	122151298	+	1	NA	intron (NM_001164572, intron 2 of 5)	intron (NM_001164572, intron 2 of 5)	34030	NM_133741	20623	Mm.257989	NM_133741	ENSMUSG00000038145	Snrk	2010012F07Rik|AI448042|AW547029|E030034B15|R74830|mKIAA0096	SNF related kinase	protein-coding
mm_149288.1	chr19	10648227	10648233	+	1	NA	promoter-TSS (NR_045316)	promoter-TSS (NR_045316)	-177	NR_045316	75096	Mm.399287	NR_045316		4930524O05Rik	-	RIKEN cDNA 4930524O05 gene	ncRNA
mm_27600.1	chr3	59153463	59153478	-	1	NA	promoter-TSS (NM_001287119)	promoter-TSS (NM_001287119)	22	NM_001287119	140795	Mm.439021	NM_133200	ENSMUSG00000036381	P2ry14	A330108O13Rik|Gpr105|P2Y14	purinergic receptor P2Y, G-protein coupled, 14	protein-coding
mm_69778.1	chr7	141018003	141018023	-	1	NA	Intergenic	B2_Mm2|SINE|B2	-1121	NM_001033632	213002	Mm.276440	NM_001033632	ENSMUSG00000059108	Ifitm6	A330075D07|Dspa2f|Fgls5|fragilis5	interferon induced transmembrane protein 6	protein-coding
mm_164073.1	chr14	120418266	120418272	+	1	NA	intron (NM_175341, intron 8 of 8)	intron (NM_175341, intron 8 of 8)	-60192	NM_029519	76108	Mm.261448	NM_029519	ENSMUSG00000051615	Rap2a	5830461H18Rik	RAS related protein 2a	protein-coding
mm_99340.1	chr11	101468356	101468373	+	1	NA	promoter-TSS (NM_009708)	promoter-TSS (NM_009708)	26	NM_009708	11858	Mm.378883	NM_009708	ENSMUSG00000001313	Rnd2	Arhn|Rohn	Rho family GTPase 2	protein-coding
mm_87914.1	chr10	62362330	62362353	+	1	NA	intron (NM_010438, intron 2 of 21)	intron (NM_010438, intron 2 of 21)	17567	NM_010438	15275	Mm.196605	NM_010438	ENSMUSG00000037012	Hk1	BB404130|Hk-1|Hk1-s|dea|mHk1-s	hexokinase 1	protein-coding
mm_95125.1	chr11	34091230	34091243	+	1	NA	3' UTR (NM_010696, exon 21 of 21)	3' UTR (NM_010696, exon 21 of 21)	44035	NM_010696	16822	Mm.265350	NM_010696	ENSMUSG00000002699	Lcp2	AI323664|BB161688|SLP-76|SLP76|m1Khoe|twm	lymphocyte cytosolic protein 2	protein-coding
mm_118424.1	chr14	7924236	7924246	+	1	NA	exon (NM_001081427, exon 32 of 46)	exon (NM_001081427, exon 32 of 46)	69941	NM_007870	13421	Mm.272258	NM_007870	ENSMUSG00000025279	Dnase1l3	DNasegamma|Dhp2|Lsd	deoxyribonuclease 1-like 3	protein-coding
mm_79093.1	chr9	46242795	46242801	+	1	NA	exon (NM_007468, exon 3 of 3)	exon (NM_007468, exon 3 of 3)	1954	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_103371.1	chr11	75297870	75297880	-	1	NA	Intergenic	Intergenic	50508	NM_001164223	68275	Mm.102574	NM_026653	ENSMUSG00000000751	Rpa1	5031405K23Rik|70kDa|AA589576|AW557552|RF-A|RP-A|Rpa	replication protein A1	protein-coding
mm_67650.1	chr7	84689795	84689821	-	1	NA	non-coding (NR_038175, exon 1 of 5)	non-coding (NR_038175, exon 1 of 5)	168	NR_038175	72495	Mm.382914	NR_038175	ENSMUSG00000085236	2610206C17Rik	-	RIKEN cDNA 2610206C17 gene	ncRNA
mm_39133.1	chr4	155154790	155154843	-	1	NA	3' UTR (NM_011385, exon 7 of 7)	3' UTR (NM_011385, exon 7 of 7)	67719	NM_011385	20481	Mm.28520	NM_011385	ENSMUSG00000029050	Ski	2310012I02Rik|2610001A11Rik|AA062172|AA589460|BC004088	ski sarcoma viral oncogene homolog (avian)	protein-coding
mm_125231.1	chr15	34141126	34141167	+	1	NA	3' UTR (NM_026002, exon 12 of 12)	3' UTR (NM_026002, exon 12 of 12)	58427	NM_026002	67154	Mm.130883	NM_026002	ENSMUSG00000022255	Mtdh	2610103J23Rik|3D3|3D3/Lyric|AEG-1|AV353288|D8Bwg1112e|Lyric	metadherin	protein-coding
mm_26441.1	chr3	142624617	142624661	+	1	NA	promoter-TSS (NR_105802)	promoter-TSS (NR_105802)	-693	NR_105802	102465200		NR_105802	ENSMUSG00000098871	Mir6381	Gm27963|mmu-mir-6381	microRNA 6381	ncRNA
mm_162998.1	chr11	30657365	30657365	+	1	NA	Intergenic	U2|snRNA|snRNA	-7969	NM_029344	75572	Mm.390319	NM_029344	ENSMUSG00000060923	Acyp2	2310004B09Rik	acylphosphatase 2, muscle type	protein-coding
mm_49247.1	chr6	17307773	17307778	+	1	NA	5' UTR (NM_001243064, exon 1 of 2)	5' UTR (NM_001243064, exon 1 of 2)	135	NM_001243064	12389	Mm.28278	NM_007616	ENSMUSG00000007655	Cav1	Cav|Cav-1	caveolin 1, caveolae protein	protein-coding
mm_101822.1	chr11	46698820	46698835	-	1	NA	promoter-TSS (NM_001161355)	promoter-TSS (NM_001161355)	3	NM_001161355	171284	Mm.234654	NM_134249	ENSMUSG00000040413	Timd2	AA816106|AU019358|AU019662|C78111|G9D3|TIM-2|Tim2	T cell immunoglobulin and mucin domain containing 2	protein-coding
mm_152082.1	chr19	6870676	6870698	-	1	NA	Intergenic	RMER4A|LTR|ERVK	-12476	NM_001081291	78317	Mm.329596	NM_198008	ENSMUSG00000047810	Ccdc88b	2610041P08Rik|Ccdc88	coiled-coil domain containing 88B	protein-coding
mm_63377.1	chr7	127212633	127212637	+	1	NA	intron (NM_016754, intron 1 of 6)	ID_B1|SINE|B4	1027	NM_016754	17907	Mm.14526	NM_016754	ENSMUSG00000030672	Mylpf	2410014J02Rik|MLC-2|Mlc2	myosin light chain, phosphorylatable, fast skeletal muscle	protein-coding
mm_129138.1	chr15	76199863	76199894	-	1	NA	promoter-TSS (NM_201392)	promoter-TSS (NM_201392)	-43	NM_001163549	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
mm_57837.1	chr6	129465489	129465504	-	1	NA	exon (NM_020008, exon 5 of 6)	exon (NM_020008, exon 5 of 6)	7283	NM_001309637	56644	Mm.239516	NM_020008	ENSMUSG00000079293	Clec7a	BGR|Clecsf12|beta-GR	C-type lectin domain family 7, member a	protein-coding
mm_6141.1	chr1	64812967	64812993	-	1	NA	intron (NM_001039493, intron 7 of 7)	intron (NM_001039493, intron 7 of 7)	-75230	NM_022721	14367	Mm.150813	NM_022721	ENSMUSG00000045005	Fzd5	5330434N09Rik|AI427138|Fz-5|Fz5|mFz5	frizzled class receptor 5	protein-coding
mm_118230.1	chr13	111489774	111489793	-	1	NA	5' UTR (NM_028487, exon 1 of 13)	5' UTR (NM_028487, exon 1 of 13)	258	NM_028487	73274	Mm.57286	NM_028487	ENSMUSG00000032745	Gpbp1	1700034P14Rik|AU019836|D230035M11Rik|Gpbp|mGPBP	GC-rich promoter binding protein 1	protein-coding
mm_84513.1	chr9	67033378	67033382	-	1	NA	intron (NM_024427, intron 4 of 8)	intron (NM_024427, intron 4 of 8)	10491	NM_001164252	22003	Mm.121878	NM_024427	ENSMUSG00000032366	Tpm1	AA986836|AI854628|TM2|Tm3|Tmpa|Tpm-1|alpha-TM	tropomyosin 1, alpha	protein-coding
mm_74897.1	chr8	25159660	25159681	-	1	NA	promoter-TSS (NR_106187)	promoter-TSS (NR_106187)	-437	NR_106187	102467006		NR_106187	ENSMUSG00000099142	Mir8108	Gm27484|mmu-mir-8108	microRNA 8108	ncRNA
mm_161267.1	chr14	6889866	6889866	-	1	NA	Intergenic	CpG	-132809	NM_001309401	100041151	Mm.396155	NM_001309401	ENSMUSG00000091754	Gm3636	100042043	predicted gene 3636	protein-coding
mm_146749.1	chr18	16690536	16690548	-	1	NA	intron (NM_007664, intron 2 of 15)	intron (NM_007664, intron 2 of 15)	118704	NM_007664	12558	Mm.257437	NM_007664	ENSMUSG00000024304	Cdh2	CDHN|N-CAD|Ncad	cadherin 2	protein-coding
mm_163995.1	chr14	64440468	64440485	-	1	NA	intron (NM_001253712, intron 1 of 5)	intron (NM_001253712, intron 1 of 5)	550	NM_001253715	110265	Mm.26713	NM_026322	ENSMUSG00000054733	Msra	2310045J23Rik|6530413P12Rik|MSR-A	methionine sulfoxide reductase A	protein-coding
mm_111655.1	chr12	102860301	102860302	-	1	NA	intron (NM_172806, intron 1 of 11)	L2c|LINE|L2	18105	NM_172806	238386	Mm.63456	NM_172806	ENSMUSG00000041702	Btbd7	5730507E09Rik|8030448M07|E130118E17Rik|FUP1|mKIAA1525	BTB (POZ) domain containing 7	protein-coding
mm_46698.1	chr5	110108155	110108204	-	1	NA	promoter-TSS (NM_145147)	promoter-TSS (NM_145147)	18	NM_145147	107999	Mm.86267	NM_145147	ENSMUSG00000033434	Gtpbp6	AV119224|Pgbpll|pgpl	GTP binding protein 6 (putative)	protein-coding
mm_155225.1	chrX	57066165	57066179	+	1	NA	exon (NM_029371, exon 9 of 9)	exon (NM_029371, exon 9 of 9)	12338	NM_029371	72459	Mm.2152	NM_028242	ENSMUSG00000067873	Htatsf1	1600023H17Rik|2600017A12Rik|2700077B20Rik|TAT-SF1	HIV TAT specific factor 1	protein-coding
mm_147366.1	chr18	43438216	43438222	-	1	NA	promoter-TSS (NM_001291455)	promoter-TSS (NM_001291455)	67	NM_001291455	22240	Mm.8180	NM_009468	ENSMUSG00000024501	Dpysl3	CRMP-4|DRP-3|TUC4|ULIP-1|Ulip|Ulip1	dihydropyrimidinase-like 3	protein-coding
mm_138160.1	chr17	34257878	34257888	+	1	NA	Intergenic	Intergenic	-5344	NM_207105	14961	Mm.254067	NM_207105	ENSMUSG00000073421	H2-Ab1	AI845868|Abeta|H-2Ab|H2-Ab|I-Abeta|IAb|Ia-2|Ia2|Rmcs1	histocompatibility 2, class II antigen A, beta 1	protein-coding
mm_95781.1	chr11	54909893	54909903	+	1	NA	TTS (NM_021327)	TTS (NM_021327)	7044	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_3112.1	chr1	134560215	134560233	+	1	NA	promoter-TSS (NM_152895)	promoter-TSS (NM_152895)	46	NM_152895	75605	Mm.28995	NM_152895	ENSMUSG00000042207	Kdm5b	2010009J12Rik|2210016I17Rik|AW556288|D1Ertd202e|Jarid1b|PLU-1|PUT1|Plu1|RBBP2H1A|Rb-Bp2|mKIAA4034	lysine (K)-specific demethylase 5B	protein-coding
mm_109098.1	chr12	105001199	105001247	+	1	NA	intron (NM_172500, intron 1 of 16)	intron (NM_172500, intron 1 of 16)	-2546	NM_001042699	212073	Mm.212688	NM_172500	ENSMUSG00000054150	Syne3	nesprin-3	spectrin repeat containing, nuclear envelope family member 3	protein-coding
mm_131580.1	chr16	18426416	18426450	+	1	NA	promoter-TSS (NM_013711)	promoter-TSS (NM_013711)	16	NM_013711	26462	Mm.390906	NM_013711	ENSMUSG00000075704	Txnrd2	AA118373|ESTM573010|TGR|Tr3|Trxr2|Trxrd2	thioredoxin reductase 2	protein-coding
mm_140166.1	chr17	80290207	80290279	+	1	NA	promoter-TSS (NM_194269)	promoter-TSS (NM_194269)	31	NM_194269	378462	Mm.45208	NM_194269	ENSMUSG00000045257	Morn2	Mopt	MORN repeat containing 2	protein-coding
mm_18976.1	chr2	76846504	76846523	-	1	NA	intron (NM_011652, intron 143 of 312)	intron (NM_011652, intron 143 of 312)	136034	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_69724.1	chr7	140769221	140769235	-	1	NA	exon (NM_021282, exon 3 of 9)	exon (NM_021282, exon 3 of 9)	5396	NM_021282	13106	Mm.21758	NM_021282	ENSMUSG00000025479	Cyp2e1	Cyp2e	cytochrome P450, family 2, subfamily e, polypeptide 1	protein-coding
mm_88116.1	chr10	69212678	69212694	+	1	NA	promoter-TSS (NM_001081347)	promoter-TSS (NM_001081347)	29	NM_001081347	69288	Mm.26659	NM_001081347	ENSMUSG00000019944	Rhobtb1	1700008H16Rik|3110048G13Rik|AI173445|AI573858|AV350930	Rho-related BTB domain containing 1	protein-coding
mm_155243.1	chrX	57223422	57223430	+	1	NA	exon (NM_011616, exon 5 of 5)	exon (NM_011616, exon 5 of 5)	11283	NM_011616	21947	Mm.4861	NM_011616	ENSMUSG00000031132	Cd40lg	CD154|CD40-L|Cd40l|HIGM1|IGM|IMD3|Ly-62|Ly62|T-BAM|TRAP|Tnfsf5|Tnlg8b|gp39	CD40 ligand	protein-coding
mm_78790.1	chr9	44043391	44043434	+	1	NA	promoter-TSS (NM_009382)	promoter-TSS (NM_009382)	28	NM_009382	21838	Mm.3951	NM_009382	ENSMUSG00000032011	Thy1	CD90|T25|Thy-1|Thy-1.2|Thy1.1|Thy1.2	thymus cell antigen 1, theta	protein-coding
mm_164262.1	chr15	100674467	100674467	-	1	NA	TTS (NM_033612)	TTS (NM_033612)	-4967	NM_001270537	668218	Mm.451225	NM_001270537	ENSMUSG00000098112	Bin2	-	bridging integrator 2	protein-coding
mm_81476.1	chr9	109931864	109931885	+	1	NA	promoter-TSS (NM_008633)	promoter-TSS (NM_008633)	100	NM_008633	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_154331.1	chrM	3114	3122	+	1	NA	NA	Intergenic	NA	NA								
mm_121567.1	chr14	122638351	122638390	+	1	NA	intron (NM_144844, intron 7 of 23)	intron (NM_144844, intron 7 of 23)	104042	NM_144844	110821	Mm.23876	NM_144844	ENSMUSG00000041650	Pcca	C79630	propionyl-Coenzyme A carboxylase, alpha polypeptide	protein-coding
mm_136521.1	chr16	97459163	97459174	-	1	NA	intron (NR_003520, intron 2 of 8)	B1_Mur3|SINE|Alu	3737	NM_010846	17857	Mm.33996	NM_010846	ENSMUSG00000000386	Mx1	AI893580|Mx|Mx-1	MX dynamin-like GTPase 1	protein-coding
mm_125992.1	chr15	76354474	76354492	+	1	NA	TTS (NM_026859)	TTS (NM_026859)	3189	NM_026859	68877	Mm.289680	NM_026859	ENSMUSG00000022553	Maf1	1110068E11Rik|AU042856	MAF1 homolog, negative regulator of RNA polymerase III	protein-coding
mm_88015.1	chr10	67184638	67184680	+	1	NA	intron (NM_207221, intron 2 of 25)	intron (NM_207221, intron 2 of 25)	-1091	NM_001242396	108829	Mm.23846	NM_207221	ENSMUSG00000037876	Jmjd1c	5430433L24Rik|D630035I23Rik|Jmjdic|TRIP8	jumonji domain containing 1C	protein-coding
mm_113296.1	chr13	30659889	30659941	+	1	NA	promoter-TSS (NM_134068)	promoter-TSS (NM_134068)	-144	NM_001037955	105352	Mm.289646	NM_134068	ENSMUSG00000069255	Dusp22	JKAP|JSP1|LMW-DSP2|MKPX	dual specificity phosphatase 22	protein-coding
mm_126418.1	chr15	80320154	80320166	+	1	NA	intron (NM_001044308, intron 2 of 36)	intron (NM_001044308, intron 2 of 36)	32922	NM_001044308	239556	Mm.291058	NM_001044308	ENSMUSG00000022416	Cacna1i	Ca(V)3.3	calcium channel, voltage-dependent, alpha 1I subunit	protein-coding
mm_26976.1	chr3	25144250	25144270	-	1	NA	Intergenic	CpG	-360254	NM_001326288	635702	Mm.448351	NM_001326288	ENSMUSG00000102758	Naaladl2	2810043G22Rik|EG635702|Gm1021	N-acetylated alpha-linked acidic dipeptidase-like 2	protein-coding
mm_125470.1	chr15	54410648	54410664	+	1	NA	promoter-TSS (NM_173422)	promoter-TSS (NM_173422)	-118	NM_173422	239447	Mm.82400	NM_173422	ENSMUSG00000038591	Colec10	CL-L1	collectin sub-family member 10	protein-coding
mm_151228.1	chr19	53717969	53717982	+	1	NA	intron (NM_001170847, intron 1 of 13)	intron (NM_001170847, intron 1 of 13)	40669	NM_001170847	73713	Mm.313695	NM_001170847	ENSMUSG00000043639	Rbm20	1110018J23Rik|2010003H22Rik|AI646761	RNA binding motif protein 20	protein-coding
mm_65883.1	chr7	29799872	29799879	-	1	NA	Intergenic	Intergenic	15085	NM_013705	22693	Mm.292690	NM_013705	ENSMUSG00000047473	Zfp30	2610306P15Rik|Zfp-30	zinc finger protein 30	protein-coding
mm_126835.1	chr15	89020302	89020319	+	1	NA	exon (NM_031260, exon 17 of 27)	exon (NM_031260, exon 17 of 27)	37316	NM_031260	83456	Mm.358791	NM_031260	ENSMUSG00000015365	Mov10l1	CHAMP|Csm	Moloney leukemia virus 10-like 1	protein-coding
mm_140249.1	chr17	84183764	84183772	+	1	NA	TTS (NM_001001806)	TTS (NM_001001806)	4179	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_57616.1	chr6	128200553	128200570	-	1	NA	Intergenic	CpG	-16758	NR_077223	330427	Mm.426356	NR_077223	ENSMUSG00000107879	9330102E08Rik	-	RIKEN cDNA 9330102E08 gene	ncRNA
mm_40560.1	chr5	61806701	61806715	+	1	NA	Intergenic	Intergenic	-2135	NM_019468	14380	Mm.347430	NM_019468	ENSMUSG00000089992	G6pd2	G6pdx-ps1|Gpd-2|Gpd2	glucose-6-phosphate dehydrogenase 2	protein-coding
mm_95214.1	chr11	43682039	43682060	+	1	NA	promoter-TSS (NM_001164231)	promoter-TSS (NM_001164231)	51	NM_001164231	70802	Mm.397449	NM_027557	ENSMUSG00000044950	Pwwp2a	4631424J17Rik|AI891583|AU024105|D930040F23Rik	PWWP domain containing 2A	protein-coding
mm_156432.1	chrX	141475386	141475468	+	1	NA	promoter-TSS (NM_001163155)	promoter-TSS (NM_001163155)	8	NM_001163155	12830	Mm.286892	NM_007736	ENSMUSG00000031274	Col4a5	-	collagen, type IV, alpha 5	protein-coding
mm_112765.1	chr13	19356529	19356551	+	1	NA	Intergenic	Intergenic	39273	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_80764.1	chr9	95559372	95559391	+	1	NA	promoter-TSS (NM_198414)	promoter-TSS (NM_198414)	-436	NM_198414	75552	Mm.151485	NM_198414	ENSMUSG00000064225	Paqr9	1700020G04Rik	progestin and adipoQ receptor family member IX	protein-coding
mm_54926.1	chr6	48048500	48048528	-	1	NA	promoter-TSS (NM_001081382)	promoter-TSS (NM_001081382)	-400	NM_001081382	72306	Mm.381553	NM_001081382	ENSMUSG00000071477	Zfp777	2500002G23Rik	zinc finger protein 777	protein-coding
mm_162181.1	chrX	102854616	102854616	-	1	NA	promoter-TSS (NM_001142691).2	promoter-TSS (NM_001142691).2	0	NM_001142691	71083	Mm.50914	NM_001142691	ENSMUSG00000067562	Dmrtc1c1	4933424F23Rik|Dmrt8.3|Dmrtc1c	DMRT-like family C1c1	protein-coding
mm_170221.1	chr17	79063002	79063019	-	1	NA	intron (NM_001316729, intron 1 of 5)	BGLII|LTR|ERVK	11104	NM_001316729	70536	Mm.293870	NM_027455	ENSMUSG00000024084	Qpct	5730422A13Rik	glutaminyl-peptide cyclotransferase (glutaminyl cyclase)	protein-coding
mm_127649.1	chr15	102487923	102487934	+	1	NA	intron (NM_001103165, intron 10 of 14)	intron (NM_001103165, intron 10 of 14)	17296	NM_001174073	18521	Mm.236513	NM_011042	ENSMUSG00000056851	Pcbp2	AW412548|Hnrpx|alphaCP-2	poly(rC) binding protein 2	protein-coding
mm_94250.1	chr11	3330817	3330830	+	1	NA	promoter-TSS (NM_178149)	promoter-TSS (NM_178149)	92	NM_178149	216505	Mm.390323	NM_178149	ENSMUSG00000034614	Pik3ip1	1500004A08Rik|5830455E04Rik|Crkd|Hgfl	phosphoinositide-3-kinase interacting protein 1	protein-coding
mm_17536.1	chr2	29772192	29772196	-	1	NA	Intergenic	Intergenic	10666	NM_001177392	433416	Mm.330112	NM_001034887	ENSMUSG00000075425	Gm13547	OTTMUSG00000012686	predicted gene 13547	protein-coding
mm_34463.1	chr4	148140700	148140767	+	1	NA	5' UTR (NM_027985, exon 1 of 8)	5' UTR (NM_027985, exon 1 of 8)	243	NM_027985	71890	Mm.9648	NM_027985	ENSMUSG00000029003	Mad2l2	2310033C13Rik|G1-453-4|MAD2B|REV7|repro22	MAD2 mitotic arrest deficient-like 2	protein-coding
mm_130328.1	chr15	97719588	97719619	-	1	NA	exon (NM_008902, exon 4 of 9)	exon (NM_008902, exon 4 of 9)	1547	NM_008902	19011	Mm.1001	NM_008902	ENSMUSG00000022468	Endou	Pp11r|Tcl-30	endonuclease, polyU-specific	protein-coding
mm_151901.1	chr19	5799283	5799293	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	-3307	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_63230.1	chr7	126457122	126457149	+	1	NA	exon (NM_007504, exon 7 of 23)	exon (NM_007504, exon 7 of 23)	5938	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_137256.1	chr17	24550046	24550062	+	1	NA	5' UTR (NM_013630, exon 1 of 46)	5' UTR (NM_013630, exon 1 of 46)	104	NM_013630	18763	Mm.30435	NM_013630	ENSMUSG00000032855	Pkd1	PC1|mFLJ00285	polycystic kidney disease 1 homolog	protein-coding
mm_68356.1	chr7	106510913	106510925	-	1	NA	Intergenic	Intergenic	-69846	NR_003967	209380	Mm.461779	NM_001001318		Gm4759	EG209380	GTPase, very large interferon inducible 1 pseudogene	pseudo
mm_157668.1	chrX	59062890	59062902	-	1	NA	3' UTR (NM_001290415, exon 5 of 5)	3' UTR (NM_001290415, exon 5 of 5)	34840	NR_030574	100124476		NR_030574	ENSMUSG00000070110	Mir504	Mirn504|mir-504|mmu-mir-504	microRNA 504	ncRNA
mm_71458.1	chr8	46526454	46526493	+	1	NA	intron (NM_001302163, intron 13 of 20)	PB1D11|SINE|Alu	-25596	NM_027973	71876	Mm.22108	NM_027973	ENSMUSG00000031629	Cenpu	1700029A22Rik|Mlf1ip	centromere protein U	protein-coding
mm_151934.1	chr19	5800403	5800412	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	2265	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_16738.1	chr2	9305048	9305052	-	1	NA	Intergenic	Tigger7|DNA|TcMar-Tigger	115535	NR_038180	73438	Mm.23558	NR_038180	ENSMUSG00000085580	1700061F12Rik	-	RIKEN cDNA 1700061F12 gene	ncRNA
mm_48478.1	chr5	141000591	141000632	-	1	NA	promoter-TSS (NM_175362)	promoter-TSS (NM_175362)	-15	NM_175362	108723	Mm.46187	NM_175362	ENSMUSG00000036526	Card11	0610008L17Rik|2410011D02Rik|BIMP3|CARMA1	caspase recruitment domain family, member 11	protein-coding
mm_158656.1	chrX	156235235	156235235	-	1	NA	Intergenic	L1_Mus1|LINE|L1	-304248	NR_033598	74941	Mm.484588	NR_033598		4930503H13Rik	-	gem (nuclear organelle) associated protein 8 pseudogene	pseudo
mm_76518.1	chr8	87470640	87470651	-	1	NA	intron (NM_019626, intron 2 of 2)	CpG	1947	NM_019626	12404	Mm.4880	NM_019626	ENSMUSG00000031654	Cbln1	AI323299	cerebellin 1 precursor protein	protein-coding
mm_22954.1	chr3	32397151	32397179	+	1	NA	Intergenic	CpG	-31500	NM_009517	22401	Mm.35705	NM_009517	ENSMUSG00000027663	Zmat3	Wig1	zinc finger matrin type 3	protein-coding
mm_69315.1	chr7	128459723	128459726	-	1	NA	intron (NM_001347641, intron 1 of 12)	intron (NM_001347641, intron 1 of 12)	1789	NM_009383	21843	Mm.242072	NM_009383	ENSMUSG00000030846	Tial1	5330433G13Rik|AL033329|TIAR|mTIAR	Tia1 cytotoxic granule-associated RNA binding protein-like 1	protein-coding
mm_59036.1	chr7	19320322	19320327	+	1	NA	Intergenic	Intergenic	-10279	NM_001347586	14282	Mm.248335	NM_008036	ENSMUSG00000003545	Fosb	-	FBJ osteosarcoma oncogene B	protein-coding
mm_111672.1	chr12	103338290	103338313	-	1	NA	intron (NM_023049, intron 2 of 9)	intron (NM_023049, intron 2 of 9)	17700	NM_023049	65256	Mm.27159	NM_023049	ENSMUSG00000021200	Asb2	1110008E15Rik	ankyrin repeat and SOCS box-containing 2	protein-coding
mm_44158.1	chr5	150522647	150522670	+	1	NA	promoter-TSS (NM_009765)	promoter-TSS (NM_009765)	37	NM_001081001	12190	Mm.236256	NM_009765	ENSMUSG00000041147	Brca2	Fancd1|RAB163	breast cancer 2, early onset	protein-coding
mm_5727.1	chr1	44118758	44118816	-	1	NA	promoter-TSS (NM_023645)	promoter-TSS (NM_023645)	-14	NM_023645	72050	Mm.281714	NM_023645	ENSMUSG00000026047	Kdelc1	1810049A15Rik|5730416C13Rik|EP58|Kdel1	KDEL (Lys-Asp-Glu-Leu) containing 1	protein-coding
mm_6417.1	chr1	73751873	73751874	-	1	NA	intron (NR_045311, intron 6 of 8)	intron (NR_045311, intron 6 of 8)	103702	NR_105769	102465179		NR_105769	ENSMUSG00000098504	Mir6351	Gm27936|mmu-mir-6351	microRNA 6351	ncRNA
mm_169998.1	chr1	71640338	71640339	-	1	NA	exon (NM_001276413, exon 10 of 44)	exon (NM_001276413, exon 10 of 44)	12896	NM_010233	14268	Mm.193099	NM_010233	ENSMUSG00000026193	Fn1	E330027I09|Fn|Fn-1	fibronectin 1	protein-coding
mm_68382.1	chr7	109175359	109175369	-	1	NA	promoter-TSS (NM_001302205)	promoter-TSS (NM_001302205)	-157	NM_001302205	109594	Mm.360145	NM_057173	ENSMUSG00000036111	Lmo1	Rbtn-1|Rbtn1|Ttg1	LIM domain only 1	protein-coding
mm_41450.1	chr5	90905445	90905456	+	1	NA	3' UTR (NM_009140, exon 4 of 4)	3' UTR (NM_009140, exon 4 of 4)	1551	NM_009140	20310	Mm.4979	NM_009140	ENSMUSG00000058427	Cxcl2	CINC-2a|GROb|Gro2|MIP-2|MIP-2a|Mgsa-b|Mip2|Scyb|Scyb2	chemokine (C-X-C motif) ligand 2	protein-coding
mm_45267.1	chr5	64467937	64467947	-	1	NA	promoter-TSS (NR_040681)	promoter-TSS (NR_040681)	0	NR_040681	69999	Mm.261413	NR_040681	ENSMUSG00000100911	1700027F09Rik	-	RIKEN cDNA 1700027F09 gene	ncRNA
mm_59189.1	chr7	24475304	24475320	+	1	NA	exon (NM_011113, exon 7 of 7)	exon (NM_011113, exon 7 of 7)	-6711	NM_153112	260299	Mm.178322	NM_153112	ENSMUSG00000054793	Cadm4	Igdf4c|Igsf4c|Tsll2	cell adhesion molecule 4	protein-coding
mm_166032.1	chr4	126753295	126753307	-	1	NA	promoter-TSS (NM_001035526)	promoter-TSS (NM_001035526)	128	NM_011986	26562	Mm.206206	NM_011986	ENSMUSG00000028833	Ncdn	AU042419|MMS10-AE|Ms10ae|mKIAA0607|norbin	neurochondrin	protein-coding
mm_169124.1	chr13	53160429	53160445	-	1	NA	intron (NM_013846, intron 1 of 8)	ORR1A1|LTR|ERVL-MaLR	125672	NM_013846	26564	Mm.342774	NM_013846	ENSMUSG00000021464	Ror2	Ntrkr2|mRor2	receptor tyrosine kinase-like orphan receptor 2	protein-coding
mm_51294.1	chr6	72305981	72306029	+	1	NA	intron (NM_147779, intron 4 of 11)	intron (NM_147779, intron 4 of 11)	1395	NM_147779	20388	Mm.46033	NM_147779	ENSMUSG00000056370	Sftpb	AI562151|SF-B|SP-B|Sftp-3|Sftp3	surfactant associated protein B	protein-coding
mm_104823.1	chr11	99003560	99003563	-	1	NA	exon (NM_011623, exon 23 of 36)	exon (NM_011623, exon 23 of 36)	-20545	NM_178596	353155	Mm.453253	NM_178596	ENSMUSG00000047197	Gjd3	Gja11|Gjc1|cx30.2	gap junction protein, delta 3	protein-coding
mm_119788.1	chr14	54192302	54192315	+	1	NA	Intergenic	Intergenic	61621	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_68242.1	chr7	105399992	105400023	-	1	NA	promoter-TSS (NM_199009)	promoter-TSS (NM_199009)	47	NM_001242364	74349	Mm.30254	NM_199009	ENSMUSG00000044465	Fam160a2	4632419K20Rik|6530415H11Rik|FHIP	family with sequence similarity 160, member A2	protein-coding
mm_113774.1	chr13	44874355	44874377	+	1	NA	exon (NM_001205043, exon 4 of 18)	exon (NM_001205043, exon 4 of 18)	127730	NM_025772	94245	Mm.352311	NM_025772	ENSMUSG00000057531	Dtnbp1	5430437B18Rik|AW048963|Bloc1s8|dysbindin|sdy	dystrobrevin binding protein 1	protein-coding
mm_149103.1	chr19	8942522	8942542	+	1	NA	TTS (NM_144872)	TTS (NM_144872)	612	NM_011842	23942	Mm.25339	NM_011842	ENSMUSG00000071646	Mta2	AW550797|Mata1l1|Mta1l1|mmta2	metastasis-associated gene family, member 2	protein-coding
mm_78202.1	chr9	21380611	21380613	+	1	NA	intron (NM_001277322, intron 2 of 21)	L3|LINE|CR1	12080	NM_001277322	16201	Mm.440026	NM_010561	ENSMUSG00000032178	Ilf3	MBII-26|MPHOSPH4|NF90|NFAR	interleukin enhancer binding factor 3	protein-coding
mm_133628.1	chr16	91647061	91647106	+	1	NA	promoter-TSS (NM_019973)	promoter-TSS (NM_019973)	-111	NM_010256	14450	Mm.4505	NM_010256	ENSMUSG00000022962	Gart	Gaps|Prgs	phosphoribosylglycinamide formyltransferase	protein-coding
mm_157346.1	chrX	36979671	36979671	-	1	NA	intron (NM_001177323, intron 1 of 9)	intron (NM_001177323, intron 1 of 9)	10024	NM_001177324	56526	Mm.260036	NM_019942	ENSMUSG00000050379	Sept6	2810035H17Rik|C920001C06Rik|Sep6|mKIAA0128	septin 6	protein-coding
mm_128046.1	chr15	25413753	25413773	-	1	NA	promoter-TSS (NM_027395)	promoter-TSS (NM_027395)	1	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	brain abundant, membrane attached signal protein 1	protein-coding
mm_35790.1	chr4	46506830	46506843	-	1	NA	3' UTR (NM_029077, exon 6 of 6)	3' UTR (NM_029077, exon 6 of 6)	17507	NM_053179	94181	Mm.249349	NM_053179	ENSMUSG00000028334	Nans	4632418E04Rik|BB056474|Sas	N-acetylneuraminic acid synthase (sialic acid synthase)	protein-coding
mm_92753.1	chr10	81025522	81025559	-	1	NA	promoter-TSS (NM_145217)	promoter-TSS (NM_145217)	-163	NM_145217	208666	Mm.44995	NM_145217	ENSMUSG00000043670	Diras1	Di-Ras1|Gbts1|RIG	DIRAS family, GTP-binding RAS-like 1	protein-coding
mm_80387.1	chr9	75625400	75625420	+	1	NA	promoter-TSS (NM_027309)	promoter-TSS (NM_027309)	-322	NM_027309	70082	Mm.19119	NM_027309	ENSMUSG00000032184	Lysmd2	2210402C18Rik|AV033872|AW538442	LysM, putative peptidoglycan-binding, domain containing 2	protein-coding
mm_167261.1	chr8	26717319	26717321	+	1	NA	Intergenic	Intergenic	107103	NR_045904	72316	Mm.490534	NR_045904	ENSMUSG00000100335	2310008N11Rik	-	RIKEN cDNA 2310008N11 gene	ncRNA
mm_46365.1	chr5	103377333	103377338	-	1	NA	Intergenic	Intergenic	-47857	NM_011204	19249	Mm.3414	NM_011204	ENSMUSG00000034573	Ptpn13	AI324989|PTP-BL|PTPL1|Ptpri|RIP	protein tyrosine phosphatase, non-receptor type 13	protein-coding
mm_149808.1	chr19	23759013	23759025	+	1	NA	5' UTR (NM_177034, exon 1 of 13)	5' UTR (NM_177034, exon 1 of 13)	143	NM_177034	319924	Mm.22879	NM_177034	ENSMUSG00000024897	Apba1	6430513E09Rik|Lin-10|Mint|Mint1|Urop11|X11|X11alpha	amyloid beta (A4) precursor protein binding, family A, member 1	protein-coding
mm_48759.1	chr5	148330110	148330121	-	1	NA	3' UTR (NM_007513, exon 13 of 13)	3' UTR (NM_007513, exon 13 of 13)	62700	NM_001301424	11987	Mm.275489	NM_007513	ENSMUSG00000041313	Slc7a1	4831426K01Rik|AI447493|Atrc-1|Atrc1|Cat1|Rec-1|Rev-1|mCAT-1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 1	protein-coding
mm_56533.1	chr6	99585257	99585260	-	1	NA	Intergenic	B1_Mur1|SINE|Alu	-64265	NM_001347345	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_139830.1	chr17	69127400	69127409	+	1	NA	Intergenic	Intergenic	-29406	NM_013813	13823	Mm.131135	NM_013813	ENSMUSG00000024044	Epb41l3	4.1B|DAL1P|Dal1|Epb4.1l3|NBL3	erythrocyte membrane protein band 4.1 like 3	protein-coding
mm_13437.1	chr2	105126610	105126629	+	1	NA	promoter-TSS (NM_144783)	promoter-TSS (NM_144783)	90	NM_144783	22431	Mm.389339	NM_144783	ENSMUSG00000016458	Wt1	D630046I19Rik|Wt-1	Wilms tumor 1 homolog	protein-coding
mm_156413.1	chrX	140664698	140664729	+	1	NA	Intergenic	Intergenic	-13315	NM_011845	23947	Mm.131097	NM_011845	ENSMUSG00000000266	Mid2	FXY2|Trim1	midline 2	protein-coding
mm_4771.1	chr1	182564995	182565010	+	1	NA	promoter-TSS (NM_001145806)	promoter-TSS (NM_001145806)	-5	NM_001145806	170725	Mm.189201	NM_130890	ENSMUSG00000038599	Capn8	nCL-2|nCL-2'	calpain 8	protein-coding
mm_11989.1	chr2	55437191	55437201	+	1	NA	5' UTR (NM_001304810, exon 2 of 3)	5' UTR (NM_001304810, exon 2 of 3)	1226	NM_008426	16519	Mm.5127	NM_008426	ENSMUSG00000026824	Kcnj3	GIRK-1|GIRK1|Kcnf3|Kir3.1	potassium inwardly-rectifying channel, subfamily J, member 3	protein-coding
mm_132259.1	chr16	32755635	32755640	+	1	NA	exon (NM_080457, exon 4 of 27)	exon (NM_080457, exon 4 of 27)	19751	NM_080457	140474	Mm.214599	NM_080457	ENSMUSG00000079620	Muc4	4933405I11Rik|Asgp	mucin 4	protein-coding
mm_112089.1	chr12	112674775	112674814	-	1	NA	promoter-TSS (NM_001165894)	promoter-TSS (NM_001165894)	90	NM_001331107	11651	Mm.6645	NM_009652	ENSMUSG00000001729	Akt1	Akt|LTR-akt|PKB|PKB/Akt|PKBalpha|Rac	thymoma viral proto-oncogene 1	protein-coding
mm_16686.1	chr2	6884583	6884603	-	1	NA	intron (NM_001110229, intron 2 of 14)	intron (NM_001110229, intron 2 of 14)	403	NM_010160	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_76050.1	chr8	77689120	77689126	-	1	NA	exon (NM_010332, exon 3 of 8)	exon (NM_010332, exon 3 of 8)	35329	NM_010332	13617	Mm.283168	NM_010332	ENSMUSG00000031616	Ednra	ET-AR|ETa|Gpcr10	endothelin receptor type A	protein-coding
mm_138568.1	chr17	35379609	35379637	+	1	NA	promoter-TSS (NM_001143689)	promoter-TSS (NM_001143689)	6	NM_001143689	15015	Mm.464284	NM_001143689	ENSMUSG00000035929	H2-Q4	H-2Q4|H2-Gs10|Qa-4|Qa4|Qat-4|Qb-1|Qb1	histocompatibility 2, Q region locus 4	protein-coding
mm_18784.1	chr2	73659998	73660067	-	1	NA	5' UTR (NM_175752, exon 1 of 7)	5' UTR (NM_175752, exon 1 of 7)	391	NM_175752	108699	Mm.257073	NM_029716	ENSMUSG00000056486	Chn1	0610007I19Rik|0710001E19Rik|1700112L09Rik|2900046J01Rik|AI413815|ARHGAP2	chimerin 1	protein-coding
mm_67457.1	chr7	80402744	80402757	-	1	NA	promoter-TSS (NM_011046)	promoter-TSS (NM_011046)	62	NM_011046	18550	Mm.5241	NM_011046	ENSMUSG00000030530	Furin	9130404I01Rik|Fur|PACE|Pcsk3|SPC1	furin (paired basic amino acid cleaving enzyme)	protein-coding
mm_165177.1	chr2	27714280	27714294	-	1	NA	intron (NM_001290482, intron 1 of 9)	intron (NM_001290482, intron 1 of 9)	3704	NM_001290482	20181	Mm.24624	NM_011305	ENSMUSG00000015846	Rxra	9530071D11Rik|Nr2b1|RXRalpha1	retinoid X receptor alpha	protein-coding
mm_20817.1	chr2	144527527	144527537	-	1	NA	promoter-TSS (NM_029763)	promoter-TSS (NM_029763)	-134	NM_172859	241688	Mm.442156	NM_172859	ENSMUSG00000037259	Dzank1	2810039F03Rik|6330439K17Rik|6430408C01|AI851115|Ankrd64	double zinc ribbon and ankyrin repeat domains 1	protein-coding
mm_8459.1	chr1	153186126	153186136	-	1	NA	intron (NM_008485, intron 1 of 23)	CpG	316	NM_008485	16782	Mm.329272	NM_008485	ENSMUSG00000026479	Lamc2	AA589349	laminin, gamma 2	protein-coding
mm_4195.1	chr1	171225712	171225751	+	1	NA	exon (NM_013474, exon 3 of 4)	exon (NM_013474, exon 3 of 4)	677	NM_013474	11807	Mm.389209	NM_013474	ENSMUSG00000005681	Apoa2	Alp-2|Apo-AII|ApoA-II|ApoAII|Apoa-2|Hdl-1	apolipoprotein A-II	protein-coding
mm_81566.1	chr9	110419807	110419809	+	1	NA	promoter-TSS (NM_008694)	promoter-TSS (NM_008694)	0	NM_008694	18054	Mm.236225	NM_008694	ENSMUSG00000032484	Ngp	bectenecin	neutrophilic granule protein	protein-coding
mm_78127.1	chr9	20652108	20652138	+	1	NA	promoter-TSS (NM_023371)	promoter-TSS (NM_023371)	-7	NM_023371	23988	Mm.7906	NM_023371	ENSMUSG00000032171	Pin1	0610025L01Rik|D9Bwg1161e	protein (peptidyl-prolyl cis/trans isomerase) NIMA-interacting 1	protein-coding
mm_39745.1	chr5	29569464	29569481	+	1	NA	5' UTR (NM_133907, exon 1 of 23)	5' UTR (NM_133907, exon 1 of 23)	230	NM_133907	100763	Mm.137746	NM_133907	ENSMUSG00000039000	Ube3c	AI853514|mKIAA0010	ubiquitin protein ligase E3C	protein-coding
mm_2444.1	chr1	98693477	98693495	+	1	NA	Intergenic	(T)n|Simple_repeat|Simple_repeat	272362	NM_027584	70866	Mm.389164	NM_027584	ENSMUSG00000026336	Slco6d1	4921511I05Rik	solute carrier organic anion transporter family, member 6d1	protein-coding
mm_154920.1	chrX	23115593	23115595	+	1	NA	Intergenic	Intergenic	151208	NM_001310466	67455	Mm.224306	NM_026167	ENSMUSG00000036782	Klhl13	1200009K10Rik|AI451128|Bklhd2|D130072F20Rik	kelch-like 13	protein-coding
mm_106415.1	chr11	119133791	119133802	-	1	NA	Intergenic	Intergenic	20341	NR_105899	102465563		NR_105899	ENSMUSG00000098704	Mir6934	Gm27523|mmu-mir-6934	microRNA 6934	ncRNA
mm_137935.1	chr17	32659022	32659041	+	1	NA	promoter-TSS (NM_001101588)	promoter-TSS (NM_001101588)	-452	NM_001101588	631304	Mm.328950	NM_001101588	ENSMUSG00000090700	Cyp4f40	EG631304	cytochrome P450, family 4, subfamily f, polypeptide 40	protein-coding
mm_159127.1	chr2	74659517	74659517	-	1	NA	promoter-TSS (NM_007967)	promoter-TSS (NM_007967)	40	NM_007967	14029	Mm.25365	NM_007967	ENSMUSG00000001815	Evx2	Evx-2	even-skipped homeobox 2	protein-coding
mm_29377.1	chr3	108798052	108798055	-	1	NA	intron (NM_011504, intron 16 of 18)	intron (NM_011504, intron 16 of 18)	42449	NM_011504	20912	Mm.316894	NM_011504	ENSMUSG00000027882	Stxbp3	Munc-18c|Stxbp3a|Sxtbp3|Unc18-3	syntaxin binding protein 3	protein-coding
mm_56153.1	chr6	87844018	87844088	-	1	NA	exon (NM_013493, exon 5 of 5)	exon (NM_013493, exon 5 of 5)	-5294	NM_133934	57905	Mm.241546	NM_133934	ENSMUSG00000030056	Isy1	5830446M03Rik|AI181014|AU020769	ISY1 splicing factor homolog	protein-coding
mm_87676.1	chr10	59136869	59136893	+	1	NA	3' UTR (NM_172788, exon 10 of 10)	3' UTR (NM_172788, exon 10 of 10)	84966	NM_001024911	103080	Mm.346842	NM_001024910	ENSMUSG00000019917	Sept10	4921515A04Rik|9430099J10Rik|AA408298|AI874685	septin 10	protein-coding
mm_128573.1	chr15	57696095	57696115	-	1	NA	intron (NM_199449, intron 1 of 3)	intron (NM_199449, intron 1 of 3)	1438	NM_199449	387609	Mm.36557	NM_199449	ENSMUSG00000071757	Zhx2	Afr-1|Afr1|Raf|mKIAA0854	zinc fingers and homeoboxes 2	protein-coding
mm_45644.1	chr5	76951208	76951232	-	1	NA	promoter-TSS (NM_025939)	promoter-TSS (NM_025939)	-191	NM_025939	67054	Mm.182931	NM_025939	ENSMUSG00000029247	Paics	2610511I09Rik|ADE2H1|AIRC|PAIS	phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoribosylaminoimidazole, succinocarboxamide synthetase	protein-coding
mm_158355.1	chrX	134595232	134595243	-	1	NA	exon (NM_013463, exon 3 of 7)	exon (NM_013463, exon 3 of 7)	5768	NM_013463	11605	Mm.1114	NM_013463	ENSMUSG00000031266	Gla	Ags	galactosidase, alpha	protein-coding
mm_151652.1	chr19	4118511	4118529	-	1	NA	intron (NM_001276284, intron 1 of 5)	L2b|LINE|L2	3055	NM_001276284	11632	Mm.10433	NM_016666	ENSMUSG00000024847	Aip	AA408703|AW476050|Ara9|D19Bwg1412e|Fkbp16|Xap2	aryl-hydrocarbon receptor-interacting protein	protein-coding
mm_95445.1	chr11	50237003	50237014	+	1	NA	intron (NR_132732, intron 4 of 4)	CpG	1524	NM_001313968	17001	Mm.245151	NM_008521	ENSMUSG00000020377	Ltc4s	-	leukotriene C4 synthase	protein-coding
mm_88639.1	chr10	79927331	79927370	+	1	NA	promoter-TSS (NM_001288625)	promoter-TSS (NM_001288625)	9	NM_001288625	13496	Mm.301282	NM_007880	ENSMUSG00000019564	Arid3a	Bright|Dri1|Dril1	AT rich interactive domain 3A (BRIGHT-like)	protein-coding
mm_122319.1	chr14	36935547	36935553	-	1	NA	promoter-TSS (NM_028407)	promoter-TSS (NM_028407)	18	NM_028407	72972	Mm.27621	NM_027045	ENSMUSG00000058690	Ccser2	1700012P13Rik|2900054P12Rik|AI035535|AW108503|Fam190b|Gcap14	coiled-coil serine rich 2	protein-coding
mm_127373.1	chr15	100790444	100790456	+	1	NA	intron (NM_001347102, intron 8 of 23)	intron (NM_001347102, intron 8 of 23)	9196	NM_001347102	59033	Mm.209856	NM_021530	ENSMUSG00000023032	Slc4a8	AW493845|C230026C11|NDCBE|kNBC-3	solute carrier family 4 (anion exchanger), member 8	protein-coding
mm_153733.1	chr19	44410458	44410466	-	1	NA	Intergenic	Intergenic	-2753	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_7097.1	chr1	88702029	88702039	-	1	NA	5' UTR (NM_177305, exon 1 of 1)	5' UTR (NM_177305, exon 1 of 1)	157	NM_177305	320982	Mm.27968	NM_177305	ENSMUSG00000049866	Arl4c	A630084M22Rik|Arl7|LAK	ADP-ribosylation factor-like 4C	protein-coding
mm_86503.1	chr10	7212335	7212362	+	1	NA	promoter-TSS (NM_172546)	promoter-TSS (NM_172546)	-111	NM_172546	215748	Mm.37984	NM_172546	ENSMUSG00000015202	Cnksr3	6820402C05|BC024086|Magi1	Cnksr family member 3	protein-coding
mm_89462.1	chr10	93309886	93309891	+	1	NA	intron (NM_013508, intron 1 of 4)	intron (NM_013508, intron 1 of 4)	1271	NM_001322268	13713	Mm.4454	NM_013508	ENSMUSG00000008398	Elk3	D430049E23Rik|Erp|Etrp|Net|Sap-2	ELK3, member of ETS oncogene family	protein-coding
mm_114241.1	chr13	56623549	56623580	+	1	NA	exon (NM_009369, exon 3 of 17)	exon (NM_009369, exon 3 of 17)	13961	NM_009369	21810	Mm.14455	NM_009369	ENSMUSG00000035493	Tgfbi	68kDa|AI181842|AI747162|Beta-ig|big-h3	transforming growth factor, beta induced	protein-coding
mm_3671.1	chr1	153665491	153665504	+	1	NA	promoter-TSS (NM_001347115)	promoter-TSS (NM_001347115)	-176	NM_001347115	67792	Mm.379143	NM_026380	ENSMUSG00000042671	Rgs8	6530413N01Rik	regulator of G-protein signaling 8	protein-coding
mm_138243.1	chr17	34564347	34564360	+	1	NA	promoter-TSS (NM_010929)	promoter-TSS (NM_010929)	58	NM_010929	18132	Mm.173813	NM_010929	ENSMUSG00000015468	Notch4	Int-3|Int3|N4	notch 4	protein-coding
mm_28736.1	chr3	95736686	95736719	-	1	NA	exon (NM_007899, exon 7 of 11)	exon (NM_007899, exon 7 of 11)	-1729	NR_105981	102466787		NR_105981	ENSMUSG00000098737	Mir7014	Gm27837|mmu-mir-7014	microRNA 7014	ncRNA
mm_119021.1	chr14	30009096	30009110	+	1	NA	promoter-TSS (NM_019583)	promoter-TSS (NM_019583)	103	NM_001136240	218865	Mm.259916	NM_172264	ENSMUSG00000015970	Chdh	AU041472|D630034H06Rik	choline dehydrogenase	protein-coding
mm_72668.1	chr8	84903572	84903607	+	1	NA	intron (NM_010635, intron 2 of 2)	CpG-14292	1661	NM_010635	16596	Mm.4847	NM_010635	ENSMUSG00000054191	Klf1	Eklf|Nan	Kruppel-like factor 1 (erythroid)	protein-coding
mm_68601.1	chr7	116237768	116237781	-	1	NA	promoter-TSS (NM_001305186)	promoter-TSS (NM_001305186)	2	NM_001305186	233765	Mm.3741	NM_172743	ENSMUSG00000045659	Plekha7	A430081P20Rik|AI414265	pleckstrin homology domain containing, family A member 7	protein-coding
mm_12584.1	chr2	73450591	73450612	+	1	NA	intron (NM_153138, intron 1 of 7)	intron (NM_153138, intron 1 of 7)	3288	NM_001289722	215280	Mm.223504	NM_153138	ENSMUSG00000075284	Wipf1	AI115543|D2Ertd120e|WIP|Waspip	WAS/WASL interacting protein family, member 1	protein-coding
mm_16474.1	chr2	180732229	180732271	+	1	NA	intron (NM_183161, intron 2 of 12)	intron (NM_183161, intron 2 of 12)	6911	NM_183161	228993	Mm.87189	NM_183161	ENSMUSG00000023393	Slc17a9	1700019H03Rik|BC019537|Vnut	solute carrier family 17, member 9	protein-coding
mm_119205.1	chr14	32856818	32856830	+	1	NA	promoter-TSS (NM_178791)	promoter-TSS (NM_178791)	68	NM_178791	320736	Mm.187910	NM_178791	ENSMUSG00000050666	Vstm4	E130203B14Rik	V-set and transmembrane domain containing 4	protein-coding
mm_42806.1	chr5	121748170	121748173	+	1	NA	intron (NM_009125, intron 4 of 24)	intron (NM_009125, intron 4 of 24)	36562	NM_009125	20239	Mm.260900	NM_009125	ENSMUSG00000042605	Atxn2	9630045M23Rik|ATX2|AW544490|Sca2	ataxin 2	protein-coding
mm_49022.1	chr6	4759511	4759524	+	1	NA	3' UTR (NM_130877, exon 2 of 2)	3' UTR (NM_130877, exon 2 of 2)	12211	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_94465.1	chr11	6474963	6475025	+	1	NA	exon (NM_011221, exon 1 of 1)	exon (NM_011221, exon 1 of 1)	1082	NM_011221	19291	Mm.296150	NM_011221	ENSMUSG00000094483	Purb	2310015K15Rik|AA114818|Cager-2|D11Bwg0414e	purine rich element binding protein B	protein-coding
mm_99085.1	chr11	99417276	99417307	+	1	NA	intron (NM_010661, intron 6 of 7)	intron (NM_010661, intron 6 of 7)	4968	NM_010661	268482	Mm.436651	NM_010661	ENSMUSG00000020912	Krt12	AI835216|K12|Krt-12|Krt1-12	keratin 12	protein-coding
mm_165583.1	chr3	29268527	29268529	+	1	NA	intron (NM_001167748, intron 4 of 12)	Lx8|LINE|L1	-148295	NR_030422	791072		NR_030422	ENSMUSG00000076120	Mir551b	Mirn551b|mir-551b	microRNA 551b	ncRNA
mm_1941.1	chr1	86303226	86303239	+	1	NA	promoter-TSS (NM_145222)	promoter-TSS (NM_145222)	11	NM_145222	227327	Mm.86467	NM_145222	ENSMUSG00000079445	B3gnt7	C330001H22Rik|beta-3GnT7	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 7	protein-coding
mm_53231.1	chr6	127233725	127233740	+	1	NA	Intergenic	Intergenic	74235	NR_073373	232386	Mm.257367	NR_073373	ENSMUSG00000107153	Gm38404	D130058E03	predicted gene, 38404	ncRNA
mm_151135.1	chr19	51792201	51792203	+	1	NA	Intergenic	Intergenic	-472095	NM_008386	16333	Mm.46269	NM_008386	ENSMUSG00000035804	Ins1	Ins-1|Ins2-rs1	insulin I	protein-coding
mm_89886.1	chr10	108543105	108543110	+	1	NA	intron (NM_001252341, intron 10 of 11)	ORR1A2|LTR|ERVL-MaLR	157053	NM_203660	368203	Mm.452758	NM_203660		Gm5136	C6.1AL|EG368203	predicted gene 5136	protein-coding
mm_106297.1	chr11	118219055	118219062	-	1	NA	intron (NM_001112699, intron 1 of 12)	intron (NM_001112699, intron 1 of 12)	-6316	NM_001112700	19157	Mm.86413	NM_011180	ENSMUSG00000017132	Cyth1	CLM1|CTH-1|CYTIP|Pscd1	cytohesin 1	protein-coding
mm_46144.1	chr5	93192943	93192946	-	1	NA	intron (NM_017367, intron 2 of 6)	intron (NM_017367, intron 2 of 6)	13551	NM_017367	12453	Mm.250419	NM_017367	ENSMUSG00000063015	Ccni	-	cyclin I	protein-coding
mm_8356.1	chr1	150393025	150393079	-	1	NA	promoter-TSS (NM_145511)	promoter-TSS (NM_145511)	3	NM_001077237	226499	Mm.222093	NM_145511	ENSMUSG00000006010	BC003331	1810053E15Rik|Odr4|odr-4	cDNA sequence BC003331	protein-coding
mm_163873.1	chr14	19419311	19419349	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	183257	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_139863.1	chr17	70521713	70521738	+	1	NA	promoter-TSS (NM_001128180)	promoter-TSS (NM_001128180)	-169	NM_001347414	224997	Mm.311840	NM_027712	ENSMUSG00000003279	Dlgap1	4933422O14Rik|9630002F18|AI845682|AI848168|BB075781|D17Bwg0511e|GKAP/SAPAP|GKPA/SAPAP|Gkap|Sapap1|mKIAA4162	discs, large (Drosophila) homolog-associated protein 1	protein-coding
mm_29403.1	chr3	108905524	108905526	-	1	NA	intron (NM_025845, intron 4 of 5)	intron (NM_025845, intron 4 of 5)	6179	NM_025845	66921	Mm.51049	NM_025845	ENSMUSG00000027881	Prpf38b	1110021E09Rik|AU018955	PRP38 pre-mRNA processing factor 38 (yeast) domain containing B	protein-coding
mm_52909.1	chr6	122819940	122819950	+	1	NA	promoter-TSS (NM_021899)	promoter-TSS (NM_021899)	-239	NM_021899	60611	Mm.87142	NM_021899	ENSMUSG00000003154	Foxj2	Fhx	forkhead box J2	protein-coding
mm_146093.1	chr18	73859367	73859399	+	1	NA	promoter-TSS (NM_001305882)	promoter-TSS (NM_001305882)	-2	NM_027741	71263	Mm.126220	NM_027741	ENSMUSG00000064036	Mro	4930507C04Rik|4933435E20Rik	maestro	protein-coding
mm_4899.1	chr1	189785260	189785272	+	1	NA	intron (NM_008976, intron 1 of 18)	intron (NM_008976, intron 1 of 18)	56998	NM_008976	19250	Mm.4498	NM_008976	ENSMUSG00000026604	Ptpn14	C130080N23Rik|OTTMUSG00000022087|PTP36	protein tyrosine phosphatase, non-receptor type 14	protein-coding
mm_142159.1	chr17	36111675	36111696	-	1	NA	promoter-TSS (NM_001271005)	promoter-TSS (NM_001271005)	-9	NM_001271005	667803	Mm.477808	NM_001271005		H2-T-ps	C920025E04Rik|H2-T11	histocompatibility 2, T region locus, pseudogene	protein-coding
mm_34859.1	chr4	155546856	155546869	+	1	NA	intron (NM_001160016, intron 7 of 11)	Tigger5b|DNA|TcMar-Tigger	-15530	NM_138671	192185	Mm.28347	NM_138671	ENSMUSG00000029063	Nadk	4432404C02Rik|BC004012	NAD kinase	protein-coding
mm_102877.1	chr11	69409885	69409906	-	1	NA	intron (NM_001017426, intron 1 of 22)	intron (NM_001017426, intron 1 of 22)	3780	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_93092.1	chr10	89647024	89647035	-	1	NA	intron (NM_198021, intron 13 of 17)	intron (NM_198021, intron 13 of 17)	-25780	NM_182959	216227	Mm.233921	NM_182959	ENSMUSG00000019935	Slc17a8	BC042593|Vglut3	solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 8	protein-coding
mm_123753.1	chr14	70195998	70196009	-	1	NA	intron (NM_001271408, intron 5 of 20)	intron (NM_001271408, intron 5 of 20)	-3757	NM_001271409	20410	Mm.5068	NM_011366	ENSMUSG00000022091	Sorbs3	SCAM-1|SH3P3|Sh3d4|vinexin-g	sorbin and SH3 domain containing 3	protein-coding
mm_120830.1	chr14	75176634	75176643	+	1	NA	intron (NM_008879, intron 1 of 16)	intron (NM_008879, intron 1 of 16)	40213	NM_008879	18826	Mm.153911	NM_008879	ENSMUSG00000021998	Lcp1	AW536232|D14Ertd310e|LCP-1|Pls2|pp65	lymphocyte cytosolic protein 1	protein-coding
mm_65836.1	chr7	29213958	29213983	-	1	NA	promoter-TSS (NM_001164658)	promoter-TSS (NM_001164658)	63	NM_001164658	320225	Mm.349382	NM_001039721	ENSMUSG00000049676	Catsperg1	A230107C01Rik|Catsperg	catsper channel auxiliary subunit gamma 1	protein-coding
mm_282.1	chr1	21262836	21262868	+	1	NA	exon (NM_010356, exon 6 of 7)	exon (NM_010356, exon 6 of 7)	22267	NM_010356	14859	Mm.394593	NM_010356	ENSMUSG00000025934	Gsta3	Gst2-3	glutathione S-transferase, alpha 3	protein-coding
mm_9360.1	chr1	172198175	172198202	-	1	NA	3' UTR (NM_001329871, exon 4 of 4)	3' UTR (NM_001329871, exon 4 of 4)	8616	NM_001329871	18611	Mm.544	NM_011063	ENSMUSG00000013698	Pea15a	Mat1|PEA-15|Pea15|Pkcs15	phosphoprotein enriched in astrocytes 15A	protein-coding
mm_157923.1	chrX	79517334	79517376	-	1	NA	promoter-TSS (NM_001099307)	promoter-TSS (NM_001099307)	-70	NM_001099307	636104	Mm.459420	NM_001099307	ENSMUSG00000073077	Gm7173	EG636104	predicted gene 7173	protein-coding
mm_139636.1	chr17	57376017	57376033	+	1	NA	intron (NM_010130, intron 2 of 21)	Lx4A|LINE|L1	17339	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_53288.1	chr6	128992972	128993054	+	1	NA	promoter-TSS (NR_015455)	promoter-TSS (NR_015455)	52	NR_015455	408064	Mm.172429	NR_015455		BC064078	-	cDNA sequence BC064078	ncRNA
mm_6237.1	chr1	66945362	66945416	-	1	NA	promoter-TSS (NM_021285)	promoter-TSS (NM_021285)	-333	NM_021285	17901	Mm.1000	NM_021285	ENSMUSG00000061816	Myl1	AI325107|MLC1f|MLC3f|Mylf	myosin, light polypeptide 1	protein-coding
mm_139809.1	chr17	66470737	66470747	+	1	NA	Intergenic	Intergenic	-20992	NM_001114098	68617	Mm.33421	NM_172963	ENSMUSG00000052105	Mtcl1	1110012J17Rik|Ccdc165|D130071O13|Kiaa0802|Soga2|mKIAA0802|t8219b25	microtubule crosslinking factor 1	protein-coding
mm_15730.1	chr2	164189598	164189600	+	1	NA	3' UTR (NM_138684, exon 3 of 3)	3' UTR (NM_138684, exon 3 of 3)	959	NM_138684	192200	Mm.6433	NM_138684	ENSMUSG00000042845	Wfdc12	Swam2|WAP2	WAP four-disulfide core domain 12	protein-coding
mm_32779.1	chr4	116708468	116708472	+	1	NA	promoter-TSS (NM_026714)	promoter-TSS (NM_026714)	-85	NM_025962	67096	Mm.252785	NM_025962	ENSMUSG00000028690	Mmachc	1810037K07Rik|CblC	methylmalonic aciduria cblC type, with homocystinuria	protein-coding
mm_16125.1	chr2	170176033	170176069	+	1	NA	Intergenic	RSINE1|SINE|B4	-33376	NM_001159683	228913	Mm.22858	NM_001033299	ENSMUSG00000052056	Zfp217	4933431C08Rik|AW987152|Gm562|ZABC1|Znf217	zinc finger protein 217	protein-coding
mm_53233.1	chr6	127446793	127446803	+	1	NA	promoter-TSS (NM_001346513)	promoter-TSS (NM_001346513)	-42	NM_001346513	101187	Mm.110818	NM_181402	ENSMUSG00000037997	Parp11	5330431N24Rik|AI851877|ARTD11|HIN1L|PARP-11	poly (ADP-ribose) polymerase family, member 11	protein-coding
mm_129672.1	chr15	81365334	81365362	-	1	NA	3' UTR (NM_133726, exon 12 of 12)	3' UTR (NM_133726, exon 12 of 12)	-4583	NM_011399	20524	Mm.222536	NM_011399	ENSMUSG00000022404	Slc25a17	34kDa|47kDa|PMP34|Pmp47	solute carrier family 25 (mitochondrial carrier, peroxisomal membrane protein), member 17	protein-coding
mm_124795.1	chr15	8169068	8169105	+	1	NA	promoter-TSS (NM_001162906)	promoter-TSS (NM_001162906)	-20	NM_001162906	73692	Mm.164436	NM_001162906	ENSMUSG00000039801	2410089E03Rik	4732468D17Rik|Hug|Jbts17|b2b012Clo	RIKEN cDNA 2410089E03 gene	protein-coding
mm_103979.1	chr11	84823719	84823729	-	1	NA	intron (NM_177564, intron 2 of 6)	intron (NM_177564, intron 2 of 6)	-4209	NM_145433	217038	Mm.280825	NM_145433	ENSMUSG00000018405	Mrm1	A530065E19Rik|ENSMUSG00000054212	mitochondrial rRNA methyltransferase 1	protein-coding
mm_128915.1	chr15	73676444	73676461	-	1	NA	Intergenic	Intergenic	31053	NM_173365	239530	Mm.122997	NM_173365	ENSMUSG00000045281	Gpr20	A430106B11Rik	G protein-coupled receptor 20	protein-coding
mm_142234.1	chr17	37481038	37481051	-	1	NA	3' UTR (NM_008204, exon 4 of 4)	3' UTR (NM_008204, exon 4 of 4)	2485	NM_008204	14990	Mm.329041	NM_008204	ENSMUSG00000016283	H2-M2	H-2M2|Thy19.4	histocompatibility 2, M region locus 2	protein-coding
mm_167163.1	chr7	135716280	135716282	-	1	NA	promoter-TSS (NM_001081117)	promoter-TSS (NM_001081117)	98	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_148490.1	chr19	4153659	4153672	+	1	NA	promoter-TSS (NM_016933)	promoter-TSS (NM_016933)	-981	NM_016933	19265	Mm.271937	NM_016933	ENSMUSG00000045826	Ptprcap	AI605264|CD-45-AP|LPAP|LSM-1	protein tyrosine phosphatase, receptor type, C polypeptide-associated protein	protein-coding
mm_145459.1	chr18	60238931	60238966	+	1	NA	intron (NM_001033767, intron 2 of 2)	intron (NM_001033767, intron 2 of 2)	26871	NM_001033767	240327	Mm.357104	NM_001033767	ENSMUSG00000073555	Gm4951	EG240327|Ifgga2	predicted gene 4951	protein-coding
mm_56497.1	chr6	99266367	99266378	-	1	NA	5' UTR (NM_001197321, exon 1 of 18)	5' UTR (NM_001197321, exon 1 of 18)	143	NM_001197321	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_102062.1	chr11	52253904	52253932	-	1	NA	exon (NM_009331, exon 10 of 10)	exon (NM_009331, exon 10 of 10)	21923	NM_011543	21402	Mm.42944	NM_011543	ENSMUSG00000036309	Skp1a	15kDa|2610043E24Rik|2610206H23Rik|EMC19|OCP-II|OCP2|SKP1|Tceb1l|p19A|p19Skp1	S-phase kinase-associated protein 1A	protein-coding
mm_126267.1	chr15	79109146	79109180	+	1	NA	5' UTR (NM_177461, exon 1 of 16)	5' UTR (NM_177461, exon 1 of 16)	180	NM_177461	27008	Mm.196480	NM_177461	ENSMUSG00000033039	Micall1	AI448246|D15Mit260|D15N2e|EST573322|EST820961|MIRab13|mKIAA1668	microtubule associated monooxygenase, calponin and LIM domain containing -like 1	protein-coding
mm_18660.1	chr2	70509268	70509293	-	1	NA	exon (NM_025744, exon 1 of 13)	exon (NM_025744, exon 1 of 13)	461	NM_025744	66748	Mm.423014	NM_025744	ENSMUSG00000075302	Erich2	4933404M02Rik	glutamate rich 2	protein-coding
mm_20085.1	chr2	120731343	120731349	-	1	NA	intron (NM_026891, intron 1 of 27)	CpG	171	NM_026891	68968	Mm.2289	NM_026891	ENSMUSG00000027284	Cdan1	1500015A01Rik|AI448026|AW492297|CDA-I|CDA1|CDAI	congenital dyserythropoietic anemia, type I (human)	protein-coding
mm_115345.1	chr13	112639466	112639477	+	1	NA	intron (NM_010029, intron 3 of 20)	RMER1B|Other|Other	12839	NM_010029	13206	Mm.12818	NM_010029	ENSMUSG00000021758	Ddx4	AV206478|Mvh|VASA	DEAD (Asp-Glu-Ala-Asp) box polypeptide 4	protein-coding
mm_129565.1	chr15	79546746	79546787	-	1	NA	promoter-TSS (NM_001040187)	promoter-TSS (NM_001040187)	-25	NM_199080	67040	Mm.29644	NM_152806	ENSMUSG00000055065	Ddx17	2610007K22Rik|A430025E01Rik|AI047725|C80929|Gm926|p72	DEAD (Asp-Glu-Ala-Asp) box polypeptide 17	protein-coding
mm_116043.1	chr13	27247829	27247870	-	1	NA	exon (NM_008865, exon 4 of 5)	exon (NM_008865, exon 4 of 5)	5419	NM_008865	18776	Mm.37203	NM_008865	ENSMUSG00000038891	Prl3b1	Csh2|Ghd8|PL|Pl-2|Pl2|mPL-II|mplII	prolactin family 3, subfamily b, member 1	protein-coding
mm_148263.1	chr18	80934055	80934077	-	1	NA	promoter-TSS (NM_015805)	promoter-TSS (NM_015805)	-8	NM_015805	50771	Mm.247138	NM_015805	ENSMUSG00000024566	Atp9b	AA934181|Atpc2b|IIb|MMR	ATPase, class II, type 9B	protein-coding
mm_22596.1	chr3	13884945	13884948	+	1	NA	intron (NM_178631, intron 3 of 9)	intron (NM_178631, intron 3 of 9)	-61426	NM_001163329	76897	Mm.422625	NM_178631	ENSMUSG00000039717	Ralyl	0710005M24Rik	RALY RNA binding protein-like	protein-coding
mm_1188.1	chr1	62703308	62703317	+	1	NA	promoter-TSS (NM_001077407)	promoter-TSS (NM_001077407)	-5	NM_001077406	18187	Mm.266341	NM_010939	ENSMUSG00000025969	Nrp2	1110048P06Rik|Np-2|Np2|Npn-2|Npn2	neuropilin 2	protein-coding
mm_84629.1	chr9	70816980	70816994	-	1	NA	intron (NM_001324473, intron 4 of 8)	intron (NM_001324473, intron 4 of 8)	117821	NM_008280	15450	Mm.390187	NM_008280	ENSMUSG00000032207	Lipc	AI256194|HL|Hpl	lipase, hepatic	protein-coding
mm_70432.1	chr8	11556437	11556466	+	1	NA	promoter-TSS (NM_011919)	promoter-TSS (NM_011919)	-6	NM_011919	26356	Mm.25709	NM_011919	ENSMUSG00000045969	Ing1	2610028J21Rik|AA407184|AI875420|mING1h|p33Ing1|p37Ing1b	inhibitor of growth family, member 1	protein-coding
mm_121267.1	chr14	103098487	103098514	+	1	NA	intron (NM_001347600, intron 1 of 4)	intron (NM_001347600, intron 1 of 4)	504	NM_001347601	50789	Mm.214746	NM_015822	ENSMUSG00000022124	Fbxl3	AU041772|AW212966|FBK|Fbl3a|Fbxl3a|Ovtm|Play68	F-box and leucine-rich repeat protein 3	protein-coding
mm_157143.1	chrX	9460683	9460693	-	1	NA	intron (NM_007807, intron 3 of 12)	intron (NM_007807, intron 3 of 12)	8636	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_97885.1	chr11	83291720	83291748	+	1	NA	promoter-TSS (NR_028363)	promoter-TSS (NR_028363)	35	NR_028363	613254	Mm.383758	NR_028363	ENSMUSG00000093483	AA465934	-	expressed sequence AA465934	ncRNA
mm_95030.1	chr11	32031174	32031186	+	1	NA	intron (NM_001290680, intron 3 of 4)	intron (NM_001290680, intron 3 of 4)	29903	NM_001290681	18197	Mm.3304	NM_008741	ENSMUSG00000020297	Nsg2	-	neuron specific gene family member 2	protein-coding
mm_102505.1	chr11	60727197	60727251	-	1	NA	promoter-TSS (NM_022009)	promoter-TSS (NM_022009)	39	NM_022009	14248	Mm.339755	NM_022009	ENSMUSG00000002812	Flii	3632430F08Rik|Fliih	flightless I actin binding protein	protein-coding
mm_42835.1	chr5	122102897	122102921	+	1	NA	intron (NM_010861, intron 3 of 6)	intron (NM_010861, intron 3 of 6)	1929	NM_010861	17906	Mm.1529	NM_010861	ENSMUSG00000013936	Myl2	MLC-2|MLC-2s/v|MLC-2v|Mlc2v|Mylpc	myosin, light polypeptide 2, regulatory, cardiac, slow	protein-coding
mm_66133.1	chr7	31073679	31073693	-	1	NA	intron (NM_008557, intron 1 of 7)	intron (NM_008557, intron 1 of 7)	3011	NM_008557	17178	Mm.263847	NM_008557	ENSMUSG00000057092	Fxyd3	Mat8	FXYD domain-containing ion transport regulator 3	protein-coding
mm_55684.1	chr6	72616726	72616756	-	1	NA	promoter-TSS (NM_009444)	promoter-TSS (NM_009444)	7	NM_009444	22135	Mm.246563	NM_009444		Tgoln2	TGN38B|TGN41|TGN46|Ttgn2	trans-golgi network protein 2	protein-coding
mm_117266.1	chr13	64408851	64408853	-	1	NA	Intergenic	ORR1C1|LTR|ERVL-MaLR	-23701	NM_053180	105278	Mm.74982	NM_053180	ENSMUSG00000021483	Cdk20	4932702G04Rik|AU019450|AW558027|CDCH|Ccrk|PNQLARE|p42	cyclin-dependent kinase 20	protein-coding
mm_31919.1	chr4	85379331	85379347	+	1	NA	exon (NM_019535, exon 6 of 9)	exon (NM_019535, exon 6 of 9)	173883	NM_019535	20404	Mm.143603	NM_019535	ENSMUSG00000028488	Sh3gl2	9530001L19Rik|AI120490|AW555077|B930049H17Rik|EEN-B1|SH3PA|Sh3d2a	SH3-domain GRB2-like 2	protein-coding
mm_66285.1	chr7	37773526	37773547	-	1	NA	Intergenic	CpG	-3784	NM_172385	243937	Mm.322505	NM_172385	ENSMUSG00000043456	Zfp536	9630010P11Rik|Znf536|mKIAA0390	zinc finger protein 536	protein-coding
mm_46078.1	chr5	92325113	92325134	-	1	NA	exon (NM_008599, exon 3 of 4)	exon (NM_008599, exon 3 of 4)	2956	NM_008599	17329	Mm.766	NM_008599	ENSMUSG00000029417	Cxcl9	BB139920|CMK|Mig|MuMIG|Scyb9|crg-10	chemokine (C-X-C motif) ligand 9	protein-coding
mm_32342.1	chr4	104766309	104766331	+	1	NA	promoter-TSS (NM_133882)	promoter-TSS (NM_133882)	3	NM_001316671	110382	Mm.87072	NM_133882	ENSMUSG00000029656	C8b	4930439B20Rik|AI595927	complement component 8, beta polypeptide	protein-coding
mm_57988.1	chr6	136171824	136171849	-	1	NA	5' UTR (NM_008171, exon 3 of 15)	5' UTR (NM_008171, exon 3 of 15)	1675	NM_008171	14812	Mm.436649	NM_008171	ENSMUSG00000030209	Grin2b	AW490526|GluN2B|NR2B|Nmdar2b	glutamate receptor, ionotropic, NMDA2B (epsilon 2)	protein-coding
mm_82195.1	chr9	123965433	123965451	+	1	NA	intron (NM_009912, intron 1 of 1)	intron (NM_009912, intron 1 of 1)	3250	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_20596.1	chr2	131179986	131180092	-	1	NA	promoter-TSS (NM_007682)	promoter-TSS (NM_007682)	28	NM_007682	12616	Mm.440169	NM_007682	ENSMUSG00000068267	Cenpb	CENP-B	centromere protein B	protein-coding
mm_42731.1	chr5	120621443	120621463	+	1	NA	intron (NM_028041, intron 10 of 19)	MIR|SINE|MIR	8323	NM_028041	71990	Mm.24495	NM_028041	ENSMUSG00000029599	Ddx54	2410015A15Rik|AI414901|DP97	DEAD (Asp-Glu-Ala-Asp) box polypeptide 54	protein-coding
mm_64731.1	chr7	4710018	4710023	-	1	NA	intron (NM_177887, intron 4 of 4)	B3|SINE|B2	15062	NM_001142792	330460	Mm.361851	NM_177887	ENSMUSG00000046456	Tmem150b	A630041N19|Tmem224	transmembrane protein 150B	protein-coding
mm_50561.1	chr6	49047928	49047938	+	1	NA	exon (NM_053110, exon 6 of 11)	exon (NM_053110, exon 6 of 11)	11415	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_169171.1	chr13	65639414	65639430	+	1	NA	Intergenic	Intergenic	360568	NM_178364	170936	Mm.151546	NM_178364	ENSMUSG00000021514	Zfp369	B930030B22Rik|D230020H11Rik|NRIF2	zinc finger protein 369	protein-coding
mm_25535.1	chr3	115674020	115674032	+	1	NA	Intergenic	Intergenic	41029	NM_007901	13609	Mm.982	NM_007901	ENSMUSG00000045092	S1pr1	AI849002|Edg1|Lpb1|S1p|S1p1	sphingosine-1-phosphate receptor 1	protein-coding
mm_93497.1	chr10	112271955	112271964	-	1	NA	exon (NM_001025581, exon 2 of 5)	exon (NM_001025581, exon 2 of 5)	836	NM_001025581	268345	Mm.336242	NM_001025581	ENSMUSG00000035681	Kcnc2	AW047325|B230117I07|KShIIIA|Kv3.2	potassium voltage gated channel, Shaw-related subfamily, member 2	protein-coding
mm_91000.1	chr10	14545197	14545205	-	1	NA	promoter-TSS (NM_001002268)	promoter-TSS (NM_001002268)	-165	NM_001002268	215798	Mm.440142	NM_001002268	ENSMUSG00000039116	Adgrg6	1190004A11Rik|AI449247|AW045736|DREG|Gm222|Gpr126	adhesion G protein-coupled receptor G6	protein-coding
mm_116220.1	chr13	32898148	32898160	-	1	NA	promoter-TSS (NM_173051)	promoter-TSS (NM_173051)	-14	NM_173051	380839	Mm.250802	NM_173051	ENSMUSG00000079049	Serpinb1c	EIC|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 1c	protein-coding
mm_36892.1	chr4	107680772	107680847	-	1	NA	exon (NM_019872, exon 2 of 4)	exon (NM_019872, exon 2 of 4)	3353	NM_019872	56296	Mm.141324	NM_019872	ENSMUSG00000028610	Dmrtb1	Dmrt6|Prp13	DMRT-like family B with proline-rich C-terminal, 1	protein-coding
mm_68506.1	chr7	111082448	111082506	-	1	NA	intron (NM_001040131, intron 1 of 20)	CpG	553	NM_001040131	13690	Mm.185453	NM_013507	ENSMUSG00000005610	Eif4g2	DAP-5|E130105L11Rik|Nat1|Natm1|p97	eukaryotic translation initiation factor 4, gamma 2	protein-coding
mm_129029.1	chr15	74958899	74958909	-	1	NA	3' UTR (NM_001164036, exon 4 of 4)	3' UTR (NM_001164036, exon 4 of 4)	3798	NM_001164040	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_160522.1	chr9	35570371	35570371	+	1	NA	promoter-TSS (NM_029762)	promoter-TSS (NM_029762)	-302	NM_029762	76832	Mm.482285	NM_029762	ENSMUSG00000050555	Hyls1	3010015K02Rik	hydrolethalus syndrome 1	protein-coding
mm_96809.1	chr11	69991634	69991638	+	1	NA	5' UTR (NM_019749, exon 1 of 4)	5' UTR (NM_019749, exon 1 of 4)	266	NM_019749	56486	Mm.272460	NM_019749	ENSMUSG00000018567	Gabarap	-	gamma-aminobutyric acid receptor associated protein	protein-coding
mm_108353.1	chr12	80519222	80519230	+	1	NA	exon (NM_001081421, exon 1 of 15)	exon (NM_001081421, exon 1 of 15)	236	NM_001081421	108760	Mm.308296	NM_001081421	ENSMUSG00000021130	Galnt16	5730405L21Rik|AI415388|Galntl1|mpp-GalNAc-T16	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 16	protein-coding
mm_21193.1	chr2	155407827	155407838	-	1	NA	exon (NM_019825, exon 10 of 14)	exon (NM_019825, exon 10 of 14)	25976	NM_178111	68728	Mm.293605	NM_178111	ENSMUSG00000038375	Trp53inp2	1110029F20Rik|Tp53inp2	transformation related protein 53 inducible nuclear protein 2	protein-coding
mm_130980.1	chr15	103344713	103344724	-	1	NA	3' UTR (NM_010577, exon 30 of 30)	3' UTR (NM_010577, exon 30 of 30)	-4632	NM_013866	29813	Mm.14099	NM_013866	ENSMUSG00000000552	Zfp385a	Hzf|Zfp385|Znf385a	zinc finger protein 385A	protein-coding
mm_136269.1	chr16	91044474	91044520	-	1	NA	promoter-TSS (NM_026110)	promoter-TSS (NM_026110)	-118	NM_026110	67367	Mm.347	NM_026110	ENSMUSG00000022974	Paxbp1	1810007M14Rik|C21orf66|Gcfc|Gcfc1|Pax3/7bp	PAX3 and PAX7 binding protein 1	protein-coding
mm_94474.1	chr11	6547276	6547295	+	1	NA	intron (NM_001190343, intron 1 of 8)	intron (NM_001190343, intron 1 of 8)	398	NM_001190343	216527	Mm.221271	NM_146014	ENSMUSG00000000378	Ccm2	BC029157	cerebral cavernous malformation 2	protein-coding
mm_141733.1	chr17	34120312	34120334	-	1	NA	promoter-TSS (NR_037970)	promoter-TSS (NR_037970)	-423	NR_037970	14312	Mm.3444	NM_010238	ENSMUSG00000024335	Brd2	AW228947|D17H6S113E|Frg-1|Fsrg-1|Fsrg1|Nat|Ring3|Rnf3|mKIAA4005	bromodomain containing 2	protein-coding
mm_22768.1	chr3	20198132	20198171	+	1	NA	Intergenic	Intergenic	24208	NR_105974	102465609		NR_105974	ENSMUSG00000099105	Mir7007	Gm27897|mmu-mir-7007	microRNA 7007	ncRNA
mm_49415.1	chr6	28867855	28867861	+	1	NA	intron (NM_019776, intron 16 of 23)	intron (NM_019776, intron 16 of 23)	-36111	NM_138682	192198	Mm.443660	NM_138682	ENSMUSG00000049939	Lrrc4	MBAG1|NGL-2|NGL2|NLG-2|Nag14	leucine rich repeat containing 4	protein-coding
mm_9249.1	chr1	171388773	171388798	-	1	NA	promoter-TSS (NM_001005508)	promoter-TSS (NM_001005508)	-175	NM_001005508	226652	Mm.251048	NM_001005508	ENSMUSG00000048865	Arhgap30	6030405P05Rik|Gm102|mFLJ00267	Rho GTPase activating protein 30	protein-coding
mm_85568.1	chr9	107231910	107231918	-	1	NA	promoter-TSS (NM_153413)	promoter-TSS (NM_153413)	-5	NM_153413	208869	Mm.150259	NM_153413	ENSMUSG00000039716	Dock3	MOCA|PBP|mKIAA0299	dedicator of cyto-kinesis 3	protein-coding
mm_143879.1	chr17	84273041	84273073	-	1	NA	intron (NM_183021, intron 29 of 37)	intron (NM_183021, intron 29 of 37)	-85110	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_154529.1	chrM	13564	13607	-	1	NA	NA	Intergenic	NA	NA								
mm_161346.1	chr14	52491209	52491209	-	1	NA	promoter-TSS (NM_020512)	promoter-TSS (NM_020512)	-163	NM_020512	57269	Mm.88822	NM_020512	ENSMUSG00000059887	Olfr1507	MOR244-1|Mor28|Or28	olfactory receptor 1507	protein-coding
mm_20134.1	chr2	121380942	121380947	-	1	NA	promoter-TSS (NM_080459)	promoter-TSS (NM_080459)	-4	NM_080459	140476	Mm.467475	NM_080459	ENSMUSG00000033498	Strc	DFNB16	stereocilin	protein-coding
mm_17947.1	chr2	36136579	36136597	-	1	NA	non-coding (NR_027515, exon 1 of 6)	non-coding (NR_027515, exon 1 of 6)	116	NM_026434	67889	Mm.205937	NM_026434	ENSMUSG00000026889	Rbm18	2010004P11Rik|AU015530	RNA binding motif protein 18	protein-coding
mm_120735.1	chr14	73165289	73165297	+	1	NA	intron (NR_033185, intron 8 of 15)	MTC|LTR|ERVL-MaLR	22508	NR_033185	105670	Mm.280068	NM_134083	ENSMUSG00000022106	Rcbtb2	2610028E02Rik|2810420M18Rik|AI448345|AW240694|Chc1l|RC/BTB2	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 2	protein-coding
mm_160105.1	chr7	23144266	23144266	-	1	NA	intron (NM_001034904, intron 1 of 3).2	MT2B2|LTR|ERVL	212	NM_001201364	100043665	Mm.335671	NM_001201364	ENSMUSG00000095683	Gm10662	ENSMUSG00000074296	predicted gene 10662	protein-coding
mm_51803.1	chr6	88724490	88724502	+	1	NA	promoter-TSS (NM_001166251)	promoter-TSS (NM_001166251)	84	NM_011844	23945	Mm.272197	NM_011844	ENSMUSG00000033174	Mgll	AA589436|Magl|Mgl	monoglyceride lipase	protein-coding
mm_73129.1	chr8	94923551	94923582	+	1	NA	promoter-TSS (NM_001145972)	promoter-TSS (NM_001145972)	-128	NM_001033468	382045	Mm.334726	NM_001033468	ENSMUSG00000061577	Adgrg5	Gm1109|Gpr114|PGR27	adhesion G protein-coupled receptor G5	protein-coding
mm_30787.1	chr4	19575534	19575562	+	1	NA	intron (NM_025476, intron 1 of 9)	intron (NM_025476, intron 1 of 9)	482	NM_025476	66302	Mm.440686	NM_025476	ENSMUSG00000028229	Rmdn1	Fam82b|RMD-1	regulator of microtubule dynamics 1	protein-coding
mm_161495.1	chr15	88712766	88712766	-	1	NA	exon (NM_001033274, exon 6 of 13)	exon (NM_001033274, exon 6 of 13)	21453	NM_001033274	223770	Mm.254438	NM_001033274	ENSMUSG00000022387	Brd1	1110059H06Rik|AI316859|mKIAA4191	bromodomain containing 1	protein-coding
mm_90190.1	chr10	120174554	120174562	+	1	NA	intron (NM_028679, intron 5 of 11)	MLTR31F_MM|LTR|ERVK	26979	NM_028679	73914	Mm.146194	NM_028679	ENSMUSG00000020227	Irak3	4833428C18Rik|AI563835|IRAK-M	interleukin-1 receptor-associated kinase 3	protein-coding
mm_131358.1	chr16	13749541	13749566	+	1	NA	Intergenic	MMERVK9C_I-int|LTR|ERVK	-19069	NM_011987	26565	Mm.4214	NM_011987	ENSMUSG00000022683	Pla2g10	GX sPLA2|PLA2GX|sPLA2-X	phospholipase A2, group X	protein-coding
mm_105915.1	chr11	114989855	114989919	-	1	NA	promoter-TSS (NM_145437)	promoter-TSS (NM_145437)	-1	NM_145437	217305	Mm.275986	NM_145437	ENSMUSG00000034641	Cd300ld	4732429D16Rik|CLM5|Cd300ld1|LMIR4|MAIR-IV|clm-5	CD300 molecule like family member d	protein-coding
mm_122436.1	chr14	45219274	45219308	-	1	NA	promoter-TSS (NM_027518)	promoter-TSS (NM_027518)	134	NM_172597	70561	Mm.28129	NM_172597	ENSMUSG00000021830	Txndc16	5730420B22Rik|C77647	thioredoxin domain containing 16	protein-coding
mm_61714.1	chr7	81523556	81523609	+	1	NA	promoter-TSS (NR_045299)	promoter-TSS (NR_045299)	32	NR_045299	100504421	Mm.217071	NR_045299	ENSMUSG00000097277	2900076A07Rik	WI1-1616M8.2	RIKEN cDNA 2900076A07 gene	ncRNA
mm_29902.1	chr3	131470959	131470959	-	1	NA	Intergenic	Intergenic	-93809	NM_001289479	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_157038.1	chrX	7964167	7964191	-	1	NA	intron (NM_008089, intron 1 of 5)	intron (NM_008089, intron 1 of 5)	3731	NM_008089	14460	Mm.335973	NM_008089	ENSMUSG00000031162	Gata1	Gata-1|Gf-1|eryf1	GATA binding protein 1	protein-coding
mm_61307.1	chr7	67952436	67952450	+	1	NA	5' UTR (NM_010513, exon 1 of 21)	5' UTR (NM_010513, exon 1 of 21)	186	NM_010513	16001	Mm.275742	NM_010513	ENSMUSG00000005533	Igf1r	A330103N21Rik|CD221|D930020L01|IGF-1R|hyft	insulin-like growth factor I receptor	protein-coding
mm_87518.1	chr10	52760936	52760951	+	1	NA	intron (NM_178675, intron 1 of 7)	intron (NM_178675, intron 1 of 7)	70442	NM_178675	215085	Mm.338690	NM_178675	ENSMUSG00000038602	Slc35f1	Duf6|E130016L02	solute carrier family 35, member F1	protein-coding
mm_101068.1	chr11	11462211	11462243	-	1	NA	exon (NM_015785, exon 1 of 8)	exon (NM_015785, exon 1 of 8)	192	NM_015785	53604	Mm.9500	NM_015785	ENSMUSG00000020193	Zpbp	4930486K01Rik|Iam38|Sp38	zona pellucida binding protein	protein-coding
mm_159470.1	chr4	12139878	12139878	+	1	NA	promoter-TSS (NM_028226)	promoter-TSS (NM_028226)	-239	NM_028226	72397	Mm.430709	NM_028226	ENSMUSG00000046667	Rbm12b1	3000004N20Rik|Rbm12b|Rbm12ba	RNA binding motif protein 12 B1	protein-coding
mm_25101.1	chr3	101286566	101286569	+	1	NA	intron (NM_013486, intron 2 of 4)	intron (NM_013486, intron 2 of 4)	1372	NM_013486	12481	Mm.22842	NM_013486	ENSMUSG00000027863	Cd2	LFA-2|Ly-37|Ly37	CD2 antigen	protein-coding
mm_12020.1	chr2	58156237	58156273	+	1	NA	intron (NM_139200, intron 1 of 7)	intron (NM_139200, intron 1 of 7)	3867	NM_139200	227929	Mm.273905	NM_139200	ENSMUSG00000026832	Cytip	A130053M09Rik|AI462064|C80816|Cbp|Cybr|Pscdbp	cytohesin 1 interacting protein	protein-coding
mm_77042.1	chr8	109575601	109575640	-	1	NA	exon (NM_017370, exon 5 of 5)	exon (NM_017370, exon 5 of 5)	3552	NM_017370	15439	Mm.26730	NM_017370	ENSMUSG00000031722	Hp	HP-1|preHP2	haptoglobin	protein-coding
mm_141123.1	chr17	26095488	26095514	-	1	NA	promoter-TSS (NM_019731)	promoter-TSS (NM_019731)	-31	NM_019731	56520	Mm.41787	NM_019731	ENSMUSG00000024177	Nme4	2610027N22Rik|2810024O08Rik|5730493H09Rik|NM23-M4|Nm23M4	NME/NM23 nucleoside diphosphate kinase 4	protein-coding
mm_17687.1	chr2	32323445	32323455	-	1	NA	non-coding (NR_125959, exon 13 of 22)	non-coding (NR_125959, exon 13 of 22)	4990	NR_029811	387239		NR_029811	ENSMUSG00000092807	Mir199b	Mirn199b|mir-199b	microRNA 199b	ncRNA
mm_147622.1	chr18	58072811	58072824	-	1	NA	intron (NM_010181, intron 25 of 64)	intron (NM_010181, intron 25 of 64)	137109	NM_010181	14119	Mm.20271	NM_010181	ENSMUSG00000024598	Fbn2	BC063774|Fib-2|mKIAA4226|sne|sy	fibrillin 2	protein-coding
mm_112596.1	chr13	14090957	14090976	+	1	NA	intron (NM_198122, intron 2 of 22)	B1_Mus2|SINE|Alu	27182	NM_198122	94246	Mm.439784	NM_194262	ENSMUSG00000039219	Arid4b	BCAA|BRCAA1|RBBP1L1|Rbp1l1|SAP180	AT rich interactive domain 4B (RBP1-like)	protein-coding
mm_82955.1	chr9	35570394	35570402	-	1	NA	promoter-TSS (NM_029762)	promoter-TSS (NM_029762)	-329	NM_029762	76832	Mm.482285	NM_029762	ENSMUSG00000050555	Hyls1	3010015K02Rik	hydrolethalus syndrome 1	protein-coding
mm_153677.1	chr19	44396546	44396571	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	11151	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_23853.1	chr3	83008697	83008718	+	1	NA	exon (NM_133862, exon 4 of 10)	exon (NM_133862, exon 4 of 10)	983	NM_001317105	99571	Mm.16422	NM_133862	ENSMUSG00000033860	Fgg	3010002H13Rik|AI256424	fibrinogen gamma chain	protein-coding
mm_169321.1	chr14	113314803	113314821	+	1	NA	Intergenic	Intergenic	1293382	NR_030150	723922		NR_030150	ENSMUSG00000070099	Mir466	Mirn466|mmu-mir-466	microRNA 466	ncRNA
mm_140668.1	chr17	12916092	12916119	-	1	NA	promoter-TSS (NM_013686)	promoter-TSS (NM_013686)	-14	NM_026310	67681	Mm.290166	NM_026310	ENSMUSG00000057388	Mrpl18	1010001C05Rik|C79879|HSPC071|MRP-L18	mitochondrial ribosomal protein L18	protein-coding
mm_61945.1	chr7	90183747	90183769	+	1	NA	intron (NM_001252520, intron 13 of 20)	B1_Mur2|SINE|Alu	53526	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_148638.1	chr19	5474879	5474895	+	1	NA	5' UTR (NM_001164352, exon 1 of 10)	5' UTR (NM_001164352, exon 1 of 10)	152	NM_001164352	58859	Mm.276367	NM_021474	ENSMUSG00000024909	Efemp2	0610011K11Rik|Fbln4|MBP1	epidermal growth factor-containing fibulin-like extracellular matrix protein 2	protein-coding
mm_163464.1	chr12	101382877	101382891	+	1	NA	Intergenic	Lx3_Mus|LINE|L1	-21789	NM_173023	271036	Mm.84218	NM_173023	ENSMUSG00000047014	Catsperb	4931410B03|4932415G16Rik	catsper channel auxiliary subunit beta	protein-coding
mm_163520.1	chr12	115224783	115224788	+	1	NA	Intergenic	Intergenic	471009	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
mm_80128.1	chr9	70580824	70580834	+	1	NA	exon (NM_025690, exon 13 of 21)	exon (NM_025690, exon 13 of 21)	37959	NM_025690	66660	Mm.22379	NM_025690	ENSMUSG00000032212	Sltm	5730455C01Rik|5730555F13Rik|9130215G10Rik|Met	SAFB-like, transcription modulator	protein-coding
mm_120498.1	chr14	65981449	65981478	+	1	NA	TTS (NM_013492)	TTS (NM_013492)	12980	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_154003.1	chr19	53028369	53028379	-	1	NA	intron (NM_133216, intron 2 of 20)	intron (NM_133216, intron 2 of 20)	10280	NM_133216	170750	Mm.99776	NM_133216	ENSMUSG00000025027	Xpnpep1	D230045I08Rik|sAMP	X-prolyl aminopeptidase (aminopeptidase P) 1, soluble	protein-coding
mm_81529.1	chr9	110062833	110062851	+	1	NA	intron (NM_001311163, intron 1 of 10)	intron (NM_001311163, intron 1 of 10)	10821	NM_001311164	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_49920.1	chr6	39205495	39205506	+	1	NA	intron (NM_001033430, intron 1 of 19)	CpG	1273	NM_001033430	338523	Mm.293175	NM_001033430	ENSMUSG00000042599	Kdm7a	A630082K20Rik|BB041802|ENSMUSG00000073143|Jhdm1d|mKIAA1718	lysine (K)-specific demethylase 7A	protein-coding
mm_122148.1	chr14	31206783	31206815	-	1	NA	promoter-TSS (NM_022656)	promoter-TSS (NM_022656)	27	NM_022656	64652	Mm.298728	NM_022656	ENSMUSG00000021910	Nisch	1200007D05Rik|3202002H23Rik|AW494485|I-1	nischarin	protein-coding
mm_1209.1	chr1	62726511	62726542	+	1	NA	intron (NM_001077405, intron 2 of 15)	intron (NM_001077405, intron 2 of 15)	23209	NM_001077405	18187	Mm.266341	NM_010939	ENSMUSG00000025969	Nrp2	1110048P06Rik|Np-2|Np2|Npn-2|Npn2	neuropilin 2	protein-coding
mm_31832.1	chr4	70553693	70553734	+	1	NA	Intergenic	RMER19B|LTR|ERVK	-18785	NM_172694	230316	Mm.251188	NM_172694	ENSMUSG00000039270	Megf9	4933405H16Rik|9630025C07|Egfl5|mKIAA0818	multiple EGF-like-domains 9	protein-coding
mm_172950.1	chr9	82611129	82611131	+	1	NA	Intergenic	RLTR10D2|LTR|ERVK	-218676	NM_001168240	65099	Mm.41415	NM_022986	ENSMUSG00000032251	Irak1bp1	4921528N06Rik|AI851240|Aabp3|Aip70|Simpl	interleukin-1 receptor-associated kinase 1 binding protein 1	protein-coding
mm_108727.1	chr12	87266697	87266760	+	1	NA	promoter-TSS (NM_001142580)	promoter-TSS (NM_001142580)	0	NM_146036	217737	Mm.22626	NM_146036	ENSMUSG00000021037	Ahsa1	BC023857|p38	AHA1, activator of heat shock protein ATPase 1	protein-coding
mm_73593.1	chr8	109997541	109997552	+	1	NA	exon (NM_146214, exon 10 of 12)	exon (NM_146214, exon 10 of 12)	7110	NM_146214	234724	Mm.28110	NM_146214	ENSMUSG00000001670	Tat	-	tyrosine aminotransferase	protein-coding
mm_30976.1	chr4	34550932	34550945	+	1	NA	5' UTR (NM_001007589, exon 1 of 5)	5' UTR (NM_001007589, exon 1 of 5)	323	NM_001007589	433693	Mm.389532	NM_026019	ENSMUSG00000028291	Akirin2	2700059D21Rik|AA114675|AA522011|AU019887|Akirin-2	akirin 2	protein-coding
mm_13068.1	chr2	91118950	91118952	+	1	NA	intron (NM_008653, intron 1 of 31)	intron (NM_008653, intron 1 of 31)	807	NM_008653	17868	Mm.10728	NM_008653	ENSMUSG00000002100	Mybpc3	-	myosin binding protein C, cardiac	protein-coding
mm_128452.1	chr15	50772708	50772720	-	1	NA	intron (NM_001310485, intron 5 of 7)	intron (NM_001310485, intron 5 of 7)	116335	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_170102.1	chr17	39844520	39844520	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	1523	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_134171.1	chr16	10796532	10796539	-	1	NA	intron (NM_013637, intron 1 of 1)	intron (NM_013637, intron 1 of 1)	288	NM_013637	19118	Mm.42733	NM_013637	ENSMUSG00000022501	Prm1	Prm-1	protamine 1	protein-coding
mm_70912.1	chr8	25720043	25720053	+	1	NA	promoter-TSS (NM_001293703)	promoter-TSS (NM_001293703)	0	NR_121642	71910	Mm.385055	NM_028000	ENSMUSG00000031570	Plpp5	1810019D05Rik|2310022A04Rik|AW045471|Ppapdc1|Ppapdc1b	phospholipid phosphatase 5	protein-coding
mm_113161.1	chr13	24803352	24803367	+	1	NA	5' UTR (NM_024473, exon 1 of 5)	5' UTR (NM_024473, exon 1 of 5)	1702	NM_024473	79555	Mm.266668	NM_024473	ENSMUSG00000019132	BC005537	8030460C05Rik|C78201	cDNA sequence BC005537	protein-coding
mm_27453.1	chr3	52056346	52056367	-	1	NA	intron (NM_001004176, intron 1 of 4)	RLTR20A4|LTR|ERVK	48650	NM_001004176	433586	Mm.234972	NM_001004176	ENSMUSG00000061143	Maml3	AV234550|BC049812|Mam-2|mKIAA1816	mastermind like 3 (Drosophila)	protein-coding
mm_117474.1	chr13	76271321	76271358	-	1	NA	Intergenic	Intergenic	-113622	NM_030174	78771	Mm.316249	NM_030174	ENSMUSG00000021596	Mctp1	2810465F10Rik	multiple C2 domains, transmembrane 1	protein-coding
mm_155032.1	chrX	42068423	42068447	+	1	NA	promoter-TSS (NR_125870)	promoter-TSS (NR_125870)	37	NR_125870	11798	Mm.259879	NM_009688	ENSMUSG00000025860	Xiap	1110015C02Rik|Aipa|Api3|Birc4|IAP3|ILP-1|MIHA	X-linked inhibitor of apoptosis	protein-coding
mm_133314.1	chr16	77643009	77643022	+	1	NA	Intergenic	Intergenic	-3258	NR_029540	723952		NR_029540	ENSMUSG00000065472	Mir125b-2	Mirn125b-2|mir-125b-2	microRNA 125b-2	ncRNA
mm_5293.1	chr1	21001438	21001452	-	1	NA	TTS (NM_177409)	TTS (NM_177409)	49819	NM_027974	71877	Mm.29178	NM_027974	ENSMUSG00000041809	Efhc1	1700029F22Rik|mRib72-1|myoclonin1	EF-hand domain (C-terminal) containing 1	protein-coding
mm_14943.1	chr2	151702183	151702213	+	1	NA	5' UTR (NM_001160363, exon 1 of 2)	5' UTR (NM_001160363, exon 1 of 2)	190	NM_001160363	108832	Mm.103494	NM_001160363	ENSMUSG00000044364	Tmem74b	5430405G05Rik	transmembrane protein 74B	protein-coding
mm_112129.1	chr12	112942091	112942097	-	1	NA	promoter-TSS (NM_001316724)	promoter-TSS (NM_001316724)	48	NM_025399	66174	Mm.7070	NM_025399	ENSMUSG00000002804	Nudt14	1110030M18Rik|UGPPase	nudix (nucleoside diphosphate linked moiety X)-type motif 14	protein-coding
mm_58953.1	chr7	18787759	18787760	+	1	NA	non-coding (NR_024208, exon 1 of 1)	non-coding (NR_024208, exon 1 of 1)	1457	NR_024208	20958	Mm.423480	NR_024208	ENSMUSG00000109116	Sycp1-ps1	Sycp1-rs	synaptonemal complex protein 1, pseudogene 1	pseudo
mm_151296.1	chr19	55464775	55464787	+	1	NA	intron (NM_001293685, intron 6 of 8)	intron (NM_001293685, intron 6 of 8)	148724	NM_001293686	53611	Mm.258637	NM_016862	ENSMUSG00000024983	Vti1a	1110014F16Rik|1110018K19Rik|4921537J05Rik|MVti1|MVti1a|Vti1|Vti1-rp2	vesicle transport through interaction with t-SNAREs 1A	protein-coding
mm_65616.1	chr7	27533698	27533709	-	1	NA	exon (NM_011116, exon 12 of 14)	exon (NM_011116, exon 12 of 14)	10442	NM_001033315	233020	Mm.429716	NM_001033315	ENSMUSG00000040424	Hipk4	Gm162	homeodomain interacting protein kinase 4	protein-coding
mm_9989.1	chr1	191348307	191348310	-	1	NA	intron (NM_025864, intron 6 of 7)	intron (NM_025864, intron 6 of 7)	22343	NM_025864	66950	Mm.236300	NM_025864	ENSMUSG00000026627	Tmem206	2310028N02Rik|AI118576	transmembrane protein 206	protein-coding
mm_88551.1	chr10	78595499	78595509	+	1	NA	Intergenic	Intergenic	-3540	NM_027875	71709	Mm.86439	NM_027875	ENSMUSG00000032714	Syde1	1200008N06Rik|BB043000|mSYD1A	synapse defective 1, Rho GTPase, homolog 1 (C. elegans)	protein-coding
mm_10544.1	chr2	16548929	16548953	+	1	NA	intron (NM_026162, intron 3 of 13)	intron (NM_026162, intron 3 of 13)	192637	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding
mm_168794.1	chr12	19490228	19490238	+	1	NA	Intergenic	CpG	975723	NM_001201330	236366	Mm.352227	NM_001033157	ENSMUSG00000073197	5730507C01Rik	-	RIKEN cDNA 5730507C01 gene	protein-coding
mm_135631.1	chr16	52304107	52304125	-	1	NA	intron (NM_009655, intron 3 of 15)	intron (NM_009655, intron 3 of 15)	148965	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_67616.1	chr7	83933489	83933500	-	1	NA	3' UTR (NM_030728, exon 29 of 29)	3' UTR (NM_030728, exon 29 of 29)	41494	NM_023403	67943	Mm.117365	NM_023403	ENSMUSG00000038503	Mesdc2	2210015O11Rik|AW537813|mKIAA0081|mesd|msd	mesoderm development candidate 2	protein-coding
mm_89899.1	chr10	110937798	110937830	+	1	NA	exon (NM_007792, exon 4 of 6)	exon (NM_007792, exon 4 of 6)	17638	NM_007792	13008	Mm.2020	NM_007792	ENSMUSG00000020186	Csrp2	AW551867|Crp2|SmLim	cysteine and glycine-rich protein 2	protein-coding
mm_69360.1	chr7	130519466	130519558	-	1	NA	promoter-TSS (NM_001136054)	promoter-TSS (NM_001136054)	68	NM_001136054	11907	Mm.216321	NM_013799	ENSMUSG00000030850	Ate1	AI225793|AW547406	arginyltransferase 1	protein-coding
mm_66066.1	chr7	30821206	30821214	-	1	NA	promoter-TSS (NM_001168512)	promoter-TSS (NM_001168512)	-18	NM_001168510	233079	Mm.97338	NM_146187	ENSMUSG00000051314	Ffar2	GPCR43|Gpr43	free fatty acid receptor 2	protein-coding
mm_131991.1	chr16	25042986	25042997	+	1	NA	Intergenic	Intergenic	-16648	NR_040374	319487	Mm.137341	NR_040374	ENSMUSG00000096960	A230028O05Rik	-	RIKEN cDNA A230028O05 gene	ncRNA
mm_80223.1	chr9	72620446	72620447	+	1	NA	3' UTR (NM_001033536, exon 9 of 9)	3' UTR (NM_001033536, exon 9 of 9)	-41901	NM_010890	17999	Mm.279923	NM_010890	ENSMUSG00000032216	Nedd4	AA959633|AL023035|AU019897|E430025J12Rik|Nedd4-1|Nedd4a|mKIAA0093	neural precursor cell expressed, developmentally down-regulated 4	protein-coding
mm_74.1	chr1	6674110	6674131	+	1	NA	intron (NM_001244693, intron 2 of 22)	Lx8|LINE|L1	-55931	NR_045189	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding
mm_31382.1	chr4	47996412	47996441	+	1	NA	Intergenic	B1_Mur1|SINE|Alu	-48879	NM_015743	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_85535.1	chr9	106550261	106550261	-	1	NA	intron (NM_026645, intron 6 of 7)	intron (NM_026645, intron 6 of 7)	11364	NM_026645	68265	Mm.141451	NM_026645	ENSMUSG00000023577	Iqcf3	1700012F17Rik|AV040440	IQ motif containing F3	protein-coding
mm_78612.1	chr9	37545175	37545181	+	1	NA	TTS (NM_020518)	TTS (NM_020518)	5923	NM_020518	57276	Mm.27478	NM_020518	ENSMUSG00000001943	Vsig2	1190004B15Rik|2210413P10Rik|AU040484|CTX|Ctm	V-set and immunoglobulin domain containing 2	protein-coding
mm_40827.1	chr5	72902587	72902617	+	1	NA	Intergenic	Intergenic	-11760	NM_001113423	75991	Mm.121285	NM_153567	ENSMUSG00000036087	Slain2	5033405K12Rik|8030444K12Rik|AI596370	SLAIN motif family, member 2	protein-coding
mm_93738.1	chr10	120142175	120142186	-	1	NA	3' UTR (NM_028679, exon 12 of 12)	3' UTR (NM_028679, exon 12 of 12)	-29215	NM_080446	117599	Mm.214703	NM_080446	ENSMUSG00000020228	Helb	AI447783|D10Ertd664e	helicase (DNA) B	protein-coding
mm_60943.1	chr7	46920150	46920176	+	1	NA	promoter-TSS (NM_021884)	promoter-TSS (NM_021884)	-233	NM_021884	22088	Mm.241334	NM_021884	ENSMUSG00000014402	Tsg101	AI255943|CC2	tumor susceptibility gene 101	protein-coding
mm_36889.1	chr4	107437681	107437685	-	1	NA	intron (NM_147221, intron 2 of 10)	intron (NM_147221, intron 2 of 10)	2964	NM_147221	230587	Mm.331757	NM_147221	ENSMUSG00000034762	Glis1	Gli5|Gli6|GliH1	GLIS family zinc finger 1	protein-coding
mm_1976.1	chr1	86526790	86526806	+	1	NA	promoter-TSS (NM_008972)	promoter-TSS (NM_008972)	62	NM_008972	19231	Mm.19187	NM_008972	ENSMUSG00000026238	Ptma	Thym	prothymosin alpha	protein-coding
mm_172170.1	chr6	44793192	44793197	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-266867	NM_001004357	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding
mm_58740.1	chr7	13034865	13034879	+	1	NA	promoter-TSS (NM_026885)	promoter-TSS (NM_026885)	-95	NM_026885	68953	Mm.295670	NM_026885	ENSMUSG00000033916	Chmp2a	1500016L11Rik	charged multivesicular body protein 2A	protein-coding
mm_132836.1	chr16	45535341	45535354	+	1	NA	promoter-TSS (NM_198106)	promoter-TSS (NM_198106)	81	NM_198106	208169	Mm.277437	NM_198106	ENSMUSG00000033210	Slc9c1	Gm610|NHE-10|Slc9a10|sNHE|spermNHE	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	protein-coding
mm_115750.1	chr13	18397802	18397832	-	1	NA	Intergenic	Intergenic	-15778	NM_175006	218030	Mm.352263	NM_175006	ENSMUSG00000009734	Pou6f2	D130006K24Rik|RPF-1	POU domain, class 6, transcription factor 2	protein-coding
mm_5648.1	chr1	40516492	40516501	-	1	NA	5' UTR (NM_010553, exon 3 of 13)	5' UTR (NM_010553, exon 3 of 13)	1134	NM_010553	16174	Mm.20466	NM_010553	ENSMUSG00000026068	Il18rap	AcPL|IL-18R-beta|IL-18RAcP|IL-18Rbeta|IL-1RAcPL	interleukin 18 receptor accessory protein	protein-coding
mm_85263.1	chr9	99420266	99420276	-	1	NA	intron (NM_008624, intron 1 of 5)	intron (NM_008624, intron 1 of 5)	16441	NM_008624	17532	Mm.2045	NM_008624	ENSMUSG00000032470	Mras	2900078C09Rik|AI326250	muscle and microspikes RAS	protein-coding
mm_67326.1	chr7	79732195	79732199	-	1	NA	intron (NM_001113471, intron 1 of 8)	intron (NM_001113471, intron 1 of 8)	579	NM_175640	103968	Mm.254917	NM_175640	ENSMUSG00000030546	Plin1	6030432J05Rik|Peri|Plin	perilipin 1	protein-coding
mm_63108.1	chr7	122670801	122670827	+	1	NA	promoter-TSS (NM_019430)	promoter-TSS (NM_019430)	-930	NM_019430	54376	Mm.444212	NM_019430	ENSMUSG00000066189	Cacng3	-	calcium channel, voltage-dependent, gamma subunit 3	protein-coding
mm_66697.1	chr7	45920389	45920421	-	1	NA	intron (NM_010129, intron 1 of 4)	intron (NM_010129, intron 1 of 4)	444	NM_001146346	13732	Mm.20829	NM_010129	ENSMUSG00000040212	Emp3	H-4|H4|HNMP-1|MI-35|Ymp	epithelial membrane protein 3	protein-coding
mm_51465.1	chr6	82652626	82652646	+	1	NA	exon (NM_025882, exon 1 of 4)	exon (NM_025882, exon 1 of 4)	229	NM_025882	66979	Mm.195753	NM_025882	ENSMUSG00000030042	Pole4	2400007P05Rik|5830430F06Rik	polymerase (DNA-directed), epsilon 4 (p12 subunit)	protein-coding
mm_38657.1	chr4	143390354	143390387	-	1	NA	Intergenic	GA-rich|Low_complexity|Low_complexity	-4071	NM_031377	83491	Mm.190607	NM_031377	ENSMUSG00000041805	Pramel1	-	preferentially expressed antigen in melanoma-like 1	protein-coding
mm_102144.1	chr11	53631700	53631710	-	1	NA	3' UTR (NM_008355, exon 4 of 4)	3' UTR (NM_008355, exon 4 of 4)	2997	NM_008355	16163	Mm.1284	NM_008355	ENSMUSG00000020383	Il13	Il-13	interleukin 13	protein-coding
mm_165250.1	chr2	71529969	71529973	+	1	NA	TTS (NR_002854)	TTS (NR_002854)	526	NM_010053	13390	Mm.475101	NM_010053	ENSMUSG00000041911	Dlx1	Dlx|Dlx-1	distal-less homeobox 1	protein-coding
mm_65904.1	chr7	30192969	30192982	-	1	NA	intron (NM_009795, intron 2 of 10)	intron (NM_009795, intron 2 of 10)	2073	NM_009795	12336	Mm.439782	NM_009795	ENSMUSG00000001794	Capns1	Capa-4|Capa4|Capn4|D7Ertd146e	calpain, small subunit 1	protein-coding
mm_106179.1	chr11	116694581	116694668	-	1	NA	promoter-TSS (NM_009180)	promoter-TSS (NM_009180)	36	NM_009180	20446	Mm.3947	NM_009180	ENSMUSG00000057286	St6galnac2	II|ST6GalNAc|Siat7|Siat7b	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2	protein-coding
mm_56891.1	chr6	119108548	119108616	-	1	NA	promoter-TSS (NM_001159534)	promoter-TSS (NM_001159534)	-87	NM_001256002	12288	Mm.41628	NM_009781	ENSMUSG00000051331	Cacna1c	Cav1.2|Cchl1a1|D930026N18Rik|MBC|MELC-CC	calcium channel, voltage-dependent, L type, alpha 1C subunit	protein-coding
mm_88821.1	chr10	80803602	80803617	+	1	NA	exon (NM_013651, exon 7 of 9)	exon (NM_013651, exon 7 of 9)	-1639	NM_007445	11705	Mm.376094	NM_007445	ENSMUSG00000035262	Amh	MIS	anti-Mullerian hormone	protein-coding
mm_156255.1	chrX	136708390	136708404	+	1	NA	intron (NM_146236, intron 1 of 1)	intron (NM_146236, intron 1 of 1)	332	NM_146236	237052	Mm.40713	NM_146236	ENSMUSG00000049536	Tceal1	0610011M09Rik|BC011290|P21|SIIR|pp21	transcription elongation factor A (SII)-like 1	protein-coding
mm_2814.1	chr1	130877789	130877800	+	1	NA	exon (NM_026976, exon 5 of 8)	exon (NM_026976, exon 5 of 8)	9617	NM_053095	93672	Mm.196691	NM_053095	ENSMUSG00000026420	Il24	FISP|Mda-7|Mda7|St16	interleukin 24	protein-coding
mm_47973.1	chr5	135910581	135910598	-	1	NA	3' UTR (NM_018871, exon 2 of 2)	3' UTR (NM_018871, exon 2 of 2)	22670	NM_013560	15507	Mm.13849	NM_013560	ENSMUSG00000004951	Hspb1	27kDa|Hsp25	heat shock protein 1	protein-coding
mm_139785.1	chr17	65800030	65800032	+	1	NA	intron (NM_001114131, intron 2 of 19)	intron (NM_001114131, intron 2 of 19)	16676	NR_104465	70351	Mm.48686	NM_146081	ENSMUSG00000061950	Ppp4r1	3110001J10Rik|Pp4r1	protein phosphatase 4, regulatory subunit 1	protein-coding
mm_85231.1	chr9	98007764	98007765	-	1	NA	intron (NR_110443, intron 1 of 1)	intron (NR_110443, intron 1 of 1)	4344	NR_110443	66737	Mm.445908	NR_110443	ENSMUSG00000090255	4921534H16Rik	-	RIKEN cDNA 4921534H16 gene	ncRNA
mm_4804.1	chr1	185270987	185271006	+	1	NA	intron (NM_001163754, intron 26 of 34)	B3|SINE|B2	28021	NR_035529	100316737		NR_035529	ENSMUSG00000105770	Mir664	mir-664|mmu-mir-664	microRNA 664	ncRNA
mm_117867.1	chr13	98872204	98872225	-	1	NA	intron (NM_001048267, intron 6 of 23)	B1_Mm|SINE|Alu	18828	NM_001048267	238799	Mm.173286	NM_178716	ENSMUSG00000009470	Tnpo1	AU021749|D13Ertd688e|IPO2|Kpnb2|MIP|MIP1|TRN	transportin 1	protein-coding
mm_70959.1	chr8	26979225	26979250	+	1	NA	exon (NM_001101502, exon 2 of 2)	exon (NM_001101502, exon 2 of 2)	1901	NM_001110508	353310	Mm.212469	NM_001101502	ENSMUSG00000085795	Zfp703	1110032O19Rik|AI430822|AL022941|Csmn1|End2|Zeppo1|Znf703|Zpo1	zinc finger protein 703	protein-coding
mm_21278.1	chr2	156928604	156928619	-	1	NA	3' UTR (NM_180956, exon 17 of 17)	3' UTR (NM_180956, exon 17 of 17)	-41533	NM_029983	77799	Mm.29264	NM_029983	ENSMUSG00000027636	Sla2	A930009E21Rik|AI430952|SLAP-2|SLAP2	Src-like-adaptor 2	protein-coding
mm_86686.1	chr10	18407837	18407855	+	1	NA	5' UTR (NM_173390, exon 1 of 7)	5' UTR (NM_173390, exon 1 of 7)	171	NM_173390	215819	Mm.297971	NM_173390	ENSMUSG00000039835	Nhsl1	5730409E15Rik|A630035H13Rik|A730096F01|BC013565|D10Bwg0940e|mKIAA1357	NHS-like 1	protein-coding
mm_15717.1	chr2	164047630	164047644	+	1	NA	intron (NM_001114079, intron 12 of 13)	intron (NM_001114079, intron 12 of 13)	22413	NM_001114079	381404	Mm.82301	NM_001114079	ENSMUSG00000054582	Pabpc1l	1810053B01Rik|Epab	poly(A) binding protein, cytoplasmic 1-like	protein-coding
mm_169749.1	chr15	89355513	89355513	-	1	NA	promoter-TSS (NM_001271601)	promoter-TSS (NM_001271601)	146	NM_178919	105847	Mm.34511	NM_178919	ENSMUSG00000022614	Lmf2	AI451006|Tmem112b|Tmem153	lipase maturation factor 2	protein-coding
mm_71420.1	chr8	46490945	46490951	+	1	NA	promoter-TSS (NM_001302163)	promoter-TSS (NM_001302163)	-18	NM_001302163	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_120452.1	chr14	65968652	65968657	+	1	NA	5' UTR (NM_013492, exon 1 of 9)	5' UTR (NM_013492, exon 1 of 9)	171	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_73819.1	chr8	117410653	117410654	+	1	NA	intron (NM_028941, intron 3 of 20)	intron (NM_028941, intron 3 of 20)	-42370	NR_106045	102466801		NR_106045	ENSMUSG00000099062	Mir7077	Gm27774|mmu-mir-7077	microRNA 7077	ncRNA
mm_133555.1	chr16	91387774	91387781	+	1	NA	intron (NM_001347258, intron 4 of 7)	intron (NM_001347258, intron 4 of 7)	14994	NM_001110498	15976	Mm.6834	NM_010509	ENSMUSG00000022971	Ifnar2	AI747302|Ifnar-2	interferon (alpha and beta) receptor 2	protein-coding
mm_34246.1	chr4	141242851	141242909	+	1	NA	promoter-TSS (NM_172520)	promoter-TSS (NM_172520)	-4	NM_172520	213649	Mm.134460	NM_172520	ENSMUSG00000028919	Arhgef19	6030432F23|6430573B13Rik|WGEF	Rho guanine nucleotide exchange factor (GEF) 19	protein-coding
mm_2945.1	chr1	132342054	132342072	+	1	NA	Intergenic	Intergenic	25885	NM_001311108	68875	Mm.273785	NM_178874	ENSMUSG00000042066	Tmcc2	1110063G11Rik	transmembrane and coiled-coil domains 2	protein-coding
mm_116146.1	chr13	29944495	29944497	-	1	NA	intron (NM_010093, intron 1 of 6)	B1_Mur3|SINE|Alu	39895	NM_001289920	13557	Mm.268356	NM_010093	ENSMUSG00000016477	E2f3	E2F3b|E2f3a	E2F transcription factor 3	protein-coding
mm_40577.1	chr5	63967921	63967921	+	1	NA	intron (NM_145923, intron 1 of 6)	intron (NM_145923, intron 1 of 6)	976	NM_145923	100532	Mm.243632	NM_145923	ENSMUSG00000047881	Rell1	AA536743	RELT-like 1	protein-coding
mm_67201.1	chr7	74285943	74285957	-	1	NA	intron (NM_001038643, intron 9 of 10)	ID2|SINE|ID	268830	NM_023908	108116	Mm.425467	NM_023908	ENSMUSG00000025790	Slco3a1	5830414C08Rik|Anr1|MJAM|OATP-D|R75096|Slc21a11	solute carrier organic anion transporter family, member 3a1	protein-coding
mm_30744.1	chr4	14864050	14864060	+	1	NA	promoter-TSS (NM_028264)	promoter-TSS (NM_028264)	-164	NM_028264	72519	Mm.279158	NM_028264	ENSMUSG00000028221	Tmem55a	2610319K07Rik|AI315591|AV001360	transmembrane protein 55A	protein-coding
mm_116869.1	chr13	55018370	55018382	-	1	NA	intron (NM_001206392, intron 1 of 17)	intron (NM_001206392, intron 1 of 17)	2443	NM_001206390	212032	Mm.267479	NM_001033245	ENSMUSG00000025877	Hk3	HK III|HK-III	hexokinase 3	protein-coding
mm_166026.1	chr4	125145528	125145545	+	1	NA	Intergenic	Intergenic	-17655	NM_153159	230738	Mm.402	NM_153159	ENSMUSG00000042677	Zc3h12a	BC036563|MCPIP|MCPIP-1|Mcpip1|Reg1	zinc finger CCCH type containing 12A	protein-coding
mm_30713.1	chr4	12561105	12561107	+	1	NA	Intergenic	Intergenic	-345731	NM_173746	208820	Mm.12057	NM_173746	ENSMUSG00000055963	Triqk	C130086A10|Gm11818|OTTMUSG00000004461	triple QxxK/R motif containing	protein-coding
mm_133985.1	chr16	4559778	4559825	-	1	NA	promoter-TSS (NM_031182)	promoter-TSS (NM_031182)	-81	NM_031182	83383	Mm.273210	NM_031182	ENSMUSG00000005718	Tfap4	AI642933|AP-4|D930048N17Rik|Tcfap4|bHLHc41	transcription factor AP4	protein-coding
mm_82759.1	chr9	26862002	26862008	-	1	NA	Intergenic	Intergenic	-1182	NM_001113323	70893	Mm.78118	NM_001113323	ENSMUSG00000031966	Glb1l3	4921509F24Rik	galactosidase, beta 1 like 3	protein-coding
mm_3025.1	chr1	133664411	133664419	+	1	NA	Intergenic	Intergenic	-3016	NM_144530	70579	Mm.245357	NM_144530	ENSMUSG00000102976	Zc3h11a	1110003F06Rik|5730454B08Rik|G630041M05Rik|Zc3hdc11a|Zc3hh11a|mKIAA0663	zinc finger CCCH type containing 11A	protein-coding
mm_20864.1	chr2	148439801	148439814	-	1	NA	3' UTR (NM_010740, exon 2 of 2)	3' UTR (NM_010740, exon 2 of 2)	3728	NM_010740	17064	Mm.681	NM_010740	ENSMUSG00000027435	Cd93	6030404G09Rik|AA145088|AA4.1|AW555904|C1qr1|C1qrp|Ly68	CD93 antigen	protein-coding
mm_171336.1	chr4	101903691	101903692	-	1	NA	Intergenic	BGLII|LTR|ERVK	-9902	NM_001331179	242574	Mm.34251	NM_001331179	ENSMUSG00000046133	C130073F10Rik	-	RIKEN cDNA C130073F10 gene	protein-coding
mm_52773.1	chr6	121210732	121210758	+	1	NA	promoter-TSS (NM_017379)	promoter-TSS (NM_017379)	11	NM_017379	53857	Mm.32884	NM_017379	ENSMUSG00000030137	Tuba8	-	tubulin, alpha 8	protein-coding
mm_78123.1	chr9	20644847	20644848	+	1	NA	promoter-TSS (NM_001310746)	promoter-TSS (NM_001310746)	23	NM_001310746	66177	Mm.390165	NM_025401	ENSMUSG00000084786	Ubl5	1110030M22Rik|beacon	ubiquitin-like 5	protein-coding
mm_56054.1	chr6	86761190	86761205	-	1	NA	intron (NM_013471, intron 2 of 12)	intron (NM_013471, intron 2 of 12)	13917	NM_001331120	11746	Mm.259702	NM_013471	ENSMUSG00000029994	Anxa4	AI265406|AIV|AW106930|Anx4|Xanx-4	annexin A4	protein-coding
mm_62709.1	chr7	110768064	110768100	+	1	NA	promoter-TSS (NM_001276301)	promoter-TSS (NM_001276301)	-124	NM_001276301	11717	Mm.3238	NM_009667	ENSMUSG00000005686	Ampd3	-	adenosine monophosphate deaminase 3	protein-coding
mm_40520.1	chr5	57867480	57867488	+	1	NA	intron (NM_001310608, intron 1 of 3)	intron (NM_001310608, intron 1 of 3)	149403	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_12947.1	chr2	87516002	87516022	+	1	NA	Intergenic	Intergenic	7554	NM_178249	347711	Mm.21815	NM_178249	ENSMUSG00000025838	Pramel6	C80453|C80515	preferentially expressed antigen in melanoma like 6	protein-coding
mm_17753.1	chr2	32716770	32716778	-	1	NA	Intergenic	RMER19B|LTR|ERVK	-3802	NR_039536	100628606		NR_039536	ENSMUSG00000105841	Mir3960	mmu-mir-3960	microRNA 3960	ncRNA
mm_8688.1	chr1	157244471	157244505	-	1	NA	intron (NM_177644, intron 3 of 17)	intron (NM_177644, intron 3 of 17)	-135808	NM_001305063	73435	Mm.116705	NM_028540	ENSMUSG00000026592	Tex35	1700057K13Rik	testis expressed 35	protein-coding
mm_93489.1	chr10	111997167	111997202	-	1	NA	promoter-TSS (NM_028608)	promoter-TSS (NM_028608)	80	NM_028608	73690	Mm.173790	NM_028608	ENSMUSG00000056888	Glipr1	2410114O14Rik|RTVP-1|RTVP1|mRTVP-1	GLI pathogenesis-related 1 (glioma)	protein-coding
mm_4957.1	chr1	191266855	191266885	+	1	NA	Intergenic	Intergenic	51248	NM_025424	66208	Mm.46444	NM_025424	ENSMUSG00000037499	Nenf	1110060M21Rik|SCIRP10|Spuf	neuron derived neurotrophic factor	protein-coding
mm_117661.1	chr13	93431048	93431052	-	1	NA	3' UTR (NM_021310, exon 11 of 11)	3' UTR (NM_021310, exon 11 of 11)	68758	NM_021310	57748	Mm.100273	NM_021310	ENSMUSG00000021690	Jmy	-	junction-mediating and regulatory protein	protein-coding
mm_53113.1	chr6	125096146	125096158	+	1	NA	promoter-TSS (NR_106012)	promoter-TSS (NR_106012)	-11	NM_145979	107932	Mm.333388	NM_145979	ENSMUSG00000063870	Chd4	9530019N15Rik|AA617397|BC005710|D6Ertd380e|Mi-2beta|mKIAA4075	chromodomain helicase DNA binding protein 4	protein-coding
mm_63167.1	chr7	124089412	124089417	+	1	NA	intron (NM_001252072, intron 1 of 1)	L1MB8|LINE|L1	106233	NM_001252072	628779	Mm.40210	NM_001252072	ENSMUSG00000078591	Hs3st4	EG628779|Gm6915	heparan sulfate (glucosamine) 3-O-sulfotransferase 4	protein-coding
mm_108834.1	chr12	95780594	95780607	+	1	NA	exon (NM_201518, exon 2 of 2)	exon (NM_201518, exon 2 of 2)	88374	NM_201518	399558	Mm.341948	NM_201518	ENSMUSG00000047414	Flrt2	-	fibronectin leucine rich transmembrane protein 2	protein-coding
mm_81954.1	chr9	120555639	120555647	+	1	NA	intron (NM_178676, intron 4 of 10)	intron (NM_178676, intron 4 of 10)	15825	NM_178676	215446	Mm.76648	NM_178676	ENSMUSG00000041608	Entpd3	Cd39l3|HB6|NTPDase-3	ectonucleoside triphosphate diphosphohydrolase 3	protein-coding
mm_26767.1	chr3	8882742	8882744	-	1	NA	intron (NM_025434, intron 2 of 2)	Lx|LINE|L1	41114	NM_025434	66230	Mm.38460	NM_025434	ENSMUSG00000040269	Mrps28	1500012D08Rik|AW061224	mitochondrial ribosomal protein S28	protein-coding
mm_163694.1	chr13	100153128	100153128	+	1	NA	intron (NM_010872, intron 12 of 15)	RSINE1|SINE|B4	28273	NM_011420	20595	Mm.2025	NM_011420	ENSMUSG00000021645	Smn1	AI849087|Gemin1|Smn	survival motor neuron 1	protein-coding
mm_27201.1	chr3	35719650	35719659	-	1	NA	Intergenic	L1_Mur3|LINE|L1	-34484	NM_029570	76295	Mm.239416	NM_029570	ENSMUSG00000037400	Atp11b	1110019I14Rik|ATPIF|ATPIR|mKIAA0956	ATPase, class VI, type 11B	protein-coding
mm_148180.1	chr18	78205868	78205878	-	1	NA	exon (NM_207651, exon 6 of 22)	exon (NM_207651, exon 6 of 22)	567	NM_001110274	27411	Mm.44158	NM_030683	ENSMUSG00000024552	Slc14a2	UT-A1|UT-A3	solute carrier family 14 (urea transporter), member 2	protein-coding
mm_32693.1	chr4	115884385	115884392	+	1	NA	promoter-TSS (NM_001039124)	promoter-TSS (NM_001039124)	-12	NM_001039124	654462	Mm.388913	NM_001039124	ENSMUSG00000073774	Kncn	Kino|L5	kinocilin	protein-coding
mm_39645.1	chr5	24645466	24645470	+	1	NA	promoter-TSS (NR_003953)	promoter-TSS (NR_003953)	15	NR_003953	72252	Mm.87446	NR_003953	ENSMUSG00000038165	1700022A21Rik	-	glycerol-3-phosphate dehydrogenase 1-like pseudogene	pseudo
mm_44883.1	chr5	34650661	34650670	-	1	NA	intron (NM_029278, intron 7 of 17)	intron (NM_029278, intron 7 of 17)	9483	NM_029278	75416	Mm.40292	NM_029278	ENSMUSG00000036693	Nop14	2610033H07Rik|Nol14	NOP14 nucleolar protein	protein-coding
mm_149742.1	chr19	22448075	22448088	+	1	NA	promoter-TSS (NM_177341)	promoter-TSS (NM_177341)	-127	NM_177341	226025	Mm.131943	NM_177341	ENSMUSG00000052387	Trpm3	6330504P12Rik|9330180E14|AU018608|B930001P07Rik|LTRPC3|MLSN2	transient receptor potential cation channel, subfamily M, member 3	protein-coding
mm_46373.1	chr5	103655745	103655751	-	1	NA	promoter-TSS (NM_001163550)	promoter-TSS (NM_001163550)	-16	NM_001163550	74218	Mm.159141	NM_028824	ENSMUSG00000029320	1700016H13Rik	-	RIKEN cDNA 1700016H13 gene	protein-coding
mm_173270.1	chrX	96484853	96484873	+	1	NA	intron (NM_181273, intron 9 of 15)	intron (NM_181273, intron 9 of 15)	28517	NM_001159627	15203	Mm.277092	NM_010417	ENSMUSG00000031209	Heph	C130006F04Rik|Cpl|mKIAA0698|sla	hephaestin	protein-coding
mm_123306.1	chr14	61690889	61690894	-	1	NA	Intergenic	Intergenic	-8518	NR_028264	668253	Mm.32886	NR_028264	ENSMUSG00000097589	Dleu2	1810047A16Rik|4932411A06Rik|7730401J12Rik|AI197277|AI788824|Alt1|Gm9069|Leu2	deleted in lymphocytic leukemia, 2	ncRNA
mm_150895.1	chr19	45472756	45472771	+	1	NA	intron (NM_001286466, intron 4 of 13)	intron (NM_001286466, intron 4 of 13)	87801	NM_001330506	56626	Mm.46509	NM_020032	ENSMUSG00000025218	Poll	1110003P06Rik|AV007317	polymerase (DNA directed), lambda	protein-coding
mm_96481.1	chr11	67683889	67683909	+	1	NA	3' UTR (NM_001277080, exon 13 of 13)	3' UTR (NM_001277080, exon 13 of 13)	-11427	NM_009038	19674	Mm.439726	NM_009038	ENSMUSG00000020907	Rcvrn	CAR|S-modulin	recoverin	protein-coding
mm_72686.1	chr8	84966784	84966810	+	1	NA	promoter-TSS (NM_027187)	promoter-TSS (NM_027187)	-786	NM_027187	69724	Mm.182470	NM_027187	ENSMUSG00000052926	Rnaseh2a	2400006P09Rik|RNASEHI|RNHIA|RNHL	ribonuclease H2, large subunit	protein-coding
mm_7052.1	chr1	87127810	87127833	-	1	NA	TTS (NM_007432)	TTS (NM_007432)	2813	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_41133.1	chr5	87788759	87788768	+	1	NA	TTS (NM_001304768)	TTS (NM_001304768)	14313	NM_007785	12993	Mm.4908	NM_007785	ENSMUSG00000061937	Csn1s2a	Csng|PP22	casein alpha s2-like A	protein-coding
mm_38611.1	chr4	141875252	141875300	-	1	NA	promoter-TSS (NM_025994)	promoter-TSS (NM_025994)	-356	NM_025994	27984	Mm.395598	NM_025994	ENSMUSG00000040659	Efhd2	2600015J22Rik|AA408606|D4Wsu27e	EF hand domain containing 2	protein-coding
mm_78566.1	chr9	35908413	35908423	+	1	NA	Intergenic	Intergenic	-58538	NR_030730	100041605	Mm.99350	NR_030730	ENSMUSG00000098705	Gm3428	-	predicted gene 3428	ncRNA
mm_46762.1	chr5	112251222	112251237	-	1	NA	intron (NM_001312884, intron 1 of 4)	intron (NM_001312884, intron 1 of 4)	1289	NM_001312884	12959	Mm.40324	NM_021351	ENSMUSG00000066975	Cryba4	-	crystallin, beta A4	protein-coding
mm_150696.1	chr19	42238614	42238624	+	1	NA	Intergenic	Intergenic	-8959	NM_001141983	71146	Mm.329851	NM_027694	ENSMUSG00000042532	Golga7b	4933417O08Rik|AI839934	golgi autoantigen, golgin subfamily a, 7B	protein-coding
mm_108542.1	chr12	84317092	84317101	+	1	NA	non-coding (NR_045615, exon 1 of 10)	non-coding (NR_045615, exon 1 of 10)	237	NM_001252583	52708	Mm.255150	NM_144833	ENSMUSG00000042472	Zfp410	Apa1|D12Ertd748e|Znf410	zinc finger protein 410	protein-coding
mm_160849.1	chr11	52214020	52214020	-	1	NA	promoter-TSS (NM_207253)	promoter-TSS (NM_207253)	-33	NM_207253	276865	Mm.377871	NM_207253	ENSMUSG00000060170	Olfr1371	GA_x6K02T2QP88-3214035-3214970|MOR256-58	olfactory receptor 1371	protein-coding
mm_124149.1	chr14	92604477	92604480	-	1	NA	Intergenic	Intergenic	1284410	NM_001271800	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding
mm_89183.1	chr10	86346017	86346024	+	1	NA	3' UTR (NM_011595, exon 5 of 5)	3' UTR (NM_011595, exon 5 of 5)	45608	NM_011595	21859	Mm.4871	NM_011595	ENSMUSG00000020044	Timp3	Timp-3	tissue inhibitor of metalloproteinase 3	protein-coding
mm_34448.1	chr4	148001326	148001338	+	1	NA	exon (NM_008725, exon 2 of 3)	exon (NM_008725, exon 2 of 3)	610	NM_008725	230899	Mm.482123	NM_008725	ENSMUSG00000041616	Nppa	ANP|Anf|Pnd	natriuretic peptide type A	protein-coding
mm_166524.1	chr6	24598023	24598036	+	1	NA	exon (NM_053098, exon 1 of 3)	exon (NM_053098, exon 1 of 3)	258	NM_053098	93677	Mm.332941	NM_053098	ENSMUSG00000029683	Lmod2	C-Lmod	leiomodin 2 (cardiac)	protein-coding
mm_14927.1	chr2	151494275	151494304	+	1	NA	5' UTR (NM_198326, exon 1 of 9)	5' UTR (NM_198326, exon 1 of 9)	107	NM_198326	386649	Mm.419479	NM_198326	ENSMUSG00000027455	Nsfl1c	Munc-18c|Stxbp3a|p47	NSFL1 (p97) cofactor (p47)	protein-coding
mm_107734.1	chr12	57564098	57564105	+	1	NA	promoter-TSS (NM_001312644)	promoter-TSS (NM_001312644)	-14	NM_001312644	70846	Mm.84118	NM_001037743	ENSMUSG00000046782	Ttc6	4921506M07Rik|EG639426|ENSMUSG00000046782|Gm69|Gm9813	tetratricopeptide repeat domain 6	protein-coding
mm_7015.1	chr1	86525277	86525310	-	1	NA	Intergenic	CpG	-1443	NM_008972	19231	Mm.19187	NM_008972	ENSMUSG00000026238	Ptma	Thym	prothymosin alpha	protein-coding
mm_82269.1	chr9	7332754	7332760	-	1	NA	Intergenic	Intergenic	-11640	NM_001320077	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_53033.1	chr6	124512714	124512735	+	1	NA	5' UTR (NM_023143, exon 1 of 11)	5' UTR (NM_023143, exon 1 of 11)	103	NM_023143	50909	Mm.333375	NM_023143	ENSMUSG00000055172	C1ra	AI132558|C1r|mC1rA	complement component 1, r subcomponent A	protein-coding
mm_11789.1	chr2	43128706	43128713	+	1	NA	Intergenic	RMER1B|Other|Other	-426616	NM_001289593	70789	Mm.105278	NM_027552	ENSMUSG00000026866	Kynu	4432411A05Rik	kynureninase (L-kynurenine hydrolase)	protein-coding
mm_121812.1	chr14	20393446	20393463	-	1	NA	TTS (NM_001163638)	TTS (NM_001163638)	101	NM_025440	66242	Mm.23747	NM_025440	ENSMUSG00000049960	Mrps16	1500011E11Rik|Mprs16	mitochondrial ribosomal protein S16	protein-coding
mm_10756.1	chr2	23207459	23207465	+	1	NA	promoter-TSS (NM_027635)	promoter-TSS (NM_027635)	-14	NM_027635	70981	Mm.314026	NM_027635	ENSMUSG00000026774	4931423N10Rik	-	RIKEN cDNA 4931423N10 gene	protein-coding
mm_50190.1	chr6	41684448	41684454	+	1	NA	promoter-TSS (NM_029671)	promoter-TSS (NM_029671)	20	NM_029671	76606	Mm.272520	NM_029671	ENSMUSG00000029867	1700034O15Rik	-	RIKEN cDNA 1700034O15 gene	protein-coding
mm_155652.1	chrX	85870267	85870297	+	1	NA	promoter-TSS (NM_001163539)	promoter-TSS (NM_001163539)	9	NM_001163539	71398	Mm.185296	NM_001163539	ENSMUSG00000025058	5430427O19Rik	-	RIKEN cDNA 5430427O19 gene	protein-coding
mm_115439.1	chr13	117602440	117602482	+	1	NA	5' UTR (NM_010408, exon 1 of 8)	5' UTR (NM_010408, exon 1 of 8)	141	NM_010408	15165	Mm.343429	NM_010408	ENSMUSG00000021730	Hcn1	Bcng1|C630013B14Rik|HAC2	hyperpolarization-activated, cyclic nucleotide-gated K+ 1	protein-coding
mm_171646.1	chr4	33270037	33270042	-	1	NA	Intergenic	LTRIS2|LTR|ERV1	-21252	NM_001033225	108767	Mm.27769	NM_001033225	ENSMUSG00000040128	Pnrc1	5730463C12Rik|B4-2|PRR2|Prol2	proline-rich nuclear receptor coactivator 1	protein-coding
mm_109345.1	chr12	109603014	109603024	+	1	NA	promoter-TSS (NR_028261)	promoter-TSS (NR_028261)	-926	NR_028261	75745	Mm.293263	NR_028261		Rian	5530401N18Rik|C130089L09Rik|Meg8	RNA imprinted and accumulated in nucleus	ncRNA
mm_87846.1	chr10	60931991	60932004	+	1	NA	intron (NR_033616, intron 1 of 2)	intron (NR_033616, intron 1 of 2)	6135	NR_033616	73616	Mm.159038	NR_033616	ENSMUSG00000037247	Pldi	1700125F08Rik|Poldi	polymorphic derived intron containing	ncRNA
mm_107023.1	chr12	12909398	12909409	+	1	NA	Intergenic	Intergenic	32433	NM_008709	18109	Mm.16469	NM_008709	ENSMUSG00000037169	Mycn	N-myc|Nmyc|Nmyc-1|Nmyc1|bHLHe37|c-nmyc	v-myc avian myelocytomatosis viral related oncogene, neuroblastoma derived	protein-coding
mm_15885.1	chr2	164839683	164839712	+	1	NA	3' UTR (NM_011125, exon 16 of 16)	3' UTR (NM_011125, exon 16 of 16)	5924	NM_008906	19025	Mm.359633	NM_008906	ENSMUSG00000017760	Ctsa	AU019505|PPCA|Ppgb	cathepsin A	protein-coding
mm_141954.1	chr17	35115472	35115520	-	1	NA	promoter-TSS (NM_148939)	promoter-TSS (NM_148939)	-96	NM_148939	266614	Mm.104680	NM_148939	ENSMUSG00000043807	Ly6g5b	-	lymphocyte antigen 6 complex, locus G5B	protein-coding
mm_50397.1	chr6	48718638	48718664	+	1	NA	promoter-TSS (NM_146167)	promoter-TSS (NM_146167)	30	NM_146167	231932	Mm.30479	NM_146167	ENSMUSG00000043931	Gimap7	IAN7|Ian3	GTPase, IMAP family member 7	protein-coding
mm_123135.1	chr14	56571809	56571820	-	1	NA	promoter-TSS (NM_001014996)	promoter-TSS (NM_001014996)	32	NM_001014996	219103	Mm.212525	NM_001014996	ENSMUSG00000064128	Cenpj	4932437H03Rik|CPAP|Gm81|LAP|LIP1|Sas4	centromere protein J	protein-coding
mm_71710.1	chr8	61936152	61936164	+	1	NA	intron (NM_001293783, intron 1 of 37)	intron (NM_001293783, intron 1 of 37)	8071	NM_001293783	234311	Mm.275233	NM_144928	ENSMUSG00000037921	Ddx60	9830118M07	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	protein-coding
mm_131558.1	chr16	18066417	18066459	+	1	NA	promoter-TSS (NM_001289814)	promoter-TSS (NM_001289814)	35	NM_001289813	13353	Mm.27155	NM_010047	ENSMUSG00000003531	Dgcr6	-	DiGeorge syndrome critical region gene 6	protein-coding
mm_77517.1	chr8	122894784	122894807	-	1	NA	non-coding (NR_037865, exon 10 of 14)	non-coding (NR_037865, exon 10 of 14)	46421	NM_007662	12555	Mm.1976	NM_007662	ENSMUSG00000031962	Cdh15	AI323380|Cdh14|Mcad	cadherin 15	protein-coding
mm_55406.1	chr6	60829827	60829849	-	1	NA	promoter-TSS (NM_001042451)	promoter-TSS (NM_001042451)	17	NM_009221	20617	Mm.17484	NM_009221	ENSMUSG00000025889	Snca	NACP|alphaSYN	synuclein, alpha	protein-coding
mm_134968.1	chr16	32003050	32003058	-	1	NA	5' UTR (NM_177103, exon 1 of 10)	5' UTR (NM_177103, exon 1 of 10)	233	NM_177103	320213	Mm.152890	NM_023801	ENSMUSG00000022772	Senp5	6230429P13Rik|A730063F07Rik|AI851888|BB189556|SMT3IP3	SUMO/sentrin specific peptidase 5	protein-coding
mm_26547.1	chr3	146220936	146220950	+	1	NA	promoter-TSS (NM_022983)	promoter-TSS (NM_022983)	-18	NM_022983	65086	Mm.155520	NM_022983	ENSMUSG00000036832	Lpar3	Edg7|lpA3	lysophosphatidic acid receptor 3	protein-coding
mm_100581.1	chr11	120784442	120784453	+	1	NA	promoter-TSS (NM_145370)	promoter-TSS (NM_145370)	-68	NM_145370	209318	Mm.30195	NM_145370	ENSMUSG00000025156	Gps1	Cops1|Csn1|R75577|Sgn1	G protein pathway suppressor 1	protein-coding
mm_143284.1	chr17	65849647	65849657	-	1	NA	3' UTR (NM_001198949, exon 10 of 10)	3' UTR (NM_001198949, exon 10 of 10)	35271	NM_001198949	19765	Mm.17009	NM_009067	ENSMUSG00000024096	Ralbp1	RLIP76|Rip1	ralA binding protein 1	protein-coding
mm_88092.1	chr10	68723762	68723786	+	1	NA	promoter-TSS (NM_177794)	promoter-TSS (NM_177794)	28	NM_177794	327766	Mm.2479	NM_177794	ENSMUSG00000060044	Tmem26	3230401A06|AI195372	transmembrane protein 26	protein-coding
mm_100547.1	chr11	120708102	120708117	+	1	NA	intron (NM_198223, intron 11 of 14)	intron (NM_198223, intron 11 of 14)	5658	NM_016665	20892	Mm.259716	NM_016665	ENSMUSG00000025144	Cenpx	Stra13	centromere protein X	protein-coding
mm_151134.1	chr19	50678930	50678936	+	1	NA	promoter-TSS (NM_021377)	promoter-TSS (NM_021377)	-287	NM_001290356	58178	Mm.313672	NM_021377	ENSMUSG00000043531	Sorcs1	Sorcs|mSorCS	sortilin-related VPS10 domain containing receptor 1	protein-coding
mm_67228.1	chr7	74555106	74555150	-	1	NA	promoter-TSS (NM_023908)	promoter-TSS (NM_023908)	-348	NM_001038643	108116	Mm.425467	NM_023908	ENSMUSG00000025790	Slco3a1	5830414C08Rik|Anr1|MJAM|OATP-D|R75096|Slc21a11	solute carrier organic anion transporter family, member 3a1	protein-coding
mm_52367.1	chr6	112976180	112976183	+	1	NA	Intergenic	Intergenic	-28915	NM_080448	259302	Mm.236401	NM_080448	ENSMUSG00000030257	Srgap3	AI452337|Arhgap14|D130026O08Rik|Gbi|MEGAP|WRP|mKIAA0411	SLIT-ROBO Rho GTPase activating protein 3	protein-coding
mm_113287.1	chr13	30166962	30166972	+	1	NA	intron (NM_153546, intron 1 of 12)	intron (NM_153546, intron 1 of 12)	30477	NM_153546	218121	Mm.89682	NM_153546	ENSMUSG00000038732	Mboat1	9130215M02Rik|BC023845|LPEAT1|Moact1|Oact1	membrane bound O-acyltransferase domain containing 1	protein-coding
mm_139702.1	chr17	57451496	57451510	+	1	NA	intron (NM_010130, intron 17 of 21)	intron (NM_010130, intron 17 of 21)	92817	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_50939.1	chr6	57707417	57707446	+	1	NA	intron (NM_133737, intron 1 of 8)	MLT1F1|LTR|ERVL-MaLR	4976	NM_133737	71835	Mm.274904	NM_133737	ENSMUSG00000062190	Lancl2	1700003F10Rik	LanC (bacterial lantibiotic synthetase component C)-like 2	protein-coding
mm_155450.1	chrX	73495334	73495402	+	1	NA	3' UTR (NM_007542, exon 8 of 8)	3' UTR (NM_007542, exon 8 of 8)	-7718	NM_001310537	320707	Mm.210095	NM_177236	ENSMUSG00000031376	Atp2b3	6430519O13Rik|Pmca3	ATPase, Ca++ transporting, plasma membrane 3	protein-coding
mm_139984.1	chr17	72837554	72837622	+	1	NA	intron (NM_027166, intron 1 of 2)	CpG	884	NM_027166	383295	Mm.277533	NM_027166	ENSMUSG00000039770	Ypel5	2310076K21Rik|CGI-127	yippee-like 5 (Drosophila)	protein-coding
mm_36349.1	chr4	73950499	73950515	-	1	NA	intron (NM_027981, intron 1 of 1)	intron (NM_027981, intron 1 of 1)	339	NM_027981	71886	Mm.158769	NM_027104	ENSMUSG00000028396	2310002L09Rik	2310003M01Rik|AV083437	RIKEN cDNA 2310002L09 gene	protein-coding
mm_156478.1	chrX	144153697	144153714	+	1	NA	promoter-TSS (NR_040271)	promoter-TSS (NR_040271)	10	NR_040271	319764	Mm.208482	NR_040271	ENSMUSG00000085139	A730046J19Rik	-	RIKEN cDNA A730046J19 gene	ncRNA
mm_61460.1	chr7	75596387	75596410	+	1	NA	intron (NM_029332, intron 5 of 36)	intron (NM_029332, intron 5 of 36)	140864	NM_029332	75547	Mm.216107	NM_029332	ENSMUSG00000066406	Akap13	1700026G02Rik|5730522G15Rik|5830460E08Rik|AKAP-13|AKAP-Lbc|BRX|Ht31|LBC|PROTO-LB|PROTO-LBC	A kinase (PRKA) anchor protein 13	protein-coding
mm_99670.1	chr11	105968516	105968523	+	1	NA	intron (NM_207624, intron 1 of 24)	intron (NM_207624, intron 1 of 24)	574	NM_207624	11421	Mm.754	NM_009598	ENSMUSG00000020681	Ace	AW208573|CD143	angiotensin I converting enzyme (peptidyl-dipeptidase A) 1	protein-coding
mm_101742.1	chr11	43379197	43379214	-	1	NA	Intergenic	Intergenic	-4744	NR_029558	387164		NR_029558	ENSMUSG00000065601	Mir146	Mirn146|miR-146a|mmu-mir-146	microRNA 146	ncRNA
mm_113440.1	chr13	34924401	34924404	+	1	NA	promoter-TSS (NM_025750)	promoter-TSS (NM_025750)	-7	NM_025750	66761	Mm.157047	NM_025750	ENSMUSG00000021415	4933417A18Rik	-	RIKEN cDNA 4933417A18 gene	protein-coding
mm_45116.1	chr5	45639445	45639457	-	1	NA	promoter-TSS (NM_021416)	promoter-TSS (NM_021416)	50	NM_021416	58227	Mm.266466	NM_021416	ENSMUSG00000015879	Fam184b	9630031F12Rik|AB041544	family with sequence similarity 184, member B	protein-coding
mm_58386.1	chr6	149309657	149309685	-	1	NA	5' UTR (NM_001289662, exon 1 of 5)	5' UTR (NM_001289662, exon 1 of 5)	257	NM_001289662	67246	Mm.333515	NM_026054	ENSMUSG00000032712	2810474O19Rik	6720435I21Rik|AA536804|AU020969|GET|Kiaa1551	RIKEN cDNA 2810474O19 gene	protein-coding
mm_25752.1	chr3	123293684	123293709	+	1	NA	exon (NM_027135, exon 5 of 23)	exon (NM_027135, exon 5 of 23)	26200	NM_027135	69608	Mm.29293	NM_027135	ENSMUSG00000039234	Sec24d	2310020L09Rik|Gm1349	Sec24 related gene family, member D (S. cerevisiae)	protein-coding
mm_30634.1	chr4	8811280	8811290	+	1	NA	intron (NM_001277149, intron 6 of 37)	intron (NM_001277149, intron 6 of 37)	120879	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_83565.1	chr9	46315905	46315914	-	1	NA	5' UTR (NM_183104, exon 3 of 13)	5' UTR (NM_183104, exon 3 of 13)	4077	NM_183104	74361	Mm.159169	NM_183104	ENSMUSG00000056617	4931429L15Rik	-	RIKEN cDNA 4931429L15 gene	protein-coding
mm_150516.1	chr19	39031355	39031361	+	1	NA	exon (NM_028089, exon 5 of 9)	exon (NM_028089, exon 5 of 9)	24339	NM_028089	72082	Mm.142581	NM_028089	ENSMUSG00000025002	Cyp2c55	2010318C06Rik	cytochrome P450, family 2, subfamily c, polypeptide 55	protein-coding
mm_113734.1	chr13	44197074	44197081	+	1	NA	intron (NR_045088, intron 3 of 3)	intron (NR_045088, intron 3 of 3)	19410	NR_045088	100503592	Mm.184925	NR_045088		A330076C08Rik	-	RIKEN cDNA A330076C08 gene	ncRNA
mm_61586.1	chr7	80014215	80014217	+	1	NA	Intergenic	Intergenic	-10598	NM_001145999	209225	Mm.290925	NM_175433	ENSMUSG00000048897	Zfp710	5430400N05Rik|9830165K13|AI324798|Znf710	zinc finger protein 710	protein-coding
mm_113676.1	chr13	42753991	42754005	+	1	NA	intron (NM_001005740, intron 1 of 12)	L2a|LINE|L2	44417	NM_001005740	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding
mm_16748.1	chr2	9834218	9834223	-	1	NA	Intergenic	Intergenic	44380	NM_008091	14462	Mm.313866	NM_008091	ENSMUSG00000015619	Gata3	Gata-3|jal	GATA binding protein 3	protein-coding
mm_60856.1	chr7	45866208	45866279	+	1	NA	exon (NM_008172, exon 1 of 12)	exon (NM_008172, exon 1 of 12)	438	NM_008172	14814	Mm.322594	NM_008172	ENSMUSG00000002771	Grin2d	GluN2D|NMDAR2D|NR2D	glutamate receptor, ionotropic, NMDA2D (epsilon 4)	protein-coding
mm_95250.1	chr11	44618579	44618591	+	1	NA	intron (NM_007897, intron 1 of 15)	CpG	485	NM_001290710	13591	Mm.439662	NM_007897	ENSMUSG00000057098	Ebf1	Ebf|O/E-1|OE-1|Olf-1|Olf1	early B cell factor 1	protein-coding
mm_162729.1	chr10	42334170	42334174	+	1	NA	intron (NM_145743, intron 10 of 12)	intron (NM_145743, intron 10 of 12)	-57430	NM_019740	56484	Mm.338613	NM_019740	ENSMUSG00000048756	Foxo3	1110048B16Rik|2010203A17Rik|C76856|FKHRL1|Fkhr2|Foxo3a	forkhead box O3	protein-coding
mm_73615.1	chr8	110117661	110117672	+	1	NA	Intergenic	Intergenic	37932	NM_175480	234725	Mm.87487	NM_175480	ENSMUSG00000044676	Zfp612	B230354B21Rik	zinc finger protein 612	protein-coding
mm_148012.1	chr18	68300150	68300193	-	1	NA	promoter-TSS (NM_026440)	promoter-TSS (NM_026440)	162	NM_153794	108654	Mm.125857	NM_153794	ENSMUSG00000038121	Fam210a	4933403F05Rik|AA987140|AV134576|AW491926	family with sequence similarity 210, member A	protein-coding
mm_106815.1	chr12	7980500	7980535	+	1	NA	exon (NM_009693, exon 4 of 29)	exon (NM_009693, exon 4 of 29)	2840	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_27001.1	chr3	25838532	25838547	-	1	NA	intron (NM_001163387, intron 3 of 5)	B3|SINE|B2	314768	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_4808.1	chr1	185332144	185332216	+	1	NA	promoter-TSS (NM_011794)	promoter-TSS (NM_011794)	21	NM_001347210	23827	Mm.227549	NM_011794	ENSMUSG00000026617	Bpnt1	BPntase	bisphosphate 3'-nucleotidase 1	protein-coding
mm_55865.1	chr6	83456813	83456862	-	1	NA	promoter-TSS (NM_001347313)	promoter-TSS (NM_001347313)	-445	NM_001347313	194388	Mm.211030	NM_183138	ENSMUSG00000034832	Tet3	B430006D22Rik|BC037432|D230004J03Rik	tet methylcytosine dioxygenase 3	protein-coding
mm_46686.1	chr5	109796271	109796286	-	1	NA	Intergenic	Intergenic	37864	NR_027964	667213	Mm.454429	NR_027964	ENSMUSG00000105044	Gm10416	EG667213|ENSMUSG00000072761	zinc finger protein pseudogene	pseudo
mm_113259.1	chr13	28417535	28417549	+	1	NA	Intergenic	Intergenic	275058	NM_023746	28078	Mm.155058	NM_023746	ENSMUSG00000017064	Prl5a1	1600013P04Rik|D13Wsu14e|Ghd24|PLP-L|Prlpl	prolactin family 5, subfamily a, member 1	protein-coding
mm_142558.1	chr17	46640061	46640072	-	1	NA	exon (NM_029091, exon 5 of 16)	exon (NM_029091, exon 5 of 16)	5078	NM_029091	74764	Mm.279599	NM_029091	ENSMUSG00000003546	Klc4	1200014P03Rik|AA408085|AW146303|Knsl8	kinesin light chain 4	protein-coding
mm_42072.1	chr5	110101178	110101216	+	1	NA	intron (NM_207279, intron 3 of 7)	intron (NM_207279, intron 3 of 7)	638	NM_001281812	403178	Mm.297057	NM_207279	ENSMUSG00000064247	Plcxd1	A330045H12Rik|Gm576	phosphatidylinositol-specific phospholipase C, X domain containing 1	protein-coding
mm_116355.1	chr13	40683886	40683896	-	1	NA	Intergenic	Intergenic	-43917	NR_125899	102633805		NR_125899	ENSMUSG00000097752	Gm26688	Tfap2a-as1	predicted gene, 26688	ncRNA
mm_140675.1	chr17	12991546	12991548	-	1	NA	intron (NM_175394, intron 1 of 5)	intron (NM_175394, intron 1 of 5)	712	NM_001113533	60532	Mm.275521	NM_175394	ENSMUSG00000060475	Wtap	2810408K05Rik|9430038B09Rik	Wilms tumour 1-associating protein	protein-coding
mm_122014.1	chr14	27337228	27337255	-	1	NA	intron (NM_001289687, intron 1 of 9)	intron (NM_001289687, intron 1 of 9)	1204	NM_001289687	71704	Mm.248606	NM_027871	ENSMUSG00000021895	Arhgef3	1200004I24Rik|9830169H03Rik|C76747|Xpln	Rho guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_72050.1	chr8	71366871	71366946	+	1	NA	promoter-TSS (NM_025917)	promoter-TSS (NM_025917)	60	NM_001145780	67023	Mm.41890	NM_025917	ENSMUSG00000002395	Use1	2010315L10Rik|5730403H22Rik|AV002165|D12|Ed2|Q-snare|p31	unconventional SNARE in the ER 1 homolog (S. cerevisiae)	protein-coding
mm_170171.1	chr17	56047588	56047605	+	1	NA	exon (NM_013733, exon 3 of 14)	exon (NM_013733, exon 3 of 14)	7180	NM_013733	27221	Mm.391010	NM_013733	ENSMUSG00000002835	Chaf1a	AL023013|AL024058|CAF-1|Cac1p	chromatin assembly factor 1, subunit A (p150)	protein-coding
mm_149647.1	chr19	17926553	17926555	+	1	NA	Intergenic	Lx3C|LINE|L1	-88922	NM_001190483	18552	Mm.3401	NM_001163144	ENSMUSG00000024713	Pcsk5	PC5|PC6|SPC6|b2b1549Clo|b2b585Clo	proprotein convertase subtilisin/kexin type 5	protein-coding
mm_27909.1	chr3	79521377	79521389	-	1	NA	intron (NM_001162999, intron 1 of 16)	B1F|SINE|Alu	46296	NM_001162999	329679	Mm.244005	NM_001162999	ENSMUSG00000061175	Fnip2	D630023B12Rik|mKIAA1450	folliculin interacting protein 2	protein-coding
mm_70955.1	chr8	26977459	26977490	+	1	NA	exon (NM_001110508, exon 1 of 3)	exon (NM_001110508, exon 1 of 3)	138	NM_001110508	353310	Mm.212469	NM_001101502	ENSMUSG00000085795	Zfp703	1110032O19Rik|AI430822|AL022941|Csmn1|End2|Zeppo1|Znf703|Zpo1	zinc finger protein 703	protein-coding
mm_33799.1	chr4	134926591	134926603	+	1	NA	intron (NM_023665, intron 3 of 4)	intron (NM_023665, intron 3 of 4)	2972	NM_023665	27981	Mm.331964	NM_023665	ENSMUSG00000037266	Rsrp1	2700043I21Rik|D4Ucla2|D4Wsu53e	arginine/serine rich protein 1	protein-coding
mm_134917.1	chr16	30314834	30314844	-	1	NA	3' UTR (NM_001128094, exon 33 of 33)	3' UTR (NM_001128094, exon 33 of 33)	-4058	NM_008148	14729	Mm.3519	NM_008148	ENSMUSG00000047953	Gp5	GPV	glycoprotein 5 (platelet)	protein-coding
mm_64360.1	chr7	142398277	142398285	+	1	NA	Intergenic	Intergenic	-10411	NM_009983	13033	Mm.231395	NM_009983	ENSMUSG00000007891	Ctsd	CD|CatD	cathepsin D	protein-coding
mm_21942.1	chr2	167060832	167060836	-	1	NA	intron (NM_001033196, intron 1 of 13)	intron (NM_001033196, intron 1 of 13)	-2100	NR_138563	68949	Mm.391959	NM_001081005		Zfas1	1500012F01Rik|Zfos1	zinc finger, NFX1-type containing 1, antisense RNA 1	ncRNA
mm_29282.1	chr3	107670572	107670575	-	1	NA	intron (NM_145542, intron 7 of 16)	intron (NM_145542, intron 7 of 16)	25975	NM_145542	229709	Mm.220328	NM_145542	ENSMUSG00000027893	Ahcyl1	1110034F20Rik|AA409031|AA414901|Ahcy-rs3|DCAL|Irbit	S-adenosylhomocysteine hydrolase-like 1	protein-coding
mm_76475.1	chr8	85432770	85432836	-	1	NA	promoter-TSS (NM_025722)	promoter-TSS (NM_025722)	38	NR_033144	66714	Mm.272748	NM_025722	ENSMUSG00000036934	4921524J17Rik	-	RIKEN cDNA 4921524J17 gene	protein-coding
mm_40040.1	chr5	33820484	33820509	+	1	NA	Intergenic	CpG	-22616	NM_175231	107823	Mm.19892	NM_175231	ENSMUSG00000057406	Whsc1	5830445G22Rik|9430010A17Rik|AW555663|C130020C13Rik|D030027O06Rik|D930023B08Rik|MMSET|NSD2|Whsc1l|mKIAA1090	Wolf-Hirschhorn syndrome candidate 1 (human)	protein-coding
mm_37897.1	chr4	132611392	132611408	-	1	NA	Intergenic	Intergenic	-27646	NM_210071	14050	Mm.227733	NM_010166	ENSMUSG00000028886	Eya3	AI844637	EYA transcriptional coactivator and phosphatase 3	protein-coding
mm_57290.1	chr6	124433491	124433515	-	1	NA	intron (NM_001346656, intron 16 of 17)	intron (NM_001346656, intron 16 of 17)	-18436	NM_001277805	19305	Mm.22418	NM_008995	ENSMUSG00000005069	Pex5	AW212715|ESTM1|PTS1R|Pxr1|X83306	peroxisomal biogenesis factor 5	protein-coding
mm_39222.1	chr4	156199655	156199666	-	1	NA	exon (NM_015783, exon 2 of 2)	exon (NM_015783, exon 2 of 2)	1158	NM_015783	100038882	Mm.4950	NM_015783	ENSMUSG00000035692	Isg15	G1p2|IGI15|IP17|Irfp|UCRP	ISG15 ubiquitin-like modifier	protein-coding
mm_136529.1	chr16	97478740	97478750	-	1	NA	intron (NM_020622, intron 3 of 7)	intron (NM_020622, intron 3 of 7)	-15839	NR_003520	17857	Mm.33996	NM_010846	ENSMUSG00000000386	Mx1	AI893580|Mx|Mx-1	MX dynamin-like GTPase 1	protein-coding
mm_56003.1	chr6	86488015	86488085	-	1	NA	non-coding (NR_040293, exon 1 of 2)	non-coding (NR_040293, exon 1 of 2)	177	NR_040293	381792	Mm.333223	NR_040292	ENSMUSG00000101655	2310040G24Rik	-	RIKEN cDNA 2310040G24 gene	ncRNA
mm_148569.1	chr19	4855148	4855269	+	1	NA	promoter-TSS (NM_019861)	promoter-TSS (NM_019861)	79	NM_019861	56464	Mm.29561	NM_019861	ENSMUSG00000083282	Ctsf	AI481912	cathepsin F	protein-coding
mm_4744.1	chr1	182124775	182124800	+	1	NA	promoter-TSS (NM_012058)	promoter-TSS (NM_012058)	50	NM_012058	27058	Mm.273196	NM_012058	ENSMUSG00000026511	Srp9	9kDa	signal recognition particle 9	protein-coding
mm_79416.1	chr9	55213854	55213866	+	1	NA	intron (NM_028049, intron 2 of 6)	intron (NM_028049, intron 2 of 6)	4925	NM_028049	71999	Mm.276429	NM_028049	ENSMUSG00000032309	Fbxo22	0610033L19Rik|1600016C16Rik	F-box protein 22	protein-coding
mm_51145.1	chr6	70572585	70572604	+	1	NA	Intergenic	Intergenic	219581	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_58279.1	chr6	145862016	145862019	-	1	NA	3' UTR (NM_001271768, exon 5 of 5)	3' UTR (NM_001271768, exon 5 of 5)	3403	NM_001271768	79362	Mm.154529	NM_024469	ENSMUSG00000030256	Bhlhe41	6430520M22Rik|Bhlhb2l|Bhlhb3|DEC2|Sharp1	basic helix-loop-helix family, member e41	protein-coding
mm_52136.1	chr6	97957012	97957017	+	1	NA	intron (NM_001113198, intron 2 of 9)	intron (NM_001113198, intron 2 of 9)	27197	NM_001178049	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_51537.1	chr6	83195877	83195881	+	1	NA	intron (NM_001347310, intron 20 of 26)	intron (NM_001347310, intron 20 of 26)	9933	NM_001347310	13191	Mm.6919	NM_007835	ENSMUSG00000031865	Dctn1	AL022633|DAP-150|DP-150|Glued|p150|p150-glued|p150<glued>	dynactin 1	protein-coding
mm_88999.1	chr10	81575546	81575557	+	1	NA	5' UTR (NM_019725, exon 1 of 21)	5' UTR (NM_019725, exon 1 of 21)	264	NM_001252401	21886	Mm.38608	NM_019725	ENSMUSG00000034771	Tle2	Grg2|mKIAA4188	transducin-like enhancer of split 2	protein-coding
mm_124808.1	chr15	8914096	8914115	+	1	NA	Intergenic	Intergenic	-53844	NM_198024	223332	Mm.321371	NM_198024	ENSMUSG00000048424	Ranbp3l	C130037N17Rik	RAN binding protein 3-like	protein-coding
mm_51961.1	chr6	91758010	91758021	+	1	NA	3' UTR (NM_009320, exon 15 of 15)	3' UTR (NM_009320, exon 15 of 15)	49378	NM_001159507	243547	Mm.333264	NM_001033353	ENSMUSG00000030098	Grip2	-	glutamate receptor interacting protein 2	protein-coding
mm_148577.1	chr19	4962309	4962332	+	1	NA	promoter-TSS (NM_025553)	promoter-TSS (NM_025553)	14	NM_025553	66419	Mm.28494	NM_025553	ENSMUSG00000024902	Mrpl11	2410001P07Rik|L11mt	mitochondrial ribosomal protein L11	protein-coding
mm_40770.1	chr5	67098672	67098686	+	1	NA	intron (NM_008888, intron 1 of 2)	intron (NM_008888, intron 1 of 2)	447	NM_008888	18935	Mm.62505	NM_008888	ENSMUSG00000012520	Phox2b	Dilp1|NBPhox|Pmx2b|Px2b	paired-like homeobox 2b	protein-coding
mm_10699.1	chr2	22755972	22755981	+	1	NA	Intergenic	RMER1A|Other|Other	-18351	NM_019456	54519	Mm.14255	NM_019456	ENSMUSG00000026786	Apbb1ip	9930118P07Rik|Prp48	amyloid beta (A4) precursor protein-binding, family B, member 1 interacting protein	protein-coding
mm_144151.1	chr18	5591427	5591446	+	1	NA	promoter-TSS (NM_011546)	promoter-TSS (NM_011546)	-424	NM_011546	21417	Mm.3929	NM_011546	ENSMUSG00000024238	Zeb1	3110032K11Rik|AREB6|BZP|MEB1|Nil2|TCF-8|Tcf18|Tcf8|Tw|ZEB|Zfhep|Zfhx1a|Zfx1a|Zfx1ha|[delta]EF1	zinc finger E-box binding homeobox 1	protein-coding
mm_125616.1	chr15	61987411	61987491	+	1	NA	intron (NM_001177353, intron 1 of 2)	CpG	2110	NM_001177352	17869	Mm.2444	NM_010849	ENSMUSG00000022346	Myc	AU016757|Myc2|Niard|Nird|bHLHe39	myelocytomatosis oncogene	protein-coding
mm_109980.1	chr12	12941442	12941443	-	1	NA	intron (NM_008709, intron 1 of 2)	intron (NM_008709, intron 1 of 2)	394	NM_008709	18109	Mm.16469	NM_008709	ENSMUSG00000037169	Mycn	N-myc|Nmyc|Nmyc-1|Nmyc1|bHLHe37|c-nmyc	v-myc avian myelocytomatosis viral related oncogene, neuroblastoma derived	protein-coding
mm_171150.1	chr3	159495088	159495100	+	1	NA	promoter-TSS (NM_001172093)	promoter-TSS (NM_001172093)	-339	NM_001172092	76131	Mm.371655	NM_029523	ENSMUSG00000028175	Depdc1a	5830484J08Rik|Depdc1	DEP domain containing 1a	protein-coding
mm_79490.1	chr9	57073736	57073754	+	1	NA	intron (NM_001110351, intron 1 of 21)	intron (NM_001110351, intron 1 of 21)	1705	NM_001110351	20466	Mm.15755	NM_011378	ENSMUSG00000042557	Sin3a	AW553200|Sin3|mKIAA4126|mSin3A	transcriptional regulator, SIN3A (yeast)	protein-coding
mm_90273.1	chr10	122757133	122757181	+	1	NA	intron (NM_176919, intron 1 of 8)	RLTR17D_Mm|LTR|ERVK	77842	NR_106182	102466884		NR_106182	ENSMUSG00000099225	Mir8104	Gm27380|mmu-mir-8104	microRNA 8104	ncRNA
mm_60968.1	chr7	47772813	47772816	+	1	NA	Intergenic	Intergenic	-171442	NM_153067	233222	Mm.240142	NM_153067	ENSMUSG00000078698	Mrgpra3	Mrga3	MAS-related GPR, member A3	protein-coding
mm_95052.1	chr11	32358690	32358700	+	1	NA	intron (NM_177364, intron 1 of 12)	intron (NM_177364, intron 1 of 12)	10884	NM_177364	268396	Mm.227616	NM_177364	ENSMUSG00000040711	Sh3pxd2b	G431001E03Rik|TSK4|fad49	SH3 and PX domains 2B	protein-coding
mm_133820.1	chr16	95769189	95769199	+	1	NA	Intergenic	Intergenic	66787	NM_011809	23872	Mm.290207	NM_011809	ENSMUSG00000022895	Ets2	AU022856|Ets-2	E26 avian leukemia oncogene 2, 3' domain	protein-coding
mm_154795.1	chrX	13202602	13202619	+	1	NA	Intergenic	Intergenic	33673	NR_045430	72122	Mm.75434	NR_045429	ENSMUSG00000100714	2010308F09Rik	-	RIKEN cDNA 2010308F09 gene	ncRNA
mm_134235.1	chr16	11909338	11909353	-	1	NA	promoter-TSS (NM_146067)	promoter-TSS (NM_146067)	78	NM_146067	223978	Mm.86360	NM_146067	ENSMUSG00000065979	Cpped1	C530044N13Rik	calcineurin-like phosphoesterase domain containing 1	protein-coding
mm_137684.1	chr17	28847977	28847980	+	1	NA	Intergenic	RLTR41B|LTR|ERV1	-10433	NM_001034885	433091	Mm.328925	NM_001034885	ENSMUSG00000043286	Pnpla1	-	patatin-like phospholipase domain containing 1	protein-coding
mm_40775.1	chr5	67260745	67260779	+	1	NA	5' UTR (NM_030108, exon 1 of 9)	5' UTR (NM_030108, exon 1 of 9)	197	NM_030108	67878	Mm.23217	NM_028975	ENSMUSG00000037720	Tmem33	1110006G02Rik|1600019D15Rik|2410089A21Rik|2700052H22Rik|5430406L04Rik|AA388285|AI314185|AI426615|db83	transmembrane protein 33	protein-coding
mm_166808.1	chr7	6774845	6774845	+	1	NA	intron (NM_021323, intron 2 of 7)	intron (NM_021323, intron 2 of 7)	-28742	NR_037213	100499513		NR_037213	ENSMUSG00000092815	Mir3099	mir-3099|mmu-mir-3099	microRNA 3099	ncRNA
mm_41111.1	chr5	87778053	87778059	+	1	NA	intron (NM_007785, intron 3 of 13)	intron (NM_007785, intron 3 of 13)	3606	NM_007785	12993	Mm.4908	NM_007785	ENSMUSG00000061937	Csn1s2a	Csng|PP22	casein alpha s2-like A	protein-coding
mm_156860.1	chrX	164402223	164402249	+	1	NA	3' UTR (NM_010216, exon 7 of 7)	3' UTR (NM_010216, exon 7 of 7)	-17551	NM_011081	18700	Mm.3781	NM_011081	ENSMUSG00000031381	Piga	AI194334|Pig-a	phosphatidylinositol glycan anchor biosynthesis, class A	protein-coding
mm_115876.1	chr13	21750536	21750543	-	1	NA	promoter-TSS (NM_178211)	promoter-TSS (NM_178211)	14	NM_178211	319160	Mm.255646	NM_178211	ENSMUSG00000064288	Hist1h4k	-	histone cluster 1, H4k	protein-coding
mm_111393.1	chr12	90726910	90726915	-	1	NA	3' UTR (NM_010050, exon 2 of 2)	3' UTR (NM_010050, exon 2 of 2)	12125	NM_010050	13371	Mm.21389	NM_010050	ENSMUSG00000007682	Dio2	5DII|AI324267|DIOII	deiodinase, iodothyronine, type II	protein-coding
mm_171165.1	chr3	25731232	25731233	+	1	NA	intron (NM_001163387, intron 3 of 5)	intron (NM_001163387, intron 3 of 5)	422075	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_35903.1	chr4	49597838	49597849	-	1	NA	promoter-TSS (NM_025944)	promoter-TSS (NM_025944)	27	NM_025944	67063	Mm.490285	NM_025944	ENSMUSG00000039611	Tmem246	2810432L12Rik|9330170P15Rik|AI835809	transmembrane protein 246	protein-coding
mm_81109.1	chr9	106453242	106453276	+	1	NA	promoter-TSS (NM_021567)	promoter-TSS (NM_021567)	-579	NM_021567	59092	Mm.286394	NM_021567	ENSMUSG00000023495	Pcbp4	1200003L19Rik|AlphaCP-4	poly(rC) binding protein 4	protein-coding
mm_63629.1	chr7	128374563	128374581	+	1	NA	intron (NM_026418, intron 4 of 4)	YREP_Mm|Unknown|Unknown	43600	NM_026418	67865	Mm.18635	NM_026418	ENSMUSG00000030844	Rgs10	2310010N19Rik	regulator of G-protein signalling 10	protein-coding
mm_126493.1	chr15	81648797	81648811	+	1	NA	exon (NM_177821, exon 31 of 31)	exon (NM_177821, exon 31 of 31)	-15085	NM_001289712	214669	Mm.280768	NM_145993	ENSMUSG00000022394	L3mbtl2	4732493N06Rik|M4mbt	l(3)mbt-like 2 (Drosophila)	protein-coding
mm_20160.1	chr2	122147503	122147520	-	1	NA	promoter-TSS (NM_009735)	promoter-TSS (NM_009735)	-176	NM_009735	12010	Mm.163	NM_009735	ENSMUSG00000060802	B2m	Ly-m11|beta2-m|beta2m	beta-2 microglobulin	protein-coding
mm_89766.1	chr10	100097024	100097035	+	1	NA	3' UTR (NM_013598, exon 10 of 10)	3' UTR (NM_013598, exon 10 of 10)	81208	NM_013598	17311	Mm.45124	NM_013598	ENSMUSG00000019966	Kitl	Clo|Con|Gb|Kitlg|Mgf|SCF|SF|SLF|Sl|blz|contrasted	kit ligand	protein-coding
mm_107329.1	chr12	31870583	31870586	+	1	NA	intron (NM_001163126, intron 16 of 22)	MER20|DNA|hAT-Charlie	79951	NM_177993	73389	Mm.390461	NM_153198	ENSMUSG00000002996	Hbp1	1700058O05Rik|BE629963|C330012F01Rik|C86454	high mobility group box transcription factor 1	protein-coding
mm_43393.1	chr5	135778466	135778471	+	1	NA	promoter-TSS (NM_029659)	promoter-TSS (NM_029659)	-83	NM_001289557	76571	Mm.247666	NM_029659	ENSMUSG00000019178	Styxl1	1700011C14Rik|Dusp24|Mkstyx	serine/threonine/tyrosine interacting-like 1	protein-coding
mm_13374.1	chr2	103606429	103606441	+	1	NA	intron (NM_178890, intron 1 of 16)	intron (NM_178890, intron 1 of 16)	40125	NM_178890	99382	Mm.35850	NM_178890	ENSMUSG00000032724	Abtb2	AW539457|BPOZ-2	ankyrin repeat and BTB (POZ) domain containing 2	protein-coding
mm_160879.1	chr11	69156877	69156877	+	1	NA	promoter-TSS (NM_009659)	promoter-TSS (NM_009659)	-195	NM_009659	11686	Mm.340329	NM_009659	ENSMUSG00000032807	Alox12b	12R-LOX|Aloxe2|e-LOX2	arachidonate 12-lipoxygenase, 12R type	protein-coding
mm_60979.1	chr7	48963898	48963916	+	1	NA	5' UTR (NM_001111016, exon 2 of 39)	5' UTR (NM_001111016, exon 2 of 39)	4834	NM_001111016	78286	Mm.333881	NM_175272	ENSMUSG00000052512	Nav2	5330421F07Rik|AU067780|BQ960892|HELAD1|POMFIL2|RAINB1|RAINB2|Unc53H2|mKIAA3015	neuron navigator 2	protein-coding
mm_56708.1	chr6	115251840	115251867	-	1	NA	promoter-TSS (NM_080639)	promoter-TSS (NM_080639)	-4	NM_080639	110595	Mm.255607	NM_080639	ENSMUSG00000030317	Timp4	TIMP-4	tissue inhibitor of metalloproteinase 4	protein-coding
mm_81293.1	chr9	108337279	108337299	+	1	NA	3' UTR (NM_016802, exon 6 of 6)	3' UTR (NM_016802, exon 6 of 6)	-1791	NM_008160	14775	Mm.1090	NM_008160	ENSMUSG00000063856	Gpx1	AI195024|AL033363|CGPx|GPx-1|GSHPx-1|Gpx	glutathione peroxidase 1	protein-coding
mm_2238.1	chr1	91053175	91053192	+	1	NA	promoter-TSS (NM_008515)	promoter-TSS (NM_008515)	-261	NM_001310732	16978	Mm.45039	NM_008515	ENSMUSG00000026305	Lrrfip1	AU024550|Fliiap1	leucine rich repeat (in FLII) interacting protein 1	protein-coding
mm_41028.1	chr5	83837190	83837195	+	1	NA	Intergenic	Lx8|LINE|L1	-481997	NM_153801	243078	Mm.126783	NM_153801	ENSMUSG00000049537	Tecrl	D330017N19Rik|Srd5a2l2	trans-2,3-enoyl-CoA reductase-like	protein-coding
mm_165208.1	chr2	34958311	34958317	+	1	NA	intron (NM_009421, intron 4 of 10)	intron (NM_009421, intron 4 of 10)	3458	NM_009421	22029	Mm.239514	NM_009421	ENSMUSG00000026875	Traf1	4732496E14Rik	TNF receptor-associated factor 1	protein-coding
mm_163225.1	chr11	102097593	102097596	-	1	NA	Intergenic	Intergenic	3706	NM_008918	19064	Mm.1269	NM_008918	ENSMUSG00000017316	Ppy	AV061413|IGSPP|PP	pancreatic polypeptide	protein-coding
mm_102329.1	chr11	57828957	57828963	-	1	NA	3' UTR (NM_008213, exon 2 of 2)	3' UTR (NM_008213, exon 2 of 2)	3187	NM_008213	15110	Mm.4746	NM_008213	ENSMUSG00000037335	Hand1	Ehand1|Hxt|Th1|Thing1|bHLHa27|eHAND	heart and neural crest derivatives expressed transcript 1	protein-coding
mm_99933.1	chr11	111026673	111026682	+	1	NA	3' UTR (NM_001252208, exon 2 of 2)	3' UTR (NM_001252208, exon 2 of 2)	2817	NM_001252208	16517	Mm.30176	NM_010604	ENSMUSG00000051497	Kcnj16	6430410F18Rik|AI132396|Kir5.1	potassium inwardly-rectifying channel, subfamily J, member 16	protein-coding
mm_27558.1	chr3	58525769	58525788	-	1	NA	promoter-TSS (NM_001005509)	promoter-TSS (NM_001005509)	-43	NM_001005509	229317	Mm.21617	NM_001005509	ENSMUSG00000027810	Eif2a	D030048D22|D3Ertd194e	eukaryotic translation initiation factor 2A	protein-coding
mm_130301.1	chr15	97019879	97019883	-	1	NA	intron (NM_027052, intron 1 of 15)	intron (NM_027052, intron 1 of 15)	36075	NM_027052	69354	Mm.250980	NM_027052	ENSMUSG00000022464	Slc38a4	1110012E16Rik|1700012A18Rik|Ata3|mATA3|mNAT3	solute carrier family 38, member 4	protein-coding
mm_93840.1	chr10	121626291	121626310	-	1	NA	promoter-TSS (NM_001081056)	promoter-TSS (NM_001081056)	16	NM_001081056	73192	Mm.25042	NM_001081056	ENSMUSG00000034667	Xpot	1110004L07Rik|3110065H13Rik|AI452076|C79645|EXPORTIN-T	exportin, tRNA (nuclear export receptor for tRNAs)	protein-coding
mm_53748.1	chr6	145212526	145212529	+	1	NA	intron (NM_001163628, intron 1 of 2)	intron (NM_001163628, intron 1 of 2)	1380	NM_133688	67636	Mm.486359	NM_133688	ENSMUSG00000040370	Lyrm5	4930469P12Rik|AL022899|Etfrf1|Ghiso	LYR motif containing 5	protein-coding
mm_9616.1	chr1	176214042	176214047	-	1	NA	promoter-TSS (NM_001195816)	promoter-TSS (NM_001195816)	-102	NM_001195816	319455	Mm.338001	NM_176916	ENSMUSG00000055214	Pld5	B230365F16Rik	phospholipase D family, member 5	protein-coding
mm_158145.1	chrX	103467290	103467338	-	1	NA	non-coding (NR_001570, exon 7 of 8)	non-coding (NR_001570, exon 7 of 8)	15919	NR_001570	213742	Mm.274770	NR_001463	ENSMUSG00000086503	Xist	A430022B11|AI314753	inactive X specific transcripts	ncRNA
mm_63517.1	chr7	127876925	127876954	+	1	NA	promoter-TSS (NM_146259)	promoter-TSS (NM_146259)	-116	NM_146259	244219	Mm.207872	NM_146259	ENSMUSG00000049728	Zfp668	BC030314|E130018B19Rik|Znf668	zinc finger protein 668	protein-coding
mm_8431.1	chr1	152592763	152592779	-	1	NA	intron (NM_001346119, intron 2 of 17)	intron (NM_001346119, intron 2 of 17)	32446	NM_016846	19731	Mm.245270	NM_016846	ENSMUSG00000026482	Rgl1	Rgl|mKIAA0959	ral guanine nucleotide dissociation stimulator,-like 1	protein-coding
mm_133501.1	chr16	90498498	90498506	+	1	NA	3' UTR (NM_015755, exon 11 of 11)	3' UTR (NM_015755, exon 11 of 11)	112105	NM_015755	26559	Mm.125874	NM_015755	ENSMUSG00000053414	Hunk	Bstk1|Mak-v	hormonally upregulated Neu-associated kinase	protein-coding
mm_110917.1	chr12	76255047	76255057	-	1	NA	promoter-TSS (NM_138745)	promoter-TSS (NM_138745)	-180	NM_138745	108156	Mm.29584	NM_138745	ENSMUSG00000021048	Mthfd1	Dcs|E430024A07Rik|Mthfd	methylenetetrahydrofolate dehydrogenase (NADP+ dependent), methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthase	protein-coding
mm_123580.1	chr14	67008526	67008542	-	1	NA	intron (NM_009761, intron 1 of 5)	CpG	343	NM_009761	12177	Mm.29820	NM_009761	ENSMUSG00000022051	Bnip3l	C86132|D14Ertd719e|Nip3L|Nix	BCL2/adenovirus E1B interacting protein 3-like	protein-coding
mm_163295.1	chr11	119916697	119916707	+	1	NA	exon (NM_001085498, exon 5 of 8)	exon (NM_001085498, exon 5 of 8)	2892	NM_001085498	208092	Mm.306673	NM_001085498	ENSMUSG00000025371	Chmp6	2400004G01Rik	charged multivesicular body protein 6	protein-coding
mm_18475.1	chr2	62412220	62412234	-	1	NA	promoter-TSS (NM_010074)	promoter-TSS (NM_010074)	4	NM_010074	13482	Mm.1151	NM_010074	ENSMUSG00000035000	Dpp4	Cd26|Dpp-4|THAM	dipeptidylpeptidase 4	protein-coding
mm_163821.1	chr14	19416755	19416765	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	185827	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_32109.1	chr4	98923725	98923743	+	1	NA	promoter-TSS (NM_146144)	promoter-TSS (NM_146144)	-76	NM_001301414	230484	Mm.371692	NM_146144	ENSMUSG00000028560	Usp1	-	ubiquitin specific peptidase 1	protein-coding
mm_156675.1	chrX	159256112	159256122	+	1	NA	5' UTR (NM_148945, exon 1 of 22)	5' UTR (NM_148945, exon 1 of 22)	335	NM_001346675	110651	Mm.328476	NM_148945	ENSMUSG00000031309	Rps6ka3	MAPKAPK-1b|MPK-9|Rsk2|S6K-alpha3|p90RSK3|pp90RSK2	ribosomal protein S6 kinase polypeptide 3	protein-coding
mm_22379.1	chr2	181156798	181156808	-	1	NA	5' UTR (NM_007906, exon 1 of 8)	5' UTR (NM_007906, exon 1 of 8)	212	NM_007906	13628	Mm.2645	NM_007906	ENSMUSG00000016349	Eef1a2	Eef1a|S1|wasted|wst	eukaryotic translation elongation factor 1 alpha 2	protein-coding
mm_53224.1	chr6	127072903	127072910	+	1	NA	promoter-TSS (NM_022657)	promoter-TSS (NM_022657)	4	NM_022657	64654	Mm.347933	NM_022657	ENSMUSG00000000182	Fgf23	-	fibroblast growth factor 23	protein-coding
mm_142299.1	chr17	42372821	42372822	-	1	NA	intron (NM_028474, intron 2 of 3)	intron (NM_028474, intron 2 of 3)	56874	NM_028474	627626	Mm.390999	NM_028474	ENSMUSG00000042256	Ptchd4	3110082D06Rik|Gm321	patched domain containing 4	protein-coding
mm_137994.1	chr17	33638121	33638123	+	1	NA	promoter-TSS (NR_028279)	promoter-TSS (NR_028279)	27	NR_028279	378460	Mm.272606	NM_001002842	ENSMUSG00000032739	Pram1	AY665714	PML-RAR alpha-regulated adaptor molecule 1	protein-coding
mm_109022.1	chr12	103551680	103551720	+	1	NA	intron (NM_028980, intron 2 of 24)	intron (NM_028980, intron 2 of 24)	19135	NM_028980	74521	Mm.248619	NM_028980	ENSMUSG00000021209	Ppp4r4	8430415E04Rik|mKIAA1622	protein phosphatase 4, regulatory subunit 4	protein-coding
mm_168846.1	chr12	23800904	23800905	-	1	NA	Intergenic	CpG	296365	NM_001256489	66808	Mm.379124	NM_001256489	ENSMUSG00000073158	9030624G23Rik	-	RIKEN cDNA 9030624G23 gene	protein-coding
mm_69741.1	chr7	140950283	140950291	-	1	NA	promoter-TSS (NM_053088)	promoter-TSS (NM_053088)	-48	NM_053088	73835	Mm.389989	NM_053088	ENSMUSG00000025489	Ifitm5	1110003J06Rik|AW213665|Bril|DSPA1|Hrmp1|Hrtm1	interferon induced transmembrane protein 5	protein-coding
mm_31408.1	chr4	48047865	48047888	+	1	NA	intron (NM_015743, intron 1 of 7)	intron (NM_015743, intron 1 of 7)	2571	NM_015743	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_21206.1	chr2	155640713	155640723	-	1	NA	intron (NM_019828, intron 12 of 18)	intron (NM_019828, intron 12 of 18)	17838	NR_030757	735275		NR_030757	ENSMUSG00000076312	Mir499	Mirn499|mir-499|mmu-mir-499	microRNA 499	ncRNA
mm_163966.1	chr14	54966513	54966537	-	1	NA	promoter-TSS (NM_010856)	promoter-TSS (NM_010856)	82	NM_001164171	17888	Mm.290003	NM_010856	ENSMUSG00000040752	Myh6	A830009F23Rik|AA517445|Myhc-a|Myhca|alpha-MHC	myosin, heavy polypeptide 6, cardiac muscle, alpha	protein-coding
mm_145078.1	chr18	42319884	42319919	+	1	NA	exon (NM_172626, exon 10 of 20)	exon (NM_172626, exon 10 of 20)	44548	NM_172626	225432	Mm.329400	NM_172626	ENSMUSG00000024491	Rbm27	A730010I06|AI043120|Psc1|mKIAA1311	RNA binding motif protein 27	protein-coding
mm_88668.1	chr10	80017602	80017639	+	1	NA	intron (NM_001347074, intron 1 of 22)	intron (NM_001347074, intron 1 of 22)	705	NM_001347074	70719	Mm.243954	NM_027521	ENSMUSG00000035697	Hmha1	6330406L22Rik|AW539505|Ha-1	histocompatibility (minor) HA-1	protein-coding
mm_154482.1	chrM	4550	4565	-	1	NA	NA	Intergenic	NA	NA								
mm_25382.1	chr3	107212827	107212834	+	1	NA	exon (NM_001111143, exon 8 of 9)	exon (NM_001111143, exon 8 of 9)	8902	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_88574.1	chr10	79682148	79682161	+	1	NA	promoter-TSS (NM_177613)	promoter-TSS (NM_177613)	-41	NM_177613	216150	Mm.21981	NM_177613	ENSMUSG00000020307	Cdc34	AI327276|UBE2R1	cell division cycle 34	protein-coding
mm_108242.1	chr12	78197073	78197086	+	1	NA	Intergenic	Intergenic	-29576	NM_172952	268566	Mm.341742	NM_145965	ENSMUSG00000047454	Gphn	5730552E08Rik|AI662856|BC027112|C230040D23|GPH|GPHRYN|geph	gephyrin	protein-coding
mm_131091.1	chr16	4886240	4886268	+	1	NA	5' UTR (NM_029657, exon 1 of 17)	5' UTR (NM_029657, exon 1 of 17)	154	NM_001252437	17237	Mm.291326	NM_029657	ENSMUSG00000022517	Mgrn1	2610042J20Rik|mKIAA0544|md|nc	mahogunin, ring finger 1	protein-coding
mm_85855.1	chr9	110742566	110742576	-	1	NA	promoter-TSS (NM_001083936)	promoter-TSS (NM_001083936)	39	NM_001083936	19228	Mm.3542	NM_011199	ENSMUSG00000032492	Pth1r	PPR|Pthr|Pthr1	parathyroid hormone 1 receptor	protein-coding
mm_96982.1	chr11	70656632	70656634	+	1	NA	promoter-TSS (NM_007933)	promoter-TSS (NM_007933)	-543	NM_001136062	13808	Mm.251322	NM_007933	ENSMUSG00000060600	Eno3	Eno-3|MSE	enolase 3, beta muscle	protein-coding
mm_139734.1	chr17	57484718	57484729	+	1	NA	Intergenic	MTE2b|LTR|ERVL-MaLR	60591	NM_001104591	224916	Mm.469889	NM_001104591	ENSMUSG00000090655	Vmn2r120	EG224916	vomeronasal 2, receptor 120	protein-coding
mm_171675.1	chr4	51254354	51254367	-	1	NA	Intergenic	Intergenic	37682	NM_001162865	74914	Mm.159368	NM_001162865	ENSMUSG00000039555	Cylc2	4930488P18Rik	cylicin, basic protein of sperm head cytoskeleton 2	protein-coding
mm_156479.1	chrX	144153717	144153765	+	1	NA	promoter-TSS (NR_040271)	promoter-TSS (NR_040271)	46	NR_040271	319764	Mm.208482	NR_040271	ENSMUSG00000085139	A730046J19Rik	-	RIKEN cDNA A730046J19 gene	ncRNA
mm_70240.1	chr8	3353610	3353620	+	1	NA	5' UTR (NM_001033378, exon 1 of 11)	5' UTR (NM_001033378, exon 1 of 11)	200	NM_001033378	319493	Mm.234565	NM_001033378	ENSMUSG00000074497	A430078G23Rik	-	RIKEN cDNA A430078G23 gene	protein-coding
mm_125869.1	chr15	75517260	75517273	+	1	NA	Intergenic	Intergenic	49382	NM_001135689	23934	Mm.22154	NM_011837	ENSMUSG00000022577	Ly6h	-	lymphocyte antigen 6 complex, locus H	protein-coding
mm_44517.1	chr5	24351629	24351647	-	1	NA	promoter-TSS (NM_013569)	promoter-TSS (NM_013569)	-34	NM_013569	16511	Mm.6539	NM_013569	ENSMUSG00000038319	Kcnh2	AI326795|ERG1|LQT|Lqt2|M-erg|Merg1|merg1a|merg1b	potassium voltage-gated channel, subfamily H (eag-related), member 2	protein-coding
mm_100900.1	chr11	6159862	6159885	-	1	NA	intron (NM_173748, intron 2 of 5)	intron (NM_173748, intron 2 of 5)	13458	NR_029471	100042173	Mm.441799	NR_029471		Rps15a-ps6	Gm11968|OTTMUSG00000005107	ribosomal protein S15A, pseudogene 6	pseudo
mm_141087.1	chr17	25942861	25942865	-	1	NA	promoter-TSS (NM_011822)	promoter-TSS (NM_011822)	-874	NM_011822	14755	Mm.362054	NM_011822	ENSMUSG00000025728	Pigq	Gpi1|Gpi1h|Gpi1p|Gpih	phosphatidylinositol glycan anchor biosynthesis, class Q	protein-coding
mm_79757.1	chr9	62374650	62374675	+	1	NA	exon (NM_009672, exon 5 of 7)	exon (NM_009672, exon 5 of 7)	33319	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	protein-coding
mm_137923.1	chr17	32506420	32506440	+	1	NA	promoter-TSS (NM_001101445)	promoter-TSS (NM_001101445)	-32	NM_001101445	208285	Mm.311422	NM_001101445	ENSMUSG00000091586	Cyp4f17	EG208285	cytochrome P450, family 4, subfamily f, polypeptide 17	protein-coding
mm_79309.1	chr9	52048247	52048319	+	1	NA	5' UTR (NM_009041, exon 1 of 14)	5' UTR (NM_009041, exon 1 of 14)	342	NM_001104617	19684	Mm.245746	NM_009041	ENSMUSG00000032050	Rdx	AA516625	radixin	protein-coding
mm_71181.1	chr8	40862183	40862250	+	1	NA	promoter-TSS (NM_001044740)	promoter-TSS (NM_001044740)	-151	NM_007514	11988	Mm.4676	NM_007514	ENSMUSG00000031596	Slc7a2	20.5|AI158848|Atrc2|CAT-2|Cat2|Tea	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	protein-coding
mm_89012.1	chr10	81643798	81643856	+	1	NA	exon (NM_027480, exon 17 of 20)	exon (NM_027480, exon 17 of 20)	-5242	NM_001142963	100233208	Mm.327168	NM_001142963	ENSMUSG00000096856	Gm10778	ENSMUSG00000074860	predicted gene 10778	protein-coding
mm_48809.1	chr5	148969918	148969939	-	1	NA	Intergenic	Intergenic	19678	NR_040686	71473	Mm.90306	NR_040686	ENSMUSG00000079069	8430423G03Rik	-	RIKEN cDNA 8430423G03 gene	ncRNA
mm_33188.1	chr4	126148458	126148527	+	1	NA	5' UTR (NM_172145, exon 1 of 3)	5' UTR (NM_172145, exon 1 of 3)	489	NM_172145	230752	Mm.41569	NM_172145	ENSMUSG00000050212	Eva1b	2610027C15Rik|Fam176b	eva-1 homolog B (C. elegans)	protein-coding
mm_139549.1	chr17	56793905	56793917	+	1	NA	intron (NM_009056, intron 5 of 16)	RLTR20A3_MM|LTR|ERVK	23635	NM_001195673	100504446	Mm.46157	NM_001195673	ENSMUSG00000090273	Prr22	Gm546	proline rich 22	protein-coding
mm_9185.1	chr1	171101118	171101118	-	1	NA	Intergenic	ORR1A1|LTR|ERVL-MaLR	-20543	NM_001081275	75472	Mm.32760	NM_029301	ENSMUSG00000026649	Cfap126	1700009P17Rik|AV282292|Flattop|Fltp	cilia and flagella associated protein 126	protein-coding
mm_111573.1	chr12	101818875	101818896	-	1	NA	5' UTR (NM_011812, exon 1 of 11)	5' UTR (NM_011812, exon 1 of 11)	234	NM_011812	23876	Mm.288381	NM_011812	ENSMUSG00000021186	Fbln5	A55|DANCE|EVEC	fibulin 5	protein-coding
mm_55873.1	chr6	83506866	83506876	-	1	NA	promoter-TSS (NM_001162521)	promoter-TSS (NM_001162521)	98	NM_013764	27369	Mm.42234	NM_013764	ENSMUSG00000014554	Dguok	dGK|dGK1|dGK2|dGK3	deoxyguanosine kinase	protein-coding
mm_47971.1	chr5	135909472	135909486	-	1	NA	3' UTR (NM_018871, exon 2 of 2)	3' UTR (NM_018871, exon 2 of 2)	21560	NM_013560	15507	Mm.13849	NM_013560	ENSMUSG00000004951	Hspb1	27kDa|Hsp25	heat shock protein 1	protein-coding
mm_155167.1	chrX	53020096	53020122	+	1	NA	exon (NM_013556, exon 7 of 9)	exon (NM_013556, exon 7 of 9)	27969	NR_030498	751532		NR_030498	ENSMUSG00000076050	Mir450b	Mirn450b|mir-450b	microRNA 450b	ncRNA
mm_685.1	chr1	40515472	40515483	+	1	NA	intron (NM_010553, intron 1 of 12)	intron (NM_010553, intron 1 of 12)	115	NM_010553	16174	Mm.20466	NM_010553	ENSMUSG00000026068	Il18rap	AcPL|IL-18R-beta|IL-18RAcP|IL-18Rbeta|IL-1RAcPL	interleukin 18 receptor accessory protein	protein-coding
mm_17534.1	chr2	29751636	29751669	-	1	NA	Intergenic	CpG	-9876	NM_001177392	433416	Mm.330112	NM_001034887	ENSMUSG00000075425	Gm13547	OTTMUSG00000012686	predicted gene 13547	protein-coding
mm_83226.1	chr9	42330977	42330998	-	1	NA	exon (NM_001324548, exon 23 of 24)	exon (NM_001324548, exon 23 of 24)	-66687	NM_172769	235293	Mm.32700	NM_172769	ENSMUSG00000032018	Sc5d	A830037K02|A830073K23Rik|Sc5dl	sterol-C5-desaturase	protein-coding
mm_172463.1	chr7	42592569	42592574	-	1	NA	Intergenic	Intergenic	50033	NM_001242388	208111	Mm.387841	NM_001034857	ENSMUSG00000074158	Zfp976	9830147E19Rik|C330019L16Rik	zinc finger protein 976	protein-coding
mm_149211.1	chr19	9983089	9983118	+	1	NA	intron (NR_073181, intron 2 of 4)	intron (NR_073181, intron 2 of 4)	457	NM_010239	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
mm_155887.1	chrX	101640057	101640108	+	1	NA	promoter-TSS (NM_001290535)	promoter-TSS (NM_001290535)	31	NM_139144	108155	Mm.487332	NM_139144	ENSMUSG00000034160	Ogt	1110038P24Rik|4831420N21Rik|AI115525|Ogtl	O-linked N-acetylglucosamine (GlcNAc) transferase (UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase)	protein-coding
mm_64569.1	chr7	144897062	144897071	+	1	NA	intron (NM_008003, intron 1 of 2)	CpG	534	NM_008003	14170	Mm.3904	NM_008003	ENSMUSG00000031073	Fgf15	FGF19	fibroblast growth factor 15	protein-coding
mm_77273.1	chr8	116571889	116571892	-	1	NA	3' UTR (NM_029441, exon 7 of 7)	3' UTR (NM_029441, exon 7 of 7)	66875	NM_029297	75465	Mm.23114	NM_029297	ENSMUSG00000034467	Dynlrb2	1700009A04Rik|DNLC2B|Dncl2b	dynein light chain roadblock-type 2	protein-coding
mm_37286.1	chr4	119127333	119127369	-	1	NA	intron (NM_011400, intron 2 of 9)	intron (NM_011400, intron 2 of 9)	18606	NM_011400	20525	Mm.21002	NM_011400	ENSMUSG00000028645	Slc2a1	Glut-1|Glut1	solute carrier family 2 (facilitated glucose transporter), member 1	protein-coding
mm_159407.1	chr3	98763092	98763092	-	1	NA	promoter-TSS (NM_001161745)	promoter-TSS (NM_001161745)	36	NM_001161743	15494	Mm.158717	NM_001012306	ENSMUSG00000062410	Hsd3b3	9030618K22Rik|AI790201	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 3	protein-coding
mm_31660.1	chr4	59933872	59933881	+	1	NA	Intergenic	L3|LINE|CR1	-18820	NM_021053	30936	Mm.284433	NM_021053	ENSMUSG00000028386	Slc46a2	5430429N04Rik|Ly110|TSO-1C12|Tscot	solute carrier family 46, member 2	protein-coding
mm_118563.1	chr14	18030723	18030726	+	1	NA	intron (NM_009380, intron 6 of 6)	intron (NM_009380, intron 6 of 6)	49080	NM_009380	21834	Mm.32563	NM_009380	ENSMUSG00000021779	Thrb	Nr1a2|T3R[b]|T3Rbeta|Thrb1|Thrb2|c-erbAbeta	thyroid hormone receptor beta	protein-coding
mm_41200.1	chr5	88328284	88328335	+	1	NA	exon (NM_008644, exon 3 of 3)	exon (NM_008644, exon 3 of 3)	10997	NM_008644	17830	Mm.200411	NM_008644	ENSMUSG00000064156	Prol1	Muc10	proline rich, lacrimal 1	protein-coding
mm_15589.1	chr2	160366231	160366244	+	1	NA	exon (NM_010658, exon 1 of 1)	exon (NM_010658, exon 1 of 1)	828	NM_010658	16658	Mm.330745	NM_010658	ENSMUSG00000074622	Mafb	Kreisler|Krml|Krml1|kr	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein B (avian)	protein-coding
mm_7615.1	chr1	126738154	126738163	-	1	NA	intron (NM_001081756, intron 1 of 16)	intron (NM_001081756, intron 1 of 16)	92474	NM_001081756	210356	Mm.377234	NM_172484	ENSMUSG00000049690	Nckap5	8430408F21|D130011D22Rik|E030049G20Rik|Erih1|Erih2|Gm1548|Nap5	NCK-associated protein 5	protein-coding
mm_162767.1	chr10	63998162	63998162	+	1	NA	intron (NM_178678, intron 2 of 2)	intron (NM_178678, intron 2 of 2)	92093	NM_178678	216028	Mm.431318	NM_178678	ENSMUSG00000042846	Lrrtm3	9630044H04Rik	leucine rich repeat transmembrane neuronal 3	protein-coding
mm_128697.1	chr15	62809290	62809298	-	1	NA	Intergenic	Intergenic	-589843	NR_003523	67552	Mm.484027	NM_026230		H2afy3	4933432H23Rik	H2A histone family, member Y3	pseudo
mm_79116.1	chr9	46280673	46280676	+	1	NA	intron (NM_011752, intron 13 of 13)	PB1D10|SINE|Alu	-2338	NM_146000	215051	Mm.32648	NM_146000	ENSMUSG00000032077	Bud13	AV305342|D030060M11Rik	BUD13 homolog	protein-coding
mm_9377.1	chr1	172210235	172210244	-	1	NA	3' UTR (NM_009813, exon 11 of 11)	3' UTR (NM_009813, exon 11 of 11)	-3435	NM_011063	18611	Mm.544	NM_011063	ENSMUSG00000013698	Pea15a	Mat1|PEA-15|Pea15|Pkcs15	phosphoprotein enriched in astrocytes 15A	protein-coding
mm_168822.1	chr12	22274802	22274814	-	1	NA	Intergenic	CpG	-118162	NR_136920	100043416		NM_001004167	ENSMUSG00000093846	Gm4425	EG432637|Gm5433	KRAB-domain protein pseudogene	pseudo
mm_125370.1	chr15	39745927	39745937	+	1	NA	promoter-TSS (NM_029422)	promoter-TSS (NM_029422)	2	NM_001289508	75766	Mm.159563	NM_029422	ENSMUSG00000022303	Dcstamp	4833414I07Rik|DC-STAMP|FIND|Tm7sf4|mDC-STAMP	dendrocyte expressed seven transmembrane protein	protein-coding
mm_35033.1	chr4	4112257	4112279	-	1	NA	Intergenic	Intergenic	26177	NM_001002927	18619	Mm.475097	NM_001002927	ENSMUSG00000045573	Penk	AI326464|ENK|PPA|Penk1	preproenkephalin	protein-coding
mm_169667.1	chr15	61289050	61289052	-	1	NA	Intergenic	L1Md_F2|LINE|L1	-367781	NM_001081067	117586	Mm.291499	NM_001081067	ENSMUSG00000022347	A1bg	C44	alpha-1-B glycoprotein	protein-coding
mm_164856.1	chr18	49706794	49706796	+	1	NA	intron (NM_001170960, intron 2 of 3)	intron (NM_001170960, intron 2 of 3)	48806	NM_026854	68857	Mm.96010	NM_026854	ENSMUSG00000024505	Dtwd2	1190002H09Rik|8030470C17Rik|AI414673|BB115449	DTW domain containing 2	protein-coding
mm_133204.1	chr16	73202098	73202098	+	1	NA	Intergenic	Intergenic	538949	NM_019413	19876	Mm.310772	NM_019413	ENSMUSG00000022883	Robo1	AW494633|AW742721|DUTT1|Gm310	roundabout guidance receptor 1	protein-coding
mm_46461.1	chr5	105118448	105118457	-	1	NA	exon (NM_001256005, exon 11 of 11)	exon (NM_001256005, exon 11 of 11)	-8160	NM_172777	236573	Mm.425261	NM_172777	ENSMUSG00000029298	Gbp9	-	guanylate-binding protein 9	protein-coding
mm_57344.1	chr6	124747970	124747994	-	1	NA	exon (NM_007881, exon 5 of 10)	exon (NM_007881, exon 5 of 10)	-6903	NM_013535	14790	Mm.439877	NM_013535	ENSMUSG00000072772	Grcc10	2310033H05Rik|C10	gene rich cluster, C10 gene	protein-coding
mm_142084.1	chr17	35731854	35731895	-	1	NA	Intergenic	Intergenic	-27735	NM_172962	12305	Mm.5021	NM_007584	ENSMUSG00000003534	Ddr1	6030432F18|AI323681|CD167a|Cak|Nep|PTK3A	discoidin domain receptor family, member 1	protein-coding
mm_49498.1	chr6	29746760	29746766	+	1	NA	intron (NM_176996, intron 1 of 11)	intron (NM_176996, intron 1 of 11)	11266	NM_176996	319757	Mm.29279	NM_176996	ENSMUSG00000001761	Smo	E130215L21Rik|Smoh|bnb|smoothened	smoothened, frizzled class receptor	protein-coding
mm_227.1	chr1	17629051	17629065	+	1	NA	3' UTR (NM_053191, exon 6 of 6)	3' UTR (NM_053191, exon 6 of 6)	27157	NM_053191	94227	Mm.442452	NM_053191	ENSMUSG00000067780	Pi15	P24TI|P25TI|PI-15|SugarCrisp	peptidase inhibitor 15	protein-coding
mm_38901.1	chr4	149909584	149909612	-	1	NA	intron (NM_029035, intron 1 of 2)	intron (NM_029035, intron 1 of 2)	45408	NM_029035	74646	Mm.30	NM_029035	ENSMUSG00000039911	Spsb1	1110014L01Rik|4930422J18Rik|AI596360|AI854583|SSB-1|SSB1	splA/ryanodine receptor domain and SOCS box containing 1	protein-coding
mm_91971.1	chr10	61432934	61432948	-	1	NA	3' UTR (NM_010124, exon 3 of 3)	3' UTR (NM_010124, exon 3 of 3)	14969	NM_013611	18119	Mm.57195	NM_013611	ENSMUSG00000037171	Nodal	Tg.413d	nodal	protein-coding
mm_25533.1	chr3	115081026	115081036	+	1	NA	promoter-TSS (NM_153157)	promoter-TSS (NM_153157)	66	NM_153157	229759	Mm.54183	NM_153157	ENSMUSG00000027965	Olfm3	B230206G02Rik	olfactomedin 3	protein-coding
mm_4478.1	chr1	173427610	173427613	+	1	NA	intron (NM_001013779, intron 1 of 8)	RMER19B|LTR|ERVK	7007	NM_001013779	383619	Mm.131453	NM_001013779	ENSMUSG00000037860	Aim2	Gm1313|Ifi210	absent in melanoma 2	protein-coding
mm_91097.1	chr10	19065153	19065163	-	1	NA	Intergenic	Intergenic	-49748	NM_009397	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_46224.1	chr5	98966791	98966799	-	1	NA	intron (NM_008926, intron 13 of 18)	intron (NM_008926, intron 13 of 18)	70284	NM_008926	19092	Mm.263002	NM_008926	ENSMUSG00000029334	Prkg2	AW212535|CGKII|Prkgr2|cGK-II	protein kinase, cGMP-dependent, type II	protein-coding
mm_118738.1	chr14	22310827	22310841	+	1	NA	intron (NM_028275, intron 2 of 6)	(TC)n|Simple_repeat|Simple_repeat	231964	NR_046307	74896	Mm.444661	NR_046307		4930405A10Rik	4930456G20Rik	RIKEN cDNA 4930405A10 gene	ncRNA
mm_23748.1	chr3	69386397	69386402	+	1	NA	intron (NM_178726, intron 1 of 3)	L1_Mur3|LINE|L1	69481	NM_178726	242083	Mm.40577	NM_178726	ENSMUSG00000027784	Ppm1l	3222401G13|5930404J21Rik|AI481720|AW045850|PP2C|PP2Cepsilon|Pp2ce|Ppp2ce|mKIAA4175	protein phosphatase 1 (formerly 2C)-like	protein-coding
mm_145430.1	chr18	58725654	58725661	+	1	NA	Intergenic	Intergenic	66175	NM_025478	66307	Mm.182574	NM_025478	ENSMUSG00000024601	Isoc1	2610034N03Rik	isochorismatase domain containing 1	protein-coding
mm_88580.1	chr10	79691187	79691191	+	1	NA	intron (NR_126325, intron 1 of 3)	(T)n|Simple_repeat|Simple_repeat	2169	NM_008504	16904	Mm.378960	NM_008504	ENSMUSG00000054206	Gzmm	Lmet1|MMET-1	granzyme M (lymphocyte met-ase 1)	protein-coding
mm_18435.1	chr2	60845765	60845768	-	1	NA	intron (NM_020296, intron 1 of 13)	intron (NM_020296, intron 1 of 13)	35672	NM_001141932	56878	Mm.259667	NM_020296	ENSMUSG00000026970	Rbms1	2600014B10Rik|AI255215|MSSP-1|MSSP-2|MSSP-3|YC1	RNA binding motif, single stranded interacting protein 1	protein-coding
mm_87893.1	chr10	62066616	62066639	+	1	NA	Intergenic	Intergenic	44386	NM_027251	69894	Mm.294126	NM_027251	ENSMUSG00000020083	2010107G23Rik	AA545165	RIKEN cDNA 2010107G23 gene	protein-coding
mm_156824.1	chrX	164162135	164162153	+	1	NA	intron (NM_001130513, intron 6 of 18)	intron (NM_001130513, intron 6 of 18)	21664	NM_027286	70008	Mm.13451	NM_027286	ENSMUSG00000015405	Ace2	2010305L05Rik	angiotensin I converting enzyme (peptidyl-dipeptidase A) 2	protein-coding
mm_164547.1	chr17	12318808	12318815	-	1	NA	promoter-TSS (NR_045290)	promoter-TSS (NR_045290)	-42	NR_045290	224523	Mm.188855	NR_045290	ENSMUSG00000097350	4732491K20Rik	-	RIKEN cDNA 4732491K20 gene	ncRNA
mm_83356.1	chr9	44406963	44407013	-	1	NA	promoter-TSS (NM_024266)	promoter-TSS (NM_024266)	560	NM_021789	60409	Mm.29814	NM_021789	ENSMUSG00000032112	Trappc4	1500017G03Rik|AI303617|HSPC172|PTD009|Sbd|Sbdn|Sdcbp2|TRS23	trafficking protein particle complex 4	protein-coding
mm_83275.1	chr9	43071163	43071171	-	1	NA	intron (NM_027144, intron 1 of 40)	intron (NM_027144, intron 1 of 40)	34551	NM_027144	69632	Mm.275266	NM_027144	ENSMUSG00000059495	Arhgef12	2310014B11Rik|AU019857|Larg|mKIAA0382	Rho guanine nucleotide exchange factor (GEF) 12	protein-coding
mm_146350.1	chr18	82559401	82559421	+	1	NA	TTS (NM_001025245)	TTS (NM_001025245)	4903	NM_001025254	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_113568.1	chr13	38345095	38345105	+	1	NA	promoter-TSS (NM_007556)	promoter-TSS (NM_007556)	-616	NM_007556	12161	Mm.385759	NM_007556	ENSMUSG00000039004	Bmp6	D13Wsu115e|Vgr1	bone morphogenetic protein 6	protein-coding
mm_34824.1	chr4	154965073	154965101	+	1	NA	intron (NM_001305804, intron 1 of 19)	intron (NM_001305804, intron 1 of 19)	964	NR_131230	269614	Mm.30042	NM_172990	ENSMUSG00000029056	Pank4	D030031I12Rik|R75150	pantothenate kinase 4	protein-coding
mm_2690.1	chr1	127487617	127487617	+	1	NA	Intergenic	Intergenic	190404	NM_028135	72160	Mm.281287	NM_028135	ENSMUSG00000026347	Tmem163	2610024A01Rik|SV31	transmembrane protein 163	protein-coding
mm_91710.1	chr10	44148848	44148858	-	1	NA	Intergenic	CpG	-21594	NR_001582	70365	Mm.87073	NR_001582	ENSMUSG00000091358	Speer5-ps1	1700007C10Rik|SPEER-5|Speer5-ps	spermatogenesis associated glutamate (E)-rich protein 5, pseudogene 1	pseudo
mm_70625.1	chr8	13677776	13677827	+	1	NA	promoter-TSS (NM_009025)	promoter-TSS (NM_009025)	-214	NM_009025	19414	Mm.18517	NM_009025	ENSMUSG00000031453	Rasa3	AI326412|C86362|E130011G04|GAPIII|hlb381|scat	RAS p21 protein activator 3	protein-coding
mm_154494.1	chrM	11144	11229	-	1	NA	NA	Intergenic	NA	NA								
mm_164489.1	chr16	85550315	85550317	-	1	NA	promoter-TSS (NM_144853)	promoter-TSS (NM_144853)	57	NM_144853	224405	Mm.213203	NM_144853	ENSMUSG00000041134	Cyyr1	-	cysteine and tyrosine-rich protein 1	protein-coding
mm_12187.1	chr2	65334311	65334320	+	1	NA	intron (NM_177074, intron 9 of 11)	intron (NM_177074, intron 9 of 11)	29711	NM_177074	320106	Mm.227703	NM_177074	ENSMUSG00000061171	Slc38a11	9330158F14Rik	solute carrier family 38, member 11	protein-coding
mm_41010.1	chr5	81021128	81021145	+	1	NA	promoter-TSS (NM_198702)	promoter-TSS (NM_198702)	-457	NM_198702	319387	Mm.273631	NM_198702	ENSMUSG00000037605	Adgrl3	5430402I23Rik|CIRL-3|D130075K09Rik|Gm1379|LEC3|Lphn3|mKIAA0768	adhesion G protein-coupled receptor L3	protein-coding
mm_82363.1	chr9	14500490	14500503	-	1	NA	promoter-TSS (NM_023153)	promoter-TSS (NM_023153)	-14	NM_173433	244694	Mm.240457	NM_173433	ENSMUSG00000053914	Kdm4d	4932416A15|Jmjd2d	lysine (K)-specific demethylase 4D	protein-coding
mm_31426.1	chr4	48083807	48083821	+	1	NA	3' UTR (NM_015743, exon 8 of 8)	3' UTR (NM_015743, exon 8 of 8)	32568	NM_001307989	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_5995.1	chr1	58721103	58721114	-	1	NA	intron (NM_009805, intron 1 of 4)	intron (NM_009805, intron 1 of 4)	7822	NM_207653	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_30310.1	chr3	149445377	149445417	-	1	NA	Intergenic	(GA)n|Simple_repeat|Simple_repeat	170660	NR_040591	381482	Mm.393866	NR_040591		Gm1653	-	predicted gene 1653	ncRNA
mm_85321.1	chr9	101251811	101251839	-	1	NA	promoter-TSS (NM_001161362)	promoter-TSS (NM_001161362)	7	NM_001161362	235542	Mm.335386	NM_172144	ENSMUSG00000043154	Ppp2r3a	3222402P14Rik|A730042E07	protein phosphatase 2, regulatory subunit B'', alpha	protein-coding
mm_19128.1	chr2	80129218	80129243	-	1	NA	promoter-TSS (NM_016744)	promoter-TSS (NM_016744)	182	NM_001159582	18573	Mm.40678	NM_016744	ENSMUSG00000059173	Pde1a	AI987702|AW125737	phosphodiesterase 1A, calmodulin-dependent	protein-coding
mm_19781.1	chr2	106974333	106974360	-	1	NA	promoter-TSS (NM_001025102)	promoter-TSS (NM_001025102)	51	NM_001025102	212772	Mm.381231	NM_173750	ENSMUSG00000027122	Arl14ep	2700007P21Rik|4930448O08Rik|ARF7EP	ADP-ribosylation factor-like 14 effector protein	protein-coding
mm_47070.1	chr5	116446708	116446740	-	1	NA	intron (NM_026886, intron 11 of 12)	CpG	8002	NR_015595	76798	Mm.444322	NR_015595	ENSMUSG00000086219	Srrm4os	2410137F16Rik	serine/arginine repetitive matrix 4, opposite strand	ncRNA
mm_93729.1	chr10	119298691	119298691	-	1	NA	Intergenic	Intergenic	-21543	NR_126086	74905	Mm.399357	NR_126085		4930477N07Rik	-	RIKEN cDNA 4930477N07 gene	ncRNA
mm_133056.1	chr16	58415475	58415483	+	1	NA	intron (NM_028523, intron 1 of 15)	intron (NM_028523, intron 1 of 15)	6944	NM_028523	73379	Mm.373589	NM_028523	ENSMUSG00000035107	Dcbld2	1700055P21Rik|AW146002|CLCP1|Esdn	discoidin, CUB and LCCL domain containing 2	protein-coding
mm_6937.1	chr1	85723820	85723824	-	1	NA	intron (NM_177055, intron 3 of 5)	B3A|SINE|B2	12784	NM_177055	319997	Mm.116691	NM_177055	ENSMUSG00000052760	A630001G21Rik	-	RIKEN cDNA A630001G21 gene	protein-coding
mm_69559.1	chr7	135700308	135700319	-	1	NA	exon (NM_001081117, exon 12 of 14)	exon (NM_001081117, exon 12 of 14)	16066	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_21909.1	chr2	166573728	166573731	-	1	NA	intron (NM_177782, intron 33 of 39)	intron (NM_177782, intron 33 of 39)	-98989	NR_105783	102465188		NR_105783	ENSMUSG00000098675	Mir6364	Gm27327|mmu-mir-6364	microRNA 6364	ncRNA
mm_4078.1	chr1	166256594	166256601	+	1	NA	intron (NM_001164528, intron 1 of 9)	intron (NM_001164528, intron 1 of 9)	2458	NM_001164528	100039795	Mm.101743	NM_001164528	ENSMUSG00000040612	Ildr2	2810478N18Rik|3110063L10Rik|AI852300|D1Ertd471e|Dbsm1|ENSMUSG00000040612|Ll	immunoglobulin-like domain containing receptor 2	protein-coding
mm_94763.1	chr11	21220982	21221015	+	1	NA	Intergenic	Intergenic	-18034	NM_139061	245944	Mm.170103	NM_139061	ENSMUSG00000020128	Vps54	Hcc8|Vps54l|mSLP8|wr	VPS54 GARP complex subunit	protein-coding
mm_107931.1	chr12	71137594	71137601	+	1	NA	promoter-TSS (NM_001286203)	promoter-TSS (NM_001286203)	749	NM_001163378	76967	Mm.87290	NM_029818	ENSMUSG00000034601	2700049A03Rik	Ta3|Talpid3|mKIAA0586	RIKEN cDNA 2700049A03 gene	protein-coding
mm_121893.1	chr14	21745205	21745235	-	1	NA	intron (NM_001007268, intron 3 of 7)	MER91C|DNA|hAT-Tip100	-2341	NM_013849	27389	Mm.390674	NM_013849	ENSMUSG00000021768	Dusp13	DUSP13A|DUSP13B|Gm1203|LMW-DSP6|MDSP|TMDP|TS-DSP6	dual specificity phosphatase 13	protein-coding
mm_161829.1	chr17	80215856	80215856	+	1	NA	promoter-TSS (NM_026351)	promoter-TSS (NM_026351)	-58	NM_026351	67737	Mm.158172	NM_026351	ENSMUSG00000046196	Ttc39d	4930560E09Rik	tetratricopeptide repeat domain 39D	protein-coding
mm_30679.1	chr4	11173833	11173881	+	1	NA	3' UTR (NM_001199105, exon 5 of 5)	3' UTR (NM_001199105, exon 5 of 5)	17416	NM_021897	60599	Mm.393018	NM_021897	ENSMUSG00000028211	Trp53inp1	2700057G22Rik|SIP|SIP18|SIP27|Stinp|Teap	transformation related protein 53 inducible nuclear protein 1	protein-coding
mm_31990.1	chr4	89302881	89302884	+	1	NA	intron (NR_132431, intron 2 of 9)	L1_Mur3|LINE|L1	7702	NR_132431	102633081	Mm.409388	NR_132431		Gm12610	Gm12609|OTTMUSG00000007716|OTTMUSG00000007717	predicted gene 12610	ncRNA
mm_18801.1	chr2	73892563	73892573	-	1	NA	promoter-TSS (NM_009715)	promoter-TSS (NM_009715)	71	NM_001284371	11909	Mm.209903	NM_009715	ENSMUSG00000027104	Atf2	Atf-2|CRE-BP|Creb2|D130078H02Rik|D18875|Tg(Gzma-Klra1)7Wum|mXBP	activating transcription factor 2	protein-coding
mm_159474.1	chr4	32417272	32417272	+	1	NA	promoter-TSS (NM_001109661)	promoter-TSS (NM_001109661)	-163	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_58276.1	chr6	145450754	145450767	-	1	NA	Intergenic	Intergenic	-15835	NM_028742	74071	Mm.441497	NM_028742	ENSMUSG00000054966	Lmntd1	4933403M22Rik|AI482300|Ifltd1|Lmna-rs1|Lmna1|OTTMUSG00000022798	lamin tail domain containing 1	protein-coding
mm_36644.1	chr4	94331614	94331626	-	1	NA	Intergenic	Intergenic	225176	NM_026368	67770	Mm.35170	NM_026368	ENSMUSG00000028578	Caap1	5830433M19Rik|AI536248|CAAP	caspase activity and apoptosis inhibitor 1	protein-coding
mm_57822.1	chr6	129462831	129462847	-	1	NA	non-coding (NR_132130, exon 6 of 6)	non-coding (NR_132130, exon 6 of 6)	9940	NM_001309637	56644	Mm.239516	NM_020008	ENSMUSG00000079293	Clec7a	BGR|Clecsf12|beta-GR	C-type lectin domain family 7, member a	protein-coding
mm_107751.1	chr12	59066909	59066931	+	1	NA	promoter-TSS (NM_008891)	promoter-TSS (NM_008891)	1	NM_008891	18949	Mm.22347	NM_008891	ENSMUSG00000020994	Pnn	AU045199|D12Ertd512e	pinin	protein-coding
mm_146075.1	chr18	70568862	70568898	+	1	NA	exon (NM_010773, exon 1 of 7)	exon (NM_010773, exon 1 of 7)	588	NM_010773	17191	Mm.322	NM_010773	ENSMUSG00000024513	Mbd2	MBD2a	methyl-CpG binding domain protein 2	protein-coding
mm_50883.1	chr6	56017490	56017517	+	1	NA	promoter-TSS (NM_011153)	promoter-TSS (NM_011153)	-12	NM_011153	19051	Mm.42096	NM_011153	ENSMUSG00000002930	Ppp1r17	G-substrate|Gsbs|Ppp1r2	protein phosphatase 1, regulatory subunit 17	protein-coding
mm_32764.1	chr4	116691053	116691059	+	1	NA	intron (NM_011034, intron 2 of 5)	PB1D10|SINE|Alu	-5034	NR_040442	100502959	Mm.395400	NR_040442		AV051173	-	expressed sequence AV051173	ncRNA
mm_172131.1	chr6	3346017	3346028	-	1	NA	Intergenic	Intergenic	53549	NM_010156	209086	Mm.196013	NM_010156	ENSMUSG00000047735	Samd9l	AA175286|ESTM25|mKIAA2005	sterile alpha motif domain containing 9-like	protein-coding
mm_117290.1	chr13	66905323	66905370	-	1	NA	promoter-TSS (NM_026219)	promoter-TSS (NM_026219)	4	NM_026219	67530	Mm.379136	NM_026219	ENSMUSG00000021520	Uqcrb	2210415M14Rik|QP-C|QPC|UQBC|UQBP|UQPC	ubiquinol-cytochrome c reductase binding protein	protein-coding
mm_4560.1	chr1	177447148	177447156	+	1	NA	exon (NM_013915, exon 1 of 1)	exon (NM_013915, exon 1 of 1)	1331	NM_013915	30928	Mm.330700	NM_013915	ENSMUSG00000063659	Zbtb18	RP58|Zfp238|Znf238	zinc finger and BTB domain containing 18	protein-coding
mm_58506.1	chr7	3981141	3981147	+	1	NA	Intergenic	Intergenic	-65643	NR_028115	18726	Mm.440989	NM_011090	ENSMUSG00000030427	Lilra6	7M1|Pira3	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	protein-coding
mm_120137.1	chr14	60299227	60299233	+	1	NA	intron (NM_144843, intron 13 of 13)	L1M5|LINE|L1	34025	NM_144843	219135	Mm.247007	NM_144843	ENSMUSG00000021987	Mtmr6	4022440C11Rik|AI428804|AU041072	myotubularin related protein 6	protein-coding
mm_40912.1	chr5	75609390	75609398	+	1	NA	exon (NM_001122733, exon 3 of 21)	exon (NM_001122733, exon 3 of 21)	34403	NM_021099	16590	Mm.247073	NM_021099	ENSMUSG00000005672	Kit	Bs|CD117|Fdc|Gsfsco1|Gsfsco5|Gsfsow3|SCO1|SCO5|SOW3|Ssm|Tr-kit|W|c-KIT	KIT proto-oncogene receptor tyrosine kinase	protein-coding
mm_133991.1	chr16	4670532	4670581	-	1	NA	exon (NM_030205, exon 4 of 28)	exon (NM_030205, exon 4 of 28)	9164	NM_030205	78885	Mm.325512	NM_030205	ENSMUSG00000039637	Coro7	0610011B16Rik|AW048373|AW556392	coronin 7	protein-coding
mm_30318.1	chr3	151731650	151731673	-	1	NA	3' UTR (NM_133871, exon 8 of 8)	3' UTR (NM_133871, exon 8 of 8)	18298	NM_133871	99899	Mm.30756	NM_133871	ENSMUSG00000028037	Ifi44	A430056A10Rik|AW261460|MTAP44|p44	interferon-induced protein 44	protein-coding
mm_64537.1	chr7	144175681	144175702	+	1	NA	5' UTR (NM_001113373, exon 1 of 16)	5' UTR (NM_001113373, exon 1 of 16)	171	NM_001113373	210274	Mm.483624	NM_001081370	ENSMUSG00000037541	Shank2	ProSAP1|mKIAA1022	SH3/ankyrin domain gene 2	protein-coding
mm_21421.1	chr2	158138865	158138889	-	1	NA	exon (NM_009373, exon 3 of 13)	exon (NM_009373, exon 3 of 13)	7515	NM_009373	21817	Mm.330731	NM_009373	ENSMUSG00000037820	Tgm2	G[a]h|TG2|TGase2|tTG|tTGas	transglutaminase 2, C polypeptide	protein-coding
mm_89429.1	chr10	91083025	91083028	+	1	NA	promoter-TSS (NM_026166)	promoter-TSS (NM_026166)	-13	NM_027078	67454	Mm.252843	NM_026166	ENSMUSG00000019975	Ikbip	1200009F10Rik|1700023M03Rik|D18354|Ikip	IKBKB interacting protein	protein-coding
mm_69856.1	chr7	141434230	141434240	-	1	NA	5' UTR (NM_026646, exon 2 of 10)	5' UTR (NM_026646, exon 2 of 10)	359	NM_001177576	68267	Mm.33729	NM_026646	ENSMUSG00000019082	Slc25a22	1300006L01Rik|AI060884|Gc1	solute carrier family 25 (mitochondrial carrier, glutamate), member 22	protein-coding
mm_33000.1	chr4	120517617	120517638	+	1	NA	intron (NM_001159630, intron 13 of 17)	intron (NM_001159630, intron 13 of 17)	-14604	NM_177570	194219	Mm.29788	NM_177570	ENSMUSG00000047518	Slfnl1	4933406A14Rik	schlafen like 1	protein-coding
mm_66451.1	chr7	44869588	44869618	-	1	NA	5' UTR (NM_133949, exon 1 of 12)	5' UTR (NM_133949, exon 1 of 12)	185	NM_133949	84113	Mm.42855	NM_133949	ENSMUSG00000038502	Ptov1	1110030G05Rik|AU041779|Gcap3	prostate tumor over expressed gene 1	protein-coding
mm_172844.1	chr9	33728178	33728180	+	1	NA	Intergenic	(CGG)n|Simple_repeat|Simple_repeat	-314192	NR_040744	77119	Mm.367930	NR_040744	ENSMUSG00000098758	7630403G23Rik	-	RIKEN cDNA 7630403G23 gene	ncRNA
mm_100490.1	chr11	120442654	120442701	+	1	NA	promoter-TSS (NM_145363)	promoter-TSS (NM_145363)	46	NM_145363	208634	Mm.209875	NM_145363	ENSMUSG00000039691	Tspan10	Ocsp	tetraspanin 10	protein-coding
mm_69789.1	chr7	141096777	141096789	-	1	NA	intron (NM_023059, intron 1 of 9)	intron (NM_023059, intron 1 of 9)	3763	NM_023059	24058	Mm.38017	NM_023059	ENSMUSG00000025494	Sigirr	AI256711|TIR8	single immunoglobulin and toll-interleukin 1 receptor (TIR) domain	protein-coding
mm_91473.1	chr10	34207487	34207511	-	1	NA	promoter-TSS (NM_172508)	promoter-TSS (NM_172508)	52	NM_172508	212898	Mm.34557	NM_172508	ENSMUSG00000039497	Dse	6030499O08|AI480506|B130024B19Rik|DS-epi1|Sart2	dermatan sulfate epimerase	protein-coding
mm_55503.1	chr6	69815124	69815143	-	1	NA	Intergenic	Intergenic	-487959	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_171368.1	chr4	119170001	119170001	-	1	NA	3' UTR (NM_001145936, exon 2 of 2)	3' UTR (NM_001145936, exon 2 of 2)	3855	NM_001145935	195522	Mm.169620	NM_183140	ENSMUSG00000045268	Zfp691	6430544H17Rik|Znf691	zinc finger protein 691	protein-coding
mm_146491.1	chr18	90541431	90541444	+	1	NA	3' UTR (NM_198295, exon 16 of 16)	3' UTR (NM_198295, exon 16 of 16)	31283	NM_198295	67988	Mm.268041	NM_198295	ENSMUSG00000024614	Tmx3	6430411B10Rik|A730024F05Rik|AV259382|Txndc10|mKIAA1830	thioredoxin-related transmembrane protein 3	protein-coding
mm_115763.1	chr13	19193614	19193622	-	1	NA	Intergenic	Intergenic	202195	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_24754.1	chr3	95427576	95427588	+	1	NA	intron (NR_033637, intron 1 of 2)	intron (NR_033637, intron 1 of 2)	233	NR_033637	100043305	Mm.412052	NR_033637		Gm4349	-	SET domain, bifurcated 1 pseudogene	pseudo
mm_91244.1	chr10	22306600	22306610	-	1	NA	promoter-TSS (NR_015465)	promoter-TSS (NR_015465)	-115	NR_015465	606736	Mm.387042	NR_015465	ENSMUSG00000097352	C920009B18Rik	-	RIKEN cDNA C920009B18 gene	ncRNA
mm_68875.1	chr7	126447206	126447218	-	1	NA	exon (NM_007504, exon 20 of 23)	exon (NM_007504, exon 20 of 23)	15861	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_172577.1	chr8	11635766	11635766	-	1	NA	promoter-TSS (NM_001167967)	promoter-TSS (NM_001167967)	-9	NM_001281974	102334	Mm.12459	NM_133971	ENSMUSG00000031508	Ankrd10	4833425P12Rik|AW549277	ankyrin repeat domain 10	protein-coding
mm_105600.1	chr11	106752228	106752238	-	1	NA	intron (NM_001033435, intron 2 of 6)	intron (NM_001033435, intron 2 of 6)	1007	NM_001033435	380732	Mm.343952	NM_001033435	ENSMUSG00000040528	Milr1	Allergin-1|Gm885|Mca32	mast cell immunoglobulin like receptor 1	protein-coding
mm_74125.1	chr8	123186238	123186262	+	1	NA	promoter-TSS (NM_007876)	promoter-TSS (NM_007876)	15	NM_007876	13479	Mm.20388	NM_007876	ENSMUSG00000019278	Dpep1	AI327012|MBD	dipeptidase 1 (renal)	protein-coding
mm_15563.1	chr2	158609602	158609612	+	1	NA	intron (NR_040358, intron 1 of 2)	intron (NR_040358, intron 1 of 2)	1116	NR_040358	100045469	Mm.143404	NR_040358	ENSMUSG00000086496	Gm14204	OTTMUSG00000015935	predicted gene 14204	ncRNA
mm_33479.1	chr4	130818849	130818859	+	1	NA	exon (NM_011520, exon 3 of 5)	exon (NM_011520, exon 3 of 5)	26317	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_162561.1	chr1	172206788	172206793	-	1	NA	promoter-TSS (NM_001329871)	promoter-TSS (NM_001329871)	14	NM_001329871	18611	Mm.544	NM_011063	ENSMUSG00000013698	Pea15a	Mat1|PEA-15|Pea15|Pkcs15	phosphoprotein enriched in astrocytes 15A	protein-coding
mm_138432.1	chr17	35108181	35108185	+	1	NA	promoter-TSS (NM_148947)	promoter-TSS (NM_148947)	-117	NM_148947	114652	Mm.222643	NM_148947	ENSMUSG00000034482	Ly6g5c	G5c|NG33	lymphocyte antigen 6 complex, locus G5C	protein-coding
mm_74661.1	chr8	13562398	13562410	-	1	NA	promoter-TSS (NM_025601)	promoter-TSS (NM_025601)	57	NM_025601	66501	Mm.46136	NM_025601	ENSMUSG00000031452	1700029H14Rik	-	RIKEN cDNA 1700029H14 gene	protein-coding
mm_116302.1	chr13	36726597	36726620	-	1	NA	3' UTR (NM_153529, exon 3 of 3)	3' UTR (NM_153529, exon 3 of 3)	7869	NM_153529	68404	Mm.232930	NM_153529	ENSMUSG00000039114	Nrn1	0710008J23Rik|Cpg15|Nrn	neuritin 1	protein-coding
mm_86982.1	chr10	25441392	25441408	+	1	NA	intron (NM_013511, intron 1 of 19)	intron (NM_013511, intron 1 of 19)	33032	NM_013511	13822	Mm.306026	NM_013511	ENSMUSG00000019978	Epb41l2	4.1G|AW555191|D10Ertd398e|Epb4.1l2|NBL2	erythrocyte membrane protein band 4.1 like 2	protein-coding
mm_168250.1	chr10	82629879	82629880	+	1	NA	promoter-TSS (NR_037190)	promoter-TSS (NR_037190)	37	NR_037190	624784	Mm.284252	NR_037190		Gm9855	ENSMUSG00000051559	thymine DNA glycosylase pseudogene	pseudo
mm_72306.1	chr8	77518098	77518131	+	1	NA	promoter-TSS (NM_030113)	promoter-TSS (NM_030113)	-207	NM_030113	78514	Mm.165974	NM_030113	ENSMUSG00000037148	Arhgap10	A930033B01Rik|PSGAP-m|PSGAP-s	Rho GTPase activating protein 10	protein-coding
mm_135275.1	chr16	38407704	38407738	-	1	NA	exon (NM_134102, exon 7 of 11)	exon (NM_134102, exon 7 of 11)	25424	NM_134102	85031	Mm.279805	NM_134102	ENSMUSG00000002847	Pla1a	AA986889|Ps-pla1|Pspla1	phospholipase A1 member A	protein-coding
mm_128148.1	chr15	31601787	31601812	-	1	NA	promoter-TSS (NM_007637)	promoter-TSS (NM_007637)	5	NM_007637	12465	Mm.282158	NM_007637	ENSMUSG00000022234	Cct5	CCT-epsilon|Ccte|TCP-1-epsilon|TCPE|mKIAA0098	chaperonin containing Tcp1, subunit 5 (epsilon)	protein-coding
mm_66597.1	chr7	45458218	45458224	-	1	NA	exon (NM_010240, exon 4 of 4)	exon (NM_010240, exon 4 of 4)	1665	NM_010240	14325	Mm.30357	NM_010240	ENSMUSG00000050708	Ftl1	Ftl|Ftl-1|L-ferritin	ferritin light polypeptide 1	protein-coding
mm_49589.1	chr6	30643537	30643582	+	1	NA	exon (NM_025350, exon 9 of 10)	exon (NM_025350, exon 9 of 10)	4341	NM_025350	109697	Mm.25377	NM_025350	ENSMUSG00000054446	Cpa1	0910001L12Rik|Cpa	carboxypeptidase A1, pancreatic	protein-coding
mm_59470.1	chr7	27309279	27309294	+	1	NA	exon (NM_175641, exon 28 of 33)	exon (NM_175641, exon 28 of 33)	24362	NM_001113549	108075	Mm.272251	NM_175641	ENSMUSG00000040488	Ltbp4	2310046A13Rik	latent transforming growth factor beta binding protein 4	protein-coding
mm_35264.1	chr4	19892564	19892572	-	1	NA	intron (NM_175406, intron 2 of 7)	intron (NM_175406, intron 2 of 7)	29998	NM_175406	242341	Mm.19298	NM_175406	ENSMUSG00000028238	Atp6v0d2	1620401A02Rik|AI324824|V-ATPase	ATPase, H+ transporting, lysosomal V0 subunit D2	protein-coding
mm_27140.1	chr3	32616480	32616564	-	1	NA	promoter-TSS (NM_013531)	promoter-TSS (NM_013531)	13	NM_013531	14696	Mm.139192	NM_013531	ENSMUSG00000027669	Gnb4	6720453A21Rik|G(beta)4	guanine nucleotide binding protein (G protein), beta 4	protein-coding
mm_23171.1	chr3	40745538	40745632	+	1	NA	promoter-TSS (NM_011020)	promoter-TSS (NM_011020)	-28	NM_011020	18415	Mm.39330	NM_011020	ENSMUSG00000025757	Hspa4l	94kDa|AI461691|APG-1|Osp94	heat shock protein 4 like	protein-coding
mm_12679.1	chr2	75832333	75832343	+	1	NA	exon (NM_172666, exon 1 of 20)	exon (NM_172666, exon 1 of 20)	161	NM_172666	228061	Mm.31227	NM_172666	ENSMUSG00000042410	Agps	5832437L22|9930035G10Rik|AW123847|Adaps|Adas|Adhaps|Adps|Aldhpsy|bs2	alkylglycerone phosphate synthase	protein-coding
mm_167821.1	chr9	124408713	124408742	+	1	NA	Intergenic	Intergenic	-14524	NR_027950	75135	Mm.476814	NR_015516		4930526I15Rik	1600027J15Rik	RIKEN cDNA 4930526I15 gene	ncRNA
mm_83113.1	chr9	40376360	40376415	-	1	NA	intron (NM_172768, intron 2 of 19)	intron (NM_172768, intron 2 of 19)	42915	NR_040728	73558	Mm.398307	NR_040728		1700110K17Rik	-	RIKEN cDNA 1700110K17 gene	ncRNA
mm_129981.1	chr15	86029962	86029994	-	1	NA	intron (NM_009886, intron 1 of 34)	intron (NM_009886, intron 1 of 34)	3799	NM_009886	12614	Mm.22680	NM_009886	ENSMUSG00000016028	Celsr1	Adgrc1|Crsh|Scy|crash	cadherin, EGF LAG seven-pass G-type receptor 1	protein-coding
mm_20236.1	chr2	126152016	126152042	-	1	NA	promoter-TSS (NM_026981)	promoter-TSS (NM_026981)	-25	NM_029455	75823	Mm.444732	NM_029455	ENSMUSG00000027209	Fam227b	4930525F21Rik	family with sequence similarity 227, member B	protein-coding
mm_96455.1	chr11	67586553	67586563	+	1	NA	promoter-TSS (NM_001109657)	promoter-TSS (NM_001109657)	58	NM_001109657	14457	Mm.40338	NM_008088	ENSMUSG00000033066	Gas7	AW124766|B230343A10Rik|Gas7-cb	growth arrest specific 7	protein-coding
mm_142822.1	chr17	51759404	51759414	-	1	NA	intron (NM_009122, intron 9 of 10)	intron (NM_009122, intron 9 of 10)	52645	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_87871.1	chr10	61418284	61418289	+	1	NA	5' UTR (NM_013611, exon 1 of 3)	5' UTR (NM_013611, exon 1 of 3)	314	NM_013611	18119	Mm.57195	NM_013611	ENSMUSG00000037171	Nodal	Tg.413d	nodal	protein-coding
mm_79024.1	chr9	45945320	45945350	+	1	NA	exon (NM_001289668, exon 15 of 27)	exon (NM_001289668, exon 15 of 27)	-5745	NR_106055	102465659		NR_106055	ENSMUSG00000098327	Mir7087	Gm27273|mmu-mir-7087	microRNA 7087	ncRNA
mm_71021.1	chr8	33516661	33516678	+	1	NA	Intergenic	Intergenic	32358	NR_033589	628431	Mm.376526	NR_033589		Hmgb1-rs17	Hmg1-rs17	high mobility group box 1, related sequence 17	pseudo
mm_35799.1	chr4	46566433	46566471	-	1	NA	promoter-TSS (NM_178893)	promoter-TSS (NM_178893)	-12	NM_178893	107684	Mm.416311	NM_178893	ENSMUSG00000028337	Coro2a	9030208C03Rik|AI563590|IR10	coronin, actin binding protein 2A	protein-coding
mm_69075.1	chr7	126976125	126976131	-	1	NA	5' UTR (NM_026638, exon 1 of 6)	5' UTR (NM_026638, exon 1 of 6)	214	NM_001347656	52858	Mm.28219	NM_026638	ENSMUSG00000030682	Cdipt	9530042F15Rik|D7Bwg0575e|Pis|Pis1	CDP-diacylglycerol--inositol 3-phosphatidyltransferase (phosphatidylinositol synthase)	protein-coding
mm_164714.1	chr17	56079610	56079610	+	1	NA	promoter-TSS (NM_001304785)	promoter-TSS (NM_001304785)	-21	NM_001304784	15193	Mm.12966	NM_008233	ENSMUSG00000002833	Hdgfrp2	HRP-2	hepatoma-derived growth factor, related protein 2	protein-coding
mm_157770.1	chrX	73716443	73716466	-	1	NA	promoter-TSS (NM_012060)	promoter-TSS (NM_012060)	-143	NM_007435	11666	Mm.365	NM_007435	ENSMUSG00000031378	Abcd1	ALDP|Ald|Aldgh	ATP-binding cassette, sub-family D (ALD), member 1	protein-coding
mm_160569.1	chr9	56956901	56956901	+	1	NA	intron (NM_178374, intron 1 of 8)	(T)n|Simple_repeat|Simple_repeat	5977	NM_178374	66069	Mm.220984	NM_178374	ENSMUSG00000055334	Snupn	0610031A09Rik|Rnut1|Snupn1	snurportin 1	protein-coding
mm_88862.1	chr10	80930946	80930955	+	1	NA	intron (NM_008655, intron 2 of 3)	intron (NM_008655, intron 2 of 3)	859	NM_008655	17873	Mm.1360	NM_008655	ENSMUSG00000015312	Gadd45b	AI323528|Myd118	growth arrest and DNA-damage-inducible 45 beta	protein-coding
mm_147402.1	chr18	44601721	44601737	-	1	NA	intron (NM_001085373, intron 3 of 18)	intron (NM_001085373, intron 3 of 18)	-59936	NR_026853	626275	Mm.427116	NR_026853	ENSMUSG00000097610	A930012L18Rik	-	RIKEN cDNA A930012L18 gene	ncRNA
mm_166087.1	chr4	138967757	138967767	-	1	NA	exon (NM_025786, exon 1 of 1)	exon (NM_025786, exon 1 of 1)	650	NM_025786	66825	Mm.252312	NM_025786	ENSMUSG00000070661	Rnf186	9130020G10Rik	ring finger protein 186	protein-coding
mm_141308.1	chr17	28350659	28350681	-	1	NA	promoter-TSS (NM_001204156)	promoter-TSS (NM_001204156)	-70	NM_001098226	21678	Mm.6655	NM_011566	ENSMUSG00000002249	Tead3	DTEF-1|ETFR-1|TEAD-3|TEF-5|Tcf13r2	TEA domain family member 3	protein-coding
mm_79267.1	chr9	50753280	50753282	+	1	NA	promoter-TSS (NM_024441)	promoter-TSS (NM_024441)	310	NM_009964	12955	Mm.178	NM_009964	ENSMUSG00000032060	Cryab	Crya-2|Crya2|HspB5|P23	crystallin, alpha B	protein-coding
mm_124047.1	chr14	77844356	77844360	-	1	NA	intron (NM_025384, intron 4 of 5)	intron (NM_025384, intron 4 of 5)	30559	NM_025384	66148	Mm.248046	NM_025384	ENSMUSG00000022013	Dnajc15	1110003P16Rik|Dnajd1	DnaJ heat shock protein family (Hsp40) member C15	protein-coding
mm_153862.1	chr19	46573097	46573207	-	1	NA	promoter-TSS (NM_053196)	promoter-TSS (NM_053196)	-67	NM_019718	56350	Mm.22085	NM_019718	ENSMUSG00000025035	Arl3	-	ADP-ribosylation factor-like 3	protein-coding
mm_152720.1	chr19	17901197	17901198	-	1	NA	Intergenic	IMPB_01|Satellite|Satellite	-63565	NM_001190483	18552	Mm.3401	NM_001163144	ENSMUSG00000024713	Pcsk5	PC5|PC6|SPC6|b2b1549Clo|b2b585Clo	proprotein convertase subtilisin/kexin type 5	protein-coding
mm_134717.1	chr16	22895335	22895346	-	1	NA	promoter-TSS (NR_110508)	promoter-TSS (NR_110508)	-954	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_35587.1	chr4	42874198	42874223	-	1	NA	promoter-TSS (NM_177785)	promoter-TSS (NM_177785)	-7	NM_177785	277773	Mm.212727	NM_177785	ENSMUSG00000050141	Fam205c	4931430D02|FAM205CP	family with sequence similarity 205, member C	protein-coding
mm_158288.1	chrX	112698351	112698373	-	1	NA	exon (NM_181579, exon 2 of 17)	exon (NM_181579, exon 2 of 17)	289	NM_181579	69693	Mm.34964	NM_181579	ENSMUSG00000034607	Pof1b	2310066B14Rik	premature ovarian failure 1B	protein-coding
mm_167540.1	chr9	23026533	23026534	-	1	NA	Intergenic	Intergenic	-196543	NM_028472	73230	Mm.335020	NM_028472	ENSMUSG00000031963	Bmper	3110056H04Rik|CV-2|Crim3|Cv2	BMP-binding endothelial regulator	protein-coding
mm_45635.1	chr5	76658311	76658336	-	1	NA	Intergenic	CpG	66609	NM_199032	381644	Mm.332452	NM_199032	ENSMUSG00000036403	Cep135	BC062951|Cep4|Gm1044	centrosomal protein 135	protein-coding
mm_9857.1	chr1	184811157	184811163	-	1	NA	5' UTR (NM_001290273, exon 1 of 7)	5' UTR (NM_001290273, exon 1 of 7)	140	NM_001290273	66112	Mm.272457	NM_001081361	ENSMUSG00000026621	Marc1	1300013F15Rik|Mosc1	mitochondrial amidoxime reducing component 1	protein-coding
mm_162746.1	chr10	56389697	56389715	+	1	NA	3' UTR (NM_010288, exon 2 of 2)	3' UTR (NM_010288, exon 2 of 2)	12406	NM_010288	14609	Mm.378921	NM_010288	ENSMUSG00000050953	Gja1	AU042049|AW546267|Cnx43|Cx43|Cx43alpha1|Gja-1|Npm1|connexin43	gap junction protein, alpha 1	protein-coding
mm_111543.1	chr12	100899360	100899385	-	1	NA	5' UTR (NM_001177674, exon 1 of 3)	5' UTR (NM_001177674, exon 1 of 3)	152	NM_001177674	238377	Mm.32160	NM_175493	ENSMUSG00000047415	Gpr68	BB131428|Ogr1	G protein-coupled receptor 68	protein-coding
mm_87435.1	chr10	51454695	51454708	+	1	NA	Intergenic	RMER15|LTR|ERVL	-25911	NM_008147	14727	Mm.439661	NM_008147	ENSMUSG00000062593	Lilr4b	Gp49a|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4B	protein-coding
mm_131896.1	chr16	23237371	23237382	+	1	NA	intron (NM_001252505, intron 1 of 7)	intron (NM_001252505, intron 1 of 7)	11355	NM_001252505	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_98189.1	chr11	87793832	87793847	+	1	NA	promoter-TSS (NM_010824)	promoter-TSS (NM_010824)	55	NM_010824	17523	Mm.4668	NM_010824	ENSMUSG00000009350	Mpo	mKIAA4033	myeloperoxidase	protein-coding
mm_17000.1	chr2	18392716	18392716	-	1	NA	5' UTR (NM_001190817, exon 1 of 13)	5' UTR (NM_001190817, exon 1 of 13)	114	NM_001190817	13418	Mm.246674	NM_007869	ENSMUSG00000026740	Dnajc1	4733401K02Rik|AA960110|D230036H06Rik|Dnajl1|ERdj1|ERj1p|MTJ1	DnaJ heat shock protein family (Hsp40) member C1	protein-coding
mm_61862.1	chr7	88430258	88430286	+	1	NA	promoter-TSS (NM_028238)	promoter-TSS (NM_028238)	-1	NM_028238	72433	Mm.276669	NM_028238	ENSMUSG00000030559	Rab38	2310011F14Rik|AU043391|cht	RAB38, member RAS oncogene family	protein-coding
mm_57046.1	chr6	122344845	122344849	-	1	NA	Intergenic	Intergenic	-4620	NM_001271579	13619	Mm.6822	NM_007905	ENSMUSG00000040669	Phc1	AW557034|Edr|Edr1|Mph1|Rae-28|rae28	polyhomeotic-like 1 (Drosophila)	protein-coding
mm_117955.1	chr13	99444528	99444552	-	1	NA	intron (NM_008634, intron 2 of 6)	intron (NM_008634, intron 2 of 6)	-31714	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_127804.1	chr15	4027395	4027419	-	1	NA	promoter-TSS (NR_028266)	promoter-TSS (NR_028266)	-1	NR_028266	414066	Mm.394461	NR_028266		BC037032	-	cDNA Sequence BC037032	ncRNA
mm_52259.1	chr6	108213087	108213123	+	1	NA	promoter-TSS (NM_010585)	promoter-TSS (NM_010585)	9	NM_010585	16438	Mm.227912	NM_010585	ENSMUSG00000030102	Itpr1	D6Pas2|ENSMUSG00000072853|Gm10429|IP3R 1|IP3R1|InsP3R|Ip3r|Itpr-1|P400|Pcp-1|Pcp1|insP3R1|opt|wblo	inositol 1,4,5-trisphosphate receptor 1	protein-coding
mm_13501.1	chr2	107306529	107306531	+	1	NA	Intergenic	Intergenic	15941	NM_021275	16492	Mm.142718	NM_021275	ENSMUSG00000042604	Kcna4	Kv1.4	potassium voltage-gated channel, shaker-related subfamily, member 4	protein-coding
mm_88444.1	chr10	77547240	77547258	+	1	NA	exon (NM_008404, exon 5 of 16)	exon (NM_008404, exon 5 of 16)	16901	NM_008404	16414	Mm.1137	NM_008404	ENSMUSG00000000290	Itgb2	2E6|AI528527|Cd18|LAD|LCAMB|Lfa1|MF17	integrin beta 2	protein-coding
mm_67596.1	chr7	83732347	83732357	-	1	NA	intron (NM_010551, intron 1 of 18)	intron (NM_010551, intron 1 of 18)	3138	NM_010551	16170	Mm.10137	NM_010551	ENSMUSG00000001741	Il16	mKIAA4048	interleukin 16	protein-coding
mm_4094.1	chr1	167308848	167308858	+	1	NA	5' UTR (NM_001039483, exon 1 of 7)	5' UTR (NM_001039483, exon 1 of 7)	183	NM_001039483	68944	Mm.330045	NM_026881	ENSMUSG00000052428	Tmco1	1190006A08Rik|4930403O06Rik|AA109065|AU022572|ESTM39	transmembrane and coiled-coil domains 1	protein-coding
mm_10956.1	chr2	25657981	25657985	+	1	NA	promoter-TSS (NM_007947)	promoter-TSS (NM_007947)	31	NM_001042630	13863	Mm.12867	NM_007947	ENSMUSG00000026937	Lcn5	E-RABP|Erabp|MEP10	lipocalin 5	protein-coding
mm_20956.1	chr2	151741223	151741226	-	1	NA	promoter-TSS (NM_001305244)	promoter-TSS (NM_001305244)	86	NM_212446	228769	Mm.146984	NM_144889	ENSMUSG00000032869	Psmf1	AW048666|BC012260|PI31	proteasome (prosome, macropain) inhibitor subunit 1	protein-coding
mm_135593.1	chr16	50722825	50722852	-	1	NA	Intergenic	MLT1A1|LTR|ERVL-MaLR	-4294	NR_105782	102466634		NR_105782	ENSMUSG00000098482	Mir6363	Gm28026|mmu-mir-6363	microRNA 6363	ncRNA
mm_63417.1	chr7	127471010	127471036	+	1	NA	promoter-TSS (NM_145589)	promoter-TSS (NM_145589)	-591	NM_145589	233895	Mm.44183	NM_145589	ENSMUSG00000030822	Prr14	BC006909	proline rich 14	protein-coding
mm_18118.1	chr2	44996861	44996870	-	1	NA	exon (NM_015753, exon 8 of 10)	exon (NM_015753, exon 8 of 10)	26312	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_63820.1	chr7	134225149	134225152	+	1	NA	promoter-TSS (NM_007400)	promoter-TSS (NM_007400)	-53	NM_007400	11489	Mm.439714	NM_007400	ENSMUSG00000054555	Adam12	Mltna	a disintegrin and metallopeptidase domain 12 (meltrin alpha)	protein-coding
mm_118910.1	chr14	26669940	26669971	+	1	NA	promoter-TSS (NM_178668)	promoter-TSS (NM_178668)	-109	NM_178668	211948	Mm.290758	NM_178668	ENSMUSG00000043702	Pde12	2'-PDE|E430028B21Rik	phosphodiesterase 12	protein-coding
mm_106353.1	chr11	118393580	118393592	-	1	NA	exon (NM_011150, exon 6 of 6)	exon (NM_011150, exon 6 of 6)	8345	NM_011150	19039	Mm.3152	NM_011150	ENSMUSG00000033880	Lgals3bp	90K|CyCAP|MAC-2BP|Ppicap|Tango10b	lectin, galactoside-binding, soluble, 3 binding protein	protein-coding
mm_141406.1	chr17	29347903	29347940	-	1	NA	promoter-TSS (NM_019880)	promoter-TSS (NM_019880)	11	NM_001347335	56462	Mm.285322	NM_019880	ENSMUSG00000024012	Mtch1	2310034O17Rik|AI255158|AU018396|C77849|PSAP	mitochondrial carrier 1	protein-coding
mm_161430.1	chr15	55133442	55133442	+	1	NA	promoter-TSS (NM_001037937)	promoter-TSS (NM_001037937)	6	NM_001037937	97998	Mm.295397	NM_145470	ENSMUSG00000022419	Deptor	Depdc6	DEP domain containing MTOR-interacting protein	protein-coding
mm_36004.1	chr4	56757321	56757329	-	1	NA	intron (NM_026079, intron 34 of 36)	intron (NM_026079, intron 34 of 36)	13903	NM_009611	11470	Mm.30959	NM_009611	ENSMUSG00000070979	Actl7a	Tact2	actin-like 7a	protein-coding
mm_36168.1	chr4	61782223	61782226	-	1	NA	promoter-TSS (NM_001135127)	promoter-TSS (NM_001135127)	0	NM_001135127	100189605	Mm.457980	NM_001135127	ENSMUSG00000078673	Mup19	100039247|Gm12552|Mup11|Mup14|Mup17|Mup6|Mup8|OTTMUSG00000007472	major urinary protein 19	protein-coding
mm_93930.1	chr10	127166317	127166340	-	1	NA	intron (NR_045166, intron 2 of 9)	intron (NR_045166, intron 2 of 9)	497	NM_001244618	14421	Mm.386762	NM_008080	ENSMUSG00000006731	B4galnt1	4933429D13Rik|Gal-NAc-T|GalNAc-T|GalNAcT|Galgt1|Ggm-2|Ggm2	beta-1,4-N-acetyl-galactosaminyl transferase 1	protein-coding
mm_82062.1	chr9	122747194	122747223	+	1	NA	promoter-TSS (NM_001199736)	promoter-TSS (NM_001199736)	-138	NM_001199736	671232	Mm.296421	NM_001199736	ENSMUSG00000094985	Topaz1	Gm9524	testis and ovary specific PAZ domain containing 1	protein-coding
mm_161183.1	chr13	48261561	48261561	+	1	NA	exon (NM_031166, exon 1 of 3)	exon (NM_031166, exon 1 of 3)	134	NM_031166	15904	Mm.458006	NM_031166	ENSMUSG00000021379	Id4	Idb4|bHLHb27	inhibitor of DNA binding 4	protein-coding
mm_117368.1	chr13	71394291	71394299	-	1	NA	Intergenic	Intergenic	287206	NR_130325	100316804		NR_130325	ENSMUSG00000080580	Mir466f-4	Mirn466f-4|mmu-mir-466f-4	microRNA 466f-4	ncRNA
mm_127633.1	chr15	102470719	102470790	+	1	NA	5' UTR (NM_001174073, exon 1 of 13)	5' UTR (NM_001174073, exon 1 of 13)	122	NM_001174073	18521	Mm.236513	NM_011042	ENSMUSG00000056851	Pcbp2	AW412548|Hnrpx|alphaCP-2	poly(rC) binding protein 2	protein-coding
mm_57596.1	chr6	127769722	127769731	-	1	NA	promoter-TSS (NM_201371)	promoter-TSS (NM_201371)	-567	NM_201371	381813	Mm.39750	NM_201371	ENSMUSG00000030350	Prmt8	Hrmt1l3|Hrmt1l4	protein arginine N-methyltransferase 8	protein-coding
mm_73714.1	chr8	111914145	111914154	+	1	NA	intron (NM_001033321, intron 6 of 6)	intron (NM_001033321, intron 6 of 6)	-3950	NM_019950	56773	Mm.432506	NM_019950	ENSMUSG00000031952	Chst5	AI173964|GST-4|Gn6st-3|I-GlcNAc-6-ST	carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 5	protein-coding
mm_76529.1	chr8	87694870	87694902	-	1	NA	intron (NM_001310520, intron 3 of 5)	intron (NM_001310520, intron 3 of 5)	-52676	NR_131165	73557		NR_131165		1700096P03Rik	-	RIKEN cDNA 1700096P03 gene	ncRNA
mm_40863.1	chr5	73651347	73651369	+	1	NA	promoter-TSS (NM_178387)	promoter-TSS (NM_178387)	-22	NM_178387	73472	Mm.87067	NM_178387	ENSMUSG00000029155	Spata18	1700067I02Rik	spermatogenesis associated 18	protein-coding
mm_172383.1	chr7	131482793	131482803	+	1	NA	Intergenic	B1_Mm|SINE|Alu	-60165	NM_008257	15373	Mm.323562	NM_008257	ENSMUSG00000040148	Hmx3	Nkx-5.1|Nkx5-1|Nkx5.1	H6 homeobox 3	protein-coding
mm_133109.1	chr16	65520504	65520518	+	1	NA	promoter-TSS (NM_008849)	promoter-TSS (NM_008849)	-118	NM_008849	18736	Mm.355440	NM_008849	ENSMUSG00000004842	Pou1f1	GHF-1|Hmp1|Pit-1|Pit1|Pit1-rs1|dw|dwarf	POU domain, class 1, transcription factor 1	protein-coding
mm_19780.1	chr2	106970394	106970407	-	1	NA	promoter-TSS (NM_173750)	promoter-TSS (NM_173750)	-9	NM_173750	212772	Mm.381231	NM_173750	ENSMUSG00000027122	Arl14ep	2700007P21Rik|4930448O08Rik|ARF7EP	ADP-ribosylation factor-like 14 effector protein	protein-coding
mm_146186.1	chr18	75820213	75820236	+	1	NA	promoter-TSS (NM_145356)	promoter-TSS (NM_145356)	46	NM_145356	207259	Mm.159332	NM_145356	ENSMUSG00000044646	Zbtb7c	B230208J24Rik|Kr-pok|Zbtb36	zinc finger and BTB domain containing 7C	protein-coding
mm_111004.1	chr12	78861637	78861641	-	1	NA	promoter-TSS (NM_026114)	promoter-TSS (NM_026114)	-1	NM_023721	73834	Mm.311549	NM_023721	ENSMUSG00000021114	Atp6v1d	1110004P10Rik|Atp6m|VATD|Vma8	ATPase, H+ transporting, lysosomal V1 subunit D	protein-coding
mm_27215.1	chr3	35933096	35933100	-	1	NA	promoter-TSS (NM_001205362)	promoter-TSS (NM_001205362)	-132	NM_001205361	114893	Mm.374810	NM_033623	ENSMUSG00000027708	Dcun1d1	Rp42|SCCRO|Tes3|pTes3	DCN1, defective in cullin neddylation 1, domain containing 1 (S. cerevisiae)	protein-coding
mm_23267.1	chr3	51484276	51484304	+	1	NA	5' UTR (NM_016858, exon 1 of 2)	5' UTR (NM_016858, exon 1 of 2)	324	NM_016858	19338	Mm.1664	NM_016858	ENSMUSG00000027739	Rab33b	-	RAB33B, member RAS oncogene family	protein-coding
mm_140486.1	chr17	3156356	3156366	-	1	NA	intron (NM_134123, intron 3 of 19)	intron (NM_134123, intron 3 of 19)	41389	NM_134123	106583	Mm.124373	NM_134123	ENSMUSG00000046201	Scaf8	A630086M08Rik|A930036P18Rik|AA408306|AI447644|AI448652|AU015035|Rbm16|mKIAA1116	SR-related CTD-associated factor 8	protein-coding
mm_36878.1	chr4	107178297	107178338	-	1	NA	promoter-TSS (NM_029565)	promoter-TSS (NM_029565)	49	NM_025617	66526	Mm.246956	NM_025617	ENSMUSG00000028619	Tceanc2	2210010B22Rik|2210012G02Rik|6330404A07Rik|AU015593|Tdeanc2	transcription elongation factor A (SII) N-terminal and central domain containing 2	protein-coding
mm_2996.1	chr1	133232026	133232050	+	1	NA	Intergenic	Intergenic	-14059	NM_001160268	240753	Mm.253559	NM_182930	ENSMUSG00000041757	Plekha6	9530028L01Rik|AU042621|Pepp3	pleckstrin homology domain containing, family A member 6	protein-coding
mm_78561.1	chr9	35740958	35740966	+	1	NA	promoter-TSS (NM_001167588)	promoter-TSS (NM_001167588)	-87	NM_001167588	100312949	Mm.475848	NM_001167588	ENSMUSG00000091174	Gm17677	Pate-n|Pate10	predicted gene, 17677	protein-coding
mm_40987.1	chr5	77266234	77266244	+	1	NA	intron (NM_011263, intron 1 of 3)	CpG	745	NM_011263	19712	Mm.28840	NM_011263	ENSMUSG00000029249	Rest	2610008J04Rik|AA407358|NRSF|REST4	RE1-silencing transcription factor	protein-coding
mm_86748.1	chr10	19494709	19494738	+	1	NA	Intergenic	Intergenic	-97226	NM_010511	15979	Mm.549	NM_010511	ENSMUSG00000020009	Ifngr1	CD119|IFN-gammaR|Ifgr|Ifngr|Nktar	interferon gamma receptor 1	protein-coding
mm_39205.1	chr4	156047933	156047972	-	1	NA	intron (NM_029264, intron 4 of 14)	intron (NM_029264, intron 4 of 14)	2865	NM_029264	330010	Mm.440232	NM_029264	ENSMUSG00000029074	Ttll10	4833412E22Rik|4930595O22Rik|AU022799|BC042775|Ttll5	tubulin tyrosine ligase-like family, member 10	protein-coding
mm_67338.1	chr7	79793208	79793233	-	1	NA	exon (NM_008588, exon 1 of 2)	exon (NM_008588, exon 1 of 2)	370	NM_008588	17292	Mm.1404	NM_008588	ENSMUSG00000030544	Mesp1	bHLHc5	mesoderm posterior 1	protein-coding
mm_40351.1	chr5	45857090	45857120	+	1	NA	promoter-TSS (NM_172153)	promoter-TSS (NM_172153)	435	NM_001163073	209707	Mm.71498	NM_172153	ENSMUSG00000015882	Lcorl	Mlr1	ligand dependent nuclear receptor corepressor-like	protein-coding
mm_21621.1	chr2	164276118	164276124	-	1	NA	3' UTR (NM_009300, exon 3 of 3)	3' UTR (NM_009300, exon 3 of 3)	2186	NM_009300	20941	Mm.1286	NM_009300	ENSMUSG00000016998	Svs4	SVS-IV|Svp-2|Svp-4|Svp2|Svp4	seminal vesicle secretory protein 4	protein-coding
mm_39184.1	chr4	155785865	155785880	-	1	NA	promoter-TSS (NM_001033394)	promoter-TSS (NM_001033394)	2	NM_001033394	320587	Mm.384382	NM_001033394	ENSMUSG00000073680	Tmem88b	A230069A22Rik	transmembrane protein 88B	protein-coding
mm_2336.1	chr1	92831820	92831875	+	1	NA	5' UTR (NM_016696, exon 1 of 9)	5' UTR (NM_016696, exon 1 of 9)	161	NM_016696	14733	Mm.297976	NM_016696	ENSMUSG00000034220	Gpc1	AI462976	glypican 1	protein-coding
mm_106403.1	chr11	118909640	118909739	-	1	NA	promoter-TSS (NM_001039167)	promoter-TSS (NM_001039167)	-117	NM_001039167	52897	Mm.341103	NM_001024931	ENSMUSG00000025576	Rbfox3	Fox-3|Hrnbp3|NeuN|Neuna60	RNA binding protein, fox-1 homolog (C. elegans) 3	protein-coding
mm_129150.1	chr15	76229493	76229511	-	1	NA	promoter-TSS (NM_201385)	promoter-TSS (NM_201385)	-5	NM_201385	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
mm_40014.1	chr5	33104221	33104240	+	1	NA	promoter-TSS (NM_019810)	promoter-TSS (NM_019810)	11	NM_019810	20537	Mm.25237	NM_019810	ENSMUSG00000011034	Slc5a1	Sglt1	solute carrier family 5 (sodium/glucose cotransporter), member 1	protein-coding
mm_6837.1	chr1	84232956	84232968	-	1	NA	intron (NM_001003948, intron 1 of 2)	GA-rich|Low_complexity|Low_complexity	-14001	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_88133.1	chr10	69398800	69398817	+	1	NA	Intergenic	CpG	-45896	NM_007659	12534	Mm.281367	NM_007659	ENSMUSG00000019942	Cdk1	Cdc2|Cdc2a|p34<CDC2>	cyclin-dependent kinase 1	protein-coding
mm_67386.1	chr7	79842475	79842509	-	1	NA	promoter-TSS (NM_008486)	promoter-TSS (NM_008486)	-140	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_163596.1	chr13	41569327	41569336	+	1	NA	Intergenic	Intergenic	-36885	NM_001163572	621976	Mm.259830	NM_001163572	ENSMUSG00000087370	Tmem170b	EG621976	transmembrane protein 170B	protein-coding
mm_20746.1	chr2	140042173	140042192	-	1	NA	intron (NR_110350, intron 3 of 12)	intron (NR_110350, intron 3 of 12)	24623	NM_001159640	75812	Mm.293449	NM_175225	ENSMUSG00000039033	Tasp1	4930485D02Rik|AW986064	taspase, threonine aspartase 1	protein-coding
mm_11426.1	chr2	31950291	31950301	+	1	NA	promoter-TSS (NM_145144)	promoter-TSS (NM_145144)	-7	NM_145144	108897	Mm.24838	NM_145144	ENSMUSG00000001864	Aif1l	2810003C17Rik|AI043124|C87647|Iba2	allograft inflammatory factor 1-like	protein-coding
mm_165484.1	chr2	164333586	164333590	+	1	NA	exon (NM_009301, exon 2 of 3)	exon (NM_009301, exon 2 of 3)	823	NM_009301	20944	Mm.140154	NM_009301	ENSMUSG00000017004	Svs5	BB115186|Semg1|Svp-1|Svp1|Svp5	seminal vesicle secretory protein 5	protein-coding
mm_143837.1	chr17	84119208	84119218	-	1	NA	Intergenic	Intergenic	40553	NR_045458	74473	Mm.399575	NR_045458		4933433H22Rik	-	RIKEN cDNA 4933433H22 gene	ncRNA
mm_139998.1	chr17	72939721	72939740	+	1	NA	3' UTR (NM_029999, exon 3 of 3)	3' UTR (NM_029999, exon 3 of 3)	21425	NM_029999	77889	Mm.154109	NM_029999	ENSMUSG00000024063	Lbh	1810009F10Rik|6720416L16Rik	limb-bud and heart	protein-coding
mm_65493.1	chr7	25689149	25689169	-	1	NA	intron (NM_011577, intron 1 of 6)	intron (NM_011577, intron 1 of 6)	2157	NM_011577	21803	Mm.248380	NM_011577	ENSMUSG00000002603	Tgfb1	TGF-beta1|TGFbeta1|Tgfb|Tgfb-1	transforming growth factor, beta 1	protein-coding
mm_56324.1	chr6	92481165	92481214	-	1	NA	5' UTR (NM_001134460, exon 1 of 8)	5' UTR (NM_001134460, exon 1 of 8)	203	NM_001134460	243548	Mm.248820	NM_001081146	ENSMUSG00000030020	Prickle2	6230400G14Rik|6720451F06Rik|mpk2	prickle planar cell polarity protein 2	protein-coding
mm_164653.1	chr17	35835865	35835901	-	1	NA	exon (NM_011655, exon 4 of 4)	exon (NM_011655, exon 4 of 4)	2418	NM_011655	22154	Mm.273538	NM_011655	ENSMUSG00000001525	Tubb5	AA408537|AI596182|B130022C14Rik|M(beta)5	tubulin, beta 5 class I	protein-coding
mm_29836.1	chr3	129804143	129804147	-	1	NA	promoter-TSS (NM_001287224)	promoter-TSS (NM_001287224)	-115	NM_001287224	242235	Mm.302549	NM_001205102	ENSMUSG00000093865	Lrit3	Gm421	leucine-rich repeat, immunoglobulin-like and transmembrane domains 3	protein-coding
mm_132765.1	chr16	44746076	44746083	+	1	NA	exon (NM_025332, exon 1 of 6)	exon (NM_025332, exon 1 of 6)	284	NM_001159329	66067	Mm.34520	NM_025332	ENSMUSG00000022668	Gtpbp8	0610037H22Rik	GTP-binding protein 8 (putative)	protein-coding
mm_38268.1	chr4	136880735	136880743	-	1	NA	exon (NM_009777, exon 3 of 3)	exon (NM_009777, exon 3 of 3)	5438	NM_009777	12260	Mm.2570	NM_009777	ENSMUSG00000036905	C1qb	-	complement component 1, q subcomponent, beta polypeptide	protein-coding
mm_144074.1	chr17	91088824	91088858	-	1	NA	5' UTR (NM_020252, exon 2 of 23)	5' UTR (NM_020252, exon 2 of 23)	764	NM_001346957	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_162077.1	chrX	24574860	24574860	-	1	NA	Intergenic	Intergenic	-1555	NM_001100446	100043216		NM_001100446	ENSMUSG00000081218	Gm4297	-	predicted gene 4297	protein-coding
mm_8673.1	chr1	156674838	156674883	-	1	NA	promoter-TSS (NM_023141)	promoter-TSS (NM_023141)	-521	NM_023141	30935	Mm.206737	NM_023141	ENSMUSG00000060519	Tor3a	Adir	torsin family 3, member A	protein-coding
mm_48352.1	chr5	139345098	139345108	-	1	NA	promoter-TSS (NM_197980)	promoter-TSS (NM_197980)	63	NM_197980	68033	Mm.261064	NM_197980	ENSMUSG00000045438	Cox19	1810074D02Rik|2810437L13Rik	cytochrome c oxidase assembly protein 19	protein-coding
mm_80564.1	chr9	83834646	83834668	+	1	NA	promoter-TSS (NM_001284272)	promoter-TSS (NM_001284272)	-32	NM_009445	22137	Mm.1904	NM_009445	ENSMUSG00000038379	Ttk	AL022661|Esk1|Mps1|PYT|esk	Ttk protein kinase	protein-coding
mm_115383.1	chr13	113136157	113136167	+	1	NA	promoter-TSS (NR_131045)	promoter-TSS (NR_131045)	86	NR_131045	76720	Mm.54263	NR_131045		1700084D21Rik	-	RIKEN cDNA 1700084D21 gene	ncRNA
mm_156757.1	chrX	160502154	160502201	+	1	NA	promoter-TSS (NM_001177878)	promoter-TSS (NM_001177878)	11	NM_001177879	110094	Mm.350712	NM_172783	ENSMUSG00000031295	Phka2	6330505C01Rik|D330034O08|Phk	phosphorylase kinase alpha 2	protein-coding
mm_82420.1	chr9	14903809	14903815	-	1	NA	5' UTR (NM_176807, exon 1 of 5)	5' UTR (NM_176807, exon 1 of 5)	139	NM_176807	64931	Mm.86738	NM_022888	ENSMUSG00000031933	Izumo1r	0910001L11Rik|C86255|Folbp3|Folr4|Juno	IZUMO1 receptor, JUNO	protein-coding
mm_98992.1	chr11	98766259	98766277	+	1	NA	intron (NM_001313983, intron 9 of 9)	intron (NM_001313983, intron 9 of 9)	9109	NM_145434	217166	Mm.390397	NM_145434	ENSMUSG00000020889	Nr1d1	A530070C09Rik|R75201	nuclear receptor subfamily 1, group D, member 1	protein-coding
mm_125625.1	chr15	61988958	61988961	+	1	NA	intron (NM_010849, intron 2 of 2)	intron (NM_010849, intron 2 of 2)	3618	NM_001177352	17869	Mm.2444	NM_010849	ENSMUSG00000022346	Myc	AU016757|Myc2|Niard|Nird|bHLHe39	myelocytomatosis oncogene	protein-coding
mm_119317.1	chr14	36970042	36970050	+	1	NA	Intergenic	Intergenic	-1282	NM_027045	72972	Mm.27621	NM_027045	ENSMUSG00000058690	Ccser2	1700012P13Rik|2900054P12Rik|AI035535|AW108503|Fam190b|Gcap14	coiled-coil serine rich 2	protein-coding
mm_123824.1	chr14	70618632	70618641	-	1	NA	promoter-TSS (NM_001252666)	promoter-TSS (NM_001252666)	-67	NM_001252666	13829	Mm.210863	NM_013514	ENSMUSG00000022099	Dmtn	AI325486|Epb4.9|Epb49|dematin	dematin actin binding protein	protein-coding
mm_87008.1	chr10	26827645	26827648	+	1	NA	intron (NM_176837, intron 1 of 14)	intron (NM_176837, intron 1 of 14)	55134	NM_176837	73910	Mm.356496	NM_176837	ENSMUSG00000039031	Arhgap18	4833419J07Rik|AI314906|AI843501	Rho GTPase activating protein 18	protein-coding
mm_163104.1	chr11	69735558	69735572	-	1	NA	exon (NM_001291068, exon 29 of 29)	exon (NM_001291068, exon 29 of 29)	23068	NM_001291068	20020	Mm.16533	NM_009089	ENSMUSG00000005198	Polr2a	220kDa|Rpb1|Rpo2-1	polymerase (RNA) II (DNA directed) polypeptide A	protein-coding
mm_88934.1	chr10	81268177	81268205	+	1	NA	promoter-TSS (NM_018758)	promoter-TSS (NM_018758)	19	NM_018758	57267	Mm.293931	NM_018758	ENSMUSG00000004931	Apba3	AW208791|Mint-3|X11gamma|lin-10|mint3	amyloid beta (A4) precursor protein-binding, family A, member 3	protein-coding
mm_75044.1	chr8	32819919	32819931	-	1	NA	Intergenic	(TATATG)n|Simple_repeat|Simple_repeat	130101	NM_001177589	100042715	Mm.291093	NM_001177589		Gm3985	-	predicted gene 3985	protein-coding
mm_21908.1	chr2	166567244	166567265	-	1	NA	3' UTR (NM_177782, exon 40 of 40)	3' UTR (NM_177782, exon 40 of 40)	-105464	NR_105783	102465188		NR_105783	ENSMUSG00000098675	Mir6364	Gm27327|mmu-mir-6364	microRNA 6364	ncRNA
mm_143085.1	chr17	57078448	57078458	-	1	NA	promoter-TSS (NM_153551)	promoter-TSS (NM_153551)	57	NM_153551	70785	Mm.284447	NM_153551	ENSMUSG00000002668	Dennd1c	4432409M07Rik	DENN/MADD domain containing 1C	protein-coding
mm_172497.1	chr7	64389770	64389774	-	1	NA	exon (NM_026483, exon 2 of 11)	exon (NM_026483, exon 2 of 11)	2464	NM_026483	67973	Mm.26973	NM_026483	ENSMUSG00000030521	Mphosph10	2810453H10Rik|5730405D16Rik|AI326008	M-phase phosphoprotein 10 (U3 small nucleolar ribonucleoprotein)	protein-coding
mm_147709.1	chr18	60812271	60812299	-	1	NA	TTS (NR_039567)	TTS (NR_039567)	209	NR_039567	100628611		NR_039567	ENSMUSG00000093327	Mir5107	mir-5107|mmu-mir-5107|mu-mir-5107	microRNA 5107	ncRNA
mm_84240.1	chr9	62282166	62282217	-	1	NA	promoter-TSS (NM_025721)	promoter-TSS (NM_025721)	-12	NM_025721	66712	Mm.263615	NM_025721	ENSMUSG00000046846	Spesp1	4921508E09Rik|AI428149	sperm equatorial segment protein 1	protein-coding
mm_41600.1	chr5	96173882	96173912	+	1	NA	Intergenic	Intergenic	-11907	NM_144910	231464	Mm.28374	NM_144910	ENSMUSG00000034724	Cnot6l	4932442K20Rik	CCR4-NOT transcription complex, subunit 6-like	protein-coding
mm_34473.1	chr4	148164218	148164239	+	1	NA	exon (NM_176848, exon 2 of 6)	exon (NM_176848, exon 2 of 6)	3560	NM_176848	230904	Mm.262287	NM_176848	ENSMUSG00000041556	Fbxo2	FBG1|FBX2|Fbs1|Fbs2|NFB42|Prpl4	F-box protein 2	protein-coding
mm_41528.1	chr5	92682783	92682805	+	1	NA	promoter-TSS (NM_015756)	promoter-TSS (NM_015756)	-641	NM_015756	27428	Mm.46014	NM_015756	ENSMUSG00000029381	Shroom3	AL022960|D5Ertd287e|Shrm|Shrm3	shroom family member 3	protein-coding
mm_43889.1	chr5	143933030	143933047	+	1	NA	Intergenic	Intergenic	23037	NM_008886	18861	Mm.2950	NM_008886	ENSMUSG00000075569	Pms2	AW555130|Pmsl2	postmeiotic segregation increased 2 (S. cerevisiae)	protein-coding
mm_118038.1	chr13	101692564	101692600	-	1	NA	promoter-TSS (NM_001024955)	promoter-TSS (NM_001024955)	48	NM_001024955	18708	Mm.259333	NM_001024955	ENSMUSG00000041417	Pik3r1	PI3K|p50alpha|p55alpha|p85alpha	phosphatidylinositol 3-kinase, regulatory subunit, polypeptide 1 (p85 alpha)	protein-coding
mm_24186.1	chr3	88594094	88594107	+	1	NA	Intergenic	Intergenic	14429	NM_025448	66256	Mm.7091	NM_025448	ENSMUSG00000041355	Ssr2	1500032E05Rik|AI315033|AU020133|TLAP|TRAPB|TRAPbeta	signal sequence receptor, beta	protein-coding
mm_57059.1	chr6	122488112	122488113	-	1	NA	Intergenic	MT2B2|LTR|ERVL	-1807	NM_027664	108653	Mm.277939	NM_027664	ENSMUSG00000040649	Rimklb	4931417E21Rik|4933426K21Rik|AA097693|AI325948|AU015629|Naags	ribosomal modification protein rimK-like family member B	protein-coding
mm_30655.1	chr4	8913020	8913029	+	1	NA	Intergenic	Intergenic	222618	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_132709.1	chr16	43474292	43474294	+	1	NA	intron (NM_181058, intron 3 of 6)	Lx4A|LINE|L1	-54097	NR_046026	626693	Mm.447083	NR_046026	ENSMUSG00000085499	Gm15713	OTTMUSG00000025617	predicted gene 15713	ncRNA
mm_13022.1	chr2	91035614	91035632	+	1	NA	promoter-TSS (NM_009023)	promoter-TSS (NM_009023)	-4	NM_009023	19400	Mm.1272	NM_009023	ENSMUSG00000002104	Rapsn	43kDa|Nraps|Raps|rapsyn	receptor-associated protein of the synapse	protein-coding
mm_21046.1	chr2	152540256	152540258	-	1	NA	promoter-TSS (NM_001001444)	promoter-TSS (NM_001001444)	-216	NM_001001444	75400	Mm.45560	NM_001001444	ENSMUSG00000044249	Defb29	0610030I09Rik|BD-29|mBD-29	defensin beta 29	protein-coding
mm_60346.1	chr7	44358499	44358509	+	1	NA	TTS (NM_001034115)	TTS (NM_001034115)	16526	NM_027049	69349	Mm.358922	NM_027049	ENSMUSG00000008028	1700008O03Rik	-	RIKEN cDNA 1700008O03 gene	protein-coding
mm_115247.1	chr13	110396613	110396647	+	1	NA	exon (NM_152804, exon 4 of 14)	exon (NM_152804, exon 4 of 14)	1586	NM_152804	20620	Mm.380	NM_152804	ENSMUSG00000021701	Plk2	Snk	polo-like kinase 2	protein-coding
mm_126624.1	chr15	83220522	83220556	+	1	NA	Intergenic	MLTR18_MM|LTR|ERVK	31192	NM_001170954	239559	Mm.323805	NM_001004150	ENSMUSG00000047878	A4galt	-	alpha 1,4-galactosyltransferase	protein-coding
mm_21988.1	chr2	167631984	167632009	-	1	NA	promoter-TSS (NM_023230)	promoter-TSS (NM_023230)	9	NM_001311146	66589	Mm.278783	NM_023230	ENSMUSG00000078923	Ube2v1	0610011J09Rik|AI256840|CROC-1|CROC1|D7Bwg1382e|UEV-1	ubiquitin-conjugating enzyme E2 variant 1	protein-coding
mm_51163.1	chr6	70726431	70726472	+	1	NA	Intergenic	Intergenic	65724	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_100191.1	chr11	116751707	116751721	+	1	NA	promoter-TSS (NR_003364)	promoter-TSS (NR_003364)	-453	NR_003364	193217	Mm.100084	NR_003364		BC018473	-	cDNA sequence BC018473	ncRNA
mm_103268.1	chr11	71740330	71740361	-	1	NA	Intergenic	Intergenic	-10358	NM_177618	216881	Mm.48648	NM_177618	ENSMUSG00000020811	Wscd1	mKIAA0523	WSC domain containing 1	protein-coding
mm_123290.1	chr14	61556666	61556674	-	1	NA	5' UTR (NM_001310603, exon 1 of 4)	5' UTR (NM_001310603, exon 1 of 4)	216	NM_025697	66674	Mm.282706	NM_025697	ENSMUSG00000021930	Spryd7	6330409N04Rik|Clld6	SPRY domain containing 7	protein-coding
mm_121362.1	chr14	117269687	117269702	+	1	NA	intron (NM_001079844, intron 2 of 9)	RSINE1|SINE|B4	344397	NM_011821	23888	Mm.440025	NM_011821	ENSMUSG00000058571	Gpc6	-	glypican 6	protein-coding
mm_171298.1	chr3	92689368	92689368	+	1	NA	Intergenic	Intergenic	-2158	NM_027137	69611	Mm.176243	NM_027137	ENSMUSG00000103243	Lce1d	2310037L11Rik|AI415320|Sprrl7	late cornified envelope 1D	protein-coding
mm_10322.1	chr2	11250463	11250474	+	1	NA	intron (NM_008859, intron 8 of 17)	C-rich|Low_complexity|Low_complexity	78086	NM_008859	18761	Mm.329993	NM_008859	ENSMUSG00000026778	Prkcq	A130035A12Rik|AW494342|PKC-0|PKC-theta|PKCtheta|Pkcq	protein kinase C, theta	protein-coding
mm_64449.1	chr7	142658861	142658899	+	1	NA	promoter-TSS (NM_010514)	promoter-TSS (NM_010514)	-76	NM_010514	16002	Mm.3862	NM_010514	ENSMUSG00000048583	Igf2	AL033362|Igf-2|Igf-II|M6pr|Mpr|Peg2	insulin-like growth factor 2	protein-coding
mm_104718.1	chr11	98053416	98053467	-	1	NA	promoter-TSS (NM_146028)	promoter-TSS (NM_146028)	21	NM_146028	217154	Mm.181008	NM_146028	ENSMUSG00000017400	Stac2	24b2|24b2/STAC2|AW240854	SH3 and cysteine rich domain 2	protein-coding
mm_159667.1	chr4	154097157	154097157	-	1	NA	promoter-TSS (NM_001126330)	promoter-TSS (NM_001126330)	16	NM_001126330	22062	Mm.78015	NM_011642	ENSMUSG00000029026	Trp73	TAp73|Tp73|deltaNp73|p73	transformation related protein 73	protein-coding
mm_113741.1	chr13	44729523	44729550	+	1	NA	Intergenic	Intergenic	-1238	NM_021878	16468	Mm.25059	NM_021878	ENSMUSG00000038518	Jarid2	Jmj|jumonji	jumonji, AT rich interactive domain 2	protein-coding
mm_64246.1	chr7	141704272	141704282	+	1	NA	exon (NM_023566, exon 27 of 46)	exon (NM_023566, exon 27 of 46)	13937	NM_023566	17831	Mm.2041	NM_023566		Muc2	2010015E03Rik|MCM|wnn	mucin 2	protein-coding
mm_16499.1	chr2	181187878	181187916	+	1	NA	intron (NM_025598, intron 3 of 4)	CpG-8989	554	NM_025598	66496	Mm.213943	NM_025598	ENSMUSG00000016344	Ppdpf	0610012G23Rik|2610317A05Rik|2700038C09Rik|3110053G12Rik	pancreatic progenitor cell differentiation and proliferation factor	protein-coding
mm_6848.1	chr1	84245165	84245176	-	1	NA	intron (NM_001003948, intron 1 of 2)	intron (NM_001003948, intron 1 of 2)	-26209	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_56668.1	chr6	113633128	113633145	-	1	NA	Intergenic	RMER1B|Other|Other	-5331	NM_172161	108960	Mm.152142	NM_172161	ENSMUSG00000060477	Irak2	6330415L08Rik|AI649099|IRAK-2	interleukin-1 receptor-associated kinase 2	protein-coding
mm_82362.1	chr9	14500429	14500460	-	1	NA	promoter-TSS (NM_023153)	promoter-TSS (NM_023153)	38	NM_173433	244694	Mm.240457	NM_173433	ENSMUSG00000053914	Kdm4d	4932416A15|Jmjd2d	lysine (K)-specific demethylase 4D	protein-coding
mm_59692.1	chr7	28467900	28467902	+	1	NA	TTS (NM_001141921)	TTS (NM_001141921)	15663	NM_001141921	80749	Mm.483073	NM_030562	ENSMUSG00000030600	Lrfn1	BC004018|SALM2|Semo1	leucine rich repeat and fibronectin type III domain containing 1	protein-coding
mm_140202.1	chr17	83729142	83729151	+	1	NA	intron (NM_001171053, intron 3 of 13)	B1_Mur2|SINE|Alu	22983	NM_001171052	116871	Mm.277668	NM_054082	ENSMUSG00000055817	Mta3	1110002J22Rik|mKIAA1266	metastasis associated 3	protein-coding
mm_128800.1	chr15	66865198	66865207	-	1	NA	Intergenic	Intergenic	-26191	NM_018865	22402	Mm.10222	NM_018865	ENSMUSG00000005124	Wisp1	AW146261|CCN4|Elm1	WNT1 inducible signaling pathway protein 1	protein-coding
mm_67231.1	chr7	74719275	74719287	-	1	NA	Intergenic	Intergenic	-164501	NM_001038643	108116	Mm.425467	NM_023908	ENSMUSG00000025790	Slco3a1	5830414C08Rik|Anr1|MJAM|OATP-D|R75096|Slc21a11	solute carrier organic anion transporter family, member 3a1	protein-coding
mm_88091.1	chr10	68723724	68723760	+	1	NA	promoter-TSS (NM_177794)	promoter-TSS (NM_177794)	-4	NM_177794	327766	Mm.2479	NM_177794	ENSMUSG00000060044	Tmem26	3230401A06|AI195372	transmembrane protein 26	protein-coding
mm_15937.1	chr2	165655321	165655351	+	1	NA	promoter-TSS (NM_010165)	promoter-TSS (NM_010165)	38	NM_010165	14049	Mm.282719	NM_010165	ENSMUSG00000017897	Eya2	Eab1	EYA transcriptional coactivator and phosphatase 2	protein-coding
mm_40171.1	chr5	35893361	35893426	+	1	NA	promoter-TSS (NM_027373)	promoter-TSS (NM_027373)	74	NM_027373	70292	Mm.125167	NM_027373	ENSMUSG00000029094	Afap1	2600003E23Rik|9630044L16Rik|AI848729|Afap|mKIAA3018	actin filament associated protein 1	protein-coding
mm_39882.1	chr5	31077773	31077810	+	1	NA	intron (NM_023525, intron 42 of 43)	intron (NM_023525, intron 42 of 43)	15736	NM_011773	22784	Mm.1396	NM_011773	ENSMUSG00000029151	Slc30a3	Znt3	solute carrier family 30 (zinc transporter), member 3	protein-coding
mm_84928.1	chr9	81633807	81633839	-	1	NA	intron (NR_040396, intron 1 of 4)	intron (NR_040396, intron 1 of 4)	-1271	NM_010482	15551	Mm.445308	NM_010482	ENSMUSG00000049511	Htr1b	-	5-hydroxytryptamine (serotonin) receptor 1B	protein-coding
mm_70442.1	chr8	11728013	11728037	+	1	NA	promoter-TSS (NM_001113517)	promoter-TSS (NM_001113517)	-80	NM_001113517	54126	Mm.244068	NM_017402	ENSMUSG00000031511	Arhgef7	Cool|PIX|Pak3bp|betaPix|betaPix-b|betaPix-c|cool-1|mKIAA0142|p85Cool1|p85SPR	Rho guanine nucleotide exchange factor (GEF7)	protein-coding
mm_90600.1	chr10	128322480	128322493	+	1	NA	promoter-TSS (NM_019953)	promoter-TSS (NM_019953)	27	NM_019953	56530	Mm.44220	NM_019953	ENSMUSG00000025381	Cnpy2	5330432A10Rik|AW229003|D10Bwg1546e|Tmem4|Zsig9	canopy FGF signaling regulator 2	protein-coding
mm_167677.1	chr9	77917463	77917473	+	1	NA	5' UTR (NM_134255, exon 1 of 8)	5' UTR (NM_134255, exon 1 of 8)	103	NM_134255	68801	Mm.430736	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	ELOVL family member 5, elongation of long chain fatty acids (yeast)	protein-coding
mm_9892.1	chr1	186705237	186705245	-	1	NA	5' UTR (NM_009367, exon 1 of 7)	5' UTR (NM_009367, exon 1 of 7)	748	NM_009367	21808	Mm.18213	NM_009367	ENSMUSG00000039239	Tgfb2	BB105277|Tgf-beta2|Tgfb-2	transforming growth factor, beta 2	protein-coding
mm_151843.1	chr19	5729619	5729700	-	1	NA	promoter-TSS (NM_181452)	promoter-TSS (NM_181452)	7	NM_181452	17826	Mm.391142	NM_023166	ENSMUSG00000024939	Fam89b	1110021A21Rik|MMTV|Mtvr2	family with sequence similarity 89, member B	protein-coding
mm_116560.1	chr13	46727933	46728005	-	1	NA	promoter-TSS (NM_175749)	promoter-TSS (NM_175749)	-120	NM_175749	218210	Mm.255398	NM_175749	ENSMUSG00000021374	Nup153	B130015D15Rik|C88147	nucleoporin 153	protein-coding
mm_17434.1	chr2	27515052	27515089	-	1	NA	promoter-TSS (NM_080848)	promoter-TSS (NM_080848)	-77	NM_080848	140858	Mm.28265	NM_080848	ENSMUSG00000026917	Wdr5	2410008O07Rik|AA408785|AA960360|Big|Big-3	WD repeat domain 5	protein-coding
mm_119323.1	chr14	37068058	37068064	+	1	NA	promoter-TSS (NM_173418)	promoter-TSS (NM_173418)	12	NM_173418	239038	Mm.134302	NM_173418	ENSMUSG00000043418	Lrit2	A930010E21Rik|Lrrc22	leucine-rich repeat, immunoglobulin-like and transmembrane domains 2	protein-coding
mm_144761.1	chr18	35771611	35771615	+	1	NA	promoter-TSS (NM_019912)	promoter-TSS (NM_019912)	54	NM_019912	56550	Mm.180052	NM_019912	ENSMUSG00000091896	Ube2d2a	1500034D03Rik|Ubc2e|Ube2d2|ubc4	ubiquitin-conjugating enzyme E2D 2A	protein-coding
mm_15602.1	chr2	160687671	160687700	+	1	NA	exon (NM_009408, exon 6 of 21)	exon (NM_009408, exon 6 of 21)	41788	NM_009408	21969	Mm.217233	NM_009408	ENSMUSG00000070544	Top1	AI467334|D130064I21Rik|Top-1	topoisomerase (DNA) I	protein-coding
mm_132267.1	chr16	32877834	32877863	+	1	NA	promoter-TSS (NM_001159349)	promoter-TSS (NM_001159349)	64	NM_001159349	69823	Mm.12831	NM_027226	ENSMUSG00000022800	Fyttd1	2010005M05Rik|3830411L18Rik|3830421F13Rik|4933423A17Rik|AI098218|AW539567|C85190	forty-two-three domain containing 1	protein-coding
mm_153047.1	chr19	32068824	32068836	-	1	NA	intron (NM_018830, intron 2 of 23)	intron (NM_018830, intron 2 of 23)	34310	NM_018830	54447	Mm.491229	NM_018830	ENSMUSG00000024887	Asah2	AI585898	N-acylsphingosine amidohydrolase 2	protein-coding
mm_78156.1	chr9	21027516	21027526	+	1	NA	exon (NM_010493, exon 6 of 7)	exon (NM_010493, exon 6 of 7)	-1852	NM_023892	78369	Mm.30220	NM_023892	ENSMUSG00000001014	Icam4	1810015M19Rik|Cd242|ICAM-4	intercellular adhesion molecule 4, Landsteiner-Wiener blood group	protein-coding
mm_164267.1	chr15	101228320	101228344	+	1	NA	intron (NM_019518, intron 2 of 7)	intron (NM_019518, intron 2 of 7)	-3146	NR_045328	380977	Mm.399924	NR_045326	ENSMUSG00000097915	A330009N23Rik	-	RIKEN cDNA A330009N23 gene	ncRNA
mm_154564.1	chrX	6400112	6400144	+	1	NA	promoter-TSS (NM_001040459)	promoter-TSS (NM_001040459)	96	NM_001040459	208431	Mm.23208	NM_001040459	ENSMUSG00000068270	Shroom4	D430043L16Rik|Gm724|Shrm4	shroom family member 4	protein-coding
mm_55867.1	chr6	83457524	83457543	-	1	NA	Intergenic	Intergenic	-1141	NM_001347313	194388	Mm.211030	NM_183138	ENSMUSG00000034832	Tet3	B430006D22Rik|BC037432|D230004J03Rik	tet methylcytosine dioxygenase 3	protein-coding
mm_96098.1	chr11	60444309	60444313	+	1	NA	3' UTR (NM_025757, exon 6 of 6)	3' UTR (NM_025757, exon 6 of 6)	-10306	NM_021354	13495	Mm.41803	NM_021354	ENSMUSG00000020537	Drg2	AI255295|AI461605	developmentally regulated GTP binding protein 2	protein-coding
mm_21274.1	chr2	156887057	156887084	-	1	NA	promoter-TSS (NM_029983)	promoter-TSS (NM_029983)	8	NM_029983	77799	Mm.29264	NM_029983	ENSMUSG00000027636	Sla2	A930009E21Rik|AI430952|SLAP-2|SLAP2	Src-like-adaptor 2	protein-coding
mm_34320.1	chr4	141821705	141821723	+	1	NA	exon (NM_007919, exon 4 of 8)	exon (NM_007919, exon 4 of 8)	4291	NM_007919	13706	Mm.45316	NM_007919	ENSMUSG00000058579	Cela2a	Ela-2|Ela2|Ela2a	chymotrypsin-like elastase family, member 2A	protein-coding
mm_77641.1	chr8	124369988	124369999	-	1	NA	3' UTR (NM_171824, exon 7 of 7)	3' UTR (NM_171824, exon 7 of 7)	63943	NM_171824	209966	Mm.234233	NM_171824	ENSMUSG00000050751	Pgbd5	2900019M05Rik|AI854313	piggyBac transposable element derived 5	protein-coding
mm_3067.1	chr1	134183479	134183487	+	1	NA	intron (NM_007695, intron 2 of 9)	intron (NM_007695, intron 2 of 9)	1079	NM_007695	12654	Mm.38274	NM_007695	ENSMUSG00000064246	Chil1	AW208766|Brp39|Chi3l1|Gp39	chitinase-like 1	protein-coding
mm_123845.1	chr14	70677335	70677340	-	1	NA	intron (NM_023045, intron 20 of 27)	B3|SINE|B2	-24253	NM_181345	328440	Mm.347749	NM_181345	ENSMUSG00000047911	Npm2	-	nucleophosmin/nucleoplasmin 2	protein-coding
mm_23343.1	chr3	54693089	54693101	+	1	NA	promoter-TSS (NM_019995)	promoter-TSS (NM_019995)	-10	NM_019995	56790	Mm.486375	NM_019995	ENSMUSG00000027751	Supt20	AA667204|AI450544|D3Ertd300e|Fam48a|Supt20h|p38IP	suppressor of Ty 20	protein-coding
mm_163138.1	chr11	79276781	79276783	+	1	NA	Intergenic	Intergenic	-22087	NM_019653	78889	Mm.307022	NM_019653	ENSMUSG00000017677	Wsb1	1110056B13Rik|2700038M07Rik	WD repeat and SOCS box-containing 1	protein-coding
mm_85793.1	chr9	109832714	109832739	-	1	NA	promoter-TSS (NM_018757)	promoter-TSS (NM_018757)	-68	NM_018757	54369	Mm.12951	NM_018757	ENSMUSG00000032478	Nme6	nm23-M6	NME/NM23 nucleoside diphosphate kinase 6	protein-coding
mm_15541.1	chr2	158384974	158384993	+	1	NA	3' UTR (NM_175692, exon 5 of 5)	3' UTR (NM_175692, exon 5 of 5)	9345	NM_175692	319317	Mm.294494	NM_175692	ENSMUSG00000044349	Snhg11	A930034L06Rik|AI854265|AL022637|AW319638|E130013N09Rik	small nucleolar RNA host gene 11	protein-coding
mm_8190.1	chr1	138101131	138101163	-	1	NA	exon (NM_001268286, exon 9 of 29)	exon (NM_001268286, exon 9 of 29)	73979	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_67811.1	chr7	98119518	98119527	-	1	NA	promoter-TSS (NM_008663)	promoter-TSS (NM_008663)	-29	NM_008663	17921	Mm.1403	NM_008663	ENSMUSG00000030761	Myo7a	Hdb|Myo7|USH1B|nmf371|polka|sh-1|sh1	myosin VIIA	protein-coding
mm_39687.1	chr5	26881534	26881534	+	1	NA	intron (NM_010075, intron 1 of 25)	MTC|LTR|ERVL-MaLR	-23244	NM_001198886	13483	Mm.42078	NM_010075	ENSMUSG00000061576	Dpp6	B930011P16Rik|D5Buc3|D5Buc4|D5Buc5|DPP VI|Dpp-6|Gm1377|In(5)6H-p|Peplb|Rw	dipeptidylpeptidase 6	protein-coding
mm_97391.1	chr11	77801326	77801355	+	1	NA	promoter-TSS (NM_001291215)	promoter-TSS (NM_001291215)	42	NM_001291215	360013	Mm.341248	NM_011586	ENSMUSG00000000631	Myo18a	MAJN|MyoPDZ|MysPDZ|SP-R210	myosin XVIIIA	protein-coding
mm_124195.1	chr14	98169092	98169102	-	1	NA	exon (NM_001038610, exon 1 of 11)	exon (NM_001038610, exon 1 of 11)	668	NM_001038610	13134	Mm.320593	NM_007826	ENSMUSG00000055639	Dach1	Dac|Dach	dachshund 1 (Drosophila)	protein-coding
mm_73005.1	chr8	93810889	93810899	+	1	NA	promoter-TSS (NM_010308)	promoter-TSS (NM_010308)	56	NM_001113384	14681	Mm.251445	NM_010308	ENSMUSG00000031748	Gnao1	AW050213|Galphao|Gnao|alphaO	guanine nucleotide binding protein, alpha O	protein-coding
mm_25199.1	chr3	103787480	103787489	+	1	NA	intron (NM_001301304, intron 1 of 15)	intron (NM_001301304, intron 1 of 15)	3791	NM_001301306	15257	Mm.20827	NM_010432	ENSMUSG00000008730	Hipk1	1110062K04Rik|Myak	homeodomain interacting protein kinase 1	protein-coding
mm_102645.1	chr11	62789403	62789443	-	1	NA	promoter-TSS (NM_138949)	promoter-TSS (NM_138949)	-6	NM_138949	192651	Mm.168530	NM_138949	ENSMUSG00000047342	Zfp286	BC027023	zinc finger protein 286	protein-coding
mm_6664.1	chr1	80287662	80287665	-	1	NA	intron (NM_001313728, intron 6 of 16)	intron (NM_001313728, intron 6 of 16)	53027	NM_001313728	26554	Mm.12665	NM_016716	ENSMUSG00000004364	Cul3	KIAA0617	cullin 3	protein-coding
mm_152672.1	chr19	14598192	14598202	-	1	NA	promoter-TSS (NM_011600)	promoter-TSS (NM_011600)	-14	NM_001302947	21888	Mm.103638	NM_011600	ENSMUSG00000024642	Tle4	5730411M05Rik|AA792082|Bce-1|Bce1|ESTM13|ESTM14|Grg4|X83332|X83333|grg-4	transducin-like enhancer of split 4	protein-coding
mm_89395.1	chr10	89916374	89916385	+	1	NA	intron (NM_001128086, intron 1 of 24)	intron (NM_001128086, intron 1 of 24)	42870	NM_001128086	77531	Mm.440605	NM_181398	ENSMUSG00000058589	Anks1b	AIDA-1b|C030032C09Rik|E530015N03Rik|ENSMUSG00000078431|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding
mm_69925.1	chr7	141902334	141902350	-	1	NA	promoter-TSS (NM_023764)	promoter-TSS (NM_023764)	64	NM_023764	54473	Mm.103551	NM_023764	ENSMUSG00000025139	Tollip	4930403G24Rik|4931428G15Rik	toll interacting protein	protein-coding
mm_96214.1	chr11	62457412	62457449	+	1	NA	promoter-TSS (NM_177229)	promoter-TSS (NM_177229)	-98	NM_177229	20185	Mm.271814	NM_011308	ENSMUSG00000018501	Ncor1	5730405M06Rik|A230020K14Rik|N-CoR|RIP13|Rxrip13|mKIAA1047	nuclear receptor co-repressor 1	protein-coding
mm_147752.1	chr18	61211452	61211454	-	1	NA	5' UTR (NM_007885, exon 1 of 4)	5' UTR (NM_007885, exon 1 of 4)	143	NM_007885	13521	Mm.24803	NM_007885	ENSMUSG00000034320	Slc26a2	Dtd|ST-OB	solute carrier family 26 (sulfate transporter), member 2	protein-coding
mm_144513.1	chr18	24709464	24709466	+	1	NA	5' UTR (NM_001289655, exon 1 of 26)	5' UTR (NM_001289655, exon 1 of 26)	842	NM_001289655	225288	Mm.329322	NM_175276	ENSMUSG00000034295	Fhod3	A930009H06Rik|FHOS2|mKIAA1695	formin homology 2 domain containing 3	protein-coding
mm_78189.1	chr9	21320721	21320807	+	1	NA	promoter-TSS (NM_001199186)	promoter-TSS (NM_001199186)	45	NM_001199186	68682	Mm.148425	NM_152808	ENSMUSG00000057193	Slc44a2	1110028E10Rik|CTL2	solute carrier family 44, member 2	protein-coding
mm_108120.1	chr12	75818295	75818356	+	1	NA	promoter-TSS (NM_001005510)	promoter-TSS (NM_001005510)	7	NM_001005510	319565	Mm.26652	NM_001005510	ENSMUSG00000063450	Syne2	6820443O06Rik|AW546258|Cpfl8|D12Ertd777e|NUA|Nesp2g|dice|mKIAA1011	spectrin repeat containing, nuclear envelope 2	protein-coding
mm_168502.1	chr11	53272017	53272031	-	1	NA	exon (NM_008300, exon 10 of 19)	exon (NM_008300, exon 10 of 19)	28455	NM_008300	15525	Mm.239865	NM_008300	ENSMUSG00000020361	Hspa4	70kDa|AI317151|APG-2|Hsp110|Hsp70RY|mKIAA4025	heat shock protein 4	protein-coding
mm_161196.1	chr13	54784183	54784183	+	1	NA	intron (NM_001039683, intron 1 of 6)	B1_Mur4|SINE|Alu	185	NM_001039683	218268	Mm.425821	NM_001033269	ENSMUSG00000074895	Eif4e1b	Eif4eloo|Gm273	eukaryotic translation initiation factor 4E family member 1B	protein-coding
mm_119751.1	chr14	54153254	54153264	+	1	NA	Intergenic	Intergenic	100670	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_33654.1	chr4	133092530	133092540	+	1	NA	Intergenic	Intergenic	-38098	NM_153423	242687	Mm.23566	NM_153423	ENSMUSG00000028868	Wasf2	AW742646|D4Ertd13e|WAVE2	WAS protein family, member 2	protein-coding
mm_46285.1	chr5	100165524	100165564	-	1	NA	Intergenic	Intergenic	-5736	NM_182841	231503	Mm.99790	NM_182841	ENSMUSG00000050640	Tmem150c	-	transmembrane protein 150C	protein-coding
mm_26019.1	chr3	135438433	135438452	+	1	NA	promoter-TSS (NM_025356)	promoter-TSS (NM_025356)	223	NR_030689	319587	Mm.358971	NR_030689	ENSMUSG00000097032	4930539J05Rik	8030475D13Rik	RIKEN cDNA 4930539J05 gene	ncRNA
mm_97948.1	chr11	83664486	83664513	+	1	NA	3' UTR (NM_013652, exon 3 of 3)	3' UTR (NM_013652, exon 3 of 3)	1915	NM_013652	20303	Mm.244263	NM_013652	ENSMUSG00000018930	Ccl4	AT744.1|Act-2|MIP-1B|Mip1b|Scya4	chemokine (C-C motif) ligand 4	protein-coding
mm_49441.1	chr6	29319230	29319237	+	1	NA	promoter-TSS (NM_001289664)	promoter-TSS (NM_001289664)	93	NM_001289664	330277	Mm.87624	NM_207258	ENSMUSG00000039742	Fam71f1	GARI-L1|Gm764|NYD-SP18	family with sequence similarity 71, member F1	protein-coding
mm_169612.1	chr15	37347765	37347766	+	1	NA	intron (NM_026496, intron 13 of 15)	intron (NM_026496, intron 13 of 15)	-77789	NM_029113	74892	Mm.107630	NM_029113	ENSMUSG00000022288	4930447A16Rik	-	RIKEN cDNA 4930447A16 gene	protein-coding
mm_74880.1	chr8	25088515	25088545	-	1	NA	intron (NM_031257, intron 1 of 11)	intron (NM_031257, intron 1 of 11)	13281	NM_031257	83436	Mm.261122	NM_031257	ENSMUSG00000031557	Plekha2	6430512N22Rik|AI851530|AU041791|TAPP2|W91773	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 2	protein-coding
mm_160530.1	chr9	38047417	38047417	+	1	NA	exon (NM_001011798, exon 1 of 1)	exon (NM_001011798, exon 1 of 1)	193	NM_001011798	257996	Mm.390162	NM_001011798	ENSMUSG00000095893	Olfr884	MOR162-11P|MOR162-13|MOR162-9P|Olfr1550-ps1	olfactory receptor 884	protein-coding
mm_89397.1	chr10	90071096	90071117	+	1	NA	exon (NM_001128086, exon 6 of 25)	exon (NM_001128086, exon 6 of 25)	197597	NM_001128086	77531	Mm.440605	NM_181398	ENSMUSG00000058589	Anks1b	AIDA-1b|C030032C09Rik|E530015N03Rik|ENSMUSG00000078431|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding
mm_109527.1	chr12	111538265	111538278	+	1	NA	intron (NM_173363, intron 1 of 11)	CpG	170	NM_173363	217869	Mm.271222	NM_173363	ENSMUSG00000021282	Eif5	2810011H21Rik|D12Ertd549e	eukaryotic translation initiation factor 5	protein-coding
mm_51784.1	chr6	88199693	88199699	+	1	NA	exon (NM_008090, exon 2 of 6)	exon (NM_008090, exon 2 of 6)	1032	NM_008090	14461	Mm.491156	NM_008090	ENSMUSG00000015053	Gata2	Gata-2	GATA binding protein 2	protein-coding
mm_116272.1	chr13	34652934	34652976	-	1	NA	promoter-TSS (NR_105041)	promoter-TSS (NR_105041)	32	NR_105041	101056149	Mm.421309	NR_105041	ENSMUSG00000086786	Gm15908	OTTMUSG00000027716	predicted gene 15908	ncRNA
mm_109582.1	chr12	112599382	112599398	+	1	NA	intron (NM_198411, intron 1 of 22)	intron (NM_198411, intron 1 of 22)	10606	NM_198411	70435	Mm.250193	NM_198411	ENSMUSG00000037679	Inf2	2610204M08Rik|AA589465|AW125550|EG629699	inverted formin, FH2 and WH2 domain containing	protein-coding
mm_22247.1	chr2	174614373	174614384	-	1	NA	Intergenic	Intergenic	-29156	NM_001099328	100043757	Mm.48711	NM_001099328	ENSMUSG00000050600	Zfp831	ENSMUSG00000050600|OTTMUSG00000017459	zinc finger protein 831	protein-coding
mm_4216.1	chr1	171315318	171315323	+	1	NA	Intergenic	RLTR6_Mm|LTR|ERV1	-13825	NM_001128609	21945	Mm.270139	NM_011615	ENSMUSG00000013973	Dedd	CASP8IP1|DEFT|Dedpro1|FLDED1|KE05	death effector domain-containing	protein-coding
mm_120320.1	chr14	63142890	63142900	+	1	NA	3' UTR (NM_007798, exon 10 of 10)	3' UTR (NM_007798, exon 10 of 10)	20433	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_14589.1	chr2	136057712	136057723	+	1	NA	promoter-TSS (NM_029530)	promoter-TSS (NM_029530)	-210	NM_029530	76161	Mm.41638	NM_029530	ENSMUSG00000027270	Lamp5	3110035N03Rik|6330527O06Rik|BAD-LAMP|LAMP-5	lysosomal-associated membrane protein family, member 5	protein-coding
mm_53185.1	chr6	125432774	125432784	+	1	NA	Intergenic	Intergenic	-52275	NM_198604	213522	Mm.333396	NM_198604	ENSMUSG00000038167	Plekhg6	BC026778|Gm155	pleckstrin homology domain containing, family G (with RhoGef domain) member 6	protein-coding
mm_102319.1	chr11	57507042	57507052	-	1	NA	intron (NM_001168667, intron 6 of 13)	intron (NM_001168667, intron 6 of 13)	11597	NM_001168667	67726	Mm.25632	NM_026342	ENSMUSG00000020523	Fam114a2	1810073G14Rik|9030624B09Rik	family with sequence similarity 114, member A2	protein-coding
mm_163090.1	chr11	69734704	69734717	-	1	NA	exon (NM_001291068, exon 29 of 29)	exon (NM_001291068, exon 29 of 29)	23923	NM_001291068	20020	Mm.16533	NM_009089	ENSMUSG00000005198	Polr2a	220kDa|Rpb1|Rpo2-1	polymerase (RNA) II (DNA directed) polypeptide A	protein-coding
mm_100053.1	chr11	115180310	115180320	+	1	NA	exon (NM_012030, exon 6 of 6)	exon (NM_012030, exon 6 of 6)	7001	NM_025400	66176	Mm.86823	NM_025400	ENSMUSG00000015542	Nat9	1110028N05Rik	N-acetyltransferase 9 (GCN5-related, putative)	protein-coding
mm_83808.1	chr9	53536729	53536747	-	1	NA	promoter-TSS (NM_001081152)	promoter-TSS (NM_001081152)	-67	NM_007499	11920	Mm.5088	NM_007499	ENSMUSG00000034218	Atm	AI256621|C030026E19Rik	ataxia telangiectasia mutated	protein-coding
mm_11672.1	chr2	35292628	35292639	+	1	NA	exon (NM_001206369, exon 5 of 17)	exon (NM_001206369, exon 5 of 17)	10253	NM_146120	227753	Mm.443	NM_146120	ENSMUSG00000026879	Gsn	ADF	gelsolin	protein-coding
mm_93285.1	chr10	96181534	96181544	-	1	NA	Intergenic	L2c|LINE|L2	-44668	NR_110448	74881	Mm.410819	NR_110448		4930459C07Rik	-	RIKEN cDNA 4930459C07 gene	ncRNA
mm_2010.1	chr1	87127621	87127626	+	1	NA	exon (NM_007432, exon 11 of 11)	exon (NM_007432, exon 11 of 11)	2615	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_170940.1	chr2	49308186	49308195	+	1	NA	intron (NM_029924, intron 15 of 16)	intron (NM_029924, intron 15 of 16)	62290	NM_001290656	109241	Mm.440436	NM_029924	ENSMUSG00000036792	Mbd5	9430004D19Rik|AA536666|AI426407|C030040A15Rik|Gm1630|OTTMUSG00000012483	methyl-CpG binding domain protein 5	protein-coding
mm_173138.1	chrX	21261571	21261585	-	1	NA	Intergenic	L1Md_T|LINE|L1	-39913	NM_001252013	100503481	Mm.272069	NM_001252013		4930453H23Rik	-	RIKEN cDNA 4930453H23 gene	protein-coding
mm_64736.1	chr7	4724517	4724541	-	1	NA	intron (NM_001142792, intron 1 of 5)	intron (NM_001142792, intron 1 of 5)	553	NM_001142792	330460	Mm.361851	NM_177887	ENSMUSG00000046456	Tmem150b	A630041N19|Tmem224	transmembrane protein 150B	protein-coding
mm_99401.1	chr11	102189841	102189870	+	1	NA	5' UTR (NM_175935, exon 1 of 6)	5' UTR (NM_175935, exon 1 of 6)	156	NM_175935	68401	Mm.22385	NM_175935	ENSMUSG00000034793	G6pc3	0710001K01Rik|AU019276|AU045429|AV128920|AW545836|UGRP	glucose 6 phosphatase, catalytic, 3	protein-coding
mm_172759.1	chr8	88587394	88587413	-	1	NA	intron (NM_001163660, intron 4 of 7)	(CCCTAA)n|Simple_repeat|Simple_repeat	48725	NM_027840	71607	Mm.270607	NM_027840	ENSMUSG00000031662	Snx20	9130017C17Rik	sorting nexin 20	protein-coding
mm_48473.1	chr5	140992363	140992399	-	1	NA	intron (NM_175362, intron 1 of 24)	L1ME3|LINE|L1	8215	NM_175362	108723	Mm.46187	NM_175362	ENSMUSG00000036526	Card11	0610008L17Rik|2410011D02Rik|BIMP3|CARMA1	caspase recruitment domain family, member 11	protein-coding
mm_63267.1	chr7	126759730	126759762	+	1	NA	exon (NM_011952, exon 1 of 9)	exon (NM_011952, exon 1 of 9)	120	NM_011952	26417	Mm.8385	NM_011952	ENSMUSG00000063065	Mapk3	Erk-1|Erk1|Ert2|Esrk1|Mnk1|Mtap2k|Prkm3|p44|p44erk1|p44mapk	mitogen-activated protein kinase 3	protein-coding
mm_92083.1	chr10	62785507	62785524	-	1	NA	exon (NM_026201, exon 3 of 25)	exon (NM_026201, exon 3 of 25)	6853	NM_026201	67500	Mm.196371	NM_026201	ENSMUSG00000020074	Ccar1	2610511G16Rik|9430036H15Rik|Carp1	cell division cycle and apoptosis regulator 1	protein-coding
mm_144130.1	chr18	4920722	4920733	+	1	NA	Intergenic	CpG	108241	NR_045881	100038439	Mm.387569	NR_045881	ENSMUSG00000097043	Gm10556	ENSMUSG00000073646	predicted gene 10556	ncRNA
mm_145112.1	chr18	44270079	44270083	+	1	NA	promoter-TSS (NM_010935)	promoter-TSS (NM_010935)	-46	NM_010935	18169	Mm.57234	NM_010935	ENSMUSG00000038071	Npy6r	-	neuropeptide Y receptor Y6	protein-coding
mm_164603.1	chr17	29842177	29842177	+	1	NA	exon (NM_001081160, exon 9 of 16)	exon (NM_001081160, exon 9 of 16)	45705	NM_001081160	74762	Mm.40901	NM_001081160	ENSMUSG00000043557	Mdga1	1200011I03Rik|GPIM|Mamdc3	MAM domain containing glycosylphosphatidylinositol anchor 1	protein-coding
mm_30501.1	chr3	157924860	157924877	-	1	NA	exon (NM_145953, exon 1 of 12)	exon (NM_145953, exon 1 of 12)	195	NM_145953	107869	Mm.28301	NM_145953	ENSMUSG00000028179	Cth	0610010I13Rik|AI314617|BC019483|CSE|Cys3	cystathionase (cystathionine gamma-lyase)	protein-coding
mm_155348.1	chrX	68678713	68678721	+	1	NA	promoter-TSS (NR_033481)	promoter-TSS (NR_033481)	176	NM_001290424	14265	Mm.3451	NM_008031	ENSMUSG00000000838	Fmr1	FMRP|Fmr-1	fragile X mental retardation syndrome 1	protein-coding
mm_76235.1	chr8	83574759	83574778	-	1	NA	intron (NM_134118, intron 1 of 12)	intron (NM_134118, intron 1 of 12)	8010	NM_025843	66916	Mm.29683	NM_025843	ENSMUSG00000033938	Ndufb7	1110002H15Rik	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 7	protein-coding
mm_139015.1	chr17	45699583	45699587	+	1	NA	Intergenic	Intergenic	13213	NM_026732	68463	Mm.379158	NM_026732	ENSMUSG00000023939	Mrpl14	1110006I11Rik|AI846816|MRP-L32|Rpml32	mitochondrial ribosomal protein L14	protein-coding
mm_25364.1	chr3	107101268	107101281	+	1	NA	promoter-TSS (NM_008417)	promoter-TSS (NM_008417)	-293	NM_008417	16490	Mm.39285	NM_008417	ENSMUSG00000040724	Kcna2	Akr6a4|ENSMUSG00000074335|Gm10672|Kca1-2|Kv1.2|Mk-2	potassium voltage-gated channel, shaker-related subfamily, member 2	protein-coding
mm_134768.1	chr16	23520779	23520793	-	1	NA	promoter-TSS (NM_008555)	promoter-TSS (NM_008555)	-196	NM_008555	17174	Mm.1213	NM_008555	ENSMUSG00000022887	Masp1	AW048060|CCPII|Crarf|Masp1/3	mannan-binding lectin serine peptidase 1	protein-coding
mm_39146.1	chr4	155361323	155361346	-	1	NA	promoter-TSS (NM_008860)	promoter-TSS (NM_008860)	94	NM_008860	18762	Mm.28561	NM_008860	ENSMUSG00000029053	Prkcz	AI098070|C80388|Pkcz|R74924|aPKCzeta|nPKC-zeta|zetaPKC	protein kinase C, zeta	protein-coding
mm_18670.1	chr2	70825727	70825820	-	1	NA	promoter-TSS (NM_172664)	promoter-TSS (NM_172664)	-293	NM_172664	228012	Mm.136511	NM_172664	ENSMUSG00000041997	Tlk1	4930545J15Rik	tousled-like kinase 1	protein-coding
mm_23815.1	chr3	79900679	79900682	+	1	NA	intron (NM_133187, intron 1 of 3)	B1_Mur2|SINE|Alu	14750	NM_133187	68659	Mm.427274	NM_133187	ENSMUSG00000027955	Fam198b	1110032E23Rik|2210419I08Rik|AV011458|Ened	family with sequence similarity 198, member B	protein-coding
mm_142718.1	chr17	47924744	47924774	-	1	NA	promoter-TSS (NM_028767)	promoter-TSS (NM_028767)	-127	NM_001110825	74123	Mm.240062	NM_028767	ENSMUSG00000023991	Foxp4	1200010K03Rik|2310007G05Rik|mFKHLA	forkhead box P4	protein-coding
mm_34682.1	chr4	151405035	151405052	+	1	NA	intron (NM_001081557, intron 5 of 23)	intron (NM_001081557, intron 5 of 23)	315473	NM_001308446	105704528	Mm.415128	NM_001308446	ENSMUSG00000078491	Gm13090	OTTMUSG00000010356	predicted gene 13090	protein-coding
mm_37311.1	chr4	119294715	119294725	-	1	NA	promoter-TSS (NM_011732)	promoter-TSS (NM_011732)	-207	NM_011732	22608	Mm.258204	NM_011732	ENSMUSG00000028639	Ybx1	1700102N10Rik|C79409|EF1A|MSY1|Nsep1|YB-1|dbpB|mYB-1a	Y box protein 1	protein-coding
mm_52441.1	chr6	113624127	113624164	+	1	NA	exon (NM_009507, exon 1 of 3)	exon (NM_009507, exon 1 of 3)	124	NM_009507	22346	Mm.29407	NM_009507	ENSMUSG00000033933	Vhl	Vhlh	von Hippel-Lindau tumor suppressor	protein-coding
mm_154734.1	chrX	9846946	9846977	+	1	NA	promoter-TSS (NM_026096)	promoter-TSS (NM_026096)	14	NM_026096	67334	Mm.46146	NM_026096	ENSMUSG00000040456	Hypm	1700054O13Rik|H2al3	huntingtin interacting protein M	protein-coding
mm_63882.1	chr7	137411129	137411169	+	1	NA	promoter-TSS (NM_029886)	promoter-TSS (NM_029886)	-393	NM_029886	77252	Mm.29184	NM_029886	ENSMUSG00000040139	9430038I01Rik	-	RIKEN cDNA 9430038I01 gene	protein-coding
mm_162222.1	chrX	144687965	144687965	-	1	NA	promoter-TSS (NM_001033795)	promoter-TSS (NM_001033795)	215	NM_009428	22067	Mm.82621	NM_009428	ENSMUSG00000041710	Trpc5	CCE2|TRP-5|TRP5|Trrp5	transient receptor potential cation channel, subfamily C, member 5	protein-coding
mm_32058.1	chr4	97777571	97777581	+	1	NA	promoter-TSS (NM_001122953)	promoter-TSS (NM_001122953)	-50	NM_001122953	18027	Mm.31274	NM_010905	ENSMUSG00000028565	Nfia	1110047K16Rik|9430022M17Rik|CTF|NF1-A|NF1A	nuclear factor I/A	protein-coding
mm_108983.1	chr12	102744022	102744047	+	1	NA	promoter-TSS (NM_001142937)	promoter-TSS (NM_001142937)	274	NM_177140	320351	Mm.86546	NM_177140	ENSMUSG00000046675	Tmem251	D230037D09Rik	transmembrane protein 251	protein-coding
mm_119113.1	chr14	31019160	31019178	+	1	NA	promoter-TSS (NM_001081251)	promoter-TSS (NM_001081251)	31	NM_001081251	66923	Mm.27913	NM_025847	ENSMUSG00000042323	Pbrm1	2610016F04Rik|AI507524|BAF180|Pb1	polybromo 1	protein-coding
mm_148910.1	chr19	6974614	6974682	+	1	NA	promoter-TSS (NM_008889)	promoter-TSS (NM_008889)	-400	NM_008889	18938	Mm.140	NM_008889	ENSMUSG00000056612	Ppp1r14b	AOM172|PHI-1|PLCB3N|Png	protein phosphatase 1, regulatory (inhibitor) subunit 14B	protein-coding
mm_151053.1	chr19	47091006	47091037	+	1	NA	promoter-TSS (NM_023211)	promoter-TSS (NM_023211)	255	NM_011053	18572	Mm.41166	NM_011053	ENSMUSG00000025047	Pdcd11	1110021I22Rik|ALG-4|Pdcd7|mKIAA0185	programmed cell death 11	protein-coding
mm_25469.1	chr3	108653980	108653986	+	1	NA	promoter-TSS (NM_145543)	promoter-TSS (NM_145543)	-7	NM_001177770	229725	Mm.214545	NM_145543	ENSMUSG00000027884	Clcc1	Mclc	chloride channel CLIC-like 1	protein-coding
mm_9957.1	chr1	191062877	191062887	-	1	NA	promoter-TSS (NM_001163422)	promoter-TSS (NM_001163422)	50	NM_001163421	68972	Mm.237188	NM_026895	ENSMUSG00000026632	Tatdn3	1500010M24Rik	TatD DNase domain containing 3	protein-coding
mm_109477.1	chr12	111423114	111423133	+	1	NA	intron (NM_001289487, intron 4 of 13)	intron (NM_001289487, intron 4 of 13)	5678	NM_001289488	74190	Mm.248640	NM_028807	ENSMUSG00000021280	Exoc3l4	1200009I06Rik|1600013K19Rik	exocyst complex component 3-like 4	protein-coding
mm_130433.1	chr15	98165614	98165616	-	1	NA	promoter-TSS (NM_001170711)	promoter-TSS (NM_001170711)	-37	NM_001170711	78541	Mm.200766	NM_030121	ENSMUSG00000048175	Asb8	4930539L19Rik|AI788835|C430011H06Rik	ankyrin repeat and SOCS box-containing 8	protein-coding
mm_172486.1	chr7	51879304	51879306	+	1	NA	5' UTR (NM_008087, exon 1 of 8)	5' UTR (NM_008087, exon 1 of 8)	338	NM_001330607	14453	Mm.207360	NM_008087	ENSMUSG00000030498	Gas2	Gas-2	growth arrest specific 2	protein-coding
mm_67189.1	chr7	73940500	73940510	-	1	NA	3' UTR (NM_009181, exon 6 of 6)	3' UTR (NM_009181, exon 6 of 6)	73177	NM_009181	20450	Mm.4954	NM_009181	ENSMUSG00000025789	St8sia2	AI323367|ST8SiaII|STX|Siat8b	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 2	protein-coding
mm_104952.1	chr11	100137769	100137787	-	1	NA	Intergenic	Intergenic	-1829	NM_008469	16665	Mm.440010	NM_008469	ENSMUSG00000054146	Krt15	AI528832|K15|Krt1-15	keratin 15	protein-coding
mm_20549.1	chr2	131068952	131068964	-	1	NA	TTS (NM_011426)	TTS (NM_011426)	-5144	NM_001163529	110751	Mm.108550	NM_033615	ENSMUSG00000027318	Adam33	Adaml	a disintegrin and metallopeptidase domain 33	protein-coding
mm_111275.1	chr12	85341574	85341586	-	1	NA	3' UTR (NM_026775, exon 5 of 5)	3' UTR (NM_026775, exon 5 of 5)	-2218	NM_145138	217718	Mm.29071	NM_145138	ENSMUSG00000034290	Nek9	C130021H08Rik	NIMA (never in mitosis gene a)-related expressed kinase 9	protein-coding
mm_100045.1	chr11	115154203	115154210	+	1	NA	promoter-TSS (NM_021411)	promoter-TSS (NM_021411)	28	NM_021411	58222	Mm.143789	NM_021411	ENSMUSG00000020732	Rab37	B230331O03Rik|B230354I04Rik	RAB37, member RAS oncogene family	protein-coding
mm_121329.1	chr14	114946047	114946058	+	1	NA	promoter-TSS (NR_126551)	promoter-TSS (NR_126551)	-104	NR_126548	74982		NR_126548		1700100I10Rik	1700085D13Rik|4930481K08Rik	RIKEN cDNA 1700100I10 gene	ncRNA
mm_41395.1	chr5	90772470	90772480	+	1	NA	promoter-TSS (NM_019932)	promoter-TSS (NM_019932)	40	NM_019932	56744	Mm.332490	NM_019932	ENSMUSG00000029373	Pf4	Cxcl4|Scyb4	platelet factor 4	protein-coding
mm_106562.1	chr11	120633356	120633374	-	1	NA	5' UTR (NM_010756, exon 1 of 3)	5' UTR (NM_010756, exon 1 of 3)	182	NM_010756	17134	Mm.268010	NM_010756	ENSMUSG00000051510	Mafg	AA545192|C630022N07Rik	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein G (avian)	protein-coding
mm_98924.1	chr11	98348753	98348763	+	1	NA	5' UTR (NM_144828, exon 1 of 7)	5' UTR (NM_144828, exon 1 of 7)	352	NM_144828	19049	Mm.45372	NM_144828	ENSMUSG00000061718	Ppp1r1b	AU040756|DARPP-32|Darpp32	protein phosphatase 1, regulatory (inhibitor) subunit 1B	protein-coding
mm_55687.1	chr6	72690780	72690789	-	1	NA	intron (NM_001079822, intron 3 of 12)	L2a|LINE|L2	60953	NR_040421	100038714	Mm.321330	NR_040421		Gm15401	ENSMUSG00000072999|OTTMUSG00000021199	predicted gene 15401	ncRNA
mm_169412.1	chr14	52077461	52077463	-	1	NA	exon (NM_001170982, exon 5 of 8)	exon (NM_001170982, exon 5 of 8)	8147	NR_028552	100217457		NR_028552	ENSMUSG00000064871	Snord58b	MBII-199	small nucleolar RNA, C/D box 58B	snoRNA
mm_37873.1	chr4	132353660	132353713	-	1	NA	promoter-TSS (NR_003270)	promoter-TSS (NR_003270)	0	NR_003270	399101	Mm.486919	NR_002904	ENSMUSG00000085241	Snhg3	Rnu17d|U17HG	small nucleolar RNA host gene 3	ncRNA
mm_29865.1	chr3	130061486	130061508	-	1	NA	promoter-TSS (NM_207209)	promoter-TSS (NM_207209)	-590	NM_207209	99683	Mm.192303	NM_207209	ENSMUSG00000001052	Sec24b	AI605202|SEC24	Sec24 related gene family, member B (S. cerevisiae)	protein-coding
mm_57719.1	chr6	128803107	128803110	-	1	NA	Intergenic	4.5SRNA|scRNA|scRNA	-14467	NM_001159904	17059	Mm.480764	NM_008527	ENSMUSG00000030325	Klrb1c	AI462337|CD161|Ly-59|Ly55c|Ly59|NK-RP1|NK1.1|NKR-P1.9|NKRP1|NKRP140|Nk-1|Nk-1.2|Nk1|Nk1.2|Nkrp1c|ly-55c	killer cell lectin-like receptor subfamily B member 1C	protein-coding
mm_161639.1	chr16	94287781	94287781	-	1	NA	promoter-TSS (NM_139145)	promoter-TSS (NM_139145)	75	NM_139145	110948	Mm.30921	NM_139145	ENSMUSG00000040820	Hlcs	410I21.SP6|D16Jhu34	holocarboxylase synthetase (biotin- [propriony-Coenzyme A-carboxylase (ATP-hydrolysing)] ligase)	protein-coding
mm_27723.1	chr3	69004453	69004467	-	1	NA	promoter-TSS (NM_133786)	promoter-TSS (NM_133786)	110	NM_026641	68259	Mm.389451	NM_026641	ENSMUSG00000027778	Ift80	4921524P20Rik|Wdr56|mKIAA1374	intraflagellar transport 80	protein-coding
mm_146630.1	chr18	10182129	10182151	-	1	NA	promoter-TSS (NM_009071)	promoter-TSS (NM_009071)	-348	NM_009071	19877	Mm.6710	NM_009071	ENSMUSG00000024290	Rock1	1110055K06Rik|Rock-I	Rho-associated coiled-coil containing protein kinase 1	protein-coding
mm_67622.1	chr7	84077564	84077565	-	1	NA	intron (NM_030728, intron 1 of 28)	MER121|DNA|TcMar?	8941	NM_030728	80982	Mm.160389	NM_030728	ENSMUSG00000052353	Cemip	12H19.01.T7|6330404C01Rik|9930013L23Rik|AY007814|Kiaa1199	cell migration inducing protein, hyaluronan binding	protein-coding
mm_10630.1	chr2	19909770	19909785	+	1	NA	Intergenic	CpG	251715	NM_027715	71198	Mm.83981	NM_027715	ENSMUSG00000043415	Otud1	4933428L19Rik	OTU domain containing 1	protein-coding
mm_38359.1	chr4	137883916	137883965	-	1	NA	intron (NM_199307, intron 1 of 19)	intron (NM_199307, intron 1 of 19)	21703	NM_199307	230857	Mm.401062	NM_199307	ENSMUSG00000057530	Ece1	AW322500|ECE-1|ECE-1a|ECE-1b|ECE-1d	endothelin converting enzyme 1	protein-coding
mm_55338.1	chr6	56369576	56369586	-	1	NA	promoter-TSS (NM_001159957)	promoter-TSS (NM_001159957)	53	NM_001159957	18575	Mm.5145	NM_011054	ENSMUSG00000004347	Pde1c	-	phosphodiesterase 1C	protein-coding
mm_159361.1	chr3	86142593	86142593	-	1	NA	promoter-TSS (NM_016959)	promoter-TSS (NM_016959)	75	NM_016959	20091	Mm.391785	NM_016959	ENSMUSG00000028081	Rps3a1	Rps3a	ribosomal protein S3A1	protein-coding
mm_58868.1	chr7	16950129	16950139	+	1	NA	Intergenic	Intergenic	5452	NM_001099636	434128	Mm.483018	NM_001099636	ENSMUSG00000070802	Pnmal2	EG434128	PNMA-like 2	protein-coding
mm_160966.1	chr11	99772913	99772913	-	1	NA	promoter-TSS (NM_001126322)	promoter-TSS (NM_001126322)	0	NM_001126322	100040276	Mm.475095	NM_001126322	ENSMUSG00000078668	Gm11595	OTTMUSG00000002543	predicted gene 11595	protein-coding
mm_110071.1	chr12	21417346	21417355	-	1	NA	promoter-TSS (NM_011739)	promoter-TSS (NM_011739)	86	NM_011739	22630	Mm.289630	NM_011739	ENSMUSG00000076432	Ywhaq	2700028P07Rik|AA409740|AU021156|R74690	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide	protein-coding
mm_152402.1	chr19	10577099	10577120	-	1	NA	promoter-TSS (NM_201351)	promoter-TSS (NM_201351)	-23	NM_001302218	72982	Mm.391194	NM_028411	ENSMUSG00000024666	Tmem138	1700113I01Rik|2900055D14Rik	transmembrane protein 138	protein-coding
mm_59221.1	chr7	24610749	24610776	+	1	NA	promoter-TSS (NM_001102613)	promoter-TSS (NM_001102613)	-566	NM_001102613	232970	Mm.333663	NM_001102613	ENSMUSG00000074277	Phldb3	EG232970|ENSMUSG00000061511|Gm10102	pleckstrin homology like domain, family B, member 3	protein-coding
mm_442.1	chr1	34849938	34849947	+	1	NA	promoter-TSS (NM_145516)	promoter-TSS (NM_145516)	-17	NM_175421	226971	Mm.292751	NM_145516	ENSMUSG00000026123	Plekhb2	2310009M15Rik|AU018239|Evt2|Phdc|evt-2	pleckstrin homology domain containing, family B (evectins) member 2	protein-coding
mm_82618.1	chr9	21794993	21794997	-	1	NA	exon (NM_145611, exon 3 of 12)	exon (NM_145611, exon 3 of 12)	3551	NM_145611	235041	Mm.257371	NM_145611	ENSMUSG00000032194	Kank2	AI504612|Ankrd25|BC010245	KN motif and ankyrin repeat domains 2	protein-coding
mm_163034.1	chr11	52241794	52241797	+	1	NA	intron (NM_011543, intron 2 of 5)	intron (NM_011543, intron 2 of 5)	9800	NM_011543	21402	Mm.42944	NM_011543	ENSMUSG00000036309	Skp1a	15kDa|2610043E24Rik|2610206H23Rik|EMC19|OCP-II|OCP2|SKP1|Tceb1l|p19A|p19Skp1	S-phase kinase-associated protein 1A	protein-coding
mm_129186.1	chr15	76309793	76309799	-	1	NA	Intergenic	Intergenic	-2551	NM_153122	75475	Mm.322738	NM_153122	ENSMUSG00000022562	Oplah	1700010G02Rik	5-oxoprolinase (ATP-hydrolysing)	protein-coding
mm_121108.1	chr14	101379078	101379079	+	1	NA	Intergenic	Intergenic	-179009	NM_029680	76627	Mm.31415	NM_029680	ENSMUSG00000042888	Prr30	1700110M21Rik	proline rich 30	protein-coding
mm_125210.1	chr15	34053753	34053761	+	1	NA	Intergenic	RLTR41|LTR|ERV1	-28962	NM_026002	67154	Mm.130883	NM_026002	ENSMUSG00000022255	Mtdh	2610103J23Rik|3D3|3D3/Lyric|AEG-1|AV353288|D8Bwg1112e|Lyric	metadherin	protein-coding
mm_147520.1	chr18	52528543	52528563	-	1	NA	intron (NM_001286181, intron 2 of 7)	intron (NM_001286181, intron 2 of 7)	1168	NM_001286181	16948	Mm.172	NM_010728	ENSMUSG00000024529	Lox	AI893619|TSC-160|rrg	lysyl oxidase	protein-coding
mm_99754.1	chr11	106750676	106750690	+	1	NA	promoter-TSS (NM_001271373)	promoter-TSS (NM_001271373)	-543	NM_001271375	380732	Mm.343952	NM_001033435	ENSMUSG00000040528	Milr1	Allergin-1|Gm885|Mca32	mast cell immunoglobulin like receptor 1	protein-coding
mm_125513.1	chr15	55886318	55886322	+	1	NA	intron (NM_016667, intron 1 of 6)	U2|snRNA|snRNA	20629	NM_016667	20649	Mm.309425	NM_016667	ENSMUSG00000060429	Sntb1	-	syntrophin, basic 1	protein-coding
mm_7991.1	chr1	134235204	134235217	-	1	NA	promoter-TSS (NM_001291928)	promoter-TSS (NM_001291928)	247	NM_001291930	11539	Mm.298908	NM_009629	ENSMUSG00000042429	Adora1	A1-AR|A1AR|A1R|AA1R|AI848715|BB176431|Ri	adenosine A1 receptor	protein-coding
mm_145420.1	chr18	58556077	58556081	+	1	NA	promoter-TSS (NM_001081072)	promoter-TSS (NM_001081072)	-161	NM_001081072	225579	Mm.258517	NM_001081072	ENSMUSG00000024600	Slc27a6	4732438L20Rik|FACVL2|FATP6|VLCS-H1	solute carrier family 27 (fatty acid transporter), member 6	protein-coding
mm_286.1	chr1	21291664	21291674	+	1	NA	intron (NR_002858, intron 3 of 5)	PB1D10|SINE|Alu	6643	NR_002858	241041	Mm.290634	NR_002858	ENSMUSG00000025936	Gm4956	EG241041	predicted gene 4956	pseudo
mm_111.1	chr1	9601457	9601487	+	1	NA	5' UTR (NM_178399, exon 1 of 6)	5' UTR (NM_178399, exon 1 of 6)	205	NM_178399	76982	Mm.491098	NM_178399	ENSMUSG00000067879	3110035E14Rik	AI415019|AV164974|R75066	RIKEN cDNA 3110035E14 gene	protein-coding
mm_100676.1	chr11	3409163	3409195	-	1	NA	promoter-TSS (NM_010718)	promoter-TSS (NM_010718)	59	NM_010718	16886	Mm.124176	NM_010718	ENSMUSG00000020451	Limk2	Limk-2|whe	LIM motif-containing protein kinase 2	protein-coding
mm_91287.1	chr10	24813744	24813747	-	1	NA	intron (NM_134005, intron 6 of 24)	L1M3d|LINE|L1	22450	NM_134005	209558	Mm.338425	NM_134005	ENSMUSG00000019989	Enpp3	AI876438|CD203c	ectonucleotide pyrophosphatase/phosphodiesterase 3	protein-coding
mm_155047.1	chrX	42151003	42151019	+	1	NA	intron (NM_021465, intron 1 of 32)	intron (NM_021465, intron 1 of 32)	310	NM_021465	20843	Mm.290422	NM_021465	ENSMUSG00000025862	Stag2	9230105L23Rik|B230112I07Rik|SA-2|SAP2	stromal antigen 2	protein-coding
mm_147241.1	chr18	38338992	38338994	-	1	NA	promoter-TSS (NM_011937)	promoter-TSS (NM_011937)	0	NM_011937	26384	Mm.22374	NM_011937	ENSMUSG00000052102	Gnpda1	GNPDA|Gnp1|Gnpi|oscillin	glucosamine-6-phosphate deaminase 1	protein-coding
mm_32104.1	chr4	98726787	98726805	+	1	NA	promoter-TSS (NM_001081202)	promoter-TSS (NM_001081202)	42	NM_001081202	381591	Mm.34340	NM_001081202	ENSMUSG00000087166	L1td1	AA546746|AB211064|D76865|ECAT11	LINE-1 type transposase domain containing 1	protein-coding
mm_66107.1	chr7	31041625	31041638	-	1	NA	TTS (NM_022007)	TTS (NM_022007)	208	NM_001111073	18301	Mm.1870	NM_008761	ENSMUSG00000009687	Fxyd5	EF-8|Oit2|RIC	FXYD domain-containing ion transport regulator 5	protein-coding
mm_58524.1	chr7	4147678	4147760	+	1	NA	TTS (NM_175529)	TTS (NM_175529)	2153	NM_175529	243813	Mm.347643	NM_175529	ENSMUSG00000043432	Leng9	9530024C23Rik|F630035L11Rik	leukocyte receptor cluster (LRC) member 9	protein-coding
mm_63474.1	chr7	127691659	127691668	+	1	NA	intron (NM_001347652, intron 5 of 5)	intron (NM_001347652, intron 5 of 5)	-16824	NR_030428	791073		NR_030428	ENSMUSG00000076454	Mir762	Mirn762|mir-762|mmu-mir-762	microRNA 762	ncRNA
mm_138202.1	chr17	34293907	34293917	+	1	NA	Intergenic	Intergenic	-6141	NM_010378	14960	Mm.235338	NM_010378	ENSMUSG00000036594	H2-Aa	Aalpha|H-2Aa|H2Aa|I-Aalpha|IAalpha|Ia-1|Ia1	histocompatibility 2, class II antigen A, alpha	protein-coding
mm_31387.1	chr4	48043516	48043541	+	1	NA	Intergenic	Intergenic	-1777	NM_015743	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_152605.1	chr19	11818807	11818883	-	1	NA	5' UTR (NM_001286543, exon 1 of 12)	5' UTR (NM_001286543, exon 1 of 12)	558	NM_001286543	20908	Mm.272264	NM_011502	ENSMUSG00000041488	Stx3	Syn-3	syntaxin 3	protein-coding
mm_156889.1	chrX	166440739	166440781	+	1	NA	promoter-TSS (NM_001313722)	promoter-TSS (NM_001313722)	5	NM_001313722	66226	Mm.279752	NM_025432	ENSMUSG00000079317	Trappc2	1110066L09Rik|1810064C02Rik|AW496358|MIP-2A|Sedl|TRS20	trafficking protein particle complex 2	protein-coding
mm_142669.1	chr17	47729279	47729281	-	1	NA	exon (NM_025973, exon 3 of 9)	exon (NM_025973, exon 3 of 9)	2438	NM_025973	109820	Mm.22957	NM_025973	ENSMUSG00000023987	Pgc	2210410L06Rik|Upg-1|Upg1	progastricsin (pepsinogen C)	protein-coding
mm_104122.1	chr11	86756997	86757018	-	1	NA	intron (NM_001003908, intron 1 of 31)	intron (NM_001003908, intron 1 of 31)	485	NM_001003908	67300	Mm.254588	NM_001003908	ENSMUSG00000047126	Cltc	3110065L21Rik|CHC|R74732	clathrin, heavy polypeptide (Hc)	protein-coding
mm_25472.1	chr3	108774884	108774902	+	1	NA	intron (NM_177859, intron 7 of 11)	intron (NM_177859, intron 7 of 11)	35235	NM_177859	329738	Mm.72322	NM_177859	ENSMUSG00000049565	Aknad1	4921525H12Rik	AKNA domain containing 1	protein-coding
mm_159750.1	chr5	81660292	81660292	+	1	NA	exon (NM_198702, exon 13 of 28)	exon (NM_198702, exon 13 of 28)	464421	NR_138557	67327	Mm.87058	NR_138557		1700031L13Rik	-	RIKEN cDNA 1700031L13 gene	ncRNA
mm_155703.1	chrX	95558100	95558108	+	1	NA	promoter-TSS (NM_001313743)	promoter-TSS (NM_001313743)	-117	NM_001313743	70392	Mm.79122	NM_080858	ENSMUSG00000031204	Asb12	2310036C05Rik|Asb-12	ankyrin repeat and SOCS box-containing 12	protein-coding
mm_6205.1	chr1	66782240	66782243	-	1	NA	intron (NM_177645, intron 2 of 13)	intron (NM_177645, intron 2 of 13)	35354	NM_177645	68691	Mm.240912	NM_177645	ENSMUSG00000026004	Kansl1l	1110028C15Rik|1190030G24|AI427598|C430010P07Rik|mKIAA4189	KAT8 regulatory NSL complex subunit 1-like	protein-coding
mm_125188.1	chr15	32357146	32357173	+	1	NA	intron (NM_009154, intron 2 of 22)	intron (NM_009154, intron 2 of 22)	112346	NM_009154	20356	Mm.260374	NM_009154	ENSMUSG00000022231	Sema5a	5930434A13|9130201M22Rik|AI464145|Semaf|semF	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A	protein-coding
mm_162878.1	chr10	99463205	99463214	+	1	NA	Intergenic	Intergenic	-145962	NR_038019	100504202	Mm.403801	NR_038019		Gm20110	-	predicted gene, 20110	ncRNA
mm_65425.1	chr7	25297637	25297653	-	1	NA	intron (NM_008776, intron 1 of 5)	CpG-12842	310	NM_008776	18476	Mm.597	NM_008776	ENSMUSG00000005447	Pafah1b3	Pafahg|mus[g]	platelet-activating factor acetylhydrolase, isoform 1b, subunit 3	protein-coding
mm_101292.1	chr11	22048027	22048031	-	1	NA	intron (NM_001252515, intron 21 of 24)	intron (NM_001252515, intron 21 of 24)	-46378	NM_011023	18423	Mm.129663	NM_011023	ENSMUSG00000005917	Otx1	A730044F23Rik|jv	orthodenticle homeobox 1	protein-coding
mm_100014.1	chr11	114881520	114881523	+	1	NA	Intergenic	Intergenic	-8520	NM_001347654	217303	Mm.294439	NM_170758	ENSMUSG00000034652	Cd300a	B230315M08Rik|Clm8|LMIR1|MAIR-I|MAIR-Ia|MMAC8|Pigr4|mcpir1	CD300A molecule	protein-coding
mm_47208.1	chr5	120955457	120955463	-	1	NA	intron (NM_001302345, intron 10 of 20)	intron (NM_001302345, intron 10 of 20)	40642	NM_133893	100535	Mm.247620	NM_133893	ENSMUSG00000032623	Oas1d	AA536864|C85127|oasl8	2'-5' oligoadenylate synthetase 1D	protein-coding
mm_45011.1	chr5	38502134	38502141	-	1	NA	promoter-TSS (NM_145559)	promoter-TSS (NM_145559)	15	NM_145559	117591	Mm.260137	NM_145559	ENSMUSG00000005107	Slc2a9	Glut9|SLC2A9B|SLC2a9A	solute carrier family 2 (facilitated glucose transporter), member 9	protein-coding
mm_17038.1	chr2	20671685	20671709	-	1	NA	intron (NM_029895, intron 4 of 18)	intron (NM_029895, intron 4 of 18)	152184	NM_001177631	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding
mm_130616.1	chr15	99967082	99967087	-	1	NA	Intergenic	Intergenic	-2981	NM_001080948	207214	Mm.28811	NM_001024526	ENSMUSG00000023025	Larp4	DXErtd793|DXErtd793e	La ribonucleoprotein domain family, member 4	protein-coding
mm_102576.1	chr11	61719979	61719998	-	1	NA	intron (NM_001033227, intron 1 of 15)	intron (NM_001033227, intron 1 of 15)	811	NM_001033227	109342	Mm.441070	NM_001033227	ENSMUSG00000042371	Slc5a10	C330021F16Rik|SGLT5	solute carrier family 5 (sodium/glucose cotransporter), member 10	protein-coding
mm_125737.1	chr15	73512615	73512640	+	1	NA	promoter-TSS (NM_001081066)	promoter-TSS (NM_001081066)	67	NM_001081066	105841	Mm.322557	NM_001081066	ENSMUSG00000036661	Dennd3	AI447457|E030003N15Rik	DENN/MADD domain containing 3	protein-coding
mm_71665.1	chr8	60655501	60655522	+	1	NA	promoter-TSS (NM_001177882)	promoter-TSS (NM_001177882)	-46	NM_001177882	71306	Mm.23242	NM_027756	ENSMUSG00000031647	Mfap3l	4933428A15Rik|5430405D20Rik|AI461995|AW125052|NYD-sp9|mKIAA0626	microfibrillar-associated protein 3-like	protein-coding
mm_8113.1	chr1	135919295	135919307	-	1	NA	promoter-TSS (NM_019645)	promoter-TSS (NM_019645)	-94	NM_019645	18772	Mm.4494	NM_019645	ENSMUSG00000026413	Pkp1	-	plakophilin 1	protein-coding
mm_74654.1	chr8	13476144	13476153	-	1	NA	exon (NM_019521, exon 8 of 15)	exon (NM_019521, exon 8 of 15)	18387	NM_019521	14456	Mm.3982	NM_019521	ENSMUSG00000031451	Gas6	Gas-6	growth arrest specific 6	protein-coding
mm_166872.1	chr7	25301469	25301471	+	1	NA	5' UTR (NM_001081294, exon 1 of 3)	5' UTR (NM_001081294, exon 1 of 3)	111	NM_001081294	623131	Mm.172160	NM_001081294	ENSMUSG00000058741	Prr19	EG623131	proline rich 19	protein-coding
mm_61693.1	chr7	81100730	81100738	+	1	NA	intron (NM_054085, intron 11 of 13)	intron (NM_054085, intron 11 of 13)	-14065	NM_001004184	434203	Mm.389909	NM_001004184	ENSMUSG00000025726	Slc28a1	Cnt1	solute carrier family 28 (sodium-coupled nucleoside transporter), member 1	protein-coding
mm_149085.1	chr19	8920433	8920446	+	1	NA	promoter-TSS (NM_024256)	promoter-TSS (NM_024256)	46	NM_024256	72727	Mm.259	NM_024256	ENSMUSG00000071649	B3gat3	2810405M13Rik	beta-1,3-glucuronyltransferase 3 (glucuronosyltransferase I)	protein-coding
mm_165461.1	chr2	159354450	159354453	+	1	NA	Intergenic	Intergenic	559644	NM_001291144	71715	Mm.315652	NM_145742	ENSMUSG00000027655	Dhx35	1200009D07Rik|Ddx35	DEAH (Asp-Glu-Ala-His) box polypeptide 35	protein-coding
mm_6120.1	chr1	64121655	64121676	-	1	NA	promoter-TSS (NM_033563)	promoter-TSS (NM_033563)	-276	NM_033563	93691	Mm.29466	NM_033563	ENSMUSG00000025959	Klf7	9830124P08Rik	Kruppel-like factor 7 (ubiquitous)	protein-coding
mm_59659.1	chr7	28187581	28187584	+	1	NA	TTS (NM_001271370)	TTS (NM_001271370)	7266	NM_001271370	13549	Mm.57249	NM_010092	ENSMUSG00000002409	Dyrk1b	Mirk	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1b	protein-coding
mm_93826.1	chr10	121498142	121498150	-	1	NA	Intergenic	Intergenic	-21896	NM_138956	192678	Mm.41265	NM_138956	ENSMUSG00000025795	Rassf3	AW212023|AW322379	Ras association (RalGDS/AF-6) domain family member 3	protein-coding
mm_89471.1	chr10	93501657	93501683	+	1	NA	intron (NM_010401, intron 14 of 19)	intron (NM_010401, intron 14 of 19)	12902	NM_010401	15109	Mm.13000	NM_010401	ENSMUSG00000020017	Hal	Hsd|his|histidase	histidine ammonia lyase	protein-coding
mm_117160.1	chr13	62466795	62466839	-	1	NA	promoter-TSS (NM_178875)	promoter-TSS (NM_178875)	-5	NM_001136496	71508	Mm.442497	NM_178875	ENSMUSG00000055228	Zfp935	8430426H19Rik|Es113	zinc finger protein 935	protein-coding
mm_27169.1	chr3	33812734	33812736	-	1	NA	3' UTR (NM_025978, exon 10 of 10)	3' UTR (NM_025978, exon 10 of 10)	12552	NM_025978	67120	Mm.275710	NM_025978	ENSMUSG00000027677	Ttc14	2700016E08Rik|4930434D01Rik|4931403I22Rik|4933402I15Rik|AI662468|AU014779|AW561908|cI-44|mKIAA1980	tetratricopeptide repeat domain 14	protein-coding
mm_106191.1	chr11	116808158	116808162	-	1	NA	intron (NM_001347633, intron 4 of 4)	intron (NM_001347633, intron 4 of 4)	19886	NM_026280	67622	Mm.64962	NM_026280	ENSMUSG00000020814	Mxra7	1810057P16Rik|E130302J09Rik	matrix-remodelling associated 7	protein-coding
mm_139726.1	chr17	57476660	57476675	+	1	NA	intron (NM_010130, intron 19 of 21)	intron (NM_010130, intron 19 of 21)	68647	NM_001104591	224916	Mm.469889	NM_001104591	ENSMUSG00000090655	Vmn2r120	EG224916	vomeronasal 2, receptor 120	protein-coding
mm_154173.1	chr19	58730497	58730524	-	1	NA	exon (NM_018874, exon 4 of 13)	exon (NM_018874, exon 4 of 13)	1623	NM_018874	18946	Mm.10753	NM_018874	ENSMUSG00000042179	Pnliprp1	Plrp1	pancreatic lipase related protein 1	protein-coding
mm_87931.1	chr10	62651667	62651677	+	1	NA	promoter-TSS (NM_053183)	promoter-TSS (NM_053183)	-474	NM_053183	94213	Mm.114116	NM_053183	ENSMUSG00000020076	Ddx50	4933429B04Rik|8430408E17Rik|GU2|RH-II	DEAD (Asp-Glu-Ala-Asp) box polypeptide 50	protein-coding
mm_525.1	chr1	37660741	37660750	+	1	NA	intron (NM_028096, intron 1 of 9)	L1M4c|LINE|L1	59066	NM_028096	72097	Mm.142607	NM_028096	ENSMUSG00000026090	2010300C02Rik	-	RIKEN cDNA 2010300C02 gene	protein-coding
mm_42455.1	chr5	115435417	115435435	+	1	NA	intron (NM_008629, intron 5 of 14)	intron (NM_008629, intron 5 of 14)	5741	NM_008629	17690	Mm.5077	NM_008629	ENSMUSG00000054256	Msi1	Msi1h|Musahi1|m-Msi-1	musashi RNA-binding protein 1	protein-coding
mm_5305.1	chr1	22315793	22315815	-	1	NA	intron (NM_001012623, intron 10 of 14)	intron (NM_001012623, intron 10 of 14)	117039	NM_053270	116837	Mm.60061	NM_053270	ENSMUSG00000041670	Rims1	C030033M19Rik|RIM1|RIM1a|RIM1alpha|Rab3ip1|Rim|Serg1|mKIAA0340	regulating synaptic membrane exocytosis 1	protein-coding
mm_134654.1	chr16	22059861	22059877	-	1	NA	3' UTR (NM_183029, exon 16 of 16)	3' UTR (NM_183029, exon 16 of 16)	50385	NR_027488	75826	Mm.297431	NM_029457	ENSMUSG00000022855	Senp2	2310007L05Rik|4930538C18Rik|AI646780|AW554757|Smt3ip2|SuPr-1|mKIAA1331	SUMO/sentrin specific peptidase 2	protein-coding
mm_34204.1	chr4	140924260	140924280	+	1	NA	intron (NM_008812, intron 3 of 15)	intron (NM_008812, intron 3 of 15)	17910	NM_008812	18600	Mm.2296	NM_008812	ENSMUSG00000028927	Padi2	Pdi|Pdi2|mKIAA0994	peptidyl arginine deiminase, type II	protein-coding
mm_152342.1	chr19	9982892	9982940	-	1	NA	exon (NM_010239, exon 1 of 4)	exon (NM_010239, exon 1 of 4)	270	NM_010239	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
mm_102618.1	chr11	62458699	62458719	-	1	NA	intron (NM_001039536, intron 1 of 6)	intron (NM_001039536, intron 1 of 6)	249	NM_001039536	327942	Mm.390358	NM_199026	ENSMUSG00000014245	Pigl	Gm737	phosphatidylinositol glycan anchor biosynthesis, class L	protein-coding
mm_11933.1	chr2	52425242	52425246	+	1	NA	promoter-TSS (NM_182994)	promoter-TSS (NM_182994)	-370	NM_182994	75423	Mm.314378	NM_182994	ENSMUSG00000036093	Arl5a	2410015N24Rik|2810410P22Rik|AA408731|AW610751|Arl5|T25534	ADP-ribosylation factor-like 5A	protein-coding
mm_45288.1	chr5	64961050	64961064	-	1	NA	Intergenic	Intergenic	-1023	NM_011604	21899	Mm.42146	NM_011604	ENSMUSG00000051498	Tlr6	-	toll-like receptor 6	protein-coding
mm_56404.1	chr6	97155038	97155041	-	1	NA	3' UTR (NM_001081111, exon 17 of 17)	3' UTR (NM_001081111, exon 17 of 17)	-6156	NM_175313	101351	Mm.116802	NM_175313	ENSMUSG00000035245	Eogt	A130022J15Rik|AI447490|AW214473|AW259391|Aer61	EGF domain-specific O-linked N-acetylglucosamine (GlcNAc) transferase	protein-coding
mm_152151.1	chr19	7217550	7217580	-	1	NA	promoter-TSS (NM_007750)	promoter-TSS (NM_007750)	51	NM_007750	12868	Mm.14022	NM_007750	ENSMUSG00000035885	Cox8a	COX8L	cytochrome c oxidase subunit VIIIa	protein-coding
mm_9290.1	chr1	171634966	171634976	-	1	NA	exon (NM_144539, exon 8 of 8)	exon (NM_144539, exon 8 of 8)	6929	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_113630.1	chr13	42049368	42049369	+	1	NA	Intergenic	Intergenic	-2653	NM_007772	110521	Mm.4808	NM_007772	ENSMUSG00000021366	Hivep1	Cryabp1	human immunodeficiency virus type I enhancer binding protein 1	protein-coding
mm_122258.1	chr14	34201651	34201663	-	1	NA	promoter-TSS (NM_183209)	promoter-TSS (NM_183209)	-24	NM_183209	432839	Mm.294643	NM_183209	ENSMUSG00000071531	Gprin2	C130040D06Rik|C230073P13|Gm286|mKIAA0514	G protein regulated inducer of neurite outgrowth 2	protein-coding
mm_133897.1	chr16	97541500	97541510	+	1	NA	intron (NM_013606, intron 2 of 13)	intron (NM_013606, intron 2 of 13)	5422	NM_013606	17858	Mm.14157	NM_013606	ENSMUSG00000023341	Mx2	AI528743|Mx-2	MX dynamin-like GTPase 2	protein-coding
mm_33851.1	chr4	135861764	135861765	+	1	NA	intron (NM_010178, intron 2 of 5)	intron (NM_010178, intron 2 of 5)	5693	NM_010178	14105	Mm.10229	NM_010178	ENSMUSG00000028676	Srsf10	FUSIP2|Fusip1|NSSR1|NSSR2|Nssr|SRrp40|Sfrs13a|Srsf13a|TASR|TASR1|TASR2	serine/arginine-rich splicing factor 10	protein-coding
mm_119138.1	chr14	31209416	31209426	+	1	NA	intron (NM_009393, intron 1 of 5)	intron (NM_009393, intron 1 of 5)	1109	NM_009393	21924	Mm.439921	NM_009393	ENSMUSG00000091898	Tnnc1	AI874626|TnC|cTnC|cTnI|tncc	troponin C, cardiac/slow skeletal	protein-coding
mm_164506.1	chr16	93424277	93424280	+	1	NA	intron (NR_040494, intron 1 of 2)	MIRb|SINE|MIR	34594	NR_040494	72264	Mm.396204	NR_040494	ENSMUSG00000099968	1700029J03Rik	-	RIKEN cDNA 1700029J03 gene	ncRNA
mm_86321.1	chr9	123021215	123021218	-	1	NA	promoter-TSS (NM_025339)	promoter-TSS (NM_025339)	-110	NM_025339	66079	Mm.482265	NM_025339	ENSMUSG00000066233	Tmem42	0610027O18Rik|4933429E06Rik|AV003444|D9Ertd662e	transmembrane protein 42	protein-coding
mm_127522.1	chr15	102073640	102073642	+	1	NA	promoter-TSS (NM_145625)	promoter-TSS (NM_145625)	-132	NM_145625	75705	Mm.290022	NM_145625	ENSMUSG00000058655	Eif4b	2310046H11Rik|AL024095|C85189|Eif4a2	eukaryotic translation initiation factor 4B	protein-coding
mm_16471.1	chr2	180710312	180710327	+	1	NA	promoter-TSS (NM_001291432)	promoter-TSS (NM_001291432)	-9	NM_001289651	76425	Mm.41464	NM_029607	ENSMUSG00000027573	Gid8	2310003C23Rik|4833420G11Rik|AI451474|Twa1	GID complex subunit 8	protein-coding
mm_6229.1	chr1	66937528	66937539	-	1	NA	intron (NM_021285, intron 1 of 6)	intron (NM_021285, intron 1 of 6)	-2167	NM_001113387	17901	Mm.1000	NM_021285	ENSMUSG00000061816	Myl1	AI325107|MLC1f|MLC3f|Mylf	myosin, light polypeptide 1	protein-coding
mm_131093.1	chr16	4886303	4886320	+	1	NA	5' UTR (NM_029657, exon 1 of 17)	5' UTR (NM_029657, exon 1 of 17)	211	NM_001252437	17237	Mm.291326	NM_029657	ENSMUSG00000022517	Mgrn1	2610042J20Rik|mKIAA0544|md|nc	mahogunin, ring finger 1	protein-coding
mm_27205.1	chr3	35754475	35754483	-	1	NA	intron (NM_029570, intron 1 of 29)	CpG	341	NM_029570	76295	Mm.239416	NM_029570	ENSMUSG00000037400	Atp11b	1110019I14Rik|ATPIF|ATPIR|mKIAA0956	ATPase, class VI, type 11B	protein-coding
mm_66.1	chr1	6635971	6635992	+	1	NA	intron (NM_001244693, intron 2 of 22)	intron (NM_001244693, intron 2 of 22)	-94070	NR_045189	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding
mm_108195.1	chr12	76782273	76782276	+	1	NA	intron (NM_206534, intron 3 of 3)	(TTTTTG)n|Simple_repeat|Simple_repeat	13280	NM_030677	14776	Mm.441856	NM_030677	ENSMUSG00000042808	Gpx2	GI-GPx|GPx-GI|GSHPx-2|GSHPx-GI	glutathione peroxidase 2	protein-coding
mm_41299.1	chr5	90464949	90464952	+	1	NA	exon (NM_009654, exon 5 of 15)	exon (NM_009654, exon 5 of 15)	4080	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_24809.1	chr3	95588929	95588953	+	1	NA	promoter-TSS (NM_001177669)	promoter-TSS (NM_001177669)	7	NM_001177670	229593	Mm.245830	NM_146133	ENSMUSG00000046519	Golph3l	2010204I15Rik|AU015439|AW549227|C77637|Gpp34r	golgi phosphoprotein 3-like	protein-coding
mm_110779.1	chr12	71007309	71007316	-	1	NA	intron (NR_045055, intron 3 of 3)	intron (NR_045055, intron 3 of 3)	8511	NR_045056	73204	Mm.363770	NR_045055	ENSMUSG00000085622	3110056K07Rik	4921536K06Rik	RIKEN cDNA 3110056K07 gene	ncRNA
mm_93634.1	chr10	117282263	117282280	-	1	NA	promoter-TSS (NM_017372)	promoter-TSS (NM_017372)	1	NM_017372	17105	Mm.45436	NM_017372	ENSMUSG00000069516	Lyz2	AI326280|Lys|Lysm|Lyzf2|Lyzs|Lzm|Lzm-s1|Lzp	lysozyme 2	protein-coding
mm_142133.1	chr17	35909678	35909700	-	1	NA	TTS (NM_025878)	TTS (NM_025878)	379	NM_001142745	73242	Mm.273155	NM_028476	ENSMUSG00000024426	Atat1	0610011P08Rik|2610008K08Rik|2610110G12Rik|3110080J08Rik|Mec17|TAT	alpha tubulin acetyltransferase 1	protein-coding
mm_112879.1	chr13	20855695	20855705	+	1	NA	intron (NM_012054, intron 4 of 20)	intron (NM_012054, intron 4 of 20)	61587	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_12477.1	chr2	71529079	71529084	+	1	NA	promoter-TSS (NM_010053)	promoter-TSS (NM_010053)	-364	NM_010053	13390	Mm.475101	NM_010053	ENSMUSG00000041911	Dlx1	Dlx|Dlx-1	distal-less homeobox 1	protein-coding
mm_48027.1	chr5	136245297	136245304	-	1	NA	promoter-TSS (NM_018825)	promoter-TSS (NM_018825)	-360	NM_018825	23921	Mm.425294	NM_018825	ENSMUSG00000005057	Sh2b2	Aps	SH2B adaptor protein 2	protein-coding
mm_78723.1	chr9	41580004	41580017	+	1	NA	intron (NR_131930, intron 3 of 3)	intron (NR_131930, intron 3 of 3)	-1243	NR_015483	73144	Mm.38166	NM_001033153	ENSMUSG00000074415	3110039I08Rik	2610203C20Rik|AI848448|D230004N17Rik|D3Mgi9|Mir100hg	RIKEN cDNA 3110039I08 gene	ncRNA
mm_153407.1	chr19	40561747	40561764	-	1	NA	intron (NM_019698, intron 14 of 18)	intron (NM_019698, intron 14 of 18)	26708	NM_019698	56454	Mm.233117	NM_019698	ENSMUSG00000025007	Aldh18a1	2810433K04Rik|AI429789|Pycs	aldehyde dehydrogenase 18 family, member A1	protein-coding
mm_24380.1	chr3	90248832	90248842	+	1	NA	intron (NM_013901, intron 1 of 3)	intron (NM_013901, intron 1 of 3)	645	NM_013901	30791	Mm.294709	NM_013901	ENSMUSG00000052310	Slc39a1	Zip1|Zirtl	solute carrier family 39 (zinc transporter), member 1	protein-coding
mm_113976.1	chr13	51800233	51800245	+	1	NA	Intergenic	Intergenic	-6492	NM_013660	20354	Mm.33903	NM_013660	ENSMUSG00000021451	Sema4d	CD100|Semacl2|Semaj|Semcl2|coll-4	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D	protein-coding
mm_160590.1	chr9	67539545	67539545	-	1	NA	intron (NM_001081242, intron 1 of 57)	intron (NM_001081242, intron 1 of 57)	20158	NM_001081242	70549	Mm.33645	NM_027458	ENSMUSG00000052698	Tln2	5730421P04Rik|AI507121|AI787438|AL118320|mKIAA0320	talin 2	protein-coding
mm_59192.1	chr7	24481992	24482076	+	1	NA	promoter-TSS (NM_153112)	promoter-TSS (NM_153112)	11	NM_153112	260299	Mm.178322	NM_153112	ENSMUSG00000054793	Cadm4	Igdf4c|Igsf4c|Tsll2	cell adhesion molecule 4	protein-coding
mm_86285.1	chr9	121857895	121857948	-	1	NA	promoter-TSS (NM_019814)	promoter-TSS (NM_019814)	79	NM_019814	56295	Mm.347915	NM_019814	ENSMUSG00000038412	Higd1a	2210020B17Rik|7420700H20Rik|AI303276|AW049839|HIMP1|Hig1	HIG1 domain family, member 1A	protein-coding
mm_43645.1	chr5	138262348	138262369	+	1	NA	intron (NM_153161, intron 5 of 10)	intron (NM_153161, intron 5 of 10)	-1687	NR_045821	69004	Mm.439868	NR_045821	ENSMUSG00000085227	6330418K02Rik	-	RIKEN cDNA 6330418K02 gene	ncRNA
mm_4540.1	chr1	176835520	176835532	+	1	NA	non-coding (NR_037996, exon 1 of 1)	non-coding (NR_037996, exon 1 of 1)	607	NR_037996	15365	Mm.441435	NR_037996		Hmga2-ps1	EG666235|Gm7996|Hmgic-ps1|[y]i-c	high mobility group AT-hook 2, pseudogene 1	pseudo
mm_138595.1	chr17	35517243	35517259	+	1	NA	promoter-TSS (NM_001163763)	promoter-TSS (NM_001163763)	135	NM_146248	240084	Mm.49544	NM_146248	ENSMUSG00000040312	Cchcr1	Hcr	coiled-coil alpha-helical rod protein 1	protein-coding
mm_165575.1	chr3	22136667	22136670	+	1	NA	intron (NM_030732, intron 1 of 15)	intron (NM_030732, intron 1 of 15)	60016	NM_030732	81004	Mm.202966	NM_030732	ENSMUSG00000027630	Tbl1xr1	8030499H02Rik|A630076E03Rik|AW539987|C21|C230089I12Rik|DC42|Ira1|TBLR1	transducin (beta)-like 1X-linked receptor 1	protein-coding
mm_24631.1	chr3	94310096	94310144	+	1	NA	promoter-TSS (NM_029431)	promoter-TSS (NM_029431)	-12	NM_029431	75778	Mm.45092	NM_029431	ENSMUSG00000028145	Them4	2700077M13Rik|4921507I02Rik	thioesterase superfamily member 4	protein-coding
mm_122001.1	chr14	26669836	26669846	-	1	NA	promoter-TSS (NM_178668)	promoter-TSS (NM_178668)	5	NM_178668	211948	Mm.290758	NM_178668	ENSMUSG00000043702	Pde12	2'-PDE|E430028B21Rik	phosphodiesterase 12	protein-coding
mm_113039.1	chr13	23555617	23555633	+	1	NA	exon (NM_145713, exon 1 of 1)	exon (NM_145713, exon 1 of 1)	593	NM_145713	14957	Mm.247046	NM_145713	ENSMUSG00000052565	Hist1h1d	H1.3|H1D|H1f3|H1s-4	histone cluster 1, H1d	protein-coding
mm_25065.1	chr3	99253334	99253345	+	1	NA	promoter-TSS (NM_009323)	promoter-TSS (NM_009323)	-421	NM_009323	21384	Mm.88761	NM_009323	ENSMUSG00000027868	Tbx15	Tbx14|Tbx8|de	T-box 15	protein-coding
mm_77012.1	chr8	107581289	107581302	-	1	NA	exon (NM_010817, exon 7 of 7)	exon (NM_010817, exon 7 of 7)	7187	NM_010817	17463	Mm.18347	NM_010817	ENSMUSG00000039067	Psmd7	AW107203|Mov-34|Mov34	proteasome (prosome, macropain) 26S subunit, non-ATPase, 7	protein-coding
mm_76000.1	chr8	72475115	72475168	-	1	NA	promoter-TSS (NM_138585)	promoter-TSS (NM_138585)	92	NM_138585	27967	Mm.30136	NM_138585	ENSMUSG00000052488	Cherp	5730408I11Rik|D8Wsu96e|DAN16|Scaf6	calcium homeostasis endoplasmic reticulum protein	protein-coding
mm_41331.1	chr5	90492638	90492683	+	1	NA	exon (NM_007423, exon 3 of 15)	exon (NM_007423, exon 3 of 15)	1946	NM_007423	11576	Mm.358570	NM_007423	ENSMUSG00000054932	Afp	-	alpha fetoprotein	protein-coding
mm_157588.1	chrX	53114363	53114368	-	1	NA	promoter-TSS (NM_019538)	promoter-TSS (NM_019538)	40	NM_019538	56096	Mm.274842	NM_019538	ENSMUSG00000061082	Plac1	DXWsu72e|Epcs26|Oosp2l	placental specific protein 1	protein-coding
mm_2147.1	chr1	88106835	88106840	+	1	NA	intron (NM_201410, intron 1 of 5)	intron (NM_201410, intron 1 of 5)	3580	NM_201410	394435	Mm.300095	NM_201410	ENSMUSG00000090145	Ugt1a6b	A9'|Ugt1a9	UDP glucuronosyltransferase 1 family, polypeptide A6B	protein-coding
mm_138588.1	chr17	35506257	35506269	+	1	NA	exon (NM_013633, exon 1 of 5)	exon (NM_013633, exon 1 of 5)	231	NM_013633	18999	Mm.17031	NM_013633	ENSMUSG00000024406	Pou5f1	NF-A3|Oct-3|Oct-3/4|Oct-4|Oct3|Oct3/4|Oct4|Otf-3|Otf-4|Otf3|Otf3-rs7|Otf3g|Otf4	POU domain, class 5, transcription factor 1	protein-coding
mm_53728.1	chr6	145115617	145115658	+	1	NA	promoter-TSS (NM_001281981)	promoter-TSS (NM_001281981)	1	NM_001281981	16970	Mm.843	NM_008511	ENSMUSG00000030263	Lrmp	D6Int3|D6Int4|D6Int5|D6Int7|D6Int8|Jaw1	lymphoid-restricted membrane protein	protein-coding
mm_110543.1	chr12	55302975	55303014	-	1	NA	promoter-TSS (NM_021529)	promoter-TSS (NM_021529)	6	NM_021529	59032	Mm.427307	NM_021529	ENSMUSG00000021022	Ppp2r3c	4930511A21Rik|5730412A08Rik|G4-1|G5pr	protein phosphatase 2, regulatory subunit B'', gamma	protein-coding
mm_74555.1	chr8	10892079	10892089	-	1	NA	Intergenic	Intergenic	-7838	NR_102285	71624	Mm.139075	NR_102285	ENSMUSG00000109089	4833411C07Rik	-	RIKEN cDNA 4833411C07 gene	ncRNA
mm_142308.1	chr17	42795927	42795962	-	1	NA	3' UTR (NM_009847, exon 18 of 18)	3' UTR (NM_009847, exon 18 of 18)	-53765	NM_001033493	435529	Mm.136350	NM_001033493	ENSMUSG00000057899	Adgrf2	Gpr111|PGR20	adhesion G protein-coupled receptor F2	protein-coding
mm_131361.1	chr16	13780506	13780523	+	1	NA	promoter-TSS (NM_001039521)	promoter-TSS (NM_001039521)	-185	NM_001039521	106298	Mm.288606	NM_001039521	ENSMUSG00000022682	Rrn3	AL023001|E130302O19Rik|R75565|TIF-1A|Tif1a	RRN3 RNA polymerase I transcription factor homolog (yeast)	protein-coding
mm_173047.1	chrX	119509616	119509617	-	1	NA	Intergenic	L1_Mur2|LINE|L1	-417580	NM_053114	93728	Mm.125979	NM_053114	ENSMUSG00000034732	Pabpc5	C820015E17	poly(A) binding protein, cytoplasmic 5	protein-coding
mm_164496.1	chr16	91354840	91354859	+	1	NA	Intergenic	ID_B1|SINE|B4	-17934	NM_010509	15976	Mm.6834	NM_010509	ENSMUSG00000022971	Ifnar2	AI747302|Ifnar-2	interferon (alpha and beta) receptor 2	protein-coding
mm_55515.1	chr6	70117632	70117657	-	1	NA	Intergenic	Intergenic	674531	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_52720.1	chr6	119902742	119902754	+	1	NA	promoter-TSS (NM_011236)	promoter-TSS (NM_011236)	50	NM_001166381	19365	Mm.149	NM_011236	ENSMUSG00000030166	Rad52	Rad52yh	RAD52 homolog, DNA repair protein	protein-coding
mm_172964.1	chr9	88731774	88731782	-	1	NA	promoter-TSS (NM_007536)	promoter-TSS (NM_007536)	72	NM_007536	12047	Mm.378888	NM_007536	ENSMUSG00000099974	Bcl2a1d	A1-d	B cell leukemia/lymphoma 2 related protein A1d	protein-coding
mm_97443.1	chr11	78188423	78188447	+	1	NA	promoter-TSS (NM_001159482)	promoter-TSS (NM_001159482)	8	NM_001159482	19376	Mm.275864	NM_033475	ENSMUSG00000002059	Rab34	AI326479|Narr|Rah|Rah1	RAB34, member RAS oncogene family	protein-coding
mm_75604.1	chr8	61785150	61785152	-	1	NA	intron (NM_001081390, intron 2 of 19)	B4A|SINE|B4	-25053	NM_001293773	72333	Mm.29933	NM_001081390	ENSMUSG00000058056	Palld	2410003B16Rik|6030492A02	palladin, cytoskeletal associated protein	protein-coding
mm_167816.1	chr9	124281241	124281271	-	1	NA	Intergenic	Intergenic	31438	NM_001243118	630836	Mm.458553	NM_001243117	ENSMUSG00000074829	2010315B03Rik	BC029716	RIKEN cDNA 2010315B03 gene	protein-coding
mm_78617.1	chr9	37555638	37555643	+	1	NA	Intergenic	Intergenic	-2895	NM_022029	64011	Mm.335065	NM_022029	ENSMUSG00000053310	Nrgn	0710001B06Rik|AI838505|NG|NG/RC3|Pss1|R75334|RC3	neurogranin	protein-coding
mm_68230.1	chr7	104446071	104446103	-	1	NA	intron (NM_009099, intron 1 of 7)	intron (NM_009099, intron 1 of 7)	19106	NM_009099	20128	Mm.295578	NM_009099	ENSMUSG00000030921	Trim30a	Rpt-1|Rpt1|Trim30	tripartite motif-containing 30A	protein-coding
mm_142101.1	chr17	35835497	35835520	-	1	NA	exon (NM_011655, exon 4 of 4)	exon (NM_011655, exon 4 of 4)	2793	NM_011655	22154	Mm.273538	NM_011655	ENSMUSG00000001525	Tubb5	AA408537|AI596182|B130022C14Rik|M(beta)5	tubulin, beta 5 class I	protein-coding
mm_46369.1	chr5	103629280	103629296	-	1	NA	5' UTR (NM_029415, exon 1 of 6)	5' UTR (NM_029415, exon 1 of 6)	115	NM_029415	75750	Mm.7446	NM_029415	ENSMUSG00000029321	Slc10a6	8430417G17Rik|C78479|Soat	solute carrier family 10 (sodium/bile acid cotransporter family), member 6	protein-coding
mm_97534.1	chr11	78536500	78536514	+	1	NA	promoter-TSS (NM_018854)	promoter-TSS (NM_018854)	71	NM_018854	55978	Mm.358671	NM_018854	ENSMUSG00000001105	Ift20	0610009H04Rik|AU015496	intraflagellar transport 20	protein-coding
mm_4057.1	chr1	165841057	165841067	+	1	NA	intron (NM_001113391, intron 1 of 7)	intron (NM_001113391, intron 1 of 7)	52381	NM_001113392	12503	Mm.217308	NM_031162	ENSMUSG00000005763	Cd247	4930549J05Rik|A430104F18Rik|AW552088|Cd3|Cd3-eta|Cd3-zeta|Cd3h|Cd3z|Cd3zeta|T3z|Tcrk|Tcrz	CD247 antigen	protein-coding
mm_30283.1	chr3	148989095	148989097	-	1	NA	Intergenic	CpG	-34461	NM_001081298	99633	Mm.9776	NM_001081298	ENSMUSG00000028184	Adgrl2	AI450192|CIRL-2|Gm619|Lec1|Lphh1|Lphn2|mKIAA0786	adhesion G protein-coupled receptor L2	protein-coding
mm_80300.1	chr9	73192455	73192458	+	1	NA	Intergenic	Intergenic	78987	NM_198609	225215	Mm.379366	NM_198609	ENSMUSG00000032215	Rsl24d1	2410159K22Rik	ribosomal L24 domain containing 1	protein-coding
mm_78625.1	chr9	38718329	38718341	+	1	NA	promoter-TSS (NM_001145957)	promoter-TSS (NM_001145957)	67	NM_172767	67776	Mm.290950	NM_172767	ENSMUSG00000023186	Vwa5a	5830475I06Rik|AW552491|BCSC-1|E130119J22|Loh11cr2a	von Willebrand factor A domain containing 5A	protein-coding
mm_160071.1	chr7	6363325	6363325	+	1	NA	promoter-TSS (NM_001025163)	promoter-TSS (NM_001025163)	17	NM_001112805	330463	Mm.136456	NM_177888	ENSMUSG00000055150	Zfp78	A330079D15|KRAB12|Zfp77	zinc finger protein 78	protein-coding
mm_7141.1	chr1	91091640	91091657	-	1	NA	exon (NM_008515, exon 9 of 23)	exon (NM_008515, exon 9 of 23)	38204	NM_008515	16978	Mm.45039	NM_008515	ENSMUSG00000026305	Lrrfip1	AU024550|Fliiap1	leucine rich repeat (in FLII) interacting protein 1	protein-coding
mm_86222.1	chr9	120135022	120135026	-	1	NA	Intergenic	B3A|SINE|B2	4590	NR_002902	104433	Mm.453530	NR_002902	ENSMUSG00000064925	Snora62	E2|MBI-13|MBI-136|Rnu108	small nucleolar RNA, H/ACA box 62	snoRNA
mm_91495.1	chr10	37135976	37135987	-	1	NA	3' UTR (NM_008538, exon 2 of 2)	3' UTR (NM_008538, exon 2 of 2)	2945	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_44327.1	chr5	11177433	11177436	-	1	NA	Intergenic	Intergenic	-5581	NM_001310021	545728	Mm.109461	NM_001310021	ENSMUSG00000095918	Gm5861	EG545728	predicted gene 5861	protein-coding
mm_20499.1	chr2	130397526	130397587	-	1	NA	promoter-TSS (NM_019696)	promoter-TSS (NM_019696)	73	NM_019696	56264	Mm.112701	NM_019696	ENSMUSG00000027408	Cpxm1	AA986902|Cpx-1|Cpx1|Cpxm	carboxypeptidase X 1 (M14 family)	protein-coding
mm_86199.1	chr9	119978268	119978277	-	1	NA	intron (NM_153287, intron 1 of 4)	intron (NM_153287, intron 1 of 4)	6386	NM_153287	215418	Mm.491094	NM_153287	ENSMUSG00000032515	Csrnp1	4931429D10Rik|Axud1|CSRNP-1|URAX1|taip-3	cysteine-serine-rich nuclear protein 1	protein-coding
mm_43559.1	chr5	137629113	137629123	+	1	NA	promoter-TSS (NM_146164)	promoter-TSS (NM_146164)	-5	NM_001168652	231798	Mm.200763	NM_146164	ENSMUSG00000029720	Lrch4	2810008P14Rik|2900069C24Rik|AI558103|LRN|LRRN4|SAP25|mFLJ00248	leucine-rich repeats and calponin homology (CH) domain containing 4	protein-coding
mm_104791.1	chr11	98729402	98729432	-	1	NA	promoter-TSS (NM_011869)	promoter-TSS (NM_011869)	18	NM_011869	23989	Mm.246493	NM_011869	ENSMUSG00000017210	Med24	911GSE|AU040102|AW547152|D11Ertd307e|DRIP100|Gse2|Pparb2|Pparbp2|R75526|Thrap4|Trap100	mediator complex subunit 24	protein-coding
mm_15631.1	chr2	162987505	162987509	+	1	NA	promoter-TSS (NM_013731)	promoter-TSS (NM_013731)	26	NM_013731	27219	Mm.26462	NM_013731	ENSMUSG00000017868	Sgk2	AI098171|AW146006|Sgkl	serum/glucocorticoid regulated kinase 2	protein-coding
mm_89777.1	chr10	100592366	100592382	+	1	NA	promoter-TSS (NM_001081246)	promoter-TSS (NM_001081246)	-12	NM_001081246	66605	Mm.72646	NM_001081246	ENSMUSG00000056912	1700017N19Rik	-	RIKEN cDNA 1700017N19 gene	protein-coding
mm_153055.1	chr19	32108133	32108220	-	1	NA	Intergenic	Intergenic	-5036	NM_018830	54447	Mm.491229	NM_018830	ENSMUSG00000024887	Asah2	AI585898	N-acylsphingosine amidohydrolase 2	protein-coding
mm_43303.1	chr5	134613992	134613999	+	1	NA	intron (NM_020044, intron 1 of 12)	intron (NM_020044, intron 1 of 12)	1030	NM_022964	56743	Mm.391375	NM_020044	ENSMUSG00000040751	Lat2	AW125574|LAB|NTAL|WSCR5|Wbscr15|Wbscr5	linker for activation of T cells family, member 2	protein-coding
mm_111288.1	chr12	85455180	85455192	-	1	NA	Intergenic	Intergenic	-18715	NM_010234	14281	Mm.246513	NM_010234	ENSMUSG00000021250	Fos	D12Rfj1|c-fos|cFos	FBJ osteosarcoma oncogene	protein-coding
mm_85785.1	chr9	109059712	109059771	-	1	NA	promoter-TSS (NM_011637)	promoter-TSS (NM_011637)	-18	NM_011637	22040	Mm.439964	NM_011637	ENSMUSG00000049734	Trex1	AU041952	three prime repair exonuclease 1	protein-coding
mm_154990.1	chrX	38316178	38316193	+	1	NA	promoter-TSS (NM_001290389)	promoter-TSS (NM_001290389)	63	NM_133690	67821	Mm.60134	NM_133690	ENSMUSG00000016327	Atp1b4	1110020B02Rik	ATPase, (Na+)/K+ transporting, beta 4 polypeptide	protein-coding
mm_139603.1	chr17	57281902	57281912	+	1	NA	intron (NM_001163816, intron 1 of 25)	RMER10A|LTR|ERVL	2807	NM_001163815	22324	Mm.248172	NM_011691	ENSMUSG00000034116	Vav1	Vav|vav-T	vav 1 oncogene	protein-coding
mm_9450.1	chr1	172602520	172602544	-	1	NA	promoter-TSS (NM_001164725)	promoter-TSS (NM_001164725)	19	NM_001164725	677296	Mm.439612	NM_001164725	ENSMUSG00000070504	Fcrl6	ENSMUSG00000070504|FcRH6|mIFGP6|moFcRH6	Fc receptor-like 6	protein-coding
mm_23604.1	chr3	65188113	65188143	+	1	NA	promoter-TSS (NM_001289450)	promoter-TSS (NM_001289450)	25	NM_001289450	16497	Mm.316402	NM_010597	ENSMUSG00000027827	Kcnab1	Akr8a8|Kvbeta1.1|mKv(beta)1	potassium voltage-gated channel, shaker-related subfamily, beta member 1	protein-coding
mm_66598.1	chr7	45458345	45458348	-	1	NA	intron (NM_010240, intron 3 of 3)	intron (NM_010240, intron 3 of 3)	1540	NM_010240	14325	Mm.30357	NM_010240	ENSMUSG00000050708	Ftl1	Ftl|Ftl-1|L-ferritin	ferritin light polypeptide 1	protein-coding
mm_63715.1	chr7	130716761	130716782	+	1	NA	exon (NM_021314, exon 2 of 18)	exon (NM_021314, exon 2 of 18)	24215	NM_021314	57752	Mm.86322	NM_021314	ENSMUSG00000030852	Tacc2	mKIAA4180	transforming, acidic coiled-coil containing protein 2	protein-coding
mm_124946.1	chr15	12350080	12350091	+	1	NA	3' UTR (NM_025673, exon 4 of 4)	3' UTR (NM_025673, exon 4 of 4)	28589	NM_025673	66629	Mm.157655	NM_025673	ENSMUSG00000022200	Golph3	4733401N08Rik|5730410D03Rik|AW413496	golgi phosphoprotein 3	protein-coding
mm_101199.1	chr11	19018404	19018428	-	1	NA	5' UTR (NM_010789, exon 1 of 12)	5' UTR (NM_010789, exon 1 of 12)	553	NM_001193271	17268	Mm.356578	NM_010789	ENSMUSG00000020160	Meis1	C530044H18Rik|Evi8	Meis homeobox 1	protein-coding
mm_136111.1	chr16	85497271	85497274	-	1	NA	intron (NM_144853, intron 2 of 3)	AT_rich|Low_complexity|Low_complexity	53101	NM_144853	224405	Mm.213203	NM_144853	ENSMUSG00000041134	Cyyr1	-	cysteine and tyrosine-rich protein 1	protein-coding
mm_167989.1	chrX	170009646	170009671	+	1	NA	Intergenic	CpG	-30741	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_97232.1	chr11	75655752	75655775	+	1	NA	promoter-TSS (NM_001080775)	promoter-TSS (NM_001080775)	-252	NM_001080775	17913	Mm.234502	NM_008659	ENSMUSG00000017774	Myo1c	C80397|MMIb|MYO1E|NMI|mm1beta|myr2	myosin IC	protein-coding
mm_121908.1	chr14	21987886	21987897	-	1	NA	5' UTR (NM_145459, exon 2 of 3)	5' UTR (NM_145459, exon 2 of 3)	1710	NM_145459	218820	Mm.292401	NM_145459	ENSMUSG00000039081	Zfp503	AI181838|B830002A16Rik|Nolz-1|Nolz1|Znf503	zinc finger protein 503	protein-coding
mm_109645.1	chr12	112829149	112829161	+	1	NA	5' UTR (NM_028023, exon 1 of 2)	5' UTR (NM_028023, exon 1 of 2)	234	NM_028023	71963	Mm.313185	NM_028023	ENSMUSG00000047832	Cdca4	2410018C03Rik|HEPP|SEI-3	cell division cycle associated 4	protein-coding
mm_93205.1	chr10	94855482	94855502	-	1	NA	intron (NM_018797, intron 9 of 30)	B4|SINE|B4	89086	NM_018797	54712	Mm.256712	NM_018797	ENSMUSG00000074785	Plxnc1	2510048K12Rik|AW742158|CD232|Vespr	plexin C1	protein-coding
mm_71343.1	chr8	45627918	45627933	+	1	NA	5' UTR (NM_001310707, exon 1 of 24)	5' UTR (NM_001310707, exon 1 of 24)	174	NM_001310707	234214	Mm.211096	NM_172752	ENSMUSG00000031626	Sorbs2	2010203O03Rik|9430041O17Rik|A530071H08|Argbp2|mKIAA0777|nArgBP2	sorbin and SH3 domain containing 2	protein-coding
mm_168213.1	chr10	75860242	75860242	-	1	NA	promoter-TSS (NM_010798)	promoter-TSS (NM_010798)	8	NM_010798	17319	Mm.2326	NM_010798	ENSMUSG00000033307	Mif	GIF|Glif	macrophage migration inhibitory factor	protein-coding
mm_40547.1	chr5	58044366	58044383	+	1	NA	intron (NM_001310608, intron 3 of 3)	intron (NM_001310608, intron 3 of 3)	326293	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_49938.1	chr6	39592570	39592588	+	1	NA	promoter-TSS (NM_026612)	promoter-TSS (NM_026612)	-4	NM_026612	68198	Mm.29415	NM_026612	ENSMUSG00000002416	Ndufb2	1810011O01Rik|8kDa|AGGG|AI325567|CI-AGGG	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 2	protein-coding
mm_5187.1	chr1	13104067	13104076	-	1	NA	Intergenic	Intergenic	23092	NM_001081209	383491	Mm.309380	NM_001081209	ENSMUSG00000042414	Prdm14	-	PR domain containing 14	protein-coding
mm_62386.1	chr7	100862737	100862741	+	1	NA	intron (NM_177073, intron 1 of 10)	intron (NM_177073, intron 1 of 10)	674	NM_177073	320100	Mm.40336	NM_177073	ENSMUSG00000008318	Relt	E430021K24Rik|Tnfrsf19l	RELT tumor necrosis factor receptor	protein-coding
mm_155242.1	chrX	57214040	57214050	+	1	NA	exon (NM_011616, exon 2 of 5)	exon (NM_011616, exon 2 of 5)	1902	NM_011616	21947	Mm.4861	NM_011616	ENSMUSG00000031132	Cd40lg	CD154|CD40-L|Cd40l|HIGM1|IGM|IMD3|Ly-62|Ly62|T-BAM|TRAP|Tnfsf5|Tnlg8b|gp39	CD40 ligand	protein-coding
mm_30290.1	chr3	148989533	148989553	-	1	NA	Intergenic	CpG	-34908	NM_001081298	99633	Mm.9776	NM_001081298	ENSMUSG00000028184	Adgrl2	AI450192|CIRL-2|Gm619|Lec1|Lphh1|Lphn2|mKIAA0786	adhesion G protein-coupled receptor L2	protein-coding
mm_116371.1	chr13	40733769	40733836	-	1	NA	promoter-TSS (NM_011547)	promoter-TSS (NM_011547)	21	NM_011547	21418	Mm.85544	NM_011547	ENSMUSG00000021359	Tfap2a	AP-2|AP2alpha|Ap-2 (a)|Ap2|Ap2tf|Tcfap2a	transcription factor AP-2, alpha	protein-coding
mm_29808.1	chr3	127790202	127790218	-	1	NA	intron (NM_145133, intron 1 of 2)	intron (NM_145133, intron 1 of 2)	297	NM_145133	211550	Mm.31852	NM_145133	ENSMUSG00000046688	Tifa	T2bp	TRAF-interacting protein with forkhead-associated domain	protein-coding
mm_7124.1	chr1	90843917	90843983	-	1	NA	promoter-TSS (NM_001243009)	promoter-TSS (NM_001243009)	21	NM_001243009	12835	Mm.7562	NM_009935	ENSMUSG00000048126	Col6a3	AI507288|Col6a-3	collagen, type VI, alpha 3	protein-coding
mm_147900.1	chr18	65349757	65349778	-	1	NA	exon (NM_001037294, exon 4 of 13)	exon (NM_001037294, exon 4 of 13)	44121	NM_001037294	225638	Mm.296528	NM_001037294	ENSMUSG00000032845	Alpk2	Gm549|Hak	alpha-kinase 2	protein-coding
mm_106058.1	chr11	116125327	116125331	-	1	NA	3' UTR (NM_178802, exon 6 of 6)	3' UTR (NM_178802, exon 6 of 6)	5799	NM_178802	338364	Mm.439976	NM_178802	ENSMUSG00000054517	Trim65	4732463G12Rik	tripartite motif-containing 65	protein-coding
mm_26811.1	chr3	10206044	10206058	-	1	NA	exon (NM_024406, exon 2 of 4)	exon (NM_024406, exon 2 of 4)	2525	NM_024406	11770	Mm.582	NM_024406	ENSMUSG00000062515	Fabp4	422/aP2|ALBP/Ap2|Ap2|Lbpl	fatty acid binding protein 4, adipocyte	protein-coding
mm_95748.1	chr11	54866414	54866459	+	1	NA	promoter-TSS (NM_008248)	promoter-TSS (NM_008248)	-2	NM_008248	15254	Mm.425	NM_008248	ENSMUSG00000020267	Hint1	AA673479|Hint|Ipk1|PKCI-1|PRKCNH1	histidine triad nucleotide binding protein 1	protein-coding
mm_124627.1	chr15	3637419	3637428	+	1	NA	Intergenic	Intergenic	-54071	NM_010284	14600	Mm.3986	NM_010284	ENSMUSG00000055737	Ghr	GHBP|GHR/BP	growth hormone receptor	protein-coding
mm_26659.1	chr3	154597353	154597363	+	1	NA	promoter-TSS (NM_172474)	promoter-TSS (NM_172474)	-260	NM_172474	209584	Mm.347513	NM_172474	ENSMUSG00000047583	Tyw3	5230400J09Rik	tRNA-yW synthesizing protein 3 homolog (S. cerevisiae)	protein-coding
mm_113792.1	chr13	46060595	46060633	+	1	NA	Intergenic	Intergenic	-95623	NM_009124	20238	Mm.342683	NM_009124	ENSMUSG00000046876	Atxn1	2900016G23Rik|Atx1|C85907|ENSMUSG00000074917|Gm10786|Sca1	ataxin 1	protein-coding
mm_90379.1	chr10	127266298	127266306	+	1	NA	promoter-TSS (NM_027151)	promoter-TSS (NM_027151)	40	NM_001190453	69654	Mm.167537	NM_027151	ENSMUSG00000025410	Dctn2	2310042E05Rik|C130077D06Rik|C87049|DCTN-50|GMP23-48K|RBP50|p50	dynactin 2	protein-coding
mm_43276.1	chr5	130677561	130677561	+	1	NA	intron (NM_021371, intron 4 of 5)	intron (NM_021371, intron 4 of 5)	228769	NM_021371	140904	Mm.40875	NM_021371	ENSMUSG00000060371	Caln1	9630012C17Rik|Cabp8|MNCb-0849	calneuron 1	protein-coding
mm_23582.1	chr3	63963632	63963643	+	1	NA	exon (NM_001272035, exon 1 of 7)	exon (NM_001272035, exon 1 of 7)	1096	NM_001331067	11416	Mm.135619	NM_015728	ENSMUSG00000027822	Slc33a1	AI315656|AI788741|Acatn|D630022N01Rik	solute carrier family 33 (acetyl-CoA transporter), member 1	protein-coding
mm_93065.1	chr10	89257516	89257527	-	1	NA	non-coding (NR_102339, exon 1 of 27)	non-coding (NR_102339, exon 1 of 27)	269	NM_001277188	320091	Mm.236464	NM_178773	ENSMUSG00000035189	Ano4	A330096O15Rik|Gm65|Tmem16d	anoctamin 4	protein-coding
mm_122821.1	chr14	54653663	54653701	-	1	NA	promoter-TSS (NM_001242606)	promoter-TSS (NM_001242606)	3	NM_001242605	56215	Mm.297078	NM_019567	ENSMUSG00000022185	Acin1	2610036I19Rik|2610510L13Rik|Acinus|Acn|C79325|acinusL|acinusS|mKIAA0670	apoptotic chromatin condensation inducer 1	protein-coding
mm_17489.1	chr2	28583196	28583230	-	1	NA	promoter-TSS (NM_001290484)	promoter-TSS (NM_001290484)	66	NM_148928	70239	Mm.274120	NM_148928	ENSMUSG00000026816	Gtf3c5	2700084A09Rik|TFIIIC63|TFiiiC2-63	general transcription factor IIIC, polypeptide 5	protein-coding
mm_51921.1	chr6	91265879	91265892	+	1	NA	intron (NM_007992, intron 12 of 17)	intron (NM_007992, intron 12 of 17)	53121	NM_007992	14115	Mm.249146	NM_007992	ENSMUSG00000064080	Fbln2	5730577E14Rik|FIBL-2	fibulin 2	protein-coding
mm_4071.1	chr1	166155007	166155017	+	1	NA	intron (NM_021610, intron 3 of 6)	intron (NM_021610, intron 3 of 6)	24552	NM_021610	59290	Mm.46357	NM_021610	ENSMUSG00000000544	Gpa33	2010310L10Rik|2210401D16Rik|BB116197	glycoprotein A33 (transmembrane)	protein-coding
mm_141542.1	chr17	31870791	31870793	-	1	NA	Intergenic	Intergenic	-15000	NM_010831	17691	Mm.290941	NM_010831	ENSMUSG00000024042	Sik1	Msk|Sik|Snf1lk	salt inducible kinase 1	protein-coding
mm_161099.1	chr12	99886663	99886663	+	1	NA	intron (NM_028354, intron 1 of 15)	intron (NM_028354, intron 1 of 15)	2148	NM_028354	104884	Mm.312323	NM_028354	ENSMUSG00000021177	Tdp1	2810481F14Rik|4921509N21Rik|AI838772|AW493413|E430034L06Rik|MLZ-501|SCAN1	tyrosyl-DNA phosphodiesterase 1	protein-coding
mm_170430.1	chr18	75899828	75899830	+	1	NA	intron (NM_145356, intron 1 of 4)	intron (NM_145356, intron 1 of 4)	79651	NM_145356	207259	Mm.159332	NM_145356	ENSMUSG00000044646	Zbtb7c	B230208J24Rik|Kr-pok|Zbtb36	zinc finger and BTB domain containing 7C	protein-coding
mm_57174.1	chr6	122847867	122847879	-	1	NA	3' UTR (NM_009779, exon 2 of 2)	3' UTR (NM_009779, exon 2 of 2)	8284	NM_009779	12267	Mm.2408	NM_009779	ENSMUSG00000040552	C3ar1	AZ3B|C3AR|HNFAG09	complement component 3a receptor 1	protein-coding
mm_153564.1	chr19	42431748	42431760	-	1	NA	promoter-TSS (NM_145123)	promoter-TSS (NM_145123)	29	NM_145123	72832	Mm.313558	NM_145123	ENSMUSG00000042401	Crtac1	2810454P21Rik|AW047536|Crtac1B|Lotus	cartilage acidic protein 1	protein-coding
mm_142586.1	chr17	46726710	46726718	-	1	NA	exon (NM_010321, exon 3 of 6)	exon (NM_010321, exon 3 of 6)	2451	NM_010321	14711	Mm.29395	NM_010321	ENSMUSG00000002769	Gnmt	-	glycine N-methyltransferase	protein-coding
mm_43683.1	chr5	138808853	138808872	+	1	NA	intron (NM_030565, intron 9 of 9)	intron (NM_030565, intron 9 of 9)	-11218	NM_001195128	384244	Mm.485002	NM_001195128	ENSMUSG00000094504	Gm5294	EG384244	predicted gene 5294	protein-coding
mm_15761.1	chr2	164289262	164289273	+	1	NA	promoter-TSS (NM_021363)	promoter-TSS (NM_021363)	0	NM_001311114	64335	Mm.389393	NM_021363	ENSMUSG00000017003	Svs3a	9530026M05Rik|BB121242|Semg2|Svp-3|Svp3|Svs3	seminal vesicle secretory protein 3A	protein-coding
mm_21321.1	chr2	157099377	157099390	-	1	NA	3' UTR (NM_001139520, exon 17 of 17)	3' UTR (NM_001139520, exon 17 of 17)	12328	NM_001177439	383766	Mm.480305	NM_001177439	ENSMUSG00000074628	Tldc2	Gm1332	TBC/LysM associated domain containing 2	protein-coding
mm_51065.1	chr6	65952562	65952621	+	1	NA	promoter-TSS (NM_001161773)	promoter-TSS (NM_001161773)	20	NM_001161773	67653	Mm.389756	NM_001161773	ENSMUSG00000036463	4930544G11Rik	-	RIKEN cDNA 4930544G11 gene	protein-coding
mm_6571.1	chr1	75192005	75192016	-	1	NA	promoter-TSS (NM_001288613)	promoter-TSS (NM_001288613)	0	NM_001003917	245860	Mm.238266	NM_001003917	ENSMUSG00000033124	Atg9a	AU019532|Apg9l1|Atg9|Atg9l1	autophagy related 9A	protein-coding
mm_35571.1	chr4	41640383	41640402	-	1	NA	promoter-TSS (NM_027147)	promoter-TSS (NM_027147)	-90	NM_027147	69638	Mm.372459	NM_027147	ENSMUSG00000028445	Enho	1110065P19Rik|2310040A07Rik	energy homeostasis associated	protein-coding
mm_54810.1	chr6	42323350	42323370	-	1	NA	intron (NM_001286584, intron 1 of 6)	intron (NM_001286584, intron 1 of 6)	1280	NM_001286584	76156	Mm.234314	NM_029528	ENSMUSG00000029861	Fam131b	6330503C03Rik|6530406I18Rik|AV277466	family with sequence similarity 131, member B	protein-coding
mm_96743.1	chr11	69846611	69846659	+	1	NA	promoter-TSS (NM_023564)	promoter-TSS (NM_023564)	-9	NR_033133	70310	Mm.28874	NM_023564	ENSMUSG00000019461	Plscr3	2210403O21Rik|2610037N06Rik|ESTM3|X83310	phospholipid scramblase 3	protein-coding
mm_134287.1	chr16	14215884	14215894	-	1	NA	exon (NM_013607, exon 25 of 42)	exon (NM_013607, exon 25 of 42)	52614	NM_001114085	67203	Mm.24105	NM_023317	ENSMUSG00000022678	Nde1	2810027M15Rik|AU042936|AW822251|Nude|mNudE	nudE neurodevelopment protein 1	protein-coding
mm_39518.1	chr5	21257841	21257848	+	1	NA	intron (NM_175437, intron 18 of 30)	intron (NM_175437, intron 18 of 30)	71577	NM_175437	212167	Mm.121705	NM_175437	ENSMUSG00000039934	Gsap	A530088I07Rik|Pion	gamma-secretase activating protein	protein-coding
mm_43992.1	chr5	146795912	146795935	+	1	NA	promoter-TSS (NM_011669)	promoter-TSS (NM_011669)	-967	NM_011669	22217	Mm.167971	NM_011669	ENSMUSG00000029640	Usp12	Ubh1	ubiquitin specific peptidase 12	protein-coding
mm_15493.1	chr2	157788552	157788557	+	1	NA	intron (NM_025680, intron 3 of 15)	intron (NM_025680, intron 3 of 15)	51153	NM_025680	66642	Mm.45193	NM_025680	ENSMUSG00000027649	Ctnnbl1	5730471K09Rik|NAP|NYD-SP19|P14L	catenin, beta like 1	protein-coding
mm_146847.1	chr18	23954571	23954607	-	1	NA	promoter-TSS (NM_027007)	promoter-TSS (NM_027007)	-99	NM_027007	69256	Mm.218343	NM_027007	ENSMUSG00000024276	Zfp397	2810411K16Rik|6720480F11Rik|AI461664	zinc finger protein 397	protein-coding
mm_154520.1	chrM	13154	13203	-	1	NA	NA	Intergenic	NA	NA								
mm_83243.1	chr9	42399805	42399877	-	1	NA	promoter-TSS (NM_001324548)	promoter-TSS (NM_001324548)	88	NM_009347	21683	Mm.42209	NM_009347	ENSMUSG00000037705	Tecta	Tctna	tectorin alpha	protein-coding
mm_76028.1	chr8	75406585	75406593	-	1	NA	Intergenic	Intergenic	-42105	NM_027944	71831	Mm.443238	NM_027944	ENSMUSG00000031620	1700007B14Rik	-	RIKEN cDNA 1700007B14 gene	protein-coding
mm_34392.1	chr4	144981397	144981433	+	1	NA	intron (NM_001276502, intron 67 of 68)	intron (NM_001276502, intron 67 of 68)	88278	NM_011303	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding
mm_121681.1	chr14	12823139	12823151	-	1	NA	promoter-TSS (NM_001042617)	promoter-TSS (NM_001042617)	-66	NM_012061	27062	Mm.260881	NM_012061	ENSMUSG00000054423	Cadps	AU067781|CAPS|CAPS1|mKIAA1121	Ca2+-dependent secretion activator	protein-coding
mm_35432.1	chr4	36664951	36664953	-	1	NA	intron (NM_001165999, intron 2 of 7)	L1_Mur2|LINE|L1	-3558	NR_105849	102465229		NR_105849	ENSMUSG00000106425	Mir873b	mmu-mir-873b	microRNA 873b	ncRNA
mm_67382.1	chr7	79842288	79842302	-	1	NA	promoter-TSS (NM_008486)	promoter-TSS (NM_008486)	57	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_20742.1	chr2	138112199	138112201	-	1	NA	Intergenic	Intergenic	-144384	NM_001025431	228662	Mm.153405	NM_145534	ENSMUSG00000062098	Btbd3	mKIAA0952	BTB (POZ) domain containing 3	protein-coding
mm_109135.1	chr12	106010276	106010339	+	1	NA	promoter-TSS (NM_011705)	promoter-TSS (NM_011705)	44	NM_001029843	22367	Mm.2981	NM_011705	ENSMUSG00000021115	Vrk1	51PK	vaccinia related kinase 1	protein-coding
mm_81895.1	chr9	119796641	119796642	+	1	NA	intron (NM_011887, intron 11 of 26)	RSINE1|SINE|B4	28815	NM_011887	24046	Mm.89981	NM_011887	ENSMUSG00000034115	Scn11a	NSS2|NaN|NaT|NaV1.9|SNS2	sodium channel, voltage-gated, type XI, alpha	protein-coding
mm_70588.1	chr8	13172584	13172599	+	1	NA	exon (NM_010684, exon 6 of 9)	exon (NM_010684, exon 6 of 9)	13430	NM_010684	16783	Mm.16716	NM_010684	ENSMUSG00000031447	Lamp1	CD107a|LGP-120|LGP-A|Lamp-1|P2B	lysosomal-associated membrane protein 1	protein-coding
mm_160798.1	chr11	4746536	4746536	-	1	NA	intron (NM_138948, intron 1 of 4)	CpG	242	NM_138948	192650	Mm.207056	NM_138948	ENSMUSG00000009075	Cabp7	-	calcium binding protein 7	protein-coding
mm_82810.1	chr9	29963206	29963210	-	1	NA	promoter-TSS (NM_172290)	promoter-TSS (NM_172290)	-79	NM_172290	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding
mm_37636.1	chr4	127534654	127534670	-	1	NA	Intergenic	Intergenic	-176498	NM_010291	14622	Mm.26859	NM_010291	ENSMUSG00000042357	Gjb5	Cnx31.1|Cx31.1|Gjb-5	gap junction protein, beta 5	protein-coding
mm_97788.1	chr11	82785371	82785378	+	1	NA	exon (NM_010716, exon 3 of 20)	exon (NM_010716, exon 3 of 20)	4265	NM_010716	16882	Mm.277136	NM_010716	ENSMUSG00000020697	Lig3	D11Wsu78e	ligase III, DNA, ATP-dependent	protein-coding
mm_71.1	chr1	6670315	6670321	+	1	NA	intron (NM_001244693, intron 2 of 22)	L1VL2|LINE|L1	-59733	NR_045189	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding
mm_165761.1	chr3	117574835	117574858	+	1	NA	promoter-TSS (NM_029425)	promoter-TSS (NM_029425)	-381	NM_029425	75769	Mm.72187	NM_029425	ENSMUSG00000033342	Plppr5	4833424O15Rik|Lppr5|PRG-5|Pap2d	phospholipid phosphatase related 5	protein-coding
mm_64867.1	chr7	13571062	13571073	-	1	NA	promoter-TSS (NM_001080942)	promoter-TSS (NM_001080942)	0	NM_001080942	77684	Mm.190482	NM_001080942	ENSMUSG00000078800	Bsph2	9230107M04Rik|Bsph2a	binder of sperm protein homolog 2	protein-coding
mm_121616.1	chr14	8259292	8259313	-	1	NA	promoter-TSS (NM_053115)	promoter-TSS (NM_053115)	-283	NM_053115	93732	Mm.28700	NM_053115	ENSMUSG00000021751	Acox2	THCCox	acyl-Coenzyme A oxidase 2, branched chain	protein-coding
mm_133263.1	chr16	77340654	77340669	+	1	NA	intron (NR_015543, intron 1 of 4)	intron (NR_015543, intron 1 of 4)	11333	NR_015543	77994	Mm.394688	NR_015543	ENSMUSG00000090386	Mir99ahg	2810055G20Rik|D730043B02Rik	Mir99a and Mirlet7c-1 host gene (non-protein coding)	ncRNA
mm_145418.1	chr18	58556012	58556047	+	1	NA	promoter-TSS (NM_001081072)	promoter-TSS (NM_001081072)	-211	NM_001081072	225579	Mm.258517	NM_001081072	ENSMUSG00000024600	Slc27a6	4732438L20Rik|FACVL2|FATP6|VLCS-H1	solute carrier family 27 (fatty acid transporter), member 6	protein-coding
mm_37324.1	chr4	119415472	119415487	-	1	NA	promoter-TSS (NM_001270435)	promoter-TSS (NM_001270435)	42	NM_001270435	73332	Mm.425204	NM_028506	ENSMUSG00000028637	Ccdc30	1700001O02Rik|1700041C02Rik|1700111D19Rik|4930445I03Rik	coiled-coil domain containing 30	protein-coding
mm_27480.1	chr3	53657300	53657308	-	1	NA	promoter-TSS (NM_172862)	promoter-TSS (NM_172862)	51	NM_172862	242022	Mm.38378	NM_172862	ENSMUSG00000037016	Frem2	6030440P17Rik|8430406N05Rik|Gm409|b2b1562Clo|my|ne|nv1	Fras1 related extracellular matrix protein 2	protein-coding
mm_26605.1	chr3	152214286	152214290	+	1	NA	intron (NM_057172, intron 2 of 19)	intron (NM_057172, intron 2 of 19)	3830	NM_057172	51886	Mm.278922	NM_057172	ENSMUSG00000028034	Fubp1	9530027K12Rik|D3Ertd330e|FBP|Fubp|Fubp4	far upstream element (FUSE) binding protein 1	protein-coding
mm_50915.1	chr6	57598605	57598617	+	1	NA	exon (NM_025992, exon 4 of 23)	exon (NM_025992, exon 4 of 23)	17619	NM_025992	67138	Mm.297393	NM_025992	ENSMUSG00000029798	Herc6	1700121D12Rik|2510038N07Rik|4930427L17Rik|AI451296|CEB1|Herc5	hect domain and RLD 6	protein-coding
mm_87399.1	chr10	45452146	45452147	+	1	NA	intron (NM_001031772, intron 2 of 4)	intron (NM_001031772, intron 2 of 4)	18055	NM_001031772	380669	Mm.440328	NM_001031772	ENSMUSG00000063804	Lin28b	2810403D23Rik|D030047M17Rik|Lin-28.2	lin-28 homolog B (C. elegans)	protein-coding
mm_63954.1	chr7	139907118	139907121	+	1	NA	intron (NM_177261, intron 3 of 30)	intron (NM_177261, intron 3 of 30)	12423	NM_177261	76484	Mm.44442	NM_177261	ENSMUSG00000066129	Kndc1	2410012C07Rik|B830014K08Rik|VKIND|very-kind	kinase non-catalytic C-lobe domain (KIND) containing 1	protein-coding
mm_149929.1	chr19	26750955	26750967	+	1	NA	intron (NM_001347439, intron 2 of 7)	(T)n|Simple_repeat|Simple_repeat	2558	NM_026003	67155	Mm.342988	NM_011416	ENSMUSG00000024921	Smarca2	2610209L14Rik|SNF2alpha|Snf2l2|brahma|brm	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	protein-coding
mm_135880.1	chr16	63864098	63864113	-	1	NA	promoter-TSS (NM_010140)	promoter-TSS (NM_010140)	52	NM_010140	13837	Mm.1977	NM_010140	ENSMUSG00000052504	Epha3	AW492086|Cek4|ETK1|End3|Hek|Hek4|Mek4|Tyro4	Eph receptor A3	protein-coding
mm_122074.1	chr14	30599418	30599432	-	1	NA	exon (NM_001310682, exon 15 of 17)	exon (NM_001310682, exon 15 of 17)	10885	NM_001310682	18753	Mm.2314	NM_011103	ENSMUSG00000021948	Prkcd	AI385711|D14Ertd420e|PKC[d]|PKCdelta|Pkcd	protein kinase C, delta	protein-coding
mm_101501.1	chr11	32199261	32199297	-	1	NA	intron (NM_001134458, intron 1 of 8)	intron (NM_001134458, intron 1 of 8)	1000	NM_001134458	16199	Mm.384	NM_008374	ENSMUSG00000020279	Il9r	-	interleukin 9 receptor	protein-coding
mm_118354.1	chr13	115056522	115056525	-	1	NA	intron (NM_001033228, intron 1 of 28)	intron (NM_001033228, intron 1 of 28)	33635	NM_134058	105083	Mm.486295	NM_134058	ENSMUSG00000042275	Pelo	AA409897|AI852218	pelota homolog (Drosophila)	protein-coding
mm_127946.1	chr15	10714799	10714816	-	1	NA	promoter-TSS (NM_001166408)	promoter-TSS (NM_001166408)	-29	NR_045063	75259	Mm.33928	NR_045063	ENSMUSG00000097058	4930556M19Rik	1700009D01Rik|C130022M03Rik	RIKEN cDNA 4930556M19 gene	ncRNA
mm_58983.1	chr7	19076402	19076409	+	1	NA	exon (NM_010058, exon 1 of 5)	exon (NM_010058, exon 1 of 5)	205	NM_010058	13401	Mm.2852	NM_010058	ENSMUSG00000030410	Dmwd	DMR-N9|Dm9	dystrophia myotonica-containing WD repeat motif	protein-coding
mm_31198.1	chr4	43669267	43669287	+	1	NA	promoter-TSS (NM_175517)	promoter-TSS (NM_175517)	306	NM_001085508	242409	Mm.171489	NM_001085508	ENSMUSG00000078716	Tmem8b	4930500O05Rik	transmembrane protein 8B	protein-coding
mm_61787.1	chr7	83883623	83883645	+	1	NA	5' UTR (NM_030705, exon 1 of 1)	5' UTR (NM_030705, exon 1 of 1)	707	NM_030705	80889	Mm.272998	NM_030705	ENSMUSG00000070462	Mesdc1	AW061151	mesoderm development candidate 1	protein-coding
mm_89640.1	chr10	96621895	96621906	+	1	NA	3' UTR (NM_007569, exon 2 of 2)	3' UTR (NM_007569, exon 2 of 2)	4899	NM_007569	12226	Mm.23811	NM_007569	ENSMUSG00000036478	Btg1	AI426953|AW546738	B cell translocation gene 1, anti-proliferative	protein-coding
mm_85846.1	chr9	110645307	110645320	-	1	NA	intron (NM_183276, intron 1 of 53)	intron (NM_183276, intron 1 of 53)	8848	NM_183276	235627	Mm.335481	NM_183276	ENSMUSG00000056724	Nbeal2	1110014F23Rik|BC042396|mKIAA0540	neurobeachin-like 2	protein-coding
mm_363.1	chr1	33908021	33908065	+	1	NA	promoter-TSS (NM_001310484)	promoter-TSS (NM_001310484)	-182	NM_001276764	13518	Mm.336625	NM_010081	ENSMUSG00000026131	Dst	2310001O04Rik|A830042E19Rik|AW554249|BP230|BPAG1-n|Bpag|Bpag1|Macf2|ah|athetoid|dt|mKIAA0728|nmf203|nmf339	dystonin	protein-coding
mm_151484.1	chr19	58677137	58677150	+	1	NA	exon (NM_026925, exon 9 of 13)	exon (NM_026925, exon 9 of 13)	6778	NM_026925	69060	Mm.20407	NM_026925	ENSMUSG00000046008	Pnlip	1810007A24Rik|PL|PTL	pancreatic lipase	protein-coding
mm_41319.1	chr5	90472058	90472073	+	1	NA	exon (NM_009654, exon 11 of 15)	exon (NM_009654, exon 11 of 15)	11195	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_28580.1	chr3	93465357	93465361	-	1	NA	Intergenic	Intergenic	-3395	NM_027762	71325	Mm.68064	NM_027762	ENSMUSG00000027908	Tchhl1	5430400H23Rik|AA589420|S100a17|Thhl1	trichohyalin-like 1	protein-coding
mm_156504.1	chrX	146610904	146610904	+	1	NA	Intergenic	Intergenic	-351609	NM_008312	15560	Mm.439670	NM_008312	ENSMUSG00000041380	Htr2c	5-HT2C|5-HT2cR|5-HTR2C|5HT1c|Htr1c|SR1	5-hydroxytryptamine (serotonin) receptor 2C	protein-coding
mm_708.1	chr1	40771375	40771402	+	1	NA	TTS (NM_172499)	TTS (NM_172499)	19269	NM_172499	211798	Mm.235443	NM_172499	ENSMUSG00000041945	Mfsd9	4931419K03Rik	major facilitator superfamily domain containing 9	protein-coding
mm_32404.1	chr4	106911518	106911529	+	1	NA	promoter-TSS (NM_198438)	promoter-TSS (NM_198438)	53	NM_023672	72475	Mm.195635	NM_023672	ENSMUSG00000061887	Ssbp3	2610021L12Rik|2610200M23Rik|5730488C10Rik|AI854733|AW551939|LAST|SSDP1	single-stranded DNA binding protein 3	protein-coding
mm_76987.1	chr8	107048574	107048631	-	1	NA	promoter-TSS (NM_026513)	promoter-TSS (NM_026513)	12	NM_026513	68023	Mm.482335	NM_026513	ENSMUSG00000078931	Pdf	2610019N19Rik	peptide deformylase (mitochondrial)	protein-coding
mm_119766.1	chr14	54173559	54173590	+	1	NA	Intergenic	Intergenic	80355	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_942.1	chr1	56971452	56971505	+	1	NA	promoter-TSS (NR_024325)	promoter-TSS (NR_024325)	9	NR_024325	329160	Mm.419039	NR_024325	ENSMUSG00000087022	9130024F11Rik	B530002L08|EG329160	RIKEN cDNA 9130024F11 gene	ncRNA
mm_159578.1	chr4	118543950	118543950	-	1	NA	promoter-TSS (NM_172383)	promoter-TSS (NM_172383)	-224	NM_172383	230678	Mm.23639	NM_172383	ENSMUSG00000050854	Tmem125	6330530A05Rik|AV223516	transmembrane protein 125	protein-coding
mm_90634.1	chr10	128489084	128489120	+	1	NA	3' UTR (NM_001114096, exon 29 of 29)	3' UTR (NM_001114096, exon 29 of 29)	3907	NM_001317220	17904	Mm.337074	NM_010860	ENSMUSG00000090841	Myl6	ESMLC|LC17|LC17-GI|MLC-3|MLC1SM|Myln	myosin, light polypeptide 6, alkali, smooth muscle and non-muscle	protein-coding
mm_117442.1	chr13	74734256	74734266	-	1	NA	promoter-TSS (NM_001301181)	promoter-TSS (NM_001301181)	0	NM_001301158	12380	Mm.29163	NM_009817	ENSMUSG00000021585	Cast	-	calpastatin	protein-coding
mm_38187.1	chr4	135325971	135325976	-	1	NA	intron (NM_016799, intron 14 of 17)	B2_Mm2|SINE|B2	27241	NM_016799	51796	Mm.1963	NM_016799	ENSMUSG00000028809	Srrm1	AA407769|POP101|Srm160	serine/arginine repetitive matrix 1	protein-coding
mm_114043.1	chr13	54071861	54071909	+	1	NA	promoter-TSS (NM_027324)	promoter-TSS (NM_027324)	40	NM_027324	14057	Mm.134191	NM_027324	ENSMUSG00000021474	Sfxn1	2810002O05Rik|A930015P12Rik|f	sideroflexin 1	protein-coding
mm_97602.1	chr11	78949650	78949663	+	1	NA	exon (NM_010927, exon 19 of 27)	exon (NM_010927, exon 19 of 27)	24365	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_96776.1	chr11	69935990	69936000	+	1	NA	promoter-TSS (NM_016875)	promoter-TSS (NM_016875)	96	NM_016875	53422	Mm.29286	NM_016875	ENSMUSG00000018554	Ybx2	Msy2	Y box protein 2	protein-coding
mm_169631.1	chr15	45140882	45140884	-	1	NA	Intergenic	ORR1A0|LTR|ERVL-MaLR	-25949	NM_026200	67498	Mm.300079	NM_026200	ENSMUSG00000022342	Kcnv1	2700023A03Rik|vibe	potassium channel, subfamily V, member 1	protein-coding
mm_111110.1	chr12	80958161	80958202	-	1	NA	exon (NM_001177561, exon 3 of 5)	exon (NM_001177561, exon 3 of 5)	9898	NM_011387	20493	Mm.486361	NM_011387	ENSMUSG00000021135	Slc10a1	Ntcp	solute carrier family 10 (sodium/bile acid cotransporter family), member 1	protein-coding
mm_45072.1	chr5	43867815	43867826	-	1	NA	promoter-TSS (NM_007646)	promoter-TSS (NM_007646)	-989	NM_007646	12494	Mm.249873	NM_007646	ENSMUSG00000029084	Cd38	ADPRC 1|Cd38-rs1|I-19	CD38 antigen	protein-coding
mm_48312.1	chr5	138754880	138754910	-	1	NA	promoter-TSS (NM_030565)	promoter-TSS (NM_030565)	-186	NM_030565	80752	Mm.320355	NM_030565	ENSMUSG00000025854	Fam20c	C76981|DMP-4|DMP4|GEF-CK|mKIAA4081	family with sequence similarity 20, member C	protein-coding
mm_84379.1	chr9	65398396	65398400	-	1	NA	promoter-TSS (NM_001162923)	promoter-TSS (NM_001162923)	-90	NM_001162923	70784	Mm.35827	NM_001033158	ENSMUSG00000041696	Rasl12	4631404I11Rik	RAS-like, family 12	protein-coding
mm_41739.1	chr5	102725167	102725190	+	1	NA	intron (NM_146161, intron 2 of 8)	intron (NM_146161, intron 2 of 8)	-43632	NM_001286468	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding
mm_19732.1	chr2	104494509	104494542	-	1	NA	promoter-TSS (NM_001145824)	promoter-TSS (NM_001145824)	-36	NM_001145824	15259	Mm.257925	NM_010434	ENSMUSG00000027177	Hipk3	DYRK6|FIST3|PKY|mir-1902	homeodomain interacting protein kinase 3	protein-coding
mm_154839.1	chrX	19202875	19202905	+	1	NA	Intergenic	Intergenic	-55919	NR_029807	723828		NR_029807	ENSMUSG00000065471	Mir222	Mirn222|mir-222|mmu-mir-222	microRNA 222	ncRNA
mm_42614.1	chr5	118010159	118010166	+	1	NA	TTS (NM_001346588)	TTS (NM_001346588)	-17662	NM_021344	57816	Mm.273285	NM_021344	ENSMUSG00000029359	Tesc	1010001A17Rik|2410011K10Rik|TE-1	tescalcin	protein-coding
mm_168730.1	chr12	113631041	113631053	-	1	NA	Intergenic	Intergenic	87139	NM_174885	238406	Mm.188683	NM_174885	ENSMUSG00000043945	Adam6a	Adam6|tMDCIV	a disintegrin and metallopeptidase domain 6A	protein-coding
mm_26266.1	chr3	142501590	142501611	+	1	NA	intron (NM_153564, intron 3 of 10)	RMER17C|LTR|ERVK	4666	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_140229.1	chr17	84002298	84002305	+	1	NA	intron (NR_130994, intron 1 of 1)	MT2A|LTR|ERVL	3749	NR_130994	78148	Mm.243918	NR_130994		8430430B14Rik	-	RIKEN cDNA 8430430B14 gene	ncRNA
mm_94949.1	chr11	29741460	29741482	+	1	NA	intron (NM_024226, intron 4 of 6)	intron (NM_024226, intron 4 of 6)	22908	NM_024226	68585	Mm.192580	NM_024226	ENSMUSG00000020458	Rtn4	1110020G17Rik|AA407876|AA409940|AA960376|ASY|C130026I10Rik|NOGO|NSP-CL|NgA|Nogo-A|Nogo-B|Nogo-C|mKIAA0886|mKIAA4153	reticulon 4	protein-coding
mm_33257.1	chr4	127168957	127168969	+	1	NA	promoter-TSS (NM_198618)	promoter-TSS (NM_198618)	-241	NM_198618	242667	Mm.331885	NM_198618	ENSMUSG00000042388	Dlgap3	BC058433|DAP-3|DAP3|Prpl8|Sapap3	discs, large (Drosophila) homolog-associated protein 3	protein-coding
mm_87981.1	chr10	63858851	63858854	+	1	NA	intron (NM_177612, intron 7 of 17)	intron (NM_177612, intron 7 of 17)	37797	NM_001164519	216033	Mm.444692	NM_177612	ENSMUSG00000060843	Ctnna3	4930429L08Rik|4933408A16|Catna3|Vr22	catenin (cadherin associated protein), alpha 3	protein-coding
mm_88877.1	chr10	81105919	81105932	+	1	NA	promoter-TSS (NM_001347144)	promoter-TSS (NM_001347144)	10	NM_001347144	26396	Mm.275436	NM_023138	ENSMUSG00000035027	Map2k2	AA589381|MEK2|MK2|Prkmk2	mitogen-activated protein kinase kinase 2	protein-coding
mm_136501.1	chr16	96441665	96441669	-	1	NA	intron (NM_008405, intron 1 of 15)	intron (NM_008405, intron 1 of 15)	1947	NM_008405	16415	Mm.12872	NM_008405	ENSMUSG00000000157	Itgb2l	5033406G21Rik|pactolus	integrin beta 2-like	protein-coding
mm_159695.1	chr5	24479642	24479642	+	1	NA	exon (NM_001256431, exon 8 of 9)	exon (NM_001256431, exon 8 of 9)	27465	NM_139153	213990	Mm.250703	NM_139153	ENSMUSG00000023353	Agap3	AGAP-3|AV028425|Centg3|Crag|Crag.|MRIP-1|cnt-g3	ArfGAP with GTPase domain, ankyrin repeat and PH domain 3	protein-coding
mm_168168.1	chr10	5289533	5289533	-	1	NA	exon (NM_001347711, exon 55 of 146)	exon (NM_001347711, exon 55 of 146)	-94826	NM_001079686	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_135059.1	chr16	34013441	34013444	-	1	NA	intron (NM_177357, intron 49 of 59)	intron (NM_177357, intron 49 of 59)	-46439	NM_009471	22247	Mm.13145	NM_009471	ENSMUSG00000022814	Umps	1700095D23Rik|AA408257|AL033308|BB164745	uridine monophosphate synthetase	protein-coding
mm_160438.1	chr8	94871138	94871138	-	1	NA	intron (NM_053246, intron 1 of 8)	C-rich|Low_complexity|Low_complexity	5174	NM_053246	114255	Mm.203949	NM_053246	ENSMUSG00000040631	Dok4	-	docking protein 4	protein-coding
mm_20268.1	chr2	126675539	126675572	-	1	NA	promoter-TSS (NM_010249)	promoter-TSS (NM_010249)	37	NM_001271469	14391	Mm.293266	NM_010249	ENSMUSG00000027361	Gabpb1	BABPB2|E4TF1|E4TF1-47|E4TF1-53|E4Tf1B|GABPB|GABPB-1|GABPB-2|GABPB1-1|GABPB1-2|NRF2B1|NRF2B2	GA repeat binding protein, beta 1	protein-coding
mm_29633.1	chr3	121758545	121758555	-	1	NA	TTS (NM_008991)	TTS (NM_008991)	35013	NM_010171	14066	Mm.273188	NM_010171	ENSMUSG00000028128	F3	AA409063|CD142|Cf-3|Cf3|TF	coagulation factor III	protein-coding
mm_127319.1	chr15	100280851	100280871	+	1	NA	promoter-TSS (NM_183109)	promoter-TSS (NM_183109)	24	NM_183109	75002	Mm.261400	NM_183109	ENSMUSG00000045631	Tmprss12	4930478A21Rik	transmembrane (C-terminal) protease, serine 12	protein-coding
mm_75338.1	chr8	43306346	43306351	-	1	NA	intron (NM_009556, intron 1 of 3)	B1_Mus1|SINE|Alu	661	NM_009556	22702	Mm.285848	NM_009556	ENSMUSG00000051176	Zfp42	Rex-1|Rex1|Zfp-42	zinc finger protein 42	protein-coding
mm_55881.1	chr6	83526916	83526933	-	1	NA	exon (NM_009610, exon 3 of 9)	exon (NM_009610, exon 3 of 9)	9327	NM_009610	11468	Mm.292865	NM_009610	ENSMUSG00000059430	Actg2	ACTA3|Act-4|Act4|SMGA	actin, gamma 2, smooth muscle, enteric	protein-coding
mm_3403.1	chr1	143777333	143777345	+	1	NA	promoter-TSS (NM_001159866)	promoter-TSS (NM_001159866)	61	NM_019562	56207	Mm.261004	NM_019562	ENSMUSG00000018189	Uchl5	5830413B11Rik|Uch37	ubiquitin carboxyl-terminal esterase L5	protein-coding
mm_131072.1	chr16	4684230	4684236	+	1	NA	exon (NM_023646, exon 1 of 12)	exon (NM_023646, exon 1 of 12)	163	NM_001135112	83945	Mm.248337	NM_023646	ENSMUSG00000004069	Dnaja3	1200003J13Rik|1810053A11Rik|C81173|Tid-1|Tid1l	DnaJ heat shock protein family (Hsp40) member A3	protein-coding
mm_141275.1	chr17	27820499	27820529	-	1	NA	promoter-TSS (NM_001271511)	promoter-TSS (NM_001271511)	28	NM_001033279	224647	Mm.196577	NM_001033279	ENSMUSG00000056692	D17Wsu92e	AU020189|C030010A15|C80239	DNA segment, Chr 17, Wayne State University 92, expressed	protein-coding
mm_155185.1	chrX	56317643	56317655	+	1	NA	promoter-TSS (NR_038168)	promoter-TSS (NR_038168)	41	NR_038168	72030	Mm.426148	NR_038168	ENSMUSG00000085114	1600025M17Rik	Gm394	RIKEN cDNA 1600025M17 gene	ncRNA
mm_57933.1	chr6	134632363	134632380	-	1	NA	5' UTR (NM_026345, exon 1 of 4)	5' UTR (NM_026345, exon 1 of 4)	117	NM_026345	67729	Mm.57648	NM_026345	ENSMUSG00000032718	Mansc1	9130403P13Rik	MANSC domain containing 1	protein-coding
mm_104460.1	chr11	95076567	95076589	-	1	NA	5' UTR (NM_001306162, exon 2 of 26)	5' UTR (NM_001306162, exon 2 of 26)	136	NM_013565	16400	Mm.57035	NM_013565	ENSMUSG00000001507	Itga3	AA407068|CD49C|GAPB3	integrin alpha 3	protein-coding
mm_68314.1	chr7	105787568	105787639	-	1	NA	promoter-TSS (NM_001162943)	promoter-TSS (NM_001162943)	-53	NM_001162943	233651	Mm.334108	NM_001162943	ENSMUSG00000036862	Dchs1	3110041P15Rik|C130033F22Rik|CDH25|FIB1|Gm165|PCDH16	dachsous 1 (Drosophila)	protein-coding
mm_139273.1	chr17	48185582	48185588	+	1	NA	Intergenic	RLTR51A_Mm|LTR|ERVK?	-18328	NM_178796	328830	Mm.470939	NM_178796	ENSMUSG00000043939	A530064D06Rik	Trem4|pdctrem	RIKEN cDNA A530064D06 gene	protein-coding
mm_119973.1	chr14	55559994	55560004	+	1	NA	promoter-TSS (NM_001199009)	promoter-TSS (NM_001199009)	-30	NR_037572	28199	Mm.11535	NM_133734	ENSMUSG00000022214	Dcaf11	0710008A13Rik|C76035|D14Ucla1|Dacf11|GLO14|Wdr23	DDB1 and CUL4 associated factor 11	protein-coding
mm_1594.1	chr1	74375144	74375172	+	1	NA	promoter-TSS (NM_013612)	promoter-TSS (NM_013612)	-45	NM_013612	18173	Mm.2913	NM_013612	ENSMUSG00000026177	Slc11a1	Bcg|Ity|Ity1|Lsh|Nramp|Nramp1|ity	solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1	protein-coding
mm_46840.1	chr5	113340050	113340085	-	1	NA	Intergenic	Intergenic	-2422	NR_106089	102466821		NR_106089	ENSMUSG00000104840	Mir7230	mmu-mir-7230	microRNA 7230	ncRNA
mm_77278.1	chr8	116677954	116677967	-	1	NA	intron (NM_029441, intron 1 of 6)	intron (NM_029441, intron 1 of 6)	55031	NM_029441	75796	Mm.159575	NM_029441	ENSMUSG00000031758	Cdyl2	1700029M19Rik|4930453I21Rik|Gm20194	chromodomain protein, Y chromosome-like 2	protein-coding
mm_18437.1	chr2	60881272	60881286	-	1	NA	5' UTR (NM_001141932, exon 1 of 15)	5' UTR (NM_001141932, exon 1 of 15)	159	NM_001141932	56878	Mm.259667	NM_020296	ENSMUSG00000026970	Rbms1	2600014B10Rik|AI255215|MSSP-1|MSSP-2|MSSP-3|YC1	RNA binding motif, single stranded interacting protein 1	protein-coding
mm_121961.1	chr14	25143240	25143261	-	1	NA	promoter-TSS (NR_045718)	promoter-TSS (NR_045718)	-9	NR_045718	75862	Mm.109191	NR_045718		4930572O13Rik	-	RIKEN cDNA 4930572O13 gene	ncRNA
mm_78938.1	chr9	45121198	45121213	+	1	NA	intron (NM_001014761, intron 1 of 3)	intron (NM_001014761, intron 1 of 3)	3329	NM_001014761	72821	Mm.229373	NM_001014761	ENSMUSG00000070304	Scn2b	2810451E09Rik|AI840361|Gm183	sodium channel, voltage-gated, type II, beta	protein-coding
mm_140443.1	chr17	88530289	88530297	+	1	NA	exon (NM_028658, exon 1 of 22)	exon (NM_028658, exon 1 of 22)	169	NM_028658	73825	Mm.271817	NM_028658	ENSMUSG00000034709	Ppp1r21	1110018J12Rik|AI426045|AW550781|Ccdc128|Klraq1	protein phosphatase 1, regulatory subunit 21	protein-coding
mm_36698.1	chr4	96664067	96664073	-	1	NA	promoter-TSS (NM_010007)	promoter-TSS (NM_010007)	49	NM_010007	13109	Mm.12838	NM_010007	ENSMUSG00000052520	Cyp2j5	-	cytochrome P450, family 2, subfamily j, polypeptide 5	protein-coding
mm_58425.1	chr7	3296806	3296821	+	1	NA	exon (NM_016969, exon 3 of 3)	exon (NM_016969, exon 3 of 3)	3785	NM_001093766	50918	Mm.29874	NM_016969	ENSMUSG00000068566	Myadm	D7Wsu62e	myeloid-associated differentiation marker	protein-coding
mm_57587.1	chr6	127732804	127732814	-	1	NA	exon (NM_201371, exon 2 of 10)	exon (NM_201371, exon 2 of 10)	36350	NM_201371	381813	Mm.39750	NM_201371	ENSMUSG00000030350	Prmt8	Hrmt1l3|Hrmt1l4	protein arginine N-methyltransferase 8	protein-coding
mm_135328.1	chr16	38800278	38800286	-	1	NA	promoter-TSS (NM_178924)	promoter-TSS (NM_178924)	-79	NM_178924	22268	Mm.130793	NM_178924	ENSMUSG00000049436	Upk1b	AI413235|Tspan20|UPIb|Upk1	uroplakin 1B	protein-coding
mm_21839.1	chr2	165793372	165793380	-	1	NA	intron (NM_027230, intron 20 of 23)	intron (NM_027230, intron 20 of 23)	64797	NM_001252585	228880	Mm.227598	NM_027230	ENSMUSG00000039671	Zmynd8	1110013E22Rik|2010005I16Rik|3632413B07Rik|AI316811|AL024039|Prkcbp1|RACK7	zinc finger, MYND-type containing 8	protein-coding
mm_69446.1	chr7	133005802	133005845	-	1	NA	intron (NM_001347623, intron 1 of 8)	intron (NM_001347623, intron 1 of 8)	9424	NM_001170744	13017	Mm.246240	NM_009980	ENSMUSG00000030970	Ctbp2	AA407280|D7Ertd45e|Gtrgeo6|Ribeye	C-terminal binding protein 2	protein-coding
mm_116378.1	chr13	41000915	41000940	-	1	NA	promoter-TSS (NM_026550)	promoter-TSS (NM_026550)	-83	NM_026550	68083	Mm.24789	NM_026550	ENSMUSG00000038683	Pak1ip1	5830431I15Rik|5930415H02Rik|AA419825|AI314040|AW556169|Gdpd1|PIP1	PAK1 interacting protein 1	protein-coding
mm_84469.1	chr9	66593107	66593120	-	1	NA	promoter-TSS (NM_144937)	promoter-TSS (NM_144937)	2	NM_144937	235441	Mm.32465	NM_144937	ENSMUSG00000032376	Usp3	AA409661|BC017156	ubiquitin specific peptidase 3	protein-coding
mm_124461.1	chr14	120806306	120806312	-	1	NA	Intergenic	Intergenic	-104885	NM_023579	70572	Mm.221452	NM_023579	ENSMUSG00000030662	Ipo5	1110011C18Rik|5730478E03Rik|AA409333|C76941|IMB3|Kpnb3|Ranbp5	importin 5	protein-coding
mm_41829.1	chr5	104092946	104093059	+	1	NA	exon (NM_010097, exon 4 of 11)	exon (NM_010097, exon 4 of 11)	-15394	NM_001163772	100271704	Mm.366664	NM_001163772	ENSMUSG00000091034	Gm17660	Scpppq1	predicted gene, 17660	protein-coding
mm_15267.1	chr2	155096057	155096063	+	1	NA	Intergenic	Intergenic	4019	NR_040634	100504268	Mm.410858	NR_040634	ENSMUSG00000087254	2310005A03Rik	-	RIKEN cDNA 2310005A03 gene	ncRNA
mm_152860.1	chr19	24200657	24200668	-	1	NA	intron (NM_011597, intron 1 of 22)	intron (NM_011597, intron 1 of 22)	24364	NM_011597	21873	Mm.104744	NM_011597	ENSMUSG00000024812	Tjp2	ZO-2	tight junction protein 2	protein-coding
mm_92546.1	chr10	79746085	79746088	-	1	NA	intron (NM_172551, intron 1 of 20)	PB1D10|SINE|Alu	495	NM_172551	216151	Mm.39001	NM_172551	ENSMUSG00000020329	Polrmt	1110018N15Rik|4932416K13	polymerase (RNA) mitochondrial (DNA directed)	protein-coding
mm_107325.1	chr12	31461697	31461704	+	1	NA	intron (NM_021353, intron 11 of 20)	intron (NM_021353, intron 11 of 20)	23481	NM_021353	13487	Mm.490454	NM_021353	ENSMUSG00000001225	Slc26a3	9030623B18Rik|9130013M11Rik|AV376035|Dra	solute carrier family 26, member 3	protein-coding
mm_146317.1	chr18	80555191	80555193	+	1	NA	Intergenic	Intergenic	-10646	NR_028424	100039348	Mm.254722	NR_028424		Gm2176	A430076E10Rik	glucosamine-6-phosphate deaminase 1 pseudogene	pseudo
mm_25320.1	chr3	106545881	106545899	+	1	NA	intron (NM_133869, intron 1 of 8)	intron (NM_133869, intron 1 of 8)	-1908	NM_001286986	67171	Mm.290488	NM_026013	ENSMUSG00000027900	Dram2	2010305N14Rik|2610318G18Rik|AI647667|Tmem77	DNA-damage regulated autophagy modulator 2	protein-coding
mm_36552.1	chr4	86749397	86749410	-	1	NA	intron (NM_184088, intron 1 of 31)	intron (NM_184088, intron 1 of 31)	848	NM_184088	329877	Mm.273718	NM_184088	ENSMUSG00000038024	Dennd4c	1700065A05Rik|AA420392	DENN/MADD domain containing 4C	protein-coding
mm_91862.1	chr10	59441802	59441808	-	1	NA	promoter-TSS (NM_010959)	promoter-TSS (NM_010959)	-26	NM_010959	18302	Mm.123013	NM_010959	ENSMUSG00000009654	Oit3	EF-9|LZP	oncoprotein induced transcript 3	protein-coding
mm_14117.1	chr2	125893336	125893342	+	1	NA	intron (NM_175154, intron 3 of 9)	intron (NM_175154, intron 3 of 9)	27116	NM_001291002	69976	Mm.20216	NM_175154	ENSMUSG00000027207	Galk2	2810017M24Rik|AI327030|Gk2	galactokinase 2	protein-coding
mm_43078.1	chr5	124446973	124446983	+	1	NA	intron (NM_001310727, intron 1 of 6)	intron (NM_001310727, intron 1 of 6)	274	NM_001310727	67956	Mm.137966	NM_030241	ENSMUSG00000049327	Kmt5a	2410195B05Rik|AA617402|AW536475|PR-SET7|PR/SET07|Setd8	lysine methyltransferase 5A	protein-coding
mm_22217.1	chr2	174327373	174327419	-	1	NA	promoter-TSS (NR_003258)	promoter-TSS (NR_003258)	-372	NM_001310083	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_103364.1	chr11	75071298	75071300	-	1	NA	intron (NM_001002764, intron 13 of 18)	intron (NM_001002764, intron 13 of 18)	-5308	NR_030454	735274		NR_030454	ENSMUSG00000106252	Mir684-1	Mirn684-1	microRNA 684-1	ncRNA
mm_109769.1	chr12	118847207	118847217	+	1	NA	intron (NM_177082, intron 1 of 2)	CpG	883	NM_177082	320145	Mm.51682	NM_177082	ENSMUSG00000048562	Sp8	D930049B17Rik|mBtd	trans-acting transcription factor 8	protein-coding
mm_165811.1	chr3	145758780	145758784	+	1	NA	promoter-TSS (NM_026993)	promoter-TSS (NM_026993)	90	NM_026993	69219	Mm.234247	NM_026993	ENSMUSG00000028194	Ddah1	2410006N07Rik|2510015N06Rik|AI987801|AW050362	dimethylarginine dimethylaminohydrolase 1	protein-coding
mm_37884.1	chr4	132510457	132510477	-	1	NA	promoter-TSS (NM_144907)	promoter-TSS (NM_144907)	-11	NM_144907	230784	Mm.23608	NM_144907	ENSMUSG00000028893	Sesn2	HI95|SEST2|Ses2	sestrin 2	protein-coding
mm_145968.1	chr18	67815488	67815501	+	1	NA	intron (NM_027556, intron 8 of 45)	intron (NM_027556, intron 8 of 45)	15387	NM_027556	70799	Mm.30857	NM_027556	ENSMUSG00000024542	Cep192	4631422C13Rik|D430014P18Rik	centrosomal protein 192	protein-coding
mm_165067.1	chr19	44407419	44407475	-	1	NA	5' UTR (NM_009127, exon 1 of 6)	5' UTR (NM_009127, exon 1 of 6)	262	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_34898.1	chr4	155626809	155626825	+	1	NA	exon (NM_007661, exon 3 of 20)	exon (NM_007661, exon 3 of 20)	1948	NM_007661	12537	Mm.267410	NM_007661	ENSMUSG00000029062	Cdk11b	AA989746|CDK11-p110|CDK11-p46|CDK11-p58|Cdc11b|Cdc2l1|Cdc2l2|Cdk11|p58	cyclin-dependent kinase 11B	protein-coding
mm_5437.1	chr1	34842940	34842944	-	1	NA	5' UTR (NM_001160236, exon 1 of 7)	5' UTR (NM_001160236, exon 1 of 7)	108	NM_001160235	214469	Mm.120151	NM_174997	ENSMUSG00000037503	Fam168b	mKIAA4042	family with sequence similarity 168, member B	protein-coding
mm_77733.1	chr8	126885657	126885672	-	1	NA	Intergenic	Intergenic	60257	NM_024214	67952	Mm.6932	NM_024214	ENSMUSG00000093904	Tomm20	1810060K07Rik|BB284719|Gm19268|MAS20|MOM19|TOM20|mKIAA0016	translocase of outer mitochondrial membrane 20 homolog (yeast)	protein-coding
mm_48815.1	chr5	149015792	149015800	-	1	NA	Intergenic	CpG	8834	NR_040429	100503307	Mm.188008	NR_040429	ENSMUSG00000086610	Gm15408	OTTMUSG00000021225	predicted gene 15408	ncRNA
mm_72846.1	chr8	88306610	88306622	+	1	NA	exon (NM_001037724, exon 4 of 28)	exon (NM_001037724, exon 4 of 28)	12412	NM_001037724	11513	Mm.288206	NM_007406	ENSMUSG00000031659	Adcy7	AA407758	adenylate cyclase 7	protein-coding
mm_129224.1	chr15	76607569	76607593	-	1	NA	promoter-TSS (NM_053193)	promoter-TSS (NM_053193)	10	NM_053193	94230	Mm.45141	NM_053193	ENSMUSG00000034022	Cpsf1	-	cleavage and polyadenylation specific factor 1	protein-coding
mm_119069.1	chr14	30825826	30825857	+	1	NA	exon (NM_028839, exon 1 of 8)	exon (NM_028839, exon 1 of 8)	247	NM_028839	69179	Mm.143025	NM_028839	ENSMUSG00000006526	Tmem110	1810038N08Rik|2310014H19Rik|AW554125|STIMATE	transmembrane protein 110	protein-coding
mm_16716.1	chr2	7144666	7144679	-	1	NA	intron (NM_001110231, intron 3 of 15)	B4|SINE|B4	-63370	NM_001160292	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_164056.1	chr14	106191005	106191005	+	1	NA	Intergenic	Intergenic	84807	NR_073203	212085	Mm.78128	NM_198601	ENSMUSG00000022113	Trim52	4921513B05Rik	tripartite motif-containing 52	protein-coding
mm_4051.1	chr1	165790184	165790186	+	1	NA	intron (NM_001113391, intron 1 of 7)	intron (NM_001113391, intron 1 of 7)	1504	NM_001113392	12503	Mm.217308	NM_031162	ENSMUSG00000005763	Cd247	4930549J05Rik|A430104F18Rik|AW552088|Cd3|Cd3-eta|Cd3-zeta|Cd3h|Cd3z|Cd3zeta|T3z|Tcrk|Tcrz	CD247 antigen	protein-coding
mm_27859.1	chr3	79157838	79157846	-	1	NA	Intergenic	L1_Mur3|LINE|L1	-11967	NM_001099624	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_28005.1	chr3	83012840	83012856	-	1	NA	exon (NM_133862, exon 8 of 10)	exon (NM_133862, exon 8 of 10)	5124	NM_001317105	99571	Mm.16422	NM_133862	ENSMUSG00000033860	Fgg	3010002H13Rik|AI256424	fibrinogen gamma chain	protein-coding
mm_87391.1	chr10	45107582	45107588	+	1	NA	intron (NM_011156, intron 6 of 14)	ORR1E|LTR|ERVL-MaLR	40371	NM_011156	19072	Mm.10281	NM_011156	ENSMUSG00000019849	Prep	AI047692|AI450383|D10Wsu136e|PEP|Pop	prolyl endopeptidase	protein-coding
mm_143335.1	chr17	66483866	66483876	-	1	NA	Intergenic	Intergenic	-34121	NM_001114098	68617	Mm.33421	NM_172963	ENSMUSG00000052105	Mtcl1	1110012J17Rik|Ccdc165|D130071O13|Kiaa0802|Soga2|mKIAA0802|t8219b25	microtubule crosslinking factor 1	protein-coding
mm_172848.1	chr9	36568464	36568464	-	1	NA	Intergenic	L1Md_T|LINE|L1	14171	NM_001167584	100312948	Mm.475849	NM_001167584	ENSMUSG00000091248	Gm17689	Pate-g|Pate8	predicted gene, 17689	protein-coding
mm_3195.1	chr1	135810895	135810933	+	1	NA	TTS (NM_021467)	TTS (NM_021467)	-7684	NM_133664	16763	Mm.36726	NM_133664	ENSMUSG00000041782	Lad1	-	ladinin	protein-coding
mm_6876.1	chr1	84363251	84363259	-	1	NA	Intergenic	Intergenic	-78610	NM_001003948	98496	Mm.187470	NM_001003948	ENSMUSG00000045658	Pid1	5033414K04Rik|NYGGF4	phosphotyrosine interaction domain containing 1	protein-coding
mm_69516.1	chr7	135196033	135196042	-	1	NA	promoter-TSS (NR_046050)	promoter-TSS (NR_046050)	-35	NR_046050	74314	Mm.415339	NR_046050	ENSMUSG00000100717	1700120G07Rik	-	RIKEN cDNA 1700120G07 gene	ncRNA
mm_45825.1	chr5	87694569	87694574	-	1	NA	exon (NM_001286023, exon 5 of 7)	exon (NM_001286023, exon 5 of 7)	4854	NM_001286020	12991	Mm.268737	NM_009972	ENSMUSG00000063157	Csn2	Csnb	casein beta	protein-coding
mm_105520.1	chr11	106300304	106300372	-	1	NA	TTS (NM_008117)	TTS (NM_008117)	1558	NM_008117	14599	Mm.343934	NM_008117	ENSMUSG00000020713	Gh	Gh1|Ghb1	growth hormone	protein-coding
mm_172167.1	chr6	44793147	44793147	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-266914	NM_001004357	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding
mm_47309.1	chr5	122456987	122456999	-	1	NA	non-coding (NR_027838, exon 20 of 21)	non-coding (NR_027838, exon 20 of 21)	34549	NM_019805	56317	Mm.37341	NM_019805	ENSMUSG00000029466	Anapc7	APC7|AW545589	anaphase promoting complex subunit 7	protein-coding
mm_83434.1	chr9	44999122	44999149	-	1	NA	3' UTR (NM_007648, exon 8 of 8)	3' UTR (NM_007648, exon 8 of 8)	10455	NM_007648	12501	Mm.210361	NM_007648	ENSMUSG00000032093	Cd3e	AI504783|CD3|CD3epsilon|T3e	CD3 antigen, epsilon polypeptide	protein-coding
mm_69903.1	chr7	141639503	141639529	-	1	NA	intron (NM_001330001, intron 31 of 33)	intron (NM_001330001, intron 31 of 33)	15803	NM_001330001	353328	Mm.246621	NM_181729	ENSMUSG00000048191	Muc6	-	mucin 6, gastric	protein-coding
mm_3801.1	chr1	157526100	157526119	+	1	NA	promoter-TSS (NM_001159986)	promoter-TSS (NM_001159986)	-61	NM_001159986	89867	Mm.87114	NM_033354	ENSMUSG00000026589	Sec16b	Lztr2|Rgpr|Rgpr-p117	SEC16 homolog B (S. cerevisiae)	protein-coding
mm_30381.1	chr3	152243976	152243987	-	1	NA	exon (NM_199465, exon 9 of 13)	exon (NM_199465, exon 9 of 13)	22339	NM_199465	68810	Mm.200188	NM_199465	ENSMUSG00000039103	Nexn	1110046H09Rik|AA553326|NELIN	nexilin	protein-coding
mm_37260.1	chr4	118437285	118437304	-	1	NA	promoter-TSS (NM_023223)	promoter-TSS (NM_023223)	49	NM_023223	107995	Mm.261764	NM_023223	ENSMUSG00000006398	Cdc20	2310042N09Rik|C87100|p55CDC	cell division cycle 20	protein-coding
mm_45010.1	chr5	38502108	38502126	-	1	NA	promoter-TSS (NM_145559)	promoter-TSS (NM_145559)	35	NM_145559	117591	Mm.260137	NM_145559	ENSMUSG00000005107	Slc2a9	Glut9|SLC2A9B|SLC2a9A	solute carrier family 2 (facilitated glucose transporter), member 9	protein-coding
mm_94363.1	chr11	5012570	5012580	+	1	NA	intron (NM_007454, intron 2 of 20)	intron (NM_007454, intron 2 of 20)	25751	NM_007454	11764	Mm.274816	NM_007454	ENSMUSG00000009090	Ap1b1	Adtb1|b2b1660Clo	adaptor protein complex AP-1, beta 1 subunit	protein-coding
mm_97744.1	chr11	80472381	80472417	+	1	NA	TTS (NM_178616)	TTS (NM_178616)	-4647	NM_009871	12569	Mm.142275	NM_009871	ENSMUSG00000048895	Cdk5r1	Cdk5r|D11Bwg0379e|p25|p35	cyclin-dependent kinase 5, regulatory subunit 1 (p35)	protein-coding
mm_119387.1	chr14	41136676	41136690	+	1	NA	TTS (NM_023134)	TTS (NM_023134)	4895	NM_023134	20387	Mm.46062	NM_023134	ENSMUSG00000021789	Sftpa1	SP-A|Sftp-1|Sftp1	surfactant associated protein A1	protein-coding
mm_45936.1	chr5	89883466	89883512	-	1	NA	promoter-TSS (NM_177872)	promoter-TSS (NM_177872)	-155	NM_001081401	330119	Mm.133062	NM_177872	ENSMUSG00000043635	Adamts3	1100001H14Rik|6330442E02Rik	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 3	protein-coding
mm_109517.1	chr12	111454412	111454423	+	1	NA	3' UTR (NM_009396, exon 12 of 12)	3' UTR (NM_009396, exon 12 of 12)	11756	NM_009396	21928	Mm.255332	NM_009396	ENSMUSG00000021281	Tnfaip2	B94|Exoc3l3|M-sec|Tnfip2|tnfb94	tumor necrosis factor, alpha-induced protein 2	protein-coding
mm_32518.1	chr4	108643142	108643150	+	1	NA	intron (NM_001347163, intron 17 of 18)	B4A|SINE|B4	23190	NM_177045	319965	Mm.151129	NM_177045	ENSMUSG00000028582	Cc2d1b	A830039B04Rik|Freud2	coiled-coil and C2 domain containing 1B	protein-coding
mm_27104.1	chr3	30599864	30599886	-	1	NA	promoter-TSS (NM_029690)	promoter-TSS (NM_029690)	-5	NM_029690	76652	Mm.116928	NM_029690	ENSMUSG00000037737	Actrt3	1700119I24Rik|ARP-T3|Arpm1	actin related protein T3	protein-coding
mm_72025.1	chr8	70755951	70755968	+	1	NA	exon (NM_001166399, exon 2 of 5)	exon (NM_001166399, exon 2 of 5)	1280	NM_001166399	19339	Mm.5083	NM_009001	ENSMUSG00000031840	Rab3a	-	RAB3A, member RAS oncogene family	protein-coding
mm_129743.1	chr15	82224365	82224379	-	1	NA	promoter-TSS (NM_028075)	promoter-TSS (NM_028075)	-36	NM_028075	72049	Mm.240047	NM_028075	ENSMUSG00000068105	Tnfrsf13c	2010006P15Rik|BAFF-R|Baffr|Bcmd|Bcmd-1|Bcmd1|Lvis22	tumor necrosis factor receptor superfamily, member 13c	protein-coding
mm_77019.1	chr8	108584354	108584360	-	1	NA	non-coding (NR_077224, exon 1 of 2)	non-coding (NR_077224, exon 1 of 2)	320	NR_077224	109215	Mm.65282	NR_077224	ENSMUSG00000110613	Lncbate1	3010033K07Rik|Lnc-BATE1	brown adipose tissue enriched long non-coding RNA 1	ncRNA
mm_105362.1	chr11	103132854	103132918	-	1	NA	promoter-TSS (NM_027658)	promoter-TSS (NM_027658)	-453	NM_001130516	71059	Mm.273871	NM_027658	ENSMUSG00000043372	Hexim2	4933402L21Rik	hexamethylene bis-acetamide inducible 2	protein-coding
mm_83938.1	chr9	56637343	56637359	-	1	NA	intron (NM_181074, intron 3 of 3)	MIRb|SINE|MIR	-1703	NM_001311076	235402	Mm.246605	NM_181074	ENSMUSG00000049556	Lingo1	4930471K13Rik|AV148400|LERN1|LINGO-1|Lrrn6a|UNQ201	leucine rich repeat and Ig domain containing 1	protein-coding
mm_94553.1	chr11	11484554	11484568	+	1	NA	intron (NM_001347068, intron 2 of 8)	Lx8|LINE|L1	-4705	NM_028669	73862	Mm.159077	NM_028669	ENSMUSG00000020191	4930415F15Rik	-	RIKEN cDNA 4930415F15 gene	protein-coding
mm_94665.1	chr11	17211897	17211908	+	1	NA	promoter-TSS (NM_178909)	promoter-TSS (NM_178909)	9	NM_178909	103784	Mm.298132	NM_178909	ENSMUSG00000078970	Wdr92	AI553587|HZGJ	WD repeat domain 92	protein-coding
mm_27024.1	chr3	26098722	26098722	-	1	NA	intron (NM_138666, intron 3 of 7)	L1Md_T|LINE|L1	54585	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_155738.1	chrX	96166552	96166564	+	1	NA	exon (NM_010833, exon 13 of 13)	exon (NM_010833, exon 13 of 13)	70513	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_84602.1	chr9	70090253	70090258	-	1	NA	3' UTR (NM_029784, exon 9 of 9)	3' UTR (NM_029784, exon 9 of 9)	51302	NM_029784	76886	Mm.44355	NM_029784	ENSMUSG00000032224	Fam81a	6430514L14Rik	family with sequence similarity 81, member A	protein-coding
mm_28326.1	chr3	89349940	89349959	-	1	NA	promoter-TSS (NM_001037722)	promoter-TSS (NM_001037722)	79	NM_001037722	11490	Mm.274049	NM_009614	ENSMUSG00000028041	Adam15	AD56|MDC15	a disintegrin and metallopeptidase domain 15 (metargidin)	protein-coding
mm_77213.1	chr8	114131579	114131595	-	1	NA	Intergenic	Intergenic	-1987	NM_024446	67528	Mm.27889	NM_024437	ENSMUSG00000031767	Nudt7	1300007B24Rik|2210404C19Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 7	protein-coding
mm_69048.1	chr7	126857316	126857343	-	1	NA	exon (NM_153580, exon 4 of 5)	exon (NM_153580, exon 4 of 5)	4134	NM_153580	233875	Mm.486253	NM_153580	ENSMUSG00000030689	Ino80e	AI225782|AI854876|Ccdc85|Ccdc95	INO80 complex subunit E	protein-coding
mm_118630.1	chr14	21271524	21271533	+	1	NA	intron (NM_001243041, intron 6 of 10)	intron (NM_001243041, intron 6 of 10)	195376	NM_001243041	11534	Mm.188734	NM_134079	ENSMUSG00000039197	Adk	2310026J05Rik|5033405D03Rik|AI255373|AI987814|Ak	adenosine kinase	protein-coding
mm_35155.1	chr4	12171760	12171770	-	1	NA	exon (NM_001310743, exon 1 of 8)	exon (NM_001310743, exon 1 of 8)	250	NM_001310743	68099	Mm.25340	NM_026558	ENSMUSG00000028218	Fam92a	6720467C03Rik|Fam92a1	family with sequence similarity 92, member A	protein-coding
mm_107803.1	chr12	64965792	64965810	+	1	NA	promoter-TSS (NM_177805)	promoter-TSS (NM_177805)	59	NM_177805	328108	Mm.138465	NM_177805	ENSMUSG00000035614	Fam179b	A430041B07Rik|BC062107|C130034K06|mKIAA0423	family with sequence similarity 179, member B	protein-coding
mm_13936.1	chr2	121140502	121140530	+	1	NA	promoter-TSS (NM_001290812)	promoter-TSS (NM_001290812)	88	NM_001290812	75894	Mm.384805	NM_029475	ENSMUSG00000027259	Adal	4930578F03Rik	adenosine deaminase-like	protein-coding
mm_125021.1	chr15	25708264	25708268	+	1	NA	intron (NM_019472, intron 3 of 40)	intron (NM_019472, intron 3 of 40)	85716	NM_019472	17909	Mm.60590	NM_019472	ENSMUSG00000022272	Myo10	AW048724|D15Ertd600e|mKIAA0799|myosin-X	myosin X	protein-coding
mm_6492.1	chr1	74181609	74181637	-	1	NA	Intergenic	Intergenic	13008	NM_178241	227288	Mm.337035	NM_178241	ENSMUSG00000048480	Cxcr1	Il8ra	chemokine (C-X-C motif) receptor 1	protein-coding
mm_164177.1	chr15	76210718	76210718	+	1	NA	intron (NM_011117, intron 1 of 31)	B4|SINE|B4	-1553	NM_201386	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
mm_81672.1	chr9	111032983	111032991	+	1	NA	intron (NM_008522, intron 13 of 16)	B3A|SINE|B2	13695	NM_008522	17002	Mm.282359	NM_008522	ENSMUSG00000032496	Ltf	Csp82|Lf|MMS10R|Ms10r	lactotransferrin	protein-coding
mm_72147.1	chr8	72144537	72144545	+	1	NA	intron (NM_001001491, intron 3 of 7)	intron (NM_001001491, intron 3 of 7)	9249	NM_001001491	326618	Mm.295124	NM_001001491	ENSMUSG00000031799	Tpm4	2610528G24Rik|Tpm4.2|Tpm4.2cy	tropomyosin 4	protein-coding
mm_67306.1	chr7	79386907	79386930	-	1	NA	5' UTR (NM_020599, exon 1 of 9)	5' UTR (NM_020599, exon 1 of 9)	109	NM_020599	19771	Mm.41653	NM_020599	ENSMUSG00000039194	Rlbp1	3110056M11Rik|CRALBP	retinaldehyde binding protein 1	protein-coding
mm_142010.1	chr17	35200366	35200378	-	1	NA	exon (NM_013693, exon 4 of 4)	exon (NM_013693, exon 4 of 4)	1635	NM_013693	21926	Mm.1293	NM_013693	ENSMUSG00000024401	Tnf	DIF|TNF-a|TNF-alpha|TNFSF2|TNFalpha|Tnfa|Tnfsf1a|Tnlg1f	tumor necrosis factor	protein-coding
mm_3103.1	chr1	134455525	134455564	+	1	NA	promoter-TSS (NM_153128)	promoter-TSS (NM_153128)	13	NM_001311136	240756	Mm.87398	NM_153128	ENSMUSG00000026455	Klhl12	C3ip1	kelch-like 12	protein-coding
mm_52105.1	chr6	97876541	97876569	+	1	NA	intron (NM_001113198, intron 1 of 9)	B4A|SINE|B4	-53262	NM_001178049	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_150878.1	chr19	45076192	45076195	+	1	NA	promoter-TSS (NM_178929)	promoter-TSS (NM_178929)	54	NM_178929	107250	Mm.24417	NM_178929	ENSMUSG00000025213	Kazald1	AI842353|Bono1|IGFBP-rP10	Kazal-type serine peptidase inhibitor domain 1	protein-coding
mm_53610.1	chr6	139599478	139599501	+	1	NA	Intergenic	Intergenic	-97580	NM_001128090	632971	Mm.475610	NM_001128090	ENSMUSG00000092164	Rergl	EG632971	RERG/RAS-like	protein-coding
mm_110502.1	chr12	54369306	54369355	-	1	NA	Intergenic	Intergenic	21988	NR_033689	665239	Mm.26856	NR_033689		Gm7550	EG665239|Gm666	predicted gene 7550	ncRNA
mm_122352.1	chr14	38833445	38833457	-	1	NA	intron (NM_001190187, intron 2 of 9)	Lx5c|LINE|L1	-64851	NR_045713	75170	Mm.372967	NR_045713	ENSMUSG00000093528	Nrg3os	4930529F24Rik	neuregulin 3, opposite strand	ncRNA
mm_81645.1	chr9	110951728	110951745	+	1	NA	intron (NM_028838, intron 1 of 8)	intron (NM_028838, intron 1 of 8)	191	NM_028838	74249	Mm.307615	NM_028838	ENSMUSG00000032495	Lrrc2	2400002D05Rik|4933431K03Rik	leucine rich repeat containing 2	protein-coding
mm_51748.1	chr6	87379364	87379374	+	1	NA	3' UTR (NM_025467, exon 6 of 6)	3' UTR (NM_025467, exon 6 of 6)	6004	NM_025467	66284	Mm.46446	NM_025467	ENSMUSG00000030049	Gkn2	1810036H07Rik|Bricd1b	gastrokine 2	protein-coding
mm_146274.1	chr18	77882251	77882261	+	1	NA	3' UTR (NM_013831, exon 15 of 15)	3' UTR (NM_013831, exon 15 of 15)	-56211	NM_001195633	100502841	Mm.297782	NM_001195633	ENSMUSG00000039840	Epg5	4732475F16|5430411K18Rik|AI661957|AW456499|mKIAA1632	ectopic P-granules autophagy protein 5 homolog (C. elegans)	protein-coding
mm_139054.1	chr17	46383544	46383566	+	1	NA	promoter-TSS (NM_021346)	promoter-TSS (NM_021346)	-211	NM_207671	57908	Mm.439916	NM_021346	ENSMUSG00000015597	Zfp318	2610034E08Rik|D530032D06Rik|TZF|Znf318	zinc finger protein 318	protein-coding
mm_146622.1	chr18	10125603	10125606	-	1	NA	intron (NM_009071, intron 9 of 32)	L1M4c|LINE|L1	56188	NM_009071	19877	Mm.6710	NM_009071	ENSMUSG00000024290	Rock1	1110055K06Rik|Rock-I	Rho-associated coiled-coil containing protein kinase 1	protein-coding
mm_44420.1	chr5	18799612	18799639	-	1	NA	Intergenic	RLTR9E|LTR|ERVK	426930	NR_102341	70832	Mm.398993	NR_102341	ENSMUSG00000097626	4921504A21Rik	-	RIKEN cDNA 4921504A21 gene	ncRNA
mm_9430.1	chr1	172500695	172500703	-	1	NA	intron (NM_178598, intron 1 of 4)	CpG	453	NM_178598	21346	Mm.271711	NM_178598	ENSMUSG00000026547	Tagln2	2700094C18Rik|SM22beta|Sm22B|Sm22a	transgelin 2	protein-coding
mm_116563.1	chr13	46929803	46929829	-	1	NA	promoter-TSS (NM_010617)	promoter-TSS (NM_010617)	-98	NM_010617	16553	Mm.342703	NM_010617	ENSMUSG00000021375	Kif13a	4930505I07Rik|mKIAA4109	kinesin family member 13A	protein-coding
mm_169113.1	chr13	48924458	48924471	+	1	NA	intron (NM_001033268, intron 5 of 17)	intron (NM_001033268, intron 5 of 17)	43364	NM_001033268	218236	Mm.426571	NM_001033268	ENSMUSG00000038014	Fam120a	C9orf10|Ossa	family with sequence similarity 120, member A	protein-coding
mm_38745.1	chr4	145270172	145270185	-	1	NA	intron (NM_009401, intron 12 of 12)	intron (NM_009401, intron 12 of 12)	-23308	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_156999.1	chrX	7567638	7567642	-	1	NA	intron (NM_138605, intron 1 of 3)	intron (NM_138605, intron 1 of 3)	-5960	NR_029473	78185	Mm.160055	NR_029473	ENSMUSG00000039545	Ppp1r3fos	4930524L23Rik	protein phosphatase 1, regulatory subunit 3F, opposite strand	ncRNA
mm_60136.1	chr7	37772843	37772871	+	1	NA	Intergenic	CpG	-3105	NM_172385	243937	Mm.322505	NM_172385	ENSMUSG00000043456	Zfp536	9630010P11Rik|Znf536|mKIAA0390	zinc finger protein 536	protein-coding
mm_125092.1	chr15	27488262	27488301	+	1	NA	intron (NM_020332, intron 1 of 11)	intron (NM_020332, intron 1 of 11)	21604	NM_020332	11732	Mm.265264	NM_020332	ENSMUSG00000022265	Ank	Ankh|D15Ertd221e|ank|mKIAA1581	progressive ankylosis	protein-coding
mm_56751.1	chr6	115994930	115994932	-	1	NA	promoter-TSS (NM_026376)	promoter-TSS (NM_026376)	74	NM_026376	67784	Mm.3085	NM_026376	ENSMUSG00000030123	Plxnd1	6230425C21Rik|b2b1863Clo|b2b553Clo	plexin D1	protein-coding
mm_166728.1	chr6	122487174	122487176	-	1	NA	promoter-TSS (NM_027664)	promoter-TSS (NM_027664)	-870	NM_027664	108653	Mm.277939	NM_027664	ENSMUSG00000040649	Rimklb	4931417E21Rik|4933426K21Rik|AA097693|AI325948|AU015629|Naags	ribosomal modification protein rimK-like family member B	protein-coding
mm_108027.1	chr12	73716174	73716184	+	1	NA	intron (NM_001313977, intron 10 of 14)	intron (NM_001313977, intron 10 of 14)	131383	NM_008856	18755	Mm.341677	NM_008856	ENSMUSG00000021108	Prkch	Pkch	protein kinase C, eta	protein-coding
mm_57966.1	chr6	135310350	135310370	-	1	NA	promoter-TSS (NM_029595)	promoter-TSS (NM_029595)	24	NM_029595	76400	Mm.293018	NM_029595	ENSMUSG00000047104	Pbp2	1700023A18Rik|AI326308|Pebp-2|Pebp2	phosphatidylethanolamine binding protein 2	protein-coding
mm_159990.1	chr6	116056889	116056889	-	1	NA	intron (NM_177412, intron 3 of 5)	intron (NM_177412, intron 3 of 5)	-61884	NM_026376	67784	Mm.3085	NM_026376	ENSMUSG00000030123	Plxnd1	6230425C21Rik|b2b1863Clo|b2b553Clo	plexin D1	protein-coding
mm_118567.1	chr14	18271309	18271321	+	1	NA	promoter-TSS (NM_025586)	promoter-TSS (NM_025586)	179	NM_023526	69721	Mm.25648	NM_023526	ENSMUSG00000021772	Nkiras1	2400004O09Rik|KBRAS1|kappaB-Ras1	NFKB inhibitor interacting Ras-like protein 1	protein-coding
mm_139844.1	chr17	69289720	69289727	+	1	NA	3' UTR (NM_013813, exon 22 of 22)	3' UTR (NM_013813, exon 22 of 22)	-12517	NR_045428	69750	Mm.439063	NR_045428	ENSMUSG00000100572	2410021H03Rik	-	RIKEN cDNA 2410021H03 gene	ncRNA
mm_30392.1	chr3	152248081	152248091	-	1	NA	exon (NM_199465, exon 7 of 13)	exon (NM_199465, exon 7 of 13)	18234	NM_199465	68810	Mm.200188	NM_199465	ENSMUSG00000039103	Nexn	1110046H09Rik|AA553326|NELIN	nexilin	protein-coding
mm_52353.1	chr6	112459650	112459652	+	1	NA	5' UTR (NM_007617, exon 1 of 2)	5' UTR (NM_007617, exon 1 of 2)	146	NM_007617	12391	Mm.3924	NM_007617	ENSMUSG00000062694	Cav3	AI385751|Cav-3|M-cav	caveolin 3	protein-coding
mm_26825.1	chr3	10346036	10346039	-	1	NA	intron (NM_025512, intron 4 of 7)	intron (NM_025512, intron 4 of 7)	5280	NM_001331015	66361	Mm.371617	NM_025512	ENSMUSG00000039795	Zfand1	2310008M20Rik|AW048890	zinc finger, AN1-type domain 1	protein-coding
mm_131309.1	chr16	11461906	11461912	+	1	NA	intron (NM_001290148, intron 6 of 13)	intron (NM_001290148, intron 6 of 13)	56261	NM_001290148	74478	Mm.325831	NM_028964	ENSMUSG00000071669	Snx29	4933437K13Rik|ENSMUSG00000079738|Gm11170|Gm1737|Gm930|Rundc2a	sorting nexin 29	protein-coding
mm_55751.1	chr6	78373232	78373242	-	1	NA	exon (NM_011036, exon 6 of 6)	exon (NM_011036, exon 6 of 6)	2352	NM_011036	18489	Mm.2553	NM_011036	ENSMUSG00000071356	Reg3b	HIP|PAP1|Pap|REG-III	regenerating islet-derived 3 beta	protein-coding
mm_36009.1	chr4	56802326	56802330	-	1	NA	promoter-TSS (NM_026079)	promoter-TSS (NM_026079)	-1	NM_001081420	230234	Mm.268148	NM_001081420	ENSMUSG00000038827	Fam206a	simiate	family with sequence similarity 206, member A	protein-coding
mm_90861.1	chr10	8885869	8885885	-	1	NA	5' UTR (NM_175155, exon 1 of 20)	5' UTR (NM_175155, exon 1 of 20)	193	NM_175155	70097	Mm.338275	NM_175155	ENSMUSG00000015305	Sash1	1100001C18Rik|2500002E12Rik|A330076K04Rik|mKIAA0790	SAM and SH3 domain containing 1	protein-coding
mm_81255.1	chr9	107992452	107992462	+	1	NA	Intergenic	Intergenic	-6541	NM_026597	68176	Mm.76166	NM_026597	ENSMUSG00000042106	Fam212a	6230427J02Rik|Inka1	family with sequence similarity 212, member A	protein-coding
mm_4670.1	chr1	180387743	180387772	+	1	NA	intron (NM_001081175, intron 2 of 7)	intron (NM_001081175, intron 2 of 7)	-57208	NR_003623	277333	Mm.389223	NM_199472		Gm5069	EG277333	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_79376.1	chr9	54699519	54699525	+	1	NA	promoter-TSS (NM_021422)	promoter-TSS (NM_021422)	-37	NM_021422	58233	Mm.489676	NM_021422	ENSMUSG00000032285	Dnaja4	1110021L12Rik|AV358213|Dj4|Hsj4|mmDjA4	DnaJ heat shock protein family (Hsp40) member A4	protein-coding
mm_120503.1	chr14	66223943	66223963	+	1	NA	intron (NM_001162365, intron 1 of 30)	intron (NM_001162365, intron 1 of 30)	-10401	NM_001162366	19229	Mm.21613	NM_172498	ENSMUSG00000059456	Ptk2b	CADTK|CAKB|CAKbeta|E430023O05Rik|FADK2|FAK2|PYK2|Raftk	PTK2 protein tyrosine kinase 2 beta	protein-coding
mm_28316.1	chr3	89279584	89279594	-	1	NA	promoter-TSS (NM_010107)	promoter-TSS (NM_010107)	56	NM_010107	13636	Mm.15675	NM_010107	ENSMUSG00000027954	Efna1	AI325262|B61|Efl1|Epl1|Eplg1|Lerk1	ephrin A1	protein-coding
mm_89445.1	chr10	93084204	93084238	+	1	NA	Intergenic	Intergenic	-2625	NM_001347060	380654	Mm.34980	NM_001347060	ENSMUSG00000020014	Cfap54	4930485B16Rik|Gm872	cilia and flagella associated protein 54	protein-coding
mm_125668.1	chr15	65810218	65810228	+	1	NA	intron (NM_133766, intron 1 of 22)	intron (NM_133766, intron 1 of 22)	23182	NM_133766	76740	Mm.260647	NM_133766	ENSMUSG00000015002	Efr3a	A130089M23Rik|BB071175|C76891|C920006C10Rik|D030063F01Rik|mKIAA0143	EFR3 homolog A	protein-coding
mm_65862.1	chr7	29354307	29354338	-	1	NA	intron (NM_001081028, intron 13 of 22)	intron (NM_001081028, intron 13 of 22)	50317	NM_013874	29861	Mm.101885	NM_013874	ENSMUSG00000030584	Dpf1	Neud4	D4, zinc and double PHD fingers family 1	protein-coding
mm_143645.1	chr17	79355049	79355073	-	1	NA	promoter-TSS (NM_026514)	promoter-TSS (NM_026514)	30	NM_026514	260409	Mm.140601	NM_026514	ENSMUSG00000036533	Cdc42ep3	3200001F04Rik|AA986861|Borg2|Cep3|UB1	CDC42 effector protein (Rho GTPase binding) 3	protein-coding
mm_167133.1	chr7	126976581	126976598	+	1	NA	5' UTR (NM_026638, exon 1 of 6)	5' UTR (NM_026638, exon 1 of 6)	675	NM_001347656	52858	Mm.28219	NM_026638	ENSMUSG00000030682	Cdipt	9530042F15Rik|D7Bwg0575e|Pis|Pis1	CDP-diacylglycerol--inositol 3-phosphatidyltransferase (phosphatidylinositol synthase)	protein-coding
mm_15466.1	chr2	157457871	157457878	+	1	NA	intron (NM_009271, intron 4 of 14)	intron (NM_009271, intron 4 of 14)	33581	NM_001025395	20779	Mm.22845	NM_009271	ENSMUSG00000027646	Src	AW259666|pp60c-src	Rous sarcoma oncogene	protein-coding
mm_3450.1	chr1	150103050	150103065	+	1	NA	intron (NM_011198, intron 5 of 9)	intron (NM_011198, intron 5 of 9)	3026	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_87999.1	chr10	66997201	66997203	+	1	NA	Intergenic	B1_Mur4|SINE|Alu	-7873	NR_110511	102634101	Mm.445258	NR_110511		Gm31763	-	predicted gene, 31763	ncRNA
mm_17813.1	chr2	33718748	33718759	-	1	NA	Intergenic	Intergenic	77560	NR_046275	100504399	Mm.72070	NM_177842		C130021I20Rik	-	Riken cDNA C130021I20 gene	ncRNA
mm_136959.1	chr17	15499909	15499959	+	1	NA	promoter-TSS (NM_013684)	promoter-TSS (NM_013684)	46	NM_013684	21374	Mm.244820	NM_013684	ENSMUSG00000014767	Tbp	GTF2D1|Gtf2d|SCA17|TFIID	TATA box binding protein	protein-coding
mm_44559.1	chr5	24603115	24603122	-	1	NA	Intergenic	Intergenic	-1116	NM_025891	66993	Mm.436539	NM_025891	ENSMUSG00000028949	Smarcd3	1500001J14Rik|2210409C08Rik|BAF60C	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3	protein-coding
mm_63414.1	chr7	127448657	127448707	+	1	NA	exon (NM_175163, exon 1 of 3)	exon (NM_175163, exon 1 of 3)	476	NM_175163	71131	Mm.474533	NM_175163	ENSMUSG00000048921	Zfp689	4933416E05Rik|Znf689	zinc finger protein 689	protein-coding
mm_157620.1	chrX	56549620	56549622	-	1	NA	promoter-TSS (NM_001033372)	promoter-TSS (NM_001033372)	-15	NM_001033372	270599	Mm.424438	NM_001033372	ENSMUSG00000064016	Gm648	-	predicted gene 648	protein-coding
mm_75974.1	chr8	72136730	72136751	-	1	NA	intron (NM_001001491, intron 1 of 7)	intron (NM_001001491, intron 1 of 7)	1448	NM_001001491	326618	Mm.295124	NM_001001491	ENSMUSG00000031799	Tpm4	2610528G24Rik|Tpm4.2|Tpm4.2cy	tropomyosin 4	protein-coding
mm_118500.1	chr14	13454195	13454233	+	1	NA	5' UTR (NM_001163032, exon 1 of 5)	5' UTR (NM_001163032, exon 1 of 5)	256	NM_001163032	72003	Mm.317515	NM_028052	ENSMUSG00000056296	Synpr	1500003F20Rik|SPO	synaptoporin	protein-coding
mm_93322.1	chr10	99132369	99132393	-	1	NA	intron (NM_027740, intron 4 of 11)	intron (NM_027740, intron 4 of 11)	24246	NM_015737	14426	Mm.314	NM_015737	ENSMUSG00000090035	Galnt4	AV011803	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 4	protein-coding
mm_2615.1	chr1	120485885	120485909	+	1	NA	exon (NM_010766, exon 9 of 17)	exon (NM_010766, exon 9 of 17)	19187	NM_010766	17167	Mm.1856	NM_010766	ENSMUSG00000026390	Marco	AI323439|Ly112|Scara2	macrophage receptor with collagenous structure	protein-coding
mm_44763.1	chr5	31596718	31596738	-	1	NA	Intergenic	Intergenic	-17223	NM_025796	66845	Mm.120763	NM_025796	ENSMUSG00000106918	Mrpl33	0610009M10Rik|L33mt|MRP-L33	mitochondrial ribosomal protein L33	protein-coding
mm_61321.1	chr7	68189565	68189586	+	1	NA	exon (NM_010513, exon 9 of 21)	exon (NM_010513, exon 9 of 21)	74658	NM_030101	78444	Mm.425468	NM_030101	ENSMUSG00000030553	Pgpep1l	C330024D12Rik	pyroglutamyl-peptidase I-like	protein-coding
mm_99110.1	chr11	100135378	100135421	+	1	NA	exon (NM_008469, exon 1 of 8)	exon (NM_008469, exon 1 of 8)	550	NM_008469	16665	Mm.440010	NM_008469	ENSMUSG00000054146	Krt15	AI528832|K15|Krt1-15	keratin 15	protein-coding
mm_1994.1	chr1	87126726	87126731	+	1	NA	exon (NM_007432, exon 8 of 11)	exon (NM_007432, exon 8 of 11)	1720	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_113908.1	chr13	49341532	49341543	+	1	NA	promoter-TSS (NM_029791)	promoter-TSS (NM_029791)	-12	NM_001039179	76895	Mm.197387	NM_029791	ENSMUSG00000037933	Bicd2	-	bicaudal D homolog 2 (Drosophila)	protein-coding
mm_80235.1	chr9	72679260	72679263	+	1	NA	intron (NM_010890, intron 5 of 28)	intron (NM_010890, intron 5 of 28)	16914	NM_010890	17999	Mm.279923	NM_010890	ENSMUSG00000032216	Nedd4	AA959633|AL023035|AU019897|E430025J12Rik|Nedd4-1|Nedd4a|mKIAA0093	neural precursor cell expressed, developmentally down-regulated 4	protein-coding
mm_96721.1	chr11	69665712	69665842	+	1	NA	exon (NM_001291058, exon 2 of 6)	exon (NM_001291058, exon 2 of 6)	393	NM_001291058	12514	Mm.15819	NM_009853	ENSMUSG00000018774	Cd68	Lamp4|Scard1|gp110	CD68 antigen	protein-coding
mm_88505.1	chr10	77864608	77864643	+	1	NA	intron (NM_001287074, intron 2 of 11)	intron (NM_001287074, intron 2 of 11)	2650	NM_001101631	100041351	Mm.441672	NM_001101631		Gm3285	-	predicted gene 3285	protein-coding
mm_114556.1	chr13	74122519	74122534	+	1	NA	intron (NM_001081060, intron 1 of 15)	(T)n|Simple_repeat|Simple_repeat	1011	NM_001081060	105243	Mm.261564	NM_001081060	ENSMUSG00000036123	Slc9a3	9030624O13Rik|AI930210|NHE-3|NHE3	solute carrier family 9 (sodium/hydrogen exchanger), member 3	protein-coding
mm_141112.1	chr17	26081612	26081621	-	1	NA	3' UTR (NM_011933, exon 9 of 9)	3' UTR (NM_011933, exon 9 of 9)	8548	NM_011933	26378	Mm.292869	NM_011933	ENSMUSG00000036775	Decr2	-	2-4-dienoyl-Coenzyme A reductase 2, peroxisomal	protein-coding
mm_125943.1	chr15	76248279	76248298	+	1	NA	promoter-TSS (NR_105918)	promoter-TSS (NR_105918)	97	NR_105918	102465575		NR_105918	ENSMUSG00000098625	Mir6953	Gm27738|mmu-mir-6953	microRNA 6953	ncRNA
mm_95535.1	chr11	52256252	52256283	+	1	NA	exon (NM_009331, exon 9 of 10)	exon (NM_009331, exon 9 of 10)	24272	NM_011543	21402	Mm.42944	NM_011543	ENSMUSG00000036309	Skp1a	15kDa|2610043E24Rik|2610206H23Rik|EMC19|OCP-II|OCP2|SKP1|Tceb1l|p19A|p19Skp1	S-phase kinase-associated protein 1A	protein-coding
mm_89114.1	chr10	84708183	84708187	+	1	NA	intron (NM_027423, intron 23 of 27)	intron (NM_027423, intron 23 of 27)	-47863	NM_001024918	71137	Mm.79070	NM_027689	ENSMUSG00000020037	Rfx4	4933412G19Rik|NYD-sp10	regulatory factor X, 4 (influences HLA class II expression)	protein-coding
mm_143384.1	chr17	67967074	67967075	-	1	NA	intron (NM_172964, intron 1 of 17)	intron (NM_172964, intron 1 of 17)	-16134	NM_001347410	268970	Mm.9935	NM_172964	ENSMUSG00000024043	Arhgap28	AU044757|AW550892|E130310N06	Rho GTPase activating protein 28	protein-coding
mm_54828.1	chr6	42585805	42585832	-	1	NA	Intergenic	Intergenic	11554	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_11596.1	chr2	33468088	33468115	+	1	NA	intron (NM_001025594, intron 1 of 2)	intron (NM_001025594, intron 1 of 2)	431	NM_027947	71834	Mm.44186	NM_027947	ENSMUSG00000026788	Zbtb43	1700010E06Rik|Zfp297b|mKIAA0414	zinc finger and BTB domain containing 43	protein-coding
mm_155716.1	chrX	96099460	96099465	+	1	NA	intron (NM_010833, intron 1 of 12)	PB1D7|SINE|Alu	3417	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_54377.1	chr6	31205947	31205951	-	1	NA	intron (NR_110469, intron 1 of 3)	intron (NR_110469, intron 1 of 3)	12525	NR_110470	232685	Mm.443019	NM_144555	ENSMUSG00000044471	Lncpint	Lincpint|MNCb-1768|Pint|linc-Pint	long non-protein coding RNA, Trp53 induced transcript	ncRNA
mm_77682.1	chr8	125699478	125699486	-	1	NA	Intergenic	RLTR41C|LTR|ERV1	29664	NM_028908	74393	Mm.41709	NM_028908	ENSMUSG00000050930	Map10	4933403G14Rik|AI835009|mKIAA1383	microtubule-associated protein 10	protein-coding
mm_147312.1	chr18	41951162	41951180	-	1	NA	promoter-TSS (NM_029942)	promoter-TSS (NM_029942)	23	NM_029942	77619	Mm.30649	NM_029942	ENSMUSG00000056671	Prelid2	1700003A01Rik|C330008K14Rik	PRELI domain containing 2	protein-coding
mm_10519.1	chr2	16360991	16361040	+	1	NA	intron (NM_026162, intron 1 of 13)	B1_Mus1|SINE|Alu	4711	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding
mm_14170.1	chr2	126675298	126675347	+	1	NA	intron (NM_001271470, intron 1 of 8)	CpG	270	NM_001271469	14391	Mm.293266	NM_010249	ENSMUSG00000027361	Gabpb1	BABPB2|E4TF1|E4TF1-47|E4TF1-53|E4Tf1B|GABPB|GABPB-1|GABPB-2|GABPB1-1|GABPB1-2|NRF2B1|NRF2B2	GA repeat binding protein, beta 1	protein-coding
mm_24902.1	chr3	96184733	96184759	+	1	NA	5' UTR (NM_022030, exon 2 of 13)	5' UTR (NM_022030, exon 2 of 13)	3519	NM_022030	64051	Mm.491135	NM_022030	ENSMUSG00000038486	Sv2a	AI746429|mKIAA0736	synaptic vesicle glycoprotein 2 a	protein-coding
mm_60965.1	chr7	47747317	47747347	+	1	NA	Intergenic	Intergenic	-145960	NM_153067	233222	Mm.240142	NM_153067	ENSMUSG00000078698	Mrgpra3	Mrga3	MAS-related GPR, member A3	protein-coding
mm_93827.1	chr10	121553942	121553963	-	1	NA	exon (NM_019786, exon 14 of 21)	exon (NM_019786, exon 14 of 21)	32842	NM_019786	56480	Mm.34580	NM_019786	ENSMUSG00000020115	Tbk1	1200008B05Rik|AI462036|AW048562	TANK-binding kinase 1	protein-coding
mm_159052.1	chr1	189344183	189344183	-	1	NA	promoter-TSS (NM_001281847)	promoter-TSS (NM_001281847)	9	NM_001281847	16526	Mm.33304	NM_010607	ENSMUSG00000037624	Kcnk2	A430027H14Rik|AI848635|TREK-1	potassium channel, subfamily K, member 2	protein-coding
mm_127882.1	chr15	8642282	8642292	-	1	NA	exon (NM_148938, exon 8 of 10)	exon (NM_148938, exon 8 of 10)	68520	NM_148938	20512	Mm.204834	NM_148938	ENSMUSG00000005360	Slc1a3	AI504299|B430115D02Rik|Eaat1|GLAST|GLAST-1|GLU-T|GluT-1|Gmt1|MGluT1	solute carrier family 1 (glial high affinity glutamate transporter), member 3	protein-coding
mm_109851.1	chr12	4712216	4712258	-	1	NA	intron (NM_011365, intron 37 of 38)	intron (NM_011365, intron 37 of 38)	26146	NM_029107	74855	Mm.269534	NM_029107	ENSMUSG00000079177	Fam228a	4930417G10Rik	family with sequence similarity 228, member A	protein-coding
mm_124893.1	chr15	10346485	10346491	+	1	NA	TTS (NM_001253782)	TTS (NM_001253782)	-12045	NM_001310736	268782	Mm.482244	NM_001031851	ENSMUSG00000089678	Agxt2	AI303810|AI663818	alanine-glyoxylate aminotransferase 2	protein-coding
mm_2204.1	chr1	89580231	89580242	+	1	NA	intron (NM_001037136, intron 1 of 16)	GC_rich|Low_complexity|Low_complexity	103656	NR_015540	74403	Mm.444291	NR_015540		4933400F21Rik	1700091C04Rik|4930565K10Rik	RIKEN cDNA 4933400F21 gene	ncRNA
mm_164300.1	chr15	103897361	103897369	-	1	NA	exon (NM_009267, exon 3 of 4)	exon (NM_009267, exon 3 of 4)	1935	NM_009268	20771	Mm.30276	NM_009268		Mucl1	Spt-2|Spt2	mucin-like 1	protein-coding
mm_148518.1	chr19	4237021	4237021	+	1	NA	Intergenic	Intergenic	4606	NR_132280	69745	Mm.32518	NM_027196	ENSMUSG00000024854	Pold4	2410012M21Rik|AI463381|AW060307|Polds|p12	polymerase (DNA-directed), delta 4	protein-coding
mm_26973.1	chr3	24858226	24858236	-	1	NA	Intergenic	Intergenic	-74225	NM_001326288	635702	Mm.448351	NM_001326288	ENSMUSG00000102758	Naaladl2	2810043G22Rik|EG635702|Gm1021	N-acetylated alpha-linked acidic dipeptidase-like 2	protein-coding
mm_77210.1	chr8	114014412	114014416	-	1	NA	Intergenic	RMER19C|LTR|ERVK	-119160	NM_024446	67528	Mm.27889	NM_024437	ENSMUSG00000031767	Nudt7	1300007B24Rik|2210404C19Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 7	protein-coding
mm_122046.1	chr14	30056326	30056339	-	1	NA	intron (NM_001302637, intron 41 of 48)	intron (NM_001302637, intron 41 of 48)	33699	NM_175343	218865	Mm.259916	NM_172264	ENSMUSG00000015970	Chdh	AU041472|D630034H06Rik	choline dehydrogenase	protein-coding
mm_145773.1	chr18	65025984	65026004	+	1	NA	intron (NM_031881, intron 1 of 29)	intron (NM_031881, intron 1 of 29)	2467	NM_031881	83814	Mm.98668	NM_031881	ENSMUSG00000024589	Nedd4l	1300012C07Rik|Nedd4-2|Nedd4b	neural precursor cell expressed, developmentally down-regulated gene 4-like	protein-coding
mm_157956.1	chrX	87779697	87779700	-	1	NA	intron (NM_001160403, intron 2 of 10)	A-rich|Low_complexity|Low_complexity	335925	NM_001160403	331461	Mm.121680	NM_001160403	ENSMUSG00000052372	Il1rapl1	6330532G10Rik|C030039N24|IL1R8|IL1RAPL|MRX34|OPHN4|TIGIRR-2	interleukin 1 receptor accessory protein-like 1	protein-coding
mm_9311.1	chr1	171641174	171641180	-	1	NA	TTS (NR_106151)	TTS (NR_106151)	723	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_117220.1	chr13	64129306	64129348	-	1	NA	promoter-TSS (NM_001001321)	promoter-TSS (NM_001001321)	3	NM_001001321	70484	Mm.133731	NM_001001321	ENSMUSG00000033114	Slc35d2	5730408I21Rik|SQV7L|UGTrel8|hfrc|mUGTrel8	solute carrier family 35, member D2	protein-coding
mm_144823.1	chr18	36343082	36343116	+	1	NA	Intergenic	Intergenic	-5525	NM_001081365	66060	Mm.272527	NM_001081365	ENSMUSG00000046727	Cystm1	0610010O12Rik	cysteine-rich transmembrane module containing 1	protein-coding
mm_134109.1	chr16	9995563	9995581	-	1	NA	Intergenic	CpG	-3039	NM_008170	14811	Mm.2953	NM_008170	ENSMUSG00000059003	Grin2a	GluN2A|NMDAR2A|NR2A	glutamate receptor, ionotropic, NMDA2A (epsilon 1)	protein-coding
mm_170962.1	chr2	57553141	57553156	+	1	NA	Intergenic	L1Md_A|LINE|L1	314766	NM_010274	14571	Mm.3711	NM_010274	ENSMUSG00000026827	Gpd2	AA408484|AI448216|AU021455|AW494132|GPDH|Gdm1|Gpd-m|Gpdh-m|TISP38	glycerol phosphate dehydrogenase 2, mitochondrial	protein-coding
mm_60546.1	chr7	44480673	44480712	+	1	NA	Intergenic	Intergenic	-3825	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_164984.1	chr19	10101257	10101269	-	1	NA	exon (NM_019699, exon 1 of 12)	exon (NM_019699, exon 1 of 12)	240	NM_019699	56473	Mm.38901	NM_019699	ENSMUSG00000024665	Fads2	2900042M13Rik|Fadsd2	fatty acid desaturase 2	protein-coding
mm_162214.1	chrX	136742893	136742893	-	1	NA	promoter-TSS (NM_001168227)	promoter-TSS (NM_001168227)	25	NM_001168227	56397	Mm.27218	NM_019768	ENSMUSG00000031422	Morf4l2	2410017O14Rik|Mrgx|Sid393p|mKIAA0026	mortality factor 4 like 2	protein-coding
mm_172265.1	chr6	75298133	75298138	-	1	NA	Intergenic	Intergenic	-1827114	NR_108032	73408	Mm.233629	NR_108032	ENSMUSG00000107408	1700065L07Rik	-	RIKEN cDNA 1700065L07 gene	ncRNA
mm_143668.1	chr17	79895958	79895966	-	1	NA	exon (NM_019717, exon 1 of 13)	exon (NM_019717, exon 1 of 13)	161	NM_178050	56298	Mm.175403	NM_019717	ENSMUSG00000059811	Atl2	2010110I21Rik|AA407293|AV334690|Aip-2|Arl6ip2	atlastin GTPase 2	protein-coding
mm_36800.1	chr4	103173354	103173364	-	1	NA	3' UTR (NM_177732, exon 10 of 10)	3' UTR (NM_177732, exon 10 of 10)	41525	NM_177732	242585	Mm.281800	NM_177732	ENSMUSG00000028521	Slc35d1	AI834976|C330011J09|UGTREL7|mKIAA0260	solute carrier family 35 (UDP-glucuronic acid/UDP-N-acetylgalactosamine dual transporter), member D1	protein-coding
mm_14590.1	chr2	136057887	136057895	+	1	NA	promoter-TSS (NM_029530)	promoter-TSS (NM_029530)	-36	NM_029530	76161	Mm.41638	NM_029530	ENSMUSG00000027270	Lamp5	3110035N03Rik|6330527O06Rik|BAD-LAMP|LAMP-5	lysosomal-associated membrane protein family, member 5	protein-coding
mm_108687.1	chr12	86867698	86867742	+	1	NA	Intergenic	Intergenic	17094	NM_145836	238330	Mm.248358	NM_145836	ENSMUSG00000034168	Irf2bpl	6430527G18Rik|Eap1	interferon regulatory factor 2 binding protein-like	protein-coding
mm_40375.1	chr5	52363926	52363955	+	1	NA	5' UTR (NM_011435, exon 1 of 2)	5' UTR (NM_011435, exon 1 of 2)	136	NM_011435	20657	Mm.2407	NM_011435	ENSMUSG00000072941	Sod3	AI314465|EC-SOD	superoxide dismutase 3, extracellular	protein-coding
mm_50225.1	chr6	42350622	42350634	+	1	NA	intron (NM_001289619, intron 2 of 8)	intron (NM_001289619, intron 2 of 8)	800	NM_001289619	22793	Mm.282303	NM_011777	ENSMUSG00000029860	Zyx	9530098H06Rik|R75157	zyxin	protein-coding
mm_63978.1	chr7	139975737	139975765	+	1	NA	intron (NM_001347613, intron 5 of 5)	intron (NM_001347613, intron 5 of 5)	3004	NM_001347614	381933	Mm.440431	NM_001033465	ENSMUSG00000073795	6430531B16Rik	Gm1093	RIKEN cDNA 6430531B16 gene	protein-coding
mm_173033.1	chrX	105889040	105889046	-	1	NA	exon (NM_009530, exon 4 of 35)	exon (NM_009530, exon 4 of 35)	40329	NM_009530	22589	Mm.10141	NM_009530	ENSMUSG00000031229	Atrx	4833408C14Rik|AI447451|ATR2|DXHXS6677E|HP1-BP38|Hp1bp2|Hp1bp38|MRXS3|RAD54L|Rad54|XH2|Xnp|ZNF-HX	alpha thalassemia/mental retardation syndrome X-linked	protein-coding
mm_106689.1	chr12	3365144	3365207	+	1	NA	promoter-TSS (NM_008445)	promoter-TSS (NM_008445)	43	NM_008445	16570	Mm.7688	NM_008445	ENSMUSG00000020668	Kif3c	mKIAA4058	kinesin family member 3C	protein-coding
mm_32307.1	chr4	103164642	103164645	+	1	NA	3' UTR (NM_027696, exon 15 of 15)	3' UTR (NM_027696, exon 15 of 15)	45253	NM_001039081	71148	Mm.288721	NM_027696	ENSMUSG00000028522	Mier1	4933425I22Rik|5830411K19Rik|er1	MEIR1 treanscription regulator	protein-coding
mm_105099.1	chr11	100939556	100939566	-	1	NA	promoter-TSS (NM_011486)	promoter-TSS (NM_011486)	-21	NM_011486	20848	Mm.249934	NM_011486	ENSMUSG00000004040	Stat3	1110034C02Rik|AW109958|Aprf	signal transducer and activator of transcription 3	protein-coding
mm_157102.1	chrX	9437652	9437662	-	1	NA	3' UTR (NM_007807, exon 13 of 13)	3' UTR (NM_007807, exon 13 of 13)	31667	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_95641.1	chr11	53720011	53720027	+	1	NA	promoter-TSS (NM_010558)	promoter-TSS (NM_010558)	-775	NM_010558	16191	Mm.4461	NM_010558	ENSMUSG00000036117	Il5	Il-5	interleukin 5	protein-coding
mm_136914.1	chr17	13017201	13017213	+	1	NA	3' UTR (NM_013671, exon 5 of 5)	3' UTR (NM_013671, exon 5 of 5)	9368	NM_013671	20656	Mm.290876	NM_013671	ENSMUSG00000006818	Sod2	MnSOD|Sod-2	superoxide dismutase 2, mitochondrial	protein-coding
mm_1885.1	chr1	85670913	85670919	+	1	NA	intron (NM_001313713, intron 7 of 15)	L1MA7|LINE|L1	20928	NM_001313714	20684	Mm.290906	NM_013673	ENSMUSG00000026222	Sp100	A430075G10Rik	nuclear antigen Sp100	protein-coding
mm_68529.1	chr7	113207093	113207111	-	1	NA	promoter-TSS (NM_007489)	promoter-TSS (NM_007489)	-363	NM_001243048	11865	Mm.33970	NM_007489	ENSMUSG00000055116	Arntl	Arnt3|BMAL1b|Bmal1|MOP3|bHLHe5|bmal1b'	aryl hydrocarbon receptor nuclear translocator-like	protein-coding
mm_47590.1	chr5	124862130	124862148	-	1	NA	promoter-TSS (NM_001081750)	promoter-TSS (NM_001081750)	82	NM_144819	215707	Mm.389693	NM_144819	ENSMUSG00000037979	Ccdc92	AW050178|D5Bwg0834e	coiled-coil domain containing 92	protein-coding
mm_164193.1	chr15	78877456	78877482	-	1	NA	5' UTR (NM_145929, exon 1 of 17)	5' UTR (NM_145929, exon 1 of 17)	279	NM_145929	106039	Mm.251331	NM_145929	ENSMUSG00000033128	Gga1	4930406E12Rik|AU016030|AW209092	golgi associated, gamma adaptin ear containing, ARF binding protein 1	protein-coding
mm_166469.1	chr5	142794687	142794697	-	1	NA	intron (NM_178242, intron 2 of 15)	intron (NM_178242, intron 2 of 15)	22695	NM_178242	231861	Mm.354649	NM_178242	ENSMUSG00000039477	Tnrc18	BC025631|EG381742|Zfp469	trinucleotide repeat containing 18	protein-coding
mm_88825.1	chr10	80804069	80804090	+	1	NA	exon (NM_013651, exon 9 of 9)	exon (NM_013651, exon 9 of 9)	-1169	NM_007445	11705	Mm.376094	NM_007445	ENSMUSG00000035262	Amh	MIS	anti-Mullerian hormone	protein-coding
mm_29297.1	chr3	107895755	107895805	-	1	NA	promoter-TSS (NM_010360)	promoter-TSS (NM_010360)	-74	NM_010360	14866	Mm.282351	NM_010360	ENSMUSG00000004032	Gstm5	-	glutathione S-transferase, mu 5	protein-coding
mm_98497.1	chr11	94951723	94951735	+	1	NA	3' UTR (NM_007742, exon 51 of 51)	3' UTR (NM_007742, exon 51 of 51)	15505	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_26918.1	chr3	20242174	20242187	-	1	NA	promoter-TSS (NM_007753)	promoter-TSS (NM_007753)	1	NM_007753	12873	Mm.1135	NM_007753	ENSMUSG00000001865	Cpa3	MC-CPA	carboxypeptidase A3, mast cell	protein-coding
mm_61506.1	chr7	78718379	78718400	+	1	NA	promoter-TSS (NR_015542)	promoter-TSS (NR_015542)	-169	NR_015542	414121	Mm.482537	NR_015542	ENSMUSG00000059146	E430016F16Rik	-	RIKEN cDNA E430016F16 gene	ncRNA
mm_133731.1	chr16	93809428	93809443	+	1	NA	intron (NM_027293, intron 36 of 36)	intron (NM_027293, intron 36 of 36)	-22686	NM_001045529	338467	Mm.287329	NM_001045529	ENSMUSG00000039456	Morc3	1110051N18Rik|AI452146|BF318192|D16Jhu32e|NXP2|Zcwcc3	microrchidia 3	protein-coding
mm_15916.1	chr2	165064929	165064939	+	1	NA	intron (NM_170703, intron 5 of 7)	intron (NM_170703, intron 5 of 7)	9298	NM_011611	21939	Mm.271833	NM_011611	ENSMUSG00000017652	Cd40	AI326936|Bp50|GP39|HIGM1|IGM|IMD3|T-BAM|TRAP|Tnfrsf5|p50	CD40 antigen	protein-coding
mm_140886.1	chr17	23893608	23893613	-	1	NA	Intergenic	Intergenic	-5112	NM_001039238	630537	Mm.436677	NM_001039238	ENSMUSG00000096278	Dcpp2	Dcpp-2|EG630537|SPT-2	demilune cell and parotid protein 2	protein-coding
mm_149351.1	chr19	10895373	10895383	+	1	NA	5' UTR (NM_134129, exon 1 of 16)	5' UTR (NM_134129, exon 1 of 16)	147	NM_001253843	28000	Mm.491104	NM_134129	ENSMUSG00000024735	Prpf19	AA617263|AL024362|D19Wsu55e|NMP200|PSO4|Prp19|Snev	pre-mRNA processing factor 19	protein-coding
mm_128255.1	chr15	36771097	36771175	-	1	NA	3' UTR (NM_001253807, exon 5 of 5)	3' UTR (NM_001253807, exon 5 of 5)	19796	NM_001253807	22631	Mm.3360	NM_011740	ENSMUSG00000022285	Ywhaz	1110013I11Rik|14-3-3zeta|AI596267|AL022924|AU020854	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide	protein-coding
mm_69740.1	chr7	140950237	140950257	-	1	NA	promoter-TSS (NM_053088)	promoter-TSS (NM_053088)	-8	NM_053088	73835	Mm.389989	NM_053088	ENSMUSG00000025489	Ifitm5	1110003J06Rik|AW213665|Bril|DSPA1|Hrmp1|Hrtm1	interferon induced transmembrane protein 5	protein-coding
mm_142191.1	chr17	36951140	36951148	-	1	NA	intron (NM_029632, intron 1 of 2)	intron (NM_029632, intron 1 of 2)	648	NM_029632	76497	Mm.46176	NM_029632	ENSMUSG00000036398	Ppp1r11	1500041B02Rik|AV117883|Hcgv|Tcte5|Tctex-5|Tctex5	protein phosphatase 1, regulatory (inhibitor) subunit 11	protein-coding
mm_9617.1	chr1	176275284	176275308	-	1	NA	promoter-TSS (NM_176916)	promoter-TSS (NM_176916)	16	NM_176916	319455	Mm.338001	NM_176916	ENSMUSG00000055214	Pld5	B230365F16Rik	phospholipase D family, member 5	protein-coding
mm_102634.1	chr11	62539282	62539288	-	1	NA	promoter-TSS (NM_028448)	promoter-TSS (NM_028448)	-24	NM_028448	73139	Mm.390409	NM_028448	ENSMUSG00000018509	Cenpv	3110013H01Rik|AA671303|Prr6	centromere protein V	protein-coding
mm_108230.1	chr12	77238997	77239035	+	1	NA	non-coding (NR_045554, exon 1 of 12)	non-coding (NR_045554, exon 1 of 12)	277	NR_045554	53618	Mm.35628	NM_016893	ENSMUSG00000021065	Fut8	-	fucosyltransferase 8	protein-coding
mm_22697.1	chr3	18008742	18008748	+	1	NA	Intergenic	L1_Mur3|LINE|L1	-45580	NM_021560	59058	Mm.149938	NM_021560	ENSMUSG00000025128	Bhlhe22	Beta3|Beta3a|Bhlhb5	basic helix-loop-helix family, member e22	protein-coding
mm_162049.1	chrX	6172979	6172979	-	1	NA	promoter-TSS (NM_001031664)	promoter-TSS (NM_001031664)	12	NM_001031664	102954	Mm.426101	NM_001031664	ENSMUSG00000073293	Nudt10	AI853080|Dipp3a	nudix (nucleoside diphosphate linked moiety X)-type motif 10	protein-coding
mm_108148.1	chr12	76294138	76294183	+	1	NA	exon (NM_138745, exon 14 of 28)	exon (NM_138745, exon 14 of 28)	-30731	NM_001101471	238276	Mm.311452	NM_001101471	ENSMUSG00000021057	Akap5	3526401B18Rik|AKAP 150|AKAP-5|AKAP150|BB098886|Gm258|P150	A kinase (PRKA) anchor protein 5	protein-coding
mm_107757.1	chr12	59071520	59071532	+	1	NA	exon (NM_008891, exon 9 of 9)	exon (NM_008891, exon 9 of 9)	4607	NM_008891	18949	Mm.22347	NM_008891	ENSMUSG00000020994	Pnn	AU045199|D12Ertd512e	pinin	protein-coding
mm_145854.1	chr18	65454103	65454111	+	1	NA	intron (NM_172833, intron 8 of 15)	intron (NM_172833, intron 8 of 15)	23110	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_103779.1	chr11	82764242	82764273	-	1	NA	promoter-TSS (NM_025884)	promoter-TSS (NM_025884)	64	NM_009839	12467	Mm.4126	NM_009839	ENSMUSG00000020698	Cct6b	CCT-zeta-2|CCTzeta-2|Cctz-2|TCP-1-zeta-2	chaperonin containing Tcp1, subunit 6b (zeta)	protein-coding
mm_173266.1	chrX	95444851	95444869	-	1	NA	promoter-TSS (NM_175179)	promoter-TSS (NM_175179)	-20	NM_175179	72345	Mm.182867	NM_175179	ENSMUSG00000050332	Amer1	2810002O09Rik|AW492303|Fam123b|Wtx	APC membrane recruitment 1	protein-coding
mm_103951.1	chr11	84068555	84068604	-	1	NA	promoter-TSS (NM_019819)	promoter-TSS (NM_019819)	-222	NM_019819	56405	Mm.240885	NM_019819	ENSMUSG00000018648	Dusp14	1110014C10Rik|2310042C07Rik|D11Ertd395e|MKP-L|Mkp6	dual specificity phosphatase 14	protein-coding
mm_28080.1	chr3	84582477	84582522	-	1	NA	5' UTR (NM_001293801, exon 1 of 8)	5' UTR (NM_001293801, exon 1 of 8)	126	NM_001081093	99889	Mm.316536	NM_001081093	ENSMUSG00000074513	Arfip1	2310030I10Rik|Arfaptin|D3Ertd598e	ADP-ribosylation factor interacting protein 1	protein-coding
mm_49603.1	chr6	30741375	30741378	+	1	NA	promoter-TSS (NR_029900)	promoter-TSS (NR_029900)	77	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_79930.1	chr9	65637840	65637852	+	1	NA	intron (NM_028030, intron 1 of 7)	ORR1C2|LTR|ERVL-MaLR	7264	NM_028030	71973	Mm.29148	NM_028030	ENSMUSG00000032387	Rbpms2	2400008B06Rik|AI316523	RNA binding protein with multiple splicing 2	protein-coding
mm_65815.1	chr7	29125143	29125160	-	1	NA	promoter-TSS (NM_009109)	promoter-TSS (NM_009109)	0	NM_009109	20190	Mm.439745	NM_009109	ENSMUSG00000030592	Ryr1	AI528790|RYR-1|Ryr|skrr	ryanodine receptor 1, skeletal muscle	protein-coding
mm_150140.1	chr19	31082983	31083046	+	1	NA	5' UTR (NM_031249, exon 1 of 1)	5' UTR (NM_031249, exon 1 of 1)	173	NM_031249	83410	Mm.22031	NM_031249	ENSMUSG00000053536	Cstf2t	64kDa|C77975|tCstF-64|tauCstF-64	cleavage stimulation factor, 3' pre-RNA subunit 2, tau	protein-coding
mm_49113.1	chr6	8509388	8509437	+	1	NA	promoter-TSS (NR_040452)	promoter-TSS (NR_040452)	-188	NM_133236	170772	Mm.210787	NM_133236	ENSMUSG00000029638	Glcci1	2310047L21Rik|A130036A18Rik|Fam117c|Gig18|Tssn1	glucocorticoid induced transcript 1	protein-coding
mm_171478.1	chr4	145864171	145864178	+	1	NA	Intergenic	Intergenic	26955	NR_033612	236069	Mm.276881	NR_033612	ENSMUSG00000096233	Gm13238	OTTMUSG00000011065	carnitine deficiency-associated gene expressed in ventricle 3 pseudogene	pseudo
mm_108085.1	chr12	73997750	73997817	+	1	NA	promoter-TSS (NM_172804)	promoter-TSS (NM_172804)	22	NM_172804	238266	Mm.311393	NM_172804	ENSMUSG00000044912	Syt16	6430703N11|Strep14|Syt14l|syt14r	synaptotagmin XVI	protein-coding
mm_157422.1	chrX	38564346	38564359	-	1	NA	intron (NM_001110142, intron 3 of 22)	G-rich|Low_complexity|Low_complexity	11844	NM_028288	72584	Mm.327675	NM_028288	ENSMUSG00000031095	Cul4b	2700050M05Rik|AA409770|CUL-4B|mKIAA0695	cullin 4B	protein-coding
mm_101004.1	chr11	8468818	8468822	-	1	NA	intron (NM_001083587, intron 20 of 30)	intron (NM_001083587, intron 20 of 30)	195715	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_72144.1	chr8	72135764	72135828	+	1	NA	intron (NM_001001491, intron 1 of 7)	CpG	504	NM_001001491	326618	Mm.295124	NM_001001491	ENSMUSG00000031799	Tpm4	2610528G24Rik|Tpm4.2|Tpm4.2cy	tropomyosin 4	protein-coding
mm_4837.1	chr1	186705014	186705022	+	1	NA	5' UTR (NM_009367, exon 1 of 7)	5' UTR (NM_009367, exon 1 of 7)	971	NM_009367	21808	Mm.18213	NM_009367	ENSMUSG00000039239	Tgfb2	BB105277|Tgf-beta2|Tgfb-2	transforming growth factor, beta 2	protein-coding
mm_29463.1	chr3	113574759	113574774	-	1	NA	promoter-TSS (NM_007446)	promoter-TSS (NM_007446)	-4	NM_007446	11722	Mm.439727	NM_007446	ENSMUSG00000074264	Amy1	Amy-1|Amy1a|C030014B17Rik	amylase 1, salivary	protein-coding
mm_61790.1	chr7	83883858	83883881	+	1	NA	5' UTR (NM_030705, exon 1 of 1)	5' UTR (NM_030705, exon 1 of 1)	472	NM_030705	80889	Mm.272998	NM_030705	ENSMUSG00000070462	Mesdc1	AW061151	mesoderm development candidate 1	protein-coding
mm_123735.1	chr14	70176788	70176824	-	1	NA	promoter-TSS (NM_001253736)	promoter-TSS (NM_001253736)	9	NM_001253736	213019	Mm.283968	NM_145978	ENSMUSG00000022090	Pdlim2	4732462F18Rik|Slim	PDZ and LIM domain 2	protein-coding
mm_26705.1	chr3	157946955	157946993	+	1	NA	promoter-TSS (NM_001013806)	promoter-TSS (NM_001013806)	-492	NM_001013806	433667	Mm.265806	NM_001013806	ENSMUSG00000039988	Ankrd13c	AI505652|AU022220	ankyrin repeat domain 13c	protein-coding
mm_72358.1	chr8	79712951	79712965	+	1	NA	intron (NM_026904, intron 1 of 4)	B1_Mus2|SINE|Alu	1138	NM_026904	68999	Mm.257445	NM_026904	ENSMUSG00000036977	Anapc10	1500026N15Rik|A830003M23Rik|APC10	anaphase promoting complex subunit 10	protein-coding
mm_57489.1	chr6	125275941	125275943	-	1	NA	Intergenic	Intergenic	10100	NM_009446	22144	Mm.287784	NM_009446	ENSMUSG00000067702	Tuba3a	AI528779|M[a]3|Tuba3	tubulin, alpha 3A	protein-coding
mm_154728.1	chrX	9436873	9436880	+	1	NA	3' UTR (NM_007807, exon 13 of 13)	3' UTR (NM_007807, exon 13 of 13)	32448	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_11977.1	chr2	55115765	55115776	+	1	NA	3' UTR (NM_173030, exon 13 of 13)	3' UTR (NM_173030, exon 13 of 13)	-320200	NM_001304810	16519	Mm.5127	NM_008426	ENSMUSG00000026824	Kcnj3	GIRK-1|GIRK1|Kcnf3|Kir3.1	potassium inwardly-rectifying channel, subfamily J, member 3	protein-coding
mm_31852.1	chr4	75549718	75549722	+	1	NA	Intergenic	Lx9|LINE|L1	-271434	NM_025849	66928	Mm.24332	NM_025849	ENSMUSG00000028398	Tmem261	1700027K24Rik|3110001D03Rik	transmembrane protein 261	protein-coding
mm_47423.1	chr5	123150180	123150183	-	1	NA	intron (NM_001040398, intron 6 of 16)	intron (NM_001040398, intron 6 of 16)	7988	NM_001040398	208043	Mm.250391	NM_177581	ENSMUSG00000038384	Setd1b	AA516740|BC035291|KMT2G|mKIAA1076	SET domain containing 1B	protein-coding
mm_56285.1	chr6	91440868	91440919	-	1	NA	promoter-TSS (NR_045980)	promoter-TSS (NR_045980)	-39	NR_045980	75787	Mm.30842	NR_045980	ENSMUSG00000097693	4930471M09Rik	4930427C17Rik	RIKEN cDNA 4930471M09 gene	ncRNA
mm_122029.1	chr14	29529652	29529652	-	1	NA	intron (NM_009785, intron 3 of 37)	intron (NM_009785, intron 3 of 37)	192212	NM_009785	12294	Mm.386754	NM_009785	ENSMUSG00000021991	Cacna2d3	Cacnad3|alapha2delta3	calcium channel, voltage-dependent, alpha2/delta subunit 3	protein-coding
mm_29315.1	chr3	108012560	108012572	-	1	NA	3' UTR (NM_010358, exon 8 of 8)	3' UTR (NM_010358, exon 8 of 8)	5407	NM_010358	14862	Mm.37199	NM_010358	ENSMUSG00000058135	Gstm1	Gstb-1|Gstb1	glutathione S-transferase, mu 1	protein-coding
mm_131094.1	chr16	4908710	4908712	+	1	NA	intron (NM_001252437, intron 2 of 16)	MTC|LTR|ERVL-MaLR	22611	NM_001252437	17237	Mm.291326	NM_029657	ENSMUSG00000022517	Mgrn1	2610042J20Rik|mKIAA0544|md|nc	mahogunin, ring finger 1	protein-coding
mm_148949.1	chr19	7268297	7268313	+	1	NA	promoter-TSS (NM_001320554)	promoter-TSS (NM_001320554)	26	NM_001320554	104383	Mm.283859	NM_054048	ENSMUSG00000024968	Rcor2	1A13|AW122124|CoREST|Rcor|Rcor1	REST corepressor 2	protein-coding
mm_150682.1	chr19	42058007	42058008	+	1	NA	intron (NM_026152, intron 1 of 6)	intron (NM_026152, intron 1 of 6)	5779	NM_025752	66765	Mm.440412	NM_025752	ENSMUSG00000090369	4933411K16Rik	-	RIKEN cDNA 4933411K16 gene	protein-coding
mm_96559.1	chr11	68968108	68968175	+	1	NA	promoter-TSS (NM_028048)	promoter-TSS (NM_028048)	10	NM_028048	71998	Mm.298622	NM_028048	ENSMUSG00000018740	Slc25a35	1810012H11Rik	solute carrier family 25, member 35	protein-coding
mm_44901.1	chr5	35525692	35525705	-	1	NA	promoter-TSS (NM_153107)	promoter-TSS (NM_153107)	-72	NM_153107	242939	Mm.108557	NM_153107	ENSMUSG00000036596	Cpz	AV136066	carboxypeptidase Z	protein-coding
mm_5204.1	chr1	13426805	13426814	-	1	NA	Intergenic	ID_B1|SINE|B4	-52726	NM_008678	17978	Mm.2537	NM_008678	ENSMUSG00000005886	Ncoa2	D1Ertd433e|GRIP-1|Grip1|KAT13C|NCoA-2|SRC-2|TIF2|bHLHe75	nuclear receptor coactivator 2	protein-coding
mm_93304.1	chr10	97596933	97596942	-	1	NA	promoter-TSS (NR_045356)	promoter-TSS (NR_045356)	-6	NR_045356	75025	Mm.159401	NR_045356		4930473O22Rik	-	RIKEN cDNA 4930473O22 gene	ncRNA
mm_121656.1	chr14	11335044	11335051	-	1	NA	Intergenic	BC1_Mm|scRNA|scRNA	52570	NR_105811	102466641		NR_105811	ENSMUSG00000099218	Mir5124b	Gm27681|mmu-mir-5124b	microRNA 5124b	ncRNA
mm_93441.1	chr10	109883739	109883782	-	1	NA	intron (NM_001081035, intron 3 of 38)	intron (NM_001081035, intron 3 of 38)	116459	NM_001081035	260315	Mm.225050	NM_177797	ENSMUSG00000020181	Nav3	4732483H20Rik|9630020C08Rik|POMFIL1|Pomfil1p|mKIAA0938|unc53H3	neuron navigator 3	protein-coding
mm_7753.1	chr1	131097827	131097844	-	1	NA	promoter-TSS (NM_008551)	promoter-TSS (NM_008551)	8	NM_008551	17164	Mm.221235	NM_008551	ENSMUSG00000016528	Mapkapk2	AA960234|MAPKAP-K2|MK-2|MK2|Rps6kc1	MAP kinase-activated protein kinase 2	protein-coding
mm_129234.1	chr15	76616842	76616876	-	1	NA	promoter-TSS (NM_028064)	promoter-TSS (NM_028064)	-7	NM_028064	72027	Mm.276829	NM_028064	ENSMUSG00000063354	Slc39a4	1600025H15Rik|AU041686|AWMS2|ZIP4	solute carrier family 39 (zinc transporter), member 4	protein-coding
mm_41218.1	chr5	88583528	88583590	+	1	NA	promoter-TSS (NM_027530)	promoter-TSS (NM_027530)	46	NM_027530	52822	Mm.270469	NM_027530	ENSMUSG00000029291	Rufy3	2810428M05Rik|6330416M07Rik|AW455998|AW538594|D5Bwg0860e|Ripx|Rpipx	RUN and FYVE domain containing 3	protein-coding
mm_166924.1	chr7	31054578	31054610	-	1	NA	intron (NM_052992, intron 1 of 7)	intron (NM_052992, intron 1 of 7)	259	NM_052991	56188	Mm.1491	NM_019503	ENSMUSG00000036570	Fxyd1	0610012C17Rik|1110006M24Rik|Plm|Pml	FXYD domain-containing ion transport regulator 1	protein-coding
mm_133802.1	chr16	95298695	95298715	+	1	NA	non-coding (NR_073406, exon 6 of 6)	non-coding (NR_073406, exon 6 of 6)	41147	NM_001271690	16516	Mm.272239	NM_019664	ENSMUSG00000062609	Kcnj15	4930414N08Rik|AI182284|AI267127|IRKK|Kir4.2	potassium inwardly-rectifying channel, subfamily J, member 15	protein-coding
mm_107600.1	chr12	49383086	49383105	+	1	NA	promoter-TSS (NM_008241)	promoter-TSS (NM_008241)	88	NM_008241	15228	Mm.4704	NM_008241	ENSMUSG00000020950	Foxg1	2900064B05Rik|BF-1|Bf1|Hfh9|Hfhbf1	forkhead box G1	protein-coding
mm_13617.1	chr2	113439781	113439781	+	1	NA	intron (NM_010230, intron 3 of 19)	intron (NM_010230, intron 3 of 19)	-1283	NM_001285459	14260	Mm.4938	NM_010230	ENSMUSG00000044042	Fmn1	Fmn|formin-1|ld	formin 1	protein-coding
mm_85343.1	chr9	103202114	103202136	-	1	NA	promoter-TSS (NM_009275)	promoter-TSS (NM_009275)	-60	NM_009275	20818	Mm.273053	NM_009275	ENSMUSG00000032553	Srprb	AA409543	signal recognition particle receptor, B subunit	protein-coding
mm_29389.1	chr3	108889913	108889917	-	1	NA	promoter-TSS (NM_177091)	promoter-TSS (NM_177091)	93	NM_177091	320181	Mm.244233	NM_177091	ENSMUSG00000045326	Fndc7	E230011A21Rik	fibronectin type III domain containing 7	protein-coding
mm_137078.1	chr17	21091221	21091228	+	1	NA	promoter-TSS (NR_137274)	promoter-TSS (NR_137274)	16	NR_137274	328766	Mm.50947	NR_137274	ENSMUSG00000102080	Gm5092	4933430A09	predicted gene 5092	ncRNA
mm_27534.1	chr3	57575761	57575836	-	1	NA	promoter-TSS (NM_133784)	promoter-TSS (NM_133784)	78	NM_133784	97064	Mm.405029	NM_133784	ENSMUSG00000027803	Wwtr1	2310058J06Rik|2610021I22Rik|C78399|Taz	WW domain containing transcription regulator 1	protein-coding
mm_7404.1	chr1	119053573	119053583	-	1	NA	promoter-TSS (NM_001081125)	promoter-TSS (NM_001081125)	41	NM_001081125	14633	Mm.273292	NM_001081125	ENSMUSG00000048402	Gli2	-	GLI-Kruppel family member GLI2	protein-coding
mm_117033.1	chr13	58274368	58274377	-	1	NA	promoter-TSS (NM_019832)	promoter-TSS (NM_019832)	-184	NM_019832	56278	Mm.296625	NM_019832	ENSMUSG00000021552	Gkap1	42kDa|4933400B15Rik|D13Ertd340e|Gkap42	G kinase anchoring protein 1	protein-coding
mm_164737.1	chr17	71019542	71019546	+	1	NA	promoter-TSS (NM_001083934)	promoter-TSS (NM_001083934)	-13	NM_010867	17929	Mm.4103	NM_010867	ENSMUSG00000024049	Myom1	D430047A17Rik	myomesin 1	protein-coding
mm_172261.1	chr6	75296651	75296655	-	1	NA	Intergenic	Intergenic	-1825632	NR_108032	73408	Mm.233629	NR_108032	ENSMUSG00000107408	1700065L07Rik	-	RIKEN cDNA 1700065L07 gene	ncRNA
mm_90622.1	chr10	128428248	128428252	+	1	NA	intron (NR_104288, intron 2 of 6)	intron (NR_104288, intron 2 of 6)	16634	NM_026259	67588	Mm.294120	NM_026259	ENSMUSG00000025373	Rnf41	2210404G21Rik|4930511A05Rik|4933415P08Rik|D10Ertd722e|FLRF|Nrdp1	ring finger protein 41	protein-coding
mm_159641.1	chr4	142210152	142210152	-	1	NA	promoter-TSS (NM_001109684)	promoter-TSS (NM_001109684)	56	NM_144531	71529	Mm.255986	NM_144531	ENSMUSG00000040606	Kazn	2310007B04Rik|9030409G11Rik|AI256607|AI666764|AW061099|Kaz|Kazrin	kazrin, periplakin interacting protein	protein-coding
mm_56255.1	chr6	90782025	90782035	-	1	NA	intron (NM_001134384, intron 1 of 13)	intron (NM_001134384, intron 1 of 13)	28093	NM_001134384	232227	Mm.196943	NM_182784	ENSMUSG00000034312	Iqsec1	AW561907|BC026481|BRAG2|D6Ertd349e|cI-43	IQ motif and Sec7 domain 1	protein-coding
mm_89637.1	chr10	96620862	96620874	+	1	NA	3' UTR (NM_007569, exon 2 of 2)	3' UTR (NM_007569, exon 2 of 2)	3867	NM_007569	12226	Mm.23811	NM_007569	ENSMUSG00000036478	Btg1	AI426953|AW546738	B cell translocation gene 1, anti-proliferative	protein-coding
mm_36589.1	chr4	88429002	88429007	-	1	NA	intron (NM_025760, intron 3 of 6)	intron (NM_025760, intron 3 of 6)	9922	NM_025760	66775	Mm.386788	NM_025760	ENSMUSG00000028497	Hacd4	4933428I03Rik|Hcad4|Ptplad2	3-hydroxyacyl-CoA dehydratase 4	protein-coding
mm_136307.1	chr16	91646907	91646960	-	1	NA	promoter-TSS (NM_019973)	promoter-TSS (NM_019973)	39	NM_010256	14450	Mm.4505	NM_010256	ENSMUSG00000022962	Gart	Gaps|Prgs	phosphoribosylglycinamide formyltransferase	protein-coding
mm_12843.1	chr2	82507650	82507666	+	1	NA	Intergenic	Intergenic	454000	NM_175513	241514	Mm.119383	NM_175513	ENSMUSG00000070866	Zfp804a	C630007C17Rik|Znf804a	zinc finger protein 804A	protein-coding
mm_16446.1	chr2	180454930	180454934	+	1	NA	Intergenic	Intergenic	-6046	NM_148933	108115	Mm.133687	NM_148933	ENSMUSG00000038963	Slco4a1	OATP-E|Slc21a12	solute carrier organic anion transporter family, member 4a1	protein-coding
mm_81777.1	chr9	114688815	114688819	+	1	NA	promoter-TSS (NM_146229)	promoter-TSS (NM_146229)	-14	NM_146229	235661	Mm.128627	NM_146229	ENSMUSG00000032435	Dync1li1	1110053F02Rik|Dnclic1|LIC-1	dynein cytoplasmic 1 light intermediate chain 1	protein-coding
mm_63976.1	chr7	139971711	139971726	+	1	NA	TTS (NM_001033465)	TTS (NM_001033465)	7037	NM_001347614	381933	Mm.440431	NM_001033465	ENSMUSG00000073795	6430531B16Rik	Gm1093	RIKEN cDNA 6430531B16 gene	protein-coding
mm_160765.1	chr10	95322892	95322892	-	1	NA	intron (NM_001330175, intron 1 of 2)	intron (NM_001330175, intron 1 of 2)	817	NM_001330138	12905	Mm.473739	NM_009950	ENSMUSG00000045867	Cradd	RAIDD	CASP2 and RIPK1 domain containing adaptor with death domain	protein-coding
mm_121468.1	chr14	120911116	120911147	+	1	NA	promoter-TSS (NM_023579)	promoter-TSS (NM_023579)	-63	NM_023579	70572	Mm.221452	NM_023579	ENSMUSG00000030662	Ipo5	1110011C18Rik|5730478E03Rik|AA409333|C76941|IMB3|Kpnb3|Ranbp5	importin 5	protein-coding
mm_150546.1	chr19	39315640	39315671	+	1	NA	intron (NM_007815, intron 5 of 8)	L1MEg|LINE|L1	28570	NM_007815	13095	Mm.20764	NM_007815	ENSMUSG00000003053	Cyp2c29	AHOH|AHOHase|AI159681|AI196010|Ah-2|Ahh-1|Cyp2c|P450-2C	cytochrome P450, family 2, subfamily c, polypeptide 29	protein-coding
mm_119065.1	chr14	30825569	30825574	+	1	NA	promoter-TSS (NM_028839)	promoter-TSS (NM_028839)	-23	NM_028839	69179	Mm.143025	NM_028839	ENSMUSG00000006526	Tmem110	1810038N08Rik|2310014H19Rik|AW554125|STIMATE	transmembrane protein 110	protein-coding
mm_118207.1	chr13	109903660	109903691	-	1	NA	promoter-TSS (NR_035442)	promoter-TSS (NR_035442)	-134	NR_035442	100316683		NR_035442	ENSMUSG00000084651	Mir1904	Mirn1904|mmu-mir-1904	microRNA 1904	ncRNA
mm_63624.1	chr7	128266364	128266374	+	1	NA	exon (NM_133254, exon 2 of 14)	exon (NM_133254, exon 2 of 14)	672	NM_133254	246787	Mm.38870	NM_133254	ENSMUSG00000030781	Slc5a2	Sglt2	solute carrier family 5 (sodium/glucose cotransporter), member 2	protein-coding
mm_105294.1	chr11	102476581	102476587	-	1	NA	3' UTR (NM_001159492, exon 8 of 8)	3' UTR (NM_001159492, exon 8 of 8)	-6701	NM_010575	16399	Mm.26646	NM_010575	ENSMUSG00000034664	Itga2b	AI172977|CD41|CD41B|GpIIb|alphaIIb	integrin alpha 2b	protein-coding
mm_147918.1	chr18	65697609	65697624	-	1	NA	promoter-TSS (NM_177028)	promoter-TSS (NM_177028)	-652	NM_177028	319888	Mm.183576	NM_177028	ENSMUSG00000046610	Oacyl	5330437I02Rik|Acyl3	O-acyltransferase like	protein-coding
mm_162792.1	chr10	75822515	75822515	-	1	NA	promoter-TSS (NM_029472)	promoter-TSS (NM_029472)	28	NM_029472	75886	Mm.268996	NM_029472	ENSMUSG00000009093	Gstt4	4930583C14Rik|AI507011	glutathione S-transferase, theta 4	protein-coding
mm_161559.1	chr16	16504167	16504167	-	1	NA	exon (NM_001301817, exon 2 of 17)	exon (NM_001301817, exon 2 of 17)	23244	NM_001301818	224014	Mm.256131	NM_139232	ENSMUSG00000022788	Fgd4	9030023J02Rik|9330209B17Rik|Frabp|ZFYVE6	FYVE, RhoGEF and PH domain containing 4	protein-coding
mm_76583.1	chr8	89015669	89015690	-	1	NA	Intergenic	Intergenic	-9056	NR_106190	102465899		NR_106190	ENSMUSG00000099078	Mir8110	Gm27571|mmu-mir-8110	microRNA 8110	ncRNA
mm_79480.1	chr9	56994864	56994874	+	1	NA	promoter-TSS (NM_019651)	promoter-TSS (NM_019651)	-99	NM_019651	56294	Mm.325643	NM_019651	ENSMUSG00000032290	Ptpn9	MEG2	protein tyrosine phosphatase, non-receptor type 9	protein-coding
mm_21119.1	chr2	153530206	153530252	-	1	NA	promoter-TSS (NM_001134300)	promoter-TSS (NM_001134300)	-258	NM_001134300	329540	Mm.50600	NM_001001986	ENSMUSG00000061411	Nol4l	4931410H15|8430427H17Rik|AI429157|Gm1636	nucleolar protein 4-like	protein-coding
mm_30382.1	chr3	152243992	152244004	-	1	NA	exon (NM_199465, exon 9 of 13)	exon (NM_199465, exon 9 of 13)	22322	NM_199465	68810	Mm.200188	NM_199465	ENSMUSG00000039103	Nexn	1110046H09Rik|AA553326|NELIN	nexilin	protein-coding
mm_144014.1	chr17	88625493	88625521	-	1	NA	Intergenic	Intergenic	-1048	NM_029858	77057	Mm.482203	NM_029858	ENSMUSG00000033855	Ston1	4921524J06Rik|C86231|Salf|Sblf	stonin 1	protein-coding
mm_4313.1	chr1	171845722	171845735	+	1	NA	intron (NM_001289470, intron 2 of 8)	intron (NM_001289470, intron 2 of 8)	6031	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_118044.1	chr13	101694717	101694760	-	1	NA	intron (NM_001077495, intron 7 of 15)	CpG	-2108	NM_001024955	18708	Mm.259333	NM_001024955	ENSMUSG00000041417	Pik3r1	PI3K|p50alpha|p55alpha|p85alpha	phosphatidylinositol 3-kinase, regulatory subunit, polypeptide 1 (p85 alpha)	protein-coding
mm_161671.1	chr17	13355300	13355300	+	1	NA	intron (NM_001167578, intron 1 of 11)	intron (NM_001167578, intron 1 of 11)	728	NM_001167578	100041352	Mm.490251	NM_001167578	ENSMUSG00000052469	Tcp10c	D17Leh66C|D17Leh66ca|Gm9880|T66C-a|Tcp-10c	t-complex protein 10c	protein-coding
mm_81750.1	chr9	113955985	113956011	+	1	NA	exon (NM_001083319, exon 5 of 17)	exon (NM_001083319, exon 5 of 17)	25064	NM_013699	22221	Mm.28052	NM_013699	ENSMUSG00000009741	Ubp1	Cp2b|LBP-1a|LBP-1b|NF2d9	upstream binding protein 1	protein-coding
mm_111799.1	chr12	104988271	104988273	-	1	NA	intron (NM_172500, intron 1 of 16)	intron (NM_172500, intron 1 of 16)	10405	NM_001042699	212073	Mm.212688	NM_172500	ENSMUSG00000054150	Syne3	nesprin-3	spectrin repeat containing, nuclear envelope family member 3	protein-coding
mm_46562.1	chr5	106926246	106926284	-	1	NA	promoter-TSS (NM_177873)	promoter-TSS (NM_177873)	-375	NM_001252516	330149	Mm.121664	NM_177873	ENSMUSG00000043410	Hfm1	A330009G12Rik|Gm1046|Mer3|Sec63d1	HFM1, ATP-dependent DNA helicase homolog	protein-coding
mm_118595.1	chr14	20682743	20682767	+	1	NA	exon (NM_172596, exon 4 of 23)	exon (NM_172596, exon 4 of 23)	-7880	NR_105911	102465571		NR_105911	ENSMUSG00000098602	Mir6946	Gm27799|mmu-mir-6946	microRNA 6946	ncRNA
mm_43028.1	chr5	123915094	123915107	+	1	NA	intron (NM_026603, intron 2 of 7)	intron (NM_026603, intron 2 of 7)	7825	NM_026603	68184	Mm.28549	NM_026603	ENSMUSG00000023106	Denr	1500003K04Rik	density-regulated protein	protein-coding
mm_16791.1	chr2	10068667	10068677	-	1	NA	exon (NM_001112738, exon 3 of 10)	exon (NM_001112738, exon 3 of 10)	11838	NM_020615	11949	Mm.12677	NM_020615	ENSMUSG00000025781	Atp5c1	1700094F02Rik	ATP synthase, H+ transporting, mitochondrial F1 complex, gamma polypeptide 1	protein-coding
mm_142699.1	chr17	47834683	47834690	-	1	NA	promoter-TSS (NM_001109973)	promoter-TSS (NM_001109973)	5	NM_001109973	17240	Mm.329100	NM_010783	ENSMUSG00000032717	Mdfi	I-mf|I-mfa	MyoD family inhibitor	protein-coding
mm_92638.1	chr10	80345215	80345260	-	1	NA	intron (NR_104339, intron 4 of 11)	intron (NR_104339, intron 4 of 11)	3211	NM_001285435	66548	Mm.71891	NM_025629	ENSMUSG00000043822	Adamtsl5	2010109H09Rik|Thsd6	ADAMTS-like 5	protein-coding
mm_72026.1	chr8	70756454	70756473	+	1	NA	exon (NM_001166399, exon 3 of 5)	exon (NM_001166399, exon 3 of 5)	1784	NM_001166399	19339	Mm.5083	NM_009001	ENSMUSG00000031840	Rab3a	-	RAB3A, member RAS oncogene family	protein-coding
mm_3056.1	chr1	134063521	134063531	+	1	NA	Intergenic	Intergenic	15629	NM_007570	12227	Mm.392646	NM_007570	ENSMUSG00000020423	Btg2	AA959598|APRO1|Pc3|TIS21	B cell translocation gene 2, anti-proliferative	protein-coding
mm_42502.1	chr5	115490327	115490329	+	1	NA	Intergenic	U4|snRNA|snRNA	-5844	NM_133760	75387	Mm.332616	NM_133760	ENSMUSG00000029524	Sirt4	4930596O17Rik	sirtuin 4	protein-coding
mm_170420.1	chr18	70326594	70326599	-	1	NA	Intergenic	RLTR10-int|LTR|ERVK	-82012	NM_029346	75577	Mm.58214	NM_029346	ENSMUSG00000024512	Dynap	2310002L13Rik	dynactin associated protein	protein-coding
mm_43298.1	chr5	134582794	134582804	+	1	NA	exon (NM_020022, exon 1 of 11)	exon (NM_020022, exon 1 of 11)	109	NM_020022	19718	Mm.332739	NM_020022	ENSMUSG00000023104	Rfc2	2610008M13Rik|40kDa|AI326953|Recc2	replication factor C (activator 1) 2	protein-coding
mm_70886.1	chr8	25518758	25518771	+	1	NA	promoter-TSS (NM_010206)	promoter-TSS (NM_010206)	5	NM_001079908	14182	Mm.265716	NM_010206	ENSMUSG00000031565	Fgfr1	AW208770|Eask|FGFR-I|FLG|Fgfr-1|Flt-2|Hspy|MFR|bFGF-R-1|c-fgr	fibroblast growth factor receptor 1	protein-coding
mm_73321.1	chr8	105269789	105269836	+	1	NA	promoter-TSS (NM_001256044)	promoter-TSS (NM_001256044)	11	NM_001256044	26386	Mm.89204	NM_011939	ENSMUSG00000033249	Hsf4	HSF 4|HSTF 4|HSTF4|ldis1|mHSF4	heat shock transcription factor 4	protein-coding
mm_19052.1	chr2	77260019	77260062	-	1	NA	intron (NM_175465, intron 1 of 17)	intron (NM_175465, intron 1 of 17)	20552	NM_175465	228071	Mm.27120	NM_175465	ENSMUSG00000042272	Sestd1	1500031J16Rik|A930010O20|Solo/Trio8	SEC14 and spectrin domains 1	protein-coding
mm_85504.1	chr9	106199254	106199286	-	1	NA	promoter-TSS (NM_026447)	promoter-TSS (NM_026447)	-37	NM_026447	67905	Mm.23018	NM_026447	ENSMUSG00000020253	Ppm1m	2810423O19Rik|AW610647|C77250|PP2Ceta	protein phosphatase 1M	protein-coding
mm_165457.1	chr2	158166703	158166712	-	1	NA	Intergenic	Intergenic	-20315	NM_009373	21817	Mm.330731	NM_009373	ENSMUSG00000037820	Tgm2	G[a]h|TG2|TGase2|tTG|tTGas	transglutaminase 2, C polypeptide	protein-coding
mm_3526.1	chr1	150165186	150165206	+	1	NA	promoter-TSS (NR_110420)	promoter-TSS (NR_110420)	-248	NR_110420	102639566	Mm.417208	NR_110420	ENSMUSG00000097754	Ptgs2os2	Gm26687|Linc-cox2|Lincrna-cox2	prostaglandin-endoperoxide synthase 2, opposite strand 2	ncRNA
mm_147179.1	chr18	36766219	36766237	-	1	NA	promoter-TSS (NM_173383)	promoter-TSS (NM_173383)	-14	NM_173383	213236	Mm.234464	NM_173383	ENSMUSG00000044595	Dnd1	BC034897|RBMS4|Ter	DND microRNA-mediated repression inhibitor 1	protein-coding
mm_114482.1	chr13	69612010	69612067	+	1	NA	promoter-TSS (NM_175283)	promoter-TSS (NM_175283)	22	NM_145354	28114	Mm.260009	NM_145354	ENSMUSG00000021595	Nsun2	D13Wsu123e|Misu	NOL1/NOP2/Sun domain family member 2	protein-coding
mm_47793.1	chr5	132338231	132338242	-	1	NA	intron (NM_177047, intron 1 of 18)	intron (NM_177047, intron 1 of 18)	204107	NM_177047	319974	Mm.409595	NM_177047	ENSMUSG00000029673	Auts2	2700063G02Rik|A730011F23Rik|D830032G16Rik	autism susceptibility candidate 2	protein-coding
mm_135635.1	chr16	52343794	52343820	-	1	NA	intron (NM_009655, intron 1 of 15)	intron (NM_009655, intron 1 of 15)	109274	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_112644.1	chr13	16017048	16017056	+	1	NA	intron (NM_008380, intron 3 of 4)	C-rich|Low_complexity|Low_complexity	5201	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_69474.1	chr7	133730861	133730875	-	1	NA	intron (NM_133941, intron 7 of 11)	intron (NM_133941, intron 7 of 11)	21535	NM_025392	66165	Mm.389983	NM_025392	ENSMUSG00000030983	Bccip	1110013J05Rik|TOK-1	BRCA2 and CDKN1A interacting protein	protein-coding
mm_26231.1	chr3	139205888	139205909	+	1	NA	promoter-TSS (NM_198659)	promoter-TSS (NM_198659)	5	NM_198659	381476	Mm.188334	NM_198659	ENSMUSG00000047940	Stpg2	B930007M17Rik|Gm1017	sperm tail PG rich repeat containing 2	protein-coding
mm_105284.1	chr11	102436163	102436197	-	1	NA	TTS (NM_199200)	TTS (NM_199200)	5858	NM_008175	14824	Mm.1568	NM_008175	ENSMUSG00000034708	Grn	Pgrn|epithelin	granulin	protein-coding
mm_155662.1	chrX	87238349	87238364	+	1	NA	intron (NM_001160403, intron 5 of 10)	intron (NM_001160403, intron 5 of 10)	877267	NM_001160403	331461	Mm.121680	NM_001160403	ENSMUSG00000052372	Il1rapl1	6330532G10Rik|C030039N24|IL1R8|IL1RAPL|MRX34|OPHN4|TIGIRR-2	interleukin 1 receptor accessory protein-like 1	protein-coding
mm_116161.1	chr13	30660231	30660242	-	1	NA	intron (NM_001037955, intron 1 of 6)	intron (NM_001037955, intron 1 of 6)	177	NM_134068	105352	Mm.289646	NM_134068	ENSMUSG00000069255	Dusp22	JKAP|JSP1|LMW-DSP2|MKPX	dual specificity phosphatase 22	protein-coding
mm_109028.1	chr12	104052727	104052755	+	1	NA	Intergenic	Intergenic	-8298	NM_026535	68054	Mm.20286	NM_026535	ENSMUSG00000041567	Serpina12	4632419J12Rik	serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 12	protein-coding
mm_68490.1	chr7	111074723	111074745	-	1	NA	exon (NM_013507, exon 18 of 22)	exon (NM_013507, exon 18 of 22)	8296	NM_001040131	13690	Mm.185453	NM_013507	ENSMUSG00000005610	Eif4g2	DAP-5|E130105L11Rik|Nat1|Natm1|p97	eukaryotic translation initiation factor 4, gamma 2	protein-coding
mm_122998.1	chr14	54992699	54992711	-	1	NA	exon (NM_080728, exon 4 of 41)	exon (NM_080728, exon 4 of 41)	1844	NM_080728	140781	Mm.457983	NM_080728	ENSMUSG00000053093	Myh7	B-MHC|MyHC-I|Myhc-b|Myhcb|beta-MHC	myosin, heavy polypeptide 7, cardiac muscle, beta	protein-coding
mm_124040.1	chr14	77036569	77036579	-	1	NA	promoter-TSS (NM_172488)	promoter-TSS (NM_172488)	43	NM_172488	210808	Mm.89278	NM_172488	ENSMUSG00000044350	Lacc1	9030625A04Rik	laccase (multicopper oxidoreductase) domain containing 1	protein-coding
mm_116536.1	chr13	45876080	45876098	-	1	NA	intron (NM_001199304, intron 2 of 6)	intron (NM_001199304, intron 2 of 6)	88902	NM_001199304	20238	Mm.342683	NM_009124	ENSMUSG00000046876	Atxn1	2900016G23Rik|Atx1|C85907|ENSMUSG00000074917|Gm10786|Sca1	ataxin 1	protein-coding
mm_65341.1	chr7	24981611	24981622	-	1	NA	exon (NM_001290469, exon 18 of 23)	exon (NM_001290469, exon 18 of 23)	6051	NR_106014	102465634		NR_106014	ENSMUSG00000099258	Mir7047	Gm27270|mmu-mir-7047	microRNA 7047	ncRNA
mm_162072.1	chrX	20460578	20460578	+	1	NA	intron (NM_199317, intron 4 of 12)	intron (NM_199317, intron 4 of 12)	34890	NM_001289684	382207	Mm.281517	NM_199317	ENSMUSG00000037315	Jade3	5730598B06|AI851988|AW544806|Phf16|mKIAA0215	jade family PHD finger 3	protein-coding
mm_7850.1	chr1	132390302	132390373	-	1	NA	promoter-TSS (NM_001311107)	promoter-TSS (NM_001311107)	-19	NM_001311107	68875	Mm.273785	NM_178874	ENSMUSG00000042066	Tmcc2	1110063G11Rik	transmembrane and coiled-coil domains 2	protein-coding
mm_81206.1	chr9	107575907	107575917	+	1	NA	Intergenic	Intergenic	-1015	NM_008317	15586	Mm.475658	NM_008317	ENSMUSG00000010051	Hyal1	Hya1|Hyal-1	hyaluronoglucosaminidase 1	protein-coding
mm_131714.1	chr16	21205044	21205065	+	1	NA	5' UTR (NM_010143, exon 1 of 16)	5' UTR (NM_010143, exon 1 of 16)	259	NM_010143	13845	Mm.6972	NM_010143	ENSMUSG00000005958	Ephb3	AW456895|Cek10|Etk2|HEK2|MDK5|Sek4|Tyro6	Eph receptor B3	protein-coding
mm_119262.1	chr14	34017039	34017051	+	1	NA	Intergenic	Intergenic	-24033	NM_001034880	432838	Mm.318383	NM_001034880	ENSMUSG00000072624	Gm5460	EG432838	predicted gene 5460	protein-coding
mm_20237.1	chr2	126315563	126315569	-	1	NA	Intergenic	RMER15|LTR|ERVL	163425	NM_026981	69185	Mm.29019	NM_026981	ENSMUSG00000023330	Dtwd1	1810033A06Rik	DTW domain containing 1	protein-coding
mm_139227.1	chr17	47730689	47730701	+	1	NA	exon (NM_025973, exon 5 of 9)	exon (NM_025973, exon 5 of 9)	3853	NM_025973	109820	Mm.22957	NM_025973	ENSMUSG00000023987	Pgc	2210410L06Rik|Upg-1|Upg1	progastricsin (pepsinogen C)	protein-coding
mm_33475.1	chr4	130818703	130818714	+	1	NA	exon (NM_011520, exon 3 of 5)	exon (NM_011520, exon 3 of 5)	26171	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_3583.1	chr1	151344011	151344033	+	1	NA	promoter-TSS (NM_001039512)	promoter-TSS (NM_001039512)	-476	NM_001039512	117198	Mm.33764	NM_028582	ENSMUSG00000023150	Ivns1abp	1190004M08Rik|1700126I16Rik|AA960440|HSPC068|ND1|NS-1|NS1-BP|Nd1-L|Nd1-S|mKIAA0850	influenza virus NS1A binding protein	protein-coding
mm_78711.1	chr9	41446678	41446688	+	1	NA	intron (NR_131928, intron 3 of 4)	intron (NR_131928, intron 3 of 4)	-28210	NR_131931	73144	Mm.38166	NM_001033153	ENSMUSG00000074415	3110039I08Rik	2610203C20Rik|AI848448|D230004N17Rik|D3Mgi9|Mir100hg	RIKEN cDNA 3110039I08 gene	ncRNA
mm_121163.1	chr14	103012825	103012844	+	1	NA	intron (NR_045657, intron 2 of 2)	intron (NR_045657, intron 2 of 2)	20969	NR_045657	71264	Mm.399572	NR_045657		4933432I03Rik	-	RIKEN cDNA 4933432I03 gene	ncRNA
mm_144085.1	chr17	94749972	94750046	-	1	NA	promoter-TSS (NM_176917)	promoter-TSS (NM_176917)	-91	NR_024720	77022	Mm.440259	NR_024720	ENSMUSG00000098090	2700099C18Rik	9430041D22Rik	NDC80 homolog, kinetochore complex component pseudogene	pseudo
mm_129116.1	chr15	76080934	76080944	-	1	NA	promoter-TSS (NM_028364)	promoter-TSS (NM_028364)	7	NM_133691	67959	Mm.29965	NM_028364	ENSMUSG00000002524	Puf60	2410104I19Rik|2810454F19Rik|SIAHBP1	poly-U binding splicing factor 60	protein-coding
mm_14615.1	chr2	136723775	136723778	+	1	NA	intron (NM_011428, intron 1 of 7)	URR1A|DNA|hAT-Charlie	10326	NM_001291056	20614	Mm.45953	NM_011428	ENSMUSG00000027273	Snap25	Bdr|GENA70|SNAP-25|SUP|sp	synaptosomal-associated protein 25	protein-coding
mm_717.1	chr1	42695715	42695721	+	1	NA	promoter-TSS (NR_027826)	promoter-TSS (NR_027826)	-893	NR_027826	66297	Mm.45203	NM_183252	ENSMUSG00000060424	Pantr1	2610017I09Rik|Pou3f3os|linc-Brn1a	POU domain, class 3, transcription factor 3 adjacent noncoding transcript 1	ncRNA
mm_38592.1	chr4	141822274	141822334	-	1	NA	exon (NM_007919, exon 3 of 8)	exon (NM_007919, exon 3 of 8)	3701	NM_007919	13706	Mm.45316	NM_007919	ENSMUSG00000058579	Cela2a	Ela-2|Ela2|Ela2a	chymotrypsin-like elastase family, member 2A	protein-coding
mm_139197.1	chr17	47630521	47630523	+	1	NA	promoter-TSS (NM_198421)	promoter-TSS (NM_198421)	-168	NM_198421	224836	Mm.59393	NM_198421	ENSMUSG00000090115	Usp49	C330046L10Rik|Gm545	ubiquitin specific peptidase 49	protein-coding
mm_40417.1	chr5	53376028	53376030	+	1	NA	Intergenic	L2|LINE|L2	108923	NM_001145433	66278	Mm.27900	NM_001145433	ENSMUSG00000061461	Smim20	1110067B18Rik|1810013D10Rik|N28078	small integral membrane protein 20	protein-coding
mm_122474.1	chr14	45610562	45610582	-	1	NA	exon (NM_001042719, exon 8 of 14)	exon (NM_001042719, exon 8 of 14)	47481	NR_039593	100628600		NR_039593	ENSMUSG00000093167	Mir5131	mmu-mir-5131|mu-mir-5131	microRNA 5131	ncRNA
mm_122578.1	chr14	50833940	50833977	-	1	NA	exon (NM_009351, exon 42 of 55)	exon (NM_009351, exon 42 of 55)	26012	NM_009632	11546	Mm.281482	NM_009632	ENSMUSG00000036023	Parp2	ARTD2|Adprt2|Adprtl2|Aspartl2|C78626|PARP-2	poly (ADP-ribose) polymerase family, member 2	protein-coding
mm_155610.1	chrX	83043293	83043306	+	1	NA	intron (NM_007868, intron 1 of 78)	intron (NM_007868, intron 1 of 78)	94429	NM_007868	13405	Mm.275608	NM_007868	ENSMUSG00000045103	Dmd	DXSmh7|DXSmh9|Dp427|Dp71|dys|mdx|pke	dystrophin, muscular dystrophy	protein-coding
mm_139158.1	chr17	47540759	47540772	+	1	NA	intron (NM_001081635, intron 1 of 6)	PB1D10|SINE|Alu	35714	NM_001081635	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_107043.1	chr12	15606368	15606390	+	1	NA	Intergenic	Intergenic	194722	NR_105809	102465204		NR_105809	ENSMUSG00000098480	Mir6387	Gm27281|mmu-mir-6387	microRNA 6387	ncRNA
mm_145655.1	chr18	61130430	61130440	+	1	NA	TTS (NM_178277)	TTS (NM_178277)	12967	NR_105949	102466212		NR_105949	ENSMUSG00000098389	Mir6983	Gm27496|mmu-mir-6983	microRNA 6983	ncRNA
mm_31493.1	chr4	53120671	53120700	+	1	NA	intron (NM_013454, intron 5 of 49)	intron (NM_013454, intron 5 of 49)	39210	NM_013454	11303	Mm.277376	NM_013454	ENSMUSG00000015243	Abca1	ABC-1|Abc1	ATP-binding cassette, sub-family A (ABC1), member 1	protein-coding
mm_83662.1	chr9	49568519	49568533	-	1	NA	TTS (NR_029465)	TTS (NR_029465)	50238	NR_029465	100036537	Mm.437541	NR_029465	ENSMUSG00000079564	Gm11149	ENSMUSG00000060603|ENSMUSG00000079564	predicted gene 11149	ncRNA
mm_53536.1	chr6	136659497	136659507	+	1	NA	intron (NM_025806, intron 1 of 10)	intron (NM_025806, intron 1 of 10)	2391	NM_025806	66857	Mm.3311	NM_025806	ENSMUSG00000030214	Plbd1	1100001H23Rik	phospholipase B domain containing 1	protein-coding
mm_129671.1	chr15	81364812	81364815	-	1	NA	TTS (NM_133726)	TTS (NM_133726)	-4048	NM_011399	20524	Mm.222536	NM_011399	ENSMUSG00000022404	Slc25a17	34kDa|47kDa|PMP34|Pmp47	solute carrier family 25 (mitochondrial carrier, peroxisomal membrane protein), member 17	protein-coding
mm_6873.1	chr1	84284549	84284628	-	1	NA	promoter-TSS (NM_001003948)	promoter-TSS (NM_001003948)	57	NM_001003948	98496	Mm.187470	NM_001003948	ENSMUSG00000045658	Pid1	5033414K04Rik|NYGGF4	phosphotyrosine interaction domain containing 1	protein-coding
mm_151452.1	chr19	57780569	57780572	+	1	NA	intron (NM_181415, intron 25 of 28)	intron (NM_181415, intron 25 of 28)	169536	NM_181415	226255	Mm.245340	NM_181415	ENSMUSG00000054843	Atrnl1	AI504415|AW555641|Alp|Atrnl|Atrnlp	attractin like 1	protein-coding
mm_151863.1	chr19	5797411	5797421	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	-1435	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_14180.1	chr2	126929026	126929030	+	1	NA	intron (NM_023220, intron 1 of 14)	MERV1_LTR|LTR|ERV1	4207	NM_023220	66552	Mm.269928	NM_023220	ENSMUSG00000027366	Sppl2a	2010106G01Rik|C130089K23Rik	signal peptide peptidase like 2A	protein-coding
mm_113543.1	chr13	37873432	37873472	+	1	NA	intron (NM_001039188, intron 1 of 9)	intron (NM_001039188, intron 1 of 9)	-14982	NR_033218	68750	Mm.491109	NM_026830	ENSMUSG00000039087	Rreb1	1110037N09Rik|AA414966|B930013M22Rik	ras responsive element binding protein 1	protein-coding
mm_157827.1	chrX	74241272	74241290	-	1	NA	exon (NM_010227, exon 8 of 46)	exon (NM_010227, exon 8 of 46)	5253	NM_010227	192176	Mm.295533	NM_010227	ENSMUSG00000031328	Flna	ABP-280|Dilp2|F730004A14Rik|Fln1|GENA 379|filamin-1	filamin, alpha	protein-coding
mm_53058.1	chr6	124829541	124829577	+	1	NA	promoter-TSS (NM_013538)	promoter-TSS (NM_013538)	-75	NM_013700	22225	Mm.3571	NM_013700	ENSMUSG00000038429	Usp5	AA407472|ISOT|ISOT-1|Ucht	ubiquitin specific peptidase 5 (isopeptidase T)	protein-coding
mm_96046.1	chr11	59559029	59559032	+	1	NA	intron (NM_145827, intron 7 of 9)	MER2|DNA|TcMar-Tigger	12708	NM_001011789	257962	Mm.377316	NM_001011789	ENSMUSG00000059610	Olfr222	MOR256-45P	olfactory receptor 222	protein-coding
mm_94657.1	chr11	17054691	17054697	+	1	NA	exon (NM_029861, exon 2 of 3)	exon (NM_029861, exon 2 of 3)	2760	NM_029861	380686	Mm.425666	NM_029861	ENSMUSG00000044629	Cnrip1	1500041B16Rik|3110054C06Rik|5330437A18Rik|AI854501|C2orf32	cannabinoid receptor interacting protein 1	protein-coding
mm_169152.1	chr13	63218130	63218146	-	1	NA	intron (NM_001289926, intron 11 of 15)	IAPLTR1_Mm|LTR|ERVK	-21891	NR_110520	72061	Mm.188105	NM_028079	ENSMUSG00000021458	2010111I01Rik	2300006M17Rik|AP-O|AW742919|Aopep|ApO|mir-23b|mir-24-1|mir-27b	RIKEN cDNA 2010111I01 gene	protein-coding
mm_80198.1	chr9	72400393	72400414	+	1	NA	Intergenic	Intergenic	-38126	NM_008613	17427	Mm.387671	NM_008613	ENSMUSG00000032221	Mns1	AW546487	meiosis-specific nuclear structural protein 1	protein-coding
mm_52575.1	chr6	116350903	116350937	+	1	NA	intron (NM_001302385, intron 2 of 6)	intron (NM_001302385, intron 2 of 6)	12898	NM_027920	71779	Mm.27064	NM_027920	ENSMUSG00000025702	March8	1300017E09Rik|MARCH-VIII|Mir	membrane-associated ring finger (C3HC4) 8	protein-coding
mm_133788.1	chr16	95258156	95258205	+	1	NA	intron (NM_001039056, intron 1 of 3)	intron (NM_001039056, intron 1 of 3)	622	NM_001271690	16516	Mm.272239	NM_019664	ENSMUSG00000062609	Kcnj15	4930414N08Rik|AI182284|AI267127|IRKK|Kir4.2	potassium inwardly-rectifying channel, subfamily J, member 15	protein-coding
mm_159366.1	chr3	88349172	88349172	+	1	NA	exon (NM_178246, exon 8 of 22)	exon (NM_178246, exon 8 of 22)	12912	NM_178246	229512	Mm.439830	NM_173188	ENSMUSG00000001415	Smg5	BC024683|mKIAA1089	Smg-5 homolog, nonsense mediated mRNA decay factor (C. elegans)	protein-coding
mm_167683.1	chr9	82985911	82985911	+	1	NA	Intergenic	Lx8b|LINE|L1	-10422	NM_001081216	83946	Mm.221688	NM_031879	ENSMUSG00000032253	Phip	2810004D21Rik|4632404O06Rik|Ndrp|Wdr11	pleckstrin homology domain interacting protein	protein-coding
mm_62918.1	chr7	118243861	118243871	+	1	NA	promoter-TSS (NM_001031814)	promoter-TSS (NM_001031814)	-41	NR_027879	67745	Mm.483404	NM_183267	ENSMUSG00000055159	4930583K01Rik	-	RIKEN cDNA 4930583K01 gene	ncRNA
mm_122256.1	chr14	34201583	34201602	-	1	NA	promoter-TSS (NM_183209)	promoter-TSS (NM_183209)	41	NM_183209	432839	Mm.294643	NM_183209	ENSMUSG00000071531	Gprin2	C130040D06Rik|C230073P13|Gm286|mKIAA0514	G protein regulated inducer of neurite outgrowth 2	protein-coding
mm_110459.1	chr12	51692052	51692058	-	1	NA	promoter-TSS (NM_001172098)	promoter-TSS (NM_001172098)	-141	NM_052973	94186	Mm.65979	NM_052973	ENSMUSG00000020954	Strn3	Gs2na|SG2NA	striatin, calmodulin binding protein 3	protein-coding
mm_1862.1	chr1	84952715	84952719	+	1	NA	Intergenic	Intergenic	-17634	NM_027921	71781	Mm.158754	NM_027921	ENSMUSG00000026220	Slc16a14	1110004H10Rik	solute carrier family 16 (monocarboxylic acid transporters), member 14	protein-coding
mm_73450.1	chr8	106305226	106305229	+	1	NA	intron (NM_021491, intron 1 of 8)	PB1|SINE|Alu	22998	NR_126090	75044	Mm.445896	NR_126090		4930506A18Rik	-	RIKEN cDNA 4930506A18 gene	ncRNA
mm_34328.1	chr4	142018008	142018034	+	1	NA	non-coding (NR_131014, exon 1 of 2)	non-coding (NR_131014, exon 1 of 2)	123	NR_131014	78917	Mm.139995	NR_131014	ENSMUSG00000085761	4930455G09Rik	-	RIKEN cDNA 4930455G09 gene	ncRNA
mm_69425.1	chr7	132786915	132786941	-	1	NA	promoter-TSS (NM_175268)	promoter-TSS (NM_175268)	7	NM_175268	77938	Mm.225649	NM_175268	ENSMUSG00000030956	Fam53b	A930008G19Rik|mKIAA0140	family with sequence similarity 53, member B	protein-coding
mm_115347.1	chr13	112660740	112660795	+	1	NA	promoter-TSS (NM_178746)	promoter-TSS (NM_178746)	1	NM_178746	268706	Mm.40834	NM_175376	ENSMUSG00000047789	Slc38a9	4833412L08Rik|6720411P22Rik|9130023D20Rik|9430067K09Rik|A730092C09	solute carrier family 38, member 9	protein-coding
mm_160650.1	chr9	110951321	110951321	+	1	NA	promoter-TSS (NM_028838)	promoter-TSS (NM_028838)	-224	NM_028838	74249	Mm.307615	NM_028838	ENSMUSG00000032495	Lrrc2	2400002D05Rik|4933431K03Rik	leucine rich repeat containing 2	protein-coding
mm_65625.1	chr7	27541779	27541798	-	1	NA	exon (NM_011116, exon 6 of 14)	exon (NM_011116, exon 6 of 14)	11430	NM_011116	18807	Mm.6483	NM_011116	ENSMUSG00000003363	Pld3	Sam-9	phospholipase D family, member 3	protein-coding
mm_126652.1	chr15	84167805	84167824	+	1	NA	promoter-TSS (NR_105816)	promoter-TSS (NR_105816)	-2	NM_054088	116939	Mm.390817	NM_054088	ENSMUSG00000041653	Pnpla3	Adpn	patatin-like phospholipase domain containing 3	protein-coding
mm_74104.1	chr8	122848408	122848437	+	1	NA	promoter-TSS (NM_007662)	promoter-TSS (NM_007662)	48	NM_007662	12555	Mm.1976	NM_007662	ENSMUSG00000031962	Cdh15	AI323380|Cdh14|Mcad	cadherin 15	protein-coding
mm_172094.1	chr6	23090910	23090925	+	1	NA	intron (NM_013930, intron 18 of 23)	ERVB7_2B-LTR_MM|LTR|ERVK	42069	NM_013930	30956	Mm.18651	NM_013930	ENSMUSG00000029695	Aass	LKR|LKR/SDH|LOR|LOR/SDH|Lorsdh|SDH	aminoadipate-semialdehyde synthase	protein-coding
mm_77397.1	chr8	120419948	120419953	-	1	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	-68916	NM_198671	382034	Mm.334856	NM_198671	ENSMUSG00000031822	Gse1	2210013I18Rik|mKIAA0182	genetic suppressor element 1, coiled-coil protein	protein-coding
mm_163928.1	chr14	47277135	47277143	+	1	NA	promoter-TSS (NM_080843)	promoter-TSS (NM_080843)	-4	NM_080843	67296	Mm.23957	NM_080843	ENSMUSG00000048379	Socs4	3110032M18Rik|A730004F22Rik|AI427843|AU015727|AU015859|Socs7	suppressor of cytokine signaling 4	protein-coding
mm_124604.1	chr15	3279158	3279183	+	1	NA	exon (NM_009155, exon 5 of 5)	exon (NM_009155, exon 5 of 5)	8193	NM_009155	20363	Mm.392203	NM_009155	ENSMUSG00000064373	Selenop	AU018766|D15Ucla1|Se-P|Sepp1|selp	selenoprotein P	protein-coding
mm_36036.1	chr4	57241006	57241008	-	1	NA	intron (NM_011207, intron 10 of 25)	intron (NM_011207, intron 10 of 25)	60830	NM_011207	545622	Mm.246552	NM_011207	ENSMUSG00000038764	Ptpn3	9530011I20Rik|PTP-H1|PTPCL	protein tyrosine phosphatase, non-receptor type 3	protein-coding
mm_62465.1	chr7	101663636	101663679	+	1	NA	promoter-TSS (NM_009191)	promoter-TSS (NM_009191)	-111	NM_009191	20480	Mm.3990	NM_009191	ENSMUSG00000001829	Clpb	AL118244|Skd3	ClpB caseinolytic peptidase B	protein-coding
mm_21522.1	chr2	163634462	163634474	-	1	NA	exon (NM_012032, exon 4 of 10)	exon (NM_012032, exon 4 of 10)	-10382	NR_028113	68386	Mm.410649	NR_028113	ENSMUSG00000058812	0610039K10Rik	-	RIKEN cDNA 0610039K10 gene	ncRNA
mm_170858.1	chr2	180725270	180725270	+	1	NA	promoter-TSS (NM_183161)	promoter-TSS (NM_183161)	-69	NM_183161	228993	Mm.87189	NM_183161	ENSMUSG00000023393	Slc17a9	1700019H03Rik|BC019537|Vnut	solute carrier family 17, member 9	protein-coding
mm_172519.1	chr7	80846894	80846905	-	1	NA	Intergenic	RLTR31C_MM|LTR|ERVK	-15209	NM_009553	22691	Mm.358645	NM_009553	ENSMUSG00000038797	Zscan2	Zfp-29|Zfp29	zinc finger and SCAN domain containing 2	protein-coding
mm_54458.1	chr6	34862573	34862613	-	1	NA	promoter-TSS (NM_197986)	promoter-TSS (NM_197986)	-553	NM_197986	68487	Mm.248440	NM_197986	ENSMUSG00000057137	Tmem140	1110007F12Rik	transmembrane protein 140	protein-coding
mm_137163.1	chr17	23806520	23806531	+	1	NA	intron (NM_175229, intron 1 of 13)	intron (NM_175229, intron 1 of 13)	3338	NM_175229	75956	Mm.5222	NM_175229	ENSMUSG00000039218	Srrm2	5033413A03Rik|AA410130|SRm300|mKIAA0324	serine/arginine repetitive matrix 2	protein-coding
mm_153882.1	chr19	46941036	46941044	-	1	NA	intron (NM_001164365, intron 2 of 17)	intron (NM_001164365, intron 2 of 17)	21311	NM_029810	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_73565.1	chr8	109575835	109575850	+	1	NA	exon (NM_017370, exon 5 of 5)	exon (NM_017370, exon 5 of 5)	3330	NM_017370	15439	Mm.26730	NM_017370	ENSMUSG00000031722	Hp	HP-1|preHP2	haptoglobin	protein-coding
mm_101242.1	chr11	20712243	20712247	-	1	NA	exon (NM_001252503, exon 3 of 8)	exon (NM_001252503, exon 3 of 8)	29311	NM_001290545	216549	Mm.356580	NM_181411	ENSMUSG00000049659	Aftph	-	aftiphilin	protein-coding
mm_91448.1	chr10	33939884	33939899	-	1	NA	intron (NM_028287, intron 5 of 9)	B3A|SINE|B2	11321	NM_028287	72580	Mm.248081	NM_028287	ENSMUSG00000039531	Zufsp	2700019D07Rik	zinc finger with UFM1-specific peptidase domain	protein-coding
mm_24594.1	chr3	93445219	93445227	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	2893	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_145194.1	chr18	49880734	49880746	+	1	NA	exon (NM_001081371, exon 19 of 43)	exon (NM_001081371, exon 19 of 43)	47743	NM_001081371	240283	Mm.257790	NM_001081371	ENSMUSG00000037416	Dmxl1	C630007L23Rik|D030030C22	Dmx-like 1	protein-coding
mm_30600.1	chr4	6385506	6385518	+	1	NA	intron (NM_001098227, intron 5 of 8)	intron (NM_001098227, intron 5 of 8)	19832	NM_001098227	53378	Mm.247473	NM_016807	ENSMUSG00000028249	Sdcbp	MDA-9|Sycl|syntenin-1	syndecan binding protein	protein-coding
mm_66876.1	chr7	57509917	57509976	-	1	NA	promoter-TSS (NM_176942)	promoter-TSS (NM_176942)	63	NM_176942	110886	Mm.273114	NM_176942	ENSMUSG00000055078	Gabra5	A230018I05Rik	gamma-aminobutyric acid (GABA) A receptor, subunit alpha 5	protein-coding
mm_54905.1	chr6	47594968	47595047	-	1	NA	promoter-TSS (NM_001146689)	promoter-TSS (NM_001146689)	23	NM_007971	14056	Mm.246688	NM_007971	ENSMUSG00000029687	Ezh2	Enx-1|Enx1h|KMT6|mKIAA4065	enhancer of zeste 2 polycomb repressive complex 2 subunit	protein-coding
mm_5364.1	chr1	25830058	25830077	-	1	NA	promoter-TSS (NM_175642)	promoter-TSS (NM_175642)	-360	NM_175642	210933	Mm.336569	NM_175642	ENSMUSG00000033569	Adgrb3	A830096D10Rik|Bai3	adhesion G protein-coupled receptor B3	protein-coding
mm_111186.1	chr12	84148450	84148499	-	1	NA	promoter-TSS (NM_027438)	promoter-TSS (NM_027438)	15	NM_027438	70481	Mm.444348	NM_027438	ENSMUSG00000054383	Pnma1	5730402C15Rik	paraneoplastic antigen MA1	protein-coding
mm_123697.1	chr14	69707547	69707567	-	1	NA	promoter-TSS (NM_001146012)	promoter-TSS (NM_001146012)	27	NM_001146012	71843	Mm.27738	NM_001146012	ENSMUSG00000034194	R3hcc1	1700020M16Rik|AA407796	R3H domain and coiled-coil containing 1	protein-coding
mm_77160.1	chr8	111687183	111687196	-	1	NA	exon (NM_025583, exon 6 of 7)	exon (NM_025583, exon 6 of 7)	2485	NR_106044	102466993		NR_106044	ENSMUSG00000099129	Mir7076	Gm27318|mmu-mir-7076	microRNA 7076	ncRNA
mm_134332.1	chr16	16456072	16456075	-	1	NA	intron (NM_001301817, intron 10 of 16)	intron (NM_001301817, intron 10 of 16)	71338	NM_001301818	224014	Mm.256131	NM_139232	ENSMUSG00000022788	Fgd4	9030023J02Rik|9330209B17Rik|Frabp|ZFYVE6	FYVE, RhoGEF and PH domain containing 4	protein-coding
mm_28737.1	chr3	95737049	95737061	-	1	NA	exon (NM_007899, exon 6 of 11)	exon (NM_007899, exon 6 of 11)	-2082	NR_105981	102466787		NR_105981	ENSMUSG00000098737	Mir7014	Gm27837|mmu-mir-7014	microRNA 7014	ncRNA
mm_166720.1	chr6	120302724	120302727	-	1	NA	Intergenic	Intergenic	-8166	NM_198884	330406	Mm.321840	NM_198884	ENSMUSG00000041372	B4galnt3	AB114826|B4GalNAcT3|C330047A21	beta-1,4-N-acetyl-galactosaminyl transferase 3	protein-coding
mm_37599.1	chr4	126752016	126752022	-	1	NA	exon (NM_011986, exon 2 of 7)	exon (NM_011986, exon 2 of 7)	1410	NM_011986	26562	Mm.206206	NM_011986	ENSMUSG00000028833	Ncdn	AU042419|MMS10-AE|Ms10ae|mKIAA0607|norbin	neurochondrin	protein-coding
mm_138747.1	chr17	37009968	37009968	+	1	NA	TTS (NM_010814)	TTS (NM_010814)	6302	NR_033137	22715	Mm.305561	NM_009559	ENSMUSG00000036036	Zfp57	G19|Zfp-57	zinc finger protein 57	protein-coding
mm_147805.1	chr18	61665402	61665416	-	1	NA	non-coding (NR_045402, exon 1 of 5)	non-coding (NR_045402, exon 1 of 5)	129	NR_045402	328968	Mm.392305	NR_045402		Carmn	Carmen|E330013P06|Gm16908|Mir143hg	cardiac mesoderm enhancer-associated non-coding RNA	ncRNA
mm_15797.1	chr2	164445423	164445433	+	1	NA	Intergenic	Intergenic	-2240	NM_011521	20971	Mm.3815	NM_011521	ENSMUSG00000017009	Sdc4	AA959608|AW108331|S4|Synd4|ryudocan|syndecan-4	syndecan 4	protein-coding
mm_114388.1	chr13	63252605	63252609	+	1	NA	intron (NR_110520, intron 2 of 5)	intron (NR_110520, intron 2 of 5)	12578	NR_110521	72061	Mm.188105	NM_028079	ENSMUSG00000021458	2010111I01Rik	2300006M17Rik|AP-O|AW742919|Aopep|ApO|mir-23b|mir-24-1|mir-27b	RIKEN cDNA 2010111I01 gene	protein-coding
mm_85621.1	chr9	107614931	107614956	-	1	NA	3' UTR (NM_008138, exon 9 of 9)	3' UTR (NM_008138, exon 9 of 9)	-5702	NM_001291539	20347	Mm.4083	NM_009153	ENSMUSG00000057969	Sema3b	SemA|Semaa|sema5|semaV	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B	protein-coding
mm_86736.1	chr10	19117430	19117446	+	1	NA	Intergenic	Intergenic	-24311	NR_038021	100504265	Mm.383417	NR_038021		Gm20139	-	predicted gene, 20139	ncRNA
mm_49573.1	chr6	30640890	30640946	+	1	NA	exon (NM_025350, exon 4 of 10)	exon (NM_025350, exon 4 of 10)	1700	NM_025350	109697	Mm.25377	NM_025350	ENSMUSG00000054446	Cpa1	0910001L12Rik|Cpa	carboxypeptidase A1, pancreatic	protein-coding
mm_83440.1	chr9	45001015	45001034	-	1	NA	exon (NM_007648, exon 6 of 8)	exon (NM_007648, exon 6 of 8)	8566	NM_007648	12501	Mm.210361	NM_007648	ENSMUSG00000032093	Cd3e	AI504783|CD3|CD3epsilon|T3e	CD3 antigen, epsilon polypeptide	protein-coding
mm_159124.1	chr2	70562765	70562765	+	1	NA	intron (NM_001312900, intron 1 of 6)	CpG	592	NR_040496	68986	Mm.437697	NR_040496	ENSMUSG00000087264	Gad1os	1500002O10Rik	glutamate decarboxylase 1, opposite strand	ncRNA
mm_77921.1	chr9	7352600	7352614	+	1	NA	intron (NM_001320077, intron 5 of 10)	L1MA6|LINE|L1	5233	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_7125.1	chr1	90843993	90844004	-	1	NA	promoter-TSS (NM_001243009)	promoter-TSS (NM_001243009)	-27	NM_001243008	12835	Mm.7562	NM_009935	ENSMUSG00000048126	Col6a3	AI507288|Col6a-3	collagen, type VI, alpha 3	protein-coding
mm_33477.1	chr4	130818767	130818788	+	1	NA	exon (NM_011520, exon 3 of 5)	exon (NM_011520, exon 3 of 5)	26240	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_27152.1	chr3	33082874	33082887	-	1	NA	5' UTR (NM_021483, exon 1 of 15)	5' UTR (NM_021483, exon 1 of 15)	180	NM_021483	58869	Mm.151332	NM_021483	ENSMUSG00000027674	Pex5l	1700016J08Rik|PXR2|Pex2|TRIP8b|pex5Rp	peroxisomal biogenesis factor 5-like	protein-coding
mm_36011.1	chr4	56846020	56846039	-	1	NA	intron (NM_018761, intron 2 of 18)	intron (NM_018761, intron 2 of 18)	19182	NM_018761	54366	Mm.218891	NM_018761	ENSMUSG00000038816	Ctnnal1	ACRP|AI616177|AW545119|C86009|Catnal1	catenin (cadherin associated protein), alpha-like 1	protein-coding
mm_33091.1	chr4	124695910	124695920	+	1	NA	Intergenic	Intergenic	-2361	NM_026031	67205	Mm.259121	NM_026031	ENSMUSG00000028907	Utp11l	2700082D03Rik|CGI-94|Cgi94|Utp11	UTP11-like, U3 small nucleolar ribonucleoprotein, (yeast)	protein-coding
mm_54711.1	chr6	39725420	39725429	-	1	NA	promoter-TSS (NM_139294)	promoter-TSS (NM_139294)	39	NM_139294	109880	Mm.245513	NM_139294	ENSMUSG00000002413	Braf	9930012E13Rik|AA120551|AA387315|AA473386|B-raf|Braf-2|Braf2|C230098H17|C87398|D6Ertd631e	Braf transforming gene	protein-coding
mm_107638.1	chr12	52446885	52446907	+	1	NA	Intergenic	Intergenic	33713	NR_136881	102638611	Mm.363799	NR_136881		Gm35135	-	predicted gene, 35135	ncRNA
mm_87862.1	chr10	61175713	61175729	+	1	NA	intron (NM_001017409, intron 1 of 3)	intron (NM_001017409, intron 1 of 3)	459	NM_023064	65971	Mm.30227	NM_023064	ENSMUSG00000020096	Tbata	1700021K02Rik|AI428928|Spatial|Titest	thymus, brain and testes associated	protein-coding
mm_113066.1	chr13	23751070	23751086	+	1	NA	promoter-TSS (NM_175660)	promoter-TSS (NM_175660)	-10	NM_175660	319172	Mm.423402	NM_175660	ENSMUSG00000061615	Hist1h2ab	H2A.1|H2a-53	histone cluster 1, H2ab	protein-coding
mm_143006.1	chr17	56434590	56434593	-	1	NA	exon (NM_001252453, exon 10 of 29)	exon (NM_001252453, exon 10 of 29)	-15682	NR_105943	102465590		NR_105943	ENSMUSG00000098339	Mir6977	Gm27922|mmu-mir-6977	microRNA 6977	ncRNA
mm_56447.1	chr6	97519093	97519096	-	1	NA	intron (NM_145148, intron 2 of 23)	ID_B1|SINE|B4	-31274	NM_001346637	232288	Mm.27789	NM_145148	ENSMUSG00000030064	Frmd4b	6030440G05Rik|C87375|GOBLIN|GRSP1|R74720	FERM domain containing 4B	protein-coding
mm_74618.1	chr8	12915734	12915778	-	1	NA	promoter-TSS (NM_178076)	promoter-TSS (NM_178076)	-137	NM_178076	17207	Mm.334413	NM_178076	ENSMUSG00000031442	Mcf2l	C130040G20Rik|Dbs|Ost|mKIAA0362	mcf.2 transforming sequence-like	protein-coding
mm_74993.1	chr8	27202525	27202535	-	1	NA	promoter-TSS (NM_029674)	promoter-TSS (NM_029674)	17	NM_029674	76615	Mm.272794	NM_029674	ENSMUSG00000039720	Got1l1	1700083M11Rik	glutamic-oxaloacetic transaminase 1-like 1	protein-coding
mm_98302.1	chr11	90032996	90033002	+	1	NA	intron (NM_026433, intron 1 of 2)	(A)n|Simple_repeat|Simple_repeat	2651	NM_026433	67888	Mm.212428	NM_026433	ENSMUSG00000069763	Tmem100	1810057C19Rik|AV011897	transmembrane protein 100	protein-coding
mm_30306.1	chr3	149445187	149445244	-	1	NA	Intergenic	Intergenic	170478	NR_040591	381482	Mm.393866	NR_040591		Gm1653	-	predicted gene 1653	ncRNA
mm_140192.1	chr17	83351006	83351016	+	1	NA	promoter-TSS (NM_001114361)	promoter-TSS (NM_001114361)	80	NM_001114362	78798	Mm.295565	NM_199466	ENSMUSG00000032624	Eml4	4930443C24Rik|AI644019	echinoderm microtubule associated protein like 4	protein-coding
mm_170140.1	chr17	39848782	39848789	+	1	NA	TTS (NR_046233)	TTS (NR_046233)	5788	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_86326.1	chr9	123061773	123061779	-	1	NA	exon (NM_177911, exon 11 of 14)	exon (NM_177911, exon 11 of 14)	27035	NM_177911	331046	Mm.195309	NM_177911	ENSMUSG00000025787	Tgm4	9530008N10Rik|Eapa1|TGP	transglutaminase 4 (prostate)	protein-coding
mm_84314.1	chr9	63719042	63719046	-	1	NA	intron (NM_016769, intron 1 of 8)	intron (NM_016769, intron 1 of 8)	38950	NM_016769	17127	Mm.7320	NM_016769	ENSMUSG00000032402	Smad3	AU022421|Madh3	SMAD family member 3	protein-coding
mm_152068.1	chr19	6542990	6543014	-	1	NA	promoter-TSS (NM_009203)	promoter-TSS (NM_009203)	68	NM_009203	20521	Mm.391146	NM_009203	ENSMUSG00000061742	Slc22a12	AI987855|OAT4L|Rst|Slc22al2|URAT1	solute carrier family 22 (organic anion/cation transporter), member 12	protein-coding
mm_170268.1	chr18	20961551	20961562	+	1	NA	intron (NM_026301, intron 1 of 5)	CpG	16931	NM_026301	67664	Mm.45980	NM_026301	ENSMUSG00000033107	Rnf125	4930553F04Rik	ring finger protein 125	protein-coding
mm_34922.1	chr4	155802914	155802924	+	1	NA	promoter-TSS (NM_025570)	promoter-TSS (NM_025570)	-699	NM_025570	66448	Mm.23825	NM_025570	ENSMUSG00000029066	Mrpl20	2610008D01Rik|4930425I20Rik	mitochondrial ribosomal protein L20	protein-coding
mm_63379.1	chr7	127212853	127212863	+	1	NA	intron (NM_016754, intron 1 of 6)	intron (NM_016754, intron 1 of 6)	1250	NM_016754	17907	Mm.14526	NM_016754	ENSMUSG00000030672	Mylpf	2410014J02Rik|MLC-2|Mlc2	myosin light chain, phosphorylatable, fast skeletal muscle	protein-coding
mm_130745.1	chr15	101256917	101256931	-	1	NA	Intergenic	Intergenic	-9922	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_133727.1	chr16	93778723	93778736	+	1	NA	intron (NM_027293, intron 23 of 36)	intron (NM_027293, intron 23 of 36)	-53392	NM_001045529	338467	Mm.287329	NM_001045529	ENSMUSG00000039456	Morc3	1110051N18Rik|AI452146|BF318192|D16Jhu32e|NXP2|Zcwcc3	microrchidia 3	protein-coding
mm_52006.1	chr6	92940595	92940619	+	1	NA	promoter-TSS (NR_015530)	promoter-TSS (NR_015530)	25	NR_015530	330385	Mm.483472	NR_015530	ENSMUSG00000097462	9530026P05Rik	B430306B02	RIKEN cDNA 9530026P05 gene	ncRNA
mm_17652.1	chr2	32045587	32045616	-	1	NA	intron (NM_172268, intron 32 of 35)	intron (NM_172268, intron 32 of 35)	-5345	NR_106135	102466844		NR_106135	ENSMUSG00000099075	Mir7674	Gm27563|mmu-mir-7674	microRNA 7674	ncRNA
mm_81751.1	chr9	113956021	113956027	+	1	NA	exon (NM_001083319, exon 5 of 17)	exon (NM_001083319, exon 5 of 17)	25090	NM_013699	22221	Mm.28052	NM_013699	ENSMUSG00000009741	Ubp1	Cp2b|LBP-1a|LBP-1b|NF2d9	upstream binding protein 1	protein-coding
mm_98470.1	chr11	94950311	94950329	+	1	NA	exon (NM_007742, exon 48 of 51)	exon (NM_007742, exon 48 of 51)	14096	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_89610.1	chr10	96026705	96026723	+	1	NA	exon (NM_001001932, exon 19 of 29)	exon (NM_001001932, exon 19 of 29)	86051	NM_001001932	216238	Mm.210035	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding
mm_142303.1	chr17	42742025	42742027	-	1	NA	5' UTR (NM_001033493, exon 1 of 6)	5' UTR (NM_001033493, exon 1 of 6)	153	NM_001033493	435529	Mm.136350	NM_001033493	ENSMUSG00000057899	Adgrf2	Gpr111|PGR20	adhesion G protein-coupled receptor F2	protein-coding
mm_50645.1	chr6	51464419	51464429	+	1	NA	intron (NR_104468, intron 7 of 10)	intron (NR_104468, intron 7 of 10)	5470	NM_182650	53379	Mm.155896	NM_016806	ENSMUSG00000004980	Hnrnpa2b1	9130414A06Rik|Hnrpa2|Hnrpa2b1|hnrnp-A	heterogeneous nuclear ribonucleoprotein A2/B1	protein-coding
mm_112600.1	chr13	14161285	14161298	+	1	NA	intron (NM_198122, intron 13 of 22)	intron (NM_198122, intron 13 of 22)	97507	NM_198122	94246	Mm.439784	NM_194262	ENSMUSG00000039219	Arid4b	BCAA|BRCAA1|RBBP1L1|Rbp1l1|SAP180	AT rich interactive domain 4B (RBP1-like)	protein-coding
mm_81964.1	chr9	120933878	120933910	+	1	NA	intron (NM_007614, intron 1 of 14)	CpG	316	NM_001165902	12387	Mm.291928	NM_007614	ENSMUSG00000006932	Ctnnb1	Bfc|Catnb|Mesc	catenin (cadherin associated protein), beta 1	protein-coding
mm_110813.1	chr12	72374325	72374348	-	1	NA	intron (NM_153457, intron 1 of 8)	intron (NM_153457, intron 1 of 8)	34718	NM_001286448	104001	Mm.221275	NM_153457	ENSMUSG00000021087	Rtn1	Nsp	reticulon 1	protein-coding
mm_165117.1	chr19	60812221	60812221	-	1	NA	intron (NM_001347464, intron 1 of 7)	intron (NM_001347464, intron 1 of 7)	651	NM_001167829	67894	Mm.26148	NM_026437	ENSMUSG00000024993	Fam45a	1810055E12Rik	family with sequence similarity 45, member A	protein-coding
mm_96726.1	chr11	69684356	69684384	+	1	NA	intron (NM_001034097, intron 10 of 12)	intron (NM_001034097, intron 10 of 12)	1184	NM_001159505	69583	Mm.8983	NM_023517	ENSMUSG00000089669	Tnfsf13	2310026N09Rik|April|Tall2|Tnlg7b|Trdl1	tumor necrosis factor (ligand) superfamily, member 13	protein-coding
mm_164751.1	chr17	78937238	78937244	+	1	NA	promoter-TSS (NM_001024806)	promoter-TSS (NM_001024806)	106	NM_028611	73694	Mm.104959	NM_028611	ENSMUSG00000024082	Ndufaf7	2410091C18Rik|AL033374|PRO1853	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex assembly factor 7	protein-coding
mm_146603.1	chr18	9508511	9508534	-	1	NA	Intergenic	Intergenic	-58372	NM_026484	67974	Mm.86523	NM_026484	ENSMUSG00000024286	Ccny	1700025H17Rik|3110050L10Rik|4631402G10Rik|5730405I09Rik	cyclin Y	protein-coding
mm_4672.1	chr1	180393345	180393348	+	1	NA	intron (NM_001081175, intron 2 of 7)	intron (NM_001081175, intron 2 of 7)	-62797	NR_003623	277333	Mm.389223	NM_199472		Gm5069	EG277333	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_70705.1	chr8	15057647	15057660	+	1	NA	promoter-TSS (NM_008664)	promoter-TSS (NM_008664)	0	NM_008664	17930	Mm.272115	NM_008664	ENSMUSG00000031461	Myom2	AW146149	myomesin 2	protein-coding
mm_51870.1	chr6	90552184	90552194	+	1	NA	intron (NM_027406, intron 1 of 22)	intron (NM_027406, intron 1 of 22)	1341	NM_027406	107747	Mm.30035	NM_027406	ENSMUSG00000030088	Aldh1l1	1810048F20Rik|FDH|Fthfd|Neut2	aldehyde dehydrogenase 1 family, member L1	protein-coding
mm_164228.1	chr15	87342064	87342066	+	1	NA	Intergenic	Intergenic	-202234	NM_001252310	106014	Mm.244319	NM_134096	ENSMUSG00000054863	Fam19a5	TAFA5|Tafa-5|Tara-5	family with sequence similarity 19, member A5	protein-coding
mm_17806.1	chr2	33431295	33431347	-	1	NA	promoter-TSS (NM_001085507)	promoter-TSS (NM_001085507)	3	NM_001085507	241311	Mm.296512	NM_001085507	ENSMUSG00000068966	Zbtb34	Gm349|mKIAA1993	zinc finger and BTB domain containing 34	protein-coding
mm_75825.1	chr8	70488116	70488126	-	1	NA	promoter-TSS (NM_182991)	promoter-TSS (NM_182991)	-763	NM_182991	67937	Mm.23002	NM_182991	ENSMUSG00000035964	Tmem59l	5330410G16Rik	transmembrane protein 59-like	protein-coding
mm_145941.1	chr18	67343754	67343764	+	1	NA	5' UTR (NM_007702, exon 1 of 5)	5' UTR (NM_007702, exon 1 of 5)	195	NM_007702	12683	Mm.449	NM_007702	ENSMUSG00000024526	Cidea	AW212747	cell death-inducing DNA fragmentation factor, alpha subunit-like effector A	protein-coding
mm_25029.1	chr3	98149083	98149109	+	1	NA	3' UTR (NM_010928, exon 34 of 34)	3' UTR (NM_010928, exon 34 of 34)	-11538	NM_027665	71078	Mm.50711	NM_027665	ENSMUSG00000043468	Adam30	4933424D07Rik|svph4	a disintegrin and metallopeptidase domain 30	protein-coding
mm_107744.1	chr12	58436963	58436973	+	1	NA	Intergenic	Intergenic	-167710	NM_025809	66864	Mm.280563	NM_025809	ENSMUSG00000045930	Clec14a	1200003C23Rik|AI642649	C-type lectin domain family 14, member a	protein-coding
mm_9983.1	chr1	191242181	191242203	-	1	NA	Intergenic	Intergenic	-58859	NM_007498	11910	Mm.2706	NM_007498	ENSMUSG00000026628	Atf3	LRG-21	activating transcription factor 3	protein-coding
mm_11739.1	chr2	37776282	37776297	+	1	NA	promoter-TSS (NM_001163566)	promoter-TSS (NM_001163566)	40	NM_001163566	241324	Mm.392369	NM_001163566	ENSMUSG00000035403	Crb2	5930402A21|BC043114	crumbs family member 2	protein-coding
mm_172975.1	chr9	93917734	93917748	-	1	NA	Intergenic	L1Md_T|LINE|L1	620340	NM_001033145	68861	Mm.258746	NM_001033145	ENSMUSG00000045414	1190002N15Rik	GoPro49|HASF	RIKEN cDNA 1190002N15 gene	protein-coding
mm_124051.1	chr14	77861317	77861343	-	1	NA	intron (NM_025384, intron 1 of 5)	RLTR8|LTR|ERVK	13587	NM_025384	66148	Mm.248046	NM_025384	ENSMUSG00000022013	Dnajc15	1110003P16Rik|Dnajd1	DnaJ heat shock protein family (Hsp40) member C15	protein-coding
mm_137832.1	chr17	30800668	30800672	+	1	NA	intron (NM_013811, intron 77 of 92)	intron (NM_013811, intron 77 of 92)	-101197	NM_021332	14652	Mm.390969	NM_021332	ENSMUSG00000024027	Glp1r	GLP-1R|GLP1Rc	glucagon-like peptide 1 receptor	protein-coding
mm_54526.1	chr6	36387846	36387861	-	1	NA	promoter-TSS (NM_203491)	promoter-TSS (NM_203491)	-231	NM_203491	243764	Mm.448632	NM_203491	ENSMUSG00000045613	Chrm2	AChR-M2|Chrm-2|M2	cholinergic receptor, muscarinic 2, cardiac	protein-coding
mm_99429.1	chr11	102407614	102407632	+	1	NA	promoter-TSS (NM_026542)	promoter-TSS (NM_026542)	-106	NM_026542	68066	Mm.44226	NM_026542	ENSMUSG00000018677	Slc25a39	3010027G13Rik|D11Ertd333e	solute carrier family 25, member 39	protein-coding
mm_26965.1	chr3	22077479	22077499	-	1	NA	intron (NM_030732, intron 1 of 15)	intron (NM_030732, intron 1 of 15)	837	NM_030732	81004	Mm.202966	NM_030732	ENSMUSG00000027630	Tbl1xr1	8030499H02Rik|A630076E03Rik|AW539987|C21|C230089I12Rik|DC42|Ira1|TBLR1	transducin (beta)-like 1X-linked receptor 1	protein-coding
mm_151990.1	chr19	5849944	5849961	-	1	NA	Intergenic	Intergenic	-4472	NR_003513	66961	Mm.281895	NR_003513	ENSMUSG00000092274	Neat1	2310043N10Rik|VINC	nuclear paraspeckle assembly transcript 1 (non-protein coding)	ncRNA
mm_9550.1	chr1	173923087	173923098	-	1	NA	intron (NM_001302649, intron 9 of 9)	BGLII_B|LTR|ERVK	-10046	NM_001033450	381308	Mm.490248	NM_001033450	ENSMUSG00000026536	Ifi211	A730048F03|Ifi205b|Mnda|ifi-205-B	interferon activated gene 211	protein-coding
mm_43116.1	chr5	124629051	124629097	+	1	NA	promoter-TSS (NM_011596)	promoter-TSS (NM_011596)	22	NM_011596	21871	Mm.1158	NM_011596	ENSMUSG00000038023	Atp6v0a2	8430408C20Rik|AI385560|ATP6a2|AW489264|Atp6n1d|Atp6n2|C76904|ISF|J6B7|SHIF|Stv1|TJ6M|TJ6s|Tj6|V-ATPase 116 kDa|V-ATPase a2	ATPase, H+ transporting, lysosomal V0 subunit A2	protein-coding
mm_126445.1	chr15	80711293	80711340	+	1	NA	promoter-TSS (NM_144812)	promoter-TSS (NM_144812)	3	NM_144812	213988	Mm.131328	NM_144812	ENSMUSG00000047888	Tnrc6b	2700090M07Rik|A730065C02Rik|AI848765|D230019K20Rik	trinucleotide repeat containing 6b	protein-coding
mm_168281.1	chr1	107800142	107800153	+	1	NA	Intergenic	MT2_Mm|LTR|ERVL	-117112	NR_102306	319596	Mm.136054	NR_102306	ENSMUSG00000100457	D830032E09Rik	-	RIKEN cDNA D830032E09 gene	ncRNA
mm_25968.1	chr3	132814989	132814999	+	1	NA	intron (NM_001163455, intron 24 of 25)	intron (NM_001163455, intron 24 of 25)	63602	NR_102297	101243624	Mm.306256	NR_102297	ENSMUSG00000106230	Gm29811	-	predicted gene, 29811	ncRNA
mm_170603.1	chr19	5844004	5844022	+	1	NA	non-coding (NR_003513, exon 1 of 1)	non-coding (NR_003513, exon 1 of 1)	1465	NR_131212	66961	Mm.281895	NR_003513	ENSMUSG00000092274	Neat1	2310043N10Rik|VINC	nuclear paraspeckle assembly transcript 1 (non-protein coding)	ncRNA
mm_133499.1	chr16	90497169	90497200	+	1	NA	3' UTR (NM_015755, exon 11 of 11)	3' UTR (NM_015755, exon 11 of 11)	110787	NM_015755	26559	Mm.125874	NM_015755	ENSMUSG00000053414	Hunk	Bstk1|Mak-v	hormonally upregulated Neu-associated kinase	protein-coding
mm_144124.1	chr18	4908907	4908940	+	1	NA	Intergenic	Intergenic	96437	NR_045881	100038439	Mm.387569	NR_045881	ENSMUSG00000097043	Gm10556	ENSMUSG00000073646	predicted gene 10556	ncRNA
mm_59509.1	chr7	27574391	27574480	+	1	NA	intron (NM_175107, intron 7 of 9)	PB1D10|SINE|Alu	13959	NM_001122767	66367	Mm.29831	NM_175107	ENSMUSG00000049643	2310022A10Rik	-	RIKEN cDNA 2310022A10 gene	protein-coding
mm_147915.1	chr18	65582159	65582186	-	1	NA	intron (NM_207255, intron 1 of 5)	intron (NM_207255, intron 1 of 5)	1942	NM_207255	328977	Mm.286232	NM_207255	ENSMUSG00000042439	Zfp532	C530030I18Rik|Znf532|mKIAA1629	zinc finger protein 532	protein-coding
mm_75168.1	chr8	36669216	36669217	-	1	NA	intron (NM_001194940, intron 5 of 17)	intron (NM_001194940, intron 5 of 17)	-55273	NM_015802	50768	Mm.125155	NM_015802	ENSMUSG00000031523	Dlc1	A730069N07Rik|Arhgap7|HP|STARD12|dlc-1	deleted in liver cancer 1	protein-coding
mm_58019.1	chr6	136661708	136661718	-	1	NA	5' UTR (NM_025806, exon 1 of 11)	5' UTR (NM_025806, exon 1 of 11)	180	NM_025806	66857	Mm.3311	NM_025806	ENSMUSG00000030214	Plbd1	1100001H23Rik	phospholipase B domain containing 1	protein-coding
mm_76744.1	chr8	95331757	95331836	-	1	NA	promoter-TSS (NM_133954)	promoter-TSS (NM_133954)	154	NM_024467	79233	Mm.350514	NM_024467	ENSMUSG00000046556	Zfp319	AI225750|AI413472|Znf319|mKIAA1388	zinc finger protein 319	protein-coding
mm_155944.1	chrX	104489036	104489039	+	1	NA	intron (NM_001081189, intron 1 of 6)	intron (NM_001081189, intron 1 of 6)	6255	NM_001081189	331487	Mm.438275	NM_001081189	ENSMUSG00000073016	Uprt	Gm774	uracil phosphoribosyltransferase	protein-coding
mm_34887.1	chr4	155601273	155601277	+	1	NA	promoter-TSS (NM_177186)	promoter-TSS (NM_177186)	-141	NM_177186	320541	Mm.306018	NM_177186	ENSMUSG00000042202	Slc35e2	A530082C11Rik|AI957035	solute carrier family 35, member E2	protein-coding
mm_12879.1	chr2	84678456	84678458	+	1	NA	promoter-TSS (NM_001290751)	promoter-TSS (NM_001290751)	55	NM_025885	381379	Mm.219643	NM_025885	ENSMUSG00000027080	Med19	2410018M14Rik|3110040A13Rik|LCMR1	mediator complex subunit 19	protein-coding
mm_173301.1	chrY	62724049	62724049	+	1	NA	Intergenic	Intergenic	-259204	NM_001160143	100040031	Mm.463839	NM_001160143	ENSMUSG00000093950	Gm20823	-	predicted gene, 20823	protein-coding
mm_113388.1	chr13	33039946	33039954	+	1	NA	exon (NM_011452, exon 7 of 7)	exon (NM_011452, exon 7 of 7)	12536	NM_011452	20706	Mm.45371	NM_011452	ENSMUSG00000021403	Serpinb9b	1600019A21Rik|R86|SPI-CI|Spi10|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 9b	protein-coding
mm_18838.1	chr2	75119311	75119321	-	1	NA	Intergenic	Intergenic	293504	NM_016804	53375	Mm.292613	NM_016804	ENSMUSG00000027099	Mtx2	1500012G02Rik	metaxin 2	protein-coding
mm_90939.1	chr10	12923104	12923143	-	1	NA	promoter-TSS (NR_038028)	promoter-TSS (NR_038028)	4	NR_038027	320273	Mm.417706	NR_038027	ENSMUSG00000097378	B230208H11Rik	-	RIKEN cDNA B230208H11 gene	ncRNA
mm_11067.1	chr2	27676419	27676421	+	1	NA	promoter-TSS (NM_011305)	promoter-TSS (NM_011305)	-781	NM_011305	20181	Mm.24624	NM_011305	ENSMUSG00000015846	Rxra	9530071D11Rik|Nr2b1|RXRalpha1	retinoid X receptor alpha	protein-coding
mm_98989.1	chr11	98753513	98753531	+	1	NA	5' UTR (NM_001313983, exon 2 of 10)	5' UTR (NM_001313983, exon 2 of 10)	11737	NM_001313983	21833	Mm.265917	NM_178060	ENSMUSG00000058756	Thra	6430529J03Rik|AW259572|Erba|Nr1a1|Rvr|T3R[a]|T3Ralpha|Thra1|Thra2|c-erbA-1|c-erbA-alpha|c-erbAalpha	thyroid hormone receptor alpha	protein-coding
mm_68190.1	chr7	104307143	104307146	-	1	NA	exon (NM_023835, exon 2 of 8)	exon (NM_023835, exon 2 of 8)	-7887	NR_040749	622070	Mm.486406	NR_040749	ENSMUSG00000087175	Gm15133	OTTMUSG00000019186	predicted gene 15133	ncRNA
mm_7922.1	chr1	133801032	133801038	-	1	NA	Intergenic	Intergenic	-47288	NM_213616	381290	Mm.188617	NM_213616	ENSMUSG00000026463	Atp2b4	Pmca4	ATPase, Ca++ transporting, plasma membrane 4	protein-coding
mm_160353.1	chr8	21297396	21297396	+	1	NA	promoter-TSS (NM_007851)	promoter-TSS (NM_007851)	2	NM_007851	13239	Mm.426634	NM_007851	ENSMUSG00000074439	Defa5	Defa29|Defcr29|Defcr5	defensin, alpha, 5	protein-coding
mm_104286.1	chr11	90121811	90121815	-	1	NA	Intergenic	Intergenic	91465	NM_026433	67888	Mm.212428	NM_026433	ENSMUSG00000069763	Tmem100	1810057C19Rik|AV011897	transmembrane protein 100	protein-coding
mm_64336.1	chr7	142376435	142376452	+	1	NA	3' UTR (NM_009983, exon 9 of 9)	3' UTR (NM_009983, exon 9 of 9)	-2697	NM_001347541	320802	Mm.154486	NM_177265	ENSMUSG00000045777	Ifitm10	6330512M04Rik|AI848576|DSPA3	interferon induced transmembrane protein 10	protein-coding
mm_19351.1	chr2	90917988	90918107	-	1	NA	promoter-TSS (NM_025576)	promoter-TSS (NM_025576)	3	NM_025576	66461	Mm.23926	NM_025576		Ptpmt1	1110001D10Rik|2810004N20Rik|PLIP	protein tyrosine phosphatase, mitochondrial 1	protein-coding
mm_157173.1	chrX	9471027	9471029	-	1	NA	Intergenic	LTR33A|LTR|ERVL	-1704	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_166892.1	chr7	28142221	28142234	+	1	NA	exon (NM_001164655, exon 6 of 20)	exon (NM_001164655, exon 6 of 20)	12761	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_65328.1	chr7	24972686	24972694	-	1	NA	promoter-TSS (NM_010261)	promoter-TSS (NM_010261)	38	NM_010261	14470	Mm.22473	NM_010261	ENSMUSG00000003380	Rabac1	2310040I06Rik|Gbpap1|PRA1|prenylin	Rab acceptor 1 (prenylated)	protein-coding
mm_105307.1	chr11	102780259	102780260	-	1	NA	TTS (NM_009613)	TTS (NM_009613)	18824	NM_001110778	11488	Mm.89854	NM_009613	ENSMUSG00000020926	Adam11	AW060611|Mdc	a disintegrin and metallopeptidase domain 11	protein-coding
mm_115005.1	chr13	98316385	98316406	+	1	NA	promoter-TSS (NR_137279)	promoter-TSS (NR_137279)	572	NM_145455	218490	Mm.371688	NM_145455	ENSMUSG00000021660	Btf3	1700054E11Rik	basic transcription factor 3	protein-coding
mm_80634.1	chr9	89211284	89211297	+	1	NA	promoter-TSS (NM_026829)	promoter-TSS (NM_026829)	100	NM_026829	107885	Mm.486274	NM_026829	ENSMUSG00000066442	Mthfs	1110034I12Rik|2310020H23Rik|AI119695	5, 10-methenyltetrahydrofolate synthetase	protein-coding
mm_44060.1	chr5	148265308	148265318	+	1	NA	intron (NM_029920, intron 7 of 14)	intron (NM_029920, intron 7 of 14)	127502	NM_001301424	11987	Mm.275489	NM_007513	ENSMUSG00000041313	Slc7a1	4831426K01Rik|AI447493|Atrc-1|Atrc1|Cat1|Rec-1|Rev-1|mCAT-1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 1	protein-coding
mm_94589.1	chr11	11744128	11744130	+	1	NA	intron (NM_001301866, intron 3 of 5)	intron (NM_001301866, intron 3 of 5)	53952	NM_001301863	22778	Mm.103545	NM_009578	ENSMUSG00000018654	Ikzf1	5832432G11Rik|Ikaros|LyF-1|Zfpn1a1|Znfn1a1|hlk-1|mKIAA4227	IKAROS family zinc finger 1	protein-coding
mm_101212.1	chr11	20077235	20077250	-	1	NA	exon (NM_146243, exon 7 of 9)	exon (NM_146243, exon 7 of 9)	35709	NM_146243	66713	Mm.259045	NM_146243	ENSMUSG00000020152	Actr2	4921510D23Rik|AA409782|Arp2|D6Ertd746e	ARP2 actin-related protein 2	protein-coding
mm_18569.1	chr2	65364012	65364066	-	1	NA	promoter-TSS (NM_177074)	promoter-TSS (NM_177074)	-13	NM_177074	320106	Mm.227703	NM_177074	ENSMUSG00000061171	Slc38a11	9330158F14Rik	solute carrier family 38, member 11	protein-coding
mm_107783.1	chr12	61524601	61524640	+	1	NA	5' UTR (NM_001310586, exon 1 of 6)	5' UTR (NM_001310586, exon 1 of 6)	1453	NM_001310586	238205	Mm.28802	NM_178714	ENSMUSG00000035653	Lrfn5	AI427653|AI604817|C130061B21|mKIAA4208	leucine rich repeat and fibronectin type III domain containing 5	protein-coding
mm_113699.1	chr13	43126021	43126034	+	1	NA	intron (NM_001005740, intron 9 of 12)	intron (NM_001005740, intron 9 of 12)	3188	NM_001005748	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding
mm_66793.1	chr7	47132399	47132412	-	1	NA	5' UTR (NM_001163565, exon 1 of 14)	5' UTR (NM_001163565, exon 1 of 14)	193	NM_001163565	19259	Mm.4654	NM_013643	ENSMUSG00000030854	Ptpn5	Step	protein tyrosine phosphatase, non-receptor type 5	protein-coding
mm_39513.1	chr5	21256772	21256786	+	1	NA	intron (NM_175437, intron 18 of 30)	B1_Mur4|SINE|Alu	70512	NM_175437	212167	Mm.121705	NM_175437	ENSMUSG00000039934	Gsap	A530088I07Rik|Pion	gamma-secretase activating protein	protein-coding
mm_158155.1	chrX	103480511	103480561	-	1	NA	non-coding (NR_001570, exon 1 of 8)	non-coding (NR_001570, exon 1 of 8)	2697	NR_001570	213742	Mm.274770	NR_001463	ENSMUSG00000086503	Xist	A430022B11|AI314753	inactive X specific transcripts	ncRNA
mm_85947.1	chr9	112108137	112108154	-	1	NA	intron (NM_001177618, intron 17 of 18)	intron (NM_001177618, intron 17 of 18)	10566	NR_029823	723815		NR_029823	ENSMUSG00000065441	Mir128-2	Mirn128-2|Mirn128b|mir-128-2|mir-128b	microRNA 128-2	ncRNA
mm_87672.1	chr10	58824464	58824470	+	1	NA	intron (NM_172788, intron 1 of 9)	(T)n|Simple_repeat|Simple_repeat	11108	NM_172788	237353	Mm.333078	NM_172788	ENSMUSG00000037990	Sh3rf3	4831416G18Rik|Igfbp5-ip|Sh3md4|Sh3rf31	SH3 domain containing ring finger 3	protein-coding
mm_120462.1	chr14	65970885	65970903	+	1	NA	intron (NM_013492, intron 1 of 8)	intron (NM_013492, intron 1 of 8)	2411	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_93910.1	chr10	127030814	127030838	-	1	NA	promoter-TSS (NM_025537)	promoter-TSS (NM_025537)	-12	NM_025537	66399	Mm.29900	NM_025537	ENSMUSG00000040521	Tsfm	2310050B20Rik|9430024O13Rik|EF-TS|EF-Tsmt	Ts translation elongation factor, mitochondrial	protein-coding
mm_638.1	chr1	40398583	40398611	+	1	NA	Intergenic	Intergenic	-30973	NM_001294171	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_113623.1	chr13	41637397	41637399	+	1	NA	3' UTR (NM_001163572, exon 3 of 3)	3' UTR (NM_001163572, exon 3 of 3)	-12045	NM_177808	328231	Mm.227476	NM_177808	ENSMUSG00000054258	Gm5082	A030008J09|EG328231	predicted gene 5082	protein-coding
mm_25155.1	chr3	103028843	103028868	+	1	NA	5' UTR (NM_001310693, exon 2 of 18)	5' UTR (NM_001310693, exon 2 of 18)	8309	NM_144901	229663	Mm.277713	NM_144901	ENSMUSG00000068823	Csde1	AA960392|BC016898|D3Jfr1|mKIAA0885|unr	cold shock domain containing E1, RNA binding	protein-coding
mm_138299.1	chr17	34630970	34630985	+	1	NA	exon (NM_030890, exon 2 of 4)	exon (NM_030890, exon 2 of 4)	1291	NM_030890	260297	Mm.390965	NM_030890	ENSMUSG00000015476	Prrt1	Bat-4|Bat4|D17H6S54E|DSPD1|G5b|NG5|ORF31	proline-rich transmembrane protein 1	protein-coding
mm_35501.1	chr4	41048125	41048140	-	1	NA	promoter-TSS (NM_007473)	promoter-TSS (NM_007473)	4	NM_007473	11832	Mm.8728	NM_007473	ENSMUSG00000028427	Aqp7	AQP7L|AQPap	aquaporin 7	protein-coding
mm_80099.1	chr9	70298284	70298292	+	1	NA	intron (NM_181072, intron 3 of 27)	intron (NM_181072, intron 3 of 27)	90938	NM_181072	71602	Mm.249311	NM_181072	ENSMUSG00000032220	Myo1e	2310020N23Rik|9130023P14Rik|AA407778|myosin-1e|myr 3	myosin IE	protein-coding
mm_118929.1	chr14	27039067	27039077	+	1	NA	promoter-TSS (NM_134437)	promoter-TSS (NM_134437)	71	NM_134437	171463	Mm.206726	NM_027265	ENSMUSG00000040717	Il17rd	2810004A10Rik|AI428510|Sef|Sef-S	interleukin 17 receptor D	protein-coding
mm_32306.1	chr4	103151032	103151072	+	1	NA	intron (NM_001039081, intron 10 of 12)	intron (NM_001039081, intron 10 of 12)	31662	NM_001039081	71148	Mm.288721	NM_027696	ENSMUSG00000028522	Mier1	4933425I22Rik|5830411K19Rik|er1	MEIR1 treanscription regulator	protein-coding
mm_169053.1	chr13	21833497	21833512	-	1	NA	promoter-TSS (NM_001110555)	promoter-TSS (NM_001110555)	-29	NM_178185	319171	Mm.250564	NM_178185	ENSMUSG00000094777	Hist1h2ap	ENSMUSG00000060262|Gm11276|OTTMUSG00000000448	histone cluster 1, H2ap	protein-coding
mm_68509.1	chr7	111082998	111083037	-	1	NA	promoter-TSS (NM_013507)	promoter-TSS (NM_013507)	13	NM_001040131	13690	Mm.185453	NM_013507	ENSMUSG00000005610	Eif4g2	DAP-5|E130105L11Rik|Nat1|Natm1|p97	eukaryotic translation initiation factor 4, gamma 2	protein-coding
mm_23992.1	chr3	86362488	86362488	+	1	NA	intron (NM_001077687, intron 30 of 50)	intron (NM_001077687, intron 30 of 50)	137798	NM_001077687	80877	Mm.439825	NM_030695	ENSMUSG00000028080	Lrba	C80285|D3Ertd775e|Lab300|Lba	LPS-responsive beige-like anchor	protein-coding
mm_42103.1	chr5	110514858	110514879	+	1	NA	promoter-TSS (NR_102290)	promoter-TSS (NR_102290)	-55	NR_102290	231603	Mm.22836	NM_173766	ENSMUSG00000048215	A630023P12Rik	-	RIKEN cDNA A630023P12 gene	ncRNA
mm_46894.1	chr5	113993874	113993902	-	1	NA	promoter-TSS (NM_198109)	promoter-TSS (NM_198109)	-131	NM_198109	231637	Mm.389682	NM_198109	ENSMUSG00000042121	Ssh1	AW551225|Gm1394|Gm1395|SSH-1|SSH-1L	slingshot homolog 1 (Drosophila)	protein-coding
mm_106451.1	chr11	119943341	119943355	-	1	NA	intron (NM_001037754, intron 1 of 13)	CpG	256	NM_130862	108100	Mm.197534	NM_130862	ENSMUSG00000025372	Baiap2	IRSp53|R75030	brain-specific angiogenesis inhibitor 1-associated protein 2	protein-coding
mm_156687.1	chrX	159414527	159414536	+	1	NA	promoter-TSS (NM_001081124)	promoter-TSS (NM_001081124)	-41	NM_001081124	78283	Mm.160079	NM_001081124	ENSMUSG00000041020	Map7d2	1600028E09Rik|2900002G04Rik|5330432J06Rik|C030036K04Rik|Mtap7d2	MAP7 domain containing 2	protein-coding
mm_43999.1	chr5	146833270	146833280	+	1	NA	intron (NM_019647, intron 1 of 5)	CpG	385	NM_019647	19933	Mm.316592	NM_019647	ENSMUSG00000041453	Rpl21	8430440E03Rik|L21	ribosomal protein L21	protein-coding
mm_12225.1	chr2	67971248	67971262	+	1	NA	Intergenic	Intergenic	-133417	NM_020283	26877	Mm.226435	NM_020283	ENSMUSG00000034780	B3galt1	beta3Gal-T1	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 1	protein-coding
mm_224.1	chr1	17601894	17601913	+	1	NA	promoter-TSS (NM_053191)	promoter-TSS (NM_053191)	2	NM_053191	94227	Mm.442452	NM_053191	ENSMUSG00000067780	Pi15	P24TI|P25TI|PI-15|SugarCrisp	peptidase inhibitor 15	protein-coding
mm_14104.1	chr2	125591642	125591656	+	1	NA	intron (NM_001081091, intron 13 of 27)	MTEa-int|LTR|ERVL-MaLR	33464	NM_001081091	99100	Mm.330545	NM_001081091	ENSMUSG00000068394	Cep152	AI851464|mKIAA0912	centrosomal protein 152	protein-coding
mm_52213.1	chr6	103510632	103510634	+	1	NA	promoter-TSS (NM_007697)	promoter-TSS (NM_007697)	-243	NM_007697	12661	Mm.251288	NM_007697	ENSMUSG00000030077	Chl1	A530023M13Rik|AI465420|CALL|LICAM2	cell adhesion molecule L1-like	protein-coding
mm_10854.1	chr2	25051643	25051684	+	1	NA	exon (NM_146251, exon 30 of 35)	exon (NM_146251, exon 30 of 35)	-2716	NM_001177654	56876	Mm.42956	NM_020276	ENSMUSG00000006476	Nsmf	Jacob|Nelf	NMDA receptor synaptonuclear signaling and neuronal migration factor	protein-coding
mm_113824.1	chr13	46986438	46986464	+	1	NA	Intergenic	Intergenic	28399	NM_175340	105193	Mm.25593	NM_175340	ENSMUSG00000044231	Nhlrc1	AI505271|B230309E09Rik|EPM2B	NHL repeat containing 1	protein-coding
mm_26542.1	chr3	146150229	146150249	+	1	NA	promoter-TSS (NM_001005846)	promoter-TSS (NM_001005846)	65	NM_001005846	68279	Mm.116862	NM_026656	ENSMUSG00000011008	Mcoln2	3300002C04Rik|AI549968|C86638|TRPML2	mucolipin 2	protein-coding
mm_104783.1	chr11	98584247	98584281	-	1	NA	intron (NM_025661, intron 1 of 3)	intron (NM_025661, intron 1 of 3)	2981	NM_025661	66612	Mm.180546	NM_025661	ENSMUSG00000038150	Ormdl3	2810011N17Rik|AI315223	ORM1-like 3 (S. cerevisiae)	protein-coding
mm_26197.1	chr3	138526439	138526458	+	1	NA	promoter-TSS (NR_035481)	promoter-TSS (NR_035481)	27	NR_035481	100316706		NR_035481	ENSMUSG00000088373	Mir1956	mir-1956|mmu-mir-1956	microRNA 1956	ncRNA
mm_171997.1	chr6	104385260	104385262	-	1	NA	Intergenic	L1Md_T|LINE|L1	-107783	NM_017383	53870	Mm.321671	NM_017383	ENSMUSG00000030092	Cntn6	NB-3	contactin 6	protein-coding
mm_39843.1	chr5	30889297	30889320	+	1	NA	promoter-TSS (NM_001294262)	promoter-TSS (NM_001294262)	-26	NM_001294262	231093	Mm.440364	NM_174849	ENSMUSG00000029165	Agbl5	9430057O19Rik|CCP5	ATP/GTP binding protein-like 5	protein-coding
mm_149626.1	chr19	17136745	17136781	+	1	NA	intron (NM_181348, intron 9 of 19)	intron (NM_181348, intron 9 of 19)	180645	NM_181348	353211	Mm.257354	NM_181348	ENSMUSG00000039126	Prune2	6330414G02Rik|A230083H22Rik|A330102H22Rik|Bmcc1|mKIAA0367	prune homolog 2	protein-coding
mm_146417.1	chr18	84589782	84589808	+	1	NA	promoter-TSS (NM_001033341)	promoter-TSS (NM_001033341)	-291	NM_001033341	240476	Mm.329575	NM_001033341	ENSMUSG00000048410	Zfp407	6430585N13Rik|Gm333|Gm334|Gm948|ZNF407	zinc finger protein 407	protein-coding
mm_35398.1	chr4	34614887	34614931	-	1	NA	promoter-TSS (NM_015824)	promoter-TSS (NM_015824)	33	NM_001159563	50793	Mm.399624	NM_015824	ENSMUSG00000040044	Orc3	Orc3l	origin recognition complex, subunit 3	protein-coding
mm_155321.1	chrX	62372178	62372189	+	1	NA	Intergenic	Intergenic	85041	NM_001199996	74437	Mm.85792	NM_001199996	ENSMUSG00000045330	4933402E13Rik	-	RIKEN cDNA 4933402E13 gene	protein-coding
mm_131474.1	chr16	17070265	17070275	+	1	NA	5' UTR (NM_023249, exon 1 of 5)	5' UTR (NM_023249, exon 1 of 5)	131	NM_001291047	106369	Mm.237941	NM_023249	ENSMUSG00000022773	Ypel1	0610009L05Rik|1700016N17Rik|1700019O22Rik|4921520K19Rik|4930511F14Rik|AV118478|DGL-1|Dgl1|Ppil2|mdgl-1	yippee-like 1 (Drosophila)	protein-coding
mm_43946.1	chr5	145128084	145128117	+	1	NA	TTS (NM_001033313)	TTS (NM_001033313)	11989	NM_001033313	231887	Mm.188851	NM_001033313	ENSMUSG00000029623	Pdap1	HASPP28|PAP|PAP1	PDGFA associated protein 1	protein-coding
mm_112106.1	chr12	112785744	112785763	-	1	NA	Intergenic	Intergenic	-23222	NM_145450	217887	Mm.186678	NM_145450	ENSMUSG00000037594	BC022687	AW050009|C130001I08Rik|Flj20080	cDNA sequence BC022687	protein-coding
mm_73163.1	chr8	95013287	95013313	+	1	NA	3' UTR (NM_001198894, exon 14 of 14)	3' UTR (NM_001198894, exon 14 of 14)	-4392	NM_173036	54672	Mm.27995	NM_173036	ENSMUSG00000060470	Adgrg3	A030001G24Rik|AW214383|Gpr97|Pb1|Pb99	adhesion G protein-coupled receptor G3	protein-coding
mm_38199.1	chr4	135494500	135494583	-	1	NA	promoter-TSS (NM_028995)	promoter-TSS (NM_028995)	-37	NM_028995	74552	Mm.26548	NM_028995	ENSMUSG00000028803	Nipal3	9130020G22Rik|AI480660|Npal3	NIPA-like domain containing 3	protein-coding
mm_32501.1	chr4	108459922	108459928	+	1	NA	intron (NM_175472, intron 1 of 30)	CpG	499	NM_175472	230594	Mm.25181	NM_175472	ENSMUSG00000034610	Zcchc11	6030404K05Rik|9230115F04Rik|PPAPD3|mKIAA0191	zinc finger, CCHC domain containing 11	protein-coding
mm_37040.1	chr4	115647711	115647728	-	1	NA	promoter-TSS (NM_007823)	promoter-TSS (NM_007823)	-14	NM_007823	13120	Mm.1840	NM_007823	ENSMUSG00000028713	Cyp4b1	-	cytochrome P450, family 4, subfamily b, polypeptide 1	protein-coding
mm_71168.1	chr8	40546596	40546617	+	1	NA	3' UTR (NM_033560, exon 12 of 12)	3' UTR (NM_033560, exon 12 of 12)	-30759	NM_001271542	18983	Mm.272551	NM_011135	ENSMUSG00000031601	Cnot7	AU022737|CAF-1|Caf1|Pop2	CCR4-NOT transcription complex, subunit 7	protein-coding
mm_28616.1	chr3	94979895	94979900	-	1	NA	intron (NM_001293716, intron 1 of 9)	intron (NM_001293716, intron 1 of 9)	5166	NM_001293716	107650	Mm.217222	NM_175356	ENSMUSG00000038861	Pi4kb	ESTM41|PI4K-beta|PI4Kbeta|Pik4cb	phosphatidylinositol 4-kinase, catalytic, beta polypeptide	protein-coding
mm_93661.1	chr10	117693136	117693144	-	1	NA	intron (NM_001288586, intron 8 of 10)	intron (NM_001288586, intron 8 of 10)	17618	NM_010786	17246	Mm.22670	NM_010786	ENSMUSG00000020184	Mdm2	1700007J15Rik|AA415488|Mdm-2	transformed mouse 3T3 cell double minute 2	protein-coding
mm_123666.1	chr14	69245248	69245258	-	1	NA	exon (NM_026331, exon 4 of 4)	exon (NM_026331, exon 4 of 4)	39850	NM_026331	67712	Mm.293635	NM_026331	ENSMUSG00000034248	Slc25a37	1700020E22Rik|4930513O14Rik|4930526G11Rik|AI848481|C330015G08Rik|Mfrn|Mfrn1|Mscp|frascati|mitoferrin	solute carrier family 25, member 37	protein-coding
mm_159355.1	chr3	80801617	80801617	-	1	NA	intron (NM_001083806, intron 2 of 15)	intron (NM_001083806, intron 2 of 15)	1174	NM_013540	14800	Mm.220224	NM_013540	ENSMUSG00000033981	Gria2	GluA2|GluR-B|Glur-2|Glur2	glutamate receptor, ionotropic, AMPA2 (alpha 2)	protein-coding
mm_105821.1	chr11	112774354	112774362	-	1	NA	Intergenic	Intergenic	-7852	NM_011448	20682	Mm.286407	NM_011448	ENSMUSG00000000567	Sox9	2010306G03Rik|AV220920|mKIAA4243	SRY (sex determining region Y)-box 9	protein-coding
mm_164935.1	chr18	84101934	84101934	+	1	NA	Intergenic	Intergenic	13776	NM_146090	225791	Mm.147052	NM_146090	ENSMUSG00000049090	Zadh2	C530046K17Rik|PTGR-3|Pthr3	zinc binding alcohol dehydrogenase, domain containing 2	protein-coding
mm_38471.1	chr4	140659534	140659544	-	1	NA	intron (NM_001290803, intron 1 of 28)	intron (NM_001290803, intron 1 of 28)	6348	NM_001290803	72754	Mm.29329	NM_172415	ENSMUSG00000040964	Arhgef10l	2810441C07Rik	Rho guanine nucleotide exchange factor (GEF) 10-like	protein-coding
mm_113593.1	chr13	40971562	40971569	+	1	NA	Intergenic	Intergenic	-29445	NM_026550	68083	Mm.24789	NM_026550	ENSMUSG00000038683	Pak1ip1	5830431I15Rik|5930415H02Rik|AA419825|AI314040|AW556169|Gdpd1|PIP1	PAK1 interacting protein 1	protein-coding
mm_72096.1	chr8	71586480	71586526	+	1	NA	3' UTR (NM_011977, exon 14 of 14)	3' UTR (NM_011977, exon 14 of 14)	-5681	NM_025396	66171	Mm.282284	NM_025396	ENSMUSG00000031807	Pgls	1110030K05Rik|AI447866|Plgs	6-phosphogluconolactonase	protein-coding
mm_36882.1	chr4	107239280	107239283	-	1	NA	intron (NM_029985, intron 5 of 7)	ORR1B1-int|LTR|ERVL-MaLR	14252	NM_029985	77809	Mm.29681	NM_029985	ENSMUSG00000028617	Lrrc42	A930011F22Rik|AA536996	leucine rich repeat containing 42	protein-coding
mm_72157.1	chr8	72169287	72169291	+	1	NA	intron (NM_023126, intron 2 of 7)	PB1D10|SINE|Alu	8089	NM_023126	17274	Mm.162811	NM_023126	ENSMUSG00000003037	Rab8a	AA409338|Mel	RAB8A, member RAS oncogene family	protein-coding
mm_124262.1	chr14	102978559	102978571	-	1	NA	3' UTR (NM_177715, exon 1 of 1)	3' UTR (NM_177715, exon 1 of 1)	4067	NR_039592	100628599		NR_039592	ENSMUSG00000092901	Mir5130	mir-5130|mmu-mir-5130|mu-mir-5130	microRNA 5130	ncRNA
mm_142709.1	chr17	47888183	47888189	-	1	NA	exon (NM_028767, exon 3 of 17)	exon (NM_028767, exon 3 of 17)	36446	NM_028767	74123	Mm.240062	NM_028767	ENSMUSG00000023991	Foxp4	1200010K03Rik|2310007G05Rik|mFKHLA	forkhead box P4	protein-coding
mm_72264.1	chr8	75097216	75097224	+	1	NA	exon (NM_010442, exon 3 of 5)	exon (NM_010442, exon 3 of 5)	3602	NM_010442	15368	Mm.276389	NM_010442	ENSMUSG00000005413	Hmox1	D8Wsu38e|HO-1|HO1|Hemox|Hmox|Hsp32	heme oxygenase 1	protein-coding
mm_65788.1	chr7	28893739	28893763	-	1	NA	TTS (NM_001110807)	TTS (NM_001110807)	12095	NM_001110807	60594	Mm.476990	NM_021894	ENSMUSG00000054083	Capn12	CANP 12	calpain 12	protein-coding
mm_84906.1	chr9	79977541	79977549	-	1	NA	5' UTR (NM_001081243, exon 1 of 6)	5' UTR (NM_001081243, exon 1 of 6)	337	NM_001081243	70598	Mm.23049	NM_001081243	ENSMUSG00000034898	Filip1	5730485H21Rik|AI843021	filamin A interacting protein 1	protein-coding
mm_34819.1	chr4	154961001	154961017	+	1	NA	promoter-TSS (NM_010419)	promoter-TSS (NM_010419)	86	NM_010419	15208	Mm.137268	NM_010419	ENSMUSG00000048001	Hes5	bHLHb38	hairy and enhancer of split 5 (Drosophila)	protein-coding
mm_67347.1	chr7	79826909	79826927	-	1	NA	exon (NM_008486, exon 16 of 20)	exon (NM_008486, exon 16 of 20)	15434	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_170637.1	chr1	98946785	98946797	+	1	NA	Intergenic	L1Md_A|LINE|L1	525667	NM_027584	70866	Mm.389164	NM_027584	ENSMUSG00000026336	Slco6d1	4921511I05Rik	solute carrier organic anion transporter family, member 6d1	protein-coding
mm_20707.1	chr2	132946053	132946066	-	1	NA	promoter-TSS (NM_198029)	promoter-TSS (NM_198029)	-23	NM_198029	241639	Mm.209784	NM_198029	ENSMUSG00000027356	Fermt1	5830467P10Rik|Kindlin-1	fermitin family member 1	protein-coding
mm_173344.1	chrY	90812968	90812968	+	1	NA	intron (NM_133362, intron 2 of 3)	(TTAGGG)n|Simple_repeat|Simple_repeat	26438	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_113534.1	chr13	37845855	37845883	+	1	NA	intron (NM_001039188, intron 1 of 9)	intron (NM_001039188, intron 1 of 9)	18476	NM_001039188	68750	Mm.491109	NM_026830	ENSMUSG00000039087	Rreb1	1110037N09Rik|AA414966|B930013M22Rik	ras responsive element binding protein 1	protein-coding
mm_116901.1	chr13	55426770	55426780	-	1	NA	promoter-TSS (NM_021489)	promoter-TSS (NM_021489)	29	NM_021489	58992	Mm.42224	NM_021489	ENSMUSG00000021492	F12	FXII|HAF	coagulation factor XII (Hageman factor)	protein-coding
mm_34385.1	chr4	144921461	144921467	+	1	NA	intron (NM_011303, intron 4 of 5)	intron (NM_011303, intron 4 of 5)	28327	NM_011303	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding
mm_48948.1	chr6	4540529	4540542	+	1	NA	exon (NM_007743, exon 52 of 52)	exon (NM_007743, exon 52 of 52)	34917	NM_007743	12843	Mm.277792	NM_007743	ENSMUSG00000029661	Col1a2	AA960264|AI325291|Col1a-2|Cola-2|Cola2|oim	collagen, type I, alpha 2	protein-coding
mm_157128.1	chrX	9446809	9446850	-	1	NA	exon (NM_007807, exon 9 of 13)	exon (NM_007807, exon 9 of 13)	22495	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_134624.1	chr16	21650108	21650108	-	1	NA	3' UTR (NM_001001881, exon 2 of 2)	3' UTR (NM_001001881, exon 2 of 2)	44557	NM_001001881	72190	Mm.131606	NM_001001881	ENSMUSG00000043391	2510009E07Rik	AI194952	RIKEN cDNA 2510009E07 gene	protein-coding
mm_60260.1	chr7	43811322	43811324	+	1	NA	promoter-TSS (NM_011872)	promoter-TSS (NM_011872)	29	NM_011872	23993	Mm.251227	NM_011872	ENSMUSG00000030713	Klk7	Prss6|SCCE	kallikrein related-peptidase 7 (chymotryptic, stratum corneum)	protein-coding
mm_167573.1	chr9	44275546	44275552	-	1	NA	intron (NM_138955, intron 12 of 14)	intron (NM_138955, intron 12 of 14)	-6950	NM_001163742	270151	Mm.3957	NM_178420	ENSMUSG00000032109	Nlrx1	BC034204|NOD9	NLR family member X1	protein-coding
mm_169730.1	chr15	81399740	81399740	-	1	NA	promoter-TSS (NM_133726)	promoter-TSS (NM_133726)	-46	NM_133726	70356	Mm.180337	NM_133726	ENSMUSG00000022403	St13	1110007I03Rik|3110002K08Rik|AW555194|HIP|HOP|HSPABP|HSPABP1|PRO0786|SNC6|p48	suppression of tumorigenicity 13	protein-coding
mm_144342.1	chr18	15011241	15011264	+	1	NA	intron (NM_134112, intron 1 of 4)	intron (NM_134112, intron 1 of 4)	22257	NR_045372	74456	Mm.391075	NR_045372		4933424G05Rik	-	RIKEN cDNA 4933424G05 gene	ncRNA
mm_104336.1	chr11	94052456	94052460	-	1	NA	intron (NM_001025429, intron 2 of 26)	PB1D9|SINE|Alu	8253	NM_001025429	70834	Mm.260737	NM_027569	ENSMUSG00000020859	Spag9	3110018C07Rik|4733401I23Rik|4831406C20Rik|AW552012|JLP|JSAP2|JSAP2a|Jip4|Mapk8ip4|syd1	sperm associated antigen 9	protein-coding
mm_131987.1	chr16	25042246	25042266	+	1	NA	Intergenic	Intergenic	-17383	NR_040374	319487	Mm.137341	NR_040374	ENSMUSG00000096960	A230028O05Rik	-	RIKEN cDNA A230028O05 gene	ncRNA
mm_145733.1	chr18	64265073	64265087	+	1	NA	intron (NM_009182, intron 2 of 5)	intron (NM_009182, intron 2 of 5)	10721	NM_009182	20451	Mm.252110	NM_009182	ENSMUSG00000056812	St8sia3	AI847333|ST8SiaIII|Siat8c	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3	protein-coding
mm_138834.1	chr17	39848419	39848427	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	5426	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_149349.1	chr19	10895226	10895272	+	1	NA	promoter-TSS (NM_134129)	promoter-TSS (NM_134129)	18	NM_001253843	28000	Mm.491104	NM_134129	ENSMUSG00000024735	Prpf19	AA617263|AL024362|D19Wsu55e|NMP200|PSO4|Prp19|Snev	pre-mRNA processing factor 19	protein-coding
mm_110685.1	chr12	67209521	67209524	-	1	NA	intron (NM_001193266, intron 1 of 16)	intron (NM_001193266, intron 1 of 16)	13027	NM_001193266	320772	Mm.227680	NM_207010	ENSMUSG00000034912	Mdga2	6720489L24Rik|9330209L04Rik|Adp|Mamdc1	MAM domain containing glycosylphosphatidylinositol anchor 2	protein-coding
mm_36533.1	chr4	86633161	86633165	-	1	NA	Intergenic	Intergenic	-21141	NM_173400	230376	Mm.74730	NM_173400	ENSMUSG00000038047	Haus6	6230416J20Rik|9830144E06|D4Ertd27e|mKIAA1574	HAUS augmin-like complex, subunit 6	protein-coding
mm_68137.1	chr7	102239626	102239653	-	1	NA	3' UTR (NM_019566, exon 2 of 2)	3' UTR (NM_019566, exon 2 of 2)	10479	NM_019566	56212	Mm.259795	NM_019566	ENSMUSG00000073982	Rhog	2810426G09Rik|Arhg|Sid10750	ras homolog family member G	protein-coding
mm_12394.1	chr2	70039268	70039306	+	1	NA	intron (NM_177376, intron 1 of 34)	intron (NM_177376, intron 1 of 34)	161	NM_177376	329421	Mm.99648	NM_177376	ENSMUSG00000042064	Myo3b	A430065P19Rik	myosin IIIB	protein-coding
mm_116981.1	chr13	56289332	56289368	-	1	NA	3' UTR (NM_019568, exon 4 of 4)	3' UTR (NM_019568, exon 4 of 4)	7201	NM_019568	57266	Mm.30211	NM_019568	ENSMUSG00000021508	Cxcl14	1110031L23Rik|1200006I23Rik|AI414372|BMAC|BRAK|KS1|Kec|MIP-2g|MIP2gamma|NJAC|Scyb14|bolekine	chemokine (C-X-C motif) ligand 14	protein-coding
mm_75032.1	chr8	32009489	32009519	-	1	NA	Intergenic	CpG	-91301	NM_178591	211323	Mm.153432	NM_178591	ENSMUSG00000062991	Nrg1	6030402G23Rik|ARIA|D230005F13Rik|GGF|GGFII|HRG|HRGalpha|Hgl|NDF|SMDF	neuregulin 1	protein-coding
mm_136503.1	chr16	96443666	96443676	-	1	NA	promoter-TSS (NM_008405)	promoter-TSS (NM_008405)	-57	NM_008405	16415	Mm.12872	NM_008405	ENSMUSG00000000157	Itgb2l	5033406G21Rik|pactolus	integrin beta 2-like	protein-coding
mm_10619.1	chr2	19371641	19371685	+	1	NA	promoter-TSS (NM_029619)	promoter-TSS (NM_029619)	27	NM_029619	76467	Mm.27166	NM_029619	ENSMUSG00000023094	Msrb2	2310050L06Rik|Mrsb|Msrb|Pilb	methionine sulfoxide reductase B2	protein-coding
mm_52323.1	chr6	108836643	108836652	+	1	NA	intron (NM_138677, intron 1 of 11)	intron (NM_138677, intron 1 of 11)	8006	NM_138677	192193	Mm.21596	NM_138677	ENSMUSG00000030104	Edem1	A130059K23Rik|EDEM|mKIAA0212	ER degradation enhancer, mannosidase alpha-like 1	protein-coding
mm_148804.1	chr19	6269041	6269073	+	1	NA	Intergenic	Intergenic	4213	NR_029720	387187		NR_029720	ENSMUSG00000065523	Mir192	Mirn192|mir-192|mmu-mir-192	microRNA 192	ncRNA
mm_173100.1	chrX	152690162	152690171	+	1	NA	intron (NM_001290684, intron 2 of 9)	BGLII|LTR|ERVK	-45618	NM_001290685	110380	Mm.40796	NM_172441	ENSMUSG00000045180	Shroom2	4832440C16|Apxl|C630003H05Rik|Shrm2	shroom family member 2	protein-coding
mm_137446.1	chr17	26532880	26532886	+	1	NA	Intergenic	Intergenic	-24411	NM_013642	19252	Mm.239041	NM_013642	ENSMUSG00000024190	Dusp1	3CH134|MKP1|Ptpn16|U19515|erp|mkp-1	dual specificity phosphatase 1	protein-coding
mm_74610.1	chr8	12478132	12478150	-	1	NA	Intergenic	Intergenic	82622	NM_009233	20664	Mm.39088	NM_009233	ENSMUSG00000096014	Sox1	BB176347|Sox-1	SRY (sex determining region Y)-box 1	protein-coding
mm_112870.1	chr13	20852728	20852741	+	1	NA	TTS (NM_001281854)	TTS (NM_001281854)	58621	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_7834.1	chr1	132139649	132139657	-	1	NA	promoter-TSS (NM_008795)	promoter-TSS (NM_008795)	32	NM_008795	18557	Mm.28130	NM_008795	ENSMUSG00000026437	Cdk18	AA682070|Ctk18|Pctk3	cyclin-dependent kinase 18	protein-coding
mm_148270.1	chr18	81924748	81924760	-	1	NA	Intergenic	Intergenic	67326	NR_039589	100628596		NR_039589	ENSMUSG00000093036	Mir5127	mmu-mir-5127|mu-mir-5127	microRNA 5127	ncRNA
mm_54669.1	chr6	39207172	39207211	-	1	NA	promoter-TSS (NM_001033430)	promoter-TSS (NM_001033430)	-418	NM_001033430	338523	Mm.293175	NM_001033430	ENSMUSG00000042599	Kdm7a	A630082K20Rik|BB041802|ENSMUSG00000073143|Jhdm1d|mKIAA1718	lysine (K)-specific demethylase 7A	protein-coding
mm_121984.1	chr14	26414629	26414667	-	1	NA	3' UTR (NM_032008, exon 23 of 23)	3' UTR (NM_032008, exon 23 of 23)	57101	NR_038005	71106	Mm.158564	NR_038005	ENSMUSG00000021874	4933413J09Rik	GCSE	RIKEN cDNA 4933413J09 gene	ncRNA
mm_58212.1	chr6	144099808	144099844	-	1	NA	intron (NM_001113559, intron 3 of 13)	intron (NM_001113559, intron 3 of 13)	109742	NM_001113559	20678	Mm.1752	NM_011444	ENSMUSG00000041540	Sox5	A730017D01Rik|AI528773	SRY (sex determining region Y)-box 5	protein-coding
mm_75136.1	chr8	35208445	35208456	-	1	NA	Intergenic	Intergenic	-167291	NM_177741	244416	Mm.247126	NM_177741	ENSMUSG00000046794	Ppp1r3b	6430576E21|AW821953|GL|PTG	protein phosphatase 1, regulatory (inhibitor) subunit 3B	protein-coding
mm_101426.1	chr11	29742913	29742916	-	1	NA	TTS (NM_146016)	TTS (NM_146016)	24351	NM_024226	68585	Mm.192580	NM_024226	ENSMUSG00000020458	Rtn4	1110020G17Rik|AA407876|AA409940|AA960376|ASY|C130026I10Rik|NOGO|NSP-CL|NgA|Nogo-A|Nogo-B|Nogo-C|mKIAA0886|mKIAA4153	reticulon 4	protein-coding
mm_4501.1	chr1	173673902	173673916	+	1	NA	5' UTR (NM_001162938, exon 1 of 7)	5' UTR (NM_001162938, exon 1 of 7)	229	NM_001162938	100033459	Mm.303377	NM_001162938	ENSMUSG00000066677	Ifi208	9830148g24rik|E430029J22Rik|Pydc3|Pyr-rv1	interferon activated gene 208	protein-coding
mm_126732.1	chr15	85646080	85646127	+	1	NA	Intergenic	CpG	-57670	NR_110483	102800312	Mm.33117	NR_110483		Lncppara	Lincppara|Mirlet7bhg|linc-Ppara	long noncoding RNA near Ppara	ncRNA
mm_157782.1	chrX	73806213	73806219	-	1	NA	intron (NM_001029868, intron 1 of 7)	intron (NM_001029868, intron 1 of 7)	18753	NM_001029868	245469	Mm.103782	NM_001029868	ENSMUSG00000002006	Pdzd4	B230341P03|D130075J17Rik|Kiaa1444-hp|LU1|PDZRN4L|Pdzk4|Pdzrnk4l|Xlu	PDZ domain containing 4	protein-coding
mm_168521.1	chr11	58215005	58215015	+	1	NA	promoter-TSS (NM_019440)	promoter-TSS (NM_019440)	33	NM_019440	54396	Mm.458517	NM_019440	ENSMUSG00000069874	Irgm2	AI481100|GTPI|Ifggd2|Iigp2	immunity-related GTPase family M member 2	protein-coding
mm_27402.1	chr3	51277312	51277443	-	1	NA	non-coding (NR_073429, exon 1 of 1)	non-coding (NR_073429, exon 1 of 1)	137	NM_001291062	69257	Mm.131038	NM_023502	ENSMUSG00000037174	Elf2	2610036A20Rik|A230104O07Rik|AW111824|BB183398|EU32|NERF|NERF-1A|NERF-1B|NERF-2	E74-like factor 2	protein-coding
mm_38316.1	chr4	137279196	137279202	-	1	NA	intron (NM_009523, intron 1 of 4)	intron (NM_009523, intron 1 of 4)	1564	NM_009523	22417	Mm.20355	NM_009523	ENSMUSG00000036856	Wnt4	Wnt-4	wingless-type MMTV integration site family, member 4	protein-coding
mm_142055.1	chr17	35643685	35643699	-	1	NA	promoter-TSS (NM_001033366)	promoter-TSS (NM_001033366)	3	NM_001033366	268949	Mm.296301	NM_001033366	ENSMUSG00000073408	Dpcr1	Gm630	diffuse panbronchiolitis critical region 1 (human)	protein-coding
mm_130962.1	chr15	103314997	103315023	-	1	NA	exon (NM_013866, exon 8 of 8)	exon (NM_013866, exon 8 of 8)	-4572	NM_030720	80910	Mm.160369	NM_030720	ENSMUSG00000063234	Gpr84	EX33	G protein-coupled receptor 84	protein-coding
mm_40419.1	chr5	53388950	53388955	+	1	NA	Intergenic	BC1_Mm|scRNA|scRNA	121846	NM_001145433	66278	Mm.27900	NM_001145433	ENSMUSG00000061461	Smim20	1110067B18Rik|1810013D10Rik|N28078	small integral membrane protein 20	protein-coding
mm_107696.1	chr12	55398921	55398931	+	1	NA	exon (NM_011968, exon 1 of 7)	exon (NM_011968, exon 1 of 7)	101	NM_011968	26443	Mm.30210	NM_011968	ENSMUSG00000021024	Psma6	IOTA	proteasome (prosome, macropain) subunit, alpha type 6	protein-coding
mm_108413.1	chr12	81860191	81860236	+	1	NA	5' UTR (NM_018814, exon 1 of 36)	5' UTR (NM_018814, exon 1 of 36)	183	NM_018814	54604	Mm.86584	NM_018814	ENSMUSG00000021140	Pcnx	2900024E21Rik|3526401J03Rik|AF096286|AI327143|AI413187|Pcnx1|Pcnxl1	pecanex homolog (Drosophila)	protein-coding
mm_110207.1	chr12	27342392	27342417	-	1	NA	exon (NM_009234, exon 1 of 1)	exon (NM_009234, exon 1 of 1)	314	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding
mm_22713.1	chr3	19188215	19188225	+	1	NA	promoter-TSS (NM_026182)	promoter-TSS (NM_026182)	-1	NM_026182	67472	Mm.45125	NM_026182	ENSMUSG00000027601	Mtfr1	1300002C08Rik|1700080D04Rik|2810026O10Rik|4930579E05Rik|Chppr|Fam54a2	mitochondrial fission regulator 1	protein-coding
mm_66621.1	chr7	45474936	45474961	-	1	NA	3' UTR (NM_027903, exon 7 of 7)	3' UTR (NM_027903, exon 7 of 7)	-8050	NM_007527	12028	Mm.19904	NM_007527	ENSMUSG00000003873	Bax	-	BCL2-associated X protein	protein-coding
mm_106903.1	chr12	8015321	8015334	+	1	NA	exon (NM_009693, exon 29 of 29)	exon (NM_009693, exon 29 of 29)	37650	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_76712.1	chr8	94666950	94666987	-	1	NA	promoter-TSS (NM_024269)	promoter-TSS (NM_024269)	-123	NM_024269	107566	Mm.393247	NM_024191	ENSMUSG00000031776	Arl2bp	1700010P10Rik|1700027H16Rik|6330544B05Rik|AI482273|AI849834|BART|Bart1	ADP-ribosylation factor-like 2 binding protein	protein-coding
mm_98429.1	chr11	94677579	94677632	+	1	NA	promoter-TSS (NM_145828)	promoter-TSS (NM_145828)	-112	NM_145828	217119	Mm.100638	NM_145828	ENSMUSG00000020868	Xylt2	E030002B02Rik|XT-II|XT2|xylT-II	xylosyltransferase II	protein-coding
mm_33605.1	chr4	132580658	132580677	+	1	NA	3' UTR (NM_001081211, exon 2 of 2)	3' UTR (NM_001081211, exon 2 of 2)	16600	NM_001081211	19204	Mm.89389	NM_001081211	ENSMUSG00000056529	Ptafr	PAFR	platelet-activating factor receptor	protein-coding
mm_91928.1	chr10	60358215	60358234	-	1	NA	exon (NM_001159572, exon 2 of 7)	exon (NM_001159572, exon 2 of 7)	11373	NM_028732	74048	Mm.273584	NM_028732	ENSMUSG00000020101	Vsir	4632428N05Rik|Dies1|PD-1H|VISTA	V-set immunoregulatory receptor	protein-coding
mm_11794.1	chr2	43366160	43366198	+	1	NA	Intergenic	Intergenic	-189146	NM_001289593	70789	Mm.105278	NM_027552	ENSMUSG00000026866	Kynu	4432411A05Rik	kynureninase (L-kynurenine hydrolase)	protein-coding
mm_155667.1	chrX	88959184	88959184	+	1	NA	Intergenic	L1M4c|LINE|L1	-199631	NR_037313	100499530		NR_037313	ENSMUSG00000084559	Mir1906-2	mmu-mir-1906-2	microRNA 1906-2	ncRNA
mm_114904.1	chr13	94817695	94817711	+	1	NA	intron (NM_009321, intron 1 of 3)	intron (NM_009321, intron 1 of 3)	28760	NM_009321	21371	Mm.379025	NM_009321	ENSMUSG00000042043	Tbca	Tbca13	tubulin cofactor A	protein-coding
mm_172224.1	chr6	66766115	66766117	+	1	NA	Intergenic	L1Md_F|LINE|L1	11014	NM_134168	171186	Mm.377167	NM_134168	ENSMUSG00000093632	Vmn1r38	V1rc13	vomeronasal 1 receptor 38	protein-coding
mm_169174.1	chr13	65699214	65699217	-	1	NA	Intergenic	Intergenic	-414238	NM_001177832	628709	Mm.390595	NM_001177832	ENSMUSG00000095909	Gm10324	ENSMUSG00000071302	predicted gene 10324	protein-coding
mm_147975.1	chr18	67401595	67401603	-	1	NA	exon (NM_026473, exon 4 of 4)	exon (NM_026473, exon 4 of 4)	10868	NM_026473	67951	Mm.181860	NM_026473	ENSMUSG00000001473	Tubb6	2310057H16Rik|BB220206	tubulin, beta 6 class V	protein-coding
mm_16715.1	chr2	7125654	7125662	-	1	NA	intron (NM_001110231, intron 3 of 15)	intron (NM_001110231, intron 3 of 15)	-44356	NM_001160292	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_57920.1	chr6	133864994	133865005	-	1	NA	Intergenic	Intergenic	-11332	NM_010594	16483	Mm.13052	NM_010594	ENSMUSG00000032758	Kap	AW146435|FKSG22	kidney androgen regulated protein	protein-coding
mm_103042.1	chr11	69795896	69795922	-	1	NA	promoter-TSS (NM_009601)	promoter-TSS (NM_009601)	28	NM_009601	11443	Mm.86425	NM_009601	ENSMUSG00000041189	Chrnb1	Achr-2|Acrb	cholinergic receptor, nicotinic, beta polypeptide 1 (muscle)	protein-coding
mm_150808.1	chr19	44376874	44376879	+	1	NA	Intergenic	Intergenic	30833	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_3109.1	chr1	134540847	134540862	+	1	NA	TTS (NM_001145300)	TTS (NM_001145300)	8828	NM_001145300	71001	Mm.158529	NM_183292	ENSMUSG00000046367	Mgat4e	4931440L10Rik	MGAT4 family, member E	protein-coding
mm_93935.1	chr10	127180580	127180583	-	1	NA	promoter-TSS (NM_177615)	promoter-TSS (NM_177615)	64	NM_177615	216441	Mm.248373	NM_177615	ENSMUSG00000040441	Slc26a10	C78409|D630010I07	solute carrier family 26, member 10	protein-coding
mm_98524.1	chr11	94990760	94990797	+	1	NA	promoter-TSS (NM_172261)	promoter-TSS (NM_172261)	-434	NM_172261	217124	Mm.229087	NM_172261	ENSMUSG00000038976	Ppp1r9b	SPL|Spn	protein phosphatase 1, regulatory subunit 9B	protein-coding
mm_87778.1	chr10	60295931	60295981	+	1	NA	exon (NM_011179, exon 7 of 15)	exon (NM_011179, exon 7 of 15)	11495	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_38484.1	chr4	140750570	140750587	-	1	NA	intron (NM_011061, intron 12 of 15)	intron (NM_011061, intron 12 of 15)	-7935	NM_153106	242726	Mm.271661	NM_153106	ENSMUSG00000040935	Padi6	Pad6|Padi5|ePAD	peptidyl arginine deiminase, type VI	protein-coding
mm_34655.1	chr4	150855065	150855081	+	1	NA	promoter-TSS (NM_133753)	promoter-TSS (NM_133753)	-18	NM_133753	74155	Mm.318841	NM_133753	ENSMUSG00000028967	Errfi1	1300002F13Rik|AI788755|Mig-6|Mig6|RALT	ERBB receptor feedback inhibitor 1	protein-coding
mm_68367.1	chr7	107209243	107209253	-	1	NA	promoter-TSS (NM_029660)	promoter-TSS (NM_029660)	-197	NM_029660	76572	Mm.128134	NM_029660	ENSMUSG00000073894	Rbmxl2	1700012H05Rik|Hnrnpg-t	RNA binding motif protein, X-linked-like 2	protein-coding
mm_28011.1	chr3	83043397	83043407	-	1	NA	exon (NM_181849, exon 7 of 8)	exon (NM_181849, exon 7 of 8)	6461	NM_181849	110135	Mm.30063	NM_181849	ENSMUSG00000033831	Fgb	2510049G14Rik	fibrinogen beta chain	protein-coding
mm_58484.1	chr7	3620112	3620122	+	1	NA	TTS (NM_001290381)	TTS (NM_001290381)	2744	NM_025348	66091	Mm.17851	NM_025348	ENSMUSG00000035674	Ndufa3	1010001M12Rik|1700022J01Rik	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 3	protein-coding
mm_119790.1	chr14	54192755	54192770	+	1	NA	Intergenic	L3b|LINE|CR1	61167	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_70960.1	chr8	26979943	26979945	+	1	NA	exon (NM_001101502, exon 2 of 2)	exon (NM_001101502, exon 2 of 2)	2608	NM_001110508	353310	Mm.212469	NM_001101502	ENSMUSG00000085795	Zfp703	1110032O19Rik|AI430822|AL022941|Csmn1|End2|Zeppo1|Znf703|Zpo1	zinc finger protein 703	protein-coding
mm_62960.1	chr7	119760919	119760934	+	1	NA	promoter-TSS (NM_016870)	promoter-TSS (NM_016870)	3	NM_212442	20216	Mm.334199	NM_016870	ENSMUSG00000030935	Acsm3	Sa|Sah	acyl-CoA synthetase medium-chain family member 3	protein-coding
mm_151312.1	chr19	55832747	55832757	+	1	NA	intron (NR_138565, intron 4 of 15)	B3A|SINE|B2	-62569	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_23166.1	chr3	40745306	40745317	+	1	NA	promoter-TSS (NM_011020)	promoter-TSS (NM_011020)	-302	NM_011020	18415	Mm.39330	NM_011020	ENSMUSG00000025757	Hspa4l	94kDa|AI461691|APG-1|Osp94	heat shock protein 4 like	protein-coding
mm_71785.1	chr8	66697265	66697273	+	1	NA	promoter-TSS (NM_010934)	promoter-TSS (NM_010934)	-153	NM_010934	18166	Mm.5112	NM_010934	ENSMUSG00000036437	Npy1r	Npyr|Y1-R	neuropeptide Y receptor Y1	protein-coding
mm_71699.1	chr8	61713582	61713592	+	1	NA	intron (NM_001081390, intron 3 of 19)	intron (NM_001081390, intron 3 of 19)	46511	NM_001293773	72333	Mm.29933	NM_001081390	ENSMUSG00000058056	Palld	2410003B16Rik|6030492A02	palladin, cytoskeletal associated protein	protein-coding
mm_40364.1	chr5	48372364	48372420	+	1	NA	promoter-TSS (NM_025755)	promoter-TSS (NM_025755)	0	NM_025755	66768	Mm.29409	NM_025755	ENSMUSG00000029089	Pacrgl	4933428G09Rik	PARK2 co-regulated-like	protein-coding
mm_140163.1	chr17	80224534	80224550	+	1	NA	promoter-TSS (NM_026053)	promoter-TSS (NM_026053)	53	NM_026053	67242	Mm.279985	NM_026053	ENSMUSG00000055760	Gemin6	2610019B15Rik|2810470M17Rik	gem (nuclear organelle) associated protein 6	protein-coding
mm_99035.1	chr11	98960436	98960485	+	1	NA	promoter-TSS (NM_001176528)	promoter-TSS (NM_001176528)	-11	NM_001176528	19401	Mm.439744	NM_009024	ENSMUSG00000037992	Rara	Nr1b1|RAR|RARalpha1	retinoic acid receptor, alpha	protein-coding
mm_151086.1	chr19	47625429	47625449	+	1	NA	exon (NM_001164639, exon 12 of 18)	exon (NM_001164639, exon 12 of 18)	45420	NM_001164639	20874	Mm.281011	NM_009289	ENSMUSG00000025060	Slk	9A2|AV021402|AW411554|Etk4|SMAK|Stk2|mKIAA0204|mSLK	STE20-like kinase	protein-coding
mm_40546.1	chr5	58042782	58042811	+	1	NA	intron (NM_001310608, intron 3 of 3)	B1_Mur2|SINE|Alu	324715	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_42396.1	chr5	114937863	114937879	+	1	NA	TTS (NM_145209)	TTS (NM_145209)	-4331	NM_028211	72357	Mm.292672	NM_028211	ENSMUSG00000029559	2210016L21Rik	-	RIKEN cDNA 2210016L21 gene	protein-coding
mm_11835.1	chr2	45110973	45111008	+	1	NA	promoter-TSS (NM_001289521)	promoter-TSS (NM_001289521)	-148	NR_110572	433424	Mm.441408	NR_110571	ENSMUSG00000052248	Zeb2os	Gm13476|OTTMUSG00000012358|Zeb2nat	zinc finger E-box binding homeobox 2, opposite strand	ncRNA
mm_120347.1	chr14	63819742	63819754	+	1	NA	exon (NM_173393, exon 3 of 3)	exon (NM_173393, exon 3 of 3)	-40564	NM_028228	72400	Mm.379214	NM_028228	ENSMUSG00000021958	Pinx1	2210403I16Rik|2610028A01Rik|67-11-3|AU024023|LPTS|LPTS1	PIN2/TERF1 interacting, telomerase inhibitor 1	protein-coding
mm_161850.1	chr18	13846945	13846945	-	1	NA	exon (NM_145492, exon 4 of 8)	exon (NM_145492, exon 4 of 8)	125788	NM_145492	225207	Mm.40325	NM_145492	ENSMUSG00000024420	Zfp521	B930086A16Rik|Evi3|Znf521	zinc finger protein 521	protein-coding
mm_18024.1	chr2	38613759	38613767	-	1	NA	intron (NM_011187, intron 5 of 7)	intron (NM_011187, intron 5 of 7)	30143	NM_011187	19177	Mm.389251	NM_011187	ENSMUSG00000026750	Psmb7	AU020723|MC14	proteasome (prosome, macropain) subunit, beta type 7	protein-coding
mm_113944.1	chr13	49814742	49814753	+	1	NA	Intergenic	Intergenic	132617	NM_172015	105148	Mm.21118	NM_172015	ENSMUSG00000037851	Iars	2510016L12Rik|AI327140|AU044614|E430001P04Rik|ILRS	isoleucine-tRNA synthetase	protein-coding
mm_4332.1	chr1	171854902	171854909	+	1	NA	3' UTR (NM_001252472, exon 3 of 3)	3' UTR (NM_001252472, exon 3 of 3)	15208	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_124155.1	chr14	93224918	93224920	-	1	NA	intron (NM_001346722, intron 4 of 4)	Lx3A|LINE|L1	663969	NM_001271800	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding
mm_90301.1	chr10	125972381	125972385	+	1	NA	intron (NM_177152, intron 2 of 18)	intron (NM_177152, intron 2 of 18)	6164	NM_177152	320398	Mm.275586	NM_177152	ENSMUSG00000020105	Lrig3	9030421L11Rik|9130004I02Rik|9430095K15Rik|mKIAA3016	leucine-rich repeats and immunoglobulin-like domains 3	protein-coding
mm_66300.1	chr7	38184520	38184524	-	1	NA	intron (NM_028166, intron 1 of 3)	PB1D10|SINE|Alu	735	NM_028166	72244	Mm.187554	NM_028166		1600014C10Rik	AI428873	RIKEN cDNA 1600014C10 gene	protein-coding
mm_101005.1	chr11	8477142	8477152	-	1	NA	intron (NM_001083587, intron 20 of 30)	intron (NM_001083587, intron 20 of 30)	187388	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_24551.1	chr3	93442372	93442389	+	1	NA	promoter-TSS (NM_001163098)	promoter-TSS (NM_001163098)	50	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_111042.1	chr12	79296267	79296310	-	1	NA	promoter-TSS (NM_009014)	promoter-TSS (NM_009014)	-6	NM_001008550	211978	Mm.297919	NM_001008550	ENSMUSG00000066440	Zfyve26	4930465A13|9330197E15Rik|A630028O16Rik|Gm893|mKIAA0321	zinc finger, FYVE domain containing 26	protein-coding
mm_120746.1	chr14	73237990	73238007	+	1	NA	5' UTR (NM_175116, exon 1 of 1)	5' UTR (NM_175116, exon 1 of 1)	107	NM_175116	67168	Mm.390681	NM_175116	ENSMUSG00000033446	Lpar6	2610302I02Rik|P2ry5|P2y5	lysophosphatidic acid receptor 6	protein-coding
mm_153575.1	chr19	43248058	43248061	-	1	NA	intron (NM_001081257, intron 3 of 11)	intron (NM_001081257, intron 3 of 11)	140296	NM_001081257	545291	Mm.442200	NM_001081257	ENSMUSG00000074852	Hpse2	Gm968|Hpa2	heparanase 2	protein-coding
mm_89910.1	chr10	111174274	111174314	+	1	NA	intron (NM_175489, intron 1 of 23)	intron (NM_175489, intron 1 of 23)	9492	NM_175489	237542	Mm.220204	NM_175489	ENSMUSG00000020189	Osbpl8	AA536976|AA536995|C730029P18Rik|D330025H14Rik|ORP-8	oxysterol binding protein-like 8	protein-coding
mm_75577.1	chr8	61289329	61289329	-	1	NA	promoter-TSS (NR_045475)	promoter-TSS (NR_045475)	-457	NR_045475	69279	Mm.417857	NR_045475	ENSMUSG00000099419	1700001D01Rik	-	RIKEN cDNA 1700001D01 gene	ncRNA
mm_67240.1	chr7	75308949	75308957	-	1	NA	promoter-TSS (NM_001109753)	promoter-TSS (NM_001109753)	251	NR_045814	68954	Mm.46960	NR_045812	ENSMUSG00000097247	1500012K07Rik	-	RIKEN cDNA 1500012K07 gene	ncRNA
mm_60482.1	chr7	44478413	44478418	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-6102	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_20600.1	chr2	131352835	131352856	-	1	NA	promoter-TSS (NM_178607)	promoter-TSS (NM_178607)	47	NM_178607	51902	Mm.477523	NM_178607	ENSMUSG00000048911	Rnf24	2810473M14Rik|4930505A13Rik|AI317164|C86507|D2Ertd504e	ring finger protein 24	protein-coding
mm_172348.1	chr7	113491481	113491484	-	1	NA	Intergenic	L1Md_T|LINE|L1	-22352	NM_001285831	67420	Mm.206919	NM_026143	ENSMUSG00000030759	Far1	2600011M19Rik|2900034E22Rik|3732409C05Rik|AI850429|Mlstd2	fatty acyl CoA reductase 1	protein-coding
mm_165247.1	chr2	69789642	69789644	+	1	NA	promoter-TSS (NM_028521)	promoter-TSS (NM_028521)	-94	NM_028521	73373	Mm.9621	NM_028521	ENSMUSG00000027088	Phospho2	1700048E23Rik|AI661517|AU021728|AV006103|Phos2	phosphatase, orphan 2	protein-coding
mm_30757.1	chr4	15266103	15266173	+	1	NA	exon (NM_181401, exon 1 of 3)	exon (NM_181401, exon 1 of 3)	318	NM_181401	100201	Mm.394111	NM_181401	ENSMUSG00000043252	Tmem64	9630015D15Rik|AI790744|AV300874	transmembrane protein 64	protein-coding
mm_52635.1	chr6	117174482	117174504	+	1	NA	3' UTR (NM_021704, exon 3 of 3)	3' UTR (NM_021704, exon 3 of 3)	5958	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_4452.1	chr1	172698047	172698063	+	1	NA	promoter-TSS (NM_007768)	promoter-TSS (NM_007768)	-1	NM_007768	12944	Mm.28767	NM_007768	ENSMUSG00000037942	Crp	AI255847	C-reactive protein, pentraxin-related	protein-coding
mm_141160.1	chr17	26508464	26508482	-	1	NA	promoter-TSS (NM_013642)	promoter-TSS (NM_013642)	-1	NM_013642	19252	Mm.239041	NM_013642	ENSMUSG00000024190	Dusp1	3CH134|MKP1|Ptpn16|U19515|erp|mkp-1	dual specificity phosphatase 1	protein-coding
mm_141411.1	chr17	29403346	29403358	-	1	NA	Intergenic	B3A|SINE|B2	42438	NM_001159538	26382	Mm.279187	NM_013710	ENSMUSG00000024013	Fgd2	Tcd-2|Tcd2|ZFYVE4|tcs-2|tcs2	FYVE, RhoGEF and PH domain containing 2	protein-coding
mm_170238.1	chr1	78955319	78955319	+	1	NA	Intergenic	L1Md_A|LINE|L1	138370	NM_021342	57814	Mm.24386	NM_021342	ENSMUSG00000047330	Kcne4	AW487937|MiRP3	potassium voltage-gated channel, Isk-related subfamily, gene 4	protein-coding
mm_38541.1	chr4	141595936	141595961	-	1	NA	5' UTR (NM_133754, exon 2 of 9)	5' UTR (NM_133754, exon 2 of 9)	3976	NM_001163256	74202	Mm.490327	NM_133754	ENSMUSG00000006219	Fblim1	2410043F08Rik|Cal|Fblp1|Gt10|migfilin|migfilin(s)	filamin binding LIM protein 1	protein-coding
mm_90524.1	chr10	128068212	128068222	+	1	NA	intron (NM_019766, intron 1 of 7)	B1_Mur4|SINE|Alu	9235	NM_019766	56351	Mm.305816	NM_019766	ENSMUSG00000071072	Ptges3	5730442A20Rik|Ptges|Tebp|cPGES|p23|sid3177	prostaglandin E synthase 3 (cytosolic)	protein-coding
mm_8874.1	chr1	162859985	162859994	-	1	NA	promoter-TSS (NM_001330291)	promoter-TSS (NM_001330291)	11	NM_001330291	14261	Mm.976	NM_010231	ENSMUSG00000040181	Fmo1	-	flavin containing monooxygenase 1	protein-coding
mm_38580.1	chr4	141819020	141819132	-	1	NA	exon (NM_007919, exon 6 of 8)	exon (NM_007919, exon 6 of 8)	6929	NM_007919	13706	Mm.45316	NM_007919	ENSMUSG00000058579	Cela2a	Ela-2|Ela2|Ela2a	chymotrypsin-like elastase family, member 2A	protein-coding
mm_99292.1	chr11	101330811	101330820	+	1	NA	5' UTR (NM_009675, exon 1 of 4)	5' UTR (NM_009675, exon 1 of 4)	209	NM_009675	11754	Mm.67281	NM_009675	ENSMUSG00000019326	Aoc3	SSAO|VAP1	amine oxidase, copper containing 3	protein-coding
mm_38138.1	chr4	134750291	134750298	-	1	NA	intron (NM_145554, intron 5 of 8)	MIRb|SINE|MIR	17710	NM_145554	100017	Mm.27486	NM_145554	ENSMUSG00000037295	Ldlrap1	AA691260|ARH2|Arh|Arh1|FHCB1|FHCB2	low density lipoprotein receptor adaptor protein 1	protein-coding
mm_132462.1	chr16	36206396	36206398	+	1	NA	Intergenic	RLTR13E|LTR|ERVK	-4006	NM_001082542	408196	Mm.432544	NM_001082542	ENSMUSG00000094733	Gm5416	EG408196|Stfna1l1	predicted gene 5416	protein-coding
mm_96736.1	chr11	69765971	69766027	+	1	NA	promoter-TSS (NM_029348)	promoter-TSS (NM_029348)	87	NM_029348	75580	Mm.426361	NM_029348	ENSMUSG00000018750	Zbtb4	2310026P19Rik|9230111I22Rik|mKIAA1538	zinc finger and BTB domain containing 4	protein-coding
mm_68650.1	chr7	118491880	118491903	-	1	NA	promoter-TSS (NM_001033380)	promoter-TSS (NM_001033380)	84	NM_001033380	319622	Mm.323386	NM_001033380	ENSMUSG00000095115	Itpripl2	C130081G24|E030018N11Rik	inositol 1,4,5-triphosphate receptor interacting protein-like 2	protein-coding
mm_59687.1	chr7	28443078	28443124	+	1	NA	intron (NM_001039192, intron 3 of 6)	MIRb|SINE|MIR	2164	NM_001039192	63986	Mm.194536	NM_022024	ENSMUSG00000060791	Gmfg	0610039G16Rik|2310057N07Rik|AI324845	glia maturation factor, gamma	protein-coding
mm_129972.1	chr15	85811240	85811248	-	1	NA	intron (NM_197998, intron 1 of 4)	CpG	453	NM_001164626	72355	Mm.33706	NM_197998	ENSMUSG00000064284	Cdpf1	2210021J22Rik	cysteine rich, DPF motif domain containing 1	protein-coding
mm_117498.1	chr13	78199836	78199855	-	1	NA	promoter-TSS (NM_010151)	promoter-TSS (NM_010151)	-972	NM_010151	13865	Mm.439653	NM_010151	ENSMUSG00000069171	Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR-3|EAR3|Erbal3|SVP44|Tcfcoup1	nuclear receptor subfamily 2, group F, member 1	protein-coding
mm_152600.1	chr19	11691027	11691058	-	1	NA	promoter-TSS (NM_133353)	promoter-TSS (NM_133353)	9	NM_133353	170834	Mm.24754	NM_133353	ENSMUSG00000041857	Oosp1	AA536827	oocyte secreted protein 1	protein-coding
mm_52480.1	chr6	114315410	114315426	+	1	NA	3' UTR (NM_178703, exon 16 of 16)	3' UTR (NM_178703, exon 16 of 16)	32783	NM_178703	232333	Mm.5260	NM_178703	ENSMUSG00000030310	Slc6a1	A730043E01|GABATHG|GABATR|GAT-1|Gabt|Gabt1|Gat1|XT-1|Xtrp1	solute carrier family 6 (neurotransmitter transporter, GABA), member 1	protein-coding
mm_35707.1	chr4	44168018	44168069	-	1	NA	promoter-TSS (NM_175201)	promoter-TSS (NM_175201)	240	NM_001038993	73469	Mm.262859	NM_175201	ENSMUSG00000035696	Rnf38	1700065B19Rik|2610202O07Rik|AA673263|Oip1	ring finger protein 38	protein-coding
mm_130006.1	chr15	86222041	86222047	-	1	NA	intron (NM_145476, intron 1 of 12)	MMERGLN_LTR|LTR|ERV1	7585	NM_145476	223754	Mm.28904	NM_145476	ENSMUSG00000051864	Tbc1d22a	BC023106|D15Ertd781e	TBC1 domain family, member 22a	protein-coding
mm_60540.1	chr7	44480485	44480488	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-4031	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_93957.1	chr10	127267027	127267046	-	1	NA	intron (NM_001190453, intron 1 of 14)	intron (NM_001190453, intron 1 of 14)	774	NM_001190453	69654	Mm.167537	NM_027151	ENSMUSG00000025410	Dctn2	2310042E05Rik|C130077D06Rik|C87049|DCTN-50|GMP23-48K|RBP50|p50	dynactin 2	protein-coding
mm_98318.1	chr11	90249488	90249503	+	1	NA	promoter-TSS (NM_026178)	promoter-TSS (NM_026178)	19	NM_026178	67468	Mm.277518	NM_026178	ENSMUSG00000003948	Mmd	1200017E07Rik|1810073C06Rik|AA690185	monocyte to macrophage differentiation-associated	protein-coding
mm_50720.1	chr6	52229972	52229980	+	1	NA	TTS (NR_029912)	TTS (NR_029912)	189	NR_029912	723820		NR_029912	ENSMUSG00000065443	Mir196b	Mirn196b|mir-196b	microRNA 196b	ncRNA
mm_85804.1	chr9	110210114	110210118	-	1	NA	intron (NM_009211, intron 24 of 27)	U2|snRNA|snRNA	-33667	NM_013884	29873	Mm.38496	NM_013884	ENSMUSG00000032482	Cspg5	Caleb|Ngc	chondroitin sulfate proteoglycan 5	protein-coding
mm_30624.1	chr4	8731998	8732000	+	1	NA	intron (NM_001277149, intron 1 of 37)	PB1|SINE|Alu	41593	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_56580.1	chr6	106791627	106791628	-	1	NA	intron (NM_175357, intron 4 of 10)	intron (NM_175357, intron 4 of 10)	8460	NM_021449	58799	Mm.290085	NM_021449	ENSMUSG00000005362	Crbn	2610203G15Rik|2900045O07Rik|AF229032|AW108261|piL	cereblon	protein-coding
mm_104615.1	chr11	97280433	97280444	-	1	NA	exon (NM_008942, exon 1 of 23)	exon (NM_008942, exon 1 of 23)	138	NM_008942	19155	Mm.29824	NM_008942	ENSMUSG00000001441	Npepps	AAP-S|MP100|Psa|R74825|goku	aminopeptidase puromycin sensitive	protein-coding
mm_26274.1	chr3	142505424	142505434	+	1	NA	exon (NM_153564, exon 7 of 11)	exon (NM_153564, exon 7 of 11)	8495	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_63593.1	chr7	128139154	128139155	+	1	NA	intron (NM_021334, intron 14 of 29)	PB1D11|SINE|Alu	9586	NM_021334	16411	Mm.22378	NM_021334	ENSMUSG00000030789	Itgax	AI449405|Cd11c|Cr4|N418	integrin alpha X	protein-coding
mm_13562.1	chr2	112265810	112265858	+	1	NA	promoter-TSS (NM_133649)	promoter-TSS (NM_133649)	-480	NM_133649	107723	Mm.491155	NM_133648	ENSMUSG00000027130	Slc12a6	9530023I19Rik|KCC3|gaxp	solute carrier family 12, member 6	protein-coding
mm_140788.1	chr17	18968982	18968998	-	1	NA	Intergenic	IAPLTR4|LTR|ERVK	54668	NM_001104549	627367	Mm.384131	NM_001104549	ENSMUSG00000091491	Vmn2r97	EG627367|Vn2r97	vomeronasal 2, receptor 97	protein-coding
mm_18156.1	chr2	45092485	45092495	-	1	NA	intron (NM_001289521, intron 1 of 8)	intron (NM_001289521, intron 1 of 8)	17787	NM_001289521	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_24989.1	chr3	97032438	97032448	+	1	NA	promoter-TSS (NM_008121)	promoter-TSS (NM_008121)	41	NM_008121	14613	Mm.281816	NM_008121	ENSMUSG00000057123	Gja5	5730555N10Rik|Cnx40|Cx40|Gja-5	gap junction protein, alpha 5	protein-coding
mm_137144.1	chr17	23660478	23660525	+	1	NA	promoter-TSS (NM_153784)	promoter-TSS (NM_153784)	-5	NM_153784	212733	Mm.59997	NM_153784	ENSMUSG00000043782	Ccdc64b	BICDR-2|Bicdl2	coiled-coil domain containing 64B	protein-coding
mm_33535.1	chr4	130932459	130932555	+	1	NA	intron (NM_010686, intron 7 of 7)	(TCCA)n|Simple_repeat|Simple_repeat	-11878	NM_010769	17180	Mm.271796	NM_010769	ENSMUSG00000040533	Matn1	CMP|Crtm|Mat1|matrilin-1	matrilin 1, cartilage matrix protein	protein-coding
mm_12946.1	chr2	87506558	87506566	+	1	NA	Intergenic	Intergenic	-1896	NM_178249	347711	Mm.21815	NM_178249	ENSMUSG00000025838	Pramel6	C80453|C80515	preferentially expressed antigen in melanoma like 6	protein-coding
mm_123969.1	chr14	75130645	75130649	-	1	NA	promoter-TSS (NM_001247984)	promoter-TSS (NM_001247984)	236	NM_027581	70859	Mm.320289	NM_027581	ENSMUSG00000021997	Lrrc63	4921509B22Rik	leucine rich repeat containing 63	protein-coding
mm_151082.1	chr19	47620377	47620391	+	1	NA	exon (NM_001164639, exon 9 of 18)	exon (NM_001164639, exon 9 of 18)	40365	NM_001164639	20874	Mm.281011	NM_009289	ENSMUSG00000025060	Slk	9A2|AV021402|AW411554|Etk4|SMAK|Stk2|mKIAA0204|mSLK	STE20-like kinase	protein-coding
mm_44240.1	chr5	5314582	5314592	-	1	NA	intron (NM_011074, intron 2 of 14)	intron (NM_011074, intron 2 of 14)	-48519	NM_001310448	18647	Mm.389061	NM_011074	ENSMUSG00000028926	Cdk14	Pftk1|mKIAA0834	cyclin-dependent kinase 14	protein-coding
mm_161109.1	chr12	103863563	103863563	-	1	NA	promoter-TSS (NM_009243)	promoter-TSS (NM_009243)	56	NM_001252569	20700	Mm.439692	NM_009243	ENSMUSG00000066366	Serpina1a	Aat-2|Aat2|Dom1|PI1|Spi1-1|Spi1-3	serine (or cysteine) peptidase inhibitor, clade A, member 1A	protein-coding
mm_109501.1	chr12	111452065	111452083	+	1	NA	intron (NM_009396, intron 11 of 11)	intron (NM_009396, intron 11 of 11)	9413	NM_009396	21928	Mm.255332	NM_009396	ENSMUSG00000021281	Tnfaip2	B94|Exoc3l3|M-sec|Tnfip2|tnfb94	tumor necrosis factor, alpha-induced protein 2	protein-coding
mm_15094.1	chr2	153291405	153291459	+	1	NA	promoter-TSS (NM_008444)	promoter-TSS (NM_008444)	16	NM_008444	16569	Mm.315560	NM_008444	ENSMUSG00000027475	Kif3b	AI854312|AW549267|mKIAA0359	kinesin family member 3B	protein-coding
mm_144731.1	chr18	35553584	35553596	+	1	NA	promoter-TSS (NR_035472)	promoter-TSS (NR_035472)	180	NR_038073	100503380	Mm.482118	NR_038073	ENSMUSG00000097769	Snhg4	Gm17457	small nucleolar RNA host gene 4	ncRNA
mm_105054.1	chr11	100703715	100703733	-	1	NA	intron (NM_030150, intron 2 of 12)	intron (NM_030150, intron 2 of 12)	547	NM_030150	80861	Mm.271830	NM_030150	ENSMUSG00000017830	Dhx58	B430001I08Rik|D11Lgp2e|LPG2|Lgp2|RLR-3	DEXH (Asp-Glu-X-His) box polypeptide 58	protein-coding
mm_164562.1	chr17	17832460	17832473	+	1	NA	intron (NM_001162909, intron 2 of 8)	intron (NM_001162909, intron 2 of 8)	1491	NM_001162909	75202	Mm.227456	NM_029205	ENSMUSG00000080316	Spaca6	4930546H06Rik|9530079D04Rik|B230206P06Rik|Ncrna00085|SPACA6A|let-7e|mir-125a|mir-99b	sperm acrosome associated 6	protein-coding
mm_159235.1	chr2	144332102	144332102	-	1	NA	promoter-TSS (NM_026924)	promoter-TSS (NM_026924)	-22	NM_026924	107586	Mm.252750	NM_026924	ENSMUSG00000037279	Ovol2	1700108N11Rik|1810007D21Rik|M-OVO|M-OVO-A|M-OVO-B|MOVO|Ovo2|Zfp339|movo2	ovo like zinc finger 2	protein-coding
mm_19188.1	chr2	84416623	84416633	-	1	NA	intron (NM_018782, intron 1 of 15)	intron (NM_018782, intron 1 of 15)	8638	NM_018782	54598	Mm.75467	NM_018782	ENSMUSG00000059588	Calcrl	AV071593|CRLR	calcitonin receptor-like	protein-coding
mm_28535.1	chr3	92720345	92720359	-	1	NA	promoter-TSS (NM_026394)	promoter-TSS (NM_026394)	-2	NM_026394	67828	Mm.158176	NM_026394	ENSMUSG00000042124	Lce1f	1110055J05Rik	late cornified envelope 1F	protein-coding
mm_54873.1	chr6	42601849	42601863	-	1	NA	Intergenic	Intergenic	-4484	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_140860.1	chr17	23740366	23740385	-	1	NA	promoter-TSS (NM_023824)	promoter-TSS (NM_023824)	-45	NM_023824	76498	Mm.491253	NM_023824	ENSMUSG00000023909	Paqr4	1500004C10Rik	progestin and adipoQ receptor family member IV	protein-coding
mm_52860.1	chr6	122294148	122294163	+	1	NA	Intergenic	RMER10A|LTR|ERVL	-11322	NM_016970	50928	Mm.20434	NM_016970	ENSMUSG00000030114	Klrg1	2F1-Ag|MAFA|MAFA-L	killer cell lectin-like receptor subfamily G, member 1	protein-coding
mm_97845.1	chr11	83065388	83065398	+	1	NA	intron (NM_011408, intron 1 of 1)	intron (NM_011408, intron 1 of 1)	281	NM_011408	20556	Mm.278689	NM_011408	ENSMUSG00000072620	Slfn2	Shlf2	schlafen 2	protein-coding
mm_29043.1	chr3	103020336	103020347	-	1	NA	promoter-TSS (NM_001310693)	promoter-TSS (NM_001310693)	-205	NM_001310693	229663	Mm.277713	NM_144901	ENSMUSG00000068823	Csde1	AA960392|BC016898|D3Jfr1|mKIAA0885|unr	cold shock domain containing E1, RNA binding	protein-coding
mm_73263.1	chr8	104340774	104340789	+	1	NA	exon (NM_024217, exon 1 of 5)	exon (NM_024217, exon 1 of 5)	187	NM_024217	68119	Mm.390108	NM_024217	ENSMUSG00000031875	Cmtm3	9430096L06Rik|AI413895|BNAS2|Cklfsf3	CKLF-like MARVEL transmembrane domain containing 3	protein-coding
mm_27604.1	chr3	59153597	59153624	-	1	NA	promoter-TSS (NR_045641)	promoter-TSS (NR_045641)	18	NR_045641	320463	Mm.484506	NR_045641	ENSMUSG00000036381	F630111L10Rik	-	RIKEN cDNA F630111L10 gene	ncRNA
mm_127555.1	chr15	102150591	102150601	+	1	NA	promoter-TSS (NM_146064)	promoter-TSS (NM_146064)	21	NM_146064	223920	Mm.358862	NM_146064	ENSMUSG00000023045	Soat2	ACAT2|D15Wsu97e	sterol O-acyltransferase 2	protein-coding
mm_153651.1	chr19	44388517	44388575	-	1	NA	Intergenic	Intergenic	19163	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_56895.1	chr6	119121128	119121149	-	1	NA	intron (NM_001255998, intron 1 of 47)	intron (NM_001255998, intron 1 of 47)	-12643	NM_001256002	12288	Mm.41628	NM_009781	ENSMUSG00000051331	Cacna1c	Cav1.2|Cchl1a1|D930026N18Rik|MBC|MELC-CC	calcium channel, voltage-dependent, L type, alpha 1C subunit	protein-coding
mm_9432.1	chr1	172506853	172506896	-	1	NA	3' UTR (NM_178598, exon 5 of 5)	3' UTR (NM_178598, exon 5 of 5)	6628	NM_178598	21346	Mm.271711	NM_178598	ENSMUSG00000026547	Tagln2	2700094C18Rik|SM22beta|Sm22B|Sm22a	transgelin 2	protein-coding
mm_11906.1	chr2	50909582	50909584	+	1	NA	promoter-TSS (NR_033595)	promoter-TSS (NR_033595)	-101	NR_033595	227885	Mm.301654	NR_033595	ENSMUSG00000083270	Gm13498	OTTMUSG00000012426	heat shock protein 90 alpha (cytosolic), class B member 1 pseudogene	pseudo
mm_72177.1	chr8	72319534	72319571	+	1	NA	exon (NM_008452, exon 2 of 3)	exon (NM_008452, exon 2 of 3)	490	NM_008452	16598	Mm.26938	NM_008452	ENSMUSG00000055148	Klf2	Lklf	Kruppel-like factor 2 (lung)	protein-coding
mm_95089.1	chr11	33534758	33534761	+	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-21013	NM_023146	66011	Mm.383775	NM_023146	ENSMUSG00000040594	Ranbp17	-	RAN binding protein 17	protein-coding
mm_112076.1	chr12	112633085	112633095	-	1	NA	exon (NM_007421, exon 5 of 13)	exon (NM_007421, exon 5 of 13)	-11738	NM_001161737	30954	Mm.289812	NM_013929	ENSMUSG00000064326	Siva1	CD27bp|Siva	SIVA1, apoptosis-inducing factor	protein-coding
mm_47558.1	chr5	124396035	124396048	-	1	NA	exon (NM_001081203, exon 16 of 32)	exon (NM_001081203, exon 16 of 32)	29873	NM_001081203	243272	Mm.23879	NM_001081203	ENSMUSG00000038095	Sbno1	9330180L10Rik|AI849128|AW557836|BC021875|Sbno|mSno1|sno	strawberry notch homolog 1 (Drosophila)	protein-coding
mm_18267.1	chr2	52319664	52319674	-	1	NA	exon (NM_010889, exon 10 of 157)	exon (NM_010889, exon 10 of 157)	19129	NM_010889	17996	Mm.389247	NM_010889	ENSMUSG00000026950	Neb	AI595938	nebulin	protein-coding
mm_81607.1	chr9	110663691	110663694	+	1	NA	intron (NM_028312, intron 1 of 6)	ORR1A2|LTR|ERVL-MaLR	7189	NM_028312	72654	Mm.249115	NM_028312	ENSMUSG00000019659	Ccdc12	2700094L05Rik|C76605	coiled-coil domain containing 12	protein-coding
mm_170342.1	chr18	48046709	48046710	+	1	NA	intron (NM_001025388, intron 1 of 1)	CpG	1374	NM_001025388	433182	Mm.70666	NM_001025388	ENSMUSG00000059040	Eno1b	EG433182|Eno1|Gm5506	enolase 1B, retrotransposed	protein-coding
mm_154783.1	chrX	13042006	13042051	+	1	NA	promoter-TSS (NR_038158)	promoter-TSS (NR_038158)	13	NR_038158	70489	Mm.383563	NR_038158	ENSMUSG00000087424	5730405O15Rik	-	RIKEN cDNA 5730405O15 gene	ncRNA
mm_20483.1	chr2	129699837	129699850	-	1	NA	promoter-TSS (NM_018863)	promoter-TSS (NM_018863)	95	NM_018863	18610	Mm.6239	NM_018863	ENSMUSG00000027400	Pdyn	Dyn	prodynorphin	protein-coding
mm_17106.1	chr2	24049357	24049380	-	1	NA	promoter-TSS (NM_080462)	promoter-TSS (NM_080462)	11	NM_080462	140483	Mm.33120	NM_080462	ENSMUSG00000026986	Hnmt	1500031F01Rik|AI788969	histamine N-methyltransferase	protein-coding
mm_21954.1	chr2	167188625	167188637	-	1	NA	5' UTR (NM_008420, exon 1 of 2)	5' UTR (NM_008420, exon 1 of 2)	187	NM_008420	16500	Mm.205341	NM_008420	ENSMUSG00000050556	Kcnb1	Kcr1-1|Kv2.1|Shab	potassium voltage gated channel, Shab-related subfamily, member 1	protein-coding
mm_125213.1	chr15	34082741	34082756	+	1	NA	promoter-TSS (NM_026002)	promoter-TSS (NM_026002)	29	NM_026002	67154	Mm.130883	NM_026002	ENSMUSG00000022255	Mtdh	2610103J23Rik|3D3|3D3/Lyric|AEG-1|AV353288|D8Bwg1112e|Lyric	metadherin	protein-coding
mm_62026.1	chr7	91672382	91672390	+	1	NA	intron (NM_011807, intron 2 of 22)	intron (NM_011807, intron 2 of 22)	-390008	NM_001243046	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_94728.1	chr11	20740655	20740681	+	1	NA	intron (NM_001290545, intron 1 of 9)	intron (NM_001290545, intron 1 of 9)	888	NM_001290545	216549	Mm.356580	NM_181411	ENSMUSG00000049659	Aftph	-	aftiphilin	protein-coding
mm_52706.1	chr6	119388873	119388888	+	1	NA	intron (NM_197985, intron 1 of 7)	CpG	28603	NM_197985	68465	Mm.291826	NM_197985	ENSMUSG00000030168	Adipor2	1110001I14Rik|ADCR2|AI115388|AW554121|D6Ucla1e|Paqr2	adiponectin receptor 2	protein-coding
mm_171941.1	chr5	69946219	69946220	+	1	NA	Intergenic	B1_Mus1|SINE|Alu	-353915	NM_001347363	67980	Mm.33830	NM_027681	ENSMUSG00000029209	Gnpda2	4921523I18Rik|4933412A11Rik|BB189630|GNPDA|Gnp2|Sb52|mKIAA4008	glucosamine-6-phosphate deaminase 2	protein-coding
mm_11531.1	chr2	32628419	32628462	+	1	NA	promoter-TSS (NM_001198792)	promoter-TSS (NM_001198792)	50	NM_001198792	11636	Mm.29189	NM_021515	ENSMUSG00000026817	Ak1	Ak-1|B430205N08Rik	adenylate kinase 1	protein-coding
mm_44108.1	chr5	149368487	149368506	+	1	NA	Intergenic	MLT1F2|LTR|ERVL-MaLR	-43310	NM_027519	70717	Mm.252139	NM_027519	ENSMUSG00000029659	Medag	6330406I15Rik|Awms3|MEDA-4|Meda4|mAWMS3	mesenteric estrogen dependent adipogenesis	protein-coding
mm_116928.1	chr13	55647693	55647727	-	1	NA	exon (NM_001282055, exon 5 of 23)	exon (NM_001282055, exon 5 of 23)	12711	NM_001282055	212880	Mm.202725	NM_145975	ENSMUSG00000021500	Ddx46	2200005K02Rik|8430438J23Rik|AI325430|AI957095|mKIAA0801	DEAD (Asp-Glu-Ala-Asp) box polypeptide 46	protein-coding
mm_143124.1	chr17	57211668	57211703	-	1	NA	exon (NM_009778, exon 29 of 41)	exon (NM_009778, exon 29 of 41)	5543	NR_105944	102465591		NR_105944	ENSMUSG00000099066	Mir6978	Gm27858|mmu-mir-6978	microRNA 6978	ncRNA
mm_74806.1	chr8	22593964	22593981	-	1	NA	promoter-TSS (NM_001198998)	promoter-TSS (NM_001198998)	-159	NM_011696	22335	Mm.227704	NM_011696	ENSMUSG00000008892	Vdac3	-	voltage-dependent anion channel 3	protein-coding
mm_73339.1	chr8	105323440	105323450	+	1	NA	intron (NM_177449, intron 1 of 4)	intron (NM_177449, intron 1 of 4)	2831	NM_177449	234684	Mm.381717	NM_177449	ENSMUSG00000041679	Lrrc29	A630024J02Rik|FBL9|FBXL9	leucine rich repeat containing 29	protein-coding
mm_95222.1	chr11	44400061	44400066	+	1	NA	promoter-TSS (NM_001303244)	promoter-TSS (NM_001303244)	0	NM_001303244	16160	Mm.239707	NM_008352	ENSMUSG00000004296	Il12b	Il-12b|Il-12p40|Il12p40|p40	interleukin 12b	protein-coding
mm_148733.1	chr19	5878591	5878611	+	1	NA	5' UTR (NM_134154, exon 1 of 6)	5' UTR (NM_134154, exon 1 of 6)	135	NM_134154	107375	Mm.5323	NM_134154	ENSMUSG00000024818	Slc25a45	AW491445	solute carrier family 25, member 45	protein-coding
mm_27371.1	chr3	50439009	50439029	-	1	NA	intron (NM_011990, intron 1 of 11)	intron (NM_011990, intron 1 of 11)	4594	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_154570.1	chrX	6778474	6778488	+	1	NA	Intergenic	Intergenic	-95003	NM_177914	331374	Mm.392752	NM_177914	ENSMUSG00000062393	Dgkk	Gm360	diacylglycerol kinase kappa	protein-coding
mm_103147.1	chr11	70322465	70322476	-	1	NA	promoter-TSS (NM_145684)	promoter-TSS (NM_145684)	48	NM_145684	11685	Mm.274093	NM_145684	ENSMUSG00000018907	Alox12e	8-LOX|AW259591|Alox12-ps1|Alox12-ps2|Aloxe|e-LOX1	arachidonate lipoxygenase, epidermal	protein-coding
mm_108812.1	chr12	95692213	95692246	+	1	NA	promoter-TSS (NM_201518)	promoter-TSS (NM_201518)	3	NM_201518	399558	Mm.341948	NM_201518	ENSMUSG00000047414	Flrt2	-	fibronectin leucine rich transmembrane protein 2	protein-coding
mm_10061.1	chr1	193370234	193370255	-	1	NA	promoter-TSS (NM_144817)	promoter-TSS (NM_144817)	38	NM_144817	215303	Mm.40329	NM_144817	ENSMUSG00000016179	Camk1g	CLICK-III|CaMKIgamma	calcium/calmodulin-dependent protein kinase I gamma	protein-coding
mm_55239.1	chr6	52260823	52260837	-	1	NA	promoter-TSS (NM_008264)	promoter-TSS (NM_008264)	50	NM_008264	15398	Mm.377086	NM_008264		Hoxa13	Hd|Hox-1.10	homeobox A13	protein-coding
mm_53542.1	chr6	136809592	136809603	+	1	NA	3' UTR (NM_177688, exon 1 of 1)	3' UTR (NM_177688, exon 1 of 1)	1349	NM_177688	232440	Mm.154564	NM_177688	ENSMUSG00000060032	H2afj	E130307C13	H2A histone family, member J	protein-coding
mm_105215.1	chr11	102167200	102167223	-	1	NA	intron (NM_172947, intron 2 of 4)	intron (NM_172947, intron 2 of 4)	-10804	NM_029649	76547	Mm.46529	NM_029649	ENSMUSG00000020921	Tmem101	2610511E22Rik	transmembrane protein 101	protein-coding
mm_114484.1	chr13	69612227	69612260	+	1	NA	promoter-TSS (NM_175283)	promoter-TSS (NM_175283)	227	NM_145354	28114	Mm.260009	NM_145354	ENSMUSG00000021595	Nsun2	D13Wsu123e|Misu	NOL1/NOP2/Sun domain family member 2	protein-coding
mm_102968.1	chr11	69666079	69666149	-	1	NA	promoter-TSS (NR_110993)	promoter-TSS (NR_110993)	56	NM_001291058	12514	Mm.15819	NM_009853	ENSMUSG00000018774	Cd68	Lamp4|Scard1|gp110	CD68 antigen	protein-coding
mm_155564.1	chrX	75668105	75668116	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	-89879	NM_175122	67790	Mm.45148	NM_175122	ENSMUSG00000031202	Rab39b	6330580M05Rik	RAB39B, member RAS oncogene family	protein-coding
mm_137849.1	chr17	31067294	31067299	+	1	NA	intron (NM_009593, intron 2 of 14)	intron (NM_009593, intron 2 of 14)	9602	NM_009593	11307	Mm.15691	NM_009593	ENSMUSG00000024030	Abcg1	AW413978|Abc8|White	ATP-binding cassette, sub-family G (WHITE), member 1	protein-coding
mm_133155.1	chr16	70321260	70321288	+	1	NA	intron (NM_028803, intron 1 of 15)	intron (NM_028803, intron 1 of 15)	7325	NM_028803	74185	Mm.396102	NM_028803	ENSMUSG00000022707	Gbe1	2310045H19Rik|2810426P10Rik|D16Ertd536e	glucan (1,4-alpha-), branching enzyme 1	protein-coding
mm_20213.1	chr2	125625066	125625123	-	1	NA	promoter-TSS (NM_001081091)	promoter-TSS (NM_001081091)	19	NM_001081091	99100	Mm.330545	NM_001081091	ENSMUSG00000068394	Cep152	AI851464|mKIAA0912	centrosomal protein 152	protein-coding
mm_172104.1	chr6	31804386	31804401	-	1	NA	Intergenic	IAPLTR1_Mm|LTR|ERVK	-240456	NM_013723	27205	Mm.89918	NM_013723	ENSMUSG00000025608	Podxl	AW121214|Ly102|PC|PCLP-1|Pclp1	podocalyxin-like	protein-coding
mm_144899.1	chr18	37186696	37186696	+	1	NA	3' UTR (NM_138663, exon 4 of 4)	3' UTR (NM_138663, exon 4 of 4)	42727	NM_001003672	353237	Mm.308500	NM_001003672	ENSMUSG00000102697	Pcdhac2	CNRc2	protocadherin alpha subfamily C, 2	protein-coding
mm_120792.1	chr14	74733647	74733672	+	1	NA	intron (NM_001285423, intron 1 of 8)	intron (NM_001285423, intron 1 of 8)	1362	NM_016903	13885	Mm.38055	NM_016903	ENSMUSG00000021996	Esd	Es-10|Es10|FGH|sid478	esterase D/formylglutathione hydrolase	protein-coding
mm_161400.1	chr14	119138254	119138254	+	1	NA	promoter-TSS (NM_015820)	promoter-TSS (NM_015820)	-11	NM_015820	50787	Mm.445777	NM_015820	ENSMUSG00000053465	Hs6st3	6OST3|HS6ST-3	heparan sulfate 6-O-sulfotransferase 3	protein-coding
mm_92752.1	chr10	81025407	81025411	-	1	NA	promoter-TSS (NM_145217)	promoter-TSS (NM_145217)	-32	NM_145217	208666	Mm.44995	NM_145217	ENSMUSG00000043670	Diras1	Di-Ras1|Gbts1|RIG	DIRAS family, GTP-binding RAS-like 1	protein-coding
mm_52466.1	chr6	113702292	113702303	+	1	NA	exon (NM_001347356, exon 3 of 8)	exon (NM_001347356, exon 3 of 8)	-4911	NR_106009	102465631		NR_106009	ENSMUSG00000106581	Mir7042	mmu-mir-7042	microRNA 7042	ncRNA
mm_37141.1	chr4	116990360	116990381	-	1	NA	exon (NM_009478, exon 10 of 10)	exon (NM_009478, exon 10 of 10)	4043	NM_009478	22275	Mm.46484	NM_009478	ENSMUSG00000028684	Urod	AI323803|UPD|Uro-d	uroporphyrinogen decarboxylase	protein-coding
mm_40681.1	chr5	65540049	65540071	+	1	NA	intron (NM_001310618, intron 1 of 4)	(T)n|Simple_repeat|Simple_repeat	2815	NM_001310619	53323	Mm.319512	NM_016786	ENSMUSG00000029203	Ube2k	AW492011|D5Ertd601e|E2-25k|HIP-2|Hip2|Hypg|Lig	ubiquitin-conjugating enzyme E2K	protein-coding
mm_783.1	chr1	45311625	45311638	+	1	NA	promoter-TSS (NM_009930)	promoter-TSS (NM_009930)	93	NM_009930	12825	Mm.249555	NM_009930	ENSMUSG00000026043	Col3a1	AW550625|Col3a-1|Tsk-2|Tsk2	collagen, type III, alpha 1	protein-coding
mm_515.1	chr1	37409619	37409622	+	1	NA	3' UTR (NM_030266, exon 26 of 26)	3' UTR (NM_030266, exon 26 of 26)	20483	NM_198006	76178	Mm.28085	NM_198006	ENSMUSG00000026112	Coa5	1700001A24Rik|6330578E17Rik|Pet191	cytochrome C oxidase assembly factor 5	protein-coding
mm_161185.1	chr13	49078133	49078133	-	1	NA	exon (NM_001290311, exon 11 of 29)	exon (NM_001290311, exon 11 of 29)	70195	NM_029361	75607	Mm.342723	NM_029361	ENSMUSG00000037989	Wnk2	1810073P09Rik|AW122246|ESTM15|X83337|mKIAA1760	WNK lysine deficient protein kinase 2	protein-coding
mm_127728.1	chr15	103253017	103253025	+	1	NA	promoter-TSS (NM_001302339)	promoter-TSS (NM_001302339)	131	NM_001302343	18022	Mm.457989	NM_008685	ENSMUSG00000058794	Nfe2	NF-E2|NF-E2/P45|p45|p45NFE2|p45nf-e2	nuclear factor, erythroid derived 2	protein-coding
mm_2481.1	chr1	105981095	105981103	+	1	NA	Intergenic	Intergenic	-9307	NM_001122676	227449	Mm.210188	NM_001122675	ENSMUSG00000038866	Zcchc2	9930114B20Rik|AW212015	zinc finger, CCHC domain containing 2	protein-coding
mm_48587.1	chr5	143732479	143732520	-	1	NA	promoter-TSS (NM_029749)	promoter-TSS (NM_029749)	-219	NM_029749	76800	Mm.259620	NM_029749	ENSMUSG00000051306	Usp42	2410140K03Rik|3110031A07Rik|A630018G05Rik|D5Ertd591e	ubiquitin specific peptidase 42	protein-coding
mm_94181.1	chr10	128922979	128923069	-	1	NA	intron (NM_015740, intron 1 of 3)	intron (NM_015740, intron 1 of 3)	500	NM_015740	14533	Mm.30118	NM_015740	ENSMUSG00000090247	Bloc1s1	AI839753|BLOS1|Gcn5l1	biogenesis of lysosomal organelles complex-1, subunit 1	protein-coding
mm_146141.1	chr18	74740112	74740146	+	1	NA	intron (NM_201600, intron 32 of 38)	ORR1E|LTR|ERVL-MaLR	38326	NR_028560	100217466		NR_028560		Scarna17	MBII-119	small Cajal body-specific RNA 17	ncRNA
mm_14633.1	chr2	136781458	136781472	+	1	NA	3' UTR (NM_001291056, exon 8 of 8)	3' UTR (NM_001291056, exon 8 of 8)	68015	NM_001291056	20614	Mm.45953	NM_011428	ENSMUSG00000027273	Snap25	Bdr|GENA70|SNAP-25|SUP|sp	synaptosomal-associated protein 25	protein-coding
mm_49019.1	chr6	4758919	4758936	+	1	NA	3' UTR (NM_130877, exon 2 of 2)	3' UTR (NM_130877, exon 2 of 2)	11621	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_154804.1	chrX	13302255	13302267	+	1	NA	Intergenic	Intergenic	21239	NM_010028	13205	Mm.289662	NM_010028	ENSMUSG00000000787	Ddx3x	D1Pas1-rs2|Ddx3|Fin14	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 3, X-linked	protein-coding
mm_1373.1	chr1	66468365	66468435	+	1	NA	promoter-TSS (NM_175510)	promoter-TSS (NM_175510)	-47	NM_175510	329178	Mm.44798	NM_175510	ENSMUSG00000055567	Unc80	C030018G13Rik|C230061B10Rik|UNC-80	unc-80, NALCN activator	protein-coding
mm_117751.1	chr13	95912555	95912567	-	1	NA	Intergenic	Intergenic	-20639	NM_027711	544963	Mm.38878	NM_027711	ENSMUSG00000021676	Iqgap2	4933417J23Rik|A630053O10|AI788777	IQ motif containing GTPase activating protein 2	protein-coding
mm_72851.1	chr8	88320778	88320813	+	1	NA	intron (NM_001037723, intron 17 of 27)	RSINE1|SINE|B4	26591	NM_001037724	11513	Mm.288206	NM_007406	ENSMUSG00000031659	Adcy7	AA407758	adenylate cyclase 7	protein-coding
mm_97250.1	chr11	75754866	75754869	+	1	NA	intron (NM_009536, intron 2 of 5)	intron (NM_009536, intron 2 of 5)	21980	NM_009536	22627	Mm.234700	NM_009536	ENSMUSG00000020849	Ywhae	AU019196	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide	protein-coding
mm_13859.1	chr2	119711486	119711495	+	1	NA	intron (NM_030112, intron 5 of 17)	intron (NM_030112, intron 5 of 17)	-30847	NM_146125	228550	Mm.65337	NM_146125	ENSMUSG00000027296	Itpka	-	inositol 1,4,5-trisphosphate 3-kinase A	protein-coding
mm_14939.1	chr2	151558810	151558813	+	1	NA	intron (NM_001302078, intron 4 of 5)	AT_rich|Low_complexity|Low_complexity	-13812	NM_145535	228765	Mm.32068	NM_145535	ENSMUSG00000027456	Sdcbp2	-	syndecan binding protein (syntenin) 2	protein-coding
mm_169931.1	chr16	57606750	57606752	-	1	NA	5' UTR (NM_025599, exon 1 of 10)	5' UTR (NM_025599, exon 1 of 10)	116	NM_025599	66497	Mm.425976	NM_025599	ENSMUSG00000022748	Cmss1	1110001A06Rik|2610528E23Rik|4930572F24Rik|AV099812|AV122629	cms small ribosomal subunit 1	protein-coding
mm_149892.1	chr19	25407018	25407028	+	1	NA	intron (NM_181404, intron 4 of 13)	intron (NM_181404, intron 4 of 13)	-98683	NM_015826	50796	Mm.391208	NM_015826	ENSMUSG00000024837	Dmrt1	-	doublesex and mab-3 related transcription factor 1	protein-coding
mm_71878.1	chr8	69808673	69808742	+	1	NA	promoter-TSS (NM_198101)	promoter-TSS (NM_198101)	20	NM_198101	78816	Mm.324305	NM_198101	ENSMUSG00000036246	Gmip	5031419I10Rik	Gem-interacting protein	protein-coding
mm_25000.1	chr3	97651752	97651765	+	1	NA	exon (NM_001161763, exon 9 of 9)	exon (NM_001161763, exon 9 of 9)	-6454	NM_182997	108097	Mm.31175	NM_182997	ENSMUSG00000038205	Prkab2	5730553K21Rik|AW049591|BB124140	protein kinase, AMP-activated, beta 2 non-catalytic subunit	protein-coding
mm_11547.1	chr2	32680267	32680300	+	1	NA	exon (NM_001146350, exon 13 of 14)	exon (NM_001146350, exon 13 of 14)	7483	NR_106168	102465885		NR_106168	ENSMUSG00000098972	Mir8093	Gm27548|mmu-mir-8093	microRNA 8093	ncRNA
mm_31892.1	chr4	82692752	82692767	+	1	NA	Intergenic	Intergenic	166902	NM_026647	68268	Mm.32047	NM_026647	ENSMUSG00000028403	Zdhhc21	9130404H11Rik|AL024349|D130004H04Rik|dep	zinc finger, DHHC domain containing 21	protein-coding
mm_74437.1	chr8	3754722	3754747	-	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	-5750	NM_133238	170786	Mm.32510	NM_133238	ENSMUSG00000031494	Cd209a	CD209|CDSIGN|CIRE|DC-SIGN|DC-SIGN1|Dcsign|SIGN-R1|SIGNR5	CD209a antigen	protein-coding
mm_164727.1	chr17	57839244	57839244	-	1	NA	intron (NM_001081653, intron 1 of 23)	intron (NM_001081653, intron 1 of 23)	69674	NM_001081653	620292	Mm.391030	NM_001081653	ENSMUSG00000038048	Cntnap5c	Caspr5-3|EG620292|Gm325	contactin associated protein-like 5C	protein-coding
mm_153573.1	chr19	42779937	42779985	-	1	NA	promoter-TSS (NM_019424)	promoter-TSS (NM_019424)	15	NM_001346703	192236	Mm.218381	NM_019424	ENSMUSG00000025188	Hps1	6030422N11Rik|BB405864|Gm21361|Hps|ep	Hermansky-Pudlak syndrome 1	protein-coding
mm_47569.1	chr5	124478285	124478295	-	1	NA	promoter-TSS (NM_030259)	promoter-TSS (NM_030259)	-55	NM_030259	80291	Mm.425280	NM_030259	ENSMUSG00000029401	Rilpl2	-	Rab interacting lysosomal protein-like 2	protein-coding
mm_132190.1	chr16	32431093	32431102	+	1	NA	promoter-TSS (NM_001163160)	promoter-TSS (NM_001163160)	77	NM_001163159	13026	Mm.98775	NM_009981	ENSMUSG00000005615	Pcyt1a	CTalpha|Cctalpha|Ctpct|Cttalpha	phosphate cytidylyltransferase 1, choline, alpha isoform	protein-coding
mm_6965.1	chr1	86124454	86124456	-	1	NA	intron (NM_027357, intron 18 of 24)	intron (NM_027357, intron 18 of 24)	-12485	NM_008311	15559	Mm.439747	NM_008311	ENSMUSG00000026228	Htr2b	5-HT2B|AJ012488|AV377389	5-hydroxytryptamine (serotonin) receptor 2B	protein-coding
mm_87470.1	chr10	51491597	51491656	+	1	NA	exon (NM_013532, exon 3 of 9)	exon (NM_013532, exon 3 of 9)	728	NM_013532	14728	Mm.34408	NM_013532	ENSMUSG00000062593	Lilrb4a	CD85K|Gp49b|HM18|ILT3|LIR-5|Lilrb4|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4A	protein-coding
mm_69775.1	chr7	141016945	141016959	-	1	NA	promoter-TSS (NM_001033632)	promoter-TSS (NM_001033632)	-60	NM_001033632	213002	Mm.276440	NM_001033632	ENSMUSG00000059108	Ifitm6	A330075D07|Dspa2f|Fgls5|fragilis5	interferon induced transmembrane protein 6	protein-coding
mm_151290.1	chr19	55316279	55316305	+	1	NA	promoter-TSS (NM_025883)	promoter-TSS (NM_025883)	235	NM_001293686	53611	Mm.258637	NM_016862	ENSMUSG00000024983	Vti1a	1110014F16Rik|1110018K19Rik|4921537J05Rik|MVti1|MVti1a|Vti1|Vti1-rp2	vesicle transport through interaction with t-SNAREs 1A	protein-coding
mm_34757.1	chr4	152338816	152338845	+	1	NA	5' UTR (NM_001081376, exon 1 of 42)	5' UTR (NM_001081376, exon 1 of 42)	179	NM_001081376	269610	Mm.40192	NM_029216	ENSMUSG00000005045	Chd5	4930532L22Rik|AW060752|B230399N07Rik|CHD-5	chromodomain helicase DNA binding protein 5	protein-coding
mm_1646.1	chr1	74601549	74601558	+	1	NA	promoter-TSS (NM_021313)	promoter-TSS (NM_021313)	98	NM_175031	269209	Mm.310974	NM_175031	ENSMUSG00000033276	Stk36	1700112N14Rik|B930045J24|FU|Fused|mKIAA1278	serine/threonine kinase 36	protein-coding
mm_150273.1	chr19	34243459	34243472	+	1	NA	exon (NM_007392, exon 8 of 9)	exon (NM_007392, exon 8 of 9)	11908	NM_007392	11475	Mm.213025	NM_007392	ENSMUSG00000035783	Acta2	0610041G09Rik|Actvs|SMalphaA|a-SMA|alphaSMA	actin, alpha 2, smooth muscle, aorta	protein-coding
mm_159420.1	chr3	107239565	107239565	-	1	NA	intron (NM_001044382, intron 1 of 2)	intron (NM_001044382, intron 1 of 2)	142	NM_001044382	246691	Mm.490697	NM_001044382	ENSMUSG00000070368	Prok1	EG-VEGF	prokineticin 1	protein-coding
mm_2151.1	chr1	88166005	88166037	+	1	NA	promoter-TSS (NM_201643)	promoter-TSS (NM_201643)	9	NM_201643	394433	Mm.300095	NM_201643	ENSMUSG00000089943	Ugt1a5	-	UDP glucuronosyltransferase 1 family, polypeptide A5	protein-coding
mm_19582.1	chr2	101773047	101773049	-	1	NA	intron (NM_001110849, intron 2 of 9)	intron (NM_001110849, intron 2 of 9)	24659	NM_175181	72446	Mm.24138	NM_175181	ENSMUSG00000032841	Prr5l	2600010E01Rik|4833411O04Rik|Protor-2|Protor2	proline rich 5 like	protein-coding
mm_74358.1	chr8	128358585	128358666	+	1	NA	promoter-TSS (NM_008737)	promoter-TSS (NM_008737)	-448	NM_008737	18186	Mm.271745	NM_008737	ENSMUSG00000025810	Nrp1	C530029I03|NP-1|NPN-1|Npn1|Nrp	neuropilin 1	protein-coding
mm_145767.1	chr18	65023716	65023721	+	1	NA	5' UTR (NM_031881, exon 1 of 30)	5' UTR (NM_031881, exon 1 of 30)	191	NM_031881	83814	Mm.98668	NM_031881	ENSMUSG00000024589	Nedd4l	1300012C07Rik|Nedd4-2|Nedd4b	neural precursor cell expressed, developmentally down-regulated gene 4-like	protein-coding
mm_90774.1	chr10	5922326	5922328	-	1	NA	promoter-TSS (NM_019958)	promoter-TSS (NM_019958)	73	NM_001161822	56533	Mm.44606	NM_019958	ENSMUSG00000019775	Rgs17	6430507P11Rik|Rgsz2	regulator of G-protein signaling 17	protein-coding
mm_84518.1	chr9	67043719	67043742	-	1	NA	5' UTR (NM_001164256, exon 1 of 8)	5' UTR (NM_001164256, exon 1 of 8)	141	NM_001164252	22003	Mm.121878	NM_024427	ENSMUSG00000032366	Tpm1	AA986836|AI854628|TM2|Tm3|Tmpa|Tpm-1|alpha-TM	tropomyosin 1, alpha	protein-coding
mm_76154.1	chr8	82356166	82356178	-	1	NA	intron (NM_008357, intron 2 of 7)	intron (NM_008357, intron 2 of 7)	46414	NM_001254747	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_113722.1	chr13	43785141	43785160	+	1	NA	promoter-TSS (NM_009856)	promoter-TSS (NM_009856)	38	NM_001289915	12522	Mm.57175	NM_009856	ENSMUSG00000015396	Cd83	-	CD83 antigen	protein-coding
mm_118784.1	chr14	24100164	24100174	+	1	NA	Intergenic	Intergenic	11292	NR_106069	102465697		NR_106069	ENSMUSG00000105723	Mir7210	mir-7210|mmu-mir-7210	microRNA 7210	ncRNA
mm_71151.1	chr8	39636157	39636174	+	1	NA	intron (NM_001113326, intron 1 of 9)	intron (NM_001113326, intron 1 of 9)	6513	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_143500.1	chr17	71526759	71526817	-	1	NA	promoter-TSS (NM_023294)	promoter-TSS (NM_023294)	69	NM_023294	67052	Mm.225956	NM_023294	ENSMUSG00000024056	Ndc80	2610020P18Rik|AV139730|HEC|HEC1|Kntc2	NDC80 kinetochore complex component	protein-coding
mm_34039.1	chr4	138206075	138206096	+	1	NA	exon (NM_001256195, exon 35 of 35)	exon (NM_001256195, exon 35 of 35)	-10527	NM_001122896	15441	Mm.348429	NM_010470	ENSMUSG00000028759	Hp1bp3	Hp1bp74	heterochromatin protein 1, binding protein 3	protein-coding
mm_112772.1	chr13	19623164	19623183	+	1	NA	promoter-TSS (NM_016687)	promoter-TSS (NM_016687)	-2	NM_016687	20379	Mm.42095	NM_016687	ENSMUSG00000021319	Sfrp4	-	secreted frizzled-related protein 4	protein-coding
mm_155661.1	chrX	86770469	86770475	+	1	NA	intron (NM_001160403, intron 8 of 10)	intron (NM_001160403, intron 8 of 10)	-415478	NR_036689	245502	Mm.490821	NR_036689		Gm41	-	melanoma antigen, family B, 4 pseudogene	pseudo
mm_36357.1	chr4	75982766	75982788	-	1	NA	intron (NM_011211, intron 31 of 39)	intron (NM_011211, intron 31 of 39)	-704491	NM_025849	66928	Mm.24332	NM_025849	ENSMUSG00000028398	Tmem261	1700027K24Rik|3110001D03Rik	transmembrane protein 261	protein-coding
mm_67043.1	chr7	67255298	67255304	-	1	NA	intron (NM_001291191, intron 7 of 10)	intron (NM_001291191, intron 7 of 10)	32685	NM_001191051	75099	Mm.121691	NM_175215	ENSMUSG00000043831	Lysmd4	4930506D23Rik	LysM, putative peptidoglycan-binding, domain containing 4	protein-coding
mm_135780.1	chr16	56885979	56885989	-	1	NA	5' UTR (NM_019631, exon 1 of 6)	5' UTR (NM_019631, exon 1 of 6)	179	NM_019631	56277	Mm.262328	NM_019631	ENSMUSG00000022754	Tmem45a	C630002M10Rik|M32486|p19.5	transmembrane protein 45a	protein-coding
mm_100370.1	chr11	119089330	119089337	+	1	NA	Intergenic	Intergenic	-3096	NM_007625	12418	Mm.268070	NM_007625	ENSMUSG00000039989	Cbx4	MPc2|PC2	chromobox 4	protein-coding
mm_86987.1	chr10	25489584	25489595	+	1	NA	intron (NM_001199265, intron 12 of 19)	intron (NM_001199265, intron 12 of 19)	46683	NM_001195596	100504474	Mm.46323	NM_001195596	ENSMUSG00000096546	Smlr1	2010003K15Rik	small leucine-rich protein 1	protein-coding
mm_48893.1	chr5	151428173	151428187	-	1	NA	intron (NR_131166, intron 3 of 3)	intron (NR_131166, intron 3 of 3)	21676	NR_131166	100042166	Mm.443286	NR_131166	ENSMUSG00000097321	Gm3704	-	predicted gene 3704	ncRNA
mm_144619.1	chr18	32837339	32837353	+	1	NA	promoter-TSS (NR_045381)	promoter-TSS (NR_045381)	-59	NR_045381	75795	Mm.382634	NR_045381	ENSMUSG00000097553	4930455D15Rik	-	RIKEN cDNA 4930455D15 gene	ncRNA
mm_13380.1	chr2	103838921	103838928	+	1	NA	Intergenic	Intergenic	-28302	NR_040514	78031	Mm.243867	NR_040514	ENSMUSG00000086687	4930547E08Rik	-	RIKEN cDNA 4930547E08 gene	ncRNA
mm_128134.1	chr15	31453497	31453507	-	1	NA	exon (NM_145852, exon 1 of 5)	exon (NM_145852, exon 1 of 5)	187	NM_145852	252967	Mm.436668	NM_145852	ENSMUSG00000022236	Ropn1l	ASP|AV047578|Akapasp	ropporin 1-like	protein-coding
mm_54234.1	chr6	28238799	28238826	-	1	NA	Intergenic	Intergenic	22789	NM_001081678	627049	Mm.84441	NM_001081678	ENSMUSG00000039841	Zfp800	AA407452|Znf800	zinc finger protein 800	protein-coding
mm_160819.1	chr11	29693523	29693523	+	1	NA	promoter-TSS (NM_194051)	promoter-TSS (NM_194051)	-251	NM_194051	68585	Mm.192580	NM_024226	ENSMUSG00000020458	Rtn4	1110020G17Rik|AA407876|AA409940|AA960376|ASY|C130026I10Rik|NOGO|NSP-CL|NgA|Nogo-A|Nogo-B|Nogo-C|mKIAA0886|mKIAA4153	reticulon 4	protein-coding
mm_119416.1	chr14	45219745	45219775	+	1	NA	promoter-TSS (NM_027518)	promoter-TSS (NM_027518)	43	NM_027518	70713	Mm.343793	NM_027518	ENSMUSG00000049092	Gpr137c	6330416L11Rik|Gm908|TM7SF1L2	G protein-coupled receptor 137C	protein-coding
mm_62548.1	chr7	102441686	102441698	+	1	NA	promoter-TSS (NM_009103)	promoter-TSS (NM_009103)	-3	NM_009103	20133	Mm.197486	NM_009103	ENSMUSG00000030978	Rrm1	RnrM1	ribonucleotide reductase M1	protein-coding
mm_116516.1	chr13	45713005	45713009	-	1	NA	intron (NM_001199305, intron 5 of 7)	L1MB5|LINE|L1	205563	NM_025508	66355	Mm.290802	NM_025508	ENSMUSG00000000253	Gmpr	2310004P21Rik|AV028449|GMPR 1	guanosine monophosphate reductase	protein-coding
mm_161189.1	chr13	50467307	50467307	+	1	NA	promoter-TSS (NM_001033400)	promoter-TSS (NM_001033400)	0	NM_001033400	328250	Mm.315205	NM_001033400	ENSMUSG00000071909	Nutm2	Fam22|Gm806	NUT family member 2	protein-coding
mm_138744.1	chr17	37002611	37002617	+	1	NA	promoter-TSS (NM_001013745)	promoter-TSS (NM_001013745)	89	NM_001013745	22715	Mm.305561	NM_009559	ENSMUSG00000036036	Zfp57	G19|Zfp-57	zinc finger protein 57	protein-coding
mm_48190.1	chr5	137529108	137529115	-	1	NA	TTS (NR_105846)	TTS (NR_105846)	483	NR_105846	102465227		NR_105846	ENSMUSG00000098597	Mir6418	Gm27629|mir-6418|mmu-mir-6418	microRNA 6418	ncRNA
mm_137259.1	chr17	24632672	24632712	+	1	NA	promoter-TSS (NM_008743)	promoter-TSS (NM_008743)	10	NM_008743	18207	Mm.148315	NM_008743	ENSMUSG00000041429	Nthl1	Nth1|Octs3	nth (endonuclease III)-like 1 (E.coli)	protein-coding
mm_146253.1	chr18	77781840	77781860	+	1	NA	exon (NM_007505, exon 11 of 12)	exon (NM_007505, exon 11 of 12)	8082	NM_007505	11946	Mm.276137	NM_007505	ENSMUSG00000025428	Atp5a1	AI035633|AL022851|AL023067|Atpm|D18Ertd206e|Mom2	ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1	protein-coding
mm_130396.1	chr15	97975700	97975717	-	1	NA	3' UTR (NM_001113515, exon 53 of 53)	3' UTR (NM_001113515, exon 53 of 53)	11479	NM_001252153	380967	Mm.196630	NM_201359	ENSMUSG00000052369	Tmem106c	AI046681|BC046621|D15Ertd405e	transmembrane protein 106C	protein-coding
mm_125073.1	chr15	25984334	25984336	+	1	NA	promoter-TSS (NM_144523)	promoter-TSS (NM_144523)	-31	NM_144523	52521	Mm.29145	NM_144523	ENSMUSG00000052253	Zfp622	1110033B05Rik|D15Ertd806e|ZPR9|Znf622	zinc finger protein 622	protein-coding
mm_124153.1	chr14	93202134	93202144	-	1	NA	intron (NM_001346722, intron 4 of 4)	intron (NM_001346722, intron 4 of 4)	686749	NM_001271800	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding
mm_134668.1	chr16	22261757	22261763	-	1	NA	intron (NM_001330555, intron 1 of 9)	intron (NM_001330555, intron 1 of 9)	4245	NM_001330554	20462	Mm.210352	NM_009186	ENSMUSG00000022858	Tra2b	5730405G21Rik|D16Ertd266e|SIG-41|Sfrs10|Silg41|TRA2beta	transformer 2 beta homolog (Drosophila)	protein-coding
mm_114298.1	chr13	59357732	59357777	+	1	NA	Intergenic	RMER17C|LTR|ERVK	186697	NM_001284221	67269	Mm.153008	NM_023328	ENSMUSG00000021557	Agtpbp1	1700020N17Rik|2310001G17Rik|2900054O13Rik|4930445M19Rik|5730402G09Rik|CCP1|Nna1|nmf243|pcd	ATP/GTP binding protein 1	protein-coding
mm_126019.1	chr15	76671627	76671710	+	1	NA	promoter-TSS (NM_033371)	promoter-TSS (NM_033371)	-12	NM_033371	73062	Mm.322901	NM_033371	ENSMUSG00000033819	Ppp1r16a	2900084E10Rik|Mypt3|R75527	protein phosphatase 1, regulatory (inhibitor) subunit 16A	protein-coding
mm_151596.1	chr19	3441266	3441276	-	1	NA	Intergenic	Intergenic	-26727	NM_010253	14419	Mm.4655	NM_010253	ENSMUSG00000024907	Gal	Galn	galanin	protein-coding
mm_18921.1	chr2	76742280	76742295	-	1	NA	exon (NM_011652, exon 275 of 313)	exon (NM_011652, exon 275 of 313)	66972	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_76462.1	chr8	85365318	85365334	-	1	NA	promoter-TSS (NM_175441)	promoter-TSS (NM_175441)	-2	NM_175441	213435	Mm.32804	NM_175441	ENSMUSG00000031698	Mylk3	D830007F02Rik|MLCK	myosin light chain kinase 3	protein-coding
mm_62764.1	chr7	112226752	112226789	+	1	NA	intron (NM_001193305, intron 1 of 25)	intron (NM_001193305, intron 1 of 25)	934	NM_001193305	320878	Mm.52312	NM_177282	ENSMUSG00000038244	Mical2	5330438E18Rik|9530064J02|MICAL-2|mKIAA0750	microtubule associated monooxygenase, calponin and LIM domain containing 2	protein-coding
mm_29945.1	chr3	132948427	132948453	-	1	NA	intron (NM_033525, intron 1 of 12)	intron (NM_033525, intron 1 of 12)	1374	NM_001287103	114249	Mm.279310	NM_033525	ENSMUSG00000040998	Npnt	1110009H02Rik|AA682063|AI314031|Nctn|POEM	nephronectin	protein-coding
mm_119983.1	chr14	55575856	55575866	+	1	NA	exon (NM_026808, exon 1 of 2)	exon (NM_026808, exon 1 of 2)	187	NM_026808	68680	Mm.36758	NM_026808	ENSMUSG00000022215	Fitm1	1110028A07Rik|AV010547|Cg10671|Fit1	fat storage-inducing transmembrane protein 1	protein-coding
mm_75572.1	chr8	60954727	60954790	-	1	NA	promoter-TSS (NM_173876)	promoter-TSS (NM_173876)	41	NM_173876	12725	Mm.25263	NM_007711	ENSMUSG00000004319	Clcn3	Clc3	chloride channel, voltage-sensitive 3	protein-coding
mm_154909.1	chrX	21360857	21360899	+	1	NA	promoter-TSS (NR_045668)	promoter-TSS (NR_045668)	13	NR_045668	331392	Mm.23126	NM_198633	ENSMUSG00000051537	Gm5124	EG331392	nucleolar and coiled-body phosphoprotein 1 pseudogene	pseudo
mm_14623.1	chr2	136773925	136773961	+	1	NA	exon (NM_001291056, exon 6 of 8)	exon (NM_001291056, exon 6 of 8)	60493	NM_001291056	20614	Mm.45953	NM_011428	ENSMUSG00000027273	Snap25	Bdr|GENA70|SNAP-25|SUP|sp	synaptosomal-associated protein 25	protein-coding
mm_55126.1	chr6	50574417	50574429	-	1	NA	exon (NM_027564, exon 10 of 10)	exon (NM_027564, exon 10 of 10)	2025	NR_105790	102465193		NR_105790	ENSMUSG00000099221	Mir6371	Gm27376|mmu-mir-6371	microRNA 6371	ncRNA
mm_82992.1	chr9	36541887	36541901	-	1	NA	promoter-TSS (NM_001033783)	promoter-TSS (NM_001033783)	69	NM_001033783	434396	Mm.118836	NM_001033783	ENSMUSG00000074448	Gm5615	EG434396|Pate-H|Pate9	predicted gene 5615	protein-coding
mm_108190.1	chr12	76742676	76742678	+	1	NA	Intergenic	RLTR6-int|LTR|ERV1	-22896	NM_206534	211151	Mm.80970	NM_206534	ENSMUSG00000090258	Churc1	1700030P15Rik|My015|chch	churchill domain containing 1	protein-coding
mm_140183.1	chr17	80996094	80996097	+	1	NA	intron (NM_026516, intron 3 of 3)	intron (NM_026516, intron 3 of 3)	51463	NM_026516	68027	Mm.357108	NM_026516	ENSMUSG00000024245	Tmem178	2810417M05Rik|Tmem178a	transmembrane protein 178	protein-coding
mm_138846.1	chr17	40561499	40561512	+	1	NA	promoter-TSS (NM_001287195)	promoter-TSS (NM_001287195)	-2	NM_001177529	433107	Mm.353122	NM_001177529	ENSMUSG00000092043	Esp6	EG433107|Esp5|Gm5494	exocrine gland secreted peptide 6	protein-coding
mm_28477.1	chr3	92123944	92123953	-	1	NA	promoter-TSS (NM_175424)	promoter-TSS (NM_175424)	-1	NM_175424	109314	Mm.440617	NM_175424	ENSMUSG00000056270	Prr9	A030004J04Rik	proline rich 9	protein-coding
mm_1047.1	chr1	58796325	58796336	+	1	NA	intron (NM_009812, intron 1 of 8)	intron (NM_009812, intron 1 of 8)	956	NM_009812	12370	Mm.336851	NM_009812	ENSMUSG00000026029	Casp8	CASP-8|FLICE|MACH|Mch5	caspase 8	protein-coding
mm_23186.1	chr3	40949964	40949968	+	1	NA	promoter-TSS (NM_001040399)	promoter-TSS (NM_001040399)	-665	NM_001040399	214048	Mm.46782	NM_027663	ENSMUSG00000025762	Larp1b	1700108L22Rik|4933421B21Rik|AA690246|Larp2	La ribonucleoprotein domain family, member 1B	protein-coding
mm_78701.1	chr9	41327070	41327092	+	1	NA	Intergenic	Intergenic	-49445	NR_040725	73144	Mm.38166	NM_001033153	ENSMUSG00000074415	3110039I08Rik	2610203C20Rik|AI848448|D230004N17Rik|D3Mgi9|Mir100hg	RIKEN cDNA 3110039I08 gene	ncRNA
mm_13747.1	chr2	118120832	118120843	+	1	NA	exon (NM_011580, exon 15 of 22)	exon (NM_011580, exon 15 of 22)	8961	NM_001313914	21825	Mm.4159	NM_011580	ENSMUSG00000040152	Thbs1	TSP-1|TSP1|Thbs-1|tbsp1	thrombospondin 1	protein-coding
mm_161807.1	chr17	61020621	61020621	+	1	NA	Intergenic	IAPLTR1a_Mm|LTR|ERVK	1860696	NM_207654	13640	Mm.7978	NM_010109	ENSMUSG00000048915	Efna5	AL-1|AV158822|EFL-5|Ephrin-A5|Epl7|LERK-7|RAGS	ephrin A5	protein-coding
mm_21318.1	chr2	157099170	157099180	-	1	NA	3' UTR (NM_001139520, exon 17 of 17)	3' UTR (NM_001139520, exon 17 of 17)	12120	NM_001177439	383766	Mm.480305	NM_001177439	ENSMUSG00000074628	Tldc2	Gm1332	TBC/LysM associated domain containing 2	protein-coding
mm_57638.1	chr6	128362668	128362686	-	1	NA	promoter-TSS (NM_008021)	promoter-TSS (NM_008021)	145	NM_001326583	72440	Mm.143908	NM_197981	ENSMUSG00000048668	Rhno1	2510047L19Rik|5930416I19Rik	RAD9-HUS1-RAD1 interacting nuclear orphan 1	protein-coding
mm_84893.1	chr9	79793379	79793409	-	1	NA	promoter-TSS (NR_040734)	promoter-TSS (NR_040734)	36	NM_133718	69981	Mm.486324	NM_133718	ENSMUSG00000032328	Tmem30a	2010200I23Rik|AW540225|Cdc50a|D9Wsu20e	transmembrane protein 30A	protein-coding
mm_128899.1	chr15	73296671	73296692	-	1	NA	exon (NM_007982, exon 12 of 32)	exon (NM_007982, exon 12 of 32)	-41799	NR_029561	387169		NR_029561	ENSMUSG00000065612	Mir151	Mirn151|mir-151|mmu-mir-151	microRNA 151	ncRNA
mm_145069.1	chr18	42052476	42052487	+	1	NA	Intergenic	Intergenic	-1229	NM_172966	269016	Mm.45472	NM_172966	ENSMUSG00000057719	Sh3rf2	2310046K19|9130023G24Rik|AI452083|Ppp1r39|RNF158	SH3 domain containing ring finger 2	protein-coding
mm_13725.1	chr2	117421647	117421670	+	1	NA	Intergenic	Intergenic	-78781	NM_011246	19419	Mm.42150	NM_011246	ENSMUSG00000027347	Rasgrp1	Rasgrp	RAS guanyl releasing protein 1	protein-coding
mm_63854.1	chr7	135667438	135667457	+	1	NA	intron (NM_001316681, intron 7 of 17)	intron (NM_001316681, intron 7 of 17)	-15133	NR_015548	67765	Mm.445272	NR_015548	ENSMUSG00000097471	5830432E09Rik	-	RIKEN cDNA 5830432E09 gene	ncRNA
mm_99112.1	chr11	100140591	100140593	+	1	NA	TTS (NM_008471)	TTS (NM_008471)	3107	NM_001313963	16669	Mm.439699	NM_008471	ENSMUSG00000020911	Krt19	AI663979|CK-19|EndoC|K19|Krt-1.19|Krt1-19	keratin 19	protein-coding
mm_2142.1	chr1	88095055	88095088	+	1	NA	promoter-TSS (NM_201642)	promoter-TSS (NM_201642)	70	NM_201642	394432	Mm.300095	NM_201642	ENSMUSG00000090124	Ugt1a7c	A10'|A13|Ugt1a10	UDP glucuronosyltransferase 1 family, polypeptide A7C	protein-coding
mm_107409.1	chr12	33928403	33928407	+	1	NA	promoter-TSS (NM_033522)	promoter-TSS (NM_033522)	-20	NM_033522	114712	Mm.204643	NM_033522	ENSMUSG00000046518	Ferd3l	Mnato3|N-twist|Nato|Nato3|Ntwist|Ptfb|bHLHa31|fer3	Fer3-like (Drosophila)	protein-coding
mm_103569.1	chr11	77893781	77893838	-	1	NA	promoter-TSS (NM_008952)	promoter-TSS (NM_008952)	63	NM_008952	19193	Mm.8543	NM_008952	ENSMUSG00000017453	Pipox	LPIPOX|Pso	pipecolic acid oxidase	protein-coding
mm_154328.1	chrM	2854	2864	+	1	NA	NA	Intergenic	NA	NA								
mm_53342.1	chr6	129268084	129268108	+	1	NA	3' UTR (NM_001033122, exon 5 of 5)	3' UTR (NM_001033122, exon 5 of 5)	7273	NM_001033122	12515	Mm.74745	NM_001033122	ENSMUSG00000030156	Cd69	5830438K24Rik|AI452015|AIM|VEA	CD69 antigen	protein-coding
mm_59017.1	chr7	19258509	19258524	+	1	NA	intron (NR_104069, intron 9 of 10)	intron (NR_104069, intron 9 of 10)	13338	NM_001282021	22323	Mm.9684	NM_009499	ENSMUSG00000030403	Vasp	-	vasodilator-stimulated phosphoprotein	protein-coding
mm_113855.1	chr13	47228499	47228508	+	1	NA	intron (NM_001170643, intron 3 of 7)	intron (NM_001170643, intron 3 of 7)	34500	NM_001170643	218215	Mm.287609	NM_146042	ENSMUSG00000038068	Rnf144b	BC025007|E130105P19Rik|Ibrdc2|Pir2	ring finger protein 144B	protein-coding
mm_134001.1	chr16	4789888	4789949	-	1	NA	promoter-TSS (NM_025670)	promoter-TSS (NM_025670)	17	NM_025670	66626	Mm.157648	NM_025670	ENSMUSG00000004071	Cdip1	2700048O17Rik|5730403B10Rik|AU018521|AW742692|CDIP	cell death inducing Trp53 target 1	protein-coding
mm_116521.1	chr13	45789177	45789196	-	1	NA	intron (NM_001199304, intron 4 of 6)	intron (NM_001199304, intron 4 of 6)	175805	NM_001199304	20238	Mm.342683	NM_009124	ENSMUSG00000046876	Atxn1	2900016G23Rik|Atx1|C85907|ENSMUSG00000074917|Gm10786|Sca1	ataxin 1	protein-coding
mm_16307.1	chr2	174289916	174290021	+	1	NA	intron (NR_002846, intron 1 of 4)	(CA)n|Simple_repeat|Simple_repeat	5468	NR_002846	56802	Mm.125770	NR_002846	ENSMUSG00000086537	Nespas	Gnas-as|Nespos	neuroendocrine secretory protein antisense	ncRNA
mm_35099.1	chr4	8913687	8913689	-	1	NA	Intergenic	Intergenic	223282	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_101103.1	chr11	11931761	11931844	-	1	NA	3' UTR (NM_010345, exon 17 of 17)	3' UTR (NM_010345, exon 17 of 17)	-33658	NM_001190448	13195	Mm.12906	NM_016672	ENSMUSG00000020182	Ddc	Aadc	dopa decarboxylase	protein-coding
mm_157576.1	chrX	52614218	52614228	-	1	NA	promoter-TSS (NM_016697)	promoter-TSS (NM_016697)	-249	NM_016697	14734	Mm.22515	NM_016697	ENSMUSG00000055653	Gpc3	OCI-5	glypican 3	protein-coding
mm_78045.1	chr9	14501887	14501919	+	1	NA	intron (NM_023153, intron 1 of 6)	intron (NM_023153, intron 1 of 6)	1284	NM_023153	66070	Mm.245938	NM_023153	ENSMUSG00000004096	Cwc15	0610040D20Rik|2900052N06Rik|Ed1|c11orf5|mED1	CWC15 spliceosome-associated protein	protein-coding
mm_58866.1	chr7	16944646	16944720	+	1	NA	promoter-TSS (NM_001099636)	promoter-TSS (NM_001099636)	1	NM_001099636	434128	Mm.483018	NM_001099636	ENSMUSG00000070802	Pnmal2	EG434128	PNMA-like 2	protein-coding
mm_77433.1	chr8	121544316	121544333	-	1	NA	promoter-TSS (NR_045903)	promoter-TSS (NR_045903)	-64	NR_045903	72259	Mm.396206	NR_045903	ENSMUSG00000097424	1700030M09Rik	-	RIKEN cDNA 1700030M09 gene	ncRNA
mm_120909.1	chr14	76114814	76114860	+	1	NA	intron (NM_013745, intron 3 of 9)	intron (NM_013745, intron 3 of 9)	3946	NM_013745	27275	Mm.21138	NM_013745	ENSMUSG00000022009	Nufip1	Nufip	nuclear fragile X mental retardation protein interacting protein 1	protein-coding
mm_169323.1	chr14	115042253	115042255	+	1	NA	Intergenic	CpG	-1417	NR_029785	723905		NR_029785	ENSMUSG00000065508	Mir17	Mirn17|mir-17|mmu-mir-17	microRNA 17	ncRNA
mm_146342.1	chr18	82475303	82475309	+	1	NA	5' UTR (NM_010777, exon 1 of 7)	5' UTR (NM_010777, exon 1 of 7)	183	NM_001025245	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_149441.1	chr19	11480330	11480358	+	1	NA	exon (NM_028595, exon 6 of 7)	exon (NM_028595, exon 6 of 7)	10976	NM_028595	73656	Mm.440719	NM_028595	ENSMUSG00000079419	Ms4a6c	2200009H22Rik|2210417N07Rik	membrane-spanning 4-domains, subfamily A, member 6C	protein-coding
mm_89569.1	chr10	95456491	95456505	+	1	NA	Intergenic	RLTR12A|LTR|ERVK	39123	NR_045338	70523	Mm.158398	NR_045338	ENSMUSG00000097766	5730420D15Rik	-	RIKEN cDNA 5730420D15 gene	ncRNA
mm_155794.1	chrX	98937469	98937538	+	1	NA	promoter-TSS (NM_207633)	promoter-TSS (NM_207633)	-278	NM_207633	77929	Mm.212290	NM_207633	ENSMUSG00000047694	Yipf6	A430107J06Rik	Yip1 domain family, member 6	protein-coding
mm_35574.1	chr4	41723130	41723179	-	1	NA	promoter-TSS (NM_001159565)	promoter-TSS (NM_001159565)	9	NM_001159565	53598	Mm.29025	NM_016890	ENSMUSG00000028447	Dctn3	p24	dynactin 3	protein-coding
mm_34343.1	chr4	144403746	144403750	+	1	NA	intron (NM_029948, intron 1 of 3)	RMER17C|LTR|ERVK	4716	NM_029948	77632	Mm.31283	NM_029948	ENSMUSG00000028591	Pramef12	4930569K13Rik|AU023001|C86578	PRAME family member 12	protein-coding
mm_38846.1	chr4	149247262	149247272	-	1	NA	exon (NM_001290995, exon 19 of 49)	exon (NM_001290995, exon 19 of 49)	60431	NM_207682	16561	Mm.402393	NM_008441	ENSMUSG00000063077	Kif1b	A530096N05Rik|AI448212|AI506502|D4Mil1e|KIF1Bp130|KIF1Bp204	kinesin family member 1B	protein-coding
mm_58808.1	chr7	16315602	16315606	+	1	NA	intron (NM_133234, intron 3 of 3)	intron (NM_133234, intron 3 of 3)	6021	NM_133234	170770	Mm.7660	NM_133234	ENSMUSG00000002083	Bbc3	PUMA|PUMA/JFY1	BCL2 binding component 3	protein-coding
mm_69053.1	chr7	126876061	126876076	-	1	NA	exon (NM_001163775, exon 9 of 16)	exon (NM_001163775, exon 9 of 16)	8899	NM_001163775	381921	Mm.259634	NM_001163774	ENSMUSG00000059981	Taok2	1110033K02Rik|B230344N16|MAP3K17|PSK|PSK1|TAO1|TAO2|mKIAA0881	TAO kinase 2	protein-coding
mm_61528.1	chr7	78920129	78920140	+	1	NA	exon (NM_020583, exon 4 of 4)	exon (NM_020583, exon 4 of 4)	5899	NM_001113527	57444	Mm.322843	NM_020583	ENSMUSG00000039236	Isg20	1600023I01Rik|2010107M23Rik|20kDa|DnaQL|HEM45	interferon-stimulated protein	protein-coding
mm_166208.1	chr5	45493375	45493384	+	1	NA	promoter-TSS (NM_024434)	promoter-TSS (NM_024434)	5	NM_024434	66988	Mm.286830	NM_024434	ENSMUSG00000039682	Lap3	2410015L10Rik|AA410100|LAP-3|Lap|Lapep|Pep-7|Pep-S|Pep7|Peps	leucine aminopeptidase 3	protein-coding
mm_50246.1	chr6	42355954	42355976	+	1	NA	exon (NM_001289618, exon 5 of 10)	exon (NM_001289618, exon 5 of 10)	6137	NM_001289619	22793	Mm.282303	NM_011777	ENSMUSG00000029860	Zyx	9530098H06Rik|R75157	zyxin	protein-coding
mm_17629.1	chr2	31036751	31036765	-	1	NA	intron (NM_001038700, intron 11 of 14)	intron (NM_001038700, intron 11 of 14)	54479	NM_028846	74270	Mm.346654	NM_028846	ENSMUSG00000026854	Usp20	1700055M05Rik|AI467231|Vdu2	ubiquitin specific peptidase 20	protein-coding
mm_32357.1	chr4	105157476	105157480	+	1	NA	5' UTR (NM_080555, exon 1 of 6)	5' UTR (NM_080555, exon 1 of 6)	131	NM_080555	67916	Mm.348326	NM_080555	ENSMUSG00000028517	Plpp3	1110003O22Rik|2610002D05Rik|AV025606|D4Bwg0538e|D4Bwg1535e|Lpp3|Ppab2b|Ppap2b	phospholipid phosphatase 3	protein-coding
mm_138695.1	chr17	35980115	35980133	+	1	NA	promoter-TSS (NM_001282025)	promoter-TSS (NM_001282025)	169	NM_008136	14670	Mm.335754	NM_008136	ENSMUSG00000024429	Gnl1	Gna-rs1|Gnal1	guanine nucleotide binding protein-like 1	protein-coding
mm_60721.1	chr7	45336030	45336049	+	1	NA	exon (NM_010473, exon 1 of 6)	exon (NM_010473, exon 1 of 6)	770	NM_010473	15464	Mm.39968	NM_010473	ENSMUSG00000038239	Hrc	-	histidine rich calcium binding protein	protein-coding
mm_65436.1	chr7	25384952	25384958	-	1	NA	exon (NM_010719, exon 5 of 10)	exon (NM_010719, exon 5 of 10)	5157	NM_001039507	16890	Mm.158548	NM_010719	ENSMUSG00000003123	Lipe	4933403G17Rik|HSL	lipase, hormone sensitive	protein-coding
mm_138622.1	chr17	35835622	35835675	+	1	NA	exon (NM_011655, exon 4 of 4)	exon (NM_011655, exon 4 of 4)	2653	NM_011655	22154	Mm.273538	NM_011655	ENSMUSG00000001525	Tubb5	AA408537|AI596182|B130022C14Rik|M(beta)5	tubulin, beta 5 class I	protein-coding
mm_24705.1	chr3	95160450	95160505	+	1	NA	promoter-TSS (NM_001272024)	promoter-TSS (NM_001272024)	57	NR_073551	20360	Mm.23662	NM_011351	ENSMUSG00000038777	Sema6c	Semay|mKIAA1869	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C	protein-coding
mm_26461.1	chr3	143017245	143017276	+	1	NA	Intergenic	Intergenic	-135256	NM_178654	109333	Mm.244236	NM_178654	ENSMUSG00000004591	Pkn2	6030436C20Rik|AI507382|PRK2|Prkcl2|Stk7	protein kinase N2	protein-coding
mm_88154.1	chr10	69572675	69572689	+	1	NA	intron (NM_170730, intron 1 of 17)	RMER17C|LTR|ERVK	38974	NM_146005	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_155218.1	chrX	56792667	56792679	+	1	NA	3' UTR (NM_010211, exon 7 of 7)	3' UTR (NM_010211, exon 7 of 7)	6146	NM_001287800	14199	Mm.3126	NM_010211	ENSMUSG00000023092	Fhl1	FHL-1|KyoT|RAM14-1|SLIM|SLIM-1	four and a half LIM domains 1	protein-coding
mm_56540.1	chr6	99712168	99712174	-	1	NA	3' UTR (NM_001170419, exon 2 of 2)	3' UTR (NM_001170419, exon 2 of 2)	14221	NM_001037539	50501	Mm.87365	NM_015768	ENSMUSG00000030069	Prok2	Bv8|PK2|Prok1	prokineticin 2	protein-coding
mm_5685.1	chr1	43170566	43170570	-	1	NA	intron (NM_001289533, intron 1 of 5)	intron (NM_001289533, intron 1 of 5)	-6607	NM_010212	14200	Mm.6799	NM_010212	ENSMUSG00000008136	Fhl2	FHL-2|SLIM-3|SLIM3	four and a half LIM domains 2	protein-coding
mm_129294.1	chr15	77245594	77245604	-	1	NA	intron (NM_053104, intron 1 of 13)	intron (NM_053104, intron 1 of 13)	61454	NM_001110827	93686	Mm.202774	NM_053104	ENSMUSG00000033565	Rbfox2	Fbm2|Fxh|Hrnbp2|Rbm9	RNA binding protein, fox-1 homolog (C. elegans) 2	protein-coding
mm_714.1	chr1	42694096	42694101	+	1	NA	intron (NR_027826, intron 1 of 3)	CpG	727	NR_027826	66297	Mm.45203	NM_183252	ENSMUSG00000060424	Pantr1	2610017I09Rik|Pou3f3os|linc-Brn1a	POU domain, class 3, transcription factor 3 adjacent noncoding transcript 1	ncRNA
mm_151445.1	chr19	57508583	57508597	+	1	NA	promoter-TSS (NR_040307)	promoter-TSS (NR_040307)	26	NR_040306	78073	Mm.12411	NR_040306		6720468P15Rik	-	RIKEN cDNA 6720468P15 gene	ncRNA
mm_3322.1	chr1	137918774	137918781	+	1	NA	Intergenic	Intergenic	-47678	NR_029795	735252		NR_029795	ENSMUSG00000065565	Mir181a-1	Mirn181a-1|Mirn213|miR-213|mir-181a-1|mmu-mir-213	microRNA 181a-1	ncRNA
mm_108382.1	chr12	80878317	80878330	+	1	NA	3' UTR (NM_178682, exon 6 of 6)	3' UTR (NM_178682, exon 6 of 6)	46124	NR_033786	67340	Mm.386790	NR_033786	ENSMUSG00000101912	1700052I22Rik	-	RIKEN cDNA 1700052I22 gene	ncRNA
mm_120618.1	chr14	70432010	70432013	+	1	NA	Intergenic	Intergenic	-2917	NM_021308	57746	Mm.85253	NM_021308	ENSMUSG00000033644	Piwil2	Piwil1l|mili	piwi-like RNA-mediated gene silencing 2	protein-coding
mm_143158.1	chr17	57223938	57223982	-	1	NA	exon (NM_009778, exon 11 of 41)	exon (NM_009778, exon 11 of 41)	4176	NM_009778	12266	Mm.19131	NM_009778	ENSMUSG00000024164	C3	AI255234|ASP|HSE-MSF|Plp	complement component 3	protein-coding
mm_14566.1	chr2	135061321	135061335	+	1	NA	intron (NM_019677, intron 3 of 32)	intron (NM_019677, intron 3 of 32)	154288	NR_040517	78805	Mm.78702	NR_040517	ENSMUSG00000085247	4930545L23Rik	-	RIKEN cDNA 4930545L23 gene	ncRNA
mm_60876.1	chr7	46050659	46050661	+	1	NA	exon (NM_153057, exon 11 of 31)	exon (NM_153057, exon 11 of 31)	16964	NM_153057	211548	Mm.274811	NM_153057	ENSMUSG00000030835	Nomo1	D7Ertd156e|Nomo|pM5	nodal modulator 1	protein-coding
mm_110014.1	chr12	16610961	16610991	-	1	NA	Intergenic	Intergenic	-21206	NM_172950	14245	Mm.153625	NM_015763	ENSMUSG00000020593	Lpin1	4631420P06|Kiaa0188|Lipin1|fld|mKIAA0188	lipin 1	protein-coding
mm_80413.1	chr9	77784295	77784309	+	1	NA	intron (NM_010295, intron 6 of 15)	intron (NM_010295, intron 6 of 15)	29767	NM_010295	14629	Mm.89888	NM_010295	ENSMUSG00000032350	Gclc	D9Wsu168e|GLCL-H|Ggcs-hs|Glclc	glutamate-cysteine ligase, catalytic subunit	protein-coding
mm_21562.1	chr2	164182714	164182720	-	1	NA	promoter-TSS (NM_145369)	promoter-TSS (NM_145369)	25	NM_145369	209232	Mm.218273	NM_145369	ENSMUSG00000040154	Wfdc5	BC019734|Prg5|Wap1	WAP four-disulfide core domain 5	protein-coding
mm_22948.1	chr3	32364393	32364404	+	1	NA	intron (NM_009517, intron 1 of 5)	intron (NM_009517, intron 1 of 5)	-1091	NR_027966	67576	Mm.435324	NR_027966		4930429B21Rik	-	RIKEN cDNA 4930429B21 gene	ncRNA
mm_74740.1	chr8	18846148	18846190	-	1	NA	promoter-TSS (NM_026792)	promoter-TSS (NM_026792)	-110	NM_026792	52123	Mm.24117	NM_026792	ENSMUSG00000031467	Agpat5	1110013A05Rik|D8Ertd319e	1-acylglycerol-3-phosphate O-acyltransferase 5 (lysophosphatidic acid acyltransferase, epsilon)	protein-coding
mm_119870.1	chr14	54681100	54681100	+	1	NA	intron (NM_001085473, intron 2 of 18)	intron (NM_001085473, intron 2 of 18)	-5071	NM_021437	58248	Mm.197509	NM_021437	ENSMUSG00000040822	1700123O20Rik	MNCb-2990	RIKEN cDNA 1700123O20 gene	protein-coding
mm_59047.1	chr7	19361187	19361201	+	1	NA	promoter-TSS (NM_001010836)	promoter-TSS (NM_001010836)	-22	NM_001010836	333654	Mm.333640	NM_001010836	ENSMUSG00000040734	Ppp1r13l	AV260376|IASPP|Nkip1|wa3	protein phosphatase 1, regulatory (inhibitor) subunit 13 like	protein-coding
mm_145094.1	chr18	43207623	43207678	+	1	NA	promoter-TSS (NM_178749)	promoter-TSS (NM_178749)	-47	NM_178749	269019	Mm.150401	NM_178749	ENSMUSG00000039954	Stk32a	A930015B13Rik|YANK1	serine/threonine kinase 32A	protein-coding
mm_98875.1	chr11	97799773	97799781	+	1	NA	5' UTR (NM_010688, exon 1 of 7)	5' UTR (NM_010688, exon 1 of 7)	105	NM_010688	16796	Mm.271967	NM_010688	ENSMUSG00000038366	Lasp1	AA408629|Def-4|SH3P6|Tg(Col1a1-lacZ)1Ngma	LIM and SH3 protein 1	protein-coding
mm_54093.1	chr6	16836863	16836888	-	1	NA	intron (NM_031198, intron 5 of 6)	(TG)n|Simple_repeat|Simple_repeat	61566	NM_031198	21426	Mm.36217	NM_031198	ENSMUSG00000029553	Tfec	BB107417|Tcfec|bHLHe34	transcription factor EC	protein-coding
mm_164026.1	chr14	76556855	76556865	-	1	NA	promoter-TSS (NR_027699)	promoter-TSS (NR_027699)	29	NR_027699	72661	Mm.320384	NM_001160326	ENSMUSG00000052584	Serp2	2810032E02Rik	stress-associated endoplasmic reticulum protein family member 2	protein-coding
mm_40518.1	chr5	57843331	57843380	+	1	NA	intron (NM_001310608, intron 1 of 3)	intron (NM_001310608, intron 1 of 3)	125274	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_131461.1	chr16	16983455	16983461	+	1	NA	promoter-TSS (NM_001038663)	promoter-TSS (NM_001038663)	76	NM_001038663	26413	Mm.196581	NM_011949	ENSMUSG00000063358	Mapk1	9030612K14Rik|AA407128|AU018647|C78273|ERK|Erk2|MAPK2|PRKM2|Prkm1|p41mapk|p42mapk	mitogen-activated protein kinase 1	protein-coding
mm_117833.1	chr13	98535893	98535918	-	1	NA	Intergenic	Intergenic	-100840	NR_045498	70090	Mm.410857	NR_045498	ENSMUSG00000099446	2310005E17Rik	-	RIKEN cDNA 2310005E17 gene	ncRNA
mm_45941.1	chr5	90243980	90244051	-	1	NA	exon (NM_030886, exon 29 of 34)	exon (NM_030886, exon 29 of 34)	-20019	NM_001163456	231430	Mm.319697	NM_001033310	ENSMUSG00000035505	Cox18	BC038311	cytochrome c oxidase assembly protein 18	protein-coding
mm_88207.1	chr10	70190427	70190438	+	1	NA	3' UTR (NM_001111121, exon 9 of 9)	3' UTR (NM_001111121, exon 9 of 9)	-14232	NM_001304739	69563	Mm.64672	NM_001304739	ENSMUSG00000019933	Mrln	2310015B20Rik|Mln	myoregulin	protein-coding
mm_56762.1	chr6	116109846	116109871	-	1	NA	intron (NM_177412, intron 3 of 5)	intron (NM_177412, intron 3 of 5)	83516	NM_177412	330401	Mm.425352	NM_177412	ENSMUSG00000030126	Tmcc1	3632431M01Rik|mKIAA0779	transmembrane and coiled coil domains 1	protein-coding
mm_67368.1	chr7	79840921	79840975	-	1	NA	exon (NM_008486, exon 3 of 20)	exon (NM_008486, exon 3 of 20)	1404	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_105281.1	chr11	102433971	102433981	-	1	NA	exon (NM_008175, exon 5 of 13)	exon (NM_008175, exon 5 of 13)	3654	NM_008175	14824	Mm.1568	NM_008175	ENSMUSG00000034708	Grn	Pgrn|epithelin	granulin	protein-coding
mm_20728.1	chr2	136891116	136891122	-	1	NA	promoter-TSS (NM_028201)	promoter-TSS (NM_028201)	-99	NM_028201	74243	Mm.330612	NM_028201	ENSMUSG00000027281	Slx4ip	2210009G21Rik|2410004I22Rik|C85661|Slxip	SLX4 interacting protein	protein-coding
mm_145631.1	chr18	61110340	61110484	+	1	NA	exon (NM_001037859, exon 4 of 22)	exon (NM_001037859, exon 4 of 22)	4840	NM_001037859	12978	Mm.22574	NM_007779	ENSMUSG00000024621	Csf1r	AI323359|CD115|CSF-1R|Csfmr|Fim-2|Fim2|Fms|M-CSF-R|M-CSFR	colony stimulating factor 1 receptor	protein-coding
mm_88391.1	chr10	76481102	76481127	+	1	NA	exon (NM_019434, exon 7 of 29)	exon (NM_019434, exon 7 of 29)	-12000	NM_172550	216119	Mm.344778	NM_172550	ENSMUSG00000033126	Ybey	1110068N23Rik|A130042E20Rik|C21orf57|ORF57|ORF66	ybeY metallopeptidase	protein-coding
mm_59986.1	chr7	30553264	30553272	+	1	NA	promoter-TSS (NM_183321)	promoter-TSS (NM_183321)	-34	NM_001012401	243912	Mm.34885	NM_001012401	ENSMUSG00000036854	Hspb6	AA387366|Gm479|Hsp20	heat shock protein, alpha-crystallin-related, B6	protein-coding
mm_129646.1	chr15	80576618	80576624	-	1	NA	intron (NM_001289442, intron 1 of 7)	MIR|SINE|MIR	4024	NM_001289442	17444	Mm.12947	NM_010815	ENSMUSG00000042351	Grap2	GRAP-2|GRB2L|GRBLG|GRID|Gads|GrbX|Grf40|GrpL|Mona|P38	GRB2-related adaptor protein 2	protein-coding
mm_55930.1	chr6	84588297	84588319	-	1	NA	intron (NM_175475, intron 1 of 6)	intron (NM_175475, intron 1 of 6)	5502	NM_175475	232174	Mm.255246	NM_175475	ENSMUSG00000063415	Cyp26b1	CP26|P450RAI-2	cytochrome P450, family 26, subfamily b, polypeptide 1	protein-coding
mm_57574.1	chr6	127148722	127148744	-	1	NA	promoter-TSS (NR_040275)	promoter-TSS (NR_040275)	-656	NR_040274	77558	Mm.358918	NR_040273	ENSMUSG00000097166	9330179D12Rik	-	RIKEN cDNA 9330179D12 gene	ncRNA
mm_147460.1	chr18	46597460	46597470	-	1	NA	promoter-TSS (NM_025698)	promoter-TSS (NM_025698)	70	NM_025698	66676	Mm.296043	NM_025698	ENSMUSG00000033184	Tmed7	3930401E15Rik|5830493P14Rik|AU044611|AW545765|TRAM	transmembrane p24 trafficking protein 7	protein-coding
mm_92439.1	chr10	77370244	77370254	-	1	NA	intron (NM_001024837, intron 1 of 10)	HAL1ME|LINE|L1	48024	NM_130895	110532	Mm.276815	NM_130895	ENSMUSG00000020262	Adarb1	1700057H01Rik|AW124433|AW558573|Adar2|BB220382|D10Bwg0447e|Red1	adenosine deaminase, RNA-specific, B1	protein-coding
mm_62255.1	chr7	99269116	99269129	+	1	NA	exon (NM_001043355, exon 1 of 3)	exon (NM_001043355, exon 1 of 3)	776	NM_001043355	17760	Mm.154087	NM_010837	ENSMUSG00000055407	Map6	2810411E12Rik|Map-6|Mtap6|STOP	microtubule-associated protein 6	protein-coding
mm_136582.1	chr17	4794687	4794698	+	1	NA	Intergenic	Intergenic	159712	NR_130984	75117	Mm.429393	NR_130984		4930517M08Rik	-	RIKEN cDNA 4930517M08 gene	ncRNA
mm_139207.1	chr17	47703170	47703182	+	1	NA	exon (NM_144939, exon 7 of 7)	exon (NM_144939, exon 7 of 7)	-1180	NR_045913	100126242	Mm.392746	NR_045912	ENSMUSG00000086930	Frs3os	4930417B13Rik|Gm14873|OTTMUSG00000018358	fibroblast growth factor receptor substrate 3, opposite strand	ncRNA
mm_117200.1	chr13	64066114	64066118	-	1	NA	intron (NM_008291, intron 6 of 10)	B4A|SINE|B4	23085	NM_008291	15487	Mm.5109	NM_008291	ENSMUSG00000033122	Hsd17b3	-	hydroxysteroid (17-beta) dehydrogenase 3	protein-coding
mm_50513.1	chr6	49038335	49038348	+	1	NA	intron (NM_053110, intron 1 of 10)	B1_Mur2|SINE|Alu	1823	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_18063.1	chr2	42058843	42058848	-	1	NA	intron (NM_053011, intron 2 of 90)	MLTR11B|LTR|ERVK	388723	NR_105754	102465171		NR_105754	ENSMUSG00000098660	Mir6336	Gm27584|mmu-mir-6336	microRNA 6336	ncRNA
mm_2053.1	chr1	87404988	87404998	+	1	NA	intron (NM_001110212, intron 9 of 28)	intron (NM_001110212, intron 9 of 28)	-10264	NM_001110227	100040591	Mm.443539	NM_001110227	ENSMUSG00000079436	Kcnj13	-	potassium inwardly-rectifying channel, subfamily J, member 13	protein-coding
mm_6717.1	chr1	82317644	82317652	-	1	NA	intron (NM_029777, intron 1 of 6)	intron (NM_029777, intron 1 of 6)	1069	NM_029777	76867	Mm.226994	NM_029777	ENSMUSG00000026142	Rhbdd1	4930418P06Rik|RRP4|mRHBDD1	rhomboid domain containing 1	protein-coding
mm_147244.1	chr18	38350101	38350133	-	1	NA	Intergenic	Intergenic	-11124	NM_011937	26384	Mm.22374	NM_011937	ENSMUSG00000052102	Gnpda1	GNPDA|Gnp1|Gnpi|oscillin	glucosamine-6-phosphate deaminase 1	protein-coding
mm_88201.1	chr10	70110301	70110307	+	1	NA	intron (NM_001111121, intron 1 of 8)	intron (NM_001111121, intron 1 of 8)	13183	NM_001111121	76551	Mm.281741	NM_001111121	ENSMUSG00000048701	Ccdc6	2810012H18Rik|AA536681|AA960498|AW061011	coiled-coil domain containing 6	protein-coding
mm_14461.1	chr2	131210364	131210476	+	1	NA	promoter-TSS (NR_110992)	promoter-TSS (NR_110992)	60	NR_110992	69596	Mm.2937	NM_027129	ENSMUSG00000068264	Ap5s1	0610038L13Rik|2310035K24Rik|AW060727|sigma5	adaptor-related protein 5 complex, sigma 1 subunit	protein-coding
mm_110893.1	chr12	75596164	75596176	-	1	NA	promoter-TSS (NM_012024)	promoter-TSS (NM_012024)	30	NM_012024	26932	Mm.259626	NM_012024	ENSMUSG00000021051	Ppp2r5e	4633401M22Rik|AI449017|B56beta	protein phosphatase 2, regulatory subunit B', epsilon	protein-coding
mm_7047.1	chr1	87126799	87126808	-	1	NA	exon (NM_007432, exon 8 of 11)	exon (NM_007432, exon 8 of 11)	1795	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_27847.1	chr3	79156621	79156635	-	1	NA	Intergenic	L1_Mur3|LINE|L1	-10753	NM_001099624	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_59043.1	chr7	19345594	19345616	+	1	NA	intron (NM_001127324, intron 1 of 6)	intron (NM_001127324, intron 1 of 6)	534	NM_007948	13870	Mm.280913	NM_007948	ENSMUSG00000003549	Ercc1	Ercc-1	excision repair cross-complementing rodent repair deficiency, complementation group 1	protein-coding
mm_116373.1	chr13	40738237	40738246	-	1	NA	Intergenic	Intergenic	-3321	NM_001301674	21418	Mm.85544	NM_011547	ENSMUSG00000021359	Tfap2a	AP-2|AP2alpha|Ap-2 (a)|Ap2|Ap2tf|Tcfap2a	transcription factor AP-2, alpha	protein-coding
mm_155513.1	chrX	74177253	74177268	+	1	NA	promoter-TSS (NM_031379)	promoter-TSS (NM_031379)	1	NM_031379	83553	Mm.25057	NM_031379	ENSMUSG00000031397	Tktl1	C79967	transketolase-like 1	protein-coding
mm_107772.1	chr12	59133800	59133816	+	1	NA	intron (NM_001165253, intron 1 of 22)	intron (NM_001165253, intron 1 of 22)	2355	NM_001165253	338320	Mm.213215	NM_146034	ENSMUSG00000021000	Mia2	Ctage5|D12Bwg0579e|Mea6|Mgea|Mgea6	melanoma inhibitory activity 2	protein-coding
mm_155376.1	chrX	71575756	71575798	+	1	NA	Intergenic	Intergenic	19860	NM_001293625	15354	Mm.336087	NM_008253	ENSMUSG00000015217	Hmgb3	Hmg2a|Hmg4	high mobility group box 3	protein-coding
mm_293.1	chr1	23271675	23271705	+	1	NA	promoter-TSS (NR_029533)	promoter-TSS (NR_029533)	-579	NR_029533	387225		NR_029533	ENSMUSG00000065405	Mir30a	Mirn30a|mir-30a|mmu-mir-30a	microRNA 30a	ncRNA
mm_39069.1	chr4	154097106	154097114	-	1	NA	promoter-TSS (NM_001126330)	promoter-TSS (NM_001126330)	63	NM_001126330	22062	Mm.78015	NM_011642	ENSMUSG00000029026	Trp73	TAp73|Tp73|deltaNp73|p73	transformation related protein 73	protein-coding
mm_25561.1	chr3	116562944	116562964	+	1	NA	promoter-TSS (NM_175413)	promoter-TSS (NM_175413)	-19	NM_027321	109245	Mm.216027	NM_027321	ENSMUSG00000027961	Lrrc39	2010005E21Rik|9430028I06Rik|Myomasp	leucine rich repeat containing 39	protein-coding
mm_143306.1	chr17	65986796	65986813	-	1	NA	exon (NM_001025572, exon 9 of 13)	exon (NM_001025572, exon 9 of 13)	-35617	NM_023053	65960	Mm.10153	NM_023053	ENSMUSG00000024098	Twsg1	1810013J15Rik|9030422N06Rik|AW552143|D17Ertd403e|Tsg|Twg	twisted gastrulation BMP signaling modulator 1	protein-coding
mm_134932.1	chr16	31081364	31081439	-	1	NA	promoter-TSS (NM_198626)	promoter-TSS (NM_198626)	31	NM_198626	268880	Mm.286693	NM_198626	ENSMUSG00000047434	Xxylt1	AI480653	xyloside xylosyltransferase 1	protein-coding
mm_28874.1	chr3	97713227	97713230	-	1	NA	exon (NM_001289701, exon 31 of 47)	exon (NM_001289701, exon 31 of 47)	-22666	NR_106084	102466229		NR_106084	ENSMUSG00000098381	Mir7225	Gm27499|mmu-mir-7225	microRNA 7225	ncRNA
mm_90733.1	chr10	5299013	5299026	-	1	NA	exon (NM_001347711, exon 51 of 146)	exon (NM_001347711, exon 51 of 146)	-104312	NM_001079686	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_36220.1	chr4	62516744	62516752	-	1	NA	intron (NM_008525, intron 1 of 11)	intron (NM_008525, intron 1 of 11)	3161	NM_001276446	17025	Mm.6988	NM_008525	ENSMUSG00000028393	Alad	ALADH|Lv	aminolevulinate, delta-, dehydratase	protein-coding
mm_27203.1	chr3	35754411	35754421	-	1	NA	intron (NM_029570, intron 1 of 29)	CpG	278	NM_029570	76295	Mm.239416	NM_029570	ENSMUSG00000037400	Atp11b	1110019I14Rik|ATPIF|ATPIR|mKIAA0956	ATPase, class VI, type 11B	protein-coding
mm_92341.1	chr10	75835359	75835373	-	1	NA	promoter-TSS (NM_010361)	promoter-TSS (NM_010361)	-485	NM_010361	14872	Mm.24118	NM_010361	ENSMUSG00000033318	Gstt2	AI266894|Yrs|mGSTT2	glutathione S-transferase, theta 2	protein-coding
mm_164708.1	chr17	52719865	52719868	+	1	NA	intron (NM_001031811, intron 1 of 15)	intron (NM_001031811, intron 1 of 15)	117157	NM_001031811	211468	Mm.399068	NM_001031811	ENSMUSG00000035580	Kcnh8	C130090D05Rik|ELK|ELK1|ELK3|Kv12.1	potassium voltage-gated channel, subfamily H (eag-related), member 8	protein-coding
mm_137136.1	chr17	23604633	23604658	+	1	NA	intron (NM_001289482, intron 1 of 3)	ID_B1|SINE|B4	3819	NM_001289482	332221	Mm.270315	NM_001033425	ENSMUSG00000023902	Zscan10	BC068284|Zfp206|Zkscan10|Znf206	zinc finger and SCAN domain containing 10	protein-coding
mm_28964.1	chr3	100685920	100686013	-	1	NA	promoter-TSS (NM_010763)	promoter-TSS (NM_010763)	-493	NM_010763	17156	Mm.271617	NM_010763	ENSMUSG00000008763	Man1a2	AI428775|AI528764|AI854422|Man1b|PCR2	mannosidase, alpha, class 1A, member 2	protein-coding
mm_140493.1	chr17	3462366	3462373	-	1	NA	intron (NM_001122998, intron 14 of 26)	intron (NM_001122998, intron 14 of 26)	-19946	NM_001286758	24001	Mm.137134	NM_011878	ENSMUSG00000023800	Tiam2	3000002F19Rik|STEF|mKIAA2016	T cell lymphoma invasion and metastasis 2	protein-coding
mm_47068.1	chr5	116422952	116423025	-	1	NA	promoter-TSS (NM_030704)	promoter-TSS (NM_030704)	-124	NM_030704	80888	Mm.21549	NM_030704	ENSMUSG00000041548	Hspb8	AU018630|AW413033|Cryac|D5Ucla4|E2IG1|H11|H11K|HSP20-like|HSP22	heat shock protein 8	protein-coding
mm_10237.1	chr2	6721168	6721181	+	1	NA	intron (NM_001347094, intron 2 of 12)	intron (NM_001347094, intron 2 of 12)	488	NM_001310447	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_115805.1	chr13	19358280	19358298	-	1	NA	intron (NM_024270, intron 8 of 8)	intron (NM_024270, intron 8 of 8)	37524	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_57352.1	chr6	124756888	124756898	-	1	NA	promoter-TSS (NM_007881)	promoter-TSS (NM_007881)	-406	NM_007881	13498	Mm.333380	NM_007881	ENSMUSG00000004263	Atn1	Atr1|Drpla|atrophin-1	atrophin 1	protein-coding
mm_157554.1	chrX	51972772	51972798	-	1	NA	promoter-TSS (NM_028851)	promoter-TSS (NM_028851)	-13	NM_028851	74279	Mm.159154	NM_028851	ENSMUSG00000031118	1700080O16Rik	-	RIKEN cDNA 1700080O16 gene	protein-coding
mm_55385.1	chr6	59016943	59016954	-	1	NA	intron (NM_153574, intron 1 of 17)	intron (NM_153574, intron 1 of 17)	7554	NM_153574	58909	Mm.28813	NM_153574	ENSMUSG00000037709	Fam13a	AI462012|D430015B01Rik|FAM13A1|Precm1	family with sequence similarity 13, member A	protein-coding
mm_71173.1	chr8	40595666	40595674	+	1	NA	intron (NM_001040699, intron 4 of 13)	intron (NM_001040699, intron 4 of 13)	39122	NM_001040699	54384	Mm.294871	NM_019433	ENSMUSG00000039431	Mtmr7	-	myotubularin related protein 7	protein-coding
mm_107530.1	chr12	40518911	40518936	+	1	NA	intron (NM_172803, intron 1 of 52)	intron (NM_172803, intron 1 of 52)	72870	NM_172803	238130	Mm.341423	NM_172803	ENSMUSG00000035954	Dock4	5330406C03|6330411N01Rik|AF263288|C030023J22|mKIAA0716	dedicator of cytokinesis 4	protein-coding
mm_105887.1	chr11	114931156	114931181	-	1	NA	intron (NM_199221, intron 1 of 3)	MIRb|SINE|MIR	3218	NM_001347651	217304	Mm.185355	NM_199221	ENSMUSG00000063193	Cd300lb	CLM-7|Clm7|Gm253|LMIR5	CD300 molecule like family member B	protein-coding
mm_1830.1	chr1	82724882	82724895	+	1	NA	promoter-TSS (NM_029409)	promoter-TSS (NM_029409)	-2	NM_001310697	75734	Mm.396863	NM_029409	ENSMUSG00000026150	Mff	5230400G24Rik|AI314724	mitochondrial fission factor	protein-coding
mm_69542.1	chr7	135695724	135695730	-	1	NA	exon (NM_001081117, exon 12 of 14)	exon (NM_001081117, exon 12 of 14)	20652	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_56111.1	chr6	87508074	87508097	-	1	NA	intron (NM_001037727, intron 1 of 10)	L1Md_F3|LINE|L1	-11758	NM_175476	232201	Mm.119564	NM_175476	ENSMUSG00000030047	Arhgap25	A130039I20Rik	Rho GTPase activating protein 25	protein-coding
mm_47346.1	chr5	122560739	122560755	-	1	NA	intron (NM_009879, intron 14 of 18)	intron (NM_009879, intron 14 of 18)	53771	NM_009879	12589	Mm.10125	NM_009879	ENSMUSG00000029469	Ift81	AW060663|Cdv-1|Cdv-1r|Cdv1	intraflagellar transport 81	protein-coding
mm_118436.1	chr14	8049541	8049544	+	1	NA	intron (NM_001331064, intron 6 of 8)	intron (NM_001331064, intron 6 of 8)	-30771	NM_025938	67053	Mm.210048	NM_025938	ENSMUSG00000023156	Rpp14	2610511E03Rik|AA682089	ribonuclease P 14 subunit	protein-coding
mm_23445.1	chr3	59825712	59825722	+	1	NA	Intergenic	Intergenic	-35334	NM_001243003	666803	Mm.389443	NM_001243003	ENSMUSG00000095522	Gm8298	EG666803	predicted gene 8298	protein-coding
mm_73894.1	chr8	119419042	119419052	+	1	NA	Intergenic	Intergenic	-18115	NM_027950	71839	Mm.272357	NM_027950	ENSMUSG00000074063	Osgin1	1700012B18Rik|Okl38	oxidative stress induced growth inhibitor 1	protein-coding
mm_35323.1	chr4	25800403	25800405	-	1	NA	promoter-TSS (NM_010243)	promoter-TSS (NM_010243)	-401	NM_010243	14348	Mm.39101	NM_010243	ENSMUSG00000055373	Fut9	AI746471|AU067636|mFUT9|mFuc-TIX	fucosyltransferase 9	protein-coding
mm_9821.1	chr1	182403188	182403206	-	1	NA	Intergenic	Intergenic	-5970	NM_173378	209456	Mm.287450	NM_173378	ENSMUSG00000026510	Trp53bp2	53BP2|AI746547|ASPP2|PPP1R13A|Tp53bp2|X98550	transformation related protein 53 binding protein 2	protein-coding
mm_142867.1	chr17	51814610	51814624	-	1	NA	intron (NM_001163632, intron 1 of 10)	intron (NM_001163632, intron 1 of 10)	-2563	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_37358.1	chr4	120570253	120570299	-	1	NA	promoter-TSS (NM_016748)	promoter-TSS (NM_016748)	0	NM_016748	51797	Mm.1815	NM_016748	ENSMUSG00000028633	Ctps	Ctps1	cytidine 5'-triphosphate synthase	protein-coding
mm_170274.1	chr18	24869874	24869878	+	1	NA	intron (NM_175276, intron 3 of 26)	intron (NM_175276, intron 3 of 26)	161253	NM_001289655	225288	Mm.329322	NM_175276	ENSMUSG00000034295	Fhod3	A930009H06Rik|FHOS2|mKIAA1695	formin homology 2 domain containing 3	protein-coding
mm_68563.1	chr7	114927780	114927781	-	1	NA	Intergenic	CpG	-20870	NR_040317	101786	Mm.395157	NR_040317	ENSMUSG00000108379	A730082K24Rik	AU044236	RIKEN cDNA A730082K24 gene	ncRNA
mm_92034.1	chr10	62486684	62486771	-	1	NA	promoter-TSS (NM_001113355)	promoter-TSS (NM_001113355)	78	NM_133672	30930	Mm.260703	NM_133672	ENSMUSG00000020078	Vps26a	AA407240|HB58|Vps26	VPS26 retromer complex component A	protein-coding
mm_32225.1	chr4	101717897	101717910	+	1	NA	5' UTR (NM_001122899, exon 1 of 19)	5' UTR (NM_001122899, exon 1 of 19)	496	NM_010704	16847	Mm.259282	NM_010704	ENSMUSG00000057722	Lepr	LEPROT|Leprb|Modb1|OB-RGRP|Obr|db|diabetes|obese-like|obl	leptin receptor	protein-coding
mm_70121.1	chr7	143008606	143008611	-	1	NA	intron (NM_001128081, intron 2 of 6)	intron (NM_001128081, intron 2 of 6)	2949	NM_001128081	27027	Mm.28172	NM_020286	ENSMUSG00000000244	Tspan32	AW208513|Art-1|BB235973|D7Wsu37e|Phemx|Tssc6	tetraspanin 32	protein-coding
mm_72571.1	chr8	84128580	84128597	+	1	NA	exon (NM_001013384, exon 6 of 10)	exon (NM_001013384, exon 6 of 10)	2599	NM_001013384	244550	Mm.334654	NM_001013384	ENSMUSG00000012889	Podnl1	5832418A03Rik|Gm506	podocan-like 1	protein-coding
mm_49059.1	chr6	5390290	5390296	+	1	NA	intron (NM_023048, intron 1 of 5)	intron (NM_023048, intron 1 of 5)	6907	NM_023048	65255	Mm.51340	NM_023048	ENSMUSG00000042607	Asb4	8430401O13Rik|AV117194|AW060255	ankyrin repeat and SOCS box-containing 4	protein-coding
mm_171632.1	chr4	19386739	19386741	+	1	NA	intron (NM_013927, intron 8 of 17)	L1_Mus2|LINE|L1	105890	NM_013927	30952	Mm.445778	NM_013927	ENSMUSG00000056494	Cngb3	CCNC2|CNG6|Cngbeta2	cyclic nucleotide gated channel beta 3	protein-coding
mm_62485.1	chr7	101884844	101884849	+	1	NA	intron (NM_001291353, intron 1 of 5)	B1_Mus2|SINE|Alu	-1014	NM_001291352	75430	Mm.284491	NM_027532	ENSMUSG00000030649	Anapc15	3200002M19Rik|6330414C15Rik|APC15	anaphase prompoting complex C subunit 15	protein-coding
mm_140269.1	chr17	84683151	84683157	+	1	NA	promoter-TSS (NM_031884)	promoter-TSS (NM_031884)	33	NM_026180	67470	Mm.26581	NM_026180	ENSMUSG00000024254	Abcg8	1300003C16Rik|AI114946|sterolin-2	ATP-binding cassette, sub-family G (WHITE), member 8	protein-coding
mm_54402.1	chr6	31528710	31528731	-	1	NA	exon (NM_013723, exon 2 of 8)	exon (NM_013723, exon 2 of 8)	35217	NM_013723	27205	Mm.89918	NM_013723	ENSMUSG00000025608	Podxl	AW121214|Ly102|PC|PCLP-1|Pclp1	podocalyxin-like	protein-coding
mm_65315.1	chr7	24869693	24869795	-	1	NA	promoter-TSS (NM_027732)	promoter-TSS (NM_027732)	-53	NM_182785	232973	Mm.189648	NM_182785	ENSMUSG00000062732	Lypd4	4933400F01Rik	Ly6/Plaur domain containing 4	protein-coding
mm_165704.1	chr3	95719154	95719160	+	1	NA	Intergenic	Intergenic	15816	NR_105981	102466787		NR_105981	ENSMUSG00000098737	Mir7014	Gm27837|mmu-mir-7014	microRNA 7014	ncRNA
mm_68729.1	chr7	120670223	120670228	-	1	NA	promoter-TSS (NM_001040137)	promoter-TSS (NM_001040137)	25	NM_001040137	67983	Mm.394441	NM_001040136	ENSMUSG00000030887	Pdzd9	4930408O21Rik	PDZ domain containing 9	protein-coding
mm_2673.1	chr1	127213413	127213430	+	1	NA	intron (NM_145128, intron 1 of 17)	ID_B1|SINE|B4	8435	NM_145128	107895	Mm.214682	NM_145128	ENSMUSG00000036155	Mgat5	4930471A21Rik|5330407H02Rik|AI480971|GlcNAc-TV	mannoside acetylglucosaminyltransferase 5	protein-coding
mm_21127.1	chr2	154015987	154016000	-	1	NA	TTS (NM_008953)	TTS (NM_008953)	7717	NM_008953	19194	Mm.29197	NM_008953	ENSMUSG00000042459	Bpifa2	Bpifa2e|Psp	BPI fold containing family A, member 2	protein-coding
mm_49959.1	chr6	40635056	40635067	+	1	NA	intron (NM_001171003, intron 1 of 47)	intron (NM_001171003, intron 1 of 47)	6230	NM_001171003	232714	Mm.33401	NM_001171003	ENSMUSG00000068587	Mgam	6030407P20Rik|MGA	maltase-glucoamylase	protein-coding
mm_80566.1	chr9	83843133	83843143	+	1	NA	exon (NM_001284272, exon 5 of 21)	exon (NM_001284272, exon 5 of 21)	8449	NM_001284272	22137	Mm.1904	NM_009445	ENSMUSG00000038379	Ttk	AL022661|Esk1|Mps1|PYT|esk	Ttk protein kinase	protein-coding
mm_139322.1	chr17	48410478	48410490	+	1	NA	promoter-TSS (NM_010913)	promoter-TSS (NM_010913)	484	NM_207219	106821	Mm.203943	NM_207219	ENSMUSG00000040771	Oard1	AI314976|AW558560	O-acyl-ADP-ribose deacylase 1	protein-coding
mm_33207.1	chr4	126466116	126466162	+	1	NA	intron (NM_001317174, intron 1 of 18)	intron (NM_001317174, intron 1 of 18)	2444	NM_001317174	236511	Mm.30800	NM_153403	ENSMUSG00000041530	Ago1	Eif2c1	argonaute RISC catalytic subunit 1	protein-coding
mm_27664.1	chr3	65380308	65380321	-	1	NA	3' UTR (NM_026155, exon 5 of 5)	3' UTR (NM_026155, exon 5 of 5)	12239	NM_026155	67437	Mm.232728	NM_026155	ENSMUSG00000027828	Ssr3	0610038P07Rik|AL022999|AU022074|AW553833|TRAPG	signal sequence receptor, gamma	protein-coding
mm_137955.1	chr17	32971604	32971606	+	1	NA	intron (NM_153063, intron 1 of 3)	B1_Mur4|SINE|Alu	5774	NM_153063	224691	Mm.328953	NM_153063	ENSMUSG00000053600	Zfp472	KRIM-1|Krim-1A|Krim-1B|Krim1	zinc finger protein 472	protein-coding
mm_97524.1	chr11	78501742	78501803	+	1	NA	exon (NM_011707, exon 7 of 8)	exon (NM_011707, exon 7 of 8)	-1741	NM_008759	18292	Mm.134360	NM_008759	ENSMUSG00000001103	Sebox	OG9|Og9x	SEBOX homeobox	protein-coding
mm_87042.1	chr10	28757209	28757213	+	1	NA	intron (NM_001305663, intron 3 of 5)	intron (NM_001305663, intron 3 of 5)	88851	NM_178666	210757	Mm.123021	NM_178666	ENSMUSG00000049109	Themis	E430004N04Rik|Gasp|Spot|Tsepa|thylex	thymocyte selection associated	protein-coding
mm_23008.1	chr3	34196743	34196756	+	1	NA	Intergenic	Intergenic	-115395	NM_026332	67713	Mm.274266	NM_026332	ENSMUSG00000027679	Dnajc19	1810055D05Rik|AA959924|Tim14	DnaJ heat shock protein family (Hsp40) member C19	protein-coding
mm_5470.1	chr1	36558183	36558212	-	1	NA	promoter-TSS (NM_001304329)	promoter-TSS (NM_001304329)	184	NM_001126047	20353	Mm.29558	NM_001126047	ENSMUSG00000026121	Sema4c	AI426163|M-Sema F|Semacl1|Semaf|Semai|sema I	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4C	protein-coding
mm_137449.1	chr17	26532935	26532955	+	1	NA	Intergenic	Intergenic	-24473	NM_013642	19252	Mm.239041	NM_013642	ENSMUSG00000024190	Dusp1	3CH134|MKP1|Ptpn16|U19515|erp|mkp-1	dual specificity phosphatase 1	protein-coding
mm_39128.1	chr4	155064047	155064066	-	1	NA	Intergenic	Intergenic	-2974	NM_001042407	668173	Mm.133114	NM_001042407	ENSMUSG00000029047	Pex10	AV128229|Gm142	peroxisomal biogenesis factor 10	protein-coding
mm_140343.1	chr17	86824571	86824591	+	1	NA	exon (NM_010137, exon 9 of 16)	exon (NM_010137, exon 9 of 16)	70717	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_47284.1	chr5	122113607	122113617	-	1	NA	intron (NM_001289809, intron 8 of 11)	intron (NM_001289809, intron 8 of 11)	12632	NM_010861	17906	Mm.1529	NM_010861	ENSMUSG00000013936	Myl2	MLC-2|MLC-2s/v|MLC-2v|Mlc2v|Mylpc	myosin, light polypeptide 2, regulatory, cardiac, slow	protein-coding
mm_36010.1	chr4	56846008	56846012	-	1	NA	intron (NM_018761, intron 2 of 18)	intron (NM_018761, intron 2 of 18)	19201	NM_018761	54366	Mm.218891	NM_018761	ENSMUSG00000038816	Ctnnal1	ACRP|AI616177|AW545119|C86009|Catnal1	catenin (cadherin associated protein), alpha-like 1	protein-coding
mm_148351.1	chr18	84681967	84682032	-	1	NA	promoter-TSS (NM_001289531)	promoter-TSS (NM_001289531)	60	NM_001289531	66054	Mm.29646	NM_023149	ENSMUSG00000024644	Cndp2	0610010E05Rik|C76600|Cn2|Dip-2|Pep-1|Pep1	CNDP dipeptidase 2 (metallopeptidase M20 family)	protein-coding
mm_79494.1	chr9	57094464	57094474	+	1	NA	exon (NM_011378, exon 5 of 22)	exon (NM_011378, exon 5 of 22)	18093	NM_011378	20466	Mm.15755	NM_011378	ENSMUSG00000042557	Sin3a	AW553200|Sin3|mKIAA4126|mSin3A	transcriptional regulator, SIN3A (yeast)	protein-coding
mm_121243.1	chr14	103056775	103056784	+	1	NA	TTS (NM_008392)	TTS (NM_008392)	9767	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_102631.1	chr11	62539184	62539194	-	1	NA	promoter-TSS (NM_028448)	promoter-TSS (NM_028448)	72	NM_028448	73139	Mm.390409	NM_028448	ENSMUSG00000018509	Cenpv	3110013H01Rik|AA671303|Prr6	centromere protein V	protein-coding
mm_22550.1	chr3	9403050	9403092	+	1	NA	promoter-TSS (NR_015499)	promoter-TSS (NR_015499)	-7	NR_015499	320088	Mm.212908	NR_015499	ENSMUSG00000097365	C030034L19Rik	A130044O20Rik	RIKEN cDNA C030034L19 gene	ncRNA
mm_167235.1	chr8	15011100	15011113	+	1	NA	promoter-TSS (NM_029116)	promoter-TSS (NM_029116)	81	NM_029116	74901	Mm.46675	NM_029116	ENSMUSG00000055675	Kbtbd11	2900016B01Rik|4930465M17Rik|mKIAA0711	kelch repeat and BTB (POZ) domain containing 11	protein-coding
mm_144764.1	chr18	35771712	35771741	+	1	NA	5' UTR (NM_019912, exon 1 of 7)	5' UTR (NM_019912, exon 1 of 7)	167	NM_019912	56550	Mm.180052	NM_019912	ENSMUSG00000091896	Ube2d2a	1500034D03Rik|Ubc2e|Ube2d2|ubc4	ubiquitin-conjugating enzyme E2D 2A	protein-coding
mm_81853.1	chr9	118703376	118703385	+	1	NA	intron (NM_133721, intron 15 of 27)	intron (NM_133721, intron 15 of 27)	-8312	NM_001113514	104099	Mm.335520	NM_133721	ENSMUSG00000039115	Itga9	(alpha)9|2610002H11Rik|6720458D17Rik|AI461869|D130073C02|D9Ertd428e	integrin alpha 9	protein-coding
mm_152433.1	chr19	10719123	10719126	-	1	NA	intron (NM_007650, intron 10 of 10)	B4|SINE|B4	19850	NM_007650	12507	Mm.779	NM_007650	ENSMUSG00000024669	Cd5	Ly-1|Ly-12|Ly-A|Lyt-1	CD5 antigen	protein-coding
mm_32493.1	chr4	108170139	108170142	+	1	NA	intron (NM_001254754, intron 2 of 8)	MIRb|SINE|MIR	4703	NM_001254754	52430	Mm.270783	NM_026728	ENSMUSG00000028601	Echdc2	1300017C12Rik|2610009M20Rik|D4Ertd765e	enoyl Coenzyme A hydratase domain containing 2	protein-coding
mm_2168.1	chr1	88259349	88259357	+	1	NA	3' UTR (NM_198652, exon 8 of 8)	3' UTR (NM_198652, exon 8 of 8)	10055	NR_040291	78605	Mm.384762	NR_040291		6430706D22Rik	-	RIKEN cDNA 6430706D22 gene	ncRNA
mm_77455.1	chr8	121885960	121885987	-	1	NA	exon (NM_011404, exon 7 of 10)	exon (NM_011404, exon 7 of 10)	21713	NM_011404	20539	Mm.22374	NM_011404	ENSMUSG00000040010	Slc7a5	4F2LC|D0H16S474E|LAT1|TA1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 5	protein-coding
mm_8699.1	chr1	158356259	158356313	-	1	NA	promoter-TSS (NM_207583)	promoter-TSS (NM_207583)	-26	NM_207583	240843	Mm.329579	NM_207583	ENSMUSG00000004031	Brinp2	6430517E21Rik|BB361039|Fam5b|mKIAA1747	bone morphogenic protein/retinoic acid inducible neural-specific 2	protein-coding
mm_96712.1	chr11	69662354	69662380	+	1	NA	promoter-TSS (NR_035455)	promoter-TSS (NR_035455)	282	NR_125917	24070	Mm.89579	NM_011900	ENSMUSG00000018761	Mpdu1	LEC35|SL15|Supl15h	mannose-P-dolichol utilization defect 1	protein-coding
mm_7851.1	chr1	132390525	132390529	-	1	NA	promoter-TSS (NM_001311107)	promoter-TSS (NM_001311107)	-209	NM_001311107	68875	Mm.273785	NM_178874	ENSMUSG00000042066	Tmcc2	1110063G11Rik	transmembrane and coiled-coil domains 2	protein-coding
mm_126848.1	chr15	89099255	89099266	+	1	NA	3' UTR (NM_001163319, exon 25 of 25)	3' UTR (NM_001163319, exon 25 of 25)	10153	NM_027905	223776	Mm.44763	NM_027905	ENSMUSG00000035757	Selenoo	1300018J18Rik|Selo	selenoprotein O	protein-coding
mm_13567.1	chr2	112266812	112266862	+	1	NA	exon (NM_133649, exon 1 of 25)	exon (NM_133649, exon 1 of 25)	523	NM_133649	107723	Mm.491155	NM_133648	ENSMUSG00000027130	Slc12a6	9530023I19Rik|KCC3|gaxp	solute carrier family 12, member 6	protein-coding
mm_14155.1	chr2	126577835	126577845	+	1	NA	intron (NM_011978, intron 5 of 9)	intron (NM_011978, intron 5 of 9)	24816	NM_011978	26458	Mm.290044	NM_011978	ENSMUSG00000027359	Slc27a2	ACSVL1|FATP2|VLCS|Vlac|Vlacs	solute carrier family 27 (fatty acid transporter), member 2	protein-coding
mm_111886.1	chr12	108272577	108272578	-	1	NA	intron (NM_001159910, intron 1 of 5)	intron (NM_001159910, intron 1 of 5)	2840	NM_001159910	668158	Mm.482792	NM_001159910	ENSMUSG00000084883	Ccdc85c	EG668158|Gm265|Gm9010	coiled-coil domain containing 85C	protein-coding
mm_167034.1	chr7	73005164	73005164	+	1	NA	Intergenic	L1M4|LINE|L1	96904	NR_046024	625243	Mm.261798	NR_046024	ENSMUSG00000108383	Gm6567	-	predicted gene 6567	ncRNA
mm_169313.1	chr14	104716061	104716073	-	1	NA	intron (NR_015593, intron 1 of 5)	LSU-rRNA_Hsa|rRNA|rRNA	76920	NR_015593	320249	Mm.320725	NR_015593		D130009I18Rik	-	RIKEN cDNA D130009I18 gene	ncRNA
mm_148102.1	chr18	74064900	74064943	-	1	NA	promoter-TSS (NM_172632)	promoter-TSS (NM_172632)	28	NM_172632	225724	Mm.254517	NM_172632	ENSMUSG00000024558	Mapk4	A330097D03Rik|Erk3|Prkm4|p63Mapk	mitogen-activated protein kinase 4	protein-coding
mm_106864.1	chr12	8009372	8009382	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	31700	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_159256.1	chr2	153257324	153257324	+	1	NA	intron (NM_080463, intron 4 of 6)	L1MA9|LINE|L1	15792	NM_080463	140484	Mm.293761	NM_080463	ENSMUSG00000046020	Pofut1	O-FucT-1|mKIAA0180	protein O-fucosyltransferase 1	protein-coding
mm_71213.1	chr8	40892254	40892280	+	1	NA	intron (NM_007514, intron 1 of 11)	intron (NM_007514, intron 1 of 11)	29900	NM_001044740	11988	Mm.4676	NM_007514	ENSMUSG00000031596	Slc7a2	20.5|AI158848|Atrc2|CAT-2|Cat2|Tea	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	protein-coding
mm_93551.1	chr10	116114242	116114263	-	1	NA	promoter-TSS (NM_001161855)	promoter-TSS (NM_001161855)	-335	NM_001161855	619332	Mm.391427	NM_001033821	ENSMUSG00000074734	4933416C03Rik	-	RIKEN cDNA 4933416C03 gene	protein-coding
mm_139412.1	chr17	52625037	52625040	+	1	NA	intron (NM_001031811, intron 1 of 15)	intron (NM_001031811, intron 1 of 15)	22329	NM_001031811	211468	Mm.399068	NM_001031811	ENSMUSG00000035580	Kcnh8	C130090D05Rik|ELK|ELK1|ELK3|Kv12.1	potassium voltage-gated channel, subfamily H (eag-related), member 8	protein-coding
mm_2442.1	chr1	98421093	98421134	+	1	NA	promoter-TSS (NM_027584)	promoter-TSS (NM_027584)	-11	NM_001164233	70866	Mm.389164	NM_027584	ENSMUSG00000026336	Slco6d1	4921511I05Rik	solute carrier organic anion transporter family, member 6d1	protein-coding
mm_113548.1	chr13	38037236	38037310	+	1	NA	promoter-TSS (NM_027724)	promoter-TSS (NM_027724)	284	NM_024242	71340	Mm.297130	NM_024242	ENSMUSG00000021428	Riok1	3110046C13Rik|5430416A05Rik|Ad034	RIO kinase 1 (yeast)	protein-coding
mm_19231.1	chr2	84678838	84678850	-	1	NA	promoter-TSS (NM_001290751)	promoter-TSS (NM_001290751)	-16	NM_025868	66958	Mm.371621	NM_025868	ENSMUSG00000050043	Tmx2	2310042M24Rik|AA589631|Txndc14	thioredoxin-related transmembrane protein 2	protein-coding
mm_95666.1	chr11	53785489	53785491	+	1	NA	TTS (NR_033332)	TTS (NR_033332)	15017	NM_001159396	16362	Mm.105218	NM_008390	ENSMUSG00000018899	Irf1	AU020929|Irf-1	interferon regulatory factor 1	protein-coding
mm_51099.1	chr6	67271909	67271920	+	1	NA	exon (NM_025814, exon 3 of 8)	exon (NM_025814, exon 3 of 8)	4935	NM_025814	66870	Mm.240490	NM_025814	ENSMUSG00000036371	Serbp1	1200009K13Rik|9330147J08Rik|AL022786|Pairbp1	serpine1 mRNA binding protein 1	protein-coding
mm_81125.1	chr9	106463784	106463816	+	1	NA	TTS (NM_001159652)	TTS (NM_001159652)	2140	NM_001159652	436090	Mm.482905	NM_001159652	ENSMUSG00000091735	Gpr62	4933402E03Rik	G protein-coupled receptor 62	protein-coding
mm_121520.1	chr14	122105124	122105143	+	1	NA	non-coding (NR_015586, exon 2 of 4)	non-coding (NR_015586, exon 2 of 4)	1841	NR_015586	319727	Mm.215552	NR_015586		A330035P11Rik	-	RIKEN cDNA A330035P11 gene	ncRNA
mm_9148.1	chr1	170913683	170913703	-	1	NA	promoter-TSS (NM_001029984)	promoter-TSS (NM_001029984)	-752	NM_001029984	435653	Mm.337931	NM_001029984	ENSMUSG00000070524	Fcrlb	FREB-2|FREB2|FcRL2|Fcrlm2|Fcry|mFCRL2	Fc receptor-like B	protein-coding
mm_34698.1	chr4	152058067	152058078	+	1	NA	intron (NM_028727, intron 11 of 11)	B2_Mm2|SINE|B2	18751	NM_028727	74035	Mm.275803	NM_028727	ENSMUSG00000028948	Nol9	4632412I24Rik|6030462G04Rik|AI449622|AW490720	nucleolar protein 9	protein-coding
mm_60681.1	chr7	45129036	45129054	+	1	NA	promoter-TSS (NM_009438)	promoter-TSS (NM_009438)	-300	NM_009438	22121	Mm.180458	NM_009438	ENSMUSG00000074129	Rpl13a	1810026N22Rik|Tstap198-7|tum-antigen	ribosomal protein L13A	protein-coding
mm_83695.1	chr9	50616881	50616932	-	1	NA	promoter-TSS (NM_028300)	promoter-TSS (NM_028300)	-415	NM_028300	72614	Mm.147232	NM_028300	ENSMUSG00000000167	Pih1d2	2700059L22Rik	PIH1 domain containing 2	protein-coding
mm_139748.1	chr17	63829936	63829950	+	1	NA	Intergenic	Intergenic	-34038	NM_001037997	14158	Mm.23039	NM_008000	ENSMUSG00000000127	Fer	AV082135|C330004K01Rik|Fert|Fert2	fer (fms/fps related) protein kinase	protein-coding
mm_162857.1	chr10	90577019	90577023	+	1	NA	exon (NM_181398, exon 1 of 10)	exon (NM_181398, exon 1 of 10)	330	NM_181398	77531	Mm.440605	NM_181398	ENSMUSG00000058589	Anks1b	AIDA-1b|C030032C09Rik|E530015N03Rik|ENSMUSG00000078431|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding
mm_93315.1	chr10	98913949	98913953	-	1	NA	Intergenic	CpG	-1201	NM_026482	67972	Mm.166944	NM_026482	ENSMUSG00000019943	Atp2b1	2810442I22Rik|E130111D10Rik|Pmca1	ATPase, Ca++ transporting, plasma membrane 1	protein-coding
mm_69900.1	chr7	141638851	141638865	-	1	NA	intron (NM_001330001, intron 31 of 33)	intron (NM_001330001, intron 31 of 33)	16461	NM_001330001	353328	Mm.246621	NM_181729	ENSMUSG00000048191	Muc6	-	mucin 6, gastric	protein-coding
mm_163272.1	chr11	115189578	115189627	+	1	NA	intron (NM_001033393, intron 2 of 9)	intron (NM_001033393, intron 2 of 9)	2115	NM_001033393	320534	Mm.260587	NM_001033393	ENSMUSG00000045980	Tmem104	C630005D06Rik|mFLJ00021	transmembrane protein 104	protein-coding
mm_155306.1	chrX	61186038	61186053	+	1	NA	promoter-TSS (NM_001166658)	promoter-TSS (NM_001166658)	-487	NM_001166658	631990	Mm.401324	NM_001166658	ENSMUSG00000090546	Cdr1	100039759|Cdr|Cdr34|EG631990|Gm2409|Gm7077	cerebellar degeneration related antigen 1	protein-coding
mm_144243.1	chr18	10725652	10725665	+	1	NA	promoter-TSS (NM_144860)	promoter-TSS (NM_144860)	33	NM_144860	225164	Mm.21500	NM_144860	ENSMUSG00000024294	Mib1	DIP-1|E430019M12Rik|Mib|mKIAA1323	mindbomb E3 ubiquitin protein ligase 1	protein-coding
mm_7473.1	chr1	120494123	120494140	-	1	NA	exon (NM_010766, exon 3 of 17)	exon (NM_010766, exon 3 of 17)	10953	NM_010766	17167	Mm.1856	NM_010766	ENSMUSG00000026390	Marco	AI323439|Ly112|Scara2	macrophage receptor with collagenous structure	protein-coding
mm_133420.1	chr16	86816886	86816902	+	1	NA	Intergenic	Intergenic	-537291	NM_001159331	67768	Mm.296532	NM_026366	ENSMUSG00000044442	N6amt1	5830445C04Rik|Hemk2|Pred28	N-6 adenine-specific DNA methyltransferase 1 (putative)	protein-coding
mm_85304.1	chr9	100546094	100546139	-	1	NA	promoter-TSS (NM_010878)	promoter-TSS (NM_010878)	18	NM_010878	17973	Mm.181485	NM_010878	ENSMUSG00000032475	Nck1	6330586M15Rik|D230010O13Rik|Nck|Nck-1	non-catalytic region of tyrosine kinase adaptor protein 1	protein-coding
mm_57833.1	chr6	129465062	129465072	-	1	NA	intron (NR_132130, intron 5 of 5)	intron (NR_132130, intron 5 of 5)	7712	NM_001309637	56644	Mm.239516	NM_020008	ENSMUSG00000079293	Clec7a	BGR|Clecsf12|beta-GR	C-type lectin domain family 7, member a	protein-coding
mm_1041.1	chr1	58795588	58795601	+	1	NA	5' UTR (NM_009812, exon 1 of 9)	5' UTR (NM_009812, exon 1 of 9)	220	NM_009812	12370	Mm.336851	NM_009812	ENSMUSG00000026029	Casp8	CASP-8|FLICE|MACH|Mch5	caspase 8	protein-coding
mm_113819.1	chr13	46736104	46736138	+	1	NA	Intergenic	Intergenic	-8272	NM_175749	218210	Mm.255398	NM_175749	ENSMUSG00000021374	Nup153	B130015D15Rik|C88147	nucleoporin 153	protein-coding
mm_130629.1	chr15	100422992	100423039	-	1	NA	promoter-TSS (NM_001146161)	promoter-TSS (NM_001146161)	40	NM_001146161	18174	Mm.234608	NM_008732	ENSMUSG00000023030	Slc11a2	DCT1|DMT1|Nramp2|mk|van	solute carrier family 11 (proton-coupled divalent metal ion transporters), member 2	protein-coding
mm_66034.1	chr7	30634748	30634772	-	1	NA	exon (NM_007959, exon 4 of 6)	exon (NM_007959, exon 4 of 6)	1092	NM_007959	14008	Mm.4829	NM_007959	ENSMUSG00000006311	Etv2	Etsrp71	ets variant 2	protein-coding
mm_170399.1	chr1	86359325	86359325	-	1	NA	promoter-TSS (NR_015507)	promoter-TSS (NR_015507)	130	NM_010880	17975	Mm.154378	NM_010880	ENSMUSG00000026234	Ncl	B530004O11Rik|C23|D0Nds28|D1Nds28|Nucl	nucleolin	protein-coding
mm_166175.1	chr5	30181804	30181805	+	1	NA	intron (NM_001289799, intron 15 of 15)	intron (NM_001289799, intron 15 of 15)	11065	NR_035486	100316709		NR_035486	ENSMUSG00000088113	Mir1960	mir-1960|mmu-mir-1960	microRNA 1960	ncRNA
mm_171493.1	chr4	146156917	146156921	+	1	NA	promoter-TSS (NM_001177545)	promoter-TSS (NM_001177545)	92	NM_001177546	667666	Mm.459230	NM_001177545	ENSMUSG00000066007	Zfp600	Gm13164|OTTMUSG00000010694	zinc finger protein 600	protein-coding
mm_16963.1	chr2	17650394	17650397	-	1	NA	intron (NM_028757, intron 2 of 6)	intron (NM_028757, intron 2 of 6)	80673	NM_028757	74103	Mm.120298	NM_028757	ENSMUSG00000053702	Nebl	1200007O21Rik|A630080F05Rik|BB140644|D830029A09Rik|Lnebl	nebulette	protein-coding
mm_268.1	chr1	20951667	20951717	+	1	NA	promoter-TSS (NM_027974)	promoter-TSS (NM_027974)	66	NM_027974	71877	Mm.29178	NM_027974	ENSMUSG00000041809	Efhc1	1700029F22Rik|mRib72-1|myoclonin1	EF-hand domain (C-terminal) containing 1	protein-coding
mm_164225.1	chr15	85581826	85581832	-	1	NA	promoter-TSS (NM_009528)	promoter-TSS (NM_009528)	-8	NM_009528	22422	Mm.306946	NM_009528	ENSMUSG00000022382	Wnt7b	Wnt-7b	wingless-type MMTV integration site family, member 7B	protein-coding
mm_29805.1	chr3	127789827	127789840	-	1	NA	promoter-TSS (NM_145133)	promoter-TSS (NM_145133)	-80	NM_145133	211550	Mm.31852	NM_145133	ENSMUSG00000046688	Tifa	T2bp	TRAF-interacting protein with forkhead-associated domain	protein-coding
mm_108754.1	chr12	88990150	88990152	+	1	NA	intron (NM_172544, intron 2 of 19)	intron (NM_172544, intron 2 of 19)	36761	NM_172544	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding
mm_22443.1	chr2	181693726	181693732	-	1	NA	promoter-TSS (NM_001291208)	promoter-TSS (NM_001291208)	81	NM_001291206	56470	Mm.274366	NM_026446	ENSMUSG00000002458	Rgs19	2610042F04Rik|AI324841|AW547781|GAIP	regulator of G-protein signaling 19	protein-coding
mm_153204.1	chr19	34640736	34640749	-	1	NA	promoter-TSS (NM_053217)	promoter-TSS (NM_053217)	1	NM_053217	112419	Mm.440727	NM_053217	ENSMUSG00000067297	Ifit1bl2	2010002M12Rik|AW412491|Ifit1b	interferon induced protein with tetratricopeptide repeats 1B like 2	protein-coding
mm_12071.1	chr2	59640368	59640371	+	1	NA	intron (NM_198294, intron 1 of 26)	ID_B1|SINE|B4	-6400	NM_001290659	66860	Mm.27917	NM_198294	ENSMUSG00000035168	Tanc1	1200003E16Rik|Tanc|mKIAA1728	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	protein-coding
mm_8143.1	chr1	136345782	136345810	-	1	NA	5' UTR (NM_001081360, exon 1 of 19)	5' UTR (NM_001081360, exon 1 of 19)	308	NM_001081360	67886	Mm.144143	NM_001081360	ENSMUSG00000041570	Camsap2	1600013L13Rik|4930541M15Rik|Camsap1l1|mKIAA1078	calmodulin regulated spectrin-associated protein family, member 2	protein-coding
mm_158473.1	chrX	141208999	141209048	-	1	NA	intron (NM_053185, intron 13 of 44)	intron (NM_053185, intron 13 of 44)	-252312	NM_001164177	53380	Mm.17640	NM_016883	ENSMUSG00000031429	Psmd10	AW554874	proteasome (prosome, macropain) 26S subunit, non-ATPase, 10	protein-coding
mm_34879.1	chr4	155577456	155577466	+	1	NA	intron (NM_138671, intron 2 of 11)	intron (NM_138671, intron 2 of 11)	13646	NM_001159637	192185	Mm.28347	NM_138671	ENSMUSG00000029063	Nadk	4432404C02Rik|BC004012	NAD kinase	protein-coding
mm_163741.1	chr13	119713903	119713905	+	1	NA	intron (NM_175538, intron 3 of 3)	intron (NM_175538, intron 3 of 3)	23553	NM_001291439	208715	Mm.61526	NM_145942	ENSMUSG00000093930	Hmgcs1	B130032C06Rik	3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1	protein-coding
mm_33880.1	chr4	136172559	136172579	+	1	NA	5' UTR (NM_177733, exon 1 of 7)	5' UTR (NM_177733, exon 1 of 7)	295	NM_177733	242705	Mm.307932	NM_177733	ENSMUSG00000018983	E2f2	E2F-2	E2F transcription factor 2	protein-coding
mm_92576.1	chr10	79961320	79961342	-	1	NA	intron (NM_175450, intron 2 of 9)	intron (NM_175450, intron 2 of 9)	1179	NM_175450	216156	Mm.35828	NM_175450	ENSMUSG00000035754	Wdr18	2310012I10Rik|AU044733|AW122032	WD repeat domain 18	protein-coding
mm_46514.1	chr5	105281788	105281797	-	1	NA	intron (NM_194336, intron 3 of 10)	intron (NM_194336, intron 3 of 10)	11907	NM_194336	100702	Mm.491210	NM_194336	ENSMUSG00000079362	Gbp6	AI595338|Mpa2l	guanylate binding protein 6	protein-coding
mm_6877.1	chr1	84363282	84363298	-	1	NA	Intergenic	Intergenic	-78645	NM_001003948	98496	Mm.187470	NM_001003948	ENSMUSG00000045658	Pid1	5033414K04Rik|NYGGF4	phosphotyrosine interaction domain containing 1	protein-coding
mm_93861.1	chr10	122982344	122982346	-	1	NA	Intergenic	B1_Mus2|SINE|Alu	3379	NR_029527	387251		NR_029527	ENSMUSG00000065406	Mirlet7i	Mirnlet7i|let-7i|mmu-let-7i	microRNA let7i	ncRNA
mm_146558.1	chr18	6226961	6226971	-	1	NA	exon (NM_008448, exon 4 of 26)	exon (NM_008448, exon 4 of 26)	14558	NM_008448	16573	Mm.223744	NM_008448	ENSMUSG00000006740	Kif5b	AL022807|Khc|Khcs|Kns1|Ukhc	kinesin family member 5B	protein-coding
mm_68892.1	chr7	126448595	126448638	-	1	NA	exon (NM_007504, exon 15 of 23)	exon (NM_007504, exon 15 of 23)	14457	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_19280.1	chr2	87496885	87496914	-	1	NA	Intergenic	Intergenic	-4481	NM_178250	347712	Mm.6018	NM_178250	ENSMUSG00000025839	Pramel7	AA675346|C81180	preferentially expressed antigen in melanoma like 7	protein-coding
mm_97784.1	chr11	82764333	82764373	+	1	NA	promoter-TSS (NM_025884)	promoter-TSS (NM_025884)	8	NM_025884	66983	Mm.29622	NM_025884	ENSMUSG00000046010	Zfp830	2410003C20Rik|AV301118|AW048207|Ccdc16|Omcg1|Znf830	zinc finger protein 830	protein-coding
mm_16027.1	chr2	167589082	167589102	+	1	NA	Intergenic	Intergenic	42913	NM_001311146	66589	Mm.278783	NM_023230	ENSMUSG00000078923	Ube2v1	0610011J09Rik|AI256840|CROC-1|CROC1|D7Bwg1382e|UEV-1	ubiquitin-conjugating enzyme E2 variant 1	protein-coding
mm_160396.1	chr8	69140732	69140732	-	1	NA	exon (NM_199364, exon 1 of 3)	exon (NM_199364, exon 1 of 3)	221	NM_199364	211134	Mm.409446	NM_199364	ENSMUSG00000036306	Lzts1	F37|FEZ1|PSD-Zip70	leucine zipper, putative tumor suppressor 1	protein-coding
mm_95240.1	chr11	44617515	44617543	+	1	NA	promoter-TSS (NM_001290711)	promoter-TSS (NM_001290711)	-571	NM_001290711	13591	Mm.439662	NM_007897	ENSMUSG00000057098	Ebf1	Ebf|O/E-1|OE-1|Olf-1|Olf1	early B cell factor 1	protein-coding
mm_79838.1	chr9	64806171	64806180	+	1	NA	Intergenic	Intergenic	-4836	NM_001162917	102442	Mm.222473	NM_176935	ENSMUSG00000053641	Dennd4a	AI115600|AI851943|F730015K02Rik	DENN/MADD domain containing 4A	protein-coding
mm_124166.1	chr14	93700910	93700914	-	1	NA	intron (NM_001346722, intron 2 of 4)	intron (NM_001346722, intron 2 of 4)	187976	NM_001271800	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding
mm_37928.1	chr4	132883334	132883339	-	1	NA	intron (NM_133887, intron 1 of 8)	intron (NM_133887, intron 1 of 8)	1122	NM_133887	100226	Mm.28237	NM_133887	ENSMUSG00000028879	Stx12	AI850350|AU041521|Stx13	syntaxin 12	protein-coding
mm_61325.1	chr7	68226617	68226655	+	1	NA	3' UTR (NM_010513, exon 21 of 21)	3' UTR (NM_010513, exon 21 of 21)	37597	NM_030101	78444	Mm.425468	NM_030101	ENSMUSG00000030553	Pgpep1l	C330024D12Rik	pyroglutamyl-peptidase I-like	protein-coding
mm_32069.1	chr4	97778127	97778136	+	1	NA	intron (NM_010905, intron 1 of 10)	CpG	505	NM_010905	18027	Mm.31274	NM_010905	ENSMUSG00000028565	Nfia	1110047K16Rik|9430022M17Rik|CTF|NF1-A|NF1A	nuclear factor I/A	protein-coding
mm_157287.1	chrX	20861213	20861244	-	1	NA	TTS (NM_009703)	TTS (NM_009703)	1954	NR_049190	100885829		NR_049190	ENSMUSG00000093408	Mir5617	Gm25192|mir-5617|mmu-mir-5617	microRNA 5617	ncRNA
mm_115357.1	chr13	112800928	112800941	+	1	NA	5' UTR (NM_008903, exon 1 of 6)	5' UTR (NM_008903, exon 1 of 6)	157	NM_008247	19012	Mm.291029	NM_008247	ENSMUSG00000021759	Plpp1	Hic53|Hpic53|LPP-1|LPP1|PAP-2a|PAP2-alpha|PAP2a|Ppap2a|mPAP	phospholipid phosphatase 1	protein-coding
mm_171723.1	chr4	86856732	86856734	-	1	NA	exon (NM_009096, exon 2 of 5)	exon (NM_009096, exon 2 of 5)	634	NM_009096	20104	Mm.379007	NM_009096	ENSMUSG00000028495	Rps6	S6R	ribosomal protein S6	protein-coding
mm_155492.1	chrX	73734102	73734128	+	1	NA	exon (NM_007435, exon 6 of 10)	exon (NM_007435, exon 6 of 10)	-16300	NM_001313698	27061	Mm.17	NM_012060	ENSMUSG00000002015	Bcap31	Bap31	B cell receptor associated protein 31	protein-coding
mm_36748.1	chr4	101172117	101172118	-	1	NA	intron (NM_146145, intron 10 of 24)	Lx8|LINE|L1	93165	NM_146145	16451	Mm.289657	NM_146145	ENSMUSG00000028530	Jak1	AA960307|BAP004|C130039L05Rik	Janus kinase 1	protein-coding
mm_88615.1	chr10	79826315	79826320	+	1	NA	exon (NM_030218, exon 2 of 5)	exon (NM_030218, exon 2 of 5)	5296	NM_030218	78906	Mm.33087	NM_030218	ENSMUSG00000035852	Misp	9130017N09Rik	mitotic spindle positioning	protein-coding
mm_105075.1	chr11	100770927	100770964	-	1	NA	promoter-TSS (NM_031871)	promoter-TSS (NM_031871)	12	NM_031871	80860	Mm.37308	NM_031871	ENSMUSG00000017747	Ghdc	D11Lgp1e	GH3 domain containing	protein-coding
mm_89357.1	chr10	88204476	88204491	+	1	NA	intron (NM_026070, intron 2 of 6)	MERVL_2A-int|LTR|ERVL	3386	NM_027487	67282	Mm.208465	NM_026070	ENSMUSG00000020056	Washc3	2900091E11Rik|5730495F03Rik|Ccdc53	WASH complex subunit 3	protein-coding
mm_172574.1	chr8	11312890	11312891	+	1	NA	promoter-TSS (NM_009932)	promoter-TSS (NM_009932)	-64	NM_009931	12826	Mm.738	NM_009931	ENSMUSG00000031502	Col4a1	Bru|Col4a-1|Raw|Svc	collagen, type IV, alpha 1	protein-coding
mm_36519.1	chr4	84546285	84546300	-	1	NA	intron (NM_172870, intron 2 of 5)	intron (NM_172870, intron 2 of 5)	128794	NM_172870	242509	Mm.190774	NM_172870	ENSMUSG00000028487	Bnc2	5031434M05Rik|8430420F16Rik	basonuclin 2	protein-coding
mm_76692.1	chr8	94173465	94173494	-	1	NA	TTS (NM_008630)	TTS (NM_008630)	861	NM_008630	17750	Mm.147226	NM_008630	ENSMUSG00000031762	Mt2	AA409533|MT-II|Mt-2	metallothionein 2	protein-coding
mm_15439.1	chr2	157283675	157283705	+	1	NA	exon (NM_019642, exon 2 of 17)	exon (NM_019642, exon 2 of 17)	-4141	NM_001039557	629499	Mm.384235	NM_001039557	ENSMUSG00000074627	Mroh8	4922505G16Rik	maestro heat-like repeat family member 8	protein-coding
mm_13103.1	chr2	91457502	91457549	+	1	NA	promoter-TSS (NM_001145857)	promoter-TSS (NM_001145857)	-6	NM_172668	228357	Mm.275149	NM_172668	ENSMUSG00000027253	Lrp4	6430526J12Rik|D230026E03|Megf7|mdig	low density lipoprotein receptor-related protein 4	protein-coding
mm_19618.1	chr2	102812493	102812504	-	1	NA	3' UTR (NM_009851, exon 19 of 19)	3' UTR (NM_009851, exon 19 of 19)	89167	NM_001177785	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_146550.1	chr18	6220870	6220881	-	1	NA	exon (NM_008448, exon 12 of 26)	exon (NM_008448, exon 12 of 26)	20649	NM_008448	16573	Mm.223744	NM_008448	ENSMUSG00000006740	Kif5b	AL022807|Khc|Khcs|Kns1|Ukhc	kinesin family member 5B	protein-coding
mm_44279.1	chr5	5783630	5783638	-	1	NA	Intergenic	Intergenic	-34317	NM_027399	70358	Mm.85429	NM_027399	ENSMUSG00000015652	Steap1	2410007B19Rik|Prss24|Steap	six transmembrane epithelial antigen of the prostate 1	protein-coding
mm_132848.1	chr16	46039498	46039519	+	1	NA	intron (NM_032465, intron 13 of 14)	RMER17A2|LTR|ERVK	-29095	NM_001134480	433022	Mm.380993	NM_001134480	ENSMUSG00000087141	Plcxd2	AW494639|EG433022	phosphatidylinositol-specific phospholipase C, X domain containing 2	protein-coding
mm_69167.1	chr7	127214747	127214763	-	1	NA	TTS (NM_016754)	TTS (NM_016754)	3147	NM_016754	17907	Mm.14526	NM_016754	ENSMUSG00000030672	Mylpf	2410014J02Rik|MLC-2|Mlc2	myosin light chain, phosphorylatable, fast skeletal muscle	protein-coding
mm_128366.1	chr15	42033840	42033862	-	1	NA	Intergenic	Intergenic	-164131	NM_175456	223513	Mm.148913	NM_175456	ENSMUSG00000042895	Abra	C130068O12Rik|STARS	actin-binding Rho activating protein	protein-coding
mm_10574.1	chr2	18064711	18064722	+	1	NA	non-coding (NR_045538, exon 1 of 23)	non-coding (NR_045538, exon 1 of 23)	131	NM_001252561	17354	Mm.209175	NM_010804	ENSMUSG00000026743	Mllt10	Af10|B130021D15Rik|D630001B22Rik|mKIAA4140	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 10	protein-coding
mm_18717.1	chr2	72446343	72446369	-	1	NA	Intergenic	Intergenic	-29863	NM_025866	66953	Mm.270676	NM_025866	ENSMUSG00000055612	Cdca7	2310021G01Rik|AU044109|JPO1	cell division cycle associated 7	protein-coding
mm_166833.1	chr7	19271540	19271544	-	1	NA	non-coding (NR_104069, exon 1 of 11)	non-coding (NR_104069, exon 1 of 11)	312	NM_001282021	22323	Mm.9684	NM_009499	ENSMUSG00000030403	Vasp	-	vasodilator-stimulated phosphoprotein	protein-coding
mm_138670.1	chr17	35879896	35879909	+	1	NA	5' UTR (NM_026987, exon 1 of 20)	5' UTR (NM_026987, exon 1 of 20)	124	NM_026987	69192	Mm.390986	NM_026987	ENSMUSG00000024422	Dhx16	2410006N22Rik|DBP2|Ddx16|mKIAA0577	DEAH (Asp-Glu-Ala-His) box polypeptide 16	protein-coding
mm_83489.1	chr9	45945164	45945193	-	1	NA	exon (NM_001289668, exon 16 of 27)	exon (NM_001289668, exon 16 of 27)	-5588	NR_106055	102465659		NR_106055	ENSMUSG00000098327	Mir7087	Gm27273|mmu-mir-7087	microRNA 7087	ncRNA
mm_65111.1	chr7	19310036	19310050	-	1	NA	promoter-TSS (NM_008036)	promoter-TSS (NM_008036)	2	NM_008036	14282	Mm.248335	NM_008036	ENSMUSG00000003545	Fosb	-	FBJ osteosarcoma oncogene B	protein-coding
mm_63147.1	chr7	123228880	123228885	+	1	NA	intron (NM_146198, intron 1 of 16)	MT2B|LTR|ERVL	14016	NM_146198	233836	Mm.211838	NM_146198	ENSMUSG00000030769	Slc5a11	2010013B02Rik|Kst1|RKST2|SMIT2|Slc5a10	solute carrier family 5 (sodium/glucose cotransporter), member 11	protein-coding
mm_22095.1	chr2	168955515	168955525	-	1	NA	promoter-TSS (NM_009564)	promoter-TSS (NM_009564)	67	NM_009564	22722	Mm.2095	NM_009564	ENSMUSG00000027551	Zfp64	-	zinc finger protein 64	protein-coding
mm_33904.1	chr4	136286116	136286150	+	1	NA	promoter-TSS (NM_009557)	promoter-TSS (NM_009557)	64	NM_009557	22704	Mm.1504	NM_009557	ENSMUSG00000051351	Zfp46	AI426962|Mlz-4|Zfp-46|Znf436	zinc finger protein 46	protein-coding
mm_80495.1	chr9	78482014	78482036	+	1	NA	promoter-TSS (NM_010106)	promoter-TSS (NM_010106)	-301	NM_010106	13627	Mm.138471	NM_010106	ENSMUSG00000037742	Eef1a1	-	eukaryotic translation elongation factor 1 alpha 1	protein-coding
mm_73446.1	chr8	106243278	106243285	+	1	NA	intron (NM_145404, intron 10 of 17)	intron (NM_145404, intron 10 of 17)	32227	NM_145404	214572	Mm.251804	NM_145404	ENSMUSG00000060098	Prmt7	4933402B05Rik|BC006705	protein arginine N-methyltransferase 7	protein-coding
mm_107502.1	chr12	38868152	38868158	+	1	NA	TTS (NM_001163154)	TTS (NM_001163154)	84444	NM_001163154	14009	Mm.4866	NM_007960	ENSMUSG00000004151	Etv1	ER81|Etsrp81	ets variant 1	protein-coding
mm_59475.1	chr7	27456003	27456006	+	1	NA	intron (NM_001290525, intron 1 of 4)	ID_B1|SINE|B4	3586	NM_001290525	233016	Mm.24021	NM_144923	ENSMUSG00000040466	Blvrb	-	biliverdin reductase B (flavin reductase (NADPH))	protein-coding
mm_93937.1	chr10	127188777	127188806	-	1	NA	intron (NM_001166413, intron 2 of 15)	CpG	1032	NM_001166413	52666	Mm.272230	NM_028027	ENSMUSG00000019467	Arhgef25	2410008H17Rik|D10Ertd610e|GEFT	Rho guanine nucleotide exchange factor (GEF) 25	protein-coding
mm_49642.1	chr6	30805458	30805467	+	1	NA	intron (NM_017478, intron 20 of 23)	intron (NM_017478, intron 20 of 23)	64163	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_69908.1	chr7	141640082	141640091	-	1	NA	intron (NM_001330001, intron 31 of 33)	intron (NM_001330001, intron 31 of 33)	15233	NM_001330001	353328	Mm.246621	NM_181729	ENSMUSG00000048191	Muc6	-	mucin 6, gastric	protein-coding
mm_65911.1	chr7	30194153	30194162	-	1	NA	intron (NM_009795, intron 1 of 10)	intron (NM_009795, intron 1 of 10)	891	NM_009795	12336	Mm.439782	NM_009795	ENSMUSG00000001794	Capns1	Capa-4|Capa4|Capn4|D7Ertd146e	calpain, small subunit 1	protein-coding
mm_80748.1	chr9	95047860	95047862	+	1	NA	intron (NM_177909, intron 11 of 15)	L1Md_F3|LINE|L1	296032	NR_106116	102465763		NR_106116	ENSMUSG00000098251	Mir7656	Gm27614|mmu-mir-7656	microRNA 7656	ncRNA
mm_22113.1	chr2	170134528	170134556	-	1	NA	intron (NM_001159683, intron 1 of 6)	intron (NM_001159683, intron 1 of 6)	-3322	NM_001033299	228913	Mm.22858	NM_001033299	ENSMUSG00000052056	Zfp217	4933431C08Rik|AW987152|Gm562|ZABC1|Znf217	zinc finger protein 217	protein-coding
mm_40249.1	chr5	38108143	38108150	+	1	NA	intron (NM_001289536, intron 4 of 9)	intron (NM_001289536, intron 4 of 9)	51321	NM_010942	18196	Mm.7414	NM_010942	ENSMUSG00000029126	Nsg1	Neep21|m234|p21	neuron specific gene family member 1	protein-coding
mm_7824.1	chr1	132067904	132067913	-	1	NA	5' UTR (NM_001114662, exon 1 of 10)	5' UTR (NM_001114662, exon 1 of 10)	154	NM_172510	213006	Mm.208445	NM_172510	ENSMUSG00000059149	Mfsd4a	A230072B04|A930031D07Rik|AI850289|Mfsd4	major facilitator superfamily domain containing 4A	protein-coding
mm_140311.1	chr17	86167778	86167795	+	1	NA	promoter-TSS (NM_011104)	promoter-TSS (NM_011104)	1	NM_011104	18754	Mm.24614	NM_011104	ENSMUSG00000045038	Prkce	5830406C15Rik|PKC[e]|PKCepsilon|Pkce|R75156	protein kinase C, epsilon	protein-coding
mm_81910.1	chr9	120074816	120074826	+	1	NA	Intergenic	Intergenic	-6525	NM_009987	13051	Mm.44065	NM_009987	ENSMUSG00000052336	Cx3cr1	-	chemokine (C-X3-C motif) receptor 1	protein-coding
mm_86080.1	chr9	114781812	114781887	-	1	NA	5' UTR (NM_133978, exon 1 of 5)	5' UTR (NM_133978, exon 1 of 5)	144	NM_133978	102545	Mm.35600	NM_133978	ENSMUSG00000032436	Cmtm7	AI481279|Cklfsf7|LNV	CKLF-like MARVEL transmembrane domain containing 7	protein-coding
mm_43440.1	chr5	136096447	136096455	+	1	NA	intron (NM_001039103, intron 6 of 19)	PB1D11|SINE|Alu	-9071	NR_106002	102465626		NR_106002	ENSMUSG00000099003	Mir7035	Gm27661|mmu-mir-7035	microRNA 7035	ncRNA
mm_100200.1	chr11	116807870	116807892	+	1	NA	3' UTR (NM_001347633, exon 5 of 5)	3' UTR (NM_001347633, exon 5 of 5)	20165	NM_026280	67622	Mm.64962	NM_026280	ENSMUSG00000020814	Mxra7	1810057P16Rik|E130302J09Rik	matrix-remodelling associated 7	protein-coding
mm_53383.1	chr6	129517526	129517539	+	1	NA	3' UTR (NM_001081186, exon 5 of 5)	3' UTR (NM_001081186, exon 5 of 5)	4975	NM_001081186	330428	Mm.44237	NM_001081186	ENSMUSG00000030160	Tmem52b	D630042F21Rik	transmembrane protein 52B	protein-coding
mm_170573.1	chr19	5288361	5288362	-	1	NA	exon (NM_030109, exon 6 of 21)	exon (NM_030109, exon 6 of 21)	7094	NM_030109	319322	Mm.196532	NM_030109	ENSMUSG00000024853	Sf3b2	145kDa|2610311M13Rik|2810441F20Rik|B230398H18Rik|SAP145|SF3b1|SF3b145|SF3b150	splicing factor 3b, subunit 2	protein-coding
mm_120846.1	chr14	75200437	75200473	+	1	NA	exon (NM_001247984, exon 4 of 16)	exon (NM_001247984, exon 4 of 16)	-41832	NM_019775	56373	Mm.24242	NM_019775	ENSMUSG00000021999	Cpb2	1110032P04Rik|4930405E17Rik|AI255929|CPR|Cpu|TAFI	carboxypeptidase B2 (plasma)	protein-coding
mm_38464.1	chr4	140617063	140617084	-	1	NA	intron (NM_001290803, intron 1 of 28)	intron (NM_001290803, intron 1 of 28)	31683	NM_001112723	72754	Mm.29329	NM_172415	ENSMUSG00000040964	Arhgef10l	2810441C07Rik	Rho guanine nucleotide exchange factor (GEF) 10-like	protein-coding
mm_12159.1	chr2	62147772	62147786	+	1	NA	intron (NM_001242378, intron 1 of 25)	intron (NM_001242378, intron 1 of 25)	101264	NM_033552	94229	Mm.314497	NM_033552	ENSMUSG00000026904	Slc4a10	NCBE|mKIAA4136	solute carrier family 4, sodium bicarbonate cotransporter-like, member 10	protein-coding
mm_147406.1	chr18	44662215	44662244	-	1	NA	promoter-TSS (NM_001085374)	promoter-TSS (NM_001085374)	37	NM_001085374	328949	Mm.312511	NM_001033406	ENSMUSG00000071856	Mcc	D18Ertd451e|E330037C19	mutated in colorectal cancers	protein-coding
mm_35062.1	chr4	6453693	6453700	-	1	NA	intron (NM_010945, intron 1 of 30)	CpG	575	NM_010945	18201	Mm.3059	NM_010945	ENSMUSG00000028245	Nsmaf	AA959567|C630007J05|Fan	neutral sphingomyelinase (N-SMase) activation associated factor	protein-coding
mm_120053.1	chr14	56668243	56668349	+	1	NA	promoter-TSS (NM_023773)	promoter-TSS (NM_023773)	48	NM_023773	75339	Mm.152466	NM_023773	ENSMUSG00000079184	Mphosph8	1500035L22Rik|4930548G07Rik|AU040635	M-phase phosphoprotein 8	protein-coding
mm_125391.1	chr15	41173660	41173687	+	1	NA	Intergenic	Intergenic	-273809	NM_001130166	170719	Mm.254267	NM_130885	ENSMUSG00000022307	Oxr1	2210416C20Rik|C7|C7B	oxidation resistance 1	protein-coding
mm_106412.1	chr11	119086232	119086250	-	1	NA	promoter-TSS (NM_007625)	promoter-TSS (NM_007625)	-4	NM_007625	12418	Mm.268070	NM_007625	ENSMUSG00000039989	Cbx4	MPc2|PC2	chromobox 4	protein-coding
mm_55610.1	chr6	72010164	72010166	-	1	NA	Intergenic	(GAAAA)n|Simple_repeat|Simple_repeat	32363	NR_046180	330350	Mm.246787	NR_046180	ENSMUSG00000108356	9130221F21Rik	9130221F21	RIKEN cDNA 9130221F21 gene	ncRNA
mm_79684.1	chr9	59942109	59942138	+	1	NA	TTS (NM_013708)	TTS (NM_013708)	7956	NM_013708	23958	Mm.103641	NM_013708	ENSMUSG00000032292	Nr2e3	A930035N01Rik|PNR|RNR|rd7	nuclear receptor subfamily 2, group E, member 3	protein-coding
mm_146781.1	chr18	20061648	20061652	-	1	NA	Intergenic	Intergenic	-2096	NM_001317365	13506	Mm.280547	NM_013505	ENSMUSG00000024331	Dsc2	AW228162	desmocollin 2	protein-coding
mm_31775.1	chr4	63558880	63558932	+	1	NA	Intergenic	CpG	-1454	NM_144905	230279	Mm.41523	NM_144905	ENSMUSG00000045917	Tmem268	6330416G13Rik|AW492431|bM230C2.2	transmembrane protein 268	protein-coding
mm_95457.1	chr11	50377070	50377086	+	1	NA	promoter-TSS (NM_021510)	promoter-TSS (NM_021510)	-641	NM_021510	59013	Mm.21740	NM_021510	ENSMUSG00000007850	Hnrnph1	AI642080|E430005G16Rik|Hnrnph|Hnrph1	heterogeneous nuclear ribonucleoprotein H1	protein-coding
mm_49222.1	chr6	15793527	15793546	+	1	NA	intron (NM_175088, intron 4 of 4)	intron (NM_175088, intron 4 of 4)	72875	NM_175088	16543	Mm.1314	NM_175088	ENSMUSG00000041390	Mdfic	Kdt1|Mdfid	MyoD family inhibitor domain containing	protein-coding
mm_124652.1	chr15	5185701	5185742	+	1	NA	5' UTR (NM_026213, exon 1 of 5)	5' UTR (NM_026213, exon 1 of 5)	161	NM_026213	67515	Mm.254979	NM_026213	ENSMUSG00000022151	Ttc33	2410099M07Rik|2900001O04Rik|AI507072|AW538342|Osrf	tetratricopeptide repeat domain 33	protein-coding
mm_146786.1	chr18	20114640	20114671	-	1	NA	5' UTR (NM_001291804, exon 1 of 16)	5' UTR (NM_001291804, exon 1 of 16)	118	NM_001291804	13505	Mm.33740	NM_013504	ENSMUSG00000044322	Dsc1	1110020A10Rik|AI507491	desmocollin 1	protein-coding
mm_133256.1	chr16	77329499	77329509	+	1	NA	non-coding (NR_015543, exon 1 of 5)	non-coding (NR_015543, exon 1 of 5)	176	NR_015543	77994	Mm.394688	NR_015543	ENSMUSG00000090386	Mir99ahg	2810055G20Rik|D730043B02Rik	Mir99a and Mirlet7c-1 host gene (non-protein coding)	ncRNA
mm_145662.1	chr18	61130891	61130901	+	1	NA	TTS (NM_178277)	TTS (NM_178277)	13428	NR_105949	102466212		NR_105949	ENSMUSG00000098389	Mir6983	Gm27496|mmu-mir-6983	microRNA 6983	ncRNA
mm_42959.1	chr5	123076276	123076354	+	1	NA	promoter-TSS (NM_001039723)	promoter-TSS (NM_001039723)	40	NM_001039723	330189	Mm.391872	NM_001039723	ENSMUSG00000054434	Tmem120b	-	transmembrane protein 120B	protein-coding
mm_45790.1	chr5	87490870	87490875	-	1	NA	promoter-TSS (NM_053184)	promoter-TSS (NM_053184)	-1	NM_053184	94215	Mm.26794	NM_053184	ENSMUSG00000106677	Ugt2a1	-	UDP glucuronosyltransferase 2 family, polypeptide A1	protein-coding
mm_79442.1	chr9	56090170	56090184	+	1	NA	5' UTR (NM_011193, exon 1 of 15)	5' UTR (NM_011193, exon 1 of 15)	201	NM_011193	19200	Mm.2534	NM_011193	ENSMUSG00000032322	Pstpip1	CD2BP1|def-2	proline-serine-threonine phosphatase-interacting protein 1	protein-coding
mm_5578.1	chr1	39551973	39551977	-	1	NA	3' UTR (NM_001033135, exon 7 of 7)	3' UTR (NM_001033135, exon 7 of 7)	-3135	NR_028555	100217461		NR_028555	ENSMUSG00000077704	Snord89	MBII-289	small nucleolar RNA, C/D box 89	snoRNA
mm_131402.1	chr16	14373330	14373335	+	1	NA	intron (NM_008576, intron 1 of 30)	intron (NM_008576, intron 1 of 30)	11774	NM_008576	17250	Mm.196634	NM_008576	ENSMUSG00000023088	Abcc1	Abcc1a|Abcc1b|MRP|Mdrap|Mrp1	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	protein-coding
mm_110284.1	chr12	32109383	32109386	-	1	NA	Intergenic	Intergenic	-48105	NM_011158	19088	Mm.25594	NM_011158	ENSMUSG00000002997	Prkar2b	AI451071|AW061005|PKARIIbeta|Pkarb2|RII(beta)	protein kinase, cAMP dependent regulatory, type II beta	protein-coding
mm_110586.1	chr12	56529447	56529451	-	1	NA	promoter-TSS (NR_045082)	promoter-TSS (NR_045082)	-29	NR_045082	104798	Mm.310950	NR_045082		E030019B13Rik	AI413669	RIKEN cDNA E030019B13 gene	ncRNA
mm_22219.1	chr2	174345114	174345129	-	1	NA	non-coding (NR_003258, exon 8 of 13)	non-coding (NR_003258, exon 8 of 13)	15032	NM_001077510	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_123005.1	chr14	54993685	54993695	-	1	NA	intron (NM_080728, intron 1 of 40)	intron (NM_080728, intron 1 of 40)	859	NM_080728	140781	Mm.457983	NM_080728	ENSMUSG00000053093	Myh7	B-MHC|MyHC-I|Myhc-b|Myhcb|beta-MHC	myosin, heavy polypeptide 7, cardiac muscle, beta	protein-coding
mm_105478.1	chr11	105937845	105937871	-	1	NA	intron (NM_007805, intron 1 of 5)	(GA)n|Simple_repeat|Simple_repeat	6289	NM_007805	13056	Mm.149403	NM_007805	ENSMUSG00000019590	Cyb561	-	cytochrome b-561	protein-coding
mm_157691.1	chrX	60403903	60403911	-	1	NA	promoter-TSS (NM_001001798)	promoter-TSS (NM_001001798)	74	NM_001001798	320940	Mm.490394	NM_001001798	ENSMUSG00000062949	Atp11c	A330005H02Rik|AI315324|Ig	ATPase, class VI, type 11C	protein-coding
mm_162793.1	chr10	75853249	75853252	+	1	NA	Intergenic	Intergenic	7000	NM_010798	17319	Mm.2326	NM_010798	ENSMUSG00000033307	Mif	GIF|Glif	macrophage migration inhibitory factor	protein-coding
mm_130501.1	chr15	98831437	98831450	-	1	NA	promoter-TSS (NM_016781)	promoter-TSS (NM_016781)	65	NM_016781	19082	Mm.6670	NM_016781	ENSMUSG00000067713	Prkag1	AA571379|BB036179|Prkaac	protein kinase, AMP-activated, gamma 1 non-catalytic subunit	protein-coding
mm_31951.1	chr4	86748619	86748623	+	1	NA	promoter-TSS (NM_184088)	promoter-TSS (NM_184088)	66	NM_184088	329877	Mm.273718	NM_184088	ENSMUSG00000038024	Dennd4c	1700065A05Rik|AA420392	DENN/MADD domain containing 4C	protein-coding
mm_129801.1	chr15	82899835	82899845	-	1	NA	intron (NR_045068, intron 1 of 3)	CpG	760	NR_045068	100504637	Mm.440928	NR_045068	ENSMUSG00000100199	Gm20324	-	predicted gene, 20324	ncRNA
mm_71654.1	chr8	60508725	60508728	+	1	NA	intron (NM_011834, intron 2 of 12)	Lx6|LINE|L1	2602	NM_011834	23923	Mm.35020	NM_011834	ENSMUSG00000057228	Aadat	AI875679|Aadt|KATII|Kat2|Kyat2|mKat-2	aminoadipate aminotransferase	protein-coding
mm_92778.1	chr10	81202045	81202059	-	1	NA	promoter-TSS (NM_027120)	promoter-TSS (NM_027120)	-15	NM_027120	69564	Mm.437211	NM_027120	ENSMUSG00000004939	Nmrk2	2310015C21Rik|Itgb1bp3|Mibp	nicotinamide riboside kinase 2	protein-coding
mm_69857.1	chr7	141434280	141434299	-	1	NA	5' UTR (NM_026646, exon 2 of 10)	5' UTR (NM_026646, exon 2 of 10)	305	NM_001177576	68267	Mm.33729	NM_026646	ENSMUSG00000019082	Slc25a22	1300006L01Rik|AI060884|Gc1	solute carrier family 25 (mitochondrial carrier, glutamate), member 22	protein-coding
mm_151683.1	chr19	4269219	4269238	-	1	NA	promoter-TSS (NM_198113)	promoter-TSS (NM_198113)	-56	NM_198113	245857	Mm.248388	NM_198113	ENSMUSG00000034616	Ssh3	BC028922|SSH-3|mSSH-3L	slingshot homolog 3 (Drosophila)	protein-coding
mm_11246.1	chr2	29890447	29890511	+	1	NA	intron (NM_013615, intron 1 of 16)	CpG	416	NM_013615	18286	Mm.330116	NM_013615	ENSMUSG00000026790	Odf2	AI848335|MMTEST29	outer dense fiber of sperm tails 2	protein-coding
mm_81993.1	chr9	121472462	121472465	+	1	NA	exon (NM_175114, exon 16 of 16)	exon (NM_175114, exon 16 of 16)	23231	NM_001284508	12424	Mm.2619	NM_031161	ENSMUSG00000032532	Cck	-	cholecystokinin	protein-coding
mm_165085.1	chr19	47228841	47228872	+	1	NA	promoter-TSS (NM_001163480)	promoter-TSS (NM_001163480)	13	NM_001163480	18011	Mm.313651	NM_021360	ENSMUSG00000006435	Neurl1a	2410129E16Rik|AI450910|AI481072|Neu1|Neur1|Neurl|Neurl1|Nlz|Rnf67	neuralized E3 ubiquitin protein ligase 1A	protein-coding
mm_27611.1	chr3	59210864	59210868	-	1	NA	promoter-TSS (NM_028808)	promoter-TSS (NM_028808)	16	NM_028808	74191	Mm.90067	NM_028808	ENSMUSG00000036362	P2ry13	2010001L06Rik|GPCR1|GPR94|Gpr86|P2Y13|P2yr13|SP174	purinergic receptor P2Y, G-protein coupled 13	protein-coding
mm_44572.1	chr5	24813994	24813998	-	1	NA	intron (NM_053075, intron 2 of 7)	intron (NM_053075, intron 2 of 7)	28365	NM_053075	19744	Mm.319175	NM_053075	ENSMUSG00000028945	Rheb	Rheb1	Ras homolog enriched in brain	protein-coding
mm_150078.1	chr19	29386925	29386983	+	1	NA	3' UTR (NM_021893, exon 7 of 7)	3' UTR (NM_021893, exon 7 of 7)	19516	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_105349.1	chr11	102999844	102999854	-	1	NA	promoter-TSS (NR_105896)	promoter-TSS (NR_105896)	72	NR_105896	102466988		NR_105896	ENSMUSG00000098613	Mir6931	Gm27303|mmu-mir-6931	microRNA 6931	ncRNA
mm_148342.1	chr18	84589917	84589943	-	1	NA	promoter-TSS (NM_001033341)	promoter-TSS (NM_001033341)	-426	NM_001033341	240476	Mm.329575	NM_001033341	ENSMUSG00000048410	Zfp407	6430585N13Rik|Gm333|Gm334|Gm948|ZNF407	zinc finger protein 407	protein-coding
mm_163761.1	chr13	119941979	119941981	+	1	NA	Intergenic	MT2B|LTR|ERVL	8826	NM_001033769	333467	Mm.387257	NM_001033769	ENSMUSG00000078537	B020031M17Rik	-	RIKEN cDNA B020031M17 gene	protein-coding
mm_147624.1	chr18	58072869	58072875	-	1	NA	intron (NM_010181, intron 25 of 64)	intron (NM_010181, intron 25 of 64)	137054	NM_010181	14119	Mm.20271	NM_010181	ENSMUSG00000024598	Fbn2	BC063774|Fib-2|mKIAA4226|sne|sy	fibrillin 2	protein-coding
mm_11798.1	chr2	43625161	43625170	+	1	NA	intron (NM_001289594, intron 8 of 10)	L1_Mur2|LINE|L1	69840	NM_027552	70789	Mm.105278	NM_027552	ENSMUSG00000026866	Kynu	4432411A05Rik	kynureninase (L-kynurenine hydrolase)	protein-coding
mm_148679.1	chr19	5645537	5645550	+	1	NA	exon (NM_009045, exon 10 of 11)	exon (NM_009045, exon 10 of 11)	8053	NM_009045	19697	Mm.249966	NM_009045	ENSMUSG00000024927	Rela	p65	v-rel reticuloendotheliosis viral oncogene homolog A (avian)	protein-coding
mm_34391.1	chr4	144977442	144977453	+	1	NA	intron (NM_001276502, intron 67 of 68)	intron (NM_001276502, intron 67 of 68)	84310	NM_011303	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding
mm_103700.1	chr11	79516433	79516447	-	1	NA	exon (NM_001077496, exon 2 of 2)	exon (NM_001077496, exon 2 of 2)	7322	NM_001077496	216984	Mm.439665	NM_001077496	ENSMUSG00000093938	Evi2b	Evi-2|Evi2	ecotropic viral integration site 2b	protein-coding
mm_1993.1	chr1	87126324	87126333	+	1	NA	exon (NM_007432, exon 6 of 11)	exon (NM_007432, exon 6 of 11)	1320	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_74757.1	chr8	19142659	19142661	-	1	NA	exon (NM_001286493, exon 3 of 3)	exon (NM_001286493, exon 3 of 3)	1901	NM_001286493	546038	Mm.99206	NM_001034905	ENSMUSG00000059463	Spag11b	EG546038|Ep2c/h|Spag11c/h	sperm associated antigen 11B	protein-coding
mm_80637.1	chr9	89218449	89218459	+	1	NA	intron (NM_026829, intron 2 of 2)	intron (NM_026829, intron 2 of 2)	7264	NM_026829	107885	Mm.486274	NM_026829	ENSMUSG00000066442	Mthfs	1110034I12Rik|2310020H23Rik|AI119695	5, 10-methenyltetrahydrofolate synthetase	protein-coding
mm_128755.1	chr15	64922291	64922315	-	1	NA	promoter-TSS (NM_009623)	promoter-TSS (NM_009623)	-7	NM_009623	11514	Mm.1425	NM_009623	ENSMUSG00000022376	Adcy8	AC8|AW060868	adenylate cyclase 8	protein-coding
mm_59947.1	chr7	30425704	30425710	+	1	NA	intron (NM_172142, intron 5 of 10)	intron (NM_172142, intron 5 of 10)	2403	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_124167.1	chr14	93710761	93710764	-	1	NA	intron (NM_001346722, intron 2 of 4)	intron (NM_001346722, intron 2 of 4)	178126	NM_001271800	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding
mm_108584.1	chr12	85122052	85122075	+	1	NA	exon (NM_030225, exon 8 of 15)	exon (NM_030225, exon 8 of 15)	11230	NM_030225	78920	Mm.296221	NM_030225	ENSMUSG00000004789	Dlst	1600017E01Rik|4632413C10Rik|4930529O08Rik|DLTS	dihydrolipoamide S-succinyltransferase (E2 component of 2-oxo-glutarate complex)	protein-coding
mm_49332.1	chr6	21215553	21215563	+	1	NA	promoter-TSS (NM_019697)	promoter-TSS (NM_019697)	-551	NM_019697	16508	Mm.425316	NM_019697	ENSMUSG00000060882	Kcnd2	AI839615|AW555701|Kv4.2|R75121|mKIAA1044	potassium voltage-gated channel, Shal-related family, member 2	protein-coding
mm_78491.1	chr9	32704175	32704185	+	1	NA	intron (NM_011808, intron 1 of 7)	intron (NM_011808, intron 1 of 7)	8138	NM_001038642	23871	Mm.292415	NM_011808	ENSMUSG00000032035	Ets1	AI196000|AI448617|D230050P06|Ets-1|Tpl1|vs	E26 avian leukemia oncogene 1, 5' domain	protein-coding
mm_161694.1	chr17	23600930	23600930	+	1	NA	5' UTR (NM_001033425, exon 1 of 6)	5' UTR (NM_001033425, exon 1 of 6)	104	NM_001289482	332221	Mm.270315	NM_001033425	ENSMUSG00000023902	Zscan10	BC068284|Zfp206|Zkscan10|Znf206	zinc finger and SCAN domain containing 10	protein-coding
mm_48544.1	chr5	142905443	142905480	-	1	NA	exon (NM_007393, exon 3 of 6)	exon (NM_007393, exon 3 of 6)	1293	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_76039.1	chr8	77452088	77452091	-	1	NA	intron (NM_030113, intron 1 of 22)	intron (NM_030113, intron 1 of 22)	-64967	NR_028125	70345	Mm.411813	NR_028125	ENSMUSG00000097882	0610038B21Rik	-	RIKEN cDNA 0610038B21 gene	ncRNA
mm_114753.1	chr13	85126565	85126590	+	1	NA	Intergenic	Intergenic	-62808	NM_001347587	66671	Mm.18474	NM_023243	ENSMUSG00000021548	Ccnh	6330408H09Rik|AI661354|AV102684|AW538719	cyclin H	protein-coding
mm_22749.1	chr3	19966346	19966356	+	1	NA	exon (NM_007752, exon 3 of 19)	exon (NM_007752, exon 3 of 19)	9297	NM_007752	12870	Mm.13787	NM_007752	ENSMUSG00000003617	Cp	D3Ertd555e	ceruloplasmin	protein-coding
mm_105738.1	chr11	109358743	109358779	-	1	NA	intron (NR_038097, intron 1 of 1)	MIRb|SINE|MIR	-4033	NM_010303	14674	Mm.193925	NM_010303	ENSMUSG00000020611	Gna13	AU024132|AU043124|Galpha13	guanine nucleotide binding protein, alpha 13	protein-coding
mm_85182.1	chr9	96631488	96631554	-	1	NA	promoter-TSS (NM_053268)	promoter-TSS (NM_053268)	-18	NM_053268	114713	Mm.124502	NM_053268	ENSMUSG00000032413	Rasa2	5430433H21Rik|AA517451|AU023900|GAP1m	RAS p21 protein activator 2	protein-coding
mm_57965.1	chr6	135254328	135254359	-	1	NA	promoter-TSS (NM_010352)	promoter-TSS (NM_010352)	-7	NM_001080553	14840	Mm.272306	NM_010352	ENSMUSG00000030206	Gsg1	-	germ cell associated 1	protein-coding
mm_96698.1	chr11	69633043	69633053	+	1	NA	promoter-TSS (NM_011814)	promoter-TSS (NM_011814)	77	NM_011814	23879	Mm.41930	NM_011814	ENSMUSG00000018765	Fxr2	Fxr2h	fragile X mental retardation, autosomal homolog 2	protein-coding
mm_78413.1	chr9	30736563	30736568	+	1	NA	Intergenic	Intergenic	184385	NM_001329420	235130	Mm.65867	NM_001024139	ENSMUSG00000033453	Adamts15	-	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 15	protein-coding
mm_169120.1	chr13	51636810	51636820	-	1	NA	Intergenic	Intergenic	-8417	NM_025415	66197	Mm.222228	NM_025415	ENSMUSG00000062248	Cks2	1110038L14Rik|CKSHS2	CDC28 protein kinase regulatory subunit 2	protein-coding
mm_125306.1	chr15	37318384	37318407	+	1	NA	intron (NM_026496, intron 8 of 15)	intron (NM_026496, intron 8 of 15)	85359	NM_026496	252973	Mm.244612	NM_026496	ENSMUSG00000022286	Grhl2	0610015A08Rik|BOM|Tcfcp2l3|clft3	grainyhead-like 2 (Drosophila)	protein-coding
mm_27385.1	chr3	50628406	50628419	-	1	NA	Intergenic	Intergenic	-184799	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_23975.1	chr3	85915704	85915735	+	1	NA	Intergenic	Intergenic	-28201	NM_177130	320302	Mm.482978	NM_177130	ENSMUSG00000031286	Glt28d2	4732486J07Rik|Glt28d1l	glycosyltransferase 28 domain containing 2	protein-coding
mm_49853.1	chr6	38433870	38433882	+	1	NA	promoter-TSS (NM_177185)	promoter-TSS (NM_177185)	-49	NM_177185	320538	Mm.302831	NM_177185	ENSMUSG00000038538	Ubn2	2900060J04Rik|6030408G03Rik|BC060116|D130059P03Rik|mKIAA2030	ubinuclein 2	protein-coding
mm_103136.1	chr11	70237887	70237919	-	1	NA	promoter-TSS (NM_001177601)	promoter-TSS (NM_001177601)	11	NM_001177601	104457	Mm.30016	NM_026757	ENSMUSG00000020831	0610010K14Rik	1110020A23Rik|AL033328|AU045833|Bap18	RIKEN cDNA 0610010K14 gene	protein-coding
mm_98709.1	chr11	96307070	96307096	+	1	NA	promoter-TSS (NR_131758)	promoter-TSS (NR_131758)	-173	NR_131758	75395	Mm.440014	NR_131758	ENSMUSG00000085645	Hoxb5os	0610040B09Rik|AV302770|Hoxb5/6as	homeobox B5 and homeobox B6, opposite strand	ncRNA
mm_102947.1	chr11	69617723	69617739	-	1	NA	intron (NM_011367, intron 1 of 7)	intron (NM_011367, intron 1 of 7)	174	NM_011367	20415	Mm.1431	NM_011367	ENSMUSG00000005202	Shbg	ABP	sex hormone binding globulin	protein-coding
mm_114972.1	chr13	97241123	97241129	+	1	NA	promoter-TSS (NM_007930)	promoter-TSS (NM_007930)	21	NM_007930	13803	Mm.241073	NM_007930	ENSMUSG00000041773	Enc1	Nrpb|PIG10	ectodermal-neural cortex 1	protein-coding
mm_67698.1	chr7	89518284	89518305	-	1	NA	promoter-TSS (NM_029614)	promoter-TSS (NM_029614)	-708	NM_029614	76453	Mm.250438	NM_029614	ENSMUSG00000039405	Prss23	2310046G15Rik|4930479H08Rik|AI790574|Spuve	protease, serine 23	protein-coding
mm_36068.1	chr4	57943806	57943829	-	1	NA	3' UTR (NM_011660, exon 5 of 5)	3' UTR (NM_011660, exon 5 of 5)	12594	NM_011660	22166	Mm.260618	NM_011660	ENSMUSG00000028367	Txn1	ADF|AW550880|Trx1|Txn	thioredoxin 1	protein-coding
mm_92818.1	chr10	81459899	81459911	-	1	NA	3' UTR (NM_176954, exon 12 of 12)	3' UTR (NM_176954, exon 12 of 12)	13226	NM_001311127	319586	Mm.152689	NM_176954	ENSMUSG00000034818	Celf5	4930565A21Rik|Brunol5	CUGBP, Elav-like family member 5	protein-coding
mm_22999.1	chr3	34046062	34046078	+	1	NA	exon (NM_001113188, exon 4 of 17)	exon (NM_001113188, exon 4 of 17)	25991	NM_001113188	14359	Mm.259021	NM_008053	ENSMUSG00000027680	Fxr1	1110050J02Rik|9530073J07Rik|AI851072|Fxr1h|Fxr1p	fragile X mental retardation gene 1, autosomal homolog	protein-coding
mm_59714.1	chr7	28766748	28766822	+	1	NA	promoter-TSS (NM_001122766)	promoter-TSS (NM_001122766)	33	NM_001122766	64383	Mm.272443	NM_022432	ENSMUSG00000015149	Sirt2	5730427M03Rik|SIR2L2|Sir2l	sirtuin 2	protein-coding
mm_111420.1	chr12	91589598	91589620	-	1	NA	promoter-TSS (NM_031391)	promoter-TSS (NM_031391)	40	NM_031391	83602	Mm.275728	NM_031391	ENSMUSG00000020962	Gtf2a1	6330549H03Rik|AA536742|AA959775|AW060250|TfIIAa/b|Tfiia1	general transcription factor II A, 1	protein-coding
mm_144419.1	chr18	20962889	20962901	+	1	NA	intron (NM_026301, intron 1 of 5)	intron (NM_026301, intron 1 of 5)	18270	NM_026301	67664	Mm.45980	NM_026301	ENSMUSG00000033107	Rnf125	4930553F04Rik	ring finger protein 125	protein-coding
mm_77448.1	chr8	121805310	121805320	-	1	NA	intron (NM_145605, intron 6 of 11)	intron (NM_145605, intron 6 of 11)	24254	NM_145605	234825	Mm.209329	NM_145605	ENSMUSG00000040263	Klhdc4	AA408426|AV352552|BC012312|G430025P05Rik	kelch domain containing 4	protein-coding
mm_34758.1	chr4	152338915	152338967	+	1	NA	5' UTR (NM_001081376, exon 1 of 42)	5' UTR (NM_001081376, exon 1 of 42)	290	NM_001081376	269610	Mm.40192	NM_029216	ENSMUSG00000005045	Chd5	4930532L22Rik|AW060752|B230399N07Rik|CHD-5	chromodomain helicase DNA binding protein 5	protein-coding
mm_69801.1	chr7	141178508	141178518	-	1	NA	Intergenic	Intergenic	-5662	NM_001172100	107702	Mm.197493	NM_145135	ENSMUSG00000038650	Rnh1	AW546468|C80305|RNH	ribonuclease/angiogenin inhibitor 1	protein-coding
mm_123944.1	chr14	73376785	73376795	-	1	NA	intron (NM_008410, intron 1 of 5)	intron (NM_008410, intron 1 of 5)	8481	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_80535.1	chr9	80305746	80305756	+	1	NA	intron (NM_001039546, intron 31 of 32)	intron (NM_001039546, intron 31 of 32)	140717	NM_001039546	17920	Mm.4040	NM_008662	ENSMUSG00000033577	Myo6	BC029719|Tlc|sv	myosin VI	protein-coding
mm_98178.1	chr11	87760534	87760551	+	1	NA	promoter-TSS (NM_172449)	promoter-TSS (NM_172449)	1	NM_172449	207777	Mm.342019	NM_172449	ENSMUSG00000034156	Bzrap1	D230016K05|PRAX-1|Tspoap1|mKIAA0612	benzodiazepine receptor associated protein 1	protein-coding
mm_52988.1	chr6	123264855	123264867	+	1	NA	intron (NM_001163161, intron 1 of 5)	Lx2A1|LINE|L1	2754	NM_010819	17474	Mm.441101	NM_010819	ENSMUSG00000030144	Clec4d	Clecsf8|Mpcl|mcl	C-type lectin domain family 4, member d	protein-coding
mm_63442.1	chr7	127483018	127483107	+	1	NA	Intergenic	Intergenic	-2159	NM_010183	14123	Mm.323505	NM_010183	ENSMUSG00000042423	Fbrs	Fbs|Fbs1	fibrosin	protein-coding
mm_102321.1	chr11	57507111	57507115	-	1	NA	intron (NM_001168667, intron 6 of 13)	intron (NM_001168667, intron 6 of 13)	11531	NM_001168667	67726	Mm.25632	NM_026342	ENSMUSG00000020523	Fam114a2	1810073G14Rik|9030624B09Rik	family with sequence similarity 114, member A2	protein-coding
mm_130212.1	chr15	95654681	95654689	-	1	NA	promoter-TSS (NM_207533)	promoter-TSS (NM_207533)	86	NM_207533	223843	Mm.152937	NM_207533	ENSMUSG00000045608	Dbx2	9430056A22Rik|9630005K15|AI846217|Gm1229	developing brain homeobox 2	protein-coding
mm_108427.1	chr12	82244643	82244673	+	1	NA	intron (NM_001167983, intron 2 of 23)	L1M4c|LINE|L1	-66691	NM_172579	217692	Mm.261333	NM_172579	ENSMUSG00000042700	Sipa1l1	4931426N11Rik|AW213287|Spar|mKIAA0440	signal-induced proliferation-associated 1 like 1	protein-coding
mm_129694.1	chr15	81586033	81586045	-	1	NA	promoter-TSS (NM_177821)	promoter-TSS (NM_177821)	-175	NM_177821	328572	Mm.258397	NM_177821	ENSMUSG00000055024	Ep300	A430090G16|A730011L11|KAT3B|p300|p300 HAT	E1A binding protein p300	protein-coding
mm_15373.1	chr2	156457243	156457243	+	1	NA	intron (NM_001291122, intron 2 of 20)	intron (NM_001291122, intron 2 of 20)	-18291	NM_001006664	13821	Mm.20852	NM_013510	ENSMUSG00000027624	Epb41l1	4.1N|Epb4.1l1|NBL1|mKIAA0338	erythrocyte membrane protein band 4.1 like 1	protein-coding
mm_56726.1	chr6	115653996	115654002	-	1	NA	intron (NM_029780, intron 1 of 16)	intron (NM_029780, intron 1 of 16)	22636	NM_029780	110157	Mm.184163	NM_029780	ENSMUSG00000000441	Raf1	6430402F14Rik|AA990557|BB129353|Craf1|D830050J10Rik|Raf-1|c-Raf|v-Raf	v-raf-leukemia viral oncogene 1	protein-coding
mm_167374.1	chr8	91313433	91313463	+	1	NA	promoter-TSS (NM_173431)	promoter-TSS (NM_173431)	-77	NM_011936	26383	Mm.4375	NM_011936	ENSMUSG00000055932	Fto	AW743446|mKIAA1752	fat mass and obesity associated	protein-coding
mm_99002.1	chr11	98798675	98798675	+	1	NA	non-coding (NR_033551, exon 3 of 3)	non-coding (NR_033551, exon 3 of 3)	2906	NM_028722	74026	Mm.258352	NM_028722	ENSMUSG00000052915	Msl1	2810017F12Rik|4121402D02Rik|4930463F05Rik|AA682082|Msl-1	male-specific lethal 1 homolog (Drosophila)	protein-coding
mm_138308.1	chr17	34647122	34647122	+	1	NA	promoter-TSS (NM_017406)	promoter-TSS (NM_017406)	-24	NM_017406	12915	Mm.4068	NM_017406	ENSMUSG00000015461	Atf6b	AA617266|ATF6beta|Creb-rp|Crebl1	activating transcription factor 6 beta	protein-coding
mm_139087.1	chr17	46812785	46812796	+	1	NA	intron (NM_001100452, intron 5 of 10)	intron (NM_001100452, intron 5 of 10)	18623	NM_001100452	210982	Mm.37642	NM_001100452	ENSMUSG00000036568	Gltscr1l	mKIAA0240	GLTSCR1-like	protein-coding
mm_36308.1	chr4	69395444	69395489	-	1	NA	Intergenic	Intergenic	-441069	NM_019967	56710	Mm.248788	NM_019967	ENSMUSG00000028351	Brinp1	BRINP|Dbc1|Dbccr1|Fam5a	bone morphogenic protein/retinoic acid inducible neural specific 1	protein-coding
mm_102584.1	chr11	61855019	61855025	-	1	NA	promoter-TSS (NM_013881)	promoter-TSS (NM_013881)	70	NM_013881	29869	Mm.162025	NM_013881	ENSMUSG00000004798	Ulk2	A830085I22Rik|AU015340|Unc51.2|mKIAA0623	unc-51 like kinase 2	protein-coding
mm_10324.1	chr2	11250488	11250498	+	1	NA	intron (NM_008859, intron 8 of 17)	intron (NM_008859, intron 8 of 17)	78111	NM_008859	18761	Mm.329993	NM_008859	ENSMUSG00000026778	Prkcq	A130035A12Rik|AW494342|PKC-0|PKC-theta|PKCtheta|Pkcq	protein kinase C, theta	protein-coding
mm_62357.1	chr7	100499299	100499316	+	1	NA	exon (NM_011671, exon 8 of 8)	exon (NM_011671, exon 8 of 8)	5949	NM_011671	22228	Mm.171378	NM_011671	ENSMUSG00000033685	Ucp2	Slc25a8	uncoupling protein 2 (mitochondrial, proton carrier)	protein-coding
mm_119313.1	chr14	36659122	36659125	+	1	NA	Intergenic	MTE-int|LTR|ERVL-MaLR	260412	NM_001347503	72972	Mm.27621	NM_027045	ENSMUSG00000058690	Ccser2	1700012P13Rik|2900054P12Rik|AI035535|AW108503|Fam190b|Gcap14	coiled-coil serine rich 2	protein-coding
mm_59804.1	chr7	29137630	29137642	+	1	NA	exon (NM_001174155, exon 2 of 17)	exon (NM_001174155, exon 2 of 17)	2703	NR_045676	233046	Mm.465324	NM_145149	ENSMUSG00000030589	Rasgrp4	-	RAS guanyl releasing protein 4	protein-coding
mm_85152.1	chr9	96333003	96333078	-	1	NA	3' UTR (NM_007502, exon 7 of 7)	3' UTR (NM_007502, exon 7 of 7)	31259	NM_007502	11933	Mm.424	NM_007502	ENSMUSG00000032412	Atp1b3	AA409958|AI664000|AW212096	ATPase, Na+/K+ transporting, beta 3 polypeptide	protein-coding
mm_128284.1	chr15	37007383	37007402	-	1	NA	promoter-TSS (NM_026521)	promoter-TSS (NM_026521)	10	NM_026521	68036	Mm.371631	NM_026521	ENSMUSG00000062397	Zfp706	3110006P09Rik|AA793007|AW536850|C77232|Znf706	zinc finger protein 706	protein-coding
mm_91815.1	chr10	54075703	54075718	-	1	NA	promoter-TSS (NM_008548)	promoter-TSS (NM_008548)	86	NM_008548	17155	Mm.117294	NM_008548	ENSMUSG00000003746	Man1a	Man1a1|PCR1	mannosidase 1, alpha	protein-coding
mm_66885.1	chr7	59228530	59228551	-	1	NA	promoter-TSS (NM_001033962)	promoter-TSS (NM_001033962)	-210	NM_173010	22215	Mm.9002	NM_011668	ENSMUSG00000025326	Ube3a	4732496B02|5830462N02Rik|A130086L21Rik|Hpve6a|mKIAA4216	ubiquitin protein ligase E3A	protein-coding
mm_26354.1	chr3	142548970	142548983	+	1	NA	3' UTR (NM_001083312, exon 11 of 11)	3' UTR (NM_001083312, exon 11 of 11)	-11076	NM_018734	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_35074.1	chr4	6989648	6989673	-	1	NA	intron (NM_145711, intron 1 of 8)	intron (NM_145711, intron 1 of 8)	1063	NM_145711	252838	Mm.435828	NM_145711	ENSMUSG00000041272	Tox	1700007F02Rik	thymocyte selection-associated high mobility group box	protein-coding
mm_7700.1	chr1	130422748	130422759	-	1	NA	intron (NM_001317361, intron 1 of 7)	intron (NM_001317361, intron 1 of 7)	290	NM_007827	13137	Mm.436759	NM_007827	ENSMUSG00000026401	Cd55b	AI323748|Daf|Daf-TM|Daf2|TM-DAF	CD55 molecule, decay accelerating factor for complement B	protein-coding
mm_9363.1	chr1	172198542	172198559	-	1	NA	3' UTR (NM_001329871, exon 4 of 4)	3' UTR (NM_001329871, exon 4 of 4)	8254	NM_001329871	18611	Mm.544	NM_011063	ENSMUSG00000013698	Pea15a	Mat1|PEA-15|Pea15|Pkcs15	phosphoprotein enriched in astrocytes 15A	protein-coding
mm_16801.1	chr2	10119535	10119545	-	1	NA	exon (NM_010582, exon 6 of 21)	exon (NM_010582, exon 6 of 21)	11143	NM_010582	16425	Mm.182043	NM_010582	ENSMUSG00000037254	Itih2	AI747202|Intin2|Itih-2	inter-alpha trypsin inhibitor, heavy chain 2	protein-coding
mm_145037.1	chr18	39362921	39362936	+	1	NA	intron (NM_175164, intron 21 of 22)	intron (NM_175164, intron 21 of 22)	124317	NM_008173	14815	Mm.129481	NM_008173	ENSMUSG00000024431	Nr3c1	GR|Grl-1|Grl1	nuclear receptor subfamily 3, group C, member 1	protein-coding
mm_125480.1	chr15	54595188	54595191	+	1	NA	intron (NM_178920, intron 2 of 3)	ERV3-16A3_LTR|LTR|ERVL	23823	NM_178920	105853	Mm.410994	NM_178920	ENSMUSG00000024479	Mal2	AI461653	mal, T cell differentiation protein 2	protein-coding
mm_172036.1	chr6	125191531	125191532	-	1	NA	promoter-TSS (NM_025595)	promoter-TSS (NM_025595)	55	NM_146171	68298	Mm.257590	NM_146171	ENSMUSG00000038252	Ncapd2	2810406C15Rik|2810465G24Rik|CAP-D2|CNAP1|mKIAA0159	non-SMC condensin I complex, subunit D2	protein-coding
mm_100595.1	chr11	120991383	120991395	+	1	NA	promoter-TSS (NM_139059)	promoter-TSS (NM_139059)	-56	NM_027874	104318	Mm.216227	NM_027874	ENSMUSG00000025162	Csnk1d	1200006A05Rik|AA409348|D930010H05Rik	casein kinase 1, delta	protein-coding
mm_148134.1	chr18	75697640	75697697	-	1	NA	promoter-TSS (NM_201354)	promoter-TSS (NM_201354)	28	NM_201354	269037	Mm.36745	NM_201354	ENSMUSG00000052928	Ctif	Gm672	CBP80/20-dependent translation initiation factor	protein-coding
mm_49986.1	chr6	41033157	41033166	+	1	NA	exon (NM_023333, exon 3 of 5)	exon (NM_023333, exon 3 of 5)	2348	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_95145.1	chr11	35544505	35544520	+	1	NA	intron (NM_011412, intron 5 of 35)	intron (NM_011412, intron 5 of 35)	-72304	NR_029799	723924		NR_029799	ENSMUSG00000065583	Mir218-2	Mirn218-2|mir-218-2	microRNA 218-2	ncRNA
mm_157014.1	chrX	7681003	7681032	-	1	NA	promoter-TSS (NM_018832)	promoter-TSS (NM_018832)	72	NM_018832	54634	Mm.67912	NM_018832	ENSMUSG00000031147	Magix	Pdzx|Sfc18	MAGI family member, X-linked	protein-coding
mm_2710.1	chr1	128103377	128103387	+	1	NA	promoter-TSS (NM_001285945)	promoter-TSS (NM_001285945)	76	NM_181750	226412	Mm.221041	NM_181750	ENSMUSG00000056211	R3hdm1	R3hdm	R3H domain containing 1	protein-coding
mm_10108.1	chr2	3664531	3664538	+	1	NA	Intergenic	Intergenic	-48924	NM_025626	66540	Mm.277864	NM_025626	ENSMUSG00000026655	Fam107b	3110001A13Rik|AA589595|AA959793|AI132312	family with sequence similarity 107, member B	protein-coding
mm_146905.1	chr18	31316960	31316970	-	1	NA	5' UTR (NM_009065, exon 1 of 5)	5' UTR (NM_009065, exon 1 of 5)	163	NM_009065	19762	Mm.5163	NM_009065	ENSMUSG00000057455	Rit2	RIBA|Rin|Roc2	Ras-like without CAAX 2	protein-coding
mm_152592.1	chr19	11604844	11604864	-	1	NA	promoter-TSS (NM_026835)	promoter-TSS (NM_026835)	-50	NM_026835	68774	Mm.290390	NM_026835	ENSMUSG00000024679	Ms4a6d	1110058E16Rik|AI447446|Ms4a11	membrane-spanning 4-domains, subfamily A, member 6D	protein-coding
mm_1056.1	chr1	58846915	58846935	+	1	NA	3' UTR (NM_001277926, exon 10 of 10)	3' UTR (NM_001277926, exon 10 of 10)	44423	NM_001080126	12370	Mm.336851	NM_009812	ENSMUSG00000026029	Casp8	CASP-8|FLICE|MACH|Mch5	caspase 8	protein-coding
mm_17865.1	chr2	34851558	34851565	-	1	NA	TTS (NM_080554)	TTS (NM_080554)	19401	NM_080554	66998	Mm.270632	NM_080554	ENSMUSG00000026869	Psmd5	1500032A03Rik|AW475925|S5b|W91691|mKIAA0072	proteasome (prosome, macropain) 26S subunit, non-ATPase, 5	protein-coding
mm_14735.1	chr2	144331479	144331483	+	1	NA	promoter-TSS (NM_152947)	promoter-TSS (NM_152947)	-119	NM_152947	107586	Mm.252750	NM_026924	ENSMUSG00000037279	Ovol2	1700108N11Rik|1810007D21Rik|M-OVO|M-OVO-A|M-OVO-B|MOVO|Ovo2|Zfp339|movo2	ovo like zinc finger 2	protein-coding
mm_149178.1	chr19	9283232	9283265	+	1	NA	Intergenic	Intergenic	-147682	NM_025610	66514	Mm.272847	NM_025610	ENSMUSG00000024654	Asrgl1	2410004D18Rik|ALP|ALP1|AU040643|AW060375	asparaginase like 1	protein-coding
mm_59251.1	chr7	24824750	24824776	+	1	NA	intron (NR_045096, intron 3 of 11)	intron (NR_045096, intron 3 of 11)	5968	NR_045096	545936	Mm.376228	NR_045096	ENSMUSG00000011350	Gm5893	EG545936|Gm477	predicted gene 5893	pseudo
mm_135652.1	chr16	52396275	52396295	-	1	NA	intron (NM_009655, intron 1 of 15)	MER2|DNA|TcMar-Tigger	56796	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_64594.1	chr7	3201260	3201267	-	1	NA	Intergenic	PB1D9|SINE|Alu	-17363	NR_029640	100049710		NR_029640	ENSMUSG00000077815	Mir290a	Mir290|Mirn290|mir-290a|mmu-miR-290|mmu-mir-290a	microRNA 290a	ncRNA
mm_118104.1	chr13	103920487	103920497	-	1	NA	promoter-TSS (NM_001289475)	promoter-TSS (NM_001289475)	94	NM_001289473	59079	Mm.277354	NM_021563	ENSMUSG00000021709	Erbin	1700028E05Rik|Erbb2ip|mKIAA1225	Erbb2 interacting protein	protein-coding
mm_143747.1	chr17	81520521	81520558	-	1	NA	intron (NR_104580, intron 2 of 8)	intron (NR_104580, intron 2 of 8)	217848	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_148969.1	chr19	7536894	7536912	+	1	NA	3' UTR (NM_001163505, exon 13 of 13)	3' UTR (NM_001163505, exon 13 of 13)	-20556	NM_139269	225845	Mm.274810	NM_139269	ENSMUSG00000060675	Pla2g16	C78643|HRSL3|Hrasls3|Hrev107|MLP-3	phospholipase A2, group XVI	protein-coding
mm_134392.1	chr16	17405878	17405888	-	1	NA	promoter-TSS (NM_023348)	promoter-TSS (NM_023348)	-117	NM_023348	67474	Mm.271992	NM_023348	ENSMUSG00000022765	Snap29	1300018G05Rik|AI891940|AU020222|BB131856|Gs32	synaptosomal-associated protein 29	protein-coding
mm_51639.1	chr6	85961716	85961760	+	1	NA	promoter-TSS (NM_028099)	promoter-TSS (NM_028099)	-71	NM_028099	72102	Mm.24007	NM_028099	ENSMUSG00000030002	Dusp11	2010300F21Rik|AI481497	dual specificity phosphatase 11 (RNA/RNP complex 1-interacting)	protein-coding
mm_31636.1	chr4	59438154	59438175	+	1	NA	intron (NM_001163288, intron 1 of 16)	CpG	469	NM_001163288	634731	Mm.483589	NM_001163288	ENSMUSG00000038578	Susd1	A530080P10|Gm12528|OTTMUSG00000007332	sushi domain containing 1	protein-coding
mm_54480.1	chr6	35100963	35100979	-	1	NA	intron (NM_016877, intron 1 of 10)	B1_Mur3|SINE|Alu	32766	NM_001164412	53621	Mm.214525	NM_016877	ENSMUSG00000038784	Cnot4	Not4|Not4h|Not4hp	CCR4-NOT transcription complex, subunit 4	protein-coding
mm_82455.1	chr9	15627821	15627834	-	1	NA	5' UTR (NM_181816, exon 1 of 12)	5' UTR (NM_181816, exon 1 of 12)	106	NM_181816	234964	Mm.32237	NM_181816	ENSMUSG00000039977	Ccdc67	4933401K09Rik|Deup1	coiled-coil domain containing 67	protein-coding
mm_102439.1	chr11	59526620	59526660	-	1	NA	Intergenic	Intergenic	-16046	NM_145827	216799	Mm.54174	NM_145827	ENSMUSG00000032691	Nlrp3	AGTAVPRL|AII/AVP|Cias1|FCAS|FCU|MWS|Mmig1|NALP3|Pypaf1	NLR family, pyrin domain containing 3	protein-coding
mm_78378.1	chr9	27790979	27790991	+	1	NA	promoter-TSS (NM_177906)	promoter-TSS (NM_177906)	-284	NM_177906	330908	Mm.379474	NM_177906	ENSMUSG00000062257	Opcml	2900075O15Rik|3732419F12|AI844366|B930023M13Rik|C230027C17|Gm181|Obcam	opioid binding protein/cell adhesion molecule-like	protein-coding
mm_106134.1	chr11	116466250	116466251	-	1	NA	Intergenic	Intergenic	-11903	NM_001033267	217341	Mm.387352	NM_001033267	ENSMUSG00000070331	Qrich2	Gm66	glutamine rich 2	protein-coding
mm_74200.1	chr8	123891927	123891939	+	1	NA	3' UTR (NM_009606, exon 7 of 7)	3' UTR (NM_009606, exon 7 of 7)	2842	NM_001272041	11459	Mm.214950	NM_009606	ENSMUSG00000031972	Acta1	AA959943|Acta-2|Acts|Actsk-1	actin, alpha 1, skeletal muscle	protein-coding
mm_8947.1	chr1	164438425	164438497	-	1	NA	exon (NM_009721, exon 6 of 6)	exon (NM_009721, exon 6 of 6)	19894	NM_009721	11931	Mm.4550	NM_009721	ENSMUSG00000026576	Atp1b1	Atp4b|Atpb|Atpb-1|NKbeta1	ATPase, Na+/K+ transporting, beta 1 polypeptide	protein-coding
mm_116990.1	chr13	56482256	56482258	-	1	NA	promoter-TSS (NM_008373)	promoter-TSS (NM_008373)	-11	NM_008373	16198	Mm.3006	NM_008373	ENSMUSG00000021538	Il9	Il-9|P40	interleukin 9	protein-coding
mm_159129.1	chr2	74705588	74705588	+	1	NA	promoter-TSS (NM_001290730)	promoter-TSS (NM_001290730)	99	NM_008276	15437	Mm.280673	NM_008276	ENSMUSG00000027102	Hoxd8	4921540P06Rik|AI047735|Hox-4.3|Hox-5.4	homeobox D8	protein-coding
mm_37111.1	chr4	116641069	116641084	-	1	NA	exon (NM_021473, exon 4 of 9)	exon (NM_021473, exon 4 of 9)	10598	NM_021473	58810	Mm.30085	NM_021473	ENSMUSG00000028692	Akr1a1	2610201A18Rik|Akr1a4	aldo-keto reductase family 1, member A1 (aldehyde reductase)	protein-coding
mm_97474.1	chr11	78323069	78323080	+	1	NA	promoter-TSS (NM_001303423)	promoter-TSS (NM_001303423)	1	NM_001303423	11676	Mm.7729	NM_009657	ENSMUSG00000017390	Aldoc	AI847350|AU040929|Aldo3|Scrg2	aldolase C, fructose-bisphosphate	protein-coding
mm_168887.1	chr1	24612694	24612703	-	1	NA	Intergenic	Intergenic	-25261	NM_007733	12823	Mm.329196	NM_007733	ENSMUSG00000026141	Col19a1	-	collagen, type XIX, alpha 1	protein-coding
mm_87806.1	chr10	60300813	60300846	+	1	NA	exon (NM_011179, exon 14 of 15)	exon (NM_011179, exon 14 of 15)	16368	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_80218.1	chr9	72532788	72532828	+	1	NA	promoter-TSS (NR_045735)	promoter-TSS (NR_045735)	568	NM_001033536	319758	Mm.32081	NM_001033536	ENSMUSG00000037674	Rfx7	2510005N23Rik|9930116O05Rik|D130086K05Rik|Rfxdc2	regulatory factor X, 7	protein-coding
mm_56240.1	chr6	90689758	90689789	-	1	NA	exon (NM_001134384, exon 3 of 14)	exon (NM_001134384, exon 3 of 14)	26756	NM_001134383	232227	Mm.196943	NM_182784	ENSMUSG00000034312	Iqsec1	AW561907|BC026481|BRAG2|D6Ertd349e|cI-43	IQ motif and Sec7 domain 1	protein-coding
mm_76422.1	chr8	84977503	84977550	-	1	NA	exon (NM_008416, exon 1 of 1)	exon (NM_008416, exon 1 of 1)	1222	NM_008416	16477	Mm.1167	NM_008416	ENSMUSG00000052837	Junb	-	jun B proto-oncogene	protein-coding
mm_171598.1	chr4	147702656	147702656	-	1	NA	promoter-TSS (NM_001127188)	promoter-TSS (NM_001127188)	-25	NM_001127188	100503584	Mm.276881	NM_001127188	ENSMUSG00000062518	Zfp534	Gm13159|OTTMUSG00000010681	zinc finger protein 534	protein-coding
mm_109129.1	chr12	105837232	105837254	+	1	NA	3' UTR (NM_001347440, exon 21 of 21)	3' UTR (NM_001347440, exon 21 of 21)	52546	NM_001347440	18789	Mm.255877	NM_011112	ENSMUSG00000021111	Papola	Pap|PapIII|Plap	poly (A) polymerase alpha	protein-coding
mm_94468.1	chr11	6476162	6476175	+	1	NA	promoter-TSS (NM_011221)	promoter-TSS (NM_011221)	-92	NM_011221	19291	Mm.296150	NM_011221	ENSMUSG00000094483	Purb	2310015K15Rik|AA114818|Cager-2|D11Bwg0414e	purine rich element binding protein B	protein-coding
mm_60834.1	chr7	45718036	45718048	+	1	NA	promoter-TSS (NM_001172561)	promoter-TSS (NM_001172561)	-29	NM_009077	19899	Mm.3459	NM_009077	ENSMUSG00000059070	Rpl18	L18|Rpl18a	ribosomal protein L18	protein-coding
mm_90590.1	chr10	128277376	128277401	+	1	NA	intron (NM_019963, intron 4 of 23)	B4|SINE|B4	6812	NM_019963	20847	Mm.293120	NM_019963	ENSMUSG00000040033	Stat2	1600010G07Rik|AW496480	signal transducer and activator of transcription 2	protein-coding
mm_113723.1	chr13	43785169	43785203	+	1	NA	promoter-TSS (NM_009856)	promoter-TSS (NM_009856)	74	NM_001289915	12522	Mm.57175	NM_009856	ENSMUSG00000015396	Cd83	-	CD83 antigen	protein-coding
mm_36072.1	chr4	57956284	57956298	-	1	NA	5' UTR (NM_011660, exon 1 of 5)	5' UTR (NM_011660, exon 1 of 5)	120	NM_011660	22166	Mm.260618	NM_011660	ENSMUSG00000028367	Txn1	ADF|AW550880|Trx1|Txn	thioredoxin 1	protein-coding
mm_122160.1	chr14	31391754	31391771	-	1	NA	intron (NM_011894, intron 3 of 8)	intron (NM_011894, intron 3 of 8)	25915	NM_001347585	24056	Mm.383198	NM_011894	ENSMUSG00000021892	Sh3bp5	AI606498|SH3BP-5|Sab	SH3-domain binding protein 5 (BTK-associated)	protein-coding
mm_34588.1	chr4	150187444	150187450	+	1	NA	exon (NM_009802, exon 8 of 8)	exon (NM_009802, exon 8 of 8)	13688	NM_009802	12353	Mm.232523	NM_009802	ENSMUSG00000028972	Car6	Ca6|DOC1	carbonic anhydrase 6	protein-coding
mm_45064.1	chr5	43233834	43233839	-	1	NA	exon (NM_001177379, exon 1 of 11)	exon (NM_001177379, exon 1 of 11)	373	NM_001177379	231207	Mm.7233	NM_175937	ENSMUSG00000039782	Cpeb2	A630055H10Rik|Cpe-bp2	cytoplasmic polyadenylation element binding protein 2	protein-coding
mm_84357.1	chr9	64704597	64704605	-	1	NA	intron (NM_001134399, intron 23 of 24)	intron (NM_001134399, intron 23 of 24)	33155	NM_017382	53869	Mm.1387	NM_017382	ENSMUSG00000004771	Rab11a	-	RAB11A, member RAS oncogene family	protein-coding
mm_113921.1	chr13	49582624	49582643	+	1	NA	promoter-TSS (NM_012050)	promoter-TSS (NM_012050)	-114	NM_012050	27047	Mm.390589	NM_012050	ENSMUSG00000048368	Omd	OSAD|SLRR2C	osteomodulin	protein-coding
mm_41717.1	chr5	102070840	102070850	+	1	NA	promoter-TSS (NM_172882)	promoter-TSS (NM_172882)	-924	NM_172882	72145	Mm.332522	NM_172882	ENSMUSG00000043940	Wdfy3	2610509D04Rik|ALFY|AW319683|B930017C24|BWF1|Bchs|D5Ertd66e|Ggtb3|ZFYVE25|mKIAA0993	WD repeat and FYVE domain containing 3	protein-coding
mm_152139.1	chr19	7089604	7089606	-	1	NA	intron (NM_134147, intron 3 of 10)	ID_B1|SINE|B4	16124	NM_201411	396184	Mm.386930	NM_201411	ENSMUSG00000047787	Flrt1	AW742165|D630040I23Rik	fibronectin leucine rich transmembrane protein 1	protein-coding
mm_12093.1	chr2	60367615	60367632	+	1	NA	intron (NM_013825, intron 3 of 34)	MTC|LTR|ERVL-MaLR	15608	NM_013825	17076	Mm.2074	NM_013825	ENSMUSG00000026980	Ly75	CD205|DEC-205|DEC205	lymphocyte antigen 75	protein-coding
mm_20793.1	chr2	144253744	144253764	-	1	NA	exon (NM_024225, exon 11 of 13)	exon (NM_024225, exon 11 of 13)	12448	NR_030762	100313519	Mm.453538	NR_030762	ENSMUSG00000077714	Snord17	MBI-43	small nucleolar RNA, C/D box 17	snoRNA
mm_31449.1	chr4	48610442	48610448	+	1	NA	exon (NM_021436, exon 3 of 10)	exon (NM_021436, exon 3 of 10)	25252	NM_021436	230157	Mm.422686	NM_021436	ENSMUSG00000028347	Tmeff1	A830033E11|M7365|Tr1	transmembrane protein with EGF-like and two follistatin-like domains 1	protein-coding
mm_90173.1	chr10	119549474	119549477	+	1	NA	intron (NM_133442, intron 1 of 21)	B1_Mm|SINE|Alu	95441	NM_001277293	74053	Mm.196692	NM_028736	ENSMUSG00000034813	Grip1	4931400F03Rik|GRIP|eb	glutamate receptor interacting protein 1	protein-coding
mm_118406.1	chr13	119409445	119409465	-	1	NA	promoter-TSS (NM_008710)	promoter-TSS (NM_008710)	-198	NM_001308506	18115	Mm.132584	NM_008710	ENSMUSG00000025453	Nnt	4930423F13Rik|AI323702|BB168308	nicotinamide nucleotide transhydrogenase	protein-coding
mm_39185.1	chr4	155785884	155785920	-	1	NA	promoter-TSS (NM_001033394)	promoter-TSS (NM_001033394)	-28	NM_001033394	320587	Mm.384382	NM_001033394	ENSMUSG00000073680	Tmem88b	A230069A22Rik	transmembrane protein 88B	protein-coding
mm_101615.1	chr11	35834519	35834530	-	1	NA	promoter-TSS (NM_025936)	promoter-TSS (NM_025936)	4	NM_025936	104458	Mm.284906	NM_025936	ENSMUSG00000018848	Rars	2610011N19Rik|2610037E21Rik|AL033339|AW985894	arginyl-tRNA synthetase	protein-coding
mm_163240.1	chr11	104637554	104637563	+	1	NA	intron (NM_016780, intron 5 of 14)	intron (NM_016780, intron 5 of 14)	29558	NM_016780	16416	Mm.87150	NM_016780	ENSMUSG00000020689	Itgb3	CD61|GP3A|INGRB3	integrin beta 3	protein-coding
mm_157025.1	chrX	7898865	7898912	-	1	NA	promoter-TSS (NM_011591)	promoter-TSS (NM_011591)	112	NM_001252528	54633	Mm.14616	NM_019478	ENSMUSG00000031157	Pqbp1	PQBP-1|Sfc2|npw38	polyglutamine binding protein 1	protein-coding
mm_46858.1	chr5	113772636	113772706	-	1	NA	promoter-TSS (NM_025526)	promoter-TSS (NM_025526)	-141	NM_025526	66383	Mm.29497	NM_025526	ENSMUSG00000025825	Iscu	2310020H20Rik|AA407971|Nifu|Nifun	iron-sulfur cluster assembly enzyme	protein-coding
mm_101635.1	chr11	36432832	36432840	-	1	NA	intron (NM_011856, intron 2 of 28)	intron (NM_011856, intron 2 of 28)	-452747	NM_170779	211652	Mm.31267	NM_170779	ENSMUSG00000018849	Wwc1	AA408228|AU017197|BC037006|Kibra|mKIAA0869	WW, C2 and coiled-coil domain containing 1	protein-coding
mm_111139.1	chr12	81663994	81664006	-	1	NA	3' UTR (NM_001033149, exon 3 of 3)	3' UTR (NM_001033149, exon 3 of 3)	32751	NM_001033149	69480	Mm.130002	NM_001033149	ENSMUSG00000042734	Ttc9	-	tetratricopeptide repeat domain 9	protein-coding
mm_17174.1	chr2	25319194	25319204	-	1	NA	promoter-TSS (NM_001177657)	promoter-TSS (NM_001177657)	-12	NM_001177656	14810	Mm.278672	NM_008169	ENSMUSG00000026959	Grin1	GluN1|GluRdelta1|GluRzeta1|M100174|NMD-R1|NMDAR1|NR1|Nmdar|Rgsc174	glutamate receptor, ionotropic, NMDA1 (zeta 1)	protein-coding
mm_78587.1	chr9	37367628	37367656	+	1	NA	promoter-TSS (NM_175189)	promoter-TSS (NM_175189)	36	NM_175189	72927	Mm.266133	NM_175189	ENSMUSG00000046240	Hepacam	2900042E01Rik|Glialcam|Hepn1	hepatocyte cell adhesion molecule	protein-coding
mm_5073.1	chr1	3489150	3489153	-	1	NA	intron (NM_001011874, intron 1 of 2)	Lx2A1|LINE|L1	182347	NM_001011874	497097	Mm.454496	NM_001011874	ENSMUSG00000051951	Xkr4	AY534250|Gm210|XRG4|mKIAA1889	X-linked Kx blood group related 4	protein-coding
mm_16655.1	chr2	6549957	6549967	-	1	NA	exon (NM_001110228, exon 12 of 14)	exon (NM_001110228, exon 12 of 14)	171700	NM_001310447	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_159337.1	chr3	54735359	54735359	-	1	NA	promoter-TSS (NM_025442)	promoter-TSS (NM_025442)	5	NM_027148	69639	Mm.29253	NM_027148	ENSMUSG00000027752	Exosc8	2310032N20Rik|CIP3|mKIAA4013	exosome component 8	protein-coding
mm_35052.1	chr4	6355346	6355352	-	1	NA	Intergenic	Intergenic	-10331	NM_016807	53378	Mm.247473	NM_016807	ENSMUSG00000028249	Sdcbp	MDA-9|Sycl|syntenin-1	syndecan binding protein	protein-coding
mm_109296.1	chr12	109559789	109559801	+	1	NA	non-coding (NR_003633, exon 5 of 5)	non-coding (NR_003633, exon 5 of 5)	-3897	NR_030427	791079		NR_030427	ENSMUSG00000076451	Mir770	Mirn770|mir-770|mmu-mir-770	microRNA 770	ncRNA
mm_128260.1	chr15	36771357	36771371	-	1	NA	3' UTR (NM_001253807, exon 5 of 5)	3' UTR (NM_001253807, exon 5 of 5)	19568	NM_001253807	22631	Mm.3360	NM_011740	ENSMUSG00000022285	Ywhaz	1110013I11Rik|14-3-3zeta|AI596267|AL022924|AU020854	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide	protein-coding
mm_56855.1	chr6	118166438	118166440	-	1	NA	intron (NM_001080780, intron 15 of 18)	intron (NM_001080780, intron 15 of 18)	-27299	NM_030165	78752	Mm.300317	NM_030165	ENSMUSG00000042042	Csgalnact2	4632415D10Rik|Galnact2	chondroitin sulfate N-acetylgalactosaminyltransferase 2	protein-coding
mm_50332.1	chr6	48413023	48413034	+	1	NA	intron (NM_001347153, intron 13 of 17)	intron (NM_001347153, intron 13 of 17)	17442	NM_001347153	77827	Mm.107646	NM_133922	ENSMUSG00000042810	Krba1	A930040G15Rik|AI448780	KRAB-A domain containing 1	protein-coding
mm_18645.1	chr2	69533638	69533648	-	1	NA	intron (NM_001081088, intron 8 of 78)	intron (NM_001081088, intron 8 of 78)	52424	NM_001081088	14725	Mm.23847	NM_001081088	ENSMUSG00000027070	Lrp2	AI315343|AW536255|D230004K18Rik|Gp330|Megalin|b2b1625.2Clo	low density lipoprotein receptor-related protein 2	protein-coding
mm_45577.1	chr5	73647712	73647718	-	1	NA	promoter-TSS (NM_011890)	promoter-TSS (NM_011890)	16	NM_011890	24051	Mm.89310	NM_011890	ENSMUSG00000029156	Sgcb	43kDa|AI747103|AI844814|beta-SG	sarcoglycan, beta (dystrophin-associated glycoprotein)	protein-coding
mm_71951.1	chr8	70493157	70493167	+	1	NA	promoter-TSS (NM_018827)	promoter-TSS (NM_018827)	31	NM_018827	12931	Mm.335584	NM_018827	ENSMUSG00000007888	Crlf1	CLF-1|CRLM-3|CRLM3|NR6|NR6.1	cytokine receptor-like factor 1	protein-coding
mm_71412.1	chr8	46472361	46472393	+	1	NA	intron (NM_007981, intron 1 of 20)	intron (NM_007981, intron 1 of 20)	1340	NM_007981	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_94889.1	chr11	28712332	28712342	+	1	NA	Intergenic	Intergenic	30773	NR_045906	72818	Mm.410846	NR_045906	ENSMUSG00000084966	2810471M01Rik	-	RIKEN cDNA 2810471M01 gene	ncRNA
mm_1397.1	chr1	67136743	67136770	+	1	NA	intron (NM_001080809, intron 1 of 37)	intron (NM_001080809, intron 1 of 37)	13729	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_1084.1	chr1	59548837	59548846	+	1	NA	intron (NM_001013771, intron 4 of 19)	intron (NM_001013771, intron 4 of 19)	32577	NM_001013771	381260	Mm.486706	NM_001013771	ENSMUSG00000047361	Gm973	AW554518	predicted gene 973	protein-coding
mm_49873.1	chr6	38577037	38577041	+	1	NA	intron (NM_001331223, intron 6 of 12)	intron (NM_001331223, intron 6 of 12)	21316	NM_001331223	192196	Mm.276133	NM_138680	ENSMUSG00000029823	Luc7l2	4930471C18Rik|AA522013|AU015269|CGI59|Cgi74	LUC7-like 2 (S. cerevisiae)	protein-coding
mm_123778.1	chr14	70323772	70323778	-	1	NA	intron (NM_001135152, intron 2 of 9)	intron (NM_001135152, intron 2 of 9)	24658	NM_001135152	213053	Mm.270647	NM_144808	ENSMUSG00000022094	Slc39a14	FAD-123|ZIP-14|Zip14|fad123	solute carrier family 39 (zinc transporter), member 14	protein-coding
mm_146028.1	chr18	69521307	69521353	+	1	NA	intron (NM_013685, intron 6 of 19)	intron (NM_013685, intron 6 of 19)	175609	NM_001083967	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding
mm_43339.1	chr5	135089885	135089896	+	1	NA	Intergenic	CpG	-11624	NM_001199677	194309	Mm.44356	NM_177574	ENSMUSG00000043614	Vps37d	Wbscr24	vacuolar protein sorting 37D	protein-coding
mm_41294.1	chr5	90464087	90464119	+	1	NA	exon (NM_009654, exon 4 of 15)	exon (NM_009654, exon 4 of 15)	3233	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_7912.1	chr1	133690091	133690097	-	1	NA	promoter-TSS (NM_001159649)	promoter-TSS (NM_001159649)	14	NM_001159649	240754	Mm.36534	NM_172842	ENSMUSG00000051998	Lax1	A530029E09|E430019B13Rik	lymphocyte transmembrane adaptor 1	protein-coding
mm_125137.1	chr15	30485864	30485880	+	1	NA	intron (NM_008729, intron 3 of 22)	intron (NM_008729, intron 3 of 22)	313279	NM_008729	18163	Mm.321648	NM_008729	ENSMUSG00000022240	Ctnnd2	Catnd2|Nprap|neurojugin	catenin (cadherin associated protein), delta 2	protein-coding
mm_149190.1	chr19	9939176	9939189	+	1	NA	Intergenic	Intergenic	-39649	NM_016692	16319	Mm.29755	NM_016692	ENSMUSG00000024660	Incenp	2700067E22Rik|AU019509|C130081E20|C77457	inner centromere protein	protein-coding
mm_8903.1	chr1	163304518	163304520	-	1	NA	intron (NM_001025570, intron 1 of 2)	intron (NM_001025570, intron 1 of 2)	9131	NM_011127	18933	Mm.288642	NM_011127	ENSMUSG00000026586	Prrx1	A230024N07Rik|AA755424|AI385634|AI843499|K-2|Pmx|Pmx1|Prx1|mHox	paired related homeobox 1	protein-coding
mm_125383.1	chr15	40655309	40655321	+	1	NA	5' UTR (NM_011766, exon 1 of 8)	5' UTR (NM_011766, exon 1 of 8)	273	NM_011766	22762	Mm.39496	NM_011766	ENSMUSG00000022306	Zfpm2	B330005D23Rik|FOG-2|FOG2	zinc finger protein, multitype 2	protein-coding
mm_40557.1	chr5	59771196	59771196	+	1	NA	Intergenic	Intergenic	214806	NR_040683	71057	Mm.50817	NR_040682	ENSMUSG00000106013	4933402J10Rik	-	RIKEN cDNA 4933402J10 gene	ncRNA
mm_60008.1	chr7	30729564	30729643	+	1	NA	promoter-TSS (NM_027215)	promoter-TSS (NM_027215)	-69	NM_027215	69804	Mm.27499	NM_027215	ENSMUSG00000006315	Tmem147	2010004E11Rik|5033425B17Rik|Nifie14	transmembrane protein 147	protein-coding
mm_119550.1	chr14	48553258	48553266	+	1	NA	Intergenic	Intergenic	106910	NR_132324	218989	Mm.85211	NM_172600	ENSMUSG00000036339	Tmem260	5930435P15|6720456H20Rik	transmembrane protein 260	protein-coding
mm_142143.1	chr17	35980198	35980235	-	1	NA	promoter-TSS (NM_001282025)	promoter-TSS (NM_001282025)	261	NM_008136	14670	Mm.335754	NM_008136	ENSMUSG00000024429	Gnl1	Gna-rs1|Gnal1	guanine nucleotide binding protein-like 1	protein-coding
mm_36298.1	chr4	66404513	66404527	-	1	NA	promoter-TSS (NM_207109)	promoter-TSS (NM_207109)	-37	NM_207109	56079	Mm.445312	NM_019514	ENSMUSG00000028373	Astn2	1d8|Astnl|bM452J22.1	astrotactin 2	protein-coding
mm_51543.1	chr6	83206119	83206130	+	1	NA	Intergenic	Intergenic	20178	NM_001347310	13191	Mm.6919	NM_007835	ENSMUSG00000031865	Dctn1	AL022633|DAP-150|DP-150|Glued|p150|p150-glued|p150<glued>	dynactin 1	protein-coding
mm_70639.1	chr8	13907749	13907816	+	1	NA	promoter-TSS (NM_025785)	promoter-TSS (NM_025785)	-24	NM_025785	66822	Mm.37950	NM_025785	ENSMUSG00000038365	Fbxo25	9130015I06Rik|AI649137|Fbx25	F-box protein 25	protein-coding
mm_65209.1	chr7	19697613	19697635	-	1	NA	exon (NM_009696, exon 3 of 4)	exon (NM_009696, exon 3 of 4)	774	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_116009.1	chr13	24613651	24613678	-	1	NA	promoter-TSS (NM_001286101)	promoter-TSS (NM_001286101)	-942	NM_001286101	193385	Mm.217319	NM_029679	ENSMUSG00000036006	Fam65b	-	family with sequence similarity 65, member B	protein-coding
mm_36302.1	chr4	68937715	68937715	-	1	NA	intron (NM_019967, intron 1 of 7)	intron (NM_019967, intron 1 of 7)	16682	NM_019967	56710	Mm.248788	NM_019967	ENSMUSG00000028351	Brinp1	BRINP|Dbc1|Dbccr1|Fam5a	bone morphogenic protein/retinoic acid inducible neural specific 1	protein-coding
mm_167982.1	chrX	164438084	164438093	+	1	NA	5' UTR (NM_026853, exon 2 of 8)	5' UTR (NM_026853, exon 2 of 8)	1094	NM_001313737	68854	Mm.33225	NM_026853	ENSMUSG00000031382	Asb11	1110067L12Rik|1600009D24Rik	ankyrin repeat and SOCS box-containing 11	protein-coding
mm_111514.1	chr12	99627965	99627985	-	1	NA	promoter-TSS (NR_045288)	promoter-TSS (NR_045288)	-1	NR_045288	73457	Mm.383439	NR_045288	ENSMUSG00000100211	1700064M15Rik	-	RIKEN cDNA 1700064M15 gene	ncRNA
mm_46595.1	chr5	107731467	107731495	-	1	NA	Intergenic	Intergenic	-5676	NM_001267621	14581	Mm.2078	NM_010278	ENSMUSG00000029275	Gfi1	AW495828|Gfi-1|Pal-1|Pal1	growth factor independent 1	protein-coding
mm_159360.1	chr3	86084419	86084419	+	1	NA	promoter-TSS (NM_001082414)	promoter-TSS (NM_001082414)	-15	NM_001082414	27059	Mm.2454	NM_012059	ENSMUSG00000028082	Sh3d19	AW011754|Kryn	SH3 domain protein D19	protein-coding
mm_153542.1	chr19	42053070	42053077	-	1	NA	exon (NM_025752, exon 1 of 1)	exon (NM_025752, exon 1 of 1)	845	NM_025752	66765	Mm.440412	NM_025752	ENSMUSG00000090369	4933411K16Rik	-	RIKEN cDNA 4933411K16 gene	protein-coding
mm_113882.1	chr13	48969089	48969111	+	1	NA	non-coding (NR_015601, exon 2 of 2)	non-coding (NR_015601, exon 2 of 2)	988	NR_015601	68128	Mm.426304	NR_015601		Fam120aos	C030044B11Rik	family with sequence similarity 120A, opposite strand	ncRNA
mm_78929.1	chr9	45079205	45079236	+	1	NA	promoter-TSS (NM_001005421)	promoter-TSS (NM_001005421)	37	NM_001005421	270152	Mm.190461	NM_001005421	ENSMUSG00000048534	Amica1	AMICA|Crea7|Gm638|Jaml	adhesion molecule, interacts with CXADR antigen 1	protein-coding
mm_48380.1	chr5	139771584	139771600	-	1	NA	exon (NM_026748, exon 7 of 47)	exon (NM_026748, exon 7 of 47)	-3649	NR_106004	102465628		NR_106004	ENSMUSG00000098574	Mir7037	Gm27447|mmu-mir-7037	microRNA 7037	ncRNA
mm_116081.1	chr13	28450506	28450510	-	1	NA	Intergenic	B4|SINE|B4	260365	NR_105787	102466635		NR_105787	ENSMUSG00000099158	Mir6368	Gm27800|mmu-mir-6368	microRNA 6368	ncRNA
mm_143895.1	chr17	84676963	84676965	-	1	NA	intron (NM_001286005, intron 1 of 11)	B1_Mur4|SINE|Alu	662	NM_001286005	67470	Mm.26581	NM_026180	ENSMUSG00000024254	Abcg8	1300003C16Rik|AI114946|sterolin-2	ATP-binding cassette, sub-family G (WHITE), member 8	protein-coding
mm_69094.1	chr7	127018579	127018596	-	1	NA	3' UTR (NM_001102563, exon 4 of 4)	3' UTR (NM_001102563, exon 4 of 4)	-1235	NM_030240	67278	Mm.345385	NM_030240	ENSMUSG00000030680	Pagr1a	2900092E17Rik|C77040|PA1|PAGR1	PAXIP1 associated glutamate rich protein 1A	protein-coding
mm_125144.1	chr15	30634744	30634756	+	1	NA	exon (NM_008729, exon 6 of 23)	exon (NM_008729, exon 6 of 23)	-404376	NR_045186	73784	Mm.66947	NR_045186		4930430F21Rik	-	RIKEN cDNA 4930430F21 gene	ncRNA
mm_34664.1	chr4	150867270	150867314	+	1	NA	exon (NM_133753, exon 4 of 4)	exon (NM_133753, exon 4 of 4)	12201	NM_133753	74155	Mm.318841	NM_133753	ENSMUSG00000028967	Errfi1	1300002F13Rik|AI788755|Mig-6|Mig6|RALT	ERBB receptor feedback inhibitor 1	protein-coding
mm_2830.1	chr1	131204700	131204739	+	1	NA	intron (NM_001313731, intron 2 of 5)	intron (NM_001313731, intron 2 of 5)	-4534	NM_001311094	54354	Mm.248291	NM_018750	ENSMUSG00000026430	Rassf5	1300019G20Rik|Maxp1|Nore1|Nore1A|Nore1B|Rapl	Ras association (RalGDS/AF-6) domain family member 5	protein-coding
mm_131487.1	chr16	17222357	17222391	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-11213	NM_178922	58180	Mm.261602	NM_178922	ENSMUSG00000050240	Hic2	AA409108|HRG22|mKIAA1020	hypermethylated in cancer 2	protein-coding
mm_74452.1	chr8	4214118	4214128	-	1	NA	exon (NM_207203, exon 6 of 7)	exon (NM_207203, exon 6 of 7)	3189	NM_207203	73072	Mm.477379	NM_207203	ENSMUSG00000064125	Prr36	-	proline rich 36	protein-coding
mm_126315.1	chr15	79687928	79687949	+	1	NA	promoter-TSS (NM_028792)	promoter-TSS (NM_028792)	-66	NM_028792	74158	Mm.323393	NM_028792	ENSMUSG00000022426	Josd1	1300006C06Rik|mKIAA0063	Josephin domain containing 1	protein-coding
mm_151631.1	chr19	3918678	3918711	-	1	NA	exon (NM_026316, exon 7 of 10)	exon (NM_026316, exon 7 of 10)	-5920	NM_001271444	225887	Mm.44227	NM_144870	ENSMUSG00000059734	Ndufs8	BC021616|CI-23kD|TYKY	NADH dehydrogenase (ubiquinone) Fe-S protein 8	protein-coding
mm_94374.1	chr11	5099660	5099677	+	1	NA	promoter-TSS (NM_007968)	promoter-TSS (NM_007968)	-80	NR_110961	279766	Mm.260866	NM_177370	ENSMUSG00000034175	Rhbdd3	Ptag	rhomboid domain containing 3	protein-coding
mm_14349.1	chr2	129596188	129596238	+	1	NA	intron (NM_001291022, intron 1 of 4)	intron (NM_001291022, intron 1 of 4)	3044	NM_001291022	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_86959.1	chr10	25053287	25053287	+	1	NA	Intergenic	Intergenic	-125817	NM_007482	11846	Mm.154144	NM_007482	ENSMUSG00000019987	Arg1	AI|AI256583|Arg-1|PGIF	arginase, liver	protein-coding
mm_152186.1	chr19	7432009	7432052	-	1	NA	exon (NM_053076, exon 4 of 7)	exon (NM_053076, exon 4 of 7)	9457	NR_105957	102466781		NR_105957	ENSMUSG00000098293	Mir6991	Gm27966|mmu-mir-6991	microRNA 6991	ncRNA
mm_16270.1	chr2	173660068	173660082	+	1	NA	promoter-TSS (NR_027957)	promoter-TSS (NR_027957)	230	NM_024436	19334	Mm.275304	NM_024436	ENSMUSG00000027519	Rab22a	3732413A17Rik|AI662177|AW319644|AW550514|E130120E14Rik|Rab22	RAB22A, member RAS oncogene family	protein-coding
mm_83357.1	chr9	44407015	44407029	-	1	NA	promoter-TSS (NM_024266)	promoter-TSS (NM_024266)	526	NM_021789	60409	Mm.29814	NM_021789	ENSMUSG00000032112	Trappc4	1500017G03Rik|AI303617|HSPC172|PTD009|Sbd|Sbdn|Sdcbp2|TRS23	trafficking protein particle complex 4	protein-coding
mm_136192.1	chr16	89420128	89420134	-	1	NA	promoter-TSS (NM_010673)	promoter-TSS (NM_010673)	-20	NM_010673	16701	Mm.3524	NM_010673	ENSMUSG00000062433	Krtap6-2	AI646275|HGTpII.4	keratin associated protein 6-2	protein-coding
mm_28990.1	chr3	101288128	101288142	-	1	NA	promoter-TSS (NM_013486)	promoter-TSS (NM_013486)	-196	NM_013486	12481	Mm.22842	NM_013486	ENSMUSG00000027863	Cd2	LFA-2|Ly-37|Ly37	CD2 antigen	protein-coding
mm_79141.1	chr9	47655117	47655151	+	1	NA	intron (NM_001025600, intron 1 of 8)	intron (NM_001025600, intron 1 of 8)	124782	NM_018770	54725	Mm.234832	NM_018770	ENSMUSG00000032076	Cadm1	2900073G06Rik|3100001I08Rik|AI987920|Bl2|Igsf4|Igsf4a|Necl2|RA175|RA175A|RA175B|RA175C|RA175N|ST17|SgIGSF|SynCam|Tslc1	cell adhesion molecule 1	protein-coding
mm_121861.1	chr14	20702972	20702985	-	1	NA	promoter-TSS (NM_025366)	promoter-TSS (NM_025366)	-49	NM_025366	66121	Mm.246996	NM_025366	ENSMUSG00000063787	Chchd1	1110001O19Rik|2400010G13Rik|MRP-S37	coiled-coil-helix-coiled-coil-helix domain containing 1	protein-coding
mm_118743.1	chr14	22318711	22318723	+	1	NA	intron (NM_028275, intron 2 of 6)	B3|SINE|B2	224081	NR_046307	74896	Mm.444661	NR_046307		4930405A10Rik	4930456G20Rik	RIKEN cDNA 4930405A10 gene	ncRNA
mm_131095.1	chr16	4913183	4913215	+	1	NA	intron (NM_001252437, intron 4 of 16)	intron (NM_001252437, intron 4 of 16)	-25912	NM_001316715	66911	Mm.428698	NM_025839	ENSMUSG00000022516	Nudt16l1	1110001K21Rik|5330437I08Rik|Sdos	nudix (nucleoside diphosphate linked moiety X)-type motif 16-like 1	protein-coding
mm_52651.1	chr6	117559695	117559700	+	1	NA	Intergenic	MT2A|LTR|ERVL	192072	NR_045731	72263	Mm.443289	NR_045731	ENSMUSG00000099869	1700030F04Rik	-	RIKEN cDNA 1700030F04 gene	ncRNA
mm_88403.1	chr10	76716253	76716299	+	1	NA	exon (NM_009933, exon 20 of 35)	exon (NM_009933, exon 20 of 35)	9768	NM_009933	12833	Mm.2509	NM_009933	ENSMUSG00000001119	Col6a1	AI747156|Col6a-1	collagen, type VI, alpha 1	protein-coding
mm_28618.1	chr3	95003411	95003414	-	1	NA	promoter-TSS (NR_105980)	promoter-TSS (NR_105980)	-756	NR_105980	102465613		NR_105980	ENSMUSG00000099033	Mir7013	Gm27488|mmu-mir-7013	microRNA 7013	ncRNA
mm_70790.1	chr8	22506555	22506571	+	1	NA	intron (NM_011394, intron 1 of 10)	intron (NM_011394, intron 1 of 10)	-29684	NM_001146117	102032	Mm.378231	NM_001012667	ENSMUSG00000031534	Smim19	AI316807|BG694986|EST-c39	small integral membrane protein 19	protein-coding
mm_32364.1	chr4	105224304	105224315	+	1	NA	intron (NM_080555, intron 5 of 5)	intron (NM_080555, intron 5 of 5)	66962	NM_080555	67916	Mm.348326	NM_080555	ENSMUSG00000028517	Plpp3	1110003O22Rik|2610002D05Rik|AV025606|D4Bwg0538e|D4Bwg1535e|Lpp3|Ppab2b|Ppap2b	phospholipid phosphatase 3	protein-coding
mm_117395.1	chr13	73678156	73678180	-	1	NA	promoter-TSS (NM_001168646)	promoter-TSS (NM_001168646)	-145	NM_001168643	22598	Mm.30370	NM_011730	ENSMUSG00000021612	Slc6a18	B0AT3|D630001K16Rik|Xt2|Xtrp2	solute carrier family 6 (neurotransmitter transporter), member 18	protein-coding
mm_61497.1	chr7	75753449	75753489	+	1	NA	3' UTR (NM_029332, exon 37 of 37)	3' UTR (NM_029332, exon 37 of 37)	-94869	NM_001122780	207952	Mm.206223	NM_029652	ENSMUSG00000055652	Klhl25	2810402K13Rik|BC027373|Enc-1	kelch-like 25	protein-coding
mm_34267.1	chr4	141421885	141421892	+	1	NA	exon (NM_013868, exon 1 of 3)	exon (NM_013868, exon 1 of 3)	1109	NM_013868	29818	Mm.46181	NM_013868	ENSMUSG00000006221	Hspb7	27kDa|Hsp25-2|cvHsp	heat shock protein family, member 7 (cardiovascular)	protein-coding
mm_128411.1	chr15	44748398	44748408	-	1	NA	5' UTR (NM_001285840, exon 1 of 7)	5' UTR (NM_001285840, exon 1 of 7)	269	NM_001285840	319613	Mm.207715	NM_176998	ENSMUSG00000022340	Sybu	Golsyn	syntabulin (syntaxin-interacting)	protein-coding
mm_57559.1	chr6	126966783	126966794	-	1	NA	intron (NM_138594, intron 10 of 13)	intron (NM_138594, intron 10 of 13)	26822	NM_138594	28040	Mm.44228	NM_138594	ENSMUSG00000030347	D6Wsu163e	C12orf4	DNA segment, Chr 6, Wayne State University 163, expressed	protein-coding
mm_149490.1	chr19	11818106	11818115	+	1	NA	intron (NM_001025307, intron 1 of 10)	intron (NM_001025307, intron 1 of 10)	1293	NM_001286543	20908	Mm.272264	NM_011502	ENSMUSG00000041488	Stx3	Syn-3	syntaxin 3	protein-coding
mm_81583.1	chr9	110422539	110422549	+	1	NA	3' UTR (NM_008694, exon 4 of 4)	3' UTR (NM_008694, exon 4 of 4)	2736	NM_008694	18054	Mm.236225	NM_008694	ENSMUSG00000032484	Ngp	bectenecin	neutrophilic granule protein	protein-coding
mm_69383.1	chr7	131329462	131329465	-	1	NA	promoter-TSS (NM_027037)	promoter-TSS (NM_027037)	36	NM_027037	69318	Mm.233840	NM_027037	ENSMUSG00000030858	1700007K09Rik	-	RIKEN cDNA 1700007K09 gene	protein-coding
mm_105211.1	chr11	102163149	102163171	-	1	NA	TTS (NM_172947)	TTS (NM_172947)	-6753	NM_029649	76547	Mm.46529	NM_029649	ENSMUSG00000020921	Tmem101	2610511E22Rik	transmembrane protein 101	protein-coding
mm_163903.1	chr14	30485099	30485107	+	1	NA	intron (NM_133761, intron 3 of 9)	intron (NM_133761, intron 3 of 9)	5538	NM_133761	75901	Mm.28733	NM_133761	ENSMUSG00000021962	Dcp1a	1110066A22Rik|4930568L04Rik|AU019772|D14Ertd817e|Mitc1|SMIF	decapping mRNA 1A	protein-coding
mm_166793.1	chr6	146850170	146850175	+	1	NA	promoter-TSS (NM_027059)	promoter-TSS (NM_027059)	62	NM_027059	69371	Mm.252733	NM_027059	ENSMUSG00000030292	Smco2	1700023A16Rik	single-pass membrane protein with coiled-coil domains 2	protein-coding
mm_131405.1	chr16	14398280	14398295	+	1	NA	intron (NM_008576, intron 5 of 30)	B2_Mm2|SINE|B2	36729	NM_008576	17250	Mm.196634	NM_008576	ENSMUSG00000023088	Abcc1	Abcc1a|Abcc1b|MRP|Mdrap|Mrp1	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	protein-coding
mm_139902.1	chr17	70858590	70858599	+	1	NA	Intergenic	AT_rich|Low_complexity|Low_complexity	-5062	NM_001164074	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_113536.1	chr13	37848708	37848716	+	1	NA	intron (NM_001039188, intron 1 of 9)	intron (NM_001039188, intron 1 of 9)	21319	NM_001039188	68750	Mm.491109	NM_026830	ENSMUSG00000039087	Rreb1	1110037N09Rik|AA414966|B930013M22Rik	ras responsive element binding protein 1	protein-coding
mm_56434.1	chr6	97354165	97354195	-	1	NA	intron (NM_001346639, intron 5 of 22)	intron (NM_001346639, intron 5 of 22)	-101400	NM_001081157	320502	Mm.68163	NM_001081157	ENSMUSG00000044086	Lmod3	5430424A14Rik	leiomodin 3 (fetal)	protein-coding
mm_82901.1	chr9	32731927	32731937	-	1	NA	intron (NM_011808, intron 3 of 7)	intron (NM_011808, intron 3 of 7)	35890	NM_001038642	23871	Mm.292415	NM_011808	ENSMUSG00000032035	Ets1	AI196000|AI448617|D230050P06|Ets-1|Tpl1|vs	E26 avian leukemia oncogene 1, 5' domain	protein-coding
mm_139280.1	chr17	48247816	48247832	+	1	NA	promoter-TSS (NM_021407)	promoter-TSS (NM_021407)	95	NM_021407	58218	Mm.302438	NM_021407	ENSMUSG00000041754	Trem3	BB134760	triggering receptor expressed on myeloid cells 3	protein-coding
mm_157695.1	chrX	60426543	60426563	-	1	NA	Intergenic	Intergenic	-22572	NM_001037863	320940	Mm.490394	NM_001001798	ENSMUSG00000062949	Atp11c	A330005H02Rik|AI315324|Ig	ATPase, class VI, type 11C	protein-coding
mm_102753.1	chr11	67297744	67297751	-	1	NA	exon (NM_177369, exon 25 of 40)	exon (NM_177369, exon 25 of 40)	20623	NM_177369	17885	Mm.340163	NM_177369	ENSMUSG00000055775	Myh8	4832426G23Rik|AI327267|MHCp|MyHC-pn|Myhs-p|Myhsp	myosin, heavy polypeptide 8, skeletal muscle, perinatal	protein-coding
mm_34743.1	chr4	152274192	152274232	+	1	NA	promoter-TSS (NM_178406)	promoter-TSS (NM_178406)	-150	NM_178406	100129	Mm.23235	NM_178406	ENSMUSG00000042804	Gpr153	1110065N12Rik|AI449320|PGR1	G protein-coupled receptor 153	protein-coding
mm_8128.1	chr1	136230308	136230332	-	1	NA	intron (NM_028872, intron 1 of 9)	intron (NM_028872, intron 1 of 9)	3960	NM_028872	67313	Mm.36763	NM_028872	ENSMUSG00000041605	5730559C18Rik	1700034M08Rik|4933426C09Rik|AI586180|D1Mgi54	RIKEN cDNA 5730559C18 gene	protein-coding
mm_47843.1	chr5	134314638	134314676	-	1	NA	5' UTR (NM_010365, exon 1 of 34)	5' UTR (NM_010365, exon 1 of 34)	103	NM_001080746	14886	Mm.261570	NM_010365	ENSMUSG00000060261	Gtf2i	6030441I21Rik|BAP-135|Diws1t|GtfII-I|Spin|TFII-I|WBSCR6	general transcription factor II I	protein-coding
mm_134275.1	chr16	13987222	13987244	-	1	NA	promoter-TSS (NM_001270718)	promoter-TSS (NM_001270718)	-366	NM_001270718	74482	Mm.484026	NM_028968	ENSMUSG00000065968	Ifitm7	4933438K12Rik|Mil4	interferon induced transmembrane protein 7	protein-coding
mm_105303.1	chr11	102579517	102579538	-	1	NA	promoter-TSS (NR_040286)	promoter-TSS (NR_040286)	-408	NR_040286	100040792	Mm.277966	NR_040286	ENSMUSG00000078640	Gm11627	OTTMUSG00000002879	predicted gene 11627	ncRNA
mm_7235.1	chr1	93445423	93445436	-	1	NA	intron (NM_133808, intron 1 of 27)	CpG	272	NM_001301364	110611	Mm.30012	NM_133808	ENSMUSG00000034088	Hdlbp	1110005P14Rik|AA960365|AI118566|D1Ertd101e	high density lipoprotein (HDL) binding protein	protein-coding
mm_147038.1	chr18	34861428	34861441	-	1	NA	5' UTR (NM_007913, exon 1 of 2)	5' UTR (NM_007913, exon 1 of 2)	227	NM_007913	13653	Mm.181959	NM_007913	ENSMUSG00000038418	Egr1	A530045N19Rik|ETR103|Egr-1|Krox-1|Krox-24|Krox24|NGF1-A|NGFI-A|NGFIA|TIS8|Zenk|Zfp-6|Zif268|egr	early growth response 1	protein-coding
mm_40122.1	chr5	34989537	34989545	+	1	NA	intron (NM_173402, intron 3 of 16)	intron (NM_173402, intron 3 of 16)	-9537	NM_001163512	71729	Mm.196208	NM_173402	ENSMUSG00000029101	Rgs12	1200016K18Rik|4632412M04Rik|AI481290|E130309H11	regulator of G-protein signaling 12	protein-coding
mm_71817.1	chr8	68886917	68886926	+	1	NA	intron (NM_008509, intron 1 of 9)	intron (NM_008509, intron 1 of 9)	6366	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_65016.1	chr7	17095087	17095091	-	1	NA	exon (NM_007676, exon 4 of 5)	exon (NM_007676, exon 4 of 5)	21049	NM_007676	26436	Mm.143686	NM_007676	ENSMUSG00000066760	Psg16	Cea11|PSG|bCEA	pregnancy specific glycoprotein 16	protein-coding
mm_130764.1	chr15	101364590	101364619	-	1	NA	intron (NM_028770, intron 1 of 8)	intron (NM_028770, intron 1 of 8)	-4748	NR_035462	100316694		NR_035462	ENSMUSG00000088459	Mir1941	mmu-mir-1941	microRNA 1941	ncRNA
mm_113691.1	chr13	43112115	43112119	+	1	NA	intron (NM_001005740, intron 8 of 12)	intron (NM_001005740, intron 8 of 12)	-10722	NM_001005748	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding
mm_113419.1	chr13	34037613	34037615	+	1	NA	promoter-TSS (NM_026512)	promoter-TSS (NM_026512)	-27	NM_026512	68021	Mm.140243	NM_026512	ENSMUSG00000038286	Bphl	2010012D11Rik|5730533B08Rik|AI115341	biphenyl hydrolase-like (serine hydrolase, breast epithelial mucin-associated antigen)	protein-coding
mm_51599.1	chr6	84008541	84008557	+	1	NA	promoter-TSS (NM_001077694)	promoter-TSS (NM_001077694)	-49	NM_001077694	26903	Mm.220982	NM_021469	ENSMUSG00000033788	Dysf	2310004N10Rik|AI604795|D6Pas3	dysferlin	protein-coding
mm_11992.1	chr2	55511543	55511546	+	1	NA	intron (NM_008426, intron 3 of 3)	L1_Mur3|LINE|L1	75574	NM_008426	16519	Mm.5127	NM_008426	ENSMUSG00000026824	Kcnj3	GIRK-1|GIRK1|Kcnf3|Kir3.1	potassium inwardly-rectifying channel, subfamily J, member 3	protein-coding
mm_19281.1	chr2	89912238	89912241	-	1	NA	Intergenic	ERVB4_3-I_MM-int|LTR|ERVK	-17572	NM_146978	258980	Mm.223370	NM_146978	ENSMUSG00000049149	Olfr1258	MOR232-3	olfactory receptor 1258	protein-coding
mm_148863.1	chr19	6408400	6408410	+	1	NA	intron (NM_011242, intron 10 of 16)	intron (NM_011242, intron 10 of 16)	7822	NM_011242	19395	Mm.77017	NM_011242	ENSMUSG00000032946	Rasgrp2	CDC25L|Caldaggef1	RAS, guanyl releasing protein 2	protein-coding
mm_48187.1	chr5	137502403	137502436	-	1	NA	promoter-TSS (NM_028753)	promoter-TSS (NM_028753)	10	NM_028753	74097	Mm.290242	NM_028753	ENSMUSG00000029715	Pop7	0610037N12Rik|AI852017|Rpp20	processing of precursor 7, ribonuclease P family, (S. cerevisiae)	protein-coding
mm_5798.1	chr1	52155402	52155412	-	1	NA	intron (NM_001205313, intron 23 of 24)	intron (NM_001205313, intron 23 of 24)	35785	NM_001205313	20846	Mm.277406	NM_009283	ENSMUSG00000026104	Stat1	2010005J02Rik|AA408197	signal transducer and activator of transcription 1	protein-coding
mm_66382.1	chr7	43979400	43979402	-	1	NA	exon (NM_010116, exon 3 of 5)	exon (NM_010116, exon 3 of 5)	3340	NM_010116	13648	Mm.440884	NM_010116	ENSMUSG00000059042	Klk1b9	EGF-BP C|Egfbp-3|Egfbp3|KAL|Klk9|kallikrein|mGk-9	kallikrein 1-related peptidase b9	protein-coding
mm_102065.1	chr11	52257001	52257025	-	1	NA	exon (NM_009331, exon 7 of 10)	exon (NM_009331, exon 7 of 10)	25018	NM_011543	21402	Mm.42944	NM_011543	ENSMUSG00000036309	Skp1a	15kDa|2610043E24Rik|2610206H23Rik|EMC19|OCP-II|OCP2|SKP1|Tceb1l|p19A|p19Skp1	S-phase kinase-associated protein 1A	protein-coding
mm_50796.1	chr6	54264840	54264863	+	1	NA	promoter-TSS (NM_001311133)	promoter-TSS (NM_001311133)	-7	NM_001311133	69993	Mm.321147	NM_023543	ENSMUSG00000004633	Chn2	1700026N20Rik|4930557O16Rik|ARHGAP3|Bch	chimerin 2	protein-coding
mm_80727.1	chr9	92542431	92542439	+	1	NA	non-coding (NR_029474, exon 1 of 1)	non-coding (NR_029474, exon 1 of 1)	212	NM_001142916	26432	Mm.79983	NM_011961	ENSMUSG00000032374	Plod2	D530025C14Rik|LH2|Plod-2	procollagen lysine, 2-oxoglutarate 5-dioxygenase 2	protein-coding
mm_157584.1	chrX	53057184	53057200	-	1	NA	promoter-TSS (NR_038185)	promoter-TSS (NR_038185)	-2	NR_038184	72575	Mm.59516	NR_038184		C430049B03Rik	2700063P19Rik|9430052C07Rik|mir-322|mir-351|mir-503	RIKEN cDNA C430049B03 gene	ncRNA
mm_66851.1	chr7	50575949	50575956	-	1	NA	promoter-TSS (NR_045928)	promoter-TSS (NR_045928)	-68	NR_045928	73515	Mm.437440	NR_045928	ENSMUSG00000085265	Nell1os	1700081H22Rik	NEL-like 1, opposite strand	ncRNA
mm_21751.1	chr2	164828530	164828537	-	1	NA	promoter-TSS (NM_029370)	promoter-TSS (NM_029370)	1	NM_029370	75642	Mm.159541	NM_029370	ENSMUSG00000017767	Spata25	1700020C07Rik|Tsg23	spermatogenesis associated 25	protein-coding
mm_102113.1	chr11	53271076	53271088	-	1	NA	intron (NM_008300, intron 10 of 18)	intron (NM_008300, intron 10 of 18)	29397	NM_008300	15525	Mm.239865	NM_008300	ENSMUSG00000020361	Hspa4	70kDa|AI317151|APG-2|Hsp110|Hsp70RY|mKIAA4025	heat shock protein 4	protein-coding
mm_3028.1	chr1	133668008	133668025	+	1	NA	Intergenic	RLTR12D|LTR|ERVK	-6617	NM_144530	70579	Mm.245357	NM_144530	ENSMUSG00000102976	Zc3h11a	1110003F06Rik|5730454B08Rik|G630041M05Rik|Zc3hdc11a|Zc3hh11a|mKIAA0663	zinc finger CCCH type containing 11A	protein-coding
mm_128073.1	chr15	27663333	27663388	-	1	NA	intron (NM_001242423, intron 4 of 7)	intron (NM_001242423, intron 4 of 7)	18182	NM_001242424	223433	Mm.266485	NM_198301	ENSMUSG00000056069	Fam105a	9830126M18	family with sequence similarity 105, member A	protein-coding
mm_64242.1	chr7	141702575	141702595	+	1	NA	exon (NM_023566, exon 26 of 46)	exon (NM_023566, exon 26 of 46)	12245	NM_023566	17831	Mm.2041	NM_023566		Muc2	2010015E03Rik|MCM|wnn	mucin 2	protein-coding
mm_168120.1	chr10	18559390	18559395	+	1	NA	Intergenic	RLTR44C|LTR|ERVK	-13316	NM_019487	56016	Mm.35551	NM_019487	ENSMUSG00000019853	Hebp2	SOUL	heme binding protein 2	protein-coding
mm_108439.1	chr12	82339761	82339776	+	1	NA	intron (NM_172579, intron 1 of 20)	intron (NM_172579, intron 1 of 20)	28419	NM_172579	217692	Mm.261333	NM_172579	ENSMUSG00000042700	Sipa1l1	4931426N11Rik|AW213287|Spar|mKIAA0440	signal-induced proliferation-associated 1 like 1	protein-coding
mm_141562.1	chr17	32229438	32229468	-	1	NA	exon (NM_001286630, exon 3 of 20)	exon (NM_001286630, exon 3 of 20)	-12467	NR_102329	100043434		NR_102329		Gm4432	-	predicted gene 4432	pseudo
mm_29372.1	chr3	108722103	108722112	-	1	NA	5' UTR (NM_029522, exon 1 of 15)	5' UTR (NM_029522, exon 1 of 15)	192	NM_029522	76123	Mm.226941	NM_029522	ENSMUSG00000027883	Gpsm2	6230410J09Rik|LGN|Pins	G-protein signalling modulator 2 (AGS3-like, C. elegans)	protein-coding
mm_29686.1	chr3	123034885	123034895	-	1	NA	promoter-TSS (NM_021503)	promoter-TSS (NM_021503)	97	NM_021503	59006	Mm.141157	NM_021503	ENSMUSG00000028116	Myoz2	1110012I24Rik|Fatz-2|Myozl2	myozenin 2	protein-coding
mm_33647.1	chr4	133039447	133039471	+	1	NA	intron (NM_146155, intron 2 of 6)	CpG	27953	NM_146155	230793	Mm.31816	NM_146155	ENSMUSG00000037692	Ahdc1	D030015G18Rik	AT hook, DNA binding motif, containing 1	protein-coding
mm_79516.1	chr9	57528947	57528955	+	1	NA	intron (NM_007747, intron 1 of 4)	intron (NM_007747, intron 1 of 4)	7719	NM_007747	12858	Mm.273403	NM_007747	ENSMUSG00000000088	Cox5a	AA959768|CcOX	cytochrome c oxidase subunit Va	protein-coding
mm_92854.1	chr10	81524382	81524390	-	1	NA	promoter-TSS (NM_010304)	promoter-TSS (NM_010304)	-161	NM_010304	14676	Mm.1546	NM_010304	ENSMUSG00000034792	Gna15	G[a]15|Galpha15	guanine nucleotide binding protein, alpha 15	protein-coding
mm_98155.1	chr11	87617212	87617222	+	1	NA	promoter-TSS (NM_001045527)	promoter-TSS (NM_001045527)	53	NM_001045527	327992	Mm.390371	NM_001045527	ENSMUSG00000070345	Hsf5	Gm739|MLZ-220	heat shock transcription factor family member 5	protein-coding
mm_10532.1	chr2	16408548	16408564	+	1	NA	intron (NM_026162, intron 1 of 13)	intron (NM_026162, intron 1 of 13)	52252	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding
mm_164684.1	chr17	47521823	47521829	+	1	NA	intron (NM_001081635, intron 1 of 6)	intron (NM_001081635, intron 1 of 6)	16775	NM_001081635	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_137836.1	chr17	30901812	30901826	+	1	NA	promoter-TSS (NM_021332)	promoter-TSS (NM_021332)	-48	NM_021332	14652	Mm.390969	NM_021332	ENSMUSG00000024027	Glp1r	GLP-1R|GLP1Rc	glucagon-like peptide 1 receptor	protein-coding
mm_113504.1	chr13	37581059	37581110	+	1	NA	Intergenic	Intergenic	235739	NM_010745	17084	Mm.2639	NM_010745	ENSMUSG00000021423	Ly86	MD-1|MD1|ly86_tv2	lymphocyte antigen 86	protein-coding
mm_1732.1	chr1	75384670	75384682	+	1	NA	promoter-TSS (NM_001085370)	promoter-TSS (NM_001085370)	-934	NM_001085370	11790	Mm.275397	NM_007463	ENSMUSG00000026207	Speg	AW125581|Apeg1|BPEG|D1Bwg1450e|SPEGalpha|SPEGbeta|mKIAA1297	SPEG complex locus	protein-coding
mm_146798.1	chr18	20683002	20683006	-	1	NA	Intergenic	Intergenic	17754	NM_013697	22139	Mm.2108	NM_013697	ENSMUSG00000061808	Ttr	AA408768|AI787086|D17860|prealbumin	transthyretin	protein-coding
mm_128983.1	chr15	74833728	74833738	-	1	NA	Intergenic	Intergenic	7910	NM_001033229	110115	Mm.322606	NM_001033229	ENSMUSG00000075604	Cyp11b1	AA389061|CPN1|Cyp11b|Cyp11b-1|FHI	cytochrome P450, family 11, subfamily b, polypeptide 1	protein-coding
mm_32315.1	chr4	103348704	103348708	+	1	NA	intron (NM_025909, intron 7 of 8)	intron (NM_025909, intron 7 of 8)	-33794	NR_040673	622167	Mm.244115	NR_040673	ENSMUSG00000086136	Gm12718	OTTMUSG00000008109	predicted gene 12718	ncRNA
mm_89247.1	chr10	87859047	87859057	+	1	NA	promoter-TSS (NM_010512)	promoter-TSS (NM_010512)	0	NM_001111275	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_128724.1	chr15	64060310	64060318	-	1	NA	5' UTR (NM_144846, exon 1 of 12)	5' UTR (NM_144846, exon 1 of 12)	134	NM_144846	223601	Mm.246108	NM_144846	ENSMUSG00000022378	Fam49b	0910001A06Rik|AW122079	family with sequence similarity 49, member B	protein-coding
mm_161191.1	chr13	51101343	51101343	+	1	NA	promoter-TSS (NR_029463)	promoter-TSS (NR_029463)	-204	NM_001283029	20729	Mm.188432	NM_011462	ENSMUSG00000021395	Spin1	Spin	spindlin 1	protein-coding
mm_111548.1	chr12	100978090	100978129	-	1	NA	intron (NM_026681, intron 4 of 29)	intron (NM_026681, intron 4 of 29)	43659	NR_035421	100316805		NR_035421	ENSMUSG00000080575	Mir1190	Mirn1190|mmu-mir-1190	microRNA 1190	ncRNA
mm_15841.1	chr2	164745980	164746025	+	1	NA	promoter-TSS (NM_133763)	promoter-TSS (NM_133763)	-13	NM_133763	76233	Mm.440009	NM_133763	ENSMUSG00000017299	Dnttip1	6430706C13Rik	deoxynucleotidyltransferase, terminal, interacting protein 1	protein-coding
mm_132543.1	chr16	37882596	37882647	+	1	NA	3' UTR (NM_177093, exon 4 of 4)	3' UTR (NM_177093, exon 4 of 4)	14221	NM_177093	320184	Mm.390882	NM_177093	ENSMUSG00000034158	Lrrc58	1810012N18Rik|C330018J07Rik	leucine rich repeat containing 58	protein-coding
mm_152738.1	chr19	19001149	19001151	-	1	NA	promoter-TSS (NM_001289921)	promoter-TSS (NM_001289921)	-33	NM_001289921	225998	Mm.234641	NM_146095	ENSMUSG00000036192	Rorb	Nr1f2|RZR-beta|RZRB|Rorbeta|hstp	RAR-related orphan receptor beta	protein-coding
mm_95575.1	chr11	52405256	52405262	+	1	NA	intron (NM_153117, intron 2 of 2)	intron (NM_153117, intron 2 of 2)	8831	NM_153117	213673	Mm.291979	NM_153117	ENSMUSG00000036275	9530068E07Rik	C85061|Kct2	RIKEN cDNA 9530068E07 gene	protein-coding
mm_59515.1	chr7	27591608	27591651	+	1	NA	promoter-TSS (NM_001110208)	promoter-TSS (NM_001110208)	77	NM_001110208	11652	Mm.177194	NM_007434	ENSMUSG00000004056	Akt2	2410016A19Rik|AW554154|PKB|PKBbeta	thymoma viral proto-oncogene 2	protein-coding
mm_52905.1	chr6	122770696	122770707	+	1	NA	Intergenic	Intergenic	-27956	NM_011401	20527	Mm.395108	NM_011401	ENSMUSG00000003153	Slc2a3	AA408729|AL023014|AL024341|AU040424|C78366|Glut-3|Glut3	solute carrier family 2 (facilitated glucose transporter), member 3	protein-coding
mm_169111.1	chr13	44869949	44869955	-	1	NA	intron (NM_001205044, intron 4 of 18)	LSU-rRNA_Hsa|rRNA|rRNA	132144	NM_025772	94245	Mm.352311	NM_025772	ENSMUSG00000057531	Dtnbp1	5430437B18Rik|AW048963|Bloc1s8|dysbindin|sdy	dystrobrevin binding protein 1	protein-coding
mm_152439.1	chr19	10738940	10738956	-	1	NA	promoter-TSS (NM_007650)	promoter-TSS (NM_007650)	26	NM_007650	12507	Mm.779	NM_007650	ENSMUSG00000024669	Cd5	Ly-1|Ly-12|Ly-A|Lyt-1	CD5 antigen	protein-coding
mm_89085.1	chr10	83590981	83591000	+	1	NA	exon (NM_001033375, exon 31 of 33)	exon (NM_001033375, exon 31 of 33)	47049	NM_001033375	319277	Mm.491194	NM_001033375	ENSMUSG00000034560	Washc4	A230046K03Rik|AA589518|Kiaa1033|mKIAA1033	WASH complex subunit 4	protein-coding
mm_145260.1	chr18	52565681	52565687	+	1	NA	Intergenic	Intergenic	-35817	NM_001286182	16948	Mm.172	NM_010728	ENSMUSG00000024529	Lox	AI893619|TSC-160|rrg	lysyl oxidase	protein-coding
mm_49042.1	chr6	4760114	4760124	+	1	NA	3' UTR (NM_130877, exon 2 of 2)	3' UTR (NM_130877, exon 2 of 2)	12813	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_116465.1	chr13	43480974	43481005	-	1	NA	promoter-TSS (NM_019930)	promoter-TSS (NM_019930)	-16	NM_019930	56705	Mm.148781	NM_019930	ENSMUSG00000038546	Ranbp9	IBAP-1|Ibap1|RanBPM	RAN binding protein 9	protein-coding
mm_44206.1	chr5	3845018	3845050	-	1	NA	promoter-TSS (NM_172879)	promoter-TSS (NM_172879)	-139	NM_172879	242838	Mm.482273	NM_172879	ENSMUSG00000040367	Lrrd1	4932412H11Rik	leucine rich repeats and death domain containing 1	protein-coding
mm_82370.1	chr9	14614894	14614906	-	1	NA	promoter-TSS (NM_001081395)	promoter-TSS (NM_001081395)	100	NM_001081395	75723	Mm.159552	NM_001081395	ENSMUSG00000013076	Amotl1	2310010G08Rik|2310067L22Rik|4932416D09Rik|JEAP|mFLJ00155	angiomotin-like 1	protein-coding
mm_99986.1	chr11	114710862	114710883	+	1	NA	exon (NM_053273, exon 12 of 14)	exon (NM_053273, exon 12 of 14)	-16540	NM_001034878	432611	Mm.212764	NM_001034878	ENSMUSG00000034706	Dnaic2	C030015H18Rik|Dnai2|Gm728	dynein, axonemal, intermediate chain 2	protein-coding
mm_108100.1	chr12	74804324	74804343	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	372999	NM_172805	238271	Mm.44465	NM_172805	ENSMUSG00000034402	Kcnh5	Eag2	potassium voltage-gated channel, subfamily H (eag-related), member 5	protein-coding
mm_139677.1	chr17	57414633	57414643	+	1	NA	intron (NM_010130, intron 10 of 21)	L1_Mur2|LINE|L1	55952	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_3478.1	chr1	150105479	150105490	+	1	NA	exon (NM_011198, exon 10 of 10)	exon (NM_011198, exon 10 of 10)	5453	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_47088.1	chr5	117305524	117305539	-	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-13735	NM_001033311	231668	Mm.298603	NM_001033311	ENSMUSG00000066894	Vsig10	-	V-set and immunoglobulin domain containing 10	protein-coding
mm_388.1	chr1	34077295	34077302	+	1	NA	intron (NM_133833, intron 1 of 92)	intron (NM_133833, intron 1 of 92)	-40061	NR_105861	102466987		NR_105861	ENSMUSG00000105982	Mir6896	mmu-mir-6896	microRNA 6896	ncRNA
mm_32417.1	chr4	107048434	107048448	+	1	NA	3' UTR (NM_198438, exon 17 of 17)	3' UTR (NM_198438, exon 17 of 17)	18425	NM_025500	56280	Mm.29517	NM_025500	ENSMUSG00000028622	Mrpl37	2300004O14Rik|AI132596|MRP-L2|Rpml2	mitochondrial ribosomal protein L37	protein-coding
mm_136952.1	chr17	14943205	14943281	+	1	NA	promoter-TSS (NM_001083881)	promoter-TSS (NM_001083881)	59	NM_026451	67912	Mm.390949	NM_026451	ENSMUSG00000050088	1600012H06Rik	-	RIKEN cDNA 1600012H06 gene	protein-coding
mm_6275.1	chr1	69683012	69683032	-	1	NA	intron (NM_011770, intron 3 of 7)	intron (NM_011770, intron 3 of 7)	2938	NM_011770	22779	Mm.106343	NM_011770	ENSMUSG00000025997	Ikzf2	A730095J18Rik|Helios|Zfpn1a2|Znfn1a2	IKAROS family zinc finger 2	protein-coding
mm_33082.1	chr4	123921503	123921508	+	1	NA	intron (NM_017475, intron 3 of 6)	intron (NM_017475, intron 3 of 6)	4072	NM_017475	54170	Mm.220922	NM_017475	ENSMUSG00000028646	Rragc	AU041672|Gtr2|RAGC|TIB929|YGR163W	Ras-related GTP binding C	protein-coding
mm_97329.1	chr11	77009266	77009280	+	1	NA	intron (NM_010484, intron 1 of 13)	intron (NM_010484, intron 1 of 13)	10676	NM_010484	15567	Mm.300318	NM_010484	ENSMUSG00000020838	Slc6a4	5-HTT|AI323329|Htt|Sert	solute carrier family 6 (neurotransmitter transporter, serotonin), member 4	protein-coding
mm_17784.1	chr2	32982008	32982086	-	1	NA	promoter-TSS (NM_019488)	promoter-TSS (NM_019488)	9	NM_019488	56017	Mm.305754	NM_019488	ENSMUSG00000026791	Slc2a8	D2Ertd44e|GLUT8|GlutX1	solute carrier family 2, (facilitated glucose transporter), member 8	protein-coding
mm_34852.1	chr4	155495215	155495226	+	1	NA	intron (NM_001160017, intron 1 of 10)	B1F|SINE|Alu	3859	NM_001160016	14688	Mm.2344	NM_008142	ENSMUSG00000029064	Gnb1	AA409223|C77571|Gnb-1	guanine nucleotide binding protein (G protein), beta 1	protein-coding
mm_108113.1	chr12	75308653	75308671	+	1	NA	5' UTR (NM_023275, exon 1 of 5)	5' UTR (NM_023275, exon 1 of 5)	349	NM_023275	80837	Mm.27467	NM_023275	ENSMUSG00000046768	Rhoj	1110005O19Rik|AW210585|Arhj|TC10L|TCL	ras homolog family member J	protein-coding
mm_82049.1	chr9	122358896	122358898	+	1	NA	intron (NM_026179, intron 1 of 6)	intron (NM_026179, intron 1 of 6)	7281	NM_026179	67469	Mm.280254	NM_026179	ENSMUSG00000032540	Abhd5	1300003D03Rik|2010002J10Rik|CDS|CGI-58|IECN5|NCIE2	abhydrolase domain containing 5	protein-coding
mm_145625.1	chr18	61109666	61109678	+	1	NA	exon (NM_001037859, exon 3 of 22)	exon (NM_001037859, exon 3 of 22)	4100	NM_001037859	12978	Mm.22574	NM_007779	ENSMUSG00000024621	Csf1r	AI323359|CD115|CSF-1R|Csfmr|Fim-2|Fim2|Fms|M-CSF-R|M-CSFR	colony stimulating factor 1 receptor	protein-coding
mm_73389.1	chr8	105701143	105701190	+	1	NA	promoter-TSS (NM_019695)	promoter-TSS (NM_019695)	18	NM_001286344	56513	Mm.472753	NM_019695	ENSMUSG00000005699	Pard6a	0710008C04Rik|2610010A15Rik|PAR-6A|PAR6alpha|Par-6|Par6|Par6c|TAX40|Tip-40	par-6 family cell polarity regulator alpha	protein-coding
mm_36476.1	chr4	82850722	82850733	-	1	NA	intron (NM_026647, intron 2 of 8)	intron (NM_026647, intron 2 of 8)	8934	NM_026647	68268	Mm.32047	NM_026647	ENSMUSG00000028403	Zdhhc21	9130404H11Rik|AL024349|D130004H04Rik|dep	zinc finger, DHHC domain containing 21	protein-coding
mm_56006.1	chr6	86488304	86488324	-	1	NA	promoter-TSS (NR_040293)	promoter-TSS (NR_040293)	-87	NR_040292	381792	Mm.333223	NR_040292	ENSMUSG00000101655	2310040G24Rik	-	RIKEN cDNA 2310040G24 gene	ncRNA
mm_5353.1	chr1	25273200	25273212	-	1	NA	intron (NM_175642, intron 16 of 30)	intron (NM_175642, intron 16 of 30)	4748	NM_001204913	100504323	Mm.484176	NM_001204913		Gm20172	-	predicted gene, 20172	protein-coding
mm_142459.1	chr17	45595843	45595867	-	1	NA	promoter-TSS (NM_001199116)	promoter-TSS (NM_001199116)	47	NM_001199114	63959	Mm.29744	NM_022880	ENSMUSG00000023942	Slc29a1	1200014D21Rik|AA407560|ENT1	solute carrier family 29 (nucleoside transporters), member 1	protein-coding
mm_50133.1	chr6	41542607	41542622	+	1	NA	Intergenic	Intergenic	20838	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_55414.1	chr6	65024705	65024725	-	1	NA	Intergenic	RLTR23|LTR|ERV1	-17952	NM_007958	13990	Mm.99113	NM_007958	ENSMUSG00000029920	Smarcad1	AV081750|AW226546|D6Pas1|Etl1|mKIAA1122	SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1	protein-coding
mm_11401.1	chr2	31489075	31489078	+	1	NA	intron (NR_002687, intron 7 of 15)	intron (NR_002687, intron 7 of 15)	18768	NR_002687	432466	Mm.333323	NR_002687	ENSMUSG00000046687	Gm5424	EG432466	argininosuccinate synthase pseudogene	pseudo
mm_73960.1	chr8	120487615	120487649	+	1	NA	Intergenic	CpG	-1234	NM_198671	382034	Mm.334856	NM_198671	ENSMUSG00000031822	Gse1	2210013I18Rik|mKIAA0182	genetic suppressor element 1, coiled-coil protein	protein-coding
mm_47314.1	chr5	122459496	122459532	-	1	NA	exon (NM_009722, exon 16 of 21)	exon (NM_009722, exon 16 of 21)	37070	NM_019805	56317	Mm.37341	NM_019805	ENSMUSG00000029466	Anapc7	APC7|AW545589	anaphase promoting complex subunit 7	protein-coding
mm_116173.1	chr13	30819806	30819810	-	1	NA	intron (NM_025588, intron 26 of 27)	intron (NM_025588, intron 26 of 27)	70575	NM_013674	16364	Mm.4677	NM_013674	ENSMUSG00000021356	Irf4	AI385587|IRF-4|LSIRF|NF-EM5|Spip	interferon regulatory factor 4	protein-coding
mm_76543.1	chr8	88108816	88108817	-	1	NA	Intergenic	L1_Rod|LINE|L1	-9943	NM_029074	382030	Mm.216574	NM_029074	ENSMUSG00000036810	Cnep1r1	5033428A16Rik|NEP1-R1|Tmem188	CTD nuclear envelope phosphatase 1 regulatory subunit 1	protein-coding
mm_107766.1	chr12	59129758	59129818	+	1	NA	promoter-TSS (NM_001165254)	promoter-TSS (NM_001165254)	42	NM_001165254	338320	Mm.213215	NM_146034	ENSMUSG00000021000	Mia2	Ctage5|D12Bwg0579e|Mea6|Mgea|Mgea6	melanoma inhibitory activity 2	protein-coding
mm_37155.1	chr4	117122316	117122353	-	1	NA	intron (NR_024078, intron 3 of 6)	intron (NR_024078, intron 3 of 6)	3391	NR_024078	78611	Mm.446227	NM_001033187		Btbd19	9530048O09Rik|BB115071	BTB (POZ) domain containing 19	ncRNA
mm_152740.1	chr19	19032244	19032249	-	1	NA	intron (NM_001043354, intron 1 of 9)	intron (NM_001043354, intron 1 of 9)	-31129	NM_001289921	225998	Mm.234641	NM_146095	ENSMUSG00000036192	Rorb	Nr1f2|RZR-beta|RZRB|Rorbeta|hstp	RAR-related orphan receptor beta	protein-coding
mm_74674.1	chr8	13974677	13974698	-	1	NA	promoter-TSS (NM_173744)	promoter-TSS (NM_173744)	90	NM_173744	72148	Mm.5727	NM_173744	ENSMUSG00000050052	Tdrp	2610019F03Rik	testis development related protein	protein-coding
mm_65407.1	chr7	25237741	25237828	-	1	NA	promoter-TSS (NM_001031667)	promoter-TSS (NM_001031667)	67	NM_001031667	606496	Mm.491101	NM_001031667	ENSMUSG00000057177	Gsk3a	2700086H06Rik	glycogen synthase kinase 3 alpha	protein-coding
mm_51970.1	chr6	91758489	91758508	+	1	NA	3' UTR (NM_009320, exon 15 of 15)	3' UTR (NM_009320, exon 15 of 15)	48895	NM_001159507	243547	Mm.333264	NM_001033353	ENSMUSG00000030098	Grip2	-	glutamate receptor interacting protein 2	protein-coding
mm_172138.1	chr6	3552785	3552804	-	1	NA	intron (NM_001167750, intron 14 of 27)	ERVB7_1-LTR_MM|LTR|ERVK	54401	NM_001167750	73288	Mm.45539	NM_024260	ENSMUSG00000001376	Vps50	1700034M03Rik|8430415E05Rik|BLM|C87205|Ccdc132|mKIAA1861	VPS50 EARP/GARPII complex subunit	protein-coding
mm_155658.1	chrX	86044205	86044214	+	1	NA	promoter-TSS (NM_028554)	promoter-TSS (NM_028554)	10	NM_028554	73495	Mm.159020	NM_028554	ENSMUSG00000035454	Samt3	1700072E05Rik	spermatogenesis associated multipass transmembrane protein 3	protein-coding
mm_38336.1	chr4	137666356	137666359	-	1	NA	intron (NR_138591, intron 1 of 23)	intron (NR_138591, intron 1 of 23)	1631	NR_138591	110351	Mm.180763	NM_029563	ENSMUSG00000041351	Rap1gap	1300019I11Rik|2310004O14Rik|AI427470|ARPP-90|Gap|Rap1GAP1|Rap1ga1	Rap1 GTPase-activating protein	protein-coding
mm_50639.1	chr6	51330651	51330665	+	1	NA	Intergenic	Intergenic	-49052	NR_110455	625167	Mm.389772	NR_110455	ENSMUSG00000107660	Gm6559	EG625167	predicted gene 6559	ncRNA
mm_73916.1	chr8	119666488	119666496	+	1	NA	5' UTR (NM_023395, exon 1 of 7)	5' UTR (NM_023395, exon 1 of 7)	127	NM_023395	67866	Mm.87599	NM_023395	ENSMUSG00000023336	Wfdc1	2310058A03Rik|ps20	WAP four-disulfide core domain 1	protein-coding
mm_130516.1	chr15	98867424	98867434	-	1	NA	intron (NM_001033276, intron 1 of 54)	intron (NM_001033276, intron 1 of 54)	3776	NM_001033276	381022	Mm.264889	NM_001033276	ENSMUSG00000048154	Kmt2d	ALR|BC032281|BC058659|C430014K11Rik|KMT2B|Mll2|Mll4	lysine (K)-specific methyltransferase 2D	protein-coding
mm_1518.1	chr1	72824483	72824501	+	1	NA	promoter-TSS (NM_008342)	promoter-TSS (NM_008342)	12	NM_008342	16008	Mm.141936	NM_008342	ENSMUSG00000039323	Igfbp2	AI255832|IBP-2|Igfbp-2|mIGFBP-2	insulin-like growth factor binding protein 2	protein-coding
mm_87306.1	chr10	42678891	42678948	+	1	NA	promoter-TSS (NM_172416)	promoter-TSS (NM_172416)	3	NM_172416	14628	Mm.46636	NM_172416	ENSMUSG00000038280	Ostm1	1200002H13Rik|HSPC019|gl	osteopetrosis associated transmembrane protein 1	protein-coding
mm_75096.1	chr8	34107817	34107842	-	1	NA	promoter-TSS (NM_001293758)	promoter-TSS (NM_001293758)	-15	NM_001293758	22428	Mm.150373	NM_011722	ENSMUSG00000031516	Dctn6	AU044699|WS-3|p27	dynactin 6	protein-coding
mm_106917.1	chr12	8220004	8220011	+	1	NA	intron (NM_001167767, intron 1 of 5)	intron (NM_001167767, intron 1 of 5)	11880	NM_001167767	68832	Mm.25608	NM_172401	ENSMUSG00000037669	Ldah	1110057K04Rik|mLDAH	lipid droplet associated hydrolase	protein-coding
mm_121421.1	chr14	120275665	120275682	+	1	NA	promoter-TSS (NM_207515)	promoter-TSS (NM_207515)	4	NM_175341	105559	Mm.238266	NM_175341	ENSMUSG00000022139	Mbnl2	1110002M11Rik|AI047808|AI837313|AI849185|AL118326|MBLL|R75232|mKIAA4072	muscleblind-like 2	protein-coding
mm_135826.1	chr16	58507642	58507662	-	1	NA	intron (NM_018784, intron 1 of 10)	intron (NM_018784, intron 1 of 10)	15660	NM_018784	54613	Mm.212742	NM_018784	ENSMUSG00000022747	St3gal6	1700023B24Rik|AI930218|AW552396|Siat10|St3galVI	ST3 beta-galactoside alpha-2,3-sialyltransferase 6	protein-coding
mm_48808.1	chr5	148969871	148969913	-	1	NA	Intergenic	Intergenic	19642	NR_040686	71473	Mm.90306	NR_040686	ENSMUSG00000079069	8430423G03Rik	-	RIKEN cDNA 8430423G03 gene	ncRNA
mm_111220.1	chr12	84546156	84546194	-	1	NA	Intergenic	Intergenic	-23653	NM_007701	12677	Mm.4405	NM_007701	ENSMUSG00000021239	Vsx2	Chx10|Hox-10|Hox10|or	visual system homeobox 2	protein-coding
mm_39026.1	chr4	152132346	152132361	-	1	NA	intron (NM_207688, intron 3 of 10)	intron (NM_207688, intron 3 of 10)	-3428	NM_019585	56226	Mm.264215	NM_019585	ENSMUSG00000028943	Espn	je	espin	protein-coding
mm_48313.1	chr5	138755412	138755432	-	1	NA	5' UTR (NM_030565, exon 1 of 10)	5' UTR (NM_030565, exon 1 of 10)	341	NM_030565	80752	Mm.320355	NM_030565	ENSMUSG00000025854	Fam20c	C76981|DMP-4|DMP4|GEF-CK|mKIAA4081	family with sequence similarity 20, member C	protein-coding
mm_18018.1	chr2	38511550	38511558	-	1	NA	promoter-TSS (NM_021606)	promoter-TSS (NM_021606)	-143	NM_021606	59126	Mm.143818	NM_021606	ENSMUSG00000026749	Nek6	1300007C09Rik	NIMA (never in mitosis gene a)-related expressed kinase 6	protein-coding
mm_162065.1	chrX	9885626	9885626	+	1	NA	promoter-TSS (NM_001290728)	promoter-TSS (NM_001290728)	5	NM_001290728	236643	Mm.246606	NM_177704	ENSMUSG00000054453	Sytl5	ENSMUSG00000054453|slp5	synaptotagmin-like 5	protein-coding
mm_134440.1	chr16	18247405	18247419	-	1	NA	exon (NM_011239, exon 2 of 6)	exon (NM_011239, exon 2 of 6)	1282	NM_011239	19385	Mm.235287	NM_011239	ENSMUSG00000005732	Ranbp1	Htf9a	RAN binding protein 1	protein-coding
mm_12102.1	chr2	61578535	61578540	+	1	NA	promoter-TSS (NM_011529)	promoter-TSS (NM_011529)	-49	NM_011529	21353	Mm.244393	NM_011529	ENSMUSG00000064289	Tank	C86182|E430026L09Rik|I-TRAF	TRAF family member-associated Nf-kappa B activator	protein-coding
mm_55502.1	chr6	69776334	69776342	-	1	NA	Intergenic	Intergenic	-449164	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_154174.1	chr19	58730565	58730582	-	1	NA	exon (NM_018874, exon 4 of 13)	exon (NM_018874, exon 4 of 13)	1686	NM_018874	18946	Mm.10753	NM_018874	ENSMUSG00000042179	Pnliprp1	Plrp1	pancreatic lipase related protein 1	protein-coding
mm_25218.1	chr3	103851270	103851279	+	1	NA	intron (NM_001142960, intron 3 of 3)	intron (NM_001142960, intron 3 of 3)	-8521	NR_104070	19260	Mm.395	NM_008979	ENSMUSG00000027843	Ptpn22	70zpep|PEP|Ptpn8	protein tyrosine phosphatase, non-receptor type 22 (lymphoid)	protein-coding
mm_18055.1	chr2	39226245	39226263	-	1	NA	promoter-TSS (NM_024209)	promoter-TSS (NM_024209)	84	NM_024209	67857	Mm.389242	NM_024209	ENSMUSG00000026753	Ppp6c	2310003C10Rik	protein phosphatase 6, catalytic subunit	protein-coding
mm_26962.1	chr3	21988293	21988312	-	1	NA	Intergenic	Intergenic	-88350	NM_030732	81004	Mm.202966	NM_030732	ENSMUSG00000027630	Tbl1xr1	8030499H02Rik|A630076E03Rik|AW539987|C21|C230089I12Rik|DC42|Ira1|TBLR1	transducin (beta)-like 1X-linked receptor 1	protein-coding
mm_55488.1	chr6	69378518	69378527	-	1	NA	Intergenic	Intergenic	-51348	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_35297.1	chr4	22486720	22486734	-	1	NA	3' UTR (NM_008899, exon 1 of 1)	3' UTR (NM_008899, exon 1 of 1)	1639	NM_008899	18992	Mm.129387	NM_008899	ENSMUSG00000095139	Pou3f2	9430075J19Rik|A230098E07Rik|Brn-2|Brn2|OTF-7|Otf7|oct-7	POU domain, class 3, transcription factor 2	protein-coding
mm_65206.1	chr7	19697505	19697522	-	1	NA	exon (NM_009696, exon 3 of 4)	exon (NM_009696, exon 3 of 4)	885	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_56920.1	chr6	119399120	119399121	-	1	NA	intron (NM_197985, intron 1 of 7)	Lx5c|LINE|L1	18363	NM_197985	68465	Mm.291826	NM_197985	ENSMUSG00000030168	Adipor2	1110001I14Rik|ADCR2|AI115388|AW554121|D6Ucla1e|Paqr2	adiponectin receptor 2	protein-coding
mm_118003.1	chr13	100552705	100552721	-	1	NA	promoter-TSS (NM_008756)	promoter-TSS (NM_008756)	-215	NM_008756	18260	Mm.4807	NM_008756	ENSMUSG00000021638	Ocln	AI503564|Ocl	occludin	protein-coding
mm_150893.1	chr19	45445549	45445558	+	1	NA	intron (NM_001286465, intron 2 of 14)	intron (NM_001286465, intron 2 of 14)	81819	NM_001037758	12234	Mm.119717	NM_009771	ENSMUSG00000025217	Btrc	Beta-Trcp1|E3RS-IkappaB|E3RSIkappaB|FWD1|Fbw1a|HOS|Slimb|b-TrCP|beta-TrCP	beta-transducin repeat containing protein	protein-coding
mm_123324.1	chr14	62966184	62966188	-	1	NA	Intergenic	Intergenic	18324	NM_001037751	432867	Mm.99387	NM_001037751	ENSMUSG00000075574	Defb48	Defb42|EG432867	defensin beta 48	protein-coding
mm_118881.1	chr14	25869636	25869636	+	1	NA	intron (NM_013469, intron 2 of 14)	intron (NM_013469, intron 2 of 14)	27481	NM_013469	11744	Mm.294083	NM_013469	ENSMUSG00000021866	Anxa11	A830099O17Rik|Anx11	annexin A11	protein-coding
mm_85921.1	chr9	111271569	111271591	-	1	NA	promoter-TSS (NM_026810)	promoter-TSS (NM_026810)	28	NM_026810	17350	Mm.486383	NM_026810	ENSMUSG00000032498	Mlh1	1110035C23Rik|AI317206|AI325952|AI561766	mutL homolog 1	protein-coding
mm_71484.1	chr8	46739842	46739846	+	1	NA	promoter-TSS (NM_008391)	promoter-TSS (NM_008391)	99	NM_008391	16363	Mm.1149	NM_008391	ENSMUSG00000031627	Irf2	9830146E22Rik|AI646973|Irf-2	interferon regulatory factor 2	protein-coding
mm_172636.1	chr8	20580135	20580139	+	1	NA	Intergenic	B3A|SINE|B2	-34790	NM_001270553	100861668	Mm.491087	NM_001270553	ENSMUSG00000095294	Gm21119	-	predicted gene, 21119	protein-coding
mm_148298.1	chr18	82687026	82687041	-	1	NA	intron (NM_177832, intron 1 of 29)	B1_Mur1|SINE|Alu	5701	NM_177832	329002	Mm.34438	NM_177832	ENSMUSG00000041258	Zfp236	AI447957|Gm335	zinc finger protein 236	protein-coding
mm_23135.1	chr3	38485196	38485211	+	1	NA	promoter-TSS (NM_001167883)	promoter-TSS (NM_001167883)	-387	NM_001167883	99696	Mm.290937	NM_001033198	ENSMUSG00000044864	Ankrd50	AI662170|E430012K20Rik|mKIAA1223|mKIAA3019	ankyrin repeat domain 50	protein-coding
mm_117338.1	chr13	69534349	69534395	-	1	NA	promoter-TSS (NM_198600)	promoter-TSS (NM_198600)	-508	NM_001169131	210106	Mm.315959	NM_198600	ENSMUSG00000034575	Papd7	LAK-1|POLK|Pols|TRF4|TRF4-1	PAP associated domain containing 7	protein-coding
mm_64708.1	chr7	4628326	4628336	-	1	NA	3' UTR (NM_023440, exon 3 of 3)	3' UTR (NM_023440, exon 3 of 3)	2151	NM_023440	68255	Mm.389784	NM_023440	ENSMUSG00000045282	Tmem86b	C330014O21Rik	transmembrane protein 86B	protein-coding
mm_24150.1	chr3	88340278	88340281	+	1	NA	intron (NM_178246, intron 1 of 21)	(T)n|Simple_repeat|Simple_repeat	4019	NM_178246	229512	Mm.439830	NM_173188	ENSMUSG00000001415	Smg5	BC024683|mKIAA1089	Smg-5 homolog, nonsense mediated mRNA decay factor (C. elegans)	protein-coding
mm_42238.1	chr5	113772787	113772827	+	1	NA	promoter-TSS (NM_025526)	promoter-TSS (NM_025526)	-5	NM_025526	66383	Mm.29497	NM_025526	ENSMUSG00000025825	Iscu	2310020H20Rik|AA407971|Nifu|Nifun	iron-sulfur cluster assembly enzyme	protein-coding
mm_22470.1	chr3	5090269	5090315	+	1	NA	Intergenic	Intergenic	-128262	NM_030708	80892	Mm.41522	NM_030708	ENSMUSG00000025255	Zfhx4	A930021B15|C130041O22Rik|Zfh-4|Zfh4	zinc finger homeodomain 4	protein-coding
mm_72962.1	chr8	92827449	92827457	+	1	NA	5' UTR (NM_008610, exon 1 of 13)	5' UTR (NM_008610, exon 1 of 13)	156	NM_008610	17390	Mm.29564	NM_008610	ENSMUSG00000031740	Mmp2	Clg4a|GelA|MMP-2	matrix metallopeptidase 2	protein-coding
mm_143471.1	chr17	71127539	71127567	-	1	NA	TTS (NM_001083934)	TTS (NM_001083934)	-56425	NM_022882	64898	Mm.227924	NM_022882	ENSMUSG00000024052	Lpin2	2610511G02Rik|AI481352|AW742896	lipin 2	protein-coding
mm_37555.1	chr4	126162645	126162655	-	1	NA	promoter-TSS (NM_025856)	promoter-TSS (NM_025856)	15	NM_025856	66938	Mm.29813	NM_025856	ENSMUSG00000073758	Sh3d21	1700029G01Rik|AU019788	SH3 domain containing 21	protein-coding
mm_143513.1	chr17	72918152	72918160	-	1	NA	promoter-TSS (NM_029999)	promoter-TSS (NM_029999)	-149	NM_029999	77889	Mm.154109	NM_029999	ENSMUSG00000024063	Lbh	1810009F10Rik|6720416L16Rik	limb-bud and heart	protein-coding
mm_101143.1	chr11	16508099	16508139	-	1	NA	exon (NM_011343, exon 1 of 4)	exon (NM_011343, exon 1 of 4)	365	NM_011343	20335	Mm.325350	NM_011343	ENSMUSG00000078974	Sec61g	-	SEC61, gamma subunit	protein-coding
mm_79074.1	chr9	46241505	46241530	+	1	NA	exon (NM_007468, exon 2 of 3)	exon (NM_007468, exon 2 of 3)	673	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_23608.1	chr3	65516122	65516136	+	1	NA	Intergenic	Intergenic	-12318	NM_178892	99929	Mm.246398	NM_178892	ENSMUSG00000034640	Tiparp	ARTD14|AW558171|PARP7	TCDD-inducible poly(ADP-ribose) polymerase	protein-coding
mm_125909.1	chr15	76009864	76009893	+	1	NA	promoter-TSS (NM_001168253)	promoter-TSS (NM_001168253)	-380	NM_001168253	105732	Mm.267178	NM_134087	ENSMUSG00000046761	Fam83h	AA409316	family with sequence similarity 83, member H	protein-coding
mm_146478.1	chr18	89197422	89197445	+	1	NA	promoter-TSS (NM_178687)	promoter-TSS (NM_178687)	6	NM_001039149	225825	Mm.139293	NM_178687	ENSMUSG00000034028	Cd226	BC051526|DNAM-1|DNAM1|Pta1|TLiSA1	CD226 antigen	protein-coding
mm_131471.1	chr16	17070128	17070215	+	1	NA	promoter-TSS (NM_023249)	promoter-TSS (NM_023249)	32	NM_001291047	106369	Mm.237941	NM_023249	ENSMUSG00000022773	Ypel1	0610009L05Rik|1700016N17Rik|1700019O22Rik|4921520K19Rik|4930511F14Rik|AV118478|DGL-1|Dgl1|Ppil2|mdgl-1	yippee-like 1 (Drosophila)	protein-coding
mm_138371.1	chr17	35001350	35001371	+	1	NA	promoter-TSS (NM_033075)	promoter-TSS (NM_033075)	453	NM_011690	22321	Mm.28420	NM_011690	ENSMUSG00000007029	Vars	Bat6|D17H6S56E|G7a|Vars2	valyl-tRNA synthetase	protein-coding
mm_92260.1	chr10	70923787	70923805	-	1	NA	3' UTR (NM_001347189, exon 22 of 22)	3' UTR (NM_001347189, exon 22 of 22)	235894	NM_031397	83675	Mm.286834	NM_031397	ENSMUSG00000014329	Bicc1	Bic-C|bpk|jcpk	BicC family RNA binding protein 1	protein-coding
mm_137558.1	chr17	27655657	27655659	+	1	NA	promoter-TSS (NM_001286743)	promoter-TSS (NM_001286743)	67	NM_001286743	23969	Mm.4926	NM_011861	ENSMUSG00000040276	Pacsin1	A830061D09Rik|H74|mKIAA1379|syndapin	protein kinase C and casein kinase substrate in neurons 1	protein-coding
mm_150557.1	chr19	39330272	39330282	+	1	NA	exon (NM_007815, exon 9 of 9)	exon (NM_007815, exon 9 of 9)	43192	NM_007815	13095	Mm.20764	NM_007815	ENSMUSG00000003053	Cyp2c29	AHOH|AHOHase|AI159681|AI196010|Ah-2|Ahh-1|Cyp2c|P450-2C	cytochrome P450, family 2, subfamily c, polypeptide 29	protein-coding
mm_37693.1	chr4	129248432	129248498	-	1	NA	promoter-TSS (NM_001033189)	promoter-TSS (NM_001033189)	-22	NM_001033189	97130	Mm.331907	NM_001033189	ENSMUSG00000050390	C77080	Kiaa1522|mKIAA1522	expressed sequence C77080	protein-coding
mm_117811.1	chr13	97747374	97747384	-	1	NA	Intergenic	Intergenic	187379	NR_046157	328314	Mm.138047	NR_046157	ENSMUSG00000110235	Gm5086	B230311A21|EG328314	predicted gene 5086	ncRNA
mm_133099.1	chr16	64852357	64852388	+	1	NA	promoter-TSS (NM_001347245)	promoter-TSS (NM_001347245)	287	NM_178647	106143	Mm.10160	NM_178647	ENSMUSG00000054604	Cggbp1	AA960172|AL023996|AW045841	CGG triplet repeat binding protein 1	protein-coding
mm_75385.1	chr8	45410365	45410387	-	1	NA	intron (NM_126166, intron 1 of 6)	intron (NM_126166, intron 1 of 6)	163	NM_126166	142980	Mm.33874	NM_126166	ENSMUSG00000031639	Tlr3	AI957183	toll-like receptor 3	protein-coding
mm_153893.1	chr19	46985364	46985368	-	1	NA	intron (NM_001164363, intron 1 of 17)	intron (NM_001164363, intron 1 of 17)	-15799	NM_001164365	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_70726.1	chr8	18595145	18595186	+	1	NA	promoter-TSS (NM_173189)	promoter-TSS (NM_173189)	-8	NM_173189	244329	Mm.235296	NM_173189	ENSMUSG00000039842	Mcph1	5430437K10Rik|BRIT1|D030046N04Rik|MCT	microcephaly, primary autosomal recessive 1	protein-coding
mm_124813.1	chr15	8968289	8968293	+	1	NA	5' UTR (NM_198024, exon 1 of 14)	5' UTR (NM_198024, exon 1 of 14)	342	NM_198024	223332	Mm.321371	NM_198024	ENSMUSG00000048424	Ranbp3l	C130037N17Rik	RAN binding protein 3-like	protein-coding
mm_158307.1	chrX	122397352	122397425	-	1	NA	promoter-TSS (NM_138742)	promoter-TSS (NM_138742)	-3	NM_138742	54561	Mm.490573	NM_138742	ENSMUSG00000055733	Nap1l3	MB20	nucleosome assembly protein 1-like 3	protein-coding
mm_82232.1	chr9	3036094	3036128	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	2632	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_105725.1	chr11	109011874	109011882	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	91529	NM_015732	12006	Mm.71710	NM_015732	ENSMUSG00000000142	Axin2	Axi1|Axil|Conductin	axin 2	protein-coding
mm_63100.1	chr7	122562219	122562222	+	1	NA	intron (NM_001316672, intron 9 of 16)	intron (NM_001316672, intron 9 of 16)	-109524	NM_019430	54376	Mm.444212	NM_019430	ENSMUSG00000066189	Cacng3	-	calcium channel, voltage-dependent, gamma subunit 3	protein-coding
mm_41495.1	chr5	92323785	92323789	+	1	NA	3' UTR (NM_008599, exon 4 of 4)	3' UTR (NM_008599, exon 4 of 4)	4292	NM_008599	17329	Mm.766	NM_008599	ENSMUSG00000029417	Cxcl9	BB139920|CMK|Mig|MuMIG|Scyb9|crg-10	chemokine (C-X-C motif) ligand 9	protein-coding
mm_91299.1	chr10	24916116	24916128	-	1	NA	exon (NM_007482, exon 7 of 8)	exon (NM_007482, exon 7 of 8)	5458	NR_105870	102465545		NR_105870	ENSMUSG00000099181	Mir6905	Gm27879|mmu-mir-6905	microRNA 6905	ncRNA
mm_18474.1	chr2	62412173	62412183	-	1	NA	promoter-TSS (NM_010074)	promoter-TSS (NM_010074)	53	NM_010074	13482	Mm.1151	NM_010074	ENSMUSG00000035000	Dpp4	Cd26|Dpp-4|THAM	dipeptidylpeptidase 4	protein-coding
mm_119107.1	chr14	31001384	31001407	+	1	NA	promoter-TSS (NM_001165930)	promoter-TSS (NM_001165930)	2	NM_001165930	76485	Mm.8766	NM_029626	ENSMUSG00000021916	Glt8d1	2410004H05Rik|5430414N14Rik|AI450005	glycosyltransferase 8 domain containing 1	protein-coding
mm_137104.1	chr17	21707771	21707799	+	1	NA	promoter-TSS (NM_001008501)	promoter-TSS (NM_001008501)	44	NM_001008501	240034	Mm.34723	NM_001008501	ENSMUSG00000067928	Zfp760	9430018I06|BC029103	zinc finger protein 760	protein-coding
mm_122207.1	chr14	31830654	31830733	-	1	NA	promoter-TSS (NM_001024604)	promoter-TSS (NM_001024604)	-278	NM_001024604	105522	Mm.37660	NM_001024604	ENSMUSG00000014496	Ankrd28	AI465466|AI604979|E430019N21Rik|mKIAA0379	ankyrin repeat domain 28	protein-coding
mm_44011.1	chr5	147077546	147077585	+	1	NA	promoter-TSS (NM_080795)	promoter-TSS (NM_080795)	219	NM_009087	20018	Mm.317557	NM_009087	ENSMUSG00000029642	Polr1d	1110003G10Rik|AC19|RPA16|Rpo1-3	polymerase (RNA) I polypeptide D	protein-coding
mm_40795.1	chr5	67608365	67608395	+	1	NA	5' UTR (NM_001033415, exon 1 of 2)	5' UTR (NM_001033415, exon 1 of 2)	497	NM_001033415	330096	Mm.442747	NM_001033415	ENSMUSG00000050010	Shisa3	D830007B15Rik	shisa family member 3	protein-coding
mm_78668.1	chr9	40730955	40730978	+	1	NA	intron (NM_133733, intron 1 of 6)	intron (NM_133733, intron 1 of 6)	45002	NM_133733	71566	Mm.280560	NM_133733	ENSMUSG00000032024	Clmp	9030425E11Rik|ACAM|ASP5|AW557819	CXADR-like membrane protein	protein-coding
mm_128283.1	chr15	37007359	37007372	-	1	NA	promoter-TSS (NM_026521)	promoter-TSS (NM_026521)	37	NM_026521	68036	Mm.371631	NM_026521	ENSMUSG00000062397	Zfp706	3110006P09Rik|AA793007|AW536850|C77232|Znf706	zinc finger protein 706	protein-coding
mm_99124.1	chr11	100206458	100206475	+	1	NA	promoter-TSS (NM_001313957)	promoter-TSS (NM_001313957)	-436	NM_001313957	16664	Mm.439898	NM_016958	ENSMUSG00000045545	Krt14	AI626930|CK-14|K14|Krt-1.14|Krt1-14	keratin 14	protein-coding
mm_115411.1	chr13	114818233	114818303	+	1	NA	promoter-TSS (NM_001113375)	promoter-TSS (NM_001113375)	31	NM_001113374	17434	Mm.19027	NM_013826	ENSMUSG00000015536	Mocs2	AI415403	molybdenum cofactor synthesis 2	protein-coding
mm_43041.1	chr5	124034793	124034802	+	1	NA	Intergenic	Intergenic	-2537	NM_177876	330192	Mm.4079	NM_177876	ENSMUSG00000066278	Vps37b	2300007F24Rik|AI415429|BC026744	vacuolar protein sorting 37B	protein-coding
mm_70140.1	chr7	143299848	143299849	-	1	NA	intron (NM_008434, intron 11 of 15)	intron (NM_008434, intron 11 of 15)	-3301	NR_001461	63830	Mm.356096	NR_001461	ENSMUSG00000101609	Kcnq1ot1	Kvlqt1-as|Lit1|Tssc8	KCNQ1 overlapping transcript 1	ncRNA
mm_7378.1	chr1	107084133	107084139	-	1	NA	promoter-TSS (NM_201376)	promoter-TSS (NM_201376)	-656	NM_201376	394252	Mm.352392	NM_201376	ENSMUSG00000058017	Serpinb3d	Serpinb3l1	serine (or cysteine) peptidase inhibitor, clade B (ovalbumin), member 3D	protein-coding
mm_148618.1	chr19	5406090	5406093	+	1	NA	promoter-TSS (NR_015545)	promoter-TSS (NR_015545)	-724	NR_015545	74931	Mm.388511	NR_015545	ENSMUSG00000086938	4930481A15Rik	-	RIKEN cDNA 4930481A15 gene	ncRNA
mm_160471.1	chr8	117082478	117082478	-	1	NA	promoter-TSS (NM_029686)	promoter-TSS (NM_029686)	-29	NM_029686	76645	Mm.159753	NM_029686	ENSMUSG00000034416	Pkd1l2	1700126L06Rik	polycystic kidney disease 1 like 2	protein-coding
mm_1129.1	chr1	60343367	60343385	+	1	NA	promoter-TSS (NM_030013)	promoter-TSS (NM_030013)	76	NM_001313721	77951	Mm.197640	NM_030013	ENSMUSG00000049439	Cyp20a1	A930011N14Rik|Cypm	cytochrome P450, family 20, subfamily a, polypeptide 1	protein-coding
mm_115423.1	chr13	117220585	117220637	+	1	NA	promoter-TSS (NM_010330)	promoter-TSS (NM_010330)	38	NM_010330	13723	Mm.274926	NM_010330	ENSMUSG00000021728	Emb	AL022799|Gp70	embigin	protein-coding
mm_81245.1	chr9	107975497	107975510	+	1	NA	promoter-TSS (NM_023738)	promoter-TSS (NM_023738)	-64	NM_023738	74153	Mm.277125	NM_023738	ENSMUSG00000032596	Uba7	1300004C08Rik|Ube1l	ubiquitin-like modifier activating enzyme 7	protein-coding
mm_121156.1	chr14	102981297	102981326	+	1	NA	3' UTR (NM_177715, exon 1 of 1)	3' UTR (NM_177715, exon 1 of 1)	1321	NR_039592	100628599		NR_039592	ENSMUSG00000092901	Mir5130	mir-5130|mmu-mir-5130|mu-mir-5130	microRNA 5130	ncRNA
mm_150650.1	chr19	41911946	41911966	+	1	NA	promoter-TSS (NM_023418)	promoter-TSS (NM_023418)	85	NM_023418	18648	Mm.16783	NM_023418	ENSMUSG00000011752	Pgam1	2310050F24Rik|Pgam-1	phosphoglycerate mutase 1	protein-coding
mm_76971.1	chr8	106282148	106282161	-	1	NA	promoter-TSS (NR_126090)	promoter-TSS (NR_126090)	-75	NR_126091	75044	Mm.445896	NR_126090		4930506A18Rik	-	RIKEN cDNA 4930506A18 gene	ncRNA
mm_46318.1	chr5	100643213	100643252	-	1	NA	Intergenic	Intergenic	31024	NM_027978	71883	Mm.260661	NM_027978	ENSMUSG00000029319	Coq2	2310002F18Rik|PHB:PPT	coenzyme Q2 4-hydroxybenzoate polyprenyltransferase	protein-coding
mm_83580.1	chr9	48340683	48340685	-	1	NA	5' UTR (NM_030069, exon 1 of 6)	5' UTR (NM_030069, exon 1 of 6)	214	NM_030069	78252	Mm.31626	NM_030069	ENSMUSG00000032028	Nxpe2	4432416J03Rik|AI323362|Fam55b	neurexophilin and PC-esterase domain family, member 2	protein-coding
mm_89405.1	chr10	90576873	90576887	+	1	NA	5' UTR (NM_181398, exon 1 of 10)	5' UTR (NM_181398, exon 1 of 10)	189	NM_181398	77531	Mm.440605	NM_181398	ENSMUSG00000058589	Anks1b	AIDA-1b|C030032C09Rik|E530015N03Rik|ENSMUSG00000078431|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding
mm_169453.1	chr14	61324974	61324992	-	1	NA	Intergenic	Intergenic	15230	NM_177337	219144	Mm.206566	NM_177337	ENSMUSG00000043157	Arl11	ARLTS1|C730007L20Rik	ADP-ribosylation factor-like 11	protein-coding
mm_6680.1	chr1	80574186	80574200	-	1	NA	exon (NM_001285927, exon 17 of 56)	exon (NM_001285927, exon 17 of 56)	91159	NM_001285927	210293	Mm.133473	NM_175291	ENSMUSG00000038608	Dock10	9330153B10Rik|A630054M16Rik|Jr4|Jr5|R75174|ZIZ3|Zizimin3|mKIAA0694	dedicator of cytokinesis 10	protein-coding
mm_119382.1	chr14	41136346	41136355	+	1	NA	TTS (NM_023134)	TTS (NM_023134)	4562	NM_023134	20387	Mm.46062	NM_023134	ENSMUSG00000021789	Sftpa1	SP-A|Sftp-1|Sftp1	surfactant associated protein A1	protein-coding
mm_149506.1	chr19	11965693	11965706	+	1	NA	promoter-TSS (NM_001033174)	promoter-TSS (NM_001033174)	-145	NM_001033174	76303	Mm.291279	NM_001033174	ENSMUSG00000024687	Osbp	1110018F06Rik|AW559088|mKIAA4220	oxysterol binding protein	protein-coding
mm_73466.1	chr8	106668613	106668629	+	1	NA	3' UTR (NM_009864, exon 16 of 16)	3' UTR (NM_009864, exon 16 of 16)	-14447	NM_173037	272538	Mm.87151	NM_173037	ENSMUSG00000041949	Tango6	AW413431|E330010G16|Tmco7	transport and golgi organization 6	protein-coding
mm_136719.1	chr17	8165559	8165593	+	1	NA	promoter-TSS (NM_201230)	promoter-TSS (NM_201230)	58	NM_201230	75296	Mm.227250	NM_201230	ENSMUSG00000069135	Fgfr1op	4930553O10Rik|FOP	Fgfr1 oncogene partner	protein-coding
mm_51580.1	chr6	83762702	83762710	+	1	NA	promoter-TSS (NR_105027)	promoter-TSS (NR_105027)	60	NM_029245	75305	Mm.391478	NM_029245	ENSMUSG00000014747	Ankrd53	4930564N15Rik	ankyrin repeat domain 53	protein-coding
mm_26751.1	chr3	7613739	7613765	-	1	NA	promoter-TSS (NM_001313889)	promoter-TSS (NM_001313889)	8	NM_008371	16196	Mm.3825	NM_008371	ENSMUSG00000040329	Il7	A630026I06Rik|Il-7|hlb368	interleukin 7	protein-coding
mm_46061.1	chr5	92262793	92262799	-	1	NA	intron (NM_025972, intron 7 of 10)	intron (NM_025972, intron 7 of 10)	-9637	NM_011148	19023	Mm.87155	NM_011148	ENSMUSG00000029410	Ppef2	-	protein phosphatase, EF hand calcium-binding domain 2	protein-coding
mm_158699.1	chrX	162019461	162019470	-	1	NA	intron (NM_001081052, intron 1 of 7)	intron (NM_001081052, intron 1 of 7)	139976	NM_001081052	195727	Mm.336313	NM_001081052	ENSMUSG00000059493	Nhs	Gm389|Gm48|Nhs1|Xcat	Nance-Horan syndrome (human)	protein-coding
mm_113960.1	chr13	51171235	51171258	+	1	NA	5' UTR (NM_029173, exon 1 of 2)	5' UTR (NM_029173, exon 1 of 2)	221	NM_029173	75124	Mm.179243	NM_029173	ENSMUSG00000021396	Nxnl2	4930519N16Rik|Rdcvf2	nucleoredoxin-like 2	protein-coding
mm_85754.1	chr9	108649062	108649073	-	1	NA	intron (NM_011790, intron 1 of 15)	CpG	313	NM_011790	23807	Mm.290447	NM_011790	ENSMUSG00000064145	Arih2	AI843547|ARI2|TRIAD1|UIP48	ariadne RBR E3 ubiquitin protein ligase 2	protein-coding
mm_114156.1	chr13	55403037	55403057	+	1	NA	exon (NM_011392, exon 7 of 13)	exon (NM_011392, exon 7 of 13)	3399	NM_011392	20505	Mm.276355	NM_011392	ENSMUSG00000021490	Slc34a1	NaPi-IIa|Npt2|Npt2a|Slc17a2	solute carrier family 34 (sodium phosphate), member 1	protein-coding
mm_29561.1	chr3	116808138	116808148	-	1	NA	promoter-TSS (NM_001081326)	promoter-TSS (NM_001081326)	23	NM_001081326	77559	Mm.237099	NM_001081326	ENSMUSG00000033400	Agl	1110061O17Rik|9430004C13Rik|9630046L06Rik|AI850929|C77197	amylo-1,6-glucosidase, 4-alpha-glucanotransferase	protein-coding
mm_13138.1	chr2	92058731	92058778	+	1	NA	Intergenic	Intergenic	-34584	NM_011957	26427	Mm.10353	NM_011957	ENSMUSG00000027230	Creb3l1	Oasis	cAMP responsive element binding protein 3-like 1	protein-coding
mm_97799.1	chr11	82952063	82952094	+	1	NA	promoter-TSS (NM_183201)	promoter-TSS (NM_183201)	-24	NM_183201	327978	Mm.42147	NM_183201	ENSMUSG00000054404	Slfn5	AI956840	schlafen 5	protein-coding
mm_16162.1	chr2	172455490	172455496	+	1	NA	intron (NM_001039560, intron 1 of 3)	PB1D11|SINE|Alu	3103	NM_001039560	654821	Mm.389337	NM_001039560	ENSMUSG00000074569	Gcnt7	A330041C17Rik|gnt	glucosaminyl (N-acetyl) transferase family member 7	protein-coding
mm_13173.1	chr2	92915123	92915127	+	1	NA	promoter-TSS (NM_030725)	promoter-TSS (NM_030725)	24	NM_030725	80976	Mm.33490	NM_030725	ENSMUSG00000027220	Syt13	5730409J20Rik|AI549909|mKIAA1427	synaptotagmin XIII	protein-coding
mm_171850.1	chr5	16904665	16904665	+	1	NA	Intergenic	L1Md_T|LINE|L1	350764	NM_001289461	15234	Mm.267078	NM_010427	ENSMUSG00000028864	Hgf	C230052L06Rik|HGF/SF|NK1|NK2|SF|SF/HGF	hepatocyte growth factor	protein-coding
mm_125928.1	chr15	76246839	76246856	+	1	NA	promoter-TSS (NM_023168)	promoter-TSS (NM_023168)	40	NM_023168	66168	Mm.41665	NM_023168	ENSMUSG00000022564	Grina	1110025J15Rik|Lag|Tmbim3	glutamate receptor, ionotropic, N-methyl D-aspartate-associated protein 1 (glutamate binding)	protein-coding
mm_59165.1	chr7	24399607	24399673	+	1	NA	promoter-TSS (NM_028047)	promoter-TSS (NM_028047)	12	NM_028047	71997	Mm.150977	NM_028047	ENSMUSG00000002210	Smg9	1500002O20Rik|AI429693|N28092	smg-9 homolog, nonsense mediated mRNA decay factor (C. elegans)	protein-coding
mm_41280.1	chr5	90366617	90366671	+	1	NA	promoter-TSS (NM_030886)	promoter-TSS (NM_030886)	-353	NR_045618	791294	Mm.30508	NR_045618	ENSMUSG00000054945	Gm9958	ENSMUSG00000054945	predicted gene 9958	ncRNA
mm_140841.1	chr17	23673558	23673577	-	1	NA	promoter-TSS (NM_181821)	promoter-TSS (NM_181821)	-41	NM_181821	353502	Mm.359030	NM_181821	ENSMUSG00000023904	Hcfc1r1	HPIP	host cell factor C1 regulator 1 (XPO1-dependent)	protein-coding
mm_157633.1	chrX	56853818	56853819	-	1	NA	Intergenic	Intergenic	-31493	NM_177293	320923	Mm.186745	NM_177293	ENSMUSG00000067878	Mtap7d3	4933424A10Rik|Map7d3	MAP7 domain containing 3	protein-coding
mm_81065.1	chr9	106178087	106178089	+	1	NA	promoter-TSS (NR_029526)	promoter-TSS (NR_029526)	-752	NR_029526	387249		NR_029526	ENSMUSG00000065440	Mirlet7g	Mirnlet7g|let-7g|mmu-let-7g	microRNA let7g	ncRNA
mm_15558.1	chr2	158502616	158502632	+	1	NA	promoter-TSS (NM_145635)	promoter-TSS (NM_145635)	12	NM_145635	246747	Mm.28800	NM_145635	ENSMUSG00000044405	Adig	SMAF-1|Smaf1	adipogenin	protein-coding
mm_116653.1	chr13	49187954	49187961	-	1	NA	intron (NM_013610, intron 1 of 3)	CpG	410	NM_013610	18081	Mm.18503	NM_013610	ENSMUSG00000037966	Ninj1	AU024536	ninjurin 1	protein-coding
mm_120887.1	chr14	75455922	75455954	+	1	NA	promoter-TSS (NM_001128093)	promoter-TSS (NM_001128093)	-44	NM_001128093	380918	Mm.484360	NM_001128093	ENSMUSG00000091722	Siah3	Gm912	seven in absentia homolog 3 (Drosophila)	protein-coding
mm_87626.1	chr10	57807901	57807933	+	1	NA	exon (NM_020561, exon 6 of 8)	exon (NM_020561, exon 6 of 8)	13373	NM_020561	57319	Mm.2379	NM_020561	ENSMUSG00000019872	Smpdl3a	0610010C24Rik|AI529588|ASM3A|ASML3|ASML3A	sphingomyelin phosphodiesterase, acid-like 3A	protein-coding
mm_9069.1	chr1	168293446	168293451	-	1	NA	intron (NM_008783, intron 2 of 7)	intron (NM_008783, intron 2 of 7)	138721	NM_001291508	18514	Mm.43358	NM_008783	ENSMUSG00000052534	Pbx1	2310056B04Rik|D230003C07Rik|Pbx-1	pre B cell leukemia homeobox 1	protein-coding
mm_39262.1	chr5	3571573	3571580	+	1	NA	promoter-TSS (NM_029843)	promoter-TSS (NM_029843)	-140	NM_029843	77036	Mm.389069	NM_029843	ENSMUSG00000008307	1700109H08Rik	-	RIKEN cDNA 1700109H08 gene	protein-coding
mm_125695.1	chr15	66891415	66891430	+	1	NA	promoter-TSS (NM_018865)	promoter-TSS (NM_018865)	29	NM_018865	22402	Mm.10222	NM_018865	ENSMUSG00000005124	Wisp1	AW146261|CCN4|Elm1	WNT1 inducible signaling pathway protein 1	protein-coding
mm_103549.1	chr11	77718660	77718666	-	1	NA	TTS (NM_001024205)	TTS (NM_001024205)	6630	NM_001313933	12957	Mm.22830	NM_009965	ENSMUSG00000000724	Cryba1	BA3/A1|Cryb	crystallin, beta A1	protein-coding
mm_41099.1	chr5	87694797	87694820	+	1	NA	exon (NM_001286023, exon 5 of 7)	exon (NM_001286023, exon 5 of 7)	4617	NM_001286020	12991	Mm.268737	NM_009972	ENSMUSG00000063157	Csn2	Csnb	casein beta	protein-coding
mm_80750.1	chr9	95168202	95168221	+	1	NA	intron (NM_177909, intron 14 of 15)	L2c|LINE|L2	239059	NM_018763	54371	Mm.212446	NM_018763	ENSMUSG00000033350	Chst2	AI428561|AW121776|C130041E03Rik|Chts2|GST-2|GlcNAc6ST|Gn6st	carbohydrate sulfotransferase 2	protein-coding
mm_64538.1	chr7	144175710	144175720	+	1	NA	5' UTR (NM_001113373, exon 1 of 16)	5' UTR (NM_001113373, exon 1 of 16)	195	NM_001113373	210274	Mm.483624	NM_001081370	ENSMUSG00000037541	Shank2	ProSAP1|mKIAA1022	SH3/ankyrin domain gene 2	protein-coding
mm_89192.1	chr10	86347506	86347523	+	1	NA	3' UTR (NM_011595, exon 5 of 5)	3' UTR (NM_011595, exon 5 of 5)	47102	NM_011595	21859	Mm.4871	NM_011595	ENSMUSG00000020044	Timp3	Timp-3	tissue inhibitor of metalloproteinase 3	protein-coding
mm_135344.1	chr16	43363062	43363068	-	1	NA	intron (NM_181058, intron 2 of 6)	LFSINE_Vert|SINE|tRNA	57131	NR_046026	626693	Mm.447083	NR_046026	ENSMUSG00000085499	Gm15713	OTTMUSG00000025617	predicted gene 15713	ncRNA
mm_111079.1	chr12	80168940	80168969	-	1	NA	exon (NM_134156, exon 20 of 21)	exon (NM_134156, exon 20 of 21)	-36110	NR_033514	69548	Mm.269712	NR_033514	ENSMUSG00000097729	2310015A10Rik	5330419I17Rik	RIKEN cDNA 2310015A10 gene	ncRNA
mm_148159.1	chr18	77687462	77687465	-	1	NA	intron (NM_178670, intron 1 of 4)	ID_B1|SINE|B4	26547	NM_178670	212163	Mm.23293	NM_178670	ENSMUSG00000047466	8030462N17Rik	Akd2|Ark2N	RIKEN cDNA 8030462N17 gene	protein-coding
mm_23530.1	chr3	60626786	60626819	+	1	NA	3' UTR (NM_001253711, exon 8 of 8)	3' UTR (NM_001253711, exon 8 of 8)	125623	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_139365.1	chr17	50698543	50698553	+	1	NA	promoter-TSS (NM_001297747)	promoter-TSS (NM_001297747)	-133	NM_001297747	12228	Mm.392910	NM_009770	ENSMUSG00000022863	Btg3	ANA|tob5	B cell translocation gene 3	protein-coding
mm_113205.1	chr13	25055965	25055975	+	1	NA	promoter-TSS (NM_177577)	promoter-TSS (NM_177577)	-34	NM_001195617	195208	Mm.284719	NM_177577	ENSMUSG00000035910	Dcdc2a	AW492955|Dcdc2|RU2	doublecortin domain containing 2a	protein-coding
mm_102386.1	chr11	58928481	58928491	-	1	NA	Intergenic	Intergenic	10420	NM_022423	108660	Mm.249986	NM_022423	ENSMUSG00000020496	Rnf187	2410016F01Rik|AB030190|RACO-1	ring finger protein 187	protein-coding
mm_62451.1	chr7	101386786	101386800	+	1	NA	exon (NM_001040111, exon 8 of 34)	exon (NM_001040111, exon 8 of 34)	1267	NM_027180	69710	Mm.277687	NM_027180	ENSMUSG00000032812	Arap1	2410002L19Rik|Centd2|mKIAA0782	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	protein-coding
mm_57553.1	chr6	126849148	126849149	-	1	NA	promoter-TSS (NM_025358)	promoter-TSS (NM_025358)	-4	NM_025358	66108	Mm.29939	NM_025358	ENSMUSG00000000399	Ndufa9	1010001N11Rik	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 9	protein-coding
mm_72109.1	chr8	71611251	71611260	+	1	NA	exon (NM_146211, exon 1 of 12)	exon (NM_146211, exon 1 of 12)	231	NM_146211	234407	Mm.240885	NM_146211	ENSMUSG00000034807	Colgalt1	2810024B22Rik|Glt25d1	collagen beta(1-O)galactosyltransferase 1	protein-coding
mm_63156.1	chr7	123418282	123418291	+	1	NA	exon (NM_025304, exon 7 of 11)	exon (NM_025304, exon 7 of 11)	40304	NM_025304	30949	Mm.260527	NM_025304	ENSMUSG00000030763	Lcmt1	AL033290|LCMT-1|Lcmt	leucine carboxyl methyltransferase 1	protein-coding
mm_107194.1	chr12	25285099	25285105	+	1	NA	Intergenic	L1_Mus3|LINE|L1	155928	NR_045844	432641	Mm.112955	NR_045844		Gm17746	-	predicted gene, 17746	ncRNA
mm_170828.1	chr2	176864490	176864501	-	1	NA	promoter-TSS (NR_040256).2	promoter-TSS (NR_040256).2	-58	NR_040256	626877	Mm.490744	NR_040256		Gm14405	OTTMUSG00000016573	predicted gene 14405	pseudo
mm_164777.1	chr18	3280951	3280951	-	1	NA	5' UTR (NM_001311067, exon 1 of 4)	5' UTR (NM_001311067, exon 1 of 4)	181	NM_001311066	12916	Mm.5244	NM_013498	ENSMUSG00000063889	Crem	ICER|ICERI	cAMP responsive element modulator	protein-coding
mm_63017.1	chr7	121032777	121032787	+	1	NA	Intergenic	Intergenic	-1663	NM_021554	59052	Mm.29122	NM_021554	ENSMUSG00000030876	Mettl9	0610012D09Rik|AA517660|Drev|MNCb-5680	methyltransferase like 9	protein-coding
mm_77751.1	chr8	128466304	128466307	-	1	NA	intron (NM_008737, intron 8 of 16)	intron (NM_008737, intron 8 of 16)	107064	NR_035436	100316680		NR_035436	ENSMUSG00000084523	Mir1903	Mirn1903|mmu-mir-1903	microRNA 1903	ncRNA
mm_32216.1	chr4	101647713	101647736	+	1	NA	promoter-TSS (NM_175036)	promoter-TSS (NM_175036)	-59	NM_175036	230514	Mm.4756	NM_175036	ENSMUSG00000035212	Leprot	LEPR|OB-RGRP|Obrgrp|VPS55	leptin receptor overlapping transcript	protein-coding
mm_140438.1	chr17	88479269	88479281	+	1	NA	intron (NM_180974, intron 3 of 5)	intron (NM_180974, intron 3 of 5)	38563	NM_180974	14236	Mm.112824	NM_180974	ENSMUSG00000034998	Foxn2	3230402J05Rik|6030465J18Rik|Fkh19|Foxn1|HTLF	forkhead box N2	protein-coding
mm_154132.1	chr19	57314844	57314893	-	1	NA	Intergenic	CpG	40908	NR_045319	78120	Mm.445892	NR_045319		4930449E18Rik	-	RIKEN cDNA 4930449E18 gene	ncRNA
mm_129242.1	chr15	76656751	76656769	-	1	NA	5' UTR (NM_001276321, exon 1 of 4)	5' UTR (NM_001276321, exon 1 of 4)	141	NM_001276321	54151	Mm.247752	NM_019396	ENSMUSG00000053929	Cyhr1	1110031M01Rik|AU042374|Chrp	cysteine and histidine rich 1	protein-coding
mm_136046.1	chr16	78546643	78546667	-	1	NA	intron (NM_025967, intron 3 of 4)	intron (NM_025967, intron 3 of 4)	-13661	NR_040569	75818	Mm.410817	NR_040569		4930478L05Rik	-	RIKEN cDNA 4930478L05 gene	ncRNA
mm_43059.1	chr5	124229723	124229734	+	1	NA	promoter-TSS (NR_045369)	promoter-TSS (NR_045369)	3	NR_045369	75927	Mm.410803	NR_045369	ENSMUSG00000090220	Pitpnm2os1	4930568K20Rik	phosphatidylinositol transfer protein, membrane-associated 2, opposite strand 1	ncRNA
mm_35872.1	chr4	49536646	49536656	-	1	NA	3' UTR (NM_144903, exon 9 of 9)	3' UTR (NM_144903, exon 9 of 9)	12895	NM_144903	230163	Mm.482116	NM_144903	ENSMUSG00000028307	Aldob	Aldo-2|Aldo2|BC016435	aldolase B, fructose-bisphosphate	protein-coding
mm_57841.1	chr6	129465566	129465574	-	1	NA	exon (NM_020008, exon 5 of 6)	exon (NM_020008, exon 5 of 6)	7209	NM_001309637	56644	Mm.239516	NM_020008	ENSMUSG00000079293	Clec7a	BGR|Clecsf12|beta-GR	C-type lectin domain family 7, member a	protein-coding
mm_160979.1	chr11	102365249	102365249	-	1	NA	promoter-TSS (NM_011403)	promoter-TSS (NM_011403)	32	NM_011403	20533	Mm.7248	NM_011403	ENSMUSG00000006574	Slc4a1	Ae1|CD233|Empb3|l11Jus51	solute carrier family 4 (anion exchanger), member 1	protein-coding
mm_126737.1	chr15	85671475	85671511	+	1	NA	Intergenic	CpG	-32280	NR_110483	102800312	Mm.33117	NR_110483		Lncppara	Lincppara|Mirlet7bhg|linc-Ppara	long noncoding RNA near Ppara	ncRNA
mm_121570.1	chr14	122876437	122876465	+	1	NA	intron (NM_144844, intron 21 of 23)	intron (NM_144844, intron 21 of 23)	36714	NM_145466	223267	Mm.379358	NM_145466	ENSMUSG00000041625	Ggact	A2ld1	gamma-glutamylamine cyclotransferase	protein-coding
mm_52474.1	chr6	114282758	114282817	+	1	NA	5' UTR (NM_178703, exon 1 of 16)	5' UTR (NM_178703, exon 1 of 16)	152	NM_178703	232333	Mm.5260	NM_178703	ENSMUSG00000030310	Slc6a1	A730043E01|GABATHG|GABATR|GAT-1|Gabt|Gabt1|Gat1|XT-1|Xtrp1	solute carrier family 6 (neurotransmitter transporter, GABA), member 1	protein-coding
mm_126984.1	chr15	93996199	93996202	+	1	NA	Intergenic	L1MA5|LINE|L1	-69089	NR_045737	77248	Mm.410768	NR_045737		9430014N10Rik	-	RIKEN cDNA 9430014N10 gene	ncRNA
mm_135726.1	chr16	55822129	55822145	-	1	NA	promoter-TSS (NM_001159394)	promoter-TSS (NM_001159394)	1	NM_001159394	80859	Mm.247272	NM_030612	ENSMUSG00000035356	Nfkbiz	AA408868|INAP|Mail	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, zeta	protein-coding
mm_2960.1	chr1	132880345	132880366	+	1	NA	promoter-TSS (NM_010732)	promoter-TSS (NM_010732)	0	NM_010732	16980	Mm.39640	NM_010732	ENSMUSG00000026443	Lrrn2	5730406J09Rik|NLRR-2	leucine rich repeat protein 2, neuronal	protein-coding
mm_9791.1	chr1	181820646	181820647	-	1	NA	intron (NM_133815, intron 9 of 13)	intron (NM_133815, intron 9 of 13)	21755	NM_133815	98386	Mm.4538	NM_133815	ENSMUSG00000004880	Lbr	AI505894|ic	lamin B receptor	protein-coding
mm_158553.1	chrX	147429190	147429192	-	1	NA	promoter-TSS (NM_008356)	promoter-TSS (NM_008356)	1	NM_001306059	16165	Mm.368330	NM_008356	ENSMUSG00000031289	Il13ra2	CD213a2|IL-13R-alpha-2	interleukin 13 receptor, alpha 2	protein-coding
mm_156489.1	chrX	144336066	144336076	+	1	NA	intron (NR_037145, intron 3 of 26)	intron (NR_037145, intron 3 of 26)	18105	NM_026247	67574	Mm.249084	NM_026247	ENSMUSG00000041718	Alg13	2810046O15Rik|4833435D08Rik|Glt28d1|MDS031|OTTMUSG00000018917	asparagine-linked glycosylation 13	protein-coding
mm_72433.1	chr8	82932447	82932460	+	1	NA	intron (NM_177378, intron 1 of 6)	Lx9|LINE|L1	69097	NM_177378	330812	Mm.491438	NM_177378	ENSMUSG00000047747	Rnf150	A630007N06Rik|C030044C12Rik|Greul5|mKIAA1214	ring finger protein 150	protein-coding
mm_34035.1	chr4	138147431	138147452	+	1	NA	intron (NM_172703, intron 13 of 34)	intron (NM_172703, intron 13 of 34)	-8923	NR_126429	73563	Mm.444294	NR_126429	ENSMUSG00000084804	1700095J12Rik	-	RIKEN cDNA 1700095J12 gene	ncRNA
mm_117319.1	chr13	67683476	67683562	-	1	NA	promoter-TSS (NM_001001187)	promoter-TSS (NM_001001187)	-7	NM_001001187	408068	Mm.435551	NM_175676	ENSMUSG00000048280	Zfp738	3830402I07Rik|6720487G11Rik	zinc finger protein 738	protein-coding
mm_120438.1	chr14	65837343	65837397	+	1	NA	promoter-TSS (NM_145944)	promoter-TSS (NM_145944)	68	NM_145944	67179	Mm.214576	NM_145944	ENSMUSG00000022035	Ccdc25	2610528H13Rik|NSrp70	coiled-coil domain containing 25	protein-coding
mm_39390.1	chr5	13399388	13399415	+	1	NA	promoter-TSS (NM_009152)	promoter-TSS (NM_009152)	92	NM_009152	20346	Mm.372039	NM_009152	ENSMUSG00000028883	Sema3a	Hsema-I|SEMA1|SemD|Semad|coll-1	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	protein-coding
mm_128861.1	chr15	72809929	72809939	-	1	NA	non-coding (NR_002864, exon 1 of 1)	non-coding (NR_002864, exon 1 of 1)	390	NR_002864	353342	Mm.440245	NR_002864	ENSMUSG00000106847	Peg13	-	paternally expressed 13	ncRNA
mm_83312.1	chr9	44047611	44047637	-	1	NA	3' UTR (NM_009382, exon 4 of 4)	3' UTR (NM_009382, exon 4 of 4)	4240	NM_009382	21838	Mm.3951	NM_009382	ENSMUSG00000032011	Thy1	CD90|T25|Thy-1|Thy-1.2|Thy1.1|Thy1.2	thymus cell antigen 1, theta	protein-coding
mm_59365.1	chr7	25687638	25687648	+	1	NA	5' UTR (NM_011577, exon 1 of 7)	5' UTR (NM_011577, exon 1 of 7)	641	NM_011577	21803	Mm.248380	NM_011577	ENSMUSG00000002603	Tgfb1	TGF-beta1|TGFbeta1|Tgfb|Tgfb-1	transforming growth factor, beta 1	protein-coding
mm_85560.1	chr9	106891381	106891391	-	1	NA	intron (NM_029103, intron 1 of 3)	intron (NM_029103, intron 1 of 3)	552	NM_029103	74840	Mm.29778	NM_029103	ENSMUSG00000032575	Manf	3230402M22Rik|AA407711|AA408789|AA673178|Armet|D17914|D18Mgi17	mesencephalic astrocyte-derived neurotrophic factor	protein-coding
mm_129061.1	chr15	75567177	75567259	-	1	NA	promoter-TSS (NM_011837)	promoter-TSS (NM_011837)	-36	NM_011837	23934	Mm.22154	NM_011837	ENSMUSG00000022577	Ly6h	-	lymphocyte antigen 6 complex, locus H	protein-coding
mm_138608.1	chr17	35649817	35649848	+	1	NA	5' UTR (NM_001163194, exon 1 of 3)	5' UTR (NM_001163194, exon 1 of 3)	124	NM_001163194	433102	Mm.136760	NM_001163194	ENSMUSG00000090509	Sfta2	EG433102	surfactant associated 2	protein-coding
mm_107959.1	chr12	72664985	72664994	+	1	NA	promoter-TSS (NM_025522)	promoter-TSS (NM_025522)	-161	NM_025522	66375	Mm.289653	NM_025522	ENSMUSG00000021094	Dhrs7	2310016E22Rik|5730564L20Rik|AW061210|Retdsr4|Retsdr4	dehydrogenase/reductase (SDR family) member 7	protein-coding
mm_99794.1	chr11	107479479	107479544	+	1	NA	promoter-TSS (NM_025894)	promoter-TSS (NM_025894)	-17	NM_025894	66997	Mm.491171	NM_025894	ENSMUSG00000020720	Psmd12	1500002F15Rik|AI480719|P55	proteasome (prosome, macropain) 26S subunit, non-ATPase, 12	protein-coding
mm_164423.1	chr16	45031137	45031141	-	1	NA	Intergenic	Intergenic	-62914	NM_026439	67896	Mm.181074	NM_026439	ENSMUSG00000022665	Ccdc80	2610001E17Rik|DRO1|Ssg1|Urb	coiled-coil domain containing 80	protein-coding
mm_148521.1	chr19	4300627	4300643	+	1	NA	intron (NM_001290818, intron 1 of 20)	intron (NM_001290818, intron 1 of 20)	5587	NM_130863	110355	Mm.254144	NM_130863	ENSMUSG00000024858	Grk2	Adrbk-1|Adrbk1|Bark-1|beta ARK|betaARK1	G protein-coupled receptor kinase 2	protein-coding
mm_172243.1	chr6	69227435	69227439	-	1	NA	Intergenic	Intergenic	99737	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_107709.1	chr12	55565262	55565267	+	1	NA	promoter-TSS (NM_001277340)	promoter-TSS (NM_001277340)	59	NM_001277340	79459	Mm.392781	NM_001277340	ENSMUSG00000063129	Aldoart2	4933425L11Rik|Aldo1-ps1|Aldoa-ps1	aldolase 1 A, retrogene 2	protein-coding
mm_135103.1	chr16	35490803	35490858	-	1	NA	promoter-TSS (NM_028295)	promoter-TSS (NM_028295)	43	NM_028295	72599	Mm.71015	NM_028295	ENSMUSG00000022844	Pdia5	2700053F16Rik|AU015525|Pdir	protein disulfide isomerase associated 5	protein-coding
mm_66058.1	chr7	30744128	30744140	-	1	NA	promoter-TSS (NM_001290631)	promoter-TSS (NM_001290631)	-453	NM_001290631	14447	Mm.436562	NM_008085	ENSMUSG00000061099	Gapdhs	Gapd-s|Gapds	glyceraldehyde-3-phosphate dehydrogenase, spermatogenic	protein-coding
mm_144510.1	chr18	24709255	24709289	+	1	NA	5' UTR (NM_001289655, exon 1 of 26)	5' UTR (NM_001289655, exon 1 of 26)	649	NM_001289655	225288	Mm.329322	NM_175276	ENSMUSG00000034295	Fhod3	A930009H06Rik|FHOS2|mKIAA1695	formin homology 2 domain containing 3	protein-coding
mm_157502.1	chrX	48594384	48594493	-	1	NA	promoter-TSS (NM_001166649)	promoter-TSS (NM_001166649)	14	NM_001166649	208968	Mm.293819	NM_153532	ENSMUSG00000036916	Zfp280c	BC028839|Suhw3|Zfp633|Znf280c|mKIAA1584	zinc finger protein 280C	protein-coding
mm_165076.1	chr19	45545337	45545345	+	1	NA	Intergenic	Intergenic	15223	NM_001330506	56626	Mm.46509	NM_020032	ENSMUSG00000025218	Poll	1110003P06Rik|AV007317	polymerase (DNA directed), lambda	protein-coding
mm_164966.1	chr19	6398738	6398764	+	1	NA	TTS (NM_011224)	TTS (NM_011224)	-1832	NM_011242	19395	Mm.77017	NM_011242	ENSMUSG00000032946	Rasgrp2	CDC25L|Caldaggef1	RAS, guanyl releasing protein 2	protein-coding
mm_141205.1	chr17	27043099	27043109	-	1	NA	Intergenic	Intergenic	13845	NM_027544	70772	Mm.440437	NM_027544	ENSMUSG00000048731	Ggnbp1	0610031G08Rik|mdf	gametogenetin binding protein 1	protein-coding
mm_142707.1	chr17	47879047	47879088	-	1	NA	intron (NM_001110824, intron 5 of 16)	intron (NM_001110824, intron 5 of 16)	-44376	NM_001109973	17240	Mm.329100	NM_010783	ENSMUSG00000032717	Mdfi	I-mf|I-mfa	MyoD family inhibitor	protein-coding
mm_85292.1	chr9	100466858	100466866	-	1	NA	intron (NM_001033543, intron 4 of 6)	intron (NM_001033543, intron 4 of 6)	19611	NM_001033543	213208	Mm.242896	NM_001033543	ENSMUSG00000044244	Il20rb	AV228068|Fndc6|Gm186|Il20R2	interleukin 20 receptor beta	protein-coding
mm_138692.1	chr17	35979908	35979924	+	1	NA	promoter-TSS (NM_001282025)	promoter-TSS (NM_001282025)	-39	NM_008136	14670	Mm.335754	NM_008136	ENSMUSG00000024429	Gnl1	Gna-rs1|Gnal1	guanine nucleotide binding protein-like 1	protein-coding
mm_5196.1	chr1	13373643	13373664	-	1	NA	intron (NM_008678, intron 1 of 22)	CpG	430	NM_008678	17978	Mm.2537	NM_008678	ENSMUSG00000005886	Ncoa2	D1Ertd433e|GRIP-1|Grip1|KAT13C|NCoA-2|SRC-2|TIF2|bHLHe75	nuclear receptor coactivator 2	protein-coding
mm_105783.1	chr11	109797354	109797361	-	1	NA	exon (NM_001162428, exon 3 of 6)	exon (NM_001162428, exon 3 of 6)	30689	NM_027038	69324	Mm.31700	NM_027038	ENSMUSG00000020617	1700012B07Rik	1700069D21Rik	RIKEN cDNA 1700012B07 gene	protein-coding
mm_169576.1	chr15	22714110	22714113	-	1	NA	exon (NM_001165971, exon 1 of 1)	exon (NM_001165971, exon 1 of 1)	873	NM_001165971	545091	Mm.475598	NM_001165971		Gm5803	EG545091	predicted gene 5803	protein-coding
mm_54913.1	chr6	47796244	47796247	-	1	NA	3' UTR (NM_009787, exon 10 of 10)	3' UTR (NM_009787, exon 10 of 10)	7407	NR_030485	735289		NR_030485	ENSMUSG00000076060	Mir704	Mirn704|mir-704|mmu-mir-704	microRNA 704	ncRNA
mm_85833.1	chr9	110462437	110462453	-	1	NA	intron (NM_177771, intron 1 of 9)	intron (NM_177771, intron 1 of 9)	14249	NM_177771	270201	Mm.41744	NM_177771	ENSMUSG00000054792	Klhl18	A930041K15|AW545966	kelch-like 18	protein-coding
mm_113713.1	chr13	43603820	43603847	+	1	NA	Intergenic	Intergenic	-11964	NM_183204	328234	Mm.40588	NM_183204	ENSMUSG00000044164	Rnf182	C630023L15Rik	ring finger protein 182	protein-coding
mm_138435.1	chr17	35110684	35110688	+	1	NA	exon (NM_148947, exon 2 of 3)	exon (NM_148947, exon 2 of 3)	2386	NM_148947	114652	Mm.222643	NM_148947	ENSMUSG00000034482	Ly6g5c	G5c|NG33	lymphocyte antigen 6 complex, locus G5C	protein-coding
mm_56893.1	chr6	119109035	119109077	-	1	NA	promoter-TSS (NM_001159534)	promoter-TSS (NM_001159534)	-561	NM_001256002	12288	Mm.41628	NM_009781	ENSMUSG00000051331	Cacna1c	Cav1.2|Cchl1a1|D930026N18Rik|MBC|MELC-CC	calcium channel, voltage-dependent, L type, alpha 1C subunit	protein-coding
mm_51039.1	chr6	65597355	65597372	+	1	NA	exon (NM_001001495, exon 4 of 8)	exon (NM_001001495, exon 4 of 8)	6965	NM_001001495	414084	Mm.117558	NM_001001495	ENSMUSG00000044162	Tnip3	9030611K07Rik|ABIN-3|LIND	TNFAIP3 interacting protein 3	protein-coding
mm_98343.1	chr11	93099241	93099249	+	1	NA	promoter-TSS (NM_028296)	promoter-TSS (NM_028296)	-45	NM_028296	72605	Mm.342160	NM_028296	ENSMUSG00000056158	Car10	2700029L05Rik|BB085816|Ca10	carbonic anhydrase 10	protein-coding
mm_46176.1	chr5	96922177	96922188	-	1	NA	intron (NR_131152, intron 2 of 2)	intron (NR_131152, intron 2 of 2)	910	NR_131152	666266	Mm.32442	NR_131152	ENSMUSG00000106357	Gm8013	EG666266	predicted gene 8013	ncRNA
mm_47538.1	chr5	124249759	124249782	-	1	NA	promoter-TSS (NM_011256)	promoter-TSS (NM_011256)	-10	NM_011256	19679	Mm.44261	NM_011256	ENSMUSG00000029406	Pitpnm2	NIR3|RDGBA2|Rdgb2|mKIAA1457	phosphatidylinositol transfer protein, membrane-associated 2	protein-coding
mm_84537.1	chr9	67262141	67262147	-	1	NA	intron (NM_001081242, intron 46 of 57)	intron (NM_001081242, intron 46 of 57)	-25418	NR_029576	387185		NR_029576	ENSMUSG00000076379	Mir190a	Mir190|Mirn190|mir-190|mir-190a|mmu-mir-190|mmu-mir-190a	microRNA 190a	ncRNA
mm_59183.1	chr7	24462476	24462496	+	1	NA	promoter-TSS (NM_011113)	promoter-TSS (NM_011113)	3	NM_011113	18793	Mm.1359	NM_011113	ENSMUSG00000046223	Plaur	Cd87|u-PAR|uPAR	plasminogen activator, urokinase receptor	protein-coding
mm_1782.1	chr1	78526570	78526602	+	1	NA	intron (NM_026713, intron 4 of 6)	intron (NM_026713, intron 4 of 6)	15526	NM_026713	68393	Mm.41325	NM_026713	ENSMUSG00000012187	Mogat1	0610030A14Rik|1110064N14Rik|Dgat2l|Dgat2l1|MGAT1|WI1-2612I11.1|mDC2	monoacylglycerol O-acyltransferase 1	protein-coding
mm_109992.1	chr12	15793170	15793173	-	1	NA	3' UTR (NM_144551, exon 3 of 3)	3' UTR (NM_144551, exon 3 of 3)	7930	NR_105809	102465204		NR_105809	ENSMUSG00000098480	Mir6387	Gm27281|mmu-mir-6387	microRNA 6387	ncRNA
mm_103602.1	chr11	78404587	78404607	-	1	NA	non-coding (NR_003282, exon 5 of 5)	non-coding (NR_003282, exon 5 of 5)	10112	NR_003282	790911	Mm.457257	NR_003282	ENSMUSG00000085747	Slc13a2os	Gm11194|OTTMUSG00000000132	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 2, opposite strand	ncRNA
mm_164936.1	chr18	84251529	84251530	+	1	NA	intron (NM_001033341, intron 8 of 8)	intron (NM_001033341, intron 8 of 8)	163371	NM_146090	225791	Mm.147052	NM_146090	ENSMUSG00000049090	Zadh2	C530046K17Rik|PTGR-3|Pthr3	zinc binding alcohol dehydrogenase, domain containing 2	protein-coding
mm_112601.1	chr13	14161307	14161327	+	1	NA	exon (NM_194262, exon 14 of 24)	exon (NM_194262, exon 14 of 24)	97533	NM_198122	94246	Mm.439784	NM_194262	ENSMUSG00000039219	Arid4b	BCAA|BRCAA1|RBBP1L1|Rbp1l1|SAP180	AT rich interactive domain 4B (RBP1-like)	protein-coding
mm_131373.1	chr16	13863381	13863382	+	1	NA	intron (NM_001291017, intron 8 of 23)	RMER15|LTR|ERVL	39764	NM_001039533	94184	Mm.171484	NM_053181	ENSMUSG00000022680	Pdxdc1	2210010A19Rik|AA415817|Kiaa0251-hp	pyridoxal-dependent decarboxylase domain containing 1	protein-coding
mm_153079.1	chr19	32349943	32349945	-	1	NA	promoter-TSS (NM_001168525)	promoter-TSS (NM_001168525)	-628	NM_001168525	208449	Mm.329810	NM_144792	ENSMUSG00000040451	Sgms1	9530058O11Rik|AI841905|C80702|Mob|Sms1|Sor1|Tmem23	sphingomyelin synthase 1	protein-coding
mm_38934.1	chr4	150193759	150193775	-	1	NA	exon (NM_009802, exon 5 of 8)	exon (NM_009802, exon 5 of 8)	7368	NM_009802	12353	Mm.232523	NM_009802	ENSMUSG00000028972	Car6	Ca6|DOC1	carbonic anhydrase 6	protein-coding
mm_70841.1	chr8	23411491	23411507	+	1	NA	promoter-TSS (NM_013834)	promoter-TSS (NM_013834)	-3	NM_013834	20377	Mm.281691	NM_013834	ENSMUSG00000031548	Sfrp1	2210415K03Rik|AW011917|AW107218|AW742929|sFRP-1	secreted frizzled-related protein 1	protein-coding
mm_105435.1	chr11	104328239	104328242	-	1	NA	3' UTR (NM_010838, exon 10 of 10)	3' UTR (NM_010838, exon 10 of 10)	96804	NM_001285454	17762	Mm.1287	NM_010838	ENSMUSG00000018411	Mapt	AI413597|AW045860|Mtapt|Tau	microtubule-associated protein tau	protein-coding
mm_84613.1	chr9	70421534	70421592	-	1	NA	promoter-TSS (NM_007630)	promoter-TSS (NM_007630)	-9	NM_007630	12442	Mm.22592	NM_007630	ENSMUSG00000032218	Ccnb2	CycB2	cyclin B2	protein-coding
mm_93727.1	chr10	119240133	119240153	-	1	NA	promoter-TSS (NM_027994)	promoter-TSS (NM_027994)	-88	NM_027994	71902	Mm.203965	NM_027994	ENSMUSG00000020114	Cand1	2310038O07Rik|6330512O03Rik|AI195005|AI846556|D10Ertd516e|Tp120a|mKIAA0829	cullin associated and neddylation disassociated 1	protein-coding
mm_122921.1	chr14	54960504	54960516	-	1	NA	exon (NM_010856, exon 13 of 39)	exon (NM_010856, exon 13 of 39)	6097	NM_001164171	17888	Mm.290003	NM_010856	ENSMUSG00000040752	Myh6	A830009F23Rik|AA517445|Myhc-a|Myhca|alpha-MHC	myosin, heavy polypeptide 6, cardiac muscle, alpha	protein-coding
mm_101324.1	chr11	22860468	22860494	-	1	NA	promoter-TSS (NM_001169114)	promoter-TSS (NM_001169114)	-145	NM_001169114	53625	Mm.395495	NM_016888	ENSMUSG00000051650	B3gnt2	AA408337|AA409404|AW260308|B3Galt6|B3gnt1|BGnT-1|BGnT-2|BGnT1|BGnT2|Beta3gnt	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 2	protein-coding
mm_169803.1	chr16	18016903	18016910	+	1	NA	Intergenic	LTRIS2|LTR|ERV1	-35954	NM_010047	13353	Mm.27155	NM_010047	ENSMUSG00000003531	Dgcr6	-	DiGeorge syndrome critical region gene 6	protein-coding
mm_73341.1	chr8	105326420	105326441	+	1	NA	promoter-TSS (NM_177449)	promoter-TSS (NM_177449)	66	NM_025486	66320	Mm.29990	NM_025486	ENSMUSG00000014856	Tmem208	1700006C06Rik|2610030K20Rik|Hspc171	transmembrane protein 208	protein-coding
mm_24282.1	chr3	89230310	89230326	+	1	NA	exon (NM_013605, exon 2 of 7)	exon (NM_013605, exon 2 of 7)	1262	NM_013605	17829	Mm.16193	NM_013605	ENSMUSG00000042784	Muc1	CD227|EMA|Muc-1	mucin 1, transmembrane	protein-coding
mm_148834.1	chr19	6343783	6343793	+	1	NA	intron (NM_009006, intron 10 of 31)	intron (NM_009006, intron 10 of 31)	2628	NR_117093	26412	Mm.25860	NM_009006	ENSMUSG00000024948	Map4k2	AI385662|BL44|GCK|Rab8ip	mitogen-activated protein kinase kinase kinase kinase 2	protein-coding
mm_4618.1	chr1	178798397	178798427	+	1	NA	intron (NM_001161665, intron 4 of 14)	intron (NM_001161665, intron 4 of 14)	269287	NM_001161665	269152	Mm.129727	NM_177724	ENSMUSG00000026494	Kif26b	4832420M10|BC056349|D230039L06Rik	kinesin family member 26B	protein-coding
mm_125329.1	chr15	38661906	38661912	+	1	NA	promoter-TSS (NM_025494)	promoter-TSS (NM_025494)	5	NM_025494	66335	Mm.276618	NM_025494	ENSMUSG00000022295	Atp6v1c1	1700025B18Rik|U13839	ATPase, H+ transporting, lysosomal V1 subunit C1	protein-coding
mm_16019.1	chr2	167503230	167503238	+	1	NA	intron (NM_030743, intron 2 of 7)	MLT1E1A|LTR|ERVL-MaLR	-10360	NM_170756	263876	Mm.34342	NM_170756	ENSMUSG00000047030	Spata2	AI504642|mKIAA0757	spermatogenesis associated 2	protein-coding
mm_156588.1	chrX	152178978	152179018	+	1	NA	promoter-TSS (NM_001005475)	promoter-TSS (NM_001005475)	-11	NM_001005475	245666	Mm.33027	NM_001005475	ENSMUSG00000041115	Iqsec2	Brag1	IQ motif and Sec7 domain 2	protein-coding
mm_80070.1	chr9	69476394	69476397	+	1	NA	intron (NM_007585, intron 4 of 12)	intron (NM_007585, intron 4 of 12)	19451	NR_037296	100526560		NR_037296	ENSMUSG00000093042	Mir3109	mir-3109|mmu-mir-3109	microRNA 3109	ncRNA
mm_53535.1	chr6	136630267	136630272	+	1	NA	intron (NM_025806, intron 6 of 10)	MLT1F1|LTR|ERVL-MaLR	31624	NM_025806	66857	Mm.3311	NM_025806	ENSMUSG00000030214	Plbd1	1100001H23Rik	phospholipase B domain containing 1	protein-coding
mm_109951.1	chr12	11435639	11435653	-	1	NA	intron (NM_012038, intron 1 of 3)	intron (NM_012038, intron 1 of 3)	1003	NM_012038	26950	Mm.27005	NM_012038	ENSMUSG00000054459	Vsnl1	VILIP|Vnsl1	visinin-like 1	protein-coding
mm_75230.1	chr8	39621678	39621684	-	1	NA	intron (NM_001113326, intron 4 of 9)	intron (NM_001113326, intron 4 of 9)	20997	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_81533.1	chr9	110082637	110082651	+	1	NA	3' UTR (NM_008633, exon 19 of 19)	3' UTR (NM_008633, exon 19 of 19)	18443	NM_001252683	72831	Mm.276305	NM_133347	ENSMUSG00000032480	Dhx30	2810477H02Rik|C130058C04Rik|Ddx30|HELG|Ret-CoR	DEAH (Asp-Glu-Ala-His) box polypeptide 30	protein-coding
mm_22493.1	chr3	6107520	6107531	+	1	NA	Intergenic	Intergenic	512918	NM_027048	69347	Mm.45822	NM_027048	ENSMUSG00000069118	1700008P02Rik	-	RIKEN cDNA 1700008P02 gene	protein-coding
mm_88303.1	chr10	75324930	75324937	+	1	NA	promoter-TSS (NM_001331096)	promoter-TSS (NM_001331096)	75	NM_001331096	11540	Mm.333734	NM_009630	ENSMUSG00000020178	Adora2a	A2AAR|A2aR|AA2AR	adenosine A2a receptor	protein-coding
mm_139790.1	chr17	65885143	65885157	+	1	NA	promoter-TSS (NM_001198949)	promoter-TSS (NM_001198949)	-227	NM_001198949	19765	Mm.17009	NM_009067	ENSMUSG00000024096	Ralbp1	RLIP76|Rip1	ralA binding protein 1	protein-coding
mm_55618.1	chr6	72234457	72234470	-	1	NA	exon (NM_153778, exon 1 of 3)	exon (NM_153778, exon 1 of 3)	1114	NM_153778	71093	Mm.87449	NM_153778	ENSMUSG00000037621	Atoh8	4933425C05Rik|Hath6|Math6|bHLHa21|okadin	atonal bHLH transcription factor 8	protein-coding
mm_71494.1	chr8	46766705	46766707	+	1	NA	intron (NM_008391, intron 1 of 8)	ORR1B1|LTR|ERVL-MaLR	26961	NM_008391	16363	Mm.1149	NM_008391	ENSMUSG00000031627	Irf2	9830146E22Rik|AI646973|Irf-2	interferon regulatory factor 2	protein-coding
mm_11954.1	chr2	52976941	52976948	+	1	NA	intron (NM_172409, intron 1 of 26)	intron (NM_172409, intron 1 of 26)	119076	NM_172409	71409	Mm.394427	NM_172409	ENSMUSG00000036053	Fmnl2	5430425K04Rik|Man	formin-like 2	protein-coding
mm_90280.1	chr10	122821176	122821179	+	1	NA	intron (NM_176919, intron 4 of 8)	intron (NM_176919, intron 4 of 8)	141862	NR_106182	102466884		NR_106182	ENSMUSG00000099225	Mir8104	Gm27380|mmu-mir-8104	microRNA 8104	ncRNA
mm_34066.1	chr4	138454904	138454917	+	1	NA	promoter-TSS (NM_025451)	promoter-TSS (NM_025451)	-238	NM_025451	66259	Mm.41603	NM_025451	ENSMUSG00000046447	Camk2n1	1810006K23Rik|AI848599|AI891706	calcium/calmodulin-dependent protein kinase II inhibitor 1	protein-coding
mm_74332.1	chr8	127063898	127063916	+	1	NA	promoter-TSS (NM_033620)	promoter-TSS (NM_033620)	-149	NM_033620	93742	Mm.299254	NM_033620	ENSMUSG00000025812	Pard3	AA960621|AI256638|Asip|D8Ertd580e|Par-3|Par3|Pard-3|Pard3a|Phip	par-3 family cell polarity regulator	protein-coding
mm_163.1	chr1	12744776	12744782	+	1	NA	intron (NM_172294, intron 2 of 21)	intron (NM_172294, intron 2 of 21)	26234	NM_172294	240725	Mm.45563	NM_172294	ENSMUSG00000016918	Sulf1	AI467640|AW121680|mKIAA1077	sulfatase 1	protein-coding
mm_47001.1	chr5	115348713	115348738	-	1	NA	intron (NM_007748, intron 1 of 2)	CpG-11401	230	NM_007748	12861	Mm.43415	NM_007748	ENSMUSG00000041697	Cox6a1	VIaL	cytochrome c oxidase subunit VIa polypeptide 1	protein-coding
mm_104713.1	chr11	98052988	98053029	-	1	NA	5' UTR (NM_146028, exon 1 of 11)	5' UTR (NM_146028, exon 1 of 11)	454	NM_146028	217154	Mm.181008	NM_146028	ENSMUSG00000017400	Stac2	24b2|24b2/STAC2|AW240854	SH3 and cysteine rich domain 2	protein-coding
mm_31308.1	chr4	46077184	46077191	+	1	NA	intron (NM_021883, intron 2 of 9)	intron (NM_021883, intron 2 of 9)	37965	NM_021883	21916	Mm.249594	NM_021883	ENSMUSG00000028328	Tmod1	E-Tmod|Tmod	tropomodulin 1	protein-coding
mm_167827.1	chr9	124423533	124423563	-	1	NA	promoter-TSS (NR_015516)	promoter-TSS (NR_015516)	-239	NR_102721	75135	Mm.476814	NR_015516		4930526I15Rik	1600027J15Rik	RIKEN cDNA 4930526I15 gene	ncRNA
mm_162345.1	chr1	52119874	52119896	+	1	NA	intron (NM_001205313, intron 1 of 24)	intron (NM_001205313, intron 1 of 24)	263	NM_001205313	20846	Mm.277406	NM_009283	ENSMUSG00000026104	Stat1	2010005J02Rik|AA408197	signal transducer and activator of transcription 1	protein-coding
mm_38497.1	chr4	141053705	141053724	-	1	NA	promoter-TSS (NM_172122)	promoter-TSS (NM_172122)	-53	NM_172122	230872	Mm.80685	NM_172122	ENSMUSG00000040860	Crocc	-	ciliary rootlet coiled-coil, rootletin	protein-coding
mm_116477.1	chr13	43559853	43559870	-	1	NA	exon (NM_001081059, exon 1 of 9)	exon (NM_001081059, exon 1 of 9)	330	NM_001081059	76137	Mm.426290	NM_001081059	ENSMUSG00000021371	Mcur1	6230416A05Rik|AU015498|AV136929|AW554392|C88263|Ccdc90a	mitochondrial calcium uniporter regulator 1	protein-coding
mm_120891.1	chr14	75845104	75845130	+	1	NA	promoter-TSS (NM_009429)	promoter-TSS (NM_009429)	-139	NM_009429	22070	Mm.297482	NM_009429	ENSMUSG00000060126	Tpt1	TCTP|Trt|p21|p23	tumor protein, translationally-controlled 1	protein-coding
mm_165463.1	chr2	161354862	161354865	+	1	NA	Intergenic	Intergenic	-245777	NR_126509	71389	Mm.122738	NM_173368	ENSMUSG00000057133	Chd6	5430439G14Rik|6330406J24Rik|CHD-6	chromodomain helicase DNA binding protein 6	protein-coding
mm_131141.1	chr16	6349022	6349095	+	1	NA	intron (NM_021477, intron 2 of 16)	CpG	373471	NR_045799	68238	Mm.434605	NR_045799	ENSMUSG00000101481	1700123O21Rik	-	RIKEN cDNA 1700123O21 gene	ncRNA
mm_38280.1	chr4	136890089	136890099	-	1	NA	exon (NM_007574, exon 3 of 3)	exon (NM_007574, exon 3 of 3)	2820	NM_007574	12262	Mm.439732	NM_007574	ENSMUSG00000036896	C1qc	AI385742|C1qg|Ciqc	complement component 1, q subcomponent, C chain	protein-coding
mm_127647.1	chr15	102486256	102486261	+	1	NA	intron (NM_001103165, intron 9 of 14)	intron (NM_001103165, intron 9 of 14)	15626	NM_001174073	18521	Mm.236513	NM_011042	ENSMUSG00000056851	Pcbp2	AW412548|Hnrpx|alphaCP-2	poly(rC) binding protein 2	protein-coding
mm_25748.1	chr3	123267182	123267202	+	1	NA	promoter-TSS (NM_027135)	promoter-TSS (NM_027135)	-304	NM_027135	69608	Mm.29293	NM_027135	ENSMUSG00000039234	Sec24d	2310020L09Rik|Gm1349	Sec24 related gene family, member D (S. cerevisiae)	protein-coding
mm_129821.1	chr15	83033295	83033312	-	1	NA	promoter-TSS (NM_001271412)	promoter-TSS (NM_001271412)	94	NM_001271412	74039	Mm.32584	NM_028728	ENSMUSG00000058099	Nfam1	4921501M20Rik|Cnaip	Nfat activating molecule with ITAM motif 1	protein-coding
mm_114406.1	chr13	64161943	64161949	+	1	NA	promoter-TSS (NM_019986)	promoter-TSS (NM_019986)	80	NM_019986	56541	Mm.40989	NM_019986	ENSMUSG00000021476	Habp4	4933413D03Rik|4933428J01Rik	hyaluronic acid binding protein 4	protein-coding
mm_144406.1	chr18	20961257	20961267	+	1	NA	intron (NM_026301, intron 1 of 5)	intron (NM_026301, intron 1 of 5)	16637	NM_026301	67664	Mm.45980	NM_026301	ENSMUSG00000033107	Rnf125	4930553F04Rik	ring finger protein 125	protein-coding
mm_152143.1	chr19	7198929	7198935	-	1	NA	TTS (NM_134147)	TTS (NM_134147)	7352	NM_134150	107260	Mm.203921	NM_134150	ENSMUSG00000024767	Otub1	AI850305	OTU domain, ubiquitin aldehyde binding 1	protein-coding
mm_39641.1	chr5	24586722	24586794	+	1	NA	promoter-TSS (NM_133913)	promoter-TSS (NM_133913)	8	NM_133913	100910	Mm.140672	NM_133913	ENSMUSG00000038181	Chpf2	2010209O12Rik|AW060945|mKIAA1402|mir-671	chondroitin polymerizing factor 2	protein-coding
mm_144168.1	chr18	6516232	6516252	+	1	NA	promoter-TSS (NM_007935)	promoter-TSS (NM_007935)	-134	NM_007935	13831	Mm.312133	NM_007935	ENSMUSG00000024240	Epc1	2400007E14Rik|5730566F07Rik|A930032N02Rik|mir-1893	enhancer of polycomb homolog 1 (Drosophila)	protein-coding
mm_30852.1	chr4	25340414	25340414	+	1	NA	Intergenic	RLTR26_Mus|LTR|ERVK	-58593	NM_026194	67490	Mm.226295	NM_026194	ENSMUSG00000040359	Ufl1	1810074P20Rik|AI429228|Kiaa0776|Maxer|Rcad|mKIAA0776	UFM1 specific ligase 1	protein-coding
mm_112998.1	chr13	21754068	21754083	+	1	NA	promoter-TSS (NM_178201)	promoter-TSS (NM_178201)	-48	NM_178201	319187		NM_178201	ENSMUSG00000095217	Hist1h2bn	-	histone cluster 1, H2bn	protein-coding
mm_120309.1	chr14	63142284	63142297	+	1	NA	exon (NM_007798, exon 10 of 10)	exon (NM_007798, exon 10 of 10)	19828	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_168349.1	chr1	112838115	112838115	+	1	NA	Intergenic	Intergenic	-973197	NM_001081316	319901	Mm.103468	NM_001081316	ENSMUSG00000038702	Dsel	9330132E09Rik|DS-epi2	dermatan sulfate epimerase-like	protein-coding
mm_100984.1	chr11	7213536	7213615	-	1	NA	exon (NM_008343, exon 1 of 5)	exon (NM_008343, exon 1 of 5)	348	NM_008343	16009	Mm.29254	NM_008343	ENSMUSG00000020427	Igfbp3	AI649005|IGFBP-3|IGgfbp3	insulin-like growth factor binding protein 3	protein-coding
mm_27568.1	chr3	58637175	58637179	-	1	NA	promoter-TSS (NM_001081262)	promoter-TSS (NM_001081262)	30	NM_001081262	545527	Mm.357722	NM_001081262	ENSMUSG00000070471	Erich6	4932431H17Rik|Fam194a	glutamate rich 6	protein-coding
mm_151758.1	chr19	5107028	5107038	-	1	NA	promoter-TSS (NM_029576)	promoter-TSS (NM_029576)	-37	NM_029576	76308	Mm.182563	NM_029576	ENSMUSG00000024870	Rab1b	1110011F09Rik	RAB1B, member RAS oncogene family	protein-coding
mm_67082.1	chr7	68276254	68276264	-	1	NA	intron (NR_040340, intron 1 of 3)	intron (NR_040340, intron 1 of 3)	335	NR_040340	100504026	Mm.426764	NR_040340	ENSMUSG00000086628	Gm16157	OTTMUSG00000031023	predicted gene 16157	ncRNA
mm_45335.1	chr5	65697834	65697848	-	1	NA	promoter-TSS (NM_001081321)	promoter-TSS (NM_001081321)	15	NM_001081321	71521	Mm.278974	NM_027818	ENSMUSG00000029202	Pds5a	9030416H16Rik|E230024D05Rik|mKIAA0648	PDS5 cohesin associated factor A	protein-coding
mm_133248.1	chr16	77236314	77236326	+	1	NA	Intergenic	Intergenic	-93008	NR_015543	77994	Mm.394688	NR_015543	ENSMUSG00000090386	Mir99ahg	2810055G20Rik|D730043B02Rik	Mir99a and Mirlet7c-1 host gene (non-protein coding)	ncRNA
mm_19296.1	chr2	90460736	90460746	-	1	NA	intron (NM_001135657, intron 7 of 25)	intron (NM_001135657, intron 7 of 25)	18433	NM_001135657	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_88005.1	chr10	67096398	67096406	+	1	NA	intron (NM_178606, intron 1 of 7)	CpG	586	NM_001204915	28193	Mm.41272	NM_178606	ENSMUSG00000019873	Reep3	D10Ucla1	receptor accessory protein 3	protein-coding
mm_38176.1	chr4	135264206	135264216	-	1	NA	intron (NM_013885, intron 1 of 5)	intron (NM_013885, intron 1 of 5)	8549	NM_013885	29876	Mm.257765	NM_013885	ENSMUSG00000037242	Clic4	D0Jmb3|TU-74|mc3s5|mtCLIC	chloride intracellular channel 4 (mitochondrial)	protein-coding
mm_135304.1	chr16	38712735	38712745	-	1	NA	5' UTR (NM_020260, exon 1 of 12)	5' UTR (NM_020260, exon 1 of 12)	295	NM_020260	12549	Mm.370848	NM_020260	ENSMUSG00000022799	Arhgap31	5830477L08Rik|AU041750|Cdgap|D330026I07Rik	Rho GTPase activating protein 31	protein-coding
mm_154907.1	chrX	21146685	21146689	+	1	NA	Intergenic	Intergenic	28273	NM_001205086	385338	Mm.298019	NM_001205086		Ssxa1	Gm1532|Ssxa	synovial sarcoma, X member A1	protein-coding
mm_142551.1	chr17	46629358	46629378	-	1	NA	5' UTR (NM_175168, exon 1 of 20)	5' UTR (NM_175168, exon 1 of 20)	136	NM_175168	71461	Mm.181833	NM_175168	ENSMUSG00000023972	Ptk7	8430404F20Rik|chz|mPTK7/CCK4	PTK7 protein tyrosine kinase 7	protein-coding
mm_80464.1	chr9	78113233	78113248	+	1	NA	promoter-TSS (NM_019987)	promoter-TSS (NM_019987)	2	NM_019987	56542	Mm.288719	NM_019987	ENSMUSG00000009828	Ick	2210420N10Rik|AI848300|Mrk	intestinal cell kinase	protein-coding
mm_32418.1	chr4	107050085	107050088	+	1	NA	TTS (NM_198438)	TTS (NM_198438)	16780	NM_025500	56280	Mm.29517	NM_025500	ENSMUSG00000028622	Mrpl37	2300004O14Rik|AI132596|MRP-L2|Rpml2	mitochondrial ribosomal protein L37	protein-coding
mm_3160.1	chr1	135231985	135232002	+	1	NA	Intergenic	Intergenic	26479	NM_001163131	13710	Mm.441439	NM_007921	ENSMUSG00000003051	Elf3	ESE-1|ESX|jen	E74-like factor 3	protein-coding
mm_83844.1	chr9	54474125	54474145	-	1	NA	intron (NM_172771, intron 3 of 43)	intron (NM_172771, intron 3 of 43)	27491	NM_172771	235380	Mm.93636	NM_172771	ENSMUSG00000041268	Dmxl2	6330586A12|6430411K14Rik|E130119P06Rik|mKIAA0856	Dmx-like 2	protein-coding
mm_125418.1	chr15	41830922	41831001	+	1	NA	promoter-TSS (NM_001130164)	promoter-TSS (NM_001130164)	3	NM_001130164	170719	Mm.254267	NM_130885	ENSMUSG00000022307	Oxr1	2210416C20Rik|C7|C7B	oxidation resistance 1	protein-coding
mm_97292.1	chr11	76243727	76243776	+	1	NA	promoter-TSS (NM_183263)	promoter-TSS (NM_183263)	15	NM_183263	67390	Mm.24886	NM_183263	ENSMUSG00000038046	Rnmtl1	4833420N02Rik|AI255153|HC90|Mrm3	RNA methyltransferase like 1	protein-coding
mm_137238.1	chr17	24454857	24454881	+	1	NA	intron (NR_125990, intron 1 of 13)	intron (NR_125990, intron 1 of 13)	523	NM_001301784	13560	Mm.163132	NM_007893	ENSMUSG00000024137	E4f1	p120E4F|phi-AP3	E4F transcription factor 1	protein-coding
mm_138996.1	chr17	45555795	45555799	+	1	NA	promoter-TSS (NM_008690)	promoter-TSS (NM_008690)	97	NM_001304956	18037	Mm.57043	NM_008690	ENSMUSG00000023947	Nfkbie	I-kappa-B-epsilon|IKBE|IkB-E|NF-kappa-BIE|ikB-epsilon	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, epsilon	protein-coding
mm_3621.1	chr1	152750524	152750526	+	1	NA	promoter-TSS (NM_001081197)	promoter-TSS (NM_001081197)	-26	NM_001081197	71281	Mm.158650	NM_001081197	ENSMUSG00000055547	Apobec4	4933431M11Rik	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 4 (putative)	protein-coding
mm_8138.1	chr1	136255859	136255876	-	1	NA	Intergenic	MIRc|SINE|MIR	5006	NM_001101516	383563	Mm.40367	NM_001101516	ENSMUSG00000052759	Gpr25	Gm1300	G protein-coupled receptor 25	protein-coding
mm_108942.1	chr12	102270416	102270417	+	1	NA	Intergenic	Intergenic	-12658	NM_177620	217835	Mm.24145	NM_177620	ENSMUSG00000044456	Rin3	6430500K07|C86933	Ras and Rab interactor 3	protein-coding
mm_143275.1	chr17	65675042	65675051	-	1	NA	intron (NM_133685, intron 5 of 6)	intron (NM_133685, intron 5 of 6)	-32842	NM_001146002	213272	Mm.255732	NM_153519	ENSMUSG00000050612	Txndc2	AU021712|Sptrx-1|Sptrx1|Trx4	thioredoxin domain containing 2 (spermatozoa)	protein-coding
mm_76411.1	chr8	84893888	84893900	-	1	NA	promoter-TSS (NM_001044744)	promoter-TSS (NM_001044744)	27	NM_001044744	270076	Mm.2475	NM_008097	ENSMUSG00000003809	Gcdh	9030411L18|AI266902|D17825|GCD	glutaryl-Coenzyme A dehydrogenase	protein-coding
mm_124076.1	chr14	78629287	78629292	-	1	NA	promoter-TSS (NM_001281794)	promoter-TSS (NM_001281794)	1	NM_001253766	380921	Mm.89591	NM_001081336	ENSMUSG00000034731	Dgkh	5930402B05Rik|D130015C16|DGK	diacylglycerol kinase, eta	protein-coding
mm_11892.1	chr2	49787676	49787695	+	1	NA	promoter-TSS (NM_027990)	promoter-TSS (NM_027990)	-1	NM_027990	71897	Mm.41381	NM_027990	ENSMUSG00000026765	Lypd6b	2310010M24Rik|AW049525	LY6/PLAUR domain containing 6B	protein-coding
mm_35174.1	chr4	15148942	15148952	-	1	NA	5' UTR (NM_178617, exon 1 of 13)	5' UTR (NM_178617, exon 1 of 13)	184	NM_178617	69352	Mm.389031	NM_178617	ENSMUSG00000040536	Necab1	1700003H21Rik|Efcbp1|STIP-1	N-terminal EF-hand calcium binding protein 1	protein-coding
mm_157086.1	chrX	9436315	9436346	-	1	NA	3' UTR (NM_007807, exon 13 of 13)	3' UTR (NM_007807, exon 13 of 13)	32994	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_95113.1	chr11	34075296	34075309	+	1	NA	intron (NM_010696, intron 10 of 20)	intron (NM_010696, intron 10 of 20)	28101	NM_010696	16822	Mm.265350	NM_010696	ENSMUSG00000002699	Lcp2	AI323664|BB161688|SLP-76|SLP76|m1Khoe|twm	lymphocyte cytosolic protein 2	protein-coding
mm_13925.1	chr2	120850120	120850135	+	1	NA	promoter-TSS (NR_038350)	promoter-TSS (NR_038350)	291	NM_001024857	140810	Mm.275698	NM_080788	ENSMUSG00000090100	Ttbk2	2610507N02Rik|AI326283|B930008N24Rik|TTK|Ttbk|Ttbk1|mKIAA0847	tau tubulin kinase 2	protein-coding
mm_48348.1	chr5	139325617	139325627	-	1	NA	promoter-TSS (NM_172723)	promoter-TSS (NM_172723)	-158	NM_172723	231821	Mm.297819	NM_172723	ENSMUSG00000056413	Adap1	4930431P11Rik|Centa1|GC1L|p42IP4	ArfGAP with dual PH domains 1	protein-coding
mm_141864.1	chr17	34804515	34804537	-	1	NA	promoter-TSS (NM_009995)	promoter-TSS (NM_009995)	-100	NM_009995	13079	Mm.440407	NM_009995	ENSMUSG00000024365	Cyp21a1	21-OH|21OH|21OHA|21OHB|CYP21OH-A|Cyp21|Cyp21-ps1|Cyp21B|Cyp21a2-ps|Cyp21a2ps|Oh21-1|Oh21-2	cytochrome P450, family 21, subfamily a, polypeptide 1	protein-coding
mm_27728.1	chr3	69006424	69006429	-	1	NA	intron (NM_133786, intron 2 of 23)	intron (NM_133786, intron 2 of 23)	1454	NM_133786	70099	Mm.206841	NM_133786	ENSMUSG00000034349	Smc4	2500002A22Rik|C79747|SMC-4|Smc4l1	structural maintenance of chromosomes 4	protein-coding
mm_119454.1	chr14	47001355	47001377	+	1	NA	promoter-TSS (NM_001163433)	promoter-TSS (NM_001163433)	26	NM_001163433	74480	Mm.214454	NM_028966	ENSMUSG00000021838	Samd4	1700024G08Rik|1700111L17Rik|4933436G17Rik|Samd4a|Smaug|Smaug1|sunk	sterile alpha motif domain containing 4	protein-coding
mm_171969.1	chr5	88162605	88162627	-	1	NA	Intergenic	ERVB7_1-LTR_MM|LTR|ERVK	76060	NM_001252680	20600	Mm.1397	NM_021289	ENSMUSG00000029281	Smr2	MSG2|Vcs2	submaxillary gland androgen regulated protein 2	protein-coding
mm_164454.1	chr16	55262156	55262159	+	1	NA	intron (NM_178720, intron 3 of 11)	MT2B|LTR|ERVL	21080	NM_178720	239852	Mm.245045	NM_178720	ENSMUSG00000064310	Zpld1	9430016A21Rik	zona pellucida like domain containing 1	protein-coding
mm_150662.1	chr19	41981662	41981706	+	1	NA	promoter-TSS (NM_028152)	promoter-TSS (NM_028152)	-79	NM_145500	226122	Mm.22948	NM_145500	ENSMUSG00000025171	Ubtd1	BC016129	ubiquitin domain containing 1	protein-coding
mm_41890.1	chr5	105495621	105495631	+	1	NA	Intergenic	Intergenic	-23845	NM_133897	100604	Mm.319847	NM_133897	ENSMUSG00000054720	Lrrc8c	AD158|AI326115|E430036I04Rik|fad158	leucine rich repeat containing 8 family, member C	protein-coding
mm_76563.1	chr8	88635977	88635987	-	1	NA	intron (NM_027840, intron 1 of 3)	intron (NM_027840, intron 1 of 3)	146	NM_027840	71607	Mm.270607	NM_027840	ENSMUSG00000031662	Snx20	9130017C17Rik	sorting nexin 20	protein-coding
mm_50321.1	chr6	48065925	48065966	+	1	NA	intron (NM_001163475, intron 6 of 6)	RLTR31D_MM|LTR|ERVK	-17831	NM_001081382	72306	Mm.381553	NM_001081382	ENSMUSG00000071477	Zfp777	2500002G23Rik	zinc finger protein 777	protein-coding
mm_68975.1	chr7	126587534	126587537	-	1	NA	exon (NM_138310, exon 2 of 4)	exon (NM_138310, exon 2 of 4)	-1718	NM_001146311	12752	Mm.268930	NM_009907	ENSMUSG00000030720	Cln3	AI323623	ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease)	protein-coding
mm_6546.1	chr1	75128644	75128655	-	1	NA	intron (NM_194333, intron 9 of 11)	intron (NM_194333, intron 9 of 11)	5241	NM_194333	22626	Mm.68157	NM_194333	ENSMUSG00000026205	Slc23a3	SVCT3|Yspl1	solute carrier family 23 (nucleobase transporters), member 3	protein-coding
mm_49278.1	chr6	17637672	17637678	+	1	NA	intron (NM_007604, intron 1 of 9)	intron (NM_007604, intron 1 of 9)	577	NM_007604	12343	Mm.392504	NM_007604	ENSMUSG00000015733	Capza2	1110053K06Rik|AW208808|Cappa2	capping protein (actin filament) muscle Z-line, alpha 2	protein-coding
mm_99447.1	chr11	102433925	102433957	+	1	NA	exon (NM_008175, exon 5 of 13)	exon (NM_008175, exon 5 of 13)	3619	NM_008175	14824	Mm.1568	NM_008175	ENSMUSG00000034708	Grn	Pgrn|epithelin	granulin	protein-coding
mm_57575.1	chr6	127148751	127148774	-	1	NA	promoter-TSS (NR_040275)	promoter-TSS (NR_040275)	-627	NR_040274	77558	Mm.358918	NR_040273	ENSMUSG00000097166	9330179D12Rik	-	RIKEN cDNA 9330179D12 gene	ncRNA
mm_117205.1	chr13	64076599	64076617	-	1	NA	intron (NM_008291, intron 2 of 10)	intron (NM_008291, intron 2 of 10)	12593	NM_008291	15487	Mm.5109	NM_008291	ENSMUSG00000033122	Hsd17b3	-	hydroxysteroid (17-beta) dehydrogenase 3	protein-coding
mm_136954.1	chr17	14945299	14945325	+	1	NA	3' UTR (NM_001083881, exon 2 of 2)	3' UTR (NM_001083881, exon 2 of 2)	2128	NM_026451	67912	Mm.390949	NM_026451	ENSMUSG00000050088	1600012H06Rik	-	RIKEN cDNA 1600012H06 gene	protein-coding
mm_158611.1	chrX	152643865	152643881	-	1	NA	5' UTR (NM_001290687, exon 1 of 6)	5' UTR (NM_001290687, exon 1 of 6)	276	NM_001290687	110380	Mm.40796	NM_172441	ENSMUSG00000045180	Shroom2	4832440C16|Apxl|C630003H05Rik|Shrm2	shroom family member 2	protein-coding
mm_90329.1	chr10	127078965	127078965	+	1	NA	promoter-TSS (NM_001301014)	promoter-TSS (NM_001301014)	58	NM_001033263	216439	Mm.336761	NM_001033263	ENSMUSG00000025422	Agap2	AGAP-2|Centg1|PIKE|cnt-g1|mKIAA0167	ArfGAP with GTPase domain, ankyrin repeat and PH domain 2	protein-coding
mm_4898.1	chr1	189782005	189782012	+	1	NA	intron (NM_008976, intron 1 of 18)	intron (NM_008976, intron 1 of 18)	53740	NM_008976	19250	Mm.4498	NM_008976	ENSMUSG00000026604	Ptpn14	C130080N23Rik|OTTMUSG00000022087|PTP36	protein tyrosine phosphatase, non-receptor type 14	protein-coding
mm_66944.1	chr7	61982291	61982306	-	1	NA	promoter-TSS (NR_037287)	promoter-TSS (NR_037287)	5	NR_015599	320026	Mm.131850	NR_015599	ENSMUSG00000109321	A330076H08Rik	Mirh1	RIKEN cDNA A330076H08 gene	ncRNA
mm_81927.1	chr9	120175476	120175485	+	1	NA	3' UTR (NM_001039364, exon 3 of 3)	3' UTR (NM_001039364, exon 3 of 3)	25738	NM_001039364	17433	Mm.486167	NM_008614	ENSMUSG00000032517	Mobp	AI835053|AI839848|MOBP155|MOBP170|MOBP69|MOBP73|MOBP81|R74645	myelin-associated oligodendrocytic basic protein	protein-coding
mm_137184.1	chr17	23816404	23816417	+	1	NA	exon (NM_175229, exon 10 of 14)	exon (NM_175229, exon 10 of 14)	12699	NM_026305	67673	Mm.153758	NM_026305	ENSMUSG00000055839	Elob	0610040H15Rik|Tceb2	elongin B	protein-coding
mm_66108.1	chr7	31041710	31041720	-	1	NA	TTS (NM_022007)	TTS (NM_022007)	124	NM_001111073	18301	Mm.1870	NM_008761	ENSMUSG00000009687	Fxyd5	EF-8|Oit2|RIC	FXYD domain-containing ion transport regulator 5	protein-coding
mm_120642.1	chr14	70521823	70521833	+	1	NA	exon (NM_011359, exon 4 of 6)	exon (NM_011359, exon 4 of 6)	-1568	NR_033241	12153	Mm.27757	NM_009755	ENSMUSG00000022098	Bmp1	Pcp|Tld	bone morphogenetic protein 1	protein-coding
mm_160622.1	chr9	97018279	97018279	-	1	NA	promoter-TSS (NM_145134)	promoter-TSS (NM_145134)	76	NM_145134	211949	Mm.491271	NM_145134	ENSMUSG00000046997	Spsb4	D030068E18Rik|SSB-4|Ssb4	splA/ryanodine receptor domain and SOCS box containing 4	protein-coding
mm_104115.1	chr11	86730303	86730371	-	1	NA	exon (NM_001003908, exon 6 of 32)	exon (NM_001003908, exon 6 of 32)	27155	NM_001003908	67300	Mm.254588	NM_001003908	ENSMUSG00000047126	Cltc	3110065L21Rik|CHC|R74732	clathrin, heavy polypeptide (Hc)	protein-coding
mm_129326.1	chr15	77771211	77771227	-	1	NA	exon (NM_022410, exon 27 of 41)	exon (NM_022410, exon 27 of 41)	-15990	NM_001081970	239552	Mm.125650	NM_001081970	ENSMUSG00000056656	Apol8	9830006J20Rik|APOL-II|Apol2	apolipoprotein L 8	protein-coding
mm_23236.1	chr3	50901030	50901064	+	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	-323400	NM_009834	12457	Mm.86541	NM_009834	ENSMUSG00000023087	Noct	AU043840|Ccr4|Ccrn4l	nocturnin	protein-coding
mm_111589.1	chr12	101975684	101975746	-	1	NA	promoter-TSS (NM_016856)	promoter-TSS (NM_016856)	-259	NM_016856	51786	Mm.716	NM_016856	ENSMUSG00000041781	Cpsf2	100kDa|2610024B04Rik|AI662483|Cpsf|MCPSF|mKIAA1367	cleavage and polyadenylation specific factor 2	protein-coding
mm_36796.1	chr4	103114813	103114836	-	1	NA	promoter-TSS (NM_146254)	promoter-TSS (NM_146254)	434	NM_001286222	71148	Mm.288721	NM_027696	ENSMUSG00000028522	Mier1	4933425I22Rik|5830411K19Rik|er1	MEIR1 treanscription regulator	protein-coding
mm_1527.1	chr1	72849080	72849086	+	1	NA	intron (NM_001310659, intron 1 of 3)	intron (NM_001310659, intron 1 of 3)	23696	NM_001310659	16008	Mm.141936	NM_008342	ENSMUSG00000039323	Igfbp2	AI255832|IBP-2|Igfbp-2|mIGFBP-2	insulin-like growth factor binding protein 2	protein-coding
mm_64981.1	chr7	16915592	16915602	-	1	NA	3' UTR (NM_007590, exon 6 of 6)	3' UTR (NM_007590, exon 6 of 6)	8435	NM_007590	12315	Mm.288630	NM_007590	ENSMUSG00000019370	Calm3	CaMA|R75142	calmodulin 3	protein-coding
mm_2269.1	chr1	91214525	91214538	+	1	NA	intron (NM_016894, intron 2 of 2)	intron (NM_016894, intron 2 of 2)	34709	NM_001168392	51801	Mm.3272	NM_016894	ENSMUSG00000034353	Ramp1	9130218E19Rik	receptor (calcitonin) activity modifying protein 1	protein-coding
mm_170183.1	chr17	6122134	6122137	-	1	NA	intron (NM_001103181, intron 1 of 13)	C-rich|Low_complexity|Low_complexity	15305	NM_001103181	68842	Mm.449307	NM_054040	ENSMUSG00000034377	Tulp4	1110057P05Rik|2210038L17Rik|Tusp	tubby like protein 4	protein-coding
mm_92254.1	chr10	70599315	70599323	-	1	NA	promoter-TSS (NM_178621)	promoter-TSS (NM_178621)	-28	NM_178621	70911	Mm.19825	NM_178621	ENSMUSG00000037747	Phyhipl	4921522K17Rik|AI267048	phytanoyl-CoA hydroxylase interacting protein-like	protein-coding
mm_101049.1	chr11	8635907	8635914	-	1	NA	intron (NM_001083587, intron 1 of 30)	intron (NM_001083587, intron 1 of 30)	28625	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_90808.1	chr10	7681119	7681163	-	1	NA	promoter-TSS (NR_033219)	promoter-TSS (NR_033219)	17	NR_033219	407824	Mm.393120	NR_033219		BC020402	-	cDNA sequence BC020402	ncRNA
mm_161537.1	chr15	102936837	102936837	+	1	NA	promoter-TSS (NM_010463)	promoter-TSS (NM_010463)	-16	NM_010463	15421	Mm.221179	NM_010463	ENSMUSG00000050328	Hoxc12	Hox-3.8	homeobox C12	protein-coding
mm_165389.1	chr2	131807223	131807223	+	1	NA	Intergenic	Intergenic	40433	NR_029381	414081	Mm.246905	NR_029381	ENSMUSG00000086822	5330413P13Rik	-	RIKEN cDNA 5330413P13 gene	ncRNA
mm_43764.1	chr5	140705077	140705091	+	1	NA	promoter-TSS (NM_181066)	promoter-TSS (NM_181066)	18	NM_001276287	231841	Mm.271932	NM_172724	ENSMUSG00000000148	Brat1	AA881470|Baat1	BRCA1-associated ATM activator 1	protein-coding
mm_17984.1	chr2	37802176	37802204	-	1	NA	exon (NM_146122, exon 21 of 22)	exon (NM_146122, exon 21 of 22)	25941	NM_001163566	241324	Mm.392369	NM_001163566	ENSMUSG00000035403	Crb2	5930402A21|BC043114	crumbs family member 2	protein-coding
mm_35846.1	chr4	48435100	48435108	-	1	NA	intron (NM_172304, intron 13 of 15)	intron (NM_172304, intron 13 of 15)	38318	NM_172304	269536	Mm.272025	NM_172304	ENSMUSG00000028345	Tex10	2610206N19Rik|2810462N03Rik|BC006867	testis expressed gene 10	protein-coding
mm_108476.1	chr12	83659429	83659439	+	1	NA	exon (NM_027349, exon 7 of 19)	exon (NM_027349, exon 7 of 19)	27200	NM_027349	67039	Mm.46005	NM_027349	ENSMUSG00000010608	Rbm25	2600011C06Rik|2610015J01Rik|A130095G20Rik|AI159652|AL023075|AU043498|RNPC7	RNA binding motif protein 25	protein-coding
mm_113240.1	chr13	27312653	27312656	+	1	NA	promoter-TSS (NM_011166)	promoter-TSS (NM_011166)	27	NM_011166	19111	Mm.7512	NM_011166	ENSMUSG00000069259	Prl6a1	Ghd10|PLP-B|Prlpb	prolactin family 6, subfamily a, member 1	protein-coding
mm_151730.1	chr19	4876871	4876880	-	1	NA	intron (NM_013456, intron 1 of 20)	intron (NM_013456, intron 1 of 20)	1034	NM_013456	11474	Mm.5316	NM_013456	ENSMUSG00000006457	Actn3	-	actinin alpha 3	protein-coding
mm_114843.1	chr13	92661015	92661060	+	1	NA	exon (NM_172588, exon 2 of 12)	exon (NM_172588, exon 2 of 12)	49899	NM_172588	218442	Mm.297970	NM_172588	ENSMUSG00000021703	Serinc5	A130038L21Rik|AIGP3|C86123|TPO1	serine incorporator 5	protein-coding
mm_163838.1	chr14	19417841	19417862	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	184736	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_65379.1	chr7	25090669	25090681	-	1	NA	TTS (NM_001163556)	TTS (NM_001163556)	6500	NR_105855	102465968		NR_105855	ENSMUSG00000098441	Mir6537	Gm27808|mmu-mir-6537	microRNA 6537	ncRNA
mm_26275.1	chr3	142505470	142505479	+	1	NA	exon (NM_153564, exon 7 of 11)	exon (NM_153564, exon 7 of 11)	8540	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_36478.1	chr4	82859572	82859679	-	1	NA	promoter-TSS (NM_026647)	promoter-TSS (NM_026647)	36	NM_026647	68268	Mm.32047	NM_026647	ENSMUSG00000028403	Zdhhc21	9130404H11Rik|AL024349|D130004H04Rik|dep	zinc finger, DHHC domain containing 21	protein-coding
mm_100591.1	chr11	120958011	120958017	+	1	NA	exon (NM_001038654, exon 5 of 5)	exon (NM_001038654, exon 5 of 5)	8947	NM_001038654	80879	Mm.28632	NM_030696	ENSMUSG00000025161	Slc16a3	Mct3|Mct4	solute carrier family 16 (monocarboxylic acid transporters), member 3	protein-coding
mm_25625.1	chr3	118777535	118777535	+	1	NA	intron (NM_170778, intron 4 of 22)	intron (NM_170778, intron 4 of 22)	215357	NM_170778	99586	Mm.27907	NM_170778	ENSMUSG00000033308	Dpyd	AI315208|DPD|E330028L06Rik	dihydropyrimidine dehydrogenase	protein-coding
mm_156055.1	chrX	109118321	109118370	+	1	NA	intron (NM_019989, intron 1 of 3)	intron (NM_019989, intron 1 of 3)	22938	NM_019989	56726	Mm.260760	NM_019989	ENSMUSG00000031246	Sh3bgrl	1190008F14Rik	SH3-binding domain glutamic acid-rich protein like	protein-coding
mm_167272.1	chr8	33517275	33517300	+	1	NA	Intergenic	CpG	32976	NR_033589	628431	Mm.376526	NR_033589		Hmgb1-rs17	Hmg1-rs17	high mobility group box 1, related sequence 17	pseudo
mm_121051.1	chr14	84445329	84445360	+	1	NA	5' UTR (NM_001013753, exon 1 of 4)	5' UTR (NM_001013753, exon 1 of 4)	1781	NM_001013753	219228	Mm.153643	NM_001013753	ENSMUSG00000035566	Pcdh17	C030033F14Rik|Gm78	protocadherin 17	protein-coding
mm_152787.1	chr19	21460883	21460884	-	1	NA	intron (NM_010266, intron 1 of 13)	ID_B1|SINE|B4	11778	NM_010266	14544	Mm.45054	NM_010266	ENSMUSG00000058624	Gda	AU015411|AW047581|GAH	guanine deaminase	protein-coding
mm_131568.1	chr16	18217874	18217884	+	1	NA	Intergenic	Intergenic	-4016	NR_015575	66779	Mm.387525	NR_015575		4933432I09Rik	-	RIKEN cDNA 4933432I09 gene	ncRNA
mm_103207.1	chr11	70652927	70652936	-	1	NA	exon (NM_011072, exon 2 of 3)	exon (NM_011072, exon 2 of 3)	1719	NM_011072	18643	Mm.2647	NM_011072	ENSMUSG00000018293	Pfn1	Pfn	profilin 1	protein-coding
mm_117497.1	chr13	78199028	78199048	-	1	NA	promoter-TSS (NM_010151)	promoter-TSS (NM_010151)	-165	NM_010151	13865	Mm.439653	NM_010151	ENSMUSG00000069171	Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR-3|EAR3|Erbal3|SVP44|Tcfcoup1	nuclear receptor subfamily 2, group F, member 1	protein-coding
mm_139175.1	chr17	47590554	47590582	+	1	NA	intron (NM_001081635, intron 2 of 6)	RLTR51A_Mm|LTR|ERVK?	-2899	NM_007632	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_158254.1	chrX	108765346	108765388	-	1	NA	intron (NM_001081477, intron 24 of 40)	intron (NM_001081477, intron 24 of 40)	68988	NM_001081477	382236	Mm.100112	NM_001081477	ENSMUSG00000063663	Brwd3	Brodl|D030064D06Rik|Gm596	bromodomain and WD repeat domain containing 3	protein-coding
mm_2510.1	chr1	106228181	106228191	+	1	NA	intron (NM_133821, intron 1 of 16)	RSINE1|SINE|B4	56317	NM_133821	98432	Mm.24115	NM_133821	ENSMUSG00000044340	Phlpp1	AI836256|Phlpp|Plekhe1|SCOP|mKIAA0606	PH domain and leucine rich repeat protein phosphatase 1	protein-coding
mm_34319.1	chr4	141821383	141821420	+	1	NA	exon (NM_007919, exon 5 of 8)	exon (NM_007919, exon 5 of 8)	4604	NM_007919	13706	Mm.45316	NM_007919	ENSMUSG00000058579	Cela2a	Ela-2|Ela2|Ela2a	chymotrypsin-like elastase family, member 2A	protein-coding
mm_97415.1	chr11	77982711	77982823	+	1	NA	promoter-TSS (NM_174852)	promoter-TSS (NM_174852)	-49	NM_174852	268448	Mm.274329	NM_174852	ENSMUSG00000037791	Phf12	2410142K10Rik|F630045O13|PF1|mKIAA1523	PHD finger protein 12	protein-coding
mm_45545.1	chr5	72868472	72868474	-	1	NA	promoter-TSS (NM_001113460)	promoter-TSS (NM_001113460)	-25	NM_001113460	21682	Mm.319581	NM_013689	ENSMUSG00000029217	Tec	-	tec protein tyrosine kinase	protein-coding
mm_55846.1	chr6	83326252	83326298	-	1	NA	intron (NM_145571, intron 1 of 5)	CpG	236	NM_145571	232157	Mm.29500	NM_145571	ENSMUSG00000043131	Mob1a	4022402H07Rik|MOB1|MOB4B|Mobk1b|Mobkl1b	MOB kinase activator 1A	protein-coding
mm_608.1	chr1	39907145	39907162	+	1	NA	intron (NM_001252200, intron 2 of 31)	intron (NM_001252200, intron 2 of 31)	6240	NM_008696	26921	Mm.491139	NM_008696	ENSMUSG00000026074	Map4k4	9430080K19Rik|AU043147|AU045934|AW046177|HGK|Nik	mitogen-activated protein kinase kinase kinase kinase 4	protein-coding
mm_15390.1	chr2	156721070	156721084	+	1	NA	promoter-TSS (NM_001042487)	promoter-TSS (NM_001042487)	112	NM_001042488	228836	Mm.22094	NM_146128	ENSMUSG00000061689	Dlgap4	AI225853|BC024558|DAP-4|DAP4|SAPAP-4|Sapap4|WBP16	discs, large homolog-associated protein 4 (Drosophila)	protein-coding
mm_30784.1	chr4	19575130	19575138	+	1	NA	promoter-TSS (NM_025476)	promoter-TSS (NM_025476)	68	NM_025476	66302	Mm.440686	NM_025476	ENSMUSG00000028229	Rmdn1	Fam82b|RMD-1	regulator of microtubule dynamics 1	protein-coding
mm_55696.1	chr6	72885426	72885429	-	1	NA	intron (NM_019715, intron 1 of 6)	intron (NM_019715, intron 1 of 6)	13865	NM_001347231	74287	Mm.29194	NM_019715	ENSMUSG00000055239	Kcmf1	1700094M07Rik|Debt91|Pmcf	potassium channel modulatory factor 1	protein-coding
mm_43179.1	chr5	127793285	127793285	+	1	NA	intron (NM_172885, intron 6 of 8)	intron (NM_172885, intron 6 of 8)	161023	NM_177005	319804	Mm.237888	NM_177005	ENSMUSG00000049971	Glt1d1	5730455A04Rik	glycosyltransferase 1 domain containing 1	protein-coding
mm_118272.1	chr13	112620677	112620683	-	1	NA	exon (NM_010029, exon 14 of 21)	exon (NM_010029, exon 14 of 21)	31630	NM_010029	13206	Mm.12818	NM_010029	ENSMUSG00000021758	Ddx4	AV206478|Mvh|VASA	DEAD (Asp-Glu-Ala-Asp) box polypeptide 4	protein-coding
mm_96176.1	chr11	61647704	61647724	+	1	NA	Intergenic	Intergenic	-5607	NM_027817	71520	Mm.202760	NM_027817	ENSMUSG00000004837	Grap	8430435N19Rik|BB233594	GRB2-related adaptor protein	protein-coding
mm_71064.1	chr8	34054635	34054647	+	1	NA	Intergenic	Intergenic	53173	NM_001293758	22428	Mm.150373	NM_011722	ENSMUSG00000031516	Dctn6	AU044699|WS-3|p27	dynactin 6	protein-coding
mm_170619.1	chr19	61313504	61313521	-	1	NA	Intergenic	Intergenic	-85094	NM_009970	12982	Mm.287228	NM_009970	ENSMUSG00000059326	Csf2ra	CD116|Csfgmra|GM-CSF-Ra|GM-CSFR	colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)	protein-coding
mm_97398.1	chr11	77838083	77838106	+	1	NA	intron (NM_001291214, intron 19 of 38)	intron (NM_001291214, intron 19 of 38)	36796	NM_001291215	360013	Mm.341248	NM_011586	ENSMUSG00000000631	Myo18a	MAJN|MyoPDZ|MysPDZ|SP-R210	myosin XVIIIA	protein-coding
mm_138534.1	chr17	35247004	35247033	+	1	NA	exon (NM_001252457, exon 5 of 11)	exon (NM_001252457, exon 5 of 11)	2943	NR_105941	102465589		NR_105941	ENSMUSG00000098499	Mir6975	Gm27693|mmu-mir-6975	microRNA 6975	ncRNA
mm_70460.1	chr8	11840515	11840530	+	1	NA	promoter-TSS (NM_029326)	promoter-TSS (NM_029326)	1	NM_029326	75528	Mm.440342	NM_029326	ENSMUSG00000031512	Tex29	1700018L24Rik	testis expressed 29	protein-coding
mm_90686.1	chr10	128933752	128933763	+	1	NA	promoter-TSS (NM_008398)	promoter-TSS (NM_008398)	-56	NM_008398	16404	Mm.179747	NM_008398	ENSMUSG00000025348	Itga7	[a]7|alpha7	integrin alpha 7	protein-coding
mm_32910.1	chr4	119132230	119132244	+	1	NA	exon (NM_011400, exon 3 of 10)	exon (NM_011400, exon 3 of 10)	23492	NM_011400	20525	Mm.21002	NM_011400	ENSMUSG00000028645	Slc2a1	Glut-1|Glut1	solute carrier family 2 (facilitated glucose transporter), member 1	protein-coding
mm_162682.1	chr10	13868757	13868776	-	1	NA	5' UTR (NM_025446, exon 1 of 6)	5' UTR (NM_025446, exon 1 of 6)	191	NM_025446	66253	Mm.45755	NM_025446	ENSMUSG00000019806	Aig1	1500031O19Rik|AV064870|AW413422|CGI-103	androgen-induced 1	protein-coding
mm_73453.1	chr8	106415320	106415396	+	1	NA	promoter-TSS (NM_011764)	promoter-TSS (NM_011764)	19	NM_011764	22751	Mm.295582	NM_011764	ENSMUSG00000031907	Zfp90	6430515L01Rik|KRAB17|NK10|Zfp64|Zfp83|mKIAA1954	zinc finger protein 90	protein-coding
mm_111697.1	chr12	103657096	103657112	-	1	NA	5' UTR (NM_007618, exon 1 of 5)	5' UTR (NM_007618, exon 1 of 5)	114	NM_007618	12401	Mm.290079	NM_007618	ENSMUSG00000060807	Serpina6	Cbg	serine (or cysteine) peptidase inhibitor, clade A, member 6	protein-coding
mm_35912.1	chr4	50827119	50827126	-	1	NA	Intergenic	L1_Mus4|LINE|L1	-389556	NM_001162865	74914	Mm.159368	NM_001162865	ENSMUSG00000039555	Cylc2	4930488P18Rik	cylicin, basic protein of sperm head cytoskeleton 2	protein-coding
mm_66224.1	chr7	34952986	34952994	-	1	NA	intron (NM_008820, intron 6 of 14)	intron (NM_008820, intron 6 of 14)	40583	NM_008820	18624	Mm.69751	NM_008820	ENSMUSG00000063931	Pepd	Pep-4|Pep4|dal	peptidase D	protein-coding
mm_13125.1	chr2	91710857	91710879	+	1	NA	promoter-TSS (NM_178724)	promoter-TSS (NM_178724)	-82	NM_178724	241547	Mm.130331	NM_178724	ENSMUSG00000027243	Harbi1	D230010M03Rik	harbinger transposase derived 1	protein-coding
mm_172195.1	chr6	51466305	51466311	-	1	NA	exon (NM_182650, exon 5 of 10)	exon (NM_182650, exon 5 of 10)	3586	NM_182650	53379	Mm.155896	NM_016806	ENSMUSG00000004980	Hnrnpa2b1	9130414A06Rik|Hnrpa2|Hnrpa2b1|hnrnp-A	heterogeneous nuclear ribonucleoprotein A2/B1	protein-coding
mm_63711.1	chr7	130692587	130692626	+	1	NA	promoter-TSS (NM_021314)	promoter-TSS (NM_021314)	50	NM_021314	57752	Mm.86322	NM_021314	ENSMUSG00000030852	Tacc2	mKIAA4180	transforming, acidic coiled-coil containing protein 2	protein-coding
mm_129614.1	chr15	80013212	80013226	-	1	NA	intron (NM_011057, intron 1 of 6)	CpG	1589	NM_011057	18591	Mm.144089	NM_011057	ENSMUSG00000000489	Pdgfb	PDGF-B|Sis	platelet derived growth factor, B polypeptide	protein-coding
mm_24044.1	chr3	87847005	87847067	+	1	NA	5' UTR (NM_021309, exon 1 of 7)	5' UTR (NM_021309, exon 1 of 7)	281	NM_021309	27371	Mm.86361	NM_021309	ENSMUSG00000028071	Sh2d2a	Lad|Ribp|Tsad	SH2 domain containing 2A	protein-coding
mm_26211.1	chr3	138744268	138744271	+	1	NA	intron (NM_019571, intron 1 of 7)	(TTTC)n|Simple_repeat|Simple_repeat	2061	NM_019571	56224	Mm.31927	NM_019571	ENSMUSG00000028152	Tspan5	2810455A09Rik|4930505M03Rik|NET-4|Tm4sf9	tetraspanin 5	protein-coding
mm_133403.1	chr16	84835044	84835056	+	1	NA	promoter-TSS (NM_001302216)	promoter-TSS (NM_001302216)	-28	NM_001302214	11957	Mm.353	NM_016755	ENSMUSG00000022890	Atp5j	CF6	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit F	protein-coding
mm_73368.1	chr8	105613227	105613243	+	1	NA	intron (NM_001081241, intron 1 of 21)	intron (NM_001081241, intron 1 of 21)	-2231	NR_035492	100316712		NR_035492	ENSMUSG00000089432	Mir1966	mir-1966|mmu-mir-1966	microRNA 1966	ncRNA
mm_84866.1	chr9	78630368	78630379	-	1	NA	intron (NM_153098, intron 2 of 32)	intron (NM_153098, intron 2 of 32)	14827	NM_153098	235505	Mm.32955	NM_153098	ENSMUSG00000046186	Cd109	9930012E15Rik|AI480638|GARP	CD109 antigen	protein-coding
mm_148658.1	chr19	5553365	5553369	+	1	NA	intron (NM_019935, intron 2 of 3)	intron (NM_019935, intron 2 of 3)	7208	NM_019935	18426	Mm.280225	NM_019935	ENSMUSG00000024922	Ovol1	BB147136|Ovo1|movo1	ovo like zinc finger 1	protein-coding
mm_49006.1	chr6	4757386	4757402	+	1	NA	3' UTR (NM_130877, exon 2 of 2)	3' UTR (NM_130877, exon 2 of 2)	10088	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_32077.1	chr4	98112025	98112030	+	1	NA	3' UTR (NM_001122953, exon 10 of 10)	3' UTR (NM_001122953, exon 10 of 10)	271238	NM_053157	94043	Mm.331719	NM_053157	ENSMUSG00000028563	Tm2d1	2310026L18Rik|AA990549|Bbp	TM2 domain containing 1	protein-coding
mm_37871.1	chr4	132353370	132353380	-	1	NA	intron (NR_003270, intron 1 of 2)	intron (NR_003270, intron 1 of 2)	311	NR_003270	399101	Mm.486919	NR_002904	ENSMUSG00000085241	Snhg3	Rnu17d|U17HG	small nucleolar RNA host gene 3	ncRNA
mm_29920.1	chr3	131490453	131490495	-	1	NA	Intergenic	CpG	-74294	NM_001289479	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_32575.1	chr4	110351481	110351487	+	1	NA	intron (NM_001163397, intron 1 of 5)	CpG	427	NM_001163397	15572	Mm.3970	NM_010488	ENSMUSG00000028546	Elavl4	Elav|Hud|PNEM	ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4 (Hu antigen D)	protein-coding
mm_133312.1	chr16	77637063	77637077	+	1	NA	Intergenic	Intergenic	-9203	NR_029540	723952		NR_029540	ENSMUSG00000065472	Mir125b-2	Mirn125b-2|mir-125b-2	microRNA 125b-2	ncRNA
mm_63993.1	chr7	140097122	140097152	+	1	NA	TTS (NM_009475)	TTS (NM_009475)	3741	NM_009475	22264	Mm.439707	NM_009475	ENSMUSG00000025467	Prap1	Upa	proline-rich acidic protein 1	protein-coding
mm_22798.1	chr3	22398923	22398923	+	1	NA	Intergenic	Intergenic	147553	NR_004439	19784		NR_004439		Rprl2	RPRH3|Rmrp3	ribonuclease P RNA-like 2	ncRNA
mm_131977.1	chr16	24984236	24984237	+	1	NA	3' UTR (NM_178665, exon 13 of 13)	3' UTR (NM_178665, exon 13 of 13)	-75403	NR_040374	319487	Mm.137341	NR_040374	ENSMUSG00000096960	A230028O05Rik	-	RIKEN cDNA A230028O05 gene	ncRNA
mm_108480.1	chr12	83660303	83660333	+	1	NA	exon (NM_027349, exon 8 of 19)	exon (NM_027349, exon 8 of 19)	28084	NM_027349	67039	Mm.46005	NM_027349	ENSMUSG00000010608	Rbm25	2600011C06Rik|2610015J01Rik|A130095G20Rik|AI159652|AL023075|AU043498|RNPC7	RNA binding motif protein 25	protein-coding
mm_78855.1	chr9	44379519	44379529	+	1	NA	promoter-TSS (NM_021395)	promoter-TSS (NM_021395)	34	NM_021395	12282	Mm.116721	NM_021395	ENSMUSG00000032115	Hyou1	AI415631|CBP-140|Cab140|Grp170|Orp150	hypoxia up-regulated 1	protein-coding
mm_167972.1	chrX	154685279	154685279	+	1	NA	Intergenic	IAPEY2_LTR|LTR|ERVK	-105949	NM_001037167	434881	Mm.357614	NM_001037167	ENSMUSG00000072888	Samt2	EG434881|Gm5647	spermatogenesis associated multipass transmembrane protein 2	protein-coding
mm_155237.1	chrX	57212078	57212097	+	1	NA	promoter-TSS (NM_011616)	promoter-TSS (NM_011616)	-56	NM_011616	21947	Mm.4861	NM_011616	ENSMUSG00000031132	Cd40lg	CD154|CD40-L|Cd40l|HIGM1|IGM|IMD3|Ly-62|Ly62|T-BAM|TRAP|Tnfsf5|Tnlg8b|gp39	CD40 ligand	protein-coding
mm_85719.1	chr9	108275072	108275082	-	1	NA	Intergenic	Intergenic	-11119	NM_001276486	13138	Mm.7524	NM_010017	ENSMUSG00000039952	Dag1	D9Wsu13e|DG|Dp427|Dp71	dystroglycan 1	protein-coding
mm_4581.1	chr1	178211142	178211190	+	1	NA	intron (NM_024282, intron 1 of 4)	intron (NM_024282, intron 1 of 4)	23749	NM_024282	78825	Mm.440132	NM_024282	ENSMUSG00000026502	Desi2	5830417C01Rik|DeSI-2|Fam152a|Pppde1	desumoylating isopeptidase 2	protein-coding
mm_65809.1	chr7	29007882	29007923	-	1	NA	intron (NM_009109, intron 101 of 105)	PB1D9|SINE|Alu	25048	NM_008279	26411	Mm.148278	NM_008279	ENSMUSG00000037337	Map4k1	Hpk1|mHPK1	mitogen-activated protein kinase kinase kinase kinase 1	protein-coding
mm_86949.1	chr10	24869999	24870050	+	1	NA	promoter-TSS (NM_001166416)	promoter-TSS (NM_001166416)	38	NM_027347	70208	Mm.28020	NM_027347	ENSMUSG00000019984	Med23	130kDa|3000002A17Rik|Crsp3|ESTM7|Sur2|X83317|mKIAA1216	mediator complex subunit 23	protein-coding
mm_159877.1	chr6	4905213	4905213	+	1	NA	intron (NM_181595, intron 1 of 15)	intron (NM_181595, intron 1 of 15)	1893	NM_181595	243725	Mm.332901	NM_181595	ENSMUSG00000032827	Ppp1r9a	2810430P21Rik|4930518N04Rik|5330407E15|A230094E16Rik|BB181831|NRB|mKIAA1222|neurabin-I	protein phosphatase 1, regulatory (inhibitor) subunit 9A	protein-coding
mm_65092.1	chr7	19266543	19266583	-	1	NA	intron (NR_104069, intron 1 of 10)	intron (NR_104069, intron 1 of 10)	5291	NM_001282021	22323	Mm.9684	NM_009499	ENSMUSG00000030403	Vasp	-	vasodilator-stimulated phosphoprotein	protein-coding
mm_78395.1	chr9	28920414	28920418	+	1	NA	3' UTR (NM_177906, exon 8 of 8)	3' UTR (NM_177906, exon 8 of 8)	1042713	NM_172290	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding
mm_138403.1	chr17	35059174	35059188	+	1	NA	TTS (NM_033444)	TTS (NM_033444)	146	NM_016765	51793	Mm.1457	NM_016765	ENSMUSG00000007039	Ddah2	1110003M04Rik|AU019324|AW413173|DDAH-2|DDAHII|Ddah|G6a|NG30	dimethylarginine dimethylaminohydrolase 2	protein-coding
mm_55835.1	chr6	83125187	83125199	-	1	NA	promoter-TSS (NM_023547)	promoter-TSS (NM_023547)	-164	NM_023547	70020	Mm.27814	NM_023547	ENSMUSG00000030034	Ino80b	2510009I23Rik|HMG1YL4|Hmga1l4|Papa1|Znhit4	INO80 complex subunit B	protein-coding
mm_92921.1	chr10	84440592	84440604	-	1	NA	promoter-TSS (NM_001004363)	promoter-TSS (NM_001004363)	-127	NM_001004363	77976	Mm.25874	NM_001004363	ENSMUSG00000020032	Nuak1	AU014801|AW494241|B230104P22Rik|Omphk1	NUAK family, SNF1-like kinase, 1	protein-coding
mm_42496.1	chr5	115476868	115476871	+	1	NA	Intergenic	ID4_|SINE|ID	7428	NM_001167691	75387	Mm.332616	NM_133760	ENSMUSG00000029524	Sirt4	4930596O17Rik	sirtuin 4	protein-coding
mm_37883.1	chr4	132463874	132463929	-	1	NA	promoter-TSS (NM_026039)	promoter-TSS (NM_026039)	20	NM_026039	67219	Mm.45929	NM_026039	ENSMUSG00000066042	Med18	2810046C01Rik	mediator complex subunit 18	protein-coding
mm_15972.1	chr2	166080749	166080759	+	1	NA	intron (NM_001252579, intron 14 of 20)	intron (NM_001252579, intron 14 of 20)	74531	NM_001252578	72043	Mm.1011	NM_028072	ENSMUSG00000006800	Sulf2	2010004N24Rik|AU020235|MSulf-2|mKIAA1247	sulfatase 2	protein-coding
mm_77475.1	chr8	122443364	122443403	-	1	NA	promoter-TSS (NM_138656)	promoter-TSS (NM_138656)	39	NM_138656	192156	Mm.28146	NM_138656	ENSMUSG00000006517	Mvd	C78718|Mpd	mevalonate (diphospho) decarboxylase	protein-coding
mm_145476.1	chr18	60376127	60376144	+	1	NA	intron (NM_021792, intron 1 of 1)	intron (NM_021792, intron 1 of 1)	106	NM_001146275	60440	Mm.261140	NM_021792	ENSMUSG00000054072	Iigp1	2900074L10Rik|AI046432|AW111922|Ifgga1|Iigp|Irga6	interferon inducible GTPase 1	protein-coding
mm_49377.1	chr6	24552857	24552859	+	1	NA	intron (NM_080847, intron 1 of 9)	intron (NM_080847, intron 1 of 9)	24714	NM_080847	78910	Mm.160150	NM_080847	ENSMUSG00000029685	Asb15	4930400E23Rik|Asb-15	ankyrin repeat and SOCS box-containing 15	protein-coding
mm_160797.1	chr11	4704334	4704334	-	1	NA	promoter-TSS (NM_026015)	promoter-TSS (NM_026015)	10	NM_197979	66152	Mm.269736	NM_197979	ENSMUSG00000059534	Uqcr10	1110020P15Rik|AA960494|Ucrc	ubiquinol-cytochrome c reductase, complex III subunit X	protein-coding
mm_136802.1	chr17	12318863	12318905	+	1	NA	promoter-TSS (NR_045290)	promoter-TSS (NR_045290)	31	NR_045290	224523	Mm.188855	NR_045290	ENSMUSG00000097350	4732491K20Rik	-	RIKEN cDNA 4732491K20 gene	ncRNA
mm_83923.1	chr9	56620687	56620697	-	1	NA	exon (NM_181074, exon 4 of 4)	exon (NM_181074, exon 4 of 4)	14956	NM_001311076	235402	Mm.246605	NM_181074	ENSMUSG00000049556	Lingo1	4930471K13Rik|AV148400|LERN1|LINGO-1|Lrrn6a|UNQ201	leucine rich repeat and Ig domain containing 1	protein-coding
mm_130270.1	chr15	96698750	96698764	-	1	NA	5' UTR (NM_175121, exon 2 of 16)	5' UTR (NM_175121, exon 2 of 16)	941	NM_175121	67760	Mm.46754	NM_175121	ENSMUSG00000022462	Slc38a2	5033402L14Rik|AI316867|ATA2|SAT2|mKIAA1382	solute carrier family 38, member 2	protein-coding
mm_6620.1	chr1	75549811	75549816	-	1	NA	intron (NM_009208, intron 6 of 22)	intron (NM_009208, intron 6 of 22)	3547	NM_009208	20536	Mm.5053	NM_009208	ENSMUSG00000006576	Slc4a3	A930038D23Rik|Ae3	solute carrier family 4 (anion exchanger), member 3	protein-coding
mm_103701.1	chr11	79516473	79516483	-	1	NA	exon (NM_001077496, exon 2 of 2)	exon (NM_001077496, exon 2 of 2)	7284	NM_001077496	216984	Mm.439665	NM_001077496	ENSMUSG00000093938	Evi2b	Evi-2|Evi2	ecotropic viral integration site 2b	protein-coding
mm_60568.1	chr7	44481475	44481485	+	1	NA	Intergenic	Intergenic	-3037	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_84713.1	chr9	73113329	73113344	-	1	NA	promoter-TSS (NM_198609)	promoter-TSS (NM_198609)	-133	NM_198609	225215	Mm.379366	NM_198609	ENSMUSG00000032215	Rsl24d1	2410159K22Rik	ribosomal L24 domain containing 1	protein-coding
mm_106040.1	chr11	116079250	116079292	-	1	NA	3' UTR (NM_016852, exon 8 of 8)	3' UTR (NM_016852, exon 8 of 8)	-1310	NM_001009573	70450	Mm.259460	NM_001009573	ENSMUSG00000057948	Unc13d	2610108D09Rik|Jinx|Munc13-4|mFLJ00067	unc-13 homolog D (C. elegans)	protein-coding
mm_135874.1	chr16	62846948	62847005	-	1	NA	promoter-TSS (NM_026577)	promoter-TSS (NM_026577)	64	NM_026577	68146	Mm.96833	NM_026577	ENSMUSG00000022911	Arl13b	A530097K21Rik|A930014M17Rik|Arl2l1|C530009C10Rik|hnn	ADP-ribosylation factor-like 13B	protein-coding
mm_103359.1	chr11	74897053	74897094	-	1	NA	promoter-TSS (NM_197943)	promoter-TSS (NM_197943)	7	NM_197943	97761	Mm.245894	NM_197943	ENSMUSG00000038351	Sgsm2	D630003G22Rik|R74628|Rutbc1|mKIAA0397	small G protein signaling modulator 2	protein-coding
mm_2435.1	chr1	97024399	97024416	+	1	NA	Intergenic	Intergenic	-26847	NR_120500	67854	Mm.263706	NM_026413	ENSMUSG00000045463	Slco6b1	1700022M03Rik	solute carrier organic anion transporter family, member 6b1	ncRNA
mm_134127.1	chr16	10395439	10395460	-	1	NA	promoter-TSS (NM_001099275)	promoter-TSS (NM_001099275)	-1	NM_001099275	70426	Mm.142181	NM_001099275	ENSMUSG00000039179	Tekt5	3300001K11Rik	tektin 5	protein-coding
mm_42729.1	chr5	120621357	120621397	+	1	NA	intron (NM_028041, intron 10 of 19)	intron (NM_028041, intron 10 of 19)	8247	NM_028041	71990	Mm.24495	NM_028041	ENSMUSG00000029599	Ddx54	2410015A15Rik|AI414901|DP97	DEAD (Asp-Glu-Ala-Asp) box polypeptide 54	protein-coding
mm_143174.1	chr17	57242710	57242710	-	1	NA	intron (NM_001308072, intron 7 of 16)	intron (NM_001308072, intron 7 of 16)	4760	NM_001308074	78308	Mm.28468	NM_030084	ENSMUSG00000005823	Gpr108	1810015L19Rik|AA589464|C79132|Lustr2	G protein-coupled receptor 108	protein-coding
mm_94360.1	chr11	5009465	5009483	+	1	NA	intron (NM_007454, intron 1 of 20)	intron (NM_007454, intron 1 of 20)	22650	NM_007454	11764	Mm.274816	NM_007454	ENSMUSG00000009090	Ap1b1	Adtb1|b2b1660Clo	adaptor protein complex AP-1, beta 1 subunit	protein-coding
mm_39867.1	chr5	31054822	31054865	+	1	NA	promoter-TSS (NM_001289522)	promoter-TSS (NM_001289522)	63	NM_001289522	69719	Mm.305535	NM_023525	ENSMUSG00000013629	Cad	2410008J01Rik|AU018859|Cpad	carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase	protein-coding
mm_26443.1	chr3	142635282	142635294	+	1	NA	exon (NM_010260, exon 9 of 11)	exon (NM_010260, exon 9 of 11)	-11342	NR_105802	102465200		NR_105802	ENSMUSG00000098871	Mir6381	Gm27963|mmu-mir-6381	microRNA 6381	ncRNA
mm_36007.1	chr4	56802243	56802262	-	1	NA	promoter-TSS (NM_026079)	promoter-TSS (NM_026079)	-77	NM_001081420	230234	Mm.268148	NM_001081420	ENSMUSG00000038827	Fam206a	simiate	family with sequence similarity 206, member A	protein-coding
mm_95867.1	chr11	58012532	58012535	+	1	NA	intron (NM_028451, intron 1 of 18)	intron (NM_028451, intron 1 of 18)	3469	NM_028451	73158	Mm.248843	NM_028451	ENSMUSG00000037331	Larp1	1810024J12Rik|3110040D16Rik|Larp|mKIAA0731	La ribonucleoprotein domain family, member 1	protein-coding
mm_113522.1	chr13	37825848	37825873	+	1	NA	promoter-TSS (NM_026830)	promoter-TSS (NM_026830)	-178	NM_026830	68750	Mm.491109	NM_026830	ENSMUSG00000039087	Rreb1	1110037N09Rik|AA414966|B930013M22Rik	ras responsive element binding protein 1	protein-coding
mm_114207.1	chr13	56144317	56144327	+	1	NA	Intergenic	Lx5|LINE|L1	-8772	NM_001159513	26914	Mm.283802	NM_012015	ENSMUSG00000015937	H2afy	H2AF12M|mH2a1|macroH2A1	H2A histone family, member Y	protein-coding
mm_60850.1	chr7	45830859	45830881	+	1	NA	promoter-TSS (NM_153419)	promoter-TSS (NM_153419)	-81	NM_153419	101612	Mm.274847	NM_153419	ENSMUSG00000053801	Grwd1	A301|AI504353|Grwd|Wdr28	glutamate-rich WD repeat containing 1	protein-coding
mm_112176.1	chr12	113421470	113421492	-	1	NA	Intergenic	Intergenic	-68084	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_130391.1	chr15	97908262	97908316	-	1	NA	promoter-TSS (NM_009504)	promoter-TSS (NM_009504)	7	NM_009504	22337	Mm.245084	NM_009504	ENSMUSG00000022479	Vdr	Nr1i1	vitamin D receptor	protein-coding
mm_134900.1	chr16	30039320	30039334	-	1	NA	non-coding (NR_045878, exon 1 of 4)	non-coding (NR_045878, exon 1 of 4)	152	NR_045878	71528	Mm.297640	NR_045878		9030404E10Rik	-	RIKEN cDNA 9030404E10 gene	ncRNA
mm_83376.1	chr9	44526470	44526501	-	1	NA	promoter-TSS (NM_007551)	promoter-TSS (NM_007551)	-64	NM_007551	12145	Mm.6246	NM_007551	ENSMUSG00000047880	Cxcr5	Blr1|CXC-R5|CXCR-5|Gpcr6|MDR15	chemokine (C-X-C motif) receptor 5	protein-coding
mm_144693.1	chr18	34860962	34860987	+	1	NA	promoter-TSS (NM_007913)	promoter-TSS (NM_007913)	-233	NM_007913	13653	Mm.181959	NM_007913	ENSMUSG00000038418	Egr1	A530045N19Rik|ETR103|Egr-1|Krox-1|Krox-24|Krox24|NGF1-A|NGFI-A|NGFIA|TIS8|Zenk|Zfp-6|Zif268|egr	early growth response 1	protein-coding
mm_57543.1	chr6	126645154	126645172	-	1	NA	5' UTR (NM_010595, exon 1 of 2)	5' UTR (NM_010595, exon 1 of 2)	638	NM_010595	16485	Mm.40424	NM_010595	ENSMUSG00000047976	Kcna1	AI840627|Kca1-1|Kv1.1|MBK1|Mk-1|Shak|mceph	potassium voltage-gated channel, shaker-related subfamily, member 1	protein-coding
mm_31674.1	chr4	62230982	62231007	+	1	NA	Intergenic	Intergenic	-22448	NM_001290350	22696	Mm.5011	NM_009554	ENSMUSG00000028389	Zfp37	Tzn|Zfp-37	zinc finger protein 37	protein-coding
mm_45974.1	chr5	90470769	90470788	-	1	NA	exon (NM_009654, exon 10 of 15)	exon (NM_009654, exon 10 of 15)	9908	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_67112.1	chr7	70360732	70360746	-	1	NA	promoter-TSS (NM_009697)	promoter-TSS (NM_009697)	-146	NM_009697	11819	Mm.158143	NM_009697	ENSMUSG00000030551	Nr2f2	2700033K02Rik|9430015G03Rik|ARP-1|Aporp1|COUP-TF2|COUP-TFII|COUPTFB|EAR3|SVP40|Tcfcoup2	nuclear receptor subfamily 2, group F, member 2	protein-coding
mm_79613.1	chr9	58629113	58629123	+	1	NA	intron (NM_001293673, intron 3 of 7)	intron (NM_001293673, intron 3 of 7)	46878	NM_009145	20320	Mm.15125	NM_009145	ENSMUSG00000032336	Nptn	AW554172|SDR-1|Sdfr1	neuroplastin	protein-coding
mm_46983.1	chr5	115300928	115300944	-	1	NA	promoter-TSS (NM_019682)	promoter-TSS (NM_019682)	54	NM_019682	56455	Mm.256858	NM_019682	ENSMUSG00000009013	Dynll1	Dlc8|Dnclc1|Pin	dynein light chain LC8-type 1	protein-coding
mm_79410.1	chr9	55149622	55149630	+	1	NA	promoter-TSS (NM_001346658)	promoter-TSS (NM_001346658)	257	NM_001346657	109161	Mm.207894	NM_180600	ENSMUSG00000032307	Ube2q2	3010021M21Rik	ubiquitin-conjugating enzyme E2Q family member 2	protein-coding
mm_77484.1	chr8	122491936	122491941	-	1	NA	intron (NM_001037298, intron 23 of 50)	intron (NM_001037298, intron 23 of 50)	15795	NM_153775	66965	Mm.482288	NM_153775	ENSMUSG00000049482	Ctu2	2310061F22Rik|C16orf84|Ncs2	cytosolic thiouridylase subunit 2	protein-coding
mm_117600.1	chr13	89909659	89909661	-	1	NA	intron (NM_028012, intron 7 of 7)	Lx5b|LINE|L1	-167148	NM_001134475	13003	Mm.158700	NM_019389	ENSMUSG00000021614	Vcan	5430420N07Rik|9430051N09|Cspg2|DPEAAE|NG2|PG-M|PG-M(V0)|PG-M(V1)|hdf	versican	protein-coding
mm_20868.1	chr2	148443430	148443444	-	1	NA	promoter-TSS (NM_010740)	promoter-TSS (NM_010740)	98	NM_010740	17064	Mm.681	NM_010740	ENSMUSG00000027435	Cd93	6030404G09Rik|AA145088|AA4.1|AW555904|C1qr1|C1qrp|Ly68	CD93 antigen	protein-coding
mm_81627.1	chr9	110849468	110849470	+	1	NA	intron (NM_183103, intron 1 of 4)	intron (NM_183103, intron 1 of 4)	4963	NM_183103	74306	Mm.87419	NM_183103	ENSMUSG00000049719	Prss46	1700112C13Rik|79H19B|Tessp6	protease, serine 46	protein-coding
mm_100932.1	chr11	6519770	6519789	-	1	NA	intron (NM_178440, intron 1 of 21)	intron (NM_178440, intron 1 of 21)	1179	NM_178440	246177	Mm.239554	NM_178440	ENSMUSG00000020437	Myo1g	E430002D17Rik	myosin IG	protein-coding
mm_142811.1	chr17	51175515	51175517	-	1	NA	intron (NM_028162, intron 1 of 21)	intron (NM_028162, intron 1 of 21)	3836	NM_028162	72238	Mm.120650	NM_028162	ENSMUSG00000023923	Tbc1d5	1600014N05Rik	TBC1 domain family, member 5	protein-coding
mm_30500.1	chr3	157909597	157909607	-	1	NA	intron (NM_145953, intron 6 of 11)	RMER12C|LTR|ERVK	15461	NM_145953	107869	Mm.28301	NM_145953	ENSMUSG00000028179	Cth	0610010I13Rik|AI314617|BC019483|CSE|Cys3	cystathionase (cystathionine gamma-lyase)	protein-coding
mm_26285.1	chr3	142505818	142505824	+	1	NA	intron (NM_153564, intron 7 of 10)	intron (NM_153564, intron 7 of 10)	8887	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_131023.1	chr16	3121448	3121454	+	1	NA	Intergenic	Intergenic	-470947	NM_146860	258859	Mm.377723	NM_146860	ENSMUSG00000051003	Olfr161	MOR131-1|OR912-47M6	olfactory receptor 161	protein-coding
mm_157897.1	chrX	77795990	77796007	-	1	NA	promoter-TSS (NM_016979)	promoter-TSS (NM_016979)	-38	NM_016979	19108	Mm.290338	NM_016979	ENSMUSG00000035725	Prkx	PKX1|Pkare	protein kinase, X-linked	protein-coding
mm_93847.1	chr10	121800575	121800578	-	1	NA	intron (NM_001242411, intron 18 of 21)	intron (NM_001242411, intron 18 of 21)	60639	NM_173022	270802	Mm.209172	NM_173022	ENSMUSG00000053684	BC048403	E030027L10	cDNA sequence BC048403	protein-coding
mm_18222.1	chr2	50523029	50523038	-	1	NA	Intergenic	Intergenic	226223	NR_040362	100502624	Mm.382825	NR_040361	ENSMUSG00000085862	Gm13483	OTTMUSG00000012382	predicted gene 13483	ncRNA
mm_145779.1	chr18	65072294	65072321	+	1	NA	intron (NM_031881, intron 1 of 29)	intron (NM_031881, intron 1 of 29)	48780	NM_031881	83814	Mm.98668	NM_031881	ENSMUSG00000024589	Nedd4l	1300012C07Rik|Nedd4-2|Nedd4b	neural precursor cell expressed, developmentally down-regulated gene 4-like	protein-coding
mm_83052.1	chr9	37545059	37545075	-	1	NA	TTS (NM_020518)	TTS (NM_020518)	5812	NM_020518	57276	Mm.27478	NM_020518	ENSMUSG00000001943	Vsig2	1190004B15Rik|2210413P10Rik|AU040484|CTX|Ctm	V-set and immunoglobulin domain containing 2	protein-coding
mm_166982.1	chr7	45639901	45639907	+	1	NA	promoter-TSS (NM_172418)	promoter-TSS (NM_172418)	-73	NM_172418	74490	Mm.107442	NM_172418	ENSMUSG00000042918	Mamstr	2810022D01Rik|5430432N15Rik|AW743872|Mastr	MEF2 activating motif and SAP domain containing transcriptional regulator	protein-coding
mm_34010.1	chr4	137993041	137993075	+	1	NA	promoter-TSS (NM_001256198)	promoter-TSS (NM_001256198)	-398	NM_001256198	230861	Mm.268903	NM_172703	ENSMUSG00000028760	Eif4g3	1500002J22Rik|4930523M17Rik|G1-419-52|eIF4GII|repro8	eukaryotic translation initiation factor 4 gamma, 3	protein-coding
mm_95439.1	chr11	50225316	50225429	+	1	NA	promoter-TSS (NM_145926)	promoter-TSS (NM_145926)	37	NM_145926	103534	Mm.86759	NM_145926	ENSMUSG00000036620	Mgat4b	AA407995|GnTIVb	mannoside acetylglucosaminyltransferase 4, isoenzyme B	protein-coding
mm_144915.1	chr18	37484956	37485028	+	1	NA	promoter-TSS (NM_053142)	promoter-TSS (NM_053142)	-29	NM_053142	93888	Mm.87553	NM_053142	ENSMUSG00000046387	Pcdhb17	Pcdhb16|PcdhbQ|mKIAA1621	protocadherin beta 17	protein-coding
mm_102592.1	chr11	61927020	61927045	-	1	NA	intron (NM_019921, intron 1 of 14)	intron (NM_019921, intron 1 of 14)	3225	NM_019921	56697	Mm.274404	NM_019921	ENSMUSG00000047804	Akap10	1500031L16Rik|B130049N18Rik|D-AKAP-2|D-AKAP2|PRKA10	A kinase (PRKA) anchor protein 10	protein-coding
mm_28560.1	chr3	93443896	93443941	-	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	1588	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_5524.1	chr1	37865129	37865139	-	1	NA	promoter-TSS (NM_207228)	promoter-TSS (NM_207228)	-52	NM_207228	211484	Mm.332756	NM_207228	ENSMUSG00000060771	Tsga10	4933432N21Rik|AI843383|Gm217|Mtsga10	testis specific 10	protein-coding
mm_171767.1	chr5	107903285	107903294	+	1	NA	exon (NM_016980, exon 4 of 8)	exon (NM_016980, exon 4 of 8)	2761	NM_016980	100503670	Mm.277897	NM_016980	ENSMUSG00000058558	Rpl5	U21RNA	ribosomal protein L5	protein-coding
mm_64368.1	chr7	142441809	142441825	+	1	NA	promoter-TSS (NM_009405)	promoter-TSS (NM_009405)	-651	NM_009405	21953	Mm.39469	NM_009405	ENSMUSG00000031097	Tnni2	-	troponin I, skeletal, fast 2	protein-coding
mm_157046.1	chrX	8005957	8005981	-	1	NA	intron (NM_027227, intron 2 of 3)	intron (NM_027227, intron 2 of 3)	12523	NM_027227	69824	Mm.279756	NM_027227	ENSMUSG00000031163	Glod5	2010001H14Rik|AV061890	glyoxalase domain containing 5	protein-coding
mm_171754.1	chr5	104860061	104860075	-	1	NA	promoter-TSS (NM_001039231)	promoter-TSS (NM_001039231)	0	NM_001039231	626391	Mm.385405	NM_001039231	ENSMUSG00000072774	Zfp951	C230055K05Rik	zinc finger protein 951	protein-coding
mm_157723.1	chrX	70344945	70344988	-	1	NA	3' UTR (NM_010498, exon 9 of 9)	3' UTR (NM_010498, exon 9 of 9)	20119	NM_010498	15931	Mm.233083	NM_010498	ENSMUSG00000035847	Ids	AW214631	iduronate 2-sulfatase	protein-coding
mm_62824.1	chr7	113513816	113513827	+	1	NA	promoter-TSS (NM_027379)	promoter-TSS (NM_027379)	-13	NM_001285831	67420	Mm.206919	NM_026143	ENSMUSG00000030759	Far1	2600011M19Rik|2900034E22Rik|3732409C05Rik|AI850429|Mlstd2	fatty acyl CoA reductase 1	protein-coding
mm_74161.1	chr8	123397922	123397930	+	1	NA	intron (NM_001286362, intron 12 of 16)	intron (NM_001286362, intron 12 of 16)	-9156	NM_008559	17199	Mm.324942	NM_008559	ENSMUSG00000074037	Mc1r	Mcr1|Mshra|Tob|e	melanocortin 1 receptor	protein-coding
mm_117724.1	chr13	95525219	95525232	-	1	NA	promoter-TSS (NM_007974)	promoter-TSS (NM_007974)	15	NM_007974	14063	Mm.1614	NM_007974	ENSMUSG00000021678	F2rl1	Gpcr11|PAR-2|Par2	coagulation factor II (thrombin) receptor-like 1	protein-coding
mm_48728.1	chr5	147426540	147426565	-	1	NA	Intergenic	Intergenic	-4028	NM_028291	72587	Mm.320469	NM_028291	ENSMUSG00000029647	Pan3	2700050F09Rik|A430027N15Rik|AU014670	PAN3 poly(A) specific ribonuclease subunit	protein-coding
mm_105526.1	chr11	106300529	106300566	-	1	NA	exon (NM_008117, exon 5 of 5)	exon (NM_008117, exon 5 of 5)	1349	NM_008117	14599	Mm.343934	NM_008117	ENSMUSG00000020713	Gh	Gh1|Ghb1	growth hormone	protein-coding
mm_22730.1	chr3	19687081	19687083	+	1	NA	intron (NM_001081281, intron 9 of 9)	L1MB2|LINE|L1	8314	NM_205769	12918	Mm.290689	NM_205769	ENSMUSG00000049796	Crh	CRF|Gm1347	corticotropin releasing hormone	protein-coding
mm_28046.1	chr3	84040101	84040147	-	1	NA	promoter-TSS (NM_172681)	promoter-TSS (NM_172681)	37	NM_172681	229473	Mm.28838	NM_172681	ENSMUSG00000033767	D930015E06Rik	Kiaa0922|mKIAA0922	RIKEN cDNA D930015E06 gene	protein-coding
mm_92992.1	chr10	86702944	86703024	-	1	NA	exon (NM_011631, exon 4 of 18)	exon (NM_011631, exon 4 of 18)	2460	NM_011631	22027	Mm.87773	NM_011631	ENSMUSG00000020048	Hsp90b1	ERp99|GRP94|TA-3|Targ2|Tra-1|Tra1|endoplasmin|gp96	heat shock protein 90, beta (Grp94), member 1	protein-coding
mm_68154.1	chr7	102250492	102250515	-	1	NA	promoter-TSS (NM_019566)	promoter-TSS (NM_019566)	-385	NM_019566	56212	Mm.259795	NM_019566	ENSMUSG00000073982	Rhog	2810426G09Rik|Arhg|Sid10750	ras homolog family member G	protein-coding
mm_46902.1	chr5	114131587	114131597	-	1	NA	intron (NM_001040691, intron 2 of 6)	CpG	436	NM_011677	22256	Mm.1393	NM_011677	ENSMUSG00000029591	Ung	UNG1|UNG2	uracil DNA glycosylase	protein-coding
mm_32447.1	chr4	107314400	107314424	+	1	NA	promoter-TSS (NM_001205156)	promoter-TSS (NM_001205156)	49	NM_001205156	230584	Mm.29118	NM_145550	ENSMUSG00000057375	Yipf1	C030002N13Rik	Yip1 domain family, member 1	protein-coding
mm_19996.1	chr2	118728431	118728446	-	1	NA	promoter-TSS (NM_177568)	promoter-TSS (NM_177568)	0	NM_177568	18796	Mm.215156	NM_177568	ENSMUSG00000040061	Plcb2	AI550384|B230205M18Rik|B230399N12	phospholipase C, beta 2	protein-coding
mm_82276.1	chr9	7354752	7354778	-	1	NA	exon (NM_008605, exon 7 of 10)	exon (NM_008605, exon 7 of 10)	7391	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_126010.1	chr15	76576387	76576457	+	1	NA	promoter-TSS (NM_172960)	promoter-TSS (NM_172960)	63	NR_073123	268822	Mm.181624	NM_172960	ENSMUSG00000022550	Adck5	A230108P17	aarF domain containing kinase 5	protein-coding
mm_170271.1	chr18	24051640	24051649	-	1	NA	Intergenic	BGLII|LTR|ERVK	-30873	NM_021559	59057	Mm.417427	NM_021559	ENSMUSG00000051469	Zfp24	3526401F17Rik|5033419P20Rik|AI480505|AI642085|AL024422|KOX17|ZF-12|Zfp191|Znf191|Znf24|Znp191	zinc finger protein 24	protein-coding
mm_57040.1	chr6	122339798	122339876	-	1	NA	promoter-TSS (NM_007905)	promoter-TSS (NM_007905)	-180	NM_007905	13619	Mm.6822	NM_007905	ENSMUSG00000040669	Phc1	AW557034|Edr|Edr1|Mph1|Rae-28|rae28	polyhomeotic-like 1 (Drosophila)	protein-coding
mm_167340.1	chr8	73353555	73353565	-	1	NA	promoter-TSS (NM_010687)	promoter-TSS (NM_010687)	-20	NM_010687	16795	Mm.324371	NM_010687	ENSMUSG00000004383	Large1	BPFD#36|Gyltl1a|Large|Mbp-1|Mbp1|enr|fg|froggy|myd	LARGE xylosyl- and glucuronyltransferase 1	protein-coding
mm_7273.1	chr1	96997597	96997610	-	1	NA	promoter-TSS (NR_120500)	promoter-TSS (NR_120500)	-43	NR_120500	67854	Mm.263706	NM_026413	ENSMUSG00000045463	Slco6b1	1700022M03Rik	solute carrier organic anion transporter family, member 6b1	ncRNA
mm_43375.1	chr5	135670028	135670042	+	1	NA	Intergenic	Intergenic	-19110	NM_008898	18984	Mm.3863	NM_008898	ENSMUSG00000005514	Por	4933424M13Rik|CPR|CYPOR|P450R	P450 (cytochrome) oxidoreductase	protein-coding
mm_76685.1	chr8	94070207	94070248	-	1	NA	intron (NM_026116, intron 15 of 16)	B1F|SINE|Alu	28584	NM_026116	67378	Mm.292107	NM_026116	ENSMUSG00000031755	Bbs2	2410125H22Rik|AI447581	Bardet-Biedl syndrome 2 (human)	protein-coding
mm_1893.1	chr1	85699637	85699650	+	1	NA	exon (NM_013673, exon 15 of 20)	exon (NM_013673, exon 15 of 20)	36963	NM_177055	319997	Mm.116691	NM_177055	ENSMUSG00000052760	A630001G21Rik	-	RIKEN cDNA A630001G21 gene	protein-coding
mm_159942.1	chr6	83277241	83277241	+	1	NA	intron (NM_001166067, intron 13 of 24)	intron (NM_001166067, intron 13 of 24)	39866	NM_001166067	232156	Mm.333189	NM_001166067	ENSMUSG00000068323	Slc4a5	C330006M16|C330016K18Rik	solute carrier family 4, sodium bicarbonate cotransporter, member 5	protein-coding
mm_130495.1	chr15	98807941	98807956	-	1	NA	promoter-TSS (NM_001013741)	promoter-TSS (NM_001013741)	-23	NM_001013741	13199	Mm.390810	NM_001013741	ENSMUSG00000059213	Ddn	Gm748	dendrin	protein-coding
mm_67234.1	chr7	75307723	75307736	-	1	NA	promoter-TSS (NR_045814)	promoter-TSS (NR_045814)	657	NM_001109753	64176	Mm.273082	NM_153579	ENSMUSG00000053025	Sv2b	A830038F04Rik|AI850768|mKIAA0735	synaptic vesicle glycoprotein 2 b	protein-coding
mm_136895.1	chr17	13013507	13013587	+	1	NA	exon (NM_013671, exon 4 of 5)	exon (NM_013671, exon 4 of 5)	5708	NM_013671	20656	Mm.290876	NM_013671	ENSMUSG00000006818	Sod2	MnSOD|Sod-2	superoxide dismutase 2, mitochondrial	protein-coding
mm_86315.1	chr9	122865939	122865999	-	1	NA	promoter-TSS (NM_173364)	promoter-TSS (NM_173364)	37	NM_173364	235682	Mm.326477	NM_173364	ENSMUSG00000047036	Zfp445	AW610627|ZNF168|Znf445|mszf29|mszf50	zinc finger protein 445	protein-coding
mm_98065.1	chr11	85832926	85832949	+	1	NA	promoter-TSS (NR_077059)	promoter-TSS (NR_077059)	322	NM_009324	21385	Mm.287052	NM_009324	ENSMUSG00000000093	Tbx2	-	T-box 2	protein-coding
mm_160363.1	chr8	21958865	21958865	+	1	NA	5' UTR (NM_001081662, exon 1 of 5)	5' UTR (NM_001081662, exon 1 of 5)	151	NM_001081662	97476	Mm.297693	NM_001081662	ENSMUSG00000079112	Fam90a1a	C86695	family with sequence similarity 90, member A1A	protein-coding
mm_169005.1	chr13	104183566	104183579	+	1	NA	intron (NM_030731, intron 1 of 9)	BGLII|LTR|ERVK	4474	NM_030731	81003	Mm.244190	NM_030731	ENSMUSG00000021712	Trim23	6330516O20Rik|AI450195|Arfd1	tripartite motif-containing 23	protein-coding
mm_63489.1	chr7	127767474	127767486	+	1	NA	exon (NM_172748, exon 10 of 11)	exon (NM_172748, exon 10 of 11)	-2335	NM_198424	269999	Mm.36852	NM_198424	ENSMUSG00000043964	Orai3	9930124N15|BC061259|Tmem142c	ORAI calcium release-activated calcium modulator 3	protein-coding
mm_67960.1	chr7	100533460	100533481	-	1	NA	Intergenic	Intergenic	-3630	NM_183270	68185	Mm.228995	NM_183270	ENSMUSG00000044881	Coa4	5330414O08Rik|AI115477|AW047259|Chchd8|E2ig2	cytochrome c oxidase assembly factor 4	protein-coding
mm_116017.1	chr13	24800779	24800789	-	1	NA	promoter-TSS (NM_024473)	promoter-TSS (NM_024473)	-873	NM_024473	79555	Mm.266668	NM_024473	ENSMUSG00000019132	BC005537	8030460C05Rik|C78201	cDNA sequence BC005537	protein-coding
mm_140488.1	chr17	3283166	3283178	-	1	NA	Intergenic	Intergenic	-43401	NM_001122998	24001	Mm.137134	NM_011878	ENSMUSG00000023800	Tiam2	3000002F19Rik|STEF|mKIAA2016	T cell lymphoma invasion and metastasis 2	protein-coding
mm_149710.1	chr19	21653198	21653213	+	1	NA	promoter-TSS (NM_025423)	promoter-TSS (NM_025423)	-104	NM_146096	226016	Mm.28796	NM_146096	ENSMUSG00000047368	Abhd17b	5730446C15Rik|Cgi67|Fam108b|Fam108b1	abhydrolase domain containing 17B	protein-coding
mm_47269.1	chr5	121859148	121859150	-	1	NA	Intergenic	Intergenic	10121	NM_175474	231717	Mm.12654	NM_175474	ENSMUSG00000044134	Fam109a	A230106M15Rik|AU017694|IPIP27A|Ses1	family with sequence similarity 109, member A	protein-coding
mm_49123.1	chr6	8521885	8521895	+	1	NA	intron (NM_001286728, intron 1 of 7)	B3A|SINE|B2	1832	NM_001286729	170772	Mm.210787	NM_133236	ENSMUSG00000029638	Glcci1	2310047L21Rik|A130036A18Rik|Fam117c|Gig18|Tssn1	glucocorticoid induced transcript 1	protein-coding
mm_82942.1	chr9	35305430	35305449	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	24334	NR_040715	71133	Mm.158577	NR_040715	ENSMUSG00000111746	4933422A05Rik	-	RIKEN cDNA 4933422A05 gene	ncRNA
mm_110492.1	chr12	52602364	52602371	-	1	NA	promoter-TSS (NR_045910)	promoter-TSS (NR_045910)	-45	NR_045910	73278	Mm.396209	NR_045910	ENSMUSG00000100315	1700031P21Rik	-	RIKEN cDNA 1700031P21 gene	ncRNA
mm_104203.1	chr11	87998272	87998285	-	1	NA	promoter-TSS (NM_001168471)	promoter-TSS (NM_001168471)	20	NM_001168471	68097	Mm.246436	NM_026556	ENSMUSG00000020483	Dynll2	1700064A15Rik|6720463E02Rik|C87222|DLC8|DLC8b|Dlc2	dynein light chain LC8-type 2	protein-coding
mm_46059.1	chr5	92256334	92256340	-	1	NA	Intergenic	Intergenic	-3178	NM_011148	19023	Mm.87155	NM_011148	ENSMUSG00000029410	Ppef2	-	protein phosphatase, EF hand calcium-binding domain 2	protein-coding
mm_132335.1	chr16	33819678	33819694	+	1	NA	3' UTR (NM_010739, exon 13 of 13)	3' UTR (NM_010739, exon 13 of 13)	-9979	NM_010580	16419	Mm.6424	NM_010580	ENSMUSG00000022817	Itgb5	AA475909|AI874634|ESTM23|[b]-5|[b]5|[b]5A|[b]5B|beta-5|beta5	integrin beta 5	protein-coding
mm_76033.1	chr8	77310938	77310947	-	1	NA	intron (NM_030113, intron 18 of 22)	intron (NM_030113, intron 18 of 22)	-206114	NR_028125	70345	Mm.411813	NR_028125	ENSMUSG00000097882	0610038B21Rik	-	RIKEN cDNA 0610038B21 gene	ncRNA
mm_73071.1	chr8	94434724	94434744	+	1	NA	intron (NR_015514, intron 1 of 2)	intron (NR_015514, intron 1 of 2)	369	NR_015514	320377	Mm.486022	NR_015514		9330175E14Rik	A630085K21	RIKEN cDNA 9330175E14 gene	ncRNA
mm_91796.1	chr10	53398704	53398728	-	1	NA	Intergenic	Intergenic	-18865	NM_001204983	100038725	Mm.441403	NM_001204983	ENSMUSG00000038594	Cep85l	ENSMUSG00000038594|Gm9766	centrosomal protein 85-like	protein-coding
mm_81485.1	chr9	109969033	109969037	+	1	NA	intron (NM_001205330, intron 1 of 18)	intron (NM_001205330, intron 1 of 18)	37261	NM_008633	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_10663.1	chr2	20737331	20737341	+	1	NA	intron (NM_029895, intron 6 of 18)	intron (NM_029895, intron 6 of 18)	217823	NM_001177631	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding
mm_154646.1	chrX	7794298	7794313	+	1	NA	intron (NM_207670, intron 4 of 24)	intron (NM_207670, intron 4 of 24)	4312	NM_207670	54645	Mm.194811	NM_207670	ENSMUSG00000031153	Gripap1	AI854681|DXImx47e|GRASP-1|Sfc10|mKIAA1167	GRIP1 associated protein 1	protein-coding
mm_16233.1	chr2	173156253	173156261	+	1	NA	intron (NM_011044, intron 6 of 9)	intron (NM_011044, intron 6 of 9)	3184	NM_011044	18534	Mm.266867	NM_011044	ENSMUSG00000027513	Pck1	AI265463|PEPCK|Pck-1	phosphoenolpyruvate carboxykinase 1, cytosolic	protein-coding
mm_34143.1	chr4	139338133	139338138	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	14441	NM_001290810	69902	Mm.27871	NM_023536	ENSMUSG00000028741	Mrto4	2610012O22Rik|Mg684|Mrt4	mRNA turnover 4, ribosome maturation factor	protein-coding
mm_68907.1	chr7	126456990	126457000	-	1	NA	exon (NM_007504, exon 8 of 23)	exon (NM_007504, exon 8 of 23)	6078	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_144688.1	chr18	34840576	34840586	+	1	NA	promoter-TSS (NM_001204914)	promoter-TSS (NM_001204914)	-8	NM_001204914	225362	Mm.293588	NM_144865	ENSMUSG00000038555	Reep2	-	receptor accessory protein 2	protein-coding
mm_88384.1	chr10	76449096	76449109	+	1	NA	promoter-TSS (NM_029816)	promoter-TSS (NM_029816)	21	NM_029816	76964	Mm.472489	NM_029816	ENSMUSG00000009114	2610028H24Rik	ORF67	RIKEN cDNA 2610028H24 gene	protein-coding
mm_5533.1	chr1	38022188	38022205	-	1	NA	exon (NM_198303, exon 6 of 24)	exon (NM_198303, exon 6 of 24)	24186	NM_198303	226982	Mm.260943	NM_198303	ENSMUSG00000026083	Eif5b	A030003E17Rik|BC018347|IF2	eukaryotic translation initiation factor 5B	protein-coding
mm_146279.1	chr18	77882552	77882564	+	1	NA	3' UTR (NM_013831, exon 15 of 15)	3' UTR (NM_013831, exon 15 of 15)	-55909	NM_001195633	100502841	Mm.297782	NM_001195633	ENSMUSG00000039840	Epg5	4732475F16|5430411K18Rik|AI661957|AW456499|mKIAA1632	ectopic P-granules autophagy protein 5 homolog (C. elegans)	protein-coding
mm_24272.1	chr3	89202995	89203010	+	1	NA	promoter-TSS (NM_001077411)	promoter-TSS (NM_001077411)	77	NR_122037	14466	Mm.5031	NM_008094	ENSMUSG00000028048	Gba	GBA1|GC|GCase|GLUC|betaGC	glucosidase, beta, acid	protein-coding
mm_156223.1	chrX	135707174	135707174	+	1	NA	Intergenic	L1_Mur2|LINE|L1	-13384	NM_027952	71841	Mm.371643	NM_027952	ENSMUSG00000058252	Tcp11x2	1700008I05Rik|C77164|TCP11|Tcp11l3	t-complex 11 family, X-linked 2	protein-coding
mm_79844.1	chr9	64811485	64811503	+	1	NA	5' UTR (NM_001162917, exon 2 of 35)	5' UTR (NM_001162917, exon 2 of 35)	483	NM_001162917	102442	Mm.222473	NM_176935	ENSMUSG00000053641	Dennd4a	AI115600|AI851943|F730015K02Rik	DENN/MADD domain containing 4A	protein-coding
mm_169382.1	chr14	4097892	4097895	-	1	NA	Intergenic	L1Md_A|LINE|L1	73952	NM_001029930	545007	Mm.449725	NM_001029930	ENSMUSG00000096775	Gm5796	-	predicted gene 5796	protein-coding
mm_73639.1	chr8	110740926	110740933	+	1	NA	TTS (NM_001135100)	TTS (NM_001135100)	15203	NM_001310591	244654	Mm.490385	NM_198625	ENSMUSG00000033763	Mtss1l	ABBA	metastasis suppressor 1-like	protein-coding
mm_49739.1	chr6	34745795	34745808	+	1	NA	exon (NM_145575, exon 3 of 12)	exon (NM_145575, exon 3 of 12)	-34631	NM_001289657	76223	Mm.150047	NM_178630	ENSMUSG00000038836	Agbl3	2900053G10Rik|4930431N21Rik|6530406M24Rik|CCP3	ATP/GTP binding protein-like 3	protein-coding
mm_60935.1	chr7	46861432	46861436	+	1	NA	intron (NM_013580, intron 1 of 7)	intron (NM_013580, intron 1 of 7)	171	NM_013580	16833	Mm.16563	NM_013580	ENSMUSG00000030851	Ldhc	LDH-C4|Ldh-3|Ldh-x|Ldh3|Ldhc4	lactate dehydrogenase C	protein-coding
mm_139293.1	chr17	48316130	48316146	+	1	NA	promoter-TSS (NM_177083)	promoter-TSS (NM_177083)	-24	NM_177083	320148	Mm.123455	NM_177083	ENSMUSG00000043740	B430306N03Rik	Treml6	RIKEN cDNA B430306N03 gene	protein-coding
mm_162245.1	chrX	159210528	159210528	+	1	NA	Intergenic	Intergenic	-45254	NM_148945	110651	Mm.328476	NM_148945	ENSMUSG00000031309	Rps6ka3	MAPKAPK-1b|MPK-9|Rsk2|S6K-alpha3|p90RSK3|pp90RSK2	ribosomal protein S6 kinase polypeptide 3	protein-coding
mm_94510.1	chr11	7977079	7977083	+	1	NA	Intergenic	MER70A|LTR|ERVL	687454	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_134888.1	chr16	29490412	29490457	-	1	NA	intron (NM_172613, intron 1 of 29)	MIRb|SINE|MIR	51049	NM_172613	224079	Mm.54954	NM_172613	ENSMUSG00000038094	Atp13a4	4631413J11Rik|4832416L12|9330174J19Rik	ATPase type 13A4	protein-coding
mm_63891.1	chr7	138846336	138846371	+	1	NA	promoter-TSS (NM_026391)	promoter-TSS (NM_026391)	-6	NM_001347618	52432	Mm.258739	NM_026391	ENSMUSG00000041769	Ppp2r2d	1300017E19Rik|D7Ertd753e|MDS026	protein phosphatase 2, regulatory subunit B, delta	protein-coding
mm_153631.1	chr19	44021732	44021762	-	1	NA	intron (NM_001001446, intron 1 of 8)	intron (NM_001001446, intron 1 of 8)	7500	NM_001001446	226143	Mm.329866	NM_001001446	ENSMUSG00000025197	Cyp2c44	AW107714|BC034834|b2b386Clo	cytochrome P450, family 2, subfamily c, polypeptide 44	protein-coding
mm_38649.1	chr4	143274030	143274034	-	1	NA	exon (NM_010329, exon 3 of 6)	exon (NM_010329, exon 3 of 6)	25532	NM_010329	14726	Mm.2976	NM_010329	ENSMUSG00000028583	Pdpn	Gp38|OTS-8|RANDAM-2|T1-alpha|T1a|T1alpha	podoplanin	protein-coding
mm_65947.1	chr7	30419769	30419776	-	1	NA	promoter-TSS (NM_011827)	promoter-TSS (NM_011827)	82	NM_011827	23900	Mm.379050	NM_011827	ENSMUSG00000064109	Hcst	DAP10|KAP10	hematopoietic cell signal transducer	protein-coding
mm_77664.1	chr8	124716695	124716706	-	1	NA	intron (NM_145607, intron 1 of 17)	intron (NM_145607, intron 1 of 17)	5275	NM_145607	234875	Mm.38436	NM_145607	ENSMUSG00000037300	Ttc13	BC017545	tetratricopeptide repeat domain 13	protein-coding
mm_40320.1	chr5	43882545	43882553	+	1	NA	intron (NM_007646, intron 1 of 7)	intron (NM_007646, intron 1 of 7)	13740	NM_007646	12494	Mm.249873	NM_007646	ENSMUSG00000029084	Cd38	ADPRC 1|Cd38-rs1|I-19	CD38 antigen	protein-coding
mm_53600.1	chr6	138147684	138147700	+	1	NA	exon (NM_019946, exon 2 of 4)	exon (NM_019946, exon 2 of 4)	6098	NM_001347489	56615	Mm.14796	NM_019946	ENSMUSG00000008540	Mgst1	1500002K10Rik|Gst	microsomal glutathione S-transferase 1	protein-coding
mm_93466.1	chr10	111010002	111010025	-	1	NA	promoter-TSS (NM_172554)	promoter-TSS (NM_172554)	53	NM_172554	320150	Mm.339281	NM_172554	ENSMUSG00000035798	Zdhhc17	A230053P19Rik|BB187739|D130071N24Rik|Hip14	zinc finger, DHHC domain containing 17	protein-coding
mm_159296.1	chr2	175372470	175372470	+	1	NA	promoter-TSS (NM_001177405).2	promoter-TSS (NM_001177405).2	8	NM_001177404	100303732	Mm.484983	NM_001177404	ENSMUSG00000095199	Zfp967	Gm14431|OTTMUSG00000016608	zinc finger protein 967	protein-coding
mm_46111.1	chr5	92361280	92361302	-	1	NA	exon (NM_019494, exon 2 of 4)	exon (NM_019494, exon 2 of 4)	1986	NM_019494	56066	Mm.131723	NM_019494	ENSMUSG00000060183	Cxcl11	Cxc11|H174|I-tac|Ip9|Itac|Scyb11|Scyb9b|b-R1|betaR1	chemokine (C-X-C motif) ligand 11	protein-coding
mm_108234.1	chr12	77239154	77239186	+	1	NA	non-coding (NR_045554, exon 1 of 12)	non-coding (NR_045554, exon 1 of 12)	431	NR_045554	53618	Mm.35628	NM_016893	ENSMUSG00000021065	Fut8	-	fucosyltransferase 8	protein-coding
mm_40504.1	chr5	57728779	57728809	+	1	NA	3' UTR (NM_018764, exon 2 of 2)	3' UTR (NM_018764, exon 2 of 2)	10713	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_71596.1	chr8	54955202	54955212	+	1	NA	5' UTR (NM_153581, exon 1 of 7)	5' UTR (NM_153581, exon 1 of 7)	479	NM_001253756	234267	Mm.241700	NM_153581	ENSMUSG00000031517	Gpm6a	Gpm6|M6A	glycoprotein m6a	protein-coding
mm_148722.1	chr19	5846849	5846860	+	1	NA	Intergenic	Intergenic	-1374	NR_003513	66961	Mm.281895	NR_003513	ENSMUSG00000092274	Neat1	2310043N10Rik|VINC	nuclear paraspeckle assembly transcript 1 (non-protein coding)	ncRNA
mm_10689.1	chr2	22622278	22622303	+	1	NA	promoter-TSS (NM_008078)	promoter-TSS (NM_008078)	-37	NM_008078	14417	Mm.4784	NM_008078	ENSMUSG00000026787	Gad2	6330404F12Rik|GAD(65)|GAD65|Gad-2	glutamic acid decarboxylase 2	protein-coding
mm_84429.1	chr9	65885077	65885091	-	1	NA	promoter-TSS (NM_001170907)	promoter-TSS (NM_001170907)	89	NM_001170907	56404	Mm.208379	NM_019797	ENSMUSG00000032386	Trip4	4930558E03Rik|ASC-1|Asc1|BB191711	thyroid hormone receptor interactor 4	protein-coding
mm_10355.1	chr2	11690097	11690134	+	1	NA	3' UTR (NM_008367, exon 8 of 8)	3' UTR (NM_008367, exon 8 of 8)	-15178	NM_001271498	16169	Mm.200196	NM_008358	ENSMUSG00000023206	Il15ra	AA690181|IL-15RA	interleukin 15 receptor, alpha chain	protein-coding
mm_98734.1	chr11	96353076	96353086	+	1	NA	exon (NM_134032, exon 2 of 2)	exon (NM_134032, exon 2 of 2)	1449	NM_134032	103889	Mm.281153	NM_134032	ENSMUSG00000075588	Hoxb2	AI894218|Hox-2.8|Hoxbes2	homeobox B2	protein-coding
mm_115863.1	chr13	21447239	21447246	-	1	NA	intron (NM_001013786, intron 3 of 3)	B1_Mur1|SINE|Alu	2082	NR_035441	100316752		NR_035441	ENSMUSG00000084590	Mir1896	Mirn1896|mmu-mir-1896	microRNA 1896	ncRNA
mm_99078.1	chr11	99388973	99388983	+	1	NA	exon (NM_010660, exon 1 of 8)	exon (NM_010660, exon 1 of 8)	386	NM_010660	16661	Mm.22662	NM_010660	ENSMUSG00000019761	Krt10	D130054E02Rik|K10|K1C1|Krt-1.10|Krt1-10	keratin 10	protein-coding
mm_30617.1	chr4	8535730	8535738	+	1	NA	promoter-TSS (NM_021518)	promoter-TSS (NM_021518)	90	NM_021518	59021	Mm.397471	NM_021518	ENSMUSG00000047187	Rab2a	9330148M11Rik|C80220|Rab2	RAB2A, member RAS oncogene family	protein-coding
mm_49183.1	chr6	15184755	15184767	+	1	NA	promoter-TSS (NM_001286607)	promoter-TSS (NM_001286607)	-745	NM_212435	114142	Mm.332919	NM_053242	ENSMUSG00000029563	Foxp2	2810043D05Rik|AI449000|CAG-16|D0Kist7	forkhead box P2	protein-coding
mm_96624.1	chr11	69142563	69142566	+	1	NA	intron (NM_011786, intron 13 of 14)	intron (NM_011786, intron 13 of 14)	-14508	NM_009659	11686	Mm.340329	NM_009659	ENSMUSG00000032807	Alox12b	12R-LOX|Aloxe2|e-LOX2	arachidonate 12-lipoxygenase, 12R type	protein-coding
mm_144315.1	chr18	12643743	12643822	+	1	NA	5' UTR (NM_028341, exon 1 of 14)	5' UTR (NM_028341, exon 1 of 14)	249	NM_028341	72747	Mm.52526	NM_028341	ENSMUSG00000024424	Ttc39c	1700008N02Rik|2810439F02Rik	tetratricopeptide repeat domain 39C	protein-coding
mm_93423.1	chr10	108796902	108796904	-	1	NA	intron (NM_001252341, intron 4 of 11)	intron (NM_001252341, intron 4 of 11)	-96743	NM_203660	368203	Mm.452758	NM_203660		Gm5136	C6.1AL|EG368203	predicted gene 5136	protein-coding
mm_109989.1	chr12	14152072	14152082	-	1	NA	promoter-TSS (NM_029007)	promoter-TSS (NM_029007)	-39	NM_029007	105005	Mm.227253	NM_029007	ENSMUSG00000020607	Fam84a	2310003N02Rik|4731402F03Rik|AW125753|Nse1	family with sequence similarity 84, member A	protein-coding
mm_131243.1	chr16	10526332	10526343	+	1	NA	3' UTR (NM_001243761, exon 19 of 19)	3' UTR (NM_001243761, exon 19 of 19)	16717	NM_021428	58239	Mm.353006	NM_021428	ENSMUSG00000038055	Dexi	1810029J14Rik|AI836170|AW413143|D16Bwg0586e|Myle	dexamethasone-induced transcript	protein-coding
mm_79967.1	chr9	66430517	66430547	+	1	NA	intron (NM_145617, intron 26 of 77)	L1MD3|LINE|L1	80082	NM_145617	235439	Mm.244179	NM_145617	ENSMUSG00000038664	Herc1	2810449H11Rik|B230218H07|D130015N03Rik|tbl	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	protein-coding
mm_93225.1	chr10	95264967	95264987	-	1	NA	intron (NM_009950, intron 2 of 2)	intron (NM_009950, intron 2 of 2)	58732	NM_001330138	12905	Mm.473739	NM_009950	ENSMUSG00000045867	Cradd	RAIDD	CASP2 and RIPK1 domain containing adaptor with death domain	protein-coding
mm_172875.1	chr9	4401107	4401123	+	1	NA	Intergenic	L1Md_A|LINE|L1	17578	NM_145609	78100	Mm.206549	NM_145609	ENSMUSG00000041124	Msantd4	8430410K20Rik|Mysantd4	Myb/SANT-like DNA-binding domain containing 4 with coiled-coils	protein-coding
mm_72503.1	chr8	83741389	83741434	+	1	NA	promoter-TSS (NM_001163029)	promoter-TSS (NM_001163029)	-100	NM_001163031	26364	Mm.334648	NM_011925	ENSMUSG00000002885	Adgre5	AA409984|Cd97|TM7LN1	adhesion G protein-coupled receptor E5	protein-coding
mm_15207.1	chr2	154213039	154213061	+	1	NA	exon (NM_153418, exon 9 of 16)	exon (NM_153418, exon 9 of 16)	-10692	NM_144890	228802	Mm.167411	NM_144890	ENSMUSG00000038572	Bpifb5	Lplunc5	BPI fold containing family B, member 5	protein-coding
mm_70831.1	chr8	23148590	23148615	+	1	NA	non-coding (NR_102386, exon 45 of 45)	non-coding (NR_102386, exon 45 of 45)	983	NM_001282148	101056408	Mm.475778	NM_001282148		Gm15816	OTTMUSG00000026380	predicted gene 15816	protein-coding
mm_1155.1	chr1	60887313	60887322	+	1	NA	Intergenic	Intergenic	-21708	NM_009843	12477	Mm.390	NM_009843	ENSMUSG00000026011	Ctla4	Cd152|Ctla-4|Ly-56	cytotoxic T-lymphocyte-associated protein 4	protein-coding
mm_97689.1	chr11	80141812	80141855	+	1	NA	intron (NM_183275, intron 1 of 3)	intron (NM_183275, intron 1 of 3)	320	NM_183275	68550	Mm.18466	NM_183275	ENSMUSG00000046909	Tefm	1110002N22Rik	transcription elongation factor, mitochondrial	protein-coding
mm_27319.1	chr3	50366961	50366971	-	1	NA	3' UTR (NM_011990, exon 12 of 12)	3' UTR (NM_011990, exon 12 of 12)	76647	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_47471.1	chr5	123693479	123693481	-	1	NA	Intergenic	Intergenic	-9119	NM_001347468	56430	Mm.241109	NM_019765	ENSMUSG00000049550	Clip1	1110007I12Rik|4631429H07Rik|AV017631|C81039|CLIP-170|CLIP170|CYLN1|Clip50|Rsn|mKIAA4046|restin	CAP-GLY domain containing linker protein 1	protein-coding
mm_129097.1	chr15	75981824	75981838	-	1	NA	exon (NM_001163518, exon 1 of 1)	exon (NM_001163518, exon 1 of 1)	454	NM_001163518	223648	Mm.17610	NM_146059	ENSMUSG00000098176	Ccdc166	2410075B13Rik	coiled-coil domain containing 166	protein-coding
mm_80516.1	chr9	80066896	80066936	+	1	NA	promoter-TSS (NM_146003)	promoter-TSS (NM_146003)	13	NM_146003	215351	Mm.28232	NM_146003	ENSMUSG00000034252	Senp6	2810017C20Rik|E130319N12Rik|Susp1|mKIAA0797	SUMO/sentrin specific peptidase 6	protein-coding
mm_62349.1	chr7	100498765	100498801	+	1	NA	exon (NM_011671, exon 7 of 8)	exon (NM_011671, exon 7 of 8)	5425	NM_011671	22228	Mm.171378	NM_011671	ENSMUSG00000033685	Ucp2	Slc25a8	uncoupling protein 2 (mitochondrial, proton carrier)	protein-coding
mm_33557.1	chr4	131843460	131843503	+	1	NA	promoter-TSS (NM_025297)	promoter-TSS (NM_025297)	10	NM_025297	26922	Mm.192706	NM_025297	ENSMUSG00000028910	Mecr	AI195831|Nrbf1	mitochondrial trans-2-enoyl-CoA reductase	protein-coding
mm_50646.1	chr6	51464439	51464448	+	1	NA	exon (NM_016806, exon 8 of 11)	exon (NM_016806, exon 8 of 11)	5451	NM_182650	53379	Mm.155896	NM_016806	ENSMUSG00000004980	Hnrnpa2b1	9130414A06Rik|Hnrpa2|Hnrpa2b1|hnrnp-A	heterogeneous nuclear ribonucleoprotein A2/B1	protein-coding
mm_126463.1	chr15	80977874	80977876	+	1	NA	intron (NM_134091, intron 1 of 21)	CpG	110	NM_134091	105835	Mm.274943	NM_134091	ENSMUSG00000042303	Sgsm3	1810012I01Rik|AI428557|BB175482|Cip85|R75178|RUSC3|Rutbc3	small G protein signaling modulator 3	protein-coding
mm_76549.1	chr8	88199321	88199355	-	1	NA	intron (NM_001164498, intron 1 of 12)	CpG	125	NM_001164498	214627	Mm.491211	NM_001164497	ENSMUSG00000036779	Papd5	5730445M16Rik|5830428A09	PAP associated domain containing 5	protein-coding
mm_152075.1	chr19	6840862	6840878	-	1	NA	promoter-TSS (NM_019924)	promoter-TSS (NM_019924)	-243	NM_019924	56613	Mm.20914	NM_019924	ENSMUSG00000024952	Rps6ka4	1110069D02Rik|90kDa|AI848992|Msk2|mMSK2	ribosomal protein S6 kinase, polypeptide 4	protein-coding
mm_155884.1	chrX	101532736	101532777	+	1	NA	promoter-TSS (NM_001290729)	promoter-TSS (NM_001290729)	21	NM_001290729	270627	Mm.261750	NM_001081008	ENSMUSG00000031314	Taf1	AU015687|B430306D02Rik|Ccg-1|Ccg1|KAT4|N-TAF1|TAFII250|Taf2a|p250	TATA-box binding protein associated factor 1	protein-coding
mm_73533.1	chr8	108703556	108703564	+	1	NA	Intergenic	Intergenic	-11084	NM_007496	11906	Mm.416972	NM_007496	ENSMUSG00000038872	Zfhx3	A230102L03Rik|Atbf1|Sci|WBP9|mKIAA4228	zinc finger homeobox 3	protein-coding
mm_137361.1	chr17	25369268	25369280	+	1	NA	Intergenic	Intergenic	-1279	NM_012034	26945	Mm.180108	NM_012034	ENSMUSG00000033200	Tpsg1	Prss31|Tmt	tryptase gamma 1	protein-coding
mm_77792.1	chr9	3027440	3027468	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	11289	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_80234.1	chr9	72679130	72679132	+	1	NA	intron (NM_010890, intron 5 of 28)	intron (NM_010890, intron 5 of 28)	16784	NM_010890	17999	Mm.279923	NM_010890	ENSMUSG00000032216	Nedd4	AA959633|AL023035|AU019897|E430025J12Rik|Nedd4-1|Nedd4a|mKIAA0093	neural precursor cell expressed, developmentally down-regulated 4	protein-coding
mm_21854.1	chr2	165879600	165879645	-	1	NA	intron (NM_027230, intron 1 of 23)	intron (NM_027230, intron 1 of 23)	-1185	NM_001291158	228880	Mm.227598	NM_027230	ENSMUSG00000039671	Zmynd8	1110013E22Rik|2010005I16Rik|3632413B07Rik|AI316811|AL024039|Prkcbp1|RACK7	zinc finger, MYND-type containing 8	protein-coding
mm_25688.1	chr3	122245626	122245722	+	1	NA	5' UTR (NM_008129, exon 1 of 7)	5' UTR (NM_008129, exon 1 of 7)	117	NM_008129	14630	Mm.292676	NM_008129	ENSMUSG00000028124	Gclm	AI649393|Gcmc|Glclr	glutamate-cysteine ligase, modifier subunit	protein-coding
mm_93389.1	chr10	107123773	107123794	-	1	NA	promoter-TSS (NM_001142804)	promoter-TSS (NM_001142804)	-119	NM_198636	380660	Mm.336072	NM_198636	ENSMUSG00000035948	Acss3	8430416H19Rik|Gm874	acyl-CoA synthetase short-chain family member 3	protein-coding
mm_135010.1	chr16	32431079	32431117	-	1	NA	promoter-TSS (NM_001163160)	promoter-TSS (NM_001163160)	78	NM_001163159	13026	Mm.98775	NM_009981	ENSMUSG00000005615	Pcyt1a	CTalpha|Cctalpha|Ctpct|Cttalpha	phosphate cytidylyltransferase 1, choline, alpha isoform	protein-coding
mm_110928.1	chr12	76369674	76369684	-	1	NA	promoter-TSS (NM_001172104)	promoter-TSS (NM_001172104)	-119	NM_028356	109929	Mm.41880	NM_028356	ENSMUSG00000056459	Zbtb25	2810462M08Rik|2900064P18Rik|AI842128|Kup|Zfp-50|Zfp50	zinc finger and BTB domain containing 25	protein-coding
mm_142964.1	chr17	56121031	56121063	-	1	NA	intron (NM_029796, intron 1 of 1)	intron (NM_029796, intron 1 of 1)	899	NM_029796	76905	Mm.348025	NM_029796	ENSMUSG00000037095	Lrg1	1300008B03Rik|2310031E04Rik|Lrg|Lrhg	leucine-rich alpha-2-glycoprotein 1	protein-coding
mm_163382.1	chr12	52621692	52621692	-	1	NA	Intergenic	Intergenic	-19370	NR_045910	73278	Mm.396209	NR_045910	ENSMUSG00000100315	1700031P21Rik	-	RIKEN cDNA 1700031P21 gene	ncRNA
mm_94817.1	chr11	23152136	23152145	+	1	NA	promoter-TSS (NR_131065)	promoter-TSS (NR_131065)	0	NR_131065	76993	Mm.59224	NR_131065	ENSMUSG00000086366	1700061J23Rik	-	RIKEN cDNA 1700061J23 gene	ncRNA
mm_102213.1	chr11	54908565	54908574	-	1	NA	exon (NM_008161, exon 3 of 5)	exon (NM_008161, exon 3 of 5)	5715	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_11938.1	chr2	52857829	52857837	+	1	NA	promoter-TSS (NM_172409)	promoter-TSS (NM_172409)	-35	NM_172409	71409	Mm.394427	NM_172409	ENSMUSG00000036053	Fmnl2	5430425K04Rik|Man	formin-like 2	protein-coding
mm_16248.1	chr2	173158740	173158750	+	1	NA	3' UTR (NM_011044, exon 10 of 10)	3' UTR (NM_011044, exon 10 of 10)	5672	NM_011044	18534	Mm.266867	NM_011044	ENSMUSG00000027513	Pck1	AI265463|PEPCK|Pck-1	phosphoenolpyruvate carboxykinase 1, cytosolic	protein-coding
mm_105317.1	chr11	102887848	102887860	-	1	NA	3' UTR (NM_010277, exon 9 of 9)	3' UTR (NM_010277, exon 9 of 9)	2685	NM_025766	66784	Mm.483216	NM_025766	ENSMUSG00000075510	Fam187a	4933439F11Rik	family with sequence similarity 187, member A	protein-coding
mm_54308.1	chr6	29609812	29609872	-	1	NA	promoter-TSS (NM_177296)	promoter-TSS (NM_177296)	-235	NM_177296	320938	Mm.276381	NM_177296	ENSMUSG00000012535	Tnpo3	5730544L10Rik|C430013M08Rik|C81142|D6Ertd313e|Trn-SR|mKIAA4133	transportin 3	protein-coding
mm_99709.1	chr11	106216972	106216976	+	1	NA	promoter-TSS (NM_026009)	promoter-TSS (NM_026009)	48	NM_028074	72047	Mm.41367	NM_028074	ENSMUSG00000020705	Ddx42	1810047H21Rik|AW319508|AW556242|B430002H05Rik|RHELP|RNAHP|SF3b125	DEAD (Asp-Glu-Ala-Asp) box polypeptide 42	protein-coding
mm_48799.1	chr5	148928930	148928951	-	1	NA	promoter-TSS (NM_153572)	promoter-TSS (NM_153572)	-293	NM_153572	231912	Mm.397405	NM_153572	ENSMUSG00000041298	Katnal1	-	katanin p60 subunit A-like 1	protein-coding
mm_29565.1	chr3	116861826	116861849	-	1	NA	intron (NM_009146, intron 1 of 16)	intron (NM_009146, intron 1 of 16)	157	NM_009146	20321	Mm.66293	NM_009146	ENSMUSG00000033386	Frrs1	AI131732|Sdfr2	ferric-chelate reductase 1	protein-coding
mm_34739.1	chr4	152217248	152217254	+	1	NA	intron (NM_001146057, intron 2 of 8)	intron (NM_001146057, intron 2 of 8)	17407	NM_001146058	70025	Mm.296191	NM_133348	ENSMUSG00000028937	Acot7	2410041A17Rik|Ach1|Act|Bach|CTE-IIa|Cte-II|Lach1	acyl-CoA thioesterase 7	protein-coding
mm_159128.1	chr2	74668128	74668128	+	1	NA	promoter-TSS (NM_008275)	promoter-TSS (NM_008275)	-182	NM_008275	15433	Mm.57227	NM_008275	ENSMUSG00000001819	Hoxd13	Hox-4.8|spdh	homeobox D13	protein-coding
mm_123012.1	chr14	55092278	55092322	-	1	NA	promoter-TSS (NM_001039198)	promoter-TSS (NM_001039198)	-252	NM_001039198	239102	Mm.441113	NM_001039198	ENSMUSG00000040721	Zfhx2	ZFH-5	zinc finger homeobox 2	protein-coding
mm_119981.1	chr14	55575716	55575801	+	1	NA	promoter-TSS (NM_026808)	promoter-TSS (NM_026808)	84	NM_026808	68680	Mm.36758	NM_026808	ENSMUSG00000022215	Fitm1	1110028A07Rik|AV010547|Cg10671|Fit1	fat storage-inducing transmembrane protein 1	protein-coding
mm_144197.1	chr18	7916019	7916034	+	1	NA	intron (NM_153085, intron 7 of 13)	intron (NM_153085, intron 7 of 13)	46829	NM_153085	225131	Mm.204524	NM_153085	ENSMUSG00000024283	Wac	1110067P07Rik|A230035H12Rik|AI256735|AI256776|Wwp4	WW domain containing adaptor with coiled-coil	protein-coding
mm_16564.1	chr2	3335983	3336012	-	1	NA	promoter-TSS (NM_030063)	promoter-TSS (NM_030063)	-171	NM_030063	78245	Mm.99733	NM_030063	ENSMUSG00000026644	Acbd7	9230116B18Rik	acyl-Coenzyme A binding domain containing 7	protein-coding
mm_56466.1	chr6	98941743	98941743	-	1	NA	intron (NM_001347345, intron 16 of 19)	intron (NM_001347345, intron 16 of 19)	86555	NM_001197322	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_2489.1	chr1	105990753	105990772	+	1	NA	5' UTR (NM_001122675, exon 1 of 13)	5' UTR (NM_001122675, exon 1 of 13)	356	NM_001122675	227449	Mm.210188	NM_001122675	ENSMUSG00000038866	Zcchc2	9930114B20Rik|AW212015	zinc finger, CCHC domain containing 2	protein-coding
mm_30737.1	chr4	13892205	13892212	+	1	NA	3' UTR (NM_009822, exon 11 of 11)	3' UTR (NM_009822, exon 11 of 11)	107426	NM_009822	12395	Mm.4909	NM_009822	ENSMUSG00000006586	Runx1t1	Cbfa2t1h|ETO|MTG8	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	protein-coding
mm_129597.1	chr15	79834225	79834245	-	1	NA	promoter-TSS (NM_001013360)	promoter-TSS (NM_001013360)	98	NM_001013360	504193	Mm.38438	NM_029079	ENSMUSG00000089837	Npcd	Cbx6-Nptxr	neuronal pentraxin chromo domain	protein-coding
mm_138178.1	chr17	34267328	34267345	+	1	NA	exon (NM_207105, exon 3 of 6)	exon (NM_207105, exon 3 of 6)	4109	NM_207105	14961	Mm.254067	NM_207105	ENSMUSG00000073421	H2-Ab1	AI845868|Abeta|H-2Ab|H2-Ab|I-Abeta|IAb|Ia-2|Ia2|Rmcs1	histocompatibility 2, class II antigen A, beta 1	protein-coding
mm_171510.1	chr4	146287056	146287062	+	1	NA	intron (NM_001083918, intron 3 of 6).2	intron (NM_001083918, intron 3 of 6).2	16674	NM_001083918	666532	Mm.392861	NM_001083918	ENSMUSG00000067916	Zfp991	Gm13139|OTTMUSG00000010657	zinc finger protein 991	protein-coding
mm_159149.1	chr2	87943631	87943631	-	1	NA	promoter-TSS (NM_146643)	promoter-TSS (NM_146643)	-5	NM_146643	258636	Mm.377605	NM_146643	ENSMUSG00000075145	Olfr1155	MOR174-10	olfactory receptor 1155	protein-coding
mm_31841.1	chr4	74251841	74251861	+	1	NA	promoter-TSS (NM_144787)	promoter-TSS (NM_144787)	-28	NM_144787	76804	Mm.209059	NM_144787	ENSMUSG00000028397	Kdm4c	2410141F18Rik|AA517467|Gasc1|Jmjd2c	lysine (K)-specific demethylase 4C	protein-coding
mm_140158.1	chr17	80207467	80207517	+	1	NA	promoter-TSS (NM_001195487)	promoter-TSS (NM_001195487)	-187	NM_001195485	225027	Mm.292016	NM_146083	ENSMUSG00000024097	Srsf7	35kDa|9430065L19Rik|9G8|NX-96|Sfrs7	serine/arginine-rich splicing factor 7	protein-coding
mm_88150.1	chr10	69534040	69534070	+	1	NA	5' UTR (NM_170688, exon 1 of 43)	5' UTR (NM_170688, exon 1 of 43)	347	NM_146005	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_48468.1	chr5	140830431	140830453	-	1	NA	promoter-TSS (NM_010302)	promoter-TSS (NM_010302)	-11	NM_010302	14673	Mm.370185	NM_010302	ENSMUSG00000000149	Gna12	AI414047|AI504261|Galpha12	guanine nucleotide binding protein, alpha 12	protein-coding
mm_136935.1	chr17	14203721	14203765	+	1	NA	promoter-TSS (NM_172826)	promoter-TSS (NM_172826)	88	NM_172826	240025	Mm.79993	NM_172826	ENSMUSG00000048826	Dact2	2900084M21Rik|A630024E20|Dpr2|Frd2|dapper2	dishevelled-binding antagonist of beta-catenin 2	protein-coding
mm_98801.1	chr11	97041074	97041110	+	1	NA	promoter-TSS (NM_026154)	promoter-TSS (NM_026154)	277	NM_027026	69297	Mm.250465	NM_027026	ENSMUSG00000020878	Lrrc46	1700006D24Rik	leucine rich repeat containing 46	protein-coding
mm_33666.1	chr4	133176337	133176361	+	1	NA	intron (NM_153423, intron 1 of 8)	intron (NM_153423, intron 1 of 8)	-19306	NR_105984	102466215		NR_105984	ENSMUSG00000099202	Mir7017	Gm27945|mmu-mir-7017	microRNA 7017	ncRNA
mm_130571.1	chr15	99458118	99458128	-	1	NA	promoter-TSS (NM_001001884)	promoter-TSS (NM_001001884)	-375	NM_001001884	380969	Mm.22915	NM_001001884	ENSMUSG00000023009	Nckap5l	C230021P08Rik|Cep169	NCK-associated protein 5-like	protein-coding
mm_93934.1	chr10	127179096	127179097	-	1	NA	intron (NM_177615, intron 2 of 16)	intron (NM_177615, intron 2 of 16)	1549	NM_177615	216441	Mm.248373	NM_177615	ENSMUSG00000040441	Slc26a10	C78409|D630010I07	solute carrier family 26, member 10	protein-coding
mm_162285.1	chr1	24177654	24177656	+	1	NA	promoter-TSS (NM_007740)	promoter-TSS (NM_007740)	45	NM_007740	12839	Mm.154662	NM_007740	ENSMUSG00000026147	Col9a1	Col9a-1	collagen, type IX, alpha 1	protein-coding
mm_114324.1	chr13	60603590	60603600	+	1	NA	intron (NM_029653, intron 2 of 25)	intron (NM_029653, intron 2 of 25)	1384	NM_134062	69635	Mm.24103	NM_029653	ENSMUSG00000021559	Dapk1	D13Ucla1|DAP-Kinase	death associated protein kinase 1	protein-coding
mm_135792.1	chr16	57189394	57189446	-	1	NA	exon (NM_026254, exon 11 of 18)	exon (NM_026254, exon 11 of 18)	-22088	NM_023175	52633	Mm.383203	NM_023175	ENSMUSG00000022751	Nit2	1190017B19Rik|D16Ertd502e	nitrilase family, member 2	protein-coding
mm_111259.1	chr12	85138734	85138743	-	1	NA	exon (NM_146244, exon 8 of 11)	exon (NM_146244, exon 8 of 11)	12526	NM_146244	238323	Mm.44829	NM_146244	ENSMUSG00000019235	Rps6kl1	A830084F09Rik|AW046440	ribosomal protein S6 kinase-like 1	protein-coding
mm_86098.1	chr9	115298123	115298125	-	1	NA	intron (NM_024222, intron 1 of 15)	intron (NM_024222, intron 1 of 15)	12297	NM_024222	68292	Mm.296158	NM_024222	ENSMUSG00000032437	Stt3b	1300006C19Rik|Simp	STT3, subunit of the oligosaccharyltransferase complex, homolog B (S. cerevisiae)	protein-coding
mm_43458.1	chr5	136245517	136245532	+	1	NA	promoter-TSS (NM_018825)	promoter-TSS (NM_018825)	-584	NM_018825	23921	Mm.425294	NM_018825	ENSMUSG00000005057	Sh2b2	Aps	SH2B adaptor protein 2	protein-coding
mm_78255.1	chr9	21826550	21826554	+	1	NA	intron (NM_177030, intron 23 of 49)	intron (NM_177030, intron 23 of 49)	-8958	NM_001080940	624219	Mm.440264	NM_001080940	ENSMUSG00000047822	Angptl8	EG624219|Gm6484|Rifl	angiopoietin-like 8	protein-coding
mm_117365.1	chr13	70841730	70841754	-	1	NA	promoter-TSS (NR_137640)	promoter-TSS (NR_137640)	69	NM_172053	271127	Mm.115970	NM_172053	ENSMUSG00000049538	Adamts16	-	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 16	protein-coding
mm_36233.1	chr4	63152672	63152686	-	1	NA	exon (NM_007443, exon 2 of 10)	exon (NM_007443, exon 2 of 10)	1493	NM_007443	11699	Mm.2197	NM_007443	ENSMUSG00000028356	Ambp	AI194774|ASPI|HI-30|Intin4|Itil|UTI	alpha 1 microglobulin/bikunin	protein-coding
mm_41336.1	chr5	90496042	90496123	+	1	NA	exon (NM_007423, exon 4 of 15)	exon (NM_007423, exon 4 of 15)	5368	NM_007423	11576	Mm.358570	NM_007423	ENSMUSG00000054932	Afp	-	alpha fetoprotein	protein-coding
mm_150658.1	chr19	41981256	41981283	+	1	NA	promoter-TSS (NM_028152)	promoter-TSS (NM_028152)	-133	NM_028152	72199	Mm.218940	NM_028152	ENSMUSG00000025159	Mms19	2410001K24Rik|2610042O15Rik|AI316855|C79368|C86341|Mms19l	MMS19 (MET18 S. cerevisiae)	protein-coding
mm_112638.1	chr13	16014422	16014439	+	1	NA	intron (NM_008380, intron 2 of 4)	intron (NM_008380, intron 2 of 4)	2579	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_16566.1	chr2	3366575	3366587	-	1	NA	promoter-TSS (NM_145921)	promoter-TSS (NM_145921)	-12	NM_145921	99035	Mm.13808	NM_145921	ENSMUSG00000026645	Olah	AI607300|E230009B14Rik|Thedc1	oleoyl-ACP hydrolase	protein-coding
mm_14339.1	chr2	129593033	129593046	+	1	NA	promoter-TSS (NM_001291022)	promoter-TSS (NM_001291022)	-130	NM_001291019	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_64975.1	chr7	16816732	16816744	-	1	NA	promoter-TSS (NM_173430)	promoter-TSS (NM_173430)	-6	NM_173430	243853	Mm.39703	NM_173430	ENSMUSG00000048920	Fkrp	A830029B19Rik|AI842067|AI847300|LGMD1I|MDC1C	fukutin related protein	protein-coding
mm_15939.1	chr2	165807529	165807575	+	1	NA	exon (NM_001291158, exon 16 of 24)	exon (NM_001291158, exon 16 of 24)	50621	NM_001252585	228880	Mm.227598	NM_027230	ENSMUSG00000039671	Zmynd8	1110013E22Rik|2010005I16Rik|3632413B07Rik|AI316811|AL024039|Prkcbp1|RACK7	zinc finger, MYND-type containing 8	protein-coding
mm_129288.1	chr15	77163117	77163177	-	1	NA	intron (NM_053104, intron 2 of 13)	intron (NM_053104, intron 2 of 13)	-9335	NM_001286418	93686	Mm.202774	NM_053104	ENSMUSG00000033565	Rbfox2	Fbm2|Fxh|Hrnbp2|Rbm9	RNA binding protein, fox-1 homolog (C. elegans) 2	protein-coding
mm_64236.1	chr7	141698706	141698719	+	1	NA	exon (NM_023566, exon 20 of 46)	exon (NM_023566, exon 20 of 46)	8372	NM_023566	17831	Mm.2041	NM_023566		Muc2	2010015E03Rik|MCM|wnn	mucin 2	protein-coding
mm_115599.1	chr13	11876469	11876470	-	1	NA	intron (NM_023868, intron 8 of 104)	B1F|SINE|Alu	230476	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding
mm_90203.1	chr10	120380717	120380718	+	1	NA	intron (NM_001347170, intron 3 of 5)	intron (NM_001347170, intron 3 of 5)	-8806	NR_040626	320626	Mm.446091	NR_040626	ENSMUSG00000090191	9230105E05Rik	-	RIKEN cDNA 9230105E05 gene	ncRNA
mm_21329.1	chr2	157101379	157101389	-	1	NA	exon (NM_001139520, exon 16 of 17)	exon (NM_001139520, exon 16 of 17)	14329	NM_001177439	383766	Mm.480305	NM_001177439	ENSMUSG00000074628	Tldc2	Gm1332	TBC/LysM associated domain containing 2	protein-coding
mm_7786.1	chr1	131424937	131424940	-	1	NA	intron (NM_001081011, intron 3 of 22)	L1MC4|LINE|L1	102423	NM_001081011	14270	Mm.276259	NM_019520	ENSMUSG00000026425	Srgap2	9930124L22Rik|AI448945|FBP2|Fnbp2|srGAP3	SLIT-ROBO Rho GTPase activating protein 2	protein-coding
mm_55676.1	chr6	72598331	72598368	-	1	NA	promoter-TSS (NM_026159)	promoter-TSS (NM_026159)	64	NM_144917	232089	Mm.167232	NM_144917	ENSMUSG00000056698	Elmod3	AI844780|C330008I15Rik|RBM29|Rbed1	ELMO/CED-12 domain containing 3	protein-coding
mm_66777.1	chr7	46909009	46909037	-	1	NA	exon (NM_021884, exon 4 of 10)	exon (NM_021884, exon 4 of 10)	10907	NM_021884	22088	Mm.241334	NM_021884	ENSMUSG00000014402	Tsg101	AI255943|CC2	tumor susceptibility gene 101	protein-coding
mm_26110.1	chr3	137623729	137623756	+	1	NA	promoter-TSS (NM_030143)	promoter-TSS (NM_030143)	70	NM_030143	73284	Mm.250841	NM_030143	ENSMUSG00000046818	Ddit4l	1700037B15Rik|1700108M02Rik|REDD2|RTP801L|Smhs1	DNA-damage-inducible transcript 4-like	protein-coding
mm_78019.1	chr9	13708916	13708929	+	1	NA	3' UTR (NM_173776, exon 4 of 4)	3' UTR (NM_173776, exon 4 of 4)	-40259	NM_023858	77116	Mm.210405	NM_023858	ENSMUSG00000031918	Mtmr2	6030445P13Rik	myotubularin related protein 2	protein-coding
mm_43963.1	chr5	145263920	145263921	+	1	NA	Intergenic	ID_B1|SINE|B4	-19423	NM_001081431	666311	Mm.260773	NM_001081431	ENSMUSG00000070420	Zscan25	EG666311|Zfp498	zinc finger and SCAN domain containing 25	protein-coding
mm_59056.1	chr7	19414226	19414255	+	1	NA	exon (NM_007710, exon 2 of 8)	exon (NM_007710, exon 2 of 8)	3146	NM_007710	12715	Mm.2375	NM_007710	ENSMUSG00000030399	Ckm	Ckmm|M-CK|MCK	creatine kinase, muscle	protein-coding
mm_48514.1	chr5	142822838	142822855	-	1	NA	Intergenic	Intergenic	-5459	NM_001122730	231861	Mm.354649	NM_178242	ENSMUSG00000039477	Tnrc18	BC025631|EG381742|Zfp469	trinucleotide repeat containing 18	protein-coding
mm_166406.1	chr5	136581644	136581648	-	1	NA	Intergenic	Intergenic	-14156	NM_001291238	13047	Mm.320317	NM_009986	ENSMUSG00000029705	Cux1	CDP|Cutl1|Cux|Cux-1	cut-like homeobox 1	protein-coding
mm_158818.1	chrX	167330510	167330579	-	1	NA	promoter-TSS (NM_001290758)	promoter-TSS (NM_001290758)	27	NM_001290757	170743	Mm.23979	NM_133211	ENSMUSG00000044583	Tlr7	-	toll-like receptor 7	protein-coding
mm_68453.1	chr7	110061539	110061552	-	1	NA	promoter-TSS (NM_009281)	promoter-TSS (NM_009281)	-157	NM_009281	20841	Mm.10815	NM_009281	ENSMUSG00000061079	Zfp143	AA959806|AU015869|D7Ertd805e|KRAB14|SBF|Staf|Zfp79|Zfp80-rs1|Znf143|pHZ-1	zinc finger protein 143	protein-coding
mm_157193.1	chrX	12080053	12080078	-	1	NA	5' UTR (NM_029510, exon 1 of 15)	5' UTR (NM_029510, exon 1 of 15)	488	NM_175045	71458	Mm.196328	NM_029510	ENSMUSG00000040363	Bcor	2900008C10Rik|5830466J11Rik|8430401K06Rik|BcorR|D930024N20Rik|mKIAA1575	BCL6 interacting corepressor	protein-coding
mm_15686.1	chr2	163631004	163631023	+	1	NA	exon (NM_012032, exon 6 of 10)	exon (NM_012032, exon 6 of 10)	-13837	NR_028113	68386	Mm.410649	NR_028113	ENSMUSG00000058812	0610039K10Rik	-	RIKEN cDNA 0610039K10 gene	ncRNA
mm_165293.1	chr2	91096886	91096894	+	1	NA	5' UTR (NM_011355, exon 1 of 5)	5' UTR (NM_011355, exon 1 of 5)	212	NM_011355	20375	Mm.1302	NM_011355	ENSMUSG00000002111	Spi1	Dis-1|Dis1|PU.1|Sfpi-1|Sfpi1|Spi-1|Tcfpu1|Tfpu.1	spleen focus forming virus (SFFV) proviral integration oncogene	protein-coding
mm_136894.1	chr17	13013461	13013499	+	1	NA	exon (NM_013671, exon 4 of 5)	exon (NM_013671, exon 4 of 5)	5641	NM_013671	20656	Mm.290876	NM_013671	ENSMUSG00000006818	Sod2	MnSOD|Sod-2	superoxide dismutase 2, mitochondrial	protein-coding
mm_148231.1	chr18	80440851	80440865	-	1	NA	intron (NM_026295, intron 10 of 12)	intron (NM_026295, intron 10 of 12)	28809	NM_026295	67655	Mm.312893	NM_026295	ENSMUSG00000033323	Ctdp1	4930563P03Rik|AW553592	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) phosphatase, subunit 1	protein-coding
mm_76220.1	chr8	83572292	83572318	-	1	NA	TTS (NM_025843)	TTS (NM_025843)	5547	NM_025843	66916	Mm.29683	NM_025843	ENSMUSG00000033938	Ndufb7	1110002H15Rik	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 7	protein-coding
mm_19589.1	chr2	101982010	101982013	-	1	NA	intron (NM_001290784, intron 4 of 5)	B3|SINE|B2	95749	NM_029635	76501	Mm.330424	NM_029635	ENSMUSG00000027163	Commd9	1810029F08Rik|AA409293	COMM domain containing 9	protein-coding
mm_72430.1	chr8	82863484	82863505	+	1	NA	5' UTR (NM_177378, exon 1 of 7)	5' UTR (NM_177378, exon 1 of 7)	138	NM_177378	330812	Mm.491438	NM_177378	ENSMUSG00000047747	Rnf150	A630007N06Rik|C030044C12Rik|Greul5|mKIAA1214	ring finger protein 150	protein-coding
mm_166622.1	chr6	72538225	72538260	+	1	NA	Intergenic	Intergenic	-6149	NM_007599	12332	Mm.18626	NM_007599	ENSMUSG00000056737	Capg	gCap39|mbh1	capping protein (actin filament), gelsolin-like	protein-coding
mm_168270.1	chr10	93889695	93889698	-	1	NA	5' UTR (NM_019648, exon 2 of 12)	5' UTR (NM_019648, exon 2 of 12)	1506	NM_019648	56307	Mm.289329	NM_019648	ENSMUSG00000036112	Metap2	4930584B20Rik|A930035J23Rik|AI047573|AL024412|AU014659|Amp2|Mnpep|p67|p67eIF2	methionine aminopeptidase 2	protein-coding
mm_143907.1	chr17	84958537	84958553	-	1	NA	promoter-TSS (NR_027930)	promoter-TSS (NR_027930)	544	NM_001159496	19043	Mm.249695	NM_011151	ENSMUSG00000061130	Ppm1b	PP2CB	protein phosphatase 1B, magnesium dependent, beta isoform	protein-coding
mm_94917.1	chr11	29463736	29463749	+	1	NA	exon (NM_176841, exon 15 of 32)	exon (NM_176841, exon 15 of 32)	51291	NM_026465	67939	Mm.251087	NM_026465	ENSMUSG00000032673	Prorsd1	2010316F05Rik|Ncrna00117|Prdxdd1	prolyl-tRNA synthetase domain containing 1	protein-coding
mm_18942.1	chr2	76764879	76764890	-	1	NA	exon (NM_011652, exon 254 of 313)	exon (NM_011652, exon 254 of 313)	89569	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_139927.1	chr17	71019525	71019535	+	1	NA	promoter-TSS (NM_001083934)	promoter-TSS (NM_001083934)	-27	NM_010867	17929	Mm.4103	NM_010867	ENSMUSG00000024049	Myom1	D430047A17Rik	myomesin 1	protein-coding
mm_23044.1	chr3	34784127	34784131	+	1	NA	Intergenic	Intergenic	12054	NR_110488	102638436	Mm.261793	NR_110488	ENSMUSG00000106519	Gm38509	Peril	predicted gene, 38509	ncRNA
mm_102730.1	chr11	67243474	67243493	-	1	NA	exon (NM_010855, exon 11 of 40)	exon (NM_010855, exon 11 of 40)	5671	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_90199.1	chr10	120227299	120227330	+	1	NA	intron (NM_025431, intron 1 of 2)	CpG	254	NM_025431	66225	Mm.291755	NM_025431	ENSMUSG00000020224	Llph	1190005P17Rik	LLP homolog, long-term synaptic facilitation (Aplysia)	protein-coding
mm_55156.1	chr6	51545283	51545322	-	1	NA	intron (NM_028035, intron 1 of 6)	intron (NM_028035, intron 1 of 6)	779	NM_001127348	71982	Mm.294166	NM_028035	ENSMUSG00000038301	Snx10	2410004M09Rik	sorting nexin 10	protein-coding
mm_9204.1	chr1	171229711	171229727	-	1	NA	3' UTR (NM_010185, exon 5 of 5)	3' UTR (NM_010185, exon 5 of 5)	4630	NM_010185	14127	Mm.22673	NM_010185	ENSMUSG00000058715	Fcer1g	AI573376|CD23|FcR-gamma|FcR[g]|FcRgamma|Fce1g|FcepsilonRI|Ly-50	Fc receptor, IgE, high affinity I, gamma polypeptide	protein-coding
mm_2716.1	chr1	128143354	128143359	+	1	NA	intron (NM_181750, intron 1 of 26)	B1_Mus2|SINE|Alu	40050	NM_181750	226412	Mm.221041	NM_181750	ENSMUSG00000056211	R3hdm1	R3hdm	R3H domain containing 1	protein-coding
mm_45364.1	chr5	66004279	66004291	-	1	NA	promoter-TSS (NR_027961)	promoter-TSS (NR_027961)	0	NR_027961	231253	Mm.436542	NM_177679	ENSMUSG00000054598	9130230L23Rik	-	RIKEN cDNA 9130230L23 gene	ncRNA
mm_40701.1	chr5	65861136	65861149	+	1	NA	Intergenic	Intergenic	-2427	NM_001081105	74734	Mm.20323	NM_001081105	ENSMUSG00000029204	Rhoh	5830400A04Rik|AU019774|Arhh	ras homolog family member H	protein-coding
mm_75072.1	chr8	33843563	33843573	-	1	NA	intron (NM_001042674, intron 4 of 7)	intron (NM_001042674, intron 4 of 7)	86295	NM_019733	19663	Mm.323997	NM_019733	ENSMUSG00000031586	Rbpms	2010300K22Rik|2700019M19Rik|AU017537|RBP-MS|hermes	RNA binding protein gene with multiple splicing	protein-coding
mm_118836.1	chr14	25607891	25607933	+	1	NA	intron (NM_001310666, intron 6 of 23)	CpG	4399	NM_001309430	100188919	Mm.473810	NM_001309430		Israa	-	immune system released activating agent	protein-coding
mm_3046.1	chr1	134040461	134040480	+	1	NA	exon (NM_021355, exon 2 of 3)	exon (NM_021355, exon 2 of 3)	2955	NM_021355	14264	Mm.287146	NM_021355	ENSMUSG00000041559	Fmod	AI131919|AU041740|SLRR2E	fibromodulin	protein-coding
mm_89204.1	chr10	86685573	86685623	+	1	NA	promoter-TSS (NR_015572)	promoter-TSS (NR_015572)	71	NR_015572	66263	Mm.392261	NR_015572		1810014B01Rik	-	RIKEN cDNA 1810014B01 gene	pseudo
mm_95179.1	chr11	41591011	41591015	+	1	NA	Intergenic	Intergenic	409701	NM_177408	14406	Mm.5309	NM_008073	ENSMUSG00000020436	Gabrg2	GABAA-R|Gabrg-2|gamma2	gamma-aminobutyric acid (GABA) A receptor, subunit gamma 2	protein-coding
mm_64669.1	chr7	4445596	4445631	-	1	NA	promoter-TSS (NM_001290411)	promoter-TSS (NM_001290411)	44	NM_175372	108841	Mm.413106	NM_175372	ENSMUSG00000008435	Rdh13	8430425D21Rik	retinol dehydrogenase 13 (all-trans and 9-cis)	protein-coding
mm_23822.1	chr3	80800547	80800555	+	1	NA	intron (NM_001083806, intron 2 of 15)	intron (NM_001083806, intron 2 of 15)	2240	NM_013540	14800	Mm.220224	NM_013540	ENSMUSG00000033981	Gria2	GluA2|GluR-B|Glur-2|Glur2	glutamate receptor, ionotropic, AMPA2 (alpha 2)	protein-coding
mm_50468.1	chr6	48977232	48977274	+	1	NA	intron (NM_001029987, intron 1 of 3)	intron (NM_001029987, intron 1 of 3)	2110	NM_001029987	243376	Mm.244112	NM_001029987	ENSMUSG00000068536	Doxl2	-	diamine oxidase-like protein 2	protein-coding
mm_13873.1	chr2	119872793	119872835	+	1	NA	Intergenic	CpG	-24414	NM_001164274	29808	Mm.87532	NM_013720	ENSMUSG00000033943	Mga	AV312082|C130042M01Rik|C80739|D030062C11Rik|Mad5	MAX gene associated	protein-coding
mm_53045.1	chr6	124712280	124712353	+	1	NA	promoter-TSS (NM_013536)	promoter-TSS (NM_013536)	27	NM_007531	12034	Mm.36241	NM_007531	ENSMUSG00000004264	Phb2	AU044498|BAP|Bap37|Bcap37|REA	prohibitin 2	protein-coding
mm_78268.1	chr9	22002993	22002999	+	1	NA	promoter-TSS (NM_029939)	promoter-TSS (NM_029939)	8	NM_008925	19089	Mm.214593	NM_008925	ENSMUSG00000003402	Prkcsh	80K-H|PKCSH	protein kinase C substrate 80K-H	protein-coding
mm_7263.1	chr1	94052578	94052587	-	1	NA	promoter-TSS (NM_008798)	promoter-TSS (NM_008798)	-29	NM_008798	18566	Mm.5024	NM_008798	ENSMUSG00000026285	Pdcd1	Ly101|PD-1|Pdc1	programmed cell death 1	protein-coding
mm_37564.1	chr4	126202584	126202698	-	1	NA	promoter-TSS (NM_146153)	promoter-TSS (NM_146153)	69	NM_146153	230753	Mm.29813	NM_146153	ENSMUSG00000043962	Thrap3	9330151F09Rik|B230333E16Rik|Trap150	thyroid hormone receptor associated protein 3	protein-coding
mm_35022.1	chr4	3938355	3938401	-	1	NA	promoter-TSS (NM_019969)	promoter-TSS (NM_019969)	27	NM_019969	56711	Mm.331467	NM_019969	ENSMUSG00000003282	Plag1	-	pleiomorphic adenoma gene 1	protein-coding
mm_171413.1	chr4	130047769	130047784	-	1	NA	promoter-TSS (NM_028266)	promoter-TSS (NM_028266)	-64	NM_028266	107581	Mm.41860	NM_028266	ENSMUSG00000040690	Col16a1	2700007F12Rik|A530052M23Rik|AI838662|CA1F	collagen, type XVI, alpha 1	protein-coding
mm_170525.1	chr19	33456428	33456441	-	1	NA	Intergenic	RLTR9D|LTR|ERVK	61336	NM_001323386	628236		NM_001323386	ENSMUSG00000079344	Lipo4	Gm6857	lipase, member O4	protein-coding
mm_126921.1	chr15	91644005	91644013	+	1	NA	Intergenic	Intergenic	-29215	NM_025730	66725	Mm.37558	NM_025730	ENSMUSG00000036273	Lrrk2	4921513O20Rik|9330188B09Rik|AW561911|D630001M17Rik|Gm927|cI-46	leucine-rich repeat kinase 2	protein-coding
mm_164587.1	chr17	26509464	26509468	-	1	NA	promoter-TSS (NM_013642)	promoter-TSS (NM_013642)	-994	NM_013642	19252	Mm.239041	NM_013642	ENSMUSG00000024190	Dusp1	3CH134|MKP1|Ptpn16|U19515|erp|mkp-1	dual specificity phosphatase 1	protein-coding
mm_14494.1	chr2	131937459	131937476	+	1	NA	3' UTR (NM_001278256, exon 4 of 4)	3' UTR (NM_001278256, exon 4 of 4)	-13394	NM_001278257	26434	Mm.180750	NM_023043	ENSMUSG00000027338	Prnd	AI450264|Dpl|PrPLP|doppel	prion protein dublet	protein-coding
mm_137939.1	chr17	32685586	32685596	+	1	NA	promoter-TSS (NM_134127)	promoter-TSS (NM_134127)	-40	NM_001346538	106648	Mm.26539	NM_134127	ENSMUSG00000073424	Cyp4f15	AI787289|Cyp4f-15	cytochrome P450, family 4, subfamily f, polypeptide 15	protein-coding
mm_133853.1	chr16	96258657	96258667	+	1	NA	intron (NM_001122993, intron 2 of 3)	intron (NM_001122993, intron 2 of 3)	-22370	NM_033149	93961	Mm.154783	NM_033149	ENSMUSG00000074892	B3galt5	1190002B21Rik|AU045265|b3Galt-V	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 5	protein-coding
mm_4617.1	chr1	178766994	178766999	+	1	NA	intron (NM_001161665, intron 4 of 14)	intron (NM_001161665, intron 4 of 14)	237871	NM_001161665	269152	Mm.129727	NM_177724	ENSMUSG00000026494	Kif26b	4832420M10|BC056349|D230039L06Rik	kinesin family member 26B	protein-coding
mm_167330.1	chr8	70544187	70544189	-	1	NA	intron (NM_007924, intron 1 of 11)	intron (NM_007924, intron 1 of 11)	4513	NM_007924	13716	Mm.271973	NM_007924	ENSMUSG00000070002	Ell	Ell1|Men	elongation factor RNA polymerase II	protein-coding
mm_83198.1	chr9	41157655	41157665	-	1	NA	promoter-TSS (NM_176860)	promoter-TSS (NM_176860)	-166	NM_176860	72828	Mm.133615	NM_176860	ENSMUSG00000032020	Ubash3b	2810457I06Rik|BB125008|TULA-2|p70	ubiquitin associated and SH3 domain containing, B	protein-coding
mm_96928.1	chr11	70511063	70511075	+	1	NA	3' UTR (NM_029360, exon 5 of 5)	3' UTR (NM_029360, exon 5 of 5)	3547	NM_001013607	327956	Mm.244514	NM_001013607	ENSMUSG00000020830	Vmo1	Gm741	vitelline membrane outer layer 1 homolog (chicken)	protein-coding
mm_170458.1	chr18	89989358	89989362	-	1	NA	Intergenic	MT2_Mm|LTR|ERVL	-220224	NM_001039173	623279	Mm.447164	NM_001039173	ENSMUSG00000073514	Dok6	Dok-6	docking protein 6	protein-coding
mm_86770.1	chr10	19957118	19957123	+	1	NA	intron (NM_008580, intron 1 of 29)	intron (NM_008580, intron 1 of 29)	22594	NM_008580	26408	Mm.6595	NM_008580	ENSMUSG00000071369	Map3k5	7420452D20Rik|ASK|ASK1|MAPKKK5|Mekk5	mitogen-activated protein kinase kinase kinase 5	protein-coding
mm_5035.1	chr1	193303374	193303386	+	1	NA	intron (NM_001277928, intron 1 of 22)	intron (NM_001277928, intron 1 of 22)	1137	NM_001277928	16780	Mm.435441	NM_008484	ENSMUSG00000026639	Lamb3	-	laminin, beta 3	protein-coding
mm_17738.1	chr2	32704124	32704139	-	1	NA	Intergenic	Intergenic	8653	NM_130860	107951	Mm.27557	NM_130860	ENSMUSG00000009555	Cdk9	PITALRE	cyclin-dependent kinase 9 (CDC2-related kinase)	protein-coding
mm_81986.1	chr9	121403415	121403528	+	1	NA	intron (NM_175114, intron 2 of 15)	intron (NM_175114, intron 2 of 15)	36513	NM_175114	67095	Mm.491112	NM_175114	ENSMUSG00000032536	Trak1	2310001H13Rik|AI413908|AI467545|hyrt|mKIAA1042	trafficking protein, kinesin binding 1	protein-coding
mm_171050.1	chr3	102936046	102936048	-	1	NA	promoter-TSS (NM_011516)	promoter-TSS (NM_011516)	53	NM_011516	20957	Mm.243849	NM_011516	ENSMUSG00000027855	Sycp1	SCP1	synaptonemal complex protein 1	protein-coding
mm_168765.1	chr12	12023002	12023020	+	1	NA	Intergenic	Intergenic	-140112	NR_003964	627110	Mm.194735	NR_003964		Tubb2a-ps2	C79445	tubulin, beta 2a, pseudogene 2	pseudo
mm_140179.1	chr17	80943827	80943857	+	1	NA	promoter-TSS (NM_026516)	promoter-TSS (NM_026516)	-790	NM_026516	68027	Mm.357108	NM_026516	ENSMUSG00000024245	Tmem178	2810417M05Rik|Tmem178a	transmembrane protein 178	protein-coding
mm_18135.1	chr2	45019143	45019155	-	1	NA	intron (NM_001289521, intron 2 of 8)	intron (NM_001289521, intron 2 of 8)	4028	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_172968.1	chr9	88956952	88956962	+	1	NA	promoter-TSS (NM_009742)	promoter-TSS (NM_009742)	37	NM_009742	12044	Mm.425593	NM_009742	ENSMUSG00000102037	Bcl2a1a	A1|BB218357|Bcl2a1|Bfl-1|Hbpa1	B cell leukemia/lymphoma 2 related protein A1a	protein-coding
mm_149990.1	chr19	29252301	29252313	+	1	NA	intron (NM_001048177, intron 1 of 23)	intron (NM_001048177, intron 1 of 23)	504	NM_008413	16452	Mm.275839	NM_008413	ENSMUSG00000024789	Jak2	Fd17	Janus kinase 2	protein-coding
mm_12219.1	chr2	67648746	67648759	+	1	NA	Intergenic	Lx5c|LINE|L1	-26705	NR_106083	102465706		NR_106083	ENSMUSG00000098299	Mir7224	Gm27971|mmu-mir-7224	microRNA 7224	ncRNA
mm_82491.1	chr9	18473612	18473682	-	1	NA	promoter-TSS (NM_028935)	promoter-TSS (NM_028935)	-88	NM_028935	72230	Mm.289689	NM_028935	ENSMUSG00000074500	Zfp558	1700007A21Rik|4932704I17Rik|Zfp558-ps	zinc finger protein 558	protein-coding
mm_151131.1	chr19	48313347	48313351	+	1	NA	intron (NM_025696, intron 1 of 26)	intron (NM_025696, intron 1 of 26)	107324	NM_025696	66673	Mm.70980	NM_025696	ENSMUSG00000063434	Sorcs3	6330404A12Rik|AW045579	sortilin-related VPS10 domain containing receptor 3	protein-coding
mm_77963.1	chr9	7764059	7764177	+	1	NA	promoter-TSS (NM_133739)	promoter-TSS (NM_133739)	41	NM_133739	71929	Mm.283293	NM_133739	ENSMUSG00000050912	Tmem123	2310075C12Rik	transmembrane protein 123	protein-coding
mm_89312.1	chr10	87923228	87923267	+	1	NA	intron (NM_001111274, intron 4 of 4)	intron (NM_001111274, intron 4 of 4)	-43424	NR_000040	22172	Mm.391420	NR_000040		Tyms-ps	-	thymidylate synthase, pseudogene	pseudo
mm_142527.1	chr17	46433702	46433715	-	1	NA	intron (NM_144856, intron 7 of 9)	intron (NM_144856, intron 7 of 9)	4766	NM_181664	114570	Mm.25168	NM_053250	ENSMUSG00000023968	Crip3	TLP|TLP-A|TLP-B|Tlmp	cysteine-rich protein 3	protein-coding
mm_155467.1	chrX	73639389	73639395	+	1	NA	promoter-TSS (NM_029352)	promoter-TSS (NM_029352)	-49	NM_029352	75590	Mm.16479	NM_029352	ENSMUSG00000031383	Dusp9	Dusp4|Mpk4|Pyst3	dual specificity phosphatase 9	protein-coding
mm_108543.1	chr12	84317103	84317147	+	1	NA	non-coding (NR_045615, exon 1 of 10)	non-coding (NR_045615, exon 1 of 10)	266	NM_001252583	52708	Mm.255150	NM_144833	ENSMUSG00000042472	Zfp410	Apa1|D12Ertd748e|Znf410	zinc finger protein 410	protein-coding
mm_137812.1	chr17	30005888	30005905	+	1	NA	intron (NM_148926, intron 1 of 4)	intron (NM_148926, intron 1 of 4)	809	NM_148926	21769	Mm.220972	NM_148926	ENSMUSG00000044477	Zfand3	AW539211|TEG-27|Tex27	zinc finger, AN1-type domain 3	protein-coding
mm_81451.1	chr9	109816644	109816669	+	1	NA	promoter-TSS (NM_183136)	promoter-TSS (NM_183136)	29	NM_183136	78709	Mm.99613	NM_183136	ENSMUSG00000050074	Spink8	C630041L24Rik	serine peptidase inhibitor, Kazal type 8	protein-coding
mm_85607.1	chr9	107605104	107605122	-	1	NA	non-coding (NR_111986, exon 2 of 18)	non-coding (NR_111986, exon 2 of 18)	289	NM_009153	20347	Mm.4083	NM_009153	ENSMUSG00000057969	Sema3b	SemA|Semaa|sema5|semaV	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B	protein-coding
mm_98788.1	chr11	96929326	96929349	+	1	NA	promoter-TSS (NM_146026)	promoter-TSS (NM_146026)	13	NM_146026	217138	Mm.342551	NM_146026	ENSMUSG00000047040	Prr15l	Atad4|BC022765|E230006A12Rik	proline rich 15-like	protein-coding
mm_87659.1	chr10	58485754	58485764	+	1	NA	exon (NM_011240, exon 24 of 29)	exon (NM_011240, exon 24 of 29)	-12178	NM_001162956	76138	Mm.211744	NM_001162956	ENSMUSG00000038010	Ccdc138	6230424H07Rik|BC042726	coiled-coil domain containing 138	protein-coding
mm_28795.1	chr3	96057824	96057874	-	1	NA	5' UTR (NM_013841, exon 1 of 15)	5' UTR (NM_013841, exon 1 of 15)	606	NM_013841	22365	Mm.263185	NM_013841	ENSMUSG00000015747	Vps45	AI462172|AW554165|mVps45	vacuolar protein sorting 45	protein-coding
mm_11078.1	chr2	27709248	27709249	+	1	NA	promoter-TSS (NM_001290481)	promoter-TSS (NM_001290481)	-44	NM_001290481	20181	Mm.24624	NM_011305	ENSMUSG00000015846	Rxra	9530071D11Rik|Nr2b1|RXRalpha1	retinoid X receptor alpha	protein-coding
mm_87647.1	chr10	58400510	58400515	+	1	NA	intron (NM_001346676, intron 2 of 9)	intron (NM_001346676, intron 2 of 9)	6139	NM_001346676	110829	Mm.57734	NM_026148	ENSMUSG00000019920	Lims1	2310016J22Rik|4921524A02Rik|AI507642|AU021743|AW551584|C430041B13Rik|Lims1l|PINCH|PINCH1	LIM and senescent cell antigen-like domains 1	protein-coding
mm_135065.1	chr16	34191784	34191787	-	1	NA	intron (NM_001164268, intron 25 of 33)	intron (NM_001164268, intron 25 of 33)	-224782	NM_009471	22247	Mm.13145	NM_009471	ENSMUSG00000022814	Umps	1700095D23Rik|AA408257|AL033308|BB164745	uridine monophosphate synthetase	protein-coding
mm_168570.1	chr11	69921389	69921390	-	1	NA	promoter-TSS (NM_001166592)	promoter-TSS (NM_001166592)	-3	NM_181582	276770	Mm.18026	NM_181582	ENSMUSG00000078812	Eif5a	AA410058|D19Wsu54e|Eif4d|Eif5a1|eIF-4D|eIF-5A|eIF-5A-1|eIF-5A1	eukaryotic translation initiation factor 5A	protein-coding
mm_94790.1	chr11	22735512	22735516	+	1	NA	Intergenic	Intergenic	124221	NM_016888	53625	Mm.395495	NM_016888	ENSMUSG00000051650	B3gnt2	AA408337|AA409404|AW260308|B3Galt6|B3gnt1|BGnT-1|BGnT-2|BGnT1|BGnT2|Beta3gnt	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 2	protein-coding
mm_81854.1	chr9	118703392	118703404	+	1	NA	intron (NM_133721, intron 15 of 27)	intron (NM_133721, intron 15 of 27)	-8294	NM_001113514	104099	Mm.335520	NM_133721	ENSMUSG00000039115	Itga9	(alpha)9|2610002H11Rik|6720458D17Rik|AI461869|D130073C02|D9Ertd428e	integrin alpha 9	protein-coding
mm_134890.1	chr16	29541542	29541558	-	1	NA	promoter-TSS (NM_001164612)	promoter-TSS (NM_001164612)	-67	NM_001164612	224079	Mm.54954	NM_172613	ENSMUSG00000038094	Atp13a4	4631413J11Rik|4832416L12|9330174J19Rik	ATPase type 13A4	protein-coding
mm_145578.1	chr18	60963652	60963656	+	1	NA	promoter-TSS (NM_001286809)	promoter-TSS (NM_001286809)	100	NM_001286809	12322	Mm.131530	NM_009792	ENSMUSG00000024617	Camk2a	CaMKII|R74975|mKIAA0968	calcium/calmodulin-dependent protein kinase II alpha	protein-coding
mm_89233.1	chr10	87566095	87566119	+	1	NA	intron (NM_008777, intron 5 of 12)	intron (NM_008777, intron 5 of 12)	44312	NM_008777	18478	Mm.263539	NM_008777	ENSMUSG00000020051	Pah	AW106920	phenylalanine hydroxylase	protein-coding
mm_32171.1	chr4	100478807	100478872	+	1	NA	promoter-TSS (NM_001033773)	promoter-TSS (NM_001033773)	-28	NM_001033773	381534	Mm.318133	NM_001033773	ENSMUSG00000069733	Ube2u	-	ubiquitin-conjugating enzyme E2U (putative)	protein-coding
mm_78260.1	chr9	21927595	21927646	+	1	NA	promoter-TSS (NM_178577)	promoter-TSS (NM_178577)	-85	NM_001253870	235043	Mm.253329	NM_178577	ENSMUSG00000040883	Tmem205	-	transmembrane protein 205	protein-coding
mm_62535.1	chr7	102249703	102249714	+	1	NA	intron (NM_019566, intron 1 of 1)	intron (NM_019566, intron 1 of 1)	410	NM_019566	56212	Mm.259795	NM_019566	ENSMUSG00000073982	Rhog	2810426G09Rik|Arhg|Sid10750	ras homolog family member G	protein-coding
mm_60617.1	chr7	44596030	44596037	+	1	NA	exon (NM_001290682, exon 2 of 5)	exon (NM_001290682, exon 2 of 5)	5147	NM_001290682	16504	Mm.40312	NM_008422	ENSMUSG00000062785	Kcnc3	KShIIID|Kcr2-3|Kv3.3	potassium voltage gated channel, Shaw-related subfamily, member 3	protein-coding
mm_127273.1	chr15	99725617	99725685	+	1	NA	promoter-TSS (NM_183256)	promoter-TSS (NM_183256)	33	NM_183256	66379	Mm.5265	NM_183256	ENSMUSG00000023020	Cox14	2310016M24Rik|AA959804	cytochrome c oxidase assembly protein 14	protein-coding
mm_58345.1	chr6	147243815	147243836	-	1	NA	Intergenic	Lx8|LINE|L1	20188	NM_008970	19227	Mm.28440	NM_008970	ENSMUSG00000048776	Pthlh	PLP|PTH-like|Pthrp	parathyroid hormone-like peptide	protein-coding
mm_105246.1	chr11	102349749	102349779	-	1	NA	3' UTR (NM_011403, exon 20 of 20)	3' UTR (NM_011403, exon 20 of 20)	15517	NM_011403	20533	Mm.7248	NM_011403	ENSMUSG00000006574	Slc4a1	Ae1|CD233|Empb3|l11Jus51	solute carrier family 4 (anion exchanger), member 1	protein-coding
mm_96705.1	chr11	69655560	69655567	+	1	NA	exon (NM_009235, exon 1 of 2)	exon (NM_009235, exon 1 of 2)	526	NM_009235	20670	Mm.347499	NM_009235	ENSMUSG00000041287	Sox15	-	SRY (sex determining region Y)-box 15	protein-coding
mm_37047.1	chr4	115964220	115964224	-	1	NA	Intergenic	Intergenic	-24296	NM_130865	140477	Mm.213206	NM_130865	ENSMUSG00000028707	Dmbx1	Atx|Cdmx|Mbx|Otx3	diencephalon/mesencephalon homeobox 1	protein-coding
mm_19693.1	chr2	103485768	103485779	-	1	NA	promoter-TSS (NM_009804)	promoter-TSS (NM_009804)	-620	NM_009804	12359	Mm.4215	NM_009804	ENSMUSG00000027187	Cat	2210418N07|Cas-1|Cas1|Cs-1	catalase	protein-coding
mm_110452.1	chr12	51636665	51636669	-	1	NA	intron (NM_052973, intron 8 of 17)	B1F|SINE|Alu	43326	NM_001198835	12810	Mm.21325	NM_007728	ENSMUSG00000020953	Coch	AW122937|Coch-5B2|D12H14S564E	cochlin	protein-coding
mm_24439.1	chr3	90600204	90600219	+	1	NA	promoter-TSS (NM_011310)	promoter-TSS (NM_011310)	-4	NM_011310	20197	Mm.440044	NM_011310	ENSMUSG00000001021	S100a3	S100E	S100 calcium binding protein A3	protein-coding
mm_142363.1	chr17	44105683	44105697	-	1	NA	5' UTR (NM_199016, exon 1 of 4)	5' UTR (NM_199016, exon 1 of 4)	118	NM_199016	224794	Mm.255971	NM_199016	ENSMUSG00000023961	Enpp4	4933413N07Rik|AA986363|AI195364|E-NPP 4|Gm90|mKIAA0879	ectonucleotide pyrophosphatase/phosphodiesterase 4	protein-coding
mm_66135.1	chr7	31110871	31110905	-	1	NA	exon (NM_001276269, exon 1 of 13)	exon (NM_001276269, exon 1 of 13)	109	NM_001276269	15451	Mm.19182	NM_008281	ENSMUSG00000001249	Hpn	Hlb320	hepsin	protein-coding
mm_23504.1	chr3	60528511	60528521	+	1	NA	intron (NM_001253710, intron 1 of 7)	intron (NM_001253710, intron 1 of 7)	27337	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_104941.1	chr11	100117441	100117454	-	1	NA	3' UTR (NM_010662, exon 8 of 8)	3' UTR (NM_010662, exon 8 of 8)	3130	NM_001313949	16663	Mm.4646	NM_010662	ENSMUSG00000044041	Krt13	CK13|K13|Krt-1.13|Krt1-13	keratin 13	protein-coding
mm_7281.1	chr1	97661625	97661635	-	1	NA	intron (NM_133825, intron 1 of 2)	CpG	388	NM_133825	52392	Mm.12309	NM_133825	ENSMUSG00000044768	D1Ertd622e	AI987691|AW047450	DNA segment, Chr 1, ERATO Doi 622, expressed	protein-coding
mm_36949.1	chr4	109102608	109102622	-	1	NA	intron (NM_133885, intron 4 of 22)	intron (NM_133885, intron 4 of 22)	15421	NM_173350	100273	Mm.366315	NM_133885	ENSMUSG00000028559	Osbpl9	2600011I06Rik|AU015843|Orp-9	oxysterol binding protein-like 9	protein-coding
mm_171469.1	chr4	145781467	145781467	+	1	NA	promoter-TSS (NM_001083918)	promoter-TSS (NM_001083918)	-76	NM_001083918	666532	Mm.392861	NM_001083918	ENSMUSG00000067916	Zfp991	Gm13139|OTTMUSG00000010657	zinc finger protein 991	protein-coding
mm_45562.1	chr5	73191949	73191961	-	1	NA	intron (NM_028194, intron 3 of 62)	intron (NM_028194, intron 3 of 62)	64663	NM_028194	72313	Mm.260594	NM_028194	ENSMUSG00000070733	Fryl	2010313D22Rik|2310004H21Rik|2510002A14Rik|9030227G01Rik|mKIAA0826	FRY like transcription coactivator	protein-coding
mm_61851.1	chr7	88297246	88297257	+	1	NA	intron (NM_009982, intron 3 of 6)	intron (NM_009982, intron 3 of 6)	19166	NM_001311790	13032	Mm.89295	NM_009982	ENSMUSG00000030560	Ctsc	AI047818|CatC|DPP1|DPPI	cathepsin C	protein-coding
mm_26491.1	chr3	145292538	145292569	+	1	NA	promoter-TSS (NM_027770)	promoter-TSS (NM_027770)	81	NM_001317733	71355	Mm.235570	NM_027770	ENSMUSG00000028197	Col24a1	5430404K19Rik	collagen, type XXIV, alpha 1	protein-coding
mm_158598.1	chrX	151414561	151414563	-	1	NA	intron (NM_198105, intron 4 of 15)	intron (NM_198105, intron 4 of 15)	70339	NM_198105	207375	Mm.391339	NM_198105	ENSMUSG00000025262	Fam120c	D930001I21Rik|ORF34	family with sequence similarity 120, member C	protein-coding
mm_117500.1	chr13	78199981	78200012	-	1	NA	intron (NR_045195, intron 1 of 2)	intron (NR_045195, intron 1 of 2)	-1123	NM_010151	13865	Mm.439653	NM_010151	ENSMUSG00000069171	Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR-3|EAR3|Erbal3|SVP44|Tcfcoup1	nuclear receptor subfamily 2, group F, member 1	protein-coding
mm_27363.1	chr3	50434387	50434396	-	1	NA	intron (NM_011990, intron 3 of 11)	intron (NM_011990, intron 3 of 11)	9222	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_74876.1	chr8	25052843	25052848	-	1	NA	intron (NM_031257, intron 9 of 11)	L1_Rod|LINE|L1	-13883	NM_001081187	330723	Mm.334452	NM_001081187	ENSMUSG00000037406	Htra4	B430206E18Rik	HtrA serine peptidase 4	protein-coding
mm_95120.1	chr11	34078504	34078514	+	1	NA	exon (NM_010696, exon 13 of 21)	exon (NM_010696, exon 13 of 21)	31308	NM_010696	16822	Mm.265350	NM_010696	ENSMUSG00000002699	Lcp2	AI323664|BB161688|SLP-76|SLP76|m1Khoe|twm	lymphocyte cytosolic protein 2	protein-coding
mm_170055.1	chr17	30005167	30005177	+	1	NA	promoter-TSS (NM_148926)	promoter-TSS (NM_148926)	85	NM_148926	21769	Mm.220972	NM_148926	ENSMUSG00000044477	Zfand3	AW539211|TEG-27|Tex27	zinc finger, AN1-type domain 3	protein-coding
mm_84819.1	chr9	77544830	77544862	-	1	NA	promoter-TSS (NM_001146048)	promoter-TSS (NM_001146048)	6	NM_001146048	214345	Mm.28534	NM_172528	ENSMUSG00000032352	Lrrc1	A430093J20Rik|AU016091|D030059I21|mKIAA4018	leucine rich repeat containing 1	protein-coding
mm_39149.1	chr4	155398012	155398028	-	1	NA	promoter-TSS (NM_008072)	promoter-TSS (NM_008072)	49	NM_008072	14403	Mm.388925	NM_008072	ENSMUSG00000029054	Gabrd	AI853201	gamma-aminobutyric acid (GABA) A receptor, subunit delta	protein-coding
mm_28130.1	chr3	87112272	87112274	-	1	NA	intron (NM_001170985, intron 2 of 15)	intron (NM_001170985, intron 2 of 15)	62474	NM_001170985	170643	Mm.89552	NM_130867	ENSMUSG00000041734	Kirrel	6720469N11Rik|Kirrel1|Neph1	kin of IRRE like (Drosophila)	protein-coding
mm_61034.1	chr7	49558591	49558607	+	1	NA	intron (NM_175272, intron 18 of 37)	intron (NM_175272, intron 18 of 37)	78236	NM_001005232	13172	Mm.307176	NM_001005232	ENSMUSG00000030507	Dbx1	AI426026|Dbx	developing brain homeobox 1	protein-coding
mm_165499.1	chr2	167349159	167349163	-	1	NA	promoter-TSS (NM_019835)	promoter-TSS (NM_019835)	17	NM_019835	56336	Mm.200886	NM_019835	ENSMUSG00000017929	B4galt5	9430078I07Rik|AW049941|AW539721	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 5	protein-coding
mm_99785.1	chr11	107338032	107338044	+	1	NA	intron (NM_145823, intron 1 of 9)	intron (NM_145823, intron 1 of 9)	132682	NM_145823	71795	Mm.397413	NM_145823	ENSMUSG00000040430	Pitpnc1	1110020B03Rik|5830436L09Rik|AI662802|AI851387|C330017I21Rik|Dnr411|RDGBB|RDGBB1|rdgB-beta	phosphatidylinositol transfer protein, cytoplasmic 1	protein-coding
mm_133855.1	chr16	96273469	96273480	+	1	NA	intron (NM_001122993, intron 2 of 3)	intron (NM_001122993, intron 2 of 3)	-7558	NM_033149	93961	Mm.154783	NM_033149	ENSMUSG00000074892	B3galt5	1190002B21Rik|AU045265|b3Galt-V	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 5	protein-coding
mm_136844.1	chr17	12762930	12762935	+	1	NA	intron (NM_010515, intron 1 of 47)	intron (NM_010515, intron 1 of 47)	6774	NM_010515	16004	Mm.26553	NM_010515	ENSMUSG00000023830	Igf2r	AI661837|CD222|CI-MPR|M6P/IGF2R|Mpr300	insulin-like growth factor 2 receptor	protein-coding
mm_30260.1	chr3	146748023	146748055	-	1	NA	exon (NM_001164199, exon 6 of 10)	exon (NM_001164199, exon 6 of 10)	22199	NM_001164198	18749	Mm.16766	NM_011100	ENSMUSG00000005034	Prkacb	CbPKA|Pkacb	protein kinase, cAMP dependent, catalytic, beta	protein-coding
mm_168303.1	chr11	106725252	106725263	+	1	NA	Intergenic	Intergenic	-9976	NM_001305157	18613	Mm.343951	NM_008816	ENSMUSG00000020717	Pecam1	C85791|Cd31|PECAM-1|Pecam	platelet/endothelial cell adhesion molecule 1	protein-coding
mm_13227.1	chr2	97480115	97480120	+	1	NA	intron (NM_001289744, intron 1 of 1)	intron (NM_001289744, intron 1 of 1)	12460	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_70994.1	chr8	27447706	27447711	+	1	NA	promoter-TSS (NM_027618)	promoter-TSS (NM_027618)	38	NM_027618	70952	Mm.158160	NM_026256	ENSMUSG00000063932	Poteg	4921537P18Rik|4930456F22Rik|Gsarp1|Gsarp2	POTE ankyrin domain family, member G	protein-coding
mm_830.1	chr1	51289286	51289315	+	1	NA	5' UTR (NM_138741, exon 1 of 2)	5' UTR (NM_138741, exon 1 of 2)	174	NM_138741	20324	Mm.398690	NM_138741	ENSMUSG00000045954	Sdpr	-	serum deprivation response	protein-coding
mm_67607.1	chr7	83794843	83794887	-	1	NA	promoter-TSS (NM_029335)	promoter-TSS (NM_029335)	-26	NM_029335	75556	Mm.17649	NM_029335	ENSMUSG00000011154	Cfap161	1700026D08Rik|AW047638|AW551802	cilia and flagella associated protein 161	protein-coding
mm_120227.1	chr14	62857562	62857594	+	1	NA	intron (NM_175546, intron 1 of 11)	(CA)n|Simple_repeat|Simple_repeat	-7964	NR_105860	102465311		NR_105860	ENSMUSG00000098858	Mir6541	Gm27311|mmu-mir-6541	microRNA 6541	ncRNA
mm_106160.1	chr11	116626926	116626937	-	1	NA	promoter-TSS (NM_172572)	promoter-TSS (NM_172572)	88	NM_172572	217344	Mm.89695	NM_172572	ENSMUSG00000020806	Rhbdf2	4732465I17Rik|Rhbdl6|cub	rhomboid 5 homolog 2	protein-coding
mm_77773.1	chr9	3015699	3015722	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	23033	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_98411.1	chr11	94363948	94363950	+	1	NA	intron (NM_029600, intron 15 of 30)	intron (NM_029600, intron 15 of 30)	29027	NM_029600	76408	Mm.23942	NM_029600	ENSMUSG00000020865	Abcc3	1700019L09Rik|ABC31|MLP2|MOAT-D|MRP3	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	protein-coding
mm_94318.1	chr11	4236800	4236806	+	1	NA	promoter-TSS (NM_001013365)	promoter-TSS (NM_001013365)	18	NM_001013365	18413	Mm.131422	NM_001013365	ENSMUSG00000058755	Osm	OncoM	oncostatin M	protein-coding
mm_121015.1	chr14	79536227	79536236	+	1	NA	5' UTR (NM_007920, exon 2 of 9)	5' UTR (NM_007920, exon 2 of 9)	20557	NM_001286411	13709	Mm.20938	NM_007920	ENSMUSG00000036461	Elf1	Elf-1|Sts1|mElf-1|p70	E74-like factor 1	protein-coding
mm_112234.1	chr12	113482347	113482349	-	1	NA	Intergenic	Intergenic	-7217	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_63143.1	chr7	123158675	123158676	+	1	NA	intron (NM_144925, intron 4 of 23)	B1_Mus1|SINE|Alu	34790	NM_144925	233833	Mm.102305	NM_144925	ENSMUSG00000052707	Tnrc6a	2010321I05Rik|3110054G10Rik|AW557223|CAGH26|D130023A07Rik|GW182|Tnrc6	trinucleotide repeat containing 6a	protein-coding
mm_53599.1	chr6	138142854	138142863	+	1	NA	intron (NM_001347489, intron 1 of 3)	intron (NM_001347489, intron 1 of 3)	1264	NM_001347489	56615	Mm.14796	NM_019946	ENSMUSG00000008540	Mgst1	1500002K10Rik|Gst	microsomal glutathione S-transferase 1	protein-coding
mm_159413.1	chr3	104777535	104777535	-	1	NA	promoter-TSS (NM_183224)	promoter-TSS (NM_183224)	12	NM_183224	329731	Mm.389494	NM_183224	ENSMUSG00000055865	Fam19a3	7530404M11Rik|TAFA3|Tafa-3	family with sequence similarity 19, member A3	protein-coding
mm_134836.1	chr16	26358790	26358792	-	1	NA	3' UTR (NM_016674, exon 4 of 4)	3' UTR (NM_016674, exon 4 of 4)	13048	NM_016674	12737	Mm.289441	NM_016674	ENSMUSG00000022512	Cldn1	AI596271	claudin 1	protein-coding
mm_28010.1	chr3	83042456	83042468	-	1	NA	exon (NM_181849, exon 8 of 8)	exon (NM_181849, exon 8 of 8)	7401	NM_181849	110135	Mm.30063	NM_181849	ENSMUSG00000033831	Fgb	2510049G14Rik	fibrinogen beta chain	protein-coding
mm_143860.1	chr17	84186176	84186197	-	1	NA	exon (NM_001001806, exon 2 of 2)	exon (NM_001001806, exon 2 of 2)	1761	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_155249.1	chrX	57223735	57223739	+	1	NA	3' UTR (NM_011616, exon 5 of 5)	3' UTR (NM_011616, exon 5 of 5)	11594	NM_011616	21947	Mm.4861	NM_011616	ENSMUSG00000031132	Cd40lg	CD154|CD40-L|Cd40l|HIGM1|IGM|IMD3|Ly-62|Ly62|T-BAM|TRAP|Tnfsf5|Tnlg8b|gp39	CD40 ligand	protein-coding
mm_145739.1	chr18	64265368	64265413	+	1	NA	5' UTR (NM_009182, exon 3 of 6)	5' UTR (NM_009182, exon 3 of 6)	11031	NM_009182	20451	Mm.252110	NM_009182	ENSMUSG00000056812	St8sia3	AI847333|ST8SiaIII|Siat8c	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3	protein-coding
mm_125793.1	chr15	74784105	74784115	+	1	NA	Intergenic	Intergenic	-5251	NR_027837	78725	Mm.171357	NM_172433	ENSMUSG00000101026	D730001G18Rik	Ly6g6g	RIKEN cDNA D730001G18 gene	ncRNA
mm_139929.1	chr17	71019584	71019600	+	1	NA	promoter-TSS (NM_001083934)	promoter-TSS (NM_001083934)	35	NM_001083934	17929	Mm.4103	NM_010867	ENSMUSG00000024049	Myom1	D430047A17Rik	myomesin 1	protein-coding
mm_96999.1	chr11	70718945	70718951	+	1	NA	intron (NM_153103, intron 17 of 22)	MIR|SINE|MIR	12958	NR_105890	102465557		NR_105890	ENSMUSG00000105932	Mir6925	mmu-mir-6925	microRNA 6925	ncRNA
mm_155771.1	chrX	96255572	96255601	+	1	NA	intron (NM_177789, intron 4 of 6)	intron (NM_177789, intron 4 of 6)	12769	NR_029801	723814		NR_029801	ENSMUSG00000076066	Mir223	Mirn223|miR-223|mmu-mir-223	microRNA 223	ncRNA
mm_153518.1	chr19	41666024	41666029	-	1	NA	intron (NM_015748, intron 4 of 36)	intron (NM_015748, intron 4 of 36)	77375	NR_106166	102465884		NR_106166	ENSMUSG00000098286	Mir8091	Gm27575|mmu-mir-8091	microRNA 8091	ncRNA
mm_104341.1	chr11	94202195	94202203	-	1	NA	Intergenic	Intergenic	-9255	NM_009427	22057	Mm.259673	NM_009427	ENSMUSG00000037573	Tob1	Tob|Trob	transducer of ErbB-2.1	protein-coding
mm_98368.1	chr11	93996083	93996099	+	1	NA	promoter-TSS (NM_001199204)	promoter-TSS (NM_001199204)	0	NM_001199203	70834	Mm.260737	NM_027569	ENSMUSG00000020859	Spag9	3110018C07Rik|4733401I23Rik|4831406C20Rik|AW552012|JLP|JSAP2|JSAP2a|Jip4|Mapk8ip4|syd1	sperm associated antigen 9	protein-coding
mm_102868.1	chr11	69407607	69407620	-	1	NA	exon (NM_001017426, exon 6 of 23)	exon (NM_001017426, exon 6 of 23)	6062	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_159955.1	chr6	86526131	86526131	-	1	NA	promoter-TSS (NM_011865)	promoter-TSS (NM_011865)	34	NM_011865	23983	Mm.274146	NM_011865	ENSMUSG00000051695	Pcbp1	WBP17|[a]CP-1|alphaCP-1|hnRNP E1	poly(rC) binding protein 1	protein-coding
mm_71147.1	chr8	39298166	39298177	+	1	NA	non-coding (NR_044988, exon 1 of 4)	non-coding (NR_044988, exon 1 of 4)	191	NR_044988	621335	Mm.208080	NR_044988	ENSMUSG00000109827	Gm6213	EG621335	predicted gene 6213	ncRNA
mm_160435.1	chr8	94136956	94136956	+	1	NA	promoter-TSS (NM_008631)	promoter-TSS (NM_008631)	-248	NM_008631	17752	Mm.1536	NM_008631	ENSMUSG00000031757	Mt4	MT-IV	metallothionein 4	protein-coding
mm_19244.1	chr2	84727356	84727372	-	1	NA	promoter-TSS (NM_133840)	promoter-TSS (NM_133840)	-96	NM_133840	98985	Mm.21583	NM_133840	ENSMUSG00000027079	Clp1	AI462438|Heab	CLP1, cleavage and polyadenylation factor I subunit	protein-coding
mm_28393.1	chr3	90020937	90020965	-	1	NA	exon (NM_001165987, exon 14 of 25)	exon (NM_001165987, exon 14 of 25)	-9741	NR_106129	102465771		NR_106129	ENSMUSG00000098397	Mir7669	Gm27996|mmu-mir-7669	microRNA 7669	ncRNA
mm_73069.1	chr8	94434344	94434354	+	1	NA	non-coding (NR_015514, exon 2 of 3)	non-coding (NR_015514, exon 2 of 3)	754	NR_015514	320377	Mm.486022	NR_015514		9330175E14Rik	A630085K21	RIKEN cDNA 9330175E14 gene	ncRNA
mm_75438.1	chr8	47352487	47352501	-	1	NA	promoter-TSS (NM_175162)	promoter-TSS (NM_175162)	-146	NM_175162	71069	Mm.23973	NM_175162	ENSMUSG00000038143	Stox2	4933409N07Rik|AI449080|AI835114|mKIAA1392	storkhead box 2	protein-coding
mm_15763.1	chr2	164316708	164316716	+	1	NA	promoter-TSS (NM_013679)	promoter-TSS (NM_013679)	-39	NM_013679	20945	Mm.439686	NM_013679	ENSMUSG00000017000	Svs6	MSVSP99|Svp6	seminal vesicle secretory protein 6	protein-coding
mm_69792.1	chr7	141100556	141100587	-	1	NA	promoter-TSS (NM_023059)	promoter-TSS (NM_023059)	-25	NM_023059	24058	Mm.38017	NM_023059	ENSMUSG00000025494	Sigirr	AI256711|TIR8	single immunoglobulin and toll-interleukin 1 receptor (TIR) domain	protein-coding
mm_72695.1	chr8	84971228	84971243	+	1	NA	intron (NM_001317385, intron 3 of 5)	intron (NM_001317385, intron 3 of 5)	1613	NM_011563	21672	Mm.347009	NM_011563	ENSMUSG00000005161	Prdx2	AL022839|Band-8|NkefB|PRP|PrxII|TDX1|TPx|TPx-B|TR|TSA|Tdpx1|Torin	peroxiredoxin 2	protein-coding
mm_145090.1	chr18	42536259	42536270	+	1	NA	exon (NM_001289526, exon 6 of 22)	exon (NM_001289526, exon 6 of 22)	24777	NR_110344	56070	Mm.270511	NM_001039474	ENSMUSG00000024498	Tcerg1	2410022J09Rik|2900090C16Rik|AI428505|CA150b|FBP23|FBP28|Taf2s|ca150|p144	transcription elongation regulator 1 (CA150)	protein-coding
mm_102086.1	chr11	52282296	52282307	-	1	NA	intron (NM_001313981, intron 2 of 10)	intron (NM_001313981, intron 2 of 10)	294	NM_009331	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_105338.1	chr11	102994705	102994735	-	1	NA	3' UTR (NM_026551, exon 5 of 5)	3' UTR (NM_026551, exon 5 of 5)	5201	NR_105896	102466988		NR_105896	ENSMUSG00000098613	Mir6931	Gm27303|mmu-mir-6931	microRNA 6931	ncRNA
mm_159174.1	chr2	109677085	109677085	+	1	NA	promoter-TSS (NM_001285419)	promoter-TSS (NM_001285419)	53	NM_001285419	12064	Mm.1442	NM_007540	ENSMUSG00000048482	Bdnf	-	brain derived neurotrophic factor	protein-coding
mm_85184.1	chr9	96685327	96685338	-	1	NA	TTS (NM_175537)	TTS (NM_175537)	46343	NM_175537	245007	Mm.485954	NM_175537	ENSMUSG00000040433	Zbtb38	A930014K01Rik|CIBZ	zinc finger and BTB domain containing 38	protein-coding
mm_10350.1	chr2	11689863	11689880	+	1	NA	3' UTR (NM_008367, exon 8 of 8)	3' UTR (NM_008367, exon 8 of 8)	-15422	NM_001271498	16169	Mm.200196	NM_008358	ENSMUSG00000023206	Il15ra	AA690181|IL-15RA	interleukin 15 receptor, alpha chain	protein-coding
mm_28690.1	chr3	95519037	95519056	-	1	NA	Intergenic	L1MB4|LINE|L1	-7740	NM_021281	13040	Mm.3619	NM_021281	ENSMUSG00000038642	Ctss	Cats	cathepsin S	protein-coding
mm_63979.1	chr7	139978932	139978956	+	1	NA	promoter-TSS (NM_001033465)	promoter-TSS (NM_001033465)	-189	NM_001347613	381933	Mm.440431	NM_001033465	ENSMUSG00000073795	6430531B16Rik	Gm1093	RIKEN cDNA 6430531B16 gene	protein-coding
mm_53678.1	chr6	142161492	142161494	+	1	NA	intron (NM_023718, intron 1 of 14)	RLTR22_Mur|LTR|ERVK	24656	NM_023718	28254	Mm.38953	NM_023718	ENSMUSG00000079262	Slco1a6	4930422F19Rik|AI790453|Oatp-5|Oatp5|Slc21a13	solute carrier organic anion transporter family, member 1a6	protein-coding
mm_74156.1	chr8	123397763	123397775	+	1	NA	intron (NM_001286362, intron 12 of 16)	intron (NM_001286362, intron 12 of 16)	-9313	NM_008559	17199	Mm.324942	NM_008559	ENSMUSG00000074037	Mc1r	Mcr1|Mshra|Tob|e	melanocortin 1 receptor	protein-coding
mm_75133.1	chr8	34979899	34979910	-	1	NA	Intergenic	Intergenic	-14214	NM_175091	21951	Mm.88364	NM_175091	ENSMUSG00000031529	Tnks	4930554K12Rik|AI662855|ARTD5|C86528|D130072O21Rik|TANK1|mTNKS1	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase	protein-coding
mm_148531.1	chr19	4558809	4558816	+	1	NA	intron (NM_001162946, intron 2 of 20)	intron (NM_001162946, intron 2 of 20)	-35507	NM_008797	18563	Mm.1845	NM_008797	ENSMUSG00000024892	Pcx	Pc|Pcb	pyruvate carboxylase	protein-coding
mm_30402.1	chr3	152253085	152253103	-	1	NA	exon (NM_199465, exon 3 of 13)	exon (NM_199465, exon 3 of 13)	13226	NM_199465	68810	Mm.200188	NM_199465	ENSMUSG00000039103	Nexn	1110046H09Rik|AA553326|NELIN	nexilin	protein-coding
mm_151611.1	chr19	3897519	3897583	-	1	NA	exon (NM_001136091, exon 15 of 20)	exon (NM_001136091, exon 15 of 20)	7679	NM_016921	27060	Mm.271689	NM_016921	ENSMUSG00000001750	Tcirg1	ATP6N1C|ATP6a3|Atp6i|OC-116|OPTB1|Stv1|TIRC7|Vph1|oc	T cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 protein A3	protein-coding
mm_26763.1	chr3	8692880	8692909	-	1	NA	Intergenic	Intergenic	-25856	NM_010423	15213	Mm.29581	NM_010423	ENSMUSG00000040289	Hey1	AI316788|AI414254|CHF2|HRT1|Herp2|Hesr1|bHLHb31|hesr-1	hairy/enhancer-of-split related with YRPW motif 1	protein-coding
mm_1952.1	chr1	86357039	86357061	+	1	NA	promoter-TSS (NR_002851)	promoter-TSS (NR_002851)	-723	NR_002851	80828		NR_002851	ENSMUSG00000064823	Snord82	Rnu82|U82|Z25	small nucleolar RNA, C/D box 82	snoRNA
mm_36679.1	chr4	96507397	96507399	-	1	NA	promoter-TSS (NM_001104927)	promoter-TSS (NM_001104927)	-12	NM_001104927	665095	Mm.331717	NM_001104927	ENSMUSG00000082932	Cyp2j8	Cyp2j8-ps|OTTMUSG00000007938	cytochrome P450, family 2, subfamily j, polypeptide 8	protein-coding
mm_85339.1	chr9	102628905	102628951	-	1	NA	intron (NM_181394, intron 1 of 2)	ID_B1|SINE|B4	2632	NM_181394	69010	Mm.2000	NM_181394	ENSMUSG00000035048	Anapc13	1810004D07Rik|APC13|SWM1	anaphase promoting complex subunit 13	protein-coding
mm_62366.1	chr7	100607557	100607618	+	1	NA	promoter-TSS (NM_024287)	promoter-TSS (NM_024287)	1	NM_001163663	19346	Mm.28650	NM_024287	ENSMUSG00000030704	Rab6a	2610028L11Rik|AA419671|Rab6	RAB6A, member RAS oncogene family	protein-coding
mm_6556.1	chr1	75141510	75141515	-	1	NA	intron (NM_026977, intron 1 of 8)	CpG	856	NM_026977	69171	Mm.28193	NM_026977	ENSMUSG00000033159	Cnppd1	1810031K17Rik|AU043960	cyclin Pas1/PHO80 domain containing 1	protein-coding
mm_1102.1	chr1	59763532	59763575	+	1	NA	promoter-TSS (NM_007561)	promoter-TSS (NM_007561)	-726	NM_007561	12168	Mm.7106	NM_007561	ENSMUSG00000067336	Bmpr2	2610024H22Rik|AL117858|AW546137|BB189135|BMP-2|BMPR-2|BMPR-II|BMPRII|BRK-3|Gm20272	bone morphogenetic protein receptor, type II (serine/threonine kinase)	protein-coding
mm_138572.1	chr17	35394098	35394099	+	1	NA	promoter-TSS (NR_051981)	promoter-TSS (NR_051981)	-1	NR_051981	15016	Mm.439648	NR_051981	ENSMUSG00000055413	H2-Q5	H-2Q5|Qa-5|Qa5|Qat-5	histocompatibility 2, Q region locus 5	pseudo
mm_146616.1	chr18	10090882	10090923	-	1	NA	exon (NM_009071, exon 23 of 33)	exon (NM_009071, exon 23 of 33)	-60753	NM_001038589	59025	Mm.329277	NM_021522	ENSMUSG00000047879	Usp14	2610005K12Rik|2610037B11Rik|AW107924|C78769|ax|nmf375	ubiquitin specific peptidase 14	protein-coding
mm_66883.1	chr7	58759447	58759461	-	1	NA	intron (NM_009728, intron 2 of 20)	intron (NM_009728, intron 2 of 20)	101252	NM_009728	11982	Mm.135129	NM_009728	ENSMUSG00000025324	Atp10a	Atp10c|pfatp	ATPase, class V, type 10A	protein-coding
mm_80053.1	chr9	69314782	69314806	+	1	NA	intron (NM_001289916, intron 1 of 9)	intron (NM_001289916, intron 1 of 9)	24953	NM_001289916	19883	Mm.378450	NM_013646	ENSMUSG00000032238	Rora	9530021D13Rik|Nr1f1|ROR1|ROR2|ROR3|nmf267|sg|staggerer|tmgc26	RAR-related orphan receptor alpha	protein-coding
mm_127704.1	chr15	102991005	102991009	+	1	NA	exon (NM_010466, exon 1 of 2)	exon (NM_010466, exon 1 of 2)	468	NM_010466	15426	Mm.6167	NM_010466	ENSMUSG00000001657	Hoxc8	D130011F21Rik|Hox-3.1	homeobox C8	protein-coding
mm_133351.1	chr16	84557150	84557168	+	1	NA	Intergenic	Intergenic	-122630	NR_040537	78023	Mm.243853	NR_040537		4930529L06Rik	-	RIKEN cDNA 4930529L06 gene	ncRNA
mm_43798.1	chr5	142818032	142818093	+	1	NA	promoter-TSS (NM_001122730)	promoter-TSS (NM_001122730)	-675	NM_001122730	231861	Mm.354649	NM_178242	ENSMUSG00000039477	Tnrc18	BC025631|EG381742|Zfp469	trinucleotide repeat containing 18	protein-coding
mm_11009.1	chr2	26581025	26581039	+	1	NA	promoter-TSS (NM_178444)	promoter-TSS (NM_178444)	-24	NM_178444	353156	Mm.268933	NM_178444	ENSMUSG00000026921	Egfl7	VE-statin|Zneu1	EGF-like domain 7	protein-coding
mm_23454.1	chr3	60472199	60472206	+	1	NA	promoter-TSS (NM_001253713)	promoter-TSS (NM_001253713)	-628	NM_001253713	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_118979.1	chr14	28152337	28152338	+	1	NA	intron (NM_177814, intron 13 of 15)	intron (NM_177814, intron 13 of 15)	-353136	NM_009524	22418	Mm.287544	NM_009524	ENSMUSG00000021994	Wnt5a	8030457G12Rik|Wnt-5a	wingless-type MMTV integration site family, member 5A	protein-coding
mm_80833.1	chr9	97103914	97103925	+	1	NA	intron (NM_138756, intron 1 of 6)	MTD|LTR|ERVL-MaLR	7122	NM_138756	192287	Mm.228067	NM_138756	ENSMUSG00000032449	Slc25a36	C330005L02Rik	solute carrier family 25, member 36	protein-coding
mm_23432.1	chr3	59091879	59091883	+	1	NA	intron (NM_177855, intron 13 of 43)	intron (NM_177855, intron 13 of 43)	9940	NM_173398	229323	Mm.123648	NM_173398	ENSMUSG00000050075	Gpr171	A630006E05|F730001G15Rik|H963	G protein-coupled receptor 171	protein-coding
mm_39495.1	chr5	21054983	21054996	+	1	NA	intron (NM_011203, intron 1 of 17)	intron (NM_011203, intron 1 of 17)	808	NM_011203	19248	Mm.319117	NM_011203	ENSMUSG00000028771	Ptpn12	P19-PTP|PTP-P19|PTP-PEST|PTPG1	protein tyrosine phosphatase, non-receptor type 12	protein-coding
mm_77054.1	chr8	109578784	109578787	-	1	NA	intron (NM_001329965, intron 1 of 4)	Charlie12|DNA|hAT-Charlie	387	NM_017370	15439	Mm.26730	NM_017370	ENSMUSG00000031722	Hp	HP-1|preHP2	haptoglobin	protein-coding
mm_57696.1	chr6	128522120	128522142	-	1	NA	exon (NM_007376, exon 6 of 36)	exon (NM_007376, exon 6 of 36)	4589	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_111026.1	chr12	79132169	79132183	-	1	NA	intron (NM_009705, intron 2 of 7)	intron (NM_009705, intron 2 of 7)	1388	NM_009705	11847	Mm.3506	NM_009705	ENSMUSG00000021125	Arg2	AII|AU022422	arginase type II	protein-coding
mm_34735.1	chr4	152190505	152190530	+	1	NA	intron (NM_001146057, intron 1 of 8)	intron (NM_001146057, intron 1 of 8)	4383	NM_001146057	70025	Mm.296191	NM_133348	ENSMUSG00000028937	Acot7	2410041A17Rik|Ach1|Act|Bach|CTE-IIa|Cte-II|Lach1	acyl-CoA thioesterase 7	protein-coding
mm_54246.1	chr6	28259923	28259936	-	1	NA	intron (NM_001081678, intron 2 of 5)	intron (NM_001081678, intron 2 of 5)	1672	NM_001081678	627049	Mm.84441	NM_001081678	ENSMUSG00000039841	Zfp800	AA407452|Znf800	zinc finger protein 800	protein-coding
mm_173050.1	chrX	121452632	121452639	+	1	NA	Intergenic	L1Md_T|LINE|L1	944750	NM_138742	54561	Mm.490573	NM_138742	ENSMUSG00000055733	Nap1l3	MB20	nucleosome assembly protein 1-like 3	protein-coding
mm_162258.1	chrX	169828134	169828134	+	1	NA	promoter-TSS (NM_001290504)	promoter-TSS (NM_001290504)	-25	NM_001290504	17318	Mm.34441	NM_010797	ENSMUSG00000035299	Mid1	61B3-R|DXHXS1141|Fxy|Trim18	midline 1	protein-coding
mm_21161.1	chr2	154603636	154603653	-	1	NA	promoter-TSS (NM_021534)	promoter-TSS (NM_021534)	29	NM_021534	59038	Mm.24673	NM_021534	ENSMUSG00000000876	Pxmp4	3010018P03Rik|Pmp24	peroxisomal membrane protein 4	protein-coding
mm_49518.1	chr6	29894727	29894733	+	1	NA	intron (NM_001347084, intron 11 of 17)	intron (NM_001347084, intron 11 of 17)	-22283	NM_001037740	320609	Mm.56097	NM_177204	ENSMUSG00000039629	Strip2	D330017J20Rik|Fam40b	striatin interacting protein 2	protein-coding
mm_59050.1	chr7	19382006	19382052	+	1	NA	promoter-TSS (NM_007949)	promoter-TSS (NM_007949)	-10	NM_007949	13871	Mm.36524	NM_007949	ENSMUSG00000030400	Ercc2	AA407812|AU020867|AW240756|CXPD|Ercc-2|Mhdarco15|RCO015|XPD	excision repair cross-complementing rodent repair deficiency, complementation group 2	protein-coding
mm_95396.1	chr11	49663604	49663621	+	1	NA	promoter-TSS (NM_054037)	promoter-TSS (NM_054037)	17	NM_170727	68662	Mm.22802	NM_054037	ENSMUSG00000064057	Scgb3a1	HIN-1|LuLeu2|Pnsp2|UGRP2|Utgrp2	secretoglobin, family 3A, member 1	protein-coding
mm_68537.1	chr7	113388564	113388578	-	1	NA	promoter-TSS (NM_020623)	promoter-TSS (NM_020623)	2	NM_020623	19226	Mm.284168	NM_020623	ENSMUSG00000059077	Pth	Pthp	parathyroid hormone	protein-coding
mm_74088.1	chr8	122564574	122564613	+	1	NA	Intergenic	MTE2a|LTR|ERVL-MaLR	-3422	NM_026014	67177	Mm.21873	NM_026014	ENSMUSG00000006585	Cdt1	2610318F11Rik|AW545653|C76791|Ris2	chromatin licensing and DNA replication factor 1	protein-coding
mm_106674.1	chr11	121741579	121741602	-	1	NA	Intergenic	Intergenic	39163	NM_144797	210029	Mm.153566	NM_144797	ENSMUSG00000039208	Metrnl	9430048M07Rik|BC019776	meteorin, glial cell differentiation regulator-like	protein-coding
mm_97402.1	chr11	77840269	77840298	+	1	NA	intron (NM_001291214, intron 19 of 38)	intron (NM_001291214, intron 19 of 38)	38985	NM_001291215	360013	Mm.341248	NM_011586	ENSMUSG00000000631	Myo18a	MAJN|MyoPDZ|MysPDZ|SP-R210	myosin XVIIIA	protein-coding
mm_46353.1	chr5	102913180	102913221	-	1	NA	exon (NM_001081567, exon 14 of 14)	exon (NM_001081567, exon 14 of 14)	68193	NM_001346585	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding
mm_81086.1	chr9	106281351	106281410	+	1	NA	5' UTR (NM_027354, exon 1 of 11)	5' UTR (NM_027354, exon 1 of 11)	319	NM_027354	70235	Mm.23054	NM_027354	ENSMUSG00000023345	Poc1a	2510040D07Rik|Wdr51a|cha	POC1 centriolar protein A	protein-coding
mm_76730.1	chr8	95020991	95021000	-	1	NA	exon (NM_173036, exon 2 of 12)	exon (NM_173036, exon 2 of 12)	3303	NM_173036	54672	Mm.27995	NM_173036	ENSMUSG00000060470	Adgrg3	A030001G24Rik|AW214383|Gpr97|Pb1|Pb99	adhesion G protein-coupled receptor G3	protein-coding
mm_3871.1	chr1	160989591	160989627	+	1	NA	exon (NM_080844, exon 3 of 8)	exon (NM_080844, exon 3 of 8)	11003	NM_080844	11905	Mm.260770	NM_080844	ENSMUSG00000026715	Serpinc1	AI114908|ATIII|At-3|At3	serine (or cysteine) peptidase inhibitor, clade C (antithrombin), member 1	protein-coding
mm_80849.1	chr9	98296904	98296912	+	1	NA	5' UTR (NM_144533, exon 1 of 5)	5' UTR (NM_144533, exon 1 of 5)	325	NM_144533	74080	Mm.294082	NM_144533	ENSMUSG00000032456	Nmnat3	4933408N02Rik|PNAT3	nicotinamide nucleotide adenylyltransferase 3	protein-coding
mm_58352.1	chr6	147531276	147531285	-	1	NA	intron (NM_025911, intron 3 of 12)	intron (NM_025911, intron 3 of 12)	55409	NM_025911	67015	Mm.209774	NM_025911	ENSMUSG00000030301	Ccdc91	1700086G08Rik|1810060J02Rik|AU045683|AW555238|p56	coiled-coil domain containing 91	protein-coding
mm_147568.1	chr18	54992526	54992540	-	1	NA	Intergenic	Intergenic	-2353	NM_175751	269023	Mm.192984	NM_175751	ENSMUSG00000052713	Zfp608	4932417D18Rik|D430007A19Rik|Znf608	zinc finger protein 608	protein-coding
mm_162391.1	chr1	75885427	75885432	+	1	NA	Intergenic	Intergenic	339163	NM_009208	20536	Mm.5053	NM_009208	ENSMUSG00000006576	Slc4a3	A930038D23Rik|Ae3	solute carrier family 4 (anion exchanger), member 3	protein-coding
mm_129071.1	chr15	75664184	75664190	-	1	NA	intron (NM_028404, intron 10 of 13)	intron (NM_028404, intron 10 of 13)	14603	NM_028404	72960	Mm.182401	NM_028404	ENSMUSG00000000934	Top1mt	2900052H09Rik	DNA topoisomerase 1, mitochondrial	protein-coding
mm_16402.1	chr2	180024904	180024914	+	1	NA	promoter-TSS (NM_177727)	promoter-TSS (NM_177727)	-78	NM_177727	241846	Mm.21577	NM_177727	ENSMUSG00000039108	Lsm14b	9430078B04|BC040823	LSM family member 14B	protein-coding
mm_75619.1	chr8	64609104	64609113	-	1	NA	exon (NM_013494, exon 5 of 9)	exon (NM_013494, exon 5 of 9)	84001	NM_013494	12876	Mm.31395	NM_013494	ENSMUSG00000037852	Cpe	CPH|Cph-1|Cph1|R74677|fat	carboxypeptidase E	protein-coding
mm_159818.1	chr5	122047858	122047858	-	1	NA	promoter-TSS (NM_007804)	promoter-TSS (NM_007804)	-33	NM_007804	13048	Mm.156172	NM_007804	ENSMUSG00000042589	Cux2	1700051K22Rik|Cutl2|Cux-2|ENSMUSG00000072641	cut-like homeobox 2	protein-coding
mm_122157.1	chr14	31374304	31374340	-	1	NA	3' UTR (NM_001347585, exon 8 of 8)	3' UTR (NM_001347585, exon 8 of 8)	37598	NM_009796	12339	Mm.201535	NM_009796	ENSMUSG00000021893	Capn7	AU022319|PalBH	calpain 7	protein-coding
mm_85342.1	chr9	103202057	103202110	-	1	NA	promoter-TSS (NM_009275)	promoter-TSS (NM_009275)	-18	NM_009275	20818	Mm.273053	NM_009275	ENSMUSG00000032553	Srprb	AA409543	signal recognition particle receptor, B subunit	protein-coding
mm_69809.1	chr7	141231494	141231499	-	1	NA	intron (NM_001081118, intron 2 of 17)	intron (NM_001081118, intron 2 of 17)	2708	NM_001081118	101471	Mm.248656	NM_207211	ENSMUSG00000038611	Phrf1	AA673488	PHD and ring finger domains 1	protein-coding
mm_104352.1	chr11	94297822	94297836	-	1	NA	exon (NM_026313, exon 7 of 11)	exon (NM_026313, exon 7 of 11)	24082	NM_026313	67684	Mm.30927	NM_026313	ENSMUSG00000020863	Luc7l3	3300001P08Rik|Luc7a	LUC7-like 3 (S. cerevisiae)	protein-coding
mm_161052.1	chr12	55230441	55230441	+	1	NA	promoter-TSS (NM_001100110)	promoter-TSS (NM_001100110)	-37	NM_001100110	100101806	Mm.471968	NM_001100110	ENSMUSG00000079108	Srp54c	E330029E12Rik	signal recognition particle 54C	protein-coding
mm_29353.1	chr3	108445184	108445211	-	1	NA	promoter-TSS (NM_011319)	promoter-TSS (NM_011319)	62	NM_011319	20226	Mm.28688	NM_011319	ENSMUSG00000068739	Sars	Sars1|Strs|serRS	seryl-aminoacyl-tRNA synthetase	protein-coding
mm_157164.1	chrX	9466728	9466731	-	1	NA	intron (NM_007807, intron 2 of 12)	intron (NM_007807, intron 2 of 12)	2595	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_31657.1	chr4	59880025	59880029	+	1	NA	intron (NM_172468, intron 4 of 8)	RLTR18|LTR|ERVK	35029	NM_021053	30936	Mm.284433	NM_021053	ENSMUSG00000028386	Slc46a2	5430429N04Rik|Ly110|TSO-1C12|Tscot	solute carrier family 46, member 2	protein-coding
mm_84854.1	chr9	78481725	78481751	-	1	NA	promoter-TSS (NM_010106)	promoter-TSS (NM_010106)	-14	NM_010106	13627	Mm.138471	NM_010106	ENSMUSG00000037742	Eef1a1	-	eukaryotic translation elongation factor 1 alpha 1	protein-coding
mm_125589.1	chr15	59620266	59620279	+	1	NA	Intergenic	Intergenic	-28382	NM_144549	211770	Mm.40298	NM_144549	ENSMUSG00000032501	Trib1	A530090O15Rik|TRB-1|Trb1	tribbles pseudokinase 1	protein-coding
mm_10518.1	chr2	16356745	16356795	+	1	NA	5' UTR (NM_026162, exon 1 of 14)	5' UTR (NM_026162, exon 1 of 14)	466	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding
mm_29857.1	chr3	130041367	130041379	-	1	NA	exon (NM_207209, exon 2 of 24)	exon (NM_207209, exon 2 of 24)	19534	NM_207209	99683	Mm.192303	NM_207209	ENSMUSG00000001052	Sec24b	AI605202|SEC24	Sec24 related gene family, member B (S. cerevisiae)	protein-coding
mm_115160.1	chr13	107063738	107063755	+	1	NA	Intergenic	Intergenic	41176	NR_015471	100040322	Mm.133867	NR_015471		3830408C21Rik	-	RIKEN cDNA 3830408C21 gene	ncRNA
mm_100422.1	chr11	119441584	119441599	+	1	NA	Intergenic	Intergenic	-49756	NM_001164636	338371	Mm.271946	NM_177394	ENSMUSG00000039850	Endov	A730011L01Rik	endonuclease V	protein-coding
mm_123880.1	chr14	72709433	72709471	-	1	NA	intron (NM_207636, intron 1 of 25)	CpG	551	NM_207636	319448	Mm.205421	NM_207636	ENSMUSG00000033487	Fndc3a	1700094E19Rik|D14Ertd453e|F730017H24Rik|Fndc3|sys	fibronectin type III domain containing 3A	protein-coding
mm_158860.1	chrY	943008	943021	+	1	NA	exon (NM_011419, exon 26 of 26)	exon (NM_011419, exon 26 of 26)	45226	NM_011419	20592	Mm.262676	NM_011419	ENSMUSG00000056673	Kdm5d	HY|Jarid1d|Smcy	lysine (K)-specific demethylase 5D	protein-coding
mm_61513.1	chr7	78888357	78888359	+	1	NA	promoter-TSS (NR_029826)	promoter-TSS (NR_029826)	81	NR_029826	723884		NR_029826	ENSMUSG00000065609	Mir7-2	Mir7a2|Mirn7-2|mir-7a-2|mir-7a2|mmu-mir-7-2|mmu-mir-7a2	microRNA 7-2	ncRNA
mm_45531.1	chr5	72736599	72736610	-	1	NA	promoter-TSS (NM_013698)	promoter-TSS (NM_013698)	-2	NM_013698	22165	Mm.3264	NM_013698	ENSMUSG00000054892	Txk	A130089B16Rik|Btkl|PTK-RL-18|PTK4|Rlk	TXK tyrosine kinase	protein-coding
mm_91910.1	chr10	60292566	60292589	-	1	NA	exon (NM_011179, exon 3 of 15)	exon (NM_011179, exon 3 of 15)	8116	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_70885.1	chr8	25518631	25518643	+	1	NA	promoter-TSS (NM_010206)	promoter-TSS (NM_010206)	-122	NM_001079909	14182	Mm.265716	NM_010206	ENSMUSG00000031565	Fgfr1	AW208770|Eask|FGFR-I|FLG|Fgfr-1|Flt-2|Hspy|MFR|bFGF-R-1|c-fgr	fibroblast growth factor receptor 1	protein-coding
mm_29778.1	chr3	127408938	127408981	-	1	NA	promoter-TSS (NM_001327939)	promoter-TSS (NM_001327939)	99	NM_001327939	109676	Mm.220242	NM_178655	ENSMUSG00000032826	Ank2	100043364|AI835472|AW491075|Ank-2|Gm4392	ankyrin 2, brain	protein-coding
mm_101589.1	chr11	34681831	34681883	-	1	NA	intron (NM_033374, intron 22 of 51)	RLTR44-int|LTR|ERVK	102048	NM_033374	94176	Mm.380679	NM_033374	ENSMUSG00000020143	Dock2	AI662014|AW122239|CED-5|Hch|MBC	dedicator of cyto-kinesis 2	protein-coding
mm_170249.1	chr17	94887165	94887175	+	1	NA	Intergenic	(TTAGGG)n|Simple_repeat|Simple_repeat	22252	NM_001024731	100044193		NM_001024731	ENSMUSG00000095193	Gm20939	-	predicted gene, 20939	protein-coding
mm_78616.1	chr9	37555615	37555628	+	1	NA	Intergenic	Intergenic	-2876	NM_022029	64011	Mm.335065	NM_022029	ENSMUSG00000053310	Nrgn	0710001B06Rik|AI838505|NG|NG/RC3|Pss1|R75334|RC3	neurogranin	protein-coding
mm_95716.1	chr11	54516800	54516802	+	1	NA	3' UTR (NM_173753, exon 18 of 18)	3' UTR (NM_173753, exon 18 of 18)	-6044	NM_001252494	192786	Mm.254404	NM_175258	ENSMUSG00000037533	Rapgef6	A530068K01|AI844632|BB085664|C030018K18Rik|PDZ-GEF2|Pdzgef2|RA-GEF-2|Ragef2|mKIAA4052	Rap guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_72645.1	chr8	84703392	84703415	+	1	NA	intron (NM_008535, intron 3 of 3)	PB1D7|SINE|Alu	1946	NM_008535	17095	Mm.4925	NM_008535	ENSMUSG00000034041	Lyl1	Lyl-1|bHLHa18	lymphoblastomic leukemia 1	protein-coding
mm_154191.1	chr19	58822537	58822558	-	1	NA	intron (NM_001327998, intron 5 of 12)	intron (NM_001327998, intron 5 of 12)	-28133	NM_026208	67507	Mm.27027	NM_026208	ENSMUSG00000026931	1700019N19Rik	-	RIKEN cDNA 1700019N19 gene	protein-coding
mm_21911.1	chr2	166581970	166582019	-	1	NA	exon (NM_177782, exon 27 of 40)	exon (NM_177782, exon 27 of 40)	-90724	NR_105783	102465188		NR_105783	ENSMUSG00000098675	Mir6364	Gm27327|mmu-mir-6364	microRNA 6364	ncRNA
mm_871.1	chr1	52153836	52153850	+	1	NA	intron (NM_001205313, intron 21 of 24)	intron (NM_001205313, intron 21 of 24)	34221	NM_001205313	20846	Mm.277406	NM_009283	ENSMUSG00000026104	Stat1	2010005J02Rik|AA408197	signal transducer and activator of transcription 1	protein-coding
mm_23864.1	chr3	83012933	83012943	+	1	NA	exon (NM_133862, exon 8 of 10)	exon (NM_133862, exon 8 of 10)	5214	NM_001317105	99571	Mm.16422	NM_133862	ENSMUSG00000033860	Fgg	3010002H13Rik|AI256424	fibrinogen gamma chain	protein-coding
mm_42237.1	chr5	113736004	113736030	+	1	NA	5' UTR (NM_001010825, exon 1 of 3)	5' UTR (NM_001010825, exon 1 of 3)	235	NM_001010825	231630	Mm.21926	NM_001010825	ENSMUSG00000053334	Ficd	D5Ertd40e|Hype	FIC domain containing	protein-coding
mm_89911.1	chr10	111174802	111174820	+	1	NA	intron (NM_175489, intron 1 of 23)	intron (NM_175489, intron 1 of 23)	10009	NM_175489	237542	Mm.220204	NM_175489	ENSMUSG00000020189	Osbpl8	AA536976|AA536995|C730029P18Rik|D330025H14Rik|ORP-8	oxysterol binding protein-like 8	protein-coding
mm_5495.1	chr1	36943801	36943809	-	1	NA	Intergenic	Intergenic	-4278	NM_018872	56030	Mm.186943	NM_018872	ENSMUSG00000026116	Tmem131	2610524E03Rik|CC28|D1Bwg0491e|Neg|RW1|YR-23|mKIAA0257	transmembrane protein 131	protein-coding
mm_7311.1	chr1	98057702	98057712	-	1	NA	intron (NM_013626, intron 1 of 25)	intron (NM_013626, intron 1 of 25)	-9914	NR_037993	78603	Mm.442597	NR_037993	ENSMUSG00000089706	B230216N24Rik	-	RIKEN cDNA B230216N24 gene	ncRNA
mm_52177.1	chr6	99264457	99264488	+	1	NA	intron (NM_001347345, intron 3 of 19)	intron (NM_001347345, intron 3 of 19)	2043	NM_001197321	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_44407.1	chr5	17848922	17848942	-	1	NA	intron (NM_001159558, intron 1 of 15)	intron (NM_001159558, intron 1 of 15)	860	NM_001159557	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_71483.1	chr8	46739813	46739824	+	1	NA	promoter-TSS (NM_008391)	promoter-TSS (NM_008391)	73	NM_008391	16363	Mm.1149	NM_008391	ENSMUSG00000031627	Irf2	9830146E22Rik|AI646973|Irf-2	interferon regulatory factor 2	protein-coding
mm_53036.1	chr6	124570305	124570315	+	1	NA	promoter-TSS (NM_001113356)	promoter-TSS (NM_001113356)	-120	NM_001113356	667277	Mm.481484	NM_001113356	ENSMUSG00000098470	C1rb	Gm8551|mC1rB	complement component 1, r subcomponent B	protein-coding
mm_157926.1	chrX	79635576	79635587	-	1	NA	promoter-TSS (NM_001113734)	promoter-TSS (NM_001113734)	1	NM_001113734	71967	Mm.379207	NM_028025	ENSMUSG00000046942	Mageb16	2410003J06Rik	melanoma antigen family B, 16	protein-coding
mm_144936.1	chr18	37736898	37736958	+	1	NA	promoter-TSS (NM_033592)	promoter-TSS (NM_033592)	-8	NM_033592	93717	Mm.247203	NM_033592	ENSMUSG00000102440	Pcdhga9	-	protocadherin gamma subfamily A, 9	protein-coding
mm_141843.1	chr17	34739989	34740005	-	1	NA	exon (NM_009780, exon 12 of 41)	exon (NM_009780, exon 12 of 41)	3900	NM_009780	12268	Mm.477109	NM_009780	ENSMUSG00000073418	C4b	C4|Ss	complement component 4B (Chido blood group)	protein-coding
mm_23960.1	chr3	84952204	84952230	+	1	NA	promoter-TSS (NM_080428)	promoter-TSS (NM_080428)	6	NM_080428	50754	Mm.196475	NM_080428	ENSMUSG00000028086	Fbxw7	1110001A17Rik|AGO|Cdc4|Fbw7|Fbwd6|Fbx30|Fbxo30|Fbxw6|SEL-10	F-box and WD-40 domain protein 7	protein-coding
mm_108878.1	chr12	99884499	99884531	+	1	NA	promoter-TSS (NM_028354)	promoter-TSS (NM_028354)	0	NM_028354	104884	Mm.312323	NM_028354	ENSMUSG00000021177	Tdp1	2810481F14Rik|4921509N21Rik|AI838772|AW493413|E430034L06Rik|MLZ-501|SCAN1	tyrosyl-DNA phosphodiesterase 1	protein-coding
mm_163237.1	chr11	104231529	104231539	+	1	NA	promoter-TSS (NM_010838)	promoter-TSS (NM_010838)	98	NM_001285454	17762	Mm.1287	NM_010838	ENSMUSG00000018411	Mapt	AI413597|AW045860|Mtapt|Tau	microtubule-associated protein tau	protein-coding
mm_73620.1	chr8	110266951	110266955	+	1	NA	promoter-TSS (NM_172916)	promoter-TSS (NM_172916)	-24	NM_172916	244653	Mm.444803	NM_172916	ENSMUSG00000059854	Hydin	1700034M11Rik|4930545D19Rik|4932703P14|A830061H17|AC069308.21gm4|hy-3|hy3|hyrh	HYDIN, axonemal central pair apparatus protein	protein-coding
mm_127612.1	chr15	102460077	102460108	+	1	NA	intron (NM_025385, intron 2 of 4)	intron (NM_025385, intron 2 of 4)	922	NM_025385	66151	Mm.393955	NM_025385	ENSMUSG00000023048	Prr13	1110020C13Rik|2010324E22Rik	proline rich 13	protein-coding
mm_45082.1	chr5	43981801	43981809	-	1	NA	promoter-TSS (NM_008009)	promoter-TSS (NM_008009)	-6	NM_001271616	14181	Mm.46053	NM_008009	ENSMUSG00000048373	Fgfbp1	FGF-BP|FGF-BP1|FGFBP-1	fibroblast growth factor binding protein 1	protein-coding
mm_152661.1	chr19	12796555	12796568	-	1	NA	promoter-TSS (NM_053009)	promoter-TSS (NM_053009)	-438	NM_053009	109910	Mm.290924	NM_053009	ENSMUSG00000024695	Zfp91	9130014I08Rik|A530054C17Rik|AL024263|AW545902|Pzf|Zfp-91	zinc finger protein 91	protein-coding
mm_66111.1	chr7	31041813	31041823	-	1	NA	promoter-TSS (NM_001111073)	promoter-TSS (NM_001111073)	21	NM_001111073	18301	Mm.1870	NM_008761	ENSMUSG00000009687	Fxyd5	EF-8|Oit2|RIC	FXYD domain-containing ion transport regulator 5	protein-coding
mm_149848.1	chr19	25052555	25052611	+	1	NA	intron (NM_028785, intron 2 of 47)	intron (NM_028785, intron 2 of 47)	53054	NM_028785	76088	Mm.102485	NM_028785	ENSMUSG00000052085	Dock8	1200017A24Rik|5830472H07Rik|A130095G14Rik|AI461977	dedicator of cytokinesis 8	protein-coding
mm_171746.1	chr4	98726817	98726819	+	1	NA	promoter-TSS (NM_001081202)	promoter-TSS (NM_001081202)	64	NM_001081202	381591	Mm.34340	NM_001081202	ENSMUSG00000087166	L1td1	AA546746|AB211064|D76865|ECAT11	LINE-1 type transposase domain containing 1	protein-coding
mm_103408.1	chr11	75449900	75449910	-	1	NA	intron (NM_138950, intron 1 of 9)	intron (NM_138950, intron 1 of 9)	4812	NM_138950	192652	Mm.340378	NM_138950	ENSMUSG00000045374	Wdr81	BC054822|Gm883|mFLJ00182|nur5	WD repeat domain 81	protein-coding
mm_45233.1	chr5	53594301	53594311	-	1	NA	intron (NM_001080927, intron 1 of 10)	PB1D10|SINE|Alu	3820	NM_001080927	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_72400.1	chr8	81769359	81769369	+	1	NA	intron (NM_001024617, intron 6 of 24)	intron (NM_001024617, intron 6 of 24)	426802	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_129875.1	chr15	83432795	83432813	-	1	NA	promoter-TSS (NM_001159510)	promoter-TSS (NM_001159510)	46	NM_011862	23970	Mm.23978	NM_011862	ENSMUSG00000016664	Pacsin2	AI197433	protein kinase C and casein kinase substrate in neurons 2	protein-coding
mm_142472.1	chr17	45659313	45659335	-	1	NA	promoter-TSS (NM_001013767)	promoter-TSS (NM_001013767)	-15	NM_001013767	268958	Mm.426026	NM_001013767	ENSMUSG00000058626	Capn11	-	calpain 11	protein-coding
mm_130972.1	chr15	103333356	103333390	-	1	NA	intron (NM_013866, intron 1 of 7)	intron (NM_013866, intron 1 of 7)	6713	NM_013866	29813	Mm.14099	NM_013866	ENSMUSG00000000552	Zfp385a	Hzf|Zfp385|Znf385a	zinc finger protein 385A	protein-coding
mm_7270.1	chr1	96872108	96872147	-	1	NA	promoter-TSS (NM_172658)	promoter-TSS (NM_172658)	44	NM_172658	227394	Mm.11662	NM_172658	ENSMUSG00000040693	Slco4c1	9530051F04|C330017E21Rik|OATP-H|OATP-M1|OATP4C1|OATPX|PRO2176|SLC21A20|oatp-R	solute carrier organic anion transporter family, member 4C1	protein-coding
mm_67042.1	chr7	67255196	67255234	-	1	NA	intron (NM_001291191, intron 7 of 10)	intron (NM_001291191, intron 7 of 10)	32599	NM_001191051	75099	Mm.121691	NM_175215	ENSMUSG00000043831	Lysmd4	4930506D23Rik	LysM, putative peptidoglycan-binding, domain containing 4	protein-coding
mm_157189.1	chrX	12053626	12053629	-	1	NA	intron (NM_001168321, intron 5 of 13)	AT_rich|Low_complexity|Low_complexity	26926	NM_175045	71458	Mm.196328	NM_029510	ENSMUSG00000040363	Bcor	2900008C10Rik|5830466J11Rik|8430401K06Rik|BcorR|D930024N20Rik|mKIAA1575	BCL6 interacting corepressor	protein-coding
mm_157656.1	chrX	57338514	57338583	-	1	NA	exon (NM_152801, exon 1 of 22)	exon (NM_152801, exon 1 of 22)	181	NM_152801	73341	Mm.261443	NM_152801	ENSMUSG00000031133	Arhgef6	1600028C08Rik|1700038J06Rik|4930592P22Rik|alpha-PIX	Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_99386.1	chr11	102097239	102097260	+	1	NA	Intergenic	Intergenic	4051	NM_008918	19064	Mm.1269	NM_008918	ENSMUSG00000017316	Ppy	AV061413|IGSPP|PP	pancreatic polypeptide	protein-coding
mm_15140.1	chr2	153974798	153974808	+	1	NA	promoter-TSS (NM_001080811)	promoter-TSS (NM_001080811)	-142	NM_001080811	545477	Mm.379973	NM_001080811	ENSMUSG00000078998	Bpifa6	EG545477|Gm5840|Splunc6	BPI fold containing family A, member 6	protein-coding
mm_111858.1	chr12	107956652	107956654	-	1	NA	intron (NM_001286343, intron 1 of 1)	ID_B1|SINE|B4	46761	NM_001079883	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_74413.1	chr8	3624971	3624983	-	1	NA	promoter-TSS (NM_001129804)	promoter-TSS (NM_001129804)	72	NM_001129804	18545	Mm.440882	NM_008790	ENSMUSG00000004630	Pcp2	L7|Pcp-2	Purkinje cell protein 2 (L7)	protein-coding
mm_31089.1	chr4	41634852	41634899	+	1	NA	intron (NM_175138, intron 18 of 19)	intron (NM_175138, intron 18 of 19)	5427	NM_027147	69638	Mm.372459	NM_027147	ENSMUSG00000028445	Enho	1110065P19Rik|2310040A07Rik	energy homeostasis associated	protein-coding
mm_92799.1	chr10	81358351	81358368	-	1	NA	intron (NM_028657, intron 1 of 9)	intron (NM_028657, intron 1 of 9)	789	NM_028657	73822	Mm.182281	NM_028657	ENSMUSG00000034854	Mfsd12	C19orf28|F630110N24Rik|Wdt1	major facilitator superfamily domain containing 12	protein-coding
mm_26204.1	chr3	138548984	138549015	+	1	NA	intron (NM_001313980, intron 4 of 7)	(T)n|Simple_repeat|Simple_repeat	21731	NM_001313980	13684	Mm.3941	NM_007917	ENSMUSG00000028156	Eif4e	EG668879|Eif4e-ps|If4e|eIF-4E	eukaryotic translation initiation factor 4E	protein-coding
mm_39091.1	chr4	154667690	154667706	-	1	NA	5' UTR (NM_028513, exon 1 of 1)	5' UTR (NM_028513, exon 1 of 1)	169	NM_028513	73353	Mm.30958	NM_028513	ENSMUSG00000051276	Actrt2	1700052K15Rik|Arp-T2|Arpm2	actin-related protein T2	protein-coding
mm_45340.1	chr5	65763963	65763976	-	1	NA	intron (NM_001024917, intron 1 of 19)	CpG	448	NM_001024917	333789	Mm.332398	NM_001024917	ENSMUSG00000037795	N4bp2	B3bp|E430014I16|Gm1791|Gm868	NEDD4 binding protein 2	protein-coding
mm_70908.1	chr8	25673980	25673991	+	1	NA	3' UTR (NM_001308482, exon 8 of 8)	3' UTR (NM_001308482, exon 8 of 8)	33408	NM_001081269	234135	Mm.217337	NM_001001735	ENSMUSG00000054823	Whsc1l1	6720429E03|A530023P05|AI528490|NSD3|WHISTLE	Wolf-Hirschhorn syndrome candidate 1-like 1 (human)	protein-coding
mm_147262.1	chr18	38867008	38867016	-	1	NA	intron (NM_010197, intron 1 of 3)	L2b|LINE|L2	-25444	NM_001033789	545253	Mm.244585	NM_001033789	ENSMUSG00000036452	Gm5820	EG545253	predicted gene 5820	protein-coding
mm_107653.1	chr12	52699298	52699411	+	1	NA	promoter-TSS (NM_198111)	promoter-TSS (NM_198111)	-29	NM_198111	238161	Mm.310822	NM_198111	ENSMUSG00000061603	Akap6	AI482140|Akapalpha|Akapbeta|PRKA	A kinase (PRKA) anchor protein 6	protein-coding
mm_8198.1	chr1	138121488	138121499	-	1	NA	intron (NM_001111316, intron 3 of 31)	intron (NM_001111316, intron 3 of 31)	53633	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_67902.1	chr7	99691624	99691634	-	1	NA	intron (NM_001252530, intron 2 of 13)	intron (NM_001252530, intron 2 of 13)	4180	NM_001252531	101488	Mm.11249	NM_175316	ENSMUSG00000030737	Slco2b1	AI060904|AI852653|OATP-B|Slc21a9	solute carrier organic anion transporter family, member 2b1	protein-coding
mm_170455.1	chr18	87044976	87044976	-	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	332911	NM_172633	12405	Mm.70775	NM_172633	ENSMUSG00000024647	Cbln2	6330593N19Rik|A730004O05	cerebellin 2 precursor protein	protein-coding
mm_134472.1	chr16	18586960	18586970	-	1	NA	promoter-TSS (NM_011532)	promoter-TSS (NM_011532)	4	NM_011532	21380	Mm.295194	NM_011532	ENSMUSG00000009097	Tbx1	-	T-box 1	protein-coding
mm_145402.1	chr18	57373879	57373887	+	1	NA	intron (NM_028447, intron 5 of 8)	RLTR16B_MM|LTR|ERVK	19150	NM_028447	73137	Mm.29889	NM_028447	ENSMUSG00000024594	Prrc1	1190002C06Rik|2310058D16Rik|3110038B19Rik|9430085A19Rik	proline-rich coiled-coil 1	protein-coding
mm_98956.1	chr11	98493109	98493111	+	1	NA	intron (NM_011771, intron 3 of 7)	intron (NM_011771, intron 3 of 7)	46276	NM_010346	14786	Mm.276702	NM_010346	ENSMUSG00000019312	Grb7	mKIAA4028	growth factor receptor bound protein 7	protein-coding
mm_76095.1	chr8	79864100	79864118	-	1	NA	Intergenic	L1_Mur2|LINE|L1	152289	NM_026904	68999	Mm.257445	NM_026904	ENSMUSG00000036977	Anapc10	1500026N15Rik|A830003M23Rik|APC10	anaphase promoting complex subunit 10	protein-coding
mm_53444.1	chr6	134414424	134414435	+	1	NA	intron (NM_025778, intron 2 of 6)	intron (NM_025778, intron 2 of 6)	18100	NM_025778	66813	Mm.474472	NM_025778	ENSMUSG00000030200	Bcl2l14	4930452K23Rik|4933405K19Rik|9030625M01Rik|AI429211|Bclg	BCL2-like 14 (apoptosis facilitator)	protein-coding
mm_3081.1	chr1	134405703	134405724	+	1	NA	promoter-TSS (NM_028057)	promoter-TSS (NM_028057)	-277	NM_028057	72017	Mm.280230	NM_028057	ENSMUSG00000026456	Cyb5r1	1500005G05Rik|B5R.1|C80155|Nqo3a2	cytochrome b5 reductase 1	protein-coding
mm_52133.1	chr6	97945176	97945190	+	1	NA	intron (NM_001113198, intron 2 of 9)	intron (NM_001113198, intron 2 of 9)	15366	NM_001178049	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_154487.1	chrM	5040	5069	-	1	NA	NA	Intergenic	NA	NA								
mm_161526.1	chr15	100936294	100936294	+	1	NA	promoter-TSS (NM_011323)	promoter-TSS (NM_011323)	23	NM_011323	20273	Mm.385012	NM_011323	ENSMUSG00000023033	Scn8a	AI853486|C630029C19Rik|NaCh6|Nav1.6|dmu|med|mnd-2|mnd2|nmf2|nmf335|nmf58|nur14|seal	sodium channel, voltage-gated, type VIII, alpha	protein-coding
mm_160408.1	chr8	71922862	71922862	+	1	NA	promoter-TSS (NM_133358)	promoter-TSS (NM_133358)	37	NM_133358	170938	Mm.480419	NM_133358	ENSMUSG00000066880	Zfp617	Zfps11-6	zinc finger protein 617	protein-coding
mm_35237.1	chr4	19877195	19877204	-	1	NA	3' UTR (NM_175406, exon 8 of 8)	3' UTR (NM_175406, exon 8 of 8)	45367	NM_175406	242341	Mm.19298	NM_175406	ENSMUSG00000028238	Atp6v0d2	1620401A02Rik|AI324824|V-ATPase	ATPase, H+ transporting, lysosomal V0 subunit D2	protein-coding
mm_104137.1	chr11	86993635	86993644	-	1	NA	5' UTR (NM_001005341, exon 1 of 5)	5' UTR (NM_001005341, exon 1 of 5)	123	NM_001005341	77864	Mm.191894	NM_001005341	ENSMUSG00000018427	Ypel2	6430570G24|E130113K08Rik	yippee-like 2 (Drosophila)	protein-coding
mm_27740.1	chr3	69093803	69093826	-	1	NA	intron (NM_008467, intron 7 of 16)	intron (NM_008467, intron 7 of 16)	33278	NM_008467	16649	Mm.30601	NM_008467	ENSMUSG00000027782	Kpna4	1110058D08Rik|IPOA3	karyopherin (importin) alpha 4	protein-coding
mm_47500.1	chr5	124034583	124034589	-	1	NA	Intergenic	Intergenic	-2326	NM_177876	330192	Mm.4079	NM_177876	ENSMUSG00000066278	Vps37b	2300007F24Rik|AI415429|BC026744	vacuolar protein sorting 37B	protein-coding
mm_85053.1	chr9	90114678	90114786	-	1	NA	promoter-TSS (NM_024431)	promoter-TSS (NM_024431)	88	NM_001039147	21761	Mm.426209	NM_024431	ENSMUSG00000062270	Morf4l1	MORFRG15|MRG15|TEG-189|Tex189|mKIAA4002	mortality factor 4 like 1	protein-coding
mm_143008.1	chr17	56440217	56440232	-	1	NA	intron (NM_001252455, intron 6 of 27)	intron (NM_001252455, intron 6 of 27)	-21315	NR_105943	102465590		NR_105943	ENSMUSG00000098339	Mir6977	Gm27922|mmu-mir-6977	microRNA 6977	ncRNA
mm_91626.1	chr10	41809621	41809654	-	1	NA	promoter-TSS (NM_001162908)	promoter-TSS (NM_001162908)	26	NM_001243075	103268	Mm.338605	NM_026643	ENSMUSG00000019813	Cep57l1	2410017P07Rik|4930484D11Rik|AI607327|cep57R	centrosomal protein 57-like 1	protein-coding
mm_109753.1	chr12	117688793	117688876	+	1	NA	intron (NM_175930, intron 12 of 27)	intron (NM_175930, intron 12 of 27)	-155027	NM_146040	217946	Mm.281149	NM_146040	ENSMUSG00000021175	Cdca7l	BC006933|JPO2	cell division cycle associated 7 like	protein-coding
mm_14629.1	chr2	136781173	136781224	+	1	NA	3' UTR (NM_001291056, exon 8 of 8)	3' UTR (NM_001291056, exon 8 of 8)	67748	NM_001291056	20614	Mm.45953	NM_011428	ENSMUSG00000027273	Snap25	Bdr|GENA70|SNAP-25|SUP|sp	synaptosomal-associated protein 25	protein-coding
mm_104355.1	chr11	94301573	94301585	-	1	NA	exon (NM_026313, exon 5 of 11)	exon (NM_026313, exon 5 of 11)	20332	NM_026313	67684	Mm.30927	NM_026313	ENSMUSG00000020863	Luc7l3	3300001P08Rik|Luc7a	LUC7-like 3 (S. cerevisiae)	protein-coding
mm_89068.1	chr10	82954557	82954567	+	1	NA	Intergenic	CpG	-30935	NM_021439	58250	Mm.360747	NM_021439	ENSMUSG00000034612	Chst11	1110020P09Rik|C4ST|C4ST-1|C4ST1|C4s	carbohydrate sulfotransferase 11	protein-coding
mm_91790.1	chr10	53349816	53349827	-	1	NA	intron (NM_001204983, intron 2 of 12)	Lx8|LINE|L1	12135	NM_001141927	18821	Mm.34145	NM_023129	ENSMUSG00000038583	Pln	Plb	phospholamban	protein-coding
mm_129225.1	chr15	76612701	76612715	-	1	NA	intron (NM_028064, intron 11 of 11)	intron (NM_028064, intron 11 of 11)	4144	NM_028064	72027	Mm.276829	NM_028064	ENSMUSG00000063354	Slc39a4	1600025H15Rik|AU041686|AWMS2|ZIP4	solute carrier family 39 (zinc transporter), member 4	protein-coding
mm_26514.1	chr3	145891994	145892009	+	1	NA	3' UTR (NM_026993, exon 6 of 6)	3' UTR (NM_026993, exon 6 of 6)	-32261	NM_009740	12042	Mm.239141	NM_009740	ENSMUSG00000028191	Bcl10	AI132454|BCL-10|C81403|CARMEN|CIPER|CLAP|ME10|cE10	B cell leukemia/lymphoma 10	protein-coding
mm_59819.1	chr7	29238324	29238394	+	1	NA	promoter-TSS (NM_001110201)	promoter-TSS (NM_001110201)	36	NM_029887	77254	Mm.36699	NM_029887	ENSMUSG00000030588	Yif1b	9430029K10Rik|Yip1b	Yip1 interacting factor homolog B (S. cerevisiae)	protein-coding
mm_89439.1	chr10	91170774	91170787	+	1	NA	promoter-TSS (NM_001283048)	promoter-TSS (NM_001283048)	-230	NM_001283048	21917	Mm.159684	NM_011605	ENSMUSG00000019961	Tmpo	5630400D24Rik|AI195756|AI606875|AW214352|AW547477|LAP2|TP	thymopoietin	protein-coding
mm_30040.1	chr3	135691940	135691981	-	1	NA	promoter-TSS (NM_008689)	promoter-TSS (NM_008689)	-413	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_122755.1	chr14	54213724	54213729	-	1	NA	Intergenic	Intergenic	40203	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_5355.1	chr1	25694125	25694129	-	1	NA	intron (NM_175642, intron 2 of 30)	intron (NM_175642, intron 2 of 30)	135580	NM_175642	210933	Mm.336569	NM_175642	ENSMUSG00000033569	Adgrb3	A830096D10Rik|Bai3	adhesion G protein-coupled receptor B3	protein-coding
mm_161220.1	chr13	67451585	67451585	-	1	NA	promoter-TSS (NM_177712)	promoter-TSS (NM_177712)	39	NM_177712	238692	Mm.486478	NM_177712	ENSMUSG00000069206	Zfp874a	C330011K17Rik|Rslcan15|Zfp874	zinc finger protein 874a	protein-coding
mm_165784.1	chr3	131357771	131357776	-	1	NA	Intergenic	Intergenic	-12850	NM_028943	74442	Mm.273360	NM_028943	ENSMUSG00000050931	Sgms2	4933405A16Rik|5133401H06Rik|AI854299	sphingomyelin synthase 2	protein-coding
mm_31570.1	chr4	57594710	57594727	+	1	NA	intron (NM_001304544, intron 1 of 8)	intron (NM_001304544, intron 1 of 8)	26470	NM_172868	242481	Mm.331630	NM_172868	ENSMUSG00000090053	Palm2	53-H12|B130066I24|R75368|pEN70	paralemmin 2	protein-coding
mm_65745.1	chr7	28544130	28544141	-	1	NA	exon (NM_001081115, exon 6 of 6)	exon (NM_001081115, exon 6 of 6)	3119	NM_001081115	233038	Mm.224815	NM_001081115	ENSMUSG00000047586	Nccrp1	1190020J12Rik|Gm163|NCCRP-1	non-specific cytotoxic cell receptor protein 1 homolog (zebrafish)	protein-coding
mm_116157.1	chr13	30551359	30551381	-	1	NA	Intergenic	Intergenic	-6054	NM_025710	66694	Mm.181933	NM_025710	ENSMUSG00000038462	Uqcrfs1	4430402G14Rik|AI875505	ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1	protein-coding
mm_54176.1	chr6	23655181	23655190	-	1	NA	promoter-TSS (NM_027754)	promoter-TSS (NM_027754)	-49	NM_027754	71300	Mm.443309	NM_027754	ENSMUSG00000078179	Rnf148	4933432M07Rik|Greul3	ring finger protein 148	protein-coding
mm_101846.1	chr11	48817333	48817389	-	1	NA	promoter-TSS (NM_145377)	promoter-TSS (NM_145377)	30	NM_145377	211007	Mm.794	NM_145377	ENSMUSG00000040365	Trim41	AW552703|BC020156|R75223|RINCK	tripartite motif-containing 41	protein-coding
mm_93797.1	chr10	120895328	120895337	-	1	NA	intron (NM_177092, intron 1 of 6)	intron (NM_177092, intron 1 of 6)	3639	NM_177092	320183	Mm.169755	NM_177092	ENSMUSG00000051236	Msrb3	D430026P16Rik|I-8-23|MsrB2	methionine sulfoxide reductase B3	protein-coding
mm_109962.1	chr12	12492907	12492913	-	1	NA	Intergenic	MLT1F-int|LTR|ERVL-MaLR	-100435	NR_045829	70858	Mm.410838	NR_045829		4921511I17Rik	-	RIKEN cDNA 4921511I17 gene	ncRNA
mm_77840.1	chr9	5299246	5299262	+	1	NA	intron (NM_009807, intron 1 of 9)	intron (NM_009807, intron 1 of 9)	737	NM_009807	12362	Mm.1051	NM_009807	ENSMUSG00000025888	Casp1	ICE|Il1bc	caspase 1	protein-coding
mm_108523.1	chr12	84100741	84100791	+	1	NA	5' UTR (NM_172580, exon 1 of 3)	5' UTR (NM_172580, exon 1 of 3)	112	NM_172580	217700	Mm.49245	NM_172580	ENSMUSG00000043487	Acot6	4632408A20Rik|A330054B07|BE688602	acyl-CoA thioesterase 6	protein-coding
mm_36773.1	chr4	102572184	102572194	-	1	NA	intron (NM_019840, intron 6 of 14)	intron (NM_019840, intron 6 of 14)	2129	NM_001177980	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_55504.1	chr6	69823940	69823971	-	1	NA	Intergenic	Intergenic	-496781	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_34230.1	chr4	141078444	141078444	+	1	NA	promoter-TSS (NM_025383)	promoter-TSS (NM_025383)	-99	NM_025383	66147	Mm.21187	NM_025383	ENSMUSG00000028923	Necap2	1110005F07Rik|AA409105|C78898	NECAP endocytosis associated 2	protein-coding
mm_149335.1	chr19	10849147	10849168	+	1	NA	intron (NM_023044, intron 2 of 7)	B4|SINE|B4	6613	NM_023044	65221	Mm.27387	NM_023044	ENSMUSG00000024737	Slc15a3	Ci1|cI-1	solute carrier family 15, member 3	protein-coding
mm_165048.1	chr19	40637776	40637784	-	1	NA	intron (NM_001304721, intron 1 of 9)	intron (NM_001304721, intron 1 of 9)	-21990	NM_009848	12495	Mm.2824	NM_009848	ENSMUSG00000048120	Entpd1	2610206B08Rik|AA408691|Cd39|NTPDase-1	ectonucleoside triphosphate diphosphohydrolase 1	protein-coding
mm_148007.1	chr18	67799925	67799975	-	1	NA	promoter-TSS (NM_027556)	promoter-TSS (NM_027556)	-7	NR_045376	75286	Mm.307315	NR_045376		4930549G23Rik	-	RIKEN cDNA 4930549G23 gene	ncRNA
mm_41093.1	chr5	87694588	87694594	+	1	NA	exon (NM_001286023, exon 5 of 7)	exon (NM_001286023, exon 5 of 7)	4834	NM_001286020	12991	Mm.268737	NM_009972	ENSMUSG00000063157	Csn2	Csnb	casein beta	protein-coding
mm_75055.1	chr8	33385471	33385517	-	1	NA	promoter-TSS (NM_001122822)	promoter-TSS (NM_001122822)	33	NM_001122822	22427	Mm.228805	NM_011721	ENSMUSG00000031583	Wrn	AI846146	Werner syndrome homolog (human)	protein-coding
mm_131345.1	chr16	13468856	13468866	+	1	NA	Intergenic	Intergenic	2319	NR_105784	102466153		NR_105784	ENSMUSG00000099214	Mir6365	Gm27683|mmu-mir-6365	microRNA 6365	ncRNA
mm_79087.1	chr9	46242606	46242630	+	1	NA	exon (NM_007468, exon 3 of 3)	exon (NM_007468, exon 3 of 3)	1774	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_124475.1	chr14	121456883	121456900	-	1	NA	Intergenic	Intergenic	48363	NM_053079	56643	Mm.155618	NM_053079	ENSMUSG00000025557	Slc15a1	D630032F02|PECT1|PEPT1	solute carrier family 15 (oligopeptide transporter), member 1	protein-coding
mm_116283.1	chr13	34993229	34993246	-	1	NA	intron (NM_001110331, intron 1 of 9)	intron (NM_001110331, intron 1 of 9)	907	NM_011868	23986	Mm.491141	NM_011868	ENSMUSG00000021417	Eci2	Acbd2|Drs1|Hca88|Peci	enoyl-Coenzyme A delta isomerase 2	protein-coding
mm_14477.1	chr2	131505659	131505661	+	1	NA	intron (NM_001177836, intron 1 of 7)	intron (NM_001177836, intron 1 of 7)	13798	NM_001177838	228608	Mm.136586	NM_145533	ENSMUSG00000027333	Smox	B130066H01Rik|PAO|PAOh1|SMO	spermine oxidase	protein-coding
mm_139235.1	chr17	47732461	47732470	+	1	NA	exon (NM_025973, exon 6 of 9)	exon (NM_025973, exon 6 of 9)	-4572	NM_001161722	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_43839.1	chr5	142972880	142972892	+	1	NA	3' UTR (NM_007984, exon 5 of 5)	3' UTR (NM_007984, exon 5 of 5)	12531	NM_007984	14086	Mm.289707	NM_007984	ENSMUSG00000029581	Fscn1	AI663989|Fan1|fascin-1	fascin actin-bundling protein 1	protein-coding
mm_155750.1	chrX	96167267	96167280	+	1	NA	3' UTR (NM_010833, exon 13 of 13)	3' UTR (NM_010833, exon 13 of 13)	71228	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_95123.1	chr11	34083617	34083629	+	1	NA	intron (NM_010696, intron 17 of 20)	intron (NM_010696, intron 17 of 20)	36422	NM_010696	16822	Mm.265350	NM_010696	ENSMUSG00000002699	Lcp2	AI323664|BB161688|SLP-76|SLP76|m1Khoe|twm	lymphocyte cytosolic protein 2	protein-coding
mm_157995.1	chrX	94540307	94540321	-	1	NA	exon (NM_019791, exon 3 of 13)	exon (NM_019791, exon 3 of 13)	1760	NM_019791	94275	Mm.27578	NM_019791	ENSMUSG00000025151	Maged1	2810433C11Rik|5430405L04Rik|DXBwg1492e|Dlixin|Dlxin-1|Dlxin1|MAGE-D1|NRAGE|mFLJ00163	melanoma antigen, family D, 1	protein-coding
mm_78526.1	chr9	34636304	34636308	+	1	NA	intron (NM_001190912, intron 1 of 15)	intron (NM_001190912, intron 1 of 15)	147575	NM_001190911	67703	Mm.220710	NM_026324	ENSMUSG00000032036	Kirrel3	1500010O20Rik|2900036G11Rik|NEPH2|SST4|mKIAA1867	kin of IRRE like 3 (Drosophila)	protein-coding
mm_9120.1	chr1	170211780	170211785	-	1	NA	intron (NM_010633, intron 2 of 7)	intron (NM_010633, intron 2 of 7)	3611	NM_010633	16589	Mm.209150	NM_010633	ENSMUSG00000026667	Uhmk1	4732477C12Rik|4930500M09Rik|AA673513|AI449218|AU021979|C820018A03Rik|KIS|Kist|OTTMUSG00000021542|P-CIP2	U2AF homology motif (UHM) kinase 1	protein-coding
mm_108581.1	chr12	85110851	85110866	+	1	NA	promoter-TSS (NM_030225)	promoter-TSS (NM_030225)	25	NM_030225	78920	Mm.296221	NM_030225	ENSMUSG00000004789	Dlst	1600017E01Rik|4632413C10Rik|4930529O08Rik|DLTS	dihydrolipoamide S-succinyltransferase (E2 component of 2-oxo-glutarate complex)	protein-coding
mm_139800.1	chr17	66111530	66111581	+	1	NA	promoter-TSS (NM_026833)	promoter-TSS (NM_026833)	9	NM_026833	68767	Mm.296545	NM_026833	ENSMUSG00000024101	Washc1	1110049F14Rik|ORF19|Wash|Wash1	WASH complex subunit 1	protein-coding
mm_94124.1	chr10	128670564	128670566	-	1	NA	exon (NM_173733, exon 4 of 4)	exon (NM_173733, exon 4 of 4)	3353	NM_173733	211389	Mm.23352	NM_173733	ENSMUSG00000049858	Suox	SO	sulfite oxidase	protein-coding
mm_50079.1	chr6	41458899	41458901	+	1	NA	promoter-TSS (NM_053243)	promoter-TSS (NM_053243)	-30	NM_053243	114228	Mm.449428	NM_053243	ENSMUSG00000062751	Prss1	Try-1|Try1|Trygn16	protease, serine 1 (trypsin 1)	protein-coding
mm_126864.1	chr15	89334987	89335017	+	1	NA	exon (NM_019977, exon 2 of 10)	exon (NM_019977, exon 2 of 10)	529	NM_019977	56727	Mm.158200	NM_019977	ENSMUSG00000022613	Miox	0610009I10Rik|AI314022|Aldrl6|C85427|RSOR	myo-inositol oxygenase	protein-coding
mm_1550.1	chr1	72934901	72934924	+	1	NA	Intergenic	Intergenic	-60047	NM_010518	16011	Mm.405761	NM_010518	ENSMUSG00000026185	Igfbp5	AI256729|AW208790|IGFBP-5|IGFBP-5P	insulin-like growth factor binding protein 5	protein-coding
mm_37072.1	chr4	116151379	116151400	-	1	NA	promoter-TSS (NM_001290658)	promoter-TSS (NM_001290658)	-42	NM_001290658	68273	Mm.196045	NM_026651	ENSMUSG00000028700	Pomgnt1	0610016I07Rik|4930467B06Rik	protein O-linked mannose beta 1,2-N-acetylglucosaminyltransferase	protein-coding
mm_69231.1	chr7	127708099	127708118	-	1	NA	promoter-TSS (NR_030428)	promoter-TSS (NR_030428)	-379	NR_030428	791073		NR_030428	ENSMUSG00000076454	Mir762	Mirn762|mir-762|mmu-mir-762	microRNA 762	ncRNA
mm_149047.1	chr19	8831586	8831597	+	1	NA	3' UTR (NM_001081196, exon 14 of 14)	3' UTR (NM_001081196, exon 14 of 14)	-5876	NM_001136064	14705	Mm.345134	NM_008144	ENSMUSG00000071657	Bscl2	2900097C17Rik|AI046355|Gng3lg	Berardinelli-Seip congenital lipodystrophy 2 (seipin)	protein-coding
mm_80324.1	chr9	74976097	74976177	+	1	NA	promoter-TSS (NM_153584)	promoter-TSS (NM_153584)	26	NM_153584	235493	Mm.208955	NM_153584	ENSMUSG00000034858	Fam214a	6330415I01Rik|AI553555|C130047D21Rik|Kiaa1370|mKIAA1370	family with sequence similarity 214, member A	protein-coding
mm_120726.1	chr14	73142491	73142564	+	1	NA	promoter-TSS (NM_001170694)	promoter-TSS (NM_001170694)	17	NM_134083	105670	Mm.280068	NM_134083	ENSMUSG00000022106	Rcbtb2	2610028E02Rik|2810420M18Rik|AI448345|AW240694|Chc1l|RC/BTB2	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 2	protein-coding
mm_142697.1	chr17	47834522	47834534	-	1	NA	5' UTR (NM_001109973, exon 1 of 5)	5' UTR (NM_001109973, exon 1 of 5)	163	NM_001109973	17240	Mm.329100	NM_010783	ENSMUSG00000032717	Mdfi	I-mf|I-mfa	MyoD family inhibitor	protein-coding
mm_39190.1	chr4	155891702	155891782	-	1	NA	promoter-TSS (NM_207223)	promoter-TSS (NM_207223)	20	NM_001033490	433813	Mm.259270	NM_001033490	ENSMUSG00000051557	Pusl1	2810021I11Rik|AI853843|D18346	pseudouridylate synthase-like 1	protein-coding
mm_44493.1	chr5	23676435	23676489	-	1	NA	Intergenic	CpG	36205	NR_038090	433855	Mm.205125	NR_015554	ENSMUSG00000105987	AI506816	-	expressed sequence AI506816	ncRNA
mm_69252.1	chr7	127848953	127848968	-	1	NA	TTS (NM_009294)	TTS (NM_009294)	7152	NM_009294	20909	Mm.24867	NM_009294	ENSMUSG00000030805	Stx4a	Stx4|Syn-4|Syn4	syntaxin 4A (placental)	protein-coding
mm_99831.1	chr11	108923278	108923286	+	1	NA	5' UTR (NM_015732, exon 2 of 11)	5' UTR (NM_015732, exon 2 of 11)	2933	NM_015732	12006	Mm.71710	NM_015732	ENSMUSG00000000142	Axin2	Axi1|Axil|Conductin	axin 2	protein-coding
mm_8009.1	chr1	134803716	134803726	-	1	NA	promoter-TSS (NR_015606)	promoter-TSS (NR_015606)	0	NR_015606	329251	Mm.188709	NM_001081307	ENSMUSG00000073557	Ppp1r12b	1810037O03Rik|9530009M10Rik|AI132431|Mypt2	protein phosphatase 1, regulatory (inhibitor) subunit 12B	protein-coding
mm_158790.1	chrX	167209469	167209474	-	1	NA	promoter-TSS (NM_021278)	promoter-TSS (NM_021278)	-253	NM_021278	19241	Mm.142729	NM_021278	ENSMUSG00000049775	Tmsb4x	Ptmb4|Tb4	thymosin, beta 4, X chromosome	protein-coding
mm_109452.1	chr12	111067892	111067913	+	1	NA	intron (NM_198023, intron 2 of 11)	intron (NM_198023, intron 2 of 11)	28104	NM_198023	217864	Mm.23808	NM_198023	ENSMUSG00000037896	Rcor1	5730409O11|6720480E22Rik|AU042633|D12Wsu95e|Rocr1|mKIAA0071	REST corepressor 1	protein-coding
mm_63944.1	chr7	139834276	139834285	+	1	NA	5' UTR (NM_177469, exon 1 of 8)	5' UTR (NM_177469, exon 1 of 8)	106	NM_177469	52389	Mm.39863	NM_177469	ENSMUSG00000025475	Adgra1	2900059M17Rik|D7Ertd680e|Gpr123	adhesion G protein-coupled receptor A1	protein-coding
mm_135373.1	chr16	44086566	44086580	-	1	NA	3' UTR (NM_007508, exon 15 of 15)	3' UTR (NM_007508, exon 15 of 15)	52446	NM_007508	11964	Mm.217787	NM_007508	ENSMUSG00000052459	Atp6v1a	AI647066|Atp6a1|Atp6a2|Atp6v1a1|VA68|VPP2	ATPase, H+ transporting, lysosomal V1 subunit A	protein-coding
mm_119410.1	chr14	44988897	44988919	+	1	NA	5' UTR (NM_008964, exon 1 of 2)	5' UTR (NM_008964, exon 1 of 2)	797	NM_008964	19217	Mm.4630	NM_008964	ENSMUSG00000037759	Ptger2	EP2|Ptgerep2	prostaglandin E receptor 2 (subtype EP2)	protein-coding
mm_127851.1	chr15	7398695	7398728	-	1	NA	promoter-TSS (NM_001289498)	promoter-TSS (NM_001289498)	-316	NM_001289498	268780	Mm.203208	NM_178748	ENSMUSG00000042961	Egflam	5930412K08|AU040377	EGF-like, fibronectin type III and laminin G domains	protein-coding
mm_95948.1	chr11	58390089	58390135	+	1	NA	exon (NM_001083884, exon 7 of 7)	exon (NM_001083884, exon 7 of 7)	9466	NM_001330197	70163	Mm.24119	NM_027339	ENSMUSG00000013643	Lypd8	2210415F13Rik	LY6/PLAUR domain containing 8	protein-coding
mm_157961.1	chrX	88115938	88115956	-	1	NA	promoter-TSS (NM_001160403)	promoter-TSS (NM_001160403)	-324	NM_001160403	331461	Mm.121680	NM_001160403	ENSMUSG00000052372	Il1rapl1	6330532G10Rik|C030039N24|IL1R8|IL1RAPL|MRX34|OPHN4|TIGIRR-2	interleukin 1 receptor accessory protein-like 1	protein-coding
mm_19679.1	chr2	103454607	103454615	-	1	NA	3' UTR (NM_009804, exon 13 of 13)	3' UTR (NM_009804, exon 13 of 13)	30542	NM_009804	12359	Mm.4215	NM_009804	ENSMUSG00000027187	Cat	2210418N07|Cas-1|Cas1|Cs-1	catalase	protein-coding
mm_38886.1	chr4	149737958	149738054	-	1	NA	promoter-TSS (NM_177672)	promoter-TSS (NM_177672)	62	NM_001284270	230917	Mm.266704	NM_177672	ENSMUSG00000044700	Tmem201	AV028368|D4Ertd429e|Net5|Samp1	transmembrane protein 201	protein-coding
mm_115135.1	chr13	104620200	104620204	+	1	NA	Intergenic	Intergenic	196751	NM_026072	67285	Mm.235398	NM_026072	ENSMUSG00000021715	Cwc27	3110009E13Rik|NY-CO-10|Sdccag10	CWC27 spliceosome-associated protein	protein-coding
mm_97166.1	chr11	75509951	75509997	+	1	NA	promoter-TSS (NM_001029938)	promoter-TSS (NM_001029938)	-120	NM_001029938	280408	Mm.41416	NM_001029938	ENSMUSG00000038195	Rilp	AI835553|Gm857	Rab interacting lysosomal protein	protein-coding
mm_126920.1	chr15	91641954	91641964	+	1	NA	Intergenic	Intergenic	-31265	NM_025730	66725	Mm.37558	NM_025730	ENSMUSG00000036273	Lrrk2	4921513O20Rik|9330188B09Rik|AW561911|D630001M17Rik|Gm927|cI-46	leucine-rich repeat kinase 2	protein-coding
mm_35355.1	chr4	32291458	32291470	-	1	NA	Intergenic	Intergenic	-125971	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_64261.1	chr7	141746633	141746642	+	1	NA	exon (NM_023566, exon 31 of 46)	exon (NM_023566, exon 31 of 46)	-42374	NM_010844	17833	Mm.334332	NM_010844	ENSMUSG00000037974	Muc5ac	2210005L13Rik|MGM	mucin 5, subtypes A and C, tracheobronchial/gastric	protein-coding
mm_83902.1	chr9	56160999	56161045	-	1	NA	promoter-TSS (NM_019793)	promoter-TSS (NM_019793)	48	NM_019793	56434	Mm.28484	NM_019793	ENSMUSG00000032324	Tspan3	1700055K04Rik|TM4-A|Tm4sf8	tetraspanin 3	protein-coding
mm_68556.1	chr7	114416627	114416637	-	1	NA	intron (NM_011055, intron 1 of 15)	intron (NM_011055, intron 1 of 15)	1378	NM_011055	18576	Mm.430730	NM_011055	ENSMUSG00000030671	Pde3b	9830102A01Rik|AI847709	phosphodiesterase 3B, cGMP-inhibited	protein-coding
mm_153426.1	chr19	40821457	40821463	-	1	NA	Intergenic	Intergenic	-9819	NM_172839	240665	Mm.309	NM_172839	ENSMUSG00000025010	Ccnj	D430039C20Rik	cyclin J	protein-coding
mm_147263.1	chr18	38867059	38867074	-	1	NA	intron (NM_010197, intron 1 of 3)	L2b|LINE|L2	-25390	NM_001033789	545253	Mm.244585	NM_001033789	ENSMUSG00000036452	Gm5820	EG545253	predicted gene 5820	protein-coding
mm_24732.1	chr3	95283075	95283112	+	1	NA	5' UTR (NM_133858, exon 1 of 10)	5' UTR (NM_133858, exon 1 of 10)	158	NM_199475	75007	Mm.279287	NM_133858	ENSMUSG00000038712	Fam63a	1810005H09Rik|4930504E06Rik|AA562754|AA960384|AW561904|cI-40|mKIAA1390|ni	family with sequence similarity 63, member A	protein-coding
mm_171582.1	chr4	147492488	147492495	+	1	NA	intron (NM_001039209, intron 1 of 2)	intron (NM_001039209, intron 1 of 2)	-60786	NM_001014397	433804	Mm.332047	NM_001014397	ENSMUSG00000065999	Zfp985	Gm13154|OTTMUSG00000010673	zinc finger protein 985	protein-coding
mm_52809.1	chr6	121343053	121343073	+	1	NA	promoter-TSS (NM_001347433)	promoter-TSS (NM_001347433)	-13	NM_001347433	14411	Mm.274506	NM_133661	ENSMUSG00000030109	Slc6a12	BGT1|GAT-2|GAT2|Gabt2	solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12	protein-coding
mm_105861.1	chr11	113797473	113797476	-	1	NA	intron (NM_172800, intron 40 of 44)	intron (NM_172800, intron 40 of 44)	-45659	NM_001163346	56699	Mm.293378	NM_020006	ENSMUSG00000041598	Cdc42ep4	1500041M20Rik|Borg4|CEP4	CDC42 effector protein (Rho GTPase binding) 4	protein-coding
mm_33295.1	chr4	128976166	128976195	+	1	NA	Intergenic	Intergenic	-13725	NM_001301841	242669	Mm.215814	NM_172875	ENSMUSG00000028789	Azin2	4933429I20Rik|Adc|Azi2|B930082O19|ODC-p|Odcp	antizyme inhibitor 2	protein-coding
mm_172436.1	chr7	29799713	29799738	-	1	NA	Intergenic	Intergenic	14935	NM_013705	22693	Mm.292690	NM_013705	ENSMUSG00000047473	Zfp30	2610306P15Rik|Zfp-30	zinc finger protein 30	protein-coding
mm_109267.1	chr12	109545391	109545443	+	1	NA	promoter-TSS (NR_003633)	promoter-TSS (NR_003633)	19	NR_003633	17263	Mm.289645	NM_144513	ENSMUSG00000021268	Meg3	2900016C05Rik|3110050O07Rik|6330408G06Rik|AI425946|AW108224|D12Bwg1266e|Gtl2|R74756|R75394	maternally expressed 3	ncRNA
mm_153635.1	chr19	44069361	44069422	-	1	NA	5' UTR (NM_001164360, exon 2 of 12)	5' UTR (NM_001164360, exon 2 of 12)	295	NM_145502	226144	Mm.279865	NM_145502	ENSMUSG00000025198	Erlin1	2810439N09Rik|C80197|Keo4|Spfh1	ER lipid raft associated 1	protein-coding
mm_163658.1	chr13	74533515	74533557	+	1	NA	Intergenic	Intergenic	-39586	NM_146231	235956	Mm.296909	NM_146231	ENSMUSG00000069208	Zfp825	-	zinc finger protein 825	protein-coding
mm_26342.1	chr3	142547266	142547270	+	1	NA	3' UTR (NM_001083312, exon 11 of 11)	3' UTR (NM_001083312, exon 11 of 11)	-12784	NM_018734	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_52268.1	chr6	108473068	108473082	+	1	NA	intron (NM_010585, intron 45 of 61)	intron (NM_010585, intron 45 of 61)	-16668	NR_106121	102465766		NR_106121	ENSMUSG00000105697	Mir7661	mmu-mir-7661	microRNA 7661	ncRNA
mm_139620.1	chr17	57362654	57362662	+	1	NA	intron (NM_010130, intron 2 of 21)	RLTR22_Mur|LTR|ERVK	3972	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_152994.1	chr19	29806532	29806552	-	1	NA	promoter-TSS (NM_172836)	promoter-TSS (NM_172836)	-533	NM_172836	240613	Mm.313351	NM_172836	ENSMUSG00000046138	9930021J03Rik	ENSMUSG00000048936|Gm9832|mKIAA2026	RIKEN cDNA 9930021J03 gene	protein-coding
mm_116432.1	chr13	42052794	42052804	-	1	NA	intron (NM_007772, intron 1 of 8)	intron (NM_007772, intron 1 of 8)	778	NM_007772	110521	Mm.4808	NM_007772	ENSMUSG00000021366	Hivep1	Cryabp1	human immunodeficiency virus type I enhancer binding protein 1	protein-coding
mm_6743.1	chr1	83277202	83277212	-	1	NA	exon (NM_172430, exon 7 of 11)	exon (NM_172430, exon 7 of 11)	117445	NM_027725	71227	Mm.256482	NM_027725	ENSMUSG00000053161	Daw1	4930563E19Rik|4933429D11Rik|Wdr69|b2b1116Clo|b2b1584Clo	dynein assembly factor with WDR repeat domains 1	protein-coding
mm_62004.1	chr7	91253276	91253285	+	1	NA	intron (NM_011807, intron 1 of 22)	intron (NM_011807, intron 1 of 22)	162494	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_26371.1	chr3	142560622	142560628	+	1	NA	5' UTR (NM_001289493, exon 1 of 11)	5' UTR (NM_001289493, exon 1 of 11)	129	NM_001289493	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_91772.1	chr10	51757159	51757170	-	1	NA	promoter-TSS (NR_045158)	promoter-TSS (NR_045158)	30	NR_045158	71090	Mm.72588	NM_027670	ENSMUSG00000062224	4933411G06Rik	-	Sumo1 pseudogene	pseudo
mm_108271.1	chr12	78861025	78861053	+	1	NA	intron (NM_023721, intron 1 of 8)	intron (NM_023721, intron 1 of 8)	599	NM_023721	73834	Mm.311549	NM_023721	ENSMUSG00000021114	Atp6v1d	1110004P10Rik|Atp6m|VATD|Vma8	ATPase, H+ transporting, lysosomal V1 subunit D	protein-coding
mm_69874.1	chr7	141539785	141539845	-	1	NA	promoter-TSS (NM_001142681)	promoter-TSS (NM_001142681)	42	NM_026522	68038	Mm.245355	NM_026522	ENSMUSG00000025512	Chid1	3110023E09Rik|AI841869	chitinase domain containing 1	protein-coding
mm_31125.1	chr4	43046015	43046043	+	1	NA	intron (NR_045567, intron 1 of 7)	intron (NR_045567, intron 1 of 7)	191	NR_045567	230088	Mm.260162	NM_172691	ENSMUSG00000036002	Fam214b	B230312A22Rik	family with sequence similarity 214, member B	protein-coding
mm_158050.1	chrX	99470677	99470748	-	1	NA	promoter-TSS (NM_001290556)	promoter-TSS (NM_001290556)	23	NM_001083110	18744	Mm.8211	NM_008853	ENSMUSG00000034403	Pja1	praja-1	praja ring finger 1, E3 ubiquitin protein ligase	protein-coding
mm_71834.1	chr8	68901146	68901219	+	1	NA	exon (NM_008509, exon 8 of 10)	exon (NM_008509, exon 8 of 10)	20627	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_31986.1	chr4	89182292	89182294	+	1	NA	Intergenic	Intergenic	44923	NM_024433	66902	Mm.28500	NM_024433	ENSMUSG00000062937	Mtap	1300019I21Rik|MSAP	methylthioadenosine phosphorylase	protein-coding
mm_87070.1	chr10	29144219	29144229	+	1	NA	5' UTR (NM_026138, exon 1 of 7)	5' UTR (NM_026138, exon 1 of 7)	228	NM_026138	67412	Mm.390264	NM_026138	ENSMUSG00000038916	Soga3	6330407J23Rik	SOGA family member 3	protein-coding
mm_28569.1	chr3	93445050	93445058	-	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	2724	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_64059.1	chr7	140847844	140847848	+	1	NA	promoter-TSS (NM_027019)	promoter-TSS (NM_027019)	-70	NM_027019	69287	Mm.56404	NM_027019	ENSMUSG00000025482	Odf3	1700011O04Rik|SHIPPO1	outer dense fiber of sperm tails 3	protein-coding
mm_152273.1	chr19	8819279	8819301	-	1	NA	promoter-TSS (NM_001081196)	promoter-TSS (NM_001081196)	4	NM_027412	70387	Mm.261082	NM_027412	ENSMUSG00000071660	Ttc9c	2210019E14Rik|6330408J23Rik	tetratricopeptide repeat domain 9C	protein-coding
mm_119121.1	chr14	31131054	31131062	+	1	NA	Intergenic	CpG	-2128	NM_001308464	66487	Mm.379116	NM_001308091	ENSMUSG00000058351	Smim4	2010107H07Rik|Gm41122	small integral membrane protein 4	protein-coding
mm_73931.1	chr8	119942025	119942057	+	1	NA	exon (NM_009462, exon 4 of 14)	exon (NM_009462, exon 4 of 14)	31681	NM_001310630	22224	Mm.256910	NM_009462	ENSMUSG00000031826	Usp10	2610014N07Rik|UBPO|Uchrp|mKIAA0190	ubiquitin specific peptidase 10	protein-coding
mm_32688.1	chr4	115847908	115847916	+	1	NA	intron (NM_001285487, intron 2 of 14)	intron (NM_001285487, intron 2 of 14)	8714	NM_001285487	17346	Mm.209327	NM_021461	ENSMUSG00000028708	Mknk1	2410048M24Rik|Mnk1	MAP kinase-interacting serine/threonine kinase 1	protein-coding
mm_54774.1	chr6	41538688	41538692	-	1	NA	Intergenic	Intergenic	16914	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_74986.1	chr8	27142336	27142353	-	1	NA	promoter-TSS (NR_045840)	promoter-TSS (NR_045840)	-566	NR_045840	71082	Mm.395259	NR_045840		4933416M07Rik	-	RIKEN cDNA 4933416M07 gene	ncRNA
mm_134023.1	chr16	4939608	4939624	-	1	NA	promoter-TSS (NR_037666)	promoter-TSS (NR_037666)	-31	NR_037666	100503704	Mm.480572	NR_037666	ENSMUSG00000097397	Gm16861	-	predicted gene, 16861	ncRNA
mm_111728.1	chr12	103768029	103768047	-	1	NA	exon (NM_009246, exon 2 of 5)	exon (NM_009246, exon 2 of 5)	5595	NM_009246	20703	Mm.439695	NM_009246	ENSMUSG00000071177	Serpina1d	AI118301|Dom4|PI4|Spi1-4	serine (or cysteine) peptidase inhibitor, clade A, member 1D	protein-coding
mm_132181.1	chr16	32400803	32400813	+	1	NA	5' UTR (NM_001160402, exon 1 of 5)	5' UTR (NM_001160402, exon 1 of 5)	302	NM_001160402	277203	Mm.484240	NM_001160402	ENSMUSG00000079625	Tm4sf19	EG277203	transmembrane 4 L six family member 19	protein-coding
mm_120980.1	chr14	78724850	78724880	+	1	NA	intron (NM_001081336, intron 1 of 28)	CpG	224	NM_001081336	380921	Mm.89591	NM_001081336	ENSMUSG00000034731	Dgkh	5930402B05Rik|D130015C16|DGK	diacylglycerol kinase, eta	protein-coding
mm_89812.1	chr10	103367749	103367836	+	1	NA	promoter-TSS (NM_175328)	promoter-TSS (NM_175328)	-16	NM_001252330	103098	Mm.458408	NM_175328	ENSMUSG00000019894	Slc6a15	AA536730|AI326450|AI326451|v7-3	solute carrier family 6 (neurotransmitter transporter), member 15	protein-coding
mm_9686.1	chr1	178334556	178334565	-	1	NA	intron (NM_016805, intron 3 of 13)	intron (NM_016805, intron 3 of 13)	3224	NM_016805	51810	Mm.86589	NM_016805	ENSMUSG00000039630	Hnrnpu	AA408410|AI256620|AL024194|AL024437|AW557595|C86794|Hnrpu|SAFA|Sp120|hnRNP U	heterogeneous nuclear ribonucleoprotein U	protein-coding
mm_5688.1	chr1	43183811	43183835	-	1	NA	intron (NM_001289533, intron 1 of 5)	ORR1A4|LTR|ERVL-MaLR	12938	NM_001289533	14200	Mm.6799	NM_010212	ENSMUSG00000008136	Fhl2	FHL-2|SLIM-3|SLIM3	four and a half LIM domains 2	protein-coding
mm_35794.1	chr4	46536097	46536130	-	1	NA	promoter-TSS (NM_029077)	promoter-TSS (NM_029077)	28	NM_029077	74735	Mm.240252	NM_029077	ENSMUSG00000039853	Trim14	5830400N10Rik|pub	tripartite motif-containing 14	protein-coding
mm_86463.1	chr10	4387508	4387551	+	1	NA	intron (NM_001033466, intron 1 of 2)	CpG	579	NM_001033466	381990	Mm.262466	NM_001033466	ENSMUSG00000075327	Zbtb2	Gm1103	zinc finger and BTB domain containing 2	protein-coding
mm_140445.1	chr17	88580396	88580407	+	1	NA	intron (NM_028658, intron 18 of 21)	intron (NM_028658, intron 18 of 21)	-46154	NM_029858	77057	Mm.482203	NM_029858	ENSMUSG00000033855	Ston1	4921524J06Rik|C86231|Salf|Sblf	stonin 1	protein-coding
mm_58514.1	chr7	4130800	4130834	+	1	NA	exon (NM_001109765, exon 9 of 14)	exon (NM_001109765, exon 9 of 14)	6109	NR_033548	100037396	Mm.447887	NR_033548	ENSMUSG00000085886	D030047H15Rik	Gm15924|OTTMUSG00000027889	RIKEN cDNA D030047H15 gene	ncRNA
mm_6565.1	chr1	75142635	75142725	-	1	NA	promoter-TSS (NM_026977)	promoter-TSS (NM_026977)	-106	NM_170755	227298	Mm.273062	NM_170755	ENSMUSG00000049339	Fam134a	-	family with sequence similarity 134, member A	protein-coding
mm_15319.1	chr2	155747140	155747148	+	1	NA	Intergenic	MT2B1|LTR|ERVL	-4073	NM_011171	19124	Mm.3243	NM_011171	ENSMUSG00000027611	Procr	AI325044|Ccca|Ccd41|Epcr	protein C receptor, endothelial	protein-coding
mm_91544.1	chr10	39692317	39692319	-	1	NA	intron (NR_038037, intron 1 of 2)	intron (NR_038037, intron 1 of 2)	39689	NR_038037	327744	Mm.295265	NM_183198	ENSMUSG00000087177	E130307A14Rik	-	RIKEN cDNA E130307A14 gene	ncRNA
mm_165294.1	chr2	91096899	91096907	+	1	NA	5' UTR (NM_011355, exon 1 of 5)	5' UTR (NM_011355, exon 1 of 5)	225	NM_011355	20375	Mm.1302	NM_011355	ENSMUSG00000002111	Spi1	Dis-1|Dis1|PU.1|Sfpi-1|Sfpi1|Spi-1|Tcfpu1|Tfpu.1	spleen focus forming virus (SFFV) proviral integration oncogene	protein-coding
mm_46334.1	chr5	101665248	101665254	-	1	NA	promoter-TSS (NM_144955)	promoter-TSS (NM_144955)	-540	NM_144955	18096	Mm.193072	NM_144955	ENSMUSG00000035187	Nkx6-1	NKX6A|Nkx6.1	NK6 homeobox 1	protein-coding
mm_6850.1	chr1	84247750	84247776	-	1	NA	intron (NM_001003948, intron 1 of 2)	intron (NM_001003948, intron 1 of 2)	-28802	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_80467.1	chr9	78113351	78113355	+	1	NA	5' UTR (NM_019987, exon 1 of 14)	5' UTR (NM_019987, exon 1 of 14)	115	NM_019987	56542	Mm.288719	NM_019987	ENSMUSG00000009828	Ick	2210420N10Rik|AI848300|Mrk	intestinal cell kinase	protein-coding
mm_152645.1	chr19	12528203	12528216	-	1	NA	Intergenic	Lx8|LINE|L1	-26213	NM_172442	207521	Mm.247695	NM_172442	ENSMUSG00000039982	Dtx4	AI449438|BC044798|D930042H13|RNF155	deltex 4, E3 ubiquitin ligase	protein-coding
mm_15940.1	chr2	165810240	165810247	+	1	NA	intron (NM_027230, intron 15 of 23)	intron (NM_027230, intron 15 of 23)	47930	NM_001252585	228880	Mm.227598	NM_027230	ENSMUSG00000039671	Zmynd8	1110013E22Rik|2010005I16Rik|3632413B07Rik|AI316811|AL024039|Prkcbp1|RACK7	zinc finger, MYND-type containing 8	protein-coding
mm_133231.1	chr16	76926208	76926216	+	1	NA	Intergenic	Intergenic	84669	NR_040573	76601	Mm.396217	NR_040573	ENSMUSG00000100857	1700041M19Rik	-	RIKEN cDNA 1700041M19 gene	ncRNA
mm_56157.1	chr6	87851012	87851054	-	1	NA	promoter-TSS (NM_013493)	promoter-TSS (NM_013493)	73	NM_001109746	12785	Mm.290251	NM_013493	ENSMUSG00000030057	Cnbp	AA408710|Cnbp1|Znf9	cellular nucleic acid binding protein	protein-coding
mm_124925.1	chr15	12146158	12146201	+	1	NA	exon (NM_011767, exon 6 of 20)	exon (NM_011767, exon 6 of 20)	-25313	NR_035443	100316684		NR_035443	ENSMUSG00000084592	Mir1898	Mirn1898|mmu-mir-1898	microRNA 1898	ncRNA
mm_142006.1	chr17	35200125	35200138	-	1	NA	3' UTR (NM_013693, exon 4 of 4)	3' UTR (NM_013693, exon 4 of 4)	1876	NM_013693	21926	Mm.1293	NM_013693	ENSMUSG00000024401	Tnf	DIF|TNF-a|TNF-alpha|TNFSF2|TNFalpha|Tnfa|Tnfsf1a|Tnlg1f	tumor necrosis factor	protein-coding
mm_39884.1	chr5	31116569	31116581	+	1	NA	promoter-TSS (NM_021447)	promoter-TSS (NM_021447)	-37	NM_021447	58522	Mm.143796	NM_021447	ENSMUSG00000062077	Trim54	4930486E09Rik|4930566I02Rik|MURF|MURF-3|MuRF3|Rnf30	tripartite motif-containing 54	protein-coding
mm_20333.1	chr2	127521359	127521375	-	1	NA	promoter-TSS (NM_019789)	promoter-TSS (NM_019789)	25	NM_001291005	56461	Mm.315292	NM_019789	ENSMUSG00000079056	Kcnip3	4933407H12Rik|AI413860|Csen|DREAM|KChIP3|R74849	Kv channel interacting protein 3, calsenilin	protein-coding
mm_69861.1	chr7	141437588	141437650	-	1	NA	TTS (NM_022654)	TTS (NM_022654)	255	NM_026646	68267	Mm.33729	NM_026646	ENSMUSG00000019082	Slc25a22	1300006L01Rik|AI060884|Gc1	solute carrier family 25 (mitochondrial carrier, glutamate), member 22	protein-coding
mm_39775.1	chr5	30020856	30020858	+	1	NA	TTS (NM_031168)	TTS (NM_031168)	7743	NM_031168	16193	Mm.1019	NM_031168	ENSMUSG00000025746	Il6	Il-6	interleukin 6	protein-coding
mm_163203.1	chr11	97435390	97435395	+	1	NA	Intergenic	Intergenic	-14768	NM_021493	58996	Mm.394118	NM_021493	ENSMUSG00000049807	Arhgap23	A330041B18Rik	Rho GTPase activating protein 23	protein-coding
mm_39855.1	chr5	30921568	30921583	+	1	NA	promoter-TSS (NM_001310524)	promoter-TSS (NM_001310524)	16	NM_001310524	16548	Mm.22451	NM_008439	ENSMUSG00000029162	Khk	-	ketohexokinase	protein-coding
mm_112030.1	chr12	111486089	111486108	-	1	NA	promoter-TSS (NM_001033248)	promoter-TSS (NM_001033248)	-275	NM_001033248	212539	Mm.81916	NM_001033248	ENSMUSG00000010529	Gm266	-	predicted gene 266	protein-coding
mm_40944.1	chr5	76822355	76822418	+	1	NA	Intergenic	Intergenic	-18213	NM_001163793	320827	Mm.101504	NM_001163793	ENSMUSG00000036377	C530008M17Rik	2810489J07Rik|4930529A19Rik|4931405B09Rik|Kiaa1211|mKIAA1211	RIKEN cDNA C530008M17 gene	protein-coding
mm_131021.1	chr15	103565070	103565088	-	1	NA	promoter-TSS (NM_008134)	promoter-TSS (NM_008134)	2	NM_001289587	14663	Mm.219621	NM_008134	ENSMUSG00000022491	Glycam1	MC26|Sgp50|glyCAM-1	glycosylation dependent cell adhesion molecule 1	protein-coding
mm_48538.1	chr5	142904745	142904783	-	1	NA	exon (NM_007393, exon 4 of 6)	exon (NM_007393, exon 4 of 6)	1990	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_116556.1	chr13	46727655	46727668	-	1	NA	5' UTR (NM_175749, exon 1 of 22)	5' UTR (NM_175749, exon 1 of 22)	188	NM_175749	218210	Mm.255398	NM_175749	ENSMUSG00000021374	Nup153	B130015D15Rik|C88147	nucleoporin 153	protein-coding
mm_80253.1	chr9	72749550	72749574	+	1	NA	3' UTR (NM_010890, exon 29 of 29)	3' UTR (NM_010890, exon 29 of 29)	-57712	NM_175485	235472	Mm.31696	NM_175485	ENSMUSG00000036030	Prtg	A230098A12Rik|Igdcc5	protogenin	protein-coding
mm_91950.1	chr10	61098844	61098923	-	1	NA	3' UTR (NM_001316673, exon 15 of 15)	3' UTR (NM_001316673, exon 15 of 15)	9552	NM_025273	13180	Mm.39473	NM_025273	ENSMUSG00000020098	Pcbd1	Dcoh|Pcbd|Pcd|Phs	pterin 4 alpha carbinolamine dehydratase/dimerization cofactor of hepatocyte nuclear factor 1 alpha (TCF1) 1	protein-coding
mm_45646.1	chr5	76971484	76971487	-	1	NA	Intergenic	Lx2B|LINE|L1	-3216	NM_025691	66661	Mm.296976	NM_025691	ENSMUSG00000036323	Srp72	5730576P14Rik|72kDa|AI132477|BC019196|C77589	signal recognition particle 72	protein-coding
mm_67903.1	chr7	99695564	99695568	-	1	NA	5' UTR (NM_001252531, exon 1 of 14)	5' UTR (NM_001252531, exon 1 of 14)	243	NM_001252531	101488	Mm.11249	NM_175316	ENSMUSG00000030737	Slco2b1	AI060904|AI852653|OATP-B|Slc21a9	solute carrier organic anion transporter family, member 2b1	protein-coding
mm_72396.1	chr8	81768062	81768105	+	1	NA	intron (NM_001297593, intron 4 of 23)	intron (NM_001297593, intron 4 of 23)	425521	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_12309.1	chr2	69113805	69113810	+	1	NA	3' UTR (NM_001347161, exon 11 of 11)	3' UTR (NM_001347161, exon 11 of 11)	-21993	NM_181547	329416	Mm.90047	NM_181547	ENSMUSG00000034738	Nostrin	Daip2|mDaIP2	nitric oxide synthase trafficker	protein-coding
mm_59002.1	chr7	19178982	19179037	+	1	NA	intron (NM_001347582, intron 1 of 21)	intron (NM_001347582, intron 1 of 21)	-2161	NM_001162996	72205	Mm.154121	NM_028153	ENSMUSG00000040811	Eml2	1600029N02Rik|EMAP-2	echinoderm microtubule associated protein like 2	protein-coding
mm_90764.1	chr10	5593518	5593524	-	1	NA	promoter-TSS (NM_026793)	promoter-TSS (NM_026793)	-207	NM_026793	68632	Mm.338242	NM_026793	ENSMUSG00000046916	Myct1	1110020B04Rik|AI225941|AI642973|Mtmc1	myc target 1	protein-coding
mm_12675.1	chr2	75808247	75808270	+	1	NA	Intergenic	Intergenic	-23919	NM_172666	228061	Mm.31227	NM_172666	ENSMUSG00000042410	Agps	5832437L22|9930035G10Rik|AW123847|Adaps|Adas|Adhaps|Adps|Aldhpsy|bs2	alkylglycerone phosphate synthase	protein-coding
mm_74176.1	chr8	123452448	123452453	+	1	NA	intron (NM_001253783, intron 5 of 13)	intron (NM_001253783, intron 5 of 13)	9191	NM_001281803	23854	Mm.275127	NM_054046	ENSMUSG00000001482	Def8	AI449518|D8Ertd713e|DEF-8	differentially expressed in FDCP 8	protein-coding
mm_115728.1	chr13	17694730	17694786	-	1	NA	promoter-TSS (NM_138654)	promoter-TSS (NM_138654)	7	NM_138654	192136	Mm.364180	NM_138654	ENSMUSG00000055137	Sugct	5033411D12Rik|D17907	succinyl-CoA glutarate-CoA transferase	protein-coding
mm_155519.1	chrX	74254878	74254888	+	1	NA	5' UTR (NM_007927, exon 1 of 6)	5' UTR (NM_007927, exon 1 of 6)	196	NM_007927	13726	Mm.18892	NM_007927	ENSMUSG00000001964	Emd	AW550900|Sta	emerin	protein-coding
mm_97457.1	chr11	78244518	78244549	+	1	NA	intron (NM_009297, intron 1 of 36)	Lx8|LINE|L1	1170	NM_009297	20926	Mm.20755	NM_009297	ENSMUSG00000002052	Supt6	5131400N11Rik|AI132449|SPT6|Supt6h|mKIAA0162	suppressor of Ty 6	protein-coding
mm_65453.1	chr7	25412903	25412913	-	1	NA	promoter-TSS (NM_153576)	promoter-TSS (NM_153576)	-22	NM_153576	232983	Mm.10545	NM_153576	ENSMUSG00000060188	Cxcl17	VCC-1|Vcc1	chemokine (C-X-C motif) ligand 17	protein-coding
mm_158110.1	chrX	102156982	102157062	-	1	NA	promoter-TSS (NM_146235)	promoter-TSS (NM_146235)	69	NM_146235	236930	Mm.31911	NM_146235	ENSMUSG00000051220	Ercc6l	BC004701|D330021P09Rik	excision repair cross-complementing rodent repair deficiency complementation group 6 like	protein-coding
mm_86670.1	chr10	18055599	18055611	+	1	NA	promoter-TSS (NM_001111065)	promoter-TSS (NM_001111065)	-335	NM_009048	19707	Mm.4479	NM_009048	ENSMUSG00000019854	Reps1	BB161292	RalBP1 associated Eps domain containing protein	protein-coding
mm_39749.1	chr5	29587567	29587567	+	1	NA	intron (NM_133907, intron 2 of 22)	intron (NM_133907, intron 2 of 22)	18325	NM_133907	100763	Mm.137746	NM_133907	ENSMUSG00000039000	Ube3c	AI853514|mKIAA0010	ubiquitin protein ligase E3C	protein-coding
mm_108104.1	chr12	75308063	75308079	+	1	NA	promoter-TSS (NM_023275)	promoter-TSS (NM_023275)	-242	NM_023275	80837	Mm.27467	NM_023275	ENSMUSG00000046768	Rhoj	1110005O19Rik|AW210585|Arhj|TC10L|TCL	ras homolog family member J	protein-coding
mm_44855.1	chr5	34243351	34243364	-	1	NA	intron (NM_001015039, intron 1 of 12)	intron (NM_001015039, intron 1 of 12)	44967	NM_001015039	231125	Mm.113388	NM_001015039	ENSMUSG00000037224	Zfyve28	9630058O20Rik|Gm146|mKIAA1643	zinc finger, FYVE domain containing 28	protein-coding
mm_84818.1	chr9	77544784	77544813	-	1	NA	promoter-TSS (NM_001146048)	promoter-TSS (NM_001146048)	54	NM_001146048	214345	Mm.28534	NM_172528	ENSMUSG00000032352	Lrrc1	A430093J20Rik|AU016091|D030059I21|mKIAA4018	leucine rich repeat containing 1	protein-coding
mm_63066.1	chr7	122132576	122132580	+	1	NA	promoter-TSS (NM_021608)	promoter-TSS (NM_021608)	368	NM_001289844	233826	Mm.38348	NM_172744	ENSMUSG00000044702	Palb2	BC066140	partner and localizer of BRCA2	protein-coding
mm_24571.1	chr3	93444541	93444549	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	2215	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_294.1	chr1	23271755	23271765	+	1	NA	promoter-TSS (NR_029533)	promoter-TSS (NR_029533)	-509	NR_029533	387225		NR_029533	ENSMUSG00000065405	Mir30a	Mirn30a|mir-30a|mmu-mir-30a	microRNA 30a	ncRNA
mm_112235.1	chr12	113482354	113482359	-	1	NA	Intergenic	Intergenic	-7209	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_169366.1	chr14	32202425	32202433	+	1	NA	promoter-TSS (NM_016897)	promoter-TSS (NM_016897)	458	NM_011960	26430	Mm.15962	NM_011960	ENSMUSG00000021911	Parg	AI413217	poly (ADP-ribose) glycohydrolase	protein-coding
mm_172312.1	chr7	105953956	105953957	-	1	NA	promoter-TSS (NM_001243039)	promoter-TSS (NM_001243039)	11	NM_001243040	100042856	Mm.425473	NM_001243039	ENSMUSG00000078606	Gm4070	VLIG-1	predicted gene 4070	protein-coding
mm_56245.1	chr6	90736113	90736151	-	1	NA	intron (NM_001134384, intron 1 of 13)	intron (NM_001134384, intron 1 of 13)	-19603	NM_001134383	232227	Mm.196943	NM_182784	ENSMUSG00000034312	Iqsec1	AW561907|BC026481|BRAG2|D6Ertd349e|cI-43	IQ motif and Sec7 domain 1	protein-coding
mm_97420.1	chr11	78032313	78032343	+	1	NA	promoter-TSS (NM_183286)	promoter-TSS (NM_183286)	15	NM_183286	70451	Mm.390342	NM_183286	ENSMUSG00000020834	Dhrs13	2610209N15Rik	dehydrogenase/reductase (SDR family) member 13	protein-coding
mm_132232.1	chr16	32736287	32736304	+	1	NA	5' UTR (NM_080457, exon 1 of 27)	5' UTR (NM_080457, exon 1 of 27)	409	NM_080457	140474	Mm.214599	NM_080457	ENSMUSG00000079620	Muc4	4933405I11Rik|Asgp	mucin 4	protein-coding
mm_22636.1	chr3	14863429	14863446	+	1	NA	promoter-TSS (NM_007606)	promoter-TSS (NM_007606)	-101	NM_007606	12350	Mm.300	NM_007606	ENSMUSG00000027559	Car3	BB219044|Ca3|Car-3	carbonic anhydrase 3	protein-coding
mm_90615.1	chr10	128377087	128377155	+	1	NA	promoter-TSS (NM_172790)	promoter-TSS (NM_172790)	-3	NM_172790	237615	Mm.440177	NM_172790	ENSMUSG00000014498	Ankrd52	6430544C07|G431002C21Rik	ankyrin repeat domain 52	protein-coding
mm_68991.1	chr7	126625049	126625061	-	1	NA	intron (NM_019738, intron 1 of 2)	intron (NM_019738, intron 1 of 2)	415	NM_019738	56312	Mm.18742	NM_019738	ENSMUSG00000030717	Nupr1	2310032H04Rik|Com1|p8	nuclear protein transcription regulator 1	protein-coding
mm_148797.1	chr19	6184364	6184375	+	1	NA	promoter-TSS (NM_001165919)	promoter-TSS (NM_001165919)	-41	NM_001165919	622554	Mm.159757	NM_001165919	ENSMUSG00000024786	Majin	1700123I01Rik	membrane anchored junction protein	protein-coding
mm_48981.1	chr6	4755398	4755408	+	1	NA	exon (NM_130877, exon 2 of 2)	exon (NM_130877, exon 2 of 2)	8097	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_64571.1	chr7	144900432	144900474	+	1	NA	3' UTR (NM_008003, exon 3 of 3)	3' UTR (NM_008003, exon 3 of 3)	3921	NM_008003	14170	Mm.3904	NM_008003	ENSMUSG00000031073	Fgf15	FGF19	fibroblast growth factor 15	protein-coding
mm_147871.1	chr18	64488947	64488976	-	1	NA	exon (NM_007998, exon 1 of 11)	exon (NM_007998, exon 1 of 11)	105	NM_007998	14151	Mm.1070	NM_007998	ENSMUSG00000024588	Fech	AI894116|Fcl|fch	ferrochelatase	protein-coding
mm_34220.1	chr4	140983551	140983565	+	1	NA	Intergenic	Intergenic	-3315	NM_029097	74772	Mm.205625	NM_029097	ENSMUSG00000036622	Atp13a2	1110012E06Rik|AA589443	ATPase type 13A2	protein-coding
mm_5842.1	chr1	52953180	52953224	-	1	NA	promoter-TSS (NM_144953)	promoter-TSS (NM_144953)	-362	NM_144953	67080	Mm.236287	NM_144953	ENSMUSG00000043629	1700019D03Rik	2410136C24Rik|AA410151|smAKAP	RIKEN cDNA 1700019D03 gene	protein-coding
mm_70477.1	chr8	12395527	12395531	+	1	NA	promoter-TSS (NM_009233)	promoter-TSS (NM_009233)	10	NM_009233	20664	Mm.39088	NM_009233	ENSMUSG00000096014	Sox1	BB176347|Sox-1	SRY (sex determining region Y)-box 1	protein-coding
mm_139231.1	chr17	47731203	47731231	+	1	NA	intron (NM_025973, intron 5 of 8)	intron (NM_025973, intron 5 of 8)	4375	NM_025973	109820	Mm.22957	NM_025973	ENSMUSG00000023987	Pgc	2210410L06Rik|Upg-1|Upg1	progastricsin (pepsinogen C)	protein-coding
mm_135468.1	chr16	45844304	45844381	-	1	NA	promoter-TSS (NM_153412)	promoter-TSS (NM_153412)	36	NM_153412	208177	Mm.211477	NM_153412	ENSMUSG00000033149	Phldb2	AV253284|C820004H04Rik|LL5b|LL5beta	pleckstrin homology like domain, family B, member 2	protein-coding
mm_67101.1	chr7	69909578	69909594	-	1	NA	Intergenic	Intergenic	413492	NR_045940	73796	Mm.410832	NR_045940	ENSMUSG00000108885	4930402F11Rik	-	RIKEN cDNA 4930402F11 gene	ncRNA
mm_27395.1	chr3	51210181	51210194	-	1	NA	Intergenic	B4A|SINE|B4	-14260	NM_009834	12457	Mm.86541	NM_009834	ENSMUSG00000023087	Noct	AU043840|Ccr4|Ccrn4l	nocturnin	protein-coding
mm_126739.1	chr15	85671810	85671816	+	1	NA	Intergenic	CpG	-31960	NR_110483	102800312	Mm.33117	NR_110483		Lncppara	Lincppara|Mirlet7bhg|linc-Ppara	long noncoding RNA near Ppara	ncRNA
mm_145527.1	chr18	60638555	60638567	+	1	NA	Intergenic	IMPB_01|Satellite|Satellite	-14256	NM_177340	104027	Mm.252321	NM_177340	ENSMUSG00000043079	Synpo	9030217H17Rik|9130229N11|9330140I15Rik|AW046661	synaptopodin	protein-coding
mm_23776.1	chr3	76637530	76637557	+	1	NA	intron (NM_001253719, intron 12 of 15)	(T)n|Simple_repeat|Simple_repeat	561960	NM_001253719	213262	Mm.379337	NM_178673	ENSMUSG00000034098	Fstl5	9130207J01Rik	follistatin-like 5	protein-coding
mm_102888.1	chr11	69411740	69411754	-	1	NA	intron (NM_001017426, intron 1 of 22)	CpG	1928	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_125689.1	chr15	66807507	66807528	+	1	NA	intron (NM_001029841, intron 1 of 7)	intron (NM_001029841, intron 1 of 7)	24312	NM_001029841	20491	Mm.7601	NM_009192	ENSMUSG00000022372	Sla	Slap|Slap-1	src-like adaptor	protein-coding
mm_127367.1	chr15	100747876	100747883	+	1	NA	Intergenic	RMER17C|LTR|ERVK	-13868	NM_021530	59033	Mm.209856	NM_021530	ENSMUSG00000023032	Slc4a8	AW493845|C230026C11|NDCBE|kNBC-3	solute carrier family 4 (anion exchanger), member 8	protein-coding
mm_65777.1	chr7	28766432	28766442	-	1	NA	promoter-TSS (NM_001122766)	promoter-TSS (NM_001122766)	207	NM_001306222	18036	Mm.220333	NM_010908	ENSMUSG00000030595	Nfkbib	I(Kappa)B(beta)|I-kappa-B-beta|IKB-beta|IKappaBbeta|IkB|IkBb|NF-kappa-BIB|ikB-B	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, beta	protein-coding
mm_111865.1	chr12	107985291	107985296	-	1	NA	intron (NM_001079883, intron 2 of 3)	intron (NM_001079883, intron 2 of 3)	18121	NM_001079883	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_107575.1	chr12	44439047	44439069	+	1	NA	intron (NM_001146031, intron 2 of 27)	intron (NM_001146031, intron 2 of 27)	110173	NM_001146031	319504	Mm.208439	NM_176930	ENSMUSG00000020598	Nrcam	Bravo|C030017F07Rik|C130076O07Rik|mKIAA0343	neuronal cell adhesion molecule	protein-coding
mm_159943.1	chr6	83711155	83711155	+	1	NA	promoter-TSS (NR_002873)	promoter-TSS (NR_002873)	-109	NM_011912	24113	Mm.307165	NM_011912	ENSMUSG00000034777	Vax2	Dres93	ventral anterior homeobox 2	protein-coding
mm_139170.1	chr17	47558406	47558432	+	1	NA	intron (NM_001081635, intron 1 of 6)	B3A|SINE|B2	-35048	NM_007632	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_28476.1	chr3	92083133	92083147	-	1	NA	promoter-TSS (NM_008508)	promoter-TSS (NM_008508)	2	NM_008508	16939	Mm.1121	NM_008508	ENSMUSG00000043165	Lor	AI036317|S77319	loricrin	protein-coding
mm_10365.1	chr2	11705731	11705767	+	1	NA	promoter-TSS (NM_001271500)	promoter-TSS (NM_001271500)	37	NM_001271500	16169	Mm.200196	NM_008358	ENSMUSG00000023206	Il15ra	AA690181|IL-15RA	interleukin 15 receptor, alpha chain	protein-coding
mm_12688.1	chr2	76028154	76028178	+	1	NA	intron (NM_001081033, intron 17 of 19)	intron (NM_001081033, intron 17 of 19)	-46199	NM_030188	78802	Mm.282339	NM_030188	ENSMUSG00000075271	Ttc30a1	4930506L13Rik	tetratricopeptide repeat domain 30A1	protein-coding
mm_1662.1	chr1	74716272	74716275	+	1	NA	intron (NM_024264, intron 1 of 8)	AT_rich|Low_complexity|Low_complexity	2738	NM_024264	104086	Mm.85083	NM_024264	ENSMUSG00000026170	Cyp27a1	1300013A03Rik|Cyp27	cytochrome P450, family 27, subfamily a, polypeptide 1	protein-coding
mm_125110.1	chr15	27924297	27924309	+	1	NA	intron (NM_001081302, intron 1 of 56)	intron (NM_001081302, intron 1 of 56)	101545	NM_001081302	223435	Mm.485422	NM_001081302	ENSMUSG00000022263	Trio	6720464I07Rik|AA408740|Solo	triple functional domain (PTPRF interacting)	protein-coding
mm_34600.1	chr4	150236817	150236819	+	1	NA	promoter-TSS (NM_001025388).2	promoter-TSS (NM_001025388).2	-379	NM_023119	13806	Mm.70666	NM_023119	ENSMUSG00000063524	Eno1	0610008I15|AL022784|Eno-1|MBP-1	enolase 1, alpha non-neuron	protein-coding
mm_144815.1	chr18	36288067	36288079	+	1	NA	exon (NM_008989, exon 2 of 2)	exon (NM_008989, exon 2 of 2)	6911	NM_008989	19290	Mm.231802	NM_008989	ENSMUSG00000043991	Pura	CAGER-1|Pur-alpha|ssCRE-BP	purine rich element binding protein A	protein-coding
mm_42633.1	chr5	118478581	118478591	+	1	NA	Intergenic	Intergenic	-82133	NM_001347445	76199	Mm.206238	NM_172424	ENSMUSG00000018076	Med13l	2210413I17Rik|6330591G05Rik|9030618F05Rik|Thrap2|Trap240L|mKIAA1025	mediator complex subunit 13-like	protein-coding
mm_112690.1	chr13	16756179	16756182	+	1	NA	Intergenic	Intergenic	744329	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_169648.1	chr15	5266861	5266861	+	1	NA	Intergenic	L1Md_T|LINE|L1	-22674	NM_008965	19219	Mm.18509	NM_008965	ENSMUSG00000039942	Ptger4	EP4|Ptgerep4	prostaglandin E receptor 4 (subtype EP4)	protein-coding
mm_150669.1	chr19	42046790	42046791	+	1	NA	intron (NM_026152, intron 1 of 6)	intron (NM_026152, intron 1 of 6)	939	NM_026152	67432	Mm.24196	NM_026152	ENSMUSG00000025176	Hoga1	0610010D20Rik|Dhdpsl|Npl2	4-hydroxy-2-oxoglutarate aldolase 1	protein-coding
mm_69622.1	chr7	137314260	137314266	-	1	NA	5' UTR (NM_001113414, exon 1 of 16)	5' UTR (NM_001113414, exon 1 of 16)	182	NM_001113415	13593	Mm.258708	NM_010096	ENSMUSG00000010476	Ebf3	3110018A08Rik|O/E-2|mKIAA4201	early B cell factor 3	protein-coding
mm_152307.1	chr19	9135604	9135635	-	1	NA	promoter-TSS (NM_025610)	promoter-TSS (NM_025610)	-53	NM_025610	66514	Mm.272847	NM_025610	ENSMUSG00000024654	Asrgl1	2410004D18Rik|ALP|ALP1|AU040643|AW060375	asparaginase like 1	protein-coding
mm_136400.1	chr16	93490288	93490294	-	1	NA	Intergenic	L1MA6|LINE|L1	-31419	NR_040494	72264	Mm.396204	NR_040494	ENSMUSG00000099968	1700029J03Rik	-	RIKEN cDNA 1700029J03 gene	ncRNA
mm_126608.1	chr15	82899019	82899035	+	1	NA	promoter-TSS (NR_027799)	promoter-TSS (NR_027799)	-53	NR_045068	100504637	Mm.440928	NR_045068	ENSMUSG00000100199	Gm20324	-	predicted gene, 20324	ncRNA
mm_121658.1	chr14	12343314	12343318	-	1	NA	intron (NM_080433, intron 4 of 4)	intron (NM_080433, intron 4 of 4)	2549	NM_080433	54713	Mm.34644	NM_080433	ENSMUSG00000021743	Fezf2	AI451466|AI852056|Fez|Fezl|Zfp312	Fez family zinc finger 2	protein-coding
mm_79118.1	chr9	46292056	46292099	+	1	NA	exon (NM_146000, exon 8 of 10)	exon (NM_146000, exon 8 of 10)	9065	NM_146000	215051	Mm.32648	NM_146000	ENSMUSG00000032077	Bud13	AV305342|D030060M11Rik	BUD13 homolog	protein-coding
mm_91861.1	chr10	59441785	59441800	-	1	NA	promoter-TSS (NM_010959)	promoter-TSS (NM_010959)	-13	NM_010959	18302	Mm.123013	NM_010959	ENSMUSG00000009654	Oit3	EF-9|LZP	oncoprotein induced transcript 3	protein-coding
mm_24884.1	chr3	96104479	96104489	+	1	NA	promoter-TSS (NM_001025614)	promoter-TSS (NM_001025614)	-43	NM_001025613	229603	Mm.272336	NM_001025613	ENSMUSG00000038495	Otud7b	2900060B22Rik|4930463P07Rik|AI462125|CEZANNE|Trabid2|Za20d1	OTU domain containing 7B	protein-coding
mm_60944.1	chr7	46920188	46920194	+	1	NA	promoter-TSS (NM_021884)	promoter-TSS (NM_021884)	-261	NM_021884	22088	Mm.241334	NM_021884	ENSMUSG00000014402	Tsg101	AI255943|CC2	tumor susceptibility gene 101	protein-coding
mm_9246.1	chr1	171345632	171345653	-	1	NA	promoter-TSS (NM_012049)	promoter-TSS (NM_012049)	3	NM_001242580	27045	Mm.12915	NM_012049	ENSMUSG00000013997	Nit1	AI255805|ESTM30|W57327	nitrilase 1	protein-coding
mm_100851.1	chr11	5803707	5803728	-	1	NA	promoter-TSS (NM_018870)	promoter-TSS (NM_018870)	79	NM_018870	56012	Mm.219627	NM_018870	ENSMUSG00000020475	Pgam2	-	phosphoglycerate mutase 2	protein-coding
mm_120623.1	chr14	70457448	70457544	+	1	NA	promoter-TSS (NM_145981)	promoter-TSS (NM_145981)	-21	NM_145981	105653	Mm.192598	NM_145981	ENSMUSG00000003469	Phyhip	AW049870|C630010D02Rik|Lnap1ip|PAHX-AP#1|PAHX-AP1	phytanoyl-CoA hydroxylase interacting protein	protein-coding
mm_121367.1	chr14	117386107	117386154	+	1	NA	intron (NM_001079844, intron 2 of 9)	intron (NM_001079844, intron 2 of 9)	460833	NM_011821	23888	Mm.440025	NM_011821	ENSMUSG00000058571	Gpc6	-	glypican 6	protein-coding
mm_124465.1	chr14	121287123	121287139	-	1	NA	3' UTR (NM_145465, exon 11 of 11)	3' UTR (NM_145465, exon 11 of 11)	92099	NM_145465	223255	Mm.390756	NM_145465	ENSMUSG00000063410	Stk24	1810013H02Rik|C76483|MST-3|Mst3|STE20	serine/threonine kinase 24	protein-coding
mm_85.1	chr1	7068364	7068364	+	1	NA	Intergenic	Intergenic	-20556	NM_183028	319263	Mm.21539	NM_183028	ENSMUSG00000051285	Pcmtd1	8430411F12Rik|A030012M09Rik	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding
mm_94396.1	chr11	5574108	5574115	+	1	NA	intron (NM_023816, intron 3 of 26)	intron (NM_023816, intron 3 of 26)	4427	NM_023816	76389	Mm.67300	NM_023816	ENSMUSG00000020481	Ankrd36	1700008J08Rik|1700012M14Rik|Ankrd48	ankyrin repeat domain 36	protein-coding
mm_128418.1	chr15	45114661	45114676	-	1	NA	5' UTR (NM_026200, exon 1 of 3)	5' UTR (NM_026200, exon 1 of 3)	266	NM_026200	67498	Mm.300079	NM_026200	ENSMUSG00000022342	Kcnv1	2700023A03Rik|vibe	potassium channel, subfamily V, member 1	protein-coding
mm_83837.1	chr9	54249818	54249829	-	1	NA	Intergenic	MamTip2|DNA|hAT-Tip100	-36663	NM_177350	235379	Mm.123549	NM_177350	ENSMUSG00000046167	Gldn	CRG-L2|Clom|Colm|Crgl2|Crlg2	gliomedin	protein-coding
mm_135555.1	chr16	49855518	49855572	-	1	NA	promoter-TSS (NM_010581)	promoter-TSS (NM_010581)	-109	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_17684.1	chr2	32312339	32312387	-	1	NA	intron (NM_001301737, intron 19 of 21)	CpG-7982	-5902	NR_128563	104795665		NR_128563	ENSMUSG00000092765	Gm23363	Mir3154|mir-3154|mmu-mir-3154	predicted gene, 23363	ncRNA
mm_26931.1	chr3	20262564	20262566	-	1	NA	exon (NM_029706, exon 9 of 11)	exon (NM_029706, exon 9 of 11)	13168	NM_029706	76703	Mm.34692	NM_029706	ENSMUSG00000011463	Cpb1	0910001A18Rik|1810063F02Rik|2210008M23Rik|AI504870	carboxypeptidase B1 (tissue)	protein-coding
mm_62527.1	chr7	102233089	102233108	+	1	NA	intron (NR_111937, intron 2 of 5)	intron (NR_111937, intron 2 of 5)	10070	NR_111937	233575	Mm.302013	NM_145583	ENSMUSG00000030990	Pgap2	1810006G21Rik|C76649|Frag1	post-GPI attachment to proteins 2	protein-coding
mm_92692.1	chr10	80666965	80666980	-	1	NA	3' UTR (NM_021462, exon 14 of 14)	3' UTR (NM_021462, exon 14 of 14)	9321	NM_021462	17347	Mm.42126	NM_021462	ENSMUSG00000020190	Mknk2	2010016G11Rik|Gprk7|Mnk2	MAP kinase-interacting serine/threonine kinase 2	protein-coding
mm_79729.1	chr9	62341894	62341926	+	1	NA	intron (NM_009672, intron 1 of 6)	CpG	567	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	protein-coding
mm_132732.1	chr16	43694363	43694373	+	1	NA	Intergenic	Intergenic	-30184	NM_001146325	100043314	Mm.390896	NM_001146325	ENSMUSG00000071552	Tigit	ENSMUSG00000071552|Vstm3	T cell immunoreceptor with Ig and ITIM domains	protein-coding
mm_135434.1	chr16	45382948	45382958	-	1	NA	3' UTR (NM_010818, exon 6 of 6)	3' UTR (NM_010818, exon 6 of 6)	26100	NM_010818	17470	Mm.245851	NM_010818	ENSMUSG00000022661	Cd200	Mox2|OX2	CD200 antigen	protein-coding
mm_47635.1	chr5	125304292	125304319	-	1	NA	exon (NM_001205082, exon 2 of 12)	exon (NM_001205082, exon 2 of 12)	36789	NM_016741	20778	Mm.282242	NM_016741	ENSMUSG00000037936	Scarb1	AI120173|CD36|Cd36l1|Chohd1|Cla-1|Cla1|D5Ertd460e|Hdlq1|Hlb398|SR-B1|SR-BI|SRBI|Srb1|mSR-BI	scavenger receptor class B, member 1	protein-coding
mm_152296.1	chr19	9083727	9083743	-	1	NA	TTS (NM_011681)	TTS (NM_011681)	4221	NM_011681	22287	Mm.2258	NM_011681	ENSMUSG00000024653	Scgb1a1	CC10|CC16|CCSP|PCB-BP|UG|UGB|Utg	secretoglobin, family 1A, member 1 (uteroglobin)	protein-coding
mm_34301.1	chr4	141746770	141746787	+	1	NA	5' UTR (NM_001081408, exon 1 of 7)	5' UTR (NM_001081408, exon 1 of 7)	103	NM_001081408	75986	Mm.30032	NM_001081408	ENSMUSG00000040706	Agmat	5033405N08Rik	agmatine ureohydrolase (agmatinase)	protein-coding
mm_89488.1	chr10	93691096	93691096	+	1	NA	intron (NM_021320, intron 3 of 9)	intron (NM_021320, intron 3 of 9)	-7774	NR_038017	100504069	Mm.391412	NR_038017	ENSMUSG00000085723	Gm15915	OTTMUSG00000027787	predicted gene 15915	ncRNA
mm_15084.1	chr2	153191795	153191808	+	1	NA	intron (NM_133847, intron 8 of 17)	intron (NM_133847, intron 8 of 17)	30500	NM_133847	99237	Mm.330674	NM_133847	ENSMUSG00000068040	Tm9sf4	AA986553|AU045326|B930079E06|mKIAA0255	transmembrane 9 superfamily protein member 4	protein-coding
mm_41390.1	chr5	90769595	90769606	+	1	NA	3' UTR (NM_023785, exon 3 of 3)	3' UTR (NM_023785, exon 3 of 3)	1082	NM_023785	57349	Mm.293614	NM_023785	ENSMUSG00000029372	Ppbp	2400003M24Rik|AI854500|CTAP3|CTAPIII|Cxcl7|LA-PF4|LDGF|MDGF|NAP-2|NAP-2-L1|Scyb7|TGB|TGB1|THBGB1|b-TG1|beta-TG	pro-platelet basic protein	protein-coding
mm_78503.1	chr9	32745308	32745310	+	1	NA	intron (NM_011808, intron 6 of 7)	intron (NM_011808, intron 6 of 7)	49267	NM_001038642	23871	Mm.292415	NM_011808	ENSMUSG00000032035	Ets1	AI196000|AI448617|D230050P06|Ets-1|Tpl1|vs	E26 avian leukemia oncogene 1, 5' domain	protein-coding
mm_3654.1	chr1	153099358	153099360	+	1	NA	intron (NM_175460, intron 8 of 10)	intron (NM_175460, intron 8 of 10)	87088	NM_008485	16782	Mm.329272	NM_008485	ENSMUSG00000026479	Lamc2	AA589349	laminin, gamma 2	protein-coding
mm_124898.1	chr15	10486009	10486077	+	1	NA	promoter-TSS (NM_011232)	promoter-TSS (NM_011232)	5	NM_001289447	19355	Mm.38376	NM_011232	ENSMUSG00000022248	Rad1	mRAD1	RAD1 checkpoint DNA exonuclease	protein-coding
mm_52518.1	chr6	115422082	115422103	+	1	NA	promoter-TSS (NM_011146)	promoter-TSS (NM_011146)	26	NM_011146	19016	Mm.3020	NM_011146	ENSMUSG00000000440	Pparg	Nr1c3|PPAR-gamma|PPAR-gamma2|PPARgamma|PPARgamma2	peroxisome proliferator activated receptor gamma	protein-coding
mm_100878.1	chr11	5972685	5972708	-	1	NA	exon (NM_001174054, exon 19 of 21)	exon (NM_001174054, exon 19 of 21)	16938	NM_019661	56418	Mm.294821	NM_019661	ENSMUSG00000002741	Ykt6	0610042I15Rik|1810013M05Rik|AW105923	YKT6 v-SNARE homolog (S. cerevisiae)	protein-coding
mm_159077.1	chr2	26225323	26225323	-	1	NA	intron (NM_001302956, intron 3 of 11)	intron (NM_001302956, intron 3 of 11)	12076	NM_153559	227638	Mm.116769	NM_153559	ENSMUSG00000036327	Qsox2	BC030934|Qscn6l1|Soxn	quiescin Q6 sulfhydryl oxidase 2	protein-coding
mm_72180.1	chr8	72319677	72319699	+	1	NA	exon (NM_008452, exon 2 of 3)	exon (NM_008452, exon 2 of 3)	626	NM_008452	16598	Mm.26938	NM_008452	ENSMUSG00000055148	Klf2	Lklf	Kruppel-like factor 2 (lung)	protein-coding
mm_122544.1	chr14	47724043	47724044	-	1	NA	exon (NM_001293636, exon 34 of 40)	exon (NM_001293636, exon 34 of 40)	60287	NM_001347522	16709	Mm.3110	NM_008477	ENSMUSG00000021843	Ktn1	-	kinectin 1	protein-coding
mm_86576.1	chr10	12956062	12956075	+	1	NA	intron (NM_029075, intron 1 of 2)	intron (NM_029075, intron 1 of 2)	8191	NM_029075	74732	Mm.248648	NM_029075	ENSMUSG00000039232	Stx11	5830405C08Rik	syntaxin 11	protein-coding
mm_142858.1	chr17	51813293	51813355	-	1	NA	intron (NM_001163632, intron 1 of 10)	CpG	-1270	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_26303.1	chr3	142510735	142510743	+	1	NA	intron (NM_153564, intron 10 of 10)	intron (NM_153564, intron 10 of 10)	13805	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_66784.1	chr7	47008247	47008275	-	1	NA	5' UTR (NM_175318, exon 1 of 6)	5' UTR (NM_175318, exon 1 of 6)	153	NM_175318	101685	Mm.155687	NM_175318	ENSMUSG00000049516	Spty2d1	5830435K17Rik|AI852426|P16H6	SPT2, Suppressor of Ty, domain containing 1 (S. cerevisiae)	protein-coding
mm_92037.1	chr10	62494772	62494783	-	1	NA	3' UTR (NM_011157, exon 3 of 3)	3' UTR (NM_011157, exon 3 of 3)	-7972	NM_133672	30930	Mm.260703	NM_133672	ENSMUSG00000020078	Vps26a	AA407240|HB58|Vps26	VPS26 retromer complex component A	protein-coding
mm_19885.1	chr2	114050346	114050354	-	1	NA	exon (NM_009608, exon 3 of 7)	exon (NM_009608, exon 3 of 7)	2525	NM_009608	11464	Mm.686	NM_009608	ENSMUSG00000068614	Actc1	Actc-1	actin, alpha, cardiac muscle 1	protein-coding
mm_162163.1	chrX	95166503	95166503	-	1	NA	promoter-TSS (NM_001290384)	promoter-TSS (NM_001290384)	36	NM_001290385	236915	Mm.44841	NM_001033329	ENSMUSG00000025656	Arhgef9	9630036L12Rik	CDC42 guanine nucleotide exchange factor (GEF) 9	protein-coding
mm_170347.1	chr18	50859062	50859070	-	1	NA	Intergenic	Intergenic	-258832	NM_001081224	71373	Mm.63546	NM_001081224	ENSMUSG00000073565	Prr16	5430406M13Rik|AI607429	proline rich 16	protein-coding
mm_22433.1	chr2	181689001	181689006	-	1	NA	TTS (NM_009326)	TTS (NM_009326)	2814	NM_001291205	56470	Mm.274366	NM_026446	ENSMUSG00000002458	Rgs19	2610042F04Rik|AI324841|AW547781|GAIP	regulator of G-protein signaling 19	protein-coding
mm_59316.1	chr7	25291084	25291098	+	1	NA	exon (NM_027882, exon 14 of 20)	exon (NM_027882, exon 14 of 20)	6864	NM_008776	18476	Mm.597	NM_008776	ENSMUSG00000005447	Pafah1b3	Pafahg|mus[g]	platelet-activating factor acetylhydrolase, isoform 1b, subunit 3	protein-coding
mm_101996.1	chr11	51220409	51220443	-	1	NA	promoter-TSS (NR_110444)	promoter-TSS (NR_110444)	-8	NR_110444	71297	Mm.390420	NR_110444	ENSMUSG00000086646	Platr20	5133400J02Rik	pluripotency associated transcript 20	ncRNA
mm_163507.1	chr12	113140667	113140670	+	1	NA	promoter-TSS (NM_001347443)	promoter-TSS (NM_001347443)	63	NM_001347443	68337	Mm.133825	NM_024223	ENSMUSG00000006356	Crip2	0610010I23Rik|AW743261|C77570|CRP2|CRP4|Crp|ESP1|Hlp	cysteine rich protein 2	protein-coding
mm_98401.1	chr11	94328098	94328108	+	1	NA	5' UTR (NM_027799, exon 1 of 5)	5' UTR (NM_027799, exon 1 of 5)	102	NM_146024	71452	Mm.141054	NM_027799	ENSMUSG00000020864	Ankrd40	1110011C06Rik|5530600A18Rik|Gcap15	ankyrin repeat domain 40	protein-coding
mm_161212.1	chr13	63565554	63565554	-	1	NA	5' UTR (NM_008957, exon 1 of 24)	5' UTR (NM_008957, exon 1 of 24)	181	NM_008957	19206	Mm.228798	NM_008957	ENSMUSG00000021466	Ptch1	A230106A15Rik|Ptc|Ptc1|Ptch|mes	patched 1	protein-coding
mm_165776.1	chr3	129332274	129332310	-	1	NA	exon (NM_007934, exon 1 of 20)	exon (NM_007934, exon 1 of 20)	457	NM_007934	13809	Mm.1193	NM_007934	ENSMUSG00000028024	Enpep	6030431M22Rik|APA|Bp-1/6C3|Ly-51|Ly51	glutamyl aminopeptidase	protein-coding
mm_100597.1	chr11	121146147	121146160	+	1	NA	promoter-TSS (NM_028602)	promoter-TSS (NM_028602)	10	NM_028602	73679	Mm.390423	NM_028602	ENSMUSG00000039329	Tex19.1	2410081M02Rik|Tex19|Tex19a|mTex19.1	testis expressed gene 19.1	protein-coding
mm_62623.1	chr7	107567446	107567461	+	1	NA	promoter-TSS (NM_172907)	promoter-TSS (NM_172907)	20	NM_172907	244198	Mm.77425	NM_172907	ENSMUSG00000051041	Olfml1	6720478C22|AV321997|BC047207|MVAL564|ONT2|mONT2	olfactomedin-like 1	protein-coding
mm_4845.1	chr1	186967640	186967646	+	1	NA	5' UTR (NM_033077, exon 1 of 1)	5' UTR (NM_033077, exon 1 of 1)	227	NM_033077	110957	Mm.108054	NM_033077	ENSMUSG00000039224	D1Pas1	Pl10	DNA segment, Chr 1, Pasteur Institute 1	protein-coding
mm_62336.1	chr7	100494892	100494896	+	1	NA	intron (NM_011671, intron 2 of 7)	intron (NM_011671, intron 2 of 7)	1536	NM_011671	22228	Mm.171378	NM_011671	ENSMUSG00000033685	Ucp2	Slc25a8	uncoupling protein 2 (mitochondrial, proton carrier)	protein-coding
mm_172562.1	chr8	107263282	107263294	-	1	NA	intron (NR_039557, intron 1 of 3).3	intron (NR_039557, intron 1 of 3).3	7124	NR_039557	100628577		NR_039557	ENSMUSG00000093061	Mir5098	mmu-mir-5098|mu-mir-5098	microRNA 5098	ncRNA
mm_54841.1	chr6	42586471	42586479	-	1	NA	TTS (NM_203396)	TTS (NM_203396)	10897	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_140909.1	chr17	24165045	24165067	-	1	NA	intron (NR_037854, intron 1 of 2)	intron (NR_037854, intron 1 of 2)	-1323	NM_172935	245847	Mm.87319	NM_172935	ENSMUSG00000036820	Amdhd2	5730457F11Rik	amidohydrolase domain containing 2	protein-coding
mm_166593.1	chr6	57485115	57485125	+	1	NA	Intergenic	Intergenic	50306	NM_175523	243382	Mm.396893	NM_175523	ENSMUSG00000037826	Ppm1k	2900063A19Rik|A930026L03Rik|PP2Cm	protein phosphatase 1K (PP2C domain containing)	protein-coding
mm_94116.1	chr10	128626673	128626689	-	1	NA	promoter-TSS (NM_013765)	promoter-TSS (NM_013765)	-175	NM_013765	27370	Mm.32118	NM_013765	ENSMUSG00000025362	Rps26	-	ribosomal protein S26	protein-coding
mm_76336.1	chr8	84713834	84713846	-	1	NA	exon (NM_010906, exon 8 of 9)	exon (NM_010906, exon 8 of 9)	12383	NM_008535	17095	Mm.4925	NM_008535	ENSMUSG00000034041	Lyl1	Lyl-1|bHLHa18	lymphoblastomic leukemia 1	protein-coding
mm_141128.1	chr17	26201306	26201312	-	1	NA	promoter-TSS (NM_008113)	promoter-TSS (NM_008113)	41	NM_008113	14570	Mm.1383	NM_008113	ENSMUSG00000073433	Arhgdig	Gdi5|RIP2|Rho-GDI-3|Rho-GDI2	Rho GDP dissociation inhibitor (GDI) gamma	protein-coding
mm_31102.1	chr4	41762336	41762351	+	1	NA	promoter-TSS (NM_010549)	promoter-TSS (NM_010549)	33	NM_010549	16157	Mm.193451	NM_010549	ENSMUSG00000073889	Il11ra1	AI314697|GP130|Il-11ra|Il11ra|Il11ra2|NR1	interleukin 11 receptor, alpha chain 1	protein-coding
mm_84222.1	chr9	61925475	61925483	-	1	NA	intron (NM_024245, intron 15 of 22)	intron (NM_024245, intron 15 of 22)	-10969	NM_018853	56040	Mm.3158	NM_018853	ENSMUSG00000007892	Rplp1	2410042H16Rik|Arpp1|C430017H15Rik	ribosomal protein, large, P1	protein-coding
mm_156541.1	chrX	151169565	151169576	+	1	NA	Intergenic	CpG	-28508	NM_001271679	279561	Mm.441474	NM_001271678	ENSMUSG00000041245	Wnk3	Prkwnk3|Wnk3-ps	WNK lysine deficient protein kinase 3	protein-coding
mm_9380.1	chr1	172210461	172210473	-	1	NA	exon (NM_009813, exon 11 of 11)	exon (NM_009813, exon 11 of 11)	-3663	NM_011063	18611	Mm.544	NM_011063	ENSMUSG00000013698	Pea15a	Mat1|PEA-15|Pea15|Pkcs15	phosphoprotein enriched in astrocytes 15A	protein-coding
mm_97168.1	chr11	75510107	75510128	+	1	NA	promoter-TSS (NM_001029938)	promoter-TSS (NM_001029938)	23	NM_001029938	280408	Mm.41416	NM_001029938	ENSMUSG00000038195	Rilp	AI835553|Gm857	Rab interacting lysosomal protein	protein-coding
mm_172493.1	chr7	59228852	59228853	+	1	NA	promoter-TSS (NM_001033962)	promoter-TSS (NM_001033962)	100	NM_011668	22215	Mm.9002	NM_011668	ENSMUSG00000025326	Ube3a	4732496B02|5830462N02Rik|A130086L21Rik|Hpve6a|mKIAA4216	ubiquitin protein ligase E3A	protein-coding
mm_66275.1	chr7	37563653	37563656	-	1	NA	intron (NM_172385, intron 4 of 5)	L1MEc|LINE|L1	206098	NM_172385	243937	Mm.322505	NM_172385	ENSMUSG00000043456	Zfp536	9630010P11Rik|Znf536|mKIAA0390	zinc finger protein 536	protein-coding
mm_148809.1	chr19	6276900	6276936	+	1	NA	promoter-TSS (NM_010119)	promoter-TSS (NM_010119)	22	NM_010119	13660	Mm.30169	NM_010119	ENSMUSG00000024772	Ehd1	AA409636|Past1|RME-1	EH-domain containing 1	protein-coding
mm_810.1	chr1	45795520	45795530	+	1	NA	promoter-TSS (NM_028599)	promoter-TSS (NM_028599)	24	NM_028599	73674	Mm.270376	NM_028599	ENSMUSG00000025995	Wdr75	1300003A18Rik|2410118I19Rik|C77608	WD repeat domain 75	protein-coding
mm_36569.1	chr4	87806333	87806345	-	1	NA	promoter-TSS (NM_029931)	promoter-TSS (NM_029931)	-16	NM_029931	70122	Mm.288898	NM_027326	ENSMUSG00000028496	Mllt3	2210011H10Rik|2610012I03Rik|3830408D16Rik|Af9|D4Ertd321e	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 3	protein-coding
mm_170345.1	chr1	85012090	85012111	+	1	NA	Intergenic	Intergenic	-77017	NM_027921	71781	Mm.158754	NM_027921	ENSMUSG00000026220	Slc16a14	1110004H10Rik	solute carrier family 16 (monocarboxylic acid transporters), member 14	protein-coding
mm_166703.1	chr6	115759727	115759732	+	1	NA	promoter-TSS (NM_144805)	promoter-TSS (NM_144805)	-730	NM_144805	94346	Mm.29739	NM_144805	ENSMUSG00000059900	Tmem40	9030407H20Rik|AV091463|W64236	transmembrane protein 40	protein-coding
mm_10260.1	chr2	9376281	9376325	+	1	NA	Intergenic	MIR|SINE|MIR	186788	NR_038180	73438	Mm.23558	NR_038180	ENSMUSG00000085580	1700061F12Rik	-	RIKEN cDNA 1700061F12 gene	ncRNA
mm_9679.1	chr1	178332188	178332204	-	1	NA	exon (NM_016805, exon 7 of 14)	exon (NM_016805, exon 7 of 14)	5588	NM_016805	51810	Mm.86589	NM_016805	ENSMUSG00000039630	Hnrnpu	AA408410|AI256620|AL024194|AL024437|AW557595|C86794|Hnrpu|SAFA|Sp120|hnRNP U	heterogeneous nuclear ribonucleoprotein U	protein-coding
mm_144526.1	chr18	25065670	25065697	+	1	NA	intron (NM_175276, intron 15 of 26)	intron (NM_175276, intron 15 of 26)	100282	NM_001142697	66648	Mm.263189	NM_001004361	ENSMUSG00000024269	Tpgs2	5730437P09Rik|5730494M16Rik|AI666318|Pgs2	tubulin polyglutamylase complex subunit 2	protein-coding
mm_74517.1	chr8	8745756	8745797	-	1	NA	Intergenic	LTR104_Mam|LTR|Gypsy	-55239	NM_176849	234023	Mm.251655	NM_176849	ENSMUSG00000040459	Arglu1	9430010O03Rik|C130008N12	arginine and glutamate rich 1	protein-coding
mm_102881.1	chr11	69410608	69410616	-	1	NA	intron (NM_001017426, intron 1 of 22)	CpG	3063	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_94352.1	chr11	4902280	4902291	+	1	NA	intron (NM_172438, intron 4 of 19)	intron (NM_172438, intron 4 of 19)	6942	NM_172438	107829	Mm.28969	NM_172438	ENSMUSG00000034274	Thoc5	1700060C24Rik|A430085L24Rik|Fmip|PK1.3|Sgk2	THO complex 5	protein-coding
mm_154049.1	chr19	55096885	55096888	-	1	NA	intron (NM_008149, intron 2 of 20)	intron (NM_008149, intron 2 of 20)	2561	NM_008149	14732	Mm.210196	NM_008149	ENSMUSG00000024978	Gpam	GPAT|GPAT1	glycerol-3-phosphate acyltransferase, mitochondrial	protein-coding
mm_126790.1	chr15	86326006	86326014	+	1	NA	intron (NM_145476, intron 8 of 12)	(CA)n|Simple_repeat|Simple_repeat	111551	NM_145476	223754	Mm.28904	NM_145476	ENSMUSG00000051864	Tbc1d22a	BC023106|D15Ertd781e	TBC1 domain family, member 22a	protein-coding
mm_52932.1	chr6	122933772	122933791	+	1	NA	exon (NM_199311, exon 6 of 6)	exon (NM_199311, exon 6 of 6)	11933	NM_199311	269799	Mm.297275	NM_199311	ENSMUSG00000049037	Clec4a1	BC049354|Dcir4	C-type lectin domain family 4, member a1	protein-coding
mm_131339.1	chr16	13392420	13392420	+	1	NA	intron (NM_153588, intron 6 of 14)	B4A|SINE|B4	33999	NM_153588	239719	Mm.270643	NM_153588	ENSMUSG00000009569	Mkl2	ENSMUSG00000075401|Gt4-1|MRTF-B|Mrtfb|mKIAA1243	MKL/myocardin-like 2	protein-coding
mm_77414.1	chr8	120634359	120634374	-	1	NA	promoter-TSS (NM_197988)	promoter-TSS (NM_197988)	16	NM_197988	68918	Mm.473736	NM_197988	ENSMUSG00000043687	1190005I06Rik	-	RIKEN cDNA 1190005I06 gene	protein-coding
mm_129136.1	chr15	76199813	76199831	-	1	NA	promoter-TSS (NM_201392)	promoter-TSS (NM_201392)	13	NM_201391	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
mm_96704.1	chr11	69655030	69655055	+	1	NA	promoter-TSS (NM_009235)	promoter-TSS (NM_009235)	5	NM_009235	20670	Mm.347499	NM_009235	ENSMUSG00000041287	Sox15	-	SRY (sex determining region Y)-box 15	protein-coding
mm_117532.1	chr13	83503534	83503543	-	1	NA	promoter-TSS (NM_025282)	promoter-TSS (NM_025282)	-496	NM_001347572	17260	Mm.24001	NM_025282	ENSMUSG00000005583	Mef2c	5430401D19Rik|9930028G15Rik|AV011172|Mef2	myocyte enhancer factor 2C	protein-coding
mm_72891.1	chr8	90493105	90493116	+	1	NA	Intergenic	Intergenic	-144858	NM_172913	244579	Mm.302755	NM_172913	ENSMUSG00000043668	Tox3	500-9|BC052044|C230068E13|CAGF9|Tnrc9	TOX high mobility group box family member 3	protein-coding
mm_26414.1	chr3	142609296	142609301	+	1	NA	intron (NM_010259, intron 8 of 10)	RLTR13D1|LTR|ERVK	-11365	NM_010260	14469	Mm.24038	NM_010260	ENSMUSG00000028270	Gbp2	-	guanylate binding protein 2	protein-coding
mm_56905.1	chr6	119196591	119196597	-	1	NA	promoter-TSS (NM_009781)	promoter-TSS (NM_009781)	-185	NM_001255999	12288	Mm.41628	NM_009781	ENSMUSG00000051331	Cacna1c	Cav1.2|Cchl1a1|D930026N18Rik|MBC|MELC-CC	calcium channel, voltage-dependent, L type, alpha 1C subunit	protein-coding
mm_30487.1	chr3	155091151	155091153	-	1	NA	intron (NM_029330, intron 2 of 3)	intron (NM_029330, intron 2 of 3)	2226	NM_029330	75540	Mm.35218	NM_029330	ENSMUSG00000053870	Fpgt	1700016E03Rik	fucose-1-phosphate guanylyltransferase	protein-coding
mm_66665.1	chr7	45717891	45717918	-	1	NA	promoter-TSS (NM_001172561)	promoter-TSS (NM_001172561)	98	NM_203280	56632	Mm.24222	NM_020011	ENSMUSG00000057342	Sphk2	C76851	sphingosine kinase 2	protein-coding
mm_98693.1	chr11	96299208	96299222	+	1	NA	promoter-TSS (NM_008269)	promoter-TSS (NM_008269)	44	NM_008269	15414	Mm.215	NM_008269	ENSMUSG00000000690	Hoxb6	Hox-2.2	homeobox B6	protein-coding
mm_104323.1	chr11	93956000	93956006	-	1	NA	promoter-TSS (NM_001077529)	promoter-TSS (NM_001077529)	-220	NM_001077529	18103	Mm.1260	NM_008705	ENSMUSG00000020857	Nme2	NM23-H2|NM23B|nm23-M2	NME/NM23 nucleoside diphosphate kinase 2	protein-coding
mm_173024.1	chrX	103129584	103129590	+	1	NA	Intergenic	L1Md_F3|LINE|L1	57077	NM_008671	17954	Mm.388694	NM_008671	ENSMUSG00000082229	Nap1l2	Bpx	nucleosome assembly protein 1-like 2	protein-coding
mm_141208.1	chr17	27101431	27101455	-	1	NA	intron (NM_080553, intron 23 of 57)	intron (NM_080553, intron 23 of 57)	10198	NR_106142	102465779		NR_106142	ENSMUSG00000098826	Mir7677	Gm27400|mmu-mir-7677	microRNA 7677	ncRNA
mm_164677.1	chr17	46572108	46572110	-	1	NA	intron (NM_175168, intron 16 of 19)	GA-rich|Low_complexity|Low_complexity	-15947	NM_020493	20807	Mm.45044	NM_020493	ENSMUSG00000015605	Srf	AW049942|AW240594	serum response factor	protein-coding
mm_146419.1	chr18	84719487	84719507	+	1	NA	promoter-TSS (NM_173770)	promoter-TSS (NM_173770)	-745	NM_173770	240479	Mm.472378	NM_173770	ENSMUSG00000047992	Fam69c	B230399E16Rik	family with sequence similarity 69, member C	protein-coding
mm_35788.1	chr4	46472123	46472168	-	1	NA	exon (NM_130889, exon 7 of 7)	exon (NM_130889, exon 7 of 7)	-17184	NM_053179	94181	Mm.249349	NM_053179	ENSMUSG00000028334	Nans	4632418E04Rik|BB056474|Sas	N-acetylneuraminic acid synthase (sialic acid synthase)	protein-coding
mm_79114.1	chr9	46270553	46270573	+	1	NA	exon (NM_080434, exon 4 of 4)	exon (NM_080434, exon 4 of 4)	1955	NM_080434	66113	Mm.29738	NM_080434	ENSMUSG00000032079	Apoa5	1300007O05Rik|Apoav|RAP3	apolipoprotein A-V	protein-coding
mm_164358.1	chr16	22617996	22618032	-	1	NA	intron (NM_001346673, intron 2 of 23)	intron (NM_001346673, intron 2 of 23)	39217	NM_138650	110197	Mm.194986	NM_138650	ENSMUSG00000022861	Dgkg	2900055E17Rik|90kDa|AI854428|Dagk3|E430001K23Rik|mKIAA4131	diacylglycerol kinase, gamma	protein-coding
mm_29147.1	chr3	105932666	105932679	-	1	NA	promoter-TSS (NM_001033780)	promoter-TSS (NM_001033780)	-8	NM_001033780	433638	Mm.239081	NM_001033780	ENSMUSG00000074342	I830077J02Rik	-	RIKEN cDNA I830077J02 gene	protein-coding
mm_93726.1	chr10	119240104	119240130	-	1	NA	promoter-TSS (NM_027994)	promoter-TSS (NM_027994)	-62	NM_027994	71902	Mm.203965	NM_027994	ENSMUSG00000020114	Cand1	2310038O07Rik|6330512O03Rik|AI195005|AI846556|D10Ertd516e|Tp120a|mKIAA0829	cullin associated and neddylation disassociated 1	protein-coding
mm_111489.1	chr12	98901416	98901472	-	1	NA	promoter-TSS (NM_001081191)	promoter-TSS (NM_001081191)	40	NM_001081191	319670	Mm.390484	NM_001081191	ENSMUSG00000051166	Eml5	BC027154|C130068M19Rik	echinoderm microtubule associated protein like 5	protein-coding
mm_132349.1	chr16	33891966	33891990	+	1	NA	intron (NM_010580, intron 5 of 14)	intron (NM_010580, intron 5 of 14)	62313	NM_001145884	16419	Mm.6424	NM_010580	ENSMUSG00000022817	Itgb5	AA475909|AI874634|ESTM23|[b]-5|[b]5|[b]5A|[b]5B|beta-5|beta5	integrin beta 5	protein-coding
mm_161206.1	chr13	59706181	59706181	-	1	NA	promoter-TSS (NM_028157)	promoter-TSS (NM_028157)	16	NM_028157	72219	Mm.233883	NM_028157	ENSMUSG00000050876	Spata31d1a	1700013B16Rik|Fam75d1a|Fam75d3	spermatogenesis associated 31 subfamily D, member 1A	protein-coding
mm_118160.1	chr13	105293005	105293015	-	1	NA	promoter-TSS (NM_027934)	promoter-TSS (NM_027934)	4	NM_027934	71816	Mm.317015	NM_027934	ENSMUSG00000021720	Rnf180	3110001E11Rik|Rines	ring finger protein 180	protein-coding
mm_154757.1	chrX	10717579	10717596	+	1	NA	5' UTR (NM_001166635, exon 1 of 2)	5' UTR (NM_001166635, exon 1 of 2)	222	NM_001166635	68041	Mm.29429	NM_026524	ENSMUSG00000008035	Mid1ip1	3110038L01Rik|Mig12|S14R	Mid1 interacting protein 1 (gastrulation specific G12-like (zebrafish))	protein-coding
mm_123409.1	chr14	63860269	63860293	-	1	NA	promoter-TSS (NM_028228)	promoter-TSS (NM_028228)	-31	NM_028228	72400	Mm.379214	NM_028228	ENSMUSG00000021958	Pinx1	2210403I16Rik|2610028A01Rik|67-11-3|AU024023|LPTS|LPTS1	PIN2/TERF1 interacting, telomerase inhibitor 1	protein-coding
mm_56039.1	chr6	86684482	86684508	-	1	NA	promoter-TSS (NM_025665)	promoter-TSS (NM_025665)	-4	NM_025665	66618	Mm.182650	NM_025665	ENSMUSG00000001158	Snrnp27	2610209M04Rik|AI449063|AU022368|Ry1	small nuclear ribonucleoprotein 27 (U4/U6.U5)	protein-coding
mm_97849.1	chr11	83069279	83069296	+	1	NA	exon (NM_011408, exon 2 of 2)	exon (NM_011408, exon 2 of 2)	4175	NM_011408	20556	Mm.278689	NM_011408	ENSMUSG00000072620	Slfn2	Shlf2	schlafen 2	protein-coding
mm_103356.1	chr11	74851187	74851202	-	1	NA	exon (NM_197943, exon 22 of 23)	exon (NM_197943, exon 22 of 23)	17000	NR_105891	102465558		NR_105891	ENSMUSG00000098317	Mir6926	Gm27949|mmu-mir-6926	microRNA 6926	ncRNA
mm_92573.1	chr10	79913686	79913703	-	1	NA	exon (NM_177994, exon 2 of 8)	exon (NM_177994, exon 2 of 8)	3236	NM_177994	109284	Mm.300416	NM_177994	ENSMUSG00000035781	R3hdm4	AI503502|C030046I01Rik	R3H domain containing 4	protein-coding
mm_50399.1	chr6	48718769	48718779	+	1	NA	intron (NM_146167, intron 1 of 1)	intron (NM_146167, intron 1 of 1)	153	NM_146167	231932	Mm.30479	NM_146167	ENSMUSG00000043931	Gimap7	IAN7|Ian3	GTPase, IMAP family member 7	protein-coding
mm_62289.1	chr7	99906517	99906525	+	1	NA	exon (NM_001164258, exon 12 of 19)	exon (NM_001164258, exon 12 of 19)	47303	NM_001164258	446101	Mm.440757	NM_001164258	ENSMUSG00000035211	Xrra1	AI449753	X-ray radiation resistance associated 1	protein-coding
mm_123894.1	chr14	73049065	73049077	-	1	NA	promoter-TSS (NM_001162412)	promoter-TSS (NM_001162412)	43	NM_133720	70086	Mm.158324	NM_133720	ENSMUSG00000033470	Cysltr2	2300001H05Rik|CYSLT2R|Cltr2|Cyslt2	cysteinyl leukotriene receptor 2	protein-coding
mm_153356.1	chr19	40163115	40163118	-	1	NA	intron (NM_145499, intron 6 of 8)	intron (NM_145499, intron 6 of 8)	24170	NM_145499	226105	Mm.29119	NM_145499	ENSMUSG00000060613	Cyp2c70	-	cytochrome P450, family 2, subfamily c, polypeptide 70	protein-coding
mm_154871.1	chrX	20681334	20681366	+	1	NA	exon (NM_009457, exon 23 of 26)	exon (NM_009457, exon 23 of 26)	-6604	NM_001310456	18555	Mm.102574	NM_011049	ENSMUSG00000031065	Cdk16	Crk5|Pctaire1|Pctk1	cyclin-dependent kinase 16	protein-coding
mm_2509.1	chr1	106223903	106223909	+	1	NA	intron (NM_133821, intron 1 of 16)	RLTR12B|LTR|ERVK	52037	NM_133821	98432	Mm.24115	NM_133821	ENSMUSG00000044340	Phlpp1	AI836256|Phlpp|Plekhe1|SCOP|mKIAA0606	PH domain and leucine rich repeat protein phosphatase 1	protein-coding
mm_43070.1	chr5	124446237	124446248	+	1	NA	promoter-TSS (NM_001310727)	promoter-TSS (NM_001310727)	-462	NM_001310727	67956	Mm.137966	NM_030241	ENSMUSG00000049327	Kmt5a	2410195B05Rik|AA617402|AW536475|PR-SET7|PR/SET07|Setd8	lysine methyltransferase 5A	protein-coding
mm_108348.1	chr12	80480230	80480244	+	1	NA	intron (NM_133798, intron 2 of 8)	intron (NM_133798, intron 2 of 8)	17142	NM_133798	97827	Mm.206631	NM_133798	ENSMUSG00000032705	Exd2	4930539P14Rik|C85658|Exdl2	exonuclease 3'-5' domain containing 2	protein-coding
mm_60386.1	chr7	44473976	44473992	+	1	NA	Intergenic	IMPB_01|Satellite|Satellite	3637	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_161143.1	chr13	21981159	21981159	+	1	NA	promoter-TSS (NM_001162929)	promoter-TSS (NM_001162929)	-22	NM_001162928	195236	Mm.204664	NM_001162928	ENSMUSG00000016982	Pom121l2	Gm24	POM121 membrane glycoprotein-like 2 (rat)	protein-coding
mm_163384.1	chr12	53737717	53737753	+	1	NA	intron (NM_013780, intron 4 of 11)	intron (NM_013780, intron 4 of 11)	466139	NM_028133	112407	Mm.133037	NM_028133	ENSMUSG00000035105	Egln3	2610021G09Rik|AI505553|AI648162|Hif-p4h-3|Phd3|SM-20	egl-9 family hypoxia-inducible factor 3	protein-coding
mm_134424.1	chr16	17894109	17894115	-	1	NA	promoter-TSS (NM_009435)	promoter-TSS (NM_009435)	-91	NM_009435	22114	Mm.439725	NM_009435	ENSMUSG00000041566	Tssk1	Stk22a|TSK-1|Tsk1|Tssk|Tssk1b	testis-specific serine kinase 1	protein-coding
mm_142381.1	chr17	44736445	44736469	-	1	NA	promoter-TSS (NM_001271631)	promoter-TSS (NM_001271631)	191	NM_001145920	12393	Mm.391013	NM_009820	ENSMUSG00000039153	Runx2	AML3|Cbf|Cbfa-1|Cbfa1|LS3|Osf2|PEBP2aA|Pebp2a1|Pebpa2a	runt related transcription factor 2	protein-coding
mm_16943.1	chr2	15049160	15049170	-	1	NA	5' UTR (NM_001165942, exon 1 of 4)	5' UTR (NM_001165942, exon 1 of 4)	147	NM_001165942	74455	Mm.478923	NM_028950	ENSMUSG00000026707	Nsun6	4933403D21Rik|4933414E04Rik|NOPD1	NOL1/NOP2/Sun domain family member 6	protein-coding
mm_87364.1	chr10	43902232	43902237	+	1	NA	promoter-TSS (NM_001081054)	promoter-TSS (NM_001081054)	427	NM_130892	170728	Mm.390253	NM_130892	ENSMUSG00000019864	Rtn4ip1	D10Ertd690e|NIMP	reticulon 4 interacting protein 1	protein-coding
mm_17236.1	chr2	25581643	25581656	-	1	NA	Intergenic	Intergenic	-1550	NM_001005424	381353	Mm.379511	NM_001005424	ENSMUSG00000029419	Gm996	-	predicted gene 996	protein-coding
mm_6633.1	chr1	78537499	78537507	-	1	NA	intron (NM_026713, intron 6 of 6)	intron (NM_026713, intron 6 of 6)	26443	NM_026713	68393	Mm.41325	NM_026713	ENSMUSG00000012187	Mogat1	0610030A14Rik|1110064N14Rik|Dgat2l|Dgat2l1|MGAT1|WI1-2612I11.1|mDC2	monoacylglycerol O-acyltransferase 1	protein-coding
mm_153364.1	chr19	40271507	40271577	-	1	NA	promoter-TSS (NM_016861)	promoter-TSS (NM_016861)	74	NM_016861	54132	Mm.5567	NM_016861	ENSMUSG00000055044	Pdlim1	CLP36|Clim1|mClim1	PDZ and LIM domain 1 (elfin)	protein-coding
mm_15592.1	chr2	160394512	160394534	+	1	NA	Intergenic	Intergenic	-27458	NM_010658	16658	Mm.330745	NM_010658	ENSMUSG00000074622	Mafb	Kreisler|Krml|Krml1|kr	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein B (avian)	protein-coding
mm_77572.1	chr8	123432554	123432562	-	1	NA	Intergenic	MuLV-int|LTR|ERV1	-10398	NM_001253784	23854	Mm.275127	NM_054046	ENSMUSG00000001482	Def8	AI449518|D8Ertd713e|DEF-8	differentially expressed in FDCP 8	protein-coding
mm_141670.1	chr17	33904051	33904067	-	1	NA	Intergenic	Intergenic	-1076	NR_040470	474160	Mm.206186	NR_040470	ENSMUSG00000092349	Platr17	-	pluripotency associated transcript 17	ncRNA
mm_37814.1	chr4	130936137	130936139	-	1	NA	TTS (NM_010686)	TTS (NM_010686)	-8247	NM_010769	17180	Mm.271796	NM_010769	ENSMUSG00000040533	Matn1	CMP|Crtm|Mat1|matrilin-1	matrilin 1, cartilage matrix protein	protein-coding
mm_85830.1	chr9	110459236	110459246	-	1	NA	intron (NM_177771, intron 1 of 9)	ID4_|SINE|ID	17453	NM_177771	270201	Mm.41744	NM_177771	ENSMUSG00000054792	Klhl18	A930041K15|AW545966	kelch-like 18	protein-coding
mm_167831.1	chr9	124424078	124424173	-	1	NA	non-coding (NR_015516, exon 1 of 1)	non-coding (NR_015516, exon 1 of 1)	338	NR_015516	75135	Mm.476814	NR_015516		4930526I15Rik	1600027J15Rik	RIKEN cDNA 4930526I15 gene	ncRNA
mm_138739.1	chr17	36994310	36994320	+	1	NA	Intergenic	RMER10A|LTR|ERVL	-4811	NM_001115075	240095	Mm.246609	NM_001115075	ENSMUSG00000024459	H2-M5	CRW2|D130003B22Rik|H-2M5	histocompatibility 2, M region locus 5	protein-coding
mm_144088.1	chr17	94834769	94834804	-	1	NA	promoter-TSS (NR_045964)	promoter-TSS (NR_045964)	13	NR_045964	100038746	Mm.456686	NR_045963	ENSMUSG00000066057	Gm1976	100038868	predicted gene 1976	ncRNA
mm_104397.1	chr11	94499963	94500002	-	1	NA	promoter-TSS (NM_027984)	promoter-TSS (NM_027984)	-8	NM_027984	71889	Mm.248620	NM_027984	ENSMUSG00000010080	Epn3	2310022G12Rik	epsin 3	protein-coding
mm_16521.1	chr2	181506703	181506706	+	1	NA	intron (NM_025482, intron 4 of 7)	intron (NM_025482, intron 4 of 7)	9562	NM_001291204	66314	Mm.136648	NM_025482	ENSMUSG00000000827	Tpd52l2	2810411G23Rik|AU016537|C86069|D54	tumor protein D52-like 2	protein-coding
mm_45382.1	chr5	66132133	66132157	-	1	NA	intron (NM_001127382, intron 2 of 7)	B1_Mur4|SINE|Alu	18833	NM_001291226	245945	Mm.36863	NM_139065	ENSMUSG00000070780	Rbm47	9530077J19Rik	RNA binding motif protein 47	protein-coding
mm_55453.1	chr6	67339640	67339657	-	1	NA	promoter-TSS (NM_001311141)	promoter-TSS (NM_001311141)	46	NM_001311141	16162	Mm.188337	NM_008354	ENSMUSG00000018341	Il12rb2	A930027I18Rik|IL-12RB2|Ifnm	interleukin 12 receptor, beta 2	protein-coding
mm_36269.1	chr4	63622422	63622448	-	1	NA	promoter-TSS (NM_029324)	promoter-TSS (NM_029324)	-6	NM_029324	75524	Mm.38543	NM_029324	ENSMUSG00000058935	1700018C11Rik	bM230C2.3	RIKEN cDNA 1700018C11 gene	protein-coding
mm_97123.1	chr11	74925817	74925833	+	1	NA	promoter-TSS (NM_001163311)	promoter-TSS (NM_001163311)	-27	NM_001163311	27364	Mm.131443	NM_013761	ENSMUSG00000001323	Srr	M100034|Rgsc34|Srs	serine racemase	protein-coding
mm_40452.1	chr5	53602540	53602556	+	1	NA	intron (NM_001277116, intron 3 of 12)	intron (NM_001277116, intron 3 of 12)	12062	NM_001080927	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_66644.1	chr7	45655641	45655650	-	1	NA	intron (NM_001271993, intron 1 of 2)	intron (NM_001271993, intron 1 of 2)	10749	NM_018876	14344	Mm.290046	NM_018876	ENSMUSG00000055978	Fut2	-	fucosyltransferase 2	protein-coding
mm_114464.1	chr13	67729232	67729244	+	1	NA	promoter-TSS (NM_145622)	promoter-TSS (NM_145622)	-24	NR_027969	68271	Mm.145530	NM_026649		Zfp85os	4930441O14Rik	zinc finger protein 85, opposite strand	ncRNA
mm_68776.1	chr7	122067040	122067080	-	1	NA	promoter-TSS (NM_138589)	promoter-TSS (NM_138589)	26	NM_026140	67417	Mm.45171	NM_026140	ENSMUSG00000030871	Ears2	3230401I01Rik|mKIAA1970	glutamyl-tRNA synthetase 2, mitochondrial	protein-coding
mm_167244.1	chr8	22340020	22340021	+	1	NA	intron (NM_199257, intron 18 of 27)	B3A|SINE|B2	56579	NM_199257	234129	Mm.450553	NM_181851	ENSMUSG00000031481	Tpte	Pten2	transmembrane phosphatase with tensin homology	protein-coding
mm_26706.1	chr3	157946996	157947041	+	1	NA	promoter-TSS (NM_001013806)	promoter-TSS (NM_001013806)	-448	NM_001013806	433667	Mm.265806	NM_001013806	ENSMUSG00000039988	Ankrd13c	AI505652|AU022220	ankyrin repeat domain 13c	protein-coding
mm_18321.1	chr2	57114906	57114916	-	1	NA	5' UTR (NM_013613, exon 1 of 8)	5' UTR (NM_013613, exon 1 of 8)	127	NM_013613	18227	Mm.3507	NM_013613	ENSMUSG00000026826	Nr4a2	HZF-3|NOT|Nurr1|RNR-1|TINOR|TINUR	nuclear receptor subfamily 4, group A, member 2	protein-coding
mm_19867.1	chr2	114047329	114047339	-	1	NA	TTS (NM_009608)	TTS (NM_009608)	5541	NM_009608	11464	Mm.686	NM_009608	ENSMUSG00000068614	Actc1	Actc-1	actin, alpha, cardiac muscle 1	protein-coding
mm_117680.1	chr13	94155696	94155701	-	1	NA	intron (NM_172589, intron 2 of 3)	intron (NM_172589, intron 2 of 3)	97902	NM_172589	218454	Mm.316553	NM_172589	ENSMUSG00000045312	Lhfpl2	6030465B15|AI447312|AW050335|mKIAA0206|vgim	lipoma HMGIC fusion partner-like 2	protein-coding
mm_73345.1	chr8	105349296	105349369	+	1	NA	5' UTR (NM_001081332, exon 1 of 16)	5' UTR (NM_001081332, exon 1 of 16)	1074	NM_001081332	277973	Mm.334766	NM_001081332	ENSMUSG00000014786	Slc9a5	Gm696	solute carrier family 9 (sodium/hydrogen exchanger), member 5	protein-coding
mm_69351.1	chr7	130264220	130264233	-	1	NA	intron (NM_001347638, intron 1 of 15)	intron (NM_001347638, intron 1 of 15)	2582	NM_010207	14183	Mm.16340	NM_010207	ENSMUSG00000030849	Fgfr2	AU043015|AW556123|Bek|Fgfr-2|Fgfr-7|Fgfr7|KGFR|KGFRTr|svs	fibroblast growth factor receptor 2	protein-coding
mm_28614.1	chr3	94886921	94886942	-	1	NA	promoter-TSS (NM_008945)	promoter-TSS (NM_008945)	27	NM_008945	19172	Mm.368	NM_008945	ENSMUSG00000005779	Psmb4	Pros-27	proteasome (prosome, macropain) subunit, beta type 4	protein-coding
mm_68567.1	chr7	115664055	115664058	-	1	NA	intron (NM_001025560, intron 5 of 15)	intron (NM_001025560, intron 5 of 15)	137553	NM_001277328	20679	Mm.323365	NM_011445	ENSMUSG00000051910	Sox6	AI987981|SOX-LZ	SRY (sex determining region Y)-box 6	protein-coding
mm_52897.1	chr6	122644267	122644270	+	1	NA	Intergenic	Intergenic	17844	NM_139218	73708	Mm.27982	NM_139218	ENSMUSG00000046323	Dppa3	2410075G02Rik|PCG7|PGC7|Stella	developmental pluripotency-associated 3	protein-coding
mm_98671.1	chr11	96283024	96283040	+	1	NA	exon (NM_010461, exon 1 of 2)	exon (NM_010461, exon 1 of 2)	1127	NM_010461	15416	Mm.4822	NM_010461	ENSMUSG00000056648	Hoxb8	Hox-2.4	homeobox B8	protein-coding
mm_95580.1	chr11	52816368	52816370	+	1	NA	intron (NM_177059, intron 3 of 15)	intron (NM_177059, intron 3 of 15)	51663	NM_177059	320027	Mm.44518	NM_177059	ENSMUSG00000036264	Fstl4	B230374F23Rik|SPIG1|mKIAA1061	follistatin-like 4	protein-coding
mm_116253.1	chr13	34002744	34002783	-	1	NA	promoter-TSS (NM_009068)	promoter-TSS (NM_009068)	31	NM_001243192	20719	Mm.252210	NM_009254	ENSMUSG00000060147	Serpinb6a	4930482L21Rik|D330015H01Rik|PI-6|Serpinb6|Spi3|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 6a	protein-coding
mm_99567.1	chr11	103894108	103894150	+	1	NA	intron (NM_008740, intron 8 of 20)	intron (NM_008740, intron 8 of 20)	59927	NM_008740	18195	Mm.260117	NM_008740	ENSMUSG00000034187	Nsf	AI316878|AU020090|AU067812|SKD2	N-ethylmaleimide sensitive fusion protein	protein-coding
mm_158103.1	chrX	101794430	101794448	-	1	NA	Intergenic	CpG	-54946	NM_001163610	100042480	Mm.232	NM_001163610	ENSMUSG00000079481	Nhsl2	1110062M06Rik|6430511F03|AI225852|AW488865|EG621083|ENSMUSG00000073037|Gm10456	NHS-like 2	protein-coding
mm_110549.1	chr12	55489810	55489824	-	1	NA	3' UTR (NM_010907, exon 6 of 6)	3' UTR (NM_010907, exon 6 of 6)	2830	NM_010907	18035	Mm.170515	NM_010907	ENSMUSG00000021025	Nfkbia	AI462015|Nfkbi	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, alpha	protein-coding
mm_52470.1	chr6	114248092	114248118	+	1	NA	3' UTR (NM_172890, exon 14 of 14)	3' UTR (NM_172890, exon 14 of 14)	-34530	NM_178703	232333	Mm.5260	NM_178703	ENSMUSG00000030310	Slc6a1	A730043E01|GABATHG|GABATR|GAT-1|Gabt|Gabt1|Gat1|XT-1|Xtrp1	solute carrier family 6 (neurotransmitter transporter, GABA), member 1	protein-coding
mm_55465.1	chr6	67535829	67535870	-	1	NA	promoter-TSS (NM_020047)	promoter-TSS (NM_020047)	-27	NM_020047	56753	Mm.439913	NM_020047	ENSMUSG00000051397	Tacstd2	C80403|EGP-1|GA733-1|Ly97|TROP2	tumor-associated calcium signal transducer 2	protein-coding
mm_122058.1	chr14	30345803	30345805	-	1	NA	intron (NM_001302637, intron 3 of 48)	intron (NM_001302637, intron 3 of 48)	7682	NM_001302637	12289	Mm.9772	NM_028981	ENSMUSG00000015968	Cacna1d	8430418G19Rik|C79217|Cach3|Cacn4|Cacnl1a2|Cav1.3|Cchl1a|Cchl1a2|D-LTCC	calcium channel, voltage-dependent, L type, alpha 1D subunit	protein-coding
mm_46589.1	chr5	107725367	107725377	-	1	NA	intron (NM_001267621, intron 1 of 6)	CpG	433	NM_001267621	14581	Mm.2078	NM_010278	ENSMUSG00000029275	Gfi1	AW495828|Gfi-1|Pal-1|Pal1	growth factor independent 1	protein-coding
mm_74992.1	chr8	27202479	27202481	-	1	NA	promoter-TSS (NM_029674)	promoter-TSS (NM_029674)	67	NM_029674	76615	Mm.272794	NM_029674	ENSMUSG00000039720	Got1l1	1700083M11Rik	glutamic-oxaloacetic transaminase 1-like 1	protein-coding
mm_44235.1	chr5	5265700	5265720	-	1	NA	5' UTR (NM_001310448, exon 1 of 14)	5' UTR (NM_001310448, exon 1 of 14)	358	NM_001310448	18647	Mm.389061	NM_011074	ENSMUSG00000028926	Cdk14	Pftk1|mKIAA0834	cyclin-dependent kinase 14	protein-coding
mm_93327.1	chr10	99261710	99261726	-	1	NA	Intergenic	CpG	-1513	NM_026268	67603	Mm.1791	NM_026268	ENSMUSG00000019960	Dusp6	1300019I03Rik|MKP-3|MKP3|PYST1	dual specificity phosphatase 6	protein-coding
mm_132294.1	chr16	33380865	33380902	+	1	NA	promoter-TSS (NR_045709)	promoter-TSS (NR_045709)	108	NM_011749	22661	Mm.392667	NM_011749	ENSMUSG00000022811	Zfp148	2210405J08Rik|AI480666|AW045217|BERF-1|BFCOL1|ZBP-89|Znf148	zinc finger protein 148	protein-coding
mm_145623.1	chr18	61109623	61109626	+	1	NA	exon (NM_001037859, exon 3 of 22)	exon (NM_001037859, exon 3 of 22)	4052	NM_001037859	12978	Mm.22574	NM_007779	ENSMUSG00000024621	Csf1r	AI323359|CD115|CSF-1R|Csfmr|Fim-2|Fim2|Fms|M-CSF-R|M-CSFR	colony stimulating factor 1 receptor	protein-coding
mm_150833.1	chr19	44756901	44756924	+	1	NA	promoter-TSS (NM_011037)	promoter-TSS (NM_011037)	-482	NM_011037	18504	Mm.192158	NM_011037	ENSMUSG00000004231	Pax2	Opdc|Pax-2	paired box 2	protein-coding
mm_37029.1	chr4	114987221	114987256	-	1	NA	promoter-TSS (NM_025647)	promoter-TSS (NM_025647)	-10	NM_025647	66588	Mm.294159	NM_025647	ENSMUSG00000028719	Cmpk1	0610011D08Rik|CK|Cmpk|UMP-CMPk	cytidine monophosphate (UMP-CMP) kinase 1	protein-coding
mm_158211.1	chrX	105875408	105875425	-	1	NA	exon (NM_009530, exon 9 of 35)	exon (NM_009530, exon 9 of 35)	53956	NM_009530	22589	Mm.10141	NM_009530	ENSMUSG00000031229	Atrx	4833408C14Rik|AI447451|ATR2|DXHXS6677E|HP1-BP38|Hp1bp2|Hp1bp38|MRXS3|RAD54L|Rad54|XH2|Xnp|ZNF-HX	alpha thalassemia/mental retardation syndrome X-linked	protein-coding
mm_76840.1	chr8	105289069	105289083	-	1	NA	TTS (NM_177788)	TTS (NM_177788)	452	NM_001166394	74356	Mm.204876	NM_028888	ENSMUSG00000014837	4931428F04Rik	AI426165|Kiaa0895l	RIKEN cDNA 4931428F04 gene	protein-coding
mm_51090.1	chr6	67146238	67146277	+	1	NA	Intergenic	Intergenic	-108850	NM_007836	13197	Mm.72235	NM_007836	ENSMUSG00000036390	Gadd45a	AA545191|Ddit1|GADD45	growth arrest and DNA-damage-inducible 45 alpha	protein-coding
mm_58802.1	chr7	16299888	16299904	+	1	NA	Intergenic	CpG	-9687	NM_133234	170770	Mm.7660	NM_133234	ENSMUSG00000002083	Bbc3	PUMA|PUMA/JFY1	BCL2 binding component 3	protein-coding
mm_113547.1	chr13	38010803	38010842	+	1	NA	intron (NM_027724, intron 11 of 12)	intron (NM_027724, intron 11 of 12)	-16632	NM_025965	107513	Mm.426670	NM_025965	ENSMUSG00000021427	Ssr1	2510001K09Rik|6330400D04|AI159733|AI452176|SSR|TRAPA	signal sequence receptor, alpha	protein-coding
mm_145116.1	chr18	44334063	44334081	+	1	NA	promoter-TSS (NM_001033621)	promoter-TSS (NM_001033621)	-2	NM_001033621	58916	Mm.143804	NM_001033621	ENSMUSG00000024471	Myot	5530402I04Rik|Ttid	myotilin	protein-coding
mm_168942.1	chr12	72049282	72049301	-	1	NA	Intergenic	Intergenic	21700	NM_181752	238252	Mm.390508	NM_181752	ENSMUSG00000043398	Gpr135	PAFR	G protein-coupled receptor 135	protein-coding
mm_39957.1	chr5	32136023	32136033	+	1	NA	promoter-TSS (NM_008037)	promoter-TSS (NM_008037)	-444	NM_008037	14284	Mm.24684	NM_008037	ENSMUSG00000029135	Fosl2	Fra-2	fos-like antigen 2	protein-coding
mm_23914.1	chr3	83044211	83044236	+	1	NA	exon (NM_181849, exon 5 of 8)	exon (NM_181849, exon 5 of 8)	5640	NM_181849	110135	Mm.30063	NM_181849	ENSMUSG00000033831	Fgb	2510049G14Rik	fibrinogen beta chain	protein-coding
mm_48654.1	chr5	145872401	145872423	-	1	NA	intron (NM_007818, intron 4 of 12)	Lx5|LINE|L1	7442	NM_007818	13112	Mm.332844	NM_007818	ENSMUSG00000056035	Cyp3a11	AI256190|Cyp3a|IIIAm1|Pcn	cytochrome P450, family 3, subfamily a, polypeptide 11	protein-coding
mm_35659.1	chr4	43558387	43558421	-	1	NA	intron (NM_011602, intron 1 of 56)	intron (NM_011602, intron 1 of 56)	4179	NM_011602	21894	Mm.208601	NM_011602	ENSMUSG00000028465	Tln1	Tln	talin 1	protein-coding
mm_70170.1	chr7	143628112	143628176	-	1	NA	promoter-TSS (NM_175649)	promoter-TSS (NM_175649)	-299	NM_175649	244237	Mm.247498	NM_175649	ENSMUSG00000045362	Tnfrsf26	Tnfrh3|Tnfrsf24	tumor necrosis factor receptor superfamily, member 26	protein-coding
mm_127275.1	chr15	99725721	99725737	+	1	NA	TTS (NM_010271)	TTS (NM_010271)	111	NM_183256	66379	Mm.5265	NM_183256	ENSMUSG00000023020	Cox14	2310016M24Rik|AA959804	cytochrome c oxidase assembly protein 14	protein-coding
mm_161968.1	chr19	9895382	9895382	-	1	NA	exon (NM_016692, exon 2 of 18)	exon (NM_016692, exon 2 of 18)	4151	NM_016692	16319	Mm.29755	NM_016692	ENSMUSG00000024660	Incenp	2700067E22Rik|AU019509|C130081E20|C77457	inner centromere protein	protein-coding
mm_25147.1	chr3	102735203	102735236	+	1	NA	promoter-TSS (NM_001243132)	promoter-TSS (NM_001243132)	4	NM_001243132	70747	Mm.27469	NM_027533	ENSMUSG00000027858	Tspan2	6330415F13Rik|B230119D02Rik|tspan-2	tetraspanin 2	protein-coding
mm_100235.1	chr11	117231861	117231890	+	1	NA	intron (NM_001113486, intron 2 of 11)	intron (NM_001113486, intron 2 of 11)	32214	NM_001113486	53860	Mm.38450	NM_017380	ENSMUSG00000059248	Sept9	MSF1|Msf|PNUTL4|Sint1	septin 9	protein-coding
mm_132023.1	chr16	26582341	26582344	+	1	NA	intron (NM_001159318, intron 1 of 10)	(T)n|Simple_repeat|Simple_repeat	637	NM_008364	16180	Mm.253424	NM_008364	ENSMUSG00000022514	Il1rap	6430709H04Rik|AI255955|AV239853|IL-1RAcP	interleukin 1 receptor accessory protein	protein-coding
mm_126518.1	chr15	81872471	81872514	+	1	NA	promoter-TSS (NM_080633)	promoter-TSS (NM_080633)	29	NM_080633	11429	Mm.154581	NM_080633	ENSMUSG00000022477	Aco2	Aco-2|Aco3|D10Wsu183e	aconitase 2, mitochondrial	protein-coding
mm_158734.1	chrX	164027966	164027994	-	1	NA	promoter-TSS (NM_181315)	promoter-TSS (NM_181315)	30	NM_181315	56078	Mm.180953	NM_181315	ENSMUSG00000031373	Car5b	7330410H16Rik|CAVB|Ca5b|CarVb|D730005F19Rik	carbonic anhydrase 5b, mitochondrial	protein-coding
mm_16493.1	chr2	181187276	181187347	+	1	NA	promoter-TSS (NM_025598)	promoter-TSS (NM_025598)	-32	NM_025598	66496	Mm.213943	NM_025598	ENSMUSG00000016344	Ppdpf	0610012G23Rik|2610317A05Rik|2700038C09Rik|3110053G12Rik	pancreatic progenitor cell differentiation and proliferation factor	protein-coding
mm_171599.1	chr4	147738800	147738812	-	1	NA	Intergenic	CpG	-36175	NM_001127188	100503584	Mm.276881	NM_001127188	ENSMUSG00000062518	Zfp534	Gm13159|OTTMUSG00000010681	zinc finger protein 534	protein-coding
mm_69632.1	chr7	137410950	137410970	-	1	NA	promoter-TSS (NM_029886)	promoter-TSS (NM_029886)	-204	NM_029886	77252	Mm.29184	NM_029886	ENSMUSG00000040139	9430038I01Rik	-	RIKEN cDNA 9430038I01 gene	protein-coding
mm_118687.1	chr14	22122434	22122453	+	1	NA	intron (NM_028275, intron 2 of 6)	L1MEg|LINE|L1	102731	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_129696.1	chr15	81586301	81586367	-	1	NA	5' UTR (NM_177821, exon 1 of 31)	5' UTR (NM_177821, exon 1 of 31)	120	NM_177821	328572	Mm.258397	NM_177821	ENSMUSG00000055024	Ep300	A430090G16|A730011L11|KAT3B|p300|p300 HAT	E1A binding protein p300	protein-coding
mm_143524.1	chr17	73870800	73870815	-	1	NA	Intergenic	Intergenic	65966	NM_020578	57440	Mm.18526	NM_020578	ENSMUSG00000024065	Ehd3	Ehd2	EH-domain containing 3	protein-coding
mm_101740.1	chr11	43379109	43379127	-	1	NA	Intergenic	Intergenic	-4657	NR_029558	387164		NR_029558	ENSMUSG00000065601	Mir146	Mirn146|miR-146a|mmu-mir-146	microRNA 146	ncRNA
mm_22970.1	chr3	32708671	32708738	+	1	NA	5' UTR (NM_019673, exon 1 of 14)	5' UTR (NM_019673, exon 1 of 14)	158	NM_019673	56456	Mm.41077	NM_019673	ENSMUSG00000027671	Actl6a	2810432C06Rik|AI851094|ARP4|Actl6|Baf53a|C79802	actin-like 6A	protein-coding
mm_9743.1	chr1	180387477	180387490	-	1	NA	intron (NM_001081175, intron 2 of 7)	intron (NM_001081175, intron 2 of 7)	-56934	NR_003623	277333	Mm.389223	NM_199472		Gm5069	EG277333	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_53492.1	chr6	135198035	135198062	+	1	NA	promoter-TSS (NM_028982)	promoter-TSS (NM_028982)	61	NM_028982	74525	Mm.34182	NM_028982	ENSMUSG00000030207	Fam234b	8430419L09Rik|Kiaa1467|mKIAA1467	family with sequence similarity 234, member B	protein-coding
mm_4494.1	chr1	173641427	173641436	+	1	NA	intron (NM_175026, intron 4 of 6)	MTD|LTR|ERVL-MaLR	10572	NM_175026	236312	Mm.447	NM_175026	ENSMUSG00000043263	Ifi209	4930422C14|AI447904|Ifix|Pyhin-1|Pyhin1	interferon activated gene 209	protein-coding
mm_158556.1	chrX	150177282	150177284	-	1	NA	Intergenic	Intergenic	136081	NM_001101501	333588	Mm.159296	NM_001101501		Gm15104	OTTMUSG00000018998	predicted gene 15104	protein-coding
mm_139694.1	chr17	57441318	57441349	+	1	NA	exon (NM_010130, exon 13 of 22)	exon (NM_010130, exon 13 of 22)	82647	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_55142.1	chr6	51464447	51464450	-	1	NA	exon (NM_016806, exon 8 of 11)	exon (NM_016806, exon 8 of 11)	5446	NM_182650	53379	Mm.155896	NM_016806	ENSMUSG00000004980	Hnrnpa2b1	9130414A06Rik|Hnrpa2|Hnrpa2b1|hnrnp-A	heterogeneous nuclear ribonucleoprotein A2/B1	protein-coding
mm_99796.1	chr11	107546847	107546890	+	1	NA	Intergenic	CpG	-1092	NM_198298	78455	Mm.272047	NM_198298	ENSMUSG00000020721	Helz	3110078M01Rik|9430093I07Rik|9630002H22Rik|AI851979|DRHC	helicase with zinc finger domain	protein-coding
mm_93026.1	chr10	87957587	87957588	-	1	NA	Intergenic	Intergenic	-9084	NR_000040	22172	Mm.391420	NR_000040		Tyms-ps	-	thymidylate synthase, pseudogene	pseudo
mm_140546.1	chr17	6828000	6828021	-	1	NA	Intergenic	CpG	-45230	NM_009510	22350	Mm.277812	NM_009510	ENSMUSG00000052397	Ezr	AW146364|R75297|Vil2|p81	ezrin	protein-coding
mm_41507.1	chr5	92371659	92371661	+	1	NA	intron (NM_001310664, intron 2 of 10)	intron (NM_001310664, intron 2 of 10)	-8364	NR_038116	56066	Mm.131723	NM_019494	ENSMUSG00000060183	Cxcl11	Cxc11|H174|I-tac|Ip9|Itac|Scyb11|Scyb9b|b-R1|betaR1	chemokine (C-X-C motif) ligand 11	protein-coding
mm_25243.1	chr3	103914614	103914624	+	1	NA	exon (NM_172684, exon 1 of 7)	exon (NM_172684, exon 1 of 7)	499	NM_172684	229675	Mm.29366	NM_172684	ENSMUSG00000044098	Rsbn1	C230004D03Rik|E330004N01|Rosbin|Rsbn|Rsbp|mKIAA3002	rosbin, round spermatid basic protein 1	protein-coding
mm_46476.1	chr5	105131616	105131623	-	1	NA	intron (NM_008620, intron 3 of 10)	GA-rich|Low_complexity|Low_complexity	7933	NM_008620	17472	Mm.440525	NM_008620	ENSMUSG00000079363	Gbp4	AW228052|Mag-2|Mpa-2|Mpa2	guanylate binding protein 4	protein-coding
mm_130355.1	chr15	97767245	97767283	-	1	NA	intron (NM_144850, intron 1 of 27)	intron (NM_144850, intron 1 of 27)	402	NM_001177810	223864	Mm.24028	NM_144850	ENSMUSG00000022469	Rapgef3	2310016P22Rik|9330170P05Rik|Epac|Epac1	Rap guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_89004.1	chr10	81620610	81620634	+	1	NA	Intergenic	Intergenic	6700	NM_001163430	50721	Mm.25643	NM_181586	ENSMUSG00000034748	Sirt6	2810449N18Rik|AI043036|Sir2l6	sirtuin 6	protein-coding
mm_3065.1	chr1	134182457	134182477	+	1	NA	promoter-TSS (NM_007695)	promoter-TSS (NM_007695)	63	NM_007695	12654	Mm.38274	NM_007695	ENSMUSG00000064246	Chil1	AW208766|Brp39|Chi3l1|Gp39	chitinase-like 1	protein-coding
mm_19680.1	chr2	103454619	103454625	-	1	NA	3' UTR (NM_009804, exon 13 of 13)	3' UTR (NM_009804, exon 13 of 13)	30531	NM_009804	12359	Mm.4215	NM_009804	ENSMUSG00000027187	Cat	2210418N07|Cas-1|Cas1|Cs-1	catalase	protein-coding
mm_41493.1	chr5	92322985	92322991	+	1	NA	3' UTR (NM_008599, exon 4 of 4)	3' UTR (NM_008599, exon 4 of 4)	5091	NM_008599	17329	Mm.766	NM_008599	ENSMUSG00000029417	Cxcl9	BB139920|CMK|Mig|MuMIG|Scyb9|crg-10	chemokine (C-X-C motif) ligand 9	protein-coding
mm_56001.1	chr6	86484884	86484888	-	1	NA	intron (NR_040292, intron 1 of 1)	B1_Mur1|SINE|Alu	3341	NR_040293	381792	Mm.333223	NR_040292	ENSMUSG00000101655	2310040G24Rik	-	RIKEN cDNA 2310040G24 gene	ncRNA
mm_113382.1	chr13	33017126	33017135	+	1	NA	3' UTR (NM_009256, exon 7 of 7)	3' UTR (NM_009256, exon 7 of 7)	-10284	NM_011452	20706	Mm.45371	NM_011452	ENSMUSG00000021403	Serpinb9b	1600019A21Rik|R86|SPI-CI|Spi10|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 9b	protein-coding
mm_168173.1	chr10	55720605	55720611	-	1	NA	Intergenic	IAPLTR2b|LTR|ERVK	-386309	NM_001163833	73390	Mm.181475	NM_133751	ENSMUSG00000047669	Msl3l2	1700060H10Rik	male-specific lethal 3-like 2 (Drosophila)	protein-coding
mm_166422.1	chr5	137151895	137151902	+	1	NA	Intergenic	Intergenic	-35691	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_7425.1	chr1	119828088	119828092	-	1	NA	intron (NM_019933, intron 1 of 26)	ID4|SINE|ID	8981	NM_019933	19258	Mm.458796	NM_019933	ENSMUSG00000026384	Ptpn4	PTPMEG|Ptn4|TEP|TEP/mPTPMEG|hPTP-MEG	protein tyrosine phosphatase, non-receptor type 4	protein-coding
mm_112411.1	chr13	3634013	3634027	+	1	NA	promoter-TSS (NM_001267724)	promoter-TSS (NM_001267724)	-12	NM_178283	142688	Mm.253061	NM_178283	ENSMUSG00000033781	Asb13	2210015B19Rik|6430573K02Rik|Asb-13|C85285	ankyrin repeat and SOCS box-containing 13	protein-coding
mm_148807.1	chr19	6276781	6276792	+	1	NA	promoter-TSS (NM_010119)	promoter-TSS (NM_010119)	-110	NM_010119	13660	Mm.30169	NM_010119	ENSMUSG00000024772	Ehd1	AA409636|Past1|RME-1	EH-domain containing 1	protein-coding
mm_4245.1	chr1	171389212	171389233	+	1	NA	TTS (NM_027893)	TTS (NM_027893)	262	NM_001005508	226652	Mm.251048	NM_001005508	ENSMUSG00000048865	Arhgap30	6030405P05Rik|Gm102|mFLJ00267	Rho GTPase activating protein 30	protein-coding
mm_108719.1	chr12	87163704	87163729	+	1	NA	exon (NM_001252556, exon 8 of 8)	exon (NM_001252556, exon 8 of 8)	-8231	NR_136901	625237	Mm.390529	NR_136901		Gm6566	EG625237	predicted gene 6566	ncRNA
mm_123908.1	chr14	73325636	73325703	-	1	NA	5' UTR (NM_009029, exon 1 of 27)	5' UTR (NM_009029, exon 1 of 27)	122	NM_009029	19645	Mm.273862	NM_009029	ENSMUSG00000022105	Rb1	Rb|Rb-1|pRb	retinoblastoma 1	protein-coding
mm_137313.1	chr17	24885976	24885991	+	1	NA	promoter-TSS (NM_001163750)	promoter-TSS (NM_001163750)	367	NM_011956	26426	Mm.36718	NM_011956	ENSMUSG00000039183	Nubp2	D17Wsu11e	nucleotide binding protein 2	protein-coding
mm_117895.1	chr13	99424413	99424416	-	1	NA	3' UTR (NM_008634, exon 7 of 7)	3' UTR (NM_008634, exon 7 of 7)	-11588	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_6293.1	chr1	71028622	71028635	-	1	NA	3' UTR (NM_007525, exon 11 of 11)	3' UTR (NM_007525, exon 11 of 11)	74344	NM_007525	12021	Mm.10764	NM_007525	ENSMUSG00000026196	Bard1	ENSMUSG00000060893|ENSMUSG00000073653	BRCA1 associated RING domain 1	protein-coding
mm_110345.1	chr12	36218173	36218187	-	1	NA	promoter-TSS (NM_027699)	promoter-TSS (NM_027699)	22	NM_027699	71156	Mm.250837	NM_027699	ENSMUSG00000020545	Lrrc72	1700108M19Rik|4933421E18Rik	leucine rich repeat containing 72	protein-coding
mm_153620.1	chr19	43986496	43986527	-	1	NA	promoter-TSS (NM_030703)	promoter-TSS (NM_030703)	9	NM_030703	93721	Mm.206774	NM_030703	ENSMUSG00000025196	Cpn1	0610011F20Rik|CPN	carboxypeptidase N, polypeptide 1	protein-coding
mm_27574.1	chr3	58692392	58692412	-	1	NA	promoter-TSS (NM_009174)	promoter-TSS (NM_009174)	-14	NM_009174	20439	Mm.2847	NM_009174	ENSMUSG00000036432	Siah2	AA415433|Sinh2	seven in absentia 2	protein-coding
mm_65500.1	chr7	25722857	25722878	-	1	NA	exon (NM_144922, exon 14 of 15)	exon (NM_144922, exon 14 of 15)	-3814	NM_028771	52132	Mm.278798	NM_028771	ENSMUSG00000002608	Ccdc97	1200014H14Rik|2810446P04Rik|AA545218|D7Ertd462e	coiled-coil domain containing 97	protein-coding
mm_74397.1	chr8	3240987	3240991	-	1	NA	intron (NM_010568, intron 2 of 20)	L1MB3|LINE|L1	38628	NM_010568	16337	Mm.268003	NM_010568	ENSMUSG00000005534	Insr	4932439J01Rik|CD220|D630014A15Rik|IR|IR-A|IR-B	insulin receptor	protein-coding
mm_85825.1	chr9	110422306	110422330	-	1	NA	exon (NM_008694, exon 4 of 4)	exon (NM_008694, exon 4 of 4)	2510	NM_008694	18054	Mm.236225	NM_008694	ENSMUSG00000032484	Ngp	bectenecin	neutrophilic granule protein	protein-coding
mm_162518.1	chr1	156723478	156723482	+	1	NA	Intergenic	B1_Mur1|SINE|Alu	-4570	NM_145413	215015	Mm.229107	NM_145413	ENSMUSG00000033557	Fam20b	C530043G21Rik|mKIAA0475	family with sequence similarity 20, member B	protein-coding
mm_100319.1	chr11	118003519	118003522	+	1	NA	intron (NM_133757, intron 6 of 9)	intron (NM_133757, intron 6 of 9)	1250	NR_105898	102466768		NR_105898	ENSMUSG00000098958	Mir6933	Gm27856|mmu-mir-6933	microRNA 6933	ncRNA
mm_17003.1	chr2	18698873	18698885	-	1	NA	promoter-TSS (NM_001001334)	promoter-TSS (NM_001001334)	-143	NM_001001334	381350	Mm.330024	NM_001001334	ENSMUSG00000037708	Spag6	Spag6l	sperm associated antigen 6	protein-coding
mm_59011.1	chr7	19228377	19228416	+	1	NA	promoter-TSS (NM_207525)	promoter-TSS (NM_207525)	7	NM_207525	403187	Mm.239583	NM_207525	ENSMUSG00000052214	Opa3	D630048P19Rik|Gm1425|Gm472	optic atrophy 3	protein-coding
mm_55207.1	chr6	52217436	52217451	-	1	NA	5' UTR (NM_010455, exon 1 of 2)	5' UTR (NM_010455, exon 1 of 2)	1130	NM_010455	15404	Mm.294826	NM_010455	ENSMUSG00000038236	Hoxa7	AV118143|Hox-1.1|M6	homeobox A7	protein-coding
mm_80731.1	chr9	94473357	94473362	+	1	NA	Intergenic	Intergenic	64722	NM_001033145	68861	Mm.258746	NM_001033145	ENSMUSG00000045414	1190002N15Rik	GoPro49|HASF	RIKEN cDNA 1190002N15 gene	protein-coding
mm_75661.1	chr8	66484016	66484025	-	1	NA	intron (NM_025465, intron 2 of 6)	intron (NM_025465, intron 2 of 6)	2487	NM_025465	66282	Mm.294985	NM_025465	ENSMUSG00000025591	Tma16	1810029B16Rik	translation machinery associated 16	protein-coding
mm_54011.1	chr6	8180215	8180258	-	1	NA	intron (NM_001037865, intron 1 of 34)	intron (NM_001037865, intron 1 of 34)	12381	NM_001037865	213945	Mm.297404	NM_001037865	ENSMUSG00000068794	Col28a1	Col28|Gm466	collagen, type XXVIII, alpha 1	protein-coding
mm_163327.1	chr12	8351366	8351375	-	1	NA	Intergenic	Intergenic	37937	NM_021429	58240	Mm.309954	NM_021429	ENSMUSG00000020605	Hs1bp3	-	HCLS1 binding protein 3	protein-coding
mm_118364.1	chr13	115101873	115101890	-	1	NA	promoter-TSS (NM_001033228)	promoter-TSS (NM_001033228)	83	NM_001033228	109700	Mm.317280	NM_001033228	ENSMUSG00000042284	Itga1	CD49A|E130012M19Rik|Vla1	integrin alpha 1	protein-coding
mm_88187.1	chr10	70006228	70006231	+	1	NA	intron (NM_146005, intron 41 of 42)	intron (NM_146005, intron 41 of 42)	80697	NM_009670	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_118317.1	chr13	113180957	113180967	-	1	NA	promoter-TSS (NM_008196)	promoter-TSS (NM_008196)	-65	NM_008196	14945	Mm.56993	NM_008196	ENSMUSG00000042385	Gzmk	-	granzyme K	protein-coding
mm_21276.1	chr2	156887232	156887240	-	1	NA	promoter-TSS (NM_029983)	promoter-TSS (NM_029983)	-158	NM_029983	77799	Mm.29264	NM_029983	ENSMUSG00000027636	Sla2	A930009E21Rik|AI430952|SLAP-2|SLAP2	Src-like-adaptor 2	protein-coding
mm_80313.1	chr9	74848733	74848735	+	1	NA	non-coding (NR_045284, exon 1 of 3)	non-coding (NR_045284, exon 1 of 3)	297	NR_045284	100503019	Mm.482658	NR_045284	ENSMUSG00000066477	Gm16551	-	predicted gene 16551	ncRNA
mm_121863.1	chr14	20733580	20733595	-	1	NA	5' UTR (NM_010811, exon 2 of 15)	5' UTR (NM_010811, exon 2 of 15)	975	NM_010811	17423	Mm.4084	NM_010811	ENSMUSG00000039308	Ndst2	Mndns|NDST-2	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 2	protein-coding
mm_89458.1	chr10	93184223	93184225	+	1	NA	intron (NM_146239, intron 1 of 16)	intron (NM_146239, intron 1 of 16)	21439	NR_035452	100316689		NR_035452	ENSMUSG00000089214	Mir1931	mir-1931|mmu-mir-1931	microRNA 1931	ncRNA
mm_103547.1	chr11	77607813	77607860	-	1	NA	promoter-TSS (NM_144825)	promoter-TSS (NM_144825)	-21	NM_144825	216965	Mm.340436	NM_144825	ENSMUSG00000017291	Taok1	2810468K05Rik|AU020252|D130018F14Rik|Map3k16|Markk|Psk2|mKIAA1361	TAO kinase 1	protein-coding
mm_137306.1	chr17	24874903	24874908	+	1	NA	Intergenic	RMER17A2|LTR|ERVK	-3865	NM_008340	16005	Mm.3135	NM_008340	ENSMUSG00000046070	Igfals	ALS|Albs|mKIAA4111	insulin-like growth factor binding protein, acid labile subunit	protein-coding
mm_20486.1	chr2	129895386	129895399	-	1	NA	Intergenic	B3A|SINE|B2	-93933	NR_029452	654409	Mm.305555	NR_029452		4932416H05Rik	-	RIKEN cDNA 4932416H05 gene	ncRNA
mm_28201.1	chr3	88281271	88281286	-	1	NA	Intergenic	MT2A|LTR|ERVL	15560	NM_029801	76927	Mm.273330	NM_029801	ENSMUSG00000010538	Tsacc	1700021C14Rik|SIP	TSSK6 activating co-chaperone	protein-coding
mm_72692.1	chr8	84969791	84969818	+	1	NA	intron (NM_011563, intron 1 of 5)	intron (NM_011563, intron 1 of 5)	182	NM_011563	21672	Mm.347009	NM_011563	ENSMUSG00000005161	Prdx2	AL022839|Band-8|NkefB|PRP|PrxII|TDX1|TPx|TPx-B|TR|TSA|Tdpx1|Torin	peroxiredoxin 2	protein-coding
mm_109435.1	chr12	110694604	110694637	+	1	NA	exon (NM_010480, exon 4 of 11)	exon (NM_010480, exon 4 of 11)	1775	NM_010480	15519	Mm.1843	NM_010480	ENSMUSG00000021270	Hsp90aa1	86kDa|89kDa|AL024080|AL024147|Hsp86-1|Hsp89|Hsp90|Hspca|hsp4	heat shock protein 90, alpha (cytosolic), class A member 1	protein-coding
mm_31298.1	chr4	45972793	45972810	+	1	NA	intron (NM_146142, intron 1 of 16)	CpG	504	NM_146142	100121	Mm.275413	NM_146142	ENSMUSG00000035517	Tdrd7	5730495N10Rik|AI447470|PCTAIRE2BP	tudor domain containing 7	protein-coding
mm_14273.1	chr2	128709092	128709107	+	1	NA	intron (NM_008587, intron 1 of 18)	RMER30|DNA|hAT-Charlie	10102	NM_008587	17289	Mm.239655	NM_008587	ENSMUSG00000014361	Mertk	Eyk|Mer|Nyk|nmf12	c-mer proto-oncogene tyrosine kinase	protein-coding
mm_50626.1	chr6	50200173	50200177	+	1	NA	Intergenic	Intergenic	61594	NM_018769	54722	Mm.248361	NM_018769	ENSMUSG00000029821	Dfna5	2310037D07Rik|4932441K13Rik|Dfna5h|EG14210|Fin15	deafness, autosomal dominant 5 (human)	protein-coding
mm_158039.1	chrX	98888397	98888401	-	1	NA	intron (NM_001313756, intron 2 of 2)	PB1D10|SINE|Alu	2626	NM_052976	94190	Mm.33536	NM_052976	ENSMUSG00000031214	Ophn1	C130037N19Rik|Wtgr	oligophrenin 1	protein-coding
mm_74530.1	chr8	9589587	9589590	-	1	NA	intron (NM_001347127, intron 1 of 3)	MusHAL1|LINE|L1	181435	NM_173446	270028	Mm.268163	NM_173446	ENSMUSG00000079157	Fam155a	6430500D16|AW121567|Tmem28	family with sequence similarity 155, member A	protein-coding
mm_57304.1	chr6	124709053	124709057	-	1	NA	intron (NM_013536, intron 1 of 5)	B1_Mur3|SINE|Alu	3123	NM_013536	14791	Mm.6390	NM_013536	ENSMUSG00000004268	Emg1	C2f|Grcc2f	EMG1 N1-specific pseudouridine methyltransferase	protein-coding
mm_104450.1	chr11	95040549	95040565	-	1	NA	intron (NM_133667, intron 1 of 10)	intron (NM_133667, intron 1 of 10)	814	NM_133667	18604	Mm.29768	NM_133667	ENSMUSG00000038967	Pdk2	-	pyruvate dehydrogenase kinase, isoenzyme 2	protein-coding
mm_24755.1	chr3	95434387	95434421	+	1	NA	promoter-TSS (NM_001037737)	promoter-TSS (NM_001037737)	14	NM_001037737	11863	Mm.250265	NM_009709	ENSMUSG00000015522	Arnt	D3Ertd557e|Drnt|ESTM42|Hif1b|W08714|bHLHe2|mKIAA4051	aryl hydrocarbon receptor nuclear translocator	protein-coding
mm_132847.1	chr16	46010774	46010776	+	1	NA	promoter-TSS (NM_001134480)	promoter-TSS (NM_001134480)	-362	NM_001134480	433022	Mm.380993	NM_001134480	ENSMUSG00000087141	Plcxd2	AW494639|EG433022	phosphatidylinositol-specific phospholipase C, X domain containing 2	protein-coding
mm_45217.1	chr5	53152875	53152877	-	1	NA	intron (NM_172710, intron 11 of 23)	L1MEd|LINE|L1	60576	NM_172710	231238	Mm.235020	NM_172710	ENSMUSG00000029189	Sel1l3	2310045A20Rik|AI429585|mKIAA0746	sel-1 suppressor of lin-12-like 3 (C. elegans)	protein-coding
mm_88853.1	chr10	80930711	80930718	+	1	NA	intron (NM_008655, intron 2 of 3)	intron (NM_008655, intron 2 of 3)	623	NM_008655	17873	Mm.1360	NM_008655	ENSMUSG00000015312	Gadd45b	AI323528|Myd118	growth arrest and DNA-damage-inducible 45 beta	protein-coding
mm_92297.1	chr10	73282183	73282187	-	1	NA	Intergenic	Intergenic	-195480	NR_040646	327768	Mm.417745	NR_040646		A330049N07Rik	-	RIKEN cDNA A330049N07 gene	ncRNA
mm_22051.1	chr2	168281121	168281144	-	1	NA	Intergenic	Intergenic	-11801	NM_001081134	241794	Mm.425102	NM_001081134	ENSMUSG00000074575	Kcng1	AW536275|OTTMUSG00000016048	potassium voltage-gated channel, subfamily G, member 1	protein-coding
mm_88728.1	chr10	80226645	80226752	+	1	NA	promoter-TSS (NM_023431)	promoter-TSS (NM_023431)	100	NM_023431	68114	Mm.273418	NM_023431	ENSMUSG00000020156	Mum1	2610019J09|9430059D04Rik|UBE-1C2	melanoma associated antigen (mutated) 1	protein-coding
mm_103006.1	chr11	69695882	69695900	-	1	NA	5' UTR (NM_001159503, exon 1 of 13)	5' UTR (NM_001159503, exon 1 of 13)	207	NM_011614	21944	Mm.8983	NM_011614	ENSMUSG00000097328	Tnfsf12	Apo3l|Dr3l|Dr3lg|Tweak	tumor necrosis factor (ligand) superfamily, member 12	protein-coding
mm_45003.1	chr5	38344327	38344328	-	1	NA	promoter-TSS (NR_046191)	promoter-TSS (NR_046191)	-62	NR_046191	78172	Mm.243835	NR_046191	ENSMUSG00000106932	4930487D11Rik	-	RIKEN cDNA 4930487D11 gene	ncRNA
mm_145867.1	chr18	65462913	65462917	+	1	NA	intron (NM_172833, intron 10 of 15)	intron (NM_172833, intron 10 of 15)	31918	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_36581.1	chr4	88032840	88032863	-	1	NA	intron (NM_027326, intron 1 of 10)	CpG	556	NM_027326	70122	Mm.288898	NM_027326	ENSMUSG00000028496	Mllt3	2210011H10Rik|2610012I03Rik|3830408D16Rik|Af9|D4Ertd321e	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 3	protein-coding
mm_110295.1	chr12	32208560	32208572	-	1	NA	promoter-TSS (NM_001146201)	promoter-TSS (NM_001146201)	83	NM_001146200	30955	Mm.101369	NM_020272	ENSMUSG00000020573	Pik3cg	5830428L06Rik|PI3Kgamma|p110gamma	phosphoinositide-3-kinase, catalytic, gamma polypeptide	protein-coding
mm_93553.1	chr10	116114284	116114299	-	1	NA	promoter-TSS (NM_001161855)	promoter-TSS (NM_001161855)	-374	NM_001161855	619332	Mm.391427	NM_001033821	ENSMUSG00000074734	4933416C03Rik	-	RIKEN cDNA 4933416C03 gene	protein-coding
mm_159528.1	chr4	62525141	62525141	+	1	NA	promoter-TSS (NM_021498)	promoter-TSS (NM_021498)	-127	NM_021498	59001	Mm.27444	NM_021498	ENSMUSG00000028394	Pole3	1810034K18Rik|YBL1	polymerase (DNA directed), epsilon 3 (p17 subunit)	protein-coding
mm_62046.1	chr7	92336591	92336628	+	1	NA	intron (NM_011807, intron 14 of 22)	B4A|SINE|B4	101639	NM_001243047	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_27460.1	chr3	52179953	52179955	-	1	NA	Intergenic	Intergenic	-74948	NM_001004176	433586	Mm.234972	NM_001004176	ENSMUSG00000061143	Maml3	AV234550|BC049812|Mam-2|mKIAA1816	mastermind like 3 (Drosophila)	protein-coding
mm_150387.1	chr19	36348507	36348550	+	1	NA	Intergenic	CpG	-30539	NM_029508	76073	Mm.259180	NM_029508	ENSMUSG00000024805	Pcgf5	0610009F02Rik|1110054A01Rik|5830406C17Rik|5830443C21Rik|9530023M17Rik|AI324127	polycomb group ring finger 5	protein-coding
mm_38507.1	chr4	141137383	141137387	-	1	NA	intron (NM_001025608, intron 1 of 3)	intron (NM_001025608, intron 1 of 3)	2411	NR_102344	213491	Mm.332006	NM_174996	ENSMUSG00000040842	Szrd1	1110022I03|D4Ertd22e	SUZ RNA binding domain containing 1	protein-coding
mm_90635.1	chr10	128494314	128494368	+	1	NA	promoter-TSS (NM_010860)	promoter-TSS (NM_010860)	-455	NM_010860	17904	Mm.337074	NM_010860	ENSMUSG00000090841	Myl6	ESMLC|LC17|LC17-GI|MLC-3|MLC1SM|Myln	myosin, light polypeptide 6, alkali, smooth muscle and non-muscle	protein-coding
mm_73185.1	chr8	95332280	95332342	+	1	NA	promoter-TSS (NM_024467)	promoter-TSS (NM_024467)	27	NM_133954	101985	Mm.29069	NM_133954	ENSMUSG00000031792	Usb1	AA960436	U6 snRNA biogenesis 1	protein-coding
mm_1506.1	chr1	72307459	72307475	+	1	NA	promoter-TSS (NM_009533)	promoter-TSS (NM_009533)	46	NM_009533	22596	Mm.246952	NM_009533	ENSMUSG00000026187	Xrcc5	AI314015|Ku80|Ku86	X-ray repair complementing defective repair in Chinese hamster cells 5	protein-coding
mm_54862.1	chr6	42597403	42597412	-	1	NA	promoter-TSS (NM_203396)	promoter-TSS (NM_203396)	-35	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_171567.1	chr4	147310538	147310538	+	1	NA	intron (NM_001039209, intron 1 of 2)	intron (NM_001039209, intron 1 of 2)	134672	NM_001039209	195531	Mm.270762	NM_001039209	ENSMUSG00000078496	Zfp982	Gm13152|OTTMUSG00000010671	zinc finger protein 982	protein-coding
mm_169963.1	chr16	97490791	97490805	+	1	NA	intron (NM_020622, intron 2 of 7)	(TGG)n|Simple_repeat|Simple_repeat	14138	NM_020622	52793	Mm.327932	NM_020622	ENSMUSG00000022938	Fam3b	2-21|9030624C24Rik|D16Jhu19e|ORF9|Pander	family with sequence similarity 3, member B	protein-coding
mm_115886.1	chr13	21897529	21897535	-	1	NA	promoter-TSS (NR_035500)	promoter-TSS (NR_035500)	-483	NR_035500	100316716		NR_035500	ENSMUSG00000088148	Mir1983	mmu-mir-1983	microRNA 1983	ncRNA
mm_1723.1	chr1	75362050	75362064	+	1	NA	intron (NM_010043, intron 1 of 8)	intron (NM_010043, intron 1 of 8)	1765	NM_010043	13346	Mm.6712	NM_010043	ENSMUSG00000026208	Des	-	desmin	protein-coding
mm_172097.1	chr6	26247641	26247642	+	1	NA	Intergenic	L1Md_A|LINE|L1	316215	NR_040771	626904	Mm.126787	NR_040771	ENSMUSG00000106799	Gm20756	-	predicted gene, 20756	ncRNA
mm_39168.1	chr4	155669120	155669163	-	1	NA	5' UTR (NM_001256107, exon 1 of 20)	5' UTR (NM_001256107, exon 1 of 20)	113	NM_001256108	76580	Mm.235738	NM_145124	ENSMUSG00000029060	Mib2	2210008I11Rik|Zzank1|skd	mindbomb E3 ubiquitin protein ligase 2	protein-coding
mm_141698.1	chr17	33996287	33996367	-	1	NA	3' UTR (NM_001001892, exon 8 of 8)	3' UTR (NM_001001892, exon 8 of 8)	4006	NM_001001892	14972	Mm.422886	NM_001001892	ENSMUSG00000061232	H2-K1	H-2K|H-2K(d)|H2-K|K-f	histocompatibility 2, K1, K region	protein-coding
mm_8314.1	chr1	144249100	144249113	-	1	NA	promoter-TSS (NM_015811)	promoter-TSS (NM_015811)	-2	NM_015811	50778	Mm.103701	NM_015811	ENSMUSG00000026358	Rgs1	BL34	regulator of G-protein signaling 1	protein-coding
mm_131687.1	chr16	20678437	20678451	+	1	NA	intron (NM_001304432, intron 6 of 31)	intron (NM_001304432, intron 6 of 31)	5717	NM_001304432	208643	Mm.260256	NM_145941	ENSMUSG00000045983	Eif4g1	E030015G23Rik|eIF-4-gamma 1|eIF-4G 1|eIF-4G1|eIF4GI	eukaryotic translation initiation factor 4, gamma 1	protein-coding
mm_93277.1	chr10	96077561	96077585	-	1	NA	Intergenic	Intergenic	136910	NM_001001932	216238	Mm.210035	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding
mm_8157.1	chr1	136949172	136949189	-	1	NA	intron (NM_030676, intron 2 of 8)	CpG-577	4450	NM_001159769	26424	Mm.16794	NM_030676	ENSMUSG00000026398	Nr5a2	AU020803|D1Ertd308e|Ftf|LRH-1|UF2-H3B	nuclear receptor subfamily 5, group A, member 2	protein-coding
mm_11297.1	chr2	30171487	30171497	+	1	NA	promoter-TSS (NM_007931)	promoter-TSS (NM_007931)	-32	NM_007931	13804	Mm.474473	NM_007931	ENSMUSG00000015337	Endog	-	endonuclease G	protein-coding
mm_83538.1	chr9	46233325	46233351	-	1	NA	exon (NM_001289755, exon 4 of 4)	exon (NM_001289755, exon 4 of 4)	1961	NM_001289833	11814	Mm.390161	NM_023114	ENSMUSG00000032081	Apoc3	apo-CIII|apoC-III	apolipoprotein C-III	protein-coding
mm_46466.1	chr5	105121193	105121236	-	1	NA	intron (NM_008620, intron 7 of 10)	intron (NM_008620, intron 7 of 10)	-10922	NM_172777	236573	Mm.425261	NM_172777	ENSMUSG00000029298	Gbp9	-	guanylate-binding protein 9	protein-coding
mm_15381.1	chr2	156538768	156538769	+	1	NA	intron (NM_001006664, intron 21 of 21)	intron (NM_001006664, intron 21 of 21)	-8808	NM_026661	68295	Mm.253648	NM_026661	ENSMUSG00000027628	Aar2	0610011L14Rik	AAR2 splicing factor homolog	protein-coding
mm_99050.1	chr11	99047316	99047326	+	1	NA	intron (NM_010517, intron 1 of 3)	intron (NM_010517, intron 1 of 3)	6061	NM_010517	16010	Mm.233799	NM_010517	ENSMUSG00000017493	Igfbp4	AI875747|Deb2|IGFBP-4	insulin-like growth factor binding protein 4	protein-coding
mm_86722.1	chr10	19061367	19061368	+	1	NA	Intergenic	Intergenic	-45957	NM_009397	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_145033.1	chr18	39353497	39353498	+	1	NA	intron (NM_175164, intron 20 of 22)	L1ME4a|LINE|L1	133748	NM_008173	14815	Mm.129481	NM_008173	ENSMUSG00000024431	Nr3c1	GR|Grl-1|Grl1	nuclear receptor subfamily 3, group C, member 1	protein-coding
mm_171329.1	chr3	98468858	98468871	-	1	NA	Intergenic	Intergenic	-11833	NM_001111336	15495	Mm.14309	NM_008294	ENSMUSG00000095143	Hsd3b4	-	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 4	protein-coding
mm_61656.1	chr7	80501235	80501239	+	1	NA	intron (NM_001042527, intron 7 of 21)	intron (NM_001042527, intron 7 of 21)	33761	NM_007550	12144	Mm.12932	NM_007550	ENSMUSG00000030528	Blm	-	Bloom syndrome, RecQ helicase-like	protein-coding
mm_10863.1	chr2	25080317	25080343	+	1	NA	promoter-TSS (NM_028093)	promoter-TSS (NM_028093)	7	NM_028093	72090	Mm.33403	NM_028093	ENSMUSG00000036813	Entpd8	-	ectonucleoside triphosphate diphosphohydrolase 8	protein-coding
mm_52379.1	chr6	113120975	113120992	+	1	NA	exon (NM_028385, exon 14 of 22)	exon (NM_028385, exon 14 of 22)	16048	NM_173005	72895	Mm.367159	NM_028385	ENSMUSG00000034269	Setd5	2900045N06Rik|C330007C20|C85544|mKIAA1757	SET domain containing 5	protein-coding
mm_2097.1	chr1	87756005	87756115	+	1	NA	promoter-TSS (NM_029846)	promoter-TSS (NM_029846)	49	NM_001205392	77040	Mm.272972	NM_029846	ENSMUSG00000026289	Atg16l1	1500009K01Rik|Apg16l|Atg16l|WDR30	autophagy related 16-like 1 (S. cerevisiae)	protein-coding
mm_98097.1	chr11	86618800	86618804	+	1	NA	intron (NM_029478, intron 7 of 11)	intron (NM_029478, intron 7 of 11)	-34644	NR_029738	387140		NR_029738	ENSMUSG00000065455	Mir21a	Mir21|Mirn21|mmu-mir-21|mmu-mir-21a	microRNA 21a	ncRNA
mm_139219.1	chr17	47729295	47729343	+	1	NA	exon (NM_025973, exon 3 of 9)	exon (NM_025973, exon 3 of 9)	2477	NM_025973	109820	Mm.22957	NM_025973	ENSMUSG00000023987	Pgc	2210410L06Rik|Upg-1|Upg1	progastricsin (pepsinogen C)	protein-coding
mm_22806.1	chr3	27064049	27064059	+	1	NA	Intergenic	Intergenic	89800	NM_007900	13605	Mm.261453	NM_007900	ENSMUSG00000027699	Ect2	AI528536|mKIAA4037	ect2 oncogene	protein-coding
mm_93422.1	chr10	108719478	108719513	-	1	NA	intron (NM_001252341, intron 4 of 11)	intron (NM_001252341, intron 4 of 11)	-19335	NM_203660	368203	Mm.452758	NM_203660		Gm5136	C6.1AL|EG368203	predicted gene 5136	protein-coding
mm_148810.1	chr19	6282064	6282067	+	1	NA	intron (NM_010119, intron 2 of 4)	B1_Mur3|SINE|Alu	5169	NM_010119	13660	Mm.30169	NM_010119	ENSMUSG00000024772	Ehd1	AA409636|Past1|RME-1	EH-domain containing 1	protein-coding
mm_58693.1	chr7	12925406	12925428	+	1	NA	exon (NM_009095, exon 3 of 6)	exon (NM_009095, exon 3 of 6)	-1999	NM_029809	381845	Mm.439896	NM_029809	ENSMUSG00000033967	Rnf225	2310014L17Rik|AV237412|C77118	ring finger protein 225	protein-coding
mm_28001.1	chr3	83008525	83008535	-	1	NA	exon (NM_133862, exon 3 of 10)	exon (NM_133862, exon 3 of 10)	806	NM_001317105	99571	Mm.16422	NM_133862	ENSMUSG00000033860	Fgg	3010002H13Rik|AI256424	fibrinogen gamma chain	protein-coding
mm_31015.1	chr4	40722462	40722512	+	1	NA	promoter-TSS (NM_001164672)	promoter-TSS (NM_001164672)	19	NM_008298	15502	Mm.27897	NM_008298	ENSMUSG00000028410	Dnaja1	HSJ-2|Hsj2|Nedd7	DnaJ heat shock protein family (Hsp40) member A1	protein-coding
mm_39816.1	chr5	30711603	30711612	+	1	NA	promoter-TSS (NM_023047)	promoter-TSS (NM_023047)	-288	NM_023047	65254	Mm.27732	NM_023047	ENSMUSG00000029168	Dpysl5	CRAM|CRMP-5|Crmp5	dihydropyrimidinase-like 5	protein-coding
mm_39830.1	chr5	30814785	30814800	+	1	NA	5' UTR (NM_133350, exon 1 of 7)	5' UTR (NM_133350, exon 1 of 7)	151	NM_133350	100732	Mm.332295	NM_133350	ENSMUSG00000029166	Mapre3	AI790651|EB2|EB3|EBF3|RP3	microtubule-associated protein, RP/EB family, member 3	protein-coding
mm_160018.1	chr6	129717264	129717264	-	1	NA	promoter-TSS (NM_001012520)	promoter-TSS (NM_001012520)	-132	NM_001012520	503550	Mm.376476	NM_001012520	ENSMUSG00000067610	Klri1	-	killer cell lectin-like receptor family I member 1	protein-coding
mm_143227.1	chr17	63312969	63312988	-	1	NA	promoter-TSS (NR_130176)	promoter-TSS (NR_130176)	-5	NR_130176	414079	Mm.444282	NR_130176	ENSMUSG00000090565	4930405O22Rik	-	RIKEN cDNA 4930405O22 gene	ncRNA
mm_40554.1	chr5	58453059	58453072	+	1	NA	promoter-TSS (NR_046190)	promoter-TSS (NR_046190)	-67	NR_046190	78163	Mm.243828	NR_046190	ENSMUSG00000105234	4930459L07Rik	-	RIKEN cDNA 4930459L07 gene	ncRNA
mm_30289.1	chr3	148989514	148989522	-	1	NA	Intergenic	CpG	-34883	NM_001081298	99633	Mm.9776	NM_001081298	ENSMUSG00000028184	Adgrl2	AI450192|CIRL-2|Gm619|Lec1|Lphh1|Lphn2|mKIAA0786	adhesion G protein-coupled receptor L2	protein-coding
mm_51967.1	chr6	91758409	91758419	+	1	NA	3' UTR (NM_009320, exon 15 of 15)	3' UTR (NM_009320, exon 15 of 15)	48979	NM_001159507	243547	Mm.333264	NM_001033353	ENSMUSG00000030098	Grip2	-	glutamate receptor interacting protein 2	protein-coding
mm_99685.1	chr11	106036868	106036924	+	1	NA	promoter-TSS (NM_027946)	promoter-TSS (NM_027946)	24	NM_027946	71833	Mm.307455	NM_027946	ENSMUSG00000049354	Dcaf7	1700012F10Rik|2610037L01Rik|C86529|HAN11|Wdr68	DDB1 and CUL4 associated factor 7	protein-coding
mm_71041.1	chr8	33660874	33660898	+	1	NA	intron (NM_010344, intron 1 of 12)	intron (NM_010344, intron 1 of 12)	7648	NM_010344	14782	Mm.283573	NM_010344	ENSMUSG00000031584	Gsr	AI325518|D8Ertd238e|Gr-1|Gr1	glutathione reductase	protein-coding
mm_24946.1	chr3	96601085	96601139	+	1	NA	promoter-TSS (NM_001163170)	promoter-TSS (NM_001163170)	-21	NM_001163170	280411	Mm.482147	NM_001163170	ENSMUSG00000049288	Lix1l	D130027M04Rik	Lix1-like	protein-coding
mm_30692.1	chr4	11558915	11558979	+	1	NA	promoter-TSS (NM_001256145)	promoter-TSS (NM_001256145)	27	NM_001256145	623474	Mm.491200	NM_177285	ENSMUSG00000078773	Rad54b	E130016E03Rik	RAD54 homolog B (S. cerevisiae)	protein-coding
mm_23178.1	chr3	40800014	40800050	+	1	NA	promoter-TSS (NM_011495)	promoter-TSS (NM_011495)	81	NR_045576	20873	Mm.3794	NM_011495	ENSMUSG00000025758	Plk4	1700028H20|AI385771|Sak|Stk18	polo-like kinase 4	protein-coding
mm_90230.1	chr10	121374351	121374368	+	1	NA	exon (NM_029364, exon 3 of 14)	exon (NM_029364, exon 3 of 14)	9269	NM_029364	75612	Mm.207683	NM_029364	ENSMUSG00000034707	Gns	2610016K11Rik|AU042285|C87209|G6S|N28088	glucosamine (N-acetyl)-6-sulfatase	protein-coding
mm_18811.1	chr2	74518959	74518986	-	1	NA	3' UTR (NM_027133, exon 13 of 13)	3' UTR (NM_027133, exon 13 of 13)	59976	NM_001110209	69605	Mm.156113	NM_027133	ENSMUSG00000009207	Lnpk	2310011O18Rik|4921514L11Rik|9530051D01Rik|AI666268|Lnp|Lnpk1|Ul|ulnaless	lunapark, ER junction formation factor	protein-coding
mm_109540.1	chr12	111583625	111583629	+	1	NA	intron (NM_022801, intron 1 of 15)	intron (NM_022801, intron 1 of 15)	9117	NM_022801	17169	Mm.260504	NM_021516	ENSMUSG00000007411	Mark3	1600015G02Rik|A430080F22Rik|C-TAK1|ETK-1|ETK1|Emk2|MPK10	MAP/microtubule affinity regulating kinase 3	protein-coding
mm_84355.1	chr9	64704582	64704584	-	1	NA	intron (NM_001134399, intron 23 of 24)	intron (NM_001134399, intron 23 of 24)	33173	NM_017382	53869	Mm.1387	NM_017382	ENSMUSG00000004771	Rab11a	-	RAB11A, member RAS oncogene family	protein-coding
mm_126887.1	chr15	89456734	89456738	+	1	NA	exon (NM_021921, exon 3 of 12)	exon (NM_021921, exon 3 of 12)	2825	NM_021921	60597	Mm.173337	NM_021921	ENSMUSG00000022619	Mapk8ip2	3230402N03Rik|AI847694|AW049958|IB2|Jip2|R75148	mitogen-activated protein kinase 8 interacting protein 2	protein-coding
mm_41715.1	chr5	101968743	101968779	+	1	NA	intron (NM_172882, intron 5 of 66)	intron (NM_172882, intron 5 of 66)	101160	NM_172882	72145	Mm.332522	NM_172882	ENSMUSG00000043940	Wdfy3	2610509D04Rik|ALFY|AW319683|B930017C24|BWF1|Bchs|D5Ertd66e|Ggtb3|ZFYVE25|mKIAA0993	WD repeat and FYVE domain containing 3	protein-coding
mm_43941.1	chr5	145127915	145127915	+	1	NA	TTS (NM_001033313)	TTS (NM_001033313)	12174	NM_001033313	231887	Mm.188851	NM_001033313	ENSMUSG00000029623	Pdap1	HASPP28|PAP|PAP1	PDGFA associated protein 1	protein-coding
mm_136898.1	chr17	13015088	13015101	+	1	NA	exon (NM_013671, exon 5 of 5)	exon (NM_013671, exon 5 of 5)	7255	NM_013671	20656	Mm.290876	NM_013671	ENSMUSG00000006818	Sod2	MnSOD|Sod-2	superoxide dismutase 2, mitochondrial	protein-coding
mm_68300.1	chr7	105745670	105745690	-	1	NA	3' UTR (NM_009906, exon 13 of 13)	3' UTR (NM_009906, exon 13 of 13)	-1342	NM_020024	24075	Mm.274846	NM_020024	ENSMUSG00000043866	Taf10	30kDa|AU041226|TAFII30|Taf2h	TATA-box binding protein associated factor 10	protein-coding
mm_3007.1	chr1	133350668	133350683	+	1	NA	promoter-TSS (NM_031192)	promoter-TSS (NM_031192)	1	NM_031192	19701	Mm.220955	NM_031192	ENSMUSG00000070645	Ren1	D19352|Ren|Ren-1|Ren-A|Ren1c|Ren1d|Rn-1|Rnr	renin 1 structural	protein-coding
mm_116680.1	chr13	49248121	49248140	-	1	NA	promoter-TSS (NM_025491)	promoter-TSS (NM_025491)	33	NM_025491	66329	Mm.34308	NM_025491	ENSMUSG00000021384	Susd3	1700017I11Rik|2810440J20Rik	sushi domain containing 3	protein-coding
mm_117311.1	chr13	67500452	67500512	-	1	NA	promoter-TSS (NM_001007575)	promoter-TSS (NM_001007575)	40	NM_001007575	238693	Mm.478914	NM_001007575	ENSMUSG00000071291	Zfp58	A530094I17Rik|Mfg-1|Mfg1|Rslcan5|Zfp817	zinc finger protein 58	protein-coding
mm_114274.1	chr13	58214929	58214934	+	1	NA	intron (NM_026842, intron 1 of 10)	intron (NM_026842, intron 1 of 10)	722	NM_152234	56085	Mm.182053	NM_026842	ENSMUSG00000005312	Ubqln1	1110046H03Rik|1810030E05Rik|AU019746|C77538|D13Ertd372e|Da41|Dsk2|Plic-1|Plic1|Xdrp1	ubiquilin 1	protein-coding
mm_108019.1	chr12	73598495	73598504	+	1	NA	intron (NM_001313977, intron 2 of 14)	intron (NM_001313977, intron 2 of 14)	13703	NM_008856	18755	Mm.341677	NM_008856	ENSMUSG00000021108	Prkch	Pkch	protein kinase C, eta	protein-coding
mm_44610.1	chr5	25472524	25472528	-	1	NA	intron (NM_001081383, intron 1 of 58)	intron (NM_001081383, intron 1 of 58)	26257	NM_001081383	231051	Mm.332268	NM_001081383	ENSMUSG00000038056	Kmt2c	E330008K23Rik|HALR|Mll3|mKIAA1506	lysine (K)-specific methyltransferase 2C	protein-coding
mm_43225.1	chr5	129794351	129794369	+	1	NA	promoter-TSS (NR_003681)	promoter-TSS (NR_003681)	-201	NR_003681	100113364	Mm.449738	NR_003681	ENSMUSG00000093413	Snora15	MBI-79	small nucleolar RNA, H/ACA box 15	snoRNA
mm_118693.1	chr14	22135728	22135729	+	1	NA	intron (NM_028275, intron 2 of 6)	MLT1A|LTR|ERVL-MaLR	116016	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_58669.1	chr7	7185665	7185665	+	1	NA	Intergenic	MTE-int|LTR|ERVL-MaLR	14312	NM_146179	232854	Mm.184857	NM_146179	ENSMUSG00000034538	Zfp418	A230102I05Rik	zinc finger protein 418	protein-coding
mm_81231.1	chr9	107729519	107729527	+	1	NA	Intergenic	Intergenic	-19048	NM_011349	20350	Mm.12903	NM_011349	ENSMUSG00000034684	Sema3f	Sema4|Semak	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F	protein-coding
mm_162773.1	chr10	68136742	68136757	-	1	NA	intron (NM_023598, intron 4 of 9)	intron (NM_023598, intron 4 of 9)	141977	NM_023598	71371	Mm.440357	NM_023598	ENSMUSG00000019947	Arid5b	4930580B11|5430435G07Rik|AI467247|Desrt|Mrf2|Mrf2alpha|Mrf2beta	AT rich interactive domain 5B (MRF1-like)	protein-coding
mm_81467.1	chr9	109875911	109876000	+	1	NA	5' UTR (NM_007658, exon 1 of 15)	5' UTR (NM_007658, exon 1 of 15)	376	NM_007658	12530	Mm.307103	NM_007658	ENSMUSG00000032477	Cdc25a	D9Ertd393e	cell division cycle 25A	protein-coding
mm_135952.1	chr16	74412117	74412131	-	1	NA	Intergenic	Intergenic	-1212	NM_175549	268902	Mm.171736	NM_175549	ENSMUSG00000052516	Robo2	2600013A04Rik|9430089E08Rik|BB097918|D230004I22Rik|mKIAA1568	roundabout guidance receptor 2	protein-coding
mm_42440.1	chr5	115429721	115429734	+	1	NA	promoter-TSS (NM_008629)	promoter-TSS (NM_008629)	42	NM_008629	17690	Mm.5077	NM_008629	ENSMUSG00000054256	Msi1	Msi1h|Musahi1|m-Msi-1	musashi RNA-binding protein 1	protein-coding
mm_50376.1	chr6	48684545	48684556	+	1	NA	promoter-TSS (NM_001243199)	promoter-TSS (NM_001243199)	-28	NM_001243200	107526	Mm.333048	NM_174990	ENSMUSG00000054435	Gimap4	AU019574|E430007K16Rik|Ian-1|Ian1|Imap4	GTPase, IMAP family member 4	protein-coding
mm_116811.1	chr13	54379540	54379578	-	1	NA	exon (NM_009946, exon 4 of 4)	exon (NM_009946, exon 4 of 4)	8210	NM_009946	12890	Mm.268902	NM_009946	ENSMUSG00000025867	Cplx2	921-L|AI413745|AW492120	complexin 2	protein-coding
mm_142981.1	chr17	56271250	56271263	-	1	NA	exon (NM_174989, exon 2 of 2)	exon (NM_174989, exon 2 of 2)	5511	NM_174989	106759	Mm.203952	NM_174989	ENSMUSG00000047123	Ticam1	AW046014|AW547018|TICAM-1|TRIF	toll-like receptor adaptor molecule 1	protein-coding
mm_89490.1	chr10	93778604	93778629	+	1	NA	Intergenic	Intergenic	-52939	NM_183199	327799	Mm.491598	NM_183199	ENSMUSG00000020020	Usp44	E430004F17Rik	ubiquitin specific peptidase 44	protein-coding
mm_115117.1	chr13	104228930	104228982	+	1	NA	promoter-TSS (NM_021790)	promoter-TSS (NM_021790)	-112	NM_172807	238831	Mm.98910	NM_172807	ENSMUSG00000021713	Ppwd1	4632422M10Rik|A330090G21Rik	peptidylprolyl isomerase domain and WD repeat containing 1	protein-coding
mm_41073.1	chr5	87668982	87669010	+	1	NA	intron (NM_001286015, intron 3 of 32)	intron (NM_001286015, intron 3 of 32)	2788	NM_001286016	12990	Mm.427467	NM_007784	ENSMUSG00000070702	Csn1s1	AA959832|AW212882|Csna	casein alpha s1	protein-coding
mm_108099.1	chr12	74804271	74804281	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	373056	NM_172805	238271	Mm.44465	NM_172805	ENSMUSG00000034402	Kcnh5	Eag2	potassium voltage-gated channel, subfamily H (eag-related), member 5	protein-coding
mm_96371.1	chr11	67236205	67236211	+	1	NA	Intergenic	Intergenic	-1604	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_160632.1	chr9	107541658	107541658	-	1	NA	promoter-TSS (NM_018879)	promoter-TSS (NM_018879)	207	NM_019720	56368	Mm.24833	NM_019720	ENSMUSG00000037190	Cyb561d2	AW049681|Tsp10	cytochrome b-561 domain containing 2	protein-coding
mm_10522.1	chr2	16363515	16363535	+	1	NA	intron (NM_026162, intron 1 of 13)	intron (NM_026162, intron 1 of 13)	7221	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding
mm_45038.1	chr5	39644602	39644619	-	1	NA	promoter-TSS (NM_010474)	promoter-TSS (NM_010474)	21	NM_010474	15476	Mm.12559	NM_010474	ENSMUSG00000051022	Hs3st1	3-Ost|D5Wsu110e|Hsg3ost	heparan sulfate (glucosamine) 3-O-sulfotransferase 1	protein-coding
mm_86062.1	chr9	114640156	114640167	-	1	NA	promoter-TSS (NM_153585)	promoter-TSS (NM_153585)	39	NM_153585	78893	Mm.283708	NM_153585	ENSMUSG00000056167	Cnot10	2600001P13Rik	CCR4-NOT transcription complex, subunit 10	protein-coding
mm_43422.1	chr5	136054469	136054475	+	1	NA	Intergenic	Intergenic	-2795	NM_027158	69665	Mm.75713	NM_027158	ENSMUSG00000006143	Upk3bl	2310043J07Rik	uroplakin 3B-like	protein-coding
mm_142595.1	chr17	46763577	46763644	-	1	NA	exon (NM_011195, exon 1 of 4)	exon (NM_011195, exon 1 of 4)	102	NM_011195	19208	Mm.215173	NM_011195	ENSMUSG00000036858	Ptcra	gp33|pT-alpha|pT-alpha-TCR|pT[a]|pTa|pTalpha	pre T cell antigen receptor alpha	protein-coding
mm_160334.1	chr8	13000655	13000655	+	1	NA	intron (NM_001159486, intron 9 of 29)	L1MD1|LINE|L1	-25379	NM_010172	14068	Mm.4827	NM_010172	ENSMUSG00000031443	F7	AI132620|Cf7|FVII	coagulation factor VII	protein-coding
mm_14521.1	chr2	132690121	132690162	+	1	NA	promoter-TSS (NM_028637)	promoter-TSS (NM_028637)	-142	NM_028637	73747	Mm.284114	NM_028637	ENSMUSG00000044991	1110034G24Rik	-	RIKEN cDNA 1110034G24 gene	protein-coding
mm_69032.1	chr7	126797897	126797928	-	1	NA	intron (NM_001177308, intron 1 of 8)	intron (NM_001177308, intron 1 of 8)	1266	NM_001177307	11674	Mm.275831	NM_007438	ENSMUSG00000030695	Aldoa	Aldo-1|Aldo1	aldolase A, fructose-bisphosphate	protein-coding
mm_93908.1	chr10	126978879	126978896	-	1	NA	5' UTR (NM_001113470, exon 1 of 8)	5' UTR (NM_001113470, exon 1 of 8)	170	NM_001113470	52468	Mm.29490	NM_146012	ENSMUSG00000078429	Ctdsp2	AI586070|D10Ertd73e|OS-4|OS4|SCP2	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 2	protein-coding
mm_61905.1	chr7	90131108	90131134	+	1	NA	intron (NM_001252520, intron 1 of 20)	intron (NM_001252520, intron 1 of 20)	889	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_9945.1	chr1	190911729	190911802	-	1	NA	promoter-TSS (NM_178775)	promoter-TSS (NM_178775)	5	NM_178775	320119	Mm.220912	NM_178775	ENSMUSG00000089872	Rps6kc1	AA682037|B130003F20Rik|C80612|Rpk118	ribosomal protein S6 kinase polypeptide 1	protein-coding
mm_23127.1	chr3	37656019	37656027	+	1	NA	Intergenic	Intergenic	16076	NM_001305442	24063	Mm.330986	NM_011896	ENSMUSG00000037211	Spry1	sprouty1|spry-1	sprouty homolog 1 (Drosophila)	protein-coding
mm_133104.1	chr16	65368352	65368360	+	1	NA	Intergenic	L1MCa|LINE|L1	-152273	NM_008849	18736	Mm.355440	NM_008849	ENSMUSG00000004842	Pou1f1	GHF-1|Hmp1|Pit-1|Pit1|Pit1-rs1|dw|dwarf	POU domain, class 1, transcription factor 1	protein-coding
mm_158500.1	chrX	142390361	142390363	-	1	NA	5' UTR (NM_207625, exon 1 of 16)	5' UTR (NM_207625, exon 1 of 16)	173	NM_001033600	50790	Mm.391337	NM_019477	ENSMUSG00000031278	Acsl4	9430020A05Rik|ACS4|AU018108|Facl4|Lacs4	acyl-CoA synthetase long-chain family member 4	protein-coding
mm_155345.1	chrX	68678627	68678639	+	1	NA	promoter-TSS (NM_008031)	promoter-TSS (NM_008031)	92	NM_001290424	14265	Mm.3451	NM_008031	ENSMUSG00000000838	Fmr1	FMRP|Fmr-1	fragile X mental retardation syndrome 1	protein-coding
mm_145704.1	chr18	62657330	62657340	+	1	NA	intron (NM_177829, intron 5 of 8)	intron (NM_177829, intron 5 of 8)	-61071	NM_001001803	408198	Mm.478742	NM_001001803	ENSMUSG00000060201	Spink7	EG408198|Ecg2	serine peptidase inhibitor, Kazal type 7 (putative)	protein-coding
mm_115768.1	chr13	19306162	19306183	-	1	NA	Intergenic	Intergenic	89641	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_28714.1	chr3	95658562	95658588	-	1	NA	promoter-TSS (NM_008562)	promoter-TSS (NM_008562)	-146	NM_008562	17210	Mm.1639	NM_008562	ENSMUSG00000038612	Mcl1	AW556805|Mcl-1	myeloid cell leukemia sequence 1	protein-coding
mm_75818.1	chr8	70420012	70420043	-	1	NA	intron (NM_001004062, intron 1 of 13)	intron (NM_001004062, intron 1 of 13)	19546	NM_001004062	382056	Mm.227767	NM_001004062	ENSMUSG00000003575	Crtc1	AI413414|Mect1|R74955|TORC1|mKIAA0616	CREB regulated transcription coactivator 1	protein-coding
mm_87982.1	chr10	63859131	63859135	+	1	NA	intron (NM_177612, intron 7 of 17)	intron (NM_177612, intron 7 of 17)	38078	NM_001164519	216033	Mm.444692	NM_177612	ENSMUSG00000060843	Ctnna3	4930429L08Rik|4933408A16|Catna3|Vr22	catenin (cadherin associated protein), alpha 3	protein-coding
mm_129307.1	chr15	77561858	77561887	-	1	NA	promoter-TSS (NR_040310)	promoter-TSS (NR_040310)	20	NR_040310	76409	Mm.183491	NR_040310	ENSMUSG00000101113	1700025B11Rik	-	RIKEN cDNA 1700025B11 gene	ncRNA
mm_11429.1	chr2	31962015	31962024	+	1	NA	intron (NM_145144, intron 2 of 5)	intron (NM_145144, intron 2 of 5)	11716	NM_145144	108897	Mm.24838	NM_145144	ENSMUSG00000001864	Aif1l	2810003C17Rik|AI043124|C87647|Iba2	allograft inflammatory factor 1-like	protein-coding
mm_20249.1	chr2	126499840	126499858	-	1	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	-8296	NM_001080944	241633	Mm.222235	NM_001080944	ENSMUSG00000060131	Atp8b4	A530043E15|Im	ATPase, class I, type 8B, member 4	protein-coding
mm_162353.1	chr1	55412213	55412213	+	1	NA	intron (NM_001114663, intron 1 of 5)	intron (NM_001114663, intron 1 of 5)	6267	NM_001114663	227120	Mm.194183	NM_001114663	ENSMUSG00000038349	Plcl1	C230017K02Rik|PLC-L|PLC-L1|PLCE|PLCL|PLDL1|PRIP|PRIP-1	phospholipase C-like 1	protein-coding
mm_49924.1	chr6	39379975	39379995	+	1	NA	Intergenic	Intergenic	-1443	NM_011226	19331	Mm.123866	NM_011226	ENSMUSG00000029923	Rab19	-	RAB19, member RAS oncogene family	protein-coding
mm_14243.1	chr2	128015184	128015187	+	1	NA	intron (NM_028765, intron 12 of 17)	L1MDb|LINE|L1	-110853	NM_207681	12125	Mm.141083	NM_009754	ENSMUSG00000027381	Bcl2l11	1500006F24Rik|Bim|Bod|bcl2-L-11	BCL2-like 11 (apoptosis facilitator)	protein-coding
mm_124843.1	chr15	9436040	9436083	+	1	NA	promoter-TSS (NM_029341)	promoter-TSS (NM_029341)	33	NM_029341	75568	Mm.82143	NM_029341	ENSMUSG00000039676	Capsl	1700028N11Rik|AW125205	calcyphosine-like	protein-coding
mm_107244.1	chr12	26479222	26479234	+	1	NA	3' UTR (NM_020557, exon 5 of 5)	3' UTR (NM_020557, exon 5 of 5)	10013	NM_020557	22169	Mm.271839	NM_020557	ENSMUSG00000020638	Cmpk2	1200004E04Rik|TDKI|Tyki	cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial	protein-coding
mm_145689.1	chr18	61952961	61952997	+	1	NA	promoter-TSS (NM_172628)	promoter-TSS (NM_172628)	-96	NM_172628	225608	Mm.262320	NM_172628	ENSMUSG00000045629	Sh3tc2	D430044G18Rik	SH3 domain and tetratricopeptide repeats 2	protein-coding
mm_107662.1	chr12	52829165	52829203	+	1	NA	intron (NM_198111, intron 2 of 13)	intron (NM_198111, intron 2 of 13)	129801	NM_198111	238161	Mm.310822	NM_198111	ENSMUSG00000061603	Akap6	AI482140|Akapalpha|Akapbeta|PRKA	A kinase (PRKA) anchor protein 6	protein-coding
mm_35425.1	chr4	35225179	35225189	-	1	NA	intron (NM_001081343, intron 1 of 10)	intron (NM_001081343, intron 1 of 10)	696	NM_001081343	73205	Mm.331544	NM_001081343	ENSMUSG00000028300	3110043O21Rik	AI840585	RIKEN cDNA 3110043O21 gene	protein-coding
mm_46520.1	chr5	105339051	105339065	-	1	NA	intron (NR_132129, intron 3 of 10)	L1MA8|LINE|L1	7414	NM_001039647	634650	Mm.458435	NM_001039647	ENSMUSG00000092021	Gbp11	EG634650|Gm7141	guanylate binding protein 11	protein-coding
mm_106618.1	chr11	120820292	120820310	-	1	NA	exon (NM_007988, exon 6 of 43)	exon (NM_007988, exon 6 of 43)	4246	NM_007988	14104	Mm.236443	NM_007988	ENSMUSG00000025153	Fasn	A630082H08Rik|FAS	fatty acid synthase	protein-coding
mm_99662.1	chr11	105901973	105901984	+	1	NA	intron (NM_181071, intron 17 of 25)	intron (NM_181071, intron 17 of 25)	42169	NM_007805	13056	Mm.149403	NM_007805	ENSMUSG00000019590	Cyb561	-	cytochrome b-561	protein-coding
mm_61759.1	chr7	82771621	82771625	+	1	NA	intron (NM_175317, intron 18 of 19)	intron (NM_175317, intron 18 of 19)	-15979	NR_046004	77800	Mm.444811	NR_046004	ENSMUSG00000086690	4933406J10Rik	A930009F24Rik	RIKEN cDNA 4933406J10 gene	ncRNA
mm_167771.1	chr9	111026061	111026082	-	1	NA	exon (NM_008522, exon 9 of 17)	exon (NM_008522, exon 9 of 17)	6779	NM_008522	17002	Mm.282359	NM_008522	ENSMUSG00000032496	Ltf	Csp82|Lf|MMS10R|Ms10r	lactotransferrin	protein-coding
mm_2362.1	chr1	93006329	93006348	+	1	NA	promoter-TSS (NM_177587)	promoter-TSS (NM_177587)	4	NM_001159658	208760	Mm.235537	NM_177587	ENSMUSG00000045091	Aqp12	AB084104|mAQP12	aquaporin 12	protein-coding
mm_120812.1	chr14	75131108	75131150	+	1	NA	promoter-TSS (NM_001247984)	promoter-TSS (NM_001247984)	6	NM_001247984	18826	Mm.153911	NM_008879	ENSMUSG00000021998	Lcp1	AW536232|D14Ertd310e|LCP-1|Pls2|pp65	lymphocyte cytosolic protein 1	protein-coding
mm_64294.1	chr7	141859145	141859154	+	1	NA	exon (NM_028801, exon 31 of 49)	exon (NM_028801, exon 31 of 49)	20077	NM_028801	74180	Mm.200752	NM_028801	ENSMUSG00000066108	Muc5b	2300002I04Rik|A130042M24|AV085033|MUC5|MUC9|mucin 5b	mucin 5, subtype B, tracheobronchial	protein-coding
mm_49320.1	chr6	18853647	18853668	+	1	NA	exon (NM_133939, exon 4 of 4)	exon (NM_133939, exon 4 of 4)	5022	NM_133939	76522	Mm.275158	NM_133939	ENSMUSG00000044155	Lsm8	2010003I05Rik|AW214405|Naa38	LSM8 homolog, U6 small nuclear RNA associated	protein-coding
mm_32752.1	chr4	116686565	116686575	+	1	NA	promoter-TSS (NR_040442)	promoter-TSS (NR_040442)	-548	NR_040442	100502959	Mm.395400	NR_040442		AV051173	-	expressed sequence AV051173	ncRNA
mm_1719.1	chr1	75360223	75360249	+	1	NA	promoter-TSS (NM_010043)	promoter-TSS (NM_010043)	-56	NM_010043	13346	Mm.6712	NM_010043	ENSMUSG00000026208	Des	-	desmin	protein-coding
mm_29516.1	chr3	116424111	116424125	-	1	NA	promoter-TSS (NM_001173553)	promoter-TSS (NM_001173553)	-86	NM_001173553	229776	Mm.17647	NM_001080818	ENSMUSG00000033502	Cdc14a	A830059A17Rik|CDC14A2|CDC14a1|Cdc14	CDC14 cell division cycle 14A	protein-coding
mm_77855.1	chr9	5311986	5311998	+	1	NA	intron (NM_007609, intron 1 of 8)	RLTR17|LTR|ERVK	3143	NM_007609	12363	Mm.1569	NM_007609	ENSMUSG00000033538	Casp4	CASP-11|CASP-4|Casp11|Caspl|ich-3	caspase 4, apoptosis-related cysteine peptidase	protein-coding
mm_116585.1	chr13	47106210	47106221	-	1	NA	promoter-TSS (NM_025900)	promoter-TSS (NM_025900)	6	NM_025900	110052	Mm.131150	NM_025900	ENSMUSG00000021377	Dek	1810019E15Rik|D13H6S231E	DEK oncogene (DNA binding)	protein-coding
mm_161001.1	chr11	116359388	116359388	-	1	NA	intron (NM_027258, intron 5 of 18)	(TG)n|Simple_repeat|Simple_repeat	-24034	NM_008240	15223	Mm.378938	NM_008240	ENSMUSG00000034227	Foxj1	FKHL-13|HFH-4|Hfh4	forkhead box J1	protein-coding
mm_18627.1	chr2	69206134	69206144	-	1	NA	promoter-TSS (NM_001199123)	promoter-TSS (NM_001199123)	74	NM_025565	66442	Mm.272969	NM_025565	ENSMUSG00000005233	Spc25	2600017H08Rik|2610205L13Rik|Spbc25	SPC25, NDC80 kinetochore complex component, homolog (S. cerevisiae)	protein-coding
mm_98941.1	chr11	98383817	98383832	+	1	NA	promoter-TSS (NM_011540)	promoter-TSS (NM_011540)	13	NM_011540	21393	Mm.10762	NM_011540	ENSMUSG00000007877	Tcap	AI503981|AJ223855	titin-cap	protein-coding
mm_103122.1	chr11	70205031	70205038	-	1	NA	Intergenic	Intergenic	-8876	NM_153081	216867	Mm.289238	NM_153081	ENSMUSG00000040938	Slc16a11	AB041591|MCT 11|MNCb-2717	solute carrier family 16 (monocarboxylic acid transporters), member 11	protein-coding
mm_131614.1	chr16	19760264	19760331	+	1	NA	promoter-TSS (NM_001159407)	promoter-TSS (NM_001159407)	63	NM_001159407	108105	Mm.33935	NM_054052	ENSMUSG00000022686	B3gnt5	beta3GnT5	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5	protein-coding
mm_55415.1	chr6	65024746	65024759	-	1	NA	Intergenic	RLTR23|LTR|ERV1	-17915	NM_007958	13990	Mm.99113	NM_007958	ENSMUSG00000029920	Smarcad1	AV081750|AW226546|D6Pas1|Etl1|mKIAA1122	SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1	protein-coding
mm_26194.1	chr3	138489774	138489785	+	1	NA	promoter-TSS (NM_175224)	promoter-TSS (NM_175224)	-397	NM_175224	75624	Mm.26833	NM_175224	ENSMUSG00000005813	Metap1	1700029C17Rik|AW047992|mKIAA0094	methionyl aminopeptidase 1	protein-coding
mm_62156.1	chr7	97140349	97140351	+	1	NA	intron (NM_001162477, intron 1 of 9)	L1MEd|LINE|L1	58599	NM_010248	14389	Mm.42033	NM_010248	ENSMUSG00000004508	Gab2	AI463667|D130058I17Rik|p97	growth factor receptor bound protein 2-associated protein 2	protein-coding
mm_161424.1	chr15	41789466	41789466	+	1	NA	promoter-TSS (NM_001130163)	promoter-TSS (NM_001130163)	-49	NM_001130163	170719	Mm.254267	NM_130885	ENSMUSG00000022307	Oxr1	2210416C20Rik|C7|C7B	oxidation resistance 1	protein-coding
mm_140114.1	chr17	78916474	78916509	+	1	NA	promoter-TSS (NM_001177403)	promoter-TSS (NM_001177403)	-8	NM_001177403	68554	Mm.391820	NM_001177402	ENSMUSG00000062691	Cebpzos	1110001A16Rik	CCAAT/enhancer binding protein (C/EBP), zeta, opposite strand	protein-coding
mm_123148.1	chr14	57099552	57099560	-	1	NA	3' UTR (NM_008125, exon 2 of 2)	3' UTR (NM_008125, exon 2 of 2)	5146	NM_008125	14619	Mm.390683	NM_008125	ENSMUSG00000046352	Gjb2	AI325222|Cnx26|Cx26|Gjb-2	gap junction protein, beta 2	protein-coding
mm_40825.1	chr5	72803098	72803100	+	1	NA	intron (NM_001113461, intron 3 of 17)	intron (NM_001113461, intron 3 of 17)	-50322	NM_001122754	22165	Mm.3264	NM_013698	ENSMUSG00000054892	Txk	A130089B16Rik|Btkl|PTK-RL-18|PTK4|Rlk	TXK tyrosine kinase	protein-coding
mm_118791.1	chr14	24118994	24119000	+	1	NA	Intergenic	B1_Mur1|SINE|Alu	30120	NR_106069	102465697		NR_106069	ENSMUSG00000105723	Mir7210	mir-7210|mmu-mir-7210	microRNA 7210	ncRNA
mm_138276.1	chr17	34605856	34605862	+	1	NA	promoter-TSS (NM_001163379)	promoter-TSS (NM_001163379)	-2	NM_001163379	55979	Mm.8684	NM_018862	ENSMUSG00000034254	Agpat1	1-AGP|1-AGPAT|AW047140	1-acylglycerol-3-phosphate O-acyltransferase 1 (lysophosphatidic acid acyltransferase, alpha)	protein-coding
mm_127338.1	chr15	100478795	100478799	+	1	NA	TTS (NM_153407)	TTS (NM_153407)	9763	NM_134093	68614	Mm.275272	NM_134093	ENSMUSG00000037353	Letmd1	1110019O13Rik|AI593524|BB130465|BB235638|HCCR-2|HCCR1|MCC-32|Mccr	LETM1 domain containing 1	protein-coding
mm_142315.1	chr17	42876617	42876676	-	1	NA	promoter-TSS (NM_009847)	promoter-TSS (NM_009847)	-222	NM_009847	12488	Mm.218637	NM_009847	ENSMUSG00000061665	Cd2ap	AL024079|C78928|METS-1|Mets1	CD2-associated protein	protein-coding
mm_160192.1	chr7	60140231	60140231	-	1	NA	promoter-TSS (NM_001082962)	promoter-TSS (NM_001082962)	-12	NM_001082962	20646	Mm.274995	NM_013670	ENSMUSG00000102252	Snrpn	2410045I01Rik|HCERN3|Peg4|Pwcr1|SMN	small nuclear ribonucleoprotein N	protein-coding
mm_110361.1	chr12	40038031	40038041	-	1	NA	promoter-TSS (NM_007487)	promoter-TSS (NM_007487)	-49	NM_001039515	11861	Mm.12723	NM_007487	ENSMUSG00000047446	Arl4a	AI467555|Arl4	ADP-ribosylation factor-like 4A	protein-coding
mm_68311.1	chr7	105787484	105787494	-	1	NA	promoter-TSS (NM_001162943)	promoter-TSS (NM_001162943)	61	NM_001162943	233651	Mm.334108	NM_001162943	ENSMUSG00000036862	Dchs1	3110041P15Rik|C130033F22Rik|CDH25|FIB1|Gm165|PCDH16	dachsous 1 (Drosophila)	protein-coding
mm_577.1	chr1	39193740	39193798	+	1	NA	promoter-TSS (NM_008719)	promoter-TSS (NM_008719)	-503	NM_008719	18143	Mm.2380	NM_008719	ENSMUSG00000026077	Npas2	MOP4|bHLHe9	neuronal PAS domain protein 2	protein-coding
mm_86184.1	chr9	119322377	119322417	-	1	NA	promoter-TSS (NM_133985)	promoter-TSS (NM_133985)	30	NR_045693	108737	Mm.293565	NM_133985	ENSMUSG00000036737	Oxsr1	2210022N24Rik|2810422B09Rik|AI462649|AW209236|Osr1|mKIAA1101	oxidative-stress responsive 1	protein-coding
mm_43544.1	chr5	137553514	137553520	+	1	NA	promoter-TSS (NM_031404)	promoter-TSS (NM_031404)	-38	NM_031404	83766	Mm.31646	NM_031404	ENSMUSG00000029712	Actl6b	Actl6|ArpNa|Baf53b	actin-like 6B	protein-coding
mm_71356.1	chr8	45658732	45658798	+	1	NA	intron (NM_001310707, intron 1 of 23)	intron (NM_001310707, intron 1 of 23)	-3228	NM_001310708	234214	Mm.211096	NM_172752	ENSMUSG00000031626	Sorbs2	2010203O03Rik|9430041O17Rik|A530071H08|Argbp2|mKIAA0777|nArgBP2	sorbin and SH3 domain containing 2	protein-coding
mm_168373.1	chr11	21259163	21259175	+	1	NA	intron (NM_139061, intron 1 of 22)	B1_Mm|SINE|Alu	20137	NM_001290628	245944	Mm.170103	NM_139061	ENSMUSG00000020128	Vps54	Hcc8|Vps54l|mSLP8|wr	VPS54 GARP complex subunit	protein-coding
mm_107106.1	chr12	17786481	17786505	+	1	NA	exon (NM_016677, exon 2 of 4)	exon (NM_016677, exon 2 of 4)	95679	NM_016677	53602	Mm.313619	NM_016677	ENSMUSG00000071379	Hpcal1	NVP-3|Nvp3|VILIP3|Vnsl3|Vsnl3	hippocalcin-like 1	protein-coding
mm_47724.1	chr5	130023229	130023233	-	1	NA	intron (NM_133768, intron 2 of 16)	intron (NM_133768, intron 2 of 16)	1100	NM_133768	109900	Mm.23869	NM_133768	ENSMUSG00000025533	Asl	2510006M18Rik	argininosuccinate lyase	protein-coding
mm_105958.1	chr11	115419933	115419953	-	1	NA	promoter-TSS (NM_027862)	promoter-TSS (NM_027862)	-24	NM_027862	71679	Mm.371641	NM_027862	ENSMUSG00000034566	Atp5h	0610009D10Rik	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit D	protein-coding
mm_47220.1	chr5	121163215	121163235	-	1	NA	exon (NM_001109992, exon 5 of 16)	exon (NM_001109992, exon 5 of 16)	28172	NM_001109992	19247	Mm.8681	NM_011202	ENSMUSG00000043733	Ptpn11	2700084A17Rik|AW536184|PTP1D|PTP2C|SAP-2|SH-PTP2|SH-PTP3|SHP-2|Shp2|Syp	protein tyrosine phosphatase, non-receptor type 11	protein-coding
mm_143106.1	chr17	57087730	57087734	-	1	NA	promoter-TSS (NM_009451)	promoter-TSS (NM_009451)	50	NM_009451	22153	Mm.7420	NM_009451	ENSMUSG00000062591	Tubb4a	AI325297|M(beta)4|Tubb|Tubb4	tubulin, beta 4A class IVA	protein-coding
mm_67405.1	chr7	80025114	80025135	-	1	NA	intron (NM_001145999, intron 1 of 4)	intron (NM_001145999, intron 1 of 4)	310	NM_001146000	209225	Mm.290925	NM_175433	ENSMUSG00000048897	Zfp710	5430400N05Rik|9830165K13|AI324798|Znf710	zinc finger protein 710	protein-coding
mm_25229.1	chr3	103860313	103860329	+	1	NA	promoter-TSS (NM_008979)	promoter-TSS (NM_008979)	44	NM_008979	19260	Mm.395	NM_008979	ENSMUSG00000027843	Ptpn22	70zpep|PEP|Ptpn8	protein tyrosine phosphatase, non-receptor type 22 (lymphoid)	protein-coding
mm_79232.1	chr9	50496777	50496801	+	1	NA	intron (NM_029639, intron 1 of 3)	intron (NM_029639, intron 1 of 3)	2264	NM_029639	76509	Mm.29959	NM_029639	ENSMUSG00000032068	Plet1	0610037B23Rik|1600029D21Rik|AA407923|AU043048	placenta expressed transcript 1	protein-coding
mm_39217.1	chr4	156186216	156186279	-	1	NA	intron (NM_021604, intron 2 of 35)	intron (NM_021604, intron 2 of 35)	11241	NM_021604	11603	Mm.273098	NM_021604	ENSMUSG00000041936	Agrn	Agrin|nmf380	agrin	protein-coding
mm_84723.1	chr9	73988237	73988250	-	1	NA	Intergenic	Intergenic	-54676	NM_001081153	208898	Mm.41035	NM_001081153	ENSMUSG00000062151	Unc13c	1500037O19Rik|AU019458|D9Ertd414e|Munc13-3|Unc13h3	unc-13 homolog C (C. elegans)	protein-coding
mm_69715.1	chr7	140154713	140154745	-	1	NA	promoter-TSS (NM_183147)	promoter-TSS (NM_183147)	-70	NM_183147	212518	Mm.246858	NM_183147	ENSMUSG00000045733	Sprn	C630041J07	shadow of prion protein	protein-coding
mm_12541.1	chr2	72297896	72297912	+	1	NA	intron (NM_023057, intron 1 of 19)	intron (NM_023057, intron 1 of 19)	12203	NM_178084	65964	Mm.304143	NM_023057	ENSMUSG00000004085	Map3k20	AV006891|B230120H23Rik|MLTK|MLTKalpha|MLTKbeta|Zak	mitogen-activated protein kinase kinase kinase 20	protein-coding
mm_11821.1	chr2	44335880	44335888	+	1	NA	intron (NM_001301831, intron 13 of 14)	intron (NM_001301831, intron 13 of 14)	-270560	NR_040622	320872	Mm.445023	NR_040622	ENSMUSG00000085089	Arhgap15os	A430092G05Rik	Rho GTPase activating protein 15, opposite strand	ncRNA
mm_29239.1	chr3	107215978	107215989	-	1	NA	exon (NM_001111143, exon 5 of 9)	exon (NM_001111143, exon 5 of 9)	5749	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_159245.1	chr2	151098243	151098243	+	1	NA	promoter-TSS (NM_001097977)	promoter-TSS (NM_001097977)	-2	NM_001097977	433486	Mm.422661	NM_001097977	ENSMUSG00000079006	Gm14151	OTTMUSG00000015806	predicted gene 14151	protein-coding
mm_104040.1	chr11	86304726	86304739	-	1	NA	TTS (NR_130959)	TTS (NR_130959)	-47164	NM_027421	70422	Mm.171304	NM_027421	ENSMUSG00000018068	Ints2	2810417D08Rik|AA408260|AI987735|mKIAA1287	integrator complex subunit 2	protein-coding
mm_90577.1	chr10	128254158	128254176	+	1	NA	promoter-TSS (NM_133996)	promoter-TSS (NM_133996)	36	NM_133996	28194	Mm.439846	NM_133996	ENSMUSG00000051716	Apon	AI195275|D10Ucla2	apolipoprotein N	protein-coding
mm_136722.1	chr17	8195965	8195976	+	1	NA	3' UTR (NM_201230, exon 12 of 12)	3' UTR (NM_201230, exon 12 of 12)	30452	NM_201230	75296	Mm.227250	NM_201230	ENSMUSG00000069135	Fgfr1op	4930553O10Rik|FOP	Fgfr1 oncogene partner	protein-coding
mm_138550.1	chr17	35264398	35264418	+	1	NA	intron (NM_010380, intron 3 of 7)	intron (NM_010380, intron 3 of 7)	1285	NM_001267808	14980	Mm.439675	NM_001267808		H2-L	H-2L	histocompatibility 2, D region locus L	protein-coding
mm_153531.1	chr19	41848291	41848310	-	1	NA	promoter-TSS (NM_177603)	promoter-TSS (NM_177603)	-168	NM_177603	212398	Mm.222723	NM_177603	ENSMUSG00000047604	Frat2	-	frequently rearranged in advanced T cell lymphomas 2	protein-coding
mm_34654.1	chr4	150854371	150854385	+	1	NA	promoter-TSS (NM_133753)	promoter-TSS (NM_133753)	571	NR_040649	73348	Mm.396218	NR_040649	ENSMUSG00000078492	1700045H11Rik	-	RIKEN cDNA 1700045H11 gene	ncRNA
mm_85222.1	chr9	97018852	97018879	-	1	NA	promoter-TSS (NM_145134)	promoter-TSS (NM_145134)	-510	NM_145134	211949	Mm.491271	NM_145134	ENSMUSG00000046997	Spsb4	D030068E18Rik|SSB-4|Ssb4	splA/ryanodine receptor domain and SOCS box containing 4	protein-coding
mm_40612.1	chr5	64781004	64781032	+	1	NA	Intergenic	Intergenic	-22505	NM_008453	16599	Mm.392759	NM_008453	ENSMUSG00000029178	Klf3	9930027G08Rik|AL024007|Bklf|Tef-2	Kruppel-like factor 3 (basic)	protein-coding
mm_6952.1	chr1	85956739	85956747	-	1	NA	intron (NM_001033290, intron 1 of 1)	intron (NM_001033290, intron 1 of 1)	4312	NM_001033290	227326	Mm.244158	NM_001033290	ENSMUSG00000049608	Gpr55	CTFL|Gm218|Lpir1	G protein-coupled receptor 55	protein-coding
mm_12048.1	chr2	59161032	59161054	+	1	NA	5' UTR (NM_026361, exon 1 of 22)	5' UTR (NM_026361, exon 1 of 22)	193	NM_175464	227937	Mm.260938	NM_026361	ENSMUSG00000026991	Pkp4	5031422I09Rik|9430019K17Rik|Armrp|p0071	plakophilin 4	protein-coding
mm_125949.1	chr15	76248817	76248842	+	1	NA	TTS (NR_105918)	TTS (NR_105918)	638	NR_105918	102465575		NR_105918	ENSMUSG00000098625	Mir6953	Gm27738|mmu-mir-6953	microRNA 6953	ncRNA
mm_35914.1	chr4	52445416	52445440	-	1	NA	intron (NM_001301412, intron 3 of 24)	intron (NM_001301412, intron 3 of 24)	6207	NM_001301412	14211	Mm.2999	NM_008017	ENSMUSG00000028312	Smc2	5730502P04Rik|AI255214|AW545314|CAP-E|CAPE|Fin16|SMC-2|Smc2l1	structural maintenance of chromosomes 2	protein-coding
mm_71408.1	chr8	46471694	46471704	+	1	NA	intron (NM_007981, intron 1 of 20)	CpG	662	NM_007981	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_11264.1	chr2	29984120	29984123	+	1	NA	intron (NM_001309460, intron 5 of 57)	B1_Mur3|SINE|Alu	-11829	NR_105963	102465603		NR_105963	ENSMUSG00000098453	Mir6997	Gm27310|mmu-mir-6997	microRNA 6997	ncRNA
mm_110661.1	chr12	59131279	59131294	-	1	NA	promoter-TSS (NM_001165253)	promoter-TSS (NM_001165253)	-167	NM_001165253	338320	Mm.213215	NM_146034	ENSMUSG00000021000	Mia2	Ctage5|D12Bwg0579e|Mea6|Mgea|Mgea6	melanoma inhibitory activity 2	protein-coding
mm_84843.1	chr9	78378547	78378562	-	1	NA	promoter-TSS (NM_026480)	promoter-TSS (NM_026480)	34	NM_026480	67968	Mm.26883	NM_026480	ENSMUSG00000032346	Ooep	2410146L05Rik|Floped|Moep19|Sddr	oocyte expressed protein	protein-coding
mm_34871.1	chr4	155558959	155558981	+	1	NA	3' UTR (NM_008142, exon 12 of 12)	3' UTR (NM_008142, exon 12 of 12)	-3422	NM_138671	192185	Mm.28347	NM_138671	ENSMUSG00000029063	Nadk	4432404C02Rik|BC004012	NAD kinase	protein-coding
mm_49458.1	chr6	29398960	29398966	+	1	NA	promoter-TSS (NM_001201378)	promoter-TSS (NM_001201378)	37	NM_001201378	232664	Mm.251303	NM_145574	ENSMUSG00000029769	Ccdc136	4921511K06Rik|BC006583	coiled-coil domain containing 136	protein-coding
mm_48945.1	chr6	4539592	4539600	+	1	NA	exon (NM_007743, exon 51 of 52)	exon (NM_007743, exon 51 of 52)	33978	NM_007743	12843	Mm.277792	NM_007743	ENSMUSG00000029661	Col1a2	AA960264|AI325291|Col1a-2|Cola-2|Cola2|oim	collagen, type I, alpha 2	protein-coding
mm_120989.1	chr14	79290213	79290251	+	1	NA	intron (NM_025427, intron 4 of 4)	intron (NM_025427, intron 4 of 4)	11403	NM_025427	66214	Mm.29811	NM_025427	ENSMUSG00000022018	Rgcc	1190002H23Rik|Rgc-32|Rgc32	regulator of cell cycle	protein-coding
mm_134497.1	chr16	18811639	18811643	-	1	NA	promoter-TSS (NM_001161623)	promoter-TSS (NM_001161623)	-2	NM_001161623	12544	Mm.1248	NM_009862	ENSMUSG00000000028	Cdc45	Cdc45l	cell division cycle 45	protein-coding
mm_32788.1	chr4	116721068	116721078	+	1	NA	5' UTR (NM_146151, exon 1 of 11)	5' UTR (NM_146151, exon 1 of 11)	118	NM_146151	230661	Mm.482431	NM_146151	ENSMUSG00000033985	Tesk2	-	testis-specific kinase 2	protein-coding
mm_101693.1	chr11	40750404	40750432	-	1	NA	3' UTR (NM_009831, exon 6 of 6)	3' UTR (NM_009831, exon 6 of 6)	4868	NM_009831	12450	Mm.2103	NM_009831	ENSMUSG00000020326	Ccng1	AI314029	cyclin G1	protein-coding
mm_111985.1	chr12	110478656	110478665	-	1	NA	intron (NM_001135001, intron 3 of 13)	intron (NM_001135001, intron 3 of 13)	-7079	NM_001081457	26931	Mm.240396	NM_012023	ENSMUSG00000017843	Ppp2r5c	2610043M05Rik|2700063L20Rik|AI060890|AW545884|C85228|D12Bwg0916e|mKIAA0044	protein phosphatase 2, regulatory subunit B', gamma	protein-coding
mm_35550.1	chr4	41507784	41507791	-	1	NA	promoter-TSS (NM_001253780)	promoter-TSS (NM_001253780)	-23	NM_001253778	73721	Mm.45614	NM_028624	ENSMUSG00000028441	1110017D15Rik	Cbe1|Smrp1	RIKEN cDNA 1110017D15 gene	protein-coding
mm_91300.1	chr10	24916132	24916139	-	1	NA	exon (NM_007482, exon 7 of 8)	exon (NM_007482, exon 7 of 8)	5471	NR_105870	102465545		NR_105870	ENSMUSG00000099181	Mir6905	Gm27879|mmu-mir-6905	microRNA 6905	ncRNA
mm_165028.1	chr19	32757681	32757695	+	1	NA	5' UTR (NM_008960, exon 1 of 9)	5' UTR (NM_008960, exon 1 of 9)	111	NM_008960	19211	Mm.245395	NM_008960	ENSMUSG00000013663	Pten	2310035O07Rik|A130070J02Rik|AI463227|B430203M17Rik|MMAC1|TEP1	phosphatase and tensin homolog	protein-coding
mm_150478.1	chr19	38930929	38930941	+	1	NA	promoter-TSS (NM_008234)	promoter-TSS (NM_008234)	-55	NM_008234	15201	Mm.57223	NM_008234	ENSMUSG00000025001	Hells	AI323785|E130115I21Rik|LSH|Lysh|PASG|YFK8	helicase, lymphoid specific	protein-coding
mm_71142.1	chr8	39046596	39046650	+	1	NA	exon (NM_030254, exon 2 of 8)	exon (NM_030254, exon 2 of 8)	40756	NM_030254	80286	Mm.272722	NM_030254	ENSMUSG00000039530	Tusc3	AU022242|BC003311|N33	tumor suppressor candidate 3	protein-coding
mm_44719.1	chr5	30960171	30960182	-	1	NA	5' UTR (NM_001294302, exon 1 of 8)	5' UTR (NM_001294302, exon 1 of 8)	151	NM_001294302	50907	Mm.272414	NM_016703	ENSMUSG00000045302	Preb	C85705	prolactin regulatory element binding	protein-coding
mm_170522.1	chr19	3282928	3282931	-	1	NA	promoter-TSS (NM_001347420)	promoter-TSS (NM_001347420)	28	NM_001347420	353242	Mm.74084	NM_172252	ENSMUSG00000024829	Mrpl21	BC028768	mitochondrial ribosomal protein L21	protein-coding
mm_84824.1	chr9	77976912	77976913	-	1	NA	exon (NM_134255, exon 5 of 8)	exon (NM_134255, exon 5 of 8)	59547	NM_134255	68801	Mm.430736	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	ELOVL family member 5, elongation of long chain fatty acids (yeast)	protein-coding
mm_45862.1	chr5	87929865	87929886	-	1	NA	exon (NM_007786, exon 4 of 5)	exon (NM_007786, exon 4 of 5)	4242	NM_007786	12994	Mm.296303	NM_007786	ENSMUSG00000001622	Csn3	AW208918|CSN10|Csnk	casein kappa	protein-coding
mm_94994.1	chr11	31871666	31871675	+	1	NA	5' UTR (NM_026252, exon 1 of 10)	5' UTR (NM_026252, exon 1 of 10)	730	NM_026252	67579	Mm.339792	NM_026252	ENSMUSG00000020300	Cpeb4	Cpe-bp4|Cpeb-4|mCPEB-4	cytoplasmic polyadenylation element binding protein 4	protein-coding
mm_29810.1	chr3	127837420	127837505	-	1	NA	promoter-TSS (NM_145964)	promoter-TSS (NM_145964)	30	NM_001346718	211556	Mm.403486	NM_145964	ENSMUSG00000074238	Ap1ar	AA407621|C78909|Gadkin	adaptor-related protein complex 1 associated regulatory protein	protein-coding
mm_76612.1	chr8	91134028	91134038	-	1	NA	promoter-TSS (NM_001302337)	promoter-TSS (NM_001302337)	-6	NM_001302268	14339	Mm.324588	NM_010241	ENSMUSG00000031667	Aktip	AL023020|Fif|Ft|Ft1|Fts	thymoma viral proto-oncogene 1 interacting protein	protein-coding
mm_89618.1	chr10	96173232	96173250	+	1	NA	Intergenic	Intergenic	-52966	NR_110448	74881	Mm.410819	NR_110448		4930459C07Rik	-	RIKEN cDNA 4930459C07 gene	ncRNA
mm_20046.1	chr2	120154601	120154611	-	1	NA	promoter-TSS (NM_133838)	promoter-TSS (NM_133838)	-31	NM_133838	98878	Mm.132226	NM_133838	ENSMUSG00000027293	Ehd4	2210022F10Rik|AI197390|AI846352|AV006278|Past2	EH-domain containing 4	protein-coding
mm_107050.1	chr12	16232290	16232310	+	1	NA	Intergenic	Intergenic	357470	NM_015763	14245	Mm.153625	NM_015763	ENSMUSG00000020593	Lpin1	4631420P06|Kiaa0188|Lipin1|fld|mKIAA0188	lipin 1	protein-coding
mm_21026.1	chr2	152413487	152413489	-	1	NA	3' UTR (NM_175126, exon 1 of 1)	3' UTR (NM_175126, exon 1 of 1)	1556	NM_175126	67917	Mm.391810	NM_175126	ENSMUSG00000074682	Zcchc3	2810406K24Rik	zinc finger, CCHC domain containing 3	protein-coding
mm_55945.1	chr6	85126089	85126099	-	1	NA	promoter-TSS (NM_001034902)	promoter-TSS (NM_001034902)	0	NM_001034902	545861	Mm.321419	NM_001034902	ENSMUSG00000072952	Gm5878	EG545861	predicted gene 5878	protein-coding
mm_37161.1	chr4	117148224	117148231	-	1	NA	Intergenic	Intergenic	6347	NR_028524	100217424		NR_028524	ENSMUSG00000065680	Snord38a	MBII-329	small nucleolar RNA, C/D box 38A	snoRNA
mm_95259.1	chr11	44667559	44667560	+	1	NA	intron (NM_007897, intron 6 of 15)	intron (NM_007897, intron 6 of 15)	49459	NM_001290710	13591	Mm.439662	NM_007897	ENSMUSG00000057098	Ebf1	Ebf|O/E-1|OE-1|Olf-1|Olf1	early B cell factor 1	protein-coding
mm_162564.1	chr1	172430950	172430956	+	1	NA	Intergenic	MYSERV6-int|LTR|ERVK	-44407	NM_029612	98365	Mm.150050	NM_029612	ENSMUSG00000026548	Slamf9	2310026I04Rik|AI462096|CD2F-10|CD84-H1|Cd2f10|SF2001	SLAM family member 9	protein-coding
mm_28036.1	chr3	83789941	83789961	-	1	NA	Intergenic	CpG	23630	NM_009144	20319	Mm.19155	NM_009144	ENSMUSG00000027996	Sfrp2	AI851596|Sdf5	secreted frizzled-related protein 2	protein-coding
mm_69748.1	chr7	140955903	140955913	-	1	NA	promoter-TSS (NM_030694)	promoter-TSS (NM_030694)	53	NM_030694	80876	Mm.379266	NM_030694	ENSMUSG00000060591	Ifitm2	DSPA2c|Ifitm3l|fragilis3|mil-3	interferon induced transmembrane protein 2	protein-coding
mm_145062.1	chr18	40513025	40513027	+	1	NA	intron (NM_026135, intron 1 of 1)	intron (NM_026135, intron 1 of 1)	254665	NM_026135	383348	Mm.76366	NM_026135	ENSMUSG00000051401	Kctd16	4930434H12Rik|Gm1267	potassium channel tetramerisation domain containing 16	protein-coding
mm_138378.1	chr17	35024108	35024113	+	1	NA	intron (NM_001347347, intron 13 of 16)	intron (NM_001347347, intron 13 of 16)	3906	NR_028258	78376	Mm.390966	NM_023893	ENSMUSG00000036185	Sapcd1	2810436B06Rik|G7d|Ng23	suppressor APC domain containing 1	protein-coding
mm_171788.1	chr5	113767092	113767108	+	1	NA	intron (NM_016926, intron 1 of 18)	intron (NM_016926, intron 1 of 18)	4549	NM_016926	53890	Mm.29594	NM_016926	ENSMUSG00000018974	Sart3	AU045857|mKIAA0156	squamous cell carcinoma antigen recognized by T cells 3	protein-coding
mm_114459.1	chr13	67451248	67451259	+	1	NA	intron (NM_177712, intron 1 of 3)	intron (NM_177712, intron 1 of 3)	371	NM_177712	238692	Mm.486478	NM_177712	ENSMUSG00000069206	Zfp874a	C330011K17Rik|Rslcan15|Zfp874	zinc finger protein 874a	protein-coding
mm_90693.1	chr10	130004357	130004361	+	1	NA	Intergenic	MMERVK9C_I-int|LTR|ERVK	-13004	NM_146675	258670	Mm.271512	NM_146675	ENSMUSG00000048745	Olfr820	MOR116-1	olfactory receptor 820	protein-coding
mm_49531.1	chr6	30102141	30102149	+	1	NA	intron (NM_010938, intron 5 of 11)	intron (NM_010938, intron 5 of 11)	25824	NM_001164229	18181	Mm.259258	NM_010938	ENSMUSG00000058440	Nrf1	C87038|D6Ertd415e	nuclear respiratory factor 1	protein-coding
mm_104157.1	chr11	87217715	87217758	-	1	NA	intron (NM_197987, intron 23 of 23)	intron (NM_197987, intron 23 of 23)	90661	NM_197987	68729	Mm.17436	NM_197987	ENSMUSG00000018548	Trim37	1110032A10Rik|2810004E07Rik|AI848587|AU043018|MUL|TEF3|mKIAA0898	tripartite motif-containing 37	protein-coding
mm_157223.1	chrX	13524182	13524182	-	1	NA	intron (NM_009806, intron 24 of 24)	intron (NM_009806, intron 24 of 24)	56510	NM_173415	236690	Mm.90233	NM_173415	ENSMUSG00000051228	Nyx	CLNP|CSNB1|CSNB4|nob	nyctalopin	protein-coding
mm_33710.1	chr4	133813535	133813561	+	1	NA	Intergenic	CpG	-59937	NM_001080819	93760	Mm.22478	NM_001080819	ENSMUSG00000007880	Arid1a	1110030E03Rik|BAF250a|Osa1|Smarcf1	AT rich interactive domain 1A (SWI-like)	protein-coding
mm_50265.1	chr6	45059583	45059638	+	1	NA	promoter-TSS (NM_001004357)	promoter-TSS (NM_001004357)	-451	NM_001004357	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding
mm_117324.1	chr13	67830907	67830911	-	1	NA	promoter-TSS (NR_045194)	promoter-TSS (NR_045194)	76	NR_045194	320163	Mm.444711	NR_045194	ENSMUSG00000097276	4930525G20Rik	-	RIKEN cDNA 4930525G20 gene	ncRNA
mm_138337.1	chr17	34898587	34898605	+	1	NA	promoter-TSS (NM_145830)	promoter-TSS (NM_145830)	104	NM_147151	110147	Mm.35345	NM_145830	ENSMUSG00000013787	Ehmt2	Bat8|D17Ertd710e|G9a|KMT1C|NG36	euchromatic histone lysine N-methyltransferase 2	protein-coding
mm_66431.1	chr7	44668491	44668501	-	1	NA	intron (NM_001271540, intron 1 of 41)	intron (NM_001271540, intron 1 of 41)	2347	NM_001271540	71960	Mm.158289	NM_028021	ENSMUSG00000030739	Myh14	2400004E04Rik|II-C|NHMCII|NMHC II-C	myosin, heavy polypeptide 14	protein-coding
mm_158079.1	chrX	101264973	101264983	-	1	NA	promoter-TSS (NM_001317221)	promoter-TSS (NM_001317221)	-986	NM_001317221	245536	Mm.212463	NM_001033362	ENSMUSG00000090141	Gm614	-	predicted gene 614	protein-coding
mm_53676.1	chr6	141876049	141876050	+	1	NA	Intergenic	RLTR48A|LTR|ERV1	-19878	NM_030687	28250	Mm.255586	NM_030687	ENSMUSG00000030237	Slco1a4	AI785519|Oatp1a4|Oatp2|Slc21a5	solute carrier organic anion transporter family, member 1a4	protein-coding
mm_154159.1	chr19	58455819	58455872	-	1	NA	promoter-TSS (NM_010279)	promoter-TSS (NM_010279)	-447	NM_010279	14585	Mm.88367	NM_010279	ENSMUSG00000025089	Gfra1	AU042498	glial cell line derived neurotrophic factor family receptor alpha 1	protein-coding
mm_94418.1	chr11	5864218	5864241	+	1	NA	exon (NM_009636, exon 2 of 21)	exon (NM_009636, exon 2 of 21)	2363	NM_001291857	11568	Mm.3317	NM_009636	ENSMUSG00000020473	Aebp1	ACLP	AE binding protein 1	protein-coding
mm_105300.1	chr11	102553223	102553226	-	1	NA	intron (NM_001159492, intron 1 of 7)	B2_Mm2|SINE|B2	2934	NM_001159492	237943	Mm.260282	NM_001159492	ENSMUSG00000034621	Gpatch8	5430405G24Rik|AU018890|ENSMUSG00000075516|Fbm1|Gpatc8|mKIAA0553	G patch domain containing 8	protein-coding
mm_87032.1	chr10	28668454	28668458	+	1	NA	promoter-TSS (NM_178666)	promoter-TSS (NM_178666)	96	NM_178666	210757	Mm.123021	NM_178666	ENSMUSG00000049109	Themis	E430004N04Rik|Gasp|Spot|Tsepa|thylex	thymocyte selection associated	protein-coding
mm_21612.1	chr2	164256273	164256309	-	1	NA	exon (NM_173377, exon 2 of 3)	exon (NM_173377, exon 2 of 3)	352	NM_173377	329557	Mm.118769	NM_173377	ENSMUSG00000050383	Svs3b	9530004A22Rik	seminal vesicle secretory protein 3B	protein-coding
mm_89201.1	chr10	86348475	86348486	+	1	NA	3' UTR (NM_011595, exon 5 of 5)	3' UTR (NM_011595, exon 5 of 5)	48068	NM_011595	21859	Mm.4871	NM_011595	ENSMUSG00000020044	Timp3	Timp-3	tissue inhibitor of metalloproteinase 3	protein-coding
mm_103118.1	chr11	70092124	70092135	-	1	NA	promoter-TSS (NM_007493)	promoter-TSS (NM_007493)	-515	NM_007493	11890	Mm.1357	NM_007493	ENSMUSG00000040963	Asgr2	ASGPR2|Asgr|Asgr-2|HL-2	asialoglycoprotein receptor 2	protein-coding
mm_117281.1	chr13	65205962	65205969	-	1	NA	promoter-TSS (NM_175290)	promoter-TSS (NM_175290)	-249	NM_175290	97895	Mm.315815	NM_175290	ENSMUSG00000032999	Nlrp4f	C330026N02Rik|C86045|Nalp-kappa|Nalp4f	NLR family, pyrin domain containing 4F	protein-coding
mm_18322.1	chr2	57114924	57114955	-	1	NA	promoter-TSS (NM_013613)	promoter-TSS (NM_013613)	99	NM_013613	18227	Mm.3507	NM_013613	ENSMUSG00000026826	Nr4a2	HZF-3|NOT|Nurr1|RNR-1|TINOR|TINUR	nuclear receptor subfamily 4, group A, member 2	protein-coding
mm_151382.1	chr19	56287944	56287974	+	1	NA	promoter-TSS (NM_001329936)	promoter-TSS (NM_001329936)	47	NM_146101	226243	Mm.25791	NM_146101	ENSMUSG00000025075	Habp2	AI035669|FSAP|HABP|HGFAL|PHBP	hyaluronic acid binding protein 2	protein-coding
mm_36675.1	chr4	96348600	96348618	-	1	NA	promoter-TSS (NM_001004141)	promoter-TSS (NM_001004141)	71	NM_001004141	100066	Mm.26915	NM_001004141	ENSMUSG00000066097	Cyp2j11	AI314783|Cyp2j11-ps	cytochrome P450, family 2, subfamily j, polypeptide 11	protein-coding
mm_91280.1	chr10	24711910	24711918	-	1	NA	exon (NM_008813, exon 1 of 25)	exon (NM_008813, exon 1 of 25)	245	NM_001308327	18605	Mm.27254	NM_008813	ENSMUSG00000037370	Enpp1	4833416E15Rik|AI428932|C76301|CD203c|E-NPP 1|E-NPP1|Ly-41|M6S1|NPP1|Npps|PC-1|Pca|Pca-1|Pdnp1|ttw|twy	ectonucleotide pyrophosphatase/phosphodiesterase 1	protein-coding
mm_96714.1	chr11	69664171	69664184	+	1	NA	TTS (NR_110993)	TTS (NR_110993)	1134	NR_035455	100316840		NR_035455	ENSMUSG00000088752	Mir1934	mir-1934|mmu-mir-1934	microRNA 1934	ncRNA
mm_142285.1	chr17	40232588	40232597	-	1	NA	exon (NM_009639, exon 5 of 8)	exon (NM_009639, exon 5 of 8)	9666	NM_009639	11572	Mm.14138	NM_009639	ENSMUSG00000025433	Crisp3	Aeg2|CRISP-3|CRS3|SGP28	cysteine-rich secretory protein 3	protein-coding
mm_58599.1	chr7	5039287	5039288	+	1	NA	promoter-TSS (NM_001039532)	promoter-TSS (NM_001039532)	-841	NM_001039532	654801	Mm.333548	NM_001039532	ENSMUSG00000043290	Zfp784	C730049F21Rik|Znf784	zinc finger protein 784	protein-coding
mm_22649.1	chr3	14869240	14869260	+	1	NA	exon (NM_007606, exon 5 of 7)	exon (NM_007606, exon 5 of 7)	5712	NM_007606	12350	Mm.300	NM_007606	ENSMUSG00000027559	Car3	BB219044|Ca3|Car-3	carbonic anhydrase 3	protein-coding
mm_77694.1	chr8	126589537	126589570	-	1	NA	3' UTR (NM_001164598, exon 2 of 2)	3' UTR (NM_001164598, exon 2 of 2)	3883	NM_001164598	270110	Mm.334918	NM_001164598	ENSMUSG00000051495	Irf2bp2	E130305N23Rik|IRF-2BP2	interferon regulatory factor 2 binding protein 2	protein-coding
mm_155505.1	chrX	73787134	73787198	+	1	NA	promoter-TSS (NM_008323)	promoter-TSS (NM_008323)	23	NM_009279	20832	Mm.831	NM_009279	ENSMUSG00000002014	Ssr4	AW743063|C78062|Trap	signal sequence receptor, delta	protein-coding
mm_258.1	chr1	20682856	20682857	+	1	NA	promoter-TSS (NR_029902)	promoter-TSS (NR_029902)	87	NR_029902	723817		NR_029902	ENSMUSG00000065480	Mir133b	Mirn133b|mir-133b	microRNA 133b	ncRNA
mm_5855.1	chr1	53352638	53352716	-	1	NA	promoter-TSS (NM_133728)	promoter-TSS (NM_133728)	75	NM_001290984	70396	Mm.285783	NM_133728	ENSMUSG00000026095	Asnsd1	2210409M21Rik	asparagine synthetase domain containing 1	protein-coding
mm_121886.1	chr14	21740423	21740445	-	1	NA	intron (NM_001007268, intron 5 of 7)	intron (NM_001007268, intron 5 of 7)	2445	NM_013849	27389	Mm.390674	NM_013849	ENSMUSG00000021768	Dusp13	DUSP13A|DUSP13B|Gm1203|LMW-DSP6|MDSP|TMDP|TS-DSP6	dual specificity phosphatase 13	protein-coding
mm_138065.1	chr17	33931360	33931373	+	1	NA	intron (NM_009059, intron 2 of 17)	intron (NM_009059, intron 2 of 17)	1472	NM_009059	19732	Mm.43777	NM_009059	ENSMUSG00000041354	Rgl2	KE1.5|Rab2l|Rgt2|Rlf	ral guanine nucleotide dissociation stimulator-like 2	protein-coding
mm_147289.1	chr18	39489881	39489915	-	1	NA	Intergenic	CpG	-2653	NM_008173	14815	Mm.129481	NM_008173	ENSMUSG00000024431	Nr3c1	GR|Grl-1|Grl1	nuclear receptor subfamily 3, group C, member 1	protein-coding
mm_22555.1	chr3	9658372	9658378	+	1	NA	Intergenic	RMER17A|LTR|ERVK	-48290	NM_133218	170753	Mm.212908	NM_133218	ENSMUSG00000040209	Zfp704	C030026M03|C030034L19Rik|Gig1|Znf704	zinc finger protein 704	protein-coding
mm_158276.1	chrX	111463150	111463173	-	1	NA	intron (NM_025949, intron 2 of 24)	CpG-15872	74798	NM_025949	67071	Mm.37617	NM_025949	ENSMUSG00000025665	Rps6ka6	2610524K04Rik|RSK4|S6K-alpha-6	ribosomal protein S6 kinase polypeptide 6	protein-coding
mm_14694.1	chr2	141182899	141182900	+	1	NA	intron (NM_001013802, intron 5 of 18)	intron (NM_001013802, intron 5 of 18)	-511423	NM_178382	71436	Mm.426781	NM_178382	ENSMUSG00000051379	Flrt3	5530600M07Rik|C430047I10Rik|mKIAA1469	fibronectin leucine rich transmembrane protein 3	protein-coding
mm_155409.1	chrX	73411098	73411125	+	1	NA	promoter-TSS (NM_001310531)	promoter-TSS (NM_001310531)	15	NM_009566	22754	Mm.5060	NM_009566	ENSMUSG00000031374	Zfp92	-	zinc finger protein 92	protein-coding
mm_51274.1	chr6	72125429	72125447	+	1	NA	intron (NM_011375, intron 1 of 6)	intron (NM_011375, intron 1 of 6)	-2241	NR_045165	71265	Mm.442035	NR_045163	ENSMUSG00000108709	4933431G14Rik	4930565C19Rik	RIKEN cDNA 4933431G14 gene	ncRNA
mm_74432.1	chr8	3720799	3720817	-	1	NA	promoter-TSS (NM_029465)	promoter-TSS (NM_029465)	-157	NM_029465	75863	Mm.109183	NM_029465	ENSMUSG00000074491	Clec4g	4930572L20Rik	C-type lectin domain family 4, member g	protein-coding
mm_33131.1	chr4	124937043	124937074	+	1	NA	promoter-TSS (NM_177573)	promoter-TSS (NM_177573)	10	NM_177573	194268	Mm.266907	NM_177573		9930104L06Rik	-	RIKEN cDNA 9930104L06 gene	protein-coding
mm_126071.1	chr15	77477045	77477048	+	1	NA	promoter-TSS (NM_177744)	promoter-TSS (NM_177744)	-1	NM_177744	245282	Mm.390820	NM_177744	ENSMUSG00000050982	Apol10a	9030421J09Rik	apolipoprotein L 10A	protein-coding
mm_1547.1	chr1	72852422	72852432	+	1	NA	TTS (NM_008342)	TTS (NM_008342)	22438	NM_010518	16011	Mm.405761	NM_010518	ENSMUSG00000026185	Igfbp5	AI256729|AW208790|IGFBP-5|IGFBP-5P	insulin-like growth factor binding protein 5	protein-coding
mm_110671.1	chr12	65073928	65073954	-	1	NA	promoter-TSS (NM_013902)	promoter-TSS (NM_013902)	-3	NM_013902	30795	Mm.28480	NM_013902	ENSMUSG00000020949	Fkbp3	25kDa|FKBP-3|FKBP25	FK506 binding protein 3	protein-coding
mm_113707.1	chr13	43398376	43398402	+	1	NA	promoter-TSS (NM_023554)	promoter-TSS (NM_023554)	13	NM_023554	70078	Mm.439927	NM_023554	ENSMUSG00000063200	Nol7	2210008F15Rik|5730556I21Rik|NOP27|RARG-1	nucleolar protein 7	protein-coding
mm_73555.1	chr8	108959477	108959480	+	1	NA	3' UTR (NM_007496, exon 10 of 10)	3' UTR (NM_007496, exon 10 of 10)	22618	NR_037295	100526511		NR_037295	ENSMUSG00000093241	Mir3108	mir-3108|mmu-mir-3108	microRNA 3108	ncRNA
mm_31319.1	chr4	46138822	46138832	+	1	NA	promoter-TSS (NM_173033)	promoter-TSS (NM_173033)	316	NM_001033201	433702	Mm.389536	NM_001033201	ENSMUSG00000028330	Ncbp1	AU014645|AW538051|CBP80	nuclear cap binding protein subunit 1	protein-coding
mm_157522.1	chrX	50942740	50942758	-	1	NA	promoter-TSS (NM_001190332)	promoter-TSS (NM_001190332)	-39	NM_001190332	385354	Mm.393050	NM_001190332	ENSMUSG00000036131	Frmd7	EG665849|Gm1533	FERM domain containing 7	protein-coding
mm_66445.1	chr7	44863393	44863397	-	1	NA	TTS (NM_021549)	TTS (NM_021549)	5992	NM_001290767	59047	Mm.238254	NM_021549	ENSMUSG00000002963	Pnkp	1810009G08Rik|PNK	polynucleotide kinase 3'- phosphatase	protein-coding
mm_43787.1	chr5	142629599	142629615	+	1	NA	promoter-TSS (NM_178398)	promoter-TSS (NM_178398)	23	NM_178398	74781	Mm.29432	NM_178398	ENSMUSG00000029578	Wipi2	1110018O08Rik|2510001I10Rik	WD repeat domain, phosphoinositide interacting 2	protein-coding
mm_122657.1	chr14	51911548	51911564	-	1	NA	intron (NM_013864, intron 1 of 15)	intron (NM_013864, intron 1 of 15)	1932	NM_001145959	29811	Mm.26722	NM_013864	ENSMUSG00000004558	Ndrg2	AI182517|AU040374|Ndr2|SYLD	N-myc downstream regulated gene 2	protein-coding
mm_81692.1	chr9	111168742	111168751	+	1	NA	intron (NM_001164838, intron 5 of 14)	intron (NM_001164838, intron 5 of 14)	50635	NM_001164838	71268	Mm.302287	NM_027742	ENSMUSG00000032497	Lrrfip2	5133400F20Rik|AI850587	leucine rich repeat (in FLII) interacting protein 2	protein-coding
mm_124681.1	chr15	6429766	6429776	+	1	NA	exon (NM_023118, exon 10 of 15)	exon (NM_023118, exon 10 of 15)	-15562	NM_013485	12279	Mm.29095	NM_013485	ENSMUSG00000022149	C9	-	complement component 9	protein-coding
mm_143701.1	chr17	80577393	80577403	-	1	NA	Intergenic	CpG	-13564	NM_001033443	381113	Mm.329216	NM_001033443	ENSMUSG00000033966	Cdkl4	AU067824|Gm942	cyclin-dependent kinase-like 4	protein-coding
mm_66292.1	chr7	38018768	38018793	-	1	NA	intron (NM_011274, intron 1 of 10)	intron (NM_011274, intron 1 of 10)	772	NM_011274	19777	Mm.387220	NM_011274	ENSMUSG00000030421	Uri1	C80913|NNX3|Rmp	URI1, prefoldin-like chaperone	protein-coding
mm_35186.1	chr4	16001473	16001475	-	1	NA	intron (NM_145950, intron 5 of 5)	B1_Mur2|SINE|Alu	12403	NM_145950	209212	Mm.46455	NM_145950	ENSMUSG00000041153	Osgin2	BC010311|C230027H09Rik	oxidative stress induced growth inhibitor family member 2	protein-coding
mm_163996.1	chr14	64440844	64440846	-	1	NA	exon (NM_026322, exon 6 of 11)	exon (NM_026322, exon 6 of 11)	181	NM_001253715	110265	Mm.26713	NM_026322	ENSMUSG00000054733	Msra	2310045J23Rik|6530413P12Rik|MSR-A	methionine sulfoxide reductase A	protein-coding
mm_143392.1	chr17	69776008	69776013	-	1	NA	Intergenic	URR1A|DNA|hAT-Charlie	-193063	NM_001347412	224997	Mm.311840	NM_027712	ENSMUSG00000003279	Dlgap1	4933422O14Rik|9630002F18|AI845682|AI848168|BB075781|D17Bwg0511e|GKAP/SAPAP|GKPA/SAPAP|Gkap|Sapap1|mKIAA4162	discs, large (Drosophila) homolog-associated protein 1	protein-coding
mm_1306.1	chr1	64690914	64690933	+	1	NA	promoter-TSS (NM_001097644)	promoter-TSS (NM_001097644)	-264	NR_038009	69941	Mm.69044	NR_038009	ENSMUSG00000087213	2810408I11Rik	-	RIKEN cDNA 2810408I11 gene	ncRNA
mm_170925.1	chr2	39005161	39005162	-	1	NA	promoter-TSS (NM_025592)	promoter-TSS (NM_025592)	-30	NM_025592	66489	Mm.345333	NM_025592	ENSMUSG00000062997	Rpl35	2410039E09Rik	ribosomal protein L35	protein-coding
mm_41323.1	chr5	90472529	90472539	+	1	NA	exon (NM_009654, exon 12 of 15)	exon (NM_009654, exon 12 of 15)	11664	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_112394.1	chr12	119238618	119238634	-	1	NA	promoter-TSS (NM_177290)	promoter-TSS (NM_177290)	-350	NM_177290	320910	Mm.217000	NM_177290	ENSMUSG00000025321	Itgb8	4832412O06Rik	integrin beta 8	protein-coding
mm_32187.1	chr4	101069084	101069094	+	1	NA	promoter-TSS (NM_183024)	promoter-TSS (NM_183024)	51	NM_183024	242570	Mm.185636	NM_183024	ENSMUSG00000035275	Raver2	A430091O22Rik	ribonucleoprotein, PTB-binding 2	protein-coding
mm_131876.1	chr16	23192145	23192171	+	1	NA	Intergenic	Lx8|LINE|L1	-32582	NM_145933	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_149806.1	chr19	23758820	23758907	+	1	NA	promoter-TSS (NM_177034)	promoter-TSS (NM_177034)	-13	NM_177034	319924	Mm.22879	NM_177034	ENSMUSG00000024897	Apba1	6430513E09Rik|Lin-10|Mint|Mint1|Urop11|X11|X11alpha	amyloid beta (A4) precursor protein binding, family A, member 1	protein-coding
mm_51649.1	chr6	86028822	86028826	+	1	NA	5' UTR (NM_001271860, exon 1 of 13)	5' UTR (NM_001271860, exon 1 of 13)	143	NM_001271860	11519	Mm.104155	NM_013458	ENSMUSG00000030000	Add2	2900072M03Rik|add97	adducin 2 (beta)	protein-coding
mm_163352.1	chr12	21496469	21496477	+	1	NA	Intergenic	Intergenic	-79037	NM_011739	22630	Mm.289630	NM_011739	ENSMUSG00000076432	Ywhaq	2700028P07Rik|AA409740|AU021156|R74690	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide	protein-coding
mm_110799.1	chr12	72212155	72212177	-	1	NA	non-coding (NR_104446, exon 7 of 7)	non-coding (NR_104446, exon 7 of 7)	23580	NR_104446	104001	Mm.221275	NM_153457	ENSMUSG00000021087	Rtn1	Nsp	reticulon 1	protein-coding
mm_136107.1	chr16	85173730	85173747	-	1	NA	promoter-TSS (NM_001198823)	promoter-TSS (NM_001198823)	-31	NM_001198826	11820	Mm.277585	NM_007471	ENSMUSG00000022892	App	Abeta|Abpp|Adap|Ag|Cvap|E030013M08Rik|betaApp	amyloid beta (A4) precursor protein	protein-coding
mm_139679.1	chr17	57415052	57415066	+	1	NA	intron (NM_010130, intron 10 of 21)	L1_Mur2|LINE|L1	56373	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_88805.1	chr10	80755197	80755239	+	1	NA	promoter-TSS (NM_199322)	promoter-TSS (NM_199322)	12	NM_199322	208266	Mm.152371	NM_199322	ENSMUSG00000061589	Dot1l	A630076O07|AW907654|Dot1|KMT4|mDot1	DOT1-like, histone H3 methyltransferase (S. cerevisiae)	protein-coding
mm_70191.1	chr7	143784276	143784326	-	1	NA	5' UTR (NM_175534, exon 1 of 2)	5' UTR (NM_175534, exon 1 of 2)	199	NM_175534	244238	Mm.183561	NM_175534	ENSMUSG00000048965	Mrgpre	C130069N09Rik|Ebrt3|Mgrf|MrgE	MAS-related GPR, member E	protein-coding
mm_150774.1	chr19	44294233	44294246	+	1	NA	5' UTR (NM_009128, exon 1 of 6)	5' UTR (NM_009128, exon 1 of 6)	563	NM_009128	20250	Mm.487021	NM_009128	ENSMUSG00000025203	Scd2	Mir5114|Scd-2|mir-5114|swty	stearoyl-Coenzyme A desaturase 2	protein-coding
mm_40992.1	chr5	77283971	77283976	+	1	NA	TTS (NM_011263)	TTS (NM_011263)	11216	NR_039557	100628577		NR_039557	ENSMUSG00000093061	Mir5098	mmu-mir-5098|mu-mir-5098	microRNA 5098	ncRNA
mm_166512.1	chr6	12749186	12749190	-	1	NA	promoter-TSS (NM_001164805)	promoter-TSS (NM_001164805)	65	NM_001164805	330267	Mm.11989	NM_001164805	ENSMUSG00000032625	Thsd7a	Gm837	thrombospondin, type I, domain containing 7A	protein-coding
mm_83461.1	chr9	45263047	45263068	-	1	NA	intron (NR_136903, intron 4 of 5)	B1_Mur1|SINE|Alu	3650	NR_106054	102466803		NR_106054	ENSMUSG00000098361	Mir7086	Gm27643|mmu-mir-7086	microRNA 7086	ncRNA
mm_109132.1	chr12	105862748	105862749	+	1	NA	Intergenic	CpG	78051	NM_001347440	18789	Mm.255877	NM_011112	ENSMUSG00000021111	Papola	Pap|PapIII|Plap	poly (A) polymerase alpha	protein-coding
mm_35561.1	chr4	41569651	41569659	-	1	NA	promoter-TSS (NM_027993)	promoter-TSS (NM_027993)	-128	NM_027993	71901	Mm.39215	NM_027993	ENSMUSG00000028439	Fam219a	2310028H24Rik	family with sequence similarity 219, member A	protein-coding
mm_143846.1	chr17	84137198	84137207	-	1	NA	Intergenic	Intergenic	50745	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_19273.1	chr2	85157775	85157808	-	1	NA	Intergenic	Intergenic	21431	NM_011784	23796	Mm.29368	NM_011784	ENSMUSG00000044338	Aplnr	APJ|Agtrl1|msr/apj	apelin receptor	protein-coding
mm_89781.1	chr10	101681676	101681686	+	1	NA	5' UTR (NM_001205098, exon 1 of 8)	5' UTR (NM_001205098, exon 1 of 8)	194	NM_001205098	67569	Mm.25252	NM_026243	ENSMUSG00000019888	Mgat4c	9130411I17Rik|GntIVh	MGAT4 family, member C	protein-coding
mm_116326.1	chr13	37994112	37994184	-	1	NA	promoter-TSS (NM_025965)	promoter-TSS (NM_025965)	42	NM_025965	107513	Mm.426670	NM_025965	ENSMUSG00000021427	Ssr1	2510001K09Rik|6330400D04|AI159733|AI452176|SSR|TRAPA	signal sequence receptor, alpha	protein-coding
mm_171666.1	chr4	46517494	46517496	+	1	NA	intron (NM_029077, intron 4 of 5)	IAPLTR1_Mm|LTR|ERVK	18646	NM_029077	74735	Mm.240252	NM_029077	ENSMUSG00000039853	Trim14	5830400N10Rik|pub	tripartite motif-containing 14	protein-coding
mm_82006.1	chr9	121710371	121710375	+	1	NA	promoter-TSS (NM_026794)	promoter-TSS (NM_026794)	-16	NM_026794	26901	Mm.24848	NM_026794	ENSMUSG00000032526	Ss18l2	1110020I04Rik|AI463209|Deb1	SS18, nBAF chromatin remodeling complex subunit like 2	protein-coding
mm_32953.1	chr4	119637693	119637697	+	1	NA	promoter-TSS (NM_008190)	promoter-TSS (NM_008190)	-37	NM_008190	14915	Mm.2614	NM_008190	ENSMUSG00000023247	Guca2a	Guca2	guanylate cyclase activator 2a (guanylin)	protein-coding
mm_61278.1	chr7	66743688	66743706	+	1	NA	exon (NM_001164201, exon 1 of 11)	exon (NM_001164201, exon 1 of 11)	193	NM_001164201	545975	Mm.380104	NM_001164201	ENSMUSG00000030510	Cers3	4930550L11Rik|Gm488|Lass3|T3L	ceramide synthase 3	protein-coding
mm_46170.1	chr5	96739665	96739686	-	1	NA	intron (NM_175473, intron 55 of 73)	intron (NM_175473, intron 55 of 73)	-53710	NM_013470	11745	Mm.7214	NM_013470	ENSMUSG00000029484	Anxa3	Anx3	annexin A3	protein-coding
mm_116392.1	chr13	41194811	41194821	-	1	NA	exon (NM_019423, exon 3 of 8)	exon (NM_019423, exon 3 of 8)	25346	NM_001311121	54326	Mm.2567	NM_019423	ENSMUSG00000021364	Elovl2	AI317360|Ssc2	elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 2	protein-coding
mm_165027.1	chr19	32757485	32757500	+	1	NA	promoter-TSS (NM_008960)	promoter-TSS (NM_008960)	-85	NM_008960	19211	Mm.245395	NM_008960	ENSMUSG00000013663	Pten	2310035O07Rik|A130070J02Rik|AI463227|B430203M17Rik|MMAC1|TEP1	phosphatase and tensin homolog	protein-coding
mm_98431.1	chr11	94742117	94742145	+	1	NA	Intergenic	Intergenic	19051	NM_001105561	217122	Mm.24063	NM_183153		Gm11545	A430060F13Rik|C86086|OTTMUSG00000002043	predicted gene 11545	protein-coding
mm_113628.1	chr13	41800773	41800782	+	1	NA	intron (NM_175417, intron 4 of 6)	MLT1A1|LTR|ERVL-MaLR	46711	NM_175417	109254	Mm.25195	NM_175417	ENSMUSG00000058022	Adtrp	9530008L14Rik	androgen dependent TFPI regulating protein	protein-coding
mm_31759.1	chr4	63381343	63381354	+	1	NA	intron (NM_001305432, intron 8 of 20)	intron (NM_001305432, intron 8 of 20)	16892	NM_001305432	100182	Mm.387725	NM_001045514	ENSMUSG00000039158	Akna	AI597013	AT-hook transcription factor	protein-coding
mm_64153.1	chr7	141328206	141328241	+	1	NA	promoter-TSS (NM_001282076)	promoter-TSS (NM_001282076)	93	NM_027797	71448	Mm.248960	NM_027797	ENSMUSG00000025505	Tmem80	5530601I19Rik	transmembrane protein 80	protein-coding
mm_173249.1	chrX	91852276	91852278	+	1	NA	Intergenic	IAPLTR1_Mm|LTR|ERVK	-69301	NM_028847	74271	Mm.141337	NM_028847	ENSMUSG00000061392	Mageb5	1700056A17Rik|mMage-b5	melanoma antigen, family B, 5	protein-coding
mm_146628.1	chr18	10182069	10182092	-	1	NA	promoter-TSS (NM_009071)	promoter-TSS (NM_009071)	-288	NM_009071	19877	Mm.6710	NM_009071	ENSMUSG00000024290	Rock1	1110055K06Rik|Rock-I	Rho-associated coiled-coil containing protein kinase 1	protein-coding
mm_31113.1	chr4	42926381	42926389	+	1	NA	intron (NM_001346526, intron 2 of 8)	intron (NM_001346526, intron 2 of 8)	9134	NM_172690	230085	Mm.240965	NM_172690	ENSMUSG00000036062	Phf24	GINIP|N28178	PHD finger protein 24	protein-coding
mm_29855.1	chr3	130041190	130041206	-	1	NA	exon (NM_207209, exon 2 of 24)	exon (NM_207209, exon 2 of 24)	19709	NM_207209	99683	Mm.192303	NM_207209	ENSMUSG00000001052	Sec24b	AI605202|SEC24	Sec24 related gene family, member B (S. cerevisiae)	protein-coding
mm_69200.1	chr7	127376029	127376055	-	1	NA	promoter-TSS (NM_175560)	promoter-TSS (NM_175560)	8	NM_175560	269997	Mm.221270	NM_175560	ENSMUSG00000054381	Zfp747	6430604K15Rik	zinc finger protein 747	protein-coding
mm_117502.1	chr13	78200168	78200205	-	1	NA	intron (NR_045195, intron 1 of 2)	intron (NR_045195, intron 1 of 2)	-1313	NM_010151	13865	Mm.439653	NM_010151	ENSMUSG00000069171	Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR-3|EAR3|Erbal3|SVP44|Tcfcoup1	nuclear receptor subfamily 2, group F, member 1	protein-coding
mm_27621.1	chr3	59344079	59344100	-	1	NA	5' UTR (NM_001162884, exon 1 of 7)	5' UTR (NM_001162884, exon 1 of 7)	167	NM_001162884	242050	Mm.228086	NM_001162884	ENSMUSG00000036334	Igsf10	6530405F15Rik|9030224D03|AA409708|AA536958|AI414626|Adlican2|CMF608	immunoglobulin superfamily, member 10	protein-coding
mm_45808.1	chr5	87669536	87669562	-	1	NA	exon (NM_007784, exon 5 of 34)	exon (NM_007784, exon 5 of 34)	3341	NM_001286016	12990	Mm.427467	NM_007784	ENSMUSG00000070702	Csn1s1	AA959832|AW212882|Csna	casein alpha s1	protein-coding
mm_53208.1	chr6	125690652	125690662	+	1	NA	5' UTR (NM_153589, exon 1 of 26)	5' UTR (NM_153589, exon 1 of 26)	238	NM_153589	243634	Mm.333398	NM_153589	ENSMUSG00000038115	Ano2	BC033409|Tmem16b	anoctamin 2	protein-coding
mm_96297.1	chr11	63133173	63133177	+	1	NA	exon (NM_008885, exon 2 of 5)	exon (NM_008885, exon 2 of 5)	372	NM_001302260	18858	Mm.1237	NM_008885	ENSMUSG00000018217	Pmp22	22kDa|Gas-3|HNPP|Tr|trembler	peripheral myelin protein 22	protein-coding
mm_101432.1	chr11	30099464	30099478	-	1	NA	TTS (NM_175836)	TTS (NM_175836)	-73438	NM_146016	237711	Mm.445271	NM_146016	ENSMUSG00000044072	Eml6	2900083P10Rik|C230094A16Rik|EMAP-6	echinoderm microtubule associated protein like 6	protein-coding
mm_22653.1	chr3	14870142	14870163	+	1	NA	exon (NM_007606, exon 6 of 7)	exon (NM_007606, exon 6 of 7)	6614	NM_007606	12350	Mm.300	NM_007606	ENSMUSG00000027559	Car3	BB219044|Ca3|Car-3	carbonic anhydrase 3	protein-coding
mm_124895.1	chr15	10358526	10358545	+	1	NA	promoter-TSS (NM_001310735)	promoter-TSS (NM_001310735)	2	NM_001310735	268782	Mm.482244	NM_001031851	ENSMUSG00000089678	Agxt2	AI303810|AI663818	alanine-glyoxylate aminotransferase 2	protein-coding
mm_53450.1	chr6	134605771	134605771	+	1	NA	Intergenic	Intergenic	26717	NM_026345	67729	Mm.57648	NM_026345	ENSMUSG00000032718	Mansc1	9130403P13Rik	MANSC domain containing 1	protein-coding
mm_140190.1	chr17	83312727	83312737	+	1	NA	Intergenic	Intergenic	-38199	NM_001114361	78798	Mm.295565	NM_199466	ENSMUSG00000032624	Eml4	4930443C24Rik|AI644019	echinoderm microtubule associated protein like 4	protein-coding
mm_155511.1	chrX	74127464	74127469	+	1	NA	promoter-TSS (NM_008106)	promoter-TSS (NM_008106)	0	NM_008106	14539	Mm.284825	NM_008106	ENSMUSG00000031394	Opn1mw	Gcp	opsin 1 (cone pigments), medium-wave-sensitive (color blindness, deutan)	protein-coding
mm_94649.1	chr11	17051602	17051625	+	1	NA	promoter-TSS (NM_029861)	promoter-TSS (NM_029861)	-321	NM_029861	380686	Mm.425666	NM_029861	ENSMUSG00000044629	Cnrip1	1500041B16Rik|3110054C06Rik|5330437A18Rik|AI854501|C2orf32	cannabinoid receptor interacting protein 1	protein-coding
mm_88243.1	chr10	72654856	72654866	+	1	NA	promoter-TSS (NM_025635)	promoter-TSS (NM_025635)	15	NM_001293683	52696	Mm.62876	NM_025635	ENSMUSG00000019923	Zwint	2010007E07Rik|2600001N01Rik|D10Ertd749e|Zwint-1	ZW10 interactor	protein-coding
mm_147949.1	chr18	66504060	66504062	-	1	NA	promoter-TSS (NR_040528)	promoter-TSS (NR_040528)	-117	NR_040528	100503565	Mm.98256	NR_040528		Gm9926	ENSMUSG00000053891	predicted gene 9926	ncRNA
mm_40634.1	chr5	64830465	64830468	+	1	NA	TTS (NM_008453)	TTS (NM_008453)	26943	NM_008453	16599	Mm.392759	NM_008453	ENSMUSG00000029178	Klf3	9930027G08Rik|AL024007|Bklf|Tef-2	Kruppel-like factor 3 (basic)	protein-coding
mm_134936.1	chr16	31143806	31143808	-	1	NA	intron (NM_030138, intron 4 of 22)	intron (NM_030138, intron 4 of 22)	57431	NM_030138	78618	Mm.274646	NM_030138	ENSMUSG00000049076	Acap2	4832442G16|9530039J15Rik|CNT-B2|Centb2|mKIAA0041	ArfGAP with coiled-coil, ankyrin repeat and PH domains 2	protein-coding
mm_87930.1	chr10	62602370	62602392	+	1	NA	promoter-TSS (NM_019553)	promoter-TSS (NM_019553)	-83	NM_019553	56200	Mm.413275	NM_019553	ENSMUSG00000020075	Ddx21	AI255159|AL022742|D10Ertd645e|D10Wsu42e	DEAD (Asp-Glu-Ala-Asp) box polypeptide 21	protein-coding
mm_138619.1	chr17	35823559	35823571	+	1	NA	TTS (NM_133662)	TTS (NM_133662)	208	NM_008027	14251	Mm.2931	NM_008027	ENSMUSG00000059714	Flot1	reggie-2	flotillin 1	protein-coding
mm_145503.1	chr18	60391488	60391494	+	1	NA	3' UTR (NM_001146275, exon 3 of 3)	3' UTR (NM_001146275, exon 3 of 3)	15462	NM_001146275	60440	Mm.261140	NM_021792	ENSMUSG00000054072	Iigp1	2900074L10Rik|AI046432|AW111922|Ifgga1|Iigp|Irga6	interferon inducible GTPase 1	protein-coding
mm_106601.1	chr11	120731894	120731903	-	1	NA	intron (NM_007621, intron 1 of 7)	intron (NM_007621, intron 1 of 7)	123	NM_007621	12409	Mm.21454	NM_007621	ENSMUSG00000025150	Cbr2	MLCR	carbonyl reductase 2	protein-coding
mm_58097.1	chr6	137537764	137537776	-	1	NA	intron (NM_001271595, intron 2 of 20)	intron (NM_001271595, intron 2 of 20)	-17875	NM_001271589	13860	Mm.235346	NM_007945	ENSMUSG00000015766	Eps8	AW261790	epidermal growth factor receptor pathway substrate 8	protein-coding
mm_895.1	chr1	53297148	53297156	+	1	NA	promoter-TSS (NM_145517)	promoter-TSS (NM_145517)	57	NM_145517	227102	Mm.212846	NM_145517	ENSMUSG00000026097	Ormdl1	C730042F17Rik	ORM1-like 1 (S. cerevisiae)	protein-coding
mm_10080.1	chr1	195131537	195131588	-	1	NA	promoter-TSS (NM_013499)	promoter-TSS (NM_013499)	8	NM_013499	12946	Mm.301652	NM_013499	ENSMUSG00000016481	Cr1l	Crry|Mcp|mCRY	complement component (3b/4b) receptor 1-like	protein-coding
mm_157484.1	chrX	48208567	48208691	-	1	NA	promoter-TSS (NM_172465)	promoter-TSS (NM_172465)	73	NM_172465	208884	Mm.207367	NM_172465	ENSMUSG00000036985	Zdhhc9	6430508G22|9530098M12Rik	zinc finger, DHHC domain containing 9	protein-coding
mm_66914.1	chr7	60005102	60005151	-	1	NA	promoter-TSS (NM_013670)	promoter-TSS (NM_013670)	30	NM_013670	20646	Mm.274995	NM_013670	ENSMUSG00000102252	Snrpn	2410045I01Rik|HCERN3|Peg4|Pwcr1|SMN	small nuclear ribonucleoprotein N	protein-coding
mm_48017.1	chr5	136170672	136170698	-	1	NA	promoter-TSS (NM_178751)	promoter-TSS (NM_178751)	-29	NM_178751	269717	Mm.308396	NM_178751	ENSMUSG00000039747	Orai2	A730041O15Rik|Tmem142b	ORAI calcium release-activated calcium modulator 2	protein-coding
mm_145342.1	chr18	56469511	56469517	+	1	NA	intron (NM_026240, intron 1 of 13)	intron (NM_026240, intron 1 of 13)	37382	NM_026240	107022	Mm.24356	NM_026240	ENSMUSG00000001700	Gramd3	9030613F08Rik|9130427A09Rik|AW061306|NS3TP2	GRAM domain containing 3	protein-coding
mm_4621.1	chr1	178828107	178828110	+	1	NA	intron (NM_001161665, intron 5 of 14)	intron (NM_001161665, intron 5 of 14)	298983	NM_001161665	269152	Mm.129727	NM_177724	ENSMUSG00000026494	Kif26b	4832420M10|BC056349|D230039L06Rik	kinesin family member 26B	protein-coding
mm_22594.1	chr3	13781747	13781750	+	1	NA	intron (NM_178631, intron 3 of 9)	intron (NM_178631, intron 3 of 9)	-128883	NR_040598	75203	Mm.490940	NR_040598		4930539N22Rik	-	RIKEN cDNA 4930539N22 gene	ncRNA
mm_157329.1	chrX	23361688	23361702	-	1	NA	intron (NM_026167, intron 1 of 8)	Ricksha_c|DNA|MULE-MuDR	3387	NM_026167	67455	Mm.224306	NM_026167	ENSMUSG00000036782	Klhl13	1200009K10Rik|AI451128|Bklhd2|D130072F20Rik	kelch-like 13	protein-coding
mm_137657.1	chr17	28627467	28627467	+	1	NA	Intergenic	PB1D9|SINE|Alu	-5013	NM_016795	20815	Mm.15252	NM_016795	ENSMUSG00000004865	Srpk1	AU017960	serine/arginine-rich protein specific kinase 1	protein-coding
mm_115762.1	chr13	19193602	19193608	-	1	NA	Intergenic	Intergenic	202208	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_9297.1	chr1	171637347	171637378	-	1	NA	exon (NM_144539, exon 6 of 8)	exon (NM_144539, exon 6 of 8)	4538	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_119271.1	chr14	34091808	34091814	+	1	NA	exon (NM_001281845, exon 4 of 12)	exon (NM_001281845, exon 4 of 12)	5832	NM_013473	11752	Mm.3267	NM_013473	ENSMUSG00000021950	Anxa8	AI466995|Anx8	annexin A8	protein-coding
mm_139049.1	chr17	46254018	46254022	+	1	NA	promoter-TSS (NM_001111142)	promoter-TSS (NM_001111142)	-145	NM_001111142	224813	Mm.70999	NM_001111142	ENSMUSG00000071073	Lrrc73	Gm88	leucine rich repeat containing 73	protein-coding
mm_131496.1	chr16	17336238	17336250	+	1	NA	5' UTR (NM_008223, exon 2 of 5)	5' UTR (NM_008223, exon 2 of 5)	4873	NM_001331047	15160	Mm.6609	NM_008223	ENSMUSG00000022766	Serpind1	AA985900|AI303446|HC-II|HCII|Hcf2	serine (or cysteine) peptidase inhibitor, clade D, member 1	protein-coding
mm_121273.1	chr14	103513329	103513377	+	1	NA	promoter-TSS (NM_022886)	promoter-TSS (NM_022886)	12	NM_022886	64929	Mm.244003	NM_022886	ENSMUSG00000022123	Scel	9230114I02Rik	sciellin	protein-coding
mm_29194.1	chr3	106760597	106760602	-	1	NA	3' UTR (NM_007651, exon 8 of 8)	3' UTR (NM_007651, exon 8 of 8)	29550	NM_007651	12508	Mm.316861	NM_007651	ENSMUSG00000040747	Cd53	AI323659|Ox-44|Tspan25	CD53 antigen	protein-coding
mm_31199.1	chr4	43669289	43669329	+	1	NA	promoter-TSS (NM_175517)	promoter-TSS (NM_175517)	338	NM_001085508	242409	Mm.171489	NM_001085508	ENSMUSG00000078716	Tmem8b	4930500O05Rik	transmembrane protein 8B	protein-coding
mm_98054.1	chr11	85821879	85821893	+	1	NA	intron (NR_077059, intron 1 of 4)	intron (NR_077059, intron 1 of 4)	10502	NR_077059	69909	Mm.440214	NR_077059	ENSMUSG00000087013	2610027K06Rik	-	RIKEN cDNA 2610027K06 gene	ncRNA
mm_23237.1	chr3	51210288	51210298	+	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	-14154	NM_009834	12457	Mm.86541	NM_009834	ENSMUSG00000023087	Noct	AU043840|Ccr4|Ccrn4l	nocturnin	protein-coding
mm_159624.1	chr4	135573803	135573803	-	1	NA	promoter-TSS (NM_001013756)	promoter-TSS (NM_001013756)	-183	NM_001013756	230824	Mm.331972	NM_001013756	ENSMUSG00000037188	Grhl3	AI561912|Get1|Som|Tfcp2l4|ct	grainyhead-like 3 (Drosophila)	protein-coding
mm_150672.1	chr19	42051785	42051832	+	1	NA	promoter-TSS (NM_025752)	promoter-TSS (NM_025752)	-420	NM_025752	66765	Mm.440412	NM_025752	ENSMUSG00000090369	4933411K16Rik	-	RIKEN cDNA 4933411K16 gene	protein-coding
mm_111176.1	chr12	83819944	83819946	-	1	NA	intron (NR_073563, intron 5 of 10)	intron (NR_073563, intron 5 of 10)	22413	NM_001272055	18222	Mm.4390	NM_010949	ENSMUSG00000021224	Numb	Nb	numb homolog (Drosophila)	protein-coding
mm_64163.1	chr7	141392217	141392227	+	1	NA	promoter-TSS (NM_011528)	promoter-TSS (NM_011528)	62	NM_011528	21351	Mm.29182	NM_011528	ENSMUSG00000025503	Taldo1	-	transaldolase 1	protein-coding
mm_67766.1	chr7	92876497	92876502	-	1	NA	intron (NM_028243, intron 1 of 8)	intron (NM_028243, intron 1 of 8)	1246	NM_028243	72461	Mm.389969	NM_028243	ENSMUSG00000061119	Prcp	2510048K03Rik|2610104A14Rik|AI451719|HUMPCP|PCP	prolylcarboxypeptidase (angiotensinase C)	protein-coding
mm_70702.1	chr8	15036821	15036831	+	1	NA	Intergenic	Intergenic	9252	NR_037972	434285	Mm.334425	NM_001007591	ENSMUSG00000049008	BB014433	-	expressed sequence BB014433	ncRNA
mm_5702.1	chr1	43310899	43310909	-	1	NA	Intergenic	Intergenic	-114143	NM_001289533	14200	Mm.6799	NM_010212	ENSMUSG00000008136	Fhl2	FHL-2|SLIM-3|SLIM3	four and a half LIM domains 2	protein-coding
mm_5806.1	chr1	52233007	52233032	-	1	NA	5' UTR (NM_001113383, exon 1 of 15)	5' UTR (NM_001113383, exon 1 of 15)	213	NM_001081081	14660	Mm.398608	NM_001081081	ENSMUSG00000026103	Gls	6330442B14|AI314027|B230365M23Rik	glutaminase	protein-coding
mm_97932.1	chr11	83648229	83648239	+	1	NA	3' UTR (NM_011337, exon 3 of 3)	3' UTR (NM_011337, exon 3 of 3)	1144	NM_011337	20302	Mm.1282	NM_011337	ENSMUSG00000000982	Ccl3	AI323804|G0S19-1|LD78alpha|MIP-1alpha|MIP1-(a)|MIP1-alpha|Mip1a|Scya3	chemokine (C-C motif) ligand 3	protein-coding
mm_113193.1	chr13	24943181	24943207	+	1	NA	promoter-TSS (NM_008156)	promoter-TSS (NM_008156)	42	NM_008156	14756	Mm.291831	NM_008156	ENSMUSG00000021340	Gpld1	6330541J12Rik|AW546131	glycosylphosphatidylinositol specific phospholipase D1	protein-coding
mm_83696.1	chr9	50617229	50617289	-	1	NA	promoter-TSS (NM_028300)	promoter-TSS (NM_028300)	-62	NM_028300	72614	Mm.147232	NM_028300	ENSMUSG00000000167	Pih1d2	2700059L22Rik	PIH1 domain containing 2	protein-coding
mm_127105.1	chr15	97842726	97842749	+	1	NA	intron (NM_001204275, intron 1 of 24)	intron (NM_001204275, intron 1 of 24)	1765	NM_001204279	56233	Mm.384027	NM_019572	ENSMUSG00000022475	Hdac7	5830434K02Rik|HD7|HD7a|Hdac7a|mFLJ00062	histone deacetylase 7	protein-coding
mm_76395.1	chr8	84844435	84844443	-	1	NA	exon (NM_007591, exon 6 of 9)	exon (NM_007591, exon 6 of 9)	2492	NM_007591	12317	Mm.1971	NM_007591	ENSMUSG00000003814	Calr	CRT|Calregulin	calreticulin	protein-coding
mm_37233.1	chr4	118012490	118012492	-	1	NA	intron (NM_009176, intron 5 of 11)	B4|SINE|B4	-82728	NM_001284192	11876	Mm.56897	NM_009711	ENSMUSG00000028539	Artn	neublastin	artemin	protein-coding
mm_83505.1	chr9	45955280	45955291	-	1	NA	promoter-TSS (NM_001289668)	promoter-TSS (NM_001289668)	-36	NM_001289668	214597	Mm.379345	NM_172257	ENSMUSG00000034908	Sidt2	B930096O19|BC023957|CGI-40	SID1 transmembrane family, member 2	protein-coding
mm_131592.1	chr16	18812287	18812336	+	1	NA	promoter-TSS (NM_001161623)	promoter-TSS (NM_001161623)	17	NM_011672	22230	Mm.237594	NM_011672	ENSMUSG00000005262	Ufd1l	Ufd1	ubiquitin fusion degradation 1 like	protein-coding
mm_168011.1	chrY	20697385	20697391	+	1	NA	Intergenic	Intergenic	-397943	NM_009220	20611	Mm.347498	NM_009220	ENSMUSG00000095267	Ssty1	Smy|Ssty	spermiogenesis specific transcript on the Y 1	protein-coding
mm_25630.1	chr3	119184127	119184130	+	1	NA	intron (NM_170778, intron 16 of 22)	B4A|SINE|B4	599260	NM_001310711	56195	Mm.29966	NM_019550	ENSMUSG00000028134	Ptbp2	Ptb2|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding
mm_58339.1	chr6	146954400	146954431	-	1	NA	promoter-TSS (NM_028509)	promoter-TSS (NM_028509)	6	NM_001164236	73344	Mm.391543	NM_028509	ENSMUSG00000040163	1700034J05Rik	-	RIKEN cDNA 1700034J05 gene	protein-coding
mm_144095.1	chr18	3338212	3338214	+	1	NA	promoter-TSS (NM_001110852)	promoter-TSS (NM_001110852)	-624	NM_001110852	12916	Mm.5244	NM_013498	ENSMUSG00000063889	Crem	ICER|ICERI	cAMP responsive element modulator	protein-coding
mm_7808.1	chr1	131527303	131527385	-	1	NA	promoter-TSS (NM_001081011)	promoter-TSS (NM_001081011)	17	NM_001081011	14270	Mm.276259	NM_019520	ENSMUSG00000026425	Srgap2	9930124L22Rik|AI448945|FBP2|Fnbp2|srGAP3	SLIT-ROBO Rho GTPase activating protein 2	protein-coding
mm_42528.1	chr5	115631903	115631933	+	1	NA	promoter-TSS (NR_027810)	promoter-TSS (NR_027810)	-69	NM_198163	77407	Mm.27553	NM_198163	ENSMUSG00000029518	Rab35	9530019H02Rik|AU040256|H-ray|RAB1C|RAY	RAB35, member RAS oncogene family	protein-coding
mm_42769.1	chr5	121233012	121233015	+	1	NA	intron (NM_181421, intron 1 of 75)	intron (NM_181421, intron 1 of 75)	12794	NM_181421	269700	Mm.184589	NM_181421	ENSMUSG00000042744	Gm15800	A130010L24|AU042671|BC019639|EG545802|OTTMUSG00000026283|mKIAA0614	predicted gene 15800	protein-coding
mm_81308.1	chr9	108347959	108347969	+	1	NA	exon (NM_011678, exon 1 of 22)	exon (NM_011678, exon 1 of 22)	133	NM_011678	22258	Mm.3974	NM_011678	ENSMUSG00000032612	Usp4	F730026I20Rik|Unp|mKIAA4155	ubiquitin specific peptidase 4 (proto-oncogene)	protein-coding
mm_43275.1	chr5	130508090	130508099	+	1	NA	intron (NM_021371, intron 2 of 5)	ID4|SINE|ID	59302	NM_021371	140904	Mm.40875	NM_021371	ENSMUSG00000060371	Caln1	9630012C17Rik|Cabp8|MNCb-0849	calneuron 1	protein-coding
mm_122555.1	chr14	49066326	49066367	-	1	NA	promoter-TSS (NM_144535)	promoter-TSS (NM_144535)	-149	NM_144535	74385	Mm.379235	NM_144535	ENSMUSG00000036291	Ap5m1	4932432K03Rik|Mu5|Mudeng	adaptor-related protein complex 5, mu 1 subunit	protein-coding
mm_131559.1	chr16	18066462	18066494	+	1	NA	promoter-TSS (NM_001289814)	promoter-TSS (NM_001289814)	75	NM_001289813	13353	Mm.27155	NM_010047	ENSMUSG00000003531	Dgcr6	-	DiGeorge syndrome critical region gene 6	protein-coding
mm_100913.1	chr11	6267719	6267755	-	1	NA	promoter-TSS (NM_026538)	promoter-TSS (NM_026538)	-8	NM_026538	52513	Mm.29810	NM_026538	ENSMUSG00000004393	Ddx56	2600001H07Rik|D11Ertd619e|Noh61	DEAD (Asp-Glu-Ala-Asp) box polypeptide 56	protein-coding
mm_75701.1	chr8	68557018	68557052	-	1	NA	5' UTR (NM_001252623, exon 4 of 11)	5' UTR (NM_001252623, exon 4 of 11)	178111	NM_001252623	234356	Mm.334569	NM_172753	ENSMUSG00000036356	Csgalnact1	4732435N03Rik|CSGalNAcT-1	chondroitin sulfate N-acetylgalactosaminyltransferase 1	protein-coding
mm_44885.1	chr5	34654463	34654511	-	1	NA	exon (NM_029278, exon 4 of 18)	exon (NM_029278, exon 4 of 18)	5661	NM_029278	75416	Mm.40292	NM_029278	ENSMUSG00000036693	Nop14	2610033H07Rik|Nol14	NOP14 nucleolar protein	protein-coding
mm_52351.1	chr6	112459596	112459604	+	1	NA	promoter-TSS (NM_007617)	promoter-TSS (NM_007617)	95	NM_007617	12391	Mm.3924	NM_007617	ENSMUSG00000062694	Cav3	AI385751|Cav-3|M-cav	caveolin 3	protein-coding
mm_139657.1	chr17	57402826	57402838	+	1	NA	exon (NM_010130, exon 5 of 22)	exon (NM_010130, exon 5 of 22)	44146	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_138678.1	chr17	35916572	35916595	+	1	NA	promoter-TSS (NM_025878)	promoter-TSS (NM_025878)	-143	NM_001347380	66973	Mm.29484	NM_025878	ENSMUSG00000024436	Mrps18b	2400002C15Rik	mitochondrial ribosomal protein S18B	protein-coding
mm_126639.1	chr15	83597036	83597039	+	1	NA	Intergenic	B1_Mur2|SINE|Alu	-1880	NM_183017	223723	Mm.46778	NM_183017	ENSMUSG00000016757	Ttll12	BC055368|D430005B17	tubulin tyrosine ligase-like family, member 12	protein-coding
mm_11493.1	chr2	32493519	32493559	+	1	NA	Intergenic	Intergenic	-41820	NM_153560	98952	Mm.4065	NM_153560	ENSMUSG00000039157	Fam102a	AI426465|C230093N12Rik|Eeig1	family with sequence similarity 102, member A	protein-coding
mm_156624.1	chrX	155172447	155172448	+	1	NA	Intergenic	Intergenic	-24598	NM_001081671	73347	Mm.63848	NM_001081671	ENSMUSG00000057402	Cldn34b2	1700042B14Rik	claudin 34B2	protein-coding
mm_30421.1	chr3	152340351	152340416	-	1	NA	promoter-TSS (NM_001162375)	promoter-TSS (NM_001162375)	24	NM_001162375	215708	Mm.135018	NM_174868	ENSMUSG00000054942	Miga1	A930038D06|AI852168|C030011O14Rik|Fam73a|Mita1	mitoguardin 1	protein-coding
mm_154632.1	chrX	7762790	7762809	+	1	NA	5' UTR (NM_001271489, exon 1 of 10)	5' UTR (NM_001271489, exon 1 of 10)	138	NM_172472	209446	Mm.249142	NM_172472	ENSMUSG00000000134	Tfe3	F830016E06Rik|Tcfe3|Tfe-3|bHLHe33	transcription factor E3	protein-coding
mm_138976.1	chr17	45433588	45433612	+	1	NA	promoter-TSS (NR_130961)	promoter-TSS (NR_130961)	107	NM_152810	71702	Mm.28270	NM_152810	ENSMUSG00000023932	Cdc5l	1200002I02Rik|AA408004|PCDC5RP	cell division cycle 5-like (S. pombe)	protein-coding
mm_147258.1	chr18	38635906	38635916	-	1	NA	Intergenic	Intergenic	-34643	NM_011898	24066	Mm.42038	NM_011898	ENSMUSG00000024427	Spry4	A030006O18Rik|sprouty4	sprouty homolog 4 (Drosophila)	protein-coding
mm_113490.1	chr13	37378696	37378712	+	1	NA	intron (NM_010745, intron 3 of 4)	MER2|DNA|TcMar-Tigger	33359	NM_010745	17084	Mm.2639	NM_010745	ENSMUSG00000021423	Ly86	MD-1|MD1|ly86_tv2	lymphocyte antigen 86	protein-coding
mm_28881.1	chr3	97824495	97824508	-	1	NA	intron (NM_001039376, intron 3 of 46)	intron (NM_001039376, intron 3 of 46)	-56487	NM_178080	83679	Mm.129840	NM_031401	ENSMUSG00000038170	Pde4dip	4732458A06Rik|9430063L05Rik|C87016|D130016K21Rik|D3Bwg1078e|Usmg4|mKIAA0454	phosphodiesterase 4D interacting protein (myomegalin)	protein-coding
mm_83462.1	chr9	45263071	45263099	-	1	NA	intron (NR_136903, intron 4 of 5)	B1_Mur1|SINE|Alu	3622	NR_106054	102466803		NR_106054	ENSMUSG00000098361	Mir7086	Gm27643|mmu-mir-7086	microRNA 7086	ncRNA
mm_116445.1	chr13	43154793	43154805	-	1	NA	exon (NM_025935, exon 6 of 8)	exon (NM_025935, exon 6 of 8)	16702	NM_001252639	67046	Mm.269213	NM_025935	ENSMUSG00000021368	Tbc1d7	2610009C09Rik	TBC1 domain family, member 7	protein-coding
mm_163578.1	chr13	33139456	33139456	-	1	NA	Intergenic	RLTR48C|LTR|ERV1	18895	NM_011453	20707	Mm.219429	NM_011453	ENSMUSG00000021404	Serpinb9c	3830421J05Rik|Nk9|Spi11	serine (or cysteine) peptidase inhibitor, clade B, member 9c	protein-coding
mm_40678.1	chr5	65537268	65537331	+	1	NA	promoter-TSS (NM_016786)	promoter-TSS (NM_016786)	54	NM_001310619	53323	Mm.319512	NM_016786	ENSMUSG00000029203	Ube2k	AW492011|D5Ertd601e|E2-25k|HIP-2|Hip2|Hypg|Lig	ubiquitin-conjugating enzyme E2K	protein-coding
mm_116414.1	chr13	41487307	41487346	-	1	NA	promoter-TSS (NM_001111324)	promoter-TSS (NM_001111324)	34	NM_001111324	18003	Mm.288980	NM_017464	ENSMUSG00000021365	Nedd9	Cas-L|CasL|HEF1|MEF1|Nedd-9|p105	neural precursor cell expressed, developmentally down-regulated gene 9	protein-coding
mm_158745.1	chrX	164373421	164373424	-	1	NA	promoter-TSS (NM_010216)	promoter-TSS (NM_010216)	-100	NM_001308489	14205	Mm.297978	NM_010216	ENSMUSG00000031380	Vegfd	AI325264|Figf|VEGF-D	vascular endothelial growth factor D	protein-coding
mm_112013.1	chr12	110987105	110987110	-	1	NA	Intergenic	Intergenic	-7291	NR_036598	77878	Mm.293198	NR_036598		6030440G07Rik	-	RIKEN cDNA 6030440G07 gene	ncRNA
mm_104132.1	chr11	86828461	86828471	-	1	NA	intron (NR_106195, intron 2 of 8)	intron (NR_106195, intron 2 of 8)	-20806	NM_026191	67487	Mm.260627	NM_026191	ENSMUSG00000018425	Dhx40	2410016C14Rik|ARG147|DDX40|PAD	DEAH (Asp-Glu-Ala-His) box polypeptide 40	protein-coding
mm_151929.1	chr19	5800231	5800233	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	2440	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_45662.1	chr5	77140278	77140299	-	1	NA	Intergenic	Intergenic	-25165	NM_175606	74318	Mm.181852	NM_175606	ENSMUSG00000059325	Hopx	1110018K11Rik|1200015P04Rik|2300002F06Rik|AI848177|AW490897|Cameo|Hdop|Hod|Hop|Ob1|Obl|Toto	HOP homeobox	protein-coding
mm_8039.1	chr1	135258450	135258465	-	1	NA	promoter-TSS (NM_001163131)	promoter-TSS (NM_001163131)	15	NM_001163131	13710	Mm.441439	NM_007921	ENSMUSG00000003051	Elf3	ESE-1|ESX|jen	E74-like factor 3	protein-coding
mm_117076.1	chr13	59556846	59556854	-	1	NA	promoter-TSS (NM_001284219)	promoter-TSS (NM_001284219)	72	NM_001284219	67269	Mm.153008	NM_023328	ENSMUSG00000021557	Agtpbp1	1700020N17Rik|2310001G17Rik|2900054O13Rik|4930445M19Rik|5730402G09Rik|CCP1|Nna1|nmf243|pcd	ATP/GTP binding protein 1	protein-coding
mm_53510.1	chr6	135382505	135382525	+	1	NA	3' UTR (NM_001288627, exon 5 of 5)	3' UTR (NM_001288627, exon 5 of 5)	15022	NM_001288627	13730	Mm.182785	NM_010128	ENSMUSG00000030208	Emp1	I-8-09|TMP	epithelial membrane protein 1	protein-coding
mm_121714.1	chr14	16243310	16243344	-	1	NA	intron (NM_027695, intron 1 of 2)	CpG	-5987	NM_021504	59007	Mm.258381	NM_021504	ENSMUSG00000021785	Ngly1	1110002C09Rik|PNGase|Png1	N-glycanase 1	protein-coding
mm_65497.1	chr7	25718802	25718815	-	1	NA	intron (NM_028771, intron 1 of 4)	intron (NM_028771, intron 1 of 4)	245	NM_028771	52132	Mm.278798	NM_028771	ENSMUSG00000002608	Ccdc97	1200014H14Rik|2810446P04Rik|AA545218|D7Ertd462e	coiled-coil domain containing 97	protein-coding
mm_53031.1	chr6	124512616	124512640	+	1	NA	promoter-TSS (NM_023143)	promoter-TSS (NM_023143)	7	NM_023143	50909	Mm.333375	NM_023143	ENSMUSG00000055172	C1ra	AI132558|C1r|mC1rA	complement component 1, r subcomponent A	protein-coding
mm_113218.1	chr13	26855205	26855208	+	1	NA	Intergenic	MTEa|LTR|ERVL-MaLR	-85041	NM_008232	15192	Mm.7411	NM_008232	ENSMUSG00000045835	Hdgfl1	4921520N01Rik|HRP-1|Hdgfrp1|Pwwp1	hepatoma derived growth factor-like 1	protein-coding
mm_45349.1	chr5	65858255	65858261	-	1	NA	Intergenic	Intergenic	-5311	NM_001081105	74734	Mm.20323	NM_001081105	ENSMUSG00000029204	Rhoh	5830400A04Rik|AU019774|Arhh	ras homolog family member H	protein-coding
mm_166642.1	chr6	83537156	83537164	-	1	NA	promoter-TSS (NM_009610)	promoter-TSS (NM_009610)	-909	NM_009610	11468	Mm.292865	NM_009610	ENSMUSG00000059430	Actg2	ACTA3|Act-4|Act4|SMGA	actin, gamma 2, smooth muscle, enteric	protein-coding
mm_120099.1	chr14	58072216	58072229	+	1	NA	promoter-TSS (NM_013518)	promoter-TSS (NM_013518)	-464	NM_013518	14180	Mm.8846	NM_013518	ENSMUSG00000021974	Fgf9	Eks	fibroblast growth factor 9	protein-coding
mm_136706.1	chr17	7925872	7925878	+	1	NA	promoter-TSS (NM_145968)	promoter-TSS (NM_145968)	-125	NM_145968	72536	Mm.119680	NM_145968	ENSMUSG00000033450	Tagap	2610315E15Rik	T cell activation Rho GTPase activating protein	protein-coding
mm_152774.1	chr19	21170926	21170939	-	1	NA	Intergenic	Intergenic	66222	NR_126458	75354	Mm.243873	NR_126458		4930554I06Rik	-	RIKEN cDNA 4930554I06 gene	ncRNA
mm_168836.1	chr12	23117863	23117864	+	1	NA	Intergenic	B1_Mm|SINE|Alu	-107620	NR_015504	69732	Mm.391403	NM_028362	ENSMUSG00000073164	2410018L13Rik	2810480C08Rik	RIKEN cDNA 2410018L13 gene	ncRNA
mm_166771.1	chr6	136120288	136120333	+	1	NA	intron (NM_008171, intron 3 of 14)	intron (NM_008171, intron 3 of 14)	53201	NM_008171	14812	Mm.436649	NM_008171	ENSMUSG00000030209	Grin2b	AW490526|GluN2B|NR2B|Nmdar2b	glutamate receptor, ionotropic, NMDA2B (epsilon 2)	protein-coding
mm_152196.1	chr19	7483213	7483229	-	1	NA	promoter-TSS (NM_053076)	promoter-TSS (NM_053076)	70	NM_001271486	20168	Mm.246990	NM_053076	ENSMUSG00000024758	Rtn3	RTN3-A1	reticulon 3	protein-coding
mm_124353.1	chr14	104522616	104522707	-	1	NA	promoter-TSS (NM_026047)	promoter-TSS (NM_026047)	5	NM_026047	72486	Mm.291811	NM_026047	ENSMUSG00000022120	Rnf219	2610206B13Rik|2810449K13Rik|AI451544	ring finger protein 219	protein-coding
mm_91713.1	chr10	44170304	44170351	-	1	NA	promoter-TSS (NR_001582)	promoter-TSS (NR_001582)	-120	NR_001582	70365	Mm.87073	NR_001582	ENSMUSG00000091358	Speer5-ps1	1700007C10Rik|SPEER-5|Speer5-ps	spermatogenesis associated glutamate (E)-rich protein 5, pseudogene 1	pseudo
mm_162732.1	chr10	49832026	49832029	+	1	NA	Intergenic	Intergenic	-43273	NM_001111268	14806	Mm.332838	NM_010349	ENSMUSG00000056073	Grik2	AW124492|GluK2|Glur-6|Glur6|Glurbeta2	glutamate receptor, ionotropic, kainate 2 (beta 2)	protein-coding
mm_57838.1	chr6	129465509	129465531	-	1	NA	exon (NM_020008, exon 5 of 6)	exon (NM_020008, exon 5 of 6)	7259	NM_001309637	56644	Mm.239516	NM_020008	ENSMUSG00000079293	Clec7a	BGR|Clecsf12|beta-GR	C-type lectin domain family 7, member a	protein-coding
mm_55741.1	chr6	77526972	77526977	-	1	NA	intron (NM_001109764, intron 8 of 19)	MTEa|LTR|ERVL-MaLR	-144499	NR_045141	70753	Mm.490700	NR_045141	ENSMUSG00000108077	6330415B21Rik	-	RIKEN cDNA 6330415B21 gene	ncRNA
mm_7401.1	chr1	119053349	119053370	-	1	NA	5' UTR (NM_001081125, exon 1 of 14)	5' UTR (NM_001081125, exon 1 of 14)	260	NM_001081125	14633	Mm.273292	NM_001081125	ENSMUSG00000048402	Gli2	-	GLI-Kruppel family member GLI2	protein-coding
mm_44313.1	chr5	9300103	9300109	-	1	NA	intron (NM_172706, intron 1 of 21)	intron (NM_172706, intron 1 of 21)	33913	NM_172706	231014	Mm.130063	NM_172706	ENSMUSG00000056004	9330182L06Rik	Eig121l	RIKEN cDNA 9330182L06 gene	protein-coding
mm_46977.1	chr5	115267179	115267181	-	1	NA	intron (NM_001302448, intron 1 of 16)	intron (NM_001302448, intron 1 of 16)	5715	NM_001302448	50849	Mm.30051	NM_016698	ENSMUSG00000041740	Rnf10	AA675014|RIE2|mKIAA0262	ring finger protein 10	protein-coding
mm_132705.1	chr16	43364103	43364139	+	1	NA	intron (NM_181058, intron 2 of 6)	intron (NM_181058, intron 2 of 6)	56075	NR_046026	626693	Mm.447083	NR_046026	ENSMUSG00000085499	Gm15713	OTTMUSG00000025617	predicted gene 15713	ncRNA
mm_141393.1	chr17	29189111	29189122	-	1	NA	intron (NM_153166, intron 8 of 20)	intron (NM_153166, intron 8 of 20)	48674	NM_153166	240058	Mm.39905	NM_153166	ENSMUSG00000024008	Cpne5	A830083G22Rik	copine V	protein-coding
mm_74701.1	chr8	16670159	16670170	-	1	NA	intron (NM_053171, intron 5 of 69)	intron (NM_053171, intron 5 of 69)	-501326	NR_037214	100526464		NR_037214	ENSMUSG00000093142	Mir3106	mir-3106|mmu-mir-3106	microRNA 3106	ncRNA
mm_49187.1	chr6	15185457	15185520	+	1	NA	promoter-TSS (NM_001286607)	promoter-TSS (NM_001286607)	-18	NM_212435	114142	Mm.332919	NM_053242	ENSMUSG00000029563	Foxp2	2810043D05Rik|AI449000|CAG-16|D0Kist7	forkhead box P2	protein-coding
mm_79386.1	chr9	54772910	54772917	+	1	NA	3' UTR (NM_001284507, exon 3 of 3)	3' UTR (NM_001284507, exon 3 of 3)	8165	NM_013496	12903	Mm.34797	NM_013496	ENSMUSG00000032291	Crabp1	AI326249|CRABP-I|Crabp-1|CrabpI|Rbp-5	cellular retinoic acid binding protein I	protein-coding
mm_101564.1	chr11	34098558	34098591	-	1	NA	Intergenic	Intergenic	51373	NM_010696	16822	Mm.265350	NM_010696	ENSMUSG00000002699	Lcp2	AI323664|BB161688|SLP-76|SLP76|m1Khoe|twm	lymphocyte cytosolic protein 2	protein-coding
mm_6199.1	chr1	65186397	65186409	-	1	NA	promoter-TSS (NM_001310624)	promoter-TSS (NM_001310624)	76	NM_001111320	15926	Mm.9925	NM_010497	ENSMUSG00000025950	Idh1	AI314845|AI788952|E030024J03Rik|Id-1|Idh-1|Idpc	isocitrate dehydrogenase 1 (NADP+), soluble	protein-coding
mm_122690.1	chr14	52020670	52020675	-	1	NA	promoter-TSS (NM_001253694)	promoter-TSS (NM_001253694)	61	NM_001253696	69890	Mm.475652	NM_027248	ENSMUSG00000049295	Zfp219	2010302A17Rik	zinc finger protein 219	protein-coding
mm_15382.1	chr2	156540111	156540160	+	1	NA	3' UTR (NM_001291121, exon 22 of 22)	3' UTR (NM_001291121, exon 22 of 22)	-7441	NM_026661	68295	Mm.253648	NM_026661	ENSMUSG00000027628	Aar2	0610011L14Rik	AAR2 splicing factor homolog	protein-coding
mm_22198.1	chr2	173305130	173305145	-	1	NA	Intergenic	Intergenic	-28604	NM_022995	65112	Mm.73682	NM_022995	ENSMUSG00000038400	Pmepa1	2210418I02Rik|AW455466|Erg1.2|N4wbp4|Stag1|Tmepai	prostate transmembrane protein, androgen induced 1	protein-coding
mm_55880.1	chr6	83526880	83526898	-	1	NA	exon (NM_009610, exon 3 of 9)	exon (NM_009610, exon 3 of 9)	9362	NM_009610	11468	Mm.292865	NM_009610	ENSMUSG00000059430	Actg2	ACTA3|Act-4|Act4|SMGA	actin, gamma 2, smooth muscle, enteric	protein-coding
mm_173177.1	chrX	50635238	50635238	-	1	NA	promoter-TSS (NR_015505)	promoter-TSS (NR_015505)	83	NR_015505	103012	Mm.482523	NR_015505	ENSMUSG00000085396	Firre	5830467J12Rik|6720401G13Rik|AW048145	functional intergenic repeating RNA element	ncRNA
mm_76576.1	chr8	89006660	89006670	-	1	NA	Intergenic	CpG	-18070	NR_106190	102465899		NR_106190	ENSMUSG00000099078	Mir8110	Gm27571|mmu-mir-8110	microRNA 8110	ncRNA
mm_115428.1	chr13	117236024	117236024	+	1	NA	intron (NM_010330, intron 2 of 8)	intron (NM_010330, intron 2 of 8)	15451	NM_010330	13723	Mm.274926	NM_010330	ENSMUSG00000021728	Emb	AL022799|Gp70	embigin	protein-coding
mm_156648.1	chrX	157702490	157702500	+	1	NA	intron (NR_045569, intron 1 of 6)	intron (NR_045569, intron 1 of 6)	3522	NR_103722	66106	Mm.140340	NM_025357	ENSMUSG00000041476	Smpx	1010001C09Rik|Csl	small muscle protein, X-linked	protein-coding
mm_40781.1	chr5	67306979	67307014	+	1	NA	promoter-TSS (NM_178651)	promoter-TSS (NM_178651)	41	NM_001310629	109108	Mm.234455	NM_178651	ENSMUSG00000029221	Slc30a9	2310024J23Rik|AL024256|GAC63|HUEL|znT-9	solute carrier family 30 (zinc transporter), member 9	protein-coding
mm_15509.1	chr2	158258204	158258209	+	1	NA	promoter-TSS (NM_177850)	promoter-TSS (NM_177850)	-35	NM_177850	329547	Mm.260883	NM_177850	ENSMUSG00000052922	Bpi	9230105K17Rik|Bpifd1	bactericidal permeablility increasing protein	protein-coding
mm_3567.1	chr1	150439078	150439104	+	1	NA	exon (NM_133780, exon 41 of 52)	exon (NM_133780, exon 41 of 52)	27074	NM_021400	96875	Mm.174256	NM_021400	ENSMUSG00000006014	Prg4	CACP|DOL54|JCAP|MSF|SZP|lubricin	proteoglycan 4 (megakaryocyte stimulating factor, articular superficial zone protein)	protein-coding
mm_97222.1	chr11	75642558	75642590	+	1	NA	intron (NM_008916, intron 7 of 11)	B1_Mus2|SINE|Alu	-8935	NM_008659	17913	Mm.234502	NM_008659	ENSMUSG00000017774	Myo1c	C80397|MMIb|MYO1E|NMI|mm1beta|myr2	myosin IC	protein-coding
mm_6685.1	chr1	80664294	80664303	-	1	NA	intron (NM_175291, intron 1 of 55)	intron (NM_175291, intron 1 of 55)	1054	NM_001285927	210293	Mm.133473	NM_175291	ENSMUSG00000038608	Dock10	9330153B10Rik|A630054M16Rik|Jr4|Jr5|R75174|ZIZ3|Zizimin3|mKIAA0694	dedicator of cytokinesis 10	protein-coding
mm_154856.1	chrX	20617758	20617816	+	1	NA	promoter-TSS (NM_145627)	promoter-TSS (NM_145627)	28	NM_145627	236732	Mm.279194	NM_145627	ENSMUSG00000031060	Rbm10	E430039K10Rik	RNA binding motif protein 10	protein-coding
mm_116757.1	chr13	52530828	52530841	-	1	NA	promoter-TSS (NM_001024474)	promoter-TSS (NM_001024474)	2	NM_001024474	68203	Mm.29362	NM_001024474	ENSMUSG00000047842	Diras2	2900052J15Rik|AI414999	DIRAS family, GTP-binding RAS-like 2	protein-coding
mm_6696.1	chr1	80756051	80756052	-	1	NA	intron (NM_175291, intron 1 of 55)	intron (NM_175291, intron 1 of 55)	2502	NM_175291	210293	Mm.133473	NM_175291	ENSMUSG00000038608	Dock10	9330153B10Rik|A630054M16Rik|Jr4|Jr5|R75174|ZIZ3|Zizimin3|mKIAA0694	dedicator of cytokinesis 10	protein-coding
mm_24632.1	chr3	94310156	94310171	+	1	NA	promoter-TSS (NM_029431)	promoter-TSS (NM_029431)	31	NM_029431	75778	Mm.45092	NM_029431	ENSMUSG00000028145	Them4	2700077M13Rik|4921507I02Rik	thioesterase superfamily member 4	protein-coding
mm_18444.1	chr2	60902835	60902840	-	1	NA	intron (NM_020296, intron 1 of 13)	intron (NM_020296, intron 1 of 13)	-21399	NM_001141931	56878	Mm.259667	NM_020296	ENSMUSG00000026970	Rbms1	2600014B10Rik|AI255215|MSSP-1|MSSP-2|MSSP-3|YC1	RNA binding motif, single stranded interacting protein 1	protein-coding
mm_83447.1	chr9	45009835	45009847	-	1	NA	promoter-TSS (NM_007648)	promoter-TSS (NM_007648)	-251	NM_007648	12501	Mm.210361	NM_007648	ENSMUSG00000032093	Cd3e	AI504783|CD3|CD3epsilon|T3e	CD3 antigen, epsilon polypeptide	protein-coding
mm_169151.1	chr13	63003563	63003582	-	1	NA	intron (NM_001289926, intron 1 of 15)	L1Md_Gf|LINE|L1	38679	NM_001289924	72061	Mm.188105	NM_028079	ENSMUSG00000021458	2010111I01Rik	2300006M17Rik|AP-O|AW742919|Aopep|ApO|mir-23b|mir-24-1|mir-27b	RIKEN cDNA 2010111I01 gene	protein-coding
mm_40316.1	chr5	43869792	43869796	+	1	NA	intron (NM_007646, intron 1 of 7)	intron (NM_007646, intron 1 of 7)	985	NM_007646	12494	Mm.249873	NM_007646	ENSMUSG00000029084	Cd38	ADPRC 1|Cd38-rs1|I-19	CD38 antigen	protein-coding
mm_123623.1	chr14	68121145	68121158	-	1	NA	exon (NM_008691, exon 3 of 3)	exon (NM_008691, exon 3 of 3)	-2601	NR_045897	100043072	Mm.242832	NR_045897		A230070E04Rik	Gm4210	RIKEN cDNA A230070E04 gene	ncRNA
mm_166743.1	chr6	124817998	124818007	-	1	NA	exon (NM_001326594, exon 16 of 20)	exon (NM_001326594, exon 16 of 20)	-3706	NM_009415	21991	Mm.4222	NM_009415	ENSMUSG00000023456	Tpi1	AI255506|Tpi|Tpi-1	triosephosphate isomerase 1	protein-coding
mm_102239.1	chr11	54973772	54973801	-	1	NA	Intergenic	Intergenic	-10846	NM_001271455	57783	Mm.259671	NM_021327	ENSMUSG00000020400	Tnip1	ABIN|ABIN-1|ABIN1|AU018810|Naf1|Nef|VAN	TNFAIP3 interacting protein 1	protein-coding
mm_115610.1	chr13	11992118	11992121	-	1	NA	intron (NM_023868, intron 1 of 104)	intron (NM_023868, intron 1 of 104)	114826	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding
mm_4716.1	chr1	181035595	181035643	+	1	NA	Intergenic	Intergenic	-15618	NM_001033819	619326	Mm.355174	NM_001033819	ENSMUSG00000038768	9130409I23Rik	-	RIKEN cDNA 9130409I23 gene	protein-coding
mm_136425.1	chr16	94223149	94223159	-	1	NA	intron (NM_139145, intron 5 of 9)	intron (NM_139145, intron 5 of 9)	64702	NM_139145	110948	Mm.30921	NM_139145	ENSMUSG00000040820	Hlcs	410I21.SP6|D16Jhu34	holocarboxylase synthetase (biotin- [propriony-Coenzyme A-carboxylase (ATP-hydrolysing)] ligase)	protein-coding
mm_55285.1	chr6	54531125	54531137	-	1	NA	intron (NM_027268, intron 3 of 7)	intron (NM_027268, intron 3 of 7)	35251	NM_027268	69938	Mm.41557	NM_027268	ENSMUSG00000019124	Scrn1	2810019K23Rik|6330535A03Rik|AI852905|SES1|mKIAA0193	secernin 1	protein-coding
mm_89179.1	chr10	86344627	86344647	+	1	NA	exon (NM_011595, exon 4 of 5)	exon (NM_011595, exon 4 of 5)	44225	NM_011595	21859	Mm.4871	NM_011595	ENSMUSG00000020044	Timp3	Timp-3	tissue inhibitor of metalloproteinase 3	protein-coding
mm_120410.1	chr14	65174062	65174071	+	1	NA	Intergenic	RMER2|LTR|ERV1	-75960	NM_018788	54616	Mm.103748	NM_018788	ENSMUSG00000021978	Extl3	2900009G18Rik|AU040105|Ext1l|mKIAA0519	exostoses (multiple)-like 3	protein-coding
mm_134818.1	chr16	25517700	25517702	-	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-166064	NM_001127259	22061	Mm.20894	NM_011641	ENSMUSG00000022510	Trp63	AI462811|Ket|P51/P63|P63|P73l|Tp63|Trp53rp1	transformation related protein 63	protein-coding
mm_118496.1	chr14	13453938	13453952	+	1	NA	promoter-TSS (NM_001163032)	promoter-TSS (NM_001163032)	-13	NM_001163032	72003	Mm.317515	NM_028052	ENSMUSG00000056296	Synpr	1500003F20Rik|SPO	synaptoporin	protein-coding
mm_103944.1	chr11	83850763	83850773	-	1	NA	promoter-TSS (NM_001291268)	promoter-TSS (NM_001291268)	-101	NM_001291268	21410	Mm.7226	NM_009330	ENSMUSG00000020679	Hnf1b	HNF-1-beta|HNF-1B|HNF-1Beta|Hnf1beta|LFB3|Tcf-2|Tcf2|vHNF1	HNF1 homeobox B	protein-coding
mm_105361.1	chr11	103131813	103131817	-	1	NA	Intergenic	Intergenic	-1524	NM_001130516	71059	Mm.273871	NM_027658	ENSMUSG00000043372	Hexim2	4933402L21Rik	hexamethylene bis-acetamide inducible 2	protein-coding
mm_20093.1	chr2	120850624	120850635	-	1	NA	promoter-TSS (NM_001024856)	promoter-TSS (NM_001024856)	-27	NR_038349	100502700	Mm.330516	NR_038349	ENSMUSG00000087519	AV039307	-	expressed sequence AV039307	ncRNA
mm_24745.1	chr3	95315283	95315302	+	1	NA	5' UTR (NM_029789, exon 1 of 11)	5' UTR (NM_029789, exon 1 of 11)	102	NM_029789	76893	Mm.181009	NM_029789	ENSMUSG00000015714	Cers2	0610013I17Rik|AI225939|Lass2|TRH3	ceramide synthase 2	protein-coding
mm_5751.1	chr1	46853483	46853571	-	1	NA	promoter-TSS (NM_172653)	promoter-TSS (NM_172653)	-18	NM_172653	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|mKIAA1265	solute carrier family 39 (zinc transporter), member 10	protein-coding
mm_87102.1	chr10	33157128	33157141	+	1	NA	exon (NM_029726, exon 3 of 38)	exon (NM_029726, exon 3 of 38)	73651	NM_029726	76757	Mm.338508	NM_029726	ENSMUSG00000019787	Trdn	2310045H21Rik|EG432451|TDN	triadin	protein-coding
mm_39787.1	chr5	30263538	30263549	+	1	NA	intron (NR_137634, intron 6 of 8)	intron (NR_137634, intron 6 of 8)	30962	NR_137634	28042	Mm.168854	NM_027652	ENSMUSG00000075703	Selenoi	4933402G07Rik|AI448296|AI452230|C79563|D5Wsu178e|Ept1|SELI|mKIAA1724	selenoprotein I	protein-coding
mm_166218.1	chr5	63693943	63693946	+	1	NA	intron (NM_177006, intron 1 of 6)	intron (NM_177006, intron 1 of 6)	44841	NM_177006	319807	Mm.319487	NM_028470	ENSMUSG00000090061	Nwd2	3110047P20Rik|B830017A01Rik|Hn1-ps2|mKIAA1239	NACHT and WD repeat domain containing 2	protein-coding
mm_30881.1	chr4	32240471	32240474	+	1	NA	Intergenic	Intergenic	-176963	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_20200.1	chr2	124711538	124711542	-	1	NA	Intergenic	Intergenic	57959	NM_199239	214968	Mm.330536	NM_172537	ENSMUSG00000027200	Sema6d	1110067B02Rik|AA409156|D330011G23|mKIAA1479	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	protein-coding
mm_171058.1	chr3	10760431	10760432	+	1	NA	Intergenic	RLTR13D6|LTR|ERVK	-320301	NM_001127191	74718	Mm.440548	NM_029068	ENSMUSG00000027534	Snx16	4930522N22Rik|AI117577|AI747675	sorting nexin 16	protein-coding
mm_84202.1	chr9	60649868	60649878	-	1	NA	intron (NM_001311095, intron 7 of 15)	intron (NM_001311095, intron 7 of 15)	37661	NM_001311095	102747	Mm.269413	NM_145616	ENSMUSG00000047766	Lrrc49	AI430817|AW050057|D430025H09Rik|PGs4|p79	leucine rich repeat containing 49	protein-coding
mm_21680.1	chr2	164426210	164426229	-	1	NA	exon (NM_011521, exon 5 of 5)	exon (NM_011521, exon 5 of 5)	16969	NM_011521	20971	Mm.3815	NM_011521	ENSMUSG00000017009	Sdc4	AA959608|AW108331|S4|Synd4|ryudocan|syndecan-4	syndecan 4	protein-coding
mm_105579.1	chr11	106615629	106615660	-	1	NA	Intergenic	Intergenic	-2714	NM_198292	21763	Mm.102407	NM_198292	ENSMUSG00000040548	Tex2	4930568E07Rik|AI553404|Def-5|Taz4	testis expressed gene 2	protein-coding
mm_116416.1	chr13	41605498	41605501	-	1	NA	promoter-TSS (NM_001163572)	promoter-TSS (NM_001163572)	-717	NM_001163572	621976	Mm.259830	NM_001163572	ENSMUSG00000087370	Tmem170b	EG621976	transmembrane protein 170B	protein-coding
mm_13234.1	chr2	98662228	98662243	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	1194578	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_30518.1	chr3	158561335	158561347	-	1	NA	5' UTR (NM_001291453, exon 1 of 26)	5' UTR (NM_001291453, exon 1 of 26)	880	NM_001291453	242274	Mm.132162	NM_001081358	ENSMUSG00000028176	Lrrc7	AK122498|densin|mKIAA1365	leucine rich repeat containing 7	protein-coding
mm_42211.1	chr5	112793278	112793297	+	1	NA	promoter-TSS (NR_040676)	promoter-TSS (NR_040676)	-5	NR_040675	67360	Mm.59218	NR_040675	ENSMUSG00000098230	1700095B10Rik	-	RIKEN cDNA 1700095B10 gene	ncRNA
mm_145487.1	chr18	60385009	60385024	+	1	NA	intron (NM_001146275, intron 2 of 2)	intron (NM_001146275, intron 2 of 2)	8987	NM_001146275	60440	Mm.261140	NM_021792	ENSMUSG00000054072	Iigp1	2900074L10Rik|AI046432|AW111922|Ifgga1|Iigp|Irga6	interferon inducible GTPase 1	protein-coding
mm_103411.1	chr11	75454657	75454721	-	1	NA	promoter-TSS (NM_138950)	promoter-TSS (NM_138950)	28	NM_138950	192652	Mm.340378	NM_138950	ENSMUSG00000045374	Wdr81	BC054822|Gm883|mFLJ00182|nur5	WD repeat domain 81	protein-coding
mm_87173.1	chr10	38965548	38965558	+	1	NA	promoter-TSS (NM_010681)	promoter-TSS (NM_010681)	38	NM_010681	16775	Mm.258065	NM_010681	ENSMUSG00000019846	Lama4	-	laminin, alpha 4	protein-coding
mm_4150.1	chr1	171018924	171018930	+	1	NA	promoter-TSS (NM_144559)	promoter-TSS (NM_144559)	1	NM_144559	246256	Mm.251254	NM_144559	ENSMUSG00000059089	Fcgr4	4833442P21Rik|CD16-2|FcgRIV|FcgammaRIV|Fcgr3a|Fcrl3	Fc receptor, IgG, low affinity IV	protein-coding
mm_91409.1	chr10	31445850	31445894	-	1	NA	promoter-TSS (NM_009413)	promoter-TSS (NM_009413)	49	NM_009413	21987	Mm.439966	NM_009413	ENSMUSG00000000296	Tpd52l1	D53	tumor protein D52-like 1	protein-coding
mm_128162.1	chr15	33687841	33687864	-	1	NA	promoter-TSS (NM_001085421)	promoter-TSS (NM_001085421)	31	NM_001085421	239364	Mm.60794	NM_001085421	ENSMUSG00000038984	Tspyl5	6330530B20|E130308C19Rik	testis-specific protein, Y-encoded-like 5	protein-coding
mm_21884.1	chr2	166155166	166155176	-	1	NA	5' UTR (NM_001252578, exon 1 of 21)	5' UTR (NM_001252578, exon 1 of 21)	114	NM_001252578	72043	Mm.1011	NM_028072	ENSMUSG00000006800	Sulf2	2010004N24Rik|AU020235|MSulf-2|mKIAA1247	sulfatase 2	protein-coding
mm_64463.1	chr7	142665786	142665794	+	1	NA	intron (NR_002855, intron 2 of 3)	intron (NR_002855, intron 2 of 3)	1026	NM_001315488	16002	Mm.3862	NM_010514	ENSMUSG00000048583	Igf2	AL033362|Igf-2|Igf-II|M6pr|Mpr|Peg2	insulin-like growth factor 2	protein-coding
mm_91075.1	chr10	19009694	19009711	-	1	NA	intron (NM_001166402, intron 1 of 7)	intron (NM_001166402, intron 1 of 7)	2261	NM_001166402	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_10280.1	chr2	9906284	9906291	+	1	NA	Intergenic	Intergenic	-16747	NR_040511	77682	Mm.488621	NR_040511	ENSMUSG00000079602	9230102O04Rik	-	RIKEN cDNA 9230102O04 gene	ncRNA
mm_124617.1	chr15	3279647	3279658	+	1	NA	TTS (NM_001166063)	TTS (NM_001166063)	8675	NM_009155	20363	Mm.392203	NM_009155	ENSMUSG00000064373	Selenop	AU018766|D15Ucla1|Se-P|Sepp1|selp	selenoprotein P	protein-coding
mm_114576.1	chr13	75089948	75089959	+	1	NA	promoter-TSS (NM_013628)	promoter-TSS (NM_013628)	-34	NM_013628	18548	Mm.1333	NM_013628	ENSMUSG00000021587	Pcsk1	Nec-1|Nec1|PC1|PC3|Phpp-1|SPC3	proprotein convertase subtilisin/kexin type 1	protein-coding
mm_26851.1	chr3	14776255	14776276	-	1	NA	exon (NM_001083957, exon 3 of 7)	exon (NM_001083957, exon 3 of 7)	2195	NM_001083957	12346	Mm.273195	NM_009799	ENSMUSG00000027556	Car1	AW555628|Ca1|Car-1	carbonic anhydrase 1	protein-coding
mm_111515.1	chr12	99642683	99642692	-	1	NA	Intergenic	Lx9|LINE|L1	-14713	NR_045288	73457	Mm.383439	NR_045288	ENSMUSG00000100211	1700064M15Rik	-	RIKEN cDNA 1700064M15 gene	ncRNA
mm_82309.1	chr9	7872815	7872876	-	1	NA	5' UTR (NM_007464, exon 1 of 9)	5' UTR (NM_007464, exon 1 of 9)	325	NM_007464	11796	Mm.2026	NM_007464	ENSMUSG00000032000	Birc3	AW107670|Api1|Api2|Birc2|C-IAP2|HIAP2|IAP1|IAP2|MIAP1|MIAP2|MIHB|MIHC|RNF49|cIAP-1|cIAP-2|cIAP1|cIAP2	baculoviral IAP repeat-containing 3	protein-coding
mm_49213.1	chr6	15727810	15727814	+	1	NA	intron (NM_175088, intron 2 of 4)	intron (NM_175088, intron 2 of 4)	7151	NM_175088	16543	Mm.1314	NM_175088	ENSMUSG00000041390	Mdfic	Kdt1|Mdfid	MyoD family inhibitor domain containing	protein-coding
mm_129766.1	chr15	82687695	82687699	-	1	NA	Intergenic	Intergenic	2361	NR_033515	627860	Mm.486636	NR_033515		Cyp2d37-ps	EG627860|Gm6800	cytochrome P450, family 2, subfamily d, polypeptide 37, pseudogene	pseudo
mm_48895.1	chr5	151651157	151651213	-	1	NA	promoter-TSS (NM_027009)	promoter-TSS (NM_027009)	23	NM_027009	69263	Mm.12553	NM_027009	ENSMUSG00000033970	Rfc3	2810416I22Rik|38kDa|AU022547|Recc3	replication factor C (activator 1) 3	protein-coding
mm_158614.1	chrX	152644419	152644429	-	1	NA	promoter-TSS (NM_001290687)	promoter-TSS (NM_001290687)	124	NM_001290686	110380	Mm.40796	NM_172441	ENSMUSG00000045180	Shroom2	4832440C16|Apxl|C630003H05Rik|Shrm2	shroom family member 2	protein-coding
mm_154588.1	chrX	7577497	7577521	+	1	NA	intron (NR_029473, intron 1 of 2)	intron (NR_029473, intron 1 of 2)	-2167	NM_001199347	20371	Mm.182291	NM_054039	ENSMUSG00000039521	Foxp3	JM2|scurfin|sf	forkhead box P3	protein-coding
mm_159907.1	chr6	43235692	43235692	+	1	NA	promoter-TSS (NM_146370)	promoter-TSS (NM_146370)	82	NM_146370	18346	Mm.222840	NM_146370	ENSMUSG00000061210	Olfr47	IB12|MOR261-9|Olfr13	olfactory receptor 47	protein-coding
mm_164994.1	chr19	14904647	14904653	+	1	NA	Intergenic	Intergenic	-306467	NM_001302947	21888	Mm.103638	NM_011600	ENSMUSG00000024642	Tle4	5730411M05Rik|AA792082|Bce-1|Bce1|ESTM13|ESTM14|Grg4|X83332|X83333|grg-4	transducin-like enhancer of split 4	protein-coding
mm_61021.1	chr7	49484532	49484543	+	1	NA	intron (NM_175272, intron 10 of 37)	intron (NM_175272, intron 10 of 37)	152298	NM_001005232	13172	Mm.307176	NM_001005232	ENSMUSG00000030507	Dbx1	AI426026|Dbx	developing brain homeobox 1	protein-coding
mm_56108.1	chr6	87496695	87496713	-	1	NA	promoter-TSS (NM_175476)	promoter-TSS (NM_175476)	-377	NM_175476	232201	Mm.119564	NM_175476	ENSMUSG00000030047	Arhgap25	A130039I20Rik	Rho GTPase activating protein 25	protein-coding
mm_162647.1	chr1	195131425	195131429	-	1	NA	5' UTR (NM_013499, exon 1 of 10)	5' UTR (NM_013499, exon 1 of 10)	143	NM_013499	12946	Mm.301652	NM_013499	ENSMUSG00000016481	Cr1l	Crry|Mcp|mCRY	complement component (3b/4b) receptor 1-like	protein-coding
mm_142530.1	chr17	46438472	46438481	-	1	NA	promoter-TSS (NM_144856)	promoter-TSS (NM_144856)	1	NM_144856	108114	Mm.387538	NM_144856	ENSMUSG00000067144	Slc22a7	NLT|OAT2	solute carrier family 22 (organic anion transporter), member 7	protein-coding
mm_72684.1	chr8	84950154	84950164	+	1	NA	5' UTR (NM_144929, exon 2 of 6)	5' UTR (NM_144929, exon 2 of 6)	3168	NM_144929	234542	Mm.461701	NM_144929	ENSMUSG00000048617	Rtbdn	A330096I21Rik|BC022744|Rtbnd	retbindin	protein-coding
mm_104084.1	chr11	86602335	86602345	-	1	NA	intron (NM_029478, intron 9 of 11)	intron (NM_029478, intron 9 of 11)	-18182	NR_029738	387140		NR_029738	ENSMUSG00000065455	Mir21a	Mir21|Mirn21|mmu-mir-21|mmu-mir-21a	microRNA 21a	ncRNA
mm_94505.1	chr11	7199854	7199856	+	1	NA	exon (NM_008341, exon 2 of 4)	exon (NM_008341, exon 2 of 4)	2068	NM_008341	16006	Mm.21300	NM_008341	ENSMUSG00000020429	Igfbp1	-	insulin-like growth factor binding protein 1	protein-coding
mm_30673.1	chr4	11156829	11156837	+	1	NA	intron (NM_021897, intron 1 of 3)	MIRb|SINE|MIR	392	NM_021897	60599	Mm.393018	NM_021897	ENSMUSG00000028211	Trp53inp1	2700057G22Rik|SIP|SIP18|SIP27|Stinp|Teap	transformation related protein 53 inducible nuclear protein 1	protein-coding
mm_15811.1	chr2	164497962	164497984	+	1	NA	exon (NM_133779, exon 2 of 12)	exon (NM_133779, exon 2 of 12)	448	NM_133779	78928	Mm.28228	NM_133779	ENSMUSG00000017721	Pigt	2510012P17Rik|4930534E15Rik|CGI-06|NDAP|Ndap7	phosphatidylinositol glycan anchor biosynthesis, class T	protein-coding
mm_26065.1	chr3	135839768	135839792	+	1	NA	non-coding (NR_040540, exon 2 of 5)	non-coding (NR_040540, exon 2 of 5)	489	NR_040540	71038	Mm.410798	NR_040540	ENSMUSG00000106306	4933401H06Rik	-	RIKEN cDNA 4933401H06 gene	ncRNA
mm_160985.1	chr11	104442917	104442917	-	1	NA	promoter-TSS (NM_001081045)	promoter-TSS (NM_001081045)	-626	NM_001081045	76719	Mm.136418	NM_001081045	ENSMUSG00000018412	Kansl1	1700081L11Rik|9430041J06Rik|mKIAA1267	KAT8 regulatory NSL complex subunit 1	protein-coding
mm_128270.1	chr15	36793596	36793637	-	1	NA	5' UTR (NM_011740, exon 2 of 7)	5' UTR (NM_011740, exon 2 of 7)	922	NM_011740	22631	Mm.3360	NM_011740	ENSMUSG00000022285	Ywhaz	1110013I11Rik|14-3-3zeta|AI596267|AL022924|AU020854	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide	protein-coding
mm_99077.1	chr11	99388787	99388853	+	1	NA	exon (NM_010660, exon 1 of 8)	exon (NM_010660, exon 1 of 8)	544	NM_010660	16661	Mm.22662	NM_010660	ENSMUSG00000019761	Krt10	D130054E02Rik|K10|K1C1|Krt-1.10|Krt1-10	keratin 10	protein-coding
mm_104314.1	chr11	93885725	93885741	-	1	NA	promoter-TSS (NM_134012)	promoter-TSS (NM_134012)	33	NM_001013375	217109	Mm.379350	NM_001013375	ENSMUSG00000054079	Utp18	6230425C22Rik|6430513M13|Wdr50	UTP18 small subunit processome component	protein-coding
mm_103564.1	chr11	77880989	77881028	-	1	NA	3' UTR (NM_008952, exon 8 of 8)	3' UTR (NM_008952, exon 8 of 8)	12864	NM_008952	19193	Mm.8543	NM_008952	ENSMUSG00000017453	Pipox	LPIPOX|Pso	pipecolic acid oxidase	protein-coding
mm_36611.1	chr4	89282114	89282151	-	1	NA	promoter-TSS (NM_001040654)	promoter-TSS (NM_001040654)	60	NM_001040654	12578	Mm.4733	NM_009877	ENSMUSG00000044303	Cdkn2a	ARF-INK4a|Arf|INK4a-ARF|Ink4a/Arf|MTS1|Pctr1|p16|p16(INK4a)|p16INK4a|p19<ARF>|p19ARF	cyclin-dependent kinase inhibitor 2A	protein-coding
mm_126093.1	chr15	77929230	77929250	+	1	NA	promoter-TSS (NM_019913)	promoter-TSS (NM_019913)	-246	NM_019913	56551	Mm.291917	NM_019913	ENSMUSG00000005354	Txn2	2510006J11Rik|AI788873|Trx2	thioredoxin 2	protein-coding
mm_103531.1	chr11	77200974	77200989	-	1	NA	Intergenic	Intergenic	-12013	NM_176965	319634	Mm.108786	NM_176965	ENSMUSG00000050944	Efcab5	4930563A03Rik	EF-hand calcium binding domain 5	protein-coding
mm_7856.1	chr1	132417971	132417980	-	1	NA	intron (NM_172516, intron 1 of 12)	CpG	522	NM_172516	213452	Mm.257120	NM_172516	ENSMUSG00000042046	Dstyk	A930019K20Rik|C430014H23Rik|C820013G01|Ripk5	dual serine/threonine and tyrosine protein kinase	protein-coding
mm_171807.1	chr5	129887321	129887324	-	1	NA	5' UTR (NM_024166, exon 1 of 4)	5' UTR (NM_024166, exon 1 of 4)	148	NM_024166	14004	Mm.30133	NM_024166	ENSMUSG00000070493	Chchd2	AL033347|Etohi6	coiled-coil-helix-coiled-coil-helix domain containing 2	protein-coding
mm_4294.1	chr1	171775160	171775162	+	1	NA	intron (NM_013730, intron 2 of 6)	intron (NM_013730, intron 2 of 6)	8029	NM_013730	27218	Mm.103648	NM_013730	ENSMUSG00000015316	Slamf1	4933415F16|AA177906|CD150|CDw150|ESTM51|IPO-3|Slam	signaling lymphocytic activation molecule family member 1	protein-coding
mm_39047.1	chr4	152477463	152477549	-	1	NA	promoter-TSS (NM_010598)	promoter-TSS (NM_010598)	43	NM_001252654	16498	Mm.388924	NM_010598	ENSMUSG00000028931	Kcnab2	F5|I2rf5|Kcnb3|kv-beta-2	potassium voltage-gated channel, shaker-related subfamily, beta member 2	protein-coding
mm_39871.1	chr5	31074846	31074883	+	1	NA	intron (NM_023525, intron 34 of 43)	intron (NM_023525, intron 34 of 43)	18663	NM_011773	22784	Mm.1396	NM_011773	ENSMUSG00000029151	Slc30a3	Znt3	solute carrier family 30 (zinc transporter), member 3	protein-coding
mm_52222.1	chr6	103511013	103511078	+	1	NA	5' UTR (NM_007697, exon 1 of 27)	5' UTR (NM_007697, exon 1 of 27)	169	NM_007697	12661	Mm.251288	NM_007697	ENSMUSG00000030077	Chl1	A530023M13Rik|AI465420|CALL|LICAM2	cell adhesion molecule L1-like	protein-coding
mm_110578.1	chr12	56513937	56513968	-	1	NA	intron (NR_045082, intron 1 of 6)	intron (NR_045082, intron 1 of 6)	15468	NR_045082	104798	Mm.310950	NR_045082		E030019B13Rik	AI413669	RIKEN cDNA E030019B13 gene	ncRNA
mm_27950.1	chr3	79825520	79825536	-	1	NA	intron (NM_027495, intron 7 of 11)	intron (NM_027495, intron 7 of 11)	17134	NM_027495	70652	Mm.46635	NM_027495	ENSMUSG00000027956	Tmem144	1110057I03Rik|5730537D05Rik	transmembrane protein 144	protein-coding
mm_33660.1	chr4	133130643	133130656	+	1	NA	promoter-TSS (NM_153423)	promoter-TSS (NM_153423)	16	NM_153423	242687	Mm.23566	NM_153423	ENSMUSG00000028868	Wasf2	AW742646|D4Ertd13e|WAVE2	WAS protein family, member 2	protein-coding
mm_58374.1	chr6	148989334	148989338	-	1	NA	3' UTR (NM_177192, exon 21 of 21)	3' UTR (NM_177192, exon 21 of 21)	-42904	NM_019643	56306	Mm.18637	NM_019643	ENSMUSG00000039985	Fam60a	Ppcs1|Pptcs1|Tera	family with sequence similarity 60, member A	protein-coding
mm_169300.1	chr14	101982783	101982802	-	1	NA	Intergenic	Intergenic	142169	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_162892.1	chr10	111010287	111010289	-	1	NA	promoter-TSS (NM_172554)	promoter-TSS (NM_172554)	-222	NM_172554	320150	Mm.339281	NM_172554	ENSMUSG00000035798	Zdhhc17	A230053P19Rik|BB187739|D130071N24Rik|Hip14	zinc finger, DHHC domain containing 17	protein-coding
mm_162877.1	chr10	99443870	99443878	+	1	NA	Intergenic	Intergenic	-165297	NR_038019	100504202	Mm.403801	NR_038019		Gm20110	-	predicted gene, 20110	ncRNA
mm_148517.1	chr19	4232784	4232804	+	1	NA	non-coding (NR_132308, exon 3 of 4)	non-coding (NR_132308, exon 3 of 4)	379	NR_132280	69745	Mm.32518	NM_027196	ENSMUSG00000024854	Pold4	2410012M21Rik|AI463381|AW060307|Polds|p12	polymerase (DNA-directed), delta 4	protein-coding
mm_12517.1	chr2	72112747	72112747	+	1	NA	intron (NM_001204166, intron 1 of 27)	MTE2a|LTR|ERVL-MaLR	58130	NM_001204166	56508	Mm.196153	NM_019688	ENSMUSG00000049044	Rapgef4	1300003D15Rik|5730402K07Rik|6330581N18Rik|EPAC 2|Epac-2|Epac2|mKIAA4040	Rap guanine nucleotide exchange factor (GEF) 4	protein-coding
mm_134494.1	chr16	18784310	18784313	-	1	NA	intron (NM_009862, intron 18 of 19)	PB1D10|SINE|Alu	7464	NM_013805	12741	Mm.22768	NM_013805	ENSMUSG00000041378	Cldn5	AI854493|MBEC1|Tmvcf	claudin 5	protein-coding
mm_22876.1	chr3	29240423	29240425	+	1	NA	intron (NM_001167748, intron 4 of 12)	B4A|SINE|B4	157847	NM_029412	75740	Mm.330948	NM_029412	ENSMUSG00000063600	Egfem1	6130401L20Rik|Efcab11	EGF-like and EMI domain containing 1	protein-coding
mm_8565.1	chr1	155417284	155417323	-	1	NA	5' UTR (NM_011273, exon 1 of 15)	5' UTR (NM_011273, exon 1 of 15)	141	NM_011273	19775	Mm.266215	NM_011273	ENSMUSG00000026469	Xpr1	Rmc-1|Rmc1|Sxv|Syg1|XR	xenotropic and polytropic retrovirus receptor 1	protein-coding
mm_88454.1	chr10	77556117	77556131	+	1	NA	exon (NM_008404, exon 9 of 16)	exon (NM_008404, exon 9 of 16)	-25643	NM_145925	108705	Mm.28853	NM_145925	ENSMUSG00000009291	Pttg1ip	1810010L20Rik|AI314311|AU018448|C79540	pituitary tumor-transforming 1 interacting protein	protein-coding
mm_47906.1	chr5	134945817	134945836	-	1	NA	3' UTR (NM_009903, exon 1 of 1)	3' UTR (NM_009903, exon 1 of 1)	1108	NM_009903	12740	Mm.7339	NM_009903	ENSMUSG00000047501	Cldn4	Cep-r|Cpetr|Cpetr1	claudin 4	protein-coding
mm_36681.1	chr4	96507478	96507486	-	1	NA	promoter-TSS (NM_001104927)	promoter-TSS (NM_001104927)	-96	NM_001104927	665095	Mm.331717	NM_001104927	ENSMUSG00000082932	Cyp2j8	Cyp2j8-ps|OTTMUSG00000007938	cytochrome P450, family 2, subfamily j, polypeptide 8	protein-coding
mm_57243.1	chr6	123283163	123283190	-	1	NA	3' UTR (NM_019948, exon 6 of 6)	3' UTR (NM_019948, exon 6 of 6)	6695	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_156910.1	chrX	169052891	169052903	+	1	NA	intron (NR_109847, intron 1 of 14)	intron (NR_109847, intron 1 of 14)	16286	NR_109847	11856	Mm.441810	NM_009707	ENSMUSG00000031355	Arhgap6	AI504284|RhoGAPX-1	Rho GTPase activating protein 6	protein-coding
mm_51862.1	chr6	90486411	90486430	+	1	NA	Intergenic	Intergenic	23794	NM_023184	66277	Mm.38343	NM_023184	ENSMUSG00000030087	Klf15	1810013I09Rik|AV048136|AW494632|CKLF|KKLF	Kruppel-like factor 15	protein-coding
mm_91356.1	chr10	27991077	27991114	-	1	NA	Intergenic	Intergenic	-83725	NM_008983	19272	Mm.332303	NM_008983	ENSMUSG00000019889	Ptprk	AI853699|PTPk|RPTPkappa	protein tyrosine phosphatase, receptor type, K	protein-coding
mm_37931.1	chr4	132884771	132884790	-	1	NA	promoter-TSS (NM_133887)	promoter-TSS (NM_133887)	-322	NM_133887	100226	Mm.28237	NM_133887	ENSMUSG00000028879	Stx12	AI850350|AU041521|Stx13	syntaxin 12	protein-coding
mm_30221.1	chr3	145032870	145032898	-	1	NA	promoter-TSS (NM_017474)	promoter-TSS (NM_017474)	-108	NM_017474	23844	Mm.33483	NM_017474	ENSMUSG00000028255	Clca1	Clca2|Clca3|gob-5|gob5	chloride channel accessory 1	protein-coding
mm_14315.1	chr2	129246358	129246361	+	1	NA	Intergenic	RLTR12C|LTR|ERVK	27390	NR_045838	329513	Mm.473529	NM_177847	ENSMUSG00000056738	A730036I17Rik	-	RIKEN cDNA A730036I17 gene	ncRNA
mm_123891.1	chr14	72710759	72710769	-	1	NA	promoter-TSS (NM_207636)	promoter-TSS (NM_207636)	-761	NM_207636	319448	Mm.205421	NM_207636	ENSMUSG00000033487	Fndc3a	1700094E19Rik|D14Ertd453e|F730017H24Rik|Fndc3|sys	fibronectin type III domain containing 3A	protein-coding
mm_143972.1	chr17	87427691	87427707	-	1	NA	promoter-TSS (NM_029298)	promoter-TSS (NM_029298)	42	NM_029298	75467	Mm.50108	NM_029298	ENSMUSG00000036557	Stpg4	1700011E24Rik|GSE	sperm tail PG rich repeat containing 4	protein-coding
mm_62713.1	chr7	110768616	110768634	+	1	NA	intron (NM_001276301, intron 1 of 14)	CpG	419	NM_001276301	11717	Mm.3238	NM_009667	ENSMUSG00000005686	Ampd3	-	adenosine monophosphate deaminase 3	protein-coding
mm_26898.1	chr3	19264998	19265005	-	1	NA	promoter-TSS (NM_008802)	promoter-TSS (NM_008802)	7	NM_008802	18583	Mm.355614	NM_008802	ENSMUSG00000069094	Pde7a	AU015378|AW047537	phosphodiesterase 7A	protein-coding
mm_108405.1	chr12	81631381	81631394	+	1	NA	5' UTR (NM_001033149, exon 1 of 3)	5' UTR (NM_001033149, exon 1 of 3)	138	NM_001033149	69480	Mm.130002	NM_001033149	ENSMUSG00000042734	Ttc9	-	tetratricopeptide repeat domain 9	protein-coding
mm_129857.1	chr15	83251721	83251736	-	1	NA	promoter-TSS (NM_001170954)	promoter-TSS (NM_001170954)	3	NM_001170954	239559	Mm.323805	NM_001004150	ENSMUSG00000047878	A4galt	-	alpha 1,4-galactosyltransferase	protein-coding
mm_17517.1	chr2	29251684	29251696	-	1	NA	intron (NR_029460, intron 1 of 1)	CpG	1303	NR_029460	76220	Mm.330108	NR_029460	ENSMUSG00000079499	6530402F18Rik	mKIAA1857	RIKEN cDNA 6530402F18 gene	ncRNA
mm_39840.1	chr5	30887609	30887612	+	1	NA	Intergenic	Intergenic	-1242	NM_174849	231093	Mm.440364	NM_174849	ENSMUSG00000029165	Agbl5	9430057O19Rik|CCP5	ATP/GTP binding protein-like 5	protein-coding
mm_47453.1	chr5	123573036	123573040	-	1	NA	promoter-TSS (NM_029929)	promoter-TSS (NM_029929)	-23	NM_029929	77573	Mm.41372	NM_029929	ENSMUSG00000029434	Vps33a	3830421M04Rik|AI503300|AW048546|AW554476|bf	VPS33A CORVET/HOPS core subunit	protein-coding
mm_54288.1	chr6	29250031	29250052	-	1	NA	Intergenic	Intergenic	-22447	NM_001190461	69573	Mm.45161	NM_023516	ENSMUSG00000043421	Hilpda	2310016C08Rik|AW049004|Hig2	hypoxia inducible lipid droplet associated	protein-coding
mm_38378.1	chr4	138624002	138624021	-	1	NA	promoter-TSS (NM_029401)	promoter-TSS (NM_029401)	-19	NM_029401	75718	Mm.251530	NM_029401	ENSMUSG00000028753	Vwa5b1	4931403E03Rik	von Willebrand factor A domain containing 5B1	protein-coding
mm_91162.1	chr10	20596379	20596404	-	1	NA	intron (NM_013875, intron 2 of 12)	B1F1|SINE|Alu	-48063	NM_001347366	29863	Mm.425617	NM_013875	ENSMUSG00000019990	Pde7b	-	phosphodiesterase 7B	protein-coding
mm_13410.1	chr2	104095797	104095805	+	1	NA	promoter-TSS (NM_001111060)	promoter-TSS (NM_001111060)	0	NM_007652	12509	Mm.247265	NM_007652	ENSMUSG00000032679	Cd59a	AA987121|Cd59|protectin	CD59a antigen	protein-coding
mm_14069.1	chr2	122738645	122738653	+	1	NA	exon (NM_019788, exon 1 of 5)	exon (NM_019788, exon 1 of 5)	144	NM_019788	18457	Mm.268921	NM_019788	ENSMUSG00000005804	Bloc1s6	BLOC-1|Pldn|Stx13bp1|pa	biogenesis of lysosomal organelles complex-1, subunit 6, pallidin	protein-coding
mm_159469.1	chr4	11706042	11706042	+	1	NA	exon (NM_010276, exon 2 of 5)	exon (NM_010276, exon 2 of 5)	1595	NM_010276	14579	Mm.247486	NM_010276	ENSMUSG00000028214	Gem	AV020497	GTP binding protein (gene overexpressed in skeletal muscle)	protein-coding
mm_54618.1	chr6	38433644	38433661	-	1	NA	promoter-TSS (NM_177185)	promoter-TSS (NM_177185)	-273	NM_177185	320538	Mm.302831	NM_177185	ENSMUSG00000038538	Ubn2	2900060J04Rik|6030408G03Rik|BC060116|D130059P03Rik|mKIAA2030	ubinuclein 2	protein-coding
mm_164216.1	chr15	84301463	84301468	+	1	NA	intron (NM_133167, intron 8 of 12)	intron (NM_133167, intron 8 of 12)	-23255	NM_022321	64099	Mm.251356	NM_022321	ENSMUSG00000022439	Parvg	AI413459	parvin, gamma	protein-coding
mm_27422.1	chr3	51517953	51517963	-	1	NA	3' UTR (NM_080793, exon 8 of 8)	3' UTR (NM_080793, exon 8 of 8)	33992	NM_016858	19338	Mm.1664	NM_016858	ENSMUSG00000027739	Rab33b	-	RAB33B, member RAS oncogene family	protein-coding
mm_102673.1	chr11	65243550	65243562	-	1	NA	intron (NM_146386, intron 1 of 12)	intron (NM_146386, intron 1 of 12)	26433	NM_145136	214384	Mm.32257	NM_145136	ENSMUSG00000020542	Myocd	BSAC2A|Srfcp	myocardin	protein-coding
mm_149397.1	chr19	11389174	11389181	+	1	NA	intron (NM_001310331, intron 5 of 6)	MER45C|DNA|hAT-Tip100	13689	NM_001310331	666907		NM_001310331	ENSMUSG00000101389	Ms4a4a	EG666907	membrane-spanning 4-domains, subfamily A, member 4A	protein-coding
mm_29632.1	chr3	121723396	121723409	-	1	NA	promoter-TSS (NM_010171)	promoter-TSS (NM_010171)	-135	NM_010171	14066	Mm.273188	NM_010171	ENSMUSG00000028128	F3	AA409063|CD142|Cf-3|Cf3|TF	coagulation factor III	protein-coding
mm_48533.1	chr5	142904384	142904415	-	1	NA	exon (NM_007393, exon 4 of 6)	exon (NM_007393, exon 4 of 6)	2355	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_4634.1	chr1	179668414	179668420	+	1	NA	exon (NM_178653, exon 1 of 12)	exon (NM_178653, exon 1 of 12)	186	NM_178653	109232	Mm.136458	NM_178653	ENSMUSG00000038936	Sccpdh	AW214504|C330023F11Rik	saccharopine dehydrogenase (putative)	protein-coding
mm_145355.1	chr18	56675692	56675698	+	1	NA	Intergenic	Intergenic	-32118	NM_010721	16906	Mm.4105	NM_010721	ENSMUSG00000024590	Lmnb1	-	lamin B1	protein-coding
mm_132526.1	chr16	37831568	37831582	+	1	NA	exon (NM_008047, exon 10 of 11)	exon (NM_008047, exon 10 of 11)	-36825	NM_177093	320184	Mm.390882	NM_177093	ENSMUSG00000034158	Lrrc58	1810012N18Rik|C330018J07Rik	leucine rich repeat containing 58	protein-coding
mm_39725.1	chr5	28317154	28317220	+	1	NA	promoter-TSS (NM_028234)	promoter-TSS (NM_028234)	-2	NM_028234	381626	Mm.304075	NM_028234	ENSMUSG00000048271	Rbm33	3200001K10Rik|6430512A10Rik|AA386890|Prr8	RNA binding motif protein 33	protein-coding
mm_62090.1	chr7	94042636	94042647	+	1	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	962762	NM_021427	58238	Mm.113787	NM_021427	ENSMUSG00000051515	Fam181b	A830059I20Rik|AB041569	family with sequence similarity 181, member B	protein-coding
mm_91212.1	chr10	21410580	21410587	-	1	NA	Intergenic	Intergenic	33283	NM_178713	237320	Mm.90181	NM_178713	ENSMUSG00000037542	Aldh8a1	Raldh4	aldehyde dehydrogenase 8 family, member A1	protein-coding
mm_116025.1	chr13	25020119	25020137	-	1	NA	exon (NM_001013389, exon 1 of 11)	exon (NM_001013389, exon 1 of 11)	189	NM_001013389	380836	Mm.387097	NM_001013389	ENSMUSG00000021339	Mrs2	Gm902|HPT|Mrs2l|RPT	MRS2 magnesium transporter	protein-coding
mm_157693.1	chrX	60404760	60404846	-	1	NA	promoter-TSS (NM_001001798)	promoter-TSS (NM_001001798)	-822	NM_001037863	320940	Mm.490394	NM_001001798	ENSMUSG00000062949	Atp11c	A330005H02Rik|AI315324|Ig	ATPase, class VI, type 11C	protein-coding
mm_31118.1	chr4	42952773	42952780	+	1	NA	promoter-TSS (NM_019874)	promoter-TSS (NM_019874)	-318	NM_019874	56323	Mm.20437	NM_019874	ENSMUSG00000036052	Dnajb5	1110058L06Rik|AI462558|Hsc40|Hsp40-3	DnaJ heat shock protein family (Hsp40) member B5	protein-coding
mm_153572.1	chr19	42767489	42767498	-	1	NA	intron (NM_001346703, intron 6 of 19)	intron (NM_001346703, intron 6 of 19)	12483	NM_001346703	192236	Mm.218381	NM_019424	ENSMUSG00000025188	Hps1	6030422N11Rik|BB405864|Gm21361|Hps|ep	Hermansky-Pudlak syndrome 1	protein-coding
mm_10953.1	chr2	25653112	25653130	+	1	NA	promoter-TSS (NM_033145)	promoter-TSS (NM_033145)	3	NM_033145	78076	Mm.196708	NM_033145	ENSMUSG00000036449	Lcn8	9230106L18Rik|EP17|Lcn5|mEP17	lipocalin 8	protein-coding
mm_79702.1	chr9	60866114	60866164	+	1	NA	intron (NM_028283, intron 13 of 18)	intron (NM_028283, intron 13 of 18)	71591	NM_028283	72565	Mm.68819	NM_028283	ENSMUSG00000034485	Uaca	2700059D02Rik|nucling	uveal autoantigen with coiled-coil domains and ankyrin repeats	protein-coding
mm_67288.1	chr7	78737229	78737232	-	1	NA	Intergenic	L1MD2|LINE|L1	-19010	NR_015542	414121	Mm.482537	NR_015542	ENSMUSG00000059146	E430016F16Rik	-	RIKEN cDNA E430016F16 gene	ncRNA
mm_20648.1	chr2	132029846	132029901	-	1	NA	5' UTR (NM_175445, exon 1 of 11)	5' UTR (NM_175445, exon 1 of 11)	115	NM_175445	215653	Mm.204737	NM_175445	ENSMUSG00000027339	Rassf2	3830431H01Rik|9030412M04Rik|AI852669|AW495050	Ras association (RalGDS/AF-6) domain family member 2	protein-coding
mm_117009.1	chr13	58007863	58007869	-	1	NA	intron (NM_001195075, intron 16 of 16)	intron (NM_001195075, intron 16 of 16)	15334	NR_030544	100124491		NR_030544	ENSMUSG00000077962	Mir874	Mirn874|mir-874|mmu-mir-874	microRNA 874	ncRNA
mm_52879.1	chr6	122513371	122513393	+	1	NA	promoter-TSS (NM_015776)	promoter-TSS (NM_015776)	-202	NM_001347434	50530	Mm.41931	NM_015776	ENSMUSG00000030116	Mfap5	MAGP-2|MFAP-5	microfibrillar associated protein 5	protein-coding
mm_103769.1	chr11	81968416	81968426	-	1	NA	promoter-TSS (NM_001034013)	promoter-TSS (NM_001034013)	-25	NM_001034013	11418	Mm.234998	NM_007384	ENSMUSG00000020704	Asic2	ACIC2|Accn1|BNC1|BNaC1|BNaC1a|Mdeg	acid-sensing (proton-gated) ion channel 2	protein-coding
mm_126130.1	chr15	78335285	78335302	+	1	NA	exon (NM_007780, exon 2 of 14)	exon (NM_007780, exon 2 of 14)	9303	NM_007780	12983	Mm.235324	NM_007780	ENSMUSG00000071713	Csf2rb	AI848964|AIC2B|Bc|CDw131|Csf2rb1|Csfgmrb|Il3r|Il3rb|Il3rb1|Il5rb	colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage)	protein-coding
mm_140415.1	chr17	87650492	87650530	+	1	NA	3' UTR (NM_008532, exon 10 of 10)	3' UTR (NM_008532, exon 10 of 10)	14532	NM_008532	17075	Mm.4259	NM_008532	ENSMUSG00000045394	Epcam	CD326|EGP|EGP-2|Egp314|Ep-CAM|EpCAM1|GA733-2|Ly74|TROP1|Tacsd1|Tacstd1|gp40	epithelial cell adhesion molecule	protein-coding
mm_123223.1	chr14	59597899	59597904	-	1	NA	promoter-TSS (NM_027986)	promoter-TSS (NM_027986)	58	NM_001168537	71891	Mm.439850	NM_027986	ENSMUSG00000021982	Cdadc1	2310010M10Rik|AI449174|AI463398|BB130816|NYD-SP15	cytidine and dCMP deaminase domain containing 1	protein-coding
mm_41787.1	chr5	103736908	103736914	+	1	NA	Intergenic	PB1D11|SINE|Alu	-17251	NM_133919	17355	Mm.6949	NM_133919	ENSMUSG00000029313	Aff1	9630032B01Rik|AW319193|Af4|Mllt2h|Rob	AF4/FMR2 family, member 1	protein-coding
mm_99549.1	chr11	103412829	103412840	+	1	NA	promoter-TSS (NM_183034)	promoter-TSS (NM_183034)	-170	NM_183034	353047	Mm.18556	NM_183034	ENSMUSG00000034247	Plekhm1	AP162|B2|BC038943|D330036J23Rik	pleckstrin homology domain containing, family M (with RUN domain) member 1	protein-coding
mm_115543.1	chr13	7175667	7175671	-	1	NA	Intergenic	RLTR9E|LTR|ERVK	-526898	NM_001291071	56421	Mm.273874	NM_019703	ENSMUSG00000021196	Pfkp	1200015H23Rik|9330125N24Rik|ATP-PFK|PFK-C|PFK-P	phosphofructokinase, platelet	protein-coding
mm_140798.1	chr17	21516940	21516960	-	1	NA	Intergenic	Intergenic	-18589	NM_144515	22710	Mm.296100	NM_144515	ENSMUSG00000051341	Zfp52	KRAB11|Zfp-52|Zfp76|mszf23-2|mszf24|mszf34|mszf75|zfec29	zinc finger protein 52	protein-coding
mm_167302.1	chr8	56344697	56344697	+	1	NA	Intergenic	Intergenic	50145	NM_008278	15446	Mm.18832	NM_008278	ENSMUSG00000031613	Hpgd	15-PGDH|AV026552	hydroxyprostaglandin dehydrogenase 15 (NAD)	protein-coding
mm_149232.1	chr19	10182907	10182917	+	1	NA	promoter-TSS (NM_146094)	promoter-TSS (NM_146094)	24	NM_146094	76267	Mm.30158	NM_146094	ENSMUSG00000010663	Fads1	0710001O03Rik|A930006B21Rik|AI317215|DSD	fatty acid desaturase 1	protein-coding
mm_11007.1	chr2	26576078	26576107	+	1	NA	Intergenic	Intergenic	-4964	NM_178444	353156	Mm.268933	NM_178444	ENSMUSG00000026921	Egfl7	VE-statin|Zneu1	EGF-like domain 7	protein-coding
mm_102813.1	chr11	68956874	68956909	-	1	NA	promoter-TSS (NM_177566)	promoter-TSS (NM_177566)	-33	NM_177566	442801	Mm.376147	NM_177566	ENSMUSG00000052921	Arhgef15	D130071N09|D530030K12Rik|E5	Rho guanine nucleotide exchange factor (GEF) 15	protein-coding
mm_151644.1	chr19	4042231	4042242	-	1	NA	promoter-TSS (NM_181796)	promoter-TSS (NM_181796)	-15	NM_181796	14869	Mm.441542	NM_181796	ENSMUSG00000038155	Gstp2	GSTpiA|Gst-3|Gst3	glutathione S-transferase, pi 2	protein-coding
mm_168126.1	chr10	23349638	23349644	-	1	NA	intron (NM_010167, intron 1 of 18)	intron (NM_010167, intron 1 of 18)	249	NM_001347372	14051	Mm.332128	NM_010167	ENSMUSG00000010461	Eya4	B130023L16Rik	EYA transcriptional coactivator and phosphatase 4	protein-coding
mm_161114.1	chr12	104752010	104752010	-	1	NA	promoter-TSS (NM_148948)	promoter-TSS (NM_148948)	-58	NM_148948	192119	Mm.21135	NM_148948	ENSMUSG00000041415	Dicer1	1110006F08Rik|D12Ertd7e|mKIAA0928	dicer 1, ribonuclease type III	protein-coding
mm_157246.1	chrX	18461386	18461402	-	1	NA	promoter-TSS (NM_175228)	promoter-TSS (NM_175228)	3	NR_132634	75905	Mm.159617	NM_175228	ENSMUSG00000037358	4930578C19Rik	-	RIKEN cDNA 4930578C19 gene	protein-coding
mm_35320.1	chr4	25800214	25800224	-	1	NA	promoter-TSS (NM_010243)	promoter-TSS (NM_010243)	-216	NM_010243	14348	Mm.39101	NM_010243	ENSMUSG00000055373	Fut9	AI746471|AU067636|mFUT9|mFuc-TIX	fucosyltransferase 9	protein-coding
mm_44600.1	chr5	25100401	25100457	-	1	NA	promoter-TSS (NR_027851)	promoter-TSS (NR_027851)	213	NM_145401	108099	Mm.33649	NM_145401	ENSMUSG00000028944	Prkag2	2410051C13Rik|AAKG|AAKG2|AI854673|H91620p|WPWS	protein kinase, AMP-activated, gamma 2 non-catalytic subunit	protein-coding
mm_151708.1	chr19	4615146	4615199	-	1	NA	5' UTR (NM_153388, exon 1 of 3)	5' UTR (NM_153388, exon 1 of 3)	495	NM_153388	225875	Mm.329675	NM_153388	ENSMUSG00000045045	Lrfn4	BC023156|Salm3	leucine rich repeat and fibronectin type III domain containing 4	protein-coding
mm_4913.1	chr1	190594301	190594314	+	1	NA	Intergenic	Intergenic	317463	NM_178775	320119	Mm.220912	NM_178775	ENSMUSG00000089872	Rps6kc1	AA682037|B130003F20Rik|C80612|Rpk118	ribosomal protein S6 kinase polypeptide 1	protein-coding
mm_139182.1	chr17	47593742	47593752	+	1	NA	exon (NM_007632, exon 1 of 5)	exon (NM_007632, exon 1 of 5)	280	NM_007632	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_18103.1	chr2	44988532	44988543	-	1	NA	3' UTR (NM_015753, exon 10 of 10)	3' UTR (NM_015753, exon 10 of 10)	34640	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_10312.1	chr2	11172310	11172327	+	1	NA	promoter-TSS (NM_008859)	promoter-TSS (NM_008859)	-64	NM_008859	18761	Mm.329993	NM_008859	ENSMUSG00000026778	Prkcq	A130035A12Rik|AW494342|PKC-0|PKC-theta|PKCtheta|Pkcq	protein kinase C, theta	protein-coding
mm_98003.1	chr11	84177631	84177653	+	1	NA	Intergenic	Intergenic	-10166	NM_001037932	628813	Mm.390389	NM_001037932	ENSMUSG00000051452	Gm11437	AI463690|OTTMUSG00000000997	predicted gene 11437	protein-coding
mm_8828.1	chr1	162570283	162570322	-	1	NA	promoter-TSS (NM_016796)	promoter-TSS (NM_016796)	-526	NM_016796	53330	Mm.10699	NM_016796	ENSMUSG00000026696	Vamp4	D1Ertd147e	vesicle-associated membrane protein 4	protein-coding
mm_4450.1	chr1	172588976	172588979	+	1	NA	intron (NM_029084, intron 1 of 4)	intron (NM_029084, intron 1 of 4)	1591	NM_029084	74748	Mm.179812	NM_029084	ENSMUSG00000053318	Slamf8	5830408F06Rik|Blame|SBBI42	SLAM family member 8	protein-coding
mm_18986.1	chr2	76856350	76856373	-	1	NA	exon (NM_011652, exon 124 of 313)	exon (NM_011652, exon 124 of 313)	126186	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_129114.1	chr15	76080876	76080893	-	1	NA	promoter-TSS (NM_028364)	promoter-TSS (NM_028364)	-14	NM_001164600	67959	Mm.29965	NM_028364	ENSMUSG00000002524	Puf60	2410104I19Rik|2810454F19Rik|SIAHBP1	poly-U binding splicing factor 60	protein-coding
mm_85280.1	chr9	99691685	99691687	-	1	NA	3' UTR (NM_001194922, exon 5 of 5)	3' UTR (NM_001194922, exon 5 of 5)	18377	NM_019815	56492	Mm.386784	NM_019815	ENSMUSG00000032473	Cldn18	-	claudin 18	protein-coding
mm_103329.1	chr11	74547101	74547112	-	1	NA	intron (NM_001015046, intron 2 of 24)	intron (NM_001015046, intron 2 of 24)	43052	NM_001015046	380711	Mm.425690	NM_001015046	ENSMUSG00000038807	Rap1gap2	AU067654|Garnl4|Gm1561|mKIAA1039	RAP1 GTPase activating protein 2	protein-coding
mm_140871.1	chr17	23786198	23786237	-	1	NA	promoter-TSS (NM_029798)	promoter-TSS (NM_029798)	-140	NM_029798	76917	Mm.269613	NM_029798	ENSMUSG00000023911	Flywch2	2810417J12Rik|3010014L17Rik|AW548203	FLYWCH family member 2	protein-coding
mm_158886.1	chr1	10232553	10232553	-	1	NA	5' UTR (NM_001102430, exon 1 of 38)	5' UTR (NM_001102430, exon 1 of 38)	117	NM_001102430	211673	Mm.229141	NM_001102430	ENSMUSG00000067851	Arfgef1	ARFGEP1|BIG1|D130059B05Rik|D730028O18Rik|P200	ADP-ribosylation factor guanine nucleotide-exchange factor 1(brefeldin A-inhibited)	protein-coding
mm_49466.1	chr6	29433249	29433267	+	1	NA	promoter-TSS (NM_001311074)	promoter-TSS (NM_001311074)	-90	NM_001311074	68794	Mm.39046	NM_026839	ENSMUSG00000068699	Flnc	1110055E19Rik|ABP-280|ABPL|Fln2	filamin C, gamma	protein-coding
mm_91829.1	chr10	56914533	56914575	-	1	NA	Intergenic	Intergenic	537254	NM_010288	14609	Mm.378921	NM_010288	ENSMUSG00000050953	Gja1	AU042049|AW546267|Cnx43|Cx43|Cx43alpha1|Gja-1|Npm1|connexin43	gap junction protein, alpha 1	protein-coding
mm_310.1	chr1	24195197	24195221	+	1	NA	promoter-TSS (NM_001290691)	promoter-TSS (NM_001290691)	6	NM_001290691	12839	Mm.154662	NM_007740	ENSMUSG00000026147	Col9a1	Col9a-1	collagen, type IX, alpha 1	protein-coding
mm_19946.1	chr2	117122874	117122890	-	1	NA	intron (NM_033524, intron 1 of 6)	intron (NM_033524, intron 1 of 6)	1811	NM_033524	114715	Mm.245890	NM_033524	ENSMUSG00000027351	Spred1	5730461F13Rik|AL024345|AW047647	sprouty protein with EVH-1 domain 1, related sequence	protein-coding
mm_96539.1	chr11	68692071	68692086	+	1	NA	5' UTR (NM_175260, exon 1 of 41)	5' UTR (NM_175260, exon 1 of 41)	163	NM_175260	77579	Mm.218233	NM_175260	ENSMUSG00000020900	Myh10	5730504C04Rik|9330167F11Rik|Fltn|Myhn-2|Myhn2|NMHC II-B|NMHC-B|NMHCII-B|NMMHC II-b|NMMHC-B|NMMHC-IIB|SMemb|mKIAA3005	myosin, heavy polypeptide 10, non-muscle	protein-coding
mm_50887.1	chr6	56714867	56714883	+	1	NA	promoter-TSS (NM_030235)	promoter-TSS (NM_030235)	-30	NM_030235	78937	Mm.105343	NM_030235	ENSMUSG00000029787	Avl9	5830411G16Rik|D730049P16Rik|mKIAA0241	AVL9 cell migration associated	protein-coding
mm_42182.1	chr5	112263516	112263526	+	1	NA	exon (NM_001312894, exon 4 of 6)	exon (NM_001312894, exon 4 of 6)	7701	NM_001312893	12960	Mm.29488	NM_023695	ENSMUSG00000029343	Crybb1	3110006K12Rik|BB1CRY	crystallin, beta B1	protein-coding
mm_57630.1	chr6	128300454	128300501	-	1	NA	5' UTR (NM_001080979, exon 1 of 11)	5' UTR (NM_001080979, exon 1 of 11)	336	NM_001080979	21679	Mm.14774	NM_011567	ENSMUSG00000030353	Tead4	ETFR-2|Etfr2|FR-19|Rtef1|TEAD-4|TEF-3|Tcf13r1|Tef3|Tefr|Tefr1|Tefr1a	TEA domain family member 4	protein-coding
mm_78369.1	chr9	27191738	27191738	+	1	NA	Intergenic	Intergenic	-36317	NM_023277	83964	Mm.28770	NM_023277	ENSMUSG00000031990	Jam3	1110002N23Rik|JAM-3|JAM-C|Jcam3	junction adhesion molecule 3	protein-coding
mm_46870.1	chr5	113830570	113830575	-	1	NA	promoter-TSS (NM_009151)	promoter-TSS (NM_009151)	-71	NM_009151	20345	Mm.332590	NM_009151	ENSMUSG00000048163	Selplg	CD162|Psgl-1|Psgl1|Selp1|Selpl	selectin, platelet (p-selectin) ligand	protein-coding
mm_75359.1	chr8	45262109	45262119	-	1	NA	promoter-TSS (NM_028066)	promoter-TSS (NM_028066)	-83	NM_028066	109821	Mm.33326	NM_028066	ENSMUSG00000031645	F11	1600027G01Rik|AI503996|Cf11|FXI|PTA	coagulation factor XI	protein-coding
mm_33387.1	chr4	129772546	129772566	+	1	NA	Intergenic	Intergenic	-30253	NR_045036	20218	Mm.8256	NM_011317	ENSMUSG00000028790	Khdrbs1	Sam68|p62|p68	KH domain containing, RNA binding, signal transduction associated 1	protein-coding
mm_66119.1	chr7	31051432	31051488	-	1	NA	promoter-TSS (NM_022007)	promoter-TSS (NM_022007)	-6	NM_022007	57780	Mm.41770	NM_022007	ENSMUSG00000036578	Fxyd7	1110035I01Rik	FXYD domain-containing ion transport regulator 7	protein-coding
mm_86965.1	chr10	25359821	25359844	+	1	NA	promoter-TSS (NM_001199265)	promoter-TSS (NM_001199265)	34	NM_001199265	13822	Mm.306026	NM_013511	ENSMUSG00000019978	Epb41l2	4.1G|AW555191|D10Ertd398e|Epb4.1l2|NBL2	erythrocyte membrane protein band 4.1 like 2	protein-coding
mm_90004.1	chr10	112726914	112726927	+	1	NA	promoter-TSS (NR_040579)	promoter-TSS (NR_040579)	-6	NR_040579	69355	Mm.84337	NR_040579	ENSMUSG00000100314	1700010J16Rik	-	RIKEN cDNA 1700010J16 gene	ncRNA
mm_20384.1	chr2	128943986	128944034	-	1	NA	promoter-TSS (NM_020594)	promoter-TSS (NM_020594)	10	NM_020594	57432	Mm.11675	NM_020594	ENSMUSG00000027387	Zc3h8	AU020882|E130108N08Rik|Fliz1|Zc3hdc8	zinc finger CCCH type containing 8	protein-coding
mm_127674.1	chr15	102762280	102762284	+	1	NA	Intergenic	Intergenic	-15373	NR_104334	102216269		NR_104334		Gm38436	Cistr|Cistr-act	predicted gene, 38436	ncRNA
mm_128987.1	chr15	74834662	74834675	-	1	NA	TTS (NM_001033229)	TTS (NM_001033229)	6975	NM_001033229	110115	Mm.322606	NM_001033229	ENSMUSG00000075604	Cyp11b1	AA389061|CPN1|Cyp11b|Cyp11b-1|FHI	cytochrome P450, family 11, subfamily b, polypeptide 1	protein-coding
mm_109681.1	chr12	113133509	113133528	+	1	NA	intron (NM_001346696, intron 17 of 19)	intron (NM_001346696, intron 17 of 19)	-6718	NM_024223	68337	Mm.133825	NM_024223	ENSMUSG00000006356	Crip2	0610010I23Rik|AW743261|C77570|CRP2|CRP4|Crp|ESP1|Hlp	cysteine rich protein 2	protein-coding
mm_42053.1	chr5	108669272	108669322	+	1	NA	TTS (NM_001310692)	TTS (NM_001310692)	5499	NM_001310692	231583	Mm.440571	NM_174870	ENSMUSG00000046959	Slc26a1	Sat1	solute carrier family 26 (sulfate transporter), member 1	protein-coding
mm_197.1	chr1	16051553	16051554	+	1	NA	Intergenic	MERV1_LTR|LTR|ERV1	41772	NM_001305227	75799	Mm.78557	NM_001243238	ENSMUSG00000067795	4930444P10Rik	-	RIKEN cDNA 4930444P10 gene	protein-coding
mm_13554.1	chr2	112261946	112261951	+	1	NA	promoter-TSS (NM_025403)	promoter-TSS (NM_025403)	22	NM_025403	66181	Mm.272346	NM_025403	ENSMUSG00000027133	Nop10	1110036B12Rik|NOP10P|Nola3	NOP10 ribonucleoprotein	protein-coding
mm_126119.1	chr15	78325724	78325750	+	1	NA	promoter-TSS (NM_007780)	promoter-TSS (NM_007780)	-253	NM_007780	12983	Mm.235324	NM_007780	ENSMUSG00000071713	Csf2rb	AI848964|AIC2B|Bc|CDw131|Csf2rb1|Csfgmrb|Il3r|Il3rb|Il3rb1|Il5rb	colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage)	protein-coding
mm_139253.1	chr17	47734407	47734421	+	1	NA	TTS (NM_025973)	TTS (NM_025973)	-2623	NM_001161722	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_24784.1	chr3	95541639	95541662	+	1	NA	intron (NM_001267695, intron 3 of 7)	intron (NM_001267695, intron 3 of 7)	14864	NM_001267695	13040	Mm.3619	NM_021281	ENSMUSG00000038642	Ctss	Cats	cathepsin S	protein-coding
mm_87086.1	chr10	31313376	31313420	+	1	NA	promoter-TSS (NM_027168)	promoter-TSS (NM_027168)	-7	NM_027168	69692	Mm.245537	NM_027168	ENSMUSG00000000295	Hddc2	2310057G13Rik	HD domain containing 2	protein-coding
mm_129746.1	chr15	82244717	82244755	-	1	NA	promoter-TSS (NM_001080158)	promoter-TSS (NM_001080158)	11	NM_178269	66570	Mm.23596	NM_025639	ENSMUSG00000068101	Cenpm	2610019I03Rik|AI853711|Pane1	centromere protein M	protein-coding
mm_17464.1	chr2	28558030	28558054	-	1	NA	exon (NM_009885, exon 8 of 11)	exon (NM_009885, exon 8 of 11)	5361	NM_009885	12613	Mm.236017	NM_009885	ENSMUSG00000026818	Cel	1810036E18Rik|BAL	carboxyl ester lipase	protein-coding
mm_37210.1	chr4	117887248	117887254	-	1	NA	promoter-TSS (NM_033617)	promoter-TSS (NM_033617)	78	NM_033617	114143	Mm.207052	NM_033617	ENSMUSG00000033379	Atp6v0b	2310024H13Rik|Atp6f|VMA16	ATPase, H+ transporting, lysosomal V0 subunit B	protein-coding
mm_65305.1	chr7	24750391	24750427	-	1	NA	exon (NM_026862, exon 13 of 17)	exon (NM_026862, exon 13 of 17)	9902	NM_026862	68891	Mm.292848	NM_026862	ENSMUSG00000052212	Cd177	1190003K14Rik|Pdp3	CD177 antigen	protein-coding
mm_157218.1	chrX	13071925	13071929	-	1	NA	intron (NM_009481, intron 1 of 44)	CpG	429	NM_009481	22284	Mm.242646	NM_009481	ENSMUSG00000031010	Usp9x	5730589N07Rik|AA407302|AA407699|AL022658|AL022749|Dffrx|FAF-X|Fafl	ubiquitin specific peptidase 9, X chromosome	protein-coding
mm_17210.1	chr2	25478076	25478094	-	1	NA	Intergenic	Intergenic	-8336	NM_008963	19215	Mm.1008	NM_008963	ENSMUSG00000015090	Ptgds	21kDa|L-PGDS|PGD2|PGDS|PGDS2|Ptgs3	prostaglandin D2 synthase (brain)	protein-coding
mm_148033.1	chr18	70141569	70141622	-	1	NA	promoter-TSS (NM_001082553)	promoter-TSS (NM_001082553)	10	NM_001082553	80718	Mm.246753	NM_030554	ENSMUSG00000024511	Rab27b	2310021G14Rik|B130064M09Rik	RAB27B, member RAS oncogene family	protein-coding
mm_158390.1	chrX	136172234	136172244	-	1	NA	promoter-TSS (NM_025703)	promoter-TSS (NM_025703)	12	NM_001168578	66684	Mm.182094	NM_025703	ENSMUSG00000051579	Tceal8	3930402F23Rik	transcription elongation factor A (SII)-like 8	protein-coding
mm_151519.1	chr19	58738355	58738365	+	1	NA	intron (NM_018874, intron 10 of 12)	intron (NM_018874, intron 10 of 12)	9473	NM_018874	18946	Mm.10753	NM_018874	ENSMUSG00000042179	Pnliprp1	Plrp1	pancreatic lipase related protein 1	protein-coding
mm_139111.1	chr17	47385376	47385380	+	1	NA	promoter-TSS (NM_146079)	promoter-TSS (NM_146079)	-15	NM_146079	107477	Mm.59151	NM_146079	ENSMUSG00000023979	Guca1b	BC018258|GCAP2	guanylate cyclase activator 1B	protein-coding
mm_142542.1	chr17	46556038	46556044	-	1	NA	5' UTR (NM_020493, exon 1 of 7)	5' UTR (NM_020493, exon 1 of 7)	121	NM_020493	20807	Mm.45044	NM_020493	ENSMUSG00000015605	Srf	AW049942|AW240594	serum response factor	protein-coding
mm_164754.1	chr17	82539158	82539171	+	1	NA	Intergenic	Intergenic	539061	NR_045094	100503434	Mm.187281	NR_045094		Gm19689	-	predicted gene, 19689	ncRNA
mm_88720.1	chr10	80167838	80167840	+	1	NA	promoter-TSS (NM_007705)	promoter-TSS (NM_007705)	-2	NM_007705	12696	Mm.17898	NM_007705	ENSMUSG00000045193	Cirbp	Cirp|R74941	cold inducible RNA binding protein	protein-coding
mm_135561.1	chr16	50070710	50070719	-	1	NA	intron (NR_045935, intron 1 of 3)	intron (NR_045935, intron 1 of 3)	2138	NR_045935	224180	Mm.146439	NM_175010		Gm4827	B130050K08|EG224180	predicted gene 4827	ncRNA
mm_140434.1	chr17	88440715	88440741	+	1	NA	promoter-TSS (NM_180974)	promoter-TSS (NM_180974)	16	NM_180974	14236	Mm.112824	NM_180974	ENSMUSG00000034998	Foxn2	3230402J05Rik|6030465J18Rik|Fkh19|Foxn1|HTLF	forkhead box N2	protein-coding
mm_14125.1	chr2	126025310	126025322	+	1	NA	intron (NM_029455, intron 11 of 16)	intron (NM_029455, intron 11 of 16)	-9342	NM_008008	14178	Mm.330557	NM_008008	ENSMUSG00000027208	Fgf7	Kgf	fibroblast growth factor 7	protein-coding
mm_1257.1	chr1	63114416	63114473	+	1	NA	promoter-TSS (NM_001114609)	promoter-TSS (NM_001114609)	-27	NR_045915	100380944	Mm.392955	NR_045914	ENSMUSG00000084799	Ino80dos	Gm11602|OTTMUSG00000002611	INO80 complex subunit D, opposite strand	ncRNA
mm_107078.1	chr12	16965491	16965565	+	1	NA	exon (NM_009072, exon 20 of 33)	exon (NM_009072, exon 20 of 33)	34590	NM_172574	217430	Mm.379451	NM_172574	ENSMUSG00000045679	Pqlc3	C78076|E030024M05Rik	PQ loop repeat containing	protein-coding
mm_132562.1	chr16	38089362	38089395	+	1	NA	promoter-TSS (NR_033221)	promoter-TSS (NR_033221)	-118	NR_033221	414072	Mm.483602	NR_033221		BC031361	-	cDNA sequence BC031361	ncRNA
mm_156218.1	chrX	134717931	134717941	+	1	NA	promoter-TSS (NM_030066)	promoter-TSS (NM_030066)	-2	NM_001166380	78248	Mm.458522	NM_030066	ENSMUSG00000033460	Armcx1	3010033I09Rik|ALEX1	armadillo repeat containing, X-linked 1	protein-coding
mm_83919.1	chr9	56549132	56549139	-	1	NA	Intergenic	RMER17C|LTR|ERVK	86513	NM_001311076	235402	Mm.246605	NM_181074	ENSMUSG00000049556	Lingo1	4930471K13Rik|AV148400|LERN1|LINGO-1|Lrrn6a|UNQ201	leucine rich repeat and Ig domain containing 1	protein-coding
mm_86384.1	chr9	123872110	123872157	-	1	NA	Intergenic	Intergenic	-10104	NM_011798	23832	Mm.390241	NM_011798	ENSMUSG00000060509	Xcr1	Ccxcr1|Gpr5|mXcr1	chemokine (C motif) receptor 1	protein-coding
mm_67647.1	chr7	84605820	84605826	-	1	NA	5' UTR (NM_010176, exon 1 of 14)	5' UTR (NM_010176, exon 1 of 14)	119	NM_010176	14085	Mm.3798	NM_010176	ENSMUSG00000030630	Fah	-	fumarylacetoacetate hydrolase	protein-coding
mm_14985.1	chr2	152179539	152179549	+	1	NA	Intergenic	B4|SINE|B4	35935	NM_009328	21407	Mm.3881	NM_009328	ENSMUSG00000068079	Tcf15	Meso1|bHLH-EC2	transcription factor 15	protein-coding
mm_34718.1	chr4	152128989	152129003	+	1	NA	promoter-TSS (NM_019585)	promoter-TSS (NM_019585)	-71	NM_019585	56226	Mm.264215	NM_019585	ENSMUSG00000028943	Espn	je	espin	protein-coding
mm_43744.1	chr5	140264378	140264398	+	1	NA	intron (NM_010752, intron 9 of 17)	intron (NM_010752, intron 9 of 17)	57164	NM_010752	17120	Mm.27250	NM_010752	ENSMUSG00000029554	Mad1l1	AI173502|AW550425|Mad1	MAD1 mitotic arrest deficient 1-like 1	protein-coding
mm_9028.1	chr1	166483459	166483473	-	1	NA	TTS (NM_001164306)	TTS (NM_001164306)	14122	NM_001164306	226601	Mm.475593	NM_001164306	ENSMUSG00000086056	Gm4846	EG226601|Fmo13	predicted gene 4846	protein-coding
mm_90563.1	chr10	128225831	128225845	+	1	NA	promoter-TSS (NM_008600)	promoter-TSS (NM_008600)	28	NM_008600	17339	Mm.31625	NM_008600	ENSMUSG00000025389	Mip	Aqp0|Cat|Cts|Hfi|Lop|MIP26|MP26|Svl|shrivelled	major intrinsic protein of lens fiber	protein-coding
mm_157637.1	chrX	57188921	57188926	-	1	NA	Intergenic	Intergenic	-11714	NR_038463	100502842	Mm.164733	NR_038463	ENSMUSG00000085808	Gm14718	OTTMUSG00000017790	predicted gene 14718	ncRNA
mm_128103.1	chr15	27968229	27968240	-	1	NA	intron (NM_001081302, intron 1 of 56)	intron (NM_001081302, intron 1 of 56)	57614	NM_001081302	223435	Mm.485422	NM_001081302	ENSMUSG00000022263	Trio	6720464I07Rik|AA408740|Solo	triple functional domain (PTPRF interacting)	protein-coding
mm_123673.1	chr14	69249717	69249721	-	1	NA	intron (NM_026331, intron 1 of 3)	intron (NM_026331, intron 1 of 3)	35384	NM_026331	67712	Mm.293635	NM_026331	ENSMUSG00000034248	Slc25a37	1700020E22Rik|4930513O14Rik|4930526G11Rik|AI848481|C330015G08Rik|Mfrn|Mfrn1|Mscp|frascati|mitoferrin	solute carrier family 25, member 37	protein-coding
mm_148389.1	chr19	3388862	3388904	+	1	NA	promoter-TSS (NM_001286558)	promoter-TSS (NM_001286558)	26	NM_001039657	17771	Mm.209941	NM_010841	ENSMUSG00000024905	Mtl5	tesmin	metallothionein-like 5, testis-specific (tesmin)	protein-coding
mm_133439.1	chr16	87700201	87700213	+	1	NA	intron (NM_007520, intron 1 of 4)	intron (NM_007520, intron 1 of 4)	1253	NM_007520	12013	Mm.26147	NM_007520	ENSMUSG00000025612	Bach1	6230421P05Rik|AI323795	BTB and CNC homology 1, basic leucine zipper transcription factor 1	protein-coding
mm_30739.1	chr4	14240199	14240209	+	1	NA	intron (NR_131155, intron 2 of 2)	intron (NR_131155, intron 2 of 2)	51105	NR_131155	100040030	Mm.366499	NR_131155		Gm2560	-	predicted gene 2560	ncRNA
mm_100585.1	chr11	120948544	120948553	+	1	NA	promoter-TSS (NM_001038654)	promoter-TSS (NM_001038654)	64	NM_030696	80879	Mm.28632	NM_030696	ENSMUSG00000025161	Slc16a3	Mct3|Mct4	solute carrier family 16 (monocarboxylic acid transporters), member 3	protein-coding
mm_144423.1	chr18	21001268	21001273	+	1	NA	promoter-TSS (NM_207623)	promoter-TSS (NM_207623)	-30	NM_019706	56515	Mm.253542	NM_019706	ENSMUSG00000024317	Rnf138	2410015A17Rik|2810480D20Rik|STRIN|Trif|Trif-d	ring finger protein 138	protein-coding
mm_113447.1	chr13	35738438	35738462	+	1	NA	intron (NM_009881, intron 3 of 9)	intron (NM_009881, intron 3 of 9)	-2952	NM_001123386	12593	Mm.29002	NM_009881	ENSMUSG00000059288	Cdyl	AI325931	chromodomain protein, Y chromosome-like	protein-coding
mm_28093.1	chr3	85887414	85887456	-	1	NA	promoter-TSS (NM_177130)	promoter-TSS (NM_177130)	83	NM_177130	320302	Mm.482978	NM_177130	ENSMUSG00000031286	Glt28d2	4732486J07Rik|Glt28d1l	glycosyltransferase 28 domain containing 2	protein-coding
mm_512.1	chr1	37299883	37299937	+	1	NA	promoter-TSS (NM_030266)	promoter-TSS (NM_030266)	72	NM_001290797	269180	Mm.5294	NM_030266	ENSMUSG00000026113	Inpp4a	107kDa|9630012D15|D130048C09Rik|R74740	inositol polyphosphate-4-phosphatase, type I	protein-coding
mm_117753.1	chr13	95957611	95957612	-	1	NA	Intergenic	Intergenic	-65689	NM_027711	544963	Mm.38878	NM_027711	ENSMUSG00000021676	Iqgap2	4933417J23Rik|A630053O10|AI788777	IQ motif containing GTPase activating protein 2	protein-coding
mm_148980.1	chr19	7591807	7591810	+	1	NA	Intergenic	MTE2b|LTR|ERVL-MaLR	15368	NM_019516	56072	Mm.298242	NM_019516	ENSMUSG00000024972	Lgals12	AW987437|Grip1	lectin, galactose binding, soluble 12	protein-coding
mm_142384.1	chr17	44814417	44814419	-	1	NA	5' UTR (NM_001271627, exon 1 of 8)	5' UTR (NM_001271627, exon 1 of 8)	209	NM_009820	12393	Mm.391013	NM_009820	ENSMUSG00000039153	Runx2	AML3|Cbf|Cbfa-1|Cbfa1|LS3|Osf2|PEBP2aA|Pebp2a1|Pebpa2a	runt related transcription factor 2	protein-coding
mm_58479.1	chr7	3423613	3423654	+	1	NA	promoter-TSS (NR_126426)	promoter-TSS (NR_126426)	-188	NR_126426	70230	Mm.458356	NR_126426	ENSMUSG00000107585	3300002P13Rik	-	RIKEN cDNA 3300002P13 gene	ncRNA
mm_67480.1	chr7	80712032	80712045	-	1	NA	3' UTR (NM_016721, exon 38 of 38)	3' UTR (NM_016721, exon 38 of 38)	-23161	NM_173863	70461	Mm.392175	NM_173863	ENSMUSG00000030527	Crtc3	2610312F20Rik|6332415K15Rik|AI429792|BC011210|TORC3	CREB regulated transcription coactivator 3	protein-coding
mm_20840.1	chr2	147977148	147977151	-	1	NA	Intergenic	Intergenic	68315	NM_001291067	15376	Mm.938	NM_010446	ENSMUSG00000037025	Foxa2	HNF3-beta|HNF3beta|Hnf-3b|Hnf3b|Tcf-3b|Tcf3b	forkhead box A2	protein-coding
mm_110401.1	chr12	44210379	44210388	-	1	NA	promoter-TSS (NM_013760)	promoter-TSS (NM_013760)	70	NR_049203	100885842		NR_049203	ENSMUSG00000093618	Mir5627	Gm23684|mir-5627|mmu-mir-5627	microRNA 5627	ncRNA
mm_689.1	chr1	40542985	40542991	+	1	NA	intron (NM_010553, intron 10 of 12)	intron (NM_010553, intron 10 of 12)	27626	NM_010553	16174	Mm.20466	NM_010553	ENSMUSG00000026068	Il18rap	AcPL|IL-18R-beta|IL-18RAcP|IL-18Rbeta|IL-1RAcPL	interleukin 18 receptor accessory protein	protein-coding
mm_36369.1	chr4	76450479	76450496	-	1	NA	intron (NM_011211, intron 10 of 39)	CpG	-1172201	NM_025849	66928	Mm.24332	NM_025849	ENSMUSG00000028398	Tmem261	1700027K24Rik|3110001D03Rik	transmembrane protein 261	protein-coding
mm_141512.1	chr17	31678132	31678166	-	1	NA	exon (NM_001278570, exon 1 of 3)	exon (NM_001278570, exon 1 of 3)	218	NM_001278570	12954	Mm.1228	NM_013501	ENSMUSG00000024041	Cryaa	Acry-1|Crya-1|Crya1|DAcry-1|lop18	crystallin, alpha A	protein-coding
mm_162250.1	chrX	163549724	163549724	-	1	NA	promoter-TSS (NM_008177)	promoter-TSS (NM_008177)	12	NM_008177	14829	Mm.4687	NM_008177	ENSMUSG00000031364	Grpr	GRP-R	gastrin releasing peptide receptor	protein-coding
mm_55393.1	chr6	60462210	60462212	-	1	NA	Intergenic	Intergenic	-58504	NR_015565	208079	Mm.131226	NM_177329	ENSMUSG00000046764	A530053G22Rik	-	RIKEN cDNA A530053G22 gene	ncRNA
mm_94747.1	chr11	21105927	21105937	+	1	NA	intron (NM_023324, intron 1 of 6)	intron (NM_023324, intron 1 of 6)	14608	NM_023324	67245	Mm.28957	NM_023324	ENSMUSG00000020134	Peli1	2810468L03Rik|A930031K15Rik|AA409794|AI586297|D11Ertd676e	pellino 1	protein-coding
mm_165792.1	chr3	138112470	138112471	+	1	NA	exon (NM_001163457, exon 11 of 20)	exon (NM_001163457, exon 11 of 20)	18907	NM_008642	17777	Mm.2941	NM_008642	ENSMUSG00000028158	Mttp	1810043K16Rik|MTP	microsomal triglyceride transfer protein	protein-coding
mm_153429.1	chr19	40894604	40894641	-	1	NA	promoter-TSS (NR_106167)	promoter-TSS (NR_106167)	-81	NR_106167	102466881		NR_106167	ENSMUSG00000099118	Mir8092	Gm27407|mmu-mir-8092	microRNA 8092	ncRNA
mm_104890.1	chr11	99566620	99566646	-	1	NA	promoter-TSS (NM_023511)	promoter-TSS (NM_023511)	-3	NM_023511	69473	Mm.158281	NM_023511	ENSMUSG00000047564	Krtap3-1	2310003K17Rik|KAP3.1|KRTAP3.1	keratin associated protein 3-1	protein-coding
mm_87322.1	chr10	42860696	42860714	+	1	NA	5' UTR (NM_172938, exon 1 of 9)	5' UTR (NM_172938, exon 1 of 9)	193	NM_172938	268297	Mm.98731	NM_172938	ENSMUSG00000044770	Scml4	9330161D17|mFLJ00197	sex comb on midleg-like 4 (Drosophila)	protein-coding
mm_27890.1	chr3	79287002	79287015	-	1	NA	Intergenic	CpG	-58368	NM_001142953	100233207	Mm.373801	NM_001142953	ENSMUSG00000091685	Gm17359	-	predicted gene, 17359	protein-coding
mm_167291.1	chr8	45409939	45409950	-	1	NA	5' UTR (NM_126166, exon 2 of 7)	5' UTR (NM_126166, exon 2 of 7)	595	NM_126166	142980	Mm.33874	NM_126166	ENSMUSG00000031639	Tlr3	AI957183	toll-like receptor 3	protein-coding
mm_149537.1	chr19	12465842	12465856	+	1	NA	TTS (NM_010821)	TTS (NM_010821)	5070	NM_010821	17476	Mm.3999	NM_010821	ENSMUSG00000046805	Mpeg1	MPS1|Mpg-1	macrophage expressed gene 1	protein-coding
mm_53964.1	chr6	5819802	5819824	-	1	NA	intron (NM_001191027, intron 5 of 15)	intron (NM_001191027, intron 5 of 15)	94174	NM_001191026	13426	Mm.20893	NM_010063	ENSMUSG00000029757	Dync1i1	DH IC-1|DHIC-1|DIC|Dncic1|IC74	dynein cytoplasmic 1 intermediate chain 1	protein-coding
mm_51642.1	chr6	86017263	86017272	+	1	NA	promoter-TSS (NM_012013)	promoter-TSS (NM_012013)	76	NM_012013	26910	Mm.8024	NM_012013	ENSMUSG00000030001	Figla	FIGalpha|bHLHc8	folliculogenesis specific basic helix-loop-helix	protein-coding
mm_87074.1	chr10	29200816	29200853	+	1	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	-10809	NM_001162537	212448	Mm.132789	NM_001162537	ENSMUSG00000004360	9330159F19Rik	-	RIKEN cDNA 9330159F19 gene	protein-coding
mm_154885.1	chrX	20719806	20719818	+	1	NA	exon (NM_145628, exon 21 of 21)	exon (NM_145628, exon 21 of 21)	15903	NM_145628	236733	Mm.34489	NM_145628	ENSMUSG00000031066	Usp11	6230415D12Rik|mKIAA4085	ubiquitin specific peptidase 11	protein-coding
mm_4603.1	chr1	178406496	178406560	+	1	NA	intron (NM_026626, intron 1 of 6)	CpG	647	NM_026626	68226	Mm.252132	NM_026626	ENSMUSG00000026495	Efcab2	1700073K01Rik|D830011E08Rik	EF-hand calcium binding domain 2	protein-coding
mm_46653.1	chr5	108660784	108660822	-	1	NA	promoter-TSS (NM_199011)	promoter-TSS (NM_199011)	-34	NM_199011	110524	Mm.260921	NM_199011	ENSMUSG00000004815	Dgkq	110kDa|DAGK|DAGK7|Dagk4|Dgkd	diacylglycerol kinase, theta	protein-coding
mm_5371.1	chr1	30642330	30642341	-	1	NA	Intergenic	Intergenic	220921	NM_001081080	213109	Mm.194486	NM_025871	ENSMUSG00000048874	Phf3	2310061N19Rik|mKIAA0244	PHD finger protein 3	protein-coding
mm_152542.1	chr19	11336053	11336069	-	1	NA	promoter-TSS (NM_027836)	promoter-TSS (NM_027836)	85	NM_001025610	109225	Mm.491251	NM_027836	ENSMUSG00000024672	Ms4a7	9130422I10Rik|A430103C15Rik|CD20l4|CFFMA	membrane-spanning 4-domains, subfamily A, member 7	protein-coding
mm_29884.1	chr3	131112625	131112633	-	1	NA	promoter-TSS (NM_001276403)	promoter-TSS (NM_001276403)	-162	NM_001276403	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_38210.1	chr4	135874074	135874078	-	1	NA	promoter-TSS (NM_026383)	promoter-TSS (NM_026383)	-230	NM_026383	52830	Mm.29159	NM_026383	ENSMUSG00000028675	Pnrc2	0610011E17Rik|D4Bwg0593e	proline-rich nuclear receptor coactivator 2	protein-coding
mm_5525.1	chr1	37890311	37890324	-	1	NA	promoter-TSS (NM_027098)	promoter-TSS (NM_027098)	94	NM_026913	69028	Mm.63984	NM_026913	ENSMUSG00000026088	Mitd1	1500032H18Rik	MIT, microtubule interacting and transport, domain containing 1	protein-coding
mm_51255.1	chr6	71912235	71912252	+	1	NA	intron (NM_009088, intron 1 of 33)	intron (NM_009088, intron 1 of 33)	3190	NM_009088	20019	Mm.135581	NM_009088	ENSMUSG00000049553	Polr1a	194kDa|3010014K16Rik|RPA194|Rpo1-4|mRPA1	polymerase (RNA) I polypeptide A	protein-coding
mm_102404.1	chr11	59163282	59163323	-	1	NA	intron (NM_001270791, intron 1 of 1)	intron (NM_001270791, intron 1 of 1)	443	NM_001270791	216792	Mm.266175	NM_173785	ENSMUSG00000049287	Iba57	4930543L23Rik|A230051G13Rik|C1orf69	IBA57 homolog, iron-sulfur cluster assembly	protein-coding
mm_62632.1	chr7	107639113	107639129	+	1	NA	intron (NM_001163557, intron 2 of 25)	B4|SINE|B4	32277	NM_001163557	19024	Mm.2817	NM_008905	ENSMUSG00000036528	Ppfibp2	Cclp1	PTPRF interacting protein, binding protein 2 (liprin beta 2)	protein-coding
mm_31616.1	chr4	59035465	59035478	+	1	NA	intron (NM_025277, intron 1 of 2)	CpG	315	NM_025277	14700	Mm.41780	NM_025277	ENSMUSG00000038607	Gng10	AV006524	guanine nucleotide binding protein (G protein), gamma 10	protein-coding
mm_73888.1	chr8	119394867	119394954	+	1	NA	promoter-TSS (NM_019966)	promoter-TSS (NM_019966)	18	NM_019966	56690	Mm.423037	NM_019966	ENSMUSG00000074064	Mlycd	AI324784|Mcd	malonyl-CoA decarboxylase	protein-coding
mm_130508.1	chr15	98845761	98845772	-	1	NA	exon (NM_001033276, exon 40 of 55)	exon (NM_001033276, exon 40 of 55)	-14258	NM_016781	19082	Mm.6670	NM_016781	ENSMUSG00000067713	Prkag1	AA571379|BB036179|Prkaac	protein kinase, AMP-activated, gamma 1 non-catalytic subunit	protein-coding
mm_112578.1	chr13	13694453	13694463	+	1	NA	intron (NM_010748, intron 29 of 52)	intron (NM_010748, intron 29 of 52)	-89601	NM_001302997	14706	Mm.215394	NM_010317	ENSMUSG00000021303	Gng4	-	guanine nucleotide binding protein (G protein), gamma 4	protein-coding
mm_27487.1	chr3	54686809	54686821	-	1	NA	Intergenic	Intergenic	-6290	NM_019995	56790	Mm.486375	NM_019995	ENSMUSG00000027751	Supt20	AA667204|AI450544|D3Ertd300e|Fam48a|Supt20h|p38IP	suppressor of Ty 20	protein-coding
mm_40317.1	chr5	43875080	43875085	+	1	NA	intron (NM_007646, intron 1 of 7)	ORR1B2|LTR|ERVL-MaLR	6273	NM_007646	12494	Mm.249873	NM_007646	ENSMUSG00000029084	Cd38	ADPRC 1|Cd38-rs1|I-19	CD38 antigen	protein-coding
mm_23215.1	chr3	45378397	45378413	+	1	NA	promoter-TSS (NR_045172)	promoter-TSS (NR_045172)	7	NM_001098171	18526	Mm.242644	NM_011043	ENSMUSG00000049100	Pcdh10	6430521D13Rik|6430703F07Rik|OL-pc|mKIAA1400	protocadherin 10	protein-coding
mm_65851.1	chr7	29281617	29281688	-	1	NA	5' UTR (NM_001082548, exon 1 of 6)	5' UTR (NM_001082548, exon 1 of 6)	325	NM_001082548	20733	Mm.295230	NM_011464	ENSMUSG00000074227	Spint2	AL024025|C76321|HAI-2	serine protease inhibitor, Kunitz type 2	protein-coding
mm_170374.1	chr18	55202263	55202282	-	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	-212092	NM_175751	269023	Mm.192984	NM_175751	ENSMUSG00000052713	Zfp608	4932417D18Rik|D430007A19Rik|Znf608	zinc finger protein 608	protein-coding
mm_19773.1	chr2	105904485	105904527	-	1	NA	promoter-TSS (NM_023876)	promoter-TSS (NM_023876)	58	NM_023876	77766	Mm.3608	NM_023876	ENSMUSG00000027167	Elp4	A330107A17Rik|Paxneb	elongator acetyltransferase complex subunit 4	protein-coding
mm_61778.1	chr7	83641820	83641834	+	1	NA	3' UTR (NM_023377, exon 6 of 6)	3' UTR (NM_023377, exon 6 of 6)	9810	NM_023377	170460	Mm.357953	NM_023377	ENSMUSG00000046027	Stard5	2310058G22Rik|AI607880|D7Ertd152e	StAR-related lipid transfer (START) domain containing 5	protein-coding
mm_157299.1	chrX	20928383	20928394	-	1	NA	exon (NM_008823, exon 5 of 9)	exon (NM_008823, exon 5 of 9)	3167	NM_008823	18636	Mm.3064	NM_008823	ENSMUSG00000001128	Cfp	BCFG|Pfc	complement factor properdin	protein-coding
mm_139543.1	chr17	56734827	56734841	+	1	NA	non-coding (NR_033644, exon 1 of 2)	non-coding (NR_033644, exon 1 of 2)	606	NR_033644	14346	Mm.160272	NR_033644		Fut4-ps1	-	fucosyltransferase 4, pseudogene 1	pseudo
mm_114960.1	chr13	97071435	97071447	+	1	NA	promoter-TSS (NM_001100458)	promoter-TSS (NM_001100458)	-202	NM_001100458	320557	Mm.458280	NM_001100458	ENSMUSG00000041817	Fam169a	B230112C05Rik|SLAP75	family with sequence similarity 169, member A	protein-coding
mm_7597.1	chr1	125912161	125912199	-	1	NA	promoter-TSS (NM_001311090)	promoter-TSS (NM_001311090)	34	NM_145100	72585	Mm.490405	NM_145100	ENSMUSG00000026344	Lypd1	2700050C12Rik|AI853408|C530008O16Rik|Lynx2|Lypdc1	Ly6/Plaur domain containing 1	protein-coding
mm_83007.1	chr9	36759240	36759253	-	1	NA	exon (NM_008408, exon 4 of 18)	exon (NM_008408, exon 4 of 18)	8332	NM_008408	16430	Mm.2863	NM_008408	ENSMUSG00000032116	Stt3a	AA408947|BB081708|Itm1	STT3, subunit of the oligosaccharyltransferase complex, homolog A (S. cerevisiae)	protein-coding
mm_63104.1	chr7	122628899	122628905	+	1	NA	3' UTR (NM_008855, exon 17 of 17)	3' UTR (NM_008855, exon 17 of 17)	-42842	NM_019430	54376	Mm.444212	NM_019430	ENSMUSG00000066189	Cacng3	-	calcium channel, voltage-dependent, gamma subunit 3	protein-coding
mm_47989.1	chr5	135957511	135957521	-	1	NA	Intergenic	Intergenic	16960	NM_001160366	109267	Mm.332750	NM_001160366	ENSMUSG00000029699	Ssc4d	C330016E03Rik|S4D-SRCRB|SRCRB-S4D|Srcrb4d	scavenger receptor cysteine rich family, 4 domains	protein-coding
mm_111587.1	chr12	101958162	101958212	-	1	NA	promoter-TSS (NM_001167914)	promoter-TSS (NM_001167914)	56	NM_029705	110616	Mm.271914	NM_029705	ENSMUSG00000021189	Atxn3	2210008M02Rik|AI463012|AI647473|ATX3|MJD1|Mjd|Sca3|ataxin-3	ataxin 3	protein-coding
mm_143876.1	chr17	84187738	84187757	-	1	NA	5' UTR (NM_001001806, exon 1 of 2)	5' UTR (NM_001001806, exon 1 of 2)	200	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_134216.1	chr16	11253767	11253771	-	1	NA	TTS (NR_035466)	TTS (NR_035466)	556	NM_001130008	14852	Mm.325827	NM_146066	ENSMUSG00000062203	Gspt1	AI314175|AI326449|AV307676|C79774|G1st|Gst-1	G1 to S phase transition 1	protein-coding
mm_19977.1	chr2	118373310	118373341	-	1	NA	promoter-TSS (NM_201367)	promoter-TSS (NM_201367)	94	NM_201367	381413	Mm.70979	NM_201367	ENSMUSG00000040133	Gpr176	Gm1012	G protein-coupled receptor 176	protein-coding
mm_129024.1	chr15	74958699	74958730	-	1	NA	3' UTR (NM_001164036, exon 4 of 4)	3' UTR (NM_001164036, exon 4 of 4)	3608	NM_001164040	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_148077.1	chr18	72351077	72351087	-	1	NA	promoter-TSS (NM_007831)	promoter-TSS (NM_007831)	-13	NM_007831	13176	Mm.167882	NM_007831	ENSMUSG00000060534	Dcc	C030036D22Rik|Igdcc1	deleted in colorectal carcinoma	protein-coding
mm_84798.1	chr9	77230387	77230403	-	1	NA	intron (NM_027150, intron 2 of 7)	intron (NM_027150, intron 2 of 7)	117475	NM_027150	69642	Mm.35008	NM_027150	ENSMUSG00000032355	Mlip	2310046A06Rik|AI931782|CIP	muscular LMNA-interacting protein	protein-coding
mm_19315.1	chr2	90550122	90550145	-	1	NA	intron (NM_008982, intron 1 of 23)	intron (NM_008982, intron 1 of 23)	30514	NM_008982	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_109412.1	chr12	110463920	110463932	+	1	NA	intron (NM_001135001, intron 2 of 13)	intron (NM_001135001, intron 2 of 13)	16747	NM_001135001	26931	Mm.240396	NM_012023	ENSMUSG00000017843	Ppp2r5c	2610043M05Rik|2700063L20Rik|AI060890|AW545884|C85228|D12Bwg0916e|mKIAA0044	protein phosphatase 2, regulatory subunit B', gamma	protein-coding
mm_100911.1	chr11	6230128	6230160	-	1	NA	5' UTR (NM_207242, exon 1 of 19)	5' UTR (NM_207242, exon 1 of 19)	101	NM_207242	237636	Mm.212492	NM_207242	ENSMUSG00000020447	Npc1l1	9130221N23Rik|Gm243	NPC1-like 1	protein-coding
mm_166427.1	chr5	137152362	137152416	+	1	NA	Intergenic	Intergenic	-36182	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_112306.1	chr12	114809904	114809909	-	1	NA	Intergenic	Intergenic	-296212	NR_106063	102465664		NR_106063	ENSMUSG00000098357	Mir7094-2	Gm27508|mmu-mir-7094-2	microRNA 7094-2	ncRNA
mm_55178.1	chr6	52012563	52012571	-	1	NA	promoter-TSS (NM_018773)	promoter-TSS (NM_018773)	-18	NM_018773	54353	Mm.221479	NM_018773	ENSMUSG00000059182	Skap2	2610021A10Rik|AA960083|BB137539|RA70|SKAP-HOM|Saps|Scap2|mSKAP55R	src family associated phosphoprotein 2	protein-coding
mm_104656.1	chr11	97576335	97576355	-	1	NA	Intergenic	Intergenic	-1219	NM_018873	56013	Mm.342665	NM_018873	ENSMUSG00000038453	Srcin1	P140|SNIP|mKIAA1684|p140Cap	SRC kinase signaling inhibitor 1	protein-coding
mm_35427.1	chr4	35225790	35225857	-	1	NA	promoter-TSS (NM_001081343)	promoter-TSS (NM_001081343)	57	NM_001081343	73205	Mm.331544	NM_001081343	ENSMUSG00000028300	3110043O21Rik	AI840585	RIKEN cDNA 3110043O21 gene	protein-coding
mm_172414.1	chr7	19991442	19991444	+	1	NA	TTS (NM_027839)	TTS (NM_027839)	-16580	NM_194058	243874	Mm.277114	NM_194058	ENSMUSG00000060508	Nlrp9b	Nalp-delta|Nalp9b|Nlrp9	NLR family, pyrin domain containing 9B	protein-coding
mm_136750.1	chr17	8525370	8525396	+	1	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	-1418	NM_001290707	23984	Mm.87161	NM_011866	ENSMUSG00000023868	Pde10a	-	phosphodiesterase 10A	protein-coding
mm_115089.1	chr13	102706290	102706293	+	1	NA	exon (NM_008533, exon 3 of 3)	exon (NM_008533, exon 3 of 3)	12733	NM_008533	17079	Mm.373974	NM_008533	ENSMUSG00000021624	Cd180	F630107B15|Ly78|RP105	CD180 antigen	protein-coding
mm_119383.1	chr14	41136411	41136424	+	1	NA	TTS (NM_023134)	TTS (NM_023134)	4629	NM_023134	20387	Mm.46062	NM_023134	ENSMUSG00000021789	Sftpa1	SP-A|Sftp-1|Sftp1	surfactant associated protein A1	protein-coding
mm_44657.1	chr5	28237880	28237888	-	1	NA	intron (NM_001310512, intron 1 of 3)	intron (NM_001310512, intron 1 of 3)	7904	NM_001310512	269637	Mm.68286	NM_175651	ENSMUSG00000044681	Cnpy1	1500012D20Rik|9630008K15Rik|AI853839	canopy FGF signaling regulator 1	protein-coding
mm_76226.1	chr8	83573107	83573121	-	1	NA	exon (NM_027179, exon 5 of 12)	exon (NM_027179, exon 5 of 12)	6356	NM_025843	66916	Mm.29683	NM_025843	ENSMUSG00000033938	Ndufb7	1110002H15Rik	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 7	protein-coding
mm_18237.1	chr2	51973220	51973234	-	1	NA	promoter-TSS (NM_001141948)	promoter-TSS (NM_001141948)	-19	NM_001141948	64685	Mm.7491	NM_019401	ENSMUSG00000026946	Nmi	-	N-myc (and STAT) interactor	protein-coding
mm_100406.1	chr11	119415727	119415733	+	1	NA	Intergenic	Intergenic	25258	NR_035453	100316690		NR_035453	ENSMUSG00000088015	Mir1932	mir-1932|mmu-mir-1932	microRNA 1932	ncRNA
mm_102024.1	chr11	51650785	51650810	-	1	NA	promoter-TSS (NR_027958)	promoter-TSS (NR_027958)	-157	NR_027958	97775	Mm.220299	NM_175289	ENSMUSG00000052563	D930048N14Rik	AI315703|R75254	RIKEN cDNA D930048N14 gene	ncRNA
mm_143080.1	chr17	57045320	57045361	-	1	NA	3' UTR (NM_025877, exon 10 of 10)	3' UTR (NM_025877, exon 10 of 10)	-3686	NM_175333	103775	Mm.33647	NM_175333	ENSMUSG00000011486	Slc25a41	4933406J04Rik|AI507137	solute carrier family 25, member 41	protein-coding
mm_58134.1	chr6	140747212	140747226	-	1	NA	Intergenic	RLTR25A|LTR|ERVK	120334	NM_001309436	11569	Mm.86453	NM_009637	ENSMUSG00000030232	Aebp2	AU023766|B230313N05Rik	AE binding protein 2	protein-coding
mm_31326.1	chr4	46450893	46450903	+	1	NA	promoter-TSS (NM_130889)	promoter-TSS (NM_130889)	-28	NM_130889	67628	Mm.263913	NM_130889	ENSMUSG00000028333	Anp32b	2410015B15Rik|PAL31|PHAPI2a|Ssp29	acidic (leucine-rich) nuclear phosphoprotein 32 family, member B	protein-coding
mm_97285.1	chr11	76202008	76202030	+	1	NA	promoter-TSS (NM_027773)	promoter-TSS (NM_027773)	-37	NM_027773	116972	Mm.188413	NM_027773	ENSMUSG00000069808	Fam57a	2310047D13Rik|4932415L08Rik|5430402E13Rik|5430420K21Rik|Wdt3	family with sequence similarity 57, member A	protein-coding
mm_153485.1	chr19	41305913	41305943	-	1	NA	intron (NM_031376, intron 9 of 16)	intron (NM_031376, intron 9 of 16)	-41924	NM_133352	107358	Mm.246440	NM_133352	ENSMUSG00000025016	Tm9sf3	1810073M23Rik|2810031D16Rik|AI115521|AI413748|AW146116|AW549777|Smbp|mKIAA4036	transmembrane 9 superfamily member 3	protein-coding
mm_63223.1	chr7	126353556	126353557	+	1	NA	Intergenic	B1F1|SINE|Alu	14489	NR_106025	102466797		NR_106025	ENSMUSG00000099017	Mir7058	Gm27766|mmu-mir-7058	microRNA 7058	ncRNA
mm_102532.1	chr11	61159329	61159361	-	1	NA	exon (NM_001004143, exon 8 of 13)	exon (NM_001004143, exon 8 of 13)	15714	NM_001004143	216825	Mm.30602	NM_001004143	ENSMUSG00000042506	Usp22	AI427806	ubiquitin specific peptidase 22	protein-coding
mm_154165.1	chr19	58673116	58673137	-	1	NA	exon (NM_026925, exon 4 of 13)	exon (NM_026925, exon 4 of 13)	2761	NM_026925	69060	Mm.20407	NM_026925	ENSMUSG00000046008	Pnlip	1810007A24Rik|PL|PTL	pancreatic lipase	protein-coding
mm_67644.1	chr7	84594816	84594827	-	1	NA	exon (NM_010176, exon 9 of 14)	exon (NM_010176, exon 9 of 14)	11121	NM_010176	14085	Mm.3798	NM_010176	ENSMUSG00000030630	Fah	-	fumarylacetoacetate hydrolase	protein-coding
mm_164121.1	chr15	38300286	38300289	+	1	NA	intron (NM_001289471, intron 1 of 4)	CpG	424	NM_013692	21847	Mm.4292	NM_013692	ENSMUSG00000037465	Klf10	AI115143|EGR[a]|Egral|Gdnfif|TIEG-1|Tieg|Tieg1|mGIF	Kruppel-like factor 10	protein-coding
mm_82444.1	chr9	15301556	15301571	-	1	NA	promoter-TSS (NM_133732)	promoter-TSS (NM_133732)	44	NM_133732	70984	Mm.261842	NM_133732	ENSMUSG00000031938	4931406C07Rik	-	RIKEN cDNA 4931406C07 gene	protein-coding
mm_159363.1	chr3	87729493	87729493	+	1	NA	exon (NM_001003912, exon 31 of 40)	exon (NM_001003912, exon 31 of 40)	19130	NM_028971	74485	Mm.474494	NM_028971	ENSMUSG00000023084	Lrrc71	4933430H15Rik	leucine rich repeat containing 71	protein-coding
mm_53009.1	chr6	123272168	123272180	+	1	NA	intron (NM_001163161, intron 5 of 5)	Lx8b|LINE|L1	10067	NM_010819	17474	Mm.441101	NM_010819	ENSMUSG00000030144	Clec4d	Clecsf8|Mpcl|mcl	C-type lectin domain family 4, member d	protein-coding
mm_46578.1	chr5	107406362	107406386	-	1	NA	intron (NM_001001804, intron 2 of 6)	intron (NM_001001804, intron 2 of 6)	2861	NM_001001804	384214	Mm.489863	NM_001001804	ENSMUSG00000033805	Ephx4	Abhd7|Ephxrp|Gm1382	epoxide hydrolase 4	protein-coding
mm_90356.1	chr10	127165366	127165398	+	1	NA	promoter-TSS (NM_027739)	promoter-TSS (NM_027739)	226	NM_001244617	14421	Mm.386762	NM_008080	ENSMUSG00000006731	B4galnt1	4933429D13Rik|Gal-NAc-T|GalNAc-T|GalNAcT|Galgt1|Ggm-2|Ggm2	beta-1,4-N-acetyl-galactosaminyl transferase 1	protein-coding
mm_78751.1	chr9	42264472	42264479	+	1	NA	promoter-TSS (NM_172769)	promoter-TSS (NM_172769)	-175	NM_172769	235293	Mm.32700	NM_172769	ENSMUSG00000032018	Sc5d	A830037K02|A830073K23Rik|Sc5dl	sterol-C5-desaturase	protein-coding
mm_162599.1	chr1	183147522	183147538	-	1	NA	promoter-TSS (NM_001278220)	promoter-TSS (NM_001278220)	27	NM_001278220	68897	Mm.327216	NM_026866	ENSMUSG00000030768	Disp1	1190008H24Rik|DispA	dispatched RND transporter family member 1	protein-coding
mm_140310.1	chr17	86167621	86167683	+	1	NA	promoter-TSS (NM_011104)	promoter-TSS (NM_011104)	-133	NM_011104	18754	Mm.24614	NM_011104	ENSMUSG00000045038	Prkce	5830406C15Rik|PKC[e]|PKCepsilon|Pkce|R75156	protein kinase C, epsilon	protein-coding
mm_79862.1	chr9	65032618	65032672	+	1	NA	intron (NM_028906, intron 1 of 20)	CpG	187	NM_028906	74388	Mm.202749	NM_028906	ENSMUSG00000032393	Dpp8	2310004I03Rik|4932434F09Rik|AI666706|DPP VIII	dipeptidylpeptidase 8	protein-coding
mm_130580.1	chr15	99527794	99527804	-	1	NA	5' UTR (NM_028224, exon 1 of 12)	5' UTR (NM_028224, exon 1 of 12)	366	NM_028224	72393	Mm.39760	NM_028224	ENSMUSG00000023011	Faim2	2900002L20Rik|Lfg|Lfg2|NMP25|Nmp35|Tmbim2	Fas apoptotic inhibitory molecule 2	protein-coding
mm_33351.1	chr4	129381416	129381438	+	1	NA	Intergenic	RMER10B|LTR|ERVL	-3399	NM_028603	73680	Mm.32997	NM_028603	ENSMUSG00000028807	Zbtb8a	2410081M15Rik|AI480941	zinc finger and BTB domain containing 8a	protein-coding
mm_158119.1	chrX	102252065	102252087	-	1	NA	promoter-TSS (NM_007709)	promoter-TSS (NM_007709)	105	NM_001276466	12705	Mm.2390	NM_007709	ENSMUSG00000051159	Cited1	AI316840|AU019144|Msg1	Cbp/p300-interacting transactivator with Glu/Asp-rich carboxy-terminal domain 1	protein-coding
mm_57237.1	chr6	123282990	123283004	-	1	NA	3' UTR (NM_019948, exon 6 of 6)	3' UTR (NM_019948, exon 6 of 6)	6874	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_167081.1	chr7	101111996	101112029	+	1	NA	intron (NM_199012, intron 2 of 20)	B1_Mm|SINE|Alu	3237	NM_199012	207278	Mm.263041	NM_199012	ENSMUSG00000030691	Fchsd2	BC034086|R74866|Sh3md3|mKIAA0769	FCH and double SH3 domains 2	protein-coding
mm_151529.1	chr19	58744115	58744125	+	1	NA	TTS (NM_018874)	TTS (NM_018874)	15233	NM_018874	18946	Mm.10753	NM_018874	ENSMUSG00000042179	Pnliprp1	Plrp1	pancreatic lipase related protein 1	protein-coding
mm_28381.1	chr3	89998657	89998704	-	1	NA	promoter-TSS (NM_011826)	promoter-TSS (NM_011826)	36	NM_011826	23897	Mm.256035	NM_011826	ENSMUSG00000027944	Hax1	HAX-1|HSP1BP-1|Hs1bp1|SIG-111|Silg111|mHAX-1s	HCLS1 associated X-1	protein-coding
mm_45977.1	chr5	90472493	90472561	-	1	NA	exon (NM_009654, exon 12 of 15)	exon (NM_009654, exon 12 of 15)	11657	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_26078.1	chr3	136670570	136670583	+	1	NA	5' UTR (NM_001293622, exon 1 of 13)	5' UTR (NM_001293622, exon 1 of 13)	510	NM_001293622	19055	Mm.331389	NM_008913	ENSMUSG00000028161	Ppp3ca	2900074D19Rik|CN|Caln|Calna|CnA	protein phosphatase 3, catalytic subunit, alpha isoform	protein-coding
mm_42145.1	chr5	111418254	111418268	+	1	NA	promoter-TSS (NM_001081235)	promoter-TSS (NM_001081235)	95	NM_001081235	433938	Mm.332576	NM_001081235	ENSMUSG00000070576	Mn1	AA003644|AA009236	meningioma 1	protein-coding
mm_116791.1	chr13	53421645	53421662	-	1	NA	intron (NR_037991, intron 4 of 7)	intron (NR_037991, intron 4 of 7)	27964	NR_037991	100040421	Mm.83967	NR_037991	ENSMUSG00000107008	Gm2762	1700025I17Rik	predicted gene 2762	ncRNA
mm_122101.1	chr14	30915717	30915736	-	1	NA	exon (NM_008407, exon 12 of 21)	exon (NM_008407, exon 12 of 21)	7861	NM_008407	16426	Mm.4517	NM_008407	ENSMUSG00000006522	Itih3	AW108094|ITI-HC3|Intin3|Itih-3	inter-alpha trypsin inhibitor, heavy chain 3	protein-coding
mm_129590.1	chr15	79789629	79789641	-	1	NA	3' UTR (NM_001013360, exon 8 of 8)	3' UTR (NM_001013360, exon 8 of 8)	15074	NM_030689	73340	Mm.38438	NM_030689	ENSMUSG00000022421	Nptxr	1200009K17Rik|1700036C17Rik|5730406O18Rik|AI452369|AI785356|D15Bwg0580e|NPR|Npcd	neuronal pentraxin receptor	protein-coding
mm_64410.1	chr7	142512248	142512256	+	1	NA	intron (NM_001347548, intron 11 of 14)	intron (NM_001347548, intron 11 of 14)	-5481	NR_033261	677289	Mm.350054	NR_033261	ENSMUSG00000043795	Prr33	ENSMUSG00000043795|Gm14492|OTTMUSG00000016823	proline rich 33	ncRNA
mm_12072.1	chr2	59645495	59645497	+	1	NA	intron (NM_198294, intron 1 of 26)	intron (NM_198294, intron 1 of 26)	-1273	NM_001290659	66860	Mm.27917	NM_198294	ENSMUSG00000035168	Tanc1	1200003E16Rik|Tanc|mKIAA1728	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	protein-coding
mm_87847.1	chr10	60932037	60932050	+	1	NA	intron (NR_033616, intron 1 of 2)	intron (NR_033616, intron 1 of 2)	6089	NR_033616	73616	Mm.159038	NR_033616	ENSMUSG00000037247	Pldi	1700125F08Rik|Poldi	polymorphic derived intron containing	ncRNA
mm_42727.1	chr5	120613389	120613390	+	1	NA	promoter-TSS (NM_029096)	promoter-TSS (NM_029096)	259	NM_028041	71990	Mm.24495	NM_028041	ENSMUSG00000029599	Ddx54	2410015A15Rik|AI414901|DP97	DEAD (Asp-Glu-Ala-Asp) box polypeptide 54	protein-coding
mm_158470.1	chrX	141207582	141207589	-	1	NA	intron (NM_053185, intron 14 of 44)	intron (NM_053185, intron 14 of 44)	-250874	NM_001164177	53380	Mm.17640	NM_016883	ENSMUSG00000031429	Psmd10	AW554874	proteasome (prosome, macropain) 26S subunit, non-ATPase, 10	protein-coding
mm_29086.1	chr3	104511813	104511933	-	1	NA	promoter-TSS (NM_001025067)	promoter-TSS (NM_001025067)	45	NM_001310698	269473	Mm.34855	NM_001025067	ENSMUSG00000032913	Lrig2	4632419I10Rik|BB096938|LIG-2	leucine-rich repeats and immunoglobulin-like domains 2	protein-coding
mm_83216.1	chr9	42124112	42124142	-	1	NA	5' UTR (NM_011436, exon 1 of 48)	5' UTR (NM_011436, exon 1 of 48)	162	NM_011436	20660	Mm.121920	NM_011436	ENSMUSG00000049313	Sorl1	2900010L19Rik|AI596264|AW261561|LR11|SorLA|gp250|mSorLA	sortilin-related receptor, LDLR class A repeats-containing	protein-coding
mm_29263.1	chr3	107329906	107329945	-	1	NA	intron (NM_001045807, intron 1 of 1)	intron (NM_001045807, intron 1 of 1)	3364	NM_001045807	229700	Mm.27966	NM_001045807	ENSMUSG00000048109	Rbm15	C230088J01Rik|mKIAA1438	RNA binding motif protein 15	protein-coding
mm_140344.1	chr17	86825649	86825663	+	1	NA	exon (NM_010137, exon 10 of 16)	exon (NM_010137, exon 10 of 16)	71792	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_1631.1	chr1	74506024	74506038	+	1	NA	promoter-TSS (NM_001310662)	promoter-TSS (NM_001310662)	-29	NM_021383	58184	Mm.291708	NM_021383	ENSMUSG00000026174	Cnot9	2610007F23Rik|AI593551|Fl10|Rqcd1	CCR4-NOT transcription complex, subunit 9	protein-coding
mm_125755.1	chr15	73751394	73751402	+	1	NA	5' UTR (NM_008975, exon 2 of 6)	5' UTR (NM_008975, exon 2 of 6)	3372	NM_008975	19245	Mm.390807	NM_008975	ENSMUSG00000059895	Ptp4a3	AV088979|Prl-3|pPtp4a3	protein tyrosine phosphatase 4a3	protein-coding
mm_97056.1	chr11	72607364	72607435	+	1	NA	5' UTR (NM_025985, exon 1 of 6)	5' UTR (NM_025985, exon 1 of 6)	138	NM_025985	67128	Mm.458052	NM_025985	ENSMUSG00000020794	Ube2g1	2700059C12Rik|AI256795|AU014992|AW552068|D130023C12Rik	ubiquitin-conjugating enzyme E2G 1	protein-coding
mm_10668.1	chr2	20968703	20968715	+	1	NA	promoter-TSS (NM_001081364)	promoter-TSS (NM_001081364)	-165	NR_033225	433408	Mm.386941	NR_033225		Gm13375	OTTMUSG00000011664	predicted gene 13375	ncRNA
mm_161897.1	chr18	44812190	44812190	-	1	NA	promoter-TSS (NM_001085373)	promoter-TSS (NM_001085373)	-8	NM_001085373	328949	Mm.312511	NM_001033406	ENSMUSG00000071856	Mcc	D18Ertd451e|E330037C19	mutated in colorectal cancers	protein-coding
mm_67090.1	chr7	68742630	68742643	-	1	NA	exon (NM_001042592, exon 4 of 8)	exon (NM_001042592, exon 4 of 8)	6602	NM_001042592	66412	Mm.251199	NM_025549	ENSMUSG00000042659	Arrdc4	2410003C09Rik|AV216361	arrestin domain containing 4	protein-coding
mm_153172.1	chr19	34493651	34493662	-	1	NA	3' UTR (NM_021460, exon 10 of 10)	3' UTR (NM_021460, exon 10 of 10)	-18521	NM_009890	12642	Mm.30824	NM_009890	ENSMUSG00000050370	Ch25h	AI462618|m25OH	cholesterol 25-hydroxylase	protein-coding
mm_69975.1	chr7	142377117	142377136	-	1	NA	exon (NM_009983, exon 7 of 9)	exon (NM_009983, exon 7 of 9)	-3380	NM_001347541	320802	Mm.154486	NM_177265	ENSMUSG00000045777	Ifitm10	6330512M04Rik|AI848576|DSPA3	interferon induced transmembrane protein 10	protein-coding
mm_40947.1	chr5	76822525	76822541	+	1	NA	Intergenic	Intergenic	-18066	NM_001163793	320827	Mm.101504	NM_001163793	ENSMUSG00000036377	C530008M17Rik	2810489J07Rik|4930529A19Rik|4931405B09Rik|Kiaa1211|mKIAA1211	RIKEN cDNA C530008M17 gene	protein-coding
mm_35622.1	chr4	43454565	43454576	-	1	NA	promoter-TSS (NM_001110320)	promoter-TSS (NM_001110320)	56	NM_001110320	12517	Mm.188157	NM_007654	ENSMUSG00000028459	Cd72	CD72c|Ly-19|Ly-32|Ly-m19|Lyb-2	CD72 antigen	protein-coding
mm_83436.1	chr9	44999222	44999257	-	1	NA	3' UTR (NM_007648, exon 8 of 8)	3' UTR (NM_007648, exon 8 of 8)	10351	NM_007648	12501	Mm.210361	NM_007648	ENSMUSG00000032093	Cd3e	AI504783|CD3|CD3epsilon|T3e	CD3 antigen, epsilon polypeptide	protein-coding
mm_112616.1	chr13	15463838	15463938	+	1	NA	5' UTR (NM_008130, exon 1 of 15)	5' UTR (NM_008130, exon 1 of 15)	165	NM_008130	14634	Mm.5098	NM_008130	ENSMUSG00000021318	Gli3	AI854843|AU023367|Bph|GLI3-190|GLI3FL|Pdn|Xt|add	GLI-Kruppel family member GLI3	protein-coding
mm_5872.1	chr1	53785165	53785189	-	1	NA	promoter-TSS (NM_133810)	promoter-TSS (NM_133810)	38	NM_133810	98267	Mm.25559	NM_133810	ENSMUSG00000026094	Stk17b	3110009A03Rik|AI120141|Drak2	serine/threonine kinase 17b (apoptosis-inducing)	protein-coding
mm_112427.1	chr13	4233731	4233758	+	1	NA	promoter-TSS (NM_001013785)	promoter-TSS (NM_001013785)	4	NM_001013785	432720	Mm.22832	NM_001013785	ENSMUSG00000071551	Akr1c19	1810010N06Rik	aldo-keto reductase family 1, member C19	protein-coding
mm_4938.1	chr1	191172365	191172411	+	1	NA	exon (NM_007498, exon 3 of 4)	exon (NM_007498, exon 3 of 4)	-7571	NM_001109759	619288	Mm.61148	NM_001109759	ENSMUSG00000091017	Fam71a	4933417M04Rik|GARI-L4	family with sequence similarity 71, member A	protein-coding
mm_114905.1	chr13	94826999	94827006	+	1	NA	intron (NM_009321, intron 1 of 3)	PB1D9|SINE|Alu	38059	NM_009321	21371	Mm.379025	NM_009321	ENSMUSG00000042043	Tbca	Tbca13	tubulin cofactor A	protein-coding
mm_10068.1	chr1	193510203	193510216	-	1	NA	Intergenic	Intergenic	-2679	NR_029592	387201		NR_029592	ENSMUSG00000065533	Mir205	Mirn205|mir-205|mmu-mir-205	microRNA 205	ncRNA
mm_65826.1	chr7	29179163	29179181	-	1	NA	exon (NM_026545, exon 2 of 7)	exon (NM_026545, exon 2 of 7)	1501	NM_026545	57296	Mm.273152	NM_026545	ENSMUSG00000030591	Psmd8	6720456J22Rik|AA407360|AL033291|AL033322|AL033323|C76433	proteasome (prosome, macropain) 26S subunit, non-ATPase, 8	protein-coding
mm_87239.1	chr10	40883521	40883598	+	1	NA	promoter-TSS (NM_027879)	promoter-TSS (NM_027879)	25	NM_031877	83767	Mm.41353	NM_031877	ENSMUSG00000019831	Wasf1	AI195380|AI838537|Scar|WAVE|WAVE-1	WAS protein family, member 1	protein-coding
mm_142417.1	chr17	45568062	45568082	-	1	NA	TTS (NM_028662)	TTS (NM_028662)	3920	NM_028662	73836	Mm.289716	NM_028662	ENSMUSG00000037089	Slc35b2	1110003M08Rik|AA407792|AI842275|PAPST1|Slc35b1	solute carrier family 35, member B2	protein-coding
mm_27854.1	chr3	79157195	79157225	-	1	NA	Intergenic	L1_Mur3|LINE|L1	-11335	NM_001099624	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_45255.1	chr5	62766400	62766412	-	1	NA	promoter-TSS (NM_178407)	promoter-TSS (NM_178407)	-229	NM_178407	212285	Mm.244403	NM_178407	ENSMUSG00000037999	Arap2	Centd1|Gm148|mKIAA0580	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2	protein-coding
mm_80417.1	chr9	77838849	77838855	+	1	NA	Intergenic	Intergenic	-78513	NM_134255	68801	Mm.430736	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	ELOVL family member 5, elongation of long chain fatty acids (yeast)	protein-coding
mm_74834.1	chr8	23208362	23208404	-	1	NA	promoter-TSS (NM_018743)	promoter-TSS (NM_018743)	70	NM_018743	102247	Mm.200898	NM_018743	ENSMUSG00000031545	Gpat4	AU041707|AW545732|Agpat6|Tsarg7	glycerol-3-phosphate acyltransferase 4	protein-coding
mm_68010.1	chr7	100939129	100939144	-	1	NA	exon (NM_183168, exon 3 of 3)	exon (NM_183168, exon 3 of 3)	-6975	NM_001081116	207212	Mm.29954	NM_001081116	ENSMUSG00000032875	Arhgef17	8030463K16|AI428794|AW558066|BC035332|mKIAA0337	Rho guanine nucleotide exchange factor (GEF) 17	protein-coding
mm_99812.1	chr11	108395927	108395951	+	1	NA	exon (NM_013475, exon 2 of 8)	exon (NM_013475, exon 2 of 8)	642	NM_013475	11818	Mm.2266	NM_013475	ENSMUSG00000000049	Apoh	B2GPI|beta-2-GPI|beta2-GPI	apolipoprotein H	protein-coding
mm_141981.1	chr17	35164845	35164851	-	1	NA	promoter-TSS (NM_020027)	promoter-TSS (NM_020027)	29	NM_001199044	53761	Mm.272462	NM_020027	ENSMUSG00000024393	Prrc2a	3110039B05Rik|Bat-2|Bat2|D17H6S51E|G2|Wbp12|mKIAA4178	proline-rich coiled-coil 2A	protein-coding
mm_43151.1	chr5	125531788	125531819	+	1	NA	promoter-TSS (NM_001190352)	promoter-TSS (NM_001190352)	-615	NM_001190352	208151	Mm.40397	NM_001190352	ENSMUSG00000070498	Tmem132b	AK220418|mKIAA1786	transmembrane protein 132B	protein-coding
mm_147215.1	chr18	37969971	37969981	-	1	NA	promoter-TSS (NM_175684)	promoter-TSS (NM_175684)	-245	NM_175684	319262	Mm.285060	NM_175684	ENSMUSG00000038524	Fchsd1	A030002D08Rik	FCH and double SH3 domains 1	protein-coding
mm_47383.1	chr5	122990461	122990463	-	1	NA	intron (NR_045820, intron 1 of 2)	intron (NR_045820, intron 1 of 2)	1108	NR_045820	109202	Mm.30769	NM_175405	ENSMUSG00000056735	A930024E05Rik	-	RIKEN cDNA A930024E05 gene	ncRNA
mm_133988.1	chr16	4624985	4624991	-	1	NA	promoter-TSS (NM_025571)	promoter-TSS (NM_025571)	-42	NM_025571	66449	Mm.354760	NM_025571	ENSMUSG00000014301	Pam16	2010110I09Rik|AV006767|CGI-136|Magmas|Tim16|Timm16	presequence translocase-asssociated motor 16 homolog (S. cerevisiae)	protein-coding
mm_32261.1	chr4	102586062	102586064	+	1	NA	intron (NM_019840, intron 6 of 14)	intron (NM_019840, intron 6 of 14)	-1495	NM_001177982	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_114490.1	chr13	69802391	69802405	+	1	NA	Intergenic	MLT1G1|LTR|ERVL-MaLR	-7484	NM_138596	28077	Mm.52583	NM_138596	ENSMUSG00000021598	Med10	AA959813|AI385605|C78613|D13Wsu50e	mediator complex subunit 10	protein-coding
mm_152793.1	chr19	21471281	21471282	-	1	NA	intron (NM_010266, intron 1 of 13)	intron (NM_010266, intron 1 of 13)	1380	NM_010266	14544	Mm.45054	NM_010266	ENSMUSG00000058624	Gda	AU015411|AW047581|GAH	guanine deaminase	protein-coding
mm_92328.1	chr10	75781037	75781110	-	1	NA	5' UTR (NM_133994, exon 1 of 5)	5' UTR (NM_133994, exon 1 of 5)	341	NM_133994	103140	Mm.5731	NM_133994	ENSMUSG00000001665	Gstt3	AI118089	glutathione S-transferase, theta 3	protein-coding
mm_117397.1	chr13	73689099	73689114	-	1	NA	exon (NM_028878, exon 6 of 12)	exon (NM_028878, exon 6 of 12)	-10720	NM_027780	71390	Mm.105251	NM_027780		Slc6a19os	5430425J12Rik	solute carrier family 6 (neurotransmitter transporter), member 19, opposite strand	protein-coding
mm_22168.1	chr2	173062103	173062128	-	1	NA	Intergenic	Intergenic	40213	NM_019547	56190	Mm.485782	NM_019547	ENSMUSG00000027510	Rbm38	Rnpc1|Seb4|Seb4l	RNA binding motif protein 38	protein-coding
mm_54285.1	chr6	29216343	29216354	-	1	NA	promoter-TSS (NM_001302934)	promoter-TSS (NM_001302934)	16	NM_001302933	23917	Mm.260707	NM_011829	ENSMUSG00000003500	Impdh1	B930086D20Rik|IMPDH-I	inosine 5'-phosphate dehydrogenase 1	protein-coding
mm_77446.1	chr8	121792263	121792273	-	1	NA	Intergenic	Intergenic	37301	NM_145605	234825	Mm.209329	NM_145605	ENSMUSG00000040263	Klhdc4	AA408426|AV352552|BC012312|G430025P05Rik	kelch domain containing 4	protein-coding
mm_169428.1	chr14	53640633	53640635	+	1	NA	Intergenic	Intergenic	613295	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_23255.1	chr3	51276848	51276863	+	1	NA	promoter-TSS (NR_073429)	promoter-TSS (NR_073429)	94	NR_073429	67746	Mm.441177	NR_073429	ENSMUSG00000087440	4930577N17Rik	-	RIKEN cDNA 4930577N17 gene	ncRNA
mm_107402.1	chr12	33348403	33348408	+	1	NA	intron (NM_001033436, intron 5 of 7)	(T)n|Simple_repeat|Simple_repeat	45890	NM_001033436	380753	Mm.41540	NM_028139	ENSMUSG00000020564	Atxn7l1	2810423G08Rik|Atxn7l4	ataxin 7-like 1	protein-coding
mm_2959.1	chr1	132880320	132880339	+	1	NA	promoter-TSS (NM_010732)	promoter-TSS (NM_010732)	-26	NM_010732	16980	Mm.39640	NM_010732	ENSMUSG00000026443	Lrrn2	5730406J09Rik|NLRR-2	leucine rich repeat protein 2, neuronal	protein-coding
mm_112815.1	chr13	20796390	20796391	+	1	NA	intron (NM_012054, intron 1 of 20)	intron (NM_012054, intron 1 of 20)	2277	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_58361.1	chr6	148354589	148354601	-	1	NA	promoter-TSS (NR_003634)	promoter-TSS (NR_003634)	-61	NR_003634	66184	Mm.391542	NM_025405	ENSMUSG00000063171	Rps4l	1110033J19Rik|AA407494|Rps4y2	ribosomal protein S4-like	pseudo
mm_47706.1	chr5	129887417	129887429	-	1	NA	promoter-TSS (NM_024166)	promoter-TSS (NM_024166)	47	NM_024166	14004	Mm.30133	NM_024166	ENSMUSG00000070493	Chchd2	AL033347|Etohi6	coiled-coil-helix-coiled-coil-helix domain containing 2	protein-coding
mm_77008.1	chr8	107581058	107581081	-	1	NA	exon (NM_010817, exon 7 of 7)	exon (NM_010817, exon 7 of 7)	7413	NM_010817	17463	Mm.18347	NM_010817	ENSMUSG00000039067	Psmd7	AW107203|Mov-34|Mov34	proteasome (prosome, macropain) 26S subunit, non-ATPase, 7	protein-coding
mm_111791.1	chr12	104864958	104864991	-	1	NA	non-coding (NR_104437, exon 1 of 14)	non-coding (NR_104437, exon 1 of 14)	102	NR_104436	94040	Mm.244078	NM_053155	ENSMUSG00000021097	Clmn	9330188N17Rik|AI428889|AI788815|mKIAA1188	calmin	protein-coding
mm_17771.1	chr2	32823174	32823200	-	1	NA	intron (NM_009295, intron 2 of 18)	intron (NM_009295, intron 2 of 18)	24045	NM_009295	20910	Mm.278865	NM_009295	ENSMUSG00000026797	Stxbp1	AI317162|AI326233|MMS10-G|Ms10g|Munc-18a|Munc18-1|N-sec1|Rb-sec1|Sxtbp1|Unc18-1|Unc18h|nsec1	syntaxin binding protein 1	protein-coding
mm_124667.1	chr15	6386760	6386785	+	1	NA	promoter-TSS (NM_001102400)	promoter-TSS (NM_001102400)	24	NM_001310446	13132	Mm.240830	NM_023118	ENSMUSG00000022150	Dab2	5730435J12Rik|AA960054|AI957090|D15Wsu122e|D630005B22Rik|Doc-2|Doc2|p96	disabled 2, mitogen-responsive phosphoprotein	protein-coding
mm_39966.1	chr5	32139062	32139064	+	1	NA	intron (NM_008037, intron 1 of 3)	intron (NM_008037, intron 1 of 3)	2591	NM_008037	14284	Mm.24684	NM_008037	ENSMUSG00000029135	Fosl2	Fra-2	fos-like antigen 2	protein-coding
mm_172837.1	chr9	26407596	26407598	-	1	NA	Intergenic	L1Md_T|LINE|L1	-326211	NM_001310766	76898	Mm.218788	NM_029792	ENSMUSG00000045994	B3gat1	0710007K08Rik|AI846286|GlcAT-P|Glcatp|Hnk1	beta-1,3-glucuronyltransferase 1 (glucuronosyltransferase P)	protein-coding
mm_51679.1	chr6	86443805	86443817	+	1	NA	5' UTR (NM_001243742, exon 2 of 10)	5' UTR (NM_001243742, exon 2 of 10)	5165	NM_001243741	232196	Mm.404040	NM_146170	ENSMUSG00000046679	C87436	-	expressed sequence C87436	protein-coding
mm_91239.1	chr10	22306368	22306383	-	1	NA	promoter-TSS (NR_015465)	promoter-TSS (NR_015465)	-345	NR_015465	606736	Mm.387042	NR_015465	ENSMUSG00000097352	C920009B18Rik	-	RIKEN cDNA C920009B18 gene	ncRNA
mm_29578.1	chr3	117077761	117077769	-	1	NA	promoter-TSS (NR_038029)	promoter-TSS (NR_038029)	0	NR_038029	433646	Mm.158997	NR_038029	ENSMUSG00000028009	1700061I17Rik	-	RIKEN cDNA 1700061I17 gene	ncRNA
mm_118305.1	chr13	113101131	113101143	-	1	NA	promoter-TSS (NM_010370)	promoter-TSS (NM_010370)	-156	NM_010370	14938	Mm.15510	NM_010370	ENSMUSG00000023132	Gzma	AW494114|Ctla-3|Ctla3|Hf|Hf1|SE1|TSP-1|TSP1	granzyme A	protein-coding
mm_121652.1	chr14	10331852	10331859	-	1	NA	intron (NM_001308286, intron 2 of 6)	(A)n|Simple_repeat|Simple_repeat	121603	NM_001308286	14198	Mm.397619	NM_010210	ENSMUSG00000060579	Fhit	AW045638|Fra14A2	fragile histidine triad gene	protein-coding
mm_63386.1	chr7	127214533	127214567	+	1	NA	TTS (NM_016754)	TTS (NM_016754)	2942	NM_016754	17907	Mm.14526	NM_016754	ENSMUSG00000030672	Mylpf	2410014J02Rik|MLC-2|Mlc2	myosin light chain, phosphorylatable, fast skeletal muscle	protein-coding
mm_124527.1	chr14	122233573	122233581	-	1	NA	promoter-TSS (NR_015532)	promoter-TSS (NR_015532)	61	NR_015532	68245	Mm.443285	NR_015532	ENSMUSG00000100585	1700108J01Rik	-	RIKEN cDNA 1700108J01 gene	ncRNA
mm_136033.1	chr16	77420280	77420308	-	1	NA	intron (NR_015543, intron 2 of 4)	intron (NR_015543, intron 2 of 4)	90966	NR_015543	77994	Mm.394688	NR_015543	ENSMUSG00000090386	Mir99ahg	2810055G20Rik|D730043B02Rik	Mir99a and Mirlet7c-1 host gene (non-protein coding)	ncRNA
mm_85990.1	chr9	112187899	112187938	-	1	NA	promoter-TSS (NM_001177620)	promoter-TSS (NM_001177620)	8	NM_001177615	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_134686.1	chr16	22439582	22439603	-	1	NA	promoter-TSS (NM_023794)	promoter-TSS (NM_023794)	-22	NM_023794	104156	Mm.155708	NM_023794	ENSMUSG00000013089	Etv5	1110005E01Rik|8430401F14Rik|ERM	ets variant 5	protein-coding
mm_25062.1	chr3	99141082	99141103	+	1	NA	promoter-TSS (NM_027462)	promoter-TSS (NM_027462)	2	NM_027462	70560	Mm.316754	NM_027462	ENSMUSG00000004233	Wars2	5730427B17Rik|9430020O07Rik|AI413375|TrpRS	tryptophanyl tRNA synthetase 2 (mitochondrial)	protein-coding
mm_10241.1	chr2	8946928	8946943	+	1	NA	Intergenic	Intergenic	-242580	NR_038180	73438	Mm.23558	NR_038180	ENSMUSG00000085580	1700061F12Rik	-	RIKEN cDNA 1700061F12 gene	ncRNA
mm_19147.1	chr2	80524703	80524711	-	1	NA	intron (NM_016965, intron 18 of 30)	intron (NM_016965, intron 18 of 30)	56475	NM_001290745	50884	Mm.25203	NM_016965	ENSMUSG00000027002	Nckap1	C79304|H19|Hem-2|Hem2|Nap1|mKIAA0587|mh19|p125Nap1	NCK-associated protein 1	protein-coding
mm_90832.1	chr10	8358326	8358356	-	1	NA	intron (NM_177387, intron 2 of 7)	intron (NM_177387, intron 2 of 7)	160484	NM_177387	338362	Mm.41163	NM_177387	ENSMUSG00000047712	Ust	D930010O20Rik|UA2OST	uronyl-2-sulfotransferase	protein-coding
mm_69491.1	chr7	134221533	134221543	-	1	NA	intron (NM_007400, intron 1 of 22)	intron (NM_007400, intron 1 of 22)	3559	NM_007400	11489	Mm.439714	NM_007400	ENSMUSG00000054555	Adam12	Mltna	a disintegrin and metallopeptidase domain 12 (meltrin alpha)	protein-coding
mm_22799.1	chr3	23461050	23461075	+	1	NA	Intergenic	Intergenic	1209692	NR_004439	19784		NR_004439		Rprl2	RPRH3|Rmrp3	ribonuclease P RNA-like 2	ncRNA
mm_108196.1	chr12	76792762	76792788	+	1	NA	exon (NM_030677, exon 2 of 2)	exon (NM_030677, exon 2 of 2)	2779	NM_030677	14776	Mm.441856	NM_030677	ENSMUSG00000042808	Gpx2	GI-GPx|GPx-GI|GSHPx-2|GSHPx-GI	glutathione peroxidase 2	protein-coding
mm_3839.1	chr1	160044489	160044497	+	1	NA	non-coding (NR_028111, exon 1 of 3)	non-coding (NR_028111, exon 1 of 3)	113	NM_001162896	67647	Mm.171518	NM_001024470	ENSMUSG00000090394	4930523C07Rik	-	RIKEN cDNA 4930523C07 gene	protein-coding
mm_59750.1	chr7	28822008	28822030	+	1	NA	3' UTR (NM_177301, exon 13 of 13)	3' UTR (NM_177301, exon 13 of 13)	-3319	NM_016772	51798	Mm.291776	NM_016772	ENSMUSG00000053898	Ech1	AA617331	enoyl coenzyme A hydratase 1, peroxisomal	protein-coding
mm_81541.1	chr9	110245383	110245417	+	1	NA	5' UTR (NM_013884, exon 1 of 5)	5' UTR (NM_013884, exon 1 of 5)	1617	NM_001166273	29873	Mm.38496	NM_013884	ENSMUSG00000032482	Cspg5	Caleb|Ngc	chondroitin sulfate proteoglycan 5	protein-coding
mm_64065.1	chr7	140857389	140857457	+	1	NA	promoter-TSS (NM_053194)	promoter-TSS (NM_053194)	26	NM_053194	101489	Mm.281916	NM_053194	ENSMUSG00000025485	Ric8a	AI114950|RIC-8|Ric8	RIC8 guanine nucleotide exchange factor A	protein-coding
mm_137888.1	chr17	31679570	31679581	+	1	NA	exon (NM_001278570, exon 2 of 3)	exon (NM_001278570, exon 2 of 3)	1644	NM_001278570	12954	Mm.1228	NM_013501	ENSMUSG00000024041	Cryaa	Acry-1|Crya-1|Crya1|DAcry-1|lop18	crystallin, alpha A	protein-coding
mm_46786.1	chr5	112590008	112590015	-	1	NA	promoter-TSS (NR_045397)	promoter-TSS (NR_045397)	-15	NR_045397	67325	Mm.490791	NR_045396	ENSMUSG00000097962	1700034G24Rik	-	RIKEN cDNA 1700034G24 gene	ncRNA
mm_74394.1	chr8	3177034	3177059	-	1	NA	intron (NM_010568, intron 10 of 20)	intron (NM_010568, intron 10 of 20)	102571	NM_010568	16337	Mm.268003	NM_010568	ENSMUSG00000005534	Insr	4932439J01Rik|CD220|D630014A15Rik|IR|IR-A|IR-B	insulin receptor	protein-coding
mm_1244.1	chr1	62798202	62798215	+	1	NA	intron (NM_010939, intron 15 of 15)	intron (NM_010939, intron 15 of 15)	-3476	NR_040601	74992	Mm.401979	NR_040601		4930487H11Rik	-	RIKEN cDNA 4930487H11 gene	ncRNA
mm_152412.1	chr19	10605468	10605470	-	1	NA	promoter-TSS (NM_015735)	promoter-TSS (NM_015735)	-156	NM_015735	13194	Mm.289915	NM_015735	ENSMUSG00000024740	Ddb1	127kDa|AA408517|p127-Ddb1	damage specific DNA binding protein 1	protein-coding
mm_37126.1	chr4	116682982	116683009	-	1	NA	Intergenic	Intergenic	-2604	NM_011034	18477	Mm.30929	NM_011034	ENSMUSG00000028691	Prdx1	MSP23|NkefA|OSF-3|OSF3|PAG|Paga|PrdxI|PrxI|TDX2|TPxA|Tdpx2|prx1	peroxiredoxin 1	protein-coding
mm_172504.1	chr7	68055149	68055150	+	1	NA	intron (NM_010513, intron 2 of 20)	intron (NM_010513, intron 2 of 20)	102892	NM_010513	16001	Mm.275742	NM_010513	ENSMUSG00000005533	Igf1r	A330103N21Rik|CD221|D930020L01|IGF-1R|hyft	insulin-like growth factor I receptor	protein-coding
mm_61348.1	chr7	68287181	68287203	+	1	NA	intron (NM_001013811, intron 1 of 8)	intron (NM_001013811, intron 1 of 8)	-10598	NR_040340	100504026	Mm.426764	NR_040340	ENSMUSG00000086628	Gm16157	OTTMUSG00000031023	predicted gene 16157	ncRNA
mm_92377.1	chr10	76416782	76416804	-	1	NA	intron (NM_008787, intron 13 of 41)	intron (NM_008787, intron 13 of 41)	26119	NM_008787	18541	Mm.251794	NM_008787	ENSMUSG00000001151	Pcnt	AW476095|C86676|KEN|Pcnt2|kendrin|m239Asp|m275Asp	pericentrin (kendrin)	protein-coding
mm_126479.1	chr15	81585339	81585381	+	1	NA	promoter-TSS (NM_177821)	promoter-TSS (NM_177821)	-854	NM_177821	328572	Mm.258397	NM_177821	ENSMUSG00000055024	Ep300	A430090G16|A730011L11|KAT3B|p300|p300 HAT	E1A binding protein p300	protein-coding
mm_106021.1	chr11	116024086	116024114	-	1	NA	intron (NM_008211, intron 1 of 3)	CpG-2838	404	NM_008211	15081	Mm.18516	NM_008211	ENSMUSG00000016559	H3f3b	9430068D06Rik|H3.3B	H3 histone, family 3B	protein-coding
mm_132446.1	chr16	35983090	35983106	+	1	NA	promoter-TSS (NM_008465)	promoter-TSS (NM_008465)	-265	NM_008465	16646	Mm.3991	NM_008465	ENSMUSG00000022905	Kpna1	AW494490|IPOA5|NPI1|Rch2|mSRP1	karyopherin (importin) alpha 1	protein-coding
mm_172762.1	chr8	90933782	90933794	+	1	NA	exon (NM_177224, exon 3 of 40)	exon (NM_177224, exon 3 of 40)	1539	NM_001310530	109151	Mm.100615	NM_177224	ENSMUSG00000056608	Chd9	1810014J18Rik|9030205D12Rik|A330063D19Rik|AD013|PRIC320|mKIAA0308	chromodomain helicase DNA binding protein 9	protein-coding
mm_171602.1	chr4	147809784	147809789	-	1	NA	promoter-TSS (NM_001127189)	promoter-TSS (NM_001127189)	2	NM_001127189	100041677	Mm.327194	NM_001127189	ENSMUSG00000078495	Zfp984	Gm13157|OTTMUSG00000010679	zinc finger protein 984	protein-coding
mm_122552.1	chr14	48742331	48742344	-	1	NA	intron (NR_029384, intron 4 of 4)	B3A|SINE|B2	73049	NR_029384	606497	Mm.165199	NR_029384	ENSMUSG00000098682	Otx2os1	-	orthodenticle homeobox 2 opposite strand 1	ncRNA
mm_128256.1	chr15	36771178	36771198	-	1	NA	3' UTR (NM_001253807, exon 5 of 5)	3' UTR (NM_001253807, exon 5 of 5)	19744	NM_001253807	22631	Mm.3360	NM_011740	ENSMUSG00000022285	Ywhaz	1110013I11Rik|14-3-3zeta|AI596267|AL022924|AU020854	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide	protein-coding
mm_47943.1	chr5	135394206	135394240	-	1	NA	exon (NM_148932, exon 1 of 13)	exon (NM_148932, exon 1 of 13)	323	NM_148932	107939	Mm.28399	NM_148932	ENSMUSG00000053293	Pom121	2610027A18Rik|C80273|mKIAA0618	nuclear pore membrane protein 121	protein-coding
mm_87842.1	chr10	60400754	60400764	+	1	NA	intron (NM_001164374, intron 1 of 1)	intron (NM_001164374, intron 1 of 1)	1033	NM_001164374	100302688	Mm.444135	NM_001164374	ENSMUSG00000090439	Gm17455	-	predicted gene, 17455	protein-coding
mm_119244.1	chr14	33590828	33590831	+	1	NA	intron (NM_008978, intron 1 of 11)	intron (NM_008978, intron 1 of 11)	1559	NM_008978	19256	Mm.8019	NM_008978	ENSMUSG00000021940	Ptpn20	typ	protein tyrosine phosphatase, non-receptor type 20	protein-coding
mm_166930.1	chr7	34725060	34725060	+	1	NA	intron (NM_175140, intron 2 of 3)	intron (NM_175140, intron 2 of 3)	-72219	NM_146188	233107	Mm.486198	NM_146188	ENSMUSG00000030499	Kctd15	BC031749	potassium channel tetramerisation domain containing 15	protein-coding
mm_145399.1	chr18	57354717	57354727	+	1	NA	promoter-TSS (NM_028447)	promoter-TSS (NM_028447)	-11	NM_028447	73137	Mm.29889	NM_028447	ENSMUSG00000024594	Prrc1	1190002C06Rik|2310058D16Rik|3110038B19Rik|9430085A19Rik	proline-rich coiled-coil 1	protein-coding
mm_11533.1	chr2	32629468	32629514	+	1	NA	promoter-TSS (NM_021515)	promoter-TSS (NM_021515)	-9	NM_021515	11636	Mm.29189	NM_021515	ENSMUSG00000026817	Ak1	Ak-1|B430205N08Rik	adenylate kinase 1	protein-coding
mm_140600.1	chr17	10319284	10319294	-	1	NA	promoter-TSS (NM_001159517)	promoter-TSS (NM_001159517)	72	NM_021881	19317	Mm.130694	NM_021881	ENSMUSG00000062078	Qk	1110003F05Rik|1500005P18|QkI|l(17)-1Wis|l17Wis1	quaking	protein-coding
mm_28300.1	chr3	89188601	89188637	-	1	NA	exon (NM_001014995, exon 12 of 12)	exon (NM_001014995, exon 12 of 12)	5394	NM_001014995	68521	Mm.274708	NM_001014995	ENSMUSG00000032657	Fam189b	1110013L07Rik	family with sequence similarity 189, member B	protein-coding
mm_167213.1	chr8	3711462	3711466	+	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	9187	NM_029465	75863	Mm.109183	NM_029465	ENSMUSG00000074491	Clec4g	4930572L20Rik	C-type lectin domain family 4, member g	protein-coding
mm_159965.1	chr6	91055665	91055665	-	1	NA	intron (NM_018815, intron 16 of 39)	intron (NM_018815, intron 16 of 39)	61161	NM_018815	54563	Mm.28162	NM_018815	ENSMUSG00000030091	Nup210	9830001L10|AI836801|Pom210|gp190|gp210	nucleoporin 210	protein-coding
mm_142198.1	chr17	36958262	36958284	-	1	NA	promoter-TSS (NM_029602)	promoter-TSS (NM_029602)	155	NM_023162	66136	Mm.486229	NM_023162	ENSMUSG00000036315	Znrd1	1110014N07Rik|Rpa12	zinc ribbon domain containing, 1	protein-coding
mm_28945.1	chr3	99352155	99352172	-	1	NA	exon (NM_009323, exon 8 of 8)	exon (NM_009323, exon 8 of 8)	98403	NM_009323	21384	Mm.88761	NM_009323	ENSMUSG00000027868	Tbx15	Tbx14|Tbx8|de	T-box 15	protein-coding
mm_129469.1	chr15	78670540	78670545	-	1	NA	3' UTR (NM_183141, exon 2 of 2)	3' UTR (NM_183141, exon 2 of 2)	47571	NM_183141	207393	Mm.323188	NM_183141	ENSMUSG00000043460	Elfn2	6330514E13|AW048948|BC094219|Lrrc62|Ppp1r29	leucine rich repeat and fibronectin type III, extracellular 2	protein-coding
mm_170760.1	chr2	159346113	159346121	+	1	NA	Intergenic	Intergenic	551310	NM_001291144	71715	Mm.315652	NM_145742	ENSMUSG00000027655	Dhx35	1200009D07Rik|Ddx35	DEAH (Asp-Glu-Ala-His) box polypeptide 35	protein-coding
mm_21738.1	chr2	164777992	164778015	-	1	NA	exon (NM_009394, exon 3 of 6)	exon (NM_009394, exon 3 of 6)	1731	NM_009394	21925	Mm.1716	NM_009394	ENSMUSG00000017300	Tnnc2	Tncs	troponin C2, fast	protein-coding
mm_42518.1	chr5	115545273	115545315	+	1	NA	intron (NM_133915, intron 3 of 11)	intron (NM_133915, intron 3 of 11)	-14173	NM_007475	11837	Mm.5286	NM_007475	ENSMUSG00000067274	Rplp0	36B4|Arbp|L10E	ribosomal protein, large, P0	protein-coding
mm_120133.1	chr14	60265190	60265215	+	1	NA	promoter-TSS (NM_144843)	promoter-TSS (NM_144843)	-3	NM_144843	219135	Mm.247007	NM_144843	ENSMUSG00000021987	Mtmr6	4022440C11Rik|AI428804|AU041072	myotubularin related protein 6	protein-coding
mm_111290.1	chr12	85468643	85468651	-	1	NA	Intergenic	Intergenic	-5254	NM_010234	14281	Mm.246513	NM_010234	ENSMUSG00000021250	Fos	D12Rfj1|c-fos|cFos	FBJ osteosarcoma oncogene	protein-coding
mm_18632.1	chr2	69342579	69342592	-	1	NA	promoter-TSS (NM_021022)	promoter-TSS (NM_021022)	31	NM_021022	27413	Mm.439855	NM_021022	ENSMUSG00000027048	Abcb11	ABC16|Bsep|Lith1|PFIC2|PGY4|SPGP	ATP-binding cassette, sub-family B (MDR/TAP), member 11	protein-coding
mm_31974.1	chr4	88353857	88353867	+	1	NA	intron (NM_001081184, intron 28 of 43)	intron (NM_001081184, intron 28 of 43)	85064	NM_025760	66775	Mm.386788	NM_025760	ENSMUSG00000028497	Hacd4	4933428I03Rik|Hcad4|Ptplad2	3-hydroxyacyl-CoA dehydratase 4	protein-coding
mm_124484.1	chr14	121698421	121698448	-	1	NA	promoter-TSS (NM_001081039)	promoter-TSS (NM_001081039)	-17	NM_001081039	105445	Mm.378591	NM_134074	ENSMUSG00000025558	Dock9	AA959601|AW538057|B230309H04Rik|D14Wsu89e|Zizimin1|mKIAA1058	dedicator of cytokinesis 9	protein-coding
mm_86489.1	chr10	5548800	5548833	+	1	NA	intron (NM_001347732, intron 1 of 145)	intron (NM_001347732, intron 1 of 145)	1876	NM_153399	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_93303.1	chr10	96958788	96958800	-	1	NA	Intergenic	RLTR18|LTR|ERVK	-76974	NR_045358	75301	Mm.108650	NR_045358		4930556N09Rik	-	RIKEN cDNA 4930556N09 gene	ncRNA
mm_103846.1	chr11	83067249	83067291	-	1	NA	intron (NM_011408, intron 1 of 1)	RLTR11A|LTR|ERVK	2158	NM_011408	20556	Mm.278689	NM_011408	ENSMUSG00000072620	Slfn2	Shlf2	schlafen 2	protein-coding
mm_154505.1	chrM	11990	12000	-	1	NA	NA	Intergenic	NA	NA								
mm_23194.1	chr3	41083430	41083449	+	1	NA	promoter-TSS (NM_027558)	promoter-TSS (NM_027558)	-393	NM_027558	70804	Mm.40321	NM_027558	ENSMUSG00000049940	Pgrmc2	4631434O19Rik|5730409G06Rik|DG6|PMBP	progesterone receptor membrane component 2	protein-coding
mm_26987.1	chr3	25698132	25698139	-	1	NA	intron (NM_001163387, intron 3 of 5)	intron (NM_001163387, intron 3 of 5)	455172	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_41568.1	chr5	93160032	93160036	+	1	NA	intron (NM_001347377, intron 5 of 10)	intron (NM_001347377, intron 5 of 10)	46461	NM_017367	12453	Mm.250419	NM_017367	ENSMUSG00000063015	Ccni	-	cyclin I	protein-coding
mm_140375.1	chr17	86981116	86981126	+	1	NA	intron (NM_145491, intron 2 of 4)	B4A|SINE|B4	18010	NM_145491	104215	Mm.826	NM_145491	ENSMUSG00000024143	Rhoq	Arhq|TC10A|Tc10	ras homolog family member Q	protein-coding
mm_79892.1	chr9	65294558	65294576	+	1	NA	intron (NM_001044389, intron 1 of 12)	CpG	307	NM_011802	270166	Mm.30088	NM_011802	ENSMUSG00000015357	Clpx	AU014732|E330029I21	caseinolytic mitochondrial matrix peptidase chaperone subunit	protein-coding
mm_156018.1	chrX	107089690	107089699	+	1	NA	5' UTR (NM_172435, exon 2 of 3)	5' UTR (NM_172435, exon 2 of 3)	359	NM_172435	78826	Mm.74639	NM_172435	ENSMUSG00000050921	P2ry10	5830408N17Rik|Lypsr2|P2Y10	purinergic receptor P2Y, G-protein coupled 10	protein-coding
mm_631.1	chr1	40324571	40324623	+	1	NA	promoter-TSS (NM_133193)	promoter-TSS (NM_133193)	-30	NM_133193	107527	Mm.155583	NM_133193	ENSMUSG00000070942	Il1rl2	AI481289|AW551444|IL-1Rrp2	interleukin 1 receptor-like 2	protein-coding
mm_111576.1	chr12	101818955	101818963	-	1	NA	5' UTR (NM_011812, exon 1 of 11)	5' UTR (NM_011812, exon 1 of 11)	160	NM_011812	23876	Mm.288381	NM_011812	ENSMUSG00000021186	Fbln5	A55|DANCE|EVEC	fibulin 5	protein-coding
mm_141097.1	chr17	26004834	26004844	-	1	NA	intron (NM_153140, intron 4 of 11)	intron (NM_153140, intron 4 of 11)	17021	NM_153140	215445	Mm.41191	NM_153140	ENSMUSG00000037098	Rab11fip3	Cart1|D030060O14Rik|Rab11-FIP3|mKIAA0665	RAB11 family interacting protein 3 (class II)	protein-coding
mm_62651.1	chr7	107691841	107691859	+	1	NA	intron (NM_001163557, intron 5 of 25)	intron (NM_001163557, intron 5 of 25)	66182	NM_001205227	320635	Mm.132828	NM_177216	ENSMUSG00000048065	Cyb5r2	D630003K02Rik|b5R.2	cytochrome b5 reductase 2	protein-coding
mm_112991.1	chr13	21717627	21717631	+	1	NA	promoter-TSS (NM_178206)	promoter-TSS (NM_178206)	1	NM_178206	319152	Mm.377874	NM_178206	ENSMUSG00000101355	Hist1h3h	H3-291	histone cluster 1, H3h	protein-coding
mm_94420.1	chr11	5871627	5871648	+	1	NA	TTS (NM_008894)	TTS (NM_008894)	6619	NM_008894	18972	Mm.35788	NM_008894	ENSMUSG00000020471	Pold2	50kDa|p50|po1D2	polymerase (DNA directed), delta 2, regulatory subunit	protein-coding
mm_139502.1	chr17	56303354	56303378	+	1	NA	promoter-TSS (NM_001111080)	promoter-TSS (NM_001111080)	29	NM_001111079	18140	Mm.42196	NM_010931	ENSMUSG00000001228	Uhrf1	AL022808|ICBP90|Np95|RNF106	ubiquitin-like, containing PHD and RING finger domains, 1	protein-coding
mm_45318.1	chr5	65453394	65453404	-	1	NA	intron (NM_133697, intron 3 of 4)	intron (NM_133697, intron 3 of 4)	-17557	NM_009466	22235	Mm.344831	NM_009466	ENSMUSG00000029201	Ugdh	Udpgdh	UDP-glucose dehydrogenase	protein-coding
mm_152009.1	chr19	5952066	5952075	-	1	NA	intron (NM_001164057, intron 7 of 17)	intron (NM_001164057, intron 7 of 17)	12136	NM_001164057	18969	Mm.209931	NM_008893	ENSMUSG00000024833	Pola2	AI573378	polymerase (DNA directed), alpha 2	protein-coding
mm_74315.1	chr8	126662928	126662965	+	1	NA	Intergenic	Intergenic	-69510	NM_001164598	270110	Mm.334918	NM_001164598	ENSMUSG00000051495	Irf2bp2	E130305N23Rik|IRF-2BP2	interferon regulatory factor 2 binding protein 2	protein-coding
mm_107152.1	chr12	24498592	24498617	+	1	NA	promoter-TSS (NM_020614)	promoter-TSS (NM_020614)	23	NR_028341	21340	Mm.39082	NM_020614	ENSMUSG00000059669	Taf1b	4930408G01Rik|A230108M10Rik|TAFI68|Tafi86|p63	TATA-box binding protein associated factor, RNA polymerase I, B	protein-coding
mm_87433.1	chr10	50969362	50969365	+	1	NA	intron (NM_011376, intron 9 of 10)	intron (NM_011376, intron 9 of 10)	73712	NM_011376	20464	Mm.4774	NM_011376	ENSMUSG00000019913	Sim1	bHLHe14|mSIM1	single-minded homolog 1 (Drosophila)	protein-coding
mm_40271.1	chr5	39798103	39798103	+	1	NA	Intergenic	Intergenic	-153472	NM_010474	15476	Mm.12559	NM_010474	ENSMUSG00000051022	Hs3st1	3-Ost|D5Wsu110e|Hsg3ost	heparan sulfate (glucosamine) 3-O-sulfotransferase 1	protein-coding
mm_152355.1	chr19	10060409	10060426	-	1	NA	TTS (NM_021890)	TTS (NM_021890)	18869	NM_021890	60527	Mm.253875	NM_021890	ENSMUSG00000024664	Fads3	AI464531	fatty acid desaturase 3	protein-coding
mm_159160.1	chr2	90677403	90677403	+	1	NA	5' UTR (NM_021512, exon 1 of 37)	5' UTR (NM_021512, exon 1 of 37)	188	NM_021512	59015	Mm.24532	NM_021512	ENSMUSG00000051329	Nup160	160kDa|2810011M03Rik|AA414952|AU020188|Gtl-13|Gtl1-13|Gtl13|mKIAA0197	nucleoporin 160	protein-coding
mm_95802.1	chr11	55109641	55109642	+	1	NA	3' UTR (NM_010299, exon 4 of 4)	3' UTR (NM_010299, exon 4 of 4)	11656	NM_010299	14667	Mm.287807	NM_010299	ENSMUSG00000000594	Gm2a	AA408702|AW215435|GM2-AP|SAP-3	GM2 ganglioside activator protein	protein-coding
mm_133074.1	chr16	58679703	58679723	+	1	NA	3' UTR (NM_007757, exon 7 of 7)	3' UTR (NM_007757, exon 7 of 7)	9505	NM_007757	12892	Mm.291519	NM_007757	ENSMUSG00000022742	Cpox	CPX|Cpo|HCP|cac|nct	coproporphyrinogen oxidase	protein-coding
mm_169718.1	chr15	77775878	77775884	-	1	NA	exon (NM_022410, exon 21 of 41)	exon (NM_022410, exon 21 of 41)	-20652	NM_001081970	239552	Mm.125650	NM_001081970	ENSMUSG00000056656	Apol8	9830006J20Rik|APOL-II|Apol2	apolipoprotein L 8	protein-coding
mm_170614.1	chr19	60769879	60769888	-	1	NA	exon (NM_010123, exon 16 of 22)	exon (NM_010123, exon 16 of 22)	4502	NR_034047	100217439		NR_034047		Snora19	MBI-51	small nucleolar RNA, H/ACA box 19	snoRNA
mm_18016.1	chr2	38369014	38369024	-	1	NA	exon (NM_010710, exon 5 of 5)	exon (NM_010710, exon 5 of 5)	17711	NM_010710	16870	Mm.142856	NM_010710	ENSMUSG00000000247	Lhx2	LH2A|Lh-2|Lim2|ap|apterous	LIM homeobox protein 2	protein-coding
mm_121576.1	chr14	122913019	122913051	+	1	NA	intron (NM_145466, intron 1 of 2)	CpG	130	NM_145466	223267	Mm.379358	NM_145466	ENSMUSG00000041625	Ggact	A2ld1	gamma-glutamylamine cyclotransferase	protein-coding
mm_166588.1	chr6	55336174	55336184	+	1	NA	promoter-TSS (NM_007472)	promoter-TSS (NM_007472)	-120	NM_007472	11826	Mm.18625	NM_007472	ENSMUSG00000004655	Aqp1	CHIP28	aquaporin 1	protein-coding
mm_49585.1	chr6	30642925	30642938	+	1	NA	exon (NM_025350, exon 8 of 10)	exon (NM_025350, exon 8 of 10)	3713	NM_025350	109697	Mm.25377	NM_025350	ENSMUSG00000054446	Cpa1	0910001L12Rik|Cpa	carboxypeptidase A1, pancreatic	protein-coding
mm_24345.1	chr3	89820174	89820197	+	1	NA	Intergenic	Intergenic	-11185	NM_172530	214547	Mm.225	NM_172530	ENSMUSG00000046280	She	9430022A14	src homology 2 domain-containing transforming protein E	protein-coding
mm_9419.1	chr1	172329262	172329307	-	1	NA	promoter-TSS (NM_008429)	promoter-TSS (NM_008429)	-21	NM_008429	16524	Mm.261168	NM_008429	ENSMUSG00000038026	Kcnj9	1700085N21Rik|Girk3|Kir3.3|mbGIRK3	potassium inwardly-rectifying channel, subfamily J, member 9	protein-coding
mm_128323.1	chr15	38059749	38059753	-	1	NA	intron (NM_001112721, intron 1 of 58)	intron (NM_001112721, intron 1 of 58)	19103	NM_001112721	70790	Mm.476840	NM_027553	ENSMUSG00000037487	Ubr5	Edd|Edd1	ubiquitin protein ligase E3 component n-recognin 5	protein-coding
mm_48821.1	chr5	149051379	149051390	-	1	NA	5' UTR (NM_001313894, exon 1 of 5)	5' UTR (NM_001313894, exon 1 of 5)	232	NM_001313894	15289	Mm.207047	NM_010439	ENSMUSG00000066551	Hmgb1	HMG-1|Hmg1|SBP-1|p30	high mobility group box 1	protein-coding
mm_162684.1	chr10	13983775	13983789	-	1	NA	intron (NM_010437, intron 1 of 8)	intron (NM_010437, intron 1 of 8)	17403	NM_010437	15273	Mm.42157	NM_010437	ENSMUSG00000015501	Hivep2	Gm20114|MIBP1|Schnurri-2|Shn-2	human immunodeficiency virus type I enhancer binding protein 2	protein-coding
mm_169466.1	chr14	66044956	66044973	+	1	NA	intron (NM_009618, intron 13 of 20)	CpG	32805	NM_009618	11495	Mm.422850	NM_009618	ENSMUSG00000022039	Adam2	AI323749|Ftnb|Ph30-beta	a disintegrin and metallopeptidase domain 2	protein-coding
mm_15607.1	chr2	160731777	160731796	+	1	NA	5' UTR (NM_021280, exon 2 of 34)	5' UTR (NM_021280, exon 2 of 34)	476	NM_021280	18803	Mm.44463	NM_021280	ENSMUSG00000016933	Plcg1	AI894140|Cded|Plc-1|Plc-gamma1|Plcg-1	phospholipase C, gamma 1	protein-coding
mm_112923.1	chr13	20934659	20934691	+	1	NA	intron (NM_012054, intron 11 of 20)	intron (NM_012054, intron 11 of 20)	138624	NM_146535	258528	Mm.377554	NM_146535	ENSMUSG00000042869	Olfr1370	MOR256-14	olfactory receptor 1370	protein-coding
mm_2396.1	chr1	93685684	93685709	+	1	NA	5' UTR (NM_016778, exon 1 of 5)	5' UTR (NM_016778, exon 1 of 5)	121	NM_016778	51800	Mm.3295	NM_016778	ENSMUSG00000026278	Bok	matador|mtd	BCL2-related ovarian killer	protein-coding
mm_11980.1	chr2	55292471	55292501	+	1	NA	Intergenic	Intergenic	-143484	NM_001304810	16519	Mm.5127	NM_008426	ENSMUSG00000026824	Kcnj3	GIRK-1|GIRK1|Kcnf3|Kir3.1	potassium inwardly-rectifying channel, subfamily J, member 3	protein-coding
mm_77108.1	chr8	111081696	111081730	-	1	NA	promoter-TSS (NM_181549)	promoter-TSS (NM_181549)	-5	NM_181549	353287	Mm.135495	NM_181549	ENSMUSG00000033633	Clec18a	Mrcl	C-type lectin domain family 18, member A	protein-coding
mm_52769.1	chr6	121183885	121183941	+	1	NA	non-coding (NR_130903, exon 1 of 7)	non-coding (NR_130903, exon 1 of 7)	246	NM_001304773	74043	Mm.491240	NM_028730	ENSMUSG00000067825	Pex26	4632428M11Rik	peroxisomal biogenesis factor 26	protein-coding
mm_146358.1	chr18	82584109	82584125	+	1	NA	exon (NM_010777, exon 7 of 7)	exon (NM_010777, exon 7 of 7)	29609	NM_001025254	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_156762.1	chrX	160505180	160505182	+	1	NA	intron (NM_172783, intron 1 of 32)	intron (NM_172783, intron 1 of 32)	2747	NM_001177878	110094	Mm.350712	NM_172783	ENSMUSG00000031295	Phka2	6330505C01Rik|D330034O08|Phk	phosphorylase kinase alpha 2	protein-coding
mm_1006.1	chr1	58726017	58726063	+	1	NA	intron (NM_009805, intron 1 of 4)	intron (NM_009805, intron 1 of 4)	-4512	NM_001293805	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_64265.1	chr7	141749923	141749933	+	1	NA	intron (NM_023566, intron 37 of 45)	intron (NM_023566, intron 37 of 45)	-39083	NM_010844	17833	Mm.334332	NM_010844	ENSMUSG00000037974	Muc5ac	2210005L13Rik|MGM	mucin 5, subtypes A and C, tracheobronchial/gastric	protein-coding
mm_92213.1	chr10	68233309	68233312	-	1	NA	intron (NM_023598, intron 3 of 9)	intron (NM_023598, intron 3 of 9)	45416	NM_023598	71371	Mm.440357	NM_023598	ENSMUSG00000019947	Arid5b	4930580B11|5430435G07Rik|AI467247|Desrt|Mrf2|Mrf2alpha|Mrf2beta	AT rich interactive domain 5B (MRF1-like)	protein-coding
mm_84263.1	chr9	62537336	62537354	-	1	NA	promoter-TSS (NM_175484)	promoter-TSS (NM_175484)	-301	NM_175484	235431	Mm.335229	NM_175484	ENSMUSG00000041729	Coro2b	CLIPINC|E130012P22Rik	coronin, actin binding protein, 2B	protein-coding
mm_8167.1	chr1	136960500	136960528	-	1	NA	promoter-TSS (NM_030676)	promoter-TSS (NM_030676)	-66	NM_030676	26424	Mm.16794	NM_030676	ENSMUSG00000026398	Nr5a2	AU020803|D1Ertd308e|Ftf|LRH-1|UF2-H3B	nuclear receptor subfamily 5, group A, member 2	protein-coding
mm_41623.1	chr5	96911738	96911792	+	1	NA	Intergenic	Intergenic	-9507	NR_131152	666266	Mm.32442	NR_131152	ENSMUSG00000106357	Gm8013	EG666266	predicted gene 8013	ncRNA
mm_30891.1	chr4	32263881	32263893	+	1	NA	Intergenic	Intergenic	-153548	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_132112.1	chr16	31456656	31456680	+	1	NA	exon (NM_001122683, exon 7 of 7)	exon (NM_001122683, exon 7 of 7)	27915	NM_001122683	71911	Mm.293470	NM_175177	ENSMUSG00000046598	Bdh1	2310032J20Rik|AI327223|Bdh	3-hydroxybutyrate dehydrogenase, type 1	protein-coding
mm_158201.1	chrX	105374809	105374813	-	1	NA	non-coding (NR_015552, exon 5 of 5)	non-coding (NR_015552, exon 5 of 5)	16943	NR_015552	100043213	Mm.388967	NR_015552	ENSMUSG00000087620	5330434G04Rik	-	RIKEN cDNA 5330434G04 gene	ncRNA
mm_172376.1	chr7	127397881	127397903	+	1	NA	Intergenic	Intergenic	-1024	NR_030454	735274		NR_030454	ENSMUSG00000106252	Mir684-1	Mirn684-1	microRNA 684-1	ncRNA
mm_67484.1	chr7	80713184	80713199	-	1	NA	3' UTR (NM_016721, exon 38 of 38)	3' UTR (NM_016721, exon 38 of 38)	-24314	NM_173863	70461	Mm.392175	NM_173863	ENSMUSG00000030527	Crtc3	2610312F20Rik|6332415K15Rik|AI429792|BC011210|TORC3	CREB regulated transcription coactivator 3	protein-coding
mm_20844.1	chr2	148038289	148038299	-	1	NA	Intergenic	Intergenic	7170	NM_001291067	15376	Mm.938	NM_010446	ENSMUSG00000037025	Foxa2	HNF3-beta|HNF3beta|Hnf-3b|Hnf3b|Tcf-3b|Tcf3b	forkhead box A2	protein-coding
mm_7333.1	chr1	105356641	105356651	-	1	NA	promoter-TSS (NM_001160368)	promoter-TSS (NM_001160368)	64	NM_178779	320311	Mm.389162	NM_178779	ENSMUSG00000047496	Rnf152	A930029B02Rik	ring finger protein 152	protein-coding
mm_47447.1	chr5	123482610	123482627	-	1	NA	promoter-TSS (NM_029594)	promoter-TSS (NM_029594)	-517	NM_029594	76399	Mm.75049	NM_029594	ENSMUSG00000029437	Il31	1700013B14Rik	interleukin 31	protein-coding
mm_126580.1	chr15	82292674	82292676	+	1	NA	3' UTR (NM_011889, exon 10 of 10)	3' UTR (NM_011889, exon 10 of 10)	-6309	NM_029066	74716	Mm.159315	NM_029066	ENSMUSG00000022455	Wbp2nl	4930521I23Rik|PAWP	WBP2 N-terminal like	protein-coding
mm_149099.1	chr19	8941866	8942050	+	1	NA	promoter-TSS (NM_011842)	promoter-TSS (NM_011842)	38	NM_011842	23942	Mm.25339	NM_011842	ENSMUSG00000071646	Mta2	AW550797|Mata1l1|Mta1l1|mmta2	metastasis-associated gene family, member 2	protein-coding
mm_36738.1	chr4	99655999	99656032	-	1	NA	promoter-TSS (NM_010425)	promoter-TSS (NM_010425)	-284	NM_010425	15221	Mm.4758	NM_010425	ENSMUSG00000067261	Foxd3	CWH3|Genesis|Hfh2	forkhead box D3	protein-coding
mm_166526.1	chr6	24598102	24598105	+	1	NA	exon (NM_053098, exon 1 of 3)	exon (NM_053098, exon 1 of 3)	332	NM_053098	93677	Mm.332941	NM_053098	ENSMUSG00000029683	Lmod2	C-Lmod	leiomodin 2 (cardiac)	protein-coding
mm_118466.1	chr14	11553524	11553542	+	1	NA	promoter-TSS (NM_008981)	promoter-TSS (NM_008981)	-20	NM_008981	19270	Mm.431266	NM_008981	ENSMUSG00000021745	Ptprg	5430405N12Rik|AW046354|AW549872|RPTPgamma	protein tyrosine phosphatase, receptor type, G	protein-coding
mm_151701.1	chr19	4477120	4477161	-	1	NA	promoter-TSS (NM_134164)	promoter-TSS (NM_134164)	3	NM_134164	171180	Mm.262270	NM_134164	ENSMUSG00000049303	Syt12	-	synaptotagmin XII	protein-coding
mm_25396.1	chr3	107230457	107230467	+	1	NA	promoter-TSS (NM_001256174)	promoter-TSS (NM_001256174)	-152	NM_001256174	319929	Mm.30453	NM_001256174	ENSMUSG00000094613	A630076J17Rik	-	RIKEN cDNA A630076J17 gene	protein-coding
mm_172949.1	chr9	82592744	82592756	-	1	NA	Intergenic	ORR1A0|LTR|ERVL-MaLR	-237056	NM_001168240	65099	Mm.41415	NM_022986	ENSMUSG00000032251	Irak1bp1	4921528N06Rik|AI851240|Aabp3|Aip70|Simpl	interleukin-1 receptor-associated kinase 1 binding protein 1	protein-coding
mm_266.1	chr1	20951593	20951603	+	1	NA	promoter-TSS (NM_027974)	promoter-TSS (NM_027974)	-28	NM_027974	71877	Mm.29178	NM_027974	ENSMUSG00000041809	Efhc1	1700029F22Rik|mRib72-1|myoclonin1	EF-hand domain (C-terminal) containing 1	protein-coding
mm_86704.1	chr10	18613458	18613465	+	1	NA	intron (NM_001033258, intron 22 of 33)	intron (NM_001033258, intron 22 of 33)	-67385	NM_019487	56016	Mm.35551	NM_019487	ENSMUSG00000019853	Hebp2	SOUL	heme binding protein 2	protein-coding
mm_24284.1	chr3	89231484	89231496	+	1	NA	intron (NM_013605, intron 3 of 6)	intron (NM_013605, intron 3 of 6)	2434	NM_013605	17829	Mm.16193	NM_013605	ENSMUSG00000042784	Muc1	CD227|EMA|Muc-1	mucin 1, transmembrane	protein-coding
mm_45013.1	chr5	38527196	38527213	-	1	NA	3' UTR (NM_011715, exon 15 of 15)	3' UTR (NM_011715, exon 15 of 15)	-25052	NM_145559	117591	Mm.260137	NM_145559	ENSMUSG00000005107	Slc2a9	Glut9|SLC2A9B|SLC2a9A	solute carrier family 2 (facilitated glucose transporter), member 9	protein-coding
mm_161911.1	chr18	65470443	65470443	+	1	NA	exon (NM_172833, exon 13 of 16)	exon (NM_172833, exon 13 of 16)	39446	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_100794.1	chr11	4939934	4939941	-	1	NA	exon (NM_010904, exon 4 of 4)	exon (NM_010904, exon 4 of 4)	-7584	NM_001243043	11764	Mm.274816	NM_007454	ENSMUSG00000009090	Ap1b1	Adtb1|b2b1660Clo	adaptor protein complex AP-1, beta 1 subunit	protein-coding
mm_134951.1	chr16	31301251	31301262	-	1	NA	intron (NM_001301353, intron 4 of 5)	intron (NM_001301353, intron 4 of 5)	13552	NM_001301353	11815	Mm.2082	NM_007470	ENSMUSG00000022548	Apod	-	apolipoprotein D	protein-coding
mm_73471.1	chr8	106683109	106683124	+	1	NA	promoter-TSS (NM_173037)	promoter-TSS (NM_173037)	48	NM_173037	272538	Mm.87151	NM_173037	ENSMUSG00000041949	Tango6	AW413431|E330010G16|Tmco7	transport and golgi organization 6	protein-coding
mm_92510.1	chr10	78427471	78427485	-	1	NA	3' UTR (NM_007793, exon 3 of 3)	3' UTR (NM_007793, exon 3 of 3)	1808	NM_007793	13014	Mm.6095	NM_007793	ENSMUSG00000005054	Cstb	AA960480|Stfb	cystatin B	protein-coding
mm_153565.1	chr19	42431779	42431792	-	1	NA	promoter-TSS (NM_145123)	promoter-TSS (NM_145123)	-2	NM_145123	72832	Mm.313558	NM_145123	ENSMUSG00000042401	Crtac1	2810454P21Rik|AW047536|Crtac1B|Lotus	cartilage acidic protein 1	protein-coding
mm_57440.1	chr6	124962426	124962438	-	1	NA	exon (NM_001164089, exon 4 of 8)	exon (NM_001164089, exon 4 of 8)	2965	NM_012003	26894	Mm.244536	NM_012003	ENSMUSG00000030127	Cops7a	D6Ertd35e	COP9 signalosome subunit 7A	protein-coding
mm_44985.1	chr5	37434755	37434761	-	1	NA	Intergenic	Intergenic	96280	NM_145920	68525	Mm.25506	NM_145920	ENSMUSG00000050248	Evc2	1110017L09Rik|Lbn|limbin	Ellis van Creveld syndrome 2	protein-coding
mm_152347.1	chr19	9984858	9984868	-	1	NA	TTS (NM_011913)	TTS (NM_011913)	2217	NM_010239	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
mm_37902.1	chr4	132732428	132732438	-	1	NA	TTS (NM_133888)	TTS (NM_133888)	113	NM_201368	381560	Mm.44558	NM_201368	ENSMUSG00000037752	Xkr8	4931440N07Rik|AI597014|Gm1031|XRG8|mXkr8	X-linked Kx blood group related 8	protein-coding
mm_85851.1	chr9	110654230	110654254	-	1	NA	promoter-TSS (NM_183276)	promoter-TSS (NM_183276)	-81	NM_183276	235627	Mm.335481	NM_183276	ENSMUSG00000056724	Nbeal2	1110014F23Rik|BC042396|mKIAA0540	neurobeachin-like 2	protein-coding
mm_103253.1	chr11	70971094	70971104	-	1	NA	intron (NM_001252413, intron 1 of 5)	MER20|DNA|hAT-Charlie	899	NM_001252415	69723	Mm.275691	NM_027186	ENSMUSG00000018449	Rpain	2400006N03Rik|Rip	RPA interacting protein	protein-coding
mm_85675.1	chr9	107757533	107757535	-	1	NA	intron (NM_148930, intron 6 of 24)	intron (NM_148930, intron 6 of 24)	13468	NM_148930	83486	Mm.259197	NM_148930	ENSMUSG00000032580	Rbm5	D030069N10Rik	RNA binding motif protein 5	protein-coding
mm_91116.1	chr10	19188477	19188544	-	1	NA	intron (NR_038022, intron 1 of 1)	intron (NR_038022, intron 1 of 1)	21272	NR_038022	100504265	Mm.383417	NR_038021		Gm20139	-	predicted gene, 20139	ncRNA
mm_129543.1	chr15	79396822	79396844	-	1	NA	intron (NM_172608, intron 1 of 8)	intron (NM_172608, intron 1 of 8)	6086	NM_001253817	223693	Mm.323358	NM_172608	ENSMUSG00000009035	Tmem184b	2610507A11|4732495E13Rik	transmembrane protein 184b	protein-coding
mm_139797.1	chr17	66005697	66005717	+	1	NA	intron (NM_001025572, intron 8 of 12)	intron (NM_001025572, intron 8 of 12)	-54520	NM_023053	65960	Mm.10153	NM_023053	ENSMUSG00000024098	Twsg1	1810013J15Rik|9030422N06Rik|AW552143|D17Ertd403e|Tsg|Twg	twisted gastrulation BMP signaling modulator 1	protein-coding
mm_51078.1	chr6	66935862	66935877	+	1	NA	intron (NM_001177556, intron 2 of 3)	intron (NM_001177556, intron 2 of 3)	38978	NM_001177558	14701	Mm.234342	NM_025278	ENSMUSG00000036402	Gng12	2010305F15Rik|AA536815|AI115529|AI314170|AI842738	guanine nucleotide binding protein (G protein), gamma 12	protein-coding
mm_88482.1	chr10	77622364	77622374	+	1	NA	promoter-TSS (NM_019803)	promoter-TSS (NM_019803)	48	NM_019803	22213	Mm.458125	NM_019803	ENSMUSG00000009293	Ube2g2	1110003O05Rik|D10Xrf369|UBC7|Ubc7p	ubiquitin-conjugating enzyme E2G 2	protein-coding
mm_121568.1	chr14	122749362	122749374	+	1	NA	intron (NM_144844, intron 19 of 23)	intron (NM_144844, intron 19 of 23)	163797	NM_145466	223267	Mm.379358	NM_145466	ENSMUSG00000041625	Ggact	A2ld1	gamma-glutamylamine cyclotransferase	protein-coding
mm_102593.1	chr11	61930198	61930243	-	1	NA	promoter-TSS (NM_019921)	promoter-TSS (NM_019921)	37	NM_019921	56697	Mm.274404	NM_019921	ENSMUSG00000047804	Akap10	1500031L16Rik|B130049N18Rik|D-AKAP-2|D-AKAP2|PRKA10	A kinase (PRKA) anchor protein 10	protein-coding
mm_162450.1	chr1	122357302	122357328	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-789335	NM_025860	66942	Mm.44219	NM_025860	ENSMUSG00000001674	Ddx18	2310005B10Rik	DEAD (Asp-Glu-Ala-Asp) box polypeptide 18	protein-coding
mm_67088.1	chr7	68285944	68285952	-	1	NA	intron (NM_001013811, intron 1 of 8)	intron (NM_001013811, intron 1 of 8)	-9354	NR_040340	100504026	Mm.426764	NR_040340	ENSMUSG00000086628	Gm16157	OTTMUSG00000031023	predicted gene 16157	ncRNA
mm_44435.1	chr5	21055990	21056035	-	1	NA	promoter-TSS (NM_011203)	promoter-TSS (NM_011203)	-215	NM_011203	19248	Mm.319117	NM_011203	ENSMUSG00000028771	Ptpn12	P19-PTP|PTP-P19|PTP-PEST|PTPG1	protein tyrosine phosphatase, non-receptor type 12	protein-coding
mm_159265.1	chr2	156174316	156174316	-	1	NA	intron (NM_133242, intron 3 of 16)	intron (NM_133242, intron 3 of 16)	5264	NM_001291115	170791	Mm.392436	NM_133242	ENSMUSG00000027620	Rbm39	1500012C14Rik|2310040E03Rik|B330012G18Rik|C79248|R75070|Rnpc2|caper	RNA binding motif protein 39	protein-coding
mm_50975.1	chr6	61204844	61204851	+	1	NA	intron (NM_183310, intron 1 of 10)	intron (NM_183310, intron 1 of 10)	-24037	NR_040287	100504262	Mm.438066	NR_040287		A730020E08Rik	-	RIKEN cDNA A730020E08 gene	ncRNA
mm_5944.1	chr1	56782166	56782210	-	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	-144737	NM_027661	71066	Mm.152656	NM_027661	ENSMUSG00000045336	Hsfy2	4933413G11Rik|Hspy2l	heat shock transcription factor, Y-linked 2	protein-coding
mm_89744.1	chr10	99107512	99107531	+	1	NA	promoter-TSS (NM_015737)	promoter-TSS (NM_015737)	350	NM_027740	382406	Mm.440656	NM_027740	ENSMUSG00000019952	Poc1b	4933430F16Rik|Wdr51b	POC1 centriolar protein B	protein-coding
mm_33732.1	chr4	134098900	134098912	+	1	NA	Intergenic	Intergenic	-3677	NR_045571	67586	Mm.282029	NM_026257	ENSMUSG00000012126	Ubxn11	4930506L07Rik|D4Bwg1540e|Soc|Soci|Ubxd5	UBX domain protein 11	protein-coding
mm_159331.1	chr3	40846797	40846797	-	1	NA	promoter-TSS (NM_028140)	promoter-TSS (NM_028140)	57	NM_028140	72175	Mm.130610	NM_028140	ENSMUSG00000025759	Mfsd8	2810423E13Rik|AI836898|AV142426|Cln7	major facilitator superfamily domain containing 8	protein-coding
mm_168134.1	chr10	27936360	27936360	+	1	NA	Intergenic	Intergenic	-138460	NM_008983	19272	Mm.332303	NM_008983	ENSMUSG00000019889	Ptprk	AI853699|PTPk|RPTPkappa	protein tyrosine phosphatase, receptor type, K	protein-coding
mm_103508.1	chr11	76617470	76617481	-	1	NA	Intergenic	ID4_|SINE|ID	-39736	NM_198894	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_112606.1	chr13	14510089	14510094	+	1	NA	intron (NM_001081348, intron 1 of 28)	RMER15|LTR|ERVL	13135	NM_001081348	94253	Mm.125298	NM_153130	ENSMUSG00000021301	Hecw1	9330116H24Rik|AV273951|E130207I19Rik|Nedl1	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	protein-coding
mm_37027.1	chr4	114970513	114970516	-	1	NA	intron (NM_025647, intron 1 of 5)	intron (NM_025647, intron 1 of 5)	16714	NM_025647	66588	Mm.294159	NM_025647	ENSMUSG00000028719	Cmpk1	0610011D08Rik|CK|Cmpk|UMP-CMPk	cytidine monophosphate (UMP-CMP) kinase 1	protein-coding
mm_144790.1	chr18	35910329	35910337	+	1	NA	Intergenic	Intergenic	-54497	NM_028707	74002	Mm.196944	NM_028707	ENSMUSG00000024347	Psd2	6330404E20Rik|AW125584|EFA6C	pleckstrin and Sec7 domain containing 2	protein-coding
mm_24341.1	chr3	89773344	89773394	+	1	NA	promoter-TSS (NR_130957)	promoter-TSS (NR_130957)	31	NR_130957	74034	Mm.386816	NR_130957	ENSMUSG00000042579	4632404H12Rik	-	RIKEN cDNA 4632404H12 gene	ncRNA
mm_83385.1	chr9	44582465	44582470	-	1	NA	Intergenic	Intergenic	-22425	NM_001110826	13209	Mm.267061	NM_007841	ENSMUSG00000032097	Ddx6	1110001P04Rik|E230023J21Rik|HLR2|mRCK/P54|p54|rck	DEAD (Asp-Glu-Ala-Asp) box polypeptide 6	protein-coding
mm_122178.1	chr14	31553234	31553240	-	1	NA	intron (NM_009937, intron 2 of 16)	intron (NM_009937, intron 2 of 16)	24146	NM_009937	382864	Mm.239821	NM_009937	ENSMUSG00000057606	Colq	A130034K24Rik	collagen-like tail subunit (single strand of homotrimer) of asymmetric acetylcholinesterase	protein-coding
mm_35182.1	chr4	15958165	15958208	-	1	NA	intron (NM_013752, intron 1 of 15)	CpG	219	NM_013752	27354	Mm.20866	NM_013752	ENSMUSG00000028224	Nbn	Nbs1	nibrin	protein-coding
mm_134421.1	chr16	17891639	17891700	-	1	NA	promoter-TSS (NM_001109750)	promoter-TSS (NM_001109750)	59	NM_010048	13356	Mm.254515	NM_010048	ENSMUSG00000003166	Dgcr2	9930034O06Rik|DGS-C|Dgsc|Idd|Lan|Sez12|mKIAA0163	DiGeorge syndrome critical region gene 2	protein-coding
mm_21390.1	chr2	157560970	157560973	-	1	NA	intron (NM_001291128, intron 2 of 2)	intron (NM_001291128, intron 2 of 2)	893	NM_180960	18111	Mm.34330	NM_010923	ENSMUSG00000067786	Nnat	5730414I02Rik|AW107673|Peg5	neuronatin	protein-coding
mm_94702.1	chr11	20226032	20226112	+	1	NA	TTS (NM_172260)	TTS (NM_172260)	23352	NM_172260	216543	Mm.260314	NM_172260	ENSMUSG00000044066	Cep68	6030463E10Rik|AI481761|BC027174|Kiaa0582	centrosomal protein 68	protein-coding
mm_163848.1	chr14	19418196	19418224	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	184377	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_37913.1	chr4	132782475	132782487	-	1	NA	3' UTR (NM_001033308, exon 6 of 6)	3' UTR (NM_001033308, exon 6 of 6)	13883	NM_001033308	230787	Mm.290912	NM_001033308	ENSMUSG00000037731	Themis2	ICB-1	thymocyte selection associated family member 2	protein-coding
mm_81053.1	chr9	105658436	105658456	+	1	NA	exon (NM_001081309, exon 7 of 20)	exon (NM_001081309, exon 7 of 20)	15451	NM_001081309	75669	Mm.274830	NM_029380	ENSMUSG00000032571	Pik3r4	2210010O15Rik|C730038E05Rik|C85833|D9Ertd418e	phosphatidylinositol 3 kinase, regulatory subunit, polypeptide 4, p150	protein-coding
mm_16465.1	chr2	180635091	180635121	+	1	NA	intron (NM_178254, intron 5 of 5)	intron (NM_178254, intron 5 of 5)	7585	NM_178254	277353	Mm.473700	NM_178254	ENSMUSG00000038932	Tcfl5	AV260129|Figlb|Sosf1	transcription factor-like 5 (basic helix-loop-helix)	protein-coding
mm_78379.1	chr9	27790993	27791003	+	1	NA	promoter-TSS (NM_177906)	promoter-TSS (NM_177906)	-271	NM_177906	330908	Mm.379474	NM_177906	ENSMUSG00000062257	Opcml	2900075O15Rik|3732419F12|AI844366|B930023M13Rik|C230027C17|Gm181|Obcam	opioid binding protein/cell adhesion molecule-like	protein-coding
mm_11130.1	chr2	28230347	28230358	+	1	NA	3' UTR (NM_001038613, exon 6 of 6)	3' UTR (NM_001038613, exon 6 of 6)	24663	NM_019498	56177	Mm.43278	NM_019498	ENSMUSG00000026833	Olfm1	AMY|AW742568|Noe1|OlfA|Pancortin|Pancortin3	olfactomedin 1	protein-coding
mm_157964.1	chrX	90744686	90744720	-	1	NA	Intergenic	Intergenic	-147439	NM_001101450	212952	Mm.477436	NM_001101450	ENSMUSG00000091497	Gm44	-	predicted gene 44	protein-coding
mm_83474.1	chr9	45827282	45827309	-	1	NA	intron (NM_001081373, intron 1 of 29)	G-rich|Low_complexity|Low_complexity	1343	NM_001081373	214552	Mm.260103	NM_172531	ENSMUSG00000043987	Cep164	AI450905|BC027092|D030051D21|mKIAA1052	centrosomal protein 164	protein-coding
mm_123459.1	chr14	65593080	65593093	-	1	NA	promoter-TSS (NM_028811)	promoter-TSS (NM_028811)	26	NM_001253812	74195	Mm.29719	NM_028811	ENSMUSG00000022031	Elp3	2610507P14Rik|KAT9	elongator acetyltransferase complex subunit 3	protein-coding
mm_71543.1	chr8	47675363	47675413	+	1	NA	promoter-TSS (NM_023503)	promoter-TSS (NM_023503)	-229	NM_023503	69260	Mm.430733	NM_023503	ENSMUSG00000063049	Ing2	2810011M06Rik|Ing1l|Ing2b|P33ING2	inhibitor of growth family, member 2	protein-coding
mm_40060.1	chr5	33996699	33996729	+	1	NA	5' UTR (NM_001001985, exon 1 of 3)	5' UTR (NM_001001985, exon 1 of 3)	730	NM_001001985	269642	Mm.274610	NM_001001985	ENSMUSG00000048142	Nat8l	1110038O08Rik|Shati	N-acetyltransferase 8-like	protein-coding
mm_108369.1	chr12	80816728	80816743	+	1	NA	intron (NM_001242419, intron 1 of 6)	intron (NM_001242419, intron 1 of 6)	26203	NM_001242419	217684	Mm.341776	NM_178682	ENSMUSG00000021133	Susd6	4933426M11Rik|mKIAA0247	sushi domain containing 6	protein-coding
mm_62216.1	chr7	98178332	98178423	+	1	NA	promoter-TSS (NM_007602)	promoter-TSS (NM_007602)	-103	NM_007602	12337	Mm.326847	NM_007602	ENSMUSG00000035547	Capn5	nCL-3	calpain 5	protein-coding
mm_75048.1	chr8	32874823	32874826	-	1	NA	Intergenic	Intergenic	75202	NM_001177589	100042715	Mm.291093	NM_001177589		Gm3985	-	predicted gene 3985	protein-coding
mm_39825.1	chr5	30798071	30798087	+	1	NA	3' UTR (NM_023047, exon 13 of 13)	3' UTR (NM_023047, exon 13 of 13)	-16562	NM_133350	100732	Mm.332295	NM_133350	ENSMUSG00000029166	Mapre3	AI790651|EB2|EB3|EBF3|RP3	microtubule-associated protein, RP/EB family, member 3	protein-coding
mm_125452.1	chr15	51877510	51877520	+	1	NA	promoter-TSS (NM_030132)	promoter-TSS (NM_030132)	74	NM_030132	78581	Mm.176347	NM_030132	ENSMUSG00000022313	Utp23	1700010I21Rik|AI662478|BB238373|D530033C11Rik	UTP23 small subunit processome component	protein-coding
mm_80432.1	chr9	77923269	77923272	+	1	NA	intron (NM_134255, intron 1 of 7)	intron (NM_134255, intron 1 of 7)	5905	NM_134255	68801	Mm.430736	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	ELOVL family member 5, elongation of long chain fatty acids (yeast)	protein-coding
mm_22592.1	chr3	13610509	13610511	+	1	NA	intron (NR_040598, intron 3 of 3)	intron (NR_040598, intron 3 of 3)	42355	NR_040598	75203	Mm.490940	NR_040598		4930539N22Rik	-	RIKEN cDNA 4930539N22 gene	ncRNA
mm_44649.1	chr5	28210032	28210034	-	1	NA	5' UTR (NM_001310511, exon 1 of 3)	5' UTR (NM_001310511, exon 1 of 3)	135	NM_001310511	269637	Mm.68286	NM_175651	ENSMUSG00000044681	Cnpy1	1500012D20Rik|9630008K15Rik|AI853839	canopy FGF signaling regulator 1	protein-coding
mm_96818.1	chr11	69994507	69994517	+	1	NA	exon (NM_019749, exon 4 of 4)	exon (NM_019749, exon 4 of 4)	-1254	NM_001291125	78246	Mm.20805	NM_030064	ENSMUSG00000018572	Phf23	JUNE-1	PHD finger protein 23	protein-coding
mm_149702.1	chr19	21396610	21396616	+	1	NA	intron (NM_010266, intron 12 of 13)	intron (NM_010266, intron 12 of 13)	76048	NM_010266	14544	Mm.45054	NM_010266	ENSMUSG00000058624	Gda	AU015411|AW047581|GAH	guanine deaminase	protein-coding
mm_54235.1	chr6	28239297	28239299	-	1	NA	TTS (NM_001081678)	TTS (NM_001081678)	22303	NM_001081678	627049	Mm.84441	NM_001081678	ENSMUSG00000039841	Zfp800	AA407452|Znf800	zinc finger protein 800	protein-coding
mm_62756.1	chr7	112023578	112023590	+	1	NA	promoter-TSS (NM_177249)	promoter-TSS (NM_177249)	78	NM_177249	74996	Mm.16974	NM_133758	ENSMUSG00000059263	Usp47	4930502N04Rik|A630020C16Rik	ubiquitin specific peptidase 47	protein-coding
mm_10318.1	chr2	11206110	11206112	+	1	NA	intron (NM_008859, intron 1 of 17)	intron (NM_008859, intron 1 of 17)	33729	NM_008859	18761	Mm.329993	NM_008859	ENSMUSG00000026778	Prkcq	A130035A12Rik|AW494342|PKC-0|PKC-theta|PKCtheta|Pkcq	protein kinase C, theta	protein-coding
mm_7109.1	chr1	89931154	89931168	-	1	NA	promoter-TSS (NM_010262)	promoter-TSS (NM_010262)	15	NM_010262	14472	Mm.204730	NM_010262	ENSMUSG00000034486	Gbx2	D130058E05Rik|Gbx-2|MMoxA|Stra7	gastrulation brain homeobox 2	protein-coding
mm_66599.1	chr7	45458393	45458413	-	1	NA	intron (NM_010240, intron 3 of 3)	intron (NM_010240, intron 3 of 3)	1483	NM_010240	14325	Mm.30357	NM_010240	ENSMUSG00000050708	Ftl1	Ftl|Ftl-1|L-ferritin	ferritin light polypeptide 1	protein-coding
mm_172155.1	chr6	42450746	42450749	+	1	NA	Intergenic	Intergenic	10270	NM_146444	258436	Mm.377501	NM_146444	ENSMUSG00000068574	Olfr458	MOR211-8P|MOR221-4|MOR257-4|Olfr301	olfactory receptor 458	protein-coding
mm_62946.1	chr7	119526324	119526334	+	1	NA	promoter-TSS (NM_178758)	promoter-TSS (NM_178758)	64	NM_178758	272428	Mm.185183	NM_178758	ENSMUSG00000030972	Acsm5	C730019D22|C730027J19Rik	acyl-CoA synthetase medium-chain family member 5	protein-coding
mm_119665.1	chr14	52304893	52304917	+	1	NA	exon (NM_019721, exon 1 of 11)	exon (NM_019721, exon 1 of 11)	219	NM_019721	56335	Mm.271759	NM_019721	ENSMUSG00000022160	Mettl3	2310024F18Rik|M6A|Spo8	methyltransferase like 3	protein-coding
mm_114170.1	chr13	55472288	55472302	+	1	NA	exon (NM_001030296, exon 2 of 3)	exon (NM_001030296, exon 2 of 3)	5481	NR_105909	102465569		NR_105909	ENSMUSG00000098341	Mir6944	Gm27710|mmu-mir-6944	microRNA 6944	ncRNA
mm_137107.1	chr17	21962731	21962752	+	1	NA	promoter-TSS (NM_001199048)	promoter-TSS (NM_001199048)	182	NM_001025373	74670	Mm.26540	NM_001025373	ENSMUSG00000053347	Zfp943	4930432O21Rik	zinc finger prtoein 943	protein-coding
mm_38736.1	chr4	145245657	145245673	-	1	NA	intron (NM_011610, intron 1 of 9)	intron (NM_011610, intron 1 of 9)	1205	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_423.1	chr1	34444858	34444904	+	1	NA	3' UTR (NM_178601, exon 9 of 9)	3' UTR (NM_178601, exon 9 of 9)	5052	NM_178601	27993	Mm.289667	NM_178601	ENSMUSG00000026127	Imp4	AA409888|AV031295|D1Wsu40e	IMP4, U3 small nucleolar ribonucleoprotein	protein-coding
mm_140293.1	chr17	85620798	85620809	+	1	NA	promoter-TSS (NM_011381)	promoter-TSS (NM_011381)	-31	NM_011381	20473	Mm.370208	NM_011381	ENSMUSG00000038805	Six3	E130112M24Rik|Six3a|Six3alpha|Six3b|Six3beta	sine oculis-related homeobox 3	protein-coding
mm_54515.1	chr6	35512060	35512072	-	1	NA	3' UTR (NM_008098, exon 4 of 4)	3' UTR (NM_008098, exon 4 of 4)	27822	NM_008098	14489	Mm.182746	NM_008098	ENSMUSG00000029840	Mtpn	5033418D15Rik|Gcdp|V1	myotrophin	protein-coding
mm_43846.1	chr5	143235144	143235251	+	1	NA	promoter-TSS (NM_001289590)	promoter-TSS (NM_001289590)	34	NM_177681	231866	Mm.55211	NM_177681	ENSMUSG00000029587	Zfp12	C530015C18|Krox-7|Zfp-12|Znf12	zinc finger protein 12	protein-coding
mm_90397.1	chr10	127324336	127324363	+	1	NA	intron (NM_146011, intron 1 of 14)	B1_Mur2|SINE|Alu	622	NM_146011	216445	Mm.227198	NM_146011	ENSMUSG00000040345	Arhgap9	AU043488	Rho GTPase activating protein 9	protein-coding
mm_56167.1	chr6	87994161	87994204	-	1	NA	Intergenic	Intergenic	12499	NR_026990	434064	Mm.371796	NR_026990	ENSMUSG00000084950	Gm5577	EG434064	predicted gene 5577	ncRNA
mm_149951.1	chr19	27430137	27430161	+	1	NA	promoter-TSS (NM_177474)	promoter-TSS (NM_177474)	112	NR_027987	107372	Mm.17942	NM_175354		C030016D13Rik	AW413347	RIKEN cDNA C030016D13 gene	ncRNA
mm_92197.1	chr10	68136572	68136612	-	1	NA	intron (NM_023598, intron 4 of 9)	intron (NM_023598, intron 4 of 9)	142134	NM_023598	71371	Mm.440357	NM_023598	ENSMUSG00000019947	Arid5b	4930580B11|5430435G07Rik|AI467247|Desrt|Mrf2|Mrf2alpha|Mrf2beta	AT rich interactive domain 5B (MRF1-like)	protein-coding
mm_100128.1	chr11	115933630	115933669	+	1	NA	promoter-TSS (NM_130454)	promoter-TSS (NM_130454)	-10	NM_020483	57230	Mm.267810	NM_020483	ENSMUSG00000020755	Sap30bp	2700016D05Rik|Hcngp	SAP30 binding protein	protein-coding
mm_100793.1	chr11	4939810	4939818	-	1	NA	exon (NM_010904, exon 4 of 4)	exon (NM_010904, exon 4 of 4)	-7707	NM_001243043	11764	Mm.274816	NM_007454	ENSMUSG00000009090	Ap1b1	Adtb1|b2b1660Clo	adaptor protein complex AP-1, beta 1 subunit	protein-coding
mm_119066.1	chr14	30825581	30825640	+	1	NA	promoter-TSS (NM_028839)	promoter-TSS (NM_028839)	16	NM_028839	69179	Mm.143025	NM_028839	ENSMUSG00000006526	Tmem110	1810038N08Rik|2310014H19Rik|AW554125|STIMATE	transmembrane protein 110	protein-coding
mm_147025.1	chr18	34651704	34651741	-	1	NA	promoter-TSS (NM_178347)	promoter-TSS (NM_178347)	14	NM_178347	52563	Mm.196638	NM_178347	ENSMUSG00000024370	Cdc23	6030435O18|D18Ertd243e	CDC23 cell division cycle 23	protein-coding
mm_104033.1	chr11	86257554	86257572	-	1	NA	promoter-TSS (NM_027421)	promoter-TSS (NM_027421)	5	NM_027421	70422	Mm.171304	NM_027421	ENSMUSG00000018068	Ints2	2810417D08Rik|AA408260|AI987735|mKIAA1287	integrator complex subunit 2	protein-coding
mm_164176.1	chr15	76199376	76199395	-	1	NA	promoter-TSS (NM_201392)	promoter-TSS (NM_201392)	21	NM_201392	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
mm_26774.1	chr3	8964368	8964401	-	1	NA	promoter-TSS (NM_001025262)	promoter-TSS (NM_001025262)	-330	NM_001025261	21985	Mm.371590	NM_009412	ENSMUSG00000027506	Tpd52	AI043038|mD52	tumor protein D52	protein-coding
mm_22753.1	chr3	19972626	19972636	+	1	NA	exon (NM_007752, exon 7 of 19)	exon (NM_007752, exon 7 of 19)	15577	NM_007752	12870	Mm.13787	NM_007752	ENSMUSG00000003617	Cp	D3Ertd555e	ceruloplasmin	protein-coding
mm_98753.1	chr11	96545477	96545481	+	1	NA	intron (NM_001033186, intron 4 of 12)	intron (NM_001033186, intron 4 of 12)	80888	NM_001177898	78473	Mm.395840	NM_001033186	ENSMUSG00000057058	Skap1	1700091G21Rik|Scap1|Skap-55	src family associated phosphoprotein 1	protein-coding
mm_7178.1	chr1	92473737	92473799	-	1	NA	promoter-TSS (NM_024197)	promoter-TSS (NM_024197)	-10	NM_024197	67273	Mm.248778	NM_024197	ENSMUSG00000026260	Ndufa10	2900053E13Rik	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex 10	protein-coding
mm_46062.1	chr5	92263655	92263675	-	1	NA	exon (NM_001163687, exon 6 of 11)	exon (NM_001163687, exon 6 of 11)	-10506	NM_011148	19023	Mm.87155	NM_011148	ENSMUSG00000029410	Ppef2	-	protein phosphatase, EF hand calcium-binding domain 2	protein-coding
mm_135951.1	chr16	74411867	74411880	-	1	NA	promoter-TSS (NM_175549)	promoter-TSS (NM_175549)	-961	NM_175549	268902	Mm.171736	NM_175549	ENSMUSG00000052516	Robo2	2600013A04Rik|9430089E08Rik|BB097918|D230004I22Rik|mKIAA1568	roundabout guidance receptor 2	protein-coding
mm_61390.1	chr7	73108266	73108304	+	1	NA	Intergenic	Intergenic	-6217	NR_046024	625243	Mm.261798	NR_046024	ENSMUSG00000108383	Gm6567	-	predicted gene 6567	ncRNA
mm_29467.1	chr3	113593132	113593135	-	1	NA	Intergenic	Lx9|LINE|L1	-15383	NM_001110505	11722	Mm.439727	NM_007446	ENSMUSG00000074264	Amy1	Amy-1|Amy1a|C030014B17Rik	amylase 1, salivary	protein-coding
mm_105875.1	chr11	114923846	114923880	-	1	NA	3' UTR (NM_199221, exon 4 of 4)	3' UTR (NM_199221, exon 4 of 4)	10523	NM_001347651	217304	Mm.185355	NM_199221	ENSMUSG00000063193	Cd300lb	CLM-7|Clm7|Gm253|LMIR5	CD300 molecule like family member B	protein-coding
mm_114946.1	chr13	96565405	96565410	+	1	NA	intron (NM_023420, intron 2 of 17)	intron (NM_023420, intron 2 of 17)	22672	NM_023420	68018	Mm.24125	NM_023420	ENSMUSG00000021669	Col4a3bp	2810404O15Rik|9230101K08Rik|AU016711|CERT|GPBP	collagen, type IV, alpha 3 (Goodpasture antigen) binding protein	protein-coding
mm_17645.1	chr2	31460431	31460446	-	1	NA	Intergenic	Intergenic	-9832	NM_007494	11898	Mm.3217	NM_007494	ENSMUSG00000076441	Ass1	AA408052|ASS|Ass-1|fold	argininosuccinate synthetase 1	protein-coding
mm_90989.1	chr10	13869751	13869781	-	1	NA	promoter-TSS (NM_025446)	promoter-TSS (NM_025446)	-809	NM_001347362	66253	Mm.45755	NM_025446	ENSMUSG00000019806	Aig1	1500031O19Rik|AV064870|AW413422|CGI-103	androgen-induced 1	protein-coding
mm_87429.1	chr10	50819583	50819599	+	1	NA	intron (NM_198007, intron 36 of 41)	Lx7|LINE|L1	-76060	NM_011376	20464	Mm.4774	NM_011376	ENSMUSG00000019913	Sim1	bHLHe14|mSIM1	single-minded homolog 1 (Drosophila)	protein-coding
mm_131711.1	chr16	20867007	20867014	+	1	NA	Intergenic	RMER10A|LTR|ERVL	-132499	NM_009379	21832	Mm.3943	NM_009379	ENSMUSG00000022847	Thpo	Mgdf|Ml|Mpllg|Tpo	thrombopoietin	protein-coding
mm_149708.1	chr19	21653114	21653124	+	1	NA	promoter-TSS (NM_025423)	promoter-TSS (NM_025423)	-190	NM_146096	226016	Mm.28796	NM_146096	ENSMUSG00000047368	Abhd17b	5730446C15Rik|Cgi67|Fam108b|Fam108b1	abhydrolase domain containing 17B	protein-coding
mm_83068.1	chr9	37607657	37607659	-	1	NA	exon (NM_011449, exon 3 of 5)	exon (NM_011449, exon 3 of 5)	6062	NM_011449	20686	Mm.8637	NM_011449	ENSMUSG00000001948	Spa17	Sp17	sperm autoantigenic protein 17	protein-coding
mm_155074.1	chrX	45090921	45090940	+	1	NA	promoter-TSS (NM_026841)	promoter-TSS (NM_026841)	26	NM_026841	68800	Mm.336041	NM_026841	ENSMUSG00000037086	Prr32	1110059M19Rik	proline rich 32	protein-coding
mm_46985.1	chr5	115312899	115312899	-	1	NA	intron (NR_131932, intron 1 of 1)	L2|LINE|L2	11779	NR_131932	102639268	Mm.319998	NR_131932		Gm13830	OTTMUSG00000014646	predicted gene 13830	ncRNA
mm_62791.1	chr7	112679427	112679431	+	1	NA	5' UTR (NM_001166584, exon 1 of 14)	5' UTR (NM_001166584, exon 1 of 14)	109	NM_009346	21676	Mm.24685	NM_009346	ENSMUSG00000055320	Tead1	2610024B07Rik|B230114H05Rik|Gtrgeo5|TEAD-1|TEF-1|Tcf13|mTEF-1	TEA domain family member 1	protein-coding
mm_6484.1	chr1	74108299	74108309	-	1	NA	intron (NM_027884, intron 1 of 34)	intron (NM_027884, intron 1 of 34)	16143	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_139907.1	chr17	70873508	70873554	+	1	NA	Intergenic	Intergenic	-19999	NM_001164074	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_116717.1	chr13	51569438	51569467	-	1	NA	Intergenic	Intergenic	-2368	NM_009167	20418	Mm.131870	NM_009167	ENSMUSG00000021448	Shc3	N-Shc|Rai|ShcC	src homology 2 domain-containing transforming protein C3	protein-coding
mm_105778.1	chr11	109722175	109722186	-	1	NA	promoter-TSS (NM_153782)	promoter-TSS (NM_153782)	76	NM_153782	208659	Mm.208662	NM_153782	ENSMUSG00000020614	Fam20a	AI606893	family with sequence similarity 20, member A	protein-coding
mm_12803.1	chr2	80159135	80159136	+	1	NA	Intergenic	Intergenic	-29723	NM_001159582	18573	Mm.40678	NM_016744	ENSMUSG00000059173	Pde1a	AI987702|AW125737	phosphodiesterase 1A, calmodulin-dependent	protein-coding
mm_32224.1	chr4	101717863	101717873	+	1	NA	5' UTR (NM_001122899, exon 1 of 19)	5' UTR (NM_001122899, exon 1 of 19)	461	NM_010704	16847	Mm.259282	NM_010704	ENSMUSG00000057722	Lepr	LEPROT|Leprb|Modb1|OB-RGRP|Obr|db|diabetes|obese-like|obl	leptin receptor	protein-coding
mm_52820.1	chr6	121356790	121356816	+	1	NA	intron (NM_001347433, intron 6 of 14)	intron (NM_001347433, intron 6 of 14)	10106	NM_133661	14411	Mm.274506	NM_133661	ENSMUSG00000030109	Slc6a12	BGT1|GAT-2|GAT2|Gabt2	solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12	protein-coding
mm_137105.1	chr17	21733705	21733722	+	1	NA	promoter-TSS (NM_001164676)	promoter-TSS (NM_001164676)	-11	NM_001164676	381067	Mm.482723	NM_001164676	ENSMUSG00000061544	Zfp229	-	zinc finger protein 229	protein-coding
mm_143242.1	chr17	63702573	63702573	-	1	NA	Intergenic	Intergenic	-161408	NM_001037997	14158	Mm.23039	NM_008000	ENSMUSG00000000127	Fer	AV082135|C330004K01Rik|Fert|Fert2	fer (fms/fps related) protein kinase	protein-coding
mm_72774.1	chr8	86286959	86286960	+	1	NA	Intergenic	MT2_Mm|LTR|ERVL	279631	NM_172912	244562	Mm.67485	NM_172912	ENSMUSG00000036872	Abcc12	4930467B22Rik|MRP9	ATP-binding cassette, sub-family C (CFTR/MRP), member 12	protein-coding
mm_167574.1	chr9	44379183	44379193	-	1	NA	promoter-TSS (NM_021395)	promoter-TSS (NM_021395)	-302	NM_021395	12282	Mm.116721	NM_021395	ENSMUSG00000032115	Hyou1	AI415631|CBP-140|Cab140|Grp170|Orp150	hypoxia up-regulated 1	protein-coding
mm_11385.1	chr2	31293186	31293194	+	1	NA	3' UTR (NM_019681, exon 8 of 8)	3' UTR (NM_019681, exon 8 of 8)	47267	NM_019681	14299	Mm.249318	NM_019681	ENSMUSG00000062661	Ncs1	9430075O15Rik|A730032G13Rik|AI836659|Freq|Mfreq|NCS-1	neuronal calcium sensor 1	protein-coding
mm_2063.1	chr1	87594546	87594556	+	1	NA	promoter-TSS (NM_015750)	promoter-TSS (NM_015750)	1	NM_015750	23956	Mm.143717	NM_015750	ENSMUSG00000079434	Neu2	MBS|MSS|MTS	neuraminidase 2	protein-coding
mm_170363.1	chr1	85270486	85270493	-	1	NA	promoter-TSS (NM_001037909)	promoter-TSS (NM_001037909)	77	NM_175219	620078	Mm.386456	NM_175219	ENSMUSG00000052477	C130026I21Rik	4930565N07Rik|OTTMUSG00000029174	RIKEN cDNA C130026I21 gene	protein-coding
mm_6727.1	chr1	82587058	82587079	-	1	NA	promoter-TSS (NM_007735)	promoter-TSS (NM_007735)	147	NM_007734	12828	Mm.389135	NM_007734	ENSMUSG00000079465	Col4a3	[a]3(IV)|alpha3(IV)	collagen, type IV, alpha 3	protein-coding
mm_122086.1	chr14	30625034	30625062	-	1	NA	intron (NM_011103, intron 1 of 17)	intron (NM_011103, intron 1 of 17)	1160	NM_011103	18753	Mm.2314	NM_011103	ENSMUSG00000021948	Prkcd	AI385711|D14Ertd420e|PKC[d]|PKCdelta|Pkcd	protein kinase C, delta	protein-coding
mm_518.1	chr1	37491974	37491989	+	1	NA	intron (NM_001290801, intron 3 of 14)	intron (NM_001290801, intron 3 of 14)	-3376	NR_024017	77633	Mm.483177	NR_024017	ENSMUSG00000103948	4930594C11Rik	-	G1 to S phase transition pseudogene	pseudo
mm_60185.1	chr7	43221766	43221768	+	1	NA	intron (NM_001177525, intron 1 of 3)	B1_Mur3|SINE|Alu	7728	NM_001177525	100170401		NM_001177525		EU599041	TU7	expressed sequence EU599041	protein-coding
mm_17121.1	chr2	24608102	24608114	-	1	NA	exon (NM_001042528, exon 45 of 47)	exon (NM_001042528, exon 45 of 47)	-132509	NM_011040	18510	Mm.2533	NM_011040	ENSMUSG00000026976	Pax8	Pax-8	paired box 8	protein-coding
mm_162414.1	chr1	87449284	87449286	+	1	NA	3' UTR (NM_001110212, exon 29 of 29)	3' UTR (NM_001110212, exon 29 of 29)	-20979	NM_028473	73234	Mm.7310	NM_028473	ENSMUSG00000026258	3110079O15Rik	Snorc	RIKEN cDNA 3110079O15 gene	protein-coding
mm_140611.1	chr17	10840107	10840120	-	1	NA	promoter-TSS (NM_016694)	promoter-TSS (NM_016694)	78	NM_027032	69310	Mm.18889	NM_027032	ENSMUSG00000037196	Pacrg	1700008H23Rik	PARK2 co-regulated	protein-coding
mm_4028.1	chr1	165767715	165767770	+	1	NA	intron (NM_011804, intron 1 of 3)	CT-rich|Low_complexity|Low_complexity	3962	NM_011804	433375	Mm.294885	NM_011804	ENSMUSG00000040713	Creg1	AA755314|Creg	cellular repressor of E1A-stimulated genes 1	protein-coding
mm_101040.1	chr11	8605292	8605302	-	1	NA	intron (NM_001083587, intron 2 of 30)	intron (NM_001083587, intron 2 of 30)	59238	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_8705.1	chr1	158828932	158828937	-	1	NA	intron (NM_001085376, intron 11 of 21)	intron (NM_001085376, intron 11 of 21)	128504	NM_001085376	23850	Mm.458621	NM_001085376	ENSMUSG00000073530	Pappa2	PAPP-A2|PLAC3|Pappe	pappalysin 2	protein-coding
mm_114180.1	chr13	55639866	55639892	+	1	NA	exon (NM_001282055, exon 3 of 23)	exon (NM_001282055, exon 3 of 23)	4880	NM_001282055	212880	Mm.202725	NM_145975	ENSMUSG00000021500	Ddx46	2200005K02Rik|8430438J23Rik|AI325430|AI957095|mKIAA0801	DEAD (Asp-Glu-Ala-Asp) box polypeptide 46	protein-coding
mm_155024.1	chrX	42066569	42066589	+	1	NA	Intergenic	Intergenic	-1257	NM_009688	11798	Mm.259879	NM_009688	ENSMUSG00000025860	Xiap	1110015C02Rik|Aipa|Api3|Birc4|IAP3|ILP-1|MIHA	X-linked inhibitor of apoptosis	protein-coding
mm_3462.1	chr1	150104278	150104287	+	1	NA	intron (NM_011198, intron 7 of 9)	intron (NM_011198, intron 7 of 9)	4251	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_32906.1	chr4	119109281	119109330	+	1	NA	intron (NM_011400, intron 1 of 9)	intron (NM_011400, intron 1 of 9)	560	NM_011400	20525	Mm.21002	NM_011400	ENSMUSG00000028645	Slc2a1	Glut-1|Glut1	solute carrier family 2 (facilitated glucose transporter), member 1	protein-coding
mm_86530.1	chr10	7832415	7832454	+	1	NA	promoter-TSS (NM_172785)	promoter-TSS (NM_172785)	-36	NM_172785	237256	Mm.140055	NM_172785	ENSMUSG00000039981	Zc3h12d	D730019B10Rik|TFL	zinc finger CCCH type containing 12D	protein-coding
mm_159728.1	chr5	43602125	43602125	+	1	NA	intron (NM_175425, intron 1 of 2)	intron (NM_175425, intron 1 of 2)	203	NM_175425	109323	Mm.275553	NM_175425	ENSMUSG00000061535	C1qtnf7	5530401N20Rik|8430425G24Rik|Ctrp7	C1q and tumor necrosis factor related protein 7	protein-coding
mm_56542.1	chr6	99726316	99726324	-	1	NA	promoter-TSS (NM_001170419)	promoter-TSS (NM_001170419)	72	NM_001037539	50501	Mm.87365	NM_015768	ENSMUSG00000030069	Prok2	Bv8|PK2|Prok1	prokineticin 2	protein-coding
mm_148590.1	chr19	5069265	5069286	+	1	NA	exon (NM_054042, exon 1 of 1)	exon (NM_054042, exon 1 of 1)	1197	NM_054042	70445	Mm.29597	NM_054042	ENSMUSG00000056481	Cd248	2610111G01Rik|AI842296|Cd164l1|Tem1	CD248 antigen, endosialin	protein-coding
mm_50185.1	chr6	41641736	41641753	+	1	NA	Intergenic	Intergenic	-5339	NM_022413	64177	Mm.296889	NM_022413	ENSMUSG00000029868	Trpv6	CAT|CaT1|Cac|Ecac2|Otrpc3	transient receptor potential cation channel, subfamily V, member 6	protein-coding
mm_110793.1	chr12	72085370	72085389	-	1	NA	promoter-TSS (NM_024205)	promoter-TSS (NM_024205)	-66	NM_026038	67217	Mm.286120	NM_026038	ENSMUSG00000019718	L3hypdh	2810055F11Rik	L-3-hydroxyproline dehydratase (trans-)	protein-coding
mm_143609.1	chr17	78684263	78684268	-	1	NA	exon (NM_011500, exon 5 of 18)	exon (NM_011500, exon 5 of 18)	52295	NM_011500	268980	Mm.311915	NM_011500	ENSMUSG00000024077	Strn	AU022939|D130055P19	striatin, calmodulin binding protein	protein-coding
mm_68697.1	chr7	119620340	119620362	-	1	NA	intron (NM_054094, intron 1 of 13)	MIR|SINE|MIR	2523	NM_054094	117147	Mm.427560	NM_054094	ENSMUSG00000033533	Acsm1	Acas3|Bucs1|Macs	acyl-CoA synthetase medium-chain family member 1	protein-coding
mm_163967.1	chr14	54966636	54966650	-	1	NA	promoter-TSS (NM_010856)	promoter-TSS (NM_010856)	-36	NM_010856	17888	Mm.290003	NM_010856	ENSMUSG00000040752	Myh6	A830009F23Rik|AA517445|Myhc-a|Myhca|alpha-MHC	myosin, heavy polypeptide 6, cardiac muscle, alpha	protein-coding
mm_153800.1	chr19	46039538	46039601	-	1	NA	promoter-TSS (NM_010697)	promoter-TSS (NM_010697)	52	NM_010697	16825	Mm.327442	NM_010697	ENSMUSG00000025223	Ldb1	CLIM2|NLI	LIM domain binding 1	protein-coding
mm_50454.1	chr6	48906535	48906546	+	1	NA	exon (NM_001161622, exon 2 of 5)	exon (NM_001161622, exon 2 of 5)	1554	NM_001161621	76507	Mm.213898	NM_029638	ENSMUSG00000029811	Aoc1	1600012D06Rik|Abp1|DAO	amine oxidase, copper-containing 1	protein-coding
mm_2212.1	chr1	89738207	89738230	+	1	NA	intron (NM_001037136, intron 10 of 16)	intron (NM_001037136, intron 10 of 16)	-54326	NR_015540	74403	Mm.444291	NR_015540		4933400F21Rik	1700091C04Rik|4930565K10Rik	RIKEN cDNA 4933400F21 gene	ncRNA
mm_140752.1	chr17	17196112	17196115	-	1	NA	Intergenic	LTRIS2|LTR|ERV1	74730	NM_011765	22759	Mm.436633	NM_011765	ENSMUSG00000095990	Zfp97	NGD16-4	zinc finger protein 97	protein-coding
mm_103509.1	chr11	76622216	76622260	-	1	NA	Intergenic	CpG	-44499	NM_198894	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_55384.1	chr6	59016834	59016878	-	1	NA	intron (NM_153574, intron 1 of 17)	intron (NM_153574, intron 1 of 17)	7646	NM_153574	58909	Mm.28813	NM_153574	ENSMUSG00000037709	Fam13a	AI462012|D430015B01Rik|FAM13A1|Precm1	family with sequence similarity 13, member A	protein-coding
mm_89098.1	chr10	84534177	84534215	+	1	NA	promoter-TSS (NM_175451)	promoter-TSS (NM_175451)	-308	NM_175451	216197	Mm.334999	NM_175451	ENSMUSG00000046841	Ckap4	5630400A09Rik|CLIMP-63|P63	cytoskeleton-associated protein 4	protein-coding
mm_36064.1	chr4	57916225	57916242	-	1	NA	promoter-TSS (NM_178727)	promoter-TSS (NM_178727)	31	NM_178727	242484	Mm.23214	NM_178727	ENSMUSG00000052117	D630039A03Rik	-	RIKEN cDNA D630039A03 gene	protein-coding
mm_97286.1	chr11	76202052	76202079	+	1	NA	promoter-TSS (NM_027773)	promoter-TSS (NM_027773)	9	NM_027773	116972	Mm.188413	NM_027773	ENSMUSG00000069808	Fam57a	2310047D13Rik|4932415L08Rik|5430402E13Rik|5430420K21Rik|Wdt3	family with sequence similarity 57, member A	protein-coding
mm_94564.1	chr11	11685676	11685742	+	1	NA	promoter-TSS (NM_009578)	promoter-TSS (NM_009578)	-216	NM_009578	22778	Mm.103545	NM_009578	ENSMUSG00000018654	Ikzf1	5832432G11Rik|Ikaros|LyF-1|Zfpn1a1|Znfn1a1|hlk-1|mKIAA4227	IKAROS family zinc finger 1	protein-coding
mm_96588.1	chr11	69089957	69089997	+	1	NA	exon (NM_009497, exon 4 of 5)	exon (NM_009497, exon 4 of 5)	1449	NM_009497	22318	Mm.28643	NM_009497	ENSMUSG00000020894	Vamp2	Syb-2|Syb2|sybII	vesicle-associated membrane protein 2	protein-coding
mm_38778.1	chr4	148068535	148068537	-	1	NA	Intergenic	Intergenic	19528	NM_009642	11610	Mm.46247	NM_009642	ENSMUSG00000029007	Agtrap	3300002E14Rik|AT1R|Atrap|D4Wsu124e	angiotensin II, type I receptor-associated protein	protein-coding
mm_80431.1	chr9	77921909	77921919	+	1	NA	intron (NM_134255, intron 1 of 7)	intron (NM_134255, intron 1 of 7)	4549	NM_134255	68801	Mm.430736	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	ELOVL family member 5, elongation of long chain fatty acids (yeast)	protein-coding
mm_102916.1	chr11	69581194	69581212	-	1	NA	intron (NM_001127233, intron 1 of 10)	intron (NM_001127233, intron 1 of 10)	844	NM_001127233	22059	Mm.222	NM_011640	ENSMUSG00000059552	Trp53	Tp53|bbl|bfy|bhy|p44|p53	transformation related protein 53	protein-coding
mm_109695.1	chr12	113152044	113152057	+	1	NA	promoter-TSS (NM_007763)	promoter-TSS (NM_007763)	38	NM_007763	12925	Mm.272368	NM_007763	ENSMUSG00000006360	Crip1	CRHP|CRP1|Crip	cysteine-rich protein 1 (intestinal)	protein-coding
mm_128226.1	chr15	36555537	36555539	-	1	NA	promoter-TSS (NM_025712)	promoter-TSS (NM_025712)	30	NM_001347022	66696	Mm.253627	NM_025712	ENSMUSG00000013611	Snx31	4631426E05Rik	sorting nexin 31	protein-coding
mm_15091.1	chr2	153278658	153278695	+	1	NA	Intergenic	Intergenic	-12740	NM_008444	16569	Mm.315560	NM_008444	ENSMUSG00000027475	Kif3b	AI854312|AW549267|mKIAA0359	kinesin family member 3B	protein-coding
mm_158354.1	chrX	134589997	134590008	-	1	NA	exon (NM_013463, exon 7 of 7)	exon (NM_013463, exon 7 of 7)	4348	NM_019865	19982	Mm.286408	NM_019865	ENSMUSG00000079435	Rpl36a	L44L|Rpl44	ribosomal protein L36A	protein-coding
mm_132700.1	chr16	43363725	43363729	+	1	NA	intron (NM_181058, intron 2 of 6)	intron (NM_181058, intron 2 of 6)	56469	NR_046026	626693	Mm.447083	NR_046026	ENSMUSG00000085499	Gm15713	OTTMUSG00000025617	predicted gene 15713	ncRNA
mm_159903.1	chr6	40491050	40491050	+	1	NA	promoter-TSS (NM_001025385)	promoter-TSS (NM_001025385)	-188	NM_001025385	574417	Mm.386354	NM_001025385	ENSMUSG00000052850	Tas2r137	T2R37|Tas2r3|mt2r41	taste receptor, type 2, member 137	protein-coding
mm_144881.1	chr18	36795103	36795128	+	1	NA	exon (NM_025594, exon 3 of 6)	exon (NM_025594, exon 3 of 6)	1192	NM_025594	66492	Mm.251155	NM_025594	ENSMUSG00000001383	Zmat2	2610510D14Rik|2900082I05Rik	zinc finger, matrin type 2	protein-coding
mm_46335.1	chr5	101835606	101835610	-	1	NA	3' UTR (NM_172882, exon 67 of 67)	3' UTR (NM_172882, exon 67 of 67)	70478	NM_173370	74596	Mm.46764	NM_173370	ENSMUSG00000029330	Cds1	4833409J18Rik|AI314024|AW125888	CDP-diacylglycerol synthase 1	protein-coding
mm_137788.1	chr17	29614801	29614844	+	1	NA	promoter-TSS (NM_021419)	promoter-TSS (NM_021419)	33	NM_021419	58230	Mm.305994	NM_021419	ENSMUSG00000090083	Rnf8	3830404E21Rik|AIP37|laXp180	ring finger protein 8	protein-coding
mm_95040.1	chr11	32276594	32276609	+	1	NA	promoter-TSS (NM_010405)	promoter-TSS (NM_010405)	1	NM_010405	15126	Mm.141758	NM_010405	ENSMUSG00000055609	Hba-x	AI450015|Hbz	hemoglobin X, alpha-like embryonic chain in Hba complex	protein-coding
mm_173323.1	chrY	90737038	90737040	+	1	NA	Intergenic	(TTAGGG)n|Simple_repeat|Simple_repeat	18011	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_55437.1	chr6	67029825	67029838	-	1	NA	Intergenic	Intergenic	-6768	NR_040278	320172	Mm.449039	NR_040278	ENSMUSG00000087231	E230016M11Rik	-	RIKEN cDNA E230016M11 gene	ncRNA
mm_153458.1	chr19	41214536	41214559	-	1	NA	3' UTR (NM_133352, exon 15 of 15)	3' UTR (NM_133352, exon 15 of 15)	-7773	NM_011904	24087	Mm.89983	NM_011904	ENSMUSG00000025013	Tll2	-	tolloid-like 2	protein-coding
mm_68020.1	chr7	100964307	100964341	-	1	NA	promoter-TSS (NM_183168)	promoter-TSS (NM_183168)	42	NM_183168	233571	Mm.235193	NM_183168	ENSMUSG00000048779	P2ry6	2010204J23Rik|P2Y6	pyrimidinergic receptor P2Y, G-protein coupled, 6	protein-coding
mm_164305.1	chr15	103897429	103897445	+	1	NA	exon (NM_009267, exon 3 of 4)	exon (NM_009267, exon 3 of 4)	1863	NM_009268	20771	Mm.30276	NM_009268		Mucl1	Spt-2|Spt2	mucin-like 1	protein-coding
mm_64501.1	chr7	143475202	143475207	+	1	NA	promoter-TSS (NM_001042760)	promoter-TSS (NM_001042760)	88	NM_001042760	18400	Mm.271740	NM_008767	ENSMUSG00000000154	Slc22a18	AW260131|BWR1A|BWSCR1A|HET|ITM|Impt1|Orctl2|Slc22a1l|TSSC5|p45-BWR1A	solute carrier family 22 (organic cation transporter), member 18	protein-coding
mm_64283.1	chr7	141839066	141839082	+	1	NA	promoter-TSS (NM_028801)	promoter-TSS (NM_028801)	2	NM_028801	74180	Mm.200752	NM_028801	ENSMUSG00000066108	Muc5b	2300002I04Rik|A130042M24|AV085033|MUC5|MUC9|mucin 5b	mucin 5, subtype B, tracheobronchial	protein-coding
mm_151307.1	chr19	55743101	55743135	+	1	NA	exon (NM_001142918, exon 3 of 15)	exon (NM_001142918, exon 3 of 15)	1308	NM_001142923	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_32107.1	chr4	98922929	98922937	+	1	NA	promoter-TSS (NM_146144)	promoter-TSS (NM_146144)	-877	NM_001301414	230484	Mm.371692	NM_146144	ENSMUSG00000028560	Usp1	-	ubiquitin specific peptidase 1	protein-coding
mm_95357.1	chr11	48838673	48838714	+	1	NA	intron (NM_001347446, intron 1 of 6)	intron (NM_001347446, intron 1 of 6)	688	NM_001347436	94089	Mm.390335	NM_053166	ENSMUSG00000040350	Trim7	AI790312	tripartite motif-containing 7	protein-coding
mm_46913.1	chr5	114380489	114380497	-	1	NA	promoter-TSS (NM_001159941)	promoter-TSS (NM_001159941)	12	NM_001159941	330171	Mm.238285	NM_026145	ENSMUSG00000001098	Kctd10	AW536343|C87062|mBACURD3	potassium channel tetramerisation domain containing 10	protein-coding
mm_665.1	chr1	40444875	40444883	+	1	NA	intron (NM_001025602, intron 6 of 10)	intron (NM_001025602, intron 6 of 10)	5250	NM_010743	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_139905.1	chr17	70870747	70870760	+	1	NA	Intergenic	Intergenic	-17221	NM_001164074	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_107528.1	chr12	40480758	40480774	+	1	NA	intron (NM_172803, intron 1 of 52)	(T)n|Simple_repeat|Simple_repeat	34713	NM_172803	238130	Mm.341423	NM_172803	ENSMUSG00000035954	Dock4	5330406C03|6330411N01Rik|AF263288|C030023J22|mKIAA0716	dedicator of cytokinesis 4	protein-coding
mm_72617.1	chr8	84636341	84636390	+	1	NA	intron (NM_001252059, intron 43 of 45)	intron (NM_001252059, intron 43 of 45)	26487	NM_010499	15936	Mm.399	NM_010499	ENSMUSG00000053560	Ier2	AI317238|Ch1|Pip92	immediate early response 2	protein-coding
mm_134207.1	chr16	11155097	11155115	-	1	NA	intron (NM_145931, intron 9 of 22)	B4|SINE|B4	-20574	NM_029582	106200	Mm.291015	NM_029582	ENSMUSG00000022498	Txndc11	2810408E11Rik|AI427833|EFP1|Txdc11	thioredoxin domain containing 11	protein-coding
mm_43586.1	chr5	137747609	137747642	+	1	NA	exon (NM_023910, exon 2 of 5)	exon (NM_023910, exon 2 of 5)	1656	NM_029805	78829	Mm.286399	NM_023910	ENSMUSG00000029723	Tsc22d4	0610009M14Rik|1700023B23Rik|AI415410|Thg-1pit|Tilz2	TSC22 domain family, member 4	protein-coding
mm_58086.1	chr6	136967626	136967666	-	1	NA	Intergenic	Intergenic	13123	NM_023898	78600	Mm.290622	NM_023898	ENSMUSG00000064330	Pde6h	A930033D18Rik|PDEgamma	phosphodiesterase 6H, cGMP-specific, cone, gamma	protein-coding
mm_127614.1	chr15	102460367	102460381	+	1	NA	exon (NM_025385, exon 4 of 5)	exon (NM_025385, exon 4 of 5)	1204	NM_025385	66151	Mm.393955	NM_025385	ENSMUSG00000023048	Prr13	1110020C13Rik|2010324E22Rik	proline rich 13	protein-coding
mm_69027.1	chr7	126795702	126795728	-	1	NA	exon (NM_001177307, exon 9 of 10)	exon (NM_001177307, exon 9 of 10)	-3244	NM_019674	56420	Mm.41998	NM_019674	ENSMUSG00000030697	Ppp4c	1110002D08Rik|AU016079|Ppx	protein phosphatase 4, catalytic subunit	protein-coding
mm_66690.1	chr7	45870965	45870986	-	1	NA	Intergenic	Intergenic	-1865	NM_133950	68137	Mm.298433	NM_133950	ENSMUSG00000002778	Kdelr1	8030486F04Rik|AW215843|Erd2.1	KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 1	protein-coding
mm_149840.1	chr19	25004644	25004674	+	1	NA	intron (NM_028785, intron 1 of 47)	Lx8|LINE|L1	5130	NM_028785	76088	Mm.102485	NM_028785	ENSMUSG00000052085	Dock8	1200017A24Rik|5830472H07Rik|A130095G14Rik|AI461977	dedicator of cytokinesis 8	protein-coding
mm_117712.1	chr13	95223452	95223466	-	1	NA	promoter-TSS (NM_001170669)	promoter-TSS (NM_001170669)	-409	NM_001170669	218461	Mm.100167	NM_172263	ENSMUSG00000021684	Pde8b	B230331L10Rik|C030047E14Rik	phosphodiesterase 8B	protein-coding
mm_85808.1	chr9	110330543	110330561	-	1	NA	Intergenic	Intergenic	-2736	NM_001103162	235623	Mm.288741	NM_001001144	ENSMUSG00000032485	Scap	9530044G19|mKIAA0199	SREBF chaperone	protein-coding
mm_10767.1	chr2	24186771	24186793	+	1	NA	intron (NM_153511, intron 1 of 4)	intron (NM_153511, intron 1 of 4)	306	NM_153511	215257	Mm.249379	NM_153511	ENSMUSG00000044103	Il1f9	Il36g	interleukin 1 family, member 9	protein-coding
mm_50844.1	chr6	54824786	54824802	+	1	NA	intron (NM_199143, intron 1 of 4)	ORR1A0|LTR|ERVL-MaLR	7878	NM_199143	387524	Mm.286149	NM_199143	ENSMUSG00000058446	Znrf2	1190002C14Rik|AU044205|D6Ertd365e	zinc and ring finger 2	protein-coding
mm_172691.1	chr8	60056727	60056727	+	1	NA	Intergenic	L1Md_T|LINE|L1	231078	NR_126087	75017	Mm.60775	NR_126087	ENSMUSG00000110406	4930470O06Rik	-	RIKEN cDNA 4930470O06 gene	ncRNA
mm_8941.1	chr1	164437945	164437958	-	1	NA	TTS (NM_001293313)	TTS (NM_001293313)	20404	NM_009721	11931	Mm.4550	NM_009721	ENSMUSG00000026576	Atp1b1	Atp4b|Atpb|Atpb-1|NKbeta1	ATPase, Na+/K+ transporting, beta 1 polypeptide	protein-coding
mm_35414.1	chr4	34882920	34882964	-	1	NA	promoter-TSS (NM_013889)	promoter-TSS (NM_013889)	6	NM_013889	30046	Mm.38193	NM_013889	ENSMUSG00000039967	Zfp292	5730450D02Rik|5830493J20Rik|9430062L07Rik|AI449016|Krox-10|Zfp-15|Zfp15|Zn-15|Zn-16|mKIAA0530	zinc finger protein 292	protein-coding
mm_8477.1	chr1	153487672	153487681	-	1	NA	promoter-TSS (NM_007842)	promoter-TSS (NM_007842)	-16	NM_007842	13211	Mm.20000	NM_007842	ENSMUSG00000042699	Dhx9	AI326842|Ddx9|HEL-5|NDHII|RHA|mHEL-5	DEAH (Asp-Glu-Ala-His) box polypeptide 9	protein-coding
mm_170599.1	chr19	5802424	5802427	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	247	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_122922.1	chr14	54960879	54960885	-	1	NA	intron (NM_001164171, intron 12 of 38)	intron (NM_001164171, intron 12 of 38)	5725	NM_001164171	17888	Mm.290003	NM_010856	ENSMUSG00000040752	Myh6	A830009F23Rik|AA517445|Myhc-a|Myhca|alpha-MHC	myosin, heavy polypeptide 6, cardiac muscle, alpha	protein-coding
mm_51157.1	chr6	70722550	70722571	+	1	NA	Intergenic	Intergenic	69615	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_7393.1	chr1	111881335	111881335	-	1	NA	Intergenic	Intergenic	-16417	NM_001081316	319901	Mm.103468	NM_001081316	ENSMUSG00000038702	Dsel	9330132E09Rik|DS-epi2	dermatan sulfate epimerase-like	protein-coding
mm_77163.1	chr8	111688541	111688543	-	1	NA	intron (NM_025583, intron 5 of 6)	intron (NM_025583, intron 5 of 6)	1132	NR_106044	102466993		NR_106044	ENSMUSG00000099129	Mir7076	Gm27318|mmu-mir-7076	microRNA 7076	ncRNA
mm_163915.1	chr14	35568496	35568499	+	1	NA	intron (NM_008166, intron 14 of 15)	intron (NM_008166, intron 14 of 15)	243481	NM_001033766	239036	Mm.239970	NM_001033766	ENSMUSG00000041068	4930596D02Rik	-	RIKEN cDNA 4930596D02 gene	protein-coding
mm_114958.1	chr13	97071332	97071356	+	1	NA	promoter-TSS (NM_001100458)	promoter-TSS (NM_001100458)	-299	NM_001100458	320557	Mm.458280	NM_001100458	ENSMUSG00000041817	Fam169a	B230112C05Rik|SLAP75	family with sequence similarity 169, member A	protein-coding
mm_141764.1	chr17	34269408	34269410	-	1	NA	TTS (NM_207105)	TTS (NM_207105)	6182	NM_207105	14961	Mm.254067	NM_207105	ENSMUSG00000073421	H2-Ab1	AI845868|Abeta|H-2Ab|H2-Ab|I-Abeta|IAb|Ia-2|Ia2|Rmcs1	histocompatibility 2, class II antigen A, beta 1	protein-coding
mm_96686.1	chr11	69586021	69586052	+	1	NA	intron (NM_001127233, intron 1 of 10)	intron (NM_001127233, intron 1 of 10)	5677	NM_001127233	22059	Mm.222	NM_011640	ENSMUSG00000059552	Trp53	Tp53|bbl|bfy|bhy|p44|p53	transformation related protein 53	protein-coding
mm_110187.1	chr12	27339184	27339220	-	1	NA	3' UTR (NM_009234, exon 1 of 1)	3' UTR (NM_009234, exon 1 of 1)	3516	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding
mm_72519.1	chr8	83955704	83955721	+	1	NA	promoter-TSS (NM_024184)	promoter-TSS (NM_024184)	18	NM_024184	66929	Mm.29680	NM_024184	ENSMUSG00000005470	Asf1b	1700003K02Rik|AA409591	anti-silencing function 1B histone chaperone	protein-coding
mm_93562.1	chr10	116517968	116517971	-	1	NA	intron (NM_028082, intron 2 of 14)	intron (NM_028082, intron 2 of 14)	-44446	NM_021452	58802	Mm.440652	NM_021452	ENSMUSG00000054934	Kcnmb4	1700058G18Rik|2900045G12Rik	potassium large conductance calcium-activated channel, subfamily M, beta member 4	protein-coding
mm_134256.1	chr16	13730684	13730696	-	1	NA	promoter-TSS (NM_011987)	promoter-TSS (NM_011987)	-206	NM_011987	26565	Mm.4214	NM_011987	ENSMUSG00000022683	Pla2g10	GX sPLA2|PLA2GX|sPLA2-X	phospholipase A2, group X	protein-coding
mm_8070.1	chr1	135495525	135495527	-	1	NA	intron (NM_173437, intron 3 of 28)	intron (NM_173437, intron 3 of 28)	-40843	NR_049188	100885827		NR_049188	ENSMUSG00000093515	Mir1231	Gm23720|mir-1231|mmu-mir-1231	microRNA 1231	ncRNA
mm_88516.1	chr10	78049935	78049962	+	1	NA	promoter-TSS (NM_001284197)	promoter-TSS (NM_001284197)	-11	NM_001284197	54427	Mm.13433	NM_019448	ENSMUSG00000000730	Dnmt3l	D6Ertd14e|ecat7	DNA (cytosine-5-)-methyltransferase 3-like	protein-coding
mm_171704.1	chr4	74643780	74643780	-	1	NA	Intergenic	L1Md_A|LINE|L1	391901	NM_144787	76804	Mm.209059	NM_144787	ENSMUSG00000028397	Kdm4c	2410141F18Rik|AA517467|Gasc1|Jmjd2c	lysine (K)-specific demethylase 4C	protein-coding
mm_31291.1	chr4	45972236	45972245	+	1	NA	promoter-TSS (NM_146142)	promoter-TSS (NM_146142)	-57	NM_146142	100121	Mm.275413	NM_146142	ENSMUSG00000035517	Tdrd7	5730495N10Rik|AI447470|PCTAIRE2BP	tudor domain containing 7	protein-coding
mm_89292.1	chr10	87906922	87906935	+	1	NA	intron (NM_001314010, intron 3 of 4)	intron (NM_001314010, intron 3 of 4)	45817	NM_001111276	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_35183.1	chr4	15958314	15958325	-	1	NA	intron (NM_013752, intron 1 of 15)	CpG	352	NM_013752	27354	Mm.20866	NM_013752	ENSMUSG00000028224	Nbn	Nbs1	nibrin	protein-coding
mm_58413.1	chr7	3289516	3289517	+	1	NA	intron (NM_001093764, intron 1 of 2)	intron (NM_001093764, intron 1 of 2)	478	NM_001093764	50918	Mm.29874	NM_016969	ENSMUSG00000068566	Myadm	D7Wsu62e	myeloid-associated differentiation marker	protein-coding
mm_133585.1	chr16	91420860	91420941	+	1	NA	intron (NM_008349, intron 5 of 6)	intron (NM_008349, intron 5 of 6)	14665	NM_008349	16155	Mm.4154	NM_008349	ENSMUSG00000022969	Il10rb	6620401D04Rik|AI528744|CRF2-4|Crfb4|D16H21S58|D21S58h|IL-10R2|Il10r2	interleukin 10 receptor, beta	protein-coding
mm_90952.1	chr10	13192731	13192800	-	1	NA	intron (NM_181470, intron 1 of 10)	intron (NM_181470, intron 1 of 10)	372	NM_181470	353258	Mm.117581	NM_181470	ENSMUSG00000019814	Ltv1	2610020N02Rik	LTV1 ribosome biogenesis factor	protein-coding
mm_140959.1	chr17	24640703	24640736	-	1	NA	intron (NM_023449, intron 4 of 5)	(CACG)n|Simple_repeat|Simple_repeat	4238	NM_023449	65962	Mm.21587	NM_023055	ENSMUSG00000002504	Slc9a3r2	0610011L07Rik|1200011K07Rik|2010007A20Rik|E3karp|NHERF-2|Nherf2|Octs2|Sip-1|Sip1|Sryip1|Tka-1	solute carrier family 9 (sodium/hydrogen exchanger), member 3 regulator 2	protein-coding
mm_67244.1	chr7	75309131	75309153	-	1	NA	promoter-TSS (NM_001109753)	promoter-TSS (NM_001109753)	120	NM_153579	64176	Mm.273082	NM_153579	ENSMUSG00000053025	Sv2b	A830038F04Rik|AI850768|mKIAA0735	synaptic vesicle glycoprotein 2 b	protein-coding
mm_20604.1	chr2	131443448	131443458	-	1	NA	intron (NR_037281, intron 1 of 2)	RMER15|LTR|ERVL	-48409	NM_001177834	228608	Mm.136586	NM_145533	ENSMUSG00000027333	Smox	B130066H01Rik|PAO|PAOh1|SMO	spermine oxidase	protein-coding
mm_55559.1	chr6	71341231	71341268	-	1	NA	Intergenic	Intergenic	18437	NM_009858	12526	Mm.333148	NM_009858	ENSMUSG00000053044	Cd8b1	Cd8b|Ly-3|Ly-C|Lyt-3	CD8 antigen, beta chain 1	protein-coding
mm_137111.1	chr17	22081226	22081252	+	1	NA	Intergenic	CpG	84738	NM_177596	210853	Mm.441622	NM_177596	ENSMUSG00000063383	Zfp947	6720451E15|EG210853|Gm4769	zinc finger protein 947	protein-coding
mm_122530.1	chr14	47381661	47381692	-	1	NA	exon (NM_010705, exon 4 of 6)	exon (NM_010705, exon 4 of 6)	7816	NM_001145953	16854	Mm.248615	NM_010705	ENSMUSG00000050335	Lgals3	GBP|L-34|Mac-2|gal3	lectin, galactose binding, soluble 3	protein-coding
mm_153644.1	chr19	44231665	44231697	-	1	NA	intron (NM_024450, intron 2 of 5)	RLTR19A|LTR|ERVK	28393	NM_024450	30049	Mm.480594	NM_024450	ENSMUSG00000025202	Scd3	4930513N16Rik	stearoyl-coenzyme A desaturase 3	protein-coding
mm_10022.1	chr1	192092367	192092375	-	1	NA	5' UTR (NM_011633, exon 1 of 10)	5' UTR (NM_011633, exon 1 of 10)	228	NM_011633	22033	Mm.380491	NM_011633		Traf5	-	TNF receptor-associated factor 5	protein-coding
mm_25706.1	chr3	122504660	122504666	+	1	NA	intron (NM_013867, intron 3 of 11)	intron (NM_013867, intron 3 of 11)	37018	NR_106117	102465764		NR_106117	ENSMUSG00000104773	Mir7657	mmu-mir-7657	microRNA 7657	ncRNA
mm_116233.1	chr13	33566243	33566252	-	1	NA	intron (NR_131140, intron 1 of 2)	RMER17D|LTR|ERVK	2622	NR_131140	619715	Mm.390575	NR_131140		Gm6093	EG619715	predicted gene 6093	ncRNA
mm_52656.1	chr6	117863070	117863103	+	1	NA	promoter-TSS (NM_008616)	promoter-TSS (NM_008616)	9	NM_001001792	22685	Mm.249661	NM_008616	ENSMUSG00000042097	Zfp239	Mok-2|Mok2|Znf239	zinc finger protein 239	protein-coding
mm_168969.1	chr1	28288819	28288838	+	1	NA	Intergenic	L1Md_T|LINE|L1	491424	NM_001013750	210962	Mm.214178	NM_001013750	ENSMUSG00000048411	Gm597	-	predicted gene 597	protein-coding
mm_41043.1	chr5	86091317	86091356	+	1	NA	intron (NM_001310639, intron 5 of 7)	intron (NM_001310639, intron 5 of 7)	19590	NM_001310639	56792	Mm.131237	NM_019992	ENSMUSG00000029254	Stap1	AI586015|Brdg1|STAP-1	signal transducing adaptor family member 1	protein-coding
mm_87828.1	chr10	60358097	60358121	+	1	NA	exon (NM_001159572, exon 2 of 7)	exon (NM_001159572, exon 2 of 7)	11258	NM_028732	74048	Mm.273584	NM_028732	ENSMUSG00000020101	Vsir	4632428N05Rik|Dies1|PD-1H|VISTA	V-set immunoregulatory receptor	protein-coding
mm_125817.1	chr15	74955612	74955629	+	1	NA	5' UTR (NM_001164036, exon 1 of 4)	5' UTR (NM_001164036, exon 1 of 4)	514	NM_001164040	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_3821.1	chr1	159268518	159268521	+	1	NA	intron (NM_011931, intron 8 of 19)	intron (NM_011931, intron 8 of 19)	-25254	NR_144489	100846986		NR_144489		Pou5f1-rs1	Gm21053|Oct4P2|Otf-3rs|Otf3-rs1|Otf3a	POU domain, class 5, transcription factor 1, related sequence 1	pseudo
mm_76910.1	chr8	105901154	105901192	-	1	NA	intron (NM_173432, intron 1 of 2)	intron (NM_173432, intron 1 of 2)	699	NM_173432	244631	Mm.27627	NM_173432	ENSMUSG00000048310	Pskh1	AW539964|E130013P03Rik|b2b1230Clo	protein serine kinase H1	protein-coding
mm_114068.1	chr13	54382085	54382095	+	1	NA	3' UTR (NM_009946, exon 4 of 4)	3' UTR (NM_009946, exon 4 of 4)	10741	NM_009946	12890	Mm.268902	NM_009946	ENSMUSG00000025867	Cplx2	921-L|AI413745|AW492120	complexin 2	protein-coding
mm_144030.1	chr17	90037189	90037204	-	1	NA	exon (NM_001347419, exon 3 of 3)	exon (NM_001347419, exon 3 of 3)	51172	NM_001346962	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_100215.1	chr11	116918902	116918908	+	1	NA	promoter-TSS (NM_172948)	promoter-TSS (NM_172948)	42	NM_172948	268510	Mm.35141	NM_172948	ENSMUSG00000043857	Mgat5b	C330018B01|GnT-IX|mGnTVB	mannoside acetylglucosaminyltransferase 5, isoenzyme B	protein-coding
mm_90665.1	chr10	128821746	128821773	+	1	NA	promoter-TSS (NM_024180)	promoter-TSS (NM_024180)	-12	NM_025364	66118	Mm.235562	NM_025364	ENSMUSG00000078427	Sarnp	1110005A23Rik|Cip29	SAP domain containing ribonucleoprotein	protein-coding
mm_106839.1	chr12	8006717	8006736	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	29049	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_52554.1	chr6	115995124	115995158	+	1	NA	promoter-TSS (NM_026376)	promoter-TSS (NM_026376)	-136	NM_026376	67784	Mm.3085	NM_026376	ENSMUSG00000030123	Plxnd1	6230425C21Rik|b2b1863Clo|b2b553Clo	plexin D1	protein-coding
mm_53895.1	chr6	3399302	3399315	-	1	NA	5' UTR (NM_010156, exon 1 of 2)	5' UTR (NM_010156, exon 1 of 2)	263	NM_010156	209086	Mm.196013	NM_010156	ENSMUSG00000047735	Samd9l	AA175286|ESTM25|mKIAA2005	sterile alpha motif domain containing 9-like	protein-coding
mm_112120.1	chr12	112860238	112860245	-	1	NA	intron (NM_019925, intron 1 of 2)	intron (NM_019925, intron 1 of 2)	675	NM_019925	56696	Mm.20455	NM_019925	ENSMUSG00000021298	Gpr132	G2a	G protein-coupled receptor 132	protein-coding
mm_116937.1	chr13	55904920	55904920	-	1	NA	Intergenic	Intergenic	-73495	NM_011097	18740	Mm.135195	NM_011097	ENSMUSG00000021506	Pitx1	Bft|P-OTX|Potx|Ptx1	paired-like homeodomain transcription factor 1	protein-coding
mm_145694.1	chr18	62182927	62182972	+	1	NA	Intergenic	Intergenic	-2968	NM_007420	11555	Mm.5598	NM_007420	ENSMUSG00000045730	Adrb2	Adrb-2|Badm|Gpcr7	adrenergic receptor, beta 2	protein-coding
mm_130625.1	chr15	100410160	100410167	-	1	NA	exon (NM_001146161, exon 3 of 16)	exon (NM_001146161, exon 3 of 16)	12892	NM_001146161	18174	Mm.234608	NM_008732	ENSMUSG00000023030	Slc11a2	DCT1|DMT1|Nramp2|mk|van	solute carrier family 11 (proton-coupled divalent metal ion transporters), member 2	protein-coding
mm_56389.1	chr6	94698857	94698859	-	1	NA	intron (NM_008377, intron 1 of 18)	intron (NM_008377, intron 1 of 18)	1287	NM_008377	16206	Mm.245210	NM_008377	ENSMUSG00000030029	Lrig1	D6Bwg0781e|Img|LIG-1	leucine-rich repeats and immunoglobulin-like domains 1	protein-coding
mm_57985.1	chr6	136003416	136003426	-	1	NA	intron (NM_008171, intron 4 of 14)	intron (NM_008171, intron 4 of 14)	170090	NM_008171	14812	Mm.436649	NM_008171	ENSMUSG00000030209	Grin2b	AW490526|GluN2B|NR2B|Nmdar2b	glutamate receptor, ionotropic, NMDA2B (epsilon 2)	protein-coding
mm_99356.1	chr11	101588907	101588924	+	1	NA	exon (NM_144830, exon 6 of 9)	exon (NM_144830, exon 6 of 9)	6673	NM_144830	217203	Mm.280559	NM_144830	ENSMUSG00000034947	Tmem106a	0610008L10Rik|AI043106|BC022145	transmembrane protein 106A	protein-coding
mm_24458.1	chr3	90614347	90614357	+	1	NA	TTS (NM_011313)	TTS (NM_011313)	1458	NM_011313	20200	Mm.100144	NM_011313	ENSMUSG00000001025	S100a6	2A9|5B10|CALCYCLIN|Cacy|PRA	S100 calcium binding protein A6 (calcyclin)	protein-coding
mm_76479.1	chr8	85548683	85548700	-	1	NA	exon (NM_019794, exon 5 of 9)	exon (NM_019794, exon 5 of 9)	6580	NM_019794	56445	Mm.475573	NM_019794	ENSMUSG00000031701	Dnaja2	1500017M13Rik|2010206B19Rik|DNAJ|DNJ3|Dnaj3|HIRIP4|PRO3015|mDj3	DnaJ heat shock protein family (Hsp40) member A2	protein-coding
mm_54525.1	chr6	36179775	36179804	-	1	NA	Intergenic	Intergenic	-208295	NM_203491	243764	Mm.448632	NM_203491	ENSMUSG00000045613	Chrm2	AChR-M2|Chrm-2|M2	cholinergic receptor, muscarinic 2, cardiac	protein-coding
mm_77476.1	chr8	122443405	122443426	-	1	NA	promoter-TSS (NM_138656)	promoter-TSS (NM_138656)	7	NM_138656	192156	Mm.28146	NM_138656	ENSMUSG00000006517	Mvd	C78718|Mpd	mevalonate (diphospho) decarboxylase	protein-coding
mm_130152.1	chr15	91190986	91190994	-	1	NA	exon (NM_011994, exon 1 of 10)	exon (NM_011994, exon 1 of 10)	817	NM_011994	26874	Mm.295456	NM_011994	ENSMUSG00000055782	Abcd2	ABC39|ALDL1|ALDR|ALDRP	ATP-binding cassette, sub-family D (ALD), member 2	protein-coding
mm_113724.1	chr13	43791030	43791053	+	1	NA	intron (NM_001289915, intron 2 of 4)	intron (NM_001289915, intron 2 of 4)	5929	NM_001289915	12522	Mm.57175	NM_009856	ENSMUSG00000015396	Cd83	-	CD83 antigen	protein-coding
mm_56552.1	chr6	100287480	100287501	-	1	NA	promoter-TSS (NM_019743)	promoter-TSS (NM_019743)	-132	NM_019743	56353	Mm.321633	NM_019743	ENSMUSG00000072872	Rybp	2410018J24Rik|DEDAF|YEAF1	RING1 and YY1 binding protein	protein-coding
mm_39862.1	chr5	30968656	30968667	+	1	NA	promoter-TSS (NM_053085)	promoter-TSS (NM_053085)	-16	NM_053085	69852	Mm.57874	NM_053085	ENSMUSG00000006642	Tcf23	2010002O16Rik|Out|bHLHa24	transcription factor 23	protein-coding
mm_105328.1	chr11	102897147	102897157	-	1	NA	promoter-TSS (NM_010277)	promoter-TSS (NM_010277)	48	NM_001131020	14580	Mm.1239	NM_010277	ENSMUSG00000020932	Gfap	AI836096	glial fibrillary acidic protein	protein-coding
mm_95365.1	chr11	49076553	49076577	+	1	NA	promoter-TSS (NM_001271677)	promoter-TSS (NM_001271677)	-22	NM_001271677	15953	Mm.24769	NM_008330	ENSMUSG00000078920	Ifi47	47kDa|IRG-47|Ifggc1|Igrd|Iigp4|Iipg4|Irgd	interferon gamma inducible protein 47	protein-coding
mm_4597.1	chr1	178338195	178338198	+	1	NA	promoter-TSS (NM_016805)	promoter-TSS (NM_016805)	-412	NM_016805	51810	Mm.86589	NM_016805	ENSMUSG00000039630	Hnrnpu	AA408410|AI256620|AL024194|AL024437|AW557595|C86794|Hnrpu|SAFA|Sp120|hnRNP U	heterogeneous nuclear ribonucleoprotein U	protein-coding
mm_172555.1	chr8	105594014	105594016	+	1	NA	Intergenic	Intergenic	-11214	NM_001081241	75687	Mm.41261	NM_001081241	ENSMUSG00000038604	Fam65a	2310066E14Rik|AI837433	family with sequence similarity 65, member A	protein-coding
mm_104846.1	chr11	99230967	99230988	-	1	NA	promoter-TSS (NM_020618)	promoter-TSS (NM_020618)	40	NM_020618	57376	Mm.379086	NM_020618	ENSMUSG00000037935	Smarce1	2810417B20Rik|5830412H02Rik|9030408N19Rik|Baf27	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1	protein-coding
mm_85888.1	chr9	111053878	111053889	-	1	NA	TTS (NM_017466)	TTS (NM_017466)	3361	NM_001302377	54199	Mm.7336	NM_017466	ENSMUSG00000043953	Ccrl2	1810047I05Rik|Ackr5|CCR11|Cmkbr1l2|E01|L-CCR	chemokine (C-C motif) receptor-like 2	protein-coding
mm_117761.1	chr13	96132544	96132567	-	1	NA	promoter-TSS (NM_029210)	promoter-TSS (NM_029210)	22	NM_029210	75209	Mm.40436	NM_029210	ENSMUSG00000051111	Sv2c	4930527L09Rik|AI841971	synaptic vesicle glycoprotein 2c	protein-coding
mm_147477.1	chr18	47112350	47112361	-	1	NA	Intergenic	Intergenic	153479	NM_178377	69456	Mm.210734	NM_178377	ENSMUSG00000042705	Commd10	2310003A05Rik|AU019438|DRWMS2	COMM domain containing 10	protein-coding
mm_145783.1	chr18	65083558	65083579	+	1	NA	intron (NM_001114386, intron 5 of 30)	intron (NM_001114386, intron 5 of 30)	60041	NM_031881	83814	Mm.98668	NM_031881	ENSMUSG00000024589	Nedd4l	1300012C07Rik|Nedd4-2|Nedd4b	neural precursor cell expressed, developmentally down-regulated gene 4-like	protein-coding
mm_167599.1	chr9	50593006	50593037	-	1	NA	Intergenic	Intergenic	10828	NM_025848	66925	Mm.10406	NM_025848	ENSMUSG00000000171	Sdhd	3110001M13Rik|AVLL5809|C78570|PRO19626	succinate dehydrogenase complex, subunit D, integral membrane protein	protein-coding
mm_44771.1	chr5	31961571	31961585	-	1	NA	intron (NM_144541, intron 7 of 11)	intron (NM_144541, intron 7 of 11)	-174894	NM_008037	14284	Mm.24684	NM_008037	ENSMUSG00000029135	Fosl2	Fra-2	fos-like antigen 2	protein-coding
mm_125464.1	chr15	52712435	52712477	+	1	NA	promoter-TSS (NM_027212)	promoter-TSS (NM_027212)	11	NM_027212	69790	Mm.195562	NM_027212	ENSMUSG00000038622	Med30	1810038N03Rik|2510044J04Rik|TRAP25|Thrap6	mediator complex subunit 30	protein-coding
mm_58971.1	chr7	19004048	19004095	+	1	NA	promoter-TSS (NM_178757)	promoter-TSS (NM_178757)	6	NM_178757	272359	Mm.274237	NM_178757	ENSMUSG00000044030	Irf2bp1	6330414O09Rik|C530033F24	interferon regulatory factor 2 binding protein 1	protein-coding
mm_99900.1	chr11	109651130	109651160	+	1	NA	intron (NM_001313976, intron 1 of 10)	CpG	224	NM_001313976	19084	Mm.30039	NM_021880	ENSMUSG00000020612	Prkar1a	1300018C22Rik|RIalpha|Tse-1|Tse1	protein kinase, cAMP dependent regulatory, type I, alpha	protein-coding
mm_136564.1	chr17	3239847	3239850	+	1	NA	Intergenic	Intergenic	-86725	NM_001122998	24001	Mm.137134	NM_011878	ENSMUSG00000023800	Tiam2	3000002F19Rik|STEF|mKIAA2016	T cell lymphoma invasion and metastasis 2	protein-coding
mm_145986.1	chr18	68228056	68228087	+	1	NA	intron (NM_172631, intron 3 of 5)	intron (NM_172631, intron 3 of 5)	32902	NR_106078	102465702		NR_106078	ENSMUSG00000098253	Mir7219	Gm27613|mmu-mir-7219	microRNA 7219	ncRNA
mm_158341.1	chrX	134162477	134162495	-	1	NA	promoter-TSS (NM_183319)	promoter-TSS (NM_183319)	-558	NM_183319	331524	Mm.235055	NM_183319	ENSMUSG00000031258	Xkrx	A630026F04	X-linked Kx blood group related, X-linked	protein-coding
mm_89923.1	chr10	111226892	111226898	+	1	NA	intron (NM_175489, intron 3 of 23)	intron (NM_175489, intron 3 of 23)	62093	NM_175489	237542	Mm.220204	NM_175489	ENSMUSG00000020189	Osbpl8	AA536976|AA536995|C730029P18Rik|D330025H14Rik|ORP-8	oxysterol binding protein-like 8	protein-coding
mm_125009.1	chr15	25414306	25414316	+	1	NA	promoter-TSS (NM_027395)	promoter-TSS (NM_027395)	119	NR_027376	432939	Mm.146555	NM_001013791		Gm5468	100040583|EG432939	predicted gene 5468	ncRNA
mm_42931.1	chr5	122850187	122850198	+	1	NA	promoter-TSS (NM_030564)	promoter-TSS (NM_030564)	4	NM_030564	80751	Mm.388529	NM_030564	ENSMUSG00000029474	Rnf34	AW061037|AW536122|BC004042|C88279|RIFF	ring finger protein 34	protein-coding
mm_68815.1	chr7	125707736	125707747	-	1	NA	promoter-TSS (NM_207239)	promoter-TSS (NM_207239)	-53	NM_207239	233863	Mm.294173	NM_207239	ENSMUSG00000032777	Gtf3c1	-	general transcription factor III C 1	protein-coding
mm_139884.1	chr17	70819673	70819682	+	1	NA	3' UTR (NM_177639, exon 12 of 12)	3' UTR (NM_177639, exon 12 of 12)	27100	NM_001164077	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_63175.1	chr7	125368987	125369003	+	1	NA	5' UTR (NM_001145759, exon 1 of 1)	5' UTR (NM_001145759, exon 1 of 1)	134	NM_001145759	75861	Mm.349600	NM_001145759		4930571K23Rik	AI428146	RIKEN cDNA 4930571K23 gene	protein-coding
mm_115328.1	chr13	112465842	112465849	+	1	NA	intron (NM_010560, intron 1 of 16)	intron (NM_010560, intron 1 of 16)	1775	NM_010560	16195	Mm.4364	NM_010560	ENSMUSG00000021756	Il6st	5133400A03Rik|AA389424|BB405851|CD130|D13Ertd699e|gp130	interleukin 6 signal transducer	protein-coding
mm_170952.1	chr2	5379176	5379186	-	1	NA	promoter-TSS (NR_030601)	promoter-TSS (NR_030601)	-209	NR_030601	100124465		NR_030601	ENSMUSG00000078031	Mir466d	Mirn466d	microRNA 466d	ncRNA
mm_26378.1	chr3	142567547	142567568	+	1	NA	exon (NM_018734, exon 7 of 11)	exon (NM_018734, exon 7 of 11)	7061	NM_001289493	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_48423.1	chr5	140389257	140389263	-	1	NA	promoter-TSS (NM_172277)	promoter-TSS (NM_172277)	48	NM_172277	231834	Mm.27098	NM_172277	ENSMUSG00000029560	Snx8	B130023O14Rik	sorting nexin 8	protein-coding
mm_118169.1	chr13	105299707	105299716	-	1	NA	Intergenic	MER34A1|LTR|ERV1	-6697	NM_027934	71816	Mm.317015	NM_027934	ENSMUSG00000021720	Rnf180	3110001E11Rik|Rines	ring finger protein 180	protein-coding
mm_148477.1	chr19	4101006	4101008	+	1	NA	5' UTR (NM_008851, exon 1 of 23)	5' UTR (NM_008851, exon 1 of 23)	385	NM_008851	18739	Mm.1860	NM_008851	ENSMUSG00000024851	Pitpnm1	DRES9|Mpt-1|Nir-2|PITPnm 1|Pitpnm|R75447|Rd9|RdgB|RdgB1	phosphatidylinositol transfer protein, membrane-associated 1	protein-coding
mm_81012.1	chr9	104063679	104063710	+	1	NA	promoter-TSS (NM_175324)	promoter-TSS (NM_175324)	-9	NM_175324	102632	Mm.41274	NM_175324	ENSMUSG00000090150	Acad11	5730439E10Rik|AI987948	acyl-Coenzyme A dehydrogenase family, member 11	protein-coding
mm_89751.1	chr10	99263295	99263314	+	1	NA	promoter-TSS (NM_026268)	promoter-TSS (NM_026268)	73	NM_026268	67603	Mm.1791	NM_026268	ENSMUSG00000019960	Dusp6	1300019I03Rik|MKP-3|MKP3|PYST1	dual specificity phosphatase 6	protein-coding
mm_113020.1	chr13	22006565	22006574	+	1	NA	intron (NM_019429, intron 7 of 11)	intron (NM_019429, intron 7 of 11)	3172	NM_019429	54373	Mm.32043	NM_019429	ENSMUSG00000006179	Prss16	AI448615|TSSP	protease, serine 16 (thymus)	protein-coding
mm_145322.1	chr18	54906890	54906923	+	1	NA	intron (NM_175751, intron 3 of 9)	intron (NM_175751, intron 3 of 9)	83274	NM_175751	269023	Mm.192984	NM_175751	ENSMUSG00000052713	Zfp608	4932417D18Rik|D430007A19Rik|Znf608	zinc finger protein 608	protein-coding
mm_25379.1	chr3	107211460	107211470	+	1	NA	exon (NM_001111143, exon 9 of 9)	exon (NM_001111143, exon 9 of 9)	10267	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_25450.1	chr3	108364914	108364943	+	1	NA	promoter-TSS (NM_026831)	promoter-TSS (NM_026831)	17	NM_026831	68753	Mm.75201	NM_026831	ENSMUSG00000068745	Mybphl	1110037P11Rik	myosin binding protein H-like	protein-coding
mm_4954.1	chr1	191239912	191239916	+	1	NA	Intergenic	Intergenic	-56581	NM_007498	11910	Mm.2706	NM_007498	ENSMUSG00000026628	Atf3	LRG-21	activating transcription factor 3	protein-coding
mm_21020.1	chr2	152398027	152398041	-	1	NA	promoter-TSS (NM_011438)	promoter-TSS (NM_011438)	12	NM_011438	20667	Mm.28424	NM_011438	ENSMUSG00000051817	Sox12	2010205A02Rik	SRY (sex determining region Y)-box 12	protein-coding
mm_151489.1	chr19	58679745	58679749	+	1	NA	intron (NM_026925, intron 10 of 12)	intron (NM_026925, intron 10 of 12)	9382	NM_026925	69060	Mm.20407	NM_026925	ENSMUSG00000046008	Pnlip	1810007A24Rik|PL|PTL	pancreatic lipase	protein-coding
mm_110610.1	chr12	56536896	56536937	-	1	NA	promoter-TSS (NM_009385)	promoter-TSS (NM_009385)	-8	NM_009385	21869	Mm.89972	NM_009385	ENSMUSG00000001496	Nkx2-1	AV026640|Nkx2.1|T/EBP|Titf1|Ttf-1	NK2 homeobox 1	protein-coding
mm_144938.1	chr18	37746972	37747023	+	1	NA	promoter-TSS (NM_033593)	promoter-TSS (NM_033593)	-191	NM_033593	93722	Mm.247203	NM_033593	ENSMUSG00000102222	Pcdhga10	-	protocadherin gamma subfamily A, 10	protein-coding
mm_82472.1	chr9	16499259	16499260	-	1	NA	Intergenic	Intergenic	-121028	NM_001080814	270120	Mm.195010	NM_001080814	ENSMUSG00000074505	Fat3	9430076A06Rik|D430038H04Rik|Gm1132|Gm510|MFAT3F	FAT atypical cadherin 3	protein-coding
mm_131029.1	chr16	3730254	3730302	+	1	NA	Intergenic	Intergenic	-12154	NM_001161791	54483	Mm.143718	NM_019453	ENSMUSG00000022534	Mefv	FMF|TRIM20|pyrin	Mediterranean fever	protein-coding
mm_16635.1	chr2	5844918	5844985	-	1	NA	promoter-TSS (NM_133837)	promoter-TSS (NM_133837)	9	NM_133837	98828	Mm.181490	NM_133837	ENSMUSG00000039128	Cdc123	AA959893|G431001I09Rik	cell division cycle 123	protein-coding
mm_39846.1	chr5	30907935	30907955	+	1	NA	promoter-TSS (NM_001134692)	promoter-TSS (NM_001134692)	-157	NM_024460	67695	Mm.21450	NM_024460	ENSMUSG00000038803	Ost4	2310016E02Rik	oligosaccharyltransferase complex subunit 4 (non-catalytic)	protein-coding
mm_53487.1	chr6	135078712	135078769	+	1	NA	exon (NM_181444, exon 2 of 4)	exon (NM_181444, exon 2 of 4)	13078	NM_181444	232431	Mm.23575	NM_181444	ENSMUSG00000046733	Gprc5a	Rai3|Raig1	G protein-coupled receptor, family C, group 5, member A	protein-coding
mm_152263.1	chr19	8798405	8798418	-	1	NA	intron (NM_026329, intron 1 of 7)	intron (NM_026329, intron 1 of 7)	146	NM_026329	67710	Mm.22117	NM_026329	ENSMUSG00000071662	Polr2g	2410046K11Rik|A230108L04Rik|C76415|RBP7|Rpo2-7l	polymerase (RNA) II (DNA directed) polypeptide G	protein-coding
mm_64992.1	chr7	16917633	16917647	-	1	NA	exon (NM_007590, exon 3 of 6)	exon (NM_007590, exon 3 of 6)	6392	NM_007590	12315	Mm.288630	NM_007590	ENSMUSG00000019370	Calm3	CaMA|R75142	calmodulin 3	protein-coding
mm_103491.1	chr11	76548436	76548439	-	1	NA	intron (NM_198894, intron 1 of 22)	MER2|DNA|TcMar-Tigger	22947	NM_198895	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_62700.1	chr7	110221725	110221739	+	1	NA	promoter-TSS (NM_009302)	promoter-TSS (NM_009302)	29	NM_009302	20947	Mm.334144	NM_009302	ENSMUSG00000031015	Swap70	70kDa|AV235546	SWA-70 protein	protein-coding
mm_41580.1	chr5	93173585	93173633	+	1	NA	3' UTR (NM_001009818, exon 10 of 10)	3' UTR (NM_001009818, exon 10 of 10)	32886	NM_017367	12453	Mm.250419	NM_017367	ENSMUSG00000063015	Ccni	-	cyclin I	protein-coding
mm_38577.1	chr4	141817948	141817968	-	1	NA	exon (NM_007919, exon 7 of 8)	exon (NM_007919, exon 7 of 8)	8047	NM_007919	13706	Mm.45316	NM_007919	ENSMUSG00000058579	Cela2a	Ela-2|Ela2|Ela2a	chymotrypsin-like elastase family, member 2A	protein-coding
mm_137171.1	chr17	23815117	23815191	+	1	NA	exon (NM_175229, exon 10 of 14)	exon (NM_175229, exon 10 of 14)	11967	NM_175229	75956	Mm.5222	NM_175229	ENSMUSG00000039218	Srrm2	5033413A03Rik|AA410130|SRm300|mKIAA0324	serine/arginine repetitive matrix 2	protein-coding
mm_101640.1	chr11	36433020	36433028	-	1	NA	intron (NM_011856, intron 2 of 28)	intron (NM_011856, intron 2 of 28)	-452935	NM_170779	211652	Mm.31267	NM_170779	ENSMUSG00000018849	Wwc1	AA408228|AU017197|BC037006|Kibra|mKIAA0869	WW, C2 and coiled-coil domain containing 1	protein-coding
mm_72511.1	chr8	83900593	83900617	+	1	NA	5' UTR (NM_181039, exon 1 of 23)	5' UTR (NM_181039, exon 1 of 23)	507	NM_181039	330814	Mm.260733	NM_181039	ENSMUSG00000013033	Adgrl1	2900070I05Rik|AI182398|CLIBA|Lec2|Lphn1|mKIAA0821	adhesion G protein-coupled receptor L1	protein-coding
mm_147033.1	chr18	34751346	34751357	-	1	NA	5' UTR (NM_009860, exon 1 of 15)	5' UTR (NM_009860, exon 1 of 15)	182	NM_009860	12532	Mm.286602	NM_009860	ENSMUSG00000044201	Cdc25c	Cdc25	cell division cycle 25C	protein-coding
mm_12034.1	chr2	58755178	58755195	+	1	NA	promoter-TSS (NM_001289659)	promoter-TSS (NM_001289659)	2	NM_029692	76654	Mm.200370	NM_029692	ENSMUSG00000026839	Upp2	1700124F02Rik|AI266885|UDRPASE2|UP2|UPASE2	uridine phosphorylase 2	protein-coding
mm_114360.1	chr13	61039077	61039126	+	1	NA	exon (NM_029636, exon 3 of 8)	exon (NM_029636, exon 3 of 8)	1496	NM_029636	104002	Mm.46088	NM_029636	ENSMUSG00000021439	Ctsq	1600010J02Rik	cathepsin Q	protein-coding
mm_75448.1	chr8	47675113	47675126	-	1	NA	promoter-TSS (NM_023503)	promoter-TSS (NM_023503)	40	NM_023503	69260	Mm.430733	NM_023503	ENSMUSG00000063049	Ing2	2810011M06Rik|Ing1l|Ing2b|P33ING2	inhibitor of growth family, member 2	protein-coding
mm_156035.1	chrX	107542566	107542577	+	1	NA	promoter-TSS (NR_033580)	promoter-TSS (NR_033580)	-11	NR_033580	71011	Mm.307348	NR_033580	ENSMUSG00000055700	4933401B06Rik	-	GLE1 RNA export mediator pseudogene	pseudo
mm_168724.1	chr12	110695079	110695080	-	1	NA	exon (NM_010480, exon 3 of 11)	exon (NM_010480, exon 3 of 11)	1316	NM_010480	15519	Mm.1843	NM_010480	ENSMUSG00000021270	Hsp90aa1	86kDa|89kDa|AL024080|AL024147|Hsp86-1|Hsp89|Hsp90|Hspca|hsp4	heat shock protein 90, alpha (cytosolic), class A member 1	protein-coding
mm_46650.1	chr5	108629687	108629707	-	1	NA	promoter-TSS (NM_153569)	promoter-TSS (NM_153569)	80	NM_153569	231580	Mm.276647	NM_153569	ENSMUSG00000062234	Gak	D130045N16Rik	cyclin G associated kinase	protein-coding
mm_130640.1	chr15	100551837	100551856	-	1	NA	intron (NM_033476, intron 1 of 15)	CpG	162	NM_033476	21422	Mm.219040	NM_033476	ENSMUSG00000009733	Tfcp2	CP-2|CP2|D230015P20Rik|LBP-1c|LBP-1d|LBP1|LSF|Tcfcp2|UBP-1	transcription factor CP2	protein-coding
mm_157205.1	chrX	12677586	12677612	-	1	NA	exon (NM_001048208, exon 31 of 31)	exon (NM_001048208, exon 31 of 31)	-3960	NM_175141	69155	Mm.15974	NM_175141	ENSMUSG00000044148	1810030O07Rik	-	RIKEN cDNA 1810030O07 gene	protein-coding
mm_90038.1	chr10	115817248	115817323	+	1	NA	promoter-TSS (NM_001168680)	promoter-TSS (NM_001168680)	1	NM_001168679	216350	Mm.22270	NM_146010	ENSMUSG00000034127	Tspan8	C76990|E330007O21Rik|Tm4sf3	tetraspanin 8	protein-coding
mm_119184.1	chr14	32202005	32202013	+	1	NA	promoter-TSS (NM_011960)	promoter-TSS (NM_011960)	38	NM_011960	26430	Mm.15962	NM_011960	ENSMUSG00000021911	Parg	AI413217	poly (ADP-ribose) glycohydrolase	protein-coding
mm_88719.1	chr10	80158746	80158773	+	1	NA	TTS (NM_001305798)	TTS (NM_001305798)	9077	NM_001305799	59090	Mm.143813	NM_021565	ENSMUSG00000035621	Midn	3000003C15Rik	midnolin	protein-coding
mm_98254.1	chr11	88624927	88624949	+	1	NA	intron (NM_054043, intron 5 of 13)	intron (NM_054043, intron 5 of 13)	5687	NR_131025	68397	Mm.426889	NR_131025		0610039H22Rik	-	RIKEN cDNA 0610039H22 gene	ncRNA
mm_84256.1	chr9	62536748	62536767	-	1	NA	5' UTR (NM_175484, exon 1 of 12)	5' UTR (NM_175484, exon 1 of 12)	287	NM_175484	235431	Mm.335229	NM_175484	ENSMUSG00000041729	Coro2b	CLIPINC|E130012P22Rik	coronin, actin binding protein, 2B	protein-coding
mm_41616.1	chr5	96799793	96799809	+	1	NA	intron (NM_013470, intron 2 of 12)	ID_B1|SINE|B4	6416	NM_013470	11745	Mm.7214	NM_013470	ENSMUSG00000029484	Anxa3	Anx3	annexin A3	protein-coding
mm_88146.1	chr10	69533703	69533723	+	1	NA	promoter-TSS (NM_170688)	promoter-TSS (NM_170688)	5	NM_146005	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_118222.1	chr13	110397751	110397768	-	1	NA	exon (NM_152804, exon 7 of 14)	exon (NM_152804, exon 7 of 14)	2715	NM_152804	20620	Mm.380	NM_152804	ENSMUSG00000021701	Plk2	Snk	polo-like kinase 2	protein-coding
mm_160874.1	chr11	68594152	68594152	+	1	NA	intron (NM_177779, intron 4 of 6)	intron (NM_177779, intron 4 of 6)	7115	NM_177779	276920	Mm.123046	NM_177779	ENSMUSG00000045915	Ccdc42	A530001H01Rik	coiled-coil domain containing 42	protein-coding
mm_17184.1	chr2	25460934	25460959	-	1	NA	5' UTR (NM_153557, exon 1 of 7)	5' UTR (NM_153557, exon 1 of 7)	148	NM_153557	227622	Mm.261780	NM_153557	ENSMUSG00000047617	BC029214	D930050G13Rik|Paxx	cDNA sequence BC029214	protein-coding
mm_119033.1	chr14	30549140	30549159	+	1	NA	promoter-TSS (NM_009388)	promoter-TSS (NM_009388)	18	NM_009388	21881	Mm.290692	NM_009388	ENSMUSG00000021957	Tkt	p68	transketolase	protein-coding
mm_93114.1	chr10	91123263	91123315	-	1	NA	intron (NM_133668, intron 2 of 7)	intron (NM_133668, intron 2 of 7)	674	NM_133668	18674	Mm.298	NM_133668	ENSMUSG00000061904	Slc25a3	5730556H19Rik|PTP|Phc	solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 3	protein-coding
mm_154629.1	chrX	7762549	7762562	+	1	NA	promoter-TSS (NM_001271489)	promoter-TSS (NM_001271489)	-106	NM_001271489	209446	Mm.249142	NM_172472	ENSMUSG00000000134	Tfe3	F830016E06Rik|Tcfe3|Tfe-3|bHLHe33	transcription factor E3	protein-coding
mm_82819.1	chr9	31030231	31030251	-	1	NA	promoter-TSS (NM_001115130)	promoter-TSS (NM_001115130)	-403	NM_001115130	235132	Mm.239355	NM_172765	ENSMUSG00000047412	Zbtb44	6030404E16Rik|Btbd15|E230011F09	zinc finger and BTB domain containing 44	protein-coding
mm_156768.1	chrX	160768110	160768122	+	1	NA	5' UTR (NM_011302, exon 1 of 6)	5' UTR (NM_011302, exon 1 of 6)	103	NM_011302	20147	Mm.41982	NM_011302	ENSMUSG00000031293	Rs1	Rs1h|Xlrs1|tmgc1	retinoschisis (X-linked, juvenile) 1 (human)	protein-coding
mm_158059.1	chrX	101067721	101067745	-	1	NA	Intergenic	Intergenic	-8094	NM_001167997	83558	Mm.134024	NM_031384	ENSMUSG00000009670	Tex11	4930565P14Rik|BB024231|ZIP4H	testis expressed gene 11	protein-coding
mm_137476.1	chr17	26781061	26781094	+	1	NA	promoter-TSS (NM_172149)	promoter-TSS (NM_172149)	-2	NM_172149	224630	Mm.21795	NM_172149	ENSMUSG00000024191	Bnip1	2010005M06Rik|5930429G21Rik|Sec20	BCL2/adenovirus E1B interacting protein 1	protein-coding
mm_19294.1	chr2	90458314	90458327	-	1	NA	exon (NM_008982, exon 10 of 24)	exon (NM_008982, exon 10 of 24)	20854	NM_001135657	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_101332.1	chr11	23257479	23257487	-	1	NA	intron (NM_001035226, intron 2 of 25)	intron (NM_001035226, intron 2 of 25)	1442	NM_134014	103573	Mm.217547	NM_134014	ENSMUSG00000020290	Xpo1	AA420417|Crm1|Exp1	exportin 1	protein-coding
mm_140581.1	chr17	10212060	10212083	-	1	NA	3' UTR (NM_001159516, exon 7 of 7)	3' UTR (NM_001159516, exon 7 of 7)	107290	NM_021881	19317	Mm.130694	NM_021881	ENSMUSG00000062078	Qk	1110003F05Rik|1500005P18|QkI|l(17)-1Wis|l17Wis1	quaking	protein-coding
mm_137582.1	chr17	28007522	28007540	+	1	NA	intron (NM_001286040, intron 11 of 24)	intron (NM_001286040, intron 11 of 24)	73053	NM_013687	21463	Mm.29758	NM_013687	ENSMUSG00000062859	Tcp11	D17Ken1|Tcp-11	t-complex protein 11	protein-coding
mm_99231.1	chr11	101063026	101063040	+	1	NA	3' UTR (NM_001243049, exon 21 of 21)	3' UTR (NM_001243049, exon 21 of 21)	-7061	NM_013792	27419	Mm.95452	NM_013792	ENSMUSG00000001751	Naglu	-	alpha-N-acetylglucosaminidase (Sanfilippo disease IIIB)	protein-coding
mm_35103.1	chr4	9451153	9451158	-	1	NA	3' UTR (NM_028940, exon 6 of 6)	3' UTR (NM_028940, exon 6 of 6)	181838	NM_028940	74438	Mm.473368	NM_028940	ENSMUSG00000041216	Clvs1	4933402J24Rik|Clvl1|Rlbp1l1	clavesin 1	protein-coding
mm_31965.1	chr4	86930750	86930759	+	1	NA	intron (NM_001290543, intron 5 of 5)	RLTR51A_Mm|LTR|ERVK?	56340	NM_139306	230379	Mm.45019	NM_139306	ENSMUSG00000038007	Acer2	2410116I05Rik|Asah3l|CRG-L1|maCER2	alkaline ceramidase 2	protein-coding
mm_150009.1	chr19	29312202	29312227	+	1	NA	3' UTR (NM_008413, exon 25 of 25)	3' UTR (NM_008413, exon 25 of 25)	13104	NM_013754	27356	Mm.306511	NM_013754	ENSMUSG00000050957	Insl6	RIF1	insulin-like 6	protein-coding
mm_59313.1	chr7	25284922	25284933	+	1	NA	exon (NM_027882, exon 2 of 20)	exon (NM_027882, exon 2 of 20)	2748	NM_027882	71722	Mm.28833	NM_027882	ENSMUSG00000005442	Cic	1200010B10Rik|mKIAA0306	capicua transcriptional repressor	protein-coding
mm_129897.1	chr15	83595167	83595177	-	1	NA	promoter-TSS (NM_183017)	promoter-TSS (NM_183017)	-15	NM_183017	223723	Mm.46778	NM_183017	ENSMUSG00000016757	Ttll12	BC055368|D430005B17	tubulin tyrosine ligase-like family, member 12	protein-coding
mm_116070.1	chr13	27640810	27640816	-	1	NA	exon (NM_001164058, exon 2 of 7)	exon (NM_001164058, exon 2 of 7)	1680	NM_001164058	19113	Mm.196424	NM_008930	ENSMUSG00000006488	Prl7a1	AA407021|AA409971|AA410116|PLP-E|PLP-G|Prlpe|Prlpg	prolactin family 7, subfamily a, member 1	protein-coding
mm_17088.1	chr2	22989241	22989260	-	1	NA	intron (NM_001331043, intron 2 of 10)	intron (NM_001331043, intron 2 of 10)	50991	NM_001077192	11308	Mm.205647	NM_007380	ENSMUSG00000058835	Abi1	E3B1|NAP1|Ssh3bp1|abi-1	abl-interactor 1	protein-coding
mm_136495.1	chr16	96135879	96135888	-	1	NA	Intergenic	ORR1A3|LTR|ERVL-MaLR	-8158	NM_008251	15312	Mm.2756	NM_008251	ENSMUSG00000040681	Hmgn1	HMG-14|Hmg14	high mobility group nucleosomal binding domain 1	protein-coding
mm_166782.1	chr6	141856185	141856191	-	1	NA	promoter-TSS (NM_030687)	promoter-TSS (NM_030687)	-17	NM_030687	28250	Mm.255586	NM_030687	ENSMUSG00000030237	Slco1a4	AI785519|Oatp1a4|Oatp2|Slc21a5	solute carrier organic anion transporter family, member 1a4	protein-coding
mm_23763.1	chr3	73066346	73066359	+	1	NA	promoter-TSS (NR_040557)	promoter-TSS (NR_040557)	1	NR_040557	626082	Mm.428099	NR_040557	ENSMUSG00000103428	Gm20754	-	predicted gene, 20754	ncRNA
mm_171273.1	chr3	88775227	88775241	+	1	NA	Intergenic	CpG	-1823	NR_028359	100302730	Mm.482358	NR_028359		5830417I10Rik	3632445O20Rik|AA387005	gon-4-like pseudogene	pseudo
mm_21769.1	chr2	164844698	164844706	-	1	NA	exon (NM_011125, exon 11 of 16)	exon (NM_011125, exon 11 of 16)	10929	NM_008906	19025	Mm.359633	NM_008906	ENSMUSG00000017760	Ctsa	AU019505|PPCA|Ppgb	cathepsin A	protein-coding
mm_26385.1	chr3	142569209	142569219	+	1	NA	exon (NM_018734, exon 8 of 11)	exon (NM_018734, exon 8 of 11)	8718	NM_001289493	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_34584.1	chr4	150148882	150148896	+	1	NA	promoter-TSS (NM_001085529)	promoter-TSS (NM_001085529)	-83	NM_001085529	435818	Mm.359648	NM_001085529	ENSMUSG00000062064	Slc2a7	OTTMUSG00000010396	solute carrier family 2 (facilitated glucose transporter), member 7	protein-coding
mm_57112.1	chr6	122595821	122595837	-	1	NA	intron (NM_031159, intron 3 of 7)	intron (NM_031159, intron 3 of 7)	6615	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_75851.1	chr8	70659646	70659696	-	1	NA	promoter-TSS (NM_023217)	promoter-TSS (NM_023217)	67	NM_023217	66522	Mm.154906	NM_023217	ENSMUSG00000056204	Pgpep1	2810003H13Rik|Gm19458|PAP-I|PGP|PGP-I|PGPI|Pcp	pyroglutamyl-peptidase I	protein-coding
mm_138347.1	chr17	34931349	34931384	+	1	NA	TTS (NM_023557)	TTS (NM_023557)	113	NM_010893	18010	Mm.8856	NM_010893	ENSMUSG00000007038	Neu1	AA407268|AA407316|Aglp|Apl|Bat-7|Bat7|G9|Map-2|Neu|Neu-1	neuraminidase 1	protein-coding
mm_157511.1	chrX	49273809	49273819	-	1	NA	intron (NM_001271450, intron 2 of 15)	intron (NM_001271450, intron 2 of 15)	14428	NM_001271449	209224	Mm.327730	NM_145951	ENSMUSG00000031109	Enox2	APK1|Cova1|tNOX	ecto-NOX disulfide-thiol exchanger 2	protein-coding
mm_85731.1	chr9	108359093	108359099	-	1	NA	intron (NM_001311157, intron 3 of 20)	intron (NM_001311157, intron 3 of 20)	11265	NM_011678	22258	Mm.3974	NM_011678	ENSMUSG00000032612	Usp4	F730026I20Rik|Unp|mKIAA4155	ubiquitin specific peptidase 4 (proto-oncogene)	protein-coding
mm_135507.1	chr16	46498583	46498588	-	1	NA	Intergenic	Intergenic	-1618	NM_021497	58998	Mm.40477	NM_021495	ENSMUSG00000022656	Nectin3	2610301B19Rik|3000002N23Rik|4921513D19Rik|AA407785|AU016832|AW538082|CD113|Pvrl3	nectin cell adhesion molecule 3	protein-coding
mm_139718.1	chr17	57466683	57466722	+	1	NA	intron (NM_010130, intron 18 of 21)	Lx|LINE|L1	78612	NM_001104591	224916	Mm.469889	NM_001104591	ENSMUSG00000090655	Vmn2r120	EG224916	vomeronasal 2, receptor 120	protein-coding
mm_56931.1	chr6	119544283	119544304	-	1	NA	promoter-TSS (NM_009525)	promoter-TSS (NM_009525)	54	NM_009525	22419	Mm.321818	NM_009525	ENSMUSG00000030170	Wnt5b	AW545702|Wnt-5b	wingless-type MMTV integration site family, member 5B	protein-coding
mm_122457.1	chr14	45388748	45388758	-	1	NA	promoter-TSS (NM_019425)	promoter-TSS (NM_019425)	43	NM_019425	54342	Mm.312945	NM_019425	ENSMUSG00000037722	Gnpnat1	AU017428|AU040593|EMeg32|Gpnat1|Gsnpat	glucosamine-phosphate N-acetyltransferase 1	protein-coding
mm_171553.1	chr4	147132045	147132052	+	1	NA	Intergenic	Intergenic	-43818	NM_001039209	195531	Mm.270762	NM_001039209	ENSMUSG00000078496	Zfp982	Gm13152|OTTMUSG00000010671	zinc finger protein 982	protein-coding
mm_115941.1	chr13	23684619	23684648	-	1	NA	promoter-TSS (NM_178189)	promoter-TSS (NM_178189)	434	NM_023422	68024	Mm.261676	NM_023422	ENSMUSG00000018102	Hist1h2bc	2610022J01Rik|H2bfs|R74621	histone cluster 1, H2bc	protein-coding
mm_33983.1	chr4	137717365	137717381	+	1	NA	intron (NM_001256218, intron 10 of 24)	intron (NM_001256218, intron 10 of 24)	-7088	NR_138592	110351	Mm.180763	NM_029563	ENSMUSG00000041351	Rap1gap	1300019I11Rik|2310004O14Rik|AI427470|ARPP-90|Gap|Rap1GAP1|Rap1ga1	Rap1 GTPase-activating protein	protein-coding
mm_156620.1	chrX	153832237	153832281	+	1	NA	promoter-TSS (NM_001005370)	promoter-TSS (NM_001005370)	-34	NM_001005370	278240	Mm.293363	NM_001005370	ENSMUSG00000046550	Spin2c	BC068162|SPIN-2C|Spin2	spindlin family, member 2C	protein-coding
mm_166704.1	chr6	115792929	115792967	+	1	NA	exon (NM_025958, exon 10 of 15)	exon (NM_025958, exon 10 of 15)	15155	NR_028546	100217451	Mm.484708	NR_028546	ENSMUSG00000064563	Snora7a	MBI-141	small nucleolar RNA, H/ACA box 7A	snoRNA
mm_90639.1	chr10	128499409	128499445	+	1	NA	promoter-TSS (NM_172259)	promoter-TSS (NM_172259)	180	NR_131151	654440	Mm.441262	NR_131150	ENSMUSG00000097353	A430046D13Rik	-	Riken cDNA A430046D13 gene	ncRNA
mm_148663.1	chr19	5601842	5601852	+	1	NA	promoter-TSS (NM_026616)	promoter-TSS (NM_026616)	-26	NM_026616	68209	Mm.246200	NM_026616	ENSMUSG00000024925	Rnaseh2c	1500026D16Rik|AYP1	ribonuclease H2, subunit C	protein-coding
mm_82948.1	chr9	35558460	35558476	-	1	NA	promoter-TSS (NM_013932)	promoter-TSS (NM_013932)	2	NM_013932	30959	Mm.291723	NM_013932	ENSMUSG00000032101	Ddx25	AW047046|GRTH	DEAD (Asp-Glu-Ala-Asp) box polypeptide 25	protein-coding
mm_64905.1	chr7	16047639	16047643	-	1	NA	Intergenic	CpG	-24204	NM_001347559	666528	Mm.290718	NM_001099277	ENSMUSG00000078796	Zfp541	EG666528|Znf541	zinc finger protein 541	protein-coding
mm_168515.1	chr11	5699996	5700000	-	1	NA	Intergenic	RLTR9D|LTR|ERVK	7701	NM_026080	64660	Mm.7328	NM_026080	ENSMUSG00000020477	Mrps24	3110030K20Rik|AI414579|Rpms24	mitochondrial ribosomal protein S24	protein-coding
mm_59453.1	chr7	27195122	27195123	+	1	NA	promoter-TSS (NM_001290511)	promoter-TSS (NM_001290511)	638	NM_001046637	53607	Mm.386890	NM_015782	ENSMUSG00000061479	Snrpa	C430021M15Rik|Rnu1a-1|Rnu1a1|U1-A|U1A	small nuclear ribonucleoprotein polypeptide A	protein-coding
mm_149133.1	chr19	9002645	9002657	+	1	NA	exon (NM_009643, exon 5 of 5)	exon (NM_009643, exon 5 of 5)	13367	NM_001286518	66395	Mm.203866	NM_009643	ENSMUSG00000069833	Ahnak	DY6	AHNAK nucleoprotein (desmoyokin)	protein-coding
mm_69600.1	chr7	135716474	135716480	-	1	NA	promoter-TSS (NM_001081117)	promoter-TSS (NM_001081117)	-98	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_122285.1	chr14	34503255	34503281	-	1	NA	promoter-TSS (NM_009758)	promoter-TSS (NM_009758)	-722	NM_009758	12166	Mm.237825	NM_009758	ENSMUSG00000021796	Bmpr1a	1110037I22Rik|ALK3|AU045487|BMPR-IA|Bmpr	bone morphogenetic protein receptor, type 1A	protein-coding
mm_129838.1	chr15	83154417	83154435	-	1	NA	3' UTR (NM_029787, exon 9 of 9)	3' UTR (NM_029787, exon 9 of 9)	4781	NR_004432	104307	Mm.471434	NR_004432	ENSMUSG00000065176	Rnu12	-	RNA U12, small nuclear	snRNA
mm_168666.1	chr1	191120996	191120996	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	22582	NM_030060	381319	Mm.6922	NM_030060	ENSMUSG00000026630	Batf3	9130211I03Rik|Snft	basic leucine zipper transcription factor, ATF-like 3	protein-coding
mm_125527.1	chr15	57892749	57892761	+	1	NA	promoter-TSS (NM_024207)	promoter-TSS (NM_024207)	-337	NM_024207	67819	Mm.289387	NM_024207	ENSMUSG00000022365	Derl1	1110021N07Rik|AI195141|AW551338|Derlin-1	Der1-like domain family, member 1	protein-coding
mm_10708.1	chr2	22774339	22774370	+	1	NA	promoter-TSS (NM_019456)	promoter-TSS (NM_019456)	27	NM_019456	54519	Mm.14255	NM_019456	ENSMUSG00000026786	Apbb1ip	9930118P07Rik|Prp48	amyloid beta (A4) precursor protein-binding, family B, member 1 interacting protein	protein-coding
mm_150242.1	chr19	34085371	34085382	+	1	NA	TTS (NM_027340)	TTS (NM_027340)	-15567	NM_023903	78753	Mm.195937	NM_023903	ENSMUSG00000056078	Lipm	4632427C23Rik|AW227514|Lipl3	lipase, family member M	protein-coding
mm_130279.1	chr15	96702548	96702556	-	1	NA	Intergenic	Intergenic	-2854	NM_175121	67760	Mm.46754	NM_175121	ENSMUSG00000022462	Slc38a2	5033402L14Rik|AI316867|ATA2|SAT2|mKIAA1382	solute carrier family 38, member 2	protein-coding
mm_114936.1	chr13	95988422	95988437	+	1	NA	intron (NM_029210, intron 6 of 12)	B4A|SINE|B4	-96507	NM_027711	544963	Mm.38878	NM_027711	ENSMUSG00000021676	Iqgap2	4933417J23Rik|A630053O10|AI788777	IQ motif containing GTPase activating protein 2	protein-coding
mm_40279.1	chr5	42615196	42615198	+	1	NA	Intergenic	Intergenic	547237	NR_131130	433882	Mm.319353	NR_131130	ENSMUSG00000067285	Gm16223	EG433882|OTTMUSG00000031875	predicted gene 16223	ncRNA
mm_157535.1	chrX	51116105	51116107	-	1	NA	3' UTR (NM_134163, exon 8 of 8)	3' UTR (NM_134163, exon 8 of 8)	89884	NM_001310515	171170	Mm.295324	NM_134163	ENSMUSG00000036109	Mbnl3	A530038J18Rik|AI661274|CHCR|E430034C16Rik|MBLX|MBLX39|MBXL	muscleblind-like 3 (Drosophila)	protein-coding
mm_167557.1	chr9	35908386	35908393	+	1	NA	Intergenic	Intergenic	-58509	NR_030730	100041605	Mm.99350	NR_030730	ENSMUSG00000098705	Gm3428	-	predicted gene 3428	ncRNA
mm_74868.1	chr8	25012618	25012622	-	1	NA	intron (NM_001270996, intron 1 of 21)	intron (NM_001270996, intron 1 of 21)	4302	NM_001270996	11502	Mm.28908	NM_007404	ENSMUSG00000031555	Adam9	AU020942|MDC9|Mltng|mKIAA0021	a disintegrin and metallopeptidase domain 9 (meltrin gamma)	protein-coding
mm_66231.1	chr7	35121925	35121928	-	1	NA	TTS (NM_001287514)	TTS (NM_001287514)	2633	NM_007678	12606	Mm.349667	NM_007678	ENSMUSG00000034957	Cebpa	C/ebpalpha|CBF-A|Cebp	CCAAT/enhancer binding protein (C/EBP), alpha	protein-coding
mm_22614.1	chr3	14578610	14578687	+	1	NA	promoter-TSS (NM_007892)	promoter-TSS (NM_007892)	-23	NM_007892	13559	Mm.153415	NM_007892	ENSMUSG00000027552	E2f5	AU024671|E2F-5	E2F transcription factor 5	protein-coding
mm_42628.1	chr5	118381647	118381658	+	1	NA	Intergenic	Intergenic	136425	NM_001081236	76792	Mm.103428	NM_001081236	ENSMUSG00000032840	2410131K14Rik	-	RIKEN cDNA 2410131K14 gene	protein-coding
mm_70917.1	chr8	25754463	25754485	+	1	NA	promoter-TSS (NM_028102)	promoter-TSS (NM_028102)	-194	NM_028102	72108	Mm.246875	NM_028102	ENSMUSG00000061313	Ddhd2	2010305K11Rik|SAMWD1|mKIAA0725	DDHD domain containing 2	protein-coding
mm_122040.1	chr14	30008979	30008999	-	1	NA	promoter-TSS (NM_001136240)	promoter-TSS (NM_001136240)	-11	NM_001136240	218865	Mm.259916	NM_172264	ENSMUSG00000015970	Chdh	AU041472|D630034H06Rik	choline dehydrogenase	protein-coding
mm_76114.1	chr8	80788822	80788853	-	1	NA	exon (NM_001301298, exon 4 of 11)	exon (NM_001301298, exon 4 of 11)	-49378	NM_053124	93762	Mm.246803	NM_053124	ENSMUSG00000031715	Smarca5	4933427E24Rik|D030040M08Rik|D330027N15Rik|MommeD4|Snf2h	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5	protein-coding
mm_159574.1	chr4	115600940	115600940	+	1	NA	promoter-TSS (NM_001100181)	promoter-TSS (NM_001100181)	2	NM_001100181	100040843	Mm.482683	NM_001100181	ENSMUSG00000063929	Cyp4a32	OTTMUSG00000008689	cytochrome P450, family 4, subfamily a, polypeptide 32	protein-coding
mm_85306.1	chr9	100987950	100987960	-	1	NA	intron (NM_025835, intron 9 of 14)	intron (NM_025835, intron 9 of 14)	46929	NM_001311149	66904	Mm.335385	NM_025835	ENSMUSG00000032527	Pccb	1300012P06Rik|AI314687|R74805	propionyl Coenzyme A carboxylase, beta polypeptide	protein-coding
mm_90406.1	chr10	127390310	127390336	+	1	NA	promoter-TSS (NM_001168292)	promoter-TSS (NM_001168292)	12	NM_001168292	71750	Mm.29342	NM_027900	ENSMUSG00000025404	R3hdm2	1300003K24Rik|AU041262|mKIAA1002	R3H domain containing 2	protein-coding
mm_103515.1	chr11	76763551	76763582	-	1	NA	promoter-TSS (NM_016810)	promoter-TSS (NM_016810)	-11	NM_016810	53334	Mm.20931	NM_016810	ENSMUSG00000010392	Gosr1	AI414660|AI426320|BB145494|GOS-28|GOSRI|GS28	golgi SNAP receptor complex member 1	protein-coding
mm_76262.1	chr8	84011477	84011486	-	1	NA	TTS (NR_035431)	TTS (NR_035431)	152	NR_035431	100316677		NR_035431	ENSMUSG00000080665	Mir1199	Mirn1199|mir-1199|mmu-mir-1199	microRNA 1199	ncRNA
mm_159815.1	chr5	120887571	120887571	-	1	NA	promoter-TSS (NR_126529)	promoter-TSS (NR_126529)	42	NM_011852	23960	Mm.389688	NM_011852	ENSMUSG00000066861	Oas1g	AI449562|L2|Mmu-L|Mmu-L2|Oas1b|Oias-1|Oias1	2'-5' oligoadenylate synthetase 1G	protein-coding
mm_135497.1	chr16	46433695	46433704	-	1	NA	intron (NM_021496, intron 7 of 8)	B1_Mm|SINE|Alu	63268	NM_021496	58998	Mm.40477	NM_021495	ENSMUSG00000022656	Nectin3	2610301B19Rik|3000002N23Rik|4921513D19Rik|AA407785|AU016832|AW538082|CD113|Pvrl3	nectin cell adhesion molecule 3	protein-coding
mm_70073.1	chr7	142653171	142653181	-	1	NA	3' UTR (NM_010514, exon 4 of 4)	3' UTR (NM_010514, exon 4 of 4)	1820	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_122520.1	chr14	47276793	47276848	-	1	NA	promoter-TSS (NM_080843)	promoter-TSS (NM_080843)	37	NM_172598	218973	Mm.265615	NM_172598	ENSMUSG00000037572	Wdhd1	A630092E18|AND-1|D630024B06Rik	WD repeat and HMG-box DNA binding protein 1	protein-coding
mm_172925.1	chr9	69464502	69464521	+	1	NA	exon (NM_007585, exon 2 of 13)	exon (NM_007585, exon 2 of 13)	7567	NR_037296	100526560		NR_037296	ENSMUSG00000093042	Mir3109	mir-3109|mmu-mir-3109	microRNA 3109	ncRNA
mm_12639.1	chr2	74711889	74711908	+	1	NA	promoter-TSS (NM_010468)	promoter-TSS (NM_010468)	-95	NM_010468	15434	Mm.430708	NM_010468	ENSMUSG00000079277	Hoxd3	Hox-4.1|Hox-5.5	homeobox D3	protein-coding
mm_22135.1	chr2	170470700	170470709	-	1	NA	Intergenic	RLTR51B_Mm|LTR|ERVK?	-25724	NM_001013369	109054	Mm.28808	NM_001013369	ENSMUSG00000052033	Pfdn4	0610025M10Rik|1810063B06Rik|C-1|C1|Pfd4	prefoldin 4	protein-coding
mm_60682.1	chr7	45154298	45154354	+	1	NA	promoter-TSS (NM_029406)	promoter-TSS (NM_029406)	23	NM_001278207	68845	Mm.181689	NM_029406	ENSMUSG00000003423	Pih1d1	1110061L23Rik|4933413A04Rik|Nop17	PIH1 domain containing 1	protein-coding
mm_170077.1	chr17	33760277	33760285	-	1	NA	5' UTR (NM_008997, exon 1 of 5)	5' UTR (NM_008997, exon 1 of 5)	205	NM_008997	19326	Mm.387587	NM_008997	ENSMUSG00000077450	Rab11b	A730055L17Rik	RAB11B, member RAS oncogene family	protein-coding
mm_148232.1	chr18	80451249	80451259	-	1	NA	exon (NM_026295, exon 7 of 13)	exon (NM_026295, exon 7 of 13)	18413	NM_026295	67655	Mm.312893	NM_026295	ENSMUSG00000033323	Ctdp1	4930563P03Rik|AW553592	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) phosphatase, subunit 1	protein-coding
mm_148553.1	chr19	4712072	4712111	+	1	NA	intron (NM_021287, intron 1 of 36)	CpG	868	NM_021287	20743	Mm.329668	NM_021287	ENSMUSG00000067889	Sptbn2	Spnb3|mKIAA0302	spectrin beta, non-erythrocytic 2	protein-coding
mm_38600.1	chr4	141859235	141859246	-	1	NA	3' UTR (NM_025994, exon 4 of 4)	3' UTR (NM_025994, exon 4 of 4)	-12881	NM_001033875	76701	Mm.489680	NM_001033875	ENSMUSG00000062478	Ctrc	1810044E12Rik	chymotrypsin C (caldecrin)	protein-coding
mm_84423.1	chr9	65765003	65765005	-	1	NA	intron (NM_172536, intron 2 of 9)	intron (NM_172536, intron 2 of 9)	62560	NM_172536	214812	Mm.139231	NM_172536	ENSMUSG00000040524	Zfp609	9830165N24|BC016271|Znf609|mKIAA0295	zinc finger protein 609	protein-coding
mm_130414.1	chr15	97997591	97997597	-	1	NA	intron (NM_031163, intron 7 of 53)	intron (NM_031163, intron 7 of 53)	7130	NM_031163	12824	Mm.2423	NM_031163	ENSMUSG00000022483	Col2a1	Col2|Col2a|Col2a-1|Del1|Dmm|Lpk|Rgsc856	collagen, type II, alpha 1	protein-coding
mm_34272.1	chr4	141424201	141424201	+	1	NA	3' UTR (NM_013868, exon 3 of 3)	3' UTR (NM_013868, exon 3 of 3)	3422	NM_013868	29818	Mm.46181	NM_013868	ENSMUSG00000006221	Hspb7	27kDa|Hsp25-2|cvHsp	heat shock protein family, member 7 (cardiovascular)	protein-coding
mm_3233.1	chr1	135850058	135850072	+	1	NA	intron (NM_001130174, intron 10 of 13)	B1_Mur2|SINE|Alu	9204	NM_001130176	21956	Mm.247470	NM_011619	ENSMUSG00000026414	Tnnt2	Tnt|cTnT	troponin T2, cardiac	protein-coding
mm_9356.1	chr1	172197846	172197874	-	1	NA	3' UTR (NM_001329871, exon 4 of 4)	3' UTR (NM_001329871, exon 4 of 4)	8944	NM_001329871	18611	Mm.544	NM_011063	ENSMUSG00000013698	Pea15a	Mat1|PEA-15|Pea15|Pkcs15	phosphoprotein enriched in astrocytes 15A	protein-coding
mm_17062.1	chr2	22589425	22589449	-	1	NA	Intergenic	Intergenic	-32890	NM_008078	14417	Mm.4784	NM_008078	ENSMUSG00000026787	Gad2	6330404F12Rik|GAD(65)|GAD65|Gad-2	glutamic acid decarboxylase 2	protein-coding
mm_74056.1	chr8	122332764	122332788	+	1	NA	intron (NM_009569, intron 5 of 9)	intron (NM_009569, intron 5 of 9)	27970	NM_133202	170732	Mm.154808	NM_133202	ENSMUSG00000039079	Trhr2	TRH-R2	thyrotropin releasing hormone receptor 2	protein-coding
mm_158090.1	chrX	101384645	101384681	-	1	NA	exon (NM_008124, exon 2 of 2)	exon (NM_008124, exon 2 of 2)	931	NM_001302497	14618	Mm.21198	NM_008124	ENSMUSG00000047797	Gjb1	Cnx32|Cx32|connexin-32	gap junction protein, beta 1	protein-coding
mm_6210.1	chr1	66817537	66817600	-	1	NA	promoter-TSS (NM_001122738)	promoter-TSS (NM_001122738)	27	NM_177645	68691	Mm.240912	NM_177645	ENSMUSG00000026004	Kansl1l	1110028C15Rik|1190030G24|AI427598|C430010P07Rik|mKIAA4189	KAT8 regulatory NSL complex subunit 1-like	protein-coding
mm_169830.1	chr16	24529416	24529420	+	1	NA	non-coding (NR_038091, exon 1 of 1)	non-coding (NR_038091, exon 1 of 1)	104	NR_038091	624582	Mm.439775	NR_038091		Morf4l1-ps1	A730098P11Rik	mortality factor 4 like 1, pseudogene 1	pseudo
mm_84015.1	chr9	57646747	57646769	-	1	NA	intron (NM_001304761, intron 2 of 14)	intron (NM_001304761, intron 2 of 14)	-1105	NM_007783	12988	Mm.21974	NM_007783	ENSMUSG00000032312	Csk	AW212630|p50CSK	c-src tyrosine kinase	protein-coding
mm_45667.1	chr5	77211193	77211207	-	1	NA	promoter-TSS (NM_001289764)	promoter-TSS (NM_001289764)	5	NM_001289767	69982	Mm.46106	NM_183284	ENSMUSG00000053030	Spink2	1700007F22Rik|AV038945|HUSI-II	serine peptidase inhibitor, Kazal type 2	protein-coding
mm_68550.1	chr7	114276108	114276125	-	1	NA	promoter-TSS (NM_011965)	promoter-TSS (NM_011965)	0	NM_011965	26440	Mm.121265	NM_011965	ENSMUSG00000030751	Psma1	C2|HC2|Pros-30|alpha-type	proteasome (prosome, macropain) subunit, alpha type 1	protein-coding
mm_123045.1	chr14	55591055	55591070	-	1	NA	promoter-TSS (NM_011190)	promoter-TSS (NM_011190)	39	NM_001029855	19188	Mm.371573	NM_011190	ENSMUSG00000079197	Psme2	AA589371|AI788882|PA28b	proteasome (prosome, macropain) activator subunit 2 (PA28 beta)	protein-coding
mm_38604.1	chr4	141860575	141860586	-	1	NA	exon (NM_025994, exon 3 of 4)	exon (NM_025994, exon 3 of 4)	-14221	NM_001033875	76701	Mm.489680	NM_001033875	ENSMUSG00000062478	Ctrc	1810044E12Rik	chymotrypsin C (caldecrin)	protein-coding
mm_167351.1	chr8	83740391	83740401	+	1	NA	intron (NM_001163031, intron 1 of 17)	intron (NM_001163031, intron 1 of 17)	915	NM_001163029	26364	Mm.334648	NM_011925	ENSMUSG00000002885	Adgre5	AA409984|Cd97|TM7LN1	adhesion G protein-coupled receptor E5	protein-coding
mm_70707.1	chr8	15058971	15058974	+	1	NA	intron (NM_008664, intron 1 of 36)	intron (NM_008664, intron 1 of 36)	1319	NM_008664	17930	Mm.272115	NM_008664	ENSMUSG00000031461	Myom2	AW146149	myomesin 2	protein-coding
mm_6072.1	chr1	60910918	60910961	-	1	NA	intron (NM_001281976, intron 1 of 2)	intron (NM_001281976, intron 1 of 2)	1914	NM_001281976	12477	Mm.390	NM_009843	ENSMUSG00000026011	Ctla4	Cd152|Ctla-4|Ly-56	cytotoxic T-lymphocyte-associated protein 4	protein-coding
mm_32842.1	chr4	117849302	117849308	+	1	NA	intron (NM_008135, intron 2 of 13)	intron (NM_008135, intron 2 of 13)	14047	NM_008135	14664	Mm.244549	NM_008135	ENSMUSG00000028542	Slc6a9	Glyt-1|Glyt1	solute carrier family 6 (neurotransmitter transporter, glycine), member 9	protein-coding
mm_55998.1	chr6	86438619	86438636	-	1	NA	promoter-TSS (NM_001243742)	promoter-TSS (NM_001243742)	-19	NM_001243742	232196	Mm.404040	NM_146170	ENSMUSG00000046679	C87436	-	expressed sequence C87436	protein-coding
mm_100626.1	chr11	121702529	121702539	+	1	NA	5' UTR (NM_144797, exon 1 of 4)	5' UTR (NM_144797, exon 1 of 4)	107	NM_144797	210029	Mm.153566	NM_144797	ENSMUSG00000039208	Metrnl	9430048M07Rik|BC019776	meteorin, glial cell differentiation regulator-like	protein-coding
mm_112335.1	chr12	115981177	115981188	-	1	NA	Intergenic	Intergenic	-66542	NM_001004066	56220	Mm.254997	NM_019565	ENSMUSG00000042063	Zfp386	Kzf1|mKIAA4205	zinc finger protein 386 (Kruppel-like)	protein-coding
mm_108764.1	chr12	89454018	89454020	+	1	NA	intron (NM_172544, intron 8 of 19)	intron (NM_172544, intron 8 of 19)	-358464	NM_001252074	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding
mm_48805.1	chr5	148959976	148960001	-	1	NA	Intergenic	Intergenic	9738	NR_040686	71473	Mm.90306	NR_040686	ENSMUSG00000079069	8430423G03Rik	-	RIKEN cDNA 8430423G03 gene	ncRNA
mm_73688.1	chr8	111556629	111556641	+	1	NA	intron (NM_001168623, intron 1 of 4)	RMER21B|LTR|ERV1	18292	NM_001168623	170737	Mm.271578	NM_133206	ENSMUSG00000033545	Znrf1	B830022L21Rik|Rnf42|Zrfp1|nin283	zinc and ring finger 1	protein-coding
mm_60431.1	chr7	44476819	44476833	+	1	NA	Intergenic	L1MEd|LINE|L1	6479	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_57625.1	chr6	128279131	128279137	-	1	NA	intron (NM_011567, intron 1 of 11)	intron (NM_011567, intron 1 of 11)	21679	NM_001080979	21679	Mm.14774	NM_011567	ENSMUSG00000030353	Tead4	ETFR-2|Etfr2|FR-19|Rtef1|TEAD-4|TEF-3|Tcf13r1|Tef3|Tefr|Tefr1|Tefr1a	TEA domain family member 4	protein-coding
mm_92868.1	chr10	81627593	81627607	-	1	NA	promoter-TSS (NM_027480)	promoter-TSS (NM_027480)	8	NM_181586	50721	Mm.25643	NM_181586	ENSMUSG00000034748	Sirt6	2810449N18Rik|AI043036|Sir2l6	sirtuin 6	protein-coding
mm_129767.1	chr15	82693063	82693082	-	1	NA	Intergenic	Intergenic	-3014	NR_033515	627860	Mm.486636	NR_033515		Cyp2d37-ps	EG627860|Gm6800	cytochrome P450, family 2, subfamily d, polypeptide 37, pseudogene	pseudo
mm_7177.1	chr1	92439785	92439792	-	1	NA	TTS (NM_024197)	TTS (NM_024197)	24754	NR_105865	102465542		NR_105865	ENSMUSG00000098288	Mir6900	Gm27708|mmu-mir-6900	microRNA 6900	ncRNA
mm_48963.1	chr6	4600659	4600676	+	1	NA	promoter-TSS (NM_145398)	promoter-TSS (NM_145398)	-399	NM_145398	213819	Mm.270703	NM_145398	ENSMUSG00000015189	Casd1	Cas1|Cast1	CAS1 domain containing 1	protein-coding
mm_103025.1	chr11	69735178	69735191	-	1	NA	exon (NM_001291068, exon 29 of 29)	exon (NM_001291068, exon 29 of 29)	23449	NM_001291068	20020	Mm.16533	NM_009089	ENSMUSG00000005198	Polr2a	220kDa|Rpb1|Rpo2-1	polymerase (RNA) II (DNA directed) polypeptide A	protein-coding
mm_129692.1	chr15	81523262	81523312	-	1	NA	Intergenic	CpG	56971	NM_019712	56438	Mm.29405	NM_019712	ENSMUSG00000022400	Rbx1	1500002P15Rik|AA517855|ROC1	ring-box 1	protein-coding
mm_153095.1	chr19	32682844	32682847	-	1	NA	intron (NM_026487, intron 8 of 9)	intron (NM_026487, intron 8 of 9)	29453	NM_026487	67979	Mm.27123	NM_026487	ENSMUSG00000013662	Atad1	4921525H23Rik|AW107648|Thorase	ATPase family, AAA domain containing 1	protein-coding
mm_106309.1	chr11	118302149	118302159	-	1	NA	3' UTR (NM_011594, exon 5 of 5)	3' UTR (NM_011594, exon 5 of 5)	-11910	NM_001033528	72344	Mm.232293	NM_001033528	ENSMUSG00000033909	Usp36	2700002L06Rik|mKIAA1453	ubiquitin specific peptidase 36	protein-coding
mm_49453.1	chr6	29374478	29374480	+	1	NA	exon (NM_184053, exon 7 of 7)	exon (NM_184053, exon 7 of 7)	6034	NM_007538	12057	Mm.56987	NM_007538	ENSMUSG00000058831	Opn1sw	AW551857|Bcp	opsin 1 (cone pigments), short-wave-sensitive (color blindness, tritan)	protein-coding
mm_154002.1	chr19	53013450	53013461	-	1	NA	exon (NM_133216, exon 5 of 21)	exon (NM_133216, exon 5 of 21)	-2699	NR_105834	102465220		NR_105834	ENSMUSG00000098730	Mir6407	Gm27832|mmu-mir-6407	microRNA 6407	ncRNA
mm_1068.1	chr1	59172087	59172113	+	1	NA	intron (NM_028717, intron 27 of 33)	intron (NM_028717, intron 27 of 33)	-8711	NM_001164682	227157	Mm.474049	NM_145143	ENSMUSG00000079550	Mpp4	Dlg6	membrane protein, palmitoylated 4 (MAGUK p55 subfamily member 4)	protein-coding
mm_139597.1	chr17	57249451	57249522	+	1	NA	promoter-TSS (NM_001242389)	promoter-TSS (NM_001242389)	35	NM_001242389	106628	Mm.37368	NM_134125	ENSMUSG00000019487	Trip10	AI646975|Cip4	thyroid hormone receptor interactor 10	protein-coding
mm_22248.1	chr2	174807860	174807868	-	1	NA	Intergenic	MT2A|LTR|ERVL	47245	NM_007903	13616	Mm.9478	NM_007903	ENSMUSG00000027524	Edn3	ET-3|PPET3|ls|tmgc48	endothelin 3	protein-coding
mm_45841.1	chr5	87697140	87697146	-	1	NA	intron (NM_001286022, intron 2 of 7)	intron (NM_001286022, intron 2 of 7)	2282	NM_001286020	12991	Mm.268737	NM_009972	ENSMUSG00000063157	Csn2	Csnb	casein beta	protein-coding
mm_85863.1	chr9	110873991	110874009	-	1	NA	5' UTR (NM_146260, exon 3 of 6)	5' UTR (NM_146260, exon 3 of 6)	6083	NM_146260	20776	Mm.390229	NM_146260	ENSMUSG00000049555	Tmie	5131400L21Rik|Mm.87012|sr	transmembrane inner ear	protein-coding
mm_93288.1	chr10	96306928	96306938	-	1	NA	Intergenic	Intergenic	80726	NR_110448	74881	Mm.410819	NR_110448		4930459C07Rik	-	RIKEN cDNA 4930459C07 gene	ncRNA
mm_71361.1	chr8	45690102	45690112	+	1	NA	intron (NM_001310708, intron 1 of 19)	intron (NM_001310708, intron 1 of 19)	28114	NM_001310708	234214	Mm.211096	NM_172752	ENSMUSG00000031626	Sorbs2	2010203O03Rik|9430041O17Rik|A530071H08|Argbp2|mKIAA0777|nArgBP2	sorbin and SH3 domain containing 2	protein-coding
mm_142689.1	chr17	47737778	47737797	-	1	NA	promoter-TSS (NM_001161723)	promoter-TSS (NM_001161723)	-144	NM_001161723	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_71998.1	chr8	70649541	70649549	+	1	NA	3' UTR (NM_023217, exon 5 of 5)	3' UTR (NM_023217, exon 5 of 5)	10193	NM_023217	66522	Mm.154906	NM_023217	ENSMUSG00000056204	Pgpep1	2810003H13Rik|Gm19458|PAP-I|PGP|PGP-I|PGPI|Pcp	pyroglutamyl-peptidase I	protein-coding
mm_51433.1	chr6	78467483	78467527	+	1	NA	exon (NM_011260, exon 4 of 6)	exon (NM_011260, exon 4 of 6)	1369	NM_011260	19695	Mm.252385	NM_011260	ENSMUSG00000030017	Reg3g	AI449515|REG-3-gamma|reg III-gamma	regenerating islet-derived 3 gamma	protein-coding
mm_113903.1	chr13	49216157	49216202	+	1	NA	promoter-TSS (NM_026738)	promoter-TSS (NM_026738)	-153	NM_026738	68480	Mm.3336	NM_026738	ENSMUSG00000037960	Card19	1110007C09Rik|AI851695|Bincard	caspase recruitment domain family, member 19	protein-coding
mm_95856.1	chr11	57973257	57973265	+	1	NA	Intergenic	Intergenic	-35803	NM_028451	73158	Mm.248843	NM_028451	ENSMUSG00000037331	Larp1	1810024J12Rik|3110040D16Rik|Larp|mKIAA0731	La ribonucleoprotein domain family, member 1	protein-coding
mm_44509.1	chr5	24100468	24100485	-	1	NA	promoter-TSS (NM_026448)	promoter-TSS (NM_026448)	-114	NM_026448	52323	Mm.273768	NM_026448	ENSMUSG00000028986	Klhl7	2700038B03Rik|D5Ertd363e|SBBI26	kelch-like 7	protein-coding
mm_96402.1	chr11	67250866	67250876	+	1	NA	exon (NM_010855, exon 22 of 40)	exon (NM_010855, exon 22 of 40)	13059	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_121805.1	chr14	20269174	20269244	-	1	NA	promoter-TSS (NM_029006)	promoter-TSS (NM_029006)	-47	NM_029006	74571	Mm.105571	NM_029006	ENSMUSG00000023387	Kcnk16	4731413G05Rik|TALK-1|TALK1	potassium channel, subfamily K, member 16	protein-coding
mm_38158.1	chr4	135214492	135214504	-	1	NA	3' UTR (NM_013885, exon 6 of 6)	3' UTR (NM_013885, exon 6 of 6)	58262	NM_013885	29876	Mm.257765	NM_013885	ENSMUSG00000037242	Clic4	D0Jmb3|TU-74|mc3s5|mtCLIC	chloride intracellular channel 4 (mitochondrial)	protein-coding
mm_134611.1	chr16	20784737	20784739	-	1	NA	Intergenic	Intergenic	-50227	NM_009379	21832	Mm.3943	NM_009379	ENSMUSG00000022847	Thpo	Mgdf|Ml|Mpllg|Tpo	thrombopoietin	protein-coding
mm_61952.1	chr7	90207726	90207732	+	1	NA	3' UTR (NM_001252521, exon 20 of 20)	3' UTR (NM_001252521, exon 20 of 20)	57703	NM_029256	75338	Mm.487222	NM_029256	ENSMUSG00000030617	Ccdc83	4930549K11Rik|4930554C01Rik|4932423M01Rik	coiled-coil domain containing 83	protein-coding
mm_149906.1	chr19	25610534	25610553	+	1	NA	promoter-TSS (NM_177360)	promoter-TSS (NM_177360)	6	NM_177360	240590	Mm.62785	NM_177360	ENSMUSG00000042372	Dmrt3	-	doublesex and mab-3 related transcription factor 3	protein-coding
mm_47825.1	chr5	134264429	134264433	-	1	NA	intron (NM_001080746, intron 14 of 34)	PB1D9|SINE|Alu	-34806	NR_104383	17969	Mm.425296	NM_010876	ENSMUSG00000015950	Ncf1	NCF-47K|NOXO2|Ncf-1|p47-phox|p47<phox>|p47phox	neutrophil cytosolic factor 1	protein-coding
mm_121385.1	chr14	118953429	118953442	+	1	NA	intron (NM_008929, intron 2 of 11)	B3A|SINE|B2	15503	NM_008929	100037258	Mm.12616	NM_008929	ENSMUSG00000022136	Dnajc3	AA408985|AU067833|Dnajc3a|Dnajc3b|Prkri|mp58|p58|p58IPK	DnaJ heat shock protein family (Hsp40) member C3	protein-coding
mm_143464.1	chr17	70998011	70998013	-	1	NA	intron (NM_026064, intron 1 of 3)	intron (NM_026064, intron 1 of 3)	4521	NM_026064	67268	Mm.489605	NM_026064	ENSMUSG00000024048	Myl12a	2900073G15Rik|AI838292|C80200	myosin, light chain 12A, regulatory, non-sarcomeric	protein-coding
mm_45264.1	chr5	64255138	64255157	-	1	NA	intron (NM_001289514, intron 1 of 18)	RSINE1|SINE|B4	24790	NM_001289514	57915	Mm.286353	NM_019636	ENSMUSG00000029174	Tbc1d1	1110062G02Rik|AI385682|AW555803|Nob1|Nobq1|Tbc1|mKIAA1108	TBC1 domain family, member 1	protein-coding
mm_126080.1	chr15	77800816	77800826	+	1	NA	intron (NM_022410, intron 3 of 40)	intron (NM_022410, intron 3 of 40)	41354	NM_022410	17886	Mm.29677	NM_022410	ENSMUSG00000022443	Myh9	Fltn|Myhn-1|Myhn1|NMHCIIA|NMMHC-A|NMMHC-IIA|TU72.6	myosin, heavy polypeptide 9, non-muscle	protein-coding
mm_56681.1	chr6	113891295	113891375	-	1	NA	5' UTR (NM_001036684, exon 1 of 20)	5' UTR (NM_001036684, exon 1 of 20)	204	NM_001036684	11941	Mm.321755	NM_009723	ENSMUSG00000030302	Atp2b2	D6Abb2e|Gena300|PMCA2|Tmy|dfw|jog|wms|wri	ATPase, Ca++ transporting, plasma membrane 2	protein-coding
mm_7515.1	chr1	124045212	124045235	-	1	NA	intron (NM_199021, intron 1 of 25)	intron (NM_199021, intron 1 of 25)	336	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_56481.1	chr6	99096197	99096240	-	1	NA	intron (NM_001347345, intron 5 of 19)	intron (NM_001347345, intron 5 of 19)	-67920	NM_001197322	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_89785.1	chr10	102158873	102158889	+	1	NA	promoter-TSS (NM_001162369)	promoter-TSS (NM_001162369)	23	NM_001162368	67569	Mm.25252	NM_026243	ENSMUSG00000019888	Mgat4c	9130411I17Rik|GntIVh	MGAT4 family, member C	protein-coding
mm_14961.1	chr2	152081109	152081137	+	1	NA	promoter-TSS (NM_001160410)	promoter-TSS (NM_001160410)	-406	NM_001160410	545474	Mm.214317	NM_001160410	ENSMUSG00000060257	Scrt2	AW060659	scratch family zinc finger 2	protein-coding
mm_91852.1	chr10	59165265	59165267	-	1	NA	intron (NM_001024911, intron 9 of 9)	intron (NM_001024911, intron 9 of 9)	56581	NM_001024911	103080	Mm.346842	NM_001024910	ENSMUSG00000019917	Sept10	4921515A04Rik|9430099J10Rik|AA408298|AI874685	septin 10	protein-coding
mm_104662.1	chr11	97629295	97629305	-	1	NA	5' UTR (NM_175332, exon 1 of 1)	5' UTR (NM_175332, exon 1 of 1)	416	NM_175332	103551	Mm.24506	NM_175332	ENSMUSG00000043439	Epop	AA409164|AI413509|AW539173|E13|E130012A19Rik|esPRC2p48	elongin BC and polycomb repressive complex 2 associated protein	protein-coding
mm_113357.1	chr13	32802008	32802152	+	1	NA	promoter-TSS (NM_030215)	promoter-TSS (NM_030215)	50	NM_030215	78903	Mm.286680	NM_030215	ENSMUSG00000021400	Wrnip1	4833444L21Rik|WHIP|Wrnip	Werner helicase interacting protein 1	protein-coding
mm_100946.1	chr11	6546754	6546793	-	1	NA	promoter-TSS (NM_001190343)	promoter-TSS (NM_001190343)	-114	NM_146014	216527	Mm.221271	NM_146014	ENSMUSG00000000378	Ccm2	BC029157	cerebral cavernous malformation 2	protein-coding
mm_55130.1	chr6	50631124	50631125	-	1	NA	Intergenic	Intergenic	23269	NM_021892	60531	Mm.157158	NM_021892	ENSMUSG00000029831	Npvf	Rfrp	neuropeptide VF precursor	protein-coding
mm_84916.1	chr9	80067362	80067370	-	1	NA	5' UTR (NM_146003, exon 1 of 23)	5' UTR (NM_146003, exon 1 of 23)	463	NM_146003	215351	Mm.28232	NM_146003	ENSMUSG00000034252	Senp6	2810017C20Rik|E130319N12Rik|Susp1|mKIAA0797	SUMO/sentrin specific peptidase 6	protein-coding
mm_131642.1	chr16	20516963	20516999	+	1	NA	promoter-TSS (NM_007889)	promoter-TSS (NM_007889)	-5	NM_001347176	13544	Mm.247259	NM_007889	ENSMUSG00000003233	Dvl3	-	dishevelled segment polarity protein 3	protein-coding
mm_15696.1	chr2	163662885	163662906	+	1	NA	intron (NM_001039390, intron 2 of 4)	B3|SINE|B2	4437	NM_001164053	18769	Mm.10091	NM_011106	ENSMUSG00000035268	Pkig	PKIgamma	protein kinase inhibitor, gamma	protein-coding
mm_17898.1	chr2	35101198	35101222	-	1	NA	promoter-TSS (NM_178885)	promoter-TSS (NM_178885)	-525	NM_001243103	98870	Mm.415380	NM_178885	ENSMUSG00000035875	AI182371	AI046667	expressed sequence AI182371	protein-coding
mm_156649.1	chrX	157702575	157702585	+	1	NA	intron (NR_045569, intron 1 of 6)	intron (NR_045569, intron 1 of 6)	3607	NR_103722	66106	Mm.140340	NM_025357	ENSMUSG00000041476	Smpx	1010001C09Rik|Csl	small muscle protein, X-linked	protein-coding
mm_138021.1	chr17	33910392	33910418	+	1	NA	intron (NM_001199733, intron 1 of 7)	intron (NM_001199733, intron 1 of 7)	804	NM_001199733	13163	Mm.271809	NM_007829	ENSMUSG00000002307	Daxx	-	Fas death domain-associated protein	protein-coding
mm_121328.1	chr14	114946038	114946042	+	1	NA	promoter-TSS (NR_126551)	promoter-TSS (NR_126551)	-92	NR_126548	74982		NR_126548		1700100I10Rik	1700085D13Rik|4930481K08Rik	RIKEN cDNA 1700100I10 gene	ncRNA
mm_128431.1	chr15	50682445	50682458	-	1	NA	intron (NM_001310481, intron 4 of 5)	intron (NM_001310481, intron 4 of 5)	206598	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_78667.1	chr9	40710110	40710115	+	1	NA	intron (NM_133733, intron 1 of 6)	intron (NM_133733, intron 1 of 6)	24148	NM_133733	71566	Mm.280560	NM_133733	ENSMUSG00000032024	Clmp	9030425E11Rik|ACAM|ASP5|AW557819	CXADR-like membrane protein	protein-coding
mm_69240.1	chr7	127777735	127777770	-	1	NA	intron (NM_178029, intron 1 of 18)	G-rich|Low_complexity|Low_complexity	363	NM_178029	233904	Mm.435494	NM_010940	ENSMUSG00000042308	Setd1a	BC010250|KMT2F|Nsccn1|mKIAA0339|mNSC1	SET domain containing 1A	protein-coding
mm_84.1	chr1	6995221	6995221	+	1	NA	Intergenic	MTB_Mm-int|LTR|ERVL-MaLR	-93699	NM_183028	319263	Mm.21539	NM_183028	ENSMUSG00000051285	Pcmtd1	8430411F12Rik|A030012M09Rik	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding
mm_160756.1	chr10	82629863	82629863	+	1	NA	promoter-TSS (NR_037190)	promoter-TSS (NR_037190)	21	NR_037190	624784	Mm.284252	NR_037190		Gm9855	ENSMUSG00000051559	thymine DNA glycosylase pseudogene	pseudo
mm_152529.1	chr19	11324525	11324545	-	1	NA	exon (NM_001276398, exon 5 of 7)	exon (NM_001276398, exon 5 of 7)	10160	NM_001276398	109225	Mm.491251	NM_027836	ENSMUSG00000024672	Ms4a7	9130422I10Rik|A430103C15Rik|CD20l4|CFFMA	membrane-spanning 4-domains, subfamily A, member 7	protein-coding
mm_125491.1	chr15	54892554	54892560	+	1	NA	intron (NM_001136077, intron 8 of 25)	intron (NM_001136077, intron 8 of 25)	27589	NM_015744	18606	Mm.250256	NM_015744	ENSMUSG00000022425	Enpp2	ATX|E-NPP 2|Npps2|PD-Ialpha|Pdnp2|lysoPLD	ectonucleotide pyrophosphatase/phosphodiesterase 2	protein-coding
mm_26919.1	chr3	20242190	20242198	-	1	NA	promoter-TSS (NM_007753)	promoter-TSS (NM_007753)	-13	NM_007753	12873	Mm.1135	NM_007753	ENSMUSG00000001865	Cpa3	MC-CPA	carboxypeptidase A3, mast cell	protein-coding
mm_80325.1	chr9	75004362	75004374	+	1	NA	exon (NM_153584, exon 2 of 12)	exon (NM_153584, exon 2 of 12)	28257	NM_153584	235493	Mm.208955	NM_153584	ENSMUSG00000034858	Fam214a	6330415I01Rik|AI553555|C130047D21Rik|Kiaa1370|mKIAA1370	family with sequence similarity 214, member A	protein-coding
mm_32931.1	chr4	119234579	119234579	+	1	NA	intron (NM_001042411, intron 1 of 14)	intron (NM_001042411, intron 1 of 14)	750	NM_001042411	56401	Mm.27961	NM_019782	ENSMUSG00000028641	P3h1	2410024C15Rik|Gros1|Lepre1	prolyl 3-hydroxylase 1	protein-coding
mm_111950.1	chr12	109458117	109458141	-	1	NA	exon (NM_010052, exon 4 of 5)	exon (NM_010052, exon 4 of 5)	4674	NM_010052	13386	Mm.157069	NM_010052	ENSMUSG00000040856	Dlk1	AW742678|DLK-1|DlkI|FA1|Ly107|Peg9|SCP1|ZOG|pG2|pref-1	delta-like 1 homolog (Drosophila)	protein-coding
mm_15358.1	chr2	156371254	156371271	+	1	NA	intron (NM_027585, intron 11 of 12)	intron (NM_027585, intron 11 of 12)	21717	NR_024329	347740	Mm.324242	NR_024329		2900097C17Rik	1810005K14Rik|4930563C06Rik	RIKEN cDNA 2900097C17 gene	ncRNA
mm_158891.1	chr1	19213927	19213927	+	1	NA	intron (NM_001025305, intron 1 of 6)	CT-rich|Low_complexity|Low_complexity	1873	NM_001025305	21419	Mm.137021	NM_009334	ENSMUSG00000025927	Tfap2b	AI606113|AP-2(beta)|E130018K07Rik|Tcfap2b	transcription factor AP-2 beta	protein-coding
mm_86433.1	chr10	3863852	3863866	+	1	NA	intron (NM_001159942, intron 2 of 16)	intron (NM_001159942, intron 2 of 16)	-8808	NM_001033253	213783	Mm.150831	NM_001033253	ENSMUSG00000040624	Plekhg1	D10Ertd733e|Gm521|mKIAA1209	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	protein-coding
mm_122181.1	chr14	31577284	31577294	-	1	NA	promoter-TSS (NM_009937)	promoter-TSS (NM_009937)	94	NM_009937	382864	Mm.239821	NM_009937	ENSMUSG00000057606	Colq	A130034K24Rik	collagen-like tail subunit (single strand of homotrimer) of asymmetric acetylcholinesterase	protein-coding
mm_41480.1	chr5	91962945	91962958	+	1	NA	promoter-TSS (NR_028429)	promoter-TSS (NR_028429)	69	NR_028429	381650	Mm.159453	NR_028429	ENSMUSG00000102644	Thap6	4930534K21Rik|AI448650	THAP domain containing 6	pseudo
mm_33201.1	chr4	126286813	126286827	+	1	NA	promoter-TSS (NM_199473)	promoter-TSS (NM_199473)	26	NM_199473	329941	Mm.296327	NM_199473	ENSMUSG00000056174	Col8a2	AI429819	collagen, type VIII, alpha 2	protein-coding
mm_2657.1	chr1	125677157	125677168	+	1	NA	5' UTR (NM_027677, exon 1 of 2)	5' UTR (NM_027677, exon 1 of 2)	166	NM_027677	71111	Mm.32727	NM_027677	ENSMUSG00000026343	Gpr39	4933415E13Rik	G protein-coupled receptor 39	protein-coding
mm_36172.1	chr4	62085991	62085997	-	1	NA	exon (NM_001039544, exon 3 of 7)	exon (NM_001039544, exon 3 of 7)	1318	NM_001039544	17842	Mm.250267	NM_010845	ENSMUSG00000066154	Mup3	MUP15|MUPIII|Mup-3|Mup25	major urinary protein 3	protein-coding
mm_59182.1	chr7	24462464	24462466	+	1	NA	promoter-TSS (NM_011113)	promoter-TSS (NM_011113)	-18	NM_011113	18793	Mm.1359	NM_011113	ENSMUSG00000046223	Plaur	Cd87|u-PAR|uPAR	plasminogen activator, urokinase receptor	protein-coding
mm_104671.1	chr11	97661730	97661754	-	1	NA	Intergenic	Intergenic	-1670	NM_139311	246198	Mm.23685	NM_139311	ENSMUSG00000038437	Mllt6	AI315037|Af17	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 6	protein-coding
mm_159319.1	chr3	15426478	15426478	-	1	NA	promoter-TSS (NM_001002898)	promoter-TSS (NM_001002898)	-51	NM_001002898	320832	Mm.330924	NM_178792	ENSMUSG00000095788	Sirpb1a	9930027N05Rik|SIRP-beta|Sirpb|Sirpb1	signal-regulatory protein beta 1A	protein-coding
mm_51464.1	chr6	82403031	82403044	+	1	NA	5' UTR (NM_009313, exon 2 of 6)	5' UTR (NM_009313, exon 2 of 6)	562	NM_009313	21336	Mm.8055	NM_009313	ENSMUSG00000030043	Tacr1	Nk1r|Spr|Tac1r	tachykinin receptor 1	protein-coding
mm_64068.1	chr7	140882382	140882426	+	1	NA	promoter-TSS (NM_001127351)	promoter-TSS (NM_001127351)	10	NM_011875	23997	Mm.29760	NM_011875	ENSMUSG00000025487	Psmd13	S11	proteasome (prosome, macropain) 26S subunit, non-ATPase, 13	protein-coding
mm_127717.1	chr15	103034658	103034676	+	1	NA	5' UTR (NM_013553, exon 1 of 2)	5' UTR (NM_013553, exon 1 of 2)	272	NM_013553	15423	Mm.1351	NM_013553	ENSMUSG00000075394	Hoxc4	Hox-3.5	homeobox C4	protein-coding
mm_42525.1	chr5	115610444	115610444	+	1	NA	intron (NM_172719, intron 42 of 57)	intron (NM_172719, intron 42 of 57)	21372	NR_027810	66123	Mm.133063	NM_021417	ENSMUSG00000107121	1110006O24Rik	-	RIKEN cDNA 1110006O24 gene	ncRNA
mm_78517.1	chr9	32926606	32926620	+	1	NA	intron (NR_131058, intron 1 of 3)	intron (NR_131058, intron 1 of 3)	2353	NR_131058	330917	Mm.488283	NR_131058		Gm27162	A430016B06	predicted gene 27162	ncRNA
mm_103194.1	chr11	70646890	70646967	-	1	NA	promoter-TSS (NM_001316728)	promoter-TSS (NM_001316728)	111	NM_024211	67863	Mm.296082	NM_024211	ENSMUSG00000014606	Slc25a11	2310022P18Rik|2oxoc	solute carrier family 25 (mitochondrial carrier oxoglutarate carrier), member 11	protein-coding
mm_1064.1	chr1	59119823	59119861	+	1	NA	promoter-TSS (NM_001037812)	promoter-TSS (NM_001037812)	-36	NM_001037812	381259	Mm.261275	NM_001033449	ENSMUSG00000038079	Tmem237	AI853305|Als2cr4|Gm972	transmembrane protein 237	protein-coding
mm_61634.1	chr7	80261203	80261257	+	1	NA	promoter-TSS (NM_031375)	promoter-TSS (NM_031375)	15	NM_031375	83485	Mm.21175	NM_031375	ENSMUSG00000047084	Ngrn	AW552001	neugrin, neurite outgrowth associated	protein-coding
mm_166192.1	chr5	34001138	34001167	+	1	NA	3' UTR (NM_001001985, exon 3 of 3)	3' UTR (NM_001001985, exon 3 of 3)	5168	NM_001001985	269642	Mm.274610	NM_001001985	ENSMUSG00000048142	Nat8l	1110038O08Rik|Shati	N-acetyltransferase 8-like	protein-coding
mm_71989.1	chr8	70616817	70616930	+	1	NA	promoter-TSS (NM_153074)	promoter-TSS (NM_153074)	29	NM_153074	211228	Mm.132939	NM_153074	ENSMUSG00000049988	Lrrc25	Mapa	leucine rich repeat containing 25	protein-coding
mm_121811.1	chr14	20388914	20388927	-	1	NA	promoter-TSS (NM_134081)	promoter-TSS (NM_134081)	-10	NM_134081	108671	Mm.2871	NM_134081	ENSMUSG00000021811	Dnajc9	5330419I01Rik|AU020082	DnaJ heat shock protein family (Hsp40) member C9	protein-coding
mm_75376.1	chr8	45333239	45333257	-	1	NA	promoter-TSS (NM_133969)	promoter-TSS (NM_133969)	-52	NM_133969	102294	Mm.245297	NM_133969	ENSMUSG00000079057	Cyp4v3	AU043077|AW111961|Cyp4v2	cytochrome P450, family 4, subfamily v, polypeptide 3	protein-coding
mm_166248.1	chr5	77266185	77266209	+	1	NA	intron (NM_011263, intron 1 of 3)	CpG	703	NM_011263	19712	Mm.28840	NM_011263	ENSMUSG00000029249	Rest	2610008J04Rik|AA407358|NRSF|REST4	RE1-silencing transcription factor	protein-coding
mm_168077.1	chr10	113119205	113119205	+	1	NA	Intergenic	IMPB_01|Satellite|Satellite	-190179	NM_001033474	382423	Mm.431239	NM_001033474	ENSMUSG00000074748	Atxn7l3b	4921506J03Rik|6230409E21Rik|AI315132|ENSMUSG00000074747	ataxin 7-like 3B	protein-coding
mm_101946.1	chr11	50217801	50217845	-	1	NA	Intergenic	Intergenic	-7003	NM_011018	18412	Mm.40828	NM_011018	ENSMUSG00000015837	Sqstm1	A170|OSF-6|Osi|STAP|STONE14|p62	sequestosome 1	protein-coding
mm_32639.1	chr4	115056764	115056782	+	1	NA	intron (NM_011527, intron 1 of 4)	CpG	347	NM_011527	21349	Mm.239869	NM_011527	ENSMUSG00000028717	Tal1	Hpt|SCL/tal-1|Scl|bHLHa17|tal-1	T cell acute lymphocytic leukemia 1	protein-coding
mm_7947.1	chr1	133915116	133915133	-	1	NA	exon (NM_054077, exon 2 of 3)	exon (NM_054077, exon 2 of 3)	6277	NM_054077	116847	Mm.214514	NM_054077	ENSMUSG00000041577	Prelp	7330409J17Rik|SLRR2A	proline arginine-rich end leucine-rich repeat	protein-coding
mm_658.1	chr1	40434799	40434819	+	1	NA	intron (NM_001294171, intron 1 of 7)	L1ME2|LINE|L1	-4820	NM_001025602	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_135448.1	chr16	45654084	45654096	-	1	NA	promoter-TSS (NM_145389)	promoter-TSS (NM_145389)	28	NM_145389	212998	Mm.97511	NM_145389	ENSMUSG00000033187	BC016579	-	cDNA sequence, BC016579	protein-coding
mm_87464.1	chr10	51485711	51485747	+	1	NA	exon (NM_008147, exon 8 of 9)	exon (NM_008147, exon 8 of 9)	5117	NM_001291892	14727	Mm.439661	NM_008147	ENSMUSG00000062593	Lilr4b	Gp49a|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4B	protein-coding
mm_152214.1	chr19	7966599	7966601	-	1	NA	promoter-TSS (NM_134256)	promoter-TSS (NM_134256)	-573	NM_134256	171405	Mm.326517	NM_134256	ENSMUSG00000067656	Slc22a27	Oat9|mOAT6-L|mOAT6-S	solute carrier family 22, member 27	protein-coding
mm_85001.1	chr9	86880404	86880412	-	1	NA	promoter-TSS (NM_001277986)	promoter-TSS (NM_001277986)	-11	NM_001277982	20616	Mm.281651	NM_013669	ENSMUSG00000033419	Snap91	91kDa|AP180|F1-20|mKIAA0656	synaptosomal-associated protein 91	protein-coding
mm_74838.1	chr8	23237624	23237681	-	1	NA	promoter-TSS (NM_024240)	promoter-TSS (NM_024240)	16	NM_024240	109145	Mm.27945	NM_024240	ENSMUSG00000031546	Gins4	2810037C03Rik|4933405K01Rik|Sld5	GINS complex subunit 4 (Sld5 homolog)	protein-coding
mm_38295.1	chr4	136892868	136892937	-	1	NA	promoter-TSS (NM_007574)	promoter-TSS (NM_007574)	12	NM_007574	12262	Mm.439732	NM_007574	ENSMUSG00000036896	C1qc	AI385742|C1qg|Ciqc	complement component 1, q subcomponent, C chain	protein-coding
mm_124854.1	chr15	9528528	9528540	+	1	NA	intron (NM_008372, intron 1 of 7)	intron (NM_008372, intron 1 of 7)	1342	NM_008372	16197	Mm.389	NM_008372	ENSMUSG00000003882	Il7r	CD127|IL-7Ralpha	interleukin 7 receptor	protein-coding
mm_19707.1	chr2	103796990	103797088	-	1	NA	promoter-TSS (NM_001111290)	promoter-TSS (NM_001111290)	39	NM_001111290	53872	Mm.427589	NM_016739	ENSMUSG00000027184	Caprin1	AL022980|Caprin-1|Gpiap|Gpiap1|Mmgpip137|P137|rng105	cell cycle associated protein 1	protein-coding
mm_89505.1	chr10	94074040	94074044	+	1	NA	intron (NM_053072, intron 2 of 20)	intron (NM_053072, intron 2 of 20)	38041	NM_053072	13998	Mm.269596	NM_053072	ENSMUSG00000020021	Fgd6	AA123052|Etohd4|ZFYVE24	FYVE, RhoGEF and PH domain containing 6	protein-coding
mm_34861.1	chr4	155553419	155553435	+	1	NA	exon (NM_008142, exon 9 of 12)	exon (NM_008142, exon 9 of 12)	-8965	NM_138671	192185	Mm.28347	NM_138671	ENSMUSG00000029063	Nadk	4432404C02Rik|BC004012	NAD kinase	protein-coding
mm_84729.1	chr9	75038471	75038474	-	1	NA	intron (NM_021548, intron 1 of 2)	intron (NM_021548, intron 1 of 2)	740	NM_021548	59046	Mm.247837	NM_021548	ENSMUSG00000007656	Arpp19	19kDa|2700024H10Rik|ARPP-19|AW559096|Arpp12	cAMP-regulated phosphoprotein 19	protein-coding
mm_74366.1	chr8	128375004	128375016	+	1	NA	intron (NM_008737, intron 2 of 16)	intron (NM_008737, intron 2 of 16)	15769	NR_035436	100316680		NR_035436	ENSMUSG00000084523	Mir1903	Mirn1903|mmu-mir-1903	microRNA 1903	ncRNA
mm_4006.1	chr1	164796759	164796769	+	1	NA	promoter-TSS (NM_019759)	promoter-TSS (NM_019759)	32	NM_019759	56429	Mm.28935	NM_019759	ENSMUSG00000026574	Dpt	1810032B19Rik|5033416F05Rik|EQ-1|Eq1	dermatopontin	protein-coding
mm_85041.1	chr9	88959104	88959110	-	1	NA	intron (NM_009742, intron 1 of 1)	intron (NM_009742, intron 1 of 1)	2187	NM_009742	12044	Mm.425593	NM_009742	ENSMUSG00000102037	Bcl2a1a	A1|BB218357|Bcl2a1|Bfl-1|Hbpa1	B cell leukemia/lymphoma 2 related protein A1a	protein-coding
mm_90644.1	chr10	128720135	128720145	+	1	NA	TTS (NM_016811)	TTS (NM_016811)	13882	NM_021882	20431	Mm.16756	NM_021882	ENSMUSG00000025359	Pmel	D10H12S53E|D12S53Eh|Pmel17|Si|Silv|gp100|gp87	premelanosome protein	protein-coding
mm_145036.1	chr18	39362562	39362597	+	1	NA	intron (NM_175164, intron 21 of 22)	intron (NM_175164, intron 21 of 22)	124666	NM_008173	14815	Mm.129481	NM_008173	ENSMUSG00000024431	Nr3c1	GR|Grl-1|Grl1	nuclear receptor subfamily 3, group C, member 1	protein-coding
mm_139949.1	chr17	71204648	71204693	+	1	NA	promoter-TSS (NM_001164885)	promoter-TSS (NM_001164885)	16	NM_001164885	64898	Mm.227924	NM_022882	ENSMUSG00000024052	Lpin2	2610511G02Rik|AI481352|AW742896	lipin 2	protein-coding
mm_20969.1	chr2	151973038	151973043	-	1	NA	intron (NM_146127, intron 1 of 1)	intron (NM_146127, intron 1 of 1)	354	NM_001289151	73847	Mm.272444	NM_028666	ENSMUSG00000027459	Fam110a	1700008J10Rik|5430432M24Rik|AI747080	family with sequence similarity 110, member A	protein-coding
mm_14950.1	chr2	151973462	151973468	+	1	NA	promoter-TSS (NM_001289151)	promoter-TSS (NM_001289151)	-71	NM_001289151	73847	Mm.272444	NM_028666	ENSMUSG00000027459	Fam110a	1700008J10Rik|5430432M24Rik|AI747080	family with sequence similarity 110, member A	protein-coding
mm_2039.1	chr1	87225912	87225938	+	1	NA	exon (NM_001039169, exon 5 of 7)	exon (NM_001039169, exon 5 of 7)	11986	NM_001039169	26987	Mm.227183	NM_023314	ENSMUSG00000026254	Eif4e2	2700069E09Rik|AI036339|AV129531|D0H0S6743E|Eif4el3	eukaryotic translation initiation factor 4E member 2	protein-coding
mm_115709.1	chr13	14613018	14613056	-	1	NA	promoter-TSS (NM_008944)	promoter-TSS (NM_008944)	0	NM_029271	75398	Mm.36511	NM_029271	ENSMUSG00000015672	Mrpl32	0610033O15Rik	mitochondrial ribosomal protein L32	protein-coding
mm_151394.1	chr19	56436682	56436712	+	1	NA	intron (NM_007611, intron 5 of 6)	intron (NM_007611, intron 5 of 6)	-24940	NM_001164263	226245	Mm.156742	NM_172641	ENSMUSG00000035818	Plekhs1	9930023K05Rik	pleckstrin homology domain containing, family S member 1	protein-coding
mm_55176.1	chr6	51990352	51990364	-	1	NA	intron (NM_018773, intron 4 of 12)	intron (NM_018773, intron 4 of 12)	22191	NM_018773	54353	Mm.221479	NM_018773	ENSMUSG00000059182	Skap2	2610021A10Rik|AA960083|BB137539|RA70|SKAP-HOM|Saps|Scap2|mSKAP55R	src family associated phosphoprotein 2	protein-coding
mm_149109.1	chr19	8953887	8953938	+	1	NA	promoter-TSS (NM_197993)	promoter-TSS (NM_197993)	80	NM_197993	70044	Mm.165979	NM_197993	ENSMUSG00000071645	Tut1	2700038E08Rik|PAPD2|Rbm21|TUTase6|U6-TUTase|star-PAP	terminal uridylyl transferase 1, U6 snRNA-specific	protein-coding
mm_69468.1	chr7	133702516	133702524	-	1	NA	promoter-TSS (NM_001302087)	promoter-TSS (NM_001302087)	-20	NM_001302087	22276	Mm.3160	NM_009479	ENSMUSG00000030979	Uros	AI415298|UROIIIS|Uros3	uroporphyrinogen III synthase	protein-coding
mm_117842.1	chr13	98692760	98692787	-	1	NA	intron (NM_001025606, intron 1 of 3)	intron (NM_001025606, intron 1 of 3)	2058	NM_001025606	380863	Mm.28264	NM_001025606	ENSMUSG00000052485	Tmem171	Gm905	transmembrane protein 171	protein-coding
mm_125324.1	chr15	38470724	38470757	+	1	NA	Intergenic	CpG	19807	NR_105916	102465574		NR_105916	ENSMUSG00000099110	Mir6951	Gm27765|mmu-mir-6951	microRNA 6951	ncRNA
mm_79062.1	chr9	46230268	46230274	+	1	NA	exon (NM_009692, exon 4 of 4)	exon (NM_009692, exon 4 of 4)	1641	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2|apo-AI|apoA-I	apolipoprotein A-I	protein-coding
mm_87639.1	chr10	58359881	58359885	+	1	NA	intron (NM_026148, intron 1 of 9)	intron (NM_026148, intron 1 of 9)	-11571	NM_201242	110829	Mm.57734	NM_026148	ENSMUSG00000019920	Lims1	2310016J22Rik|4921524A02Rik|AI507642|AU021743|AW551584|C430041B13Rik|Lims1l|PINCH|PINCH1	LIM and senescent cell antigen-like domains 1	protein-coding
mm_80814.1	chr9	96525565	96525573	+	1	NA	Intergenic	Intergenic	-46894	NM_001311135	19823	Mm.28235	NM_011279	ENSMUSG00000051234	Rnf7	Rbx2|SAG	ring finger protein 7	protein-coding
mm_59574.1	chr7	28115623	28115627	+	1	NA	intron (NM_001122603, intron 17 of 19)	intron (NM_001122603, intron 17 of 19)	-13841	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_127308.1	chr15	100227928	100227943	+	1	NA	promoter-TSS (NM_007497)	promoter-TSS (NM_007497)	76	NM_007497	11908	Mm.676	NM_007497	ENSMUSG00000023027	Atf1	-	activating transcription factor 1	protein-coding
mm_9156.1	chr1	170959740	170959771	-	1	NA	TTS (NM_001077189)	TTS (NM_001077189)	16316	NM_001077189	14130	Mm.425062	NM_010187	ENSMUSG00000026656	Fcgr2b	AI528646|CD32|F630109E10Rik|Fc[g]RII|FcgRII|Fcgr2|Fcgr2a|Fcr-2|Fcr-3|Ly-17|Ly-m20|LyM-1|Lym-1|fcRII	Fc receptor, IgG, low affinity IIb	protein-coding
mm_43197.1	chr5	129020434	129020440	+	1	NA	intron (NM_009391, intron 1 of 6)	CpG	281	NM_009391	19384	Mm.297440	NM_009391	ENSMUSG00000029430	Ran	-	RAN, member RAS oncogene family	protein-coding
mm_159662.1	chr4	150406301	150406301	+	1	NA	5' UTR (NM_001085492, exon 2 of 23)	5' UTR (NM_001085492, exon 2 of 23)	124385	NM_001085492	68703	Mm.291274	NM_001085492	ENSMUSG00000039852	Rere	1110033A15Rik|AI414665|ARG|ARP|ATN1L|AW742570|Atr2|DNB1|eye<m03Jus>|eyes3|mKIAA0458	arginine glutamic acid dipeptide (RE) repeats	protein-coding
mm_152109.1	chr19	6941822	6941830	-	1	NA	promoter-TSS (NM_001177360)	promoter-TSS (NM_001177360)	-35	NM_007522	12015	Mm.4387	NM_007522	ENSMUSG00000024959	Bad	AI325008|Bbc2	BCL2-associated agonist of cell death	protein-coding
mm_24505.1	chr3	92484116	92484160	+	1	NA	3' UTR (NM_009264, exon 2 of 2)	3' UTR (NM_009264, exon 2 of 2)	1743	NM_009264	20753	Mm.331191	NM_009264	ENSMUSG00000050359	Sprr1a	AI528815|SPR1a|mSPRR1A	small proline-rich protein 1A	protein-coding
mm_72835.1	chr8	88276311	88276359	+	1	NA	intron (NM_007406, intron 1 of 27)	ID|SINE|ID	3932	NM_007406	11513	Mm.288206	NM_007406	ENSMUSG00000031659	Adcy7	AA407758	adenylate cyclase 7	protein-coding
mm_26765.1	chr3	8829715	8829731	-	1	NA	intron (NM_025434, intron 2 of 2)	Lx8|LINE|L1	94134	NM_025434	66230	Mm.38460	NM_025434	ENSMUSG00000040269	Mrps28	1500012D08Rik|AW061224	mitochondrial ribosomal protein S28	protein-coding
mm_123100.1	chr14	55882051	55882051	-	1	NA	3' UTR (NM_019820, exon 3 of 3)	3' UTR (NM_019820, exon 3 of 3)	2205	NM_019820	56410	Mm.97163	NM_019820	ENSMUSG00000040380	Cbln3	-	cerebellin 3 precursor protein	protein-coding
mm_160480.1	chr8	122495370	122495370	-	1	NA	intron (NM_001037298, intron 21 of 50)	intron (NM_001037298, intron 21 of 50)	19227	NM_153775	66965	Mm.482288	NM_153775	ENSMUSG00000049482	Ctu2	2310061F22Rik|C16orf84|Ncs2	cytosolic thiouridylase subunit 2	protein-coding
mm_107110.1	chr12	17992831	17992836	+	1	NA	Intergenic	CpG	302019	NM_016677	53602	Mm.313619	NM_016677	ENSMUSG00000071379	Hpcal1	NVP-3|Nvp3|VILIP3|Vnsl3|Vsnl3	hippocalcin-like 1	protein-coding
mm_13274.1	chr2	99800214	99800217	+	1	NA	Intergenic	RLTR43C|LTR|ERVK	-1824533	NM_009020	19374	Mm.4988	NM_009020	ENSMUSG00000032864	Rag2	Rag-2	recombination activating gene 2	protein-coding
mm_16529.1	chr2	181550378	181550388	+	1	NA	non-coding (NR_073369, exon 6 of 6)	non-coding (NR_073369, exon 6 of 6)	-28097	NR_027289	100271841	Mm.438007	NR_027289	ENSMUSG00000010492	Uckl1os	Gm16119|OTTMUSG00000030649	uridine-cytidine kinase 1-like 1, opposite strand	ncRNA
mm_50211.1	chr6	42265042	42265124	+	1	NA	promoter-TSS (NM_007610)	promoter-TSS (NM_007610)	98	NM_007610	12366	Mm.3921	NM_007610	ENSMUSG00000029863	Casp2	CASP-2|ICH-1|NEDD-2|Nedd2	caspase 2	protein-coding
mm_89894.1	chr10	110878127	110878134	+	1	NA	intron (NR_045979, intron 2 of 2)	intron (NR_045979, intron 2 of 2)	18377	NR_045979	75630	Mm.392786	NR_045979	ENSMUSG00000101801	1700020G17Rik	4930480D05Rik	RIKEN cDNA 1700020G17 gene	ncRNA
mm_132685.1	chr16	43072195	43072209	+	1	NA	intron (NM_001285805, intron 2 of 10)	intron (NM_001285805, intron 2 of 10)	116622	NR_002445	170658	Mm.375824	NR_002445		BC002163	-	NADH dehydrogenase Fe-S protein 5 pseudogene	pseudo
mm_138217.1	chr17	34312068	34312072	+	1	NA	intron (NM_010382, intron 2 of 5)	intron (NM_010382, intron 2 of 5)	6203	NM_010382	14969	Mm.22564	NM_010382	ENSMUSG00000060586	H2-Eb1	Eb|H-2Eb|H2Eb|Ia-4|Ia4	histocompatibility 2, class II antigen E beta	protein-coding
mm_71982.1	chr8	70596826	70596851	+	1	NA	TTS (NM_133772)	TTS (NM_133772)	2357	NM_023627	71780	Mm.29357	NM_023627	ENSMUSG00000019139	Isyna1	1300017C10Rik|AU018670	myo-inositol 1-phosphate synthase A1	protein-coding
mm_58850.1	chr7	16845812	16845826	+	1	NA	exon (NM_178900, exon 2 of 18)	exon (NM_178900, exon 2 of 18)	2754	NM_178900	101540	Mm.1881	NM_178900	ENSMUSG00000041187	Prkd2	AI325941|PKD2	protein kinase D2	protein-coding
mm_153614.1	chr19	43986125	43986133	-	1	NA	exon (NM_030703, exon 1 of 9)	exon (NM_030703, exon 1 of 9)	391	NM_030703	93721	Mm.206774	NM_030703	ENSMUSG00000025196	Cpn1	0610011F20Rik|CPN	carboxypeptidase N, polypeptide 1	protein-coding
mm_161345.1	chr14	52411040	52411040	-	1	NA	promoter-TSS (NM_146431)	promoter-TSS (NM_146431)	-113	NM_146431	258423	Mm.377492	NM_146431	ENSMUSG00000063106	Olfr1510	MOR223-6	olfactory receptor 1510	protein-coding
mm_165669.1	chr3	89226230	89226268	+	1	NA	TTS (NR_030579)	TTS (NR_030579)	949	NR_030579	100124470		NR_030579	ENSMUSG00000076255	Mir92b	Mirn92b|mir-92b|mmu-mir-92b	microRNA 92b	ncRNA
mm_62330.1	chr7	100493350	100493370	+	1	NA	promoter-TSS (NM_011671)	promoter-TSS (NM_011671)	2	NM_011671	22228	Mm.171378	NM_011671	ENSMUSG00000033685	Ucp2	Slc25a8	uncoupling protein 2 (mitochondrial, proton carrier)	protein-coding
mm_47417.1	chr5	123140101	123140125	-	1	NA	Intergenic	Intergenic	-2080	NM_001040398	208043	Mm.250391	NM_177581	ENSMUSG00000038384	Setd1b	AA516740|BC035291|KMT2G|mKIAA1076	SET domain containing 1B	protein-coding
mm_69819.1	chr7	141265244	141265258	-	1	NA	exon (NM_001252601, exon 4 of 10)	exon (NM_001252601, exon 4 of 10)	1173	NM_001252601	54123	Mm.3233	NM_016850	ENSMUSG00000025498	Irf7	-	interferon regulatory factor 7	protein-coding
mm_62073.1	chr7	92761356	92761385	+	1	NA	intron (NM_029494, intron 1 of 4)	intron (NM_029494, intron 1 of 4)	19656	NM_029494	75985	Mm.323004	NM_029494	ENSMUSG00000030643	Rab30	5033421K01Rik|AI323892|Rsb30	RAB30, member RAS oncogene family	protein-coding
mm_153138.1	chr19	34246136	34246144	-	1	NA	exon (NM_007392, exon 6 of 9)	exon (NM_007392, exon 6 of 9)	9233	NM_007392	11475	Mm.213025	NM_007392	ENSMUSG00000035783	Acta2	0610041G09Rik|Actvs|SMalphaA|a-SMA|alphaSMA	actin, alpha 2, smooth muscle, aorta	protein-coding
mm_112138.1	chr12	113000659	113000695	-	1	NA	promoter-TSS (NM_028193)	promoter-TSS (NM_028193)	-56	NM_028193	72308	Mm.196721	NM_028193	ENSMUSG00000011158	Brf1	2510002F24Rik|GTF3B|TAF3C|TAFIII90|TFIIIB90|mTFIIIB90	BRF1, RNA polymerase III transcription initiation factor 90 kDa subunit	protein-coding
mm_28118.1	chr3	86902006	86902016	-	1	NA	intron (NM_001195497, intron 2 of 15)	(A)n|Simple_repeat|Simple_repeat	18873	NM_001195496	70762	Mm.44490	NM_027539	ENSMUSG00000028078	Dclk2	6330415M09Rik|AU044875|CL2|CLICK2|Click-II|Dcamkl2	doublecortin-like kinase 2	protein-coding
mm_32570.1	chr4	109843802	109843816	+	1	NA	intron (NM_007983, intron 12 of 18)	intron (NM_007983, intron 12 of 18)	-134216	NM_172296	242620	Mm.32825	NM_172296	ENSMUSG00000047143	Dmrta2	Dmrt5	doublesex and mab-3 related transcription factor like family A2	protein-coding
mm_50456.1	chr6	48907677	48907681	+	1	NA	exon (NM_001161622, exon 3 of 5)	exon (NM_001161622, exon 3 of 5)	2693	NM_001161621	76507	Mm.213898	NM_029638	ENSMUSG00000029811	Aoc1	1600012D06Rik|Abp1|DAO	amine oxidase, copper-containing 1	protein-coding
mm_16597.1	chr2	4959775	4959778	-	1	NA	Intergenic	Intergenic	-16346	NM_001311208	68527	Mm.27791	NM_026754	ENSMUSG00000026668	Ucma	1110017I16Rik|AW121955|Grp	upper zone of growth plate and cartilage matrix associated	protein-coding
mm_46613.1	chr5	108065519	108065540	-	1	NA	promoter-TSS (NM_013827)	promoter-TSS (NM_013827)	-145	NM_001253877	17765	Mm.257149	NM_013827	ENSMUSG00000029267	Mtf2	9230112N11Rik|AA537621|C76717|M96|Pcl2	metal response element binding transcription factor 2	protein-coding
mm_112057.1	chr12	111907999	111908017	-	1	NA	promoter-TSS (NM_011625)	promoter-TSS (NM_011625)	47	NM_011625	21981	Mm.313076	NM_011625	ENSMUSG00000021285	Ppp1r13b	AI449786|ASPP1|AW545810|Tp53bp2|Trp53bp2|p85	protein phosphatase 1, regulatory (inhibitor) subunit 13B	protein-coding
mm_137898.1	chr17	31681661	31681677	+	1	NA	TTS (NM_001278570)	TTS (NM_001278570)	3738	NM_001278570	12954	Mm.1228	NM_013501	ENSMUSG00000024041	Cryaa	Acry-1|Crya-1|Crya1|DAcry-1|lop18	crystallin, alpha A	protein-coding
mm_91127.1	chr10	19591853	19591856	-	1	NA	promoter-TSS (NM_010511)	promoter-TSS (NM_010511)	-95	NM_010511	15979	Mm.549	NM_010511	ENSMUSG00000020009	Ifngr1	CD119|IFN-gammaR|Ifgr|Ifngr|Nktar	interferon gamma receptor 1	protein-coding
mm_28402.1	chr3	90242493	90242554	-	1	NA	promoter-TSS (NM_001307935)	promoter-TSS (NM_001307935)	27	NM_001307935	78284	Mm.299952	NM_030080	ENSMUSG00000027938	Creb3l4	1700012K17Rik|5330432F22Rik|AIBZIP|AV040530|AV258827|CREB4|JAL|TISP40|acre1	cAMP responsive element binding protein 3-like 4	protein-coding
mm_38385.1	chr4	138806274	138806288	-	1	NA	intron (NM_011110, intron 1 of 4)	intron (NM_011110, intron 1 of 4)	12976	NM_011110	18784	Mm.486532	NM_011110	ENSMUSG00000041193	Pla2g5	PLA2|sPLA2	phospholipase A2, group V	protein-coding
mm_47830.1	chr5	134275047	134275051	-	1	NA	intron (NM_001080749, intron 9 of 32)	intron (NM_001080749, intron 9 of 32)	39711	NM_001080746	14886	Mm.261570	NM_010365	ENSMUSG00000060261	Gtf2i	6030441I21Rik|BAP-135|Diws1t|GtfII-I|Spin|TFII-I|WBSCR6	general transcription factor II I	protein-coding
mm_49914.1	chr6	39035543	39035572	+	1	NA	intron (NM_011539, intron 9 of 12)	B4A|SINE|B4	32029	NR_040523	69986	Mm.490941	NR_040523	ENSMUSG00000100121	1700025N23Rik	-	RIKEN cDNA 1700025N23 gene	ncRNA
mm_56257.1	chr6	90782511	90782529	-	1	NA	intron (NM_001134384, intron 1 of 13)	intron (NM_001134384, intron 1 of 13)	27603	NM_001134384	232227	Mm.196943	NM_182784	ENSMUSG00000034312	Iqsec1	AW561907|BC026481|BRAG2|D6Ertd349e|cI-43	IQ motif and Sec7 domain 1	protein-coding
mm_23190.1	chr3	40955037	40955044	+	1	NA	intron (NM_001040399, intron 1 of 9)	(T)n|Simple_repeat|Simple_repeat	4409	NM_001040399	214048	Mm.46782	NM_027663	ENSMUSG00000025762	Larp1b	1700108L22Rik|4933421B21Rik|AA690246|Larp2	La ribonucleoprotein domain family, member 1B	protein-coding
mm_59775.1	chr7	28835860	28835875	+	1	NA	exon (NM_010707, exon 3 of 9)	exon (NM_010707, exon 3 of 9)	1697	NM_010707	16857	Mm.210336	NM_010707		Lgals6	galectin-6	lectin, galactose binding, soluble 6	protein-coding
mm_90216.1	chr10	121033961	121033983	+	1	NA	promoter-TSS (NM_011915)	promoter-TSS (NM_011915)	-32	NM_011915	24117	Mm.32831	NM_011915	ENSMUSG00000020218	Wif1	AW107799|WIF-1	Wnt inhibitory factor 1	protein-coding
mm_62524.1	chr7	102231026	102231069	+	1	NA	intron (NR_111937, intron 2 of 5)	intron (NR_111937, intron 2 of 5)	8019	NR_111937	233575	Mm.302013	NM_145583	ENSMUSG00000030990	Pgap2	1810006G21Rik|C76649|Frag1	post-GPI attachment to proteins 2	protein-coding
mm_32343.1	chr4	104766335	104766389	+	1	NA	promoter-TSS (NM_133882)	promoter-TSS (NM_133882)	45	NM_001316671	110382	Mm.87072	NM_133882	ENSMUSG00000029656	C8b	4930439B20Rik|AI595927	complement component 8, beta polypeptide	protein-coding
mm_141529.1	chr17	31844374	31844378	-	1	NA	3' UTR (NM_010831, exon 14 of 14)	3' UTR (NM_010831, exon 14 of 14)	11416	NM_010831	17691	Mm.290941	NM_010831	ENSMUSG00000024042	Sik1	Msk|Sik|Snf1lk	salt inducible kinase 1	protein-coding
mm_10257.1	chr2	9368463	9368511	+	1	NA	Intergenic	Intergenic	178972	NR_038180	73438	Mm.23558	NR_038180	ENSMUSG00000085580	1700061F12Rik	-	RIKEN cDNA 1700061F12 gene	ncRNA
mm_158639.1	chrX	155216339	155216369	-	1	NA	promoter-TSS (NM_009121)	promoter-TSS (NM_009121)	95	NM_009121	20229	Mm.2734	NM_009121	ENSMUSG00000025283	Sat1	AA617398|SSAT|Sat	spermidine/spermine N1-acetyl transferase 1	protein-coding
mm_172877.1	chr9	44604641	44604656	+	1	NA	promoter-TSS (NM_001110826)	promoter-TSS (NM_001110826)	-244	NM_001110826	13209	Mm.267061	NM_007841	ENSMUSG00000032097	Ddx6	1110001P04Rik|E230023J21Rik|HLR2|mRCK/P54|p54|rck	DEAD (Asp-Glu-Ala-Asp) box polypeptide 6	protein-coding
mm_102497.1	chr11	60417023	60417056	-	1	NA	promoter-TSS (NM_145427)	promoter-TSS (NM_145427)	60	NM_145427	246782	Mm.41651	NM_145427	ENSMUSG00000042709	Atpaf2	ATP12|ATP12p	ATP synthase mitochondrial F1 complex assembly factor 2	protein-coding
mm_88469.1	chr10	77581775	77581800	+	1	NA	promoter-TSS (NM_145925)	promoter-TSS (NM_145925)	20	NM_145925	108705	Mm.28853	NM_145925	ENSMUSG00000009291	Pttg1ip	1810010L20Rik|AI314311|AU018448|C79540	pituitary tumor-transforming 1 interacting protein	protein-coding
mm_138269.1	chr17	34604784	34604790	+	1	NA	Intergenic	Intergenic	-1074	NM_001163379	55979	Mm.8684	NM_018862	ENSMUSG00000034254	Agpat1	1-AGP|1-AGPAT|AW047140	1-acylglycerol-3-phosphate O-acyltransferase 1 (lysophosphatidic acid acyltransferase, alpha)	protein-coding
mm_58183.1	chr6	142964109	142964128	-	1	NA	5' UTR (NM_011374, exon 1 of 5)	5' UTR (NM_011374, exon 1 of 5)	334	NM_011374	20449	Mm.260838	NM_011374	ENSMUSG00000030283	St8sia1	9330109E03Rik|GD3S|Sia-T|Siat8|Siat8a	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 1	protein-coding
mm_125772.1	chr15	74588410	74588415	+	1	NA	intron (NM_174991, intron 30 of 30)	intron (NM_174991, intron 30 of 30)	47906	NM_001177437	69439	Mm.263708	NM_001177437	ENSMUSG00000022603	Mroh4	1700016M24Rik	maestro heat-like repeat family member 4	protein-coding
mm_167578.1	chr9	44767401	44767424	+	1	NA	intron (NM_145985, intron 1 of 9)	CpG	396	NM_145985	213827	Mm.371682	NM_145985	ENSMUSG00000032096	Arcn1	4632432M07Rik|nur17	archain 1	protein-coding
mm_35293.1	chr4	21890655	21890660	-	1	NA	intron (NM_172687, intron 1 of 6)	B3|SINE|B2	10982	NM_172687	230027	Mm.5662	NM_172687	ENSMUSG00000028247	Coq3	4732433J24|C77934	coenzyme Q3 methyltransferase	protein-coding
mm_164590.1	chr17	26535332	26535357	+	1	NA	Intergenic	Intergenic	-26168	NM_026170	67458	Mm.30496	NM_026170	ENSMUSG00000001576	Ergic1	1200007D18Rik|maa-136	endoplasmic reticulum-golgi intermediate compartment (ERGIC) 1	protein-coding
mm_11819.1	chr2	44243128	44243155	+	1	NA	exon (NM_153820, exon 12 of 14)	exon (NM_153820, exon 12 of 14)	-177817	NR_040622	320872	Mm.445023	NR_040622	ENSMUSG00000085089	Arhgap15os	A430092G05Rik	Rho GTPase activating protein 15, opposite strand	ncRNA
mm_15863.1	chr2	164832882	164832935	+	1	NA	promoter-TSS (NM_008906)	promoter-TSS (NM_008906)	36	NM_001038492	19025	Mm.359633	NM_008906	ENSMUSG00000017760	Ctsa	AU019505|PPCA|Ppgb	cathepsin A	protein-coding
mm_116796.1	chr13	53533240	53533286	-	1	NA	Intergenic	Intergenic	-60483	NM_013601	17702	Mm.1763	NM_013601	ENSMUSG00000021469	Msx2	BB122635|Hox-8|Hox8|Hox8.1	msh homeobox 2	protein-coding
mm_126020.1	chr15	76690559	76690579	+	1	NA	5' UTR (NM_033371, exon 2 of 11)	5' UTR (NM_033371, exon 2 of 11)	-6157	NM_182805	76282	Mm.30130	NM_182805	ENSMUSG00000022546	Gpt	1300007J06Rik|2310022B03Rik|ALT|ALT1|Gpt-1|Gpt1	glutamic pyruvic transaminase, soluble	protein-coding
mm_21152.1	chr2	154421263	154421276	-	1	NA	Intergenic	Intergenic	-13185	NM_009228	20648	Mm.1541	NM_009228	ENSMUSG00000027488	Snta1	AW228934|Snt1	syntrophin, acidic 1	protein-coding
mm_5954.1	chr1	56971282	56971305	-	1	NA	promoter-TSS (NR_024325)	promoter-TSS (NR_024325)	41	NM_139146	212712	Mm.145599	NM_139146	ENSMUSG00000038331	Satb2	mKIAA1034	special AT-rich sequence binding protein 2	protein-coding
mm_134838.1	chr16	26371656	26371681	-	1	NA	5' UTR (NM_016674, exon 1 of 4)	5' UTR (NM_016674, exon 1 of 4)	171	NM_016674	12737	Mm.289441	NM_016674	ENSMUSG00000022512	Cldn1	AI596271	claudin 1	protein-coding
mm_102655.1	chr11	63887766	63887769	-	1	NA	3' UTR (NM_018805, exon 2 of 2)	3' UTR (NM_018805, exon 2 of 2)	34517	NM_018805	54710	Mm.274426	NM_018805	ENSMUSG00000070407	Hs3st3b1	3-OST-3B|3OST3B1|3Ost3b|AU041882|AW536289|Hs3st3b|m3-OST-3B	heparan sulfate (glucosamine) 3-O-sulfotransferase 3B1	protein-coding
mm_79810.1	chr9	64177753	64177780	+	1	NA	exon (NM_024212, exon 8 of 10)	exon (NM_024212, exon 8 of 10)	-1531	NM_183316	330959	Mm.24082	NM_183316	ENSMUSG00000032398	Snapc5	2010103A03Rik	small nuclear RNA activating complex, polypeptide 5	protein-coding
mm_168386.1	chr11	24040868	24040875	-	1	NA	Intergenic	B1_Mm|SINE|Alu	-37185	NM_016707	14025	Mm.53687	NM_016707	ENSMUSG00000000861	Bcl11a	2810047E18Rik|BCL-11A|Ctip1|D930021L15Rik|Evi9|Evi9a|Evi9b|Evi9c|mKIAA1809	B cell CLL/lymphoma 11A (zinc finger protein)	protein-coding
mm_4207.1	chr1	171250417	171250433	+	1	NA	5' UTR (NM_172845, exon 1 of 9)	5' UTR (NM_172845, exon 1 of 9)	296	NM_172845	240913	Mm.491147	NM_172845	ENSMUSG00000006403	Adamts4	ADAM-TS4|ADAMTS-2|ADMP-1	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 4	protein-coding
mm_145889.1	chr18	65582282	65582310	+	1	NA	intron (NM_207255, intron 1 of 5)	intron (NM_207255, intron 1 of 5)	2066	NM_207255	328977	Mm.286232	NM_207255	ENSMUSG00000042439	Zfp532	C530030I18Rik|Znf532|mKIAA1629	zinc finger protein 532	protein-coding
mm_25235.1	chr3	103886238	103886248	+	1	NA	exon (NM_008979, exon 13 of 21)	exon (NM_008979, exon 13 of 21)	25966	NM_008979	19260	Mm.395	NM_008979	ENSMUSG00000027843	Ptpn22	70zpep|PEP|Ptpn8	protein tyrosine phosphatase, non-receptor type 22 (lymphoid)	protein-coding
mm_119613.1	chr14	51114369	51114379	+	1	NA	Intergenic	Intergenic	-2179	NM_203508	219026	Mm.297297	NM_203508	ENSMUSG00000072575	Eddm3b	Fam12|Gm75	epididymal protein 3B	protein-coding
mm_146410.1	chr18	84088187	84088206	+	1	NA	promoter-TSS (NM_146090)	promoter-TSS (NM_146090)	38	NM_146090	225791	Mm.147052	NM_146090	ENSMUSG00000049090	Zadh2	C530046K17Rik|PTGR-3|Pthr3	zinc binding alcohol dehydrogenase, domain containing 2	protein-coding
mm_70013.1	chr7	142472103	142472153	-	1	NA	5' UTR (NM_019391, exon 1 of 11)	5' UTR (NM_019391, exon 1 of 11)	285	NM_019391	16985	Mm.234003	NM_019391	ENSMUSG00000018819	Lsp1	Lsp-1|WP34|p50|pp52	lymphocyte specific 1	protein-coding
mm_97050.1	chr11	72441342	72441386	+	1	NA	promoter-TSS (NM_016776)	promoter-TSS (NM_016776)	-14	NM_016776	18432	Mm.147946	NM_016776	ENSMUSG00000040463	Mybbp1a	AL024407|AU019902|P160|p160MBP|p67MBP	MYB binding protein (P160) 1a	protein-coding
mm_168.1	chr1	13094904	13094906	+	1	NA	Intergenic	RLTR24|LTR|ERV1	32258	NM_001081209	383491	Mm.309380	NM_001081209	ENSMUSG00000042414	Prdm14	-	PR domain containing 14	protein-coding
mm_108575.1	chr12	84996437	84996441	+	1	NA	5' UTR (NM_001347421, exon 1 of 20)	5' UTR (NM_001347421, exon 1 of 20)	118	NM_178363	56531	Mm.153183	NM_178363	ENSMUSG00000021244	Ylpm1	A930013E17Rik|ZAP|Zap3	YLP motif containing 1	protein-coding
mm_105000.1	chr11	100362157	100362157	-	1	NA	Intergenic	Intergenic	-6016	NM_010404	15114	Mm.281700	NM_010404	ENSMUSG00000006930	Hap1	HAP-1	huntingtin-associated protein 1	protein-coding
mm_89482.1	chr10	93640978	93641002	+	1	NA	promoter-TSS (NM_021320)	promoter-TSS (NM_021320)	-59	NM_021320	57764	Mm.483868	NM_021320	ENSMUSG00000020019	Ntn4	-	netrin 4	protein-coding
mm_118023.1	chr13	100833316	100833367	-	1	NA	promoter-TSS (NM_022885)	promoter-TSS (NM_022885)	86	NM_022885	69048	Mm.402215	NM_022885	ENSMUSG00000021629	Slc30a5	1810010K08Rik|AF233321|ZNT5|ZTL1|ZnT-5|Zntl1	solute carrier family 30 (zinc transporter), member 5	protein-coding
mm_79890.1	chr9	65294428	65294437	+	1	NA	5' UTR (NM_011802, exon 1 of 14)	5' UTR (NM_011802, exon 1 of 14)	172	NM_011802	270166	Mm.30088	NM_011802	ENSMUSG00000015357	Clpx	AU014732|E330029I21	caseinolytic mitochondrial matrix peptidase chaperone subunit	protein-coding
mm_62767.1	chr7	112241864	112241874	+	1	NA	intron (NM_001193305, intron 2 of 25)	intron (NM_001193305, intron 2 of 25)	16033	NM_001193305	320878	Mm.52312	NM_177282	ENSMUSG00000038244	Mical2	5330438E18Rik|9530064J02|MICAL-2|mKIAA0750	microtubule associated monooxygenase, calponin and LIM domain containing 2	protein-coding
mm_97117.1	chr11	74830889	74830903	+	1	NA	promoter-TSS (NM_010813)	promoter-TSS (NM_010813)	-28	NM_010813	17428	Mm.3759	NM_010813	ENSMUSG00000000282	Mnt	Rox|bHLHd3	max binding protein	protein-coding
mm_33144.1	chr4	125127452	125127463	+	1	NA	intron (NM_153159, intron 1 of 5)	intron (NM_153159, intron 1 of 5)	424	NM_153159	230738	Mm.402	NM_153159	ENSMUSG00000042677	Zc3h12a	BC036563|MCPIP|MCPIP-1|Mcpip1|Reg1	zinc finger CCCH type containing 12A	protein-coding
mm_78361.1	chr9	26733744	26733815	+	1	NA	promoter-TSS (NM_001310766)	promoter-TSS (NM_001310766)	-29	NM_001310766	76898	Mm.218788	NM_029792	ENSMUSG00000045994	B3gat1	0710007K08Rik|AI846286|GlcAT-P|Glcatp|Hnk1	beta-1,3-glucuronyltransferase 1 (glucuronosyltransferase P)	protein-coding
mm_72837.1	chr8	88289079	88289091	+	1	NA	promoter-TSS (NM_001037723)	promoter-TSS (NM_001037723)	19	NM_001037723	11513	Mm.288206	NM_007406	ENSMUSG00000031659	Adcy7	AA407758	adenylate cyclase 7	protein-coding
mm_134597.1	chr16	20619827	20619871	-	1	NA	TTS (NM_025462)	TTS (NM_025462)	1429	NM_028420	73047	Mm.425977	NM_028420	ENSMUSG00000051146	Camk2n2	2900075A18Rik	calcium/calmodulin-dependent protein kinase II inhibitor 2	protein-coding
mm_31764.1	chr4	63399520	63399522	+	1	NA	intron (NM_001045514, intron 1 of 21)	intron (NM_001045514, intron 1 of 21)	-1281	NM_001305432	100182	Mm.387725	NM_001045514	ENSMUSG00000039158	Akna	AI597013	AT-hook transcription factor	protein-coding
mm_141487.1	chr17	31268355	31268358	-	1	NA	intron (NM_025290, intron 3 of 8)	intron (NM_025290, intron 3 of 8)	9000	NM_025290	22092	Mm.12743	NM_025290	ENSMUSG00000024033	Rsph1	MCA|Tsga2	radial spoke head 1 homolog (Chlamydomonas)	protein-coding
mm_57694.1	chr6	128522066	128522080	-	1	NA	exon (NM_007376, exon 6 of 36)	exon (NM_007376, exon 6 of 36)	4647	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_88144.1	chr10	69533634	69533666	+	1	NA	promoter-TSS (NM_170688)	promoter-TSS (NM_170688)	-58	NM_170729	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_3215.1	chr1	135840858	135840878	+	1	NA	promoter-TSS (NM_001130176)	promoter-TSS (NM_001130176)	7	NM_001130176	21956	Mm.247470	NM_011619	ENSMUSG00000026414	Tnnt2	Tnt|cTnT	troponin T2, cardiac	protein-coding
mm_106629.1	chr11	120866620	120866639	-	1	NA	exon (NM_027745, exon 16 of 19)	exon (NM_027745, exon 16 of 19)	-42082	NM_007988	14104	Mm.236443	NM_007988	ENSMUSG00000025153	Fasn	A630082H08Rik|FAS	fatty acid synthase	protein-coding
mm_145448.1	chr18	60212586	60212608	+	1	NA	5' UTR (NM_001033767, exon 2 of 3)	5' UTR (NM_001033767, exon 2 of 3)	520	NM_001033767	240327	Mm.357104	NM_001033767	ENSMUSG00000073555	Gm4951	EG240327|Ifgga2	predicted gene 4951	protein-coding
mm_78775.1	chr9	43744027	43744036	+	1	NA	promoter-TSS (NM_021424)	promoter-TSS (NM_021424)	-545	NM_021424	58235	Mm.335096	NM_021424	ENSMUSG00000032012	Nectin1	AI835281|AW549174|Cd111|HIgR|HveC|PRR|PRR1|Pvrl1|nectin-1	nectin cell adhesion molecule 1	protein-coding
mm_140267.1	chr17	84683114	84683128	+	1	NA	promoter-TSS (NM_031884)	promoter-TSS (NM_031884)	0	NM_001347418	67470	Mm.26581	NM_026180	ENSMUSG00000024254	Abcg8	1300003C16Rik|AI114946|sterolin-2	ATP-binding cassette, sub-family G (WHITE), member 8	protein-coding
mm_138281.1	chr17	34608998	34609021	+	1	NA	promoter-TSS (NM_018862)	promoter-TSS (NM_018862)	-5	NM_018862	55979	Mm.8684	NM_018862	ENSMUSG00000034254	Agpat1	1-AGP|1-AGPAT|AW047140	1-acylglycerol-3-phosphate O-acyltransferase 1 (lysophosphatidic acid acyltransferase, alpha)	protein-coding
mm_51953.1	chr6	91755159	91755174	+	1	NA	3' UTR (NM_009320, exon 15 of 15)	3' UTR (NM_009320, exon 15 of 15)	52227	NM_001159507	243547	Mm.333264	NM_001033353	ENSMUSG00000030098	Grip2	-	glutamate receptor interacting protein 2	protein-coding
mm_16210.1	chr2	173065979	173065980	+	1	NA	Intergenic	RLTR10D|LTR|ERVK	44077	NM_019547	56190	Mm.485782	NM_019547	ENSMUSG00000027510	Rbm38	Rnpc1|Seb4|Seb4l	RNA binding motif protein 38	protein-coding
mm_82176.1	chr9	123851325	123851335	+	1	NA	TTS (NM_011798)	TTS (NM_011798)	331	NM_148925	17281	Mm.252941	NM_148925	ENSMUSG00000025241	Fyco1	2810409M01Rik|Mem2|RUFY3|ZFYVE7	FYVE and coiled-coil domain containing 1	protein-coding
mm_40716.1	chr5	65934923	65935006	+	1	NA	Intergenic	Intergenic	-32160	NM_001081104	231252	Mm.140015	NM_001081104	ENSMUSG00000029205	Chrna9	2410015I05Rik|Acra9|EG666827|Gm8311	cholinergic receptor, nicotinic, alpha polypeptide 9	protein-coding
mm_47166.1	chr5	120743643	120743663	-	1	NA	intron (NM_001347448, intron 3 of 11)	RLTR17B_Mm|LTR|ERVK	6195	NM_145227	246728	Mm.260926	NM_145227	ENSMUSG00000032690	Oas2	Oasl11	2'-5' oligoadenylate synthetase 2	protein-coding
mm_109922.1	chr12	8539561	8539614	-	1	NA	promoter-TSS (NM_001286385)	promoter-TSS (NM_001286385)	-21	NM_001286385	328059	Mm.46326	NM_177802	ENSMUSG00000020600	Slc7a15	Arpat	solute carrier family 7 (cationic amino acid transporter, y+ system), member 15	protein-coding
mm_40266.1	chr5	38505293	38505293	+	1	NA	Intergenic	Intergenic	-3141	NM_145559	117591	Mm.260137	NM_145559	ENSMUSG00000005107	Slc2a9	Glut9|SLC2A9B|SLC2a9A	solute carrier family 2 (facilitated glucose transporter), member 9	protein-coding
mm_131255.1	chr16	10769989	10769995	+	1	NA	Intergenic	Intergenic	15544	NM_009896	12703	Mm.130	NM_009896	ENSMUSG00000038037	Socs1	Cish1|Cish7|JAB|SOCS-1|SSI-1	suppressor of cytokine signaling 1	protein-coding
mm_4387.1	chr1	172219517	172219528	+	1	NA	exon (NM_009813, exon 1 of 11)	exon (NM_009813, exon 1 of 11)	373	NM_009813	12372	Mm.12829	NM_009813	ENSMUSG00000007122	Casq1	CSQ|CSQ-1|CSQ1|sCSQ	calsequestrin 1	protein-coding
mm_58378.1	chr6	149101675	149101686	-	1	NA	promoter-TSS (NM_177192)	promoter-TSS (NM_177192)	0	NM_177192	320560	Mm.426874	NM_177192	ENSMUSG00000030313	Dennd5b	9330160C06Rik|AI852444|D030011O10Rik|ENSMUSG00000072657|Gm17524	DENN/MADD domain containing 5B	protein-coding
mm_160792.1	chr11	3202377	3202377	+	1	NA	promoter-TSS (NM_001166549)	promoter-TSS (NM_001166549)	24	NM_001166548	74203	Mm.255649	NM_023743	ENSMUSG00000020454	Eif4enif1	2610509L04Rik|A930019J01Rik|AA410001|AU021239|Clast4|D11Ertd166e	eukaryotic translation initiation factor 4E nuclear import factor 1	protein-coding
mm_126799.1	chr15	87327232	87327233	+	1	NA	Intergenic	Intergenic	-217067	NM_001252310	106014	Mm.244319	NM_134096	ENSMUSG00000054863	Fam19a5	TAFA5|Tafa-5|Tara-5	family with sequence similarity 19, member A5	protein-coding
mm_64606.1	chr7	3249622	3249633	-	1	NA	5' UTR (NM_001033431, exon 1 of 10)	5' UTR (NM_001033431, exon 1 of 10)	113	NM_001033431	378425	Mm.277152	NM_001033431	ENSMUSG00000078817	Nlrp12	Nalp12|PYPAF7	NLR family, pyrin domain containing 12	protein-coding
mm_123645.1	chr14	68655765	68655774	-	1	NA	promoter-TSS (NM_010082)	promoter-TSS (NM_010082)	73	NM_010082	13522	Mm.117450	NM_010082	ENSMUSG00000014725	Adam28	C130072N01Rik|D430033C21Rik|Dtgn1|MDC-L|MDCL|TECADAM|eMDCII	a disintegrin and metallopeptidase domain 28	protein-coding
mm_73356.1	chr8	105518737	105518753	+	1	NA	promoter-TSS (NM_008289)	promoter-TSS (NM_008289)	-1	NM_008289	15484	Mm.5079	NM_008289	ENSMUSG00000031891	Hsd11b2	11HSD2	hydroxysteroid 11-beta dehydrogenase 2	protein-coding
mm_172386.1	chr7	133179862	133179877	+	1	NA	Intergenic	BGLII|LTR|ERVK	51618	NR_046279	74970	Mm.491044	NR_046279	ENSMUSG00000109816	4930483O08Rik	-	RIKEN cDNA 4930483O08 gene	ncRNA
mm_99284.1	chr11	101320724	101320737	+	1	NA	exon (NM_011192, exon 10 of 11)	exon (NM_011192, exon 10 of 11)	-4333	NM_178932	237940	Mm.302277	NM_178932	ENSMUSG00000078651	Aoc2	RAO	amine oxidase, copper containing 2 (retina-specific)	protein-coding
mm_37958.1	chr4	133339284	133339334	-	1	NA	promoter-TSS (NM_199306)	promoter-TSS (NM_199306)	6	NM_199306	230796	Mm.226576	NM_199306	ENSMUSG00000037622	Wdtc1	Gm695|adipose|adp	WD and tetratricopeptide repeats 1	protein-coding
mm_157670.1	chrX	59134380	59134392	-	1	NA	promoter-TSS (NM_010200)	promoter-TSS (NM_010200)	50	NM_010200	14168	Mm.7995	NM_010200	ENSMUSG00000031137	Fgf13	Fhf2	fibroblast growth factor 13	protein-coding
mm_126924.1	chr15	91673061	91673076	+	1	NA	promoter-TSS (NM_025730)	promoter-TSS (NM_025730)	-156	NM_025730	66725	Mm.37558	NM_025730	ENSMUSG00000036273	Lrrk2	4921513O20Rik|9330188B09Rik|AW561911|D630001M17Rik|Gm927|cI-46	leucine-rich repeat kinase 2	protein-coding
mm_170251.1	chr1	80967827	80967838	+	1	NA	Intergenic	RLTR10D2|LTR|ERVK	-109485	NM_172849	241134	Mm.313904	NM_172849	ENSMUSG00000054976	Nyap2	9430031J16Rik|Jr6|Kiaa1486	neuronal tyrosine-phophorylated phosphoinositide 3-kinase adaptor 2	protein-coding
mm_9596.1	chr1	175453992	175453996	-	1	NA	intron (NM_001347195, intron 2 of 17)	intron (NM_001347195, intron 2 of 17)	38551	NM_011880	24012	Mm.7956	NM_011880	ENSMUSG00000026527	Rgs7	-	regulator of G protein signaling 7	protein-coding
mm_74241.1	chr8	124792974	124792980	+	1	NA	promoter-TSS (NM_198632)	promoter-TSS (NM_198632)	-42	NM_198632	330863	Mm.422769	NM_198632	ENSMUSG00000036913	Trim67	D130049O21Rik|TNL	tripartite motif-containing 67	protein-coding
mm_160496.1	chr9	4383522	4383522	+	1	NA	promoter-TSS (NM_145609)	promoter-TSS (NM_145609)	-15	NM_145609	78100	Mm.206549	NM_145609	ENSMUSG00000041124	Msantd4	8430410K20Rik|Mysantd4	Myb/SANT-like DNA-binding domain containing 4 with coiled-coils	protein-coding
mm_28819.1	chr3	96269436	96269473	-	1	NA	promoter-TSS (NM_175666)	promoter-TSS (NM_175666)	-246	NM_175666	319189	Mm.297655	NM_175666	ENSMUSG00000105827	Hist2h2bb	H2b-616	histone cluster 2, H2bb	protein-coding
mm_118114.1	chr13	103921812	103921837	-	1	NA	Intergenic	Intergenic	-1238	NM_001005868	59079	Mm.277354	NM_021563	ENSMUSG00000021709	Erbin	1700028E05Rik|Erbb2ip|mKIAA1225	Erbb2 interacting protein	protein-coding
mm_20799.1	chr2	144266187	144266218	-	1	NA	promoter-TSS (NR_030762)	promoter-TSS (NR_030762)	0	NR_030762	100313519	Mm.453538	NR_030762	ENSMUSG00000077714	Snord17	MBI-43	small nucleolar RNA, C/D box 17	snoRNA
mm_166364.1	chr5	124186652	124186676	+	1	NA	intron (NM_011256, intron 2 of 24)	intron (NM_011256, intron 2 of 24)	518	NM_001289472	19679	Mm.44261	NM_011256	ENSMUSG00000029406	Pitpnm2	NIR3|RDGBA2|Rdgb2|mKIAA1457	phosphatidylinositol transfer protein, membrane-associated 2	protein-coding
mm_158451.1	chrX	140543161	140543166	-	1	NA	promoter-TSS (NM_010286)	promoter-TSS (NM_010286)	24	NM_010286	14605	Mm.22216	NM_010286	ENSMUSG00000031431	Tsc22d3	DIP|Dsip1|Gilz|TSC-22R|Tilz3	TSC22 domain family, member 3	protein-coding
mm_96498.1	chr11	68153876	68153882	+	1	NA	intron (NM_018768, intron 7 of 7)	MTD|LTR|ERVL-MaLR	-67013	NR_105833	102465219		NR_105833	ENSMUSG00000099174	Mir6406	Gm27981|mmu-mir-6406	microRNA 6406	ncRNA
mm_164894.1	chr18	65023742	65023744	+	1	NA	5' UTR (NM_031881, exon 1 of 30)	5' UTR (NM_031881, exon 1 of 30)	216	NM_031881	83814	Mm.98668	NM_031881	ENSMUSG00000024589	Nedd4l	1300012C07Rik|Nedd4-2|Nedd4b	neural precursor cell expressed, developmentally down-regulated gene 4-like	protein-coding
mm_50614.1	chr6	49823675	49823686	+	1	NA	exon (NM_023456, exon 2 of 4)	exon (NM_023456, exon 2 of 4)	970	NM_023456	109648	Mm.154796	NM_023456	ENSMUSG00000029819	Npy	0710005A05Rik	neuropeptide Y	protein-coding
mm_105902.1	chr11	114983003	114983023	-	1	NA	3' UTR (NM_145437, exon 4 of 4)	3' UTR (NM_145437, exon 4 of 4)	6873	NM_145437	217305	Mm.275986	NM_145437	ENSMUSG00000034641	Cd300ld	4732429D16Rik|CLM5|Cd300ld1|LMIR4|MAIR-IV|clm-5	CD300 molecule like family member d	protein-coding
mm_159251.1	chr2	152415769	152415769	+	1	NA	promoter-TSS (NM_175126)	promoter-TSS (NM_175126)	182	NR_110368	228778	Mm.70959	NM_177656	ENSMUSG00000032680	6820408C15Rik	-	RIKEN cDNA 6820408C15 gene	protein-coding
mm_2608.1	chr1	120340570	120340580	+	1	NA	promoter-TSS (NM_207233)	promoter-TSS (NM_207233)	-7	NM_207233	226359	Mm.337409	NM_207233	ENSMUSG00000036907	C1ql2	BC040774|CTRP10	complement component 1, q subcomponent-like 2	protein-coding
mm_120958.1	chr14	77520131	77520139	+	1	NA	intron (NM_001253759, intron 7 of 19)	RLTR25A|LTR|ERVK	-13267	NR_033141	629678	Mm.390721	NM_001037935	ENSMUSG00000067973	Gm6994	EG629678	predicted gene 6994	ncRNA
mm_25844.1	chr3	129217891	129217922	+	1	NA	intron (NM_011098, intron 4 of 4)	intron (NM_011098, intron 4 of 4)	3974	NM_001287048	18741	Mm.246804	NM_011098	ENSMUSG00000028023	Pitx2	9430085M16Rik|Brx1|Brx1b|Munc30|Otlx2|Ptx2|Rieg	paired-like homeodomain transcription factor 2	protein-coding
mm_9723.1	chr1	180193159	180193180	-	1	NA	intron (NM_023341, intron 1 of 14)	intron (NM_023341, intron 1 of 14)	316	NM_001163290	67426	Mm.38330	NM_023341	ENSMUSG00000026489	Coq8a	4632432J16Rik|AI462003|Adck3|Cabc1|mKIAA0451	coenzyme Q8A	protein-coding
mm_46945.1	chr5	114910987	114911003	-	1	NA	exon (NM_011854, exon 6 of 6)	exon (NM_011854, exon 6 of 6)	-12245	NM_145209	231655	Mm.95479	NM_145209	ENSMUSG00000041827	Oasl1	7530414C13Rik|oasl9	2'-5' oligoadenylate synthetase-like 1	protein-coding
mm_76904.1	chr8	105827643	105827666	-	1	NA	promoter-TSS (NM_024445)	promoter-TSS (NM_024445)	-90	NM_024445	72236	Mm.386810	NM_024445	ENSMUSG00000031893	Tsnaxip1	1700016K08Rik|TXI1	translin-associated factor X (Tsnax) interacting protein 1	protein-coding
mm_120815.1	chr14	75131533	75131563	+	1	NA	promoter-TSS (NM_027581)	promoter-TSS (NM_027581)	425	NM_001247984	18826	Mm.153911	NM_008879	ENSMUSG00000021998	Lcp1	AW536232|D14Ertd310e|LCP-1|Pls2|pp65	lymphocyte cytosolic protein 1	protein-coding
mm_170196.1	chr17	6655815	6655817	-	1	NA	promoter-TSS (NM_001166630).2	promoter-TSS (NM_001166630).2	15	NM_001166630	100040563	Mm.457381	NM_001166630	ENSMUSG00000000579	Dynlt1c	100040603|Dynlt1d	dynein light chain Tctex-type 1C	protein-coding
mm_167616.1	chr9	57075436	57075443	+	1	NA	promoter-TSS (NM_011378)	promoter-TSS (NM_011378)	-937	NM_001110350	20466	Mm.15755	NM_011378	ENSMUSG00000042557	Sin3a	AW553200|Sin3|mKIAA4126|mSin3A	transcriptional regulator, SIN3A (yeast)	protein-coding
mm_58869.1	chr7	16950158	16950164	+	1	NA	Intergenic	Intergenic	5479	NM_001099636	434128	Mm.483018	NM_001099636	ENSMUSG00000070802	Pnmal2	EG434128	PNMA-like 2	protein-coding
mm_140857.1	chr17	23726265	23726307	-	1	NA	promoter-TSS (NM_023058)	promoter-TSS (NM_023058)	-50	NM_023058	268930	Mm.182193	NM_023058	ENSMUSG00000023908	Pkmyt1	6230424P17|AW209059|Myt1	protein kinase, membrane associated tyrosine/threonine 1	protein-coding
mm_144051.1	chr17	90456031	90456049	-	1	NA	promoter-TSS (NM_001346961)	promoter-TSS (NM_001346961)	-160	NM_001346959	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_102924.1	chr11	69600644	69600653	-	1	NA	3' UTR (NM_013415, exon 7 of 7)	3' UTR (NM_013415, exon 7 of 7)	5312	NM_013415	11932	Mm.235204	NM_013415	ENSMUSG00000041329	Atp1b2	Amog|Atpb-2	ATPase, Na+/K+ transporting, beta 2 polypeptide	protein-coding
mm_68780.1	chr7	122186225	122186231	-	1	NA	promoter-TSS (NM_001316689)	promoter-TSS (NM_001316689)	3	NM_012016	26918	Mm.20452	NM_012016	ENSMUSG00000030866	Ern2	Ern1|Ire1|Ire1b|ire1-beta|mIre1	endoplasmic reticulum (ER) to nucleus signalling 2	protein-coding
mm_172129.1	chr6	3268684	3268701	-	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	-19827	NR_036696	667335	Mm.380219	NR_036696	ENSMUSG00000106779	Gm8579	EG667335	spermatogenesis associated glutamate (E)-rich protein 4a pseudogene	pseudo
mm_105291.1	chr11	102469840	102469866	-	1	NA	promoter-TSS (NM_010575)	promoter-TSS (NM_010575)	30	NM_010575	16399	Mm.26646	NM_010575	ENSMUSG00000034664	Itga2b	AI172977|CD41|CD41B|GpIIb|alphaIIb	integrin alpha 2b	protein-coding
mm_34902.1	chr4	155638559	155638574	+	1	NA	exon (NM_007661, exon 7 of 20)	exon (NM_007661, exon 7 of 20)	13697	NM_007661	12537	Mm.267410	NM_007661	ENSMUSG00000029062	Cdk11b	AA989746|CDK11-p110|CDK11-p46|CDK11-p58|Cdc11b|Cdc2l1|Cdc2l2|Cdk11|p58	cyclin-dependent kinase 11B	protein-coding
mm_145857.1	chr18	65455859	65455882	+	1	NA	intron (NM_172833, intron 8 of 15)	intron (NM_172833, intron 8 of 15)	24873	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_22725.1	chr3	19644468	19644474	+	1	NA	promoter-TSS (NM_001081281)	promoter-TSS (NM_001081281)	11	NM_001081281	381485	Mm.35419	NM_001081281	ENSMUSG00000060913	Trim55	D830041C10Rik|Murf2|Rnf29	tripartite motif-containing 55	protein-coding
mm_63211.1	chr7	126272464	126272474	+	1	NA	promoter-TSS (NM_145587)	promoter-TSS (NM_145587)	-150	NM_145587	104175	Mm.29660	NM_145587	ENSMUSG00000042978	Sbk1	Sbk	SH3-binding kinase 1	protein-coding
mm_10839.1	chr2	24949748	24949801	+	1	NA	promoter-TSS (NM_147179)	promoter-TSS (NM_147179)	-3	NM_026021	67187	Mm.296106	NM_026021	ENSMUSG00000026974	Zmynd19	2700064H14Rik|AA536891|AU014915|mizip	zinc finger, MYND domain containing 19	protein-coding
mm_27971.1	chr3	80802591	80802601	-	1	NA	5' UTR (NM_013540, exon 1 of 16)	5' UTR (NM_013540, exon 1 of 16)	195	NM_013540	14800	Mm.220224	NM_013540	ENSMUSG00000033981	Gria2	GluA2|GluR-B|Glur-2|Glur2	glutamate receptor, ionotropic, AMPA2 (alpha 2)	protein-coding
mm_132798.1	chr16	45094082	45094091	+	1	NA	promoter-TSS (NM_026439)	promoter-TSS (NM_026439)	33	NM_026439	67896	Mm.181074	NM_026439	ENSMUSG00000022665	Ccdc80	2610001E17Rik|DRO1|Ssg1|Urb	coiled-coil domain containing 80	protein-coding
mm_139591.1	chr17	57225250	57225282	+	1	NA	exon (NM_009778, exon 5 of 41)	exon (NM_009778, exon 5 of 41)	2870	NM_009778	12266	Mm.19131	NM_009778	ENSMUSG00000024164	C3	AI255234|ASP|HSE-MSF|Plp	complement component 3	protein-coding
mm_116716.1	chr13	51569342	51569345	-	1	NA	Intergenic	Intergenic	-2259	NM_009167	20418	Mm.131870	NM_009167	ENSMUSG00000021448	Shc3	N-Shc|Rai|ShcC	src homology 2 domain-containing transforming protein C3	protein-coding
mm_40526.1	chr5	57919816	57919826	+	1	NA	intron (NM_001122758, intron 2 of 2)	B4A|SINE|B4	201740	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_59381.1	chr7	26099126	26099129	+	1	NA	Intergenic	Lx4B|LINE|L1	37632	NM_007813	13089	Mm.482696	NM_007813	ENSMUSG00000040583	Cyp2b13	-	cytochrome P450, family 2, subfamily b, polypeptide 13	protein-coding
mm_42740.1	chr5	120678549	120678556	+	1	NA	intron (NM_013832, intron 20 of 21)	intron (NM_013832, intron 20 of 21)	29364	NM_001281999	19415	Mm.41209	NM_013832	ENSMUSG00000029602	Rasal1	MRASAL	RAS protein activator like 1 (GAP1 like)	protein-coding
mm_173309.1	chrY	90734700	90734700	+	1	NA	Intergenic	IMPB_01|Satellite|Satellite	20350	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_142894.1	chr17	51833279	51833299	-	1	NA	promoter-TSS (NM_001163632)	promoter-TSS (NM_001163632)	1	NM_001163632	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_158873.1	chrY	1286518	1286548	-	1	NA	promoter-TSS (NM_012008)	promoter-TSS (NM_012008)	80	NM_012008	26900	Mm.302938	NM_012008	ENSMUSG00000069045	Ddx3y	8030469F12Rik|D1Pas1-rs1|Dby	DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, Y-linked	protein-coding
mm_58667.1	chr7	6995487	6995498	+	1	NA	exon (NM_001080965, exon 1 of 7)	exon (NM_001080965, exon 1 of 7)	107	NM_001080965	20871	Mm.261572	NM_020572	ENSMUSG00000070837	Aurkc	AIE1|AIK3|ARK-3|IAK3|Stk13	aurora kinase C	protein-coding
mm_156415.1	chrX	140664872	140664882	+	1	NA	Intergenic	CpG	-13151	NM_011845	23947	Mm.131097	NM_011845	ENSMUSG00000000266	Mid2	FXY2|Trim1	midline 2	protein-coding
mm_159445.1	chr3	130474604	130474604	+	1	NA	intron (NM_029838, intron 7 of 37)	intron (NM_029838, intron 7 of 37)	-142844	NM_001163587	71760	Mm.29125	NM_027907	ENSMUSG00000019232	Etnppl	1300019H02Rik|AI195447|Agxt2l1	ethanolamine phosphate phospholyase	protein-coding
mm_59100.1	chr7	19697466	19697498	+	1	NA	exon (NM_009696, exon 3 of 4)	exon (NM_009696, exon 3 of 4)	916	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_155605.1	chrX	82954203	82954204	+	1	NA	intron (NM_007868, intron 1 of 78)	intron (NM_007868, intron 1 of 78)	5333	NM_007868	13405	Mm.275608	NM_007868	ENSMUSG00000045103	Dmd	DXSmh7|DXSmh9|Dp427|Dp71|dys|mdx|pke	dystrophin, muscular dystrophy	protein-coding
mm_10298.1	chr2	10449085	10449104	+	1	NA	intron (NM_001198808, intron 8 of 22)	(T)n|Simple_repeat|Simple_repeat	-17569	NR_130333	100526481		NR_130333	ENSMUSG00000092793	Mir466m	mmu-mir-466m	microRNA 466m	ncRNA
mm_156406.1	chrX	140277757	140277765	+	1	NA	Intergenic	CpG	-33187	NR_037208	100499512		NR_037208	ENSMUSG00000093102	Mir3475	mir-3475|mmu-mir-3475	microRNA 3475	ncRNA
mm_126577.1	chr15	82274980	82275034	+	1	NA	promoter-TSS (NM_011889)	promoter-TSS (NM_011889)	72	NM_011889	24050	Mm.309707	NM_011889	ENSMUSG00000022456	Sept3	3110018K01Rik|AV154067|B530002E20Rik|Sep3	septin 3	protein-coding
mm_151738.1	chr19	4943050	4943101	-	1	NA	promoter-TSS (NM_172835)	promoter-TSS (NM_172835)	17	NM_172835	240518	Mm.277580	NM_172835	ENSMUSG00000024901	Peli3	6030441F14Rik|A930011L17|BC028931	pellino 3	protein-coding
mm_11234.1	chr2	29803619	29803634	+	1	NA	intron (NM_011989, intron 1 of 12)	intron (NM_011989, intron 1 of 12)	946	NM_011989	26569	Mm.330113	NM_011989	ENSMUSG00000059316	Slc27a4	BB144259|FATP4	solute carrier family 27 (fatty acid transporter), member 4	protein-coding
mm_50119.1	chr6	41535077	41535097	+	1	NA	Intergenic	Intergenic	13311	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_142105.1	chr17	35835763	35835783	-	1	NA	exon (NM_011655, exon 4 of 4)	exon (NM_011655, exon 4 of 4)	2528	NM_011655	22154	Mm.273538	NM_011655	ENSMUSG00000001525	Tubb5	AA408537|AI596182|B130022C14Rik|M(beta)5	tubulin, beta 5 class I	protein-coding
mm_36901.1	chr4	107803382	107803392	-	1	NA	intron (NR_033496, intron 2 of 20)	CpG-10112	1128	NM_001080926	16975	Mm.442134	NM_053073	ENSMUSG00000028613	Lrp8	4932703M08Rik|AA921429|AI848122|ApoER2|Lr8b	low density lipoprotein receptor-related protein 8, apolipoprotein e receptor	protein-coding
mm_118255.1	chr13	112354250	112354271	-	1	NA	intron (NM_001168403, intron 7 of 11)	intron (NM_001168403, intron 7 of 11)	65742	NM_001168404	77318	Mm.159895	NM_029898	ENSMUSG00000049985	Ankrd55	C030011J08Rik	ankyrin repeat domain 55	protein-coding
mm_60754.1	chr7	45513702	45513710	+	1	NA	promoter-TSS (NM_008807)	promoter-TSS (NM_008807)	0	NM_008807	56734	Mm.439742	NM_008807	ENSMUSG00000023467	Tulp2	Pdet	tubby-like protein 2	protein-coding
mm_123175.1	chr14	57571552	57571588	-	1	NA	promoter-TSS (NM_026526)	promoter-TSS (NM_026526)	-1	NM_026526	68043	Mm.45225	NM_026526	ENSMUSG00000021951	Eef1akmt1	2510005D08Rik|AW045965|Ayu21-96|Gt(pU21)96Imeg|GtAyu21-96|N6amt2	eukaryotic translation elongation factor 1 alpha lysine methyltransferase 1	protein-coding
mm_58582.1	chr7	4922598	4922613	+	1	NA	TTS (NM_170759)	TTS (NM_170759)	354	NM_201355	269854	Mm.42652	NM_201355	ENSMUSG00000035285	Nat14	BC047219	N-acetyltransferase 14	protein-coding
mm_56.1	chr1	6537392	6537423	+	1	NA	intron (NM_001244693, intron 2 of 22)	L1Md_F2|LINE|L1	50176	NM_001244692	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding
mm_107875.1	chr12	69963413	69963440	+	1	NA	promoter-TSS (NR_036607)	promoter-TSS (NR_036607)	17	NR_036607	100040999	Mm.394588	NR_036607	ENSMUSG00000079076	Gm3086	-	RuvB-like protein 1 pseudogene	pseudo
mm_26072.1	chr3	136670257	136670264	+	1	NA	5' UTR (NM_001293622, exon 1 of 13)	5' UTR (NM_001293622, exon 1 of 13)	194	NM_001293622	19055	Mm.331389	NM_008913	ENSMUSG00000028161	Ppp3ca	2900074D19Rik|CN|Caln|Calna|CnA	protein phosphatase 3, catalytic subunit, alpha isoform	protein-coding
mm_17350.1	chr2	26608067	26608073	-	1	NA	Intergenic	GA-rich|Low_complexity|Low_complexity	-3653	NM_026212	67512	Mm.24244	NM_026212	ENSMUSG00000026922	Agpat2	2510002J07Rik|AV000834|BSCL|BSCL1|LPAAB|LPAAT-beta	1-acylglycerol-3-phosphate O-acyltransferase 2 (lysophosphatidic acid acyltransferase, beta)	protein-coding
mm_66495.1	chr7	45061629	45061647	-	1	NA	promoter-TSS (NM_025533)	promoter-TSS (NM_025533)	14	NM_022999	65116	Mm.379098	NM_022999	ENSMUSG00000007837	Prrg2	1600014G02Rik|2510041M06Rik|N4WBP1	proline-rich Gla (G-carboxyglutamic acid) polypeptide 2	protein-coding
mm_61164.1	chr7	59228954	59228967	+	1	NA	5' UTR (NM_001033962, exon 1 of 11)	5' UTR (NM_001033962, exon 1 of 11)	208	NM_011668	22215	Mm.9002	NM_011668	ENSMUSG00000025326	Ube3a	4732496B02|5830462N02Rik|A130086L21Rik|Hpve6a|mKIAA4216	ubiquitin protein ligase E3A	protein-coding
mm_68817.1	chr7	126082084	126082098	-	1	NA	exon (NM_001101488, exon 1 of 7)	exon (NM_001101488, exon 1 of 7)	320	NM_001101488	269994	Mm.39599	NM_001101488	ENSMUSG00000046182	Gsg1l	AI852434|C230098I05Rik|G630023A01Rik|Gm637|g1l	GSG1-like	protein-coding
mm_11023.1	chr2	26628466	26628550	+	1	NA	promoter-TSS (NM_019833)	promoter-TSS (NM_019833)	51	NM_019833	56279	Mm.279863	NM_019833	ENSMUSG00000036186	Fam69b	AB030186|AW209000|B230317C12Rik|PIP49	family with sequence similarity 69, member B	protein-coding
mm_162028.1	chr19	53143908	53143908	+	1	NA	promoter-TSS (NM_013758)	promoter-TSS (NM_013758)	-89	NM_013758	27360	Mm.426080	NM_013758	ENSMUSG00000025026	Add3	AI463285|R75380	adducin 3 (gamma)	protein-coding
mm_52501.1	chr6	115238968	115238978	+	1	NA	promoter-TSS (NM_001326560)	promoter-TSS (NM_001326560)	-21	NM_001326560	20965	Mm.441431	NM_013681	ENSMUSG00000009394	Syn2	2900074L19Rik|AI836018|AI841723	synapsin II	protein-coding
mm_152031.1	chr19	6084699	6084731	-	1	NA	promoter-TSS (NM_026410)	promoter-TSS (NM_026410)	176	NM_024231	81909	Mm.289471	NM_024231	ENSMUSG00000024792	Zfpl1	1500015B20Rik	zinc finger like protein 1	protein-coding
mm_24365.1	chr3	90086343	90086353	+	1	NA	intron (NM_001293749, intron 1 of 7)	intron (NM_001293749, intron 1 of 7)	6827	NM_001293749	59069	Mm.240839	NM_022314	ENSMUSG00000027940	Tpm3	TM30nm|TMnm|Tm5NM|Tpm-5|Tpm5|Trop-5|gamma-TM|hTM30nm|hTMnm	tropomyosin 3, gamma	protein-coding
mm_59523.1	chr7	27607998	27608009	+	1	NA	intron (NM_001331109, intron 1 of 13)	intron (NM_001331109, intron 1 of 13)	667	NM_001331109	11652	Mm.177194	NM_007434	ENSMUSG00000004056	Akt2	2410016A19Rik|AW554154|PKB|PKBbeta	thymoma viral proto-oncogene 2	protein-coding
mm_164009.1	chr14	69840388	69840391	+	1	NA	promoter-TSS (NM_028526)	promoter-TSS (NM_028526)	-18	NM_028560	73523	Mm.23509	NM_028526	ENSMUSG00000022085	Pebp4	PEBP-4	phosphatidylethanolamine binding protein 4	protein-coding
mm_70239.1	chr8	3353500	3353525	+	1	NA	promoter-TSS (NM_001033378)	promoter-TSS (NM_001033378)	97	NM_001033378	319493	Mm.234565	NM_001033378	ENSMUSG00000074497	A430078G23Rik	-	RIKEN cDNA A430078G23 gene	protein-coding
mm_114519.1	chr13	73264603	73264603	+	1	NA	intron (NM_018885, intron 1 of 5)	intron (NM_018885, intron 1 of 5)	4106	NM_018885	50916	Mm.103784	NM_018885	ENSMUSG00000021604	Irx4	-	Iroquois related homeobox 4 (Drosophila)	protein-coding
mm_65140.1	chr7	19573373	19573377	-	1	NA	promoter-TSS (NM_027189)	promoter-TSS (NM_027189)	-32	NM_027189	69731	Mm.24540	NM_027189	ENSMUSG00000044709	Gemin7	2400008I04Rik|AI120175|AI461688	gem (nuclear organelle) associated protein 7	protein-coding
mm_28256.1	chr3	88554446	88554460	-	1	NA	intron (NM_033526, intron 1 of 10)	intron (NM_033526, intron 1 of 10)	737	NM_033526	94232	Mm.303059	NM_033526	ENSMUSG00000008604	Ubqln4	A1Up|A1u|AI663987|CIP75|UBIN	ubiquilin 4	protein-coding
mm_46631.1	chr5	108449180	108449190	-	1	NA	promoter-TSS (NM_172883)	promoter-TSS (NM_172883)	-294	NM_172883	243197	Mm.106818	NM_172883	ENSMUSG00000029490	Mfsd7a	4732482E20Rik|Mfsd7	major facilitator superfamily domain containing 7A	protein-coding
mm_46999.1	chr5	115348597	115348628	-	1	NA	exon (NM_007748, exon 2 of 3)	exon (NM_007748, exon 2 of 3)	343	NM_007748	12861	Mm.43415	NM_007748	ENSMUSG00000041697	Cox6a1	VIaL	cytochrome c oxidase subunit VIa polypeptide 1	protein-coding
mm_62067.1	chr7	92637170	92637221	+	1	NA	promoter-TSS (NM_028665)	promoter-TSS (NM_028665)	-53	NM_028665	73845	Mm.73248	NM_028665	ENSMUSG00000041343	Ankrd42	4931426M20|4933417L02Rik|Ikbn	ankyrin repeat domain 42	protein-coding
mm_101883.1	chr11	48945242	48945263	-	1	NA	TTS (NM_001281472)	TTS (NM_001281472)	1158	NM_001281472	621823	Mm.440151	NM_001281472	ENSMUSG00000078153	Psme2b	PA28b-p|PA28b2|Psme2-like|Psme2b-ps	protease (prosome, macropain) activator subunit 2B	protein-coding
mm_120651.1	chr14	70530900	70530910	+	1	NA	promoter-TSS (NM_145219)	promoter-TSS (NM_145219)	84	NM_145219	213469	Mm.41708	NM_145219	ENSMUSG00000033595	Lgi3	AI841179|AW049851	leucine-rich repeat LGI family, member 3	protein-coding
mm_28987.1	chr3	101287842	101287861	-	1	NA	promoter-TSS (NM_013486)	promoter-TSS (NM_013486)	88	NM_013486	12481	Mm.22842	NM_013486	ENSMUSG00000027863	Cd2	LFA-2|Ly-37|Ly37	CD2 antigen	protein-coding
mm_107120.1	chr12	18610122	18610133	+	1	NA	Intergenic	CpG	95617	NM_001201330	236366	Mm.352227	NM_001033157	ENSMUSG00000073197	5730507C01Rik	-	RIKEN cDNA 5730507C01 gene	protein-coding
mm_156609.1	chrX	153359576	153359590	+	1	NA	intron (NM_173780, intron 2 of 6)	intron (NM_173780, intron 2 of 6)	121538	NM_173780	245671	Mm.260751	NM_173780	ENSMUSG00000041649	Klf8	A830097P10Rik|BKLF3|ZNF74	Kruppel-like factor 8	protein-coding
mm_76585.1	chr8	89033370	89033385	-	1	NA	exon (NM_021390, exon 3 of 4)	exon (NM_021390, exon 3 of 4)	8642	NR_106190	102465899		NR_106190	ENSMUSG00000099078	Mir8110	Gm27571|mmu-mir-8110	microRNA 8110	ncRNA
mm_60292.1	chr7	44012655	44012659	+	1	NA	promoter-TSS (NM_010644)	promoter-TSS (NM_010644)	-21	NM_010644	16618	Mm.439663	NM_010644	ENSMUSG00000053719	Klk1b26	Egfbp2|Klk26|PRECE-2|mGK-26|mGK26	kallikrein 1-related petidase b26	protein-coding
mm_33631.1	chr4	132883938	132883982	+	1	NA	intron (NM_133887, intron 1 of 8)	intron (NM_133887, intron 1 of 8)	498	NM_133887	100226	Mm.28237	NM_133887	ENSMUSG00000028879	Stx12	AI850350|AU041521|Stx13	syntaxin 12	protein-coding
mm_93317.1	chr10	98914990	98915009	-	1	NA	promoter-TSS (NM_026482)	promoter-TSS (NM_026482)	-153	NM_026482	67972	Mm.166944	NM_026482	ENSMUSG00000019943	Atp2b1	2810442I22Rik|E130111D10Rik|Pmca1	ATPase, Ca++ transporting, plasma membrane 1	protein-coding
mm_69520.1	chr7	135528646	135528661	-	1	NA	promoter-TSS (NM_178669)	promoter-TSS (NM_178669)	1	NM_178669	212070	Mm.39721	NM_178669	ENSMUSG00000050866	Clrn3	AI649392|Tmem12	clarin 3	protein-coding
mm_54470.1	chr6	34910503	34910515	-	1	NA	intron (NM_001013366, intron 1 of 14)	MIR3|SINE|MIR	322	NM_001013366	101240	Mm.152120	NM_001013366	ENSMUSG00000058486	Wdr91	9530020G05Rik|AI987683|AU018665	WD repeat domain 91	protein-coding
mm_165859.1	chr4	24430731	24430742	-	1	NA	Intergenic	Intergenic	-65726	NM_199467	212377	Mm.120919	NM_199467	ENSMUSG00000045751	Mms22l	F730047E07Rik|Gm134	MMS22-like, DNA repair protein	protein-coding
mm_32720.1	chr4	116221690	116221698	+	1	NA	promoter-TSS (NM_181585)	promoter-TSS (NM_181585)	-220	NM_181585	18710	Mm.253819	NM_181585	ENSMUSG00000028698	Pik3r3	AA414954|p55pik	phosphatidylinositol 3 kinase, regulatory subunit, polypeptide 3 (p55)	protein-coding
mm_153693.1	chr19	44397259	44397269	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	10445	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_75854.1	chr8	70698335	70698364	-	1	NA	5' UTR (NM_001286944, exon 1 of 1)	5' UTR (NM_001286944, exon 1 of 1)	610	NM_001286944	16478	Mm.419851	NM_010592	ENSMUSG00000071076	Jund	Jund1	jun D proto-oncogene	protein-coding
mm_70022.1	chr7	142575839	142575854	-	1	NA	non-coding (NR_130974, exon 5 of 5)	non-coding (NR_130974, exon 5 of 5)	1301	NR_030416	735280		NR_030416	ENSMUSG00000076275	Mir675	Mirn675|mir-675|mmu-mir-675	microRNA 675	ncRNA
mm_21287.1	chr2	156970503	156970520	-	1	NA	intron (NM_013865, intron 1 of 15)	MLT1F2|LTR|ERVL-MaLR	21600	NM_013865	29812	Mm.279256	NM_013865	ENSMUSG00000027634	Ndrg3	4833415O14Rik|AI747193|Ndr3	N-myc downstream regulated gene 3	protein-coding
mm_90149.1	chr10	118141886	118141898	+	1	NA	5' UTR (NM_010785, exon 1 of 13)	5' UTR (NM_010785, exon 1 of 13)	105	NM_010785	17245	Mm.101191	NM_010785	ENSMUSG00000020212	Mdm1	Arrd2|Mdm-1	transformed mouse 3T3 cell double minute 1	protein-coding
mm_20378.1	chr2	128467526	128467531	-	1	NA	Intergenic	Intergenic	-38177	NR_028590	100043424	Mm.297222	NR_028589		Gm14005	OTTMUSG00000015351	predicted gene 14005	ncRNA
mm_15768.1	chr2	164332724	164332736	+	1	NA	promoter-TSS (NM_009301)	promoter-TSS (NM_009301)	-35	NM_009301	20944	Mm.140154	NM_009301	ENSMUSG00000017004	Svs5	BB115186|Semg1|Svp-1|Svp1|Svp5	seminal vesicle secretory protein 5	protein-coding
mm_76053.1	chr8	77689214	77689232	-	1	NA	intron (NM_010332, intron 2 of 7)	intron (NM_010332, intron 2 of 7)	35229	NM_010332	13617	Mm.283168	NM_010332	ENSMUSG00000031616	Ednra	ET-AR|ETa|Gpcr10	endothelin receptor type A	protein-coding
mm_20385.1	chr2	128967234	128967262	-	1	NA	promoter-TSS (NM_178404)	promoter-TSS (NM_178404)	-154	NM_178404	78751	Mm.26377	NM_178404	ENSMUSG00000042851	Zc3h6	4631426G04Rik|4833425H18Rik|AU024389|AW060453|Zc3hdc6|mKIAA2035	zinc finger CCCH type containing 6	protein-coding
mm_170634.1	chr1	98589508	98589518	+	1	NA	Intergenic	IAP1-MM_LTR|LTR|ERVK	168389	NM_027584	70866	Mm.389164	NM_027584	ENSMUSG00000026336	Slco6d1	4921511I05Rik	solute carrier organic anion transporter family, member 6d1	protein-coding
mm_65474.1	chr7	25537071	25537086	-	1	NA	intron (NR_015569, intron 6 of 6)	intron (NR_015569, intron 6 of 6)	2926	NM_001113368	26367	Mm.439731	NM_007543	ENSMUSG00000054385	Ceacam2	AI267129|Bgp2|Ceacam2-L	carcinoembryonic antigen-related cell adhesion molecule 2	protein-coding
mm_45818.1	chr5	87680940	87680944	-	1	NA	exon (NM_007784, exon 32 of 34)	exon (NM_007784, exon 32 of 34)	14734	NM_001286016	12990	Mm.427467	NM_007784	ENSMUSG00000070702	Csn1s1	AA959832|AW212882|Csna	casein alpha s1	protein-coding
mm_82256.1	chr9	4796197	4796216	-	1	NA	promoter-TSS (NM_001113181)	promoter-TSS (NM_001113181)	28	NM_001113180	14802	Mm.209263	NM_019691	ENSMUSG00000025892	Gria4	GluA4|GluR-D|Glur-4|Glur4|Gluralpha4|spkw1	glutamate receptor, ionotropic, AMPA4 (alpha 4)	protein-coding
mm_11336.1	chr2	30654872	30654880	+	1	NA	Intergenic	Intergenic	23135	NR_136917	665635	Mm.450149	NR_136917		Gm14486	OTTMUSG00000016802	predicted gene 14486	ncRNA
mm_54211.1	chr6	25689593	25689608	-	1	NA	5' UTR (NM_010338, exon 1 of 2)	5' UTR (NM_010338, exon 1 of 2)	380	NM_010338	14763	Mm.409670	NM_010338	ENSMUSG00000039904	Gpr37	AI848630|Pael-R	G protein-coupled receptor 37	protein-coding
mm_4015.1	chr1	165485169	165485206	+	1	NA	promoter-TSS (NM_173029)	promoter-TSS (NM_173029)	4	NM_173029	271639	Mm.66952	NM_173029	ENSMUSG00000026567	Adcy10	4930431D04Rik|4931412F17|Sacy|sAC	adenylate cyclase 10	protein-coding
mm_3629.1	chr1	152807773	152807790	+	1	NA	5' UTR (NM_010877, exon 2 of 16)	5' UTR (NM_010877, exon 2 of 16)	7628	NM_010877	17970	Mm.270307	NM_010877	ENSMUSG00000026480	Ncf2	NOXA2|Ncf-2|p67phox	neutrophil cytosolic factor 2	protein-coding
mm_47791.1	chr5	132259009	132259028	-	1	NA	exon (NM_177047, exon 2 of 19)	exon (NM_177047, exon 2 of 19)	283325	NM_177047	319974	Mm.409595	NM_177047	ENSMUSG00000029673	Auts2	2700063G02Rik|A730011F23Rik|D830032G16Rik	autism susceptibility candidate 2	protein-coding
mm_127813.1	chr15	5099126	5099155	-	1	NA	exon (NM_001163138, exon 4 of 4)	exon (NM_001163138, exon 4 of 4)	9393	NM_001163138	239319	Mm.31252	NM_001163138	ENSMUSG00000041849	Card6	D730008L15	caspase recruitment domain family, member 6	protein-coding
mm_87436.1	chr10	51459259	51459265	+	1	NA	Intergenic	Intergenic	-21350	NM_008147	14727	Mm.439661	NM_008147	ENSMUSG00000062593	Lilr4b	Gp49a|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4B	protein-coding
mm_144393.1	chr18	20673627	20673697	+	1	NA	exon (NM_013697, exon 4 of 4)	exon (NM_013697, exon 4 of 4)	8412	NM_013697	22139	Mm.2108	NM_013697	ENSMUSG00000061808	Ttr	AA408768|AI787086|D17860|prealbumin	transthyretin	protein-coding
mm_152918.1	chr19	28009894	28009906	-	1	NA	intron (NM_011265, intron 1 of 16)	intron (NM_011265, intron 1 of 16)	1266	NM_011265	19726	Mm.313321	NM_011265	ENSMUSG00000040929	Rfx3	C230093O12Rik|MRFX3	regulatory factor X, 3 (influences HLA class II expression)	protein-coding
mm_29995.1	chr3	135587989	135588011	-	1	NA	intron (NM_008689, intron 24 of 24)	intron (NM_008689, intron 24 of 24)	102389	NM_027288	110173	Mm.280536	NM_027288	ENSMUSG00000028164	Manba	2410030O07Rik|B930014J03Rik|Bmn	mannosidase, beta A, lysosomal	protein-coding
mm_130379.1	chr15	97844255	97844318	-	1	NA	5' UTR (NM_001204278, exon 1 of 24)	5' UTR (NM_001204278, exon 1 of 24)	216	NM_001204279	56233	Mm.384027	NM_019572	ENSMUSG00000022475	Hdac7	5830434K02Rik|HD7|HD7a|Hdac7a|mFLJ00062	histone deacetylase 7	protein-coding
mm_71850.1	chr8	68906024	68906034	+	1	NA	3' UTR (NM_008509, exon 10 of 10)	3' UTR (NM_008509, exon 10 of 10)	25474	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_89950.1	chr10	111289837	111289855	+	1	NA	exon (NM_001003717, exon 21 of 23)	exon (NM_001003717, exon 21 of 23)	-8833	NM_027914	71769	Mm.45256	NM_027914	ENSMUSG00000035759	Bbs10	1300007O09Rik|AI452285	Bardet-Biedl syndrome 10 (human)	protein-coding
mm_150824.1	chr19	44554956	44554957	+	1	NA	exon (NM_026061, exon 2 of 5)	exon (NM_026061, exon 2 of 5)	459	NM_026061	67264	Mm.2060	NM_026061	ENSMUSG00000025204	Ndufb8	2900010I05Rik|AI987932	NADH dehydrogenase (ubiquinone) 1 beta subcomplex 8	protein-coding
mm_76738.1	chr8	95143247	95143257	-	1	NA	promoter-TSS (NM_010631)	promoter-TSS (NM_010631)	-712	NM_001145831	16582	Mm.378951	NM_010631	ENSMUSG00000031788	Kifc3	AI325457|BB123200	kinesin family member C3	protein-coding
mm_65632.1	chr7	27553105	27553115	-	1	NA	promoter-TSS (NM_175107)	promoter-TSS (NM_175107)	108	NM_011116	18807	Mm.6483	NM_011116	ENSMUSG00000003363	Pld3	Sam-9	phospholipase D family, member 3	protein-coding
mm_115127.1	chr13	104287492	104287498	+	1	NA	promoter-TSS (NM_001081020)	promoter-TSS (NM_001081020)	-340	NR_136938	108154	Mm.208125	NM_175496	ENSMUSG00000046169	Adamts6	A930019D11Rik|ADAM-TS6|b2b1879.1Clo|b2b2029Clo|b2b2182Clo|b2b2187.1Clo|b2b2228Clo	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 6	protein-coding
mm_13736.1	chr2	118112655	118112665	+	1	NA	exon (NM_011580, exon 2 of 22)	exon (NM_011580, exon 2 of 22)	784	NM_001313914	21825	Mm.4159	NM_011580	ENSMUSG00000040152	Thbs1	TSP-1|TSP1|Thbs-1|tbsp1	thrombospondin 1	protein-coding
mm_35556.1	chr4	41569405	41569415	-	1	NA	promoter-TSS (NM_175138)	promoter-TSS (NM_175138)	117	NM_001159583	71901	Mm.39215	NM_027993	ENSMUSG00000028439	Fam219a	2310028H24Rik	family with sequence similarity 219, member A	protein-coding
mm_117334.1	chr13	69069939	69069962	-	1	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	-70409	NM_153534	210044	Mm.390617	NM_153534	ENSMUSG00000021536	Adcy2	mKIAA1060	adenylate cyclase 2	protein-coding
mm_166974.1	chr7	44669368	44669370	-	1	NA	intron (NM_001271540, intron 1 of 41)	CpG	1474	NM_001271540	71960	Mm.158289	NM_028021	ENSMUSG00000030739	Myh14	2400004E04Rik|II-C|NHMCII|NMHC II-C	myosin, heavy polypeptide 14	protein-coding
mm_42122.1	chr5	110895206	110895241	+	1	NA	intron (NM_001267622, intron 2 of 22)	intron (NM_001267622, intron 2 of 22)	15420	NM_001267622	209683	Mm.295660	NM_024477	ENSMUSG00000033209	Ttc28	2310015L07Rik|6030435N04|AI428795|AI851761|BC002262|TPRBK	tetratricopeptide repeat domain 28	protein-coding
mm_103484.1	chr11	76509209	76509228	-	1	NA	5' UTR (NM_198018, exon 1 of 22)	5' UTR (NM_198018, exon 1 of 22)	201	NM_198018	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_59261.1	chr7	24884612	24884644	+	1	NA	promoter-TSS (NM_023133)	promoter-TSS (NM_023133)	-86	NM_023133	20085	Mm.300281	NM_023133	ENSMUSG00000040952	Rps19	Dsk3	ribosomal protein S19	protein-coding
mm_75393.1	chr8	45999861	45999873	-	1	NA	promoter-TSS (NM_001039562)	promoter-TSS (NM_001039562)	-17	NM_001039562	654824	Mm.334517	NM_001039562	ENSMUSG00000050914	Ankrd37	-	ankyrin repeat domain 37	protein-coding
mm_22926.1	chr3	31121405	31121423	+	1	NA	3' UTR (NM_001039090, exon 7 of 7)	3' UTR (NM_001039090, exon 7 of 7)	26356	NM_001039090	20482	Mm.15406	NM_011386	ENSMUSG00000027660	Skil	Skir|SnoN|sno	SKI-like	protein-coding
mm_102348.1	chr11	58168468	58168544	-	1	NA	promoter-TSS (NM_001166670)	promoter-TSS (NM_001166670)	33	NM_172558	216766	Mm.275349	NM_172558	ENSMUSG00000037275	Gemin5	AA407055|AA407208|AI451603|BB194447|C330013N08	gem (nuclear organelle) associated protein 5	protein-coding
mm_21429.1	chr2	158320330	158320346	-	1	NA	exon (NM_008489, exon 8 of 15)	exon (NM_008489, exon 8 of 15)	13845	NM_008489	16803	Mm.218846	NM_008489	ENSMUSG00000016024	Lbp	Bpifd2|Ly88	lipopolysaccharide binding protein	protein-coding
mm_135093.1	chr16	34958803	34958813	-	1	NA	promoter-TSS (NR_045722)	promoter-TSS (NR_045722)	56	NR_045722	278725	Mm.436927	NR_045722		E130310I04Rik	A930019C19Rik	RIKEN cDNA E130310I04 gene	ncRNA
mm_156083.1	chrX	109445396	109445453	+	1	NA	Intergenic	Intergenic	248668	NM_001037917	622976	Mm.482747	NM_001037917	ENSMUSG00000048621	Gm6377	EG622976	predicted gene 6377	protein-coding
mm_3838.1	chr1	160044474	160044484	+	1	NA	promoter-TSS (NR_028111)	promoter-TSS (NR_028111)	99	NM_001162896	67647	Mm.171518	NM_001024470	ENSMUSG00000090394	4930523C07Rik	-	RIKEN cDNA 4930523C07 gene	protein-coding
mm_166392.1	chr5	134938453	134938453	+	1	NA	intron (NM_024479, intron 5 of 5)	MLTR14|LTR|ERV1	6080	NM_001347490	79565	Mm.34235	NM_024479	ENSMUSG00000040557	Wbscr27	AW492986|BC002286	Williams Beuren syndrome chromosome region 27 (human)	protein-coding
mm_112185.1	chr12	113422512	113422518	-	1	NA	Intergenic	Intergenic	-67050	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_164959.1	chr19	5799027	5799030	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	-3047	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_49930.1	chr6	39420574	39420597	+	1	NA	promoter-TSS (NM_018810)	promoter-TSS (NM_018810)	-216	NM_018810	54484	Mm.270484	NM_018810	ENSMUSG00000029922	Mkrn1	RFP	makorin, ring finger protein, 1	protein-coding
mm_44316.1	chr5	9300140	9300144	-	1	NA	intron (NM_172706, intron 1 of 21)	intron (NM_172706, intron 1 of 21)	33949	NM_172706	231014	Mm.130063	NM_172706	ENSMUSG00000056004	9330182L06Rik	Eig121l	RIKEN cDNA 9330182L06 gene	protein-coding
mm_8636.1	chr1	156421110	156421119	-	1	NA	promoter-TSS (NM_001346967)	promoter-TSS (NM_001346967)	-199	NM_001346967	77352	Mm.428709	NM_001033180	ENSMUSG00000026601	Axdnd1	9430070O13Rik|Gm979	axonemal dynein light chain domain containing 1	protein-coding
mm_4372.1	chr1	172121745	172121795	+	1	NA	3' UTR (NM_009938, exon 33 of 33)	3' UTR (NM_009938, exon 33 of 33)	-4985	NM_001159525	19298	Mm.247764	NM_023041	ENSMUSG00000003464	Pex19	Pxf	peroxisomal biogenesis factor 19	protein-coding
mm_144907.1	chr18	37404054	37404058	+	1	NA	TTS (NM_053134)	TTS (NM_053134)	3201	NM_053134	93880	Mm.286019	NM_053134	ENSMUSG00000051242	Pcdhb9	Pcdhb4C|PcdhbI	protocadherin beta 9	protein-coding
mm_106756.1	chr12	4225722	4225730	+	1	NA	intron (NM_134046, intron 3 of 6)	intron (NM_134046, intron 3 of 6)	-8301	NM_001204912	69709	Mm.250552	NM_001204912	ENSMUSG00000096199	Ptrhd1	2410017P09Rik	peptidyl-tRNA hydrolase domain containing 1	protein-coding
mm_38640.1	chr4	143162098	143162134	-	1	NA	exon (NM_001081355, exon 6 of 10)	exon (NM_001081355, exon 6 of 10)	-25954	NR_105988	102465618		NR_105988	ENSMUSG00000106597	Mir7021	mmu-mir-7021	microRNA 7021	ncRNA
mm_1037.1	chr1	58756807	58756823	+	1	NA	3' UTR (NM_207653, exon 10 of 10)	3' UTR (NM_207653, exon 10 of 10)	26263	NM_001293805	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_76961.1	chr8	106134934	106134943	-	1	NA	promoter-TSS (NR_040346)	promoter-TSS (NR_040346)	-462	NR_040345	69771	Mm.393274	NR_040344		1810019D21Rik	-	RIKEN cDNA 1810019D21 gene	ncRNA
mm_32428.1	chr4	107178419	107178466	+	1	NA	promoter-TSS (NM_029565)	promoter-TSS (NM_029565)	-76	NM_025617	66526	Mm.246956	NM_025617	ENSMUSG00000028619	Tceanc2	2210010B22Rik|2210012G02Rik|6330404A07Rik|AU015593|Tdeanc2	transcription elongation factor A (SII) N-terminal and central domain containing 2	protein-coding
mm_68870.1	chr7	126446582	126446588	-	1	NA	TTS (NM_030566)	TTS (NM_030566)	16488	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_87629.1	chr10	58323480	58323499	+	1	NA	promoter-TSS (NM_026148)	promoter-TSS (NM_026148)	23	NM_026148	110829	Mm.57734	NM_026148	ENSMUSG00000019920	Lims1	2310016J22Rik|4921524A02Rik|AI507642|AU021743|AW551584|C430041B13Rik|Lims1l|PINCH|PINCH1	LIM and senescent cell antigen-like domains 1	protein-coding
mm_126511.1	chr15	81802795	81802805	+	1	NA	exon (NM_153484, exon 1 of 4)	exon (NM_153484, exon 1 of 4)	127	NM_153484	21685	Mm.270278	NM_017376	ENSMUSG00000022389	Tef	2310028D20Rik	thyrotroph embryonic factor	protein-coding
mm_53769.1	chr6	145865676	145865693	+	1	NA	promoter-TSS (NM_001271768)	promoter-TSS (NM_001271768)	-264	NM_024469	79362	Mm.154529	NM_024469	ENSMUSG00000030256	Bhlhe41	6430520M22Rik|Bhlhb2l|Bhlhb3|DEC2|Sharp1	basic helix-loop-helix family, member e41	protein-coding
mm_126822.1	chr15	88819695	88819717	+	1	NA	promoter-TSS (NM_001142357)	promoter-TSS (NM_001142357)	60	NM_029720	76737	Mm.292567	NM_029720	ENSMUSG00000023272	Creld2	5730592L21Rik|C85758	cysteine-rich with EGF-like domains 2	protein-coding
mm_41304.1	chr5	90467359	90467372	+	1	NA	exon (NM_009654, exon 7 of 15)	exon (NM_009654, exon 7 of 15)	6495	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_36985.1	chr4	109666611	109666653	-	1	NA	5' UTR (NM_001301368, exon 1 of 3)	5' UTR (NM_001301368, exon 1 of 3)	124	NM_001301368	12580	Mm.1912	NM_007671	ENSMUSG00000028551	Cdkn2c	C77269|INK4c|p18|p18-INK4c|p18-INK6|p18INK4c	cyclin-dependent kinase inhibitor 2C (p18, inhibits CDK4)	protein-coding
mm_171829.1	chr5	145271984	145271986	-	1	NA	Intergenic	RLTR10B2|LTR|ERVK	-11358	NM_001081431	666311	Mm.260773	NM_001081431	ENSMUSG00000070420	Zscan25	EG666311|Zfp498	zinc finger and SCAN domain containing 25	protein-coding
mm_98377.1	chr11	94044332	94044342	+	1	NA	5' UTR (NM_001199205, exon 1 of 27)	5' UTR (NM_001199205, exon 1 of 27)	132	NM_001025429	70834	Mm.260737	NM_027569	ENSMUSG00000020859	Spag9	3110018C07Rik|4733401I23Rik|4831406C20Rik|AW552012|JLP|JSAP2|JSAP2a|Jip4|Mapk8ip4|syd1	sperm associated antigen 9	protein-coding
mm_81477.1	chr9	109931895	109931915	+	1	NA	5' UTR (NM_008633, exon 1 of 19)	5' UTR (NM_008633, exon 1 of 19)	131	NM_008633	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_128823.1	chr15	67128988	67129005	-	1	NA	intron (NM_009177, intron 2 of 8)	intron (NM_009177, intron 2 of 8)	47886	NM_009177	20442	Mm.248334	NM_009177	ENSMUSG00000013846	St3gal1	5330418N22Rik|AI467004|ST3GalI|Siat4|Siat4a|St3gal-1	ST3 beta-galactoside alpha-2,3-sialyltransferase 1	protein-coding
mm_72748.1	chr8	85095334	85095351	+	1	NA	exon (NM_010764, exon 18 of 24)	exon (NM_010764, exon 18 of 24)	12073	NM_010764	17159	Mm.4219	NM_010764	ENSMUSG00000005142	Man2b1	AW107687|LAMAN	mannosidase 2, alpha B1	protein-coding
mm_78530.1	chr9	35054234	35054238	+	1	NA	intron (NM_009178, intron 5 of 10)	intron (NM_009178, intron 5 of 10)	-62492	NR_029475	78934	Mm.391688	NR_029475	ENSMUSG00000070315	4930581F22Rik	-	RIKEN cDNA 4930581F22 gene	ncRNA
mm_9574.1	chr1	173980024	173980034	-	1	NA	intron (NM_008327, intron 1 of 6)	Lx9|LINE|L1	2815	NM_008327	26388	Mm.218770	NM_008327	ENSMUSG00000026535	Ifi202b	Ifbip-1|Ifi202|Ifi202a|p202	interferon activated gene 202B	protein-coding
mm_26813.1	chr3	10254201	10254208	-	1	NA	intron (NM_029310, intron 2 of 5)	intron (NM_029310, intron 2 of 5)	-45628	NM_024406	11770	Mm.582	NM_024406	ENSMUSG00000062515	Fabp4	422/aP2|ALBP/Ap2|Ap2|Lbpl	fatty acid binding protein 4, adipocyte	protein-coding
mm_74181.1	chr8	123477935	123477945	+	1	NA	promoter-TSS (NR_028260)	promoter-TSS (NR_028260)	78	NR_028260	114896	Mm.287475	NM_054070	ENSMUSG00000031967	Afg3l1	1700047G05Rik|3110061K15Rik	AFG3-like AAA ATPase 1	protein-coding
mm_110561.1	chr12	55783318	55783318	-	1	NA	intron (NM_001003719, intron 6 of 39)	intron (NM_001003719, intron 6 of 39)	38198	NM_019994	56784	Mm.292180	NM_019994	ENSMUSG00000021027	Ralgapa1	2310003F20Rik|4930400K19Rik|AI563624|GRIPE|Garnl1|Tulip1|mKIAA0884	Ral GTPase activating protein, alpha subunit 1	protein-coding
mm_132491.1	chr16	36934592	36934594	+	1	NA	promoter-TSS (NM_008225)	promoter-TSS (NM_008225)	-390	NM_008225	15163	Mm.4091	NM_008225	ENSMUSG00000022831	Hcls1	AW213261|HS1	hematopoietic cell specific Lyn substrate 1	protein-coding
mm_28121.1	chr3	86920396	86920413	-	1	NA	5' UTR (NM_001195500, exon 1 of 12)	5' UTR (NM_001195500, exon 1 of 12)	480	NM_001195496	70762	Mm.44490	NM_027539	ENSMUSG00000028078	Dclk2	6330415M09Rik|AU044875|CL2|CLICK2|Click-II|Dcamkl2	doublecortin-like kinase 2	protein-coding
mm_29404.1	chr3	108906981	108906984	-	1	NA	intron (NM_025845, intron 4 of 5)	intron (NM_025845, intron 4 of 5)	4722	NM_025845	66921	Mm.51049	NM_025845	ENSMUSG00000027881	Prpf38b	1110021E09Rik|AU018955	PRP38 pre-mRNA processing factor 38 (yeast) domain containing B	protein-coding
mm_169311.1	chr14	104715955	104715955	-	1	NA	intron (NR_015593, intron 1 of 5)	LSU-rRNA_Hsa|rRNA|rRNA	76808	NR_015593	320249	Mm.320725	NR_015593		D130009I18Rik	-	RIKEN cDNA D130009I18 gene	ncRNA
mm_135274.1	chr16	38407679	38407696	-	1	NA	exon (NM_134102, exon 7 of 11)	exon (NM_134102, exon 7 of 11)	25458	NM_134102	85031	Mm.279805	NM_134102	ENSMUSG00000002847	Pla1a	AA986889|Ps-pla1|Pspla1	phospholipase A1 member A	protein-coding
mm_94452.1	chr11	6389443	6389453	+	1	NA	Intergenic	(CGG)n|Simple_repeat|Simple_repeat	-5677	NM_001005867	52915	Mm.1144	NM_028601	ENSMUSG00000041164	Zmiz2	Zimp7	zinc finger, MIZ-type containing 2	protein-coding
mm_48033.1	chr5	136266715	136266727	-	1	NA	3' UTR (NM_009986, exon 24 of 24)	3' UTR (NM_009986, exon 24 of 24)	-21781	NM_018825	23921	Mm.425294	NM_018825	ENSMUSG00000005057	Sh2b2	Aps	SH2B adaptor protein 2	protein-coding
mm_69217.1	chr7	127585172	127585208	-	1	NA	exon (NM_001033040, exon 6 of 9)	exon (NM_001033040, exon 6 of 9)	3405	NM_001033040	233899	Mm.25220	NM_001033040	ENSMUSG00000057176	Ccdc189	Gm166	coiled-coil domain containing 189	protein-coding
mm_39025.1	chr4	152131874	152131886	-	1	NA	intron (NM_207688, intron 3 of 10)	CpG-10714	-2955	NM_019585	56226	Mm.264215	NM_019585	ENSMUSG00000028943	Espn	je	espin	protein-coding
mm_107083.1	chr12	17274449	17274465	+	1	NA	exon (NM_027959, exon 4 of 13)	exon (NM_027959, exon 4 of 13)	7862	NM_027959	71853	Mm.222825	NM_027959	ENSMUSG00000020571	Pdia6	1700015E05Rik|AL023058|C77895|CaBP5|P5|Txndc7	protein disulfide isomerase associated 6	protein-coding
mm_62868.1	chr7	114722452	114722483	+	1	NA	intron (NM_054084, intron 4 of 4)	intron (NM_054084, intron 4 of 4)	3824	NM_054084	116903	Mm.273838	NM_054084	ENSMUSG00000030666	Calcb	CGRP2|Calc2	calcitonin-related polypeptide, beta	protein-coding
mm_74435.1	chr8	3754475	3754491	-	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	-5499	NM_133238	170786	Mm.32510	NM_133238	ENSMUSG00000031494	Cd209a	CD209|CDSIGN|CIRE|DC-SIGN|DC-SIGN1|Dcsign|SIGN-R1|SIGNR5	CD209a antigen	protein-coding
mm_117282.1	chr13	65278710	65278752	-	1	NA	promoter-TSS (NM_178364)	promoter-TSS (NM_178364)	-123	NM_178364	170936	Mm.151546	NM_178364	ENSMUSG00000021514	Zfp369	B930030B22Rik|D230020H11Rik|NRIF2	zinc finger protein 369	protein-coding
mm_41222.1	chr5	88584176	88584200	+	1	NA	exon (NM_027530, exon 1 of 13)	exon (NM_027530, exon 1 of 13)	675	NM_027530	52822	Mm.270469	NM_027530	ENSMUSG00000029291	Rufy3	2810428M05Rik|6330416M07Rik|AW455998|AW538594|D5Bwg0860e|Ripx|Rpipx	RUN and FYVE domain containing 3	protein-coding
mm_157643.1	chrX	57304838	57304888	-	1	NA	intron (NM_152801, intron 2 of 21)	intron (NM_152801, intron 2 of 21)	33866	NM_152801	73341	Mm.261443	NM_152801	ENSMUSG00000031133	Arhgef6	1600028C08Rik|1700038J06Rik|4930592P22Rik|alpha-PIX	Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_38717.1	chr4	145234752	145234756	-	1	NA	intron (NM_011610, intron 1 of 9)	intron (NM_011610, intron 1 of 9)	12116	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_167738.1	chr9	106561650	106561653	-	1	NA	promoter-TSS (NM_026645)	promoter-TSS (NM_026645)	-26	NM_026645	68265	Mm.141451	NM_026645	ENSMUSG00000023577	Iqcf3	1700012F17Rik|AV040440	IQ motif containing F3	protein-coding
mm_54735.1	chr6	40940933	40940946	-	1	NA	promoter-TSS (NM_028550)	promoter-TSS (NM_028550)	-382	NM_028550	73481	Mm.333010	NM_028550	ENSMUSG00000029883	1700074P13Rik	AV047902|Tryx5	RIKEN cDNA 1700074P13 gene	protein-coding
mm_163638.1	chr13	60602556	60602576	-	1	NA	exon (NM_134062, exon 2 of 27)	exon (NM_134062, exon 2 of 27)	355	NM_134062	69635	Mm.24103	NM_029653	ENSMUSG00000021559	Dapk1	D13Ucla1|DAP-Kinase	death associated protein kinase 1	protein-coding
mm_28274.1	chr3	88913801	88913811	-	1	NA	exon (NM_144898, exon 1 of 14)	exon (NM_144898, exon 1 of 14)	144	NM_144898	229524	Mm.440405	NM_144898	ENSMUSG00000068922	Msto1	BC008103|mst	misato 1, mitochondrial distribution and morphology regulator	protein-coding
mm_122534.1	chr14	47385683	47385702	-	1	NA	3' UTR (NM_010705, exon 6 of 6)	3' UTR (NM_010705, exon 6 of 6)	11832	NM_001145953	16854	Mm.248615	NM_010705	ENSMUSG00000050335	Lgals3	GBP|L-34|Mac-2|gal3	lectin, galactose binding, soluble 3	protein-coding
mm_110609.1	chr12	56536799	56536810	-	1	NA	5' UTR (NM_009385, exon 1 of 3)	5' UTR (NM_009385, exon 1 of 3)	104	NM_009385	21869	Mm.89972	NM_009385	ENSMUSG00000001496	Nkx2-1	AV026640|Nkx2.1|T/EBP|Titf1|Ttf-1	NK2 homeobox 1	protein-coding
mm_74370.1	chr8	128487357	128487360	+	1	NA	intron (NM_008737, intron 11 of 16)	intron (NM_008737, intron 11 of 16)	128117	NR_035436	100316680		NR_035436	ENSMUSG00000084523	Mir1903	Mirn1903|mmu-mir-1903	microRNA 1903	ncRNA
mm_36037.1	chr4	57241043	57241056	-	1	NA	intron (NM_011207, intron 10 of 25)	intron (NM_011207, intron 10 of 25)	60788	NM_011207	545622	Mm.246552	NM_011207	ENSMUSG00000038764	Ptpn3	9530011I20Rik|PTP-H1|PTPCL	protein tyrosine phosphatase, non-receptor type 3	protein-coding
mm_22953.1	chr3	32397108	32397144	+	1	NA	Intergenic	CpG	-31461	NM_009517	22401	Mm.35705	NM_009517	ENSMUSG00000027663	Zmat3	Wig1	zinc finger matrin type 3	protein-coding
mm_107805.1	chr12	65021820	65021835	+	1	NA	3' UTR (NM_177805, exon 20 of 20)	3' UTR (NM_177805, exon 20 of 20)	-14507	NM_177806	328110	Mm.283339	NM_177806	ENSMUSG00000035597	Prpf39	Srcs1	pre-mRNA processing factor 39	protein-coding
mm_123862.1	chr14	72539146	72539175	-	1	NA	3' UTR (NM_207636, exon 26 of 26)	3' UTR (NM_207636, exon 26 of 26)	170843	NM_207636	319448	Mm.205421	NM_207636	ENSMUSG00000033487	Fndc3a	1700094E19Rik|D14Ertd453e|F730017H24Rik|Fndc3|sys	fibronectin type III domain containing 3A	protein-coding
mm_123139.1	chr14	56620560	56620564	-	1	NA	exon (NM_001145978, exon 22 of 35)	exon (NM_001145978, exon 22 of 35)	44943	NM_001145978	328417	Mm.379357	NM_001145978	ENSMUSG00000054509	Parp4	Adprtl1|C030027K23Rik|E230037B21Rik|Gm743|PARPL|PH5P|VAULT3|VPARP|p193	poly (ADP-ribose) polymerase family, member 4	protein-coding
mm_58290.1	chr6	145863818	145863835	-	1	NA	exon (NM_001271768, exon 5 of 5)	exon (NM_001271768, exon 5 of 5)	1594	NM_001271768	79362	Mm.154529	NM_024469	ENSMUSG00000030256	Bhlhe41	6430520M22Rik|Bhlhb2l|Bhlhb3|DEC2|Sharp1	basic helix-loop-helix family, member e41	protein-coding
mm_125311.1	chr15	38079045	38079094	+	1	NA	promoter-TSS (NM_001081359)	promoter-TSS (NM_001081359)	-215	NM_001081359	70790	Mm.476840	NM_027553	ENSMUSG00000037487	Ubr5	Edd|Edd1	ubiquitin protein ligase E3 component n-recognin 5	protein-coding
mm_69636.1	chr7	138397627	138397643	-	1	NA	promoter-TSS (NM_183289)	promoter-TSS (NM_183289)	95	NM_183289	70571	Mm.334297	NM_183289	ENSMUSG00000091002	Tcerg1l	5730476P14Rik	transcription elongation regulator 1-like	protein-coding
mm_58559.1	chr7	4741795	4741812	+	1	NA	5' UTR (NM_001115018, exon 2 of 9)	5' UTR (NM_001115018, exon 2 of 9)	1676	NM_001115018	232811	Mm.247844	NM_146177	ENSMUSG00000059851	Kmt5c	BC024816|Suv4-20h2|Suv420h2	lysine methyltransferase 5C	protein-coding
mm_46560.1	chr5	106879912	106879915	-	1	NA	intron (NM_177873, intron 24 of 39)	PB1D7|SINE|Alu	45977	NM_177873	330149	Mm.121664	NM_177873	ENSMUSG00000043410	Hfm1	A330009G12Rik|Gm1046|Mer3|Sec63d1	HFM1, ATP-dependent DNA helicase homolog	protein-coding
mm_51852.1	chr6	90428521	90428565	+	1	NA	promoter-TSS (NM_173775)	promoter-TSS (NM_173775)	-63	NM_173775	243538	Mm.386876	NM_173775	ENSMUSG00000048794	Cfap100	AW048498|C030041G11Rik|C230069K22Rik|Ccdc37	cilia and flagella associated protein 100	protein-coding
mm_64915.1	chr7	16239777	16239794	-	1	NA	intron (NM_176912, intron 1 of 1)	intron (NM_176912, intron 1 of 1)	2546	NM_001146005	319430	Mm.239570	NM_176912	ENSMUSG00000074361	C5ar2	C5L2|E030029A11Rik|Gpr77	complement component 5a receptor 2	protein-coding
mm_113485.1	chr13	37345458	37345480	+	1	NA	exon (NM_010745, exon 1 of 5)	exon (NM_010745, exon 1 of 5)	124	NM_010745	17084	Mm.2639	NM_010745	ENSMUSG00000021423	Ly86	MD-1|MD1|ly86_tv2	lymphocyte antigen 86	protein-coding
mm_99878.1	chr11	109425941	109425952	+	1	NA	promoter-TSS (NM_025275)	promoter-TSS (NM_025275)	0	NM_025275	13929	Mm.211850	NM_025275	ENSMUSG00000020610	Amz2	AA408420|ESTM12|X83328	archaelysin family metallopeptidase 2	protein-coding
mm_16916.1	chr2	13558506	13558512	-	1	NA	Intergenic	Intergenic	-13845	NM_010067	13434	Mm.6979	NM_010067	ENSMUSG00000026723	Trdmt1	Dnmt2|Rnmt2	tRNA aspartic acid methyltransferase 1	protein-coding
mm_85767.1	chr9	108937171	108937182	-	1	NA	intron (NM_025407, intron 2 of 12)	CpG-15416	528	NM_025407	22273	Mm.335460	NM_025407	ENSMUSG00000025651	Uqcrc1	1110032G10Rik	ubiquinol-cytochrome c reductase core protein 1	protein-coding
mm_91637.1	chr10	42270922	42270941	-	1	NA	intron (NM_019740, intron 2 of 3)	intron (NM_019740, intron 2 of 3)	5811	NM_019740	56484	Mm.338613	NM_019740	ENSMUSG00000048756	Foxo3	1110048B16Rik|2010203A17Rik|C76856|FKHRL1|Fkhr2|Foxo3a	forkhead box O3	protein-coding
mm_69551.1	chr7	135697931	135697958	-	1	NA	exon (NM_001081117, exon 12 of 14)	exon (NM_001081117, exon 12 of 14)	18435	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_11149.1	chr2	28517483	28517484	+	1	NA	intron (NM_001145834, intron 1 of 17)	intron (NM_001145834, intron 1 of 17)	4316	NM_001145834	19730	Mm.5236	NM_009058	ENSMUSG00000026821	Ralgds	Gnds|Rgds|mKIAA1308	ral guanine nucleotide dissociation stimulator	protein-coding
mm_65781.1	chr7	28767113	28767117	-	1	NA	promoter-TSS (NM_010908)	promoter-TSS (NM_010908)	363	NM_001122766	64383	Mm.272443	NM_022432	ENSMUSG00000015149	Sirt2	5730427M03Rik|SIR2L2|Sir2l	sirtuin 2	protein-coding
mm_23283.1	chr3	51682614	51682625	+	1	NA	TTS (NM_174995)	TTS (NM_174995)	21440	NM_001310482	211666	Mm.24679	NM_174995	ENSMUSG00000074604	Mgst2	GST2|MGST-II	microsomal glutathione S-transferase 2	protein-coding
mm_32564.1	chr4	109676653	109676702	+	1	NA	promoter-TSS (NM_007983)	promoter-TSS (NM_007983)	50	NM_007983	14084	Mm.318259	NM_007983	ENSMUSG00000010517	Faf1	AA408698|Dffrx|Fam	Fas-associated factor 1	protein-coding
mm_125427.1	chr15	43477214	43477270	+	1	NA	promoter-TSS (NM_025736)	promoter-TSS (NM_025736)	13	NM_025736	66736	Mm.244512	NM_025736	ENSMUSG00000022337	Emc2	4921531G14Rik|AV060620|AW209495|Ttc35	ER membrane protein complex subunit 2	protein-coding
mm_139146.1	chr17	47527790	47527806	+	1	NA	intron (NM_001081635, intron 1 of 6)	intron (NM_001081635, intron 1 of 6)	22747	NM_001081635	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_114206.1	chr13	56104934	56104949	+	1	NA	exon (NM_001159515, exon 3 of 9)	exon (NM_001159515, exon 3 of 9)	30609	NM_012015	26914	Mm.283802	NM_012015	ENSMUSG00000015937	H2afy	H2AF12M|mH2a1|macroH2A1	H2A histone family, member Y	protein-coding
mm_141250.1	chr17	27556506	27556511	-	1	NA	promoter-TSS (NM_001166545)	promoter-TSS (NM_001166545)	-66	NM_001166536	15361	Mm.4438	NM_016660	ENSMUSG00000046711	Hmga1	AL023995|Hmga1a|Hmga1b|Hmgi|Hmgiy|Hmgy	high mobility group AT-hook 1	protein-coding
mm_14206.1	chr2	127248054	127248064	+	1	NA	promoter-TSS (NM_175145)	promoter-TSS (NM_175145)	84	NM_175145	69470	Mm.200889	NM_175145	ENSMUSG00000034850	Tmem127	2310003P10Rik|AI314202|AI317350	transmembrane protein 127	protein-coding
mm_115156.1	chr13	107034285	107034306	+	1	NA	TTS (NR_015471)	TTS (NR_015471)	11725	NR_015471	100040322	Mm.133867	NR_015471		3830408C21Rik	-	RIKEN cDNA 3830408C21 gene	ncRNA
mm_104876.1	chr11	99432287	99432299	-	1	NA	exon (NM_023256, exon 4 of 8)	exon (NM_023256, exon 4 of 8)	5860	NM_023256	66809	Mm.28042	NM_023256	ENSMUSG00000035775	Krt20	9030623C06Rik|Ck-20|Ck20|K20|Krt21	keratin 20	protein-coding
mm_109709.1	chr12	113422530	113422542	+	1	NA	Intergenic	Intergenic	-67029	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_47151.1	chr5	120588663	120588669	-	1	NA	promoter-TSS (NM_145853)	promoter-TSS (NM_145853)	-53	NM_145853	252972	Mm.114054	NM_145853	ENSMUSG00000032741	Tpcn1	5730403B01Rik|Tpc1|mKIAA1169	two pore channel 1	protein-coding
mm_49343.1	chr6	21949989	21950062	+	1	NA	intron (NM_001311061, intron 1 of 11)	CpG	410	NM_023626	71777	Mm.39999	NM_023626	ENSMUSG00000029670	Ing3	1300013A07Rik|P47ING3	inhibitor of growth family, member 3	protein-coding
mm_86512.1	chr10	7663400	7663417	+	1	NA	promoter-TSS (NR_030698)	promoter-TSS (NR_030698)	37	NR_030698	320642	Mm.398806	NR_030698		A630066F11Rik	-	RIKEN cDNA A630066F11 gene	ncRNA
mm_163393.1	chr12	64474918	64474920	-	1	NA	promoter-TSS (NM_001163271)	promoter-TSS (NM_001163271)	-21	NM_001163271	623046	Mm.189552	NM_001163271	ENSMUSG00000043060	Fscb	EG623046	fibrous sheath CABYR binding protein	protein-coding
mm_108232.1	chr12	77239110	77239126	+	1	NA	non-coding (NR_045554, exon 1 of 12)	non-coding (NR_045554, exon 1 of 12)	379	NR_045554	53618	Mm.35628	NM_016893	ENSMUSG00000021065	Fut8	-	fucosyltransferase 8	protein-coding
mm_154518.1	chrM	12905	12928	-	1	NA	NA	Intergenic	NA	NA								
mm_79394.1	chr9	54863852	54863859	+	1	NA	promoter-TSS (NM_022655)	promoter-TSS (NM_022655)	100	NM_022655	64602	Mm.208991	NM_022655	ENSMUSG00000032293	Ireb2	D9Ertd85e|Irp2	iron responsive element binding protein 2	protein-coding
mm_24374.1	chr3	90220872	90220877	+	1	NA	promoter-TSS (NM_026677)	promoter-TSS (NM_026677)	90	NM_026677	68328	Mm.29355	NM_026677	ENSMUSG00000027935	Rab13	0610007N03Rik|B230212B15Rik	RAB13, member RAS oncogene family	protein-coding
mm_38796.1	chr4	148149685	148149696	-	1	NA	intron (NM_001163707, intron 1 of 5)	intron (NM_001163707, intron 1 of 5)	2235	NM_001163705	50762	Mm.27445	NM_015797	ENSMUSG00000055401	Fbxo6	AA408845|FBG2|Fbs2|Fbx6b|Fbxo6b	F-box protein 6	protein-coding
mm_158610.1	chrX	152643850	152643861	-	1	NA	5' UTR (NM_001290687, exon 1 of 6)	5' UTR (NM_001290687, exon 1 of 6)	294	NM_001290687	110380	Mm.40796	NM_172441	ENSMUSG00000045180	Shroom2	4832440C16|Apxl|C630003H05Rik|Shrm2	shroom family member 2	protein-coding
mm_140963.1	chr17	24647776	24647846	-	1	NA	intron (NM_023055, intron 1 of 6)	intron (NM_023055, intron 1 of 6)	2494	NM_023055	65962	Mm.21587	NM_023055	ENSMUSG00000002504	Slc9a3r2	0610011L07Rik|1200011K07Rik|2010007A20Rik|E3karp|NHERF-2|Nherf2|Octs2|Sip-1|Sip1|Sryip1|Tka-1	solute carrier family 9 (sodium/hydrogen exchanger), member 3 regulator 2	protein-coding
mm_65201.1	chr7	19696915	19696943	-	1	NA	exon (NM_009696, exon 4 of 4)	exon (NM_009696, exon 4 of 4)	1469	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_4939.1	chr1	191182375	191182400	+	1	NA	intron (NM_007498, intron 1 of 3)	intron (NM_007498, intron 1 of 3)	946	NM_007498	11910	Mm.2706	NM_007498	ENSMUSG00000026628	Atf3	LRG-21	activating transcription factor 3	protein-coding
mm_126953.1	chr15	92161411	92161431	+	1	NA	promoter-TSS (NM_001159647)	promoter-TSS (NM_001159647)	64	NM_001159647	12805	Mm.4911	NM_007727	ENSMUSG00000055022	Cntn1	AW495098|CNTN|F3cam|usl	contactin 1	protein-coding
mm_121897.1	chr14	21845515	21845522	-	1	NA	TTS (NM_026965)	TTS (NM_026965)	-2060	NM_176925	319486	Mm.390671	NM_176925	ENSMUSG00000090564	A430057M04Rik	-	RIKEN cDNA A430057M04 gene	protein-coding
mm_151261.1	chr19	54020382	54020386	+	1	NA	intron (NM_001168505, intron 4 of 8)	intron (NM_001168505, intron 4 of 8)	-24798	NM_007417	11551	Mm.235195	NM_007417	ENSMUSG00000033717	Adra2a	AW122659|Adra-2|Adra-2a|alpha(2A)AR|alpha2-C10|alpha2A|alpha2A-AR	adrenergic receptor, alpha 2a	protein-coding
mm_637.1	chr1	40381464	40381474	+	1	NA	Intergenic	Intergenic	-48101	NM_001294171	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_153341.1	chr19	38789103	38789110	-	1	NA	3' UTR (NM_021315, exon 21 of 21)	3' UTR (NM_021315, exon 21 of 21)	30131	NM_021315	57753	Mm.86482	NM_021315	ENSMUSG00000024999	Noc3l	AF233884|Fad24	NOC3 like DNA replication regulator	protein-coding
mm_37984.1	chr4	133622523	133622533	-	1	NA	intron (NM_001017968, intron 2 of 7)	intron (NM_001017968, intron 2 of 7)	10901	NM_001017968	503610	Mm.331948	NM_001017968	ENSMUSG00000037553	Zdhhc18	-	zinc finger, DHHC domain containing 18	protein-coding
mm_123621.1	chr14	68121067	68121075	-	1	NA	exon (NM_008691, exon 3 of 3)	exon (NM_008691, exon 3 of 3)	-2681	NR_045897	100043072	Mm.242832	NR_045897		A230070E04Rik	Gm4210	RIKEN cDNA A230070E04 gene	ncRNA
mm_78916.1	chr9	44999445	44999461	+	1	NA	3' UTR (NM_007648, exon 8 of 8)	3' UTR (NM_007648, exon 8 of 8)	10137	NM_007648	12501	Mm.210361	NM_007648	ENSMUSG00000032093	Cd3e	AI504783|CD3|CD3epsilon|T3e	CD3 antigen, epsilon polypeptide	protein-coding
mm_170027.1	chr17	21679986	21679988	+	1	NA	Intergenic	Intergenic	-10225	NR_045766	100310809	Mm.293030	NR_045766		Gm10509	ENSMUSG00000073448	zinc finger protein 51 pseudogene	pseudo
mm_55845.1	chr6	83325964	83325975	-	1	NA	promoter-TSS (NM_145571)	promoter-TSS (NM_145571)	-70	NM_145571	232157	Mm.29500	NM_145571	ENSMUSG00000043131	Mob1a	4022402H07Rik|MOB1|MOB4B|Mobk1b|Mobkl1b	MOB kinase activator 1A	protein-coding
mm_78728.1	chr9	41580969	41581004	+	1	NA	promoter-TSS (NR_029822)	promoter-TSS (NR_029822)	-267	NR_015483	73144	Mm.38166	NM_001033153	ENSMUSG00000074415	3110039I08Rik	2610203C20Rik|AI848448|D230004N17Rik|D3Mgi9|Mir100hg	RIKEN cDNA 3110039I08 gene	ncRNA
mm_101706.1	chr11	42000473	42000481	-	1	NA	5' UTR (NM_008073, exon 1 of 10)	5' UTR (NM_008073, exon 1 of 10)	237	NM_177408	14406	Mm.5309	NM_008073	ENSMUSG00000020436	Gabrg2	GABAA-R|Gabrg-2|gamma2	gamma-aminobutyric acid (GABA) A receptor, subunit gamma 2	protein-coding
mm_149079.1	chr19	8888947	8888953	+	1	NA	promoter-TSS (NM_025463)	promoter-TSS (NM_025463)	67	NR_104416	66276	Mm.27503	NM_025463	ENSMUSG00000071653	1810009A15Rik	-	RIKEN cDNA 1810009A15 gene	protein-coding
mm_28067.1	chr3	84270705	84270713	-	1	NA	promoter-TSS (NM_001271725)	promoter-TSS (NM_001271725)	74	NM_001271725	80890	Mm.44876	NM_030706	ENSMUSG00000027993	Trim2	mKIAA0517|narf	tripartite motif-containing 2	protein-coding
mm_82112.1	chr9	123150942	123151021	+	1	NA	promoter-TSS (NM_011606)	promoter-TSS (NM_011606)	35	NM_011606	21922	Mm.34588	NM_011606	ENSMUSG00000025784	Clec3b	Tna	C-type lectin domain family 3, member b	protein-coding
mm_9494.1	chr1	173729632	173729642	-	1	NA	exon (NM_001204910, exon 5 of 8)	exon (NM_001204910, exon 5 of 8)	12172	NM_001204910	226691	Mm.440876	NM_001204910	ENSMUSG00000073490	Ifi207	AI607873|Pyhin-A	interferon activated gene 207	protein-coding
mm_131939.1	chr16	23986467	23986485	+	1	NA	intron (NM_009744, intron 1 of 9)	intron (NM_009744, intron 1 of 9)	2136	NM_009744	12053	Mm.347398	NM_009744	ENSMUSG00000022508	Bcl6	Bcl5	B cell leukemia/lymphoma 6	protein-coding
mm_14409.1	chr2	130277198	130277201	+	1	NA	promoter-TSS (NR_028528)	promoter-TSS (NR_028528)	-827	NR_028528	100217428		NR_028528	ENSMUSG00000065272	Snord57	MBII-434	small nucleolar RNA, C/D box 57	snoRNA
mm_74144.1	chr8	123280612	123280640	+	1	NA	intron (NM_016925, intron 30 of 42)	RLTR17B_Mm|LTR|ERVK	-26404	NM_028200	72325	Mm.276193	NM_028200	ENSMUSG00000001062	Vps9d1	1300018I17Rik|2410004N05Rik|5DOS1|Vsp9d1	VPS9 domain containing 1	protein-coding
mm_111287.1	chr12	85430084	85430087	-	1	NA	Intergenic	Intergenic	-43816	NM_010234	14281	Mm.246513	NM_010234	ENSMUSG00000021250	Fos	D12Rfj1|c-fos|cFos	FBJ osteosarcoma oncogene	protein-coding
mm_110531.1	chr12	54999121	54999142	-	1	NA	Intergenic	Intergenic	-12795	NM_013815	217578	Mm.479583	NM_013815	ENSMUSG00000035021	Baz1a	Acf1|B930060C03|BC065123|Gtl5|Wcrf180|cbp146	bromodomain adjacent to zinc finger domain 1A	protein-coding
mm_38246.1	chr4	136602620	136602634	-	1	NA	promoter-TSS (NM_133872)	promoter-TSS (NM_133872)	96	NM_133872	99982	Mm.28540	NM_133872	ENSMUSG00000036940	Kdm1a	1810043O07Rik|AA408884|Aof2|D4Ertd478e|Kdm1|Lsd1|mKIAA0601	lysine (K)-specific demethylase 1A	protein-coding
mm_62199.1	chr7	97788593	97788616	+	1	NA	Intergenic	CpG	-50357	NM_175105	66333	Mm.29756	NM_175105	ENSMUSG00000042797	Aqp11	1700015P13Rik|AI648923|sjds	aquaporin 11	protein-coding
mm_160921.1	chr11	84880116	84880116	+	1	NA	promoter-TSS (NM_027388)	promoter-TSS (NM_027388)	79	NM_027388	70325	Mm.390414	NM_027388	ENSMUSG00000045140	Pigw	2610044A17Rik|Gwt1	phosphatidylinositol glycan anchor biosynthesis, class W	protein-coding
mm_130892.1	chr15	102366315	102366338	-	1	NA	promoter-TSS (NM_130458)	promoter-TSS (NM_130458)	-55	NM_130458	170574	Mm.263284	NM_130458	ENSMUSG00000060284	Sp7	6430578P22Rik|C22|Osx	Sp7 transcription factor 7	protein-coding
mm_150612.1	chr19	40894693	40894736	+	1	NA	promoter-TSS (NR_106167)	promoter-TSS (NR_106167)	9	NM_028319	72672	Mm.313523	NM_028319	ENSMUSG00000049164	Zfp518a	2810401C22Rik|6330417C12Rik|AI426493|Zfp518|Znf518|Znf518a|mKIAA0335	zinc finger protein 518A	protein-coding
mm_155788.1	chrX	96713509	96713520	+	1	NA	promoter-TSS (NM_029536)	promoter-TSS (NM_029536)	46	NM_029536	76206	Mm.256065	NM_029536	ENSMUSG00000031210	Gpr165	6530406P05Rik	G protein-coupled receptor 165	protein-coding
mm_48072.1	chr5	136581781	136581785	-	1	NA	Intergenic	Intergenic	-14293	NM_001291238	13047	Mm.320317	NM_009986	ENSMUSG00000029705	Cux1	CDP|Cutl1|Cux|Cux-1	cut-like homeobox 1	protein-coding
mm_48607.1	chr5	144255964	144256002	-	1	NA	intron (NM_018772, intron 2 of 2)	intron (NM_018772, intron 2 of 2)	758	NM_018772	55950	Mm.38011	NM_018772	ENSMUSG00000047843	Bri3	I3	brain protein I3	protein-coding
mm_134354.1	chr16	16718091	16718103	-	1	NA	promoter-TSS (NR_045920)	promoter-TSS (NR_045920)	24	NR_045920	74066	Mm.61161	NM_028739		4933404G15Rik	4933401J20Rik	RIKEN cDNA 4933404G15 gene	ncRNA
mm_158851.1	chrX	169994074	169994083	-	1	NA	Intergenic	CpG	-15161	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_150448.1	chr19	38096859	38096889	+	1	NA	promoter-TSS (NM_181748)	promoter-TSS (NM_181748)	-205	NM_181748	107221	Mm.35288	NM_181748	ENSMUSG00000054200	Ffar4	AI552415|GT01|Gpr120|Gpr129|KPG_013|O3far1|Pgr4	free fatty acid receptor 4	protein-coding
mm_171209.1	chr3	5860444	5860444	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-284196	NM_001163305	19302	Mm.132336	NM_008994	ENSMUSG00000040374	Pex2	D3Ertd138e|PAF-1|PMP35|Pxmp3	peroxisomal biogenesis factor 2	protein-coding
mm_116471.1	chr13	43481174	43481191	-	1	NA	promoter-TSS (NM_019930)	promoter-TSS (NM_019930)	-209	NM_019930	56705	Mm.148781	NM_019930	ENSMUSG00000038546	Ranbp9	IBAP-1|Ibap1|RanBPM	RAN binding protein 9	protein-coding
mm_45909.1	chr5	89419050	89419053	-	1	NA	intron (NM_008096, intron 12 of 12)	intron (NM_008096, intron 12 of 12)	38847	NM_008096	14473	Mm.196595	NM_008096	ENSMUSG00000035540	Gc	DBP|VDB	group specific component	protein-coding
mm_59499.1	chr7	27541085	27541112	+	1	NA	exon (NM_011116, exon 7 of 14)	exon (NM_011116, exon 7 of 14)	12120	NM_011116	18807	Mm.6483	NM_011116	ENSMUSG00000003363	Pld3	Sam-9	phospholipase D family, member 3	protein-coding
mm_92879.1	chr10	82623201	82623248	-	1	NA	promoter-TSS (NM_001135567)	promoter-TSS (NM_001135567)	4	NM_001135569	544717	Mm.334867	NM_001135567	ENSMUSG00000063320	1190007I07Rik	-	RIKEN cDNA 1190007I07 gene	protein-coding
mm_119373.1	chr14	41122817	41122828	+	1	NA	3' UTR (NM_133653, exon 10 of 10)	3' UTR (NM_133653, exon 10 of 10)	-8966	NM_023134	20387	Mm.46062	NM_023134	ENSMUSG00000021789	Sftpa1	SP-A|Sftp-1|Sftp1	surfactant associated protein A1	protein-coding
mm_91655.1	chr10	42583629	42583639	-	1	NA	promoter-TSS (NM_152229)	promoter-TSS (NM_152229)	-46	NM_152229	21907	Mm.287100	NM_152229	ENSMUSG00000019803	Nr2e1	Mtl1|Mtll|TLL|Tlx|XTLL|fierce|frc|tailless	nuclear receptor subfamily 2, group E, member 1	protein-coding
mm_27737.1	chr3	69073562	69073575	-	1	NA	3' UTR (NM_008467, exon 17 of 17)	3' UTR (NM_008467, exon 17 of 17)	-28826	NM_025863	66949	Mm.176695	NM_025863	ENSMUSG00000034317	Trim59	2310035M22Rik|2700022F13Rik|Mrf1|TSBF1	tripartite motif-containing 59	protein-coding
mm_158032.1	chrX	97377164	97377187	-	1	NA	promoter-TSS (NM_001161432)	promoter-TSS (NM_001161432)	34	NM_001161432	245527	Mm.189270	NM_175540	ENSMUSG00000034457	Eda2r	9430060M22Rik|TNFRSF27|Xedar	ectodysplasin A2 receptor	protein-coding
mm_70377.1	chr8	10006785	10006810	+	1	NA	5' UTR (NM_033622, exon 1 of 7)	5' UTR (NM_033622, exon 1 of 7)	164	NM_033622	24099	Mm.28835	NM_033622	ENSMUSG00000031497	Tnfsf13b	BAFF|BLyS|D8Ertd387e|TALL-1|TALL1|THANK|TNFSF20|Tnlg7a|zTNF4	tumor necrosis factor (ligand) superfamily, member 13b	protein-coding
mm_148628.1	chr19	5450234	5450282	+	1	NA	exon (NM_010235, exon 2 of 4)	exon (NM_010235, exon 2 of 4)	2560	NM_010235	14283	Mm.6215	NM_010235	ENSMUSG00000024912	Fosl1	AW538199|Fra1|fra-1	fos-like antigen 1	protein-coding
mm_146514.1	chr18	3337682	3337698	-	1	NA	promoter-TSS (NM_001110852)	promoter-TSS (NM_001110852)	-101	NM_001110852	12916	Mm.5244	NM_013498	ENSMUSG00000063889	Crem	ICER|ICERI	cAMP responsive element modulator	protein-coding
mm_11118.1	chr2	28205649	28205672	+	1	NA	promoter-TSS (NM_019498)	promoter-TSS (NM_019498)	-29	NM_001038612	56177	Mm.43278	NM_019498	ENSMUSG00000026833	Olfm1	AMY|AW742568|Noe1|OlfA|Pancortin|Pancortin3	olfactomedin 1	protein-coding
mm_167492.1	chr9	7558240	7558246	-	1	NA	promoter-TSS (NM_008611)	promoter-TSS (NM_008611)	-186	NM_008611	17394	Mm.16415	NM_008611	ENSMUSG00000005800	Mmp8	BB138268	matrix metallopeptidase 8	protein-coding
mm_23341.1	chr3	54693035	54693055	+	1	NA	promoter-TSS (NM_019995)	promoter-TSS (NM_019995)	-60	NM_019995	56790	Mm.486375	NM_019995	ENSMUSG00000027751	Supt20	AA667204|AI450544|D3Ertd300e|Fam48a|Supt20h|p38IP	suppressor of Ty 20	protein-coding
mm_91195.1	chr10	21150385	21150407	-	1	NA	exon (NM_001198914, exon 6 of 16)	exon (NM_001198914, exon 6 of 16)	10588	NM_001198914	17863	Mm.52109	NM_010848	ENSMUSG00000019982	Myb	AI550390|M16449|c-myb	myeloblastosis oncogene	protein-coding
mm_4365.1	chr1	172082510	172082543	+	1	NA	promoter-TSS (NM_009938)	promoter-TSS (NM_009938)	-3	NM_009938	12847	Mm.30041	NM_009938	ENSMUSG00000026553	Copa	AU040324|xenin	coatomer protein complex subunit alpha	protein-coding
mm_8629.1	chr1	156303363	156303388	-	1	NA	promoter-TSS (NM_001134741)	promoter-TSS (NM_001134741)	-27	NM_001134741	214575	Mm.252800	NM_001134741	ENSMUSG00000060985	Tdrd5	Gm103	tudor domain containing 5	protein-coding
mm_54472.1	chr6	34910553	34910588	-	1	NA	intron (NM_001013366, intron 1 of 14)	MIR3|SINE|MIR	261	NM_001013366	101240	Mm.152120	NM_001013366	ENSMUSG00000058486	Wdr91	9530020G05Rik|AI987683|AU018665	WD repeat domain 91	protein-coding
mm_160645.1	chr9	109978959	109978959	+	1	NA	exon (NM_008633, exon 2 of 19)	exon (NM_008633, exon 2 of 19)	47185	NM_008633	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_134909.1	chr16	30260777	30260790	-	1	NA	exon (NM_027904, exon 2 of 2)	exon (NM_027904, exon 2 of 2)	6749	NM_027904	71756	Mm.290614	NM_027904	ENSMUSG00000023176	Cpn2	1300018K11Rik	carboxypeptidase N, polypeptide 2	protein-coding
mm_148551.1	chr19	4711955	4711982	+	1	NA	intron (NM_021287, intron 1 of 36)	CpG	745	NM_021287	20743	Mm.329668	NM_021287	ENSMUSG00000067889	Sptbn2	Spnb3|mKIAA0302	spectrin beta, non-erythrocytic 2	protein-coding
mm_14427.1	chr2	130539430	130539438	+	1	NA	intron (NM_001163688, intron 10 of 20)	intron (NM_001163688, intron 10 of 20)	24315	NR_040348	321014	Mm.442588	NR_040348	ENSMUSG00000060029	4930473A02Rik	-	RIKEN cDNA 4930473A02 gene	ncRNA
mm_98336.1	chr11	90804683	90804699	+	1	NA	promoter-TSS (NR_045956)	promoter-TSS (NR_045956)	0	NR_045956	73922	Mm.233289	NR_045956	ENSMUSG00000085940	4930405D11Rik	-	RIKEN cDNA 4930405D11 gene	ncRNA
mm_93193.1	chr10	94035790	94035816	-	1	NA	promoter-TSS (NM_053072)	promoter-TSS (NM_053072)	-4	NM_001304575	215008	Mm.124177	NM_172538	ENSMUSG00000036099	Vezt	A630071D13Rik|AI848282	vezatin, adherens junctions transmembrane protein	protein-coding
mm_104778.1	chr11	98546057	98546081	-	1	NA	promoter-TSS (NM_011771)	promoter-TSS (NM_011771)	-38	NM_011771	22780	Mm.133367	NM_011771	ENSMUSG00000018168	Ikzf3	5830411O07Rik|Aiolos|Zfpn1a3|Znfn1a3	IKAROS family zinc finger 3	protein-coding
mm_147348.1	chr18	43324348	43324364	-	1	NA	exon (NM_001291455, exon 14 of 14)	exon (NM_001291455, exon 14 of 14)	48916	NM_001136086	22240	Mm.8180	NM_009468	ENSMUSG00000024501	Dpysl3	CRMP-4|DRP-3|TUC4|ULIP-1|Ulip|Ulip1	dihydropyrimidinase-like 3	protein-coding
mm_148670.1	chr19	5637529	5637548	+	1	NA	promoter-TSS (NM_009045)	promoter-TSS (NM_009045)	48	NM_009045	19697	Mm.249966	NM_009045	ENSMUSG00000024927	Rela	p65	v-rel reticuloendotheliosis viral oncogene homolog A (avian)	protein-coding
mm_99843.1	chr11	109359585	109359614	+	1	NA	intron (NR_038097, intron 1 of 1)	intron (NR_038097, intron 1 of 1)	-3195	NM_010303	14674	Mm.193925	NM_010303	ENSMUSG00000020611	Gna13	AU024132|AU043124|Galpha13	guanine nucleotide binding protein, alpha 13	protein-coding
mm_103382.1	chr11	75415128	75415141	-	1	NA	intron (NM_011340, intron 4 of 7)	intron (NM_011340, intron 4 of 7)	7489	NM_011340	20317	Mm.2044	NM_011340	ENSMUSG00000000753	Serpinf1	AI195227|EPC-1|Pedf|Pedfl|Sdf3	serine (or cysteine) peptidase inhibitor, clade F, member 1	protein-coding
mm_154089.1	chr19	56815785	56815798	-	1	NA	Intergenic	Intergenic	-2108	NM_170757	213993	Mm.469677	NM_170757	ENSMUSG00000035173	Ccdc186	1810028B20Rik|A630007B06Rik|AI159700|Otg1	coiled-coil domain containing 186	protein-coding
mm_78454.1	chr9	32372410	32372425	+	1	NA	promoter-TSS (NM_019659)	promoter-TSS (NM_019659)	-1	NM_019659	56379	Mm.390168	NM_019659	ENSMUSG00000041248	Kcnj1	Kir1.1|ROMK|Romk2	potassium inwardly-rectifying channel, subfamily J, member 1	protein-coding
mm_24709.1	chr3	95217418	95217484	+	1	NA	promoter-TSS (NR_108026)	promoter-TSS (NR_108026)	-6	NR_108026	100504029	Mm.478537	NR_108026	ENSMUSG00000097167	Gm16740	-	predicted gene, 16740	ncRNA
mm_125181.1	chr15	31604795	31604832	+	1	NA	intron (NM_026546, intron 1 of 4)	B3A|SINE|B2	2697	NM_026546	68073	Mm.119185	NM_026546	ENSMUSG00000039065	Fam173b	A930016P21Rik|AA987072	family with sequence similarity 173, member B	protein-coding
mm_7031.1	chr1	87099526	87099535	-	1	NA	exon (NM_001081082, exon 9 of 11)	exon (NM_001081082, exon 9 of 11)	2076	NM_001081082	76768	Mm.58068	NM_001081082	ENSMUSG00000079440	Alpi	2010001C14Rik|Akp6|gIAP	alkaline phosphatase, intestinal	protein-coding
mm_18385.1	chr2	60113780	60113807	-	1	NA	intron (NM_001001182, intron 1 of 35)	L1MA5A|LINE|L1	11947	NM_001001182	407823	Mm.228071	NM_001001182	ENSMUSG00000026987	Baz2b	5830435C13Rik|BC053917|D2Ertd794e	bromodomain adjacent to zinc finger domain, 2B	protein-coding
mm_102296.1	chr11	55419905	55419915	-	1	NA	5' UTR (NM_009242, exon 1 of 10)	5' UTR (NM_009242, exon 1 of 10)	170	NM_009242	20692	Mm.291442	NM_009242	ENSMUSG00000018593	Sparc	BM-40|ON	secreted acidic cysteine rich glycoprotein	protein-coding
mm_122761.1	chr14	54233251	54233261	-	1	NA	Intergenic	Intergenic	20673	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_144707.1	chr18	34864656	34864665	+	1	NA	3' UTR (NM_007913, exon 2 of 2)	3' UTR (NM_007913, exon 2 of 2)	3453	NM_007913	13653	Mm.181959	NM_007913	ENSMUSG00000038418	Egr1	A530045N19Rik|ETR103|Egr-1|Krox-1|Krox-24|Krox24|NGF1-A|NGFI-A|NGFIA|TIS8|Zenk|Zfp-6|Zif268|egr	early growth response 1	protein-coding
mm_118984.1	chr14	28504566	28504605	+	1	NA	promoter-TSS (NM_009524)	promoter-TSS (NM_009524)	-888	NM_009524	22418	Mm.287544	NM_009524	ENSMUSG00000021994	Wnt5a	8030457G12Rik|Wnt-5a	wingless-type MMTV integration site family, member 5A	protein-coding
mm_26408.1	chr3	142608188	142608198	+	1	NA	exon (NM_010259, exon 8 of 11)	exon (NM_010259, exon 8 of 11)	-12470	NM_010260	14469	Mm.24038	NM_010260	ENSMUSG00000028270	Gbp2	-	guanylate binding protein 2	protein-coding
mm_36527.1	chr4	86558267	86558307	-	1	NA	promoter-TSS (NM_001081096)	promoter-TSS (NM_001081096)	16	NM_001081096	75811	Mm.56451	NM_001081096	ENSMUSG00000028492	Saxo1	4930500O09Rik|Fam154a	stabilizer of axonemal microtubules 1	protein-coding
mm_29927.1	chr3	131491276	131491288	-	1	NA	Intergenic	Intergenic	-73486	NM_001289479	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_158111.1	chrX	102157066	102157096	-	1	NA	promoter-TSS (NM_146235)	promoter-TSS (NM_146235)	10	NM_146235	236930	Mm.31911	NM_146235	ENSMUSG00000051220	Ercc6l	BC004701|D330021P09Rik	excision repair cross-complementing rodent repair deficiency complementation group 6 like	protein-coding
mm_75122.1	chr8	34807072	34807085	-	1	NA	promoter-TSS (NM_176933)	promoter-TSS (NM_176933)	-532	NM_176933	319520	Mm.170276	NM_176933	ENSMUSG00000031530	Dusp4	2700078F24Rik|AI844617|BB104621|E130306H24Rik|MKP2	dual specificity phosphatase 4	protein-coding
mm_32497.1	chr4	108431376	108431382	+	1	NA	Intergenic	Intergenic	-24666	NM_024198	67305	Mm.20164	NM_024198	ENSMUSG00000028597	Gpx7	3110050F08Rik|AI327032|GPX6	glutathione peroxidase 7	protein-coding
mm_9662.1	chr1	177796611	177796619	-	1	NA	promoter-TSS (NM_007422)	promoter-TSS (NM_007422)	-106	NM_007422	11566	Mm.338021	NM_007422	ENSMUSG00000015961	Adss	AI314886|AS|Adss2	adenylosuccinate synthetase, non muscle	protein-coding
mm_109667.1	chr12	113050502	113050513	+	1	NA	intron (NM_001291444, intron 5 of 23)	intron (NM_001291444, intron 5 of 23)	-23995	NM_029381	75671	Mm.23377	NM_029381	ENSMUSG00000012211	Tex22	1700028O09Rik|AV210422|Tep22	testis expressed gene 22	protein-coding
mm_170985.1	chr2	73867938	73867940	+	1	NA	intron (NM_001284374, intron 3 of 11)	LSU-rRNA_Hsa|rRNA|rRNA	24700	NM_001284371	11909	Mm.209903	NM_009715	ENSMUSG00000027104	Atf2	Atf-2|CRE-BP|Creb2|D130078H02Rik|D18875|Tg(Gzma-Klra1)7Wum|mXBP	activating transcription factor 2	protein-coding
mm_9469.1	chr1	173333505	173333520	-	1	NA	promoter-TSS (NM_010045)	promoter-TSS (NM_010045)	-9	NM_010045	13349	Mm.6393	NM_010045	ENSMUSG00000037872	Ackr1	AA162249|CCBP1|CD234|Darc|Dfy|ESTM35|FY|GPD	atypical chemokine receptor 1 (Duffy blood group)	protein-coding
mm_527.1	chr1	37660793	37660798	+	1	NA	intron (NM_028096, intron 1 of 9)	L1M4c|LINE|L1	59016	NM_028096	72097	Mm.142607	NM_028096	ENSMUSG00000026090	2010300C02Rik	-	RIKEN cDNA 2010300C02 gene	protein-coding
mm_15342.1	chr2	156008089	156008138	+	1	NA	promoter-TSS (NM_001145352)	promoter-TSS (NM_001145352)	-12	NM_025516	66366	Mm.141276	NM_025516	ENSMUSG00000005881	Ergic3	2310015B14Rik|AV318804|CGI-54|D2Ucla1|NY-BR-84|Sdbcag84	ERGIC and golgi 3	protein-coding
mm_32909.1	chr4	119132157	119132212	+	1	NA	exon (NM_011400, exon 3 of 10)	exon (NM_011400, exon 3 of 10)	23439	NM_011400	20525	Mm.21002	NM_011400	ENSMUSG00000028645	Slc2a1	Glut-1|Glut1	solute carrier family 2 (facilitated glucose transporter), member 1	protein-coding
mm_129883.1	chr15	83484018	83484042	-	1	NA	3' UTR (NM_178869, exon 12 of 12)	3' UTR (NM_178869, exon 12 of 12)	-19424	NM_001159509	23970	Mm.23978	NM_011862	ENSMUSG00000016664	Pacsin2	AI197433	protein kinase C and casein kinase substrate in neurons 2	protein-coding
mm_111628.1	chr12	102439091	102439099	-	1	NA	intron (NM_011175, intron 1 of 13)	intron (NM_011175, intron 1 of 13)	718	NM_011175	19141	Mm.17185	NM_011175	ENSMUSG00000021190	Lgmn	AEP|AI746452|AU022324|Prsc1	legumain	protein-coding
mm_28558.1	chr3	93443865	93443884	-	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	1544	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_123075.1	chr14	55721897	55721930	-	1	NA	5' UTR (NM_019519, exon 1 of 16)	5' UTR (NM_019519, exon 1 of 16)	263	NM_019519	56187	Mm.87216	NM_019519	ENSMUSG00000040472	Rabggta	gm	Rab geranylgeranyl transferase, a subunit	protein-coding
mm_45542.1	chr5	72846431	72846469	-	1	NA	intron (NM_001113461, intron 1 of 17)	intron (NM_001113461, intron 1 of 17)	21998	NM_001113461	21682	Mm.319581	NM_013689	ENSMUSG00000029217	Tec	-	tec protein tyrosine kinase	protein-coding
mm_50556.1	chr6	49047776	49047786	+	1	NA	exon (NM_053110, exon 6 of 11)	exon (NM_053110, exon 6 of 11)	11263	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_173123.1	chrX	165466242	165466242	+	1	NA	Intergenic	Lx2|LINE|L1	-139261	NM_183427	237213	Mm.113877	NM_183427	ENSMUSG00000018589	Glra2	-	glycine receptor, alpha 2 subunit	protein-coding
mm_72761.1	chr8	85509182	85509205	+	1	NA	exon (NM_173866, exon 5 of 12)	exon (NM_173866, exon 5 of 12)	16576	NM_173866	108682	Mm.200423	NM_173866	ENSMUSG00000031700	Gpt2	4631422C05Rik|ALT2|AU014768|AU041193|C87201	glutamic pyruvate transaminase (alanine aminotransferase) 2	protein-coding
mm_1497.1	chr1	72074381	72074400	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-69195	NR_040454	71134	Mm.370574	NR_040454	ENSMUSG00000101848	4933417E11Rik	-	RIKEN cDNA 4933417E11 gene	ncRNA
mm_144528.1	chr18	25065841	25065851	+	1	NA	intron (NM_175276, intron 15 of 26)	intron (NM_175276, intron 15 of 26)	100119	NM_001142697	66648	Mm.263189	NM_001004361	ENSMUSG00000024269	Tpgs2	5730437P09Rik|5730494M16Rik|AI666318|Pgs2	tubulin polyglutamylase complex subunit 2	protein-coding
mm_26952.1	chr3	20275660	20275675	-	1	NA	promoter-TSS (NM_029706)	promoter-TSS (NM_029706)	66	NM_029706	76703	Mm.34692	NM_029706	ENSMUSG00000011463	Cpb1	0910001A18Rik|1810063F02Rik|2210008M23Rik|AI504870	carboxypeptidase B1 (tissue)	protein-coding
mm_166876.1	chr7	25412948	25412950	-	1	NA	promoter-TSS (NM_153576)	promoter-TSS (NM_153576)	-63	NM_153576	232983	Mm.10545	NM_153576	ENSMUSG00000060188	Cxcl17	VCC-1|Vcc1	chemokine (C-X-C motif) ligand 17	protein-coding
mm_148075.1	chr18	72351010	72351022	-	1	NA	promoter-TSS (NM_007831)	promoter-TSS (NM_007831)	53	NM_007831	13176	Mm.167882	NM_007831	ENSMUSG00000060534	Dcc	C030036D22Rik|Igdcc1	deleted in colorectal carcinoma	protein-coding
mm_157842.1	chrX	74373236	74373249	-	1	NA	non-coding (NR_103489, exon 1 of 6)	non-coding (NR_103489, exon 1 of 6)	107	NM_001256104	214601	Mm.19931	NM_145406	ENSMUSG00000032806	Slc10a3	DXHXS253E|DXS253Eh|DXSmhG28|P3	solute carrier family 10 (sodium/bile acid cotransporter family), member 3	protein-coding
mm_39110.1	chr4	154928157	154928174	-	1	NA	promoter-TSS (NM_178931)	promoter-TSS (NM_178931)	-88	NM_178931	230979	Mm.215147	NM_178931	ENSMUSG00000042333	Tnfrsf14	Atar|HveA|Hvem|Tnfrs14	tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)	protein-coding
mm_85599.1	chr9	107542111	107542155	-	1	NA	promoter-TSS (NM_019720)	promoter-TSS (NM_019720)	-76	NM_018879	56032	Mm.11337	NM_018879	ENSMUSG00000010057	Nprl2	2810446G01Rik|G21|NPR2L|Tusc4	nitrogen permease regulator-like 2	protein-coding
mm_31384.1	chr4	47996464	47996470	+	1	NA	Intergenic	B1_Mur1|SINE|Alu	-48838	NM_015743	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_25359.1	chr3	107090949	107090963	+	1	NA	Intergenic	L2a|LINE|L2	-10611	NM_008417	16490	Mm.39285	NM_008417	ENSMUSG00000040724	Kcna2	Akr6a4|ENSMUSG00000074335|Gm10672|Kca1-2|Kv1.2|Mk-2	potassium voltage-gated channel, shaker-related subfamily, member 2	protein-coding
mm_155043.1	chrX	42150673	42150721	+	1	NA	promoter-TSS (NM_021465)	promoter-TSS (NM_021465)	-4	NM_021465	20843	Mm.290422	NM_021465	ENSMUSG00000025862	Stag2	9230105L23Rik|B230112I07Rik|SA-2|SAP2	stromal antigen 2	protein-coding
mm_49789.1	chr6	35185240	35185244	+	1	NA	intron (NM_027513, intron 2 of 42)	intron (NM_027513, intron 2 of 42)	7626	NM_027513	70699	Mm.261208	NM_027513	ENSMUSG00000038759	Nup205	3830404O05Rik|AV248391|mKIAA0225	nucleoporin 205	protein-coding
mm_133296.1	chr16	77500211	77500232	+	1	NA	intron (NR_015543, intron 3 of 4)	intron (NR_015543, intron 3 of 4)	-98715	NR_029535	387229		NR_029535	ENSMUSG00000065530	Mir99a	Mirn99a|mir-99a|mmu-mir-99a	microRNA 99a	ncRNA
mm_9828.1	chr1	182517565	182517615	-	1	NA	promoter-TSS (NM_009794)	promoter-TSS (NM_009794)	-107	NM_009794	12334	Mm.19306	NM_009794	ENSMUSG00000026509	Capn2	AI326419|Capa-2|Capa2|m-calpain|m-calpin	calpain 2	protein-coding
mm_163948.1	chr14	51923143	51923149	-	1	NA	promoter-TSS (NM_001011687)	promoter-TSS (NM_001011687)	-373	NM_001011687	497071	Mm.378602	NM_001011687	ENSMUSG00000068392	Rnase13	-	ribonuclease, RNase A family, 13 (non-active)	protein-coding
mm_75915.1	chr8	71463577	71463593	-	1	NA	promoter-TSS (NM_022419)	promoter-TSS (NM_022419)	72	NM_022419	64296	Mm.276383	NM_022419	ENSMUSG00000007950	Abhd8	0910001L24Rik|AB030191	abhydrolase domain containing 8	protein-coding
mm_96105.1	chr11	60537990	60538074	+	1	NA	5' UTR (NM_172943, exon 1 of 4)	5' UTR (NM_172943, exon 1 of 4)	349	NM_172943	268420	Mm.262056	NM_172943	ENSMUSG00000042650	Alkbh5	AW050020|AW215868|Abh5|E130207K11|Ofoxd	alkB homolog 5, RNA demethylase	protein-coding
mm_131172.1	chr16	7069789	7069793	+	1	NA	promoter-TSS (NM_183188)	promoter-TSS (NM_183188)	-44	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_114197.1	chr13	55905298	55905301	+	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-73874	NM_011097	18740	Mm.135195	NM_011097	ENSMUSG00000021506	Pitx1	Bft|P-OTX|Potx|Ptx1	paired-like homeodomain transcription factor 1	protein-coding
mm_113165.1	chr13	24812712	24812722	+	1	NA	exon (NM_024473, exon 5 of 5)	exon (NM_024473, exon 5 of 5)	11060	NM_024473	79555	Mm.266668	NM_024473	ENSMUSG00000019132	BC005537	8030460C05Rik|C78201	cDNA sequence BC005537	protein-coding
mm_70448.1	chr8	11758330	11758375	+	1	NA	promoter-TSS (NM_001113518)	promoter-TSS (NM_001113518)	22	NM_001113518	54126	Mm.244068	NM_017402	ENSMUSG00000031511	Arhgef7	Cool|PIX|Pak3bp|betaPix|betaPix-b|betaPix-c|cool-1|mKIAA0142|p85Cool1|p85SPR	Rho guanine nucleotide exchange factor (GEF7)	protein-coding
mm_98108.1	chr11	86900247	86900250	+	1	NA	intron (NR_106195, intron 4 of 8)	RMER19B|LTR|ERVK	-92588	NM_026191	67487	Mm.260627	NM_026191	ENSMUSG00000018425	Dhx40	2410016C14Rik|ARG147|DDX40|PAD	DEAH (Asp-Glu-Ala-His) box polypeptide 40	protein-coding
mm_99081.1	chr11	99389086	99389129	+	1	NA	exon (NM_010660, exon 1 of 8)	exon (NM_010660, exon 1 of 8)	257	NM_010660	16661	Mm.22662	NM_010660	ENSMUSG00000019761	Krt10	D130054E02Rik|K10|K1C1|Krt-1.10|Krt1-10	keratin 10	protein-coding
mm_82671.1	chr9	22130612	22130640	-	1	NA	promoter-TSS (NM_007388)	promoter-TSS (NM_007388)	-28	NM_007388	11433	Mm.46354	NM_007388	ENSMUSG00000001348	Acp5	TRACP|TRAP	acid phosphatase 5, tartrate resistant	protein-coding
mm_53129.1	chr6	125145236	125145250	+	1	NA	promoter-TSS (NM_001039669)	promoter-TSS (NM_001039669)	19	NM_001302779	320678	Mm.129415	NM_178787	ENSMUSG00000038271	Iffo1	4733401N06Rik|A930037G23Rik|HOM-TES-103|Iffo	intermediate filament family orphan 1	protein-coding
mm_52524.1	chr6	115601952	115601979	+	1	NA	promoter-TSS (NM_023290)	promoter-TSS (NM_023290)	27	NM_023290	67027	Mm.101316	NM_023290	ENSMUSG00000000439	Mkrn2	2610002L04Rik|C81377	makorin, ring finger protein, 2	protein-coding
mm_65575.1	chr7	27195718	27195725	-	1	NA	promoter-TSS (NM_001046637)	promoter-TSS (NM_001046637)	39	NM_001046637	53607	Mm.386890	NM_015782	ENSMUSG00000061479	Snrpa	C430021M15Rik|Rnu1a-1|Rnu1a1|U1-A|U1A	small nuclear ribonucleoprotein polypeptide A	protein-coding
mm_77123.1	chr8	111310209	111310211	-	1	NA	Intergenic	Intergenic	-9988	NM_146218	234736	Mm.334816	NM_146218	ENSMUSG00000033596	Rfwd3	BC027246	ring finger and WD repeat domain 3	protein-coding
mm_486.1	chr1	36764513	36764523	+	1	NA	promoter-TSS (NM_001289766)	promoter-TSS (NM_001289766)	3	NM_001289766	22637	Mm.8038	NM_009539	ENSMUSG00000026117	Zap70	Srk|ZAP-70|mrtle|mur	zeta-chain (TCR) associated protein kinase	protein-coding
mm_40566.1	chr5	62818594	62818597	+	1	NA	exon (NM_001170705, exon 2 of 9)	exon (NM_001170705, exon 2 of 9)	4772	NM_001170705	100322896	Mm.479821	NM_001170705	ENSMUSG00000090326	Dthd1	Gm17384	death domain containing 1	protein-coding
mm_29292.1	chr3	107760235	107760249	-	1	NA	5' UTR (NM_007778, exon 1 of 9)	5' UTR (NM_007778, exon 1 of 9)	227	NM_001113530	12977	Mm.795	NM_007778	ENSMUSG00000014599	Csf1	C87615|Csfm|MCSF|op	colony stimulating factor 1 (macrophage)	protein-coding
mm_53404.1	chr6	131782169	131782176	+	1	NA	Intergenic	Intergenic	-92109	NM_207019	387346	Mm.377908	NM_207019	ENSMUSG00000063478	Tas2r114	T2R14|Tas2r14|mGR14|mt2r46	taste receptor, type 2, member 114	protein-coding
mm_22756.1	chr3	19985633	19985643	+	1	NA	exon (NM_007752, exon 15 of 19)	exon (NM_007752, exon 15 of 19)	28584	NM_007752	12870	Mm.13787	NM_007752	ENSMUSG00000003617	Cp	D3Ertd555e	ceruloplasmin	protein-coding
mm_73473.1	chr8	106716388	106716407	+	1	NA	intron (NM_173037, intron 7 of 17)	intron (NM_173037, intron 7 of 17)	33329	NM_173037	272538	Mm.87151	NM_173037	ENSMUSG00000041949	Tango6	AW413431|E330010G16|Tmco7	transport and golgi organization 6	protein-coding
mm_103943.1	chr11	83850718	83850760	-	1	NA	promoter-TSS (NM_001291268)	promoter-TSS (NM_001291268)	-130	NM_001291268	21410	Mm.7226	NM_009330	ENSMUSG00000020679	Hnf1b	HNF-1-beta|HNF-1B|HNF-1Beta|Hnf1beta|LFB3|Tcf-2|Tcf2|vHNF1	HNF1 homeobox B	protein-coding
mm_3846.1	chr1	160055068	160055072	+	1	NA	intron (NM_001162896, intron 1 of 2)	intron (NM_001162896, intron 1 of 2)	10690	NM_001162896	67647	Mm.171518	NM_001024470	ENSMUSG00000090394	4930523C07Rik	-	RIKEN cDNA 4930523C07 gene	protein-coding
mm_89063.1	chr10	82896914	82896934	+	1	NA	3' UTR (NM_001042523, exon 15 of 15)	3' UTR (NM_001042523, exon 15 of 15)	30298	NM_025499	66341	Mm.443284	NM_025499	ENSMUSG00000109864	Eid3	1700027M21Rik|NS4EB	EP300 interacting inhibitor of differentiation 3	protein-coding
mm_110379.1	chr12	40209669	40209689	-	1	NA	intron (NM_013562, intron 8 of 11)	intron (NM_013562, intron 8 of 11)	-10364	NM_001033437	380755	Mm.390463	NM_001033437	ENSMUSG00000071342	Lsmem1	Gm889	leucine-rich single-pass membrane protein 1	protein-coding
mm_11499.1	chr2	32535283	32535290	+	1	NA	promoter-TSS (NM_153560)	promoter-TSS (NM_153560)	-73	NM_153560	98952	Mm.4065	NM_153560	ENSMUSG00000039157	Fam102a	AI426465|C230093N12Rik|Eeig1	family with sequence similarity 102, member A	protein-coding
mm_172700.1	chr8	63933315	63933326	-	1	NA	intron (NM_001195687, intron 5 of 7)	intron (NM_001195687, intron 5 of 7)	18850	NM_001195687	244495	Mm.485331	NM_001195687	ENSMUSG00000094443	Sgol2b	EG244495|Gm4975|Sgo2B	shugoshin like 2b (S. pombe)	protein-coding
mm_167586.1	chr9	46197083	46197094	+	1	NA	intron (NM_027498, intron 11 of 24)	intron (NM_027498, intron 11 of 24)	-31542	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2|apo-AI|apoA-I	apolipoprotein A-I	protein-coding
mm_137985.1	chr17	33608054	33608056	+	1	NA	TTS (NM_053214)	TTS (NM_053214)	-21037	NR_034153	328801	Mm.181488	NM_026712	ENSMUSG00000073423	Zfp414	0610030H11Rik|Znf414	zinc finger protein 414	protein-coding
mm_110425.1	chr12	46818927	46818937	-	1	NA	promoter-TSS (NM_021361)	promoter-TSS (NM_021361)	-157	NM_021361	664883	Mm.247195	NM_021361	ENSMUSG00000021047	Nova1	9430099M15Rik|G630039L02|Nova-1	neuro-oncological ventral antigen 1	protein-coding
mm_100213.1	chr11	116918827	116918837	+	1	NA	promoter-TSS (NM_172948)	promoter-TSS (NM_172948)	-31	NM_172948	268510	Mm.35141	NM_172948	ENSMUSG00000043857	Mgat5b	C330018B01|GnT-IX|mGnTVB	mannoside acetylglucosaminyltransferase 5, isoenzyme B	protein-coding
mm_1252.1	chr1	62816814	62816826	+	1	NA	3' UTR (NM_010939, exon 16 of 16)	3' UTR (NM_010939, exon 16 of 16)	-22088	NR_040601	74992	Mm.401979	NR_040601		4930487H11Rik	-	RIKEN cDNA 4930487H11 gene	ncRNA
mm_57320.1	chr6	124733022	124733032	-	1	NA	5' UTR (NM_013545, exon 1 of 16)	5' UTR (NM_013545, exon 1 of 16)	127	NM_013545	15170	Mm.271799	NM_013545	ENSMUSG00000004266	Ptpn6	70Z-SHP|Hcph|PTPTY-42|Ptp1C|SH-PTP1|SHP-1|hcp|me	protein tyrosine phosphatase, non-receptor type 6	protein-coding
mm_101927.1	chr11	50202873	50202891	-	1	NA	exon (NM_011018, exon 6 of 8)	exon (NM_011018, exon 6 of 8)	7938	NM_001290769	18412	Mm.40828	NM_011018	ENSMUSG00000015837	Sqstm1	A170|OSF-6|Osi|STAP|STONE14|p62	sequestosome 1	protein-coding
mm_168106.1	chr10	14745893	14745898	-	1	NA	intron (NR_045824, intron 3 of 5)	intron (NR_045824, intron 3 of 5)	-14394	NM_008703	18101	Mm.487342	NM_008703	ENSMUSG00000019865	Nmbr	BB182387	neuromedin B receptor	protein-coding
mm_64603.1	chr7	3216983	3217010	-	1	NA	Intergenic	Intergenic	-1630	NR_029640	100049710		NR_029640	ENSMUSG00000077815	Mir290a	Mir290|Mirn290|mir-290a|mmu-miR-290|mmu-mir-290a	microRNA 290a	ncRNA
mm_130626.1	chr15	100415745	100415759	-	1	NA	intron (NM_008732, intron 1 of 16)	intron (NM_008732, intron 1 of 16)	7303	NM_001146161	18174	Mm.234608	NM_008732	ENSMUSG00000023030	Slc11a2	DCT1|DMT1|Nramp2|mk|van	solute carrier family 11 (proton-coupled divalent metal ion transporters), member 2	protein-coding
mm_137661.1	chr17	28691463	28691471	+	1	NA	5' UTR (NM_011951, exon 1 of 12)	5' UTR (NM_011951, exon 1 of 12)	125	NM_001168514	26416	Mm.311337	NM_011951	ENSMUSG00000053436	Mapk14	CSBP2|Crk1|Csbp1|Mxi2|PRKM14|PRKM15|p38|p38-alpha|p38MAPK|p38a|p38alpha	mitogen-activated protein kinase 14	protein-coding
mm_23639.1	chr3	67092501	67092504	+	1	NA	intron (NM_025822, intron 4 of 9)	intron (NM_025822, intron 4 of 9)	106830	NM_025822	66880	Mm.316418	NM_025822	ENSMUSG00000034544	Rsrc1	1200013F24Rik|SRrp53	arginine/serine-rich coiled-coil 1	protein-coding
mm_143159.1	chr17	57224122	57224163	-	1	NA	exon (NM_009778, exon 10 of 41)	exon (NM_009778, exon 10 of 41)	3994	NM_009778	12266	Mm.19131	NM_009778	ENSMUSG00000024164	C3	AI255234|ASP|HSE-MSF|Plp	complement component 3	protein-coding
mm_28644.1	chr3	95228170	95228261	-	1	NA	promoter-TSS (NM_172395)	promoter-TSS (NM_172395)	-209	NM_172395	57912	Mm.28189	NM_172395	ENSMUSG00000046722	Cdc42se1	1300002M12Rik|AW558204|Cdcse1|SCIP1|Spec1	CDC42 small effector 1	protein-coding
mm_44574.1	chr5	24842308	24842318	-	1	NA	promoter-TSS (NM_053075)	promoter-TSS (NM_053075)	48	NM_053075	19744	Mm.319175	NM_053075	ENSMUSG00000028945	Rheb	Rheb1	Ras homolog enriched in brain	protein-coding
mm_139942.1	chr17	71183577	71183598	+	1	NA	promoter-TSS (NM_022882)	promoter-TSS (NM_022882)	-391	NM_022882	64898	Mm.227924	NM_022882	ENSMUSG00000024052	Lpin2	2610511G02Rik|AI481352|AW742896	lipin 2	protein-coding
mm_153225.1	chr19	34879179	34879194	-	1	NA	5' UTR (NM_001114339, exon 1 of 7)	5' UTR (NM_001114339, exon 1 of 7)	269	NM_001114339	75735	Mm.24742	NM_023792	ENSMUSG00000033610	Pank1	Pank|Pank1b	pantothenate kinase 1	protein-coding
mm_27868.1	chr3	79159623	79159631	-	1	NA	Intergenic	B3|SINE|B2	-13752	NM_001099624	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_153048.1	chr19	32068860	32068862	-	1	NA	intron (NM_018830, intron 2 of 23)	intron (NM_018830, intron 2 of 23)	34279	NM_018830	54447	Mm.491229	NM_018830	ENSMUSG00000024887	Asah2	AI585898	N-acylsphingosine amidohydrolase 2	protein-coding
mm_78519.1	chr9	32963054	32963079	+	1	NA	Intergenic	Intergenic	-34100	NR_131058	330917	Mm.488283	NR_131058		Gm27162	A430016B06	predicted gene 27162	ncRNA
mm_123528.1	chr14	66803539	66803560	-	1	NA	3' UTR (NM_009955, exon 14 of 14)	3' UTR (NM_009955, exon 14 of 14)	65051	NM_009955	12934	Mm.352648	NM_009955	ENSMUSG00000022048	Dpysl2	AI851130|Crmp2|DRP2|Musunc33|TOAD-64|Ulip2	dihydropyrimidinase-like 2	protein-coding
mm_11369.1	chr2	30995540	30995569	+	1	NA	intron (NM_028846, intron 1 of 24)	intron (NM_028846, intron 1 of 24)	13275	NM_028846	74270	Mm.346654	NM_028846	ENSMUSG00000026854	Usp20	1700055M05Rik|AI467231|Vdu2	ubiquitin specific peptidase 20	protein-coding
mm_118971.1	chr14	27876160	27876172	+	1	NA	intron (NM_177814, intron 3 of 15)	intron (NM_177814, intron 3 of 15)	253759	NM_177814	238988	Mm.318004	NM_177814	ENSMUSG00000040640	Erc2	6430531D06|CAST|CAST1/ERC2|D14Ertd171e|ELKS2alpha	ELKS/RAB6-interacting/CAST family member 2	protein-coding
mm_165876.1	chr4	41124288	41124292	-	1	NA	promoter-TSS (NM_139236)	promoter-TSS (NM_139236)	49	NM_139236	230082	Mm.285797	NM_139236	ENSMUSG00000028430	Nol6	AA410091|Nrap	nucleolar protein family 6 (RNA-associated)	protein-coding
mm_149006.1	chr19	8723479	8723514	+	1	NA	promoter-TSS (NR_002896)	promoter-TSS (NR_002896)	9	NR_002896	83673	Mm.292489	NR_002896	ENSMUSG00000108414	Snhg1	-	small nucleolar RNA host gene 1	ncRNA
mm_15815.1	chr2	164507393	164507433	+	1	NA	exon (NM_133779, exon 12 of 12)	exon (NM_133779, exon 12 of 12)	9888	NM_133779	78928	Mm.28228	NM_133779	ENSMUSG00000017721	Pigt	2510012P17Rik|4930534E15Rik|CGI-06|NDAP|Ndap7	phosphatidylinositol glycan anchor biosynthesis, class T	protein-coding
mm_112177.1	chr12	113421633	113421692	-	1	NA	Intergenic	Intergenic	-67903	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_146293.1	chr18	79958944	79958955	+	1	NA	Intergenic	Intergenic	-87946	NM_053117	93737	Mm.24678	NM_053117	ENSMUSG00000056214	Pard6g	2410049N21Rik|Par6a	par-6 family cell polarity regulator gamma	protein-coding
mm_52258.1	chr6	108065036	108065053	+	1	NA	promoter-TSS (NM_001276356)	promoter-TSS (NM_001276356)	-1	NM_001276356	74729	Mm.56539	NM_178391	ENSMUSG00000034639	Setmar	5830404F24Rik|Etet2	SET domain without mariner transposase fusion	protein-coding
mm_12545.1	chr2	72390720	72390739	+	1	NA	TTS (NM_178084)	TTS (NM_178084)	-85490	NM_025866	66953	Mm.270676	NM_025866	ENSMUSG00000055612	Cdca7	2310021G01Rik|AU044109|JPO1	cell division cycle associated 7	protein-coding
mm_4424.1	chr1	172502581	172502592	+	1	NA	intron (NM_178598, intron 1 of 4)	intron (NM_178598, intron 1 of 4)	2340	NM_178598	21346	Mm.271711	NM_178598	ENSMUSG00000026547	Tagln2	2700094C18Rik|SM22beta|Sm22B|Sm22a	transgelin 2	protein-coding
mm_71783.1	chr8	66697163	66697209	+	1	NA	promoter-TSS (NM_010934)	promoter-TSS (NM_010934)	-236	NM_010934	18166	Mm.5112	NM_010934	ENSMUSG00000036437	Npy1r	Npyr|Y1-R	neuropeptide Y receptor Y1	protein-coding
mm_123465.1	chr14	65953729	65953794	-	1	NA	promoter-TSS (NM_172604)	promoter-TSS (NM_172604)	-17	NM_172604	219151	Mm.344095	NM_172604	ENSMUSG00000034463	Scara3	APC7|C130058N24Rik|CSR|CSR1|MSLR1|MSRL1	scavenger receptor class A, member 3	protein-coding
mm_1062.1	chr1	58973703	58973717	+	1	NA	promoter-TSS (NM_172406)	promoter-TSS (NM_172406)	139	NM_172656	227154	Mm.286006	NM_172656	ENSMUSG00000026027	Stradb	AA792893|Als2cr2|B830008M19|D1Ucla2|ILPIP|ILPIPA|PRO1038|Papk|Syradb	STE20-related kinase adaptor beta	protein-coding
mm_25534.1	chr3	115384542	115384542	+	1	NA	Intergenic	Intergenic	303577	NM_153157	229759	Mm.54183	NM_153157	ENSMUSG00000027965	Olfm3	B230206G02Rik	olfactomedin 3	protein-coding
mm_112846.1	chr13	20835962	20835966	+	1	NA	intron (NM_012054, intron 2 of 20)	intron (NM_012054, intron 2 of 20)	41851	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_16613.1	chr2	5339869	5339873	-	1	NA	intron (NM_001290374, intron 4 of 9)	intron (NM_001290374, intron 4 of 9)	-39519	NR_030601	100124465		NR_030601	ENSMUSG00000078031	Mir466d	Mirn466d	microRNA 466d	ncRNA
mm_131123.1	chr16	5476343	5476346	+	1	NA	Intergenic	B4|SINE|B4	-220388	NM_027446	70511	Mm.45780	NM_027446	ENSMUSG00000022544	Eef2kmt	5730409G15Rik|Fam86|Fam86a|eEF2-KMT	eukaryotic elongation factor 2 lysine methyltransferase	protein-coding
mm_28967.1	chr3	101003755	101003789	-	1	NA	exon (NM_001167906, exon 8 of 9)	exon (NM_001167906, exon 8 of 9)	25723	NM_001167906	630146	Mm.190915	NM_001099332	ENSMUSG00000086564	Cd101	EWI-101|Gm1016|Gm734|Igsf2	CD101 antigen	protein-coding
mm_144895.1	chr18	36973800	36973816	+	1	NA	promoter-TSS (NM_009957)	promoter-TSS (NM_009957)	6	NM_001301259	103611159		NM_001301259		Gm38667	Pcdha7-g	predicted gene, 38667	protein-coding
mm_263.1	chr1	20890596	20890617	+	1	NA	promoter-TSS (NR_040492)	promoter-TSS (NR_040492)	-16	NM_028829	74229	Mm.40780	NM_028829	ENSMUSG00000025931	Paqr8	1700019B16Rik|3110001D06Rik	progestin and adipoQ receptor family member VIII	protein-coding
mm_37890.1	chr4	132533175	132533196	-	1	NA	intron (NM_007512, intron 3 of 3)	intron (NM_007512, intron 3 of 3)	2229	NM_007512	11983	Mm.2171	NM_007512	ENSMUSG00000054428	Atpif1	Atpi|IF(1)|If1	ATPase inhibitory factor 1	protein-coding
mm_3465.1	chr1	150104350	150104394	+	1	NA	exon (NM_011198, exon 8 of 10)	exon (NM_011198, exon 8 of 10)	4341	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_35109.1	chr4	9651334	9651336	-	1	NA	intron (NM_001290367, intron 1 of 22)	B4A|SINE|B4	-7618	NM_001177852	65973	Mm.222206	NM_023066	ENSMUSG00000028207	Asph	2310005F16Rik|3110001L23Rik|AI848629|AW261690|AW561901|BAH|C79816|cI-37	aspartate-beta-hydroxylase	protein-coding
mm_96071.1	chr11	59810310	59810334	+	1	NA	promoter-TSS (NM_001271357)	promoter-TSS (NM_001271357)	242	NR_045686	100504104	Mm.391737	NR_045686	ENSMUSG00000087249	Gm16062	ENSMUSG00000072890|OTTMUSG00000029633	predicted gene 16062	ncRNA
mm_13688.1	chr2	117120828	117120855	+	1	NA	promoter-TSS (NM_001277256)	promoter-TSS (NM_001277256)	-230	NM_001277256	114715	Mm.245890	NM_033524	ENSMUSG00000027351	Spred1	5730461F13Rik|AL024345|AW047647	sprouty protein with EVH-1 domain 1, related sequence	protein-coding
mm_167581.1	chr9	45944841	45944848	-	1	NA	intron (NM_172257, intron 15 of 25)	intron (NM_172257, intron 15 of 25)	-5254	NR_106055	102465659		NR_106055	ENSMUSG00000098327	Mir7087	Gm27273|mmu-mir-7087	microRNA 7087	ncRNA
mm_143650.1	chr17	79451650	79451664	-	1	NA	Intergenic	Intergenic	26228	NR_033463	74622	Mm.311921	NR_033463		4930429F11Rik	-	RIKEN cDNA 4930429F11 gene	ncRNA
mm_73045.1	chr8	94347407	94347419	+	1	NA	intron (NM_019415, intron 17 of 24)	ID_B1|SINE|B4	18205	NM_001205311	20497	Mm.25804	NM_019415	ENSMUSG00000031766	Slc12a3	AI035291|NCC|NCCT|TSC	solute carrier family 12, member 3	protein-coding
mm_20694.1	chr2	132793331	132793383	-	1	NA	exon (NM_007694, exon 4 of 5)	exon (NM_007694, exon 4 of 5)	12079	NM_007694	12653	Mm.255241	NM_007694	ENSMUSG00000027350	Chgb	Scg-1	chromogranin B	protein-coding
mm_159682.1	chr5	5749352	5749352	-	1	NA	promoter-TSS (NM_027399)	promoter-TSS (NM_027399)	-35	NM_027399	70358	Mm.85429	NM_027399	ENSMUSG00000015652	Steap1	2410007B19Rik|Prss24|Steap	six transmembrane epithelial antigen of the prostate 1	protein-coding
mm_146029.1	chr18	69521356	69521360	+	1	NA	intron (NM_013685, intron 6 of 19)	intron (NM_013685, intron 6 of 19)	175637	NM_001083967	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding
mm_12489.1	chr2	71745825	71745861	+	1	NA	intron (NR_039557, intron 2 of 3).2	RMER10A|LTR|ERVL	26426	NR_037979	381371	Mm.330284	NM_201366	ENSMUSG00000064263	Platr26	Gm1631	pluripotency associated transcript 26	ncRNA
mm_27282.1	chr3	41494897	41494905	-	1	NA	Intergenic	ID_B1|SINE|B4	-1702	NR_040385	78706	Mm.366094	NR_040385	ENSMUSG00000097639	Platr4	C430002E04Rik	pluripotency associated transcript 4	ncRNA
mm_111556.1	chr12	101066411	101066414	-	1	NA	intron (NM_211355, intron 2 of 14)	intron (NM_211355, intron 2 of 14)	-16039	NR_038048	319760	Mm.440198	NM_176997	ENSMUSG00000097121	D130020L05Rik	9430007L23Rik	RIKEN cDNA D130020L05 gene	ncRNA
mm_1394.1	chr1	67129116	67129152	+	1	NA	intron (NM_001080809, intron 1 of 37)	intron (NM_001080809, intron 1 of 37)	6107	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_17582.1	chr2	30415510	30415560	-	1	NA	promoter-TSS (NM_138748)	promoter-TSS (NM_138748)	213	NM_007760	12908	Mm.20396	NM_007760	ENSMUSG00000026853	Crat	AW107812|CARAT	carnitine acetyltransferase	protein-coding
mm_45053.1	chr5	41799919	41799938	-	1	NA	exon (NM_001081422, exon 20 of 27)	exon (NM_001081422, exon 20 of 27)	-35708	NM_007524	12020	Mm.2530	NM_007524	ENSMUSG00000049691	Nkx3-2	Bapx1|NKX3.2|Nkx-3.2	NK3 homeobox 2	protein-coding
mm_37329.1	chr4	119539517	119539544	-	1	NA	promoter-TSS (NM_001290696)	promoter-TSS (NM_001290696)	-131	NM_001290696	230700	Mm.259227	NM_172699	ENSMUSG00000032998	Foxj3	C330039G02Rik|Fhd6	forkhead box J3	protein-coding
mm_107281.1	chr12	29724423	29724430	+	1	NA	intron (NM_001093778, intron 3 of 24)	B4|SINE|B4	-37981	NR_046080	328075	Mm.447832	NR_046080		C630031E19Rik	C630031E19	RIKEN cDNA C630031E19 gene	ncRNA
mm_95570.1	chr11	52396483	52396494	+	1	NA	promoter-TSS (NM_153117)	promoter-TSS (NM_153117)	60	NM_153117	213673	Mm.291979	NM_153117	ENSMUSG00000036275	9530068E07Rik	C85061|Kct2	RIKEN cDNA 9530068E07 gene	protein-coding
mm_140773.1	chr17	17855201	17855205	-	1	NA	promoter-TSS (NM_008215)	promoter-TSS (NM_008215)	-15	NM_008215	15116	Mm.255701	NM_008215	ENSMUSG00000003665	Has1	HAS	hyaluronan synthase1	protein-coding
mm_126636.1	chr15	83563584	83563620	+	1	NA	promoter-TSS (NM_009775)	promoter-TSS (NM_009775)	29	NM_009775	12257	Mm.1508	NM_009775	ENSMUSG00000041736	Tspo	Bzrp|IBP|PBR|Tspo1	translocator protein	protein-coding
mm_35338.1	chr4	31970577	31970583	-	1	NA	intron (NM_172688, intron 1 of 15)	RMER10B|LTR|ERVL	6473	NM_172688	26409	Mm.258589	NM_009316	ENSMUSG00000028284	Map3k7	B430101B05|C87327|Tak1	mitogen-activated protein kinase kinase kinase 7	protein-coding
mm_26317.1	chr3	142521316	142521330	+	1	NA	3' UTR (NM_153564, exon 11 of 11)	3' UTR (NM_153564, exon 11 of 11)	-9013	NM_001083312	229900	Mm.45740	NM_145545	ENSMUSG00000040253	Gbp7	9830147J24Rik	guanylate binding protein 7	protein-coding
mm_85586.1	chr9	107307551	107307570	-	1	NA	Intergenic	Intergenic	10901	NM_009895	12700	Mm.4592	NM_009895	ENSMUSG00000032578	Cish	CIS-1|CIS1|Cis|F17|F23|SOCS	cytokine inducible SH2-containing protein	protein-coding
mm_109065.1	chr12	104345270	104345275	+	1	NA	exon (NM_011458, exon 5 of 5)	exon (NM_011458, exon 5 of 5)	6786	NM_011458	20714	Mm.291569	NM_011458	ENSMUSG00000058207	Serpina3k	1300001I07Rik|D12Rp54|MMCM2|MMSpi2|RP54|Spi-2|Spi2|contrapsin	serine (or cysteine) peptidase inhibitor, clade A, member 3K	protein-coding
mm_148115.1	chr18	74958020	74958026	-	1	NA	intron (NM_010720, intron 1 of 9)	B1F|SINE|Alu	3240	NM_010720	16891	Mm.299647	NM_010720	ENSMUSG00000053846	Lipg	3110013K01Rik|EL|lipase|mEDL	lipase, endothelial	protein-coding
mm_7978.1	chr1	134099121	134099129	-	1	NA	Intergenic	Intergenic	-12117	NM_001284524	71884	Mm.328268	NM_027979	ENSMUSG00000026450	Chit1	2300002L19Rik	chitinase 1 (chitotriosidase)	protein-coding
mm_88927.1	chr10	81257057	81257060	+	1	NA	promoter-TSS (NM_001285854)	promoter-TSS (NM_001285854)	-241	NM_001285854	17179	Mm.2918	NM_010768	ENSMUSG00000004933	Matk	CHK|HYL|Ntk|p56ntk	megakaryocyte-associated tyrosine kinase	protein-coding
mm_86280.1	chr9	121839471	121839497	-	1	NA	promoter-TSS (NM_028384)	promoter-TSS (NM_028384)	-23	NM_028384	100502861	Mm.335550	NM_028384	ENSMUSG00000079235	Ccdc13	2900041A11Rik|Gm188	coiled-coil domain containing 13	protein-coding
mm_74528.1	chr8	9559258	9559269	-	1	NA	intron (NM_001347127, intron 1 of 3)	B4A|SINE|B4	211760	NM_173446	270028	Mm.268163	NM_173446	ENSMUSG00000079157	Fam155a	6430500D16|AW121567|Tmem28	family with sequence similarity 155, member A	protein-coding
mm_134475.1	chr16	18588773	18588784	-	1	NA	intron (NM_001285472, intron 1 of 8)	CpG	-1809	NM_001285476	21380	Mm.295194	NM_011532	ENSMUSG00000009097	Tbx1	-	T-box 1	protein-coding
mm_43640.1	chr5	138255715	138255725	+	1	NA	5' UTR (NM_001081108, exon 1 of 4)	5' UTR (NM_001081108, exon 1 of 4)	238	NM_001081108	66096	Mm.206901	NM_001081108	ENSMUSG00000050552	Lamtor4	0910001L09Rik|AV006840	late endosomal/lysosomal adaptor, MAPK and MTOR activator 4	protein-coding
mm_149456.1	chr19	11516474	11516497	+	1	NA	Intergenic	Lx4A|LINE|L1	-2074	NM_027209	69774	Mm.436639	NM_027209	ENSMUSG00000024677	Ms4a6b	1810027D10Rik	membrane-spanning 4-domains, subfamily A, member 6B	protein-coding
mm_36706.1	chr4	97523701	97523710	-	1	NA	Intergenic	Intergenic	-58238	NM_001122952	18027	Mm.31274	NM_010905	ENSMUSG00000028565	Nfia	1110047K16Rik|9430022M17Rik|CTF|NF1-A|NF1A	nuclear factor I/A	protein-coding
mm_44432.1	chr5	21008639	21008644	-	1	NA	intron (NM_011203, intron 8 of 17)	ID_B1|SINE|B4	47156	NM_011203	19248	Mm.319117	NM_011203	ENSMUSG00000028771	Ptpn12	P19-PTP|PTP-P19|PTP-PEST|PTPG1	protein tyrosine phosphatase, non-receptor type 12	protein-coding
mm_93049.1	chr10	88503953	88503973	-	1	NA	promoter-TSS (NM_001146690)	promoter-TSS (NM_001146690)	7	NR_027477	212862	Mm.288897	NM_144807	ENSMUSG00000060002	Chpt1	-	choline phosphotransferase 1	protein-coding
mm_149998.1	chr19	29271537	29271550	+	1	NA	intron (NM_001048177, intron 3 of 23)	intron (NM_001048177, intron 3 of 23)	19740	NM_008413	16452	Mm.275839	NM_008413	ENSMUSG00000024789	Jak2	Fd17	Janus kinase 2	protein-coding
mm_49159.1	chr6	13413335	13413361	+	1	NA	promoter-TSS (NR_038149)	promoter-TSS (NR_038149)	11	NR_038149	69413	Mm.177847	NR_038149	ENSMUSG00000101894	1700016P04Rik	-	RIKEN cDNA 1700016P04 gene	ncRNA
mm_46261.1	chr5	99728802	99728812	-	1	NA	non-coding (NR_030692, exon 1 of 4)	non-coding (NR_030692, exon 1 of 4)	253	NR_030692	319818	Mm.295233	NR_030692	ENSMUSG00000089809	A930011G23Rik	-	RIKEN cDNA A930011G23 gene	ncRNA
mm_25831.1	chr3	129199517	129199526	+	1	NA	promoter-TSS (NM_001042504)	promoter-TSS (NM_001042504)	-357	NM_001286942	18741	Mm.246804	NM_011098	ENSMUSG00000028023	Pitx2	9430085M16Rik|Brx1|Brx1b|Munc30|Otlx2|Ptx2|Rieg	paired-like homeodomain transcription factor 2	protein-coding
mm_19786.1	chr2	107057321	107057323	-	1	NA	exon (NM_008045, exon 3 of 3)	exon (NM_008045, exon 3 of 3)	2329	NM_008045	14308	Mm.249525	NM_008045	ENSMUSG00000027120	Fshb	FSH|FSH-B|FSH-beta|Fshbeta	follicle stimulating hormone beta	protein-coding
mm_55744.1	chr6	77979483	77979500	-	1	NA	5' UTR (NM_145732, exon 1 of 19)	5' UTR (NM_145732, exon 1 of 19)	176	NM_145732	12386	Mm.34637	NM_009819	ENSMUSG00000063063	Ctnna2	AI481747|Catna|Catna2|cdf|chp	catenin (cadherin associated protein), alpha 2	protein-coding
mm_120192.1	chr14	61598301	61598310	+	1	NA	promoter-TSS (NM_001164220)	promoter-TSS (NM_001164220)	79	NM_001164220	66597	Mm.491258	NM_023233	ENSMUSG00000035235	Trim13	3110001L12Rik|CAR|LEU5|RNF77|Rfp2	tripartite motif-containing 13	protein-coding
mm_161340.1	chr14	51717183	51717183	-	1	NA	promoter-TSS (NM_001034102)	promoter-TSS (NM_001034102)	-51	NM_001034102	545047	Mm.425915	NM_001034102	ENSMUSG00000068506	Gm5800	EG545047	predicted gene 5800	protein-coding
mm_12854.1	chr2	83724077	83724106	+	1	NA	promoter-TSS (NM_008402)	promoter-TSS (NM_008402)	-306	NM_008402	16410	Mm.227	NM_008402	ENSMUSG00000027087	Itgav	1110004F14Rik|2610028E01Rik|CD51|D430040G12Rik	integrin alpha V	protein-coding
mm_165664.1	chr3	88454879	88454887	-	1	NA	intron (NM_001163489, intron 1 of 14)	intron (NM_001163489, intron 1 of 14)	878	NM_013658	20351	Mm.439752	NM_013658	ENSMUSG00000028064	Sema4a	AI132332|SemB|Semab	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A	protein-coding
mm_138306.1	chr17	34644782	34644797	+	1	NA	promoter-TSS (NM_019873)	promoter-TSS (NM_019873)	-94	NM_019873	56299	Mm.10025	NM_019873	ENSMUSG00000033739	Fkbpl	DIR1|NG7|Ppiase-X|Wisp39	FK506 binding protein-like	protein-coding
mm_163315.1	chr12	6595844	6595851	+	1	NA	Intergenic	RLTR9E|LTR|ERVK	784483	NR_045045	73575	Mm.179463	NR_045045	ENSMUSG00000102096	1700101O22Rik	-	RIKEN cDNA 1700101O22 gene	ncRNA
mm_102760.1	chr11	67589163	67589164	-	1	NA	intron (NM_001109657, intron 1 of 13)	intron (NM_001109657, intron 1 of 13)	2663	NM_001109657	14457	Mm.40338	NM_008088	ENSMUSG00000033066	Gas7	AW124766|B230343A10Rik|Gas7-cb	growth arrest specific 7	protein-coding
mm_131888.1	chr16	23226089	23226113	+	1	NA	promoter-TSS (NM_001252505)	promoter-TSS (NM_001252505)	80	NM_001252505	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_134679.1	chr16	22411823	22411850	-	1	NA	exon (NM_023794, exon 7 of 13)	exon (NM_023794, exon 7 of 13)	27734	NM_023794	104156	Mm.155708	NM_023794	ENSMUSG00000013089	Etv5	1110005E01Rik|8430401F14Rik|ERM	ets variant 5	protein-coding
mm_78556.1	chr9	35559461	35559493	+	1	NA	promoter-TSS (NM_023292)	promoter-TSS (NM_023292)	11	NM_023292	67049	Mm.425574	NM_023292	ENSMUSG00000032103	Pus3	2610020J05Rik|5730412F04Rik	pseudouridine synthase 3	protein-coding
mm_63178.1	chr7	125487411	125487425	+	1	NA	intron (NM_026330, intron 1 of 7)	intron (NM_026330, intron 1 of 7)	4124	NM_026330	67711	Mm.4467	NM_026330	ENSMUSG00000030750	Nsmce1	2510027N19Rik	NSE1 homolog, SMC5-SMC6 complex component	protein-coding
mm_172480.1	chr7	4951042	4951049	-	1	NA	Intergenic	Intergenic	13303	NM_001146329	381836	Mm.297829	NM_001146329	ENSMUSG00000030433	Sbk2	Gm1079|Sgk069	SH3-binding domain kinase family, member 2	protein-coding
mm_97477.1	chr11	78323152	78323166	+	1	NA	promoter-TSS (NM_001303423)	promoter-TSS (NM_001303423)	86	NM_001303423	11676	Mm.7729	NM_009657	ENSMUSG00000017390	Aldoc	AI847350|AU040929|Aldo3|Scrg2	aldolase C, fructose-bisphosphate	protein-coding
mm_74264.1	chr8	124898437	124898449	+	1	NA	promoter-TSS (NM_198103)	promoter-TSS (NM_198103)	557	NM_001111141	244666	Mm.482915	NM_001111141	ENSMUSG00000031986	Sprtn	Gm505	SprT-like N-terminal domain	protein-coding
mm_127201.1	chr15	99126514	99126616	+	1	NA	promoter-TSS (NM_139140)	promoter-TSS (NM_139140)	-280	NM_139140	72572	Mm.276650	NM_139140	ENSMUSG00000051934	Spats2	2700012F11Rik|59kDa|Scr59|p59	spermatogenesis associated, serine-rich 2	protein-coding
mm_172676.1	chr8	4818722	4818727	-	1	NA	Intergenic	RLTR9E|LTR|ERVK	-39190	NM_011369	20419	Mm.37801	NM_011369	ENSMUSG00000022322	Shcbp1	mPAL	Shc SH2-domain binding protein 1	protein-coding
mm_75687.1	chr8	68204916	68204919	-	1	NA	Intergenic	B4|SINE|B4	-71611	NM_028182	72281	Mm.40974	NM_028182	ENSMUSG00000053886	Sh2d4a	2210402M20Rik|SH2A	SH2 domain containing 4A	protein-coding
mm_155890.1	chrX	101652359	101652375	+	1	NA	intron (NM_139144, intron 4 of 21)	intron (NM_139144, intron 4 of 21)	12149	NM_001290535	108155	Mm.487332	NM_139144	ENSMUSG00000034160	Ogt	1110038P24Rik|4831420N21Rik|AI115525|Ogtl	O-linked N-acetylglucosamine (GlcNAc) transferase (UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase)	protein-coding
mm_40988.1	chr5	77266280	77266293	+	1	NA	intron (NM_011263, intron 1 of 3)	CpG	792	NM_011263	19712	Mm.28840	NM_011263	ENSMUSG00000029249	Rest	2610008J04Rik|AA407358|NRSF|REST4	RE1-silencing transcription factor	protein-coding
mm_4879.1	chr1	187943335	187943345	+	1	NA	intron (NM_001243792, intron 2 of 7)	intron (NM_001243792, intron 2 of 7)	-54487	NM_011935	26381	Mm.89989	NM_011935	ENSMUSG00000026610	Esrrg	ERR3|Errg|NR3B3|mKIAA0832	estrogen-related receptor gamma	protein-coding
mm_97757.1	chr11	80810358	80810404	+	1	NA	promoter-TSS (NM_029537)	promoter-TSS (NM_029537)	-34	NM_029537	103743	Mm.27682	NM_029537	ENSMUSG00000035413	Tmem98	6530411B15Rik|AI463522	transmembrane protein 98	protein-coding
mm_89645.1	chr10	96725126	96725133	+	1	NA	Intergenic	Intergenic	108128	NM_007569	12226	Mm.23811	NM_007569	ENSMUSG00000036478	Btg1	AI426953|AW546738	B cell translocation gene 1, anti-proliferative	protein-coding
mm_137676.1	chr17	28801151	28801173	+	1	NA	promoter-TSS (NM_001081315)	promoter-TSS (NM_001081315)	36	NM_001081315	268936	Mm.291877	NM_199061	ENSMUSG00000063952	Brpf3	AI413466|AW493400|mKIAA1286	bromodomain and PHD finger containing, 3	protein-coding
mm_171352.1	chr4	109676610	109676611	+	1	NA	promoter-TSS (NM_007983)	promoter-TSS (NM_007983)	-17	NM_007983	14084	Mm.318259	NM_007983	ENSMUSG00000010517	Faf1	AA408698|Dffrx|Fam	Fas-associated factor 1	protein-coding
mm_64580.1	chr7	145284058	145284101	+	1	NA	promoter-TSS (NM_146206)	promoter-TSS (NM_146206)	-68	NR_132642	233979	Mm.102235	NM_146206	ENSMUSG00000048677	Tpcn2	D830047E22Rik|Gm35086	two pore segment channel 2	protein-coding
mm_45397.1	chr5	66151531	66151541	-	1	NA	promoter-TSS (NM_001291226)	promoter-TSS (NM_001291226)	418	NM_001127382	245945	Mm.36863	NM_139065	ENSMUSG00000070780	Rbm47	9530077J19Rik	RNA binding motif protein 47	protein-coding
mm_165726.1	chr3	104478803	104478823	+	1	NA	intron (NM_001310698, intron 11 of 17)	B3|SINE|B2	33105	NM_001310698	269473	Mm.34855	NM_001025067	ENSMUSG00000032913	Lrig2	4632419I10Rik|BB096938|LIG-2	leucine-rich repeats and immunoglobulin-like domains 2	protein-coding
mm_25809.1	chr3	127789987	127790001	+	1	NA	promoter-TSS (NM_145133)	promoter-TSS (NM_145133)	81	NM_145133	211550	Mm.31852	NM_145133	ENSMUSG00000046688	Tifa	T2bp	TRAF-interacting protein with forkhead-associated domain	protein-coding
mm_8.1	chr1	4807867	4807928	+	1	NA	promoter-TSS (NM_008866)	promoter-TSS (NM_008866)	4	NM_008866	18777	Mm.299955	NM_008866	ENSMUSG00000025903	Lypla1	Pla1a	lysophospholipase 1	protein-coding
mm_48641.1	chr5	145201876	145201891	-	1	NA	promoter-TSS (NM_023322)	promoter-TSS (NM_023322)	-1	NM_023322	67235	Mm.432480	NM_023322	ENSMUSG00000029627	Zkscan14	2310046C23Rik|2810437E14Rik|Zfp99|Znf394	zinc finger with KRAB and SCAN domains 14	protein-coding
mm_91061.1	chr10	18957942	18957989	-	1	NA	Intergenic	L1M2|LINE|L1	53998	NM_001166402	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_152892.1	chr19	24861859	24861865	-	1	NA	promoter-TSS (NM_175013)	promoter-TSS (NM_175013)	-20	NM_175013	226041	Mm.105222	NM_175013	ENSMUSG00000041731	Pgm5	4833423B07|9530034F03Rik|D830025G17|aciculin	phosphoglucomutase 5	protein-coding
mm_138375.1	chr17	35004696	35004728	+	1	NA	intron (NM_011690, intron 4 of 29)	intron (NM_011690, intron 4 of 29)	3805	NM_011690	22321	Mm.28420	NM_011690	ENSMUSG00000007029	Vars	Bat6|D17H6S56E|G7a|Vars2	valyl-tRNA synthetase	protein-coding
mm_92532.1	chr10	79587070	79587076	-	1	NA	promoter-TSS (NM_199226)	promoter-TSS (NM_199226)	63	NM_199226	21830	Mm.89197	NM_011583	ENSMUSG00000020317	Theg	-	testicular haploid expressed gene	protein-coding
mm_107775.1	chr12	59153078	59153081	+	1	NA	intron (NM_001329047, intron 14 of 29)	intron (NM_001329047, intron 14 of 29)	21626	NM_001165253	338320	Mm.213215	NM_146034	ENSMUSG00000021000	Mia2	Ctage5|D12Bwg0579e|Mea6|Mgea|Mgea6	melanoma inhibitory activity 2	protein-coding
mm_51501.1	chr6	83109251	83109277	+	1	NA	TTS (NM_001081266)	TTS (NM_001081266)	156	NM_026744	68499	Mm.333183	NM_026744	ENSMUSG00000030037	Mrpl53	1110007K17Rik	mitochondrial ribosomal protein L53	protein-coding
mm_46065.1	chr5	92278176	92278186	-	1	NA	promoter-TSS (NM_001163687)	promoter-TSS (NM_001163687)	0	NM_001163687	67111	Mm.28890	NM_025972	ENSMUSG00000029413	Naaa	2210023K21Rik|3830414F09Rik|Asahl	N-acylethanolamine acid amidase	protein-coding
mm_142646.1	chr17	47501900	47501946	-	1	NA	intron (NM_022015, intron 1 of 8)	intron (NM_022015, intron 1 of 8)	364	NM_022015	63856	Mm.275901	NM_022015	ENSMUSG00000023980	Taf8	AW260255|Tbn	TATA-box binding protein associated factor 8	protein-coding
mm_84770.1	chr9	75642112	75642123	-	1	NA	Intergenic	Intergenic	16385	NM_027309	70082	Mm.19119	NM_027309	ENSMUSG00000032184	Lysmd2	2210402C18Rik|AV033872|AW538442	LysM, putative peptidoglycan-binding, domain containing 2	protein-coding
mm_40718.1	chr5	65955654	65955664	+	1	NA	Intergenic	Intergenic	-11465	NM_001081104	231252	Mm.140015	NM_001081104	ENSMUSG00000029205	Chrna9	2410015I05Rik|Acra9|EG666827|Gm8311	cholinergic receptor, nicotinic, alpha polypeptide 9	protein-coding
mm_122191.1	chr14	31729015	31729017	-	1	NA	intron (NM_001024604, intron 13 of 27)	intron (NM_001024604, intron 13 of 27)	87959	NM_025295	26363	Mm.282679	NM_025295	ENSMUSG00000021900	Btd	-	biotinidase	protein-coding
mm_84979.1	chr9	85348045	85348065	-	1	NA	Intergenic	RMER15-int|LTR|ERVL	-20905	NM_001160379	212943	Mm.74610	NM_001160378	ENSMUSG00000032265	Fam46a	BAP014|D930050G01Rik	family with sequence similarity 46, member A	protein-coding
mm_169167.1	chr13	65503934	65503944	+	1	NA	Intergenic	Intergenic	225085	NM_178364	170936	Mm.151546	NM_178364	ENSMUSG00000021514	Zfp369	B930030B22Rik|D230020H11Rik|NRIF2	zinc finger protein 369	protein-coding
mm_88661.1	chr10	80015790	80015838	+	1	NA	promoter-TSS (NM_001142701)	promoter-TSS (NM_001142701)	-858	NM_001142701	70719	Mm.243954	NM_027521	ENSMUSG00000035697	Hmha1	6330406L22Rik|AW539505|Ha-1	histocompatibility (minor) HA-1	protein-coding
mm_120338.1	chr14	63493674	63493681	+	1	NA	intron (NM_021480, intron 8 of 8)	CpG	15415	NM_021480	58865	Mm.354229	NM_021480	ENSMUSG00000021953	Tdh	-	L-threonine dehydrogenase	protein-coding
mm_163947.1	chr14	51923108	51923116	-	1	NA	promoter-TSS (NM_001011687)	promoter-TSS (NM_001011687)	-339	NM_001011687	497071	Mm.378602	NM_001011687	ENSMUSG00000068392	Rnase13	-	ribonuclease, RNase A family, 13 (non-active)	protein-coding
mm_19889.1	chr2	114050495	114050497	-	1	NA	exon (NM_009608, exon 3 of 7)	exon (NM_009608, exon 3 of 7)	2379	NM_009608	11464	Mm.686	NM_009608	ENSMUSG00000068614	Actc1	Actc-1	actin, alpha, cardiac muscle 1	protein-coding
mm_23533.1	chr3	60627867	60627993	+	1	NA	3' UTR (NM_001253711, exon 8 of 8)	3' UTR (NM_001253711, exon 8 of 8)	126751	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_130405.1	chr15	97976725	97976735	-	1	NA	exon (NM_001113515, exon 52 of 53)	exon (NM_001113515, exon 52 of 53)	12501	NM_001252153	380967	Mm.196630	NM_201359	ENSMUSG00000052369	Tmem106c	AI046681|BC046621|D15Ertd405e	transmembrane protein 106C	protein-coding
mm_128391.1	chr15	43170810	43170834	-	1	NA	promoter-TSS (NM_172815)	promoter-TSS (NM_172815)	-4	NM_172815	239405	Mm.193274	NM_172815	ENSMUSG00000051920	Rspo2	2610028F08Rik|AA673245|D430027K22|ftls	R-spondin 2	protein-coding
mm_18189.1	chr2	45113202	45113214	-	1	NA	promoter-TSS (NM_015753)	promoter-TSS (NM_015753)	71	NM_015753	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_129823.1	chr15	83122089	83122131	-	1	NA	intron (NM_029101, intron 1 of 6)	intron (NM_029101, intron 1 of 6)	691	NM_029101	74778	Mm.30056	NM_029101	ENSMUSG00000018040	Rrp7a	1110014J01Rik|AA408146|Kheg1	ribosomal RNA processing 7 homolog A (S. cerevisiae)	protein-coding
mm_17163.1	chr2	25255349	25255397	-	1	NA	promoter-TSS (NM_001082476)	promoter-TSS (NM_001082476)	41	NM_001252541	78797	Mm.40020	NM_178239	ENSMUSG00000006471	Ndor1	4930447P04Rik|NR1|Ndor	NADPH dependent diflavin oxidoreductase 1	protein-coding
mm_3468.1	chr1	150104468	150104486	+	1	NA	exon (NM_011198, exon 8 of 10)	exon (NM_011198, exon 8 of 10)	4446	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_90162.1	chr10	119131106	119131114	+	1	NA	Intergenic	Intergenic	38205	NR_045348	73400	Mm.416864	NR_045348	ENSMUSG00000100681	1700064J06Rik	-	RIKEN cDNA 1700064J06 gene	ncRNA
mm_158901.1	chr1	32547293	32547293	-	1	NA	promoter-TSS (NM_001164286)	promoter-TSS (NM_001164286)	0	NM_001164286	408191	Mm.479439	NM_001164286	ENSMUSG00000091318	Gm5415	EG408191|Senp14	predicted gene 5415	protein-coding
mm_143374.1	chr17	67632708	67632728	-	1	NA	promoter-TSS (NM_001033340)	promoter-TSS (NM_001033340)	5	NM_001033340	240131	Mm.295736	NM_001033340	ENSMUSG00000073375	Lrrc30	Gm326	leucine rich repeat containing 30	protein-coding
mm_83360.1	chr9	44407302	44407343	-	1	NA	promoter-TSS (NM_024266)	promoter-TSS (NM_024266)	226	NM_021789	60409	Mm.29814	NM_021789	ENSMUSG00000032112	Trappc4	1500017G03Rik|AI303617|HSPC172|PTD009|Sbd|Sbdn|Sdcbp2|TRS23	trafficking protein particle complex 4	protein-coding
mm_71907.1	chr8	70074451	70074477	+	1	NA	intron (NM_181540, intron 2 of 9)	intron (NM_181540, intron 2 of 9)	1540	NM_181540	107770	Mm.37974	NM_181540	ENSMUSG00000036151	Tm6sf2	-	transmembrane 6 superfamily member 2	protein-coding
mm_65957.1	chr7	30428599	30428611	-	1	NA	3' UTR (NM_172142, exon 11 of 11)	3' UTR (NM_172142, exon 11 of 11)	5301	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_87056.1	chr10	28837556	28837559	+	1	NA	intron (NM_001305663, intron 5 of 5)	intron (NM_001305663, intron 5 of 5)	85950	NR_033601	114676	Mm.390292	NR_033601		4930519F09Rik	-	pyruvate dehydrogenase E1 alpha 1 pseudogene	pseudo
mm_8422.1	chr1	152386676	152386684	-	1	NA	promoter-TSS (NM_025677)	promoter-TSS (NM_025677)	2	NM_025677	66637	Mm.379120	NM_025677	ENSMUSG00000014980	Tsen15	5730449L18Rik|AL023077|Sen15	tRNA splicing endonuclease subunit 15	protein-coding
mm_112968.1	chr13	21286428	21286434	+	1	NA	TTS (NM_010343)	TTS (NM_010343)	6255	NM_010343	14780	Mm.1332	NM_010343	ENSMUSG00000004344	Gpx5	AV379049|Arep	glutathione peroxidase 5	protein-coding
mm_72381.1	chr8	81558886	81558896	+	1	NA	intron (NM_001297591, intron 2 of 24)	RMER19A|LTR|ERVK	216329	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_122373.1	chr14	39473514	39473529	-	1	NA	promoter-TSS (NM_008734)	promoter-TSS (NM_008734)	-433	NM_008734	18183	Mm.258705	NM_008734	ENSMUSG00000041014	Nrg3	ska	neuregulin 3	protein-coding
mm_9562.1	chr1	173975064	173975121	-	1	NA	exon (NM_011940, exon 3 of 7)	exon (NM_011940, exon 3 of 7)	7752	NM_008327	26388	Mm.218770	NM_008327	ENSMUSG00000026535	Ifi202b	Ifbip-1|Ifi202|Ifi202a|p202	interferon activated gene 202B	protein-coding
mm_133431.1	chr16	87553518	87553530	+	1	NA	5' UTR (NM_144854, exon 1 of 5)	5' UTR (NM_144854, exon 1 of 5)	194	NM_144854	224419	Mm.194466	NM_144854	ENSMUSG00000025610	Map3k7cl	C21orf7|ORF63|Tak1l	Map3k7 C-terminal like	protein-coding
mm_18407.1	chr2	60383297	60383303	-	1	NA	promoter-TSS (NM_013825)	promoter-TSS (NM_013825)	-69	NM_013825	17076	Mm.2074	NM_013825	ENSMUSG00000026980	Ly75	CD205|DEC-205|DEC205	lymphocyte antigen 75	protein-coding
mm_107091.1	chr12	17544861	17544892	+	1	NA	promoter-TSS (NM_013614)	promoter-TSS (NM_013614)	3	NM_013614	18263	Mm.34102	NM_013614	ENSMUSG00000011179	Odc1	ODC	ornithine decarboxylase, structural 1	protein-coding
mm_129090.1	chr15	75909569	75909593	-	1	NA	promoter-TSS (NM_001285431)	promoter-TSS (NM_001285431)	-25	NM_001285429	66656	Mm.258927	NM_023240	ENSMUSG00000055762	Eef1d	EF-1-delta	eukaryotic translation elongation factor 1 delta (guanine nucleotide exchange protein)	protein-coding
mm_152827.1	chr19	23140638	23140653	-	1	NA	promoter-TSS (NM_010638)	promoter-TSS (NM_010638)	-581	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_123723.1	chr14	70153652	70153678	-	1	NA	TTS (NM_001112735)	TTS (NM_001112735)	126	NM_146055	219158	Mm.218284	NM_146055	ENSMUSG00000033712	Ccar2	2610301G19Rik|Dbc1|mKIAA1967	cell cycle activator and apoptosis regulator 2	protein-coding
mm_141201.1	chr17	27028621	27028631	-	1	NA	promoter-TSS (NM_027544)	promoter-TSS (NM_027544)	0	NM_007523	12018	Mm.2443	NM_007523	ENSMUSG00000057789	Bak1	Bak|N-BAK1|N-Bak	BCL2-antagonist/killer 1	protein-coding
mm_74982.1	chr8	27141877	27141892	-	1	NA	3' UTR (NM_001080813, exon 6 of 6)	3' UTR (NM_001080813, exon 6 of 6)	-1026	NR_045840	71082	Mm.395259	NR_045840		4933416M07Rik	-	RIKEN cDNA 4933416M07 gene	ncRNA
mm_117831.1	chr13	98316865	98316890	-	1	NA	promoter-TSS (NR_137279)	promoter-TSS (NR_137279)	90	NM_145455	218490	Mm.371688	NM_145455	ENSMUSG00000021660	Btf3	1700054E11Rik	basic transcription factor 3	protein-coding
mm_59442.1	chr7	27132577	27132596	+	1	NA	exon (NM_007817, exon 9 of 10)	exon (NM_007817, exon 9 of 10)	12631	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_164315.1	chr15	103899301	103899316	-	1	NA	promoter-TSS (NM_009268)	promoter-TSS (NM_009268)	4	NM_009267	20770	Mm.1280	NM_009267	ENSMUSG00000036925	Mucl2	Spt-1|Spt1	mucin-like 2	protein-coding
mm_71382.1	chr8	45975515	45975558	+	1	NA	promoter-TSS (NM_138668)	promoter-TSS (NM_138668)	8	NM_138668	192169	Mm.210882	NM_138668	ENSMUSG00000031634	Ufsp2	1810047C23Rik	UFM1-specific peptidase 2	protein-coding
mm_98345.1	chr11	93099666	93099676	+	1	NA	5' UTR (NM_028296, exon 1 of 9)	5' UTR (NM_028296, exon 1 of 9)	381	NM_028296	72605	Mm.342160	NM_028296	ENSMUSG00000056158	Car10	2700029L05Rik|BB085816|Ca10	carbonic anhydrase 10	protein-coding
mm_79351.1	chr9	53771647	53771663	+	1	NA	5' UTR (NM_028060, exon 1 of 8)	5' UTR (NM_028060, exon 1 of 8)	120	NM_028060	72022	Mm.26159	NM_028060	ENSMUSG00000042195	Slc35f2	1500009K05Rik|AU019213	solute carrier family 35, member F2	protein-coding
mm_82007.1	chr9	121710379	121710386	+	1	NA	promoter-TSS (NM_026794)	promoter-TSS (NM_026794)	-7	NM_026794	26901	Mm.24848	NM_026794	ENSMUSG00000032526	Ss18l2	1110020I04Rik|AI463209|Deb1	SS18, nBAF chromatin remodeling complex subunit like 2	protein-coding
mm_75872.1	chr8	70764603	70764616	-	1	NA	exon (NM_023065, exon 5 of 8)	exon (NM_023065, exon 5 of 8)	2054	NM_023065	65972	Mm.30241	NM_023065	ENSMUSG00000031838	Ifi30	GILT|IP30	interferon gamma inducible protein 30	protein-coding
mm_124414.1	chr14	118012997	118013007	-	1	NA	3' UTR (NM_010024, exon 8 of 8)	3' UTR (NM_010024, exon 8 of 8)	39244	NM_010024	13190	Mm.19987	NM_010024	ENSMUSG00000022129	Dct	DT|TRP-2|TRP2|Tyrp-2|Tyrp2|slaty|slt	dopachrome tautomerase	protein-coding
mm_86581.1	chr10	12976319	12976327	+	1	NA	Intergenic	Intergenic	-12064	NM_001163591	74732	Mm.248648	NM_029075	ENSMUSG00000039232	Stx11	5830405C08Rik	syntaxin 11	protein-coding
mm_99879.1	chr11	109425968	109426010	+	1	NA	promoter-TSS (NM_025275)	promoter-TSS (NM_025275)	43	NM_025275	13929	Mm.211850	NM_025275	ENSMUSG00000020610	Amz2	AA408420|ESTM12|X83328	archaelysin family metallopeptidase 2	protein-coding
mm_124584.1	chr14	124677551	124677561	-	1	NA	promoter-TSS (NM_207667)	promoter-TSS (NM_207667)	-429	NM_207667	14169	Mm.206362	NM_010201	ENSMUSG00000025551	Fgf14	FHF-4|Fhf4|mFHF-4(1B)	fibroblast growth factor 14	protein-coding
mm_101971.1	chr11	50311736	50311780	-	1	NA	exon (NM_001110500, exon 2 of 15)	exon (NM_001110500, exon 2 of 15)	13915	NM_001110499	12330	Mm.248827	NM_007597	ENSMUSG00000020368	Canx	1110069N15Rik|AI988026|Cnx|D11Ertd153e	calnexin	protein-coding
mm_17576.1	chr2	30414170	30414180	-	1	NA	intron (NM_007760, intron 1 of 13)	intron (NM_007760, intron 1 of 13)	1573	NM_007760	12908	Mm.20396	NM_007760	ENSMUSG00000026853	Crat	AW107812|CARAT	carnitine acetyltransferase	protein-coding
mm_159911.1	chr6	48413129	48413129	+	1	NA	exon (NM_133922, exon 14 of 18)	exon (NM_133922, exon 14 of 18)	17543	NM_001347153	77827	Mm.107646	NM_133922	ENSMUSG00000042810	Krba1	A930040G15Rik|AI448780	KRAB-A domain containing 1	protein-coding
mm_68029.1	chr7	101012015	101012023	-	1	NA	promoter-TSS (NM_001302347)	promoter-TSS (NM_001302347)	-21	NM_008773	18442	Mm.3000	NM_008773	ENSMUSG00000032860	P2ry2	P2U1|P2Y2	purinergic receptor P2Y, G-protein coupled 2	protein-coding
mm_52434.1	chr6	113537811	113537811	+	1	NA	intron (NM_001347350, intron 6 of 42)	intron (NM_001347350, intron 6 of 42)	6129	NM_001347350	211651	Mm.160061	NM_001033244	ENSMUSG00000034023	Fancd2	2410150O07Rik|AU015151|BB137857|FA-D2|FA4|FACD|FAD|FANCD	Fanconi anemia, complementation group D2	protein-coding
mm_35715.1	chr4	44525028	44525030	-	1	NA	Intergenic	Intergenic	-177771	NR_073462	70602	Mm.491142	NR_073462	ENSMUSG00000103995	5730488B01Rik	-	RIKEN cDNA 5730488B01 gene	ncRNA
mm_118088.1	chr13	103768456	103768458	-	1	NA	Intergenic	Intergenic	-3875	NM_172592	218543	Mm.458176	NM_172592	ENSMUSG00000032621	Srek1	8430401B01|AI450757|AI462342|SRrp508|SRrp86|Sfrs12|Srsf12	splicing regulatory glutamine/lysine-rich protein 1	protein-coding
mm_123527.1	chr14	66803461	66803474	-	1	NA	3' UTR (NM_009955, exon 14 of 14)	3' UTR (NM_009955, exon 14 of 14)	65133	NM_009955	12934	Mm.352648	NM_009955	ENSMUSG00000022048	Dpysl2	AI851130|Crmp2|DRP2|Musunc33|TOAD-64|Ulip2	dihydropyrimidinase-like 2	protein-coding
mm_100227.1	chr11	117143817	117143865	+	1	NA	exon (NM_001166506, exon 6 of 16)	exon (NM_001166506, exon 6 of 16)	28669	NM_001166506	74136	Mm.272312	NM_028777	ENSMUSG00000020823	Sec14l1	1200017E04Rik|2810012L19Rik|Naa-35	SEC14-like lipid binding 1	protein-coding
mm_108186.1	chr12	76571524	76571539	+	1	NA	intron (NM_153804, intron 13 of 18)	intron (NM_153804, intron 13 of 18)	-23606	NR_046044	100504549	Mm.440349	NR_046044		AI463170	-	expressed sequence AI463170	ncRNA
mm_144776.1	chr18	35829799	35829821	+	1	NA	promoter-TSS (NM_133687)	promoter-TSS (NM_133687)	-8	NM_133687	67393	Mm.94560	NM_133687	ENSMUSG00000046668	Cxxc5	4930415K17Rik	CXXC finger 5	protein-coding
mm_27686.1	chr3	65958545	65958561	-	1	NA	promoter-TSS (NM_019937)	promoter-TSS (NM_019937)	-328	NM_019937	56706	Mm.175612	NM_019937	ENSMUSG00000027829	Ccnl1	2610030E23Rik|AU018493|Ccnl|ania-6a	cyclin L1	protein-coding
mm_71122.1	chr8	36248544	36248578	+	1	NA	intron (NM_001081150, intron 1 of 11)	CpG	955	NM_001081150	244421	Mm.324032	NM_001081150	ENSMUSG00000039633	Lonrf1	-	LON peptidase N-terminal domain and ring finger 1	protein-coding
mm_101802.1	chr11	46287009	46287011	-	1	NA	intron (NM_133769, intron 3 of 30)	intron (NM_133769, intron 3 of 30)	25348	NM_001252460	76884	Mm.154358	NM_133769	ENSMUSG00000020340	Cyfip2	1500004I01Rik|6430511D02Rik|AA930218|AU022376|Pir121|mKIAA1168	cytoplasmic FMR1 interacting protein 2	protein-coding
mm_115579.1	chr13	11584742	11584746	-	1	NA	intron (NM_023868, intron 95 of 104)	ID4_|SINE|ID	62692	NR_027813	664793	Mm.410565	NR_027813		Zp4-ps	EG664793|Zp4|Zpb	zona pellucida glycoprotein 4, pseudogene	pseudo
mm_133339.1	chr16	81200709	81200717	+	1	NA	promoter-TSS (NM_010954)	promoter-TSS (NM_010954)	16	NM_010954	17968	Mm.433941	NM_010954	ENSMUSG00000022762	Ncam2	Ncam-2|Ocam|RNCAM	neural cell adhesion molecule 2	protein-coding
mm_151545.1	chr19	59284215	59284238	+	1	NA	intron (NM_172523, intron 11 of 15)	intron (NM_172523, intron 11 of 15)	23348	NM_172523	214084	Mm.268797	NM_172523	ENSMUSG00000025094	Slc18a2	1110037L13Rik|9330105E13|Vmat2	solute carrier family 18 (vesicular monoamine), member 2	protein-coding
mm_43588.1	chr5	137747715	137747734	+	1	NA	exon (NM_023910, exon 2 of 5)	exon (NM_023910, exon 2 of 5)	1755	NM_029805	78829	Mm.286399	NM_023910	ENSMUSG00000029723	Tsc22d4	0610009M14Rik|1700023B23Rik|AI415410|Thg-1pit|Tilz2	TSC22 domain family, member 4	protein-coding
mm_114243.1	chr13	56625643	56625666	+	1	NA	exon (NM_009369, exon 5 of 17)	exon (NM_009369, exon 5 of 17)	16051	NM_009369	21810	Mm.14455	NM_009369	ENSMUSG00000035493	Tgfbi	68kDa|AI181842|AI747162|Beta-ig|big-h3	transforming growth factor, beta induced	protein-coding
mm_86908.1	chr10	22649004	22649009	+	1	NA	intron (NM_178934, intron 1 of 4)	intron (NM_178934, intron 1 of 4)	3995	NM_178934	353169	Mm.473705	NM_178934	ENSMUSG00000037490	Slc2a12	GLUT-12|Glut12	solute carrier family 2 (facilitated glucose transporter), member 12	protein-coding
mm_113245.1	chr13	27349008	27349013	+	1	NA	exon (NM_010088, exon 2 of 6)	exon (NM_010088, exon 2 of 6)	3337	NM_001289919	13529	Mm.291450	NM_010088	ENSMUSG00000018259	Prl8a2	D/tPRP|DPRP|Dtprp|Ghd11|mdPRP	prolactin family 8, subfamily a, member 2	protein-coding
mm_58903.1	chr7	17163694	17163702	+	1	NA	TTS (NM_054059)	TTS (NM_054059)	13298	NM_054059	384557	Mm.486145	NM_054059	ENSMUSG00000053228	Ceacam3	EG384557|Psg24|cea12	carcinoembryonic antigen-related cell adhesion molecule 3	protein-coding
mm_135466.1	chr16	45843478	45843481	-	1	NA	intron (NM_001252442, intron 1 of 18)	intron (NM_001252442, intron 1 of 18)	899	NM_153412	208177	Mm.211477	NM_153412	ENSMUSG00000033149	Phldb2	AV253284|C820004H04Rik|LL5b|LL5beta	pleckstrin homology like domain, family B, member 2	protein-coding
mm_85003.1	chr9	86880482	86880484	-	1	NA	promoter-TSS (NM_001277986)	promoter-TSS (NM_001277986)	-34	NM_001277983	20616	Mm.281651	NM_013669	ENSMUSG00000033419	Snap91	91kDa|AP180|F1-20|mKIAA0656	synaptosomal-associated protein 91	protein-coding
mm_164533.1	chr17	6296730	6296732	+	1	NA	intron (NM_001033178, intron 7 of 16)	intron (NM_001033178, intron 7 of 16)	20743	NM_001166629	100310872	Mm.381893	NM_001166629	ENSMUSG00000092074	Dynlt1a	-	dynein light chain Tctex-type 1A	protein-coding
mm_10904.1	chr2	25332733	25332782	+	1	NA	promoter-TSS (NR_027448)	promoter-TSS (NR_027448)	14	NM_001029983	227619	Mm.270798	NM_001029983	ENSMUSG00000036646	Man1b1	E430019H13Rik|ERMan1|Gm108|MANA-ER	mannosidase, alpha, class 1B, member 1	protein-coding
mm_169746.1	chr1	58646612	58646613	+	1	NA	Intergenic	Intergenic	-6029	NR_045007	100504501	Mm.440933	NR_045007	ENSMUSG00000102059	Gm20257	-	caspase 8 pseudogene	pseudo
mm_61728.1	chr7	81859329	81859337	+	1	NA	non-coding (NR_111910, exon 1 of 8)	non-coding (NR_111910, exon 1 of 8)	332	NM_145375	107769	Mm.221412	NM_145375	ENSMUSG00000038623	Tm6sf1	AI428514|BC023123|C630016D09Rik	transmembrane 6 superfamily member 1	protein-coding
mm_172225.1	chr6	66875708	66875711	-	1	NA	Intergenic	Intergenic	-20688	NM_001177557	14701	Mm.234342	NM_025278	ENSMUSG00000036402	Gng12	2010305F15Rik|AA536815|AI115529|AI314170|AI842738	guanine nucleotide binding protein (G protein), gamma 12	protein-coding
mm_88566.1	chr10	79665501	79665510	+	1	NA	exon (NM_013591, exon 3 of 5)	exon (NM_013591, exon 3 of 5)	931	NM_013591	17123	Mm.391556	NM_013591	ENSMUSG00000020310	Madcam1	AV211525	mucosal vascular addressin cell adhesion molecule 1	protein-coding
mm_146532.1	chr18	5334740	5334751	-	1	NA	promoter-TSS (NM_178722)	promoter-TSS (NM_178722)	-306	NM_178722	240186	Mm.118257	NM_178722	ENSMUSG00000050945	Zfp438	9430031G09|9430091M14Rik|B830013J05Rik	zinc finger protein 438	protein-coding
mm_77050.1	chr8	109577159	109577212	-	1	NA	exon (NM_017370, exon 3 of 5)	exon (NM_017370, exon 3 of 5)	1987	NM_017370	15439	Mm.26730	NM_017370	ENSMUSG00000031722	Hp	HP-1|preHP2	haptoglobin	protein-coding
mm_139140.1	chr17	47509630	47509650	+	1	NA	intron (NM_001081635, intron 1 of 6)	intron (NM_001081635, intron 1 of 6)	4589	NM_001081635	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_84351.1	chr9	64340984	64340994	-	1	NA	promoter-TSS (NM_001177784)	promoter-TSS (NM_001177784)	-216	NM_001177784	213550	Mm.268341	NM_172519	ENSMUSG00000032396	Dis3l	AV340375	DIS3 like exosome 3'-5' exoribonuclease	protein-coding
mm_41711.1	chr5	101814487	101814524	+	1	NA	exon (NM_173370, exon 10 of 13)	exon (NM_173370, exon 10 of 13)	49375	NM_173370	74596	Mm.46764	NM_173370	ENSMUSG00000029330	Cds1	4833409J18Rik|AI314024|AW125888	CDP-diacylglycerol synthase 1	protein-coding
mm_161461.1	chr15	77447440	77447440	-	1	NA	promoter-TSS (NM_001024848)	promoter-TSS (NM_001024848)	20	NM_001024848	278679	Mm.440965	NM_001024848	ENSMUSG00000068252	Apol7b	-	apolipoprotein L 7b	protein-coding
mm_121415.1	chr14	119655057	119655060	+	1	NA	intron (NM_015820, intron 1 of 1)	intron (NM_015820, intron 1 of 1)	-94169	NR_045621	75432	Mm.443277	NR_045621	ENSMUSG00000100274	1700006F04Rik	-	RIKEN cDNA 1700006F04 gene	ncRNA
mm_31925.1	chr4	85413992	85413996	+	1	NA	Intergenic	Intergenic	208538	NM_019535	20404	Mm.143603	NM_019535	ENSMUSG00000028488	Sh3gl2	9530001L19Rik|AI120490|AW555077|B930049H17Rik|EEN-B1|SH3PA|Sh3d2a	SH3-domain GRB2-like 2	protein-coding
mm_107006.1	chr12	11311568	11311571	+	1	NA	intron (NM_025695, intron 24 of 26)	intron (NM_025695, intron 24 of 26)	11682	NR_106136	102465775		NR_106136	ENSMUSG00000098879	Mir7675	Gm27965|mmu-mir-7675	microRNA 7675	ncRNA
mm_149350.1	chr19	10895275	10895313	+	1	NA	promoter-TSS (NM_134129)	promoter-TSS (NM_134129)	63	NM_001253843	28000	Mm.491104	NM_134129	ENSMUSG00000024735	Prpf19	AA617263|AL024362|D19Wsu55e|NMP200|PSO4|Prp19|Snev	pre-mRNA processing factor 19	protein-coding
mm_120356.1	chr14	64085508	64085521	+	1	NA	promoter-TSS (NM_001081063)	promoter-TSS (NM_001081063)	-125	NM_001081063	71037	Mm.19977	NM_001081063	ENSMUSG00000034623	Prss55	4933401F05Rik	protease, serine 55	protein-coding
mm_43924.1	chr5	144771328	144771340	+	1	NA	intron (NM_001081362, intron 2 of 70)	intron (NM_001081362, intron 2 of 70)	2542	NM_001081362	100683	Mm.273570	NM_001081362	ENSMUSG00000045482	Trrap	AI481500	transformation/transcription domain-associated protein	protein-coding
mm_163553.1	chr13	23839626	23839628	+	1	NA	5' UTR (NM_001164743, exon 1 of 12)	5' UTR (NM_001164743, exon 1 of 12)	193	NM_134069	105355	Mm.27038	NM_134069	ENSMUSG00000036083	Slc17a3	AW261723|Npt4	solute carrier family 17 (sodium phosphate), member 3	protein-coding
mm_58970.1	chr7	18992430	18992439	+	1	NA	exon (NM_145579, exon 2 of 3)	exon (NM_145579, exon 2 of 3)	1189	NM_145579	232934	Mm.440069	NM_145579	ENSMUSG00000048481	Mypop	Myodysa|P42pop	Myb-related transcription factor, partner of profilin	protein-coding
mm_3234.1	chr1	135850098	135850110	+	1	NA	intron (NM_001130174, intron 10 of 13)	intron (NM_001130174, intron 10 of 13)	9243	NM_001130176	21956	Mm.247470	NM_011619	ENSMUSG00000026414	Tnnt2	Tnt|cTnT	troponin T2, cardiac	protein-coding
mm_167963.1	chrX	150552268	150552282	+	1	NA	exon (NM_009653, exon 2 of 11)	exon (NM_009653, exon 2 of 11)	-4830	NR_106147	102465782		NR_106147	ENSMUSG00000099172	Mir3620	Gm27984|mmu-mir-3620	microRNA 3620	ncRNA
mm_105651.1	chr11	107189256	107189307	-	1	NA	promoter-TSS (NM_001161329)	promoter-TSS (NM_001161329)	100	NM_133702	68979	Mm.294617	NM_133702	ENSMUSG00000018433	Nol11	1500002M01Rik|AU015220|AU019874	nucleolar protein 11	protein-coding
mm_86518.1	chr10	7725998	7726014	+	1	NA	promoter-TSS (NM_011835)	promoter-TSS (NM_011835)	6	NM_011835	23924	Mm.28127	NM_011835	ENSMUSG00000019794	Katna1	-	katanin p60 (ATPase-containing) subunit A1	protein-coding
mm_91466.1	chr10	34151913	34151916	-	1	NA	3' UTR (NM_172508, exon 6 of 6)	3' UTR (NM_172508, exon 6 of 6)	-23942	NM_175449	215900	Mm.34479	NM_175449	ENSMUSG00000046031	Fam26f	A630077B13Rik	family with sequence similarity 26, member F	protein-coding
mm_47640.1	chr5	125341012	125341027	-	1	NA	promoter-TSS (NM_001205082)	promoter-TSS (NM_001205082)	75	NM_016741	20778	Mm.282242	NM_016741	ENSMUSG00000037936	Scarb1	AI120173|CD36|Cd36l1|Chohd1|Cla-1|Cla1|D5Ertd460e|Hdlq1|Hlb398|SR-B1|SR-BI|SRBI|Srb1|mSR-BI	scavenger receptor class B, member 1	protein-coding
mm_59456.1	chr7	27195815	27195830	+	1	NA	promoter-TSS (NM_001046637)	promoter-TSS (NM_001046637)	41	NM_001243888	414069	Mm.379069	NM_001243888	ENSMUSG00000078786	BC024978	-	cDNA sequence BC024978	protein-coding
mm_126721.1	chr15	85393435	85393450	+	1	NA	exon (NM_016843, exon 9 of 12)	exon (NM_016843, exon 9 of 12)	57061	NM_016843	54138	Mm.248906	NM_016843	ENSMUSG00000016541	Atxn10	AI325283|C77170|E46|Sca10|TEG-169|Tex169	ataxin 10	protein-coding
mm_116704.1	chr13	50934148	50934186	-	1	NA	Intergenic	Intergenic	166560	NR_029463	77428	Mm.405630	NR_029463		9430083A17Rik	-	RIKEN cDNA 9430083A17 gene	ncRNA
mm_87166.1	chr10	37078625	37078627	+	1	NA	Intergenic	Intergenic	60300	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_26034.1	chr3	135485606	135485668	+	1	NA	promoter-TSS (NM_027288)	promoter-TSS (NM_027288)	26	NM_027288	110173	Mm.280536	NM_027288	ENSMUSG00000028164	Manba	2410030O07Rik|B930014J03Rik|Bmn	mannosidase, beta A, lysosomal	protein-coding
mm_155717.1	chrX	96107046	96107051	+	1	NA	intron (NM_010833, intron 1 of 12)	intron (NM_010833, intron 1 of 12)	11003	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_102392.1	chr11	58999221	58999237	-	1	NA	exon (NM_001171512, exon 93 of 104)	exon (NM_001171512, exon 93 of 104)	21136	NM_053168	94091	Mm.248049	NM_053168	ENSMUSG00000020455	Trim11	-	tripartite motif-containing 11	protein-coding
mm_38713.1	chr4	145225453	145225492	-	1	NA	exon (NM_011610, exon 4 of 10)	exon (NM_011610, exon 4 of 10)	21398	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_29135.1	chr3	105785857	105785860	-	1	NA	intron (NM_145541, intron 1 of 7)	Lx5c|LINE|L1	15523	NM_145541	109905	Mm.101922	NM_145541	ENSMUSG00000068798	Rap1a	AI848598|G-22K|Krev-1|Rap1	RAS-related protein-1a	protein-coding
mm_128477.1	chr15	50889666	50889688	-	1	NA	promoter-TSS (NR_035444)	promoter-TSS (NR_035444)	364	NM_032000	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_135926.1	chr16	70006479	70006510	-	1	NA	Intergenic	Lx4A|LINE|L1	-142750	NM_173069	224318	Mm.212743	NM_173069	ENSMUSG00000063163	Speer2	SPEER-2	spermatogenesis associated glutamate (E)-rich protein 2	protein-coding
mm_22765.1	chr3	20058337	20058352	+	1	NA	promoter-TSS (NR_105047)	promoter-TSS (NR_105047)	53	NR_105047	20585	Mm.209650	NM_009210	ENSMUSG00000002428	Hltf	AF010600|BC057116|P113|Smarca3|Snf2l3	helicase-like transcription factor	protein-coding
mm_138784.1	chr17	37270671	37270696	+	1	NA	exon (NM_013819, exon 2 of 8)	exon (NM_013819, exon 2 of 8)	449	NM_013819	14991	Mm.14437	NM_013819	ENSMUSG00000016206	H2-M3	H-2M3|Hmt|M3a|MuprM3|MuprM301|MuprM302|R4B2	histocompatibility 2, M region locus 3	protein-coding
mm_164642.1	chr17	35067111	35067119	+	1	NA	promoter-TSS (NM_023463)	promoter-TSS (NM_023463)	-210	NM_023463	68468	Mm.215096	NM_023463	ENSMUSG00000092586	Ly6g6c	1110003M04Rik|AU016360|G6c|NG24	lymphocyte antigen 6 complex, locus G6C	protein-coding
mm_128747.1	chr15	64382938	64382958	-	1	NA	promoter-TSS (NM_001276467)	promoter-TSS (NM_001276467)	-29	NM_010026	13196	Mm.277236	NM_010026	ENSMUSG00000022377	Asap1	AV239055|DEF-1|Ddef1|PAP|mKIAA1249|s19	ArfGAP with SH3 domain, ankyrin repeat and PH domain1	protein-coding
mm_169558.1	chr15	103917247	103917251	-	1	NA	Intergenic	RLTR10D2|LTR|ERVK	-17937	NM_009267	20770	Mm.1280	NM_009267	ENSMUSG00000036925	Mucl2	Spt-1|Spt1	mucin-like 2	protein-coding
mm_152190.1	chr19	7441581	7441616	-	1	NA	intron (NM_053076, intron 1 of 6)	intron (NM_053076, intron 1 of 6)	19025	NR_105957	102466781		NR_105957	ENSMUSG00000098293	Mir6991	Gm27966|mmu-mir-6991	microRNA 6991	ncRNA
mm_3047.1	chr1	134040739	134040754	+	1	NA	exon (NM_021355, exon 2 of 3)	exon (NM_021355, exon 2 of 3)	3231	NM_021355	14264	Mm.287146	NM_021355	ENSMUSG00000041559	Fmod	AI131919|AU041740|SLRR2E	fibromodulin	protein-coding
mm_48085.1	chr5	136987502	136987569	-	1	NA	promoter-TSS (NM_001310748)	promoter-TSS (NM_001310748)	424	NM_027318	70103	Mm.273147	NM_027318	ENSMUSG00000059518	Znhit1	2700001K05Rik|ZNFN4A1	zinc finger, HIT domain containing 1	protein-coding
mm_131497.1	chr16	17336260	17336310	+	1	NA	5' UTR (NM_008223, exon 2 of 5)	5' UTR (NM_008223, exon 2 of 5)	4914	NM_001331047	15160	Mm.6609	NM_008223	ENSMUSG00000022766	Serpind1	AA985900|AI303446|HC-II|HCII|Hcf2	serine (or cysteine) peptidase inhibitor, clade D, member 1	protein-coding
mm_146205.1	chr18	76595741	76595744	+	1	NA	Intergenic	Intergenic	-260663	NM_001109743	664805	Mm.329543	NM_001109743	ENSMUSG00000091519	Skor2	Corl2|EG664805|Fussel18|Gm7348	SKI family transcriptional corepressor 2	protein-coding
mm_47327.1	chr5	122489314	122489326	-	1	NA	exon (NM_009722, exon 5 of 21)	exon (NM_009722, exon 5 of 21)	12905	NM_001110140	11938	Mm.227583	NM_009722	ENSMUSG00000029467	Atp2a2	9530097L16Rik|D5Wsu150e|SERCA2|SERCA2B|Serca2a|mKIAA4195	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	protein-coding
mm_54303.1	chr6	29526461	29526499	-	1	NA	promoter-TSS (NM_012057)	promoter-TSS (NM_012057)	-145	NM_001311083	27056	Mm.6479	NM_012057	ENSMUSG00000029771	Irf5	AW491843|mirf5	interferon regulatory factor 5	protein-coding
mm_35047.1	chr4	4765404	4765407	-	1	NA	3' UTR (NM_177730, exon 5 of 5)	3' UTR (NM_177730, exon 5 of 5)	27901	NM_177730	242291	Mm.218889	NM_177730	ENSMUSG00000066324	Impad1	1110001C20Rik|AA408880|AI451589|AL022796|B230207P20|Jaws|gPAPP	inositol monophosphatase domain containing 1	protein-coding
mm_127591.1	chr15	102386924	102386934	+	1	NA	Intergenic	Intergenic	-19387	NM_013672	20683	Mm.4618	NM_013672	ENSMUSG00000001280	Sp1	1110003E12Rik|AA450830|AI845540|Sp1-1	trans-acting transcription factor 1	protein-coding
mm_103036.1	chr11	69758631	69758642	-	1	NA	promoter-TSS (NM_001291068)	promoter-TSS (NM_001291068)	-3	NM_001291068	20020	Mm.16533	NM_009089	ENSMUSG00000005198	Polr2a	220kDa|Rpb1|Rpo2-1	polymerase (RNA) II (DNA directed) polypeptide A	protein-coding
mm_15799.1	chr2	164460946	164461018	+	1	NA	promoter-TSS (NM_025575)	promoter-TSS (NM_025575)	11	NM_025575	66460	Mm.44218	NM_025575	ENSMUSG00000045503	Sys1	2610042O14Rik|AI266964|C87389	SYS1 Golgi-localized integral membrane protein homolog (S. cerevisiae)	protein-coding
mm_73217.1	chr8	97142156	97142158	+	1	NA	Intergenic	Lx6|LINE|L1	-596184	NR_039538	100628567		NR_039538	ENSMUSG00000104794	Mir28c	mmu-mir-28c	microRNA 28c	ncRNA
mm_66298.1	chr7	38107453	38107485	-	1	NA	promoter-TSS (NM_007633)	promoter-TSS (NM_007633)	21	NM_007633	12447	Mm.16110	NM_007633	ENSMUSG00000002068	Ccne1	AW538188|CycE1	cyclin E1	protein-coding
mm_21619.1	chr2	164276084	164276093	-	1	NA	3' UTR (NM_009300, exon 3 of 3)	3' UTR (NM_009300, exon 3 of 3)	2219	NM_009300	20941	Mm.1286	NM_009300	ENSMUSG00000016998	Svs4	SVS-IV|Svp-2|Svp-4|Svp2|Svp4	seminal vesicle secretory protein 4	protein-coding
mm_92450.1	chr10	77751421	77751425	-	1	NA	intron (NM_001287074, intron 1 of 11)	(TG)n|Simple_repeat|Simple_repeat	19902	NM_001101630	100041261	Mm.477434	NM_001101630	ENSMUSG00000095817	Gm3238	-	predicted gene 3238	protein-coding
mm_77897.1	chr9	7348624	7348647	+	1	NA	exon (NM_008605, exon 2 of 10)	exon (NM_008605, exon 2 of 10)	1261	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_132076.1	chr16	30067128	30067145	+	1	NA	exon (NM_008235, exon 4 of 4)	exon (NM_008235, exon 4 of 4)	1779	NM_008235	15205	Mm.390859	NM_008235	ENSMUSG00000022528	Hes1	Hry|bHLHb39	hairy and enhancer of split 1 (Drosophila)	protein-coding
mm_74900.1	chr8	25201350	25201459	-	1	NA	5' UTR (NM_177089, exon 1 of 13)	5' UTR (NM_177089, exon 1 of 13)	138	NM_199323	320165	Mm.308452	NM_177089	ENSMUSG00000065954	Tacc1	4833447E04Rik|AA960202|B230378H13Rik	transforming, acidic coiled-coil containing protein 1	protein-coding
mm_170362.1	chr1	85270356	85270359	-	1	NA	5' UTR (NM_001037909, exon 1 of 7)	5' UTR (NM_001037909, exon 1 of 7)	209	NM_175219	620078	Mm.386456	NM_175219	ENSMUSG00000052477	C130026I21Rik	4930565N07Rik|OTTMUSG00000029174	RIKEN cDNA C130026I21 gene	protein-coding
mm_139296.1	chr17	48316217	48316232	+	1	NA	promoter-TSS (NM_177083)	promoter-TSS (NM_177083)	62	NM_177083	320148	Mm.123455	NM_177083	ENSMUSG00000043740	B430306N03Rik	Treml6	RIKEN cDNA B430306N03 gene	protein-coding
mm_32391.1	chr4	106622425	106622477	+	1	NA	promoter-TSS (NM_177667)	promoter-TSS (NM_177667)	2	NM_177667	230576	Mm.41945	NM_177667	ENSMUSG00000034919	Ttc22	4732467L16Rik	tetratricopeptide repeat domain 22	protein-coding
mm_119624.1	chr14	51129086	51129113	+	1	NA	promoter-TSS (NM_030098)	promoter-TSS (NM_030098)	31	NM_030098	78416	Mm.103835	NM_030098	ENSMUSG00000021880	Rnase6	9530043P15Rik|BB119466	ribonuclease, RNase A family, 6	protein-coding
mm_73467.1	chr8	106668724	106668752	+	1	NA	3' UTR (NM_009864, exon 16 of 16)	3' UTR (NM_009864, exon 16 of 16)	-14330	NM_173037	272538	Mm.87151	NM_173037	ENSMUSG00000041949	Tango6	AW413431|E330010G16|Tmco7	transport and golgi organization 6	protein-coding
mm_124836.1	chr15	9279842	9279865	+	1	NA	promoter-TSS (NM_207216)	promoter-TSS (NM_207216)	24	NM_207216	105887	Mm.482274	NM_207216	ENSMUSG00000072664	Ugt3a1	AI746432	UDP glycosyltransferases 3 family, polypeptide A1	protein-coding
mm_104574.1	chr11	96944934	96944946	-	1	NA	promoter-TSS (NM_134021)	promoter-TSS (NM_134021)	794	NR_003293	319371	Mm.436865	NR_003293	ENSMUSG00000078700	D030028A08Rik	-	RIKEN cDNA D030028A08 gene	ncRNA
mm_71653.1	chr8	60506110	60506125	+	1	NA	promoter-TSS (NM_011834)	promoter-TSS (NM_011834)	-7	NM_011834	23923	Mm.35020	NM_011834	ENSMUSG00000057228	Aadat	AI875679|Aadt|KATII|Kat2|Kyat2|mKat-2	aminoadipate aminotransferase	protein-coding
mm_54405.1	chr6	31563856	31563880	-	1	NA	promoter-TSS (NM_013723)	promoter-TSS (NM_013723)	69	NM_013723	27205	Mm.89918	NM_013723	ENSMUSG00000025608	Podxl	AW121214|Ly102|PC|PCLP-1|Pclp1	podocalyxin-like	protein-coding
mm_46143.1	chr5	93190278	93190285	-	1	NA	intron (NM_017367, intron 2 of 6)	intron (NM_017367, intron 2 of 6)	16214	NM_017367	12453	Mm.250419	NM_017367	ENSMUSG00000063015	Ccni	-	cyclin I	protein-coding
mm_77270.1	chr8	116529386	116529392	-	1	NA	Intergenic	Intergenic	24374	NM_029297	75465	Mm.23114	NM_029297	ENSMUSG00000034467	Dynlrb2	1700009A04Rik|DNLC2B|Dncl2b	dynein light chain roadblock-type 2	protein-coding
mm_22955.1	chr3	32397239	32397265	+	1	NA	Intergenic	CpG	-31587	NM_009517	22401	Mm.35705	NM_009517	ENSMUSG00000027663	Zmat3	Wig1	zinc finger matrin type 3	protein-coding
mm_82088.1	chr9	123046534	123046549	+	1	NA	exon (NM_177911, exon 5 of 14)	exon (NM_177911, exon 5 of 14)	11800	NM_177911	331046	Mm.195309	NM_177911	ENSMUSG00000025787	Tgm4	9530008N10Rik|Eapa1|TGP	transglutaminase 4 (prostate)	protein-coding
mm_13345.1	chr2	102941055	102941077	+	1	NA	Intergenic	Intergenic	-39401	NM_001039150	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_66172.1	chr7	33944987	33944988	-	1	NA	promoter-TSS (NM_178308)	promoter-TSS (NM_178308)	-2	NM_178308	110187	Mm.155750	NM_178308	ENSMUSG00000066586	Scgb2b26	Abpbg26|Abpbg4|Abpg|C2d|Scgb2b4	secretoglobin, family 2B, member 26	protein-coding
mm_115222.1	chr13	109685556	109685584	+	1	NA	intron (NM_011056, intron 3 of 16)	intron (NM_011056, intron 3 of 16)	-218239	NR_035442	100316683		NR_035442	ENSMUSG00000084651	Mir1904	Mirn1904|mmu-mir-1904	microRNA 1904	ncRNA
mm_13110.1	chr2	91537815	91537835	+	1	NA	Intergenic	Intergenic	-8497	NM_001165989	75786	Mm.168478	NM_029437	ENSMUSG00000040549	Ckap5	3110043H24Rik|4930432B04Rik|D730027C18Rik|T25636|mKIAA0097	cytoskeleton associated protein 5	protein-coding
mm_86421.1	chr10	3740349	3740430	+	1	NA	promoter-TSS (NM_001159942)	promoter-TSS (NM_001159942)	12	NM_001159942	213783	Mm.150831	NM_001033253	ENSMUSG00000040624	Plekhg1	D10Ertd733e|Gm521|mKIAA1209	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	protein-coding
mm_51125.1	chr6	68219945	68219957	+	1	NA	Intergenic	Intergenic	-654252	NR_003100	75070	Mm.463364	NR_003100		4930515G16Rik	-	myc induced nuclear antigen pseudogene	pseudo
mm_132759.1	chr16	44531223	44531229	+	1	NA	intron (NM_172506, intron 1 of 18)	intron (NM_172506, intron 1 of 18)	26903	NR_037242	100526478		NR_037242	ENSMUSG00000093046	Mir3081	mir-3081|mmu-mir-3081	microRNA 3081	ncRNA
mm_105044.1	chr11	100613385	100613389	-	1	NA	intron (NM_019795, intron 1 of 13)	intron (NM_019795, intron 1 of 13)	6781	NM_019795	56354	Mm.402409	NM_019795	ENSMUSG00000014195	Dnajc7	2010003F24Rik|2010004G07Rik|CCRP|Ttc2|mDj11|mTpr2	DnaJ heat shock protein family (Hsp40) member C7	protein-coding
mm_145777.1	chr18	65072218	65072260	+	1	NA	intron (NM_031881, intron 1 of 29)	intron (NM_031881, intron 1 of 29)	48712	NM_031881	83814	Mm.98668	NM_031881	ENSMUSG00000024589	Nedd4l	1300012C07Rik|Nedd4-2|Nedd4b	neural precursor cell expressed, developmentally down-regulated gene 4-like	protein-coding
mm_82621.1	chr9	21798503	21798561	-	1	NA	promoter-TSS (NM_145611)	promoter-TSS (NM_145611)	14	NM_145611	235041	Mm.257371	NM_145611	ENSMUSG00000032194	Kank2	AI504612|Ankrd25|BC010245	KN motif and ankyrin repeat domains 2	protein-coding
mm_124600.1	chr15	3275709	3275729	+	1	NA	exon (NM_009155, exon 3 of 5)	exon (NM_009155, exon 3 of 5)	4742	NM_009155	20363	Mm.392203	NM_009155	ENSMUSG00000064373	Selenop	AU018766|D15Ucla1|Se-P|Sepp1|selp	selenoprotein P	protein-coding
mm_134771.1	chr16	23520999	23521006	-	1	NA	promoter-TSS (NM_008555)	promoter-TSS (NM_008555)	-412	NM_008555	17174	Mm.1213	NM_008555	ENSMUSG00000022887	Masp1	AW048060|CCPII|Crarf|Masp1/3	mannan-binding lectin serine peptidase 1	protein-coding
mm_141992.1	chr17	35175996	35176038	-	1	NA	promoter-TSS (NM_019467)	promoter-TSS (NM_019467)	-16	NM_019467	11629	Mm.10747	NM_019467	ENSMUSG00000024397	Aif1	AI607846|AIF-1|D17H6S50E|G1|Iba1	allograft inflammatory factor 1	protein-coding
mm_118113.1	chr13	103921788	103921807	-	1	NA	Intergenic	CpG	-1211	NM_001005868	59079	Mm.277354	NM_021563	ENSMUSG00000021709	Erbin	1700028E05Rik|Erbb2ip|mKIAA1225	Erbb2 interacting protein	protein-coding
mm_86283.1	chr9	121857558	121857572	-	1	NA	5' UTR (NM_019814, exon 1 of 4)	5' UTR (NM_019814, exon 1 of 4)	435	NM_019814	56295	Mm.347915	NM_019814	ENSMUSG00000038412	Higd1a	2210020B17Rik|7420700H20Rik|AI303276|AW049839|HIMP1|Hig1	HIG1 domain family, member 1A	protein-coding
mm_43643.1	chr5	138256068	138256123	+	1	NA	intron (NM_001081108, intron 1 of 3)	intron (NM_001081108, intron 1 of 3)	613	NM_001081108	66096	Mm.206901	NM_001081108	ENSMUSG00000050552	Lamtor4	0910001L09Rik|AV006840	late endosomal/lysosomal adaptor, MAPK and MTOR activator 4	protein-coding
mm_39059.1	chr4	154023788	154023798	-	1	NA	exon (NM_001163722, exon 3 of 4)	exon (NM_001163722, exon 3 of 4)	2251	NM_001163722	68859	Mm.477488	NM_001033144	ENSMUSG00000078350	Smim1	0610011H04Rik|1190007F08Rik|2700009I11Rik	small integral membrane protein 1	protein-coding
mm_61950.1	chr7	90195993	90196014	+	1	NA	intron (NM_001252520, intron 19 of 20)	intron (NM_001252520, intron 19 of 20)	65771	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_47407.1	chr5	123132405	123132434	-	1	NA	5' UTR (NM_175092, exon 1 of 5)	5' UTR (NM_175092, exon 1 of 5)	210	NM_175092	23912	Mm.253876	NM_175092	ENSMUSG00000029449	Rhof	AI845056|AV026554|Arhf|Ifld1|Rif	ras homolog family member F (in filopodia)	protein-coding
mm_20399.1	chr2	129199182	129199197	-	1	NA	intron (NM_001159593, intron 1 of 5)	CpG	416	NM_001159593	20515	Mm.272675	NM_015747	ENSMUSG00000027397	Slc20a1	AI607883|Glvr-1|Glvr1	solute carrier family 20, member 1	protein-coding
mm_92357.1	chr10	75921547	75921553	-	1	NA	promoter-TSS (NM_001161853)	promoter-TSS (NM_001161853)	64	NM_011418	20587	Mm.279751	NM_011418	ENSMUSG00000000902	Smarcb1	AU020204|Baf47|Ini1|SNF5/INI1|Snf5	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1	protein-coding
mm_46153.1	chr5	96092515	96092518	-	1	NA	intron (NM_144910, intron 7 of 11)	intron (NM_144910, intron 7 of 11)	69031	NM_001285511	231464	Mm.28374	NM_144910	ENSMUSG00000034724	Cnot6l	4932442K20Rik	CCR4-NOT transcription complex, subunit 6-like	protein-coding
mm_66216.1	chr7	34389576	34389638	-	1	NA	promoter-TSS (NM_025948)	promoter-TSS (NM_025948)	-67	NM_025948	67070	Mm.276503	NM_025948	ENSMUSG00000066568	Lsm14a	2700023B17Rik|AA407828|AU017544|Tral	LSM14A mRNA processing body assembly factor	protein-coding
mm_101711.1	chr11	42000870	42000887	-	1	NA	promoter-TSS (NM_008073)	promoter-TSS (NM_008073)	-164	NM_008073	14406	Mm.5309	NM_008073	ENSMUSG00000020436	Gabrg2	GABAA-R|Gabrg-2|gamma2	gamma-aminobutyric acid (GABA) A receptor, subunit gamma 2	protein-coding
mm_168927.1	chr12	63691592	63691592	-	1	NA	Intergenic	L1Md_T|LINE|L1	783306	NM_001163271	623046	Mm.189552	NM_001163271	ENSMUSG00000043060	Fscb	EG623046	fibrous sheath CABYR binding protein	protein-coding
mm_142952.1	chr17	56109816	56109824	-	1	NA	promoter-TSS (NM_020568)	promoter-TSS (NM_020568)	-18	NM_020568	57435	Mm.12966	NM_020568	ENSMUSG00000002831	Plin4	S3-12|mKIAA1881	perilipin 4	protein-coding
mm_80998.1	chr9	103425065	103425067	+	1	NA	3' UTR (NM_001002896, exon 7 of 7)	3' UTR (NM_001002896, exon 7 of 7)	1488	NR_040466	100529079	Mm.437003	NR_040466	ENSMUSG00000086236	5830418P13Rik	-	RIKEN cDNA 5830418P13 gene	ncRNA
mm_56406.1	chr6	97179072	97179095	-	1	NA	promoter-TSS (NM_001081111)	promoter-TSS (NM_001081111)	41	NM_001081111	232286	Mm.30893	NM_001081111	ENSMUSG00000030059	Tmf1	7030402D04Rik|Gm153|Tmf1`	TATA element modulatory factor 1	protein-coding
mm_28785.1	chr3	95995663	95995692	-	1	NA	intron (NM_023320, intron 1 of 5)	CpG-9390	162	NM_023320	67220	Mm.458147	NM_023320	ENSMUSG00000015745	Plekho1	2810052M02Rik|CKIP-1|Ckip1|JZA-20|Jza2	pleckstrin homology domain containing, family O member 1	protein-coding
mm_80339.1	chr9	75071398	75071418	+	1	NA	5' UTR (NM_010864, exon 1 of 41)	5' UTR (NM_010864, exon 1 of 41)	202	NM_010864	17918	Mm.3645	NM_010864	ENSMUSG00000034593	Myo5a	9630007J19Rik|AI413174|AI661011|Dbv|MVa|Myo5|MyoVA|Sev-1|d|d-120J|flail|flr	myosin VA	protein-coding
mm_96669.1	chr11	69410552	69410582	+	1	NA	intron (NM_001017426, intron 1 of 22)	CpG	3108	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_100787.1	chr11	4849324	4849343	-	1	NA	5' UTR (NM_001252252, exon 1 of 16)	5' UTR (NM_001252252, exon 1 of 16)	211	NM_001252250	18016	Mm.297109	NM_010898	ENSMUSG00000009073	Nf2	merlin	neurofibromin 2	protein-coding
mm_39936.1	chr5	31698776	31698802	+	1	NA	intron (NM_181280, intron 1 of 12)	intron (NM_181280, intron 1 of 12)	739	NM_144541	107976	Mm.482126	NM_144541	ENSMUSG00000052139	Bre	6030405P19Rik|AI429776|B830038C02Rik	brain and reproductive organ-expressed protein	protein-coding
mm_121875.1	chr14	21049443	21049461	-	1	NA	intron (NM_018829, intron 1 of 8)	intron (NM_018829, intron 1 of 8)	2990	NM_018829	55946	Mm.376269	NM_018829	ENSMUSG00000021824	Ap3m1	1200013D09Rik|C78982|R75378	adaptor-related protein complex 3, mu 1 subunit	protein-coding
mm_127325.1	chr15	100304228	100304243	+	1	NA	promoter-TSS (NM_027334)	promoter-TSS (NM_027334)	-582	NM_027334	70152	Mm.488086	NM_027334	ENSMUSG00000054619	Mettl7a1	2210414H16Rik|3300001H21Rik|Aam-B|Mettl7a|UbiE1	methyltransferase like 7A1	protein-coding
mm_94520.1	chr11	8773638	8773646	+	1	NA	Intergenic	Intergenic	-109107	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_139022.1	chr17	46124264	46124278	+	1	NA	intron (NM_026768, intron 3 of 5)	intron (NM_026768, intron 3 of 5)	13267	NM_026768	68565	Mm.287443	NM_026768	ENSMUSG00000023967	Mrps18a	1110004O20Rik|C79712	mitochondrial ribosomal protein S18A	protein-coding
mm_14942.1	chr2	151572629	151572673	+	1	NA	promoter-TSS (NM_145535)	promoter-TSS (NM_145535)	28	NM_145535	228765	Mm.32068	NM_145535	ENSMUSG00000027456	Sdcbp2	-	syndecan binding protein (syntenin) 2	protein-coding
mm_136853.1	chr17	12793936	12793938	+	1	NA	intron (NR_027784, intron 2 of 2)	intron (NR_027784, intron 2 of 2)	-24231	NM_010515	16004	Mm.26553	NM_010515	ENSMUSG00000023830	Igf2r	AI661837|CD222|CI-MPR|M6P/IGF2R|Mpr300	insulin-like growth factor 2 receptor	protein-coding
mm_146140.1	chr18	74733835	74733854	+	1	NA	intron (NM_201600, intron 30 of 38)	intron (NM_201600, intron 30 of 38)	44611	NR_028560	100217466		NR_028560		Scarna17	MBII-119	small Cajal body-specific RNA 17	ncRNA
mm_160720.1	chr10	63429972	63429972	+	1	NA	promoter-TSS (NM_177612)	promoter-TSS (NM_177612)	-126	NM_177612	216033	Mm.444692	NM_177612	ENSMUSG00000060843	Ctnna3	4930429L08Rik|4933408A16|Catna3|Vr22	catenin (cadherin associated protein), alpha 3	protein-coding
mm_51092.1	chr6	67226446	67226456	+	1	NA	Intergenic	Intergenic	-40528	NM_001113564	66870	Mm.240490	NM_025814	ENSMUSG00000036371	Serbp1	1200009K13Rik|9330147J08Rik|AL022786|Pairbp1	serpine1 mRNA binding protein 1	protein-coding
mm_109006.1	chr12	103336856	103336882	+	1	NA	intron (NM_023049, intron 3 of 9)	intron (NM_023049, intron 3 of 9)	19132	NM_023049	65256	Mm.27159	NM_023049	ENSMUSG00000021200	Asb2	1110008E15Rik	ankyrin repeat and SOCS box-containing 2	protein-coding
mm_123934.1	chr14	73368322	73368333	-	1	NA	exon (NM_008410, exon 2 of 6)	exon (NM_008410, exon 2 of 6)	16944	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_6817.1	chr1	84183099	84183102	-	1	NA	intron (NM_001003948, intron 1 of 2)	intron (NM_001003948, intron 1 of 2)	35861	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_16111.1	chr2	169664923	169664938	+	1	NA	intron (NM_080455, intron 1 of 1)	intron (NM_080455, intron 1 of 1)	31284	NM_080455	228911	Mm.315789	NM_080455	ENSMUSG00000047907	Tshz2	2900073F20Rik|B830045G17|Mtsh2|Sdccag33l|Tsh2|Zfp218|mKIAA4248|teashirt2	teashirt zinc finger family member 2	protein-coding
mm_16772.1	chr2	9881044	9881050	-	1	NA	promoter-TSS (NR_024257)	promoter-TSS (NR_024257)	-199	NR_024257	381347	Mm.441450	NR_024257		4930412O13Rik	ENSMUSG00000075535|Gm10853	RIKEN cDNA 4930412O13 gene	ncRNA
mm_32969.1	chr4	120032735	120032753	+	1	NA	intron (NM_010657, intron 2 of 8)	GC_rich|Low_complexity|Low_complexity	-128462	NM_007902	13615	Mm.284855	NM_007902	ENSMUSG00000028635	Edn2	ET-2|PPET2|VIC	endothelin 2	protein-coding
mm_70988.1	chr8	27262747	27262760	+	1	NA	intron (NM_007918, intron 1 of 2)	intron (NM_007918, intron 1 of 2)	2426	NM_007918	13685	Mm.6700	NM_007918	ENSMUSG00000031490	Eif4ebp1	4e-bp1|AA959816|PHAS-I	eukaryotic translation initiation factor 4E binding protein 1	protein-coding
mm_105979.1	chr11	115590855	115590860	-	1	NA	intron (NM_001252067, intron 7 of 15)	intron (NM_001252067, intron 7 of 15)	13059	NM_001252067	260302	Mm.119479	NM_173048	ENSMUSG00000020740	Gga3	C230037M19Rik|mKIAA0154	golgi associated, gamma adaptin ear containing, ARF binding protein 3	protein-coding
mm_141574.1	chr17	32321103	32321116	-	1	NA	TTS (NM_017476)	TTS (NM_017476)	129	NM_019774	56399	Mm.328945	NM_019774	ENSMUSG00000024045	Akap8	1200016A02Rik|AA673585|AKAP-8|AKAP95|AU015639	A kinase (PRKA) anchor protein 8	protein-coding
mm_26288.1	chr3	142506745	142506758	+	1	NA	exon (NM_153564, exon 8 of 11)	exon (NM_153564, exon 8 of 11)	9817	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_79489.1	chr9	57072066	57072076	+	1	NA	promoter-TSS (NM_001110351)	promoter-TSS (NM_001110351)	31	NM_001110351	20466	Mm.15755	NM_011378	ENSMUSG00000042557	Sin3a	AW553200|Sin3|mKIAA4126|mSin3A	transcriptional regulator, SIN3A (yeast)	protein-coding
mm_29702.1	chr3	123225134	123225137	-	1	NA	intron (NM_080451, intron 1 of 4)	intron (NM_080451, intron 1 of 4)	11014	NM_080451	118449	Mm.34359	NM_080451	ENSMUSG00000050315	Synpo2	1110069I04Rik|2310068J10Rik|9530006G20Rik|AI848603|Myo	synaptopodin 2	protein-coding
mm_78872.1	chr9	44482532	44482552	+	1	NA	Intergenic	Intergenic	-16594	NM_030256	80288	Mm.370270	NM_030256	ENSMUSG00000063382	Bcl9l	B9L|BC003321|BCL9-2|DLNB11	B cell CLL/lymphoma 9-like	protein-coding
mm_122462.1	chr14	45477857	45477870	-	1	NA	intron (NM_146054, intron 4 of 14)	intron (NM_146054, intron 4 of 14)	52202	NM_146054	218952	Mm.210018	NM_146054	ENSMUSG00000037712	Fermt2	AA960555|Kindlin-2|Mig2|Plekhc1	fermitin family member 2	protein-coding
mm_165911.1	chr4	57779070	57779073	+	1	NA	intron (NM_001304544, intron 6 of 8)	intron (NM_001304544, intron 6 of 8)	-66177	NM_009649	11641	Mm.467752	NM_009649	ENSMUSG00000038729	Akap2	AA959716|AI649048|Akap-2|Akap-kl|B230340M18Rik|Prka2	A kinase (PRKA) anchor protein 2	protein-coding
mm_56777.1	chr6	116633306	116633316	-	1	NA	3' UTR (NM_178045, exon 11 of 11)	3' UTR (NM_178045, exon 11 of 11)	-4312	NM_026057	67255	Mm.18810	NM_026057	ENSMUSG00000059878	Zfp422	2900028O21Rik|AU041373|KOX15|Krox-25-2|Krox-26|Krox25|Krox26|Znf22	zinc finger protein 422	protein-coding
mm_66650.1	chr7	45706906	45706919	-	1	NA	exon (NM_016974, exon 2 of 4)	exon (NM_016974, exon 2 of 4)	1665	NM_016974	13170	Mm.24222	NM_016974	ENSMUSG00000059824	Dbp	-	D site albumin promoter binding protein	protein-coding
mm_143800.1	chr17	83221201	83221218	-	1	NA	exon (NM_134117, exon 3 of 7)	exon (NM_134117, exon 3 of 7)	5926	NM_134117	106522	Mm.311974	NM_134117	ENSMUSG00000024247	Pkdcc	AI115348|AW548124|Adtk1|ESTM17|MAd1|Sgk493|Vlk|X83346	protein kinase domain containing, cytoplasmic	protein-coding
mm_129541.1	chr15	79357790	79357800	-	1	NA	exon (NM_001304830, exon 3 of 3)	exon (NM_001304830, exon 3 of 3)	9393	NM_001304832	17133	Mm.86646	NM_010755	ENSMUSG00000042622	Maff	-	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein F (avian)	protein-coding
mm_125058.1	chr15	25910499	25910514	+	1	NA	intron (NM_001034851, intron 3 of 8)	intron (NM_001034851, intron 3 of 8)	-23046	NM_001277318	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_23036.1	chr3	34699946	34699947	+	1	NA	intron (NR_038347, intron 4 of 4)	intron (NR_038347, intron 4 of 4)	16716	NR_038347	100041108	Mm.24764	NR_038347	ENSMUSG00000105153	Gm3143	-	predicted gene 3143	ncRNA
mm_146649.1	chr18	11051374	11051387	-	1	NA	intron (NR_105022, intron 1 of 3)	intron (NR_105022, intron 1 of 3)	-1130	NM_010258	14465	Mm.329287	NM_010258	ENSMUSG00000005836	Gata6	AA410133|GATA-6	GATA binding protein 6	protein-coding
mm_167431.1	chr8	118438120	118438131	+	1	NA	intron (NM_019707, intron 1 of 13)	intron (NM_019707, intron 1 of 13)	154514	NM_019707	12554	Mm.334841	NM_019707	ENSMUSG00000031841	Cdh13	4932416G01Rik|Cdht|Tcad	cadherin 13	protein-coding
mm_118709.1	chr14	22180337	22180341	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	160627	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_165054.1	chr19	41339478	41339496	+	1	NA	intron (NM_031376, intron 2 of 16)	intron (NM_031376, intron 2 of 16)	45583	NM_031376	83490	Mm.222266	NM_031376	ENSMUSG00000025017	Pik3ap1	1810044J04Rik|BCAP	phosphoinositide-3-kinase adaptor protein 1	protein-coding
mm_84472.1	chr9	66795299	66795319	-	1	NA	exon (NM_177583, exon 1 of 6)	exon (NM_177583, exon 1 of 6)	114	NM_177583	208117	Mm.41291	NM_177583	ENSMUSG00000032375	Aph1b	2310057K14Rik|Aph1c	aph1 homolog B, gamma secretase subunit	protein-coding
mm_41832.1	chr5	104202610	104202624	+	1	NA	promoter-TSS (NM_016779)	promoter-TSS (NM_016779)	0	NM_016779	13406	Mm.199008	NM_016779	ENSMUSG00000029307	Dmp1	AV020965|Dmp|PP	dentin matrix protein 1	protein-coding
mm_43884.1	chr5	143817850	143817865	+	1	NA	Intergenic	CpG	-54005	NM_013557	15467	Mm.389709	NM_013557	ENSMUSG00000029613	Eif2ak1	HCR|Hri	eukaryotic translation initiation factor 2 alpha kinase 1	protein-coding
mm_124709.1	chr15	6569482	6569497	+	1	NA	Intergenic	Intergenic	-10358	NM_001278269	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_110395.1	chr12	44203211	44203220	-	1	NA	Intergenic	Intergenic	6853	NM_013760	27362	Mm.27432	NM_013760	ENSMUSG00000014905	Dnajb9	AA408011|AA673251|AA673481|AW556981|ERdj4|Mdg1|mDj7	DnaJ heat shock protein family (Hsp40) member B9	protein-coding
mm_85019.1	chr9	88380209	88380233	-	1	NA	exon (NM_172926, exon 26 of 28)	exon (NM_172926, exon 26 of 28)	52612	NM_011851	23959	Mm.244235	NM_011851	ENSMUSG00000032420	Nt5e	2210401F01Rik|5'-NT|AI447961|CD73|NT|Nt5|eNT	5' nucleotidase, ecto	protein-coding
mm_161022.1	chr11	121207822	121207822	+	1	NA	intron (NM_001001333, intron 2 of 12)	intron (NM_001001333, intron 2 of 12)	179	NM_001146073	238023	Mm.275130	NM_001001333	ENSMUSG00000039307	Hexdc	BC069960	hexosaminidase (glycosyl hydrolase family 20, catalytic domain) containing	protein-coding
mm_103139.1	chr11	70238394	70238420	-	1	NA	promoter-TSS (NM_001177601)	promoter-TSS (NM_001177601)	-493	NM_145758	104457	Mm.30016	NM_026757	ENSMUSG00000020831	0610010K14Rik	1110020A23Rik|AL033328|AU045833|Bap18	RIKEN cDNA 0610010K14 gene	protein-coding
mm_58052.1	chr6	136857249	136857260	-	1	NA	5' UTR (NM_026639, exon 1 of 3)	5' UTR (NM_026639, exon 1 of 3)	346	NM_026639	109978	Mm.31840	NM_026639	ENSMUSG00000030217	Art4	4432404K01Rik|ARTC4|DO|DOK1	ADP-ribosyltransferase 4	protein-coding
mm_168816.1	chr12	21960200	21960201	+	1	NA	Intergenic	B1_Mm|SINE|Alu	196446	NR_136920	100043416		NM_001004167	ENSMUSG00000093846	Gm4425	EG432637|Gm5433	KRAB-domain protein pseudogene	pseudo
mm_30387.1	chr3	152247211	152247219	-	1	NA	exon (NM_199465, exon 8 of 13)	exon (NM_199465, exon 8 of 13)	19105	NM_199465	68810	Mm.200188	NM_199465	ENSMUSG00000039103	Nexn	1110046H09Rik|AA553326|NELIN	nexilin	protein-coding
mm_115766.1	chr13	19304438	19304451	-	1	NA	Intergenic	Intergenic	91369	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_93705.1	chr10	118556527	118556542	-	1	NA	promoter-TSS (NR_104123)	promoter-TSS (NR_104123)	-9	NR_104123	103214	Mm.30529	NR_104123		Tmevpg1	AI447422	Theiler's murine encephalomyelitis virus persistence candidate gene 1	ncRNA
mm_149051.1	chr19	8837600	8837608	+	1	NA	5' UTR (NM_001136064, exon 1 of 12)	5' UTR (NM_001136064, exon 1 of 12)	137	NM_001136064	14705	Mm.345134	NM_008144	ENSMUSG00000071657	Bscl2	2900097C17Rik|AI046355|Gng3lg	Berardinelli-Seip congenital lipodystrophy 2 (seipin)	protein-coding
mm_35993.1	chr4	55532281	55532322	-	1	NA	5' UTR (NM_010637, exon 1 of 5)	5' UTR (NM_010637, exon 1 of 5)	174	NM_010637	16600	Mm.4325	NM_010637	ENSMUSG00000003032	Klf4	EZF|Gklf|Zie	Kruppel-like factor 4 (gut)	protein-coding
mm_57263.1	chr6	123285566	123285589	-	1	NA	exon (NM_019948, exon 5 of 6)	exon (NM_019948, exon 5 of 6)	4294	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_36171.1	chr4	62054113	62054117	-	1	NA	promoter-TSS (NM_001012323)	promoter-TSS (NM_001012323)	2	NM_001012323	381530	Mm.460005	NM_001012323	ENSMUSG00000078672	Mup20	Gm12560|Mup24|OTTMUSG00000007485|darcin	major urinary protein 20	protein-coding
mm_7528.1	chr1	124208465	124208473	-	1	NA	Intergenic	B3A|SINE|B2	-162910	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_65027.1	chr7	18475015	18475023	-	1	NA	3' UTR (NM_001029893, exon 5 of 5)	3' UTR (NM_001029893, exon 5 of 5)	9130	NM_001029893	574429	Mm.296754	NM_001029893	ENSMUSG00000070799	Psg26	EG574429|cea14	pregnancy-specific glycoprotein 26	protein-coding
mm_157089.1	chrX	9437042	9437054	-	1	NA	3' UTR (NM_007807, exon 13 of 13)	3' UTR (NM_007807, exon 13 of 13)	32276	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_23906.1	chr3	83032093	83032100	+	1	NA	3' UTR (NM_010196, exon 5 of 5)	3' UTR (NM_010196, exon 5 of 5)	5943	NM_001111048	14161	Mm.88793	NM_010196	ENSMUSG00000028001	Fga	ENSMUSG00000059807|Fib	fibrinogen alpha chain	protein-coding
mm_140974.1	chr17	24696198	24696206	-	1	NA	promoter-TSS (NM_027988)	promoter-TSS (NM_027988)	-32	NM_027988	71893	Mm.390971	NM_027988	ENSMUSG00000019320	Noxo1	2310034C04Rik|P41NOX|P41NOXA|P41NOXB|P41NOXC|Snx28|hslt	NADPH oxidase organizer 1	protein-coding
mm_46382.1	chr5	103977361	103977403	-	1	NA	promoter-TSS (NM_001163486)	promoter-TSS (NM_001163486)	6	NM_198030	243168	Mm.284944	NM_198030	ENSMUSG00000034528	Hsd17b13	AI047820|PAN1B-like|Pan1b	hydroxysteroid (17-beta) dehydrogenase 13	protein-coding
mm_17762.1	chr2	32788286	32788294	-	1	NA	3' UTR (NM_001113569, exon 20 of 20)	3' UTR (NM_001113569, exon 20 of 20)	-3885	NM_025619	227736	Mm.441499	NM_025619	ENSMUSG00000038987	Cfap157	1700019L03Rik	cilia and flagella associated protein 157	protein-coding
mm_71352.1	chr8	45658300	45658308	+	1	NA	intron (NM_001310707, intron 1 of 23)	intron (NM_001310707, intron 1 of 23)	-3689	NM_001310708	234214	Mm.211096	NM_172752	ENSMUSG00000031626	Sorbs2	2010203O03Rik|9430041O17Rik|A530071H08|Argbp2|mKIAA0777|nArgBP2	sorbin and SH3 domain containing 2	protein-coding
mm_116345.1	chr13	38528413	38528472	-	1	NA	promoter-TSS (NM_145367)	promoter-TSS (NM_145367)	42	NM_145367	105245	Mm.28622	NM_145367	ENSMUSG00000038991	Txndc5	AL022641|ERp46|PC-TRP	thioredoxin domain containing 5	protein-coding
mm_170966.1	chr2	58256773	58256777	+	1	NA	Intergenic	Intergenic	-20004	NR_040365	100502932	Mm.417207	NR_040365	ENSMUSG00000086995	Gm13544	OTTMUSG00000012672	predicted gene 13544	ncRNA
mm_118475.1	chr14	11617663	11617691	+	1	NA	intron (NM_008981, intron 1 of 29)	intron (NM_008981, intron 1 of 29)	64124	NM_008981	19270	Mm.431266	NM_008981	ENSMUSG00000021745	Ptprg	5430405N12Rik|AW046354|AW549872|RPTPgamma	protein tyrosine phosphatase, receptor type, G	protein-coding
mm_99620.1	chr11	104633576	104633615	+	1	NA	exon (NM_016780, exon 4 of 15)	exon (NM_016780, exon 4 of 15)	25595	NM_016780	16416	Mm.87150	NM_016780	ENSMUSG00000020689	Itgb3	CD61|GP3A|INGRB3	integrin beta 3	protein-coding
mm_3929.1	chr1	162857243	162857248	+	1	NA	intron (NM_001330318, intron 2 of 4)	intron (NM_001330318, intron 2 of 4)	2755	NM_001330291	14261	Mm.976	NM_010231	ENSMUSG00000040181	Fmo1	-	flavin containing monooxygenase 1	protein-coding
mm_12161.1	chr2	62147829	62147873	+	1	NA	intron (NM_001242378, intron 1 of 25)	intron (NM_001242378, intron 1 of 25)	101336	NM_033552	94229	Mm.314497	NM_033552	ENSMUSG00000026904	Slc4a10	NCBE|mKIAA4136	solute carrier family 4, sodium bicarbonate cotransporter-like, member 10	protein-coding
mm_21554.1	chr2	164077903	164077909	-	1	NA	intron (NM_021420, intron 1 of 10)	intron (NM_021420, intron 1 of 10)	3728	NM_021420	58231	Mm.234472	NM_021420	ENSMUSG00000018209	Stk4	AI447339|AU020804|Kas-2|Mst1|Ysk3	serine/threonine kinase 4	protein-coding
mm_133600.1	chr16	91465166	91465193	+	1	NA	promoter-TSS (NR_077219)	promoter-TSS (NR_077219)	75	NR_077219	100503120	Mm.387130	NR_077219	ENSMUSG00000084866	A930006K02Rik	-	RIKEN cDNA A930006K02 gene	ncRNA
mm_147478.1	chr18	47247890	47247903	-	1	NA	3' UTR (NM_018744, exon 19 of 19)	3' UTR (NM_018744, exon 19 of 19)	120972	NM_018744	20358	Mm.40909	NM_018744	ENSMUSG00000019647	Sema6a	A730020P05Rik|AI851735|Sema6A-1|Semaq|VIa	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A	protein-coding
mm_44880.1	chr5	34637068	34637081	-	1	NA	promoter-TSS (NM_026660)	promoter-TSS (NM_026660)	40	NM_026660	68294	Mm.34564	NM_026660	ENSMUSG00000001082	Mfsd10	0610009O03Rik|Tetran	major facilitator superfamily domain containing 10	protein-coding
mm_167975.1	chrX	157711585	157711590	+	1	NA	intron (NR_045569, intron 3 of 6)	Lx9|LINE|L1	12614	NR_103722	66106	Mm.140340	NM_025357	ENSMUSG00000041476	Smpx	1010001C09Rik|Csl	small muscle protein, X-linked	protein-coding
mm_146470.1	chr18	88587463	88587479	+	1	NA	Intergenic	Intergenic	306736	NM_018821	54607	Mm.91920	NM_018821	ENSMUSG00000056153	Socs6	1500012M23Rik|5830401B18Rik|AI447482|Cis4|Cish4|HSPC060|SOCS-4|SOCS-6|SSI4|STAI4|STATI4|Socs4	suppressor of cytokine signaling 6	protein-coding
mm_89851.1	chr10	107271828	107271850	+	1	NA	promoter-TSS (NM_001039354)	promoter-TSS (NM_001039354)	8	NM_001033223	108030	Mm.268025	NM_001033223	ENSMUSG00000019906	Lin7a	AI848705|LIN-7A|MALS-1|TIP-33|Veli|Veli1	lin-7 homolog A (C. elegans)	protein-coding
mm_127182.1	chr15	98983941	98983951	+	1	NA	Intergenic	Intergenic	-2019	NR_045991	75951	Mm.441657	NR_045991	ENSMUSG00000097587	4930578M01Rik	3010001K12Rik	RIKEN cDNA 4930578M01 gene	ncRNA
mm_133474.1	chr16	89306927	89306937	+	1	NA	Intergenic	Intergenic	96842	NM_028621	170656	Mm.46109	NM_028621	ENSMUSG00000058368	Krtap21-1	1110017B05Rik|AI506979|KAP21.1|Krtap16-7	keratin associated protein 21-1	protein-coding
mm_172394.1	chr7	140891087	140891091	+	1	NA	intron (NM_011875, intron 9 of 12)	intron (NM_011875, intron 9 of 12)	8695	NM_011875	23997	Mm.29760	NM_011875	ENSMUSG00000025487	Psmd13	S11	proteasome (prosome, macropain) 26S subunit, non-ATPase, 13	protein-coding
mm_84989.1	chr9	86571119	86571130	-	1	NA	promoter-TSS (NM_001145969)	promoter-TSS (NM_001145969)	718	NM_001163746	109785	Mm.390201	NM_028352	ENSMUSG00000056131	Pgm3	2810473H05Rik|Agm1|BB187688|C77933|PAGM|Pgm-3	phosphoglucomutase 3	protein-coding
mm_36148.1	chr4	59475902	59475921	-	1	NA	3' UTR (NM_144904, exon 15 of 15)	3' UTR (NM_144904, exon 15 of 15)	-37278	NM_001163288	634731	Mm.483589	NM_001163288	ENSMUSG00000038578	Susd1	A530080P10|Gm12528|OTTMUSG00000007332	sushi domain containing 1	protein-coding
mm_76311.1	chr8	84661542	84661555	-	1	NA	3' UTR (NM_010499, exon 1 of 1)	3' UTR (NM_010499, exon 1 of 1)	1304	NM_010499	15936	Mm.399	NM_010499	ENSMUSG00000053560	Ier2	AI317238|Ch1|Pip92	immediate early response 2	protein-coding
mm_61134.1	chr7	55962521	55962552	+	1	NA	promoter-TSS (NM_023647)	promoter-TSS (NM_023647)	5	NR_015495	320845	Mm.274484	NM_001033396		A230056P14Rik	OTTMUSG00000027345	RIKEN cDNA A230056P14 gene	ncRNA
mm_109718.1	chr12	116055346	116055351	+	1	NA	intron (NM_001004066, intron 2 of 2)	intron (NM_001004066, intron 2 of 2)	7624	NM_019565	56220	Mm.254997	NM_019565	ENSMUSG00000042063	Zfp386	Kzf1|mKIAA4205	zinc finger protein 386 (Kruppel-like)	protein-coding
mm_156325.1	chrX	137709007	137709009	+	1	NA	intron (NM_030688, intron 2 of 10)	MYSERV16_I-int|LTR|ERVK	138254	NM_030688	60367	Mm.328321	NM_030688	ENSMUSG00000059203	Il1rapl2	-	interleukin 1 receptor accessory protein-like 2	protein-coding
mm_159657.1	chr4	148643293	148643293	+	1	NA	promoter-TSS (NM_001085505)	promoter-TSS (NM_001085505)	-24	NM_001085505	230909	Mm.332067	NM_001085505	ENSMUSG00000070577	Gm572	b2b1167Clo	predicted gene 572	protein-coding
mm_155650.1	chrX	85777011	85777020	+	1	NA	promoter-TSS (NM_212444)	promoter-TSS (NM_212444)	-196	NM_001294138	14933	Mm.246682	NM_008194	ENSMUSG00000025059	Gk	D930012N15Rik|Gyk	glycerol kinase	protein-coding
mm_105836.1	chr11	113650042	113650100	-	1	NA	intron (NM_013581, intron 1 of 13)	CpG	542	NM_013581	16834	Mm.261620	NM_013581	ENSMUSG00000018661	Cog1	6030445I15|Ldlb|mKIAA1381	component of oligomeric golgi complex 1	protein-coding
mm_90929.1	chr10	12868175	12868187	-	1	NA	Intergenic	Intergenic	-6446	NM_011682	22288	Mm.331784	NM_011682	ENSMUSG00000019820	Utrn	AA589569|DRP|Dmdl	utrophin	protein-coding
mm_35411.1	chr4	34806308	34806348	-	1	NA	exon (NM_013889, exon 8 of 8)	exon (NM_013889, exon 8 of 8)	-27962	NM_025471	66291	Mm.28071	NM_025471	ENSMUSG00000028295	Smim8	1810030N24Rik|2810406B13Rik	small integral membrane protein 8	protein-coding
mm_39677.1	chr5	25529968	25530049	+	1	NA	promoter-TSS (NR_027388)	promoter-TSS (NR_027388)	-10	NR_027388	73571	Mm.105263	NR_027388	ENSMUSG00000101856	1700096K18Rik	-	RIKEN cDNA 1700096K18 gene	ncRNA
mm_110354.1	chr12	39975034	39975037	-	1	NA	Intergenic	RLTR35B_MM|LTR|ERVL	62341	NM_007487	11861	Mm.12723	NM_007487	ENSMUSG00000047446	Arl4a	AI467555|Arl4	ADP-ribosylation factor-like 4A	protein-coding
mm_153519.1	chr19	41743645	41743662	-	1	NA	5' UTR (NM_015748, exon 1 of 37)	5' UTR (NM_015748, exon 1 of 37)	203	NM_015748	20562	Mm.39155	NM_015748	ENSMUSG00000025020	Slit1	Slil1|mKIAA0813	slit homolog 1 (Drosophila)	protein-coding
mm_158308.1	chrX	124109792	124109803	-	1	NA	Intergenic	Intergenic	26113	NM_001100616	100038941	Mm.388852	NM_001100616	ENSMUSG00000072049	Vmn2r121	EG625699	vomeronasal 2, receptor 121	protein-coding
mm_94782.1	chr11	21601142	21601144	+	1	NA	intron (NM_145425, intron 1 of 17)	ORR1A3|LTR|ERVL-MaLR	28862	NM_145425	216560	Mm.138090	NM_145425	ENSMUSG00000020319	Wdpcp	AV249152	WD repeat containing planar cell polarity effector	protein-coding
mm_17672.1	chr2	32236352	32236363	-	1	NA	promoter-TSS (NM_145145)	promoter-TSS (NM_145145)	-326	NM_145145	99011	Mm.31192	NM_145145	ENSMUSG00000039254	Pomt1	AI505244	protein-O-mannosyltransferase 1	protein-coding
mm_75916.1	chr8	71463601	71463680	-	1	NA	promoter-TSS (NM_022419)	promoter-TSS (NM_022419)	17	NM_022419	64296	Mm.276383	NM_022419	ENSMUSG00000007950	Abhd8	0910001L24Rik|AB030191	abhydrolase domain containing 8	protein-coding
mm_126475.1	chr15	81522339	81522391	+	1	NA	Intergenic	Intergenic	56049	NM_019712	56438	Mm.29405	NM_019712	ENSMUSG00000022400	Rbx1	1500002P15Rik|AA517855|ROC1	ring-box 1	protein-coding
mm_150716.1	chr19	43468381	43468383	+	1	NA	intron (NM_031396, intron 3 of 10)	intron (NM_031396, intron 3 of 10)	27946	NM_031396	83674	Mm.329864	NM_031396	ENSMUSG00000025189	Cnnm1	AI846314|Acdp1|CLP-1	cyclin M1	protein-coding
mm_54297.1	chr6	29380518	29380520	-	1	NA	promoter-TSS (NM_007538)	promoter-TSS (NM_007538)	-6	NM_007538	12057	Mm.56987	NM_007538	ENSMUSG00000058831	Opn1sw	AW551857|Bcp	opsin 1 (cone pigments), short-wave-sensitive (color blindness, tritan)	protein-coding
mm_139508.1	chr17	56304340	56304355	+	1	NA	promoter-TSS (NM_001111080)	promoter-TSS (NM_001111080)	34	NM_001111080	18140	Mm.42196	NM_010931	ENSMUSG00000001228	Uhrf1	AL022808|ICBP90|Np95|RNF106	ubiquitin-like, containing PHD and RING finger domains, 1	protein-coding
mm_100291.1	chr11	117813756	117813766	+	1	NA	3' UTR (NM_009304, exon 4 of 4)	3' UTR (NM_009304, exon 4 of 4)	4094	NM_009304	20973	Mm.468228	NM_009304	ENSMUSG00000048277	Syngr2	Clast2|cellugyrin	synaptogyrin 2	protein-coding
mm_147720.1	chr18	60822982	60822992	-	1	NA	exon (NM_011552, exon 17 of 25)	exon (NM_011552, exon 17 of 25)	10911	NR_039567	100628611		NR_039567	ENSMUSG00000093327	Mir5107	mir-5107|mmu-mir-5107|mu-mir-5107	microRNA 5107	ncRNA
mm_77162.1	chr8	111688488	111688497	-	1	NA	intron (NM_025583, intron 5 of 6)	intron (NM_025583, intron 5 of 6)	1182	NR_106044	102466993		NR_106044	ENSMUSG00000099129	Mir7076	Gm27318|mmu-mir-7076	microRNA 7076	ncRNA
mm_21656.1	chr2	164372736	164372759	-	1	NA	Intergenic	Intergenic	-16240	NM_011414	20568	Mm.371583	NM_011414	ENSMUSG00000017002	Slpi	-	secretory leukocyte peptidase inhibitor	protein-coding
mm_101390.1	chr11	24386033	24386033	-	1	NA	Intergenic	Intergenic	-95876	NR_045857	71316	Mm.79162	NR_045857	ENSMUSG00000086892	4933430M04Rik	-	RIKEN cDNA 4933430M04 gene	ncRNA
mm_108865.1	chr12	98950100	98950116	+	1	NA	intron (NM_029553, intron 6 of 13)	B4A|SINE|B4	29496	NM_198311	76260	Mm.282660	NM_029553	ENSMUSG00000021013	Ttc8	0610012F22Rik|AV001447|BBS8	tetratricopeptide repeat domain 8	protein-coding
mm_102625.1	chr11	62537250	62537253	-	1	NA	intron (NM_028448, intron 1 of 4)	intron (NM_028448, intron 1 of 4)	2010	NM_028448	73139	Mm.390409	NM_028448	ENSMUSG00000018509	Cenpv	3110013H01Rik|AA671303|Prr6	centromere protein V	protein-coding
mm_52063.1	chr6	97431495	97431512	+	1	NA	intron (NM_145148, intron 2 of 23)	intron (NM_145148, intron 2 of 23)	27783	NM_001346639	232288	Mm.27789	NM_145148	ENSMUSG00000030064	Frmd4b	6030440G05Rik|C87375|GOBLIN|GRSP1|R74720	FERM domain containing 4B	protein-coding
mm_132646.1	chr16	41020137	41020142	+	1	NA	Intergenic	T-rich|Low_complexity|Low_complexity	-512687	NM_001347236	268890	Mm.310524	NM_175548	ENSMUSG00000061080	Lsamp	5430428I19|AW046674|B130007O04Rik|D930023J12Rik|Lam|Lamp	limbic system-associated membrane protein	protein-coding
mm_2828.1	chr1	131153188	131153261	+	1	NA	promoter-TSS (NM_010709)	promoter-TSS (NM_010709)	17	NM_010709	16865	Mm.276294	NM_010709	ENSMUSG00000026427	Eif2d	D1Ertd5e|Lgtn	eukaryotic translation initiation factor 2D	protein-coding
mm_166105.1	chr4	146904958	146904970	-	1	NA	Intergenic	Intergenic	-116886	NM_001177767	100043034	Mm.422606	NM_001177767	ENSMUSG00000067919	Rex2	Gm13138|OTTMUSG00000010655	reduced expression 2	protein-coding
mm_62145.1	chr7	97101609	97101643	+	1	NA	intron (NM_001162477, intron 1 of 9)	B3A|SINE|B2	19875	NM_010248	14389	Mm.42033	NM_010248	ENSMUSG00000004508	Gab2	AI463667|D130058I17Rik|p97	growth factor receptor bound protein 2-associated protein 2	protein-coding
mm_1592.1	chr1	74352448	74352468	+	1	NA	3' UTR (NM_019999, exon 9 of 9)	3' UTR (NM_019999, exon 9 of 9)	-9650	NM_001033345	241112	Mm.310460	NM_001033345	ENSMUSG00000073650	Catip	Gm216	ciliogenesis associated TTC17 interacting protein	protein-coding
mm_88502.1	chr10	77852811	77852816	+	1	NA	promoter-TSS (NM_001162944)	promoter-TSS (NM_001162944)	-46	NM_001162944	622629	Mm.426393	NM_001162944		Gm10318	EG622629|ENSMUSG00000071195	predicted gene 10318	protein-coding
mm_27962.1	chr3	80688136	80688146	-	1	NA	3' UTR (NM_013540, exon 16 of 16)	3' UTR (NM_013540, exon 16 of 16)	114650	NM_013540	14800	Mm.220224	NM_013540	ENSMUSG00000033981	Gria2	GluA2|GluR-B|Glur-2|Glur2	glutamate receptor, ionotropic, AMPA2 (alpha 2)	protein-coding
mm_57340.1	chr6	124746942	124746958	-	1	NA	exon (NM_007881, exon 5 of 10)	exon (NM_007881, exon 5 of 10)	-5871	NM_013535	14790	Mm.439877	NM_013535	ENSMUSG00000072772	Grcc10	2310033H05Rik|C10	gene rich cluster, C10 gene	protein-coding
mm_134588.1	chr16	20426294	20426314	-	1	NA	promoter-TSS (NM_013790)	promoter-TSS (NM_013790)	90	NM_013790	27416	Mm.20845	NM_013790	ENSMUSG00000022822	Abcc5	2900011L11Rik|AI132311|Abcc5a|Abcc5b|Mrp5	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	protein-coding
mm_2102.1	chr1	87803898	87803906	+	1	NA	5' UTR (NM_009118, exon 1 of 16)	5' UTR (NM_009118, exon 1 of 16)	222	NM_009118	20215	Mm.1276	NM_009118	ENSMUSG00000056055	Sag	A930001K18Rik|Arr1|Irbp|arrestin	S-antigen, retina and pineal gland (arrestin)	protein-coding
mm_133421.1	chr16	86816905	86816920	+	1	NA	Intergenic	Intergenic	-537273	NM_001159331	67768	Mm.296532	NM_026366	ENSMUSG00000044442	N6amt1	5830445C04Rik|Hemk2|Pred28	N-6 adenine-specific DNA methyltransferase 1 (putative)	protein-coding
mm_56278.1	chr6	91116837	91116858	-	1	NA	promoter-TSS (NM_018815)	promoter-TSS (NM_018815)	-21	NM_018815	54563	Mm.28162	NM_018815	ENSMUSG00000030091	Nup210	9830001L10|AI836801|Pom210|gp190|gp210	nucleoporin 210	protein-coding
mm_123448.1	chr14	65174925	65174934	-	1	NA	Intergenic	MLTR73|LTR|ERV1	-76823	NM_018788	54616	Mm.103748	NM_018788	ENSMUSG00000021978	Extl3	2900009G18Rik|AU040105|Ext1l|mKIAA0519	exostoses (multiple)-like 3	protein-coding
mm_149731.1	chr19	21851418	21851430	+	1	NA	intron (NM_001033759, intron 21 of 23)	RCHARR1|DNA|hAT-Charlie	73084	NM_031997	83921	Mm.329776	NM_031997	ENSMUSG00000024754	Tmem2	-	transmembrane protein 2	protein-coding
mm_167696.1	chr9	88523048	88523096	+	1	NA	promoter-TSS (NR_040721)	promoter-TSS (NR_040721)	-175	NR_040721	72655	Mm.21798	NR_040721	ENSMUSG00000097195	Snhg5	2810026P18Rik|4933428I09Rik|mU50HG-b	small nucleolar RNA host gene 5	ncRNA
mm_132007.1	chr16	25802044	25802056	+	1	NA	5' UTR (NM_001127262, exon 1 of 11)	5' UTR (NM_001127262, exon 1 of 11)	134	NM_001127264	22061	Mm.20894	NM_011641	ENSMUSG00000022510	Trp63	AI462811|Ket|P51/P63|P63|P73l|Tp63|Trp53rp1	transformation related protein 63	protein-coding
mm_50825.1	chr6	54595273	54595292	+	1	NA	5' UTR (NM_001164361, exon 1 of 14)	5' UTR (NM_001164361, exon 1 of 14)	171	NM_001164361	231999	Mm.35416	NM_001001335	ENSMUSG00000005225	Plekha8	6330400G01|AA517676|BC052360|Fapp-2|Fapp2	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 8	protein-coding
mm_70940.1	chr8	26082604	26082625	+	1	NA	promoter-TSS (NR_110583)	promoter-TSS (NR_110583)	5	NR_110583	76604	Mm.437190	NR_110583	ENSMUSG00000085437	1700047A11Rik	4930554C15Rik	RIKEN cDNA 1700047A11 gene	ncRNA
mm_90345.1	chr10	127149373	127149380	+	1	NA	Intergenic	RMER6BA|LTR|ERVK	-15780	NR_045166	14421	Mm.386762	NM_008080	ENSMUSG00000006731	B4galnt1	4933429D13Rik|Gal-NAc-T|GalNAc-T|GalNAcT|Galgt1|Ggm-2|Ggm2	beta-1,4-N-acetyl-galactosaminyl transferase 1	protein-coding
mm_36970.1	chr4	109476429	109476437	-	1	NA	promoter-TSS (NM_013876)	promoter-TSS (NM_013876)	72	NM_013876	29864	Mm.392580	NM_013876	ENSMUSG00000028557	Rnf11	-	ring finger protein 11	protein-coding
mm_23998.1	chr3	86551757	86551783	+	1	NA	intron (NM_001077687, intron 40 of 50)	intron (NM_001077687, intron 40 of 50)	-3487	NM_011839	23937	Mm.389466	NM_011839	ENSMUSG00000057777	Mab21l2	-	mab-21-like 2 (C. elegans)	protein-coding
mm_36113.1	chr4	58885473	58885502	-	1	NA	exon (NM_172381, exon 2 of 49)	exon (NM_172381, exon 2 of 49)	27238	NM_172381	230249	Mm.234801	NM_172381	ENSMUSG00000050812	AI314180	AW558785|BB181316|mKIAA0368	expressed sequence AI314180	protein-coding
mm_44951.1	chr5	36586240	36586248	-	1	NA	promoter-TSS (NM_001113362)	promoter-TSS (NM_001113362)	-18	NM_001113362	100855	Mm.486203	NM_133910	ENSMUSG00000029192	Tbc1d14	2810413P16Rik|AU043625|C86258|D5Ertd110e|mKIAA1322	TBC1 domain family, member 14	protein-coding
mm_80124.1	chr9	70579318	70579331	+	1	NA	exon (NM_025690, exon 10 of 21)	exon (NM_025690, exon 10 of 21)	36454	NM_025690	66660	Mm.22379	NM_025690	ENSMUSG00000032212	Sltm	5730455C01Rik|5730555F13Rik|9130215G10Rik|Met	SAFB-like, transcription modulator	protein-coding
mm_72738.1	chr8	85085412	85085423	+	1	NA	exon (NM_010764, exon 4 of 24)	exon (NM_010764, exon 4 of 24)	2148	NM_010764	17159	Mm.4219	NM_010764	ENSMUSG00000005142	Man2b1	AW107687|LAMAN	mannosidase 2, alpha B1	protein-coding
mm_66353.1	chr7	43527527	43527563	-	1	NA	TTS (NM_001111058)	TTS (NM_001111058)	5626	NM_001111058	12489	Mm.140157	NM_021293	ENSMUSG00000004609	Cd33	Siglec-3|gp67	CD33 antigen	protein-coding
mm_156890.1	chrX	166510184	166510223	+	1	NA	intron (NM_001007577, intron 1 of 4)	CpG	275	NM_001007577	245695	Mm.336318	NM_001007577	ENSMUSG00000051224	Tceanc	A630018P17Rik|Gm390	transcription elongation factor A (SII) N-terminal and central domain containing	protein-coding
mm_65740.1	chr7	28436235	28436245	-	1	NA	promoter-TSS (NM_175021)	promoter-TSS (NM_175021)	-49	NM_175021	233033	Mm.54120	NM_175021	ENSMUSG00000109336	Samd4b	BC042901	sterile alpha motif domain containing 4B	protein-coding
mm_90.1	chr1	7089188	7089200	+	1	NA	5' UTR (NM_183028, exon 1 of 6)	5' UTR (NM_183028, exon 1 of 6)	274	NM_183028	319263	Mm.21539	NM_183028	ENSMUSG00000051285	Pcmtd1	8430411F12Rik|A030012M09Rik	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding
mm_21563.1	chr2	164182730	164182766	-	1	NA	promoter-TSS (NM_145369)	promoter-TSS (NM_145369)	-6	NM_145369	209232	Mm.218273	NM_145369	ENSMUSG00000040154	Wfdc5	BC019734|Prg5|Wap1	WAP four-disulfide core domain 5	protein-coding
mm_157398.1	chrX	38420893	38420911	-	1	NA	3' UTR (NM_010685, exon 9 of 9)	3' UTR (NM_010685, exon 9 of 9)	35558	NM_010685	16784	Mm.486	NM_010685	ENSMUSG00000016534	Lamp2	CD107b|LGP-B|Lamp II|Lamp-2|Lamp-2a|Lamp-2b|Lamp-2c|Mac3	lysosomal-associated membrane protein 2	protein-coding
mm_120898.1	chr14	75846144	75846147	+	1	NA	intron (NM_009429, intron 2 of 5)	intron (NM_009429, intron 2 of 5)	889	NM_009429	22070	Mm.297482	NM_009429	ENSMUSG00000060126	Tpt1	TCTP|Trt|p21|p23	tumor protein, translationally-controlled 1	protein-coding
mm_120032.1	chr14	55854126	55854206	+	1	NA	promoter-TSS (NM_001040072)	promoter-TSS (NM_001040072)	51	NM_001040072	277154	Mm.319347	NM_001040072	ENSMUSG00000075592	Nynrin	AA409373|C80530|mKIAA1305	NYN domain and retroviral integrase containing	protein-coding
mm_35620.1	chr4	43452590	43452613	-	1	NA	exon (NM_001110320, exon 5 of 9)	exon (NM_001110320, exon 5 of 9)	2025	NM_001110320	12517	Mm.188157	NM_007654	ENSMUSG00000028459	Cd72	CD72c|Ly-19|Ly-32|Ly-m19|Lyb-2	CD72 antigen	protein-coding
mm_32532.1	chr4	109000607	109000706	+	1	NA	promoter-TSS (NM_146150)	promoter-TSS (NM_146150)	1	NM_001346554	230598	Mm.274950	NM_146150	ENSMUSG00000053510	Nrd1	2600011I06Rik|AI875733|NRD-C|Nrdc	nardilysin, N-arginine dibasic convertase, NRD convertase 1	protein-coding
mm_102014.1	chr11	51606891	51606895	-	1	NA	promoter-TSS (NM_010448)	promoter-TSS (NM_010448)	-12	NM_010448	15384	Mm.256875	NM_010448	ENSMUSG00000020358	Hnrnpab	3010025C11Rik|CBF-A|Cgbfa|Hnrpab	heterogeneous nuclear ribonucleoprotein A/B	protein-coding
mm_127457.1	chr15	101271800	101271813	+	1	NA	exon (NM_010444, exon 3 of 7)	exon (NM_010444, exon 3 of 7)	4960	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_127177.1	chr15	98953745	98953769	+	1	NA	promoter-TSS (NM_011653)	promoter-TSS (NM_011653)	-256	NM_011653	22142	Mm.405359	NM_011653	ENSMUSG00000072235	Tuba1a	Tuba-1|Tuba1	tubulin, alpha 1A	protein-coding
mm_139113.1	chr17	47385414	47385439	+	1	NA	promoter-TSS (NM_146079)	promoter-TSS (NM_146079)	33	NM_146079	107477	Mm.59151	NM_146079	ENSMUSG00000023979	Guca1b	BC018258|GCAP2	guanylate cyclase activator 1B	protein-coding
mm_154061.1	chr19	55127248	55127257	-	1	NA	Intergenic	Intergenic	-27805	NM_008149	14732	Mm.210196	NM_008149	ENSMUSG00000024978	Gpam	GPAT|GPAT1	glycerol-3-phosphate acyltransferase, mitochondrial	protein-coding
mm_66546.1	chr7	45210431	45210451	-	1	NA	exon (NM_015789, exon 3 of 5)	exon (NM_015789, exon 3 of 5)	1442	NM_015789	50722	Mm.27287	NM_015789	ENSMUSG00000030792	Dkkl1	AI414495|SGY|SGY-1|SGY1|Soggy|mSgy	dickkopf-like 1	protein-coding
mm_144660.1	chr18	34313186	34313202	+	1	NA	exon (NM_007462, exon 16 of 16)	exon (NM_007462, exon 16 of 16)	-17951	NM_025527	66384	Mm.29452	NM_025527	ENSMUSG00000014504	Srp19	2310020D23Rik	signal recognition particle 19	protein-coding
mm_103831.1	chr11	83020220	83020231	-	1	NA	intron (NM_181545, intron 1 of 5)	intron (NM_181545, intron 1 of 5)	497	NM_001167743	276950	Mm.491599	NM_181545	ENSMUSG00000035208	Slfn8	-	schlafen 8	protein-coding
mm_125586.1	chr15	59618286	59618295	+	1	NA	Intergenic	MTEb|LTR|ERVL-MaLR	-30364	NM_144549	211770	Mm.40298	NM_144549	ENSMUSG00000032501	Trib1	A530090O15Rik|TRB-1|Trb1	tribbles pseudokinase 1	protein-coding
mm_30651.1	chr4	8842378	8842381	+	1	NA	intron (NM_001277149, intron 19 of 37)	L1M5|LINE|L1	151973	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_4707.1	chr1	180904741	180904783	+	1	NA	exon (NM_133705, exon 2 of 7)	exon (NM_133705, exon 2 of 7)	488	NM_133705	69051	Mm.274180	NM_133705	ENSMUSG00000026520	Pycr2	1810018M05Rik|P5cr2	pyrroline-5-carboxylate reductase family, member 2	protein-coding
mm_48477.1	chr5	141000559	141000589	-	1	NA	promoter-TSS (NM_175362)	promoter-TSS (NM_175362)	22	NM_175362	108723	Mm.46187	NM_175362	ENSMUSG00000036526	Card11	0610008L17Rik|2410011D02Rik|BIMP3|CARMA1	caspase recruitment domain family, member 11	protein-coding
mm_165424.1	chr2	151974229	151974235	-	1	NA	promoter-TSS (NM_001289151)	promoter-TSS (NM_001289151)	-251	NM_028666	73847	Mm.272444	NM_028666	ENSMUSG00000027459	Fam110a	1700008J10Rik|5430432M24Rik|AI747080	family with sequence similarity 110, member A	protein-coding
mm_98858.1	chr11	97683107	97683111	+	1	NA	3' UTR (NM_139311, exon 20 of 20)	3' UTR (NM_139311, exon 20 of 20)	-2843	NM_001085500	217149	Mm.29659	NM_001085500	ENSMUSG00000078695	Cisd3	Mel-13|Mel13	CDGSH iron sulfur domain 3	protein-coding
mm_99805.1	chr11	107995406	107995411	+	1	NA	intron (NM_011101, intron 8 of 16)	intron (NM_011101, intron 8 of 16)	-1440	NR_106082	102465705		NR_106082	ENSMUSG00000098989	Mir7223	Gm28009|mmu-mir-7223	microRNA 7223	ncRNA
mm_55666.1	chr6	72520632	72520643	-	1	NA	Intergenic	Intergenic	-23754	NM_007599	12332	Mm.18626	NM_007599	ENSMUSG00000056737	Capg	gCap39|mbh1	capping protein (actin filament), gelsolin-like	protein-coding
mm_96040.1	chr11	59556489	59556500	+	1	NA	intron (NM_145827, intron 6 of 9)	ID_B1|SINE|B4	13808	NM_145827	216799	Mm.54174	NM_145827	ENSMUSG00000032691	Nlrp3	AGTAVPRL|AII/AVP|Cias1|FCAS|FCU|MWS|Mmig1|NALP3|Pypaf1	NLR family, pyrin domain containing 3	protein-coding
mm_102819.1	chr11	69008423	69008477	-	1	NA	promoter-TSS (NM_001159519)	promoter-TSS (NM_001159519)	10	NM_001159519	237823	Mm.340288	NM_001159519	ENSMUSG00000020899	Pfas	4432409B16Rik|FGAMS|FGAR-AT|FGARAT|Gm18|PURL|Sofa	phosphoribosylformylglycinamidine synthase (FGAR amidotransferase)	protein-coding
mm_58236.1	chr6	145047506	145047523	-	1	NA	intron (NM_007532, intron 1 of 10)	intron (NM_007532, intron 1 of 10)	1298	NM_001024468	12035	Mm.4606	NM_007532	ENSMUSG00000030268	Bcat1	BCATc|Eca39	branched chain aminotransferase 1, cytosolic	protein-coding
mm_137220.1	chr17	24171564	24171565	+	1	NA	Intergenic	Intergenic	-2135	NM_009729	11984	Mm.30155	NM_009729	ENSMUSG00000024121	Atp6v0c	Atp6c|Atp6c2|Atp6l|Atpl|Atpl-rs1|PL16|VATL|Vma3	ATPase, H+ transporting, lysosomal V0 subunit C	protein-coding
mm_103138.1	chr11	70238373	70238388	-	1	NA	promoter-TSS (NM_001177601)	promoter-TSS (NM_001177601)	-466	NM_145758	104457	Mm.30016	NM_026757	ENSMUSG00000020831	0610010K14Rik	1110020A23Rik|AL033328|AU045833|Bap18	RIKEN cDNA 0610010K14 gene	protein-coding
mm_60277.1	chr7	43950615	43950647	+	1	NA	promoter-TSS (NM_008457)	promoter-TSS (NM_008457)	-35	NM_008457	16624	Mm.435488	NM_008457	ENSMUSG00000063089	Klk1b8	Klk8|Nrpn|TADG14|kallikrein|mGK-8	kallikrein 1-related peptidase b8	protein-coding
mm_120329.1	chr14	63317714	63317731	+	1	NA	Intergenic	Intergenic	-72451	NM_001310610	14463	Mm.247669	NM_008092	ENSMUSG00000021944	Gata4	Gata-4	GATA binding protein 4	protein-coding
mm_91101.1	chr10	19065296	19065310	-	1	NA	Intergenic	Intergenic	-49893	NM_009397	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_107349.1	chr12	32820438	32820486	+	1	NA	5' UTR (NM_021524, exon 1 of 11)	5' UTR (NM_021524, exon 1 of 11)	127	NM_021524	59027	Mm.202727	NM_021524	ENSMUSG00000020572	Nampt	1110035O14Rik|AI314458|AI480535|NAmPRTase|Pbef|Pbef1|Visfatin	nicotinamide phosphoribosyltransferase	protein-coding
mm_42475.1	chr5	115466153	115466159	+	1	NA	promoter-TSS (NM_011107)	promoter-TSS (NM_011107)	-110	NM_011107	18778	Mm.20190	NM_011107	ENSMUSG00000029522	Pla2g1b	Pla2a|sPLA2IB	phospholipase A2, group IB, pancreas	protein-coding
mm_22103.1	chr2	169686888	169686892	-	1	NA	intron (NM_080455, intron 1 of 1)	intron (NM_080455, intron 1 of 1)	53244	NM_080455	228911	Mm.315789	NM_080455	ENSMUSG00000047907	Tshz2	2900073F20Rik|B830045G17|Mtsh2|Sdccag33l|Tsh2|Zfp218|mKIAA4248|teashirt2	teashirt zinc finger family member 2	protein-coding
mm_24018.1	chr3	87525647	87525667	+	1	NA	promoter-TSS (NM_012051)	promoter-TSS (NM_012051)	79	NM_012051	27049	Mm.219460	NM_012051	ENSMUSG00000003382	Etv3	AI414410|METS|Pe1	ets variant 3	protein-coding
mm_68008.1	chr7	100939028	100939049	-	1	NA	exon (NM_183168, exon 3 of 3)	exon (NM_183168, exon 3 of 3)	-6877	NM_001081116	207212	Mm.29954	NM_001081116	ENSMUSG00000032875	Arhgef17	8030463K16|AI428794|AW558066|BC035332|mKIAA0337	Rho guanine nucleotide exchange factor (GEF) 17	protein-coding
mm_111528.1	chr12	100239528	100239564	-	1	NA	Intergenic	MLT1H|LTR|ERVL-MaLR	-37063	NR_045741	100038713	Mm.470751	NR_045741		Gm10432	ENSMUSG00000072882	predicted gene 10432	ncRNA
mm_90227.1	chr10	121316771	121316776	+	1	NA	Intergenic	Intergenic	-5584	NM_029057	74694	Mm.233833	NM_029057	ENSMUSG00000052302	Tbc1d30	4930505D03Rik	TBC1 domain family, member 30	protein-coding
mm_19124.1	chr2	80129014	80129023	-	1	NA	promoter-TSS (NM_016744)	promoter-TSS (NM_016744)	-47	NM_016744	18573	Mm.40678	NM_016744	ENSMUSG00000059173	Pde1a	AI987702|AW125737	phosphodiesterase 1A, calmodulin-dependent	protein-coding
mm_4499.1	chr1	173673703	173673710	+	1	NA	promoter-TSS (NM_001162938)	promoter-TSS (NM_001162938)	26	NM_001162938	100033459	Mm.303377	NM_001162938	ENSMUSG00000066677	Ifi208	9830148g24rik|E430029J22Rik|Pydc3|Pyr-rv1	interferon activated gene 208	protein-coding
mm_129250.1	chr15	76669812	76669820	-	1	NA	exon (NM_007989, exon 1 of 3)	exon (NM_007989, exon 1 of 3)	132	NM_007989	14106	Mm.42011	NM_007989	ENSMUSG00000033837	Foxh1	Fast1|Fast2|fast-1|fast-2	forkhead box H1	protein-coding
mm_165403.1	chr2	137528352	137528352	+	1	NA	Intergenic	Intergenic	-411832	NM_013822	16449	Mm.22398	NM_013822	ENSMUSG00000027276	Jag1	ABE2|Gsfabe2|Htu|Ozz|Ser-1	jagged 1	protein-coding
mm_159135.1	chr2	76687072	76687072	+	1	NA	intron (NM_031256, intron 4 of 7)	RLTR20A|LTR|ERVK	11757	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_37692.1	chr4	129248416	129248430	-	1	NA	promoter-TSS (NM_001033189)	promoter-TSS (NM_001033189)	20	NM_001033189	97130	Mm.331907	NM_001033189	ENSMUSG00000050390	C77080	Kiaa1522|mKIAA1522	expressed sequence C77080	protein-coding
mm_170950.1	chr2	53191287	53191292	-	1	NA	promoter-TSS (NM_018785)	promoter-TSS (NM_018785)	-102	NM_018785	56194	Mm.257474	NM_018785	ENSMUSG00000061136	Prpf40a	2810012K09Rik|FBP-11|FBP11|Fnbp11|Fnbp3	pre-mRNA processing factor 40A	protein-coding
mm_167014.1	chr7	63127130	63127132	+	1	NA	intron (NM_007390, intron 4 of 9)	L1MDa|LINE|L1	85395	NM_007390	11441	Mm.113464	NM_007390	ENSMUSG00000030525	Chrna7	Acra7|alpha7|nAchR	cholinergic receptor, nicotinic, alpha polypeptide 7	protein-coding
mm_164582.1	chr17	25736215	25736240	+	1	NA	5' UTR (NM_177822, exon 1 of 16)	5' UTR (NM_177822, exon 1 of 16)	187	NM_177822	328783	Mm.183275	NM_177822	ENSMUSG00000041062	Mslnl	4732467B22	mesothelin-like	protein-coding
mm_27281.1	chr3	41493178	41493202	-	1	NA	promoter-TSS (NR_040385)	promoter-TSS (NR_040385)	9	NR_040385	78706	Mm.366094	NR_040385	ENSMUSG00000097639	Platr4	C430002E04Rik	pluripotency associated transcript 4	ncRNA
mm_166535.1	chr6	30639976	30640011	+	1	NA	exon (NM_025350, exon 2 of 10)	exon (NM_025350, exon 2 of 10)	775	NM_025350	109697	Mm.25377	NM_025350	ENSMUSG00000054446	Cpa1	0910001L12Rik|Cpa	carboxypeptidase A1, pancreatic	protein-coding
mm_124058.1	chr14	77904395	77904403	-	1	NA	5' UTR (NM_029495, exon 1 of 12)	5' UTR (NM_029495, exon 1 of 12)	160	NM_029495	108670	Mm.68134	NM_029495	ENSMUSG00000022014	Epsti1	2310046K10Rik|5033415K03Rik|BRESI1	epithelial stromal interaction 1 (breast)	protein-coding
mm_42399.1	chr5	114942217	114942223	+	1	NA	promoter-TSS (NM_028211)	promoter-TSS (NM_028211)	18	NM_028211	72357	Mm.292672	NM_028211	ENSMUSG00000029559	2210016L21Rik	-	RIKEN cDNA 2210016L21 gene	protein-coding
mm_51486.1	chr6	83054723	83054739	+	1	NA	promoter-TSS (NM_019752)	promoter-TSS (NM_019752)	-160	NM_019752	64704	Mm.21880	NM_019752	ENSMUSG00000068329	Htra2	AI481710|Omi|Prss25|mnd2	HtrA serine peptidase 2	protein-coding
mm_153914.1	chr19	47205736	47205736	-	1	NA	intron (NM_021360, intron 1 of 5)	intron (NM_021360, intron 1 of 5)	-23107	NM_001163480	18011	Mm.313651	NM_021360	ENSMUSG00000006435	Neurl1a	2410129E16Rik|AI450910|AI481072|Neu1|Neur1|Neurl|Neurl1|Nlz|Rnf67	neuralized E3 ubiquitin protein ligase 1A	protein-coding
mm_144296.1	chr18	12256183	12256206	+	1	NA	intron (NM_001190371, intron 9 of 9)	Charlie1a|DNA|hAT-Charlie	-19808	NM_008720	18145	Mm.3484	NM_008720	ENSMUSG00000024413	Npc1	A430089E03Rik|C85354|D18Ertd139e|D18Ertd723e|lcsd|nmf164|spm	Niemann-Pick type C1	protein-coding
mm_135675.1	chr16	52419911	52419919	-	1	NA	intron (NM_009655, intron 1 of 15)	intron (NM_009655, intron 1 of 15)	33166	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_115931.1	chr13	23574200	23574229	-	1	NA	promoter-TSS (NM_178188)	promoter-TSS (NM_178188)	-24	NM_178195	319180		NM_178195	ENSMUSG00000069268	Hist1h2bf	-	histone cluster 1, H2bf	protein-coding
mm_90254.1	chr10	122198770	122198774	+	1	NA	Intergenic	Intergenic	79075	NR_027637	100043513	Mm.429141	NR_027637		Gm4489	Gm241	predicted gene 4489	ncRNA
mm_126441.1	chr15	80671649	80671677	+	1	NA	promoter-TSS (NM_145986)	promoter-TSS (NM_145986)	-184	NM_145986	213956	Mm.132439	NM_145986	ENSMUSG00000022408	Fam83f	AW544981	family with sequence similarity 83, member F	protein-coding
mm_45459.1	chr5	67784213	67784223	-	1	NA	intron (NM_001284345, intron 6 of 36)	intron (NM_001284345, intron 6 of 36)	63213	NM_009727	11980	Mm.153230	NM_009727	ENSMUSG00000037685	Atp8a1	AI481521|AI853962|APLT|AW743152|AW822227|Atp3a2|B230107D19Rik|ClassI	ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1	protein-coding
mm_13037.1	chr2	91081377	91081393	+	1	NA	Intergenic	Intergenic	-11070	NM_001290765	68427	Mm.192375	NM_026721	ENSMUSG00000002105	Slc39a13	1100001L14Rik|AA387663|ZIP-13|ZIP13	solute carrier family 39 (metal ion transporter), member 13	protein-coding
mm_43103.1	chr5	124483472	124483491	+	1	NA	intron (NM_029532, intron 1 of 1)	CpG	326	NM_029532	76167	Mm.156035	NM_029532	ENSMUSG00000029402	Snrnp35	6330548G22Rik	small nuclear ribonucleoprotein 35 (U11/U12)	protein-coding
mm_133478.1	chr16	89826124	89826146	+	1	NA	intron (NM_009384, intron 15 of 27)	intron (NM_009384, intron 15 of 27)	-7783	NM_001145887	21844	Mm.310902	NM_009384	ENSMUSG00000002489	Tiam1	AI847750|D16Ium10|D16Ium10e	T cell lymphoma invasion and metastasis 1	protein-coding
mm_3786.1	chr1	156838916	156838978	+	1	NA	promoter-TSS (NM_028333)	promoter-TSS (NM_028333)	-76	NM_028333	72713	Mm.389206	NM_028333	ENSMUSG00000033544	Angptl1	2810039D03Rik|ANG3|ANGPT3|ANGY|ARP1	angiopoietin-like 1	protein-coding
mm_41666.1	chr5	99336761	99336768	+	1	NA	intron (NR_030692, intron 3 of 3)	intron (NR_030692, intron 3 of 3)	-83837	NM_145839	320292	Mm.259074	NM_145839	ENSMUSG00000089809	Rasgef1b	4732452O09Rik|GPIgamma4|Gpig4	RasGEF domain family, member 1B	protein-coding
mm_168381.1	chr11	23256209	23256213	+	1	NA	intron (NM_001035226, intron 1 of 25)	CpG	170	NM_134014	103573	Mm.217547	NM_134014	ENSMUSG00000020290	Xpo1	AA420417|Crm1|Exp1	exportin 1	protein-coding
mm_148010.1	chr18	68231081	68231094	-	1	NA	intron (NM_172631, intron 3 of 5)	intron (NM_172631, intron 3 of 5)	29886	NR_106078	102465702		NR_106078	ENSMUSG00000098253	Mir7219	Gm27613|mmu-mir-7219	microRNA 7219	ncRNA
mm_86152.1	chr9	117588674	117588675	-	1	NA	intron (NM_001172121, intron 1 of 14)	intron (NM_001172121, intron 1 of 14)	41239	NM_001172121	207181	Mm.326411	NM_178660	ENSMUSG00000039607	Rbms3	6720477E09Rik|8430436O14Rik	RNA binding motif, single stranded interacting protein	protein-coding
mm_43512.1	chr5	137046143	137046178	+	1	NA	promoter-TSS (NM_007457)	promoter-TSS (NM_007457)	-100	NM_007457	11769	Mm.833	NM_007457	ENSMUSG00000004849	Ap1s1	AP19	adaptor protein complex AP-1, sigma 1	protein-coding
mm_6836.1	chr1	84230546	84230553	-	1	NA	intron (NM_001003948, intron 1 of 2)	MTD|LTR|ERVL-MaLR	-11588	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_28444.1	chr3	90509457	90509506	-	1	NA	promoter-TSS (NM_001293782)	promoter-TSS (NM_001293782)	17	NM_001293776	66511	Mm.154136	NM_023215	ENSMUSG00000001017	Chtop	2500003M10Rik|Fop|Srag	chromatin target of PRMT1	protein-coding
mm_133632.1	chr16	91651747	91651777	+	1	NA	exon (NM_019973, exon 2 of 5)	exon (NM_019973, exon 2 of 5)	3938	NM_178880	20658	Mm.46401	NM_019973	ENSMUSG00000022961	Son	2900011L12Rik|AA409051|AU067731|C81487|mKIAA1019|nrebp	Son DNA binding protein	protein-coding
mm_142371.1	chr17	44654426	44654465	-	1	NA	intron (NM_001271631, intron 2 of 4)	intron (NM_001271631, intron 2 of 4)	81731	NR_073425	12393	Mm.391013	NM_009820	ENSMUSG00000039153	Runx2	AML3|Cbf|Cbfa-1|Cbfa1|LS3|Osf2|PEBP2aA|Pebp2a1|Pebpa2a	runt related transcription factor 2	protein-coding
mm_35668.1	chr4	43562479	43562497	-	1	NA	promoter-TSS (NM_013497)	promoter-TSS (NM_013497)	95	NM_011602	21894	Mm.208601	NM_011602	ENSMUSG00000028465	Tln1	Tln	talin 1	protein-coding
mm_165924.1	chr4	63214025	63214037	+	1	NA	Intergenic	CpG	-1381	NM_025685	373864	Mm.194116	NM_025685	ENSMUSG00000045672	Col27a1	5730512J02Rik|AI449266	collagen, type XXVII, alpha 1	protein-coding
mm_144154.1	chr18	5593348	5593351	+	1	NA	promoter-TSS (NR_033552)	promoter-TSS (NR_033552)	-912	NR_033552	791318	Mm.84339	NR_033552	ENSMUSG00000063087	Gm10125	ENSMUSG00000063087|Zeb1os	predicted gene 10125	ncRNA
mm_85309.1	chr9	101034893	101034904	-	1	NA	promoter-TSS (NM_001311149)	promoter-TSS (NM_001311149)	-14	NM_025835	66904	Mm.335385	NM_025835	ENSMUSG00000032527	Pccb	1300012P06Rik|AI314687|R74805	propionyl Coenzyme A carboxylase, beta polypeptide	protein-coding
mm_137922.1	chr17	32492169	32492199	+	1	NA	intron (NM_177307, intron 13 of 13)	MIRb|SINE|MIR	-14278	NM_001101445	208285	Mm.311422	NM_001101445	ENSMUSG00000091586	Cyp4f17	EG208285	cytochrome P450, family 4, subfamily f, polypeptide 17	protein-coding
mm_117133.1	chr13	60939407	60939415	-	1	NA	3' UTR (NM_009411, exon 5 of 5)	3' UTR (NM_009411, exon 5 of 5)	2524	NM_009411	21984	Mm.2372	NM_009411	ENSMUSG00000033834	Tpbpa	AV033951|Tb-1|Tb1|Tpbp|b2b1247Clo	trophoblast specific protein alpha	protein-coding
mm_173118.1	chrX	161546749	161546753	-	1	NA	Intergenic	L1Md_T|LINE|L1	-170285	NM_001103367	24004	Mm.328503	NM_198409	ENSMUSG00000043518	Rai2	3f8	retinoic acid induced 2	protein-coding
mm_143598.1	chr17	75518394	75518422	-	1	NA	intron (NM_001166493, intron 13 of 16)	intron (NM_001166493, intron 13 of 16)	33538	NM_133747	72722	Mm.24641	NM_133747	ENSMUSG00000002017	Fam98a	2810405J04Rik|AL024114	family with sequence similarity 98, member A	protein-coding
mm_149852.1	chr19	25075597	25075600	+	1	NA	intron (NM_028785, intron 4 of 47)	intron (NM_028785, intron 4 of 47)	76069	NM_028785	76088	Mm.102485	NM_028785	ENSMUSG00000052085	Dock8	1200017A24Rik|5830472H07Rik|A130095G14Rik|AI461977	dedicator of cytokinesis 8	protein-coding
mm_166274.1	chr5	90490816	90490820	+	1	NA	exon (NM_007423, exon 1 of 15)	exon (NM_007423, exon 1 of 15)	104	NM_007423	11576	Mm.358570	NM_007423	ENSMUSG00000054932	Afp	-	alpha fetoprotein	protein-coding
mm_76946.1	chr8	105979404	105979412	-	1	NA	promoter-TSS (NM_027960)	promoter-TSS (NM_027960)	11	NM_027960	71854	Mm.173395	NM_027960	ENSMUSG00000031898	Dpep3	1700018F16Rik|AI507039|MBD-3|MLZ-136	dipeptidase 3	protein-coding
mm_43185.1	chr5	128600801	128600816	+	1	NA	promoter-TSS (NM_175284)	promoter-TSS (NM_175284)	-121	NR_015517	319616	Mm.387738	NR_015517	ENSMUSG00000072591	5930412G12Rik	-	RIKEN cDNA 5930412G12 gene	ncRNA
mm_156185.1	chrX	133908419	133908430	+	1	NA	promoter-TSS (NM_026838)	promoter-TSS (NM_026838)	-1	NM_026838	68792	Mm.263553	NM_026838	ENSMUSG00000031253	Srpx2	1110039C07Rik|SRP|SRPUL	sushi-repeat-containing protein, X-linked 2	protein-coding
mm_78576.1	chr9	36767882	36767892	+	1	NA	promoter-TSS (NM_008408)	promoter-TSS (NM_008408)	-309	NM_008408	16430	Mm.2863	NM_008408	ENSMUSG00000032116	Stt3a	AA408947|BB081708|Itm1	STT3, subunit of the oligosaccharyltransferase complex, homolog A (S. cerevisiae)	protein-coding
mm_13740.1	chr2	118118242	118118264	+	1	NA	exon (NM_011580, exon 9 of 22)	exon (NM_011580, exon 9 of 22)	6377	NM_001313914	21825	Mm.4159	NM_011580	ENSMUSG00000040152	Thbs1	TSP-1|TSP1|Thbs-1|tbsp1	thrombospondin 1	protein-coding
mm_8098.1	chr1	135848054	135848087	-	1	NA	exon (NM_001130176, exon 7 of 13)	exon (NM_001130176, exon 7 of 13)	7209	NM_001130176	21956	Mm.247470	NM_011619	ENSMUSG00000026414	Tnnt2	Tnt|cTnT	troponin T2, cardiac	protein-coding
mm_164316.1	chr15	103899539	103899545	-	1	NA	promoter-TSS (NM_009268)	promoter-TSS (NM_009268)	-230	NM_009267	20770	Mm.1280	NM_009267	ENSMUSG00000036925	Mucl2	Spt-1|Spt1	mucin-like 2	protein-coding
mm_96495.1	chr11	67975532	67975537	+	1	NA	intron (NM_018768, intron 3 of 7)	(T)n|Simple_repeat|Simple_repeat	9051	NM_018768	55943	Mm.3973	NM_018768	ENSMUSG00000020903	Stx8	0610007H08Rik|1110002H11Rik|4930571E13Rik|CARB	syntaxin 8	protein-coding
mm_22343.1	chr2	180889704	180889715	-	1	NA	Intergenic	Intergenic	-4331	NR_029538	723951		NR_029538	ENSMUSG00000065454	Mir124a-3	Mirn124a-3|mir-124-3|mir-124a-3	microRNA 124a-3	ncRNA
mm_63093.1	chr7	122366165	122366176	+	1	NA	intron (NM_001316672, intron 2 of 16)	intron (NM_001316672, intron 2 of 16)	77045	NM_008855	18751	Mm.207496	NM_008855	ENSMUSG00000052889	Prkcb	PKC-B|PKC-Beta|Pkcb|Prkcb1|Prkcb2	protein kinase C, beta	protein-coding
mm_6862.1	chr1	84278344	84278379	-	1	NA	intron (NM_001003948, intron 1 of 2)	intron (NM_001003948, intron 1 of 2)	6284	NM_001003948	98496	Mm.187470	NM_001003948	ENSMUSG00000045658	Pid1	5033414K04Rik|NYGGF4	phosphotyrosine interaction domain containing 1	protein-coding
mm_164825.1	chr18	36719954	36719960	-	1	NA	Intergenic	L3|LINE|CR1	6858	NM_009841	12475	Mm.3460	NM_009841	ENSMUSG00000051439	Cd14	-	CD14 antigen	protein-coding
mm_22766.1	chr3	20062648	20062659	+	1	NA	intron (NR_105047, intron 2 of 23)	Lx8|LINE|L1	4362	NR_105047	20585	Mm.209650	NM_009210	ENSMUSG00000002428	Hltf	AF010600|BC057116|P113|Smarca3|Snf2l3	helicase-like transcription factor	protein-coding
mm_56995.1	chr6	120971399	120971437	-	1	NA	intron (NM_001270475, intron 21 of 31)	intron (NM_001270475, intron 21 of 31)	12574	NR_138099	215458	Mm.122399	NR_138099		LOC215458	-	uncharacterized LOC215458	ncRNA
mm_145455.1	chr18	60229688	60229691	+	1	NA	intron (NM_001033767, intron 2 of 2)	Lx5|LINE|L1	17612	NM_001033767	240327	Mm.357104	NM_001033767	ENSMUSG00000073555	Gm4951	EG240327|Ifgga2	predicted gene 4951	protein-coding
mm_115984.1	chr13	24281225	24281277	-	1	NA	promoter-TSS (NM_026825)	promoter-TSS (NM_026825)	-461	NM_026825	68732	Mm.211047	NM_026825	ENSMUSG00000021338	Carmil1	1110037D04Rik|AI425970|CARMIL|CARML1|D130057M20|Lrrc16|Lrrc16a	capping protein regulator and myosin 1 linker 1	protein-coding
mm_75024.1	chr8	31918353	31918368	-	1	NA	promoter-TSS (NM_178591)	promoter-TSS (NM_178591)	-157	NM_178591	211323	Mm.153432	NM_178591	ENSMUSG00000062991	Nrg1	6030402G23Rik|ARIA|D230005F13Rik|GGF|GGFII|HRG|HRGalpha|Hgl|NDF|SMDF	neuregulin 1	protein-coding
mm_73837.1	chr8	117461065	117461095	+	1	NA	3' UTR (NM_001163262, exon 21 of 21)	3' UTR (NM_001163262, exon 21 of 21)	1815	NR_106046	102465653		NR_106046	ENSMUSG00000098483	Mir7078	Gm27386|mmu-mir-7078	microRNA 7078	ncRNA
mm_65008.1	chr7	17060886	17060922	-	1	NA	intron (NM_001162950, intron 1 of 14)	intron (NM_001162950, intron 1 of 14)	1523	NM_001162950	53417	Mm.135110	NM_016868	ENSMUSG00000004328	Hif3a	Ipas|MOP7|NEPAS|bHLHe17	hypoxia inducible factor 3, alpha subunit	protein-coding
mm_77777.1	chr9	3018761	3018779	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	19973	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_88943.1	chr10	81321188	81321247	+	1	NA	exon (NM_027381, exon 1 of 9)	exon (NM_027381, exon 1 of 9)	114	NM_027381	70312	Mm.87628	NM_027381	ENSMUSG00000034889	Cactin	2510012J08Rik	cactin, spliceosome C complex subunit	protein-coding
mm_63378.1	chr7	127212660	127212672	+	1	NA	intron (NM_016754, intron 1 of 6)	ID_B1|SINE|B4	1058	NM_016754	17907	Mm.14526	NM_016754	ENSMUSG00000030672	Mylpf	2410014J02Rik|MLC-2|Mlc2	myosin light chain, phosphorylatable, fast skeletal muscle	protein-coding
mm_142162.1	chr17	36145700	36145723	-	1	NA	intron (NR_033517, intron 1 of 3)	CpG	693	NR_033517	675325	Mm.75890	NR_033517	ENSMUSG00000038311	2410017I17Rik	-	RIKEN cDNA 2410017I17 gene	ncRNA
mm_124911.1	chr15	11064765	11064797	+	1	NA	promoter-TSS (NM_175501)	promoter-TSS (NM_175501)	8	NM_175501	239337	Mm.224825	NM_175501	ENSMUSG00000047497	Adamts12	ADAMTS-12|AI605170	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 12	protein-coding
mm_21501.1	chr2	163472637	163472668	-	1	NA	promoter-TSS (NM_173397)	promoter-TSS (NM_173397)	-23	NM_173397	228859	Mm.242917	NM_173397	ENSMUSG00000048486	Fitm2	AI414861|D930001I22Rik|Fit2	fat storage-inducing transmembrane protein 2	protein-coding
mm_21812.1	chr2	165234659	165234681	-	1	NA	promoter-TSS (NM_174988)	promoter-TSS (NM_174988)	67	NM_174988	104010	Mm.151819	NM_174988	ENSMUSG00000053166	Cdh22	-	cadherin 22	protein-coding
mm_129657.1	chr15	81067010	81067020	-	1	NA	intron (NM_001082536, intron 2 of 13)	intron (NM_001082536, intron 2 of 13)	38032	NM_153049	223701	Mm.439814	NM_153049	ENSMUSG00000042292	Mkl1	AMKL|Bsac|Mal|Mrtf-A	MKL (megakaryoblastic leukemia)/myocardin-like 1	protein-coding
mm_86942.1	chr10	24596041	24596071	+	1	NA	exon (NM_010217, exon 2 of 5)	exon (NM_010217, exon 2 of 5)	614	NM_010217	14219	Mm.390287	NM_010217	ENSMUSG00000019997	Ctgf	Ccn2|Fisp12|Hcs24|fisp-12	connective tissue growth factor	protein-coding
mm_28929.1	chr3	98859754	98859769	-	1	NA	promoter-TSS (NM_001304800)	promoter-TSS (NM_001304800)	33	NM_001304800	15492	Mm.140811	NM_008293	ENSMUSG00000027871	Hsd3b1	3-beta-HSD I|D3Ertd383e	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1	protein-coding
mm_120314.1	chr14	63142662	63142702	+	1	NA	3' UTR (NM_007798, exon 10 of 10)	3' UTR (NM_007798, exon 10 of 10)	20220	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_8670.1	chr1	156669676	156669685	-	1	NA	intron (NM_023141, intron 2 of 5)	intron (NM_023141, intron 2 of 5)	4659	NM_023141	30935	Mm.206737	NM_023141	ENSMUSG00000060519	Tor3a	Adir	torsin family 3, member A	protein-coding
mm_34519.1	chr4	148941177	148941188	+	1	NA	intron (NM_027195, intron 11 of 15)	intron (NM_027195, intron 11 of 15)	136790	NM_027195	69743	Mm.233879	NM_027195	ENSMUSG00000028977	Casz1	2410019P08Rik|AV096627|BC040081|Cst|D4Ertd432e	castor zinc finger 1	protein-coding
mm_120492.1	chr14	65979845	65979855	+	1	NA	exon (NM_013492, exon 7 of 9)	exon (NM_013492, exon 7 of 9)	11367	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_150532.1	chr19	39291092	39291109	+	1	NA	exon (NM_007815, exon 3 of 9)	exon (NM_007815, exon 3 of 9)	4015	NM_007815	13095	Mm.20764	NM_007815	ENSMUSG00000003053	Cyp2c29	AHOH|AHOHase|AI159681|AI196010|Ah-2|Ahh-1|Cyp2c|P450-2C	cytochrome P450, family 2, subfamily c, polypeptide 29	protein-coding
mm_121208.1	chr14	103053629	103053659	+	1	NA	intron (NM_008392, intron 4 of 4)	Lx8|LINE|L1	6632	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_3072.1	chr1	134193433	134193445	+	1	NA	promoter-TSS (NM_016749)	promoter-TSS (NM_016749)	-9	NM_016749	53311	Mm.379067	NM_016749	ENSMUSG00000042451	Mybph	AI385643|MyBP-H	myosin binding protein H	protein-coding
mm_133239.1	chr16	77074852	77074873	+	1	NA	exon (NM_013918, exon 11 of 24)	exon (NM_013918, exon 11 of 24)	60793	NM_013918	30940	Mm.40986	NM_013918	ENSMUSG00000022867	Usp25	-	ubiquitin specific peptidase 25	protein-coding
mm_43066.1	chr5	124439892	124439991	+	1	NA	promoter-TSS (NM_030241)	promoter-TSS (NM_030241)	11	NM_001310725	67956	Mm.137966	NM_030241	ENSMUSG00000049327	Kmt5a	2410195B05Rik|AA617402|AW536475|PR-SET7|PR/SET07|Setd8	lysine methyltransferase 5A	protein-coding
mm_5271.1	chr1	18145896	18145922	-	1	NA	promoter-TSS (NM_001347048)	promoter-TSS (NM_001347048)	-7	NM_001347048	78081	Mm.319913	NM_030033	ENSMUSG00000025774	Crisp4	9230112K08Rik	cysteine-rich secretory protein 4	protein-coding
mm_23669.1	chr3	68572395	68572420	+	1	NA	promoter-TSS (NM_013928)	promoter-TSS (NM_013928)	39	NM_013928	30953	Mm.331064	NM_013928	ENSMUSG00000027777	Schip1	Nf2ip|Schip-1	schwannomin interacting protein 1	protein-coding
mm_95623.1	chr11	53583895	53583906	+	1	NA	exon (NM_008443, exon 7 of 18)	exon (NM_008443, exon 7 of 18)	16531	NM_001290806	16568	Mm.88694	NM_008443	ENSMUSG00000018395	Kif3a	Kif3|Kifl|Kns3	kinesin family member 3A	protein-coding
mm_44950.1	chr5	36586220	36586229	-	1	NA	promoter-TSS (NM_001113362)	promoter-TSS (NM_001113362)	2	NM_001113362	100855	Mm.486203	NM_133910	ENSMUSG00000029192	Tbc1d14	2810413P16Rik|AU043625|C86258|D5Ertd110e|mKIAA1322	TBC1 domain family, member 14	protein-coding
mm_75814.1	chr8	70316204	70316217	-	1	NA	intron (NM_138647, intron 1 of 7)	intron (NM_138647, intron 1 of 7)	435	NM_001163282	14559	Mm.258280	NM_008107	ENSMUSG00000087408	Gdf1	AI385651|Gdf-1	growth differentiation factor 1	protein-coding
mm_58381.1	chr6	149188649	149188725	-	1	NA	promoter-TSS (NM_001113424)	promoter-TSS (NM_001113424)	25	NM_001113424	232566	Mm.209147	NM_001113424	ENSMUSG00000068250	Amn1	5830467E07Rik|A230083D09|C730024G19Rik	antagonist of mitotic exit network 1	protein-coding
mm_133955.1	chr16	4017096	4017098	-	1	NA	Intergenic	Intergenic	-15419	NM_177472	52864	Mm.29935	NM_177472	ENSMUSG00000039738	Slx4	AI256635|AI426760|Btbd12|D16Bwg1016e	SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)	protein-coding
mm_23457.1	chr3	60472632	60472666	+	1	NA	promoter-TSS (NM_001253713)	promoter-TSS (NM_001253713)	-181	NM_001253713	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_135579.1	chr16	50432295	50432301	-	1	NA	promoter-TSS (NM_027444)	promoter-TSS (NM_027444)	91	NM_027444	70508	Mm.28940	NM_027444	ENSMUSG00000022641	Bbx	5530401J07Rik|5730403O13Rik	bobby sox HMG box containing	protein-coding
mm_77971.1	chr9	7793298	7793312	+	1	NA	3' UTR (NM_133739, exon 5 of 5)	3' UTR (NM_133739, exon 5 of 5)	8915	NR_049191	100885830		NR_049191	ENSMUSG00000093615	Mir5618	Gm23685|mmu-mir-5618	microRNA 5618	ncRNA
mm_155736.1	chrX	96166467	96166478	+	1	NA	exon (NM_010833, exon 13 of 13)	exon (NM_010833, exon 13 of 13)	70427	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_77267.1	chr8	115713513	115713520	-	1	NA	Intergenic	Intergenic	-6622	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_87350.1	chr10	43583897	43583900	+	1	NA	3' UTR (NM_009846, exon 2 of 2)	3' UTR (NM_009846, exon 2 of 2)	4729	NM_009846	12484	Mm.29742	NM_009846	ENSMUSG00000047139	Cd24a	Cd24|HSA|Ly-52|nectadrin	CD24a antigen	protein-coding
mm_153787.1	chr19	45816240	45816252	-	1	NA	promoter-TSS (NM_030716)	promoter-TSS (NM_030716)	-183	NM_145703	80906	Mm.213204	NM_030716	ENSMUSG00000025221	Kcnip2	KChIP2	Kv channel-interacting protein 2	protein-coding
mm_50976.1	chr6	61350979	61350983	+	1	NA	intron (NM_001164316, intron 3 of 10)	LTR40a|LTR|ERVL	-170171	NR_040287	100504262	Mm.438066	NR_040287		A730020E08Rik	-	RIKEN cDNA A730020E08 gene	ncRNA
mm_21141.1	chr2	154220211	154220230	-	1	NA	3' UTR (NM_153418, exon 16 of 16)	3' UTR (NM_153418, exon 16 of 16)	-3522	NM_144890	228802	Mm.167411	NM_144890	ENSMUSG00000038572	Bpifb5	Lplunc5	BPI fold containing family B, member 5	protein-coding
mm_81556.1	chr9	110344186	110344204	+	1	NA	intron (NM_001001144, intron 1 of 22)	RSINE1|SINE|B4	10839	NM_001001144	235623	Mm.288741	NM_001001144	ENSMUSG00000032485	Scap	9530044G19|mKIAA0199	SREBF chaperone	protein-coding
mm_143673.1	chr17	79981614	79981624	-	1	NA	Intergenic	Intergenic	80649	NM_144802	72692	Mm.64579	NM_144802	ENSMUSG00000024095	Hnrnpll	2510028H02Rik|2810036L13Rik|AI256697|AI852082|Hnrpll	heterogeneous nuclear ribonucleoprotein L-like	protein-coding
mm_137802.1	chr17	29846531	29846535	+	1	NA	exon (NM_001081160, exon 7 of 16)	exon (NM_001081160, exon 7 of 16)	41349	NM_001081160	74762	Mm.40901	NM_001081160	ENSMUSG00000043557	Mdga1	1200011I03Rik|GPIM|Mamdc3	MAM domain containing glycosylphosphatidylinositol anchor 1	protein-coding
mm_49578.1	chr6	30642294	30642298	+	1	NA	intron (NM_025350, intron 6 of 9)	intron (NM_025350, intron 6 of 9)	3078	NM_025350	109697	Mm.25377	NM_025350	ENSMUSG00000054446	Cpa1	0910001L12Rik|Cpa	carboxypeptidase A1, pancreatic	protein-coding
mm_104822.1	chr11	99003043	99003071	-	1	NA	exon (NM_011623, exon 24 of 36)	exon (NM_011623, exon 24 of 36)	-20041	NM_178596	353155	Mm.453253	NM_178596	ENSMUSG00000047197	Gjd3	Gja11|Gjc1|cx30.2	gap junction protein, delta 3	protein-coding
mm_17017.1	chr2	18998040	18998059	-	1	NA	promoter-TSS (NR_024323)	promoter-TSS (NR_024323)	72	NM_008845	18718	Mm.313977	NM_008845	ENSMUSG00000026737	Pip4k2a	AW742916|Pip5k2a	phosphatidylinositol-5-phosphate 4-kinase, type II, alpha	protein-coding
mm_170628.1	chr19	7516901	7516905	+	1	NA	exon (NM_001163505, exon 4 of 13)	exon (NM_001163505, exon 4 of 13)	22465	NM_146091	109168	Mm.264016	NM_146091	ENSMUSG00000024759	Atl3	4633402C03Rik|5730596K20Rik|AI465397|AW228836	atlastin GTPase 3	protein-coding
mm_35581.1	chr4	41741015	41741053	-	1	NA	intron (NM_011014, intron 1 of 3)	CpG-9828	325	NM_001286540	18391	Mm.425181	NM_011014	ENSMUSG00000036078	Sigmar1	Oprs1|Sig1R|sigma1R	sigma non-opioid intracellular receptor 1	protein-coding
mm_53275.1	chr6	128648873	128648886	+	1	NA	Intergenic	Intergenic	-13506	NM_053165	94071	Mm.197689	NM_053165	ENSMUSG00000030364	Clec2h	Clrf|clr-f	C-type lectin domain family 2, member h	protein-coding
mm_8340.1	chr1	150164905	150164916	-	1	NA	promoter-TSS (NR_110420)	promoter-TSS (NR_110420)	38	NR_110420	102639566	Mm.417208	NR_110420	ENSMUSG00000097754	Ptgs2os2	Gm26687|Linc-cox2|Lincrna-cox2	prostaglandin-endoperoxide synthase 2, opposite strand 2	ncRNA
mm_9119.1	chr1	170211769	170211775	-	1	NA	intron (NM_010633, intron 2 of 7)	intron (NM_010633, intron 2 of 7)	3621	NM_010633	16589	Mm.209150	NM_010633	ENSMUSG00000026667	Uhmk1	4732477C12Rik|4930500M09Rik|AA673513|AI449218|AU021979|C820018A03Rik|KIS|Kist|OTTMUSG00000021542|P-CIP2	U2AF homology motif (UHM) kinase 1	protein-coding
mm_130927.1	chr15	103097785	103097787	-	1	NA	Intergenic	B1F|SINE|Alu	49042	NR_045743	432989	Mm.383979	NR_045743	ENSMUSG00000097003	D930007P13Rik	-	Riken cDNA D930007P13 gene	ncRNA
mm_152611.1	chr19	11912102	11912104	-	1	NA	promoter-TSS (NM_172635)	promoter-TSS (NM_172635)	-296	NM_172635	225929	Mm.42711	NM_172635	ENSMUSG00000046139	Patl1	AV312086|Pat1b	protein associated with topoisomerase II homolog 1 (yeast)	protein-coding
mm_83217.1	chr9	42124154	42124164	-	1	NA	5' UTR (NM_011436, exon 1 of 48)	5' UTR (NM_011436, exon 1 of 48)	130	NM_011436	20660	Mm.121920	NM_011436	ENSMUSG00000049313	Sorl1	2900010L19Rik|AI596264|AW261561|LR11|SorLA|gp250|mSorLA	sortilin-related receptor, LDLR class A repeats-containing	protein-coding
mm_142918.1	chr17	53689232	53689253	-	1	NA	promoter-TSS (NM_028232)	promoter-TSS (NM_028232)	73	NM_028232	72415	Mm.153202	NM_028232	ENSMUSG00000023940	Sgol1	3300001M08Rik|C81037|Sgo1	shugoshin-like 1 (S. pombe)	protein-coding
mm_70004.1	chr7	142387896	142387906	-	1	NA	promoter-TSS (NM_009983)	promoter-TSS (NM_009983)	-31	NM_009983	13033	Mm.231395	NM_009983	ENSMUSG00000007891	Ctsd	CD|CatD	cathepsin D	protein-coding
mm_28045.1	chr3	84039876	84039905	-	1	NA	intron (NM_172681, intron 1 of 34)	CpG	271	NM_172681	229473	Mm.28838	NM_172681	ENSMUSG00000033767	D930015E06Rik	Kiaa0922|mKIAA0922	RIKEN cDNA D930015E06 gene	protein-coding
mm_75082.1	chr8	33916140	33916148	-	1	NA	intron (NM_001042674, intron 1 of 7)	URR1A|DNA|hAT-Charlie	13719	NM_019733	19663	Mm.323997	NM_019733	ENSMUSG00000031586	Rbpms	2010300K22Rik|2700019M19Rik|AU017537|RBP-MS|hermes	RNA binding protein gene with multiple splicing	protein-coding
mm_21798.1	chr2	164879736	164879804	-	1	NA	intron (NM_146129, intron 1 of 16)	CpG	402	NM_146129	228866	Mm.241134	NM_146129	ENSMUSG00000039849	Pcif1	2310022K11Rik|C20orf67|F730014I05Rik	PDX1 C-terminal inhibiting factor 1	protein-coding
mm_18317.1	chr2	57108277	57108285	-	1	NA	exon (NM_013613, exon 8 of 8)	exon (NM_013613, exon 8 of 8)	6757	NM_013613	18227	Mm.3507	NM_013613	ENSMUSG00000026826	Nr4a2	HZF-3|NOT|Nurr1|RNR-1|TINOR|TINUR	nuclear receptor subfamily 4, group A, member 2	protein-coding
mm_114124.1	chr13	55209806	55209812	+	1	NA	promoter-TSS (NM_008739)	promoter-TSS (NM_008739)	27	NM_008739	18193	Mm.12964	NM_008739	ENSMUSG00000021488	Nsd1	AI528500|KMT3B	nuclear receptor-binding SET-domain protein 1	protein-coding
mm_8170.1	chr1	137751423	137751430	-	1	NA	Intergenic	Intergenic	-215029	NR_029795	735252		NR_029795	ENSMUSG00000065565	Mir181a-1	Mirn181a-1|Mirn213|miR-213|mir-181a-1|mmu-mir-213	microRNA 181a-1	ncRNA
mm_25915.1	chr3	131136147	131136150	+	1	NA	intron (NM_001276403, intron 3 of 11)	Lx8b|LINE|L1	23357	NM_001276403	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_111639.1	chr12	102652641	102652652	-	1	NA	intron (NM_172584, intron 2 of 9)	intron (NM_172584, intron 2 of 9)	32374	NR_035457	100316812		NR_035457	ENSMUSG00000089324	Mir1936	mir-1936|mmu-mir-1936	microRNA 1936	ncRNA
mm_79640.1	chr9	59557336	59557367	+	1	NA	exon (NM_010421, exon 5 of 14)	exon (NM_010421, exon 5 of 14)	17811	NM_010421	15211	Mm.2284	NM_010421	ENSMUSG00000025232	Hexa	Hex-1	hexosaminidase A	protein-coding
mm_22098.1	chr2	169081773	169081783	-	1	NA	Intergenic	Lx8|LINE|L1	103509	NR_040326	75508	Mm.271256	NR_040326	ENSMUSG00000086348	1700017J07Rik	-	RIKEN cDNA 1700017J07 gene	ncRNA
mm_59209.1	chr7	24530724	24530734	+	1	NA	promoter-TSS (NM_153134)	promoter-TSS (NM_153134)	81	NM_153134	210146	Mm.41108	NM_153134	ENSMUSG00000041037	Irgq	AF322649|FKSG27|Irgq1	immunity-related GTPase family, Q	protein-coding
mm_166442.1	chr5	137263906	137263950	-	1	NA	Intergenic	Intergenic	-24326	NM_009599	11423	Mm.255464	NM_009599	ENSMUSG00000023328	Ache	-	acetylcholinesterase	protein-coding
mm_51395.1	chr6	78371190	78371206	+	1	NA	intron (NM_011036, intron 1 of 5)	intron (NM_011036, intron 1 of 5)	313	NM_011036	18489	Mm.2553	NM_011036	ENSMUSG00000071356	Reg3b	HIP|PAP1|Pap|REG-III	regenerating islet-derived 3 beta	protein-coding
mm_156891.1	chrX	166661619	166661625	+	1	NA	promoter-TSS (NR_046015)	promoter-TSS (NR_046015)	-403	NR_046015	382255	Mm.336320	NR_046015	ENSMUSG00000086860	Gm1720	-	predicted gene 1720	ncRNA
mm_78805.1	chr9	44066967	44066988	+	1	NA	promoter-TSS (NM_198092)	promoter-TSS (NM_198092)	-44	NM_198092	53376	Mm.272770	NM_016808	ENSMUSG00000032010	Usp2	B930035K21Rik|Ubp41	ubiquitin specific peptidase 2	protein-coding
mm_139581.1	chr17	57105402	57105421	+	1	NA	promoter-TSS (NM_009404)	promoter-TSS (NM_009404)	26	NM_009404	21950	Mm.41171	NM_009404	ENSMUSG00000035678	Tnfsf9	4-1BB-L|4-1BBL|AI848817|Cd137l|Ly63l	tumor necrosis factor (ligand) superfamily, member 9	protein-coding
mm_160037.1	chr6	133292216	133292216	+	1	NA	promoter-TSS (NM_027784)	promoter-TSS (NM_027784)	0	NM_027784	232426	Mm.158689	NM_027784	ENSMUSG00000055594	5530400C23Rik	GRP	RIKEN cDNA 5530400C23 gene	protein-coding
mm_54717.1	chr6	40049670	40049717	-	1	NA	Intergenic	Intergenic	-60560	NM_001004182	434008	Mm.130209	NM_001004182	ENSMUSG00000057716	Tmem178b	EG434008|Gm5567	transmembrane protein 178B	protein-coding
mm_67842.1	chr7	98539131	98539137	-	1	NA	Intergenic	L1MB8|LINE|L1	44912	NM_001113379	434215	Mm.323057	NM_001113379	ENSMUSG00000090958	Lrrc32	AI426318|D11S833Eh|D7H11S833E|EG434215|Garp	leucine rich repeat containing 32	protein-coding
mm_142157.1	chr17	36046562	36046570	-	1	NA	intron (NM_001034909, intron 1 of 2)	B1_Mus1|SINE|Alu	3605	NM_001034909	547347	Mm.484641	NM_001034909	ENSMUSG00000073407	Gm6034	EG547347|H2-gs14-2	predicted gene 6034	protein-coding
mm_166767.1	chr6	134567232	134567249	-	1	NA	promoter-TSS (NM_008514)	promoter-TSS (NM_008514)	-327	NM_008514	16974	Mm.321990	NM_008514	ENSMUSG00000030201	Lrp6	C030016K15Rik|Cd|Gw|ska26|ska<m26Jus>|skax26	low density lipoprotein receptor-related protein 6	protein-coding
mm_20567.1	chr2	131083363	131083376	-	1	NA	exon (NM_011426, exon 5 of 21)	exon (NM_011426, exon 5 of 21)	3396	NM_011426	20612	Mm.1374	NM_011426	ENSMUSG00000027322	Siglec1	Cd169|Siglec-1|Sn	sialic acid binding Ig-like lectin 1, sialoadhesin	protein-coding
mm_84129.1	chr9	59036203	59036221	-	1	NA	5' UTR (NM_008684, exon 1 of 29)	5' UTR (NM_008684, exon 1 of 29)	229	NM_008684	18007	Mm.42249	NM_008684	ENSMUSG00000032340	Neo1	2610028H22Rik|AI327052|D930014N22Rik|Igdcc2	neogenin	protein-coding
mm_20310.1	chr2	127247705	127247765	-	1	NA	promoter-TSS (NM_175145)	promoter-TSS (NM_175145)	81	NM_025296	26371	Mm.45179	NM_025296	ENSMUSG00000003662	Ciao1	AW210570|Wdr39	cytosolic iron-sulfur protein assembly 1	protein-coding
mm_173282.1	chrY	1561178	1561178	+	1	NA	Intergenic	L1Md_T|LINE|L1	-101396	NM_148943	107868	Mm.347376	NM_148943	ENSMUSG00000069044	Usp9y	Dffry|Fafl2	ubiquitin specific peptidase 9, Y chromosome	protein-coding
mm_153017.1	chr19	30674592	30674595	-	1	NA	intron (NM_011160, intron 9 of 17)	intron (NM_011160, intron 9 of 17)	-125097	NM_010051	13380	Mm.214717	NM_010051	ENSMUSG00000024868	Dkk1	mdkk-1	dickkopf WNT signaling pathway inhibitor 1	protein-coding
mm_147196.1	chr18	37655839	37655858	-	1	NA	intron (NM_001301259, intron 1 of 3)	intron (NM_001301259, intron 1 of 3)	-6097	NM_033584	93709	Mm.247203	NM_033584	ENSMUSG00000103144	Pcdhga1	-	protocadherin gamma subfamily A, 1	protein-coding
mm_57259.1	chr6	123285298	123285325	-	1	NA	intron (NM_019948, intron 5 of 5)	intron (NM_019948, intron 5 of 5)	4560	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_121668.1	chr14	12346646	12346651	-	1	NA	promoter-TSS (NM_080433)	promoter-TSS (NM_080433)	-783	NM_080433	54713	Mm.34644	NM_080433	ENSMUSG00000021743	Fezf2	AI451466|AI852056|Fez|Fezl|Zfp312	Fez family zinc finger 2	protein-coding
mm_104193.1	chr11	87828336	87828348	-	1	NA	Intergenic	Intergenic	-2228	NM_080420	76113	Mm.41236	NM_080420	ENSMUSG00000009356	Lpo	5830499B15Rik	lactoperoxidase	protein-coding
mm_101745.1	chr11	43379370	43379379	-	1	NA	Intergenic	Intergenic	-4913	NR_029558	387164		NR_029558	ENSMUSG00000065601	Mir146	Mirn146|miR-146a|mmu-mir-146	microRNA 146	ncRNA
mm_32252.1	chr4	102570498	102570507	+	1	NA	5' UTR (NM_001177980, exon 1 of 10)	5' UTR (NM_001177980, exon 1 of 10)	442	NM_001177980	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_155343.1	chrX	68678572	68678589	+	1	NA	promoter-TSS (NM_008031)	promoter-TSS (NM_008031)	39	NM_001290424	14265	Mm.3451	NM_008031	ENSMUSG00000000838	Fmr1	FMRP|Fmr-1	fragile X mental retardation syndrome 1	protein-coding
mm_71555.1	chr8	48632860	48632863	+	1	NA	intron (NM_011857, intron 2 of 28)	intron (NM_011857, intron 2 of 28)	41829	NM_001145937	23965	Mm.42191	NM_011857	ENSMUSG00000031561	Tenm3	2610100B16Rik|Odz1|Odz3|Ten-m3|mKIAA1455	teneurin transmembrane protein 3	protein-coding
mm_67907.1	chr7	99695841	99695855	-	1	NA	promoter-TSS (NM_001252531)	promoter-TSS (NM_001252531)	-39	NM_001252531	101488	Mm.11249	NM_175316	ENSMUSG00000030737	Slco2b1	AI060904|AI852653|OATP-B|Slc21a9	solute carrier organic anion transporter family, member 2b1	protein-coding
mm_76936.1	chr8	105939827	105939864	-	1	NA	exon (NM_008490, exon 6 of 6)	exon (NM_008490, exon 6 of 6)	-1453	NM_013640	19171	Mm.787	NM_013640	ENSMUSG00000031897	Psmb10	Mecl-1|Mecl1	proteasome (prosome, macropain) subunit, beta type 10	protein-coding
mm_14272.1	chr2	128709056	128709065	+	1	NA	intron (NM_008587, intron 1 of 18)	RMER30|DNA|hAT-Charlie	10063	NM_008587	17289	Mm.239655	NM_008587	ENSMUSG00000014361	Mertk	Eyk|Mer|Nyk|nmf12	c-mer proto-oncogene tyrosine kinase	protein-coding
mm_3173.1	chr1	135719796	135719815	+	1	NA	Intergenic	Intergenic	-9392	NM_007791	13007	Mm.196484	NM_007791	ENSMUSG00000026421	Csrp1	AA408841|AA959891|AW545626|CRP1|Csrp	cysteine and glycine-rich protein 1	protein-coding
mm_65789.1	chr7	28893840	28893850	-	1	NA	TTS (NM_001110807)	TTS (NM_001110807)	12189	NM_001110807	60594	Mm.476990	NM_021894	ENSMUSG00000054083	Capn12	CANP 12	calpain 12	protein-coding
mm_134307.1	chr16	15863120	15863126	-	1	NA	5' UTR (NM_029354, exon 1 of 3)	5' UTR (NM_029354, exon 1 of 3)	199	NM_029354	72083	Mm.22351	NM_029354	ENSMUSG00000022671	Mzt2	2410018G20Rik|2610001E06Rik|Fam128|Fam128b	mitotic spindle organizing protein 2	protein-coding
mm_118055.1	chr13	101768155	101768194	-	1	NA	promoter-TSS (NM_001077495)	promoter-TSS (NM_001077495)	43	NM_001077495	18708	Mm.259333	NM_001024955	ENSMUSG00000041417	Pik3r1	PI3K|p50alpha|p55alpha|p85alpha	phosphatidylinositol 3-kinase, regulatory subunit, polypeptide 1 (p85 alpha)	protein-coding
mm_115887.1	chr13	21901114	21901116	-	1	NA	Intergenic	LTRIS2|LTR|ERV1	-4066	NR_035500	100316716		NR_035500	ENSMUSG00000088148	Mir1983	mmu-mir-1983	microRNA 1983	ncRNA
mm_133174.1	chr16	72027684	72027694	+	1	NA	Intergenic	Intergenic	206638	NR_131116	319533	Mm.373754	NR_131115		8030451O07Rik	-	RIKEN cDNA 8030451O07 gene	ncRNA
mm_13559.1	chr2	112265709	112265719	+	1	NA	promoter-TSS (NM_133649)	promoter-TSS (NM_133649)	-600	NM_133649	107723	Mm.491155	NM_133648	ENSMUSG00000027130	Slc12a6	9530023I19Rik|KCC3|gaxp	solute carrier family 12, member 6	protein-coding
mm_156491.1	chrX	144336096	144336108	+	1	NA	intron (NR_037145, intron 3 of 26)	intron (NR_037145, intron 3 of 26)	18136	NM_026247	67574	Mm.249084	NM_026247	ENSMUSG00000041718	Alg13	2810046O15Rik|4833435D08Rik|Glt28d1|MDS031|OTTMUSG00000018917	asparagine-linked glycosylation 13	protein-coding
mm_75853.1	chr8	70698318	70698327	-	1	NA	5' UTR (NM_001286944, exon 1 of 1)	5' UTR (NM_001286944, exon 1 of 1)	583	NM_001286944	16478	Mm.419851	NM_010592	ENSMUSG00000071076	Jund	Jund1	jun D proto-oncogene	protein-coding
mm_15527.1	chr2	158382701	158382734	+	1	NA	3' UTR (NM_175692, exon 5 of 5)	3' UTR (NM_175692, exon 5 of 5)	7079	NM_175692	319317	Mm.294494	NM_175692	ENSMUSG00000044349	Snhg11	A930034L06Rik|AI854265|AL022637|AW319638|E130013N09Rik	small nucleolar RNA host gene 11	protein-coding
mm_71547.1	chr8	47836928	47836929	+	1	NA	intron (NM_133791, intron 21 of 22)	ORR1A1-int|LTR|ERVL-MaLR	12446	NM_029383	75677	Mm.390033	NM_029383	ENSMUSG00000038064	Cldn22	2210404A22Rik|5330431C14Rik|9530051B05Rik	claudin 22	protein-coding
mm_51894.1	chr6	90619145	90619158	+	1	NA	promoter-TSS (NM_001037493)	promoter-TSS (NM_001037493)	-95	NM_001037493	71699	Mm.272633	NM_027868	ENSMUSG00000030089	Slc41a3	1010001P06Rik|AI480742|SLC41A1-L2	solute carrier family 41, member 3	protein-coding
mm_129779.1	chr15	82793167	82793195	-	1	NA	exon (NM_029562, exon 2 of 9)	exon (NM_029562, exon 2 of 9)	1064	NM_029562	76279	Mm.439931	NM_029562	ENSMUSG00000022445	Cyp2d26	1300006E06Rik	cytochrome P450, family 2, subfamily d, polypeptide 26	protein-coding
mm_94095.1	chr10	128547723	128547768	-	1	NA	promoter-TSS (NM_134003)	promoter-TSS (NM_134003)	-1	NM_134003	103284	Mm.68289	NM_134003	ENSMUSG00000039810	Zc3h10	AI790326	zinc finger CCCH type containing 10	protein-coding
mm_78948.1	chr9	45138601	45138613	+	1	NA	promoter-TSS (NM_001013390)	promoter-TSS (NM_001013390)	-435	NM_001013390	399548	Mm.335112	NM_001013390	ENSMUSG00000046480	Scn4b	Gm1471	sodium channel, type IV, beta	protein-coding
mm_29560.1	chr3	116808068	116808136	-	1	NA	promoter-TSS (NM_001081326)	promoter-TSS (NM_001081326)	64	NM_001081326	77559	Mm.237099	NM_001081326	ENSMUSG00000033400	Agl	1110061O17Rik|9430004C13Rik|9630046L06Rik|AI850929|C77197	amylo-1,6-glucosidase, 4-alpha-glucanotransferase	protein-coding
mm_66113.1	chr7	31042088	31042091	-	1	NA	promoter-TSS (NM_001111073)	promoter-TSS (NM_001111073)	242	NM_008761	18301	Mm.1870	NM_008761	ENSMUSG00000009687	Fxyd5	EF-8|Oit2|RIC	FXYD domain-containing ion transport regulator 5	protein-coding
mm_135254.1	chr16	37654409	37654450	-	1	NA	promoter-TSS (NM_026610)	promoter-TSS (NM_026610)	-61	NM_026610	68194	Mm.379154	NM_026610	ENSMUSG00000022820	Ndufb4	0610006N12Rik|1300010H20Rik	NADH dehydrogenase (ubiquinone) 1 beta subcomplex 4	protein-coding
mm_36452.1	chr4	82499329	82499355	-	1	NA	intron (NM_001113210, intron 1 of 11)	intron (NM_001113210, intron 1 of 11)	6437	NM_001286127	18028	Mm.317947	NM_008687	ENSMUSG00000008575	Nfib	6720429L07Rik|CTF|E030026I10Rik|NF-I/B|NF1-B|NFI-B	nuclear factor I/B	protein-coding
mm_164666.1	chr17	44279903	44279917	+	1	NA	3' UTR (NM_172621, exon 6 of 6)	3' UTR (NM_172621, exon 6 of 6)	91338	NM_172621	224796	Mm.37666	NM_172621	ENSMUSG00000023959	Clic5	5730531E12Rik|B330005L24|Gm322|jbg	chloride intracellular channel 5	protein-coding
mm_168868.1	chr12	35047231	35047231	+	1	NA	promoter-TSS (NM_001014973)	promoter-TSS (NM_001014973)	42	NM_001014973	217463	Mm.213991	NM_001014973	ENSMUSG00000020590	Snx13	Rgs-px1|mKIAA0713	sorting nexin 13	protein-coding
mm_91096.1	chr10	19062196	19062200	-	1	NA	Intergenic	Intergenic	-46788	NM_009397	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_144286.1	chr18	12128595	12128606	+	1	NA	promoter-TSS (NM_024182)	promoter-TSS (NM_024182)	-250	NM_024182	66878	Mm.28551	NM_024182	ENSMUSG00000024404	Riok3	1200013N13Rik|D18Ertd331e|E130306C24Rik|Sudd	RIO kinase 3	protein-coding
mm_43767.1	chr5	140735557	140735567	+	1	NA	intron (NM_173405, intron 2 of 7)	CpG	11435	NM_173405	231842	Mm.491298	NM_173405	ENSMUSG00000050022	Amz1	5330426I05|6530401C20Rik	archaelysin family metallopeptidase 1	protein-coding
mm_16506.1	chr2	181306750	181306760	+	1	NA	3' UTR (NM_009133, exon 5 of 5)	3' UTR (NM_009133, exon 5 of 5)	7745	NM_009133	20262	Mm.2319	NM_009133	ENSMUSG00000027581	Stmn3	9330161A03Rik|AI604839|R75323|Sclip	stathmin-like 3	protein-coding
mm_112165.1	chr12	113366504	113366538	-	1	NA	Intergenic	Intergenic	-123044	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_134115.1	chr16	10292359	10292381	-	1	NA	5' UTR (NM_007929, exon 2 of 5)	5' UTR (NM_007929, exon 2 of 5)	21598	NM_007929	13731	Mm.246009	NM_007929	ENSMUSG00000022505	Emp2	XMP	epithelial membrane protein 2	protein-coding
mm_15740.1	chr2	164237306	164237307	+	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	1035	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_128878.1	chr15	73060214	73060259	-	1	NA	intron (NM_180662, intron 1 of 21)	intron (NM_180662, intron 1 of 21)	968	NM_001164641	76510	Mm.158902	NM_029640	ENSMUSG00000047921	Trappc9	1810044A24Rik|2900005P22Rik|4632408O18Rik|Ibp|Nibp|TRS130|mKIAA1882	trafficking protein particle complex 9	protein-coding
mm_117476.1	chr13	76271939	76271953	-	1	NA	Intergenic	Intergenic	-113015	NM_030174	78771	Mm.316249	NM_030174	ENSMUSG00000021596	Mctp1	2810465F10Rik	multiple C2 domains, transmembrane 1	protein-coding
mm_144947.1	chr18	37807011	37807023	+	1	NA	exon (NM_033581, exon 1 of 4)	exon (NM_033581, exon 1 of 4)	607	NM_033581	93706	Mm.247203	NM_033581	ENSMUSG00000102918	Pcdhgc3	PC43|Pcdh2	protocadherin gamma subfamily C, 3	protein-coding
mm_137086.1	chr17	21488983	21489060	+	1	NA	promoter-TSS (NM_013843)	promoter-TSS (NM_013843)	33	NM_013843	24132	Mm.42140	NM_013843	ENSMUSG00000057409	Zfp53	D030067O06Rik|KRAZ1|Zfp-53|Zfp118|zfas8	zinc finger protein 53	protein-coding
mm_90241.1	chr10	121396763	121396775	+	1	NA	3' UTR (NM_029364, exon 14 of 14)	3' UTR (NM_029364, exon 14 of 14)	31679	NM_029364	75612	Mm.207683	NM_029364	ENSMUSG00000034707	Gns	2610016K11Rik|AU042285|C87209|G6S|N28088	glucosamine (N-acetyl)-6-sulfatase	protein-coding
mm_2287.1	chr1	91366413	91366433	+	1	NA	promoter-TSS (NM_173395)	promoter-TSS (NM_173395)	-7	NM_173395	227358	Mm.389157	NM_173395	ENSMUSG00000047443	Erfe	4832406C22|Fam132b|myonectin	erythroferrone	protein-coding
mm_111757.1	chr12	103958879	103958889	-	1	NA	Intergenic	Intergenic	-1987	NM_009247	20704	Mm.312593	NM_009247	ENSMUSG00000072849	Serpina1e	Dom5|PI5|Spi1-5	serine (or cysteine) peptidase inhibitor, clade A, member 1E	protein-coding
mm_11920.1	chr2	52072334	52072346	+	1	NA	promoter-TSS (NM_175238)	promoter-TSS (NM_175238)	-497	NM_175238	51869	Mm.254530	NM_175238	ENSMUSG00000036202	Rif1	5730435J01Rik|6530403D07Rik|AU016181|AW549474|D2Ertd145e	replication timing regulatory factor 1	protein-coding
mm_102110.1	chr11	53266042	53266054	-	1	NA	exon (NM_008300, exon 15 of 19)	exon (NM_008300, exon 15 of 19)	34431	NM_008300	15525	Mm.239865	NM_008300	ENSMUSG00000020361	Hspa4	70kDa|AI317151|APG-2|Hsp110|Hsp70RY|mKIAA4025	heat shock protein 4	protein-coding
mm_167012.1	chr7	60005174	60005182	-	1	NA	promoter-TSS (NM_013670)	promoter-TSS (NM_013670)	-22	NM_033174	84704	Mm.274995	NM_033174	ENSMUSG00000000948	Snurf	2410045I01Rik|Snrpn	SNRPN upstream reading frame	protein-coding
mm_55063.1	chr6	49048027	49048108	-	1	NA	exon (NM_053110, exon 6 of 11)	exon (NM_053110, exon 6 of 11)	11549	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_141426.1	chr17	29437305	29437336	-	1	NA	Intergenic	CpG	-53725	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_25431.1	chr3	107895913	107895913	+	1	NA	promoter-TSS (NM_010360)	promoter-TSS (NM_010360)	59	NM_010360	14866	Mm.282351	NM_010360	ENSMUSG00000004032	Gstm5	-	glutathione S-transferase, mu 5	protein-coding
mm_28276.1	chr3	88913978	88914004	-	1	NA	promoter-TSS (NM_144898)	promoter-TSS (NM_144898)	-41	NM_144898	229524	Mm.440405	NM_144898	ENSMUSG00000068922	Msto1	BC008103|mst	misato 1, mitochondrial distribution and morphology regulator	protein-coding
mm_41346.1	chr5	90501431	90501436	+	1	NA	exon (NM_007423, exon 8 of 15)	exon (NM_007423, exon 8 of 15)	10719	NM_007423	11576	Mm.358570	NM_007423	ENSMUSG00000054932	Afp	-	alpha fetoprotein	protein-coding
mm_23254.1	chr3	51276258	51276274	+	1	NA	promoter-TSS (NR_073429)	promoter-TSS (NR_073429)	-495	NR_073429	67746	Mm.441177	NR_073429	ENSMUSG00000087440	4930577N17Rik	-	RIKEN cDNA 4930577N17 gene	ncRNA
mm_22359.1	chr2	181029303	181029319	-	1	NA	exon (NM_015730, exon 5 of 6)	exon (NM_015730, exon 5 of 6)	9866	NM_015730	11438	Mm.252369	NM_015730	ENSMUSG00000027577	Chrna4	Acra-4|Acra4|EBN1|ENFL1	cholinergic receptor, nicotinic, alpha polypeptide 4	protein-coding
mm_89167.1	chr10	86309977	86309985	+	1	NA	intron (NM_011595, intron 1 of 4)	intron (NM_011595, intron 1 of 4)	9569	NM_011595	21859	Mm.4871	NM_011595	ENSMUSG00000020044	Timp3	Timp-3	tissue inhibitor of metalloproteinase 3	protein-coding
mm_129255.1	chr15	76698016	76698025	-	1	NA	exon (NM_182805, exon 5 of 11)	exon (NM_182805, exon 5 of 11)	1294	NM_182805	76282	Mm.30130	NM_182805	ENSMUSG00000022546	Gpt	1300007J06Rik|2310022B03Rik|ALT|ALT1|Gpt-1|Gpt1	glutamic pyruvic transaminase, soluble	protein-coding
mm_161707.1	chr17	24804353	24804353	+	1	NA	promoter-TSS (NM_029197)	promoter-TSS (NM_029197)	-29	NM_029197	75178	Mm.52592	NM_029197	ENSMUSG00000024155	Meiob	4930528F23Rik|MLZ-675	meiosis specific with OB domains	protein-coding
mm_33021.1	chr4	121041760	121041771	+	1	NA	intron (NM_007741, intron 2 of 31)	intron (NM_007741, intron 2 of 31)	2199	NM_007741	12840	Mm.269384	NM_007741	ENSMUSG00000028626	Col9a2	AI427499|Col9a-2	collagen, type IX, alpha 2	protein-coding
mm_72878.1	chr8	88697309	88697393	+	1	NA	intron (NM_173369, intron 1 of 16)	CpG	323	NM_001128171	74256	Mm.490395	NM_173369	ENSMUSG00000036712	Cyld	2010013M14Rik|2900009M21Rik|C130039D01Rik|CDMT|CYLD1|EAC|mKIAA0849	CYLD lysine 63 deubiquitinase	protein-coding
mm_70758.1	chr8	21249714	21249720	+	1	NA	promoter-TSS (NM_001177487)	promoter-TSS (NM_001177487)	-45	NM_001177487	100041787	Mm.437206	NM_001177487	ENSMUSG00000074441	Gm15292	ENSMUSG00000074441|OTTMUSG00000019784	predicted gene 15292	protein-coding
mm_119479.1	chr14	47319581	47319595	+	1	NA	3' UTR (NM_178684, exon 4 of 4)	3' UTR (NM_178684, exon 4 of 4)	21274	NM_178684	218975	Mm.212297	NM_178684	ENSMUSG00000021840	Mapk1ip1l	9130202B12|C130032J12Rik	mitogen-activated protein kinase 1 interacting protein 1-like	protein-coding
mm_97479.1	chr11	78324254	78324272	+	1	NA	promoter-TSS (NM_009657)	promoter-TSS (NM_009657)	65	NM_009657	11676	Mm.7729	NM_009657	ENSMUSG00000017390	Aldoc	AI847350|AU040929|Aldo3|Scrg2	aldolase C, fructose-bisphosphate	protein-coding
mm_47384.1	chr5	122990478	122990495	-	1	NA	intron (NR_045820, intron 1 of 2)	intron (NR_045820, intron 1 of 2)	1132	NR_045820	109202	Mm.30769	NM_175405	ENSMUSG00000056735	A930024E05Rik	-	RIKEN cDNA A930024E05 gene	ncRNA
mm_128965.1	chr15	74832118	74832120	-	1	NA	Intergenic	B3|SINE|B2	9524	NM_001033229	110115	Mm.322606	NM_001033229	ENSMUSG00000075604	Cyp11b1	AA389061|CPN1|Cyp11b|Cyp11b-1|FHI	cytochrome P450, family 11, subfamily b, polypeptide 1	protein-coding
mm_77692.1	chr8	126588675	126588692	-	1	NA	3' UTR (NM_001164598, exon 2 of 2)	3' UTR (NM_001164598, exon 2 of 2)	4753	NM_001164598	270110	Mm.334918	NM_001164598	ENSMUSG00000051495	Irf2bp2	E130305N23Rik|IRF-2BP2	interferon regulatory factor 2 binding protein 2	protein-coding
mm_89900.1	chr10	110937917	110937929	+	1	NA	intron (NM_007792, intron 4 of 5)	intron (NM_007792, intron 4 of 5)	17747	NM_007792	13008	Mm.2020	NM_007792	ENSMUSG00000020186	Csrp2	AW551867|Crp2|SmLim	cysteine and glycine-rich protein 2	protein-coding
mm_86288.1	chr9	121914820	121914864	-	1	NA	exon (NM_010012, exon 1 of 1)	exon (NM_010012, exon 1 of 1)	1463	NM_010012	13124	Mm.20889	NM_010012	ENSMUSG00000050445	Cyp8b1	-	cytochrome P450, family 8, subfamily b, polypeptide 1	protein-coding
mm_11237.1	chr2	29858248	29858268	+	1	NA	Intergenic	Intergenic	-11236	NM_207298	99151	Mm.296336	NM_207298	ENSMUSG00000039787	Cercam	2600006K01Rik|AL024097|Ceecam1	cerebral endothelial cell adhesion molecule	protein-coding
mm_43648.1	chr5	138280338	138280355	+	1	NA	promoter-TSS (NM_016964)	promoter-TSS (NM_016964)	-163	NM_016964	50878	Mm.285609	NM_016964	ENSMUSG00000036928	Stag3	SA-2	stromal antigen 3	protein-coding
mm_112542.1	chr13	11840268	11840268	+	1	NA	intron (NM_023868, intron 12 of 104)	intron (NM_023868, intron 12 of 104)	266677	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding
mm_115201.1	chr13	109116231	109116241	+	1	NA	intron (NM_011056, intron 3 of 16)	intron (NM_011056, intron 3 of 16)	-208508	NR_030644	100124489		NR_030644	ENSMUSG00000076946	Mir582	Mirn582|mir-582|mmu-mir-582	microRNA 582	ncRNA
mm_120915.1	chr14	76414795	76414823	+	1	NA	promoter-TSS (NM_001310646)	promoter-TSS (NM_001310646)	-152	NM_001310646	21807	Mm.153272	NM_009366	ENSMUSG00000022010	Tsc22d1	AA589566|AW105905|Egr5|TSC-22|Tgfb1i4|Tsc|Tsc22	TSC22 domain family, member 1	protein-coding
mm_166749.1	chr6	125237095	125237101	-	1	NA	promoter-TSS (NM_001042564)	promoter-TSS (NM_001042564)	-71	NM_001286753	21940	Mm.367714	NM_001033126	ENSMUSG00000030336	Cd27	S152|Tnfrsf7|Tp55	CD27 antigen	protein-coding
mm_8654.1	chr1	156462319	156462326	-	1	NA	intron (NM_009230, intron 2 of 15)	AT_rich|Low_complexity|Low_complexity	12006	NM_009230	20652	Mm.28099	NM_009230	ENSMUSG00000026600	Soat1	8430426K15Rik|ACAT-1|AW550831|Acact|ald|hid	sterol O-acyltransferase 1	protein-coding
mm_132219.1	chr16	32631019	32631030	+	1	NA	3' UTR (NM_011638, exon 19 of 19)	3' UTR (NM_011638, exon 19 of 19)	-13619	NM_001110147	51789	Mm.251115	NM_016788	ENSMUSG00000022791	Tnk2	Ack|Ack-1|Ack1|Cdgip|Pyk1	tyrosine kinase, non-receptor, 2	protein-coding
mm_81877.1	chr9	119323048	119323064	+	1	NA	promoter-TSS (NM_133985)	promoter-TSS (NM_133985)	-629	NM_133985	108737	Mm.293565	NM_133985	ENSMUSG00000036737	Oxsr1	2210022N24Rik|2810422B09Rik|AI462649|AW209236|Osr1|mKIAA1101	oxidative-stress responsive 1	protein-coding
mm_62027.1	chr7	91672431	91672448	+	1	NA	intron (NM_011807, intron 2 of 22)	intron (NM_011807, intron 2 of 22)	-389955	NM_001243046	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_153540.1	chr19	41966659	41966661	-	1	NA	intron (NM_028152, intron 2 of 30)	B1_Mus1|SINE|Alu	14476	NM_028152	72199	Mm.218940	NM_028152	ENSMUSG00000025159	Mms19	2410001K24Rik|2610042O15Rik|AI316855|C79368|C86341|Mms19l	MMS19 (MET18 S. cerevisiae)	protein-coding
mm_48059.1	chr5	136566364	136566375	-	1	NA	promoter-TSS (NM_001291240)	promoter-TSS (NM_001291240)	-388	NM_001291233	13047	Mm.320317	NM_009986	ENSMUSG00000029705	Cux1	CDP|Cutl1|Cux|Cux-1	cut-like homeobox 1	protein-coding
mm_44544.1	chr5	24555429	24555440	-	1	NA	promoter-TSS (NM_177676)	promoter-TSS (NM_177676)	35	NR_033188	231045	Mm.255800	NM_177676	ENSMUSG00000038199	4931409K22Rik	Iqca1l|Iqca1p1	RIKEN cDNA 4931409K22 gene	protein-coding
mm_41416.1	chr5	90804149	90804151	+	1	NA	Intergenic	Intergenic	9616	NM_011339	20309	Mm.64326	NM_011339	ENSMUSG00000029375	Cxcl15	Il8|Scyb15|lungkine|weche	chemokine (C-X-C motif) ligand 15	protein-coding
mm_81618.1	chr9	110797244	110797264	+	1	NA	promoter-TSS (NM_153099)	promoter-TSS (NM_153099)	-931	NM_153099	235628	Mm.292285	NM_153099	ENSMUSG00000044664	Prss42	Tessp2	protease, serine 42	protein-coding
mm_101530.1	chr11	33163073	33163087	-	1	NA	5' UTR (NM_001252261, exon 1 of 10)	5' UTR (NM_001252261, exon 1 of 10)	126	NM_001252261	18148	Mm.485384	NM_008722	ENSMUSG00000057113	Npm1	B23|NO38|Npm	nucleophosmin 1	protein-coding
mm_89681.1	chr10	97517641	97517651	+	1	NA	exon (NM_007833, exon 8 of 8)	exon (NM_007833, exon 8 of 8)	35315	NM_007833	13179	Mm.56769	NM_007833	ENSMUSG00000019929	Dcn	DC|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding
mm_70748.1	chr8	19225475	19225482	+	1	NA	promoter-TSS (NM_054074)	promoter-TSS (NM_054074)	0	NM_054074	116746	Mm.358822	NM_054074	ENSMUSG00000050756	Defb6	BD-6	defensin beta 6	protein-coding
mm_88998.1	chr10	81575307	81575327	+	1	NA	promoter-TSS (NM_019725)	promoter-TSS (NM_019725)	30	NM_001252401	21886	Mm.38608	NM_019725	ENSMUSG00000034771	Tle2	Grg2|mKIAA4188	transducin-like enhancer of split 2	protein-coding
mm_35769.1	chr4	46196299	46196332	-	1	NA	promoter-TSS (NM_011728)	promoter-TSS (NM_011728)	-4	NM_011728	22590	Mm.247036	NM_011728	ENSMUSG00000028329	Xpa	AI573865|Xpac	xeroderma pigmentosum, complementation group A	protein-coding
mm_27122.1	chr3	31310268	31310324	-	1	NA	promoter-TSS (NM_172861)	promoter-TSS (NM_172861)	23	NM_172861	241919	Mm.285366	NM_172861	ENSMUSG00000069072	Slc7a14	A930013N06|BC061928	solute carrier family 7 (cationic amino acid transporter, y+ system), member 14	protein-coding
mm_72929.1	chr8	91115717	91115727	+	1	NA	exon (NM_001282001, exon 21 of 22)	exon (NM_001282001, exon 21 of 22)	18305	NM_001302337	14339	Mm.324588	NM_010241	ENSMUSG00000031667	Aktip	AL023020|Fif|Ft|Ft1|Fts	thymoma viral proto-oncogene 1 interacting protein	protein-coding
mm_118134.1	chr13	104816909	104816951	-	1	NA	promoter-TSS (NM_026072)	promoter-TSS (NM_026072)	23	NM_026072	67285	Mm.235398	NM_026072	ENSMUSG00000021715	Cwc27	3110009E13Rik|NY-CO-10|Sdccag10	CWC27 spliceosome-associated protein	protein-coding
mm_34102.1	chr4	138983702	138983723	+	1	NA	5' UTR (NM_029857, exon 3 of 17)	5' UTR (NM_029857, exon 3 of 17)	10807	NM_029857	77056	Mm.122336	NM_029857	ENSMUSG00000041143	Tmco4	4632413C14Rik|AI430825	transmembrane and coiled-coil domains 4	protein-coding
mm_162556.1	chr1	171849655	171849656	+	1	NA	intron (NM_001289470, intron 2 of 8)	intron (NM_001289470, intron 2 of 8)	9958	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_153008.1	chr19	30175475	30175487	-	1	NA	promoter-TSS (NM_138595)	promoter-TSS (NM_138595)	-40	NM_138595	104174	Mm.274852	NM_138595	ENSMUSG00000024827	Gldc	D030049L12Rik|D19Wsu57e	glycine decarboxylase	protein-coding
mm_73020.1	chr8	94010484	94010490	+	1	NA	intron (NM_011787, intron 1 of 13)	intron (NM_011787, intron 1 of 13)	2153	NM_011787	23802	Mm.34641	NM_011787	ENSMUSG00000031751	Amfr	gp78	autocrine motility factor receptor	protein-coding
mm_133316.1	chr16	77651958	77651981	+	1	NA	Intergenic	IMPB_01|Satellite|Satellite	5696	NR_029540	723952		NR_029540	ENSMUSG00000065472	Mir125b-2	Mirn125b-2|mir-125b-2	microRNA 125b-2	ncRNA
mm_124738.1	chr15	6581056	6581067	+	1	NA	intron (NM_011815, intron 1 of 17)	intron (NM_011815, intron 1 of 17)	1214	NM_011815	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_9498.1	chr1	173730050	173730079	-	1	NA	exon (NM_001204910, exon 5 of 8)	exon (NM_001204910, exon 5 of 8)	11745	NM_001204910	226691	Mm.440876	NM_001204910	ENSMUSG00000073490	Ifi207	AI607873|Pyhin-A	interferon activated gene 207	protein-coding
mm_143970.1	chr17	87306915	87306954	-	1	NA	exon (NM_028639, exon 4 of 20)	exon (NM_028639, exon 4 of 20)	24048	NM_028639	225049	Mm.77396	NM_028639	ENSMUSG00000036918	Ttc7	1110035E02Rik|1700007L07Rik|Ttc7a|fsn|hea	tetratricopeptide repeat domain 7	protein-coding
mm_92186.1	chr10	68097576	68097617	-	1	NA	exon (NM_023598, exon 10 of 10)	exon (NM_023598, exon 10 of 10)	117998	NM_001081346	170799	Mm.209844	NM_133244	ENSMUSG00000037846	Rtkn2	B130039D23Rik|Mbf|Plekhk1	rhotekin 2	protein-coding
mm_145041.1	chr18	39519813	39519847	+	1	NA	Intergenic	Intergenic	-32585	NM_008173	14815	Mm.129481	NM_008173	ENSMUSG00000024431	Nr3c1	GR|Grl-1|Grl1	nuclear receptor subfamily 3, group C, member 1	protein-coding
mm_118933.1	chr14	27114896	27114909	+	1	NA	Intergenic	CpG	-29091	NM_001289686	71704	Mm.248606	NM_027871	ENSMUSG00000021895	Arhgef3	1200004I24Rik|9830169H03Rik|C76747|Xpln	Rho guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_163436.1	chr12	85455614	85455628	+	1	NA	Intergenic	Intergenic	-18280	NM_010234	14281	Mm.246513	NM_010234	ENSMUSG00000021250	Fos	D12Rfj1|c-fos|cFos	FBJ osteosarcoma oncogene	protein-coding
mm_15559.1	chr2	158502634	158502698	+	1	NA	promoter-TSS (NM_145635)	promoter-TSS (NM_145635)	54	NM_145635	246747	Mm.28800	NM_145635	ENSMUSG00000044405	Adig	SMAF-1|Smaf1	adipogenin	protein-coding
mm_122513.1	chr14	47175649	47175664	-	1	NA	intron (NM_008102, intron 1 of 5)	intron (NM_008102, intron 1 of 5)	13746	NM_008102	14528	Mm.10651	NM_008102	ENSMUSG00000037580	Gch1	GTP-CH|GTPCH|Gch	GTP cyclohydrolase 1	protein-coding
mm_592.1	chr1	39551730	39551738	+	1	NA	3' UTR (NM_001033135, exon 7 of 7)	3' UTR (NM_001033135, exon 7 of 7)	-2894	NR_028555	100217461		NR_028555	ENSMUSG00000077704	Snord89	MBII-289	small nucleolar RNA, C/D box 89	snoRNA
mm_51592.1	chr6	83867418	83867423	+	1	NA	Intergenic	CpG	-35679	NM_146169	232164	Mm.404420	NM_146169	ENSMUSG00000045896	Paip2b	-	poly(A) binding protein interacting protein 2B	protein-coding
mm_131024.1	chr16	3542192	3542231	+	1	NA	Intergenic	IAPLTR3|LTR|ERVK	-50187	NM_146860	258859	Mm.377723	NM_146860	ENSMUSG00000051003	Olfr161	MOR131-1|OR912-47M6	olfactory receptor 161	protein-coding
mm_113607.1	chr13	41249877	41249950	+	1	NA	promoter-TSS (NM_001135577)	promoter-TSS (NM_001135577)	69	NM_001135577	108934	Mm.38578	NM_001135577	ENSMUSG00000091264	Smim13	2900036K02Rik	small integral membrane protein 13	protein-coding
mm_83645.1	chr9	49505198	49505225	-	1	NA	3' UTR (NM_001311065, exon 18 of 18)	3' UTR (NM_001311065, exon 18 of 18)	-13077	NR_029465	100036537	Mm.437541	NR_029465	ENSMUSG00000079564	Gm11149	ENSMUSG00000060603|ENSMUSG00000079564	predicted gene 11149	ncRNA
mm_144482.1	chr18	23954877	23954922	+	1	NA	intron (NM_027007, intron 1 of 3)	CpG	211	NM_027007	69256	Mm.218343	NM_027007	ENSMUSG00000024276	Zfp397	2810411K16Rik|6720480F11Rik|AI461664	zinc finger protein 397	protein-coding
mm_127863.1	chr15	8351697	8351712	-	1	NA	exon (NM_027707, exon 10 of 47)	exon (NM_027707, exon 10 of 47)	92759	NM_027707	71175	Mm.240329	NM_027707	ENSMUSG00000022141	Nipbl	Idn3	Nipped-B homolog (Drosophila)	protein-coding
mm_113204.1	chr13	25055465	25055497	+	1	NA	promoter-TSS (NM_177577)	promoter-TSS (NM_177577)	-523	NM_001195617	195208	Mm.284719	NM_177577	ENSMUSG00000035910	Dcdc2a	AW492955|Dcdc2|RU2	doublecortin domain containing 2a	protein-coding
mm_169894.1	chr16	48283761	48283764	+	1	NA	promoter-TSS (NM_028610)	promoter-TSS (NM_028610)	27	NM_001018002	73693	Mm.35597	NM_028610	ENSMUSG00000058550	Dppa4	2410091M23Rik|C76608|ECAT15-1	developmental pluripotency associated 4	protein-coding
mm_116036.1	chr13	26770111	26770119	-	1	NA	promoter-TSS (NM_008232)	promoter-TSS (NM_008232)	50	NM_008232	15192	Mm.7411	NM_008232	ENSMUSG00000045835	Hdgfl1	4921520N01Rik|HRP-1|Hdgfrp1|Pwwp1	hepatoma derived growth factor-like 1	protein-coding
mm_143910.1	chr17	85162681	85162687	-	1	NA	intron (NM_028576, intron 3 of 10)	PB1|SINE|Alu	71984	NM_028576	73582	Mm.260753	NM_028576	ENSMUSG00000071037	Camkmt	1700106N22Rik|AI480743|AV099781|CLNMT|CaM KMT	calmodulin-lysine N-methyltransferase	protein-coding
mm_71608.1	chr8	56305704	56305705	+	1	NA	intron (NM_008278, intron 3 of 6)	MTD|LTR|ERVL-MaLR	11152	NM_008278	15446	Mm.18832	NM_008278	ENSMUSG00000031613	Hpgd	15-PGDH|AV026552	hydroxyprostaglandin dehydrogenase 15 (NAD)	protein-coding
mm_160962.1	chr11	99543139	99543139	-	1	NA	promoter-TSS (NM_001039666)	promoter-TSS (NM_001039666)	19	NM_001039666	406221	Mm.422372	NM_001039666	ENSMUSG00000059169	Krt40	CK-40|K40	keratin 40	protein-coding
mm_93200.1	chr10	94688556	94688612	-	1	NA	promoter-TSS (NM_029852)	promoter-TSS (NM_029852)	29	NR_015524	67723	Mm.116284	NR_015524	ENSMUSG00000097164	Cep83os	4932415G12Rik|Ccdc41os1	centrosomal protein 83, opposite strand	ncRNA
mm_136517.1	chr16	97454016	97454030	-	1	NA	intron (NM_010846, intron 7 of 10)	intron (NM_010846, intron 7 of 10)	8882	NM_010846	17857	Mm.33996	NM_010846	ENSMUSG00000000386	Mx1	AI893580|Mx|Mx-1	MX dynamin-like GTPase 1	protein-coding
mm_60644.1	chr7	44849950	44850026	+	1	NA	promoter-TSS (NM_001253920)	promoter-TSS (NM_001253920)	-19	NM_001253920	67605	Mm.148007	NM_026270	ENSMUSG00000011096	Akt1s1	1110012J22Rik|AI227026|Lobe|Lobel|PRAS40	AKT1 substrate 1 (proline-rich)	protein-coding
mm_161128.1	chr12	111844822	111844822	-	1	NA	exon (NM_011625, exon 6 of 17)	exon (NM_011625, exon 6 of 17)	30652	NM_026752	68520	Mm.390497	NM_026752	ENSMUSG00000021286	Zfyve21	1110013H04Rik|AW558780|C85416	zinc finger, FYVE domain containing 21	protein-coding
mm_114069.1	chr13	54382536	54382552	+	1	NA	3' UTR (NM_009946, exon 4 of 4)	3' UTR (NM_009946, exon 4 of 4)	11195	NM_009946	12890	Mm.268902	NM_009946	ENSMUSG00000025867	Cplx2	921-L|AI413745|AW492120	complexin 2	protein-coding
mm_162850.1	chr10	88224751	88224753	+	1	NA	intron (NM_026070, intron 5 of 6)	intron (NM_026070, intron 5 of 6)	23655	NM_027487	67282	Mm.208465	NM_026070	ENSMUSG00000020056	Washc3	2900091E11Rik|5730495F03Rik|Ccdc53	WASH complex subunit 3	protein-coding
mm_150424.1	chr19	37434835	37434847	+	1	NA	promoter-TSS (NM_008245)	promoter-TSS (NM_008245)	0	NM_008245	15242	Mm.33896	NM_008245	ENSMUSG00000024986	Hhex	Hex|Hex1|Hhex-rs2|Prh|Prhx	hematopoietically expressed homeobox	protein-coding
mm_163487.1	chr12	109453604	109453616	+	1	NA	non-coding (NR_033813, exon 2 of 6)	non-coding (NR_033813, exon 2 of 6)	155	NM_010052	13386	Mm.157069	NM_010052	ENSMUSG00000040856	Dlk1	AW742678|DLK-1|DlkI|FA1|Ly107|Peg9|SCP1|ZOG|pG2|pref-1	delta-like 1 homolog (Drosophila)	protein-coding
mm_9238.1	chr1	171294825	171294839	-	1	NA	intron (NM_025388, intron 1 of 6)	intron (NM_025388, intron 1 of 6)	150	NM_025388	66155	Mm.2815	NM_025388	ENSMUSG00000062963	Ufc1	1110021H02Rik|AA062310|ESTM29	ubiquitin-fold modifier conjugating enzyme 1	protein-coding
mm_153499.1	chr19	41332680	41332724	-	1	NA	intron (NM_031376, intron 2 of 16)	intron (NM_031376, intron 2 of 16)	52368	NM_031376	83490	Mm.222266	NM_031376	ENSMUSG00000025017	Pik3ap1	1810044J04Rik|BCAP	phosphoinositide-3-kinase adaptor protein 1	protein-coding
mm_49969.1	chr6	40768711	40768726	+	1	NA	3' UTR (NM_001171003, exon 48 of 48)	3' UTR (NM_001171003, exon 48 of 48)	118776	NM_139296	194357	Mm.207087	NM_139296	ENSMUSG00000029885	Moxd2	Dbhl1	monooxygenase, DBH-like 2	protein-coding
mm_108361.1	chr12	80790585	80790595	+	1	NA	promoter-TSS (NM_178682)	promoter-TSS (NM_178682)	58	NM_001242419	217684	Mm.341776	NM_178682	ENSMUSG00000021133	Susd6	4933426M11Rik|mKIAA0247	sushi domain containing 6	protein-coding
mm_72216.1	chr8	72687197	72687208	+	1	NA	intron (NM_176940, intron 10 of 18)	RMER17A2|LTR|ERVK	-36068	NM_001113248	20467	Mm.2137	NM_009188	ENSMUSG00000031622	Sin3b	2810430C10Rik	transcriptional regulator, SIN3B (yeast)	protein-coding
mm_77384.1	chr8	120101474	120101506	-	1	NA	promoter-TSS (NM_133967)	promoter-TSS (NM_133967)	-18	NM_133967	102193	Mm.240076	NM_133967	ENSMUSG00000031823	Zdhhc7	AL024087|Gramp2	zinc finger, DHHC domain containing 7	protein-coding
mm_146682.1	chr18	12860141	12860155	-	1	NA	intron (NM_207530, intron 15 of 27)	intron (NM_207530, intron 15 of 27)	2565	NM_001252493	64291	Mm.259470	NM_020573	ENSMUSG00000044252	Osbpl1a	G430090F17Rik|Gm753|ORP-1|Osbpl1b	oxysterol binding protein-like 1A	protein-coding
mm_109648.1	chr12	112855419	112855427	+	1	NA	intron (NM_019925, intron 2 of 2)	intron (NM_019925, intron 2 of 2)	5493	NM_019925	56696	Mm.20455	NM_019925	ENSMUSG00000021298	Gpr132	G2a	G protein-coupled receptor 132	protein-coding
mm_137374.1	chr17	25579162	25579209	+	1	NA	promoter-TSS (NM_029624)	promoter-TSS (NM_029624)	11	NR_045520	76483	Mm.12787	NM_029624	ENSMUSG00000002279	Lmf1	2400010G15Rik|AW822050|Tmem112|cld	lipase maturation factor 1	protein-coding
mm_169092.1	chr13	39939580	39939580	+	1	NA	Intergenic	Intergenic	348431	NM_172143	218165	Mm.364096	NM_172143	ENSMUSG00000047094	Ofcc1	opo	orofacial cleft 1 candidate 1	protein-coding
mm_44758.1	chr5	31526694	31526747	-	1	NA	promoter-TSS (NM_009206)	promoter-TSS (NM_009206)	42	NM_028150	72195	Mm.164187	NM_028150	ENSMUSG00000053134	Supt7l	2610524B01Rik|6030455L14Rik	suppressor of Ty 7-like	protein-coding
mm_120664.1	chr14	70545386	70545394	+	1	NA	5' UTR (NM_180588, exon 1 of 8)	5' UTR (NM_180588, exon 1 of 8)	139	NM_180588	72549	Mm.46742	NM_180588	ENSMUSG00000033589	Reep4	2700029E10Rik	receptor accessory protein 4	protein-coding
mm_156168.1	chrX	130116160	130116187	+	1	NA	intron (NM_172493, intron 22 of 26)	intron (NM_172493, intron 22 of 26)	366431	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diaph2	Dia3|Diap2|Drf2|E430022I22Rik	diaphanous related formin 2	protein-coding
mm_155535.1	chrX	74303939	74303984	+	1	NA	exon (NM_018794, exon 10 of 10)	exon (NM_018794, exon 10 of 10)	-1051	NM_010273	14567	Mm.205830	NM_010273	ENSMUSG00000015291	Gdi1	GDIA|GDIalpha	guanosine diphosphate (GDP) dissociation inhibitor 1	protein-coding
mm_153403.1	chr19	40511821	40511823	-	1	NA	intron (NM_009166, intron 1 of 23)	intron (NM_009166, intron 1 of 23)	1914	NM_178362	20411	Mm.210815	NM_009166	ENSMUSG00000025006	Sorbs1	2310065E01Rik|9530001P15Rik|CAP|SH3P12|Sh3d5|mKIAA1296	sorbin and SH3 domain containing 1	protein-coding
mm_83867.1	chr9	54850065	54850068	-	1	NA	Intergenic	MERVL_2A-int|LTR|ERVL	-13689	NM_022655	64602	Mm.208991	NM_022655	ENSMUSG00000032293	Ireb2	D9Ertd85e|Irp2	iron responsive element binding protein 2	protein-coding
mm_121078.1	chr14	99046407	99046429	+	1	NA	promoter-TSS (NM_175245)	promoter-TSS (NM_175245)	41	NM_175265	77744	Mm.23503	NM_175265	ENSMUSG00000022070	Bora	6720463M24Rik|AI317232	bora, aurora kinase A activator	protein-coding
mm_56967.1	chr6	120114756	120114802	-	1	NA	intron (NM_016718, intron 1 of 3)	intron (NM_016718, intron 1 of 3)	21399	NM_016718	29862	Mm.103668	NM_016718	ENSMUSG00000041377	Ninj2	-	ninjurin 2	protein-coding
mm_169393.1	chr14	43694580	43694580	+	1	NA	Intergenic	BGLII|LTR|ERVK	-86567	NM_001098269	100042342	Mm.429750	NM_001098269	ENSMUSG00000095528	Gm10375	ENSMUSG00000072602	predicted gene 10375	protein-coding
mm_18681.1	chr2	71347823	71347851	-	1	NA	intron (NM_172436, intron 2 of 17)	intron (NM_172436, intron 2 of 17)	19717	NM_172436	78830	Mm.30928	NM_172436	ENSMUSG00000027010	Slc25a12	2610002D09Rik|AI839531|B230107K20Rik|BB129864	solute carrier family 25 (mitochondrial carrier, Aralar), member 12	protein-coding
mm_171016.1	chr2	83960701	83960718	+	1	NA	Intergenic	CpG	-19483	NM_027964	71861	Mm.116957	NM_027964	ENSMUSG00000034552	Zswim2	1700025P14Rik|4933437F18Rik|MEX	zinc finger SWIM-type containing 2	protein-coding
mm_125362.1	chr15	39434568	39434580	+	1	NA	intron (NM_001256382, intron 3 of 26)	intron (NM_001256382, intron 3 of 26)	-224937	NM_001256384	116838	Mm.309296	NM_053271	ENSMUSG00000037386	Rims2	2810036I15Rik|AW048769|RIM2|Rab3ip2|Rim2(+40A)|Rim2(+44A)|Rim2(+4A)|Serg2|Syt3-rs|mKIAA0751	regulating synaptic membrane exocytosis 2	protein-coding
mm_146396.1	chr18	82910659	82910678	+	1	NA	promoter-TSS (NM_183033)	promoter-TSS (NM_183033)	-211	NM_183033	329003	Mm.326526	NM_183033	ENSMUSG00000058881	Zfp516	C330029B10Rik|D230016L03|Zfp26l|Znf516|mKIAA0222	zinc finger protein 516	protein-coding
mm_111841.1	chr12	107931309	107931310	-	1	NA	intron (NM_001286343, intron 1 of 1)	intron (NM_001286343, intron 1 of 1)	72105	NM_001079883	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_110096.1	chr12	25189603	25189614	-	1	NA	Intergenic	Intergenic	60434	NR_045844	432641	Mm.112955	NR_045844		Gm17746	-	predicted gene, 17746	ncRNA
mm_17316.1	chr2	26445111	26445116	-	1	NA	5' UTR (NM_153125, exon 1 of 30)	5' UTR (NM_153125, exon 1 of 30)	103	NM_153125	227648	Mm.206371	NM_153125	ENSMUSG00000026924	Sec16a	AU024582|C230052J16Rik	SEC16 homolog A, endoplasmic reticulum export factor	protein-coding
mm_30271.1	chr3	146781352	146781431	-	1	NA	promoter-TSS (NM_001164200)	promoter-TSS (NM_001164200)	25	NM_001164200	18749	Mm.16766	NM_011100	ENSMUSG00000005034	Prkacb	CbPKA|Pkacb	protein kinase, cAMP dependent, catalytic, beta	protein-coding
mm_100484.1	chr11	120236494	120236524	+	1	NA	intron (NM_001347621, intron 1 of 27)	CpG	3562	NM_198423	268515	Mm.309498	NM_198423	ENSMUSG00000039741	Bahcc1	B930044J06|BC060615	BAH domain and coiled-coil containing 1	protein-coding
mm_117447.1	chr13	74770627	74770669	-	1	NA	promoter-TSS (NM_001301157)	promoter-TSS (NM_001301157)	88	NM_001301156	12380	Mm.29163	NM_009817	ENSMUSG00000021585	Cast	-	calpastatin	protein-coding
mm_142821.1	chr17	51756453	51756467	-	1	NA	intron (NM_009122, intron 9 of 10)	intron (NM_009122, intron 9 of 10)	55594	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_41340.1	chr5	90497277	90497297	+	1	NA	exon (NM_007423, exon 5 of 15)	exon (NM_007423, exon 5 of 15)	6573	NM_007423	11576	Mm.358570	NM_007423	ENSMUSG00000054932	Afp	-	alpha fetoprotein	protein-coding
mm_23926.1	chr3	83766603	83766613	+	1	NA	exon (NM_009144, exon 1 of 3)	exon (NM_009144, exon 1 of 3)	287	NM_009144	20319	Mm.19155	NM_009144	ENSMUSG00000027996	Sfrp2	AI851596|Sdf5	secreted frizzled-related protein 2	protein-coding
mm_53016.1	chr6	123283419	123283442	+	1	NA	3' UTR (NM_019948, exon 6 of 6)	3' UTR (NM_019948, exon 6 of 6)	6441	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_136374.1	chr16	92825606	92825641	-	1	NA	exon (NM_001111021, exon 2 of 8)	exon (NM_001111021, exon 2 of 8)	451	NM_001111021	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_86685.1	chr10	18407779	18407783	+	1	NA	5' UTR (NM_173390, exon 1 of 7)	5' UTR (NM_173390, exon 1 of 7)	106	NM_173390	215819	Mm.297971	NM_173390	ENSMUSG00000039835	Nhsl1	5730409E15Rik|A630035H13Rik|A730096F01|BC013565|D10Bwg0940e|mKIAA1357	NHS-like 1	protein-coding
mm_52612.1	chr6	117173799	117173816	+	1	NA	3' UTR (NM_021704, exon 3 of 3)	3' UTR (NM_021704, exon 3 of 3)	5272	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_22158.1	chr2	172901973	172901986	-	1	NA	intron (NM_007557, intron 2 of 6)	intron (NM_007557, intron 2 of 6)	38342	NM_007557	12162	Mm.595	NM_007557	ENSMUSG00000008999	Bmp7	OP1	bone morphogenetic protein 7	protein-coding
mm_162209.1	chrX	136033367	136033367	+	1	NA	promoter-TSS (NM_029541)	promoter-TSS (NM_029541)	0	NM_029541	76219	Mm.482965	NM_029541	ENSMUSG00000048355	Arxes1	6530401D17Rik|Spc22/23|Spcs3	adipocyte-related X-chromosome expressed sequence 1	protein-coding
mm_4644.1	chr1	180199800	180199816	+	1	NA	Intergenic	L2a|LINE|L2	-3788	NM_023341	67426	Mm.38330	NM_023341	ENSMUSG00000026489	Coq8a	4632432J16Rik|AI462003|Adck3|Cabc1|mKIAA0451	coenzyme Q8A	protein-coding
mm_106551.1	chr11	120598347	120598405	-	1	NA	promoter-TSS (NM_011568)	promoter-TSS (NM_011568)	-11	NM_011568	21681	Mm.1886	NM_011568	ENSMUSG00000025134	Alyref	ALY|REF1|Refbp1|Thoc4	Aly/REF export factor	protein-coding
mm_24434.1	chr3	90541259	90541276	+	1	NA	promoter-TSS (NM_026416)	promoter-TSS (NM_026416)	44	NM_026416	67860	Mm.331185	NM_026416	ENSMUSG00000074457	S100a16	2300002L21Rik|AI325039|AI663996|DT1P1A7|S100F	S100 calcium binding protein A16	protein-coding
mm_167098.1	chr7	109798673	109798678	+	1	NA	TTS (NM_020052)	TTS (NM_020052)	-17130	NM_020610	78593	Mm.275374	NM_020610	ENSMUSG00000034825	Nrip3	A330103B05Rik|D7H11orf14|ICRFP703B1614Q5.2	nuclear receptor interacting protein 3	protein-coding
mm_42871.1	chr5	122240656	122240671	+	1	NA	exon (NM_001042489, exon 8 of 8)	exon (NM_001042489, exon 8 of 8)	23797	NR_104441	654470	Mm.28804	NM_001039153	ENSMUSG00000038593	Tctn1	G730031O11Rik|Tect1	tectonic family member 1	protein-coding
mm_94812.1	chr11	23067993	23068005	+	1	NA	Intergenic	CpG	54612	NM_028672	73873	Mm.252406	NM_028672	ENSMUSG00000049811	Fam161a	4930430E16Rik	family with sequence similarity 161, member A	protein-coding
mm_51079.1	chr6	66957027	66957031	+	1	NA	intron (NM_001177560, intron 3 of 4)	intron (NM_001177560, intron 3 of 4)	60138	NM_001177558	14701	Mm.234342	NM_025278	ENSMUSG00000036402	Gng12	2010305F15Rik|AA536815|AI115529|AI314170|AI842738	guanine nucleotide binding protein (G protein), gamma 12	protein-coding
mm_102283.1	chr11	55399219	55399238	-	1	NA	exon (NM_009242, exon 7 of 10)	exon (NM_009242, exon 7 of 10)	20852	NM_009242	20692	Mm.291442	NM_009242	ENSMUSG00000018593	Sparc	BM-40|ON	secreted acidic cysteine rich glycoprotein	protein-coding
mm_40010.1	chr5	33018888	33018903	+	1	NA	promoter-TSS (NM_011738)	promoter-TSS (NM_011738)	79	NM_011738	22629	Mm.332314	NM_011738	ENSMUSG00000018965	Ywhah	-	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta polypeptide	protein-coding
mm_96914.1	chr11	70460072	70460112	+	1	NA	promoter-TSS (NM_023158)	promoter-TSS (NM_023158)	-108	NM_023158	66102	Mm.425692	NM_023158	ENSMUSG00000018920	Cxcl16	0910001K24Rik|AV290116|BB024863|CXCL16v1|CXCL16v2|SR-PSOX|Zmynd15|b2b498Clo	chemokine (C-X-C motif) ligand 16	protein-coding
mm_159195.1	chr2	119208633	119208633	+	1	NA	promoter-TSS (NM_028054)	promoter-TSS (NM_028054)	-87	NM_001164827	72008	Mm.386807	NM_028054	ENSMUSG00000068580	Zfyve19	1500041L05Rik|ANCHR	zinc finger, FYVE domain containing 19	protein-coding
mm_68052.1	chr7	101585594	101585607	-	1	NA	Intergenic	Intergenic	-4439	NM_019915	11872	Mm.57008	NM_019915	ENSMUSG00000030651	Art2b	ART2.2|ARTC2|Art|Ly92b|Rt-6|Rt6|Rt6-2	ADP-ribosyltransferase 2b	protein-coding
mm_63760.1	chr7	131112140	131112152	+	1	NA	exon (NM_007769, exon 44 of 47)	exon (NM_007769, exon 44 of 47)	34137	NM_173409	233918	Mm.78341	NM_173409	ENSMUSG00000013668	4933402N03Rik	4930412O05	RIKEN cDNA 4933402N03 gene	protein-coding
mm_13452.1	chr2	105425979	105425983	+	1	NA	Intergenic	Intergenic	-26662	NM_009037	19672	Mm.4876	NM_009037	ENSMUSG00000005973	Rcn1	Rcn	reticulocalbin 1	protein-coding
mm_55829.1	chr6	83124769	83124779	-	1	NA	exon (NM_023547, exon 2 of 5)	exon (NM_023547, exon 2 of 5)	255	NM_023547	70020	Mm.27814	NM_023547	ENSMUSG00000030034	Ino80b	2510009I23Rik|HMG1YL4|Hmga1l4|Papa1|Znhit4	INO80 complex subunit B	protein-coding
mm_138063.1	chr17	33930847	33930930	+	1	NA	intron (NM_009059, intron 2 of 17)	intron (NM_009059, intron 2 of 17)	994	NM_009059	19732	Mm.43777	NM_009059	ENSMUSG00000041354	Rgl2	KE1.5|Rab2l|Rgt2|Rlf	ral guanine nucleotide dissociation stimulator-like 2	protein-coding
mm_31507.1	chr4	53631397	53631457	+	1	NA	promoter-TSS (NM_176966)	promoter-TSS (NM_176966)	-44	NM_176966	319636	Mm.103464	NM_176966	ENSMUSG00000054752	Fsd1l	A230072O16Rik|Ccdc10|Csdufd1|Fsd1nl|OTTMUSG00000007002	fibronectin type III and SPRY domain containing 1-like	protein-coding
mm_85331.1	chr9	102354643	102354672	-	1	NA	promoter-TSS (NM_173447)	promoter-TSS (NM_173447)	36	NM_001168296	270190	Mm.22897	NM_173447	ENSMUSG00000032537	Ephb1	9330129L11|AW488255|C130099E04Rik|Cek6|ENSMUSG00000074119|Elk|Elkh|Hek6|Net	Eph receptor B1	protein-coding
mm_125206.1	chr15	33221381	33221391	+	1	NA	intron (NM_176073, intron 2 of 7)	intron (NM_176073, intron 2 of 7)	138257	NM_176073	54381	Mm.158251	NM_018755	ENSMUSG00000039007	Cpq	1190003P12Rik|2610034C17Rik|Hls2|Lal-1|Pgcp	carboxypeptidase Q	protein-coding
mm_18510.1	chr2	62617328	62617347	-	1	NA	exon (NM_027835, exon 5 of 16)	exon (NM_027835, exon 5 of 16)	28918	NM_027835	71586	Mm.136224	NM_027835	ENSMUSG00000026896	Ifih1	9130009C22Rik|Helicard|Hlcd|MDA5|RLR-2	interferon induced with helicase C domain 1	protein-coding
mm_10307.1	chr2	11172081	11172140	+	1	NA	promoter-TSS (NM_008859)	promoter-TSS (NM_008859)	-272	NM_008859	18761	Mm.329993	NM_008859	ENSMUSG00000026778	Prkcq	A130035A12Rik|AW494342|PKC-0|PKC-theta|PKCtheta|Pkcq	protein kinase C, theta	protein-coding
mm_129301.1	chr15	77307044	77307058	-	1	NA	promoter-TSS (NM_175387)	promoter-TSS (NM_175387)	2	NM_001110827	93686	Mm.202774	NM_053104	ENSMUSG00000033565	Rbfox2	Fbm2|Fxh|Hrnbp2|Rbm9	RNA binding protein, fox-1 homolog (C. elegans) 2	protein-coding
mm_70168.1	chr7	143627842	143627846	-	1	NA	promoter-TSS (NM_175649)	promoter-TSS (NM_175649)	1	NM_175649	244237	Mm.247498	NM_175649	ENSMUSG00000045362	Tnfrsf26	Tnfrh3|Tnfrsf24	tumor necrosis factor receptor superfamily, member 26	protein-coding
mm_122517.1	chr14	47186954	47186957	-	1	NA	intron (NM_008102, intron 1 of 5)	intron (NM_008102, intron 1 of 5)	2447	NM_008102	14528	Mm.10651	NM_008102	ENSMUSG00000037580	Gch1	GTP-CH|GTPCH|Gch	GTP cyclohydrolase 1	protein-coding
mm_151527.1	chr19	58744073	58744094	+	1	NA	TTS (NM_018874)	TTS (NM_018874)	15196	NM_018874	18946	Mm.10753	NM_018874	ENSMUSG00000042179	Pnliprp1	Plrp1	pancreatic lipase related protein 1	protein-coding
mm_157756.1	chrX	73494857	73494878	-	1	NA	3' UTR (NM_007542, exon 8 of 8)	3' UTR (NM_007542, exon 8 of 8)	-8219	NM_001310537	320707	Mm.210095	NM_177236	ENSMUSG00000031376	Atp2b3	6430519O13Rik|Pmca3	ATPase, Ca++ transporting, plasma membrane 3	protein-coding
mm_75532.1	chr8	57320367	57320379	-	1	NA	promoter-TSS (NM_010402)	promoter-TSS (NM_010402)	486	NR_110474	102636514		NR_110474	ENSMUSG00000100510	Uph	-	upperhand	ncRNA
mm_106780.1	chr12	4635614	4635629	+	1	NA	exon (NM_001198969, exon 13 of 17)	exon (NM_001198969, exon 13 of 17)	42613	NM_001198968	20403	Mm.341204	NM_011365	ENSMUSG00000020640	Itsn2	AI327390|Ese2|Sh3d1B|Sh3p18|mKIAA1256	intersectin 2	protein-coding
mm_166574.1	chr6	50247515	50247516	-	1	NA	intron (NM_018769, intron 2 of 9)	intron (NM_018769, intron 2 of 9)	14254	NM_018769	54722	Mm.248361	NM_018769	ENSMUSG00000029821	Dfna5	2310037D07Rik|4932441K13Rik|Dfna5h|EG14210|Fin15	deafness, autosomal dominant 5 (human)	protein-coding
mm_91706.1	chr10	44058911	44058922	-	1	NA	Intergenic	Intergenic	-54070	NM_172393	11630	Mm.292082	NM_172393	ENSMUSG00000019866	Aim1	AI462491|AI463325	absent in melanoma 1	protein-coding
mm_8735.1	chr1	160212612	160212623	-	1	NA	intron (NM_009786, intron 1 of 5)	CpG	275	NM_009786	12301	Mm.10702	NM_009786	ENSMUSG00000014226	Cacybp	SIP	calcyclin binding protein	protein-coding
mm_7858.1	chr1	132523682	132523706	-	1	NA	exon (NM_177129, exon 11 of 23)	exon (NM_177129, exon 11 of 23)	17464	NM_029025	74626	Mm.34611	NM_029025	ENSMUSG00000048174	Tmem81	4930429O20Rik|AI465369	transmembrane protein 81	protein-coding
mm_159230.1	chr2	135741806	135741806	+	1	NA	promoter-TSS (NM_013829)	promoter-TSS (NM_013829)	-24	NM_013829	18798	Mm.38009	NM_013829	ENSMUSG00000039943	Plcb4	A930039J07Rik|AI854601|C230058B11Rik	phospholipase C, beta 4	protein-coding
mm_64819.1	chr7	7298739	7298749	-	1	NA	promoter-TSS (NM_001302387)	promoter-TSS (NM_001302387)	92	NM_001302387	12727	Mm.297883	NM_011334	ENSMUSG00000000605	Clcn4	Clc4-2|Clcn4-2	chloride channel, voltage-sensitive 4	protein-coding
mm_1089.1	chr1	59619399	59619415	+	1	NA	intron (NM_001013771, intron 13 of 19)	intron (NM_001013771, intron 13 of 19)	51427	NM_009460	22218	Mm.362118	NM_009460	ENSMUSG00000026021	Sumo1	GMP1|PIC1|SENTRIN|SMT3|SMT3H3|SMTP3|SUMO-1|Smt3C|Ubl1	small ubiquitin-like modifier 1	protein-coding
mm_3379.1	chr1	139454748	139454825	+	1	NA	promoter-TSS (NM_009791)	promoter-TSS (NM_009791)	13	NM_009791	12316	Mm.168523	NM_009791	ENSMUSG00000033952	Aspm	Calmbp1|D330028K02Rik|MCPH5|Sha1	asp (abnormal spindle)-like, microcephaly associated (Drosophila)	protein-coding
mm_147739.1	chr18	61108562	61108592	-	1	NA	intron (NM_001037859, intron 2 of 21)	intron (NM_001037859, intron 2 of 21)	3005	NM_001037859	12978	Mm.22574	NM_007779	ENSMUSG00000024621	Csf1r	AI323359|CD115|CSF-1R|Csfmr|Fim-2|Fim2|Fms|M-CSF-R|M-CSFR	colony stimulating factor 1 receptor	protein-coding
mm_137620.1	chr17	28298339	28298361	+	1	NA	exon (NM_011145, exon 6 of 8)	exon (NM_011145, exon 6 of 8)	-15180	NR_028297	72775	Mm.201859	NM_028348	ENSMUSG00000007570	Fance	2810451D06Rik|AI415634|AW209126	Fanconi anemia, complementation group E	protein-coding
mm_147466.1	chr18	46713410	46713412	-	1	NA	3' UTR (NM_033037, exon 5 of 5)	3' UTR (NM_033037, exon 5 of 5)	14931	NM_033037	12583	Mm.241056	NM_033037	ENSMUSG00000033022	Cdo1	1300002L19Rik|Cdo|D18Ucla3	cysteine dioxygenase 1, cytosolic	protein-coding
mm_104527.1	chr11	96111959	96111992	-	1	NA	promoter-TSS (NM_001271018)	promoter-TSS (NM_001271018)	-13	NM_001271018	76815	Mm.296049	NM_029755	ENSMUSG00000006056	Calcoco2	2410154J16Rik|C77254|Ndp52|Ndp52l1	calcium binding and coiled-coil domain 2	protein-coding
mm_106824.1	chr12	7987790	7987800	+	1	NA	exon (NM_009693, exon 9 of 29)	exon (NM_009693, exon 9 of 29)	10118	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_145107.1	chr18	44104650	44104666	+	1	NA	exon (NM_030061, exon 1 of 4)	exon (NM_030061, exon 1 of 4)	135	NM_030061	78242	Mm.99782	NM_030061	ENSMUSG00000061144	Spink12	9230117E20Rik	serine peptidase inhibitor, Kazal type 12	protein-coding
mm_38756.1	chr4	147848359	147848425	-	1	NA	promoter-TSS (NM_198619)	promoter-TSS (NM_198619)	-17	NM_198619	242747	Mm.332053	NM_198619	ENSMUSG00000059423	Zfp933	2810408P10Rik	zinc finger protein 933	protein-coding
mm_125129.1	chr15	30187960	30187964	+	1	NA	intron (NM_008729, intron 1 of 22)	intron (NM_008729, intron 1 of 22)	15369	NM_008729	18163	Mm.321648	NM_008729	ENSMUSG00000022240	Ctnnd2	Catnd2|Nprap|neurojugin	catenin (cadherin associated protein), delta 2	protein-coding
mm_80943.1	chr9	102718425	102718490	+	1	NA	intron (NM_019764, intron 1 of 9)	CpG	653	NM_019764	56332	Mm.21145	NM_019764	ENSMUSG00000032531	Amotl2	AW549739|C79691|Lccp|MASCOT|mKIAA0989	angiomotin-like 2	protein-coding
mm_124522.1	chr14	122105835	122105841	-	1	NA	non-coding (NR_015586, exon 1 of 4)	non-coding (NR_015586, exon 1 of 4)	1136	NR_015586	319727	Mm.215552	NR_015586		A330035P11Rik	-	RIKEN cDNA A330035P11 gene	ncRNA
mm_82442.1	chr9	15288049	15288081	-	1	NA	intron (NM_133732, intron 6 of 7)	intron (NM_133732, intron 6 of 7)	-8198	NM_144933	234959	Mm.44151	NM_144933	ENSMUSG00000031935	Med17	77kDa|C330002H14Rik|Crsp6|Trap80	mediator complex subunit 17	protein-coding
mm_137852.1	chr17	31098018	31098020	+	1	NA	intron (NM_009593, intron 4 of 14)	ORR1A3|LTR|ERVL-MaLR	31592	NM_011575	21786	Mm.4641	NM_011575	ENSMUSG00000024029	Tff3	ITF|mITF	trefoil factor 3, intestinal	protein-coding
mm_18562.1	chr2	65238786	65238796	-	1	NA	promoter-TSS (NM_177025)	promoter-TSS (NM_177025)	-165	NM_027225	319876	Mm.34159	NM_027225	ENSMUSG00000034903	Cobll1	1810047P18Rik|Coblr1|D430044D16Rik	Cobl-like 1	protein-coding
mm_101563.1	chr11	34098540	34098556	-	1	NA	Intergenic	Intergenic	51347	NM_010696	16822	Mm.265350	NM_010696	ENSMUSG00000002699	Lcp2	AI323664|BB161688|SLP-76|SLP76|m1Khoe|twm	lymphocyte cytosolic protein 2	protein-coding
mm_18132.1	chr2	45005257	45005274	-	1	NA	intron (NM_001289521, intron 3 of 8)	intron (NM_001289521, intron 3 of 8)	17912	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_103855.1	chr11	83286665	83286679	-	1	NA	promoter-TSS (NM_001166028)	promoter-TSS (NM_001166028)	54	NM_001166028	237890	Mm.297670	NM_001166028	ENSMUSG00000082101	Slfn14	Gm20|Slfn14-ps	schlafen 14	protein-coding
mm_16115.1	chr2	169723963	169723977	+	1	NA	intron (NM_080455, intron 1 of 1)	intron (NM_080455, intron 1 of 1)	90324	NM_080455	228911	Mm.315789	NM_080455	ENSMUSG00000047907	Tshz2	2900073F20Rik|B830045G17|Mtsh2|Sdccag33l|Tsh2|Zfp218|mKIAA4248|teashirt2	teashirt zinc finger family member 2	protein-coding
mm_76859.1	chr8	105467906	105467934	-	1	NA	exon (NM_026481, exon 4 of 4)	exon (NM_026481, exon 4 of 4)	3502	NM_026481	67971	Mm.29358	NM_026481	ENSMUSG00000014846	Tppp3	2700055K07Rik|CGI-38|Ceacam9|mmCGM8	tubulin polymerization-promoting protein family member 3	protein-coding
mm_88828.1	chr10	80804212	80804227	+	1	NA	exon (NM_013651, exon 9 of 9)	exon (NM_013651, exon 9 of 9)	-1029	NM_007445	11705	Mm.376094	NM_007445	ENSMUSG00000035262	Amh	MIS	anti-Mullerian hormone	protein-coding
mm_82678.1	chr9	22132284	22132300	-	1	NA	promoter-TSS (NM_001102404)	promoter-TSS (NM_001102404)	-427	NM_001102404	11433	Mm.46354	NM_007388	ENSMUSG00000001348	Acp5	TRACP|TRAP	acid phosphatase 5, tartrate resistant	protein-coding
mm_86542.1	chr10	8884063	8884098	+	1	NA	intron (NM_175155, intron 1 of 19)	intron (NM_175155, intron 1 of 19)	1990	NM_175155	70097	Mm.338275	NM_175155	ENSMUSG00000015305	Sash1	1100001C18Rik|2500002E12Rik|A330076K04Rik|mKIAA0790	SAM and SH3 domain containing 1	protein-coding
mm_112607.1	chr13	14522497	14522505	+	1	NA	intron (NM_001081348, intron 1 of 28)	intron (NM_001081348, intron 1 of 28)	725	NM_001081348	94253	Mm.125298	NM_153130	ENSMUSG00000021301	Hecw1	9330116H24Rik|AV273951|E130207I19Rik|Nedl1	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	protein-coding
mm_27049.1	chr3	27194196	27194206	-	1	NA	intron (NM_178772, intron 1 of 4)	L3|LINE|CR1	11197	NM_178772	320024	Mm.24576	NM_178772	ENSMUSG00000027698	Nceh1	Aadacl1|B230106I24Rik|CPO-BP|Nceh	neutral cholesterol ester hydrolase 1	protein-coding
mm_162171.1	chrX	101288337	101288337	+	1	NA	intron (NM_021521, intron 30 of 44)	intron (NM_021521, intron 30 of 44)	-10842	NM_172932	245537	Mm.121508	NM_172932	ENSMUSG00000031302	Nlgn3	A230085M13Rik|HNL3|NL3	neuroligin 3	protein-coding
mm_95488.1	chr11	51605590	51605609	+	1	NA	exon (NM_010448, exon 3 of 7)	exon (NM_010448, exon 3 of 7)	1282	NM_001048061	15384	Mm.256875	NM_010448	ENSMUSG00000020358	Hnrnpab	3010025C11Rik|CBF-A|Cgbfa|Hnrpab	heterogeneous nuclear ribonucleoprotein A/B	protein-coding
mm_119266.1	chr14	34052738	34052748	+	1	NA	promoter-TSS (NM_172808)	promoter-TSS (NM_172808)	-727	NM_172808	239029	Mm.477093	NM_172808	ENSMUSG00000047441	Antxrl	1700112N15Rik|4933430J11	anthrax toxin receptor-like	protein-coding
mm_51562.1	chr6	83523192	83523240	+	1	NA	exon (NM_009610, exon 4 of 9)	exon (NM_009610, exon 4 of 9)	13035	NM_009610	11468	Mm.292865	NM_009610	ENSMUSG00000059430	Actg2	ACTA3|Act-4|Act4|SMGA	actin, gamma 2, smooth muscle, enteric	protein-coding
mm_76090.1	chr8	79638712	79638717	-	1	NA	promoter-TSS (NM_001256033)	promoter-TSS (NM_001256033)	-962	NM_001256033	73945	Mm.34348	NM_001081164	ENSMUSG00000036990	Otud4	4930431L18Rik|AI449692|D8Ertd69e|mKIAA1046	OTU domain containing 4	protein-coding
mm_97237.1	chr11	75656004	75656037	+	1	NA	promoter-TSS (NM_001080775)	promoter-TSS (NM_001080775)	5	NM_001080775	17913	Mm.234502	NM_008659	ENSMUSG00000017774	Myo1c	C80397|MMIb|MYO1E|NMI|mm1beta|myr2	myosin IC	protein-coding
mm_111932.1	chr12	108888777	108888783	-	1	NA	intron (NM_001164314, intron 1 of 9)	intron (NM_001164314, intron 1 of 9)	4418	NM_001164488	22375	Mm.38433	NM_011710	ENSMUSG00000021266	Wars	TrpRS|WRS	tryptophanyl-tRNA synthetase	protein-coding
mm_117017.1	chr13	58127105	58127116	-	1	NA	3' UTR (NM_029872, exon 1 of 1)	3' UTR (NM_029872, exon 1 of 1)	1446	NM_029872	77134	Mm.490274	NM_029872	ENSMUSG00000007836	Hnrnpa0	1110055B05Rik|3010025E17Rik|Hnrpa0|hnRNP A0	heterogeneous nuclear ribonucleoprotein A0	protein-coding
mm_98534.1	chr11	95009765	95009782	+	1	NA	promoter-TSS (NM_146025)	promoter-TSS (NM_146025)	-106	NM_146025	217125	Mm.297199	NM_146025	ENSMUSG00000047181	Samd14	AI839049|AI854782|BC034054	sterile alpha motif domain containing 14	protein-coding
mm_5157.1	chr1	9991920	9991930	-	1	NA	intron (NR_110971, intron 5 of 6)	intron (NR_110971, intron 5 of 6)	17211	NR_110971	69312	Mm.386795	NM_027033	ENSMUSG00000025916	Ppp1r42	1700011J18Rik|4930418G15Rik|Lrrc67|TLRR	protein phosphatase 1, regulatory subunit 42	protein-coding
mm_55434.1	chr6	66875651	66875689	-	1	NA	Intergenic	Intergenic	-20727	NM_001177557	14701	Mm.234342	NM_025278	ENSMUSG00000036402	Gng12	2010305F15Rik|AA536815|AI115529|AI314170|AI842738	guanine nucleotide binding protein (G protein), gamma 12	protein-coding
mm_77769.1	chr9	3005621	3005636	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	33115	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_9408.1	chr1	172274432	172274454	-	1	NA	3' UTR (NM_178405, exon 23 of 23)	3' UTR (NM_178405, exon 23 of 23)	-16019	NM_013734	27222	Mm.482392	NM_013734	ENSMUSG00000007107	Atp1a4	-	ATPase, Na+/K+ transporting, alpha 4 polypeptide	protein-coding
mm_1635.1	chr1	74506379	74506387	+	1	NA	promoter-TSS (NM_001310662)	promoter-TSS (NM_001310662)	323	NM_021383	58184	Mm.291708	NM_021383	ENSMUSG00000026174	Cnot9	2610007F23Rik|AI593551|Fl10|Rqcd1	CCR4-NOT transcription complex, subunit 9	protein-coding
mm_71764.1	chr8	66400507	66400528	+	1	NA	intron (NM_175188, intron 5 of 7)	Lx8|LINE|L1	14216	NM_001166375	72925	Mm.380457	NM_175188	ENSMUSG00000036469	March1	2900024D24Rik|BB085186	membrane-associated ring finger (C3HC4) 1	protein-coding
mm_125066.1	chr15	25941030	25941047	+	1	NA	5' UTR (NM_001277315, exon 1 of 7)	5' UTR (NM_001277315, exon 1 of 7)	212	NM_025459	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_16216.1	chr2	173073288	173073298	+	1	NA	Intergenic	Intergenic	46232	NM_001081387	664799	Mm.389396	NM_001081387	ENSMUSG00000070495	Ctcfl	Boris|OTTMUSG00000016680	CCCTC-binding factor (zinc finger protein)-like	protein-coding
mm_162920.1	chr10	120653363	120653374	-	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-112364	NR_038000	70874	Mm.427286	NR_038000	ENSMUSG00000044544	4921513I03Rik	-	RIKEN cDNA 4921513I03 gene	ncRNA
mm_52044.1	chr6	96592988	96592988	+	1	NA	intron (NM_182808, intron 3 of 4)	intron (NM_182808, intron 3 of 4)	-426783	NR_003643	78482	Mm.391486	NM_030107	ENSMUSG00000072878	1700123L14Rik	-	nucleoporin 50 pseudogene	pseudo
mm_100374.1	chr11	119229093	119229131	+	1	NA	promoter-TSS (NM_172443)	promoter-TSS (NM_172443)	540	NM_175430	207607	Mm.189885	NM_175430	ENSMUSG00000039963	Ccdc40	B930008I02Rik	coiled-coil domain containing 40	protein-coding
mm_154080.1	chr19	56566080	56566127	-	1	NA	intron (NM_025811, intron 2 of 10)	intron (NM_025811, intron 2 of 10)	17842	NM_025811	66866	Mm.46346	NM_025811	ENSMUSG00000025078	Nhlrc2	1200003G01Rik|AI835049|AV002846|AW496455	NHL repeat containing 2	protein-coding
mm_8896.1	chr1	162898712	162898728	-	1	NA	promoter-TSS (NM_018881)	promoter-TSS (NM_018881)	-8	NM_018881	55990	Mm.10929	NM_018881	ENSMUSG00000040170	Fmo2	2310008D08Rik|2310042I22Rik|AW107733	flavin containing monooxygenase 2	protein-coding
mm_139733.1	chr17	57483855	57483859	+	1	NA	TTS (NM_010130)	TTS (NM_010130)	61457	NM_001104591	224916	Mm.469889	NM_001104591	ENSMUSG00000090655	Vmn2r120	EG224916	vomeronasal 2, receptor 120	protein-coding
mm_149765.1	chr19	22927073	22927073	+	1	NA	TTS (NM_001035244)	TTS (NM_001035244)	176468	NR_029591	387200		NR_029591	ENSMUSG00000065507	Mir204	Mirn204|mir-204|mmu-mir-204	microRNA 204	ncRNA
mm_71652.1	chr8	60505898	60505910	+	1	NA	promoter-TSS (NM_011834)	promoter-TSS (NM_011834)	-220	NM_011834	23923	Mm.35020	NM_011834	ENSMUSG00000057228	Aadat	AI875679|Aadt|KATII|Kat2|Kyat2|mKat-2	aminoadipate aminotransferase	protein-coding
mm_123248.1	chr14	60485639	60485649	-	1	NA	Intergenic	Intergenic	107358	NM_001164705	72125	Mm.275499	NM_028113	ENSMUSG00000021986	Amer2	2600011E07Rik|Fam123a	APC membrane recruitment 2	protein-coding
mm_173290.1	chrY	2314451	2314451	+	1	NA	Intergenic	RLTR10C|LTR|ERVK	-144042	NM_009571	22768	Mm.411381	NM_009571	ENSMUSG00000000103	Zfy2	Zfy-2	zinc finger protein 2, Y-linked	protein-coding
mm_30605.1	chr4	6394733	6394752	+	1	NA	3' UTR (NM_016807, exon 9 of 9)	3' UTR (NM_016807, exon 9 of 9)	29062	NM_001098227	53378	Mm.247473	NM_016807	ENSMUSG00000028249	Sdcbp	MDA-9|Sycl|syntenin-1	syndecan binding protein	protein-coding
mm_139275.1	chr17	48233867	48233886	+	1	NA	intron (NM_001347399, intron 1 of 2)	AT_rich|Low_complexity|Low_complexity	1137	NM_021406	58217	Mm.248352	NM_021406	ENSMUSG00000042265	Trem1	-	triggering receptor expressed on myeloid cells 1	protein-coding
mm_100199.1	chr11	116753276	116753287	+	1	NA	intron (NR_003364, intron 1 of 3)	intron (NR_003364, intron 1 of 3)	1114	NR_003364	193217	Mm.100084	NR_003364		BC018473	-	cDNA sequence BC018473	ncRNA
mm_52861.1	chr6	122294175	122294185	+	1	NA	Intergenic	RMER10A|LTR|ERVL	-11347	NM_016970	50928	Mm.20434	NM_016970	ENSMUSG00000030114	Klrg1	2F1-Ag|MAFA|MAFA-L	killer cell lectin-like receptor subfamily G, member 1	protein-coding
mm_64170.1	chr7	141448801	141448808	+	1	NA	promoter-TSS (NR_034049)	promoter-TSS (NR_034049)	1	NR_034049	100217419		NR_034049	ENSMUSG00000064666	Snora52	MBI-20	small nucleolar RNA, H/ACA box 52	snoRNA
mm_139861.1	chr17	69982413	69982414	+	1	NA	intron (NM_001347411, intron 1 of 14)	intron (NM_001347411, intron 1 of 14)	13340	NM_001347411	224997	Mm.311840	NM_027712	ENSMUSG00000003279	Dlgap1	4933422O14Rik|9630002F18|AI845682|AI848168|BB075781|D17Bwg0511e|GKAP/SAPAP|GKPA/SAPAP|Gkap|Sapap1|mKIAA4162	discs, large (Drosophila) homolog-associated protein 1	protein-coding
mm_105254.1	chr11	102354359	102354375	-	1	NA	exon (NM_011403, exon 14 of 20)	exon (NM_011403, exon 14 of 20)	10914	NM_011403	20533	Mm.7248	NM_011403	ENSMUSG00000006574	Slc4a1	Ae1|CD233|Empb3|l11Jus51	solute carrier family 4 (anion exchanger), member 1	protein-coding
mm_162643.1	chr1	193338569	193338587	+	1	NA	intron (NM_008484, intron 18 of 22)	intron (NM_008484, intron 18 of 22)	31704	NM_144817	215303	Mm.40329	NM_144817	ENSMUSG00000016179	Camk1g	CLICK-III|CaMKIgamma	calcium/calmodulin-dependent protein kinase I gamma	protein-coding
mm_9237.1	chr1	171294753	171294787	-	1	NA	5' UTR (NM_025388, exon 2 of 7)	5' UTR (NM_025388, exon 2 of 7)	212	NM_025388	66155	Mm.2815	NM_025388	ENSMUSG00000062963	Ufc1	1110021H02Rik|AA062310|ESTM29	ubiquitin-fold modifier conjugating enzyme 1	protein-coding
mm_108126.1	chr12	75983692	75983696	+	1	NA	intron (NM_001005510, intron 53 of 115)	intron (NM_001005510, intron 53 of 115)	74591	NR_039560	100628610		NR_039560	ENSMUSG00000092922	Mir5101	mmu-mir-5101|mu-mir-5101	microRNA 5101	ncRNA
mm_92043.1	chr10	62494935	62494961	-	1	NA	exon (NM_011157, exon 3 of 3)	exon (NM_011157, exon 3 of 3)	-8143	NM_133672	30930	Mm.260703	NM_133672	ENSMUSG00000020078	Vps26a	AA407240|HB58|Vps26	VPS26 retromer complex component A	protein-coding
mm_34623.1	chr4	150568817	150568835	+	1	NA	intron (NM_001085492, intron 11 of 22)	intron (NM_001085492, intron 11 of 22)	83348	NM_173774	242773	Mm.29280	NM_173774	ENSMUSG00000039838	Slc45a1	C230078B22|Dnb5	solute carrier family 45, member 1	protein-coding
mm_47250.1	chr5	121593483	121593493	-	1	NA	5' UTR (NM_001308450, exon 1 of 11)	5' UTR (NM_001308450, exon 1 of 11)	336	NM_009656	11669	Mm.284446	NM_009656	ENSMUSG00000029455	Aldh2	AHD-M1|ALDH-E2|ALDHI|Ahd-5|Ahd5	aldehyde dehydrogenase 2, mitochondrial	protein-coding
mm_110975.1	chr12	76962179	76962240	-	1	NA	promoter-TSS (NM_001146176)	promoter-TSS (NM_001146176)	39	NM_008558	17187	Mm.268548	NM_008558	ENSMUSG00000059436	Max	AA960152|AI875693|bHLHd4|bHLHd5|bHLHd6|bHLHd7|bHLHd8	Max protein	protein-coding
mm_106027.1	chr11	116030083	116030121	-	1	NA	promoter-TSS (NM_001286006)	promoter-TSS (NM_001286006)	-214	NM_001286006	217331	Mm.297706	NM_172569	ENSMUSG00000020770	Unk	B230379M23Rik|Zc3h5|Zc3hdc5|mKIAA1753	unkempt family zinc finger	protein-coding
mm_102121.1	chr11	53307629	53307640	-	1	NA	Intergenic	Intergenic	-7155	NM_008300	15525	Mm.239865	NM_008300	ENSMUSG00000020361	Hspa4	70kDa|AI317151|APG-2|Hsp110|Hsp70RY|mKIAA4025	heat shock protein 4	protein-coding
mm_88884.1	chr10	81135274	81135291	+	1	NA	promoter-TSS (NM_010731)	promoter-TSS (NM_010731)	-989	NM_010731	16969	Mm.20920	NM_010731	ENSMUSG00000035011	Zbtb7a	9030619K07Rik|9130006G12Rik|AI452336|FBI-1|Lrf|Pokemon|Zbtb7	zinc finger and BTB domain containing 7a	protein-coding
mm_104297.1	chr11	90390758	90390779	-	1	NA	5' UTR (NM_172563, exon 1 of 4)	5' UTR (NM_172563, exon 1 of 4)	149	NM_172563	217082	Mm.158903	NM_172563	ENSMUSG00000003949	Hlf	E230015K02Rik	hepatic leukemia factor	protein-coding
mm_84606.1	chr9	70141485	70141559	-	1	NA	promoter-TSS (NM_029784)	promoter-TSS (NM_029784)	35	NM_029784	76886	Mm.44355	NM_029784	ENSMUSG00000032224	Fam81a	6430514L14Rik	family with sequence similarity 81, member A	protein-coding
mm_26729.1	chr3	5220772	5220795	-	1	NA	promoter-TSS (NR_045905)	promoter-TSS (NR_045905)	40	NR_045905	72608	Mm.384359	NR_045905		2700069I18Rik	-	RIKEN cDNA 2700069I18 gene	ncRNA
mm_101046.1	chr11	8624675	8624695	-	1	NA	intron (NM_001083587, intron 1 of 30)	CpG	39850	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_157618.1	chrX	56549516	56549544	-	1	NA	promoter-TSS (NM_001033372)	promoter-TSS (NM_001033372)	76	NM_001033372	270599	Mm.424438	NM_001033372	ENSMUSG00000064016	Gm648	-	predicted gene 648	protein-coding
mm_124490.1	chr14	121738915	121738959	-	1	NA	promoter-TSS (NM_001128307)	promoter-TSS (NM_001128307)	-8	NM_001128307	105445	Mm.378591	NM_134074	ENSMUSG00000025558	Dock9	AA959601|AW538057|B230309H04Rik|D14Wsu89e|Zizimin1|mKIAA1058	dedicator of cytokinesis 9	protein-coding
mm_97599.1	chr11	78949156	78949175	+	1	NA	exon (NM_010927, exon 18 of 27)	exon (NM_010927, exon 18 of 27)	23874	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_76773.1	chr8	95864758	95864796	-	1	NA	3' UTR (NM_010325, exon 10 of 10)	3' UTR (NM_010325, exon 10 of 10)	-11286	NM_172758	234595	Mm.29267	NM_172758	ENSMUSG00000036534	Slc38a7	D430050E18	solute carrier family 38, member 7	protein-coding
mm_99837.1	chr11	109011987	109011994	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	91641	NM_015732	12006	Mm.71710	NM_015732	ENSMUSG00000000142	Axin2	Axi1|Axil|Conductin	axin 2	protein-coding
mm_91939.1	chr10	60752774	60752820	-	1	NA	promoter-TSS (NM_023596)	promoter-TSS (NM_023596)	-15	NM_023596	71279	Mm.284462	NM_023596	ENSMUSG00000020100	Slc29a3	4933435C21Rik|AW987637|Ent3	solute carrier family 29 (nucleoside transporters), member 3	protein-coding
mm_157222.1	chrX	13518936	13518936	-	1	NA	3' UTR (NM_001284505, exon 26 of 26)	3' UTR (NM_001284505, exon 26 of 26)	51264	NM_173415	236690	Mm.90233	NM_173415	ENSMUSG00000051228	Nyx	CLNP|CSNB1|CSNB4|nob	nyctalopin	protein-coding
mm_103003.1	chr11	69695640	69695713	-	1	NA	exon (NM_001159503, exon 1 of 13)	exon (NM_001159503, exon 1 of 13)	422	NM_011614	21944	Mm.8983	NM_011614	ENSMUSG00000097328	Tnfsf12	Apo3l|Dr3l|Dr3lg|Tweak	tumor necrosis factor (ligand) superfamily, member 12	protein-coding
mm_10340.1	chr2	11653557	11653561	+	1	NA	intron (NM_008367, intron 1 of 7)	intron (NM_008367, intron 1 of 7)	10767	NM_008367	16184	Mm.915	NM_008367	ENSMUSG00000026770	Il2ra	CD25|Il2r|Ly-43	interleukin 2 receptor, alpha chain	protein-coding
mm_143919.1	chr17	85618364	85618370	-	1	NA	promoter-TSS (NR_015387)	promoter-TSS (NR_015387)	29	NR_038084	100043902	Mm.150838	NR_015385	ENSMUSG00000093460	Six3os1	D17Mgi26|E130112H22Rik|Rncr1|Six3os	SIX homeobox 3, opposite strand 1	ncRNA
mm_38751.1	chr4	145577335	145577336	-	1	NA	Intergenic	Intergenic	-7865	NM_001324416	433801	Mm.276881	NM_001013808	ENSMUSG00000078502	Gm13212	OTTMUSG00000010965	predicted gene 13212	protein-coding
mm_127083.1	chr15	97718712	97718728	+	1	NA	intron (NM_001168693, intron 6 of 9)	intron (NM_001168693, intron 6 of 9)	2430	NM_008902	19011	Mm.1001	NM_008902	ENSMUSG00000022468	Endou	Pp11r|Tcl-30	endonuclease, polyU-specific	protein-coding
mm_73913.1	chr8	119666273	119666277	+	1	NA	promoter-TSS (NM_023395)	promoter-TSS (NM_023395)	-90	NM_023395	67866	Mm.87599	NM_023395	ENSMUSG00000023336	Wfdc1	2310058A03Rik|ps20	WAP four-disulfide core domain 1	protein-coding
mm_156934.1	chrX	169879597	169879656	+	1	NA	promoter-TSS (NM_001290505)	promoter-TSS (NM_001290505)	7	NM_001290505	17318	Mm.34441	NM_010797	ENSMUSG00000035299	Mid1	61B3-R|DXHXS1141|Fxy|Trim18	midline 1	protein-coding
mm_102575.1	chr11	61653124	61653138	-	1	NA	promoter-TSS (NM_027817)	promoter-TSS (NM_027817)	-190	NM_027817	71520	Mm.202760	NM_027817	ENSMUSG00000004837	Grap	8430435N19Rik|BB233594	GRB2-related adaptor protein	protein-coding
mm_30164.1	chr3	144188990	144189006	-	1	NA	3' UTR (NM_010723, exon 5 of 5)	3' UTR (NM_010723, exon 5 of 5)	13334	NM_001161770	16911	Mm.29187	NM_010723	ENSMUSG00000028266	Lmo4	A730077C12Rik|Crp3|Etohi4	LIM domain only 4	protein-coding
mm_52337.1	chr6	110648797	110648798	+	1	NA	intron (NM_001346640, intron 1 of 10)	intron (NM_001346640, intron 1 of 10)	3199	NM_177328	108073	Mm.240881	NM_177328	ENSMUSG00000056755	Grm7	6330570A01Rik|BB176677|C030018L03|E130018M02Rik|Gpr1g|Gprc1g|SMN2|Tg(SMN2)89Ahmb|mGluR7	glutamate receptor, metabotropic 7	protein-coding
mm_6248.1	chr1	68184416	68184420	-	1	NA	intron (NM_010154, intron 20 of 26)	MTD|LTR|ERVL-MaLR	923641	NM_010154	13869	Mm.442420	NM_010154	ENSMUSG00000062209	Erbb4	Her4|c-erbB-4	erb-b2 receptor tyrosine kinase 4	protein-coding
mm_8479.1	chr1	153518945	153518959	-	1	NA	exon (NM_028749, exon 7 of 12)	exon (NM_028749, exon 7 of 12)	30762	NM_028749	74091	Mm.24887	NM_028749	ENSMUSG00000042684	Npl	0610033B02Rik	N-acetylneuraminate pyruvate lyase	protein-coding
mm_16168.1	chr2	172545713	172545728	+	1	NA	Intergenic	Intergenic	-3873	NM_009335	21420	Mm.3629	NM_009335	ENSMUSG00000028640	Tfap2c	AA409384|AP2gamma|Ap-2.2|Stra2|Tcfap2c	transcription factor AP-2, gamma	protein-coding
mm_22740.1	chr3	19956926	19956930	+	1	NA	promoter-TSS (NM_007752)	promoter-TSS (NM_007752)	-126	NM_001276250	12870	Mm.13787	NM_007752	ENSMUSG00000003617	Cp	D3Ertd555e	ceruloplasmin	protein-coding
mm_75834.1	chr8	70523086	70523114	-	1	NA	promoter-TSS (NM_029366)	promoter-TSS (NM_029366)	80	NM_029366	75620	Mm.482129	NM_029366	ENSMUSG00000055553	Kxd1	0610030B01Rik|2810422J05Rik|C78305	KxDL motif containing 1	protein-coding
mm_75362.1	chr8	45283323	45283331	-	1	NA	exon (NM_008455, exon 5 of 15)	exon (NM_008455, exon 5 of 15)	11508	NM_008455	16621	Mm.482691	NM_008455	ENSMUSG00000109764	Klkb1	APS|Kal-3|Kal3|Klk3|PSA	kallikrein B, plasma 1	protein-coding
mm_153798.1	chr19	46039209	46039229	-	1	NA	5' UTR (NM_010697, exon 1 of 11)	5' UTR (NM_010697, exon 1 of 11)	402	NM_010697	16825	Mm.327442	NM_010697	ENSMUSG00000025223	Ldb1	CLIM2|NLI	LIM domain binding 1	protein-coding
mm_151233.1	chr19	53793267	53793275	+	1	NA	intron (NM_001170847, intron 1 of 13)	intron (NM_001170847, intron 1 of 13)	-98960	NM_011050	18569	Mm.1605	NM_011050	ENSMUSG00000024975	Pdcd4	D19Ucla1|Ma3|Tis	programmed cell death 4	protein-coding
mm_161319.1	chr14	44724987	44724987	-	1	NA	promoter-TSS (NM_001162954)	promoter-TSS (NM_001162954)	0	NM_001162954	666744	Mm.387002	NM_001162954	ENSMUSG00000091923	Gm8267	EG666744	predicted gene 8267	protein-coding
mm_110050.1	chr12	17882017	17882044	-	1	NA	Intergenic	CpG	191216	NM_016677	53602	Mm.313619	NM_016677	ENSMUSG00000071379	Hpcal1	NVP-3|Nvp3|VILIP3|Vnsl3|Vsnl3	hippocalcin-like 1	protein-coding
mm_70819.1	chr8	23130758	23130772	+	1	NA	intron (NM_001277280, intron 37 of 42)	intron (NM_001277280, intron 37 of 42)	-8265	NM_001310436	11733	Mm.334444	NM_031158	ENSMUSG00000031543	Ank1	Ank-1|nb|pale	ankyrin 1, erythroid	protein-coding
mm_64256.1	chr7	141744699	141744711	+	1	NA	exon (NM_023566, exon 28 of 46)	exon (NM_023566, exon 28 of 46)	-44306	NM_010844	17833	Mm.334332	NM_010844	ENSMUSG00000037974	Muc5ac	2210005L13Rik|MGM	mucin 5, subtypes A and C, tracheobronchial/gastric	protein-coding
mm_92724.1	chr10	80813487	80813533	-	1	NA	promoter-TSS (NM_028001)	promoter-TSS (NM_028001)	-12	NM_028001	71912	Mm.45137	NM_028001	ENSMUSG00000020216	Jsrp1	2300003C06Rik|2310032K21Rik|JP-45|JP45	junctional sarcoplasmic reticulum protein 1	protein-coding
mm_21894.1	chr2	166155625	166155671	-	1	NA	promoter-TSS (NM_028072)	promoter-TSS (NM_028072)	35	NM_001252579	72043	Mm.1011	NM_028072	ENSMUSG00000006800	Sulf2	2010004N24Rik|AU020235|MSulf-2|mKIAA1247	sulfatase 2	protein-coding
mm_134224.1	chr16	11254343	11254352	-	1	NA	promoter-TSS (NM_001130008)	promoter-TSS (NM_001130008)	-22	NM_146066	14852	Mm.325827	NM_146066	ENSMUSG00000062203	Gspt1	AI314175|AI326449|AV307676|C79774|G1st|Gst-1	G1 to S phase transition 1	protein-coding
mm_45236.1	chr5	53671441	53671447	-	1	NA	Intergenic	RLTR23|LTR|ERV1	27144	NR_024201	19866		NR_024201	ENSMUSG00000089083	Rnu7	-	U7 small nuclear RNA	snRNA
mm_62209.1	chr7	97843040	97843059	+	1	NA	5' UTR (NM_011035, exon 1 of 15)	5' UTR (NM_011035, exon 1 of 15)	110	NM_011035	18479	Mm.260227	NM_011035	ENSMUSG00000030774	Pak1	AW045634|PAK-1|Paka	p21 protein (Cdc42/Rac)-activated kinase 1	protein-coding
mm_114982.1	chr13	97294023	97294025	+	1	NA	Intergenic	Intergenic	52919	NM_007930	13803	Mm.241073	NM_007930	ENSMUSG00000041773	Enc1	Nrpb|PIG10	ectodermal-neural cortex 1	protein-coding
mm_132243.1	chr16	32751036	32751049	+	1	NA	exon (NM_080457, exon 2 of 27)	exon (NM_080457, exon 2 of 27)	15156	NM_080457	140474	Mm.214599	NM_080457	ENSMUSG00000079620	Muc4	4933405I11Rik|Asgp	mucin 4	protein-coding
mm_59460.1	chr7	27196977	27196998	+	1	NA	promoter-TSS (NM_015782)	promoter-TSS (NM_015782)	-716	NM_001285825	53607	Mm.386890	NM_015782	ENSMUSG00000061479	Snrpa	C430021M15Rik|Rnu1a-1|Rnu1a1|U1-A|U1A	small nuclear ribonucleoprotein polypeptide A	protein-coding
mm_19210.1	chr2	84531427	84531437	-	1	NA	Intergenic	MTEa|LTR|ERVL-MaLR	-24559	NR_046046	672763	Mm.491046	NR_046046	ENSMUSG00000087362	Gm13710	OTTMUSG00000013441	predicted gene 13710	ncRNA
mm_159620.1	chr4	134402946	134402946	+	1	NA	promoter-TSS (NM_001285877)	promoter-TSS (NM_001285877)	-24	NM_001285877	100163	Mm.22116	NM_133880	ENSMUSG00000037366	Pafah2	2310074E22Rik|AI507170	platelet-activating factor acetylhydrolase 2	protein-coding
mm_58674.1	chr7	10687792	10687792	+	1	NA	promoter-TSS (NM_172481)	promoter-TSS (NM_172481)	-1	NM_172481	210045	Mm.95244	NM_172481	ENSMUSG00000034087	Nlrp4b	AU022726|E330024M09|Nalp-gamma|Nalp4b	NLR family, pyrin domain containing 4B	protein-coding
mm_171333.1	chr3	98820942	98820957	+	1	NA	Intergenic	Intergenic	-6506	NM_013821	15497	Mm.14435	NM_013821	ENSMUSG00000027869	Hsd3b6	D19210	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 6	protein-coding
mm_83880.1	chr9	55283651	55283660	-	1	NA	promoter-TSS (NM_032002)	promoter-TSS (NM_032002)	-30	NM_032002	83961	Mm.443874	NM_032002	ENSMUSG00000032311	Nrg4	AI552600	neuregulin 4	protein-coding
mm_135495.1	chr16	46120427	46120437	-	1	NA	promoter-TSS (NM_032465)	promoter-TSS (NM_032465)	-184	NM_032465	84544	Mm.29204	NM_032465	ENSMUSG00000022657	Cd96	1700109I12Rik|Tactile	CD96 antigen	protein-coding
mm_59718.1	chr7	28767627	28767642	+	1	NA	promoter-TSS (NM_010908)	promoter-TSS (NM_010908)	882	NM_001122766	64383	Mm.272443	NM_022432	ENSMUSG00000015149	Sirt2	5730427M03Rik|SIR2L2|Sir2l	sirtuin 2	protein-coding
mm_71240.1	chr8	40908732	40908742	+	1	NA	intron (NM_007514, intron 7 of 11)	intron (NM_007514, intron 7 of 11)	-17496	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_21028.1	chr2	152414773	152414809	-	1	NA	promoter-TSS (NM_177656)	promoter-TSS (NM_177656)	253	NM_175126	67917	Mm.391810	NM_175126	ENSMUSG00000074682	Zcchc3	2810406K24Rik	zinc finger, CCHC domain containing 3	protein-coding
mm_38063.1	chr4	134018830	134018836	-	1	NA	promoter-TSS (NM_145833)	promoter-TSS (NM_145833)	-17	NM_145833	83557	Mm.302567	NM_145833	ENSMUSG00000050966	Lin28a	AL024421|ENSMUSG00000070700|Gm10299|Lin-28|Lin28|Tex17|lin-28A	lin-28 homolog A (C. elegans)	protein-coding
mm_69915.1	chr7	141702767	141702783	-	1	NA	exon (NM_023566, exon 26 of 46)	exon (NM_023566, exon 26 of 46)	12435	NM_023566	17831	Mm.2041	NM_023566		Muc2	2010015E03Rik|MCM|wnn	mucin 2	protein-coding
mm_152375.1	chr19	10225248	10225262	-	1	NA	intron (NM_001033481, intron 4 of 25)	intron (NM_001033481, intron 4 of 25)	15493	NM_001033481	225908	Mm.329716	NM_001033481	ENSMUSG00000036098	Myrf	6030439E18|Gm1804|Gm98|Mrf	myelin regulatory factor	protein-coding
mm_109077.1	chr12	104406705	104406728	+	1	NA	promoter-TSS (NM_009252)	promoter-TSS (NM_009252)	8	NM_009252	20716	Mm.482074	NM_009252	ENSMUSG00000021091	Serpina3n	Spi2-2|Spi2.2|Spi2/eb.4	serine (or cysteine) peptidase inhibitor, clade A, member 3N	protein-coding
mm_125402.1	chr15	41487360	41487362	+	1	NA	intron (NM_001130166, intron 1 of 16)	intron (NM_001130166, intron 1 of 16)	39879	NM_001130166	170719	Mm.254267	NM_130885	ENSMUSG00000022307	Oxr1	2210416C20Rik|C7|C7B	oxidation resistance 1	protein-coding
mm_54392.1	chr6	31220288	31220297	-	1	NA	promoter-TSS (NR_040262)	promoter-TSS (NR_040262)	-59	NR_040258	73652	Mm.441297	NR_040257	ENSMUSG00000087380	2210408F21Rik	-	RIKEN cDNA 2210408F21 gene	ncRNA
mm_86388.1	chr9	123940180	123940190	-	1	NA	Intergenic	(ATGTG)n|Simple_repeat|Simple_repeat	28507	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_43748.1	chr5	140392931	140392957	+	1	NA	Intergenic	Intergenic	-3636	NM_172277	231834	Mm.27098	NM_172277	ENSMUSG00000029560	Snx8	B130023O14Rik	sorting nexin 8	protein-coding
mm_97003.1	chr11	70869662	70869669	+	1	NA	intron (NM_001291143, intron 2 of 18)	(T)n|Simple_repeat|Simple_repeat	24904	NM_001291142	54189	Mm.7087	NM_019400	ENSMUSG00000020817	Rabep1	Rab5ep|rabaptin-5|rabaptin-5alpha	rabaptin, RAB GTPase binding effector protein 1	protein-coding
mm_108491.1	chr12	83675036	83675053	+	1	NA	exon (NM_027349, exon 16 of 19)	exon (NM_027349, exon 16 of 19)	-13519	NM_008943	19164	Mm.998	NM_008943	ENSMUSG00000019969	Psen1	Ad3h|PS-1|PS1|S182	presenilin 1	protein-coding
mm_87332.1	chr10	42940413	42940444	+	1	NA	intron (NM_172938, intron 6 of 8)	intron (NM_172938, intron 6 of 8)	79916	NM_172938	268297	Mm.98731	NM_172938	ENSMUSG00000044770	Scml4	9330161D17|mFLJ00197	sex comb on midleg-like 4 (Drosophila)	protein-coding
mm_166591.1	chr6	56715007	56715015	+	1	NA	5' UTR (NM_030235, exon 1 of 16)	5' UTR (NM_030235, exon 1 of 16)	106	NM_030235	78937	Mm.105343	NM_030235	ENSMUSG00000029787	Avl9	5830411G16Rik|D730049P16Rik|mKIAA0241	AVL9 cell migration associated	protein-coding
mm_102347.1	chr11	58139541	58139551	-	1	NA	exon (NM_001166670, exon 17 of 28)	exon (NM_001166670, exon 17 of 28)	28993	NM_172558	216766	Mm.275349	NM_172558	ENSMUSG00000037275	Gemin5	AA407055|AA407208|AI451603|BB194447|C330013N08	gem (nuclear organelle) associated protein 5	protein-coding
mm_130873.1	chr15	102231921	102231941	-	1	NA	promoter-TSS (NM_013566)	promoter-TSS (NM_013566)	4	NM_013566	16421	Mm.58	NM_013566	ENSMUSG00000001281	Itgb7	Ly69	integrin beta 7	protein-coding
mm_104716.1	chr11	98053297	98053337	-	1	NA	5' UTR (NM_146028, exon 1 of 11)	5' UTR (NM_146028, exon 1 of 11)	145	NM_146028	217154	Mm.181008	NM_146028	ENSMUSG00000017400	Stac2	24b2|24b2/STAC2|AW240854	SH3 and cysteine rich domain 2	protein-coding
mm_112174.1	chr12	113421189	113421199	-	1	NA	Intergenic	Intergenic	-68371	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_160475.1	chr8	120144723	120144723	+	1	NA	promoter-TSS (NM_001163760)	promoter-TSS (NM_001163760)	-206	NM_001163760	234797	Mm.101958	NM_172286	ENSMUSG00000031824	6430548M08Rik	AW049007|Kiaa0513|mKIAA0513	RIKEN cDNA 6430548M08 gene	protein-coding
mm_130261.1	chr15	96642853	96642875	-	1	NA	promoter-TSS (NM_001166456)	promoter-TSS (NM_001166456)	49	NM_001166458	105727	Mm.103568	NM_134086	ENSMUSG00000023169	Slc38a1	AA408026|AA409865|AL022800|AU015942|NAT2	solute carrier family 38, member 1	protein-coding
mm_159061.1	chr2	13793565	13793565	-	1	NA	promoter-TSS (NM_145838)	promoter-TSS (NM_145838)	-45	NM_145838	241230	Mm.330004	NM_145838	ENSMUSG00000003418	St8sia6	1700007J08Rik|AI314453|AI875066|ST8SiaVI|Siat8f	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 6	protein-coding
mm_138256.1	chr17	34590794	34590829	+	1	NA	exon (NM_134116, exon 3 of 4)	exon (NM_134116, exon 3 of 4)	1005	NM_134116	106512	Mm.26584	NM_134116	ENSMUSG00000034786	Gpsm3	AA960287|AGS4	G-protein signalling modulator 3 (AGS3-like, C. elegans)	protein-coding
mm_37641.1	chr4	128260889	128260900	-	1	NA	promoter-TSS (NM_027036)	promoter-TSS (NM_027036)	1	NM_027036	69317	Mm.331893	NM_027036	ENSMUSG00000048686	Hmgb4	1700001F22Rik|AI326135	high-mobility group box 4	protein-coding
mm_88147.1	chr10	69533762	69533776	+	1	NA	promoter-TSS (NM_170688)	promoter-TSS (NM_170688)	61	NM_146005	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_120092.1	chr14	57889812	57889846	+	1	NA	intron (NM_029492, intron 1 of 12)	CpG	433	NM_029492	75965	Mm.29044	NM_029492	ENSMUSG00000021969	Zdhhc20	4930542A17Rik|5033406L14Rik|AI448102|B230110O18Rik|ENSMUSG00000055956|HK11	zinc finger, DHHC domain containing 20	protein-coding
mm_145262.1	chr18	52616025	52616033	+	1	NA	5' UTR (NM_025749, exon 1 of 2)	5' UTR (NM_025749, exon 1 of 2)	114	NM_025749	66758	Mm.251599	NM_025749	ENSMUSG00000046886	Zfp474	4933409D10Rik|Znf474	zinc finger protein 474	protein-coding
mm_18121.1	chr2	44997279	44997291	-	1	NA	exon (NM_015753, exon 8 of 10)	exon (NM_015753, exon 8 of 10)	25892	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_158137.1	chrX	103186619	103186671	-	1	NA	promoter-TSS (NM_008671)	promoter-TSS (NM_008671)	19	NM_008671	17954	Mm.388694	NM_008671	ENSMUSG00000082229	Nap1l2	Bpx	nucleosome assembly protein 1-like 2	protein-coding
mm_169438.1	chr14	56262265	56262265	-	1	NA	promoter-TSS (NM_013542)	promoter-TSS (NM_013542)	69	NM_013542	14939	Mm.14874	NM_013542	ENSMUSG00000015437	Gzmb	AI553453|CCP-1/C11|CCP1|Ctla-1|Ctla1|GZB	granzyme B	protein-coding
mm_164232.1	chr15	89542586	89542588	+	1	NA	intron (NM_021423, intron 18 of 21)	intron (NM_021423, intron 18 of 21)	-25739	NM_013455	11434	Mm.57	NM_013455	ENSMUSG00000022622	Acr	-	acrosin prepropeptide	protein-coding
mm_25325.1	chr3	106565912	106565916	+	1	NA	intron (NM_001025582, intron 4 of 6)	intron (NM_001025582, intron 4 of 6)	-18112	NM_133869	99712	Mm.429443	NM_133869	ENSMUSG00000040774	Cept1	9930118K05Rik|mCEPT1	choline/ethanolaminephosphotransferase 1	protein-coding
mm_76293.1	chr8	84202013	84202017	-	1	NA	Intergenic	B1F|SINE|Alu	-6503	NR_029740	387216		NR_029740	ENSMUSG00000065611	Mir23a	Mirn23a|mir-23a|mmu-mir-23a	microRNA 23a	ncRNA
mm_145741.1	chr18	64288336	64288336	+	1	NA	Intergenic	Intergenic	-11156	NR_045366	73588	Mm.65475	NR_045366	ENSMUSG00000086128	St8sia3os	1700091E21Rik	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3, opposite strand	ncRNA
mm_164690.1	chr17	47729311	47729313	-	1	NA	exon (NM_025973, exon 3 of 9)	exon (NM_025973, exon 3 of 9)	2470	NM_025973	109820	Mm.22957	NM_025973	ENSMUSG00000023987	Pgc	2210410L06Rik|Upg-1|Upg1	progastricsin (pepsinogen C)	protein-coding
mm_148800.1	chr19	6241700	6241734	+	1	NA	promoter-TSS (NM_194348)	promoter-TSS (NM_194348)	49	NM_194348	329015	Mm.277384	NM_194348	ENSMUSG00000024773	Atg2a	1810013C15Rik|A830054M12|BC023754|mKIAA0404	autophagy related 2A	protein-coding
mm_66248.1	chr7	35556079	35556089	-	1	NA	promoter-TSS (NM_033080)	promoter-TSS (NM_033080)	-156	NM_033080	110959	Mm.410206	NM_033080	ENSMUSG00000034875	Nudt19	D7Rp2|D7Rp2-r|D7Rp2-s|D7Rp2e|RP2-r|RP2-s	nudix (nucleoside diphosphate linked moiety X)-type motif 19	protein-coding
mm_149347.1	chr19	10859823	10859833	+	1	NA	intron (NM_133804, intron 9 of 10)	intron (NM_133804, intron 9 of 10)	9951	NM_133804	98170	Mm.490254	NM_133804	ENSMUSG00000024736	Tmem132a	6720481D13Rik|Hspa5bp1|Orai1|R74613	transmembrane protein 132A	protein-coding
mm_89496.1	chr10	93833910	93833953	+	1	NA	intron (NM_001206851, intron 1 of 6)	CpG	2376	NM_001206851	327799	Mm.491598	NM_183199	ENSMUSG00000020020	Usp44	E430004F17Rik	ubiquitin specific peptidase 44	protein-coding
mm_45618.1	chr5	75835934	75835940	-	1	NA	Intergenic	Intergenic	142491	NM_010612	16542	Mm.285	NM_010612	ENSMUSG00000062960	Kdr	6130401C07|Flk-1|Flk1|Krd-1|Ly73|VEGFR-2|VEGFR2|sVEGFR-2	kinase insert domain protein receptor	protein-coding
mm_35594.1	chr4	43010500	43010537	-	1	NA	promoter-TSS (NM_053081)	promoter-TSS (NM_053081)	-217	NM_053081	60534	Mm.23122	NM_053081	ENSMUSG00000028453	Fancg	AU041407|Xrcc9	Fanconi anemia, complementation group G	protein-coding
mm_52924.1	chr6	122921806	122921865	+	1	NA	promoter-TSS (NM_199311)	promoter-TSS (NM_199311)	-13	NM_199311	269799	Mm.297275	NM_199311	ENSMUSG00000049037	Clec4a1	BC049354|Dcir4	C-type lectin domain family 4, member a1	protein-coding
mm_163334.1	chr12	11436519	11436540	-	1	NA	5' UTR (NM_012038, exon 1 of 4)	5' UTR (NM_012038, exon 1 of 4)	120	NM_012038	26950	Mm.27005	NM_012038	ENSMUSG00000054459	Vsnl1	VILIP|Vnsl1	visinin-like 1	protein-coding
mm_54989.1	chr6	48770736	48770741	-	1	NA	5' UTR (NM_031247, exon 1 of 5)	5' UTR (NM_031247, exon 1 of 5)	113	NM_031247	83408	Mm.333050	NM_031247	ENSMUSG00000039264	Gimap3	2010110D23Rik|Gimap5|Ian4	GTPase, IMAP family member 3	protein-coding
mm_61673.1	chr7	80830746	80830756	+	1	NA	Intergenic	Intergenic	-27420	NM_016721	29875	Mm.207619	NM_016721	ENSMUSG00000030536	Iqgap1	AA682088|D7Ertd237e|D7Ertd257e|mKIAA0051	IQ motif containing GTPase activating protein 1	protein-coding
mm_139993.1	chr17	72918496	72918547	+	1	NA	5' UTR (NM_029999, exon 1 of 3)	5' UTR (NM_029999, exon 1 of 3)	216	NM_029999	77889	Mm.154109	NM_029999	ENSMUSG00000024063	Lbh	1810009F10Rik|6720416L16Rik	limb-bud and heart	protein-coding
mm_122179.1	chr14	31553781	31553828	-	1	NA	exon (NM_009937, exon 2 of 17)	exon (NM_009937, exon 2 of 17)	23579	NM_009937	382864	Mm.239821	NM_009937	ENSMUSG00000057606	Colq	A130034K24Rik	collagen-like tail subunit (single strand of homotrimer) of asymmetric acetylcholinesterase	protein-coding
mm_18252.1	chr2	52232967	52232995	-	1	NA	exon (NM_010889, exon 76 of 157)	exon (NM_010889, exon 76 of 157)	-58021	NR_040620	78049	Mm.243883	NR_040620		4930573O16Rik	-	RIKEN cDNA 4930573O16 gene	ncRNA
mm_47019.1	chr5	115489956	115489981	-	1	NA	Intergenic	CpG	-5484	NM_133760	75387	Mm.332616	NM_133760	ENSMUSG00000029524	Sirt4	4930596O17Rik	sirtuin 4	protein-coding
mm_96851.1	chr11	70045320	70045323	+	1	NA	3' UTR (NM_007864, exon 20 of 20)	3' UTR (NM_007864, exon 20 of 20)	-8803	NM_001291131	11889	Mm.6559	NM_009714	ENSMUSG00000020884	Asgr1	ASGPR1|Asgr|Asgr-1|HL-1	asialoglycoprotein receptor 1	protein-coding
mm_37549.1	chr4	125127849	125127891	-	1	NA	promoter-TSS (NM_153159)	promoter-TSS (NM_153159)	11	NM_153159	230738	Mm.402	NM_153159	ENSMUSG00000042677	Zc3h12a	BC036563|MCPIP|MCPIP-1|Mcpip1|Reg1	zinc finger CCCH type containing 12A	protein-coding
mm_171407.1	chr4	129212741	129212741	+	1	NA	intron (NM_134151, intron 8 of 12)	B2_Mm1t|SINE|B2	15170	NM_001285866	97130	Mm.331907	NM_001033189	ENSMUSG00000050390	C77080	Kiaa1522|mKIAA1522	expressed sequence C77080	protein-coding
mm_166739.1	chr6	124570289	124570296	+	1	NA	promoter-TSS (NM_001113356)	promoter-TSS (NM_001113356)	-138	NM_001113356	667277	Mm.481484	NM_001113356	ENSMUSG00000098470	C1rb	Gm8551|mC1rB	complement component 1, r subcomponent B	protein-coding
mm_111156.1	chr12	83439911	83439934	-	1	NA	intron (NM_058212, intron 1 of 8)	intron (NM_058212, intron 1 of 8)	47814	NM_001267626	70127	Mm.151308	NM_058212	ENSMUSG00000021221	Dpf3	2810403B03Rik|6530402L11Rik|BAF45C|C78788|CERD4|cer-d4	D4, zinc and double PHD fingers, family 3	protein-coding
mm_120052.1	chr14	56648078	56648102	+	1	NA	exon (NM_001145978, exon 32 of 35)	exon (NM_001145978, exon 32 of 35)	-20158	NM_023773	75339	Mm.152466	NM_023773	ENSMUSG00000079184	Mphosph8	1500035L22Rik|4930548G07Rik|AU040635	M-phase phosphoprotein 8	protein-coding
mm_122061.1	chr14	30363897	30363897	-	1	NA	intron (NM_028981, intron 1 of 46)	intron (NM_028981, intron 1 of 46)	-10411	NM_001083616	12289	Mm.9772	NM_028981	ENSMUSG00000015968	Cacna1d	8430418G19Rik|C79217|Cach3|Cacn4|Cacnl1a2|Cav1.3|Cchl1a|Cchl1a2|D-LTCC	calcium channel, voltage-dependent, L type, alpha 1D subunit	protein-coding
mm_95832.1	chr11	55496568	55496574	+	1	NA	intron (NM_013716, intron 8 of 11)	B4|SINE|B4	13865	NR_028480	100303747	Mm.453534	NR_028480	ENSMUSG00000065061	Gm12238	Mbi-39|OTTMUSG00000005697	predicted gene 12238	snoRNA
mm_159069.1	chr2	25080409	25080409	+	1	NA	promoter-TSS (NM_028093)	promoter-TSS (NM_028093)	86	NM_028093	72090	Mm.33403	NM_028093	ENSMUSG00000036813	Entpd8	-	ectonucleoside triphosphate diphosphohydrolase 8	protein-coding
mm_106246.1	chr11	117813378	117813437	-	1	NA	exon (NM_009304, exon 4 of 4)	exon (NM_009304, exon 4 of 4)	3740	NM_009304	20973	Mm.468228	NM_009304	ENSMUSG00000048277	Syngr2	Clast2|cellugyrin	synaptogyrin 2	protein-coding
mm_13432.1	chr2	105017115	105017153	+	1	NA	promoter-TSS (NM_145380)	promoter-TSS (NM_145380)	-107	NM_145380	98221	Mm.379278	NM_145380	ENSMUSG00000027170	Eif3m	Ga17|Pcid1|Tango7	eukaryotic translation initiation factor 3, subunit M	protein-coding
mm_107750.1	chr12	59066897	59066907	+	1	NA	promoter-TSS (NM_008891)	promoter-TSS (NM_008891)	-17	NM_008891	18949	Mm.22347	NM_008891	ENSMUSG00000020994	Pnn	AU045199|D12Ertd512e	pinin	protein-coding
mm_26094.1	chr3	136903019	136903024	+	1	NA	intron (NM_008913, intron 8 of 13)	intron (NM_008913, intron 8 of 13)	232955	NM_001293622	19055	Mm.331389	NM_008913	ENSMUSG00000028161	Ppp3ca	2900074D19Rik|CN|Caln|Calna|CnA	protein phosphatase 3, catalytic subunit, alpha isoform	protein-coding
mm_91858.1	chr10	59438911	59438913	-	1	NA	exon (NM_010959, exon 2 of 9)	exon (NM_010959, exon 2 of 9)	2867	NM_010959	18302	Mm.123013	NM_010959	ENSMUSG00000009654	Oit3	EF-9|LZP	oncoprotein induced transcript 3	protein-coding
mm_157694.1	chrX	60426276	60426319	-	1	NA	Intergenic	Intergenic	-22316	NM_001037863	320940	Mm.490394	NM_001001798	ENSMUSG00000062949	Atp11c	A330005H02Rik|AI315324|Ig	ATPase, class VI, type 11C	protein-coding
mm_5912.1	chr1	55022091	55022095	-	1	NA	intron (NM_031179, intron 1 of 24)	B1_Mur1|SINE|Alu	5385	NM_031179	81898	Mm.279736	NM_031179	ENSMUSG00000025982	Sf3b1	155kDa|2810001M05Rik|AA409119|Prp10|SAP155|SF3b155|TA-8|Targ4	splicing factor 3b, subunit 1	protein-coding
mm_52785.1	chr6	121256984	121256994	+	1	NA	intron (NM_011909, intron 4 of 10)	L1M2|LINE|L1	11083	NM_011909	24110	Mm.326911	NM_011909	ENSMUSG00000030107	Usp18	1110058H21Rik|AW047653|UBP43|Ubp15	ubiquitin specific peptidase 18	protein-coding
mm_82857.1	chr9	31464207	31464222	-	1	NA	promoter-TSS (NM_144936)	promoter-TSS (NM_144936)	24	NM_144936	235135	Mm.390134	NM_144936	ENSMUSG00000041737	Tmem45b	BC018222	transmembrane protein 45b	protein-coding
mm_1042.1	chr1	58795619	58795639	+	1	NA	5' UTR (NM_009812, exon 1 of 9)	5' UTR (NM_009812, exon 1 of 9)	255	NM_009812	12370	Mm.336851	NM_009812	ENSMUSG00000026029	Casp8	CASP-8|FLICE|MACH|Mch5	caspase 8	protein-coding
mm_170537.1	chr19	38869789	38869818	-	1	NA	intron (NM_145952, intron 2 of 12)	RLTRETN_Mm|LTR|ERVK	33224	NM_145952	209478	Mm.391153	NM_145952	ENSMUSG00000048720	Tbc1d12	BC033574	TBC1D12: TBC1 domain family, member 12	protein-coding
mm_119009.1	chr14	29968318	29968334	+	1	NA	promoter-TSS (NM_019979)	promoter-TSS (NM_019979)	-54	NM_019979	80795	Mm.104491	NM_019979	ENSMUSG00000042682	Selenok	1110001C03Rik|AA673253|HSPC030|Hsp30|Selk	selenoprotein K	protein-coding
mm_67966.1	chr7	100590853	100590862	-	1	NA	intron (NR_003559, intron 1 of 7)	intron (NR_003559, intron 1 of 7)	-7727	NM_198831	52443	Mm.473730	NM_198831	ENSMUSG00000030706	Mrpl48	1810030E20Rik|2610028L11Rik|CGI-118|D4Ertd786e	mitochondrial ribosomal protein L48	protein-coding
mm_127200.1	chr15	99125894	99125909	+	1	NA	promoter-TSS (NM_139140)	promoter-TSS (NM_139140)	-944	NM_139140	72572	Mm.276650	NM_139140	ENSMUSG00000051934	Spats2	2700012F11Rik|59kDa|Scr59|p59	spermatogenesis associated, serine-rich 2	protein-coding
mm_97501.1	chr11	78394494	78394505	+	1	NA	promoter-TSS (NR_003282)	promoter-TSS (NR_003282)	14	NR_003282	790911	Mm.457257	NR_003282	ENSMUSG00000085747	Slc13a2os	Gm11194|OTTMUSG00000000132	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 2, opposite strand	ncRNA
mm_122870.1	chr14	54925582	54925599	-	1	NA	5' UTR (NM_010112, exon 1 of 6)	5' UTR (NM_010112, exon 1 of 6)	1198	NM_010112	13644	Mm.236438	NM_010112	ENSMUSG00000022203	Efs	-	embryonal Fyn-associated substrate	protein-coding
mm_17125.1	chr2	24763183	24763196	-	1	NA	promoter-TSS (NM_001042528)	promoter-TSS (NM_001042528)	-37	NM_007579	12287	Mm.4424	NM_007579	ENSMUSG00000004113	Cacna1b	AW050276|AW060892|AW822256|BIII|Cav2.2|Cchn1a|alpha(1B)	calcium channel, voltage-dependent, N type, alpha 1B subunit	protein-coding
mm_18798.1	chr2	73892215	73892240	-	1	NA	intron (NM_001284374, intron 1 of 11)	CpG	412	NM_001284371	11909	Mm.209903	NM_009715	ENSMUSG00000027104	Atf2	Atf-2|CRE-BP|Creb2|D130078H02Rik|D18875|Tg(Gzma-Klra1)7Wum|mXBP	activating transcription factor 2	protein-coding
mm_15051.1	chr2	152876546	152876582	+	1	NA	intron (NM_001141977, intron 6 of 17)	intron (NM_001141977, intron 6 of 17)	11497	NR_049195	100885834		NR_049195	ENSMUSG00000093746	Mir5622	Gm24421|mmu-mir-5622	microRNA 5622	ncRNA
mm_54936.1	chr6	48445731	48445741	-	1	NA	promoter-TSS (NM_001085417)	promoter-TSS (NM_001085417)	89	NM_020589	68910	Mm.2464	NM_020589	ENSMUSG00000068551	Zfp467	1190001I08Rik|AB041616|AI426952|AV017623|EZI|MNCb-3350|Znf467	zinc finger protein 467	protein-coding
mm_146741.1	chr18	15403681	15403687	-	1	NA	promoter-TSS (NM_009700)	promoter-TSS (NM_009700)	74	NM_001317729	11829	Mm.250786	NM_009700	ENSMUSG00000024411	Aqp4	WCH4	aquaporin 4	protein-coding
mm_149799.1	chr19	23687174	23687212	+	1	NA	promoter-TSS (NM_028208)	promoter-TSS (NM_028208)	-207	NM_028208	72351	Mm.474795	NM_028208	ENSMUSG00000074925	Ptar1	1700084D09Rik|2010013L17Rik|4930428J16Rik|AI449677	protein prenyltransferase alpha subunit repeat containing 1	protein-coding
mm_86955.1	chr10	24920767	24920781	+	1	NA	exon (NM_007482, exon 3 of 8)	exon (NM_007482, exon 3 of 8)	6696	NM_007482	11846	Mm.154144	NM_007482	ENSMUSG00000019987	Arg1	AI|AI256583|Arg-1|PGIF	arginase, liver	protein-coding
mm_152697.1	chr19	17125585	17125598	-	1	NA	exon (NM_181348, exon 9 of 20)	exon (NM_181348, exon 9 of 20)	169473	NM_181348	353211	Mm.257354	NM_181348	ENSMUSG00000039126	Prune2	6330414G02Rik|A230083H22Rik|A330102H22Rik|Bmcc1|mKIAA0367	prune homolog 2	protein-coding
mm_165858.1	chr4	20032264	20032292	+	1	NA	Intergenic	Intergenic	-9774	NM_010281	14590	Mm.20461	NM_010281	ENSMUSG00000073987	Ggh	gamma-GH	gamma-glutamyl hydrolase	protein-coding
mm_54448.1	chr6	34745936	34746010	-	1	NA	exon (NM_145575, exon 3 of 12)	exon (NM_145575, exon 3 of 12)	-34459	NM_001289657	76223	Mm.150047	NM_178630	ENSMUSG00000038836	Agbl3	2900053G10Rik|4930431N21Rik|6530406M24Rik|CCP3	ATP/GTP binding protein-like 3	protein-coding
mm_40742.1	chr5	66686199	66686203	+	1	NA	intron (NM_011670, intron 8 of 8)	MER58A|DNA|hAT-Charlie	-9704	NR_102714	101202684	Mm.381468	NR_102714	ENSMUSG00000087601	Uchl1os	Gm16832|Uchl1as	ubiquitin carboxy-terminal hydrolase L1, opposite strand	ncRNA
mm_28542.1	chr3	92827240	92827257	-	1	NA	promoter-TSS (NM_028629)	promoter-TSS (NM_028629)	-1	NM_028629	433619	Mm.28359	NM_028629	ENSMUSG00000059832	Kprp	1110001M24Rik|AA589586	keratinocyte expressed, proline-rich	protein-coding
mm_93448.1	chr10	109904013	109904022	-	1	NA	intron (NM_001081035, intron 1 of 38)	intron (NM_001081035, intron 1 of 38)	96202	NM_001081035	260315	Mm.225050	NM_177797	ENSMUSG00000020181	Nav3	4732483H20Rik|9630020C08Rik|POMFIL1|Pomfil1p|mKIAA0938|unc53H3	neuron navigator 3	protein-coding
mm_48051.1	chr5	136472412	136472417	-	1	NA	intron (NM_001291239, intron 2 of 22)	intron (NM_001291239, intron 2 of 22)	93567	NM_001291239	13047	Mm.320317	NM_009986	ENSMUSG00000029705	Cux1	CDP|Cutl1|Cux|Cux-1	cut-like homeobox 1	protein-coding
mm_150572.1	chr19	40119748	40119765	+	1	NA	Intergenic	Lx2|LINE|L1	30077	NM_001167875	107141	Mm.474575	NM_134144	ENSMUSG00000054827	Cyp2c50	AI266900	cytochrome P450, family 2, subfamily c, polypeptide 50	protein-coding
mm_29712.1	chr3	123690124	123690176	-	1	NA	intron (NR_121616, intron 1 of 13)	intron (NR_121616, intron 1 of 13)	702	NR_121616	83398	Mm.443908	NM_031186	ENSMUSG00000027977	Ndst3	4921531K01Rik|4930511P15Rik|N-HSST 3|NDST-3	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 3	protein-coding
mm_76868.1	chr8	105497090	105497094	-	1	NA	promoter-TSS (NM_175160)	promoter-TSS (NM_175160)	-222	NM_175160	70796	Mm.100917	NM_175160	ENSMUSG00000039199	Zdhhc1	4432412D04Rik	zinc finger, DHHC domain containing 1	protein-coding
mm_109641.1	chr12	112808915	112809002	+	1	NA	promoter-TSS (NM_145450)	promoter-TSS (NM_145450)	-17	NM_145450	217887	Mm.186678	NM_145450	ENSMUSG00000037594	BC022687	AW050009|C130001I08Rik|Flj20080	cDNA sequence BC022687	protein-coding
mm_141079.1	chr17	25868670	25868674	-	1	NA	promoter-TSS (NM_026633)	promoter-TSS (NM_026633)	66	NM_026633	68241	Mm.328870	NM_026633	ENSMUSG00000025732	Fam195a	9530058B02Rik|Mcrip2	family with sequence similarity 195, member A	protein-coding
mm_146336.1	chr18	82475082	82475103	+	1	NA	promoter-TSS (NM_010777)	promoter-TSS (NM_010777)	-31	NM_010777	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_9648.1	chr1	177260505	177260531	-	1	NA	Intergenic	Intergenic	-11751	NM_011785	23797	Mm.235194	NM_011785	ENSMUSG00000019699	Akt3	AI851531|D930002M15Rik|Nmf350	thymoma viral proto-oncogene 3	protein-coding
mm_4448.1	chr1	172588708	172588716	+	1	NA	intron (NM_029084, intron 1 of 4)	intron (NM_029084, intron 1 of 4)	1856	NM_029084	74748	Mm.179812	NM_029084	ENSMUSG00000053318	Slamf8	5830408F06Rik|Blame|SBBI42	SLAM family member 8	protein-coding
mm_124016.1	chr14	76506622	76506632	-	1	NA	exon (NM_207652, exon 3 of 3)	exon (NM_207652, exon 3 of 3)	2117	NM_009366	21807	Mm.153272	NM_009366	ENSMUSG00000022010	Tsc22d1	AA589566|AW105905|Egr5|TSC-22|Tgfb1i4|Tsc|Tsc22	TSC22 domain family, member 1	protein-coding
mm_84298.1	chr9	63377961	63377980	-	1	NA	promoter-TSS (NM_011840)	promoter-TSS (NM_011840)	-118	NM_011840	23938	Mm.325746	NM_011840	ENSMUSG00000058444	Map2k5	AI324775|AI428457|MEK5|Mapkk5|Prkmk5	mitogen-activated protein kinase kinase 5	protein-coding
mm_41658.1	chr5	98854554	98854562	+	1	NA	5' UTR (NM_001310677, exon 1 of 3)	5' UTR (NM_001310677, exon 1 of 3)	143	NM_001310677	110075	Mm.136461	NM_173404	ENSMUSG00000029335	Bmp3	9530029I04Rik	bone morphogenetic protein 3	protein-coding
mm_155517.1	chrX	74254737	74254750	+	1	NA	promoter-TSS (NM_007927)	promoter-TSS (NM_007927)	56	NM_007927	13726	Mm.18892	NM_007927	ENSMUSG00000001964	Emd	AW550900|Sta	emerin	protein-coding
mm_66350.1	chr7	43525224	43525235	-	1	NA	Intergenic	B3A|SINE|B2	7942	NM_001111058	12489	Mm.140157	NM_021293	ENSMUSG00000004609	Cd33	Siglec-3|gp67	CD33 antigen	protein-coding
mm_76731.1	chr8	95021008	95021016	-	1	NA	exon (NM_173036, exon 2 of 12)	exon (NM_173036, exon 2 of 12)	3320	NM_173036	54672	Mm.27995	NM_173036	ENSMUSG00000060470	Adgrg3	A030001G24Rik|AW214383|Gpr97|Pb1|Pb99	adhesion G protein-coupled receptor G3	protein-coding
mm_124605.1	chr15	3279266	3279272	+	1	NA	exon (NM_009155, exon 5 of 5)	exon (NM_009155, exon 5 of 5)	8292	NM_009155	20363	Mm.392203	NM_009155	ENSMUSG00000064373	Selenop	AU018766|D15Ucla1|Se-P|Sepp1|selp	selenoprotein P	protein-coding
mm_109304.1	chr12	109560659	109560682	+	1	NA	non-coding (NR_003633, exon 5 of 5)	non-coding (NR_003633, exon 5 of 5)	-3022	NR_030427	791079		NR_030427	ENSMUSG00000076451	Mir770	Mirn770|mir-770|mmu-mir-770	microRNA 770	ncRNA
mm_111124.1	chr12	81333524	81333552	-	1	NA	promoter-TSS (NM_080440)	promoter-TSS (NM_080440)	-358	NM_080440	110893	Mm.443748	NM_080440	ENSMUSG00000079055	Slc8a3	AW742262|Ncx3	solute carrier family 8 (sodium/calcium exchanger), member 3	protein-coding
mm_36896.1	chr4	107680959	107680985	-	1	NA	intron (NM_019872, intron 1 of 3)	intron (NM_019872, intron 1 of 3)	3190	NM_019872	56296	Mm.141324	NM_019872	ENSMUSG00000028610	Dmrtb1	Dmrt6|Prp13	DMRT-like family B with proline-rich C-terminal, 1	protein-coding
mm_54958.1	chr6	48707619	48707634	-	1	NA	intron (NM_153175, intron 1 of 2)	intron (NM_153175, intron 1 of 2)	618	NM_153175	231931	Mm.321047	NM_153175	ENSMUSG00000047867	Gimap6	4833419H03Rik|Ian6|mFLJ00102	GTPase, IMAP family member 6	protein-coding
mm_115475.1	chr13	119488488	119488529	+	1	NA	promoter-TSS (NR_027974)	promoter-TSS (NR_027974)	-124	NR_027974	67304	Mm.474382	NM_026084	ENSMUSG00000074635	3110070M22Rik	-	RIKEN cDNA 3110070M22 gene	ncRNA
mm_29437.1	chr3	109808256	109808258	-	1	NA	intron (NM_001163349, intron 5 of 5)	intron (NM_001163349, intron 5 of 5)	234250	NM_146139	57257	Mm.282257	NM_020505	ENSMUSG00000033721	Vav3	A530094I06Rik|AA986410|Idd18.1	vav 3 oncogene	protein-coding
mm_73347.1	chr8	105413615	105413631	+	1	NA	promoter-TSS (NM_177791)	promoter-TSS (NM_177791)	1	NM_001170788	270091	Mm.212709	NM_001033371	ENSMUSG00000054320	Lrrc36	BC036564	leucine rich repeat containing 36	protein-coding
mm_93329.1	chr10	99270443	99270448	-	1	NA	Intergenic	Intergenic	7214	NM_026268	67603	Mm.1791	NM_026268	ENSMUSG00000019960	Dusp6	1300019I03Rik|MKP-3|MKP3|PYST1	dual specificity phosphatase 6	protein-coding
mm_99839.1	chr11	109343925	109343955	+	1	NA	Intergenic	Intergenic	-2927	NR_027883	67927	Mm.394490	NR_027883	ENSMUSG00000099630	1700096J18Rik	-	RIKEN cDNA 1700096J18 gene	ncRNA
mm_162112.1	chrX	51681511	51681511	-	1	NA	promoter-TSS (NM_001290467)	promoter-TSS (NM_001290467)	91	NM_001077202	50786	Mm.252561	NM_015819	ENSMUSG00000062184	Hs6st2	6OST2	heparan sulfate 6-O-sulfotransferase 2	protein-coding
mm_169414.1	chr14	52862753	52862753	-	1	NA	Intergenic	Intergenic	-367058	NM_001170918	57269	Mm.88822	NM_020512	ENSMUSG00000059887	Olfr1507	MOR244-1|Mor28|Or28	olfactory receptor 1507	protein-coding
mm_111817.1	chr12	105685180	105685231	-	1	NA	promoter-TSS (NM_178613)	promoter-TSS (NM_178613)	36	NM_029654	76559	Mm.114362	NM_029654	ENSMUSG00000041341	Atg2b	2410024A21Rik|AI047755|AI503411|AW558123|C030004M05Rik|C630028L02Rik|mKIAA4067	autophagy related 2B	protein-coding
mm_34420.1	chr4	145274187	145274202	+	1	NA	intron (NM_009401, intron 12 of 12)	intron (NM_009401, intron 12 of 12)	-27324	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_98674.1	chr11	96284080	96284093	+	1	NA	intron (NM_010461, intron 1 of 1)	CpG	2181	NM_010461	15416	Mm.4822	NM_010461	ENSMUSG00000056648	Hoxb8	Hox-2.4	homeobox B8	protein-coding
mm_43305.1	chr5	134676690	134676713	+	1	NA	intron (NM_010717, intron 2 of 15)	intron (NM_010717, intron 2 of 15)	1547	NM_001305875	16885	Mm.15409	NM_010717	ENSMUSG00000029674	Limk1	KIZ-1|LIMK-1|Limk	LIM-domain containing, protein kinase	protein-coding
mm_754.1	chr1	43730812	43730875	+	1	NA	5' UTR (NM_024283, exon 1 of 4)	5' UTR (NM_024283, exon 1 of 4)	241	NM_024283	78896	Mm.50109	NM_024283	ENSMUSG00000026051	1500015O10Rik	Ecrg4	RIKEN cDNA 1500015O10 gene	protein-coding
mm_6339.1	chr1	71632077	71632095	-	1	NA	exon (NM_001276413, exon 13 of 44)	exon (NM_001276413, exon 13 of 44)	21148	NM_010233	14268	Mm.193099	NM_010233	ENSMUSG00000026193	Fn1	E330027I09|Fn|Fn-1	fibronectin 1	protein-coding
mm_50679.1	chr6	51557515	51557544	+	1	NA	intron (NM_028035, intron 1 of 6)	ORR1A3|LTR|ERVL-MaLR	13006	NM_001127348	71982	Mm.294166	NM_028035	ENSMUSG00000038301	Snx10	2410004M09Rik	sorting nexin 10	protein-coding
mm_50941.1	chr6	57824486	57824498	+	1	NA	intron (NM_146168, intron 1 of 4)	CpG	633	NM_146168	232023	Mm.24642	NM_146168	ENSMUSG00000037788	Vopp1	AW146242|Ecop	vesicular, overexpressed in cancer, prosurvival protein 1	protein-coding
mm_98719.1	chr11	96318862	96318872	+	1	NA	exon (NM_010459, exon 1 of 2)	exon (NM_010459, exon 1 of 2)	600	NM_010459	15412	Mm.3546	NM_010459	ENSMUSG00000038692	Hoxb4	Hox-2.6	homeobox B4	protein-coding
mm_109359.1	chr12	109633209	109633212	+	1	NA	intron (NR_028261, intron 6 of 20)	AT_rich|Low_complexity|Low_complexity	-2802	NR_046302	449562		NR_046302	ENSMUSG00000088294	AF357425	MBII-48	snoRNA AF357425	snoRNA
mm_153238.1	chr19	36113022	36113025	-	1	NA	intron (NM_013468, intron 8 of 8)	intron (NM_013468, intron 8 of 8)	6821	NM_013468	107765	Mm.10279	NM_013468	ENSMUSG00000024803	Ankrd1	Alrp|CARP|Crap|MARP1	ankyrin repeat domain 1 (cardiac muscle)	protein-coding
mm_160.1	chr1	12718497	12718513	+	1	NA	promoter-TSS (NM_172294)	promoter-TSS (NM_172294)	-40	NM_172294	240725	Mm.45563	NM_172294	ENSMUSG00000016918	Sulf1	AI467640|AW121680|mKIAA1077	sulfatase 1	protein-coding
mm_2616.1	chr1	120488191	120488226	+	1	NA	exon (NM_010766, exon 8 of 17)	exon (NM_010766, exon 8 of 17)	16876	NM_010766	17167	Mm.1856	NM_010766	ENSMUSG00000026390	Marco	AI323439|Ly112|Scara2	macrophage receptor with collagenous structure	protein-coding
mm_137452.1	chr17	26538331	26538352	+	1	NA	Intergenic	Intergenic	-23171	NM_026170	67458	Mm.30496	NM_026170	ENSMUSG00000001576	Ergic1	1200007D18Rik|maa-136	endoplasmic reticulum-golgi intermediate compartment (ERGIC) 1	protein-coding
mm_151509.1	chr19	58733345	58733408	+	1	NA	exon (NM_018874, exon 6 of 13)	exon (NM_018874, exon 6 of 13)	4489	NM_018874	18946	Mm.10753	NM_018874	ENSMUSG00000042179	Pnliprp1	Plrp1	pancreatic lipase related protein 1	protein-coding
mm_80059.1	chr9	69397930	69397937	+	1	NA	promoter-TSS (NM_145618)	promoter-TSS (NM_145618)	-65	NM_145618	93697	Mm.35911	NM_145618	ENSMUSG00000032235	Ice2	B230343B06Rik|Narg2	interactor of little elongation complex ELL subunit 2	protein-coding
mm_156800.1	chrX	163909099	163909099	+	1	NA	promoter-TSS (NM_026887)	promoter-TSS (NM_026887)	82	NM_001290379	108012	Mm.426783	NM_026887	ENSMUSG00000031367	Ap1s2	1500012A13Rik|AI853648|EST1	adaptor-related protein complex 1, sigma 2 subunit	protein-coding
mm_104900.1	chr11	99620433	99620436	-	1	NA	promoter-TSS (NM_001177537)	promoter-TSS (NM_001177537)	-30	NM_001177537	100502803	Mm.351892	NM_001177537	ENSMUSG00000062278	Gm11562	OTTMUSG00000002199	predicted gene 11562	protein-coding
mm_54953.1	chr6	48682350	48682395	-	1	NA	Intergenic	Intergenic	-2206	NM_001243200	107526	Mm.333048	NM_174990	ENSMUSG00000054435	Gimap4	AU019574|E430007K16Rik|Ian-1|Ian1|Imap4	GTPase, IMAP family member 4	protein-coding
mm_135022.1	chr16	32496150	32496160	-	1	NA	promoter-TSS (NM_199309)	promoter-TSS (NM_199309)	-126	NM_199309	245308	Mm.76859	NM_199309	ENSMUSG00000052363	Zdhhc19	Gm1744|Gm616	zinc finger, DHHC domain containing 19	protein-coding
mm_159485.1	chr4	42153415	42153415	+	1	NA	promoter-TSS (NM_001199961)	promoter-TSS (NM_001199961)	-30	NM_001199962	100039863	Mm.6660	NM_001164046	ENSMUSG00000073877	Gm13306	OTTMUSG00000011352	predicted gene 13306	protein-coding
mm_40952.1	chr5	76856651	76856666	+	1	NA	exon (NM_001163793, exon 6 of 9)	exon (NM_001163793, exon 6 of 9)	16059	NM_001163793	320827	Mm.101504	NM_001163793	ENSMUSG00000036377	C530008M17Rik	2810489J07Rik|4930529A19Rik|4931405B09Rik|Kiaa1211|mKIAA1211	RIKEN cDNA C530008M17 gene	protein-coding
mm_114113.1	chr13	54949364	54949386	+	1	NA	promoter-TSS (NM_153131)	promoter-TSS (NM_153131)	-36	NM_001311128	107448	Mm.23573	NM_153131	ENSMUSG00000025876	Unc5a	Unc5h1|mKIAA1976	unc-5 netrin receptor A	protein-coding
mm_130499.1	chr15	98809488	98809492	-	1	NA	Intergenic	Intergenic	-1565	NM_001013741	13199	Mm.390810	NM_001013741	ENSMUSG00000059213	Ddn	Gm748	dendrin	protein-coding
mm_78446.1	chr9	32224269	32224281	+	1	NA	promoter-TSS (NM_177379)	promoter-TSS (NM_177379)	26	NM_177379	330914	Mm.46683	NM_177379	ENSMUSG00000041444	Arhgap32	3426406O18Rik|Gc-gap|Grit|Px-rics|Rics|mKIAA0712|p200Rhogap|p250Gap	Rho GTPase activating protein 32	protein-coding
mm_131444.1	chr16	16232429	16232432	+	1	NA	intron (NM_026163, intron 4 of 12)	B3|SINE|B2	19085	NM_026163	67451	Mm.2252	NM_026163	ENSMUSG00000041957	Pkp2	1200008D14Rik|1200012P04Rik|AA516617|Pkp2l	plakophilin 2	protein-coding
mm_14575.1	chr2	135659160	135659174	+	1	NA	Intergenic	CpG	-75947	NR_015544	320684	Mm.421433	NR_015544	ENSMUSG00000085631	9630028H03Rik	-	RIKEN cDNA 9630028H03 gene	ncRNA
mm_37499.1	chr4	123687320	123687356	-	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	-2978	NM_001199136	11426	Mm.402299	NM_009600	ENSMUSG00000028649	Macf1	ABP620|Acf7|Aclp7|MACF|R74989|mKIAA0465	microtubule-actin crosslinking factor 1	protein-coding
mm_18845.1	chr2	75633533	75633543	-	1	NA	Intergenic	RMER20B|LTR|ERVK	-25721	NM_146130	229279	Mm.316306	NM_053263	ENSMUSG00000059005	Hnrnpa3	2410013L13Rik|2610209F03Rik|2610510D13Rik|Hnrpa3	heterogeneous nuclear ribonucleoprotein A3	protein-coding
mm_77011.1	chr8	107581242	107581269	-	1	NA	exon (NM_010817, exon 7 of 7)	exon (NM_010817, exon 7 of 7)	7227	NM_010817	17463	Mm.18347	NM_010817	ENSMUSG00000039067	Psmd7	AW107203|Mov-34|Mov34	proteasome (prosome, macropain) 26S subunit, non-ATPase, 7	protein-coding
mm_110105.1	chr12	26415200	26415214	-	1	NA	promoter-TSS (NR_105856)	promoter-TSS (NR_105856)	55	NM_001081977	108089	Mm.214932	NM_080563	ENSMUSG00000020642	Rnf144a	Rnf144|UIP4|Ubce7ip4	ring finger protein 144A	protein-coding
mm_112515.1	chr13	9093894	9093927	+	1	NA	promoter-TSS (NM_172585)	promoter-TSS (NM_172585)	29	NM_172585	217980	Mm.234944	NM_172585	ENSMUSG00000033499	Larp4b	A630096F19|AI256361|D13Wsu64e|Larp5	La ribonucleoprotein domain family, member 4B	protein-coding
mm_38288.1	chr4	136890372	136890384	-	1	NA	exon (NM_007574, exon 3 of 3)	exon (NM_007574, exon 3 of 3)	2536	NM_007574	12262	Mm.439732	NM_007574	ENSMUSG00000036896	C1qc	AI385742|C1qg|Ciqc	complement component 1, q subcomponent, C chain	protein-coding
mm_101001.1	chr11	8468572	8468580	-	1	NA	intron (NM_001083587, intron 20 of 30)	intron (NM_001083587, intron 20 of 30)	195959	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_168926.1	chr12	63113064	63113071	-	1	NA	Intergenic	BGLII|LTR|ERVK	425280	NR_131949	73309	Mm.276558	NR_131949		Spanxn4	1700047L15Rik	SPANX family, member N4	ncRNA
mm_39538.1	chr5	21424935	21425013	+	1	NA	promoter-TSS (NM_177869)	promoter-TSS (NM_177869)	71	NM_177869	330050	Mm.40655	NM_177869	ENSMUSG00000047221	Fam185a	4631428I10|AI847670	family with sequence similarity 185, member A	protein-coding
mm_123380.1	chr14	63271683	63271702	-	1	NA	Intergenic	Intergenic	-26421	NM_001310610	14463	Mm.247669	NM_008092	ENSMUSG00000021944	Gata4	Gata-4	GATA binding protein 4	protein-coding
mm_116750.1	chr13	51801150	51801154	-	1	NA	Intergenic	Intergenic	-7405	NM_013660	20354	Mm.33903	NM_013660	ENSMUSG00000021451	Sema4d	CD100|Semacl2|Semaj|Semcl2|coll-4	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D	protein-coding
mm_77696.1	chr8	126589613	126589626	-	1	NA	3' UTR (NM_001164598, exon 2 of 2)	3' UTR (NM_001164598, exon 2 of 2)	3817	NM_001164598	270110	Mm.334918	NM_001164598	ENSMUSG00000051495	Irf2bp2	E130305N23Rik|IRF-2BP2	interferon regulatory factor 2 binding protein 2	protein-coding
mm_118073.1	chr13	102969440	102969442	-	1	NA	intron (NM_175171, intron 4 of 28)	intron (NM_175171, intron 4 of 28)	209186	NR_130171	76624	Mm.426384	NR_130171	ENSMUSG00000091906	1700099I09Rik	-	RIKEN cDNA 1700099I09 gene	ncRNA
mm_142482.1	chr17	45721067	45721106	-	1	NA	Intergenic	Intergenic	12758	NM_028164	72240	Mm.482897	NM_028164	ENSMUSG00000094690	1600014C23Rik	-	RIKEN cDNA 1600014C23 gene	protein-coding
mm_149319.1	chr19	10839879	10839898	+	1	NA	Intergenic	Intergenic	-2656	NM_023044	65221	Mm.27387	NM_023044	ENSMUSG00000024737	Slc15a3	Ci1|cI-1	solute carrier family 15, member 3	protein-coding
mm_72732.1	chr8	85083270	85083297	+	1	NA	promoter-TSS (NM_010764)	promoter-TSS (NM_010764)	14	NM_010764	17159	Mm.4219	NM_010764	ENSMUSG00000005142	Man2b1	AW107687|LAMAN	mannosidase 2, alpha B1	protein-coding
mm_48445.1	chr5	140648981	140649014	-	1	NA	promoter-TSS (NM_175274)	promoter-TSS (NM_175274)	34	NM_001308040	78339	Mm.28947	NM_175274	ENSMUSG00000036565	Ttyh3	2900029G13Rik|AI414930|TTY3|mTTY3	tweety family member 3	protein-coding
mm_16492.1	chr2	181155253	181155293	+	1	NA	exon (NM_007906, exon 2 of 8)	exon (NM_007906, exon 2 of 8)	1742	NM_007906	13628	Mm.2645	NM_007906	ENSMUSG00000016349	Eef1a2	Eef1a|S1|wasted|wst	eukaryotic translation elongation factor 1 alpha 2	protein-coding
mm_71514.1	chr8	46846498	46846521	+	1	NA	3' UTR (NM_008391, exon 9 of 9)	3' UTR (NM_008391, exon 9 of 9)	106764	NM_008391	16363	Mm.1149	NM_008391	ENSMUSG00000031627	Irf2	9830146E22Rik|AI646973|Irf-2	interferon regulatory factor 2	protein-coding
mm_11997.1	chr2	57115127	57115162	+	1	NA	promoter-TSS (NM_013613)	promoter-TSS (NM_013613)	-106	NM_013613	18227	Mm.3507	NM_013613	ENSMUSG00000026826	Nr4a2	HZF-3|NOT|Nurr1|RNR-1|TINOR|TINUR	nuclear receptor subfamily 4, group A, member 2	protein-coding
mm_64757.1	chr7	4844711	4844725	-	1	NA	promoter-TSS (NM_172737)	promoter-TSS (NM_172737)	-22	NM_172737	232813	Mm.44666	NM_172737	ENSMUSG00000053550	Shisa7	ckamp59	shisa family member 7	protein-coding
mm_23917.1	chr3	83046665	83046676	+	1	NA	exon (NM_181849, exon 2 of 8)	exon (NM_181849, exon 2 of 8)	3193	NM_181849	110135	Mm.30063	NM_181849	ENSMUSG00000033831	Fgb	2510049G14Rik	fibrinogen beta chain	protein-coding
mm_161557.1	chr16	13984612	13984612	-	1	NA	intron (NM_001270718, intron 1 of 2)	intron (NM_001270718, intron 1 of 2)	-2025	NM_144518	67254	Mm.216217	NM_144518	ENSMUSG00000044117	2900011O08Rik	MINP	RIKEN cDNA 2900011O08 gene	protein-coding
mm_142348.1	chr17	43612183	43612203	-	1	NA	TTS (NM_013737)	TTS (NM_013737)	18106	NM_001161366	210510	Mm.329058	NM_198418	ENSMUSG00000040140	Tdrd6	AB097085|Tdr2	tudor domain containing 6	protein-coding
mm_66689.1	chr7	45870228	45870238	-	1	NA	Intergenic	Intergenic	-2607	NM_133950	68137	Mm.298433	NM_133950	ENSMUSG00000002778	Kdelr1	8030486F04Rik|AW215843|Erd2.1	KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 1	protein-coding
mm_64901.1	chr7	15964373	15964427	-	1	NA	intron (NM_153068, intron 1 of 5)	intron (NM_153068, intron 1 of 5)	3135	NM_153068	259300	Mm.138215	NM_153068	ENSMUSG00000074364	Ehd2	BC027084|C130052H20Rik	EH-domain containing 2	protein-coding
mm_66028.1	chr7	30620903	30620907	-	1	NA	intron (NM_025628, intron 3 of 3)	B1F|SINE|Alu	5246	NM_025628	110323	Mm.400	NM_025628	ENSMUSG00000036751	Cox6b1	2010000G05Rik|Cox6b	cytochrome c oxidase, subunit VIb polypeptide 1	protein-coding
mm_2728.1	chr1	128202423	128202429	+	1	NA	promoter-TSS (NR_029543)	promoter-TSS (NR_029543)	65	NR_029543	387147		NR_029543	ENSMUSG00000065520	Mir128-1	Mirn128|Mirn128-1|Mirn128a|mir-128-1	microRNA 128-1	ncRNA
mm_90127.1	chr10	117710075	117710085	+	1	NA	intron (NM_001288586, intron 1 of 10)	CpG-1528	678	NM_010786	17246	Mm.22670	NM_010786	ENSMUSG00000020184	Mdm2	1700007J15Rik|AA415488|Mdm-2	transformed mouse 3T3 cell double minute 2	protein-coding
mm_43371.1	chr5	135632682	135632694	+	1	NA	promoter-TSS (NM_146002)	promoter-TSS (NM_146002)	34	NM_146002	215160	Mm.295438	NM_031398	ENSMUSG00000039917	Rhbdd2	0610011L13Rik|AI480532|Rhbdl7|Usmg1	rhomboid domain containing 2	protein-coding
mm_127496.1	chr15	101411121	101411138	+	1	NA	Intergenic	Intergenic	-1274	NM_033073	110310	Mm.486285	NM_033073	ENSMUSG00000023039	Krt7	D15Wsu77e|K7|Krt2-7	keratin 7	protein-coding
mm_40396.1	chr5	52834010	52834031	+	1	NA	promoter-TSS (NM_024213)	promoter-TSS (NM_024213)	-115	NM_024213	52206	Mm.272568	NM_024213	ENSMUSG00000029176	Anapc4	2610306D21Rik|APC4|D5Ertd249e	anaphase promoting complex subunit 4	protein-coding
mm_172717.1	chr8	70691785	70691785	-	1	NA	Intergenic	Intergenic	-5954	NM_010592	16478	Mm.419851	NM_010592	ENSMUSG00000071076	Jund	Jund1	jun D proto-oncogene	protein-coding
mm_164081.1	chr15	4077169	4077170	+	1	NA	intron (NM_024188, intron 7 of 16)	intron (NM_024188, intron 7 of 16)	-49763	NR_028266	414066	Mm.394461	NR_028266		BC037032	-	cDNA Sequence BC037032	ncRNA
mm_70054.1	chr7	142651115	142651125	-	1	NA	3' UTR (NM_010514, exon 4 of 4)	3' UTR (NM_010514, exon 4 of 4)	3876	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_29937.1	chr3	132655800	132655811	-	1	NA	Intergenic	Intergenic	25614	NM_001270430	433653		NM_001270430	ENSMUSG00000091721	Gimd1	EG433653|Gm5549	GIMAP family P-loop NTPase domain containing 1	protein-coding
mm_131263.1	chr16	10827391	10827395	+	1	NA	Intergenic	RLTR8|LTR|ERVK	-7666	NM_001162932	223970	Mm.325777	NM_001033278	ENSMUSG00000037991	Rmi2	A630055G03Rik|Gm537|Gm929	RecQ mediated genome instability 2	protein-coding
mm_37485.1	chr4	123573072	123573081	-	1	NA	intron (NM_001199136, intron 1 of 97)	intron (NM_001199136, intron 1 of 97)	-43344	NR_105824	102465214		NR_105824	ENSMUSG00000099005	Mir6398	Gm27657|mmu-mir-6398	microRNA 6398	ncRNA
mm_4531.1	chr1	175698553	175698560	+	1	NA	promoter-TSS (NM_029453)	promoter-TSS (NM_029453)	-37	NM_029453	75820	Mm.50361	NM_029453	ENSMUSG00000026523	Wdr64	4930415O10Rik|4930511H01Rik	WD repeat domain 64	protein-coding
mm_89685.1	chr10	97565416	97565431	+	1	NA	promoter-TSS (NM_008524)	promoter-TSS (NM_008524)	-78	NM_008524	17022	Mm.18888	NM_008524	ENSMUSG00000036446	Lum	Ldc|SLRR2D	lumican	protein-coding
mm_104182.1	chr11	87796422	87796434	-	1	NA	exon (NM_010824, exon 7 of 14)	exon (NM_010824, exon 7 of 14)	2644	NM_010824	17523	Mm.4668	NM_010824	ENSMUSG00000009350	Mpo	mKIAA4033	myeloperoxidase	protein-coding
mm_4627.1	chr1	179546522	179546538	+	1	NA	promoter-TSS (NM_146105)	promoter-TSS (NM_146105)	1	NM_146105	226744	Mm.87662	NM_146105	ENSMUSG00000038949	Cnst	9630058J23Rik	consortin, connexin sorting protein	protein-coding
mm_173039.1	chrX	112162754	112162758	+	1	NA	Intergenic	Intergenic	69236	NM_031382	83556	Mm.190608	NM_031382	ENSMUSG00000034555	Tex16	OTTMUSG00000018437	testis expressed gene 16	protein-coding
mm_85437.1	chr9	104102317	104102340	-	1	NA	5' UTR (NM_145700, exon 2 of 3)	5' UTR (NM_145700, exon 2 of 3)	24315	NM_145700	252837	Mm.269254	NM_145700	ENSMUSG00000079355	Ackr4	A630091E18Rik|CCBP2|CCR11|CCX-CKR|CCX-CKR1|Ccrl1|Cmkbrl1|PPR1|VSHK1	atypical chemokine receptor 4	protein-coding
mm_91969.1	chr10	61432712	61432746	-	1	NA	3' UTR (NM_010124, exon 3 of 3)	3' UTR (NM_010124, exon 3 of 3)	14757	NM_013611	18119	Mm.57195	NM_013611	ENSMUSG00000037171	Nodal	Tg.413d	nodal	protein-coding
mm_55706.1	chr6	72958098	72958244	-	1	NA	promoter-TSS (NM_001039392)	promoter-TSS (NM_001039392)	61	NM_001039392	19240	Mm.3532	NM_025284	ENSMUSG00000079523	Tmsb10	Ptmb10|Tb10	thymosin, beta 10	protein-coding
mm_50566.1	chr6	49048028	49048064	+	1	NA	exon (NM_053110, exon 6 of 11)	exon (NM_053110, exon 6 of 11)	11528	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_53469.1	chr6	134921190	134921208	+	1	NA	exon (NM_009875, exon 1 of 3)	exon (NM_009875, exon 1 of 3)	798	NM_009875	12576	Mm.2958	NM_009875	ENSMUSG00000003031	Cdkn1b	AA408329|AI843786|Kip1|p27|p27Kip1	cyclin-dependent kinase inhibitor 1B	protein-coding
mm_111356.1	chr12	86990485	86990494	-	1	NA	Intergenic	CpG	-1813	NM_001080943	238331	Mm.185890	NM_001080943	ENSMUSG00000048483	Zdhhc22	Gm262	zinc finger, DHHC-type containing 22	protein-coding
mm_134778.1	chr16	23977844	23977863	-	1	NA	intron (NM_009744, intron 2 of 9)	MIRc|SINE|MIR	10759	NM_009744	12053	Mm.347398	NM_009744	ENSMUSG00000022508	Bcl6	Bcl5	B cell leukemia/lymphoma 6	protein-coding
mm_13694.1	chr2	117121052	117121149	+	1	NA	promoter-TSS (NM_001277256)	promoter-TSS (NM_001277256)	29	NM_033524	114715	Mm.245890	NM_033524	ENSMUSG00000027351	Spred1	5730461F13Rik|AL024345|AW047647	sprouty protein with EVH-1 domain 1, related sequence	protein-coding
mm_4312.1	chr1	171845703	171845718	+	1	NA	intron (NM_001289470, intron 2 of 8)	intron (NM_001289470, intron 2 of 8)	6013	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_155318.1	chrX	62283498	62283500	+	1	NA	promoter-TSS (NM_001199997)	promoter-TSS (NM_001199997)	0	NM_001199997	74437	Mm.85792	NM_001199996	ENSMUSG00000045330	4933402E13Rik	-	RIKEN cDNA 4933402E13 gene	protein-coding
mm_128553.1	chr15	55906066	55906102	-	1	NA	exon (NM_016667, exon 1 of 7)	exon (NM_016667, exon 1 of 7)	865	NM_016667	20649	Mm.309425	NM_016667	ENSMUSG00000060429	Sntb1	-	syntrophin, basic 1	protein-coding
mm_124563.1	chr14	123627032	123627057	-	1	NA	promoter-TSS (NM_177393)	promoter-TSS (NM_177393)	100	NM_177393	338370	Mm.255348	NM_177393	ENSMUSG00000000197	Nalcn	A530023G15Rik|AI849508|Vgcnl1	sodium leak channel, non-selective	protein-coding
mm_125496.1	chr15	55112453	55112484	+	1	NA	non-coding (NR_045093, exon 2 of 5)	non-coding (NR_045093, exon 2 of 5)	151	NM_145470	97998	Mm.295397	NM_145470	ENSMUSG00000022419	Deptor	Depdc6	DEP domain containing MTOR-interacting protein	protein-coding
mm_143774.1	chr17	81704783	81704810	-	1	NA	intron (NR_104580, intron 1 of 8)	intron (NR_104580, intron 1 of 8)	33591	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_27351.1	chr3	50416064	50416078	-	1	NA	intron (NM_011990, intron 6 of 11)	intron (NM_011990, intron 6 of 11)	27542	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_12637.1	chr2	74709714	74709714	+	1	NA	TTS (NR_027899)	TTS (NR_027899)	-2279	NM_010468	15434	Mm.430708	NM_010468	ENSMUSG00000079277	Hoxd3	Hox-4.1|Hox-5.5	homeobox D3	protein-coding
mm_17927.1	chr2	35462455	35462503	-	1	NA	Intergenic	CpG	-1030	NM_001145821	14594	Mm.281124	NM_010283	ENSMUSG00000035778	Ggta1	AW108479|GALT|Gal|Ggta|Ggta-1|alpha Gal|alpha3GalT	glycoprotein galactosyltransferase alpha 1, 3	protein-coding
mm_137013.1	chr17	17831138	17831145	+	1	NA	TTS (NR_029539)	TTS (NR_029539)	166	NM_001162909	75202	Mm.227456	NM_029205	ENSMUSG00000080316	Spaca6	4930546H06Rik|9530079D04Rik|B230206P06Rik|Ncrna00085|SPACA6A|let-7e|mir-125a|mir-99b	sperm acrosome associated 6	protein-coding
mm_74077.1	chr8	122470197	122470212	+	1	NA	exon (NM_001033142, exon 2 of 6)	exon (NM_001033142, exon 2 of 6)	5860	NM_001033142	68718	Mm.34356	NM_001033142	ENSMUSG00000014470	Rnf166	1110031E24Rik|AW555115|Zfp313l	ring finger protein 166	protein-coding
mm_43961.1	chr5	145249408	145249410	+	1	NA	Intergenic	Intergenic	17650	NM_028298	72611	Mm.206555	NM_028298	ENSMUSG00000007812	Zfp655	2700038I16Rik|9030409O18Rik|mKIAA4222	zinc finger protein 655	protein-coding
mm_28014.1	chr3	83043867	83043877	-	1	NA	exon (NM_181849, exon 6 of 8)	exon (NM_181849, exon 6 of 8)	5991	NM_181849	110135	Mm.30063	NM_181849	ENSMUSG00000033831	Fgb	2510049G14Rik	fibrinogen beta chain	protein-coding
mm_136910.1	chr17	13016737	13016740	+	1	NA	3' UTR (NM_013671, exon 5 of 5)	3' UTR (NM_013671, exon 5 of 5)	8899	NM_013671	20656	Mm.290876	NM_013671	ENSMUSG00000006818	Sod2	MnSOD|Sod-2	superoxide dismutase 2, mitochondrial	protein-coding
mm_105655.1	chr11	107289224	107289227	-	1	NA	intron (NM_145823, intron 5 of 9)	B3|SINE|B2	-99844	NM_001161329	68979	Mm.294617	NM_133702	ENSMUSG00000018433	Nol11	1500002M01Rik|AU015220|AU019874	nucleolar protein 11	protein-coding
mm_128925.1	chr15	73986113	73986153	-	1	NA	Intergenic	Intergenic	-146462	NM_001033365	268816	Mm.440635	NM_001033365	ENSMUSG00000072487	Mroh5	Gm628	maestro heat-like repeat family member 5	protein-coding
mm_124319.1	chr14	103346724	103346734	-	1	NA	promoter-TSS (NM_207215)	promoter-TSS (NM_207215)	71	NM_207215	105689	Mm.6478	NM_207215	ENSMUSG00000033004	Mycbp2	AU023734|AW107953|AW546647|C130061D10Rik|Pam|Phr1|R75243	MYC binding protein 2	protein-coding
mm_169352.1	chr14	20982717	20982718	+	1	NA	exon (NM_009502, exon 3 of 21)	exon (NM_009502, exon 3 of 21)	53284	NM_009502	22330	Mm.279361	NM_009502	ENSMUSG00000021823	Vcl	9430097D22|AA571387|AI462105|AW545629	vinculin	protein-coding
mm_136636.1	chr17	5718012	5718028	+	1	NA	intron (NM_146073, intron 5 of 8)	intron (NM_146073, intron 5 of 8)	-80637	NR_045081	78512	Mm.23696	NR_045079	ENSMUSG00000096965	3300005D01Rik	-	RIKEN cDNA 3300005D01 gene	ncRNA
mm_158578.1	chrX	150657123	150657133	-	1	NA	intron (NM_001290770, intron 1 of 12)	intron (NM_001290770, intron 1 of 12)	308	NM_019548	56191	Mm.3597	NM_019548	ENSMUSG00000025272	Tro	AA409408|Maged3|Maged3l|Tnn|Trol|magphinin	trophinin	protein-coding
mm_85612.1	chr9	107606674	107606688	-	1	NA	5' UTR (NM_001291538, exon 2 of 20)	5' UTR (NM_001291538, exon 2 of 20)	411	NM_001291538	20347	Mm.4083	NM_009153	ENSMUSG00000057969	Sema3b	SemA|Semaa|sema5|semaV	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B	protein-coding
mm_39488.1	chr5	20950772	20950775	+	1	NA	promoter-TSS (NR_030699)	promoter-TSS (NR_030699)	-216	NR_030699	320770	Mm.491217	NR_030699	ENSMUSG00000101013	A630072M18Rik	Aptr	RIKEN cDNA A630072M18 gene	ncRNA
mm_128649.1	chr15	59646355	59646358	-	1	NA	Intergenic	Intergenic	-2298	NM_144549	211770	Mm.40298	NM_144549	ENSMUSG00000032501	Trib1	A530090O15Rik|TRB-1|Trb1	tribbles pseudokinase 1	protein-coding
mm_18286.1	chr2	52558579	52558601	-	1	NA	promoter-TSS (NM_146123)	promoter-TSS (NM_146123)	21	NM_146123	12298	Mm.330223	NM_146123	ENSMUSG00000017412	Cacnb4	3110038O15Rik|Cchb4|lh	calcium channel, voltage-dependent, beta 4 subunit	protein-coding
mm_53802.1	chr6	146850121	146850159	+	1	NA	promoter-TSS (NM_027059)	promoter-TSS (NM_027059)	30	NM_027059	69371	Mm.252733	NM_027059	ENSMUSG00000030292	Smco2	1700023A16Rik	single-pass membrane protein with coiled-coil domains 2	protein-coding
mm_132742.1	chr16	44136809	44136819	+	1	NA	intron (NM_007508, intron 1 of 14)	B4A|SINE|B4	2205	NM_007508	11964	Mm.217787	NM_007508	ENSMUSG00000052459	Atp6v1a	AI647066|Atp6a1|Atp6a2|Atp6v1a1|VA68|VPP2	ATPase, H+ transporting, lysosomal V1 subunit A	protein-coding
mm_105870.1	chr11	114248323	114248347	-	1	NA	Intergenic	MLTR14|LTR|ERV1	50077	NR_045930	73536	Mm.54275	NR_045930	ENSMUSG00000078600	1700092K14Rik	-	RIKEN cDNA 1700092K14 gene	ncRNA
mm_64790.1	chr7	6173103	6173130	-	1	NA	intron (NM_028316, intron 1 of 3)	intron (NM_028316, intron 1 of 3)	603	NM_001146024	72667	Mm.274089	NM_028316	ENSMUSG00000044876	Zfp444	2810031J10Rik|6230401O10Rik|mFLJ00134	zinc finger protein 444	protein-coding
mm_33777.1	chr4	134506672	134506676	+	1	NA	5' UTR (NM_001285845, exon 2 of 3)	5' UTR (NM_001285845, exon 2 of 3)	-4325	NM_001081099	69885	Mm.141592	NM_001081099	ENSMUSG00000078521	Aunip	2610002D18Rik|Clhc1	aurora kinase A and ninein interacting protein	protein-coding
mm_63208.1	chr7	126272414	126272424	+	1	NA	promoter-TSS (NM_145587)	promoter-TSS (NM_145587)	-200	NM_145587	104175	Mm.29660	NM_145587	ENSMUSG00000042978	Sbk1	Sbk	SH3-binding kinase 1	protein-coding
mm_34041.1	chr4	138216300	138216324	+	1	NA	promoter-TSS (NM_001122896)	promoter-TSS (NM_001122896)	-300	NM_001122896	15441	Mm.348429	NM_010470	ENSMUSG00000028759	Hp1bp3	Hp1bp74	heterochromatin protein 1, binding protein 3	protein-coding
mm_21208.1	chr2	155651825	155651829	-	1	NA	intron (NM_001163452, intron 8 of 18)	intron (NM_001163452, intron 8 of 18)	28947	NR_030757	735275		NR_030757	ENSMUSG00000076312	Mir499	Mirn499|mir-499|mmu-mir-499	microRNA 499	ncRNA
mm_85066.1	chr9	91051105	91051106	-	1	NA	Intergenic	Lx8b|LINE|L1	314694	NM_009573	22771	Mm.335350	NM_009573	ENSMUSG00000032368	Zic1	ZIC|ZNF201	zinc finger protein of the cerebellum 1	protein-coding
mm_70677.1	chr8	14961902	14961913	+	1	NA	intron (NM_172751, intron 16 of 28)	intron (NM_172751, intron 16 of 28)	-49118	NM_029116	74901	Mm.46675	NM_029116	ENSMUSG00000055675	Kbtbd11	2900016B01Rik|4930465M17Rik|mKIAA0711	kelch repeat and BTB (POZ) domain containing 11	protein-coding
mm_150720.1	chr19	43528341	43528351	+	1	NA	Intergenic	Intergenic	-3741	NM_010324	14718	Mm.19039	NM_010324	ENSMUSG00000025190	Got1	AI789014|Got-1|cAspAT|cCAT	glutamic-oxaloacetic transaminase 1, soluble	protein-coding
mm_96843.1	chr11	70030073	70030083	+	1	NA	intron (NM_001109752, intron 2 of 19)	intron (NM_001109752, intron 2 of 19)	11473	NM_007864	13385	Mm.27256	NM_007864	ENSMUSG00000020886	Dlg4	Dlgh4|PSD-95|PSD95|SAP90|SAP90A	discs, large homolog 4 (Drosophila)	protein-coding
mm_92734.1	chr10	80906424	80906442	-	1	NA	promoter-TSS (NM_001347140)	promoter-TSS (NM_001347140)	-21	NM_001347140	16907	Mm.7362	NM_010722	ENSMUSG00000062075	Lmnb2	-	lamin B2	protein-coding
mm_75512.1	chr8	54529403	54529414	-	1	NA	intron (NM_029701, intron 1 of 4)	intron (NM_029701, intron 1 of 4)	590	NM_029701	76687	Mm.86437	NM_029701	ENSMUSG00000054408	Spcs3	1810011E08Rik|SPC22/23	signal peptidase complex subunit 3 homolog (S. cerevisiae)	protein-coding
mm_96480.1	chr11	67683507	67683531	+	1	NA	3' UTR (NM_001277080, exon 13 of 13)	3' UTR (NM_001277080, exon 13 of 13)	-11807	NM_009038	19674	Mm.439726	NM_009038	ENSMUSG00000020907	Rcvrn	CAR|S-modulin	recoverin	protein-coding
mm_121975.1	chr14	25768811	25768865	-	1	NA	promoter-TSS (NM_001101433)	promoter-TSS (NM_001101433)	18	NM_001101433	71918	Mm.41904	NM_001101433	ENSMUSG00000055538	Zcchc24	2310047A01Rik	zinc finger, CCHC domain containing 24	protein-coding
mm_8036.1	chr1	135167607	135167629	-	1	NA	promoter-TSS (NM_134438)	promoter-TSS (NM_134438)	63	NM_134438	171469	Mm.272290	NM_134438	ENSMUSG00000026424	Gpr37l1	AW047233|CAG-18|D0Kist8	G protein-coupled receptor 37-like 1	protein-coding
mm_35995.1	chr4	55533323	55533331	-	1	NA	promoter-TSS (NM_010637)	promoter-TSS (NM_010637)	-852	NM_010637	16600	Mm.4325	NM_010637	ENSMUSG00000003032	Klf4	EZF|Gklf|Zie	Kruppel-like factor 4 (gut)	protein-coding
mm_79801.1	chr9	64139274	64139277	+	1	NA	intron (NM_026507, intron 18 of 18)	IAPEY4_LTR|LTR|ERVK	22128	NM_145835	235435	Mm.436581	NM_145835	ENSMUSG00000032401	Lctl	E130104I05Rik|KLPH	lactase-like	protein-coding
mm_111748.1	chr12	103948160	103948169	-	1	NA	exon (NM_009247, exon 4 of 5)	exon (NM_009247, exon 4 of 5)	8733	NM_009247	20704	Mm.312593	NM_009247	ENSMUSG00000072849	Serpina1e	Dom5|PI5|Spi1-5	serine (or cysteine) peptidase inhibitor, clade A, member 1E	protein-coding
mm_56729.1	chr6	115676473	115676578	-	1	NA	5' UTR (NM_029780, exon 1 of 17)	5' UTR (NM_029780, exon 1 of 17)	110	NM_029780	110157	Mm.184163	NM_029780	ENSMUSG00000000441	Raf1	6430402F14Rik|AA990557|BB129353|Craf1|D830050J10Rik|Raf-1|c-Raf|v-Raf	v-raf-leukemia viral oncogene 1	protein-coding
mm_38925.1	chr4	150010990	150011000	-	1	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	-1972	NM_173371	100198	Mm.22183	NM_173371	ENSMUSG00000028980	H6pd	AI785303|G6pd1|Gpd-1|Gpd1	hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase)	protein-coding
mm_153574.1	chr19	43112412	43112412	-	1	NA	intron (NM_001081257, intron 3 of 11)	Lx8b|LINE|L1	275943	NM_001081257	545291	Mm.442200	NM_001081257	ENSMUSG00000074852	Hpse2	Gm968|Hpa2	heparanase 2	protein-coding
mm_25579.1	chr3	116861911	116861928	+	1	NA	intron (NM_009146, intron 1 of 16)	intron (NM_009146, intron 1 of 16)	239	NM_009146	20321	Mm.66293	NM_009146	ENSMUSG00000033386	Frrs1	AI131732|Sdfr2	ferric-chelate reductase 1	protein-coding
mm_163901.1	chr14	29669435	29669436	+	1	NA	intron (NM_009785, intron 2 of 37)	GA-rich|Low_complexity|Low_complexity	52429	NM_009785	12294	Mm.386754	NM_009785	ENSMUSG00000021991	Cacna2d3	Cacnad3|alapha2delta3	calcium channel, voltage-dependent, alpha2/delta subunit 3	protein-coding
mm_105826.1	chr11	113171943	113171959	-	1	NA	intron (NR_015556, intron 1 of 2)	intron (NR_015556, intron 1 of 2)	29887	NR_015556	72386	Mm.266961	NR_015556	ENSMUSG00000087259	2610035D17Rik	-	RIKEN cDNA 2610035D17 gene	ncRNA
mm_148164.1	chr18	77732725	77732739	-	1	NA	Intergenic	Intergenic	18548	NR_027978	67640	Mm.482903	NM_026289		4930465K10Rik	-	RIKEN cDNA 4930465K10 gene	ncRNA
mm_26994.1	chr3	25790595	25790638	-	1	NA	intron (NM_001163387, intron 3 of 5)	intron (NM_001163387, intron 3 of 5)	362691	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_105101.1	chr11	100955210	100955213	-	1	NA	Intergenic	Intergenic	15406	NM_008986	19285	Mm.21864	NM_008986	ENSMUSG00000004044	Ptrf	2310075E07Rik|AW546441|Cav-p60|Cavin	polymerase I and transcript release factor	protein-coding
mm_85646.1	chr9	107656174	107656184	-	1	NA	exon (NM_001199218, exon 10 of 16)	exon (NM_001199218, exon 10 of 16)	11220	NM_023805	76257	Mm.296560	NM_023805	ENSMUSG00000010064	Slc38a3	0610012J02Rik|D9Ucla2|Nat1|Slc38-3|Sn1|Snat3|mNAT	solute carrier family 38, member 3	protein-coding
mm_111717.1	chr12	103730277	103730304	-	1	NA	exon (NM_009244, exon 3 of 5)	exon (NM_009244, exon 3 of 5)	7899	NM_009244	20701	Mm.439692	NM_009244	ENSMUSG00000071178	Serpina1b	D12Ucla2|Dom2|PI2|Spi1-2	serine (or cysteine) preptidase inhibitor, clade A, member 1B	protein-coding
mm_136572.1	chr17	3453256	3453276	+	1	NA	intron (NM_001122998, intron 12 of 26)	intron (NM_001122998, intron 12 of 26)	-29049	NM_001286758	24001	Mm.137134	NM_011878	ENSMUSG00000023800	Tiam2	3000002F19Rik|STEF|mKIAA2016	T cell lymphoma invasion and metastasis 2	protein-coding
mm_30200.1	chr3	144720217	144720233	-	1	NA	5' UTR (NM_019464, exon 1 of 9)	5' UTR (NM_019464, exon 1 of 9)	110	NM_001282042	54673	Mm.271775	NM_019464	ENSMUSG00000037062	Sh3glb1	AA409932|AI314629|AU015566|Bif-1|mKIAA0491	SH3-domain GRB2-like B1 (endophilin)	protein-coding
mm_103218.1	chr11	70655162	70655182	-	1	NA	promoter-TSS (NM_011072)	promoter-TSS (NM_011072)	-522	NM_011072	18643	Mm.2647	NM_011072	ENSMUSG00000018293	Pfn1	Pfn	profilin 1	protein-coding
mm_163381.1	chr12	52504310	52504318	+	1	NA	Intergenic	CpG	-11763	NM_009706	11855	Mm.35059	NM_009706	ENSMUSG00000035133	Arhgap5	p190-B|p190B	Rho GTPase activating protein 5	protein-coding
mm_114677.1	chr13	80885746	80885765	+	1	NA	intron (NM_001042591, intron 1 of 7)	CpG	2333	NM_001042591	105171	Mm.423137	NM_001042591	ENSMUSG00000074794	Arrdc3	AI450344|mKIAA1376	arrestin domain containing 3	protein-coding
mm_113126.1	chr13	24603245	24603252	+	1	NA	intron (NR_024599, intron 1 of 1)	intron (NR_024599, intron 1 of 1)	1519	NR_024599	76024	Mm.440710	NR_024599		Gm11346	5830431A10Rik|AI447617|Gm11347|OTTMUSG00000000601|OTTMUSG00000000602	X-linked lymphocyte-regulated 5 pseudogene	pseudo
mm_93680.1	chr10	117792639	117792658	-	1	NA	promoter-TSS (NM_134010)	promoter-TSS (NM_134010)	57	NM_134010	103468	Mm.12568	NM_134010	ENSMUSG00000052798	Nup107	AW541137|C76801	nucleoporin 107	protein-coding
mm_24534.1	chr3	93279455	93279514	+	1	NA	Intergenic	Intergenic	-40265	NM_133698	68723	Mm.208047	NM_133698	ENSMUSG00000041991	Hrnr	1110033K19Rik|A530063N20Rik|S100a18	hornerin	protein-coding
mm_146502.1	chr18	3299518	3299523	-	1	NA	promoter-TSS (NM_001110853)	promoter-TSS (NM_001110853)	36	NM_001110853	12916	Mm.5244	NM_013498	ENSMUSG00000063889	Crem	ICER|ICERI	cAMP responsive element modulator	protein-coding
mm_139507.1	chr17	56304264	56304274	+	1	NA	promoter-TSS (NM_001111080)	promoter-TSS (NM_001111080)	-44	NM_001111078	18140	Mm.42196	NM_010931	ENSMUSG00000001228	Uhrf1	AL022808|ICBP90|Np95|RNF106	ubiquitin-like, containing PHD and RING finger domains, 1	protein-coding
mm_110667.1	chr12	64963365	64963374	-	1	NA	intron (NM_025707, intron 1 of 4)	MamRep605|LTR?|LTR?	2167	NM_025707	66689	Mm.248678	NM_025707	ENSMUSG00000020948	Klhl28	2810440N09Rik|4122402F11Rik|4931401E10Rik|Btbd5	kelch-like 28	protein-coding
mm_86783.1	chr10	20171090	20171100	+	1	NA	intron (NM_001198635, intron 1 of 17)	intron (NM_001198635, intron 1 of 17)	22175	NM_001198635	17761	Mm.20928	NM_008635	ENSMUSG00000019996	Map7	E-MAP-115|MAP-7|Mtap7|R75000|mshi|mste|ste	microtubule-associated protein 7	protein-coding
mm_95505.1	chr11	51916907	51916919	+	1	NA	Intergenic	Intergenic	-50718	NM_029976	52626	Mm.289456	NM_029976	ENSMUSG00000020392	Cdkn2aipnl	A430101B06Rik|AA409260|D11Ertd497e|MNCb-1520	CDKN2A interacting protein N-terminal like	protein-coding
mm_172449.1	chr7	32298525	32298526	+	1	NA	Intergenic	L1Md_T|LINE|L1	28720	NM_001281508	668379	Mm.380094	NM_001281508	ENSMUSG00000097982	Scgb2b12	Abpbg12|EG668379|Gm9138	secretoglobin, family 2B, member 12	protein-coding
mm_64954.1	chr7	16476766	16476792	-	1	NA	promoter-TSS (NM_008718)	promoter-TSS (NM_008718)	1	NM_008718	18142	Mm.145821	NM_008718	ENSMUSG00000001988	Npas1	MOP5|bHLHe11	neuronal PAS domain protein 1	protein-coding
mm_132916.1	chr16	49699199	49699299	+	1	NA	promoter-TSS (NM_028680)	promoter-TSS (NM_028680)	-45	NM_028680	73916	Mm.241276	NM_028680	ENSMUSG00000032965	Ift57	4833420A15Rik|Esrrbl1|Hippi|MHS4R2	intraflagellar transport 57	protein-coding
mm_9048.1	chr1	167285051	167285068	-	1	NA	promoter-TSS (NM_030724)	promoter-TSS (NM_030724)	68	NM_030724	80914	Mm.280895	NM_030724	ENSMUSG00000026558	Uck2	AA407809|AI481316|AU018180|AU020720|TSA903|UK|UMK|Umpk	uridine-cytidine kinase 2	protein-coding
mm_166626.1	chr6	78371895	78371912	-	1	NA	exon (NM_011036, exon 3 of 6)	exon (NM_011036, exon 3 of 6)	1018	NM_011036	18489	Mm.2553	NM_011036	ENSMUSG00000071356	Reg3b	HIP|PAP1|Pap|REG-III	regenerating islet-derived 3 beta	protein-coding
mm_120103.1	chr14	59178885	59178892	+	1	NA	promoter-TSS (NM_001004158)	promoter-TSS (NM_001004158)	-139	NM_001004158	380907	Mm.81009	NM_001004158	ENSMUSG00000053868	Gm5142	EG380907	predicted gene 5142	protein-coding
mm_90293.1	chr10	125308997	125309005	+	1	NA	intron (NM_011391, intron 1 of 6)	intron (NM_011391, intron 1 of 6)	19534	NM_011391	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|Mct2	solute carrier family 16 (monocarboxylic acid transporters), member 7	protein-coding
mm_8154.1	chr1	136929300	136929310	-	1	NA	intron (NM_030676, intron 6 of 8)	B1_Mm|SINE|Alu	24325	NM_001159769	26424	Mm.16794	NM_030676	ENSMUSG00000026398	Nr5a2	AU020803|D1Ertd308e|Ftf|LRH-1|UF2-H3B	nuclear receptor subfamily 5, group A, member 2	protein-coding
mm_65700.1	chr7	28377222	28377254	-	1	NA	3' UTR (NM_011756, exon 2 of 2)	3' UTR (NM_011756, exon 2 of 2)	1990	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_55550.1	chr6	71225459	71225474	-	1	NA	exon (NM_001160127, exon 6 of 10)	exon (NM_001160127, exon 6 of 10)	25578	NM_017399	14080	Mm.22126	NM_017399	ENSMUSG00000054422	Fabp1	Fabpl|L-FABP	fatty acid binding protein 1, liver	protein-coding
mm_40254.1	chr5	38220629	38220649	+	1	NA	promoter-TSS (NM_029162)	promoter-TSS (NM_029162)	157	NM_025281	17089	Mm.28560	NM_025281	ENSMUSG00000067367	Lyar	MLZ-264	Ly1 antibody reactive clone	protein-coding
mm_98972.1	chr11	98685906	98685914	+	1	NA	intron (NM_009439, intron 2 of 11)	intron (NM_009439, intron 2 of 11)	3356	NM_009439	22123	Mm.12194	NM_009439	ENSMUSG00000017221	Psmd3	AI255837|AntP91a|D11Bwg1349e|Psd3|Tstap91a	proteasome (prosome, macropain) 26S subunit, non-ATPase, 3	protein-coding
mm_106457.1	chr11	120020161	120020190	-	1	NA	intron (NM_001198787, intron 2 of 13)	intron (NM_001198787, intron 2 of 13)	-5313	NR_029767	723844		NR_029767	ENSMUSG00000065600	Mir338	Mirn338|mir-338|mmu-mir-338	microRNA 338	ncRNA
mm_170524.1	chr19	33456271	33456275	-	1	NA	Intergenic	ETnERV2-int|LTR|ERVK	61497	NM_001323386	628236		NM_001323386	ENSMUSG00000079344	Lipo4	Gm6857	lipase, member O4	protein-coding
mm_56641.1	chr6	113326636	113326685	-	1	NA	promoter-TSS (NM_010957)	promoter-TSS (NM_010957)	-316	NM_010957	18294	Mm.43612	NM_010957	ENSMUSG00000030271	Ogg1	Mmh	8-oxoguanine DNA-glycosylase 1	protein-coding
mm_141960.1	chr17	35118571	35118582	-	1	NA	intron (NM_001303445, intron 3 of 6)	intron (NM_001303445, intron 3 of 6)	2716	NM_001303476	13001	Mm.378901	NM_009975	ENSMUSG00000024387	Csnk2b	CK II beta	casein kinase 2, beta polypeptide	protein-coding
mm_99874.1	chr11	109413910	109413927	+	1	NA	Intergenic	Intergenic	-12028	NM_025275	13929	Mm.211850	NM_025275	ENSMUSG00000020610	Amz2	AA408420|ESTM12|X83328	archaelysin family metallopeptidase 2	protein-coding
mm_109389.1	chr12	109741648	109741652	+	1	NA	promoter-TSS (NR_030263)	promoter-TSS (NR_030263)	-759	NR_030263	723941		NR_030263	ENSMUSG00000076052	Mir541	Mirn541|mir-541|mmu-mir-541	microRNA 541	ncRNA
mm_151451.1	chr19	57747601	57747613	+	1	NA	intron (NM_181415, intron 21 of 28)	intron (NM_181415, intron 21 of 28)	136573	NM_181415	226255	Mm.245340	NM_181415	ENSMUSG00000054843	Atrnl1	AI504415|AW555641|Alp|Atrnl|Atrnlp	attractin like 1	protein-coding
mm_123484.1	chr14	66009151	66009159	-	1	NA	promoter-TSS (NM_178747)	promoter-TSS (NM_178747)	55	NM_178747	268756	Mm.26207	NM_178747	ENSMUSG00000034450	Gulo	5730581M22|AU018375|BC028822|GLO|LGO|sfx|unh|unhip	gulonolactone (L-) oxidase	protein-coding
mm_60833.1	chr7	45718019	45718024	+	1	NA	promoter-TSS (NM_001172561)	promoter-TSS (NM_001172561)	-19	NM_001172561	56632	Mm.24222	NM_020011	ENSMUSG00000057342	Sphk2	C76851	sphingosine kinase 2	protein-coding
mm_34131.1	chr4	139280536	139280556	+	1	NA	exon (NM_001271405, exon 6 of 9)	exon (NM_001271405, exon 6 of 9)	30154	NM_145384	212555	Mm.45131	NM_145384	ENSMUSG00000028744	Pqlc2	BC019216	PQ loop repeat containing 2	protein-coding
mm_63834.1	chr7	135534980	135534986	+	1	NA	Intergenic	Intergenic	-2841	NM_011212	19267	Mm.945	NM_011212	ENSMUSG00000041836	Ptpre	PTPe|PTPepsilon|RPTPepsilon	protein tyrosine phosphatase, receptor type, E	protein-coding
mm_17691.1	chr2	32332110	32332125	-	1	NA	intron (NM_010065, intron 10 of 20)	intron (NM_010065, intron 10 of 20)	13657	NR_029811	387239		NR_029811	ENSMUSG00000092807	Mir199b	Mirn199b|mir-199b	microRNA 199b	ncRNA
mm_63146.1	chr7	123214861	123214886	+	1	NA	promoter-TSS (NM_146198)	promoter-TSS (NM_146198)	7	NM_146198	233836	Mm.211838	NM_146198	ENSMUSG00000030769	Slc5a11	2010013B02Rik|Kst1|RKST2|SMIT2|Slc5a10	solute carrier family 5 (sodium/glucose cotransporter), member 11	protein-coding
mm_151961.1	chr19	5801566	5801597	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	1091	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_43362.1	chr5	135230283	135230312	+	1	NA	exon (NM_011714, exon 12 of 19)	exon (NM_011714, exon 12 of 19)	20750	NM_010246	14371	Mm.6256	NM_010246	ENSMUSG00000049551	Fzd9	mfz9	frizzled class receptor 9	protein-coding
mm_133557.1	chr16	91388065	91388081	+	1	NA	exon (NM_010509, exon 5 of 9)	exon (NM_010509, exon 5 of 9)	15290	NM_001110498	15976	Mm.6834	NM_010509	ENSMUSG00000022971	Ifnar2	AI747302|Ifnar-2	interferon (alpha and beta) receptor 2	protein-coding
mm_94087.1	chr10	128498648	128498675	-	1	NA	promoter-TSS (NM_172259)	promoter-TSS (NM_172259)	24	NM_172259	216459	Mm.291688	NM_172259	ENSMUSG00000039824	Myl6b	5730437E04Rik|BC037527|MLC1SA	myosin, light polypeptide 6B	protein-coding
mm_87051.1	chr10	28823065	28823067	+	1	NA	intron (NM_001305663, intron 5 of 5)	intron (NM_001305663, intron 5 of 5)	100441	NR_033601	114676	Mm.390292	NR_033601		4930519F09Rik	-	pyruvate dehydrogenase E1 alpha 1 pseudogene	pseudo
mm_74212.1	chr8	123896235	123896276	+	1	NA	TTS (NM_172288)	TTS (NM_172288)	-1480	NM_009606	11459	Mm.214950	NM_009606	ENSMUSG00000031972	Acta1	AA959943|Acta-2|Acts|Actsk-1	actin, alpha 1, skeletal muscle	protein-coding
mm_106055.1	chr11	116110267	116110283	-	1	NA	promoter-TSS (NM_001205081)	promoter-TSS (NM_001205081)	-40	NM_172570	217333	Mm.347770	NM_172570	ENSMUSG00000020773	Trim47	2210023F24Rik	tripartite motif-containing 47	protein-coding
mm_164321.1	chr16	4037372	4037387	+	1	NA	5' UTR (NM_010061, exon 1 of 9)	5' UTR (NM_010061, exon 1 of 9)	234	NM_010061	13419	Mm.291048	NM_010061	ENSMUSG00000005980	Dnase1	AI788650|DNaseI|Dnl1	deoxyribonuclease I	protein-coding
mm_115440.1	chr13	117602503	117602513	+	1	NA	5' UTR (NM_010408, exon 1 of 8)	5' UTR (NM_010408, exon 1 of 8)	188	NM_010408	15165	Mm.343429	NM_010408	ENSMUSG00000021730	Hcn1	Bcng1|C630013B14Rik|HAC2	hyperpolarization-activated, cyclic nucleotide-gated K+ 1	protein-coding
mm_151392.1	chr19	56425717	56425742	+	1	NA	intron (NM_007611, intron 2 of 6)	intron (NM_007611, intron 2 of 6)	28600	NM_007611	12369	Mm.35687	NM_007611	ENSMUSG00000025076	Casp7	AI314680|CMH-1|ICE-IAP3|Mch3|caspase-7|mCASP-7	caspase 7	protein-coding
mm_47642.1	chr5	125388870	125388872	-	1	NA	intron (NM_019639, intron 1 of 1)	intron (NM_019639, intron 1 of 1)	1146	NM_019639	22190	Mm.331	NM_019639	ENSMUSG00000008348	Ubc	2700054O04Rik|AI194771|Rps27a|TI-225|Uba52|Ubb	ubiquitin C	protein-coding
mm_70229.1	chr7	145284381	145284391	-	1	NA	promoter-TSS (NM_146206)	promoter-TSS (NM_146206)	-375	NR_132642	233979	Mm.102235	NM_146206	ENSMUSG00000048677	Tpcn2	D830047E22Rik|Gm35086	two pore segment channel 2	protein-coding
mm_73248.1	chr8	104264483	104264508	+	1	NA	3' UTR (NM_001037841, exon 3 of 3)	3' UTR (NM_001037841, exon 3 of 3)	13634	NM_001286383	75458	Mm.269219	NM_029295	ENSMUSG00000054400	Cklf	1700001C14Rik|1810018M11Rik|A730028G07Rik|C32|CKLF1|CKLF3|CKLF4|CKLF5|Cklf2|Cklf6|HSPC224|UCK-1	chemokine-like factor	protein-coding
mm_106811.1	chr12	7379887	7379909	+	1	NA	intron (NR_045045, intron 1 of 2)	intron (NR_045045, intron 1 of 2)	432	NR_045045	73575	Mm.179463	NR_045045	ENSMUSG00000102096	1700101O22Rik	-	RIKEN cDNA 1700101O22 gene	ncRNA
mm_168782.1	chr12	18514443	18514446	+	1	NA	promoter-TSS (NM_001201330)	promoter-TSS (NM_001201330)	-66	NM_001033157	236366	Mm.352227	NM_001033157	ENSMUSG00000073197	5730507C01Rik	-	RIKEN cDNA 5730507C01 gene	protein-coding
mm_126079.1	chr15	77800758	77800791	+	1	NA	intron (NM_022410, intron 3 of 40)	intron (NM_022410, intron 3 of 40)	41401	NM_022410	17886	Mm.29677	NM_022410	ENSMUSG00000022443	Myh9	Fltn|Myhn-1|Myhn1|NMHCIIA|NMMHC-A|NMMHC-IIA|TU72.6	myosin, heavy polypeptide 9, non-muscle	protein-coding
mm_75447.1	chr8	47674836	47674868	-	1	NA	5' UTR (NM_023503, exon 1 of 2)	5' UTR (NM_023503, exon 1 of 2)	307	NM_023503	69260	Mm.430733	NM_023503	ENSMUSG00000063049	Ing2	2810011M06Rik|Ing1l|Ing2b|P33ING2	inhibitor of growth family, member 2	protein-coding
mm_13768.1	chr2	118598210	118598226	+	1	NA	promoter-TSS (NM_009773)	promoter-TSS (NM_009773)	7	NM_009773	12236	Mm.29133	NM_009773	ENSMUSG00000040084	Bub1b	AU045529|BUBR1	BUB1B, mitotic checkpoint serine/threonine kinase	protein-coding
mm_65193.1	chr7	19696712	19696748	-	1	NA	exon (NM_009696, exon 4 of 4)	exon (NM_009696, exon 4 of 4)	1668	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_172927.1	chr9	71120563	71120566	-	1	NA	intron (NR_073483, intron 6 of 6)	MT2_Mm|LTR|ERVL	42069	NM_001271843	64008	Mm.449427	NM_022026	ENSMUSG00000032204	Aqp9	1700020I22Rik|AI266899|AQP-9	aquaporin 9	protein-coding
mm_156538.1	chrX	151168764	151168807	+	1	NA	Intergenic	Intergenic	-29293	NM_001271679	279561	Mm.441474	NM_001271678	ENSMUSG00000041245	Wnk3	Prkwnk3|Wnk3-ps	WNK lysine deficient protein kinase 3	protein-coding
mm_38763.1	chr4	147903762	147903776	-	1	NA	intron (NM_001285920, intron 1 of 19)	intron (NM_001285920, intron 1 of 19)	929	NM_001285923	170731	Mm.154312	NM_133201	ENSMUSG00000029020	Mfn2	D630023P19Rik|Fzo	mitofusin 2	protein-coding
mm_12658.1	chr2	75582447	75582449	+	1	NA	Intergenic	Intergenic	-76811	NM_146130	229279	Mm.316306	NM_053263	ENSMUSG00000059005	Hnrnpa3	2410013L13Rik|2610209F03Rik|2610510D13Rik|Hnrpa3	heterogeneous nuclear ribonucleoprotein A3	protein-coding
mm_95384.1	chr11	49203466	49203524	+	1	NA	promoter-TSS (NM_001024846)	promoter-TSS (NM_001024846)	-5	NM_001024846	22720	Mm.16650	NM_009562	ENSMUSG00000046311	Zfp62	-	zinc finger protein 62	protein-coding
mm_125135.1	chr15	30457628	30457710	+	1	NA	intron (NM_008729, intron 2 of 22)	intron (NM_008729, intron 2 of 22)	285076	NM_008729	18163	Mm.321648	NM_008729	ENSMUSG00000022240	Ctnnd2	Catnd2|Nprap|neurojugin	catenin (cadherin associated protein), delta 2	protein-coding
mm_55818.1	chr6	83053723	83053773	-	1	NA	promoter-TSS (NR_125891)	promoter-TSS (NR_125891)	-773	NR_125891	11993	Mm.386752	NM_007517	ENSMUSG00000068328	Aup1	AA589454	ancient ubiquitous protein 1	protein-coding
mm_27837.1	chr3	79144407	79144410	-	1	NA	intron (NM_001099624, intron 1 of 23)	intron (NM_001099624, intron 1 of 23)	479	NM_001310536	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_107559.1	chr12	41498938	41498939	+	1	NA	intron (NM_053122, intron 4 of 6)	intron (NM_053122, intron 4 of 6)	-12881	NM_010733	16981	Mm.404786	NM_010733	ENSMUSG00000036295	Lrrn3	NLRR-3	leucine rich repeat protein 3, neuronal	protein-coding
mm_151056.1	chr19	47179039	47179079	+	1	NA	5' UTR (NM_021360, exon 1 of 6)	5' UTR (NM_021360, exon 1 of 6)	239	NM_021360	18011	Mm.313651	NM_021360	ENSMUSG00000006435	Neurl1a	2410129E16Rik|AI450910|AI481072|Neu1|Neur1|Neurl|Neurl1|Nlz|Rnf67	neuralized E3 ubiquitin protein ligase 1A	protein-coding
mm_3481.1	chr1	150105576	150105586	+	1	NA	exon (NM_011198, exon 10 of 10)	exon (NM_011198, exon 10 of 10)	5550	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_2131.1	chr1	88055491	88055495	+	1	NA	promoter-TSS (NM_201641)	promoter-TSS (NM_201641)	82	NM_201641	394430	Mm.300095	NM_201641	ENSMUSG00000090165	Ugt1a10	A13|Ugt1a13	UDP glycosyltransferase 1 family, polypeptide A10	protein-coding
mm_158102.1	chrX	101794400	101794417	-	1	NA	Intergenic	CpG	-54977	NM_001163610	100042480	Mm.232	NM_001163610	ENSMUSG00000079481	Nhsl2	1110062M06Rik|6430511F03|AI225852|AW488865|EG621083|ENSMUSG00000073037|Gm10456	NHS-like 2	protein-coding
mm_51213.1	chr6	71352969	71352979	+	1	NA	Intergenic	Intergenic	-20453	NM_009857	12525	Mm.1858	NM_009857	ENSMUSG00000053977	Cd8a	BB154331|Ly-2|Ly-35|Ly-B|Lyt-2	CD8 antigen, alpha chain	protein-coding
mm_135120.1	chr16	35841486	35841496	-	1	NA	exon (NM_001039530, exon 13 of 17)	exon (NM_001039530, exon 13 of 17)	29891	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_173159.1	chrX	36864160	36864160	-	1	NA	promoter-TSS (NM_029951)	promoter-TSS (NM_029951)	86	NM_029951	77644	Mm.290704	NM_029951	ENSMUSG00000006423	C330007P06Rik	-	RIKEN cDNA C330007P06 gene	protein-coding
mm_128375.1	chr15	42676744	42676760	-	1	NA	5' UTR (NM_001286062, exon 1 of 9)	5' UTR (NM_001286062, exon 1 of 9)	225	NM_001286062	11600	Mm.309336	NM_009640	ENSMUSG00000022309	Angpt1	1110046O21Rik|Ang-1|Ang1	angiopoietin 1	protein-coding
mm_168047.1	chrY	90811706	90811717	+	1	NA	intron (NM_133362, intron 2 of 3)	IMPB_01|Satellite|Satellite	26269	NM_133362	170942	Mm.76062	NM_133362	ENSMUSG00000096768	Erdr1	edr	erythroid differentiation regulator 1	protein-coding
mm_98239.1	chr11	88155836	88155837	+	1	NA	intron (NM_198013, intron 1 of 10)	intron (NM_198013, intron 1 of 10)	-13729	NM_001172099	103841	Mm.374846	NM_198013	ENSMUSG00000018378	Cuedc1	AI841487|C330016O16Rik	CUE domain containing 1	protein-coding
mm_87304.1	chr10	42583788	42583811	+	1	NA	promoter-TSS (NM_152229)	promoter-TSS (NM_152229)	-211	NM_152229	21907	Mm.287100	NM_152229	ENSMUSG00000019803	Nr2e1	Mtl1|Mtll|TLL|Tlx|XTLL|fierce|frc|tailless	nuclear receptor subfamily 2, group E, member 1	protein-coding
mm_106453.1	chr11	120017177	120017186	-	1	NA	intron (NM_001198787, intron 3 of 13)	intron (NM_001198787, intron 3 of 13)	-2319	NR_029767	723844		NR_029767	ENSMUSG00000065600	Mir338	Mirn338|mir-338|mmu-mir-338	microRNA 338	ncRNA
mm_103744.1	chr11	80142124	80142162	-	1	NA	promoter-TSS (NM_183275)	promoter-TSS (NM_183275)	10	NM_183275	68550	Mm.18466	NM_183275	ENSMUSG00000046909	Tefm	1110002N22Rik	transcription elongation factor, mitochondrial	protein-coding
mm_82591.1	chr9	21239054	21239088	-	1	NA	5' UTR (NM_016679, exon 1 of 5)	5' UTR (NM_016679, exon 1 of 5)	261	NM_016679	50868	Mm.248266	NM_016679	ENSMUSG00000003308	Keap1	INRF2|mKIAA0132	kelch-like ECH-associated protein 1	protein-coding
mm_47685.1	chr5	129007524	129007526	-	1	NA	intron (NM_001286033, intron 1 of 9)	intron (NM_001286033, intron 1 of 9)	1047	NM_001286034	13852	Mm.260716	NM_007941	ENSMUSG00000029428	Stx2	AW538950|Epim|G1-536-1|Syn-2|repro34	syntaxin 2	protein-coding
mm_81653.1	chr9	110960453	110960477	+	1	NA	intron (NM_028838, intron 2 of 8)	ID_B1|SINE|B4	8920	NM_028838	74249	Mm.307615	NM_028838	ENSMUSG00000032495	Lrrc2	2400002D05Rik|4933431K03Rik	leucine rich repeat containing 2	protein-coding
mm_133936.1	chr16	3884439	3884470	-	1	NA	promoter-TSS (NM_001290689)	promoter-TSS (NM_001290689)	-165	NM_029090	74763	Mm.28403	NM_029090	ENSMUSG00000005982	Naa60	1200013P24Rik|AI315146|Nat15	N(alpha)-acetyltransferase 60, NatF catalytic subunit	protein-coding
mm_120448.1	chr14	65968595	65968597	+	1	NA	5' UTR (NM_013492, exon 1 of 9)	5' UTR (NM_013492, exon 1 of 9)	113	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_35025.1	chr4	4016485	4016497	-	1	NA	intron (NM_181989, intron 1 of 6)	intron (NM_181989, intron 1 of 6)	3172	NM_181989	242285	Mm.98096	NM_181989	ENSMUSG00000028236	Sdr16c5	Rdhe2|Scdr9	short chain dehydrogenase/reductase family 16C, member 5	protein-coding
mm_17644.1	chr2	31460388	31460397	-	1	NA	Intergenic	Intergenic	-9878	NM_007494	11898	Mm.3217	NM_007494	ENSMUSG00000076441	Ass1	AA408052|ASS|Ass-1|fold	argininosuccinate synthetase 1	protein-coding
mm_125293.1	chr15	36792666	36792691	+	1	NA	intron (NM_001253806, intron 1 of 5)	CpG	-1746	NM_001253807	22631	Mm.3360	NM_011740	ENSMUSG00000022285	Ywhaz	1110013I11Rik|14-3-3zeta|AI596267|AL022924|AU020854	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide	protein-coding
mm_6690.1	chr1	80709500	80709516	-	1	NA	intron (NM_175291, intron 1 of 55)	intron (NM_175291, intron 1 of 55)	-44156	NM_001285927	210293	Mm.133473	NM_175291	ENSMUSG00000038608	Dock10	9330153B10Rik|A630054M16Rik|Jr4|Jr5|R75174|ZIZ3|Zizimin3|mKIAA0694	dedicator of cytokinesis 10	protein-coding
mm_107252.1	chr12	28649602	28649649	+	1	NA	promoter-TSS (NM_001286865)	promoter-TSS (NM_001286865)	23	NM_001286865	19819	Mm.10152	NM_011275	ENSMUSG00000020630	Rnaseh1	-	ribonuclease H1	protein-coding
mm_138885.1	chr17	43389543	43389562	+	1	NA	promoter-TSS (NM_001081178)	promoter-TSS (NM_001081178)	86	NM_001081178	224792	Mm.23478	NM_001081178	ENSMUSG00000056492	Adgrf5	8430401C09Rik|9330185D23|AI528491|Gpr116|mKIAA0758	adhesion G protein-coupled receptor F5	protein-coding
mm_101320.1	chr11	22859634	22859647	-	1	NA	promoter-TSS (NM_016888)	promoter-TSS (NM_016888)	95	NM_016888	53625	Mm.395495	NM_016888	ENSMUSG00000051650	B3gnt2	AA408337|AA409404|AW260308|B3Galt6|B3gnt1|BGnT-1|BGnT-2|BGnT1|BGnT2|Beta3gnt	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 2	protein-coding
mm_1091.1	chr1	59684950	59685023	+	1	NA	promoter-TSS (NM_018868)	promoter-TSS (NM_018868)	-20	NM_018868	55989	Mm.220367	NM_018868	ENSMUSG00000026020	Nop58	MSSP|Nol5|SIK|nop5	NOP58 ribonucleoprotein	protein-coding
mm_97810.1	chr11	82962113	82962129	+	1	NA	3' UTR (NM_183201, exon 6 of 6)	3' UTR (NM_183201, exon 6 of 6)	-1440	NR_045932	76392	Mm.295205	NR_045932	ENSMUSG00000086327	Slfn5os	1700003F17Rik	schlafen 5, opposite strand	ncRNA
mm_92115.1	chr10	63203931	63203956	-	1	NA	promoter-TSS (NM_182992)	promoter-TSS (NM_182992)	9	NM_182992	68802	Mm.259767	NM_182992	ENSMUSG00000020067	Mypn	1110056A04Rik|9830112J03|AI853556|mKIAA4170	myopalladin	protein-coding
mm_130037.1	chr15	88978959	88978992	-	1	NA	promoter-TSS (NM_133241)	promoter-TSS (NM_133241)	-422	NM_133241	170790	Mm.32780	NM_133241	ENSMUSG00000035805	Mlc1	AW048630|BB074274|Kiaa0027-hp|LVM|MLC|VL|WKL1|mKIAA0027	megalencephalic leukoencephalopathy with subcortical cysts 1 homolog (human)	protein-coding
mm_160766.1	chr10	95415518	95415518	-	1	NA	promoter-TSS (NM_001168657)	promoter-TSS (NM_001168657)	-34	NM_001168656	216233	Mm.474283	NM_007706	ENSMUSG00000020027	Socs2	8030460M17|AI527257|AW108012|CIS2|Cish2|D130043N08Rik|JAB|SOCS-2|SSI-2|hg	suppressor of cytokine signaling 2	protein-coding
mm_17492.1	chr2	28615336	28615346	-	1	NA	exon (NM_001160406, exon 2 of 7)	exon (NM_001160406, exon 2 of 7)	6641	NM_008114	14582	Mm.373385	NM_008114	ENSMUSG00000026815	Gfi1b	Gfi-1B	growth factor independent 1B	protein-coding
mm_30267.1	chr3	146770577	146770602	-	1	NA	promoter-TSS (NM_001164198)	promoter-TSS (NM_001164198)	104	NM_001164199	18749	Mm.16766	NM_011100	ENSMUSG00000005034	Prkacb	CbPKA|Pkacb	protein kinase, cAMP dependent, catalytic, beta	protein-coding
mm_107308.1	chr12	31073971	31074003	+	1	NA	promoter-TSS (NM_027828)	promoter-TSS (NM_027828)	19	NM_027828	104943	Mm.248938	NM_027828	ENSMUSG00000036136	Fam110c	9030611O19Rik|AU019489	family with sequence similarity 110, member C	protein-coding
mm_152394.1	chr19	10525183	10525197	-	1	NA	promoter-TSS (NM_025333)	promoter-TSS (NM_025333)	19	NM_025333	66072	Mm.180063	NM_025333	ENSMUSG00000024668	Sdhaf2	0610038F07Rik|AA407634|AW049997	succinate dehydrogenase complex assembly factor 2	protein-coding
mm_159348.1	chr3	65188106	65188106	+	1	NA	promoter-TSS (NM_001289450)	promoter-TSS (NM_001289450)	3	NM_001289450	16497	Mm.316402	NM_010597	ENSMUSG00000027827	Kcnab1	Akr8a8|Kvbeta1.1|mKv(beta)1	potassium voltage-gated channel, shaker-related subfamily, beta member 1	protein-coding
mm_311.1	chr1	24195231	24195271	+	1	NA	promoter-TSS (NM_001290691)	promoter-TSS (NM_001290691)	48	NM_001290691	12839	Mm.154662	NM_007740	ENSMUSG00000026147	Col9a1	Col9a-1	collagen, type IX, alpha 1	protein-coding
mm_91704.1	chr10	44022269	44022280	-	1	NA	Intergenic	Intergenic	-17428	NM_172393	11630	Mm.292082	NM_172393	ENSMUSG00000019866	Aim1	AI462491|AI463325	absent in melanoma 1	protein-coding
mm_23459.1	chr3	60472732	60472741	+	1	NA	promoter-TSS (NM_001253713)	promoter-TSS (NM_001253713)	-94	NM_001253713	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_25676.1	chr3	122044472	122044491	+	1	NA	promoter-TSS (NM_007378)	promoter-TSS (NM_007378)	21	NM_007378	11304	Mm.3918	NM_007378	ENSMUSG00000028125	Abca4	AW050280|Abc10|Abcr|D430003I15Rik|RmP	ATP-binding cassette, sub-family A (ABC1), member 4	protein-coding
mm_46970.1	chr5	115158337	115158347	-	1	NA	promoter-TSS (NM_175403)	promoter-TSS (NM_175403)	-166	NM_175403	109154	Mm.153963	NM_175403	ENSMUSG00000048578	Mlec	2410014A08Rik|AI850530|ESTM19|X83352|mKIAA0152	malectin	protein-coding
mm_39210.1	chr4	156050786	156050796	-	1	NA	promoter-TSS (NM_029264)	promoter-TSS (NM_029264)	26	NM_029264	330010	Mm.440232	NM_029264	ENSMUSG00000029074	Ttll10	4833412E22Rik|4930595O22Rik|AU022799|BC042775|Ttll5	tubulin tyrosine ligase-like family, member 10	protein-coding
mm_154180.1	chr19	58792795	58792812	-	1	NA	intron (NM_026208, intron 1 of 5)	intron (NM_026208, intron 1 of 5)	1611	NM_026208	67507	Mm.27027	NM_026208	ENSMUSG00000026931	1700019N19Rik	-	RIKEN cDNA 1700019N19 gene	protein-coding
mm_1854.1	chr1	84362665	84362670	+	1	NA	Intergenic	Intergenic	-78022	NM_001003948	98496	Mm.187470	NM_001003948	ENSMUSG00000045658	Pid1	5033414K04Rik|NYGGF4	phosphotyrosine interaction domain containing 1	protein-coding
mm_64940.1	chr7	16312409	16312425	-	1	NA	intron (NM_133234, intron 2 of 3)	CpG-12701	2834	NM_133234	170770	Mm.7660	NM_133234	ENSMUSG00000002083	Bbc3	PUMA|PUMA/JFY1	BCL2 binding component 3	protein-coding
mm_52522.1	chr6	115581099	115581109	+	1	NA	Intergenic	Intergenic	11472	NM_001101431	70291	Mm.133694	NM_001101431	ENSMUSG00000068011	Mkrn2os	2510049J12Rik	makorin, ring finger protein 2, opposite strand	protein-coding
mm_147072.1	chr18	35258983	35258985	-	1	NA	Intergenic	Intergenic	-43960	NM_178005	107065	Mm.39900	NM_178005	ENSMUSG00000071862	Lrrtm2	AI851755|BB129880|C630011A14Rik|mKIAA0416	leucine rich repeat transmembrane neuronal 2	protein-coding
mm_352.1	chr1	32172712	32172792	+	1	NA	promoter-TSS (NM_133235)	promoter-TSS (NM_133235)	-54	NM_133235	170771	Mm.336594	NM_133235	ENSMUSG00000026058	Khdrbs2	6330586C16Rik|Slim1|Slm-1|Slm1|mSLM-1	KH domain containing, RNA binding, signal transduction associated 2	protein-coding
mm_94905.1	chr11	29373591	29373613	+	1	NA	promoter-TSS (NM_176841)	promoter-TSS (NM_176841)	-570	NM_176841	108686	Mm.338284	NM_176841	ENSMUSG00000032740	Ccdc88a	A430106J12Rik|AI848406|Ape|C130096N06Rik|C330012F17Rik|D130005J21Rik|Girdin|Giv|Grdn|Hkrp1	coiled coil domain containing 88A	protein-coding
mm_1681.1	chr1	74855204	74855216	+	1	NA	exon (NM_009872, exon 1 of 1)	exon (NM_009872, exon 1 of 1)	181	NM_009872	12570	Mm.153833	NM_009872	ENSMUSG00000090071	Cdk5r2	B230310J22Rik|p39	cyclin-dependent kinase 5, regulatory subunit 2 (p39)	protein-coding
mm_159350.1	chr3	72966778	72966778	-	1	NA	promoter-TSS (NM_001081137)	promoter-TSS (NM_001081137)	88	NM_001081137	69983	Mm.261054	NM_001081137	ENSMUSG00000027790	Sis	2010204N08Rik|SI|Si-s	sucrase isomaltase (alpha-glucosidase)	protein-coding
mm_97270.1	chr11	75765363	75765373	+	1	NA	3' UTR (NM_009536, exon 6 of 6)	3' UTR (NM_009536, exon 6 of 6)	-30441	NR_136933	102641247	Mm.411386	NR_136932		Gm12339	OTTMUSG00000006218	predicted gene 12339	ncRNA
mm_83209.1	chr9	41988240	41988269	-	1	NA	intron (NM_011436, intron 37 of 47)	RLTR20A4|LTR|ERVK	136035	NM_011436	20660	Mm.121920	NM_011436	ENSMUSG00000049313	Sorl1	2900010L19Rik|AI596264|AW261561|LR11|SorLA|gp250|mSorLA	sortilin-related receptor, LDLR class A repeats-containing	protein-coding
mm_93479.1	chr10	111993587	111993605	-	1	NA	exon (NM_028608, exon 2 of 6)	exon (NM_028608, exon 2 of 6)	3668	NM_028608	73690	Mm.173790	NM_028608	ENSMUSG00000056888	Glipr1	2410114O14Rik|RTVP-1|RTVP1|mRTVP-1	GLI pathogenesis-related 1 (glioma)	protein-coding
mm_73904.1	chr8	119446923	119446947	+	1	NA	TTS (NM_027950)	TTS (NM_027950)	216	NM_054095	117148	Mm.356184	NM_054095	ENSMUSG00000031837	Necab2	Efcbp2	N-terminal EF-hand calcium binding protein 2	protein-coding
mm_63674.1	chr7	130525711	130525741	+	1	NA	Intergenic	Intergenic	-5357	NM_001271343	11907	Mm.216321	NM_013799	ENSMUSG00000030850	Ate1	AI225793|AW547406	arginyltransferase 1	protein-coding
mm_55037.1	chr6	48987460	48987462	-	1	NA	exon (NM_172888, exon 1 of 5)	exon (NM_172888, exon 1 of 5)	600	NM_172888	243377	Mm.446302	NM_172888	ENSMUSG00000039215	Svs1	9530003A11	seminal vesicle secretory protein 1	protein-coding
mm_149530.1	chr19	12461111	12461160	+	1	NA	5' UTR (NM_010821, exon 2 of 2)	5' UTR (NM_010821, exon 2 of 2)	356	NM_010821	17476	Mm.3999	NM_010821	ENSMUSG00000046805	Mpeg1	MPS1|Mpg-1	macrophage expressed gene 1	protein-coding
mm_41510.1	chr5	92371722	92371732	+	1	NA	intron (NM_001310664, intron 2 of 10)	intron (NM_001310664, intron 2 of 10)	-8431	NR_038116	56066	Mm.131723	NM_019494	ENSMUSG00000060183	Cxcl11	Cxc11|H174|I-tac|Ip9|Itac|Scyb11|Scyb9b|b-R1|betaR1	chemokine (C-X-C motif) ligand 11	protein-coding
mm_38673.1	chr4	144892297	144892363	-	1	NA	promoter-TSS (NM_001172424)	promoter-TSS (NM_001172424)	-497	NM_001172424	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding
mm_60147.1	chr7	38186236	38186249	+	1	NA	intron (NM_028166, intron 1 of 3)	intron (NM_028166, intron 1 of 3)	2455	NM_028166	72244	Mm.187554	NM_028166		1600014C10Rik	AI428873	RIKEN cDNA 1600014C10 gene	protein-coding
mm_100300.1	chr11	117849224	117849234	+	1	NA	promoter-TSS (NM_009689)	promoter-TSS (NM_009689)	-8	NM_001012273	11799	Mm.8552	NM_009689	ENSMUSG00000017716	Birc5	AAC-11|Api4|TIAP|survivin40	baculoviral IAP repeat-containing 5	protein-coding
mm_57420.1	chr6	124913859	124913886	-	1	NA	3' UTR (NM_026988, exon 5 of 5)	3' UTR (NM_026988, exon 5 of 5)	-2167	NM_008479	16768	Mm.4528	NM_008479	ENSMUSG00000030124	Lag3	CD223|LAG-3|Ly66	lymphocyte-activation gene 3	protein-coding
mm_33834.1	chr4	135686037	135686054	+	1	NA	promoter-TSS (NM_174851)	promoter-TSS (NM_174851)	-412	NM_174851	242700	Mm.259623	NM_174851	ENSMUSG00000062157	Ifnlr1	CRF2-12|Il28ra	interferon lambda receptor 1	protein-coding
mm_152889.1	chr19	24859401	24859406	-	1	NA	intron (NM_175013, intron 1 of 10)	ORR1C2|LTR|ERVL-MaLR	2439	NM_175013	226041	Mm.105222	NM_175013	ENSMUSG00000041731	Pgm5	4833423B07|9530034F03Rik|D830025G17|aciculin	phosphoglucomutase 5	protein-coding
mm_172905.1	chr9	58582970	58582977	+	1	NA	intron (NM_001293673, intron 1 of 7)	intron (NM_001293673, intron 1 of 7)	733	NM_009145	20320	Mm.15125	NM_009145	ENSMUSG00000032336	Nptn	AW554172|SDR-1|Sdfr1	neuroplastin	protein-coding
mm_22270.1	chr2	178506061	178506069	-	1	NA	Intergenic	Intergenic	75550	NM_198656	381409	Mm.330860	NM_198656	ENSMUSG00000039155	Cdh26	Gm1010	cadherin-like 26	protein-coding
mm_53302.1	chr6	129180614	129180630	+	1	NA	promoter-TSS (NM_053109)	promoter-TSS (NM_053109)	7	NM_053109	93694	Mm.197536	NM_053109	ENSMUSG00000030157	Clec2d	Clr-b|Clrb|Ocil	C-type lectin domain family 2, member d	protein-coding
mm_8104.1	chr1	135850738	135850787	-	1	NA	exon (NM_001130176, exon 10 of 13)	exon (NM_001130176, exon 10 of 13)	9901	NM_001130176	21956	Mm.247470	NM_011619	ENSMUSG00000026414	Tnnt2	Tnt|cTnT	troponin T2, cardiac	protein-coding
mm_40932.1	chr5	76588788	76588803	+	1	NA	Intergenic	CpG	-2919	NM_199032	381644	Mm.332452	NM_199032	ENSMUSG00000036403	Cep135	BC062951|Cep4|Gm1044	centrosomal protein 135	protein-coding
mm_66051.1	chr7	30729506	30729556	-	1	NA	promoter-TSS (NM_027215)	promoter-TSS (NM_027215)	3	NM_027215	69804	Mm.27499	NM_027215	ENSMUSG00000006315	Tmem147	2010004E11Rik|5033425B17Rik|Nifie14	transmembrane protein 147	protein-coding
mm_114413.1	chr13	64363796	64363805	+	1	NA	3' UTR (NM_009984, exon 8 of 8)	3' UTR (NM_009984, exon 8 of 8)	6720	NM_009984	13039	Mm.930	NM_009984	ENSMUSG00000021477	Ctsl	1190035F06Rik|CatL|Ctsl1|MEP|fs|nkt	cathepsin L	protein-coding
mm_98511.1	chr11	94952356	94952369	+	1	NA	3' UTR (NM_007742, exon 51 of 51)	3' UTR (NM_007742, exon 51 of 51)	-15231	NM_018792	54388	Mm.30482	NM_018792	ENSMUSG00000038994	Hils1	H1.9|TISP64	histone H1-like protein in spermatids 1	protein-coding
mm_1316.1	chr1	65080521	65080525	+	1	NA	exon (NM_144761, exon 3 of 3)	exon (NM_144761, exon 3 of 3)	1767	NM_144761	12965	Mm.440053	NM_144761	ENSMUSG00000073658	Crygb	Cryg-3|DGcry-3|Nop	crystallin, gamma B	protein-coding
mm_162652.1	chr10	3758393	3758400	+	1	NA	intron (NM_001159942, intron 1 of 16)	intron (NM_001159942, intron 1 of 16)	18019	NM_001159942	213783	Mm.150831	NM_001033253	ENSMUSG00000040624	Plekhg1	D10Ertd733e|Gm521|mKIAA1209	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	protein-coding
mm_12340.1	chr2	69723040	69723068	+	1	NA	promoter-TSS (NM_001081086)	promoter-TSS (NM_001081086)	-34	NM_001081086	228005	Mm.11815	NM_001081086	ENSMUSG00000042133	Ppig	AU019516|AU022200|B230312B02Rik|CYP|SRCyp	peptidyl-prolyl isomerase G (cyclophilin G)	protein-coding
mm_87960.1	chr10	63244003	63244013	+	1	NA	5' UTR (NM_026101, exon 1 of 25)	5' UTR (NM_026101, exon 1 of 25)	211	NM_026101	67345	Mm.234437	NM_026101	ENSMUSG00000020064	Herc4	1700056O17Rik|4921531D01Rik|9530080M15Rik|mKIAA1593	hect domain and RLD 4	protein-coding
mm_19830.1	chr2	112203041	112203071	-	1	NA	Intergenic	Lx9|LINE|L1	-36785	NM_207206	99010	Mm.33438	NM_207206	ENSMUSG00000027134	Lpcat4	AI505034|Agpat7|Aytl3|LPEAT2	lysophosphatidylcholine acyltransferase 4	protein-coding
mm_89014.1	chr10	81651652	81651652	+	1	NA	intron (NM_001142963, intron 1 of 3)	B1_Mus2|SINE|Alu	2583	NM_001142963	100233208	Mm.327168	NM_001142963	ENSMUSG00000096856	Gm10778	ENSMUSG00000074860	predicted gene 10778	protein-coding
mm_145025.1	chr18	39024143	39024181	+	1	NA	intron (NM_175164, intron 1 of 22)	B1_Mur3|SINE|Alu	31017	NM_175164	71302	Mm.329396	NM_175164	ENSMUSG00000036452	Arhgap26	1810044B20Rik|2610010G17Rik|4933432P15Rik|AI853435|mKIAA0621	Rho GTPase activating protein 26	protein-coding
mm_61179.1	chr7	60155683	60155722	+	1	NA	Intergenic	Intergenic	-15483	NM_001082962	20646	Mm.274995	NM_013670	ENSMUSG00000102252	Snrpn	2410045I01Rik|HCERN3|Peg4|Pwcr1|SMN	small nuclear ribonucleoprotein N	protein-coding
mm_118885.1	chr14	26357534	26357551	+	1	NA	promoter-TSS (NR_038005)	promoter-TSS (NR_038005)	-5	NR_038005	71106	Mm.158564	NR_038005	ENSMUSG00000021874	4933413J09Rik	GCSE	RIKEN cDNA 4933413J09 gene	ncRNA
mm_146164.1	chr18	75183843	75183865	+	1	NA	intron (NM_027727, intron 13 of 16)	intron (NM_027727, intron 13 of 16)	113463	NR_045394	100503117	Mm.250517	NR_045393	ENSMUSG00000102047	2010010A06Rik	5033420E22Rik	RIKEN cDNA 2010010A06 gene	ncRNA
mm_148533.1	chr19	4594338	4594361	+	1	NA	promoter-TSS (NM_008797)	promoter-TSS (NM_008797)	30	NM_008797	18563	Mm.1845	NM_008797	ENSMUSG00000024892	Pcx	Pc|Pcb	pyruvate carboxylase	protein-coding
mm_131854.1	chr16	23067723	23067725	+	1	NA	exon (NM_001102411, exon 4 of 10)	exon (NM_001102411, exon 4 of 10)	9424	NM_001102412	16644	Mm.2160	NM_023125	ENSMUSG00000022875	Kng1	Kng	kininogen 1	protein-coding
mm_131653.1	chr16	20538221	20538250	+	1	NA	intron (NM_001302970, intron 2 of 10)	intron (NM_001302970, intron 2 of 10)	2755	NM_009679	11773	Mm.18946	NM_009679	ENSMUSG00000022841	Ap2m1	-	adaptor-related protein complex 2, mu 1 subunit	protein-coding
mm_127469.1	chr15	101272799	101272809	+	1	NA	exon (NM_010444, exon 5 of 7)	exon (NM_010444, exon 5 of 7)	5958	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_72083.1	chr8	71573995	71573999	+	1	NA	intron (NM_011977, intron 3 of 13)	intron (NM_011977, intron 3 of 13)	5070	NM_011977	26457	Mm.38165	NM_011977	ENSMUSG00000031808	Slc27a1	FATP1|Fatp	solute carrier family 27 (fatty acid transporter), member 1	protein-coding
mm_60029.1	chr7	30973832	30973849	+	1	NA	promoter-TSS (NM_017405)	promoter-TSS (NM_017405)	36	NR_038860	76415	Mm.259739	NM_175240	ENSMUSG00000046826	Fam187b	1700020B09Rik|Tmem162	family with sequence similarity 187, member B	protein-coding
mm_127859.1	chr15	8350877	8350890	-	1	NA	exon (NM_027707, exon 10 of 47)	exon (NM_027707, exon 10 of 47)	93580	NM_027707	71175	Mm.240329	NM_027707	ENSMUSG00000022141	Nipbl	Idn3	Nipped-B homolog (Drosophila)	protein-coding
mm_118565.1	chr14	18271123	18271178	+	1	NA	promoter-TSS (NM_025586)	promoter-TSS (NM_025586)	14	NM_023526	69721	Mm.25648	NM_023526	ENSMUSG00000021772	Nkiras1	2400004O09Rik|KBRAS1|kappaB-Ras1	NFKB inhibitor interacting Ras-like protein 1	protein-coding
mm_71304.1	chr8	41316012	41316029	+	1	NA	exon (NM_023662, exon 29 of 38)	exon (NM_023662, exon 29 of 38)	58677	NM_019734	11886	Mm.22547	NM_019734	ENSMUSG00000031591	Asah1	2310081N20Rik|AC|Asah	N-acylsphingosine amidohydrolase 1	protein-coding
mm_133232.1	chr16	77013701	77013775	+	1	NA	promoter-TSS (NM_013918)	promoter-TSS (NM_013918)	-331	NM_013918	30940	Mm.40986	NM_013918	ENSMUSG00000022867	Usp25	-	ubiquitin specific peptidase 25	protein-coding
mm_15042.1	chr2	152821269	152821282	+	1	NA	intron (NM_001289717, intron 2 of 2)	intron (NM_001289717, intron 2 of 2)	9442	NM_001289716	12048	Mm.238213	NM_009743	ENSMUSG00000007659	Bcl2l1	Bcl(X)L|Bcl-XL|Bcl2l|BclX|bcl-x|bcl2-L-1	BCL2-like 1	protein-coding
mm_39176.1	chr4	155774564	155774574	-	1	NA	promoter-TSS (NM_147776)	promoter-TSS (NM_147776)	-8	NM_147776	246228	Mm.26515	NM_147776	ENSMUSG00000042116	Vwa1	4932416A11Rik|WARP	von Willebrand factor A domain containing 1	protein-coding
mm_85278.1	chr9	99568641	99568678	-	1	NA	5' UTR (NM_001166138, exon 1 of 12)	5' UTR (NM_001166138, exon 1 of 12)	240	NM_001166138	74125	Mm.234823	NM_028768	ENSMUSG00000032468	Armc8	1200015K23Rik|Gid5|HSPC056	armadillo repeat containing 8	protein-coding
mm_69059.1	chr7	126897342	126897354	-	1	NA	intron (NM_026827, intron 1 of 5)	MIRc|SINE|MIR	930	NM_026827	68742	Mm.248646	NM_026827	ENSMUSG00000060538	Tmem219	1110032O16Rik|2900045G02Rik|IGFBP-3R	transmembrane protein 219	protein-coding
mm_117781.1	chr13	97022315	97022324	-	1	NA	non-coding (NR_104276, exon 3 of 3)	non-coding (NR_104276, exon 3 of 3)	12043	NM_025585	66479	Mm.390629	NM_025585	ENSMUSG00000052075	1700029F12Rik	-	RIKEN cDNA 1700029F12 gene	protein-coding
mm_75333.1	chr8	43304674	43304676	-	1	NA	intron (NM_009556, intron 1 of 3)	intron (NM_009556, intron 1 of 3)	2334	NM_009556	22702	Mm.285848	NM_009556	ENSMUSG00000051176	Zfp42	Rex-1|Rex1|Zfp-42	zinc finger protein 42	protein-coding
mm_94112.1	chr10	128626454	128626458	-	1	NA	promoter-TSS (NM_013765)	promoter-TSS (NM_013765)	50	NM_013765	27370	Mm.32118	NM_013765	ENSMUSG00000025362	Rps26	-	ribosomal protein S26	protein-coding
mm_44163.1	chr5	150673885	150673937	+	1	NA	promoter-TSS (NM_175310)	promoter-TSS (NM_175310)	84	NM_001346503	100710	Mm.32959	NM_175310	ENSMUSG00000034021	Pds5b	AI646570|AS3|AW212954|Aprin|Tg(Wap-ERBB2)229Wzw|WAP-Her-2|mKIAA0979	PDS5 cohesin associated factor B	protein-coding
mm_107986.1	chr12	73086480	73086490	+	1	NA	Intergenic	Intergenic	26760	NM_011382	20474	Mm.249575	NM_011382	ENSMUSG00000034460	Six4	AI047561|AREC3|TrexBF	sine oculis-related homeobox 4	protein-coding
mm_160245.1	chr7	105056411	105056411	+	1	NA	exon (NM_146358, exon 1 of 1)	exon (NM_146358, exon 1 of 1)	163	NM_146358	258355	Mm.377452	NM_146358	ENSMUSG00000073914	Olfr677	MOR32-11	olfactory receptor 677	protein-coding
mm_169105.1	chr13	44869639	44869639	-	1	NA	intron (NM_001205044, intron 4 of 18)	LSU-rRNA_Hsa|rRNA|rRNA	132457	NM_025772	94245	Mm.352311	NM_025772	ENSMUSG00000057531	Dtnbp1	5430437B18Rik|AW048963|Bloc1s8|dysbindin|sdy	dystrobrevin binding protein 1	protein-coding
mm_107425.1	chr12	35135987	35136005	+	1	NA	intron (NM_001014973, intron 22 of 25)	L1_Mus3|LINE|L1	88807	NM_001014973	217463	Mm.213991	NM_001014973	ENSMUSG00000020590	Snx13	Rgs-px1|mKIAA0713	sorting nexin 13	protein-coding
mm_30085.1	chr3	138131390	138131400	-	1	NA	promoter-TSS (NM_008642)	promoter-TSS (NM_008642)	-18	NM_008642	17777	Mm.2941	NM_008642	ENSMUSG00000028158	Mttp	1810043K16Rik|MTP	microsomal triglyceride transfer protein	protein-coding
mm_111732.1	chr12	103773632	103773640	-	1	NA	promoter-TSS (NM_009246)	promoter-TSS (NM_009246)	-3	NM_009246	20703	Mm.439695	NM_009246	ENSMUSG00000071177	Serpina1d	AI118301|Dom4|PI4|Spi1-4	serine (or cysteine) peptidase inhibitor, clade A, member 1D	protein-coding
mm_67392.1	chr7	79846433	79846443	-	1	NA	Intergenic	Intergenic	-4086	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_20752.1	chr2	140389732	140389738	-	1	NA	promoter-TSS (NM_001033296)	promoter-TSS (NM_001033296)	-25	NM_001033296	228684	Mm.486585	NM_001033296	ENSMUSG00000074764	Sel1l2	Gm118	sel-1 suppressor of lin-12-like 2 (C. elegans)	protein-coding
mm_157753.1	chrX	73494619	73494677	-	1	NA	exon (NM_007542, exon 8 of 8)	exon (NM_007542, exon 8 of 8)	-8438	NM_001310537	320707	Mm.210095	NM_177236	ENSMUSG00000031376	Atp2b3	6430519O13Rik|Pmca3	ATPase, Ca++ transporting, plasma membrane 3	protein-coding
mm_104013.1	chr11	85235066	85235137	-	1	NA	promoter-TSS (NM_025825)	promoter-TSS (NM_025825)	19	NM_025825	66884	Mm.271997	NM_025825	ENSMUSG00000018481	Appbp2	1300003O07Rik|AI465480|PAT1	amyloid beta precursor protein (cytoplasmic tail) binding protein 2	protein-coding
mm_36398.1	chr4	77788568	77788571	-	1	NA	intron (NM_011211, intron 2 of 39)	intron (NM_011211, intron 2 of 39)	423326	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding
mm_132465.1	chr16	36307993	36308005	+	1	NA	Intergenic	Intergenic	26333	NM_001001332	100038854	Mm.383561	NM_001001332	ENSMUSG00000079594	BC117090	Gm1975	cDNA sequence BC1179090	protein-coding
mm_56152.1	chr6	87843796	87843855	-	1	NA	3' UTR (NM_013493, exon 5 of 5)	3' UTR (NM_013493, exon 5 of 5)	-5066	NM_133934	57905	Mm.241546	NM_133934	ENSMUSG00000030056	Isy1	5830446M03Rik|AI181014|AU020769	ISY1 splicing factor homolog	protein-coding
mm_56449.1	chr6	97606473	97606475	-	1	NA	intron (NM_145148, intron 1 of 23)	intron (NM_145148, intron 1 of 23)	11183	NM_145148	232288	Mm.27789	NM_145148	ENSMUSG00000030064	Frmd4b	6030440G05Rik|C87375|GOBLIN|GRSP1|R74720	FERM domain containing 4B	protein-coding
mm_104628.1	chr11	97315623	97315634	-	1	NA	promoter-TSS (NM_025927)	promoter-TSS (NM_025927)	-88	NM_025927	67036	Mm.5381	NM_025927	ENSMUSG00000018882	Mrpl45	2600005P05Rik|AU043542|R75241	mitochondrial ribosomal protein L45	protein-coding
mm_137593.1	chr17	28098017	28098018	+	1	NA	Intergenic	Intergenic	-17378	NM_001085555	21463	Mm.29758	NM_013687	ENSMUSG00000062859	Tcp11	D17Ken1|Tcp-11	t-complex protein 11	protein-coding
mm_66962.1	chr7	62464418	62464440	-	1	NA	promoter-TSS (NM_013788)	promoter-TSS (NM_013788)	81	NM_013788	27412	Mm.422745	NM_013788	ENSMUSG00000070526	Peg12	Frat3	paternally expressed 12	protein-coding
mm_145498.1	chr18	60390650	60390676	+	1	NA	exon (NM_001146275, exon 3 of 3)	exon (NM_001146275, exon 3 of 3)	14634	NM_001146275	60440	Mm.261140	NM_021792	ENSMUSG00000054072	Iigp1	2900074L10Rik|AI046432|AW111922|Ifgga1|Iigp|Irga6	interferon inducible GTPase 1	protein-coding
mm_141341.1	chr17	28552531	28552533	-	1	NA	TTS (NM_001034871)	TTS (NM_001034871)	3045	NM_001034871	328788	Mm.99400	NM_001034871	ENSMUSG00000024224	Clpsl2	Gm749	colipase-like 2	protein-coding
mm_149059.1	chr19	8839472	8839493	+	1	NA	promoter-TSS (NM_010316)	promoter-TSS (NM_010316)	154	NM_008144	14705	Mm.345134	NM_008144	ENSMUSG00000071657	Bscl2	2900097C17Rik|AI046355|Gng3lg	Berardinelli-Seip congenital lipodystrophy 2 (seipin)	protein-coding
mm_7534.1	chr1	124419896	124419901	-	1	NA	Intergenic	Intergenic	-374339	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_16608.1	chr2	5083840	5083852	-	1	NA	Intergenic	Intergenic	-19908	NM_181848	71648	Mm.116942	NM_181848	ENSMUSG00000026672	Optn	4930441O07Rik|FIP2|HYPL|NRP	optineurin	protein-coding
mm_80462.1	chr9	78051939	78051948	+	1	NA	promoter-TSS (NM_008103)	promoter-TSS (NM_008103)	-15	NM_008103	14531	Mm.1400	NM_008103	ENSMUSG00000023333	Gcm1	GCMa|Gcm-rs2|Gcm1-rs1|glide	glial cells missing homolog 1 (Drosophila)	protein-coding
mm_23825.1	chr3	81036966	81037011	+	1	NA	5' UTR (NM_019971, exon 1 of 6)	5' UTR (NM_019971, exon 1 of 6)	572	NM_019971	54635	Mm.331089	NM_019971	ENSMUSG00000028019	Pdgfc	1110064L01Rik|AI647969|PDGF-C	platelet-derived growth factor, C polypeptide	protein-coding
mm_100614.1	chr11	121519421	121519436	+	1	NA	promoter-TSS (NM_178763)	promoter-TSS (NM_178763)	-86	NM_178763	319530	Mm.11395	NM_178763	ENSMUSG00000039238	Zfp750	A030007D23Rik|Znf750	zinc finger protein 750	protein-coding
mm_8600.1	chr1	156034801	156034814	-	1	NA	promoter-TSS (NM_001160180)	promoter-TSS (NM_001160180)	10	NM_001160019	208263	Mm.211654	NM_144791	ENSMUSG00000026466	Tor1aip1	LAP1|Lap1B	torsin A interacting protein 1	protein-coding
mm_1312.1	chr1	65043786	65043789	+	1	NA	Intergenic	RLTR43C|LTR|ERVK	7376	NM_007777	12968	Mm.258170	NM_007777	ENSMUSG00000070870	Cryge	Cryg-2|Cryg-6|DGcry-2|Elo	crystallin, gamma E	protein-coding
mm_3597.1	chr1	151530739	151530757	+	1	NA	Intergenic	ORR1B2|LTR|ERVL-MaLR	-29925	NM_011277	19821	Mm.474038	NM_011277	ENSMUSG00000026484	Rnf2	AI326319|AI450156|AU019207|Ring1B|dinG	ring finger protein 2	protein-coding
mm_83029.1	chr9	37255404	37255419	-	1	NA	5' UTR (NM_001145960, exon 1 of 19)	5' UTR (NM_001145960, exon 1 of 19)	327	NM_020258	56857	Mm.440037	NM_020258	ENSMUSG00000032122	Slc37a2	G3PP|Slc37a1|cI-2|ci2	solute carrier family 37 (glycerol-3-phosphate transporter), member 2	protein-coding
mm_75931.1	chr8	71525702	71525713	-	1	NA	Intergenic	CpG	11730	NM_198095	69550	Mm.260325	NM_198095	ENSMUSG00000046718	Bst2	2310015I10Rik|Bst-2|C87040|CD317|DAMP-1|GREG	bone marrow stromal cell antigen 2	protein-coding
mm_75401.1	chr8	46208518	46208543	-	1	NA	exon (NM_007450, exon 3 of 4)	exon (NM_007450, exon 3 of 4)	2479	NM_007450	11739	Mm.16228	NM_007450	ENSMUSG00000031633	Slc25a4	AU019225|Ant1	solute carrier family 25 (mitochondrial carrier, adenine nucleotide translocator), member 4	protein-coding
mm_171888.1	chr5	36779337	36779337	+	1	NA	Intergenic	B1_Mus2|SINE|Alu	17417	NM_026242	67568	Mm.332336	NM_026242	ENSMUSG00000055302	Mrfap1	9130413I22Rik|AL022827|Pam14	Morf4 family associated protein 1	protein-coding
mm_13794.1	chr2	118901382	118901403	+	1	NA	promoter-TSS (NM_001045523)	promoter-TSS (NM_001045523)	-223	NM_001045523	228536	Mm.330487	NM_001045523	ENSMUSG00000040007	Bahd1	AL022997|AW541238|Gm117|mKIAA0945	bromo adjacent homology domain containing 1	protein-coding
mm_30359.1	chr3	151764249	151764260	-	1	NA	Intergenic	Intergenic	-1363	NM_031367	15061	Mm.219544	NM_031367	ENSMUSG00000039146	Ifi44l	H-28|H28|H28-1|NS1178	interferon-induced protein 44 like	protein-coding
mm_32613.1	chr4	112288674	112288683	+	1	NA	intron (NM_001102474, intron 8 of 9)	Lx2|LINE|L1	56257	NM_001102474	195564	Mm.259652	NM_177578	ENSMUSG00000070868	Skint3	A430090E18Rik|Skint-3	selection and upkeep of intraepithelial T cells 3	protein-coding
mm_135502.1	chr16	46496944	46496954	-	1	NA	promoter-TSS (NM_021495)	promoter-TSS (NM_021495)	18	NM_021496	58998	Mm.40477	NM_021495	ENSMUSG00000022656	Nectin3	2610301B19Rik|3000002N23Rik|4921513D19Rik|AA407785|AU016832|AW538082|CD113|Pvrl3	nectin cell adhesion molecule 3	protein-coding
mm_77600.1	chr8	123892889	123892904	-	1	NA	exon (NM_009606, exon 4 of 7)	exon (NM_009606, exon 4 of 7)	1879	NM_001272041	11459	Mm.214950	NM_009606	ENSMUSG00000031972	Acta1	AA959943|Acta-2|Acts|Actsk-1	actin, alpha 1, skeletal muscle	protein-coding
mm_150103.1	chr19	29488693	29488708	+	1	NA	Intergenic	Intergenic	33287	NR_015567	77779	Mm.458738	NR_015567	ENSMUSG00000097855	A930007I19Rik	-	RIKEN cDNA A930007I19 gene	ncRNA
mm_24362.1	chr3	90079547	90079565	+	1	NA	promoter-TSS (NM_001253740)	promoter-TSS (NM_001253740)	35	NM_001293749	59069	Mm.240839	NM_022314	ENSMUSG00000027940	Tpm3	TM30nm|TMnm|Tm5NM|Tpm-5|Tpm5|Trop-5|gamma-TM|hTM30nm|hTMnm	tropomyosin 3, gamma	protein-coding
mm_35072.1	chr4	6989108	6989122	-	1	NA	intron (NM_145711, intron 1 of 8)	intron (NM_145711, intron 1 of 8)	1608	NM_145711	252838	Mm.435828	NM_145711	ENSMUSG00000041272	Tox	1700007F02Rik	thymocyte selection-associated high mobility group box	protein-coding
mm_19475.1	chr2	92540955	92540961	-	1	NA	Intergenic	Intergenic	-51248	NR_106080	102466819		NR_106080	ENSMUSG00000099223	Mir7221	Gm27378|mmu-mir-7221	microRNA 7221	ncRNA
mm_149547.1	chr19	12595718	12595751	+	1	NA	intron (NR_015503, intron 1 of 1)	intron (NR_015503, intron 1 of 1)	832	NR_015503	74333	Mm.329744	NR_015503	ENSMUSG00000086213	A330040F15Rik	-	RIKEN cDNA A330040F15 gene	ncRNA
mm_10493.1	chr2	14824173	14824185	+	1	NA	promoter-TSS (NM_001252533)	promoter-TSS (NM_001252533)	87	NM_001252533	12296	Mm.313930	NM_023116	ENSMUSG00000057914	Cacnb2	AW060387|CAB2|Cavbeta2|Cchb2	calcium channel, voltage-dependent, beta 2 subunit	protein-coding
mm_64498.1	chr7	143475095	143475115	+	1	NA	promoter-TSS (NM_001042760)	promoter-TSS (NM_001042760)	-11	NM_001042760	18400	Mm.271740	NM_008767	ENSMUSG00000000154	Slc22a18	AW260131|BWR1A|BWSCR1A|HET|ITM|Impt1|Orctl2|Slc22a1l|TSSC5|p45-BWR1A	solute carrier family 22 (organic cation transporter), member 18	protein-coding
mm_57964.1	chr6	135254321	135254322	-	1	NA	promoter-TSS (NM_010352)	promoter-TSS (NM_010352)	15	NM_010352	14840	Mm.272306	NM_010352	ENSMUSG00000030206	Gsg1	-	germ cell associated 1	protein-coding
mm_141113.1	chr17	26082080	26082098	-	1	NA	3' UTR (NM_011933, exon 9 of 9)	3' UTR (NM_011933, exon 9 of 9)	8075	NM_011933	26378	Mm.292869	NM_011933	ENSMUSG00000036775	Decr2	-	2-4-dienoyl-Coenzyme A reductase 2, peroxisomal	protein-coding
mm_26389.1	chr3	142570896	142570933	+	1	NA	exon (NM_018734, exon 10 of 11)	exon (NM_018734, exon 10 of 11)	10418	NM_001289493	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_63573.1	chr7	128117788	128117798	+	1	NA	3' UTR (NM_008401, exon 30 of 30)	3' UTR (NM_008401, exon 30 of 30)	-11775	NM_021334	16411	Mm.22378	NM_021334	ENSMUSG00000030789	Itgax	AI449405|Cd11c|Cr4|N418	integrin alpha X	protein-coding
mm_59233.1	chr7	24777173	24777247	+	1	NA	promoter-TSS (NM_007675)	promoter-TSS (NM_007675)	6	NM_007675	26366	Mm.30300	NM_007675	ENSMUSG00000054169	Ceacam10	Bgp3|Cea10	carcinoembryonic antigen-related cell adhesion molecule 10	protein-coding
mm_24119.1	chr3	88167595	88167654	+	1	NA	exon (NM_001310593, exon 9 of 11)	exon (NM_001310593, exon 9 of 11)	10161	NR_045997	76642	Mm.424420	NR_045997	ENSMUSG00000096935	1700113A16Rik	2210408E11Rik|AA408983	RIKEN cDNA 1700113A16 gene	ncRNA
mm_112488.1	chr13	6548136	6548146	+	1	NA	promoter-TSS (NM_145131)	promoter-TSS (NM_145131)	-16	NM_145131	69617	Mm.41933	NM_145131	ENSMUSG00000021193	Pitrm1	2310012C15Rik|AA410010|MP-1|MP1|Ntup1|PreP|mKIAA1104	pitrilysin metallepetidase 1	protein-coding
mm_53910.1	chr6	3968572	3968610	-	1	NA	promoter-TSS (NM_009364)	promoter-TSS (NM_009364)	-216	NM_009364	21789	Mm.25612	NM_009364	ENSMUSG00000029664	Tfpi2	AV000670|PP5/TFPI-2	tissue factor pathway inhibitor 2	protein-coding
mm_167224.1	chr8	12647193	12647194	+	1	NA	intron (NM_198031, intron 11 of 21)	B3A|SINE|B2	24907	NM_198031	259279	Mm.142095	NM_198031	ENSMUSG00000000759	Tubgcp3	GCP3|Spc98p	tubulin, gamma complex associated protein 3	protein-coding
mm_111510.1	chr12	99563957	99563959	-	1	NA	intron (NR_136760, intron 1 of 3)	intron (NR_136760, intron 1 of 3)	117	NR_136760	102639404	Mm.396324	NR_136760	ENSMUSG00000097917	Gm26839	-	predicted gene, 26839	ncRNA
mm_150564.1	chr19	39510908	39510918	+	1	NA	promoter-TSS (NM_010003)	promoter-TSS (NM_010003)	91	NM_010003	13098	Mm.42101	NM_010003	ENSMUSG00000025003	Cyp2c39	CYPIIC39	cytochrome P450, family 2, subfamily c, polypeptide 39	protein-coding
mm_74873.1	chr8	25029705	25029742	-	1	NA	exon (NM_001081187, exon 8 of 9)	exon (NM_001081187, exon 8 of 9)	9239	NM_001081187	330723	Mm.334452	NM_001081187	ENSMUSG00000037406	Htra4	B430206E18Rik	HtrA serine peptidase 4	protein-coding
mm_78923.1	chr9	45042628	45042660	+	1	NA	5' UTR (NM_007962, exon 1 of 6)	5' UTR (NM_007962, exon 1 of 6)	300	NM_007962	14012	Mm.33240	NM_007962	ENSMUSG00000032092	Mpzl2	Eva|Eva1	myelin protein zero-like 2	protein-coding
mm_135454.1	chr16	45724527	45724545	-	1	NA	promoter-TSS (NM_019754)	promoter-TSS (NM_019754)	-5	NM_019754	56370	Mm.24183	NM_019754	ENSMUSG00000022658	Tagln3	2700038H05Rik|2900005O10Rik|AI426007|Np25	transgelin 3	protein-coding
mm_68713.1	chr7	119895651	119895659	-	1	NA	promoter-TSS (NM_001285961)	promoter-TSS (NM_001285961)	90	NM_001163703	233805	Mm.31539	NM_173408	ENSMUSG00000048787	Dcun1d3	1700020A13Rik|BC030335	DCN1, defective in cullin neddylation 1, domain containing 3 (S. cerevisiae)	protein-coding
mm_52784.1	chr6	121256934	121256947	+	1	NA	intron (NM_011909, intron 4 of 10)	L1M2|LINE|L1	11034	NM_011909	24110	Mm.326911	NM_011909	ENSMUSG00000030107	Usp18	1110058H21Rik|AW047653|UBP43|Ubp15	ubiquitin specific peptidase 18	protein-coding
mm_81159.1	chr9	107296224	107296235	+	1	NA	promoter-TSS (NM_009895)	promoter-TSS (NM_009895)	-430	NM_001317354	12700	Mm.4592	NM_009895	ENSMUSG00000032578	Cish	CIS-1|CIS1|Cis|F17|F23|SOCS	cytokine inducible SH2-containing protein	protein-coding
mm_16358.1	chr2	174439707	174439727	+	1	NA	promoter-TSS (NM_022325)	promoter-TSS (NM_022325)	-678	NM_022325	64138	Mm.156919	NM_022325	ENSMUSG00000016256	Ctsz	AI787083|AU019819|CTSX|D2Wsu143e	cathepsin Z	protein-coding
mm_99467.1	chr11	102435796	102435864	+	1	NA	exon (NM_008175, exon 11 of 13)	exon (NM_008175, exon 11 of 13)	5508	NM_008175	14824	Mm.1568	NM_008175	ENSMUSG00000034708	Grn	Pgrn|epithelin	granulin	protein-coding
mm_49588.1	chr6	30643021	30643027	+	1	NA	exon (NM_025350, exon 8 of 10)	exon (NM_025350, exon 8 of 10)	3806	NM_025350	109697	Mm.25377	NM_025350	ENSMUSG00000054446	Cpa1	0910001L12Rik|Cpa	carboxypeptidase A1, pancreatic	protein-coding
mm_9883.1	chr1	186558505	186558521	-	1	NA	non-coding (NR_131124, exon 1 of 3)	non-coding (NR_131124, exon 1 of 3)	168	NR_131124	320449	Mm.404477	NR_131124	ENSMUSG00000103690	A730004F24Rik	-	RIKEN cDNA A730004F24 gene	ncRNA
mm_10783.1	chr2	24336934	24336945	+	1	NA	promoter-TSS (NM_031167)	promoter-TSS (NM_031167)	79	NM_031167	16181	Mm.882	NM_031167	ENSMUSG00000026981	Il1rn	F630041P17Rik|IL-1ra	interleukin 1 receptor antagonist	protein-coding
mm_172222.1	chr6	66515973	66515991	+	1	NA	Intergenic	Intergenic	-19486	NM_019499	56150	Mm.489653	NM_019499	ENSMUSG00000029910	Mad2l1	AA673185|MAD2	MAD2 mitotic arrest deficient-like 1	protein-coding
mm_59618.1	chr7	28147423	28147430	+	1	NA	exon (NM_001164655, exon 9 of 20)	exon (NM_001164655, exon 9 of 20)	17960	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_92552.1	chr10	79766793	79766803	-	1	NA	exon (NM_144528, exon 1 of 9)	exon (NM_144528, exon 1 of 9)	154	NM_144528	70294	Mm.466670	NM_144528	ENSMUSG00000035890	Rnf126	2610010O19Rik	ring finger protein 126	protein-coding
mm_153277.1	chr19	37194066	37194067	-	1	NA	intron (NR_045329, intron 2 of 2)	intron (NR_045329, intron 2 of 2)	4042	NM_001290829	208922	Mm.391176	NM_198300	ENSMUSG00000039652	Cpeb3	4831444O18Rik|CPE-BP3|mKIAA0940	cytoplasmic polyadenylation element binding protein 3	protein-coding
mm_160349.1	chr8	21084401	21084401	+	1	NA	promoter-TSS (NM_007849)	promoter-TSS (NM_007849)	-41	NM_007849	13236	Mm.376982	NM_007849	ENSMUSG00000094687	Defa25	Defcr-2|Defcr2|Defcr25	defensin, alpha, 25	protein-coding
mm_514.1	chr1	37408828	37408872	+	1	NA	3' UTR (NM_030266, exon 26 of 26)	3' UTR (NM_030266, exon 26 of 26)	21253	NM_198006	76178	Mm.28085	NM_198006	ENSMUSG00000026112	Coa5	1700001A24Rik|6330578E17Rik|Pet191	cytochrome C oxidase assembly factor 5	protein-coding
mm_41449.1	chr5	90905411	90905417	+	1	NA	3' UTR (NM_009140, exon 4 of 4)	3' UTR (NM_009140, exon 4 of 4)	1515	NM_009140	20310	Mm.4979	NM_009140	ENSMUSG00000058427	Cxcl2	CINC-2a|GROb|Gro2|MIP-2|MIP-2a|Mgsa-b|Mip2|Scyb|Scyb2	chemokine (C-X-C motif) ligand 2	protein-coding
mm_61903.1	chr7	90130286	90130300	+	1	NA	promoter-TSS (NM_001252521)	promoter-TSS (NM_001252521)	61	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_89874.1	chr10	108277723	108277734	+	1	NA	TTS (NM_027892)	TTS (NM_027892)	-54461	NM_054056	114774	Mm.391419	NM_054056	ENSMUSG00000035873	Pawr	2310001G03Rik|PAR4|Par-4	PRKC, apoptosis, WT1, regulator	protein-coding
mm_3052.1	chr1	134061073	134061090	+	1	NA	Intergenic	Intergenic	18074	NM_007570	12227	Mm.392646	NM_007570	ENSMUSG00000020423	Btg2	AA959598|APRO1|Pc3|TIS21	B cell translocation gene 2, anti-proliferative	protein-coding
mm_87023.1	chr10	28089231	28089240	+	1	NA	intron (NM_008983, intron 1 of 31)	(T)n|Simple_repeat|Simple_repeat	14415	NM_008983	19272	Mm.332303	NM_008983	ENSMUSG00000019889	Ptprk	AI853699|PTPk|RPTPkappa	protein tyrosine phosphatase, receptor type, K	protein-coding
mm_156849.1	chrX	164400856	164400868	+	1	NA	exon (NM_001308489, exon 6 of 6)	exon (NM_001308489, exon 6 of 6)	-18925	NM_011081	18700	Mm.3781	NM_011081	ENSMUSG00000031381	Piga	AI194334|Pig-a	phosphatidylinositol glycan anchor biosynthesis, class A	protein-coding
mm_128447.1	chr15	50769556	50769571	-	1	NA	intron (NM_001310485, intron 5 of 7)	intron (NM_001310485, intron 5 of 7)	119486	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_128689.1	chr15	61546440	61546450	-	1	NA	Intergenic	Intergenic	228006	NR_040350	432956	Mm.404918	NR_040350		D030024E09Rik	-	RIKEN cDNA D030024E09 gene	ncRNA
mm_26136.1	chr3	137914935	137914947	+	1	NA	Intergenic	Intergenic	-3614	NM_019920	56692	Mm.331392	NM_019920	ENSMUSG00000091512	Lamtor3	AW556229|Map2k1ip1|Mapbp|Mapksp1|Mp1	late endosomal/lysosomal adaptor, MAPK and MTOR activator 3	protein-coding
mm_115896.1	chr13	22042952	22042978	-	1	NA	promoter-TSS (NM_178186)	promoter-TSS (NM_178186)	-16	NM_178186	319167	Mm.263165	NM_178186	ENSMUSG00000069301	Hist1h2ag	-	histone cluster 1, H2ag	protein-coding
mm_48184.1	chr5	137472227	137472239	-	1	NA	exon (NM_011741, exon 7 of 88)	exon (NM_011741, exon 7 of 88)	4831	NM_011741	22635	Mm.7984	NM_011741	ENSMUSG00000079173	Zan	Zan-test	zonadhesin	protein-coding
mm_155144.1	chrX	52788317	52788319	+	1	NA	Intergenic	L2a|LINE|L2	-2882	NM_001034059	434778	Mm.23411	NM_001034059	ENSMUSG00000073207	Ccdc160	6330534C20Rik	coiled-coil domain containing 160	protein-coding
mm_67838.1	chr7	98415623	98415625	-	1	NA	Intergenic	Intergenic	-24792	NM_001130693	14918	Mm.389928	NM_001034890	ENSMUSG00000074003	Gucy2d	-	guanylate cyclase 2d	protein-coding
mm_38159.1	chr4	135214507	135214519	-	1	NA	3' UTR (NM_013885, exon 6 of 6)	3' UTR (NM_013885, exon 6 of 6)	58247	NM_013885	29876	Mm.257765	NM_013885	ENSMUSG00000037242	Clic4	D0Jmb3|TU-74|mc3s5|mtCLIC	chloride intracellular channel 4 (mitochondrial)	protein-coding
mm_104854.1	chr11	99346536	99346539	-	1	NA	intron (NM_010666, intron 6 of 7)	intron (NM_010666, intron 6 of 7)	4581	NM_010666	16675	Mm.440476	NM_010666	ENSMUSG00000017588	Krt27	CK-27|Krt1-c29|mIRSa3.1|stpm	keratin 27	protein-coding
mm_167511.1	chr9	13514716	13514744	+	1	NA	Intergenic	Intergenic	83369	NR_028271	18689	Mm.41972	NM_008835	ENSMUSG00000031802	Phxr4	Sp5	per-hexamer repeat gene 4	ncRNA
mm_50658.1	chr6	51470609	51470620	+	1	NA	promoter-TSS (NM_007624)	promoter-TSS (NM_007624)	-2	NM_007624	12417	Mm.280968	NM_007624	ENSMUSG00000029836	Cbx3	HP1g|M32	chromobox 3	protein-coding
mm_63793.1	chr7	132782071	132782075	+	1	NA	intron (NM_212473, intron 1 of 4)	intron (NM_212473, intron 1 of 4)	4862	NM_175268	77938	Mm.225649	NM_175268	ENSMUSG00000030956	Fam53b	A930008G19Rik|mKIAA0140	family with sequence similarity 53, member B	protein-coding
mm_15078.1	chr2	153147484	153147492	+	1	NA	intron (NM_001172117, intron 11 of 12)	intron (NM_001172117, intron 11 of 12)	-13813	NM_133847	99237	Mm.330674	NM_133847	ENSMUSG00000068040	Tm9sf4	AA986553|AU045326|B930079E06|mKIAA0255	transmembrane 9 superfamily protein member 4	protein-coding
mm_135081.1	chr16	34263212	34263249	-	1	NA	intron (NM_001164268, intron 10 of 33)	intron (NM_001164268, intron 10 of 33)	250797	NM_001164268	545156	Mm.82274	NM_177357	ENSMUSG00000061751	Kalrn	2210407G14Rik|AV235988|DUET|E530005C20Rik|Gm539|Hapip|TRAD	kalirin, RhoGEF kinase	protein-coding
mm_4180.1	chr1	171158768	171158779	+	1	NA	exon (NM_008623, exon 5 of 8)	exon (NM_008623, exon 5 of 8)	3255	NM_001315500	17528	Mm.9986	NM_008623	ENSMUSG00000056569	Mpz	Mpp|P-zero|P0	myelin protein zero	protein-coding
mm_8444.1	chr1	152857410	152857421	-	1	NA	intron (NM_001005507, intron 8 of 21)	intron (NM_001005507, intron 8 of 21)	20753	NM_001160257	226517	Mm.270775	NM_001005507	ENSMUSG00000042772	Smg7	9430023P16Rik|mKIAA0250	Smg-7 homolog, nonsense mediated mRNA decay factor (C. elegans)	protein-coding
mm_168202.1	chr10	6982915	6982924	-	1	NA	intron (NM_001039652, intron 4 of 5)	intron (NM_001039652, intron 4 of 5)	-2454	NM_001170801	320495	Mm.331674	NM_001033391	ENSMUSG00000064065	Ipcef1	A130090K04Rik	interaction protein for cytohesin exchange factors 1	protein-coding
mm_61742.1	chr7	82264438	82264444	+	1	NA	intron (NM_001277954, intron 2 of 8)	RMER13B|LTR|ERVK	4533	NM_001277954	20408	Mm.736	NM_017400	ENSMUSG00000030638	Sh3gl3	EEN-B2|SH3P13|Sh3d2c|Sh3d2c2	SH3-domain GRB2-like 3	protein-coding
mm_118870.1	chr14	25855731	25855741	+	1	NA	intron (NM_013469, intron 1 of 14)	intron (NM_013469, intron 1 of 14)	13581	NM_013469	11744	Mm.294083	NM_013469	ENSMUSG00000021866	Anxa11	A830099O17Rik|Anx11	annexin A11	protein-coding
mm_27956.1	chr3	79843437	79843442	-	1	NA	promoter-TSS (NM_027495)	promoter-TSS (NM_027495)	-777	NM_027495	70652	Mm.46635	NM_027495	ENSMUSG00000027956	Tmem144	1110057I03Rik|5730537D05Rik	transmembrane protein 144	protein-coding
mm_123163.1	chr14	57133564	57133575	-	1	NA	promoter-TSS (NM_001271663)	promoter-TSS (NM_001271663)	42	NM_001271663	14623	Mm.25652	NM_008128	ENSMUSG00000040055	Gjb6	AA958971|Cx30|D14Bwg0506e	gap junction protein, beta 6	protein-coding
mm_117429.1	chr13	74522424	74522443	-	1	NA	Intergenic	Intergenic	-28483	NM_146231	235956	Mm.296909	NM_146231	ENSMUSG00000069208	Zfp825	-	zinc finger protein 825	protein-coding
mm_60514.1	chr7	44479751	44479758	+	1	NA	Intergenic	Intergenic	-4763	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_59444.1	chr7	27133245	27133268	+	1	NA	exon (NM_007817, exon 10 of 10)	exon (NM_007817, exon 10 of 10)	13301	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_43107.1	chr5	124522642	124522646	+	1	NA	intron (NM_021430, intron 1 of 6)	intron (NM_021430, intron 1 of 6)	8747	NM_021430	75695	Mm.41180	NM_021430	ENSMUSG00000029392	Rilpl1	2900002H16Rik|6330559I19Rik|GOSPEL	Rab interacting lysosomal protein-like 1	protein-coding
mm_52100.1	chr6	97868792	97868806	+	1	NA	intron (NM_001113198, intron 1 of 9)	intron (NM_001113198, intron 1 of 9)	-61018	NM_001178049	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_15173.1	chr2	154130333	154130356	+	1	NA	promoter-TSS (NM_028528)	promoter-TSS (NM_028528)	8	NM_028528	73388	Mm.71904	NM_028528	ENSMUSG00000027482	Bpifa3	1700058C13Rik|Splunc3	BPI fold containing family A, member 3	protein-coding
mm_101930.1	chr11	50203018	50203039	-	1	NA	exon (NM_011018, exon 6 of 8)	exon (NM_011018, exon 6 of 8)	7792	NM_001290769	18412	Mm.40828	NM_011018	ENSMUSG00000015837	Sqstm1	A170|OSF-6|Osi|STAP|STONE14|p62	sequestosome 1	protein-coding
mm_105043.1	chr11	100613335	100613368	-	1	NA	intron (NM_019795, intron 1 of 13)	intron (NM_019795, intron 1 of 13)	6817	NM_019795	56354	Mm.402409	NM_019795	ENSMUSG00000014195	Dnajc7	2010003F24Rik|2010004G07Rik|CCRP|Ttc2|mDj11|mTpr2	DnaJ heat shock protein family (Hsp40) member C7	protein-coding
mm_87614.1	chr10	57786283	57786305	+	1	NA	exon (NM_021272, exon 3 of 4)	exon (NM_021272, exon 3 of 4)	1371	NM_021272	12140	Mm.3644	NM_021272	ENSMUSG00000019874	Fabp7	B-FABP|BFABP|Blbp|MRG	fatty acid binding protein 7, brain	protein-coding
mm_123838.1	chr14	70635947	70635969	-	1	NA	promoter-TSS (NM_001252664)	promoter-TSS (NM_001252664)	90	NM_001252664	13829	Mm.210863	NM_013514	ENSMUSG00000022099	Dmtn	AI325486|Epb4.9|Epb49|dematin	dematin actin binding protein	protein-coding
mm_122516.1	chr14	47177876	47177886	-	1	NA	intron (NM_008102, intron 1 of 5)	intron (NM_008102, intron 1 of 5)	11521	NM_008102	14528	Mm.10651	NM_008102	ENSMUSG00000037580	Gch1	GTP-CH|GTPCH|Gch	GTP cyclohydrolase 1	protein-coding
mm_139820.1	chr17	67697254	67697276	+	1	NA	promoter-TSS (NM_008480)	promoter-TSS (NM_008480)	0	NM_008480	16772	Mm.303386	NM_008480	ENSMUSG00000032796	Lama1	AA408497|Lama	laminin, alpha 1	protein-coding
mm_29535.1	chr3	116662591	116662641	-	1	NA	promoter-TSS (NM_008246)	promoter-TSS (NM_008246)	61	NM_008246	15247	Mm.280077	NM_008246	ENSMUSG00000089911	Mfsd14a	Hiat1	major facilitator superfamily domain containing 14A	protein-coding
mm_117086.1	chr13	59731769	59731773	-	1	NA	promoter-TSS (NM_177711)	promoter-TSS (NM_177711)	-19	NM_177711	238663	Mm.444776	NM_177711	ENSMUSG00000043986	Spata31d1d	4932411G14Rik|Fam75d1d	spermatogenesis associated 31 subfamily D, member 1D	protein-coding
mm_106342.1	chr11	118393256	118393266	-	1	NA	exon (NM_011150, exon 6 of 6)	exon (NM_011150, exon 6 of 6)	8670	NM_011150	19039	Mm.3152	NM_011150	ENSMUSG00000033880	Lgals3bp	90K|CyCAP|MAC-2BP|Ppicap|Tango10b	lectin, galactoside-binding, soluble, 3 binding protein	protein-coding
mm_131008.1	chr15	103562922	103562929	-	1	NA	exon (NM_008134, exon 4 of 4)	exon (NM_008134, exon 4 of 4)	2156	NM_001289587	14663	Mm.219621	NM_008134	ENSMUSG00000022491	Glycam1	MC26|Sgp50|glyCAM-1	glycosylation dependent cell adhesion molecule 1	protein-coding
mm_117392.1	chr13	73677990	73677998	-	1	NA	promoter-TSS (NM_001168646)	promoter-TSS (NM_001168646)	29	NM_001168646	22598	Mm.30370	NM_011730	ENSMUSG00000021612	Slc6a18	B0AT3|D630001K16Rik|Xt2|Xtrp2	solute carrier family 6 (neurotransmitter transporter), member 18	protein-coding
mm_156119.1	chrX	114907576	114907586	+	1	NA	promoter-TSS (NM_001081661)	promoter-TSS (NM_001081661)	-1	NM_001081661	75097	Mm.50414	NM_001081661	ENSMUSG00000047079	Ube2dnl2	4930524E20Rik	ubiquitin-conjugating enzyme E2D N-terminal like 2	protein-coding
mm_88804.1	chr10	80755124	80755132	+	1	NA	promoter-TSS (NM_199322)	promoter-TSS (NM_199322)	-78	NM_199322	208266	Mm.152371	NM_199322	ENSMUSG00000061589	Dot1l	A630076O07|AW907654|Dot1|KMT4|mDot1	DOT1-like, histone H3 methyltransferase (S. cerevisiae)	protein-coding
mm_138915.1	chr17	43604598	43604615	+	1	NA	exon (NM_013737, exon 9 of 12)	exon (NM_013737, exon 9 of 12)	-13097	NR_045444	73504	Mm.9277	NR_045444	ENSMUSG00000090307	1700071M16Rik	-	RIKEN cDNA 1700071M16 gene	ncRNA
mm_76888.1	chr8	105637404	105637497	-	1	NA	intron (NM_181322, intron 1 of 11)	CpG	912	NM_181322	13018	Mm.269474	NM_181322	ENSMUSG00000005698	Ctcf	AW108038	CCCTC-binding factor	protein-coding
mm_88025.1	chr10	67219410	67219422	+	1	NA	exon (NM_001242396, exon 7 of 25)	exon (NM_001242396, exon 7 of 25)	33666	NM_001242396	108829	Mm.23846	NM_207221	ENSMUSG00000037876	Jmjd1c	5430433L24Rik|D630035I23Rik|Jmjdic|TRIP8	jumonji domain containing 1C	protein-coding
mm_61.1	chr1	6591616	6591623	+	1	NA	intron (NM_001244693, intron 2 of 22)	intron (NM_001244693, intron 2 of 22)	104388	NM_001244692	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding
mm_67224.1	chr7	74543669	74543676	-	1	NA	intron (NM_001038643, intron 1 of 10)	ID_B1|SINE|B4	11108	NM_023908	108116	Mm.425467	NM_023908	ENSMUSG00000025790	Slco3a1	5830414C08Rik|Anr1|MJAM|OATP-D|R75096|Slc21a11	solute carrier organic anion transporter family, member 3a1	protein-coding
mm_139127.1	chr17	47505086	47505105	+	1	NA	promoter-TSS (NM_001081636)	promoter-TSS (NM_001081636)	44	NM_001081635	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_120852.1	chr14	75222959	75222973	+	1	NA	intron (NM_008879, intron 14 of 16)	intron (NM_008879, intron 14 of 16)	-19321	NM_019775	56373	Mm.24242	NM_019775	ENSMUSG00000021999	Cpb2	1110032P04Rik|4930405E17Rik|AI255929|CPR|Cpu|TAFI	carboxypeptidase B2 (plasma)	protein-coding
mm_103335.1	chr11	74590188	74590215	-	1	NA	promoter-TSS (NM_001015046)	promoter-TSS (NM_001015046)	-43	NM_001015046	380711	Mm.425690	NM_001015046	ENSMUSG00000038807	Rap1gap2	AU067654|Garnl4|Gm1561|mKIAA1039	RAP1 GTPase activating protein 2	protein-coding
mm_966.1	chr1	58115420	58115433	+	1	NA	intron (NM_023617, intron 2 of 34)	B4|SINE|B4	2290	NM_023617	71724	Mm.20108	NM_023617	ENSMUSG00000064294	Aox3	1200011D03Rik|AI326299|Aoh1|Aoh2	aldehyde oxidase 3	protein-coding
mm_52946.1	chr6	122952702	122952763	+	1	NA	promoter-TSS (NM_153197)	promoter-TSS (NM_153197)	88	NM_153197	73149	Mm.25684	NM_153197	ENSMUSG00000043832	Clec4a3	3110037K17Rik|Dcir3	C-type lectin domain family 4, member a3	protein-coding
mm_76234.1	chr8	83574732	83574747	-	1	NA	intron (NM_134118, intron 1 of 12)	intron (NM_134118, intron 1 of 12)	7981	NM_025843	66916	Mm.29683	NM_025843	ENSMUSG00000033938	Ndufb7	1110002H15Rik	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 7	protein-coding
mm_60010.1	chr7	30729796	30729806	+	1	NA	promoter-TSS (NM_027215)	promoter-TSS (NM_027215)	-267	NM_027215	69804	Mm.27499	NM_027215	ENSMUSG00000006315	Tmem147	2010004E11Rik|5033425B17Rik|Nifie14	transmembrane protein 147	protein-coding
mm_132876.1	chr16	48630155	48630166	+	1	NA	intron (NM_010816, intron 26 of 26)	intron (NM_010816, intron 26 of 26)	141796	NM_198297	77647	Mm.167298	NM_198297	ENSMUSG00000030775	Trat1	C030046M14Rik|Tcrim|Trim	T cell receptor associated transmembrane adaptor 1	protein-coding
mm_55554.1	chr6	71270715	71270726	-	1	NA	promoter-TSS (NR_106192)	promoter-TSS (NR_106192)	-951	NR_106192	102465900		NR_106192	ENSMUSG00000098623	Mir8112	Gm27739|mmu-mir-8112	microRNA 8112	ncRNA
mm_39118.1	chr4	154944178	154944188	-	1	NA	Intergenic	Intergenic	-16106	NM_178931	230979	Mm.215147	NM_178931	ENSMUSG00000042333	Tnfrsf14	Atar|HveA|Hvem|Tnfrs14	tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)	protein-coding
mm_68351.1	chr7	106509507	106509514	-	1	NA	Intergenic	Intergenic	-68437	NR_003967	209380	Mm.461779	NM_001001318		Gm4759	EG209380	GTPase, very large interferon inducible 1 pseudogene	pseudo
mm_133746.1	chr16	94085227	94085250	+	1	NA	promoter-TSS (NM_011377)	promoter-TSS (NM_011377)	-22	NM_011377	20465	Mm.4775	NM_011377	ENSMUSG00000062713	Sim2	bHLHe15	single-minded homolog 2 (Drosophila)	protein-coding
mm_122514.1	chr14	47177305	47177337	-	1	NA	intron (NM_008102, intron 1 of 5)	intron (NM_008102, intron 1 of 5)	12081	NM_008102	14528	Mm.10651	NM_008102	ENSMUSG00000037580	Gch1	GTP-CH|GTPCH|Gch	GTP cyclohydrolase 1	protein-coding
mm_96890.1	chr11	70436656	70436694	+	1	NA	exon (NM_001271358, exon 5 of 15)	exon (NM_001271358, exon 5 of 15)	-1580	NR_106064	102465670		NR_106064	ENSMUSG00000099109	Mir7115	Gm27902|mmu-mir-7115	microRNA 7115	ncRNA
mm_167444.1	chr8	121796251	121796260	-	1	NA	TTS (NM_145605)	TTS (NM_145605)	33314	NM_145605	234825	Mm.209329	NM_145605	ENSMUSG00000040263	Klhdc4	AA408426|AV352552|BC012312|G430025P05Rik	kelch domain containing 4	protein-coding
mm_48875.1	chr5	150665418	150665444	-	1	NA	intron (NM_201369, intron 1 of 5)	CpG	181	NM_201369	381695	Mm.246934	NM_201369	ENSMUSG00000029655	N4bp2l2	2700092H06Rik|zag1	NEDD4 binding protein 2-like 2	protein-coding
mm_80976.1	chr9	103181452	103181469	+	1	NA	3' UTR (NM_173781, exon 8 of 8)	3' UTR (NM_173781, exon 8 of 8)	20605	NM_009275	20818	Mm.273053	NM_009275	ENSMUSG00000032553	Srprb	AA409543	signal recognition particle receptor, B subunit	protein-coding
mm_122240.1	chr14	33371272	33371272	-	1	NA	Intergenic	Intergenic	39752	NM_001310452	26419	Mm.21495	NM_016700	ENSMUSG00000021936	Mapk8	AI849689|JNK|JNK1|Prkm8|SAPK1	mitogen-activated protein kinase 8	protein-coding
mm_167304.1	chr8	57801293	57801302	-	1	NA	intron (NM_175032, intron 10 of 11)	intron (NM_175032, intron 10 of 11)	-148242	NM_144731	108150	Mm.62886	NM_144731	ENSMUSG00000031608	Galnt7	AI225872	UDP-N-acetyl-alpha-D-galactosamine: polypeptide N-acetylgalactosaminyltransferase 7	protein-coding
mm_129866.1	chr15	83367268	83367287	-	1	NA	promoter-TSS (NR_027980)	promoter-TSS (NR_027980)	20	NR_027980	69291	Mm.66794	NM_001033147		1700001L05Rik	-	RIKEN cDNA 1700001L05 gene	ncRNA
mm_90796.1	chr10	7212198	7212220	-	1	NA	promoter-TSS (NM_172546)	promoter-TSS (NM_172546)	28	NM_172546	215748	Mm.37984	NM_172546	ENSMUSG00000015202	Cnksr3	6820402C05|BC024086|Magi1	Cnksr family member 3	protein-coding
mm_162568.1	chr1	172894906	172894912	-	1	NA	5' UTR (NM_011318, exon 1 of 2)	5' UTR (NM_011318, exon 1 of 2)	145	NM_011318	20219	Mm.330510	NM_011318	ENSMUSG00000026542	Apcs	Sap	serum amyloid P-component	protein-coding
mm_117619.1	chr13	91807659	91807708	-	1	NA	promoter-TSS (NM_145453)	promoter-TSS (NM_145453)	13	NM_145453	69085	Mm.52356	NM_145453	ENSMUSG00000021621	Zcchc9	1810019C21Rik	zinc finger, CCHC domain containing 9	protein-coding
mm_155490.1	chrX	73716787	73716799	+	1	NA	promoter-TSS (NM_012060)	promoter-TSS (NM_012060)	196	NM_007435	11666	Mm.365	NM_007435	ENSMUSG00000031378	Abcd1	ALDP|Ald|Aldgh	ATP-binding cassette, sub-family D (ALD), member 1	protein-coding
mm_48512.1	chr5	142822349	142822388	-	1	NA	Intergenic	Intergenic	-4981	NM_001122730	231861	Mm.354649	NM_178242	ENSMUSG00000039477	Tnrc18	BC025631|EG381742|Zfp469	trinucleotide repeat containing 18	protein-coding
mm_130669.1	chr15	100674603	100674618	-	1	NA	3' UTR (NM_033612, exon 8 of 8)	3' UTR (NM_033612, exon 8 of 8)	-5110	NM_001270537	668218	Mm.451225	NM_001270537	ENSMUSG00000098112	Bin2	-	bridging integrator 2	protein-coding
mm_120615.1	chr14	70289531	70289585	+	1	NA	promoter-TSS (NM_001304992)	promoter-TSS (NM_001304992)	-61	NM_001304992	19057	Mm.439683	NM_008915	ENSMUSG00000022092	Ppp3cc	Calnc|PP2BA gamma	protein phosphatase 3, catalytic subunit, gamma isoform	protein-coding
mm_142137.1	chr17	35963663	35963677	-	1	NA	exon (NM_013854, exon 6 of 23)	exon (NM_013854, exon 6 of 23)	-2856	NR_030608	100124459		NR_030608	ENSMUSG00000077931	Mir877	Mirn877|mir-877|mmu-mir-877	microRNA 877	ncRNA
mm_157604.1	chrX	53643718	53643769	-	1	NA	promoter-TSS (NM_024170)	promoter-TSS (NM_024170)	20	NM_024170	66158	Mm.391252	NM_024170	ENSMUSG00000067925	Cxx1a	1110012O05Rik|Mar8.2A/B|Mart8b	CAAX box 1A	protein-coding
mm_25556.1	chr3	116008405	116008415	+	1	NA	5' UTR (NM_001163514, exon 1 of 5)	5' UTR (NM_001163514, exon 1 of 5)	113	NM_001163514	58193	Mm.41739	NM_021388	ENSMUSG00000027963	Extl2	3000001D04Rik|AW146439	exostoses (multiple)-like 2	protein-coding
mm_40159.1	chr5	35588044	35588044	+	1	NA	intron (NR_045807, intron 2 of 3)	intron (NR_045807, intron 2 of 3)	719	NR_045807	74364	Mm.473123	NM_175208	ENSMUSG00000055061	4931431C16Rik	-	RIKEN cDNA 4931431C16 gene	ncRNA
mm_138464.1	chr17	35170988	35170997	+	1	NA	TTS (NM_019467)	TTS (NM_019467)	5009	NM_019467	11629	Mm.10747	NM_019467	ENSMUSG00000024397	Aif1	AI607846|AIF-1|D17H6S50E|G1|Iba1	allograft inflammatory factor 1	protein-coding
mm_76151.1	chr8	82353496	82353531	-	1	NA	intron (NM_008357, intron 2 of 7)	intron (NM_008357, intron 2 of 7)	49073	NM_001254747	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_72368.1	chr8	80948949	80948966	+	1	NA	Intergenic	Intergenic	65949	NM_027554	74841	Mm.246018	NM_027554	ENSMUSG00000038250	Usp38	4631402N15Rik|4833420O05Rik|AA536967|AU044701|AW544820|mKIAA1891	ubiquitin specific peptidase 38	protein-coding
mm_160713.1	chr10	60820553	60820553	-	1	NA	intron (NM_029770, intron 1 of 16)	intron (NM_029770, intron 1 of 16)	11028	NM_029770	107449	Mm.290433	NM_029770	ENSMUSG00000020099	Unc5b	6330415E02Rik|A630020F16|D10Bwg0792e|Unc5h2	unc-5 netrin receptor B	protein-coding
mm_154204.1	chr19	59041954	59041970	-	1	NA	intron (NM_175172, intron 3 of 14)	intron (NM_175172, intron 3 of 14)	34107	NM_175172	71653	Mm.37338	NM_175172	ENSMUSG00000041362	Shtn1	4930506M07Rik|Kiaa1598|Shootin1|mKIAA1598	shootin 1	protein-coding
mm_58727.1	chr7	13027898	13027910	+	1	NA	exon (NM_011588, exon 5 of 17)	exon (NM_011588, exon 5 of 17)	3752	NM_011588	21849	Mm.15701	NM_011588	ENSMUSG00000005566	Trim28	AA408787|KAP-1|KRIP-1|MommeD9|Tif1b|Tif1beta	tripartite motif-containing 28	protein-coding
mm_22575.1	chr3	10351512	10351552	+	1	NA	promoter-TSS (NM_001331013)	promoter-TSS (NM_001331013)	-215	NM_001331014	66361	Mm.371617	NM_025512	ENSMUSG00000039795	Zfand1	2310008M20Rik|AW048890	zinc finger, AN1-type domain 1	protein-coding
mm_18020.1	chr2	38613675	38613685	-	1	NA	intron (NM_011187, intron 5 of 7)	intron (NM_011187, intron 5 of 7)	30226	NM_011187	19177	Mm.389251	NM_011187	ENSMUSG00000026750	Psmb7	AU020723|MC14	proteasome (prosome, macropain) subunit, beta type 7	protein-coding
mm_83031.1	chr9	37255445	37255461	-	1	NA	5' UTR (NM_001145960, exon 1 of 19)	5' UTR (NM_001145960, exon 1 of 19)	285	NM_020258	56857	Mm.440037	NM_020258	ENSMUSG00000032122	Slc37a2	G3PP|Slc37a1|cI-2|ci2	solute carrier family 37 (glycerol-3-phosphate transporter), member 2	protein-coding
mm_6901.1	chr1	84786127	84786135	-	1	NA	exon (NM_133975, exon 4 of 41)	exon (NM_133975, exon 4 of 41)	53173	NM_133975	14897	Mm.209265	NM_133975	ENSMUSG00000026219	Trip12	1110036I07Rik|6720416K24Rik|AA410158|Gtl6|TRIP-12	thyroid hormone receptor interactor 12	protein-coding
mm_170147.1	chr17	45450683	45450693	+	1	NA	intron (NM_027649, intron 6 of 7)	B1_Mus1|SINE|Alu	16857	NR_130961	105246278	Mm.206588	NR_130960	ENSMUSG00000097119	B230354K17Rik	-	RIKEN cDNA B230354K17 gene	ncRNA
mm_2754.1	chr1	129273437	129273470	+	1	NA	5' UTR (NM_172485, exon 1 of 28)	5' UTR (NM_172485, exon 1 of 28)	149	NM_172485	210417	Mm.380518	NM_172485	ENSMUSG00000042581	Thsd7b	1700074E13Rik|B930082A18|D130067I03Rik	thrombospondin, type I, domain containing 7B	protein-coding
mm_140901.1	chr17	24141543	24141591	-	1	NA	promoter-TSS (NM_011062)	promoter-TSS (NM_011062)	27	NM_011062	18607	Mm.10504	NM_011062	ENSMUSG00000024122	Pdpk1	Pdk1	3-phosphoinositide dependent protein kinase 1	protein-coding
mm_126890.1	chr15	89497984	89497994	+	1	NA	Intergenic	Intergenic	-1868	NM_021423	58234	Mm.146855	NM_021423	ENSMUSG00000022623	Shank3	AI841104|SHANK3c-3|SHANK3c-4|Shank3b	SH3/ankyrin domain gene 3	protein-coding
mm_63942.1	chr7	139834203	139834218	+	1	NA	promoter-TSS (NM_177469)	promoter-TSS (NM_177469)	36	NM_177469	52389	Mm.39863	NM_177469	ENSMUSG00000025475	Adgra1	2900059M17Rik|D7Ertd680e|Gpr123	adhesion G protein-coupled receptor A1	protein-coding
mm_139566.1	chr17	56990399	56990410	+	1	NA	exon (NM_017393, exon 1 of 6)	exon (NM_017393, exon 1 of 6)	140	NM_017393	53895	Mm.287892	NM_017393	ENSMUSG00000002660	Clpp	AU019820|D17Wsu160e	caseinolytic mitochondrial matrix peptidase proteolytic subunit	protein-coding
mm_101865.1	chr11	48872350	48872358	-	1	NA	Intergenic	Intergenic	-1008	NM_008326	15944	Mm.29938	NM_008326	ENSMUSG00000046879	Irgm1	Ifggd3|Ifi1|Iigp3|Iipg3|Irgm|LRG-47	immunity-related GTPase family M member 1	protein-coding
mm_130364.1	chr15	97791325	97791354	-	1	NA	3' UTR (NM_026353, exon 3 of 3)	3' UTR (NM_026353, exon 3 of 3)	6974	NM_026353	67739	Mm.28955	NM_026353	ENSMUSG00000081534	Slc48a1	4930570C03Rik	solute carrier family 48 (heme transporter), member 1	protein-coding
mm_149302.1	chr19	10712956	10712968	+	1	NA	exon (NM_181403, exon 5 of 5)	exon (NM_181403, exon 5 of 5)	24147	NM_181403	107305	Mm.19091	NM_181403	ENSMUSG00000048832	Vps37c	5730409F24Rik|AU042646	vacuolar protein sorting 37C	protein-coding
mm_98190.1	chr11	87794020	87794032	+	1	NA	5' UTR (NM_010824, exon 1 of 14)	5' UTR (NM_010824, exon 1 of 14)	242	NM_010824	17523	Mm.4668	NM_010824	ENSMUSG00000009350	Mpo	mKIAA4033	myeloperoxidase	protein-coding
mm_73659.1	chr8	111033862	111033886	+	1	NA	promoter-TSS (NM_146217)	promoter-TSS (NM_146217)	32	NM_146217	234734	Mm.24174	NM_146217	ENSMUSG00000031960	Aars	AI316495|C76919|sti	alanyl-tRNA synthetase	protein-coding
mm_5264.1	chr1	17082459	17082462	-	1	NA	intron (NM_020604, intron 2 of 4)	B1_Mur2|SINE|Alu	15429	NM_020604	57339	Mm.143761	NM_020604	ENSMUSG00000042686	Jph1	ENSMUSG00000054314|JP-1|Jp1	junctophilin 1	protein-coding
mm_151176.1	chr19	53310859	53310871	+	1	NA	exon (NM_001008542, exon 1 of 6)	exon (NM_001008542, exon 1 of 6)	359	NM_001008542	17859	Mm.2154	NM_010847	ENSMUSG00000025025	Mxi1	ENSMUSG00000067085|Gm10197|Mad2|bHLHc11	MAX interactor 1, dimerization protein	protein-coding
mm_579.1	chr1	39352445	39352445	+	1	NA	intron (NM_008719, intron 19 of 20)	L1M4b|LINE|L1	-15406	NM_053257	114641	Mm.379302	NM_053257	ENSMUSG00000073702	Rpl31	Dts	ribosomal protein L31	protein-coding
mm_44481.1	chr5	23435254	23435264	-	1	NA	promoter-TSS (NR_040469)	promoter-TSS (NR_040469)	830	NM_026984	69188	Mm.205190	NM_026984	ENSMUSG00000029004	Kmt2e	1810033J14Rik|9530077A04Rik|D230038D11Rik|Mll5|NKp44L	lysine (K)-specific methyltransferase 2E	protein-coding
mm_68585.1	chr7	116033607	116033624	-	1	NA	intron (NM_001025559, intron 1 of 15)	intron (NM_001025559, intron 1 of 15)	-2568	NM_001025560	20679	Mm.323365	NM_011445	ENSMUSG00000051910	Sox6	AI987981|SOX-LZ	SRY (sex determining region Y)-box 6	protein-coding
mm_94028.1	chr10	127751708	127751737	-	1	NA	promoter-TSS (NM_007412)	promoter-TSS (NM_007412)	76	NM_007412	11536	Mm.2857	NM_007412	ENSMUSG00000058396	Gpr182	AM-R|Admr|G10-D|Gpcr17|Gpcr22|MB10|NOW	G protein-coupled receptor 182	protein-coding
mm_74572.1	chr8	11199736	11199776	-	1	NA	non-coding (NR_133670, exon 53 of 53)	non-coding (NR_133670, exon 53 of 53)	-113049	NM_009932	12827	Mm.181021	NM_009932	ENSMUSG00000031503	Col4a2	Col4a-2	collagen, type IV, alpha 2	protein-coding
mm_22941.1	chr3	31954753	31954784	+	1	NA	intron (NM_028231, intron 2 of 5)	intron (NM_028231, intron 2 of 5)	52065	NM_028231	72413	Mm.64790	NM_028231	ENSMUSG00000037610	Kcnmb2	2700049B16Rik|3110031N04Rik	potassium large conductance calcium-activated channel, subfamily M, beta member 2	protein-coding
mm_39972.1	chr5	32232681	32232729	+	1	NA	promoter-TSS (NM_030072)	promoter-TSS (NM_030072)	-3	NM_030072	665270	Mm.160067	NM_030072	ENSMUSG00000029134	Plb1	4632413E21Rik|4930433E17Rik|4930539A06Rik|BC033606	phospholipase B1	protein-coding
mm_135768.1	chr16	56795824	56795899	-	1	NA	promoter-TSS (NM_172825)	promoter-TSS (NM_172825)	-3	NM_172825	239853	Mm.258979	NM_172825	ENSMUSG00000022755	Adgrg7	9130020O16Rik|Gpr128	adhesion G protein-coupled receptor G7	protein-coding
mm_59815.1	chr7	29172340	29172346	+	1	NA	exon (NM_182694, exon 2 of 3)	exon (NM_182694, exon 2 of 3)	1953	NM_182696	243897	Mm.389886	NM_182694	ENSMUSG00000031493	Ggn	AI593290	gametogenetin	protein-coding
mm_48128.1	chr5	137149851	137149857	-	1	NA	Intergenic	Intergenic	-33647	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_167290.1	chr8	45409927	45409935	-	1	NA	5' UTR (NM_126166, exon 2 of 7)	5' UTR (NM_126166, exon 2 of 7)	608	NM_126166	142980	Mm.33874	NM_126166	ENSMUSG00000031639	Tlr3	AI957183	toll-like receptor 3	protein-coding
mm_55891.1	chr6	83536241	83536270	-	1	NA	promoter-TSS (NM_009610)	promoter-TSS (NM_009610)	-4	NM_009610	11468	Mm.292865	NM_009610	ENSMUSG00000059430	Actg2	ACTA3|Act-4|Act4|SMGA	actin, gamma 2, smooth muscle, enteric	protein-coding
mm_109470.1	chr12	111420485	111420537	+	1	NA	intron (NM_001289487, intron 2 of 13)	intron (NM_001289487, intron 2 of 13)	3066	NM_001289488	74190	Mm.248640	NM_028807	ENSMUSG00000021280	Exoc3l4	1200009I06Rik|1600013K19Rik	exocyst complex component 3-like 4	protein-coding
mm_94740.1	chr11	21092941	21092971	+	1	NA	intron (NM_023324, intron 1 of 6)	intron (NM_023324, intron 1 of 6)	1632	NM_023324	67245	Mm.28957	NM_023324	ENSMUSG00000020134	Peli1	2810468L03Rik|A930031K15Rik|AA409794|AI586297|D11Ertd676e	pellino 1	protein-coding
mm_142739.1	chr17	48408986	48408996	-	1	NA	intron (NM_001110832, intron 1 of 9)	intron (NM_001110832, intron 1 of 9)	829	NM_001110832	18044	Mm.4929	NM_010913	ENSMUSG00000023994	Nfya	AA407810|Cbf-b|SEZ-10|SEZ10	nuclear transcription factor-Y alpha	protein-coding
mm_140167.1	chr17	80307302	80307306	+	1	NA	promoter-TSS (NM_001145452)	promoter-TSS (NM_001145452)	-103	NM_001145452	381112	Mm.360004	NM_001145452	ENSMUSG00000054901	Arhgef33	Gm941	Rho guanine nucleotide exchange factor (GEF) 33	protein-coding
mm_79919.1	chr9	65579221	65579231	+	1	NA	intron (NM_153119, intron 1 of 5)	intron (NM_153119, intron 1 of 5)	861	NM_153119	102595	Mm.247303	NM_153119	ENSMUSG00000050721	Plekho2	AI840980|Plekhq1	pleckstrin homology domain containing, family O member 2	protein-coding
mm_109823.1	chr12	3862235	3862256	-	1	NA	promoter-TSS (NR_045884)	promoter-TSS (NR_045884)	-1	NR_045884	100038522	Mm.417270	NR_045884	ENSMUSG00000073242	Dnmt3aos	ENSMUSG00000073242|Gm10485	DNA methyltransferase 3A, opposite strand	ncRNA
mm_94741.1	chr11	21093031	21093033	+	1	NA	intron (NM_023324, intron 1 of 6)	intron (NM_023324, intron 1 of 6)	1708	NM_023324	67245	Mm.28957	NM_023324	ENSMUSG00000020134	Peli1	2810468L03Rik|A930031K15Rik|AA409794|AI586297|D11Ertd676e	pellino 1	protein-coding
mm_167716.1	chr9	98425084	98425104	+	1	NA	intron (NM_011254, intron 1 of 3)	CpG	2133	NM_011254	19659	Mm.279741	NM_011254	ENSMUSG00000046402	Rbp1	CRBPI|Crbp|Rbp-1	retinol binding protein 1, cellular	protein-coding
mm_62490.1	chr7	101921310	101921320	+	1	NA	promoter-TSS (NM_001162974)	promoter-TSS (NM_001162974)	-541	NM_001162974	69358	Mm.214841	NM_027053	ENSMUSG00000064307	Lrrc51	1700008D07Rik|Lrtomt	leucine rich repeat containing 51	protein-coding
mm_92247.1	chr10	70367852	70367862	-	1	NA	Intergenic	Intergenic	-72811	NM_001143777	71721	Mm.477813	NM_024244	ENSMUSG00000043259	Fam13c	1200015N20Rik|C030038O19Rik|mKIAA1796	family with sequence similarity 13, member C	protein-coding
mm_141576.1	chr17	32350536	32350568	-	1	NA	promoter-TSS (NM_017476)	promoter-TSS (NM_017476)	25	NM_017476	54194	Mm.281005	NM_017476	ENSMUSG00000002625	Akap8l	HAP95|Nakap95	A kinase (PRKA) anchor protein 8-like	protein-coding
mm_155460.1	chrX	73503154	73503170	+	1	NA	promoter-TSS (NM_177236)	promoter-TSS (NM_177236)	76	NM_177236	320707	Mm.210095	NM_177236	ENSMUSG00000031376	Atp2b3	6430519O13Rik|Pmca3	ATPase, Ca++ transporting, plasma membrane 3	protein-coding
mm_98280.1	chr11	89029393	89029431	+	1	NA	Intergenic	LTR75|LTR|ERVL	30009	NM_009546	217069	Mm.248445	NM_009546	ENSMUSG00000000275	Trim25	AA960166|AL022677|EFP|Zfp147	tripartite motif-containing 25	protein-coding
mm_61062.1	chr7	49975229	49975340	+	1	NA	promoter-TSS (NM_001037906)	promoter-TSS (NM_001037906)	-66	NM_001037906	338352	Mm.383528	NM_001037906	ENSMUSG00000055409	Nell1	B230343H07Rik|l7R6	NEL-like 1	protein-coding
mm_61201.1	chr7	64001874	64001887	+	1	NA	Intergenic	Intergenic	-62965	NM_021366	50794	Mm.240473	NM_021366	ENSMUSG00000052040	Klf13	0610043C13Rik|9430029L20Rik|Bteb3|FKLF-2|FKLF2|NSLP1|RFLAT-1|RFLAT1	Kruppel-like factor 13	protein-coding
mm_159622.1	chr4	135385653	135385653	-	1	NA	promoter-TSS (NM_001243305)	promoter-TSS (NM_001243305)	19	NM_001168498	230822	Mm.35548	NM_145555	ENSMUSG00000043924	Ncmap	A330049M08Rik|AA545175|Mp11	noncompact myelin associated protein	protein-coding
mm_67592.1	chr7	83661079	83661090	-	1	NA	exon (NM_010551, exon 12 of 19)	exon (NM_010551, exon 12 of 19)	29067	NM_023377	170460	Mm.357953	NM_023377	ENSMUSG00000046027	Stard5	2310058G22Rik|AI607880|D7Ertd152e	StAR-related lipid transfer (START) domain containing 5	protein-coding
mm_129815.1	chr15	82999055	82999088	-	1	NA	3' UTR (NM_028728, exon 6 of 6)	3' UTR (NM_028728, exon 6 of 6)	24067	NM_028728	74039	Mm.32584	NM_028728	ENSMUSG00000058099	Nfam1	4921501M20Rik|Cnaip	Nfat activating molecule with ITAM motif 1	protein-coding
mm_20952.1	chr2	151729928	151729966	-	1	NA	intron (NM_001305244, intron 1 of 4)	intron (NM_001305244, intron 1 of 4)	11363	NM_212446	228769	Mm.146984	NM_144889	ENSMUSG00000032869	Psmf1	AW048666|BC012260|PI31	proteasome (prosome, macropain) inhibitor subunit 1	protein-coding
mm_90576.1	chr10	128247267	128247332	+	1	NA	intron (NM_011589, intron 16 of 28)	intron (NM_011589, intron 16 of 28)	-6832	NM_133996	28194	Mm.439846	NM_133996	ENSMUSG00000051716	Apon	AI195275|D10Ucla2	apolipoprotein N	protein-coding
mm_27812.1	chr3	78594438	78594449	-	1	NA	Intergenic	Intergenic	550444	NM_001310536	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_135113.1	chr16	35771371	35771374	-	1	NA	intron (NM_175111, intron 1 of 7)	RMER17C|LTR|ERVK	986	NM_175111	66667	Mm.45272	NM_175111	ENSMUSG00000022849	Hspbap1	3830421G21Rik	Hspb associated protein 1	protein-coding
mm_129445.1	chr15	78544667	78544686	-	1	NA	promoter-TSS (NM_009218)	promoter-TSS (NM_009218)	-331	NM_009218	20607	Mm.211411	NM_009218	ENSMUSG00000044933	Sstr3	Smstr-3|Smstr3|sst3	somatostatin receptor 3	protein-coding
mm_140772.1	chr17	17838203	17838208	-	1	NA	exon (NM_001162909, exon 7 of 9)	exon (NM_001162909, exon 7 of 9)	7230	NM_001162909	75202	Mm.227456	NM_029205	ENSMUSG00000080316	Spaca6	4930546H06Rik|9530079D04Rik|B230206P06Rik|Ncrna00085|SPACA6A|let-7e|mir-125a|mir-99b	sperm acrosome associated 6	protein-coding
mm_114874.1	chr13	94130772	94130780	+	1	NA	intron (NM_172589, intron 2 of 3)	intron (NM_172589, intron 2 of 3)	72980	NM_172589	218454	Mm.316553	NM_172589	ENSMUSG00000045312	Lhfpl2	6030465B15|AI447312|AW050335|mKIAA0206|vgim	lipoma HMGIC fusion partner-like 2	protein-coding
mm_152006.1	chr19	5919849	5919851	-	1	NA	intron (NM_026772, intron 1 of 1)	PB1D9|SINE|Alu	4966	NM_026772	104252	Mm.491103	NM_026772	ENSMUSG00000045664	Cdc42ep2	1110008C05Rik|Borg1|Cep2|D19Bwg1013e	CDC42 effector protein (Rho GTPase binding) 2	protein-coding
mm_169793.1	chr16	15452219	15452237	+	1	NA	Intergenic	Intergenic	142290	NM_001159351	70620	Mm.235407	NM_023585	ENSMUSG00000022674	Ube2v2	1110021H13Rik|4632410D19Rik|5730524P06Rik|6820402M05|AI848315|C81524|MMS2	ubiquitin-conjugating enzyme E2 variant 2	protein-coding
mm_6522.1	chr1	74505788	74505844	-	1	NA	promoter-TSS (NM_001310662)	promoter-TSS (NM_001310662)	5	NM_001310662	319651	Mm.66568	NM_176972	ENSMUSG00000033364	Usp37	4932415L06Rik|C330008N13Rik	ubiquitin specific peptidase 37	protein-coding
mm_74962.1	chr8	26158025	26158058	-	1	NA	promoter-TSS (NM_199042)	promoter-TSS (NM_199042)	-128	NM_199042	73754	Mm.383241	NM_199042	ENSMUSG00000037214	Thap1	4833431A01Rik|AW490810	THAP domain containing, apoptosis associated protein 1	protein-coding
mm_130922.1	chr15	102722062	102722114	-	1	NA	promoter-TSS (NM_026192)	promoter-TSS (NM_026192)	90	NM_026192	67488	Mm.71682	NM_026192	ENSMUSG00000023055	Calcoco1	1810009B06Rik|Cocoa|Gcap11|mKIAA1536	calcium binding and coiled coil domain 1	protein-coding
mm_141084.1	chr17	25941883	25941889	-	1	NA	TTS (NM_001039038)	TTS (NM_001039038)	103	NM_001291025	14755	Mm.362054	NM_011822	ENSMUSG00000025728	Pigq	Gpi1|Gpi1h|Gpi1p|Gpih	phosphatidylinositol glycan anchor biosynthesis, class Q	protein-coding
mm_158044.1	chrX	98890620	98890638	-	1	NA	5' UTR (NM_052976, exon 1 of 25)	5' UTR (NM_052976, exon 1 of 25)	396	NM_052976	94190	Mm.33536	NM_052976	ENSMUSG00000031214	Ophn1	C130037N19Rik|Wtgr	oligophrenin 1	protein-coding
mm_171289.1	chr3	90079856	90079859	+	1	NA	exon (NM_001253740, exon 1 of 8)	exon (NM_001253740, exon 1 of 8)	336	NM_001293749	59069	Mm.240839	NM_022314	ENSMUSG00000027940	Tpm3	TM30nm|TMnm|Tm5NM|Tpm-5|Tpm5|Trop-5|gamma-TM|hTM30nm|hTMnm	tropomyosin 3, gamma	protein-coding
mm_168934.1	chr12	6770942	6770947	+	1	NA	Intergenic	Intergenic	609386	NR_045045	73575	Mm.179463	NR_045045	ENSMUSG00000102096	1700101O22Rik	-	RIKEN cDNA 1700101O22 gene	ncRNA
mm_80074.1	chr9	69767619	69767637	+	1	NA	intron (NR_040765, intron 1 of 4)	intron (NR_040765, intron 1 of 4)	6482	NR_040765	319970	Mm.186434	NR_040765	ENSMUSG00000097623	B230323A14Rik	-	RIKEN cDNA B230323A14 gene	ncRNA
mm_16041.1	chr2	167693455	167693461	+	1	NA	intron (NR_015500, intron 1 of 1)	intron (NR_015500, intron 1 of 1)	2281	NR_015500	329562	Mm.123101	NM_177851	ENSMUSG00000006462	A530013C23Rik	-	RIKEN cDNA A530013C23 gene	ncRNA
mm_124751.1	chr15	6633672	6633685	+	1	NA	intron (NM_011815, intron 5 of 17)	ORR1B1|LTR|ERVL-MaLR	53831	NM_011815	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_118427.1	chr14	7951193	7951222	+	1	NA	3' UTR (NM_001081427, exon 46 of 46)	3' UTR (NM_001081427, exon 46 of 46)	42975	NM_007870	13421	Mm.272258	NM_007870	ENSMUSG00000025279	Dnase1l3	DNasegamma|Dhp2|Lsd	deoxyribonuclease 1-like 3	protein-coding
mm_114323.1	chr13	60602183	60602231	+	1	NA	promoter-TSS (NM_134062)	promoter-TSS (NM_134062)	-4	NM_134062	69635	Mm.24103	NM_029653	ENSMUSG00000021559	Dapk1	D13Ucla1|DAP-Kinase	death associated protein kinase 1	protein-coding
mm_120761.1	chr14	73368346	73368359	+	1	NA	exon (NM_008410, exon 2 of 6)	exon (NM_008410, exon 2 of 6)	16919	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_123103.1	chr14	55882670	55882714	-	1	NA	3' UTR (NM_019820, exon 3 of 3)	3' UTR (NM_019820, exon 3 of 3)	1564	NM_019820	56410	Mm.97163	NM_019820	ENSMUSG00000040380	Cbln3	-	cerebellin 3 precursor protein	protein-coding
mm_90912.1	chr10	12383865	12383868	-	1	NA	3' UTR (NM_011682, exon 74 of 74)	3' UTR (NM_011682, exon 74 of 74)	477869	NM_011682	22288	Mm.331784	NM_011682	ENSMUSG00000019820	Utrn	AA589569|DRP|Dmdl	utrophin	protein-coding
mm_20783.1	chr2	143989095	143989108	-	1	NA	exon (NM_133626, exon 2 of 3)	exon (NM_133626, exon 2 of 3)	22162	NM_133626	81910	Mm.13705	NM_024281	ENSMUSG00000027422	Rrbp1	1700087N07Rik|5730465C04Rik|ES/130|mKIAA1398|mRRp0|mRRp1.8|mRRp10|mRRp15a|mRRp15b|mRRp16.8|mRRp2|mRRp41|mRRp47|mRRp5.4|p180	ribosome binding protein 1	protein-coding
mm_100712.1	chr11	3775134	3775162	-	1	NA	intron (NM_152818, intron 2 of 13)	intron (NM_152818, intron 2 of 13)	-52921	NM_001302630	74309	Mm.61022	NM_152818	ENSMUSG00000020435	Osbp2	1700095P05Rik|C630001G20Rik|Gm244|ORP-4|OSBPL1	oxysterol binding protein 2	protein-coding
mm_141987.1	chr17	35165155	35165160	-	1	NA	promoter-TSS (NM_020027)	promoter-TSS (NM_020027)	-280	NM_020027	53761	Mm.272462	NM_020027	ENSMUSG00000024393	Prrc2a	3110039B05Rik|Bat-2|Bat2|D17H6S51E|G2|Wbp12|mKIAA4178	proline-rich coiled-coil 2A	protein-coding
mm_24020.1	chr3	87526510	87526532	+	1	NA	intron (NM_001286844, intron 1 of 4)	intron (NM_001286844, intron 1 of 4)	943	NM_012051	27049	Mm.219460	NM_012051	ENSMUSG00000003382	Etv3	AI414410|METS|Pe1	ets variant 3	protein-coding
mm_145640.1	chr18	61117544	61117571	+	1	NA	promoter-TSS (NR_105949)	promoter-TSS (NR_105949)	89	NR_105949	102466212		NR_105949	ENSMUSG00000098389	Mir6983	Gm27496|mmu-mir-6983	microRNA 6983	ncRNA
mm_151234.1	chr19	53793292	53793341	+	1	NA	intron (NM_001170847, intron 1 of 13)	intron (NM_001170847, intron 1 of 13)	-98915	NM_011050	18569	Mm.1605	NM_011050	ENSMUSG00000024975	Pdcd4	D19Ucla1|Ma3|Tis	programmed cell death 4	protein-coding
mm_130200.1	chr15	94589833	94589864	-	1	NA	promoter-TSS (NM_008971)	promoter-TSS (NM_008971)	-24	NM_008971	19230	Mm.490250	NM_008971	ENSMUSG00000022451	Twf1	A6|Ptk9|twinfilin	twinfilin actin binding protein 1	protein-coding
mm_19472.1	chr2	92459784	92459797	-	1	NA	promoter-TSS (NM_211358)	promoter-TSS (NM_211358)	4	NM_211358	228368	Mm.273990	NM_145832	ENSMUSG00000049922	Slc35c1	E430007K15Rik|fuct1	solute carrier family 35, member C1	protein-coding
mm_92769.1	chr10	81148421	81148432	-	1	NA	exon (NM_010731, exon 3 of 3)	exon (NM_010731, exon 3 of 3)	12155	NM_010731	16969	Mm.20920	NM_010731	ENSMUSG00000035011	Zbtb7a	9030619K07Rik|9130006G12Rik|AI452336|FBI-1|Lrf|Pokemon|Zbtb7	zinc finger and BTB domain containing 7a	protein-coding
mm_22902.1	chr3	30855947	30856002	+	1	NA	promoter-TSS (NM_027965)	promoter-TSS (NM_027965)	24	NM_001286994	71862	Mm.272019	NM_027965	ENSMUSG00000037661	Gpr160	1700025D19Rik|GPCR150	G protein-coupled receptor 160	protein-coding
mm_21304.1	chr2	157079082	157079121	-	1	NA	5' UTR (NM_001164663, exon 1 of 15)	5' UTR (NM_001164663, exon 1 of 15)	164	NM_001164663	320706	Mm.79466	NM_001164663	ENSMUSG00000055485	Soga1	9830001H06Rik|AI426038|D430036N24Rik|Soga	suppressor of glucose, autophagy associated 1	protein-coding
mm_106783.1	chr12	4712356	4712377	+	1	NA	intron (NM_011365, intron 37 of 38)	intron (NM_011365, intron 37 of 38)	26017	NM_029107	74855	Mm.269534	NM_029107	ENSMUSG00000079177	Fam228a	4930417G10Rik	family with sequence similarity 228, member A	protein-coding
mm_112160.1	chr12	113329702	113329716	-	1	NA	Intergenic	Intergenic	143806	NM_153776	69195	Mm.313244	NM_153776	ENSMUSG00000049036	Tmem121	2410008J05Rik|Hole	transmembrane protein 121	protein-coding
mm_159255.1	chr2	152754990	152754990	+	1	NA	intron (NM_053091, intron 1 of 4)	URR1B|DNA|hAT-Charlie	817	NM_053091	84682	Mm.196668	NM_053091	ENSMUSG00000009876	Cox4i2	Cox4b|CoxIV-2	cytochrome c oxidase subunit IV isoform 2	protein-coding
mm_94068.1	chr10	128401193	128401214	-	1	NA	promoter-TSS (NM_028092)	promoter-TSS (NM_028092)	21	NM_001136237	72002	Mm.22983	NM_028051	ENSMUSG00000039878	Slc39a5	1810013D05Rik|2010205A06Rik|Zip5	solute carrier family 39 (metal ion transporter), member 5	protein-coding
mm_3124.1	chr1	134709260	134709289	+	1	NA	intron (NM_009307, intron 2 of 9)	CpG	62593	NM_009307	20980	Mm.5102	NM_009307	ENSMUSG00000026452	Syt2	IP4BP|R74640|mKIAA4194	synaptotagmin II	protein-coding
mm_68138.1	chr7	102239717	102239725	-	1	NA	exon (NM_019566, exon 2 of 2)	exon (NM_019566, exon 2 of 2)	10397	NM_019566	56212	Mm.259795	NM_019566	ENSMUSG00000073982	Rhog	2810426G09Rik|Arhg|Sid10750	ras homolog family member G	protein-coding
mm_39344.1	chr5	8893857	8893896	+	1	NA	5' UTR (NM_008830, exon 1 of 28)	5' UTR (NM_008830, exon 1 of 28)	155	NM_008830	18670	Mm.297825	NM_008830	ENSMUSG00000042476	Abcb4	Mdr2|Pgy-2|Pgy2|mdr-2	ATP-binding cassette, sub-family B (MDR/TAP), member 4	protein-coding
mm_71539.1	chr8	47220753	47220763	+	1	NA	intron (NM_175162, intron 1 of 4)	intron (NM_175162, intron 1 of 4)	68644	NM_001286376	71069	Mm.23973	NM_175162	ENSMUSG00000038143	Stox2	4933409N07Rik|AI449080|AI835114|mKIAA1392	storkhead box 2	protein-coding
mm_70539.1	chr8	13039359	13039359	+	1	NA	intron (NM_001242368, intron 2 of 8)	MTEa|LTR|ERVL-MaLR	2051	NM_001242368	14058	Mm.262589	NM_007972	ENSMUSG00000031444	F10	Cf10|fX	coagulation factor X	protein-coding
mm_39678.1	chr5	25555927	25555954	+	1	NA	Intergenic	ORR1B2-int|LTR|ERVL-MaLR	25922	NR_027388	73571	Mm.105263	NR_027388	ENSMUSG00000101856	1700096K18Rik	-	RIKEN cDNA 1700096K18 gene	ncRNA
mm_147008.1	chr18	34506742	34506768	-	1	NA	promoter-TSS (NM_146084)	promoter-TSS (NM_146084)	68	NM_146084	225358	Mm.226899	NM_146084	ENSMUSG00000036501	Fam13b	2610024E20Rik|AW060714|AW546153	family with sequence similarity 13, member B	protein-coding
mm_52257.1	chr6	107554437	107554439	+	1	NA	intron (NM_008516, intron 1 of 1)	intron (NM_008516, intron 1 of 1)	24712	NM_008516	16979	Mm.428543	NM_008516	ENSMUSG00000034648	Lrrn1	2810047E21Rik|NLRR-1	leucine rich repeat protein 1, neuronal	protein-coding
mm_146881.1	chr18	25679581	25679589	-	1	NA	intron (NM_001146292, intron 1 of 12)	intron (NM_001146292, intron 1 of 12)	74398	NM_133195	108013	Mm.266435	NM_133195	ENSMUSG00000024268	Celf4	A230070D14Rik|BRUNOL-4|Brul4|Brunol4|C130060B05Rik	CUGBP, Elav-like family member 4	protein-coding
mm_22422.1	chr2	181581997	181582007	-	1	NA	promoter-TSS (NM_026765)	promoter-TSS (NM_026765)	-29	NM_026765	68556	Mm.232400	NM_026765	ENSMUSG00000089917	Uckl1	1110007H10Rik|Urkl1	uridine-cytidine kinase 1-like 1	protein-coding
mm_122047.1	chr14	30056351	30056359	-	1	NA	intron (NM_001302637, intron 41 of 48)	intron (NM_001302637, intron 41 of 48)	33722	NM_175343	218865	Mm.259916	NM_172264	ENSMUSG00000015970	Chdh	AU041472|D630034H06Rik	choline dehydrogenase	protein-coding
mm_115771.1	chr13	19307861	19307891	-	1	NA	Intergenic	Intergenic	87937	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_117100.1	chr13	59823073	59823143	-	1	NA	promoter-TSS (NM_153538)	promoter-TSS (NM_153538)	39	NM_153538	214290	Mm.233082	NM_153538	ENSMUSG00000035248	Zcchc6	6030448M23Rik|AA420405	zinc finger, CCHC domain containing 6	protein-coding
mm_10360.1	chr2	11705321	11705346	+	1	NA	promoter-TSS (NM_001271498)	promoter-TSS (NM_001271498)	40	NM_001271497	16169	Mm.200196	NM_008358	ENSMUSG00000023206	Il15ra	AA690181|IL-15RA	interleukin 15 receptor, alpha chain	protein-coding
mm_3585.1	chr1	151344473	151344530	+	1	NA	promoter-TSS (NM_001039512)	promoter-TSS (NM_001039512)	3	NM_001039511	117198	Mm.33764	NM_028582	ENSMUSG00000023150	Ivns1abp	1190004M08Rik|1700126I16Rik|AA960440|HSPC068|ND1|NS-1|NS1-BP|Nd1-L|Nd1-S|mKIAA0850	influenza virus NS1A binding protein	protein-coding
mm_89327.1	chr10	87932073	87932084	+	1	NA	3' UTR (NM_010512, exon 5 of 5)	3' UTR (NM_010512, exon 5 of 5)	-34593	NR_000040	22172	Mm.391420	NR_000040		Tyms-ps	-	thymidylate synthase, pseudogene	pseudo
mm_133932.1	chr16	3872232	3872249	-	1	NA	5' UTR (NM_001033159, exon 1 of 3)	5' UTR (NM_001033159, exon 1 of 3)	134	NM_001033159	71063	Mm.379190	NM_001033159	ENSMUSG00000039789	Zfp597	4933407K12Rik|AI462383|AI666357	zinc finger protein 597	protein-coding
mm_120460.1	chr14	65970629	65970655	+	1	NA	intron (NM_013492, intron 1 of 8)	intron (NM_013492, intron 1 of 8)	2159	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_19448.1	chr2	91986221	91986242	-	1	NA	exon (NM_011957, exon 10 of 12)	exon (NM_011957, exon 10 of 12)	-22668	NM_138306	104418	Mm.314923	NM_138306	ENSMUSG00000040479	Dgkz	E130307B02Rik|ENSMUSG00000075035|F730209L11Rik|mDGK[z]	diacylglycerol kinase zeta	protein-coding
mm_110888.1	chr12	75549644	75549661	-	1	NA	intron (NM_012024, intron 2 of 13)	intron (NM_012024, intron 2 of 13)	46548	NM_012024	26932	Mm.259626	NM_012024	ENSMUSG00000021051	Ppp2r5e	4633401M22Rik|AI449017|B56beta	protein phosphatase 2, regulatory subunit B', epsilon	protein-coding
mm_91642.1	chr10	42276689	42276743	-	1	NA	promoter-TSS (NM_019740)	promoter-TSS (NM_019740)	26	NM_019740	56484	Mm.338613	NM_019740	ENSMUSG00000048756	Foxo3	1110048B16Rik|2010203A17Rik|C76856|FKHRL1|Fkhr2|Foxo3a	forkhead box O3	protein-coding
mm_23824.1	chr3	81036639	81036738	+	1	NA	5' UTR (NM_019971, exon 1 of 6)	5' UTR (NM_019971, exon 1 of 6)	272	NM_019971	54635	Mm.331089	NM_019971	ENSMUSG00000028019	Pdgfc	1110064L01Rik|AI647969|PDGF-C	platelet-derived growth factor, C polypeptide	protein-coding
mm_71460.1	chr8	46528568	46528626	+	1	NA	exon (NM_007981, exon 15 of 21)	exon (NM_007981, exon 15 of 21)	-23472	NM_027973	71876	Mm.22108	NM_027973	ENSMUSG00000031629	Cenpu	1700029A22Rik|Mlf1ip	centromere protein U	protein-coding
mm_160553.1	chr9	49016682	49016682	+	1	NA	exon (NM_175482, exon 11 of 24)	exon (NM_175482, exon 11 of 24)	31297	NM_175482	235323	Mm.21630	NM_175482	ENSMUSG00000032267	Usp28	9830148O20Rik|AU022237|mKIAA1515	ubiquitin specific peptidase 28	protein-coding
mm_33147.1	chr4	125158286	125158320	+	1	NA	Intergenic	Intergenic	-30422	NM_153159	230738	Mm.402	NM_153159	ENSMUSG00000042677	Zc3h12a	BC036563|MCPIP|MCPIP-1|Mcpip1|Reg1	zinc finger CCCH type containing 12A	protein-coding
mm_59074.1	chr7	19517621	19517631	+	1	NA	Intergenic	MIRc|SINE|MIR	-1105	NM_027116	69547	Mm.77325	NM_027116	ENSMUSG00000060621	Nkpd1	2310015G09Rik	NTPase, KAP family P-loop domain containing 1	protein-coding
mm_41095.1	chr5	87694706	87694719	+	1	NA	exon (NM_001286023, exon 5 of 7)	exon (NM_001286023, exon 5 of 7)	4713	NM_001286020	12991	Mm.268737	NM_009972	ENSMUSG00000063157	Csn2	Csnb	casein beta	protein-coding
mm_77609.1	chr8	123893443	123893453	-	1	NA	exon (NM_009606, exon 3 of 7)	exon (NM_009606, exon 3 of 7)	1327	NM_001272041	11459	Mm.214950	NM_009606	ENSMUSG00000031972	Acta1	AA959943|Acta-2|Acts|Actsk-1	actin, alpha 1, skeletal muscle	protein-coding
mm_18059.1	chr2	39226446	39226456	-	1	NA	promoter-TSS (NM_024209)	promoter-TSS (NM_024209)	-113	NM_024209	67857	Mm.389242	NM_024209	ENSMUSG00000026753	Ppp6c	2310003C10Rik	protein phosphatase 6, catalytic subunit	protein-coding
mm_43031.1	chr5	123930724	123930754	+	1	NA	promoter-TSS (NM_001134767)	promoter-TSS (NM_001134767)	50	NM_001134767	208908	Mm.243679	NM_001134767	ENSMUSG00000061882	Ccdc62	AI661708|Gm150	coiled-coil domain containing 62	protein-coding
mm_83279.1	chr9	43104541	43104545	-	1	NA	intron (NM_027144, intron 1 of 40)	intron (NM_027144, intron 1 of 40)	1175	NM_027144	69632	Mm.275266	NM_027144	ENSMUSG00000059495	Arhgef12	2310014B11Rik|AU019857|Larg|mKIAA0382	Rho guanine nucleotide exchange factor (GEF) 12	protein-coding
mm_1848.1	chr1	83060928	83060933	+	1	NA	promoter-TSS (NM_027778)	promoter-TSS (NM_027778)	0	NM_027778	71386	Mm.389133	NM_027778	ENSMUSG00000101315	Krtap28-13	5530401N06Rik	keratin associated protein 28-13	protein-coding
mm_153018.1	chr19	30681862	30681865	-	1	NA	intron (NM_011160, intron 9 of 17)	intron (NM_011160, intron 9 of 17)	-132367	NM_010051	13380	Mm.214717	NM_010051	ENSMUSG00000024868	Dkk1	mdkk-1	dickkopf WNT signaling pathway inhibitor 1	protein-coding
mm_80839.1	chr9	97275728	97275754	+	1	NA	Intergenic	RLTR44A|LTR|ERVK	94217	NM_030219	78911	Mm.108347	NM_030219	ENSMUSG00000032451	Trim42	4930486B16Rik	tripartite motif-containing 42	protein-coding
mm_103698.1	chr11	79516379	79516412	-	1	NA	exon (NM_001077496, exon 2 of 2)	exon (NM_001077496, exon 2 of 2)	7367	NM_001077496	216984	Mm.439665	NM_001077496	ENSMUSG00000093938	Evi2b	Evi-2|Evi2	ecotropic viral integration site 2b	protein-coding
mm_162874.1	chr10	96617547	96617557	+	1	NA	intron (NM_007569, intron 1 of 1)	CpG	551	NM_007569	12226	Mm.23811	NM_007569	ENSMUSG00000036478	Btg1	AI426953|AW546738	B cell translocation gene 1, anti-proliferative	protein-coding
mm_22969.1	chr3	32708268	32708270	+	1	NA	promoter-TSS (NM_019673)	promoter-TSS (NM_019673)	-277	NM_019673	56456	Mm.41077	NM_019673	ENSMUSG00000027671	Actl6a	2810432C06Rik|AI851094|ARP4|Actl6|Baf53a|C79802	actin-like 6A	protein-coding
mm_98638.1	chr11	96194280	96194287	+	1	NA	promoter-TSS (NM_008267)	promoter-TSS (NM_008267)	-78	NM_008267	15408	Mm.57221	NM_008267	ENSMUSG00000049604	Hoxb13	-	homeobox B13	protein-coding
mm_87344.1	chr10	43518587	43518600	+	1	NA	Intergenic	Intergenic	22401	NM_026411	67851	Mm.209953	NM_026411	ENSMUSG00000019797	1700021F05Rik	-	RIKEN cDNA 1700021F05 gene	protein-coding
mm_105753.1	chr11	109473066	109473079	-	1	NA	promoter-TSS (NM_028710)	promoter-TSS (NM_028710)	157	NM_134038	104681	Mm.265874	NM_134038	ENSMUSG00000041920	Slc16a6	AW743111|ESTM12|MCT 6|MCT 7|MCT6	solute carrier family 16 (monocarboxylic acid transporters), member 6	protein-coding
mm_123474.1	chr14	65974991	65975009	-	1	NA	exon (NM_013492, exon 4 of 9)	exon (NM_013492, exon 4 of 9)	6517	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_31147.1	chr4	43384339	43384350	+	1	NA	intron (NM_001037709, intron 1 of 11)	intron (NM_001037709, intron 1 of 11)	2362	NM_001037709	100213	Mm.235730	NM_199057	ENSMUSG00000035969	Rusc2	AI840675|mKIAA0375	RUN and SH3 domain containing 2	protein-coding
mm_126498.1	chr15	81745058	81745131	+	1	NA	5' UTR (NM_001081016, exon 1 of 23)	5' UTR (NM_001081016, exon 1 of 23)	246	NM_001081016	20286	Mm.432075	NM_001081016	ENSMUSG00000022390	Zc3h7b	Gm627|Scrg3|Zc2h7b|mKIAA1031	zinc finger CCCH type containing 7B	protein-coding
mm_139672.1	chr17	57412328	57412336	+	1	NA	intron (NM_010130, intron 9 of 21)	intron (NM_010130, intron 9 of 21)	53646	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_101828.1	chr11	47379279	47379297	-	1	NA	promoter-TSS (NM_011891)	promoter-TSS (NM_011891)	14	NM_011891	24052	Mm.338890	NM_011891	ENSMUSG00000020354	Sgcd	35kDa|delta-SG	sarcoglycan, delta (dystrophin-associated glycoprotein)	protein-coding
mm_18019.1	chr2	38536292	38536334	-	1	NA	intron (NM_001159631, intron 1 of 9)	intron (NM_001159631, intron 1 of 9)	24437	NM_001159631	59126	Mm.143818	NM_021606	ENSMUSG00000026749	Nek6	1300007C09Rik	NIMA (never in mitosis gene a)-related expressed kinase 6	protein-coding
mm_141718.1	chr17	34031645	34031667	-	1	NA	promoter-TSS (NM_001205216)	promoter-TSS (NM_001205216)	34	NM_001077709	14977	Mm.18556	NM_008202	ENSMUSG00000024327	Slc39a7	AA408174|AI117660|AL024048|H-2Ke4|H2-Ke4|Ke-4|Ke4|Ring5|Zip7	solute carrier family 39 (zinc transporter), member 7	protein-coding
mm_48674.1	chr5	146160539	146160554	-	1	NA	Intergenic	Intergenic	24758	NM_001008547	69282	Mm.373573	NM_001008547	ENSMUSG00000095040	1700001J03Rik	-	RIKEN cDNA 1700001J03 gene	protein-coding
mm_135945.1	chr16	74411508	74411543	-	1	NA	promoter-TSS (NM_175549)	promoter-TSS (NM_175549)	-613	NM_175549	268902	Mm.171736	NM_175549	ENSMUSG00000052516	Robo2	2600013A04Rik|9430089E08Rik|BB097918|D230004I22Rik|mKIAA1568	roundabout guidance receptor 2	protein-coding
mm_140122.1	chr17	79134166	79134166	+	1	NA	Intergenic	RLTR41A2|LTR|ERV1	82260	NM_001316729	70536	Mm.293870	NM_027455	ENSMUSG00000024084	Qpct	5730422A13Rik	glutaminyl-peptide cyclotransferase (glutaminyl cyclase)	protein-coding
mm_11006.1	chr2	26516029	26516039	+	1	NA	Intergenic	ID4|SINE|ID	12107	NR_132655	102639736		NR_132655		Gm35978	-	predicted gene, 35978	ncRNA
mm_74717.1	chr8	17372134	17372143	-	1	NA	intron (NM_053171, intron 1 of 69)	intron (NM_053171, intron 1 of 69)	163247	NM_053171	94109	Mm.436988	NM_053171	ENSMUSG00000060924	Csmd1	B930082H09|mKIAA1890	CUB and Sushi multiple domains 1	protein-coding
mm_91368.1	chr10	29362013	29362029	-	1	NA	5' UTR (NM_001110198, exon 1 of 4)	5' UTR (NM_001110198, exon 1 of 4)	421	NM_026518	68031	Mm.28930	NM_026518	ENSMUSG00000038876	Rnf146	2610509H23Rik|Iduna	ring finger protein 146	protein-coding
mm_146758.1	chr18	16808578	16808608	-	1	NA	5' UTR (NM_007664, exon 1 of 16)	5' UTR (NM_007664, exon 1 of 16)	653	NM_007664	12558	Mm.257437	NM_007664	ENSMUSG00000024304	Cdh2	CDHN|N-CAD|Ncad	cadherin 2	protein-coding
mm_67568.1	chr7	81934278	81934288	-	1	NA	5' UTR (NM_013886, exon 1 of 6)	5' UTR (NM_013886, exon 1 of 6)	176	NM_013886	29877	Mm.392934	NM_013886	ENSMUSG00000025104	Hdgfrp3	2700022B06Rik|HRP-3	hepatoma-derived growth factor, related protein 3	protein-coding
mm_20928.1	chr2	150855829	150855848	-	1	NA	intron (NM_024465, intron 2 of 12)	IMPB_01|Satellite|Satellite	48893	NM_024465	76192	Mm.112632	NM_024465	ENSMUSG00000032046	Abhd12	1500011G07Rik|6330583M11Rik|AI431047|AW547313	abhydrolase domain containing 12	protein-coding
mm_29685.1	chr3	123033008	123033015	-	1	NA	intron (NM_021503, intron 2 of 5)	intron (NM_021503, intron 2 of 5)	1976	NM_021503	59006	Mm.141157	NM_021503	ENSMUSG00000028116	Myoz2	1110012I24Rik|Fatz-2|Myozl2	myozenin 2	protein-coding
mm_49053.1	chr6	5048265	5048274	+	1	NA	intron (NM_181595, intron 3 of 15)	intron (NM_181595, intron 3 of 15)	144949	NM_181595	243725	Mm.332901	NM_181595	ENSMUSG00000032827	Ppp1r9a	2810430P21Rik|4930518N04Rik|5330407E15|A230094E16Rik|BB181831|NRB|mKIAA1222|neurabin-I	protein phosphatase 1, regulatory (inhibitor) subunit 9A	protein-coding
mm_145597.1	chr18	60987935	60987937	+	1	NA	3' UTR (NM_001286809, exon 6 of 6)	3' UTR (NM_001286809, exon 6 of 6)	24382	NM_001286809	12322	Mm.131530	NM_009792	ENSMUSG00000024617	Camk2a	CaMKII|R74975|mKIAA0968	calcium/calmodulin-dependent protein kinase II alpha	protein-coding
mm_169520.1	chr14	8800291	8800299	-	1	NA	Intergenic	Intergenic	133905	NR_045968	74859	Mm.84041	NR_045968	ENSMUSG00000097898	4930455B14Rik	1700027C12Rik	RIKEN cDNA 4930455B14 gene	ncRNA
mm_54513.1	chr6	35511704	35511724	-	1	NA	3' UTR (NM_008098, exon 4 of 4)	3' UTR (NM_008098, exon 4 of 4)	28174	NM_008098	14489	Mm.182746	NM_008098	ENSMUSG00000029840	Mtpn	5033418D15Rik|Gcdp|V1	myotrophin	protein-coding
mm_106496.1	chr11	120348496	120348508	-	1	NA	promoter-TSS (NM_009609)	promoter-TSS (NM_009609)	-7	NM_009609	11465	Mm.196173	NM_009609	ENSMUSG00000062825	Actg1	AL023024|Actg|Actl|E51	actin, gamma, cytoplasmic 1	protein-coding
mm_109698.1	chr12	113155363	113155384	+	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	-1048	NM_134041	104732	Mm.87616	NM_134041	ENSMUSG00000037466	4930427A07Rik	AA536649|mFLJ00116	RIKEN cDNA 4930427A07 gene	protein-coding
mm_65569.1	chr7	27181048	27181137	-	1	NA	promoter-TSS (NM_019394)	promoter-TSS (NM_019394)	57	NM_019394	12587	Mm.262447	NM_019394	ENSMUSG00000089661	Mia	CD-RAP|Cdrap|Mia1	melanoma inhibitory activity	protein-coding
mm_31293.1	chr4	45972338	45972365	+	1	NA	promoter-TSS (NM_146142)	promoter-TSS (NM_146142)	54	NM_146142	100121	Mm.275413	NM_146142	ENSMUSG00000035517	Tdrd7	5730495N10Rik|AI447470|PCTAIRE2BP	tudor domain containing 7	protein-coding
mm_67665.1	chr7	86775940	86775948	-	1	NA	promoter-TSS (NM_001159706)	promoter-TSS (NM_001159706)	-80	NM_001159706	53320	Mm.269137	NM_016770	ENSMUSG00000001773	Folh1	GCP2|mopsm	folate hydrolase 1	protein-coding
mm_76649.1	chr8	93131275	93131291	-	1	NA	promoter-TSS (NM_007954)	promoter-TSS (NM_007954)	0	NM_007954	13884	Mm.88078	NM_007954	ENSMUSG00000057400	Ces1c	Ces-N|Ee-1|Ee1|Es-4|Es-N|Es1|Es4|EsN|PESN	carboxylesterase 1C	protein-coding
mm_131748.1	chr16	22265567	22265586	+	1	NA	intron (NM_001330555, intron 1 of 9)	CpG	429	NM_001330554	20462	Mm.210352	NM_009186	ENSMUSG00000022858	Tra2b	5730405G21Rik|D16Ertd266e|SIG-41|Sfrs10|Silg41|TRA2beta	transformer 2 beta homolog (Drosophila)	protein-coding
mm_44675.1	chr5	29736413	29736428	-	1	NA	promoter-TSS (NR_028426)	promoter-TSS (NR_028426)	-484	NR_028426	332993	Mm.473746	NR_028426		Gm5129	EG332993|ENSMUSG00000053121	predicted gene 5129	ncRNA
mm_72192.1	chr8	72492983	72492993	+	1	NA	promoter-TSS (NM_177766)	promoter-TSS (NM_177766)	-374	NM_177766	270066	Mm.291461	NM_177766	ENSMUSG00000019731	Slc35e1	6030458H05|AA408278	solute carrier family 35, member E1	protein-coding
mm_44022.1	chr5	147418632	147418637	+	1	NA	promoter-TSS (NR_033625)	promoter-TSS (NR_033625)	14	NR_033625	100039805	Mm.394705	NR_033625	ENSMUSG00000106820	D5Ertd605e	Gm2433	DNA segment, Chr 5, ERATO Doi 605, expressed	ncRNA
mm_80702.1	chr9	92249716	92249729	+	1	NA	promoter-TSS (NM_011636)	promoter-TSS (NM_011636)	-472	NM_011636	22038	Mm.421956	NM_011636	ENSMUSG00000032369	Plscr1	MmTRA1a|MmTRA1b|Nor1|Tra1|Tra1a|Tra1b|Tras1|Tras2	phospholipid scramblase 1	protein-coding
mm_117300.1	chr13	67108547	67108609	-	1	NA	intron (NM_001256052, intron 2 of 6)	intron (NM_001256052, intron 2 of 6)	5450	NM_001256052	432770	Mm.124021	NM_001256052	ENSMUSG00000074824	Rslcan18	mszf51	regulator of sex-limitation candidate 18	protein-coding
mm_91283.1	chr10	24712134	24712146	-	1	NA	promoter-TSS (NM_008813)	promoter-TSS (NM_008813)	19	NM_001308327	18605	Mm.27254	NM_008813	ENSMUSG00000037370	Enpp1	4833416E15Rik|AI428932|C76301|CD203c|E-NPP 1|E-NPP1|Ly-41|M6S1|NPP1|Npps|PC-1|Pca|Pca-1|Pdnp1|ttw|twy	ectonucleotide pyrophosphatase/phosphodiesterase 1	protein-coding
mm_152987.1	chr19	29646160	29646198	-	1	NA	exon (NM_001081213, exon 2 of 15)	exon (NM_001081213, exon 2 of 15)	2241	NM_001081213	226090	Mm.267131	NM_146098	ENSMUSG00000046324	Ermp1	D19Ertd410e|D19Wsu12e|Fxna|mKIAA1815	endoplasmic reticulum metallopeptidase 1	protein-coding
mm_24257.1	chr3	89186747	89186757	+	1	NA	intron (NM_001014995, intron 7 of 11)	intron (NM_001014995, intron 7 of 11)	3527	NM_001014995	68521	Mm.274708	NM_001014995	ENSMUSG00000032657	Fam189b	1110013L07Rik	family with sequence similarity 189, member B	protein-coding
mm_41132.1	chr5	87788733	87788747	+	1	NA	TTS (NM_001304768)	TTS (NM_001304768)	14290	NM_007785	12993	Mm.4908	NM_007785	ENSMUSG00000061937	Csn1s2a	Csng|PP22	casein alpha s2-like A	protein-coding
mm_24655.1	chr3	94443287	94443295	+	1	NA	promoter-TSS (NM_030116)	promoter-TSS (NM_030116)	-45	NM_030116	78523	Mm.218515	NM_030116	ENSMUSG00000028140	Mrpl9	8030480E20Rik|AA409733|C330013D18Rik|L9mt	mitochondrial ribosomal protein L9	protein-coding
mm_77331.1	chr8	119501762	119501766	-	1	NA	promoter-TSS (NM_001009950)	promoter-TSS (NM_001009950)	-66	NM_001009950	234788	Mm.302096	NM_001009950	ENSMUSG00000034224	Slc38a8	Gm587	solute carrier family 38, member 8	protein-coding
mm_52165.1	chr6	98275916	98275923	+	1	NA	intron (NM_001128092, intron 2 of 3)	intron (NM_001128092, intron 2 of 3)	66835	NM_001128092	330390	Mm.484161	NM_001128092	ENSMUSG00000090667	Gm765	-	predicted gene 765	protein-coding
mm_73689.1	chr8	111560939	111560946	+	1	NA	intron (NM_001168623, intron 1 of 4)	ID_B1|SINE|B4	22599	NM_001168623	170737	Mm.271578	NM_133206	ENSMUSG00000033545	Znrf1	B830022L21Rik|Rnf42|Zrfp1|nin283	zinc and ring finger 1	protein-coding
mm_93522.1	chr10	115289933	115289937	-	1	NA	TTS (NM_024454)	TTS (NM_024454)	25656	NM_024454	216344	Mm.21936	NM_024454	ENSMUSG00000020132	Rab21	9630024B22	RAB21, member RAS oncogene family	protein-coding
mm_4529.1	chr1	175632170	175632185	+	1	NA	promoter-TSS (NM_133809)	promoter-TSS (NM_133809)	-16	NM_133809	98256	Mm.27217	NM_133809	ENSMUSG00000039783	Kmo	AI046660	kynurenine 3-monooxygenase (kynurenine 3-hydroxylase)	protein-coding
mm_11784.1	chr2	40555683	40555693	+	1	NA	Intergenic	Intergenic	-1329350	NM_024209	67857	Mm.389242	NM_024209	ENSMUSG00000026753	Ppp6c	2310003C10Rik	protein phosphatase 6, catalytic subunit	protein-coding
mm_20193.1	chr2	122702728	122702785	-	1	NA	promoter-TSS (NM_011774)	promoter-TSS (NM_011774)	-93	NM_001290993	22785	Mm.27801	NM_011774	ENSMUSG00000005802	Slc30a4	Znt4|lm|znT-4	solute carrier family 30 (zinc transporter), member 4	protein-coding
mm_100669.1	chr11	3335813	3335836	-	1	NA	intron (NM_178149, intron 5 of 5)	intron (NM_178149, intron 5 of 5)	5093	NM_178149	216505	Mm.390323	NM_178149	ENSMUSG00000034614	Pik3ip1	1500004A08Rik|5830455E04Rik|Crkd|Hgfl	phosphoinositide-3-kinase interacting protein 1	protein-coding
mm_12580.1	chr2	73274800	73274808	+	1	NA	3' UTR (NM_001005343, exon 2 of 2)	3' UTR (NM_001005343, exon 2 of 2)	2878	NM_001005343	381373	Mm.330293	NM_001005343	ENSMUSG00000068859	Sp9	-	trans-acting transcription factor 9	protein-coding
mm_44636.1	chr5	27919265	27919287	-	1	NA	Intergenic	Intergenic	77329	NM_008314	15563	Mm.4835	NM_008314	ENSMUSG00000039106	Htr5a	Htr5	5-hydroxytryptamine (serotonin) receptor 5A	protein-coding
mm_134493.1	chr16	18776649	18776681	-	1	NA	promoter-TSS (NM_013805)	promoter-TSS (NM_013805)	-182	NM_013805	12741	Mm.22768	NM_013805	ENSMUSG00000041378	Cldn5	AI854493|MBEC1|Tmvcf	claudin 5	protein-coding
mm_14597.1	chr2	136058246	136058263	+	1	NA	5' UTR (NM_029530, exon 1 of 6)	5' UTR (NM_029530, exon 1 of 6)	327	NM_029530	76161	Mm.41638	NM_029530	ENSMUSG00000027270	Lamp5	3110035N03Rik|6330527O06Rik|BAD-LAMP|LAMP-5	lysosomal-associated membrane protein family, member 5	protein-coding
mm_10632.1	chr2	19909833	19909843	+	1	NA	Intergenic	CpG	251776	NM_027715	71198	Mm.83981	NM_027715	ENSMUSG00000043415	Otud1	4933428L19Rik	OTU domain containing 1	protein-coding
mm_38721.1	chr4	145234808	145234820	-	1	NA	intron (NM_011610, intron 1 of 9)	intron (NM_011610, intron 1 of 9)	12056	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_90875.1	chr10	9071151	9071154	-	1	NA	Intergenic	Lx10|LINE|L1	-185082	NM_175155	70097	Mm.338275	NM_175155	ENSMUSG00000015305	Sash1	1100001C18Rik|2500002E12Rik|A330076K04Rik|mKIAA0790	SAM and SH3 domain containing 1	protein-coding
mm_139730.1	chr17	57477239	57477258	+	1	NA	intron (NM_010130, intron 19 of 21)	intron (NM_010130, intron 19 of 21)	68066	NM_001104591	224916	Mm.469889	NM_001104591	ENSMUSG00000090655	Vmn2r120	EG224916	vomeronasal 2, receptor 120	protein-coding
mm_36322.1	chr4	70378176	70378194	-	1	NA	intron (NM_145990, intron 4 of 36)	GSAT_MM|Satellite|Satellite	32250	NM_001313762	214444	Mm.370777	NM_145990	ENSMUSG00000039298	Cdk5rap2	2900018K03Rik|an|mKIAA1633	CDK5 regulatory subunit associated protein 2	protein-coding
mm_14140.1	chr2	126499066	126499076	+	1	NA	Intergenic	Intergenic	-7518	NM_001080944	241633	Mm.222235	NM_001080944	ENSMUSG00000060131	Atp8b4	A530043E15|Im	ATPase, class I, type 8B, member 4	protein-coding
mm_14411.1	chr2	130295149	130295236	+	1	NA	promoter-TSS (NM_001110513)	promoter-TSS (NM_001110513)	-747	NM_001110513	228598	Mm.32582	NM_152993	ENSMUSG00000053552	Ebf4	Ebf3|O/E-4|Olf-1	early B cell factor 4	protein-coding
mm_76280.1	chr8	84192061	84192108	-	1	NA	Intergenic	Intergenic	-13123	NR_029821	723819		NR_029821	ENSMUSG00000065483	Mir181c	Mirn181c|mir-181c	microRNA 181c	ncRNA
mm_9172.1	chr1	170978615	170978643	-	1	NA	Intergenic	RMER1B|Other|Other	-2558	NM_010187	14130	Mm.425062	NM_010187	ENSMUSG00000026656	Fcgr2b	AI528646|CD32|F630109E10Rik|Fc[g]RII|FcgRII|Fcgr2|Fcgr2a|Fcr-2|Fcr-3|Ly-17|Ly-m20|LyM-1|Lym-1|fcRII	Fc receptor, IgG, low affinity IIb	protein-coding
mm_168064.1	chr10	102432942	102432962	-	1	NA	Intergenic	L1Md_T|LINE|L1	57466	NM_024435	67405	Mm.64201	NM_024435	ENSMUSG00000019890	Nts	5033428E16Rik|NMN-125|NN|NT|NT/N|NTS1	neurotensin	protein-coding
mm_170235.1	chr17	87590280	87590282	-	1	NA	Intergenic	LTRIS3|LTR|ERV1	-45698	NM_008532	17075	Mm.4259	NM_008532	ENSMUSG00000045394	Epcam	CD326|EGP|EGP-2|Egp314|Ep-CAM|EpCAM1|GA733-2|Ly74|TROP1|Tacsd1|Tacstd1|gp40	epithelial cell adhesion molecule	protein-coding
mm_18611.1	chr2	68386676	68386693	-	1	NA	intron (NM_016866, intron 5 of 17)	intron (NM_016866, intron 5 of 17)	85297	NM_016866	53416	Mm.198414	NM_016866	ENSMUSG00000027030	Stk39	AW227544|AW556857|DCHT|RF005|Rnl5|SPAK	serine/threonine kinase 39	protein-coding
mm_77376.1	chr8	119834414	119834425	-	1	NA	intron (NM_028071, intron 2 of 3)	intron (NM_028071, intron 2 of 3)	6160	NM_028071	72042	Mm.393405	NM_028071	ENSMUSG00000031827	Cotl1	1810074P22Rik|2010004C08Rik|Clp	coactosin-like 1 (Dictyostelium)	protein-coding
mm_48976.1	chr6	4754430	4754440	+	1	NA	exon (NM_130877, exon 2 of 2)	exon (NM_130877, exon 2 of 2)	7129	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_57362.1	chr6	124763066	124763076	-	1	NA	exon (NM_013509, exon 9 of 12)	exon (NM_013509, exon 9 of 12)	-6584	NM_007881	13498	Mm.333380	NM_007881	ENSMUSG00000004263	Atn1	Atr1|Drpla|atrophin-1	atrophin 1	protein-coding
mm_34778.1	chr4	154012282	154012299	+	1	NA	exon (NM_201226, exon 1 of 7)	exon (NM_201226, exon 1 of 7)	487	NM_201226	72946	Mm.260690	NM_201226	ENSMUSG00000029028	Lrrc47	2900010D03Rik|AA960559|mKIAA1185	leucine rich repeat containing 47	protein-coding
mm_103556.1	chr11	77720936	77720946	-	1	NA	exon (NM_009965, exon 4 of 6)	exon (NM_009965, exon 4 of 6)	4352	NM_001313933	12957	Mm.22830	NM_009965	ENSMUSG00000000724	Cryba1	BA3/A1|Cryb	crystallin, beta A1	protein-coding
mm_105360.1	chr11	103115399	103115423	-	1	NA	promoter-TSS (NM_138753)	promoter-TSS (NM_138753)	-914	NM_138753	192231	Mm.8763	NM_138753	ENSMUSG00000048878	Hexim1	7330426E13Rik|CLP-1|Clp1|HIS1	hexamethylene bis-acetamide inducible 1	protein-coding
mm_73410.1	chr8	106052701	106052711	+	1	NA	intron (NM_001301176, intron 13 of 14)	intron (NM_001301176, intron 13 of 14)	-6897	NM_010901	18021	Mm.383185	NM_010901	ENSMUSG00000031902	Nfatc3	C80703|D8Ertd281e|NFAT4|NFATx	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 3	protein-coding
mm_137641.1	chr17	28523276	28523314	+	1	NA	Intergenic	CpG	-7566	NM_026290	67645	Mm.46170	NM_026290	ENSMUSG00000024223	Armc12	4930511I11Rik|AV041658	armadillo repeat containing 12	protein-coding
mm_109503.1	chr12	111452107	111452127	+	1	NA	intron (NM_009396, intron 11 of 11)	(TCTA)n|Simple_repeat|Simple_repeat	9456	NM_009396	21928	Mm.255332	NM_009396	ENSMUSG00000021281	Tnfaip2	B94|Exoc3l3|M-sec|Tnfip2|tnfb94	tumor necrosis factor, alpha-induced protein 2	protein-coding
mm_114522.1	chr13	73328511	73328553	+	1	NA	promoter-TSS (NM_010888)	promoter-TSS (NM_010888)	-50	NM_010888	407785	Mm.29897	NM_010888	ENSMUSG00000021606	Ndufs6	BC059730|IP13	NADH dehydrogenase (ubiquinone) Fe-S protein 6	protein-coding
mm_7816.1	chr1	131911108	131911125	-	1	NA	intron (NM_175294, intron 1 of 6)	CpG	658	NM_001145804	98415	Mm.246869	NM_175294	ENSMUSG00000026434	Nucks1	2700010L10Rik|8430423A01Rik|AI647518|C78391|Nucks	nuclear casein kinase and cyclin-dependent kinase substrate 1	protein-coding
mm_152830.1	chr19	23142371	23142420	-	1	NA	intron (NM_010638, intron 1 of 1)	CpG	1169	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_70014.1	chr7	142496927	142496979	-	1	NA	intron (NR_033261, intron 1 of 2)	intron (NR_033261, intron 1 of 2)	-1883	NM_001347549	21957	Mm.389992	NM_011620	ENSMUSG00000061723	Tnnt3	fTnT	troponin T3, skeletal, fast	protein-coding
mm_116920.1	chr13	55528563	55528580	-	1	NA	promoter-TSS (NM_013739)	promoter-TSS (NM_013739)	-33	NM_013739	27261	Mm.33910	NM_013739	ENSMUSG00000035711	Dok3	AI450713|Dokl	docking protein 3	protein-coding
mm_89487.1	chr10	93682477	93682487	+	1	NA	exon (NM_021320, exon 3 of 10)	exon (NM_021320, exon 3 of 10)	840	NR_038017	100504069	Mm.391412	NR_038017	ENSMUSG00000085723	Gm15915	OTTMUSG00000027787	predicted gene 15915	ncRNA
mm_169056.1	chr13	22788595	22788595	+	1	NA	Intergenic	Intergenic	-15270	NM_134218	171252	Mm.390562	NM_134218	ENSMUSG00000071493	Vmn1r208	V1rh9|Vmn1r208-ps	vomeronasal 1 receptor 208	protein-coding
mm_85178.1	chr9	96611412	96611424	-	1	NA	exon (NM_053268, exon 2 of 24)	exon (NM_053268, exon 2 of 24)	20085	NM_053268	114713	Mm.124502	NM_053268	ENSMUSG00000032413	Rasa2	5430433H21Rik|AA517451|AU023900|GAP1m	RAS p21 protein activator 2	protein-coding
mm_96234.1	chr11	62551449	62551457	+	1	NA	promoter-TSS (NR_002875).2	promoter-TSS (NR_002875).2	-51	NR_002875	218963	Mm.282093	NR_002875		Gm1821	-	ubiquitin pseudogene	pseudo
mm_95430.1	chr11	50202811	50202860	+	1	NA	exon (NM_011018, exon 6 of 8)	exon (NM_011018, exon 6 of 8)	7985	NM_001290769	18412	Mm.40828	NM_011018	ENSMUSG00000015837	Sqstm1	A170|OSF-6|Osi|STAP|STONE14|p62	sequestosome 1	protein-coding
mm_133473.1	chr16	89288328	89288334	+	1	NA	Intergenic	Intergenic	82470	NM_001163615	622935	Mm.459837	NM_001163615	ENSMUSG00000091039	Krtap20-2	1190004K03Rik|EG622935|Gm6371	keratin associated protein 20-2	protein-coding
mm_141563.1	chr17	32229597	32229615	-	1	NA	exon (NM_001286630, exon 3 of 20)	exon (NM_001286630, exon 3 of 20)	-12314	NR_102329	100043434		NR_102329		Gm4432	-	predicted gene 4432	pseudo
mm_87581.1	chr10	56504522	56504535	+	1	NA	Intergenic	Intergenic	127228	NM_010288	14609	Mm.378921	NM_010288	ENSMUSG00000050953	Gja1	AU042049|AW546267|Cnx43|Cx43|Cx43alpha1|Gja-1|Npm1|connexin43	gap junction protein, alpha 1	protein-coding
mm_92064.1	chr10	62514392	62514400	-	1	NA	Intergenic	Intergenic	-6641	NM_011157	19073	Mm.338790	NM_011157	ENSMUSG00000020077	Srgn	Prg|Prg1|Sgc	serglycin	protein-coding
mm_77710.1	chr8	126591986	126592000	-	1	NA	intron (NM_001164598, intron 1 of 1)	intron (NM_001164598, intron 1 of 1)	1443	NM_001164598	270110	Mm.334918	NM_001164598	ENSMUSG00000051495	Irf2bp2	E130305N23Rik|IRF-2BP2	interferon regulatory factor 2 binding protein 2	protein-coding
mm_115769.1	chr13	19306303	19306316	-	1	NA	Intergenic	Intergenic	89504	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_95763.1	chr11	54907133	54907160	+	1	NA	exon (NM_008161, exon 2 of 5)	exon (NM_008161, exon 2 of 5)	4292	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_61658.1	chr7	80583245	80583290	+	1	NA	Intergenic	Intergenic	-48148	NM_001042527	12144	Mm.12932	NM_007550	ENSMUSG00000030528	Blm	-	Bloom syndrome, RecQ helicase-like	protein-coding
mm_120168.1	chr14	60768099	60768118	+	1	NA	promoter-TSS (NM_183175)	promoter-TSS (NM_183175)	-26	NM_183175	239126	Mm.319636	NM_183175	ENSMUSG00000071347	C1qtnf9	9130217G22Rik|CTRP9|Ciqtnf9	C1q and tumor necrosis factor related protein 9	protein-coding
mm_13307.1	chr2	102658641	102658669	+	1	NA	promoter-TSS (NM_001077514)	promoter-TSS (NM_001077514)	-28	NM_001077514	20511	Mm.267547	NM_011393	ENSMUSG00000005089	Slc1a2	1700091C19Rik|2900019G14Rik|AI159670|Eaat2|GLT-1|GLT1|MGLT1	solute carrier family 1 (glial high affinity glutamate transporter), member 2	protein-coding
mm_89890.1	chr10	110660095	110660129	+	1	NA	Intergenic	Intergenic	59462	NR_028438	109335	Mm.367727	NR_028438		9230102K24Rik	-	RIKEN cDNA 9230102K24 gene	ncRNA
mm_13247.1	chr2	98663714	98663719	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	1196059	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_63424.1	chr7	127471710	127471724	+	1	NA	5' UTR (NM_145589, exon 1 of 11)	5' UTR (NM_145589, exon 1 of 11)	103	NM_145589	233895	Mm.44183	NM_145589	ENSMUSG00000030822	Prr14	BC006909	proline rich 14	protein-coding
mm_59958.1	chr7	30427459	30427472	+	1	NA	exon (NM_172142, exon 10 of 11)	exon (NM_172142, exon 10 of 11)	4161	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_123110.1	chr14	55884280	55884311	-	1	NA	promoter-TSS (NM_019820)	promoter-TSS (NM_019820)	-39	NM_019820	56410	Mm.97163	NM_019820	ENSMUSG00000040380	Cbln3	-	cerebellin 3 precursor protein	protein-coding
mm_55099.1	chr6	49733492	49733500	-	1	NA	Intergenic	RMER19B|LTR|ERVK	-89214	NM_023456	109648	Mm.154796	NM_023456	ENSMUSG00000029819	Npy	0710005A05Rik	neuropeptide Y	protein-coding
mm_154780.1	chrX	12977857	12977893	+	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	41002	NM_001272033	245350	Mm.302695	NM_001272033		AA414768	OTTMUSG00000017000	expressed sequence AA414768	protein-coding
mm_160589.1	chr9	65890362	65890362	+	1	NA	promoter-TSS (NM_026515)	promoter-TSS (NM_026515)	39	NM_026515	68026	Mm.351273	NM_026515	ENSMUSG00000040204	Pclaf	2810417H13Rik|AA409629|Ns5apt9|Ns5atp9|PAF15|Paf|mKIAA0101|p15(PAF)	PCNA clamp associated factor	protein-coding
mm_50186.1	chr6	41684354	41684358	+	1	NA	promoter-TSS (NM_029671)	promoter-TSS (NM_029671)	-75	NM_029671	76606	Mm.272520	NM_029671	ENSMUSG00000029867	1700034O15Rik	-	RIKEN cDNA 1700034O15 gene	protein-coding
mm_17019.1	chr2	18998105	18998118	-	1	NA	promoter-TSS (NR_024323)	promoter-TSS (NR_024323)	10	NM_008845	18718	Mm.313977	NM_008845	ENSMUSG00000026737	Pip4k2a	AW742916|Pip5k2a	phosphatidylinositol-5-phosphate 4-kinase, type II, alpha	protein-coding
mm_104360.1	chr11	94309649	94309667	-	1	NA	exon (NM_026313, exon 2 of 11)	exon (NM_026313, exon 2 of 11)	12253	NM_026313	67684	Mm.30927	NM_026313	ENSMUSG00000020863	Luc7l3	3300001P08Rik|Luc7a	LUC7-like 3 (S. cerevisiae)	protein-coding
mm_96841.1	chr11	70026816	70026853	+	1	NA	intron (NM_001109752, intron 1 of 19)	intron (NM_001109752, intron 1 of 19)	8229	NM_007864	13385	Mm.27256	NM_007864	ENSMUSG00000020886	Dlg4	Dlgh4|PSD-95|PSD95|SAP90|SAP90A	discs, large homolog 4 (Drosophila)	protein-coding
mm_87751.1	chr10	60277540	60277542	+	1	NA	promoter-TSS (NM_011179)	promoter-TSS (NM_011179)	-87	NM_001146123	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_142053.1	chr17	35638140	35638153	-	1	NA	exon (NM_001033366, exon 2 of 3)	exon (NM_001033366, exon 2 of 3)	5549	NM_001033366	268949	Mm.296301	NM_001033366	ENSMUSG00000073408	Dpcr1	Gm630	diffuse panbronchiolitis critical region 1 (human)	protein-coding
mm_119047.1	chr14	30626598	30626603	+	1	NA	promoter-TSS (NM_011103)	promoter-TSS (NM_011103)	-392	NM_011103	18753	Mm.2314	NM_011103	ENSMUSG00000021948	Prkcd	AI385711|D14Ertd420e|PKC[d]|PKCdelta|Pkcd	protein kinase C, delta	protein-coding
mm_27266.1	chr3	38558857	38558861	-	1	NA	Intergenic	Intergenic	-74043	NM_001167883	99696	Mm.290937	NM_001033198	ENSMUSG00000044864	Ankrd50	AI662170|E430012K20Rik|mKIAA1223|mKIAA3019	ankyrin repeat domain 50	protein-coding
mm_102708.1	chr11	66526987	66527018	-	1	NA	promoter-TSS (NM_001034874)	promoter-TSS (NM_001034874)	-876	NM_001034874	380702	Mm.351764	NM_001034874	ENSMUSG00000053930	Shisa6	Gm879|ckamp52	shisa family member 6	protein-coding
mm_117295.1	chr13	66933015	66933069	-	1	NA	promoter-TSS (NM_025547)	promoter-TSS (NM_025547)	30	NM_025547	66410	Mm.347939	NM_025547	ENSMUSG00000021519	Mterf3	2410017I18Rik|Mterfd1	mitochondrial transcription termination factor 3	protein-coding
mm_131705.1	chr16	20732761	20732806	+	1	NA	promoter-TSS (NM_009893)	promoter-TSS (NM_009893)	-344	NM_001278041	12667	Mm.20457	NM_009893	ENSMUSG00000006958	Chrd	Chd	chordin	protein-coding
mm_84848.1	chr9	78443160	78443175	-	1	NA	promoter-TSS (NM_173386)	promoter-TSS (NM_173386)	70	NR_125721	214763	Mm.101559	NM_173386	ENSMUSG00000032344	Mb21d1	E330016A19Rik|cGAS	Mab-21 domain containing 1	protein-coding
mm_67070.1	chr7	67803490	67803532	-	1	NA	promoter-TSS (NR_045954)	promoter-TSS (NR_045954)	-15	NR_045954	73904	Mm.70992	NR_045954	ENSMUSG00000097697	4833412C05Rik	Bigheart	RIKEN cDNA 4833412C05 gene	ncRNA
mm_78824.1	chr9	44102066	44102078	+	1	NA	exon (NM_001190314, exon 2 of 14)	exon (NM_001190314, exon 2 of 14)	302	NM_147126	259172	Mm.227110	NM_147126	ENSMUSG00000034739	Mfrp	rd6	membrane frizzled-related protein	protein-coding
mm_164377.1	chr16	27849829	27849849	+	1	NA	promoter-TSS (NR_033475)	promoter-TSS (NR_033475)	-91	NR_033475	100038623	Mm.387135	NR_033475		Gm10823	ENSMUSG00000075290	predicted gene 10823	ncRNA
mm_47881.1	chr5	134703183	134703187	-	1	NA	3' UTR (NM_007925, exon 37 of 37)	3' UTR (NM_007925, exon 37 of 37)	-14595	NM_010717	16885	Mm.15409	NM_010717	ENSMUSG00000029674	Limk1	KIZ-1|LIMK-1|Limk	LIM-domain containing, protein kinase	protein-coding
mm_152728.1	chr19	18748516	18748519	-	1	NA	Intergenic	Intergenic	-1466	NM_153417	225997	Mm.215171	NM_153417	ENSMUSG00000024727	Trpm6	CHAK2|TRPM6/CHAK2	transient receptor potential cation channel, subfamily M, member 6	protein-coding
mm_3506.1	chr1	150107092	150107100	+	1	NA	3' UTR (NM_011198, exon 10 of 10)	3' UTR (NM_011198, exon 10 of 10)	7065	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_33187.1	chr4	126140830	126140850	+	1	NA	3' UTR (NM_028800, exon 11 of 11)	3' UTR (NM_028800, exon 11 of 11)	-7163	NM_172145	230752	Mm.41569	NM_172145	ENSMUSG00000050212	Eva1b	2610027C15Rik|Fam176b	eva-1 homolog B (C. elegans)	protein-coding
mm_108750.1	chr12	88917272	88917276	+	1	NA	intron (NM_001198587, intron 3 of 19)	intron (NM_001198587, intron 3 of 19)	-36116	NM_172544	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding
mm_102817.1	chr11	68973365	68973382	-	1	NA	TTS (NM_028048)	TTS (NM_028048)	482	NM_021329	57785	Mm.143774	NM_021329	ENSMUSG00000032892	Rangrf	2400006H24Rik|Mog1|Rangnrf	RAN guanine nucleotide release factor	protein-coding
mm_72763.1	chr8	85515835	85515868	+	1	NA	intron (NM_173866, intron 6 of 11)	intron (NM_173866, intron 6 of 11)	23234	NM_173866	108682	Mm.200423	NM_173866	ENSMUSG00000031700	Gpt2	4631422C05Rik|ALT2|AU014768|AU041193|C87201	glutamic pyruvate transaminase (alanine aminotransferase) 2	protein-coding
mm_96525.1	chr11	68496685	68496703	+	1	NA	3' UTR (NM_177320, exon 19 of 19)	3' UTR (NM_177320, exon 19 of 19)	-6325	NM_001004435	104709	Mm.234573	NM_001004435	ENSMUSG00000046207	Pik3r6	BB220380|p84|p84 PIKAP|p87(PIKAP)|p87PIKAP	phosphoinositide-3-kinase, regulatory subunit 6	protein-coding
mm_39872.1	chr5	31077005	31077011	+	1	NA	intron (NM_023525, intron 39 of 43)	intron (NM_023525, intron 39 of 43)	16519	NM_011773	22784	Mm.1396	NM_011773	ENSMUSG00000029151	Slc30a3	Znt3	solute carrier family 30 (zinc transporter), member 3	protein-coding
mm_166096.1	chr4	141723440	141723454	-	1	NA	promoter-TSS (NM_001017966)	promoter-TSS (NM_001017966)	-28	NM_001017966	68817	Mm.393721	NM_001017966	ENSMUSG00000078515	Ddi2	1110056G13Rik|1700027M01Rik|9130022E05Rik|AI604911|AU040698	DNA-damage inducible protein 2	protein-coding
mm_147732.1	chr18	61035776	61035818	-	1	NA	exon (NM_009880, exon 1 of 3)	exon (NM_009880, exon 1 of 3)	402	NM_009880	12590	Mm.144448	NM_009880	ENSMUSG00000024619	Cdx1	Cdx|Cdx-1	caudal type homeobox 1	protein-coding
mm_153654.1	chr19	44394792	44394794	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	12916	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_171395.1	chr4	12233622	12233636	+	1	NA	Intergenic	(TGG)n|Simple_repeat|Simple_repeat	-61614	NM_026558	68099	Mm.25340	NM_026558	ENSMUSG00000028218	Fam92a	6720467C03Rik|Fam92a1	family with sequence similarity 92, member A	protein-coding
mm_36136.1	chr4	59349942	59349990	-	1	NA	exon (NM_001163288, exon 12 of 17)	exon (NM_001163288, exon 12 of 17)	88667	NM_001163288	634731	Mm.483589	NM_001163288	ENSMUSG00000038578	Susd1	A530080P10|Gm12528|OTTMUSG00000007332	sushi domain containing 1	protein-coding
mm_73813.1	chr8	117379390	117379404	+	1	NA	intron (NM_028941, intron 2 of 20)	intron (NM_028941, intron 2 of 20)	30227	NM_028941	74440	Mm.233181	NM_028941	ENSMUSG00000034390	Cmip	4933407C03Rik|5830471E12Rik|AI314065|AI464126	c-Maf inducing protein	protein-coding
mm_105102.1	chr11	100956922	100956927	-	1	NA	3' UTR (NM_008986, exon 2 of 2)	3' UTR (NM_008986, exon 2 of 2)	13693	NM_008986	19285	Mm.21864	NM_008986	ENSMUSG00000004044	Ptrf	2310075E07Rik|AW546441|Cav-p60|Cavin	polymerase I and transcript release factor	protein-coding
mm_121480.1	chr14	121035683	121035693	+	1	NA	5' UTR (NM_134082, exon 1 of 27)	5' UTR (NM_134082, exon 1 of 27)	114	NM_134082	223254	Mm.223980	NM_134082	ENSMUSG00000025555	Farp1	AW228844|BC030329|Cdep	FERM, RhoGEF (Arhgef) and pleckstrin domain protein 1 (chondrocyte-derived)	protein-coding
mm_105591.1	chr11	106736412	106736441	-	1	NA	Intergenic	PB1D9|SINE|Alu	-14800	NM_001271375	380732	Mm.343952	NM_001033435	ENSMUSG00000040528	Milr1	Allergin-1|Gm885|Mca32	mast cell immunoglobulin like receptor 1	protein-coding
mm_2196.1	chr1	89454887	89454920	+	1	NA	promoter-TSS (NM_178119)	promoter-TSS (NM_178119)	92	NM_001037136	347722	Mm.291135	NM_178119	ENSMUSG00000055013	Agap1	Centg2|Ggap1|R75364|mKIAA1099	ArfGAP with GTPase domain, ankyrin repeat and PH domain 1	protein-coding
mm_85542.1	chr9	106682200	106682214	-	1	NA	intron (NM_001286498, intron 2 of 5)	intron (NM_001286498, intron 2 of 5)	3609	NM_011573	21767	Mm.22266	NM_011573	ENSMUSG00000040813	Tex264	TEG-264	testis expressed gene 264	protein-coding
mm_132403.1	chr16	35001454	35001465	+	1	NA	3' UTR (NM_139300, exon 32 of 32)	3' UTR (NM_139300, exon 32 of 32)	-20962	NM_023587	70757	Mm.27286	NM_023587	ENSMUSG00000035376	Hacd2	6330408J20Rik|AI255777|AI481689|Hcad2|Ptplb	3-hydroxyacyl-CoA dehydratase 2	protein-coding
mm_148729.1	chr19	5877854	5877870	+	1	NA	promoter-TSS (NM_134154)	promoter-TSS (NM_134154)	-604	NM_134154	107375	Mm.5323	NM_134154	ENSMUSG00000024818	Slc25a45	AW491445	solute carrier family 25, member 45	protein-coding
mm_158507.1	chrX	142852513	142852516	-	1	NA	TTS (NM_019496)	TTS (NM_019496)	113514	NR_030523	723976		NR_030523	ENSMUSG00000076011	Mir652	Mirn652|miRX|mmu-mir-652	microRNA 652	ncRNA
mm_110820.1	chr12	72408689	72408740	-	1	NA	5' UTR (NM_001286448, exon 1 of 7)	5' UTR (NM_001286448, exon 1 of 7)	340	NM_001286448	104001	Mm.221275	NM_153457	ENSMUSG00000021087	Rtn1	Nsp	reticulon 1	protein-coding
mm_30268.1	chr3	146770604	146770664	-	1	NA	promoter-TSS (NM_001164199)	promoter-TSS (NM_001164199)	59	NM_001164199	18749	Mm.16766	NM_011100	ENSMUSG00000005034	Prkacb	CbPKA|Pkacb	protein kinase, cAMP dependent, catalytic, beta	protein-coding
mm_62716.1	chr7	110772733	110772754	+	1	NA	5' UTR (NM_009667, exon 1 of 15)	5' UTR (NM_009667, exon 1 of 15)	139	NM_009667	11717	Mm.3238	NM_009667	ENSMUSG00000005686	Ampd3	-	adenosine monophosphate deaminase 3	protein-coding
mm_146018.1	chr18	69475599	69475601	+	1	NA	intron (NM_013685, intron 5 of 19)	intron (NM_013685, intron 5 of 19)	129879	NM_001083967	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding
mm_28620.1	chr3	95015417	95015462	-	1	NA	promoter-TSS (NM_030074)	promoter-TSS (NM_030074)	-201	NM_030074	78266	Mm.389478	NM_030074	ENSMUSG00000019338	Zfp687	4931408L03Rik|Znf687|mKIAA1441	zinc finger protein 687	protein-coding
mm_149439.1	chr19	11478282	11478319	+	1	NA	exon (NM_028595, exon 5 of 7)	exon (NM_028595, exon 5 of 7)	8932	NM_028595	73656	Mm.440719	NM_028595	ENSMUSG00000079419	Ms4a6c	2200009H22Rik|2210417N07Rik	membrane-spanning 4-domains, subfamily A, member 6C	protein-coding
mm_34439.1	chr4	147868831	147868896	+	1	NA	promoter-TSS (NM_010244)	promoter-TSS (NM_010244)	-116	NM_010244	14349	Mm.422607	NM_010244	ENSMUSG00000070583	Fv1	Fv-1|Rv-1|Rv1	Friend virus susceptibility 1	protein-coding
mm_28718.1	chr3	95659560	95659579	-	1	NA	intron (NM_008562, intron 1 of 2)	intron (NM_008562, intron 1 of 2)	848	NM_008562	17210	Mm.1639	NM_008562	ENSMUSG00000038612	Mcl1	AW556805|Mcl-1	myeloid cell leukemia sequence 1	protein-coding
mm_20570.1	chr2	131085074	131085093	-	1	NA	exon (NM_011426, exon 3 of 21)	exon (NM_011426, exon 3 of 21)	1682	NM_011426	20612	Mm.1374	NM_011426	ENSMUSG00000027322	Siglec1	Cd169|Siglec-1|Sn	sialic acid binding Ig-like lectin 1, sialoadhesin	protein-coding
mm_68673.1	chr7	118976675	118976691	-	1	NA	intron (NM_022420, intron 2 of 3)	intron (NM_022420, intron 2 of 3)	18528	NM_022420	64297	Mm.103439	NM_022420	ENSMUSG00000008734	Gprc5b	AW125761|Raig2	G protein-coupled receptor, family C, group 5, member B	protein-coding
mm_118521.1	chr14	14716977	14716980	+	1	NA	intron (NM_001033270, intron 1 of 24)	Lx4A|LINE|L1	13953	NM_001033270	218756	Mm.258893	NM_001033270	ENSMUSG00000021733	Slc4a7	E430014N10Rik|NBC3|NBCn1|NBCn1-G	solute carrier family 4, sodium bicarbonate cotransporter, member 7	protein-coding
mm_111433.1	chr12	91788367	91788376	-	1	NA	Intergenic	MT2A|LTR|ERVL	-1935	NM_175367	108800	Mm.23125	NM_175367	ENSMUSG00000020961	Ston2	4933401N24Rik|AI425999|AW544599	stonin 2	protein-coding
mm_21184.1	chr2	155130015	155130037	-	1	NA	Intergenic	Intergenic	-3455	NM_001243712	16396	Mm.208286	NM_008395	ENSMUSG00000027598	Itch	6720481N21Rik|8030492O04Rik|A130065M08|AIP4|C230047C07Rik	itchy, E3 ubiquitin protein ligase	protein-coding
mm_32110.1	chr4	98923752	98923777	+	1	NA	promoter-TSS (NM_146144)	promoter-TSS (NM_146144)	-46	NM_001301414	230484	Mm.371692	NM_146144	ENSMUSG00000028560	Usp1	-	ubiquitin specific peptidase 1	protein-coding
mm_38647.1	chr4	143268072	143268103	-	1	NA	3' UTR (NM_010329, exon 6 of 6)	3' UTR (NM_010329, exon 6 of 6)	31477	NM_010329	14726	Mm.2976	NM_010329	ENSMUSG00000028583	Pdpn	Gp38|OTS-8|RANDAM-2|T1-alpha|T1a|T1alpha	podoplanin	protein-coding
mm_18341.1	chr2	58156805	58156818	-	1	NA	intron (NM_139200, intron 1 of 7)	intron (NM_139200, intron 1 of 7)	3311	NM_139200	227929	Mm.273905	NM_139200	ENSMUSG00000026832	Cytip	A130053M09Rik|AI462064|C80816|Cbp|Cybr|Pscdbp	cytohesin 1 interacting protein	protein-coding
mm_46668.1	chr5	108760056	108760069	-	1	NA	Intergenic	Intergenic	-3780	NR_040691	73295	Mm.416858	NR_040691	ENSMUSG00000101762	1700047L14Rik	-	RIKEN cDNA 1700047L14 gene	ncRNA
mm_69823.1	chr7	141265929	141265941	-	1	NA	5' UTR (NM_001252601, exon 2 of 10)	5' UTR (NM_001252601, exon 2 of 10)	489	NM_001252601	54123	Mm.3233	NM_016850	ENSMUSG00000025498	Irf7	-	interferon regulatory factor 7	protein-coding
mm_61855.1	chr7	88308050	88308058	+	1	NA	exon (NM_009982, exon 6 of 7)	exon (NM_009982, exon 6 of 7)	29969	NM_001311790	13032	Mm.89295	NM_009982	ENSMUSG00000030560	Ctsc	AI047818|CatC|DPP1|DPPI	cathepsin C	protein-coding
mm_110355.1	chr12	40014483	40014494	-	1	NA	Intergenic	Intergenic	22888	NM_007487	11861	Mm.12723	NM_007487	ENSMUSG00000047446	Arl4a	AI467555|Arl4	ADP-ribosylation factor-like 4A	protein-coding
mm_136746.1	chr17	8500465	8500480	+	1	NA	Intergenic	Intergenic	-26329	NM_001290707	23984	Mm.87161	NM_011866	ENSMUSG00000023868	Pde10a	-	phosphodiesterase 10A	protein-coding
mm_14912.1	chr2	150667386	150667421	+	1	NA	promoter-TSS (NR_040331)	promoter-TSS (NR_040331)	-91	NR_040331	109344	Mm.440012	NR_040331	ENSMUSG00000087406	E130215H24Rik	-	RIKEN cDNA E130215H24 gene	ncRNA
mm_79348.1	chr9	53667132	53667149	+	1	NA	exon (NM_001161618, exon 1 of 18)	exon (NM_001161618, exon 1 of 18)	367	NM_001161618	75717	Mm.218910	NM_027807	ENSMUSG00000032030	Cul5	4921514I20Rik|8430423K24Rik|AI852817|C030032G03Rik|C330021I08Rik|VACM-1|VACM1	cullin 5	protein-coding
mm_108276.1	chr12	78862540	78862554	+	1	NA	promoter-TSS (NM_023721)	promoter-TSS (NM_023721)	475	NM_026114	13665	Mm.196220	NM_026114	ENSMUSG00000021116	Eif2s1	0910001O23Rik|2410026C18Rik|35kDa|Eif2a|eIF2alpha	eukaryotic translation initiation factor 2, subunit 1 alpha	protein-coding
mm_161783.1	chr17	43630187	43630187	-	1	NA	5' UTR (NM_198418, exon 1 of 5)	5' UTR (NM_198418, exon 1 of 5)	112	NM_001161366	210510	Mm.329058	NM_198418	ENSMUSG00000040140	Tdrd6	AB097085|Tdr2	tudor domain containing 6	protein-coding
mm_107374.1	chr12	32953856	32953870	+	1	NA	promoter-TSS (NM_198710)	promoter-TSS (NM_198710)	-74	NR_044986	74076	Mm.50114	NR_044986	ENSMUSG00000097494	4933406C10Rik	-	RIKEN cDNA 4933406C10 gene	ncRNA
mm_157591.1	chrX	53114556	53114566	-	1	NA	promoter-TSS (NM_019538)	promoter-TSS (NM_019538)	-156	NM_019538	56096	Mm.274842	NM_019538	ENSMUSG00000061082	Plac1	DXWsu72e|Epcs26|Oosp2l	placental specific protein 1	protein-coding
mm_167059.1	chr7	90071661	90071692	+	1	NA	Intergenic	Intergenic	42517	NR_110364	319711	Mm.31753	NR_015614	ENSMUSG00000097585	E230029C05Rik	AI452102|B230337J15	RIKEN cDNA E230029C05 gene	ncRNA
mm_102897.1	chr11	69423909	69423911	-	1	NA	exon (NM_001081330, exon 78 of 86)	exon (NM_001081330, exon 78 of 86)	-10235	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_116916.1	chr13	55512358	55512369	-	1	NA	exon (NM_001114088, exon 2 of 13)	exon (NM_001114088, exon 2 of 13)	1083	NM_026131	67399	Mm.275648	NM_026131	ENSMUSG00000021493	Pdlim7	LMP	PDZ and LIM domain 7	protein-coding
mm_42700.1	chr5	119884320	119884321	+	1	NA	3' UTR (NM_011537, exon 9 of 9)	3' UTR (NM_011537, exon 9 of 9)	49657	NM_011537	21388	Mm.103636	NM_011537	ENSMUSG00000018263	Tbx5	-	T-box 5	protein-coding
mm_165572.1	chr3	19992797	19992817	+	1	NA	3' UTR (NM_007752, exon 19 of 19)	3' UTR (NM_007752, exon 19 of 19)	35753	NM_007752	12870	Mm.13787	NM_007752	ENSMUSG00000003617	Cp	D3Ertd555e	ceruloplasmin	protein-coding
mm_42885.1	chr5	122372495	122372513	+	1	NA	promoter-TSS (NM_026883)	promoter-TSS (NM_026883)	-4	NM_024216	68080	Mm.266328	NM_024216	ENSMUSG00000029464	Gpn3	A930018B01Rik|Atpbd1c|D5Ertd708e	GPN-loop GTPase 3	protein-coding
mm_121841.1	chr14	20607872	20607900	-	1	NA	5' UTR (NM_030180, exon 2 of 21)	5' UTR (NM_030180, exon 2 of 21)	10468	NM_030180	78787	Mm.301173	NM_030180	ENSMUSG00000034235	Usp54	4930429G18Rik|AI115571|C030002J06Rik	ubiquitin specific peptidase 54	protein-coding
mm_139124.1	chr17	47504950	47504960	+	1	NA	promoter-TSS (NM_001081636)	promoter-TSS (NM_001081636)	-96	NM_001081636	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_41572.1	chr5	93171367	93171386	+	1	NA	3' UTR (NM_001009818, exon 10 of 10)	3' UTR (NM_001009818, exon 10 of 10)	35119	NM_017367	12453	Mm.250419	NM_017367	ENSMUSG00000063015	Ccni	-	cyclin I	protein-coding
mm_9190.1	chr1	171136149	171136160	-	1	NA	exon (NM_025321, exon 5 of 6)	exon (NM_025321, exon 5 of 6)	14449	NM_025321	66052	Mm.198138	NM_025321	ENSMUSG00000058076	Sdhc	0610010E03Rik|AI316496|AU019277	succinate dehydrogenase complex, subunit C, integral membrane protein	protein-coding
mm_34084.1	chr4	138831775	138831780	+	1	NA	promoter-TSS (NR_002926)	promoter-TSS (NR_002926)	-80	NR_002926	18780	Mm.4675	NM_011108	ENSMUSG00000058908	Pla2g2a	EF|Mom1|Pla2|sPLA2|sPla2-IIA	phospholipase A2, group IIA (platelets, synovial fluid)	protein-coding
mm_163911.1	chr14	32085547	32085558	-	1	NA	promoter-TSS (NM_145460)	promoter-TSS (NM_145460)	140	NR_104303	105638	Mm.2519	NM_172254	ENSMUSG00000021905	Dph3	DELGIP1|DelgipP1|Desr1|KTI11|Zcsl2	diphthamine biosynthesis 3	protein-coding
mm_117206.1	chr13	64084485	64084491	-	1	NA	intron (NM_008291, intron 2 of 10)	intron (NM_008291, intron 2 of 10)	4713	NM_008291	15487	Mm.5109	NM_008291	ENSMUSG00000033122	Hsd17b3	-	hydroxysteroid (17-beta) dehydrogenase 3	protein-coding
mm_68948.1	chr7	126563068	126563099	-	1	NA	exon (NM_146200, exon 7 of 21)	exon (NM_146200, exon 7 of 21)	3283	NM_146200	56347	Mm.22776	NM_146200	ENSMUSG00000030738	Eif3c	110kDa|3230401O13Rik|Eif3s8|NIPIL(A3)|NipilA3|Xs|Xsl	eukaryotic translation initiation factor 3, subunit C	protein-coding
mm_38.1	chr1	6453843	6453853	+	1	NA	Intergenic	Intergenic	-33383	NM_001244693	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding
mm_107606.1	chr12	49384367	49384398	+	1	NA	5' UTR (NM_008241, exon 2 of 2)	5' UTR (NM_008241, exon 2 of 2)	1375	NM_008241	15228	Mm.4704	NM_008241	ENSMUSG00000020950	Foxg1	2900064B05Rik|BF-1|Bf1|Hfh9|Hfhbf1	forkhead box G1	protein-coding
mm_45245.1	chr5	57718959	57718964	-	1	NA	5' UTR (NM_001310606, exon 1 of 3)	5' UTR (NM_001310606, exon 1 of 3)	880	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_21771.1	chr2	164844740	164844757	-	1	NA	exon (NM_011125, exon 11 of 16)	exon (NM_011125, exon 11 of 16)	10975	NM_008906	19025	Mm.359633	NM_008906	ENSMUSG00000017760	Ctsa	AU019505|PPCA|Ppgb	cathepsin A	protein-coding
mm_33128.1	chr4	124850739	124850786	+	1	NA	promoter-TSS (NM_001142727)	promoter-TSS (NM_001142727)	3	NM_153566	230734	Mm.258568	NM_153566	ENSMUSG00000028889	Yrdc	AV303379|BC023823|IRIP|ITIP	yrdC domain containing (E.coli)	protein-coding
mm_21681.1	chr2	164426237	164426249	-	1	NA	intron (NM_011521, intron 4 of 4)	intron (NM_011521, intron 4 of 4)	16945	NM_011521	20971	Mm.3815	NM_011521	ENSMUSG00000017009	Sdc4	AA959608|AW108331|S4|Synd4|ryudocan|syndecan-4	syndecan 4	protein-coding
mm_71556.1	chr8	48843518	48843528	+	1	NA	Intergenic	CpG	-168833	NM_011857	23965	Mm.42191	NM_011857	ENSMUSG00000031561	Tenm3	2610100B16Rik|Odz1|Odz3|Ten-m3|mKIAA1455	teneurin transmembrane protein 3	protein-coding
mm_122832.1	chr14	54712398	54712408	-	1	NA	promoter-TSS (NM_207131)	promoter-TSS (NM_207131)	-229	NM_207131	110794	Mm.236223	NM_207131	ENSMUSG00000052435	Cebpe	C/EBPe|CRP1|Gm294	CCAAT/enhancer binding protein (C/EBP), epsilon	protein-coding
mm_136630.1	chr17	5661701	5661712	+	1	NA	intron (NM_146073, intron 2 of 8)	intron (NM_146073, intron 2 of 8)	-136951	NR_045081	78512	Mm.23696	NR_045079	ENSMUSG00000096965	3300005D01Rik	-	RIKEN cDNA 3300005D01 gene	ncRNA
mm_20108.1	chr2	121116455	121116465	-	1	NA	Intergenic	Intergenic	-6669	NM_001160424	640543	Mm.478785	NM_001160424	ENSMUSG00000079103	Tgm7	TGMZ|TGz	transglutaminase 7	protein-coding
mm_52593.1	chr6	116673913	116673954	+	1	NA	promoter-TSS (NM_178045)	promoter-TSS (NM_178045)	-97	NM_178045	213391	Mm.257931	NM_178045	ENSMUSG00000042129	Rassf4	3830411C14Rik|AD037|AI586137	Ras association (RalGDS/AF-6) domain family member 4	protein-coding
mm_122163.1	chr14	31401007	31401012	-	1	NA	intron (NM_011894, intron 3 of 8)	intron (NM_011894, intron 3 of 8)	16668	NM_001347585	24056	Mm.383198	NM_011894	ENSMUSG00000021892	Sh3bp5	AI606498|SH3BP-5|Sab	SH3-domain binding protein 5 (BTK-associated)	protein-coding
mm_17241.1	chr2	25608448	25608486	-	1	NA	promoter-TSS (NM_001024616)	promoter-TSS (NM_001024616)	-21	NM_001024616	227624	Mm.29600	NM_001024616	ENSMUSG00000015087	Rabl6	B230208H17Rik|Rbel1|Rbel1a|Rbel1b|parf	RAB, member RAS oncogene family-like 6	protein-coding
mm_62147.1	chr7	97129205	97129215	+	1	NA	intron (NM_001162477, intron 1 of 9)	intron (NM_001162477, intron 1 of 9)	47459	NM_010248	14389	Mm.42033	NM_010248	ENSMUSG00000004508	Gab2	AI463667|D130058I17Rik|p97	growth factor receptor bound protein 2-associated protein 2	protein-coding
mm_91214.1	chr10	21785854	21785860	-	1	NA	Intergenic	Intergenic	95012	NR_045843	432436	Mm.244553	NM_001004162		Gm5420	EG432436	predicted gene 5420	ncRNA
mm_43796.1	chr5	142816726	142816741	+	1	NA	intron (NM_178242, intron 1 of 15)	CpG-11746	654	NM_178242	231861	Mm.354649	NM_178242	ENSMUSG00000039477	Tnrc18	BC025631|EG381742|Zfp469	trinucleotide repeat containing 18	protein-coding
mm_114965.1	chr13	97088545	97088582	+	1	NA	intron (NM_001100458, intron 1 of 12)	intron (NM_001100458, intron 1 of 12)	16920	NM_001100458	320557	Mm.458280	NM_001100458	ENSMUSG00000041817	Fam169a	B230112C05Rik|SLAP75	family with sequence similarity 169, member A	protein-coding
mm_101696.1	chr11	40751043	40751055	-	1	NA	exon (NM_009831, exon 6 of 6)	exon (NM_009831, exon 6 of 6)	4237	NM_009831	12450	Mm.2103	NM_009831	ENSMUSG00000020326	Ccng1	AI314029	cyclin G1	protein-coding
mm_101404.1	chr11	26593971	26594007	-	1	NA	promoter-TSS (NM_027260)	promoter-TSS (NM_027260)	-69	NM_001252447	69922	Mm.285351	NM_027260	ENSMUSG00000064090	Vrk2	2810003O05Rik|AI447698	vaccinia related kinase 2	protein-coding
mm_150575.1	chr19	40276040	40276056	+	1	NA	Intergenic	Intergenic	-4432	NM_016861	54132	Mm.5567	NM_016861	ENSMUSG00000055044	Pdlim1	CLP36|Clim1|mClim1	PDZ and LIM domain 1 (elfin)	protein-coding
mm_16126.1	chr2	170184846	170184856	+	1	NA	Intergenic	Intergenic	-42176	NM_001159683	228913	Mm.22858	NM_001033299	ENSMUSG00000052056	Zfp217	4933431C08Rik|AW987152|Gm562|ZABC1|Znf217	zinc finger protein 217	protein-coding
mm_169930.1	chr16	57391608	57391608	-	1	NA	intron (NM_001040397, intron 1 of 4)	LSU-rRNA_Hsa|rRNA|rRNA	38331	NM_001040397	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding
mm_41526.1	chr5	92603040	92603050	+	1	NA	promoter-TSS (NM_175096)	promoter-TSS (NM_175096)	-6	NM_175096	52331	Mm.21965	NM_175096	ENSMUSG00000047963	Stbd1	D530019K15Rik|D5Ertd593e	starch binding domain 1	protein-coding
mm_4067.1	chr1	166130412	166130424	+	1	NA	promoter-TSS (NM_021610)	promoter-TSS (NM_021610)	-42	NM_021610	59290	Mm.46357	NM_021610	ENSMUSG00000000544	Gpa33	2010310L10Rik|2210401D16Rik|BB116197	glycoprotein A33 (transmembrane)	protein-coding
mm_96352.1	chr11	66957923	66957937	+	1	NA	promoter-TSS (NR_130646)	promoter-TSS (NR_130646)	36	NR_130646	71576	Mm.340077	NR_130315	ENSMUSG00000085683	9130409J20Rik	-	RIKEN cDNA 9130409J20 gene	ncRNA
mm_71536.1	chr8	46986914	46986962	+	1	NA	promoter-TSS (NM_177304)	promoter-TSS (NM_177304)	51	NM_177304	320981	Mm.211429	NM_177304	ENSMUSG00000038173	Enpp6	4833421B01Rik|B830047L21Rik|D8Ertd514e|E-NPP 6|GPC-Cpde|Npp6	ectonucleotide pyrophosphatase/phosphodiesterase 6	protein-coding
mm_132783.1	chr16	44943666	44943676	+	1	NA	promoter-TSS (NM_029018)	promoter-TSS (NM_029018)	-7	NM_001128133	74603	Mm.297337	NM_027578	ENSMUSG00000036172	Cd200r3	4733401I18Rik|4833409J19Rik|AI505817|BB106877|mCD200RLb	CD200 receptor 3	protein-coding
mm_152308.1	chr19	9559205	9559248	-	1	NA	promoter-TSS (NR_073559)	promoter-TSS (NR_073559)	22	NR_073559	619371	Mm.316894	NM_001030317		Stxbp3-ps	Munc18c(L)|Stxbp3-1|Stxbp3b	syntaxin-binding protein 3, pseudogene	pseudo
mm_36956.1	chr4	109138658	109138663	-	1	NA	intron (NM_001346502, intron 3 of 23)	intron (NM_001346502, intron 3 of 23)	-20624	NM_001134791	100273	Mm.366315	NM_133885	ENSMUSG00000028559	Osbpl9	2600011I06Rik|AU015843|Orp-9	oxysterol binding protein-like 9	protein-coding
mm_62655.1	chr7	107693269	107693278	+	1	NA	intron (NM_001163557, intron 5 of 25)	intron (NM_001163557, intron 5 of 25)	64759	NM_001205227	320635	Mm.132828	NM_177216	ENSMUSG00000048065	Cyb5r2	D630003K02Rik|b5R.2	cytochrome b5 reductase 2	protein-coding
mm_152577.1	chr19	11602088	11602101	-	1	NA	intron (NM_026835, intron 2 of 6)	intron (NM_026835, intron 2 of 6)	2710	NM_026835	68774	Mm.290390	NM_026835	ENSMUSG00000024679	Ms4a6d	1110058E16Rik|AI447446|Ms4a11	membrane-spanning 4-domains, subfamily A, member 6D	protein-coding
mm_92141.1	chr10	67011168	67011209	-	1	NA	3' UTR (NM_001204915, exon 9 of 9)	3' UTR (NM_001204915, exon 9 of 9)	6113	NR_110511	102634101	Mm.445258	NR_110511		Gm31763	-	predicted gene, 31763	ncRNA
mm_128241.1	chr15	36608693	36608720	-	1	NA	5' UTR (NM_008774, exon 1 of 15)	5' UTR (NM_008774, exon 1 of 15)	267	NM_008774	18458	Mm.371570	NM_008774	ENSMUSG00000022283	Pabpc1	PABP|Pabp1|PabpI|Pabpl1|ePAB	poly(A) binding protein, cytoplasmic 1	protein-coding
mm_162588.1	chr1	180944058	180944071	+	1	NA	intron (NM_144794, intron 1 of 22)	intron (NM_144794, intron 1 of 22)	1546	NM_144794	208795	Mm.185518	NM_144794	ENSMUSG00000026519	Tmem63a	BC014795|Tmem64a	transmembrane protein 63a	protein-coding
mm_126855.1	chr15	89212310	89212311	+	1	NA	intron (NM_027805, intron 1 of 7)	intron (NM_027805, intron 1 of 7)	751	NM_027805	71474	Mm.184055	NM_026813	ENSMUSG00000036561	Ppp6r2	1110033O10Rik|8430411H09Rik|B230107H12Rik|Pp6r2|Saps2	protein phosphatase 6, regulatory subunit 2	protein-coding
mm_4737.1	chr1	181842516	181842548	+	1	NA	promoter-TSS (NM_133815)	promoter-TSS (NM_133815)	-131	NM_133815	98386	Mm.4538	NM_133815	ENSMUSG00000004880	Lbr	AI505894|ic	lamin B receptor	protein-coding
mm_146523.1	chr18	4353246	4353256	-	1	NA	promoter-TSS (NM_007746)	promoter-TSS (NM_007746)	-296	NR_040328	73915	Mm.482777	NR_040328		4833419F23Rik	-	RIKEN cDNA 4833419F23 gene	ncRNA
mm_13301.1	chr2	102550100	102550113	+	1	NA	promoter-TSS (NM_173749)	promoter-TSS (NM_173749)	85	NM_173749	210622	Mm.28649	NM_173749	ENSMUSG00000027188	Pamr1	5930437L24|E430002G05Rik|Ramp	peptidase domain containing associated with muscle regeneration 1	protein-coding
mm_58429.1	chr7	3297426	3297443	+	1	NA	exon (NM_016969, exon 3 of 3)	exon (NM_016969, exon 3 of 3)	4406	NM_001093766	50918	Mm.29874	NM_016969	ENSMUSG00000068566	Myadm	D7Wsu62e	myeloid-associated differentiation marker	protein-coding
mm_20393.1	chr2	129174827	129174827	-	1	NA	Intergenic	Intergenic	5846	NR_045264	100048701	Mm.428544	NR_045264	ENSMUSG00000084826	AI847159	OTTMUSG00000015420	expressed sequence AI847159	ncRNA
mm_109220.1	chr12	108792947	108792988	+	1	NA	promoter-TSS (NM_009537)	promoter-TSS (NM_009537)	-344	NM_009537	22632	Mm.3868	NM_009537	ENSMUSG00000021264	Yy1	AW488674|NF-E1	YY1 transcription factor	protein-coding
mm_84226.1	chr9	61946769	61946779	-	1	NA	promoter-TSS (NM_024245)	promoter-TSS (NM_024245)	25	NM_024245	71819	Mm.259374	NM_024245	ENSMUSG00000032254	Kif23	3110001D19Rik|C87313|CHO1|Knsl5|MKLP-1|MKLP1	kinesin family member 23	protein-coding
mm_8490.1	chr1	153808164	153808168	-	1	NA	intron (NM_001243223, intron 10 of 20)	intron (NM_001243223, intron 10 of 20)	35975	NM_001243223	240816	Mm.329340	NM_001243223	ENSMUSG00000042641	Rgsl1	4930415K13Rik|Gm202|Rgsl2	regulator of G-protein signaling like 1	protein-coding
mm_135643.1	chr16	52366447	52366455	-	1	NA	intron (NM_009655, intron 1 of 15)	L1_Mus2|LINE|L1	86630	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_88313.1	chr10	75518012	75518029	+	1	NA	promoter-TSS (NM_026095)	promoter-TSS (NM_026095)	-22	NM_026095	67332	Mm.45151	NM_026095	ENSMUSG00000020180	Snrpd3	1700043E15Rik|2310009E13Rik|AW046420|SMD3	small nuclear ribonucleoprotein D3	protein-coding
mm_72821.1	chr8	88199195	88199224	+	1	NA	promoter-TSS (NM_001164497)	promoter-TSS (NM_001164497)	-4	NM_001164499	214627	Mm.491211	NM_001164497	ENSMUSG00000036779	Papd5	5730445M16Rik|5830428A09	PAP associated domain containing 5	protein-coding
mm_27743.1	chr3	69126842	69126885	-	1	NA	5' UTR (NM_008467, exon 1 of 17)	5' UTR (NM_008467, exon 1 of 17)	229	NM_008467	16649	Mm.30601	NM_008467	ENSMUSG00000027782	Kpna4	1110058D08Rik|IPOA3	karyopherin (importin) alpha 4	protein-coding
mm_162968.1	chr11	10545136	10545136	+	1	NA	Intergenic	Intergenic	-568880	NM_177033	319922	Mm.337851	NM_177033	ENSMUSG00000050830	Vwc2	A930041G11Rik|G11|PSST739|UNQ739|cradin	von Willebrand factor C domain containing 2	protein-coding
mm_66376.1	chr7	43660140	43660179	-	1	NA	promoter-TSS (NM_031181)	promoter-TSS (NM_031181)	2	NM_031181	83382	Mm.157702	NM_031181	ENSMUSG00000030474	Siglece	Cd170|Siglec12|Siglec5|Siglec9|Siglecl1|mSiglec-E	sialic acid binding Ig-like lectin E	protein-coding
mm_31797.1	chr4	63979936	63979946	+	1	NA	intron (NM_011607, intron 15 of 25)	intron (NM_011607, intron 15 of 25)	67074	NM_011607	21923	Mm.980	NM_011607	ENSMUSG00000028364	Tnc	AI528729|C130033P17Rik|Hxb|TN|TN-C|Ten|cytotactin|tenascin-C	tenascin C	protein-coding
mm_154458.1	chrM	2845	2855	-	1	NA	NA	Intergenic	NA	NA								
mm_109369.1	chr12	109646437	109646458	+	1	NA	non-coding (NR_028261, exon 11 of 21)	non-coding (NR_028261, exon 11 of 21)	-3170	NR_046304	100861570		NR_046304	ENSMUSG00000084549	DQ267100	-	snoRNA DQ267100	snoRNA
mm_150081.1	chr19	29387118	29387148	+	1	NA	3' UTR (NM_021893, exon 7 of 7)	3' UTR (NM_021893, exon 7 of 7)	19695	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_96869.1	chr11	70167203	70167222	+	1	NA	intron (NM_001204252, intron 1 of 9)	intron (NM_001204252, intron 1 of 9)	589	NM_010796	17312	Mm.252405	NM_010796	ENSMUSG00000000318	Clec10a	CD301a|M-ASGP-BP-1|Mgl|Mgl1	C-type lectin domain family 10, member A	protein-coding
mm_1886.1	chr1	85673707	85673723	+	1	NA	exon (NM_013673, exon 8 of 20)	exon (NM_013673, exon 8 of 20)	23727	NM_001313714	20684	Mm.290906	NM_013673	ENSMUSG00000026222	Sp100	A430075G10Rik	nuclear antigen Sp100	protein-coding
mm_45754.1	chr5	86783203	86783213	-	1	NA	Intergenic	Intergenic	-21058	NM_001347375	231386	Mm.196325	NM_177680	ENSMUSG00000035851	Ythdc1	A730098D12Rik|C80342|mKIAA1966	YTH domain containing 1	protein-coding
mm_67000.1	chr7	64907580	64907581	-	1	NA	intron (NM_183087, intron 2 of 9)	RSINE1|SINE|B4	-34540	NM_023239	66647	Mm.19944	NM_023239	ENSMUSG00000070520	Ndnl2	5730494G16Rik|AI642138|BB044375|HCA4|Mageg1|Nsmce3|mage-g1	necdin-like 2	protein-coding
mm_29599.1	chr3	119783506	119783516	-	1	NA	promoter-TSS (NM_019550)	promoter-TSS (NM_019550)	-123	NM_019550	56195	Mm.29966	NM_019550	ENSMUSG00000028134	Ptbp2	Ptb2|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding
mm_14271.1	chr2	128708757	128708783	+	1	NA	intron (NM_008587, intron 1 of 18)	intron (NM_008587, intron 1 of 18)	9773	NM_008587	17289	Mm.239655	NM_008587	ENSMUSG00000014361	Mertk	Eyk|Mer|Nyk|nmf12	c-mer proto-oncogene tyrosine kinase	protein-coding
mm_41573.1	chr5	93172473	93172484	+	1	NA	3' UTR (NM_001009818, exon 10 of 10)	3' UTR (NM_001009818, exon 10 of 10)	34017	NM_017367	12453	Mm.250419	NM_017367	ENSMUSG00000063015	Ccni	-	cyclin I	protein-coding
mm_61086.1	chr7	51622447	51622510	+	1	NA	5' UTR (NM_080853, exon 1 of 12)	5' UTR (NM_080853, exon 1 of 12)	648	NM_080853	140919	Mm.256618	NM_080853	ENSMUSG00000030500	Slc17a6	2900073D12Rik|DNPI|VGLUT2	solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 6	protein-coding
mm_74234.1	chr8	124340567	124340569	+	1	NA	intron (NM_139272, intron 14 of 15)	intron (NM_139272, intron 14 of 15)	93368	NM_171824	209966	Mm.234233	NM_171824	ENSMUSG00000050751	Pgbd5	2900019M05Rik|AI854313	piggyBac transposable element derived 5	protein-coding
mm_87718.1	chr10	60106187	60106193	+	1	NA	promoter-TSS (NM_052994)	promoter-TSS (NM_052994)	-67	NM_052994	94214	Mm.153429	NM_052994	ENSMUSG00000058297	Spock2	AA407235|Gcap26|mKIAA0275	sparc/osteonectin, cwcv and kazal-like domains proteoglycan 2	protein-coding
mm_89416.1	chr10	90834238	90834239	+	1	NA	intron (NM_001347053, intron 1 of 8)	intron (NM_001347053, intron 1 of 8)	4395	NM_001347053	77531	Mm.440605	NM_181398	ENSMUSG00000058589	Anks1b	AIDA-1b|C030032C09Rik|E530015N03Rik|ENSMUSG00000078431|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding
mm_23170.1	chr3	40745469	40745498	+	1	NA	promoter-TSS (NM_011020)	promoter-TSS (NM_011020)	-130	NM_011020	18415	Mm.39330	NM_011020	ENSMUSG00000025757	Hspa4l	94kDa|AI461691|APG-1|Osp94	heat shock protein 4 like	protein-coding
mm_135514.1	chr16	48772037	48772051	-	1	NA	promoter-TSS (NM_198297)	promoter-TSS (NM_198297)	-88	NM_198297	77647	Mm.167298	NM_198297	ENSMUSG00000030775	Trat1	C030046M14Rik|Tcrim|Trim	T cell receptor associated transmembrane adaptor 1	protein-coding
mm_113662.1	chr13	42681688	42681706	+	1	NA	intron (NM_001302635, intron 1 of 13)	intron (NM_001302635, intron 1 of 13)	898	NM_001302635	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding
mm_34572.1	chr4	150052631	150052633	+	1	NA	Intergenic	L1MCa|LINE|L1	-15822	NR_029751	723848		NR_029751	ENSMUSG00000065493	Mir34a	Mirn34a|mir-34a|mmu-mir-34a	microRNA 34a	ncRNA
mm_82413.1	chr9	14860078	14860105	-	1	NA	promoter-TSS (NM_010287)	promoter-TSS (NM_010287)	-119	NM_001310734	14608	Mm.4672	NM_010287	ENSMUSG00000031932	Gpr83	AW045253|Gir|Gpr72|RP105|RP39|RP82	G protein-coupled receptor 83	protein-coding
mm_107691.1	chr12	55377140	55377158	+	1	NA	exon (NM_025373, exon 5 of 7)	exon (NM_025373, exon 5 of 7)	6454	NR_035430	100316807		NR_035430	ENSMUSG00000080645	Mir1198	Mirn1198|mmu-mir-1198	microRNA 1198	ncRNA
mm_133289.1	chr16	77483569	77483591	+	1	NA	intron (NR_015543, intron 3 of 4)	intron (NR_015543, intron 3 of 4)	-115356	NR_029535	387229		NR_029535	ENSMUSG00000065530	Mir99a	Mirn99a|mir-99a|mmu-mir-99a	microRNA 99a	ncRNA
mm_158237.1	chrX	106485368	106485424	-	1	NA	promoter-TSS (NM_001007580)	promoter-TSS (NM_001007580)	-167	NM_001007580	333564	Mm.298000	NM_001007580	ENSMUSG00000033737	Fndc3c1	Fndc3c|Gm784	fibronectin type III domain containing 3C1	protein-coding
mm_9559.1	chr1	173971708	173971731	-	1	NA	exon (NM_011940, exon 5 of 7)	exon (NM_011940, exon 5 of 7)	11125	NM_008327	26388	Mm.218770	NM_008327	ENSMUSG00000026535	Ifi202b	Ifbip-1|Ifi202|Ifi202a|p202	interferon activated gene 202B	protein-coding
mm_32214.1	chr4	101550800	101550824	+	1	NA	exon (NM_001164583, exon 1 of 19)	exon (NM_001164583, exon 1 of 19)	218	NM_001164583	72685	Mm.76494	NM_198412	ENSMUSG00000028528	Dnajc6	2810027M23Rik|mKIAA0473	DnaJ heat shock protein family (Hsp40) member C6	protein-coding
mm_76230.1	chr8	83573452	83573465	-	1	NA	intron (NM_134118, intron 3 of 12)	intron (NM_134118, intron 3 of 12)	6700	NM_025843	66916	Mm.29683	NM_025843	ENSMUSG00000033938	Ndufb7	1110002H15Rik	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 7	protein-coding
mm_57801.1	chr6	129331787	129331791	-	1	NA	promoter-TSS (NM_199034)	promoter-TSS (NM_199034)	-8	NM_199034	381816	Mm.46114	NM_199034	ENSMUSG00000047720	4922502D21Rik	Clec2m|Gm1074|SPATA78	RIKEN cDNA 4922502D21 gene	protein-coding
mm_75586.1	chr8	61550101	61550128	-	1	NA	exon (NM_001293773, exon 10 of 20)	exon (NM_001293773, exon 10 of 20)	41055	NM_001293774	72333	Mm.29933	NM_001081390	ENSMUSG00000058056	Palld	2410003B16Rik|6030492A02	palladin, cytoskeletal associated protein	protein-coding
mm_100383.1	chr11	119314828	119314859	+	1	NA	promoter-TSS (NM_130886)	promoter-TSS (NM_130886)	56	NM_130886	170720	Mm.130832	NM_130886	ENSMUSG00000013483	Card14	Bimp2|CARMA2	caspase recruitment domain family, member 14	protein-coding
mm_164772.1	chr17	88583683	88583725	+	1	NA	intron (NM_028658, intron 20 of 21)	intron (NM_028658, intron 20 of 21)	-42851	NM_029858	77057	Mm.482203	NM_029858	ENSMUSG00000033855	Ston1	4921524J06Rik|C86231|Salf|Sblf	stonin 1	protein-coding
mm_31366.1	chr4	47288435	47288455	+	1	NA	intron (NM_009928, intron 22 of 39)	intron (NM_009928, intron 22 of 39)	-64777	NM_001312868	21812	Mm.197552	NM_009370	ENSMUSG00000007613	Tgfbr1	ALK5|AU017191|Alk-5|ESK2|TGFR-1|TbetaR-I|TbetaRI	transforming growth factor, beta receptor I	protein-coding
mm_31722.1	chr4	62674202	62674238	+	1	NA	5' UTR (NM_001310706, exon 1 of 7)	5' UTR (NM_001310706, exon 1 of 7)	246	NM_001310706	50780	Mm.286753	NM_019492	ENSMUSG00000059810	Rgs3	4930506N09Rik|C2PA-RGS3|C2pa|PDZ-RGS3|RGS3S	regulator of G-protein signaling 3	protein-coding
mm_162121.1	chrX	68893050	68893050	-	1	NA	promoter-TSS (NM_001098842)	promoter-TSS (NM_001098842)	3	NM_001098842	627927	Mm.391264	NM_001098842	ENSMUSG00000056815	Gm6812	EG627927	predicted gene 6812	protein-coding
mm_33635.1	chr4	132972336	132972343	+	1	NA	Intergenic	Intergenic	-1756	NM_010208	14191	Mm.271665	NM_010208	ENSMUSG00000028874	Fgr	-	FGR proto-oncogene, Src family tyrosine kinase	protein-coding
mm_83123.1	chr9	40411732	40411734	-	1	NA	intron (NM_172768, intron 2 of 19)	intron (NM_172768, intron 2 of 19)	44031	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_150325.1	chr19	34574408	34574424	+	1	NA	exon (NM_008332, exon 3 of 3)	exon (NM_008332, exon 3 of 3)	-9113	NM_010501	15959	Mm.426079	NM_010501	ENSMUSG00000074896	Ifit3	Ifi49|P49	interferon-induced protein with tetratricopeptide repeats 3	protein-coding
mm_116079.1	chr13	28419980	28419992	-	1	NA	Intergenic	Intergenic	277502	NM_023746	28078	Mm.155058	NM_023746	ENSMUSG00000017064	Prl5a1	1600013P04Rik|D13Wsu14e|Ghd24|PLP-L|Prlpl	prolactin family 5, subfamily a, member 1	protein-coding
mm_93310.1	chr10	98857093	98857096	-	1	NA	Intergenic	Intergenic	-58058	NM_026482	67972	Mm.166944	NM_026482	ENSMUSG00000019943	Atp2b1	2810442I22Rik|E130111D10Rik|Pmca1	ATPase, Ca++ transporting, plasma membrane 1	protein-coding
mm_143630.1	chr17	78915847	78915866	-	1	NA	promoter-TSS (NM_001177403)	promoter-TSS (NM_001177403)	-643	NM_001177403	68554	Mm.391820	NM_001177402	ENSMUSG00000062691	Cebpzos	1110001A16Rik	CCAAT/enhancer binding protein (C/EBP), zeta, opposite strand	protein-coding
mm_92670.1	chr10	80522107	80522110	-	1	NA	exon (NM_026094, exon 26 of 28)	exon (NM_026094, exon 26 of 28)	17016	NM_026094	67331	Mm.52511	NM_026094	ENSMUSG00000003341	Atp8b3	1700042F02Rik|1700056N23Rik|ATPIK|SAPLT	ATPase, class I, type 8B, member 3	protein-coding
mm_55135.1	chr6	51270897	51270941	-	1	NA	Intergenic	CpG	-1009	NR_029719	387166		NR_029719	ENSMUSG00000065505	Mir148a	Mirn148|Mirn148a|mir-148a	microRNA 148a	ncRNA
mm_8442.1	chr1	152810610	152810617	-	1	NA	intron (NM_010877, intron 2 of 15)	B3|SINE|B2	10460	NM_010877	17970	Mm.270307	NM_010877	ENSMUSG00000026480	Ncf2	NOXA2|Ncf-2|p67phox	neutrophil cytosolic factor 2	protein-coding
mm_95790.1	chr11	54960562	54960573	+	1	NA	intron (NM_001199275, intron 1 of 18)	ID_B1|SINE|B4	2373	NM_021327	57783	Mm.259671	NM_021327	ENSMUSG00000020400	Tnip1	ABIN|ABIN-1|ABIN1|AU018810|Naf1|Nef|VAN	TNFAIP3 interacting protein 1	protein-coding
mm_101022.1	chr11	8577233	8577247	-	1	NA	intron (NM_001083587, intron 4 of 30)	intron (NM_001083587, intron 4 of 30)	87295	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_127812.1	chr15	5098914	5098934	-	1	NA	exon (NM_001163138, exon 4 of 4)	exon (NM_001163138, exon 4 of 4)	9609	NM_001163138	239319	Mm.31252	NM_001163138	ENSMUSG00000041849	Card6	D730008L15	caspase recruitment domain family, member 6	protein-coding
mm_155029.1	chrX	42068223	42068232	+	1	NA	promoter-TSS (NR_125870)	promoter-TSS (NR_125870)	-171	NM_001301639	11798	Mm.259879	NM_009688	ENSMUSG00000025860	Xiap	1110015C02Rik|Aipa|Api3|Birc4|IAP3|ILP-1|MIHA	X-linked inhibitor of apoptosis	protein-coding
mm_31141.1	chr4	43383118	43383121	+	1	NA	intron (NM_001037709, intron 1 of 11)	intron (NM_001037709, intron 1 of 11)	1137	NM_001037709	100213	Mm.235730	NM_199057	ENSMUSG00000035969	Rusc2	AI840675|mKIAA0375	RUN and SH3 domain containing 2	protein-coding
mm_103144.1	chr11	70239767	70239772	-	1	NA	promoter-TSS (NM_173742)	promoter-TSS (NM_173742)	83	NM_173742	52898	Mm.29852	NM_173742	ENSMUSG00000040904	Rnasek	2310033H11Rik|AA571397|D11Bwg0434e	ribonuclease, RNase K	protein-coding
mm_102240.1	chr11	54982745	54982749	-	1	NA	intron (NR_138556, intron 23 of 24)	B2_Mm2|SINE|B2	-19807	NM_001271455	57783	Mm.259671	NM_021327	ENSMUSG00000020400	Tnip1	ABIN|ABIN-1|ABIN1|AU018810|Naf1|Nef|VAN	TNFAIP3 interacting protein 1	protein-coding
mm_35409.1	chr4	34778323	34778381	-	1	NA	promoter-TSS (NM_001330755)	promoter-TSS (NM_001330755)	14	NR_138487	66291	Mm.28071	NM_025471	ENSMUSG00000028295	Smim8	1810030N24Rik|2810406B13Rik	small integral membrane protein 8	protein-coding
mm_22007.1	chr2	167774951	167774969	-	1	NA	Intergenic	Intergenic	83783	NR_015500	329562	Mm.123101	NM_177851	ENSMUSG00000006462	A530013C23Rik	-	RIKEN cDNA A530013C23 gene	ncRNA
mm_35374.1	chr4	33031296	33031354	-	1	NA	promoter-TSS (NM_019586)	promoter-TSS (NM_019586)	-2	NR_036602	100504166	Mm.426309	NR_036602	ENSMUSG00000085037	4933421O10Rik	-	RIKEN cDNA 4933421O10 gene	ncRNA
mm_50411.1	chr6	48739869	48739877	+	1	NA	intron (NM_175860, intron 1 of 2)	intron (NM_175860, intron 1 of 2)	826	NM_008376	16205	Mm.252599	NM_008376	ENSMUSG00000090019	Gimap1	IAP38|Imap38|imap	GTPase, IMAP family member 1	protein-coding
mm_16557.1	chr2	181850944	181850955	+	1	NA	intron (NM_153594, intron 5 of 6)	intron (NM_153594, intron 5 of 6)	13095	NM_001291211	245867	Mm.491085	NM_153594	ENSMUSG00000027589	Pcmtd2	5330414D10Rik|AI314201	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 2	protein-coding
mm_168446.1	chr11	40714830	40714832	-	1	NA	exon (NM_013552, exon 10 of 18)	exon (NM_013552, exon 10 of 18)	18606	NM_013552	15366	Mm.116997	NM_013552	ENSMUSG00000020330	Hmmr	AA386826|CD168|Rhamm	hyaluronan mediated motility receptor (RHAMM)	protein-coding
mm_64667.1	chr7	4445206	4445243	-	1	NA	intron (NM_175372, intron 1 of 6)	intron (NM_175372, intron 1 of 6)	433	NM_175372	108841	Mm.413106	NM_175372	ENSMUSG00000008435	Rdh13	8430425D21Rik	retinol dehydrogenase 13 (all-trans and 9-cis)	protein-coding
mm_50898.1	chr6	57580995	57581015	+	1	NA	promoter-TSS (NM_025992)	promoter-TSS (NM_025992)	13	NM_025992	67138	Mm.297393	NM_025992	ENSMUSG00000029798	Herc6	1700121D12Rik|2510038N07Rik|4930427L17Rik|AI451296|CEB1|Herc5	hect domain and RLD 6	protein-coding
mm_153996.1	chr19	50678643	50678702	-	1	NA	promoter-TSS (NM_021377)	promoter-TSS (NM_021377)	-26	NM_001290356	58178	Mm.313672	NM_021377	ENSMUSG00000043531	Sorcs1	Sorcs|mSorCS	sortilin-related VPS10 domain containing receptor 1	protein-coding
mm_71075.1	chr8	34156881	34156885	+	1	NA	intron (NM_026432, intron 1 of 5)	intron (NM_026432, intron 1 of 5)	2320	NM_026432	67887	Mm.290353	NM_026432	ENSMUSG00000031532	Saraf	1810045K07Rik|Tmem66	store-operated calcium entry-associated regulatory factor	protein-coding
mm_58056.1	chr6	136857591	136857610	-	1	NA	promoter-TSS (NM_026639)	promoter-TSS (NM_026639)	0	NM_026639	109978	Mm.31840	NM_026639	ENSMUSG00000030217	Art4	4432404K01Rik|ARTC4|DO|DOK1	ADP-ribosyltransferase 4	protein-coding
mm_74450.1	chr8	4213736	4213750	-	1	NA	exon (NM_207203, exon 6 of 7)	exon (NM_207203, exon 6 of 7)	3569	NM_207203	73072	Mm.477379	NM_207203	ENSMUSG00000064125	Prr36	-	proline rich 36	protein-coding
mm_123956.1	chr14	74804026	74804029	-	1	NA	intron (NM_001252132, intron 13 of 18)	intron (NM_001252132, intron 13 of 18)	71730	NM_016903	13885	Mm.38055	NM_016903	ENSMUSG00000021996	Esd	Es-10|Es10|FGH|sid478	esterase D/formylglutathione hydrolase	protein-coding
mm_24120.1	chr3	88170325	88170336	+	1	NA	3' UTR (NM_001310593, exon 11 of 11)	3' UTR (NM_001310593, exon 11 of 11)	7455	NR_045997	76642	Mm.424420	NR_045997	ENSMUSG00000096935	1700113A16Rik	2210408E11Rik|AA408983	RIKEN cDNA 1700113A16 gene	ncRNA
mm_106713.1	chr12	3826624	3826635	+	1	NA	intron (NM_001271753, intron 1 of 22)	intron (NM_001271753, intron 1 of 22)	19469	NM_001271753	13435	Mm.5001	NM_007872	ENSMUSG00000020661	Dnmt3a	MmuIIIA	DNA methyltransferase 3A	protein-coding
mm_162447.1	chr1	119906838	119906842	+	1	NA	Intergenic	B3A|SINE|B2	6328	NM_175106	66343	Mm.49942	NM_175106	ENSMUSG00000036975	Tmem177	2300008B03Rik	transmembrane protein 177	protein-coding
mm_147216.1	chr18	37987171	37987174	-	1	NA	intron (NM_001205336, intron 16 of 32)	B1F2|SINE|Alu	3773	NR_105946	102466913		NR_105946	ENSMUSG00000098297	Mir6980	Gm27969|mmu-mir-6980	microRNA 6980	ncRNA
mm_75980.1	chr8	72268436	72268477	-	1	NA	Intergenic	Intergenic	28438	NM_007456	11767	Mm.290086	NM_007456	ENSMUSG00000003033	Ap1m1	AA408894|AP47|Adtm1A|Cltnm|mu1A	adaptor-related protein complex AP-1, mu subunit 1	protein-coding
mm_40164.1	chr5	35757876	35757946	+	1	NA	promoter-TSS (NM_177678)	promoter-TSS (NM_177678)	31	NM_001177698	231148	Mm.254446	NM_177678	ENSMUSG00000029095	Ablim2	AI606905|C230091L11	actin-binding LIM protein 2	protein-coding
mm_117745.1	chr13	95891882	95891902	-	1	NA	promoter-TSS (NM_027711)	promoter-TSS (NM_027711)	30	NM_027711	544963	Mm.38878	NM_027711	ENSMUSG00000021676	Iqgap2	4933417J23Rik|A630053O10|AI788777	IQ motif containing GTPase activating protein 2	protein-coding
mm_16073.1	chr2	168159067	168159077	+	1	NA	Intergenic	Intergenic	-4559	NR_040327	77017	Mm.407822	NR_040327	ENSMUSG00000087648	E130018N17Rik	-	RIKEN cDNA E130018N17 gene	ncRNA
mm_90204.1	chr10	120388610	120388628	+	1	NA	promoter-TSS (NR_040626)	promoter-TSS (NR_040626)	-904	NR_040626	320626	Mm.446091	NR_040626	ENSMUSG00000090191	9230105E05Rik	-	RIKEN cDNA 9230105E05 gene	ncRNA
mm_90421.1	chr10	127481648	127481672	+	1	NA	intron (NM_027900, intron 13 of 23)	intron (NM_027900, intron 13 of 23)	-20057	NM_177707	237611	Mm.32087	NM_177707	ENSMUSG00000040287	Stac3	9830125E18	SH3 and cysteine rich domain 3	protein-coding
mm_17463.1	chr2	28557998	28558022	-	1	NA	exon (NM_009885, exon 8 of 11)	exon (NM_009885, exon 8 of 11)	5393	NM_009885	12613	Mm.236017	NM_009885	ENSMUSG00000026818	Cel	1810036E18Rik|BAL	carboxyl ester lipase	protein-coding
mm_27974.1	chr3	80802652	80802672	-	1	NA	5' UTR (NM_013540, exon 1 of 16)	5' UTR (NM_013540, exon 1 of 16)	129	NM_013540	14800	Mm.220224	NM_013540	ENSMUSG00000033981	Gria2	GluA2|GluR-B|Glur-2|Glur2	glutamate receptor, ionotropic, AMPA2 (alpha 2)	protein-coding
mm_44228.1	chr5	5108444	5108447	-	1	NA	intron (NM_011074, intron 6 of 14)	intron (NM_011074, intron 6 of 14)	157623	NM_001310448	18647	Mm.389061	NM_011074	ENSMUSG00000028926	Cdk14	Pftk1|mKIAA0834	cyclin-dependent kinase 14	protein-coding
mm_16820.1	chr2	11473754	11473796	-	1	NA	3' UTR (NM_001177754, exon 16 of 16)	3' UTR (NM_001177754, exon 16 of 16)	28315	NM_001177754	170768	Mm.19669	NM_133232	ENSMUSG00000026773	Pfkfb3	E330010H22Rik|iPFK-2|uPFK-2	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	protein-coding
mm_25738.1	chr3	122896734	122896773	+	1	NA	exon (NM_007980, exon 2 of 4)	exon (NM_007980, exon 2 of 4)	1681	NM_007980	14079	Mm.28398	NM_007980	ENSMUSG00000023057	Fabp2	Fabpi|I-FABP	fatty acid binding protein 2, intestinal	protein-coding
mm_83688.1	chr9	50555171	50555183	-	1	NA	promoter-TSS (NM_133217)	promoter-TSS (NM_133217)	-39	NM_133217	170752	Mm.390149	NM_133217	ENSMUSG00000032066	Bco2	B-diox-II|Bcdo2|Bcmo2|CMO2	beta-carotene oxygenase 2	protein-coding
mm_130346.1	chr15	97748503	97748521	-	1	NA	intron (NM_144850, intron 24 of 27)	intron (NM_144850, intron 24 of 27)	-17107	NM_001168693	19011	Mm.1001	NM_008902	ENSMUSG00000022468	Endou	Pp11r|Tcl-30	endonuclease, polyU-specific	protein-coding
mm_121587.1	chr14	7791769	7791778	-	1	NA	Intergenic	CpG	-26184	NM_001081427	286940	Mm.489652	NM_134080	ENSMUSG00000025278	Flnb	AL024016|Fln-b	filamin, beta	protein-coding
mm_31419.1	chr4	48051368	48051372	+	1	NA	exon (NM_015743, exon 3 of 8)	exon (NM_015743, exon 3 of 8)	124	NM_001307989	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_61427.1	chr7	73687169	73687174	+	1	NA	promoter-TSS (NR_033604)	promoter-TSS (NR_033604)	-608	NR_033604	244061	Mm.484605	NR_033604	ENSMUSG00000108337	Gm4971	EG244061	Smad nuclear interacting protein 1 pseudogene	pseudo
mm_101325.1	chr11	22860589	22860610	-	1	NA	promoter-TSS (NM_001169114)	promoter-TSS (NM_001169114)	-263	NM_001169114	53625	Mm.395495	NM_016888	ENSMUSG00000051650	B3gnt2	AA408337|AA409404|AW260308|B3Galt6|B3gnt1|BGnT-1|BGnT-2|BGnT1|BGnT2|Beta3gnt	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 2	protein-coding
mm_154260.1	chr19	60769928	60769938	-	1	NA	exon (NM_010123, exon 16 of 22)	exon (NM_010123, exon 16 of 22)	4452	NR_034047	100217439		NR_034047		Snora19	MBI-51	small nucleolar RNA, H/ACA box 19	snoRNA
mm_69962.1	chr7	142376576	142376601	-	1	NA	exon (NM_009983, exon 9 of 9)	exon (NM_009983, exon 9 of 9)	-2842	NM_001347541	320802	Mm.154486	NM_177265	ENSMUSG00000045777	Ifitm10	6330512M04Rik|AI848576|DSPA3	interferon induced transmembrane protein 10	protein-coding
mm_65638.1	chr7	27912627	27912628	-	1	NA	intron (NM_028538, intron 3 of 3)	L1_Mur3|LINE|L1	16803	NM_028538	73430	Mm.379224	NM_028538	ENSMUSG00000070709	Zfp974	1700049G17Rik|AV321011|BB026409	zinc finger protein 974	protein-coding
mm_131623.1	chr16	20097556	20097596	+	1	NA	promoter-TSS (NM_029436)	promoter-TSS (NM_029436)	22	NM_029436	75785	Mm.392450	NM_029436	ENSMUSG00000062901	Klhl24	1110046J11Rik|4930429H24Rik|6530402O20Rik|C85082	kelch-like 24	protein-coding
mm_103351.1	chr11	74830660	74830689	-	1	NA	promoter-TSS (NM_010813)	promoter-TSS (NM_010813)	-250	NM_010813	17428	Mm.3759	NM_010813	ENSMUSG00000000282	Mnt	Rox|bHLHd3	max binding protein	protein-coding
mm_126596.1	chr15	82358545	82358584	+	1	NA	Intergenic	Intergenic	-4273	NM_025987	67130	Mm.27570	NM_025987	ENSMUSG00000022450	Ndufa6	14kDa|2700038D15Rik|B230217P19Rik	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 6 (B14)	protein-coding
mm_138563.1	chr17	35343150	35343161	+	1	NA	exon (NM_010392, exon 3 of 7)	exon (NM_010392, exon 3 of 7)	822	NM_010392	15013	Mm.427969	NM_010392	ENSMUSG00000091705	H2-Q2	BE136769|ENSMUSG00000079507|Gm11132|H-2Q2|gs14-2	histocompatibility 2, Q region locus 2	protein-coding
mm_165839.1	chr3	158949716	158949741	+	1	NA	Intergenic	(CAGT)n|Simple_repeat|Simple_repeat	-126636	NR_040750	624759	Mm.491054	NR_040750	ENSMUSG00000106053	Gm20752	-	predicted gene, 20752	ncRNA
mm_81443.1	chr9	109812208	109812218	+	1	NA	Intergenic	Intergenic	-4414	NM_183136	78709	Mm.99613	NM_183136	ENSMUSG00000050074	Spink8	C630041L24Rik	serine peptidase inhibitor, Kazal type 8	protein-coding
mm_40166.1	chr5	35786152	35786178	+	1	NA	intron (NM_001177696, intron 1 of 21)	intron (NM_001177696, intron 1 of 21)	28285	NM_001177698	231148	Mm.254446	NM_177678	ENSMUSG00000029095	Ablim2	AI606905|C230091L11	actin-binding LIM protein 2	protein-coding
mm_41576.1	chr5	93172936	93172950	+	1	NA	3' UTR (NM_001009818, exon 10 of 10)	3' UTR (NM_001009818, exon 10 of 10)	33552	NM_017367	12453	Mm.250419	NM_017367	ENSMUSG00000063015	Ccni	-	cyclin I	protein-coding
mm_85276.1	chr9	99437556	99437564	-	1	NA	promoter-TSS (NM_008624)	promoter-TSS (NM_008624)	-848	NM_008624	17532	Mm.2045	NM_008624	ENSMUSG00000032470	Mras	2900078C09Rik|AI326250	muscle and microspikes RAS	protein-coding
mm_90523.1	chr10	128061341	128061344	+	1	NA	intron (NM_019766, intron 1 of 7)	PB1D9|SINE|Alu	2360	NM_019766	56351	Mm.305816	NM_019766	ENSMUSG00000071072	Ptges3	5730442A20Rik|Ptges|Tebp|cPGES|p23|sid3177	prostaglandin E synthase 3 (cytosolic)	protein-coding
mm_148598.1	chr19	5111321	5111334	+	1	NA	intron (NR_045528, intron 8 of 15)	intron (NR_045528, intron 8 of 15)	-4331	NM_029576	76308	Mm.182563	NM_029576	ENSMUSG00000024870	Rab1b	1110011F09Rik	RAB1B, member RAS oncogene family	protein-coding
mm_26306.1	chr3	142512062	142512091	+	1	NA	intron (NM_153564, intron 10 of 10)	intron (NM_153564, intron 10 of 10)	15142	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_143584.1	chr17	74338602	74338614	-	1	NA	promoter-TSS (NM_001162870)	promoter-TSS (NM_001162870)	-379	NM_001162870	50850	Mm.19804	NM_016962	ENSMUSG00000024068	Spast	Spg4|mKIAA1083	spastin	protein-coding
mm_28732.1	chr3	95736081	95736121	-	1	NA	exon (NM_007899, exon 8 of 11)	exon (NM_007899, exon 8 of 11)	-1128	NR_105981	102466787		NR_105981	ENSMUSG00000098737	Mir7014	Gm27837|mmu-mir-7014	microRNA 7014	ncRNA
mm_140620.1	chr17	11861191	11861192	-	1	NA	intron (NM_016694, intron 9 of 11)	intron (NM_016694, intron 9 of 11)	21998	NR_045808	52027	Mm.442257	NR_045808		D17Ertd648e	-	DNA segment, Chr 17, ERATO Doi 648, expressed	ncRNA
mm_145488.1	chr18	60385704	60385705	+	1	NA	intron (NM_001146275, intron 2 of 2)	intron (NM_001146275, intron 2 of 2)	9675	NM_001146275	60440	Mm.261140	NM_021792	ENSMUSG00000054072	Iigp1	2900074L10Rik|AI046432|AW111922|Ifgga1|Iigp|Irga6	interferon inducible GTPase 1	protein-coding
mm_91925.1	chr10	60350403	60350444	-	1	NA	intron (NM_028732, intron 1 of 6)	intron (NM_028732, intron 1 of 6)	3572	NM_028732	74048	Mm.273584	NM_028732	ENSMUSG00000020101	Vsir	4632428N05Rik|Dies1|PD-1H|VISTA	V-set immunoregulatory receptor	protein-coding
mm_10143.1	chr2	4285237	4285253	+	1	NA	intron (NM_172475, intron 1 of 22)	intron (NM_172475, intron 1 of 22)	-115731	NM_001177843	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding
mm_129747.1	chr15	82332448	82332472	-	1	NA	exon (NM_008669, exon 8 of 10)	exon (NM_008669, exon 8 of 10)	6366	NM_008669	17939	Mm.20325	NM_008669	ENSMUSG00000022453	Naga	-	N-acetyl galactosaminidase, alpha	protein-coding
mm_78219.1	chr9	21545114	21545136	+	1	NA	3' UTR (NM_206536, exon 6 of 6)	3' UTR (NM_206536, exon 6 of 6)	-1769	NM_021531	59035	Mm.178115	NM_021531	ENSMUSG00000032185	Carm1	Prmt4	coactivator-associated arginine methyltransferase 1	protein-coding
mm_88223.1	chr10	70365776	70365825	+	1	NA	Intergenic	Intergenic	-74868	NM_001143777	71721	Mm.477813	NM_024244	ENSMUSG00000043259	Fam13c	1200015N20Rik|C030038O19Rik|mKIAA1796	family with sequence similarity 13, member C	protein-coding
mm_83393.1	chr9	44672257	44672262	-	1	NA	promoter-TSS (NM_001277851)	promoter-TSS (NM_001277851)	-974	NM_001277851	58866	Mm.45380	NM_021481	ENSMUSG00000032098	Treh	2210412M19Rik	trehalase (brush-border membrane glycoprotein)	protein-coding
mm_10862.1	chr2	25080297	25080310	+	1	NA	promoter-TSS (NM_028093)	promoter-TSS (NM_028093)	-20	NM_028093	72090	Mm.33403	NM_028093	ENSMUSG00000036813	Entpd8	-	ectonucleoside triphosphate diphosphohydrolase 8	protein-coding
mm_108203.1	chr12	76902188	76902201	+	1	NA	intron (NM_145927, intron 7 of 11)	ORR1C2|LTR|ERVL-MaLR	60054	NM_008558	17187	Mm.268548	NM_008558	ENSMUSG00000059436	Max	AA960152|AI875693|bHLHd4|bHLHd5|bHLHd6|bHLHd7|bHLHd8	Max protein	protein-coding
mm_84068.1	chr9	58201475	58201519	-	1	NA	5' UTR (NM_001161537, exon 1 of 3)	5' UTR (NM_001161537, exon 1 of 3)	218	NM_001161535	320563	Mm.186499	NM_177193	ENSMUSG00000051243	Islr2	B930052A04Rik|Linx|Mbu-3|mKIAA1465	immunoglobulin superfamily containing leucine-rich repeat 2	protein-coding
mm_70784.1	chr8	22476736	22476778	+	1	NA	promoter-TSS (NM_011394)	promoter-TSS (NM_011394)	57	NM_011394	20516	Mm.323901	NM_011394	ENSMUSG00000037656	Slc20a2	MolPit2|Pit-2|Pit2|Ram-1|Ram1	solute carrier family 20, member 2	protein-coding
mm_161540.1	chr15	102998556	102998556	+	1	NA	Intergenic	Intergenic	8017	NM_010466	15426	Mm.6167	NM_010466	ENSMUSG00000001657	Hoxc8	D130011F21Rik|Hox-3.1	homeobox C8	protein-coding
mm_35058.1	chr4	6357508	6357551	-	1	NA	Intergenic	Intergenic	-8151	NM_016807	53378	Mm.247473	NM_016807	ENSMUSG00000028249	Sdcbp	MDA-9|Sycl|syntenin-1	syndecan binding protein	protein-coding
mm_20467.1	chr2	129369724	129369761	-	1	NA	promoter-TSS (NR_015474)	promoter-TSS (NR_015474)	-160	NR_015474	329514	Mm.207315	NM_177848	ENSMUSG00000074805	Il1bos	9430083I22|Gm14047|OTTMUSG00000015529	interleukin 1 beta, opposite strand	ncRNA
mm_75211.1	chr8	39605393	39605409	-	1	NA	3' UTR (NM_031195, exon 9 of 9)	3' UTR (NM_031195, exon 9 of 9)	37277	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_123039.1	chr14	55580126	55580164	-	1	NA	exon (NM_011189, exon 5 of 11)	exon (NM_011189, exon 5 of 11)	1651	NM_011189	19186	Mm.830	NM_011189	ENSMUSG00000022216	Psme1	AW413925|PA28a	proteasome (prosome, macropain) activator subunit 1 (PA28 alpha)	protein-coding
mm_112707.1	chr13	18781418	18781435	+	1	NA	intron (NM_172120, intron 4 of 28)	intron (NM_172120, intron 4 of 28)	64134	NM_172120	218035	Mm.27389	NM_172120	ENSMUSG00000041236	Vps41	AI317346|Vam2|mVam2	VPS41 HOPS complex subunit	protein-coding
mm_47305.1	chr5	122391742	122391762	-	1	NA	promoter-TSS (NM_019824)	promoter-TSS (NM_019824)	-126	NM_019824	56378	Mm.275942	NM_019824	ENSMUSG00000029465	Arpc3	1110006A04Rik|p21-ARC|p21-Ar|p21Arc	actin related protein 2/3 complex, subunit 3	protein-coding
mm_158998.1	chr1	143740341	143740341	+	1	NA	promoter-TSS (NM_001038594)	promoter-TSS (NM_001038594)	-106	NM_001038594	69367	Mm.272727	NM_023505	ENSMUSG00000018196	Glrx2	1700010P22Rik|AI645710|Grx2	glutaredoxin 2 (thioltransferase)	protein-coding
mm_46183.1	chr5	97392333	97392352	-	1	NA	promoter-TSS (NM_001033191)	promoter-TSS (NM_001033191)	-12	NM_001033191	97243	Mm.11746	NM_001033191	ENSMUSG00000046000	Naa11	Ard1b|Ard2|C80008	N(alpha)-acetyltransferase 11, NatA catalytic subunit	protein-coding
mm_128160.1	chr15	33550728	33550746	-	1	NA	intron (NM_176073, intron 7 of 7)	intron (NM_176073, intron 7 of 7)	102699	NR_045070	75880	Mm.396109	NR_045070		4930592A05Rik	-	RIKEN cDNA 4930592A05 gene	ncRNA
mm_86330.1	chr9	123061847	123061877	-	1	NA	exon (NM_177911, exon 11 of 14)	exon (NM_177911, exon 11 of 14)	27121	NM_177911	331046	Mm.195309	NM_177911	ENSMUSG00000025787	Tgm4	9530008N10Rik|Eapa1|TGP	transglutaminase 4 (prostate)	protein-coding
mm_4256.1	chr1	171411344	171411382	+	1	NA	promoter-TSS (NM_001305678)	promoter-TSS (NM_001305678)	50	NM_001305676	22278	Mm.8	NM_009480	ENSMUSG00000026641	Usf1	bHLHb11	upstream transcription factor 1	protein-coding
mm_136159.1	chr16	88290200	88290226	-	1	NA	promoter-TSS (NM_001346964)	promoter-TSS (NM_001346964)	45	NM_146072	14805	Mm.5134	NM_010348	ENSMUSG00000022935	Grik1	A830007B11Rik|D16Ium24|D16Ium24e|GluK1|GluK5|Glur-5|Glur5|Glurbeta1	glutamate receptor, ionotropic, kainate 1	protein-coding
mm_132678.1	chr16	42921862	42921868	+	1	NA	intron (NM_001285805, intron 1 of 10)	intron (NM_001285805, intron 1 of 10)	-9795	NR_040402	100503040	Mm.490721	NR_040402		Gm19522	-	predicted gene, 19522	ncRNA
mm_124514.1	chr14	121954749	121954771	-	1	NA	exon (NM_183031, exon 2 of 2)	exon (NM_183031, exon 2 of 2)	10433	NM_183031	321019	Mm.265618	NM_183031	ENSMUSG00000051212	Gpr183	Ebi2	G protein-coupled receptor 183	protein-coding
mm_69981.1	chr7	142380812	142380814	-	1	NA	exon (NM_009983, exon 5 of 9)	exon (NM_009983, exon 5 of 9)	7057	NM_009983	13033	Mm.231395	NM_009983	ENSMUSG00000007891	Ctsd	CD|CatD	cathepsin D	protein-coding
mm_64232.1	chr7	141694605	141694614	+	1	NA	exon (NM_023566, exon 9 of 46)	exon (NM_023566, exon 9 of 46)	4269	NM_023566	17831	Mm.2041	NM_023566		Muc2	2010015E03Rik|MCM|wnn	mucin 2	protein-coding
mm_156149.1	chrX	129885396	129885404	+	1	NA	intron (NM_172493, intron 4 of 26)	intron (NM_172493, intron 4 of 26)	135658	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diaph2	Dia3|Diap2|Drf2|E430022I22Rik	diaphanous related formin 2	protein-coding
mm_90969.1	chr10	13443683	13443694	-	1	NA	intron (NM_001195065, intron 1 of 12)	B2_Mm2|SINE|B2	30708	NM_001195065	215789	Mm.283359	NM_001033257	ENSMUSG00000062866	Phactr2	AV158170|BC012871	phosphatase and actin regulator 2	protein-coding
mm_156463.1	chrX	143483030	143483057	+	1	NA	Intergenic	SYNREP_MM|Satellite|Satellite	-35548	NM_001195048	18481	Mm.40035	NM_008778	ENSMUSG00000031284	Pak3	PAK-3|Pak65alpha|Pak65beta|Stk4	p21 protein (Cdc42/Rac)-activated kinase 3	protein-coding
mm_43960.1	chr5	145244078	145244108	+	1	NA	exon (NM_028298, exon 4 of 4)	exon (NM_028298, exon 4 of 4)	12334	NM_028298	72611	Mm.206555	NM_028298	ENSMUSG00000007812	Zfp655	2700038I16Rik|9030409O18Rik|mKIAA4222	zinc finger protein 655	protein-coding
mm_89367.1	chr10	88731057	88731073	+	1	NA	promoter-TSS (NM_025859)	promoter-TSS (NM_025859)	36	NM_001037166	237433	Mm.478763	NM_001037166		Gm4925	EG237433	predicted gene 4925	protein-coding
mm_70573.1	chr8	13165844	13165858	+	1	NA	exon (NM_010684, exon 2 of 9)	exon (NM_010684, exon 2 of 9)	6690	NM_010684	16783	Mm.16716	NM_010684	ENSMUSG00000031447	Lamp1	CD107a|LGP-120|LGP-A|Lamp-1|P2B	lysosomal-associated membrane protein 1	protein-coding
mm_110467.1	chr12	51829499	51829517	-	1	NA	promoter-TSS (NM_144788)	promoter-TSS (NM_144788)	28	NM_144788	207304	Mm.249391	NM_144788	ENSMUSG00000035247	Hectd1	A630086P08Rik|AI844876|b2b327Clo|opm	HECT domain containing 1	protein-coding
mm_143462.1	chr17	70997920	70997955	-	1	NA	intron (NM_026064, intron 1 of 3)	intron (NM_026064, intron 1 of 3)	4596	NM_026064	67268	Mm.489605	NM_026064	ENSMUSG00000024048	Myl12a	2900073G15Rik|AI838292|C80200	myosin, light chain 12A, regulatory, non-sarcomeric	protein-coding
mm_7743.1	chr1	131037984	131037984	-	1	NA	Intergenic	L1M2|LINE|L1	18139	NM_010548	16153	Mm.874	NM_010548	ENSMUSG00000016529	Il10	CSIF|Il-10	interleukin 10	protein-coding
mm_18197.1	chr2	45117401	45117411	-	1	NA	Intergenic	Intergenic	-4127	NM_015753	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_104821.1	chr11	99001395	99001397	-	1	NA	exon (NM_011623, exon 25 of 36)	exon (NM_011623, exon 25 of 36)	-18380	NM_178596	353155	Mm.453253	NM_178596	ENSMUSG00000047197	Gjd3	Gja11|Gjc1|cx30.2	gap junction protein, delta 3	protein-coding
mm_73886.1	chr8	119345622	119345632	+	1	NA	exon (NM_024219, exon 3 of 4)	exon (NM_024219, exon 3 of 4)	1089	NM_024219	68196	Mm.358714	NM_024219	ENSMUSG00000031839	Hsbp1	0610007A03Rik|AA408769|Hsp25	heat shock factor binding protein 1	protein-coding
mm_27788.1	chr3	75268332	75268342	-	1	NA	intron (NM_026460, intron 1 of 8)	intron (NM_026460, intron 1 of 8)	1741	NM_026460	67931	Mm.259446	NM_026460	ENSMUSG00000034139	Serpini2	Spi14	serine (or cysteine) peptidase inhibitor, clade I, member 2	protein-coding
mm_159484.1	chr4	41730443	41730443	-	1	NA	intron (NM_001252622, intron 1 of 6)	intron (NM_001252622, intron 1 of 6)	699	NM_001017362	550619	Mm.425179	NM_001017362	ENSMUSG00000066224	Arid3c	OTTMUSG00000006683	AT rich interactive domain 3C (BRIGHT-like)	protein-coding
mm_130319.1	chr15	97373884	97373895	-	1	NA	intron (NM_172293, intron 4 of 5)	intron (NM_172293, intron 4 of 5)	-126602	NM_001164602	105827	Mm.24005	NM_178114	ENSMUSG00000048218	Amigo2	AI415330|AMIGO-2|AW208913|Ali1	adhesion molecule with Ig like domain 2	protein-coding
mm_70502.1	chr8	12867113	12867116	+	1	NA	non-coding (NR_121603, exon 30 of 30)	non-coding (NR_121603, exon 30 of 30)	-35195	NR_045775	100504249	Mm.441494	NR_045775	ENSMUSG00000084780	Gm15350	OTTMUSG00000020611	predicted gene 15350	ncRNA
mm_26861.1	chr3	14993967	14993970	-	1	NA	intron (NR_040550, intron 3 of 3)	RLTR41|LTR|ERV1	22767	NR_040550	77127	Mm.195792	NR_040549	ENSMUSG00000098008	A930001A20Rik	-	RIKEN cDNA A930001A20 gene	ncRNA
mm_31196.1	chr4	43663932	43663947	+	1	NA	intron (NM_175517, intron 3 of 6)	intron (NM_175517, intron 3 of 6)	4920	NM_175517	242408	Mm.440423	NM_175517	ENSMUSG00000043633	Fam221b	4930412F15Rik	family with sequence similarity 221, member B	protein-coding
mm_19196.1	chr2	84442783	84442793	-	1	NA	3' UTR (NM_001177319, exon 8 of 8)	3' UTR (NM_001177319, exon 8 of 8)	-17522	NM_018782	54598	Mm.75467	NM_018782	ENSMUSG00000059588	Calcrl	AV071593|CRLR	calcitonin receptor-like	protein-coding
mm_62022.1	chr7	91563080	91563086	+	1	NA	intron (NM_011807, intron 2 of 22)	intron (NM_011807, intron 2 of 22)	472297	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_121441.1	chr14	120430102	120430142	+	1	NA	3' UTR (NM_207515, exon 8 of 8)	3' UTR (NM_207515, exon 8 of 8)	-48339	NM_029519	76108	Mm.261448	NM_029519	ENSMUSG00000051615	Rap2a	5830461H18Rik	RAS related protein 2a	protein-coding
mm_10046.1	chr1	193173376	193173389	-	1	NA	promoter-TSS (NM_181048)	promoter-TSS (NM_181048)	-87	NM_001160360	319266	Mm.482460	NM_181048	ENSMUSG00000079144	A130010J15Rik	-	RIKEN cDNA A130010J15 gene	protein-coding
mm_52127.1	chr6	97943300	97943311	+	1	NA	intron (NM_001113198, intron 2 of 9)	intron (NM_001113198, intron 2 of 9)	13488	NM_001178049	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_135550.1	chr16	49840029	49840046	-	1	NA	Intergenic	Intergenic	-15617	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_95426.1	chr11	50174840	50174884	+	1	NA	promoter-TSS (NM_026543)	promoter-TSS (NM_026543)	11	NM_026543	68067	Mm.40828	NM_026543	ENSMUSG00000020381	Mrnip	2900016G09Rik|3010026O09Rik|AI851514|AW475975	MRN complex interacting protein	protein-coding
mm_156296.1	chrX	136837583	136837587	+	1	NA	3' UTR (NM_011123, exon 7 of 7)	3' UTR (NM_011123, exon 7 of 7)	14839	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_109395.1	chr12	109854063	109854063	+	1	NA	Intergenic	L1M4b|LINE|L1	106185	NR_037233	100499517		NR_037233	ENSMUSG00000093351	Mir3072	mir-3072|mmu-mir-3072	microRNA 3072	ncRNA
mm_76556.1	chr8	88362043	88362049	-	1	NA	5' UTR (NM_012047, exon 1 of 17)	5' UTR (NM_012047, exon 1 of 17)	145	NM_012047	26992	Mm.5400	NM_012047	ENSMUSG00000031660	Brd7	BP75|CELTIX1|Ptpn13ip	bromodomain containing 7	protein-coding
mm_110672.1	chr12	65159204	65159205	-	1	NA	intron (NM_172578, intron 2 of 13)	intron (NM_172578, intron 2 of 13)	13376	NM_172578	217653	Mm.21144	NM_172578	ENSMUSG00000047534	Mis18bp1	6720403H11|C79407|Knl2|mKIAA1903	MIS18 binding protein 1	protein-coding
mm_4953.1	chr1	191225441	191225467	+	1	NA	Intergenic	Intergenic	-42121	NM_007498	11910	Mm.2706	NM_007498	ENSMUSG00000026628	Atf3	LRG-21	activating transcription factor 3	protein-coding
mm_37297.1	chr4	119190006	119190016	-	1	NA	promoter-TSS (NM_013848)	promoter-TSS (NM_013848)	0	NM_013848	27028	Mm.290753	NM_013848	ENSMUSG00000028644	Ermap	AA409279|AI666418	erythroblast membrane-associated protein	protein-coding
mm_84410.1	chr9	65556867	65556888	-	1	NA	exon (NM_153119, exon 6 of 6)	exon (NM_153119, exon 6 of 6)	23210	NM_153119	102595	Mm.247303	NM_153119	ENSMUSG00000050721	Plekho2	AI840980|Plekhq1	pleckstrin homology domain containing, family O member 2	protein-coding
mm_141907.1	chr17	34959233	34959238	-	1	NA	promoter-TSS (NM_010478)	promoter-TSS (NM_010478)	3	NM_010478	15511	Mm.372314	NM_010478	ENSMUSG00000090877	Hspa1b	Hsp70|Hsp70-1|Hsp70.1|hsp68	heat shock protein 1B	protein-coding
mm_81732.1	chr9	113756341	113756353	+	1	NA	intron (NM_001286599, intron 1 of 10)	RMER13A1|LTR|ERVK	14874	NM_001114347	76499	Mm.222272	NM_029633	ENSMUSG00000033392	Clasp2	1500004F14Rik|8030404L10Rik|C77448|CLASP2beta|mKIAA0627	CLIP associating protein 2	protein-coding
mm_111849.1	chr12	107938949	107938958	-	1	NA	intron (NM_001286343, intron 1 of 1)	(TG)n|Simple_repeat|Simple_repeat	64461	NM_001079883	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_2179.1	chr1	88472403	88472412	+	1	NA	Intergenic	Intergenic	37659	NM_008132	14659	Mm.5187	NM_008132	ENSMUSG00000062310	Glrp1	GRP-1	glutamine repeat protein 1	protein-coding
mm_131389.1	chr16	14209651	14209682	+	1	NA	exon (NM_013607, exon 28 of 42)	exon (NM_013607, exon 28 of 42)	46391	NM_001114085	67203	Mm.24105	NM_023317	ENSMUSG00000022678	Nde1	2810027M15Rik|AU042936|AW822251|Nude|mNudE	nudE neurodevelopment protein 1	protein-coding
mm_1524.1	chr1	72826619	72826632	+	1	NA	intron (NM_001310659, intron 1 of 3)	intron (NM_001310659, intron 1 of 3)	1238	NM_001310659	16008	Mm.141936	NM_008342	ENSMUSG00000039323	Igfbp2	AI255832|IBP-2|Igfbp-2|mIGFBP-2	insulin-like growth factor binding protein 2	protein-coding
mm_83897.1	chr9	56136461	56136517	-	1	NA	3' UTR (NM_019793, exon 7 of 7)	3' UTR (NM_019793, exon 7 of 7)	24581	NM_019793	56434	Mm.28484	NM_019793	ENSMUSG00000032324	Tspan3	1700055K04Rik|TM4-A|Tm4sf8	tetraspanin 3	protein-coding
mm_78643.1	chr9	40269452	40269472	+	1	NA	5' UTR (NM_001083917, exon 1 of 7)	5' UTR (NM_001083917, exon 1 of 7)	246	NM_178227	235281	Mm.290083	NM_153522	ENSMUSG00000049281	Scn3b	1110001K16Rik|4833414B02Rik|Scnb3	sodium channel, voltage-gated, type III, beta	protein-coding
mm_68249.1	chr7	105565572	105565589	-	1	NA	exon (NM_001253887, exon 9 of 14)	exon (NM_001253887, exon 9 of 14)	3197	NM_001310600	11785	Mm.38469	NM_009685	ENSMUSG00000037032	Apbb1	Fe65|Rir	amyloid beta (A4) precursor protein-binding, family B, member 1	protein-coding
mm_89144.1	chr10	85927401	85927408	+	1	NA	Intergenic	Intergenic	-1087	NM_001163614	67341	Mm.382315	NM_001163614	ENSMUSG00000085111	Ascl4	1700054F16Rik|bHLHa44	achaete-scute family bHLH transcription factor 4	protein-coding
mm_3665.1	chr1	153486897	153486921	+	1	NA	intron (NM_007842, intron 1 of 27)	intron (NM_007842, intron 1 of 27)	751	NM_007842	13211	Mm.20000	NM_007842	ENSMUSG00000042699	Dhx9	AI326842|Ddx9|HEL-5|NDHII|RHA|mHEL-5	DEAH (Asp-Glu-Ala-His) box polypeptide 9	protein-coding
mm_6567.1	chr1	75180350	75180407	-	1	NA	promoter-TSS (NM_023732)	promoter-TSS (NM_023732)	14	NM_023732	74104	Mm.28663	NM_023732	ENSMUSG00000026198	Abcb6	1200005B17Rik	ATP-binding cassette, sub-family B (MDR/TAP), member 6	protein-coding
mm_81860.1	chr9	118835493	118835506	+	1	NA	intron (NM_001113514, intron 6 of 13)	B3A|SINE|B2	-91037	NM_133710	69274	Mm.439928	NM_133710	ENSMUSG00000047409	Ctdspl	2810418J22Rik|AI426263|HYA22|SCP3	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase-like	protein-coding
mm_11082.1	chr2	27714490	27714499	+	1	NA	intron (NM_001290482, intron 1 of 9)	intron (NM_001290482, intron 1 of 9)	3911	NM_001290482	20181	Mm.24624	NM_011305	ENSMUSG00000015846	Rxra	9530071D11Rik|Nr2b1|RXRalpha1	retinoid X receptor alpha	protein-coding
mm_36482.1	chr4	82885104	82885110	-	1	NA	promoter-TSS (NM_009887)	promoter-TSS (NM_009887)	44	NM_009887	12622	Mm.6780	NM_009887	ENSMUSG00000038192	Cer1	Cerl|Cerl1|Cerr1|cer-1	cerberus 1, DAN family BMP antagonist	protein-coding
mm_158855.1	chrX	169997113	169997121	-	1	NA	Intergenic	CpG	-18200	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_129904.1	chr15	83936083	83936104	-	1	NA	promoter-TSS (NM_001161628)	promoter-TSS (NM_001161628)	2	NM_001161628	77627	Mm.196288	NM_029946	ENSMUSG00000022441	Efcab6	4931407K02Rik|4932408N08Rik|bM150J22.2|mKIAA1672	EF-hand calcium binding domain 6	protein-coding
mm_34092.1	chr4	138833265	138833277	+	1	NA	non-coding (NR_002926, exon 4 of 5)	non-coding (NR_002926, exon 4 of 5)	1395	NM_001082531	18780	Mm.4675	NM_011108	ENSMUSG00000058908	Pla2g2a	EF|Mom1|Pla2|sPLA2|sPla2-IIA	phospholipase A2, group IIA (platelets, synovial fluid)	protein-coding
mm_119216.1	chr14	33214041	33214069	+	1	NA	Intergenic	Intergenic	-2768	NM_153800	239027	Mm.318350	NM_153800	ENSMUSG00000063506	Arhgap22	B230341L19Rik|RHOGAP2|p68RacGAP	Rho GTPase activating protein 22	protein-coding
mm_33332.1	chr4	129136878	129136903	+	1	NA	promoter-TSS (NM_027402)	promoter-TSS (NM_027402)	-109	NM_027402	384061	Mm.44075	NM_027402	ENSMUSG00000001334	Fndc5	1500001L03Rik|AI836596|C87088|PeP|Pxp	fibronectin type III domain containing 5	protein-coding
mm_116591.1	chr13	48513395	48513452	-	1	NA	promoter-TSS (NM_026450)	promoter-TSS (NM_026450)	-13	NM_001164575	67911	Mm.251375	NM_026450	ENSMUSG00000050954	Zfp169	1700025J14Rik|4930429A13Rik|BE688704	zinc finger protein 169	protein-coding
mm_11461.1	chr2	32236602	32236622	+	1	NA	promoter-TSS (NM_145145)	promoter-TSS (NM_145145)	-71	NM_145145	99011	Mm.31192	NM_145145	ENSMUSG00000039254	Pomt1	AI505244	protein-O-mannosyltransferase 1	protein-coding
mm_131526.1	chr16	17640875	17640923	+	1	NA	exon (NM_029945, exon 16 of 20)	exon (NM_029945, exon 16 of 20)	-5571	NM_001166164	72315	Mm.297777	NM_001166164	ENSMUSG00000041617	Ccdc74a	2310015A05Rik	coiled-coil domain containing 74A	protein-coding
mm_122113.1	chr14	31000964	31000976	-	1	NA	promoter-TSS (NM_001165930)	promoter-TSS (NM_001165930)	-423	NM_001165930	76485	Mm.8766	NM_029626	ENSMUSG00000021916	Glt8d1	2410004H05Rik|5430414N14Rik|AI450005	glycosyltransferase 8 domain containing 1	protein-coding
mm_107689.1	chr12	55303242	55303284	+	1	NA	promoter-TSS (NM_021529)	promoter-TSS (NM_021529)	-263	NM_021529	59032	Mm.427307	NM_021529	ENSMUSG00000021022	Ppp2r3c	4930511A21Rik|5730412A08Rik|G4-1|G5pr	protein phosphatase 2, regulatory subunit B'', gamma	protein-coding
mm_165724.1	chr3	103020452	103020469	-	1	NA	promoter-TSS (NM_001310693)	promoter-TSS (NM_001310693)	-86	NM_001310693	229663	Mm.277713	NM_144901	ENSMUSG00000068823	Csde1	AA960392|BC016898|D3Jfr1|mKIAA0885|unr	cold shock domain containing E1, RNA binding	protein-coding
mm_75731.1	chr8	69395493	69395553	-	1	NA	promoter-TSS (NR_038043)	promoter-TSS (NR_038043)	21	NR_038044	378466	Mm.37846	NM_194351	ENSMUSG00000110444	Gm10033	9330175B10Rik|ENSMUSG00000057924|Gm10311	predicted gene 10033	ncRNA
mm_86294.1	chr9	122187606	122187634	-	1	NA	intron (NM_001271873, intron 12 of 12)	intron (NM_001271873, intron 12 of 12)	70354	NM_133741	20623	Mm.257989	NM_133741	ENSMUSG00000038145	Snrk	2010012F07Rik|AI448042|AW547029|E030034B15|R74830|mKIAA0096	SNF related kinase	protein-coding
mm_43654.1	chr5	138441472	138441530	+	1	NA	promoter-TSS (NM_028130)	promoter-TSS (NM_028130)	25	NM_028130	72154	Mm.20263	NM_028130	ENSMUSG00000036898	Zfp157	2610020C11Rik|A630094N24Rik|AI327407|mszf12|mszf23-1	zinc finger protein 157	protein-coding
mm_49911.1	chr6	39024306	39024307	+	1	NA	intron (NM_011539, intron 8 of 12)	B1_Mus2|SINE|Alu	43280	NR_040523	69986	Mm.490941	NR_040523	ENSMUSG00000100121	1700025N23Rik	-	RIKEN cDNA 1700025N23 gene	ncRNA
mm_151099.1	chr19	47855023	47855047	+	1	NA	promoter-TSS (NM_010362)	promoter-TSS (NM_010362)	62	NM_010362	14873	Mm.378931	NM_010362	ENSMUSG00000025068	Gsto1	AA407097|AI194287|AU018802|Gsto-1|Gstx|Spg-r|p28	glutathione S-transferase omega 1	protein-coding
mm_7230.1	chr1	93425364	93425388	-	1	NA	exon (NM_133808, exon 12 of 28)	exon (NM_133808, exon 12 of 28)	20325	NM_001301364	110611	Mm.30012	NM_133808	ENSMUSG00000034088	Hdlbp	1110005P14Rik|AA960365|AI118566|D1Ertd101e	high density lipoprotein (HDL) binding protein	protein-coding
mm_165891.1	chr4	44328910	44328913	+	1	NA	intron (NM_010790, intron 10 of 17)	B3A|SINE|B2	27994	NM_010790	17279	Mm.268668	NM_010790	ENSMUSG00000035683	Melk	AI327312|MPK38|mKIAA0175	maternal embryonic leucine zipper kinase	protein-coding
mm_53915.1	chr6	4030895	4030901	-	1	NA	TTS (NR_131108)	TTS (NR_131108)	16686	NR_131108	78034	Mm.243851	NR_131108	ENSMUSG00000107681	4930528H21Rik	-	RIKEN cDNA 4930528H21 gene	ncRNA
mm_743.1	chr1	43522302	43522309	+	1	NA	intron (NM_010879, intron 2 of 4)	intron (NM_010879, intron 2 of 4)	76554	NM_010879	17974	Mm.389903	NM_010879	ENSMUSG00000066877	Nck2	4833426I10Rik|Grb4|NCKbeta|Nck-2	non-catalytic region of tyrosine kinase adaptor protein 2	protein-coding
mm_40153.1	chr5	35395657	35395662	+	1	NA	Intergenic	Intergenic	6542	NM_010445	15371	Mm.358606	NM_010445	ENSMUSG00000067438	Hmx1	Nkx5-3	H6 homeobox 1	protein-coding
mm_172730.1	chr8	77907117	77907132	+	1	NA	Intergenic	L1Md_T|LINE|L1	-182672	NM_010332	13617	Mm.283168	NM_010332	ENSMUSG00000031616	Ednra	ET-AR|ETa|Gpcr10	endothelin receptor type A	protein-coding
mm_25785.1	chr3	126780363	126780390	+	1	NA	exon (NM_001293663, exon 7 of 20)	exon (NM_001293663, exon 7 of 20)	163010	NM_001034168	109676	Mm.220242	NM_178655	ENSMUSG00000032826	Ank2	100043364|AI835472|AW491075|Ank-2|Gm4392	ankyrin 2, brain	protein-coding
mm_162426.1	chr1	92774999	92775008	-	1	NA	Intergenic	Intergenic	-56683	NM_016696	14733	Mm.297976	NM_016696	ENSMUSG00000034220	Gpc1	AI462976	glypican 1	protein-coding
mm_137665.1	chr17	28692619	28692651	+	1	NA	promoter-TSS (NM_001168513)	promoter-TSS (NM_001168513)	67	NM_001168513	26416	Mm.311337	NM_011951	ENSMUSG00000053436	Mapk14	CSBP2|Crk1|Csbp1|Mxi2|PRKM14|PRKM15|p38|p38-alpha|p38MAPK|p38a|p38alpha	mitogen-activated protein kinase 14	protein-coding
mm_1613.1	chr1	74391480	74391495	+	1	NA	promoter-TSS (NM_153088)	promoter-TSS (NM_153088)	-122	NM_153088	227292	Mm.165042	NM_153088	ENSMUSG00000026176	Ctdsp1	GIP|NLIIF|Nif3|SCP1	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 1	protein-coding
mm_116529.1	chr13	45828022	45828029	-	1	NA	intron (NM_001199304, intron 3 of 6)	intron (NM_001199304, intron 3 of 6)	136966	NM_001199304	20238	Mm.342683	NM_009124	ENSMUSG00000046876	Atxn1	2900016G23Rik|Atx1|C85907|ENSMUSG00000074917|Gm10786|Sca1	ataxin 1	protein-coding
mm_49100.1	chr6	7846978	7846982	+	1	NA	intron (NM_052993, intron 1 of 3)	intron (NM_052993, intron 1 of 3)	1756	NM_052993	94192	Mm.102752	NM_052993	ENSMUSG00000042460	C1galt1	2210410E06Rik|AV284120|T-synthase	core 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase, 1	protein-coding
mm_126474.1	chr15	81466666	81466711	+	1	NA	intron (NM_019712, intron 1 of 4)	CpG	372	NM_019712	56438	Mm.29405	NM_019712	ENSMUSG00000022400	Rbx1	1500002P15Rik|AA517855|ROC1	ring-box 1	protein-coding
mm_48756.1	chr5	148329939	148329981	-	1	NA	3' UTR (NM_007513, exon 13 of 13)	3' UTR (NM_007513, exon 13 of 13)	62855	NM_001301424	11987	Mm.275489	NM_007513	ENSMUSG00000041313	Slc7a1	4831426K01Rik|AI447493|Atrc-1|Atrc1|Cat1|Rec-1|Rev-1|mCAT-1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 1	protein-coding
mm_146643.1	chr18	10785479	10785482	-	1	NA	promoter-TSS (NR_035413)	promoter-TSS (NR_035413)	34	NR_035413	100316783		NR_035413	ENSMUSG00000080662	Mir1b	Mir1-2-as|Mir1-2as|Mirn1-2as|mir-1b|mmu-mir-1-2-as|mmu-mir-1b	microRNA 1b	ncRNA
mm_156632.1	chrX	155622786	155622811	+	1	NA	intron (NM_001093750, intron 1 of 2)	CpG	529	NM_001093750	211612	Mm.218811	NM_001093750	ENSMUSG00000041552	Ptchd1	9630036J22Rik|AI848149|Gm387	patched domain containing 1	protein-coding
mm_168354.1	chr1	113904266	113904277	-	1	NA	Intergenic	L1Md_F3|LINE|L1	-1780866	NM_001077425	636808	Mm.101576	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding
mm_170003.1	chr1	71652927	71652927	-	1	NA	promoter-TSS (NR_040308)	promoter-TSS (NR_040308)	307	NM_010233	14268	Mm.193099	NM_010233	ENSMUSG00000026193	Fn1	E330027I09|Fn|Fn-1	fibronectin 1	protein-coding
mm_47824.1	chr5	134256917	134256944	-	1	NA	intron (NM_001080746, intron 17 of 34)	intron (NM_001080746, intron 17 of 34)	-27305	NR_104383	17969	Mm.425296	NM_010876	ENSMUSG00000015950	Ncf1	NCF-47K|NOXO2|Ncf-1|p47-phox|p47<phox>|p47phox	neutrophil cytosolic factor 1	protein-coding
mm_149996.1	chr19	29266662	29266682	+	1	NA	intron (NM_001048177, intron 2 of 23)	L1M4c|LINE|L1	14869	NM_008413	16452	Mm.275839	NM_008413	ENSMUSG00000024789	Jak2	Fd17	Janus kinase 2	protein-coding
mm_96756.1	chr11	69911330	69911348	+	1	NA	intron (NM_001013414, intron 25 of 28)	intron (NM_001013414, intron 25 of 28)	-2853	NM_019726	56310	Mm.477738	NM_019726	ENSMUSG00000023170	Gps2	AI505953	G protein pathway suppressor 2	protein-coding
mm_150985.1	chr19	46515840	46515856	+	1	NA	3' UTR (NM_053100, exon 6 of 6)	3' UTR (NM_053100, exon 6 of 6)	14200	NM_053100	93679	Mm.392177	NM_053100	ENSMUSG00000025034	Trim8	AA408830|BB006755|GERP|Rnf27	tripartite motif-containing 8	protein-coding
mm_32392.1	chr4	106622487	106622511	+	1	NA	promoter-TSS (NM_177667)	promoter-TSS (NM_177667)	50	NM_177667	230576	Mm.41945	NM_177667	ENSMUSG00000034919	Ttc22	4732467L16Rik	tetratricopeptide repeat domain 22	protein-coding
mm_90911.1	chr10	11869255	11869300	-	1	NA	Intergenic	Intergenic	260053	NM_013898	30058	Mm.214504	NM_013898	ENSMUSG00000048007	Timm8a1	DXHXS1274E|Ddp1|Fci-12|Tim8a|Timm8a	translocase of inner mitochondrial membrane 8A1	protein-coding
mm_57472.1	chr6	125232923	125232934	-	1	NA	3' UTR (NM_001042564, exon 4 of 4)	3' UTR (NM_001042564, exon 4 of 4)	-1068	NM_145391	213233	Mm.296902	NM_145391	ENSMUSG00000038213	Tapbpl	BC017613|TAPBPL-R|Tapbplr	TAP binding protein-like	protein-coding
mm_139894.1	chr17	70852016	70852023	+	1	NA	promoter-TSS (NM_001164075)	promoter-TSS (NM_001164075)	-285	NM_001164075	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_79222.1	chr9	49518338	49518340	+	1	NA	promoter-TSS (NR_029465)	promoter-TSS (NR_029465)	51	NR_029465	100036537	Mm.437541	NR_029465	ENSMUSG00000079564	Gm11149	ENSMUSG00000060603|ENSMUSG00000079564	predicted gene 11149	ncRNA
mm_112609.1	chr13	14613244	14613272	+	1	NA	promoter-TSS (NM_008944)	promoter-TSS (NM_008944)	16	NM_008944	19166	Mm.252255	NM_008944	ENSMUSG00000015671	Psma2	Lmpc3	proteasome (prosome, macropain) subunit, alpha type 2	protein-coding
mm_145644.1	chr18	61121970	61121979	+	1	NA	intron (NM_001037859, intron 11 of 21)	B3|SINE|B2	4506	NR_105949	102466212		NR_105949	ENSMUSG00000098389	Mir6983	Gm27496|mmu-mir-6983	microRNA 6983	ncRNA
mm_148251.1	chr18	80713572	80713590	-	1	NA	promoter-TSS (NM_001164109)	promoter-TSS (NM_001164109)	-510	NM_001164109	18018	Mm.329560	NM_016791	ENSMUSG00000033016	Nfatc1	2210017P03Rik|AI449492|AV076380|NF-ATc|NFAT2|NFATc|Nfatcb	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 1	protein-coding
mm_31033.1	chr4	40948494	40948504	+	1	NA	promoter-TSS (NM_001171739)	promoter-TSS (NM_001171739)	-54	NM_029814	76959	Mm.212763	NM_029814	ENSMUSG00000028419	Chmp5	2210412K09Rik|AW545668	charged multivesicular body protein 5	protein-coding
mm_171771.1	chr5	108763006	108763020	+	1	NA	promoter-TSS (NR_040691)	promoter-TSS (NR_040691)	-829	NR_040691	73295	Mm.416858	NR_040691	ENSMUSG00000101762	1700047L14Rik	-	RIKEN cDNA 1700047L14 gene	ncRNA
mm_133850.1	chr16	96214009	96214022	+	1	NA	exon (NM_015825, exon 3 of 8)	exon (NM_015825, exon 3 of 8)	13545	NM_015825	50795	Mm.28638	NM_015825	ENSMUSG00000040666	Sh3bgr	5430437A18Rik	SH3-binding domain glutamic acid-rich protein	protein-coding
mm_141859.1	chr17	34804065	34804078	-	1	NA	exon (NM_009995, exon 2 of 10)	exon (NM_009995, exon 2 of 10)	355	NM_009995	13079	Mm.440407	NM_009995	ENSMUSG00000024365	Cyp21a1	21-OH|21OH|21OHA|21OHB|CYP21OH-A|Cyp21|Cyp21-ps1|Cyp21B|Cyp21a2-ps|Cyp21a2ps|Oh21-1|Oh21-2	cytochrome P450, family 21, subfamily a, polypeptide 1	protein-coding
mm_76515.1	chr8	87470099	87470109	-	1	NA	3' UTR (NM_019626, exon 3 of 3)	3' UTR (NM_019626, exon 3 of 3)	2488	NM_019626	12404	Mm.4880	NM_019626	ENSMUSG00000031654	Cbln1	AI323299	cerebellin 1 precursor protein	protein-coding
mm_76385.1	chr8	84842594	84842598	-	1	NA	3' UTR (NM_007591, exon 9 of 9)	3' UTR (NM_007591, exon 9 of 9)	-1931	NM_009010	19358	Mm.255539	NM_009010	ENSMUSG00000003813	Rad23a	2310040P19Rik|AL024030|HR23A|mHR23A	RAD23 homolog A, nucleotide excision repair protein	protein-coding
mm_116774.1	chr13	52979839	52979844	-	1	NA	intron (NM_017373, intron 1 of 1)	intron (NM_017373, intron 1 of 1)	1198	NM_017373	18030	Mm.136604	NM_017373	ENSMUSG00000056749	Nfil3	AV225605|E4BP4	nuclear factor, interleukin 3, regulated	protein-coding
mm_162416.1	chr1	87901267	87901285	+	1	NA	intron (NM_177646, intron 3 of 29)	intron (NM_177646, intron 3 of 29)	-46977	NR_136921	100503175	Mm.426422	NR_136921	ENSMUSG00000101942	Gm19582	-	predicted gene, 19582	ncRNA
mm_140439.1	chr17	88530114	88530142	+	1	NA	promoter-TSS (NM_028658)	promoter-TSS (NM_028658)	4	NM_028658	73825	Mm.271817	NM_028658	ENSMUSG00000034709	Ppp1r21	1110018J12Rik|AI426045|AW550781|Ccdc128|Klraq1	protein phosphatase 1, regulatory subunit 21	protein-coding
mm_80974.1	chr9	103143367	103143385	+	1	NA	intron (NM_173781, intron 2 of 7)	intron (NM_173781, intron 2 of 7)	31302	NM_173781	270192	Mm.490252	NM_173781	ENSMUSG00000032549	Rab6b	9630015C03|AI844641|C330006L04Rik|D9Bwg0185e	RAB6B, member RAS oncogene family	protein-coding
mm_108161.1	chr12	76367330	76367339	+	1	NA	intron (NM_028356, intron 1 of 2)	intron (NM_028356, intron 1 of 2)	2130	NM_001172104	109929	Mm.41880	NM_028356	ENSMUSG00000056459	Zbtb25	2810462M08Rik|2900064P18Rik|AI842128|Kup|Zfp-50|Zfp50	zinc finger and BTB domain containing 25	protein-coding
mm_152051.1	chr19	6235805	6235860	-	1	NA	promoter-TSS (NM_198168)	promoter-TSS (NM_198168)	8	NM_198168	225849	Mm.118076	NM_198168	ENSMUSG00000024777	Ppp2r5b	B'beta|BC026670	protein phosphatase 2, regulatory subunit B', beta	protein-coding
mm_36532.1	chr4	86612010	86612062	-	1	NA	promoter-TSS (NM_173400)	promoter-TSS (NM_173400)	-14	NM_173400	230376	Mm.74730	NM_173400	ENSMUSG00000038047	Haus6	6230416J20Rik|9830144E06|D4Ertd27e|mKIAA1574	HAUS augmin-like complex, subunit 6	protein-coding
mm_62180.1	chr7	97451317	97451331	+	1	NA	promoter-TSS (NM_001136235)	promoter-TSS (NM_001136235)	-10	NM_001136235	233529	Mm.334033	NM_001010826	ENSMUSG00000051727	Kctd14	AI449310|D7Ertd760e	potassium channel tetramerisation domain containing 14	protein-coding
mm_83506.1	chr9	45984378	45984381	-	1	NA	intron (NM_008775, intron 1 of 5)	intron (NM_008775, intron 1 of 5)	492	NM_008775	18475	Mm.200859	NM_008775	ENSMUSG00000003131	Pafah1b2	AI747451|AU021353|Pafahb|mus[b]	platelet-activating factor acetylhydrolase, isoform 1b, subunit 2	protein-coding
mm_102749.1	chr11	67255712	67255730	-	1	NA	exon (NM_010855, exon 32 of 40)	exon (NM_010855, exon 32 of 40)	17909	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_35803.1	chr4	46602194	46602224	-	1	NA	promoter-TSS (NM_001164804)	promoter-TSS (NM_001164804)	-280	NM_001164804	107684	Mm.416311	NM_178893	ENSMUSG00000028337	Coro2a	9030208C03Rik|AI563590|IR10	coronin, actin binding protein 2A	protein-coding
mm_12622.1	chr2	74697947	74697951	+	1	NA	5' UTR (NM_013555, exon 1 of 2)	5' UTR (NM_013555, exon 1 of 2)	186	NM_013555	15438	Mm.26544	NM_013555	ENSMUSG00000043342	Hoxd9	Hox-4.4|Hox-5.2	homeobox D9	protein-coding
mm_17793.1	chr2	33130222	33130251	-	1	NA	Intergenic	CpG	-43032	NM_178888	99326	Mm.41290	NM_178888	ENSMUSG00000038860	Garnl3	AW120551	GTPase activating RANGAP domain-like 3	protein-coding
mm_29326.1	chr3	108044802	108044882	-	1	NA	promoter-TSS (NM_001160411)	promoter-TSS (NM_001160411)	14	NM_026764	14865	Mm.31203	NM_026764	ENSMUSG00000027890	Gstm4	1110004G14Rik|GSTM7-7|Gstb-4|Gstb4	glutathione S-transferase, mu 4	protein-coding
mm_50291.1	chr6	47454683	47454701	+	1	NA	intron (NM_012042, intron 1 of 21)	CpG	368	NM_012042	26965	Mm.87611	NM_012042	ENSMUSG00000029686	Cul1	-	cullin 1	protein-coding
mm_56592.1	chr6	108472537	108472549	-	1	NA	intron (NM_010585, intron 45 of 61)	ORR1F|LTR|ERVL-MaLR	-17200	NR_106121	102465766		NR_106121	ENSMUSG00000105697	Mir7661	mmu-mir-7661	microRNA 7661	ncRNA
mm_11561.1	chr2	32775842	32775851	+	1	NA	promoter-TSS (NM_001290563)	promoter-TSS (NM_001290563)	25	NM_178595	329384	Mm.268037	NM_178595	ENSMUSG00000053746	Ptrh1	2210013M04Rik|AW046744	peptidyl-tRNA hydrolase 1 homolog	protein-coding
mm_104357.1	chr11	94303869	94303891	-	1	NA	exon (NM_026313, exon 4 of 11)	exon (NM_026313, exon 4 of 11)	18031	NM_026313	67684	Mm.30927	NM_026313	ENSMUSG00000020863	Luc7l3	3300001P08Rik|Luc7a	LUC7-like 3 (S. cerevisiae)	protein-coding
mm_78140.1	chr9	20897887	20897915	+	1	NA	exon (NM_016876, exon 4 of 11)	exon (NM_016876, exon 4 of 11)	689	NM_016876	53356	Mm.427309	NM_016876	ENSMUSG00000070319	Eif3g	44kDa|D0Jmb4|Eif3s4|TU-189B2|eIF3-p44|p44	eukaryotic translation initiation factor 3, subunit G	protein-coding
mm_12301.1	chr2	69105058	69105076	+	1	NA	exon (NM_001347161, exon 9 of 11)	exon (NM_001347161, exon 9 of 11)	-30733	NM_181547	329416	Mm.90047	NM_181547	ENSMUSG00000034738	Nostrin	Daip2|mDaIP2	nitric oxide synthase trafficker	protein-coding
mm_56261.1	chr6	90810163	90810219	-	1	NA	promoter-TSS (NM_001134384)	promoter-TSS (NM_001134384)	-68	NM_001134384	232227	Mm.196943	NM_182784	ENSMUSG00000034312	Iqsec1	AW561907|BC026481|BRAG2|D6Ertd349e|cI-43	IQ motif and Sec7 domain 1	protein-coding
mm_107985.1	chr12	73086462	73086474	+	1	NA	Intergenic	Intergenic	26777	NM_011382	20474	Mm.249575	NM_011382	ENSMUSG00000034460	Six4	AI047561|AREC3|TrexBF	sine oculis-related homeobox 4	protein-coding
mm_158101.1	chrX	101794376	101794387	-	1	NA	Intergenic	CpG	-55004	NM_001163610	100042480	Mm.232	NM_001163610	ENSMUSG00000079481	Nhsl2	1110062M06Rik|6430511F03|AI225852|AW488865|EG621083|ENSMUSG00000073037|Gm10456	NHS-like 2	protein-coding
mm_105208.1	chr11	102146241	102146260	-	1	NA	intron (NM_145829, intron 1 of 6)	intron (NM_145829, intron 1 of 6)	737	NM_145829	217214	Mm.31686	NM_145829	ENSMUSG00000048217	Nags	1700120E20Rik|argA	N-acetylglutamate synthase	protein-coding
mm_18863.1	chr2	75705014	75705022	-	1	NA	promoter-TSS (NM_010902)	promoter-TSS (NM_010902)	-355	NM_010902	18024	Mm.1025	NM_010902	ENSMUSG00000015839	Nfe2l2	Nrf2	nuclear factor, erythroid derived 2, like 2	protein-coding
mm_27616.1	chr3	59262826	59262851	-	1	NA	promoter-TSS (NM_027571)	promoter-TSS (NM_027571)	-7	NM_027571	70839	Mm.422675	NM_027571	ENSMUSG00000036353	P2ry12	2900079B22Rik|4921504D23Rik|P2Y12	purinergic receptor P2Y, G-protein coupled 12	protein-coding
mm_119652.1	chr14	52016850	52016879	+	1	NA	promoter-TSS (NM_001033805)	promoter-TSS (NM_001033805)	-1	NM_001033805	619301	Mm.475177	NM_001033805	ENSMUSG00000072571	Tmem253	G630016D24Rik	transmembrane protein 253	protein-coding
mm_60401.1	chr7	44475754	44475754	+	1	NA	Intergenic	Intergenic	5407	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_6066.1	chr1	60786450	60786452	-	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	40063	NM_007642	12487	Mm.255003	NM_007642	ENSMUSG00000026012	Cd28	-	CD28 antigen	protein-coding
mm_11384.1	chr2	31284145	31284157	+	1	NA	exon (NM_019681, exon 5 of 8)	exon (NM_019681, exon 5 of 8)	38228	NM_019681	14299	Mm.249318	NM_019681	ENSMUSG00000062661	Ncs1	9430075O15Rik|A730032G13Rik|AI836659|Freq|Mfreq|NCS-1	neuronal calcium sensor 1	protein-coding
mm_16235.1	chr2	173156305	173156312	+	1	NA	intron (NM_011044, intron 6 of 9)	intron (NM_011044, intron 6 of 9)	3235	NM_011044	18534	Mm.266867	NM_011044	ENSMUSG00000027513	Pck1	AI265463|PEPCK|Pck-1	phosphoenolpyruvate carboxykinase 1, cytosolic	protein-coding
mm_33679.1	chr4	133251411	133251421	+	1	NA	exon (NM_016693, exon 24 of 29)	exon (NM_016693, exon 24 of 29)	10598	NM_016693	53608	Mm.36640	NM_016693	ENSMUSG00000028862	Map3k6	Ask2|MAPKKK6|MEKK6	mitogen-activated protein kinase kinase kinase 6	protein-coding
mm_5468.1	chr1	36556662	36556691	-	1	NA	intron (NM_001304329, intron 1 of 14)	intron (NM_001304329, intron 1 of 14)	881	NM_001304330	20353	Mm.29558	NM_001126047	ENSMUSG00000026121	Sema4c	AI426163|M-Sema F|Semacl1|Semaf|Semai|sema I	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4C	protein-coding
mm_171331.1	chr3	98580522	98580530	-	1	NA	Intergenic	Intergenic	-16488	NM_008294	15495	Mm.14309	NM_008294	ENSMUSG00000095143	Hsd3b4	-	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 4	protein-coding
mm_136591.1	chr17	4995983	4995989	+	1	NA	exon (NM_001085355, exon 1 of 20)	exon (NM_001085355, exon 1 of 20)	912	NM_001085355	239985	Mm.133401	NM_001085355	ENSMUSG00000069729	Arid1b	8030481M12|9330189K18Rik|AI836955|Ardi1b|B230217J03Rik|mKIAA1235	AT rich interactive domain 1B (SWI-like)	protein-coding
mm_112771.1	chr13	19395998	19396010	+	1	NA	promoter-TSS (NM_024270)	promoter-TSS (NM_024270)	-191	NM_001347485	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_92157.1	chr10	67537386	67537396	-	1	NA	promoter-TSS (NM_010118)	promoter-TSS (NM_010118)	-478	NM_010118	13654	Mm.290421	NM_010118	ENSMUSG00000037868	Egr2	Egr-2|Krox-20|Krox20|NGF1-B|Zfp-25|Zfp-6	early growth response 2	protein-coding
mm_167764.1	chr9	110529227	110529229	+	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-3369	NM_001081340	235626	Mm.288949	NM_001081340	ENSMUSG00000044791	Setd2	4921524K10Rik|BC031601|KMT3A	SET domain containing 2	protein-coding
mm_151357.1	chr19	55908506	55908517	+	1	NA	exon (NM_001142918, exon 5 of 15)	exon (NM_001142918, exon 5 of 15)	13190	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_129412.1	chr15	78314518	78314530	-	1	NA	Intergenic	Intergenic	-8803	NM_001287389	12984	Mm.1940	NM_007781	ENSMUSG00000071714	Csf2rb2	AIC2A|BetaIl3|Bil3|Csfgmrb|Il3r|Il3rb|Il3rb2	colony stimulating factor 2 receptor, beta 2, low-affinity (granulocyte-macrophage)	protein-coding
mm_7113.1	chr1	89968687	89968690	-	1	NA	exon (NM_139152, exon 4 of 6)	exon (NM_139152, exon 4 of 6)	-37512	NM_010262	14472	Mm.204730	NM_010262	ENSMUSG00000034486	Gbx2	D130058E05Rik|Gbx-2|MMoxA|Stra7	gastrulation brain homeobox 2	protein-coding
mm_28221.1	chr3	88441000	88441006	-	1	NA	promoter-TSS (NR_105978)	promoter-TSS (NR_105978)	-52	NR_105978	102465611		NR_105978	ENSMUSG00000098655	Mir7011	Gm27677|mmu-mir-7011	microRNA 7011	ncRNA
mm_107485.1	chr12	38730110	38730114	+	1	NA	Intergenic	LTRIS2|LTR|ERV1	-49970	NM_001347379	14009	Mm.4866	NM_007960	ENSMUSG00000004151	Etv1	ER81|Etsrp81	ets variant 1	protein-coding
mm_47273.1	chr5	121916721	121916757	-	1	NA	intron (NM_001312908, intron 4 of 22)	intron (NM_001312908, intron 4 of 22)	67711	NM_175474	231717	Mm.12654	NM_175474	ENSMUSG00000044134	Fam109a	A230106M15Rik|AU017694|IPIP27A|Ses1	family with sequence similarity 109, member A	protein-coding
mm_112423.1	chr13	4191164	4191200	+	1	NA	promoter-TSS (NM_013778)	promoter-TSS (NM_013778)	-5	NM_013778	27384	Mm.27447	NM_013778	ENSMUSG00000021213	Akr1c13	mKIAA4014	aldo-keto reductase family 1, member C13	protein-coding
mm_44488.1	chr5	23669165	23669167	-	1	NA	Intergenic	B1_Mur4|SINE|Alu	43501	NR_038090	433855	Mm.205125	NR_015554	ENSMUSG00000105987	AI506816	-	expressed sequence AI506816	ncRNA
mm_18295.1	chr2	52730687	52730691	-	1	NA	intron (NM_019667, intron 1 of 13)	intron (NM_019667, intron 1 of 13)	11460	NM_019667	56324	Mm.263639	NM_019667	ENSMUSG00000055371	Stam2	1200004O12Rik|5730456G07Rik|BB145015|Hbp	signal transducing adaptor molecule (SH3 domain and ITAM motif) 2	protein-coding
mm_57776.1	chr6	129238041	129238051	-	1	NA	promoter-TSS (NR_040265)	promoter-TSS (NR_040265)	-1	NR_040265	76432	Mm.261738	NR_040265	ENSMUSG00000097354	2310001H17Rik	AI646108	RIKEN cDNA 2310001H17 gene	ncRNA
mm_39870.1	chr5	31074823	31074833	+	1	NA	intron (NM_023525, intron 34 of 43)	intron (NM_023525, intron 34 of 43)	18699	NM_011773	22784	Mm.1396	NM_011773	ENSMUSG00000029151	Slc30a3	Znt3	solute carrier family 30 (zinc transporter), member 3	protein-coding
mm_28547.1	chr3	93015680	93015694	-	1	NA	promoter-TSS (NM_028798)	promoter-TSS (NM_028798)	-1	NM_028798	74175	Mm.35806	NM_028798	ENSMUSG00000027913	Crct1	2300002G24Rik|AA589624|Nice-1	cysteine-rich C-terminal 1	protein-coding
mm_46816.1	chr5	113138405	113138448	-	1	NA	5' UTR (NM_001347397, exon 1 of 8)	5' UTR (NM_001347397, exon 1 of 8)	159	NM_001347397	243219	Mm.160131	NM_172884	ENSMUSG00000051339	2900026A02Rik	8430408O14Rik|A530094D01|AW539426|Gm449|Kiaa1671|mKIAA1671	RIKEN cDNA 2900026A02 gene	protein-coding
mm_165207.1	chr2	34957176	34957177	+	1	NA	intron (NM_009421, intron 5 of 10)	intron (NM_009421, intron 5 of 10)	4596	NM_009421	22029	Mm.239514	NM_009421	ENSMUSG00000026875	Traf1	4732496E14Rik	TNF receptor-associated factor 1	protein-coding
mm_60930.1	chr7	46850218	46850230	+	1	NA	exon (NM_001136069, exon 4 of 8)	exon (NM_001136069, exon 4 of 8)	3142	NM_001136069	16828	Mm.29324	NM_010699	ENSMUSG00000063229	Ldha	Ldh1|Ldhm|l7R2	lactate dehydrogenase A	protein-coding
mm_136929.1	chr17	13874539	13874557	+	1	NA	intron (NM_010806, intron 22 of 32)	intron (NM_010806, intron 22 of 32)	-73825	NM_001122977	635895	Mm.388844	NM_001122977	ENSMUSG00000067941	Gm7168	EG635895	predicted gene 7168	protein-coding
mm_86045.1	chr9	114496610	114496620	-	1	NA	promoter-TSS (NM_009916)	promoter-TSS (NM_009916)	-71	NM_009916	12773	Mm.1337	NM_009916	ENSMUSG00000047898	Ccr4	C-C CKR-4|CHEMR1|Cmkbr4|LESTR|Sdf1r	chemokine (C-C motif) receptor 4	protein-coding
mm_43405.1	chr5	135863043	135863054	+	1	NA	intron (NM_021403, intron 11 of 14)	B4|SINE|B4	-24871	NM_013560	15507	Mm.13849	NM_013560	ENSMUSG00000004951	Hspb1	27kDa|Hsp25	heat shock protein 1	protein-coding
mm_151667.1	chr19	4175471	4175484	-	1	NA	promoter-TSS (NM_134148)	promoter-TSS (NM_134148)	2	NM_134148	107239	Mm.482310	NM_134148	ENSMUSG00000075289	Carns1	AI790298|Atpgd1|mKIAA1394	carnosine synthase 1	protein-coding
mm_48953.1	chr6	4540631	4540671	+	1	NA	exon (NM_007743, exon 52 of 52)	exon (NM_007743, exon 52 of 52)	35033	NM_007743	12843	Mm.277792	NM_007743	ENSMUSG00000029661	Col1a2	AA960264|AI325291|Col1a-2|Cola-2|Cola2|oim	collagen, type I, alpha 2	protein-coding
mm_103481.1	chr11	76495291	76495308	-	1	NA	promoter-TSS (NM_001346670)	promoter-TSS (NM_001346670)	-804	NM_001346670	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_39132.1	chr4	155154426	155154438	-	1	NA	3' UTR (NM_011385, exon 7 of 7)	3' UTR (NM_011385, exon 7 of 7)	67855	NM_001081100	76866	Mm.200590	NM_001081100	ENSMUSG00000029049	Morn1	2900057D20Rik|4930417P05Rik|AU042805	MORN repeat containing 1	protein-coding
mm_57622.1	chr6	128233845	128233851	-	1	NA	intron (NM_011567, intron 9 of 11)	L1MA4|LINE|L1	-50045	NR_077223	330427	Mm.426356	NR_077223	ENSMUSG00000107879	9330102E08Rik	-	RIKEN cDNA 9330102E08 gene	ncRNA
mm_149977.1	chr19	29101366	29101376	+	1	NA	promoter-TSS (NM_021525)	promoter-TSS (NM_021525)	-4	NM_021525	59028	Mm.28630	NM_021525	ENSMUSG00000024785	Rcl1	2310040A02Rik|AI789745|C76567|RPCL1|Rnac	RNA terminal phosphate cyclase-like 1	protein-coding
mm_166891.1	chr7	28140143	28140150	+	1	NA	exon (NM_001164655, exon 5 of 20)	exon (NM_001164655, exon 5 of 20)	10680	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_135419.1	chr16	45158651	45158683	-	1	NA	promoter-TSS (NM_028756)	promoter-TSS (NM_028756)	6	NM_028756	74102	Mm.264984	NM_028756	ENSMUSG00000022664	Slc35a5	1010001J06Rik|AU021179|BB097433|D16Ertd450e|D730043G07Rik	solute carrier family 35, member A5	protein-coding
mm_148669.1	chr19	5637502	5637517	+	1	NA	promoter-TSS (NM_009045)	promoter-TSS (NM_009045)	19	NM_009045	19697	Mm.249966	NM_009045	ENSMUSG00000024927	Rela	p65	v-rel reticuloendotheliosis viral oncogene homolog A (avian)	protein-coding
mm_156086.1	chrX	110814396	110814413	+	1	NA	promoter-TSS (NM_008901)	promoter-TSS (NM_008901)	25	NM_008901	18994	Mm.56946	NM_008901	ENSMUSG00000056854	Pou3f4	Brn-4|Brn4|OTF-9|Otf9|Slf|oct-9	POU domain, class 3, transcription factor 4	protein-coding
mm_126846.1	chr15	89079333	89079336	+	1	NA	intron (NM_026485, intron 1 of 9)	B1_Mus2|SINE|Alu	3270	NM_026485	67976	Mm.284710	NM_026485	ENSMUSG00000015363	Trabd	5730502D15Rik|AL023039	TraB domain containing	protein-coding
mm_19192.1	chr2	84425259	84425273	-	1	NA	promoter-TSS (NM_018782)	promoter-TSS (NM_018782)	0	NM_018782	54598	Mm.75467	NM_018782	ENSMUSG00000059588	Calcrl	AV071593|CRLR	calcitonin receptor-like	protein-coding
mm_62780.1	chr7	112427672	112427680	+	1	NA	promoter-TSS (NM_020606)	promoter-TSS (NM_020606)	-30	NM_020606	57342	Mm.143763	NM_020606	ENSMUSG00000030770	Parva	2010012A22Rik|5430400F08Rik|AI225929|AU042898|Actp|CH-ILKBP|Parvin	parvin, alpha	protein-coding
mm_53205.1	chr6	125690373	125690381	+	1	NA	promoter-TSS (NM_153589)	promoter-TSS (NM_153589)	-42	NM_153589	243634	Mm.333398	NM_153589	ENSMUSG00000038115	Ano2	BC033409|Tmem16b	anoctamin 2	protein-coding
mm_115060.1	chr13	100686196	100686199	+	1	NA	intron (NM_183115, intron 6 of 11)	intron (NM_183115, intron 6 of 11)	16716	NM_001168386	76041	Mm.23977	NM_183115	ENSMUSG00000048924	Ccdc125	5830436D01Rik|AL023012	coiled-coil domain containing 125	protein-coding
mm_7784.1	chr1	131279545	131279570	-	1	NA	promoter-TSS (NM_019777)	promoter-TSS (NM_019777)	6	NM_019777	56489	Mm.386783	NM_019777	ENSMUSG00000042349	Ikbke	AW558201|IKK-i|IKKepsilon|Ikki	inhibitor of kappaB kinase epsilon	protein-coding
mm_170015.1	chr17	17346203	17346221	-	1	NA	Intergenic	CpG	-28120	NM_025934	67045	Mm.35117	NM_025934	ENSMUSG00000023852	Riok2	2010110K24Rik|2410085M17Rik	RIO kinase 2 (yeast)	protein-coding
mm_121008.1	chr14	79530674	79530687	+	1	NA	intron (NM_001286411, intron 1 of 8)	intron (NM_001286411, intron 1 of 8)	15006	NM_001286411	13709	Mm.20938	NM_007920	ENSMUSG00000036461	Elf1	Elf-1|Sts1|mElf-1|p70	E74-like factor 1	protein-coding
mm_123482.1	chr14	65981535	65981549	-	1	NA	TTS (NM_013492)	TTS (NM_013492)	13059	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_94453.1	chr11	6389554	6389573	+	1	NA	Intergenic	(CGG)n|Simple_repeat|Simple_repeat	-5562	NM_001005867	52915	Mm.1144	NM_028601	ENSMUSG00000041164	Zmiz2	Zimp7	zinc finger, MIZ-type containing 2	protein-coding
mm_51702.1	chr6	86628190	86628208	+	1	NA	promoter-TSS (NM_026414)	promoter-TSS (NM_026414)	25	NM_026414	67855	Mm.183043	NM_026414	ENSMUSG00000033508	Asprv1	2300003P22Rik|AA986851|SASP|SASPase|Taps	aspartic peptidase, retroviral-like 1	protein-coding
mm_93093.1	chr10	89674191	89674195	-	1	NA	intron (NM_198021, intron 2 of 17)	intron (NM_198021, intron 2 of 17)	12092	NM_198021	213326	Mm.27651	NM_198021	ENSMUSG00000069539	Scyl2	AU015688|AW536445|BC030932|CVAK104|D10Ertd802e	SCY1-like 2 (S. cerevisiae)	protein-coding
mm_92686.1	chr10	80645538	80645549	-	1	NA	intron (NM_145361, intron 4 of 8)	intron (NM_145361, intron 4 of 8)	11528	NM_145361	208198	Mm.60720	NM_145361	ENSMUSG00000003344	Btbd2	2610037C03Rik|4930512K17Rik	BTB (POZ) domain containing 2	protein-coding
mm_73340.1	chr8	105326355	105326411	+	1	NA	promoter-TSS (NM_177449)	promoter-TSS (NM_177449)	19	NM_025486	66320	Mm.29990	NM_025486	ENSMUSG00000014856	Tmem208	1700006C06Rik|2610030K20Rik|Hspc171	transmembrane protein 208	protein-coding
mm_130591.1	chr15	99651581	99651630	-	1	NA	promoter-TSS (NM_001253809)	promoter-TSS (NM_001253809)	51	NM_001253808	26934	Mm.273804	NM_012025	ENSMUSG00000023015	Racgap1	AI227039|AI327394|Band25|GTPase|MgcRacGAP|gtl11|mKIAA1478	Rac GTPase-activating protein 1	protein-coding
mm_136834.1	chr17	12745852	12745887	+	1	NA	intron (NR_027773, intron 1 of 2)	intron (NR_027773, intron 1 of 2)	4558	NR_027784	104103	Mm.26553	NR_002853	ENSMUSG00000078247	Airn	2810051F02Rik|2810434M15Rik|AI256653|AI597500|AW049873|Air|B930018I07Rik|D17Ertd663e|IGF2RAS	antisense Igf2r RNA	ncRNA
mm_80852.1	chr9	98424780	98424832	+	1	NA	5' UTR (NM_011254, exon 1 of 4)	5' UTR (NM_011254, exon 1 of 4)	1845	NM_011254	19659	Mm.279741	NM_011254	ENSMUSG00000046402	Rbp1	CRBPI|Crbp|Rbp-1	retinol binding protein 1, cellular	protein-coding
mm_72753.1	chr8	85299697	85299706	+	1	NA	promoter-TSS (NM_019716)	promoter-TSS (NM_019716)	69	NR_028268	56452	Mm.29709	NM_019716	ENSMUSG00000031697	Orc6	6720420I10Rik|Orc6l	origin recognition complex, subunit 6	protein-coding
mm_135046.1	chr16	33186232	33186256	-	1	NA	intron (NM_176840, intron 1 of 12)	intron (NM_176840, intron 1 of 12)	1173	NM_176840	106326	Mm.486405	NM_176840	ENSMUSG00000022807	Osbpl11	9430097N02Rik|AI132306|AU019795|ORP-11	oxysterol binding protein-like 11	protein-coding
mm_115506.1	chr13	4279358	4279373	-	1	NA	promoter-TSS (NM_013777)	promoter-TSS (NM_013777)	34	NM_013777	622402	Mm.27447	NM_013777	ENSMUSG00000021211	Akr1c12	AI266976|Akra	aldo-keto reductase family 1, member C12	protein-coding
mm_146882.1	chr18	25679674	25679688	-	1	NA	intron (NM_001146292, intron 1 of 12)	intron (NM_001146292, intron 1 of 12)	74302	NM_133195	108013	Mm.266435	NM_133195	ENSMUSG00000024268	Celf4	A230070D14Rik|BRUNOL-4|Brul4|Brunol4|C130060B05Rik	CUGBP, Elav-like family member 4	protein-coding
mm_159717.1	chr5	33722288	33722288	+	1	NA	promoter-TSS (NM_001163217)	promoter-TSS (NM_001163217)	-18	NM_001163217	14184	Mm.6904	NM_008010	ENSMUSG00000054252	Fgfr3	CD333|FR3|Fgfr-3|Flg-2|HBGFR|Mfr3|sam3	fibroblast growth factor receptor 3	protein-coding
mm_105109.1	chr11	100970539	100970551	-	1	NA	promoter-TSS (NM_008986)	promoter-TSS (NM_008986)	72	NM_008986	19285	Mm.21864	NM_008986	ENSMUSG00000004044	Ptrf	2310075E07Rik|AW546441|Cav-p60|Cavin	polymerase I and transcript release factor	protein-coding
mm_114814.1	chr13	91581827	91581831	+	1	NA	intron (NM_024186, intron 4 of 15)	intron (NM_024186, intron 4 of 15)	120732	NM_024186	66970	Mm.343095	NM_024186	ENSMUSG00000003992	Ssbp2	1500004K09Rik|2310079I02Rik|9330163K02Rik|A830008M03Rik|AU067692|AW558684|Hspc116|SSDP2	single-stranded DNA binding protein 2	protein-coding
mm_161418.1	chr15	34837420	34837420	+	1	NA	promoter-TSS (NM_181317)	promoter-TSS (NM_181317)	65	NM_181317	16539	Mm.71045	NM_181317	ENSMUSG00000050963	Kcns2	E130006J24Rik|Kv9.2	K+ voltage-gated channel, subfamily S, 2	protein-coding
mm_147368.1	chr18	43438245	43438267	-	1	NA	promoter-TSS (NM_001291455)	promoter-TSS (NM_001291455)	30	NM_001291455	22240	Mm.8180	NM_009468	ENSMUSG00000024501	Dpysl3	CRMP-4|DRP-3|TUC4|ULIP-1|Ulip|Ulip1	dihydropyrimidinase-like 3	protein-coding
mm_121777.1	chr14	19890459	19890473	-	1	NA	intron (NM_001038637, intron 4 of 4)	RSINE1|SINE|B4	51541	NR_105025	52512	Mm.483998	NR_105025		D14Ertd670e	-	DNA segment, Chr 14, ERATO Doi 670, expressed	ncRNA
mm_76547.1	chr8	88171939	88171943	-	1	NA	TTS (NM_172757)	TTS (NM_172757)	-27272	NM_001164499	214627	Mm.491211	NM_001164497	ENSMUSG00000036779	Papd5	5730445M16Rik|5830428A09	PAP associated domain containing 5	protein-coding
mm_26143.1	chr3	138065058	138065078	+	1	NA	intron (NR_037975, intron 1 of 3)	intron (NR_037975, intron 1 of 3)	2320	NR_037975	329763	Mm.169710	NM_177860	ENSMUSG00000049349	Gm5105	D830013H12|EG329763	predicted gene 5105	ncRNA
mm_121960.1	chr14	25032748	25032749	-	1	NA	Intergenic	Intergenic	110493	NR_045718	75862	Mm.109191	NR_045718		4930572O13Rik	-	RIKEN cDNA 4930572O13 gene	ncRNA
mm_160552.1	chr9	48965060	48965060	-	1	NA	promoter-TSS (NM_020274)	promoter-TSS (NM_020274)	-70	NM_020274	57014	Mm.117131	NM_020274	ENSMUSG00000008590	Htr3b	5-HT3B	5-hydroxytryptamine (serotonin) receptor 3B	protein-coding
mm_10305.1	chr2	11172034	11172053	+	1	NA	promoter-TSS (NM_008859)	promoter-TSS (NM_008859)	-339	NM_008859	18761	Mm.329993	NM_008859	ENSMUSG00000026778	Prkcq	A130035A12Rik|AW494342|PKC-0|PKC-theta|PKCtheta|Pkcq	protein kinase C, theta	protein-coding
mm_28113.1	chr3	86551266	86551283	-	1	NA	intron (NM_001077687, intron 40 of 50)	intron (NM_001077687, intron 40 of 50)	-2991	NM_011839	23937	Mm.389466	NM_011839	ENSMUSG00000057777	Mab21l2	-	mab-21-like 2 (C. elegans)	protein-coding
mm_77031.1	chr8	109251699	109251713	-	1	NA	non-coding (NR_126329, exon 10 of 10)	non-coding (NR_126329, exon 10 of 10)	89202	NR_002928	384864	Mm.390083	NR_002928		Gm1943	-	WD repeat domain 70 pseudogene	pseudo
mm_138843.1	chr17	40520020	40520028	+	1	NA	promoter-TSS (NM_001177584)	promoter-TSS (NM_001177584)	2	NM_001177584	100126778	Mm.422023	NM_001177584	ENSMUSG00000090747	Esp8	Gm17495	exocrine gland secreted peptide 8	protein-coding
mm_130628.1	chr15	100418106	100418111	-	1	NA	intron (NM_008732, intron 1 of 16)	intron (NM_008732, intron 1 of 16)	4947	NM_001146161	18174	Mm.234608	NM_008732	ENSMUSG00000023030	Slc11a2	DCT1|DMT1|Nramp2|mk|van	solute carrier family 11 (proton-coupled divalent metal ion transporters), member 2	protein-coding
mm_159594.1	chr4	126239952	126239952	-	1	NA	intron (NM_001347198, intron 5 of 17)	intron (NM_001347198, intron 5 of 17)	16367	NM_144941	245877	Mm.266716	NM_144941	ENSMUSG00000028849	Map7d1	AV028413|BC019977|Mtap7d1|Parcc1|Rprc1|mKIAA1187	MAP7 domain containing 1	protein-coding
mm_53396.1	chr6	129588119	129588126	+	1	NA	Intergenic	Intergenic	-3689	NM_010654	16643	Mm.391515	NM_010654	ENSMUSG00000030165	Klrd1	CD94	killer cell lectin-like receptor, subfamily D, member 1	protein-coding
mm_55949.1	chr6	85213901	85213906	-	1	NA	3' UTR (NM_178639, exon 14 of 14)	3' UTR (NM_178639, exon 14 of 14)	25972	NM_010131	13796	Mm.391473	NM_010131	ENSMUSG00000033726	Emx1	-	empty spiracles homeobox 1	protein-coding
mm_74134.1	chr8	123212852	123212856	+	1	NA	promoter-TSS (NM_145606)	promoter-TSS (NM_145606)	-4	NM_177279	320869	Mm.258354	NM_177279	ENSMUSG00000048478	Spata33	4732415M23Rik|AI847264	spermatogenesis associated 33	protein-coding
mm_112504.1	chr13	8301496	8301500	+	1	NA	intron (NR_110345, intron 1 of 10)	intron (NR_110345, intron 1 of 10)	98632	NM_052977	94191	Mm.425794	NM_052977	ENSMUSG00000052551	Adarb2	Adar3|RED2	adenosine deaminase, RNA-specific, B2	protein-coding
mm_157727.1	chrX	70365021	70365042	-	1	NA	promoter-TSS (NM_010498)	promoter-TSS (NM_010498)	54	NM_010498	15931	Mm.233083	NM_010498	ENSMUSG00000035847	Ids	AW214631	iduronate 2-sulfatase	protein-coding
mm_96125.1	chr11	60777532	60777563	+	1	NA	promoter-TSS (NM_001085440)	promoter-TSS (NM_001085440)	22	NM_175491	237782	Mm.57726	NM_175491	ENSMUSG00000049323	Smcr8	2310076G09Rik|AI642055|D030073L15Rik	Smith-Magenis syndrome chromosome region, candidate 8 homolog (human)	protein-coding
mm_137123.1	chr17	22674382	22674388	+	1	NA	Intergenic	Intergenic	73237	NM_001104575	628185	Mm.390947	NM_001104575	ENSMUSG00000094921	Vmn2r112	EG628185|V2rp1	vomeronasal 2, receptor 112	protein-coding
mm_142034.1	chr17	35242703	35242708	-	1	NA	promoter-TSS (NM_001252457)	promoter-TSS (NM_001252457)	-112	NM_001252457	53817	Mm.439827	NM_019693	ENSMUSG00000019432	Ddx39b	0610030D10Rik|AI428441|Bat-1|Bat1|Bat1a|D17H6S81E|D17H6S81E-1|D6S81Eh	DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B	protein-coding
mm_32766.1	chr4	116691927	116691937	+	1	NA	intron (NM_011034, intron 3 of 5)	intron (NM_011034, intron 3 of 5)	-5910	NR_040442	100502959	Mm.395400	NR_040442		AV051173	-	expressed sequence AV051173	ncRNA
mm_4819.1	chr1	185431949	185431960	+	1	NA	non-coding (NR_038006, exon 2 of 2)	non-coding (NR_038006, exon 2 of 2)	9865	NR_038006	319562	Mm.184335	NM_176943	ENSMUSG00000051295	9630028B13Rik	-	RIKEN cDNA 9630028B13 gene	ncRNA
mm_71531.1	chr8	46890530	46890569	+	1	NA	Intergenic	Intergenic	-96338	NM_177304	320981	Mm.211429	NM_177304	ENSMUSG00000038173	Enpp6	4833421B01Rik|B830047L21Rik|D8Ertd514e|E-NPP 6|GPC-Cpde|Npp6	ectonucleotide pyrophosphatase/phosphodiesterase 6	protein-coding
mm_130941.1	chr15	103240749	103240758	-	1	NA	promoter-TSS (NM_001076789)	promoter-TSS (NM_001076789)	299	NR_002883	434858	Mm.391346	NR_002883		Gm5643	EG434858	heterogeneous nuclear ribonucleoprotein A1 pseudogene	pseudo
mm_26406.1	chr3	142606831	142606850	+	1	NA	exon (NM_010259, exon 7 of 11)	exon (NM_010259, exon 7 of 11)	11993	NM_010259	14468	Mm.457978	NM_010259	ENSMUSG00000040264	Gbp2b	Gbp-1|Gbp1|Mag-1|Mpa-1|Mpa1	guanylate binding protein 2b	protein-coding
mm_149413.1	chr19	11421255	11421269	+	1	NA	exon (NM_029499, exon 6 of 7)	exon (NM_029499, exon 6 of 7)	13601	NM_029499	64380	Mm.440715	NM_029499	ENSMUSG00000024675	Ms4a4c	5830413L19Rik|AI449185|Ms4a9	membrane-spanning 4-domains, subfamily A, member 4C	protein-coding
mm_21417.1	chr2	158127305	158127310	-	1	NA	exon (NM_009373, exon 9 of 13)	exon (NM_009373, exon 9 of 13)	19085	NM_009373	21817	Mm.330731	NM_009373	ENSMUSG00000037820	Tgm2	G[a]h|TG2|TGase2|tTG|tTGas	transglutaminase 2, C polypeptide	protein-coding
mm_102948.1	chr11	69617862	69617873	-	1	NA	promoter-TSS (NM_011367)	promoter-TSS (NM_011367)	38	NM_011367	20415	Mm.1431	NM_011367	ENSMUSG00000005202	Shbg	ABP	sex hormone binding globulin	protein-coding
mm_13010.1	chr2	90917299	90917392	+	1	NA	intron (NM_025576, intron 3 of 4)	intron (NM_025576, intron 3 of 4)	705	NM_025576	66461	Mm.23926	NM_025576		Ptpmt1	1110001D10Rik|2810004N20Rik|PLIP	protein tyrosine phosphatase, mitochondrial 1	protein-coding
mm_37878.1	chr4	132422379	132422390	-	1	NA	promoter-TSS (NM_175306)	promoter-TSS (NM_175306)	62	NM_001161797	100169	Mm.158361	NM_175306	ENSMUSG00000066043	Phactr4	3110001B12Rik|AI527228|AW495572|C330013F19Rik|N28169|mKIAA4120	phosphatase and actin regulator 4	protein-coding
mm_134465.1	chr16	18426514	18426542	-	1	NA	exon (NM_013711, exon 1 of 18)	exon (NM_013711, exon 1 of 18)	111	NM_013711	26462	Mm.390906	NM_013711	ENSMUSG00000075704	Txnrd2	AA118373|ESTM573010|TGR|Tr3|Trxr2|Trxrd2	thioredoxin reductase 2	protein-coding
mm_14765.1	chr2	145460242	145460246	+	1	NA	intron (NM_053195, intron 3 of 16)	intron (NM_053195, intron 3 of 16)	94738	NM_001037929	627302	Mm.445953	NM_001037929		Gm14092	OTTMUSG00000015643	predicted gene 14092	protein-coding
mm_38028.1	chr4	133872305	133872346	-	1	NA	intron (NM_001285505, intron 2 of 21)	intron (NM_001285505, intron 2 of 21)	2406	NM_001285506	20111	Mm.301827	NM_009097	ENSMUSG00000003644	Rps6ka1	Mapkapk-1a|Rsk|Rsk-1|Rsk1|S6K-alpha-1|p90-Rsk1|p90Rsk1|p90S6K|p90rsk	ribosomal protein S6 kinase polypeptide 1	protein-coding
mm_168257.1	chr10	87180839	87180841	-	1	NA	intron (NM_029685, intron 4 of 5)	intron (NM_029685, intron 4 of 5)	122794	NM_029685	76640	Mm.78423	NM_029685	ENSMUSG00000047129	1700113H08Rik	-	RIKEN cDNA 1700113H08 gene	protein-coding
mm_37277.1	chr4	118636362	118636372	-	1	NA	Intergenic	Intergenic	9963	NR_029469	100041290	Mm.472885	NR_029469		D4Ertd617e	-	DNA segment, Chr 4, ERATO Doi 617, expressed	ncRNA
mm_115379.1	chr13	113095909	113095920	+	1	NA	exon (NM_010370, exon 4 of 5)	exon (NM_010370, exon 4 of 5)	5067	NM_010370	14938	Mm.15510	NM_010370	ENSMUSG00000023132	Gzma	AW494114|Ctla-3|Ctla3|Hf|Hf1|SE1|TSP-1|TSP1	granzyme A	protein-coding
mm_67676.1	chr7	89188311	89188315	-	1	NA	intron (NM_028343, intron 6 of 14)	intron (NM_028343, intron 6 of 14)	150474	NM_028343	72759	Mm.208477	NM_028343	ENSMUSG00000039428	Tmem135	2810439K08Rik|AW319712|PMP52	transmembrane protein 135	protein-coding
mm_119116.1	chr14	31019701	31019704	+	1	NA	promoter-TSS (NM_153547)	promoter-TSS (NM_153547)	564	NM_001081251	66923	Mm.27913	NM_025847	ENSMUSG00000042323	Pbrm1	2610016F04Rik|AI507524|BAF180|Pb1	polybromo 1	protein-coding
mm_163985.1	chr14	61046543	61046553	-	1	NA	5' UTR (NM_013869, exon 1 of 10)	5' UTR (NM_013869, exon 1 of 10)	307	NM_013869	29820	Mm.281356	NM_013869	ENSMUSG00000060548	Tnfrsf19	AL023044|AW123854|TAJ|TAJ-ALPHA|TRADE|Troy	tumor necrosis factor receptor superfamily, member 19	protein-coding
mm_127553.1	chr15	102150406	102150418	+	1	NA	promoter-TSS (NM_146064)	promoter-TSS (NM_146064)	-163	NM_146064	223920	Mm.358862	NM_146064	ENSMUSG00000023045	Soat2	ACAT2|D15Wsu97e	sterol O-acyltransferase 2	protein-coding
mm_88889.1	chr10	81136535	81136608	+	1	NA	5' UTR (NM_010731, exon 1 of 3)	5' UTR (NM_010731, exon 1 of 3)	300	NM_010731	16969	Mm.20920	NM_010731	ENSMUSG00000035011	Zbtb7a	9030619K07Rik|9130006G12Rik|AI452336|FBI-1|Lrf|Pokemon|Zbtb7	zinc finger and BTB domain containing 7a	protein-coding
mm_167257.1	chr8	25363941	25363947	-	1	NA	Intergenic	Intergenic	-57674	NR_040352	74489	Mm.256468	NR_040352	ENSMUSG00000110140	5430421F17Rik	-	RIKEN cDNA 5430421F17 gene	ncRNA
mm_55784.1	chr6	82652467	82652485	-	1	NA	intron (NM_025882, intron 1 of 3)	intron (NM_025882, intron 1 of 3)	389	NM_025882	66979	Mm.195753	NM_025882	ENSMUSG00000030042	Pole4	2400007P05Rik|5830430F06Rik	polymerase (DNA-directed), epsilon 4 (p12 subunit)	protein-coding
mm_25521.1	chr3	114030837	114030865	+	1	NA	5' UTR (NM_007729, exon 1 of 67)	5' UTR (NM_007729, exon 1 of 67)	311	NM_007729	12814	Mm.209715	NM_007729	ENSMUSG00000027966	Col11a1	C530001D20Rik|cho	collagen, type XI, alpha 1	protein-coding
mm_158973.1	chr1	109982455	109982455	+	1	NA	promoter-TSS (NM_001316743)	promoter-TSS (NM_001316743)	-445	NM_001316743	241201	Mm.213407	NM_172853	ENSMUSG00000026312	Cdh7	9330156F07Rik|CDH7L1	cadherin 7, type 2	protein-coding
mm_11292.1	chr2	30133752	30133806	+	1	NA	promoter-TSS (NM_146252)	promoter-TSS (NM_146252)	33	NM_146252	70296	Mm.19172	NM_146252	ENSMUSG00000039678	Tbc1d13	2600014A06Rik|BC025586	TBC1 domain family, member 13	protein-coding
mm_160748.1	chr10	81343330	81343330	-	1	NA	promoter-TSS (NM_148951)	promoter-TSS (NM_148951)	-64	NM_148951	209047	Mm.218755	NM_148951	ENSMUSG00000034872	Gipc3	Ahl5|Rgs19ip3	GIPC PDZ domain containing family, member 3	protein-coding
mm_153392.1	chr19	40383138	40383146	-	1	NA	intron (NM_001034963, intron 4 of 22)	intron (NM_001034963, intron 4 of 22)	19168	NM_001034964	20411	Mm.210815	NM_009166	ENSMUSG00000025006	Sorbs1	2310065E01Rik|9530001P15Rik|CAP|SH3P12|Sh3d5|mKIAA1296	sorbin and SH3 domain containing 1	protein-coding
mm_69739.1	chr7	140941459	140941461	-	1	NA	promoter-TSS (NM_145387)	promoter-TSS (NM_145387)	-121	NM_145387	212974	Mm.260139	NM_145387	ENSMUSG00000062031	Pgghg	5730511L01Rik|Athl1|BC023151	protein glucosylgalactosylhydroxylysine glucosidase	protein-coding
mm_152455.1	chr19	10845501	10845525	-	1	NA	intron (NM_023044, intron 1 of 7)	intron (NM_023044, intron 1 of 7)	2969	NM_023044	65221	Mm.27387	NM_023044	ENSMUSG00000024737	Slc15a3	Ci1|cI-1	solute carrier family 15, member 3	protein-coding
mm_63498.1	chr7	127800609	127800615	+	1	NA	promoter-TSS (NM_133943)	promoter-TSS (NM_133943)	3	NM_001040684	101502	Mm.157103	NM_133943	ENSMUSG00000042289	Hsd3b7	AI195443|BB098564	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 7	protein-coding
mm_105907.1	chr11	114983205	114983205	-	1	NA	3' UTR (NM_145437, exon 4 of 4)	3' UTR (NM_145437, exon 4 of 4)	6681	NM_145437	217305	Mm.275986	NM_145437	ENSMUSG00000034641	Cd300ld	4732429D16Rik|CLM5|Cd300ld1|LMIR4|MAIR-IV|clm-5	CD300 molecule like family member d	protein-coding
mm_51959.1	chr6	91757820	91757829	+	1	NA	3' UTR (NM_009320, exon 15 of 15)	3' UTR (NM_009320, exon 15 of 15)	49569	NM_001159507	243547	Mm.333264	NM_001033353	ENSMUSG00000030098	Grip2	-	glutamate receptor interacting protein 2	protein-coding
mm_135195.1	chr16	36450566	36450581	-	1	NA	TTS (NM_025288)	TTS (NM_025288)	4819	NM_025288	20863	Mm.136573	NM_025288	ENSMUSG00000054905	Stfa3	Stf3	stefin A3	protein-coding
mm_138661.1	chr17	35868719	35868730	+	1	NA	exon (NM_001146711, exon 2 of 4)	exon (NM_001146711, exon 2 of 4)	2109	NM_175242	76448	Mm.359982	NM_175242	ENSMUSG00000034595	Ppp1r18	2310014H01Rik|AA407849|AI450394	protein phosphatase 1, regulatory subunit 18	protein-coding
mm_155297.1	chrX	61185518	61185563	+	1	NA	promoter-TSS (NM_001166658)	promoter-TSS (NM_001166658)	18	NM_001166658	631990	Mm.401324	NM_001166658	ENSMUSG00000090546	Cdr1	100039759|Cdr|Cdr34|EG631990|Gm2409|Gm7077	cerebellar degeneration related antigen 1	protein-coding
mm_13240.1	chr2	98662574	98662604	+	1	NA	Intergenic	SYNREP_MM|Satellite|Satellite	1194932	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_161250.1	chr13	101768150	101768150	-	1	NA	promoter-TSS (NM_001077495)	promoter-TSS (NM_001077495)	67	NM_001077495	18708	Mm.259333	NM_001024955	ENSMUSG00000041417	Pik3r1	PI3K|p50alpha|p55alpha|p85alpha	phosphatidylinositol 3-kinase, regulatory subunit, polypeptide 1 (p85 alpha)	protein-coding
mm_111094.1	chr12	80441546	80441546	-	1	NA	Intergenic	Intergenic	-4945	NM_177267	320808	Mm.220310	NM_177267	ENSMUSG00000049106	Dcaf5	9430020B07Rik|AI325023|AI430035|AI848110|AW124614|BCRG2|BCRP2|Wdr22	DDB1 and CUL4 associated factor 5	protein-coding
mm_116919.1	chr13	55528512	55528561	-	1	NA	promoter-TSS (NM_013739)	promoter-TSS (NM_013739)	2	NM_013739	27261	Mm.33910	NM_013739	ENSMUSG00000035711	Dok3	AI450713|Dokl	docking protein 3	protein-coding
mm_155888.1	chrX	101641059	101641069	+	1	NA	intron (NM_001290535, intron 1 of 21)	intron (NM_001290535, intron 1 of 21)	846	NM_001290535	108155	Mm.487332	NM_139144	ENSMUSG00000034160	Ogt	1110038P24Rik|4831420N21Rik|AI115525|Ogtl	O-linked N-acetylglucosamine (GlcNAc) transferase (UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase)	protein-coding
mm_151537.1	chr19	58980119	58980127	+	1	NA	intron (NM_175172, intron 14 of 14)	intron (NM_175172, intron 14 of 14)	-36451	NM_001327998	73442	Mm.39739	NM_175199	ENSMUSG00000025092	Hspa12a	1700063D12Rik|AI118035|AI840429|AW048913|AW556406|D5Mgi40|Gm19925|mKIAA0417	heat shock protein 12A	protein-coding
mm_63064.1	chr7	122080007	122080025	+	1	NA	3' UTR (NM_138589, exon 7 of 7)	3' UTR (NM_138589, exon 7 of 7)	12818	NM_138589	28018	Mm.282122	NM_138589	ENSMUSG00000030870	Ubfd1	AI467302|D7Wsu105e|D7Wsu128e|Ubph	ubiquitin family domain containing 1	protein-coding
mm_13614.1	chr2	113405175	113405192	+	1	NA	intron (NM_001285458, intron 2 of 16)	intron (NM_001285458, intron 2 of 16)	-35881	NM_001285459	14260	Mm.4938	NM_010230	ENSMUSG00000044042	Fmn1	Fmn|formin-1|ld	formin 1	protein-coding
mm_75000.1	chr8	27228214	27228229	-	1	NA	exon (NM_013462, exon 2 of 4)	exon (NM_013462, exon 2 of 4)	1367	NM_013462	11556	Mm.278475	NM_013462	ENSMUSG00000031489	Adrb3	Adrb-3	adrenergic receptor, beta 3	protein-coding
mm_23887.1	chr3	83031296	83031314	+	1	NA	exon (NM_010196, exon 5 of 5)	exon (NM_010196, exon 5 of 5)	5152	NM_001111048	14161	Mm.88793	NM_010196	ENSMUSG00000028001	Fga	ENSMUSG00000059807|Fib	fibrinogen alpha chain	protein-coding
mm_15585.1	chr2	158794854	158794892	+	1	NA	promoter-TSS (NM_001291144)	promoter-TSS (NM_001291144)	66	NM_001291144	71715	Mm.315652	NM_145742	ENSMUSG00000027655	Dhx35	1200009D07Rik|Ddx35	DEAH (Asp-Glu-Ala-His) box polypeptide 35	protein-coding
mm_74972.1	chr8	27107443	27107480	-	1	NA	intron (NM_054044, intron 2 of 18)	intron (NM_054044, intron 2 of 18)	21171	NM_025686	66653	Mm.334467	NM_025686	ENSMUSG00000031487	Brf2	2700059M06Rik|5730512K07Rik|AU018504|AU022602|BRFU|TFIIIB50	BRF2, RNA polymerase III transcription initiation factor 50kDa subunit	protein-coding
mm_160923.1	chr11	85171060	85171060	+	1	NA	promoter-TSS (NM_028589)	promoter-TSS (NM_028589)	-36	NM_028589	73634	Mm.48850	NM_028589	ENSMUSG00000018479	1700125H20Rik	-	RIKEN cDNA 1700125H20 gene	protein-coding
mm_146245.1	chr18	77714192	77714214	+	1	NA	promoter-TSS (NM_178670)	promoter-TSS (NM_178670)	19	NR_027978	67640	Mm.482903	NM_026289		4930465K10Rik	-	RIKEN cDNA 4930465K10 gene	ncRNA
mm_24317.1	chr3	89430274	89430289	+	1	NA	promoter-TSS (NM_026869)	promoter-TSS (NM_026869)	67	NM_001293763	68911	Mm.22521	NM_026869	ENSMUSG00000047824	Pygo2	1190004M21Rik	pygopus 2	protein-coding
mm_26731.1	chr3	5515331	5515338	-	1	NA	Intergenic	RMER17A2|LTR|ERVK	60914	NM_001163301	19302	Mm.132336	NM_008994	ENSMUSG00000040374	Pex2	D3Ertd138e|PAF-1|PMP35|Pxmp3	peroxisomal biogenesis factor 2	protein-coding
mm_11852.1	chr2	45680040	45680042	+	1	NA	Intergenic	Intergenic	-16564	NR_040497	69405	Mm.396184	NR_040497	ENSMUSG00000086202	1700019E08Rik	-	RIKEN cDNA 1700019E08 gene	ncRNA
mm_27925.1	chr3	79550356	79550394	-	1	NA	intron (NM_001162999, intron 1 of 16)	intron (NM_001162999, intron 1 of 16)	17304	NM_001162999	329679	Mm.244005	NM_001162999	ENSMUSG00000061175	Fnip2	D630023B12Rik|mKIAA1450	folliculin interacting protein 2	protein-coding
mm_165135.1	chr2	11172383	11172385	+	1	NA	promoter-TSS (NM_008859)	promoter-TSS (NM_008859)	2	NM_008859	18761	Mm.329993	NM_008859	ENSMUSG00000026778	Prkcq	A130035A12Rik|AW494342|PKC-0|PKC-theta|PKCtheta|Pkcq	protein kinase C, theta	protein-coding
mm_90215.1	chr10	120979407	120979425	+	1	NA	promoter-TSS (NM_001081193)	promoter-TSS (NM_001081193)	-86	NM_001081193	380664	Mm.339371	NM_001081193	ENSMUSG00000048661	Lemd3	AI316861|Man1	LEM domain containing 3	protein-coding
mm_91719.1	chr10	44458716	44458751	-	1	NA	promoter-TSS (NM_007548)	promoter-TSS (NM_007548)	15	NM_007548	12142	Mm.4800	NM_007548	ENSMUSG00000038151	Prdm1	Blimp-1|Blimp1|PRDI-BF1|ZNFPR1A1|b2b1765Clo	PR domain containing 1, with ZNF domain	protein-coding
mm_73818.1	chr8	117403823	117403858	+	1	NA	intron (NM_028941, intron 3 of 20)	intron (NM_028941, intron 3 of 20)	-49183	NR_106045	102466801		NR_106045	ENSMUSG00000099062	Mir7077	Gm27774|mmu-mir-7077	microRNA 7077	ncRNA
mm_97449.1	chr11	78189597	78189608	+	1	NA	exon (NM_001159482, exon 3 of 11)	exon (NM_001159482, exon 3 of 11)	854	NM_033475	19376	Mm.275864	NM_033475	ENSMUSG00000002059	Rab34	AI326479|Narr|Rah|Rah1	RAB34, member RAS oncogene family	protein-coding
mm_49000.1	chr6	4756798	4756816	+	1	NA	exon (NM_130877, exon 2 of 2)	exon (NM_130877, exon 2 of 2)	9501	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_152244.1	chr19	8714201	8714207	-	1	NA	promoter-TSS (NM_008577)	promoter-TSS (NM_008577)	-307	NM_008577	17254	Mm.4114	NM_008577	ENSMUSG00000010095	Slc3a2	4F2|4F2HC|AI314110|Cd98|Ly-10|Ly-m10|Ly10|Mdu1|Mgp-2hc|NACAE	solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2	protein-coding
mm_38535.1	chr4	141571483	141571489	-	1	NA	Intergenic	Intergenic	25324	NR_030695	320456	Mm.32859	NM_177163		B330016D10Rik	-	RIKEN cDNA B330016D10 gene	ncRNA
mm_140123.1	chr17	79611782	79611788	+	1	NA	Intergenic	AmnSINE2|SINE|Deu	-3115	NM_201361	381110	Mm.209801	NM_201361	ENSMUSG00000036368	Rmdn2	AW061290|Fam82a1|RMD-2|mRMD-2	regulator of microtubule dynamics 2	protein-coding
mm_37537.1	chr4	125066586	125066596	-	1	NA	promoter-TSS (NM_175246)	promoter-TSS (NM_175246)	-102	NM_175246	76793	Mm.22548	NM_175246	ENSMUSG00000050213	Snip1	2410133M08Rik	Smad nuclear interacting protein 1	protein-coding
mm_83362.1	chr9	44407527	44407551	-	1	NA	promoter-TSS (NM_021789)	promoter-TSS (NM_021789)	9	NM_021789	60409	Mm.29814	NM_021789	ENSMUSG00000032112	Trappc4	1500017G03Rik|AI303617|HSPC172|PTD009|Sbd|Sbdn|Sdcbp2|TRS23	trafficking protein particle complex 4	protein-coding
mm_127117.1	chr15	97984187	97984188	+	1	NA	intron (NM_031163, intron 34 of 53)	intron (NM_031163, intron 34 of 53)	19958	NM_001252153	380967	Mm.196630	NM_201359	ENSMUSG00000052369	Tmem106c	AI046681|BC046621|D15Ertd405e	transmembrane protein 106C	protein-coding
mm_28582.1	chr3	93511169	93511185	-	1	NA	Intergenic	Intergenic	-9319	NM_016740	20195	Mm.280038	NM_016740	ENSMUSG00000027907	S100a11	EMAPI|Emap1|S100a14|S100c|cal	S100 calcium binding protein A11	protein-coding
mm_9117.1	chr1	170198768	170198791	-	1	NA	TTS (NM_010633)	TTS (NM_010633)	16614	NM_010633	16589	Mm.209150	NM_010633	ENSMUSG00000026667	Uhmk1	4732477C12Rik|4930500M09Rik|AA673513|AI449218|AU021979|C820018A03Rik|KIS|Kist|OTTMUSG00000021542|P-CIP2	U2AF homology motif (UHM) kinase 1	protein-coding
mm_79059.1	chr9	46230203	46230230	+	1	NA	exon (NM_009692, exon 4 of 4)	exon (NM_009692, exon 4 of 4)	1586	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2|apo-AI|apoA-I	apolipoprotein A-I	protein-coding
mm_168856.1	chr12	26456464	26456474	-	1	NA	promoter-TSS (NM_021384)	promoter-TSS (NM_021384)	-17	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_16606.1	chr2	5080568	5080573	-	1	NA	Intergenic	MURVY-LTR|LTR|ERV1	-16632	NM_181848	71648	Mm.116942	NM_181848	ENSMUSG00000026672	Optn	4930441O07Rik|FIP2|HYPL|NRP	optineurin	protein-coding
mm_168099.1	chr10	128911827	128911832	+	1	NA	exon (NM_007653, exon 4 of 8)	exon (NM_007653, exon 4 of 8)	1963	NM_007653	12512	Mm.371552	NM_007653	ENSMUSG00000025351	Cd63	C75951|ME491|Tspan30	CD63 antigen	protein-coding
mm_167296.1	chr8	47425614	47425615	+	1	NA	Intergenic	Intergenic	-73266	NM_175162	71069	Mm.23973	NM_175162	ENSMUSG00000038143	Stox2	4933409N07Rik|AI449080|AI835114|mKIAA1392	storkhead box 2	protein-coding
mm_8279.1	chr1	139990669	139990672	-	1	NA	Intergenic	Lx5c|LINE|L1	-131971	NM_001025575	545366	Mm.439660	NM_001025575	ENSMUSG00000033898	Cfhr2	Cfhrb_4/2	complement factor H-related 2	protein-coding
mm_111081.1	chr12	80231473	80231498	-	1	NA	intron (NM_001346669, intron 1 of 20)	intron (NM_001346669, intron 1 of 20)	28886	NM_134156	109711	Mm.253564	NM_134156	ENSMUSG00000015143	Actn1	3110023F10Rik|Actn1a	actinin, alpha 1	protein-coding
mm_108874.1	chr12	99645460	99645497	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-17504	NR_045288	73457	Mm.383439	NR_045288	ENSMUSG00000100211	1700064M15Rik	-	RIKEN cDNA 1700064M15 gene	ncRNA
mm_155798.1	chrX	98948596	98948599	+	1	NA	3' UTR (NM_207633, exon 7 of 7)	3' UTR (NM_207633, exon 7 of 7)	10816	NM_207633	77929	Mm.212290	NM_207633	ENSMUSG00000047694	Yipf6	A430107J06Rik	Yip1 domain family, member 6	protein-coding
mm_21460.1	chr2	160872946	160872972	-	1	NA	promoter-TSS (NM_177263)	promoter-TSS (NM_177263)	31	NM_177263	320799	Mm.436734	NM_177263	ENSMUSG00000035877	Zhx3	1810059C13Rik|4932418O04Rik|9530010N21Rik|Tix1|mKIAA0395	zinc fingers and homeoboxes 3	protein-coding
mm_72583.1	chr8	84205230	84205235	+	1	NA	Intergenic	AT_rich|Low_complexity|Low_complexity	-3286	NR_029740	387216		NR_029740	ENSMUSG00000065611	Mir23a	Mirn23a|mir-23a|mmu-mir-23a	microRNA 23a	ncRNA
mm_130110.1	chr15	89476141	89476184	-	1	NA	promoter-TSS (NR_077233)	promoter-TSS (NR_077233)	-90	NR_077233	100532730	Mm.461541	NR_077233		C230037L18Rik	-	RIKEN cDNA C230037L18 gene	ncRNA
mm_110437.1	chr12	49381825	49381830	-	1	NA	Intergenic	Intergenic	-1056	NM_001160112	15228	Mm.4704	NM_008241	ENSMUSG00000020950	Foxg1	2900064B05Rik|BF-1|Bf1|Hfh9|Hfhbf1	forkhead box G1	protein-coding
mm_16752.1	chr2	9863561	9863577	-	1	NA	intron (NM_008091, intron 4 of 5)	intron (NM_008091, intron 4 of 5)	15031	NM_008091	14462	Mm.313866	NM_008091	ENSMUSG00000015619	Gata3	Gata-3|jal	GATA binding protein 3	protein-coding
mm_52892.1	chr6	122602672	122602705	+	1	NA	promoter-TSS (NM_031159)	promoter-TSS (NM_031159)	-244	NM_001134391	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_59318.1	chr7	25301344	25301362	+	1	NA	promoter-TSS (NM_001081294)	promoter-TSS (NM_001081294)	-6	NM_001081294	623131	Mm.172160	NM_001081294	ENSMUSG00000058741	Prr19	EG623131	proline rich 19	protein-coding
mm_35220.1	chr4	19656214	19656226	-	1	NA	intron (NR_074090, intron 8 of 24)	intron (NR_074090, intron 8 of 24)	52784	NM_177327	107568	Mm.78312	NM_177327	ENSMUSG00000041058	Wwp1	8030445B08Rik|AIP5|SDRP1|Tiul1	WW domain containing E3 ubiquitin protein ligase 1	protein-coding
mm_34201.1	chr4	140906336	140906353	+	1	NA	promoter-TSS (NM_008812)	promoter-TSS (NM_008812)	-16	NM_008812	18600	Mm.2296	NM_008812	ENSMUSG00000028927	Padi2	Pdi|Pdi2|mKIAA0994	peptidyl arginine deiminase, type II	protein-coding
mm_75771.1	chr8	69986151	69986153	-	1	NA	intron (NM_145596, intron 1 of 12)	intron (NM_145596, intron 1 of 12)	10232	NM_001286450	234366	Mm.270044	NM_145596	ENSMUSG00000036180	Gatad2a	1110066C11Rik|BC031407|C80248	GATA zinc finger domain containing 2A	protein-coding
mm_94899.1	chr11	29172949	29172996	+	1	NA	promoter-TSS (NM_134034)	promoter-TSS (NM_134034)	65	NM_134034	104570	Mm.276386	NM_134034	ENSMUSG00000020463	Smek2	AW011752|AW557776|Ppp4r3b|mKIAA1387	SMEK homolog 2, suppressor of mek1 (Dictyostelium)	protein-coding
mm_38106.1	chr4	134517589	134517597	-	1	NA	intron (NM_001081099, intron 1 of 2)	intron (NM_001081099, intron 1 of 2)	6594	NM_001081099	69885	Mm.141592	NM_001081099	ENSMUSG00000078521	Aunip	2610002D18Rik|Clhc1	aurora kinase A and ninein interacting protein	protein-coding
mm_51167.1	chr6	70726533	70726537	+	1	NA	Intergenic	Intergenic	65640	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_17567.1	chr2	30205795	30205835	-	1	NA	promoter-TSS (NM_172404)	promoter-TSS (NM_172404)	-116	NM_172404	70266	Mm.216089	NM_172404	ENSMUSG00000039648	Kyat1	2010009K05Rik|AI182306|Ccbl1|Gtk|Kat1|KatI	kynurenine aminotransferase 1	protein-coding
mm_42996.1	chr5	123394731	123394739	+	1	NA	promoter-TSS (NM_177582)	promoter-TSS (NM_177582)	-63	NM_133917	208104	Mm.83277	NM_133917	ENSMUSG00000038342	Mlxip	AW228700|Mir|bHLHe36	MLX interacting protein	protein-coding
mm_118925.1	chr14	27000706	27000716	+	1	NA	5' UTR (NM_010420, exon 1 of 4)	5' UTR (NM_010420, exon 1 of 4)	349	NM_010420	15209	Mm.4802	NM_010420	ENSMUSG00000040726	Hesx1	HES-1|Rpx	homeobox gene expressed in ES cells	protein-coding
mm_172012.1	chr6	109505461	109505472	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	676825	NM_138677	192193	Mm.21596	NM_138677	ENSMUSG00000030104	Edem1	A130059K23Rik|EDEM|mKIAA0212	ER degradation enhancer, mannosidase alpha-like 1	protein-coding
mm_17358.1	chr2	26617478	26617483	-	1	NA	Intergenic	RMER1C|Other|Other	-10977	NM_019833	56279	Mm.279863	NM_019833	ENSMUSG00000036186	Fam69b	AB030186|AW209000|B230317C12Rik|PIP49	family with sequence similarity 69, member B	protein-coding
mm_148461.1	chr19	4066411	4066425	+	1	NA	Intergenic	B3A|SINE|B2	-7124	NM_144869	225884	Mm.440201	NM_144869	ENSMUSG00000058216	Gstp3	-	glutathione S-transferase pi 3	protein-coding
mm_156498.1	chrX	144352687	144352697	+	1	NA	non-coding (NR_037145, exon 19 of 27)	non-coding (NR_037145, exon 19 of 27)	34726	NM_026247	67574	Mm.249084	NM_026247	ENSMUSG00000041718	Alg13	2810046O15Rik|4833435D08Rik|Glt28d1|MDS031|OTTMUSG00000018917	asparagine-linked glycosylation 13	protein-coding
mm_28360.1	chr3	89870178	89870194	-	1	NA	3' UTR (NM_010559, exon 10 of 10)	3' UTR (NM_010559, exon 10 of 10)	38816	NM_172530	214547	Mm.225	NM_172530	ENSMUSG00000046280	She	9430022A14	src homology 2 domain-containing transforming protein E	protein-coding
mm_29387.1	chr3	108889828	108889830	-	1	NA	5' UTR (NM_177091, exon 1 of 13)	5' UTR (NM_177091, exon 1 of 13)	179	NM_177091	320181	Mm.244233	NM_177091	ENSMUSG00000045326	Fndc7	E230011A21Rik	fibronectin type III domain containing 7	protein-coding
mm_17291.1	chr2	26204657	26204661	-	1	NA	intron (NM_010711, intron 1 of 5)	intron (NM_010711, intron 1 of 5)	1916	NM_001039653	16871	Mm.386765	NM_010711	ENSMUSG00000026934	Lhx3	Lim3|P-LIM|mLIM3|mLim-3	LIM homeobox protein 3	protein-coding
mm_62635.1	chr7	107661894	107661901	+	1	NA	intron (NM_001163557, intron 3 of 25)	(T)n|Simple_repeat|Simple_repeat	55053	NM_001163557	19024	Mm.2817	NM_008905	ENSMUSG00000036528	Ppfibp2	Cclp1	PTPRF interacting protein, binding protein 2 (liprin beta 2)	protein-coding
mm_64887.1	chr7	15920779	15920791	-	1	NA	intron (NM_009156, intron 1 of 5)	intron (NM_009156, intron 1 of 5)	1586	NM_009156	20364	Mm.42829	NM_009156	ENSMUSG00000041571	Selenow	Sepw1|selW	selenoprotein W	protein-coding
mm_10921.1	chr2	25424633	25424673	+	1	NA	5' UTR (NM_013524, exon 2 of 3)	5' UTR (NM_013524, exon 2 of 3)	959	NM_001177367	14347	Mm.1203	NM_013524	ENSMUSG00000036587	Fut7	AI853193|FTVII|Fuc-TVII|FucT-VII	fucosyltransferase 7	protein-coding
mm_87004.1	chr10	26801400	26801446	+	1	NA	intron (NM_176837, intron 1 of 14)	intron (NM_176837, intron 1 of 14)	28911	NM_176837	73910	Mm.356496	NM_176837	ENSMUSG00000039031	Arhgap18	4833419J07Rik|AI314906|AI843501	Rho GTPase activating protein 18	protein-coding
mm_57043.1	chr6	122340526	122340543	-	1	NA	promoter-TSS (NM_001271579)	promoter-TSS (NM_001271579)	-307	NM_001271579	13619	Mm.6822	NM_007905	ENSMUSG00000040669	Phc1	AW557034|Edr|Edr1|Mph1|Rae-28|rae28	polyhomeotic-like 1 (Drosophila)	protein-coding
mm_149036.1	chr19	8819583	8819608	+	1	NA	promoter-TSS (NM_027412)	promoter-TSS (NM_027412)	194	NM_001081196	68693	Mm.476519	NM_001081196	ENSMUSG00000071659	Hnrnpul2	1110031M08Rik|AI465155|Hnrpul2	heterogeneous nuclear ribonucleoprotein U-like 2	protein-coding
mm_11501.1	chr2	32535397	32535405	+	1	NA	promoter-TSS (NM_153560)	promoter-TSS (NM_153560)	42	NM_153560	98952	Mm.4065	NM_153560	ENSMUSG00000039157	Fam102a	AI426465|C230093N12Rik|Eeig1	family with sequence similarity 102, member A	protein-coding
mm_122140.1	chr14	31168588	31168606	-	1	NA	promoter-TSS (NM_138672)	promoter-TSS (NM_138672)	44	NM_138672	192187	Mm.220821	NM_138672	ENSMUSG00000042286	Stab1	FEEL-1|FELE-1|MFEEL-1|MS-1|STAB-1|mKIAA0246	stabilin 1	protein-coding
mm_51678.1	chr6	86438749	86438758	+	1	NA	5' UTR (NM_001243742, exon 1 of 10)	5' UTR (NM_001243742, exon 1 of 10)	107	NM_001243741	232196	Mm.404040	NM_146170	ENSMUSG00000046679	C87436	-	expressed sequence C87436	protein-coding
mm_78783.1	chr9	43993983	43993993	+	1	NA	Intergenic	MLTR14|LTR|ERV1	-49396	NM_009382	21838	Mm.3951	NM_009382	ENSMUSG00000032011	Thy1	CD90|T25|Thy-1|Thy-1.2|Thy1.1|Thy1.2	thymus cell antigen 1, theta	protein-coding
mm_126149.1	chr15	78406184	78406187	+	1	NA	promoter-TSS (NM_138670)	promoter-TSS (NM_138670)	-326	NM_009437	22117	Mm.15312	NM_009437	ENSMUSG00000044986	Tst	Rhodanese	thiosulfate sulfurtransferase, mitochondrial	protein-coding
mm_112328.1	chr12	115742675	115742703	-	1	NA	Intergenic	Intergenic	-46895	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
mm_171028.1	chr2	88241397	88241412	+	1	NA	Intergenic	L1Md_T|LINE|L1	-16374	NM_146532	258525	Mm.377552	NM_146532	ENSMUSG00000075133	Olfr1170	MOR174-12	olfactory receptor 1170	protein-coding
mm_63613.1	chr7	128237285	128237329	+	1	NA	promoter-TSS (NM_146205)	promoter-TSS (NM_146205)	-50	NM_146205	233912	Mm.475117	NM_146205	ENSMUSG00000042178	Armc5	AW049683|BC032200	armadillo repeat containing 5	protein-coding
mm_129961.1	chr15	85577870	85577902	-	1	NA	5' UTR (NM_001163634, exon 1 of 4)	5' UTR (NM_001163634, exon 1 of 4)	184	NM_001163634	22422	Mm.306946	NM_009528	ENSMUSG00000022382	Wnt7b	Wnt-7b	wingless-type MMTV integration site family, member 7B	protein-coding
mm_151369.1	chr19	55931498	55931530	+	1	NA	exon (NM_001142922, exon 14 of 14)	exon (NM_001142922, exon 14 of 14)	36193	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_131105.1	chr16	5007564	5007593	+	1	NA	intron (NR_045596, intron 1 of 2)	intron (NR_045596, intron 1 of 2)	262	NR_045596	432995	Mm.271618	NM_001253796	ENSMUSG00000096215	Smim22	EG432995|Gm5480	small integral membrane protein 22	protein-coding
mm_109004.1	chr12	103314968	103314974	+	1	NA	promoter-TSS (NM_001195726)	promoter-TSS (NM_001195726)	12	NM_001195726	100504156	Mm.425749	NM_001195726	ENSMUSG00000096753	Fam181a	EG544888	family with sequence similarity 181, member A	protein-coding
mm_118509.1	chr14	14013126	14013195	+	1	NA	exon (NM_139227, exon 2 of 12)	exon (NM_139227, exon 2 of 12)	669	NM_139227	246103	Mm.133625	NM_139227	ENSMUSG00000021738	Atxn7	A430107N12Rik|AI627028|Sca7|ataxin-7	ataxin 7	protein-coding
mm_163755.1	chr13	119790772	119790793	-	1	NA	promoter-TSS (NM_028245)	promoter-TSS (NM_028245)	24	NM_028245	72465	Mm.139115	NM_028245	ENSMUSG00000094870	Zfp131	2610109I01Rik|AW558871|Znf131	zinc finger protein 131	protein-coding
mm_148555.1	chr19	4712205	4712218	+	1	NA	intron (NM_021287, intron 1 of 36)	CpG	988	NM_021287	20743	Mm.329668	NM_021287	ENSMUSG00000067889	Sptbn2	Spnb3|mKIAA0302	spectrin beta, non-erythrocytic 2	protein-coding
mm_98358.1	chr11	93886138	93886154	+	1	NA	promoter-TSS (NM_134012)	promoter-TSS (NM_134012)	-61	NM_001346525	103537	Mm.210334	NM_134012	ENSMUSG00000059474	Mbtd1	AA408199|AI194990|hemp	mbt domain containing 1	protein-coding
mm_71713.1	chr8	61942778	61942787	+	1	NA	intron (NM_001293783, intron 5 of 37)	B3A|SINE|B2	14695	NM_001293783	234311	Mm.275233	NM_144928	ENSMUSG00000037921	Ddx60	9830118M07	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	protein-coding
mm_127526.1	chr15	102074190	102074201	+	1	NA	intron (NM_145625, intron 1 of 14)	CpG	422	NM_145625	75705	Mm.290022	NM_145625	ENSMUSG00000058655	Eif4b	2310046H11Rik|AL024095|C85189|Eif4a2	eukaryotic translation initiation factor 4B	protein-coding
mm_76964.1	chr8	106136891	106136901	-	1	NA	promoter-TSS (NM_176838)	promoter-TSS (NM_176838)	78	NM_176838	77411	Mm.183003	NM_176838	ENSMUSG00000084128	Esrp2	9530027K23Rik|Rbm35b	epithelial splicing regulatory protein 2	protein-coding
mm_131271.1	chr16	10976351	10976363	+	1	NA	intron (NM_019980, intron 1 of 3)	intron (NM_019980, intron 1 of 3)	16764	NM_019980	56722	Mm.294753	NM_019980	ENSMUSG00000022500	Litaf	3222402J11Rik|C85531|N4WBP3|TBX1	LPS-induced TN factor	protein-coding
mm_134237.1	chr16	11909384	11909390	-	1	NA	promoter-TSS (NM_146067)	promoter-TSS (NM_146067)	36	NM_146067	223978	Mm.86360	NM_146067	ENSMUSG00000065979	Cpped1	C530044N13Rik	calcineurin-like phosphoesterase domain containing 1	protein-coding
mm_165681.1	chr3	90692778	90692790	+	1	NA	exon (NM_001281852, exon 3 of 3)	exon (NM_001281852, exon 3 of 3)	2937	NM_001281852	20202	Mm.2128	NM_009114	ENSMUSG00000056071	S100a9	60B8Ag|AW546964|BEE22|Cagb|GAGB|L1Ag|MRP14|p14	S100 calcium binding protein A9 (calgranulin B)	protein-coding
mm_79075.1	chr9	46241549	46241560	+	1	NA	exon (NM_007468, exon 2 of 3)	exon (NM_007468, exon 2 of 3)	710	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_33427.1	chr4	130050742	130050749	+	1	NA	intron (NM_028266, intron 2 of 69)	intron (NM_028266, intron 2 of 69)	2905	NM_028266	107581	Mm.41860	NM_028266	ENSMUSG00000040690	Col16a1	2700007F12Rik|A530052M23Rik|AI838662|CA1F	collagen, type XVI, alpha 1	protein-coding
mm_8396.1	chr1	151472100	151472110	-	1	NA	intron (NM_011277, intron 5 of 6)	(A)n|Simple_repeat|Simple_repeat	28718	NM_011277	19821	Mm.474038	NM_011277	ENSMUSG00000026484	Rnf2	AI326319|AI450156|AU019207|Ring1B|dinG	ring finger protein 2	protein-coding
mm_138489.1	chr17	35200340	35200352	+	1	NA	exon (NM_013693, exon 4 of 4)	exon (NM_013693, exon 4 of 4)	1661	NM_013693	21926	Mm.1293	NM_013693	ENSMUSG00000024401	Tnf	DIF|TNF-a|TNF-alpha|TNFSF2|TNFalpha|Tnfa|Tnfsf1a|Tnlg1f	tumor necrosis factor	protein-coding
mm_54608.1	chr6	38343067	38343074	-	1	NA	intron (NM_001347122, intron 1 of 12)	intron (NM_001347122, intron 1 of 12)	11533	NM_028864	78781	Mm.25243	NM_028421	ENSMUSG00000029826	Zc3hav1	1200014N16Rik|2900058M19Rik|9130009D18Rik|9830115L13Rik|ARTD13|D6Bwg1452e|ZAP	zinc finger CCCH type, antiviral 1	protein-coding
mm_67815.1	chr7	98162458	98162471	-	1	NA	promoter-TSS (NM_001301250)	promoter-TSS (NM_001301250)	-122	NM_001301250	12337	Mm.326847	NM_007602	ENSMUSG00000035547	Capn5	nCL-3	calpain 5	protein-coding
mm_110950.1	chr12	76668697	76668709	-	1	NA	intron (NM_013675, intron 1 of 35)	RSINE1|SINE|B4	41844	NM_013675	20741	Mm.32881	NM_013675	ENSMUSG00000021061	Sptb	AI842465|D330027P03Rik|Gm1301|Spnb-1|Spnb1|ja|jaundiced|mKIAA4219	spectrin beta, erythrocytic	protein-coding
mm_121081.1	chr14	99099877	99099962	+	1	NA	promoter-TSS (NM_028315)	promoter-TSS (NM_028315)	-149	NM_028315	72662	Mm.163339	NM_028315	ENSMUSG00000033166	Dis3	2810028N01Rik	DIS3 homolog, exosome endoribonuclease and 3'-5' exoribonuclease	protein-coding
mm_172239.1	chr6	68632452	68632471	-	1	NA	Intergenic	Intergenic	694713	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_94506.1	chr11	7199885	7199894	+	1	NA	exon (NM_008341, exon 2 of 4)	exon (NM_008341, exon 2 of 4)	2102	NM_008341	16006	Mm.21300	NM_008341	ENSMUSG00000020429	Igfbp1	-	insulin-like growth factor binding protein 1	protein-coding
mm_79135.1	chr9	47618638	47618681	+	1	NA	intron (NM_001025600, intron 1 of 8)	intron (NM_001025600, intron 1 of 8)	88307	NM_018770	54725	Mm.234832	NM_018770	ENSMUSG00000032076	Cadm1	2900073G06Rik|3100001I08Rik|AI987920|Bl2|Igsf4|Igsf4a|Necl2|RA175|RA175A|RA175B|RA175C|RA175N|ST17|SgIGSF|SynCam|Tslc1	cell adhesion molecule 1	protein-coding
mm_53151.1	chr6	125265539	125265545	+	1	NA	promoter-TSS (NR_015527)	promoter-TSS (NR_015527)	17	NR_015527	73870	Mm.440681	NR_015527	ENSMUSG00000108129	4930417O13Rik	-	RIKEN cDNA 4930417O13 gene	ncRNA
mm_169932.1	chr16	59092385	59092390	+	1	NA	Intergenic	RLTR10C|LTR|ERVK	-5906	NM_001011807	258035	Mm.377334	NM_001011807	ENSMUSG00000094539	Olfr191	MOR183-5P	olfactory receptor 191	protein-coding
mm_47134.1	chr5	120494401	120494421	-	1	NA	exon (NM_023625, exon 3 of 12)	exon (NM_023625, exon 3 of 12)	9212	NM_023625	71772	Mm.100065	NM_023625	ENSMUSG00000029598	Plbd2	1300012G16Rik|AU019810|P76	phospholipase B domain containing 2	protein-coding
mm_15303.1	chr2	155386871	155386896	+	1	NA	3' UTR (NM_178111, exon 4 of 4)	3' UTR (NM_178111, exon 4 of 4)	5027	NM_178111	68728	Mm.293605	NM_178111	ENSMUSG00000038375	Trp53inp2	1110029F20Rik|Tp53inp2	transformation related protein 53 inducible nuclear protein 2	protein-coding
mm_147990.1	chr18	67641258	67641284	-	1	NA	promoter-TSS (NM_001081073)	promoter-TSS (NM_001081073)	65	NM_001081073	225659	Mm.111928	NM_001081073	ENSMUSG00000073542	Cep76	6230425F05Rik|9630013E05	centrosomal protein 76	protein-coding
mm_152859.1	chr19	24200642	24200652	-	1	NA	intron (NM_011597, intron 1 of 22)	intron (NM_011597, intron 1 of 22)	24379	NM_011597	21873	Mm.104744	NM_011597	ENSMUSG00000024812	Tjp2	ZO-2	tight junction protein 2	protein-coding
mm_27006.1	chr3	25847429	25847440	-	1	NA	intron (NM_001163387, intron 3 of 5)	intron (NM_001163387, intron 3 of 5)	305873	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_89036.1	chr10	82795925	82795954	+	1	NA	Intergenic	Intergenic	-16184	NR_038042	70003	Mm.48789	NR_038042	ENSMUSG00000056821	1700028I16Rik	-	RIKEN cDNA 1700028I16 gene	ncRNA
mm_64751.1	chr7	4792813	4792823	-	1	NA	promoter-TSS (NM_009081)	promoter-TSS (NM_009081)	-147	NM_009081	19943	Mm.379002	NM_009081	ENSMUSG00000030432	Rpl28	D7Wsu21e	ribosomal protein L28	protein-coding
mm_29627.1	chr3	121548098	121548106	-	1	NA	Intergenic	Intergenic	-15758	NM_145394	213603	Mm.33062	NM_145394	ENSMUSG00000039865	Slc44a3	BC010552	solute carrier family 44, member 3	protein-coding
mm_9581.1	chr1	174028368	174028378	-	1	NA	exon (NM_172648, exon 2 of 7)	exon (NM_172648, exon 2 of 7)	3382	NM_172648	226695	Mm.425061	NM_172648	ENSMUSG00000054203	Ifi205	D3|D3cDNA|Ifi205a	interferon activated gene 205	protein-coding
mm_156214.1	chrX	134686529	134686536	+	1	NA	promoter-TSS (NR_045454)	promoter-TSS (NR_045454)	13	NM_001202500	100503043	Mm.31961	NM_001202500	ENSMUSG00000049804	Armcx4	AI448196|Gm195	armadillo repeat containing, X-linked 4	protein-coding
mm_171893.1	chr5	3893910	3893920	-	1	NA	promoter-TSS (NM_172135)	promoter-TSS (NM_172135)	18	NM_001013023	545725	Mm.99593	NM_172135	ENSMUSG00000040429	Mterf1a	4931431L11Rik|9230106K09Rik|Mterf|Mterf1|mTERF1b	mitochondrial transcription termination factor 1a	protein-coding
mm_78485.1	chr9	32698248	32698274	+	1	NA	intron (NM_011808, intron 1 of 7)	intron (NM_011808, intron 1 of 7)	2219	NM_001038642	23871	Mm.292415	NM_011808	ENSMUSG00000032035	Ets1	AI196000|AI448617|D230050P06|Ets-1|Tpl1|vs	E26 avian leukemia oncogene 1, 5' domain	protein-coding
mm_143449.1	chr17	70919897	70919919	-	1	NA	Intergenic	Intergenic	-66376	NM_001164074	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_99239.1	chr11	101078355	101078361	+	1	NA	promoter-TSS (NM_010475)	promoter-TSS (NM_010475)	-53	NM_010475	15485	Mm.188939	NM_010475	ENSMUSG00000019301	Hsd17b1	17HSDB1|17beta-HSD|E2DH|Hsd17ba	hydroxysteroid (17-beta) dehydrogenase 1	protein-coding
mm_20312.1	chr2	127272754	127272757	-	1	NA	intron (NM_139308, intron 1 of 7)	BC1_Mm|scRNA|scRNA	2526	NM_139308	99138	Mm.41271	NM_139308	ENSMUSG00000027367	Stard7	AI852671|AL022671|AW544915	START domain containing 7	protein-coding
mm_73256.1	chr8	104340386	104340403	+	1	NA	promoter-TSS (NM_024217)	promoter-TSS (NM_024217)	-200	NM_024217	68119	Mm.390108	NM_024217	ENSMUSG00000031875	Cmtm3	9430096L06Rik|AI413895|BNAS2|Cklfsf3	CKLF-like MARVEL transmembrane domain containing 3	protein-coding
mm_26122.1	chr3	137865869	137865871	+	1	NA	intron (NM_001316995, intron 3 of 4)	intron (NM_001316995, intron 3 of 4)	1383	NM_016750	51788	Mm.117541	NM_016750	ENSMUSG00000037894	H2afz	H2A.Z|H2a.z-1	H2A histone family, member Z	protein-coding
mm_123712.1	chr14	69816009	69816034	-	1	NA	Intergenic	Intergenic	-10476	NM_153514	246710	Mm.102367	NM_153514	ENSMUSG00000022075	Rhobtb2	Dbc2|E130206H14Rik|mKIAA0717	Rho-related BTB domain containing 2	protein-coding
mm_87157.1	chr10	36525388	36525392	+	1	NA	intron (NM_001081208, intron 1 of 3)	intron (NM_001081208, intron 1 of 3)	18583	NM_001253356	319415	Mm.332442	NM_001081208	ENSMUSG00000044499	Hs3st5	D930005L05Rik|Gm1151|Hs3ost5	heparan sulfate (glucosamine) 3-O-sulfotransferase 5	protein-coding
mm_105385.1	chr11	103360365	103360402	-	1	NA	exon (NM_183288, exon 3 of 3)	exon (NM_183288, exon 3 of 3)	3309	NM_183288	544817	Mm.259113	NM_133715	ENSMUSG00000034255	Arhgap27	2310069I04Rik|5730442P18Rik|Gm21552|Sh3d20	Rho GTPase activating protein 27	protein-coding
mm_55197.1	chr6	52204240	52204250	-	1	NA	exon (NM_010453, exon 1 of 2)	exon (NM_010453, exon 1 of 2)	342	NM_010453	15402	Mm.173	NM_010453	ENSMUSG00000038253	Hoxa5	Hox-1.3	homeobox A5	protein-coding
mm_77469.1	chr8	122426241	122426260	-	1	NA	exon (NM_007806, exon 5 of 6)	exon (NM_007806, exon 5 of 6)	4165	NM_145834	234836	Mm.222808	NM_145834	ENSMUSG00000046108	Il17c	IL-17C	interleukin 17C	protein-coding
mm_150328.1	chr19	34574726	34574736	+	1	NA	3' UTR (NM_008332, exon 3 of 3)	3' UTR (NM_008332, exon 3 of 3)	-8798	NM_010501	15959	Mm.426079	NM_010501	ENSMUSG00000074896	Ifit3	Ifi49|P49	interferon-induced protein with tetratricopeptide repeats 3	protein-coding
mm_129670.1	chr15	81360832	81360853	-	1	NA	promoter-TSS (NM_011399)	promoter-TSS (NM_011399)	-77	NM_011399	20524	Mm.222536	NM_011399	ENSMUSG00000022404	Slc25a17	34kDa|47kDa|PMP34|Pmp47	solute carrier family 25 (mitochondrial carrier, peroxisomal membrane protein), member 17	protein-coding
mm_26868.1	chr3	16183834	16183844	-	1	NA	intron (NR_027375, intron 1 of 5)	intron (NR_027375, intron 1 of 5)	656	NM_001145919	229096	Mm.23834	NM_172677	ENSMUSG00000047213	Ythdf3	9130022A11Rik	YTH domain family 3	protein-coding
mm_5002.1	chr1	191928642	191928650	+	1	NA	Intergenic	Intergenic	-21119	NR_030669	98736	Mm.379232	NM_001024489	ENSMUSG00000055833	1700034H15Rik	4930557M11Rik|BB016121	RIKEN cDNA 1700034H15 gene	ncRNA
mm_158993.1	chr1	136008128	136008128	+	1	NA	promoter-TSS (NM_001160145)	promoter-TSS (NM_001160145)	-91	NM_001160145	66241	Mm.41773	NM_025439	ENSMUSG00000026411	Tmem9	1500015G18Rik|AW545782	transmembrane protein 9	protein-coding
mm_121389.1	chr14	118981934	118981947	+	1	NA	TTS (NM_008929)	TTS (NM_008929)	44008	NM_008929	100037258	Mm.12616	NM_008929	ENSMUSG00000022136	Dnajc3	AA408985|AU067833|Dnajc3a|Dnajc3b|Prkri|mp58|p58|p58IPK	DnaJ heat shock protein family (Hsp40) member C3	protein-coding
mm_151777.1	chr19	5349341	5349358	-	1	NA	5' UTR (NM_028623, exon 1 of 3)	5' UTR (NM_028623, exon 1 of 3)	225	NM_028623	73720	Mm.36816	NM_028623	ENSMUSG00000024846	Cst6	1110017E11Rik|N28197|ichq	cystatin E/M	protein-coding
mm_166413.1	chr5	137151471	137151479	-	1	NA	Intergenic	Intergenic	-35268	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_11419.1	chr2	31688402	31688415	+	1	NA	promoter-TSS (NM_001283047)	promoter-TSS (NM_001283047)	-129	NM_001283047	11350	Mm.1318	NM_009594	ENSMUSG00000026842	Abl1	AI325092|Abl|E430008G22Rik|c-Abl	c-abl oncogene 1, non-receptor tyrosine kinase	protein-coding
mm_173264.1	chrX	94911537	94911554	+	1	NA	Intergenic	Intergenic	-113256	NR_003292	668171	Mm.426134	NR_003292		Zxda	4933406P09Rik|AW413531	zinc finger, X-linked, duplicated A	pseudo
mm_71600.1	chr8	54985951	54985956	+	1	NA	intron (NM_001253756, intron 1 of 5)	(T)n|Simple_repeat|Simple_repeat	31225	NM_001253756	234267	Mm.241700	NM_153581	ENSMUSG00000031517	Gpm6a	Gpm6|M6A	glycoprotein m6a	protein-coding
mm_28871.1	chr3	97702679	97702685	-	1	NA	intron (NM_001039376, intron 36 of 46)	intron (NM_001039376, intron 36 of 46)	-12120	NR_106084	102466229		NR_106084	ENSMUSG00000098381	Mir7225	Gm27499|mmu-mir-7225	microRNA 7225	ncRNA
mm_120760.1	chr14	73368302	73368312	+	1	NA	exon (NM_008410, exon 2 of 6)	exon (NM_008410, exon 2 of 6)	16964	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_170973.1	chr2	64313360	64313361	+	1	NA	Intergenic	L1Md_T|LINE|L1	-215322	NM_001267847	60344	Mm.130769	NM_021716	ENSMUSG00000075324	Fign	fi|fidget	fidgetin	protein-coding
mm_96534.1	chr11	68614219	68614221	+	1	NA	Intergenic	Intergenic	27183	NM_177779	276920	Mm.123046	NM_177779	ENSMUSG00000045915	Ccdc42	A530001H01Rik	coiled-coil domain containing 42	protein-coding
mm_110258.1	chr12	31713742	31713748	-	1	NA	5' UTR (NM_175191, exon 1 of 3)	5' UTR (NM_175191, exon 1 of 3)	181	NM_175191	73010	Mm.441517	NM_175191	ENSMUSG00000044067	Gpr22	2900068K05Rik|AW061316	G protein-coupled receptor 22	protein-coding
mm_146238.1	chr18	77186088	77186117	+	1	NA	exon (NM_013666, exon 1 of 8)	exon (NM_013666, exon 1 of 8)	255	NM_013666	225742	Mm.365178	NM_013666	ENSMUSG00000025425	St8sia5	ST8SiaV|Siat8e	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 5	protein-coding
mm_148743.1	chr19	6036716	6036716	+	1	NA	Intergenic	MTB|LTR|ERVL-MaLR	-9860	NM_028769	74126	Mm.149870	NM_028769	ENSMUSG00000024807	Syvn1	1200010C09Rik|AW211966|C85322|D530017H19Rik|Hrd1	synovial apoptosis inhibitor 1, synoviolin	protein-coding
mm_59155.1	chr7	24370317	24370332	+	1	NA	promoter-TSS (NM_001163510)	promoter-TSS (NM_001163510)	61	NM_008433	16534	Mm.9911	NM_008433	ENSMUSG00000054342	Kcnn4	IK1|IKCA1|KCA4|KCa3.1|SK4|SKCas|mIKCa1	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4	protein-coding
mm_47390.1	chr5	123015896	123015910	-	1	NA	intron (NM_175423, intron 1 of 1)	intron (NM_175423, intron 1 of 1)	829	NM_175423	109305	Mm.218582	NM_175423	ENSMUSG00000049686	Orai1	D730049H07Rik|Tmem142a|orai-1	ORAI calcium release-activated calcium modulator 1	protein-coding
mm_585.1	chr1	39369185	39369198	+	1	NA	intron (NM_001252218, intron 1 of 3)	intron (NM_001252218, intron 1 of 3)	1340	NM_001252218	114641	Mm.379302	NM_053257	ENSMUSG00000073702	Rpl31	Dts	ribosomal protein L31	protein-coding
mm_68093.1	chr7	101921752	101921793	-	1	NA	promoter-TSS (NM_001162974)	promoter-TSS (NM_001162974)	-998	NM_001162974	69358	Mm.214841	NM_027053	ENSMUSG00000064307	Lrrc51	1700008D07Rik|Lrtomt	leucine rich repeat containing 51	protein-coding
mm_171814.1	chr5	137338354	137338367	-	1	NA	Intergenic	Intergenic	-4778	NM_031406	83704	Mm.235625	NM_031406	ENSMUSG00000037344	Slc12a9	CIP1	solute carrier family 12 (potassium/chloride transporters), member 9	protein-coding
mm_164720.1	chr17	56866331	56866344	+	1	NA	intron (NM_001039114, intron 3 of 14)	intron (NM_001039114, intron 3 of 14)	8110	NM_001039114	328845	Mm.179421	NM_001039114	ENSMUSG00000024207	Acsbg2	Bgr	acyl-CoA synthetase bubblegum family member 2	protein-coding
mm_22975.1	chr3	32712190	32712195	+	1	NA	exon (NM_019673, exon 3 of 14)	exon (NM_019673, exon 3 of 14)	3646	NM_019673	56456	Mm.41077	NM_019673	ENSMUSG00000027671	Actl6a	2810432C06Rik|AI851094|ARP4|Actl6|Baf53a|C79802	actin-like 6A	protein-coding
mm_156706.1	chrX	159627236	159627258	+	1	NA	promoter-TSS (NM_001135727)	promoter-TSS (NM_001135727)	-25	NM_001135727	58194	Mm.286495	NM_021389	ENSMUSG00000040990	Sh3kbp1	1200007H22Rik|1700125L08Rik|5830464D22Rik|AI447724|Cin85|IN85|Ruk|Seta	SH3-domain kinase binding protein 1	protein-coding
mm_136920.1	chr17	13846089	13846093	+	1	NA	intron (NM_010806, intron 13 of 32)	intron (NM_010806, intron 13 of 32)	-84697	NM_022311	21646	Mm.486358	NM_022311	ENSMUSG00000038347	Tcte2	AI429268|Tcte-2	t-complex-associated testis expressed 2	protein-coding
mm_22441.1	chr2	181693655	181693670	-	1	NA	5' UTR (NM_001291208, exon 1 of 5)	5' UTR (NM_001291208, exon 1 of 5)	148	NM_001291206	56470	Mm.274366	NM_026446	ENSMUSG00000002458	Rgs19	2610042F04Rik|AI324841|AW547781|GAIP	regulator of G-protein signaling 19	protein-coding
mm_116437.1	chr13	42245761	42245768	-	1	NA	Intergenic	Intergenic	-55712	NM_010104	13614	Mm.14543	NM_010104	ENSMUSG00000021367	Edn1	ET-1|PPET1|preproET	endothelin 1	protein-coding
mm_60437.1	chr7	44476933	44476958	+	1	NA	Intergenic	L1MEd|LINE|L1	6598	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_12364.1	chr2	69789622	69789626	+	1	NA	promoter-TSS (NM_028521)	promoter-TSS (NM_028521)	-113	NM_028521	73373	Mm.9621	NM_028521	ENSMUSG00000027088	Phospho2	1700048E23Rik|AI661517|AU021728|AV006103|Phos2	phosphatase, orphan 2	protein-coding
mm_2806.1	chr1	130865747	130865768	+	1	NA	promoter-TSS (NM_026976)	promoter-TSS (NM_026976)	-20	NM_026976	69169	Mm.46042	NM_026976	ENSMUSG00000042474	Fcmr	1810037B05Rik|Faim3|FcmuR|Toso	Fc fragment of IgM receptor	protein-coding
mm_154682.1	chrX	7922078	7922106	+	1	NA	exon (NM_013892, exon 2 of 3)	exon (NM_013892, exon 2 of 3)	2270	NM_013892	30052	Mm.4881	NM_013892	ENSMUSG00000039278	Pcsk1n	AI848336|KEP|PEN|PEN19|PEN20|Pan3|SAAS|SAASCT|bLEN|lLEN|proSAAS	proprotein convertase subtilisin/kexin type 1 inhibitor	protein-coding
mm_9046.1	chr1	167284668	167284676	-	1	NA	intron (NM_030724, intron 1 of 6)	CpG	455	NM_030724	80914	Mm.280895	NM_030724	ENSMUSG00000026558	Uck2	AA407809|AI481316|AU018180|AU020720|TSA903|UK|UMK|Umpk	uridine-cytidine kinase 2	protein-coding
mm_143576.1	chr17	74316275	74316285	-	1	NA	promoter-TSS (NM_001146224)	promoter-TSS (NM_001146224)	-69	NM_001146224	66310	Mm.28536	NM_024428	ENSMUSG00000024067	Dpy30	2810410M20Rik|C87842	dpy-30, histone methyltransferase complex regulatory subunit	protein-coding
mm_58059.1	chr6	136857692	136857708	-	1	NA	promoter-TSS (NM_026639)	promoter-TSS (NM_026639)	-100	NM_026639	109978	Mm.31840	NM_026639	ENSMUSG00000030217	Art4	4432404K01Rik|ARTC4|DO|DOK1	ADP-ribosyltransferase 4	protein-coding
mm_39694.1	chr5	27049545	27049572	+	1	NA	5' UTR (NM_207282, exon 1 of 26)	5' UTR (NM_207282, exon 1 of 26)	359	NM_207282	13483	Mm.42078	NM_010075	ENSMUSG00000061576	Dpp6	B930011P16Rik|D5Buc3|D5Buc4|D5Buc5|DPP VI|Dpp-6|Gm1377|In(5)6H-p|Peplb|Rw	dipeptidylpeptidase 6	protein-coding
mm_73915.1	chr8	119666468	119666480	+	1	NA	5' UTR (NM_023395, exon 1 of 7)	5' UTR (NM_023395, exon 1 of 7)	109	NM_023395	67866	Mm.87599	NM_023395	ENSMUSG00000023336	Wfdc1	2310058A03Rik|ps20	WAP four-disulfide core domain 1	protein-coding
mm_56344.1	chr6	92908344	92908347	-	1	NA	Intergenic	Intergenic	-6904	NM_175314	101401	Mm.158235	NM_175314	ENSMUSG00000030022	Adamts9	1810011L16Rik|8430403M15Rik|AW743315|E030027K14Rik	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 9	protein-coding
mm_80322.1	chr9	74953157	74953209	+	1	NA	5' UTR (NM_001113283, exon 1 of 13)	5' UTR (NM_001113283, exon 1 of 13)	130	NM_001113283	235493	Mm.208955	NM_153584	ENSMUSG00000034858	Fam214a	6330415I01Rik|AI553555|C130047D21Rik|Kiaa1370|mKIAA1370	family with sequence similarity 214, member A	protein-coding
mm_50032.1	chr6	41130266	41130292	+	1	NA	Intergenic	Intergenic	-94770	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_81068.1	chr9	106189249	106189252	+	1	NA	3' UTR (NM_029896, exon 9 of 9)	3' UTR (NM_029896, exon 9 of 9)	9689	NM_198931	67905	Mm.23018	NM_026447	ENSMUSG00000020253	Ppm1m	2810423O19Rik|AW610647|C77250|PP2Ceta	protein phosphatase 1M	protein-coding
mm_109338.1	chr12	109585048	109585063	+	1	NA	promoter-TSS (NR_029765)	promoter-TSS (NR_029765)	-734	NR_029765	723843		NR_029765	ENSMUSG00000065526	Mir337	Mirn337|mir-337|mmu-mir-337	microRNA 337	ncRNA
mm_12164.1	chr2	62395147	62395169	+	1	NA	intron (NM_001159543, intron 2 of 24)	Lx4A|LINE|L1	17073	NM_010074	13482	Mm.1151	NM_010074	ENSMUSG00000035000	Dpp4	Cd26|Dpp-4|THAM	dipeptidylpeptidase 4	protein-coding
mm_157492.1	chrX	48429232	48429236	-	1	NA	intron (NM_019680, intron 1 of 8)	BC1_Mm|scRNA|scRNA	33898	NM_019680	56501	Mm.36808	NM_019680	ENSMUSG00000031103	Elf4	AV314029|BC042423|ENSMUSG00000053512|Gm9907|Mef	E74-like factor 4 (ets domain transcription factor)	protein-coding
mm_13288.1	chr2	101649826	101649830	+	1	NA	promoter-TSS (NM_009019)	promoter-TSS (NM_009019)	-296	NM_009019	19373	Mm.828	NM_009019	ENSMUSG00000061311	Rag1	Rag-1	recombination activating gene 1	protein-coding
mm_23156.1	chr3	40531549	40531562	+	1	NA	Intergenic	CpG	-8643	NR_040445	100040882	Mm.272869	NR_040445	ENSMUSG00000037884	1700017G19Rik	-	RIKEN cDNA 1700017G19 gene	ncRNA
mm_53235.1	chr6	127446876	127446888	+	1	NA	promoter-TSS (NM_001346513)	promoter-TSS (NM_001346513)	42	NM_001346513	101187	Mm.110818	NM_181402	ENSMUSG00000037997	Parp11	5330431N24Rik|AI851877|ARTD11|HIN1L|PARP-11	poly (ADP-ribose) polymerase family, member 11	protein-coding
mm_100603.1	chr11	121245364	121245407	+	1	NA	exon (NM_026272, exon 6 of 11)	exon (NM_026272, exon 6 of 11)	8149	NM_026272	67608	Mm.291832	NM_026272	ENSMUSG00000000056	Narf	4430402O11Rik	nuclear prelamin A recognition factor	protein-coding
mm_23182.1	chr3	40949782	40949814	+	1	NA	promoter-TSS (NM_001040399)	promoter-TSS (NM_001040399)	-833	NM_001040399	214048	Mm.46782	NM_027663	ENSMUSG00000025762	Larp1b	1700108L22Rik|4933421B21Rik|AA690246|Larp2	La ribonucleoprotein domain family, member 1B	protein-coding
mm_33874.1	chr4	136144773	136144804	+	1	NA	intron (NM_008321, intron 2 of 2)	CpG-10505	966	NM_008321	15903	Mm.110	NM_008321	ENSMUSG00000007872	Id3	Hlh462|Idb3|bHLHb25	inhibitor of DNA binding 3	protein-coding
mm_74157.1	chr8	123397777	123397787	+	1	NA	intron (NM_001286362, intron 12 of 16)	intron (NM_001286362, intron 12 of 16)	-9300	NM_008559	17199	Mm.324942	NM_008559	ENSMUSG00000074037	Mc1r	Mcr1|Mshra|Tob|e	melanocortin 1 receptor	protein-coding
mm_100399.1	chr11	119392947	119392958	+	1	NA	Intergenic	Intergenic	2480	NR_035453	100316690		NR_035453	ENSMUSG00000088015	Mir1932	mir-1932|mmu-mir-1932	microRNA 1932	ncRNA
mm_113836.1	chr13	47122720	47122761	+	1	NA	promoter-TSS (NM_146042)	promoter-TSS (NM_146042)	20	NM_146042	218215	Mm.287609	NM_146042	ENSMUSG00000038068	Rnf144b	BC025007|E130105P19Rik|Ibrdc2|Pir2	ring finger protein 144B	protein-coding
mm_149499.1	chr19	11912390	11912475	+	1	NA	promoter-TSS (NM_172635)	promoter-TSS (NM_172635)	33	NM_172635	225929	Mm.42711	NM_172635	ENSMUSG00000046139	Patl1	AV312086|Pat1b	protein associated with topoisomerase II homolog 1 (yeast)	protein-coding
mm_161415.1	chr15	21111332	21111332	+	1	NA	promoter-TSS (NM_001008420)	promoter-TSS (NM_001008420)	-120	NM_001008420	215654	Mm.300909	NM_001008420	ENSMUSG00000040452	Cdh12	Cdhb	cadherin 12	protein-coding
mm_25317.1	chr3	106482608	106482660	+	1	NA	non-coding (NR_033207, exon 2 of 2)	non-coding (NR_033207, exon 2 of 2)	184	NM_001278941	72121	Mm.14816	NM_028110	ENSMUSG00000027901	Dennd2d	2010308M01Rik|AI451421	DENN/MADD domain containing 2D	protein-coding
mm_168582.1	chr11	72292099	72292105	-	1	NA	Intergenic	RLTR1B|LTR|ERV1	-9527	NM_001291153	327959	Mm.291131	NM_001037713	ENSMUSG00000040483	Xaf1	Fbox39	XIAP associated factor 1	protein-coding
mm_64244.1	chr7	141702619	141702631	+	1	NA	exon (NM_023566, exon 26 of 46)	exon (NM_023566, exon 26 of 46)	12285	NM_023566	17831	Mm.2041	NM_023566		Muc2	2010015E03Rik|MCM|wnn	mucin 2	protein-coding
mm_151749.1	chr19	5085484	5085501	-	1	NA	promoter-TSS (NM_001001885)	promoter-TSS (NM_001001885)	-15	NM_001001885	381199	Mm.329663	NM_001001885	ENSMUSG00000061451	Tmem151a	AW125688|Gm961|Tmem151	transmembrane protein 151A	protein-coding
mm_109320.1	chr12	109561636	109561650	+	1	NA	non-coding (NR_003633, exon 5 of 5)	non-coding (NR_003633, exon 5 of 5)	-2049	NR_030427	791079		NR_030427	ENSMUSG00000076451	Mir770	Mirn770|mir-770|mmu-mir-770	microRNA 770	ncRNA
mm_149942.1	chr19	27312971	27312975	+	1	NA	Intergenic	MTEa|LTR|ERVL-MaLR	-9646	NM_183179	240595	Mm.269759	NM_183179	ENSMUSG00000047298	Kcnv2	KV11.1	potassium channel, subfamily V, member 2	protein-coding
mm_163709.1	chr13	108498503	108498550	-	1	NA	Intergenic	Intergenic	-155651	NM_011056	238871	Mm.434429	NM_011056	ENSMUSG00000021699	Pde4d	9630011N22Rik|Dpde3	phosphodiesterase 4D, cAMP specific	protein-coding
mm_140746.1	chr17	15831033	15831102	-	1	NA	Intergenic	CpG	-4481	NM_178615	68799	Mm.293466	NM_178615	ENSMUSG00000048027	Rgmb	1110059F19Rik|DRAGON	repulsive guidance molecule family member B	protein-coding
mm_152124.1	chr19	6992571	6992594	-	1	NA	promoter-TSS (NM_020566)	promoter-TSS (NM_020566)	-310	NM_020566	57431	Mm.10721	NM_020566	ENSMUSG00000024963	Dnajc4	2010301J22Rik|Hspf2|Mcg18	DnaJ heat shock protein family (Hsp40) member C4	protein-coding
mm_16225.1	chr2	173154732	173154748	+	1	NA	exon (NM_011044, exon 4 of 10)	exon (NM_011044, exon 4 of 10)	1667	NM_011044	18534	Mm.266867	NM_011044	ENSMUSG00000027513	Pck1	AI265463|PEPCK|Pck-1	phosphoenolpyruvate carboxykinase 1, cytosolic	protein-coding
mm_12680.1	chr2	75832453	75832461	+	1	NA	exon (NM_172666, exon 1 of 20)	exon (NM_172666, exon 1 of 20)	280	NM_172666	228061	Mm.31227	NM_172666	ENSMUSG00000042410	Agps	5832437L22|9930035G10Rik|AW123847|Adaps|Adas|Adhaps|Adps|Aldhpsy|bs2	alkylglycerone phosphate synthase	protein-coding
mm_72245.1	chr8	75058274	75058284	+	1	NA	intron (NM_001136259, intron 8 of 15)	intron (NM_001136259, intron 8 of 15)	24593	NM_011622	21968	Mm.1967	NM_011622	ENSMUSG00000042870	Tom1	-	target of myb1 trafficking protein	protein-coding
mm_50427.1	chr6	48842625	48842638	+	1	NA	exon (NM_025326, exon 3 of 7)	exon (NM_025326, exon 3 of 7)	975	NM_001098271	66058	Mm.27061	NM_025326	ENSMUSG00000023367	Tmem176a	0610011I04Rik|AU040201|AU041743|Keg2	transmembrane protein 176A	protein-coding
mm_36409.1	chr4	78048897	78048907	-	1	NA	intron (NM_011211, intron 1 of 39)	intron (NM_011211, intron 1 of 39)	162993	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding
mm_112440.1	chr13	5804545	5804550	+	1	NA	Intergenic	Intergenic	53545	NR_045891	71867	Mm.179181	NR_045891	ENSMUSG00000100625	1700016G22Rik	-	RIKEN cDNA 1700016G22 gene	ncRNA
mm_89066.1	chr10	82897435	82897446	+	1	NA	3' UTR (NM_001042523, exon 15 of 15)	3' UTR (NM_001042523, exon 15 of 15)	30814	NM_025499	66341	Mm.443284	NM_025499	ENSMUSG00000109864	Eid3	1700027M21Rik|NS4EB	EP300 interacting inhibitor of differentiation 3	protein-coding
mm_6955.1	chr1	85986918	85986951	-	1	NA	Intergenic	Intergenic	-25879	NM_001033290	227326	Mm.244158	NM_001033290	ENSMUSG00000049608	Gpr55	CTFL|Gm218|Lpir1	G protein-coupled receptor 55	protein-coding
mm_29748.1	chr3	126998409	126998463	-	1	NA	promoter-TSS (NM_178655)	promoter-TSS (NM_178655)	16	NM_178655	109676	Mm.220242	NM_178655	ENSMUSG00000032826	Ank2	100043364|AI835472|AW491075|Ank-2|Gm4392	ankyrin 2, brain	protein-coding
mm_132693.1	chr16	43247279	43247309	+	1	NA	promoter-TSS (NM_019778)	promoter-TSS (NM_019778)	10	NM_019778	56490	Mm.136238	NM_019778	ENSMUSG00000022708	Zbtb20	1300017A20Rik|7330412A13Rik|A930017C21Rik|D16Wsu73e|DPZF|HOF|ODA-8S|Oda8|Zfp288	zinc finger and BTB domain containing 20	protein-coding
mm_100375.1	chr11	119258948	119258960	+	1	NA	intron (NM_175430, intron 16 of 18)	intron (NM_175430, intron 16 of 18)	-9009	NM_001159324	14387	Mm.4793	NM_008064	ENSMUSG00000025579	Gaa	E430018M07Rik	glucosidase, alpha, acid	protein-coding
mm_145850.1	chr18	65453396	65453401	+	1	NA	intron (NM_172833, intron 7 of 15)	L1MA5|LINE|L1	22401	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_40299.1	chr5	43662387	43662406	+	1	NA	promoter-TSS (NM_172274)	promoter-TSS (NM_172274)	17	NM_172274	231214	Mm.44434	NM_172274	ENSMUSG00000039765	Cc2d2a	5730509K17Rik|b2b1035Clo	coiled-coil and C2 domain containing 2A	protein-coding
mm_159616.1	chr4	133519026	133519026	+	1	NA	promoter-TSS (NM_001083916)	promoter-TSS (NM_001083916)	63	NM_133707	69073	Mm.299081	NM_133707	ENSMUSG00000037600	Kdf1	1810019J16Rik	keratinocyte differentiation factor 1	protein-coding
mm_121203.1	chr14	103052471	103052498	+	1	NA	intron (NM_008392, intron 4 of 4)	Lx8|LINE|L1	5472	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_36257.1	chr4	63410706	63410726	-	1	NA	Intergenic	CpG	-7271	NM_001045514	100182	Mm.387725	NM_001045514	ENSMUSG00000039158	Akna	AI597013	AT-hook transcription factor	protein-coding
mm_67796.1	chr7	97737995	97738056	-	1	NA	5' UTR (NM_175105, exon 1 of 3)	5' UTR (NM_175105, exon 1 of 3)	222	NM_175105	66333	Mm.29756	NM_175105	ENSMUSG00000042797	Aqp11	1700015P13Rik|AI648923|sjds	aquaporin 11	protein-coding
mm_85912.1	chr9	111057423	111057435	-	1	NA	promoter-TSS (NM_017466)	promoter-TSS (NM_017466)	89	NM_001302376	54199	Mm.7336	NM_017466	ENSMUSG00000043953	Ccrl2	1810047I05Rik|Ackr5|CCR11|Cmkbr1l2|E01|L-CCR	chemokine (C-C motif) receptor-like 2	protein-coding
mm_57368.1	chr6	124779638	124779648	-	1	NA	promoter-TSS (NM_001302555)	promoter-TSS (NM_001302555)	84	NM_001302555	16977	Mm.3207	NM_013588	ENSMUSG00000030125	Lrrc23	4921537K05Rik|B7|Lrpb7	leucine rich repeat containing 23	protein-coding
mm_129975.1	chr15	85821473	85821514	-	1	NA	exon (NM_011105, exon 1 of 1)	exon (NM_011105, exon 1 of 1)	240	NM_011105	18766	Mm.89965	NM_011105	ENSMUSG00000052496	Pkdrej	-	polycystin (PKD) family receptor for egg jelly	protein-coding
mm_45970.1	chr5	90468665	90468691	-	1	NA	exon (NM_009654, exon 8 of 15)	exon (NM_009654, exon 8 of 15)	7808	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_50178.1	chr6	41582087	41582089	+	1	NA	Intergenic	Intergenic	-23394	NM_001146351	13848	Mm.271976	NM_007680	ENSMUSG00000029869	Ephb6	Cekl|Mep	Eph receptor B6	protein-coding
mm_160091.1	chr7	16815901	16815901	+	1	NA	promoter-TSS (NM_001039878)	promoter-TSS (NM_001039878)	12	NM_001039878	97387	Mm.21612	NM_133789	ENSMUSG00000030374	Strn4	C80611|ZIN|zinedin	striatin, calmodulin binding protein 4	protein-coding
mm_136436.1	chr16	94371833	94371848	-	1	NA	promoter-TSS (NM_019543)	promoter-TSS (NM_019543)	-825	NM_001159617	56176	Mm.474449	NM_019543	ENSMUSG00000022940	Pigp	Dcrc|Dscr5	phosphatidylinositol glycan anchor biosynthesis, class P	protein-coding
mm_4619.1	chr1	178798449	178798467	+	1	NA	intron (NM_001161665, intron 4 of 14)	intron (NM_001161665, intron 4 of 14)	269333	NM_001161665	269152	Mm.129727	NM_177724	ENSMUSG00000026494	Kif26b	4832420M10|BC056349|D230039L06Rik	kinesin family member 26B	protein-coding
mm_42559.1	chr5	117133568	117133649	+	1	NA	promoter-TSS (NM_183306)	promoter-TSS (NM_183306)	20	NM_183306	330177	Mm.24343	NM_183306	ENSMUSG00000061288	Taok3	2900006A08Rik|A130052D22|A430105I05Rik	TAO kinase 3	protein-coding
mm_160425.1	chr8	86651795	86651795	+	1	NA	intron (NM_001168591, intron 1 of 8)	intron (NM_001168591, intron 1 of 8)	226	NM_001168591	66887	Mm.324550	NM_025827	ENSMUSG00000047866	Lonp2	1300002A08Rik|AU015403|Lonp	lon peptidase 2, peroxisomal	protein-coding
mm_61610.1	chr7	80040044	80040057	+	1	NA	intron (NM_175433, intron 1 of 4)	B1F|SINE|Alu	13822	NM_175433	209225	Mm.290925	NM_175433	ENSMUSG00000048897	Zfp710	5430400N05Rik|9830165K13|AI324798|Znf710	zinc finger protein 710	protein-coding
mm_90484.1	chr10	127901960	127901980	+	1	NA	intron (NM_027301, intron 1 of 3)	intron (NM_027301, intron 1 of 3)	3435	NM_027301	70061	Mm.158320	NM_027301	ENSMUSG00000040127	Sdr9c7	1810054F20Rik|Rdh20|Rdhs|SDR-O|Sdro	4short chain dehydrogenase/reductase family 9C, member 7	protein-coding
mm_29098.1	chr3	104804638	104804650	-	1	NA	exon (NM_008619, exon 3 of 20)	exon (NM_008619, exon 3 of 20)	13661	NM_008619	17454	Mm.1597	NM_008619	ENSMUSG00000002227	Mov10	C77703|Mov-10	Moloney leukemia virus 10	protein-coding
mm_137652.1	chr17	28558761	28558793	+	1	NA	promoter-TSS (NR_105935)	promoter-TSS (NR_105935)	-276	NR_105935	102465585		NR_105935	ENSMUSG00000099152	Mir6969	Gm27305|mmu-mir-6969	microRNA 6969	ncRNA
mm_160373.1	chr8	36457641	36457641	+	1	NA	Intergenic	Intergenic	-31550	NM_176952	319582	Mm.180924	NM_176952	ENSMUSG00000039620	6430573F11Rik	Kiaa1456|TRM9L	RIKEN cDNA 6430573F11 gene	protein-coding
mm_104189.1	chr11	87825773	87825789	-	1	NA	5' UTR (NM_080420, exon 1 of 13)	5' UTR (NM_080420, exon 1 of 13)	333	NM_080420	76113	Mm.41236	NM_080420	ENSMUSG00000009356	Lpo	5830499B15Rik	lactoperoxidase	protein-coding
mm_134432.1	chr16	17928137	17928215	-	1	NA	promoter-TSS (NM_153150)	promoter-TSS (NM_153150)	43	NM_153150	13358	Mm.229291	NM_153150	ENSMUSG00000003528	Slc25a1	1300019P08Rik|2610100G11Rik|AI194714|Ctp|Dgsj|Slc20a3	solute carrier family 25 (mitochondrial carrier, citrate transporter), member 1	protein-coding
mm_134042.1	chr16	5195598	5195622	-	1	NA	non-coding (NR_027804, exon 9 of 9)	non-coding (NR_027804, exon 9 of 9)	8402	NM_013796	27426	Mm.215641	NM_013796	ENSMUSG00000023143	Nagpa	AI596180|UCE	N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase	protein-coding
mm_67684.1	chr7	89338710	89338795	-	1	NA	promoter-TSS (NM_028343)	promoter-TSS (NM_028343)	35	NM_028343	72759	Mm.208477	NM_028343	ENSMUSG00000039428	Tmem135	2810439K08Rik|AW319712|PMP52	transmembrane protein 135	protein-coding
mm_26294.1	chr3	142507713	142507727	+	1	NA	exon (NM_153564, exon 9 of 11)	exon (NM_153564, exon 9 of 11)	10786	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_79824.1	chr9	64485970	64485973	+	1	NA	intron (NM_172522, intron 1 of 22)	intron (NM_172522, intron 1 of 22)	100345	NM_001134399	214058	Mm.127721	NM_172522	ENSMUSG00000036466	Megf11	2410080H04Rik|D130061K05	multiple EGF-like-domains 11	protein-coding
mm_12974.1	chr2	90773571	90773572	+	1	NA	intron (NM_018828, intron 12 of 16)	ID_B1|SINE|B4	-9173	NM_178755	271813	Mm.61146	NM_178755	ENSMUSG00000040812	Agbl2	4930524K04|A430081C19Rik|CCP2	ATP/GTP binding protein-like 2	protein-coding
mm_84630.1	chr9	70835181	70835184	-	1	NA	intron (NM_001324473, intron 1 of 8)	RSINE1|SINE|B4	99626	NM_008280	15450	Mm.390187	NM_008280	ENSMUSG00000032207	Lipc	AI256194|HL|Hpl	lipase, hepatic	protein-coding
mm_64407.1	chr7	142511475	142511501	+	1	NA	exon (NM_001163669, exon 12 of 17)	exon (NM_001163669, exon 12 of 17)	-4717	NR_033261	677289	Mm.350054	NR_033261	ENSMUSG00000043795	Prr33	ENSMUSG00000043795|Gm14492|OTTMUSG00000016823	proline rich 33	ncRNA
mm_30875.1	chr4	32238884	32238890	+	1	NA	Intergenic	CpG	-178548	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_14393.1	chr2	129800743	129800765	+	1	NA	exon (NM_183262, exon 1 of 4)	exon (NM_183262, exon 1 of 4)	237	NM_001038635	67333	Mm.389329	NM_183262	ENSMUSG00000037885	Stk35	1700054C12Rik|CLIK1|Stk35l1	serine/threonine kinase 35	protein-coding
mm_67146.1	chr7	73466099	73466108	-	1	NA	intron (NM_001081345, intron 26 of 38)	L1M4|LINE|L1	75643	NM_001081345	244059	Mm.34539	NM_001081345	ENSMUSG00000078671	Chd2	2810013C04Rik|2810040A01Rik|5630401D06Rik|AI851092|BC029703|CHD-2	chromodomain helicase DNA binding protein 2	protein-coding
mm_20506.1	chr2	130563718	130563726	-	1	NA	promoter-TSS (NM_207207)	promoter-TSS (NM_207207)	27	NR_040348	321014	Mm.442588	NR_040348	ENSMUSG00000060029	4930473A02Rik	-	RIKEN cDNA 4930473A02 gene	ncRNA
mm_18570.1	chr2	65458751	65458753	-	1	NA	3' UTR (NM_018732, exon 27 of 27)	3' UTR (NM_018732, exon 27 of 27)	-94352	NR_105755	102466151		NR_105755	ENSMUSG00000099184	Mir6337	Gm27877|mmu-mir-6337	microRNA 6337	ncRNA
mm_102827.1	chr11	69070726	69070757	-	1	NA	promoter-TSS (NM_025838)	promoter-TSS (NM_025838)	-68	NM_025838	66910	Mm.33964	NM_025838	ENSMUSG00000020895	Tmem107	1110004B13Rik|2810049P21Rik	transmembrane protein 107	protein-coding
mm_165532.1	chr2	180025257	180025268	+	1	NA	exon (NM_177727, exon 1 of 9)	exon (NM_177727, exon 1 of 9)	275	NM_177727	241846	Mm.21577	NM_177727	ENSMUSG00000039108	Lsm14b	9430078B04|BC040823	LSM family member 14B	protein-coding
mm_103216.1	chr11	70655047	70655125	-	1	NA	promoter-TSS (NM_011072)	promoter-TSS (NM_011072)	-436	NM_011072	18643	Mm.2647	NM_011072	ENSMUSG00000018293	Pfn1	Pfn	profilin 1	protein-coding
mm_47781.1	chr5	131966090	131966092	-	1	NA	intron (NM_177047, intron 4 of 18)	intron (NM_177047, intron 4 of 18)	85822	NR_040704	75369	Mm.389696	NR_040704	ENSMUSG00000105773	4930563F08Rik	-	RIKEN cDNA 4930563F08 gene	ncRNA
mm_53647.1	chr6	140642209	140642223	+	1	NA	exon (NM_178803, exon 4 of 8)	exon (NM_178803, exon 4 of 8)	15331	NM_001309436	11569	Mm.86453	NM_009637	ENSMUSG00000030232	Aebp2	AU023766|B230313N05Rik	AE binding protein 2	protein-coding
mm_135100.1	chr16	35363843	35363891	-	1	NA	promoter-TSS (NM_133704)	promoter-TSS (NM_133704)	51	NM_133704	317717	Mm.259164	NM_133704	ENSMUSG00000034473	Sec22a	1810005C06Rik|Sec22l2	SEC22 homolog A, vesicle trafficking protein	protein-coding
mm_121133.1	chr14	101884039	101884045	+	1	NA	intron (NM_001347628, intron 4 of 26)	intron (NM_001347628, intron 4 of 26)	43419	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_95226.1	chr11	44518518	44518536	+	1	NA	promoter-TSS (NM_001166553)	promoter-TSS (NM_001166553)	-437	NM_028862	74315	Mm.156771	NM_028862	ENSMUSG00000019189	Rnf145	3732413I11Rik|TMRF1	ring finger protein 145	protein-coding
mm_86129.1	chr9	116175717	116175732	-	1	NA	promoter-TSS (NM_029575)	promoter-TSS (NM_029575)	-361	NM_009371	21813	Mm.172346	NM_009371	ENSMUSG00000032440	Tgfbr2	1110020H15Rik|AU042018|DNIIR|RIIDN|TBR-II|TbetaR-II|TbetaRII	transforming growth factor, beta receptor II	protein-coding
mm_25566.1	chr3	116594960	116595031	+	1	NA	promoter-TSS (NM_001289571)	promoter-TSS (NM_001289571)	37	NM_001289571	72776	Mm.440836	NM_028349	ENSMUSG00000027959	Sass6	2810453L12Rik	SAS-6 centriolar assembly protein	protein-coding
mm_16865.1	chr2	11777571	11777581	-	1	NA	promoter-TSS (NM_177268)	promoter-TSS (NM_177268)	-49	NM_015792	50755	Mm.24088	NM_015792	ENSMUSG00000058594	Fbxo18	AU015756|Fbh1|Fbx18	F-box protein 18	protein-coding
mm_111949.1	chr12	109073413	109073445	-	1	NA	Intergenic	Intergenic	-5212	NM_001163175	380785	Mm.342085	NM_001163175	ENSMUSG00000040867	Begain	BM948371|Gm897	brain-enriched guanylate kinase-associated	protein-coding
mm_47112.1	chr5	119570737	119570739	-	1	NA	intron (NR_045702, intron 3 of 4)	intron (NR_045702, intron 3 of 4)	9620	NR_045702	100993	Mm.381453	NR_045702	ENSMUSG00000087516	AW549542	-	expressed sequence AW549542	ncRNA
mm_132645.1	chr16	40908185	40908190	+	1	NA	Intergenic	Intergenic	-624639	NM_001347236	268890	Mm.310524	NM_175548	ENSMUSG00000061080	Lsamp	5430428I19|AW046674|B130007O04Rik|D930023J12Rik|Lam|Lamp	limbic system-associated membrane protein	protein-coding
mm_115182.1	chr13	108449722	108449734	+	1	NA	Intergenic	Intergenic	133391	NM_178683	218581	Mm.32318	NM_178683	ENSMUSG00000021697	Depdc1b	9830132O03|AW260467|XTP1	DEP domain containing 1B	protein-coding
mm_4036.1	chr1	165774324	165774333	+	1	NA	3' UTR (NM_011804, exon 4 of 4)	3' UTR (NM_011804, exon 4 of 4)	10548	NM_011804	433375	Mm.294885	NM_011804	ENSMUSG00000040713	Creg1	AA755314|Creg	cellular repressor of E1A-stimulated genes 1	protein-coding
mm_2125.1	chr1	87909042	87909056	+	1	NA	intron (NM_177646, intron 3 of 29)	intron (NM_177646, intron 3 of 29)	-54750	NR_136921	100503175	Mm.426422	NR_136921	ENSMUSG00000101942	Gm19582	-	predicted gene, 19582	ncRNA
mm_122664.1	chr14	51913571	51913577	-	1	NA	promoter-TSS (NM_001145959)	promoter-TSS (NM_001145959)	-86	NM_013864	29811	Mm.26722	NM_013864	ENSMUSG00000004558	Ndrg2	AI182517|AU040374|Ndr2|SYLD	N-myc downstream regulated gene 2	protein-coding
mm_17069.1	chr2	22744765	22744786	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-29552	NM_019456	54519	Mm.14255	NM_019456	ENSMUSG00000026786	Apbb1ip	9930118P07Rik|Prp48	amyloid beta (A4) precursor protein-binding, family B, member 1 interacting protein	protein-coding
mm_50952.1	chr6	58831457	58831504	+	1	NA	Intergenic	Intergenic	-2220	NM_028705	73998	Mm.191892	NM_028705	ENSMUSG00000029804	Herc3	5730409F18Rik|AI646603|mKIAA0032	hect domain and RLD 3	protein-coding
mm_123514.1	chr14	66258199	66258201	-	1	NA	intron (NM_001162365, intron 1 of 30)	intron (NM_001162365, intron 1 of 30)	22852	NM_172498	19229	Mm.21613	NM_172498	ENSMUSG00000059456	Ptk2b	CADTK|CAKB|CAKbeta|E430023O05Rik|FADK2|FAK2|PYK2|Raftk	PTK2 protein tyrosine kinase 2 beta	protein-coding
mm_163414.1	chr12	78980537	78980538	-	1	NA	intron (NM_178745, intron 1 of 2)	intron (NM_178745, intron 1 of 2)	2941	NM_001170401	268567	Mm.341747	NM_178745	ENSMUSG00000046157	Tmem229b	6330442E10Rik|9830138K24|AU019070	transmembrane protein 229B	protein-coding
mm_141069.1	chr17	25832869	25832877	-	1	NA	5' UTR (NM_019719, exon 1 of 7)	5' UTR (NM_019719, exon 1 of 7)	488	NM_019719	56424	Mm.277599	NM_019719	ENSMUSG00000039615	Stub1	0610033N24Rik|2210017D18Rik|2310040B03Rik|AW046544|Chip	STIP1 homology and U-Box containing protein 1	protein-coding
mm_5397.1	chr1	33669729	33669739	-	1	NA	promoter-TSS (NR_033199)	promoter-TSS (NR_033199)	60	NM_008922	19076	Mm.27705	NM_008922	ENSMUSG00000026134	Prim2	AI323589	DNA primase, p58 subunit	protein-coding
mm_130726.1	chr15	101215684	101215687	-	1	NA	Intergenic	Intergenic	-5562	NR_045996	105968	Mm.120798	NR_045996		AU021063	-	expressed sequence AU021063	ncRNA
mm_119763.1	chr14	54172110	54172112	+	1	NA	Intergenic	Intergenic	81818	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_105018.1	chr11	100441007	100441038	-	1	NA	promoter-TSS (NM_001102650)	promoter-TSS (NM_001102650)	67	NM_026561	68106	Mm.28738	NM_026561	ENSMUSG00000017176	Nt5c3b	2610037D24Rik|AI841843|C330027I04Rik|Nt5c3l	5'-nucleotidase, cytosolic IIIB	protein-coding
mm_20423.1	chr2	129303795	129303807	-	1	NA	intron (NM_010554, intron 5 of 6)	intron (NM_010554, intron 5 of 6)	6171	NM_010554	16175	Mm.15534	NM_010554	ENSMUSG00000027399	Il1a	Il-1a	interleukin 1 alpha	protein-coding
mm_136415.1	chr16	93914335	93914357	-	1	NA	Intergenic	Intergenic	15221	NM_001165925	56173	Mm.328716	NM_019500	ENSMUSG00000047109	Cldn14	AI851731	claudin 14	protein-coding
mm_40629.1	chr5	64822118	64822173	+	1	NA	exon (NM_008453, exon 3 of 6)	exon (NM_008453, exon 3 of 6)	18622	NM_008453	16599	Mm.392759	NM_008453	ENSMUSG00000029178	Klf3	9930027G08Rik|AL024007|Bklf|Tef-2	Kruppel-like factor 3 (basic)	protein-coding
mm_93189.1	chr10	93891118	93891136	-	1	NA	promoter-TSS (NM_019648)	promoter-TSS (NM_019648)	75	NM_019648	56307	Mm.289329	NM_019648	ENSMUSG00000036112	Metap2	4930584B20Rik|A930035J23Rik|AI047573|AL024412|AU014659|Amp2|Mnpep|p67|p67eIF2	methionine aminopeptidase 2	protein-coding
mm_35083.1	chr4	7455237	7455249	-	1	NA	Intergenic	Intergenic	-105445	NR_040645	71510	Mm.410775	NR_040645	ENSMUSG00000086070	8430436N08Rik	-	RIKEN cDNA 8430436N08 gene	ncRNA
mm_38340.1	chr4	137766434	137766444	-	1	NA	promoter-TSS (NM_001287172)	promoter-TSS (NM_001287172)	36	NM_001287172	11647	Mm.288186	NM_007431	ENSMUSG00000028766	Alpl	ALP|APTNAP|Akp-2|Akp2|TNAP|TNSALP	alkaline phosphatase, liver/bone/kidney	protein-coding
mm_133742.1	chr16	94010935	94010943	+	1	NA	Intergenic	Intergenic	-2102	NM_019500	56173	Mm.328716	NM_019500	ENSMUSG00000047109	Cldn14	AI851731	claudin 14	protein-coding
mm_101805.1	chr11	46312284	46312338	-	1	NA	promoter-TSS (NM_001252460)	promoter-TSS (NM_001252460)	47	NM_001252460	76884	Mm.154358	NM_133769	ENSMUSG00000020340	Cyfip2	1500004I01Rik|6430511D02Rik|AA930218|AU022376|Pir121|mKIAA1168	cytoplasmic FMR1 interacting protein 2	protein-coding
mm_83812.1	chr9	53594721	53594740	-	1	NA	exon (NM_144784, exon 4 of 12)	exon (NM_144784, exon 4 of 12)	15620	NM_144784	110446	Mm.293233	NM_144784	ENSMUSG00000032047	Acat1	6330585C21Rik|Acat	acetyl-Coenzyme A acetyltransferase 1	protein-coding
mm_116347.1	chr13	38658992	38659038	-	1	NA	promoter-TSS (NM_025380)	promoter-TSS (NM_025380)	13	NM_025380	66143	Mm.490319	NM_025380	ENSMUSG00000001707	Eef1e1	1110003A02Rik	eukaryotic translation elongation factor 1 epsilon 1	protein-coding
mm_137699.1	chr17	29081577	29081587	+	1	NA	Intergenic	Intergenic	-2456	NR_036469	100504267	Mm.438550	NR_036469	ENSMUSG00000085912	Trp53cor1	Gm16197|OTTMUSG00000031656|linc-p21|lincRNA-p21	tumor protein p53 pathway corepressor 1	ncRNA
mm_124888.1	chr15	10314021	10314025	+	1	NA	intron (NM_001253781, intron 2 of 9)	intron (NM_001253781, intron 2 of 9)	20372	NM_001253782	19116	Mm.10516	NM_011169	ENSMUSG00000005268	Prlr	AI987712|Pr-1|Pr-3|Prlr-rs1	prolactin receptor	protein-coding
mm_67034.1	chr7	66689614	66689624	-	1	NA	promoter-TSS (NR_003961)	promoter-TSS (NR_003961)	-58	NR_003961	117589	Mm.34785	NM_080443	ENSMUSG00000030509	Asb7	AI449039|Asb-7|D030055C23Rik	ankyrin repeat and SOCS box-containing 7	protein-coding
mm_22761.1	chr3	19992624	19992639	+	1	NA	3' UTR (NM_007752, exon 19 of 19)	3' UTR (NM_007752, exon 19 of 19)	35577	NM_007752	12870	Mm.13787	NM_007752	ENSMUSG00000003617	Cp	D3Ertd555e	ceruloplasmin	protein-coding
mm_89847.1	chr10	106949203	106949208	+	1	NA	intron (NM_001142804, intron 12 of 15)	intron (NM_001142804, intron 12 of 15)	174459	NM_001142804	380660	Mm.336072	NM_198636	ENSMUSG00000035948	Acss3	8430416H19Rik|Gm874	acyl-CoA synthetase short-chain family member 3	protein-coding
mm_169944.1	chr1	66948952	66948969	-	1	NA	Intergenic	Intergenic	-3904	NM_021285	17901	Mm.1000	NM_021285	ENSMUSG00000061816	Myl1	AI325107|MLC1f|MLC3f|Mylf	myosin, light polypeptide 1	protein-coding
mm_106492.1	chr11	120237601	120237646	-	1	NA	intron (NM_001347621, intron 2 of 27)	CpG-2934	4676	NM_198423	268515	Mm.309498	NM_198423	ENSMUSG00000039741	Bahcc1	B930044J06|BC060615	BAH domain and coiled-coil containing 1	protein-coding
mm_170989.1	chr2	7415091	7415100	+	1	NA	Intergenic	L1Md_T|LINE|L1	-18897	NM_001110231	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_132359.1	chr16	34660753	34660758	+	1	NA	intron (NM_030744, intron 1 of 5)	intron (NM_030744, intron 1 of 5)	9544	NM_030744	76378	Mm.23515	NM_030744	ENSMUSG00000022832	Ropn1	1700008N21Rik|ODF6|RHPNAP1|Rppn|ropporin	ropporin, rhophilin associated protein 1	protein-coding
mm_81678.1	chr9	111058108	111058116	+	1	NA	promoter-TSS (NM_017466)	promoter-TSS (NM_017466)	-594	NM_001302376	54199	Mm.7336	NM_017466	ENSMUSG00000043953	Ccrl2	1810047I05Rik|Ackr5|CCR11|Cmkbr1l2|E01|L-CCR	chemokine (C-C motif) receptor-like 2	protein-coding
mm_110319.1	chr12	34714310	34714328	-	1	NA	intron (NM_001271386, intron 3 of 27)	intron (NM_001271386, intron 3 of 27)	-185430	NM_024124	79221	Mm.310551	NM_024124	ENSMUSG00000004698	Hdac9	AV022454|D030072B18Rik|HD7B|HD9|HDRP|Hdac7b|Mitr|mKIAA0744	histone deacetylase 9	protein-coding
mm_112754.1	chr13	19342155	19342161	+	1	NA	Intergenic	Intergenic	53655	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_152123.1	chr19	6992479	6992524	-	1	NA	promoter-TSS (NM_020566)	promoter-TSS (NM_020566)	-229	NM_020566	57431	Mm.10721	NM_020566	ENSMUSG00000024963	Dnajc4	2010301J22Rik|Hspf2|Mcg18	DnaJ heat shock protein family (Hsp40) member C4	protein-coding
mm_171902.1	chr5	42136154	42136158	+	1	NA	intron (NR_131130, intron 1 of 2)	intron (NR_131130, intron 1 of 2)	68196	NR_131130	433882	Mm.319353	NR_131130	ENSMUSG00000067285	Gm16223	EG433882|OTTMUSG00000031875	predicted gene 16223	ncRNA
mm_27272.1	chr3	40522910	40522918	-	1	NA	promoter-TSS (NR_040445)	promoter-TSS (NR_040445)	-2	NR_040445	100040882	Mm.272869	NR_040445	ENSMUSG00000037884	1700017G19Rik	-	RIKEN cDNA 1700017G19 gene	ncRNA
mm_77103.1	chr8	111031713	111031747	-	1	NA	promoter-TSS (NM_001190786)	promoter-TSS (NM_001190786)	21	NM_001190786	234733	Mm.482176	NM_172284	ENSMUSG00000033658	Ddx19b	2810457M08Rik|4921519L13Rik|AW260119	DEAD (Asp-Glu-Ala-Asp) box polypeptide 19b	protein-coding
mm_55607.1	chr6	71881170	71881171	-	1	NA	exon (NM_027275, exon 24 of 24)	exon (NM_027275, exon 24 of 24)	27592	NM_027275	69956	Mm.30256	NM_027275	ENSMUSG00000063884	Ptcd3	2610034F17Rik|2810422B04Rik|AA589622|AU045708|MRP-S39	pentatricopeptide repeat domain 3	protein-coding
mm_95696.1	chr11	54370599	54370613	+	1	NA	promoter-TSS (NM_029105)	promoter-TSS (NM_029105)	-46	NM_029105	74847	Mm.486538	NM_029105	ENSMUSG00000020332	Meikin	4930404A10Rik	meiotic kinetochore factor	protein-coding
mm_84041.1	chr9	57792188	57792209	-	1	NA	3' UTR (NM_019689, exon 8 of 8)	3' UTR (NM_019689, exon 8 of 8)	-26338	NM_007713	102414	Mm.25720	NM_007713	ENSMUSG00000032316	Clk3	AI256811	CDC-like kinase 3	protein-coding
mm_3.1	chr1	4522817	4522864	+	1	NA	Intergenic	Intergenic	-25486	NM_001289465	20671	Mm.279103	NM_011441	ENSMUSG00000025902	Sox17	-	SRY (sex determining region Y)-box 17	protein-coding
mm_14056.1	chr2	122609705	122609723	+	1	NA	exon (NM_025961, exon 2 of 9)	exon (NM_025961, exon 2 of 9)	1563	NM_025961	67092	Mm.29975	NM_025961	ENSMUSG00000027199	Gatm	1810003P21Rik|AI314789|AT	glycine amidinotransferase (L-arginine:glycine amidinotransferase)	protein-coding
mm_108038.1	chr12	73901320	73901324	+	1	NA	promoter-TSS (NM_001313920)	promoter-TSS (NM_001313920)	-2	NM_001313920	15251	Mm.3879	NM_010431	ENSMUSG00000021109	Hif1a	AA959795|HIF-1-alpha|HIF1-alpha|HIF1alpha|MOP1|bHLHe78	hypoxia inducible factor 1, alpha subunit	protein-coding
mm_56022.1	chr6	86585217	86585217	-	1	NA	Intergenic	Intergenic	-42957	NM_026414	67855	Mm.183043	NM_026414	ENSMUSG00000033508	Asprv1	2300003P22Rik|AA986851|SASP|SASPase|Taps	aspartic peptidase, retroviral-like 1	protein-coding
mm_146277.1	chr18	77882498	77882515	+	1	NA	3' UTR (NM_013831, exon 15 of 15)	3' UTR (NM_013831, exon 15 of 15)	-55961	NM_001195633	100502841	Mm.297782	NM_001195633	ENSMUSG00000039840	Epg5	4732475F16|5430411K18Rik|AI661957|AW456499|mKIAA1632	ectopic P-granules autophagy protein 5 homolog (C. elegans)	protein-coding
mm_101428.1	chr11	29879761	29879781	-	1	NA	intron (NM_146016, intron 7 of 41)	intron (NM_146016, intron 7 of 41)	-54103	NM_176829	216622	Mm.443260	NM_176829	ENSMUSG00000078157	4931440F15Rik	Fem1ab	RIKEN cDNA 4931440F15 gene	protein-coding
mm_93290.1	chr10	96332960	96332968	-	1	NA	Intergenic	MIR3|SINE|MIR	106757	NR_110448	74881	Mm.410819	NR_110448		4930459C07Rik	-	RIKEN cDNA 4930459C07 gene	ncRNA
mm_43085.1	chr5	124450175	124450184	+	1	NA	intron (NM_001310725, intron 2 of 6)	intron (NM_001310725, intron 2 of 6)	3475	NM_001310727	67956	Mm.137966	NM_030241	ENSMUSG00000049327	Kmt5a	2410195B05Rik|AA617402|AW536475|PR-SET7|PR/SET07|Setd8	lysine methyltransferase 5A	protein-coding
mm_166900.1	chr7	28442740	28442745	-	1	NA	intron (NM_001039192, intron 3 of 6)	intron (NM_001039192, intron 3 of 6)	1805	NM_001039192	63986	Mm.194536	NM_022024	ENSMUSG00000060791	Gmfg	0610039G16Rik|2310057N07Rik|AI324845	glia maturation factor, gamma	protein-coding
mm_51054.1	chr6	65631501	65631517	+	1	NA	3' UTR (NM_001001495, exon 8 of 8)	3' UTR (NM_001001495, exon 8 of 8)	-40102	NM_172399	68169	Mm.52392	NM_172399	ENSMUSG00000049001	Ndnf	A930038C07Rik|epidermacan	neuron-derived neurotrophic factor	protein-coding
mm_146897.1	chr18	30146551	30146551	-	1	NA	Intergenic	Intergenic	-126345	NM_181414	225326	Mm.194127	NM_181414	ENSMUSG00000033628	Pik3c3	5330434F23Rik|Vps34	phosphoinositide-3-kinase, class 3	protein-coding
mm_135887.1	chr16	64851434	64851446	-	1	NA	promoter-TSS (NM_178647)	promoter-TSS (NM_178647)	283	NM_001347245	72020	Mm.25960	NM_028059	ENSMUSG00000047141	Zfp654	1600021C16Rik|1810008K20Rik|433036|Gm5488|Znf654	zinc finger protein 654	protein-coding
mm_33684.1	chr4	133370190	133370229	+	1	NA	TTS (NR_039582)	TTS (NR_039582)	433	NR_039582	100628620		NR_039582	ENSMUSG00000092745	Mir5122	mmu-mir-5122|mu-mir-5122	microRNA 5122	ncRNA
mm_89861.1	chr10	108162146	108162169	+	1	NA	promoter-TSS (NM_027892)	promoter-TSS (NM_027892)	-243	NM_027892	17931	Mm.422959	NM_027892	ENSMUSG00000019907	Ppp1r12a	1200015F06Rik|5730577I22Rik|AA792106|AV099298|D10Ertd625e|Mypt1	protein phosphatase 1, regulatory (inhibitor) subunit 12A	protein-coding
mm_62643.1	chr7	107665681	107665720	+	1	NA	intron (NM_001163557, intron 3 of 25)	intron (NM_001163557, intron 3 of 25)	58856	NM_001163557	19024	Mm.2817	NM_008905	ENSMUSG00000036528	Ppfibp2	Cclp1	PTPRF interacting protein, binding protein 2 (liprin beta 2)	protein-coding
mm_117567.1	chr13	85288032	85288042	-	1	NA	intron (NM_145452, intron 1 of 24)	intron (NM_145452, intron 1 of 24)	1449	NM_145452	218397	Mm.259653	NM_145452	ENSMUSG00000021549	Rasa1	Gap|RasGAP|Rasa	RAS p21 protein activator 1	protein-coding
mm_109710.1	chr12	113430228	113430240	+	1	NA	Intergenic	Intergenic	-59331	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_5164.1	chr1	10038107	10038169	-	1	NA	promoter-TSS (NM_013715)	promoter-TSS (NM_013715)	21	NR_102282	26754	Mm.402384	NM_013715	ENSMUSG00000025917	Cops5	AI303502|CSN5|Jab1|Mov34|Sgn5	COP9 signalosome subunit 5	protein-coding
mm_122081.1	chr14	30607824	30607824	-	1	NA	intron (NM_011103, intron 3 of 17)	intron (NM_011103, intron 3 of 17)	2486	NM_001310682	18753	Mm.2314	NM_011103	ENSMUSG00000021948	Prkcd	AI385711|D14Ertd420e|PKC[d]|PKCdelta|Pkcd	protein kinase C, delta	protein-coding
mm_33599.1	chr4	132568579	132568593	+	1	NA	intron (NM_001081211, intron 1 of 1)	B4|SINE|B4	4519	NM_001081211	19204	Mm.89389	NM_001081211	ENSMUSG00000056529	Ptafr	PAFR	platelet-activating factor receptor	protein-coding
mm_115224.1	chr13	109757193	109757199	+	1	NA	intron (NM_011056, intron 4 of 16)	intron (NM_011056, intron 4 of 16)	-146613	NR_035442	100316683		NR_035442	ENSMUSG00000084651	Mir1904	Mirn1904|mmu-mir-1904	microRNA 1904	ncRNA
mm_132680.1	chr16	42930950	42930970	+	1	NA	intron (NM_001285805, intron 1 of 10)	Lx8b|LINE|L1	-18890	NR_040402	100503040	Mm.490721	NR_040402		Gm19522	-	predicted gene, 19522	ncRNA
mm_127574.1	chr15	102279731	102279764	+	1	NA	intron (NM_134100, intron 1 of 1)	CpG	291	NM_134100	106073	Mm.287740	NM_134100	ENSMUSG00000045665	Mfsd5	AA409375|AW556797|D15Mgi27	major facilitator superfamily domain containing 5	protein-coding
mm_4932.1	chr1	191097867	191097887	+	1	NA	promoter-TSS (NM_030060)	promoter-TSS (NM_030060)	-537	NM_030060	381319	Mm.6922	NM_030060	ENSMUSG00000026630	Batf3	9130211I03Rik|Snft	basic leucine zipper transcription factor, ATF-like 3	protein-coding
mm_97308.1	chr11	76679901	76679903	+	1	NA	promoter-TSS (NM_177709)	promoter-TSS (NM_177709)	29	NM_177709	237858	Mm.127006	NM_177709	ENSMUSG00000046275	Tusc5	C130069F04Rik|DSPB1|Lost1	tumor suppressor candidate 5	protein-coding
mm_91390.1	chr10	30655842	30655852	-	1	NA	promoter-TSS (NM_001111267)	promoter-TSS (NM_001111267)	20	NM_001111267	211329	Mm.297903	NM_172495	ENSMUSG00000039697	Ncoa7	9030406N13Rik	nuclear receptor coactivator 7	protein-coding
mm_64417.1	chr7	142555606	142555622	+	1	NA	non-coding (NR_002452, exon 2 of 3)	non-coding (NR_002452, exon 2 of 3)	2984	NR_002452	330677	Mm.265130	NR_002452	ENSMUSG00000087090	Nctc1	9530074L01|Rhit1	non-coding transcript 1	ncRNA
mm_45764.1	chr5	86916978	86916987	-	1	NA	3' UTR (NM_152811, exon 6 of 6)	3' UTR (NM_152811, exon 6 of 6)	9521	NM_152811	71773	Mm.26741	NM_152811	ENSMUSG00000035836	Ugt2b1	1300012D20Rik	UDP glucuronosyltransferase 2 family, polypeptide B1	protein-coding
mm_127129.1	chr15	98156324	98156329	+	1	NA	intron (NM_001170711, intron 1 of 3)	RLTR23|LTR|ERV1	9252	NM_001170711	78541	Mm.200766	NM_030121	ENSMUSG00000048175	Asb8	4930539L19Rik|AI788835|C430011H06Rik	ankyrin repeat and SOCS box-containing 8	protein-coding
mm_164016.1	chr14	71263771	71263773	-	1	NA	intron (NR_046075, intron 2 of 2)	Lx7|LINE|L1	12499	NR_046076	100043132	Mm.399336	NR_046075		Gm4251	-	predicted gene 4251	ncRNA
mm_103347.1	chr11	74756726	74756730	-	1	NA	Intergenic	Intergenic	-14135	NM_026197	67493	Mm.45748	NM_026197	ENSMUSG00000010554	Mettl16	2610100D03Rik|2810013M15Rik|A830095F14Rik|AI846133|Mett10d	methyltransferase like 16	protein-coding
mm_170673.1	chr2	121414171	121414179	+	1	NA	promoter-TSS (NM_153075)	promoter-TSS (NM_153075)	273	NM_007952	14827	Mm.263177	NM_007952	ENSMUSG00000027248	Pdia3	58kDa|ERp57|ERp60|ERp61|Erp|Grp58|PDI|PDI-Q2|PI-PLC|PLC[a]|Plca	protein disulfide isomerase associated 3	protein-coding
mm_125029.1	chr15	25753199	25753212	+	1	NA	intron (NM_019472, intron 19 of 40)	intron (NM_019472, intron 19 of 40)	-90093	NM_001034851	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_111068.1	chr12	80115696	80115711	-	1	NA	Intergenic	CpG	-2690	NM_007564	12192	Mm.235132	NM_007564	ENSMUSG00000021127	Zfp36l1	AW742437|AW743212|Berg36|Brf1|D530020L18Rik|ERF1|TIS11b|cMG1	zinc finger protein 36, C3H type-like 1	protein-coding
mm_66400.1	chr7	44359778	44359788	-	1	NA	TTS (NM_027049)	TTS (NM_027049)	15247	NM_027049	69349	Mm.358922	NM_027049	ENSMUSG00000008028	1700008O03Rik	-	RIKEN cDNA 1700008O03 gene	protein-coding
mm_110318.1	chr12	34639518	34639519	-	1	NA	intron (NM_001271386, intron 3 of 27)	intron (NM_001271386, intron 3 of 27)	-110629	NM_024124	79221	Mm.310551	NM_024124	ENSMUSG00000004698	Hdac9	AV022454|D030072B18Rik|HD7B|HD9|HDRP|Hdac7b|Mitr|mKIAA0744	histone deacetylase 9	protein-coding
mm_82534.1	chr9	20746263	20746280	-	1	NA	Intergenic	Intergenic	-18057	NM_173777	244723	Mm.293552	NM_173777	ENSMUSG00000032172	Olfm2	A030009A06Rik	olfactomedin 2	protein-coding
mm_70355.1	chr8	5639500	5639512	+	1	NA	Intergenic	Intergenic	-534219	NM_011388	20494	Mm.3500	NM_011388	ENSMUSG00000023073	Slc10a2	9130221J18Rik|AI605518|ASBT|IBAT|ISBT	solute carrier family 10, member 2	protein-coding
mm_159800.1	chr5	112475504	112475504	-	1	NA	exon (NM_001253916, exon 2 of 17)	exon (NM_001253916, exon 2 of 17)	26078	NM_001177504	625464	Mm.389676	NM_001177504	ENSMUSG00000072722	Gm6588	EG625464	predicted gene 6588	protein-coding
mm_160919.1	chr11	84019262	84019262	+	1	NA	intron (NM_194341, intron 13 of 19)	intron (NM_194341, intron 13 of 19)	49095	NM_019819	56405	Mm.240885	NM_019819	ENSMUSG00000018648	Dusp14	1110014C10Rik|2310042C07Rik|D11Ertd395e|MKP-L|Mkp6	dual specificity phosphatase 14	protein-coding
mm_100960.1	chr11	6635579	6635583	-	1	NA	TTS (NM_011709)	TTS (NM_011709)	3068	NM_011709	22373	Mm.268094	NM_011709	ENSMUSG00000000381	Wap	-	whey acidic protein	protein-coding
mm_40074.1	chr5	34336929	34336937	+	1	NA	promoter-TSS (NM_001304270)	promoter-TSS (NM_001304270)	1	NM_001304270	19822	Mm.21281	NM_011278	ENSMUSG00000029110	Rnf4	AU018689|Gtrgeo8|SNURF	ring finger protein 4	protein-coding
mm_84574.1	chr9	69034341	69034350	-	1	NA	intron (NM_013646, intron 1 of 10)	intron (NM_013646, intron 1 of 10)	-255496	NM_001289916	19883	Mm.378450	NM_013646	ENSMUSG00000032238	Rora	9530021D13Rik|Nr1f1|ROR1|ROR2|ROR3|nmf267|sg|staggerer|tmgc26	RAR-related orphan receptor alpha	protein-coding
mm_170074.1	chr17	33524018	33524036	+	1	NA	promoter-TSS (NM_001329152)	promoter-TSS (NM_001329152)	-58	NR_137628	224697	Mm.29304	NM_172619	ENSMUSG00000024299	Adamts10	9430006O18|AW045948|Adam-ts10|Adamts-10|Znmp	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 10	protein-coding
mm_41934.1	chr5	105700883	105700893	+	1	NA	promoter-TSS (NM_178701)	promoter-TSS (NM_178701)	78	NM_178701	231549	Mm.23837	NM_178701	ENSMUSG00000046079	Lrrc8d	2810473G09Rik|4930525N13Rik|A930019F03|Lrrc5	leucine rich repeat containing 8D	protein-coding
mm_98885.1	chr11	97825560	97825581	+	1	NA	intron (NM_010688, intron 4 of 6)	intron (NM_010688, intron 4 of 6)	-15210	NM_001080935	68127	Mm.110270	NM_001080935	ENSMUSG00000050538	B230217C12Rik	AI840637	RIKEN cDNA B230217C12 gene	protein-coding
mm_3006.1	chr1	133323964	133323967	+	1	NA	TTS (NM_026680)	TTS (NM_026680)	-3247	NM_178260	280287	Mm.458301	NM_178260	ENSMUSG00000098306	Kiss1	kisspeptin|metastatin	KiSS-1 metastasis-suppressor	protein-coding
mm_142866.1	chr17	51814463	51814487	-	1	NA	intron (NM_001163632, intron 1 of 10)	intron (NM_001163632, intron 1 of 10)	-2421	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_136385.1	chr16	93127755	93127775	-	1	NA	Intergenic	Intergenic	225424	NR_040486	69857	Mm.81192	NR_040486	ENSMUSG00000100277	1810053B23Rik	1810008L18Rik|1810056K14Rik	RIKEN cDNA 1810053B23 gene	ncRNA
mm_104276.1	chr11	89403524	89403539	-	1	NA	intron (NM_001327810, intron 19 of 19)	RLTR27|LTR|ERVK	15417	NM_172534	382543	Mm.60997	NM_172534	ENSMUSG00000047773	Ankfn1	4932411E22Rik|Gm1175|nmf9	ankyrin-repeat and fibronectin type III domain containing 1	protein-coding
mm_126477.1	chr15	81523389	81523446	+	1	NA	Intergenic	Intergenic	57101	NM_019712	56438	Mm.29405	NM_019712	ENSMUSG00000022400	Rbx1	1500002P15Rik|AA517855|ROC1	ring-box 1	protein-coding
mm_111478.1	chr12	98683767	98683783	-	1	NA	intron (NM_011877, intron 13 of 18)	intron (NM_011877, intron 13 of 18)	50870	NM_011877	24000	Mm.4420	NM_011877	ENSMUSG00000021009	Ptpn21	PTPD1|PTPRL10	protein tyrosine phosphatase, non-receptor type 21	protein-coding
mm_98535.1	chr11	95009853	95009890	+	1	NA	promoter-TSS (NM_146025)	promoter-TSS (NM_146025)	-8	NM_146025	217125	Mm.297199	NM_146025	ENSMUSG00000047181	Samd14	AI839049|AI854782|BC034054	sterile alpha motif domain containing 14	protein-coding
mm_61823.1	chr7	87586496	87586565	+	1	NA	intron (NM_001143834, intron 1 of 10)	intron (NM_001143834, intron 1 of 10)	2362	NM_001143834	108071	Mm.235018	NM_001033224	ENSMUSG00000049583	Grm5	6430542K11Rik|AI850523|Glu5R|Gprc1e|mGluR5|mGluR5b	glutamate receptor, metabotropic 5	protein-coding
mm_11065.1	chr2	27625196	27625200	+	1	NA	Intergenic	Intergenic	-52003	NM_011305	20181	Mm.24624	NM_011305	ENSMUSG00000015846	Rxra	9530071D11Rik|Nr2b1|RXRalpha1	retinoid X receptor alpha	protein-coding
mm_120143.1	chr14	60378296	60378371	+	1	NA	promoter-TSS (NM_001164705)	promoter-TSS (NM_001164705)	47	NM_001164705	72125	Mm.275499	NM_028113	ENSMUSG00000021986	Amer2	2600011E07Rik|Fam123a	APC membrane recruitment 2	protein-coding
mm_145626.1	chr18	61109711	61109733	+	1	NA	exon (NM_001037859, exon 3 of 22)	exon (NM_001037859, exon 3 of 22)	4150	NM_001037859	12978	Mm.22574	NM_007779	ENSMUSG00000024621	Csf1r	AI323359|CD115|CSF-1R|Csfmr|Fim-2|Fim2|Fms|M-CSF-R|M-CSFR	colony stimulating factor 1 receptor	protein-coding
mm_72248.1	chr8	75060323	75060333	+	1	NA	intron (NM_001136259, intron 11 of 15)	intron (NM_001136259, intron 11 of 15)	26642	NM_011622	21968	Mm.1967	NM_011622	ENSMUSG00000042870	Tom1	-	target of myb1 trafficking protein	protein-coding
mm_59540.1	chr7	27838543	27838556	+	1	NA	promoter-TSS (NM_011762)	promoter-TSS (NM_011762)	-35	NM_011762	22717	Mm.379046	NM_011762	ENSMUSG00000078779	Zfp59	Mfg-2|Mfg2	zinc finger protein 59	protein-coding
mm_63847.1	chr7	135652530	135652536	+	1	NA	promoter-TSS (NR_015548)	promoter-TSS (NR_015548)	-219	NR_015548	67765	Mm.445272	NR_015548	ENSMUSG00000097471	5830432E09Rik	-	RIKEN cDNA 5830432E09 gene	ncRNA
mm_82120.1	chr9	123478658	123478681	+	1	NA	promoter-TSS (NM_013860)	promoter-TSS (NM_013860)	-32	NM_013860	29806	Mm.10987	NM_013860	ENSMUSG00000025239	Limd1	AW822033|D9Ertd192e	LIM domains containing 1	protein-coding
mm_62325.1	chr7	100472930	100472938	+	1	NA	promoter-TSS (NM_009464)	promoter-TSS (NM_009464)	-57	NM_009464	22229	Mm.6254	NM_009464	ENSMUSG00000032942	Ucp3	AI645527|Slc25a9|UCP-3	uncoupling protein 3 (mitochondrial, proton carrier)	protein-coding
mm_94146.1	chr10	128742713	128742719	-	1	NA	intron (NM_016811, intron 1 of 23)	intron (NM_016811, intron 1 of 23)	1340	NM_016811	13139	Mm.291235	NM_016811	ENSMUSG00000025357	Dgka	80kDa|AW146112|Dagk1	diacylglycerol kinase, alpha	protein-coding
mm_144449.1	chr18	23217176	23217186	+	1	NA	promoter-TSS (NR_110491)	promoter-TSS (NR_110491)	-415	NR_110491	665797	Mm.328158	NR_110491		Gm7788	EG665797	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_37285.1	chr4	119107979	119107998	-	1	NA	promoter-TSS (NM_011400)	promoter-TSS (NM_011400)	-757	NM_011400	20525	Mm.21002	NM_011400	ENSMUSG00000028645	Slc2a1	Glut-1|Glut1	solute carrier family 2 (facilitated glucose transporter), member 1	protein-coding
mm_13249.1	chr2	98663760	98663769	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	1196107	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_43691.1	chr5	139150201	139150209	+	1	NA	promoter-TSS (NM_001081265)	promoter-TSS (NM_001081265)	-18	NM_001081265	433956	Mm.5547	NM_001081265	ENSMUSG00000025857	Dnaaf5	BC053401|C76907|Heatr2	dynein, axonemal assembly factor 5	protein-coding
mm_149646.1	chr19	17517271	17517275	+	1	NA	intron (NM_001190483, intron 21 of 37)	intron (NM_001190483, intron 21 of 37)	123230	NM_019437	54391	Mm.7013	NM_019437	ENSMUSG00000024712	Rfk	0610038L10Rik|AF031381|KOI-4	riboflavin kinase	protein-coding
mm_31212.1	chr4	43957679	43957735	+	1	NA	promoter-TSS (NM_027450)	promoter-TSS (NM_027450)	5	NM_027450	384009	Mm.22213	NM_027450	ENSMUSG00000028480	Glipr2	5730414A08Rik|C77180|GAPR-1	GLI pathogenesis-related 2	protein-coding
mm_143966.1	chr17	87264240	87264265	-	1	NA	5' UTR (NM_176808, exon 2 of 5)	5' UTR (NM_176808, exon 2 of 5)	1695	NM_176808	193813	Mm.30251	NM_139295	ENSMUSG00000024150	Mcfd2	1810021C21Rik|F5f8d|Lman1ip|Sdnsf	multiple coagulation factor deficiency 2	protein-coding
mm_105316.1	chr11	102887788	102887798	-	1	NA	3' UTR (NM_010277, exon 9 of 9)	3' UTR (NM_010277, exon 9 of 9)	2624	NM_025766	66784	Mm.483216	NM_025766	ENSMUSG00000075510	Fam187a	4933439F11Rik	family with sequence similarity 187, member A	protein-coding
mm_37262.1	chr4	118437363	118437374	-	1	NA	promoter-TSS (NM_023223)	promoter-TSS (NM_023223)	-25	NM_023223	107995	Mm.261764	NM_023223	ENSMUSG00000006398	Cdc20	2310042N09Rik|C87100|p55CDC	cell division cycle 20	protein-coding
mm_162827.1	chr10	81343249	81343254	-	1	NA	promoter-TSS (NM_148951)	promoter-TSS (NM_148951)	15	NM_148951	209047	Mm.218755	NM_148951	ENSMUSG00000034872	Gipc3	Ahl5|Rgs19ip3	GIPC PDZ domain containing family, member 3	protein-coding
mm_112097.1	chr12	112785174	112785210	-	1	NA	Intergenic	Intergenic	-23783	NM_145450	217887	Mm.186678	NM_145450	ENSMUSG00000037594	BC022687	AW050009|C130001I08Rik|Flj20080	cDNA sequence BC022687	protein-coding
mm_162972.1	chr11	12035991	12036008	-	1	NA	intron (NM_010345, intron 1 of 16)	intron (NM_010345, intron 1 of 16)	1421	NM_010345	14783	Mm.273117	NM_010345	ENSMUSG00000020176	Grb10	5730571D09Rik|AI325020|Meg1|mKIAA0207	growth factor receptor bound protein 10	protein-coding
mm_133292.1	chr16	77497520	77497548	+	1	NA	intron (NR_015543, intron 3 of 4)	intron (NR_015543, intron 3 of 4)	-101402	NR_029535	387229		NR_029535	ENSMUSG00000065530	Mir99a	Mirn99a|mir-99a|mmu-mir-99a	microRNA 99a	ncRNA
mm_1296.1	chr1	64532791	64532815	+	1	NA	promoter-TSS (NM_009952)	promoter-TSS (NM_009952)	-1	NM_133828	12912	Mm.422634	NM_009952	ENSMUSG00000025958	Creb1	2310001E10Rik|3526402H21Rik|AV083133|Creb|Creb-1	cAMP responsive element binding protein 1	protein-coding
mm_129758.1	chr15	82380180	82380263	-	1	NA	promoter-TSS (NM_019823)	promoter-TSS (NM_019823)	39	NM_019823	56448	Mm.474216	NM_019823	ENSMUSG00000061740	Cyp2d22	2D22	cytochrome P450, family 2, subfamily d, polypeptide 22	protein-coding
mm_77460.1	chr8	121974131	121974131	-	1	NA	intron (NM_016812, intron 1 of 13)	intron (NM_016812, intron 1 of 13)	-3893	NR_106096	102466915		NR_106096	ENSMUSG00000099140	Mir7237	Gm27482|mmu-mir-7237	microRNA 7237	ncRNA
mm_72660.1	chr8	84872070	84872075	+	1	NA	promoter-TSS (NR_031759)	promoter-TSS (NR_031759)	-39	NR_031759	71846	Mm.229128	NM_027954	ENSMUSG00000003824	Syce2	1700013H19Rik|AA407907|Cesc1	synaptonemal complex central element protein 2	protein-coding
mm_115006.1	chr13	98316416	98316421	+	1	NA	promoter-TSS (NR_137279)	promoter-TSS (NR_137279)	549	NM_145455	218490	Mm.371688	NM_145455	ENSMUSG00000021660	Btf3	1700054E11Rik	basic transcription factor 3	protein-coding
mm_132154.1	chr16	32142820	32142826	+	1	NA	TTS (NM_001347181)	TTS (NM_001347181)	22653	NM_146069	224109	Mm.33498	NM_146069	ENSMUSG00000052384	Nrros	E430025L02Rik|Lrcc33|Lrrc33	negative regulator of reactive oxygen species	protein-coding
mm_157645.1	chrX	57304979	57304987	-	1	NA	intron (NM_152801, intron 2 of 21)	intron (NM_152801, intron 2 of 21)	33746	NM_152801	73341	Mm.261443	NM_152801	ENSMUSG00000031133	Arhgef6	1600028C08Rik|1700038J06Rik|4930592P22Rik|alpha-PIX	Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_84724.1	chr9	74528606	74528616	-	1	NA	Intergenic	Intergenic	-319826	NR_045284	100503019	Mm.482658	NR_045284	ENSMUSG00000066477	Gm16551	-	predicted gene 16551	ncRNA
mm_123637.1	chr14	68582041	68582053	-	1	NA	promoter-TSS (NM_021475)	promoter-TSS (NM_021475)	25	NM_021475	58860	Mm.36742	NM_021475	ENSMUSG00000022057	Adamdec1	2210414L24Rik|AI574231|Dcsn	ADAM-like, decysin 1	protein-coding
mm_168551.1	chr11	64299140	64299144	+	1	NA	Intergenic	Intergenic	-136190	NM_178870	15478	Mm.340214	NM_178870	ENSMUSG00000047759	Hs3st3a1	3Ost3a|Hs3st3a	heparan sulfate (glucosamine) 3-O-sulfotransferase 3A1	protein-coding
mm_65532.1	chr7	25803432	25803450	-	1	NA	3' UTR (NM_028775, exon 9 of 9)	3' UTR (NM_028775, exon 9 of 9)	13089	NM_028775	74134	Mm.275188	NM_028775	ENSMUSG00000040703	Cyp2s1	1200011C15Rik|AU041727|C79779	cytochrome P450, family 2, subfamily s, polypeptide 1	protein-coding
mm_127838.1	chr15	6874232	6874248	-	1	NA	promoter-TSS (NM_011019)	promoter-TSS (NM_011019)	73	NM_011019	18414	Mm.10760	NM_011019	ENSMUSG00000022146	Osmr	OSMRB	oncostatin M receptor	protein-coding
mm_156100.1	chrX	112600723	112600738	+	1	NA	5' UTR (NM_177747, exon 1 of 9)	5' UTR (NM_177747, exon 1 of 9)	204	NM_177747	245595	Mm.259846	NM_177747	ENSMUSG00000025529	Zfp711	2810409C01Rik|A230078I01Rik|Znf711	zinc finger protein 711	protein-coding
mm_144174.1	chr18	6733894	6733898	+	1	NA	Intergenic	MIR|SINE|MIR	-31271	NM_181070	19330	Mm.132802	NM_181070	ENSMUSG00000073639	Rab18	AA959686	RAB18, member RAS oncogene family	protein-coding
mm_23026.1	chr3	34643116	34643120	+	1	NA	intron (NR_015580, intron 3 of 4)	intron (NR_015580, intron 3 of 4)	4654	NR_035433	100316679		NR_035433	ENSMUSG00000104797	Mir1897	Mirn1897|mmu-mir-1897	microRNA 1897	ncRNA
mm_99608.1	chr11	104577368	104577387	+	1	NA	intron (NM_010858, intron 2 of 8)	intron (NM_010858, intron 2 of 8)	-15179	NR_130177	100415912	Mm.446786	NR_130177		Gm11665	Gm11664|OTTMUSG00000003182|OTTMUSG00000003183	predicted gene 11665	ncRNA
mm_61874.1	chr7	89426924	89426926	+	1	NA	intron (NR_102276, intron 1 of 1)	intron (NR_102276, intron 1 of 1)	619	NR_102276	101521	Mm.26902	NR_102276	ENSMUSG00000109311	AI314278	-	expressed sequence AI314278	ncRNA
mm_52329.1	chr6	108876288	108876293	+	1	NA	Intergenic	Intergenic	47649	NM_138677	192193	Mm.21596	NM_138677	ENSMUSG00000030104	Edem1	A130059K23Rik|EDEM|mKIAA0212	ER degradation enhancer, mannosidase alpha-like 1	protein-coding
mm_17521.1	chr2	29252828	29252832	-	1	NA	non-coding (NR_029460, exon 1 of 2)	non-coding (NR_029460, exon 1 of 2)	163	NR_029460	76220	Mm.330108	NR_029460	ENSMUSG00000079499	6530402F18Rik	mKIAA1857	RIKEN cDNA 6530402F18 gene	ncRNA
mm_66435.1	chr7	44813318	44813344	-	1	NA	exon (NM_030693, exon 3 of 3)	exon (NM_030693, exon 3 of 3)	2327	NM_030693	107503	Mm.389890	NM_030693	ENSMUSG00000038539	Atf5	AFTA|Atf7|Atfx|ODA-10	activating transcription factor 5	protein-coding
mm_165315.1	chr2	103411750	103411750	+	1	NA	promoter-TSS (NM_001145813)	promoter-TSS (NM_001145813)	-348	NM_001145813	13711	Mm.20888	NM_010125	ENSMUSG00000027186	Elf5	ESE-2|ESE-5|ESE-5.	E74-like factor 5	protein-coding
mm_59529.1	chr7	27653907	27653960	+	1	NA	promoter-TSS (NM_028417)	promoter-TSS (NM_028417)	9	NM_028417	73032	Mm.44095	NM_028417	ENSMUSG00000007944	Ttc9b	2900074C18Rik	tetratricopeptide repeat domain 9B	protein-coding
mm_65088.1	chr7	19262031	19262059	-	1	NA	exon (NM_001282022, exon 4 of 13)	exon (NM_001282022, exon 4 of 13)	9809	NM_001282021	22323	Mm.9684	NM_009499	ENSMUSG00000030403	Vasp	-	vasodilator-stimulated phosphoprotein	protein-coding
mm_4852.1	chr1	187215738	187215748	+	1	NA	promoter-TSS (NM_029067)	promoter-TSS (NM_029067)	232	NM_026367	67769	Mm.138321	NM_026367	ENSMUSG00000039210	Gpatch2	5830433G22Rik|5830436K05Rik|AI427714|AI447508|AW107440|AW491060|Gpatc2	G patch domain containing 2	protein-coding
mm_14072.1	chr2	122765378	122765404	+	1	NA	promoter-TSS (NM_001162503)	promoter-TSS (NM_001162503)	32	NM_001162503	59010	Mm.28986	NM_021507	ENSMUSG00000005803	Sqrdl	0610039J17Rik|4930557M22Rik|SQOR	sulfide quinone reductase-like (yeast)	protein-coding
mm_69460.1	chr7	133123410	133123419	-	1	NA	promoter-TSS (NM_009980)	promoter-TSS (NM_009980)	69	NM_009980	13017	Mm.246240	NM_009980	ENSMUSG00000030970	Ctbp2	AA407280|D7Ertd45e|Gtrgeo6|Ribeye	C-terminal binding protein 2	protein-coding
mm_7070.1	chr1	87853154	87853167	-	1	NA	promoter-TSS (NM_177646)	promoter-TSS (NM_177646)	-127	NM_177646	227333	Mm.277217	NM_177646	ENSMUSG00000070738	Dgkd	AI841987|D330025K09|DGKdelta|dgkd-2	diacylglycerol kinase, delta	protein-coding
mm_169999.1	chr1	71649216	71649216	-	1	NA	exon (NM_001276413, exon 4 of 44)	exon (NM_001276413, exon 4 of 44)	4018	NM_010233	14268	Mm.193099	NM_010233	ENSMUSG00000026193	Fn1	E330027I09|Fn|Fn-1	fibronectin 1	protein-coding
mm_122933.1	chr14	54962717	54962737	-	1	NA	exon (NM_010856, exon 8 of 39)	exon (NM_010856, exon 8 of 39)	3880	NM_001164171	17888	Mm.290003	NM_010856	ENSMUSG00000040752	Myh6	A830009F23Rik|AA517445|Myhc-a|Myhca|alpha-MHC	myosin, heavy polypeptide 6, cardiac muscle, alpha	protein-coding
mm_103401.1	chr11	75438924	75438946	-	1	NA	intron (NM_008878, intron 1 of 9)	intron (NM_008878, intron 1 of 9)	566	NM_008878	18816	Mm.279733	NM_008878	ENSMUSG00000038224	Serpinf2	AI747498|Pli|Serpimf2	serine (or cysteine) peptidase inhibitor, clade F, member 2	protein-coding
mm_80518.1	chr9	80066988	80067006	+	1	NA	promoter-TSS (NM_146003)	promoter-TSS (NM_146003)	94	NM_146003	215351	Mm.28232	NM_146003	ENSMUSG00000034252	Senp6	2810017C20Rik|E130319N12Rik|Susp1|mKIAA0797	SUMO/sentrin specific peptidase 6	protein-coding
mm_74941.1	chr8	25840441	25840461	-	1	NA	promoter-TSS (NM_001286207)	promoter-TSS (NM_001286207)	6	NM_001286207	23808	Mm.27706	NM_011791	ENSMUSG00000031575	Ash2l	-	ash2 (absent, small, or homeotic)-like (Drosophila)	protein-coding
mm_49800.1	chr6	35996995	35997007	+	1	NA	Intergenic	MT2A|LTR|ERVL	-391083	NM_203491	243764	Mm.448632	NM_203491	ENSMUSG00000045613	Chrm2	AChR-M2|Chrm-2|M2	cholinergic receptor, muscarinic 2, cardiac	protein-coding
mm_151810.1	chr19	5468488	5468506	-	1	NA	promoter-TSS (NM_009985)	promoter-TSS (NM_009985)	10	NM_009985	13041	Mm.113590	NM_009985	ENSMUSG00000024910	Ctsw	lymphopain	cathepsin W	protein-coding
mm_156347.1	chrX	139179244	139179246	+	1	NA	Intergenic	Intergenic	-30799	NM_175541	245631	Mm.131001	NM_175541	ENSMUSG00000042515	Mum1l1	9430086K21Rik	melanoma associated antigen (mutated) 1-like 1	protein-coding
mm_137417.1	chr17	26123567	26123579	+	1	NA	promoter-TSS (NM_024227)	promoter-TSS (NM_024227)	70	NM_024227	68611	Mm.273102	NM_024227	ENSMUSG00000024181	Mrpl28	1110015G04Rik|L28mt|MAAT1|MRP-L28|p15	mitochondrial ribosomal protein L28	protein-coding
mm_46880.1	chr5	113844257	113844274	-	1	NA	3' UTR (NM_011779, exon 11 of 11)	3' UTR (NM_011779, exon 11 of 11)	-13764	NM_009151	20345	Mm.332590	NM_009151	ENSMUSG00000048163	Selplg	CD162|Psgl-1|Psgl1|Selp1|Selpl	selectin, platelet (p-selectin) ligand	protein-coding
mm_13229.1	chr2	97502513	97502516	+	1	NA	intron (NM_001289744, intron 1 of 1)	intron (NM_001289744, intron 1 of 1)	34857	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_47120.1	chr5	119671499	119671510	-	1	NA	5' UTR (NM_011535, exon 1 of 8)	5' UTR (NM_011535, exon 1 of 8)	271	NM_011535	21386	Mm.219139	NM_011535	ENSMUSG00000018604	Tbx3	D5Ertd189e	T-box 3	protein-coding
mm_55713.1	chr6	73060289	73060309	-	1	NA	exon (NM_001164669, exon 61 of 77)	exon (NM_001164669, exon 61 of 77)	-101551	NM_001190327	19240	Mm.3532	NM_025284	ENSMUSG00000079523	Tmsb10	Ptmb10|Tb10	thymosin, beta 10	protein-coding
mm_91452.1	chr10	34019470	34019478	-	1	NA	5' UTR (NM_025614, exon 1 of 7)	5' UTR (NM_025614, exon 1 of 7)	142	NM_025614	66521	Mm.28528	NM_025614	ENSMUSG00000019782	Rwdd1	0710001K08Rik|2610002D06Rik|2700069A07Rik|IH1	RWD domain containing 1	protein-coding
mm_27003.1	chr3	25847285	25847297	-	1	NA	intron (NM_001163387, intron 3 of 5)	intron (NM_001163387, intron 3 of 5)	306016	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_132583.1	chr16	38362165	38362178	+	1	NA	promoter-TSS (NM_022318)	promoter-TSS (NM_022318)	-19	NM_001081984	64082	Mm.390856	NM_022318	ENSMUSG00000022803	Popdc2	AV006127|Pop2	popeye domain containing 2	protein-coding
mm_123316.1	chr14	62481134	62481143	-	1	NA	Intergenic	Intergenic	-24849	NM_172810	239134	Mm.236557	NM_172810	ENSMUSG00000021933	Gucy1b2	B930025B03|GC-SB2	guanylate cyclase 1, soluble, beta 2	protein-coding
mm_136335.1	chr16	92466248	92466274	-	1	NA	promoter-TSS (NM_001081549)	promoter-TSS (NM_001081549)	-92	NM_001081549	54720	Mm.265744	NM_019466	ENSMUSG00000022951	Rcan1	Adapt78|CALP1L|CSP1|DSC1|Dscr1|MCIP1|RCN1	regulator of calcineurin 1	protein-coding
mm_101362.1	chr11	23741383	23741398	-	1	NA	TTS (NM_009044)	TTS (NM_009044)	29580	NM_009044	19696	Mm.4869	NM_009044	ENSMUSG00000020275	Rel	c-Rel	reticuloendotheliosis oncogene	protein-coding
mm_150909.1	chr19	46003469	46003547	+	1	NA	promoter-TSS (NM_176785)	promoter-TSS (NM_176785)	30	NM_176785	20170	Mm.101110	NM_176785	ENSMUSG00000074811	Hps6	5330434M19Rik|BLOC2|ru	Hermansky-Pudlak syndrome 6	protein-coding
mm_62409.1	chr7	101214222	101214231	+	1	NA	intron (NM_199012, intron 8 of 20)	intron (NM_199012, intron 8 of 20)	87862	NM_001111111	73683	Mm.275744	NM_001111111	ENSMUSG00000047767	Atg16l2	2410118P20Rik	autophagy related 16-like 2 (S. cerevisiae)	protein-coding
mm_93326.1	chr10	99241940	99241970	-	1	NA	Intergenic	Intergenic	-21276	NM_026268	67603	Mm.1791	NM_026268	ENSMUSG00000019960	Dusp6	1300019I03Rik|MKP-3|MKP3|PYST1	dual specificity phosphatase 6	protein-coding
mm_21375.1	chr2	157346648	157346663	-	1	NA	promoter-TSS (NM_010285)	promoter-TSS (NM_010285)	0	NM_010285	14601	Mm.389327	NM_010285	ENSMUSG00000027643	Ghrh	GRF|Ghrf	growth hormone releasing hormone	protein-coding
mm_135086.1	chr16	34514206	34514211	-	1	NA	promoter-TSS (NM_177357)	promoter-TSS (NM_177357)	-181	NM_177357	545156	Mm.82274	NM_177357	ENSMUSG00000061751	Kalrn	2210407G14Rik|AV235988|DUET|E530005C20Rik|Gm539|Hapip|TRAD	kalirin, RhoGEF kinase	protein-coding
mm_68796.1	chr7	124629122	124629125	-	1	NA	intron (NR_045907, intron 1 of 3)	ORR1A2|LTR|ERVL-MaLR	79812	NR_045907	73076	Mm.417827	NR_045907	ENSMUSG00000086254	3100003L05Rik	-	RIKEN cDNA 3100003L05 gene	ncRNA
mm_161736.1	chr17	31583684	31583684	+	1	NA	intron (NR_027493, intron 2 of 11)	intron (NR_027493, intron 2 of 11)	18911	NM_016670	18771	Mm.259295	NM_016670	ENSMUSG00000006705	Pknox1	D17Wsu76e|PREP1	Pbx/knotted 1 homeobox	protein-coding
mm_140873.1	chr17	23802821	23802852	-	1	NA	promoter-TSS (NM_175229)	promoter-TSS (NM_175229)	-351	NM_175229	75956	Mm.5222	NM_175229	ENSMUSG00000039218	Srrm2	5033413A03Rik|AA410130|SRm300|mKIAA0324	serine/arginine repetitive matrix 2	protein-coding
mm_14472.1	chr2	131491884	131491940	+	1	NA	promoter-TSS (NM_001177840)	promoter-TSS (NM_001177840)	50	NM_001177838	228608	Mm.136586	NM_145533	ENSMUSG00000027333	Smox	B130066H01Rik|PAO|PAOh1|SMO	spermine oxidase	protein-coding
mm_148872.1	chr19	6497759	6497764	+	1	NA	intron (NM_001205234, intron 17 of 22)	CpG	45309	NM_009203	20521	Mm.391146	NM_009203	ENSMUSG00000061742	Slc22a12	AI987855|OAT4L|Rst|Slc22al2|URAT1	solute carrier family 22 (organic anion/cation transporter), member 12	protein-coding
mm_165750.1	chr3	108146176	108146196	+	1	NA	promoter-TSS (NM_010306)	promoter-TSS (NM_010306)	-34	NM_010306	14679	Mm.271703	NM_010306	ENSMUSG00000000001	Gnai3	AI158965|AW537698|Galphai3|Gnai-3	guanine nucleotide binding protein (G protein), alpha inhibiting 3	protein-coding
mm_137768.1	chr17	29490776	29490799	+	1	NA	promoter-TSS (NM_008842)	promoter-TSS (NM_008842)	-258	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_20392.1	chr2	129100908	129100957	-	1	NA	promoter-TSS (NM_009086)	promoter-TSS (NM_009086)	-64	NM_009086	20017	Mm.259078	NM_009086	ENSMUSG00000027395	Polr1b	128kDa|D630020H17Rik|RPA116|RPA135|RPA2|Rpo1-2	polymerase (RNA) I polypeptide B	protein-coding
mm_54932.1	chr6	48439613	48439624	-	1	NA	intron (NM_001085415, intron 4 of 4)	intron (NM_001085415, intron 4 of 4)	5472	NM_001085415	68910	Mm.2464	NM_020589	ENSMUSG00000068551	Zfp467	1190001I08Rik|AB041616|AI426952|AV017623|EZI|MNCb-3350|Znf467	zinc finger protein 467	protein-coding
mm_130071.1	chr15	89355469	89355498	-	1	NA	promoter-TSS (NM_001271601)	promoter-TSS (NM_001271601)	176	NM_178919	105847	Mm.34511	NM_178919	ENSMUSG00000022614	Lmf2	AI451006|Tmem112b|Tmem153	lipase maturation factor 2	protein-coding
mm_123202.1	chr14	59323198	59323233	-	1	NA	exon (NM_001164327, exon 7 of 9)	exon (NM_001164327, exon 7 of 9)	18115	NM_001164327	236451	Mm.247736	NM_001164327	ENSMUSG00000091649	Phf11b	EG236451|Gm4902	PHD finger protein 11B	protein-coding
mm_90972.1	chr10	13474282	13474324	-	1	NA	promoter-TSS (NM_001195065)	promoter-TSS (NM_001195065)	93	NM_001195065	215789	Mm.283359	NM_001033257	ENSMUSG00000062866	Phactr2	AV158170|BC012871	phosphatase and actin regulator 2	protein-coding
mm_11988.1	chr2	55437101	55437182	+	1	NA	5' UTR (NM_001304810, exon 2 of 3)	5' UTR (NM_001304810, exon 2 of 3)	1171	NM_008426	16519	Mm.5127	NM_008426	ENSMUSG00000026824	Kcnj3	GIRK-1|GIRK1|Kcnf3|Kir3.1	potassium inwardly-rectifying channel, subfamily J, member 3	protein-coding
mm_53541.1	chr6	136808264	136808345	+	1	NA	promoter-TSS (NM_177688)	promoter-TSS (NM_177688)	56	NM_177688	232440	Mm.154564	NM_177688	ENSMUSG00000060032	H2afj	E130307C13	H2A histone family, member J	protein-coding
mm_103016.1	chr11	69734893	69734903	-	1	NA	exon (NM_001291068, exon 29 of 29)	exon (NM_001291068, exon 29 of 29)	23735	NM_001291068	20020	Mm.16533	NM_009089	ENSMUSG00000005198	Polr2a	220kDa|Rpb1|Rpo2-1	polymerase (RNA) II (DNA directed) polypeptide A	protein-coding
mm_162237.1	chrX	154120652	154120652	-	1	NA	promoter-TSS (NM_030036).4	promoter-TSS (NM_030036).4	33	NM_001201358	667256	Mm.46855	NM_001201358	ENSMUSG00000094577	4921511M17Rik	-	RIKEN cDNA 4921511M17 gene	protein-coding
mm_98060.1	chr11	85831757	85831775	+	1	NA	promoter-TSS (NM_009324)	promoter-TSS (NM_009324)	622	NR_077059	69909	Mm.440214	NR_077059	ENSMUSG00000087013	2610027K06Rik	-	RIKEN cDNA 2610027K06 gene	ncRNA
mm_121152.1	chr14	101934000	101934036	+	1	NA	3' UTR (NM_201529, exon 31 of 31)	3' UTR (NM_201529, exon 31 of 31)	93395	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_81944.1	chr9	120492605	120492615	+	1	NA	promoter-TSS (NM_026892)	promoter-TSS (NM_026892)	4	NM_026892	68969	Mm.28753	NM_026892	ENSMUSG00000006941	Eif1b	1500010M16Rik|3110001N14Rik|Gc20	eukaryotic translation initiation factor 1B	protein-coding
mm_166625.1	chr6	76381221	76381222	+	1	NA	Intergenic	Intergenic	-861496	NM_028880	74342	Mm.292568	NM_028880	ENSMUSG00000060780	Lrrtm1	4632401D06Rik|AW125451	leucine rich repeat transmembrane neuronal 1	protein-coding
mm_124181.1	chr14	93877305	93877323	-	1	NA	intron (NM_001346722, intron 2 of 4)	intron (NM_001346722, intron 2 of 4)	11574	NM_001271800	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding
mm_164428.1	chr16	45383060	45383068	-	1	NA	3' UTR (NM_010818, exon 6 of 6)	3' UTR (NM_010818, exon 6 of 6)	25989	NM_010818	17470	Mm.245851	NM_010818	ENSMUSG00000022661	Cd200	Mox2|OX2	CD200 antigen	protein-coding
mm_15670.1	chr2	163438456	163438536	+	1	NA	promoter-TSS (NM_144891)	promoter-TSS (NM_144891)	29	NM_144891	228858	Mm.102080	NM_144891	ENSMUSG00000017943	Gdap1l1	Gdap1l	ganglioside-induced differentiation-associated protein 1-like 1	protein-coding
mm_130039.1	chr15	88982668	88982706	-	1	NA	promoter-TSS (NM_031260)	promoter-TSS (NM_031260)	-307	NM_031260	83456	Mm.358791	NM_031260	ENSMUSG00000015365	Mov10l1	CHAMP|Csm	Moloney leukemia virus 10-like 1	protein-coding
mm_156141.1	chrX	129749741	129749822	+	1	NA	promoter-TSS (NM_172493)	promoter-TSS (NM_172493)	39	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diaph2	Dia3|Diap2|Drf2|E430022I22Rik	diaphanous related formin 2	protein-coding
mm_90605.1	chr10	128322636	128322648	+	1	NA	5' UTR (NM_019953, exon 1 of 6)	5' UTR (NM_019953, exon 1 of 6)	183	NM_019953	56530	Mm.44220	NM_019953	ENSMUSG00000025381	Cnpy2	5330432A10Rik|AW229003|D10Bwg1546e|Tmem4|Zsig9	canopy FGF signaling regulator 2	protein-coding
mm_61680.1	chr7	80993700	80993714	+	1	NA	promoter-TSS (NM_178707)	promoter-TSS (NM_178707)	23	NM_178707	233410	Mm.29525	NM_178707	ENSMUSG00000005621	Zfp592	8430405N24|A730014M16Rik|Znf592|mKIAA0211	zinc finger protein 592	protein-coding
mm_53511.1	chr6	135707412	135707422	+	1	NA	Intergenic	ORR1C2|LTR|ERVL-MaLR	48504	NR_126088	75024	Mm.399147	NR_126088	ENSMUSG00000107396	4930425L21Rik	4930473P14Rik	RIKEN cDNA 4930425L21 gene	ncRNA
mm_92497.1	chr10	78351691	78351708	-	1	NA	promoter-TSS (NM_053014)	promoter-TSS (NM_053014)	1	NM_053014	28169	Mm.141230	NM_053014	ENSMUSG00000001211	Agpat3	AW061257|AW493985|D10Jhu12e|lpaat3	1-acylglycerol-3-phosphate O-acyltransferase 3	protein-coding
mm_6171.1	chr1	65080254	65080260	-	1	NA	TTS (NM_144761)	TTS (NM_144761)	2033	NM_144761	12965	Mm.440053	NM_144761	ENSMUSG00000073658	Crygb	Cryg-3|DGcry-3|Nop	crystallin, gamma B	protein-coding
mm_136604.1	chr17	5195702	5195737	+	1	NA	intron (NM_001085355, intron 4 of 19)	intron (NM_001085355, intron 4 of 19)	200645	NM_001085355	239985	Mm.133401	NM_001085355	ENSMUSG00000069729	Arid1b	8030481M12|9330189K18Rik|AI836955|Ardi1b|B230217J03Rik|mKIAA1235	AT rich interactive domain 1B (SWI-like)	protein-coding
mm_152632.1	chr19	12501548	12501630	-	1	NA	5' UTR (NM_172442, exon 1 of 9)	5' UTR (NM_172442, exon 1 of 9)	407	NM_172442	207521	Mm.247695	NM_172442	ENSMUSG00000039982	Dtx4	AI449438|BC044798|D930042H13|RNF155	deltex 4, E3 ubiquitin ligase	protein-coding
mm_43003.1	chr5	123462472	123462508	+	1	NA	Intergenic	T-rich|Low_complexity|Low_complexity	19611	NM_029594	76399	Mm.75049	NM_029594	ENSMUSG00000029437	Il31	1700013B14Rik	interleukin 31	protein-coding
mm_125820.1	chr15	74956424	74956481	+	1	NA	intron (NM_001164039, intron 2 of 4)	intron (NM_001164039, intron 2 of 4)	1346	NM_001164040	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_162724.1	chr10	39533261	39533273	+	1	NA	intron (NM_001122892, intron 9 of 12)	intron (NM_001122892, intron 9 of 12)	-79667	NM_134000	103213	Mm.436686	NM_134000	ENSMUSG00000019842	Traf3ip2	AI429613|Act1|CIKS	TRAF3 interacting protein 2	protein-coding
mm_147207.1	chr18	37935379	37935393	-	1	NA	promoter-TSS (NM_001305981)	promoter-TSS (NM_001305981)	90	NM_001305980	13367	Mm.195916	NM_007858	ENSMUSG00000024456	Diaph1	D18Wsu154e|Dia1|Diap1|Drf1|p140mDia	diaphanous related formin 1	protein-coding
mm_7123.1	chr1	90822422	90822424	-	1	NA	intron (NM_001243008, intron 3 of 43)	intron (NM_001243008, intron 3 of 43)	21548	NM_001243009	12835	Mm.7562	NM_009935	ENSMUSG00000048126	Col6a3	AI507288|Col6a-3	collagen, type VI, alpha 3	protein-coding
mm_137887.1	chr17	31678925	31678934	+	1	NA	intron (NM_001278569, intron 2 of 3)	intron (NM_001278569, intron 2 of 3)	998	NM_001278570	12954	Mm.1228	NM_013501	ENSMUSG00000024041	Cryaa	Acry-1|Crya-1|Crya1|DAcry-1|lop18	crystallin, alpha A	protein-coding
mm_43943.1	chr5	145127984	145127999	+	1	NA	TTS (NM_001033313)	TTS (NM_001033313)	12098	NM_001033313	231887	Mm.188851	NM_001033313	ENSMUSG00000029623	Pdap1	HASPP28|PAP|PAP1	PDGFA associated protein 1	protein-coding
mm_157657.1	chrX	57338599	57338610	-	1	NA	5' UTR (NM_152801, exon 1 of 22)	5' UTR (NM_152801, exon 1 of 22)	125	NM_152801	73341	Mm.261443	NM_152801	ENSMUSG00000031133	Arhgef6	1600028C08Rik|1700038J06Rik|4930592P22Rik|alpha-PIX	Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_86805.1	chr10	20325376	20325399	+	1	NA	exon (NM_001025393, exon 5 of 12)	exon (NM_001025393, exon 5 of 12)	12918	NM_001025393	72567	Mm.294783	NM_153787	ENSMUSG00000037608	Bclaf1	2610102K23Rik|2700025J07Rik|2810454G14Rik|5730534O06Rik|AI450190|AW556225|Btf|mKIAA0164	BCL2-associated transcription factor 1	protein-coding
mm_39865.1	chr5	31049030	31049034	+	1	NA	promoter-TSS (NM_177870)	promoter-TSS (NM_177870)	-108	NM_001177622	330064	Mm.205463	NM_177870	ENSMUSG00000006641	Slc5a6	E430023I20	solute carrier family 5 (sodium-dependent vitamin transporter), member 6	protein-coding
mm_8898.1	chr1	162937526	162937555	-	1	NA	promoter-TSS (NM_001178038)	promoter-TSS (NM_001178038)	-315	NM_001178038	226565	Mm.270516	NM_001178038	ENSMUSG00000095576	Fmo6	-	flavin containing monooxygenase 6	protein-coding
mm_117814.1	chr13	97781213	97781221	-	1	NA	Intergenic	Intergenic	221217	NR_046157	328314	Mm.138047	NR_046157	ENSMUSG00000110235	Gm5086	B230311A21|EG328314	predicted gene 5086	ncRNA
mm_67150.1	chr7	73517522	73517534	-	1	NA	intron (NM_001081345, intron 3 of 38)	intron (NM_001081345, intron 3 of 38)	24218	NM_001081345	244059	Mm.34539	NM_001081345	ENSMUSG00000078671	Chd2	2810013C04Rik|2810040A01Rik|5630401D06Rik|AI851092|BC029703|CHD-2	chromodomain helicase DNA binding protein 2	protein-coding
mm_169126.1	chr13	54190131	54190132	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-1998	NM_001010973	15466	Mm.57243	NM_008286	ENSMUSG00000034987	Hrh2	-	histamine receptor H2	protein-coding
mm_20510.1	chr2	130638095	130638113	-	1	NA	intron (NM_197945, intron 1 of 4)	intron (NM_197945, intron 1 of 4)	4740	NM_197945	241638	Mm.440130	NM_197945	ENSMUSG00000037703	Lzts3	Prosapip1	leucine zipper, putative tumor suppressor family member 3	protein-coding
mm_30324.1	chr3	151731881	151731891	-	1	NA	3' UTR (NM_133871, exon 8 of 8)	3' UTR (NM_133871, exon 8 of 8)	18073	NM_133871	99899	Mm.30756	NM_133871	ENSMUSG00000028037	Ifi44	A430056A10Rik|AW261460|MTAP44|p44	interferon-induced protein 44	protein-coding
mm_7998.1	chr1	134361934	134361998	-	1	NA	promoter-TSS (NM_001042485)	promoter-TSS (NM_001042485)	33	NM_001042485	57439	Mm.393140	NM_020588	ENSMUSG00000042305	Tmem183a	1300007B12Rik|1700020N19Rik|Tmem183	transmembrane protein 183A	protein-coding
mm_4870.1	chr1	187796265	187796268	+	1	NA	intron (NM_001243792, intron 2 of 7)	intron (NM_001243792, intron 2 of 7)	187260	NM_001243792	26381	Mm.89989	NM_011935	ENSMUSG00000026610	Esrrg	ERR3|Errg|NR3B3|mKIAA0832	estrogen-related receptor gamma	protein-coding
mm_11191.1	chr2	29122714	29122739	+	1	NA	Intergenic	Lx8|LINE|L1	-2266	NM_198033	269254	Mm.41867	NM_198033	ENSMUSG00000043535	Setx	A130090N03|A930037J23Rik|AOA2|AW060766|Als4|SCAR1|Sen1|mKIAA0625	senataxin	protein-coding
mm_83766.1	chr9	52048686	52048696	-	1	NA	promoter-TSS (NR_023357)	promoter-TSS (NR_023357)	14	NR_023357	629557	Mm.422775	NR_023357		Gm6981	EG629557	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_49122.1	chr6	8520009	8520047	+	1	NA	promoter-TSS (NM_001286729)	promoter-TSS (NM_001286729)	-30	NM_001286728	170772	Mm.210787	NM_133236	ENSMUSG00000029638	Glcci1	2310047L21Rik|A130036A18Rik|Fam117c|Gig18|Tssn1	glucocorticoid induced transcript 1	protein-coding
mm_11511.1	chr2	32575837	32575848	+	1	NA	5' UTR (NM_198191, exon 1 of 10)	5' UTR (NM_198191, exon 1 of 10)	124	NM_198191	227733	Mm.78923	NM_198191	ENSMUSG00000046854	Pip5kl1	BC028795	phosphatidylinositol-4-phosphate 5-kinase-like 1	protein-coding
mm_171546.1	chr4	147022053	147022058	+	1	NA	intron (NM_001177767, intron 1 of 4)	intron (NM_001177767, intron 1 of 4)	205	NM_001177767	100043034	Mm.422606	NM_001177767	ENSMUSG00000067919	Rex2	Gm13138|OTTMUSG00000010655	reduced expression 2	protein-coding
mm_92649.1	chr10	80399345	80399384	-	1	NA	5' UTR (NM_013595, exon 1 of 7)	5' UTR (NM_013595, exon 1 of 7)	167	NM_013595	17192	Mm.7142	NM_013595	ENSMUSG00000035478	Mbd3	AI181826|AU019209	methyl-CpG binding domain protein 3	protein-coding
mm_158335.1	chrX	133981723	133981754	-	1	NA	promoter-TSS (NM_001290718)	promoter-TSS (NM_001290718)	74	NM_001290718	27359	Mm.38674	NM_013757	ENSMUSG00000031255	Sytl4	Gph|Slp4	synaptotagmin-like 4	protein-coding
mm_6318.1	chr1	71602382	71602402	-	1	NA	exon (NM_001276413, exon 32 of 44)	exon (NM_001276413, exon 32 of 44)	45236	NM_026195	108147	Mm.38010	NM_026195	ENSMUSG00000026192	Atic	2610509C24Rik|AA536954|AW212393	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	protein-coding
mm_163918.1	chr14	37131255	37131271	-	1	NA	intron (NM_078478, intron 4 of 8)	B2_Mm2|SINE|B2	3876	NM_001199122	66092	Mm.182912	NM_078478	ENSMUSG00000041028	Ghitm	1010001P14Rik|C77840|MICS1|PTD010|Tmbim5	growth hormone inducible transmembrane protein	protein-coding
mm_92148.1	chr10	67096893	67096901	-	1	NA	promoter-TSS (NM_001204915)	promoter-TSS (NM_001204915)	91	NM_001204915	28193	Mm.41272	NM_178606	ENSMUSG00000019873	Reep3	D10Ucla1	receptor accessory protein 3	protein-coding
mm_61203.1	chr7	64153842	64153851	+	1	NA	promoter-TSS (NM_001039104)	promoter-TSS (NM_001039104)	11	NM_001039104	17364	Mm.38875	NM_018752	ENSMUSG00000030523	Trpm1	4732499L03Rik|AI606771|Ltrpc1|Mlsn1	transient receptor potential cation channel, subfamily M, member 1	protein-coding
mm_42565.1	chr5	117142187	117142206	+	1	NA	intron (NM_001081308, intron 1 of 19)	intron (NM_001081308, intron 1 of 19)	8608	NM_183306	330177	Mm.24343	NM_183306	ENSMUSG00000061288	Taok3	2900006A08Rik|A130052D22|A430105I05Rik	TAO kinase 3	protein-coding
mm_5968.1	chr1	56981119	56981127	-	1	NA	Intergenic	Intergenic	9654	NR_024325	329160	Mm.419039	NR_024325	ENSMUSG00000087022	9130024F11Rik	B530002L08|EG329160	RIKEN cDNA 9130024F11 gene	ncRNA
mm_109101.1	chr12	105019532	105019557	+	1	NA	Intergenic	Intergenic	-9735	NM_172500	212073	Mm.212688	NM_172500	ENSMUSG00000054150	Syne3	nesprin-3	spectrin repeat containing, nuclear envelope family member 3	protein-coding
mm_38668.1	chr4	144686410	144686422	-	1	NA	promoter-TSS (NM_001085504)	promoter-TSS (NM_001085504)	-48	NM_001085504	230890	Mm.457843	NM_001085504	ENSMUSG00000078505	Gm436	-	predicted gene 436	protein-coding
mm_146307.1	chr18	80256301	80256326	+	1	NA	promoter-TSS (NM_001164424)	promoter-TSS (NM_001164424)	7	NM_001164423	66943	Mm.29247	NM_025861	ENSMUSG00000034006	Pqlc1	2310009N05Rik|4933425L21Rik|5730564E11Rik|C78974	PQ loop repeat containing 1	protein-coding
mm_164399.1	chr16	34034452	34034457	-	1	NA	intron (NM_177357, intron 42 of 59)	intron (NM_177357, intron 42 of 59)	-67451	NM_009471	22247	Mm.13145	NM_009471	ENSMUSG00000022814	Umps	1700095D23Rik|AA408257|AL033308|BB164745	uridine monophosphate synthetase	protein-coding
mm_5580.1	chr1	39552028	39552045	-	1	NA	3' UTR (NM_001033135, exon 7 of 7)	3' UTR (NM_001033135, exon 7 of 7)	-3196	NR_028555	100217461		NR_028555	ENSMUSG00000077704	Snord89	MBII-289	small nucleolar RNA, C/D box 89	snoRNA
mm_1120.1	chr1	59913484	59913536	+	1	NA	exon (NM_001037725, exon 1 of 8)	exon (NM_001037725, exon 1 of 8)	504	NM_001037725	72750	Mm.258250	NM_001037725	ENSMUSG00000041040	Fam117b	2810425F24Rik|6330416D14Rik|Als2cr13	family with sequence similarity 117, member B	protein-coding
mm_170262.1	chr18	15489919	15489921	-	1	NA	intron (NM_199055, intron 3 of 3)	intron (NM_199055, intron 3 of 3)	-78938	NM_001308646	11829	Mm.250786	NM_009700	ENSMUSG00000024411	Aqp4	WCH4	aquaporin 4	protein-coding
mm_147573.1	chr18	55839026	55839034	-	1	NA	Intergenic	MTEa-int|LTR|ERVL-MaLR	-593102	NM_026240	107022	Mm.24356	NM_026240	ENSMUSG00000001700	Gramd3	9030613F08Rik|9130427A09Rik|AW061306|NS3TP2	GRAM domain containing 3	protein-coding
mm_56684.1	chr6	113910486	113910497	-	1	NA	intron (NM_001347365, intron 2 of 23)	intron (NM_001347365, intron 2 of 23)	-18952	NM_001036684	11941	Mm.321755	NM_009723	ENSMUSG00000030302	Atp2b2	D6Abb2e|Gena300|PMCA2|Tmy|dfw|jog|wms|wri	ATPase, Ca++ transporting, plasma membrane 2	protein-coding
mm_40833.1	chr5	72914508	72914520	+	1	NA	5' UTR (NM_001113423, exon 1 of 8)	5' UTR (NM_001113423, exon 1 of 8)	152	NM_153567	75991	Mm.121285	NM_153567	ENSMUSG00000036087	Slain2	5033405K12Rik|8030444K12Rik|AI596370	SLAIN motif family, member 2	protein-coding
mm_90606.1	chr10	128322658	128322729	+	1	NA	5' UTR (NM_019953, exon 1 of 6)	5' UTR (NM_019953, exon 1 of 6)	234	NM_019953	56530	Mm.44220	NM_019953	ENSMUSG00000025381	Cnpy2	5330432A10Rik|AW229003|D10Bwg1546e|Tmem4|Zsig9	canopy FGF signaling regulator 2	protein-coding
mm_68594.1	chr7	116039565	116039577	-	1	NA	promoter-TSS (NM_001025559)	promoter-TSS (NM_001025559)	-827	NM_001025559	20679	Mm.323365	NM_011445	ENSMUSG00000051910	Sox6	AI987981|SOX-LZ	SRY (sex determining region Y)-box 6	protein-coding
mm_108261.1	chr12	78486863	78486868	+	1	NA	intron (NM_145965, intron 6 of 22)	intron (NM_145965, intron 6 of 22)	-204670	NM_027597	70897	Mm.56514	NM_027597	ENSMUSG00000056987	Fam71d	4921509E07Rik|4930516C23Rik|GARI-L2	family with sequence similarity 71, member D	protein-coding
mm_106563.1	chr11	120633540	120633591	-	1	NA	promoter-TSS (NM_010756)	promoter-TSS (NM_010756)	-18	NM_010756	17134	Mm.268010	NM_010756	ENSMUSG00000051510	Mafg	AA545192|C630022N07Rik	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein G (avian)	protein-coding
mm_89249.1	chr10	87859108	87859126	+	1	NA	promoter-TSS (NM_010512)	promoter-TSS (NM_010512)	65	NM_010512	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_14613.1	chr2	136713508	136713528	+	1	NA	promoter-TSS (NM_001291056)	promoter-TSS (NM_001291056)	68	NM_001291056	20614	Mm.45953	NM_011428	ENSMUSG00000027273	Snap25	Bdr|GENA70|SNAP-25|SUP|sp	synaptosomal-associated protein 25	protein-coding
mm_27314.1	chr3	50366724	50366741	-	1	NA	3' UTR (NM_011990, exon 12 of 12)	3' UTR (NM_011990, exon 12 of 12)	76881	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_71373.1	chr8	45784754	45784757	+	1	NA	intron (NM_001310708, intron 10 of 19)	intron (NM_001310708, intron 10 of 19)	34542	NR_045739	319940	Mm.441720	NR_045739	ENSMUSG00000085440	Sorbs2os	D330022K07Rik	sorbin and SH3 domain containing 2, opposite strand	ncRNA
mm_46049.1	chr5	92083456	92083466	-	1	NA	promoter-TSS (NM_001080797)	promoter-TSS (NM_001080797)	137	NM_001080794	23881	Mm.290530	NM_011816	ENSMUSG00000029405	G3bp2	AA409541|E430034L04Rik|G3BP|mKIAA0660	GTPase activating protein (SH3 domain) binding protein 2	protein-coding
mm_67130.1	chr7	70367043	70367051	-	1	NA	promoter-TSS (NM_183261)	promoter-TSS (NM_183261)	-301	NM_183261	11819	Mm.158143	NM_009697	ENSMUSG00000030551	Nr2f2	2700033K02Rik|9430015G03Rik|ARP-1|Aporp1|COUP-TF2|COUP-TFII|COUPTFB|EAR3|SVP40|Tcfcoup2	nuclear receptor subfamily 2, group F, member 2	protein-coding
mm_113925.1	chr13	49608006	49608024	+	1	NA	promoter-TSS (NM_008760)	promoter-TSS (NM_008760)	-56	NM_008760	18295	Mm.4258	NM_008760	ENSMUSG00000021390	Ogn	3110079A16Rik|OG|OIF|SLRR3A|mimecan|mimican	osteoglycin	protein-coding
mm_146973.1	chr18	33463859	33463904	-	1	NA	promoter-TSS (NM_001267717)	promoter-TSS (NM_001267717)	148	NM_001109988	27528	Mm.407415	NM_053078	ENSMUSG00000042834	Nrep	AI325076|D0H4S114|Harp|P311|PTZ17|SEZ17	neuronal regeneration related protein	protein-coding
mm_18762.1	chr2	73453919	73453933	-	1	NA	promoter-TSS (NM_001289722)	promoter-TSS (NM_001289722)	-37	NM_001289722	215280	Mm.223504	NM_153138	ENSMUSG00000075284	Wipf1	AI115543|D2Ertd120e|WIP|Waspip	WAS/WASL interacting protein family, member 1	protein-coding
mm_78508.1	chr9	32754647	32754650	+	1	NA	3' UTR (NM_001038642, exon 7 of 7)	3' UTR (NM_001038642, exon 7 of 7)	58606	NM_001038642	23871	Mm.292415	NM_011808	ENSMUSG00000032035	Ets1	AI196000|AI448617|D230050P06|Ets-1|Tpl1|vs	E26 avian leukemia oncogene 1, 5' domain	protein-coding
mm_132156.1	chr16	32177664	32177675	+	1	NA	Intergenic	Intergenic	-2131	NM_001033539	328660	Mm.441006	NM_001033539	ENSMUSG00000075269	Bex6	B020003O03Rik	brain expressed family member 6	protein-coding
mm_159010.1	chr1	164123604	164123604	+	1	NA	intron (NM_011347, intron 1 of 15)	intron (NM_011347, intron 1 of 15)	8340	NM_011347	20344	Mm.3337	NM_011347	ENSMUSG00000026580	Selp	CD62P|GMP-140|Grmp|LECAM3|PADGEM	selectin, platelet	protein-coding
mm_114196.1	chr13	55905092	55905105	+	1	NA	Intergenic	Intergenic	-73673	NM_011097	18740	Mm.135195	NM_011097	ENSMUSG00000021506	Pitx1	Bft|P-OTX|Potx|Ptx1	paired-like homeodomain transcription factor 1	protein-coding
mm_22385.1	chr2	181156994	181157017	-	1	NA	promoter-TSS (NM_007906)	promoter-TSS (NM_007906)	10	NM_007906	13628	Mm.2645	NM_007906	ENSMUSG00000016349	Eef1a2	Eef1a|S1|wasted|wst	eukaryotic translation elongation factor 1 alpha 2	protein-coding
mm_7554.1	chr1	124678309	124678312	-	1	NA	Intergenic	MTE2a|LTR|ERVL-MaLR	-632751	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_5989.1	chr1	58504920	58504942	-	1	NA	5' UTR (NM_001271526, exon 1 of 18)	5' UTR (NM_001271526, exon 1 of 18)	178	NM_001271526	18393	Mm.3411	NM_008765	ENSMUSG00000026037	Orc2	AU041563|Orc2l	origin recognition complex, subunit 2	protein-coding
mm_52298.1	chr6	108783250	108783262	+	1	NA	exon (NM_026011, exon 1 of 7)	exon (NM_026011, exon 1 of 7)	197	NM_026011	67166	Mm.271178	NM_026011	ENSMUSG00000030105	Arl8b	2610313E07Rik|3100002J04Rik|Arl10c|gie1	ADP-ribosylation factor-like 8B	protein-coding
mm_100584.1	chr11	120948494	120948533	+	1	NA	promoter-TSS (NM_001038654)	promoter-TSS (NM_001038654)	29	NM_030696	80879	Mm.28632	NM_030696	ENSMUSG00000025161	Slc16a3	Mct3|Mct4	solute carrier family 16 (monocarboxylic acid transporters), member 3	protein-coding
mm_55094.1	chr6	49264015	49264060	-	1	NA	promoter-TSS (NM_198102)	promoter-TSS (NM_198102)	15	NM_001347209	101214	Mm.196598	NM_198102	ENSMUSG00000029817	Tra2a	1500010G04Rik|AL022798|G430041M01Rik|mAWMS1	transformer 2 alpha homolog (Drosophila)	protein-coding
mm_33536.1	chr4	130932557	130932612	+	1	NA	intron (NM_010686, intron 7 of 7)	(TCCA)n|Simple_repeat|Simple_repeat	-11801	NM_010769	17180	Mm.271796	NM_010769	ENSMUSG00000040533	Matn1	CMP|Crtm|Mat1|matrilin-1	matrilin 1, cartilage matrix protein	protein-coding
mm_158113.1	chrX	102189311	102189338	-	1	NA	promoter-TSS (NM_009094)	promoter-TSS (NM_009094)	67	NM_009094	20102	Mm.66	NM_009094	ENSMUSG00000031320	Rps4x	Rps4|Rps4-1	ribosomal protein S4, X-linked	protein-coding
mm_122078.1	chr14	30606698	30606713	-	1	NA	intron (NM_011103, intron 6 of 17)	intron (NM_011103, intron 6 of 17)	3605	NM_001310682	18753	Mm.2314	NM_011103	ENSMUSG00000021948	Prkcd	AI385711|D14Ertd420e|PKC[d]|PKCdelta|Pkcd	protein kinase C, delta	protein-coding
mm_29614.1	chr3	121277186	121277198	-	1	NA	Intergenic	Intergenic	-13876	NM_178936	99887	Mm.26088	NM_178936	ENSMUSG00000028132	Tmem56	4930577M16Rik|AU018104|AW109744|C730036B01Rik	transmembrane protein 56	protein-coding
mm_122186.1	chr14	31637739	31637744	-	1	NA	intron (NM_019975, intron 2 of 16)	intron (NM_019975, intron 2 of 16)	3224	NM_019975	56794	Mm.38887	NM_019975	ENSMUSG00000021884	Hacl1	1600020H07Rik|Hpcl|Phyh2	2-hydroxyacyl-CoA lyase 1	protein-coding
mm_122559.1	chr14	49245390	49245441	-	1	NA	promoter-TSS (NM_025956)	promoter-TSS (NM_025956)	13	NM_025956	67082	Mm.87439	NM_025956	ENSMUSG00000021850	1700011H14Rik	-	RIKEN cDNA 1700011H14 gene	protein-coding
mm_108409.1	chr12	81780285	81780303	+	1	NA	intron (NM_001174107, intron 1 of 10)	intron (NM_001174107, intron 1 of 10)	876	NM_177395	338372	Mm.35284	NM_177395	ENSMUSG00000042724	Map3k9	E130314H24Rik|Mlk1|Prke1	mitogen-activated protein kinase kinase kinase 9	protein-coding
mm_147943.1	chr18	66212351	66212354	-	1	NA	intron (NM_178793, intron 2 of 10)	intron (NM_178793, intron 2 of 10)	6981	NR_030467	751558		NR_030467	ENSMUSG00000076147	Mir694	Mirn694|mir-694|mmu-mir-694	microRNA 694	ncRNA
mm_13519.1	chr2	110003567	110003571	+	1	NA	intron (NM_172671, intron 12 of 17)	intron (NM_172671, intron 12 of 17)	-14248	NM_026613	68201	Mm.181767	NM_026613	ENSMUSG00000027160	Ccdc34	2810027O19Rik|4930522P10Rik|AI596202	coiled-coil domain containing 34	protein-coding
mm_132923.1	chr16	49791160	49791169	+	1	NA	Intergenic	Intergenic	-64490	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_165262.1	chr2	73561115	73561121	+	1	NA	Intergenic	Intergenic	19220	NM_007389	11435	Mm.4583	NM_007389	ENSMUSG00000027107	Chrna1	AI385656|AI608266|Achr-1|Acra	cholinergic receptor, nicotinic, alpha polypeptide 1 (muscle)	protein-coding
mm_161014.1	chr11	119229051	119229051	+	1	NA	promoter-TSS (NM_172443)	promoter-TSS (NM_172443)	479	NM_175430	207607	Mm.189885	NM_175430	ENSMUSG00000039963	Ccdc40	B930008I02Rik	coiled-coil domain containing 40	protein-coding
mm_47009.1	chr5	115474591	115474600	-	1	NA	exon (NM_011107, exon 4 of 4)	exon (NM_011107, exon 4 of 4)	8329	NM_011107	18778	Mm.20190	NM_011107	ENSMUSG00000029522	Pla2g1b	Pla2a|sPLA2IB	phospholipase A2, group IB, pancreas	protein-coding
mm_97997.1	chr11	84129758	84129784	+	1	NA	promoter-TSS (NM_172562)	promoter-TSS (NM_172562)	-203	NM_172562	217031	Mm.45159	NM_172562	ENSMUSG00000018651	Tada2a	AV319371|D030022J10Rik|Tada2l	transcriptional adaptor 2A	protein-coding
mm_129948.1	chr15	84987959	84988018	-	1	NA	promoter-TSS (NM_001033273)	promoter-TSS (NM_001033273)	-17	NM_001033273	223739	Mm.323925	NM_001033273	ENSMUSG00000036046	5031439G07Rik	AW554572|mKIAA0930	RIKEN cDNA 5031439G07 gene	protein-coding
mm_23538.1	chr3	61002787	61002811	+	1	NA	promoter-TSS (NM_001282016)	promoter-TSS (NM_001282016)	14	NM_001282016	18441	Mm.281452	NM_008772	ENSMUSG00000027765	P2ry1	P2Y1	purinergic receptor P2Y, G-protein coupled 1	protein-coding
mm_129631.1	chr15	80228429	80228440	-	1	NA	Intergenic	Intergenic	-5646	NM_178719	239555	Mm.307163	NM_178719	ENSMUSG00000022412	Mief1	A230016E22|AI452372|Smcr7l	mitochondrial elongation factor 1	protein-coding
mm_79766.1	chr9	62783521	62783539	+	1	NA	3' UTR (NM_176922, exon 30 of 30)	3' UTR (NM_176922, exon 30 of 30)	28118	NM_010193	14155	Mm.24069	NM_010193	ENSMUSG00000032244	Fem1b	mKIAA0396	feminization 1 homolog b (C. elegans)	protein-coding
mm_128962.1	chr15	74818723	74818735	-	1	NA	promoter-TSS (NM_010416)	promoter-TSS (NM_010416)	86	NM_001177524	625599	Mm.390785	NM_001177524	ENSMUSG00000068349	Gml	EG625599|HemT	glycosylphosphatidylinositol anchored molecule like	protein-coding
mm_80829.1	chr9	96905396	96905404	+	1	NA	Intergenic	Intergenic	-15926	NM_001289645	235534	Mm.233031	NM_153420	ENSMUSG00000043587	Pxylp1	9430094M07Rik|Acpl2|BB177120|C130099A20Rik	2-phosphoxylose phosphatase 1	protein-coding
mm_8596.1	chr1	156032949	156032978	-	1	NA	intron (NM_001160018, intron 2 of 9)	intron (NM_001160018, intron 2 of 9)	1854	NM_001160019	208263	Mm.211654	NM_144791	ENSMUSG00000026466	Tor1aip1	LAP1|Lap1B	torsin A interacting protein 1	protein-coding
mm_161863.1	chr18	32815373	32815373	+	1	NA	promoter-TSS (NM_021367)	promoter-TSS (NM_021367)	-10	NM_021367	53603	Mm.143716	NM_021367	ENSMUSG00000024379	Tslp	-	thymic stromal lymphopoietin	protein-coding
mm_149777.1	chr19	23133810	23133816	+	1	NA	Intergenic	Intergenic	-7413	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_11249.1	chr2	29890556	29890556	+	1	NA	intron (NM_013615, intron 1 of 16)	CpG	493	NM_013615	18286	Mm.330116	NM_013615	ENSMUSG00000026790	Odf2	AI848335|MMTEST29	outer dense fiber of sperm tails 2	protein-coding
mm_151900.1	chr19	5799219	5799230	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	-3243	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_45114.1	chr5	45639294	45639311	-	1	NA	promoter-TSS (NR_102378)	promoter-TSS (NR_102378)	27	NR_102378	319251	Mm.402857	NR_102378	ENSMUSG00000097825	9630001P10Rik	-	RIKEN cDNA 9630001P10 gene	ncRNA
mm_91611.1	chr10	41490336	41490368	-	1	NA	promoter-TSS (NM_009213)	promoter-TSS (NM_009213)	-12	NM_009213	20598	Mm.953	NM_009213	ENSMUSG00000019822	Smpd2	AW108287|nSMase|nSMase1	sphingomyelin phosphodiesterase 2, neutral	protein-coding
mm_19003.1	chr2	76872866	76872879	-	1	NA	exon (NM_011652, exon 99 of 313)	exon (NM_011652, exon 99 of 313)	109675	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_82730.1	chr9	25151716	25151757	-	1	NA	promoter-TSS (NM_020586)	promoter-TSS (NM_020586)	45	NM_020586	80517	Mm.142843	NM_020586	ENSMUSG00000008429	Herpud2	5031400M07Rik|AB041580	HERPUD family member 2	protein-coding
mm_125665.1	chr15	65787101	65787117	+	1	NA	promoter-TSS (NM_133766)	promoter-TSS (NM_133766)	68	NM_133766	76740	Mm.260647	NM_133766	ENSMUSG00000015002	Efr3a	A130089M23Rik|BB071175|C76891|C920006C10Rik|D030063F01Rik|mKIAA0143	EFR3 homolog A	protein-coding
mm_56207.1	chr6	89258247	89258277	-	1	NA	Intergenic	Intergenic	27463	NR_131021	75131	Mm.391482	NR_131021	ENSMUSG00000107622	4930512J16Rik	-	RIKEN cDNA 4930512J16 gene	ncRNA
mm_109933.1	chr12	10900314	10900318	-	1	NA	Intergenic	Intergenic	-147497	NR_045860	71457	Mm.95280	NR_045860		7420701I03Rik	-	RIKEN cDNA 7420701I03 gene	ncRNA
mm_47743.1	chr5	130255344	130255378	-	1	NA	promoter-TSS (NM_178897)	promoter-TSS (NM_178897)	169	NM_023248	66711	Mm.280484	NM_023248	ENSMUSG00000025337	Sbds	4733401P19Rik|AI836084|CGI-97|SDS	Shwachman-Bodian-Diamond syndrome homolog (human)	protein-coding
mm_54851.1	chr6	42591898	42591907	-	1	NA	exon (NM_203396, exon 4 of 7)	exon (NM_203396, exon 4 of 7)	5470	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_140041.1	chr17	74489479	74489491	+	1	NA	promoter-TSS (NM_026417)	promoter-TSS (NM_026417)	-8	NM_026417	67864	Mm.41891	NM_026417	ENSMUSG00000024072	Yipf4	2310034L04Rik	Yip1 domain family, member 4	protein-coding
mm_123881.1	chr14	72709535	72709549	-	1	NA	intron (NM_207636, intron 1 of 25)	CpG	461	NM_207636	319448	Mm.205421	NM_207636	ENSMUSG00000033487	Fndc3a	1700094E19Rik|D14Ertd453e|F730017H24Rik|Fndc3|sys	fibronectin type III domain containing 3A	protein-coding
mm_63921.1	chr7	139330803	139330808	+	1	NA	Intergenic	RMER19C|LTR|ERVK	-58304	NM_183144	212111	Mm.28308	NM_183144	ENSMUSG00000025477	Inpp5a	-	inositol polyphosphate-5-phosphatase A	protein-coding
mm_98379.1	chr11	94081329	94081374	+	1	NA	exon (NM_001199205, exon 6 of 27)	exon (NM_001199205, exon 6 of 27)	37146	NM_001025429	70834	Mm.260737	NM_027569	ENSMUSG00000020859	Spag9	3110018C07Rik|4733401I23Rik|4831406C20Rik|AW552012|JLP|JSAP2|JSAP2a|Jip4|Mapk8ip4|syd1	sperm associated antigen 9	protein-coding
mm_116008.1	chr13	24613615	24613623	-	1	NA	promoter-TSS (NM_001286101)	promoter-TSS (NM_001286101)	-987	NM_001286101	193385	Mm.217319	NM_029679	ENSMUSG00000036006	Fam65b	-	family with sequence similarity 65, member B	protein-coding
mm_86331.1	chr9	123071314	123071316	-	1	NA	TTS (NM_026917)	TTS (NM_026917)	36574	NM_177911	331046	Mm.195309	NM_177911	ENSMUSG00000025787	Tgm4	9530008N10Rik|Eapa1|TGP	transglutaminase 4 (prostate)	protein-coding
mm_125082.1	chr15	26309040	26309055	+	1	NA	promoter-TSS (NM_001310774)	promoter-TSS (NM_001310774)	-1	NM_177597	211147	Mm.54257	NM_177597	ENSMUSG00000022269	March11	9630025C22	membrane-associated ring finger (C3HC4) 11	protein-coding
mm_119344.1	chr14	41104319	41104334	+	1	NA	promoter-TSS (NM_133653)	promoter-TSS (NM_133653)	-707	NM_133653	11720	Mm.14064	NM_133653	ENSMUSG00000037798	Mat1a	AI046368|AdoMet|Ams|MAT|MATA1|SAMS|SAMS1	methionine adenosyltransferase I, alpha	protein-coding
mm_128705.1	chr15	63649120	63649129	-	1	NA	Intergenic	(A)n|Simple_repeat|Simple_repeat	159615	NM_031378	83492	Mm.335619	NM_031378	ENSMUSG00000079025	Gsdmc	Gsdmc1|Mlze	gasdermin C	protein-coding
mm_117727.1	chr13	95531799	95531802	-	1	NA	Intergenic	Intergenic	-6560	NM_007974	14063	Mm.1614	NM_007974	ENSMUSG00000021678	F2rl1	Gpcr11|PAR-2|Par2	coagulation factor II (thrombin) receptor-like 1	protein-coding
mm_50672.1	chr6	51544588	51544609	+	1	NA	promoter-TSS (NM_001127348)	promoter-TSS (NM_001127348)	75	NM_001127348	71982	Mm.294166	NM_028035	ENSMUSG00000038301	Snx10	2410004M09Rik	sorting nexin 10	protein-coding
mm_59917.1	chr7	30419615	30419665	+	1	NA	intron (NM_011827, intron 1 of 3)	intron (NM_011827, intron 1 of 3)	214	NM_011827	23900	Mm.379050	NM_011827	ENSMUSG00000064109	Hcst	DAP10|KAP10	hematopoietic cell signal transducer	protein-coding
mm_48880.1	chr5	151127574	151127597	-	1	NA	intron (NM_146258, intron 1 of 13)	intron (NM_146258, intron 1 of 13)	62608	NM_001163493	243362	Mm.209272	NM_146258	ENSMUSG00000016128	Stard13	DLC2|GT650	StAR-related lipid transfer (START) domain containing 13	protein-coding
mm_85712.1	chr9	108190467	108190483	-	1	NA	promoter-TSS (NM_007567)	promoter-TSS (NM_007567)	-92	NM_007567	12217	Mm.20425	NM_007567	ENSMUSG00000032589	Bsn	-	bassoon	protein-coding
mm_14148.1	chr2	126552905	126552915	+	1	NA	promoter-TSS (NM_011978)	promoter-TSS (NM_011978)	-114	NM_011978	26458	Mm.290044	NM_011978	ENSMUSG00000027359	Slc27a2	ACSVL1|FATP2|VLCS|Vlac|Vlacs	solute carrier family 27 (fatty acid transporter), member 2	protein-coding
mm_6616.1	chr1	75506414	75506424	-	1	NA	promoter-TSS (NM_178884)	promoter-TSS (NM_178884)	33	NM_178884	98733	Mm.236454	NM_178884	ENSMUSG00000026211	Obsl1	AW822216	obscurin-like 1	protein-coding
mm_10228.1	chr2	6322787	6322860	+	1	NA	promoter-TSS (NM_001080548)	promoter-TSS (NM_001080548)	66	NM_001080548	98910	Mm.40673	NM_181399	ENSMUSG00000039046	Usp6nl	AI316785|RNTRE|TRE2NL|mKIAA0019	USP6 N-terminal like	protein-coding
mm_12198.1	chr2	65845736	65845744	+	1	NA	promoter-TSS (NM_153409)	promoter-TSS (NM_153409)	-27	NM_001290666	77771	Mm.102025	NM_153409	ENSMUSG00000044647	Csrnp3	A330102K23Rik|CSRNP-3|Csnrp3|Mbu1|taip-2	cysteine-serine-rich nuclear protein 3	protein-coding
mm_109349.1	chr12	109606788	109606791	+	1	NA	intron (NR_028261, intron 2 of 20)	intron (NR_028261, intron 2 of 20)	2844	NR_028261	75745	Mm.293263	NR_028261		Rian	5530401N18Rik|C130089L09Rik|Meg8	RNA imprinted and accumulated in nucleus	ncRNA
mm_41163.1	chr5	87932446	87932454	+	1	NA	TTS (NM_007786)	TTS (NM_007786)	6817	NM_007786	12994	Mm.296303	NM_007786	ENSMUSG00000001622	Csn3	AW208918|CSN10|Csnk	casein kappa	protein-coding
mm_162658.1	chr10	4358629	4358646	+	1	NA	3' UTR (NM_031185, exon 4 of 4)	3' UTR (NM_031185, exon 4 of 4)	29471	NM_001033466	381990	Mm.262466	NM_001033466	ENSMUSG00000075327	Zbtb2	Gm1103	zinc finger and BTB domain containing 2	protein-coding
mm_34964.1	chr4	156008639	156008651	+	1	NA	intron (NM_001302468, intron 4 of 6)	intron (NM_001302468, intron 4 of 6)	-5050	NM_011659	22163	Mm.13885	NM_011659	ENSMUSG00000029075	Tnfrsf4	ACT35|CD134|Ly-70|Ox40|TXGP1L|Txgp1	tumor necrosis factor receptor superfamily, member 4	protein-coding
mm_40215.1	chr5	37050909	37050922	+	1	NA	promoter-TSS (NM_178394)	promoter-TSS (NM_178394)	58	NM_178394	76071	Mm.85280	NM_178394	ENSMUSG00000063646	Jakmip1	5830437M04Rik|C330021K24Rik|Gababrbp|Marlin-1	janus kinase and microtubule interacting protein 1	protein-coding
mm_156318.1	chrX	137038115	137038127	+	1	NA	intron (NM_001082412, intron 1 of 6)	CpG	181	NM_001082412	67062	Mm.276518	NM_001082412	ENSMUSG00000044348	Slc25a53	2310046F18Rik|2810402A17Rik|AI448995|AI841128|Mcart6	solute carrier family 25, member 53	protein-coding
mm_2503.1	chr1	106194440	106194442	+	1	NA	intron (NM_133821, intron 1 of 16)	intron (NM_133821, intron 1 of 16)	22572	NM_133821	98432	Mm.24115	NM_133821	ENSMUSG00000044340	Phlpp1	AI836256|Phlpp|Plekhe1|SCOP|mKIAA0606	PH domain and leucine rich repeat protein phosphatase 1	protein-coding
mm_49654.1	chr6	31113771	31113780	+	1	NA	intron (NR_110471, intron 3 of 3)	intron (NR_110471, intron 3 of 3)	-50682	NR_029532	387223		NR_029532	ENSMUSG00000065604	Mir29b-1	Mirn29b|Mirn29b-1|mir-29b-1	microRNA 29b-1	ncRNA
mm_85388.1	chr9	103228451	103228457	-	1	NA	intron (NM_133977, intron 1 of 16)	intron (NM_133977, intron 1 of 16)	1832	NM_133977	22041	Mm.37214	NM_133977	ENSMUSG00000032554	Trf	AI266983|Cd176|HP|Tf|Tfn|hpx	transferrin	protein-coding
mm_123768.1	chr14	70211894	70211921	-	1	NA	Intergenic	Intergenic	-4236	NM_011366	20410	Mm.5068	NM_011366	ENSMUSG00000022091	Sorbs3	SCAM-1|SH3P3|Sh3d4|vinexin-g	sorbin and SH3 domain containing 3	protein-coding
mm_86720.1	chr10	19015698	19015707	+	1	NA	promoter-TSS (NM_009397)	promoter-TSS (NM_009397)	-292	NM_009397	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_148429.1	chr19	3941895	3941911	+	1	NA	exon (NM_019449, exon 5 of 11)	exon (NM_019449, exon 5 of 11)	6717	NM_001161428	54445	Mm.262094	NM_019449	ENSMUSG00000036908	Unc93b1	Unc-93B1|Unc93b	unc-93 homolog B1 (C. elegans)	protein-coding
mm_76152.1	chr8	82353551	82353584	-	1	NA	intron (NM_008357, intron 2 of 7)	intron (NM_008357, intron 2 of 7)	49019	NM_001254747	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_17033.1	chr2	20654601	20654606	-	1	NA	intron (NM_029895, intron 3 of 18)	AT_rich|Low_complexity|Low_complexity	135090	NM_001177631	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding
mm_25097.1	chr3	101131050	101131065	+	1	NA	Intergenic	Intergenic	-20891	NM_011197	19221	Mm.24807	NM_011197	ENSMUSG00000027864	Ptgfrn	4833445A08Rik|AU042434|CD9P-1|FPRP|Trim45	prostaglandin F2 receptor negative regulator	protein-coding
mm_3657.1	chr1	153116570	153116573	+	1	NA	3' UTR (NM_175460, exon 11 of 11)	3' UTR (NM_175460, exon 11 of 11)	69876	NM_008485	16782	Mm.329272	NM_008485	ENSMUSG00000026479	Lamc2	AA589349	laminin, gamma 2	protein-coding
mm_53540.1	chr6	136808249	136808261	+	1	NA	promoter-TSS (NM_177688)	promoter-TSS (NM_177688)	7	NM_177688	232440	Mm.154564	NM_177688	ENSMUSG00000060032	H2afj	E130307C13	H2A histone family, member J	protein-coding
mm_74812.1	chr8	22671656	22671679	-	1	NA	exon (NM_010546, exon 12 of 21)	exon (NM_010546, exon 12 of 21)	-18230	NM_011130	18970	Mm.123211	NM_011130	ENSMUSG00000031536	Polb	A430088C08Rik	polymerase (DNA directed), beta	protein-coding
mm_25267.1	chr3	104794083	104794110	+	1	NA	TTS (NM_008619)	TTS (NM_008619)	5062	NM_007484	11853	Mm.262	NM_007484	ENSMUSG00000002233	Rhoc	AI324259|Arh9|Arhc	ras homolog family member C	protein-coding
mm_7269.1	chr1	96556719	96556728	-	1	NA	Intergenic	RMER5|LTR|ERV1	105850	NR_040478	75159	Mm.243854	NR_040478	ENSMUSG00000100589	4930533P14Rik	-	RIKEN cDNA 4930533P14 gene	ncRNA
mm_147163.1	chr18	36726109	36726116	-	1	NA	exon (NM_009841, exon 2 of 2)	exon (NM_009841, exon 2 of 2)	703	NM_009841	12475	Mm.3460	NM_009841	ENSMUSG00000051439	Cd14	-	CD14 antigen	protein-coding
mm_71758.1	chr8	66386189	66386214	+	1	NA	promoter-TSS (NM_001166375)	promoter-TSS (NM_001166375)	-100	NM_001166375	72925	Mm.380457	NM_175188	ENSMUSG00000036469	March1	2900024D24Rik|BB085186	membrane-associated ring finger (C3HC4) 1	protein-coding
mm_173124.1	chrX	166854182	166854190	+	1	NA	Intergenic	Intergenic	192161	NR_046015	382255	Mm.336320	NR_046015	ENSMUSG00000086860	Gm1720	-	predicted gene 1720	ncRNA
mm_91370.1	chr10	29535788	29535801	-	1	NA	promoter-TSS (NM_028351)	promoter-TSS (NM_028351)	73	NM_028351	72780	Mm.45191	NM_028351	ENSMUSG00000019880	Rspo3	2810459H04Rik|AW742308|Cristin1|Thsd2	R-spondin 3	protein-coding
mm_98193.1	chr11	87794207	87794212	+	1	NA	intron (NM_010824, intron 1 of 13)	intron (NM_010824, intron 1 of 13)	425	NM_010824	17523	Mm.4668	NM_010824	ENSMUSG00000009350	Mpo	mKIAA4033	myeloperoxidase	protein-coding
mm_14755.1	chr2	144714784	144714794	+	1	NA	intron (NM_025314, intron 4 of 5)	RMER13B|LTR|ERVK	-108877	NM_025490	66328	Mm.45377	NM_025490	ENSMUSG00000027431	Scp2d1	1700010M22Rik	SCP2 sterol-binding domain containing 1	protein-coding
mm_68666.1	chr7	118855985	118856014	-	1	NA	promoter-TSS (NM_001168218)	promoter-TSS (NM_001168218)	-1	NM_023197	66356	Mm.482278	NM_023197	ENSMUSG00000030980	Knop1	2310008H09Rik|Tsg118	lysine rich nucleolar protein 1	protein-coding
mm_160125.1	chr7	28371467	28371467	-	1	NA	intron (NM_138752, intron 1 of 18)	intron (NM_138752, intron 1 of 18)	1195	NM_138752	101497	Mm.235700	NM_138752	ENSMUSG00000037552	Plekhg2	AI194308|Clg|Cslg	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	protein-coding
mm_121946.1	chr14	24176667	24176667	-	1	NA	exon (NM_027726, exon 6 of 31)	exon (NM_027726, exon 6 of 31)	69253	NM_001163513	71228	Mm.68971	NM_027726	ENSMUSG00000021782	Dlg5	4933429D20Rik|T25557|mKIAA0583	discs, large homolog 5 (Drosophila)	protein-coding
mm_132518.1	chr16	37580275	37580289	+	1	NA	non-coding (NR_027778, exon 1 of 13)	non-coding (NR_027778, exon 1 of 13)	129	NM_013547	15233	Mm.157442	NM_013547	ENSMUSG00000022821	Hgd	Hgo|aku	homogentisate 1, 2-dioxygenase	protein-coding
mm_71548.1	chr8	47853850	47853850	+	1	NA	intron (NM_133791, intron 16 of 22)	intron (NM_133791, intron 16 of 22)	29368	NM_029383	75677	Mm.390033	NM_029383	ENSMUSG00000038064	Cldn22	2210404A22Rik|5330431C14Rik|9530051B05Rik	claudin 22	protein-coding
mm_6821.1	chr1	84194350	84194362	-	1	NA	intron (NM_001003948, intron 1 of 2)	B4|SINE|B4	24605	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_596.1	chr1	39555473	39555485	+	1	NA	exon (NM_001033135, exon 6 of 7)	exon (NM_001033135, exon 6 of 7)	-6639	NR_028555	100217461		NR_028555	ENSMUSG00000077704	Snord89	MBII-289	small nucleolar RNA, C/D box 89	snoRNA
mm_137549.1	chr17	27557899	27557915	+	1	NA	intron (NM_001166537, intron 1 of 4)	CpG-6152	1254	NM_001166477	111241	Mm.426212	NM_001166476	ENSMUSG00000078249	Hmga1-rs1	ENSMUSG00000041059|Hmgi-rs1	high mobility group AT-hook I, related sequence 1	protein-coding
mm_73393.1	chr8	105708319	105708326	+	1	NA	promoter-TSS (NM_198299)	promoter-TSS (NM_198299)	19	NM_027655	71046	Mm.280888	NM_027655	ENSMUSG00000013158	4933405L10Rik	-	RIKEN cDNA 4933405L10 gene	protein-coding
mm_121836.1	chr14	20544688	20544697	-	1	NA	intron (NM_001310427, intron 1 of 12)	B2_Mm1t|SINE|B2	-1601	NR_033571	75602	Mm.437061	NR_033571	ENSMUSG00000084925	1810062O18Rik	-	RIKEN cDNA 1810062O18 gene	ncRNA
mm_104287.1	chr11	90130236	90130258	-	1	NA	Intergenic	Intergenic	99899	NM_026433	67888	Mm.212428	NM_026433	ENSMUSG00000069763	Tmem100	1810057C19Rik|AV011897	transmembrane protein 100	protein-coding
mm_13309.1	chr2	102658727	102658742	+	1	NA	promoter-TSS (NM_001077514)	promoter-TSS (NM_001077514)	51	NM_001077514	20511	Mm.267547	NM_011393	ENSMUSG00000005089	Slc1a2	1700091C19Rik|2900019G14Rik|AI159670|Eaat2|GLT-1|GLT1|MGLT1	solute carrier family 1 (glial high affinity glutamate transporter), member 2	protein-coding
mm_109957.1	chr12	12491874	12491878	-	1	NA	Intergenic	Intergenic	-99401	NR_045829	70858	Mm.410838	NR_045829		4921511I17Rik	-	RIKEN cDNA 4921511I17 gene	ncRNA
mm_10038.1	chr1	192855684	192855715	-	1	NA	promoter-TSS (NM_198247)	promoter-TSS (NM_198247)	53	NM_198247	214791	Mm.22806	NM_198247	ENSMUSG00000016262	Sertad4	4833404A09|C130018M11Rik	SERTA domain containing 4	protein-coding
mm_138887.1	chr17	43455438	43455449	+	1	NA	3' UTR (NM_001081178, exon 21 of 21)	3' UTR (NM_001081178, exon 21 of 21)	47330	NM_008585	17287	Mm.5346	NM_008585	ENSMUSG00000023914	Mep1a	AI098089|AW107200|Mep-1|Mep-1a|Mep1	meprin 1 alpha	protein-coding
mm_63388.1	chr7	127232885	127232904	+	1	NA	promoter-TSS (NM_146201)	promoter-TSS (NM_146201)	236	NR_030674	100043580	Mm.482209	NR_030674	ENSMUSG00000000486	Gm4532	-	predicted gene 4532	ncRNA
mm_67174.1	chr7	73558488	73558534	-	1	NA	promoter-TSS (NR_037569)	promoter-TSS (NR_037569)	-116	NR_037569	69170	Mm.34539	NR_037569	ENSMUSG00000101970	1810026B05Rik	-	RIKEN cDNA 1810026B05 gene	ncRNA
mm_20534.1	chr2	131041358	131041368	-	1	NA	promoter-TSS (NR_105969)	promoter-TSS (NR_105969)	-965	NR_105969	102465606		NR_105969	ENSMUSG00000098686	Mir6973b	Gm27815|mmu-mir-6973b	microRNA 6973b	ncRNA
mm_163117.1	chr11	75438369	75438372	+	1	NA	intron (NM_008878, intron 2 of 9)	intron (NM_008878, intron 2 of 9)	1131	NM_008878	18816	Mm.279733	NM_008878	ENSMUSG00000038224	Serpinf2	AI747498|Pli|Serpimf2	serine (or cysteine) peptidase inhibitor, clade F, member 2	protein-coding
mm_8359.1	chr1	150454592	150454609	-	1	NA	exon (NM_021400, exon 7 of 13)	exon (NM_021400, exon 7 of 13)	11565	NM_021400	96875	Mm.174256	NM_021400	ENSMUSG00000006014	Prg4	CACP|DOL54|JCAP|MSF|SZP|lubricin	proteoglycan 4 (megakaryocyte stimulating factor, articular superficial zone protein)	protein-coding
mm_166101.1	chr4	145246843	145246843	-	1	NA	promoter-TSS (NM_011610)	promoter-TSS (NM_011610)	27	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_99931.1	chr11	110997545	110997552	+	1	NA	promoter-TSS (NM_001252209)	promoter-TSS (NM_001252209)	61	NM_001252209	16517	Mm.30176	NM_010604	ENSMUSG00000051497	Kcnj16	6430410F18Rik|AI132396|Kir5.1	potassium inwardly-rectifying channel, subfamily J, member 16	protein-coding
mm_92755.1	chr10	81026186	81026204	-	1	NA	promoter-TSS (NM_145217)	promoter-TSS (NM_145217)	-818	NM_145217	208666	Mm.44995	NM_145217	ENSMUSG00000043670	Diras1	Di-Ras1|Gbts1|RIG	DIRAS family, GTP-binding RAS-like 1	protein-coding
mm_3582.1	chr1	151136345	151136347	+	1	NA	Intergenic	Intergenic	-1688	NR_038011	402734	Mm.337666	NR_038011		C730036E19Rik	lncLSTR	RIKEN cDNA C730036E19 gene	ncRNA
mm_63864.1	chr7	135684214	135684225	+	1	NA	3' UTR (NM_011212, exon 21 of 21)	3' UTR (NM_011212, exon 21 of 21)	-31905	NR_015548	67765	Mm.445272	NR_015548	ENSMUSG00000097471	5830432E09Rik	-	RIKEN cDNA 5830432E09 gene	ncRNA
mm_76637.1	chr8	92355886	92355915	-	1	NA	non-coding (NR_033641, exon 1 of 7)	non-coding (NR_033641, exon 1 of 7)	220	NR_110452	71296	Mm.86664	NR_033641	ENSMUSG00000031736	Crnde	4933436C20Rik	colorectal neoplasia differentially expressed (non-protein coding)	ncRNA
mm_3325.1	chr1	137924893	137924904	+	1	NA	Intergenic	Intergenic	-41557	NR_029795	735252		NR_029795	ENSMUSG00000065565	Mir181a-1	Mirn181a-1|Mirn213|miR-213|mir-181a-1|mmu-mir-213	microRNA 181a-1	ncRNA
mm_46736.1	chr5	110810044	110810062	-	1	NA	promoter-TSS (NM_009469)	promoter-TSS (NM_009469)	28	NM_009469	22241	Mm.271898	NM_009469	ENSMUSG00000029512	Ulk1	AU041434|Unc51.1|mKIAA0722	unc-51 like kinase 1	protein-coding
mm_22803.1	chr3	26637619	26637637	+	1	NA	promoter-TSS (NM_029150)	promoter-TSS (NM_029150)	-3	NM_029150	70862	Mm.330943	NM_027583	ENSMUSG00000039335	Spata16	4921511F01Rik|4930503K02Rik|Nyd-sp12	spermatogenesis associated 16	protein-coding
mm_57379.1	chr6	124814152	124814168	-	1	NA	TTS (NM_001326594)	TTS (NM_001326594)	136	NM_009415	21991	Mm.4222	NM_009415	ENSMUSG00000023456	Tpi1	AI255506|Tpi|Tpi-1	triosephosphate isomerase 1	protein-coding
mm_64271.1	chr7	141805650	141805660	+	1	NA	exon (NM_010844, exon 30 of 50)	exon (NM_010844, exon 30 of 50)	16644	NM_010844	17833	Mm.334332	NM_010844	ENSMUSG00000037974	Muc5ac	2210005L13Rik|MGM	mucin 5, subtypes A and C, tracheobronchial/gastric	protein-coding
mm_143404.1	chr17	70761394	70761406	-	1	NA	exon (NM_177639, exon 7 of 12)	exon (NM_177639, exon 7 of 12)	85377	NM_001164077	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_151541.1	chr19	59171745	59171749	+	1	NA	Intergenic	CpG	-1718	NM_009501	22326	Mm.23801	NM_009501	ENSMUSG00000006270	Vax1	-	ventral anterior homeobox 1	protein-coding
mm_117396.1	chr13	73689071	73689079	-	1	NA	exon (NM_028878, exon 6 of 12)	exon (NM_028878, exon 6 of 12)	-10751	NM_027780	71390	Mm.105251	NM_027780		Slc6a19os	5430425J12Rik	solute carrier family 6 (neurotransmitter transporter), member 19, opposite strand	protein-coding
mm_8414.1	chr1	152090182	152090209	-	1	NA	5' UTR (NM_197990, exon 1 of 6)	5' UTR (NM_197990, exon 1 of 6)	125	NM_197990	69399	Mm.278031	NM_197990	ENSMUSG00000032666	1700025G04Rik	2610510E02Rik|2900042O04Rik|ENSMUSG00000073540	RIKEN cDNA 1700025G04 gene	protein-coding
mm_23293.1	chr3	52129465	52129470	+	1	NA	Intergenic	RMER17B|LTR|ERVK	-24461	NM_001004176	433586	Mm.234972	NM_001004176	ENSMUSG00000061143	Maml3	AV234550|BC049812|Mam-2|mKIAA1816	mastermind like 3 (Drosophila)	protein-coding
mm_19849.1	chr2	113749056	113749062	-	1	NA	3' UTR (NM_011824, exon 2 of 2)	3' UTR (NM_011824, exon 2 of 2)	9589	NM_011824	23892	Mm.166318	NM_011824	ENSMUSG00000074934	Grem1	Cktsf1b1|Drm|Grem|ld	gremlin 1, DAN family BMP antagonist	protein-coding
mm_22894.1	chr3	30793034	30793067	+	1	NA	5' UTR (NM_027016, exon 1 of 8)	5' UTR (NM_027016, exon 1 of 8)	174	NM_027016	69276	Mm.26017	NM_027016	ENSMUSG00000027706	Sec62	3100002M17Rik|AI844545|AW545092|Dtrp1|HTP1|Tloc1	SEC62 homolog (S. cerevisiae)	protein-coding
mm_136763.1	chr17	8801743	8801751	+	1	NA	promoter-TSS (NM_011866)	promoter-TSS (NM_011866)	2	NM_011866	23984	Mm.87161	NM_011866	ENSMUSG00000023868	Pde10a	-	phosphodiesterase 10A	protein-coding
mm_81980.1	chr9	121314388	121314393	+	1	NA	Intergenic	Intergenic	-37218	NM_177589	209012	Mm.371804	NM_177589	ENSMUSG00000040936	Ulk4	4932415A06Rik|A730098P15	unc-51-like kinase 4	protein-coding
mm_92065.1	chr10	62527388	62527400	-	1	NA	Intergenic	Intergenic	-19639	NM_011157	19073	Mm.338790	NM_011157	ENSMUSG00000020077	Srgn	Prg|Prg1|Sgc	serglycin	protein-coding
mm_43589.1	chr5	137748967	137748970	+	1	NA	intron (NM_029805, intron 2 of 5)	AT_rich|Low_complexity|Low_complexity	2999	NM_029805	78829	Mm.286399	NM_023910	ENSMUSG00000029723	Tsc22d4	0610009M14Rik|1700023B23Rik|AI415410|Thg-1pit|Tilz2	TSC22 domain family, member 4	protein-coding
mm_28424.1	chr3	90451410	90451484	-	1	NA	intron (NM_008727, intron 20 of 21)	intron (NM_008727, intron 20 of 21)	14419	NM_008727	18160	Mm.4627	NM_008727	ENSMUSG00000027931	Npr1	AI893888|GC-A|NPR-A|NPRA|Pndr	natriuretic peptide receptor 1	protein-coding
mm_166109.1	chr4	147104010	147104038	+	1	NA	Intergenic	Intergenic	-35588	NR_045446	71270	Mm.460830	NR_045446	ENSMUSG00000093617	4933438K21Rik	-	RIKEN cDNA 4933438K21 gene	ncRNA
mm_160619.1	chr9	89623107	89623107	-	1	NA	promoter-TSS (NM_153509)	promoter-TSS (NM_153509)	-121	NM_153509	209743	Mm.242899	NM_153509	ENSMUSG00000039313	AF529169	DD1|Kiaa1024	cDNA sequence AF529169	protein-coding
mm_52694.1	chr6	118880153	118880163	+	1	NA	promoter-TSS (NR_046053)	promoter-TSS (NR_046053)	0	NR_046053	74363	Mm.399403	NR_046053		4931430N09Rik	-	RIKEN cDNA 4931430N09 gene	ncRNA
mm_77998.1	chr9	8900491	8900502	+	1	NA	exon (NM_008829, exon 1 of 8)	exon (NM_008829, exon 1 of 8)	663	NM_008829	18667	Mm.12798	NM_008829	ENSMUSG00000031870	Pgr	9930019P03Rik|BB114106|ENSMUSG00000074510|NR3C3|PR|PR-A|PR-B	progesterone receptor	protein-coding
mm_57731.1	chr6	128961085	128961086	-	1	NA	intron (NR_045009, intron 1 of 1)	RMER17C2|LTR|ERVK	-10075	NM_001168224	70809	Mm.439891	NM_027562	ENSMUSG00000000248	Clec2g	4632413B12Rik|Clr-c|Clr-d|Clrc|Clrd|Clrx|Ddv10|Ocilrp1	C-type lectin domain family 2, member g	protein-coding
mm_123403.1	chr14	63543659	63543683	-	1	NA	5' UTR (NM_177594, exon 1 of 10)	5' UTR (NM_177594, exon 1 of 10)	282	NM_177594	210376	Mm.441613	NM_177594	ENSMUSG00000035078	Mtmr9	9430075G12Rik|AA516943|AF073881|LIP-STYX|MTMR8|mMTMH3	myotubularin related protein 9	protein-coding
mm_64643.1	chr7	4008377	4008393	-	1	NA	3' UTR (NM_178611, exon 7 of 7)	3' UTR (NM_178611, exon 7 of 7)	54819	NM_001302677	52855	Mm.290880	NM_178611	ENSMUSG00000055541	Lair1	5133400O11Rik|BB115266|D7Bwg0421e|Lair-1	leukocyte-associated Ig-like receptor 1	protein-coding
mm_96612.1	chr11	69097763	69097773	+	1	NA	Intergenic	Intergenic	-1188	NM_011065	18626	Mm.7373	NM_011065	ENSMUSG00000020893	Per1	Hftm|Per|m-rigui|mPer1	period circadian clock 1	protein-coding
mm_81418.1	chr9	109055598	109055633	+	1	NA	intron (NM_026381, intron 1 of 3)	intron (NM_026381, intron 1 of 3)	749	NM_026381	66940	Mm.196533	NM_025858	ENSMUSG00000025647	Shisa5	2310008D10Rik|6430628I05Rik|Scotin|mShisa5	shisa family member 5	protein-coding
mm_158982.1	chr1	130740267	130740267	+	1	NA	intron (NM_177604, intron 2 of 3)	intron (NM_177604, intron 2 of 3)	8291	NM_177604	212439	Mm.268547	NM_177604	ENSMUSG00000042510	AA986860	E030025M07|Sarg	expressed sequence AA986860	protein-coding
mm_13793.1	chr2	118900380	118900397	+	1	NA	Intergenic	Intergenic	-1227	NM_001045523	228536	Mm.330487	NM_001045523	ENSMUSG00000040007	Bahd1	AL022997|AW541238|Gm117|mKIAA0945	bromo adjacent homology domain containing 1	protein-coding
mm_21665.1	chr2	164425339	164425360	-	1	NA	3' UTR (NM_011521, exon 5 of 5)	3' UTR (NM_011521, exon 5 of 5)	17839	NM_011521	20971	Mm.3815	NM_011521	ENSMUSG00000017009	Sdc4	AA959608|AW108331|S4|Synd4|ryudocan|syndecan-4	syndecan 4	protein-coding
mm_106098.1	chr11	116206478	116206484	-	1	NA	intron (NM_027107, intron 3 of 3)	intron (NM_027107, intron 3 of 3)	-7436	NM_015729	11430	Mm.356689	NM_015729	ENSMUSG00000020777	Acox1	AOX|Acox|D130055E20Rik|Paox	acyl-Coenzyme A oxidase 1, palmitoyl	protein-coding
mm_142150.1	chr17	36020494	36020509	-	1	NA	promoter-TSS (NM_008207)	promoter-TSS (NM_008207)	59	NM_008207	15042	Mm.439654	NM_008207	ENSMUSG00000053835	H2-T24	H-2T24	histocompatibility 2, T region locus 24	protein-coding
mm_68147.1	chr7	102249455	102249474	-	1	NA	intron (NM_019566, intron 1 of 1)	intron (NM_019566, intron 1 of 1)	654	NM_019566	56212	Mm.259795	NM_019566	ENSMUSG00000073982	Rhog	2810426G09Rik|Arhg|Sid10750	ras homolog family member G	protein-coding
mm_169843.1	chr16	3115729	3115747	-	1	NA	Intergenic	Intergenic	-476660	NM_146860	258859	Mm.377723	NM_146860	ENSMUSG00000051003	Olfr161	MOR131-1|OR912-47M6	olfactory receptor 161	protein-coding
mm_109692.1	chr12	113146312	113146335	+	1	NA	TTS (NM_024223)	TTS (NM_024223)	-5689	NM_007763	12925	Mm.272368	NM_007763	ENSMUSG00000006360	Crip1	CRHP|CRP1|Crip	cysteine-rich protein 1 (intestinal)	protein-coding
mm_94050.1	chr10	128180102	128180112	-	1	NA	5' UTR (NM_001039080, exon 1 of 14)	5' UTR (NM_001039080, exon 1 of 14)	190	NM_001039080	56516	Mm.42247	NM_019711	ENSMUSG00000040043	Rbms2	2610315E04Rik|Scr3	RNA binding motif, single stranded interacting protein 2	protein-coding
mm_132398.1	chr16	35001206	35001221	+	1	NA	3' UTR (NM_139300, exon 32 of 32)	3' UTR (NM_139300, exon 32 of 32)	-21208	NM_023587	70757	Mm.27286	NM_023587	ENSMUSG00000035376	Hacd2	6330408J20Rik|AI255777|AI481689|Hcad2|Ptplb	3-hydroxyacyl-CoA dehydratase 2	protein-coding
mm_60109.1	chr7	35449056	35449111	+	1	NA	promoter-TSS (NM_001199016)	promoter-TSS (NM_001199016)	-9	NM_001199015	30962	Mm.45874	NM_021291	ENSMUSG00000030492	Slc7a9	CSNU3	solute carrier family 7 (cationic amino acid transporter, y+ system), member 9	protein-coding
mm_54519.1	chr6	35539708	35539718	-	1	NA	5' UTR (NM_008098, exon 1 of 4)	5' UTR (NM_008098, exon 1 of 4)	175	NM_008098	14489	Mm.182746	NM_008098	ENSMUSG00000029840	Mtpn	5033418D15Rik|Gcdp|V1	myotrophin	protein-coding
mm_35704.1	chr4	44167889	44167900	-	1	NA	promoter-TSS (NM_175201)	promoter-TSS (NM_175201)	-356	NM_175201	73469	Mm.262859	NM_175201	ENSMUSG00000035696	Rnf38	1700065B19Rik|2610202O07Rik|AA673263|Oip1	ring finger protein 38	protein-coding
mm_159822.1	chr5	123445617	123445617	+	1	NA	exon (NM_177582, exon 9 of 9)	exon (NM_177582, exon 9 of 9)	36484	NM_029594	76399	Mm.75049	NM_029594	ENSMUSG00000029437	Il31	1700013B14Rik	interleukin 31	protein-coding
mm_149474.1	chr19	11747549	11747581	+	1	NA	promoter-TSS (NM_008118)	promoter-TSS (NM_008118)	6	NM_008118	14603	Mm.456	NM_008118	ENSMUSG00000024682	Gif	AV073125	gastric intrinsic factor	protein-coding
mm_69208.1	chr7	127448614	127448660	-	1	NA	intron (NM_175163, intron 1 of 2)	CpG	521	NM_175163	71131	Mm.474533	NM_175163	ENSMUSG00000048921	Zfp689	4933416E05Rik|Znf689	zinc finger protein 689	protein-coding
mm_125187.1	chr15	32268139	32268143	+	1	NA	intron (NM_009154, intron 1 of 22)	intron (NM_009154, intron 1 of 22)	23328	NM_009154	20356	Mm.260374	NM_009154	ENSMUSG00000022231	Sema5a	5930434A13|9130201M22Rik|AI464145|Semaf|semF	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A	protein-coding
mm_83065.1	chr9	37552726	37552741	-	1	NA	promoter-TSS (NM_022029)	promoter-TSS (NM_022029)	12	NM_022029	64011	Mm.335065	NM_022029	ENSMUSG00000053310	Nrgn	0710001B06Rik|AI838505|NG|NG/RC3|Pss1|R75334|RC3	neurogranin	protein-coding
mm_92781.1	chr10	81266907	81266933	-	1	NA	promoter-TSS (NM_025317)	promoter-TSS (NM_025317)	6	NM_025317	66047	Mm.43397	NM_025317	ENSMUSG00000034932	Mrpl54	0610008M19Rik|D10Sut1e	mitochondrial ribosomal protein L54	protein-coding
mm_156459.1	chrX	142832497	142832517	+	1	NA	exon (NM_001199357, exon 5 of 7)	exon (NM_001199357, exon 5 of 7)	93507	NR_030523	723976		NR_030523	ENSMUSG00000076011	Mir652	Mirn652|miRX|mmu-mir-652	microRNA 652	ncRNA
mm_76123.1	chr8	80869157	80869204	-	1	NA	intron (NM_021356, intron 1 of 9)	intron (NM_021356, intron 1 of 9)	11299	NM_021356	14388	Mm.277409	NM_021356	ENSMUSG00000031714	Gab1	AA408973|AW107238	growth factor receptor bound protein 2-associated protein 1	protein-coding
mm_37216.1	chr4	117914702	117914712	-	1	NA	5' UTR (NM_146152, exon 1 of 20)	5' UTR (NM_146152, exon 1 of 20)	292	NM_146152	230673	Mm.287810	NM_146152	ENSMUSG00000033365	Ipo13	Imp13|Kap13|Ranbp13	importin 13	protein-coding
mm_82106.1	chr9	123067474	123067525	+	1	NA	TTS (NM_177911)	TTS (NM_177911)	32758	NM_177911	331046	Mm.195309	NM_177911	ENSMUSG00000025787	Tgm4	9530008N10Rik|Eapa1|TGP	transglutaminase 4 (prostate)	protein-coding
mm_103917.1	chr11	83589342	83589418	-	1	NA	exon (NM_009139, exon 3 of 4)	exon (NM_009139, exon 3 of 4)	3707	NM_009139	20305	Mm.137	NM_009139	ENSMUSG00000018927	Ccl6	MRP-1|Scya6|c10	chemokine (C-C motif) ligand 6	protein-coding
mm_97493.1	chr11	78343438	78343444	+	1	NA	promoter-TSS (NM_011676)	promoter-TSS (NM_011676)	-54	NM_001313985	22248	Mm.284811	NM_011676	ENSMUSG00000002058	Unc119	D11Bhm52|HRG4|MRG4|Rg4|Rtg4|Unc119h	unc-119 lipid binding chaperone	protein-coding
mm_14661.1	chr2	138256531	138256615	+	1	NA	promoter-TSS (NM_001025431)	promoter-TSS (NM_001025431)	-11	NM_001025431	228662	Mm.153405	NM_145534	ENSMUSG00000062098	Btbd3	mKIAA0952	BTB (POZ) domain containing 3	protein-coding
mm_50299.1	chr6	47522333	47522336	+	1	NA	intron (NM_012042, intron 17 of 21)	intron (NM_012042, intron 17 of 21)	68010	NM_012042	26965	Mm.87611	NM_012042	ENSMUSG00000029686	Cul1	-	cullin 1	protein-coding
mm_5638.1	chr1	40439537	40439546	-	1	NA	promoter-TSS (NM_010743)	promoter-TSS (NM_010743)	-88	NM_001025602	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_106535.1	chr11	120575487	120575521	-	1	NA	Intergenic	Intergenic	-2568	NM_011032	18453	Mm.16660	NM_011032	ENSMUSG00000025130	P4hb	ERp59|PDI|Pdia1|Thbp	prolyl 4-hydroxylase, beta polypeptide	protein-coding
mm_112715.1	chr13	19185038	19185048	+	1	NA	Intergenic	Intergenic	210770	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_9725.1	chr1	180193654	180193666	-	1	NA	promoter-TSS (NM_001163290)	promoter-TSS (NM_001163290)	-175	NM_001163290	67426	Mm.38330	NM_023341	ENSMUSG00000026489	Coq8a	4632432J16Rik|AI462003|Adck3|Cabc1|mKIAA0451	coenzyme Q8A	protein-coding
mm_144380.1	chr18	20666444	20666474	+	1	NA	exon (NM_013697, exon 2 of 4)	exon (NM_013697, exon 2 of 4)	1209	NM_013697	22139	Mm.2108	NM_013697	ENSMUSG00000061808	Ttr	AA408768|AI787086|D17860|prealbumin	transthyretin	protein-coding
mm_153388.1	chr19	40382573	40382600	-	1	NA	exon (NM_001034964, exon 4 of 22)	exon (NM_001034964, exon 4 of 22)	19724	NM_001034964	20411	Mm.210815	NM_009166	ENSMUSG00000025006	Sorbs1	2310065E01Rik|9530001P15Rik|CAP|SH3P12|Sh3d5|mKIAA1296	sorbin and SH3 domain containing 1	protein-coding
mm_91850.1	chr10	58675690	58675713	-	1	NA	promoter-TSS (NM_010100)	promoter-TSS (NM_010100)	-5	NM_010100	13608	Mm.174523	NM_010100	ENSMUSG00000003227	Edar	ED1R|ED3|ED5|EDA-A1R|EDA3|dl	ectodysplasin-A receptor	protein-coding
mm_79358.1	chr9	54286333	54286343	+	1	NA	promoter-TSS (NM_177350)	promoter-TSS (NM_177350)	-148	NM_177350	235379	Mm.123549	NM_177350	ENSMUSG00000046167	Gldn	CRG-L2|Clom|Colm|Crgl2|Crlg2	gliomedin	protein-coding
mm_69573.1	chr7	135700905	135700915	-	1	NA	exon (NM_001081117, exon 12 of 14)	exon (NM_001081117, exon 12 of 14)	15469	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_149494.1	chr19	11821823	11821850	+	1	NA	Intergenic	L1_Mur3|LINE|L1	-2433	NM_001025307	20908	Mm.272264	NM_011502	ENSMUSG00000041488	Stx3	Syn-3	syntaxin 3	protein-coding
mm_87115.1	chr10	33256526	33256540	+	1	NA	promoter-TSS (NR_040657)	promoter-TSS (NR_040657)	-176	NR_040657	442820	Mm.490725	NR_040657		D830005E20Rik	-	RIKEN cDNA D830005E20 gene	ncRNA
mm_167873.1	chrX	36872431	36872432	+	1	NA	Intergenic	MLT1E3|LTR|ERVL-MaLR	-1864	NM_001313696	22209	Mm.395649	NM_019668	ENSMUSG00000016308	Ube2a	HHR6A|HR6A|Mhr6a	ubiquitin-conjugating enzyme E2A	protein-coding
mm_171018.1	chr2	83972321	83972338	+	1	NA	Intergenic	CpG	-31103	NM_027964	71861	Mm.116957	NM_027964	ENSMUSG00000034552	Zswim2	1700025P14Rik|4933437F18Rik|MEX	zinc finger SWIM-type containing 2	protein-coding
mm_96827.1	chr11	69997442	69997501	+	1	NA	promoter-TSS (NM_001291127)	promoter-TSS (NM_001291127)	9	NM_001291127	78246	Mm.20805	NM_030064	ENSMUSG00000018572	Phf23	JUNE-1	PHD finger protein 23	protein-coding
mm_9755.1	chr1	180813592	180813605	-	1	NA	promoter-TSS (NM_008210)	promoter-TSS (NM_008210)	7	NM_008210	15078	Mm.138832	NM_008210	ENSMUSG00000060743	H3f3a	H3.3A	H3 histone, family 3A	protein-coding
mm_14238.1	chr2	127695858	127695875	+	1	NA	Intergenic	(GGGGA)n|Simple_repeat|Simple_repeat	34031	NM_145532	228576	Mm.133036	NM_145532	ENSMUSG00000027377	Mall	BC012256|BENE	mal, T cell differentiation protein-like	protein-coding
mm_121950.1	chr14	24245914	24245925	-	1	NA	promoter-TSS (NM_027726)	promoter-TSS (NM_027726)	1	NM_001163513	71228	Mm.68971	NM_027726	ENSMUSG00000021782	Dlg5	4933429D20Rik|T25557|mKIAA0583	discs, large homolog 5 (Drosophila)	protein-coding
mm_6706.1	chr1	82283818	82283819	-	1	NA	intron (NM_010570, intron 1 of 1)	intron (NM_010570, intron 1 of 1)	7621	NM_010570	16367	Mm.4952	NM_010570	ENSMUSG00000055980	Irs1	G972R|IRS-1	insulin receptor substrate 1	protein-coding
mm_41306.1	chr5	90468477	90468548	+	1	NA	exon (NM_009654, exon 8 of 15)	exon (NM_009654, exon 8 of 15)	7642	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_39700.1	chr5	27261917	27261980	+	1	NA	promoter-TSS (NM_001136060)	promoter-TSS (NM_001136060)	13	NM_001136060	13483	Mm.42078	NM_010075	ENSMUSG00000061576	Dpp6	B930011P16Rik|D5Buc3|D5Buc4|D5Buc5|DPP VI|Dpp-6|Gm1377|In(5)6H-p|Peplb|Rw	dipeptidylpeptidase 6	protein-coding
mm_47026.1	chr5	115535774	115535794	-	1	NA	intron (NM_133915, intron 1 of 11)	intron (NM_133915, intron 1 of 11)	-23683	NM_007475	11837	Mm.5286	NM_007475	ENSMUSG00000067274	Rplp0	36B4|Arbp|L10E	ribosomal protein, large, P0	protein-coding
mm_89510.1	chr10	94142839	94142849	+	1	NA	3' UTR (NM_053072, exon 21 of 21)	3' UTR (NM_053072, exon 21 of 21)	-5087	NM_011629	22025	Mm.107483	NM_011629	ENSMUSG00000005897	Nr2c1	4831444H07Rik|80.3|Eenr|TR2|Tr2-11	nuclear receptor subfamily 2, group C, member 1	protein-coding
mm_78865.1	chr9	44398429	44398435	+	1	NA	5' UTR (NM_008063, exon 1 of 8)	5' UTR (NM_008063, exon 1 of 8)	256	NM_008063	14385	Mm.30087	NM_008063	ENSMUSG00000032114	Slc37a4	100043178|G6PT|G6pt1|GSD-1b|mG6PT	solute carrier family 37 (glucose-6-phosphate transporter), member 4	protein-coding
mm_26896.1	chr3	19264928	19264939	-	1	NA	promoter-TSS (NM_008802)	promoter-TSS (NM_008802)	75	NM_008802	18583	Mm.355614	NM_008802	ENSMUSG00000069094	Pde7a	AU015378|AW047537	phosphodiesterase 7A	protein-coding
mm_29300.1	chr3	107929000	107929008	-	1	NA	intron (NM_026672, intron 6 of 7)	intron (NM_026672, intron 6 of 7)	2741	NM_026672	68312	Mm.458189	NM_026672	ENSMUSG00000004035	Gstm7	0610005A07Rik|AI894236|Cd203c	glutathione S-transferase, mu 7	protein-coding
mm_2015.1	chr1	87127904	87127913	+	1	NA	TTS (NM_007432)	TTS (NM_007432)	2900	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_102158.1	chr11	53724391	53724409	-	1	NA	3' UTR (NM_010558, exon 4 of 4)	3' UTR (NM_010558, exon 4 of 4)	3606	NM_010558	16191	Mm.4461	NM_010558	ENSMUSG00000036117	Il5	Il-5	interleukin 5	protein-coding
mm_88255.1	chr10	73202153	73202162	+	1	NA	Intergenic	Intergenic	-115452	NR_040646	327768	Mm.417745	NR_040646		A330049N07Rik	-	RIKEN cDNA A330049N07 gene	ncRNA
mm_79557.1	chr9	58016358	58016371	+	1	NA	exon (NM_019779, exon 2 of 9)	exon (NM_019779, exon 2 of 9)	1412	NM_019779	13070	Mm.302865	NM_019779	ENSMUSG00000032323	Cyp11a1	Cyp11a|Cypxia1|D9Ertd411e|P450scc|Scc|cscc	cytochrome P450, family 11, subfamily a, polypeptide 1	protein-coding
mm_35456.1	chr4	40703124	40703134	-	1	NA	promoter-TSS (NM_025545)	promoter-TSS (NM_025545)	65	NM_001025444	66408	Mm.430710	NM_025545	ENSMUSG00000028411	Aptx	2410016G21Rik|AA388047|FHA-HIT	aprataxin	protein-coding
mm_38524.1	chr4	141424559	141424600	-	1	NA	3' UTR (NM_013868, exon 3 of 3)	3' UTR (NM_013868, exon 3 of 3)	3800	NM_013868	29818	Mm.46181	NM_013868	ENSMUSG00000006221	Hspb7	27kDa|Hsp25-2|cvHsp	heat shock protein family, member 7 (cardiovascular)	protein-coding
mm_161499.1	chr15	89378804	89378804	-	1	NA	exon (NM_001013022, exon 2 of 5)	exon (NM_001013022, exon 2 of 5)	450	NM_001013022	70113	Mm.247273	NM_001013022	ENSMUSG00000047394	Odf3b	2010001J22Rik	outer dense fiber of sperm tails 3B	protein-coding
mm_120313.1	chr14	63142584	63142649	+	1	NA	3' UTR (NM_007798, exon 10 of 10)	3' UTR (NM_007798, exon 10 of 10)	20154	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_104926.1	chr11	99986607	99986608	-	1	NA	promoter-TSS (NM_001256057)	promoter-TSS (NM_001256057)	-14	NM_001256057	100504183	Mm.426560	NM_001256057	ENSMUSG00000078253	Krtap16-1	Gm11570|OTTMUSG00000002209	keratin associated protein 16-1	protein-coding
mm_161938.1	chr19	3905004	3905004	-	1	NA	intron (NM_001136091, intron 1 of 19)	B1_Mus1|SINE|Alu	226	NM_016921	27060	Mm.271689	NM_016921	ENSMUSG00000001750	Tcirg1	ATP6N1C|ATP6a3|Atp6i|OC-116|OPTB1|Stv1|TIRC7|Vph1|oc	T cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 protein A3	protein-coding
mm_172704.1	chr8	65454018	65454026	+	1	NA	Intergenic	L1Md_T|LINE|L1	-164018	NM_001293784	72925	Mm.380457	NM_175188	ENSMUSG00000036469	March1	2900024D24Rik|BB085186	membrane-associated ring finger (C3HC4) 1	protein-coding
mm_154669.1	chrX	7882174	7882187	+	1	NA	exon (NM_138606, exon 5 of 6)	exon (NM_138606, exon 5 of 6)	-2064	NM_001083937	22232	Mm.214976	NM_078484	ENSMUSG00000031156	Slc35a2	AI327289|Had-1|Had1|Sfc8|UGT|Ugalt	solute carrier family 35 (UDP-galactose transporter), member A2	protein-coding
mm_115463.1	chr13	119428584	119428612	+	1	NA	promoter-TSS (NM_001079849)	promoter-TSS (NM_001079849)	-2	NM_001079849	218693	Mm.490243	NM_145457	ENSMUSG00000025451	Paip1	PAIP-1	polyadenylate binding protein-interacting protein 1	protein-coding
mm_26642.1	chr3	153844218	153844225	+	1	NA	promoter-TSS (NM_025758)	promoter-TSS (NM_025758)	-26	NM_025758	66772	Mm.116960	NM_025758	ENSMUSG00000038997	Asb17	4933436O18Rik	ankyrin repeat and SOCS box-containing 17	protein-coding
mm_131728.1	chr16	21835971	21835973	+	1	NA	Intergenic	Intergenic	41625	NR_037957	100043489	Mm.326535	NR_037957	ENSMUSG00000097290	1300002E11Rik	1500026P21Rik	RIKEN cDNA 1300002E11 gene	ncRNA
mm_2202.1	chr1	89580184	89580202	+	1	NA	intron (NM_001037136, intron 1 of 16)	intron (NM_001037136, intron 1 of 16)	103699	NR_015540	74403	Mm.444291	NR_015540		4933400F21Rik	1700091C04Rik|4930565K10Rik	RIKEN cDNA 4933400F21 gene	ncRNA
mm_11576.1	chr2	32916583	32916628	+	1	NA	intron (NM_146119, intron 5 of 13)	intron (NM_146119, intron 5 of 13)	40471	NM_146119	227737	Mm.301646	NM_146119	ENSMUSG00000026796	Fam129b	9130404D14Rik	family with sequence similarity 129, member B	protein-coding
mm_27307.1	chr3	50366413	50366430	-	1	NA	3' UTR (NM_011990, exon 12 of 12)	3' UTR (NM_011990, exon 12 of 12)	77192	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_42185.1	chr5	112267545	112267557	+	1	NA	intron (NM_023695, intron 5 of 5)	intron (NM_023695, intron 5 of 5)	-9140	NM_001326590	22022	Mm.250631	NM_009419	ENSMUSG00000029344	Tpst2	AI448750|D5Ucla3|Tango13b|grm|grt	protein-tyrosine sulfotransferase 2	protein-coding
mm_19694.1	chr2	103605806	103605810	-	1	NA	intron (NM_178890, intron 1 of 16)	MIR|SINE|MIR	39498	NM_178890	99382	Mm.35850	NM_178890	ENSMUSG00000032724	Abtb2	AW539457|BPOZ-2	ankyrin repeat and BTB (POZ) domain containing 2	protein-coding
mm_153726.1	chr19	44407660	44407668	-	1	NA	promoter-TSS (NM_009127)	promoter-TSS (NM_009127)	45	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_14652.1	chr2	136915362	136915381	+	1	NA	intron (NM_001038641, intron 2 of 7)	intron (NM_001038641, intron 2 of 7)	16020	NM_001038641	74243	Mm.330612	NM_028201	ENSMUSG00000027281	Slx4ip	2210009G21Rik|2410004I22Rik|C85661|Slxip	SLX4 interacting protein	protein-coding
mm_65483.1	chr7	25651334	25651375	-	1	NA	intron (NM_007533, intron 1 of 8)	intron (NM_007533, intron 1 of 8)	7407	NM_007533	12039	Mm.25848	NM_007533	ENSMUSG00000060376	Bckdha	-	branched chain ketoacid dehydrogenase E1, alpha polypeptide	protein-coding
mm_26498.1	chr3	145652362	145652377	+	1	NA	Intergenic	Intergenic	-2384	NM_010516	16007	Mm.1231	NM_010516	ENSMUSG00000028195	Cyr61	AI325051|CCN1|Igfbp10	cysteine rich protein 61	protein-coding
mm_49847.1	chr6	38354769	38354780	+	1	NA	promoter-TSS (NM_028421)	promoter-TSS (NM_028421)	-171	NM_028421	78781	Mm.25243	NM_028421	ENSMUSG00000029826	Zc3hav1	1200014N16Rik|2900058M19Rik|9130009D18Rik|9830115L13Rik|ARTD13|D6Bwg1452e|ZAP	zinc finger CCCH type, antiviral 1	protein-coding
mm_134461.1	chr16	18426394	18426420	-	1	NA	promoter-TSS (NM_013711)	promoter-TSS (NM_013711)	-10	NM_013711	26462	Mm.390906	NM_013711	ENSMUSG00000075704	Txnrd2	AA118373|ESTM573010|TGR|Tr3|Trxr2|Trxrd2	thioredoxin reductase 2	protein-coding
mm_125610.1	chr15	61389636	61389636	+	1	NA	Intergenic	Intergenic	384815	NR_040350	432956	Mm.404918	NR_040350		D030024E09Rik	-	RIKEN cDNA D030024E09 gene	ncRNA
mm_108114.1	chr12	75394002	75394031	+	1	NA	exon (NM_023275, exon 4 of 5)	exon (NM_023275, exon 4 of 5)	22765	NM_175644	217674	Mm.252250	NM_175644	ENSMUSG00000048982	Gphb5	OGH|Zlut1	glycoprotein hormone beta 5	protein-coding
mm_7716.1	chr1	130647469	130647473	-	1	NA	intron (NM_007576, intron 6 of 9)	L1M2|LINE|L1	14147	NM_007576	12269	Mm.306720	NM_007576	ENSMUSG00000026405	C4bp	AI195242|C4bpa	complement component 4 binding protein	protein-coding
mm_150962.1	chr19	46463943	46463944	+	1	NA	intron (NM_001025391, intron 8 of 11)	intron (NM_001025391, intron 8 of 11)	-37705	NM_053100	93679	Mm.392177	NM_053100	ENSMUSG00000025034	Trim8	AA408830|BB006755|GERP|Rnf27	tripartite motif-containing 8	protein-coding
mm_72139.1	chr8	71957722	71957724	+	1	NA	intron (NM_001164581, intron 1 of 3)	L1VL4|LINE|L1	6657	NM_001164581	234413	Mm.334607	NM_001164581	ENSMUSG00000052446	Zfp961	A230105L22Rik|BC065788|mszf37|mszf55-2	zinc finger protein 961	protein-coding
mm_10254.1	chr2	9313364	9313366	+	1	NA	Intergenic	Intergenic	123850	NR_038180	73438	Mm.23558	NR_038180	ENSMUSG00000085580	1700061F12Rik	-	RIKEN cDNA 1700061F12 gene	ncRNA
mm_97242.1	chr11	75692603	75692620	+	1	NA	exon (NM_133656, exon 2 of 3)	exon (NM_133656, exon 2 of 3)	13352	NM_001277221	12928	Mm.280125	NM_133656	ENSMUSG00000017776	Crk	Crk-I|Crk-II|Crk-III|Crk3|CrkIII|Crko|c-Crk|p38	v-crk avian sarcoma virus CT10 oncogene homolog	protein-coding
mm_144148.1	chr18	5035072	5035114	+	1	NA	Intergenic	Intergenic	-11496	NM_153153	225115	Mm.136791	NM_153153	ENSMUSG00000024236	Svil	AU024053|B430302E16Rik	supervillin	protein-coding
mm_168535.1	chr1	161036389	161036391	+	1	NA	non-coding (NR_002840, exon 1 of 4)	non-coding (NR_002840, exon 1 of 4)	1224	NR_002840	14455	Mm.270065	NR_002840	ENSMUSG00000053332	Gas5	Gas-5|Mir5117|Snhg2	growth arrest specific 5	ncRNA
mm_139362.1	chr17	50539469	50539487	+	1	NA	intron (NM_013880, intron 1 of 5)	intron (NM_013880, intron 1 of 5)	29931	NM_013880	224860	Mm.217362	NM_013880	ENSMUSG00000038910	Plcl2	PLC-L2|PRIP-2|Plce2|mKIAA1092	phospholipase C-like 2	protein-coding
mm_17160.1	chr2	25234228	25234251	-	1	NA	promoter-TSS (NM_080854)	promoter-TSS (NM_080854)	-5	NM_080854	142681	Mm.346652	NM_080854	ENSMUSG00000006469	Slc34a3	AI649385|Npt2c|Npt2c-v1|NptIIc|naPi-2c	solute carrier family 34 (sodium phosphate), member 3	protein-coding
mm_33673.1	chr4	133194501	133194540	+	1	NA	exon (NM_153423, exon 8 of 9)	exon (NM_153423, exon 8 of 9)	-1135	NR_105984	102466215		NR_105984	ENSMUSG00000099202	Mir7017	Gm27945|mmu-mir-7017	microRNA 7017	ncRNA
mm_81638.1	chr9	110880351	110880364	+	1	NA	promoter-TSS (NM_001146060)	promoter-TSS (NM_001146060)	35	NM_001146060	235633	Mm.86338	NM_146228	ENSMUSG00000044037	Als2cl	79H19D|79H19E|BC022645|D930044G19Rik|mRn.49018	ALS2 C-terminal like	protein-coding
mm_137603.1	chr17	28218214	28218217	+	1	NA	intron (NM_027185, intron 3 of 10)	intron (NM_027185, intron 3 of 10)	10437	NM_027185	23853	Mm.204731	NM_027185	ENSMUSG00000002257	Def6	2410003F05Rik|6430538D02Rik|AV094905|Ibp|Slat|Slat2|Slat6	differentially expressed in FDCP 6	protein-coding
mm_65015.1	chr7	17095051	17095061	-	1	NA	exon (NM_007676, exon 4 of 5)	exon (NM_007676, exon 4 of 5)	21016	NM_007676	26436	Mm.143686	NM_007676	ENSMUSG00000066760	Psg16	Cea11|PSG|bCEA	pregnancy specific glycoprotein 16	protein-coding
mm_114348.1	chr13	60934772	60934778	+	1	NA	3' UTR (NM_001145799, exon 5 of 5)	3' UTR (NM_001145799, exon 5 of 5)	1791	NM_001145799	13024	Mm.482089	NM_007796	ENSMUSG00000044258	Ctla2a	Ctla-2a	cytotoxic T lymphocyte-associated protein 2 alpha	protein-coding
mm_28944.1	chr3	99253582	99253599	-	1	NA	promoter-TSS (NM_009323)	promoter-TSS (NM_009323)	-170	NM_009323	21384	Mm.88761	NM_009323	ENSMUSG00000027868	Tbx15	Tbx14|Tbx8|de	T-box 15	protein-coding
mm_131427.1	chr16	14906623	14906680	+	1	NA	promoter-TSS (NM_025769)	promoter-TSS (NM_025769)	5	NM_025769	66793	Mm.100270	NM_025769	ENSMUSG00000068617	Efcab1	4930449A16Rik|5430404L10Rik	EF hand calcium binding domain 1	protein-coding
mm_44306.1	chr5	8997090	8997093	-	1	NA	promoter-TSS (NM_023733)	promoter-TSS (NM_023733)	55	NM_023733	74114	Mm.28197	NM_023733	ENSMUSG00000003623	Crot	1200003H03Rik	carnitine O-octanoyltransferase	protein-coding
mm_101991.1	chr11	50931613	50931642	-	1	NA	promoter-TSS (NM_013744)	promoter-TSS (NM_013744)	8	NM_013744	27274	Mm.74670	NM_013744	ENSMUSG00000020335	Zfp354b	Kid2|Tcf17l1|Znf354b	zinc finger protein 354B	protein-coding
mm_61880.1	chr7	89632484	89632492	+	1	NA	promoter-TSS (NM_181407)	promoter-TSS (NM_181407)	-330	NM_181407	109264	Mm.334011	NM_181407	ENSMUSG00000030621	Me3	1700020C08Rik|B230207H15Rik	malic enzyme 3, NADP(+)-dependent, mitochondrial	protein-coding
mm_123843.1	chr14	70659782	70659791	-	1	NA	3' UTR (NM_023045, exon 28 of 28)	3' UTR (NM_023045, exon 28 of 28)	-6702	NM_181345	328440	Mm.347749	NM_181345	ENSMUSG00000047911	Npm2	-	nucleophosmin/nucleoplasmin 2	protein-coding
mm_106644.1	chr11	121039401	121039463	-	1	NA	promoter-TSS (NM_009854)	promoter-TSS (NM_009854)	46	NM_009854	12516	Mm.4100	NM_009854	ENSMUSG00000025163	Cd7	-	CD7 antigen	protein-coding
mm_94687.1	chr11	19924266	19924276	+	1	NA	promoter-TSS (NM_033523)	promoter-TSS (NM_033523)	-171	NM_033523	114716	Mm.266627	NM_033523	ENSMUSG00000045671	Spred2	C79158	sprouty-related, EVH1 domain containing 2	protein-coding
mm_104996.1	chr11	100356079	100356096	-	1	NA	promoter-TSS (NM_177981)	promoter-TSS (NM_177981)	54	NM_177981	15114	Mm.281700	NM_010404	ENSMUSG00000006930	Hap1	HAP-1	huntingtin-associated protein 1	protein-coding
mm_2140.1	chr1	88087872	88087881	+	1	NA	intron (NM_201644, intron 1 of 4)	intron (NM_201644, intron 1 of 4)	-7125	NM_201642	394432	Mm.300095	NM_201642	ENSMUSG00000090124	Ugt1a7c	A10'|A13|Ugt1a10	UDP glucuronosyltransferase 1 family, polypeptide A7C	protein-coding
mm_135638.1	chr16	52354273	52354287	-	1	NA	intron (NM_009655, intron 1 of 15)	intron (NM_009655, intron 1 of 15)	98801	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_115367.1	chr13	112993841	112993869	+	1	NA	promoter-TSS (NM_001037914)	promoter-TSS (NM_001037914)	-13	NM_001037914	622408	Mm.360976	NM_001037914	ENSMUSG00000074651	Mcidas	EG622408|Gm6320|Idas|Mci|Mcin	multiciliate differentiation and DNA synthesis associated cell cycle protein	protein-coding
mm_122533.1	chr14	47385579	47385653	-	1	NA	exon (NM_010705, exon 6 of 6)	exon (NM_010705, exon 6 of 6)	11756	NM_001145953	16854	Mm.248615	NM_010705	ENSMUSG00000050335	Lgals3	GBP|L-34|Mac-2|gal3	lectin, galactose binding, soluble 3	protein-coding
mm_118635.1	chr14	21345574	21345592	+	1	NA	intron (NM_001243041, intron 7 of 10)	intron (NM_001243041, intron 7 of 10)	-154187	NM_001205241	54169	Mm.248967	NM_017479	ENSMUSG00000021767	Kat6b	AI507552|B130044K16Rik|MYST-4|Morf|Myst4|mKIAA0383|qkf|querkopf	K(lysine) acetyltransferase 6B	protein-coding
mm_81373.1	chr9	108854090	108854110	+	1	NA	promoter-TSS (NM_134420)	promoter-TSS (NM_134420)	57	NM_134420	171429	Mm.45201	NM_134420	ENSMUSG00000023259	Slc26a6	B930010B04Rik|CFEX|Pat-1|Pat1	solute carrier family 26, member 6	protein-coding
mm_67979.1	chr7	100658370	100658386	-	1	NA	promoter-TSS (NM_001291336)	promoter-TSS (NM_001291336)	78	NM_001163185	27276	Mm.491216	NM_013746	ENSMUSG00000030701	Plekhb1	AI315628|PHR1|Phret1|evt-1	pleckstrin homology domain containing, family B (evectins) member 1	protein-coding
mm_16626.1	chr2	5677534	5677545	-	1	NA	intron (NM_001290374, intron 1 of 9)	intron (NM_001290374, intron 1 of 9)	-1493	NM_001290376	227541	Mm.191949	NM_177343	ENSMUSG00000039145	Camk1d	A630059D12Rik|CKLiK|CaMKIdelta|E030025C11Rik|mCKLiK	calcium/calmodulin-dependent protein kinase ID	protein-coding
mm_42389.1	chr5	114936974	114936986	+	1	NA	exon (NM_145209, exon 7 of 7)	exon (NM_145209, exon 7 of 7)	-5222	NM_028211	72357	Mm.292672	NM_028211	ENSMUSG00000029559	2210016L21Rik	-	RIKEN cDNA 2210016L21 gene	protein-coding
mm_126942.1	chr15	92051154	92051170	+	1	NA	promoter-TSS (NM_001159648)	promoter-TSS (NM_001159648)	-3	NM_001159648	12805	Mm.4911	NM_007727	ENSMUSG00000055022	Cntn1	AW495098|CNTN|F3cam|usl	contactin 1	protein-coding
mm_74568.1	chr8	11009462	11009499	-	1	NA	intron (NR_046017, intron 1 of 4)	CpG-13826	-1050	NM_001081212	384783	Mm.407207	NM_001081212	ENSMUSG00000038894	Irs2	Irs-2	insulin receptor substrate 2	protein-coding
mm_3981.1	chr1	164263480	164263522	+	1	NA	exon (NM_054087, exon 6 of 6)	exon (NM_054087, exon 6 of 6)	-12097	NM_029115	74895	Mm.167258	NM_029115	ENSMUSG00000026578	Ccdc181	4930455F23Rik|AI427889	coiled-coil domain containing 181	protein-coding
mm_153850.1	chr19	46348969	46349001	-	1	NA	promoter-TSS (NR_040418)	promoter-TSS (NR_040418)	3	NR_040418	75579	Mm.436708	NR_040418		2310034G01Rik	-	RIKEN cDNA 2310034G01 gene	ncRNA
mm_96995.1	chr11	70700607	70700615	+	1	NA	promoter-TSS (NM_213729)	promoter-TSS (NM_213729)	63	NM_153103	16562	Mm.99996	NM_153103	ENSMUSG00000020821	Kif1c	B430105J22Rik|D11Bwg1349e|Ltxs1|Orch3	kinesin family member 1C	protein-coding
mm_154190.1	chr19	58822522	58822532	-	1	NA	intron (NM_001327998, intron 5 of 12)	intron (NM_001327998, intron 5 of 12)	-28113	NM_026208	67507	Mm.27027	NM_026208	ENSMUSG00000026931	1700019N19Rik	-	RIKEN cDNA 1700019N19 gene	protein-coding
mm_129762.1	chr15	82407188	82407203	-	1	NA	promoter-TSS (NM_010005)	promoter-TSS (NM_010005)	-1	NM_010005	13101	Mm.174372	NM_010005	ENSMUSG00000094806	Cyp2d10	AI303445|Cyp2d|P450-2D	cytochrome P450, family 2, subfamily d, polypeptide 10	protein-coding
mm_89522.1	chr10	94357042	94357057	+	1	NA	Intergenic	Intergenic	-58346	NR_033209	215472	Mm.255656	NM_174999	ENSMUSG00000053420	Gm4792	E130012K09|EG215472	predicted gene 4792	ncRNA
mm_168218.1	chr10	76440206	76440215	-	1	NA	exon (NM_001282992, exon 2 of 42)	exon (NM_001282992, exon 2 of 42)	2702	NM_008787	18541	Mm.251794	NM_008787	ENSMUSG00000001151	Pcnt	AW476095|C86676|KEN|Pcnt2|kendrin|m239Asp|m275Asp	pericentrin (kendrin)	protein-coding
mm_133852.1	chr16	96258590	96258621	+	1	NA	intron (NM_001122993, intron 2 of 3)	intron (NM_001122993, intron 2 of 3)	-22427	NM_033149	93961	Mm.154783	NM_033149	ENSMUSG00000074892	B3galt5	1190002B21Rik|AU045265|b3Galt-V	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 5	protein-coding
mm_142901.1	chr17	52162651	52162678	-	1	NA	Intergenic	Intergenic	279937	NR_045095	100504169	Mm.417731	NR_045095		Gm20098	-	predicted gene, 20098	ncRNA
mm_11769.1	chr2	38587910	38587913	+	1	NA	TTS (NM_011187)	TTS (NM_011187)	55995	NM_011187	19177	Mm.389251	NM_011187	ENSMUSG00000026750	Psmb7	AU020723|MC14	proteasome (prosome, macropain) subunit, beta type 7	protein-coding
mm_47401.1	chr5	123130825	123130834	-	1	NA	intron (NM_175092, intron 2 of 4)	intron (NM_175092, intron 2 of 4)	1800	NM_175092	23912	Mm.253876	NM_175092	ENSMUSG00000029449	Rhof	AI845056|AV026554|Arhf|Ifld1|Rif	ras homolog family member F (in filopodia)	protein-coding
mm_75323.1	chr8	42083303	42083316	-	1	NA	Intergenic	MT2B1|LTR|ERVL	256042	NR_045497	69966	Mm.416903	NR_045497	ENSMUSG00000102046	2810404M03Rik	-	RIKEN cDNA 2810404M03 gene	ncRNA
mm_108166.1	chr12	76371128	76371140	+	1	NA	intron (NM_178744, intron 1 of 1)	CpG-3289	868	NM_178744	268564	Mm.77065	NM_178744	ENSMUSG00000033454	Zbtb1	9430077A12|AI256369|Bsg2|C430003J21Rik	zinc finger and BTB domain containing 1	protein-coding
mm_78090.1	chr9	18292272	18292334	+	1	NA	promoter-TSS (NM_025844)	promoter-TSS (NM_025844)	36	NM_025844	66917	Mm.103534	NM_025844	ENSMUSG00000001774	Chordc1	1110001O09Rik|AA409036|Chp-1|morgana	cysteine and histidine-rich domain (CHORD)-containing, zinc-binding protein 1	protein-coding
mm_82107.1	chr9	123112891	123112908	+	1	NA	promoter-TSS (NM_001081188)	promoter-TSS (NM_001081188)	306	NM_026917	69035	Mm.28300	NM_026917	ENSMUSG00000025786	Zdhhc3	1110020O22Rik|1810006O10Rik|2210017C02Rik|DHHC-3|GODZ|Gramp1|Zfp373	zinc finger, DHHC domain containing 3	protein-coding
mm_66109.1	chr7	31041733	31041776	-	1	NA	promoter-TSS (NM_001111073)	promoter-TSS (NM_001111073)	85	NM_001111073	18301	Mm.1870	NM_008761	ENSMUSG00000009687	Fxyd5	EF-8|Oit2|RIC	FXYD domain-containing ion transport regulator 5	protein-coding
mm_85205.1	chr9	96787743	96787753	-	1	NA	Intergenic	Intergenic	22186	NR_102296	319707	Mm.392191	NR_102293	ENSMUSG00000101581	C430002N11Rik	-	RIKEN cDNA C430002N11 gene	ncRNA
mm_165893.1	chr4	44771437	44771446	+	1	NA	intron (NM_138590, intron 2 of 8)	B1_Mus1|SINE|Alu	14882	NM_138590	319885	Mm.331576	NM_138590	ENSMUSG00000035649	Zcchc7	4930572I07Rik|D4Wsu132e	zinc finger, CCHC domain containing 7	protein-coding
mm_69663.1	chr7	139980410	139980417	-	1	NA	intron (NM_007403, intron 22 of 23)	intron (NM_007403, intron 22 of 23)	-1658	NM_001347613	381933	Mm.440431	NM_001033465	ENSMUSG00000073795	6430531B16Rik	Gm1093	RIKEN cDNA 6430531B16 gene	protein-coding
mm_94208.1	chr11	3105539	3105542	+	1	NA	Intergenic	Intergenic	-18481	NR_003517	236604	Mm.247625	NM_001004146		Pisd-ps1	-	phosphatidylserine decarboxylase, pseudogene 1	pseudo
mm_7659.1	chr1	128414024	128414028	-	1	NA	intron (NM_177445, intron 2 of 15)	intron (NM_177445, intron 2 of 15)	3390	NM_177445	226414	Mm.28693	NM_145507	ENSMUSG00000026356	Dars	5730439G15Rik	aspartyl-tRNA synthetase	protein-coding
mm_106349.1	chr11	118393492	118393514	-	1	NA	exon (NM_011150, exon 6 of 6)	exon (NM_011150, exon 6 of 6)	8428	NM_011150	19039	Mm.3152	NM_011150	ENSMUSG00000033880	Lgals3bp	90K|CyCAP|MAC-2BP|Ppicap|Tango10b	lectin, galactoside-binding, soluble, 3 binding protein	protein-coding
mm_171405.1	chr4	126070297	126070317	-	1	NA	intron (NM_172701, intron 1 of 9)	B1_Mus1|SINE|Alu	11742	NM_172701	230751	Mm.38907	NM_172701	ENSMUSG00000042616	Oscp1	1810007P19Rik|5730415O04|6030436A01Rik	organic solute carrier partner 1	protein-coding
mm_61854.1	chr7	88302264	88302275	+	1	NA	exon (NM_009982, exon 5 of 7)	exon (NM_009982, exon 5 of 7)	24184	NM_001311790	13032	Mm.89295	NM_009982	ENSMUSG00000030560	Ctsc	AI047818|CatC|DPP1|DPPI	cathepsin C	protein-coding
mm_139538.1	chr17	56710005	56710017	+	1	NA	intron (NR_045519, intron 14 of 16)	intron (NR_045519, intron 14 of 16)	6910	NM_178926	106639	Mm.37290	NM_178926	ENSMUSG00000054723	Vmac	AI662250	vimentin-type intermediate filament associated coiled-coil protein	protein-coding
mm_120903.1	chr14	75962416	75962447	+	1	NA	5' UTR (NM_026214, exon 2 of 2)	5' UTR (NM_026214, exon 2 of 2)	7428	NM_026214	67516	Mm.390712	NM_026214	ENSMUSG00000046523	Kctd4	2210017A09Rik|AU017169	potassium channel tetramerisation domain containing 4	protein-coding
mm_22960.1	chr3	32510566	32510641	+	1	NA	promoter-TSS (NM_144519)	promoter-TSS (NM_144519)	11	NM_144519	67778	Mm.285620	NM_144519	ENSMUSG00000027667	Zfp639	6230400O18Rik|ANC-2H01|ZASC1|Znf639	zinc finger protein 639	protein-coding
mm_161463.1	chr15	77643286	77643286	-	1	NA	promoter-TSS (NM_001143686)	promoter-TSS (NM_001143686)	0	NM_001143686	328563	Mm.17957	NM_001143686	ENSMUSG00000091694	Apol11b	A330102K04Rik	apolipoprotein L 11b	protein-coding
mm_127000.1	chr15	95790885	95790900	+	1	NA	promoter-TSS (NM_001253813)	promoter-TSS (NM_001253813)	49	NM_001253813	105722	Mm.38087	NM_175344	ENSMUSG00000064210	Ano6	2900059G15Rik|AA407480|AW554778|F730003B03Rik|Tmem16f	anoctamin 6	protein-coding
mm_107319.1	chr12	31270240	31270242	+	1	NA	intron (NM_008482, intron 3 of 32)	B2_Mm1t|SINE|B2	4947	NM_008482	16777	Mm.172674	NM_008482	ENSMUSG00000002900	Lamb1	C77966|C80098|C81607|D130003D08Rik|Lamb-1|Lamb1-1	laminin B1	protein-coding
mm_143030.1	chr17	56609805	56609819	-	1	NA	promoter-TSS (NM_153152)	promoter-TSS (NM_153152)	-41	NM_153152	224904	Mm.34002	NM_153152	ENSMUSG00000049760	2410015M20Rik	Mic13|QIL1|sr104	RIKEN cDNA 2410015M20 gene	protein-coding
mm_24691.1	chr3	95006590	95006602	+	1	NA	TTS (NM_030074)	TTS (NM_030074)	2428	NR_105980	102465613		NR_105980	ENSMUSG00000099033	Mir7013	Gm27488|mmu-mir-7013	microRNA 7013	ncRNA
mm_101552.1	chr11	33755104	33755107	-	1	NA	intron (NM_001190885, intron 1 of 8)	intron (NM_001190885, intron 1 of 8)	88480	NM_027398	70357	Mm.252514	NM_027398	ENSMUSG00000053519	Kcnip1	KCHIP1|Kchip1.2	Kv channel-interacting protein 1	protein-coding
mm_26749.1	chr3	7613695	7613704	-	1	NA	promoter-TSS (NM_001313889)	promoter-TSS (NM_001313889)	61	NM_008371	16196	Mm.3825	NM_008371	ENSMUSG00000040329	Il7	A630026I06Rik|Il-7|hlb368	interleukin 7	protein-coding
mm_131119.1	chr16	5382382	5382388	+	1	NA	Intergenic	Intergenic	-126429	NM_027446	70511	Mm.45780	NM_027446	ENSMUSG00000022544	Eef2kmt	5730409G15Rik|Fam86|Fam86a|eEF2-KMT	eukaryotic elongation factor 2 lysine methyltransferase	protein-coding
mm_170413.1	chr18	68692132	68692137	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-47266	NR_105774	102465183		NR_105774	ENSMUSG00000099300	Mir6356	Gm27461|mmu-mir-6356	microRNA 6356	ncRNA
mm_33778.1	chr4	134511003	134511076	+	1	NA	promoter-TSS (NM_001081099)	promoter-TSS (NM_001081099)	40	NM_001081099	69885	Mm.141592	NM_001081099	ENSMUSG00000078521	Aunip	2610002D18Rik|Clhc1	aurora kinase A and ninein interacting protein	protein-coding
mm_38494.1	chr4	140979185	140979196	-	1	NA	TTS (NM_023374)	TTS (NM_023374)	-7683	NM_029097	74772	Mm.205625	NM_029097	ENSMUSG00000036622	Atp13a2	1110012E06Rik|AA589443	ATPase type 13A2	protein-coding
mm_134384.1	chr16	17201491	17201507	-	1	NA	promoter-TSS (NM_009456)	promoter-TSS (NM_009456)	-7	NM_009456	22195	Mm.3074	NM_009456	ENSMUSG00000038965	Ube2l3	C79827|UbcM4|Ubce7	ubiquitin-conjugating enzyme E2L 3	protein-coding
mm_559.1	chr1	38021754	38021788	+	1	NA	exon (NM_198303, exon 5 of 24)	exon (NM_198303, exon 5 of 24)	23761	NM_198303	226982	Mm.260943	NM_198303	ENSMUSG00000026083	Eif5b	A030003E17Rik|BC018347|IF2	eukaryotic translation initiation factor 5B	protein-coding
mm_35128.1	chr4	11235545	11235565	-	1	NA	exon (NM_001159595, exon 9 of 27)	exon (NM_001159595, exon 9 of 27)	18704	NM_178112	72656	Mm.246713	NM_178112	ENSMUSG00000040738	Ints8	2810013E07Rik|AV063769|D130008D20Rik	integrator complex subunit 8	protein-coding
mm_106501.1	chr11	120378693	120378779	-	1	NA	promoter-TSS (NM_027980)	promoter-TSS (NM_027980)	10	NM_027980	71885	Mm.274890	NM_027980	ENSMUSG00000025384	Faap100	2310003H01Rik	Fanconi anemia core complex associated protein 100	protein-coding
mm_172061.1	chr6	132731985	132731991	-	1	NA	Intergenic	RLTR9E|LTR|ERVK	5998	NM_207020	353325	Mm.377892	NM_207020	ENSMUSG00000071149	Tas2r115	T2R15|Tas2r15|mGR15|mt2r49	taste receptor, type 2, member 115	protein-coding
mm_107853.1	chr12	69447709	69447712	+	1	NA	Intergenic	Intergenic	27840	NR_038060	76062	Mm.380755	NR_038060		5830428M24Rik	100040862|Gm3007	RIKEN cDNA 5830428M24 gene	ncRNA
mm_153230.1	chr19	34879333	34879398	-	1	NA	promoter-TSS (NM_001114339)	promoter-TSS (NM_001114339)	90	NM_001114339	75735	Mm.24742	NM_023792	ENSMUSG00000033610	Pank1	Pank|Pank1b	pantothenate kinase 1	protein-coding
mm_108697.1	chr12	86947370	86947430	+	1	NA	promoter-TSS (NM_173735)	promoter-TSS (NM_173735)	57	NM_001289432	217732	Mm.22337	NM_173735	ENSMUSG00000034157	Cipc	2310044G17Rik|AI842544|AI853744|Kiaa1737|mKIAA1737	CLOCK interacting protein, circadian	protein-coding
mm_158224.1	chrX	106011875	106011891	-	1	NA	promoter-TSS (NM_001190409)	promoter-TSS (NM_001190409)	16	NM_001190409	67075	Mm.275943	NM_025952	ENSMUSG00000031232	Magt1	2410001C15Rik|2610529C04Rik|2810482I07Rik|IAG2|IAP	magnesium transporter 1	protein-coding
mm_55823.1	chr6	83070362	83070377	-	1	NA	promoter-TSS (NM_009392)	promoter-TSS (NM_009392)	-144	NM_009392	21909	Mm.37	NM_009392	ENSMUSG00000068327	Tlx2	Enx|Hox11L.1|Hox11l1|NCX|Ncx1|Tlx1l1|Tlx1l2	T cell leukemia, homeobox 2	protein-coding
mm_41893.1	chr5	105518747	105518757	+	1	NA	promoter-TSS (NM_133897)	promoter-TSS (NM_133897)	-719	NM_133897	100604	Mm.319847	NM_133897	ENSMUSG00000054720	Lrrc8c	AD158|AI326115|E430036I04Rik|fad158	leucine rich repeat containing 8 family, member C	protein-coding
mm_107284.1	chr12	29783846	29783865	+	1	NA	exon (NM_001093776, exon 7 of 25)	exon (NM_001093776, exon 7 of 25)	-97410	NR_046080	328075	Mm.447832	NR_046080		C630031E19Rik	C630031E19	RIKEN cDNA C630031E19 gene	ncRNA
mm_48951.1	chr6	4540587	4540591	+	1	NA	exon (NM_007743, exon 52 of 52)	exon (NM_007743, exon 52 of 52)	34971	NM_007743	12843	Mm.277792	NM_007743	ENSMUSG00000029661	Col1a2	AA960264|AI325291|Col1a-2|Cola-2|Cola2|oim	collagen, type I, alpha 2	protein-coding
mm_28907.1	chr3	98645519	98645564	-	1	NA	promoter-TSS (NM_008295)	promoter-TSS (NM_008295)	-7	NM_008295	15496	Mm.17910	NM_008295	ENSMUSG00000038092	Hsd3b5	-	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 5	protein-coding
mm_94335.1	chr11	4637720	4637726	+	1	NA	promoter-TSS (NM_029291)	promoter-TSS (NM_029291)	-70	NM_029291	75452	Mm.439906	NM_029291	ENSMUSG00000020412	Ascc2	1700011I11Rik|2610034L15Rik|AI482016|ASC1p100|AW046480	activating signal cointegrator 1 complex subunit 2	protein-coding
mm_119584.1	chr14	50925178	50925235	+	1	NA	promoter-TSS (NM_133676)	promoter-TSS (NM_133676)	257	NM_009687	11792	Mm.203	NM_009687	ENSMUSG00000035960	Apex1	APE|Apex|HAP1|Ref-1	apurinic/apyrimidinic endonuclease 1	protein-coding
mm_51688.1	chr6	86525891	86525907	+	1	NA	exon (NM_011865, exon 1 of 1)	exon (NM_011865, exon 1 of 1)	266	NM_011865	23983	Mm.274146	NM_011865	ENSMUSG00000051695	Pcbp1	WBP17|[a]CP-1|alphaCP-1|hnRNP E1	poly(rC) binding protein 1	protein-coding
mm_123865.1	chr14	72539598	72539609	-	1	NA	3' UTR (NM_207636, exon 26 of 26)	3' UTR (NM_207636, exon 26 of 26)	170400	NM_207636	319448	Mm.205421	NM_207636	ENSMUSG00000033487	Fndc3a	1700094E19Rik|D14Ertd453e|F730017H24Rik|Fndc3|sys	fibronectin type III domain containing 3A	protein-coding
mm_21717.1	chr2	164613601	164613630	-	1	NA	promoter-TSS (NM_001080550)	promoter-TSS (NM_001080550)	11	NM_001080550	277343	Mm.383292	NM_001080550	ENSMUSG00000070533	Wfdc8	Gm706	WAP four-disulfide core domain 8	protein-coding
mm_171177.1	chr3	35131249	35131250	-	1	NA	Intergenic	L1Md_T|LINE|L1	-208598	NR_105799	102466155		NR_105799	ENSMUSG00000098862	Mir6378	Gm27706|mmu-mir-6378	microRNA 6378	ncRNA
mm_89476.1	chr10	93540627	93540653	+	1	NA	promoter-TSS (NM_027908)	promoter-TSS (NM_027908)	8	NM_175488	237465	Mm.477086	NM_175488	ENSMUSG00000036168	Ccdc38	4933417K05Rik	coiled-coil domain containing 38	protein-coding
mm_57745.1	chr6	129097261	129097272	-	1	NA	intron (NM_153506, intron 2 of 4)	intron (NM_153506, intron 2 of 4)	3637	NM_153506	232409	Mm.30870	NM_153506	ENSMUSG00000030155	Clec2e	Clra|clr-a	C-type lectin domain family 2, member e	protein-coding
mm_161066.1	chr12	73113459	73113459	-	1	NA	promoter-TSS (NM_011382)	promoter-TSS (NM_011382)	-214	NM_011382	20474	Mm.249575	NM_011382	ENSMUSG00000034460	Six4	AI047561|AREC3|TrexBF	sine oculis-related homeobox 4	protein-coding
mm_13663.1	chr2	114061164	114061176	+	1	NA	non-coding (NR_028422, exon 3 of 3)	non-coding (NR_028422, exon 3 of 3)	6774	NR_028422	100303644	Mm.330469	NR_028422	ENSMUSG00000092397	C130080G10Rik	-	RIKEN cDNA C130080G10 gene	ncRNA
mm_21500.1	chr2	163472562	163472635	-	1	NA	promoter-TSS (NR_028122)	promoter-TSS (NR_028122)	31	NM_173397	228859	Mm.242917	NM_173397	ENSMUSG00000048486	Fitm2	AI414861|D930001I22Rik|Fit2	fat storage-inducing transmembrane protein 2	protein-coding
mm_18930.1	chr2	76747064	76747074	-	1	NA	exon (NM_011652, exon 275 of 313)	exon (NM_011652, exon 275 of 313)	71754	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_55242.1	chr6	52548864	52548886	-	1	NA	exon (NM_145567, exon 7 of 8)	exon (NM_145567, exon 7 of 8)	56424	NR_046049	74304	Mm.490579	NR_046049	ENSMUSG00000107895	1700094M24Rik	-	RIKEN cDNA 1700094M24 gene	ncRNA
mm_144787.1	chr18	35873503	35873505	+	1	NA	Intergenic	CpG	43686	NM_133687	67393	Mm.94560	NM_133687	ENSMUSG00000046668	Cxxc5	4930415K17Rik	CXXC finger 5	protein-coding
mm_40389.1	chr5	52741667	52741677	+	1	NA	promoter-TSS (NM_025951)	promoter-TSS (NM_025951)	98	NM_025951	67073	Mm.248647	NM_025951	ENSMUSG00000029186	Pi4k2b	2610042N09Rik|4933409G22Rik	phosphatidylinositol 4-kinase type 2 beta	protein-coding
mm_21188.1	chr2	155314580	155314590	-	1	NA	exon (NM_001004721, exon 7 of 12)	exon (NM_001004721, exon 7 of 12)	38221	NR_046364	66734	Mm.196239	NM_025735	ENSMUSG00000027602	Map1lc3a	1010001H21Rik|4922501H04Rik|LC3|LC3a	microtubule-associated protein 1 light chain 3 alpha	protein-coding
mm_28498.1	chr3	92484618	92484627	-	1	NA	exon (NM_009264, exon 2 of 2)	exon (NM_009264, exon 2 of 2)	1259	NM_009264	20753	Mm.331191	NM_009264	ENSMUSG00000050359	Sprr1a	AI528815|SPR1a|mSPRR1A	small proline-rich protein 1A	protein-coding
mm_120630.1	chr14	70466540	70466541	+	1	NA	intron (NM_145981, intron 4 of 4)	intron (NM_145981, intron 4 of 4)	9023	NM_145981	105653	Mm.192598	NM_145981	ENSMUSG00000003469	Phyhip	AW049870|C630010D02Rik|Lnap1ip|PAHX-AP#1|PAHX-AP1	phytanoyl-CoA hydroxylase interacting protein	protein-coding
mm_6602.1	chr1	75317537	75317545	-	1	NA	promoter-TSS (NM_016878)	promoter-TSS (NM_016878)	96	NM_001110831	13437	Mm.24680	NM_016878	ENSMUSG00000026209	Dnpep	AA407814	aspartyl aminopeptidase	protein-coding
mm_167177.1	chr7	140203675	140203685	+	1	NA	promoter-TSS (NM_001011814)	promoter-TSS (NM_001011814)	-912	NM_001011814	258055	Mm.377339	NM_001011814	ENSMUSG00000050366	Olfr524	MOR103-14P	olfactory receptor 524	protein-coding
mm_73861.1	chr8	118283790	118283803	+	1	NA	5' UTR (NM_019707, exon 1 of 14)	5' UTR (NM_019707, exon 1 of 14)	185	NM_019707	12554	Mm.334841	NM_019707	ENSMUSG00000031841	Cdh13	4932416G01Rik|Cdht|Tcad	cadherin 13	protein-coding
mm_116813.1	chr13	54399247	54399251	-	1	NA	Intergenic	Tigger5b|DNA|TcMar-Tigger	27900	NM_009946	12890	Mm.268902	NM_009946	ENSMUSG00000025867	Cplx2	921-L|AI413745|AW492120	complexin 2	protein-coding
mm_112703.1	chr13	17967337	17967343	+	1	NA	Intergenic	RMER19C|LTR|ERVK	-23123	NM_019491	56044	Mm.27348	NM_019491	ENSMUSG00000008859	Rala	3010001O15Rik|AW322615|Ral|Rasl1	v-ral simian leukemia viral oncogene A (ras related)	protein-coding
mm_122212.1	chr14	32145709	32145725	-	1	NA	intron (NM_020597, intron 1 of 3)	intron (NM_020597, intron 1 of 3)	3694	NM_020597	17695	Mm.2540	NM_020597	ENSMUSG00000021907	Msmb	PIP|PSP94|beta-MSP	beta-microseminoprotein	protein-coding
mm_163480.1	chr12	105785070	105785077	-	1	NA	intron (NM_011112, intron 1 of 21)	CpG	376	NM_001347440	18789	Mm.255877	NM_011112	ENSMUSG00000021111	Papola	Pap|PapIII|Plap	poly (A) polymerase alpha	protein-coding
mm_140954.1	chr17	24614393	24614414	-	1	NA	exon (NM_001286716, exon 19 of 40)	exon (NM_001286716, exon 19 of 40)	18224	NM_011647	22084	Mm.30435	NM_011647	ENSMUSG00000002496	Tsc2	Nafld|Tcs2	tuberous sclerosis 2	protein-coding
mm_82204.1	chr9	124102111	124102166	+	1	NA	promoter-TSS (NM_009915)	promoter-TSS (NM_009915)	-45	NM_009915	12772	Mm.6272	NM_009915	ENSMUSG00000049103	Ccr2	Cc-ckr-2|Ccr2a|Ccr2b|Ckr2|Ckr2a|Ckr2b|Cmkbr2|mJe-r	chemokine (C-C motif) receptor 2	protein-coding
mm_73582.1	chr8	109855004	109855017	+	1	NA	exon (NM_009677, exon 20 of 24)	exon (NM_009677, exon 20 of 24)	-13593	NM_001122594	244650	Mm.23494	NM_001122594	ENSMUSG00000031732	Phlpp2	AI481772|C130044A18Rik|Phlppl	PH domain and leucine rich repeat protein phosphatase 2	protein-coding
mm_158189.1	chrX	104413863	104413871	-	1	NA	promoter-TSS (NM_009592)	promoter-TSS (NM_009592)	-21	NM_009592	11306	Mm.426128	NM_009592	ENSMUSG00000031333	Abcb7	AA517758|AU019072|Abc7	ATP-binding cassette, sub-family B (MDR/TAP), member 7	protein-coding
mm_153673.1	chr19	44396194	44396213	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	11506	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_55034.1	chr6	48987335	48987340	-	1	NA	exon (NM_172888, exon 1 of 5)	exon (NM_172888, exon 1 of 5)	476	NM_172888	243377	Mm.446302	NM_172888	ENSMUSG00000039215	Svs1	9530003A11	seminal vesicle secretory protein 1	protein-coding
mm_153750.1	chr19	45046619	45046645	-	1	NA	promoter-TSS (NM_053197)	promoter-TSS (NM_053197)	-860	NM_001195265	100503041	Mm.329877	NM_177605	ENSMUSG00000074818	Pdzd7	9130207N01|EG435601|Pdzk7	PDZ domain containing 7	protein-coding
mm_39167.1	chr4	155655006	155655024	-	1	NA	intron (NM_001256108, intron 19 of 19)	intron (NM_001256108, intron 19 of 19)	-1631	NM_011985	26561	Mm.29373	NM_011985	ENSMUSG00000029061	Mmp23	CA-MMP	matrix metallopeptidase 23	protein-coding
mm_136642.1	chr17	5803911	5803923	+	1	NA	TTS (NR_045081)	TTS (NR_045081)	4427	NR_045080	78512	Mm.23696	NR_045079	ENSMUSG00000096965	3300005D01Rik	-	RIKEN cDNA 3300005D01 gene	ncRNA
mm_7261.1	chr1	94035484	94035491	-	1	NA	Intergenic	Intergenic	14994	NM_001310769	241159	Mm.214565	NM_173772	ENSMUSG00000034000	Neu4	9330166I04	sialidase 4	protein-coding
mm_49861.1	chr6	38551433	38551493	+	1	NA	5' UTR (NM_001170849, exon 1 of 8)	5' UTR (NM_001170849, exon 1 of 8)	129	NM_001170848	192196	Mm.276133	NM_138680	ENSMUSG00000029823	Luc7l2	4930471C18Rik|AA522013|AU015269|CGI59|Cgi74	LUC7-like 2 (S. cerevisiae)	protein-coding
mm_122877.1	chr14	54926338	54926355	-	1	NA	5' UTR (NM_010112, exon 1 of 6)	5' UTR (NM_010112, exon 1 of 6)	442	NM_010112	13644	Mm.236438	NM_010112	ENSMUSG00000022203	Efs	-	embryonal Fyn-associated substrate	protein-coding
mm_92276.1	chr10	71238008	71238024	-	1	NA	promoter-TSS (NM_009360)	promoter-TSS (NM_009360)	28	NM_009360	21780	Mm.229292	NM_009360	ENSMUSG00000003923	Tfam	AI661103|Hmgts|mtTFA|tsHMG	transcription factor A, mitochondrial	protein-coding
mm_142367.1	chr17	44105918	44105963	-	1	NA	promoter-TSS (NM_199016)	promoter-TSS (NM_199016)	-132	NM_199016	224794	Mm.255971	NM_199016	ENSMUSG00000023961	Enpp4	4933413N07Rik|AA986363|AI195364|E-NPP 4|Gm90|mKIAA0879	ectonucleotide pyrophosphatase/phosphodiesterase 4	protein-coding
mm_73634.1	chr8	110727111	110727131	+	1	NA	exon (NM_198625, exon 4 of 14)	exon (NM_198625, exon 4 of 14)	1395	NM_001310591	244654	Mm.490385	NM_198625	ENSMUSG00000033763	Mtss1l	ABBA	metastasis suppressor 1-like	protein-coding
mm_135658.1	chr16	52402490	52402492	-	1	NA	intron (NM_009655, intron 1 of 15)	intron (NM_009655, intron 1 of 15)	50590	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_77165.1	chr8	111689165	111689228	-	1	NA	TTS (NR_106044)	TTS (NR_106044)	478	NR_106044	102466993		NR_106044	ENSMUSG00000099129	Mir7076	Gm27318|mmu-mir-7076	microRNA 7076	ncRNA
mm_121827.1	chr14	20480077	20480079	-	1	NA	promoter-TSS (NM_001110794)	promoter-TSS (NM_001110794)	55	NM_001110794	11750	Mm.280231	NM_009674	ENSMUSG00000021814	Anxa7	AI265384|AI316497|Anx7|synexin	annexin A7	protein-coding
mm_160999.1	chr11	115979381	115979381	+	1	NA	exon (NM_133663, exon 4 of 39)	exon (NM_133663, exon 4 of 39)	4656	NM_133663	192897	Mm.213873	NM_133663	ENSMUSG00000020758	Itgb4	AA407042|C230078O20|CD104	integrin beta 4	protein-coding
mm_43693.1	chr5	139150825	139150833	+	1	NA	exon (NM_001081265, exon 1 of 13)	exon (NM_001081265, exon 1 of 13)	606	NM_001081265	433956	Mm.5547	NM_001081265	ENSMUSG00000025857	Dnaaf5	BC053401|C76907|Heatr2	dynein, axonemal assembly factor 5	protein-coding
mm_142761.1	chr17	49113478	49113520	-	1	NA	promoter-TSS (NR_038142)	promoter-TSS (NR_038142)	34	NR_038141	69311	Mm.46140	NR_038141	ENSMUSG00000101012	1700008K24Rik	-	RIKEN cDNA 1700008K24 gene	ncRNA
mm_28567.1	chr3	93444974	93445020	-	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	2667	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_113927.1	chr13	49609034	49609044	+	1	NA	intron (NM_008760, intron 1 of 6)	intron (NM_008760, intron 1 of 6)	968	NM_008760	18295	Mm.4258	NM_008760	ENSMUSG00000021390	Ogn	3110079A16Rik|OG|OIF|SLRR3A|mimecan|mimican	osteoglycin	protein-coding
mm_37505.1	chr4	123750299	123750309	-	1	NA	promoter-TSS (NM_023423)	promoter-TSS (NM_023423)	-5	NM_023423	68050	Mm.27903	NM_023423	ENSMUSG00000023075	Akirin1	6330407G11Rik	akirin 1	protein-coding
mm_21282.1	chr2	156953364	156953378	-	1	NA	intron (NM_013865, intron 3 of 15)	intron (NM_013865, intron 3 of 15)	38740	NM_013865	29812	Mm.279256	NM_013865	ENSMUSG00000027634	Ndrg3	4833415O14Rik|AI747193|Ndr3	N-myc downstream regulated gene 3	protein-coding
mm_91636.1	chr10	42270342	42270346	-	1	NA	intron (NM_019740, intron 2 of 3)	intron (NM_019740, intron 2 of 3)	6398	NM_019740	56484	Mm.338613	NM_019740	ENSMUSG00000048756	Foxo3	1110048B16Rik|2010203A17Rik|C76856|FKHRL1|Fkhr2|Foxo3a	forkhead box O3	protein-coding
mm_171640.1	chr4	28461497	28461502	+	1	NA	Intergenic	Intergenic	-351632	NM_001290434	13841	Mm.257266	NM_010141	ENSMUSG00000028289	Epha7	Cek11|Ebk|Ehk3|Hek11|Mdk1	Eph receptor A7	protein-coding
mm_31268.1	chr4	45320419	45320429	+	1	NA	exon (NM_025513, exon 1 of 4)	exon (NM_025513, exon 1 of 4)	179	NM_025513	66362	Mm.275788	NM_025513	ENSMUSG00000028322	Exosc3	2310005D06Rik|AI593501|Rrp40	exosome component 3	protein-coding
mm_159869.1	chr5	146009619	146009619	-	1	NA	promoter-TSS (NM_019792)	promoter-TSS (NM_019792)	-1	NR_030782	56388	Mm.301900	NM_019792	ENSMUSG00000029630	Cyp3a25	AI327008	cytochrome P450, family 3, subfamily a, polypeptide 25	protein-coding
mm_124981.1	chr15	20744236	20744238	+	1	NA	Intergenic	Lx3A|LINE|L1	-77487	NM_022816	64833	Mm.352763	NM_022816	ENSMUSG00000047565	Acot10	Acate3|MT-ACT48|p48	acyl-CoA thioesterase 10	protein-coding
mm_12306.1	chr2	69112539	69112583	+	1	NA	3' UTR (NM_001347161, exon 11 of 11)	3' UTR (NM_001347161, exon 11 of 11)	-23239	NM_181547	329416	Mm.90047	NM_181547	ENSMUSG00000034738	Nostrin	Daip2|mDaIP2	nitric oxide synthase trafficker	protein-coding
mm_61623.1	chr7	80198391	80198458	+	1	NA	intron (NM_013659, intron 1 of 14)	CpG	11583	NM_013659	20352	Mm.275909	NM_013659	ENSMUSG00000030539	Sema4b	SemC|Semac|mKIAA1745	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B	protein-coding
mm_123422.1	chr14	64417782	64417790	-	1	NA	promoter-TSS (NM_001253716)	promoter-TSS (NM_001253716)	-507	NM_001347639	110265	Mm.26713	NM_026322	ENSMUSG00000054733	Msra	2310045J23Rik|6530413P12Rik|MSR-A	methionine sulfoxide reductase A	protein-coding
mm_11382.1	chr2	31246070	31246120	+	1	NA	5' UTR (NM_019681, exon 1 of 8)	5' UTR (NM_019681, exon 1 of 8)	172	NM_019681	14299	Mm.249318	NM_019681	ENSMUSG00000062661	Ncs1	9430075O15Rik|A730032G13Rik|AI836659|Freq|Mfreq|NCS-1	neuronal calcium sensor 1	protein-coding
mm_3378.1	chr1	139422197	139422263	+	1	NA	promoter-TSS (NM_172643)	promoter-TSS (NM_172643)	-153	NM_172643	226470	Mm.119711	NM_172643	ENSMUSG00000033964	Zbtb41	8430415N23Rik|9430031N01|9830132G07Rik|AI316857	zinc finger and BTB domain containing 41	protein-coding
mm_170705.1	chr2	140105514	140105514	+	1	NA	Intergenic	Intergenic	-38709	NR_110351	75812	Mm.293449	NM_175225	ENSMUSG00000039033	Tasp1	4930485D02Rik|AW986064	taspase, threonine aspartase 1	protein-coding
mm_119970.1	chr14	55540352	55540370	+	1	NA	promoter-TSS (NM_028994)	promoter-TSS (NM_028994)	95	NM_028994	74551	Mm.29856	NM_028994	ENSMUSG00000040618	Pck2	1810010O14Rik|9130022B02Rik|PEPCK-M	phosphoenolpyruvate carboxykinase 2 (mitochondrial)	protein-coding
mm_27171.1	chr3	33844256	33844313	-	1	NA	promoter-TSS (NM_026222)	promoter-TSS (NM_026222)	26	NM_026222	51938	Mm.275710	NM_026222	ENSMUSG00000027676	Ccdc39	4921507O14Rik|AI447426|AI844750|D3Ertd789e|b2b1304Clo|b2b1735Clo|b2b2025.1Clo	coiled-coil domain containing 39	protein-coding
mm_156963.1	chrX	169989963	169989973	+	1	NA	3' UTR (NM_001290504, exon 10 of 10)	3' UTR (NM_001290504, exon 10 of 10)	-11051	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_94893.1	chr11	28854301	28854322	+	1	NA	intron (NM_146015, intron 1 of 10)	intron (NM_146015, intron 1 of 10)	1106	NM_146015	216616	Mm.44176	NM_146015	ENSMUSG00000020467	Efemp1	-	epidermal growth factor-containing fibulin-like extracellular matrix protein 1	protein-coding
mm_45229.1	chr5	53589255	53589265	-	1	NA	intron (NM_001080928, intron 1 of 10)	CpG	-1086	NM_009035	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_99370.1	chr11	101936674	101936685	+	1	NA	Intergenic	Lx8|LINE|L1	-15742	NR_045806	73887	Mm.159084	NR_045806	ENSMUSG00000071818	4930417O22Rik	-	RIKEN cDNA 4930417O22 gene	ncRNA
mm_63970.1	chr7	139944692	139944710	+	1	NA	exon (NM_009482, exon 2 of 2)	exon (NM_009482, exon 2 of 2)	845	NM_009482	22286	Mm.10205	NM_009482	ENSMUSG00000047751	Utf1	AI505934	undifferentiated embryonic cell transcription factor 1	protein-coding
mm_51623.1	chr6	85441706	85441716	+	1	NA	intron (NM_144918, intron 7 of 12)	intron (NM_144918, intron 7 of 12)	9591	NM_001163427	73327	Mm.379221	NM_028505	ENSMUSG00000030008	Pradc1	1700040I03Rik|Pap21	protease-associated domain containing 1	protein-coding
mm_150616.1	chr19	40965765	40965770	+	1	NA	intron (NM_008528, intron 3 of 16)	MER5A1|DNA|hAT-Charlie	28768	NM_008528	17060	Mm.9749	NM_008528	ENSMUSG00000061132	Blnk	BASH|Bca|Ly-57|Ly57|Lyw-57|SLP-65	B cell linker	protein-coding
mm_122676.1	chr14	52009185	52009204	-	1	NA	exon (NM_001253694, exon 4 of 6)	exon (NM_001253694, exon 4 of 6)	5364	NM_001253695	69890	Mm.475652	NM_027248	ENSMUSG00000049295	Zfp219	2010302A17Rik	zinc finger protein 219	protein-coding
mm_49076.1	chr6	6248676	6248693	+	1	NA	promoter-TSS (NR_136906)	promoter-TSS (NR_136906)	25	NR_136905	101056138	Mm.389085	NR_136904	ENSMUSG00000093482	Gm20619	-	predicted gene 20619	ncRNA
mm_126064.1	chr15	77017708	77017732	+	1	NA	exon (NM_013593, exon 3 of 4)	exon (NM_013593, exon 3 of 4)	5007	NM_001164048	17189	Mm.404074	NM_013593	ENSMUSG00000018893	Mb	AI325109	myoglobin	protein-coding
mm_134136.1	chr16	10683534	10683544	-	1	NA	intron (NM_001204229, intron 18 of 22)	intron (NM_001204229, intron 18 of 22)	101997	NM_009896	12703	Mm.130	NM_009896	ENSMUSG00000038037	Socs1	Cish1|Cish7|JAB|SOCS-1|SSI-1	suppressor of cytokine signaling 1	protein-coding
mm_49743.1	chr6	34745895	34745910	+	1	NA	exon (NM_145575, exon 3 of 12)	exon (NM_145575, exon 3 of 12)	-34530	NM_001289657	76223	Mm.150047	NM_178630	ENSMUSG00000038836	Agbl3	2900053G10Rik|4930431N21Rik|6530406M24Rik|CCP3	ATP/GTP binding protein-like 3	protein-coding
mm_126033.1	chr15	76870943	76870958	+	1	NA	5' UTR (NM_001007568, exon 1 of 4)	5' UTR (NM_001007568, exon 1 of 4)	485	NM_001007568	71591	Mm.38195	NM_001007568	ENSMUSG00000022526	Zfp251	9130001M19Rik|AV339307	zinc finger protein 251	protein-coding
mm_13117.1	chr2	91663926	91663948	+	1	NA	intron (NR_027371, intron 5 of 13)	intron (NR_027371, intron 5 of 13)	10729	NM_146124	228359	Mm.22413	NM_146124	ENSMUSG00000027247	Arhgap1	B230365D05Rik|C76222|Cdc42GAP|p50rhoGAP	Rho GTPase activating protein 1	protein-coding
mm_86640.1	chr10	14108826	14108830	+	1	NA	intron (NM_010437, intron 2 of 8)	intron (NM_010437, intron 2 of 8)	142449	NM_010437	15273	Mm.42157	NM_010437	ENSMUSG00000015501	Hivep2	Gm20114|MIBP1|Schnurri-2|Shn-2	human immunodeficiency virus type I enhancer binding protein 2	protein-coding
mm_158230.1	chrX	106255368	106255376	-	1	NA	promoter-TSS (NM_001033424)	promoter-TSS (NM_001033424)	0	NM_001033424	331491	Mm.426150	NM_001033424	ENSMUSG00000073012	Fnd3c2	5031408O05Rik|Gm775	fibronectin type III domain containing 3C2	protein-coding
mm_138165.1	chr17	34263225	34263256	+	1	NA	promoter-TSS (NM_207105)	promoter-TSS (NM_207105)	13	NM_207105	14961	Mm.254067	NM_207105	ENSMUSG00000073421	H2-Ab1	AI845868|Abeta|H-2Ab|H2-Ab|I-Abeta|IAb|Ia-2|Ia2|Rmcs1	histocompatibility 2, class II antigen A, beta 1	protein-coding
mm_153284.1	chr19	37263922	37263928	-	1	NA	non-coding (NR_040299, exon 1 of 3)	non-coding (NR_040299, exon 1 of 3)	170	NR_040299	77059	Mm.251476	NR_040298		4931408D14Rik	-	RIKEN cDNA 4931408D14 gene	ncRNA
mm_1251.1	chr1	62816655	62816666	+	1	NA	3' UTR (NM_010939, exon 16 of 16)	3' UTR (NM_010939, exon 16 of 16)	-21928	NR_040601	74992	Mm.401979	NR_040601		4930487H11Rik	-	RIKEN cDNA 4930487H11 gene	ncRNA
mm_72733.1	chr8	85083304	85083323	+	1	NA	promoter-TSS (NM_010764)	promoter-TSS (NM_010764)	44	NM_010764	17159	Mm.4219	NM_010764	ENSMUSG00000005142	Man2b1	AW107687|LAMAN	mannosidase 2, alpha B1	protein-coding
mm_56535.1	chr6	99628943	99628945	-	1	NA	intron (NM_025829, intron 6 of 6)	B4A|SINE|B4	37827	NM_025829	66892	Mm.32889	NM_025829	ENSMUSG00000093661	Eif4e3	1300018P11Rik|AI451927|eIF4E-3	eukaryotic translation initiation factor 4E member 3	protein-coding
mm_7977.1	chr1	134093904	134093927	-	1	NA	Intergenic	Intergenic	-14760	NM_007570	12227	Mm.392646	NM_007570	ENSMUSG00000020423	Btg2	AA959598|APRO1|Pc3|TIS21	B cell translocation gene 2, anti-proliferative	protein-coding
mm_161826.1	chr17	79052153	79052153	+	1	NA	5' UTR (NM_001316729, exon 1 of 6)	5' UTR (NM_001316729, exon 1 of 6)	247	NM_001316729	70536	Mm.293870	NM_027455	ENSMUSG00000024084	Qpct	5730422A13Rik	glutaminyl-peptide cyclotransferase (glutaminyl cyclase)	protein-coding
mm_37923.1	chr4	132796362	132796389	-	1	NA	promoter-TSS (NM_001033308)	promoter-TSS (NM_001033308)	-11	NM_001033308	230787	Mm.290912	NM_001033308	ENSMUSG00000037731	Themis2	ICB-1	thymocyte selection associated family member 2	protein-coding
mm_82559.1	chr9	21028385	21028409	-	1	NA	promoter-TSS (NM_023892)	promoter-TSS (NM_023892)	-976	NM_023892	78369	Mm.30220	NM_023892	ENSMUSG00000001014	Icam4	1810015M19Rik|Cd242|ICAM-4	intercellular adhesion molecule 4, Landsteiner-Wiener blood group	protein-coding
mm_22333.1	chr2	180709041	180709074	-	1	NA	intron (NM_177852, intron 1 of 14)	intron (NM_177852, intron 1 of 14)	942	NM_177852	23856	Mm.253836	NM_011805	ENSMUSG00000038914	Dido1	6720461J16Rik|D130048F08Rik|DATF-1|DIO-1|Datf1|dido	death inducer-obliterator 1	protein-coding
mm_112622.1	chr13	15613838	15613850	+	1	NA	exon (NM_008130, exon 4 of 15)	exon (NM_008130, exon 4 of 15)	150121	NM_008130	14634	Mm.5098	NM_008130	ENSMUSG00000021318	Gli3	AI854843|AU023367|Bph|GLI3-190|GLI3FL|Pdn|Xt|add	GLI-Kruppel family member GLI3	protein-coding
mm_99010.1	chr11	98836837	98836859	+	1	NA	promoter-TSS (NM_001080925)	promoter-TSS (NM_001080925)	63	NM_001080925	268480	Mm.340766	NM_001080925	ENSMUSG00000038020	Rapgefl1	B230105J10	Rap guanine nucleotide exchange factor (GEF)-like 1	protein-coding
mm_71094.1	chr8	34821529	34821547	+	1	NA	Intergenic	Intergenic	13928	NM_176933	319520	Mm.170276	NM_176933	ENSMUSG00000031530	Dusp4	2700078F24Rik|AI844617|BB104621|E130306H24Rik|MKP2	dual specificity phosphatase 4	protein-coding
mm_123196.1	chr14	59142887	59142898	-	1	NA	promoter-TSS (NM_026461)	promoter-TSS (NM_026461)	1	NM_026461	67932	Mm.65550	NM_026461	ENSMUSG00000021977	1700129C05Rik	-	RIKEN cDNA 1700129C05 gene	protein-coding
mm_5643.1	chr1	40475786	40475790	-	1	NA	intron (NM_008365, intron 3 of 10)	intron (NM_008365, intron 3 of 10)	9782	NM_008365	16182	Mm.253664	NM_008365	ENSMUSG00000026070	Il18r1	Il18ralpha|Il1rrp	interleukin 18 receptor 1	protein-coding
mm_105782.1	chr11	109797312	109797333	-	1	NA	exon (NM_001162428, exon 3 of 6)	exon (NM_001162428, exon 3 of 6)	30724	NM_027038	69324	Mm.31700	NM_027038	ENSMUSG00000020617	1700012B07Rik	1700069D21Rik	RIKEN cDNA 1700012B07 gene	protein-coding
mm_35351.1	chr4	32258154	32258165	-	1	NA	Intergenic	Intergenic	-159276	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_69407.1	chr7	132323529	132323550	-	1	NA	Intergenic	MLT2B4|LTR|ERVL	-6384	NM_029935	77590	Mm.213582	NM_029935	ENSMUSG00000030930	Chst15	4631426J05Rik|BRAG|GalNAcS-6ST|MAd5|mKIAA0598	carbohydrate (N-acetylgalactosamine 4-sulfate 6-O) sulfotransferase 15	protein-coding
mm_165034.1	chr19	35783545	35783545	+	1	NA	Intergenic	Intergenic	273815	NM_001347442	15566	Mm.254266	NM_008315	ENSMUSG00000024798	Htr7	5-HT7	5-hydroxytryptamine (serotonin) receptor 7	protein-coding
mm_21685.1	chr2	164431262	164431273	-	1	NA	exon (NM_011521, exon 2 of 5)	exon (NM_011521, exon 2 of 5)	11921	NM_011521	20971	Mm.3815	NM_011521	ENSMUSG00000017009	Sdc4	AA959608|AW108331|S4|Synd4|ryudocan|syndecan-4	syndecan 4	protein-coding
mm_100436.1	chr11	119486185	119486204	+	1	NA	Intergenic	Intergenic	-5153	NM_001164636	338371	Mm.271946	NM_177394	ENSMUSG00000039850	Endov	A730011L01Rik	endonuclease V	protein-coding
mm_155514.1	chrX	74202413	74202420	+	1	NA	intron (NM_031379, intron 8 of 12)	intron (NM_031379, intron 8 of 12)	25157	NM_031379	83553	Mm.25057	NM_031379	ENSMUSG00000031397	Tktl1	C79967	transketolase-like 1	protein-coding
mm_127065.1	chr15	97373389	97373402	+	1	NA	intron (NM_172293, intron 4 of 5)	intron (NM_172293, intron 4 of 5)	-126108	NM_001164602	105827	Mm.24005	NM_178114	ENSMUSG00000048218	Amigo2	AI415330|AMIGO-2|AW208913|Ali1	adhesion molecule with Ig like domain 2	protein-coding
mm_93904.1	chr10	126905945	126905963	-	1	NA	Intergenic	CpG	-4583	NM_001159559	68876	Mm.276769	NM_026858	ENSMUSG00000025436	Xrcc6bp1	1110068E08Rik|2410012H02Rik|Atp23	XRCC6 binding protein 1	protein-coding
mm_63679.1	chr7	130552908	130552918	+	1	NA	Intergenic	Intergenic	-5532	NM_001162855	67872	Mm.21714	NM_001162855	ENSMUSG00000040331	Nsmce4a	2410003A14Rik	NSE4 homolog A, SMC5-SMC6 complex component	protein-coding
mm_91978.1	chr10	61680041	61680064	-	1	NA	promoter-TSS (NM_009120)	promoter-TSS (NM_009120)	238	NR_126477	75539		NR_126477		1700022H01Rik	-	RIKEN cDNA 1700022H01 gene	ncRNA
mm_8759.1	chr1	160352086	160352116	-	1	NA	promoter-TSS (NM_001038621)	promoter-TSS (NM_001038621)	-530	NM_001038621	29809	Mm.25833	NM_013862	ENSMUSG00000026721	Rabgap1l	5830411O09Rik|8430421H08Rik|9630005B12Rik|AW049894|HHL|Hh1|mKIAA0471	RAB GTPase activating protein 1-like	protein-coding
mm_131224.1	chr16	9133266	9133277	+	1	NA	Intergenic	RLTR41C|LTR|ERV1	303171	NM_001081400	69053	Mm.390868	NM_001081400	ENSMUSG00000022507	1810013L24Rik	1110017P05Rik|3010002C02Rik|AA792997|AW124177|Gm19906|R74903	RIKEN cDNA 1810013L24 gene	protein-coding
mm_8045.1	chr1	135313730	135313760	-	1	NA	promoter-TSS (NM_011590)	promoter-TSS (NM_011590)	-8	NM_011590	21854	Mm.2368	NM_011590	ENSMUSG00000062580	Timm17a	17kDa|mTim17a	translocase of inner mitochondrial membrane 17a	protein-coding
mm_172479.1	chr7	4948654	4948657	+	1	NA	Intergenic	Intergenic	15693	NM_001146329	381836	Mm.297829	NM_001146329	ENSMUSG00000030433	Sbk2	Gm1079|Sgk069	SH3-binding domain kinase family, member 2	protein-coding
mm_87286.1	chr10	42308421	42308425	+	1	NA	Intergenic	Intergenic	-31681	NM_019740	56484	Mm.338613	NM_019740	ENSMUSG00000048756	Foxo3	1110048B16Rik|2010203A17Rik|C76856|FKHRL1|Fkhr2|Foxo3a	forkhead box O3	protein-coding
mm_134314.1	chr16	15895708	15895721	-	1	NA	intron (NM_146068, intron 17 of 19)	intron (NM_146068, intron 17 of 19)	8428	NM_007679	12609	Mm.347407	NM_007679	ENSMUSG00000071637	Cebpd	c/EBPdelta	CCAAT/enhancer binding protein (C/EBP), delta	protein-coding
mm_98323.1	chr11	90257362	90257378	+	1	NA	intron (NM_026178, intron 1 of 6)	intron (NM_026178, intron 1 of 6)	7894	NM_026178	67468	Mm.277518	NM_026178	ENSMUSG00000003948	Mmd	1200017E07Rik|1810073C06Rik|AA690185	monocyte to macrophage differentiation-associated	protein-coding
mm_138869.1	chr17	43045918	43045933	+	1	NA	intron (NM_178589, intron 3 of 5)	B1F|SINE|Alu	29370	NM_178589	94185	Mm.200792	NM_178589	ENSMUSG00000023915	Tnfrsf21	AA959878|DR6|R74815|TR7	tumor necrosis factor receptor superfamily, member 21	protein-coding
mm_157571.1	chrX	52578139	52578142	-	1	NA	intron (NR_045367, intron 1 of 4)	MIRc|SINE|MIR	2297	NR_045367	100504594	Mm.447008	NR_045367	ENSMUSG00000055110	A630012P03Rik	-	RIKEN cDNA A630012P03 gene	ncRNA
mm_67172.1	chr7	73557946	73557966	-	1	NA	intron (NR_037569, intron 1 of 4)	CpG	439	NR_037569	69170	Mm.34539	NR_037569	ENSMUSG00000101970	1810026B05Rik	-	RIKEN cDNA 1810026B05 gene	ncRNA
mm_132986.1	chr16	52413924	52413933	+	1	NA	intron (NM_009655, intron 1 of 15)	intron (NM_009655, intron 1 of 15)	39153	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_170874.1	chr2	20899897	20899899	+	1	NA	intron (NM_001128084, intron 3 of 24)	LSU-rRNA_Hsa|rRNA|rRNA	67823	NM_001081364	71435	Mm.28507	NM_001081364	ENSMUSG00000036591	Arhgap21	5530401C11Rik|AA416458|ARHGAP10	Rho GTPase activating protein 21	protein-coding
mm_20532.1	chr2	131041294	131041313	-	1	NA	promoter-TSS (NR_105969)	promoter-TSS (NR_105969)	-905	NR_105969	102465606		NR_105969	ENSMUSG00000098686	Mir6973b	Gm27815|mmu-mir-6973b	microRNA 6973b	ncRNA
mm_34308.1	chr4	141814958	141814971	+	1	NA	TTS (NM_007919)	TTS (NM_007919)	11041	NM_007919	13706	Mm.45316	NM_007919	ENSMUSG00000058579	Cela2a	Ela-2|Ela2|Ela2a	chymotrypsin-like elastase family, member 2A	protein-coding
mm_116150.1	chr13	29984300	29984353	-	1	NA	promoter-TSS (NM_001289920)	promoter-TSS (NM_001289920)	65	NM_001289920	13557	Mm.268356	NM_010093	ENSMUSG00000016477	E2f3	E2F3b|E2f3a	E2F transcription factor 3	protein-coding
mm_28591.1	chr3	94435889	94435893	-	1	NA	intron (NM_016901, intron 2 of 4)	intron (NM_016901, intron 2 of 4)	760	NM_016901	53814	Mm.440422	NM_016901	ENSMUSG00000028141	Oaz3	AZ3|Az-3|Oaz-t	ornithine decarboxylase antizyme 3	protein-coding
mm_167654.1	chr9	67420200	67420201	+	1	NA	intron (NM_001081242, intron 2 of 57)	intron (NM_001081242, intron 2 of 57)	139503	NM_001081242	70549	Mm.33645	NM_027458	ENSMUSG00000052698	Tln2	5730421P04Rik|AI507121|AI787438|AL118320|mKIAA0320	talin 2	protein-coding
mm_150807.1	chr19	44376782	44376797	+	1	NA	Intergenic	Intergenic	30920	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_148406.1	chr19	3851973	3851981	+	1	NA	non-coding (NR_073190, exon 1 of 13)	non-coding (NR_073190, exon 1 of 13)	204	NR_073190	12660	Mm.225505	NM_013490	ENSMUSG00000024843	Chka	CK|CK/EK-alpha|Chetk-alpha|Chk|ChoK|EK|EtnK-alpha	choline kinase alpha	protein-coding
mm_51013.1	chr6	65022192	65022202	+	1	NA	Intergenic	Intergenic	-20470	NM_007958	13990	Mm.99113	NM_007958	ENSMUSG00000029920	Smarcad1	AV081750|AW226546|D6Pas1|Etl1|mKIAA1122	SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1	protein-coding
mm_3030.1	chr1	133754894	133754895	+	1	NA	Intergenic	Intergenic	-1147	NM_213616	381290	Mm.188617	NM_213616	ENSMUSG00000026463	Atp2b4	Pmca4	ATPase, Ca++ transporting, plasma membrane 4	protein-coding
mm_138328.1	chr17	34850560	34850576	+	1	NA	promoter-TSS (NM_021337)	promoter-TSS (NM_021337)	177	NM_001045864	27632	Mm.653	NM_138580	ENSMUSG00000024369	Nelfe	D17H6S45|NELF-E|RD|Rdbp	negative elongation factor complex member E, Rdbp	protein-coding
mm_137525.1	chr17	27342454	27342470	+	1	NA	Intergenic	Intergenic	-13276	NR_106076	102465701		NR_106076	ENSMUSG00000106578	Mir7217	mmu-mir-7217	microRNA 7217	ncRNA
mm_24077.1	chr3	87930438	87930449	+	1	NA	promoter-TSS (NM_153562)	promoter-TSS (NM_153562)	129	NM_177663	229504	Mm.45744	NM_177663	ENSMUSG00000048039	Isg20l2	4930429N24|C80587	interferon stimulated exonuclease gene 20-like 2	protein-coding
mm_66393.1	chr7	44241225	44241240	-	1	NA	Intergenic	PB1D7|SINE|Alu	-5110	NR_029436	70004	Mm.158317	NR_029436	ENSMUSG00000038782	1700028J19Rik	-	RIKEN cDNA 1700028J19 gene	ncRNA
mm_107172.1	chr12	24713693	24713699	+	1	NA	3' UTR (NM_009104, exon 10 of 10)	3' UTR (NM_009104, exon 10 of 10)	5442	NM_009104	20135	Mm.99	NM_009104	ENSMUSG00000020649	Rrm2	AA407299|R2	ribonucleotide reductase M2	protein-coding
mm_38386.1	chr4	138809805	138809812	-	1	NA	intron (NM_011110, intron 1 of 4)	intron (NM_011110, intron 1 of 4)	9449	NM_011110	18784	Mm.486532	NM_011110	ENSMUSG00000041193	Pla2g5	PLA2|sPLA2	phospholipase A2, group V	protein-coding
mm_7371.1	chr1	106759661	106759688	-	1	NA	promoter-TSS (NM_027534)	promoter-TSS (NM_027534)	68	NM_027534	70750	Mm.458911	NM_027534	ENSMUSG00000009905	Kdsr	6330410P18Rik|9430079B08Rik|Fvt1	3-ketodihydrosphingosine reductase	protein-coding
mm_141532.1	chr17	31849572	31849597	-	1	NA	exon (NM_010831, exon 9 of 14)	exon (NM_010831, exon 9 of 14)	6208	NM_010831	17691	Mm.290941	NM_010831	ENSMUSG00000024042	Sik1	Msk|Sik|Snf1lk	salt inducible kinase 1	protein-coding
mm_121620.1	chr14	8298367	8298375	-	1	NA	3' UTR (NM_183187, exon 4 of 4)	3' UTR (NM_183187, exon 4 of 4)	11405	NM_183187	268709	Mm.256058	NM_183187	ENSMUSG00000021750	Fam107a	DRR1	family with sequence similarity 107, member A	protein-coding
mm_13469.1	chr2	105682489	105682491	+	1	NA	promoter-TSS (NM_001310145)	promoter-TSS (NM_001310145)	27	NM_001310145	18508	Mm.3608	NM_013627	ENSMUSG00000027168	Pax6	1500038E17Rik|AEY11|Dey|Gsfaey11|Pax-6|Sey	paired box 6	protein-coding
mm_153385.1	chr19	40377052	40377064	-	1	NA	intron (NM_178362, intron 6 of 28)	intron (NM_178362, intron 6 of 28)	25252	NM_001034964	20411	Mm.210815	NM_009166	ENSMUSG00000025006	Sorbs1	2310065E01Rik|9530001P15Rik|CAP|SH3P12|Sh3d5|mKIAA1296	sorbin and SH3 domain containing 1	protein-coding
mm_124258.1	chr14	102828184	102828198	-	1	NA	Intergenic	Intergenic	154441	NR_039592	100628599		NR_039592	ENSMUSG00000092901	Mir5130	mir-5130|mmu-mir-5130|mu-mir-5130	microRNA 5130	ncRNA
mm_33019.1	chr4	121039682	121039697	+	1	NA	5' UTR (NM_007741, exon 1 of 32)	5' UTR (NM_007741, exon 1 of 32)	123	NM_007741	12840	Mm.269384	NM_007741	ENSMUSG00000028626	Col9a2	AI427499|Col9a-2	collagen, type IX, alpha 2	protein-coding
mm_31470.1	chr4	49632047	49632110	+	1	NA	promoter-TSS (NM_001163263)	promoter-TSS (NM_001163263)	18	NM_182999	109331	Mm.24765	NM_182999	ENSMUSG00000028309	Rnf20	4833430L21Rik|AW540162|C79397|mKIAA4116	ring finger protein 20	protein-coding
mm_45927.1	chr5	89445318	89445328	-	1	NA	exon (NM_008096, exon 3 of 13)	exon (NM_008096, exon 3 of 13)	12575	NM_008096	14473	Mm.196595	NM_008096	ENSMUSG00000035540	Gc	DBP|VDB	group specific component	protein-coding
mm_73057.1	chr8	94377897	94377907	+	1	NA	Intergenic	Intergenic	-8598	NM_022331	64209	Mm.29151	NM_022331	ENSMUSG00000031770	Herpud1	Herp|Mifl|SUP	homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1	protein-coding
mm_113605.1	chr13	41249812	41249837	+	1	NA	promoter-TSS (NM_001135577)	promoter-TSS (NM_001135577)	-20	NM_001135577	108934	Mm.38578	NM_001135577	ENSMUSG00000091264	Smim13	2900036K02Rik	small integral membrane protein 13	protein-coding
mm_103330.1	chr11	74572682	74572690	-	1	NA	intron (NM_001015046, intron 1 of 24)	intron (NM_001015046, intron 1 of 24)	17472	NM_001015046	380711	Mm.425690	NM_001015046	ENSMUSG00000038807	Rap1gap2	AU067654|Garnl4|Gm1561|mKIAA1039	RAP1 GTPase activating protein 2	protein-coding
mm_140129.1	chr17	79615237	79615252	+	1	NA	intron (NM_201361, intron 1 of 10)	CpG	344	NM_201361	381110	Mm.209801	NM_201361	ENSMUSG00000036368	Rmdn2	AW061290|Fam82a1|RMD-2|mRMD-2	regulator of microtubule dynamics 2	protein-coding
mm_5791.1	chr1	51896068	51896083	-	1	NA	intron (NM_001290982, intron 1 of 28)	intron (NM_001290982, intron 1 of 28)	19903	NM_001290982	17912	Mm.3390	NM_010863	ENSMUSG00000018417	Myo1b	AA406997|MIH-L|MMIa	myosin IB	protein-coding
mm_48206.1	chr5	137600627	137600645	-	1	NA	promoter-TSS (NM_001254762)	promoter-TSS (NM_001254762)	72	NM_001254762	68929	Mm.41355	NM_030037	ENSMUSG00000037221	Mospd3	1190005J19Rik|5133401H10Rik|Gtig2|R124	motile sperm domain containing 3	protein-coding
mm_62575.1	chr7	104332099	104332110	+	1	NA	intron (NM_001243916, intron 3 of 6)	intron (NM_001243916, intron 3 of 6)	2633	NM_001243916	434218	Mm.485757	NM_001243916	ENSMUSG00000090215	Trim34b	Gm15134|OTTMUSG00000019188|Trim34-2	tripartite motif-containing 34B	protein-coding
mm_147860.1	chr18	64277158	64277169	-	1	NA	promoter-TSS (NR_045366)	promoter-TSS (NR_045366)	17	NR_045366	73588	Mm.65475	NR_045366	ENSMUSG00000086128	St8sia3os	1700091E21Rik	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3, opposite strand	ncRNA
mm_98856.1	chr11	97663196	97663281	+	1	NA	promoter-TSS (NM_139311)	promoter-TSS (NM_139311)	-174	NM_139311	246198	Mm.23685	NM_139311	ENSMUSG00000038437	Mllt6	AI315037|Af17	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 6	protein-coding
mm_123815.1	chr14	70523454	70523462	-	1	NA	intron (NM_011359, intron 1 of 5)	RSINE1|SINE|B4	623	NM_011359	20389	Mm.24040	NM_011359	ENSMUSG00000022097	Sftpc	Bricd6|SP-C|SP5|SPC|Sftp-2|Sftp2|pro-SpC	surfactant associated protein C	protein-coding
mm_148795.1	chr19	6174864	6174908	+	1	NA	Intergenic	Intergenic	-9524	NM_001165919	622554	Mm.159757	NM_001165919	ENSMUSG00000024786	Majin	1700123I01Rik	membrane anchored junction protein	protein-coding
mm_30694.1	chr4	11579648	11579674	+	1	NA	promoter-TSS (NM_001256142)	promoter-TSS (NM_001256142)	-1	NM_001256142	100503583	Mm.249437	NM_001256142	ENSMUSG00000094595	Fsbp	-	fibrinogen silencer binding protein	protein-coding
mm_9181.1	chr1	171059349	171059379	-	1	NA	promoter-TSS (NM_010188)	promoter-TSS (NM_010188)	39	NM_010188	14131	Mm.22119	NM_010188	ENSMUSG00000059498	Fcgr3	CD16	Fc receptor, IgG, low affinity III	protein-coding
mm_72698.1	chr8	84977765	84977798	+	1	NA	exon (NM_008416, exon 1 of 1)	exon (NM_008416, exon 1 of 1)	967	NM_008416	16477	Mm.1167	NM_008416	ENSMUSG00000052837	Junb	-	jun B proto-oncogene	protein-coding
mm_77647.1	chr8	124563767	124563777	-	1	NA	exon (NM_007428, exon 2 of 5)	exon (NM_007428, exon 2 of 5)	5935	NM_007428	11606	Mm.301626	NM_007428	ENSMUSG00000031980	Agt	AI265500|AngI|AngII|Aogen|Serpina8	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	protein-coding
mm_9536.1	chr1	173872947	173872967	-	1	NA	exon (NM_001170853, exon 5 of 10)	exon (NM_001170853, exon 5 of 10)	7230	NM_001170853	100040462	Mm.463437	NM_001170853	ENSMUSG00000090272	Mndal	Gm2785|Ifi212	myeloid nuclear differentiation antigen like	protein-coding
mm_499.1	chr1	36984594	36984629	+	1	NA	Intergenic	RMER10A|LTR|ERVL	-45084	NM_018872	56030	Mm.186943	NM_018872	ENSMUSG00000026116	Tmem131	2610524E03Rik|CC28|D1Bwg0491e|Neg|RW1|YR-23|mKIAA0257	transmembrane protein 131	protein-coding
mm_137633.1	chr17	28329370	28329387	+	1	NA	exon (NM_011287, exon 4 of 6)	exon (NM_011287, exon 4 of 6)	907	NM_011287	19896	Mm.336955	NM_011287	ENSMUSG00000037805	Rpl10a	CsA-19|Nedd6	ribosomal protein L10A	protein-coding
mm_43925.1	chr5	144789024	144789029	+	1	NA	intron (NM_001081362, intron 13 of 70)	MTD|LTR|ERVL-MaLR	20234	NM_001081362	100683	Mm.273570	NM_001081362	ENSMUSG00000045482	Trrap	AI481500	transformation/transcription domain-associated protein	protein-coding
mm_145083.1	chr18	42394563	42394575	+	1	NA	promoter-TSS (NM_138945)	promoter-TSS (NM_138945)	-28	NM_138945	18998	Mm.488204	NM_138945	ENSMUSG00000024497	Pou4f3	Brn3.1|Brn3c|ddl|dreidel	POU domain, class 4, transcription factor 3	protein-coding
mm_154618.1	chrX	7697189	7697219	+	1	NA	promoter-TSS (NM_173747)	promoter-TSS (NM_173747)	70	NM_173747	209416	Mm.148753	NM_173747	ENSMUSG00000031148	Gpkow	4432411B18|DXErtd697e|DXImx41e|T54	G patch domain and KOW motifs	protein-coding
mm_56048.1	chr6	86737767	86737778	-	1	NA	exon (NM_001331120, exon 13 of 13)	exon (NM_001331120, exon 13 of 13)	-4394	NM_011818	23885	Mm.321452	NM_011818	ENSMUSG00000001157	Gmcl1	2810049L19Rik|Btbd13|DIP|Gcl|Gcl-1|glc-1|mglc-1	germ cell-less, spermatogenesis associated 1	protein-coding
mm_122979.1	chr14	54983349	54983359	-	1	NA	exon (NM_080728, exon 25 of 41)	exon (NM_080728, exon 25 of 41)	-7578	NR_030607	100124433		NR_030607	ENSMUSG00000077928	Mir208b	Mirn208b|mir-208b	microRNA 208b	ncRNA
mm_98413.1	chr11	94507461	94507474	+	1	NA	intron (NM_170671, intron 12 of 18)	intron (NM_170671, intron 12 of 18)	-7493	NM_027984	71889	Mm.248620	NM_027984	ENSMUSG00000010080	Epn3	2310022G12Rik	epsin 3	protein-coding
mm_4882.1	chr1	187997822	187997834	+	1	NA	promoter-TSS (NM_011935)	promoter-TSS (NM_011935)	1	NM_011935	26381	Mm.89989	NM_011935	ENSMUSG00000026610	Esrrg	ERR3|Errg|NR3B3|mKIAA0832	estrogen-related receptor gamma	protein-coding
mm_147453.1	chr18	46574301	46574311	-	1	NA	5' UTR (NM_173394, exon 1 of 3)	5' UTR (NM_173394, exon 1 of 3)	227	NM_173394	225471	Mm.149280	NM_173394	ENSMUSG00000056130	Ticam2	B430113A10|TICAM-2|TRAM|Tirp|Trif	toll-like receptor adaptor molecule 2	protein-coding
mm_4315.1	chr1	171848048	171848060	+	1	NA	intron (NM_001289470, intron 2 of 8)	MLT1J|LTR|ERVL-MaLR	8357	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_146855.1	chr18	24178836	24178875	-	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	-26489	NM_013814	14423	Mm.30249	NM_013814	ENSMUSG00000000420	Galnt1	-	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 1	protein-coding
mm_96246.1	chr11	62574574	62574584	+	1	NA	promoter-TSS (NM_011706)	promoter-TSS (NM_011706)	93	NM_011706	22368	Mm.288064	NM_011706	ENSMUSG00000018507	Trpv2	GRC|OTRPC2|VRL-1|Vrl1	transient receptor potential cation channel, subfamily V, member 2	protein-coding
mm_119256.1	chr14	33940972	33940982	+	1	NA	promoter-TSS (NM_019506)	promoter-TSS (NM_019506)	-62	NM_019506	12165	Mm.422844	NM_019506	ENSMUSG00000072625	Gdf2	Bmp9	growth differentiation factor 2	protein-coding
mm_156805.1	chrX	163909598	163909606	+	1	NA	intron (NM_001290379, intron 1 of 5)	CpG	585	NM_001290379	108012	Mm.426783	NM_026887	ENSMUSG00000031367	Ap1s2	1500012A13Rik|AI853648|EST1	adaptor-related protein complex 1, sigma 2 subunit	protein-coding
mm_165045.1	chr19	39510840	39510840	+	1	NA	promoter-TSS (NM_010003)	promoter-TSS (NM_010003)	18	NM_010003	13098	Mm.42101	NM_010003	ENSMUSG00000025003	Cyp2c39	CYPIIC39	cytochrome P450, family 2, subfamily c, polypeptide 39	protein-coding
mm_124659.1	chr15	5539557	5539562	+	1	NA	intron (NR_045274, intron 1 of 4)	intron (NR_045274, intron 1 of 4)	43241	NR_045274	71432	Mm.291087	NR_045274		5430437J10Rik	-	RIKEN cDNA 5430437J10 gene	ncRNA
mm_122407.1	chr14	41008257	41008275	-	1	NA	promoter-TSS (NM_001316740)	promoter-TSS (NM_001316740)	0	NM_001316732	70564	Mm.27227	NM_027464	ENSMUSG00000021792	Fam213a	5730469M10Rik|AU040822|Adrx|Pamm	family with sequence similarity 213, member A	protein-coding
mm_58473.1	chr7	3390910	3390920	+	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	-3127	NM_133190	81905	Mm.357990	NM_133190	ENSMUSG00000053395	Cacng8	-	calcium channel, voltage-dependent, gamma subunit 8	protein-coding
mm_16700.1	chr2	6921422	6921424	-	1	NA	intron (NM_001110229, intron 2 of 14)	intron (NM_001110229, intron 2 of 14)	7299	NR_027890	68144	Mm.483289	NM_026575		5031426D15Rik	-	RIKEN cDNA 5031426D15 gene	ncRNA
mm_166805.1	chr7	5020473	5020481	+	1	NA	5' UTR (NM_001290426, exon 1 of 3)	5' UTR (NM_001290426, exon 1 of 3)	101	NM_001033383	319748	Mm.86607	NM_001033383	ENSMUSG00000074405	Zfp865	6430526N21Rik|Znf865	zinc finger protein 865	protein-coding
mm_144409.1	chr18	20961357	20961381	+	1	NA	intron (NM_026301, intron 1 of 5)	CpG	16744	NM_026301	67664	Mm.45980	NM_026301	ENSMUSG00000033107	Rnf125	4930553F04Rik	ring finger protein 125	protein-coding
mm_85521.1	chr9	106447693	106447706	-	1	NA	promoter-TSS (NM_145919)	promoter-TSS (NM_145919)	-21	NM_001110272	68644	Mm.268925	NM_145919	ENSMUSG00000042210	Abhd14a	1110013B16Rik|AW558221|Dorz1	abhydrolase domain containing 14A	protein-coding
mm_4170.1	chr1	171121631	171121637	+	1	NA	promoter-TSS (NM_001081275)	promoter-TSS (NM_001081275)	-27	NM_001081275	75472	Mm.32760	NM_029301	ENSMUSG00000026649	Cfap126	1700009P17Rik|AV282292|Flattop|Fltp	cilia and flagella associated protein 126	protein-coding
mm_8434.1	chr1	152625125	152625138	-	1	NA	promoter-TSS (NM_016846)	promoter-TSS (NM_016846)	86	NM_016846	19731	Mm.245270	NM_016846	ENSMUSG00000026482	Rgl1	Rgl|mKIAA0959	ral guanine nucleotide dissociation stimulator,-like 1	protein-coding
mm_173040.1	chrX	114267908	114267925	-	1	NA	Intergenic	L1Md_T|LINE|L1	-206417	NM_001290478	237010	Mm.132583	NM_172781	ENSMUSG00000025597	Klhl4	B130014A11|C130018J01Rik	kelch-like 4	protein-coding
mm_98366.1	chr11	93995401	93995414	+	1	NA	promoter-TSS (NM_001199204)	promoter-TSS (NM_001199204)	-684	NM_001199203	70834	Mm.260737	NM_027569	ENSMUSG00000020859	Spag9	3110018C07Rik|4733401I23Rik|4831406C20Rik|AW552012|JLP|JSAP2|JSAP2a|Jip4|Mapk8ip4|syd1	sperm associated antigen 9	protein-coding
mm_153463.1	chr19	41263932	41264008	-	1	NA	promoter-TSS (NM_133352)	promoter-TSS (NM_133352)	34	NM_133352	107358	Mm.246440	NM_133352	ENSMUSG00000025016	Tm9sf3	1810073M23Rik|2810031D16Rik|AI115521|AI413748|AW146116|AW549777|Smbp|mKIAA4036	transmembrane 9 superfamily member 3	protein-coding
mm_154769.1	chrX	12609488	12609513	+	1	NA	intron (NM_027439, intron 8 of 8)	intron (NM_027439, intron 8 of 8)	21741	NM_027439	70495	Mm.25148	NM_027439	ENSMUSG00000031007	Atp6ap2	(P)RR|5730403E06Rik|APT6M8-9|ATP6M8-9|Atp6ip2|M8-9|PRR	ATPase, H+ transporting, lysosomal accessory protein 2	protein-coding
mm_16523.1	chr2	181520514	181520531	+	1	NA	promoter-TSS (NM_001271585)	promoter-TSS (NM_001271585)	37	NM_001271584	13002	Mm.140761	NM_016775	ENSMUSG00000000826	Dnajc5	2610314I24Rik|AU018536|Csp	DnaJ heat shock protein family (Hsp40) member C5	protein-coding
mm_106090.1	chr11	116197988	116197997	-	1	NA	promoter-TSS (NM_027107)	promoter-TSS (NM_027107)	-863	NM_027107	69535	Mm.390347	NM_027107	ENSMUSG00000020778	Ten1	2310004N24Rik	TEN1 telomerase capping complex subunit	protein-coding
mm_95957.1	chr11	58782984	58782988	+	1	NA	Intergenic	Intergenic	-3153	NM_001011760	257917	Mm.377302	NM_001011760	ENSMUSG00000059504	Olfr314	MOR278-2	olfactory receptor 314	protein-coding
mm_113561.1	chr13	38181173	38181185	+	1	NA	exon (NM_023842, exon 12 of 24)	exon (NM_023842, exon 12 of 24)	-23760	NM_026382	67797	Mm.250783	NM_026382	ENSMUSG00000021431	Snrnp48	1110050F08Rik|6530403A03Rik|C6orf151	small nuclear ribonucleoprotein 48 (U11/U12)	protein-coding
mm_38608.1	chr4	141864429	141864434	-	1	NA	intron (NM_025994, intron 1 of 3)	MTE2a|LTR|ERVL-MaLR	10489	NM_025994	27984	Mm.395598	NM_025994	ENSMUSG00000040659	Efhd2	2600015J22Rik|AA408606|D4Wsu27e	EF hand domain containing 2	protein-coding
mm_26043.1	chr3	135571718	135571747	+	1	NA	TTS (NM_027288)	TTS (NM_027288)	86121	NM_027288	110173	Mm.280536	NM_027288	ENSMUSG00000028164	Manba	2410030O07Rik|B930014J03Rik|Bmn	mannosidase, beta A, lysosomal	protein-coding
mm_95359.1	chr11	48871863	48871869	+	1	NA	promoter-TSS (NM_008326)	promoter-TSS (NM_008326)	-520	NM_008326	15944	Mm.29938	NM_008326	ENSMUSG00000046879	Irgm1	Ifggd3|Ifi1|Iigp3|Iipg3|Irgm|LRG-47	immunity-related GTPase family M member 1	protein-coding
mm_2953.1	chr1	132470265	132470275	+	1	NA	Intergenic	ORR1A1|LTR|ERVL-MaLR	-7097	NM_172517	213464	Mm.132868	NM_172517	ENSMUSG00000026439	Rbbp5	4933411J24Rik|C330016J05	retinoblastoma binding protein 5	protein-coding
mm_6079.1	chr1	62729435	62729436	-	1	NA	intron (NM_001077405, intron 2 of 15)	intron (NM_001077405, intron 2 of 15)	26118	NM_001077405	18187	Mm.266341	NM_010939	ENSMUSG00000025969	Nrp2	1110048P06Rik|Np-2|Np2|Npn-2|Npn2	neuropilin 2	protein-coding
mm_58533.1	chr7	4412322	4412330	+	1	NA	Intergenic	Intergenic	-14582	NM_001163014	243816	Mm.248662	NM_001163014	ENSMUSG00000078810	Gp6	9830166G18Rik|Gm469|Gpvi	glycoprotein 6 (platelet)	protein-coding
mm_110705.1	chr12	69320400	69320402	-	1	NA	exon (NM_025441, exon 25 of 33)	exon (NM_025441, exon 25 of 33)	23720	NM_027117	69554	Mm.234368	NM_027117	ENSMUSG00000020978	Klhdc2	2310022K15Rik|D12Ertd522e|HCLP-1|LCP	kelch domain containing 2	protein-coding
mm_150524.1	chr19	39042275	39042286	+	1	NA	3' UTR (NM_028089, exon 9 of 9)	3' UTR (NM_028089, exon 9 of 9)	-18726	NM_028191	72303	Mm.482578	NM_028191	ENSMUSG00000067231	Cyp2c65	2210009K14Rik	cytochrome P450, family 2, subfamily c, polypeptide 65	protein-coding
mm_40999.1	chr5	77351289	77351328	+	1	NA	exon (NM_008048, exon 4 of 5)	exon (NM_008048, exon 4 of 5)	40824	NM_153798	231329	Mm.273217	NM_153798	ENSMUSG00000029250	Polr2b	Pol2rb|Rpb140|Rpb2	polymerase (RNA) II (DNA directed) polypeptide B	protein-coding
mm_173234.1	chrX	80457483	80457497	+	1	NA	Intergenic	(TGG)n|Simple_repeat|Simple_repeat	-613154	NM_138751	192216	Mm.490421	NM_138751	ENSMUSG00000025666	Tmem47	3010015F07Rik|AI115536|BCMP1|Tm4sf10	transmembrane protein 47	protein-coding
mm_67419.1	chr7	80324116	80324137	-	1	NA	5' UTR (NM_173445, exon 1 of 9)	5' UTR (NM_173445, exon 1 of 9)	328	NM_173445	269955	Mm.474502	NM_173445	ENSMUSG00000038930	Rccd1	5830436H09|E430018M08Rik	RCC1 domain containing 1	protein-coding
mm_11344.1	chr2	30807371	30807391	+	1	NA	promoter-TSS (NM_170592)	promoter-TSS (NM_170592)	-596	NM_170592	66617	Mm.33167	NM_170592	ENSMUSG00000026857	Ntmt1	2610205E22Rik|AL033331|AL033332|Mettl11a|NTM1A	N-terminal Xaa-Pro-Lys N-methyltransferase 1	protein-coding
mm_133663.1	chr16	92015401	92015407	+	1	NA	Intergenic	Intergenic	-42918	NM_017391	53881	Mm.217354	NM_017391	ENSMUSG00000089774	Slc5a3	AA623876|BF642829|Smit1	solute carrier family 5 (inositol transporters), member 3	protein-coding
mm_105449.1	chr11	104443507	104443518	-	1	NA	Intergenic	Intergenic	-1221	NM_001081045	76719	Mm.136418	NM_001081045	ENSMUSG00000018412	Kansl1	1700081L11Rik|9430041J06Rik|mKIAA1267	KAT8 regulatory NSL complex subunit 1	protein-coding
mm_129143.1	chr15	76200624	76200634	-	1	NA	promoter-TSS (NM_201391)	promoter-TSS (NM_201391)	-22	NM_201390	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
mm_93602.1	chr10	117224481	117224499	-	1	NA	promoter-TSS (NM_026570)	promoter-TSS (NM_026570)	17	NM_026570	64050	Mm.233529	NM_026570	ENSMUSG00000020171	Yeats4	4930573H17Rik|B230215M10Rik|GAS41|NuBI-1	YEATS domain containing 4	protein-coding
mm_33767.1	chr4	134401610	134401630	+	1	NA	intron (NM_001285872, intron 1 of 10)	intron (NM_001285872, intron 1 of 10)	-1292	NM_001285874	100163	Mm.22116	NM_133880	ENSMUSG00000037366	Pafah2	2310074E22Rik|AI507170	platelet-activating factor acetylhydrolase 2	protein-coding
mm_70509.1	chr8	12926269	12926291	+	1	NA	intron (NM_178076, intron 1 of 30)	intron (NM_178076, intron 1 of 30)	10387	NM_178076	17207	Mm.334413	NM_178076	ENSMUSG00000031442	Mcf2l	C130040G20Rik|Dbs|Ost|mKIAA0362	mcf.2 transforming sequence-like	protein-coding
mm_128248.1	chr15	36609541	36609566	-	1	NA	promoter-TSS (NM_008774)	promoter-TSS (NM_008774)	-580	NM_008774	18458	Mm.371570	NM_008774	ENSMUSG00000022283	Pabpc1	PABP|Pabp1|PabpI|Pabpl1|ePAB	poly(A) binding protein, cytoplasmic 1	protein-coding
mm_161890.1	chr18	40258139	40258139	+	1	NA	promoter-TSS (NM_026135)	promoter-TSS (NM_026135)	-222	NM_026135	383348	Mm.76366	NM_026135	ENSMUSG00000051401	Kctd16	4930434H12Rik|Gm1267	potassium channel tetramerisation domain containing 16	protein-coding
mm_66169.1	chr7	33901816	33901822	-	1	NA	Intergenic	Intergenic	43166	NM_178308	110187	Mm.155750	NM_178308	ENSMUSG00000066586	Scgb2b26	Abpbg26|Abpbg4|Abpg|C2d|Scgb2b4	secretoglobin, family 2B, member 26	protein-coding
mm_63029.1	chr7	121053731	121053734	+	1	NA	intron (NM_021554, intron 3 of 4)	intron (NM_021554, intron 3 of 4)	19287	NM_021554	59052	Mm.29122	NM_021554	ENSMUSG00000030876	Mettl9	0610012D09Rik|AA517660|Drev|MNCb-5680	methyltransferase like 9	protein-coding
mm_107565.1	chr12	44221353	44221355	+	1	NA	promoter-TSS (NR_045113)	promoter-TSS (NR_045113)	-2	NR_045113	100039062	Mm.490648	NR_045113		Gm2027	-	nuclear assembly factor 1 homolog pseudogene	pseudo
mm_91739.1	chr10	47102690	47102700	-	1	NA	Intergenic	Intergenic	857946	NR_028276	108637		NR_028276	ENSMUSG00000096263	Snord14c	Gm23107|Rnu14|U14	small nucleolar RNA, C/D box 14C	snoRNA
mm_34536.1	chr4	149485317	149485327	+	1	NA	promoter-TSS (NM_026963)	promoter-TSS (NM_026963)	-11	NM_026963	69151	Mm.464434	NM_026963	ENSMUSG00000028990	Lzic	1810030J04Rik|AW047580	leucine zipper and CTNNBIP1 domain containing	protein-coding
mm_120011.1	chr14	55672372	55672391	+	1	NA	promoter-TSS (NM_008683)	promoter-TSS (NM_008683)	146	NM_177992	105446	Mm.390685	NM_177992	ENSMUSG00000002326	Gmpr2	1810008P16Rik|5730544D12Rik|AA959850|GMPR 2	guanosine monophosphate reductase 2	protein-coding
mm_120514.1	chr14	66636666	66636696	+	1	NA	intron (NM_001271760, intron 1 of 3)	(T)n|Simple_repeat|Simple_repeat	1430	NM_001271760	11549	Mm.57064	NM_013461	ENSMUSG00000045875	Adra1a	Adra1c	adrenergic receptor, alpha 1a	protein-coding
mm_45615.1	chr5	75835817	75835825	-	1	NA	Intergenic	Intergenic	142607	NM_010612	16542	Mm.285	NM_010612	ENSMUSG00000062960	Kdr	6130401C07|Flk-1|Flk1|Krd-1|Ly73|VEGFR-2|VEGFR2|sVEGFR-2	kinase insert domain protein receptor	protein-coding
mm_139145.1	chr17	47521927	47521936	+	1	NA	intron (NM_001081635, intron 1 of 6)	intron (NM_001081635, intron 1 of 6)	16880	NM_001081635	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_110991.1	chr12	77191723	77191724	-	1	NA	Intergenic	RLTR48C|LTR|ERV1	-46381	NM_001252614	53618	Mm.35628	NM_016893	ENSMUSG00000021065	Fut8	-	fucosyltransferase 8	protein-coding
mm_61843.1	chr7	88290874	88290888	+	1	NA	3' UTR (NM_001311790, exon 4 of 4)	3' UTR (NM_001311790, exon 4 of 4)	12796	NM_001311790	13032	Mm.89295	NM_009982	ENSMUSG00000030560	Ctsc	AI047818|CatC|DPP1|DPPI	cathepsin C	protein-coding
mm_88623.1	chr10	79874506	79874516	+	1	NA	non-coding (NR_033210, exon 1 of 6)	non-coding (NR_033210, exon 1 of 6)	123	NM_181681	216152	Mm.29678	NM_181681	ENSMUSG00000035835	Plppr3	Lppr3|Prg2	phospholipid phosphatase related 3	protein-coding
mm_44928.1	chr5	36146791	36146794	-	1	NA	intron (NM_030889, intron 3 of 26)	intron (NM_030889, intron 3 of 26)	-57229	NM_175249	76943	Mm.44242	NM_175249	ENSMUSG00000043430	Psapl1	2310020A21Rik	prosaposin-like 1	protein-coding
mm_163127.1	chr11	78100886	78100897	-	1	NA	intron (NM_001346762, intron 1 of 2)	intron (NM_001346762, intron 1 of 2)	6218	NM_145430	216971	Mm.119387	NM_145430	ENSMUSG00000037750	Fam222b	9630020I17Rik	family with sequence similarity 222, member B	protein-coding
mm_47995.1	chr5	136135990	136136087	-	1	NA	promoter-TSS (NM_027891)	promoter-TSS (NM_027891)	36	NM_027891	71735	Mm.425292	NM_027891	ENSMUSG00000029703	Lrwd1	1200011O22Rik|AU042569|AW548074|Orca	leucine-rich repeats and WD repeat domain containing 1	protein-coding
mm_29786.1	chr3	127522374	127522399	-	1	NA	Intergenic	Intergenic	-22842	NR_030403	723948		NR_030403	ENSMUSG00000076252	Mir302b	Mirn302b|mir-302b	microRNA 302b	ncRNA
mm_43364.1	chr5	135369943	135369997	+	1	NA	promoter-TSS (NM_145414)	promoter-TSS (NM_145414)	17	NM_145414	100609	Mm.281189	NM_145414	ENSMUSG00000000916	Nsun5	9830109N13Rik|AI326939|Nol1r|Wbscr20|Wbscr20a	NOL1/NOP2/Sun domain family, member 5	protein-coding
mm_98915.1	chr11	98217207	98217212	+	1	NA	intron (NM_001109628, intron 2 of 13)	intron (NM_001109628, intron 2 of 13)	13904	NM_001109626	69131	Mm.260516	NM_026952	ENSMUSG00000003119	Cdk12	1810022J16Rik|AI646528|Crk7|Crkrs|D11Ertd752e|Pksc	cyclin-dependent kinase 12	protein-coding
mm_108515.1	chr12	84038364	84038379	+	1	NA	promoter-TSS (NM_134247)	promoter-TSS (NM_134247)	-8	NM_134247	171282	Mm.482217	NM_134247	ENSMUSG00000052392	Acot4	B430212I04Rik|PTE-Ib|Pte1b|Pte2b	acyl-CoA thioesterase 4	protein-coding
mm_13577.1	chr2	112368047	112368078	+	1	NA	promoter-TSS (NM_026519)	promoter-TSS (NM_026519)	-35	NM_026519	68032	Mm.220942	NM_026519	ENSMUSG00000027131	Emc4	2610318K02Rik|Tmem85	ER membrane protein complex subunit 4	protein-coding
mm_14014.1	chr2	122149218	122149258	+	1	NA	intron (NM_009735, intron 1 of 3)	B1_Mm|SINE|Alu	1551	NM_009735	12010	Mm.163	NM_009735	ENSMUSG00000060802	B2m	Ly-m11|beta2-m|beta2m	beta-2 microglobulin	protein-coding
mm_140559.1	chr17	7945845	7945891	-	1	NA	exon (NM_025789, exon 1 of 8)	exon (NM_025789, exon 1 of 8)	254	NM_025789	66832	Mm.29830	NM_025789	ENSMUSG00000073471	Rsph3a	1700012G05Rik|4930524H12Rik|R74860|Rshl2|Rshl2a	radial spoke 3A homolog (Chlamydomonas)	protein-coding
mm_58829.1	chr7	16781342	16781352	+	1	NA	promoter-TSS (NM_009201)	promoter-TSS (NM_009201)	1	NM_009201	20514	Mm.1056	NM_009201	ENSMUSG00000001918	Slc1a5	AAAT|ASCT2|ATBO|M7V1|M7VS1|R16|RDRC|Slc1a7	solute carrier family 1 (neutral amino acid transporter), member 5	protein-coding
mm_163725.1	chr13	118714606	118714616	+	1	NA	promoter-TSS (NM_008002)	promoter-TSS (NM_008002)	-88	NM_008002	14165	Mm.317323	NM_008002	ENSMUSG00000021732	Fgf10	AEY17|BB213776|Fgf-10|Gsfaey17	fibroblast growth factor 10	protein-coding
mm_114162.1	chr13	55413569	55413575	+	1	NA	exon (NM_011392, exon 13 of 13)	exon (NM_011392, exon 13 of 13)	1660	NM_029303	75477	Mm.432537	NM_029303	ENSMUSG00000044444	Pfn3	1700012P12Rik	profilin 3	protein-coding
mm_118916.1	chr14	26693286	26693296	+	1	NA	Intergenic	Intergenic	-23445	NM_178668	211948	Mm.290758	NM_178668	ENSMUSG00000043702	Pde12	2'-PDE|E430028B21Rik	phosphodiesterase 12	protein-coding
mm_87870.1	chr10	61416531	61416545	+	1	NA	Intergenic	Intergenic	-1434	NM_013611	18119	Mm.57195	NM_013611	ENSMUSG00000037171	Nodal	Tg.413d	nodal	protein-coding
mm_111364.1	chr12	87147884	87147908	-	1	NA	promoter-TSS (NM_153415)	promoter-TSS (NM_153415)	6	NM_153415	217734	Mm.388249	NM_153415	ENSMUSG00000034126	Pomt2	-	protein-O-mannosyltransferase 2	protein-coding
mm_74048.1	chr8	122181789	122181795	+	1	NA	Intergenic	L1MB7|LINE|L1	-100349	NM_009569	22761	Mm.3105	NM_009569	ENSMUSG00000049577	Zfpm1	FOG|Fog1	zinc finger protein, multitype 1	protein-coding
mm_39150.1	chr4	155398038	155398055	-	1	NA	promoter-TSS (NM_008072)	promoter-TSS (NM_008072)	23	NM_008072	14403	Mm.388925	NM_008072	ENSMUSG00000029054	Gabrd	AI853201	gamma-aminobutyric acid (GABA) A receptor, subunit delta	protein-coding
mm_60370.1	chr7	44463110	44463111	+	1	NA	3' UTR (NM_198250, exon 3 of 3)	3' UTR (NM_198250, exon 3 of 3)	-2325	NM_026690	68352	Mm.88478	NM_026690	ENSMUSG00000038704	Aspdh	0610012D14Rik	aspartate dehydrogenase domain containing	protein-coding
mm_114686.1	chr13	81657733	81657846	+	1	NA	promoter-TSS (NM_030257)	promoter-TSS (NM_030257)	-17	NM_030257	80289	Mm.259969	NM_030257	ENSMUSG00000035840	Lysmd3	1110030H10Rik|BC003322	LysM, putative peptidoglycan-binding, domain containing 3	protein-coding
mm_80779.1	chr9	95637624	95637632	+	1	NA	promoter-TSS (NM_029620)	promoter-TSS (NM_029620)	0	NM_029620	76477	Mm.46016	NM_029620	ENSMUSG00000015354	Pcolce2	2400001O18Rik|Pcpe2	procollagen C-endopeptidase enhancer 2	protein-coding
mm_84245.1	chr9	62344640	62344668	-	1	NA	intron (NM_009672, intron 1 of 6)	CpG	3311	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	protein-coding
mm_41605.1	chr5	96374168	96374213	+	1	NA	5' UTR (NM_175473, exon 1 of 74)	5' UTR (NM_175473, exon 1 of 74)	235	NM_175473	231470	Mm.291120	NM_175473	ENSMUSG00000034687	Fras1	E130113P14Rik|bl|mKIAA1500	Fraser extracellular matrix complex subunit 1	protein-coding
mm_119938.1	chr14	54976817	54976832	+	1	NA	intron (NM_080728, intron 30 of 40)	RMER4B|LTR|ERVK	-1048	NR_030607	100124433		NR_030607	ENSMUSG00000077928	Mir208b	Mirn208b|mir-208b	microRNA 208b	ncRNA
mm_36899.1	chr4	107684229	107684231	-	1	NA	promoter-TSS (NM_019872)	promoter-TSS (NM_019872)	-68	NM_019872	56296	Mm.141324	NM_019872	ENSMUSG00000028610	Dmrtb1	Dmrt6|Prp13	DMRT-like family B with proline-rich C-terminal, 1	protein-coding
mm_22410.1	chr2	181314279	181314298	-	1	NA	5' UTR (NM_009133, exon 1 of 5)	5' UTR (NM_009133, exon 1 of 5)	212	NM_009133	20262	Mm.2319	NM_009133	ENSMUSG00000027581	Stmn3	9330161A03Rik|AI604839|R75323|Sclip	stathmin-like 3	protein-coding
mm_42736.1	chr5	120630095	120630101	+	1	NA	exon (NM_001195094, exon 5 of 7)	exon (NM_001195094, exon 5 of 7)	4137	NM_001195094	546886	Mm.464847	NM_001195094	ENSMUSG00000094282	Cfap73	Ccdc42b|Gm5988	cilia and flagella associated protein 73	protein-coding
mm_53439.1	chr6	134190061	134190062	+	1	NA	intron (NM_001303102, intron 3 of 8)	intron (NM_001303102, intron 3 of 8)	154361	NM_007961	14011	Mm.269995	NM_007961	ENSMUSG00000030199	Etv6	AW123102|AW557856|Tel	ets variant 6	protein-coding
mm_135237.1	chr16	36990163	36990173	-	1	NA	Intergenic	Intergenic	-11032	NM_001037321	207215	Mm.211899	NM_001037321	ENSMUSG00000047746	Fbxo40	9830003A13Rik|mKIAA1195	F-box protein 40	protein-coding
mm_24758.1	chr3	95454373	95454373	+	1	NA	intron (NM_009709, intron 3 of 20)	MTD|LTR|ERVL-MaLR	19983	NM_001037737	11863	Mm.250265	NM_009709	ENSMUSG00000015522	Arnt	D3Ertd557e|Drnt|ESTM42|Hif1b|W08714|bHLHe2|mKIAA4051	aryl hydrocarbon receptor nuclear translocator	protein-coding
mm_130183.1	chr15	93519500	93519526	-	1	NA	intron (NM_001033217, intron 1 of 7)	CpG	76378	NM_001033217	106042	Mm.150314	NM_001033217	ENSMUSG00000036158	Prickle1	1110058P22Rik|AW215793|Prickle|b2b019Clo|mpk1	prickle planar cell polarity protein 1	protein-coding
mm_97187.1	chr11	75572513	75572545	+	1	NA	3' UTR (NM_001199283, exon 14 of 14)	3' UTR (NM_001199283, exon 14 of 14)	-15550	NM_008850	18738	Mm.3128	NM_008850	ENSMUSG00000017781	Pitpna	Pitpn|vb|vibrator	phosphatidylinositol transfer protein, alpha	protein-coding
mm_165936.1	chr4	70625225	70625229	+	1	NA	Intergenic	RMER1C|Other|Other	-90299	NM_172694	230316	Mm.251188	NM_172694	ENSMUSG00000039270	Megf9	4933405H16Rik|9630025C07|Egfl5|mKIAA0818	multiple EGF-like-domains 9	protein-coding
mm_129977.1	chr15	85963518	85963523	-	1	NA	intron (NM_009886, intron 2 of 34)	MTD|LTR|ERVL-MaLR	70257	NM_009886	12614	Mm.22680	NM_009886	ENSMUSG00000016028	Celsr1	Adgrc1|Crsh|Scy|crash	cadherin, EGF LAG seven-pass G-type receptor 1	protein-coding
mm_124546.1	chr14	122474155	122474193	-	1	NA	intron (NR_045046, intron 2 of 4)	CpG	1025	NR_045046	69248	Mm.235369	NR_045046	ENSMUSG00000085555	2610035F20Rik	-	RIKEN cDNA 2610035F20 gene	ncRNA
mm_42233.1	chr5	113550907	113550923	+	1	NA	5' UTR (NM_177292, exon 1 of 8)	5' UTR (NM_177292, exon 1 of 8)	495	NM_177292	320916	Mm.102783	NM_177292	ENSMUSG00000063430	Wscd2	4933413A10Rik|C530024P05Rik|Gm450	WSC domain containing 2	protein-coding
mm_160581.1	chr9	61914533	61914533	-	1	NA	promoter-TSS (NM_018853)	promoter-TSS (NM_018853)	-23	NM_018853	56040	Mm.3158	NM_018853	ENSMUSG00000007892	Rplp1	2410042H16Rik|Arpp1|C430017H15Rik	ribosomal protein, large, P1	protein-coding
mm_166126.1	chr4	154636911	154636934	+	1	NA	promoter-TSS (NM_027504)	promoter-TSS (NM_027504)	-49	NM_027504	70673	Mm.257785	NM_027504	ENSMUSG00000039410	Prdm16	5730557K01Rik|csp1|mel1	PR domain containing 16	protein-coding
mm_153178.1	chr19	34493915	34493925	-	1	NA	3' UTR (NM_021460, exon 10 of 10)	3' UTR (NM_021460, exon 10 of 10)	-18785	NM_009890	12642	Mm.30824	NM_009890	ENSMUSG00000050370	Ch25h	AI462618|m25OH	cholesterol 25-hydroxylase	protein-coding
mm_150551.1	chr19	39324934	39324942	+	1	NA	exon (NM_007815, exon 7 of 9)	exon (NM_007815, exon 7 of 9)	37853	NM_007815	13095	Mm.20764	NM_007815	ENSMUSG00000003053	Cyp2c29	AHOH|AHOHase|AI159681|AI196010|Ah-2|Ahh-1|Cyp2c|P450-2C	cytochrome P450, family 2, subfamily c, polypeptide 29	protein-coding
mm_42792.1	chr5	121619033	121619087	+	1	NA	promoter-TSS (NM_178799)	promoter-TSS (NM_178799)	-122	NM_178799	338350	Mm.482918	NM_178799	ENSMUSG00000042647	Acad12	9330129D05Rik	acyl-Coenzyme A dehydrogenase family, member 12	protein-coding
mm_90758.1	chr10	5550600	5550613	-	1	NA	promoter-TSS (NM_153399)	promoter-TSS (NM_153399)	86	NM_153399	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_69827.1	chr7	141269452	141269475	-	1	NA	exon (NM_028069, exon 14 of 14)	exon (NM_028069, exon 14 of 14)	-3039	NM_001252600	54123	Mm.3233	NM_016850	ENSMUSG00000025498	Irf7	-	interferon regulatory factor 7	protein-coding
mm_52331.1	chr6	109739788	109739805	+	1	NA	Intergenic	Intergenic	-905716	NM_001346640	108073	Mm.240881	NM_177328	ENSMUSG00000056755	Grm7	6330570A01Rik|BB176677|C030018L03|E130018M02Rik|Gpr1g|Gprc1g|SMN2|Tg(SMN2)89Ahmb|mGluR7	glutamate receptor, metabotropic 7	protein-coding
mm_105194.1	chr11	102082465	102082493	-	1	NA	intron (NM_016695, intron 2 of 12)	intron (NM_016695, intron 2 of 12)	6036	NM_016695	50997	Mm.36242	NM_016695	ENSMUSG00000017314	Mpp2	D11Bwg0652e|Dlg2|Dlgh2|Pals4	membrane protein, palmitoylated 2 (MAGUK p55 subfamily member 2)	protein-coding
mm_168191.1	chr10	62864832	62864836	-	1	NA	exon (NM_001253857, exon 2 of 12)	exon (NM_001253857, exon 2 of 12)	15180	NM_027384	52463	Mm.17774	NM_027384	ENSMUSG00000047146	Tet1	2510010B09Rik|AA517754|BB001228|Cxxc6|D10Ertd17e|LCX|mKIAA1676	tet methylcytosine dioxygenase 1	protein-coding
mm_86419.1	chr10	3718153	3718168	+	1	NA	Intergenic	Intergenic	-22217	NM_001159942	213783	Mm.150831	NM_001033253	ENSMUSG00000040624	Plekhg1	D10Ertd733e|Gm521|mKIAA1209	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	protein-coding
mm_72195.1	chr8	72530970	72531003	+	1	NA	intron (NM_027485, intron 1 of 2)	intron (NM_027485, intron 1 of 2)	17324	NM_027485	70625	Mm.235885	NM_027485	ENSMUSG00000045248	Med26	5730493L18Rik|AI414941|AW495270|Crsp7	mediator complex subunit 26	protein-coding
mm_75752.1	chr8	69901986	69902007	-	1	NA	promoter-TSS (NM_032004)	promoter-TSS (NM_032004)	-188	NM_032004	83984	Mm.432504	NM_032004	ENSMUSG00000047654	Tssk6	Sstk|TSK-6|TSSK-6	testis-specific serine kinase 6	protein-coding
mm_170338.1	chr18	46597775	46597775	+	1	NA	promoter-TSS (NM_025698)	promoter-TSS (NM_025698)	71	NM_010120	13664	Mm.262037	NM_010120	ENSMUSG00000057561	Eif1a	C76390|Ef1a|Eftu|Eif4c|eIF-1A|eIF-4C	eukaryotic translation initiation factor 1A	protein-coding
mm_154493.1	chrM	6395	6410	-	1	NA	NA	Intergenic	NA	NA								
mm_84229.1	chr9	61976564	61976576	-	1	NA	intron (NM_028748, intron 2 of 7)	intron (NM_028748, intron 2 of 7)	-29771	NM_024245	71819	Mm.259374	NM_024245	ENSMUSG00000032254	Kif23	3110001D19Rik|C87313|CHO1|Knsl5|MKLP-1|MKLP1	kinesin family member 23	protein-coding
mm_115473.1	chr13	119488117	119488124	+	1	NA	promoter-TSS (NM_001177666)	promoter-TSS (NM_001177666)	81	NM_001039244	633640	Mm.46679	NM_001039244	ENSMUSG00000074634	Tmem267	EG633640|Gm7120	transmembrane protein 267	protein-coding
mm_65237.1	chr7	19764691	19764701	-	1	NA	exon (NM_020486, exon 7 of 15)	exon (NM_020486, exon 7 of 15)	5836	NM_020486	57278	Mm.29236	NM_020486	ENSMUSG00000002980	Bcam	1200005K12Rik|B-CAM|Gplu|Lu	basal cell adhesion molecule	protein-coding
mm_106380.1	chr11	118494173	118494183	-	1	NA	exon (NM_001039167, exon 14 of 15)	exon (NM_001039167, exon 14 of 15)	17218	NM_172573	217364	Mm.473963	NM_172573	ENSMUSG00000033857	Engase	C130099A03|D230014K01Rik	endo-beta-N-acetylglucosaminidase	protein-coding
mm_65971.1	chr7	30440029	30440045	-	1	NA	exon (NM_007467, exon 10 of 17)	exon (NM_007467, exon 10 of 17)	5545	NM_007467	11803	Mm.2381	NM_007467	ENSMUSG00000006651	Aplp1	-	amyloid beta (A4) precursor-like protein 1	protein-coding
mm_142805.1	chr17	50495391	50495399	-	1	NA	Intergenic	Intergenic	-14152	NM_013880	224860	Mm.217362	NM_013880	ENSMUSG00000038910	Plcl2	PLC-L2|PRIP-2|Plce2|mKIAA1092	phospholipase C-like 2	protein-coding
mm_122057.1	chr14	30330180	30330226	-	1	NA	intron (NM_001302637, intron 3 of 48)	intron (NM_001302637, intron 3 of 48)	23283	NM_001302637	12289	Mm.9772	NM_028981	ENSMUSG00000015968	Cacna1d	8430418G19Rik|C79217|Cach3|Cacn4|Cacnl1a2|Cav1.3|Cchl1a|Cchl1a2|D-LTCC	calcium channel, voltage-dependent, L type, alpha 1D subunit	protein-coding
mm_53621.1	chr6	140432963	140432984	+	1	NA	intron (NM_144920, intron 3 of 30)	intron (NM_144920, intron 3 of 30)	8874	NM_144920	109135	Mm.247670	NM_144920	ENSMUSG00000030231	Plekha5	2810431N21Rik|AI428202|AK129423|AMH-Cre|Ayu21-9|Gt(pU21)9Imeg|Pepp2|Tg(AMH-cre)1Flor	pleckstrin homology domain containing, family A member 5	protein-coding
mm_169080.1	chr13	3375185	3375197	-	1	NA	Intergenic	Intergenic	-103112	NR_015522	76937	Mm.487240	NR_015522	ENSMUSG00000097709	2810429I04Rik	AI256682	RIKEN cDNA 2810429I04 gene	ncRNA
mm_26159.1	chr3	138217839	138217847	+	1	NA	promoter-TSS (NM_009626)	promoter-TSS (NM_009626)	70	NM_009626	11529	Mm.8473	NM_009626	ENSMUSG00000055301	Adh7	AI325182|Adh-3|Adh-3e|Adh-3t|Adh3|Adh3-e|Adh3-t|Adh4|Adt-1	alcohol dehydrogenase 7 (class IV), mu or sigma polypeptide	protein-coding
mm_54146.1	chr6	22329608	22329625	-	1	NA	intron (NM_138587, intron 3 of 9)	intron (NM_138587, intron 3 of 9)	26465	NM_138587	27999	Mm.490307	NM_138587	ENSMUSG00000029672	Fam3c	D6Wsu176e|Ilei	family with sequence similarity 3, member C	protein-coding
mm_8718.1	chr1	160025704	160025732	-	1	NA	Intergenic	PB1D10|SINE|Alu	-18662	NR_028111	67647	Mm.171518	NM_001024470	ENSMUSG00000090394	4930523C07Rik	-	RIKEN cDNA 4930523C07 gene	protein-coding
mm_158871.1	chrY	1270622	1270625	-	1	NA	intron (NM_012008, intron 6 of 16)	intron (NM_012008, intron 6 of 16)	15990	NM_012008	26900	Mm.302938	NM_012008	ENSMUSG00000069045	Ddx3y	8030469F12Rik|D1Pas1-rs1|Dby	DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, Y-linked	protein-coding
mm_15570.1	chr2	158624904	158624930	+	1	NA	promoter-TSS (NM_175419)	promoter-TSS (NM_175419)	4	NM_175419	109275	Mm.27747	NM_175419	ENSMUSG00000037761	Actr5	AA545173|B430109J19Rik	ARP5 actin-related protein 5	protein-coding
mm_70001.1	chr7	142386850	142386879	-	1	NA	intron (NM_009983, intron 1 of 8)	intron (NM_009983, intron 1 of 8)	1006	NM_009983	13033	Mm.231395	NM_009983	ENSMUSG00000007891	Ctsd	CD|CatD	cathepsin D	protein-coding
mm_158743.1	chrX	164258187	164258199	-	1	NA	promoter-TSS (NM_009759)	promoter-TSS (NM_009759)	0	NM_009759	12169	Mm.504	NM_009759	ENSMUSG00000031377	Bmx	Etk|Etk/Bmx|Tyro8	BMX non-receptor tyrosine kinase	protein-coding
mm_101368.1	chr11	23758397	23758399	-	1	NA	intron (NM_009044, intron 2 of 9)	intron (NM_009044, intron 2 of 9)	12572	NM_009044	19696	Mm.4869	NM_009044	ENSMUSG00000020275	Rel	c-Rel	reticuloendotheliosis oncogene	protein-coding
mm_92229.1	chr10	68822758	68822778	-	1	NA	Intergenic	RMER20A|LTR|ERVK	99022	NM_177794	327766	Mm.2479	NM_177794	ENSMUSG00000060044	Tmem26	3230401A06|AI195372	transmembrane protein 26	protein-coding
mm_27222.1	chr3	36053492	36053501	-	1	NA	promoter-TSS (NM_178418)	promoter-TSS (NM_178418)	51	NM_178418	241943	Mm.269018	NM_178418	ENSMUSG00000047696	Ccdc144b	-	coiled-coil domain containing 144B	protein-coding
mm_98646.1	chr11	96251173	96251226	+	1	NA	promoter-TSS (NR_037977)	promoter-TSS (NR_037977)	-461	NR_037977	193022	Mm.169508	NR_037977		Gm53	-	predicted gene 53	ncRNA
mm_69566.1	chr7	135700619	135700637	-	1	NA	exon (NM_001081117, exon 12 of 14)	exon (NM_001081117, exon 12 of 14)	15751	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_108641.1	chr12	85824634	85824648	+	1	NA	promoter-TSS (NM_001081423)	promoter-TSS (NM_001081423)	-96	NM_021446	58520	Mm.143795	NM_021446	ENSMUSG00000021252	0610007P14Rik	1190004E09Rik|AU019315|C77855|ORF11	RIKEN cDNA 0610007P14 gene	protein-coding
mm_58744.1	chr7	13277255	13277270	+	1	NA	promoter-TSS (NM_001199310)	promoter-TSS (NM_001199310)	-51	NM_001199310	16881	Mm.288179	NM_010715	ENSMUSG00000056394	Lig1	AL033288|LigI	ligase I, DNA, ATP-dependent	protein-coding
mm_149240.1	chr19	10186825	10186835	+	1	NA	exon (NM_146094, exon 5 of 12)	exon (NM_146094, exon 5 of 12)	3942	NM_146094	76267	Mm.30158	NM_146094	ENSMUSG00000010663	Fads1	0710001O03Rik|A930006B21Rik|AI317215|DSD	fatty acid desaturase 1	protein-coding
mm_170970.1	chr2	62001542	62001542	+	1	NA	Intergenic	RLTR9E|LTR|ERVK	-44973	NM_001242382	94229	Mm.314497	NM_033552	ENSMUSG00000026904	Slc4a10	NCBE|mKIAA4136	solute carrier family 4, sodium bicarbonate cotransporter-like, member 10	protein-coding
mm_32483.1	chr4	107890095	107890129	+	1	NA	exon (NM_028754, exon 1 of 7)	exon (NM_028754, exon 1 of 7)	213	NM_028754	74098	Mm.274853	NM_028754	ENSMUSG00000028608	0610037L13Rik	1110008H16Rik	RIKEN cDNA 0610037L13 gene	protein-coding
mm_34175.1	chr4	140691302	140691305	+	1	NA	Intergenic	RMER17C|LTR|ERVK	-10170	NM_173867	108911	Mm.253	NM_173867	ENSMUSG00000040945	Rcc2	2610510H01Rik|2610529N02Rik|AA536646|AA675016|Td60|mKIAA1470	regulator of chromosome condensation 2	protein-coding
mm_53624.1	chr6	140479826	140479836	+	1	NA	intron (NM_144920, intron 3 of 30)	L1MA4|LINE|L1	55732	NM_144920	109135	Mm.247670	NM_144920	ENSMUSG00000030231	Plekha5	2810431N21Rik|AI428202|AK129423|AMH-Cre|Ayu21-9|Gt(pU21)9Imeg|Pepp2|Tg(AMH-cre)1Flor	pleckstrin homology domain containing, family A member 5	protein-coding
mm_97870.1	chr11	83175246	83175256	+	1	NA	promoter-TSS (NM_011410)	promoter-TSS (NM_011410)	65	NM_001302559	20558	Mm.38192	NM_011410	ENSMUSG00000000204	Slfn4	AI450778	schlafen 4	protein-coding
mm_98945.1	chr11	98412462	98412566	+	1	NA	promoter-TSS (NM_001003817)	promoter-TSS (NM_001003817)	30	NM_001003817	13866	Mm.290822	NM_001003817	ENSMUSG00000062312	Erbb2	Erbb-2|HER-2|HER2|Neu|c-erbB2|c-neu|l11Jus8|mKIAA3023	erb-b2 receptor tyrosine kinase 2	protein-coding
mm_161734.1	chr17	31295392	31295392	+	1	NA	promoter-TSS (NM_153062)	promoter-TSS (NM_153062)	-91	NM_153062	224674	Mm.311395	NM_153062	ENSMUSG00000024036	Slc37a1	G3PP	solute carrier family 37 (glycerol-3-phosphate transporter), member 1	protein-coding
mm_65637.1	chr7	27861029	27861039	-	1	NA	intron (NM_001024726, intron 1 of 4)	intron (NM_001024726, intron 1 of 4)	449	NM_001024726	545938	Mm.458180	NM_001024726	ENSMUSG00000020420	Zfp607a	4732475C15Rik|Zfp607	zinc finger protein 607A	protein-coding
mm_133176.1	chr16	72083109	72083111	+	1	NA	Intergenic	Intergenic	151217	NR_131116	319533	Mm.373754	NR_131115		8030451O07Rik	-	RIKEN cDNA 8030451O07 gene	ncRNA
mm_125054.1	chr15	25843512	25843542	+	1	NA	exon (NM_001034851, exon 1 of 9)	exon (NM_001034851, exon 1 of 9)	229	NM_001034851	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_132780.1	chr16	44794791	44794807	+	1	NA	3' UTR (NM_021325, exon 7 of 7)	3' UTR (NM_021325, exon 7 of 7)	-25929	NM_207244	239849	Mm.445045	NM_207244	ENSMUSG00000062082	Cd200r4	F630107N04Rik|MCD200RLa	CD200 receptor 4	protein-coding
mm_87064.1	chr10	29030070	29030118	+	1	NA	Intergenic	Intergenic	-43788	NM_026336	67719	Mm.440480	NM_026336	ENSMUSG00000015519	2310057J18Rik	2210414P04Rik|Leg1	RIKEN cDNA 2310057J18 gene	protein-coding
mm_125466.1	chr15	52959041	52959067	+	1	NA	Intergenic	MIR|SINE|MIR	246609	NM_027212	69790	Mm.195562	NM_027212	ENSMUSG00000038622	Med30	1810038N03Rik|2510044J04Rik|TRAP25|Thrap6	mediator complex subunit 30	protein-coding
mm_25435.1	chr3	107979601	107979613	+	1	NA	Intergenic	Intergenic	6829	NM_008183	14863	Mm.440086	NM_008183	ENSMUSG00000040562	Gstm2	Gstb-2|Gstb2	glutathione S-transferase, mu 2	protein-coding
mm_12682.1	chr2	75834635	75834638	+	1	NA	intron (NM_172666, intron 1 of 19)	B1_Mus1|SINE|Alu	2459	NM_172666	228061	Mm.31227	NM_172666	ENSMUSG00000042410	Agps	5832437L22|9930035G10Rik|AW123847|Adaps|Adas|Adhaps|Adps|Aldhpsy|bs2	alkylglycerone phosphate synthase	protein-coding
mm_157983.1	chrX	94136106	94136109	-	1	NA	Intergenic	PB1D11|SINE|Alu	-12700	NM_001044386	22764	Mm.919	NM_011768	ENSMUSG00000079509	Zfx	Zfx5|Zfx5,6|Zfx6	zinc finger protein X-linked	protein-coding
mm_38030.1	chr4	133873049	133873061	-	1	NA	intron (NM_001285505, intron 2 of 21)	intron (NM_001285505, intron 2 of 21)	1676	NM_001285506	20111	Mm.301827	NM_009097	ENSMUSG00000003644	Rps6ka1	Mapkapk-1a|Rsk|Rsk-1|Rsk1|S6K-alpha-1|p90-Rsk1|p90Rsk1|p90S6K|p90rsk	ribosomal protein S6 kinase polypeptide 1	protein-coding
mm_75273.1	chr8	40862255	40862307	-	1	NA	promoter-TSS (NM_001044740)	promoter-TSS (NM_001044740)	-86	NM_007514	11988	Mm.4676	NM_007514	ENSMUSG00000031596	Slc7a2	20.5|AI158848|Atrc2|CAT-2|Cat2|Tea	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	protein-coding
mm_60097.1	chr7	35119626	35119650	+	1	NA	exon (NM_001287514, exon 1 of 1)	exon (NM_001287514, exon 1 of 1)	345	NM_007678	12606	Mm.349667	NM_007678	ENSMUSG00000034957	Cebpa	C/ebpalpha|CBF-A|Cebp	CCAAT/enhancer binding protein (C/EBP), alpha	protein-coding
mm_131327.1	chr16	13109797	13109812	+	1	NA	promoter-TSS (NM_015769)	promoter-TSS (NM_015769)	68	NM_015769	50505	Mm.287837	NM_015769	ENSMUSG00000022545	Ercc4	AI606920|Xpf	excision repair cross-complementing rodent repair deficiency, complementation group 4	protein-coding
mm_132854.1	chr16	48281654	48281665	+	1	NA	Intergenic	Intergenic	-2076	NM_028610	73693	Mm.35597	NM_028610	ENSMUSG00000058550	Dppa4	2410091M23Rik|C76608|ECAT15-1	developmental pluripotency associated 4	protein-coding
mm_120559.1	chr14	68120626	68120693	+	1	NA	exon (NM_008691, exon 3 of 3)	exon (NM_008691, exon 3 of 3)	-3093	NR_045897	100043072	Mm.242832	NR_045897		A230070E04Rik	Gm4210	RIKEN cDNA A230070E04 gene	ncRNA
mm_117573.1	chr13	85289462	85289491	-	1	NA	promoter-TSS (NM_145452)	promoter-TSS (NM_145452)	10	NM_145452	218397	Mm.259653	NM_145452	ENSMUSG00000021549	Rasa1	Gap|RasGAP|Rasa	RAS p21 protein activator 1	protein-coding
mm_50558.1	chr6	49047819	49047832	+	1	NA	exon (NM_053110, exon 6 of 11)	exon (NM_053110, exon 6 of 11)	11307	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_72815.1	chr8	87563923	87563931	+	1	NA	promoter-TSS (NM_177901)	promoter-TSS (NM_177901)	20	NM_177901	330820	Mm.212913	NM_177901	ENSMUSG00000069971	4933402J07Rik	-	RIKEN cDNA 4933402J07 gene	protein-coding
mm_27285.1	chr3	41497060	41497075	-	1	NA	Intergenic	MER31-int|LTR|ERV1	-3868	NR_040385	78706	Mm.366094	NR_040385	ENSMUSG00000097639	Platr4	C430002E04Rik	pluripotency associated transcript 4	ncRNA
mm_17523.1	chr2	29252869	29252893	-	1	NA	non-coding (NR_029460, exon 1 of 2)	non-coding (NR_029460, exon 1 of 2)	112	NR_029460	76220	Mm.330108	NR_029460	ENSMUSG00000079499	6530402F18Rik	mKIAA1857	RIKEN cDNA 6530402F18 gene	ncRNA
mm_43117.1	chr5	124629100	124629113	+	1	NA	promoter-TSS (NM_011596)	promoter-TSS (NM_011596)	54	NM_011596	21871	Mm.1158	NM_011596	ENSMUSG00000038023	Atp6v0a2	8430408C20Rik|AI385560|ATP6a2|AW489264|Atp6n1d|Atp6n2|C76904|ISF|J6B7|SHIF|Stv1|TJ6M|TJ6s|Tj6|V-ATPase 116 kDa|V-ATPase a2	ATPase, H+ transporting, lysosomal V0 subunit A2	protein-coding
mm_151242.1	chr19	53863617	53863626	+	1	NA	intron (NM_001170847, intron 13 of 13)	intron (NM_001170847, intron 13 of 13)	-28610	NM_011050	18569	Mm.1605	NM_011050	ENSMUSG00000024975	Pdcd4	D19Ucla1|Ma3|Tis	programmed cell death 4	protein-coding
mm_38565.1	chr4	141708403	141708414	-	1	NA	exon (NM_001017966, exon 3 of 10)	exon (NM_001017966, exon 3 of 10)	15011	NM_001017966	68817	Mm.393721	NM_001017966	ENSMUSG00000078515	Ddi2	1110056G13Rik|1700027M01Rik|9130022E05Rik|AI604911|AU040698	DNA-damage inducible protein 2	protein-coding
mm_19563.1	chr2	100407793	100407802	-	1	NA	Intergenic	Intergenic	-1216951	NM_009020	19374	Mm.4988	NM_009020	ENSMUSG00000032864	Rag2	Rag-2	recombination activating gene 2	protein-coding
mm_144721.1	chr18	35120233	35120236	+	1	NA	intron (NM_009818, intron 1 of 17)	intron (NM_009818, intron 1 of 17)	1322	NM_009818	12385	Mm.18962	NM_009818	ENSMUSG00000037815	Ctnna1	2010010M04Rik|AA517462|AI988031|Catna1	catenin (cadherin associated protein), alpha 1	protein-coding
mm_72694.1	chr8	84970069	84970093	+	1	NA	intron (NM_011563, intron 1 of 5)	intron (NM_011563, intron 1 of 5)	459	NM_011563	21672	Mm.347009	NM_011563	ENSMUSG00000005161	Prdx2	AL022839|Band-8|NkefB|PRP|PrxII|TDX1|TPx|TPx-B|TR|TSA|Tdpx1|Torin	peroxiredoxin 2	protein-coding
mm_47185.1	chr5	120753969	120753985	-	1	NA	3' UTR (NM_145226, exon 16 of 16)	3' UTR (NM_145226, exon 16 of 16)	-4129	NM_001347448	246728	Mm.260926	NM_145227	ENSMUSG00000032690	Oas2	Oasl11	2'-5' oligoadenylate synthetase 2	protein-coding
mm_138152.1	chr17	34211941	34211945	+	1	NA	exon (NM_011530, exon 6 of 12)	exon (NM_011530, exon 6 of 12)	7464	NM_011530	21355	Mm.14814	NM_011530	ENSMUSG00000024339	Tap2	ABC18|AI462429|APT2|Abcb3|Ham-2|Ham2|MTP2|PSF2|RING11|Tap-2|Y1|jas	transporter 2, ATP-binding cassette, sub-family B (MDR/TAP)	protein-coding
mm_21790.1	chr2	164857167	164857182	-	1	NA	intron (NM_011125, intron 1 of 15)	CpG-8831	534	NM_011125	18830	Mm.6105	NM_011125	ENSMUSG00000017754	Pltp	Bpife|OD107	phospholipid transfer protein	protein-coding
mm_117246.1	chr13	64363937	64364054	-	1	NA	3' UTR (NM_009984, exon 8 of 8)	3' UTR (NM_009984, exon 8 of 8)	6525	NM_009984	13039	Mm.930	NM_009984	ENSMUSG00000021477	Ctsl	1190035F06Rik|CatL|Ctsl1|MEP|fs|nkt	cathepsin L	protein-coding
mm_89817.1	chr10	104659648	104659650	+	1	NA	Intergenic	Intergenic	372380	NR_105838	102465222		NR_105838	ENSMUSG00000099264	Mir6411	Gm27767|mmu-mir-6411	microRNA 6411	ncRNA
mm_76690.1	chr8	94154007	94154021	-	1	NA	3' UTR (NM_013603, exon 3 of 3)	3' UTR (NM_013603, exon 3 of 3)	1407	NM_013603	17751	Mm.2064	NM_013603	ENSMUSG00000031760	Mt3	Mt-3	metallothionein 3	protein-coding
mm_121906.1	chr14	21987557	21987573	-	1	NA	5' UTR (NM_145459, exon 2 of 3)	5' UTR (NM_145459, exon 2 of 3)	2036	NM_145459	218820	Mm.292401	NM_145459	ENSMUSG00000039081	Zfp503	AI181838|B830002A16Rik|Nolz-1|Nolz1|Znf503	zinc finger protein 503	protein-coding
mm_138333.1	chr17	34894687	34894700	+	1	NA	5' UTR (NM_198886, exon 1 of 2)	5' UTR (NM_198886, exon 1 of 2)	134	NM_198886	193736	Mm.161119	NM_198886	ENSMUSG00000049823	Zbtb12	BC020447|Bat-9|Bat9|G10|NG35	zinc finger and BTB domain containing 12	protein-coding
mm_154727.1	chrX	9436742	9436763	+	1	NA	3' UTR (NM_007807, exon 13 of 13)	3' UTR (NM_007807, exon 13 of 13)	32572	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_1921.1	chr1	86039639	86039643	+	1	NA	Intergenic	Intergenic	-6222	NM_001144993	72792	Mm.54981	NM_001144992	ENSMUSG00000026227	2810459M11Rik	-	RIKEN cDNA 2810459M11 gene	protein-coding
mm_33621.1	chr4	132709939	132709969	+	1	NA	exon (NM_010166, exon 15 of 18)	exon (NM_010166, exon 15 of 18)	22592	NM_201368	381560	Mm.44558	NM_201368	ENSMUSG00000037752	Xkr8	4931440N07Rik|AI597014|Gm1031|XRG8|mXkr8	X-linked Kx blood group related 8	protein-coding
mm_73731.1	chr8	113635849	113635862	+	1	NA	promoter-TSS (NM_173015)	promoter-TSS (NM_173015)	56	NM_173015	270096	Mm.74689	NM_173015	ENSMUSG00000078908	Mon1b	5031407H10|5033413H12Rik	MON1 homolog B, secretory traffciking associated	protein-coding
mm_111864.1	chr12	107980787	107980804	-	1	NA	intron (NM_001079883, intron 2 of 3)	intron (NM_001079883, intron 2 of 3)	22619	NM_001079883	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_172811.1	chr9	123689472	123689475	-	1	NA	Intergenic	(CCA)n|Simple_repeat|Simple_repeat	-10641	NM_139142	102680	Mm.440867	NM_139142	ENSMUSG00000036814	Slc6a20a	A730081N20Rik|AU022428|Xt3s1|Xtrp3s1	solute carrier family 6 (neurotransmitter transporter), member 20A	protein-coding
mm_98111.1	chr11	87109182	87109195	+	1	NA	promoter-TSS (NM_175563)	promoter-TSS (NM_175563)	-73	NM_025377	66140	Mm.45008	NM_025377	ENSMUSG00000020492	Ska2	1110001A07Rik|C78640|Fam33a	spindle and kinetochore associated complex subunit 2	protein-coding
mm_42369.1	chr5	114923388	114923400	+	1	NA	intron (NM_145209, intron 1 of 6)	intron (NM_145209, intron 1 of 6)	154	NM_145209	231655	Mm.95479	NM_145209	ENSMUSG00000041827	Oasl1	7530414C13Rik|oasl9	2'-5' oligoadenylate synthetase-like 1	protein-coding
mm_110280.1	chr12	32061195	32061208	-	1	NA	promoter-TSS (NM_011158)	promoter-TSS (NM_011158)	78	NM_011158	19088	Mm.25594	NM_011158	ENSMUSG00000002997	Prkar2b	AI451071|AW061005|PKARIIbeta|Pkarb2|RII(beta)	protein kinase, cAMP dependent regulatory, type II beta	protein-coding
mm_86740.1	chr10	19185210	19185224	+	1	NA	intron (NR_038022, intron 1 of 1)	intron (NR_038022, intron 1 of 1)	17979	NR_038022	100504265	Mm.383417	NR_038021		Gm20139	-	predicted gene, 20139	ncRNA
mm_59981.1	chr7	30465489	30465499	+	1	NA	promoter-TSS (NR_004443)	promoter-TSS (NR_004443)	97	NR_004443	445267	Mm.398140	NR_004443	ENSMUSG00000087009	Nphs1os	Nphs1as	nephrosis 1 homolog, nephrin, opposite strand	ncRNA
mm_102416.1	chr11	59202377	59202394	-	1	NA	promoter-TSS (NM_026035)	promoter-TSS (NM_026035)	46	NR_037964	72203	Mm.339566	NR_037964		2610507I01Rik	5033414D05Rik	RIKEN cDNA 2610507I01 gene	ncRNA
mm_58163.1	chr6	142507911	142507962	-	1	NA	promoter-TSS (NM_008492)	promoter-TSS (NM_008492)	21	NM_008492	16832	Mm.9745	NM_008492	ENSMUSG00000030246	Ldhb	AI790582|H-Ldh|LDH-B|LDH-H|Ldh-2|Ldh2	lactate dehydrogenase B	protein-coding
mm_56901.1	chr6	119196449	119196518	-	1	NA	promoter-TSS (NM_009781)	promoter-TSS (NM_009781)	-74	NM_001255999	12288	Mm.41628	NM_009781	ENSMUSG00000051331	Cacna1c	Cav1.2|Cchl1a1|D930026N18Rik|MBC|MELC-CC	calcium channel, voltage-dependent, L type, alpha 1C subunit	protein-coding
mm_106471.1	chr11	120099419	120099467	-	1	NA	promoter-TSS (NM_183137)	promoter-TSS (NM_183137)	509	NM_001110242	208501	Mm.46699	NM_001110242	ENSMUSG00000078572	Ndufaf8	1810043H04Rik	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex assembly factor 8	protein-coding
mm_23489.1	chr3	60501885	60501908	+	1	NA	intron (NM_001253710, intron 1 of 7)	intron (NM_001253710, intron 1 of 7)	717	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_103344.1	chr11	74724306	74724329	-	1	NA	promoter-TSS (NR_037610)	promoter-TSS (NR_037610)	67	NM_013625	18472	Mm.397111	NM_013625	ENSMUSG00000020745	Pafah1b1	LIS-1|Lis1|MMS10-U|Mdsh|Ms10u|Pafaha	platelet-activating factor acetylhydrolase, isoform 1b, subunit 1	protein-coding
mm_131984.1	chr16	25040286	25040294	+	1	NA	Intergenic	Intergenic	-19349	NR_040374	319487	Mm.137341	NR_040374	ENSMUSG00000096960	A230028O05Rik	-	RIKEN cDNA A230028O05 gene	ncRNA
mm_143345.1	chr17	66595333	66595337	-	1	NA	promoter-TSS (NM_028998)	promoter-TSS (NM_028998)	-713	NM_028998	74556	Mm.218634	NM_028998	ENSMUSG00000024105	Themis3	9130404H23Rik	thymocyte selection associated family member 3	protein-coding
mm_158582.1	chrX	150812790	150812805	-	1	NA	intron (NM_030700, intron 1 of 12)	intron (NM_030700, intron 1 of 12)	906	NM_001199246	80884	Mm.22575	NM_030700	ENSMUSG00000025268	Maged2	4833439A22Rik|Mage-d2|ORF1	melanoma antigen, family D, 2	protein-coding
mm_1579.1	chr1	74281215	74281223	+	1	NA	intron (NM_001190444, intron 8 of 10)	intron (NM_001190444, intron 8 of 10)	2619	NM_174985	227289	Mm.246587	NM_174985	ENSMUSG00000064272	Gpbar1	BG37|GPCR|GPR131|M-BAR|TGR5	G protein-coupled bile acid receptor 1	protein-coding
mm_47149.1	chr5	120564727	120564741	-	1	NA	intron (NM_145853, intron 2 of 27)	RLTR20C2_MM|LTR|ERVK	23879	NM_145853	252972	Mm.114054	NM_145853	ENSMUSG00000032741	Tpcn1	5730403B01Rik|Tpc1|mKIAA1169	two pore channel 1	protein-coding
mm_99587.1	chr11	104306641	104306654	+	1	NA	exon (NM_010838, exon 5 of 10)	exon (NM_010838, exon 5 of 10)	75211	NM_001285454	17762	Mm.1287	NM_010838	ENSMUSG00000018411	Mapt	AI413597|AW045860|Mtapt|Tau	microtubule-associated protein tau	protein-coding
mm_147393.1	chr18	44196168	44196179	-	1	NA	promoter-TSS (NM_001048217)	promoter-TSS (NM_001048217)	4	NM_001048217	433181	Mm.117440	NM_001048217	ENSMUSG00000073573	Spink11	9230112K01Rik	serine peptidase inhibitor, Kazal type 11	protein-coding
mm_75255.1	chr8	40511299	40511346	-	1	NA	promoter-TSS (NM_033560)	promoter-TSS (NM_033560)	432	NM_001271543	18983	Mm.272551	NM_011135	ENSMUSG00000031601	Cnot7	AU022737|CAF-1|Caf1|Pop2	CCR4-NOT transcription complex, subunit 7	protein-coding
mm_103269.1	chr11	72037453	72037459	-	1	NA	promoter-TSS (NM_053245)	promoter-TSS (NM_053245)	53	NM_053245	114230	Mm.95707	NM_053245	ENSMUSG00000040554	Aipl1	A930007I01Rik	aryl hydrocarbon receptor-interacting protein-like 1	protein-coding
mm_131209.1	chr16	8680812	8680817	+	1	NA	promoter-TSS (NM_001324517)	promoter-TSS (NM_001324517)	44	NM_001324517	436336	Mm.357666	NM_001324517		Gm5767	EG436336	predicted gene 5767	protein-coding
mm_25136.1	chr3	102469919	102469932	+	1	NA	promoter-TSS (NM_013609)	promoter-TSS (NM_013609)	6	NM_013609	18049	Mm.1259	NM_013609	ENSMUSG00000027859	Ngf	Ngfb	nerve growth factor	protein-coding
mm_156776.1	chrX	161162745	161162775	+	1	NA	promoter-TSS (NM_001290652)	promoter-TSS (NM_001290652)	10	NM_001290651	107815	Mm.159173	NM_133194	ENSMUSG00000000037	Scml2	4932420G07Rik	sex comb on midleg-like 2 (Drosophila)	protein-coding
mm_143472.1	chr17	71127569	71127606	-	1	NA	TTS (NM_001083934)	TTS (NM_001083934)	-56391	NM_022882	64898	Mm.227924	NM_022882	ENSMUSG00000024052	Lpin2	2610511G02Rik|AI481352|AW742896	lipin 2	protein-coding
mm_162921.1	chr10	120882660	120882687	+	1	NA	intron (NM_177092, intron 1 of 6)	intron (NM_177092, intron 1 of 6)	16298	NM_177092	320183	Mm.169755	NM_177092	ENSMUSG00000051236	Msrb3	D430026P16Rik|I-8-23|MsrB2	methionine sulfoxide reductase B3	protein-coding
mm_73656.1	chr8	110957762	110957774	+	1	NA	exon (NM_009179, exon 2 of 7)	exon (NM_009179, exon 2 of 7)	37903	NM_009179	20444	Mm.200388	NM_009179	ENSMUSG00000031749	St3gal2	AI429591|AW822065|ST3GalII|Siat5	ST3 beta-galactoside alpha-2,3-sialyltransferase 2	protein-coding
mm_18384.1	chr2	60108003	60108006	-	1	NA	intron (NM_001001182, intron 1 of 35)	PB1D11|SINE|Alu	17736	NM_001001182	407823	Mm.228071	NM_001001182	ENSMUSG00000026987	Baz2b	5830435C13Rik|BC053917|D2Ertd794e	bromodomain adjacent to zinc finger domain, 2B	protein-coding
mm_12244.1	chr2	68868922	68868951	+	1	NA	intron (NM_172856, intron 1 of 9)	B3A|SINE|B2	7495	NM_001347161	241447	Mm.222222	NM_172856	ENSMUSG00000027035	Cers6	4732462C07Rik|AW544719|Lass6|T1L	ceramide synthase 6	protein-coding
mm_134357.1	chr16	16829244	16829253	-	1	NA	5' UTR (NM_015773, exon 1 of 11)	5' UTR (NM_015773, exon 1 of 11)	115	NM_015773	50525	Mm.31701	NM_015773	ENSMUSG00000022783	Spag6l	PF16|Spag6|Spag6l1	sperm associated antigen 6-like	protein-coding
mm_153232.1	chr19	34922203	34922250	-	1	NA	promoter-TSS (NM_183046)	promoter-TSS (NM_183046)	-132	NM_183046	240641	Mm.278471	NM_183046	ENSMUSG00000024795	Kif20b	33cex|B130024C23|C330014J10Rik|Mphosph1|magoo	kinesin family member 20B	protein-coding
mm_123402.1	chr14	63508767	63508773	-	1	NA	5' UTR (NM_021480, exon 1 of 9)	5' UTR (NM_021480, exon 1 of 9)	322	NM_021480	58865	Mm.354229	NM_021480	ENSMUSG00000021953	Tdh	-	L-threonine dehydrogenase	protein-coding
mm_131134.1	chr16	6068494	6068509	+	1	NA	intron (NM_021477, intron 1 of 16)	intron (NM_021477, intron 1 of 16)	92914	NR_045799	68238	Mm.434605	NR_045799	ENSMUSG00000101481	1700123O21Rik	-	RIKEN cDNA 1700123O21 gene	ncRNA
mm_133563.1	chr16	91397126	91397130	+	1	NA	intron (NM_001347258, intron 7 of 7)	intron (NM_001347258, intron 7 of 7)	-9107	NM_008349	16155	Mm.4154	NM_008349	ENSMUSG00000022969	Il10rb	6620401D04Rik|AI528744|CRF2-4|Crfb4|D16H21S58|D21S58h|IL-10R2|Il10r2	interleukin 10 receptor, beta	protein-coding
mm_8233.1	chr1	138175693	138175704	-	1	NA	promoter-TSS (NM_001268286)	promoter-TSS (NM_001268286)	-393	NM_001268286	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_152881.1	chr19	24529040	24529062	-	1	NA	intron (NM_008846, intron 1 of 14)	intron (NM_008846, intron 1 of 14)	26776	NM_008846	18719	Mm.217214	NM_008846	ENSMUSG00000024867	Pip5k1b	PI4P5K-I[b]|PIP5K1-beta|PIP5KIbeta|Pipk5b|STM7	phosphatidylinositol-4-phosphate 5-kinase, type 1 beta	protein-coding
mm_138829.1	chr17	39848054	39848055	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	5057	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_93595.1	chr10	117116489	117116492	-	1	NA	intron (NM_177798, intron 1 of 9)	intron (NM_177798, intron 1 of 9)	31984	NM_177798	327826	Mm.135965	NM_177798	ENSMUSG00000020170	Frs2	4732458E18|C330018A15Rik|Frs2alpha|SNT1	fibroblast growth factor receptor substrate 2	protein-coding
mm_22516.1	chr3	7620144	7620146	+	1	NA	Intergenic	Intergenic	-6385	NM_001313888	16196	Mm.3825	NM_008371	ENSMUSG00000040329	Il7	A630026I06Rik|Il-7|hlb368	interleukin 7	protein-coding
mm_60730.1	chr7	45420907	45420914	+	1	NA	promoter-TSS (NM_008497)	promoter-TSS (NM_008497)	-36	NM_008497	16866	Mm.57061	NM_008497	ENSMUSG00000100916	Lhb	Gm29035|LH|LH-B|LSH-B|LSH-beta	luteinizing hormone beta	protein-coding
mm_135732.1	chr16	55831290	55831294	-	1	NA	intron (NM_030612, intron 2 of 13)	B4|SINE|B4	7349	NM_030612	80859	Mm.247272	NM_030612	ENSMUSG00000035356	Nfkbiz	AA408868|INAP|Mail	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, zeta	protein-coding
mm_18239.1	chr2	52169121	52169141	-	1	NA	exon (NM_010889, exon 136 of 157)	exon (NM_010889, exon 136 of 157)	96294	NM_175238	51869	Mm.254530	NM_175238	ENSMUSG00000036202	Rif1	5730435J01Rik|6530403D07Rik|AU016181|AW549474|D2Ertd145e	replication timing regulatory factor 1	protein-coding
mm_162347.1	chr1	53313744	53313748	+	1	NA	non-coding (NR_104361, exon 1 of 9)	non-coding (NR_104361, exon 1 of 9)	122	NR_104360	72085	Mm.482256	NM_028091	ENSMUSG00000026096	Osgepl1	2610001M19Rik|AA416452	O-sialoglycoprotein endopeptidase-like 1	protein-coding
mm_78536.1	chr9	35211254	35211264	+	1	NA	promoter-TSS (NM_172291)	promoter-TSS (NM_172291)	56	NM_026130	67398	Mm.284688	NM_026130	ENSMUSG00000032042	Srpr	1300011P19Rik|D11Mgi27|Srpra	signal recognition particle receptor ('docking protein')	protein-coding
mm_107726.1	chr12	57230466	57230503	+	1	NA	promoter-TSS (NM_001164370)	promoter-TSS (NM_001164370)	59	NM_001164370	73490	Mm.268180	NM_001164370	ENSMUSG00000047022	Mipol1	1700081O04Rik|6030439O22Rik|AU021838|AW536152|D12Ertd19e	mirror-image polydactyly 1	protein-coding
mm_153869.1	chr19	46690139	46690173	-	1	NA	intron (NM_025563, intron 1 of 4)	intron (NM_025563, intron 1 of 4)	250	NM_025563	66439	Mm.87163	NM_025563	ENSMUSG00000062376	Borcs7	2010012O05Rik|4930569L17Rik|AI413851|AI467257	BLOC-1 related complex subunit 7	protein-coding
mm_18038.1	chr2	38926339	38926354	-	1	NA	5' UTR (NM_010264, exon 1 of 11)	5' UTR (NM_010264, exon 1 of 11)	115	NM_010264	14536	Mm.439703	NM_010264	ENSMUSG00000063972	Nr6a1	1700113M01Rik|Gcnf|NCNF|RTR	nuclear receptor subfamily 6, group A, member 1	protein-coding
mm_169288.1	chr13	9834347	9834347	-	1	NA	Intergenic	L1Md_T|LINE|L1	-69026	NM_144516	66505	Mm.397307	NM_144516	ENSMUSG00000021156	Zmynd11	2210402G22Rik|BS69	zinc finger, MYND domain containing 11	protein-coding
mm_36553.1	chr4	86857118	86857146	-	1	NA	intron (NM_009096, intron 1 of 4)	CpG	235	NM_009096	20104	Mm.379007	NM_009096	ENSMUSG00000028495	Rps6	S6R	ribosomal protein S6	protein-coding
mm_6780.1	chr1	84137925	84137935	-	1	NA	intron (NM_001003948, intron 2 of 2)	Lx7|LINE|L1	81031	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_100088.1	chr11	115480929	115480950	+	1	NA	intron (NM_177778, intron 2 of 2)	B1_Mur4|SINE|Alu	5262	NM_177778	276905	Mm.38019	NM_177778	ENSMUSG00000057219	Armc7	A630084C13|BC023126	armadillo repeat containing 7	protein-coding
mm_95524.1	chr11	52224673	52224683	+	1	NA	Intergenic	Intergenic	-7317	NM_011543	21402	Mm.42944	NM_011543	ENSMUSG00000036309	Skp1a	15kDa|2610043E24Rik|2610206H23Rik|EMC19|OCP-II|OCP2|SKP1|Tceb1l|p19A|p19Skp1	S-phase kinase-associated protein 1A	protein-coding
mm_83039.1	chr9	37348340	37348366	-	1	NA	promoter-TSS (NM_001081429)	promoter-TSS (NM_001081429)	39	NM_001081429	245902	Mm.390150	NM_001081429	ENSMUSG00000034303	Ccdc15	A630039F14Rik|D030074L19	coiled-coil domain containing 15	protein-coding
mm_156918.1	chrX	169099153	169099166	+	1	NA	intron (NR_109847, intron 1 of 14)	Lx8|LINE|L1	-13719	NM_001287530	11856	Mm.441810	NM_009707	ENSMUSG00000031355	Arhgap6	AI504284|RhoGAPX-1	Rho GTPase activating protein 6	protein-coding
mm_145595.1	chr18	60987530	60987548	+	1	NA	3' UTR (NM_001286809, exon 6 of 6)	3' UTR (NM_001286809, exon 6 of 6)	23985	NM_001286809	12322	Mm.131530	NM_009792	ENSMUSG00000024617	Camk2a	CaMKII|R74975|mKIAA0968	calcium/calmodulin-dependent protein kinase II alpha	protein-coding
mm_54032.1	chr6	12724615	12724618	-	1	NA	intron (NM_001164805, intron 1 of 26)	intron (NM_001164805, intron 1 of 26)	24637	NM_001164805	330267	Mm.11989	NM_001164805	ENSMUSG00000032625	Thsd7a	Gm837	thrombospondin, type I, domain containing 7A	protein-coding
mm_157681.1	chrX	59568103	59568130	-	1	NA	intron (NM_001290414, intron 1 of 6)	CpG	17456	NM_001290414	14168	Mm.7995	NM_010200	ENSMUSG00000031137	Fgf13	Fhf2	fibroblast growth factor 13	protein-coding
mm_87724.1	chr10	60106368	60106400	+	1	NA	5' UTR (NM_052994, exon 1 of 11)	5' UTR (NM_052994, exon 1 of 11)	127	NM_052994	94214	Mm.153429	NM_052994	ENSMUSG00000058297	Spock2	AA407235|Gcap26|mKIAA0275	sparc/osteonectin, cwcv and kazal-like domains proteoglycan 2	protein-coding
mm_106770.1	chr12	4598892	4598930	+	1	NA	intron (NM_011365, intron 1 of 38)	intron (NM_011365, intron 1 of 38)	5903	NM_001198968	20403	Mm.341204	NM_011365	ENSMUSG00000020640	Itsn2	AI327390|Ese2|Sh3d1B|Sh3p18|mKIAA1256	intersectin 2	protein-coding
mm_34438.1	chr4	147868788	147868825	+	1	NA	promoter-TSS (NM_010244)	promoter-TSS (NM_010244)	-87	NM_001025365	28010	Mm.250504	NM_133873	ENSMUSG00000029022	Miip	AA553001|AI853621|D4Wsu114e|IIP45	migration and invasion inhibitory protein	protein-coding
mm_152932.1	chr19	28560976	28560987	-	1	NA	intron (NM_175459, intron 2 of 10)	intron (NM_175459, intron 2 of 10)	-117243	NR_045330	320176	Mm.406716	NR_045330	ENSMUSG00000097735	D930032P07Rik	-	RIKEN cDNA D930032P07 gene	ncRNA
mm_90313.1	chr10	127048236	127048246	+	1	NA	promoter-TSS (NM_010009)	promoter-TSS (NM_010009)	-5	NM_010009	13115	Mm.6216	NM_010009	ENSMUSG00000006724	Cyp27b1	Cp2b|Cyp1|Cyp27b|Cyp40|P450c1|Pddr|Vdd1|Vddr|VddrI|Vdr	cytochrome P450, family 27, subfamily b, polypeptide 1	protein-coding
mm_22934.1	chr3	31163378	31163388	+	1	NA	3' UTR (NM_008770, exon 3 of 3)	3' UTR (NM_008770, exon 3 of 3)	13463	NM_008770	18417	Mm.4425	NM_008770	ENSMUSG00000037625	Cldn11	Claudin-11|Claudin11|Osp|Otm	claudin 11	protein-coding
mm_33926.1	chr4	136802145	136802159	+	1	NA	intron (NM_001290753, intron 1 of 15)	(TG)n|Simple_repeat|Simple_repeat	33860	NM_001290753	13844	Mm.250981	NM_010142	ENSMUSG00000028664	Ephb2	Cek5|Drt|ETECK|Erk|Hek5|Nuk|Prkm5|Qek5|Sek3|Tyro5	Eph receptor B2	protein-coding
mm_163552.1	chr13	23710923	23710931	-	1	NA	promoter-TSS (NM_001347493)	promoter-TSS (NM_001347493)	-73	NM_010424	15216	Mm.2681	NM_010424	ENSMUSG00000006611	Hfe	MR2	hemochromatosis	protein-coding
mm_141731.1	chr17	34118477	34118522	-	1	NA	intron (NR_037970, intron 1 of 12)	CpG	1401	NR_037970	14312	Mm.3444	NM_010238	ENSMUSG00000024335	Brd2	AW228947|D17H6S113E|Frg-1|Fsrg-1|Fsrg1|Nat|Ring3|Rnf3|mKIAA4005	bromodomain containing 2	protein-coding
mm_40440.1	chr5	53591060	53591066	+	1	NA	intron (NM_001080927, intron 1 of 10)	CpG	577	NM_001080927	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_55613.1	chr6	72042545	72042560	-	1	NA	promoter-TSS (NR_046180)	promoter-TSS (NR_046180)	-24	NR_046180	330350	Mm.246787	NR_046180	ENSMUSG00000108356	9130221F21Rik	9130221F21	RIKEN cDNA 9130221F21 gene	ncRNA
mm_71658.1	chr8	60524206	60524212	+	1	NA	intron (NM_011834, intron 4 of 12)	L1VL4|LINE|L1	18085	NM_011834	23923	Mm.35020	NM_011834	ENSMUSG00000057228	Aadat	AI875679|Aadt|KATII|Kat2|Kyat2|mKat-2	aminoadipate aminotransferase	protein-coding
mm_156637.1	chrX	157540681	157540685	+	1	NA	promoter-TSS (NR_040420)	promoter-TSS (NR_040420)	-121	NR_040420	625253	Mm.463485	NR_040420		Gm6568	EG625253	DnaJ (Hsp40) homolog, subfamily B, member 9 pseudogene	pseudo
mm_84132.1	chr9	59036324	59036344	-	1	NA	5' UTR (NM_008684, exon 1 of 29)	5' UTR (NM_008684, exon 1 of 29)	107	NM_008684	18007	Mm.42249	NM_008684	ENSMUSG00000032340	Neo1	2610028H22Rik|AI327052|D930014N22Rik|Igdcc2	neogenin	protein-coding
mm_145012.1	chr18	38602240	38602260	+	1	NA	promoter-TSS (NM_011898)	promoter-TSS (NM_011898)	-982	NM_011898	24066	Mm.42038	NM_011898	ENSMUSG00000024427	Spry4	A030006O18Rik|sprouty4	sprouty homolog 4 (Drosophila)	protein-coding
mm_152029.1	chr19	6080312	6080336	-	1	NA	TTS (NM_024231)	TTS (NM_024231)	286	NM_001111317	433215	Mm.437186	NM_001111317	ENSMUSG00000047733	Tmem262	-	transmembrane protein 262	protein-coding
mm_63719.1	chr7	130820108	130820140	+	1	NA	intron (NM_001081038, intron 12 of 15)	intron (NM_001081038, intron 12 of 15)	-45600	NM_001346515	101476	Mm.323554	NM_133942	ENSMUSG00000040268	Plekha1	AA960558|C920009D07Rik|TAPP1	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 1	protein-coding
mm_68547.1	chr7	114254649	114254657	-	1	NA	promoter-TSS (NM_033370)	promoter-TSS (NM_033370)	27	NM_033370	70349	Mm.277024	NM_033370	ENSMUSG00000030754	Copb1	2610019B04Rik	coatomer protein complex, subunit beta 1	protein-coding
mm_114610.1	chr13	75840072	75840085	+	1	NA	exon (NM_053108, exon 1 of 3)	exon (NM_053108, exon 1 of 3)	192	NM_053108	93692	Mm.25844	NM_053108	ENSMUSG00000021591	Glrx	C86710|D13Wsu156e|Glrx1|Grx1|TTase	glutaredoxin	protein-coding
mm_43483.1	chr5	136908182	136908202	+	1	NA	promoter-TSS (NM_026073)	promoter-TSS (NM_026073)	42	NM_026073	67286	Mm.41779	NM_026073	ENSMUSG00000007987	Ift22	3110017O03Rik|AI835745|AI847427|Rabl5	intraflagellar transport 22	protein-coding
mm_138427.1	chr17	35076919	35076931	+	1	NA	promoter-TSS (NM_027366)	promoter-TSS (NM_027366)	-17	NM_027366	70274	Mm.250491	NM_027366	ENSMUSG00000013766	Ly6g6e	2310011I02Rik|G6e	lymphocyte antigen 6 complex, locus G6E	protein-coding
mm_33763.1	chr4	134396360	134396409	+	1	NA	promoter-TSS (NM_001285875)	promoter-TSS (NM_001285875)	64	NM_001285875	100163	Mm.22116	NM_133880	ENSMUSG00000037366	Pafah2	2310074E22Rik|AI507170	platelet-activating factor acetylhydrolase 2	protein-coding
mm_109039.1	chr12	104214513	104214532	+	1	NA	promoter-TSS (NM_001168295)	promoter-TSS (NM_001168295)	-22	NM_001168294	238393	Mm.483584	NM_001033335	ENSMUSG00000066363	Serpina3f	2A1|BC049975	serine (or cysteine) peptidase inhibitor, clade A, member 3F	protein-coding
mm_11300.1	chr2	30171544	30171554	+	1	NA	promoter-TSS (NM_007931)	promoter-TSS (NM_007931)	25	NM_007931	13804	Mm.474473	NM_007931	ENSMUSG00000015337	Endog	-	endonuclease G	protein-coding
mm_163684.1	chr13	94548342	94548344	-	1	NA	intron (NM_009680, intron 26 of 26)	intron (NM_009680, intron 26 of 26)	189383	NM_009680	11774	Mm.21185	NM_009680	ENSMUSG00000021686	Ap3b1	AP-3|AU015684|C78395|Hps2|beta3A|pe|pearl|rim2	adaptor-related protein complex 3, beta 1 subunit	protein-coding
mm_157262.1	chrX	19167238	19167244	-	1	NA	Intergenic	Intergenic	-20270	NR_029807	723828		NR_029807	ENSMUSG00000065471	Mir222	Mirn222|mir-222|mmu-mir-222	microRNA 222	ncRNA
mm_76613.1	chr8	91135660	91135668	-	1	NA	promoter-TSS (NM_010241)	promoter-TSS (NM_010241)	-170	NM_010241	14339	Mm.324588	NM_010241	ENSMUSG00000031667	Aktip	AL023020|Fif|Ft|Ft1|Fts	thymoma viral proto-oncogene 1 interacting protein	protein-coding
mm_55507.1	chr6	69900659	69900665	-	1	NA	Intergenic	Intergenic	-573488	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_78511.1	chr9	32906590	32906598	+	1	NA	non-coding (NR_131058, exon 4 of 4)	non-coding (NR_131058, exon 4 of 4)	22372	NR_131058	330917	Mm.488283	NR_131058		Gm27162	A430016B06	predicted gene 27162	ncRNA
mm_113639.1	chr13	42053011	42053022	+	1	NA	intron (NM_007772, intron 1 of 8)	intron (NM_007772, intron 1 of 8)	995	NM_007772	110521	Mm.4808	NM_007772	ENSMUSG00000021366	Hivep1	Cryabp1	human immunodeficiency virus type I enhancer binding protein 1	protein-coding
mm_118981.1	chr14	28380066	28380069	+	1	NA	intron (NM_001347497, intron 19 of 19)	intron (NM_001347497, intron 19 of 19)	-125406	NM_009524	22418	Mm.287544	NM_009524	ENSMUSG00000021994	Wnt5a	8030457G12Rik|Wnt-5a	wingless-type MMTV integration site family, member 5A	protein-coding
mm_131587.1	chr16	18548715	18548722	+	1	NA	intron (NM_001285494, intron 6 of 7)	intron (NM_001285494, intron 6 of 7)	38251	NM_011532	21380	Mm.295194	NM_011532	ENSMUSG00000009097	Tbx1	-	T-box 1	protein-coding
mm_84992.1	chr9	86695641	86695656	-	1	NA	non-coding (NR_045835, exon 1 of 3)	non-coding (NR_045835, exon 1 of 3)	206	NR_045835	319556	Mm.386894	NR_045835	ENSMUSG00000087466	A330041J22Rik	-	RIKEN cDNA A330041J22 gene	ncRNA
mm_98531.1	chr11	95006324	95006335	+	1	NA	3' UTR (NM_172261, exon 10 of 10)	3' UTR (NM_172261, exon 10 of 10)	-3550	NM_146025	217125	Mm.297199	NM_146025	ENSMUSG00000047181	Samd14	AI839049|AI854782|BC034054	sterile alpha motif domain containing 14	protein-coding
mm_29409.1	chr3	108911671	108911684	-	1	NA	promoter-TSS (NM_025845)	promoter-TSS (NM_025845)	27	NM_025845	66921	Mm.51049	NM_025845	ENSMUSG00000027881	Prpf38b	1110021E09Rik|AU018955	PRP38 pre-mRNA processing factor 38 (yeast) domain containing B	protein-coding
mm_163707.1	chr13	108335898	108335898	+	1	NA	intron (NM_178683, intron 2 of 10)	intron (NM_178683, intron 2 of 10)	19561	NM_178683	218581	Mm.32318	NM_178683	ENSMUSG00000021697	Depdc1b	9830132O03|AW260467|XTP1	DEP domain containing 1B	protein-coding
mm_62161.1	chr7	97190633	97190648	+	1	NA	intron (NM_001162477, intron 1 of 9)	intron (NM_001162477, intron 1 of 9)	108889	NM_010248	14389	Mm.42033	NM_010248	ENSMUSG00000004508	Gab2	AI463667|D130058I17Rik|p97	growth factor receptor bound protein 2-associated protein 2	protein-coding
mm_97109.1	chr11	74649974	74649984	+	1	NA	intron (NM_001081158, intron 1 of 25)	CpG	484	NM_001081158	74148	Mm.214574	NM_001081158	ENSMUSG00000020741	Cluh	1300001I01Rik|Kiaa0664|mKIAA0664	clustered mitochondria (cluA/CLU1) homolog	protein-coding
mm_74532.1	chr8	9672682	9672697	-	1	NA	intron (NM_001347127, intron 1 of 3)	intron (NM_001347127, intron 1 of 3)	98334	NM_173446	270028	Mm.268163	NM_173446	ENSMUSG00000079157	Fam155a	6430500D16|AW121567|Tmem28	family with sequence similarity 155, member A	protein-coding
mm_146892.1	chr18	26918064	26918072	-	1	NA	Intergenic	Intergenic	-1164085	NM_001174074	108013	Mm.266435	NM_133195	ENSMUSG00000024268	Celf4	A230070D14Rik|BRUNOL-4|Brul4|Brunol4|C130060B05Rik	CUGBP, Elav-like family member 4	protein-coding
mm_110891.1	chr12	75589543	75589544	-	1	NA	intron (NM_012024, intron 2 of 13)	intron (NM_012024, intron 2 of 13)	6657	NM_012024	26932	Mm.259626	NM_012024	ENSMUSG00000021051	Ppp2r5e	4633401M22Rik|AI449017|B56beta	protein phosphatase 2, regulatory subunit B', epsilon	protein-coding
mm_68038.1	chr7	101354416	101354422	-	1	NA	intron (NM_001040111, intron 1 of 33)	intron (NM_001040111, intron 1 of 33)	6350	NM_001040111	69710	Mm.277687	NM_027180	ENSMUSG00000032812	Arap1	2410002L19Rik|Centd2|mKIAA0782	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	protein-coding
mm_31289.1	chr4	45949390	45949440	+	1	NA	intron (NM_198660, intron 36 of 37)	intron (NM_198660, intron 36 of 37)	-15920	NM_001290475	100121	Mm.275413	NM_146142	ENSMUSG00000035517	Tdrd7	5730495N10Rik|AI447470|PCTAIRE2BP	tudor domain containing 7	protein-coding
mm_171140.1	chr3	150225674	150225674	-	1	NA	Intergenic	Intergenic	950937	NR_040591	381482	Mm.393866	NR_040591		Gm1653	-	predicted gene 1653	ncRNA
mm_163054.1	chr11	59331389	59331391	+	1	NA	3' UTR (NM_139298, exon 4 of 4)	3' UTR (NM_139298, exon 4 of 4)	24460	NM_139298	216795	Mm.218794	NM_139298	ENSMUSG00000000126	Wnt9a	Wnt14	wingless-type MMTV integration site family, member 9A	protein-coding
mm_1396.1	chr1	67134838	67134839	+	1	NA	intron (NM_001080809, intron 1 of 37)	intron (NM_001080809, intron 1 of 37)	11811	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_73612.1	chr8	110090112	110090141	+	1	NA	exon (NM_175480, exon 5 of 5)	exon (NM_175480, exon 5 of 5)	10392	NM_175480	234725	Mm.87487	NM_175480	ENSMUSG00000044676	Zfp612	B230354B21Rik	zinc finger protein 612	protein-coding
mm_3635.1	chr1	152807949	152807959	+	1	NA	5' UTR (NM_010877, exon 2 of 16)	5' UTR (NM_010877, exon 2 of 16)	7801	NM_010877	17970	Mm.270307	NM_010877	ENSMUSG00000026480	Ncf2	NOXA2|Ncf-2|p67phox	neutrophil cytosolic factor 2	protein-coding
mm_141190.1	chr17	26939544	26939554	-	1	NA	promoter-TSS (NM_026307)	promoter-TSS (NM_026307)	-11	NM_026307	67675	Mm.439919	NM_026307	ENSMUSG00000024194	Cuta	0610039D01Rik|1810022E02Rik|1810060C03Rik|2700094G22Rik|AI326454	cutA divalent cation tolerance homolog	protein-coding
mm_132191.1	chr16	32431226	32431280	+	1	NA	promoter-TSS (NM_001163160)	promoter-TSS (NM_001163160)	23	NM_001163160	13026	Mm.98775	NM_009981	ENSMUSG00000005615	Pcyt1a	CTalpha|Cctalpha|Ctpct|Cttalpha	phosphate cytidylyltransferase 1, choline, alpha isoform	protein-coding
mm_31806.1	chr4	65407977	65407985	+	1	NA	intron (NM_019514, intron 19 of 21)	Lx5|LINE|L1	-197005	NM_053084	69807	Mm.22786	NM_053084	ENSMUSG00000051675	Trim32	1810045E12Rik|3f3|BBS11|Zfp117	tripartite motif-containing 32	protein-coding
mm_41569.1	chr5	93161185	93161220	+	1	NA	exon (NM_001310669, exon 6 of 11)	exon (NM_001310669, exon 6 of 11)	45293	NM_017367	12453	Mm.250419	NM_017367	ENSMUSG00000063015	Ccni	-	cyclin I	protein-coding
mm_103827.1	chr11	83012468	83012479	-	1	NA	intron (NM_181545, intron 4 of 5)	intron (NM_181545, intron 4 of 5)	8249	NM_001167743	276950	Mm.491599	NM_181545	ENSMUSG00000035208	Slfn8	-	schlafen 8	protein-coding
mm_45720.1	chr5	86020847	86020854	-	1	NA	exon (NM_001345902, exon 16 of 20)	exon (NM_001345902, exon 16 of 20)	44733	NM_001345902	12617	Mm.4649	NM_007683	ENSMUSG00000029253	Cenpc1	CENP-C|Cenpc	centromere protein C1	protein-coding
mm_158268.1	chrX	109191058	109191068	-	1	NA	Intergenic	Intergenic	-5693	NM_001037917	622976	Mm.482747	NM_001037917	ENSMUSG00000048621	Gm6377	EG622976	predicted gene 6377	protein-coding
mm_121834.1	chr14	20531846	20531867	-	1	NA	exon (NM_008914, exon 2 of 14)	exon (NM_008914, exon 2 of 14)	-14437	NR_033571	75602	Mm.437061	NR_033571	ENSMUSG00000084925	1810062O18Rik	-	RIKEN cDNA 1810062O18 gene	ncRNA
mm_5110.1	chr1	6214516	6214534	-	1	NA	promoter-TSS (NM_009826)	promoter-TSS (NM_009826)	-137	NM_009826	12421	Mm.293811	NM_009826	ENSMUSG00000025907	Rb1cc1	2900055E04Rik|5930404L04Rik|Cc1|FIP200|LaXp180	RB1-inducible coiled-coil 1	protein-coding
mm_68761.1	chr7	121589852	121589853	-	1	NA	promoter-TSS (NR_131051)	promoter-TSS (NR_131051)	-16	NR_102286	75793	Mm.23397	NR_102286		4933432K03Rik	1700001C18Rik|4930433G11Rik|AI428127	RIKEN cDNA 4933432K03 gene	ncRNA
mm_65531.1	chr7	25801922	25801925	-	1	NA	TTS (NM_028775)	TTS (NM_028775)	-13190	NM_001190975	26362	Mm.4128	NM_009465	ENSMUSG00000002602	Axl	AI323647|Ark|Tyro7|Ufo	AXL receptor tyrosine kinase	protein-coding
mm_159277.1	chr2	165316365	165316365	-	1	NA	promoter-TSS (NM_001302754)	promoter-TSS (NM_001302754)	-14	NM_001302754	140579	Mm.35064	NM_080287	ENSMUSG00000017670	Elmo2	1190002F24Rik|CED-12	engulfment and cell motility 2	protein-coding
mm_16048.1	chr2	167750270	167750280	+	1	NA	Intergenic	Intergenic	59098	NR_015500	329562	Mm.123101	NM_177851	ENSMUSG00000006462	A530013C23Rik	-	RIKEN cDNA A530013C23 gene	ncRNA
mm_144747.1	chr18	35599199	35599215	+	1	NA	intron (NM_026420, intron 1 of 3)	CpG	540	NM_026420	67869	Mm.126534	NM_026420	ENSMUSG00000037058	Paip2	2310050K10Rik|AU045972	polyadenylate-binding protein-interacting protein 2	protein-coding
mm_106275.1	chr11	117991826	117991837	-	1	NA	intron (NM_133757, intron 1 of 9)	intron (NM_133757, intron 1 of 9)	4974	NM_133757	74451	Mm.28864	NM_133757	ENSMUSG00000017715	Pgs1	2610019F11Rik|4933424M23Rik|SAF	phosphatidylglycerophosphate synthase 1	protein-coding
mm_130456.1	chr15	98567590	98567620	-	1	NA	promoter-TSS (NM_009833)	promoter-TSS (NM_009833)	31	NM_009833	12455	Mm.29941	NM_009833	ENSMUSG00000011960	Ccnt1	2810478G24Rik|AI115585|CycT1	cyclin T1	protein-coding
mm_76383.1	chr8	84842513	84842521	-	1	NA	3' UTR (NM_007591, exon 9 of 9)	3' UTR (NM_007591, exon 9 of 9)	-1852	NM_009010	19358	Mm.255539	NM_009010	ENSMUSG00000003813	Rad23a	2310040P19Rik|AL024030|HR23A|mHR23A	RAD23 homolog A, nucleotide excision repair protein	protein-coding
mm_81930.1	chr9	120179865	120179873	+	1	NA	Intergenic	L1ME3Cz|LINE|L1	30127	NM_001039364	17433	Mm.486167	NM_008614	ENSMUSG00000032517	Mobp	AI835053|AI839848|MOBP155|MOBP170|MOBP69|MOBP73|MOBP81|R74645	myelin-associated oligodendrocytic basic protein	protein-coding
mm_65307.1	chr7	24752053	24752063	-	1	NA	exon (NM_026862, exon 11 of 17)	exon (NM_026862, exon 11 of 17)	8253	NM_026862	68891	Mm.292848	NM_026862	ENSMUSG00000052212	Cd177	1190003K14Rik|Pdp3	CD177 antigen	protein-coding
mm_88188.1	chr10	70024953	70024956	+	1	NA	3' UTR (NM_170688, exon 43 of 43)	3' UTR (NM_170688, exon 43 of 43)	-72167	NM_001111121	76551	Mm.281741	NM_001111121	ENSMUSG00000048701	Ccdc6	2810012H18Rik|AA536681|AA960498|AW061011	coiled-coil domain containing 6	protein-coding
mm_55519.1	chr6	70315468	70315473	-	1	NA	Intergenic	Intergenic	476705	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_9468.1	chr1	173333475	173333488	-	1	NA	promoter-TSS (NM_010045)	promoter-TSS (NM_010045)	22	NM_010045	13349	Mm.6393	NM_010045	ENSMUSG00000037872	Ackr1	AA162249|CCBP1|CD234|Darc|Dfy|ESTM35|FY|GPD	atypical chemokine receptor 1 (Duffy blood group)	protein-coding
mm_131887.1	chr16	23226015	23226077	+	1	NA	promoter-TSS (NM_001252505)	promoter-TSS (NM_001252505)	25	NM_001252505	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_164407.1	chr16	36098033	36098037	-	1	NA	Intergenic	RLTR1B|LTR|ERV1	16760	NM_001159422	381045	Mm.310434	NM_198645	ENSMUSG00000075229	Ccdc58	A930007B11Rik|AI413631	coiled-coil domain containing 58	protein-coding
mm_25717.1	chr3	122729120	122729134	+	1	NA	promoter-TSS (NM_153422)	promoter-TSS (NM_153422)	-31	NM_153422	242202	Mm.134911	NM_153422	ENSMUSG00000053965	Pde5a	Cgbpde|Cn5n|PDE5a2|Pde5|Pde5a1	phosphodiesterase 5A, cGMP-specific	protein-coding
mm_35752.1	chr4	45770739	45770743	-	1	NA	Intergenic	Intergenic	-6518	NR_046068	100040567	Mm.490816	NR_046068	ENSMUSG00000085876	Gm12409	OTTMUSG00000006726	predicted gene 12409	ncRNA
mm_30342.1	chr3	151737316	151737327	-	1	NA	intron (NM_133871, intron 7 of 7)	intron (NM_133871, intron 7 of 7)	12638	NM_133871	99899	Mm.30756	NM_133871	ENSMUSG00000028037	Ifi44	A430056A10Rik|AW261460|MTAP44|p44	interferon-induced protein 44	protein-coding
mm_93698.1	chr10	117982632	117982655	-	1	NA	Intergenic	Intergenic	57184	NR_045342	71067	Mm.410793	NR_045342		4933411E08Rik	-	RIKEN cDNA 4933411E08 gene	ncRNA
mm_19111.1	chr2	79456627	79456644	-	1	NA	promoter-TSS (NM_010894)	promoter-TSS (NM_010894)	1	NM_010894	18012	Mm.4636	NM_010894	ENSMUSG00000034701	Neurod1	BETA2|BHF-1|Nd1|Neurod|bHLHa3	neurogenic differentiation 1	protein-coding
mm_55078.1	chr6	49214162	49214179	-	1	NA	intron (NM_023670, intron 1 of 14)	CpG	784	NM_023670	140488	Mm.281018	NM_023670	ENSMUSG00000029814	Igf2bp3	2610101N11Rik|AA522010|AL022933|AU045931|IMP-3|IMP3|Koc13|Neilsen|mimp3	insulin-like growth factor 2 mRNA binding protein 3	protein-coding
mm_75957.1	chr8	71701797	71701841	-	1	NA	promoter-TSS (NM_028189)	promoter-TSS (NM_028189)	-19	NM_028189	72297	Mm.290837	NM_028189	ENSMUSG00000031803	B3gnt3	2210008L19Rik	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 3	protein-coding
mm_16250.1	chr2	173158825	173158837	+	1	NA	3' UTR (NM_011044, exon 10 of 10)	3' UTR (NM_011044, exon 10 of 10)	5758	NM_011044	18534	Mm.266867	NM_011044	ENSMUSG00000027513	Pck1	AI265463|PEPCK|Pck-1	phosphoenolpyruvate carboxykinase 1, cytosolic	protein-coding
mm_86308.1	chr9	122805440	122805456	-	1	NA	promoter-TSS (NM_001013405)	promoter-TSS (NM_001013405)	-99	NM_001013405	382117	Mm.215892	NM_001013405	ENSMUSG00000046603	Tcaim	D9Ertd402e|Gm1129|TOAG-1	T cell activation inhibitor, mitochondrial	protein-coding
mm_60896.1	chr7	46397802	46397820	+	1	NA	exon (NM_001112739, exon 1 of 4)	exon (NM_001112739, exon 1 of 4)	1343	NM_001112739	16502	Mm.249386	NM_008421	ENSMUSG00000058975	Kcnc1	C230009H10Rik|KShIIIB|KV4|Kcr2-1|Kv3.1|NGK2|Shaw	potassium voltage gated channel, Shaw-related subfamily, member 1	protein-coding
mm_134955.1	chr16	31311072	31311081	-	1	NA	exon (NM_007470, exon 3 of 6)	exon (NM_007470, exon 3 of 6)	3732	NM_001301353	11815	Mm.2082	NM_007470	ENSMUSG00000022548	Apod	-	apolipoprotein D	protein-coding
mm_5019.1	chr1	193153122	193153165	+	1	NA	promoter-TSS (NM_016851)	promoter-TSS (NM_016851)	31	NM_016851	54139	Mm.273695	NM_016851	ENSMUSG00000026638	Irf6	AI876454|E230028I05Rik|mirf6	interferon regulatory factor 6	protein-coding
mm_37227.1	chr4	117929750	117929776	-	1	NA	promoter-TSS (NM_001284191)	promoter-TSS (NM_001284191)	0	NM_001284191	11876	Mm.56897	NM_009711	ENSMUSG00000028539	Artn	neublastin	artemin	protein-coding
mm_145904.1	chr18	65800544	65800599	+	1	NA	promoter-TSS (NM_025468)	promoter-TSS (NM_025468)	-7	NM_025468	66286	Mm.27800	NM_025468	ENSMUSG00000024516	Sec11c	1810029G24Rik|Sec11l3	SEC11 homolog C, signal peptidase complex subunit	protein-coding
mm_34083.1	chr4	138775798	138775814	+	1	NA	promoter-TSS (NM_011109)	promoter-TSS (NM_011109)	71	NM_011109	18782	Mm.71913	NM_011109	ENSMUSG00000041202	Pla2g2d	Splash|mGIID	phospholipase A2, group IID	protein-coding
mm_58291.1	chr6	145864689	145864722	-	1	NA	intron (NM_024469, intron 2 of 4)	intron (NM_024469, intron 2 of 4)	715	NM_001271768	79362	Mm.154529	NM_024469	ENSMUSG00000030256	Bhlhe41	6430520M22Rik|Bhlhb2l|Bhlhb3|DEC2|Sharp1	basic helix-loop-helix family, member e41	protein-coding
mm_107994.1	chr12	73286869	73286913	+	1	NA	promoter-TSS (NM_029580)	promoter-TSS (NM_029580)	43	NM_001037717	625098	Mm.32075	NM_001037717	ENSMUSG00000044712	Slc38a6	AW322671|EG625098	solute carrier family 38, member 6	protein-coding
mm_115662.1	chr13	12461539	12461549	-	1	NA	5' UTR (NM_001291060, exon 1 of 9)	5' UTR (NM_001291060, exon 1 of 9)	194	NM_001291060	56048	Mm.474138	NM_018886	ENSMUSG00000057554	Lgals8	1200015E08Rik|AI326142|D13Ertd524e|Lgals-8	lectin, galactose binding, soluble 8	protein-coding
mm_105840.1	chr11	113683878	113683886	-	1	NA	promoter-TSS (NM_177777)	promoter-TSS (NM_177777)	269	NM_138598	28081	Mm.351688	NM_138598	ENSMUSG00000041629	Fam104a	D11Wsu99e	family with sequence similarity 104, member A	protein-coding
mm_13998.1	chr2	121956136	121956165	+	1	NA	promoter-TSS (NM_008545)	promoter-TSS (NM_008545)	-58	NM_008545	17147	Mm.389349	NM_008545	ENSMUSG00000074881	Mageb3	Mage-b3|Mage-ps1|Mage-rs3|Smage3	melanoma antigen, family B, 3	protein-coding
mm_22387.1	chr2	181157059	181157069	-	1	NA	promoter-TSS (NM_007906)	promoter-TSS (NM_007906)	-49	NM_007906	13628	Mm.2645	NM_007906	ENSMUSG00000016349	Eef1a2	Eef1a|S1|wasted|wst	eukaryotic translation elongation factor 1 alpha 2	protein-coding
mm_82135.1	chr9	123561638	123561641	+	1	NA	intron (NM_030692, intron 7 of 19)	intron (NM_030692, intron 7 of 19)	31757	NM_030692	83493	Mm.273671	NM_030692	ENSMUSG00000025240	Sacm1l	SAC1|Sac1p|mKIAA0851	SAC1 suppressor of actin mutations 1-like (yeast)	protein-coding
mm_41766.1	chr5	103501114	103501131	+	1	NA	intron (NM_011204, intron 6 of 47)	intron (NM_011204, intron 6 of 47)	75930	NM_011204	19249	Mm.3414	NM_011204	ENSMUSG00000034573	Ptpn13	AI324989|PTP-BL|PTPL1|Ptpri|RIP	protein tyrosine phosphatase, non-receptor type 13	protein-coding
mm_59053.1	chr7	19414111	19414161	+	1	NA	5' UTR (NM_007710, exon 2 of 8)	5' UTR (NM_007710, exon 2 of 8)	3042	NM_007710	12715	Mm.2375	NM_007710	ENSMUSG00000030399	Ckm	Ckmm|M-CK|MCK	creatine kinase, muscle	protein-coding
mm_103529.1	chr11	77200925	77200944	-	1	NA	Intergenic	Intergenic	-11966	NM_176965	319634	Mm.108786	NM_176965	ENSMUSG00000050944	Efcab5	4930563A03Rik	EF-hand calcium binding domain 5	protein-coding
mm_10150.1	chr2	4300750	4300765	+	1	NA	intron (NM_172475, intron 1 of 22)	intron (NM_172475, intron 1 of 22)	-100219	NM_001177843	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding
mm_160744.1	chr10	81033724	81033724	-	1	NA	exon (NM_134135, exon 1 of 2)	exon (NM_134135, exon 1 of 2)	188	NM_134135	106947	Mm.5353	NM_134135	ENSMUSG00000046822	Slc39a3	AI845814|Zip3	solute carrier family 39 (zinc transporter), member 3	protein-coding
mm_133045.1	chr16	57549233	57549264	+	1	NA	promoter-TSS (NM_001177871)	promoter-TSS (NM_001177871)	6	NM_001177871	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding
mm_18044.1	chr2	39007952	39007974	-	1	NA	promoter-TSS (NM_028809)	promoter-TSS (NM_028809)	-176	NM_028809	74192	Mm.38155	NM_028809	ENSMUSG00000026755	Arpc5l	2010015J01Rik|AI852867|ARC16-2|AW555592|AW742746	actin related protein 2/3 complex, subunit 5-like	protein-coding
mm_40497.1	chr5	57718036	57718104	+	1	NA	promoter-TSS (NM_001310606)	promoter-TSS (NM_001310606)	-11	NM_001122758	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_131753.1	chr16	22515008	22515024	+	1	NA	intron (NR_130988, intron 1 of 1)	intron (NR_130988, intron 1 of 1)	3536	NR_130988	78082	Mm.243927	NR_130988	ENSMUSG00000089874	9230117E06Rik	-	RIKEN cDNA 9230117E06 gene	ncRNA
mm_15249.1	chr2	154691266	154691288	+	1	NA	exon (NM_029362, exon 3 of 5)	exon (NM_029362, exon 3 of 5)	34251	NM_029362	75608	Mm.262480	NM_029362	ENSMUSG00000038467	Chmp4b	2010012F05Rik|C76846|Snf7-2	charged multivesicular body protein 4B	protein-coding
mm_31662.1	chr4	59964133	59964140	+	1	NA	Intergenic	RLTR9A3A|LTR|ERVK	-3471	NM_008648	17843	Mm.457982	NM_008648	ENSMUSG00000041333	Mup4	Mup-4|Mup1	major urinary protein 4	protein-coding
mm_52679.1	chr6	117917360	117917377	+	1	NA	promoter-TSS (NM_001166427)	promoter-TSS (NM_001166427)	74	NM_001166427	98758	Mm.422979	NM_133834	ENSMUSG00000042079	Hnrnpf	4833420I20Rik|AA407306|Hnrpf	heterogeneous nuclear ribonucleoprotein F	protein-coding
mm_126727.1	chr15	85580179	85580190	+	1	NA	promoter-TSS (NR_040433)	promoter-TSS (NR_040433)	545	NM_001163633	22422	Mm.306946	NM_009528	ENSMUSG00000022382	Wnt7b	Wnt-7b	wingless-type MMTV integration site family, member 7B	protein-coding
mm_102845.1	chr11	69369237	69369247	-	1	NA	exon (NM_146019, exon 1 of 40)	exon (NM_146019, exon 1 of 40)	184	NM_146019	216848	Mm.178246	NM_146019	ENSMUSG00000018474	Chd3	2600010P09Rik|AF020312|Chd7|Prp7|Prp9-1	chromodomain helicase DNA binding protein 3	protein-coding
mm_143105.1	chr17	57087638	57087657	-	1	NA	5' UTR (NM_009451, exon 1 of 4)	5' UTR (NM_009451, exon 1 of 4)	135	NM_009451	22153	Mm.7420	NM_009451	ENSMUSG00000062591	Tubb4a	AI325297|M(beta)4|Tubb|Tubb4	tubulin, beta 4A class IVA	protein-coding
mm_148559.1	chr19	4721277	4721283	+	1	NA	intron (NM_021287, intron 2 of 36)	intron (NM_021287, intron 2 of 36)	10057	NM_021287	20743	Mm.329668	NM_021287	ENSMUSG00000067889	Sptbn2	Spnb3|mKIAA0302	spectrin beta, non-erythrocytic 2	protein-coding
mm_129135.1	chr15	76198219	76198227	-	1	NA	promoter-TSS (NM_201393)	promoter-TSS (NM_201393)	-14	NM_201393	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
mm_96731.1	chr11	69686708	69686742	+	1	NA	3' UTR (NM_011614, exon 7 of 7)	3' UTR (NM_011614, exon 7 of 7)	-1171	NM_023517	69583	Mm.8983	NM_023517	ENSMUSG00000089669	Tnfsf13	2310026N09Rik|April|Tall2|Tnlg7b|Trdl1	tumor necrosis factor (ligand) superfamily, member 13	protein-coding
mm_32072.1	chr4	97906154	97906192	+	1	NA	intron (NM_010905, intron 2 of 10)	intron (NM_010905, intron 2 of 10)	128547	NM_010905	18027	Mm.31274	NM_010905	ENSMUSG00000028565	Nfia	1110047K16Rik|9430022M17Rik|CTF|NF1-A|NF1A	nuclear factor I/A	protein-coding
mm_72425.1	chr8	82774791	82774796	+	1	NA	promoter-TSS (NM_145600)	promoter-TSS (NM_145600)	-667	NM_145600	30932	Mm.269248	NM_145600	ENSMUSG00000031711	Zfp330	BC008086|Noa36|Znf330	zinc finger protein 330	protein-coding
mm_123047.1	chr14	55591480	55591506	-	1	NA	promoter-TSS (NM_011190)	promoter-TSS (NM_011190)	-297	NM_194346	268749	Mm.23748	NM_194346	ENSMUSG00000047098	Rnf31	AL033293|BC031509|Flj10111|HOIP|Paul|mFLJ00217	ring finger protein 31	protein-coding
mm_13711.1	chr2	117161813	117161817	+	1	NA	intron (NM_033524, intron 2 of 6)	MTEb|LTR|ERVL-MaLR	-23312	NR_030440	732489		NR_030440	ENSMUSG00000076376	Mir674	Mirn674|mir-674|mmu-mir-674	microRNA 674	ncRNA
mm_13418.1	chr2	104122850	104122854	+	1	NA	promoter-TSS (NM_026634)	promoter-TSS (NM_026634)	83	NM_026634	68243	Mm.158191	NM_026634	ENSMUSG00000032671	A930018P22Rik	-	RIKEN cDNA A930018P22 gene	protein-coding
mm_7429.1	chr1	119837339	119837386	-	1	NA	promoter-TSS (NM_019933)	promoter-TSS (NM_019933)	-291	NM_019933	19258	Mm.458796	NM_019933	ENSMUSG00000026384	Ptpn4	PTPMEG|Ptn4|TEP|TEP/mPTPMEG|hPTP-MEG	protein tyrosine phosphatase, non-receptor type 4	protein-coding
mm_147640.1	chr18	60269633	60269654	-	1	NA	3' UTR (NM_001034859, exon 2 of 2)	3' UTR (NM_001034859, exon 2 of 2)	3624	NM_001034859	225594	Mm.329460	NM_001034859	ENSMUSG00000068606	Gm4841	EG225594|Ifgga3	predicted gene 4841	protein-coding
mm_2088.1	chr1	87698147	87698157	+	1	NA	exon (NM_001110192, exon 13 of 27)	exon (NM_001110192, exon 13 of 27)	-57859	NM_029846	77040	Mm.272972	NM_029846	ENSMUSG00000026289	Atg16l1	1500009K01Rik|Apg16l|Atg16l|WDR30	autophagy related 16-like 1 (S. cerevisiae)	protein-coding
mm_45172.1	chr5	51497306	51497311	-	1	NA	intron (NR_132764, intron 3 of 12)	intron (NR_132764, intron 3 of 12)	56613	NR_027710	19017	Mm.259072	NM_008904	ENSMUSG00000029167	Ppargc1a	A830037N07Rik|ENSMUSG00000079510|Gm11133|PGC-1|PPARGC-1-alpha|Pgc-1alpha|Pgc1|Pgco1|Ppargc1	peroxisome proliferative activated receptor, gamma, coactivator 1 alpha	protein-coding
mm_152854.1	chr19	24147036	24147076	-	1	NA	intron (NM_011597, intron 1 of 22)	intron (NM_011597, intron 1 of 22)	27084	NM_001198985	21873	Mm.104744	NM_011597	ENSMUSG00000024812	Tjp2	ZO-2	tight junction protein 2	protein-coding
mm_59829.1	chr7	29296632	29296634	+	1	NA	Intergenic	Intergenic	7313	NM_026731	68458	Mm.2343	NM_026731	ENSMUSG00000037166	Ppp1r14a	1110001M11Rik|Cpi17	protein phosphatase 1, regulatory (inhibitor) subunit 14A	protein-coding
mm_48205.1	chr5	137599783	137599819	-	1	NA	exon (NM_030037, exon 4 of 6)	exon (NM_030037, exon 4 of 6)	907	NM_001254762	68929	Mm.41355	NM_030037	ENSMUSG00000037221	Mospd3	1190005J19Rik|5133401H10Rik|Gtig2|R124	motile sperm domain containing 3	protein-coding
mm_159546.1	chr4	91399985	91399985	-	1	NA	promoter-TSS (NM_207685)	promoter-TSS (NM_207685)	-1	NM_207685	15569	Mm.318042	NM_010486	ENSMUSG00000008489	Elavl2	Hub|mel-N1	ELAV (embryonic lethal, abnormal vision, Drosophila)-like 2 (Hu antigen B)	protein-coding
mm_111745.1	chr12	103904945	103904955	-	1	NA	promoter-TSS (NM_009245)	promoter-TSS (NM_009245)	0	NM_009245	20702	Mm.439692	NM_009245	ENSMUSG00000079015	Serpina1c	Pi3|Pi6|Skalp|Spi1-3|Spi1-6|Wap3	serine (or cysteine) peptidase inhibitor, clade A, member 1C	protein-coding
mm_103495.1	chr11	76571374	76571403	-	1	NA	promoter-TSS (NM_198895)	promoter-TSS (NM_198895)	-4	NM_198895	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_97014.1	chr11	71019627	71019638	+	1	NA	promoter-TSS (NM_001291148)	promoter-TSS (NM_001291148)	21	NM_025993	67139	Mm.28227	NM_025993	ENSMUSG00000040599	Mis12	2510025F08Rik|AU044651|Misc12	MIS12 kinetochore complex component	protein-coding
mm_156848.1	chrX	164400752	164400762	+	1	NA	exon (NM_010216, exon 6 of 7)	exon (NM_010216, exon 6 of 7)	-19030	NM_011081	18700	Mm.3781	NM_011081	ENSMUSG00000031381	Piga	AI194334|Pig-a	phosphatidylinositol glycan anchor biosynthesis, class A	protein-coding
mm_99262.1	chr11	101246064	101246068	+	1	NA	promoter-TSS (NM_019444)	promoter-TSS (NM_019444)	-268	NM_019444	54409	Mm.260698	NM_019444	ENSMUSG00000001240	Ramp2	-	receptor (calcitonin) activity modifying protein 2	protein-coding
mm_76136.1	chr8	81014846	81014862	-	1	NA	promoter-TSS (NM_027554)	promoter-TSS (NM_027554)	52	NM_027554	74841	Mm.246018	NM_027554	ENSMUSG00000038250	Usp38	4631402N15Rik|4833420O05Rik|AA536967|AU044701|AW544820|mKIAA1891	ubiquitin specific peptidase 38	protein-coding
mm_75287.1	chr8	41041670	41041676	-	1	NA	5' UTR (NM_001005865, exon 1 of 10)	5' UTR (NM_001005865, exon 1 of 10)	258	NM_001005865	102103	Mm.149438	NM_001005863	ENSMUSG00000045636	Mtus1	AI481402|ATBP135|Atip1|B430010I23Rik|B430305I03Rik|C85752|Cctsg1-440|MD44|MTSG1|mKIAA1288	mitochondrial tumor suppressor 1	protein-coding
mm_70665.1	chr8	14888837	14888874	+	1	NA	5' UTR (NM_012000, exon 1 of 3)	5' UTR (NM_012000, exon 1 of 3)	319	NM_012000	26889	Mm.254027	NM_012000	ENSMUSG00000026317	Cln8	mnd	ceroid-lipofuscinosis, neuronal 8	protein-coding
mm_104596.1	chr11	97115328	97115332	-	1	NA	promoter-TSS (NM_019507)	promoter-TSS (NM_019507)	1	NM_019507	57765	Mm.94519	NM_019507	ENSMUSG00000001444	Tbx21	TBT1|Tbet|Tblym	T-box 21	protein-coding
mm_67950.1	chr7	100498209	100498276	-	1	NA	exon (NM_011671, exon 5 of 8)	exon (NM_011671, exon 5 of 8)	4884	NM_011671	22228	Mm.171378	NM_011671	ENSMUSG00000033685	Ucp2	Slc25a8	uncoupling protein 2 (mitochondrial, proton carrier)	protein-coding
mm_127724.1	chr15	103240022	103240070	+	1	NA	promoter-TSS (NM_010447)	promoter-TSS (NM_010447)	-230	NM_001076789	12419	Mm.262059	NM_007626	ENSMUSG00000009575	Cbx5	2610029O15Rik|C75991|HP1|Hp1a|Hp1alpha	chromobox 5	protein-coding
mm_138906.1	chr17	43588615	43588647	+	1	NA	exon (NM_013737, exon 2 of 12)	exon (NM_013737, exon 2 of 12)	2878	NR_045445	73504	Mm.9277	NR_045444	ENSMUSG00000090307	1700071M16Rik	-	RIKEN cDNA 1700071M16 gene	ncRNA
mm_108438.1	chr12	82339725	82339750	+	1	NA	intron (NM_172579, intron 1 of 20)	intron (NM_172579, intron 1 of 20)	28388	NM_172579	217692	Mm.261333	NM_172579	ENSMUSG00000042700	Sipa1l1	4931426N11Rik|AW213287|Spar|mKIAA0440	signal-induced proliferation-associated 1 like 1	protein-coding
mm_22712.1	chr3	19188113	19188122	+	1	NA	promoter-TSS (NM_026182)	promoter-TSS (NM_026182)	-104	NM_026182	67472	Mm.45125	NM_026182	ENSMUSG00000027601	Mtfr1	1300002C08Rik|1700080D04Rik|2810026O10Rik|4930579E05Rik|Chppr|Fam54a2	mitochondrial fission regulator 1	protein-coding
mm_107728.1	chr12	57414151	57414166	+	1	NA	intron (NM_001164370, intron 8 of 9)	intron (NM_001164370, intron 8 of 9)	131963	NM_008259	15375	Mm.4578	NM_008259	ENSMUSG00000035451	Foxa1	Hnf-3a|Hnf3a|Tcf-3a|Tcf3a	forkhead box A1	protein-coding
mm_43279.1	chr5	130845120	130845141	+	1	NA	Intergenic	Intergenic	396338	NM_021371	140904	Mm.40875	NM_021371	ENSMUSG00000060371	Caln1	9630012C17Rik|Cabp8|MNCb-0849	calneuron 1	protein-coding
mm_110573.1	chr12	56373711	56373733	-	1	NA	Intergenic	Intergenic	-27828	NM_145442	217588	Mm.25656	NM_145442	ENSMUSG00000021028	Mbip	4933408E06Rik	MAP3K12 binding inhibitory protein 1	protein-coding
mm_38667.1	chr4	144565268	144565274	-	1	NA	promoter-TSS (NM_001085542)	promoter-TSS (NM_001085542)	-137	NM_001085542	627085	Mm.457899	NM_001085542	ENSMUSG00000078506	Gm13124	OTTMUSG00000010546	predicted gene 13124	protein-coding
mm_62262.1	chr7	99381496	99381555	+	1	NA	promoter-TSS (NM_201352)	promoter-TSS (NM_201352)	-24	NM_201352	233552	Mm.286317	NM_201352	ENSMUSG00000035314	Gdpd5	BC024955|Gde2	glycerophosphodiester phosphodiesterase domain containing 5	protein-coding
mm_138728.1	chr17	36943274	36943322	+	1	NA	exon (NM_001099632, exon 1 of 4)	exon (NM_001099632, exon 1 of 4)	247	NM_001099632	386454	Mm.105324	NM_001099632	ENSMUSG00000036492	Rnf39	BC038661|Gm1786|Gm1787|Gm320|LIRF	ring finger protein 39	protein-coding
mm_90499.1	chr10	128035481	128035520	+	1	NA	5' UTR (NM_013608, exon 1 of 8)	5' UTR (NM_013608, exon 1 of 8)	154	NM_001113199	17938	Mm.3746	NM_013608	ENSMUSG00000061315	Naca	AL022831|AL024382|Gm1878|mKIAA0363|skNAC	nascent polypeptide-associated complex alpha polypeptide	protein-coding
mm_89883.1	chr10	108414486	108414491	+	1	NA	TTS (NM_054056)	TTS (NM_054056)	82299	NM_054056	114774	Mm.391419	NM_054056	ENSMUSG00000035873	Pawr	2310001G03Rik|PAR4|Par-4	PRKC, apoptosis, WT1, regulator	protein-coding
mm_123358.1	chr14	63142717	63142726	-	1	NA	3' UTR (NM_007798, exon 10 of 10)	3' UTR (NM_007798, exon 10 of 10)	20259	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_164066.1	chr14	118428377	118428382	+	1	NA	Intergenic	Intergenic	62501	NR_045624	73306	Mm.362328	NR_045624	ENSMUSG00000099911	1700044C05Rik	-	RIKEN cDNA 1700044C05 gene	ncRNA
mm_142004.1	chr17	35200022	35200033	-	1	NA	3' UTR (NM_013693, exon 4 of 4)	3' UTR (NM_013693, exon 4 of 4)	1980	NM_013693	21926	Mm.1293	NM_013693	ENSMUSG00000024401	Tnf	DIF|TNF-a|TNF-alpha|TNFSF2|TNFalpha|Tnfa|Tnfsf1a|Tnlg1f	tumor necrosis factor	protein-coding
mm_128026.1	chr15	25135623	25135651	-	1	NA	Intergenic	Intergenic	278127	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	brain abundant, membrane attached signal protein 1	protein-coding
mm_11725.1	chr2	36389003	36389048	+	1	NA	promoter-TSS (NR_030454).6	promoter-TSS (NR_030454).6	-886	NR_030454	735274		NR_030454	ENSMUSG00000106252	Mir684-1	Mirn684-1	microRNA 684-1	ncRNA
mm_129361.1	chr15	77956659	77956723	-	1	NA	promoter-TSS (NM_001017983)	promoter-TSS (NM_001017983)	31	NM_001168260	239554	Mm.295605	NM_001017983	ENSMUSG00000016552	Foxred2	A430097D04Rik|D15Bwg0759e|Gm304	FAD-dependent oxidoreductase domain containing 2	protein-coding
mm_42977.1	chr5	123167578	123167598	+	1	NA	3' UTR (NM_001040398, exon 17 of 17)	3' UTR (NM_001040398, exon 17 of 17)	15098	NM_008277	15445	Mm.439709	NM_008277	ENSMUSG00000029445	Hpd	Fla|Flp|Hppd|Laf	4-hydroxyphenylpyruvic acid dioxygenase	protein-coding
mm_54950.1	chr6	48680571	48680581	-	1	NA	Intergenic	Intergenic	-4002	NM_001243200	107526	Mm.333048	NM_174990	ENSMUSG00000054435	Gimap4	AU019574|E430007K16Rik|Ian-1|Ian1|Imap4	GTPase, IMAP family member 4	protein-coding
mm_113838.1	chr13	47193850	47193868	+	1	NA	promoter-TSS (NM_001170643)	promoter-TSS (NM_001170643)	-144	NM_001170643	218215	Mm.287609	NM_146042	ENSMUSG00000038068	Rnf144b	BC025007|E130105P19Rik|Ibrdc2|Pir2	ring finger protein 144B	protein-coding
mm_114687.1	chr13	81711408	81711457	+	1	NA	promoter-TSS (NM_028372)	promoter-TSS (NM_028372)	15	NM_028372	72852	Mm.31095	NM_028372	ENSMUSG00000051098	Mblac2	2900024O10Rik	metallo-beta-lactamase domain containing 2	protein-coding
mm_8727.1	chr1	160053097	160053110	-	1	NA	intron (NM_001162896, intron 1 of 2)	intron (NM_001162896, intron 1 of 2)	8723	NM_001162896	67647	Mm.171518	NM_001024470	ENSMUSG00000090394	4930523C07Rik	-	RIKEN cDNA 4930523C07 gene	protein-coding
mm_154397.1	chrM	13482	13492	+	1	NA	NA	Intergenic	NA	NA								
mm_119168.1	chr14	32085754	32085800	+	1	NA	promoter-TSS (NM_001284346)	promoter-TSS (NM_001284346)	49	NM_145460	218885	Mm.202257	NM_145460	ENSMUSG00000021906	Oxnad1	2410002F01Rik|AW492292|BC019806	oxidoreductase NAD-binding domain containing 1	protein-coding
mm_116444.1	chr13	43154778	43154790	-	1	NA	exon (NM_025935, exon 6 of 8)	exon (NM_025935, exon 6 of 8)	16717	NM_001252639	67046	Mm.269213	NM_025935	ENSMUSG00000021368	Tbc1d7	2610009C09Rik	TBC1 domain family, member 7	protein-coding
mm_129932.1	chr15	84675189	84675199	-	1	NA	intron (NM_001346662, intron 1 of 8)	intron (NM_001346662, intron 1 of 8)	-5804	NM_146061	109270	Mm.291372	NM_146061	ENSMUSG00000036106	Prr5	AU043908|Arhgap8|C030017C09Rik|C78947|Protor-1|Protor1	proline rich 5 (renal)	protein-coding
mm_14381.1	chr2	129630919	129630929	+	1	NA	3' UTR (NM_001291022, exon 5 of 5)	3' UTR (NM_001291022, exon 5 of 5)	37755	NM_001291022	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_39771.1	chr5	30013971	30013979	+	1	NA	intron (NM_001314054, intron 2 of 4)	intron (NM_001314054, intron 2 of 4)	861	NM_031168	16193	Mm.1019	NM_031168	ENSMUSG00000025746	Il6	Il-6	interleukin 6	protein-coding
mm_51337.1	chr6	72414302	72414319	+	1	NA	promoter-TSS (NM_019802)	promoter-TSS (NM_019802)	2	NM_019802	56316	Mm.19937	NM_019802	ENSMUSG00000053460	Ggcx	-	gamma-glutamyl carboxylase	protein-coding
mm_104141.1	chr11	86993802	86993820	-	1	NA	promoter-TSS (NM_001005341)	promoter-TSS (NM_001005341)	-49	NM_001005341	77864	Mm.191894	NM_001005341	ENSMUSG00000018427	Ypel2	6430570G24|E130113K08Rik	yippee-like 2 (Drosophila)	protein-coding
mm_70063.1	chr7	142652268	142652280	-	1	NA	3' UTR (NM_010514, exon 4 of 4)	3' UTR (NM_010514, exon 4 of 4)	2722	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_70041.1	chr7	142577867	142577875	-	1	NA	promoter-TSS (NR_030416)	promoter-TSS (NR_030416)	275	NR_130974	14955	Mm.14802	NR_001592	ENSMUSG00000000031	H19	AI747191	H19, imprinted maternally expressed transcript	ncRNA
mm_115256.1	chr13	110399818	110399833	+	1	NA	exon (NM_152804, exon 13 of 14)	exon (NM_152804, exon 13 of 14)	4781	NM_152804	20620	Mm.380	NM_152804	ENSMUSG00000021701	Plk2	Snk	polo-like kinase 2	protein-coding
mm_106673.1	chr11	121703304	121703311	-	1	NA	intron (NM_144797, intron 1 of 3)	intron (NM_144797, intron 1 of 3)	880	NM_144797	210029	Mm.153566	NM_144797	ENSMUSG00000039208	Metrnl	9430048M07Rik|BC019776	meteorin, glial cell differentiation regulator-like	protein-coding
mm_46696.1	chr5	110101206	110101240	-	1	NA	intron (NM_207279, intron 3 of 7)	intron (NM_207279, intron 3 of 7)	664	NM_001281812	403178	Mm.297057	NM_207279	ENSMUSG00000064247	Plcxd1	A330045H12Rik|Gm576	phosphatidylinositol-specific phospholipase C, X domain containing 1	protein-coding
mm_157087.1	chrX	9436351	9436364	-	1	NA	3' UTR (NM_007807, exon 13 of 13)	3' UTR (NM_007807, exon 13 of 13)	32967	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_97630.1	chr11	78959701	78959711	+	1	NA	exon (NM_010927, exon 27 of 27)	exon (NM_010927, exon 27 of 27)	25218	NM_001159301	16859	Mm.341434	NM_010708	ENSMUSG00000001123	Lgals9	AA407335|AI194909|AI265545|LGALS35|Lgals5|gal-9|galectin-9	lectin, galactose binding, soluble 9	protein-coding
mm_163756.1	chr13	119790802	119790842	-	1	NA	promoter-TSS (NM_028245)	promoter-TSS (NM_028245)	-16	NM_001302549	72465	Mm.139115	NM_028245	ENSMUSG00000094870	Zfp131	2610109I01Rik|AW558871|Znf131	zinc finger protein 131	protein-coding
mm_45223.1	chr5	53378661	53378670	-	1	NA	Intergenic	Intergenic	111559	NM_001145433	66278	Mm.27900	NM_001145433	ENSMUSG00000061461	Smim20	1110067B18Rik|1810013D10Rik|N28078	small integral membrane protein 20	protein-coding
mm_51990.1	chr6	92091547	92091557	+	1	NA	promoter-TSS (NM_001347342)	promoter-TSS (NM_001347342)	134	NM_011630	22026	Mm.87062	NM_011630	ENSMUSG00000005893	Nr2c2	TAK1|Tr4|mKIAA4145	nuclear receptor subfamily 2, group C, member 2	protein-coding
mm_33142.1	chr4	125125001	125125021	+	1	NA	intron (NM_153159, intron 2 of 5)	intron (NM_153159, intron 2 of 5)	2870	NM_153159	230738	Mm.402	NM_153159	ENSMUSG00000042677	Zc3h12a	BC036563|MCPIP|MCPIP-1|Mcpip1|Reg1	zinc finger CCCH type containing 12A	protein-coding
mm_37695.1	chr4	129263476	129263482	-	1	NA	Intergenic	Intergenic	-2075	NM_001285867	97130	Mm.331907	NM_001033189	ENSMUSG00000050390	C77080	Kiaa1522|mKIAA1522	expressed sequence C77080	protein-coding
mm_65515.1	chr7	25755111	25755160	-	1	NA	promoter-TSS (NM_178089)	promoter-TSS (NM_178089)	-415	NM_144922	232989	Mm.254223	NM_144922	ENSMUSG00000040725	Hnrnpul1	E130317O14Rik|E1B-AP5|E1BAP5|Hnrnpul|Hnrpul1	heterogeneous nuclear ribonucleoprotein U-like 1	protein-coding
mm_76608.1	chr8	90817083	90817091	-	1	NA	Intergenic	Intergenic	-11748	NM_177224	109151	Mm.100615	NM_177224	ENSMUSG00000056608	Chd9	1810014J18Rik|9030205D12Rik|A330063D19Rik|AD013|PRIC320|mKIAA0308	chromodomain helicase DNA binding protein 9	protein-coding
mm_96973.1	chr11	70651101	70651124	+	1	NA	TTS (NM_011072)	TTS (NM_011072)	3538	NM_011072	18643	Mm.2647	NM_011072	ENSMUSG00000018293	Pfn1	Pfn	profilin 1	protein-coding
mm_155572.1	chrX	77511003	77511100	+	1	NA	promoter-TSS (NM_020601)	promoter-TSS (NM_020601)	-176	NM_020601	21372	Mm.258476	NM_020601	ENSMUSG00000025246	Tbl1x	5330429M20|Tbl1	transducin (beta)-like 1 X-linked	protein-coding
mm_66759.1	chr7	46715888	46715916	-	1	NA	promoter-TSS (NM_011315)	promoter-TSS (NM_011315)	-226	NM_011315	20210	Mm.14277	NM_011315	ENSMUSG00000040026	Saa3	AV098916|Saa-3|l7R3	serum amyloid A 3	protein-coding
mm_88011.1	chr10	67127083	67127102	+	1	NA	promoter-TSS (NM_207221)	promoter-TSS (NM_207221)	-166	NM_207221	108829	Mm.23846	NM_207221	ENSMUSG00000037876	Jmjd1c	5430433L24Rik|D630035I23Rik|Jmjdic|TRIP8	jumonji domain containing 1C	protein-coding
mm_52382.1	chr6	113147960	113147962	+	1	NA	intron (NM_173005, intron 18 of 20)	intron (NM_173005, intron 18 of 20)	43026	NM_173005	72895	Mm.367159	NM_028385	ENSMUSG00000034269	Setd5	2900045N06Rik|C330007C20|C85544|mKIAA1757	SET domain containing 5	protein-coding
mm_170351.1	chr1	85109473	85109480	-	1	NA	5' UTR (NM_213615, exon 1 of 7)	5' UTR (NM_213615, exon 1 of 7)	377	NM_213615	381287	Mm.487565	NM_213615	ENSMUSG00000089844	A530032D15Rik	Gm1888	RIKEN cDNA A530032D15Rik gene	protein-coding
mm_36696.1	chr4	96664032	96664044	-	1	NA	promoter-TSS (NM_010007)	promoter-TSS (NM_010007)	81	NM_010007	13109	Mm.12838	NM_010007	ENSMUSG00000052520	Cyp2j5	-	cytochrome P450, family 2, subfamily j, polypeptide 5	protein-coding
mm_4767.1	chr1	182484196	182484212	+	1	NA	exon (NM_009794, exon 10 of 21)	exon (NM_009794, exon 10 of 21)	33279	NM_009794	12334	Mm.19306	NM_009794	ENSMUSG00000026509	Capn2	AI326419|Capa-2|Capa2|m-calpain|m-calpin	calpain 2	protein-coding
mm_85460.1	chr9	105480182	105480194	-	1	NA	intron (NM_001253831, intron 1 of 26)	L1M3|LINE|L1	14945	NM_175025	235574	Mm.326247	NM_175025	ENSMUSG00000032570	Atp2c1	1700121J11Rik|ATP2C1A|AW061228|BCPM|D930003G21Rik|HHD|SPCA|pmr1	ATPase, Ca++-sequestering	protein-coding
mm_9909.1	chr1	187215486	187215494	-	1	NA	promoter-TSS (NM_029067)	promoter-TSS (NM_029067)	-21	NM_026367	67769	Mm.138321	NM_026367	ENSMUSG00000039210	Gpatch2	5830433G22Rik|5830436K05Rik|AI427714|AI447508|AW107440|AW491060|Gpatc2	G patch domain containing 2	protein-coding
mm_170127.1	chr17	39847130	39847133	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	4134	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_170797.1	chr2	175435795	175435814	-	1	NA	promoter-TSS (NM_001177543).2	promoter-TSS (NM_001177543).2	-27	NM_001101804	668039	Mm.466613	NM_001101804	ENSMUSG00000078881	Gm14434	OTTMUSG00000016611	predicted gene 14434	protein-coding
mm_58006.1	chr6	136449451	136449463	-	1	NA	Intergenic	Intergenic	-33888	NM_001201390	100502936	Mm.21182	NM_001201390	ENSMUSG00000045291	E330021D16Rik	C85549	RIKEN cDNA E330021D16 gene	protein-coding
mm_131716.1	chr16	21333364	21333377	+	1	NA	promoter-TSS (NR_131983)	promoter-TSS (NR_131983)	-14	NR_131983	76222	Mm.86031	NR_131983		Magef1	6430590I03Rik	melanoma antigen family F, 1	pseudo
mm_139206.1	chr17	47702896	47702908	+	1	NA	promoter-TSS (NR_045913)	promoter-TSS (NR_045913)	-906	NR_045913	100126242	Mm.392746	NR_045912	ENSMUSG00000086930	Frs3os	4930417B13Rik|Gm14873|OTTMUSG00000018358	fibroblast growth factor receptor substrate 3, opposite strand	ncRNA
mm_28421.1	chr3	90433583	90433600	-	1	NA	promoter-TSS (NM_178876)	promoter-TSS (NM_178876)	45	NM_145540	229543	Mm.268564	NM_145540	ENSMUSG00000027933	Ints3	C77668	integrator complex subunit 3	protein-coding
mm_148487.1	chr19	4151577	4151588	+	1	NA	exon (NM_011778, exon 8 of 11)	exon (NM_011778, exon 8 of 11)	2919	NM_011778	23789	Mm.276859	NM_011778	ENSMUSG00000024835	Coro1b	-	coronin, actin binding protein 1B	protein-coding
mm_143491.1	chr17	71452879	71452883	-	1	NA	intron (NM_028887, intron 5 of 47)	intron (NM_028887, intron 5 of 47)	22462	NM_028887	74355	Mm.194450	NM_028887	ENSMUSG00000024054	Smchd1	4931400A14Rik|AW554188|MommeD1|mKIAA0650	SMC hinge domain containing 1	protein-coding
mm_56348.1	chr6	92943514	92943539	-	1	NA	intron (NR_015530, intron 1 of 2)	CpG	2944	NR_015530	330385	Mm.483472	NR_015530	ENSMUSG00000097462	9530026P05Rik	B430306B02	RIKEN cDNA 9530026P05 gene	ncRNA
mm_92318.1	chr10	75517870	75517887	-	1	NA	promoter-TSS (NM_026095)	promoter-TSS (NM_026095)	94	NM_001347201	68778	Mm.29382	NM_175133	ENSMUSG00000033416	Gucd1	1110038D17Rik	guanylyl cyclase domain containing 1	protein-coding
mm_80239.1	chr9	72694031	72694077	+	1	NA	intron (NM_010890, intron 6 of 28)	intron (NM_010890, intron 6 of 28)	31707	NM_010890	17999	Mm.279923	NM_010890	ENSMUSG00000032216	Nedd4	AA959633|AL023035|AU019897|E430025J12Rik|Nedd4-1|Nedd4a|mKIAA0093	neural precursor cell expressed, developmentally down-regulated 4	protein-coding
mm_124222.1	chr14	100284818	100284849	-	1	NA	Intergenic	Intergenic	-135037	NM_010636	16597	Mm.396499	NM_010636	ENSMUSG00000072294	Klf12	2700063E05Rik|AI225908|AI315654|AP-2rep|B130052C06Rik|D530033K05Rik	Kruppel-like factor 12	protein-coding
mm_165516.1	chr2	173275336	173275362	+	1	NA	intron (NM_022995, intron 1 of 3)	intron (NM_022995, intron 1 of 3)	1184	NM_022995	65112	Mm.73682	NM_022995	ENSMUSG00000038400	Pmepa1	2210418I02Rik|AW455466|Erg1.2|N4wbp4|Stag1|Tmepai	prostate transmembrane protein, androgen induced 1	protein-coding
mm_132303.1	chr16	33523700	33523730	+	1	NA	intron (NM_001083902, intron 1 of 11)	(CCTG)n|Simple_repeat|Simple_repeat	5120	NM_001083902	171286	Mm.35253	NM_134251	ENSMUSG00000035506	Slc12a8	CCC9|E330020C02Rik	solute carrier family 12 (potassium/chloride transporters), member 8	protein-coding
mm_163098.1	chr11	69735250	69735262	-	1	NA	exon (NM_001291068, exon 29 of 29)	exon (NM_001291068, exon 29 of 29)	23377	NM_001291068	20020	Mm.16533	NM_009089	ENSMUSG00000005198	Polr2a	220kDa|Rpb1|Rpo2-1	polymerase (RNA) II (DNA directed) polypeptide A	protein-coding
mm_52349.1	chr6	111453673	111453674	+	1	NA	intron (NM_001346640, intron 8 of 10)	Lx3C|LINE|L1	-757035	NR_027865	67336	Mm.378014	NR_027865	ENSMUSG00000100219	1700054K19Rik	-	RIKEN cDNA 1700054K19 gene	ncRNA
mm_147840.1	chr18	62615718	62615723	-	1	NA	intron (NM_001168423, intron 1 of 4)	intron (NM_001168423, intron 1 of 4)	-19456	NM_001001803	408198	Mm.478742	NM_001001803	ENSMUSG00000060201	Spink7	EG408198|Ecg2	serine peptidase inhibitor, Kazal type 7 (putative)	protein-coding
mm_113048.1	chr13	23591480	23591529	+	1	NA	intron (NM_001177653, intron 1 of 1)	intron (NM_001177653, intron 1 of 1)	-5534	NM_001290530	319179	Mm.440391	NM_178194	ENSMUSG00000047246	Hist1h2be	-	histone cluster 1, H2be	protein-coding
mm_72944.1	chr8	91800407	91800429	+	1	NA	exon (NM_001253822, exon 2 of 4)	exon (NM_001253822, exon 2 of 4)	1236	NM_001253822	16373	Mm.238044	NM_008393	ENSMUSG00000031734	Irx3	AI894186	Iroquois related homeobox 3	protein-coding
mm_170779.1	chr2	170701503	170701505	-	1	NA	Intergenic	MTA_Mm|LTR|ERVL-MaLR	-30303	NM_029761	76829	Mm.41633	NM_029761	ENSMUSG00000027560	Dok5	2700055C10Rik	docking protein 5	protein-coding
mm_79776.1	chr9	62846001	62846004	+	1	NA	exon (NM_001033175, exon 3 of 7)	exon (NM_001033175, exon 3 of 7)	7215	NM_001033175	76524	Mm.283636	NM_001033175	ENSMUSG00000032245	Cln6	1810065L06Rik|AW743417|D9Bwg1455e|nclf	ceroid-lipofuscinosis, neuronal 6	protein-coding
mm_70306.1	chr8	4166557	4166593	+	1	NA	promoter-TSS (NM_001039578)	promoter-TSS (NM_001039578)	8	NM_001346730	213027	Mm.437106	NM_153536	ENSMUSG00000011832	Evi5l	1700084G18Rik|2310039H16Rik|3110007G05Rik|B130050I23Rik	ecotropic viral integration site 5 like	protein-coding
mm_172783.1	chr8	99467115	99467131	+	1	NA	intron (NR_132435, intron 1 of 4)	L1Md_T|LINE|L1	50449	NR_132435	234624	Mm.124595	NM_175479	ENSMUSG00000052479	A330008L17Rik	-	RIKEN cDNA A330008L17 gene	ncRNA
mm_61929.1	chr7	90165506	90165548	+	1	NA	exon (NM_001252521, exon 4 of 20)	exon (NM_001252521, exon 4 of 20)	35295	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_107809.1	chr12	65049189	65049198	+	1	NA	intron (NM_177806, intron 5 of 13)	intron (NM_177806, intron 5 of 13)	12859	NM_177806	328110	Mm.283339	NM_177806	ENSMUSG00000035597	Prpf39	Srcs1	pre-mRNA processing factor 39	protein-coding
mm_8142.1	chr1	136280584	136280601	-	1	NA	exon (NM_001081360, exon 13 of 19)	exon (NM_001081360, exon 13 of 19)	-19719	NM_001101516	383563	Mm.40367	NM_001101516	ENSMUSG00000052759	Gpr25	Gm1300	G protein-coupled receptor 25	protein-coding
mm_130494.1	chr15	98807911	98807932	-	1	NA	promoter-TSS (NM_001013741)	promoter-TSS (NM_001013741)	4	NM_001013741	13199	Mm.390810	NM_001013741	ENSMUSG00000059213	Ddn	Gm748	dendrin	protein-coding
mm_115606.1	chr13	11991611	11991621	-	1	NA	intron (NM_023868, intron 1 of 104)	(TG)n|Simple_repeat|Simple_repeat	115329	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding
mm_126107.1	chr15	78248060	78248073	+	1	NA	intron (NM_008677, intron 1 of 9)	intron (NM_008677, intron 1 of 9)	3255	NM_008677	17972	Mm.2068	NM_008677	ENSMUSG00000071715	Ncf4	AI451400|p40phox	neutrophil cytosolic factor 4	protein-coding
mm_71291.1	chr8	41044163	41044164	+	1	NA	intron (NM_001005863, intron 5 of 13)	L1MB1|LINE|L1	-2232	NM_001005865	102103	Mm.149438	NM_001005863	ENSMUSG00000045636	Mtus1	AI481402|ATBP135|Atip1|B430010I23Rik|B430305I03Rik|C85752|Cctsg1-440|MD44|MTSG1|mKIAA1288	mitochondrial tumor suppressor 1	protein-coding
mm_70837.1	chr8	23272549	23272574	+	1	NA	Intergenic	MLTR31FA_MM|LTR|ERVK	-15481	NM_001042484	57437	Mm.196269	NM_020585	ENSMUSG00000015341	Golga7	AB041568|C130038N16Rik|GCP16|GOLGA3AP1|HSPC041|R75586	golgi autoantigen, golgin subfamily a, 7	protein-coding
mm_126950.1	chr15	92161239	92161311	+	1	NA	promoter-TSS (NM_001159647)	promoter-TSS (NM_001159647)	-82	NM_001159647	12805	Mm.4911	NM_007727	ENSMUSG00000055022	Cntn1	AW495098|CNTN|F3cam|usl	contactin 1	protein-coding
mm_73575.1	chr8	109778592	109778651	+	1	NA	promoter-TSS (NM_009677)	promoter-TSS (NM_009677)	38	NM_001301211	11765	Mm.37210	NM_009677	ENSMUSG00000031731	Ap1g1	AA409002|AU041323|AW551707|Adtg|D8Ertd374e	adaptor protein complex AP-1, gamma 1 subunit	protein-coding
mm_123943.1	chr14	73376589	73376607	-	1	NA	intron (NM_008410, intron 1 of 5)	intron (NM_008410, intron 1 of 5)	8673	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_130710.1	chr15	100732713	100732740	-	1	NA	promoter-TSS (NR_045782)	promoter-TSS (NR_045782)	11	NR_045781	619313	Mm.123436	NR_045781		I730030J21Rik	-	RIKEN cDNA I730030J21 gene	ncRNA
mm_114446.1	chr13	66918569	66918577	+	1	NA	intron (NM_025547, intron 4 of 7)	RMER17B|LTR|ERVK	13158	NM_001177750	100038538	Mm.405005	NM_001177750	ENSMUSG00000074826	Gm10767	ENSMUSG00000074826	predicted gene 10767	protein-coding
mm_163180.1	chr11	89841297	89841310	-	1	NA	Intergenic	Intergenic	-144367	NM_001327810	382543	Mm.60997	NM_172534	ENSMUSG00000047773	Ankfn1	4932411E22Rik|Gm1175|nmf9	ankyrin-repeat and fibronectin type III domain containing 1	protein-coding
mm_16876.1	chr2	12419402	12419419	-	1	NA	promoter-TSS (NM_024185)	promoter-TSS (NM_024185)	50	NM_024185	66960	Mm.34059	NM_024185	ENSMUSG00000026767	Fam188a	1810041E18Rik|2310047O13Rik|5830410F13Rik|AI447827|AW111958	family with sequence similarity 188, member A	protein-coding
mm_57056.1	chr6	122486253	122486304	-	1	NA	promoter-TSS (NM_027664)	promoter-TSS (NM_027664)	27	NM_027664	108653	Mm.277939	NM_027664	ENSMUSG00000040649	Rimklb	4931417E21Rik|4933426K21Rik|AA097693|AI325948|AU015629|Naags	ribosomal modification protein rimK-like family member B	protein-coding
mm_107490.1	chr12	38781094	38781128	+	1	NA	intron (NM_001347379, intron 2 of 11)	intron (NM_001347379, intron 2 of 11)	1029	NM_007960	14009	Mm.4866	NM_007960	ENSMUSG00000004151	Etv1	ER81|Etsrp81	ets variant 1	protein-coding
mm_77719.1	chr8	126595947	126595983	-	1	NA	Intergenic	Intergenic	-2529	NM_001164598	270110	Mm.334918	NM_001164598	ENSMUSG00000051495	Irf2bp2	E130305N23Rik|IRF-2BP2	interferon regulatory factor 2 binding protein 2	protein-coding
mm_71835.1	chr8	68901226	68901279	+	1	NA	exon (NM_008509, exon 8 of 10)	exon (NM_008509, exon 8 of 10)	20697	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_146604.1	chr18	9552695	9552704	-	1	NA	Intergenic	MMVL30-int|LTR|ERV1	66770	NM_007593	26369	Mm.195831	NM_007593	ENSMUSG00000050996	Cetn1	caltractin	centrin 1	protein-coding
mm_33308.1	chr4	129058099	129058122	+	1	NA	promoter-TSS (NM_029219)	promoter-TSS (NM_029219)	-161	NM_029219	75234	Mm.259672	NM_029219	ENSMUSG00000028793	Rnf19b	4930534K13Rik|4930555L03Rik|Ibrdc3	ring finger protein 19B	protein-coding
mm_40853.1	chr5	73502626	73502638	+	1	NA	intron (NM_001190733, intron 1 of 9)	intron (NM_001190733, intron 1 of 9)	11606	NM_178896	100737	Mm.220312	NM_178896	ENSMUSG00000051674	Dcun1d4	AI836376	DCN1, defective in cullin neddylation 1, domain containing 4 (S. cerevisiae)	protein-coding
mm_148065.1	chr18	72327649	72327660	-	1	NA	intron (NM_007831, intron 1 of 28)	B1_Mur2|SINE|Alu	23415	NM_007831	13176	Mm.167882	NM_007831	ENSMUSG00000060534	Dcc	C030036D22Rik|Igdcc1	deleted in colorectal carcinoma	protein-coding
mm_166370.1	chr5	125389845	125389869	+	1	NA	intron (NM_019639, intron 1 of 1)	CpG	160	NM_019639	22190	Mm.331	NM_019639	ENSMUSG00000008348	Ubc	2700054O04Rik|AI194771|Rps27a|TI-225|Uba52|Ubb	ubiquitin C	protein-coding
mm_68794.1	chr7	123500504	123500578	-	1	NA	promoter-TSS (NM_001081329)	promoter-TSS (NM_001081329)	-92	NM_001081329	210162	Mm.135397	NM_175435	ENSMUSG00000030757	Zkscan2	9430065N20Rik|AW493225|Zfp694	zinc finger with KRAB and SCAN domains 2	protein-coding
mm_27209.1	chr3	35925615	35925617	-	1	NA	intron (NM_001205361, intron 1 of 6)	B1_Mur1|SINE|Alu	4458	NM_033623	114893	Mm.374810	NM_033623	ENSMUSG00000027708	Dcun1d1	Rp42|SCCRO|Tes3|pTes3	DCN1, defective in cullin neddylation 1, domain containing 1 (S. cerevisiae)	protein-coding
mm_44537.1	chr5	24540385	24540395	-	1	NA	promoter-TSS (NM_080444)	promoter-TSS (NM_080444)	67	NM_080444	117590	Mm.207071	NM_080444	ENSMUSG00000038204	Asb10	Asb-10|BB137407	ankyrin repeat and SOCS box-containing 10	protein-coding
mm_7821.1	chr1	132008003	132008054	-	1	NA	intron (NM_007923, intron 1 of 4)	CpG	423	NM_007923	13714	Mm.254233	NM_007923	ENSMUSG00000026436	Elk4	2310011G17Rik|A130026I01Rik|BB162516|SAP-1|Sap1	ELK4, member of ETS oncogene family	protein-coding
mm_84303.1	chr9	63399265	63399302	-	1	NA	promoter-TSS (NM_027090)	promoter-TSS (NM_027090)	-39	NM_027090	69478	Mm.113942	NM_027090	ENSMUSG00000032403	2300009A05Rik	-	RIKEN cDNA 2300009A05 gene	protein-coding
mm_37495.1	chr4	123665469	123665488	-	1	NA	promoter-TSS (NR_136925)	promoter-TSS (NR_136925)	-403	NR_136925	102633214	Mm.399387	NR_136925		Gm12925	OTTMUSG00000009214	predicted gene 12925	ncRNA
mm_1143.1	chr1	60714054	60714057	+	1	NA	Intergenic	Intergenic	-32333	NM_007642	12487	Mm.255003	NM_007642	ENSMUSG00000026012	Cd28	-	CD28 antigen	protein-coding
mm_149648.1	chr19	18581430	18581439	+	1	NA	intron (NM_017375, intron 9 of 9)	intron (NM_017375, intron 9 of 9)	50379	NM_017375	20409	Mm.172222	NM_017375	ENSMUSG00000024725	Ostf1	C78236|SH3P2|Sh3d3	osteoclast stimulating factor 1	protein-coding
mm_29788.1	chr3	127541482	127541495	-	1	NA	intron (NM_138593, intron 10 of 12)	intron (NM_138593, intron 10 of 12)	-3740	NR_030403	723948		NR_030403	ENSMUSG00000076252	Mir302b	Mirn302b|mir-302b	microRNA 302b	ncRNA
mm_89005.1	chr10	81621079	81621091	+	1	NA	TTS (NM_001163430)	TTS (NM_001163430)	6237	NM_001163430	50721	Mm.25643	NM_181586	ENSMUSG00000034748	Sirt6	2810449N18Rik|AI043036|Sir2l6	sirtuin 6	protein-coding
mm_156856.1	chrX	164401813	164401822	+	1	NA	TTS (NM_001308489)	TTS (NM_001308489)	-17970	NM_011081	18700	Mm.3781	NM_011081	ENSMUSG00000031381	Piga	AI194334|Pig-a	phosphatidylinositol glycan anchor biosynthesis, class A	protein-coding
mm_19546.1	chr2	98662976	98662993	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	1195327	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_83596.1	chr9	48494378	48494408	-	1	NA	promoter-TSS (NM_001004191)	promoter-TSS (NM_001004191)	937	NM_001326355	67010	Mm.76911	NM_144948	ENSMUSG00000042396	Rbm7	1200007M24Rik|1500011D06Rik|AU041934|AW554393	RNA binding motif protein 7	protein-coding
mm_25085.1	chr3	100489509	100489560	+	1	NA	promoter-TSS (NM_001142952)	promoter-TSS (NM_001142952)	-342	NM_001142952	74645	Mm.226900	NM_001142952	ENSMUSG00000044468	Fam46c	4930431B09Rik|AI449797	family with sequence similarity 46, member C	protein-coding
mm_89195.1	chr10	86347669	86347687	+	1	NA	3' UTR (NM_011595, exon 5 of 5)	3' UTR (NM_011595, exon 5 of 5)	47266	NM_011595	21859	Mm.4871	NM_011595	ENSMUSG00000020044	Timp3	Timp-3	tissue inhibitor of metalloproteinase 3	protein-coding
mm_119202.1	chr14	32833956	32833966	+	1	NA	promoter-TSS (NM_001164485)	promoter-TSS (NM_001164485)	-1	NM_001164485	105511	Mm.32231	NM_001164485	ENSMUSG00000078127	Fam170b	4922501K12Rik|AI449756	family with sequence similarity 170, member B	protein-coding
mm_21770.1	chr2	164844711	164844730	-	1	NA	exon (NM_011125, exon 11 of 16)	exon (NM_011125, exon 11 of 16)	10947	NM_008906	19025	Mm.359633	NM_008906	ENSMUSG00000017760	Ctsa	AU019505|PPCA|Ppgb	cathepsin A	protein-coding
mm_4561.1	chr1	177447190	177447200	+	1	NA	exon (NM_013915, exon 1 of 1)	exon (NM_013915, exon 1 of 1)	1374	NM_013915	30928	Mm.330700	NM_013915	ENSMUSG00000063659	Zbtb18	RP58|Zfp238|Znf238	zinc finger and BTB domain containing 18	protein-coding
mm_145275.1	chr18	53050356	53050357	+	1	NA	Intergenic	Intergenic	-126009	NM_026386	67804	Mm.252171	NM_026386	ENSMUSG00000034484	Snx2	0610030A03Rik	sorting nexin 2	protein-coding
mm_144778.1	chr18	35829841	35829851	+	1	NA	promoter-TSS (NM_133687)	promoter-TSS (NM_133687)	28	NM_133687	67393	Mm.94560	NM_133687	ENSMUSG00000046668	Cxxc5	4930415K17Rik	CXXC finger 5	protein-coding
mm_54628.1	chr6	38689532	38689555	-	1	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	26474	NM_001101507	665180	Mm.349066	NM_001101507	ENSMUSG00000079598	Clec2l	AI414054|AW122724|Gm1064	C-type lectin domain family 2, member L	protein-coding
mm_52422.1	chr6	113471482	113471513	+	1	NA	promoter-TSS (NM_178942)	promoter-TSS (NM_178942)	42	NM_134159	171095	Mm.213397	NM_134159	ENSMUSG00000030281	Il17rc	1110025H02Rik|Gm19850|IL-17RC|IL17-RC|IL17-RL|Il17rl	interleukin 17 receptor C	protein-coding
mm_123088.1	chr14	55758332	55758342	-	1	NA	promoter-TSS (NM_009894)	promoter-TSS (NM_009894)	87	NM_009894	12684	Mm.466766	NM_009894	ENSMUSG00000022219	Cideb	1110030C18Rik|AI790179|CIDE-B	cell death-inducing DNA fragmentation factor, alpha subunit-like effector B	protein-coding
mm_84734.1	chr9	75072482	75072517	-	1	NA	intron (NM_010864, intron 1 of 40)	ID4_|SINE|ID	1293	NM_010864	17918	Mm.3645	NM_010864	ENSMUSG00000034593	Myo5a	9630007J19Rik|AI413174|AI661011|Dbv|MVa|Myo5|MyoVA|Sev-1|d|d-120J|flail|flr	myosin VA	protein-coding
mm_45035.1	chr5	39615067	39615100	-	1	NA	exon (NM_010474, exon 2 of 2)	exon (NM_010474, exon 2 of 2)	-11509	NR_045416	75095	Mm.332354	NR_045416	ENSMUSG00000106741	4930513D17Rik	-	RIKEN cDNA 4930513D17 gene	ncRNA
mm_165888.1	chr4	43655538	43655540	+	1	NA	intron (NM_026871, intron 1 of 4)	intron (NM_026871, intron 1 of 4)	906	NM_026871	68917	Mm.25285	NM_026871	ENSMUSG00000028470	Hint2	1190005L05Rik	histidine triad nucleotide binding protein 2	protein-coding
mm_84164.1	chr9	59617089	59617136	-	1	NA	promoter-TSS (NM_029922)	promoter-TSS (NM_029922)	-172	NR_038075	67287	Mm.439943	NM_029922	ENSMUSG00000025237	Parp6	1700119G14Rik|2310028P13Rik|3110038K10Rik|ARTD17|C030013N01Rik|PARP-6	poly (ADP-ribose) polymerase family, member 6	protein-coding
mm_59994.1	chr7	30563299	30563349	+	1	NA	promoter-TSS (NM_025498)	promoter-TSS (NM_025498)	-16	NM_170760	233073	Mm.34790	NM_170760	ENSMUSG00000078765	U2af1l4	AA407033|AF419339|AI451269|AW553050|U2af26	U2 small nuclear RNA auxiliary factor 1-like 4	protein-coding
mm_122198.1	chr14	31781449	31781471	-	1	NA	intron (NM_001024604, intron 1 of 27)	intron (NM_001024604, intron 1 of 27)	48955	NM_001024604	105522	Mm.37660	NM_001024604	ENSMUSG00000014496	Ankrd28	AI465466|AI604979|E430019N21Rik|mKIAA0379	ankyrin repeat domain 28	protein-coding
mm_83561.1	chr9	46243441	46243459	-	1	NA	TTS (NM_007468)	TTS (NM_007468)	2606	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_101884.1	chr11	48945486	48945517	-	1	NA	TTS (NM_001114679)	TTS (NM_001114679)	909	NM_001281472	621823	Mm.440151	NM_001281472	ENSMUSG00000078153	Psme2b	PA28b-p|PA28b2|Psme2-like|Psme2b-ps	protease (prosome, macropain) activator subunit 2B	protein-coding
mm_164693.1	chr17	48234862	48234871	+	1	NA	intron (NM_001347399, intron 1 of 2)	intron (NM_001347399, intron 1 of 2)	2127	NM_021406	58217	Mm.248352	NM_021406	ENSMUSG00000042265	Trem1	-	triggering receptor expressed on myeloid cells 1	protein-coding
mm_9253.1	chr1	171531661	171531688	-	1	NA	exon (NM_010584, exon 4 of 8)	exon (NM_010584, exon 4 of 8)	3620	NM_010584	16429	Mm.247426	NM_010584	ENSMUSG00000038209	Itln1	IntL|Itln|Itln2|Itln3|Itln5|Itlna|Lfr	intelectin 1 (galactofuranose binding)	protein-coding
mm_148400.1	chr19	3851801	3851811	+	1	NA	promoter-TSS (NM_001271496)	promoter-TSS (NM_001271496)	33	NR_073190	12660	Mm.225505	NM_013490	ENSMUSG00000024843	Chka	CK|CK/EK-alpha|Chetk-alpha|Chk|ChoK|EK|EtnK-alpha	choline kinase alpha	protein-coding
mm_23625.1	chr3	65958710	65958721	+	1	NA	promoter-TSS (NM_019937)	promoter-TSS (NM_019937)	-490	NM_019937	56706	Mm.175612	NM_019937	ENSMUSG00000027829	Ccnl1	2610030E23Rik|AU018493|Ccnl|ania-6a	cyclin L1	protein-coding
mm_172465.1	chr7	42692797	42692802	-	1	NA	promoter-TSS (NM_001008427)	promoter-TSS (NM_001008427)	-81	NM_001008427	434179	Mm.284947	NM_001008427	ENSMUSG00000069727	Zfp975	EG434179|Gm5595|mszf88	zinc finger protein 975	protein-coding
mm_104747.1	chr11	98463422	98463432	-	1	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	16593	NM_010346	14786	Mm.276702	NM_010346	ENSMUSG00000019312	Grb7	mKIAA4028	growth factor receptor bound protein 7	protein-coding
mm_52138.1	chr6	97957040	97957049	+	1	NA	intron (NM_001113198, intron 2 of 9)	intron (NM_001113198, intron 2 of 9)	27227	NM_001178049	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_91290.1	chr10	24842797	24842829	-	1	NA	Intergenic	MTD-int|LTR|ERVL-MaLR	-6618	NM_134005	209558	Mm.338425	NM_134005	ENSMUSG00000019989	Enpp3	AI876438|CD203c	ectonucleotide pyrophosphatase/phosphodiesterase 3	protein-coding
mm_52210.1	chr6	101272014	101272029	+	1	NA	intron (NM_018884, intron 3 of 9)	intron (NM_018884, intron 3 of 9)	105876	NM_018884	55983	Mm.321654	NM_018884	ENSMUSG00000035357	Pdzrn3	1110020C07Rik|AI429718|AL023082|LNX3|SEMACAP3|Semcap3	PDZ domain containing RING finger 3	protein-coding
mm_43335.1	chr5	135023507	135023507	+	1	NA	promoter-TSS (NM_016801)	promoter-TSS (NM_016801)	25	NR_133683	20907	Mm.6225	NM_016801	ENSMUSG00000007207	Stx1a	HPC-1	syntaxin 1A (brain)	protein-coding
mm_119017.1	chr14	30008951	30008961	+	1	NA	promoter-TSS (NM_001136240)	promoter-TSS (NM_001136240)	-44	NM_001136240	218865	Mm.259916	NM_172264	ENSMUSG00000015970	Chdh	AU041472|D630034H06Rik	choline dehydrogenase	protein-coding
mm_114103.1	chr13	54731776	54731790	+	1	NA	intron (NM_001033364, intron 23 of 31)	PB1D10|SINE|Alu	18091	NM_001316710	26913	Mm.41812	NM_012014	ENSMUSG00000069227	Gprin1	GRIN1|Z16	G protein-regulated inducer of neurite outgrowth 1	protein-coding
mm_130709.1	chr15	100729327	100729381	-	1	NA	promoter-TSS (NM_172451)	promoter-TSS (NM_172451)	22	NM_001161767	207839	Mm.22969	NM_172451	ENSMUSG00000037280	Galnt6	4632410F13|AW047994|GalNAc-T6	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 6	protein-coding
mm_86871.1	chr10	21995347	21995350	+	1	NA	intron (NM_001161848, intron 2 of 11)	intron (NM_001161848, intron 2 of 11)	682	NM_011361	20393	Mm.28405	NM_011361	ENSMUSG00000019970	Sgk1	Sgk	serum/glucocorticoid regulated kinase 1	protein-coding
mm_36073.1	chr4	58009075	58009083	-	1	NA	promoter-TSS (NM_026132)	promoter-TSS (NM_026132)	45	NM_026132	67402	Mm.87357	NM_026132	ENSMUSG00000038709	Txndc8	4930429J24Rik|Sptrx-3|Sptrx3|Trx6	thioredoxin domain containing 8	protein-coding
mm_84241.1	chr9	62341156	62341165	-	1	NA	promoter-TSS (NM_009672)	promoter-TSS (NM_009672)	-183	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	protein-coding
mm_41601.1	chr5	96209464	96209488	+	1	NA	promoter-TSS (NM_053158)	promoter-TSS (NM_053158)	-639	NM_001039084	94061	Mm.295499	NM_053158	ENSMUSG00000029486	Mrpl1	2410002L03Rik|5830418D04Rik|AI462572|L1mt	mitochondrial ribosomal protein L1	protein-coding
mm_129324.1	chr15	77769874	77769892	-	1	NA	exon (NM_022410, exon 28 of 41)	exon (NM_022410, exon 28 of 41)	-14654	NM_001081970	239552	Mm.125650	NM_001081970	ENSMUSG00000056656	Apol8	9830006J20Rik|APOL-II|Apol2	apolipoprotein L 8	protein-coding
mm_82121.1	chr9	123478694	123478733	+	1	NA	promoter-TSS (NM_013860)	promoter-TSS (NM_013860)	12	NM_013860	29806	Mm.10987	NM_013860	ENSMUSG00000025239	Limd1	AW822033|D9Ertd192e	LIM domains containing 1	protein-coding
mm_54004.1	chr6	7693185	7693244	-	1	NA	promoter-TSS (NM_012055)	promoter-TSS (NM_012055)	-32	NM_012055	27053	Mm.2942	NM_012055	ENSMUSG00000029752	Asns	-	asparagine synthetase	protein-coding
mm_10027.1	chr1	192099291	192099293	-	1	NA	3' UTR (NM_144814, exon 10 of 10)	3' UTR (NM_144814, exon 10 of 10)	-6693	NM_011633	22033	Mm.380491	NM_011633		Traf5	-	TNF receptor-associated factor 5	protein-coding
mm_50020.1	chr6	41116038	41116055	+	1	NA	Intergenic	Intergenic	-80537	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_16568.1	chr2	3419025	3419061	-	1	NA	intron (NM_008579, intron 1 of 2)	CpG	3605	NM_008579	104362	Mm.2688	NM_008579	ENSMUSG00000026650	Meig1	MLZ-278|Meg1	meiosis expressed gene 1	protein-coding
mm_11137.1	chr2	28469836	28469853	+	1	NA	exon (NM_001166031, exon 4 of 4)	exon (NM_001166031, exon 4 of 4)	1778	NM_001166031	118451	Mm.294951	NM_080452	ENSMUSG00000035772	Mrps2	1500019M10Rik	mitochondrial ribosomal protein S2	protein-coding
mm_52859.1	chr6	122294095	122294111	+	1	NA	Intergenic	Intergenic	-11270	NM_016970	50928	Mm.20434	NM_016970	ENSMUSG00000030114	Klrg1	2F1-Ag|MAFA|MAFA-L	killer cell lectin-like receptor subfamily G, member 1	protein-coding
mm_85473.1	chr9	105819554	105819554	-	1	NA	intron (NM_001102607, intron 1 of 36)	LSU-rRNA_Hsa|rRNA|rRNA	8531	NM_001102607	245026	Mm.482507	NM_172927	ENSMUSG00000043719	Col6a6	E330019B14|E330026B02Rik	collagen, type VI, alpha 6	protein-coding
mm_84292.1	chr9	63281225	63281240	-	1	NA	intron (NM_011840, intron 12 of 21)	intron (NM_011840, intron 12 of 21)	96620	NM_011840	23938	Mm.325746	NM_011840	ENSMUSG00000058444	Map2k5	AI324775|AI428457|MEK5|Mapkk5|Prkmk5	mitogen-activated protein kinase kinase 5	protein-coding
mm_41652.1	chr5	98254323	98254334	+	1	NA	5' UTR (NM_001277268, exon 1 of 2)	5' UTR (NM_001277268, exon 1 of 2)	144	NM_001277268	14176	Mm.5055	NM_010203	ENSMUSG00000029337	Fgf5	Fgf-5|HBGF-5|angora|go	fibroblast growth factor 5	protein-coding
mm_7936.1	chr1	133914622	133914631	-	1	NA	exon (NM_054077, exon 2 of 3)	exon (NM_054077, exon 2 of 3)	-6627	NM_001160420	269120	Mm.59985	NM_054076	ENSMUSG00000010311	Optc	-	opticin	protein-coding
mm_167664.1	chr9	71896116	71896116	-	1	NA	promoter-TSS (NM_001253864)	promoter-TSS (NM_001253864)	-20	NM_001253863	21406	Mm.171615	NM_011544	ENSMUSG00000032228	Tcf12	A130037E08Rik|ALF1|HEB|HEBAlt|HTF-4|HTF4|ME1|REB|bHLHb20	transcription factor 12	protein-coding
mm_65897.1	chr7	30187269	30187284	-	1	NA	3' UTR (NM_009795, exon 11 of 11)	3' UTR (NM_009795, exon 11 of 11)	3105	NM_009944	12865	Mm.423030	NM_009944	ENSMUSG00000074218	Cox7a1	COX7A|COX7AH|COX7AM	cytochrome c oxidase subunit VIIa 1	protein-coding
mm_13612.1	chr2	113405115	113405127	+	1	NA	intron (NM_001285458, intron 2 of 16)	intron (NM_001285458, intron 2 of 16)	-35943	NM_001285459	14260	Mm.4938	NM_010230	ENSMUSG00000044042	Fmn1	Fmn|formin-1|ld	formin 1	protein-coding
mm_141912.1	chr17	34981761	34981829	-	1	NA	promoter-TSS (NM_001110101)	promoter-TSS (NM_001110101)	-59	NM_001110101	27756	Mm.165735	NM_030597	ENSMUSG00000007050	Lsm2	D17H6S56E-2|D17H6S56E2|Dmapl|Dmpkap|G7b|Sm-X5|SmX5|snRNP	LSM2 homolog, U6 small nuclear RNA and mRNA degradation associated	protein-coding
mm_9639.1	chr1	177071326	177071344	-	1	NA	intron (NM_011785, intron 7 of 12)	intron (NM_011785, intron 7 of 12)	177432	NM_011785	23797	Mm.235194	NM_011785	ENSMUSG00000019699	Akt3	AI851531|D930002M15Rik|Nmf350	thymoma viral proto-oncogene 3	protein-coding
mm_29183.1	chr3	106542165	106542192	-	1	NA	intron (NM_133869, intron 1 of 8)	PB1D11|SINE|Alu	-5620	NM_001286986	67171	Mm.290488	NM_026013	ENSMUSG00000027900	Dram2	2010305N14Rik|2610318G18Rik|AI647667|Tmem77	DNA-damage regulated autophagy modulator 2	protein-coding
mm_153026.1	chr19	31664357	31664372	-	1	NA	promoter-TSS (NM_011160)	promoter-TSS (NM_011160)	6	NM_011160	19091	Mm.381170	NM_011160	ENSMUSG00000052920	Prkg1	AW125416|CGKI|Gm19690|Prkg1b|Prkgr1b	protein kinase, cGMP-dependent, type I	protein-coding
mm_100776.1	chr11	4804004	4804023	-	1	NA	intron (NM_001252251, intron 6 of 16)	intron (NM_001252251, intron 6 of 16)	29122	NM_001252253	18016	Mm.297109	NM_010898	ENSMUSG00000009073	Nf2	merlin	neurofibromin 2	protein-coding
mm_118052.1	chr13	101739915	101739919	-	1	NA	intron (NM_001077495, intron 2 of 15)	intron (NM_001077495, intron 2 of 15)	28300	NM_001077495	18708	Mm.259333	NM_001024955	ENSMUSG00000041417	Pik3r1	PI3K|p50alpha|p55alpha|p85alpha	phosphatidylinositol 3-kinase, regulatory subunit, polypeptide 1 (p85 alpha)	protein-coding
mm_144091.1	chr18	3336690	3336703	+	1	NA	non-coding (NR_033457, exon 1 of 2)	non-coding (NR_033457, exon 1 of 2)	280	NR_033457	633947	Mm.461446	NR_033457	ENSMUSG00000097746	Gm6225	EG621440	predicted gene 6225	ncRNA
mm_69893.1	chr7	141637670	141637692	-	1	NA	intron (NM_001330001, intron 31 of 33)	intron (NM_001330001, intron 31 of 33)	16980	NR_106030	102466798		NR_106030	ENSMUSG00000098759	Mir7063	Gm27654|mmu-mir-7063	microRNA 7063	ncRNA
mm_169050.1	chr13	17949603	17949626	+	1	NA	Intergenic	Intergenic	-5397	NM_019491	56044	Mm.27348	NM_019491	ENSMUSG00000008859	Rala	3010001O15Rik|AW322615|Ral|Rasl1	v-ral simian leukemia viral oncogene A (ras related)	protein-coding
mm_38117.1	chr4	134540883	134540888	-	1	NA	exon (NM_029100, exon 10 of 12)	exon (NM_029100, exon 10 of 12)	-5498	NM_029759	76824	Mm.30153	NM_029759	ENSMUSG00000046671	Mtfr1l	2410166I05Rik|AI480750|Fam54b	mitochondrial fission regulator 1-like	protein-coding
mm_127208.1	chr15	99224580	99224618	+	1	NA	promoter-TSS (NM_010601)	promoter-TSS (NM_010601)	-377	NM_010601	16512	Mm.374793	NM_010601	ENSMUSG00000037579	Kcnh3	AU019351|C030044P22Rik|Elk2|Kv12.2|Melk2	potassium voltage-gated channel, subfamily H (eag-related), member 3	protein-coding
mm_147639.1	chr18	60269623	60269629	-	1	NA	3' UTR (NM_001034859, exon 2 of 2)	3' UTR (NM_001034859, exon 2 of 2)	3641	NM_001034859	225594	Mm.329460	NM_001034859	ENSMUSG00000068606	Gm4841	EG225594|Ifgga3	predicted gene 4841	protein-coding
mm_111935.1	chr12	108893362	108893369	-	1	NA	promoter-TSS (NM_177602)	promoter-TSS (NM_177602)	-154	NM_011710	22375	Mm.38433	NM_011710	ENSMUSG00000021266	Wars	TrpRS|WRS	tryptophanyl-tRNA synthetase	protein-coding
mm_116336.1	chr13	38109137	38109139	-	1	NA	Intergenic	Intergenic	-42156	NM_023842	109620	Mm.355327	NM_023842	ENSMUSG00000054889	Dsp	2300002E22Rik|5730453H04Rik|AA407887|AA407888|AW109828|DP|rul	desmoplakin	protein-coding
mm_165801.1	chr3	142881722	142881724	-	1	NA	5' UTR (NM_178654, exon 1 of 22)	5' UTR (NM_178654, exon 1 of 22)	281	NM_178654	109333	Mm.244236	NM_178654	ENSMUSG00000004591	Pkn2	6030436C20Rik|AI507382|PRK2|Prkcl2|Stk7	protein kinase N2	protein-coding
mm_75465.1	chr8	47948360	47948373	-	1	NA	intron (NM_133791, intron 1 of 22)	intron (NM_133791, intron 1 of 22)	42185	NM_133791	52357	Mm.235074	NM_133791	ENSMUSG00000031563	Wwc2	5330431C14Rik|AU022508|C85457|D8Ertd594e	WW, C2 and coiled-coil domain containing 2	protein-coding
mm_57500.1	chr6	125379891	125379917	-	1	NA	5' UTR (NM_198604, exon 2 of 17)	5' UTR (NM_198604, exon 2 of 17)	600	NM_198604	213522	Mm.333396	NM_198604	ENSMUSG00000038167	Plekhg6	BC026778|Gm155	pleckstrin homology domain containing, family G (with RhoGef domain) member 6	protein-coding
mm_51690.1	chr6	86526645	86526719	+	1	NA	promoter-TSS (NM_011865)	promoter-TSS (NM_011865)	-517	NM_011865	23983	Mm.274146	NM_011865	ENSMUSG00000051695	Pcbp1	WBP17|[a]CP-1|alphaCP-1|hnRNP E1	poly(rC) binding protein 1	protein-coding
mm_94770.1	chr11	21239280	21239302	+	1	NA	5' UTR (NM_001290628, exon 1 of 23)	5' UTR (NM_001290628, exon 1 of 23)	259	NM_001290628	245944	Mm.170103	NM_139061	ENSMUSG00000020128	Vps54	Hcc8|Vps54l|mSLP8|wr	VPS54 GARP complex subunit	protein-coding
mm_110908.1	chr12	75928926	75928927	-	1	NA	intron (NM_001005510, intron 27 of 115)	intron (NM_001005510, intron 27 of 115)	19823	NR_039560	100628610		NR_039560	ENSMUSG00000092922	Mir5101	mmu-mir-5101|mu-mir-5101	microRNA 5101	ncRNA
mm_28804.1	chr3	96238982	96238985	-	1	NA	TTS (NM_178212)	TTS (NM_178212)	144	NM_054045	97114	Mm.358797	NM_054045	ENSMUSG00000081058	Hist2h3c2	H3-614|H3.2-614|Hist2h3c2-ps|Hist2h3ca1|M32461	histone cluster 2, H3c2	protein-coding
mm_59631.1	chr7	28157070	28157074	+	1	NA	exon (NM_001164655, exon 15 of 20)	exon (NM_001164655, exon 15 of 20)	-12676	NM_007991	14113	Mm.4595	NM_007991	ENSMUSG00000046865	Fbl	AL022665|FIB|FLRN|RNU3IP1	fibrillarin	protein-coding
mm_55366.1	chr6	57535500	57535513	-	1	NA	promoter-TSS (NM_175523)	promoter-TSS (NM_175523)	-80	NM_175523	243382	Mm.396893	NM_175523	ENSMUSG00000037826	Ppm1k	2900063A19Rik|A930026L03Rik|PP2Cm	protein phosphatase 1K (PP2C domain containing)	protein-coding
mm_164114.1	chr15	31342292	31342323	+	1	NA	intron (NM_027496, intron 1 of 3)	intron (NM_027496, intron 1 of 3)	25452	NM_001164441	67434	Mm.102470	NM_026153	ENSMUSG00000022237	Ankrd33b	0610012A05Rik|3021401C12Rik|5730557B15Rik	ankyrin repeat domain 33B	protein-coding
mm_20027.1	chr2	119473864	119473868	-	1	NA	intron (NM_026574, intron 1 of 35)	intron (NM_026574, intron 1 of 35)	3763	NM_026574	68142	Mm.330496	NM_026574	ENSMUSG00000034154	Ino80	2310079N15Rik|4632409L19Rik|Inoc1	INO80 complex subunit	protein-coding
mm_33267.1	chr4	127371757	127371759	+	1	NA	Intergenic	Intergenic	-13594	NM_010291	14622	Mm.26859	NM_010291	ENSMUSG00000042357	Gjb5	Cnx31.1|Cx31.1|Gjb-5	gap junction protein, beta 5	protein-coding
mm_88635.1	chr10	79890904	79890918	+	1	NA	promoter-TSS (NM_013459)	promoter-TSS (NM_013459)	58	NM_001291915	11537	Mm.4407	NM_013459	ENSMUSG00000061780	Cfd	Adn|DF	complement factor D (adipsin)	protein-coding
mm_19019.1	chr2	76938404	76938413	-	1	NA	exon (NM_011652, exon 37 of 313)	exon (NM_011652, exon 37 of 313)	44139	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_46814.1	chr5	113138115	113138151	-	1	NA	5' UTR (NM_001347397, exon 1 of 8)	5' UTR (NM_001347397, exon 1 of 8)	452	NM_001347397	243219	Mm.160131	NM_172884	ENSMUSG00000051339	2900026A02Rik	8430408O14Rik|A530094D01|AW539426|Gm449|Kiaa1671|mKIAA1671	RIKEN cDNA 2900026A02 gene	protein-coding
mm_89912.1	chr10	111174874	111174887	+	1	NA	intron (NM_175489, intron 1 of 23)	intron (NM_175489, intron 1 of 23)	10078	NM_175489	237542	Mm.220204	NM_175489	ENSMUSG00000020189	Osbpl8	AA536976|AA536995|C730029P18Rik|D330025H14Rik|ORP-8	oxysterol binding protein-like 8	protein-coding
mm_84277.1	chr9	62811593	62811659	-	1	NA	promoter-TSS (NM_010193)	promoter-TSS (NM_010193)	22	NM_010193	14155	Mm.24069	NM_010193	ENSMUSG00000032244	Fem1b	mKIAA0396	feminization 1 homolog b (C. elegans)	protein-coding
mm_41637.1	chr5	97700799	97700815	+	1	NA	Intergenic	Intergenic	-243799	NM_010294	14626	Mm.61206	NM_010294	ENSMUSG00000050553	Gk2	GKTA|Gk-rs2	glycerol kinase 2	protein-coding
mm_115240.1	chr13	109952106	109952109	+	1	NA	3' UTR (NM_011056, exon 17 of 17)	3' UTR (NM_011056, exon 17 of 17)	48298	NR_035442	100316683		NR_035442	ENSMUSG00000084651	Mir1904	Mirn1904|mmu-mir-1904	microRNA 1904	ncRNA
mm_62100.1	chr7	96211826	96211837	+	1	NA	5' UTR (NM_001310760, exon 1 of 33)	5' UTR (NM_001310760, exon 1 of 33)	160	NM_001310760	23966	Mm.254610	NM_011858	ENSMUSG00000048078	Tenm4	Doc4|ELM2|Odz4|R75022|Ten-m4|l(7)-3Rn|l7Rn3|mKIAA1302	teneurin transmembrane protein 4	protein-coding
mm_36682.1	chr4	96547805	96547809	-	1	NA	intron (NM_010008, intron 1 of 8)	intron (NM_010008, intron 1 of 8)	5844	NM_010008	13110	Mm.98200	NM_010008	ENSMUSG00000052914	Cyp2j6	-	cytochrome P450, family 2, subfamily j, polypeptide 6	protein-coding
mm_72233.1	chr8	74873271	74873283	+	1	NA	5' UTR (NM_027837, exon 1 of 4)	5' UTR (NM_027837, exon 1 of 4)	103	NM_001294278	71597	Mm.158735	NM_027837	ENSMUSG00000031621	Isx	9130012O13Rik|Pix-1	intestine specific homeobox	protein-coding
mm_149381.1	chr19	11380879	11380896	+	1	NA	intron (NM_001310331, intron 2 of 6)	intron (NM_001310331, intron 2 of 6)	5399	NM_001310331	666907		NM_001310331	ENSMUSG00000101389	Ms4a4a	EG666907	membrane-spanning 4-domains, subfamily A, member 4A	protein-coding
mm_80031.1	chr9	68728269	68728269	+	1	NA	intron (NM_013646, intron 1 of 10)	intron (NM_013646, intron 1 of 10)	-37077	NR_033299	320440	Mm.483129	NM_177159		9530091C08Rik	-	RIKEN cDNA 9530091C08 gene	ncRNA
mm_138035.1	chr17	33919680	33919690	+	1	NA	TTS (NM_020625)	TTS (NM_020625)	207	NM_009318	21356	Mm.154457	NM_009318	ENSMUSG00000024308	Tapbp	D17Wsu91e|TPN	TAP binding protein	protein-coding
mm_38002.1	chr4	133686674	133686694	-	1	NA	exon (NM_001080819, exon 15 of 20)	exon (NM_001080819, exon 15 of 20)	-14037	NM_001145956	230801	Mm.217004	NM_178698	ENSMUSG00000043257	Pigv	B330013B03|D430024F16Rik	phosphatidylinositol glycan anchor biosynthesis, class V	protein-coding
mm_107872.1	chr12	69930904	69930906	+	1	NA	intron (NM_178628, intron 3 of 14)	7SK|RNA|RNA	-32504	NR_036607	100040999	Mm.394588	NR_036607	ENSMUSG00000079076	Gm3086	-	RuvB-like protein 1 pseudogene	pseudo
mm_50637.1	chr6	51329872	51329883	+	1	NA	Intergenic	Intergenic	-49833	NR_110455	625167	Mm.389772	NR_110455	ENSMUSG00000107660	Gm6559	EG625167	predicted gene 6559	ncRNA
mm_93463.1	chr10	110896502	110896539	-	1	NA	promoter-TSS (NR_045979)	promoter-TSS (NR_045979)	-13	NR_045979	75630	Mm.392786	NR_045979	ENSMUSG00000101801	1700020G17Rik	4930480D05Rik	RIKEN cDNA 1700020G17 gene	ncRNA
mm_9919.1	chr1	189343708	189343749	-	1	NA	promoter-TSS (NM_010607)	promoter-TSS (NM_010607)	-21	NM_010607	16526	Mm.33304	NM_010607	ENSMUSG00000037624	Kcnk2	A430027H14Rik|AI848635|TREK-1	potassium channel, subfamily K, member 2	protein-coding
mm_167626.1	chr9	60687444	60687452	-	1	NA	promoter-TSS (NM_001146047)	promoter-TSS (NM_001146047)	86	NM_001311095	102747	Mm.269413	NM_145616	ENSMUSG00000047766	Lrrc49	AI430817|AW050057|D430025H09Rik|PGs4|p79	leucine rich repeat containing 49	protein-coding
mm_74823.1	chr8	23095548	23095563	-	1	NA	intron (NR_102385, intron 11 of 45)	GSAT_MM|Satellite|Satellite	37296	NR_102385	11733	Mm.334444	NM_031158	ENSMUSG00000031543	Ank1	Ank-1|nb|pale	ankyrin 1, erythroid	protein-coding
mm_144092.1	chr18	3336728	3336742	+	1	NA	non-coding (NR_033457, exon 1 of 2)	non-coding (NR_033457, exon 1 of 2)	319	NR_033457	633947	Mm.461446	NR_033457	ENSMUSG00000097746	Gm6225	EG621440	predicted gene 6225	ncRNA
mm_35813.1	chr4	46941185	46941201	-	1	NA	intron (NM_001081141, intron 1 of 18)	ID4_|SINE|ID	50521	NM_001081141	242425	Mm.101909	NM_001081141	ENSMUSG00000039809	Gabbr2	GABABR2|Gb2|Gm425|Gpr51	gamma-aminobutyric acid (GABA) B receptor, 2	protein-coding
mm_30517.1	chr3	158543349	158543375	-	1	NA	intron (NM_001081358, intron 1 of 27)	intron (NM_001081358, intron 1 of 27)	18859	NM_001291453	242274	Mm.132162	NM_001081358	ENSMUSG00000028176	Lrrc7	AK122498|densin|mKIAA1365	leucine rich repeat containing 7	protein-coding
mm_141194.1	chr17	27020656	27020682	-	1	NA	3' UTR (NM_007523, exon 6 of 6)	3' UTR (NM_007523, exon 6 of 6)	2634	NM_001251881	70772	Mm.440437	NM_027544	ENSMUSG00000048731	Ggnbp1	0610031G08Rik|mdf	gametogenetin binding protein 1	protein-coding
mm_31807.1	chr4	65604985	65605052	+	1	NA	promoter-TSS (NM_053084)	promoter-TSS (NM_053084)	32	NM_001161782	69807	Mm.22786	NM_053084	ENSMUSG00000051675	Trim32	1810045E12Rik|3f3|BBS11|Zfp117	tripartite motif-containing 32	protein-coding
mm_108402.1	chr12	81532951	81532990	+	1	NA	promoter-TSS (NM_025292)	promoter-TSS (NM_025292)	-59	NM_001309848	105940408		NM_001309847	ENSMUSG00000021139	Synj2bp-cox16	ARIP2a	Synj2bp-cox16 readthrough	protein-coding
mm_114718.1	chr13	83663722	83663730	+	1	NA	3' UTR (NM_025282, exon 11 of 11)	3' UTR (NM_025282, exon 11 of 11)	-64380	NR_015561	320203	Mm.245636	NM_177100	ENSMUSG00000050334	C130071C03Rik	2810449C10Rik	RIKEN cDNA C130071C03 gene	ncRNA
mm_62831.1	chr7	113765776	113765795	+	1	NA	promoter-TSS (NM_145584)	promoter-TSS (NM_145584)	-213	NM_145584	233744	Mm.334160	NM_145584	ENSMUSG00000038156	Spon1	AI666765|AW455831|BC020531|D330035F22Rik|FSP	spondin 1, (f-spondin) extracellular matrix protein	protein-coding
mm_169192.1	chr13	66108593	66108612	-	1	NA	Intergenic	Intergenic	-4851	NM_001177832	628709	Mm.390595	NM_001177832	ENSMUSG00000095909	Gm10324	ENSMUSG00000071302	predicted gene 10324	protein-coding
mm_79833.1	chr9	64797705	64797711	+	1	NA	Intergenic	Intergenic	-13303	NM_001162917	102442	Mm.222473	NM_176935	ENSMUSG00000053641	Dennd4a	AI115600|AI851943|F730015K02Rik	DENN/MADD domain containing 4A	protein-coding
mm_9707.1	chr1	179517977	179517989	-	1	NA	promoter-TSS (NM_027188)	promoter-TSS (NM_027188)	20	NM_027188	69726	Mm.222338	NM_027188	ENSMUSG00000055067	Smyd3	2410008A19Rik|Zmynd1	SET and MYND domain containing 3	protein-coding
mm_366.1	chr1	33911579	33911584	+	1	NA	intron (NM_001276764, intron 2 of 102)	intron (NM_001276764, intron 2 of 102)	3356	NM_001276764	13518	Mm.336625	NM_010081	ENSMUSG00000026131	Dst	2310001O04Rik|A830042E19Rik|AW554249|BP230|BPAG1-n|Bpag|Bpag1|Macf2|ah|athetoid|dt|mKIAA0728|nmf203|nmf339	dystonin	protein-coding
mm_72666.1	chr8	84893990	84894021	+	1	NA	promoter-TSS (NM_001044744)	promoter-TSS (NM_001044744)	-84	NM_008097	270076	Mm.2475	NM_008097	ENSMUSG00000003809	Gcdh	9030411L18|AI266902|D17825|GCD	glutaryl-Coenzyme A dehydrogenase	protein-coding
mm_22882.1	chr3	29732831	29732834	+	1	NA	Intergenic	Intergenic	96088	NR_105796	102466637		NR_105796	ENSMUSG00000098315	Mir21b	Gm27951|mmu-mir-21b	microRNA 21b	ncRNA
mm_127365.1	chr15	100695801	100695824	+	1	NA	intron (NM_001161767, intron 10 of 11)	MTD|LTR|ERVL-MaLR	-7892	NM_033612	109901	Mm.2131	NM_033612	ENSMUSG00000023031	Cela1	1810009A17Rik|1810062B19Rik|Ela-1|Ela1|PC-TsF	chymotrypsin-like elastase family, member 1	protein-coding
mm_130076.1	chr15	89373832	89373860	-	1	NA	promoter-TSS (NM_001111288)	promoter-TSS (NM_001111288)	-28	NM_001111288	100126824	Mm.287977	NM_001111288	ENSMUSG00000091780	Sco2	-	SCO2 cytochrome c oxidase assembly protein	protein-coding
mm_139055.1	chr17	46383570	46383622	+	1	NA	promoter-TSS (NM_021346)	promoter-TSS (NM_021346)	-170	NM_207671	57908	Mm.439916	NM_021346	ENSMUSG00000015597	Zfp318	2610034E08Rik|D530032D06Rik|TZF|Znf318	zinc finger protein 318	protein-coding
mm_153688.1	chr19	44396920	44396930	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	10784	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_32398.1	chr4	106859722	106859755	+	1	NA	Intergenic	Intergenic	-51732	NM_198438	72475	Mm.195635	NM_023672	ENSMUSG00000061887	Ssbp3	2610021L12Rik|2610200M23Rik|5730488C10Rik|AI854733|AW551939|LAST|SSDP1	single-stranded DNA binding protein 3	protein-coding
mm_157498.1	chrX	48463114	48463158	-	1	NA	promoter-TSS (NM_019680)	promoter-TSS (NM_019680)	-4	NM_019680	56501	Mm.36808	NM_019680	ENSMUSG00000031103	Elf4	AV314029|BC042423|ENSMUSG00000053512|Gm9907|Mef	E74-like factor 4 (ets domain transcription factor)	protein-coding
mm_160351.1	chr8	21162279	21162279	+	1	NA	promoter-TSS (NM_207658)	promoter-TSS (NM_207658)	2	NM_207658	382059	Mm.42715	NM_207658	ENSMUSG00000074443	Defa22	Defcr22	defensin, alpha, 22	protein-coding
mm_84741.1	chr9	75387469	75387489	-	1	NA	3' UTR (NM_015806, exon 6 of 6)	3' UTR (NM_015806, exon 6 of 6)	21880	NM_027418	50772	Mm.480076	NM_015806	ENSMUSG00000042688	Mapk6	2610021I23Rik|D130053K17Rik|Erk3|Mapk4|Mapk63|Prkm4|Prkm6	mitogen-activated protein kinase 6	protein-coding
mm_36121.1	chr4	58912250	58912276	-	1	NA	intron (NM_172381, intron 1 of 48)	CpG	462	NM_172381	230249	Mm.234801	NM_172381	ENSMUSG00000050812	AI314180	AW558785|BB181316|mKIAA0368	expressed sequence AI314180	protein-coding
mm_79296.1	chr9	51656863	51656863	+	1	NA	Intergenic	Lx6|LINE|L1	-108489	NM_175535	244867	Mm.400352	NM_175535	ENSMUSG00000053199	Arhgap20	6530403F17Rik|A530023E23Rik|RARhoGAP|mKIAA1391	Rho GTPase activating protein 20	protein-coding
mm_119619.1	chr14	51128931	51128947	+	1	NA	promoter-TSS (NM_030098)	promoter-TSS (NM_030098)	-129	NM_030098	78416	Mm.103835	NM_030098	ENSMUSG00000021880	Rnase6	9530043P15Rik|BB119466	ribonuclease, RNase A family, 6	protein-coding
mm_6587.1	chr1	75256824	75256847	-	1	NA	intron (NM_008985, intron 8 of 22)	intron (NM_008985, intron 8 of 22)	7373	NM_008985	19275	Mm.2902	NM_008985	ENSMUSG00000026204	Ptprn	IA-2|mIA-A|mKIAA4064	protein tyrosine phosphatase, receptor type, N	protein-coding
mm_9760.1	chr1	180850861	180850864	-	1	NA	promoter-TSS (NM_145943)	promoter-TSS (NM_145943)	-289	NM_145943	208768	Mm.272625	NM_145943	ENSMUSG00000038806	Sde2	-	SDE2 telomere maintenance homolog (S. pombe)	protein-coding
mm_18232.1	chr2	51934944	51935015	-	1	NA	promoter-TSS (NM_001141981)	promoter-TSS (NM_001141981)	30	NM_030243	71684	Mm.28309	NM_030243	ENSMUSG00000036249	Rbm43	0610033I05Rik	RNA binding motif protein 43	protein-coding
mm_89473.1	chr10	93516926	93516945	+	1	NA	TTS (NM_010401)	TTS (NM_010401)	23098	NM_027908	71761	Mm.244518	NM_027908	ENSMUSG00000015890	Amdhd1	1300019J08Rik	amidohydrolase domain containing 1	protein-coding
mm_15944.1	chr2	165875028	165875049	+	1	NA	intron (NM_027230, intron 2 of 23)	intron (NM_027230, intron 2 of 23)	3399	NM_001291158	228880	Mm.227598	NM_027230	ENSMUSG00000039671	Zmynd8	1110013E22Rik|2010005I16Rik|3632413B07Rik|AI316811|AL024039|Prkcbp1|RACK7	zinc finger, MYND-type containing 8	protein-coding
mm_166116.1	chr4	150139329	150139343	+	1	NA	intron (NM_019741, intron 7 of 13)	intron (NM_019741, intron 7 of 13)	-9636	NM_001085529	435818	Mm.359648	NM_001085529	ENSMUSG00000062064	Slc2a7	OTTMUSG00000010396	solute carrier family 2 (facilitated glucose transporter), member 7	protein-coding
mm_19076.1	chr2	77816880	77816931	-	1	NA	promoter-TSS (NM_178723)	promoter-TSS (NM_178723)	-89	NM_178723	241494	Mm.490320	NM_178723	ENSMUSG00000027016	Zfp385b	B830010L13Rik|C130013B13Rik|Zfp533|Znf385b	zinc finger protein 385B	protein-coding
mm_154729.1	chrX	9442547	9442568	+	1	NA	exon (NM_007807, exon 11 of 13)	exon (NM_007807, exon 11 of 13)	26767	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_81399.1	chr9	109007885	109007916	+	1	NA	intron (NM_173019, intron 6 of 13)	intron (NM_173019, intron 6 of 13)	15998	NM_173019	270198	Mm.132391	NM_173019	ENSMUSG00000025648	Pfkfb4	C230090D14	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4	protein-coding
mm_79835.1	chr9	64806077	64806079	+	1	NA	Intergenic	Intergenic	-4933	NM_001162917	102442	Mm.222473	NM_176935	ENSMUSG00000053641	Dennd4a	AI115600|AI851943|F730015K02Rik	DENN/MADD domain containing 4A	protein-coding
mm_75582.1	chr8	61533534	61533554	-	1	NA	exon (NM_001293774, exon 5 of 12)	exon (NM_001293774, exon 5 of 12)	45810	NM_145595	234309	Mm.29059	NM_145595	ENSMUSG00000031641	Cbr4	A730083J17Rik|BC009118	carbonyl reductase 4	protein-coding
mm_18311.1	chr2	54085490	54085541	-	1	NA	promoter-TSS (NM_023396)	promoter-TSS (NM_023396)	37	NM_023396	67874	Mm.27086	NM_023396	ENSMUSG00000075334	Rprm	2410012A13Rik|Reprimo	reprimo, TP53 dependent G2 arrest mediator candidate	protein-coding
mm_86461.1	chr10	4387127	4387175	+	1	NA	intron (NM_001033466, intron 1 of 2)	CpG	957	NM_001033466	381990	Mm.262466	NM_001033466	ENSMUSG00000075327	Zbtb2	Gm1103	zinc finger and BTB domain containing 2	protein-coding
mm_20140.1	chr2	121413826	121413836	-	1	NA	promoter-TSS (NM_007952)	promoter-TSS (NM_007952)	-39	NM_153075	212670	Mm.384318	NM_153075	ENSMUSG00000033486	Catsper2	-	cation channel, sperm associated 2	protein-coding
mm_77526.1	chr8	122986847	122986850	-	1	NA	intron (NM_001081379, intron 1 of 12)	ID_B1|SINE|B4	55436	NR_037865	77087	Mm.31567	NM_001081379	ENSMUSG00000035569	Ankrd11	2410104C19Rik|3010027A04Rik|6330578C09Rik|9530048I21Rik|AA930108|Gm176|Yod	ankyrin repeat domain 11	protein-coding
mm_48273.1	chr5	137963043	137963056	-	1	NA	promoter-TSS (NM_080450)	promoter-TSS (NM_080450)	-90	NM_080450	118446	Mm.332771	NM_080450	ENSMUSG00000056966	Gjc3	Cx29|Gje1	gap junction protein, gamma 3	protein-coding
mm_172454.1	chr7	35647380	35647386	-	1	NA	promoter-TSS (NM_019746)	promoter-TSS (NM_019746)	99	NM_019746	56330	Mm.371609	NM_019746	ENSMUSG00000030417	Pdcd5	2200003D22Rik|AA408513|Tfar19	programmed cell death 5	protein-coding
mm_63141.1	chr7	123124641	123124681	+	1	NA	intron (NM_144925, intron 1 of 23)	intron (NM_144925, intron 1 of 23)	776	NM_144925	233833	Mm.102305	NM_144925	ENSMUSG00000052707	Tnrc6a	2010321I05Rik|3110054G10Rik|AW557223|CAGH26|D130023A07Rik|GW182|Tnrc6	trinucleotide repeat containing 6a	protein-coding
mm_131067.1	chr16	4639938	4639944	+	1	NA	promoter-TSS (NM_139307)	promoter-TSS (NM_139307)	-4	NM_139307	246154	Mm.482140	NM_139307	ENSMUSG00000039646	Vasn	2610528G05Rik|Atia|Slitl2	vasorin	protein-coding
mm_93494.1	chr10	112160305	112160313	-	1	NA	Intergenic	Intergenic	-3312	NM_001310675	353025	Mm.194428	NM_178278	ENSMUSG00000035694	Caps2	D630005B03Rik	calcyphosphine 2	protein-coding
mm_27794.1	chr3	75556925	75556939	-	1	NA	promoter-TSS (NM_009250)	promoter-TSS (NM_009250)	-80	NM_019745	56426	Mm.316473	NM_019745	ENSMUSG00000027835	Pdcd10	2410003B13Rik|Ccm3|Tfa15|Tfar15	programmed cell death 10	protein-coding
mm_75819.1	chr8	70439558	70439612	-	1	NA	promoter-TSS (NM_001004062)	promoter-TSS (NM_001004062)	-12	NM_001004062	382056	Mm.227767	NM_001004062	ENSMUSG00000003575	Crtc1	AI413414|Mect1|R74955|TORC1|mKIAA0616	CREB regulated transcription coactivator 1	protein-coding
mm_4495.1	chr1	173641442	173641454	+	1	NA	intron (NM_175026, intron 4 of 6)	MTD|LTR|ERVL-MaLR	10589	NM_175026	236312	Mm.447	NM_175026	ENSMUSG00000043263	Ifi209	4930422C14|AI447904|Ifix|Pyhin-1|Pyhin1	interferon activated gene 209	protein-coding
mm_139067.1	chr17	46623988	46624011	+	1	NA	intron (NM_175168, intron 1 of 19)	intron (NM_175168, intron 1 of 19)	5505	NM_175168	71461	Mm.181833	NM_175168	ENSMUSG00000023972	Ptk7	8430404F20Rik|chz|mPTK7/CCK4	PTK7 protein tyrosine kinase 7	protein-coding
mm_172732.1	chr8	78139880	78139882	-	1	NA	Intergenic	ERVB7_1-LTR_MM|LTR|ERVK	-73461	NM_183096	73301	Mm.61243	NM_183096	ENSMUSG00000037101	Ttc29	1700031F13Rik	tetratricopeptide repeat domain 29	protein-coding
mm_47809.1	chr5	133790809	133790815	-	1	NA	Intergenic	Intergenic	-308936	NM_030719	80909	Mm.45218	NM_030719	ENSMUSG00000015944	Gatsl2	7530428J21Rik|AW742413|Gats|Gatsl1	GATS protein-like 2	protein-coding
mm_162859.1	chr10	91040050	91040052	+	1	NA	intron (NM_009684, intron 14 of 26)	intron (NM_009684, intron 14 of 26)	42692	NM_001042558	11783	Mm.220289	NM_009684	ENSMUSG00000019979	Apaf1	6230400I06Rik|Apaf-1|Apaf1l|fog|mKIAA0413	apoptotic peptidase activating factor 1	protein-coding
mm_64715.1	chr7	4635374	4635381	-	1	NA	intron (NM_172894, intron 17 of 23)	intron (NM_172894, intron 17 of 23)	-4895	NM_023440	68255	Mm.389784	NM_023440	ENSMUSG00000045282	Tmem86b	C330014O21Rik	transmembrane protein 86B	protein-coding
mm_162592.1	chr1	181282035	181282040	+	1	NA	Intergenic	Intergenic	-70059	NM_145514	226757	Mm.289082	NM_145514	ENSMUSG00000038733	Wdr26	1600024A01Rik|AA693241|AI447817|AU044014|C77982|Gid7	WD repeat domain 26	protein-coding
mm_135140.1	chr16	35853731	35853765	-	1	NA	exon (NM_001039530, exon 7 of 17)	exon (NM_001039530, exon 7 of 17)	17634	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_107403.1	chr12	33374485	33374488	+	1	NA	intron (NR_131031, intron 2 of 3)	intron (NR_131031, intron 2 of 3)	20274	NR_131031	75836	Mm.410807	NR_131031	ENSMUSG00000085664	Atxn7l1os2	4930556N08Rik	ataxin 7-like 1, opposite strand 2	ncRNA
mm_142365.1	chr17	44105775	44105845	-	1	NA	promoter-TSS (NM_199016)	promoter-TSS (NM_199016)	-2	NM_199016	224794	Mm.255971	NM_199016	ENSMUSG00000023961	Enpp4	4933413N07Rik|AA986363|AI195364|E-NPP 4|Gm90|mKIAA0879	ectonucleotide pyrophosphatase/phosphodiesterase 4	protein-coding
mm_77014.1	chr8	107588393	107588463	-	1	NA	promoter-TSS (NM_010817)	promoter-TSS (NM_010817)	54	NM_010817	17463	Mm.18347	NM_010817	ENSMUSG00000039067	Psmd7	AW107203|Mov-34|Mov34	proteasome (prosome, macropain) 26S subunit, non-ATPase, 7	protein-coding
mm_13588.1	chr2	112455023	112455063	+	1	NA	promoter-TSS (NM_133749)	promoter-TSS (NM_133749)	18	NM_133749	73024	Mm.268027	NM_133749	ENSMUSG00000055943	Emc7	2900064A13Rik|AI451465|ORF3|c11orf3	ER membrane protein complex subunit 7	protein-coding
mm_34346.1	chr4	144522230	144522247	+	1	NA	exon (NM_198662, exon 2 of 4)	exon (NM_198662, exon 2 of 4)	2416	NM_198662	381572	Mm.184290	NM_198662	ENSMUSG00000028593	9430007A20Rik	Aadacl4|Gm1034	RIKEN cDNA 9430007A20 gene	protein-coding
mm_44358.1	chr5	17796988	17797000	-	1	NA	intron (NM_007643, intron 10 of 14)	intron (NM_007643, intron 10 of 14)	38902	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_114562.1	chr13	74406985	74407002	+	1	NA	promoter-TSS (NR_035409)	promoter-TSS (NR_035409)	-72	NR_035409	100124641		NR_035409	ENSMUSG00000076033	Mir692-3	Mir692-2b|Mirn692-2b|mmu-mir-692-3	microRNA 692-3	ncRNA
mm_61210.1	chr7	64185538	64185560	+	1	NA	promoter-TSS (NM_018752)	promoter-TSS (NM_018752)	90	NM_018752	17364	Mm.38875	NM_018752	ENSMUSG00000030523	Trpm1	4732499L03Rik|AI606771|Ltrpc1|Mlsn1	transient receptor potential cation channel, subfamily M, member 1	protein-coding
mm_154490.1	chrM	5929	5943	-	1	NA	NA	Intergenic	NA	NA								
mm_119715.1	chr14	53876689	53876713	+	1	NA	Intergenic	Intergenic	377228	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_90513.1	chr10	128042893	128042911	+	1	NA	exon (NM_001113199, exon 3 of 9)	exon (NM_001113199, exon 3 of 9)	7556	NM_001113199	17938	Mm.3746	NM_013608	ENSMUSG00000061315	Naca	AL022831|AL024382|Gm1878|mKIAA0363|skNAC	nascent polypeptide-associated complex alpha polypeptide	protein-coding
mm_143654.1	chr17	79707500	79707519	-	1	NA	3' UTR (NM_009994, exon 3 of 3)	3' UTR (NM_009994, exon 3 of 3)	7532	NM_009994	13078	Mm.214016	NM_009994	ENSMUSG00000024087	Cyp1b1	CP1B|P4501b1	cytochrome P450, family 1, subfamily b, polypeptide 1	protein-coding
mm_98381.1	chr11	94133480	94133490	+	1	NA	Intergenic	Intergenic	-77969	NM_009427	22057	Mm.259673	NM_009427	ENSMUSG00000037573	Tob1	Tob|Trob	transducer of ErbB-2.1	protein-coding
mm_44151.1	chr5	150295383	150295433	+	1	NA	intron (NM_172887, intron 1 of 60)	intron (NM_172887, intron 1 of 60)	35478	NM_172887	320365	Mm.216590	NM_172887	ENSMUSG00000056602	Fry	13CDNA73|9330186A19Rik|AF346502|AI462658|C87180|D930046M03|cg003|mKIAA4143	FRY microtubule binding protein	protein-coding
mm_36180.1	chr4	62208540	62208561	-	1	NA	promoter-TSS (NM_009554)	promoter-TSS (NM_009554)	-4	NM_001290350	22696	Mm.5011	NM_009554	ENSMUSG00000028389	Zfp37	Tzn|Zfp-37	zinc finger protein 37	protein-coding
mm_79814.1	chr9	64179290	64179349	+	1	NA	promoter-TSS (NM_183316)	promoter-TSS (NM_183316)	22	NM_183316	330959	Mm.24082	NM_183316	ENSMUSG00000032398	Snapc5	2010103A03Rik	small nuclear RNA activating complex, polypeptide 5	protein-coding
mm_114954.1	chr13	96924705	96924730	+	1	NA	promoter-TSS (NM_001166065)	promoter-TSS (NM_001166065)	28	NM_001166065	218476	Mm.483490	NM_001166065	ENSMUSG00000091387	Gcnt4	C2gnt3|Gm279|Gm73	glucosaminyl (N-acetyl) transferase 4, core 2 (beta-1,6-N-acetylglucosaminyltransferase)	protein-coding
mm_13896.1	chr2	120450733	120450743	+	1	NA	intron (NM_172672, intron 18 of 23)	intron (NM_172672, intron 18 of 23)	-12855	NM_001177799	12335	Mm.458021	NM_007601	ENSMUSG00000079110	Capn3	AI323605|Capa-3|Capa3|Lp82|p94	calpain 3	protein-coding
mm_147553.1	chr18	54956744	54956754	-	1	NA	intron (NM_175751, intron 2 of 9)	intron (NM_175751, intron 2 of 9)	33431	NM_175751	269023	Mm.192984	NM_175751	ENSMUSG00000052713	Zfp608	4932417D18Rik|D430007A19Rik|Znf608	zinc finger protein 608	protein-coding
mm_15708.1	chr2	164017472	164017485	+	1	NA	3' UTR (NM_018753, exon 6 of 6)	3' UTR (NM_018753, exon 6 of 6)	-7746	NM_001114079	381404	Mm.82301	NM_001114079	ENSMUSG00000054582	Pabpc1l	1810053B01Rik|Epab	poly(A) binding protein, cytoplasmic 1-like	protein-coding
mm_146041.1	chr18	69592955	69592971	+	1	NA	intron (NM_013685, intron 8 of 19)	intron (NM_013685, intron 8 of 19)	247242	NM_001083967	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding
mm_50571.1	chr6	49051287	49051319	+	1	NA	intron (NM_053110, intron 8 of 10)	intron (NM_053110, intron 8 of 10)	14785	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_69502.1	chr7	134232126	134232144	-	1	NA	Intergenic	Intergenic	-7038	NM_007400	11489	Mm.439714	NM_007400	ENSMUSG00000054555	Adam12	Mltna	a disintegrin and metallopeptidase domain 12 (meltrin alpha)	protein-coding
mm_37490.1	chr4	123613757	123613768	-	1	NA	intron (NM_001199136, intron 1 of 97)	intron (NM_001199136, intron 1 of 97)	-2658	NR_105824	102465214		NR_105824	ENSMUSG00000099005	Mir6398	Gm27657|mmu-mir-6398	microRNA 6398	ncRNA
mm_39287.1	chr5	4005315	4005336	+	1	NA	intron (NM_194462, intron 18 of 47)	intron (NM_194462, intron 18 of 47)	77139	NM_194462	100986	Mm.46044	NM_194462	ENSMUSG00000040407	Akap9	5730481H23Rik|AKAP-9|AKAP450|AW545847|C79026|G1-448-15|PRKA9|mKIAA0803|mei2-5|repro12	A kinase (PRKA) anchor protein (yotiao) 9	protein-coding
mm_167844.1	chrM	14408	14424	-	1	NA	NA	Intergenic	NA	NA								
mm_59211.1	chr7	24531412	24531423	+	1	NA	exon (NM_153134, exon 2 of 3)	exon (NM_153134, exon 2 of 3)	769	NM_153134	210146	Mm.41108	NM_153134	ENSMUSG00000041037	Irgq	AF322649|FKSG27|Irgq1	immunity-related GTPase family, Q	protein-coding
mm_41771.1	chr5	103501591	103501601	+	1	NA	exon (NM_011204, exon 7 of 48)	exon (NM_011204, exon 7 of 48)	76404	NM_011204	19249	Mm.3414	NM_011204	ENSMUSG00000034573	Ptpn13	AI324989|PTP-BL|PTPL1|Ptpri|RIP	protein tyrosine phosphatase, non-receptor type 13	protein-coding
mm_61213.1	chr7	64287470	64287503	+	1	NA	promoter-TSS (NM_172742)	promoter-TSS (NM_172742)	-184	NM_172742	233315	Mm.214959	NM_172742	ENSMUSG00000030522	Mtmr10	BB128963|C79734	myotubularin related protein 10	protein-coding
mm_112433.1	chr13	4574076	4574088	+	1	NA	promoter-TSS (NM_029901)	promoter-TSS (NM_029901)	7	NM_029901	77337	Mm.27085	NM_029901	ENSMUSG00000021207	Akr1c21	9430025F20Rik|AI315367	aldo-keto reductase family 1, member C21	protein-coding
mm_144683.1	chr18	34768279	34768287	+	1	NA	exon (NM_175104, exon 4 of 5)	exon (NM_175104, exon 4 of 5)	-8725	NM_001081256	277250	Mm.277906	NM_029518	ENSMUSG00000038773	Kdm3b	5830462I21Rik|JHDM2B|Jmjd1b|mKIAA1082	KDM3B lysine (K)-specific demethylase 3B	protein-coding
mm_170854.1	chr2	180225884	180225884	-	1	NA	promoter-TSS (NM_001081171)	promoter-TSS (NM_001081171)	-25	NM_001081171	16776	Mm.4339	NM_001081171	ENSMUSG00000015647	Lama5	AA408760|AA408762|AI853660|[a]5|laminin-511|mKIAA0533	laminin, alpha 5	protein-coding
mm_85734.1	chr9	108452751	108452803	-	1	NA	intron (NM_030075, intron 5 of 10)	intron (NM_030075, intron 5 of 10)	-7741	NM_133744	72454	Mm.46488	NM_133744	ENSMUSG00000049305	Ccdc71	2600016J21Rik	coiled-coil domain containing 71	protein-coding
mm_38733.1	chr4	145245068	145245090	-	1	NA	intron (NM_011610, intron 1 of 9)	intron (NM_011610, intron 1 of 9)	1791	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_119117.1	chr14	31030641	31030645	+	1	NA	intron (NM_001081251, intron 4 of 32)	intron (NM_001081251, intron 4 of 32)	11505	NM_001081251	66923	Mm.27913	NM_025847	ENSMUSG00000042323	Pbrm1	2610016F04Rik|AI507524|BAF180|Pb1	polybromo 1	protein-coding
mm_87337.1	chr10	43478623	43478651	+	1	NA	promoter-TSS (NM_199028)	promoter-TSS (NM_199028)	-503	NM_199028	331623	Mm.490388	NM_199028	ENSMUSG00000038214	Bend3	mKIAA1553	BEN domain containing 3	protein-coding
mm_145913.1	chr18	66475624	66475642	+	1	NA	Intergenic	Intergenic	17029	NM_021451	58801	Mm.271878	NM_021451	ENSMUSG00000024521	Pmaip1	Noxa	phorbol-12-myristate-13-acetate-induced protein 1	protein-coding
mm_78398.1	chr9	28920475	28920482	+	1	NA	3' UTR (NM_177906, exon 8 of 8)	3' UTR (NM_177906, exon 8 of 8)	1042651	NM_172290	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding
mm_87995.1	chr10	66698257	66698265	+	1	NA	Intergenic	Intergenic	222123	NR_138560	68488	Mm.338835	NR_138560		1110002J07Rik	-	RIKEN cDNA 1110002J07 gene	ncRNA
mm_60667.1	chr7	45017916	45017931	+	1	NA	promoter-TSS (NM_009101)	promoter-TSS (NM_009101)	-84	NM_009101	20130	Mm.389894	NM_009101	ENSMUSG00000038387	Rras	AI573426	related RAS viral (r-ras) oncogene	protein-coding
mm_62790.1	chr7	112679402	112679422	+	1	NA	promoter-TSS (NM_001166584)	promoter-TSS (NM_001166584)	92	NM_009346	21676	Mm.24685	NM_009346	ENSMUSG00000055320	Tead1	2610024B07Rik|B230114H05Rik|Gtrgeo5|TEAD-1|TEF-1|Tcf13|mTEF-1	TEA domain family member 1	protein-coding
mm_119875.1	chr14	54723954	54723965	+	1	NA	3' UTR (NM_016972, exon 11 of 11)	3' UTR (NM_016972, exon 11 of 11)	-11785	NM_207131	110794	Mm.236223	NM_207131	ENSMUSG00000052435	Cebpe	C/EBPe|CRP1|Gm294	CCAAT/enhancer binding protein (C/EBP), epsilon	protein-coding
mm_20099.1	chr2	121036696	121036735	-	1	NA	5' UTR (NM_013513, exon 1 of 13)	5' UTR (NM_013513, exon 1 of 13)	162	NM_013513	13828	Mm.240051	NM_013513	ENSMUSG00000023216	Epb42	Epb4.2	erythrocyte membrane protein band 4.2	protein-coding
mm_74028.1	chr8	121730588	121730589	+	1	NA	promoter-TSS (NM_020605)	promoter-TSS (NM_020605)	29	NM_020605	57340	Mm.306870	NM_020605	ENSMUSG00000025318	Jph3	JP-3|Jp3	junctophilin 3	protein-coding
mm_27739.1	chr3	69093558	69093574	-	1	NA	intron (NM_008467, intron 7 of 16)	intron (NM_008467, intron 7 of 16)	33526	NM_008467	16649	Mm.30601	NM_008467	ENSMUSG00000027782	Kpna4	1110058D08Rik|IPOA3	karyopherin (importin) alpha 4	protein-coding
mm_147957.1	chr18	67057232	67057235	-	1	NA	Intergenic	Intergenic	-31065	NM_177137	14680	Mm.440746	NM_010307	ENSMUSG00000024524	Gnal	2610011C15Rik|9630020G10Rik|Galphaolf|Gna10|Golf	guanine nucleotide binding protein, alpha stimulating, olfactory type	protein-coding
mm_5241.1	chr1	16104397	16104435	-	1	NA	promoter-TSS (NM_011291)	promoter-TSS (NM_011291)	17	NM_011291	19989	Mm.319659	NM_011291	ENSMUSG00000043716	Rpl7	Rpl7a|Surf-3	ribosomal protein L7	protein-coding
mm_50042.1	chr6	41151151	41151161	+	1	NA	Intergenic	Lx2A1|LINE|L1	-115647	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_885.1	chr1	52637509	52637513	+	1	NA	intron (NR_024590, intron 2 of 8)	intron (NR_024590, intron 2 of 8)	6806	NM_001142647	227094	Mm.83541	NM_172654	ENSMUSG00000043015	Nemp2	5330401P04Rik|9830163O08|Tmem194b	nuclear envelope integral membrane protein 2	protein-coding
mm_17215.1	chr2	25493467	25493479	-	1	NA	intron (NM_029958, intron 1 of 5)	intron (NM_029958, intron 1 of 5)	438	NM_029958	77701	Mm.99123	NM_029958	ENSMUSG00000026943	Lcn12	9230102M18Rik	lipocalin 12	protein-coding
mm_110596.1	chr12	56535192	56535207	-	1	NA	intron (NM_009385, intron 1 of 2)	CpG-3195	1709	NM_009385	21869	Mm.89972	NM_009385	ENSMUSG00000001496	Nkx2-1	AV026640|Nkx2.1|T/EBP|Titf1|Ttf-1	NK2 homeobox 1	protein-coding
mm_78700.1	chr9	41217201	41217244	+	1	NA	intron (NR_040392, intron 3 of 4)	ORR1F|LTR|ERVL-MaLR	11067	NR_040392	78500	Mm.275715	NR_040392	ENSMUSG00000100837	1700063D05Rik	-	RIKEN cDNA 1700063D05 gene	ncRNA
mm_140003.1	chr17	73069439	73069443	+	1	NA	Intergenic	RLTR12E|LTR|ERVK	-38544	NM_001177968	225010	Mm.329194	NM_001081071	ENSMUSG00000054469	Lclat1	AI181996|Agpat8|Alcat1|Gm91|Lycat	lysocardiolipin acyltransferase 1	protein-coding
mm_150162.1	chr19	32387575	32387585	+	1	NA	intron (NM_144792, intron 1 of 9)	CpG	874	NM_144792	208449	Mm.329810	NM_144792	ENSMUSG00000040451	Sgms1	9530058O11Rik|AI841905|C80702|Mob|Sms1|Sor1|Tmem23	sphingomyelin synthase 1	protein-coding
mm_85207.1	chr9	96787844	96787850	-	1	NA	Intergenic	Intergenic	22285	NR_102296	319707	Mm.392191	NR_102293	ENSMUSG00000101581	C430002N11Rik	-	RIKEN cDNA C430002N11 gene	ncRNA
mm_58789.1	chr7	16130253	16130269	+	1	NA	5' UTR (NM_148946, exon 1 of 10)	5' UTR (NM_148946, exon 1 of 10)	435	NM_148946	110891	Mm.241147	NM_148946	ENSMUSG00000030376	Slc8a2	Ncx2	solute carrier family 8 (sodium/calcium exchanger), member 2	protein-coding
mm_137748.1	chr17	29393860	29393888	+	1	NA	Intergenic	Intergenic	32960	NM_001159538	26382	Mm.279187	NM_013710	ENSMUSG00000024013	Fgd2	Tcd-2|Tcd2|ZFYVE4|tcs-2|tcs2	FYVE, RhoGEF and PH domain containing 2	protein-coding
mm_109990.1	chr12	15050396	15050407	-	1	NA	promoter-TSS (NR_045960)	promoter-TSS (NR_045960)	-12	NR_045960	73972	Mm.107680	NR_045960		4930448C13Rik	-	RIKEN cDNA 4930448C13 gene	ncRNA
mm_71840.1	chr8	68904692	68904710	+	1	NA	3' UTR (NM_008509, exon 10 of 10)	3' UTR (NM_008509, exon 10 of 10)	24146	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_23842.1	chr3	82380155	82380171	+	1	NA	exon (NM_001081230, exon 9 of 14)	exon (NM_001081230, exon 9 of 14)	22091	NM_001081230	213582	Mm.271269	NM_001081230	ENSMUSG00000033900	Map9	5033421J10Rik|5330427D05Rik|ASAP|Mtap9	microtubule-associated protein 9	protein-coding
mm_137034.1	chr17	17890589	17890600	+	1	NA	intron (NM_008039, intron 1 of 1)	RMER15|LTR|ERVL	2770	NM_008039	14289	Mm.378918	NM_008039	ENSMUSG00000052270	Fpr2	E330010I07Rik|Fpr-rs2	formyl peptide receptor 2	protein-coding
mm_155622.1	chrX	83591938	83591943	+	1	NA	intron (NM_007868, intron 7 of 78)	HAL1b|LINE|L1	-104016	NM_021898	100502723	Mm.383210	NM_021898	ENSMUSG00000035522	Tsga8	Halap-X|Halapx	testis specific gene A8	protein-coding
mm_106388.1	chr11	118569688	118569732	-	1	NA	intron (NM_001285436, intron 3 of 13)	CpG	92750	NM_172573	217364	Mm.473963	NM_172573	ENSMUSG00000033857	Engase	C130099A03|D230014K01Rik	endo-beta-N-acetylglucosaminidase	protein-coding
mm_118096.1	chr13	103899573	103899599	-	1	NA	intron (NM_001005868, intron 1 of 26)	intron (NM_001005868, intron 1 of 26)	21000	NM_001289473	59079	Mm.277354	NM_021563	ENSMUSG00000021709	Erbin	1700028E05Rik|Erbb2ip|mKIAA1225	Erbb2 interacting protein	protein-coding
mm_50111.1	chr6	41533819	41533835	+	1	NA	Intergenic	Intergenic	12051	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_71749.1	chr8	65209195	65209206	+	1	NA	Intergenic	RLTR9A3A|LTR|ERVK	-79663	NR_033217	407795	Mm.387876	NR_033217	ENSMUSG00000074300	BC030870	-	cDNA sequence BC030870	ncRNA
mm_168340.1	chr11	120347211	120347212	-	1	NA	TTS (NR_105900)	TTS (NR_105900)	202	NR_105900	102465564		NR_105900	ENSMUSG00000098955	Mir6935	Gm27344|mmu-mir-6935	microRNA 6935	ncRNA
mm_35179.1	chr4	15149756	15149773	-	1	NA	promoter-TSS (NM_178617)	promoter-TSS (NM_178617)	-633	NM_178617	69352	Mm.389031	NM_178617	ENSMUSG00000040536	Necab1	1700003H21Rik|Efcbp1|STIP-1	N-terminal EF-hand calcium binding protein 1	protein-coding
mm_124760.1	chr15	6647640	6647651	+	1	NA	intron (NM_011815, intron 12 of 17)	intron (NM_011815, intron 12 of 17)	-60736	NM_030168	78757	Mm.275811	NM_030168	ENSMUSG00000050310	Rictor	4921505C17Rik|6030405M08Rik|AVO3|AW492497|D530039E11Rik	RPTOR independent companion of MTOR, complex 2	protein-coding
mm_78227.1	chr9	21588896	21588910	+	1	NA	non-coding (NR_038062, exon 9 of 9)	non-coding (NR_038062, exon 9 of 9)	-3819	NM_178619	69773	Mm.39704	NM_178619	ENSMUSG00000048429	Timm29	1810026J23Rik	translocase of inner mitochondrial membrane 29	protein-coding
mm_120026.1	chr14	55824862	55824889	+	1	NA	promoter-TSS (NM_001168346)	promoter-TSS (NM_001168346)	80	NM_023699	73181	Mm.27908	NM_023699	ENSMUSG00000023411	Nfatc4	3110041H08Rik|AW107667|AW546455|Nfat3	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 4	protein-coding
mm_141755.1	chr17	34263048	34263056	-	1	NA	promoter-TSS (NM_207105)	promoter-TSS (NM_207105)	-175	NM_207105	14961	Mm.254067	NM_207105	ENSMUSG00000073421	H2-Ab1	AI845868|Abeta|H-2Ab|H2-Ab|I-Abeta|IAb|Ia-2|Ia2|Rmcs1	histocompatibility 2, class II antigen A, beta 1	protein-coding
mm_161455.1	chr15	75747698	75747698	-	1	NA	exon (NM_194350, exon 1 of 1)	exon (NM_194350, exon 1 of 1)	224	NM_194350	378435	Mm.309589	NM_194350	ENSMUSG00000047591	Mafa	RIPE3b1	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein A (avian)	protein-coding
mm_2227.1	chr1	90858007	90858018	+	1	NA	Intergenic	Intergenic	-14041	NM_001243008	12835	Mm.7562	NM_009935	ENSMUSG00000048126	Col6a3	AI507288|Col6a-3	collagen, type VI, alpha 3	protein-coding
mm_129609.1	chr15	79932717	79932782	-	1	NA	promoter-TSS (NM_144811)	promoter-TSS (NM_144811)	-103	NM_144811	52609	Mm.323442	NM_144811	ENSMUSG00000053411	Cbx7	1600014J01Rik|AI851678|D15Ertd417e	chromobox 7	protein-coding
mm_94008.1	chr10	127620943	127620943	-	1	NA	5' UTR (NM_008512, exon 1 of 89)	5' UTR (NM_008512, exon 1 of 89)	205	NM_008512	16971	Mm.271854	NM_008512	ENSMUSG00000040249	Lrp1	A2mr|AI316852|CD91|Lrp|b2b1554Clo	low density lipoprotein receptor-related protein 1	protein-coding
mm_46222.1	chr5	98943823	98943840	-	1	NA	intron (NM_008926, intron 15 of 18)	intron (NM_008926, intron 15 of 18)	89416	NM_001310677	110075	Mm.136461	NM_173404	ENSMUSG00000029335	Bmp3	9530029I04Rik	bone morphogenetic protein 3	protein-coding
mm_23062.1	chr3	35932884	35932915	+	1	NA	promoter-TSS (NM_001205362)	promoter-TSS (NM_001205362)	67	NM_001205361	114893	Mm.374810	NM_033623	ENSMUSG00000027708	Dcun1d1	Rp42|SCCRO|Tes3|pTes3	DCN1, defective in cullin neddylation 1, domain containing 1 (S. cerevisiae)	protein-coding
mm_86057.1	chr9	114564339	114564349	-	1	NA	promoter-TSS (NM_001042503)	promoter-TSS (NM_001042503)	25	NM_001042503	636931	Mm.17857	NM_001042503	ENSMUSG00000079259	Trim71	2610206G21Rik|AL022943|Gm1127|Lin41|lin-41|mLin41|mlin-41	tripartite motif-containing 71	protein-coding
mm_43417.1	chr5	135984206	135984216	+	1	NA	exon (NM_011776, exon 3 of 8)	exon (NM_011776, exon 3 of 8)	4106	NM_011776	22788	Mm.1381	NM_011776	ENSMUSG00000004948	Zp3	Zp-3	zona pellucida glycoprotein 3	protein-coding
mm_62286.1	chr7	99906327	99906353	+	1	NA	intron (NM_001164258, intron 11 of 18)	intron (NM_001164258, intron 11 of 18)	47122	NM_001164258	446101	Mm.440757	NM_001164258	ENSMUSG00000035211	Xrra1	AI449753	X-ray radiation resistance associated 1	protein-coding
mm_3386.1	chr1	140245711	140245732	+	1	NA	promoter-TSS (NM_001081027)	promoter-TSS (NM_001081027)	-536	NM_001081027	240776	Mm.483845	NM_001081027	ENSMUSG00000052726	Kcnt2	E330038N15Rik|Slick	potassium channel, subfamily T, member 2	protein-coding
mm_26881.1	chr3	17785608	17785616	-	1	NA	Intergenic	Intergenic	-4309	NR_033490	70441	Mm.458192	NR_033490	ENSMUSG00000100252	Mir124-2hg	100040120|2610100L16Rik|6430547I21Rik|A930005K07Rik|AW125202|Gm2612	Mir124-2 host gene (non-protein coding)	ncRNA
mm_159601.1	chr4	128618510	128618510	-	1	NA	5' UTR (NM_205823, exon 1 of 1)	5' UTR (NM_205823, exon 1 of 1)	109	NM_205823	384059	Mm.331901	NM_205823	ENSMUSG00000062545	Tlr12	Gm1365|Tlr11	toll-like receptor 12	protein-coding
mm_118956.1	chr14	27379667	27379682	+	1	NA	exon (NM_027871, exon 4 of 11)	exon (NM_027871, exon 4 of 11)	18285	NM_001289688	71704	Mm.248606	NM_027871	ENSMUSG00000021895	Arhgef3	1200004I24Rik|9830169H03Rik|C76747|Xpln	Rho guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_18553.1	chr2	65171796	65171809	-	1	NA	intron (NM_027225, intron 1 of 12)	GA-rich|Low_complexity|Low_complexity	66824	NM_177025	319876	Mm.34159	NM_027225	ENSMUSG00000034903	Cobll1	1810047P18Rik|Coblr1|D430044D16Rik	Cobl-like 1	protein-coding
mm_133741.1	chr16	94010861	94010884	+	1	NA	Intergenic	Intergenic	-2035	NM_019500	56173	Mm.328716	NM_019500	ENSMUSG00000047109	Cldn14	AI851731	claudin 14	protein-coding
mm_98812.1	chr11	97188555	97188580	+	1	NA	promoter-TSS (NM_008379)	promoter-TSS (NM_008379)	-675	NM_008379	16211	Mm.251013	NM_008379	ENSMUSG00000001440	Kpnb1	AA409963|IPOB|Impnb	karyopherin (importin) beta 1	protein-coding
mm_146853.1	chr18	24112090	24112108	-	1	NA	intron (NM_172625, intron 3 of 4)	intron (NM_172625, intron 3 of 4)	9720	NM_172625	225280	Mm.258973	NM_172625	ENSMUSG00000047989	Ino80c	D030070L09Rik	INO80 complex subunit C	protein-coding
mm_151389.1	chr19	56397232	56397265	+	1	NA	5' UTR (NM_007611, exon 1 of 7)	5' UTR (NM_007611, exon 1 of 7)	119	NM_007611	12369	Mm.35687	NM_007611	ENSMUSG00000025076	Casp7	AI314680|CMH-1|ICE-IAP3|Mch3|caspase-7|mCASP-7	caspase 7	protein-coding
mm_59335.1	chr7	25452090	25452118	+	1	NA	intron (NR_015569, intron 4 of 6)	MIR|SINE|MIR	25521	NM_001039185	26365	Mm.322502	NM_011926	ENSMUSG00000074272	Ceacam1	Bgp|Bgp1|C-CAM|CD66a|Cc1|Cea-1|Cea-7|Cea1|Cea7|Hv-2|Hv2|MHVR|MHVR1|Mhv-1|bb-1|mCEA1|mmCGM1|mmCGM1a|mmCGM2	carcinoembryonic antigen-related cell adhesion molecule 1	protein-coding
mm_90592.1	chr10	128278772	128278788	+	1	NA	exon (NM_019963, exon 8 of 24)	exon (NM_019963, exon 8 of 24)	8204	NM_019963	20847	Mm.293120	NM_019963	ENSMUSG00000040033	Stat2	1600010G07Rik|AW496480	signal transducer and activator of transcription 2	protein-coding
mm_10598.1	chr2	18677106	18677118	+	1	NA	promoter-TSS (NM_007552)	promoter-TSS (NM_007552)	94	NM_007552	12151	Mm.289584	NM_007552	ENSMUSG00000026739	Bmi1	AW546694|Bmi-1|Pcgf4	Bmi1 polycomb ring finger oncogene	protein-coding
mm_131338.1	chr16	13358456	13358469	+	1	NA	promoter-TSS (NM_153588)	promoter-TSS (NM_153588)	41	NM_153588	239719	Mm.270643	NM_153588	ENSMUSG00000009569	Mkl2	ENSMUSG00000075401|Gt4-1|MRTF-B|Mrtfb|mKIAA1243	MKL/myocardin-like 2	protein-coding
mm_90919.1	chr10	12614561	12614572	-	1	NA	intron (NM_011682, intron 50 of 73)	intron (NM_011682, intron 50 of 73)	247169	NM_011682	22288	Mm.331784	NM_011682	ENSMUSG00000019820	Utrn	AA589569|DRP|Dmdl	utrophin	protein-coding
mm_53303.1	chr6	129180640	129180656	+	1	NA	promoter-TSS (NM_053109)	promoter-TSS (NM_053109)	33	NM_053109	93694	Mm.197536	NM_053109	ENSMUSG00000030157	Clec2d	Clr-b|Clrb|Ocil	C-type lectin domain family 2, member d	protein-coding
mm_110225.1	chr12	28635915	28635952	-	1	NA	promoter-TSS (NM_011300)	promoter-TSS (NM_011300)	20	NM_011300	20115	Mm.279839	NM_011300	ENSMUSG00000061477	Rps7	Mtu|Rps7A|S7	ribosomal protein S7	protein-coding
mm_13564.1	chr2	112266395	112266404	+	1	NA	promoter-TSS (NM_133649)	promoter-TSS (NM_133649)	85	NM_133649	107723	Mm.491155	NM_133648	ENSMUSG00000027130	Slc12a6	9530023I19Rik|KCC3|gaxp	solute carrier family 12, member 6	protein-coding
mm_81580.1	chr9	110422491	110422506	+	1	NA	3' UTR (NM_008694, exon 4 of 4)	3' UTR (NM_008694, exon 4 of 4)	2690	NM_008694	18054	Mm.236225	NM_008694	ENSMUSG00000032484	Ngp	bectenecin	neutrophilic granule protein	protein-coding
mm_69201.1	chr7	127387133	127387151	-	1	NA	promoter-TSS (NM_030226)	promoter-TSS (NM_030226)	24	NM_030226	78921	Mm.200950	NM_030226	ENSMUSG00000030823	9130019O22Rik	-	RIKEN cDNA 9130019O22 gene	protein-coding
mm_72596.1	chr8	84414656	84414671	+	1	NA	promoter-TSS (NM_001252060)	promoter-TSS (NM_001252060)	-701	NM_001252060	12286	Mm.334658	NM_007578	ENSMUSG00000034656	Cacna1a	APCA|BI|Caca1a|Cacnl1a4|Cav2.1|Ccha1a|EA2|FHM|HPCA|MHP|MHP1|SCA6|alpha1A|la|nmf352|rkr|smrl|tg	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	protein-coding
mm_103282.1	chr11	72214986	72215020	-	1	NA	promoter-TSS (NM_001163728)	promoter-TSS (NM_001163728)	-135	NM_001163728	75304	Mm.340776	NM_001163728		4930563E22Rik	-	RIKEN cDNA 4930563E22 gene	protein-coding
mm_45758.1	chr5	86890120	86890149	-	1	NA	3' UTR (NM_153598, exon 6 of 6)	3' UTR (NM_153598, exon 6 of 6)	16803	NM_153598	100727	Mm.281844	NM_153598	ENSMUSG00000029260	Ugt2b34	AI788959	UDP glucuronosyltransferase 2 family, polypeptide B34	protein-coding
mm_22287.1	chr2	180225813	180225872	-	1	NA	promoter-TSS (NM_001081171)	promoter-TSS (NM_001081171)	17	NM_001081171	16776	Mm.4339	NM_001081171	ENSMUSG00000015647	Lama5	AA408760|AA408762|AI853660|[a]5|laminin-511|mKIAA0533	laminin, alpha 5	protein-coding
mm_27054.1	chr3	27316981	27317000	-	1	NA	promoter-TSS (NM_009425)	promoter-TSS (NM_009425)	-87	NM_009425	22035	Mm.1062	NM_009425	ENSMUSG00000039304	Tnfsf10	A330042I21Rik|AI448571|APO-2L|Ly81|TL2|Tnlg6a|Trail	tumor necrosis factor (ligand) superfamily, member 10	protein-coding
mm_49131.1	chr6	8948428	8948438	+	1	NA	Intergenic	Intergenic	-1586	NM_008751	18231	Mm.46954	NM_008751	ENSMUSG00000046178	Nxph1	C130005L03Rik	neurexophilin 1	protein-coding
mm_7593.1	chr1	125435745	125435753	-	1	NA	promoter-TSS (NM_023735)	promoter-TSS (NM_023735)	-22	NM_001205386	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding
mm_6123.1	chr1	64302981	64302990	-	1	NA	Intergenic	Intergenic	-181596	NM_033563	93691	Mm.29466	NM_033563	ENSMUSG00000025959	Klf7	9830124P08Rik	Kruppel-like factor 7 (ubiquitous)	protein-coding
mm_75127.1	chr8	34918494	34918502	-	1	NA	intron (NM_175091, intron 2 of 26)	intron (NM_175091, intron 2 of 26)	47192	NM_175091	21951	Mm.88364	NM_175091	ENSMUSG00000031529	Tnks	4930554K12Rik|AI662855|ARTD5|C86528|D130072O21Rik|TANK1|mTNKS1	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase	protein-coding
mm_61748.1	chr7	82679035	82679038	+	1	NA	intron (NM_175317, intron 7 of 19)	intron (NM_175317, intron 7 of 19)	30422	NM_175317	101592	Mm.238020	NM_175317	ENSMUSG00000038563	Efl1	4932434J20Rik|6030468D11Rik|AI451340|AU019507|AU022896|D7Ertd791e|Eftud1	elongation factor like GPTase 1	protein-coding
mm_152305.1	chr19	9135037	9135051	-	1	NA	intron (NM_025610, intron 1 of 6)	intron (NM_025610, intron 1 of 6)	522	NM_025610	66514	Mm.272847	NM_025610	ENSMUSG00000024654	Asrgl1	2410004D18Rik|ALP|ALP1|AU040643|AW060375	asparaginase like 1	protein-coding
mm_130577.1	chr15	99521234	99521257	-	1	NA	exon (NM_028224, exon 3 of 12)	exon (NM_028224, exon 3 of 12)	6920	NM_028224	72393	Mm.39760	NM_028224	ENSMUSG00000023011	Faim2	2900002L20Rik|Lfg|Lfg2|NMP25|Nmp35|Tmbim2	Fas apoptotic inhibitory molecule 2	protein-coding
mm_76969.1	chr8	106281045	106281058	-	1	NA	intron (NM_021491, intron 2 of 8)	intron (NM_021491, intron 2 of 8)	-1178	NR_126091	75044	Mm.445896	NR_126090		4930506A18Rik	-	RIKEN cDNA 4930506A18 gene	ncRNA
mm_109591.1	chr12	112632552	112632574	+	1	NA	intron (NM_007421, intron 3 of 12)	intron (NM_007421, intron 3 of 12)	-12265	NM_001161737	30954	Mm.289812	NM_013929	ENSMUSG00000064326	Siva1	CD27bp|Siva	SIVA1, apoptosis-inducing factor	protein-coding
mm_30132.1	chr3	142144758	142144771	-	1	NA	intron (NM_001277216, intron 1 of 11)	intron (NM_001277216, intron 1 of 11)	24464	NM_001277217	12167	Mm.39089	NM_007560	ENSMUSG00000052430	Bmpr1b	AI385617|ALK-6|AV355320|Acvrlk6|Alk6|BMPR-1B|BMPR-IB|CFK-43a|SKR6	bone morphogenetic protein receptor, type 1B	protein-coding
mm_159586.1	chr4	121622127	121622127	-	1	NA	promoter-TSS (NM_001099309)	promoter-TSS (NM_001099309)	-2	NM_001099309	666927	Mm.465133	NM_001099309	ENSMUSG00000078575	Gm12887	OTTMUSG00000008910	predicted gene 12887	protein-coding
mm_171910.1	chr5	52317379	52317379	+	1	NA	Intergenic	RMER20C_Mm|LTR|ERVK	-46425	NM_011435	20657	Mm.2407	NM_011435	ENSMUSG00000072941	Sod3	AI314465|EC-SOD	superoxide dismutase 3, extracellular	protein-coding
mm_132236.1	chr16	32750634	32750648	+	1	NA	exon (NM_080457, exon 2 of 27)	exon (NM_080457, exon 2 of 27)	14755	NM_080457	140474	Mm.214599	NM_080457	ENSMUSG00000079620	Muc4	4933405I11Rik|Asgp	mucin 4	protein-coding
mm_153500.1	chr19	41333030	41333040	-	1	NA	intron (NM_031376, intron 2 of 16)	MTE2a|LTR|ERVL-MaLR	52035	NM_031376	83490	Mm.222266	NM_031376	ENSMUSG00000025017	Pik3ap1	1810044J04Rik|BCAP	phosphoinositide-3-kinase adaptor protein 1	protein-coding
mm_86227.1	chr9	120135928	120135936	-	1	NA	Intergenic	Intergenic	5498	NR_002902	104433	Mm.453530	NR_002902	ENSMUSG00000064925	Snora62	E2|MBI-13|MBI-136|Rnu108	small nucleolar RNA, H/ACA box 62	snoRNA
mm_143893.1	chr17	84543248	84543261	-	1	NA	intron (NM_177606, intron 2 of 29)	intron (NM_177606, intron 2 of 29)	31359	NM_177606	213556	Mm.215159	NM_177606	ENSMUSG00000040852	Plekhh2	AI256725|E030001K05|mKIAA2028	pleckstrin homology domain containing, family H (with MyTH4 domain) member 2	protein-coding
mm_12944.1	chr2	85136601	85136623	+	1	NA	5' UTR (NM_011784, exon 1 of 1)	5' UTR (NM_011784, exon 1 of 1)	252	NM_011784	23796	Mm.29368	NM_011784	ENSMUSG00000044338	Aplnr	APJ|Agtrl1|msr/apj	apelin receptor	protein-coding
mm_87124.1	chr10	33364445	33364453	+	1	NA	intron (NM_029726, intron 21 of 37)	intron (NM_029726, intron 21 of 37)	-108092	NR_040657	442820	Mm.490725	NR_040657		D830005E20Rik	-	RIKEN cDNA D830005E20 gene	ncRNA
mm_16470.1	chr2	180710292	180710300	+	1	NA	promoter-TSS (NM_001291432)	promoter-TSS (NM_001291432)	-32	NM_001289651	76425	Mm.41464	NM_029607	ENSMUSG00000027573	Gid8	2310003C23Rik|4833420G11Rik|AI451474|Twa1	GID complex subunit 8	protein-coding
mm_80812.1	chr9	96525304	96525324	+	1	NA	Intergenic	Intergenic	-46639	NM_001311135	19823	Mm.28235	NM_011279	ENSMUSG00000051234	Rnf7	Rbx2|SAG	ring finger protein 7	protein-coding
mm_82879.1	chr9	32452124	32452136	-	1	NA	intron (NM_008026, intron 5 of 8)	intron (NM_008026, intron 5 of 8)	58145	NM_001168354	56379	Mm.390168	NM_019659	ENSMUSG00000041248	Kcnj1	Kir1.1|ROMK|Romk2	potassium inwardly-rectifying channel, subfamily J, member 1	protein-coding
mm_135321.1	chr16	38783603	38783613	-	1	NA	intron (NM_178924, intron 5 of 7)	intron (NM_178924, intron 5 of 7)	16595	NM_178924	22268	Mm.130793	NM_178924	ENSMUSG00000049436	Upk1b	AI413235|Tspan20|UPIb|Upk1	uroplakin 1B	protein-coding
mm_131570.1	chr16	18248867	18248919	+	1	NA	promoter-TSS (NM_011239)	promoter-TSS (NM_011239)	10	NM_001081000	15547	Mm.271798	NM_008307	ENSMUSG00000022721	Trmt2a	Htf9c	TRM2 tRNA methyltransferase 2A	protein-coding
mm_103277.1	chr11	72170771	72170787	-	1	NA	intron (NM_028963, intron 12 of 18)	L1MD1|LINE|L1	32592	NM_028963	74477	Mm.289697	NM_028963	ENSMUSG00000020807	4933427D14Rik	C85113|Kiaa0753|MNR	RIKEN cDNA 4933427D14 gene	protein-coding
mm_25355.1	chr3	107038928	107038944	+	1	NA	promoter-TSS (NR_033498)	promoter-TSS (NR_033498)	-568	NR_033498	229694	Mm.347584	NM_173787	ENSMUSG00000056145	AI504432	A230102G19	expressed sequence AI504432	ncRNA
mm_142592.1	chr17	46752114	46752153	-	1	NA	promoter-TSS (NM_001305990)	promoter-TSS (NM_001305990)	81	NM_001305989	72029	Mm.240325	NM_028065	ENSMUSG00000023973	Cnpy3	1600025D17Rik|2410050O22Rik|AI413153|CAG4A|ERDA5|PRAT4A|Tnrc5	canopy FGF signaling regulator 3	protein-coding
mm_40206.1	chr5	37046996	37047014	+	1	NA	Intergenic	Intergenic	-3852	NM_178394	76071	Mm.85280	NM_178394	ENSMUSG00000063646	Jakmip1	5830437M04Rik|C330021K24Rik|Gababrbp|Marlin-1	janus kinase and microtubule interacting protein 1	protein-coding
mm_69159.1	chr7	127195869	127195880	-	1	NA	5' UTR (NM_001285907, exon 1 of 7)	5' UTR (NM_001285907, exon 1 of 7)	203	NM_001285907	70233	Mm.28050	NM_027353	ENSMUSG00000042502	Cd2bp2	1500011B02Rik|2410024K20Rik|AW048183	CD2 antigen (cytoplasmic tail) binding protein 2	protein-coding
mm_60611.1	chr7	44590907	44590917	+	1	NA	promoter-TSS (NM_001290682)	promoter-TSS (NM_001290682)	26	NM_001290682	16504	Mm.40312	NM_008422	ENSMUSG00000062785	Kcnc3	KShIIID|Kcr2-3|Kv3.3	potassium voltage gated channel, Shaw-related subfamily, member 3	protein-coding
mm_161406.1	chr15	3270892	3270892	+	1	NA	promoter-TSS (NM_009155)	promoter-TSS (NM_009155)	81	NM_001042614	20363	Mm.392203	NM_009155	ENSMUSG00000064373	Selenop	AU018766|D15Ucla1|Se-P|Sepp1|selp	selenoprotein P	protein-coding
mm_9637.1	chr1	177050200	177050213	-	1	NA	exon (NM_011785, exon 10 of 13)	exon (NM_011785, exon 10 of 13)	198561	NM_011785	23797	Mm.235194	NM_011785	ENSMUSG00000019699	Akt3	AI851531|D930002M15Rik|Nmf350	thymoma viral proto-oncogene 3	protein-coding
mm_133972.1	chr16	4420381	4420399	-	1	NA	5' UTR (NM_009624, exon 1 of 11)	5' UTR (NM_009624, exon 1 of 11)	108	NM_001291910	11515	Mm.439750	NM_009624	ENSMUSG00000005580	Adcy9	AC9|ACtp10|AW125421|D16Wsu65e|mKIAA0520	adenylate cyclase 9	protein-coding
mm_42830.1	chr5	122101164	122101177	+	1	NA	intron (NM_010861, intron 1 of 6)	intron (NM_010861, intron 1 of 6)	190	NM_010861	17906	Mm.1529	NM_010861	ENSMUSG00000013936	Myl2	MLC-2|MLC-2s/v|MLC-2v|Mlc2v|Mylpc	myosin, light polypeptide 2, regulatory, cardiac, slow	protein-coding
mm_79406.1	chr9	55149414	55149432	+	1	NA	promoter-TSS (NM_180600)	promoter-TSS (NM_180600)	54	NM_001346657	109161	Mm.207894	NM_180600	ENSMUSG00000032307	Ube2q2	3010021M21Rik	ubiquitin-conjugating enzyme E2Q family member 2	protein-coding
mm_55008.1	chr6	48840458	48840466	-	1	NA	5' UTR (NM_023056, exon 1 of 7)	5' UTR (NM_023056, exon 1 of 7)	526	NM_023056	65963	Mm.28385	NM_023056	ENSMUSG00000029810	Tmem176b	1810009M01Rik|Clast1|Lr8	transmembrane protein 176B	protein-coding
mm_161974.1	chr19	12268040	12268040	+	1	NA	promoter-TSS (NM_146686)	promoter-TSS (NM_146686)	-192	NM_146686	258681	Mm.271522	NM_146686	ENSMUSG00000060049	Olfr235	MOR214-3|Olfr232|Olfr232-ps1|Olfr235-ps1|Olfr245|Olfr245-ps1	olfactory receptor 235	protein-coding
mm_165898.1	chr4	46562959	46562968	-	1	NA	exon (NM_001164804, exon 2 of 12)	exon (NM_001164804, exon 2 of 12)	3477	NM_178893	107684	Mm.416311	NM_178893	ENSMUSG00000028337	Coro2a	9030208C03Rik|AI563590|IR10	coronin, actin binding protein 2A	protein-coding
mm_81996.1	chr9	121587017	121587046	+	1	NA	promoter-TSS (NR_040740)	promoter-TSS (NR_040740)	11	NR_040740	75384	Mm.445955	NR_040740	ENSMUSG00000084995	Lyzl4os	4930589B17Rik|4930596M17Rik	lysozyme-like 4, opposite strand	ncRNA
mm_140064.1	chr17	74717744	74717773	+	1	NA	promoter-TSS (NM_152817)	promoter-TSS (NM_152817)	8	NM_152817	74196	Mm.209503	NM_152817	ENSMUSG00000024078	Ttc27	2610511O17Rik	tetratricopeptide repeat domain 27	protein-coding
mm_110367.1	chr12	40124663	40124679	-	1	NA	exon (NM_001146196, exon 3 of 16)	exon (NM_001146196, exon 3 of 16)	9557	NM_009132	20259	Mm.2416	NM_009132	ENSMUSG00000002565	Scin	AW545522|adseverin	scinderin	protein-coding
mm_161027.1	chr12	4234250	4234250	-	1	NA	promoter-TSS (NM_134046)	promoter-TSS (NM_134046)	44	NM_134046	52504	Mm.70546	NM_134046	ENSMUSG00000020652	Cenpo	2810429O05Rik|8430427C03Rik|D12Ertd482e	centromere protein O	protein-coding
mm_24618.1	chr3	93506607	93506613	+	1	NA	Intergenic	Intergenic	-13886	NM_016740	20195	Mm.280038	NM_016740	ENSMUSG00000027907	S100a11	EMAPI|Emap1|S100a14|S100c|cal	S100 calcium binding protein A11	protein-coding
mm_14317.1	chr2	129300434	129300444	+	1	NA	3' UTR (NM_010554, exon 7 of 7)	3' UTR (NM_010554, exon 7 of 7)	3069	NR_040371	100503468	Mm.446943	NR_040371	ENSMUSG00000085498	Gm14023	OTTMUSG00000015408	predicted gene 14023	ncRNA
mm_93181.1	chr10	93683336	93683349	-	1	NA	promoter-TSS (NR_038017)	promoter-TSS (NR_038017)	-20	NR_038017	100504069	Mm.391412	NR_038017	ENSMUSG00000085723	Gm15915	OTTMUSG00000027787	predicted gene 15915	ncRNA
mm_27223.1	chr3	36053505	36053510	-	1	NA	promoter-TSS (NM_178418)	promoter-TSS (NM_178418)	40	NM_178418	241943	Mm.269018	NM_178418	ENSMUSG00000047696	Ccdc144b	-	coiled-coil domain containing 144B	protein-coding
mm_137438.1	chr17	26508649	26508680	+	1	NA	promoter-TSS (NM_013642)	promoter-TSS (NM_013642)	-192	NM_013642	19252	Mm.239041	NM_013642	ENSMUSG00000024190	Dusp1	3CH134|MKP1|Ptpn16|U19515|erp|mkp-1	dual specificity phosphatase 1	protein-coding
mm_125074.1	chr15	25984360	25984373	+	1	NA	promoter-TSS (NM_144523)	promoter-TSS (NM_144523)	0	NM_144523	52521	Mm.29145	NM_144523	ENSMUSG00000052253	Zfp622	1110033B05Rik|D15Ertd806e|ZPR9|Znf622	zinc finger protein 622	protein-coding
mm_44854.1	chr5	34242465	34242491	-	1	NA	intron (NM_001015039, intron 2 of 12)	intron (NM_001015039, intron 2 of 12)	45846	NM_001015039	231125	Mm.113388	NM_001015039	ENSMUSG00000037224	Zfyve28	9630058O20Rik|Gm146|mKIAA1643	zinc finger, FYVE domain containing 28	protein-coding
mm_148366.1	chr18	88866781	88866807	-	1	NA	Intergenic	Intergenic	27413	NM_018821	54607	Mm.91920	NM_018821	ENSMUSG00000056153	Socs6	1500012M23Rik|5830401B18Rik|AI447482|Cis4|Cish4|HSPC060|SOCS-4|SOCS-6|SSI4|STAI4|STATI4|Socs4	suppressor of cytokine signaling 6	protein-coding
mm_13746.1	chr2	118120269	118120284	+	1	NA	exon (NM_011580, exon 14 of 22)	exon (NM_011580, exon 14 of 22)	8400	NM_001313914	21825	Mm.4159	NM_011580	ENSMUSG00000040152	Thbs1	TSP-1|TSP1|Thbs-1|tbsp1	thrombospondin 1	protein-coding
mm_14954.1	chr2	151999887	151999901	+	1	NA	promoter-TSS (NM_001164819)	promoter-TSS (NM_001164819)	28	NM_001164820	69698	Mm.258262	NM_027172	ENSMUSG00000027463	Slc52a3	2310046K01Rik|RFT2	solute carrier protein family 52, member 3	protein-coding
mm_96658.1	chr11	69395830	69395862	+	1	NA	promoter-TSS (NM_030083)	promoter-TSS (NM_030083)	55	NM_030083	78304	Mm.45683	NM_030083	ENSMUSG00000059278	Naa38	1500034E06Rik|Lsmd1	N(alpha)-acetyltransferase 38, NatC auxiliary subunit	protein-coding
mm_137039.1	chr17	17891415	17891426	+	1	NA	intron (NM_008039, intron 1 of 1)	intron (NM_008039, intron 1 of 1)	3596	NM_008039	14289	Mm.378918	NM_008039	ENSMUSG00000052270	Fpr2	E330010I07Rik|Fpr-rs2	formyl peptide receptor 2	protein-coding
mm_88069.1	chr10	67785744	67785755	+	1	NA	Intergenic	Intergenic	126913	NM_178679	216049	Mm.268346	NM_178679	ENSMUSG00000037855	Zfp365	AI839779|AV340892|DBZ|Su48|Znf365|talanin	zinc finger protein 365	protein-coding
mm_129468.1	chr15	78670514	78670535	-	1	NA	3' UTR (NM_183141, exon 2 of 2)	3' UTR (NM_183141, exon 2 of 2)	47589	NM_183141	207393	Mm.323188	NM_183141	ENSMUSG00000043460	Elfn2	6330514E13|AW048948|BC094219|Lrrc62|Ppp1r29	leucine rich repeat and fibronectin type III, extracellular 2	protein-coding
mm_109939.1	chr12	11325907	11325919	-	1	NA	3' UTR (NM_012038, exon 4 of 4)	3' UTR (NM_012038, exon 4 of 4)	26026	NR_106136	102465775		NR_106136	ENSMUSG00000098879	Mir7675	Gm27965|mmu-mir-7675	microRNA 7675	ncRNA
mm_138295.1	chr17	34630514	34630529	+	1	NA	intron (NM_030890, intron 1 of 3)	intron (NM_030890, intron 1 of 3)	835	NM_030890	260297	Mm.390965	NM_030890	ENSMUSG00000015476	Prrt1	Bat-4|Bat4|D17H6S54E|DSPD1|G5b|NG5|ORF31	proline-rich transmembrane protein 1	protein-coding
mm_161693.1	chr17	23599730	23599730	-	1	NA	promoter-TSS (NM_011747)	promoter-TSS (NM_011747)	-243	NM_011747	22654	Mm.40326	NM_011747	ENSMUSG00000062012	Zfp13	4933429B21|AI835008|Krox-8|Rhit|Zfp-13	zinc finger protein 13	protein-coding
mm_35296.1	chr4	22486680	22486685	-	1	NA	3' UTR (NM_008899, exon 1 of 1)	3' UTR (NM_008899, exon 1 of 1)	1684	NM_008899	18992	Mm.129387	NM_008899	ENSMUSG00000095139	Pou3f2	9430075J19Rik|A230098E07Rik|Brn-2|Brn2|OTF-7|Otf7|oct-7	POU domain, class 3, transcription factor 2	protein-coding
mm_171960.1	chr5	82906864	82906864	+	1	NA	Intergenic	Lx4A|LINE|L1	-107799	NR_035415	100316803		NR_035415	ENSMUSG00000080586	Mir1187	Mirn1187|mir-1187|mmu-mir-1187	microRNA 1187	ncRNA
mm_129695.1	chr15	81586052	81586078	-	1	NA	promoter-TSS (NM_177821)	promoter-TSS (NM_177821)	-149	NM_177821	328572	Mm.258397	NM_177821	ENSMUSG00000055024	Ep300	A430090G16|A730011L11|KAT3B|p300|p300 HAT	E1A binding protein p300	protein-coding
mm_35701.1	chr4	44167581	44167608	-	1	NA	promoter-TSS (NM_175201)	promoter-TSS (NM_175201)	-56	NM_175201	73469	Mm.262859	NM_175201	ENSMUSG00000035696	Rnf38	1700065B19Rik|2610202O07Rik|AA673263|Oip1	ring finger protein 38	protein-coding
mm_64175.1	chr7	141457586	141457634	+	1	NA	non-coding (NR_028142, exon 4 of 10)	non-coding (NR_028142, exon 4 of 10)	2422	NM_001163689	66853	Mm.29998	NM_025802	ENSMUSG00000025509	Pnpla2	0610039C21Rik|1110001C14Rik|Atgl|TTS-2.2	patatin-like phospholipase domain containing 2	protein-coding
mm_67017.1	chr7	65635963	65635973	-	1	NA	Intergenic	Intergenic	-8930	NM_172310	272396	Mm.35127	NM_172310	ENSMUSG00000030515	Tarsl2	A530046H20Rik	threonyl-tRNA synthetase-like 2	protein-coding
mm_135184.1	chr16	36071523	36071604	-	1	NA	promoter-TSS (NM_001159421)	promoter-TSS (NM_001159421)	-48	NM_027342	70186	Mm.212991	NM_027342	ENSMUSG00000003955	Fam162a	2310056P07Rik|HGTD-P	family with sequence similarity 162, member A	protein-coding
mm_81822.1	chr9	118049710	118049725	+	1	NA	intron (NM_001286507, intron 3 of 6)	intron (NM_001286507, intron 3 of 6)	9195	NM_013727	27215	Mm.92705	NM_013727	ENSMUSG00000039285	Azi2	AA410145|AZ2	5-azacytidine induced gene 2	protein-coding
mm_21733.1	chr2	164745897	164745914	-	1	NA	promoter-TSS (NM_133763)	promoter-TSS (NM_133763)	-110	NM_133763	76233	Mm.440009	NM_133763	ENSMUSG00000017299	Dnttip1	6430706C13Rik	deoxynucleotidyltransferase, terminal, interacting protein 1	protein-coding
mm_111854.1	chr12	107939207	107939223	-	1	NA	intron (NM_001286343, intron 1 of 1)	intron (NM_001286343, intron 1 of 1)	64199	NM_001079883	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_62040.1	chr7	92234975	92234997	+	1	NA	promoter-TSS (NM_001243047)	promoter-TSS (NM_001243047)	16	NM_001243047	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_41071.1	chr5	87668326	87668330	+	1	NA	intron (NM_001286015, intron 3 of 32)	intron (NM_001286015, intron 3 of 32)	2120	NM_001286016	12990	Mm.427467	NM_007784	ENSMUSG00000070702	Csn1s1	AA959832|AW212882|Csna	casein alpha s1	protein-coding
mm_19775.1	chr2	106003182	106003277	-	1	NA	non-coding (NR_033993, exon 1 of 4)	non-coding (NR_033993, exon 1 of 4)	320	NM_026992	99349	Mm.25661	NM_026992	ENSMUSG00000027166	Dnajc24	1700030A21Rik|2610027M02Rik|AV066965|AW240712|Dph4|MmDjC7|Zcsl3	DnaJ heat shock protein family (Hsp40) member C24	protein-coding
mm_147407.1	chr18	44662252	44662264	-	1	NA	promoter-TSS (NM_001085374)	promoter-TSS (NM_001085374)	8	NM_001085374	328949	Mm.312511	NM_001033406	ENSMUSG00000071856	Mcc	D18Ertd451e|E330037C19	mutated in colorectal cancers	protein-coding
mm_4104.1	chr1	167598327	167598351	+	1	NA	promoter-TSS (NM_009107)	promoter-TSS (NM_009107)	-23	NM_009107	20183	Mm.3475	NM_009107	ENSMUSG00000015843	Rxrg	Nr2b3	retinoid X receptor gamma	protein-coding
mm_102878.1	chr11	69410369	69410380	-	1	NA	intron (NM_001017426, intron 1 of 22)	CpG	3301	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_100389.1	chr11	119375900	119375938	+	1	NA	intron (NM_178743, intron 12 of 16)	intron (NM_178743, intron 12 of 16)	-14553	NR_035453	100316690		NR_035453	ENSMUSG00000088015	Mir1932	mir-1932|mmu-mir-1932	microRNA 1932	ncRNA
mm_108964.1	chr12	102400177	102400208	+	1	NA	exon (NM_011175, exon 9 of 14)	exon (NM_011175, exon 9 of 14)	39621	NM_011175	19141	Mm.17185	NM_011175	ENSMUSG00000021190	Lgmn	AEP|AI746452|AU022324|Prsc1	legumain	protein-coding
mm_61825.1	chr7	87844031	87844039	+	1	NA	intron (NM_001143834, intron 4 of 10)	(T)n|Simple_repeat|Simple_repeat	259867	NM_001143834	108071	Mm.235018	NM_001033224	ENSMUSG00000049583	Grm5	6430542K11Rik|AI850523|Glu5R|Gprc1e|mGluR5|mGluR5b	glutamate receptor, metabotropic 5	protein-coding
mm_145434.1	chr18	58836351	58836374	+	1	NA	promoter-TSS (NM_175506)	promoter-TSS (NM_175506)	-1	NM_175506	240322	Mm.71963	NM_175506	ENSMUSG00000053441	Adamts19	4831407I23Rik|AU015154|D230034E10Rik	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 19	protein-coding
mm_79996.1	chr9	67041133	67041142	+	1	NA	intron (NM_001164249, intron 2 of 8)	intron (NM_001164249, intron 2 of 8)	2734	NM_001164252	22003	Mm.121878	NM_024427	ENSMUSG00000032366	Tpm1	AA986836|AI854628|TM2|Tm3|Tmpa|Tpm-1|alpha-TM	tropomyosin 1, alpha	protein-coding
mm_70924.1	chr8	25809863	25809874	+	1	NA	exon (NM_011485, exon 3 of 7)	exon (NM_011485, exon 3 of 7)	1394	NM_011485	20845	Mm.293314	NM_011485	ENSMUSG00000031574	Star	AV363654|D8Ertd419e|stARD1	steroidogenic acute regulatory protein	protein-coding
mm_98109.1	chr11	87015985	87015989	+	1	NA	intron (NR_106195, intron 4 of 8)	B1_Mur2|SINE|Alu	-22225	NM_001005341	77864	Mm.191894	NM_001005341	ENSMUSG00000018427	Ypel2	6430570G24|E130113K08Rik	yippee-like 2 (Drosophila)	protein-coding
mm_131954.1	chr16	24457796	24457810	+	1	NA	intron (NM_001145952, intron 2 of 11)	Charlie23a|DNA|hAT-Charlie	9712	NM_001145952	210126	Mm.209385	NM_178665	ENSMUSG00000033306	Lpp	9430020K16Rik|AA959454|AU024130|B130055L10Rik|C79715|D630048H16	LIM domain containing preferred translocation partner in lipoma	protein-coding
mm_133088.1	chr16	62854282	62854288	+	1	NA	promoter-TSS (NM_011173)	promoter-TSS (NM_011173)	-22	NM_011173	19128	Mm.127156	NM_011173	ENSMUSG00000022912	Pros1	AW214361	protein S (alpha)	protein-coding
mm_94952.1	chr11	29808904	29808925	+	1	NA	intron (NM_146016, intron 17 of 41)	intron (NM_146016, intron 17 of 41)	16754	NM_176829	216622	Mm.443260	NM_176829	ENSMUSG00000078157	4931440F15Rik	Fem1ab	RIKEN cDNA 4931440F15 gene	protein-coding
mm_93268.1	chr10	95767760	95767774	-	1	NA	Intergenic	Intergenic	-172896	NM_001001932	216238	Mm.210035	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding
mm_163454.1	chr12	91357333	91357338	-	1	NA	intron (NM_181815, intron 5 of 25)	intron (NM_181815, intron 5 of 25)	27074	NM_181815	75216	Mm.312204	NM_181815	ENSMUSG00000061533	Cep128	4930534B04Rik|5430424K18Rik|AI449708|AI480494|E230024F20	centrosomal protein 128	protein-coding
mm_72721.1	chr8	85036927	85036937	+	1	NA	promoter-TSS (NM_145390)	promoter-TSS (NM_145390)	17	NM_145390	212999	Mm.220357	NM_145390	ENSMUSG00000031691	Tnpo2	1110034O24Rik|AA414969|AI464345|AI852433|IPO3|Knpb2b|Kpnb2b|TRN2	transportin 2 (importin 3, karyopherin beta 2b)	protein-coding
mm_17637.1	chr2	31142003	31142017	-	1	NA	promoter-TSS (NM_019406)	promoter-TSS (NM_019406)	-2	NM_001038700	14269	Mm.52297	NM_019406	ENSMUSG00000075415	Fnbp1	1110057E06Rik|2210010H06Rik|FBP1|Fbp17	formin binding protein 1	protein-coding
mm_60300.1	chr7	44020804	44020811	+	1	NA	Intergenic	Intergenic	8110	NM_010115	13647	Mm.439663	NM_010115		Egfbp2	Egfbp-2|Klk1b26|mGk-13	epidermal growth factor binding protein type B	protein-coding
mm_128315.1	chr15	37961060	37961107	-	1	NA	promoter-TSS (NM_199476)	promoter-TSS (NM_199476)	-28	NM_199476	382985	Mm.24738	NM_199476	ENSMUSG00000022292	Rrm2b	p53R2	ribonucleotide reductase M2 B (TP53 inducible)	protein-coding
mm_127456.1	chr15	101271769	101271779	+	1	NA	exon (NM_010444, exon 3 of 7)	exon (NM_010444, exon 3 of 7)	4928	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_40502.1	chr5	57727293	57727294	+	1	NA	intron (NM_001310608, intron 1 of 3)	intron (NM_001310608, intron 1 of 3)	9212	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_119239.1	chr14	33471533	33471540	+	1	NA	Intergenic	Intergenic	-24378	NM_016700	26419	Mm.21495	NM_016700	ENSMUSG00000021936	Mapk8	AI849689|JNK|JNK1|Prkm8|SAPK1	mitogen-activated protein kinase 8	protein-coding
mm_56372.1	chr6	94028837	94028839	-	1	NA	intron (NM_001029850, intron 1 of 23)	intron (NM_001029850, intron 1 of 23)	-115148	NM_001083320	14924	Mm.217216	NM_010367	ENSMUSG00000045095	Magi1	AIP3|BAP1|Baiap1|Gukmi1|MAGI1c|Magi-1|TNRC19|WWP3|mKIAA4129	membrane associated guanylate kinase, WW and PDZ domain containing 1	protein-coding
mm_49640.1	chr6	30805203	30805212	+	1	NA	intron (NM_017478, intron 20 of 23)	intron (NM_017478, intron 20 of 23)	63908	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_23128.1	chr3	37668816	37668834	+	1	NA	Intergenic	Intergenic	28878	NM_001305442	24063	Mm.330986	NM_011896	ENSMUSG00000037211	Spry1	sprouty1|spry-1	sprouty homolog 1 (Drosophila)	protein-coding
mm_129009.1	chr15	74909557	74909567	-	1	NA	Intergenic	Intergenic	-27858	NM_025929	67038	Mm.154566	NM_025929	ENSMUSG00000063522	2010109I03Rik	Ly6m	RIKEN cDNA 2010109I03 gene	protein-coding
mm_15307.1	chr2	155389094	155389098	+	1	NA	3' UTR (NM_178111, exon 4 of 4)	3' UTR (NM_178111, exon 4 of 4)	7240	NM_178111	68728	Mm.293605	NM_178111	ENSMUSG00000038375	Trp53inp2	1110029F20Rik|Tp53inp2	transformation related protein 53 inducible nuclear protein 2	protein-coding
mm_104092.1	chr11	86671170	86671186	-	1	NA	intron (NM_029478, intron 1 of 11)	L2|LINE|L2	12644	NM_029478	75909	Mm.390398	NM_029478	ENSMUSG00000018171	Vmp1	3110098I04Rik|4930579A11Rik|AI787464|Tango5|Tmem49|mir-21a|ni-2	vacuole membrane protein 1	protein-coding
mm_11666.1	chr2	35282300	35282318	+	1	NA	promoter-TSS (NM_146120)	promoter-TSS (NM_146120)	-71	NM_146120	227753	Mm.443	NM_146120	ENSMUSG00000026879	Gsn	ADF	gelsolin	protein-coding
mm_77780.1	chr9	3022178	3022189	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	16560	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_58705.1	chr7	12962010	12962022	+	1	NA	Intergenic	Intergenic	-3848	NM_178732	243834	Mm.133086	NM_178732	ENSMUSG00000004500	Zfp324	A930002M05|D430030K24Rik|ZF5128	zinc finger protein 324	protein-coding
mm_119087.1	chr14	30890645	30890670	+	1	NA	exon (NM_001289633, exon 6 of 22)	exon (NM_001289633, exon 6 of 22)	4181	NM_001289632	16427	Mm.34819	NM_018746	ENSMUSG00000021922	Itih4	ITI-HC4|Itih-4|PK-120	inter alpha-trypsin inhibitor, heavy chain 4	protein-coding
mm_61526.1	chr7	78914527	78914535	+	1	NA	exon (NM_020583, exon 2 of 4)	exon (NM_020583, exon 2 of 4)	296	NM_001113527	57444	Mm.322843	NM_020583	ENSMUSG00000039236	Isg20	1600023I01Rik|2010107M23Rik|20kDa|DnaQL|HEM45	interferon-stimulated protein	protein-coding
mm_117238.1	chr13	64312569	64312623	-	1	NA	exon (NM_025370, exon 1 of 6)	exon (NM_025370, exon 1 of 6)	114	NM_025370	66129	Mm.491110	NM_025370	ENSMUSG00000021482	Aaed1	1110018J18Rik|AI849003	AhpC/TSA antioxidant enzyme domain containing 1	protein-coding
mm_6223.1	chr1	66928799	66928810	-	1	NA	intron (NM_021285, intron 3 of 6)	intron (NM_021285, intron 3 of 6)	6562	NM_001113387	17901	Mm.1000	NM_021285	ENSMUSG00000061816	Myl1	AI325107|MLC1f|MLC3f|Mylf	myosin, light polypeptide 1	protein-coding
mm_114045.1	chr13	54106803	54106822	+	1	NA	3' UTR (NM_027324, exon 11 of 11)	3' UTR (NM_027324, exon 11 of 11)	34967	NM_027324	14057	Mm.134191	NM_027324	ENSMUSG00000021474	Sfxn1	2810002O05Rik|A930015P12Rik|f	sideroflexin 1	protein-coding
mm_160990.1	chr11	106084961	106084961	+	1	NA	promoter-TSS (NM_011947)	promoter-TSS (NM_011947)	59	NM_011947	26406	Mm.27041	NM_011947	ENSMUSG00000020700	Map3k3	AW548911|MAPKKK3|Mekk3|mKIAA4031	mitogen-activated protein kinase kinase kinase 3	protein-coding
mm_66217.1	chr7	34389685	34389695	-	1	NA	promoter-TSS (NM_025948)	promoter-TSS (NM_025948)	-150	NM_025948	67070	Mm.276503	NM_025948	ENSMUSG00000066568	Lsm14a	2700023B17Rik|AA407828|AU017544|Tral	LSM14A mRNA processing body assembly factor	protein-coding
mm_119385.1	chr14	41136591	41136607	+	1	NA	TTS (NM_023134)	TTS (NM_023134)	4811	NM_023134	20387	Mm.46062	NM_023134	ENSMUSG00000021789	Sftpa1	SP-A|Sftp-1|Sftp1	surfactant associated protein A1	protein-coding
mm_161224.1	chr13	69533780	69533780	-	1	NA	promoter-TSS (NM_198600)	promoter-TSS (NM_198600)	84	NM_198600	210106	Mm.315959	NM_198600	ENSMUSG00000034575	Papd7	LAK-1|POLK|Pols|TRF4|TRF4-1	PAP associated domain containing 7	protein-coding
mm_165788.1	chr3	131490006	131490031	+	1	NA	Intergenic	CpG	-74750	NM_001289479	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_144437.1	chr18	21651390	21651406	+	1	NA	promoter-TSS (NM_001271580)	promoter-TSS (NM_001271580)	-167	NM_001271580	74644	Mm.329311	NM_001271580		4930426D05Rik	-	RIKEN cDNA 4930426D05 gene	protein-coding
mm_98826.1	chr11	97373060	97373069	+	1	NA	intron (NM_138657, intron 1 of 9)	intron (NM_138657, intron 1 of 9)	10513	NM_138657	192157	Mm.34339	NM_138657	ENSMUSG00000038485	Socs7	2310063P06Rik|C85125|Nap4	suppressor of cytokine signaling 7	protein-coding
mm_97850.1	chr11	83069328	83069349	+	1	NA	exon (NM_011408, exon 2 of 2)	exon (NM_011408, exon 2 of 2)	4226	NM_011408	20556	Mm.278689	NM_011408	ENSMUSG00000072620	Slfn2	Shlf2	schlafen 2	protein-coding
mm_53779.1	chr6	146501706	146501723	+	1	NA	intron (NM_010586, intron 1 of 55)	CpG	509	NM_010586	16439	Mm.7800	NM_010586	ENSMUSG00000030287	Itpr2	AI649341|InsP3R-2|InsP3R-5|Ip3r2|Itpr5|insP3R2	inositol 1,4,5-triphosphate receptor 2	protein-coding
mm_49290.1	chr6	17666673	17666686	+	1	NA	TTS (NM_007604)	TTS (NM_007604)	-27315	NM_001289624	64213	Mm.12051	NM_022332	ENSMUSG00000029534	St7	9430001H04Rik|Fam4a2|HELG|RAY1|SEN4|TSG7	suppression of tumorigenicity 7	protein-coding
mm_42311.1	chr5	114853709	114853721	+	1	NA	promoter-TSS (NM_026263)	promoter-TSS (NM_026263)	1	NM_026263	67593	Mm.251409	NM_026263	ENSMUSG00000029564	4930519G04Rik	1700014B12Rik	RIKEN cDNA 4930519G04 gene	protein-coding
mm_4247.1	chr1	171403198	171403246	+	1	NA	exon (NM_001005508, exon 6 of 12)	exon (NM_001005508, exon 6 of 12)	-8091	NM_001305678	22278	Mm.8	NM_009480	ENSMUSG00000026641	Usf1	bHLHb11	upstream transcription factor 1	protein-coding
mm_9868.1	chr1	184882992	184883031	-	1	NA	promoter-TSS (NM_178692)	promoter-TSS (NM_178692)	25	NM_178692	226777	Mm.169542	NM_178692	ENSMUSG00000039349	C130074G19Rik	-	RIKEN cDNA C130074G19 gene	protein-coding
mm_30890.1	chr4	32258663	32258674	+	1	NA	Intergenic	Intergenic	-158767	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_28887.1	chr3	97868224	97868228	-	1	NA	intron (NM_001039376, intron 1 of 46)	CpG	20481	NM_001289702	83679	Mm.129840	NM_031401	ENSMUSG00000038170	Pde4dip	4732458A06Rik|9430063L05Rik|C87016|D130016K21Rik|D3Bwg1078e|Usmg4|mKIAA0454	phosphodiesterase 4D interacting protein (myomegalin)	protein-coding
mm_83431.1	chr9	44987186	44987200	-	1	NA	TTS (NM_013487)	TTS (NM_013487)	5407	NM_013487	12500	Mm.4527	NM_013487	ENSMUSG00000032094	Cd3d	T3d	CD3 antigen, delta polypeptide	protein-coding
mm_70326.1	chr8	4349597	4349611	+	1	NA	promoter-TSS (NM_009138)	promoter-TSS (NM_009138)	16	NM_009138	20300	Mm.7275	NM_009138	ENSMUSG00000023235	Ccl25	A130072A22Rik|AI852536|CKb15|Scya25|TECK	chemokine (C-C motif) ligand 25	protein-coding
mm_63535.1	chr7	127973626	127973629	+	1	NA	intron (NM_001347649, intron 6 of 14)	intron (NM_001347649, intron 6 of 14)	6148	NM_139149	233908	Mm.277680	NM_139149	ENSMUSG00000030795	Fus	D430004D17Rik|D930039C12Rik|Fus1|Tls	fused in sarcoma	protein-coding
mm_43079.1	chr5	124447010	124447018	+	1	NA	intron (NM_001310727, intron 1 of 6)	intron (NM_001310727, intron 1 of 6)	310	NM_001310727	67956	Mm.137966	NM_030241	ENSMUSG00000049327	Kmt5a	2410195B05Rik|AA617402|AW536475|PR-SET7|PR/SET07|Setd8	lysine methyltransferase 5A	protein-coding
mm_134420.1	chr16	17872624	17872665	-	1	NA	exon (NM_001109750, exon 2 of 10)	exon (NM_001109750, exon 2 of 10)	19084	NM_010048	13356	Mm.254515	NM_010048	ENSMUSG00000003166	Dgcr2	9930034O06Rik|DGS-C|Dgsc|Idd|Lan|Sez12|mKIAA0163	DiGeorge syndrome critical region gene 2	protein-coding
mm_161496.1	chr15	88751716	88751716	+	1	NA	promoter-TSS (NM_181412)	promoter-TSS (NM_181412)	5	NM_181412	223773	Mm.396622	NM_181412	ENSMUSG00000034333	Zbed4	1700009F06Rik	zinc finger, BED type containing 4	protein-coding
mm_7779.1	chr1	131276878	131276888	-	1	NA	intron (NM_019777, intron 2 of 21)	intron (NM_019777, intron 2 of 21)	2680	NM_019777	56489	Mm.386783	NM_019777	ENSMUSG00000042349	Ikbke	AW558201|IKK-i|IKKepsilon|Ikki	inhibitor of kappaB kinase epsilon	protein-coding
mm_104406.1	chr11	94549166	94549222	-	1	NA	promoter-TSS (NM_001013381)	promoter-TSS (NM_001013381)	13	NM_001013381	237926	Mm.342275	NM_001013381	ENSMUSG00000039096	Rsad1	B430319G23|BC056485	radical S-adenosyl methionine domain containing 1	protein-coding
mm_96012.1	chr11	59542749	59542775	+	1	NA	promoter-TSS (NM_145827)	promoter-TSS (NM_145827)	76	NM_145827	216799	Mm.54174	NM_145827	ENSMUSG00000032691	Nlrp3	AGTAVPRL|AII/AVP|Cias1|FCAS|FCU|MWS|Mmig1|NALP3|Pypaf1	NLR family, pyrin domain containing 3	protein-coding
mm_39915.1	chr5	31452684	31452688	+	1	NA	intron (NM_172993, intron 1 of 13)	intron (NM_172993, intron 1 of 13)	250	NM_172993	269639	Mm.259127	NM_172993	ENSMUSG00000062761	Zfp512	2500002M11Rik|AI450173|D230008H22|Znf512	zinc finger protein 512	protein-coding
mm_156047.1	chrX	108893150	108893196	+	1	NA	Intergenic	Intergenic	58695	NR_015493	69964	Mm.160066	NR_015493	ENSMUSG00000086629	2810403D21Rik	1810022M18Rik|4632410B05Rik|AU017716	RIKEN cDNA 2810403D21 gene	ncRNA
mm_107917.1	chr12	71036966	71036976	+	1	NA	intron (NM_001081195, intron 5 of 23)	ORR1B1|LTR|ERVL-MaLR	21004	NM_001081195	238247	Mm.241601	NM_001081195	ENSMUSG00000048118	Arid4a	A630009N03|A630067N03Rik|MmRBBP1|Rbbp1	AT rich interactive domain 4A (RBP1-like)	protein-coding
mm_63106.1	chr7	122632303	122632307	+	1	NA	3' UTR (NM_008855, exon 17 of 17)	3' UTR (NM_008855, exon 17 of 17)	-39439	NM_019430	54376	Mm.444212	NM_019430	ENSMUSG00000066189	Cacng3	-	calcium channel, voltage-dependent, gamma subunit 3	protein-coding
mm_151448.1	chr19	57646262	57646266	+	1	NA	intron (NM_181415, intron 5 of 28)	intron (NM_181415, intron 5 of 28)	35230	NM_181415	226255	Mm.245340	NM_181415	ENSMUSG00000054843	Atrnl1	AI504415|AW555641|Alp|Atrnl|Atrnlp	attractin like 1	protein-coding
mm_113100.1	chr13	24376135	24376145	+	1	NA	intron (NM_001284519, intron 2 of 17)	intron (NM_001284519, intron 2 of 17)	-38982	NM_007717	12763	Mm.8396	NM_007717	ENSMUSG00000016756	Cmah	-	cytidine monophospho-N-acetylneuraminic acid hydroxylase	protein-coding
mm_87908.1	chr10	62253091	62253108	+	1	NA	exon (NM_009314, exon 1 of 5)	exon (NM_009314, exon 1 of 5)	661	NM_009314	21337	Mm.8054	NM_009314	ENSMUSG00000020081	Tacr2	Nk2r|Skr|Tac2r	tachykinin receptor 2	protein-coding
mm_27078.1	chr3	28897158	28897171	-	1	NA	intron (NM_001033479, intron 2 of 14)	(GTCTG)n|Simple_repeat|Simple_repeat	4547	NM_001033479	385263	Mm.60893	NM_001033479	ENSMUSG00000074655	Gm1527	Gm1136	predicted gene 1527	protein-coding
mm_164813.1	chr18	32985299	32985318	+	1	NA	intron (NM_009793, intron 1 of 10)	intron (NM_009793, intron 1 of 10)	46267	NM_009793	12326	Mm.222329	NM_009793	ENSMUSG00000038128	Camk4	A430110E23Rik|AI666733|CaMKIV|CaMKIV/Gr|D18Bwg0362e	calcium/calmodulin-dependent protein kinase IV	protein-coding
mm_29918.1	chr3	131489938	131489966	-	1	NA	Intergenic	Intergenic	-74816	NM_001289479	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_135186.1	chr16	36072232	36072234	-	1	NA	promoter-TSS (NM_027342)	promoter-TSS (NM_027342)	573	NM_001159421	381045	Mm.310434	NM_198645	ENSMUSG00000075229	Ccdc58	A930007B11Rik|AI413631	coiled-coil domain containing 58	protein-coding
mm_12786.1	chr2	79587752	79587771	+	1	NA	Intergenic	Intergenic	-47664	NM_080558	70599	Mm.272881	NM_080558	ENSMUSG00000027007	Ssfa2	5730488C15Rik|CS-1|CS1|KRAP|SPAG13|mKIAA1927	sperm specific antigen 2	protein-coding
mm_16155.1	chr2	172370659	172370744	+	1	NA	promoter-TSS (NM_001291185)	promoter-TSS (NM_001291185)	-131	NM_011497	20878	Mm.249363	NM_011497	ENSMUSG00000027496	Aurka	AIRK1|ARK-1|AU019385|AW539821|Ark1|Aurora-A|Ayk1|IAK|IAK1|Stk6	aurora kinase A	protein-coding
mm_41788.1	chr5	103737344	103737369	+	1	NA	Intergenic	Intergenic	-16806	NM_133919	17355	Mm.6949	NM_133919	ENSMUSG00000029313	Aff1	9630032B01Rik|AW319193|Af4|Mllt2h|Rob	AF4/FMR2 family, member 1	protein-coding
mm_103051.1	chr11	69815317	69815349	-	1	NA	Intergenic	Intergenic	3107	NM_175368	108803	Mm.73263	NM_175368	ENSMUSG00000044084	4933402P03Rik	-	RIKEN cDNA 4933402P03 gene	protein-coding
mm_148445.1	chr19	3972323	3972345	+	1	NA	promoter-TSS (NM_001177438)	promoter-TSS (NM_001177438)	6	NM_001177438	621603	Mm.34137	NM_001177438	ENSMUSG00000075296	Aldh3b2	AI848594|C130048D07Rik	aldehyde dehydrogenase 3 family, member B2	protein-coding
mm_27268.1	chr3	39359157	39359160	-	1	NA	Intergenic	Intergenic	472218	NM_183221	329628	Mm.316210	NM_183221	ENSMUSG00000046743	Fat4	6030410K14Rik|9430004M15	FAT atypical cadherin 4	protein-coding
mm_59663.1	chr7	28316397	28316411	+	1	NA	exon (NM_013676, exon 26 of 30)	exon (NM_013676, exon 26 of 30)	-4358	NM_025616	66525	Mm.167913	NM_025616	ENSMUSG00000003438	Timm50	2810403L02Rik|AU015082|TIM50L	translocase of inner mitochondrial membrane 50	protein-coding
mm_144670.1	chr18	34542321	34542335	+	1	NA	promoter-TSS (NM_009290)	promoter-TSS (NM_009290)	0	NM_009290	20890	Mm.558	NM_009290	ENSMUSG00000012282	Wnt8a	Stra11|Wnt-8A|Wnt-8D|Wnt8d	wingless-type MMTV integration site family, member 8A	protein-coding
mm_132520.1	chr16	37616791	37616801	+	1	NA	non-coding (NR_027778, exon 8 of 13)	non-coding (NR_027778, exon 8 of 13)	36643	NM_013547	15233	Mm.157442	NM_013547	ENSMUSG00000022821	Hgd	Hgo|aku	homogentisate 1, 2-dioxygenase	protein-coding
mm_33087.1	chr4	124659549	124659561	+	1	NA	3' UTR (NM_011141, exon 1 of 1)	3' UTR (NM_011141, exon 1 of 1)	1909	NM_011141	18991	Mm.297371	NM_011141	ENSMUSG00000090125	Pou3f1	Oct-6|Oct6|Otf-6|Otf6|Scip|Test1|Tst-1|Tst1	POU domain, class 3, transcription factor 1	protein-coding
mm_90123.1	chr10	117285285	117285302	+	1	NA	Intergenic	Intergenic	-3021	NM_017372	17105	Mm.45436	NM_017372	ENSMUSG00000069516	Lyz2	AI326280|Lys|Lysm|Lyzf2|Lyzs|Lzm|Lzm-s1|Lzp	lysozyme 2	protein-coding
mm_139059.1	chr17	46428918	46428929	+	1	NA	promoter-TSS (NM_181664)	promoter-TSS (NM_181664)	-19	NM_053250	114570	Mm.25168	NM_053250	ENSMUSG00000023968	Crip3	TLP|TLP-A|TLP-B|Tlmp	cysteine-rich protein 3	protein-coding
mm_8289.1	chr1	143093696	143093714	-	1	NA	Intergenic	Intergenic	-546992	NM_020025	26878	Mm.285580	NM_020025	ENSMUSG00000033849	B3galt2	-	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 2	protein-coding
mm_14001.1	chr2	121987979	121987982	+	1	NA	intron (NM_212450, intron 6 of 12)	B2_Mm1a|SINE|B2	-31888	NM_008545	17147	Mm.389349	NM_008545	ENSMUSG00000074881	Mageb3	Mage-b3|Mage-ps1|Mage-rs3|Smage3	melanoma antigen, family B, 3	protein-coding
mm_83718.1	chr9	50756629	50756632	-	1	NA	TTS (NM_001289784)	TTS (NM_001289784)	3659	NM_009964	12955	Mm.178	NM_009964	ENSMUSG00000032060	Cryab	Crya-2|Crya2|HspB5|P23	crystallin, alpha B	protein-coding
mm_79226.1	chr9	49954903	49954911	+	1	NA	Intergenic	Intergenic	-155514	NM_001311065	17967	Mm.4974	NM_010875	ENSMUSG00000039542	Ncam1	CD56|E-NCAM|NCAM-1|Ncam	neural cell adhesion molecule 1	protein-coding
mm_151286.1	chr19	55285971	55285992	+	1	NA	intron (NM_027976, intron 12 of 21)	intron (NM_027976, intron 12 of 21)	30051	NM_025883	66980	Mm.386789	NM_025883	ENSMUSG00000024982	Zdhhc6	2400007G07Rik|5930409M18Rik|AI462345|C77369	zinc finger, DHHC domain containing 6	protein-coding
mm_82727.1	chr9	25151646	25151654	-	1	NA	5' UTR (NM_020586, exon 1 of 8)	5' UTR (NM_020586, exon 1 of 8)	131	NM_020586	80517	Mm.142843	NM_020586	ENSMUSG00000008429	Herpud2	5031400M07Rik|AB041580	HERPUD family member 2	protein-coding
mm_130761.1	chr15	101351275	101351283	-	1	NA	intron (NM_028770, intron 6 of 8)	intron (NM_028770, intron 6 of 8)	-18073	NR_035462	100316694		NR_035462	ENSMUSG00000088459	Mir1941	mmu-mir-1941	microRNA 1941	ncRNA
mm_173086.1	chrX	147239794	147239797	-	1	NA	Intergenic	Intergenic	81585	NR_029956	723914		NR_029956	ENSMUSG00000065450	Mir448	Mirn448|mir-448|mmu-mir-448	microRNA 448	ncRNA
mm_170687.1	chr2	130397599	130397599	-	1	NA	promoter-TSS (NM_019696)	promoter-TSS (NM_019696)	30	NM_019696	56264	Mm.112701	NM_019696	ENSMUSG00000027408	Cpxm1	AA986902|Cpx-1|Cpx1|Cpxm	carboxypeptidase X 1 (M14 family)	protein-coding
mm_110570.1	chr12	56345773	56345788	-	1	NA	exon (NM_145442, exon 1 of 9)	exon (NM_145442, exon 1 of 9)	114	NM_145442	217588	Mm.25656	NM_145442	ENSMUSG00000021028	Mbip	4933408E06Rik	MAP3K12 binding inhibitory protein 1	protein-coding
mm_76162.1	chr8	82372896	82372899	-	1	NA	intron (NM_008357, intron 2 of 7)	intron (NM_008357, intron 2 of 7)	29689	NM_001254747	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_155655.1	chrX	85870706	85870713	+	1	NA	intron (NM_001163539, intron 1 of 1)	intron (NM_001163539, intron 1 of 1)	436	NM_001163539	71398	Mm.185296	NM_001163539	ENSMUSG00000025058	5430427O19Rik	-	RIKEN cDNA 5430427O19 gene	protein-coding
mm_33030.1	chr4	122689263	122689283	+	1	NA	promoter-TSS (NM_023865)	promoter-TSS (NM_023865)	14	NM_023865	77432	Mm.491436	NM_023865	ENSMUSG00000023263	9530002B09Rik	Aump|Vpp1|Vppl	RIKEN cDNA 9530002B09 gene	protein-coding
mm_132627.1	chr16	38902326	38902364	+	1	NA	promoter-TSS (NM_170599)	promoter-TSS (NM_170599)	0	NM_170599	207683	Mm.245564	NM_170599	ENSMUSG00000022790	Igsf11	1700025L02Rik|BT-IgSF|Igsf13	immunoglobulin superfamily, member 11	protein-coding
mm_86400.1	chr9	123968700	123968714	-	1	NA	promoter-TSS (NM_009912)	promoter-TSS (NM_009912)	-15	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_144407.1	chr18	20961277	20961290	+	1	NA	intron (NM_026301, intron 1 of 5)	intron (NM_026301, intron 1 of 5)	16658	NM_026301	67664	Mm.45980	NM_026301	ENSMUSG00000033107	Rnf125	4930553F04Rik	ring finger protein 125	protein-coding
mm_19314.1	chr2	90549073	90549092	-	1	NA	intron (NM_008982, intron 1 of 23)	intron (NM_008982, intron 1 of 23)	31565	NM_008982	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_60491.1	chr7	44478642	44478646	+	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	-5873	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_139950.1	chr17	71204699	71204701	+	1	NA	promoter-TSS (NM_001164885)	promoter-TSS (NM_001164885)	46	NM_001164885	64898	Mm.227924	NM_022882	ENSMUSG00000024052	Lpin2	2610511G02Rik|AI481352|AW742896	lipin 2	protein-coding
mm_119489.1	chr14	47376293	47376304	+	1	NA	intron (NM_001145953, intron 1 of 5)	B1F2|SINE|Alu	2438	NM_001145953	16854	Mm.248615	NM_010705	ENSMUSG00000050335	Lgals3	GBP|L-34|Mac-2|gal3	lectin, galactose binding, soluble 3	protein-coding
mm_108628.1	chr12	85608323	85608340	+	1	NA	exon (NM_001205053, exon 2 of 4)	exon (NM_001205053, exon 2 of 4)	8313	NM_001205053	81703	Mm.103560	NM_030887	ENSMUSG00000034271	Jdp2	Jundm2|Jundp2|TIF	Jun dimerization protein 2	protein-coding
mm_77450.1	chr8	121806263	121806284	-	1	NA	intron (NM_145605, intron 6 of 11)	intron (NM_145605, intron 6 of 11)	23296	NM_145605	234825	Mm.209329	NM_145605	ENSMUSG00000040263	Klhdc4	AA408426|AV352552|BC012312|G430025P05Rik	kelch domain containing 4	protein-coding
mm_86362.1	chr9	123781496	123781504	-	1	NA	3' UTR (NM_001166625, exon 4 of 4)	3' UTR (NM_001166625, exon 4 of 4)	14289	NM_001166625	12769	Mm.440604	NM_009913	ENSMUSG00000029530	Ccr9	A130091K22Rik|Cmkbr10|GPR-9-6	chemokine (C-C motif) receptor 9	protein-coding
mm_103571.1	chr11	77893856	77893856	-	1	NA	promoter-TSS (NM_008952)	promoter-TSS (NM_008952)	16	NM_008952	19193	Mm.8543	NM_008952	ENSMUSG00000017453	Pipox	LPIPOX|Pso	pipecolic acid oxidase	protein-coding
mm_43722.1	chr5	139484682	139484721	+	1	NA	promoter-TSS (NM_001159908)	promoter-TSS (NM_001159908)	-210	NM_001159908	100494	Mm.24521	NM_133349	ENSMUSG00000053581	Zfand2a	AA407930|AU016206|Airap	zinc finger, AN1-type domain 2A	protein-coding
mm_53134.1	chr6	125192155	125192170	+	1	NA	promoter-TSS (NM_025595)	promoter-TSS (NM_025595)	-38	NM_025595	66493	Mm.138749	NM_025595	ENSMUSG00000030335	Mrpl51	2610511M02Rik|CDA09|HSPC241|Mrp64	mitochondrial ribosomal protein L51	protein-coding
mm_138313.1	chr17	34660458	34660516	+	1	NA	Intergenic	Intergenic	-10048	NM_031176	81877	Mm.290527	NM_031176	ENSMUSG00000033327	Tnxb	Tn-mhc|Tnx	tenascin XB	protein-coding
mm_11189.1	chr2	29122603	29122613	+	1	NA	Intergenic	Lx8|LINE|L1	-2384	NM_198033	269254	Mm.41867	NM_198033	ENSMUSG00000043535	Setx	A130090N03|A930037J23Rik|AOA2|AW060766|Als4|SCAR1|Sen1|mKIAA0625	senataxin	protein-coding
mm_109917.1	chr12	8482154	8482216	-	1	NA	Intergenic	Intergenic	17800	NM_007483	11852	Mm.687	NM_007483	ENSMUSG00000054364	Rhob	AA017882|Arh6|Arhb	ras homolog family member B	protein-coding
mm_79576.1	chr9	58134880	58134891	+	1	NA	intron (NM_001162479, intron 1 of 18)	intron (NM_001162479, intron 1 of 18)	220	NM_001162479	20897	Mm.10801	NM_009291	ENSMUSG00000032327	Stra6	AI891933	stimulated by retinoic acid gene 6	protein-coding
mm_72170.1	chr8	72268606	72268618	+	1	NA	Intergenic	Intergenic	28594	NM_007456	11767	Mm.290086	NM_007456	ENSMUSG00000003033	Ap1m1	AA408894|AP47|Adtm1A|Cltnm|mu1A	adaptor-related protein complex AP-1, mu subunit 1	protein-coding
mm_169698.1	chr15	75086446	75086450	+	1	NA	Intergenic	Intergenic	25501	NM_001099217	100041546	Mm.482110	NM_001099217	ENSMUSG00000022584	Ly6c2	Ly-6C.2|Ly-6C2	lymphocyte antigen 6 complex, locus C2	protein-coding
mm_80736.1	chr9	94669946	94669956	+	1	NA	promoter-TSS (NM_177909)	promoter-TSS (NM_177909)	59	NM_177909	331004	Mm.326125	NM_177909	ENSMUSG00000031129	Slc9a9	5730527A11Rik|9930105B05|AI854429|Nhe9	solute carrier family 9 (sodium/hydrogen exchanger), member 9	protein-coding
mm_8236.1	chr1	138175897	138175912	-	1	NA	promoter-TSS (NM_001268286)	promoter-TSS (NM_001268286)	-599	NM_001268286	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_34048.1	chr4	138226050	138226050	+	1	NA	intron (NM_001285478, intron 5 of 12)	intron (NM_001285478, intron 5 of 12)	8923	NM_001122897	15441	Mm.348429	NM_010470	ENSMUSG00000028759	Hp1bp3	Hp1bp74	heterochromatin protein 1, binding protein 3	protein-coding
mm_46648.1	chr5	108594419	108594422	-	1	NA	intron (NM_001282052, intron 14 of 26)	B1_Mur1|SINE|Alu	35357	NM_153569	231580	Mm.276647	NM_153569	ENSMUSG00000062234	Gak	D130045N16Rik	cyclin G associated kinase	protein-coding
mm_35877.1	chr4	49536855	49536876	-	1	NA	exon (NM_144903, exon 9 of 9)	exon (NM_144903, exon 9 of 9)	12681	NM_144903	230163	Mm.482116	NM_144903	ENSMUSG00000028307	Aldob	Aldo-2|Aldo2|BC016435	aldolase B, fructose-bisphosphate	protein-coding
mm_142432.1	chr17	45570437	45570504	-	1	NA	exon (NM_008302, exon 6 of 11)	exon (NM_008302, exon 6 of 11)	2791	NM_008302	15516	Mm.2180	NM_008302	ENSMUSG00000023944	Hsp90ab1	90kDa|AL022974|C81438|Hsp84|Hsp84-1|Hsp90|Hspcb	heat shock protein 90 alpha (cytosolic), class B member 1	protein-coding
mm_67136.1	chr7	72306741	72306755	-	1	NA	promoter-TSS (NM_001024703)	promoter-TSS (NM_001024703)	-153	NM_001024703	244049	Mm.217412	NM_001024703	ENSMUSG00000032776	Mctp2	Gm489	multiple C2 domains, transmembrane 2	protein-coding
mm_80152.1	chr9	70928771	70928779	+	1	NA	intron (NM_001324473, intron 1 of 8)	intron (NM_001324473, intron 1 of 8)	6033	NM_008280	15450	Mm.390187	NM_008280	ENSMUSG00000032207	Lipc	AI256194|HL|Hpl	lipase, hepatic	protein-coding
mm_41007.1	chr5	81020058	81020105	+	1	NA	promoter-TSS (NM_001347367)	promoter-TSS (NM_001347367)	-490	NM_001347367	319387	Mm.273631	NM_198702	ENSMUSG00000037605	Adgrl3	5430402I23Rik|CIRL-3|D130075K09Rik|Gm1379|LEC3|Lphn3|mKIAA0768	adhesion G protein-coupled receptor L3	protein-coding
mm_98029.1	chr11	85311191	85311210	+	1	NA	promoter-TSS (NM_016910)	promoter-TSS (NM_016910)	-54	NM_016910	53892	Mm.45609	NM_016910	ENSMUSG00000020525	Ppm1d	AV338790|Wip1	protein phosphatase 1D magnesium-dependent, delta isoform	protein-coding
mm_161341.1	chr14	51988767	51988767	+	1	NA	promoter-TSS (NR_045728)	promoter-TSS (NR_045728)	62	NR_045728	100502764	Mm.437219	NR_045728	ENSMUSG00000097633	Gm16617	-	predicted gene, 16617	ncRNA
mm_165665.1	chr3	88503030	88503039	-	1	NA	exon (NM_001111102, exon 1 of 10)	exon (NM_001111102, exon 1 of 10)	318	NM_001111102	16905	Mm.243014	NM_019390	ENSMUSG00000028063	Lmna	Dhe	lamin A	protein-coding
mm_55278.1	chr6	54279070	54279082	-	1	NA	intron (NM_023543, intron 1 of 6)	intron (NM_023543, intron 1 of 6)	6254	NM_023543	69993	Mm.321147	NM_023543	ENSMUSG00000004633	Chn2	1700026N20Rik|4930557O16Rik|ARHGAP3|Bch	chimerin 2	protein-coding
mm_3333.1	chr1	137946006	137946009	+	1	NA	Intergenic	B1_Mus2|SINE|Alu	-20448	NR_029795	735252		NR_029795	ENSMUSG00000065565	Mir181a-1	Mirn181a-1|Mirn213|miR-213|mir-181a-1|mmu-mir-213	microRNA 181a-1	ncRNA
mm_60832.1	chr7	45715514	45715534	+	1	NA	promoter-TSS (NM_020011)	promoter-TSS (NM_020011)	-317	NM_020011	56632	Mm.24222	NM_020011	ENSMUSG00000057342	Sphk2	C76851	sphingosine kinase 2	protein-coding
mm_138478.1	chr17	35195021	35195039	+	1	NA	promoter-TSS (NR_105939)	promoter-TSS (NR_105939)	58	NR_105939	102465588		NR_105939	ENSMUSG00000098291	Mir6973a	Gm27967|mmu-mir-6973a	microRNA 6973a	ncRNA
mm_73534.1	chr8	108703594	108703617	+	1	NA	Intergenic	Intergenic	-11039	NM_007496	11906	Mm.416972	NM_007496	ENSMUSG00000038872	Zfhx3	A230102L03Rik|Atbf1|Sci|WBP9|mKIAA4228	zinc finger homeobox 3	protein-coding
mm_132576.1	chr16	38244392	38244407	+	1	NA	3' UTR (NM_019827, exon 11 of 11)	3' UTR (NM_019827, exon 11 of 11)	50425	NM_010936	18171	Mm.8509	NM_010936	ENSMUSG00000022809	Nr1i2	PXR|PXR.1|PXR.2|PXR1|SXR|mPXR	nuclear receptor subfamily 1, group I, member 2	protein-coding
mm_77219.1	chr8	115693799	115693804	-	1	NA	Intergenic	Intergenic	13093	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_6472.1	chr1	74068684	74068713	-	1	NA	intron (NM_027884, intron 2 of 34)	CpG-274	55749	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_142322.1	chr17	43457018	43457022	-	1	NA	3' UTR (NM_001081178, exon 21 of 21)	3' UTR (NM_001081178, exon 21 of 21)	45753	NM_008585	17287	Mm.5346	NM_008585	ENSMUSG00000023914	Mep1a	AI098089|AW107200|Mep-1|Mep-1a|Mep1	meprin 1 alpha	protein-coding
mm_161273.1	chr14	8259034	8259034	-	1	NA	promoter-TSS (NM_053115)	promoter-TSS (NM_053115)	-15	NM_053115	93732	Mm.28700	NM_053115	ENSMUSG00000021751	Acox2	THCCox	acyl-Coenzyme A oxidase 2, branched chain	protein-coding
mm_109214.1	chr12	108684648	108684659	+	1	NA	intron (NM_001163394, intron 11 of 13)	intron (NM_001163394, intron 11 of 13)	17653	NM_001171002	70059	Mm.207605	NM_027299	ENSMUSG00000021263	Degs2	2210008A03Rik|AI852933|DES2	delta(4)-desaturase, sphingolipid 2	protein-coding
mm_29045.1	chr3	103028893	103028919	-	1	NA	5' UTR (NM_001310693, exon 2 of 18)	5' UTR (NM_001310693, exon 2 of 18)	8360	NM_144901	229663	Mm.277713	NM_144901	ENSMUSG00000068823	Csde1	AA960392|BC016898|D3Jfr1|mKIAA0885|unr	cold shock domain containing E1, RNA binding	protein-coding
mm_31963.1	chr4	86930715	86930726	+	1	NA	intron (NM_001290543, intron 5 of 5)	RLTR51A_Mm|LTR|ERVK?	56306	NM_139306	230379	Mm.45019	NM_139306	ENSMUSG00000038007	Acer2	2410116I05Rik|Asah3l|CRG-L1|maCER2	alkaline ceramidase 2	protein-coding
mm_138076.1	chr17	33955809	33955819	+	1	NA	promoter-TSS (NM_011296)	promoter-TSS (NM_011296)	-68	NM_172620	224705	Mm.448614	NM_172620	ENSMUSG00000024319	Vps52	ARE1|D130068D18|D430041K17Rik|SAC2|Sacm2l|tclw5	VPS52 GARP complex subunit	protein-coding
mm_50801.1	chr6	54269166	54269172	+	1	NA	promoter-TSS (NM_001311134)	promoter-TSS (NM_001311134)	13	NM_001311134	69993	Mm.321147	NM_023543	ENSMUSG00000004633	Chn2	1700026N20Rik|4930557O16Rik|ARHGAP3|Bch	chimerin 2	protein-coding
mm_58585.1	chr7	4943841	4943854	+	1	NA	exon (NM_173008, exon 14 of 14)	exon (NM_173008, exon 14 of 14)	18003	NM_173008	269855	Mm.44190	NM_173008	ENSMUSG00000035279	Ssc5d	A430110N23Rik|S5D-SRCRB	scavenger receptor cysteine rich family, 5 domains	protein-coding
mm_99053.1	chr11	99051534	99051545	+	1	NA	exon (NM_010517, exon 4 of 4)	exon (NM_010517, exon 4 of 4)	10279	NM_010517	16010	Mm.233799	NM_010517	ENSMUSG00000017493	Igfbp4	AI875747|Deb2|IGFBP-4	insulin-like growth factor binding protein 4	protein-coding
mm_153934.1	chr19	47450604	47450652	-	1	NA	intron (NM_001164717, intron 1 of 13)	intron (NM_001164717, intron 1 of 13)	13783	NM_001164717	14218	Mm.127560	NM_008018	ENSMUSG00000053617	Sh3pxd2a	2310014D11Rik|AA589508|AI256723|AI413738|C230050L11|EG329070|Fish|Gm5098|Sh3md1|TSK5|Tks5	SH3 and PX domains 2A	protein-coding
mm_132964.1	chr16	50552108	50552121	+	1	NA	intron (NR_040379, intron 4 of 5)	MLTR11B|LTR|ERVK	23612	NR_040379	619312	Mm.427671	NR_040379		G730013B05Rik	linc-Cblb|linc1610	RIKEN cDNA G730013B05 gene	ncRNA
mm_115656.1	chr13	12457451	12457462	-	1	NA	intron (NM_001291060, intron 1 of 8)	intron (NM_001291060, intron 1 of 8)	1860	NM_001291055	56048	Mm.474138	NM_018886	ENSMUSG00000057554	Lgals8	1200015E08Rik|AI326142|D13Ertd524e|Lgals-8	lectin, galactose binding, soluble 8	protein-coding
mm_79242.1	chr9	50506396	50506398	+	1	NA	TTS (NM_029639)	TTS (NM_029639)	-1592	NR_040714	69631	Mm.414996	NR_040714	ENSMUSG00000101304	Plet1os	2310014F07Rik	placenta expressed transcript 1, opposite strand	ncRNA
mm_31526.1	chr4	55008879	55008919	+	1	NA	exon (NM_172867, exon 3 of 13)	exon (NM_172867, exon 3 of 13)	60954	NM_172867	242466	Mm.102904	NM_172867	ENSMUSG00000060206	Zfp462	6030417H05|9430078C22Rik|Gt4-2|Zfpip	zinc finger protein 462	protein-coding
mm_35652.1	chr4	43533355	43533374	-	1	NA	exon (NM_011602, exon 53 of 57)	exon (NM_011602, exon 53 of 57)	-9810	NM_001277875	22004	Mm.646	NM_009416	ENSMUSG00000028464	Tpm2	Tpm-2|Trop-2	tropomyosin 2, beta	protein-coding
mm_51320.1	chr6	72314876	72314892	+	1	NA	TTS (NM_001282071)	TTS (NM_001282071)	10274	NM_147779	20388	Mm.46033	NM_147779	ENSMUSG00000056370	Sftpb	AI562151|SF-B|SP-B|Sftp-3|Sftp3	surfactant associated protein B	protein-coding
mm_92806.1	chr10	81378399	81378456	-	1	NA	promoter-TSS (NM_019757)	promoter-TSS (NM_019757)	-57	NM_019757	56371	Mm.24202	NM_019757	ENSMUSG00000020235	Fzr1	AW108046|Cdh1|FZR|FZR2|Fyr|HCDH|HCDH1	fizzy/cell division cycle 20 related 1 (Drosophila)	protein-coding
mm_165826.1	chr3	151294532	151294546	+	1	NA	Intergenic	Intergenic	-143343	NM_133222	170757	Mm.317261	NM_133222	ENSMUSG00000039167	Adgrl4	1110033N21Rik|ETL1|Eltd1|Etl	adhesion G protein-coupled receptor L4	protein-coding
mm_111843.1	chr12	107938673	107938691	-	1	NA	intron (NM_001286343, intron 1 of 1)	(TG)n|Simple_repeat|Simple_repeat	64732	NM_001079883	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_6408.1	chr1	72874146	72874208	-	1	NA	5' UTR (NM_010518, exon 1 of 4)	5' UTR (NM_010518, exon 1 of 4)	688	NM_010518	16011	Mm.405761	NM_010518	ENSMUSG00000026185	Igfbp5	AI256729|AW208790|IGFBP-5|IGFBP-5P	insulin-like growth factor binding protein 5	protein-coding
mm_38310.1	chr4	136956785	136956871	-	1	NA	promoter-TSS (NM_007939)	promoter-TSS (NM_007939)	-12	NM_007939	13842	Mm.1390	NM_007939	ENSMUSG00000028661	Epha8	AW047546|Eek|Hek3|mKIAA1459	Eph receptor A8	protein-coding
mm_154391.1	chrM	12976	13016	+	1	NA	NA	Intergenic	NA	NA								
mm_32090.1	chr4	98437311	98437317	+	1	NA	intron (NM_001005784, intron 11 of 19)	intron (NM_001005784, intron 11 of 19)	41488	NM_172696	12695	Mm.90218	NM_007704	ENSMUSG00000061859	Patj	Cipp|Inadl	PATJ, crumbs cell polarity complex component	protein-coding
mm_118452.1	chr14	8367413	8367419	+	1	NA	intron (NM_146050, intron 1 of 9)	RMER17C|LTR|ERVK	11347	NM_146050	18300	Mm.25351	NM_146050	ENSMUSG00000021749	Oit1	2310076N21Rik|AV067083|EF-7|Fam3d	oncoprotein induced transcript 1	protein-coding
mm_82560.1	chr9	21033323	21033337	-	1	NA	exon (NM_008319, exon 2 of 11)	exon (NM_008319, exon 2 of 11)	-1002	NR_035438	100316681		NR_035438	ENSMUSG00000084663	Mir1900	Mirn1900|mmu-mir-1900	microRNA 1900	ncRNA
mm_12124.1	chr2	61630802	61630817	+	1	NA	intron (NM_011529, intron 4 of 7)	intron (NM_011529, intron 4 of 7)	37712	NM_001164071	21353	Mm.244393	NM_011529	ENSMUSG00000064289	Tank	C86182|E430026L09Rik|I-TRAF	TRAF family member-associated Nf-kappa B activator	protein-coding
mm_27298.1	chr3	46447940	46447980	-	1	NA	promoter-TSS (NM_001101479)	promoter-TSS (NM_001101479)	-19	NM_001101479	241989	Mm.119234	NM_001101479	ENSMUSG00000090919	Pabpc4l	C330050A14Rik|EG241989	poly(A) binding protein, cytoplasmic 4-like	protein-coding
mm_140346.1	chr17	86830973	86830977	+	1	NA	exon (NM_010137, exon 16 of 16)	exon (NM_010137, exon 16 of 16)	77111	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_171874.1	chr5	29736018	29736021	+	1	NA	promoter-TSS (NR_028426)	promoter-TSS (NR_028426)	-83	NR_028426	332993	Mm.473746	NR_028426		Gm5129	EG332993|ENSMUSG00000053121	predicted gene 5129	ncRNA
mm_5975.1	chr1	57970009	57970022	-	1	NA	promoter-TSS (NM_001159864)	promoter-TSS (NM_001159864)	69	NM_001159864	51960	Mm.339711	NM_030211	ENSMUSG00000054770	Kctd18	4932411A20Rik|6530404F10Rik	potassium channel tetramerisation domain containing 18	protein-coding
mm_60650.1	chr7	44857310	44857354	+	1	NA	promoter-TSS (NM_001290767)	promoter-TSS (NM_001290767)	-71	NM_001290767	59047	Mm.238254	NM_021549	ENSMUSG00000002963	Pnkp	1810009G08Rik|PNK	polynucleotide kinase 3'- phosphatase	protein-coding
mm_144736.1	chr18	35562287	35562297	+	1	NA	5' UTR (NM_010771, exon 1 of 15)	5' UTR (NM_010771, exon 1 of 15)	134	NM_010771	17184	Mm.215034	NM_010771	ENSMUSG00000037236	Matr3	1110061A14Rik|2810017I02Rik|AI841759|AW555618|D030046F20Rik|mKIAA0723	matrin 3	protein-coding
mm_70970.1	chr8	27085521	27085580	+	1	NA	promoter-TSS (NM_054044)	promoter-TSS (NM_054044)	-291	NM_054044	78560	Mm.87046	NM_054044	ENSMUSG00000031486	Adgra2	8430414O08Rik|9530074E10Rik|Gpr124|Tem5|mKIAA1531	adhesion G protein-coupled receptor A2	protein-coding
mm_149666.1	chr19	18749746	18749768	+	1	NA	promoter-TSS (NM_153417)	promoter-TSS (NM_153417)	-226	NM_153417	225997	Mm.215171	NM_153417	ENSMUSG00000024727	Trpm6	CHAK2|TRPM6/CHAK2	transient receptor potential cation channel, subfamily M, member 6	protein-coding
mm_66937.1	chr7	61615288	61615301	-	1	NA	promoter-TSS (NR_045727)	promoter-TSS (NR_045727)	33	NR_045727	319752	Mm.294476	NR_045727		B230209E15Rik	-	RIKEN cDNA B230209E15 gene	ncRNA
mm_53459.1	chr6	134830765	134830774	+	1	NA	intron (NM_177687, intron 1 of 4)	(T)n|Simple_repeat|Simple_repeat	570	NM_177687	232430	Mm.267010	NM_177687	ENSMUSG00000032652	Crebl2	AI046348|B230205M03	cAMP responsive element binding protein-like 2	protein-coding
mm_148407.1	chr19	3896050	3896056	+	1	NA	TTS (NM_001136091)	TTS (NM_001136091)	9177	NM_016921	27060	Mm.271689	NM_016921	ENSMUSG00000001750	Tcirg1	ATP6N1C|ATP6a3|Atp6i|OC-116|OPTB1|Stv1|TIRC7|Vph1|oc	T cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 protein A3	protein-coding
mm_55919.1	chr6	83831706	83831720	-	1	NA	promoter-TSS (NM_146169)	promoter-TSS (NM_146169)	28	NM_146169	232164	Mm.404420	NM_146169	ENSMUSG00000045896	Paip2b	-	poly(A) binding protein interacting protein 2B	protein-coding
mm_84477.1	chr9	66834623	66834634	-	1	NA	promoter-TSS (NM_026674)	promoter-TSS (NM_026674)	78	NM_026674	68318	Mm.284229	NM_026674	ENSMUSG00000053040	Aph1c	0610008A10Rik|APH-1b|Aph1b	aph1 homolog C, gamma secretase subunit	protein-coding
mm_83136.1	chr9	40437246	40437257	-	1	NA	intron (NM_172768, intron 1 of 19)	B3|SINE|B2	18513	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_41837.1	chr5	104309366	104309400	+	1	NA	exon (NM_008318, exon 6 of 7)	exon (NM_008318, exon 6 of 7)	10096	NM_008318	15891	Mm.4987	NM_008318	ENSMUSG00000029306	Ibsp	BSP|BSP II|BSPII|Bsp2	integrin binding sialoprotein	protein-coding
mm_166312.1	chr5	108694200	108694217	+	1	NA	promoter-TSS (NM_001164259)	promoter-TSS (NM_001164259)	-21	NM_001164259	116701	Mm.35691	NM_054071	ENSMUSG00000008090	Fgfrl1	FGFR5|FGFR5beta|FGFR5gamma	fibroblast growth factor receptor-like 1	protein-coding
mm_54097.1	chr6	16837215	16837231	-	1	NA	intron (NM_031198, intron 5 of 6)	L1_Mus3|LINE|L1	61218	NM_031198	21426	Mm.36217	NM_031198	ENSMUSG00000029553	Tfec	BB107417|Tcfec|bHLHe34	transcription factor EC	protein-coding
mm_124487.1	chr14	121738544	121738553	-	1	NA	5' UTR (NM_001128307, exon 1 of 56)	5' UTR (NM_001128307, exon 1 of 56)	381	NM_001128308	105445	Mm.378591	NM_134074	ENSMUSG00000025558	Dock9	AA959601|AW538057|B230309H04Rik|D14Wsu89e|Zizimin1|mKIAA1058	dedicator of cytokinesis 9	protein-coding
mm_134682.1	chr16	22411918	22411926	-	1	NA	intron (NM_023794, intron 6 of 12)	intron (NM_023794, intron 6 of 12)	27648	NM_023794	104156	Mm.155708	NM_023794	ENSMUSG00000013089	Etv5	1110005E01Rik|8430401F14Rik|ERM	ets variant 5	protein-coding
mm_91394.1	chr10	30763558	30763561	-	1	NA	intron (NM_172495, intron 2 of 15)	intron (NM_172495, intron 2 of 15)	39548	NM_172495	211329	Mm.297903	NM_172495	ENSMUSG00000039697	Ncoa7	9030406N13Rik	nuclear receptor coactivator 7	protein-coding
mm_4443.1	chr1	172521107	172521150	+	1	NA	promoter-TSS (NM_027972)	promoter-TSS (NM_027972)	-2	NM_027972	71870	Mm.78373	NM_027972	ENSMUSG00000026546	Cfap45	1700028D05Rik|Ccdc19|Nesg1	cilia and flagella associated protein 45	protein-coding
mm_60088.1	chr7	34659959	34659969	+	1	NA	Intergenic	Intergenic	-7123	NM_146188	233107	Mm.486198	NM_146188	ENSMUSG00000030499	Kctd15	BC031749	potassium channel tetramerisation domain containing 15	protein-coding
mm_107921.1	chr12	71063201	71063212	+	1	NA	exon (NM_001081195, exon 15 of 24)	exon (NM_001081195, exon 15 of 24)	47239	NM_001081195	238247	Mm.241601	NM_001081195	ENSMUSG00000048118	Arid4a	A630009N03|A630067N03Rik|MmRBBP1|Rbbp1	AT rich interactive domain 4A (RBP1-like)	protein-coding
mm_19164.1	chr2	83941221	83941230	-	1	NA	promoter-TSS (NM_027964)	promoter-TSS (NM_027964)	1	NM_027964	71861	Mm.116957	NM_027964	ENSMUSG00000034552	Zswim2	1700025P14Rik|4933437F18Rik|MEX	zinc finger SWIM-type containing 2	protein-coding
mm_76538.1	chr8	87960621	87960642	-	1	NA	Intergenic	CpG-14330	-1036	NM_033327	94187	Mm.23452	NM_033327	ENSMUSG00000045333	Zfp423	Ebfaz|Roaz|Zfp104|Znf423|ataxia1|mKIAA0760|nur12	zinc finger protein 423	protein-coding
mm_64539.1	chr7	144238691	144238705	+	1	NA	intron (NM_001113373, intron 4 of 15)	intron (NM_001113373, intron 4 of 15)	-45687	NM_001081370	210274	Mm.483624	NM_001081370	ENSMUSG00000037541	Shank2	ProSAP1|mKIAA1022	SH3/ankyrin domain gene 2	protein-coding
mm_133468.1	chr16	89215930	89215932	+	1	NA	Intergenic	Intergenic	10070	NM_001163615	622935	Mm.459837	NM_001163615	ENSMUSG00000091039	Krtap20-2	1190004K03Rik|EG622935|Gm6371	keratin associated protein 20-2	protein-coding
mm_73825.1	chr8	117459376	117459407	+	1	NA	TTS (NR_106046)	TTS (NR_106046)	126	NR_106046	102465653		NR_106046	ENSMUSG00000098483	Mir7078	Gm27386|mmu-mir-7078	microRNA 7078	ncRNA
mm_56753.1	chr6	115994954	115995010	-	1	NA	promoter-TSS (NM_026376)	promoter-TSS (NM_026376)	23	NM_026376	67784	Mm.3085	NM_026376	ENSMUSG00000030123	Plxnd1	6230425C21Rik|b2b1863Clo|b2b553Clo	plexin D1	protein-coding
mm_51228.1	chr6	71373495	71373584	+	1	NA	5' UTR (NM_009857, exon 1 of 4)	5' UTR (NM_009857, exon 1 of 4)	112	NM_001081110	12525	Mm.1858	NM_009857	ENSMUSG00000053977	Cd8a	BB154331|Ly-2|Ly-35|Ly-B|Lyt-2	CD8 antigen, alpha chain	protein-coding
mm_161214.1	chr13	65205837	65205837	-	1	NA	promoter-TSS (NM_175290)	promoter-TSS (NM_175290)	-121	NM_175290	97895	Mm.315815	NM_175290	ENSMUSG00000032999	Nlrp4f	C330026N02Rik|C86045|Nalp-kappa|Nalp4f	NLR family, pyrin domain containing 4F	protein-coding
mm_165778.1	chr3	129753715	129753752	+	1	NA	promoter-TSS (NR_040589)	promoter-TSS (NR_040589)	-25	NR_040589	319224	Mm.477035	NR_040589	ENSMUSG00000105960	6330410L21Rik	-	RIKEN cDNA 6330410L21 gene	ncRNA
mm_37032.1	chr4	115134064	115134084	-	1	NA	promoter-TSS (NM_001003947)	promoter-TSS (NM_001003947)	-97	NM_001003947	81906	Mm.215544	NM_001003947	ENSMUSG00000047155	Cyp4x1	A230025G20|CYPIVX1|CYP_a|Cyp4a28-ps	cytochrome P450, family 4, subfamily x, polypeptide 1	protein-coding
mm_104045.1	chr11	86356130	86356132	-	1	NA	intron (NM_001080931, intron 1 of 29)	intron (NM_001080931, intron 1 of 29)	1394	NM_001080931	327987	Mm.341886	NM_001080931	ENSMUSG00000034297	Med13	1110067M05Rik|D030023K18|Thrap1|Trap240	mediator complex subunit 13	protein-coding
mm_172754.1	chr8	85299463	85299481	-	1	NA	promoter-TSS (NM_019716)	promoter-TSS (NM_019716)	25	NM_022997	65114	Mm.296520	NM_022997	ENSMUSG00000031696	Vps35	AI647796|Mem3	VPS35 retromer complex component	protein-coding
mm_118744.1	chr14	22318729	22318752	+	1	NA	intron (NM_028275, intron 2 of 6)	B3|SINE|B2	224058	NR_046307	74896	Mm.444661	NR_046307		4930405A10Rik	4930456G20Rik	RIKEN cDNA 4930405A10 gene	ncRNA
mm_50294.1	chr6	47455000	47455008	+	1	NA	intron (NM_012042, intron 1 of 21)	CpG	680	NM_012042	26965	Mm.87611	NM_012042	ENSMUSG00000029686	Cul1	-	cullin 1	protein-coding
mm_14404.1	chr2	130123311	130123314	+	1	NA	promoter-TSS (NM_177726)	promoter-TSS (NM_177726)	37	NM_177726	241636	Mm.83437	NM_177726	ENSMUSG00000027403	Tgm6	TGM3L|TGY	transglutaminase 6	protein-coding
mm_59207.1	chr7	24512645	24512651	+	1	NA	intron (NR_110958, intron 2 of 2)	intron (NR_110958, intron 2 of 2)	5561	NR_110958	232969	Mm.181332	NM_146183	ENSMUSG00000064264	Zfp428	2410005H09Rik|AV271806|AW047854|Znf428	zinc finger protein 428	protein-coding
mm_85557.1	chr9	106887060	106887094	-	1	NA	promoter-TSS (NM_175402)	promoter-TSS (NM_175402)	-77	NM_175402	109095	Mm.431589	NM_175402	ENSMUSG00000074102	Rbm15b	1810017N16Rik	RNA binding motif protein 15B	protein-coding
mm_68809.1	chr7	125492544	125492590	-	1	NA	Intergenic	Intergenic	-1025	NM_026330	67711	Mm.4467	NM_026330	ENSMUSG00000030750	Nsmce1	2510027N19Rik	NSE1 homolog, SMC5-SMC6 complex component	protein-coding
mm_58251.1	chr6	145048840	145048853	-	1	NA	promoter-TSS (NM_001024468)	promoter-TSS (NM_001024468)	-34	NM_001024468	12035	Mm.4606	NM_007532	ENSMUSG00000030268	Bcat1	BCATc|Eca39	branched chain aminotransferase 1, cytosolic	protein-coding
mm_132942.1	chr16	49857881	49857890	+	1	NA	intron (NM_010581, intron 1 of 9)	intron (NM_010581, intron 1 of 9)	2231	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_78497.1	chr9	32728602	32728608	+	1	NA	intron (NM_011808, intron 1 of 7)	intron (NM_011808, intron 1 of 7)	32563	NM_001038642	23871	Mm.292415	NM_011808	ENSMUSG00000032035	Ets1	AI196000|AI448617|D230050P06|Ets-1|Tpl1|vs	E26 avian leukemia oncogene 1, 5' domain	protein-coding
mm_122374.1	chr14	39473619	39473630	-	1	NA	promoter-TSS (NM_008734)	promoter-TSS (NM_008734)	-536	NM_008734	18183	Mm.258705	NM_008734	ENSMUSG00000041014	Nrg3	ska	neuregulin 3	protein-coding
mm_52969.1	chr6	123207514	123207517	+	1	NA	Intergenic	RMER19B|LTR|ERVK	-22328	NM_020001	56620	Mm.271782	NM_020001	ENSMUSG00000023349	Clec4n	Clec6a|Clecsf10|Nkcl	C-type lectin domain family 4, member n	protein-coding
mm_158694.1	chrX	160994666	160994686	-	1	NA	promoter-TSS (NM_001024624)	promoter-TSS (NM_001024624)	5	NM_001024624	382253	Mm.443717	NM_001024624	ENSMUSG00000031292	Cdkl5	BC038161|Stk9	cyclin-dependent kinase-like 5	protein-coding
mm_132575.1	chr16	38240823	38240840	+	1	NA	3' UTR (NM_019827, exon 11 of 11)	3' UTR (NM_019827, exon 11 of 11)	53993	NM_010936	18171	Mm.8509	NM_010936	ENSMUSG00000022809	Nr1i2	PXR|PXR.1|PXR.2|PXR1|SXR|mPXR	nuclear receptor subfamily 1, group I, member 2	protein-coding
mm_158347.1	chrX	134474987	134475016	-	1	NA	intron (NM_028958, intron 1 of 12)	CpG	1489	NM_028958	74469	Mm.103259	NM_028958	ENSMUSG00000009596	Taf7l	4933438I11Rik|Taf2q	TATA-box binding protein associated factor 7 like	protein-coding
mm_21291.1	chr2	156991988	156992005	-	1	NA	intron (NM_013865, intron 1 of 15)	CpG	115	NM_013865	29812	Mm.279256	NM_013865	ENSMUSG00000027634	Ndrg3	4833415O14Rik|AI747193|Ndr3	N-myc downstream regulated gene 3	protein-coding
mm_157177.1	chrX	9655660	9655672	-	1	NA	3' UTR (NM_025975, exon 5 of 5)	3' UTR (NM_025975, exon 5 of 5)	7317	NM_025975	67117	Mm.29150	NM_025975	ENSMUSG00000031176	Dynlt3	2310075M16Rik|AU042796|Tcte1l	dynein light chain Tctex-type 3	protein-coding
mm_62812.1	chr7	113220645	113220652	+	1	NA	intron (NM_001243048, intron 1 of 16)	intron (NM_001243048, intron 1 of 16)	13183	NM_007489	11865	Mm.33970	NM_007489	ENSMUSG00000055116	Arntl	Arnt3|BMAL1b|Bmal1|MOP3|bHLHe5|bmal1b'	aryl hydrocarbon receptor nuclear translocator-like	protein-coding
mm_121436.1	chr14	120414786	120414790	+	1	NA	intron (NM_175341, intron 8 of 8)	B4A|SINE|B4	-63673	NM_029519	76108	Mm.261448	NM_029519	ENSMUSG00000051615	Rap2a	5830461H18Rik	RAS related protein 2a	protein-coding
mm_56061.1	chr6	86775162	86775183	-	1	NA	promoter-TSS (NM_001331120)	promoter-TSS (NM_001331120)	-58	NM_001331120	11746	Mm.259702	NM_013471	ENSMUSG00000029994	Anxa4	AI265406|AIV|AW106930|Anx4|Xanx-4	annexin A4	protein-coding
mm_161778.1	chr17	37850379	37850379	+	1	NA	promoter-TSS (NM_146890)	promoter-TSS (NM_146890)	-215	NM_146890	258892	Mm.377736	NM_146890	ENSMUSG00000109212	Olfr126	MOR218-1	olfactory receptor 126	protein-coding
mm_8558.1	chr1	155244461	155244497	-	1	NA	Intergenic	CpG	85776	NM_021433	58244	Mm.66264	NM_021433	ENSMUSG00000026470	Stx6	2310039E05Rik|2410005I16Rik|AA437559|AI415714|AI845861	syntaxin 6	protein-coding
mm_48529.1	chr5	142903795	142903800	-	1	NA	3' UTR (NM_007393, exon 6 of 6)	3' UTR (NM_007393, exon 6 of 6)	2957	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_90588.1	chr10	128270547	128270577	+	1	NA	promoter-TSS (NM_019963)	promoter-TSS (NM_019963)	-14	NM_019963	20847	Mm.293120	NM_019963	ENSMUSG00000040033	Stat2	1600010G07Rik|AW496480	signal transducer and activator of transcription 2	protein-coding
mm_167719.1	chr9	99035757	99035769	-	1	NA	promoter-TSS (NM_001080776)	promoter-TSS (NM_001080776)	-73	NM_001080776	382097	Mm.293727	NM_001080776	ENSMUSG00000044860	Gm1123	AV052824|CLSP	predicted gene 1123	protein-coding
mm_161263.1	chr14	3395093	3395093	+	1	NA	promoter-TSS (NM_001270806).2	promoter-TSS (NM_001270806).2	0	NM_029288	100041774	Mm.360540	NM_029288	ENSMUSG00000095533	Gm10413	100038846|1700001E04Rik|ENSMUSG00000072749|Gm1973	predicted gene 10413	protein-coding
mm_56581.1	chr6	106794188	106794197	-	1	NA	exon (NM_021449, exon 4 of 11)	exon (NM_021449, exon 4 of 11)	5895	NM_021449	58799	Mm.290085	NM_021449	ENSMUSG00000005362	Crbn	2610203G15Rik|2900045O07Rik|AF229032|AW108261|piL	cereblon	protein-coding
mm_106204.1	chr11	116843456	116843505	-	1	NA	promoter-TSS (NM_028865)	promoter-TSS (NM_028865)	-31	NM_033398	107817	Mm.481684	NM_033398	ENSMUSG00000056962	Jmjd6	5730436I23Rik|D11Ertd195e|PSR|PtdSerR|Ptdsr|mKIAA0585	jumonji domain containing 6	protein-coding
mm_66189.1	chr7	34196642	34196675	-	1	NA	promoter-TSS (NM_026549)	promoter-TSS (NM_026549)	-11	NM_026549	68079	Mm.38173	NM_026549	ENSMUSG00000002635	Pdcd2l	6030457N17Rik	programmed cell death 2-like	protein-coding
mm_160234.1	chr7	102857081	102857081	-	1	NA	exon (NM_001011536, exon 1 of 1)	exon (NM_001011536, exon 1 of 1)	190	NM_001011536	258168	Mm.377368	NM_001011536	ENSMUSG00000060888	Olfr566	GA_x5J8B7W5P47-379997-380552|MOR14-7P	olfactory receptor 566	protein-coding
mm_72921.1	chr8	91082170	91082189	+	1	NA	intron (NM_001282000, intron 4 of 20)	intron (NM_001282000, intron 4 of 20)	12122	NM_001282000	19651	Mm.235580	NM_011250	ENSMUSG00000031666	Rbl2	PRB2|RBR-2|Rb2|p130	retinoblastoma-like 2	protein-coding
mm_108428.1	chr12	82245519	82245527	+	1	NA	intron (NM_001167983, intron 2 of 23)	L1M4c|LINE|L1	-65826	NM_172579	217692	Mm.261333	NM_172579	ENSMUSG00000042700	Sipa1l1	4931426N11Rik|AW213287|Spar|mKIAA0440	signal-induced proliferation-associated 1 like 1	protein-coding
mm_34812.1	chr4	154936235	154936243	+	1	NA	Intergenic	B3A|SINE|B2	-8162	NM_178931	230979	Mm.215147	NM_178931	ENSMUSG00000042333	Tnfrsf14	Atar|HveA|Hvem|Tnfrs14	tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)	protein-coding
mm_85658.1	chr9	107667376	107667390	-	1	NA	promoter-TSS (NM_001199217)	promoter-TSS (NM_001199217)	16	NM_023805	76257	Mm.296560	NM_023805	ENSMUSG00000010064	Slc38a3	0610012J02Rik|D9Ucla2|Nat1|Slc38-3|Sn1|Snat3|mNAT	solute carrier family 38, member 3	protein-coding
mm_167478.1	chr8	129067130	129067141	+	1	NA	promoter-TSS (NM_029292)	promoter-TSS (NM_029292)	1	NM_001168369	75453	Mm.286964	NM_029292	ENSMUSG00000056018	Ccdc7b	1700008F21Rik	coiled-coil domain containing 7B	protein-coding
mm_18089.1	chr2	44984562	44984574	-	1	NA	3' UTR (NM_015753, exon 10 of 10)	3' UTR (NM_015753, exon 10 of 10)	38609	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_134943.1	chr16	31275219	31275234	-	1	NA	promoter-TSS (NM_025800)	promoter-TSS (NM_025800)	51	NM_025800	66849	Mm.291593	NM_025800	ENSMUSG00000047714	Ppp1r2	0610025N14Rik|2310007G06Rik|4930440J04Rik|5430408E15Rik|D16Ertd248e|IPP-2	protein phosphatase 1, regulatory (inhibitor) subunit 2	protein-coding
mm_170269.1	chr18	21536612	21536619	+	1	NA	Intergenic	L1Md_T|LINE|L1	-114950	NM_001271580	74644	Mm.329311	NM_001271580		4930426D05Rik	-	RIKEN cDNA 4930426D05 gene	protein-coding
mm_161492.1	chr15	85979037	85979037	-	1	NA	exon (NM_009886, exon 2 of 35)	exon (NM_009886, exon 2 of 35)	54740	NM_009886	12614	Mm.22680	NM_009886	ENSMUSG00000016028	Celsr1	Adgrc1|Crsh|Scy|crash	cadherin, EGF LAG seven-pass G-type receptor 1	protein-coding
mm_122092.1	chr14	30625896	30625937	-	1	NA	intron (NM_011103, intron 1 of 17)	CpG	292	NM_011103	18753	Mm.2314	NM_011103	ENSMUSG00000021948	Prkcd	AI385711|D14Ertd420e|PKC[d]|PKCdelta|Pkcd	protein kinase C, delta	protein-coding
mm_128412.1	chr15	44748423	44748442	-	1	NA	5' UTR (NM_001285840, exon 1 of 7)	5' UTR (NM_001285840, exon 1 of 7)	240	NM_001285840	319613	Mm.207715	NM_176998	ENSMUSG00000022340	Sybu	Golsyn	syntabulin (syntaxin-interacting)	protein-coding
mm_161158.1	chr13	26769963	26769963	-	1	NA	exon (NM_008232, exon 1 of 1)	exon (NM_008232, exon 1 of 1)	202	NM_008232	15192	Mm.7411	NM_008232	ENSMUSG00000045835	Hdgfl1	4921520N01Rik|HRP-1|Hdgfrp1|Pwwp1	hepatoma derived growth factor-like 1	protein-coding
mm_123927.1	chr14	73365744	73365756	-	1	NA	intron (NM_008410, intron 4 of 5)	intron (NM_008410, intron 4 of 5)	19521	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_125898.1	chr15	75940994	75941015	+	1	NA	promoter-TSS (NM_030199)	promoter-TSS (NM_030199)	52	NM_030199	78834	Mm.273264	NM_030199	ENSMUSG00000050846	Zfp623	2610029D06Rik|AI847036	zinc finger protein 623	protein-coding
mm_96291.1	chr11	63131517	63131539	+	1	NA	promoter-TSS (NM_008885)	promoter-TSS (NM_008885)	71	NM_001302255	18858	Mm.1237	NM_008885	ENSMUSG00000018217	Pmp22	22kDa|Gas-3|HNPP|Tr|trembler	peripheral myelin protein 22	protein-coding
mm_123922.1	chr14	73365456	73365487	-	1	NA	intron (NM_008410, intron 4 of 5)	RSINE1|SINE|B4	19800	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_12876.1	chr2	84659066	84659082	+	1	NA	promoter-TSS (NM_001145100)	promoter-TSS (NM_001145100)	-5	NM_001145100	100270744	Mm.393636	NM_001145100	ENSMUSG00000086598	Btbd18	Btbd18-ps|Gm13718|OTTMUSG00000013494	BTB (POZ) domain containing 18	protein-coding
mm_128588.1	chr15	58112134	58112137	-	1	NA	intron (NM_027435, intron 13 of 27)	intron (NM_027435, intron 13 of 27)	22947	NM_027435	70472	Mm.221758	NM_027435	ENSMUSG00000022360	Atad2	2610509G12Rik	ATPase family, AAA domain containing 2	protein-coding
mm_130424.1	chr15	98093330	98093410	-	1	NA	5' UTR (NM_144851, exon 1 of 18)	5' UTR (NM_144851, exon 1 of 18)	199	NM_144851	223870	Mm.384023	NM_144851	ENSMUSG00000033075	Senp1	2310046A20Rik|D15Ertd528e|E330036L07Rik|suPr-2	SUMO1/sentrin specific peptidase 1	protein-coding
mm_119746.1	chr14	54136741	54136750	+	1	NA	Intergenic	Intergenic	117184	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_93394.1	chr10	107494748	107494761	-	1	NA	promoter-TSS (NM_008657)	promoter-TSS (NM_008657)	-25	NM_008657	17878	Mm.11	NM_008657	ENSMUSG00000035923	Myf6	MRF4|bHLHc4|herculin	myogenic factor 6	protein-coding
mm_4217.1	chr1	171329016	171329027	+	1	NA	promoter-TSS (NM_001128609)	promoter-TSS (NM_001128609)	-124	NM_001128609	21945	Mm.270139	NM_011615	ENSMUSG00000013973	Dedd	CASP8IP1|DEFT|Dedpro1|FLDED1|KE05	death effector domain-containing	protein-coding
mm_164156.1	chr15	66782881	66782882	-	1	NA	intron (NM_009192, intron 8 of 8)	intron (NM_009192, intron 8 of 8)	48948	NM_001029841	20491	Mm.7601	NM_009192	ENSMUSG00000022372	Sla	Slap|Slap-1	src-like adaptor	protein-coding
mm_10787.1	chr2	24345408	24345422	+	1	NA	promoter-TSS (NM_001039701)	promoter-TSS (NM_001039701)	44	NM_001039701	16181	Mm.882	NM_031167	ENSMUSG00000026981	Il1rn	F630041P17Rik|IL-1ra	interleukin 1 receptor antagonist	protein-coding
mm_163160.1	chr11	84068787	84068797	-	1	NA	promoter-TSS (NM_019819)	promoter-TSS (NM_019819)	-435	NM_019819	56405	Mm.240885	NM_019819	ENSMUSG00000018648	Dusp14	1110014C10Rik|2310042C07Rik|D11Ertd395e|MKP-L|Mkp6	dual specificity phosphatase 14	protein-coding
mm_162421.1	chr1	91459472	91459489	+	1	NA	promoter-TSS (NM_011066)	promoter-TSS (NM_011066)	-152	NM_011066	18627	Mm.482463	NM_011066	ENSMUSG00000055866	Per2	mKIAA0347|mPer2	period circadian clock 2	protein-coding
mm_19782.1	chr2	106974362	106974381	-	1	NA	promoter-TSS (NM_001025102)	promoter-TSS (NM_001025102)	26	NM_001025102	212772	Mm.381231	NM_173750	ENSMUSG00000027122	Arl14ep	2700007P21Rik|4930448O08Rik|ARF7EP	ADP-ribosylation factor-like 14 effector protein	protein-coding
mm_73462.1	chr8	106659649	106659665	+	1	NA	exon (NM_009864, exon 9 of 16)	exon (NM_009864, exon 9 of 16)	-23411	NM_173037	272538	Mm.87151	NM_173037	ENSMUSG00000041949	Tango6	AW413431|E330010G16|Tmco7	transport and golgi organization 6	protein-coding
mm_92250.1	chr10	70592783	70592848	-	1	NA	promoter-TSS (NM_001162846)	promoter-TSS (NM_001162846)	-3	NM_001162846	70911	Mm.19825	NM_178621	ENSMUSG00000037747	Phyhipl	4921522K17Rik|AI267048	phytanoyl-CoA hydroxylase interacting protein-like	protein-coding
mm_11758.1	chr2	38511671	38511747	+	1	NA	promoter-TSS (NM_021606)	promoter-TSS (NM_021606)	12	NM_021606	59126	Mm.143818	NM_021606	ENSMUSG00000026749	Nek6	1300007C09Rik	NIMA (never in mitosis gene a)-related expressed kinase 6	protein-coding
mm_78660.1	chr9	40487663	40487685	+	1	NA	Intergenic	Intergenic	-31910	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_109491.1	chr12	111445966	111445997	+	1	NA	exon (NM_009396, exon 3 of 12)	exon (NM_009396, exon 3 of 12)	3320	NM_009396	21928	Mm.255332	NM_009396	ENSMUSG00000021281	Tnfaip2	B94|Exoc3l3|M-sec|Tnfip2|tnfb94	tumor necrosis factor, alpha-induced protein 2	protein-coding
mm_99825.1	chr11	108920400	108920493	+	1	NA	promoter-TSS (NM_015732)	promoter-TSS (NM_015732)	97	NM_015732	12006	Mm.71710	NM_015732	ENSMUSG00000000142	Axin2	Axi1|Axil|Conductin	axin 2	protein-coding
mm_47728.1	chr5	130171542	130171568	-	1	NA	promoter-TSS (NM_001199059)	promoter-TSS (NM_001199059)	-264	NM_001199059	56715	Mm.288639	NM_019983	ENSMUSG00000025340	Rabgef1	Rab5ef|Rabex5|Rin2	RAB guanine nucleotide exchange factor (GEF) 1	protein-coding
mm_105511.1	chr11	106216319	106216363	-	1	NA	promoter-TSS (NM_026009)	promoter-TSS (NM_026009)	26	NM_026009	67163	Mm.22109	NM_026009	ENSMUSG00000078622	Ccdc47	2610204L23Rik|C88307|asp4|calumin	coiled-coil domain containing 47	protein-coding
mm_17678.1	chr2	32287986	32287996	-	1	NA	promoter-TSS (NM_133852)	promoter-TSS (NM_133852)	78	NR_110965	72931	Mm.27344	NM_175190	ENSMUSG00000044627	Swi5	1500019F05Rik|2900010J23Rik|AI046671	SWI5 recombination repair homolog (yeast)	protein-coding
mm_94393.1	chr11	5541933	5541942	+	1	NA	exon (NM_134033, exon 1 of 5)	exon (NM_134033, exon 1 of 5)	280	NM_134033	104479	Mm.210403	NM_134033	ENSMUSG00000020482	Ccdc117	1110004K02Rik|1700026O03Rik|AU018638|AU042822|AV173073|BC018601	coiled-coil domain containing 117	protein-coding
mm_156546.1	chrX	151344208	151344240	+	1	NA	promoter-TSS (NM_198105)	promoter-TSS (NM_198105)	1	NM_198105	207375	Mm.391339	NM_198105	ENSMUSG00000025262	Fam120c	D930001I21Rik|ORF34	family with sequence similarity 120, member C	protein-coding
mm_22817.1	chr3	27194261	27194266	+	1	NA	intron (NM_178772, intron 1 of 4)	L3|LINE|CR1	11259	NM_178772	320024	Mm.24576	NM_178772	ENSMUSG00000027698	Nceh1	Aadacl1|B230106I24Rik|CPO-BP|Nceh	neutral cholesterol ester hydrolase 1	protein-coding
mm_22943.1	chr3	31954822	31954832	+	1	NA	intron (NM_028231, intron 2 of 5)	intron (NM_028231, intron 2 of 5)	52124	NM_028231	72413	Mm.64790	NM_028231	ENSMUSG00000037610	Kcnmb2	2700049B16Rik|3110031N04Rik	potassium large conductance calcium-activated channel, subfamily M, beta member 2	protein-coding
mm_12410.1	chr2	70509422	70509470	+	1	NA	exon (NM_025744, exon 1 of 13)	exon (NM_025744, exon 1 of 13)	627	NM_025744	66748	Mm.423014	NM_025744	ENSMUSG00000075302	Erich2	4933404M02Rik	glutamate rich 2	protein-coding
mm_2581.1	chr1	118597273	118597276	+	1	NA	intron (NM_001293300, intron 38 of 40)	intron (NM_001293300, intron 38 of 40)	-30671	NM_023755	81879	Mm.24621	NM_023755	ENSMUSG00000026380	Tfcp2l1	1810030F05Rik|4932442M07Rik|AA575098|Cp2l1|Crtr-1|D930018N21Rik|LBP-9|Tcfcp2l1	transcription factor CP2-like 1	protein-coding
mm_41401.1	chr5	90786364	90786384	+	1	NA	exon (NM_203320, exon 2 of 4)	exon (NM_203320, exon 2 of 4)	273	NM_203320	330122	Mm.244289	NM_203320	ENSMUSG00000029379	Cxcl3	Dcip1|Gm1960	chemokine (C-X-C motif) ligand 3	protein-coding
mm_144886.1	chr18	36801827	36801842	+	1	NA	promoter-TSS (NR_027885)	promoter-TSS (NR_027885)	71	NR_027885	378472	Mm.482379	NR_027885		Vaultrc5	Gm22653|Mvg1	vault RNA component 5	ncRNA
mm_95723.1	chr11	54523314	54523360	+	1	NA	intron (NM_175258, intron 1 of 27)	intron (NM_175258, intron 1 of 27)	492	NM_001252496	192786	Mm.254404	NM_175258	ENSMUSG00000037533	Rapgef6	A530068K01|AI844632|BB085664|C030018K18Rik|PDZ-GEF2|Pdzgef2|RA-GEF-2|Ragef2|mKIAA4052	Rap guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_135188.1	chr16	36131157	36131191	-	1	NA	promoter-TSS (NM_001033239)	promoter-TSS (NM_001033239)	15	NM_001033239	209294	Mm.300592	NM_001033239	ENSMUSG00000034362	Csta1	Csta	cystatin A1	protein-coding
mm_101625.1	chr11	35980474	35980579	-	1	NA	promoter-TSS (NM_170779)	promoter-TSS (NM_170779)	-437	NM_170779	211652	Mm.31267	NM_170779	ENSMUSG00000018849	Wwc1	AA408228|AU017197|BC037006|Kibra|mKIAA0869	WW, C2 and coiled-coil domain containing 1	protein-coding
mm_114640.1	chr13	76510623	76510671	+	1	NA	intron (NM_030174, intron 1 of 20)	intron (NM_030174, intron 1 of 20)	125686	NM_030174	78771	Mm.316249	NM_030174	ENSMUSG00000021596	Mctp1	2810465F10Rik	multiple C2 domains, transmembrane 1	protein-coding
mm_152946.1	chr19	28975635	28975644	-	1	NA	Intergenic	Intergenic	-11485	NM_198651	381218	Mm.280653	NM_198651	ENSMUSG00000064202	4430402I18Rik	AW122618|Spata6l	RIKEN cDNA 4430402I18 gene	protein-coding
mm_35201.1	chr4	19122529	19122531	-	1	NA	Intergenic	Intergenic	-158320	NM_013927	30952	Mm.445778	NM_013927	ENSMUSG00000056494	Cngb3	CCNC2|CNG6|Cngbeta2	cyclic nucleotide gated channel beta 3	protein-coding
mm_140662.1	chr17	12895594	12895609	-	1	NA	intron (NM_001034866, intron 10 of 18)	intron (NM_001034866, intron 10 of 18)	14399	NM_001034866	240023	Mm.242315	NM_001034866	ENSMUSG00000073460	Pnldc1	Gm313	poly(A)-specific ribonuclease (PARN)-like domain containing 1	protein-coding
mm_144304.1	chr18	12504117	12504125	+	1	NA	promoter-TSS (NM_001347461)	promoter-TSS (NM_001347461)	-78	NM_001347461	16774	Mm.42012	NM_010680	ENSMUSG00000024421	Lama3	Lama3B|[a]3B	laminin, alpha 3	protein-coding
mm_171713.1	chr4	80502211	80502211	-	1	NA	Intergenic	B2_Mm2|SINE|B2	-332002	NM_031202	22178	Mm.30438	NM_031202	ENSMUSG00000005994	Tyrp1	Oca3|TRP-1|TRP1|Tyrp|b|brown|isa	tyrosinase-related protein 1	protein-coding
mm_81261.1	chr9	108002059	108002065	+	1	NA	promoter-TSS (NM_013785)	promoter-TSS (NM_013785)	-586	NM_013785	27399	Mm.276155	NM_013785	ENSMUSG00000032594	Ip6k1	1200016D08Rik|AU022776|Ihpk1|InsP6|InsP6k1|Itpk6	inositol hexaphosphate kinase 1	protein-coding
mm_17864.1	chr2	34826188	34826240	-	1	NA	promoter-TSS (NM_013890)	promoter-TSS (NM_013890)	21	NM_001164770	30050	Mm.4465	NM_013890	ENSMUSG00000035949	Fbxw2	2700071L08Rik|FBW2|Fwd2|MD6	F-box and WD-40 domain protein 2	protein-coding
mm_44765.1	chr5	31697599	31697632	-	1	NA	promoter-TSS (NM_181282)	promoter-TSS (NM_181282)	-5	NM_153196	71336	Mm.22519	NM_153196	ENSMUSG00000029136	Rbks	5230400M11Rik|AI326806|RBSK|RK	ribokinase	protein-coding
mm_39275.1	chr5	3845172	3845192	+	1	NA	promoter-TSS (NM_172879)	promoter-TSS (NM_172879)	9	NM_172879	242838	Mm.482273	NM_172879	ENSMUSG00000040367	Lrrd1	4932412H11Rik	leucine rich repeats and death domain containing 1	protein-coding
mm_98608.1	chr11	95842284	95842307	+	1	NA	promoter-TSS (NM_001284397)	promoter-TSS (NM_001284397)	0	NM_023121	14710	Mm.46299	NM_023121	ENSMUSG00000038811	Gngt2	AV096488	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 2	protein-coding
mm_53359.1	chr6	129353432	129353454	+	1	NA	exon (NM_177686, exon 2 of 6)	exon (NM_177686, exon 2 of 6)	3199	NM_177686	232413	Mm.90241	NM_177686	ENSMUSG00000053063	Clec12a	CLL-1|D230024O04|KLRL1|Micl	C-type lectin domain family 12, member a	protein-coding
mm_123215.1	chr14	59441089	59441097	-	1	NA	promoter-TSS (NM_001320721)	promoter-TSS (NM_001320721)	112	NM_026908	69008	Mm.179091	NM_026908	ENSMUSG00000021981	Cab39l	1500031K13Rik|2810425O13Rik|4930520C08Rik|AA589432|MO2L	calcium binding protein 39-like	protein-coding
mm_118329.1	chr13	113663652	113663662	-	1	NA	promoter-TSS (NM_019960)	promoter-TSS (NM_019960)	19	NM_019960	56534	Mm.41410	NM_019960	ENSMUSG00000051456	Hspb3	2310035K17Rik|AI844863|Hsbp3|spb3	heat shock protein 3	protein-coding
mm_89320.1	chr10	87930953	87930965	+	1	NA	3' UTR (NM_010512, exon 5 of 5)	3' UTR (NM_010512, exon 5 of 5)	-35712	NR_000040	22172	Mm.391420	NR_000040		Tyms-ps	-	thymidylate synthase, pseudogene	pseudo
mm_23134.1	chr3	38438658	38438658	+	1	NA	Intergenic	RMER6A|LTR|ERVK	46158	NM_001167883	99696	Mm.290937	NM_001033198	ENSMUSG00000044864	Ankrd50	AI662170|E430012K20Rik|mKIAA1223|mKIAA3019	ankyrin repeat domain 50	protein-coding
mm_103461.1	chr11	76399079	76399103	-	1	NA	promoter-TSS (NM_008750)	promoter-TSS (NM_008750)	50	NM_008750	18230	Mm.27915	NM_008750	ENSMUSG00000020844	Nxn	l11Jus13	nucleoredoxin	protein-coding
mm_37545.1	chr4	125125022	125125036	-	1	NA	intron (NM_153159, intron 2 of 5)	intron (NM_153159, intron 2 of 5)	2852	NM_153159	230738	Mm.402	NM_153159	ENSMUSG00000042677	Zc3h12a	BC036563|MCPIP|MCPIP-1|Mcpip1|Reg1	zinc finger CCCH type containing 12A	protein-coding
mm_145894.1	chr18	65587485	65587497	+	1	NA	intron (NM_207255, intron 2 of 5)	intron (NM_207255, intron 2 of 5)	7261	NM_207255	328977	Mm.286232	NM_207255	ENSMUSG00000042439	Zfp532	C530030I18Rik|Znf532|mKIAA1629	zinc finger protein 532	protein-coding
mm_127127.1	chr15	98112070	98112092	+	1	NA	promoter-TSS (NM_021514)	promoter-TSS (NM_021514)	21	NM_021514	18642	Mm.272582	NM_021514	ENSMUSG00000033065	Pfkm	AI131669|ATP-PFK|PFK-A|PFK-M|Pfk-4|Pfk4|Pfka|Pfkx	phosphofructokinase, muscle	protein-coding
mm_122378.1	chr14	40294740	40294742	-	1	NA	Intergenic	Intergenic	598224	NM_177816	328381	Mm.235694	NM_177816	ENSMUSG00000037833	Sh2d4b	A430109M18Rik|D030001E08	SH2 domain containing 4B	protein-coding
mm_93204.1	chr10	94829512	94829532	-	1	NA	intron (NM_018797, intron 20 of 30)	intron (NM_018797, intron 20 of 30)	115056	NM_018797	54712	Mm.256712	NM_018797	ENSMUSG00000074785	Plxnc1	2510048K12Rik|AW742158|CD232|Vespr	plexin C1	protein-coding
mm_149980.1	chr19	29101485	29101497	+	1	NA	5' UTR (NM_021525, exon 1 of 9)	5' UTR (NM_021525, exon 1 of 9)	116	NM_021525	59028	Mm.28630	NM_021525	ENSMUSG00000024785	Rcl1	2310040A02Rik|AI789745|C76567|RPCL1|Rnac	RNA terminal phosphate cyclase-like 1	protein-coding
mm_124723.1	chr15	6580072	6580080	+	1	NA	exon (NM_001278269, exon 1 of 17)	exon (NM_001278269, exon 1 of 17)	229	NM_011815	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_6430.1	chr1	73952793	73952804	-	1	NA	exon (NM_001289895, exon 19 of 33)	exon (NM_001289895, exon 19 of 33)	-88332	NR_045311	109198	Mm.359721	NR_045311	ENSMUSG00000100301	6030407O03Rik	-	RIKEN cDNA 6030407O03 gene	ncRNA
mm_9553.1	chr1	173933459	173933468	-	1	NA	intron (NM_001302649, intron 6 of 9)	MMERVK10C-int|LTR|ERVK	9029	NM_001302649	15950	Mm.463437	NM_008328	ENSMUSG00000039997	Ifi203	Mndal	interferon activated gene 203	protein-coding
mm_6145.1	chr1	64928062	64928066	-	1	NA	intron (NM_001039493, intron 2 of 7)	intron (NM_001039493, intron 2 of 7)	28760	NM_001039493	241075	Mm.239534	NM_175509	ENSMUSG00000051344	Plekhm3	9430067K14Rik|A230102O09Rik|AI449570|DAPR|Plekhm1l	pleckstrin homology domain containing, family M, member 3	protein-coding
mm_110648.1	chr12	59011976	59011992	-	1	NA	promoter-TSS (NM_009147)	promoter-TSS (NM_009147)	33	NM_009147	20334	Mm.491137	NM_009147	ENSMUSG00000020986	Sec23a	Msec23|Sec23r	SEC23 homolog A, COPII coat complex component	protein-coding
mm_159159.1	chr2	89836162	89836162	-	1	NA	promoter-TSS (NM_146983)	promoter-TSS (NM_146983)	-219	NM_146983	258985	Mm.223374	NM_146983	ENSMUSG00000075073	Olfr1256	MOR231-1	olfactory receptor 1256	protein-coding
mm_71169.1	chr8	40546622	40546640	+	1	NA	3' UTR (NM_033560, exon 12 of 12)	3' UTR (NM_033560, exon 12 of 12)	-30784	NM_001271542	18983	Mm.272551	NM_011135	ENSMUSG00000031601	Cnot7	AU022737|CAF-1|Caf1|Pop2	CCR4-NOT transcription complex, subunit 7	protein-coding
mm_170326.1	chr18	42877733	42877733	-	1	NA	intron (NM_028392, intron 1 of 8)	intron (NM_028392, intron 1 of 8)	21773	NR_073583	72930	Mm.26134	NM_027531	ENSMUSG00000024500	Ppp2r2b	2900026H06Rik|6330404L05Rik|E130009M08Rik|PP2A-PR55B|PR55-BETA|SCA12	protein phosphatase 2, regulatory subunit B, beta	protein-coding
mm_114013.1	chr13	52610724	52610734	+	1	NA	intron (NM_011518, intron 1 of 13)	intron (NM_011518, intron 1 of 13)	13847	NM_011518	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_62899.1	chr7	116504410	116504430	+	1	NA	promoter-TSS (NM_001130479)	promoter-TSS (NM_001130479)	51	NM_001130479	53322	Mm.9901	NM_016773	ENSMUSG00000030659	Nucb2	AI607786|Calnuc|Nefa|Nesfatin-1	nucleobindin 2	protein-coding
mm_76469.1	chr8	85386246	85386259	-	1	NA	Intergenic	Intergenic	-5211	NM_001297612	213435	Mm.32804	NM_175441	ENSMUSG00000031698	Mylk3	D830007F02Rik|MLCK	myosin light chain kinase 3	protein-coding
mm_169503.1	chr14	78725795	78725795	-	1	NA	promoter-TSS (NM_001081336)	promoter-TSS (NM_001081336)	-706	NM_001081336	380921	Mm.89591	NM_001081336	ENSMUSG00000034731	Dgkh	5930402B05Rik|D130015C16|DGK	diacylglycerol kinase, eta	protein-coding
mm_81116.1	chr9	106454248	106454258	+	1	NA	intron (NM_021567, intron 1 of 12)	intron (NM_021567, intron 1 of 12)	415	NM_021567	59092	Mm.286394	NM_021567	ENSMUSG00000023495	Pcbp4	1200003L19Rik|AlphaCP-4	poly(rC) binding protein 4	protein-coding
mm_130221.1	chr15	96198010	96198028	-	1	NA	promoter-TSS (NR_040423)	promoter-TSS (NR_040423)	-45	NR_040423	70040	Mm.437832	NR_040423		2610037D02Rik	AU024679	RIKEN cDNA 2610037D02 gene	ncRNA
mm_1869.1	chr1	85599083	85599095	+	1	NA	promoter-TSS (NM_030194)	promoter-TSS (NM_030194)	-279	NM_030194	109032	Mm.335802	NM_030194	ENSMUSG00000070034	Sp110	5031415C07Rik|52kDa|5830484A20Rik|ENSMUSG00000075603|Ifi75|Ipr1	Sp110 nuclear body protein	protein-coding
mm_87619.1	chr10	57794666	57794672	+	1	NA	5' UTR (NM_020561, exon 1 of 8)	5' UTR (NM_020561, exon 1 of 8)	125	NM_020561	57319	Mm.2379	NM_020561	ENSMUSG00000019872	Smpdl3a	0610010C24Rik|AI529588|ASM3A|ASML3|ASML3A	sphingomyelin phosphodiesterase, acid-like 3A	protein-coding
mm_121058.1	chr14	87416695	87416723	+	1	NA	5' UTR (NM_001253755, exon 1 of 12)	5' UTR (NM_001253755, exon 1 of 12)	126	NM_001253755	219249	Mm.35168	NM_172605	ENSMUSG00000022019	Tdrd3	4732418C03Rik|6720468N18	tudor domain containing 3	protein-coding
mm_26218.1	chr3	138804522	138804530	+	1	NA	intron (NM_019571, intron 1 of 7)	L1MEg|LINE|L1	62318	NM_019571	56224	Mm.31927	NM_019571	ENSMUSG00000028152	Tspan5	2810455A09Rik|4930505M03Rik|NET-4|Tm4sf9	tetraspanin 5	protein-coding
mm_158876.1	chrY	1459772	1459782	-	1	NA	promoter-TSS (NM_148943)	promoter-TSS (NM_148943)	5	NM_148943	107868	Mm.347376	NM_148943	ENSMUSG00000069044	Usp9y	Dffry|Fafl2	ubiquitin specific peptidase 9, Y chromosome	protein-coding
mm_118882.1	chr14	25872858	25872870	+	1	NA	exon (NM_013469, exon 4 of 15)	exon (NM_013469, exon 4 of 15)	30029	NM_207229	211623	Mm.439926	NM_207229	ENSMUSG00000095304	Plac9a	Plac9	placenta specific 9a	protein-coding
mm_33275.1	chr4	128688727	128688750	+	1	NA	promoter-TSS (NM_018774)	promoter-TSS (NM_018774)	0	NM_018774	54383	Mm.473738	NM_018774	ENSMUSG00000028796	Phc2	A3galt2|AA415044|D130050K19Rik|D4Ertd810e|Edr2|Mph2|p36	polyhomeotic-like 2 (Drosophila)	protein-coding
mm_131647.1	chr16	20532480	20532509	+	1	NA	TTS (NM_007889)	TTS (NM_007889)	-2986	NM_001302970	11773	Mm.18946	NM_009679	ENSMUSG00000022841	Ap2m1	-	adaptor-related protein complex 2, mu 1 subunit	protein-coding
mm_135678.1	chr16	52420020	52420030	-	1	NA	intron (NM_009655, intron 1 of 15)	intron (NM_009655, intron 1 of 15)	33056	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_101164.1	chr11	16973440	16973499	-	1	NA	3' UTR (NM_019549, exon 10 of 10)	3' UTR (NM_019549, exon 10 of 10)	22059	NM_176982	319701	Mm.120672	NM_176982	ENSMUSG00000044966	Fbxo48	A630050E13Rik	F-box protein 48	protein-coding
mm_42304.1	chr5	114774940	114774957	+	1	NA	promoter-TSS (NM_026718)	promoter-TSS (NM_026718)	35	NR_027872	67642	Mm.482535	NM_175120	ENSMUSG00000092183	4930515G01Rik	-	RIKEN cDNA 4930515G01 gene	ncRNA
mm_53282.1	chr6	128838449	128838452	+	1	NA	Intergenic	Intergenic	-12135	NM_030599	80782	Mm.6180	NM_030599	ENSMUSG00000079298	Klrb1b	Klrb1d|Ly55b|Ly55d|NKR-P1B|NKR-P1D|Nkrp1-b|Nkrp1d|ly-55b|ly-55d	killer cell lectin-like receptor subfamily B member 1B	protein-coding
mm_144191.1	chr18	7869343	7869381	+	1	NA	5' UTR (NM_001146298, exon 1 of 13)	5' UTR (NM_001146298, exon 1 of 13)	165	NM_153085	225131	Mm.204524	NM_153085	ENSMUSG00000024283	Wac	1110067P07Rik|A230035H12Rik|AI256735|AI256776|Wwp4	WW domain containing adaptor with coiled-coil	protein-coding
mm_19242.1	chr2	84715311	84715324	-	1	NA	promoter-TSS (NM_144887)	promoter-TSS (NM_144887)	-153	NM_144887	228136	Mm.288508	NM_144887	ENSMUSG00000034075	Zdhhc5	1110032A17Rik|AI451382|Zisp	zinc finger, DHHC domain containing 5	protein-coding
mm_80474.1	chr9	78175930	78175953	+	1	NA	promoter-TSS (NR_040401)	promoter-TSS (NR_040401)	27	NR_040401	320295	Mm.131285	NR_040401	ENSMUSG00000097574	C920006O11Rik	-	RIKEN cDNA C920006O11 gene	ncRNA
mm_80309.1	chr9	74157238	74157258	+	1	NA	intron (NM_001033500, intron 12 of 19)	intron (NM_001033500, intron 12 of 19)	46914	NM_001033500	546144	Mm.335289	NM_177908	ENSMUSG00000044976	Wdr72	AW558070|D230040E23	WD repeat domain 72	protein-coding
mm_83789.1	chr9	52168839	52168871	-	1	NA	promoter-TSS (NM_001162921)	promoter-TSS (NM_001162921)	-744	NM_001162921	244871	Mm.295686	NM_001162921	ENSMUSG00000035164	Zc3h12c	A230108E06|C230027N18Rik|mKIAA1726	zinc finger CCCH type containing 12C	protein-coding
mm_104844.1	chr11	99230891	99230901	-	1	NA	5' UTR (NM_020618, exon 1 of 11)	5' UTR (NM_020618, exon 1 of 11)	121	NM_020618	57376	Mm.379086	NM_020618	ENSMUSG00000037935	Smarce1	2810417B20Rik|5830412H02Rik|9030408N19Rik|Baf27	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1	protein-coding
mm_27767.1	chr3	70807285	70807297	-	1	NA	promoter-TSS (NR_040556)	promoter-TSS (NR_040556)	0	NR_040556	625901	Mm.366028	NR_040556	ENSMUSG00000097252	Gm6634	EG625901	predicted gene 6634	ncRNA
mm_112445.1	chr13	5861531	5861550	+	1	NA	promoter-TSS (NM_011803)	promoter-TSS (NM_011803)	51	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_123122.1	chr14	56132591	56132595	-	1	NA	promoter-TSS (NM_010372)	promoter-TSS (NM_010372)	0	NM_010372	14941	Mm.482071	NM_010372	ENSMUSG00000059256	Gzmd	CCP5|Ctla-5|Ctla5	granzyme D	protein-coding
mm_25269.1	chr3	104795896	104795907	+	1	NA	exon (NM_008619, exon 17 of 20)	exon (NM_008619, exon 17 of 20)	6867	NM_007484	11853	Mm.262	NM_007484	ENSMUSG00000002233	Rhoc	AI324259|Arh9|Arhc	ras homolog family member C	protein-coding
mm_83115.1	chr9	40376831	40376847	-	1	NA	intron (NM_172768, intron 2 of 19)	intron (NM_172768, intron 2 of 19)	43367	NR_040728	73558	Mm.398307	NR_040728		1700110K17Rik	-	RIKEN cDNA 1700110K17 gene	ncRNA
mm_144384.1	chr18	20666704	20666714	+	1	NA	intron (NM_013697, intron 2 of 3)	B3|SINE|B2	1459	NM_013697	22139	Mm.2108	NM_013697	ENSMUSG00000061808	Ttr	AA408768|AI787086|D17860|prealbumin	transthyretin	protein-coding
mm_117977.1	chr13	100104028	100104053	-	1	NA	promoter-TSS (NM_001081061)	promoter-TSS (NM_001081061)	30	NM_001081061	544971	Mm.288546	NM_001081061	ENSMUSG00000049658	Bdp1	AI662220|AW049390|AW456745|B130055N23Rik|G630013P12Rik|TAF3B1|TFC5|TFIIIB150|TFIIIB90|Tfnr|mKIAA1241	B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB	protein-coding
mm_95687.1	chr11	54304049	54304059	+	1	NA	promoter-TSS (NM_144823)	promoter-TSS (NM_144823)	-150	NM_144823	216739	Mm.267478	NM_144823	ENSMUSG00000020333	Acsl6	A330035H04Rik|AW050338|Facl6|LACS|Lacsl|mKIAA0837	acyl-CoA synthetase long-chain family member 6	protein-coding
mm_166482.1	chr5	146070231	146070246	-	1	NA	Intergenic	Intergenic	-9020	NM_001105160	100041449	Mm.301900	NM_001105160	ENSMUSG00000061292	Cyp3a59	ENSMUSG00000061292	cytochrome P450, family 3, subfamily a, polypeptide 59	protein-coding
mm_149005.1	chr19	8722945	8722962	+	1	NA	promoter-TSS (NR_002896)	promoter-TSS (NR_002896)	416	NM_001161413	17254	Mm.4114	NM_008577	ENSMUSG00000010095	Slc3a2	4F2|4F2HC|AI314110|Cd98|Ly-10|Ly-m10|Ly10|Mdu1|Mgp-2hc|NACAE	solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2	protein-coding
mm_89103.1	chr10	84572532	84572548	+	1	NA	Intergenic	Intergenic	-4407	NM_146008	216198	Mm.296142	NM_146008	ENSMUSG00000020034	Tcp11l2	E430026E19Rik	t-complex 11 (mouse) like 2	protein-coding
mm_68346.1	chr7	106506604	106506628	-	1	NA	Intergenic	Intergenic	-65543	NR_003967	209380	Mm.461779	NM_001001318		Gm4759	EG209380	GTPase, very large interferon inducible 1 pseudogene	pseudo
mm_150235.1	chr19	34008301	34008310	+	1	NA	promoter-TSS (NM_172837)	promoter-TSS (NM_172837)	51	NM_001205349	240633	Mm.58924	NM_172837	ENSMUSG00000024771	Lipk	9930115F20|BC055815|Lipl2	lipase, family member K	protein-coding
mm_153842.1	chr19	46332696	46332708	-	1	NA	intron (NM_001164291, intron 1 of 8)	intron (NM_001164291, intron 1 of 8)	4518	NM_133694	68431	Mm.19973	NM_133694	ENSMUSG00000025226	Fbxl15	0710008C12Rik|Fbxo37	F-box and leucine-rich repeat protein 15	protein-coding
mm_167086.1	chr7	102250260	102250276	+	1	NA	promoter-TSS (NM_019566)	promoter-TSS (NM_019566)	-150	NM_019566	56212	Mm.259795	NM_019566	ENSMUSG00000073982	Rhog	2810426G09Rik|Arhg|Sid10750	ras homolog family member G	protein-coding
mm_55773.1	chr6	78468523	78468531	-	1	NA	exon (NM_011260, exon 2 of 6)	exon (NM_011260, exon 2 of 6)	347	NM_011260	19695	Mm.252385	NM_011260	ENSMUSG00000030017	Reg3g	AI449515|REG-3-gamma|reg III-gamma	regenerating islet-derived 3 gamma	protein-coding
mm_123313.1	chr14	62414280	62414327	-	1	NA	exon (NM_001204340, exon 10 of 17)	exon (NM_001204340, exon 10 of 17)	41986	NM_001204340	239134	Mm.236557	NM_172810	ENSMUSG00000021933	Gucy1b2	B930025B03|GC-SB2	guanylate cyclase 1, soluble, beta 2	protein-coding
mm_152803.1	chr19	21674888	21674909	-	1	NA	intron (NM_146096, intron 1 of 3)	RLTR31A_Mm|LTR|ERVK	21589	NM_146096	226016	Mm.28796	NM_146096	ENSMUSG00000047368	Abhd17b	5730446C15Rik|Cgi67|Fam108b|Fam108b1	abhydrolase domain containing 17B	protein-coding
mm_124211.1	chr14	99339719	99339749	-	1	NA	Intergenic	Intergenic	41043	NM_009769	12224	Mm.30262	NM_009769	ENSMUSG00000005148	Klf5	4930520J07Rik|Bteb2|CKLF|IKLF	Kruppel-like factor 5	protein-coding
mm_11785.1	chr2	40556897	40556910	+	1	NA	Intergenic	Intergenic	-1330565	NM_024209	67857	Mm.389242	NM_024209	ENSMUSG00000026753	Ppp6c	2310003C10Rik	protein phosphatase 6, catalytic subunit	protein-coding
mm_61806.1	chr7	87246657	87246661	+	1	NA	promoter-TSS (NM_001285835)	promoter-TSS (NM_001285835)	10	NM_001285833	50490	Mm.31748	NM_015760	ENSMUSG00000030562	Nox4	AI648021	NADPH oxidase 4	protein-coding
mm_82384.1	chr9	14662926	14662950	-	1	NA	Intergenic	Intergenic	-47938	NM_001081395	75723	Mm.159552	NM_001081395	ENSMUSG00000013076	Amotl1	2310010G08Rik|2310067L22Rik|4932416D09Rik|JEAP|mFLJ00155	angiomotin-like 1	protein-coding
mm_7388.1	chr1	110977367	110977382	-	1	NA	promoter-TSS (NM_001081386)	promoter-TSS (NM_001081386)	-2	NM_001081386	227485	Mm.322070	NM_001081386	ENSMUSG00000047216	Cdh19	-	cadherin 19, type 2	protein-coding
mm_169513.1	chr1	4857810	4857811	+	1	NA	promoter-TSS (NM_001159751)	promoter-TSS (NM_001159751)	116	NM_011541	21399	Mm.207263	NM_011541	ENSMUSG00000033813	Tcea1	S-II	transcription elongation factor A (SII) 1	protein-coding
mm_74127.1	chr8	123186318	123186397	+	1	NA	5' UTR (NM_007876, exon 1 of 11)	5' UTR (NM_007876, exon 1 of 11)	122	NM_007876	13479	Mm.20388	NM_007876	ENSMUSG00000019278	Dpep1	AI327012|MBD	dipeptidase 1 (renal)	protein-coding
mm_87987.1	chr10	64055037	64055045	+	1	NA	intron (NM_178678, intron 2 of 2)	intron (NM_178678, intron 2 of 2)	35214	NM_178678	216028	Mm.431318	NM_178678	ENSMUSG00000042846	Lrrtm3	9630044H04Rik	leucine rich repeat transmembrane neuronal 3	protein-coding
mm_148895.1	chr19	6909693	6909721	+	1	NA	promoter-TSS (NM_026306)	promoter-TSS (NM_026306)	9	NM_026306	67674	Mm.318804	NM_026306	ENSMUSG00000038812	Trmt112	0610038D11Rik|Trm112p	tRNA methyltransferase 11-2	protein-coding
mm_18054.1	chr2	39226072	39226118	-	1	NA	intron (NM_024209, intron 1 of 6)	CpG	243	NM_024209	67857	Mm.389242	NM_024209	ENSMUSG00000026753	Ppp6c	2310003C10Rik	protein phosphatase 6, catalytic subunit	protein-coding
mm_48451.1	chr5	140702242	140702321	-	1	NA	promoter-TSS (NM_028833)	promoter-TSS (NM_028833)	97	NM_028833	74239	Mm.179704	NM_028833	ENSMUSG00000036555	Iqce	1700028P05Rik|mKIAA1023	IQ motif containing E	protein-coding
mm_130592.1	chr15	99702484	99702539	-	1	NA	intron (NM_031842, intron 1 of 12)	intron (NM_031842, intron 1 of 12)	224	NM_031842	83797	Mm.273756	NM_031842	ENSMUSG00000023018	Smarcd1	AA407987|Baf60a|D15Kz1	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1	protein-coding
mm_77333.1	chr8	119558413	119558462	-	1	NA	intron (NM_019709, intron 1 of 23)	CpG	324	NM_001167910	56453	Mm.206934	NM_019709	ENSMUSG00000031835	Mbtps1	0610038M03Rik|AV003995|S1P|SKI-1|Ski1|mKIAA0091	membrane-bound transcription factor peptidase, site 1	protein-coding
mm_161738.1	chr17	32387843	32387843	-	1	NA	promoter-TSS (NM_212438)	promoter-TSS (NM_212438)	-26	NM_212438	22404	Mm.274948	NM_011717	ENSMUSG00000024050	Wiz	-	widely-interspaced zinc finger motifs	protein-coding
mm_162817.1	chr10	79888127	79888133	-	1	NA	TTS (NM_015779)	TTS (NM_015779)	1818	NM_015779	50701	Mm.262194	NM_015779	ENSMUSG00000020125	Elane	Ela2|F430011M15Rik|NE	elastase, neutrophil expressed	protein-coding
mm_133918.1	chr16	97558070	97558083	+	1	NA	intron (NM_013606, intron 12 of 13)	B3A|SINE|B2	21993	NM_013606	17858	Mm.14157	NM_013606	ENSMUSG00000023341	Mx2	AI528743|Mx-2	MX dynamin-like GTPase 2	protein-coding
mm_47093.1	chr5	117484305	117484328	-	1	NA	intron (NM_001312914, intron 1 of 19)	L1MA5A|LINE|L1	70314	NM_001312914	333050	Mm.437947	NM_001034873	ENSMUSG00000061578	Ksr2	-	kinase suppressor of ras 2	protein-coding
mm_61131.1	chr7	55904678	55904682	+	1	NA	intron (NM_011370, intron 20 of 30)	(T)n|Simple_repeat|Simple_repeat	57813	NM_001256133	93790	Mm.37249	NM_023647	ENSMUSG00000030452	Nipa2	2600017P10Rik|3830408P04Rik|AB041581	non imprinted in Prader-Willi/Angelman syndrome 2 homolog (human)	protein-coding
mm_72530.1	chr8	83989531	83989549	+	1	NA	intron (NM_001277898, intron 5 of 9)	intron (NM_001277898, intron 5 of 9)	-8132	NM_001081415	666704	Mm.298091	NM_001081415	ENSMUSG00000079003	Samd1	AA589507	sterile alpha motif domain containing 1	protein-coding
mm_149653.1	chr19	18670813	18670849	+	1	NA	promoter-TSS (NM_026120)	promoter-TSS (NM_026120)	51	NM_026120	67383	Mm.306602	NM_026120	ENSMUSG00000024726	Carnmt1	2410127L17Rik	carnosine N-methyltransferase 1	protein-coding
mm_50815.1	chr6	54429545	54429547	+	1	NA	non-coding (NR_033635, exon 1 of 14)	non-coding (NR_033635, exon 1 of 14)	675	NR_033635	100042056	Mm.448157	NM_198118	ENSMUSG00000073067	9130019P16Rik	6430501H15Rik|OTTMUSG00000023151	RIKEN cDNA 9130019P16 gene	ncRNA
mm_19066.1	chr2	77621279	77621286	-	1	NA	intron (NM_178723, intron 3 of 9)	intron (NM_178723, intron 3 of 9)	81990	NM_001113399	241494	Mm.490320	NM_178723	ENSMUSG00000027016	Zfp385b	B830010L13Rik|C130013B13Rik|Zfp533|Znf385b	zinc finger protein 385B	protein-coding
mm_38437.1	chr4	139599122	139599145	-	1	NA	intron (NM_001205173, intron 1 of 8)	intron (NM_001205173, intron 1 of 8)	-23761	NM_175438	212647	Mm.273571	NM_175438	ENSMUSG00000028737	Aldh4a1	A930035F14Rik|Ahd-1|Ahd1|Aldh4|Aldh5a1|E330022C09|P5cd|P5cdh|P5cdhl|P5cdhs|Ssdh1	aldehyde dehydrogenase 4 family, member A1	protein-coding
mm_146900.1	chr18	30609056	30609056	-	1	NA	Intergenic	Intergenic	336160	NM_181414	225326	Mm.194127	NM_181414	ENSMUSG00000033628	Pik3c3	5330434F23Rik|Vps34	phosphoinositide-3-kinase, class 3	protein-coding
mm_12050.1	chr2	59161966	59161973	+	1	NA	intron (NM_175464, intron 1 of 20)	CpG	1119	NM_175464	227937	Mm.260938	NM_026361	ENSMUSG00000026991	Pkp4	5031422I09Rik|9430019K17Rik|Armrp|p0071	plakophilin 4	protein-coding
mm_39506.1	chr5	21208622	21208633	+	1	NA	intron (NM_175437, intron 5 of 30)	intron (NM_175437, intron 5 of 30)	22360	NM_175437	212167	Mm.121705	NM_175437	ENSMUSG00000039934	Gsap	A530088I07Rik|Pion	gamma-secretase activating protein	protein-coding
mm_79709.1	chr9	61370770	61370807	+	1	NA	Intergenic	CpG	-1578	NM_001083928	21887	Mm.24255	NM_009389	ENSMUSG00000032280	Tle3	2610103N05Rik|ESG|Grg3a|Grg3b|mKIAA1547	transducin-like enhancer of split 3	protein-coding
mm_49710.1	chr6	34419394	34419409	+	1	NA	intron (NM_009731, intron 5 of 9)	(T)n|Simple_repeat|Simple_repeat	7039	NM_009731	11997	Mm.482073	NM_009731	ENSMUSG00000052131	Akr1b7	AR|Avdp|MVDP	aldo-keto reductase family 1, member B7	protein-coding
mm_44288.1	chr5	8368119	8368152	-	1	NA	promoter-TSS (NM_001007221)	promoter-TSS (NM_001007221)	25	NM_001007221	11496	Mm.275895	NM_001007220	ENSMUSG00000040537	Adam22	2900022I03Rik|AI854032|MDC2	a disintegrin and metallopeptidase domain 22	protein-coding
mm_160484.1	chr8	125054147	125054147	+	1	NA	promoter-TSS (NM_174854)	promoter-TSS (NM_174854)	-48	NM_174853	244667	Mm.233504	NM_170596	ENSMUSG00000043051	Disc1	-	disrupted in schizophrenia 1	protein-coding
mm_66295.1	chr7	38019506	38019552	-	1	NA	promoter-TSS (NM_011274)	promoter-TSS (NM_011274)	23	NM_011274	19777	Mm.387220	NM_011274	ENSMUSG00000030421	Uri1	C80913|NNX3|Rmp	URI1, prefoldin-like chaperone	protein-coding
mm_139276.1	chr17	48247713	48247741	+	1	NA	promoter-TSS (NM_021407)	promoter-TSS (NM_021407)	-2	NM_021407	58218	Mm.302438	NM_021407	ENSMUSG00000041754	Trem3	BB134760	triggering receptor expressed on myeloid cells 3	protein-coding
mm_125509.1	chr15	55557576	55557604	+	1	NA	promoter-TSS (NM_026759)	promoter-TSS (NM_026759)	182	NM_001168250	105837	Mm.390829	NM_134092	ENSMUSG00000022369	Mtbp	AI429604|MDM2BP	Mdm2, transformed 3T3 cell double minute p53 binding protein	protein-coding
mm_25409.1	chr3	107291216	107291280	+	1	NA	promoter-TSS (NM_146136)	promoter-TSS (NM_146136)	18	NM_001310705	229699	Mm.38384	NM_146136	ENSMUSG00000027896	Slc16a4	AW146050|MCT 5	solute carrier family 16 (monocarboxylic acid transporters), member 4	protein-coding
mm_70072.1	chr7	142653128	142653148	-	1	NA	3' UTR (NM_010514, exon 4 of 4)	3' UTR (NM_010514, exon 4 of 4)	1858	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_129929.1	chr15	84557588	84557639	-	1	NA	5' UTR (NM_177630, exon 1 of 1)	5' UTR (NM_177630, exon 1 of 1)	210	NM_177630	223732	Mm.6471	NM_177630	ENSMUSG00000055745	Ldoc1l	BC058638|Mar6|Mart6	leucine zipper, down-regulated in cancer 1-like	protein-coding
mm_59163.1	chr7	24388000	24388009	+	1	NA	Intergenic	ID4_|SINE|ID	-11624	NM_028047	71997	Mm.150977	NM_028047	ENSMUSG00000002210	Smg9	1500002O20Rik|AI429693|N28092	smg-9 homolog, nonsense mediated mRNA decay factor (C. elegans)	protein-coding
mm_40053.1	chr5	33996049	33996061	+	1	NA	promoter-TSS (NM_001001985)	promoter-TSS (NM_001001985)	71	NM_001001985	269642	Mm.274610	NM_001001985	ENSMUSG00000048142	Nat8l	1110038O08Rik|Shati	N-acetyltransferase 8-like	protein-coding
mm_154858.1	chrX	20658390	20658402	+	1	NA	promoter-TSS (NM_009457)	promoter-TSS (NM_009457)	94	NM_009457	22201	Mm.1104	NM_009457	ENSMUSG00000001924	Uba1	A1S9|Sbx|Ube-1|Ube1x	ubiquitin-like modifier activating enzyme 1	protein-coding
mm_17808.1	chr2	33468494	33468572	-	1	NA	promoter-TSS (NM_027947)	promoter-TSS (NM_027947)	-1	NM_001025594	71834	Mm.44186	NM_027947	ENSMUSG00000026788	Zbtb43	1700010E06Rik|Zfp297b|mKIAA0414	zinc finger and BTB domain containing 43	protein-coding
mm_63285.1	chr7	126777767	126777798	+	1	NA	5' UTR (NM_026875, exon 2 of 5)	5' UTR (NM_026875, exon 2 of 5)	807	NM_025347	66090	Mm.27114	NM_025347	ENSMUSG00000042675	Ypel3	0610043B10Rik|1190001G19Rik|Suap	yippee-like 3 (Drosophila)	protein-coding
mm_86356.1	chr9	123678874	123678878	-	1	NA	promoter-TSS (NM_139142)	promoter-TSS (NM_139142)	-44	NM_139142	102680	Mm.440867	NM_139142	ENSMUSG00000036814	Slc6a20a	A730081N20Rik|AU022428|Xt3s1|Xtrp3s1	solute carrier family 6 (neurotransmitter transporter), member 20A	protein-coding
mm_43716.1	chr5	139406447	139406466	+	1	NA	promoter-TSS (NM_177000)	promoter-TSS (NM_177000)	69	NM_177000	319772	Mm.440271	NM_177000	ENSMUSG00000044092	C130050O18Rik	-	RIKEN cDNA C130050O18 gene	protein-coding
mm_140103.1	chr17	78508137	78508164	+	1	NA	promoter-TSS (NM_001197028)	promoter-TSS (NM_001197028)	87	NM_028813	74199	Mm.292983	NM_028813	ENSMUSG00000024076	Vit	1700052E02Rik|1700110E08Rik|2810429K11Rik	vitrin	protein-coding
mm_14667.1	chr2	138714630	138714640	+	1	NA	Intergenic	Intergenic	-105294	NR_035477	100316816		NR_035477	ENSMUSG00000088983	Mir1952	mmu-mir-1952	microRNA 1952	ncRNA
mm_171500.1	chr4	146263540	146263552	+	1	NA	Intergenic	CpG	-6839	NM_001083918	666532	Mm.392861	NM_001083918	ENSMUSG00000067916	Zfp991	Gm13139|OTTMUSG00000010657	zinc finger protein 991	protein-coding
mm_39768.1	chr5	30013796	30013805	+	1	NA	intron (NM_001314054, intron 2 of 4)	intron (NM_001314054, intron 2 of 4)	686	NM_031168	16193	Mm.1019	NM_031168	ENSMUSG00000025746	Il6	Il-6	interleukin 6	protein-coding
mm_102649.1	chr11	63119258	63119268	-	1	NA	intron (NR_105772, intron 5 of 6)	RMER16C|LTR|ERVK	-9719	NM_001302258	18858	Mm.1237	NM_008885	ENSMUSG00000018217	Pmp22	22kDa|Gas-3|HNPP|Tr|trembler	peripheral myelin protein 22	protein-coding
mm_83043.1	chr9	37433113	37433123	-	1	NA	promoter-TSS (NM_001164767)	promoter-TSS (NM_001164767)	57	NM_001164767	19649	Mm.212826	NM_011248	ENSMUSG00000032128	Robo3	Rbig1|Rig-1|Rig1|Robo3a|Robo3b	roundabout guidance receptor 3	protein-coding
mm_138052.1	chr17	33926412	33926414	+	1	NA	intron (NM_001025313, intron 5 of 7)	intron (NM_001025313, intron 5 of 7)	-3481	NM_009059	19732	Mm.43777	NM_009059	ENSMUSG00000041354	Rgl2	KE1.5|Rab2l|Rgt2|Rlf	ral guanine nucleotide dissociation stimulator-like 2	protein-coding
mm_120270.1	chr14	63123883	63123916	+	1	NA	intron (NM_007798, intron 1 of 9)	intron (NM_007798, intron 1 of 9)	1437	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_137305.1	chr17	24850743	24850752	+	1	NA	promoter-TSS (NM_023480)	promoter-TSS (NM_023480)	80	NM_001159626	14651	Mm.43784	NM_024284	ENSMUSG00000024158	Hagh	BC019817|Glo-2|Glo2|Rsp29	hydroxyacyl glutathione hydrolase	protein-coding
mm_10465.1	chr2	14315349	14315361	+	1	NA	exon (NM_008625, exon 22 of 30)	exon (NM_008625, exon 22 of 30)	54352	NR_030609	100124488		NR_030609	ENSMUSG00000077897	Mir511	Mirn511|mir-511|mmu-mir-511	microRNA 511	ncRNA
mm_65820.1	chr7	29155964	29155995	-	1	NA	exon (NM_001146023, exon 2 of 8)	exon (NM_001146023, exon 2 of 8)	231	NM_001146023	73833	Mm.260890	NM_028661	ENSMUSG00000030590	Fam98c	1110006G06Rik|AI836081|AV026483|B230110F21Rik	family with sequence similarity 98, member C	protein-coding
mm_118569.1	chr14	18531324	18531354	+	1	NA	Intergenic	Intergenic	-199495	NM_009455	22194	Mm.4429	NM_009455	ENSMUSG00000021774	Ube2e1	UbcM3|Ubce5|ubcM2	ubiquitin-conjugating enzyme E2E 1	protein-coding
mm_87025.1	chr10	28247787	28247791	+	1	NA	intron (NM_008983, intron 2 of 31)	intron (NM_008983, intron 2 of 31)	172969	NM_008983	19272	Mm.332303	NM_008983	ENSMUSG00000019889	Ptprk	AI853699|PTPk|RPTPkappa	protein tyrosine phosphatase, receptor type, K	protein-coding
mm_71198.1	chr8	40884829	40884839	+	1	NA	intron (NM_007514, intron 1 of 11)	intron (NM_007514, intron 1 of 11)	22467	NM_001044740	11988	Mm.4676	NM_007514	ENSMUSG00000031596	Slc7a2	20.5|AI158848|Atrc2|CAT-2|Cat2|Tea	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	protein-coding
mm_42293.1	chr5	114412826	114412836	+	1	NA	intron (NM_001331219, intron 22 of 26)	intron (NM_001331219, intron 22 of 26)	8363	NR_105994	102465621		NR_105994	ENSMUSG00000098731	Mir7027	Gm27831|mmu-mir-7027	microRNA 7027	ncRNA
mm_72613.1	chr8	84601421	84601440	+	1	NA	exon (NM_001252060, exon 32 of 48)	exon (NM_001252060, exon 32 of 48)	61422	NM_010499	15936	Mm.399	NM_010499	ENSMUSG00000053560	Ier2	AI317238|Ch1|Pip92	immediate early response 2	protein-coding
mm_125704.1	chr15	67996654	67996655	+	1	NA	Intergenic	Intergenic	262202	NM_001145888	380993	Mm.309526	NM_198644	ENSMUSG00000022335	Zfat	Gm922|Zfat1|Zfp406	zinc finger and AT hook domain containing	protein-coding
mm_155979.1	chrX	106126877	106126921	+	1	NA	3' UTR (NM_009726, exon 23 of 23)	3' UTR (NM_009726, exon 23 of 23)	-16376	NM_205820	279572	Mm.336203	NM_205820	ENSMUSG00000033777	Tlr13	AI666735|Gm713	toll-like receptor 13	protein-coding
mm_80312.1	chr9	74848468	74848531	+	1	NA	promoter-TSS (NR_045284)	promoter-TSS (NR_045284)	62	NR_045284	100503019	Mm.482658	NR_045284	ENSMUSG00000066477	Gm16551	-	predicted gene 16551	ncRNA
mm_3886.1	chr1	161142662	161142701	+	1	NA	promoter-TSS (NM_028664)	promoter-TSS (NM_028664)	-31	NM_028664	73844	Mm.38830	NM_028664	ENSMUSG00000044835	Ankrd45	4933409K03Rik	ankyrin repeat domain 45	protein-coding
mm_35636.1	chr4	43515702	43515765	-	1	NA	3' UTR (NM_009416, exon 9 of 9)	3' UTR (NM_009416, exon 9 of 9)	7821	NM_009416	22004	Mm.646	NM_009416	ENSMUSG00000028464	Tpm2	Tpm-2|Trop-2	tropomyosin 2, beta	protein-coding
mm_48758.1	chr5	148330065	148330078	-	1	NA	3' UTR (NM_007513, exon 13 of 13)	3' UTR (NM_007513, exon 13 of 13)	62744	NM_001301424	11987	Mm.275489	NM_007513	ENSMUSG00000041313	Slc7a1	4831426K01Rik|AI447493|Atrc-1|Atrc1|Cat1|Rec-1|Rev-1|mCAT-1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 1	protein-coding
mm_81240.1	chr9	107928716	107928726	+	1	NA	exon (NM_026338, exon 1 of 1)	exon (NM_026338, exon 1 of 1)	252	NM_026338	67722	Mm.390222	NM_026338	ENSMUSG00000066368	Actl11	4921517D21Rik	actin-like 11	protein-coding
mm_107174.1	chr12	24831570	24831578	+	1	NA	promoter-TSS (NM_026037)	promoter-TSS (NM_026037)	-25	NM_026037	67216	Mm.167671	NM_026037	ENSMUSG00000020646	Mboat2	2810049G06Rik|AU022889|AW547221|LPCAT4|Moact2|Oact2	membrane bound O-acyltransferase domain containing 2	protein-coding
mm_130589.1	chr15	99637788	99637796	-	1	NA	intron (NM_012025, intron 4 of 17)	intron (NM_012025, intron 4 of 17)	13864	NM_001253808	26934	Mm.273804	NM_012025	ENSMUSG00000023015	Racgap1	AI227039|AI327394|Band25|GTPase|MgcRacGAP|gtl11|mKIAA1478	Rac GTPase-activating protein 1	protein-coding
mm_137881.1	chr17	31585882	31585912	+	1	NA	intron (NR_027493, intron 3 of 11)	intron (NR_027493, intron 3 of 11)	21124	NM_016670	18771	Mm.259295	NM_016670	ENSMUSG00000006705	Pknox1	D17Wsu76e|PREP1	Pbx/knotted 1 homeobox	protein-coding
mm_166955.1	chr7	44476531	44476533	+	1	NA	Intergenic	L1MEd|LINE|L1	6185	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_12716.1	chr2	77462641	77462647	+	1	NA	promoter-TSS (NR_040368)	promoter-TSS (NR_040368)	0	NR_040368	100503106	Mm.443215	NR_040368	ENSMUSG00000085845	Gm13944	OTTMUSG00000015155	predicted gene 13944	ncRNA
mm_88196.1	chr10	70097103	70097211	+	1	NA	promoter-TSS (NM_001111121)	promoter-TSS (NM_001111121)	36	NM_001111121	76551	Mm.281741	NM_001111121	ENSMUSG00000048701	Ccdc6	2810012H18Rik|AA536681|AA960498|AW061011	coiled-coil domain containing 6	protein-coding
mm_110651.1	chr12	59040336	59040345	-	1	NA	Intergenic	U2|snRNA|snRNA	21132	NM_001306218	78232	Mm.290070	NM_030057	ENSMUSG00000020993	Trappc6b	5830498C14Rik|C79212	trafficking protein particle complex 6B	protein-coding
mm_35457.1	chr4	40703155	40703187	-	1	NA	promoter-TSS (NM_025545)	promoter-TSS (NM_025545)	23	NM_001025444	66408	Mm.430710	NM_025545	ENSMUSG00000028411	Aptx	2410016G21Rik|AA388047|FHA-HIT	aprataxin	protein-coding
mm_86926.1	chr10	24149292	24149376	+	1	NA	promoter-TSS (NM_016797)	promoter-TSS (NM_016797)	17	NM_016797	53331	Mm.248042	NM_016797	ENSMUSG00000019998	Stx7	AI315064|AI317144|AW107239|Syn7	syntaxin 7	protein-coding
mm_154788.1	chrX	13071501	13071576	+	1	NA	promoter-TSS (NM_009481)	promoter-TSS (NM_009481)	40	NM_009481	22284	Mm.242646	NM_009481	ENSMUSG00000031010	Usp9x	5730589N07Rik|AA407302|AA407699|AL022658|AL022749|Dffrx|FAF-X|Fafl	ubiquitin specific peptidase 9, X chromosome	protein-coding
mm_56884.1	chr6	119031028	119031045	-	1	NA	intron (NM_001256002, intron 3 of 47)	HAL1|LINE|L1	77459	NM_001159534	12288	Mm.41628	NM_009781	ENSMUSG00000051331	Cacna1c	Cav1.2|Cchl1a1|D930026N18Rik|MBC|MELC-CC	calcium channel, voltage-dependent, L type, alpha 1C subunit	protein-coding
mm_38555.1	chr4	141642131	141642147	-	1	NA	intron (NM_001347237, intron 3 of 18)	intron (NM_001347237, intron 3 of 18)	-18305	NM_001013780	384071	Mm.295682	NM_001013780	ENSMUSG00000040740	Slc25a34	Gm1369	solute carrier family 25, member 34	protein-coding
mm_32074.1	chr4	98041582	98041610	+	1	NA	exon (NM_001122952, exon 7 of 11)	exon (NM_001122952, exon 7 of 11)	263970	NM_010905	18027	Mm.31274	NM_010905	ENSMUSG00000028565	Nfia	1110047K16Rik|9430022M17Rik|CTF|NF1-A|NF1A	nuclear factor I/A	protein-coding
mm_123099.1	chr14	55881979	55881994	-	1	NA	3' UTR (NM_019820, exon 3 of 3)	3' UTR (NM_019820, exon 3 of 3)	2270	NM_019820	56410	Mm.97163	NM_019820	ENSMUSG00000040380	Cbln3	-	cerebellin 3 precursor protein	protein-coding
mm_45086.1	chr5	44099189	44099194	-	1	NA	intron (NM_001163577, intron 1 of 27)	intron (NM_001163577, intron 1 of 27)	2545	NM_008935	19126	Mm.6250	NM_008935	ENSMUSG00000029086	Prom1	4932416E19Rik|AC133|CD133|Prom|Prom-1|Proml1	prominin 1	protein-coding
mm_43466.1	chr5	136693085	136693104	+	1	NA	promoter-TSS (NM_021611)	promoter-TSS (NM_021611)	-52	NM_001303019	59310	Mm.5178	NM_021611	ENSMUSG00000005474	Myl10	1700027I08Rik|Mylc2pl|PLRLC	myosin, light chain 10, regulatory	protein-coding
mm_90252.1	chr10	121626655	121626661	+	1	NA	promoter-TSS (NM_001081056)	promoter-TSS (NM_001081056)	-342	NM_001081056	73192	Mm.25042	NM_001081056	ENSMUSG00000034667	Xpot	1110004L07Rik|3110065H13Rik|AI452076|C79645|EXPORTIN-T	exportin, tRNA (nuclear export receptor for tRNAs)	protein-coding
mm_95276.1	chr11	45852032	45852032	+	1	NA	promoter-TSS (NM_001045520)	promoter-TSS (NM_001045520)	68	NM_001045520	216705	Mm.169673	NM_001045520	ENSMUSG00000006169	Clint1	AI642036|AW537616|C530049I24Rik|Enth|Epn4|F630206G17Rik|mKIAA0171	clathrin interactor 1	protein-coding
mm_13077.1	chr2	91203259	91203267	+	1	NA	intron (NM_007387, intron 1 of 10)	(T)n|Simple_repeat|Simple_repeat	351	NM_007387	11432	Mm.45570	NM_007387	ENSMUSG00000002103	Acp2	Acp-2|LAP	acid phosphatase 2, lysosomal	protein-coding
mm_47857.1	chr5	134563835	134563854	-	1	NA	Intergenic	Intergenic	-3673	NM_001013751	214292	Mm.425290	NM_001013751	ENSMUSG00000085957	Syna	Gm453|Gm52|syncytin-A	syncytin a	protein-coding
mm_9540.1	chr1	173880142	173880164	-	1	NA	promoter-TSS (NM_001170853)	promoter-TSS (NM_001170853)	34	NM_001170853	100040462	Mm.463437	NM_001170853	ENSMUSG00000090272	Mndal	Gm2785|Ifi212	myeloid nuclear differentiation antigen like	protein-coding
mm_112303.1	chr12	114746755	114746761	-	1	NA	Intergenic	Intergenic	-233064	NR_106063	102465664		NR_106063	ENSMUSG00000098357	Mir7094-2	Gm27508|mmu-mir-7094-2	microRNA 7094-2	ncRNA
mm_111861.1	chr12	107970713	107970716	-	1	NA	intron (NM_001079883, intron 2 of 3)	intron (NM_001079883, intron 2 of 3)	32700	NM_001079883	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_33342.1	chr4	129287699	129287713	+	1	NA	promoter-TSS (NM_023485)	promoter-TSS (NM_023485)	85	NM_023485	68828	Mm.132243	NM_023485	ENSMUSG00000001333	Sync	1110057H03Rik|SNIP4	syncoilin	protein-coding
mm_72200.1	chr8	72572014	72572024	+	1	NA	promoter-TSS (NM_172396)	promoter-TSS (NM_172396)	-84	NM_144534	74166	Mm.212927	NM_144534	ENSMUSG00000031791	Tmem38a	1110001E17Rik|AI413399|TRIC-A|mg33a	transmembrane protein 38A	protein-coding
mm_5134.1	chr1	9700344	9700386	-	1	NA	promoter-TSS (NM_001290397)	promoter-TSS (NM_001290397)	-156	NM_008651	17864	Mm.479	NM_008651	ENSMUSG00000025912	Mybl1	A-myb|G1-419-6|repro9	myeloblastosis oncogene-like 1	protein-coding
mm_970.1	chr1	58278310	58278311	+	1	NA	promoter-TSS (NM_001008419)	promoter-TSS (NM_001008419)	-16	NM_001008419	213043	Mm.414292	NM_001008419	ENSMUSG00000079554	Aox2	Aoh3|Aox3l1	aldehyde oxidase 2	protein-coding
mm_112163.1	chr12	113330519	113330523	-	1	NA	Intergenic	Intergenic	144618	NM_153776	69195	Mm.313244	NM_153776	ENSMUSG00000049036	Tmem121	2410008J05Rik|Hole	transmembrane protein 121	protein-coding
mm_76029.1	chr8	76551848	76551854	-	1	NA	Intergenic	RMER17B|LTR|ERVK	348322	NR_028579	100039211	Mm.367571	NR_028579	ENSMUSG00000074235	Gm10649	ENSMUSG00000074235	predicted gene 10649	ncRNA
mm_140088.1	chr17	75465481	75465491	+	1	NA	promoter-TSS (NM_207246)	promoter-TSS (NM_207246)	-52	NM_207246	240168	Mm.329203	NM_207246	ENSMUSG00000071042	Rasgrp3	BC066069|Gm327	RAS, guanyl releasing protein 3	protein-coding
mm_51751.1	chr6	87496414	87496439	+	1	NA	promoter-TSS (NM_175476)	promoter-TSS (NM_175476)	-99	NM_175476	232201	Mm.119564	NM_175476	ENSMUSG00000030047	Arhgap25	A130039I20Rik	Rho GTPase activating protein 25	protein-coding
mm_146877.1	chr18	25486971	25487050	-	1	NA	intron (NM_001174074, intron 10 of 11)	CpG-6790	266973	NM_133195	108013	Mm.266435	NM_133195	ENSMUSG00000024268	Celf4	A230070D14Rik|BRUNOL-4|Brul4|Brunol4|C130060B05Rik	CUGBP, Elav-like family member 4	protein-coding
mm_20202.1	chr2	125100889	125100892	-	1	NA	intron (NM_010852, intron 9 of 15)	intron (NM_010852, intron 9 of 15)	22770	NM_001162417	17876	Mm.18535	NM_010852	ENSMUSG00000027201	Myef2	9430071B01|mKIAA1341	myelin basic protein expression factor 2, repressor	protein-coding
mm_29035.1	chr3	102167697	102167726	-	1	NA	intron (NM_177545, intron 4 of 7)	intron (NM_177545, intron 4 of 7)	36982	NM_177545	229658	Mm.118004	NM_177545	ENSMUSG00000027860	Vangl1	Kitenin|Lpp2|Stb2|Stbm	vang-like 1 (van gogh, Drosophila)	protein-coding
mm_142267.1	chr17	39846009	39846024	-	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	3019	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_76474.1	chr8	85432755	85432763	-	1	NA	promoter-TSS (NM_025722)	promoter-TSS (NM_025722)	82	NR_033144	66714	Mm.272748	NM_025722	ENSMUSG00000036934	4921524J17Rik	-	RIKEN cDNA 4921524J17 gene	protein-coding
mm_20671.1	chr2	132247668	132247698	-	1	NA	5' UTR (NM_027478, exon 1 of 4)	5' UTR (NM_027478, exon 1 of 4)	105	NM_027478	70612	Mm.30116	NM_027478	ENSMUSG00000027341	Tmem230	5730494N06Rik|AA407821	transmembrane protein 230	protein-coding
mm_114460.1	chr13	67499482	67499503	+	1	NA	intron (NM_001007575, intron 1 of 3)	intron (NM_001007575, intron 1 of 3)	1030	NM_001007575	238693	Mm.478914	NM_001007575	ENSMUSG00000071291	Zfp58	A530094I17Rik|Mfg-1|Mfg1|Rslcan5|Zfp817	zinc finger protein 58	protein-coding
mm_15464.1	chr2	157456016	157456026	+	1	NA	intron (NM_009271, intron 3 of 14)	intron (NM_009271, intron 3 of 14)	31728	NM_001025395	20779	Mm.22845	NM_009271	ENSMUSG00000027646	Src	AW259666|pp60c-src	Rous sarcoma oncogene	protein-coding
mm_2342.1	chr1	92859693	92859703	+	1	NA	3' UTR (NM_016696, exon 9 of 9)	3' UTR (NM_016696, exon 9 of 9)	9320	NR_029559	387167		NR_029559	ENSMUSG00000065470	Mir149	Mirn149|mir-149|mmu-mir-149	microRNA 149	ncRNA
mm_23256.1	chr3	51340166	51340192	+	1	NA	intron (NM_023502, intron 1 of 9)	CpG	465	NM_001291059	69257	Mm.131038	NM_023502	ENSMUSG00000037174	Elf2	2610036A20Rik|A230104O07Rik|AW111824|BB183398|EU32|NERF|NERF-1A|NERF-1B|NERF-2	E74-like factor 2	protein-coding
mm_57644.1	chr6	128434384	128434396	-	1	NA	exon (NM_010219, exon 5 of 10)	exon (NM_010219, exon 5 of 10)	4241	NM_010219	14228	Mm.12758	NM_010219	ENSMUSG00000030357	Fkbp4	59kDa|AL022792|AW208983|FKBP-4|FKBP-52|FKBP52|FKPB52|p59	FK506 binding protein 4	protein-coding
mm_106507.1	chr11	120453474	120453482	-	1	NA	promoter-TSS (NM_012065)	promoter-TSS (NM_012065)	22	NR_126089	18588	Mm.39200	NM_012065	ENSMUSG00000025386	Pde6g	Pdeg|p3AT	phosphodiesterase 6G, cGMP-specific, rod, gamma	protein-coding
mm_93598.1	chr10	117150401	117150413	-	1	NA	Intergenic	MER5A|DNA|hAT-Charlie	-1933	NM_177798	327826	Mm.135965	NM_177798	ENSMUSG00000020170	Frs2	4732458E18|C330018A15Rik|Frs2alpha|SNT1	fibroblast growth factor receptor substrate 2	protein-coding
mm_36605.1	chr4	88938878	88938888	-	1	NA	non-coding (NR_132734, exon 2 of 4)	non-coding (NR_132734, exon 2 of 4)	3159	NR_132734	106557447	Mm.484668	NR_132734		LOC106557447	-	uncharacterized LOC106557447	ncRNA
mm_169829.1	chr16	24529376	24529377	+	1	NA	promoter-TSS (NR_038091)	promoter-TSS (NR_038091)	62	NR_038091	624582	Mm.439775	NR_038091		Morf4l1-ps1	A730098P11Rik	mortality factor 4 like 1, pseudogene 1	pseudo
mm_40501.1	chr5	57721999	57722009	+	1	NA	exon (NM_001310606, exon 1 of 3)	exon (NM_001310606, exon 1 of 3)	3923	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_148725.1	chr19	5846965	5846989	+	1	NA	Intergenic	PB1D7|SINE|Alu	-1497	NR_003513	66961	Mm.281895	NR_003513	ENSMUSG00000092274	Neat1	2310043N10Rik|VINC	nuclear paraspeckle assembly transcript 1 (non-protein coding)	ncRNA
mm_28235.1	chr3	88455727	88455733	-	1	NA	promoter-TSS (NM_013658)	promoter-TSS (NM_013658)	31	NM_013658	20351	Mm.439752	NM_013658	ENSMUSG00000028064	Sema4a	AI132332|SemB|Semab	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A	protein-coding
mm_31716.1	chr4	62638577	62638584	+	1	NA	intron (NM_134257, intron 7 of 15)	AT_rich|Low_complexity|Low_complexity	18908	NM_134257	50780	Mm.286753	NM_019492	ENSMUSG00000059810	Rgs3	4930506N09Rik|C2PA-RGS3|C2pa|PDZ-RGS3|RGS3S	regulator of G-protein signaling 3	protein-coding
mm_83964.1	chr9	57148339	57148374	-	1	NA	Intergenic	Intergenic	-1322	NM_028347	72774	Mm.35749	NM_028347	ENSMUSG00000032298	Neil1	2810450N13Rik|Nei1	nei endonuclease VIII-like 1 (E. coli)	protein-coding
mm_64458.1	chr7	142660578	142660584	+	1	NA	non-coding (NR_002855, exon 1 of 4)	non-coding (NR_002855, exon 1 of 4)	690	NM_001122736	16002	Mm.3862	NM_010514	ENSMUSG00000048583	Igf2	AL033362|Igf-2|Igf-II|M6pr|Mpr|Peg2	insulin-like growth factor 2	protein-coding
mm_141671.1	chr17	33909144	33909157	-	1	NA	promoter-TSS (NM_001199733)	promoter-TSS (NM_001199733)	28	NR_045146	407803	Mm.250393	NR_045146	ENSMUSG00000092564	BC051226	-	cDNA sequence BC051226	ncRNA
mm_33491.1	chr4	130823384	130823399	+	1	NA	3' UTR (NM_011520, exon 5 of 5)	3' UTR (NM_011520, exon 5 of 5)	30854	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_71681.1	chr8	60993190	60993247	+	1	NA	promoter-TSS (NM_001293639)	promoter-TSS (NM_001293639)	25	NM_175089	18004	Mm.486881	NM_175089	ENSMUSG00000031644	Nek1	D8Ertd790e|kat	NIMA (never in mitosis gene a)-related expressed kinase 1	protein-coding
mm_46230.1	chr5	99215396	99215421	-	1	NA	Intergenic	Intergenic	37519	NM_181318	320292	Mm.259074	NM_145839	ENSMUSG00000089809	Rasgef1b	4732452O09Rik|GPIgamma4|Gpig4	RasGEF domain family, member 1B	protein-coding
mm_18017.1	chr2	38484667	38484707	-	1	NA	Intergenic	Intergenic	-27010	NM_021606	59126	Mm.143818	NM_021606	ENSMUSG00000026749	Nek6	1300007C09Rik	NIMA (never in mitosis gene a)-related expressed kinase 6	protein-coding
mm_157521.1	chrX	50635284	50635328	-	1	NA	promoter-TSS (NR_015505)	promoter-TSS (NR_015505)	15	NR_015505	103012	Mm.482523	NR_015505	ENSMUSG00000085396	Firre	5830467J12Rik|6720401G13Rik|AW048145	functional intergenic repeating RNA element	ncRNA
mm_135183.1	chr16	35983911	35983920	-	1	NA	intron (NM_008465, intron 1 of 13)	CpG	552	NM_008465	16646	Mm.3991	NM_008465	ENSMUSG00000022905	Kpna1	AW494490|IPOA5|NPI1|Rch2|mSRP1	karyopherin (importin) alpha 1	protein-coding
mm_118570.1	chr14	19127757	19127777	+	1	NA	Intergenic	Intergenic	-234140	NM_144839	218793	Mm.23551	NM_144839	ENSMUSG00000058317	Ube2e2	BC016265	ubiquitin-conjugating enzyme E2E 2	protein-coding
mm_27684.1	chr3	65958258	65958263	-	1	NA	promoter-TSS (NM_019937)	promoter-TSS (NM_019937)	-35	NM_019937	56706	Mm.175612	NM_019937	ENSMUSG00000027829	Ccnl1	2610030E23Rik|AU018493|Ccnl|ania-6a	cyclin L1	protein-coding
mm_164389.1	chr16	32487616	32487632	-	1	NA	5' UTR (NM_145932, exon 1 of 9)	5' UTR (NM_145932, exon 1 of 9)	255	NM_145932	106407	Mm.476915	NM_145932	ENSMUSG00000035699	Slc51a	AV001382|AW261577|D630035O19Rik|OSTalpha|Osta	solute carrier family 51, alpha subunit	protein-coding
mm_7233.1	chr1	93429478	93429489	-	1	NA	exon (NM_133808, exon 9 of 28)	exon (NM_133808, exon 9 of 28)	16218	NM_001301364	110611	Mm.30012	NM_133808	ENSMUSG00000034088	Hdlbp	1110005P14Rik|AA960365|AI118566|D1Ertd101e	high density lipoprotein (HDL) binding protein	protein-coding
mm_128021.1	chr15	24724840	24724849	-	1	NA	Intergenic	Intergenic	688920	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	brain abundant, membrane attached signal protein 1	protein-coding
mm_114886.1	chr13	94294043	94294052	+	1	NA	Intergenic	Intergenic	-8216	NM_001346609	107767	Mm.201455	NM_029153	ENSMUSG00000021687	Scamp1	4930505M11Rik|AI415563|AW122395	secretory carrier membrane protein 1	protein-coding
mm_111767.1	chr12	104013754	104013776	-	1	NA	promoter-TSS (NM_027997)	promoter-TSS (NM_027997)	-113	NM_027997	71907	Mm.326723	NM_027997	ENSMUSG00000058260	Serpina9	2310014L03Rik|AW049635|Centerin	serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9	protein-coding
mm_90255.1	chr10	122387004	122387016	+	1	NA	Intergenic	Intergenic	-61489	NM_016847	54140	Mm.4351	NM_016847	ENSMUSG00000020123	Avpr1a	AVPR|Avpr1|V1a|V1aR	arginine vasopressin receptor 1A	protein-coding
mm_80294.1	chr9	73096612	73096615	+	1	NA	3' UTR (NM_023635, exon 6 of 6)	3' UTR (NM_023635, exon 6 of 6)	-5785	NM_025890	66991	Mm.471745	NM_025890	ENSMUSG00000092622	Khdc3	2410004A20Rik|AI467128|FILIA|OEEP48	KH domain containing 3, subcortical maternal complex member	protein-coding
mm_4013.1	chr1	165461242	165461271	+	1	NA	promoter-TSS (NM_028759)	promoter-TSS (NM_028759)	48	NM_027430	70456	Mm.195625	NM_027430	ENSMUSG00000026568	Mpc2	0610006C01Rik|2010002I07Rik|2610205H19Rik|AA108335|Brp44|ESTM43	mitochondrial pyruvate carrier 2	protein-coding
mm_164486.1	chr16	76132461	76132463	+	1	NA	intron (NR_040575, intron 1 of 2)	intron (NR_040575, intron 1 of 2)	9849	NR_040575	78215	Mm.243885	NR_040575		4930578N18Rik	-	RIKEN cDNA 4930578N18 gene	ncRNA
mm_12563.1	chr2	72609118	72609125	+	1	NA	Intergenic	(TA)n|Simple_repeat|Simple_repeat	-94389	NR_040503	74541	Mm.410774	NR_040503	ENSMUSG00000085252	8430437L04Rik	-	RIKEN cDNA 8430437L04 gene	ncRNA
mm_25263.1	chr3	104788794	104788841	+	1	NA	promoter-TSS (NM_007484)	promoter-TSS (NM_007484)	-217	NM_001291859	11853	Mm.262	NM_007484	ENSMUSG00000002233	Rhoc	AI324259|Arh9|Arhc	ras homolog family member C	protein-coding
mm_147673.1	chr18	60648928	60648944	-	1	NA	Intergenic	Intergenic	-14474	NR_045401	328963	Mm.417203	NR_045401		G630071F17Rik	G630071F17	RIKEN cDNA G630071F17 gene	ncRNA
mm_17683.1	chr2	32312163	32312202	-	1	NA	non-coding (NR_125959, exon 20 of 22)	non-coding (NR_125959, exon 20 of 22)	-6083	NR_128563	104795665		NR_128563	ENSMUSG00000092765	Gm23363	Mir3154|mir-3154|mmu-mir-3154	predicted gene, 23363	ncRNA
mm_75423.1	chr8	46868319	46868329	-	1	NA	Intergenic	Intergenic	-118563	NM_177304	320981	Mm.211429	NM_177304	ENSMUSG00000038173	Enpp6	4833421B01Rik|B830047L21Rik|D8Ertd514e|E-NPP 6|GPC-Cpde|Npp6	ectonucleotide pyrophosphatase/phosphodiesterase 6	protein-coding
mm_89799.1	chr10	102512395	102512409	+	1	NA	5' UTR (NM_146240, exon 1 of 2)	5' UTR (NM_146240, exon 1 of 2)	180	NM_146240	237504	Mm.282672	NM_146240	ENSMUSG00000044921	Rassf9	AW322107|Pamci	Ras association (RalGDS/AF-6) domain family (N-terminal) member 9	protein-coding
mm_153521.1	chr19	41747576	41747584	-	1	NA	non-coding (NR_040320, exon 2 of 3)	non-coding (NR_040320, exon 2 of 3)	619	NR_040320	100502871	Mm.394485	NR_040320		Gm19424	-	predicted gene, 19424	ncRNA
mm_61738.1	chr7	82174871	82174875	+	1	NA	Intergenic	CpG	-85035	NM_001277955	20408	Mm.736	NM_017400	ENSMUSG00000030638	Sh3gl3	EEN-B2|SH3P13|Sh3d2c|Sh3d2c2	SH3-domain GRB2-like 3	protein-coding
mm_144900.1	chr18	37300811	37300835	+	1	NA	promoter-TSS (NM_053128)	promoter-TSS (NM_053128)	24	NM_053128	93874	Mm.82308	NM_053128	ENSMUSG00000045498	Pcdhb3	PcdhbC	protocadherin beta 3	protein-coding
mm_86299.1	chr9	122310897	122310910	-	1	NA	Intergenic	MLT1F1|LTR|ERVL-MaLR	-16480	NM_133979	102566	Mm.87676	NM_133979	ENSMUSG00000037949	Ano10	AI604832|Tmem16k	anoctamin 10	protein-coding
mm_152479.1	chr19	11047903	11047915	-	1	NA	non-coding (NR_102366, exon 3 of 3)	non-coding (NR_102366, exon 3 of 3)	2657	NR_102366	107350	Mm.6381	NM_001177351	ENSMUSG00000075010	AW112010	-	expressed sequence AW112010	ncRNA
mm_43659.1	chr5	138707558	138707585	+	1	NA	Intergenic	RMER15|LTR|ERVL	-47510	NM_030565	80752	Mm.320355	NM_030565	ENSMUSG00000025854	Fam20c	C76981|DMP-4|DMP4|GEF-CK|mKIAA4081	family with sequence similarity 20, member C	protein-coding
mm_72115.1	chr8	71676234	71676254	+	1	NA	promoter-TSS (NM_001190830)	promoter-TSS (NM_001190830)	-139	NM_001190830	16453	Mm.249645	NM_010589	ENSMUSG00000031805	Jak3	fae|wil	Janus kinase 3	protein-coding
mm_87474.1	chr10	51492052	51492066	+	1	NA	exon (NM_013532, exon 4 of 9)	exon (NM_013532, exon 4 of 9)	1161	NM_013532	14728	Mm.34408	NM_013532	ENSMUSG00000062593	Lilrb4a	CD85K|Gp49b|HM18|ILT3|LIR-5|Lilrb4|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4A	protein-coding
mm_9030.1	chr1	166503873	166503878	-	1	NA	Intergenic	Intergenic	-6287	NM_001164306	226601	Mm.475593	NM_001164306	ENSMUSG00000086056	Gm4846	EG226601|Fmo13	predicted gene 4846	protein-coding
mm_108487.1	chr12	83668122	83668158	+	1	NA	exon (NM_027349, exon 11 of 19)	exon (NM_027349, exon 11 of 19)	-20423	NM_008943	19164	Mm.998	NM_008943	ENSMUSG00000019969	Psen1	Ad3h|PS-1|PS1|S182	presenilin 1	protein-coding
mm_55996.1	chr6	86388697	86388716	-	1	NA	3' UTR (NM_025823, exon 6 of 6)	3' UTR (NM_025823, exon 6 of 6)	8444	NM_025823	66881	Mm.30849	NM_025823	ENSMUSG00000029998	Pcyox1	1200015P13Rik|AI115532|AI448340|PCL1|Pcly	prenylcysteine oxidase 1	protein-coding
mm_8365.1	chr1	150466192	150466236	-	1	NA	promoter-TSS (NM_021400)	promoter-TSS (NM_021400)	-49	NM_001110146	96875	Mm.174256	NM_021400	ENSMUSG00000006014	Prg4	CACP|DOL54|JCAP|MSF|SZP|lubricin	proteoglycan 4 (megakaryocyte stimulating factor, articular superficial zone protein)	protein-coding
mm_132350.1	chr16	33985035	33985036	+	1	NA	intron (NM_177357, intron 57 of 59)	intron (NM_177357, intron 57 of 59)	-18032	NM_009471	22247	Mm.13145	NM_009471	ENSMUSG00000022814	Umps	1700095D23Rik|AA408257|AL033308|BB164745	uridine monophosphate synthetase	protein-coding
mm_165475.1	chr2	164316692	164316698	+	1	NA	promoter-TSS (NM_013679)	promoter-TSS (NM_013679)	-56	NM_013679	20945	Mm.439686	NM_013679	ENSMUSG00000017000	Svs6	MSVSP99|Svp6	seminal vesicle secretory protein 6	protein-coding
mm_67374.1	chr7	79841947	79841960	-	1	NA	exon (NM_008486, exon 1 of 20)	exon (NM_008486, exon 1 of 20)	399	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_20734.1	chr2	137095569	137095572	-	1	NA	intron (NM_013822, intron 6 of 25)	intron (NM_013822, intron 6 of 25)	20950	NM_013822	16449	Mm.22398	NM_013822	ENSMUSG00000027276	Jag1	ABE2|Gsfabe2|Htu|Ozz|Ser-1	jagged 1	protein-coding
mm_39758.1	chr5	29736113	29736140	+	1	NA	promoter-TSS (NR_028426)	promoter-TSS (NR_028426)	-190	NR_028426	332993	Mm.473746	NR_028426		Gm5129	EG332993|ENSMUSG00000053121	predicted gene 5129	ncRNA
mm_126088.1	chr15	77881970	77882008	+	1	NA	Intergenic	Intergenic	-39814	NM_022410	17886	Mm.29677	NM_022410	ENSMUSG00000022443	Myh9	Fltn|Myhn-1|Myhn1|NMHCIIA|NMMHC-A|NMMHC-IIA|TU72.6	myosin, heavy polypeptide 9, non-muscle	protein-coding
mm_105992.1	chr11	115628234	115628250	-	1	NA	promoter-TSS (NM_001252384)	promoter-TSS (NM_001252384)	53	NM_001252394	67283	Mm.383426	NM_026071	ENSMUSG00000020744	Slc25a19	2900089E13Rik|DNC|MUP1|TPC	solute carrier family 25 (mitochondrial thiamine pyrophosphate carrier), member 19	protein-coding
mm_16287.1	chr2	174111051	174111073	+	1	NA	intron (NM_213733, intron 1 of 11)	intron (NM_213733, intron 1 of 11)	711	NM_213733	228961	Mm.295629	NM_213733	ENSMUSG00000039263	Npepl1	BC023239|C85514|mKIAA1974	aminopeptidase-like 1	protein-coding
mm_62584.1	chr7	105554379	105554487	+	1	NA	promoter-TSS (NM_011421)	promoter-TSS (NM_011421)	73	NM_011421	20597	Mm.4628	NM_011421	ENSMUSG00000037049	Smpd1	A-SMase|ASM|Zn-SMase|aSMase	sphingomyelin phosphodiesterase 1, acid lysosomal	protein-coding
mm_21784.1	chr2	164854400	164854424	-	1	NA	exon (NM_011125, exon 5 of 16)	exon (NM_011125, exon 5 of 16)	3296	NM_011125	18830	Mm.6105	NM_011125	ENSMUSG00000017754	Pltp	Bpife|OD107	phospholipid transfer protein	protein-coding
mm_36742.1	chr4	99829363	99829395	-	1	NA	promoter-TSS (NM_145549)	promoter-TSS (NM_145549)	-121	NM_145549	230500	Mm.331727	NM_145549	ENSMUSG00000073791	Efcab7	mKIAA1799	EF-hand calcium binding domain 7	protein-coding
mm_74655.1	chr8	13494480	13494546	-	1	NA	promoter-TSS (NM_019521)	promoter-TSS (NM_019521)	22	NM_019521	14456	Mm.3982	NM_019521	ENSMUSG00000031451	Gas6	Gas-6	growth arrest specific 6	protein-coding
mm_69493.1	chr7	134224990	134225042	-	1	NA	promoter-TSS (NM_007400)	promoter-TSS (NM_007400)	81	NM_007400	11489	Mm.439714	NM_007400	ENSMUSG00000054555	Adam12	Mltna	a disintegrin and metallopeptidase domain 12 (meltrin alpha)	protein-coding
mm_149850.1	chr19	25057198	25057223	+	1	NA	intron (NM_028785, intron 2 of 47)	intron (NM_028785, intron 2 of 47)	57681	NM_028785	76088	Mm.102485	NM_028785	ENSMUSG00000052085	Dock8	1200017A24Rik|5830472H07Rik|A130095G14Rik|AI461977	dedicator of cytokinesis 8	protein-coding
mm_15931.1	chr2	165503895	165503913	+	1	NA	promoter-TSS (NM_130451)	promoter-TSS (NM_130451)	7	NM_130451	170441	Mm.34147	NM_130451	ENSMUSG00000027661	Slc2a10	AA450473|Glut10	solute carrier family 2 (facilitated glucose transporter), member 10	protein-coding
mm_134804.1	chr16	24393418	24393459	-	1	NA	promoter-TSS (NM_178665)	promoter-TSS (NM_178665)	88	NM_178665	210126	Mm.209385	NM_178665	ENSMUSG00000033306	Lpp	9430020K16Rik|AA959454|AU024130|B130055L10Rik|C79715|D630048H16	LIM domain containing preferred translocation partner in lipoma	protein-coding
mm_113386.1	chr13	33039829	33039842	+	1	NA	exon (NM_011452, exon 7 of 7)	exon (NM_011452, exon 7 of 7)	12421	NM_011452	20706	Mm.45371	NM_011452	ENSMUSG00000021403	Serpinb9b	1600019A21Rik|R86|SPI-CI|Spi10|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 9b	protein-coding
mm_33063.1	chr4	123233844	123233869	+	1	NA	5' UTR (NM_013905, exon 1 of 5)	5' UTR (NM_013905, exon 1 of 5)	300	NM_013905	56198	Mm.103615	NM_013905	ENSMUSG00000032744	Heyl	Hey3|Hrt3|bHLHb33|hesr3	hairy/enhancer-of-split related with YRPW motif-like	protein-coding
mm_160738.1	chr10	79688878	79688878	+	1	NA	promoter-TSS (NM_008504)	promoter-TSS (NM_008504)	-142	NM_001302485	16904	Mm.378960	NM_008504	ENSMUSG00000054206	Gzmm	Lmet1|MMET-1	granzyme M (lymphocyte met-ase 1)	protein-coding
mm_29331.1	chr3	108086591	108086707	-	1	NA	promoter-TSS (NM_028779)	promoter-TSS (NM_028779)	17	NM_028779	109674	Mm.274335	NM_028779	ENSMUSG00000027889	Ampd2	1200014F01Rik|AI552571|Ampd-2|m4521Dajl	adenosine monophosphate deaminase 2	protein-coding
mm_7293.1	chr1	97822999	97823015	-	1	NA	intron (NM_013626, intron 24 of 25)	(A)n|Simple_repeat|Simple_repeat	52835	NM_026250	252876	Mm.86090	NM_026250	ENSMUSG00000026333	Gin1	4930429M06Rik|8430411H10Rik|Gin-1|Zh2c2	gypsy retrotransposon integrase 1	protein-coding
mm_147166.1	chr18	36726279	36726301	-	1	NA	exon (NM_009841, exon 2 of 2)	exon (NM_009841, exon 2 of 2)	525	NM_009841	12475	Mm.3460	NM_009841	ENSMUSG00000051439	Cd14	-	CD14 antigen	protein-coding
mm_27075.1	chr3	28805329	28805360	-	1	NA	promoter-TSS (NM_026517)	promoter-TSS (NM_026517)	-167	NM_001347226	68028	Mm.371630	NM_026517	ENSMUSG00000039221	Rpl22l1	3110001N18Rik|AU041196	ribosomal protein L22 like 1	protein-coding
mm_124919.1	chr15	12117814	12117846	+	1	NA	promoter-TSS (NM_011767)	promoter-TSS (NM_011767)	-21	NM_011767	22763	Mm.273496	NM_011767	ENSMUSG00000022201	Zfr	C920030H05Rik	zinc finger RNA binding protein	protein-coding
mm_164649.1	chr17	35567406	35567420	+	1	NA	promoter-TSS (NM_175148)	promoter-TSS (NM_175148)	-72	NM_175148	69542	Mm.265291	NM_175148	ENSMUSG00000039269	2300002M23Rik	Stg|emprin	RIKEN cDNA 2300002M23 gene	protein-coding
mm_35032.1	chr4	4077511	4077540	-	1	NA	promoter-TSS (NM_001080710)	promoter-TSS (NM_001080710)	-11	NM_001080710	242286	Mm.298546	NM_001080710	ENSMUSG00000071019	Sdr16c6	4833413O15Rik|Gm423	short chain dehydrogenase/reductase family 16C, member 6	protein-coding
mm_29978.1	chr3	133791494	133791502	-	1	NA	Intergenic	Intergenic	-247108	NM_001040400	214133	Mm.347816	NM_145989	ENSMUSG00000040943	Tet2	Ayu17-449|E130014J05Rik|mKIAA1546	tet methylcytosine dioxygenase 2	protein-coding
mm_133693.1	chr16	92612756	92612776	+	1	NA	intron (NM_001111023, intron 5 of 5)	intron (NM_001111023, intron 5 of 5)	84563	NM_001111023	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_80909.1	chr9	100643606	100643626	+	1	NA	promoter-TSS (NM_009282)	promoter-TSS (NM_009282)	-7	NM_009282	20842	Mm.42135	NM_009282	ENSMUSG00000037286	Stag1	AU045003|SA-1|Scc3	stromal antigen 1	protein-coding
mm_71570.1	chr8	54077244	54077256	+	1	NA	promoter-TSS (NM_009506)	promoter-TSS (NM_009506)	-282	NM_009506	22341	Mm.1402	NM_009506	ENSMUSG00000031520	Vegfc	AW228853|VEGF-C	vascular endothelial growth factor C	protein-coding
mm_31578.1	chr4	57734718	57734736	+	1	NA	intron (NM_001304544, intron 5 of 8)	B4A|SINE|B4	-110521	NM_009649	11641	Mm.467752	NM_009649	ENSMUSG00000038729	Akap2	AA959716|AI649048|Akap-2|Akap-kl|B230340M18Rik|Prka2	A kinase (PRKA) anchor protein 2	protein-coding
mm_105659.1	chr11	107337831	107337869	-	1	NA	intron (NM_145823, intron 1 of 9)	intron (NM_145823, intron 1 of 9)	132870	NM_145823	71795	Mm.397413	NM_145823	ENSMUSG00000040430	Pitpnc1	1110020B03Rik|5830436L09Rik|AI662802|AI851387|C330017I21Rik|Dnr411|RDGBB|RDGBB1|rdgB-beta	phosphatidylinositol transfer protein, cytoplasmic 1	protein-coding
mm_90081.1	chr10	116581546	116581585	+	1	NA	promoter-TSS (NM_028082)	promoter-TSS (NM_028082)	-54	NM_001037846	72068	Mm.351553	NM_028082	ENSMUSG00000020166	Cnot2	2600016M12Rik|2810470K03Rik|AA537049|AA959607|AW557563|C79650	CCR4-NOT transcription complex, subunit 2	protein-coding
mm_3066.1	chr1	134183335	134183358	+	1	NA	intron (NM_007695, intron 2 of 9)	intron (NM_007695, intron 2 of 9)	942	NM_007695	12654	Mm.38274	NM_007695	ENSMUSG00000064246	Chil1	AW208766|Brp39|Chi3l1|Gp39	chitinase-like 1	protein-coding
mm_68583.1	chr7	116030972	116031000	-	1	NA	promoter-TSS (NM_001025560)	promoter-TSS (NM_001025560)	61	NM_001025560	20679	Mm.323365	NM_011445	ENSMUSG00000051910	Sox6	AI987981|SOX-LZ	SRY (sex determining region Y)-box 6	protein-coding
mm_6025.1	chr1	59161595	59161628	-	1	NA	promoter-TSS (NM_145143)	promoter-TSS (NM_145143)	25	NM_145143	227157	Mm.474049	NM_145143	ENSMUSG00000079550	Mpp4	Dlg6	membrane protein, palmitoylated 4 (MAGUK p55 subfamily member 4)	protein-coding
mm_159468.1	chr4	9844408	9844408	+	1	NA	promoter-TSS (NM_013526)	promoter-TSS (NM_013526)	36	NM_013526	242316	Mm.302555	NM_013526	ENSMUSG00000051279	Gdf6	BMP-13|BMP13|GDF16	growth differentiation factor 6	protein-coding
mm_65122.1	chr7	19415017	19415057	-	1	NA	exon (NM_007710, exon 3 of 8)	exon (NM_007710, exon 3 of 8)	3943	NM_007710	12715	Mm.2375	NM_007710	ENSMUSG00000030399	Ckm	Ckmm|M-CK|MCK	creatine kinase, muscle	protein-coding
mm_112945.1	chr13	21001725	21001741	+	1	NA	intron (NM_012054, intron 16 of 20)	ORR1F|LTR|ERVL-MaLR	71566	NM_146535	258528	Mm.377554	NM_146535	ENSMUSG00000042869	Olfr1370	MOR256-14	olfactory receptor 1370	protein-coding
mm_128442.1	chr15	50731430	50731435	-	1	NA	intron (NM_001310481, intron 4 of 5)	intron (NM_001310481, intron 4 of 5)	157617	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_107130.1	chr12	21213041	21213060	+	1	NA	intron (NM_001135192, intron 8 of 28)	(CGTG)n|Simple_repeat|Simple_repeat	73187	NM_008403	16413	Mm.273333	NM_008403	ENSMUSG00000062352	Itgb1bp1	AI449260|AU019480|Icap1	integrin beta 1 binding protein 1	protein-coding
mm_22651.1	chr3	14870040	14870084	+	1	NA	exon (NM_007606, exon 6 of 7)	exon (NM_007606, exon 6 of 7)	6524	NM_007606	12350	Mm.300	NM_007606	ENSMUSG00000027559	Car3	BB219044|Ca3|Car-3	carbonic anhydrase 3	protein-coding
mm_23804.1	chr3	79885025	79885090	+	1	NA	promoter-TSS (NM_133187)	promoter-TSS (NM_133187)	-873	NM_133187	68659	Mm.427274	NM_133187	ENSMUSG00000027955	Fam198b	1110032E23Rik|2210419I08Rik|AV011458|Ened	family with sequence similarity 198, member B	protein-coding
mm_110839.1	chr12	72938867	72938870	-	1	NA	Intergenic	Intergenic	-1014	NM_011384	20476	Mm.57138	NM_011384	ENSMUSG00000021099	Six6	Optx2|Six9	sine oculis-related homeobox 6	protein-coding
mm_5235.1	chr1	14755985	14755998	-	1	NA	promoter-TSS (NM_010827)	promoter-TSS (NM_010827)	-25	NM_010827	17681	Mm.5820	NM_010827	ENSMUSG00000025930	Msc	MyoR|bHLHa22	musculin	protein-coding
mm_155150.1	chrX	52793042	52793076	+	1	NA	intron (NM_001034059, intron 1 of 1)	intron (NM_001034059, intron 1 of 1)	1859	NM_001034059	434778	Mm.23411	NM_001034059	ENSMUSG00000073207	Ccdc160	6330534C20Rik	coiled-coil domain containing 160	protein-coding
mm_77399.1	chr8	120489333	120489344	-	1	NA	intron (NM_198671, intron 1 of 15)	CpG-14576	472	NM_198671	382034	Mm.334856	NM_198671	ENSMUSG00000031822	Gse1	2210013I18Rik|mKIAA0182	genetic suppressor element 1, coiled-coil protein	protein-coding
mm_157734.1	chrX	71492593	71492658	-	1	NA	5' UTR (NM_138309, exon 1 of 9)	5' UTR (NM_138309, exon 1 of 9)	224	NM_138309	171486	Mm.283879	NM_138309	ENSMUSG00000035776	Cd99l2	AW548191|Mic2l1|Xap89	CD99 antigen-like 2	protein-coding
mm_34364.1	chr4	144892844	144892870	+	1	NA	promoter-TSS (NM_001172424)	promoter-TSS (NM_001172424)	30	NM_001172424	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding
mm_121532.1	chr14	122280719	122280732	+	1	NA	intron (NM_029556, intron 1 of 7)	intron (NM_029556, intron 1 of 7)	-47087	NR_015532	68245	Mm.443285	NR_015532	ENSMUSG00000100585	1700108J01Rik	-	RIKEN cDNA 1700108J01 gene	ncRNA
mm_39006.1	chr4	152027602	152027624	-	1	NA	promoter-TSS (NM_133879)	promoter-TSS (NM_133879)	58	NM_133879	100090	Mm.24661	NM_133879	ENSMUSG00000028952	Zbtb48	0610011D15Rik|AI327031|Hkr3	zinc finger and BTB domain containing 48	protein-coding
mm_738.1	chr1	43451065	43451098	+	1	NA	intron (NM_010879, intron 1 of 4)	MTC|LTR|ERVL-MaLR	5330	NM_010879	17974	Mm.389903	NM_010879	ENSMUSG00000066877	Nck2	4833426I10Rik|Grb4|NCKbeta|Nck-2	non-catalytic region of tyrosine kinase adaptor protein 2	protein-coding
mm_70099.1	chr7	142661044	142661058	-	1	NA	5' UTR (NM_001122736, exon 1 of 4)	intron (NR_002855, intron 1 of 3)	220	NM_001122736	16002	Mm.3862	NM_010514	ENSMUSG00000048583	Igf2	AL033362|Igf-2|Igf-II|M6pr|Mpr|Peg2	insulin-like growth factor 2	protein-coding
mm_16751.1	chr2	9863314	9863316	-	1	NA	intron (NM_008091, intron 4 of 5)	intron (NM_008091, intron 4 of 5)	15285	NM_008091	14462	Mm.313866	NM_008091	ENSMUSG00000015619	Gata3	Gata-3|jal	GATA binding protein 3	protein-coding
mm_156154.1	chrX	129955011	129955026	+	1	NA	intron (NM_172493, intron 10 of 26)	intron (NM_172493, intron 10 of 26)	205276	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diaph2	Dia3|Diap2|Drf2|E430022I22Rik	diaphanous related formin 2	protein-coding
mm_71318.1	chr8	44935265	44935314	+	1	NA	Intergenic	CpG	-14919	NM_001081286	14107	Mm.27365	NM_001081286	ENSMUSG00000070047	Fat1	2310038E12Rik|AU023433|Fath|mFat1	FAT atypical cadherin 1	protein-coding
mm_10379.1	chr2	12300679	12300687	+	1	NA	promoter-TSS (NR_040353)	promoter-TSS (NR_040353)	-563	NR_040353	338535	Mm.483275	NR_040353	ENSMUSG00000086843	E030013I19Rik	-	RIKEN cDNA E030013I19 gene	ncRNA
mm_105950.1	chr11	115297497	115297501	-	1	NA	promoter-TSS (NM_178035)	promoter-TSS (NM_178035)	47	NM_178035	328035	Mm.21995	NM_178035	ENSMUSG00000044788	Fads6	BC044804|OTTMUSG00000021749	fatty acid desaturase domain family, member 6	protein-coding
mm_84436.1	chr9	66093579	66093588	-	1	NA	intron (NM_019727, intron 10 of 14)	intron (NM_019727, intron 10 of 14)	-23852	NM_001025612	382083	Mm.477103	NM_001025612	ENSMUSG00000039452	Snx22	Gm1120	sorting nexin 22	protein-coding
mm_114443.1	chr13	66488196	66488235	+	1	NA	Intergenic	Intergenic	-47097	NM_001290196	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
mm_27475.1	chr3	53463201	53463232	-	1	NA	promoter-TSS (NM_172501)	promoter-TSS (NM_172501)	42	NM_172501	212114	Mm.85744	NM_172501	ENSMUSG00000042997	Nhlrc3	4833441N19|8030451K01Rik|mKIAA4083	NHL repeat containing 3	protein-coding
mm_77700.1	chr8	126590058	126590104	-	1	NA	3' UTR (NM_001164598, exon 2 of 2)	3' UTR (NM_001164598, exon 2 of 2)	3355	NM_001164598	270110	Mm.334918	NM_001164598	ENSMUSG00000051495	Irf2bp2	E130305N23Rik|IRF-2BP2	interferon regulatory factor 2 binding protein 2	protein-coding
mm_13191.1	chr2	93198514	93198558	+	1	NA	intron (NM_001025246, intron 4 of 7)	intron (NM_001025246, intron 4 of 7)	10952	NM_001025246	277414	Mm.41033	NM_001025246	ENSMUSG00000068735	Trp53i11	Tp53i11	transformation related protein 53 inducible protein 11	protein-coding
mm_49066.1	chr6	5398400	5398411	+	1	NA	exon (NM_023048, exon 3 of 6)	exon (NM_023048, exon 3 of 6)	15019	NM_023048	65255	Mm.51340	NM_023048	ENSMUSG00000042607	Asb4	8430401O13Rik|AV117194|AW060255	ankyrin repeat and SOCS box-containing 4	protein-coding
mm_83637.1	chr9	49490332	49490363	-	1	NA	Intergenic	Intergenic	-4122	NM_172770	235330	Mm.177413	NM_172770	ENSMUSG00000040219	Ttc12	E330017O07Rik	tetratricopeptide repeat domain 12	protein-coding
mm_1110.1	chr1	59815978	59815981	+	1	NA	intron (NM_007561, intron 3 of 12)	intron (NM_007561, intron 3 of 12)	51700	NM_007561	12168	Mm.7106	NM_007561	ENSMUSG00000067336	Bmpr2	2610024H22Rik|AL117858|AW546137|BB189135|BMP-2|BMPR-2|BMPR-II|BMPRII|BRK-3|Gm20272	bone morphogenetic protein receptor, type II (serine/threonine kinase)	protein-coding
mm_62688.1	chr7	110044121	110044125	+	1	NA	intron (NM_181517, intron 10 of 24)	intron (NM_181517, intron 10 of 24)	-2241	NR_033336	100379145	Mm.484711	NR_033336	ENSMUSG00000064451	Snora23	MBI-1	small nucleolar RNA, H/ACA box 23	snoRNA
mm_48026.1	chr5	136245251	136245263	-	1	NA	promoter-TSS (NM_018825)	promoter-TSS (NM_018825)	-317	NM_018825	23921	Mm.425294	NM_018825	ENSMUSG00000005057	Sh2b2	Aps	SH2B adaptor protein 2	protein-coding
mm_129345.1	chr15	77857753	77857765	-	1	NA	Intergenic	CpG	-15584	NM_022410	17886	Mm.29677	NM_022410	ENSMUSG00000022443	Myh9	Fltn|Myhn-1|Myhn1|NMHCIIA|NMMHC-A|NMMHC-IIA|TU72.6	myosin, heavy polypeptide 9, non-muscle	protein-coding
mm_152144.1	chr19	7199986	7200002	-	1	NA	exon (NM_134150, exon 4 of 7)	exon (NM_134150, exon 4 of 7)	6290	NM_134150	107260	Mm.203921	NM_134150	ENSMUSG00000024767	Otub1	AI850305	OTU domain, ubiquitin aldehyde binding 1	protein-coding
mm_34368.1	chr4	144893128	144893151	+	1	NA	promoter-TSS (NM_011303)	promoter-TSS (NM_011303)	2	NM_011303	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding
mm_123592.1	chr14	67695620	67695623	-	1	NA	intron (NM_001110162, intron 11 of 14)	intron (NM_001110162, intron 11 of 14)	19989	NM_001110162	108912	Mm.33831	NM_175384	ENSMUSG00000048922	Cdca2	2610311M19Rik|AI586158	cell division cycle associated 2	protein-coding
mm_22284.1	chr2	180104464	180104478	-	1	NA	promoter-TSS (NM_133849)	promoter-TSS (NM_133849)	-64	NM_133849	99296	Mm.285360	NM_133849	ENSMUSG00000039059	Hrh3	AW049250|H3R|HH3R	histamine receptor H3	protein-coding
mm_77962.1	chr9	7699505	7699515	+	1	NA	TTS (NM_010810)	TTS (NM_010810)	-3879	NR_126562	102722	Mm.334941	NR_126562	ENSMUSG00000086381	AV064505	-	expressed sequence AV064505	ncRNA
mm_133925.1	chr16	3633156	3633191	-	1	NA	Intergenic	RLTR46B|LTR|ERVK	40775	NM_146860	258859	Mm.377723	NM_146860	ENSMUSG00000051003	Olfr161	MOR131-1|OR912-47M6	olfactory receptor 161	protein-coding
mm_95603.1	chr11	53351851	53351890	+	1	NA	intron (NM_033565, intron 1 of 20)	intron (NM_033565, intron 1 of 20)	1103	NM_033565	93736	Mm.395281	NM_033565	ENSMUSG00000049470	Aff4	AF5Q31|Alf4|Laf4l|MCEF	AF4/FMR2 family, member 4	protein-coding
mm_125410.1	chr15	41751692	41751701	+	1	NA	intron (NM_001130166, intron 3 of 16)	intron (NM_001130166, intron 3 of 16)	-37338	NM_001130165	170719	Mm.254267	NM_130885	ENSMUSG00000022307	Oxr1	2210416C20Rik|C7|C7B	oxidation resistance 1	protein-coding
mm_120141.1	chr14	60377708	60377742	+	1	NA	promoter-TSS (NM_001164705)	promoter-TSS (NM_001164705)	-561	NM_028113	72125	Mm.275499	NM_028113	ENSMUSG00000021986	Amer2	2600011E07Rik|Fam123a	APC membrane recruitment 2	protein-coding
mm_1838.1	chr1	82839450	82839518	+	1	NA	promoter-TSS (NM_010472)	promoter-TSS (NM_010472)	24	NM_001347077	15463	Mm.392569	NM_010472	ENSMUSG00000026159	Agfg1	AU045498|C130049H11Rik|C85612|D730048C23Rik|Hrb|RAB|Rip	ArfGAP with FG repeats 1	protein-coding
mm_35235.1	chr4	19837946	19837951	-	1	NA	intron (NM_028746, intron 2 of 3)	RMER19C|LTR|ERVK	19221	NM_028746	74087	Mm.173833	NM_028746	ENSMUSG00000041052	Slc7a13	0610009O04Rik|AGT-1|AGT1|XAT2	solute carrier family 7, (cationic amino acid transporter, y+ system) member 13	protein-coding
mm_79982.1	chr9	66946396	66946424	+	1	NA	intron (NM_001311101, intron 1 of 4)	CpG	334	NM_026467	67941	Mm.30120	NM_026467	ENSMUSG00000036781	Rps27l	1810034D23Rik	ribosomal protein S27-like	protein-coding
mm_34612.1	chr4	150294007	150294010	+	1	NA	intron (NM_001085492, intron 1 of 22)	intron (NM_001085492, intron 1 of 22)	12092	NM_001085492	68703	Mm.291274	NM_001085492	ENSMUSG00000039852	Rere	1110033A15Rik|AI414665|ARG|ARP|ATN1L|AW742570|Atr2|DNB1|eye<m03Jus>|eyes3|mKIAA0458	arginine glutamic acid dipeptide (RE) repeats	protein-coding
mm_18483.1	chr2	62596134	62596143	-	1	NA	3' UTR (NM_027835, exon 16 of 16)	3' UTR (NM_027835, exon 16 of 16)	-22117	NM_007986	14089	Mm.41816	NM_007986	ENSMUSG00000000392	Fap	SIMP	fibroblast activation protein	protein-coding
mm_97939.1	chr11	83662535	83662544	+	1	NA	promoter-TSS (NM_013652)	promoter-TSS (NM_013652)	-45	NM_013652	20303	Mm.244263	NM_013652	ENSMUSG00000018930	Ccl4	AT744.1|Act-2|MIP-1B|Mip1b|Scya4	chemokine (C-C motif) ligand 4	protein-coding
mm_118455.1	chr14	8368273	8368281	+	1	NA	intron (NM_146050, intron 1 of 9)	intron (NM_146050, intron 1 of 9)	10486	NM_146050	18300	Mm.25351	NM_146050	ENSMUSG00000021749	Oit1	2310076N21Rik|AV067083|EF-7|Fam3d	oncoprotein induced transcript 1	protein-coding
mm_170001.1	chr1	71652069	71652071	-	1	NA	intron (NM_001276409, intron 1 of 44)	B1F|SINE|Alu	1164	NM_010233	14268	Mm.193099	NM_010233	ENSMUSG00000026193	Fn1	E330027I09|Fn|Fn-1	fibronectin 1	protein-coding
mm_18889.1	chr2	76709701	76709712	-	1	NA	exon (NM_011652, exon 307 of 313)	exon (NM_011652, exon 307 of 313)	34391	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_6915.1	chr1	84839529	84839535	-	1	NA	promoter-TSS (NM_025386)	promoter-TSS (NM_025386)	-228	NM_133975	14897	Mm.209265	NM_133975	ENSMUSG00000026219	Trip12	1110036I07Rik|6720416K24Rik|AA410158|Gtl6|TRIP-12	thyroid hormone receptor interactor 12	protein-coding
mm_146840.1	chr18	23038659	23038676	-	1	NA	promoter-TSS (NM_001161483)	promoter-TSS (NM_001161483)	-4	NM_001161483	319211	Mm.209896	NM_199024	ENSMUSG00000041923	Nol4	1700013J13Rik|4930568N03Rik|Gm1262	nucleolar protein 4	protein-coding
mm_32108.1	chr4	98923660	98923676	+	1	NA	promoter-TSS (NM_146144)	promoter-TSS (NM_146144)	-142	NM_001301414	230484	Mm.371692	NM_146144	ENSMUSG00000028560	Usp1	-	ubiquitin specific peptidase 1	protein-coding
mm_23476.1	chr3	60481002	60481024	+	1	NA	intron (NM_001253713, intron 2 of 9)	intron (NM_001253713, intron 2 of 9)	8183	NM_001253713	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_88409.1	chr10	77032231	77032255	+	1	NA	promoter-TSS (NM_031196)	promoter-TSS (NM_031196)	-496	NM_001199271	20509	Mm.265060	NM_031196	ENSMUSG00000001436	Slc19a1	AI323572|RFC|RFC-1|RFC1	solute carrier family 19 (folate transporter), member 1	protein-coding
mm_30996.1	chr4	40143081	40143107	+	1	NA	promoter-TSS (NM_007386)	promoter-TSS (NM_007386)	-171	NM_007386	11428	Mm.331547	NM_007386	ENSMUSG00000028405	Aco1	Aco-1|Irebp|Irp1	aconitase 1	protein-coding
mm_81224.1	chr9	107614657	107614675	+	1	NA	3' UTR (NM_008138, exon 9 of 9)	3' UTR (NM_008138, exon 9 of 9)	-5425	NM_001291539	20347	Mm.4083	NM_009153	ENSMUSG00000057969	Sema3b	SemA|Semaa|sema5|semaV	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B	protein-coding
mm_156435.1	chrX	141980281	141980306	+	1	NA	Intergenic	Intergenic	216643	NM_001007576	245650	Mm.208511	NM_001007576	ENSMUSG00000042282	Gucy2f	A930002I06|GC-F|GC2	guanylate cyclase 2f	protein-coding
mm_93299.1	chr10	96621264	96621271	-	1	NA	3' UTR (NM_007569, exon 2 of 2)	3' UTR (NM_007569, exon 2 of 2)	4266	NM_007569	12226	Mm.23811	NM_007569	ENSMUSG00000036478	Btg1	AI426953|AW546738	B cell translocation gene 1, anti-proliferative	protein-coding
mm_120729.1	chr14	73143047	73143072	+	1	NA	non-coding (NR_033185, exon 1 of 16)	non-coding (NR_033185, exon 1 of 16)	274	NR_033185	105670	Mm.280068	NM_134083	ENSMUSG00000022106	Rcbtb2	2610028E02Rik|2810420M18Rik|AI448345|AW240694|Chc1l|RC/BTB2	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 2	protein-coding
mm_152032.1	chr19	6084874	6084940	-	1	NA	promoter-TSS (NM_024231)	promoter-TSS (NM_024231)	-16	NM_024231	81909	Mm.289471	NM_024231	ENSMUSG00000024792	Zfpl1	1500015B20Rik	zinc finger like protein 1	protein-coding
mm_45482.1	chr5	70842374	70842388	-	1	NA	5' UTR (NM_010252, exon 1 of 9)	5' UTR (NM_010252, exon 1 of 9)	236	NM_010252	14405	Mm.255292	NM_010252	ENSMUSG00000001260	Gabrg1	GabaA|GabaA/BZ	gamma-aminobutyric acid (GABA) A receptor, subunit gamma 1	protein-coding
mm_11693.1	chr2	35691894	35691953	+	1	NA	promoter-TSS (NM_001290640)	promoter-TSS (NM_001290640)	-71	NM_001001602	69601	Mm.29629	NM_001001602	ENSMUSG00000026883	Dab2ip	2310011D08Rik|AI480459|Aip1|mKIAA1743	disabled 2 interacting protein	protein-coding
mm_40747.1	chr5	66745497	66745510	+	1	NA	promoter-TSS (NM_001001980)	promoter-TSS (NM_001001980)	-337	NM_001001980	77569	Mm.374778	NM_001001980	ENSMUSG00000037736	Limch1	3732412D22Rik|mKIAA1102	LIM and calponin homology domains 1	protein-coding
mm_15158.1	chr2	154009188	154009194	+	1	NA	exon (NM_008953, exon 2 of 9)	exon (NM_008953, exon 2 of 9)	915	NM_008953	19194	Mm.29197	NM_008953	ENSMUSG00000042459	Bpifa2	Bpifa2e|Psp	BPI fold containing family A, member 2	protein-coding
mm_144864.1	chr18	36725789	36725833	+	1	NA	exon (NM_009841, exon 2 of 2)	exon (NM_009841, exon 2 of 2)	1004	NM_009841	12475	Mm.3460	NM_009841	ENSMUSG00000051439	Cd14	-	CD14 antigen	protein-coding
mm_12708.1	chr2	76675291	76675321	+	1	NA	promoter-TSS (NM_031256)	promoter-TSS (NM_031256)	-9	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_92710.1	chr10	80757128	80757148	-	1	NA	intron (NM_199322, intron 1 of 27)	intron (NM_199322, intron 1 of 27)	1932	NM_199322	208266	Mm.152371	NM_199322	ENSMUSG00000061589	Dot1l	A630076O07|AW907654|Dot1|KMT4|mDot1	DOT1-like, histone H3 methyltransferase (S. cerevisiae)	protein-coding
mm_118579.1	chr14	19763750	19763768	+	1	NA	exon (NM_008695, exon 3 of 21)	exon (NM_008695, exon 3 of 21)	12502	NM_008695	18074	Mm.20348	NM_008695	ENSMUSG00000021806	Nid2	AW547149|Ly111|NID-2|entactin-2|nidogen-2	nidogen 2	protein-coding
mm_47919.1	chr5	135001289	135001361	-	1	NA	promoter-TSS (NR_026907)	promoter-TSS (NR_026907)	25	NR_026907	71304	Mm.482317	NR_026907	ENSMUSG00000054909	Wbscr25	4933433J03Rik|4933439O14Rik	Williams Beuren syndrome chromosome region 25 (human)	ncRNA
mm_145099.1	chr18	43764318	43764333	+	1	NA	promoter-TSS (NM_001289644)	promoter-TSS (NM_001289644)	24	NM_001289644	117158	Mm.210437	NM_054038	ENSMUSG00000038791	Scgb3a2	LuLeu1|Pnsp1|UGRP1|Utgrp1	secretoglobin, family 3A, member 2	protein-coding
mm_152593.1	chr19	11623679	11623709	-	1	NA	promoter-TSS (NM_013516)	promoter-TSS (NM_013516)	25	NM_001276330	14126	Mm.329735	NM_013516	ENSMUSG00000024680	Ms4a2	FcRB|Fce1b|Fcer1b|Fcrbeta|Ms4a1|fcERI	membrane-spanning 4-domains, subfamily A, member 2	protein-coding
mm_113900.1	chr13	49213891	49213902	+	1	NA	intron (NM_026738, intron 1 of 5)	intron (NM_026738, intron 1 of 5)	2130	NM_026738	68480	Mm.3336	NM_026738	ENSMUSG00000037960	Card19	1110007C09Rik|AI851695|Bincard	caspase recruitment domain family, member 19	protein-coding
mm_163016.1	chr11	46055948	46055967	+	1	NA	promoter-TSS (NM_009616)	promoter-TSS (NM_009616)	-27	NM_009616	11492	Mm.89940	NM_009616	ENSMUSG00000011256	Adam19	AL024287|MADDAM|MTLNB|Mltnb	a disintegrin and metallopeptidase domain 19 (meltrin beta)	protein-coding
mm_56877.1	chr6	118968355	118968360	-	1	NA	intron (NM_001256002, intron 3 of 47)	intron (NM_001256002, intron 3 of 47)	88199	NR_046053	74363	Mm.399403	NR_046053		4931430N09Rik	-	RIKEN cDNA 4931430N09 gene	ncRNA
mm_101363.1	chr11	23741882	23741889	-	1	NA	3' UTR (NM_009044, exon 10 of 10)	3' UTR (NM_009044, exon 10 of 10)	29085	NM_009044	19696	Mm.4869	NM_009044	ENSMUSG00000020275	Rel	c-Rel	reticuloendotheliosis oncogene	protein-coding
mm_93571.1	chr10	116564993	116565001	-	1	NA	intron (NM_001037846, intron 1 of 15)	intron (NM_001037846, intron 1 of 15)	16514	NM_001037848	72068	Mm.351553	NM_028082	ENSMUSG00000020166	Cnot2	2600016M12Rik|2810470K03Rik|AA537049|AA959607|AW557563|C79650	CCR4-NOT transcription complex, subunit 2	protein-coding
mm_20122.1	chr2	121241832	121241835	-	1	NA	intron (NM_001290830, intron 11 of 26)	ID_B1|SINE|B4	29574	NM_001290830	27223	Mm.215389	NM_013735	ENSMUSG00000043909	Trp53bp1	53BP1|Tp53bp1|m53BP1|p53BP1	transformation related protein 53 binding protein 1	protein-coding
mm_16736.1	chr2	9178718	9178725	-	1	NA	Intergenic	Intergenic	-10794	NR_038180	73438	Mm.23558	NR_038180	ENSMUSG00000085580	1700061F12Rik	-	RIKEN cDNA 1700061F12 gene	ncRNA
mm_4168.1	chr1	171113978	171114048	+	1	NA	Intergenic	Intergenic	-7648	NM_001081275	75472	Mm.32760	NM_029301	ENSMUSG00000026649	Cfap126	1700009P17Rik|AV282292|Flattop|Fltp	cilia and flagella associated protein 126	protein-coding
mm_69820.1	chr7	141265454	141265479	-	1	NA	exon (NM_001252601, exon 3 of 10)	exon (NM_001252601, exon 3 of 10)	958	NM_001252601	54123	Mm.3233	NM_016850	ENSMUSG00000025498	Irf7	-	interferon regulatory factor 7	protein-coding
mm_103126.1	chr11	70220795	70220832	-	1	NA	5' UTR (NM_172371, exon 1 of 4)	5' UTR (NM_172371, exon 1 of 4)	181	NM_172371	69309	Mm.93266	NM_172371	ENSMUSG00000044367	Slc16a13	1700007D07Rik	solute carrier family 16 (monocarboxylic acid transporters), member 13	protein-coding
mm_17343.1	chr2	26604201	26604227	-	1	NA	5' UTR (NM_026212, exon 1 of 6)	5' UTR (NM_026212, exon 1 of 6)	203	NM_026212	67512	Mm.24244	NM_026212	ENSMUSG00000026922	Agpat2	2510002J07Rik|AV000834|BSCL|BSCL1|LPAAB|LPAAT-beta	1-acylglycerol-3-phosphate O-acyltransferase 2 (lysophosphatidic acid acyltransferase, beta)	protein-coding
mm_23480.1	chr3	60487713	60487731	+	1	NA	intron (NM_001253713, intron 2 of 9)	B3A|SINE|B2	-13457	NM_001253711	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_61072.1	chr7	51596315	51596316	+	1	NA	non-coding (NR_073508, exon 21 of 21)	non-coding (NR_073508, exon 21 of 21)	-25515	NM_080853	140919	Mm.256618	NM_080853	ENSMUSG00000030500	Slc17a6	2900073D12Rik|DNPI|VGLUT2	solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 6	protein-coding
mm_172584.1	chr8	123172832	123172848	+	1	NA	Intergenic	RLTR10D2|LTR|ERVK	-13395	NM_007876	13479	Mm.20388	NM_007876	ENSMUSG00000019278	Dpep1	AI327012|MBD	dipeptidase 1 (renal)	protein-coding
mm_72249.1	chr8	75067493	75067520	+	1	NA	intron (NM_001136259, intron 13 of 15)	intron (NM_001136259, intron 13 of 15)	-26112	NM_010442	15368	Mm.276389	NM_010442	ENSMUSG00000005413	Hmox1	D8Wsu38e|HO-1|HO1|Hemox|Hmox|Hsp32	heme oxygenase 1	protein-coding
mm_1616.1	chr1	74391578	74391594	+	1	NA	promoter-TSS (NM_153088)	promoter-TSS (NM_153088)	-23	NM_153088	227292	Mm.165042	NM_153088	ENSMUSG00000026176	Ctdsp1	GIP|NLIIF|Nif3|SCP1	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 1	protein-coding
mm_61963.1	chr7	90386976	90387018	+	1	NA	promoter-TSS (NM_001040087)	promoter-TSS (NM_001040087)	16	NM_001040088	83671	Mm.26751	NM_031394	ENSMUSG00000030616	Sytl2	AI266830|Slp2|mKIAA1597	synaptotagmin-like 2	protein-coding
mm_88026.1	chr10	67220110	67220123	+	1	NA	exon (NM_001242396, exon 7 of 25)	exon (NM_001242396, exon 7 of 25)	34366	NM_001242396	108829	Mm.23846	NM_207221	ENSMUSG00000037876	Jmjd1c	5430433L24Rik|D630035I23Rik|Jmjdic|TRIP8	jumonji domain containing 1C	protein-coding
mm_74126.1	chr8	123186272	123186282	+	1	NA	promoter-TSS (NM_007876)	promoter-TSS (NM_007876)	42	NM_007876	13479	Mm.20388	NM_007876	ENSMUSG00000019278	Dpep1	AI327012|MBD	dipeptidase 1 (renal)	protein-coding
mm_54768.1	chr6	41446063	41446086	-	1	NA	promoter-TSS (NM_001103153)	promoter-TSS (NM_001103153)	23	NM_001103153	100040233	Mm.297485	NM_001103153	ENSMUSG00000071517	Gm10334	ENSMUSG00000071517	predicted gene 10334	protein-coding
mm_154406.1	chrM	14567	14577	+	1	NA	NA	Intergenic	NA	NA								
mm_3679.1	chr1	153695367	153695374	+	1	NA	3' UTR (NM_026380, exon 7 of 7)	3' UTR (NM_026380, exon 7 of 7)	29697	NM_001347115	67792	Mm.379143	NM_026380	ENSMUSG00000042671	Rgs8	6530413N01Rik	regulator of G-protein signaling 8	protein-coding
mm_118204.1	chr13	108310984	108310985	-	1	NA	Intergenic	Intergenic	-5353	NM_178683	218581	Mm.32318	NM_178683	ENSMUSG00000021697	Depdc1b	9830132O03|AW260467|XTP1	DEP domain containing 1B	protein-coding
mm_84443.1	chr9	66124873	66124883	-	1	NA	promoter-TSS (NM_019727)	promoter-TSS (NM_019727)	8	NM_019727	56440	Mm.271891	NM_019727	ENSMUSG00000032382	Snx1	-	sorting nexin 1	protein-coding
mm_153306.1	chr19	38022765	38022777	-	1	NA	intron (NM_001302140, intron 2 of 53)	intron (NM_001302140, intron 2 of 53)	20806	NM_001099634	226101	Mm.34674	NM_177035	ENSMUSG00000048612	Myof	2310004N10Rik|2310051D19Rik|E030042N20Rik|Fer1l3	myoferlin	protein-coding
mm_44490.1	chr5	23675815	23675838	-	1	NA	Intergenic	CpG	36841	NR_038090	433855	Mm.205125	NR_015554	ENSMUSG00000105987	AI506816	-	expressed sequence AI506816	ncRNA
mm_41803.1	chr5	103753981	103753987	+	1	NA	promoter-TSS (NM_133919)	promoter-TSS (NM_133919)	-178	NM_133919	17355	Mm.6949	NM_133919	ENSMUSG00000029313	Aff1	9630032B01Rik|AW319193|Af4|Mllt2h|Rob	AF4/FMR2 family, member 1	protein-coding
mm_162628.1	chr1	185283292	185283293	+	1	NA	intron (NM_001163754, intron 33 of 34)	intron (NM_001163754, intron 33 of 34)	-30027	NR_029580	387189		NR_029580	ENSMUSG00000065581	Mir194-1	Mirn194|Mirn194-1|miR-194|mir-194-1	microRNA 194-1	ncRNA
mm_18223.1	chr2	51130861	51130863	-	1	NA	3' UTR (NM_028810, exon 5 of 5)	3' UTR (NM_028810, exon 5 of 5)	18249	NM_028810	74194	Mm.46497	NM_028810	ENSMUSG00000017144	Rnd3	2610017M01Rik|AI661404|Arhe|Rhoe	Rho family GTPase 3	protein-coding
mm_77180.1	chr8	111721077	111721125	-	1	NA	exon (NM_009954, exon 2 of 7)	exon (NM_009954, exon 2 of 7)	11035	NM_001198839	12927	Mm.3758	NM_009954	ENSMUSG00000031955	Bcar1	AI385681|Cas|Crkas	breast cancer anti-estrogen resistance 1	protein-coding
mm_145191.1	chr18	49832691	49832699	+	1	NA	promoter-TSS (NM_001081371)	promoter-TSS (NM_001081371)	-302	NM_001081371	240283	Mm.257790	NM_001081371	ENSMUSG00000037416	Dmxl1	C630007L23Rik|D030030C22	Dmx-like 1	protein-coding
mm_48720.1	chr5	147322388	147322410	-	1	NA	promoter-TSS (NM_001039678)	promoter-TSS (NM_001039678)	41	NM_001039678	231903	Mm.291286	NM_001039678	ENSMUSG00000075543	Urad	EG231903|Prhoxnb	ureidoimidazoline (2-oxo-4-hydroxy-4-carboxy-5) decarboxylase	protein-coding
mm_57035.1	chr6	122339103	122339114	-	1	NA	intron (NM_001271579, intron 1 of 14)	intron (NM_001271579, intron 1 of 14)	549	NM_001042623	13619	Mm.6822	NM_007905	ENSMUSG00000040669	Phc1	AW557034|Edr|Edr1|Mph1|Rae-28|rae28	polyhomeotic-like 1 (Drosophila)	protein-coding
mm_64629.1	chr7	3692907	3693032	-	1	NA	promoter-TSS (NM_001164205)	promoter-TSS (NM_001164205)	556	NM_029934	77582	Mm.397541	NM_029934	ENSMUSG00000035596	Mboat7	5730589L02Rik|BB1|Leng4|Lpiat|Lpiat1|mBB1	membrane bound O-acyltransferase domain containing 7	protein-coding
mm_72955.1	chr8	92358309	92358327	+	1	NA	exon (NM_018826, exon 1 of 3)	exon (NM_018826, exon 1 of 3)	522	NM_018826	54352	Mm.101153	NM_018826	ENSMUSG00000031737	Irx5	-	Iroquois related homeobox 5 (Drosophila)	protein-coding
mm_72650.1	chr8	84803694	84803709	+	1	NA	Intergenic	Intergenic	-3363	NM_001081982	18032	Mm.9394	NM_010906	ENSMUSG00000001911	Nfix	CTF|NF-I/X|NF1-X|NFI-X	nuclear factor I/X	protein-coding
mm_151004.1	chr19	46654822	46654843	+	1	NA	3' UTR (NM_001177813, exon 4 of 4)	3' UTR (NM_001177813, exon 4 of 4)	18168	NM_007809	13074	Mm.1262	NM_007809	ENSMUSG00000003555	Cyp17a1	Cyp17|p450c17	cytochrome P450, family 17, subfamily a, polypeptide 1	protein-coding
mm_55588.1	chr6	71440525	71440566	-	1	NA	promoter-TSS (NM_024288)	promoter-TSS (NM_024288)	92	NM_024288	68477	Mm.28474	NM_024288	ENSMUSG00000002222	Rmnd5a	1110007A06Rik|AJ237586|AW125795|Gid2|MTA.D02.090	required for meiotic nuclear division 5 homolog A	protein-coding
mm_29278.1	chr3	107631682	107631705	-	1	NA	promoter-TSS (NM_153563)	promoter-TSS (NM_153563)	17	NM_153563	229707	Mm.278643	NM_153563	ENSMUSG00000014601	Strip1	6330569M22Rik|6530401O14Rik|Fam40a	striatin interacting protein 1	protein-coding
mm_71565.1	chr8	53511816	53511838	+	1	NA	exon (NM_001205054, exon 1 of 9)	exon (NM_001205054, exon 1 of 9)	125	NM_001005847	11593	Mm.334535	NM_001005847	ENSMUSG00000031521	Aga	AW060726	aspartylglucosaminidase	protein-coding
mm_146911.1	chr18	31439684	31439689	-	1	NA	3' UTR (NM_009308, exon 4 of 4)	3' UTR (NM_009308, exon 4 of 4)	7729	NM_009308	20983	Mm.233846	NM_009308	ENSMUSG00000024261	Syt4	SytIV	synaptotagmin IV	protein-coding
mm_23601.1	chr3	65109344	65109420	+	1	NA	promoter-TSS (NM_010597)	promoter-TSS (NM_010597)	14	NM_010597	16497	Mm.316402	NM_010597	ENSMUSG00000027827	Kcnab1	Akr8a8|Kvbeta1.1|mKv(beta)1	potassium voltage-gated channel, shaker-related subfamily, beta member 1	protein-coding
mm_121801.1	chr14	20145861	20145906	-	1	NA	intron (NM_021542, intron 2 of 4)	intron (NM_021542, intron 2 of 4)	35899	NM_021542	16529	Mm.68998	NM_021542	ENSMUSG00000023243	Kcnk5	KCNK5b|TASK-2	potassium channel, subfamily K, member 5	protein-coding
mm_161446.1	chr15	73839427	73839427	-	1	NA	intron (NM_001033365, intron 1 of 10)	CpG	244	NM_001033365	268816	Mm.440635	NM_001033365	ENSMUSG00000072487	Mroh5	Gm628	maestro heat-like repeat family member 5	protein-coding
mm_86481.1	chr10	4819488	4819491	+	1	NA	intron (NM_001302531, intron 4 of 8)	intron (NM_001302531, intron 4 of 8)	109331	NM_001302533	13982	Mm.9213	NM_007956	ENSMUSG00000019768	Esr1	ER|ER-alpha|ERa|ERalpha|ESR|Estr|Estra|Nr3a1	estrogen receptor 1 (alpha)	protein-coding
mm_58888.1	chr7	17090452	17090459	+	1	NA	5' UTR (NM_007676, exon 2 of 5)	5' UTR (NM_007676, exon 2 of 5)	16415	NM_007676	26436	Mm.143686	NM_007676	ENSMUSG00000066760	Psg16	Cea11|PSG|bCEA	pregnancy specific glycoprotein 16	protein-coding
mm_2480.1	chr1	105847006	105847023	+	1	NA	3' UTR (NM_009399, exon 10 of 10)	3' UTR (NM_009399, exon 10 of 10)	66291	NM_009399	21934	Mm.6251	NM_009399	ENSMUSG00000026321	Tnfrsf11a	Ly109|ODFR|OFE|Rank|TRANCE-R|mRANK	tumor necrosis factor receptor superfamily, member 11a, NFKB activator	protein-coding
mm_28138.1	chr3	87249660	87249673	-	1	NA	Intergenic	MLT2F|LTR|ERVL	13858	NM_030707	80891	Mm.45173	NM_030707	ENSMUSG00000015852	Fcrls	2810439C17Rik|9330158F12|FcRH2sc|Fcrh2|IFGP2|IgSR|MMAN-g|Msr2|moFcRH2sc	Fc receptor-like S, scavenger receptor	protein-coding
mm_172389.1	chr7	136810815	136810815	+	1	NA	Intergenic	Intergenic	-83796	NM_008598	17314	Mm.440219	NM_008598	ENSMUSG00000054612	Mgmt	AGT|AI267024|Agat	O-6-methylguanine-DNA methyltransferase	protein-coding
mm_55528.1	chr6	70726648	70726657	-	1	NA	Intergenic	Intergenic	65523	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_23016.1	chr3	34560361	34560386	+	1	NA	promoter-TSS (NR_015580)	promoter-TSS (NR_015580)	-8	NR_015580	320478	Mm.444063	NR_015580	ENSMUSG00000105265	Sox2ot	B230215L15Rik	SOX2 overlapping transcript (non-protein coding)	ncRNA
mm_53035.1	chr6	124556021	124556021	+	1	NA	Intergenic	B4A|SINE|B4	-13662	NM_001097617	50908	Mm.219527	NM_144938	ENSMUSG00000038521	C1s1	AA959438|AI255193|AI327365|C1s|C1sa	complement component 1, s subcomponent 1	protein-coding
mm_142642.1	chr17	47433433	47433456	-	1	NA	intron (NM_029296, intron 2 of 3)	intron (NM_029296, intron 2 of 3)	-3195	NM_145489	224833	Mm.218444	NM_145489	ENSMUSG00000034382	AI661453	-	expressed sequence AI661453	protein-coding
mm_154295.1	chr19	61198770	61198781	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-22466	NM_001177513	633057	Mm.426097	NM_001177513	ENSMUSG00000094649	Gm7102	EG633057	predicted gene 7102	protein-coding
mm_113445.1	chr13	35659857	35659870	+	1	NA	promoter-TSS (NM_009881)	promoter-TSS (NM_009881)	1	NM_009881	12593	Mm.29002	NM_009881	ENSMUSG00000059288	Cdyl	AI325931	chromodomain protein, Y chromosome-like	protein-coding
mm_87026.1	chr10	28277276	28277278	+	1	NA	intron (NM_008983, intron 3 of 31)	(T)n|Simple_repeat|Simple_repeat	202457	NM_008983	19272	Mm.332303	NM_008983	ENSMUSG00000019889	Ptprk	AI853699|PTPk|RPTPkappa	protein tyrosine phosphatase, receptor type, K	protein-coding
mm_157060.1	chrX	8132513	8132581	-	1	NA	5' UTR (NM_026137, exon 1 of 9)	5' UTR (NM_026137, exon 1 of 9)	311	NM_001290783	73447	Mm.284162	NM_026137	ENSMUSG00000031166	Wdr13	1700060B08Rik|5730411P10Rik|DXHXS7467e|W51679|mMg21	WD repeat domain 13	protein-coding
mm_41045.1	chr5	86093230	86093240	+	1	NA	intron (NM_001310639, intron 5 of 7)	intron (NM_001310639, intron 5 of 7)	21489	NM_001310639	56792	Mm.131237	NM_019992	ENSMUSG00000029254	Stap1	AI586015|Brdg1|STAP-1	signal transducing adaptor family member 1	protein-coding
mm_139933.1	chr17	71085353	71085395	+	1	NA	intron (NM_010867, intron 19 of 37)	intron (NM_010867, intron 19 of 37)	65817	NM_001083934	17929	Mm.4103	NM_010867	ENSMUSG00000024049	Myom1	D430047A17Rik	myomesin 1	protein-coding
mm_153081.1	chr19	32387871	32387897	-	1	NA	intron (NM_144792, intron 1 of 9)	CpG	570	NM_144792	208449	Mm.329810	NM_144792	ENSMUSG00000040451	Sgms1	9530058O11Rik|AI841905|C80702|Mob|Sms1|Sor1|Tmem23	sphingomyelin synthase 1	protein-coding
mm_48779.1	chr5	148552252	148552273	-	1	NA	5' UTR (NM_011908, exon 1 of 5)	5' UTR (NM_011908, exon 1 of 5)	526	NM_011908	24109	Mm.21846	NM_011908	ENSMUSG00000001687	Ubl3	AW108023|HCG	ubiquitin-like 3	protein-coding
mm_89732.1	chr10	98990498	98990512	+	1	NA	intron (NM_026482, intron 5 of 20)	intron (NM_026482, intron 5 of 20)	75353	NM_026482	67972	Mm.166944	NM_026482	ENSMUSG00000019943	Atp2b1	2810442I22Rik|E130111D10Rik|Pmca1	ATPase, Ca++ transporting, plasma membrane 1	protein-coding
mm_89270.1	chr10	87860250	87860267	+	1	NA	promoter-TSS (NM_001111276)	promoter-TSS (NM_001111276)	-853	NM_001111274	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_45787.1	chr5	87379950	87379954	-	1	NA	Intergenic	Intergenic	-42757	NM_028094	72094	Mm.482739	NM_028094	ENSMUSG00000035780	Ugt2a3	2010321J07Rik	UDP glucuronosyltransferase 2 family, polypeptide A3	protein-coding
mm_153839.1	chr19	46327122	46327154	-	1	NA	promoter-TSS (NM_001347454)	promoter-TSS (NM_001347454)	18	NM_028627	73728	Mm.268532	NM_028627	ENSMUSG00000037126	Psd	1110007H17Rik|A930015K15|Efa6|Efa6a|Psdl|mKIAA2011	pleckstrin and Sec7 domain containing	protein-coding
mm_152507.1	chr19	11232434	11232459	-	1	NA	intron (NR_045317, intron 1 of 2)	intron (NR_045317, intron 1 of 2)	33705	NM_007641	12482	Mm.4046	NM_007641	ENSMUSG00000024673	Ms4a1	AA960661|Cd20|Ly-44|Ms4a2	membrane-spanning 4-domains, subfamily A, member 1	protein-coding
mm_24459.1	chr3	90614371	90614383	+	1	NA	TTS (NM_011313)	TTS (NM_011313)	1483	NM_011313	20200	Mm.100144	NM_011313	ENSMUSG00000001025	S100a6	2A9|5B10|CALCYCLIN|Cacy|PRA	S100 calcium binding protein A6 (calcyclin)	protein-coding
mm_25028.1	chr3	98147168	98147178	+	1	NA	exon (NM_010928, exon 34 of 34)	exon (NM_010928, exon 34 of 34)	-13461	NM_027665	71078	Mm.50711	NM_027665	ENSMUSG00000043468	Adam30	4933424D07Rik|svph4	a disintegrin and metallopeptidase domain 30	protein-coding
mm_40288.1	chr5	43233733	43233741	+	1	NA	exon (NM_001177379, exon 1 of 11)	exon (NM_001177379, exon 1 of 11)	274	NM_001177379	231207	Mm.7233	NM_175937	ENSMUSG00000039782	Cpeb2	A630055H10Rik|Cpe-bp2	cytoplasmic polyadenylation element binding protein 2	protein-coding
mm_131641.1	chr16	20516886	20516896	+	1	NA	promoter-TSS (NM_007889)	promoter-TSS (NM_007889)	-95	NM_001347176	13544	Mm.247259	NM_007889	ENSMUSG00000003233	Dvl3	-	dishevelled segment polarity protein 3	protein-coding
mm_154537.1	chrM	13976	13985	-	1	NA	NA	Intergenic	NA	NA								
mm_83458.1	chr9	45259627	45259641	-	1	NA	intron (NR_136903, intron 5 of 5)	RLTR17B_Mm|LTR|ERVK	7073	NR_106054	102466803		NR_106054	ENSMUSG00000098361	Mir7086	Gm27643|mmu-mir-7086	microRNA 7086	ncRNA
mm_170834.1	chr2	177032663	177032676	+	1	NA	Intergenic	Intergenic	-104856	NM_001305133	102639598	Mm.379980	NM_029813	ENSMUSG00000074527	Gm14296	-	predicted gene 14296	protein-coding
mm_77181.1	chr8	111726107	111726139	-	1	NA	intron (NM_009954, intron 1 of 6)	intron (NM_009954, intron 1 of 6)	6013	NM_001198839	12927	Mm.3758	NM_009954	ENSMUSG00000031955	Bcar1	AI385681|Cas|Crkas	breast cancer anti-estrogen resistance 1	protein-coding
mm_18320.1	chr2	57114749	57114780	-	1	NA	5' UTR (NM_013613, exon 1 of 8)	5' UTR (NM_013613, exon 1 of 8)	274	NM_013613	18227	Mm.3507	NM_013613	ENSMUSG00000026826	Nr4a2	HZF-3|NOT|Nurr1|RNR-1|TINOR|TINUR	nuclear receptor subfamily 4, group A, member 2	protein-coding
mm_144628.1	chr18	32938956	32938967	+	1	NA	promoter-TSS (NM_009793)	promoter-TSS (NM_009793)	-80	NM_009793	12326	Mm.222329	NM_009793	ENSMUSG00000038128	Camk4	A430110E23Rik|AI666733|CaMKIV|CaMKIV/Gr|D18Bwg0362e	calcium/calmodulin-dependent protein kinase IV	protein-coding
mm_80983.1	chr9	103220902	103220934	+	1	NA	exon (NM_133977, exon 9 of 17)	exon (NM_133977, exon 9 of 17)	9368	NM_133977	22041	Mm.37214	NM_133977	ENSMUSG00000032554	Trf	AI266983|Cd176|HP|Tf|Tfn|hpx	transferrin	protein-coding
mm_144905.1	chr18	37341745	37341756	+	1	NA	promoter-TSS (NM_053132)	promoter-TSS (NM_053132)	48	NM_053132	93878	Mm.44755	NM_053132	ENSMUSG00000045062	Pcdhb7	Pcdhb4B|PcdhbG	protocadherin beta 7	protein-coding
mm_11925.1	chr2	52073100	52073141	+	1	NA	intron (NM_175238, intron 1 of 35)	CpG	283	NM_175238	51869	Mm.254530	NM_175238	ENSMUSG00000036202	Rif1	5730435J01Rik|6530403D07Rik|AU016181|AW549474|D2Ertd145e	replication timing regulatory factor 1	protein-coding
mm_44750.1	chr5	31254686	31254722	-	1	NA	exon (NM_026298, exon 43 of 48)	exon (NM_026298, exon 43 of 48)	2998	NM_027221	69815	Mm.389609	NM_027221	ENSMUSG00000029149	Krtcap3	2010001C09Rik|AW321088|Kcp3	keratinocyte associated protein 3	protein-coding
mm_70180.1	chr7	143756995	143757034	-	1	NA	Intergenic	Intergenic	9979	NM_203492	381974	Mm.297839	NM_203492	ENSMUSG00000050276	Mrgprg	Gm1098|Mrgg	MAS-related GPR, member G	protein-coding
mm_126885.1	chr15	89454125	89454145	+	1	NA	5' UTR (NM_021921, exon 1 of 12)	5' UTR (NM_021921, exon 1 of 12)	224	NM_021921	60597	Mm.173337	NM_021921	ENSMUSG00000022619	Mapk8ip2	3230402N03Rik|AI847694|AW049958|IB2|Jip2|R75148	mitogen-activated protein kinase 8 interacting protein 2	protein-coding
mm_62160.1	chr7	97177253	97177264	+	1	NA	intron (NM_001162477, intron 1 of 9)	PB1|SINE|Alu	95507	NM_010248	14389	Mm.42033	NM_010248	ENSMUSG00000004508	Gab2	AI463667|D130058I17Rik|p97	growth factor receptor bound protein 2-associated protein 2	protein-coding
mm_57004.1	chr6	121044125	121044128	-	1	NA	intron (NM_001270475, intron 1 of 31)	intron (NM_001270475, intron 1 of 31)	-20338	NR_138098	100043793	Mm.448053	NR_138098		Gm4651	-	predicted gene 4651	ncRNA
mm_61159.1	chr7	58751026	58751030	+	1	NA	intron (NM_009728, intron 2 of 20)	intron (NM_009728, intron 2 of 20)	92826	NM_009728	11982	Mm.135129	NM_009728	ENSMUSG00000025324	Atp10a	Atp10c|pfatp	ATPase, class V, type 10A	protein-coding
mm_137960.1	chr17	33139732	33139740	+	1	NA	promoter-TSS (NM_177719)	promoter-TSS (NM_177719)	-53	NM_177719	240069	Mm.157765	NM_177719	ENSMUSG00000048602	Morc2b	4932411A10Rik|Tce6	microrchidia 2B	protein-coding
mm_11714.1	chr2	36237732	36237747	+	1	NA	exon (NM_008969, exon 4 of 11)	exon (NM_008969, exon 4 of 11)	7313	NM_008969	19224	Mm.275434	NM_008969	ENSMUSG00000047250	Ptgs1	COX1|Cox-1|Cox-3|PGHS-1|PHS 1|Pghs1	prostaglandin-endoperoxide synthase 1	protein-coding
mm_101969.1	chr11	50310409	50310435	-	1	NA	exon (NM_001110500, exon 4 of 15)	exon (NM_001110500, exon 4 of 15)	15251	NM_001110499	12330	Mm.248827	NM_007597	ENSMUSG00000020368	Canx	1110069N15Rik|AI988026|Cnx|D11Ertd153e	calnexin	protein-coding
mm_28590.1	chr3	94417955	94417956	-	1	NA	intron (NM_028307, intron 1 of 12)	intron (NM_028307, intron 1 of 12)	4637	NM_028307	72634	Mm.331198	NM_028307	ENSMUSG00000041912	Tdrkh	2700091C21Rik|Tdrd2	tudor and KH domain containing protein	protein-coding
mm_100553.1	chr11	120722042	120722071	+	1	NA	TTS (NM_153545)	TTS (NM_153545)	588	NM_133223	170758	Mm.34008	NM_133223	ENSMUSG00000018012	Rac3	Rac1B	RAS-related C3 botulinum substrate 3	protein-coding
mm_166231.1	chr5	66719917	66719923	-	1	NA	Intergenic	Intergenic	-25920	NM_001001980	77569	Mm.374778	NM_001001980	ENSMUSG00000037736	Limch1	3732412D22Rik|mKIAA1102	LIM and calponin homology domains 1	protein-coding
mm_172652.1	chr8	35053420	35053424	-	1	NA	Intergenic	Intergenic	-87732	NM_175091	21951	Mm.88364	NM_175091	ENSMUSG00000031529	Tnks	4930554K12Rik|AI662855|ARTD5|C86528|D130072O21Rik|TANK1|mTNKS1	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase	protein-coding
mm_63583.1	chr7	128118185	128118210	+	1	NA	3' UTR (NM_008401, exon 30 of 30)	3' UTR (NM_008401, exon 30 of 30)	-11371	NM_021334	16411	Mm.22378	NM_021334	ENSMUSG00000030789	Itgax	AI449405|Cd11c|Cr4|N418	integrin alpha X	protein-coding
mm_134821.1	chr16	25960393	25960403	-	1	NA	TTS (NM_173379)	TTS (NM_173379)	145386	NM_173379	210530	Mm.326869	NM_173379	ENSMUSG00000038168	P3h2	4832416N06|AW553532|Leprel1|Mlat4	prolyl 3-hydroxylase 2	protein-coding
mm_129280.1	chr15	77153697	77153724	-	1	NA	5' UTR (NM_001110830, exon 1 of 13)	5' UTR (NM_001110830, exon 1 of 13)	102	NM_001110830	93686	Mm.202774	NM_053104	ENSMUSG00000033565	Rbfox2	Fbm2|Fxh|Hrnbp2|Rbm9	RNA binding protein, fox-1 homolog (C. elegans) 2	protein-coding
mm_110161.1	chr12	26834791	26834801	-	1	NA	Intergenic	RMER17B|LTR|ERVK	280199	NR_045052	100504347	Mm.130500	NR_045052		Gm20187	-	predicted gene, 20187	ncRNA
mm_60672.1	chr7	45018092	45018111	+	1	NA	promoter-TSS (NM_009101)	promoter-TSS (NM_009101)	94	NM_009101	20130	Mm.389894	NM_009101	ENSMUSG00000038387	Rras	AI573426	related RAS viral (r-ras) oncogene	protein-coding
mm_23252.1	chr3	51228323	51228327	+	1	NA	intron (NM_009834, intron 1 of 2)	intron (NM_009834, intron 1 of 2)	3878	NM_009834	12457	Mm.86541	NM_009834	ENSMUSG00000023087	Noct	AU043840|Ccr4|Ccrn4l	nocturnin	protein-coding
mm_169782.1	chr16	11144252	11144254	+	1	NA	intron (NR_027502, intron 19 of 22)	LSU-rRNA_Hsa|rRNA|rRNA	-9721	NM_029582	106200	Mm.291015	NM_029582	ENSMUSG00000022498	Txndc11	2810408E11Rik|AI427833|EFP1|Txdc11	thioredoxin domain containing 11	protein-coding
mm_151235.1	chr19	53793348	53793392	+	1	NA	intron (NM_001170847, intron 1 of 13)	intron (NM_001170847, intron 1 of 13)	-98861	NM_011050	18569	Mm.1605	NM_011050	ENSMUSG00000024975	Pdcd4	D19Ucla1|Ma3|Tis	programmed cell death 4	protein-coding
mm_69537.1	chr7	135695114	135695124	-	1	NA	exon (NM_001081117, exon 12 of 14)	exon (NM_001081117, exon 12 of 14)	21260	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_110901.1	chr12	75716413	75716424	-	1	NA	exon (NM_030750, exon 3 of 3)	exon (NM_030750, exon 3 of 3)	19311	NM_030750	81535	Mm.280199	NM_030750	ENSMUSG00000021054	Sgpp1	AI463453|SPP|SPP1|Spph1	sphingosine-1-phosphate phosphatase 1	protein-coding
mm_149055.1	chr19	8839299	8839346	+	1	NA	promoter-TSS (NM_008144)	promoter-TSS (NM_008144)	-6	NM_008144	14705	Mm.345134	NM_008144	ENSMUSG00000071657	Bscl2	2900097C17Rik|AI046355|Gng3lg	Berardinelli-Seip congenital lipodystrophy 2 (seipin)	protein-coding
mm_83639.1	chr9	49504062	49504076	-	1	NA	3' UTR (NM_001311065, exon 18 of 18)	3' UTR (NM_001311065, exon 18 of 18)	-14219	NR_029465	100036537	Mm.437541	NR_029465	ENSMUSG00000079564	Gm11149	ENSMUSG00000060603|ENSMUSG00000079564	predicted gene 11149	ncRNA
mm_127986.1	chr15	12549287	12549296	-	1	NA	intron (NM_001081064, intron 1 of 23)	intron (NM_001081064, intron 1 of 23)	43265	NM_001081064	68070	Mm.423205	NM_001081064	ENSMUSG00000022197	Pdzd2	4930537L06Rik|A930022H17Rik|Gm21706|Gm82|Pdzk3|mKIAA0300	PDZ domain containing 2	protein-coding
mm_61027.1	chr7	49522731	49522737	+	1	NA	intron (NM_175272, intron 11 of 37)	intron (NM_175272, intron 11 of 37)	114101	NM_001005232	13172	Mm.307176	NM_001005232	ENSMUSG00000030507	Dbx1	AI426026|Dbx	developing brain homeobox 1	protein-coding
mm_154207.1	chr19	59075584	59075592	-	1	NA	5' UTR (NM_001114312, exon 1 of 17)	5' UTR (NM_001114312, exon 1 of 17)	481	NM_175172	71653	Mm.37338	NM_175172	ENSMUSG00000041362	Shtn1	4930506M07Rik|Kiaa1598|Shootin1|mKIAA1598	shootin 1	protein-coding
mm_170185.1	chr17	6132599	6132620	-	1	NA	intron (NM_001103181, intron 1 of 13)	intron (NM_001103181, intron 1 of 13)	-5539	NM_054040	68842	Mm.449307	NM_054040	ENSMUSG00000034377	Tulp4	1110057P05Rik|2210038L17Rik|Tusp	tubby like protein 4	protein-coding
mm_157208.1	chrX	12761955	12761969	-	1	NA	promoter-TSS (NM_001048208)	promoter-TSS (NM_001048208)	11	NM_012005	26896	Mm.17616	NM_012005	ENSMUSG00000064127	Med14	9930001L01Rik|AU041628|Crsp2|ENSMUSG00000073278|Gm641|ORF1|Trap170	mediator complex subunit 14	protein-coding
mm_106359.1	chr11	118393829	118393837	-	1	NA	exon (NM_011150, exon 6 of 6)	exon (NM_011150, exon 6 of 6)	8098	NM_011150	19039	Mm.3152	NM_011150	ENSMUSG00000033880	Lgals3bp	90K|CyCAP|MAC-2BP|Ppicap|Tango10b	lectin, galactoside-binding, soluble, 3 binding protein	protein-coding
mm_70483.1	chr8	12395893	12395919	+	1	NA	5' UTR (NM_009233, exon 1 of 1)	5' UTR (NM_009233, exon 1 of 1)	387	NM_009233	20664	Mm.39088	NM_009233	ENSMUSG00000096014	Sox1	BB176347|Sox-1	SRY (sex determining region Y)-box 1	protein-coding
mm_67761.1	chr7	92741418	92741444	-	1	NA	promoter-TSS (NM_029494)	promoter-TSS (NM_029494)	28	NR_015510	666737	Mm.473620	NR_015510	ENSMUSG00000074024	4632427E13Rik	AU015482	RIKEN cDNA 4632427E13 gene	ncRNA
mm_59536.1	chr7	27749546	27749550	+	1	NA	exon (NM_029531, exon 5 of 5)	exon (NM_029531, exon 5 of 5)	-16125	NR_033484	100043229	Mm.458666	NR_033484	ENSMUSG00000109143	Gm10046	ENSMUSG00000058661	predicted gene 10046	ncRNA
mm_91309.1	chr10	24921800	24921810	-	1	NA	intron (NM_007482, intron 2 of 7)	intron (NM_007482, intron 2 of 7)	5665	NM_007482	11846	Mm.154144	NM_007482	ENSMUSG00000019987	Arg1	AI|AI256583|Arg-1|PGIF	arginase, liver	protein-coding
mm_107203.1	chr12	26346732	26346743	+	1	NA	promoter-TSS (NR_130981)	promoter-TSS (NR_130981)	27	NR_130981	75243	Mm.444753	NR_130981		4930549C15Rik	-	RIKEN cDNA 4930549C15 gene	ncRNA
mm_39932.1	chr5	31697666	31697709	+	1	NA	promoter-TSS (NM_181282)	promoter-TSS (NM_181282)	-77	NM_153196	71336	Mm.22519	NM_153196	ENSMUSG00000029136	Rbks	5230400M11Rik|AI326806|RBSK|RK	ribokinase	protein-coding
mm_1826.1	chr1	82604047	82604057	+	1	NA	intron (NM_007734, intron 1 of 51)	intron (NM_007734, intron 1 of 51)	17131	NM_007734	12828	Mm.389135	NM_007734	ENSMUSG00000079465	Col4a3	[a]3(IV)|alpha3(IV)	collagen, type IV, alpha 3	protein-coding
mm_31929.1	chr4	86053660	86053681	+	1	NA	promoter-TSS (NM_029967)	promoter-TSS (NM_029967)	-245	NM_029967	77739	Mm.331690	NM_029967	ENSMUSG00000066113	Adamtsl1	5930437A14Rik|6720426B09Rik|ADAMTSL-1	ADAMTS-like 1	protein-coding
mm_32146.1	chr4	99656663	99656672	+	1	NA	exon (NM_010425, exon 1 of 1)	exon (NM_010425, exon 1 of 1)	368	NM_010425	15221	Mm.4758	NM_010425	ENSMUSG00000067261	Foxd3	CWH3|Genesis|Hfh2	forkhead box D3	protein-coding
mm_44169.1	chr5	150800699	150800719	+	1	NA	exon (NM_175310, exon 32 of 35)	exon (NM_175310, exon 32 of 35)	126882	NM_001346503	100710	Mm.32959	NM_175310	ENSMUSG00000034021	Pds5b	AI646570|AS3|AW212954|Aprin|Tg(Wap-ERBB2)229Wzw|WAP-Her-2|mKIAA0979	PDS5 cohesin associated factor B	protein-coding
mm_68906.1	chr7	126456786	126456796	-	1	NA	exon (NM_007504, exon 8 of 23)	exon (NM_007504, exon 8 of 23)	6282	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_1839.1	chr1	82839561	82839571	+	1	NA	5' UTR (NM_010472, exon 1 of 13)	5' UTR (NM_010472, exon 1 of 13)	106	NM_001347077	15463	Mm.392569	NM_010472	ENSMUSG00000026159	Agfg1	AU045498|C130049H11Rik|C85612|D730048C23Rik|Hrb|RAB|Rip	ArfGAP with FG repeats 1	protein-coding
mm_37784.1	chr4	130275214	130275228	-	1	NA	promoter-TSS (NM_001253386)	promoter-TSS (NM_001253386)	-1	NM_001253386	230779	Mm.45132	NM_172702	ENSMUSG00000023232	Serinc2	2310004K20Rik|AW121759|FKSG84|TDE2|Tde2l	serine incorporator 2	protein-coding
mm_115746.1	chr13	17944152	17944239	-	1	NA	promoter-TSS (NM_019491)	promoter-TSS (NM_019491)	22	NM_019491	56044	Mm.27348	NM_019491	ENSMUSG00000008859	Rala	3010001O15Rik|AW322615|Ral|Rasl1	v-ral simian leukemia viral oncogene A (ras related)	protein-coding
mm_97914.1	chr11	83525805	83525823	+	1	NA	TTS (NM_013653)	TTS (NM_013653)	-3715	NM_001045543	629303	Mm.390417	NM_001045543	ENSMUSG00000018925	Heatr9	Gm11435|OTTMUSG00000000990	HEAT repeat containing 9	protein-coding
mm_50802.1	chr6	54272767	54272777	+	1	NA	promoter-TSS (NM_023543)	promoter-TSS (NM_023543)	-50	NM_023543	69993	Mm.321147	NM_023543	ENSMUSG00000004633	Chn2	1700026N20Rik|4930557O16Rik|ARHGAP3|Bch	chimerin 2	protein-coding
mm_51336.1	chr6	72395779	72395784	+	1	NA	Intergenic	(T)n|Simple_repeat|Simple_repeat	-5114	NM_016794	22320	Mm.1838	NM_016794	ENSMUSG00000050732	Vamp8	AU041171|Edb|endobrevin	vesicle-associated membrane protein 8	protein-coding
mm_124729.1	chr15	6580536	6580544	+	1	NA	exon (NM_001278269, exon 1 of 17)	exon (NM_001278269, exon 1 of 17)	693	NM_011815	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_132217.1	chr16	32630689	32630730	+	1	NA	3' UTR (NM_011638, exon 19 of 19)	3' UTR (NM_011638, exon 19 of 19)	-13934	NM_001110147	51789	Mm.251115	NM_016788	ENSMUSG00000022791	Tnk2	Ack|Ack-1|Ack1|Cdgip|Pyk1	tyrosine kinase, non-receptor, 2	protein-coding
mm_2432.1	chr1	95668486	95668488	+	1	NA	promoter-TSS (NM_001159745)	promoter-TSS (NM_001159745)	-893	NM_001159745	20452	Mm.306228	NM_009183	ENSMUSG00000040710	St8sia4	PST|PST-1|SIAT8-D|ST8SiaIV|Siat8d	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4	protein-coding
mm_86159.1	chr9	118150172	118150182	-	1	NA	promoter-TSS (NM_026442)	promoter-TSS (NM_026442)	19	NM_026442	67899	Mm.9953	NM_026442	ENSMUSG00000039163	Cmc1	2010110K16Rik|2010312P05Rik|AI596001	COX assembly mitochondrial protein 1	protein-coding
mm_43519.1	chr5	137150781	137150796	+	1	NA	Intergenic	Intergenic	-34581	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_64517.1	chr7	143830179	143830189	+	1	NA	5' UTR (NM_007856, exon 2 of 9)	5' UTR (NM_007856, exon 2 of 9)	7017	NM_007856	13360	Mm.249342	NM_007856	ENSMUSG00000058454	Dhcr7	AA409147	7-dehydrocholesterol reductase	protein-coding
mm_164190.1	chr15	78611415	78611425	+	1	NA	intron (NM_028195, intron 7 of 12)	intron (NM_028195, intron 7 of 12)	14373	NM_028195	72318	Mm.32911	NM_028195	ENSMUSG00000018008	Cyth4	2510004M07Rik|5830469K17Rik|AI467541|Pscd4|mFLJ00017	cytohesin 4	protein-coding
mm_106341.1	chr11	118393188	118393196	-	1	NA	exon (NM_011150, exon 6 of 6)	exon (NM_011150, exon 6 of 6)	8739	NM_011150	19039	Mm.3152	NM_011150	ENSMUSG00000033880	Lgals3bp	90K|CyCAP|MAC-2BP|Ppicap|Tango10b	lectin, galactoside-binding, soluble, 3 binding protein	protein-coding
mm_92994.1	chr10	86704328	86704353	-	1	NA	exon (NM_011631, exon 2 of 18)	exon (NM_011631, exon 2 of 18)	1104	NM_011631	22027	Mm.87773	NM_011631	ENSMUSG00000020048	Hsp90b1	ERp99|GRP94|TA-3|Targ2|Tra-1|Tra1|endoplasmin|gp96	heat shock protein 90, beta (Grp94), member 1	protein-coding
mm_144651.1	chr18	34220955	34220976	+	1	NA	promoter-TSS (NM_007462)	promoter-TSS (NM_007462)	-19	NM_007462	11789	Mm.384171	NM_007462	ENSMUSG00000005871	Apc	AI047805|AU020952|AW124434|CC1|Min|mAPC	adenomatosis polyposis coli	protein-coding
mm_119463.1	chr14	47189627	47189646	+	1	NA	promoter-TSS (NM_008102)	promoter-TSS (NM_008102)	-234	NM_008102	14528	Mm.10651	NM_008102	ENSMUSG00000037580	Gch1	GTP-CH|GTPCH|Gch	GTP cyclohydrolase 1	protein-coding
mm_168293.1	chr11	102492623	102492640	-	1	NA	intron (NM_001159492, intron 6 of 7)	intron (NM_001159492, intron 6 of 7)	-22748	NM_010575	16399	Mm.26646	NM_010575	ENSMUSG00000034664	Itga2b	AI172977|CD41|CD41B|GpIIb|alphaIIb	integrin alpha 2b	protein-coding
mm_147604.1	chr18	56863041	56863044	-	1	NA	intron (NM_177115, intron 1 of 4)	L1MB7|LINE|L1	62506	NM_177115	320253	Mm.312623	NM_177115	ENSMUSG00000032656	March3	6330411I15Rik|A530081L18Rik|AI843639|MARCH-III	membrane-associated ring finger (C3HC4) 3	protein-coding
mm_123938.1	chr14	73368411	73368428	-	1	NA	exon (NM_008410, exon 2 of 6)	exon (NM_008410, exon 2 of 6)	16852	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_41999.1	chr5	107900533	107900577	+	1	NA	promoter-TSS (NM_016980)	promoter-TSS (NM_016980)	27	NM_016980	100503670	Mm.277897	NM_016980	ENSMUSG00000058558	Rpl5	U21RNA	ribosomal protein L5	protein-coding
mm_156103.1	chrX	113298284	113298294	+	1	NA	promoter-TSS (NM_001142570)	promoter-TSS (NM_001142570)	33	NM_001142570	93837	Mm.79760	NM_033605	ENSMUSG00000025592	Dach2	9430028N04Rik	dachshund 2 (Drosophila)	protein-coding
mm_47376.1	chr5	122988684	122988705	-	1	NA	promoter-TSS (NR_045820)	promoter-TSS (NR_045820)	405	NM_001003953	30841	Mm.86406	NM_013910	ENSMUSG00000029475	Kdm2b	Cxxc2|Fbl10|Fbxl10|Jhdm1b|PCCX2	lysine (K)-specific demethylase 2B	protein-coding
mm_16095.1	chr2	168978251	168978260	+	1	NA	promoter-TSS (NR_040326)	promoter-TSS (NR_040326)	-14	NR_040326	75508	Mm.271256	NR_040326	ENSMUSG00000086348	1700017J07Rik	-	RIKEN cDNA 1700017J07 gene	ncRNA
mm_26960.1	chr3	21987817	21987837	-	1	NA	Intergenic	MLT2D|LTR|ERVL	-88825	NM_030732	81004	Mm.202966	NM_030732	ENSMUSG00000027630	Tbl1xr1	8030499H02Rik|A630076E03Rik|AW539987|C21|C230089I12Rik|DC42|Ira1|TBLR1	transducin (beta)-like 1X-linked receptor 1	protein-coding
mm_143059.1	chr17	57007064	57007090	-	1	NA	exon (NM_133801, exon 5 of 13)	exon (NM_133801, exon 5 of 13)	4211	NM_133801	98053	Mm.24632	NM_133801	ENSMUSG00000002658	Gtf2f1	2810405L04Rik|C76800|RAP74	general transcription factor IIF, polypeptide 1	protein-coding
mm_161899.1	chr18	49832972	49832972	+	1	NA	promoter-TSS (NM_001081371)	promoter-TSS (NM_001081371)	-25	NM_001081371	240283	Mm.257790	NM_001081371	ENSMUSG00000037416	Dmxl1	C630007L23Rik|D030030C22	Dmx-like 1	protein-coding
mm_98006.1	chr11	84179793	84179849	+	1	NA	Intergenic	CpG	-12345	NM_001037932	628813	Mm.390389	NM_001037932	ENSMUSG00000051452	Gm11437	AI463690|OTTMUSG00000000997	predicted gene 11437	protein-coding
mm_19399.1	chr2	91635851	91635862	-	1	NA	exon (NM_010168, exon 2 of 14)	exon (NM_010168, exon 2 of 14)	601	NM_010168	14061	Mm.89048	NM_010168	ENSMUSG00000027249	F2	Cf-2|Cf2|FII	coagulation factor II	protein-coding
mm_109386.1	chr12	109737366	109737369	+	1	NA	intron (NR_028265, intron 1 of 7)	intron (NR_028265, intron 1 of 7)	-1066	NR_029564	387172		NR_029564	ENSMUSG00000065448	Mir154	Mirn154|mir-154|mmu-mir-154	microRNA 154	ncRNA
mm_126334.1	chr15	79895092	79895104	+	1	NA	promoter-TSS (NM_001347041)	promoter-TSS (NM_001347041)	75	NM_001347041	80287	Mm.284059	NM_030255	ENSMUSG00000009585	Apobec3	Apobec|Arp3|BC003314|Cem15|Rfv3	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 3	protein-coding
mm_115169.1	chr13	108044056	108044105	+	1	NA	promoter-TSS (NM_001048250)	promoter-TSS (NM_001048250)	-394	NM_001048250	75616	Mm.491164	NM_001048250	ENSMUSG00000071180	Smim15	2810008M24Rik	small integral membrane protein 15	protein-coding
mm_168146.1	chr10	35207392	35207402	+	1	NA	Intergenic	BGLII|LTR|ERVK	723997	NM_010237	14302	Mm.332432	NM_010237	ENSMUSG00000019779	Frk	BSK|BSK/IYK|C85044|GTK|RAK	fyn-related kinase	protein-coding
mm_99454.1	chr11	102434392	102434438	+	1	NA	exon (NM_008175, exon 7 of 13)	exon (NM_008175, exon 7 of 13)	4093	NM_008175	14824	Mm.1568	NM_008175	ENSMUSG00000034708	Grn	Pgrn|epithelin	granulin	protein-coding
mm_86747.1	chr10	19494638	19494649	+	1	NA	Intergenic	Intergenic	-97306	NM_010511	15979	Mm.549	NM_010511	ENSMUSG00000020009	Ifngr1	CD119|IFN-gammaR|Ifgr|Ifngr|Nktar	interferon gamma receptor 1	protein-coding
mm_164089.1	chr15	9140599	9140610	+	1	NA	promoter-TSS (NM_013787)	promoter-TSS (NM_013787)	34	NM_177178	320506	Mm.259886	NM_177178	ENSMUSG00000039704	Lmbrd2	9930036E21Rik	LMBR1 domain containing 2	protein-coding
mm_146814.1	chr18	20896343	20896400	-	1	NA	promoter-TSS (NM_029491)	promoter-TSS (NM_029491)	-293	NM_029491	75964	Mm.273769	NM_029491	ENSMUSG00000033382	Trappc8	5033403J15Rik|AI845423|D030074E01Rik|Trs85|mKIAA1012	trafficking protein particle complex 8	protein-coding
mm_91846.1	chr10	58536386	58536396	-	1	NA	intron (NM_001162956, intron 10 of 15)	RLTR9E|LTR|ERVK	38454	NM_001162956	76138	Mm.211744	NM_001162956	ENSMUSG00000038010	Ccdc138	6230424H07Rik|BC042726	coiled-coil domain containing 138	protein-coding
mm_104547.1	chr11	96773378	96773388	-	1	NA	intron (NM_001163389, intron 3 of 7)	B1F2|SINE|Alu	4172	NM_028965	74479	Mm.270781	NM_028965	ENSMUSG00000020876	Snx11	4933439F10Rik|A930041K09Rik|AI117694	sorting nexin 11	protein-coding
mm_95021.1	chr11	32001687	32001723	+	1	NA	intron (NM_001290681, intron 1 of 4)	intron (NM_001290681, intron 1 of 4)	428	NM_001290681	18197	Mm.3304	NM_008741	ENSMUSG00000020297	Nsg2	-	neuron specific gene family member 2	protein-coding
mm_168164.1	chr10	51480660	51480675	+	1	NA	promoter-TSS (NM_008147)	promoter-TSS (NM_008147)	55	NM_001291892	14727	Mm.439661	NM_008147	ENSMUSG00000062593	Lilr4b	Gp49a|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4B	protein-coding
mm_38173.1	chr4	135257686	135257689	-	1	NA	intron (NM_013885, intron 1 of 5)	PB1D10|SINE|Alu	15073	NM_013885	29876	Mm.257765	NM_013885	ENSMUSG00000037242	Clic4	D0Jmb3|TU-74|mc3s5|mtCLIC	chloride intracellular channel 4 (mitochondrial)	protein-coding
mm_74713.1	chr8	17290126	17290140	-	1	NA	intron (NM_053171, intron 1 of 69)	(GA)n|Simple_repeat|Simple_repeat	245252	NM_053171	94109	Mm.436988	NM_053171	ENSMUSG00000060924	Csmd1	B930082H09|mKIAA1890	CUB and Sushi multiple domains 1	protein-coding
mm_2730.1	chr1	128244182	128244199	+	1	NA	promoter-TSS (NM_026390)	promoter-TSS (NM_026390)	9	NM_026390	67812	Mm.293321	NM_026390	ENSMUSG00000026353	Ubxn4	1300013G12Rik|Ubxd2|mKIAA0242	UBX domain protein 4	protein-coding
mm_46906.1	chr5	114274034	114274081	-	1	NA	promoter-TSS (NM_148935)	promoter-TSS (NM_148935)	-296	NM_148935	116810	Mm.17709	NM_148935	ENSMUSG00000042002	Foxn4	-	forkhead box N4	protein-coding
mm_91962.1	chr10	61180380	61180423	-	1	NA	exon (NM_001017407, exon 4 of 4)	exon (NM_001017407, exon 4 of 4)	5139	NM_023064	65971	Mm.30227	NM_023064	ENSMUSG00000020096	Tbata	1700021K02Rik|AI428928|Spatial|Titest	thymus, brain and testes associated	protein-coding
mm_167109.1	chr7	113760219	113760221	+	1	NA	Intergenic	Intergenic	-5778	NM_145584	233744	Mm.334160	NM_145584	ENSMUSG00000038156	Spon1	AI666765|AW455831|BC020531|D330035F22Rik|FSP	spondin 1, (f-spondin) extracellular matrix protein	protein-coding
mm_85181.1	chr9	96631183	96631196	-	1	NA	intron (NM_053268, intron 1 of 23)	CpG	314	NM_053268	114713	Mm.124502	NM_053268	ENSMUSG00000032413	Rasa2	5430433H21Rik|AA517451|AU023900|GAP1m	RAS p21 protein activator 2	protein-coding
mm_112095.1	chr12	112785112	112785122	-	1	NA	Intergenic	Intergenic	-23858	NM_145450	217887	Mm.186678	NM_145450	ENSMUSG00000037594	BC022687	AW050009|C130001I08Rik|Flj20080	cDNA sequence BC022687	protein-coding
mm_160291.1	chr7	127588551	127588551	-	1	NA	promoter-TSS (NM_001033040)	promoter-TSS (NM_001033040)	44	NM_001033040	233899	Mm.25220	NM_001033040	ENSMUSG00000057176	Ccdc189	Gm166	coiled-coil domain containing 189	protein-coding
mm_147430.1	chr18	46311892	46311926	-	1	NA	promoter-TSS (NM_001160399)	promoter-TSS (NM_001160399)	19	NM_001160399	240261	Mm.329416	NM_001160399	ENSMUSG00000071855	Ccdc112	8430438M01Rik|AW108467	coiled-coil domain containing 112	protein-coding
mm_13549.1	chr2	112239756	112239764	+	1	NA	promoter-TSS (NM_207206)	promoter-TSS (NM_207206)	-81	NM_207206	99010	Mm.33438	NM_207206	ENSMUSG00000027134	Lpcat4	AI505034|Agpat7|Aytl3|LPEAT2	lysophosphatidylcholine acyltransferase 4	protein-coding
mm_51965.1	chr6	91758336	91758346	+	1	NA	3' UTR (NM_009320, exon 15 of 15)	3' UTR (NM_009320, exon 15 of 15)	49052	NM_001159507	243547	Mm.333264	NM_001033353	ENSMUSG00000030098	Grip2	-	glutamate receptor interacting protein 2	protein-coding
mm_91471.1	chr10	34207202	34207265	-	1	NA	5' UTR (NM_172508, exon 1 of 6)	5' UTR (NM_172508, exon 1 of 6)	318	NM_172508	212898	Mm.34557	NM_172508	ENSMUSG00000039497	Dse	6030499O08|AI480506|B130024B19Rik|DS-epi1|Sart2	dermatan sulfate epimerase	protein-coding
mm_111753.1	chr12	103951294	103951307	-	1	NA	exon (NM_009247, exon 2 of 5)	exon (NM_009247, exon 2 of 5)	5597	NM_009247	20704	Mm.312593	NM_009247	ENSMUSG00000072849	Serpina1e	Dom5|PI5|Spi1-5	serine (or cysteine) peptidase inhibitor, clade A, member 1E	protein-coding
mm_27276.1	chr3	41075190	41075194	-	1	NA	intron (NM_027558, intron 1 of 2)	intron (NM_027558, intron 1 of 2)	7854	NM_027558	70804	Mm.40321	NM_027558	ENSMUSG00000049940	Pgrmc2	4631434O19Rik|5730409G06Rik|DG6|PMBP	progesterone receptor membrane component 2	protein-coding
mm_132406.1	chr16	35001818	35001828	+	1	NA	3' UTR (NM_139300, exon 32 of 32)	3' UTR (NM_139300, exon 32 of 32)	-20598	NM_023587	70757	Mm.27286	NM_023587	ENSMUSG00000035376	Hacd2	6330408J20Rik|AI255777|AI481689|Hcad2|Ptplb	3-hydroxyacyl-CoA dehydratase 2	protein-coding
mm_4285.1	chr1	171682005	171682071	+	1	NA	promoter-TSS (NM_007649)	promoter-TSS (NM_007649)	-17	NM_007649	12506	Mm.1738	NM_007649	ENSMUSG00000015355	Cd48	AI449234|AW610730|BCM1|BLAST|BLAST-1|BLAST1|Bcm-1|MEM-102|SLAMF2|Sgp-60	CD48 antigen	protein-coding
mm_35169.1	chr4	14796054	14796065	-	1	NA	promoter-TSS (NM_028499)	promoter-TSS (NM_028499)	-7	NM_028499	73314	Mm.52613	NM_028499	ENSMUSG00000023151	Lrrc69	1700034K16Rik	leucine rich repeat containing 69	protein-coding
mm_157720.1	chrX	70344357	70344377	-	1	NA	3' UTR (NM_010498, exon 9 of 9)	3' UTR (NM_010498, exon 9 of 9)	20718	NM_010498	15931	Mm.233083	NM_010498	ENSMUSG00000035847	Ids	AW214631	iduronate 2-sulfatase	protein-coding
mm_10834.1	chr2	24481337	24481364	+	1	NA	Intergenic	Intergenic	-5751	NM_011040	18510	Mm.2533	NM_011040	ENSMUSG00000026976	Pax8	Pax-8	paired box 8	protein-coding
mm_89747.1	chr10	99233096	99233109	+	1	NA	Intergenic	Intergenic	-30129	NM_026268	67603	Mm.1791	NM_026268	ENSMUSG00000019960	Dusp6	1300019I03Rik|MKP-3|MKP3|PYST1	dual specificity phosphatase 6	protein-coding
mm_84483.1	chr9	66845539	66845552	-	1	NA	3' UTR (NM_173413, exon 8 of 8)	3' UTR (NM_173413, exon 8 of 8)	-10839	NM_026674	68318	Mm.284229	NM_026674	ENSMUSG00000053040	Aph1c	0610008A10Rik|APH-1b|Aph1b	aph1 homolog C, gamma secretase subunit	protein-coding
mm_41843.1	chr5	104434525	104434552	+	1	NA	promoter-TSS (NM_001204203)	promoter-TSS (NM_001204203)	-573	NM_001204201	20750	Mm.288474	NM_009263	ENSMUSG00000029304	Spp1	2AR|Apl-1|BNSP|BSPI|Bsp|ETA-1|Eta|OP|Opn|Opnl|Ric|Spp-1	secreted phosphoprotein 1	protein-coding
mm_38801.1	chr4	148152156	148152176	-	1	NA	promoter-TSS (NM_001163707)	promoter-TSS (NM_001163707)	-31	NM_001163707	50762	Mm.27445	NM_015797	ENSMUSG00000055401	Fbxo6	AA408845|FBG2|Fbs2|Fbx6b|Fbxo6b	F-box protein 6	protein-coding
mm_136451.1	chr16	94997375	94997437	-	1	NA	5' UTR (NM_010606, exon 1 of 4)	5' UTR (NM_010606, exon 1 of 4)	290	NM_001025584	16522	Mm.328720	NM_010606	ENSMUSG00000043301	Kcnj6	BIR1|GIRK2|KATP2|KCNJ7|Kir3.2|weaver|wv	potassium inwardly-rectifying channel, subfamily J, member 6	protein-coding
mm_72276.1	chr8	75100170	75100183	+	1	NA	3' UTR (NM_010442, exon 5 of 5)	3' UTR (NM_010442, exon 5 of 5)	6558	NM_010442	15368	Mm.276389	NM_010442	ENSMUSG00000005413	Hmox1	D8Wsu38e|HO-1|HO1|Hemox|Hmox|Hsp32	heme oxygenase 1	protein-coding
mm_144649.1	chr18	34007168	34007178	+	1	NA	promoter-TSS (NM_013512)	promoter-TSS (NM_013512)	33	NM_013512	13824	Mm.3465	NM_013512	ENSMUSG00000024376	Epb41l4a	Epb4.1l4|Epb4.1l4a|NBL4	erythrocyte membrane protein band 4.1 like 4a	protein-coding
mm_150500.1	chr19	39019429	39019466	+	1	NA	intron (NM_028089, intron 4 of 8)	Lx2A1|LINE|L1	12428	NM_028089	72082	Mm.142581	NM_028089	ENSMUSG00000025002	Cyp2c55	2010318C06Rik	cytochrome P450, family 2, subfamily c, polypeptide 55	protein-coding
mm_100522.1	chr11	120573815	120573856	+	1	NA	promoter-TSS (NM_011032)	promoter-TSS (NM_011032)	-899	NM_011032	18453	Mm.16660	NM_011032	ENSMUSG00000025130	P4hb	ERp59|PDI|Pdia1|Thbp	prolyl 4-hydroxylase, beta polypeptide	protein-coding
mm_85365.1	chr9	103220928	103220939	-	1	NA	exon (NM_133977, exon 9 of 17)	exon (NM_133977, exon 9 of 17)	9353	NM_133977	22041	Mm.37214	NM_133977	ENSMUSG00000032554	Trf	AI266983|Cd176|HP|Tf|Tfn|hpx	transferrin	protein-coding
mm_13479.1	chr2	106003354	106003386	+	1	NA	non-coding (NR_033993, exon 1 of 4)	non-coding (NR_033993, exon 1 of 4)	179	NM_026992	99349	Mm.25661	NM_026992	ENSMUSG00000027166	Dnajc24	1700030A21Rik|2610027M02Rik|AV066965|AW240712|Dph4|MmDjC7|Zcsl3	DnaJ heat shock protein family (Hsp40) member C24	protein-coding
mm_49840.1	chr6	38284471	38284472	+	1	NA	Intergenic	Intergenic	14788	NM_172467	209032	Mm.101389	NM_172467	ENSMUSG00000047749	Zc3hav1l	B130055L09Rik|E430016P22Rik	zinc finger CCCH-type, antiviral 1-like	protein-coding
mm_93511.1	chr10	115222692	115222702	-	1	NA	intron (NM_025706, intron 5 of 16)	intron (NM_025706, intron 5 of 16)	28796	NM_025706	66687	Mm.22252	NM_025706	ENSMUSG00000020130	Tbc1d15	4432405K22Rik|AU022358|AU023730|AW557774|Ly6dl|Rab7-GAP	TBC1 domain family, member 15	protein-coding
mm_154131.1	chr19	57314803	57314815	-	1	NA	Intergenic	CpG	40849	NR_045319	78120	Mm.445892	NR_045319		4930449E18Rik	-	RIKEN cDNA 4930449E18 gene	ncRNA
mm_12890.1	chr2	84794273	84794273	+	1	NA	Intergenic	LTRIS4|LTR|ERV1	-4555	NM_019949	56791	Mm.38261	NM_019949	ENSMUSG00000027078	Ube2l6	2810489I21Rik|RIG-B|UBCH8|Ubce8|Ubcm8	ubiquitin-conjugating enzyme E2L 6	protein-coding
mm_4872.1	chr1	187804969	187804988	+	1	NA	intron (NM_001243792, intron 2 of 7)	(T)n|Simple_repeat|Simple_repeat	-192849	NM_011935	26381	Mm.89989	NM_011935	ENSMUSG00000026610	Esrrg	ERR3|Errg|NR3B3|mKIAA0832	estrogen-related receptor gamma	protein-coding
mm_5124.1	chr1	9299670	9299689	-	1	NA	5' UTR (NM_001290390, exon 1 of 21)	5' UTR (NM_001290390, exon 1 of 21)	198	NM_001290390	71096	Mm.336395	NM_027671	ENSMUSG00000025909	Sntg1	4933426D16Rik|G1SYN|SYN4	syntrophin, gamma 1	protein-coding
mm_153051.1	chr19	32103073	32103092	-	1	NA	promoter-TSS (NM_018830)	promoter-TSS (NM_018830)	58	NM_018830	54447	Mm.491229	NM_018830	ENSMUSG00000024887	Asah2	AI585898	N-acylsphingosine amidohydrolase 2	protein-coding
mm_111993.1	chr12	110695824	110695859	-	1	NA	intron (NM_010480, intron 1 of 10)	CpG	554	NM_010480	15519	Mm.1843	NM_010480	ENSMUSG00000021270	Hsp90aa1	86kDa|89kDa|AL024080|AL024147|Hsp86-1|Hsp89|Hsp90|Hspca|hsp4	heat shock protein 90, alpha (cytosolic), class A member 1	protein-coding
mm_64659.1	chr7	4164502	4164576	-	1	NA	5' UTR (NM_021454, exon 1 of 3)	5' UTR (NM_021454, exon 1 of 3)	160	NM_021454	58804	Mm.34268	NM_021454	ENSMUSG00000063838	Cdc42ep5	1700027J19Rik|2010007O02Rik|Borg3|C85526|CEP5	CDC42 effector protein (Rho GTPase binding) 5	protein-coding
mm_129431.1	chr15	78494359	78494369	-	1	NA	intron (NM_008368, intron 1 of 9)	intron (NM_008368, intron 1 of 9)	702	NM_008368	16185	Mm.35287	NM_008368	ENSMUSG00000068227	Il2rb	CD122|IL-15Rbeta|IL15Rbeta|Il-2/15Rbeta|Il-2Rbeta|p70	interleukin 2 receptor, beta chain	protein-coding
mm_19075.1	chr2	77816759	77816815	-	1	NA	promoter-TSS (NM_178723)	promoter-TSS (NM_178723)	29	NM_178723	241494	Mm.490320	NM_178723	ENSMUSG00000027016	Zfp385b	B830010L13Rik|C130013B13Rik|Zfp533|Znf385b	zinc finger protein 385B	protein-coding
mm_91837.1	chr10	57517134	57517179	-	1	NA	3' UTR (NM_019760, exon 9 of 9)	3' UTR (NM_019760, exon 9 of 9)	15373	NM_019760	56442	Mm.29344	NM_019760	ENSMUSG00000019877	Serinc1	1500011D18Rik|AI315070|AIGP-2|TMS-2|Tde1l|Tde2|Tms2|mKIAA1253	serine incorporator 1	protein-coding
mm_135510.1	chr16	48412409	48412421	-	1	NA	promoter-TSS (NR_015373)	promoter-TSS (NR_015373)	1	NR_015373	433023	Mm.483302	NR_015373	ENSMUSG00000110573	Gm5485	EG433023	predicted gene 5485	ncRNA
mm_26787.1	chr3	9610234	9610247	-	1	NA	promoter-TSS (NM_133218)	promoter-TSS (NM_133218)	-155	NM_133218	170753	Mm.212908	NM_133218	ENSMUSG00000040209	Zfp704	C030026M03|C030034L19Rik|Gig1|Znf704	zinc finger protein 704	protein-coding
mm_102428.1	chr11	59472433	59472460	-	1	NA	promoter-TSS (NM_178417)	promoter-TSS (NM_178417)	28	NM_178417	237775	Mm.339604	NM_178417	ENSMUSG00000054519	Zfp867	-	zinc finger protein 867	protein-coding
mm_140005.1	chr17	73108083	73108087	+	1	NA	promoter-TSS (NM_001081071)	promoter-TSS (NM_001081071)	100	NM_001177967	225010	Mm.329194	NM_001081071	ENSMUSG00000054469	Lclat1	AI181996|Agpat8|Alcat1|Gm91|Lycat	lysocardiolipin acyltransferase 1	protein-coding
mm_138134.1	chr17	34193311	34193324	+	1	NA	intron (NM_013683, intron 7 of 10)	intron (NM_013683, intron 7 of 10)	-4878	NM_010724	16913	Mm.180191	NM_010724	ENSMUSG00000024338	Psmb8	Lmp-7|Lmp7	proteasome (prosome, macropain) subunit, beta type 8 (large multifunctional peptidase 7)	protein-coding
mm_114403.1	chr13	64161797	64161832	+	1	NA	promoter-TSS (NM_019986)	promoter-TSS (NM_019986)	-52	NM_019986	56541	Mm.40989	NM_019986	ENSMUSG00000021476	Habp4	4933413D03Rik|4933428J01Rik	hyaluronic acid binding protein 4	protein-coding
mm_143689.1	chr17	80253287	80253291	-	1	NA	intron (NM_198942, intron 14 of 22)	intron (NM_198942, intron 14 of 22)	28800	NM_026053	67242	Mm.279985	NM_026053	ENSMUSG00000055760	Gemin6	2610019B15Rik|2810470M17Rik	gem (nuclear organelle) associated protein 6	protein-coding
mm_11916.1	chr2	52071572	52071597	+	1	NA	Intergenic	PB1D7|SINE|Alu	-1253	NM_175238	51869	Mm.254530	NM_175238	ENSMUSG00000036202	Rif1	5730435J01Rik|6530403D07Rik|AU016181|AW549474|D2Ertd145e	replication timing regulatory factor 1	protein-coding
mm_164630.1	chr17	33552071	33552072	+	1	NA	intron (NR_137629, intron 23 of 23)	T-rich|Low_complexity|Low_complexity	-3636	NM_053214	17916	Mm.42019	NM_053214	ENSMUSG00000024300	Myo1f	C330006B10Rik	myosin IF	protein-coding
mm_144771.1	chr18	35806455	35806465	+	1	NA	3' UTR (NM_019912, exon 7 of 7)	3' UTR (NM_019912, exon 7 of 7)	-23358	NM_133687	67393	Mm.94560	NM_133687	ENSMUSG00000046668	Cxxc5	4930415K17Rik	CXXC finger 5	protein-coding
mm_147060.1	chr18	34954256	34954266	-	1	NA	promoter-TSS (NM_010481)	promoter-TSS (NM_010481)	90	NM_010481	15526	Mm.209419	NM_010481	ENSMUSG00000024359	Hspa9	74kDa|Csa|Grp75|Hsc74|Hsp74|Hsp74a|Hspa9a|Mortalin|Mot-2|Mot2|Mthsp70|Pbp74	heat shock protein 9	protein-coding
mm_61776.1	chr7	83641378	83641388	+	1	NA	3' UTR (NM_023377, exon 6 of 6)	3' UTR (NM_023377, exon 6 of 6)	9366	NM_023377	170460	Mm.357953	NM_023377	ENSMUSG00000046027	Stard5	2310058G22Rik|AI607880|D7Ertd152e	StAR-related lipid transfer (START) domain containing 5	protein-coding
mm_118430.1	chr14	8002950	8002979	+	1	NA	promoter-TSS (NM_001331065)	promoter-TSS (NM_001331065)	-2	NM_001331064	66082	Mm.181473	NM_025341	ENSMUSG00000025277	Abhd6	0610041D24Rik|AA673485|AV065425	abhydrolase domain containing 6	protein-coding
mm_64371.1	chr7	142442357	142442367	+	1	NA	promoter-TSS (NM_009405)	promoter-TSS (NM_009405)	-106	NM_009405	21953	Mm.39469	NM_009405	ENSMUSG00000031097	Tnni2	-	troponin I, skeletal, fast 2	protein-coding
mm_63307.1	chr7	126861921	126861936	+	1	NA	promoter-TSS (NM_153580)	promoter-TSS (NM_153580)	-44	NM_172746	233876	Mm.363427	NM_172746	ENSMUSG00000042606	Hirip3	B130036O03|C86302	HIRA interacting protein 3	protein-coding
mm_153879.1	chr19	46925559	46925562	-	1	NA	intron (NM_001164365, intron 2 of 17)	PB1D11|SINE|Alu	36791	NM_029810	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_125580.1	chr15	59489993	59490024	+	1	NA	intron (NM_026746, intron 4 of 6)	intron (NM_026746, intron 4 of 6)	115810	NM_001164604	68501	Mm.27762	NM_026746	ENSMUSG00000059586	Nsmce2	1110014D18Rik|AI661537	NSE2/MMS21 homolog, SMC5-SMC6 complex SUMO ligase	protein-coding
mm_42812.1	chr5	121837241	121837255	+	1	NA	promoter-TSS (NM_001306128)	promoter-TSS (NM_001306128)	-389	NM_008507	16923	Mm.65493	NM_008507	ENSMUSG00000042594	Sh2b3	AI429800|Lnk	SH2B adaptor protein 3	protein-coding
mm_101704.1	chr11	42000269	42000279	-	1	NA	exon (NM_008073, exon 1 of 10)	exon (NM_008073, exon 1 of 10)	440	NM_177408	14406	Mm.5309	NM_008073	ENSMUSG00000020436	Gabrg2	GABAA-R|Gabrg-2|gamma2	gamma-aminobutyric acid (GABA) A receptor, subunit gamma 2	protein-coding
mm_54483.1	chr6	35133732	35133742	-	1	NA	promoter-TSS (NM_001164412)	promoter-TSS (NM_001164412)	0	NM_001164412	53621	Mm.214525	NM_016877	ENSMUSG00000038784	Cnot4	Not4|Not4h|Not4hp	CCR4-NOT transcription complex, subunit 4	protein-coding
mm_66750.1	chr7	46712244	46712251	-	1	NA	exon (NM_011315, exon 4 of 4)	exon (NM_011315, exon 4 of 4)	-1596	NM_030233	78935	Mm.289866	NM_030233	ENSMUSG00000006763	Saal1	5031425D22Rik|SPACIA1	serum amyloid A-like 1	protein-coding
mm_121224.1	chr14	103055478	103055482	+	1	NA	exon (NM_008392, exon 5 of 5)	exon (NM_008392, exon 5 of 5)	8468	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_69148.1	chr7	127107785	127107789	-	1	NA	TTS (NM_133686)	TTS (NM_133686)	14242	NM_133686	67375	Mm.26928	NM_133686	ENSMUSG00000030674	Qprt	2410027J01Rik|AI647766|QPRTase	quinolinate phosphoribosyltransferase	protein-coding
mm_93100.1	chr10	89745796	89745807	-	1	NA	intron (NM_029166, intron 1 of 20)	CpG	810	NM_029166	75089	Mm.268922	NM_029166	ENSMUSG00000019951	Uhrf1bp1l	2010319N22Rik|4930506D01Rik|AA589495|C80672|E030041M21Rik|mKIAA0701	UHRF1 (ICBP90) binding protein 1-like	protein-coding
mm_154290.1	chr19	60994273	60994298	-	1	NA	intron (NM_018869, intron 2 of 15)	intron (NM_018869, intron 2 of 15)	104536	NM_018869	14773	Mm.279400	NM_018869	ENSMUSG00000003228	Grk5	Gprk5	G protein-coupled receptor kinase 5	protein-coding
mm_94545.1	chr11	9255628	9255628	+	1	NA	intron (NM_178259, intron 5 of 61)	intron (NM_178259, intron 5 of 61)	63686	NM_178259	268379	Mm.39270	NM_178259	ENSMUSG00000004668	Abca13	9830132L24|A930002G16Rik|AI956815	ATP-binding cassette, sub-family A (ABC1), member 13	protein-coding
mm_147712.1	chr18	60812420	60812422	-	1	NA	TTS (NR_039567)	TTS (NR_039567)	345	NR_039567	100628611		NR_039567	ENSMUSG00000093327	Mir5107	mir-5107|mmu-mir-5107|mu-mir-5107	microRNA 5107	ncRNA
mm_139220.1	chr17	47730081	47730137	+	1	NA	exon (NM_025973, exon 4 of 9)	exon (NM_025973, exon 4 of 9)	3267	NM_025973	109820	Mm.22957	NM_025973	ENSMUSG00000023987	Pgc	2210410L06Rik|Upg-1|Upg1	progastricsin (pepsinogen C)	protein-coding
mm_104038.1	chr11	86301155	86301173	-	1	NA	exon (NM_001080931, exon 14 of 30)	exon (NM_001080931, exon 14 of 30)	-43596	NM_027421	70422	Mm.171304	NM_027421	ENSMUSG00000018068	Ints2	2810417D08Rik|AA408260|AI987735|mKIAA1287	integrator complex subunit 2	protein-coding
mm_56123.1	chr6	87532957	87532965	-	1	NA	5' UTR (NM_001286610, exon 1 of 10)	5' UTR (NM_001286610, exon 1 of 10)	298	NM_001037727	232201	Mm.119564	NM_175476	ENSMUSG00000030047	Arhgap25	A130039I20Rik	Rho GTPase activating protein 25	protein-coding
mm_74062.1	chr8	122376677	122376701	+	1	NA	promoter-TSS (NM_001310650)	promoter-TSS (NM_001310650)	73	NM_001029993	76014	Mm.241489	NM_001029993	ENSMUSG00000017478	Zc3h18	1190001B23Rik|5830416A07Rik|Nhn1	zinc finger CCCH-type containing 18	protein-coding
mm_140573.1	chr17	9669669	9669705	-	1	NA	promoter-TSS (NM_001163836)	promoter-TSS (NM_001163836)	17	NM_001163836	67543	Mm.26987	NM_026226	ENSMUSG00000046173	Pabpc6	4932702K14Rik|AI428050|Pabpc3	poly(A) binding protein, cytoplasmic 6	protein-coding
mm_47064.1	chr5	116422740	116422780	-	1	NA	5' UTR (NM_030704, exon 1 of 3)	5' UTR (NM_030704, exon 1 of 3)	104	NM_030704	80888	Mm.21549	NM_030704	ENSMUSG00000041548	Hspb8	AU018630|AW413033|Cryac|D5Ucla4|E2IG1|H11|H11K|HSP20-like|HSP22	heat shock protein 8	protein-coding
mm_82261.1	chr9	5440780	5440784	-	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	95306	NM_009808	12364	Mm.42163	NM_009808	ENSMUSG00000025887	Casp12	-	caspase 12	protein-coding
mm_64779.1	chr7	5020503	5020516	-	1	NA	5' UTR (NM_001290426, exon 1 of 3)	5' UTR (NM_001290426, exon 1 of 3)	133	NM_001033383	319748	Mm.86607	NM_001033383	ENSMUSG00000074405	Zfp865	6430526N21Rik|Znf865	zinc finger protein 865	protein-coding
mm_128867.1	chr15	72921421	72921452	-	1	NA	intron (NM_029640, intron 15 of 21)	intron (NM_029640, intron 15 of 21)	-111112	NR_002864	353342	Mm.440245	NR_002864	ENSMUSG00000106847	Peg13	-	paternally expressed 13	ncRNA
mm_137904.1	chr17	31912729	31912737	+	1	NA	Intergenic	Intergenic	-56941	NM_010831	17691	Mm.290941	NM_010831	ENSMUSG00000024042	Sik1	Msk|Sik|Snf1lk	salt inducible kinase 1	protein-coding
mm_157228.1	chrX	14955991	14956005	-	1	NA	Intergenic	Intergenic	155491	NR_033171	67395	Mm.50369	NM_026128	ENSMUSG00000045217	Ppp1r2-ps9	4930403L05Rik	protein phosphatase 1, regulatory (inhibitor) subunit 2, pseudogene 9	pseudo
mm_117337.1	chr13	69534166	69534191	-	1	NA	promoter-TSS (NM_198600)	promoter-TSS (NM_198600)	-314	NM_001169131	210106	Mm.315959	NM_198600	ENSMUSG00000034575	Papd7	LAK-1|POLK|Pols|TRF4|TRF4-1	PAP associated domain containing 7	protein-coding
mm_133521.1	chr16	90830831	90830878	+	1	NA	promoter-TSS (NM_001316761)	promoter-TSS (NM_001316761)	-5	NR_133572	70967	Mm.253077	NM_027627	ENSMUSG00000039903	Eva1c	1700092M14Rik|4931408A02Rik|Fam176c	eva-1 homolog C (C. elegans)	protein-coding
mm_149268.1	chr19	10582185	10582207	+	1	NA	intron (NM_001282067, intron 4 of 8)	intron (NM_001282067, intron 4 of 8)	-4810	NR_126092	72982	Mm.391194	NM_028411	ENSMUSG00000024666	Tmem138	1700113I01Rik|2900055D14Rik	transmembrane protein 138	protein-coding
mm_129909.1	chr15	84105600	84105658	-	1	NA	5' UTR (NM_013873, exon 1 of 7)	5' UTR (NM_013873, exon 1 of 7)	125	NM_013873	29859	Mm.248796	NM_013873	ENSMUSG00000018865	Sult4a1	2400007A17Rik|AI853543|BR-STL-1|ST4A1|Sultx3	sulfotransferase family 4A, member 1	protein-coding
mm_142063.1	chr17	35673706	35673721	-	1	NA	promoter-TSS (NM_010364)	promoter-TSS (NM_010364)	30	NM_010364	14885	Mm.10182	NM_010364	ENSMUSG00000001524	Gtf2h4	AW545633|BTF2 p52|p52	general transcription factor II H, polypeptide 4	protein-coding
mm_62865.1	chr7	114719587	114719621	+	1	NA	intron (NM_054084, intron 1 of 4)	intron (NM_054084, intron 1 of 4)	961	NM_054084	116903	Mm.273838	NM_054084	ENSMUSG00000030666	Calcb	CGRP2|Calc2	calcitonin-related polypeptide, beta	protein-coding
mm_65389.1	chr7	25092388	25092453	-	1	NA	3' UTR (NM_001163556, exon 14 of 14)	3' UTR (NM_001163556, exon 14 of 14)	4755	NR_105855	102465968		NR_105855	ENSMUSG00000098441	Mir6537	Gm27808|mmu-mir-6537	microRNA 6537	ncRNA
mm_118034.1	chr13	101692287	101692299	-	1	NA	5' UTR (NM_001024955, exon 1 of 10)	5' UTR (NM_001024955, exon 1 of 10)	337	NM_001024955	18708	Mm.259333	NM_001024955	ENSMUSG00000041417	Pik3r1	PI3K|p50alpha|p55alpha|p85alpha	phosphatidylinositol 3-kinase, regulatory subunit, polypeptide 1 (p85 alpha)	protein-coding
mm_149324.1	chr19	10842764	10842768	+	1	NA	5' UTR (NM_023044, exon 1 of 8)	5' UTR (NM_023044, exon 1 of 8)	222	NM_023044	65221	Mm.27387	NM_023044	ENSMUSG00000024737	Slc15a3	Ci1|cI-1	solute carrier family 15, member 3	protein-coding
mm_89407.1	chr10	90747671	90747672	+	1	NA	intron (NM_001177396, intron 3 of 11)	intron (NM_001177396, intron 3 of 11)	-81983	NM_001347054	77531	Mm.440605	NM_181398	ENSMUSG00000058589	Anks1b	AIDA-1b|C030032C09Rik|E530015N03Rik|ENSMUSG00000078431|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding
mm_155105.1	chrX	48347512	48347515	+	1	NA	intron (NM_178782, intron 2 of 14)	intron (NM_178782, intron 2 of 14)	6155	NM_178782	320376	Mm.210146	NM_178782	ENSMUSG00000036959	Bcorl1	6720425J07Rik|B930011H20Rik	BCL6 co-repressor-like 1	protein-coding
mm_45352.1	chr5	65912325	65912349	-	1	NA	Intergenic	Intergenic	48768	NM_001081105	74734	Mm.20323	NM_001081105	ENSMUSG00000029204	Rhoh	5830400A04Rik|AU019774|Arhh	ras homolog family member H	protein-coding
mm_90482.1	chr10	127898539	127898549	+	1	NA	promoter-TSS (NM_027301)	promoter-TSS (NM_027301)	9	NM_027301	70061	Mm.158320	NM_027301	ENSMUSG00000040127	Sdr9c7	1810054F20Rik|Rdh20|Rdhs|SDR-O|Sdro	4short chain dehydrogenase/reductase family 9C, member 7	protein-coding
mm_56761.1	chr6	116107850	116107881	-	1	NA	intron (NM_177412, intron 3 of 5)	intron (NM_177412, intron 3 of 5)	85509	NM_177412	330401	Mm.425352	NM_177412	ENSMUSG00000030126	Tmcc1	3632431M01Rik|mKIAA0779	transmembrane and coiled coil domains 1	protein-coding
mm_7705.1	chr1	130448999	130449027	-	1	NA	intron (NM_010016, intron 7 of 9)	intron (NM_010016, intron 7 of 9)	13731	NM_010016	13136	Mm.101591	NM_010016	ENSMUSG00000026399	Cd55	Daf|Daf-GPI|Daf1|GPI-DAF	CD55 molecule, decay accelerating factor for complement	protein-coding
mm_105077.1	chr11	100803973	100803986	-	1	NA	intron (NM_001113563, intron 3 of 18)	PB1D7|SINE|Alu	18591	NM_011489	20851	Mm.34064	NM_011489	ENSMUSG00000020919	Stat5b	-	signal transducer and activator of transcription 5B	protein-coding
mm_88511.1	chr10	77980669	77980669	+	1	NA	intron (NM_026431, intron 3 of 6)	intron (NM_026431, intron 3 of 6)	2019	NM_026431	67884	Mm.297512	NM_026431	ENSMUSG00000020284	1810043G02Rik	AV026620|D10Jhu13e	RIKEN cDNA 1810043G02 gene	protein-coding
mm_35618.1	chr4	43452519	43452543	-	1	NA	exon (NM_001110320, exon 5 of 9)	exon (NM_001110320, exon 5 of 9)	2095	NM_001110320	12517	Mm.188157	NM_007654	ENSMUSG00000028459	Cd72	CD72c|Ly-19|Ly-32|Ly-m19|Lyb-2	CD72 antigen	protein-coding
mm_116686.1	chr13	49298650	49298657	-	1	NA	intron (NM_015759, intron 1 of 17)	intron (NM_015759, intron 1 of 17)	10555	NM_015759	30938	Mm.291089	NM_015759	ENSMUSG00000037946	Fgd3	5830461L01Rik|ZFYVE5	FYVE, RhoGEF and PH domain containing 3	protein-coding
mm_125083.1	chr15	26362201	26362201	+	1	NA	intron (NM_001310774, intron 2 of 2)	intron (NM_001310774, intron 2 of 2)	53153	NM_001310774	211147	Mm.54257	NM_177597	ENSMUSG00000022269	March11	9630025C22	membrane-associated ring finger (C3HC4) 11	protein-coding
mm_42571.1	chr5	117210095	117210124	+	1	NA	intron (NM_001081308, intron 8 of 19)	B3|SINE|B2	76521	NM_183306	330177	Mm.24343	NM_183306	ENSMUSG00000061288	Taok3	2900006A08Rik|A130052D22|A430105I05Rik	TAO kinase 3	protein-coding
mm_165157.1	chr2	23138479	23138481	+	1	NA	intron (NM_025979, intron 6 of 11)	intron (NM_025979, intron 6 of 11)	17544	NM_025979	67121	Mm.253721	NM_025979	ENSMUSG00000026779	Mastl	2700091H24Rik|C88295|GW|GWL|MAST-L|THC2	microtubule associated serine/threonine kinase-like	protein-coding
mm_78954.1	chr9	45138865	45138880	+	1	NA	promoter-TSS (NM_001013390)	promoter-TSS (NM_001013390)	-170	NM_001013390	399548	Mm.335112	NM_001013390	ENSMUSG00000046480	Scn4b	Gm1471	sodium channel, type IV, beta	protein-coding
mm_35479.1	chr4	40853779	40853802	-	1	NA	exon (NM_022305, exon 1 of 6)	exon (NM_022305, exon 1 of 6)	747	NM_022305	14595	Mm.15622	NM_022305	ENSMUSG00000028413	B4galt1	B-1,4-GalT|B-1,4-GalT1|GalT|Ggtb|Ggtb2|b4Gal-T1|beta-1,4-GalT|beta-1,4-GalT1|beta4Gal-T1	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1	protein-coding
mm_115003.1	chr13	98263327	98263337	+	1	NA	promoter-TSS (NM_178918)	promoter-TSS (NM_178918)	256	NM_001271388	68558	Mm.209642	NM_023472	ENSMUSG00000021661	Ankra2	1110004M18Rik|Ankra	ankyrin repeat, family A (RFXANK-like), 2	protein-coding
mm_10329.1	chr2	11339732	11339750	+	1	NA	non-coding (NR_040369, exon 1 of 4)	non-coding (NR_040369, exon 1 of 4)	252	NR_040369	100503147	Mm.91961	NR_040369	ENSMUSG00000086006	Gm13293	OTTMUSG00000011311	predicted gene 13293	ncRNA
mm_19653.1	chr2	102900227	102900229	-	1	NA	intron (NM_001039150, intron 1 of 13)	intron (NM_001039150, intron 1 of 13)	1437	NM_001177785	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_102846.1	chr11	69369347	69369366	-	1	NA	promoter-TSS (NM_146019)	promoter-TSS (NM_146019)	70	NM_146019	216848	Mm.178246	NM_146019	ENSMUSG00000018474	Chd3	2600010P09Rik|AF020312|Chd7|Prp7|Prp9-1	chromodomain helicase DNA binding protein 3	protein-coding
mm_30262.1	chr3	146770026	146770089	-	1	NA	5' UTR (NM_001164198, exon 1 of 10)	5' UTR (NM_001164198, exon 1 of 10)	181	NM_001164198	18749	Mm.16766	NM_011100	ENSMUSG00000005034	Prkacb	CbPKA|Pkacb	protein kinase, cAMP dependent, catalytic, beta	protein-coding
mm_18757.1	chr2	73437593	73437607	-	1	NA	exon (NM_153138, exon 5 of 8)	exon (NM_153138, exon 5 of 8)	16289	NM_001289722	215280	Mm.223504	NM_153138	ENSMUSG00000075284	Wipf1	AI115543|D2Ertd120e|WIP|Waspip	WAS/WASL interacting protein family, member 1	protein-coding
mm_21156.1	chr2	154569151	154569196	-	1	NA	exon (NM_001291105, exon 1 of 7)	exon (NM_001291105, exon 1 of 7)	253	NM_001291105	13555	Mm.18036	NM_007891	ENSMUSG00000027490	E2f1	E2F-1|mKIAA4009	E2F transcription factor 1	protein-coding
mm_54726.1	chr6	40577734	40577745	-	1	NA	3' UTR (NM_021364, exon 6 of 6)	3' UTR (NM_021364, exon 6 of 6)	6351	NM_146383	258381	Mm.377469	NM_146383	ENSMUSG00000045514	Olfr460	MOR120-2	olfactory receptor 460	protein-coding
mm_110391.1	chr12	41412656	41412677	-	1	NA	intron (NM_053122, intron 4 of 6)	intron (NM_053122, intron 4 of 6)	73391	NM_001271708	16981	Mm.404786	NM_010733	ENSMUSG00000036295	Lrrn3	NLRR-3	leucine rich repeat protein 3, neuronal	protein-coding
mm_40523.1	chr5	57918727	57918738	+	1	NA	intron (NM_001122758, intron 2 of 2)	intron (NM_001122758, intron 2 of 2)	200651	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_44334.1	chr5	14723732	14723740	-	1	NA	intron (NM_001110796, intron 9 of 19)	intron (NM_001110796, intron 9 of 19)	191153	NM_198666	381714	Mm.368256	NM_198666	ENSMUSG00000033219	Gm9758	ENSMUSG00000033219	predicted gene 9758	protein-coding
mm_61918.1	chr7	90153285	90153286	+	1	NA	intron (NM_001252520, intron 1 of 20)	intron (NM_001252520, intron 1 of 20)	23053	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_158914.1	chr1	46836131	46836131	-	1	NA	exon (NM_172653, exon 2 of 10)	exon (NM_172653, exon 2 of 10)	17378	NM_172653	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|mKIAA1265	solute carrier family 39 (zinc transporter), member 10	protein-coding
mm_87925.1	chr10	62543666	62543678	+	1	NA	Intergenic	Intergenic	34785	NM_028197	72320	Mm.258955	NM_028197	ENSMUSG00000036955	Kif1bp	0710007C18Rik|2510003E04Rik|KBP|mKIAA1279	KIF1 binding protein	protein-coding
mm_152505.1	chr19	11196685	11196692	-	1	NA	promoter-TSS (NR_045317)	promoter-TSS (NR_045317)	35	NM_198224	73466	Mm.272723	NM_198224	ENSMUSG00000057240	Ms4a13	1700060E18Rik|Tetm4.2	membrane-spanning 4-domains, subfamily A, member 13	protein-coding
mm_74365.1	chr8	128359386	128359406	+	1	NA	TTS (NR_035436)	TTS (NR_035436)	155	NR_035436	100316680		NR_035436	ENSMUSG00000084523	Mir1903	Mirn1903|mmu-mir-1903	microRNA 1903	ncRNA
mm_151490.1	chr19	58680035	58680057	+	1	NA	exon (NM_026925, exon 11 of 13)	exon (NM_026925, exon 11 of 13)	9681	NM_026925	69060	Mm.20407	NM_026925	ENSMUSG00000046008	Pnlip	1810007A24Rik|PL|PTL	pancreatic lipase	protein-coding
mm_29809.1	chr3	127817267	127817273	-	1	NA	intron (NM_001346718, intron 4 of 8)	intron (NM_001346718, intron 4 of 8)	20222	NM_001346718	211556	Mm.403486	NM_145964	ENSMUSG00000074238	Ap1ar	AA407621|C78909|Gadkin	adaptor-related protein complex 1 associated regulatory protein	protein-coding
mm_66748.1	chr7	46712134	46712188	-	1	NA	exon (NM_011315, exon 4 of 4)	exon (NM_011315, exon 4 of 4)	-1510	NM_030233	78935	Mm.289866	NM_030233	ENSMUSG00000006763	Saal1	5031425D22Rik|SPACIA1	serum amyloid A-like 1	protein-coding
mm_133703.1	chr16	93104147	93104150	+	1	NA	Intergenic	Intergenic	249041	NR_040486	69857	Mm.81192	NR_040486	ENSMUSG00000100277	1810053B23Rik	1810008L18Rik|1810056K14Rik	RIKEN cDNA 1810053B23 gene	ncRNA
mm_108948.1	chr12	102283257	102283274	+	1	NA	promoter-TSS (NM_001161365)	promoter-TSS (NM_001161365)	191	NM_177620	217835	Mm.24145	NM_177620	ENSMUSG00000044456	Rin3	6430500K07|C86933	Ras and Rab interactor 3	protein-coding
mm_24573.1	chr3	93444637	93444641	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	2309	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_72328.1	chr8	79017544	79017554	+	1	NA	Intergenic	Intergenic	-10888	NM_001294279	622675	Mm.48724	NM_178267	ENSMUSG00000071064	Zfp827	2810449M09Rik|D630040G17Rik|Znf827	zinc finger protein 827	protein-coding
mm_98564.1	chr11	95377593	95377608	+	1	NA	exon (NM_172543, exon 6 of 8)	exon (NM_172543, exon 6 of 8)	-7322	NM_016752	110172	Mm.4593	NM_016752	ENSMUSG00000020873	Slc35b1	Ugalt2	solute carrier family 35, member B1	protein-coding
mm_147884.1	chr18	64661065	64661081	-	1	NA	promoter-TSS (NM_001001488)	promoter-TSS (NM_001001488)	-73	NM_001001488	54670	Mm.270043	NM_001001488	ENSMUSG00000039529	Atp8b1	AI451886|FIC1|Ic	ATPase, class I, type 8B, member 1	protein-coding
mm_35822.1	chr4	47011127	47011139	-	1	NA	Intergenic	Intergenic	-19419	NM_001081141	242425	Mm.101909	NM_001081141	ENSMUSG00000039809	Gabbr2	GABABR2|Gb2|Gm425|Gpr51	gamma-aminobutyric acid (GABA) B receptor, 2	protein-coding
mm_102141.1	chr11	53617276	53617295	-	1	NA	promoter-TSS (NR_027491)	promoter-TSS (NR_027491)	53	NR_027491	16189	Mm.276360	NM_021283	ENSMUSG00000000869	Il4	BSF-1|Il-4	interleukin 4	protein-coding
mm_17693.1	chr2	32338030	32338040	-	1	NA	non-coding (NR_125959, exon 5 of 22)	non-coding (NR_125959, exon 5 of 22)	15294	NM_001301737	13429	Mm.44736	NM_010065	ENSMUSG00000026825	Dnm1	AI838169|Dnm|Ftfl|mKIAA4093	dynamin 1	protein-coding
mm_15655.1	chr2	163204429	163204442	+	1	NA	Intergenic	CpG	-21019	NM_001098799	269389	Mm.207709	NM_001098799	ENSMUSG00000074607	Tox2	AI851523|AV026525|BI987407|Gcx1|RxHMG1	TOX high mobility group box family member 2	protein-coding
mm_83131.1	chr9	40435102	40435106	-	1	NA	intron (NM_172768, intron 1 of 19)	intron (NM_172768, intron 1 of 19)	20660	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_59106.1	chr7	19756203	19756237	+	1	NA	TTS (NM_020486)	TTS (NM_020486)	-6647	NM_001159724	19294	Mm.4341	NM_008990	ENSMUSG00000062300	Nectin2	AI325026|AI987993|Cd112|MPH|Pvr|Pvrl2|Pvs|nectin-2	nectin cell adhesion molecule 2	protein-coding
mm_45032.1	chr5	39338897	39338910	-	1	NA	Intergenic	Intergenic	264671	NR_045416	75095	Mm.332354	NR_045416	ENSMUSG00000106741	4930513D17Rik	-	RIKEN cDNA 4930513D17 gene	ncRNA
mm_116113.1	chr13	28950182	28950218	-	1	NA	TTS (NM_009238)	TTS (NM_009238)	3482	NM_009238	20677	Mm.240627	NM_009238	ENSMUSG00000076431	Sox4	AA682046|Sox-4	SRY (sex determining region Y)-box 4	protein-coding
mm_95441.1	chr11	50230691	50230733	+	1	NA	exon (NM_145926, exon 2 of 15)	exon (NM_145926, exon 2 of 15)	-1533	NR_105884	102466765		NR_105884	ENSMUSG00000098474	Mir6919	Gm27889|mmu-mir-6919	microRNA 6919	ncRNA
mm_102316.1	chr11	57112424	57112458	-	1	NA	intron (NM_001252403, intron 2 of 15)	intron (NM_001252403, intron 2 of 15)	99395	NM_001252403	14799	Mm.4920	NM_008165	ENSMUSG00000020524	Gria1	2900051M01Rik|Glr-1|Glr1|GluA1|GluR-A|GluRA|Glur-1|Glur1|HIPA1|gluR-K1	glutamate receptor, ionotropic, AMPA1 (alpha 1)	protein-coding
mm_57851.1	chr6	129470981	129470997	-	1	NA	exon (NM_020008, exon 2 of 6)	exon (NM_020008, exon 2 of 6)	1790	NM_001309637	56644	Mm.239516	NM_020008	ENSMUSG00000079293	Clec7a	BGR|Clecsf12|beta-GR	C-type lectin domain family 7, member a	protein-coding
mm_47778.1	chr5	131950609	131950616	-	1	NA	intron (NM_177047, intron 4 of 18)	intron (NM_177047, intron 4 of 18)	70343	NR_040704	75369	Mm.389696	NR_040704	ENSMUSG00000105773	4930563F08Rik	-	RIKEN cDNA 4930563F08 gene	ncRNA
mm_118516.1	chr14	14349962	14349975	+	1	NA	intron (NM_008369, intron 5 of 11)	intron (NM_008369, intron 5 of 11)	3473	NM_008369	16188	Mm.425857	NM_008369	ENSMUSG00000068758	Il3ra	CD123|CDw123|SUT-1	interleukin 3 receptor, alpha chain	protein-coding
mm_154163.1	chr19	58671733	58671739	-	1	NA	exon (NM_026925, exon 3 of 13)	exon (NM_026925, exon 3 of 13)	1371	NM_026925	69060	Mm.20407	NM_026925	ENSMUSG00000046008	Pnlip	1810007A24Rik|PL|PTL	pancreatic lipase	protein-coding
mm_97822.1	chr11	82964520	82964528	+	1	NA	3' UTR (NM_183201, exon 6 of 6)	3' UTR (NM_183201, exon 6 of 6)	-3843	NR_045932	76392	Mm.295205	NR_045932	ENSMUSG00000086327	Slfn5os	1700003F17Rik	schlafen 5, opposite strand	ncRNA
mm_146694.1	chr18	12889077	12889102	-	1	NA	intron (NM_207530, intron 13 of 27)	intron (NM_207530, intron 13 of 27)	-9110	NM_001252489	64291	Mm.259470	NM_020573	ENSMUSG00000044252	Osbpl1a	G430090F17Rik|Gm753|ORP-1|Osbpl1b	oxysterol binding protein-like 1A	protein-coding
mm_38563.1	chr4	141679550	141679551	-	1	NA	Intergenic	Intergenic	6166	NM_023544	69994	Mm.441022	NM_023544	ENSMUSG00000040715	Rsc1a1	1700027M01Rik|OTTMUSG00000010365|Rs1	regulatory solute carrier protein, family 1, member 1	protein-coding
mm_122142.1	chr14	31182788	31182835	-	1	NA	TTS (NM_001347583)	TTS (NM_001347583)	-14170	NM_138672	192187	Mm.220821	NM_138672	ENSMUSG00000042286	Stab1	FEEL-1|FELE-1|MFEEL-1|MS-1|STAB-1|mKIAA0246	stabilin 1	protein-coding
mm_170964.1	chr2	58156850	58156854	-	1	NA	intron (NM_139200, intron 1 of 7)	intron (NM_139200, intron 1 of 7)	3270	NM_139200	227929	Mm.273905	NM_139200	ENSMUSG00000026832	Cytip	A130053M09Rik|AI462064|C80816|Cbp|Cybr|Pscdbp	cytohesin 1 interacting protein	protein-coding
mm_140127.1	chr17	79615193	79615203	+	1	NA	intron (NM_201361, intron 1 of 10)	CpG	298	NM_201361	381110	Mm.209801	NM_201361	ENSMUSG00000036368	Rmdn2	AW061290|Fam82a1|RMD-2|mRMD-2	regulator of microtubule dynamics 2	protein-coding
mm_76363.1	chr8	84773432	84773466	-	1	NA	5' UTR (NM_001081981, exon 1 of 11)	5' UTR (NM_001081981, exon 1 of 11)	920	NM_001081981	18032	Mm.9394	NM_010906	ENSMUSG00000001911	Nfix	CTF|NF-I/X|NF1-X|NFI-X	nuclear factor I/X	protein-coding
mm_172220.1	chr6	65208656	65208674	-	1	NA	Intergenic	L1Md_T|LINE|L1	-63935	NM_019455	54486	Mm.410688	NM_019455	ENSMUSG00000029919	Hpgds	H-PGDS|Ptgds2	hematopoietic prostaglandin D synthase	protein-coding
mm_107159.1	chr12	24572622	24572633	+	1	NA	intron (NM_001161406, intron 1 of 15)	CpG	340	NM_001161406	195733	Mm.263068	NM_145890	ENSMUSG00000020656	Grhl1	LBP-32|MGR|Tcfcp2l2	grainyhead-like 1 (Drosophila)	protein-coding
mm_50229.1	chr6	42350979	42350987	+	1	NA	exon (NM_001289618, exon 3 of 10)	exon (NM_001289618, exon 3 of 10)	1155	NM_001289619	22793	Mm.282303	NM_011777	ENSMUSG00000029860	Zyx	9530098H06Rik|R75157	zyxin	protein-coding
mm_27827.1	chr3	79092759	79092778	-	1	NA	exon (NM_001099624, exon 9 of 24)	exon (NM_001099624, exon 9 of 24)	52119	NM_001310536	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_42062.1	chr5	109055619	109055629	+	1	NA	intron (NM_001104622, intron 1 of 5)	RLTR9A3B|LTR|ERVK	3828	NM_001104622	384219	Mm.469885	NM_001104622	ENSMUSG00000091450	Vmn2r11	EG384219	vomeronasal 2, receptor 11	protein-coding
mm_62674.1	chr7	109439193	109439203	+	1	NA	promoter-TSS (NM_054103)	promoter-TSS (NM_054103)	-145	NM_054103	117229	Mm.389950	NM_054103	ENSMUSG00000031027	Stk33	4921505G21Rik|AW061264	serine/threonine kinase 33	protein-coding
mm_11502.1	chr2	32535725	32535739	+	1	NA	5' UTR (NM_153560, exon 1 of 11)	5' UTR (NM_153560, exon 1 of 11)	373	NM_153560	98952	Mm.4065	NM_153560	ENSMUSG00000039157	Fam102a	AI426465|C230093N12Rik|Eeig1	family with sequence similarity 102, member A	protein-coding
mm_32512.1	chr4	108579482	108579489	+	1	NA	promoter-TSS (NM_172697)	promoter-TSS (NM_172697)	31	NM_011015	18392	Mm.294154	NM_011015	ENSMUSG00000028587	Orc1	AA545195|MmORC1|Orc1l	origin recognition complex, subunit 1	protein-coding
mm_162808.1	chr10	78412921	78412927	-	1	NA	exon (NM_010925, exon 1 of 13)	exon (NM_010925, exon 1 of 13)	119	NM_010925	18114	Mm.38344	NM_010925	ENSMUSG00000061032	Rrp1	AL033305|AL033306|AU018604|NNP-1|Nnp1	ribosomal RNA processing 1 homolog (S. cerevisiae)	protein-coding
mm_95846.1	chr11	57645418	57645489	+	1	NA	promoter-TSS (NM_134189)	promoter-TSS (NM_134189)	11	NM_134189	171212	Mm.271670	NM_134189	ENSMUSG00000020520	Galnt10	AU018154|C330012K04Rik|GalNAc-T10|GalNAc-T9|Galnt9|ppGaNTase	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 10	protein-coding
mm_169699.1	chr15	75086466	75086468	+	1	NA	Intergenic	B1_Mur4|SINE|Alu	25482	NM_001099217	100041546	Mm.482110	NM_001099217	ENSMUSG00000022584	Ly6c2	Ly-6C.2|Ly-6C2	lymphocyte antigen 6 complex, locus C2	protein-coding
mm_31778.1	chr4	63560242	63560266	+	1	NA	promoter-TSS (NM_144905)	promoter-TSS (NM_144905)	-106	NM_144905	230279	Mm.41523	NM_144905	ENSMUSG00000045917	Tmem268	6330416G13Rik|AW492431|bM230C2.2	transmembrane protein 268	protein-coding
mm_44519.1	chr5	24373938	24373963	-	1	NA	intron (NM_008713, intron 13 of 25)	intron (NM_008713, intron 13 of 25)	9131	NM_008713	18127	Mm.258415	NM_008713	ENSMUSG00000028978	Nos3	2310065A03Rik|Nos-3|eNOS|ecNOS	nitric oxide synthase 3, endothelial cell	protein-coding
mm_48315.1	chr5	138976513	138976516	-	1	NA	TTS (NM_008808)	TTS (NM_008808)	18439	NM_008808	18590	Mm.2675	NM_008808	ENSMUSG00000025856	Pdgfa	-	platelet derived growth factor, alpha	protein-coding
mm_86575.1	chr10	12868968	12868981	+	1	NA	Intergenic	CpG	-7239	NM_011682	22288	Mm.331784	NM_011682	ENSMUSG00000019820	Utrn	AA589569|DRP|Dmdl	utrophin	protein-coding
mm_114307.1	chr13	59657243	59657260	+	1	NA	intron (NM_027307, intron 4 of 10)	intron (NM_027307, intron 4 of 10)	18533	NM_001035122	105348	Mm.171335	NM_027307	ENSMUSG00000021556	Golm1	2310001L02Rik|AW125446|D030064E01Rik|GP73|Golph2|PSEC0257	golgi membrane protein 1	protein-coding
mm_10215.1	chr2	5852846	5852857	+	1	NA	intron (NM_016918, intron 1 of 9)	B1F2|SINE|Alu	7817	NM_016918	53893	Mm.251904	NM_016918	ENSMUSG00000025817	Nudt5	-	nudix (nucleoside diphosphate linked moiety X)-type motif 5	protein-coding
mm_101648.1	chr11	36559188	36559214	-	1	NA	intron (NM_011856, intron 2 of 28)	intron (NM_011856, intron 2 of 28)	385040	NM_001290702	23964	Mm.439889	NM_011856	ENSMUSG00000049336	Tenm2	Odz2|Odz3|Ten-2|Ten-m2	teneurin transmembrane protein 2	protein-coding
mm_127970.1	chr15	12032590	12032633	-	1	NA	Intergenic	Intergenic	-36604	NM_011294	20024	Mm.41746	NM_011294	ENSMUSG00000022205	Sub1	AI842364|P15|P9|Pc4|Rpo2tc1	SUB1 homolog (S. cerevisiae)	protein-coding
mm_139221.1	chr17	47730143	47730152	+	1	NA	exon (NM_025973, exon 4 of 9)	exon (NM_025973, exon 4 of 9)	3305	NM_025973	109820	Mm.22957	NM_025973	ENSMUSG00000023987	Pgc	2210410L06Rik|Upg-1|Upg1	progastricsin (pepsinogen C)	protein-coding
mm_21435.1	chr2	158606636	158606639	-	1	NA	intron (NR_040358, intron 1 of 2)	intron (NR_040358, intron 1 of 2)	4086	NR_040358	100045469	Mm.143404	NR_040358	ENSMUSG00000086496	Gm14204	OTTMUSG00000015935	predicted gene 14204	ncRNA
mm_81555.1	chr9	110344164	110344180	+	1	NA	intron (NM_001001144, intron 1 of 22)	RSINE1|SINE|B4	10816	NM_001001144	235623	Mm.288741	NM_001001144	ENSMUSG00000032485	Scap	9530044G19|mKIAA0199	SREBF chaperone	protein-coding
mm_158749.1	chrX	164980311	164980355	-	1	NA	promoter-TSS (NM_175027)	promoter-TSS (NM_175027)	42	NM_001290523	76763	Mm.291758	NM_029730	ENSMUSG00000061778	Mospd2	2410013I23Rik	motile sperm domain containing 2	protein-coding
mm_137079.1	chr17	21383726	21383766	+	1	NA	promoter-TSS (NM_172486)	promoter-TSS (NM_172486)	-2	NM_172486	210503	Mm.33443	NM_172486	ENSMUSG00000062743	Zfp677	A830058L05Rik|Tce8	zinc finger protein 677	protein-coding
mm_155885.1	chrX	101532793	101532875	+	1	NA	promoter-TSS (NM_001290729)	promoter-TSS (NM_001290729)	99	NM_001290729	270627	Mm.261750	NM_001081008	ENSMUSG00000031314	Taf1	AU015687|B430306D02Rik|Ccg-1|Ccg1|KAT4|N-TAF1|TAFII250|Taf2a|p250	TATA-box binding protein associated factor 1	protein-coding
mm_162130.1	chrX	73117646	73117646	-	1	NA	promoter-TSS (NM_001045539)	promoter-TSS (NM_001045539)	56	NM_001045539	574438	Mm.435653	NM_001045539	ENSMUSG00000058328	Xlr5a	Xlr5d	X-linked lymphocyte-regulated 5A	protein-coding
mm_51874.1	chr6	90552500	90552517	+	1	NA	intron (NM_027406, intron 1 of 22)	(CA)n|Simple_repeat|Simple_repeat	1660	NM_027406	107747	Mm.30035	NM_027406	ENSMUSG00000030088	Aldh1l1	1810048F20Rik|FDH|Fthfd|Neut2	aldehyde dehydrogenase 1 family, member L1	protein-coding
mm_160795.1	chr11	4257406	4257406	+	1	NA	promoter-TSS (NM_008501)	promoter-TSS (NM_008501)	-162	NM_008501	16878	Mm.4964	NM_008501	ENSMUSG00000034394	Lif	-	leukemia inhibitory factor	protein-coding
mm_108451.1	chr12	82616513	82616542	+	1	NA	promoter-TSS (NM_001282061)	promoter-TSS (NM_001282061)	-398	NM_001310478	50779	Mm.126176	NM_015812	ENSMUSG00000021219	Rgs6	-	regulator of G-protein signaling 6	protein-coding
mm_119153.1	chr14	31500124	31500125	+	1	NA	exon (NM_028932, exon 3 of 6)	exon (NM_028932, exon 3 of 6)	5045	NM_028932	74427	Mm.491208	NM_028932	ENSMUSG00000021890	Eaf1	4933403C17Rik|AI666536	ELL associated factor 1	protein-coding
mm_110982.1	chr12	77064223	77064245	-	1	NA	Intergenic	LTR50|LTR|ERVL	-101986	NM_001146176	17187	Mm.268548	NM_008558	ENSMUSG00000059436	Max	AA960152|AI875693|bHLHd4|bHLHd5|bHLHd6|bHLHd7|bHLHd8	Max protein	protein-coding
mm_153031.1	chr19	31765001	31765015	-	1	NA	promoter-TSS (NM_001013833)	promoter-TSS (NM_001013833)	25	NM_001013833	19091	Mm.381170	NM_011160	ENSMUSG00000052920	Prkg1	AW125416|CGKI|Gm19690|Prkg1b|Prkgr1b	protein kinase, cGMP-dependent, type I	protein-coding
mm_50142.1	chr6	41543355	41543379	+	1	NA	Intergenic	Intergenic	21591	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_107184.1	chr12	25042663	25042666	+	1	NA	intron (NM_001081378, intron 26 of 31)	intron (NM_001081378, intron 26 of 31)	53428	NM_010496	15902	Mm.34871	NM_010496	ENSMUSG00000020644	Id2	AI255428|C78922|Idb2|bHLHb26	inhibitor of DNA binding 2	protein-coding
mm_93793.1	chr10	120782333	120782344	-	1	NA	3' UTR (NM_177092, exon 7 of 7)	3' UTR (NM_177092, exon 7 of 7)	16606	NR_038003	70874	Mm.427286	NR_038000	ENSMUSG00000044544	4921513I03Rik	-	RIKEN cDNA 4921513I03 gene	ncRNA
mm_134269.1	chr16	13903052	13903069	-	1	NA	promoter-TSS (NM_053181)	promoter-TSS (NM_053181)	85	NM_001039533	94184	Mm.171484	NM_053181	ENSMUSG00000022680	Pdxdc1	2210010A19Rik|AA415817|Kiaa0251-hp	pyridoxal-dependent decarboxylase domain containing 1	protein-coding
mm_128032.1	chr15	25363752	25363805	-	1	NA	3' UTR (NM_027395, exon 2 of 2)	3' UTR (NM_027395, exon 2 of 2)	49986	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	brain abundant, membrane attached signal protein 1	protein-coding
mm_4018.1	chr1	165655511	165655539	+	1	NA	exon (NM_001038846, exon 5 of 6)	exon (NM_001038846, exon 5 of 6)	-20984	NM_001083897	68481	Mm.46438	NM_001001880	ENSMUSG00000026566	Mpzl1	1110007A10Rik|PZR	myelin protein zero-like 1	protein-coding
mm_126366.1	chr15	80099152	80099163	+	1	NA	intron (NM_207708, intron 1 of 3)	intron (NM_207708, intron 1 of 3)	7823	NM_207708	20972	Mm.230301	NM_009303	ENSMUSG00000022415	Syngr1	R75468|Syngr1b|p29	synaptogyrin 1	protein-coding
mm_88700.1	chr10	80142540	80142544	+	1	NA	exon (NM_025313, exon 1 of 4)	exon (NM_025313, exon 1 of 4)	227	NM_025313	66043	Mm.278560	NM_025313	ENSMUSG00000003072	Atp5d	0610008F14Rik|1500000I11Rik|AA960090|AI876556|AU020773|C85518	ATP synthase, H+ transporting, mitochondrial F1 complex, delta subunit	protein-coding
mm_29675.1	chr3	122871574	122871582	-	1	NA	Intergenic	MLTR14|LTR|ERV1	-23494	NM_007980	14079	Mm.28398	NM_007980	ENSMUSG00000023057	Fabp2	Fabpi|I-FABP	fatty acid binding protein 2, intestinal	protein-coding
mm_125906.1	chr15	75993757	75993832	+	1	NA	promoter-TSS (NM_177922)	promoter-TSS (NM_177922)	25	NM_177922	332110	Mm.40843	NM_177922	ENSMUSG00000063704	Mapk15	BC048082	mitogen-activated protein kinase 15	protein-coding
mm_141167.1	chr17	26532638	26532647	-	1	NA	Intergenic	Intergenic	-24170	NM_013642	19252	Mm.239041	NM_013642	ENSMUSG00000024190	Dusp1	3CH134|MKP1|Ptpn16|U19515|erp|mkp-1	dual specificity phosphatase 1	protein-coding
mm_146454.1	chr18	86395185	86395233	+	1	NA	5' UTR (NM_144946, exon 1 of 11)	5' UTR (NM_144946, exon 1 of 11)	257	NM_144946	246317	Mm.329578	NM_144946	ENSMUSG00000050321	Neto1	AI851453|Btcl1|C130005O10Rik	neuropilin (NRP) and tolloid (TLL)-like 1	protein-coding
mm_55674.1	chr6	72552725	72552781	-	1	NA	intron (NM_001271395, intron 1 of 9)	intron (NM_001271395, intron 1 of 9)	3106	NM_001271395	12332	Mm.18626	NM_007599	ENSMUSG00000056737	Capg	gCap39|mbh1	capping protein (actin filament), gelsolin-like	protein-coding
mm_107785.1	chr12	61534224	61534226	+	1	NA	intron (NM_178714, intron 1 of 3)	intron (NM_178714, intron 1 of 3)	11058	NM_001310586	238205	Mm.28802	NM_178714	ENSMUSG00000035653	Lrfn5	AI427653|AI604817|C130061B21|mKIAA4208	leucine rich repeat and fibronectin type III domain containing 5	protein-coding
mm_161705.1	chr17	24658256	24658256	-	1	NA	exon (NM_001099664, exon 1 of 2)	exon (NM_001099664, exon 1 of 2)	169	NM_001099664	381073	Mm.291772	NM_001099664	ENSMUSG00000071230	Npw	Gm935	neuropeptide W	protein-coding
mm_77716.1	chr8	126593973	126593997	-	1	NA	promoter-TSS (NM_001164598)	promoter-TSS (NM_001164598)	-549	NM_001164598	270110	Mm.334918	NM_001164598	ENSMUSG00000051495	Irf2bp2	E130305N23Rik|IRF-2BP2	interferon regulatory factor 2 binding protein 2	protein-coding
mm_138419.1	chr17	35069451	35069472	+	1	NA	exon (NM_023463, exon 3 of 3)	exon (NM_023463, exon 3 of 3)	2136	NM_023463	68468	Mm.215096	NM_023463	ENSMUSG00000092586	Ly6g6c	1110003M04Rik|AU016360|G6c|NG24	lymphocyte antigen 6 complex, locus G6C	protein-coding
mm_32486.1	chr4	107895803	107895815	+	1	NA	intron (NM_001347160, intron 7 of 7)	RMER12B|LTR|ERVK	5910	NM_028754	74098	Mm.274853	NM_028754	ENSMUSG00000028608	0610037L13Rik	1110008H16Rik	RIKEN cDNA 0610037L13 gene	protein-coding
mm_139168.1	chr17	47557847	47557865	+	1	NA	intron (NM_001081635, intron 1 of 6)	intron (NM_001081635, intron 1 of 6)	-35611	NM_007632	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_92763.1	chr10	81092576	81092633	-	1	NA	5' UTR (NM_145365, exon 3 of 12)	5' UTR (NM_145365, exon 3 of 12)	6268	NM_145365	208677	Mm.294693	NM_145365	ENSMUSG00000035041	Creb3l3	BC010786|CREB-H|D10Bur1e	cAMP responsive element binding protein 3-like 3	protein-coding
mm_69871.1	chr7	141475132	141475168	-	1	NA	promoter-TSS (NM_025593)	promoter-TSS (NM_025593)	3	NM_025593	66491	Mm.380115	NM_025593	ENSMUSG00000038489	Polr2l	2510029B14Rik	polymerase (RNA) II (DNA directed) polypeptide L	protein-coding
mm_10467.1	chr2	14331064	14331081	+	1	NA	exon (NM_008625, exon 30 of 30)	exon (NM_008625, exon 30 of 30)	-57326	NM_001012305	277468	Mm.44662	NM_001012305	ENSMUSG00000036949	Slc39a12	AW046938|Gm731	solute carrier family 39 (zinc transporter), member 12	protein-coding
mm_25880.1	chr3	130817846	130817859	+	1	NA	Intergenic	Intergenic	-87454	NM_001005859	68436	Mm.140568	NM_026724	ENSMUSG00000062006	Rpl34	1100001I22Rik	ribosomal protein L34	protein-coding
mm_123478.1	chr14	65976936	65976994	-	1	NA	exon (NM_013492, exon 6 of 9)	exon (NM_013492, exon 6 of 9)	8482	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_49574.1	chr6	30641504	30641513	+	1	NA	exon (NM_025350, exon 5 of 10)	exon (NM_025350, exon 5 of 10)	2290	NM_025350	109697	Mm.25377	NM_025350	ENSMUSG00000054446	Cpa1	0910001L12Rik|Cpa	carboxypeptidase A1, pancreatic	protein-coding
mm_165495.1	chr2	166117061	166117068	+	1	NA	exon (NM_028072, exon 3 of 21)	exon (NM_028072, exon 3 of 21)	38221	NM_001252578	72043	Mm.1011	NM_028072	ENSMUSG00000006800	Sulf2	2010004N24Rik|AU020235|MSulf-2|mKIAA1247	sulfatase 2	protein-coding
mm_35429.1	chr4	36006005	36006007	-	1	NA	intron (NM_001165999, intron 6 of 7)	ORR1B1-int|LTR|ERVL-MaLR	-160802	NM_175516	242384	Mm.132507	NM_175516	ENSMUSG00000045083	Lingo2	B230217C06Rik|Lern3|Lrrn6c	leucine rich repeat and Ig domain containing 2	protein-coding
mm_130716.1	chr15	101047421	101047429	-	1	NA	Intergenic	CpG	6974	NM_001214911	668225	Mm.385011	NM_001214911	ENSMUSG00000095440	Fignl2	EG668225	fidgetin-like 2	protein-coding
mm_153530.1	chr19	41848234	41848246	-	1	NA	promoter-TSS (NM_177603)	promoter-TSS (NM_177603)	-108	NM_177603	212398	Mm.222723	NM_177603	ENSMUSG00000047604	Frat2	-	frequently rearranged in advanced T cell lymphomas 2	protein-coding
mm_60192.1	chr7	43408229	43408256	+	1	NA	promoter-TSS (NM_172900)	promoter-TSS (NM_172900)	-38	NM_172900	243958	Mm.24444	NM_172900	ENSMUSG00000030468	Siglecg	9830164H23|A630096C01Rik|Siglec-G|Siglec10|mSiglec-G	sialic acid binding Ig-like lectin G	protein-coding
mm_2528.1	chr1	106934442	106934464	+	1	NA	promoter-TSS (NM_027971)	promoter-TSS (NM_027971)	4	NM_027971	71869	Mm.321740	NM_027971	ENSMUSG00000059956	Serpinb12	2300003F07Rik|4833409F13Rik	serine (or cysteine) peptidase inhibitor, clade B (ovalbumin), member 12	protein-coding
mm_12970.1	chr2	90745456	90745469	+	1	NA	promoter-TSS (NM_018828)	promoter-TSS (NM_018828)	92	NM_018828	55935	Mm.489638	NM_018828	ENSMUSG00000008200	Fnbp4	FBP30|Fnbp30|mKIAA1014	formin binding protein 4	protein-coding
mm_157374.1	chrX	37878563	37878565	-	1	NA	exon (NM_001004193, exon 2 of 4)	exon (NM_001004193, exon 2 of 4)	380	NM_001004193	434768	Mm.336025	NM_001004193	ENSMUSG00000064137	Rhox8	Tox	reproductive homeobox 8	protein-coding
mm_164260.1	chr15	100306874	100306905	+	1	NA	intron (NM_027334, intron 1 of 1)	intron (NM_027334, intron 1 of 1)	2072	NM_027334	70152	Mm.488086	NM_027334	ENSMUSG00000054619	Mettl7a1	2210414H16Rik|3300001H21Rik|Aam-B|Mettl7a|UbiE1	methyltransferase like 7A1	protein-coding
mm_60426.1	chr7	44476626	44476651	+	1	NA	Intergenic	L1MEd|LINE|L1	6291	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_167413.1	chr8	107168092	107168127	+	1	NA	intron (NM_025558, intron 1 of 4)	intron (NM_025558, intron 1 of 4)	17448	NM_025558	66427	Mm.20242	NM_025558	ENSMUSG00000031924	Cyb5b	1810044O22Rik|AU015618|Cyb5m	cytochrome b5 type B	protein-coding
mm_135399.1	chr16	44558865	44558875	-	1	NA	promoter-TSS (NR_037242)	promoter-TSS (NR_037242)	0	NM_172506	117606	Mm.41561	NM_172506	ENSMUSG00000022687	Boc	4732455C11|mFLJ00376	biregional cell adhesion molecule-related/down-regulated by oncogenes (Cdon) binding protein	protein-coding
mm_99665.1	chr11	105943348	105943358	+	1	NA	intron (NM_007805, intron 1 of 5)	intron (NM_007805, intron 1 of 5)	794	NM_007805	13056	Mm.149403	NM_007805	ENSMUSG00000019590	Cyb561	-	cytochrome b-561	protein-coding
mm_32383.1	chr4	106561046	106561065	+	1	NA	promoter-TSS (NM_053272)	promoter-TSS (NM_053272)	17	NM_053272	74754	Mm.133370	NM_053272	ENSMUSG00000034926	Dhcr24	2310076D10Rik|5830417J06Rik|mKIAA0018	24-dehydrocholesterol reductase	protein-coding
mm_75842.1	chr8	70608262	70608330	-	1	NA	promoter-TSS (NM_133772)	promoter-TSS (NM_133772)	18	NM_133772	76900	Mm.6667	NM_133772	ENSMUSG00000070003	Ssbp4	1210002E11Rik|AW743380|Sspb4	single stranded DNA binding protein 4	protein-coding
mm_63409.1	chr7	127333651	127333667	+	1	NA	3' UTR (NM_001253873, exon 31 of 31)	3' UTR (NM_001253873, exon 31 of 31)	11655	NM_146202	233890	Mm.23031	NM_146202	ENSMUSG00000047371	Zfp768	BC026432|Znf768	zinc finger protein 768	protein-coding
mm_108407.1	chr12	81663359	81663378	+	1	NA	intron (NM_001033149, intron 2 of 2)	intron (NM_001033149, intron 2 of 2)	32119	NM_001033149	69480	Mm.130002	NM_001033149	ENSMUSG00000042734	Ttc9	-	tetratricopeptide repeat domain 9	protein-coding
mm_30107.1	chr3	138975382	138975393	-	1	NA	intron (NM_145544, intron 4 of 13)	L1_Mur3|LINE|L1	99814	NM_145544	229877	Mm.28893	NM_145544	ENSMUSG00000028149	Rap1gds1	BC011279|GDS1	RAP1, GTP-GDP dissociation stimulator 1	protein-coding
mm_77698.1	chr8	126589777	126589787	-	1	NA	3' UTR (NM_001164598, exon 2 of 2)	3' UTR (NM_001164598, exon 2 of 2)	3654	NM_001164598	270110	Mm.334918	NM_001164598	ENSMUSG00000051495	Irf2bp2	E130305N23Rik|IRF-2BP2	interferon regulatory factor 2 binding protein 2	protein-coding
mm_147985.1	chr18	67610762	67610770	-	1	NA	Intergenic	CpG	30570	NM_001081073	225659	Mm.111928	NM_001081073	ENSMUSG00000073542	Cep76	6230425F05Rik|9630013E05	centrosomal protein 76	protein-coding
mm_93084.1	chr10	89548229	89548251	-	1	NA	Intergenic	Intergenic	-14618	NM_001163504	20186	Mm.3095	NM_009108	ENSMUSG00000047638	Nr1h4	AI957360|Fxr|HRR1|RIP14|Rxrip14	nuclear receptor subfamily 1, group H, member 4	protein-coding
mm_13124.1	chr2	91664583	91664605	+	1	NA	intron (NR_027371, intron 5 of 13)	IMPB_01|Satellite|Satellite	11386	NM_146124	228359	Mm.22413	NM_146124	ENSMUSG00000027247	Arhgap1	B230365D05Rik|C76222|Cdc42GAP|p50rhoGAP	Rho GTPase activating protein 1	protein-coding
mm_87818.1	chr10	60302266	60302279	+	1	NA	TTS (NM_001252635)	TTS (NM_001252635)	17811	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_19673.1	chr2	103454350	103454390	-	1	NA	3' UTR (NM_009804, exon 13 of 13)	3' UTR (NM_009804, exon 13 of 13)	30302	NM_010125	13711	Mm.20888	NM_010125	ENSMUSG00000027186	Elf5	ESE-2|ESE-5|ESE-5.	E74-like factor 5	protein-coding
mm_119005.1	chr14	29018246	29018278	+	1	NA	promoter-TSS (NM_176920)	promoter-TSS (NM_176920)	54	NM_176920	319476	Mm.95780	NM_176920	ENSMUSG00000045776	Lrtm1	A930016D02Rik	leucine-rich repeats and transmembrane domains 1	protein-coding
mm_80108.1	chr9	70399356	70399394	+	1	NA	3' UTR (NM_181072, exon 28 of 28)	3' UTR (NM_181072, exon 28 of 28)	6378	NR_049200	100885839		NR_049200	ENSMUSG00000093763	Mir5626	Gm25590|mir-5626|mmu-mir-5626	microRNA 5626	ncRNA
mm_124602.1	chr15	3277212	3277232	+	1	NA	exon (NM_009155, exon 4 of 5)	exon (NM_009155, exon 4 of 5)	6245	NM_009155	20363	Mm.392203	NM_009155	ENSMUSG00000064373	Selenop	AU018766|D15Ucla1|Se-P|Sepp1|selp	selenoprotein P	protein-coding
mm_93988.1	chr10	127521125	127521134	-	1	NA	intron (NM_028230, intron 1 of 11)	intron (NM_028230, intron 1 of 11)	1315	NM_001252316	108037	Mm.29890	NM_028230	ENSMUSG00000025403	Shmt2	2700043D08Rik|AA408223|AA986903	serine hydroxymethyltransferase 2 (mitochondrial)	protein-coding
mm_111383.1	chr12	87421015	87421016	-	1	NA	Intergenic	Intergenic	16742	NR_037228	100526546		NR_037228	ENSMUSG00000105428	Mir3068	mir-3068|mmu-mir-3068	microRNA 3068	ncRNA
mm_892.1	chr1	53061638	53061642	+	1	NA	promoter-TSS (NM_010834)	promoter-TSS (NM_010834)	0	NM_010834	17700	Mm.3514	NM_010834	ENSMUSG00000026100	Mstn	Cmpt|Gdf8	myostatin	protein-coding
mm_31940.1	chr4	86576911	86576921	+	1	NA	3' UTR (NM_178376, exon 1 of 1)	3' UTR (NM_178376, exon 1 of 1)	1243	NM_178376	68441	Mm.31178	NM_178376	ENSMUSG00000070934	Rraga	1300010C19Rik|AI255374|FIP-1|RAGA	Ras-related GTP binding A	protein-coding
mm_132608.1	chr16	38564220	38564257	+	1	NA	exon (NM_026407, exon 2 of 9)	exon (NM_026407, exon 2 of 9)	1424	NM_026407	67846	Mm.310476	NM_026407	ENSMUSG00000002845	Tmem39a	2610033C09Rik	transmembrane protein 39a	protein-coding
mm_131827.1	chr16	22951095	22951123	+	1	NA	promoter-TSS (NM_053176)	promoter-TSS (NM_053176)	37	NM_053176	94175	Mm.358794	NM_053176	ENSMUSG00000022877	Hrg	AI265597|AW413091|D16jh2|D18020|Hprg|Hrgp	histidine-rich glycoprotein	protein-coding
mm_165272.1	chr2	75704645	75704679	-	1	NA	promoter-TSS (NM_010902)	promoter-TSS (NM_010902)	1	NR_132727	18024	Mm.1025	NM_010902	ENSMUSG00000015839	Nfe2l2	Nrf2	nuclear factor, erythroid derived 2, like 2	protein-coding
mm_157934.1	chrX	81822877	81822890	-	1	NA	Intergenic	Intergenic	-364761	NM_173435	245492	Mm.109633	NM_173435	ENSMUSG00000060673	4930595M18Rik	-	RIKEN cDNA 4930595M18 gene	protein-coding
mm_110761.1	chr12	70113733	70113768	-	1	NA	Intergenic	Intergenic	-1715	NR_104397	18080	Mm.244047	NM_008697	ENSMUSG00000021068	Nin	3110068G20Rik|AI385615|AU024711|mKIAA1565	ninein	protein-coding
mm_88950.1	chr10	81364286	81364301	+	1	NA	TTS (NM_028657)	TTS (NM_028657)	1527	NM_001014836	432479	Mm.440450	NM_001014836	ENSMUSG00000020234	4930404N11Rik	2210409H10Rik|5730551K18Rik|AI854616	RIKEN cDNA 4930404N11 gene	protein-coding
mm_107558.1	chr12	41395738	41395742	+	1	NA	intron (NM_053122, intron 4 of 6)	intron (NM_053122, intron 4 of 6)	90317	NM_001271708	16981	Mm.404786	NM_010733	ENSMUSG00000036295	Lrrn3	NLRR-3	leucine rich repeat protein 3, neuronal	protein-coding
mm_92209.1	chr10	68212068	68212116	-	1	NA	intron (NM_023598, intron 3 of 9)	intron (NM_023598, intron 3 of 9)	66634	NM_023598	71371	Mm.440357	NM_023598	ENSMUSG00000019947	Arid5b	4930580B11|5430435G07Rik|AI467247|Desrt|Mrf2|Mrf2alpha|Mrf2beta	AT rich interactive domain 5B (MRF1-like)	protein-coding
mm_132609.1	chr16	38585359	38585375	+	1	NA	exon (NM_026407, exon 6 of 9)	exon (NM_026407, exon 6 of 9)	22553	NM_026407	67846	Mm.310476	NM_026407	ENSMUSG00000002845	Tmem39a	2610033C09Rik	transmembrane protein 39a	protein-coding
mm_19301.1	chr2	90471249	90471259	-	1	NA	exon (NM_008982, exon 3 of 24)	exon (NM_008982, exon 3 of 24)	7920	NM_001135657	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_7952.1	chr1	133915393	133915405	-	1	NA	exon (NM_054077, exon 2 of 3)	exon (NM_054077, exon 2 of 3)	6002	NM_054077	116847	Mm.214514	NM_054077	ENSMUSG00000041577	Prelp	7330409J17Rik|SLRR2A	proline arginine-rich end leucine-rich repeat	protein-coding
mm_70599.1	chr8	13338746	13338756	+	1	NA	promoter-TSS (NM_001291765)	promoter-TSS (NM_001291765)	0	NM_001291765	21781	Mm.925	NM_009361	ENSMUSG00000038482	Tfdp1	Dp1|Drtf1	transcription factor Dp 1	protein-coding
mm_58112.1	chr6	138422899	138422915	-	1	NA	promoter-TSS (NR_126073)	promoter-TSS (NR_126073)	-198	NR_126073	319702	Mm.403785	NR_126072	ENSMUSG00000089957	A830011K09Rik	-	RIKEN cDNA A830011K09 gene	ncRNA
mm_34239.1	chr4	141180203	141180207	+	1	NA	intron (NM_172518, intron 3 of 9)	intron (NM_172518, intron 3 of 9)	32283	NM_172518	213499	Mm.28865	NM_172518	ENSMUSG00000028920	Fbxo42	6720460I06Rik|mKIAA1332	F-box protein 42	protein-coding
mm_72877.1	chr8	88697119	88697138	+	1	NA	promoter-TSS (NM_001128171)	promoter-TSS (NM_001128171)	100	NM_001128171	74256	Mm.490395	NM_173369	ENSMUSG00000036712	Cyld	2010013M14Rik|2900009M21Rik|C130039D01Rik|CDMT|CYLD1|EAC|mKIAA0849	CYLD lysine 63 deubiquitinase	protein-coding
mm_95431.1	chr11	50202925	50203003	+	1	NA	exon (NM_011018, exon 6 of 8)	exon (NM_011018, exon 6 of 8)	7856	NM_001290769	18412	Mm.40828	NM_011018	ENSMUSG00000015837	Sqstm1	A170|OSF-6|Osi|STAP|STONE14|p62	sequestosome 1	protein-coding
mm_6276.1	chr1	69683051	69683064	-	1	NA	intron (NM_011770, intron 3 of 7)	intron (NM_011770, intron 3 of 7)	2903	NM_011770	22779	Mm.106343	NM_011770	ENSMUSG00000025997	Ikzf2	A730095J18Rik|Helios|Zfpn1a2|Znfn1a2	IKAROS family zinc finger 2	protein-coding
mm_172755.1	chr8	85553298	85553313	-	1	NA	exon (NM_019794, exon 3 of 9)	exon (NM_019794, exon 3 of 9)	1966	NM_019794	56445	Mm.475573	NM_019794	ENSMUSG00000031701	Dnaja2	1500017M13Rik|2010206B19Rik|DNAJ|DNJ3|Dnaj3|HIRIP4|PRO3015|mDj3	DnaJ heat shock protein family (Hsp40) member A2	protein-coding
mm_90900.1	chr10	10558200	10558250	-	1	NA	promoter-TSS (NM_026405)	promoter-TSS (NM_026405)	-18	NM_026405	67844	Mm.31486	NM_026405	ENSMUSG00000019832	Rab32	2810011A17Rik|AU022057	RAB32, member RAS oncogene family	protein-coding
mm_119670.1	chr14	52567183	52567203	+	1	NA	Intergenic	Intergenic	-71498	NM_001170918	57269	Mm.88822	NM_020512	ENSMUSG00000059887	Olfr1507	MOR244-1|Mor28|Or28	olfactory receptor 1507	protein-coding
mm_131879.1	chr16	23224806	23224816	+	1	NA	promoter-TSS (NM_145933)	promoter-TSS (NM_145933)	71	NM_145933	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_48559.1	chr5	143154974	143154994	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	10767	NR_040426	100042605	Mm.332809	NR_040424	ENSMUSG00000104529	Rbakdn	Gm3925	RB-associated KRAB zinc finger downstream neighbor (non-protein coding)	ncRNA
mm_489.1	chr1	36767460	36767469	+	1	NA	intron (NM_001289765, intron 1 of 12)	intron (NM_001289765, intron 1 of 12)	530	NM_001289765	22637	Mm.8038	NM_009539	ENSMUSG00000026117	Zap70	Srk|ZAP-70|mrtle|mur	zeta-chain (TCR) associated protein kinase	protein-coding
mm_79129.1	chr9	47540616	47540634	+	1	NA	intron (NM_001025600, intron 1 of 8)	intron (NM_001025600, intron 1 of 8)	10273	NM_018770	54725	Mm.234832	NM_018770	ENSMUSG00000032076	Cadm1	2900073G06Rik|3100001I08Rik|AI987920|Bl2|Igsf4|Igsf4a|Necl2|RA175|RA175A|RA175B|RA175C|RA175N|ST17|SgIGSF|SynCam|Tslc1	cell adhesion molecule 1	protein-coding
mm_111173.1	chr12	83668195	83668275	-	1	NA	exon (NM_027349, exon 11 of 19)	exon (NM_027349, exon 11 of 19)	-20328	NM_008943	19164	Mm.998	NM_008943	ENSMUSG00000019969	Psen1	Ad3h|PS-1|PS1|S182	presenilin 1	protein-coding
mm_114327.1	chr13	60613810	60613815	+	1	NA	intron (NM_029653, intron 2 of 25)	B1_Mur4|SINE|Alu	11601	NM_134062	69635	Mm.24103	NM_029653	ENSMUSG00000021559	Dapk1	D13Ucla1|DAP-Kinase	death associated protein kinase 1	protein-coding
mm_88810.1	chr10	80765657	80765660	+	1	NA	intron (NM_199322, intron 2 of 27)	intron (NM_199322, intron 2 of 27)	10452	NM_199322	208266	Mm.152371	NM_199322	ENSMUSG00000061589	Dot1l	A630076O07|AW907654|Dot1|KMT4|mDot1	DOT1-like, histone H3 methyltransferase (S. cerevisiae)	protein-coding
mm_13585.1	chr2	112379309	112379322	+	1	NA	5' UTR (NM_024254, exon 1 of 10)	5' UTR (NM_024254, exon 1 of 10)	104	NM_024254	72425	Mm.425091	NM_024254	ENSMUSG00000027132	Katnbl1	2410042D21Rik|AA166487|AA473307|AI467442	katanin p80 subunit B like 1	protein-coding
mm_38453.1	chr4	140246919	140246946	-	1	NA	promoter-TSS (NM_198610)	promoter-TSS (NM_198610)	-121	NM_198610	230868	Mm.298731	NM_198610	ENSMUSG00000040972	Igsf21	BC055811|Gm141	immunoglobulin superfamily, member 21	protein-coding
mm_56119.1	chr6	87532271	87532319	-	1	NA	intron (NM_001037727, intron 1 of 10)	intron (NM_001037727, intron 1 of 10)	964	NM_001037727	232201	Mm.119564	NM_175476	ENSMUSG00000030047	Arhgap25	A130039I20Rik	Rho GTPase activating protein 25	protein-coding
mm_100570.1	chr11	120762819	120762829	+	1	NA	Intergenic	Intergenic	21380	NM_009053	19719	Mm.871	NM_009053	ENSMUSG00000025158	Rfng	-	RFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	protein-coding
mm_39811.1	chr5	30648006	30648029	+	1	NA	promoter-TSS (NM_175675)	promoter-TSS (NM_175675)	78	NM_175675	74919	Mm.247985	NM_175675	ENSMUSG00000029175	Slc35f6	4930471M23Rik|5730478O19Rik|ANT2BP|P40|Tango9	solute carrier family 35, member F6	protein-coding
mm_140337.1	chr17	86778761	86778781	+	1	NA	intron (NM_010137, intron 1 of 15)	intron (NM_010137, intron 1 of 15)	24907	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_71211.1	chr8	40890705	40890717	+	1	NA	intron (NM_007514, intron 1 of 11)	intron (NM_007514, intron 1 of 11)	28344	NM_001044740	11988	Mm.4676	NM_007514	ENSMUSG00000031596	Slc7a2	20.5|AI158848|Atrc2|CAT-2|Cat2|Tea	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	protein-coding
mm_22209.1	chr2	174169704	174169708	-	1	NA	intron (NR_040530, intron 1 of 3)	L1MA7|LINE|L1	14212	NR_040530	100038374	Mm.127249	NR_040530	ENSMUSG00000074555	Gm10714	ENSMUSG00000074555	predicted gene 10714	ncRNA
mm_60171.1	chr7	40987550	40987570	+	1	NA	promoter-TSS (NM_207248)	promoter-TSS (NM_207248)	-49	NM_207248	243944	Mm.333806	NM_207248	ENSMUSG00000091692	4930433I11Rik	Gm481	RIKEN cDNA 4930433I11 gene	protein-coding
mm_84651.1	chr9	71592313	71592343	-	1	NA	promoter-TSS (NM_001033208)	promoter-TSS (NM_001033208)	32	NM_001033208	102371	Mm.27585	NM_001033208	ENSMUSG00000041361	Myzap	AA407270|AV006038|Gcom1|Gm640|Grinl1a7|Myozap	myocardial zonula adherens protein	protein-coding
mm_134644.1	chr16	21775490	21775495	-	1	NA	exon (NM_023737, exon 3 of 7)	exon (NM_023737, exon 3 of 7)	12342	NM_023737	74147	Mm.28100	NM_023737	ENSMUSG00000022853	Ehhadh	1300002P22Rik|HD|L-PBE|LBFP|LBP|MFP|MFP1|PBFE	enoyl-Coenzyme A, hydratase/3-hydroxyacyl Coenzyme A dehydrogenase	protein-coding
mm_152910.1	chr19	27262265	27262273	-	1	NA	Intergenic	Intergenic	45249	NM_001161420	22359	Mm.4141	NM_013703	ENSMUSG00000024924	Vldlr	AA408956|AI451093|AW047288	very low density lipoprotein receptor	protein-coding
mm_51749.1	chr6	87428987	87429000	+	1	NA	promoter-TSS (NM_009756)	promoter-TSS (NM_009756)	-1	NM_009756	12154	Mm.483321	NM_009756	ENSMUSG00000030046	Bmp10	-	bone morphogenetic protein 10	protein-coding
mm_48363.1	chr5	139408512	139408520	-	1	NA	intron (NM_177000, intron 1 of 1)	intron (NM_177000, intron 1 of 1)	2129	NM_177000	319772	Mm.440271	NM_177000	ENSMUSG00000044092	C130050O18Rik	-	RIKEN cDNA C130050O18 gene	protein-coding
mm_134129.1	chr16	10447320	10447331	-	1	NA	promoter-TSS (NM_001013778)	promoter-TSS (NM_001013778)	25	NM_001013778	383103	Mm.325732	NM_001013778	ENSMUSG00000050908	Tvp23a	Fam18a	trans-golgi network vesicle protein 23A	protein-coding
mm_139835.1	chr17	69156601	69156607	+	1	NA	promoter-TSS (NM_013813)	promoter-TSS (NM_013813)	-206	NM_013813	13823	Mm.131135	NM_013813	ENSMUSG00000024044	Epb41l3	4.1B|DAL1P|Dal1|Epb4.1l3|NBL3	erythrocyte membrane protein band 4.1 like 3	protein-coding
mm_49558.1	chr6	30554597	30554601	+	1	NA	intron (NM_001024698, intron 9 of 10)	PB1D10|SINE|Alu	12957	NM_001024698	232680	Mm.268855	NM_001024698	ENSMUSG00000071553	Cpa2	-	carboxypeptidase A2, pancreatic	protein-coding
mm_52853.1	chr6	121865820	121865848	+	1	NA	exon (NM_008645, exon 15 of 36)	exon (NM_008645, exon 15 of 36)	27293	NM_008645	17836	Mm.1311	NM_008645	ENSMUSG00000059908	Mug1	-	murinoglobulin 1	protein-coding
mm_11027.1	chr2	26910748	26910769	+	1	NA	promoter-TSS (NM_001033908)	promoter-TSS (NM_001033908)	-49	NM_013721	27176	Mm.328601	NM_013721	ENSMUSG00000062647	Rpl7a	Surf3	ribosomal protein L7A	protein-coding
mm_27187.1	chr3	34651037	34651047	-	1	NA	exon (NM_011443, exon 1 of 1)	exon (NM_011443, exon 1 of 1)	1047	NM_011443	20674	Mm.65396	NM_011443	ENSMUSG00000074637	Sox2	Sox-2|lcc|ysb	SRY (sex determining region Y)-box 2	protein-coding
mm_118820.1	chr14	25529873	25529885	+	1	NA	intron (NM_001310666, intron 2 of 23)	intron (NM_001310666, intron 2 of 23)	-4560	NR_037236	100526533		NR_037236	ENSMUSG00000093081	Mir3075	mir-3075|mmu-mir-3075	microRNA 3075	ncRNA
mm_49522.1	chr6	29957550	29957551	+	1	NA	non-coding (NR_104576, exon 21 of 21)	non-coding (NR_104576, exon 21 of 21)	-27779	NR_040264	76419	Mm.84522	NR_040263	ENSMUSG00000045709	Smkr-ps	1700023L04Rik	smal lysine rich protein 1, pseudogene	ncRNA
mm_68425.1	chr7	109760209	109760213	-	1	NA	3' UTR (NM_020610, exon 7 of 7)	3' UTR (NM_020610, exon 7 of 7)	-7948	NM_020050	56786	Mm.240668	NM_020050	ENSMUSG00000031021	Tmem9b	2310004K06Rik|AW539847|D7H11orf15|ICRFP703B1614Q5.3	TMEM9 domain family, member B	protein-coding
mm_111215.1	chr12	84408974	84408983	-	1	NA	promoter-TSS (NM_028377)	promoter-TSS (NM_028377)	51	NM_007647	12499	Mm.10211	NM_007647	ENSMUSG00000021236	Entpd5	AI196558|AI987697|Cd39l4|ER-UDPase|NTPDase-5|NTPDase5|Pcph|mNTPase	ectonucleoside triphosphate diphosphohydrolase 5	protein-coding
mm_143270.1	chr17	65642213	65642223	-	1	NA	promoter-TSS (NM_001146002)	promoter-TSS (NM_001146002)	-14	NM_001146002	213272	Mm.255732	NM_153519	ENSMUSG00000050612	Txndc2	AU021712|Sptrx-1|Sptrx1|Trx4	thioredoxin domain containing 2 (spermatozoa)	protein-coding
mm_100599.1	chr11	121204444	121204497	+	1	NA	promoter-TSS (NM_001001333)	promoter-TSS (NM_001001333)	37	NM_001001333	238023	Mm.275130	NM_001001333	ENSMUSG00000039307	Hexdc	BC069960	hexosaminidase (glycosyl hydrolase family 20, catalytic domain) containing	protein-coding
mm_118413.1	chr14	7791440	7791442	+	1	NA	Intergenic	CpG	-26516	NM_001081427	286940	Mm.489652	NM_134080	ENSMUSG00000025278	Flnb	AL024016|Fln-b	filamin, beta	protein-coding
mm_67756.1	chr7	92669866	92669877	-	1	NA	promoter-TSS (NM_029078)	promoter-TSS (NM_029078)	41	NM_029078	74737	Mm.288645	NM_029078	ENSMUSG00000041328	Pcf11	2500001H09Rik|5730417B17Rik|C77803	PCF11 cleavage and polyadenylation factor subunit	protein-coding
mm_116388.1	chr13	41184434	41184446	-	1	NA	3' UTR (NM_019423, exon 8 of 8)	3' UTR (NM_019423, exon 8 of 8)	35722	NM_001311121	54326	Mm.2567	NM_019423	ENSMUSG00000021364	Elovl2	AI317360|Ssc2	elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 2	protein-coding
mm_55396.1	chr6	60760194	60760215	-	1	NA	intron (NM_009221, intron 4 of 5)	intron (NM_009221, intron 4 of 5)	68800	NM_001042451	20617	Mm.17484	NM_009221	ENSMUSG00000025889	Snca	NACP|alphaSYN	synuclein, alpha	protein-coding
mm_94313.1	chr11	4223643	4223653	+	1	NA	Intergenic	Intergenic	5397	NM_028022	71962	Mm.7852	NM_028022	ENSMUSG00000020424	Gatsl3	2410008K03Rik	GATS protein-like 3	protein-coding
mm_38144.1	chr4	134853295	134853324	-	1	NA	promoter-TSS (NM_025382)	promoter-TSS (NM_025382)	36	NM_025382	66146	Mm.99793	NM_025382	ENSMUSG00000028826	Tmem57	1110007C24Rik|9230118A01Rik|AI317300|AI606104|C61	transmembrane protein 57	protein-coding
mm_125555.1	chr15	58872647	58872696	+	1	NA	promoter-TSS (NM_026642)	promoter-TSS (NM_026642)	22	NM_026642	68260	Mm.278805	NM_026642	ENSMUSG00000037085	Trmt12	4632406N01Rik|AI449275|Tyw2	tRNA methyltranferase 12	protein-coding
mm_22811.1	chr3	27183741	27183745	+	1	NA	intron (NM_178772, intron 1 of 4)	intron (NM_178772, intron 1 of 4)	739	NM_178772	320024	Mm.24576	NM_178772	ENSMUSG00000027698	Nceh1	Aadacl1|B230106I24Rik|CPO-BP|Nceh	neutral cholesterol ester hydrolase 1	protein-coding
mm_172506.1	chr7	68275958	68275958	+	1	NA	promoter-TSS (NR_040341)	promoter-TSS (NR_040341)	636	NR_040340	100504026	Mm.426764	NR_040340	ENSMUSG00000086628	Gm16157	OTTMUSG00000031023	predicted gene 16157	ncRNA
mm_60695.1	chr7	45175218	45175231	+	1	NA	3' UTR (NM_182993, exon 12 of 12)	3' UTR (NM_182993, exon 12 of 12)	1921	NR_106022	102465638		NR_106022	ENSMUSG00000106470	Mir7055	mmu-mir-7055	microRNA 7055	ncRNA
mm_10627.1	chr2	19658056	19658072	+	1	NA	promoter-TSS (NR_033642)	promoter-TSS (NR_033642)	2	NM_027715	71198	Mm.83981	NM_027715	ENSMUSG00000043415	Otud1	4933428L19Rik	OTU domain containing 1	protein-coding
mm_84865.1	chr9	78615646	78615657	-	1	NA	5' UTR (NM_153098, exon 1 of 33)	5' UTR (NM_153098, exon 1 of 33)	105	NM_153098	235505	Mm.32955	NM_153098	ENSMUSG00000046186	Cd109	9930012E15Rik|AI480638|GARP	CD109 antigen	protein-coding
mm_138502.1	chr17	35220285	35220291	+	1	NA	3' UTR (NM_010909, exon 4 of 4)	3' UTR (NM_010909, exon 4 of 4)	-14722	NM_001347351	66237	Mm.396107	NM_023179	ENSMUSG00000024403	Atp6v1g2	1500002D01Rik|Atp6g2|NG38|VAG2	ATPase, H+ transporting, lysosomal V1 subunit G2	protein-coding
mm_46165.1	chr5	96163577	96163579	-	1	NA	Intergenic	Intergenic	-1588	NM_144910	231464	Mm.28374	NM_144910	ENSMUSG00000034724	Cnot6l	4932442K20Rik	CCR4-NOT transcription complex, subunit 6-like	protein-coding
mm_142635.1	chr17	47414730	47414736	-	1	NA	promoter-TSS (NM_001172091)	promoter-TSS (NM_001172091)	-22	NM_001172091	75462	Mm.46129	NM_029296	ENSMUSG00000047150	1700001C19Rik	-	RIKEN cDNA 1700001C19 gene	protein-coding
mm_38798.1	chr4	148151879	148151934	-	1	NA	promoter-TSS (NM_001163705)	promoter-TSS (NM_001163705)	19	NM_001163705	50762	Mm.27445	NM_015797	ENSMUSG00000055401	Fbxo6	AA408845|FBG2|Fbs2|Fbx6b|Fbxo6b	F-box protein 6	protein-coding
mm_63666.1	chr7	129601532	129601552	+	1	NA	intron (NM_172255, intron 4 of 28)	intron (NM_172255, intron 4 of 28)	9679	NM_172255	207425	Mm.229323	NM_172255	ENSMUSG00000042055	Wdr11	2900055P10Rik|AW489876|Brwd2|mKIAA1351	WD repeat domain 11	protein-coding
mm_60477.1	chr7	44478283	44478303	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-6224	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_143388.1	chr17	68874249	68874252	-	1	NA	Intergenic	Intergenic	37114	NM_001206661	622645	Mm.86422	NM_001206661	ENSMUSG00000095407	Tmem200c	EG622645|Gm6338	transmembrane protein 200C	protein-coding
mm_90394.1	chr10	127323701	127323736	+	1	NA	promoter-TSS (NM_146011)	promoter-TSS (NM_146011)	-9	NM_146011	216445	Mm.227198	NM_146011	ENSMUSG00000040345	Arhgap9	AU043488	Rho GTPase activating protein 9	protein-coding
mm_70541.1	chr8	13039538	13039549	+	1	NA	exon (NM_007972, exon 3 of 9)	exon (NM_007972, exon 3 of 9)	2235	NM_001242368	14058	Mm.262589	NM_007972	ENSMUSG00000031444	F10	Cf10|fX	coagulation factor X	protein-coding
mm_67905.1	chr7	99695629	99695630	-	1	NA	5' UTR (NM_001252531, exon 1 of 14)	5' UTR (NM_001252531, exon 1 of 14)	180	NM_001252531	101488	Mm.11249	NM_175316	ENSMUSG00000030737	Slco2b1	AI060904|AI852653|OATP-B|Slc21a9	solute carrier organic anion transporter family, member 2b1	protein-coding
mm_149132.1	chr19	9002464	9002509	+	1	NA	exon (NM_009643, exon 5 of 5)	exon (NM_009643, exon 5 of 5)	13202	NM_001286518	66395	Mm.203866	NM_009643	ENSMUSG00000069833	Ahnak	DY6	AHNAK nucleoprotein (desmoyokin)	protein-coding
mm_122384.1	chr14	40899309	40899334	-	1	NA	Intergenic	Intergenic	-6356	NM_177816	328381	Mm.235694	NM_177816	ENSMUSG00000037833	Sh2d4b	A430109M18Rik|D030001E08	SH2 domain containing 4B	protein-coding
mm_119451.1	chr14	46889362	46889378	+	1	NA	intron (NM_001037221, intron 2 of 12)	intron (NM_001037221, intron 2 of 12)	6405	NM_001037221	74480	Mm.214454	NM_028966	ENSMUSG00000021838	Samd4	1700024G08Rik|1700111L17Rik|4933436G17Rik|Samd4a|Smaug|Smaug1|sunk	sterile alpha motif domain containing 4	protein-coding
mm_163610.1	chr13	50885853	50885859	+	1	NA	Intergenic	Intergenic	-120608	NR_045364	71654	Mm.427318	NR_045364		4930518P08Rik	-	RIKEN cDNA 4930518P08 gene	ncRNA
mm_172029.1	chr6	123195714	123195716	-	1	NA	intron (NM_001004159, intron 3 of 5)	Lx2B2|LINE|L1	22692	NM_001004159	381809	Mm.333372	NM_001004159	ENSMUSG00000067767	Clec4b2	Aplra1|F830043G12Rik|mDCAR1	C-type lectin domain family 4, member b2	protein-coding
mm_48447.1	chr5	140692533	140692557	-	1	NA	intron (NM_001347517, intron 4 of 22)	RSINE1|SINE|B4	9833	NM_028833	74239	Mm.179704	NM_028833	ENSMUSG00000036555	Iqce	1700028P05Rik|mKIAA1023	IQ motif containing E	protein-coding
mm_16977.1	chr2	18027449	18027493	-	1	NA	non-coding (NR_028376, exon 2 of 2)	non-coding (NR_028376, exon 2 of 2)	222	NR_028378	100034739	Mm.401643	NR_028378		Gm17762	-	predicted gene, 17762	ncRNA
mm_107296.1	chr12	30884266	30884272	+	1	NA	promoter-TSS (NM_001159743)	promoter-TSS (NM_001159743)	-55	NM_001159743	100294583	Mm.399726	NM_001159743	ENSMUSG00000054204	Fam150b	6230419C23Rik	family with sequence similarity 150, member B	protein-coding
mm_3419.1	chr1	146323198	146323206	+	1	NA	Intergenic	RLTR9D|LTR|ERVK	-172464	NM_153539	215378	Mm.441817	NM_153539	ENSMUSG00000035131	Brinp3	B830045N13Rik|Fam5c	bone morphogenetic protein/retinoic acid inducible neural specific 3	protein-coding
mm_26252.1	chr3	142000683	142000686	+	1	NA	intron (NM_001277217, intron 1 of 11)	intron (NM_001277217, intron 1 of 11)	-18420	NM_007560	12167	Mm.39089	NM_007560	ENSMUSG00000052430	Bmpr1b	AI385617|ALK-6|AV355320|Acvrlk6|Alk6|BMPR-1B|BMPR-IB|CFK-43a|SKR6	bone morphogenetic protein receptor, type 1B	protein-coding
mm_162803.1	chr10	77537067	77537101	+	1	NA	intron (NM_008404, intron 1 of 15)	intron (NM_008404, intron 1 of 15)	6736	NM_008404	16414	Mm.1137	NM_008404	ENSMUSG00000000290	Itgb2	2E6|AI528527|Cd18|LAD|LCAMB|Lfa1|MF17	integrin beta 2	protein-coding
mm_59447.1	chr7	27133431	27133457	+	1	NA	3' UTR (NM_007817, exon 10 of 10)	3' UTR (NM_007817, exon 10 of 10)	13489	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_17061.1	chr2	22589045	22589087	-	1	NA	Intergenic	Intergenic	-33261	NM_008078	14417	Mm.4784	NM_008078	ENSMUSG00000026787	Gad2	6330404F12Rik|GAD(65)|GAD65|Gad-2	glutamic acid decarboxylase 2	protein-coding
mm_50916.1	chr6	57602839	57602857	+	1	NA	intron (NM_025992, intron 5 of 22)	B3|SINE|B2	21856	NM_025992	67138	Mm.297393	NM_025992	ENSMUSG00000029798	Herc6	1700121D12Rik|2510038N07Rik|4930427L17Rik|AI451296|CEB1|Herc5	hect domain and RLD 6	protein-coding
mm_1253.1	chr1	62818242	62818263	+	1	NA	3' UTR (NM_010939, exon 16 of 16)	3' UTR (NM_010939, exon 16 of 16)	-23520	NR_040601	74992	Mm.401979	NR_040601		4930487H11Rik	-	RIKEN cDNA 4930487H11 gene	ncRNA
mm_93693.1	chr10	117844315	117844322	-	1	NA	intron (NM_024457, intron 1 of 7)	intron (NM_024457, intron 1 of 7)	1656	NM_024457	215449	Mm.233009	NM_024457	ENSMUSG00000052681	Rap1b	2810443E11Rik	RAS related protein 1b	protein-coding
mm_44579.1	chr5	24842552	24842571	-	1	NA	promoter-TSS (NM_053075)	promoter-TSS (NM_053075)	-200	NM_053075	19744	Mm.319175	NM_053075	ENSMUSG00000028945	Rheb	Rheb1	Ras homolog enriched in brain	protein-coding
mm_162281.1	chr1	20356415	20356421	+	1	NA	promoter-TSS (NR_045734)	promoter-TSS (NR_045734)	-36	NR_045734	75028	Mm.417820	NR_045734	ENSMUSG00000089914	4930486I03Rik	-	RIKEN cDNA 4930486I03 gene	ncRNA
mm_38999.1	chr4	151853265	151853268	-	1	NA	intron (NM_001081557, intron 1 of 23)	intron (NM_001081557, intron 1 of 23)	8502	NM_001081557	100072	Mm.318846	NM_001081557	ENSMUSG00000014592	Camta1	1810059M14Rik|2310058O09Rik|AI316882|AW987475|mKIAA0833	calmodulin binding transcription activator 1	protein-coding
mm_141655.1	chr17	33713354	33713364	-	1	NA	intron (NR_045522, intron 1 of 6)	intron (NR_045522, intron 1 of 6)	5318	NM_145486	224703	Mm.311439	NM_145486	ENSMUSG00000079557	March2	9530046H09Rik|MARCH-II	membrane-associated ring finger (C3HC4) 2	protein-coding
mm_123419.1	chr14	64413499	64413501	-	1	NA	intron (NM_001253712, intron 1 of 5)	intron (NM_001253712, intron 1 of 5)	3456	NM_001253716	110265	Mm.26713	NM_026322	ENSMUSG00000054733	Msra	2310045J23Rik|6530413P12Rik|MSR-A	methionine sulfoxide reductase A	protein-coding
mm_25204.1	chr3	103803634	103803642	+	1	NA	exon (NM_133865, exon 4 of 4)	exon (NM_133865, exon 4 of 4)	509	NR_040412	100503157	Mm.445554	NR_040412	ENSMUSG00000084997	Gm15471	OTTMUSG00000022448	predicted gene 15471	ncRNA
mm_70530.1	chr8	13031930	13031950	+	1	NA	intron (NM_010172, intron 4 of 7)	intron (NM_010172, intron 4 of 7)	-5368	NM_007972	14058	Mm.262589	NM_007972	ENSMUSG00000031444	F10	Cf10|fX	coagulation factor X	protein-coding
mm_90303.1	chr10	126928469	126928483	+	1	NA	Intergenic	CpG	-27105	NM_001159559	68876	Mm.276769	NM_026858	ENSMUSG00000025436	Xrcc6bp1	1110068E08Rik|2410012H02Rik|Atp23	XRCC6 binding protein 1	protein-coding
mm_83566.1	chr9	46315922	46315948	-	1	NA	5' UTR (NM_183104, exon 3 of 13)	5' UTR (NM_183104, exon 3 of 13)	4051	NM_183104	74361	Mm.159169	NM_183104	ENSMUSG00000056617	4931429L15Rik	-	RIKEN cDNA 4931429L15 gene	protein-coding
mm_157692.1	chrX	60403948	60404015	-	1	NA	promoter-TSS (NM_001001798)	promoter-TSS (NM_001001798)	0	NM_001001798	320940	Mm.490394	NM_001001798	ENSMUSG00000062949	Atp11c	A330005H02Rik|AI315324|Ig	ATPase, class VI, type 11C	protein-coding
mm_104641.1	chr11	97533161	97533163	-	1	NA	exon (NM_018873, exon 11 of 20)	exon (NM_018873, exon 11 of 20)	-32822	NM_001289118	100141474	Mm.482426	NM_001289118	ENSMUSG00000047988	4933428G20Rik	-	RIKEN cDNA 4933428G20 gene	protein-coding
mm_114117.1	chr13	55016785	55016801	+	1	NA	intron (NM_001206392, intron 1 of 17)	intron (NM_001206392, intron 1 of 17)	4026	NM_001206390	212032	Mm.267479	NM_001033245	ENSMUSG00000025877	Hk3	HK III|HK-III	hexokinase 3	protein-coding
mm_52130.1	chr6	97944343	97944353	+	1	NA	intron (NM_001113198, intron 2 of 9)	intron (NM_001113198, intron 2 of 9)	14531	NM_001178049	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_70717.1	chr8	15086240	15086246	+	1	NA	intron (NM_008664, intron 13 of 36)	RSINE1|SINE|B4	28590	NM_008664	17930	Mm.272115	NM_008664	ENSMUSG00000031461	Myom2	AW146149	myomesin 2	protein-coding
mm_59840.1	chr7	29519159	29519169	+	1	NA	Intergenic	CpG	-13704	NM_001081028	74206	Mm.447042	NM_001081028	ENSMUSG00000030583	Sipa1l3	2610511M17Rik	signal-induced proliferation-associated 1 like 3	protein-coding
mm_51769.1	chr6	88048073	88048088	+	1	NA	Intergenic	Intergenic	-2810	NM_009005	19349	Mm.333233	NM_009005	ENSMUSG00000079477	Rab7	Rab7a	RAB7, member RAS oncogene family	protein-coding
mm_39524.1	chr5	21265551	21265564	+	1	NA	intron (NM_175437, intron 19 of 30)	intron (NM_175437, intron 19 of 30)	79290	NM_175437	212167	Mm.121705	NM_175437	ENSMUSG00000039934	Gsap	A530088I07Rik|Pion	gamma-secretase activating protein	protein-coding
mm_75091.1	chr8	34055899	34055909	-	1	NA	Intergenic	Intergenic	51910	NM_001293758	22428	Mm.150373	NM_011722	ENSMUSG00000031516	Dctn6	AU044699|WS-3|p27	dynactin 6	protein-coding
mm_2309.1	chr1	91541075	91541089	+	1	NA	promoter-TSS (NM_023046)	promoter-TSS (NM_023046)	2	NM_023046	65247	Mm.234152	NM_023046	ENSMUSG00000026311	Asb1	1700029O08Rik|1700054C17Rik|AI426616|AI851378|mKIAA1146	ankyrin repeat and SOCS box-containing 1	protein-coding
mm_102200.1	chr11	54726799	54726844	-	1	NA	intron (NM_178626, intron 3 of 5)	intron (NM_178626, intron 3 of 5)	60882	NM_178626	72729	Mm.29476	NM_178626	ENSMUSG00000052298	Cdc42se2	2810404F18Rik|AA408783|AA536669|SPEC2	CDC42 small effector 2	protein-coding
mm_29964.1	chr3	133464944	133464947	-	1	NA	3' UTR (NM_001346736, exon 12 of 12)	3' UTR (NM_001346736, exon 12 of 12)	79445	NM_001346736	214133	Mm.347816	NM_145989	ENSMUSG00000040943	Tet2	Ayu17-449|E130014J05Rik|mKIAA1546	tet methylcytosine dioxygenase 2	protein-coding
mm_78421.1	chr9	31041888	31041888	+	1	NA	intron (NM_172765, intron 1 of 5)	intron (NM_172765, intron 1 of 5)	11244	NM_172765	235132	Mm.239355	NM_172765	ENSMUSG00000047412	Zbtb44	6030404E16Rik|Btbd15|E230011F09	zinc finger and BTB domain containing 44	protein-coding
mm_53866.1	chr6	149328530	149328563	+	1	NA	exon (NM_001289662, exon 3 of 5)	exon (NM_001289662, exon 3 of 5)	19132	NM_001289662	67246	Mm.333515	NM_026054	ENSMUSG00000032712	2810474O19Rik	6720435I21Rik|AA536804|AU020969|GET|Kiaa1551	RIKEN cDNA 2810474O19 gene	protein-coding
mm_114378.1	chr13	63239552	63239576	+	1	NA	promoter-TSS (NR_110521)	promoter-TSS (NR_110521)	-465	NR_110520	72061	Mm.188105	NM_028079	ENSMUSG00000021458	2010111I01Rik	2300006M17Rik|AP-O|AW742919|Aopep|ApO|mir-23b|mir-24-1|mir-27b	RIKEN cDNA 2010111I01 gene	protein-coding
mm_146760.1	chr18	16808765	16808850	-	1	NA	5' UTR (NM_007664, exon 1 of 16)	5' UTR (NM_007664, exon 1 of 16)	439	NM_007664	12558	Mm.257437	NM_007664	ENSMUSG00000024304	Cdh2	CDHN|N-CAD|Ncad	cadherin 2	protein-coding
mm_83620.1	chr9	48822099	48822101	-	1	NA	intron (NM_001033324, intron 2 of 6)	intron (NM_001033324, intron 2 of 6)	13845	NM_001033324	235320	Mm.457803	NM_001033324	ENSMUSG00000066687	Zbtb16	AI467657|PLZF|Zfp145|lu	zinc finger and BTB domain containing 16	protein-coding
mm_34190.1	chr4	140701834	140701839	+	1	NA	intron (NM_173867, intron 1 of 12)	CpG	363	NM_173867	108911	Mm.253	NM_173867	ENSMUSG00000040945	Rcc2	2610510H01Rik|2610529N02Rik|AA536646|AA675016|Td60|mKIAA1470	regulator of chromosome condensation 2	protein-coding
mm_94929.1	chr11	29692313	29692328	+	1	NA	promoter-TSS (NM_194054)	promoter-TSS (NM_194054)	-578	NM_194053	68585	Mm.192580	NM_024226	ENSMUSG00000020458	Rtn4	1110020G17Rik|AA407876|AA409940|AA960376|ASY|C130026I10Rik|NOGO|NSP-CL|NgA|Nogo-A|Nogo-B|Nogo-C|mKIAA0886|mKIAA4153	reticulon 4	protein-coding
mm_166129.1	chr4	155111290	155111292	+	1	NA	intron (NM_001081100, intron 9 of 13)	intron (NM_001081100, intron 9 of 13)	24714	NM_001081100	76866	Mm.200590	NM_001081100	ENSMUSG00000029049	Morn1	2900057D20Rik|4930417P05Rik|AU042805	MORN repeat containing 1	protein-coding
mm_92501.1	chr10	78352098	78352114	-	1	NA	promoter-TSS (NM_053014)	promoter-TSS (NM_053014)	-406	NM_053014	28169	Mm.141230	NM_053014	ENSMUSG00000001211	Agpat3	AW061257|AW493985|D10Jhu12e|lpaat3	1-acylglycerol-3-phosphate O-acyltransferase 3	protein-coding
mm_171639.1	chr4	24200906	24200909	+	1	NA	Intergenic	L1Md_T|LINE|L1	-295555	NM_199467	212377	Mm.120919	NM_199467	ENSMUSG00000045751	Mms22l	F730047E07Rik|Gm134	MMS22-like, DNA repair protein	protein-coding
mm_61476.1	chr7	75642723	75642764	+	1	NA	intron (NM_029332, intron 8 of 36)	intron (NM_029332, intron 8 of 36)	187209	NM_029332	75547	Mm.216107	NM_029332	ENSMUSG00000066406	Akap13	1700026G02Rik|5730522G15Rik|5830460E08Rik|AKAP-13|AKAP-Lbc|BRX|Ht31|LBC|PROTO-LB|PROTO-LBC	A kinase (PRKA) anchor protein 13	protein-coding
mm_135582.1	chr16	50529556	50529569	-	1	NA	intron (NR_040379, intron 1 of 5)	CpG	1060	NR_040379	619312	Mm.427671	NR_040379		G730013B05Rik	linc-Cblb|linc1610	RIKEN cDNA G730013B05 gene	ncRNA
mm_109050.1	chr12	104339196	104339237	+	1	NA	intron (NM_011458, intron 1 of 4)	intron (NM_011458, intron 1 of 4)	730	NM_011458	20714	Mm.291569	NM_011458	ENSMUSG00000058207	Serpina3k	1300001I07Rik|D12Rp54|MMCM2|MMSpi2|RP54|Spi-2|Spi2|contrapsin	serine (or cysteine) peptidase inhibitor, clade A, member 3K	protein-coding
mm_91870.1	chr10	59469501	59469509	-	1	NA	intron (NM_001033259, intron 2 of 7)	L1MEf|LINE|L1	-27726	NM_010959	18302	Mm.123013	NM_010959	ENSMUSG00000009654	Oit3	EF-9|LZP	oncoprotein induced transcript 3	protein-coding
mm_170721.1	chr2	148875496	148875496	-	1	NA	promoter-TSS (NM_009976)	promoter-TSS (NM_009976)	16	NM_009976	13010	Mm.4263	NM_009976	ENSMUSG00000027447	Cst3	CysC	cystatin C	protein-coding
mm_164919.1	chr18	75930398	75930401	+	1	NA	intron (NM_145356, intron 2 of 4)	intron (NM_145356, intron 2 of 4)	110221	NM_145356	207259	Mm.159332	NM_145356	ENSMUSG00000044646	Zbtb7c	B230208J24Rik|Kr-pok|Zbtb36	zinc finger and BTB domain containing 7C	protein-coding
mm_47588.1	chr5	124861958	124861964	-	1	NA	promoter-TSS (NM_001081750)	promoter-TSS (NM_001081750)	260	NM_144819	215707	Mm.389693	NM_144819	ENSMUSG00000037979	Ccdc92	AW050178|D5Bwg0834e	coiled-coil domain containing 92	protein-coding
mm_61749.1	chr7	82755723	82755728	+	1	NA	promoter-TSS (NR_046004)	promoter-TSS (NR_046004)	-81	NR_046004	77800	Mm.444811	NR_046004	ENSMUSG00000086690	4933406J10Rik	A930009F24Rik	RIKEN cDNA 4933406J10 gene	ncRNA
mm_159515.1	chr4	60139991	60139991	-	1	NA	promoter-TSS (NM_001286096).3	promoter-TSS (NM_001286096).3	-133	NM_001200004	100039150	Mm.237772	NM_001200004	ENSMUSG00000096674	Mup15	Gm2068|Mup13	major urinary protein 15	protein-coding
mm_124044.1	chr14	77036927	77036953	-	1	NA	promoter-TSS (NM_172488)	promoter-TSS (NM_172488)	168	NM_001310649	108811	Mm.102168	NM_175369	ENSMUSG00000034795	Ccdc122	4933415L06Rik	coiled-coil domain containing 122	protein-coding
mm_59734.1	chr7	28810929	28810951	+	1	NA	promoter-TSS (NM_177301)	promoter-TSS (NM_177301)	50	NM_177301	15388	Mm.9043	NM_177301	ENSMUSG00000015165	Hnrnpl	C79783|D830027H13Rik|Hnrpl	heterogeneous nuclear ribonucleoprotein L	protein-coding
mm_113320.1	chr13	30764878	30764888	+	1	NA	3' UTR (NM_013674, exon 9 of 9)	3' UTR (NM_013674, exon 9 of 9)	15650	NM_013674	16364	Mm.4677	NM_013674	ENSMUSG00000021356	Irf4	AI385587|IRF-4|LSIRF|NF-EM5|Spip	interferon regulatory factor 4	protein-coding
mm_76836.1	chr8	105281426	105281440	-	1	NA	3' UTR (NM_028888, exon 8 of 8)	3' UTR (NM_028888, exon 8 of 8)	4986	NM_030152	78688	Mm.475715	NM_030152	ENSMUSG00000014776	Nol3	ARC|B430311C09Rik|MYC|NOP|Nop30	nucleolar protein 3 (apoptosis repressor with CARD domain)	protein-coding
mm_2251.1	chr1	91068548	91068574	+	1	NA	intron (NM_001310732, intron 1 of 24)	intron (NM_001310732, intron 1 of 24)	15117	NM_008515	16978	Mm.45039	NM_008515	ENSMUSG00000026305	Lrrfip1	AU024550|Fliiap1	leucine rich repeat (in FLII) interacting protein 1	protein-coding
mm_145166.1	chr18	46741904	46741930	+	1	NA	promoter-TSS (NM_026217)	promoter-TSS (NM_026217)	41	NM_001303015	11777	Mm.312536	NM_009681	ENSMUSG00000024480	Ap3s1	-	adaptor-related protein complex 3, sigma 1 subunit	protein-coding
mm_22870.1	chr3	28986640	28986642	+	1	NA	Intergenic	Intergenic	94024	NM_001033479	385263	Mm.60893	NM_001033479	ENSMUSG00000074655	Gm1527	Gm1136	predicted gene 1527	protein-coding
mm_31055.1	chr4	41190980	41191010	+	1	NA	3' UTR (NM_026275, exon 5 of 5)	3' UTR (NM_026275, exon 5 of 5)	54974	NM_026275	67615	Mm.389540	NM_026275	ENSMUSG00000036241	Ube2r2	1200003M11Rik|Cdc34b|Ubc3b	ubiquitin-conjugating enzyme E2R 2	protein-coding
mm_56745.1	chr6	115853347	115853389	-	1	NA	promoter-TSS (NM_031177)	promoter-TSS (NM_031177)	-27	NM_010774	17193	Mm.259308	NM_010774	ENSMUSG00000030322	Mbd4	Med1	methyl-CpG binding domain protein 4	protein-coding
mm_129.1	chr1	9932093	9932107	+	1	NA	exon (NM_177722, exon 12 of 15)	exon (NM_177722, exon 12 of 15)	10443	NR_004410	266793		NR_004410	ENSMUSG00000093178	Snord87	MBII-276|Rnu87|U87	small nucleolar RNA, C/D box 87	snoRNA
mm_37651.1	chr4	128806104	128806167	-	1	NA	promoter-TSS (NM_001081098)	promoter-TSS (NM_001081098)	-23	NM_001081098	230761	Mm.22616	NM_001081098	ENSMUSG00000028799	Zfp362	-	zinc finger protein 362	protein-coding
mm_31497.1	chr4	53246185	53246202	+	1	NA	promoter-TSS (NR_040665)	promoter-TSS (NR_040665)	-3	NR_040665	78180	Mm.243847	NR_040665	ENSMUSG00000086947	4930522O17Rik	-	RIKEN cDNA 4930522O17 gene	ncRNA
mm_83548.1	chr9	46241519	46241599	-	1	NA	exon (NM_007468, exon 2 of 3)	exon (NM_007468, exon 2 of 3)	715	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_73479.1	chr8	107013928	107013973	+	1	NA	3' UTR (NM_009229, exon 7 of 7)	3' UTR (NM_009229, exon 7 of 7)	-17376	NM_126165	116733	Mm.236004	NM_126165	ENSMUSG00000031913	Vps4a	4930589C15Rik|AI325971|AW553189	vacuolar protein sorting 4A	protein-coding
mm_96660.1	chr11	69405179	69405195	+	1	NA	exon (NM_001017426, exon 11 of 23)	exon (NM_001017426, exon 11 of 23)	-6953	NM_025915	67020	Mm.390406	NM_025915	ENSMUSG00000045377	Tmem88	2600017H02Rik	transmembrane protein 88	protein-coding
mm_60662.1	chr7	44997609	44997619	+	1	NA	promoter-TSS (NM_016849)	promoter-TSS (NM_016849)	-34	NR_045611	54131	Mm.3960	NM_016849	ENSMUSG00000003184	Irf3	C920001K05Rik|IRF-3	interferon regulatory factor 3	protein-coding
mm_124264.1	chr14	102979747	102979766	-	1	NA	3' UTR (NM_177715, exon 1 of 1)	3' UTR (NM_177715, exon 1 of 1)	2876	NR_039592	100628599		NR_039592	ENSMUSG00000092901	Mir5130	mir-5130|mmu-mir-5130|mu-mir-5130	microRNA 5130	ncRNA
mm_109825.1	chr12	3862332	3862342	-	1	NA	promoter-TSS (NR_045884)	promoter-TSS (NR_045884)	-93	NR_045884	100038522	Mm.417270	NR_045884	ENSMUSG00000073242	Dnmt3aos	ENSMUSG00000073242|Gm10485	DNA methyltransferase 3A, opposite strand	ncRNA
mm_77061.1	chr8	109693216	109693226	-	1	NA	promoter-TSS (NM_028018)	promoter-TSS (NM_028018)	73	NM_028018	71955	Mm.290036	NM_028018	ENSMUSG00000031729	Ist1	2400003C14Rik|AW536298|mKIAA0174	increased sodium tolerance 1 homolog (yeast)	protein-coding
mm_123531.1	chr14	66804873	66804890	-	1	NA	3' UTR (NM_009955, exon 14 of 14)	3' UTR (NM_009955, exon 14 of 14)	63719	NM_009955	12934	Mm.352648	NM_009955	ENSMUSG00000022048	Dpysl2	AI851130|Crmp2|DRP2|Musunc33|TOAD-64|Ulip2	dihydropyrimidinase-like 2	protein-coding
mm_126396.1	chr15	80212113	80212137	+	1	NA	exon (NM_010795, exon 2 of 2)	exon (NM_010795, exon 2 of 2)	-21955	NM_178719	239555	Mm.307163	NM_178719	ENSMUSG00000022412	Mief1	A230016E22|AI452372|Smcr7l	mitochondrial elongation factor 1	protein-coding
mm_122197.1	chr14	31781424	31781440	-	1	NA	intron (NM_001024604, intron 1 of 27)	intron (NM_001024604, intron 1 of 27)	48983	NM_001024604	105522	Mm.37660	NM_001024604	ENSMUSG00000014496	Ankrd28	AI465466|AI604979|E430019N21Rik|mKIAA0379	ankyrin repeat domain 28	protein-coding
mm_83371.1	chr9	44479753	44479780	-	1	NA	Intergenic	Intergenic	-19370	NM_030256	80288	Mm.370270	NM_030256	ENSMUSG00000063382	Bcl9l	B9L|BC003321|BCL9-2|DLNB11	B cell CLL/lymphoma 9-like	protein-coding
mm_134309.1	chr16	15863264	15863273	-	1	NA	promoter-TSS (NM_029354)	promoter-TSS (NM_029354)	54	NM_029354	72083	Mm.22351	NM_029354	ENSMUSG00000022671	Mzt2	2410018G20Rik|2610001E06Rik|Fam128|Fam128b	mitotic spindle organizing protein 2	protein-coding
mm_75671.1	chr8	67833875	67833877	-	1	NA	intron (NM_030263, intron 6 of 12)	intron (NM_030263, intron 6 of 12)	-15581	NM_027626	234353	Mm.32525	NM_027626	ENSMUSG00000030465	Psd3	4931420C21Rik|AI661273|BC003498|D430018P08|EFA6D	pleckstrin and Sec7 domain containing 3	protein-coding
mm_44242.1	chr5	5314612	5314624	-	1	NA	intron (NM_011074, intron 2 of 14)	intron (NM_011074, intron 2 of 14)	-48550	NM_001310448	18647	Mm.389061	NM_011074	ENSMUSG00000028926	Cdk14	Pftk1|mKIAA0834	cyclin-dependent kinase 14	protein-coding
mm_52121.1	chr6	97941142	97941153	+	1	NA	exon (NM_001178049, exon 2 of 10)	exon (NM_001178049, exon 2 of 10)	11330	NM_001178049	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_111578.1	chr12	101819024	101819034	-	1	NA	promoter-TSS (NM_011812)	promoter-TSS (NM_011812)	90	NM_011812	23876	Mm.288381	NM_011812	ENSMUSG00000021186	Fbln5	A55|DANCE|EVEC	fibulin 5	protein-coding
mm_16868.1	chr2	12128536	12128552	-	1	NA	intron (NR_138462, intron 28 of 30)	intron (NR_138462, intron 28 of 30)	-172702	NR_040353	338535	Mm.483275	NR_040353	ENSMUSG00000086843	E030013I19Rik	-	RIKEN cDNA E030013I19 gene	ncRNA
mm_93109.1	chr10	91082705	91082773	-	1	NA	promoter-TSS (NM_026166)	promoter-TSS (NM_026166)	4	NM_001042558	11783	Mm.220289	NM_009684	ENSMUSG00000019979	Apaf1	6230400I06Rik|Apaf-1|Apaf1l|fog|mKIAA0413	apoptotic peptidase activating factor 1	protein-coding
mm_118054.1	chr13	101759663	101759666	-	1	NA	intron (NM_001077495, intron 1 of 15)	intron (NM_001077495, intron 1 of 15)	8553	NM_001077495	18708	Mm.259333	NM_001024955	ENSMUSG00000041417	Pik3r1	PI3K|p50alpha|p55alpha|p85alpha	phosphatidylinositol 3-kinase, regulatory subunit, polypeptide 1 (p85 alpha)	protein-coding
mm_94223.1	chr11	3202909	3202933	+	1	NA	promoter-TSS (NM_001166549)	promoter-TSS (NM_001166549)	-74	NM_001166547	74203	Mm.255649	NM_023743	ENSMUSG00000020454	Eif4enif1	2610509L04Rik|A930019J01Rik|AA410001|AU021239|Clast4|D11Ertd166e	eukaryotic translation initiation factor 4E nuclear import factor 1	protein-coding
mm_148957.1	chr19	7383144	7383160	+	1	NA	promoter-TSS (NM_001033139)	promoter-TSS (NM_001033139)	-126	NM_001167831	68229	Mm.34766	NM_001033139	ENSMUSG00000024970	AI846148	1700105P06Rik	expressed sequence AI846148	protein-coding
mm_172085.1	chr6	145933003	145933023	-	1	NA	intron (NM_001310837, intron 1 of 2)	LSU-rRNA_Hsa|rRNA|rRNA	-1134	NM_010656	16651	Mm.49689	NM_010656	ENSMUSG00000030255	Sspn	Krag	sarcospan	protein-coding
mm_171813.1	chr5	137300357	137300359	-	1	NA	exon (NM_031405, exon 6 of 20)	exon (NM_031405, exon 6 of 20)	-3670	NR_106003	102465627		NR_106003	ENSMUSG00000098624	Mir7036	Gm27973|mmu-mir-7036|mmu-mir-7036a	microRNA 7036	ncRNA
mm_17252.1	chr2	25785675	25785693	-	1	NA	intron (NR_045340, intron 2 of 2)	intron (NR_045340, intron 2 of 2)	1067	NR_045340	620858	Mm.210572	NR_045340	ENSMUSG00000085484	Gm13539	OTTMUSG00000012632	predicted gene 13539	ncRNA
mm_120699.1	chr14	70925892	70925904	+	1	NA	exon (NM_008115, exon 4 of 9)	exon (NM_008115, exon 4 of 9)	35791	NM_001302094	14586	Mm.32619	NM_008115	ENSMUSG00000022103	Gfra2	-	glial cell line derived neurotrophic factor family receptor alpha 2	protein-coding
mm_79305.1	chr9	52047932	52047961	+	1	NA	promoter-TSS (NM_009041)	promoter-TSS (NM_009041)	5	NM_001104617	19684	Mm.245746	NM_009041	ENSMUSG00000032050	Rdx	AA516625	radixin	protein-coding
mm_167160.1	chr7	134883449	134883453	-	1	NA	3' UTR (NM_001143802, exon 4 of 4)	3' UTR (NM_001143802, exon 4 of 4)	54979	NM_001143802	627214	Mm.323610	NM_001143802	ENSMUSG00000073805	Fam196a	B830028B13Rik	family with sequence similarity 196, member A	protein-coding
mm_31482.1	chr4	52440109	52440113	+	1	NA	intron (NM_001301412, intron 1 of 24)	intron (NM_001301412, intron 1 of 24)	890	NM_001301412	14211	Mm.2999	NM_008017	ENSMUSG00000028312	Smc2	5730502P04Rik|AI255214|AW545314|CAP-E|CAPE|Fin16|SMC-2|Smc2l1	structural maintenance of chromosomes 2	protein-coding
mm_53843.1	chr6	148831545	148831558	+	1	NA	promoter-TSS (NM_001081113)	promoter-TSS (NM_001081113)	-84	NM_001081113	320727	Mm.260105	NM_001081113	ENSMUSG00000040029	Ipo8	6230418K12Rik|Abcc10|C130009K11Rik|MRP7|OM-1|Om1|Ranbp8	importin 8	protein-coding
mm_53456.1	chr6	134830146	134830179	+	1	NA	promoter-TSS (NM_177687)	promoter-TSS (NM_177687)	-37	NM_177687	232430	Mm.267010	NM_177687	ENSMUSG00000032652	Crebl2	AI046348|B230205M03	cAMP responsive element binding protein-like 2	protein-coding
mm_144861.1	chr18	36713670	36713718	+	1	NA	Intergenic	Intergenic	13121	NM_009841	12475	Mm.3460	NM_009841	ENSMUSG00000051439	Cd14	-	CD14 antigen	protein-coding
mm_19364.1	chr2	91115746	91115757	-	1	NA	TTS (NM_011355)	TTS (NM_011355)	-2393	NM_008653	17868	Mm.10728	NM_008653	ENSMUSG00000002100	Mybpc3	-	myosin binding protein C, cardiac	protein-coding
mm_160673.1	chr10	7052632	7052632	-	1	NA	Intergenic	Intergenic	-29447	NM_001033391	320495	Mm.331674	NM_001033391	ENSMUSG00000064065	Ipcef1	A130090K04Rik	interaction protein for cytohesin exchange factors 1	protein-coding
mm_64845.1	chr7	13014241	13014274	-	1	NA	Intergenic	Intergenic	-4457	NM_001024699	232879	Mm.279272	NM_001024699	ENSMUSG00000049600	Zbtb45	BB161562|Gm157|Zfp499	zinc finger and BTB domain containing 45	protein-coding
mm_172325.1	chr7	106644672	106644672	-	1	NA	promoter-TSS (NM_001277183)	promoter-TSS (NM_001277183)	-27	NM_001277182	434223	Mm.276443	NM_001277179		Gm1966	-	predicted gene 1966	protein-coding
mm_117918.1	chr13	99433245	99433253	-	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-20423	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_135604.1	chr16	52147392	52147402	-	1	NA	intron (NM_001033238, intron 9 of 17)	intron (NM_001033238, intron 9 of 17)	115848	NM_001033238	208650	Mm.328206	NM_001033238	ENSMUSG00000022637	Cblb	AI429560|AI851073|Cbl-b	Casitas B-lineage lymphoma b	protein-coding
mm_147134.1	chr18	36255150	36255158	-	1	NA	Intergenic	RMER20C_Mm|LTR|ERVK	-26008	NM_008989	19290	Mm.231802	NM_008989	ENSMUSG00000043991	Pura	CAGER-1|Pur-alpha|ssCRE-BP	purine rich element binding protein A	protein-coding
mm_57859.1	chr6	129507178	129507181	-	1	NA	promoter-TSS (NM_138648)	promoter-TSS (NM_138648)	-14	NM_138648	108078	Mm.293626	NM_138648	ENSMUSG00000030162	Olr1	LOX-1|SR-EI|Scare1	oxidized low density lipoprotein (lectin-like) receptor 1	protein-coding
mm_83297.1	chr9	43239818	43239842	-	1	NA	promoter-TSS (NM_178644)	promoter-TSS (NM_178644)	-14	NM_178644	102644	Mm.246479	NM_178644	ENSMUSG00000032014	Oaf	AL024221|D130038B21Rik|D9Ucla1	out at first homolog	protein-coding
mm_8499.1	chr1	153899728	153899742	-	1	NA	promoter-TSS (NM_008131)	promoter-TSS (NM_008131)	-191	NR_106194	102466257		NR_106194	ENSMUSG00000099227	Mir8114	Gm27382|mmu-mir-8114	microRNA 8114	ncRNA
mm_3604.1	chr1	151632351	151632353	+	1	NA	intron (NM_022018, intron 1 of 13)	intron (NM_022018, intron 1 of 13)	60979	NM_022018	63913	Mm.157700	NM_022018	ENSMUSG00000026483	Fam129a	AI256368|AU019833|Niban	family with sequence similarity 129, member A	protein-coding
mm_97833.1	chr11	83064520	83064540	+	1	NA	promoter-TSS (NM_011408)	promoter-TSS (NM_011408)	-582	NM_011408	20556	Mm.278689	NM_011408	ENSMUSG00000072620	Slfn2	Shlf2	schlafen 2	protein-coding
mm_57937.1	chr6	134791343	134791367	-	1	NA	intron (NM_001048054, intron 1 of 6)	intron (NM_001048054, intron 1 of 6)	1273	NM_130447	70686	Mm.491182	NM_130447	ENSMUSG00000030203	Dusp16	3830417M17Rik|AW558566|D6Ertd213e|MKP-7|MKP7|Mkpm	dual specificity phosphatase 16	protein-coding
mm_71164.1	chr8	40518826	40518869	+	1	NA	intron (NM_033560, intron 1 of 11)	ORR1F|LTR|ERVL-MaLR	-3000	NM_001271542	18983	Mm.272551	NM_011135	ENSMUSG00000031601	Cnot7	AU022737|CAF-1|Caf1|Pop2	CCR4-NOT transcription complex, subunit 7	protein-coding
mm_53556.1	chr6	136924032	136924052	+	1	NA	3' UTR (NM_007486, exon 6 of 6)	3' UTR (NM_007486, exon 6 of 6)	-1862	NM_026983	69187	Mm.33692	NM_026983	ENSMUSG00000030219	Erp27	1810033M07Rik|1810047B09Rik	endoplasmic reticulum protein 27	protein-coding
mm_27464.1	chr3	52198061	52198073	-	1	NA	Intergenic	Intergenic	-70270	NM_019739	56458	Mm.29891	NM_019739	ENSMUSG00000044167	Foxo1	AI876417|Afxh|FKHR|Fkhr1|Foxo1a	forkhead box O1	protein-coding
mm_137908.1	chr17	32036400	32036453	+	1	NA	5' UTR (NM_028244, exon 1 of 16)	5' UTR (NM_028244, exon 1 of 16)	264	NM_028244	72462	Mm.102761	NM_028244	ENSMUSG00000058392	Rrp1b	2600005C20Rik|D030064A17|Kiaa0179|mKIAA0179	ribosomal RNA processing 1 homolog B (S. cerevisiae)	protein-coding
mm_138815.1	chr17	39847019	39847059	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	4042	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_142661.1	chr17	47690893	47690897	-	1	NA	non-coding (NR_045945, exon 3 of 3)	non-coding (NR_045945, exon 3 of 3)	-2509	NM_001164729	66119	Mm.89912	NM_025365	ENSMUSG00000033475	Tomm6	1110002E23Rik|AI663970	translocase of outer mitochondrial membrane 6 homolog (yeast)	protein-coding
mm_113222.1	chr13	27059433	27059439	+	1	NA	exon (NM_011164, exon 2 of 5)	exon (NM_011164, exon 2 of 5)	1866	NM_011164	19109	Mm.1270	NM_011164	ENSMUSG00000021342	Prl	AV290867|Gha1|Prl1a1	prolactin	protein-coding
mm_3003.1	chr1	133256083	133256099	+	1	NA	intron (NR_037984, intron 3 of 3)	intron (NR_037984, intron 3 of 3)	9994	NM_182930	240753	Mm.253559	NM_182930	ENSMUSG00000041757	Plekha6	9530028L01Rik|AU042621|Pepp3	pleckstrin homology domain containing, family A member 6	protein-coding
mm_4881.1	chr1	187981767	187981770	+	1	NA	intron (NM_001243792, intron 2 of 7)	intron (NM_001243792, intron 2 of 7)	-16059	NM_011935	26381	Mm.89989	NM_011935	ENSMUSG00000026610	Esrrg	ERR3|Errg|NR3B3|mKIAA0832	estrogen-related receptor gamma	protein-coding
mm_38036.1	chr4	133887766	133887804	-	1	NA	promoter-TSS (NM_009097)	promoter-TSS (NM_009097)	12	NM_001285505	20111	Mm.301827	NM_009097	ENSMUSG00000003644	Rps6ka1	Mapkapk-1a|Rsk|Rsk-1|Rsk1|S6K-alpha-1|p90-Rsk1|p90Rsk1|p90S6K|p90rsk	ribosomal protein S6 kinase polypeptide 1	protein-coding
mm_110678.1	chr12	66560953	66560981	-	1	NA	intron (NM_001193266, intron 9 of 16)	intron (NM_001193266, intron 9 of 16)	-276566	NM_001162933	238217	Mm.188575	NM_001162933	ENSMUSG00000060499	Rpl10l	EG238217	ribosomal protein L10-like	protein-coding
mm_109991.1	chr12	15051619	15051635	-	1	NA	Intergenic	Intergenic	-1238	NR_045960	73972	Mm.107680	NR_045960		4930448C13Rik	-	RIKEN cDNA 4930448C13 gene	ncRNA
mm_89340.1	chr10	87935209	87935217	+	1	NA	3' UTR (NM_010512, exon 5 of 5)	3' UTR (NM_010512, exon 5 of 5)	-31458	NR_000040	22172	Mm.391420	NR_000040		Tyms-ps	-	thymidylate synthase, pseudogene	pseudo
mm_64717.1	chr7	4656095	4656123	-	1	NA	intron (NM_172894, intron 1 of 23)	intron (NM_172894, intron 1 of 23)	2841	NM_172894	243819	Mm.258670	NM_172894	ENSMUSG00000052296	Ppp6r1	2010309P17Rik|AI836219|B430201G11Rik|D030074N20Rik|Pp6r1|Saps1|mKIAA1115	protein phosphatase 6, regulatory subunit 1	protein-coding
mm_150609.1	chr19	40840722	40840758	+	1	NA	intron (NM_172839, intron 3 of 5)	intron (NM_172839, intron 3 of 5)	9461	NM_172839	240665	Mm.309	NM_172839	ENSMUSG00000025010	Ccnj	D430039C20Rik	cyclin J	protein-coding
mm_164293.1	chr15	103895936	103895952	-	1	NA	TTS (NM_009267)	TTS (NM_009267)	3356	NM_009268	20771	Mm.30276	NM_009268		Mucl1	Spt-2|Spt2	mucin-like 1	protein-coding
mm_19183.1	chr2	84405371	84405396	-	1	NA	intron (NM_018782, intron 2 of 15)	intron (NM_018782, intron 2 of 15)	19883	NM_018782	54598	Mm.75467	NM_018782	ENSMUSG00000059588	Calcrl	AV071593|CRLR	calcitonin receptor-like	protein-coding
mm_141540.1	chr17	31858054	31858069	-	1	NA	Intergenic	Intergenic	-2269	NM_010831	17691	Mm.290941	NM_010831	ENSMUSG00000024042	Sik1	Msk|Sik|Snf1lk	salt inducible kinase 1	protein-coding
mm_34287.1	chr4	141546142	141546202	+	1	NA	promoter-TSS (NR_030695)	promoter-TSS (NR_030695)	10	NR_030695	320456	Mm.32859	NM_177163		B330016D10Rik	-	RIKEN cDNA B330016D10 gene	ncRNA
mm_34750.1	chr4	152297330	152297368	+	1	NA	non-coding (NR_037908, exon 1 of 6)	non-coding (NR_037908, exon 1 of 6)	135	NM_133788	57295	Mm.277464	NM_133788	ENSMUSG00000039662	Icmt	1700008E11Rik|C80758|Gm13095|HSTE14|OTTMUSG00000010406|PPMT|STE14|pcCMT	isoprenylcysteine carboxyl methyltransferase	protein-coding
mm_78689.1	chr9	40802367	40802369	+	1	NA	intron (NM_031165, intron 2 of 8)	intron (NM_031165, intron 2 of 8)	1095	NM_031165	15481	Mm.290774	NM_031165	ENSMUSG00000015656	Hspa8	2410008N15Rik|Hsc70|Hsc71|Hsc73|Hsp73|Hspa10	heat shock protein 8	protein-coding
mm_13481.1	chr2	106080994	106081004	+	1	NA	Intergenic	Intergenic	-77450	NR_033993	99349	Mm.25661	NM_026992	ENSMUSG00000027166	Dnajc24	1700030A21Rik|2610027M02Rik|AV066965|AW240712|Dph4|MmDjC7|Zcsl3	DnaJ heat shock protein family (Hsp40) member C24	protein-coding
mm_82501.1	chr9	20450085	20450087	-	1	NA	intron (NM_011753, intron 2 of 9)	L1_Mur3|LINE|L1	10074	NM_011753	22688	Mm.107441	NM_011753	ENSMUSG00000063108	Zfp26	5033428C05Rik|KRAB15|Zfp-26|Zfp70|Zfp81-rs1|mKIAA4196|mkr-3|mszf14|mszf52	zinc finger protein 26	protein-coding
mm_136477.1	chr16	95901473	95901496	-	1	NA	intron (NR_040484, intron 1 of 3)	intron (NR_040484, intron 1 of 3)	-2771	NR_040485	69776	Mm.120470	NR_040484	ENSMUSG00000086899	1600002D24Rik	-	RIKEN cDNA 1600002D24 gene	ncRNA
mm_31895.1	chr4	83121519	83121525	+	1	NA	Intergenic	Intergenic	-69355	NM_001198811	329872	Mm.242337	NM_177863	ENSMUSG00000059049	Frem1	BC037594|D430009N09|D630008K06|crf11|eye<m02Jus>|eyes2|heb|qbrick	Fras1 related extracellular matrix protein 1	protein-coding
mm_786.1	chr1	45332131	45332142	+	1	NA	exon (NM_009930, exon 20 of 51)	exon (NM_009930, exon 20 of 51)	20598	NM_009930	12825	Mm.249555	NM_009930	ENSMUSG00000026043	Col3a1	AW550625|Col3a-1|Tsk-2|Tsk2	collagen, type III, alpha 1	protein-coding
mm_165474.1	chr2	164290275	164290281	+	1	NA	exon (NM_021363, exon 2 of 3)	exon (NM_021363, exon 2 of 3)	1010	NM_021363	64335	Mm.389393	NM_021363	ENSMUSG00000017003	Svs3a	9530026M05Rik|BB121242|Semg2|Svp-3|Svp3|Svs3	seminal vesicle secretory protein 3A	protein-coding
mm_89642.1	chr10	96640885	96640889	+	1	NA	Intergenic	Intergenic	23886	NM_007569	12226	Mm.23811	NM_007569	ENSMUSG00000036478	Btg1	AI426953|AW546738	B cell translocation gene 1, anti-proliferative	protein-coding
mm_110155.1	chr12	26455603	26455623	-	1	NA	intron (NM_021384, intron 1 of 5)	(CA)n|Simple_repeat|Simple_repeat	839	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_131639.1	chr16	20498848	20498866	+	1	NA	promoter-TSS (NM_172265)	promoter-TSS (NM_172265)	40	NM_172265	224045	Mm.233855	NM_172265	ENSMUSG00000003235	Eif2b5	C81315	eukaryotic translation initiation factor 2B, subunit 5 epsilon	protein-coding
mm_70156.1	chr7	143502755	143502793	-	1	NA	promoter-TSS (NM_009434)	promoter-TSS (NM_009434)	-250	NM_009434	22113	Mm.334344	NM_009434	ENSMUSG00000010760	Phlda2	Ipl|Tssc3	pleckstrin homology like domain, family A, member 2	protein-coding
mm_44806.1	chr5	33274955	33274965	-	1	NA	promoter-TSS (NM_001198861)	promoter-TSS (NM_001198861)	44	NM_001310535	13016	Mm.7286	NM_013502	ENSMUSG00000037373	Ctbp1	BARS|CtBP3/BARS|D4S115h|D5H4S115|D5H4S115E	C-terminal binding protein 1	protein-coding
mm_61943.1	chr7	90183022	90183133	+	1	NA	intron (NM_001252520, intron 13 of 20)	intron (NM_001252520, intron 13 of 20)	52845	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_33507.1	chr4	130913218	130913226	+	1	NA	promoter-TSS (NM_010686)	promoter-TSS (NM_010686)	-112	NM_010686	16792	Mm.271868	NM_010686	ENSMUSG00000028581	Laptm5	E3	lysosomal-associated protein transmembrane 5	protein-coding
mm_173348.1	chrY	90813183	90813183	+	1	NA	intron (NM_133362, intron 2 of 3)	(TTAGGG)n|Simple_repeat|Simple_repeat	26223	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_76939.1	chr8	105940122	105940145	-	1	NA	exon (NM_008490, exon 6 of 6)	exon (NM_008490, exon 6 of 6)	-1741	NM_013640	19171	Mm.787	NM_013640	ENSMUSG00000031897	Psmb10	Mecl-1|Mecl1	proteasome (prosome, macropain) subunit, beta type 10	protein-coding
mm_161408.1	chr15	5243709	5243709	-	1	NA	5' UTR (NM_001136079, exon 1 of 3)	5' UTR (NM_001136079, exon 1 of 3)	478	NM_001136079	19219	Mm.18509	NM_008965	ENSMUSG00000039942	Ptger4	EP4|Ptgerep4	prostaglandin E receptor 4 (subtype EP4)	protein-coding
mm_162503.1	chr1	143908238	143908239	+	1	NA	Intergenic	Intergenic	95911	NM_009061	19735	Mm.28262	NM_009061	ENSMUSG00000026360	Rgs2	GOS8	regulator of G-protein signaling 2	protein-coding
mm_163238.1	chr11	104306718	104306724	+	1	NA	exon (NM_010838, exon 5 of 10)	exon (NM_010838, exon 5 of 10)	75285	NM_001285454	17762	Mm.1287	NM_010838	ENSMUSG00000018411	Mapt	AI413597|AW045860|Mtapt|Tau	microtubule-associated protein tau	protein-coding
mm_132972.1	chr16	52032072	52032126	+	1	NA	intron (NM_001033238, intron 1 of 17)	CpG	550	NM_001033238	208650	Mm.328206	NM_001033238	ENSMUSG00000022637	Cblb	AI429560|AI851073|Cbl-b	Casitas B-lineage lymphoma b	protein-coding
mm_31012.1	chr4	40703270	40703320	+	1	NA	promoter-TSS (NM_025545)	promoter-TSS (NM_025545)	-101	NM_001025445	66408	Mm.430710	NM_025545	ENSMUSG00000028411	Aptx	2410016G21Rik|AA388047|FHA-HIT	aprataxin	protein-coding
mm_63279.1	chr7	126764284	126764295	+	1	NA	exon (NM_011952, exon 6 of 9)	exon (NM_011952, exon 6 of 9)	-2125	NM_024228	68616	Mm.246881	NM_024228	ENSMUSG00000030703	Gdpd3	1110015E22Rik	glycerophosphodiester phosphodiesterase domain containing 3	protein-coding
mm_54420.1	chr6	32962063	32962066	-	1	NA	intron (NM_025336, intron 4 of 7)	intron (NM_025336, intron 4 of 7)	98088	NM_025336	66075	Mm.21501	NM_025336	ENSMUSG00000053768	Chchd3	0610041L09Rik|1700039J09Rik|AW558177	coiled-coil-helix-coiled-coil-helix domain containing 3	protein-coding
mm_4334.1	chr1	171855042	171855060	+	1	NA	TTS (NM_001252472)	TTS (NM_001252472)	15354	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_67895.1	chr7	99482927	99482934	-	1	NA	promoter-TSS (NR_002172)	promoter-TSS (NR_002172)	2	NR_002172	449630	Mm.454449	NR_002172	ENSMUSG00000065822	Snord15a	EG449630|Gm5774|RNU15A|Rnu15-a|U15A	small nucleolar RNA, C/D box 15A	snoRNA
mm_43392.1	chr5	135776627	135776636	+	1	NA	intron (NM_001289556, intron 1 of 7)	intron (NM_001289556, intron 1 of 7)	1670	NM_001289554	76571	Mm.247666	NM_029659	ENSMUSG00000019178	Styxl1	1700011C14Rik|Dusp24|Mkstyx	serine/threonine/tyrosine interacting-like 1	protein-coding
mm_66081.1	chr7	30956743	30956781	-	1	NA	promoter-TSS (NM_011680)	promoter-TSS (NM_011680)	41	NM_011680	22282	Mm.322453	NM_011680	ENSMUSG00000058239	Usf2	Usf-2|bHLHb12	upstream transcription factor 2	protein-coding
mm_49771.1	chr6	34866964	34866972	+	1	NA	intron (NM_197986, intron 1 of 1)	B4|SINE|B4	3822	NM_197986	68487	Mm.248440	NM_197986	ENSMUSG00000057137	Tmem140	1110007F12Rik	transmembrane protein 140	protein-coding
mm_145085.1	chr18	42440976	42440985	+	1	NA	Intergenic	Intergenic	46383	NM_138945	18998	Mm.488204	NM_138945	ENSMUSG00000024497	Pou4f3	Brn3.1|Brn3c|ddl|dreidel	POU domain, class 4, transcription factor 3	protein-coding
mm_151737.1	chr19	4928242	4928259	-	1	NA	promoter-TSS (NM_133803)	promoter-TSS (NM_133803)	37	NM_133803	75221	Mm.234769	NM_133803	ENSMUSG00000063904	Dpp3	4930533O14Rik|C86324	dipeptidylpeptidase 3	protein-coding
mm_150756.1	chr19	43939757	43939759	+	1	NA	intron (NM_028029, intron 1 of 15)	intron (NM_028029, intron 1 of 15)	440	NM_028029	71972	Mm.159024	NM_028029	ENSMUSG00000025195	Dnmbp	2410003L07Rik|2410003M15Rik|TUBA	dynamin binding protein	protein-coding
mm_101630.1	chr11	36181451	36181455	-	1	NA	intron (NM_011856, intron 7 of 28)	Lx8b|LINE|L1	-201364	NM_170779	211652	Mm.31267	NM_170779	ENSMUSG00000018849	Wwc1	AA408228|AU017197|BC037006|Kibra|mKIAA0869	WW, C2 and coiled-coil domain containing 1	protein-coding
mm_164030.1	chr14	77156867	77156875	+	1	NA	5' UTR (NM_172813, exon 1 of 19)	5' UTR (NM_172813, exon 1 of 19)	108	NM_172813	239188	Mm.441158	NM_172813	ENSMUSG00000022012	Enox1	B230207J08|D230005D02Rik	ecto-NOX disulfide-thiol exchanger 1	protein-coding
mm_307.1	chr1	23773260	23773263	+	1	NA	intron (NM_172124, intron 1 of 3)	ORR1B1|LTR|ERVL-MaLR	11335	NM_172124	280645	Mm.471661	NM_172124	ENSMUSG00000026156	B3gat2	GlcAT-S|Glcats	beta-1,3-glucuronyltransferase 2 (glucuronosyltransferase S)	protein-coding
mm_18287.1	chr2	52572554	52572556	-	1	NA	intron (NM_001285426, intron 2 of 13)	ORR1B1-int|LTR|ERVL-MaLR	-13944	NM_001285427	12298	Mm.330223	NM_146123	ENSMUSG00000017412	Cacnb4	3110038O15Rik|Cchb4|lh	calcium channel, voltage-dependent, beta 4 subunit	protein-coding
mm_166629.1	chr6	78466835	78466845	-	1	NA	exon (NM_011260, exon 5 of 6)	exon (NM_011260, exon 5 of 6)	2034	NM_011260	19695	Mm.252385	NM_011260	ENSMUSG00000030017	Reg3g	AI449515|REG-3-gamma|reg III-gamma	regenerating islet-derived 3 gamma	protein-coding
mm_109356.1	chr12	109629073	109629083	+	1	NA	intron (NR_028261, intron 6 of 20)	intron (NR_028261, intron 6 of 20)	-6934	NR_046302	449562		NR_046302	ENSMUSG00000088294	AF357425	MBII-48	snoRNA AF357425	snoRNA
mm_132662.1	chr16	41974742	41974757	+	1	NA	intron (NM_001347236, intron 3 of 6)	MIRc|SINE|MIR	328720	NR_105858	102466172		NR_105858	ENSMUSG00000098300	Mir6540	Gm27780|mir-6540|mmu-mir-6540	microRNA 6540	ncRNA
mm_99148.1	chr11	100553340	100553343	+	1	NA	intron (NM_028918, intron 5 of 11)	intron (NM_028918, intron 5 of 11)	7709	NM_028918	74407	Mm.31590	NM_028918	ENSMUSG00000006784	Ttc25	4933404O19Rik	tetratricopeptide repeat domain 25	protein-coding
mm_45266.1	chr5	64467919	64467923	-	1	NA	promoter-TSS (NR_040681)	promoter-TSS (NR_040681)	21	NR_040681	69999	Mm.261413	NR_040681	ENSMUSG00000100911	1700027F09Rik	-	RIKEN cDNA 1700027F09 gene	ncRNA
mm_60091.1	chr7	34912401	34912415	+	1	NA	promoter-TSS (NM_008820)	promoter-TSS (NM_008820)	1	NM_008820	18624	Mm.69751	NM_008820	ENSMUSG00000063931	Pepd	Pep-4|Pep4|dal	peptidase D	protein-coding
mm_87000.1	chr10	26784412	26784415	+	1	NA	intron (NM_176837, intron 1 of 14)	intron (NM_176837, intron 1 of 14)	11901	NM_176837	73910	Mm.356496	NM_176837	ENSMUSG00000039031	Arhgap18	4833419J07Rik|AI314906|AI843501	Rho GTPase activating protein 18	protein-coding
mm_77990.1	chr9	8134581	8134591	+	1	NA	promoter-TSS (NM_001045524)	promoter-TSS (NM_001045524)	-292	NM_001045524	234915	Mm.101341	NM_001045524	ENSMUSG00000040729	Cep126	Kiaa1377|mKIAA1377	centrosomal protein 126	protein-coding
mm_82868.1	chr9	32422926	32422929	-	1	NA	3' UTR (NM_008026, exon 9 of 9)	3' UTR (NM_008026, exon 9 of 9)	28942	NM_001168354	56379	Mm.390168	NM_019659	ENSMUSG00000041248	Kcnj1	Kir1.1|ROMK|Romk2	potassium inwardly-rectifying channel, subfamily J, member 1	protein-coding
mm_94045.1	chr10	128176624	128176645	-	1	NA	promoter-TSS (NM_019711)	promoter-TSS (NM_019711)	-66	NM_019711	56516	Mm.42247	NM_019711	ENSMUSG00000040043	Rbms2	2610315E04Rik|Scr3	RNA binding motif, single stranded interacting protein 2	protein-coding
mm_917.1	chr1	55052832	55052882	+	1	NA	promoter-TSS (NM_001039710)	promoter-TSS (NM_001039710)	87	NM_001039710	67876	Mm.281019	NM_026424	ENSMUSG00000025981	Coq10b	1500041J02Rik|1700030I21Rik|9530077A17Rik|AV002237|AW742641	coenzyme Q10B	protein-coding
mm_163092.1	chr11	69734731	69734742	-	1	NA	exon (NM_001291068, exon 29 of 29)	exon (NM_001291068, exon 29 of 29)	23897	NM_001291068	20020	Mm.16533	NM_009089	ENSMUSG00000005198	Polr2a	220kDa|Rpb1|Rpo2-1	polymerase (RNA) II (DNA directed) polypeptide A	protein-coding
mm_85922.1	chr9	111461630	111461633	-	1	NA	intron (NM_172928, intron 1 of 4)	intron (NM_172928, intron 1 of 4)	22550	NM_172928	245038	Mm.26361	NM_172928	ENSMUSG00000032500	Dclk3	BC056929|C730036H08|Dcamkl3	doublecortin-like kinase 3	protein-coding
mm_24944.1	chr3	96596629	96596662	+	1	NA	promoter-TSS (NM_001024851)	promoter-TSS (NM_001024851)	9	NM_001024851	545554	Mm.267664	NM_001024851	ENSMUSG00000049097	Ankrd34a	AW060394|Ankrd34	ankyrin repeat domain 34A	protein-coding
mm_43937.1	chr5	145114281	145114300	+	1	NA	promoter-TSS (NM_023142)	promoter-TSS (NM_023142)	34	NM_023142	11867	Mm.30010	NM_023142	ENSMUSG00000029622	Arpc1b	41kDa|AA408064|AA408534|AA571392|AF007010|AW208418|L72|SOP2Hs|p41-ARC	actin related protein 2/3 complex, subunit 1B	protein-coding
mm_44876.1	chr5	34634954	34634958	-	1	NA	exon (NM_026660, exon 8 of 13)	exon (NM_026660, exon 8 of 13)	2158	NM_026660	68294	Mm.34564	NM_026660	ENSMUSG00000001082	Mfsd10	0610009O03Rik|Tetran	major facilitator superfamily domain containing 10	protein-coding
mm_161331.1	chr14	50533564	50533564	+	1	NA	exon (NM_001177508, exon 1 of 1)	exon (NM_001177508, exon 1 of 1)	150	NM_001177508	219019	Mm.480303	NM_001177508	ENSMUSG00000094285	Olfr743	GA_x6K02T2PMLR-6243196-6244132|MOR106-14|MOR106-8P|Olfr264|Olfr264-ps1|Olfr265|Olfr265-ps1|Olfr743-ps1	olfactory receptor 743	protein-coding
mm_105505.1	chr11	106193490	106193501	-	1	NA	5' UTR (NM_001252449, exon 1 of 11)	5' UTR (NM_001252449, exon 1 of 11)	108	NM_001252448	72149	Mm.403722	NM_028126	ENSMUSG00000069631	Strada	2610019A05Rik|6030402H20Rik|AI480680|E130112C09Rik	STE20-related kinase adaptor alpha	protein-coding
mm_165655.1	chr3	85879036	85879038	+	1	NA	intron (NM_177130, intron 1 of 1)	intron (NM_177130, intron 1 of 1)	8481	NM_177130	320302	Mm.482978	NM_177130	ENSMUSG00000031286	Glt28d2	4732486J07Rik|Glt28d1l	glycosyltransferase 28 domain containing 2	protein-coding
mm_66953.1	chr7	62314609	62314612	-	1	NA	Intergenic	L1_Mur2|LINE|L1	-33667	NM_010882	17984	Mm.400253	NM_010882	ENSMUSG00000033585	Ndn	AI528698|Peg6	necdin	protein-coding
mm_146146.1	chr18	74787084	74787100	+	1	NA	intron (NM_177470, intron 1 of 9)	intron (NM_177470, intron 1 of 9)	7880	NM_177470	52538	Mm.245724	NM_177470	ENSMUSG00000036880	Acaa2	0610011L04Rik|AI255831|AI265397|D18Ertd240e	acetyl-Coenzyme A acyltransferase 2 (mitochondrial 3-oxoacyl-Coenzyme A thiolase)	protein-coding
mm_55474.1	chr6	68835331	68835336	-	1	NA	Intergenic	Intergenic	491841	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_133142.1	chr16	69863835	69863840	+	1	NA	promoter-TSS (NM_173069)	promoter-TSS (NM_173069)	-93	NM_173069	224318	Mm.212743	NM_173069	ENSMUSG00000063163	Speer2	SPEER-2	spermatogenesis associated glutamate (E)-rich protein 2	protein-coding
mm_85355.1	chr9	103214413	103214475	-	1	NA	intron (NM_133977, intron 14 of 16)	L2c|LINE|L2	-12379	NM_009275	20818	Mm.273053	NM_009275	ENSMUSG00000032553	Srprb	AA409543	signal recognition particle receptor, B subunit	protein-coding
mm_62211.1	chr7	97870756	97870756	+	1	NA	intron (NM_011035, intron 4 of 14)	intron (NM_011035, intron 4 of 14)	27817	NM_011035	18479	Mm.260227	NM_011035	ENSMUSG00000030774	Pak1	AW045634|PAK-1|Paka	p21 protein (Cdc42/Rac)-activated kinase 1	protein-coding
mm_110637.1	chr12	57546694	57546706	-	1	NA	promoter-TSS (NM_008259)	promoter-TSS (NM_008259)	-579	NM_008259	15375	Mm.4578	NM_008259	ENSMUSG00000035451	Foxa1	Hnf-3a|Hnf3a|Tcf-3a|Tcf3a	forkhead box A1	protein-coding
mm_72024.1	chr8	70755881	70755892	+	1	NA	exon (NM_001166399, exon 2 of 5)	exon (NM_001166399, exon 2 of 5)	1207	NM_001166399	19339	Mm.5083	NM_009001	ENSMUSG00000031840	Rab3a	-	RAB3A, member RAS oncogene family	protein-coding
mm_8715.1	chr1	158980453	158980469	-	1	NA	Intergenic	Intergenic	-23023	NM_001085376	23850	Mm.458621	NM_001085376	ENSMUSG00000073530	Pappa2	PAPP-A2|PLAC3|Pappe	pappalysin 2	protein-coding
mm_120524.1	chr14	66869285	66869289	+	1	NA	promoter-TSS (NM_009955)	promoter-TSS (NM_009955)	437	NM_001034881	432870	Mm.425890	NM_001034881	ENSMUSG00000075553	Gm5464	EG432870	predicted gene 5464	protein-coding
mm_13830.1	chr2	119288800	119288824	+	1	NA	promoter-TSS (NM_172269)	promoter-TSS (NM_172269)	70	NM_172269	228545	Mm.294761	NM_172269	ENSMUSG00000034216	Vps18	9930024E13Rik	VPS18 CORVET/HOPS core subunit	protein-coding
mm_37667.1	chr4	129112090	129112101	-	1	NA	TTS (NM_001290706)	TTS (NM_001290706)	6547	NM_001290706	66260	Mm.25295	NM_025452	ENSMUSG00000028786	Tmem54	1810017F10Rik|AI507302	transmembrane protein 54	protein-coding
mm_147458.1	chr18	46574505	46574518	-	1	NA	promoter-TSS (NM_173394)	promoter-TSS (NM_173394)	22	NM_173394	225471	Mm.149280	NM_173394	ENSMUSG00000056130	Ticam2	B430113A10|TICAM-2|TRAM|Tirp|Trif	toll-like receptor adaptor molecule 2	protein-coding
mm_38255.1	chr4	136785791	136785791	-	1	NA	intron (NM_001290753, intron 1 of 15)	MER2|DNA|TcMar-Tigger	50221	NM_001290753	13844	Mm.250981	NM_010142	ENSMUSG00000028664	Ephb2	Cek5|Drt|ETECK|Erk|Hek5|Nuk|Prkm5|Qek5|Sek3|Tyro5	Eph receptor B2	protein-coding
mm_110.1	chr1	9601337	9601348	+	1	NA	promoter-TSS (NM_178399)	promoter-TSS (NM_178399)	75	NM_178399	76982	Mm.491098	NM_178399	ENSMUSG00000067879	3110035E14Rik	AI415019|AV164974|R75066	RIKEN cDNA 3110035E14 gene	protein-coding
mm_93097.1	chr10	89732254	89732324	-	1	NA	promoter-TSS (NM_025914)	promoter-TSS (NM_025914)	6	NM_025914	67019	Mm.335292	NM_025914	ENSMUSG00000019948	Actr6	2010200J04Rik|AU044443|Arp6|ArpX|CDA12	ARP6 actin-related protein 6	protein-coding
mm_27005.1	chr3	25847362	25847370	-	1	NA	intron (NM_001163387, intron 3 of 5)	intron (NM_001163387, intron 3 of 5)	305941	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_49744.1	chr6	34745971	34745980	+	1	NA	exon (NM_145575, exon 3 of 12)	exon (NM_145575, exon 3 of 12)	-34457	NM_001289657	76223	Mm.150047	NM_178630	ENSMUSG00000038836	Agbl3	2900053G10Rik|4930431N21Rik|6530406M24Rik|CCP3	ATP/GTP binding protein-like 3	protein-coding
mm_13096.1	chr2	91256882	91256895	+	1	NA	promoter-TSS (NM_028733)	promoter-TSS (NM_028733)	75	NM_001289678	80708	Mm.236650	NM_028733	ENSMUSG00000027257	Pacsin3	4921507A02Rik|6330413E15Rik|AW413130	protein kinase C and casein kinase substrate in neurons 3	protein-coding
mm_126574.1	chr15	82256297	82256313	+	1	NA	non-coding (NR_037698, exon 1 of 2)	non-coding (NR_037698, exon 1 of 2)	282	NR_037698	76505	Mm.23023	NR_037697	ENSMUSG00000068099	1500009C09Rik	-	RIKEN cDNA 1500009C09 gene	ncRNA
mm_101357.1	chr11	23740182	23740184	-	1	NA	Intergenic	Intergenic	30787	NM_009044	19696	Mm.4869	NM_009044	ENSMUSG00000020275	Rel	c-Rel	reticuloendotheliosis oncogene	protein-coding
mm_19779.1	chr2	106970368	106970374	-	1	NA	promoter-TSS (NM_173750)	promoter-TSS (NM_173750)	20	NM_173750	212772	Mm.381231	NM_173750	ENSMUSG00000027122	Arl14ep	2700007P21Rik|4930448O08Rik|ARF7EP	ADP-ribosylation factor-like 14 effector protein	protein-coding
mm_76923.1	chr8	105933866	105933874	-	1	NA	promoter-TSS (NM_023182)	promoter-TSS (NM_023182)	-8	NM_023182	109660	Mm.2745	NM_023182	ENSMUSG00000031896	Ctrl	0910001G08Rik|1810004D15Rik|AV005227|Ctra-1|Ctra1|chymopasin|mFLJ00366	chymotrypsin-like	protein-coding
mm_94197.1	chr11	3101246	3101286	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	-22755	NR_003517	236604	Mm.247625	NM_001004146		Pisd-ps1	-	phosphatidylserine decarboxylase, pseudogene 1	pseudo
mm_21813.1	chr2	165234690	165234750	-	1	NA	promoter-TSS (NM_174988)	promoter-TSS (NM_174988)	17	NM_174988	104010	Mm.151819	NM_174988	ENSMUSG00000053166	Cdh22	-	cadherin 22	protein-coding
mm_44792.1	chr5	32354842	32354855	-	1	NA	exon (NM_001081407, exon 56 of 59)	exon (NM_001081407, exon 56 of 59)	1268	NM_172147	665270	Mm.160067	NM_030072	ENSMUSG00000029134	Plb1	4632413E21Rik|4930433E17Rik|4930539A06Rik|BC033606	phospholipase B1	protein-coding
mm_62563.1	chr7	103918958	103918958	+	1	NA	intron (NM_001271020, intron 3 of 3)	B1_Mus2|SINE|Alu	3896	NM_001271020	258961	Mm.438897	NM_146959	ENSMUSG00000042219	Olfr631	MOR3-1	olfactory receptor 631	protein-coding
mm_166777.1	chr6	137545235	137545235	+	1	NA	intron (NM_001271588, intron 1 of 20)	intron (NM_001271588, intron 1 of 20)	-25340	NM_001271589	13860	Mm.235346	NM_007945	ENSMUSG00000015766	Eps8	AW261790	epidermal growth factor receptor pathway substrate 8	protein-coding
mm_157641.1	chrX	57224334	57224338	-	1	NA	TTS (NM_011616)	TTS (NM_011616)	12193	NM_011616	21947	Mm.4861	NM_011616	ENSMUSG00000031132	Cd40lg	CD154|CD40-L|Cd40l|HIGM1|IGM|IMD3|Ly-62|Ly62|T-BAM|TRAP|Tnfsf5|Tnlg8b|gp39	CD40 ligand	protein-coding
mm_86127.1	chr9	116175319	116175329	-	1	NA	promoter-TSS (NM_029575)	promoter-TSS (NM_029575)	39	NM_029575	21813	Mm.172346	NM_009371	ENSMUSG00000032440	Tgfbr2	1110020H15Rik|AU042018|DNIIR|RIIDN|TBR-II|TbetaR-II|TbetaRII	transforming growth factor, beta receptor II	protein-coding
mm_122724.1	chr14	52316114	52316142	-	1	NA	5' UTR (NM_001244916, exon 1 of 2)	5' UTR (NM_001244916, exon 1 of 2)	195	NM_001244916	50524	Mm.39487	NM_015772	ENSMUSG00000049532	Sall2	AI225809|AW559097|Msal-2|Sal-2|mKIAA0360|p150(Sal2)	sal-like 2 (Drosophila)	protein-coding
mm_5889.1	chr1	54195190	54195211	-	1	NA	promoter-TSS (NM_172655)	promoter-TSS (NM_172655)	-166	NM_172655	329152	Mm.132150	NM_172655	ENSMUSG00000042807	Hecw2	A730039N16Rik|D030049F17Rik|Gm971|Nedl2|mKIAA1301	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2	protein-coding
mm_65444.1	chr7	25395534	25395538	-	1	NA	exon (NM_010719, exon 1 of 10)	exon (NM_010719, exon 1 of 10)	451	NM_010719	16890	Mm.158548	NM_010719	ENSMUSG00000003123	Lipe	4933403G17Rik|HSL	lipase, hormone sensitive	protein-coding
mm_105491.1	chr11	106098245	106098251	-	1	NA	intron (NM_011947, intron 2 of 15)	intron (NM_011947, intron 2 of 15)	13346	NM_011947	26406	Mm.27041	NM_011947	ENSMUSG00000020700	Map3k3	AW548911|MAPKKK3|Mekk3|mKIAA4031	mitogen-activated protein kinase kinase kinase 3	protein-coding
mm_12270.1	chr2	68979451	68979473	+	1	NA	intron (NM_172856, intron 3 of 9)	intron (NM_172856, intron 3 of 9)	118021	NM_001347161	241447	Mm.222222	NM_172856	ENSMUSG00000027035	Cers6	4732462C07Rik|AW544719|Lass6|T1L	ceramide synthase 6	protein-coding
mm_22354.1	chr2	180954648	180954670	-	1	NA	promoter-TSS (NM_001141933)	promoter-TSS (NM_001141933)	40	NM_001141933	58237	Mm.40361	NM_021426	ENSMUSG00000027574	Nkain4	AB030182|C030019F02Rik	Na+/K+ transporting ATPase interacting 4	protein-coding
mm_115814.1	chr13	19732731	19732755	-	1	NA	5' UTR (NM_175688, exon 1 of 2)	5' UTR (NM_175688, exon 1 of 2)	208	NM_175688	319293	Mm.246657	NM_175688	ENSMUSG00000047462	A530099J19Rik	-	RIKEN cDNA A530099J19 gene	protein-coding
mm_145188.1	chr18	49772793	49772825	+	1	NA	Intergenic	Intergenic	-17208	NM_001170960	68857	Mm.96010	NM_026854	ENSMUSG00000024505	Dtwd2	1190002H09Rik|8030470C17Rik|AI414673|BB115449	DTW domain containing 2	protein-coding
mm_149276.1	chr19	10605628	10605644	+	1	NA	promoter-TSS (NM_015735)	promoter-TSS (NM_015735)	11	NM_015735	13194	Mm.289915	NM_015735	ENSMUSG00000024740	Ddb1	127kDa|AA408517|p127-Ddb1	damage specific DNA binding protein 1	protein-coding
mm_111760.1	chr12	103958940	103958945	-	1	NA	Intergenic	Intergenic	-2045	NM_009247	20704	Mm.312593	NM_009247	ENSMUSG00000072849	Serpina1e	Dom5|PI5|Spi1-5	serine (or cysteine) peptidase inhibitor, clade A, member 1E	protein-coding
mm_89418.1	chr10	90875138	90875148	+	1	NA	intron (NM_001347053, intron 1 of 8)	(TCC)n|Simple_repeat|Simple_repeat	45300	NM_001347053	77531	Mm.440605	NM_181398	ENSMUSG00000058589	Anks1b	AIDA-1b|C030032C09Rik|E530015N03Rik|ENSMUSG00000078431|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding
mm_26968.1	chr3	24547113	24547116	-	1	NA	intron (NM_001326288, intron 2 of 13)	MTC|LTR|ERVL-MaLR	236892	NM_001326288	635702	Mm.448351	NM_001326288	ENSMUSG00000102758	Naaladl2	2810043G22Rik|EG635702|Gm1021	N-acetylated alpha-linked acidic dipeptidase-like 2	protein-coding
mm_18411.1	chr2	60553304	60553317	-	1	NA	promoter-TSS (NM_008867)	promoter-TSS (NM_008867)	-2	NM_008867	18779	Mm.5092	NM_008867	ENSMUSG00000054580	Pla2r1	Pla2-r|Pla2g1br|Pla2r	phospholipase A2 receptor 1	protein-coding
mm_94451.1	chr11	6389429	6389435	+	1	NA	Intergenic	(CGG)n|Simple_repeat|Simple_repeat	-5693	NM_001005867	52915	Mm.1144	NM_028601	ENSMUSG00000041164	Zmiz2	Zimp7	zinc finger, MIZ-type containing 2	protein-coding
mm_1371.1	chr1	66468226	66468264	+	1	NA	promoter-TSS (NM_175510)	promoter-TSS (NM_175510)	-202	NM_175510	329178	Mm.44798	NM_175510	ENSMUSG00000055567	Unc80	C030018G13Rik|C230061B10Rik|UNC-80	unc-80, NALCN activator	protein-coding
mm_152992.1	chr19	29787307	29787312	-	1	NA	intron (NM_172836, intron 1 of 7)	intron (NM_172836, intron 1 of 7)	18700	NM_172836	240613	Mm.313351	NM_172836	ENSMUSG00000046138	9930021J03Rik	ENSMUSG00000048936|Gm9832|mKIAA2026	RIKEN cDNA 9930021J03 gene	protein-coding
mm_140533.1	chr17	6754828	6754838	-	1	NA	exon (NM_009510, exon 4 of 13)	exon (NM_009510, exon 4 of 13)	27947	NM_009510	22350	Mm.277812	NM_009510	ENSMUSG00000052397	Ezr	AW146364|R75297|Vil2|p81	ezrin	protein-coding
mm_114160.1	chr13	55412271	55412279	+	1	NA	exon (NM_011392, exon 12 of 13)	exon (NM_011392, exon 12 of 13)	2957	NM_029303	75477	Mm.432537	NM_029303	ENSMUSG00000044444	Pfn3	1700012P12Rik	profilin 3	protein-coding
mm_24581.1	chr3	93444789	93444795	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	2462	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_56894.1	chr6	119110958	119110961	-	1	NA	intron (NM_001255998, intron 1 of 47)	intron (NM_001255998, intron 1 of 47)	-2464	NM_001256002	12288	Mm.41628	NM_009781	ENSMUSG00000051331	Cacna1c	Cav1.2|Cchl1a1|D930026N18Rik|MBC|MELC-CC	calcium channel, voltage-dependent, L type, alpha 1C subunit	protein-coding
mm_96526.1	chr11	68496708	68496720	+	1	NA	3' UTR (NM_177320, exon 19 of 19)	3' UTR (NM_177320, exon 19 of 19)	-6305	NM_001004435	104709	Mm.234573	NM_001004435	ENSMUSG00000046207	Pik3r6	BB220380|p84|p84 PIKAP|p87(PIKAP)|p87PIKAP	phosphoinositide-3-kinase, regulatory subunit 6	protein-coding
mm_87138.1	chr10	34300842	34300858	+	1	NA	3' UTR (NM_030203, exon 1 of 1)	3' UTR (NM_030203, exon 1 of 1)	3429	NM_030203	72480	Mm.21485	NM_030203	ENSMUSG00000039485	Tspyl4	2610102M01Rik|B230210I21Rik|D10Bwg0791e	TSPY-like 4	protein-coding
mm_138835.1	chr17	39848450	39848501	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	5478	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_102764.1	chr11	67922161	67922188	-	1	NA	promoter-TSS (NM_173754)	promoter-TSS (NM_173754)	-21	NM_173754	216835	Mm.158885	NM_173754	ENSMUSG00000020905	Usp43	-	ubiquitin specific peptidase 43	protein-coding
mm_115433.1	chr13	117264436	117264451	+	1	NA	exon (NM_010330, exon 5 of 9)	exon (NM_010330, exon 5 of 9)	43870	NM_010330	13723	Mm.274926	NM_010330	ENSMUSG00000021728	Emb	AL022799|Gp70	embigin	protein-coding
mm_123774.1	chr14	70289431	70289509	-	1	NA	promoter-TSS (NM_001304992)	promoter-TSS (NM_001304992)	27	NM_008915	19057	Mm.439683	NM_008915	ENSMUSG00000022092	Ppp3cc	Calnc|PP2BA gamma	protein phosphatase 3, catalytic subunit, gamma isoform	protein-coding
mm_120093.1	chr14	57889991	57889999	+	1	NA	intron (NM_029492, intron 1 of 12)	CpG	267	NM_029492	75965	Mm.29044	NM_029492	ENSMUSG00000021969	Zdhhc20	4930542A17Rik|5033406L14Rik|AI448102|B230110O18Rik|ENSMUSG00000055956|HK11	zinc finger, DHHC domain containing 20	protein-coding
mm_46459.1	chr5	105118318	105118326	-	1	NA	exon (NM_001256005, exon 11 of 11)	exon (NM_001256005, exon 11 of 11)	-8030	NM_172777	236573	Mm.425261	NM_172777	ENSMUSG00000029298	Gbp9	-	guanylate-binding protein 9	protein-coding
mm_57437.1	chr6	124917940	124917955	-	1	NA	promoter-TSS (NM_026988)	promoter-TSS (NM_026988)	-1	NM_026988	69202	Mm.142187	NM_026988	ENSMUSG00000030122	Ptms	2610009E16Rik	parathymosin	protein-coding
mm_50971.1	chr6	61179975	61180002	+	1	NA	promoter-TSS (NM_183310)	promoter-TSS (NM_183310)	-337	NM_001164316	232035	Mm.150324	NM_183310	ENSMUSG00000039578	Ccser1	6230405M12Rik|C130092O11Rik|Fam190a	coiled-coil serine rich 1	protein-coding
mm_14874.1	chr2	148799874	148799891	+	1	NA	intron (NM_009978, intron 1 of 3)	intron (NM_009978, intron 1 of 3)	1043	NM_009978	13012	Mm.20435	NM_009978	ENSMUSG00000027442	Cst8	Cres|Cst-rs1	cystatin 8 (cystatin-related epididymal spermatogenic)	protein-coding
mm_67860.1	chr7	99020433	99020439	-	1	NA	intron (NM_178635, intron 6 of 14)	intron (NM_178635, intron 6 of 14)	120708	NM_178635	78610	Mm.323072	NM_178635	ENSMUSG00000035354	Uvrag	9530039D02Rik|AI648770|BB124205|Uvrag1|Uvragl	UV radiation resistance associated gene	protein-coding
mm_121555.1	chr14	122479721	122479731	+	1	NA	3' UTR (NM_009574, exon 3 of 3)	3' UTR (NM_009574, exon 3 of 3)	4342	NM_009574	22772	Mm.308936	NM_009574	ENSMUSG00000061524	Zic2	HPE5|Ku	zinc finger protein of the cerebellum 2	protein-coding
mm_6170.1	chr1	65073528	65073537	-	1	NA	promoter-TSS (NM_007775)	promoter-TSS (NM_007775)	0	NM_007775	12966	Mm.491115	NM_007775	ENSMUSG00000025952	Crygc	Cryg-5	crystallin, gamma C	protein-coding
mm_108091.1	chr12	74296693	74296697	+	1	NA	promoter-TSS (NM_198866)	promoter-TSS (NM_198866)	-779	NM_198866	386753	Mm.341686	NM_198866	ENSMUSG00000029878	Dbpht2	Spot2	DNA binding protein with his-thr domain	protein-coding
mm_19278.1	chr2	85519046	85519056	-	1	NA	promoter-TSS (NM_001081664)	promoter-TSS (NM_001081664)	-116	NM_001081664	228151	Mm.17636	NM_001081664	ENSMUSG00000075217	4833423E24Rik	Fads2p1|Gm113	RIKEN cDNA 4833423E24 gene	protein-coding
mm_131142.1	chr16	6349120	6349145	+	1	NA	intron (NM_021477, intron 2 of 16)	CpG	373545	NR_045799	68238	Mm.434605	NR_045799	ENSMUSG00000101481	1700123O21Rik	-	RIKEN cDNA 1700123O21 gene	ncRNA
mm_102130.1	chr11	53430446	53430464	-	1	NA	intron (NM_001326614, intron 2 of 2)	intron (NM_001326614, intron 2 of 2)	376	NM_025352	22272	Mm.251621	NM_025352	ENSMUSG00000044894	Uqcrq	1100001F06Rik|1500040F11Rik|5830407L17Rik|9.5kDa|AA959903|QP-C|Qpc|Uqcrb|c1502	ubiquinol-cytochrome c reductase, complex III subunit VII	protein-coding
mm_1721.1	chr1	75360343	75360353	+	1	NA	promoter-TSS (NM_010043)	promoter-TSS (NM_010043)	56	NM_010043	13346	Mm.6712	NM_010043	ENSMUSG00000026208	Des	-	desmin	protein-coding
mm_113762.1	chr13	44766621	44766623	+	1	NA	intron (NM_001205044, intron 2 of 18)	(TTTTC)n|Simple_repeat|Simple_repeat	35351	NM_001205043	16468	Mm.25059	NM_021878	ENSMUSG00000038518	Jarid2	Jmj|jumonji	jumonji, AT rich interactive domain 2	protein-coding
mm_51539.1	chr6	83195961	83195977	+	1	NA	exon (NM_001198867, exon 23 of 28)	exon (NM_001198867, exon 23 of 28)	10023	NM_001347310	13191	Mm.6919	NM_007835	ENSMUSG00000031865	Dctn1	AL022633|DAP-150|DP-150|Glued|p150|p150-glued|p150<glued>	dynactin 1	protein-coding
mm_82298.1	chr9	7836981	7837096	-	1	NA	promoter-TSS (NM_007465)	promoter-TSS (NM_007465)	19	NM_007465	11797	Mm.335659	NM_007465	ENSMUSG00000057367	Birc2	AW146227|Api1|Api2|Birc3|C-IAP1|C330006D17Rik|HIAP1|HIAP2|IAP1|IAP2|MIAP1|MIAP2|MIHB|MIHC|RNF48|cIAP1|cIAP2|mcIAP1	baculoviral IAP repeat-containing 2	protein-coding
mm_22202.1	chr2	173578189	173578199	-	1	NA	exon (NM_001199955, exon 1 of 2)	exon (NM_001199955, exon 1 of 2)	147	NM_001199955	70065	Mm.425115	NM_027303	ENSMUSG00000027517	Ankrd60	1700019A24Rik|1700030G11Rik	ankyrin repeat domain 60	protein-coding
mm_64883.1	chr7	15879881	15879900	-	1	NA	promoter-TSS (NM_007770)	promoter-TSS (NM_007770)	65	NM_007770	12951	Mm.441911	NM_007770	ENSMUSG00000041578	Crx	Crx1	cone-rod homeobox	protein-coding
mm_114608.1	chr13	75839898	75839928	+	1	NA	promoter-TSS (NM_053108)	promoter-TSS (NM_053108)	27	NM_053108	93692	Mm.25844	NM_053108	ENSMUSG00000021591	Glrx	C86710|D13Wsu156e|Glrx1|Grx1|TTase	glutaredoxin	protein-coding
mm_166007.1	chr4	117272151	117272162	+	1	NA	3' UTR (NM_001310729, exon 14 of 14)	3' UTR (NM_001310729, exon 14 of 14)	17299	NM_001310730	66743	Mm.318331	NM_025739	ENSMUSG00000028677	Rnf220	4732477A13|4931406I20Rik|5730503K05Rik|AV302541	ring finger protein 220	protein-coding
mm_52402.1	chr6	113327226	113327241	+	1	NA	exon (NM_010957, exon 1 of 7)	exon (NM_010957, exon 1 of 7)	257	NM_010957	18294	Mm.43612	NM_010957	ENSMUSG00000030271	Ogg1	Mmh	8-oxoguanine DNA-glycosylase 1	protein-coding
mm_128273.1	chr15	36794233	36794280	-	1	NA	5' UTR (NM_011740, exon 1 of 7)	5' UTR (NM_011740, exon 1 of 7)	282	NM_011740	22631	Mm.3360	NM_011740	ENSMUSG00000022285	Ywhaz	1110013I11Rik|14-3-3zeta|AI596267|AL022924|AU020854	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide	protein-coding
mm_152012.1	chr19	5964133	5964210	-	1	NA	promoter-TSS (NM_008893)	promoter-TSS (NM_008893)	35	NM_001164057	18969	Mm.209931	NM_008893	ENSMUSG00000024833	Pola2	AI573378	polymerase (DNA directed), alpha 2	protein-coding
mm_35950.1	chr4	53116220	53116262	-	1	NA	intron (NM_013454, intron 5 of 49)	intron (NM_013454, intron 5 of 49)	43654	NM_013454	11303	Mm.277376	NM_013454	ENSMUSG00000015243	Abca1	ABC-1|Abc1	ATP-binding cassette, sub-family A (ABC1), member 1	protein-coding
mm_5584.1	chr1	39552306	39552316	-	1	NA	3' UTR (NM_001033135, exon 7 of 7)	3' UTR (NM_001033135, exon 7 of 7)	-3471	NR_028555	100217461		NR_028555	ENSMUSG00000077704	Snord89	MBII-289	small nucleolar RNA, C/D box 89	snoRNA
mm_50786.1	chr6	54039498	54039556	+	1	NA	promoter-TSS (NM_001163640)	promoter-TSS (NM_001163640)	-405	NM_001163640	69993	Mm.321147	NM_023543	ENSMUSG00000004633	Chn2	1700026N20Rik|4930557O16Rik|ARHGAP3|Bch	chimerin 2	protein-coding
mm_130997.1	chr15	103446649	103446668	-	1	NA	intron (NM_177631, intron 1 of 6)	intron (NM_177631, intron 1 of 6)	1801	NM_177631	223927	Mm.243718	NM_177631	ENSMUSG00000053508	BC048502	-	cDNA sequence BC048502	protein-coding
mm_167251.1	chr8	24725841	24725861	-	1	NA	promoter-TSS (NM_001324489)	promoter-TSS (NM_001324489)	1	NM_009619	11497	Mm.5168	NM_009619	ENSMUSG00000031553	Adam3	Cyrn1|Taz83|tMDC	a disintegrin and metallopeptidase domain 3 (cyritestin)	protein-coding
mm_12474.1	chr2	71528539	71528547	+	1	NA	promoter-TSS (NM_010053)	promoter-TSS (NM_010053)	-902	NM_010053	13390	Mm.475101	NM_010053	ENSMUSG00000041911	Dlx1	Dlx|Dlx-1	distal-less homeobox 1	protein-coding
mm_4391.1	chr1	172341305	172341322	+	1	NA	5' UTR (NM_001039484, exon 1 of 2)	5' UTR (NM_001039484, exon 1 of 2)	103	NM_001039484	16513	Mm.254563	NM_020269	ENSMUSG00000044708	Kcnj10	BIR10|BIRK-1|Kir1.2|Kir4.1	potassium inwardly-rectifying channel, subfamily J, member 10	protein-coding
mm_2289.1	chr1	91413383	91413413	+	1	NA	promoter-TSS (NM_019479)	promoter-TSS (NM_019479)	-176	NM_019479	55927	Mm.280029	NM_019479	ENSMUSG00000067071	Hes6	AI326893|bHLHb41	hairy and enhancer of split 6	protein-coding
mm_57585.1	chr6	127154728	127154748	-	1	NA	intron (NR_040275, intron 1 of 1)	intron (NR_040275, intron 1 of 1)	-3690	NM_009829	12444	Mm.333406	NM_009829	ENSMUSG00000000184	Ccnd2	2600016F06Rik|AI256817|BF642806|C86853|Vin-1|Vin1|cD2	cyclin D2	protein-coding
mm_88219.1	chr10	70293523	70293531	+	1	NA	Intergenic	Intergenic	48251	NM_025807	66859	Mm.19325	NM_025807	ENSMUSG00000037762	Slc16a9	1200003C15Rik|4930425B13Rik|AI552636	solute carrier family 16 (monocarboxylic acid transporters), member 9	protein-coding
mm_28703.1	chr3	95545526	95545537	-	1	NA	exon (NM_021281, exon 5 of 8)	exon (NM_021281, exon 5 of 8)	-14146	NM_026489	67981	Mm.179050	NM_026489	ENSMUSG00000028109	Hormad1	4921522K05Rik|Nohma	HORMA domain containing 1	protein-coding
mm_80150.1	chr9	70928138	70928151	+	1	NA	intron (NM_001324473, intron 1 of 8)	intron (NM_001324473, intron 1 of 8)	6664	NM_008280	15450	Mm.390187	NM_008280	ENSMUSG00000032207	Lipc	AI256194|HL|Hpl	lipase, hepatic	protein-coding
mm_119637.1	chr14	51893633	51893677	+	1	NA	promoter-TSS (NM_001039676)	promoter-TSS (NM_001039676)	45	NM_001039676	214922	Mm.281343	NM_001039676	ENSMUSG00000072572	Slc39a2	F730005G13Rik|Gm1789|Gm289|Zip2	solute carrier family 39 (zinc transporter), member 2	protein-coding
mm_166255.1	chr5	87254801	87254818	-	1	NA	promoter-TSS (NM_053215)	promoter-TSS (NM_053215)	-21	NM_053215	112417	Mm.160362	NM_053215	ENSMUSG00000057425	Ugt2b37	0610033E06Rik	UDP glucuronosyltransferase 2 family, polypeptide B37	protein-coding
mm_118833.1	chr14	25607756	25607794	+	1	NA	intron (NM_001310666, intron 6 of 23)	CpG	4262	NM_001309430	100188919	Mm.473810	NM_001309430		Israa	-	immune system released activating agent	protein-coding
mm_648.1	chr1	40427523	40427536	+	1	NA	Intergenic	Intergenic	-2041	NM_001294171	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_10888.1	chr2	25263200	25263210	+	1	NA	exon (NM_175286, exon 1 of 4)	exon (NM_175286, exon 1 of 4)	607	NM_175286	97031	Mm.308539	NM_175286	ENSMUSG00000048707	Tprn	C430004E15Rik|C87750	taperin	protein-coding
mm_51807.1	chr6	88733583	88733586	+	1	NA	intron (NM_011844, intron 2 of 7)	intron (NM_011844, intron 2 of 7)	8880	NM_001166251	23945	Mm.272197	NM_011844	ENSMUSG00000033174	Mgll	AA589436|Magl|Mgl	monoglyceride lipase	protein-coding
mm_101122.1	chr11	12027959	12027973	-	1	NA	promoter-TSS (NM_001177629)	promoter-TSS (NM_001177629)	5	NM_001177629	14783	Mm.273117	NM_010345	ENSMUSG00000020176	Grb10	5730571D09Rik|AI325020|Meg1|mKIAA0207	growth factor receptor bound protein 10	protein-coding
mm_166236.1	chr5	67847306	67847310	-	1	NA	5' UTR (NM_009727, exon 1 of 36)	5' UTR (NM_009727, exon 1 of 36)	123	NM_009727	11980	Mm.153230	NM_009727	ENSMUSG00000037685	Atp8a1	AI481521|AI853962|APLT|AW743152|AW822227|Atp3a2|B230107D19Rik|ClassI	ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1	protein-coding
mm_77457.1	chr8	121907679	121907694	-	1	NA	promoter-TSS (NM_011404)	promoter-TSS (NM_011404)	0	NM_011404	20539	Mm.22374	NM_011404	ENSMUSG00000040010	Slc7a5	4F2LC|D0H16S474E|LAT1|TA1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 5	protein-coding
mm_32663.1	chr4	115096137	115096172	+	1	NA	Intergenic	Intergenic	7446	NM_001164557	67182	Mm.30181	NM_026018	ENSMUSG00000028716	Pdzk1ip1	0610007F13Rik|2700030M23Rik|AU046042|Map17	PDZK1 interacting protein 1	protein-coding
mm_112014.1	chr12	110987131	110987145	-	1	NA	Intergenic	Intergenic	-7260	NR_036598	77878	Mm.293198	NR_036598		6030440G07Rik	-	RIKEN cDNA 6030440G07 gene	ncRNA
mm_110268.1	chr12	31950553	31950560	-	1	NA	promoter-TSS (NM_153198)	promoter-TSS (NM_153198)	-21	NM_153198	73389	Mm.390461	NM_153198	ENSMUSG00000002996	Hbp1	1700058O05Rik|BE629963|C330012F01Rik|C86454	high mobility group box transcription factor 1	protein-coding
mm_168369.1	chr11	18327584	18327595	-	1	NA	Intergenic	Intergenic	231603	NR_131129	327872		NR_131129	ENSMUSG00000085453	Gm12018	OTTMUSG00000005202	predicted gene 12018	ncRNA
mm_151595.1	chr19	3440891	3440907	-	1	NA	Intergenic	Intergenic	-26355	NM_010253	14419	Mm.4655	NM_010253	ENSMUSG00000024907	Gal	Galn	galanin	protein-coding
mm_57508.1	chr6	125463712	125463743	-	1	NA	exon (NM_007657, exon 4 of 8)	exon (NM_007657, exon 4 of 8)	31028	NM_007657	12527	Mm.210676	NM_007657	ENSMUSG00000030342	Cd9	Tspan29	CD9 antigen	protein-coding
mm_122125.1	chr14	31155544	31155567	-	1	NA	intron (NM_138672, intron 22 of 68)	intron (NM_138672, intron 22 of 68)	13086	NM_138672	192187	Mm.220821	NM_138672	ENSMUSG00000042286	Stab1	FEEL-1|FELE-1|MFEEL-1|MS-1|STAB-1|mKIAA0246	stabilin 1	protein-coding
mm_121883.1	chr14	21714551	21714567	-	1	NA	promoter-TSS (NM_001013826)	promoter-TSS (NM_001013826)	17	NM_001013826	435391	Mm.295860	NM_001013826	ENSMUSG00000063821	Dupd1	EG435391	dual specificity phosphatase and pro isomerase domain containing 1	protein-coding
mm_131403.1	chr16	14373625	14373650	+	1	NA	intron (NM_008576, intron 1 of 30)	B1_Mm|SINE|Alu	12079	NM_008576	17250	Mm.196634	NM_008576	ENSMUSG00000023088	Abcc1	Abcc1a|Abcc1b|MRP|Mdrap|Mrp1	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	protein-coding
mm_8450.1	chr1	152902758	152902779	-	1	NA	promoter-TSS (NM_001160256)	promoter-TSS (NM_001160256)	-122	NM_001005507	226517	Mm.270775	NM_001005507	ENSMUSG00000042772	Smg7	9430023P16Rik|mKIAA0250	Smg-7 homolog, nonsense mediated mRNA decay factor (C. elegans)	protein-coding
mm_131026.1	chr16	3723323	3723324	+	1	NA	Intergenic	Intergenic	-5199	NM_001161791	54483	Mm.143718	NM_019453	ENSMUSG00000022534	Mefv	FMF|TRIM20|pyrin	Mediterranean fever	protein-coding
mm_39165.1	chr4	155624734	155624773	-	1	NA	promoter-TSS (NM_007661)	promoter-TSS (NM_007661)	2	NR_040441	100502734	Mm.306018	NR_040441	ENSMUSG00000086682	Gm16023	OTTMUSG00000029160	predicted gene 16023	ncRNA
mm_91078.1	chr10	19011898	19011913	-	1	NA	promoter-TSS (NM_001166402)	promoter-TSS (NM_001166402)	58	NM_001166402	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_29019.1	chr3	101924379	101924408	-	1	NA	promoter-TSS (NM_001039371)	promoter-TSS (NM_001039371)	60	NM_001039371	242126	Mm.90204	NM_001039371	ENSMUSG00000033147	Slc22a15	2610034P21Rik|4930477M19|A530052I06Rik|BB219042	solute carrier family 22 (organic anion/cation transporter), member 15	protein-coding
mm_24723.1	chr3	95281359	95281391	+	1	NA	intron (NM_173347, intron 1 of 7)	CpG	701	NM_173347	229589	Mm.14155	NM_173347	ENSMUSG00000015711	Prune1	9230112O05Rik|C130058A12|DRES-17|HTCD37|PRUNEM1|Prune|Prune-M1	prune exopolyphosphatase	protein-coding
mm_130896.1	chr15	102398673	102398689	-	1	NA	Intergenic	Intergenic	-7635	NM_013672	20683	Mm.4618	NM_013672	ENSMUSG00000001280	Sp1	1110003E12Rik|AA450830|AI845540|Sp1-1	trans-acting transcription factor 1	protein-coding
mm_168805.1	chr12	20615044	20615045	+	1	NA	Intergenic	CpG	200735	NR_015521	69513	Mm.273972	NR_015521	ENSMUSG00000099759	1700030C10Rik	-	RIKEN cDNA 1700030C10 gene	ncRNA
mm_63009.1	chr7	120940618	120940659	+	1	NA	exon (NM_001164096, exon 17 of 20)	exon (NM_001164096, exon 17 of 20)	22894	NM_001164096	26939	Mm.193632	NM_025298	ENSMUSG00000030880	Polr3e	RPC5|Sin	polymerase (RNA) III (DNA directed) polypeptide E	protein-coding
mm_95366.1	chr11	49076585	49076601	+	1	NA	promoter-TSS (NM_001271677)	promoter-TSS (NM_001271677)	6	NM_001271677	15953	Mm.24769	NM_008330	ENSMUSG00000078920	Ifi47	47kDa|IRG-47|Ifggc1|Igrd|Iigp4|Iipg4|Irgd	interferon gamma inducible protein 47	protein-coding
mm_137312.1	chr17	24885963	24885971	+	1	NA	promoter-TSS (NM_001163750)	promoter-TSS (NM_001163750)	383	NM_011956	26426	Mm.36718	NM_011956	ENSMUSG00000039183	Nubp2	D17Wsu11e	nucleotide binding protein 2	protein-coding
mm_27022.1	chr3	26046432	26046440	-	1	NA	intron (NM_138666, intron 3 of 7)	intron (NM_138666, intron 3 of 7)	106871	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_154525.1	chrM	13457	13483	-	1	NA	NA	Intergenic	NA	NA								
mm_5563.1	chr1	38836632	38836647	-	1	NA	Intergenic	CpG	-15424	NM_001029878	381338	Mm.487137	NM_028403	ENSMUSG00000048814	Lonrf2	2900060P06Rik|AI851349	LON peptidase N-terminal domain and ring finger 2	protein-coding
mm_29823.1	chr3	129613895	129613921	-	1	NA	intron (NM_130450, intron 3 of 4)	intron (NM_130450, intron 3 of 4)	81522	NM_130450	170439	Mm.314113	NM_130450	ENSMUSG00000041220	Elovl6	C77826|FAE|LCE	ELOVL family member 6, elongation of long chain fatty acids (yeast)	protein-coding
mm_164140.1	chr15	57975689	57975703	-	1	NA	Intergenic	Intergenic	-10207	NM_173862	239463	Mm.221241	NM_173862	ENSMUSG00000051225	Fam83a	-	family with sequence similarity 83, member A	protein-coding
mm_86619.1	chr10	13965884	13965892	+	1	NA	promoter-TSS (NM_010437)	promoter-TSS (NM_010437)	-491	NM_010437	15273	Mm.42157	NM_010437	ENSMUSG00000015501	Hivep2	Gm20114|MIBP1|Schnurri-2|Shn-2	human immunodeficiency virus type I enhancer binding protein 2	protein-coding
mm_85736.1	chr9	108490522	108490547	-	1	NA	promoter-TSS (NM_001168373)	promoter-TSS (NM_001168373)	-142	NM_001168372	71472	Mm.289706	NM_027804	ENSMUSG00000006676	Usp19	8430421I07Rik|AI047774|Zmynd9	ubiquitin specific peptidase 19	protein-coding
mm_99365.1	chr11	101732953	101732965	+	1	NA	promoter-TSS (NM_144831)	promoter-TSS (NM_144831)	3	NM_144831	217207	Mm.28186	NM_144831	ENSMUSG00000034931	Dhx8	Ddx8|mDEAH6|mKIAA4096	DEAH (Asp-Glu-Ala-His) box polypeptide 8	protein-coding
mm_95751.1	chr11	54902744	54902769	+	1	NA	promoter-TSS (NM_008161)	promoter-TSS (NM_008161)	-98	NM_001329860	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_155619.1	chrX	83376352	83376353	+	1	NA	intron (NM_007868, intron 5 of 78)	intron (NM_007868, intron 5 of 78)	111572	NM_021898	100502723	Mm.383210	NM_021898	ENSMUSG00000035522	Tsga8	Halap-X|Halapx	testis specific gene A8	protein-coding
mm_125788.1	chr15	74721194	74721234	+	1	NA	promoter-TSS (NM_198607)	promoter-TSS (NM_198607)	-20	NM_198607	223626	Mm.268603	NM_198607	ENSMUSG00000056665	Them6	4930572J05Rik	thioesterase superfamily member 6	protein-coding
mm_56250.1	chr6	90757462	90757472	-	1	NA	intron (NM_001134384, intron 1 of 13)	intron (NM_001134384, intron 1 of 13)	-40938	NM_001134383	232227	Mm.196943	NM_182784	ENSMUSG00000034312	Iqsec1	AW561907|BC026481|BRAG2|D6Ertd349e|cI-43	IQ motif and Sec7 domain 1	protein-coding
mm_46217.1	chr5	98855089	98855092	-	1	NA	5' UTR (NM_001310677, exon 1 of 3)	5' UTR (NM_001310677, exon 1 of 3)	675	NM_001310677	110075	Mm.136461	NM_173404	ENSMUSG00000029335	Bmp3	9530029I04Rik	bone morphogenetic protein 3	protein-coding
mm_118571.1	chr14	19133107	19133114	+	1	NA	Intergenic	ERVB7_2-LTR_MM|LTR|ERVK	-239483	NM_144839	218793	Mm.23551	NM_144839	ENSMUSG00000058317	Ube2e2	BC016265	ubiquitin-conjugating enzyme E2E 2	protein-coding
mm_86821.1	chr10	20952598	20952683	+	1	NA	promoter-TSS (NM_026203)	promoter-TSS (NM_026203)	93	NM_026203	52906	Mm.253280	NM_026203	ENSMUSG00000019986	Ahi1	1700015F03Rik|Ahi-1|D10Bwg0629e	Abelson helper integration site 1	protein-coding
mm_140133.1	chr17	79622814	79622823	+	1	NA	intron (NM_201361, intron 2 of 10)	intron (NM_201361, intron 2 of 10)	7918	NM_201361	381110	Mm.209801	NM_201361	ENSMUSG00000036368	Rmdn2	AW061290|Fam82a1|RMD-2|mRMD-2	regulator of microtubule dynamics 2	protein-coding
mm_18294.1	chr2	52676601	52676631	-	1	NA	promoter-TSS (NM_001037099)	promoter-TSS (NM_001037099)	-7	NM_001037099	12298	Mm.330223	NM_146123	ENSMUSG00000017412	Cacnb4	3110038O15Rik|Cchb4|lh	calcium channel, voltage-dependent, beta 4 subunit	protein-coding
mm_15146.1	chr2	153986485	153986487	+	1	NA	exon (NM_001080811, exon 4 of 11)	exon (NM_001080811, exon 4 of 11)	11541	NM_001080811	545477	Mm.379973	NM_001080811	ENSMUSG00000078998	Bpifa6	EG545477|Gm5840|Splunc6	BPI fold containing family A, member 6	protein-coding
mm_113768.1	chr13	44837082	44837091	+	1	NA	intron (NM_001205044, intron 3 of 18)	(T)n|Simple_repeat|Simple_repeat	105815	NM_001205043	16468	Mm.25059	NM_021878	ENSMUSG00000038518	Jarid2	Jmj|jumonji	jumonji, AT rich interactive domain 2	protein-coding
mm_4931.1	chr1	191097834	191097859	+	1	NA	promoter-TSS (NM_030060)	promoter-TSS (NM_030060)	-568	NM_030060	381319	Mm.6922	NM_030060	ENSMUSG00000026630	Batf3	9130211I03Rik|Snft	basic leucine zipper transcription factor, ATF-like 3	protein-coding
mm_42823.1	chr5	122093569	122093595	+	1	NA	Intergenic	Intergenic	-7398	NM_010861	17906	Mm.1529	NM_010861	ENSMUSG00000013936	Myl2	MLC-2|MLC-2s/v|MLC-2v|Mlc2v|Mylpc	myosin, light polypeptide 2, regulatory, cardiac, slow	protein-coding
mm_37135.1	chr4	116820881	116820887	-	1	NA	exon (NM_146256, exon 1 of 1)	exon (NM_146256, exon 1 of 1)	624	NM_146256	242642	Mm.279897	NM_146256	ENSMUSG00000043155	Hpdl	A830048M07Rik|BC034099|Gloxd1	4-hydroxyphenylpyruvate dioxygenase-like	protein-coding
mm_9634.1	chr1	176835939	176835951	-	1	NA	non-coding (NR_037996, exon 1 of 1)	non-coding (NR_037996, exon 1 of 1)	188	NR_037996	15365	Mm.441435	NR_037996		Hmga2-ps1	EG666235|Gm7996|Hmgic-ps1|[y]i-c	high mobility group AT-hook 2, pseudogene 1	pseudo
mm_134868.1	chr16	28668798	28668806	-	1	NA	intron (NM_010199, intron 2 of 5)	intron (NM_010199, intron 2 of 5)	-68759	NR_030463	751543		NR_030463	ENSMUSG00000076064	Mir690	Mirn690|mir-690|mmu-mir-690	microRNA 690	ncRNA
mm_29224.1	chr3	107212845	107212855	-	1	NA	exon (NM_001111143, exon 8 of 9)	exon (NM_001111143, exon 8 of 9)	8882	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_32118.1	chr4	99031162	99031172	+	1	NA	exon (NM_013913, exon 1 of 7)	exon (NM_013913, exon 1 of 7)	213	NM_013913	30924	Mm.28341	NM_013913	ENSMUSG00000028553	Angptl3	hypl	angiopoietin-like 3	protein-coding
mm_140526.1	chr17	6743810	6743820	-	1	NA	intron (NM_009510, intron 7 of 12)	intron (NM_009510, intron 7 of 12)	37985	NM_183368	83672	Mm.442201	NM_031395	ENSMUSG00000041831	Sytl3	A430092N21|Slp3|Slp3-a|Slp3-b|mFLJ00307	synaptotagmin-like 3	protein-coding
mm_59955.1	chr7	30427126	30427130	+	1	NA	exon (NM_172142, exon 9 of 11)	exon (NM_172142, exon 9 of 11)	3824	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_166640.1	chr6	83507082	83507106	+	1	NA	promoter-TSS (NM_001162521)	promoter-TSS (NM_001162521)	-125	NM_001162521	27369	Mm.42234	NM_013764	ENSMUSG00000014554	Dguok	dGK|dGK1|dGK2|dGK3	deoxyguanosine kinase	protein-coding
mm_8280.1	chr1	140018869	140018882	-	1	NA	Intergenic	Intergenic	-160176	NM_001025575	545366	Mm.439660	NM_001025575	ENSMUSG00000033898	Cfhr2	Cfhrb_4/2	complement factor H-related 2	protein-coding
mm_42730.1	chr5	120621415	120621436	+	1	NA	intron (NM_028041, intron 10 of 19)	MIR|SINE|MIR	8295	NM_028041	71990	Mm.24495	NM_028041	ENSMUSG00000029599	Ddx54	2410015A15Rik|AI414901|DP97	DEAD (Asp-Glu-Ala-Asp) box polypeptide 54	protein-coding
mm_148391.1	chr19	3652039	3652045	+	1	NA	intron (NM_008513, intron 3 of 22)	intron (NM_008513, intron 3 of 22)	34522	NM_008513	16973	Mm.274581	NM_008513	ENSMUSG00000024913	Lrp5	BMND1|HBM|LR3|LRP7|OPPG|mKIAA4142	low density lipoprotein receptor-related protein 5	protein-coding
mm_38356.1	chr4	137796351	137796361	-	1	NA	promoter-TSS (NM_007431)	promoter-TSS (NM_007431)	28	NM_007431	11647	Mm.288186	NM_007431	ENSMUSG00000028766	Alpl	ALP|APTNAP|Akp-2|Akp2|TNAP|TNSALP	alkaline phosphatase, liver/bone/kidney	protein-coding
mm_127751.1	chr15	103479130	103479144	+	1	NA	intron (NM_153505, intron 20 of 30)	ID_B1|SINE|B4	-23897	NM_008800	18574	Mm.390792	NM_008800	ENSMUSG00000022489	Pde1b	Pde1b1	phosphodiesterase 1B, Ca2+-calmodulin dependent	protein-coding
mm_141340.1	chr17	28517510	28517558	-	1	NA	Intergenic	Intergenic	-13327	NM_026290	67645	Mm.46170	NM_026290	ENSMUSG00000024223	Armc12	4930511I11Rik|AV041658	armadillo repeat containing 12	protein-coding
mm_17154.1	chr2	25218648	25218674	-	1	NA	promoter-TSS (NM_026624)	promoter-TSS (NM_026624)	-84	NM_026624	68222	Mm.227260	NM_026624	ENSMUSG00000026969	Fam166a	4931415M17	family with sequence similarity 166, member A	protein-coding
mm_70124.1	chr7	143079556	143079584	-	1	NA	intron (NM_020277, intron 16 of 24)	intron (NM_020277, intron 16 of 24)	10202	NM_001115085	56844	Mm.139675	NM_020285	ENSMUSG00000045752	Tssc4	AA241958|ESTM671070	tumor-suppressing subchromosomal transferable fragment 4	protein-coding
mm_132386.1	chr16	34952540	34952561	+	1	NA	non-coding (NR_045722, exon 3 of 3)	non-coding (NR_045722, exon 3 of 3)	6314	NR_045722	278725	Mm.436927	NR_045722		E130310I04Rik	A930019C19Rik	RIKEN cDNA E130310I04 gene	ncRNA
mm_52782.1	chr6	121252933	121252955	+	1	NA	intron (NM_011909, intron 2 of 10)	intron (NM_011909, intron 2 of 10)	7038	NM_011909	24110	Mm.326911	NM_011909	ENSMUSG00000030107	Usp18	1110058H21Rik|AW047653|UBP43|Ubp15	ubiquitin specific peptidase 18	protein-coding
mm_20970.1	chr2	151973272	151973281	-	1	NA	intron (NM_146127, intron 1 of 1)	intron (NM_146127, intron 1 of 1)	118	NM_001289151	73847	Mm.272444	NM_028666	ENSMUSG00000027459	Fam110a	1700008J10Rik|5430432M24Rik|AI747080	family with sequence similarity 110, member A	protein-coding
mm_1135.1	chr1	60596659	60596661	+	1	NA	Intergenic	Intergenic	-29895	NM_001045513	77300	Mm.440325	NM_001045513	ENSMUSG00000026014	Raph1	9430025M21Rik|C730009O10Rik|Lpd	Ras association (RalGDS/AF-6) and pleckstrin homology domains 1	protein-coding
mm_85604.1	chr9	107576818	107576840	-	1	NA	promoter-TSS (NM_008317)	promoter-TSS (NM_008317)	-98	NM_008317	15586	Mm.475658	NM_008317	ENSMUSG00000010051	Hyal1	Hya1|Hyal-1	hyaluronoglucosaminidase 1	protein-coding
mm_61132.1	chr7	55926439	55926442	+	1	NA	exon (NM_001164662, exon 29 of 31)	exon (NM_001164662, exon 29 of 31)	36053	NM_001256133	93790	Mm.37249	NM_023647	ENSMUSG00000030452	Nipa2	2600017P10Rik|3830408P04Rik|AB041581	non imprinted in Prader-Willi/Angelman syndrome 2 homolog (human)	protein-coding
mm_142396.1	chr17	45433484	45433494	-	1	NA	promoter-TSS (NR_130961)	promoter-TSS (NR_130961)	218	NM_152810	71702	Mm.28270	NM_152810	ENSMUSG00000023932	Cdc5l	1200002I02Rik|AA408004|PCDC5RP	cell division cycle 5-like (S. pombe)	protein-coding
mm_72980.1	chr8	92901449	92901466	+	1	NA	promoter-TSS (NM_027112)	promoter-TSS (NM_027112)	62	NM_027112	69543	Mm.440514	NM_027112	ENSMUSG00000078144	Capns2	2310005G05Rik|30K-2	calpain, small subunit 2	protein-coding
mm_91052.1	chr10	18789474	18789474	-	1	NA	Intergenic	Intergenic	-2681	NM_177706	237300	Mm.444821	NM_177706	ENSMUSG00000044624	Gm4922	4933423E17|EG237300	predicted gene 4922	protein-coding
mm_116119.1	chr13	28950506	28950512	-	1	NA	TTS (NM_009238)	TTS (NM_009238)	3173	NM_009238	20677	Mm.240627	NM_009238	ENSMUSG00000076431	Sox4	AA682046|Sox-4	SRY (sex determining region Y)-box 4	protein-coding
mm_80242.1	chr9	72735155	72735210	+	1	NA	exon (NM_010890, exon 19 of 29)	exon (NM_010890, exon 19 of 29)	-72092	NM_175485	235472	Mm.31696	NM_175485	ENSMUSG00000036030	Prtg	A230098A12Rik|Igdcc5	protogenin	protein-coding
mm_116463.1	chr13	43435213	43435213	-	1	NA	intron (NM_019930, intron 3 of 13)	intron (NM_019930, intron 3 of 13)	36837	NM_023554	70078	Mm.439927	NM_023554	ENSMUSG00000063200	Nol7	2210008F15Rik|5730556I21Rik|NOP27|RARG-1	nucleolar protein 7	protein-coding
mm_68281.1	chr7	105599698	105599715	-	1	NA	exon (NM_017371, exon 3 of 10)	exon (NM_017371, exon 3 of 10)	410	NM_017371	15458	Mm.3485	NM_017371	ENSMUSG00000030895	Hpx	Hpxn|hx	hemopexin	protein-coding
mm_57203.1	chr6	122850885	122850938	-	1	NA	exon (NM_009779, exon 2 of 2)	exon (NM_009779, exon 2 of 2)	5246	NM_009779	12267	Mm.2408	NM_009779	ENSMUSG00000040552	C3ar1	AZ3B|C3AR|HNFAG09	complement component 3a receptor 1	protein-coding
mm_120523.1	chr14	66847864	66847885	+	1	NA	intron (NM_009955, intron 3 of 13)	intron (NM_009955, intron 3 of 13)	20726	NM_009955	12934	Mm.352648	NM_009955	ENSMUSG00000022048	Dpysl2	AI851130|Crmp2|DRP2|Musunc33|TOAD-64|Ulip2	dihydropyrimidinase-like 2	protein-coding
mm_128429.1	chr15	50309879	50309882	-	1	NA	Intergenic	Lx5|LINE|L1	579169	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_119782.1	chr14	54181517	54181548	+	1	NA	Intergenic	Intergenic	72397	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_126870.1	chr15	89373904	89373928	+	1	NA	promoter-TSS (NM_001111288)	promoter-TSS (NM_001111288)	-98	NM_001111288	100126824	Mm.287977	NM_001111288	ENSMUSG00000091780	Sco2	-	SCO2 cytochrome c oxidase assembly protein	protein-coding
mm_131346.1	chr16	13671859	13671918	+	1	NA	promoter-TSS (NM_001177552)	promoter-TSS (NM_001177552)	30	NM_025653	67118	Mm.223689	NM_025653	ENSMUSG00000022684	Bfar	3010001A07Rik|3110001I22Rik|AI666707|AW107665|Bar|Rnf47	bifunctional apoptosis regulator	protein-coding
mm_38858.1	chr4	149426355	149426366	-	1	NA	5' UTR (NM_022022, exon 1 of 27)	5' UTR (NM_022022, exon 1 of 27)	271	NM_022022	63958	Mm.415260	NM_022022	ENSMUSG00000028960	Ube4b	4930551I19Rik|4933406G05Rik|AU014668|D4Bwg0973e|UFD2|UFD2a|Ufd2p|mKIAA0684	ubiquitination factor E4B	protein-coding
mm_21542.1	chr2	163750208	163750233	-	1	NA	promoter-TSS (NM_001272052)	promoter-TSS (NM_001272052)	19	NM_007398	11486	Mm.388	NM_007398	ENSMUSG00000017697	Ada	-	adenosine deaminase	protein-coding
mm_54564.1	chr6	37442160	37442172	-	1	NA	promoter-TSS (NM_178661)	promoter-TSS (NM_178661)	-18	NM_178661	208647	Mm.169929	NM_178661	ENSMUSG00000038648	Creb3l2	BBF2H7|C530025K05Rik|SCIRR69	cAMP responsive element binding protein 3-like 2	protein-coding
mm_38618.1	chr4	141952933	141952946	-	1	NA	intron (NM_177868, intron 12 of 31)	B4|SINE|B4	-30053	NR_040672	545691	Mm.332015	NR_040672	ENSMUSG00000085424	Fhad1os1	Gm13037|OTTMUSG00000010113	forkhead-associated (FHA) phosphopeptide binding domain 1, opposite strand 1	ncRNA
mm_94100.1	chr10	128562873	128562906	-	1	NA	exon (NM_011119, exon 5 of 12)	exon (NM_011119, exon 5 of 12)	3045	NM_011119	18813	Mm.4742	NM_011119	ENSMUSG00000025364	Pa2g4	38kDa|AA672939|Ebp1|Plfap	proliferation-associated 2G4	protein-coding
mm_9196.1	chr1	171222509	171222519	-	1	NA	promoter-TSS (NM_001037170)	promoter-TSS (NM_001037170)	0	NM_001037170	641376	Mm.288374	NM_001037170	ENSMUSG00000005674	Tomm40l	-	translocase of outer mitochondrial membrane 40 homolog-like (yeast)	protein-coding
mm_21990.1	chr2	167643540	167643564	-	1	NA	3' UTR (NM_145538, exon 6 of 6)	3' UTR (NM_145538, exon 6 of 6)	-11547	NM_023230	66589	Mm.278783	NM_023230	ENSMUSG00000078923	Ube2v1	0610011J09Rik|AI256840|CROC-1|CROC1|D7Bwg1382e|UEV-1	ubiquitin-conjugating enzyme E2 variant 1	protein-coding
mm_57393.1	chr6	124840193	124840205	-	1	NA	promoter-TSS (NM_013530)	promoter-TSS (NM_013530)	76	NM_013530	14695	Mm.68889	NM_013530	ENSMUSG00000023439	Gnb3	Gnb-3	guanine nucleotide binding protein (G protein), beta 3	protein-coding
mm_148412.1	chr19	3935204	3935247	+	1	NA	promoter-TSS (NM_019449)	promoter-TSS (NM_019449)	39	NM_001161428	54445	Mm.262094	NM_019449	ENSMUSG00000036908	Unc93b1	Unc-93B1|Unc93b	unc-93 homolog B1 (C. elegans)	protein-coding
mm_42148.1	chr5	111419015	111419061	+	1	NA	exon (NM_001081235, exon 1 of 2)	exon (NM_001081235, exon 1 of 2)	872	NM_001081235	433938	Mm.332576	NM_001081235	ENSMUSG00000070576	Mn1	AA003644|AA009236	meningioma 1	protein-coding
mm_74463.1	chr8	4217019	4217043	-	1	NA	intron (NM_207203, intron 1 of 6)	intron (NM_207203, intron 1 of 6)	281	NM_207203	73072	Mm.477379	NM_207203	ENSMUSG00000064125	Prr36	-	proline rich 36	protein-coding
mm_113282.1	chr13	30136602	30136610	+	1	NA	5' UTR (NM_153546, exon 1 of 13)	5' UTR (NM_153546, exon 1 of 13)	116	NM_153546	218121	Mm.89682	NM_153546	ENSMUSG00000038732	Mboat1	9130215M02Rik|BC023845|LPEAT1|Moact1|Oact1	membrane bound O-acyltransferase domain containing 1	protein-coding
mm_89711.1	chr10	97714768	97714789	+	1	NA	promoter-TSS (NR_130993)	promoter-TSS (NR_130993)	6	NR_130992	78127	Mm.376175	NR_130992		4930525C09Rik	-	RIKEN cDNA 4930525C09 gene	ncRNA
mm_106805.1	chr12	5643129	5643153	+	1	NA	Intergenic	Intergenic	266639	NR_015579	72669	Mm.10434	NM_028318		2810032G03Rik	AI461720	RIKEN cDNA 2810032G03 gene	ncRNA
mm_99498.1	chr11	102885161	102885174	+	1	NA	promoter-TSS (NM_025766)	promoter-TSS (NM_025766)	-2	NM_025766	66784	Mm.483216	NM_025766	ENSMUSG00000075510	Fam187a	4933439F11Rik	family with sequence similarity 187, member A	protein-coding
mm_166887.1	chr7	28085355	28085365	+	1	NA	exon (NM_001122603, exon 4 of 20)	exon (NM_001122603, exon 4 of 20)	14124	NM_001122603	215384	Mm.292276	NM_175444	ENSMUSG00000047730	Fcgbp	A430096B05Rik	Fc fragment of IgG binding protein	protein-coding
mm_155853.1	chrX	101276673	101276681	+	1	NA	exon (NM_021521, exon 7 of 45)	exon (NM_021521, exon 7 of 45)	2586	NM_021521	59024	Mm.20873	NM_021521	ENSMUSG00000079487	Med12	230kDa|Mopa|OPA-1|Tnrc11|Trap230	mediator complex subunit 12	protein-coding
mm_137905.1	chr17	31930563	31930565	+	1	NA	Intergenic	Intergenic	-74772	NM_010831	17691	Mm.290941	NM_010831	ENSMUSG00000024042	Sik1	Msk|Sik|Snf1lk	salt inducible kinase 1	protein-coding
mm_51656.1	chr6	86089686	86089688	+	1	NA	intron (NM_001271857, intron 4 of 15)	B4|SINE|B4	11639	NM_001271859	11519	Mm.104155	NM_013458	ENSMUSG00000030000	Add2	2900072M03Rik|add97	adducin 2 (beta)	protein-coding
mm_140352.1	chr17	86831314	86831324	+	1	NA	3' UTR (NM_010137, exon 16 of 16)	3' UTR (NM_010137, exon 16 of 16)	77455	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_128386.1	chr15	43090431	43090434	-	1	NA	intron (NM_172815, intron 3 of 5)	AT_rich|Low_complexity|Low_complexity	80386	NM_172815	239405	Mm.193274	NM_172815	ENSMUSG00000051920	Rspo2	2610028F08Rik|AA673245|D430027K22|ftls	R-spondin 2	protein-coding
mm_85576.1	chr9	107289707	107289786	-	1	NA	promoter-TSS (NM_001316691)	promoter-TSS (NM_001316691)	131	NM_178907	102626	Mm.222612	NM_178907	ENSMUSG00000032577	Mapkapk3	3PK|AI874665|MAPKAP-K3|MAPKAP3|MK-3|MK3|MapkKapk3	mitogen-activated protein kinase-activated protein kinase 3	protein-coding
mm_100477.1	chr11	120164775	120164792	+	1	NA	Intergenic	Intergenic	-13432	NM_001164798	72055	Mm.253403	NM_024249	ENSMUSG00000061306	Slc38a10	1810073N04Rik	solute carrier family 38, member 10	protein-coding
mm_842.1	chr1	51594249	51594251	+	1	NA	Intergenic	Intergenic	-115851	NM_001310549	109019	Mm.196290	NM_028696	ENSMUSG00000026107	Nabp1	4930434H03Rik|4930442A21Rik|4930488J04Rik|4933440J18Rik|5830411E10Rik|AI852561|Nbp1|Obfc2a|Ssb2	nucleic acid binding protein 1	protein-coding
mm_145922.1	chr18	67088233	67088248	+	1	NA	promoter-TSS (NM_177137)	promoter-TSS (NM_177137)	-58	NM_177137	14680	Mm.440746	NM_010307	ENSMUSG00000024524	Gnal	2610011C15Rik|9630020G10Rik|Galphaolf|Gna10|Golf	guanine nucleotide binding protein, alpha stimulating, olfactory type	protein-coding
mm_157470.1	chrX	47892503	47892525	-	1	NA	promoter-TSS (NM_001290708)	promoter-TSS (NM_001290708)	38	NM_053123	93761	Mm.229151	NM_053123	ENSMUSG00000031099	Smarca1	5730494M04Rik|Snf2l	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1	protein-coding
mm_9094.1	chr1	169046870	169046878	-	1	NA	Intergenic	Intergenic	484590	NM_023284	66977	Mm.151315	NM_023284	ENSMUSG00000026683	Nuf2	2410003C07Rik|AU044112|C85691|Cdca1|NUF2R	NUF2, NDC80 kinetochore complex component	protein-coding
mm_50440.1	chr6	48872837	48872860	+	1	NA	Intergenic	MLT2B5|LTR|ERVL	-22407	NM_029638	76507	Mm.213898	NM_029638	ENSMUSG00000029811	Aoc1	1600012D06Rik|Abp1|DAO	amine oxidase, copper-containing 1	protein-coding
mm_90982.1	chr10	13553156	13553166	-	1	NA	promoter-TSS (NM_019961)	promoter-TSS (NM_019961)	-19	NM_001347361	56535	Mm.282711	NM_019961	ENSMUSG00000019809	Pex3	1700014F15Rik|2810027F19Rik|2900010N04Rik	peroxisomal biogenesis factor 3	protein-coding
mm_58966.1	chr7	18987519	18987524	+	1	NA	promoter-TSS (NM_194064)	promoter-TSS (NM_194064)	-3	NM_194064	378430	Mm.277153	NM_194064	ENSMUSG00000051965	Nanos2	nos2	nanos homolog 2 (Drosophila)	protein-coding
mm_6101.1	chr1	64030166	64030176	-	1	NA	Intergenic	Intergenic	12330	NR_105864	102466760		NR_105864	ENSMUSG00000098487	Mir6899	Gm27384|mmu-mir-6899	microRNA 6899	ncRNA
mm_152534.1	chr19	11327105	11327118	-	1	NA	intron (NM_027836, intron 3 of 6)	intron (NM_027836, intron 3 of 6)	7584	NM_001276398	109225	Mm.491251	NM_027836	ENSMUSG00000024672	Ms4a7	9130422I10Rik|A430103C15Rik|CD20l4|CFFMA	membrane-spanning 4-domains, subfamily A, member 7	protein-coding
mm_28705.1	chr3	95556171	95556193	-	1	NA	exon (NM_021281, exon 8 of 8)	exon (NM_021281, exon 8 of 8)	-3495	NM_026489	67981	Mm.179050	NM_026489	ENSMUSG00000028109	Hormad1	4921522K05Rik|Nohma	HORMA domain containing 1	protein-coding
mm_90467.1	chr10	127776437	127776443	+	1	NA	promoter-TSS (NM_153133)	promoter-TSS (NM_153133)	35	NM_153133	103142	Mm.235814	NM_153133	ENSMUSG00000056148	Rdh9	AI121090|Crad3	retinol dehydrogenase 9	protein-coding
mm_42109.1	chr5	110565584	110565592	+	1	NA	intron (NM_198306, intron 1 of 10)	intron (NM_198306, intron 1 of 10)	21233	NM_198306	231605	Mm.275748	NM_198306	ENSMUSG00000033316	Galnt9	GalNAc-T9	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 9	protein-coding
mm_86250.1	chr9	121454740	121454744	-	1	NA	intron (NM_175114, intron 13 of 15)	intron (NM_175114, intron 13 of 15)	40952	NM_001284508	12424	Mm.2619	NM_031161	ENSMUSG00000032532	Cck	-	cholecystokinin	protein-coding
mm_43610.1	chr5	137985383	137985390	+	1	NA	exon (NM_013478, exon 2 of 4)	exon (NM_013478, exon 2 of 4)	3865	NM_013478	12007	Mm.30061	NM_013478	ENSMUSG00000037053	Azgp1	Zag	alpha-2-glycoprotein 1, zinc	protein-coding
mm_76121.1	chr8	80861102	80861119	-	1	NA	intron (NM_021356, intron 1 of 9)	intron (NM_021356, intron 1 of 9)	19369	NM_021356	14388	Mm.277409	NM_021356	ENSMUSG00000031714	Gab1	AA408973|AW107238	growth factor receptor bound protein 2-associated protein 1	protein-coding
mm_33805.1	chr4	134931218	134931229	+	1	NA	exon (NM_026780, exon 2 of 7)	exon (NM_026780, exon 2 of 7)	243	NM_026780	68592	Mm.29989	NM_026780	ENSMUSG00000028821	Syf2	1110018L13Rik|Cbpin|D4Bwg1551e|Gcipip|Ntc31|mp29|p29	SYF2 homolog, RNA splicing factor (S. cerevisiae)	protein-coding
mm_167445.1	chr8	121796484	121796493	-	1	NA	3' UTR (NM_145605, exon 12 of 12)	3' UTR (NM_145605, exon 12 of 12)	33081	NM_145605	234825	Mm.209329	NM_145605	ENSMUSG00000040263	Klhdc4	AA408426|AV352552|BC012312|G430025P05Rik	kelch domain containing 4	protein-coding
mm_76284.1	chr8	84197926	84197959	-	1	NA	Intergenic	Intergenic	-10576	NR_029740	387216		NR_029740	ENSMUSG00000065611	Mir23a	Mirn23a|mir-23a|mmu-mir-23a	microRNA 23a	ncRNA
mm_22807.1	chr3	27154021	27154031	+	1	NA	promoter-TSS (NM_001177626)	promoter-TSS (NM_001177626)	0	NR_040548	76657	Mm.417839	NR_040548	ENSMUSG00000097584	1700125G22Rik	-	RIKEN cDNA 1700125G22 gene	ncRNA
mm_156875.1	chrX	166170450	166170512	+	1	NA	promoter-TSS (NM_001310724)	promoter-TSS (NM_001310724)	27	NM_001310724	237221	Mm.209490	NM_146238	ENSMUSG00000040621	Gemin8	B130034M20Rik|B930082C09Rik|BC023488|gemin-8	gem (nuclear organelle) associated protein 8	protein-coding
mm_117467.1	chr13	76018525	76018605	-	1	NA	promoter-TSS (NM_178916)	promoter-TSS (NM_178916)	-3	NM_178916	218341	Mm.266515	NM_178916	ENSMUSG00000043190	Rfesd	AI256775|D030068K09	Rieske (Fe-S) domain containing	protein-coding
mm_43923.1	chr5	144768556	144768568	+	1	NA	promoter-TSS (NM_001081362)	promoter-TSS (NM_001081362)	-230	NM_001081362	100683	Mm.273570	NM_001081362	ENSMUSG00000045482	Trrap	AI481500	transformation/transcription domain-associated protein	protein-coding
mm_107112.1	chr12	17992861	17992888	+	1	NA	Intergenic	CpG	302060	NM_016677	53602	Mm.313619	NM_016677	ENSMUSG00000071379	Hpcal1	NVP-3|Nvp3|VILIP3|Vnsl3|Vsnl3	hippocalcin-like 1	protein-coding
mm_120269.1	chr14	63122886	63122936	+	1	NA	intron (NM_007798, intron 1 of 9)	intron (NM_007798, intron 1 of 9)	449	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_104482.1	chr11	95574393	95574406	-	1	NA	exon (NM_033217, exon 4 of 6)	exon (NM_033217, exon 4 of 6)	13299	NM_033217	18053	Mm.283893	NM_033217	ENSMUSG00000000120	Ngfr	LNGFR|Tnfrsf16|p75|p75NGFR|p75NTR	nerve growth factor receptor (TNFR superfamily, member 16)	protein-coding
mm_66868.1	chr7	57313093	57313096	-	1	NA	intron (NM_008074, intron 3 of 9)	Lx8|LINE|L1	73777	NM_008074	14407	Mm.434343	NM_008074	ENSMUSG00000055026	Gabrg3	B230362M20Rik|Gabrg-3	gamma-aminobutyric acid (GABA) A receptor, subunit gamma 3	protein-coding
mm_128994.1	chr15	74839037	74839045	-	1	NA	exon (NM_001033229, exon 4 of 9)	exon (NM_001033229, exon 4 of 9)	2602	NM_001033229	110115	Mm.322606	NM_001033229	ENSMUSG00000075604	Cyp11b1	AA389061|CPN1|Cyp11b|Cyp11b-1|FHI	cytochrome P450, family 11, subfamily b, polypeptide 1	protein-coding
mm_1739.1	chr1	75441007	75441028	+	1	NA	intron (NM_133708, intron 7 of 12)	intron (NM_133708, intron 7 of 12)	5074	NM_133708	69080	Mm.23951	NM_133708	ENSMUSG00000033021	Gmppa	1810012N01Rik	GDP-mannose pyrophosphorylase A	protein-coding
mm_39583.1	chr5	23479047	23479049	+	1	NA	intron (NM_026984, intron 10 of 25)	B1F|SINE|Alu	44619	NM_026984	69188	Mm.205190	NM_026984	ENSMUSG00000029004	Kmt2e	1810033J14Rik|9530077A04Rik|D230038D11Rik|Mll5|NKp44L	lysine (K)-specific methyltransferase 2E	protein-coding
mm_13174.1	chr2	92915132	92915142	+	1	NA	promoter-TSS (NM_030725)	promoter-TSS (NM_030725)	36	NM_030725	80976	Mm.33490	NM_030725	ENSMUSG00000027220	Syt13	5730409J20Rik|AI549909|mKIAA1427	synaptotagmin XIII	protein-coding
mm_113700.1	chr13	43135251	43135263	+	1	NA	3' UTR (NM_001302636, exon 13 of 13)	3' UTR (NM_001302636, exon 13 of 13)	12418	NM_001005748	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding
mm_139893.1	chr17	70851337	70851364	+	1	NA	promoter-TSS (NM_009372)	promoter-TSS (NM_009372)	-140	NM_009372	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_78894.1	chr9	44608536	44608544	+	1	NA	intron (NM_007841, intron 2 of 13)	B1_Mur4|SINE|Alu	3648	NM_181324	13209	Mm.267061	NM_007841	ENSMUSG00000032097	Ddx6	1110001P04Rik|E230023J21Rik|HLR2|mRCK/P54|p54|rck	DEAD (Asp-Glu-Ala-Asp) box polypeptide 6	protein-coding
mm_120570.1	chr14	69040683	69040700	+	1	NA	3' UTR (NM_009285, exon 4 of 4)	3' UTR (NM_009285, exon 4 of 4)	11402	NM_009285	20855	Mm.20911	NM_009285	ENSMUSG00000014813	Stc1	Stc	stanniocalcin 1	protein-coding
mm_12109.1	chr2	61590172	61590179	+	1	NA	intron (NM_011529, intron 1 of 7)	L1_Rod|LINE|L1	-2922	NM_001164072	21353	Mm.244393	NM_011529	ENSMUSG00000064289	Tank	C86182|E430026L09Rik|I-TRAF	TRAF family member-associated Nf-kappa B activator	protein-coding
mm_102779.1	chr11	68386944	68386970	-	1	NA	promoter-TSS (NM_008744)	promoter-TSS (NM_008744)	-131	NM_008744	18208	Mm.39095	NM_008744	ENSMUSG00000020902	Ntn1	AI561871|BC019633|Netrin-1	netrin 1	protein-coding
mm_10195.1	chr2	4925592	4925624	+	1	NA	exon (NM_010726, exon 3 of 9)	exon (NM_010726, exon 3 of 9)	6612	NM_010726	16922	Mm.391704	NM_010726	ENSMUSG00000026664	Phyh	AI256161|AI265699|Lnap1|PAHX	phytanoyl-CoA hydroxylase	protein-coding
mm_83550.1	chr9	46242404	46242438	-	1	NA	exon (NM_007468, exon 3 of 3)	exon (NM_007468, exon 3 of 3)	1577	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_97741.1	chr11	80465502	80465523	+	1	NA	intron (NM_178616, intron 9 of 13)	B3A|SINE|B2	-11534	NM_009871	12569	Mm.142275	NM_009871	ENSMUSG00000048895	Cdk5r1	Cdk5r|D11Bwg0379e|p25|p35	cyclin-dependent kinase 5, regulatory subunit 1 (p35)	protein-coding
mm_24243.1	chr3	89136134	89136183	+	1	NA	promoter-TSS (NM_001099779)	promoter-TSS (NM_001099779)	16	NM_013631	18770	Mm.383180	NM_013631	ENSMUSG00000041237	Pklr	Pk-1|Pk1|R-PK	pyruvate kinase liver and red blood cell	protein-coding
mm_40756.1	chr5	66898411	66898463	+	1	NA	intron (NM_001001980, intron 3 of 25)	intron (NM_001001980, intron 3 of 25)	-69979	NM_001256122	77569	Mm.374778	NM_001001980	ENSMUSG00000037736	Limch1	3732412D22Rik|mKIAA1102	LIM and calponin homology domains 1	protein-coding
mm_146959.1	chr18	33213787	33213827	-	1	NA	promoter-TSS (NM_001347624)	promoter-TSS (NM_001347624)	55	NM_001347624	170459	Mm.127058	NM_133774	ENSMUSG00000024378	Stard4	4632419C16Rik|9030213J02Rik	StAR-related lipid transfer (START) domain containing 4	protein-coding
mm_152021.1	chr19	6015843	6015871	-	1	NA	promoter-TSS (NM_007600)	promoter-TSS (NM_007600)	-32	NM_001110504	12333	Mm.6221	NM_007600	ENSMUSG00000024942	Capn1	Capa-1|Capa1|mu-calpin	calpain 1	protein-coding
mm_57828.1	chr6	129464426	129464434	-	1	NA	intron (NR_132130, intron 5 of 5)	intron (NR_132130, intron 5 of 5)	8349	NM_001309637	56644	Mm.239516	NM_020008	ENSMUSG00000079293	Clec7a	BGR|Clecsf12|beta-GR	C-type lectin domain family 7, member a	protein-coding
mm_72789.1	chr8	86888402	86888419	+	1	NA	Intergenic	Intergenic	-3152	NM_030563	80750	Mm.25117	NM_030563	ENSMUSG00000031652	N4bp1	AI481586|C81621	NEDD4 binding protein 1	protein-coding
mm_67786.1	chr7	97549778	97549790	-	1	NA	TTS (NM_183251)	TTS (NM_183251)	29713	NM_001177945	66273	Mm.41583	NM_183251	ENSMUSG00000035642	Aamdc	1810020D17Rik|1810037D19Rik|LI2	adipogenesis associated Mth938 domain containing	protein-coding
mm_134638.1	chr16	21762580	21762586	-	1	NA	exon (NM_023737, exon 7 of 7)	exon (NM_023737, exon 7 of 7)	25251	NM_023737	74147	Mm.28100	NM_023737	ENSMUSG00000022853	Ehhadh	1300002P22Rik|HD|L-PBE|LBFP|LBP|MFP|MFP1|PBFE	enoyl-Coenzyme A, hydratase/3-hydroxyacyl Coenzyme A dehydrogenase	protein-coding
mm_13910.1	chr2	120501212	120501253	+	1	NA	exon (NM_007601, exon 16 of 24)	exon (NM_007601, exon 16 of 24)	24323	NM_001109761	12335	Mm.458021	NM_007601	ENSMUSG00000079110	Capn3	AI323605|Capa-3|Capa3|Lp82|p94	calpain 3	protein-coding
mm_20414.1	chr2	129300530	129300568	-	1	NA	3' UTR (NM_010554, exon 7 of 7)	3' UTR (NM_010554, exon 7 of 7)	3179	NR_040371	100503468	Mm.446943	NR_040371	ENSMUSG00000085498	Gm14023	OTTMUSG00000015408	predicted gene 14023	ncRNA
mm_81616.1	chr9	110769742	110769757	+	1	NA	TTS (NM_010859)	TTS (NM_010859)	6068	NM_010859	17897	Mm.7353	NM_010859	ENSMUSG00000059741	Myl3	MLC1s|MLC1v|Mylc|VLC1	myosin, light polypeptide 3	protein-coding
mm_87675.1	chr10	59085766	59085769	+	1	NA	intron (NM_172788, intron 6 of 9)	RMER13B|LTR|ERVK	136080	NM_001024911	103080	Mm.346842	NM_001024910	ENSMUSG00000019917	Sept10	4921515A04Rik|9430099J10Rik|AA408298|AI874685	septin 10	protein-coding
mm_141704.1	chr17	33999491	33999508	-	1	NA	exon (NM_001001892, exon 3 of 8)	exon (NM_001001892, exon 3 of 8)	834	NM_001001892	14972	Mm.422886	NM_001001892	ENSMUSG00000061232	H2-K1	H-2K|H-2K(d)|H2-K|K-f	histocompatibility 2, K1, K region	protein-coding
mm_60658.1	chr7	44929765	44929773	+	1	NA	promoter-TSS (NM_001077264)	promoter-TSS (NM_001077264)	-279	NM_001077264	11771	Mm.6877	NM_007458	ENSMUSG00000060279	Ap2a1	Adtaa	adaptor-related protein complex 2, alpha 1 subunit	protein-coding
mm_118400.1	chr13	119408130	119408148	-	1	NA	intron (NM_001308506, intron 1 of 16)	intron (NM_001308506, intron 1 of 16)	872	NM_008710	18115	Mm.132584	NM_008710	ENSMUSG00000025453	Nnt	4930423F13Rik|AI323702|BB168308	nicotinamide nucleotide transhydrogenase	protein-coding
mm_13273.1	chr2	99734822	99734830	+	1	NA	Intergenic	Lx9|LINE|L1	-1889922	NM_009020	19374	Mm.4988	NM_009020	ENSMUSG00000032864	Rag2	Rag-2	recombination activating gene 2	protein-coding
mm_50022.1	chr6	41118496	41118506	+	1	NA	Intergenic	Intergenic	-82992	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_8173.1	chr1	137898378	137898419	-	1	NA	Intergenic	Intergenic	-68057	NR_029795	735252		NR_029795	ENSMUSG00000065565	Mir181a-1	Mirn181a-1|Mirn213|miR-213|mir-181a-1|mmu-mir-213	microRNA 181a-1	ncRNA
mm_139489.1	chr17	56081458	56081489	+	1	NA	intron (NM_001331053, intron 1 of 15)	intron (NM_001331053, intron 1 of 15)	1842	NM_001304785	15193	Mm.12966	NM_008233	ENSMUSG00000002833	Hdgfrp2	HRP-2	hepatoma-derived growth factor, related protein 2	protein-coding
mm_40270.1	chr5	39307124	39307133	+	1	NA	Intergenic	Intergenic	296446	NR_045416	75095	Mm.332354	NR_045416	ENSMUSG00000106741	4930513D17Rik	-	RIKEN cDNA 4930513D17 gene	ncRNA
mm_44705.1	chr5	30625467	30625506	-	1	NA	TTS (NM_010608)	TTS (NM_010608)	-22450	NR_049199	100885838		NR_049199	ENSMUSG00000093710	Mir5625	Gm23930|mmu-mir-5625	microRNA 5625	ncRNA
mm_171242.1	chr3	74765669	74765676	-	1	NA	Intergenic	L1Md_T|LINE|L1	378100	NM_001310529	213234	Mm.80075	NM_172515	ENSMUSG00000034151	Zbbx	4931432L23	zinc finger, B-box domain containing	protein-coding
mm_99300.1	chr11	101367543	101367565	+	1	NA	promoter-TSS (NM_008061)	promoter-TSS (NM_008061)	-162	NM_008061	14377	Mm.18064	NM_008061	ENSMUSG00000078650	G6pc	AW107337|G6Pase|G6pt|Glc-6-Pase	glucose-6-phosphatase, catalytic	protein-coding
mm_90628.1	chr10	128459569	128459609	+	1	NA	TTS (NR_106183)	TTS (NR_106183)	353	NM_001114097	68094	Mm.417338	NM_198160	ENSMUSG00000025369	Smarcc2	5930405J04Rik	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2	protein-coding
mm_170946.1	chr2	52089569	52089582	+	1	NA	exon (NM_175238, exon 12 of 36)	exon (NM_175238, exon 12 of 36)	16738	NM_175238	51869	Mm.254530	NM_175238	ENSMUSG00000036202	Rif1	5730435J01Rik|6530403D07Rik|AU016181|AW549474|D2Ertd145e	replication timing regulatory factor 1	protein-coding
mm_25924.1	chr3	131184655	131184701	+	1	NA	exon (NM_001276402, exon 4 of 10)	exon (NM_001276402, exon 4 of 10)	71887	NM_001276403	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_128636.1	chr15	59082296	59082323	-	1	NA	promoter-TSS (NM_144800)	promoter-TSS (NM_144800)	-283	NM_144800	211401	Mm.215481	NM_144800	ENSMUSG00000022353	Mtss1	2310003N14Rik|BC024131|D130001D01Rik|Mim|mKIAA0429	metastasis suppressor 1	protein-coding
mm_133281.1	chr16	77421648	77421658	+	1	NA	intron (NR_015543, intron 2 of 4)	intron (NR_015543, intron 2 of 4)	92325	NR_015543	77994	Mm.394688	NR_015543	ENSMUSG00000090386	Mir99ahg	2810055G20Rik|D730043B02Rik	Mir99a and Mirlet7c-1 host gene (non-protein coding)	ncRNA
mm_68974.1	chr7	126585776	126585840	-	1	NA	promoter-TSS (NM_001146311)	promoter-TSS (NM_001146311)	9	NM_001146311	12752	Mm.268930	NM_009907	ENSMUSG00000030720	Cln3	AI323623	ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease)	protein-coding
mm_2299.1	chr1	91500803	91500859	+	1	NA	exon (NM_028718, exon 4 of 15)	exon (NM_028718, exon 4 of 15)	6163	NM_028718	74019	Mm.318430	NM_028718	ENSMUSG00000034292	Traf3ip1	3930402D05Rik|AU041749|MIP-T3	TRAF3 interacting protein 1	protein-coding
mm_53882.1	chr6	3345888	3345894	-	1	NA	Intergenic	Intergenic	53680	NM_010156	209086	Mm.196013	NM_010156	ENSMUSG00000047735	Samd9l	AA175286|ESTM25|mKIAA2005	sterile alpha motif domain containing 9-like	protein-coding
mm_74827.1	chr8	23181421	23181423	-	1	NA	intron (NM_018743, intron 5 of 12)	intron (NM_018743, intron 5 of 12)	27031	NM_018743	102247	Mm.200898	NM_018743	ENSMUSG00000031545	Gpat4	AU041707|AW545732|Agpat6|Tsarg7	glycerol-3-phosphate acyltransferase 4	protein-coding
mm_69269.1	chr7	127926910	127926920	-	1	NA	intron (NM_133351, intron 4 of 5)	intron (NM_133351, intron 4 of 5)	3198	NM_133351	76560	Mm.5875	NM_133351	ENSMUSG00000030800	Prss8	2410039E18Rik|AI313909|C79772|CAP1|fr|mCAP1	protease, serine 8 (prostasin)	protein-coding
mm_8300.1	chr1	143776974	143777039	-	1	NA	promoter-TSS (NM_001159866)	promoter-TSS (NM_001159866)	45	NM_013835	20822	Mm.40370	NM_013835	ENSMUSG00000018199	Trove2	1810007I17Rik|A530054J02Rik|AI646302|SS-A/Ro|Ssa|Ssa2	TROVE domain family, member 2	protein-coding
mm_22647.1	chr3	14868386	14868402	+	1	NA	exon (NM_007606, exon 4 of 7)	exon (NM_007606, exon 4 of 7)	4856	NM_007606	12350	Mm.300	NM_007606	ENSMUSG00000027559	Car3	BB219044|Ca3|Car-3	carbonic anhydrase 3	protein-coding
mm_23689.1	chr3	68691497	68691511	+	1	NA	promoter-TSS (NM_008351)	promoter-TSS (NM_008351)	80	NM_008351	16159	Mm.103783	NM_008351	ENSMUSG00000027776	Il12a	IL-12p35|Il-12a|Ll12a|p35	interleukin 12a	protein-coding
mm_92984.1	chr10	86695517	86695545	-	1	NA	exon (NM_011631, exon 11 of 18)	exon (NM_011631, exon 11 of 18)	9913	NM_011631	22027	Mm.87773	NM_011631	ENSMUSG00000020048	Hsp90b1	ERp99|GRP94|TA-3|Targ2|Tra-1|Tra1|endoplasmin|gp96	heat shock protein 90, beta (Grp94), member 1	protein-coding
mm_72088.1	chr8	71579414	71579448	+	1	NA	exon (NM_011977, exon 4 of 14)	exon (NM_011977, exon 4 of 14)	10504	NM_011977	26457	Mm.38165	NM_011977	ENSMUSG00000031808	Slc27a1	FATP1|Fatp	solute carrier family 27 (fatty acid transporter), member 1	protein-coding
mm_157555.1	chrX	52052283	52052287	-	1	NA	TTS (NM_008150)	TTS (NM_008150)	-79513	NM_028851	74279	Mm.159154	NM_028851	ENSMUSG00000031118	1700080O16Rik	-	RIKEN cDNA 1700080O16 gene	protein-coding
mm_45262.1	chr5	63968868	63968901	-	1	NA	promoter-TSS (NM_145923)	promoter-TSS (NM_145923)	13	NM_145923	100532	Mm.243632	NM_145923	ENSMUSG00000047881	Rell1	AA536743	RELT-like 1	protein-coding
mm_98089.1	chr11	86593261	86593271	+	1	NA	intron (NM_029478, intron 10 of 11)	intron (NM_029478, intron 10 of 11)	-9108	NR_029738	387140		NR_029738	ENSMUSG00000065455	Mir21a	Mir21|Mirn21|mmu-mir-21|mmu-mir-21a	microRNA 21a	ncRNA
mm_18656.1	chr2	69799688	69799688	-	1	NA	Intergenic	Intergenic	9951	NM_028521	73373	Mm.9621	NM_028521	ENSMUSG00000027088	Phospho2	1700048E23Rik|AI661517|AU021728|AV006103|Phos2	phosphatase, orphan 2	protein-coding
mm_9284.1	chr1	171634643	171634653	-	1	NA	3' UTR (NM_144539, exon 8 of 8)	3' UTR (NM_144539, exon 8 of 8)	7252	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_61281.1	chr7	66839727	66839750	+	1	NA	promoter-TSS (NM_001033877)	promoter-TSS (NM_001033877)	3	NM_001033877	233332	Mm.445763	NM_001033877	ENSMUSG00000058145	Adamts17	AU023434	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 17	protein-coding
mm_139342.1	chr17	50181244	50181251	+	1	NA	intron (NM_181397, intron 1 of 9)	intron (NM_181397, intron 1 of 9)	9250	NM_181397	76438	Mm.41854	NM_181397	ENSMUSG00000039316	Rftn1	2310015N21Rik|AI853526	raftlin lipid raft linker 1	protein-coding
mm_62117.1	chr7	96647638	96647686	+	1	NA	intron (NM_001310760, intron 6 of 32)	intron (NM_001310760, intron 6 of 32)	153887	NR_045874	791381	Mm.402112	NR_045874	ENSMUSG00000053049	Gm15413	ENSMUSG00000053049|OTTMUSG00000021246	predicted gene 15413	ncRNA
mm_149007.1	chr19	8723994	8723997	+	1	NA	promoter-TSS (NM_001161413)	promoter-TSS (NM_001161413)	508	NR_002896	83673	Mm.292489	NR_002896	ENSMUSG00000108414	Snhg1	-	small nucleolar RNA host gene 1	ncRNA
mm_154289.1	chr19	60874565	60874568	-	1	NA	promoter-TSS (NM_007452)	promoter-TSS (NM_007452)	-28	NM_007452	11757	Mm.29821	NM_007452	ENSMUSG00000024997	Prdx3	AW822249|Aop1|D0Tohi1|Ef2l|Mer5|Prx3|SP22|TDXM	peroxiredoxin 3	protein-coding
mm_158663.1	chrX	157492062	157492081	-	1	NA	promoter-TSS (NM_009214)	promoter-TSS (NM_009214)	-25	NM_009214	20603	Mm.18652	NM_009214	ENSMUSG00000071708	Sms	AI427066|Gy|SPMSY|SpmST|gyro	spermine synthase	protein-coding
mm_78279.1	chr9	22101135	22101152	+	1	NA	exon (NM_009922, exon 2 of 7)	exon (NM_009922, exon 2 of 7)	1890	NM_009922	12797	Mm.4356	NM_009922	ENSMUSG00000001349	Cnn1	CN|CnnI	calponin 1	protein-coding
mm_106405.1	chr11	118909849	118909863	-	1	NA	promoter-TSS (NM_001039167)	promoter-TSS (NM_001039167)	-284	NM_001039167	52897	Mm.341103	NM_001024931	ENSMUSG00000025576	Rbfox3	Fox-3|Hrnbp3|NeuN|Neuna60	RNA binding protein, fox-1 homolog (C. elegans) 3	protein-coding
mm_68748.1	chr7	121064680	121064702	-	1	NA	3' UTR (NM_030691, exon 6 of 6)	3' UTR (NM_030691, exon 6 of 6)	9839	NM_030691	80719	Mm.160384	NM_030691	ENSMUSG00000035004	Igsf6	-	immunoglobulin superfamily, member 6	protein-coding
mm_117137.1	chr13	60940227	60940233	-	1	NA	exon (NM_009411, exon 3 of 5)	exon (NM_009411, exon 3 of 5)	1705	NM_009411	21984	Mm.2372	NM_009411	ENSMUSG00000033834	Tpbpa	AV033951|Tb-1|Tb1|Tpbp|b2b1247Clo	trophoblast specific protein alpha	protein-coding
mm_14695.1	chr2	141611825	141611826	+	1	NA	intron (NM_001013802, intron 6 of 18)	L1VL4|LINE|L1	-940349	NM_178382	71436	Mm.426781	NM_178382	ENSMUSG00000051379	Flrt3	5530600M07Rik|C430047I10Rik|mKIAA1469	fibronectin leucine rich transmembrane protein 3	protein-coding
mm_71288.1	chr8	40926221	40926266	+	1	NA	promoter-TSS (NM_026840)	promoter-TSS (NM_026840)	10	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_161718.1	chr17	25965423	25965423	-	1	NA	promoter-TSS (NM_015830)	promoter-TSS (NM_015830)	82	NM_015830	50817	Mm.216072	NM_015830	ENSMUSG00000037326	Capn15	Solh	calpain 15	protein-coding
mm_62668.1	chr7	108950629	108950679	+	1	NA	Intergenic	CpG	16239	NM_025344	66085	Mm.182962	NM_025344	ENSMUSG00000031029	Eif3f	0610037M02Rik|AA409853|Eif3s5	eukaryotic translation initiation factor 3, subunit F	protein-coding
mm_61568.1	chr7	79710378	79710406	+	1	NA	exon (NM_010626, exon 4 of 18)	exon (NM_010626, exon 4 of 18)	3794	NM_010626	16576	Mm.101633	NM_010626	ENSMUSG00000050382	Kif7	-	kinesin family member 7	protein-coding
mm_171084.1	chr3	122276326	122276328	+	1	NA	exon (NM_153806, exon 2 of 7)	exon (NM_153806, exon 2 of 7)	1913	NM_153806	99480	Mm.398647	NM_153806	ENSMUSG00000039756	Dnttip2	4930588M11Rik|AA408582|AU014960|HSU15552	deoxynucleotidyltransferase, terminal, interacting protein 2	protein-coding
mm_139259.1	chr17	47749100	47749114	+	1	NA	intron (NM_001161723, intron 1 of 8)	intron (NM_001161723, intron 1 of 8)	11176	NM_001161723	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_64316.1	chr7	141865012	141865016	+	1	NA	exon (NM_028801, exon 31 of 49)	exon (NM_028801, exon 31 of 49)	25942	NM_028801	74180	Mm.200752	NM_028801	ENSMUSG00000066108	Muc5b	2300002I04Rik|A130042M24|AV085033|MUC5|MUC9|mucin 5b	mucin 5, subtype B, tracheobronchial	protein-coding
mm_172680.1	chr8	51943846	51943846	-	1	NA	Intergenic	RLTR10A|LTR|ERVK	-1567856	NM_001205054	11593	Mm.334535	NM_001005847	ENSMUSG00000031521	Aga	AW060726	aspartylglucosaminidase	protein-coding
mm_135842.1	chr16	58555750	58555752	-	1	NA	Intergenic	Intergenic	-32439	NM_018784	54613	Mm.212742	NM_018784	ENSMUSG00000022747	St3gal6	1700023B24Rik|AI930218|AW552396|Siat10|St3galVI	ST3 beta-galactoside alpha-2,3-sialyltransferase 6	protein-coding
mm_3979.1	chr1	164249234	164249286	+	1	NA	exon (NM_054087, exon 1 of 6)	exon (NM_054087, exon 1 of 6)	214	NM_001276455	116914	Mm.35444	NM_054087	ENSMUSG00000040918	Slc19a2	AV276020|AW322295|DDA1|THTR1|TRMA	solute carrier family 19 (thiamine transporter), member 2	protein-coding
mm_81807.1	chr9	117252522	117252559	+	1	NA	promoter-TSS (NM_001172126)	promoter-TSS (NM_001172126)	-57	NM_001172126	207181	Mm.326411	NM_178660	ENSMUSG00000039607	Rbms3	6720477E09Rik|8430436O14Rik	RNA binding motif, single stranded interacting protein	protein-coding
mm_116429.1	chr13	41847585	41847598	-	1	NA	promoter-TSS (NM_001145875)	promoter-TSS (NM_001145875)	25	NM_001145875	109254	Mm.25195	NM_175417	ENSMUSG00000058022	Adtrp	9530008L14Rik	androgen dependent TFPI regulating protein	protein-coding
mm_138901.1	chr17	43568690	43568704	+	1	NA	5' UTR (NM_013737, exon 1 of 12)	5' UTR (NM_013737, exon 1 of 12)	246	NM_013737	27226	Mm.9277	NM_013737	ENSMUSG00000023913	Pla2g7	PAF-AH|R75400	phospholipase A2, group VII (platelet-activating factor acetylhydrolase, plasma)	protein-coding
mm_137749.1	chr17	29394403	29394435	+	1	NA	Intergenic	Intergenic	33505	NM_001159538	26382	Mm.279187	NM_013710	ENSMUSG00000024013	Fgd2	Tcd-2|Tcd2|ZFYVE4|tcs-2|tcs2	FYVE, RhoGEF and PH domain containing 2	protein-coding
mm_37570.1	chr4	126242116	126242126	-	1	NA	exon (NM_144941, exon 2 of 17)	exon (NM_144941, exon 2 of 17)	14198	NM_144941	245877	Mm.266716	NM_144941	ENSMUSG00000028849	Map7d1	AV028413|BC019977|Mtap7d1|Parcc1|Rprc1|mKIAA1187	MAP7 domain containing 1	protein-coding
mm_91540.1	chr10	39534761	39534775	-	1	NA	intron (NM_001122892, intron 11 of 12)	intron (NM_001122892, intron 11 of 12)	-78166	NM_134000	103213	Mm.436686	NM_134000	ENSMUSG00000019842	Traf3ip2	AI429613|Act1|CIKS	TRAF3 interacting protein 2	protein-coding
mm_152421.1	chr19	10674902	10674930	-	1	NA	exon (NM_021453, exon 4 of 9)	exon (NM_021453, exon 4 of 9)	3155	NM_021453	58803	Mm.34037	NM_021453	ENSMUSG00000024738	Pga5	1110035E17Rik|Pepf	pepsinogen 5, group I	protein-coding
mm_57918.1	chr6	133852090	133852090	-	1	NA	exon (NM_010594, exon 2 of 4)	exon (NM_010594, exon 2 of 4)	1577	NM_010594	16483	Mm.13052	NM_010594	ENSMUSG00000032758	Kap	AW146435|FKSG22	kidney androgen regulated protein	protein-coding
mm_41197.1	chr5	88328146	88328178	+	1	NA	exon (NM_008644, exon 3 of 3)	exon (NM_008644, exon 3 of 3)	10850	NM_008644	17830	Mm.200411	NM_008644	ENSMUSG00000064156	Prol1	Muc10	proline rich, lacrimal 1	protein-coding
mm_66726.1	chr7	46179930	46180032	-	1	NA	promoter-TSS (NM_011510)	promoter-TSS (NM_011510)	52	NM_011510	20927	Mm.259076	NM_011510	ENSMUSG00000040136	Abcc8	D930031B21Rik|SUR1|Sur	ATP-binding cassette, sub-family C (CFTR/MRP), member 8	protein-coding
mm_111369.1	chr12	87236995	87237004	-	1	NA	intron (NM_027744, intron 2 of 7)	intron (NM_027744, intron 2 of 7)	1602	NM_027744	71275	Mm.79198	NM_027744	ENSMUSG00000072919	Noxred1	4933437F05Rik	NADP+ dependent oxidoreductase domain containing 1	protein-coding
mm_147369.1	chr18	43438281	43438297	-	1	NA	promoter-TSS (NM_001291455)	promoter-TSS (NM_001291455)	-3	NM_001291455	22240	Mm.8180	NM_009468	ENSMUSG00000024501	Dpysl3	CRMP-4|DRP-3|TUC4|ULIP-1|Ulip|Ulip1	dihydropyrimidinase-like 3	protein-coding
mm_71128.1	chr8	36538238	36538244	+	1	NA	Intergenic	Intergenic	49050	NM_176952	319582	Mm.180924	NM_176952	ENSMUSG00000039620	6430573F11Rik	Kiaa1456|TRM9L	RIKEN cDNA 6430573F11 gene	protein-coding
mm_90751.1	chr10	5488268	5488289	-	1	NA	promoter-TSS (NM_001347711)	promoter-TSS (NM_001347711)	36	NM_001347711	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_52643.1	chr6	117178788	117178801	+	1	NA	3' UTR (NM_001012477, exon 4 of 4)	3' UTR (NM_001012477, exon 4 of 4)	10259	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_27112.1	chr3	30942444	30942487	-	1	NA	exon (NM_153421, exon 7 of 15)	exon (NM_153421, exon 7 of 15)	26950	NM_001165954	241915	Mm.233173	NM_153421	ENSMUSG00000037652	Phc3	E030046K01Rik|Edr3|Hph3	polyhomeotic-like 3 (Drosophila)	protein-coding
mm_72286.1	chr8	75117612	75117627	+	1	NA	exon (NM_008566, exon 8 of 17)	exon (NM_008566, exon 8 of 17)	8110	NM_008566	17218	Mm.5048	NM_008566	ENSMUSG00000005410	Mcm5	AA617332|AI324988|AL033333|Cdc46|Mcmd5|P1-CDC46	minichromosome maintenance complex component 5	protein-coding
mm_45780.1	chr5	87296267	87296267	-	1	NA	Intergenic	L1Md_A|LINE|L1	40928	NM_028094	72094	Mm.482739	NM_028094	ENSMUSG00000035780	Ugt2a3	2010321J07Rik	UDP glucuronosyltransferase 2 family, polypeptide A3	protein-coding
mm_148859.1	chr19	6399858	6399890	+	1	NA	promoter-TSS (NM_011242)	promoter-TSS (NM_011242)	-709	NM_011242	19395	Mm.77017	NM_011242	ENSMUSG00000032946	Rasgrp2	CDC25L|Caldaggef1	RAS, guanyl releasing protein 2	protein-coding
mm_121085.1	chr14	99226166	99226174	+	1	NA	intron (NM_029320, intron 16 of 17)	intron (NM_029320, intron 16 of 17)	-72521	NM_009769	12224	Mm.30262	NM_009769	ENSMUSG00000005148	Klf5	4930520J07Rik|Bteb2|CKLF|IKLF	Kruppel-like factor 5	protein-coding
mm_128799.1	chr15	66831626	66831668	-	1	NA	5' UTR (NM_001029841, exon 1 of 8)	5' UTR (NM_001029841, exon 1 of 8)	182	NM_001029841	20491	Mm.7601	NM_009192	ENSMUSG00000022372	Sla	Slap|Slap-1	src-like adaptor	protein-coding
mm_28465.1	chr3	90695373	90695381	-	1	NA	intron (NM_001281852, intron 1 of 2)	intron (NM_001281852, intron 1 of 2)	344	NM_001281852	20202	Mm.2128	NM_009114	ENSMUSG00000056071	S100a9	60B8Ag|AW546964|BEE22|Cagb|GAGB|L1Ag|MRP14|p14	S100 calcium binding protein A9 (calgranulin B)	protein-coding
mm_70447.1	chr8	11756186	11756189	+	1	NA	intron (NM_001113517, intron 1 of 18)	Tigger17|DNA|TcMar-Tigger	-2143	NM_017402	54126	Mm.244068	NM_017402	ENSMUSG00000031511	Arhgef7	Cool|PIX|Pak3bp|betaPix|betaPix-b|betaPix-c|cool-1|mKIAA0142|p85Cool1|p85SPR	Rho guanine nucleotide exchange factor (GEF7)	protein-coding
mm_114420.1	chr13	64370443	64370464	+	1	NA	promoter-TSS (NM_009984)	promoter-TSS (NM_009984)	67	NM_009984	13039	Mm.930	NM_009984	ENSMUSG00000021477	Ctsl	1190035F06Rik|CatL|Ctsl1|MEP|fs|nkt	cathepsin L	protein-coding
mm_28236.1	chr3	88455736	88455788	-	1	NA	promoter-TSS (NM_013658)	promoter-TSS (NM_013658)	-1	NM_013658	20351	Mm.439752	NM_013658	ENSMUSG00000028064	Sema4a	AI132332|SemB|Semab	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A	protein-coding
mm_115159.1	chr13	107063720	107063736	+	1	NA	Intergenic	Intergenic	41158	NR_015471	100040322	Mm.133867	NR_015471		3830408C21Rik	-	RIKEN cDNA 3830408C21 gene	ncRNA
mm_106185.1	chr11	116749909	116749938	-	1	NA	Intergenic	Intergenic	-2244	NR_003364	193217	Mm.100084	NR_003364		BC018473	-	cDNA sequence BC018473	ncRNA
mm_68225.1	chr7	104434754	104434784	-	1	NA	intron (NM_009099, intron 2 of 7)	Lx7|LINE|L1	30424	NM_009099	20128	Mm.295578	NM_009099	ENSMUSG00000030921	Trim30a	Rpt-1|Rpt1|Trim30	tripartite motif-containing 30A	protein-coding
mm_26990.1	chr3	25712391	25712402	-	1	NA	intron (NM_001163387, intron 3 of 5)	RMER17D2|LTR|ERVK	440911	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_65993.1	chr7	30552256	30552316	-	1	NA	promoter-TSS (NM_183321)	promoter-TSS (NM_183321)	-14	NM_183321	333193	Mm.34885	NM_183321	ENSMUSG00000036864	Proser3	-	proline and serine rich 3	protein-coding
mm_92435.1	chr10	77182791	77182799	-	1	NA	Intergenic	Intergenic	-16265	NM_009929	12822	Mm.4352	NM_009929	ENSMUSG00000001435	Col18a1	-	collagen, type XVIII, alpha 1	protein-coding
mm_89512.1	chr10	94147983	94148009	+	1	NA	promoter-TSS (NM_011629)	promoter-TSS (NM_011629)	65	NM_011629	22025	Mm.107483	NM_011629	ENSMUSG00000005897	Nr2c1	4831444H07Rik|80.3|Eenr|TR2|Tr2-11	nuclear receptor subfamily 2, group C, member 1	protein-coding
mm_106120.1	chr11	116359427	116359444	-	1	NA	intron (NM_027258, intron 5 of 18)	intron (NM_027258, intron 5 of 18)	-24081	NM_008240	15223	Mm.378938	NM_008240	ENSMUSG00000034227	Foxj1	FKHL-13|HFH-4|Hfh4	forkhead box J1	protein-coding
mm_13767.1	chr2	118560440	118560442	+	1	NA	Intergenic	BC1_Mm|scRNA|scRNA	-10755	NM_138313	171543	Mm.210125	NM_138313	ENSMUSG00000040093	Bmf	AW260063|AW411872	BCL2 modifying factor	protein-coding
mm_38681.1	chr4	145024743	145024746	-	1	NA	intron (NM_001276502, intron 64 of 68)	intron (NM_001276502, intron 64 of 68)	131607	NM_011303	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding
mm_2737.1	chr1	128252196	128252218	+	1	NA	exon (NM_026390, exon 2 of 13)	exon (NM_026390, exon 2 of 13)	8026	NM_026390	67812	Mm.293321	NM_026390	ENSMUSG00000026353	Ubxn4	1300013G12Rik|Ubxd2|mKIAA0242	UBX domain protein 4	protein-coding
mm_36483.1	chr4	82885148	82885152	-	1	NA	promoter-TSS (NM_009887)	promoter-TSS (NM_009887)	1	NM_009887	12622	Mm.6780	NM_009887	ENSMUSG00000038192	Cer1	Cerl|Cerl1|Cerr1|cer-1	cerberus 1, DAN family BMP antagonist	protein-coding
mm_79561.1	chr9	58079359	58079382	+	1	NA	intron (NM_001166282, intron 6 of 19)	intron (NM_001166282, intron 6 of 19)	22855	NM_029212	382077	Mm.335193	NM_029212	ENSMUSG00000037716	Ccdc33	4930535E21Rik|Gm1117|Tzip1	coiled-coil domain containing 33	protein-coding
mm_3201.1	chr1	135818767	135818773	+	1	NA	5' UTR (NM_133664, exon 1 of 10)	5' UTR (NM_133664, exon 1 of 10)	172	NM_133664	16763	Mm.36726	NM_133664	ENSMUSG00000041782	Lad1	-	ladinin	protein-coding
mm_5337.1	chr1	24005609	24005646	-	1	NA	promoter-TSS (NM_026503)	promoter-TSS (NM_026503)	13	NM_026503	68002	Mm.250424	NM_026503	ENSMUSG00000026154	Sdhaf4	1110058L19Rik|1700001E18Rik|C6orf57	succinate dehydrogenase complex assembly factor 4	protein-coding
mm_154547.1	chrM	14842	14867	-	1	NA	NA	Intergenic	NA	NA								
mm_55883.1	chr6	83527367	83527373	-	1	NA	exon (NM_009610, exon 2 of 9)	exon (NM_009610, exon 2 of 9)	8881	NM_009610	11468	Mm.292865	NM_009610	ENSMUSG00000059430	Actg2	ACTA3|Act-4|Act4|SMGA	actin, gamma 2, smooth muscle, enteric	protein-coding
mm_95551.1	chr11	52307861	52307863	+	1	NA	Intergenic	Intergenic	-24848	NM_001313981	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_76876.1	chr8	105565986	105566071	-	1	NA	promoter-TSS (NM_013477)	promoter-TSS (NM_013477)	12	NM_013477	11972	Mm.17708	NM_013477	ENSMUSG00000013160	Atp6v0d1	AI267038|Ac39|Atp6d|P39|VATX|Vma6	ATPase, H+ transporting, lysosomal V0 subunit D1	protein-coding
mm_137594.1	chr17	28124038	28124044	+	1	NA	Intergenic	Intergenic	-18485	NM_001004366	268935	Mm.258491	NM_001004366	ENSMUSG00000038677	Scube3	CEGF3|D030038I21Rik	signal peptide, CUB domain, EGF-like 3	protein-coding
mm_120686.1	chr14	70774339	70774353	+	1	NA	promoter-TSS (NM_010071)	promoter-TSS (NM_010071)	-35	NM_010071	13449	Mm.243323	NM_010071	ENSMUSG00000022102	Dok2	DokR|Frip	docking protein 2	protein-coding
mm_93720.1	chr10	119239501	119239516	-	1	NA	intron (NM_027994, intron 1 of 14)	CpG	547	NM_027994	71902	Mm.203965	NM_027994	ENSMUSG00000020114	Cand1	2310038O07Rik|6330512O03Rik|AI195005|AI846556|D10Ertd516e|Tp120a|mKIAA0829	cullin associated and neddylation disassociated 1	protein-coding
mm_129629.1	chr15	80219855	80219862	-	1	NA	Intergenic	Intergenic	-14222	NM_178719	239555	Mm.307163	NM_178719	ENSMUSG00000022412	Mief1	A230016E22|AI452372|Smcr7l	mitochondrial elongation factor 1	protein-coding
mm_115515.1	chr13	5804637	5804648	-	1	NA	Intergenic	Intergenic	53450	NR_045891	71867	Mm.179181	NR_045891	ENSMUSG00000100625	1700016G22Rik	-	RIKEN cDNA 1700016G22 gene	ncRNA
mm_31241.1	chr4	44756687	44756697	+	1	NA	5' UTR (NM_138590, exon 1 of 9)	5' UTR (NM_138590, exon 1 of 9)	133	NM_138590	319885	Mm.331576	NM_138590	ENSMUSG00000035649	Zcchc7	4930572I07Rik|D4Wsu132e	zinc finger, CCHC domain containing 7	protein-coding
mm_112517.1	chr13	9127943	9127959	+	1	NA	intron (NM_001311117, intron 3 of 16)	intron (NM_001311117, intron 3 of 16)	34070	NM_172585	217980	Mm.234944	NM_172585	ENSMUSG00000033499	Larp4b	A630096F19|AI256361|D13Wsu64e|Larp5	La ribonucleoprotein domain family, member 4B	protein-coding
mm_144540.1	chr18	25839102	25839115	+	1	NA	Intergenic	Intergenic	-85125	NM_001174074	108013	Mm.266435	NM_133195	ENSMUSG00000024268	Celf4	A230070D14Rik|BRUNOL-4|Brul4|Brunol4|C130060B05Rik	CUGBP, Elav-like family member 4	protein-coding
mm_72219.1	chr8	72688456	72688466	+	1	NA	intron (NM_176940, intron 11 of 18)	B3A|SINE|B2	-34809	NM_001113248	20467	Mm.2137	NM_009188	ENSMUSG00000031622	Sin3b	2810430C10Rik	transcriptional regulator, SIN3B (yeast)	protein-coding
mm_2651.1	chr1	125676862	125676874	+	1	NA	promoter-TSS (NM_027677)	promoter-TSS (NM_027677)	-128	NM_027677	71111	Mm.32727	NM_027677	ENSMUSG00000026343	Gpr39	4933415E13Rik	G protein-coupled receptor 39	protein-coding
mm_51924.1	chr6	91265963	91265972	+	1	NA	exon (NM_001081437, exon 12 of 17)	exon (NM_001081437, exon 12 of 17)	53203	NM_007992	14115	Mm.249146	NM_007992	ENSMUSG00000064080	Fbln2	5730577E14Rik|FIBL-2	fibulin 2	protein-coding
mm_68942.1	chr7	126503409	126503477	-	1	NA	promoter-TSS (NM_183020)	promoter-TSS (NM_183020)	-141	NM_183020	233871	Mm.231450	NM_183020	ENSMUSG00000032637	Atxn2l	A2D|A2LG|A2RP|A2lp|Atxnl2	ataxin 2-like	protein-coding
mm_102794.1	chr11	68825319	68825320	-	1	NA	intron (NM_023668, intron 8 of 8)	intron (NM_023668, intron 8 of 8)	27812	NM_023668	83431	Mm.31979	NM_023668	ENSMUSG00000018736	Ndel1	2600006O07Rik|MITAP1|NUDEL|mNudel	nudE neurodevelopment protein 1 like 1	protein-coding
mm_85350.1	chr9	103210617	103210672	-	1	NA	exon (NM_133977, exon 16 of 17)	exon (NM_133977, exon 16 of 17)	-8579	NM_009275	20818	Mm.273053	NM_009275	ENSMUSG00000032553	Srprb	AA409543	signal recognition particle receptor, B subunit	protein-coding
mm_10588.1	chr2	18307935	18307981	+	1	NA	exon (NM_001190817, exon 5 of 13)	exon (NM_001190817, exon 5 of 13)	84872	NM_001190817	13418	Mm.246674	NM_007869	ENSMUSG00000026740	Dnajc1	4733401K02Rik|AA960110|D230036H06Rik|Dnajl1|ERdj1|ERj1p|MTJ1	DnaJ heat shock protein family (Hsp40) member C1	protein-coding
mm_105437.1	chr11	104352385	104352387	-	1	NA	intron (NM_001081045, intron 6 of 13)	ID4_|SINE|ID	89905	NM_001081045	76719	Mm.136418	NM_001081045	ENSMUSG00000018412	Kansl1	1700081L11Rik|9430041J06Rik|mKIAA1267	KAT8 regulatory NSL complex subunit 1	protein-coding
mm_40791.1	chr5	67453467	67453469	+	1	NA	Intergenic	Intergenic	-10430	NR_110363	320479	Mm.387187	NR_015582	ENSMUSG00000107385	C330024D21Rik	-	RIKEN cDNA C330024D21 gene	ncRNA
mm_33914.1	chr4	136424575	136424590	+	1	NA	promoter-TSS (NM_001285484)	promoter-TSS (NM_001285484)	-30	NM_001285484	15552	Mm.40573	NM_008309	ENSMUSG00000070687	Htr1d	5-HT-1D|5-HT1D|AI853647|Gpcr14|Htr1db	5-hydroxytryptamine (serotonin) receptor 1D	protein-coding
mm_62940.1	chr7	118937121	118937123	+	1	NA	intron (NM_001081446, intron 7 of 8)	intron (NM_001081446, intron 7 of 8)	58089	NM_022420	64297	Mm.103439	NM_022420	ENSMUSG00000008734	Gprc5b	AW125761|Raig2	G protein-coupled receptor, family C, group 5, member B	protein-coding
mm_61438.1	chr7	75060691	75060694	+	1	NA	intron (NR_131122, intron 6 of 7)	Lx8b|LINE|L1	30481	NR_131122	75205	Mm.399304	NR_131122	ENSMUSG00000108803	4930533N22Rik	-	RIKEN cDNA 4930533N22 gene	ncRNA
mm_21659.1	chr2	164404826	164404857	-	1	NA	promoter-TSS (NM_013592)	promoter-TSS (NM_013592)	-23	NM_013592	17183	Mm.29428	NM_013592	ENSMUSG00000016995	Matn4	matrilin-4	matrilin 4	protein-coding
mm_49421.1	chr6	29216473	29216502	+	1	NA	promoter-TSS (NM_001302934)	promoter-TSS (NM_001302934)	-123	NM_001302934	23917	Mm.260707	NM_011829	ENSMUSG00000003500	Impdh1	B930086D20Rik|IMPDH-I	inosine 5'-phosphate dehydrogenase 1	protein-coding
mm_160616.1	chr9	88839310	88839310	+	1	NA	5' UTR (NM_001177858, exon 1 of 7)	5' UTR (NM_001177858, exon 1 of 7)	146	NM_001177858	666731	Mm.446951	NM_001177858	ENSMUSG00000067399	Trim43c	EG666731|Trim43	tripartite motif-containing 43C	protein-coding
mm_98601.1	chr11	95831325	95831337	+	1	NA	3' UTR (NM_001163464, exon 8 of 8)	3' UTR (NM_001163464, exon 8 of 8)	6831	NM_153104	237928	Mm.133075	NM_153104	ENSMUSG00000050860	Phospho1	D11Moh36|Phospo1	phosphatase, orphan 1	protein-coding
mm_172073.1	chr6	140738706	140738706	-	1	NA	Intergenic	ERVB7_1-LTR_MM|LTR|ERVK	111821	NM_001309436	11569	Mm.86453	NM_009637	ENSMUSG00000030232	Aebp2	AU023766|B230313N05Rik	AE binding protein 2	protein-coding
mm_144370.1	chr18	20510270	20510290	+	1	NA	promoter-TSS (NM_030596)	promoter-TSS (NM_030596)	6	NM_030596	13512	Mm.106811	NM_030596	ENSMUSG00000056632	Dsg3	bal	desmoglein 3	protein-coding
mm_58584.1	chr7	4925803	4925868	+	1	NA	promoter-TSS (NM_173008)	promoter-TSS (NM_173008)	-9	NM_173008	269855	Mm.44190	NM_173008	ENSMUSG00000035279	Ssc5d	A430110N23Rik|S5D-SRCRB	scavenger receptor cysteine rich family, 5 domains	protein-coding
mm_121429.1	chr14	120326688	120326732	+	1	NA	intron (NM_175341, intron 2 of 8)	B4|SINE|B4	51041	NM_175341	105559	Mm.238266	NM_175341	ENSMUSG00000022139	Mbnl2	1110002M11Rik|AI047808|AI837313|AI849185|AL118326|MBLL|R75232|mKIAA4072	muscleblind-like 2	protein-coding
mm_130418.1	chr15	98074286	98074289	-	1	NA	intron (NM_144851, intron 6 of 17)	B1F|SINE|Alu	-18302	NM_001163488	18642	Mm.272582	NM_021514	ENSMUSG00000033065	Pfkm	AI131669|ATP-PFK|PFK-A|PFK-M|Pfk-4|Pfk4|Pfka|Pfkx	phosphofructokinase, muscle	protein-coding
mm_108272.1	chr12	78861679	78861688	+	1	NA	promoter-TSS (NM_026114)	promoter-TSS (NM_026114)	-45	NM_023721	73834	Mm.311549	NM_023721	ENSMUSG00000021114	Atp6v1d	1110004P10Rik|Atp6m|VATD|Vma8	ATPase, H+ transporting, lysosomal V1 subunit D	protein-coding
mm_6004.1	chr1	58973336	58973354	-	1	NA	promoter-TSS (NM_172656)	promoter-TSS (NM_172656)	137	NM_172406	70827	Mm.222887	NM_172406	ENSMUSG00000026028	Trak2	2900022D04Rik|4733401O11Rik|AI480836|AW046271|Als2cr3|CALS-C|GRIF-1|GRIF1|OIP98|mKIAA0549	trafficking protein, kinesin binding 2	protein-coding
mm_142962.1	chr17	56120833	56120848	-	1	NA	exon (NM_029796, exon 2 of 2)	exon (NM_029796, exon 2 of 2)	1106	NM_029796	76905	Mm.348025	NM_029796	ENSMUSG00000037095	Lrg1	1300008B03Rik|2310031E04Rik|Lrg|Lrhg	leucine-rich alpha-2-glycoprotein 1	protein-coding
mm_14931.1	chr2	151542508	151542515	+	1	NA	promoter-TSS (NM_008019)	promoter-TSS (NM_008019)	28	NM_001302078	14225	Mm.278458	NM_008019	ENSMUSG00000032966	Fkbp1a	FKBP12|Fkbp|Fkbp1	FK506 binding protein 1a	protein-coding
mm_159064.1	chr2	20967731	20967731	-	1	NA	promoter-TSS (NM_001081364)	promoter-TSS (NM_001081364)	-10	NM_001128084	71435	Mm.28507	NM_001081364	ENSMUSG00000036591	Arhgap21	5530401C11Rik|AA416458|ARHGAP10	Rho GTPase activating protein 21	protein-coding
mm_25360.1	chr3	107091409	107091423	+	1	NA	Intergenic	Intergenic	-10151	NM_008417	16490	Mm.39285	NM_008417	ENSMUSG00000040724	Kcna2	Akr6a4|ENSMUSG00000074335|Gm10672|Kca1-2|Kv1.2|Mk-2	potassium voltage-gated channel, shaker-related subfamily, member 2	protein-coding
mm_56403.1	chr6	97148909	97148930	-	1	NA	promoter-TSS (NM_175313)	promoter-TSS (NM_175313)	-36	NM_175313	101351	Mm.116802	NM_175313	ENSMUSG00000035245	Eogt	A130022J15Rik|AI447490|AW214473|AW259391|Aer61	EGF domain-specific O-linked N-acetylglucosamine (GlcNAc) transferase	protein-coding
mm_85366.1	chr9	103220943	103220953	-	1	NA	exon (NM_133977, exon 9 of 17)	exon (NM_133977, exon 9 of 17)	9338	NM_133977	22041	Mm.37214	NM_133977	ENSMUSG00000032554	Trf	AI266983|Cd176|HP|Tf|Tfn|hpx	transferrin	protein-coding
mm_95943.1	chr11	58384720	58384728	+	1	NA	exon (NM_001083884, exon 5 of 7)	exon (NM_001083884, exon 5 of 7)	4078	NM_001330197	70163	Mm.24119	NM_027339	ENSMUSG00000013643	Lypd8	2210415F13Rik	LY6/PLAUR domain containing 8	protein-coding
mm_44740.1	chr5	31193022	31193052	-	1	NA	promoter-TSS (NM_153680)	promoter-TSS (NM_153680)	102	NM_001127355	13667	Mm.29394	NM_010122	ENSMUSG00000029145	Eif2b4	Eif2b	eukaryotic translation initiation factor 2B, subunit 4 delta	protein-coding
mm_156644.1	chrX	157699114	157699134	+	1	NA	non-coding (NR_103722, exon 1 of 6)	non-coding (NR_103722, exon 1 of 6)	151	NR_103722	66106	Mm.140340	NM_025357	ENSMUSG00000041476	Smpx	1010001C09Rik|Csl	small muscle protein, X-linked	protein-coding
mm_73798.1	chr8	117274676	117274709	+	1	NA	intron (NM_001163262, intron 1 of 20)	B4A|SINE|B4	17673	NM_001163262	74440	Mm.233181	NM_028941	ENSMUSG00000034390	Cmip	4933407C03Rik|5830471E12Rik|AI314065|AI464126	c-Maf inducing protein	protein-coding
mm_118873.1	chr14	25857582	25857586	+	1	NA	intron (NM_013469, intron 1 of 14)	intron (NM_013469, intron 1 of 14)	15429	NM_013469	11744	Mm.294083	NM_013469	ENSMUSG00000021866	Anxa11	A830099O17Rik|Anx11	annexin A11	protein-coding
mm_35444.1	chr4	40234405	40234434	-	1	NA	intron (NM_172689, intron 2 of 17)	PB1D9|SINE|Alu	5406	NM_172689	230073	Mm.86382	NM_172689	ENSMUSG00000040296	Ddx58	6430573D20Rik|C330021E21|RIG-I|RLR-1	DEAD (Asp-Glu-Ala-Asp) box polypeptide 58	protein-coding
mm_133680.1	chr16	92423730	92423751	+	1	NA	intron (NM_001081549, intron 1 of 3)	intron (NM_001081549, intron 1 of 3)	-23662	NM_019466	54720	Mm.265744	NM_019466	ENSMUSG00000022951	Rcan1	Adapt78|CALP1L|CSP1|DSC1|Dscr1|MCIP1|RCN1	regulator of calcineurin 1	protein-coding
mm_145619.1	chr18	61105906	61105910	+	1	NA	5' UTR (NM_001037859, exon 2 of 22)	5' UTR (NM_001037859, exon 2 of 22)	336	NM_001037859	12978	Mm.22574	NM_007779	ENSMUSG00000024621	Csf1r	AI323359|CD115|CSF-1R|Csfmr|Fim-2|Fim2|Fms|M-CSF-R|M-CSFR	colony stimulating factor 1 receptor	protein-coding
mm_40495.1	chr5	57717662	57717673	+	1	NA	promoter-TSS (NM_001310606)	promoter-TSS (NM_001310606)	252	NR_015588	319216	Mm.332387	NR_015588	ENSMUSG00000097216	4932441J04Rik	-	RIKEN cDNA 4932441J04 gene	ncRNA
mm_31116.1	chr4	42950452	42950475	+	1	NA	Intergenic	Intergenic	-2631	NM_019874	56323	Mm.20437	NM_019874	ENSMUSG00000036052	Dnajb5	1110058L06Rik|AI462558|Hsc40|Hsp40-3	DnaJ heat shock protein family (Hsp40) member B5	protein-coding
mm_142606.1	chr17	46812177	46812187	-	1	NA	intron (NM_001100452, intron 5 of 10)	B1_Mur1|SINE|Alu	19231	NM_001100452	210982	Mm.37642	NM_001100452	ENSMUSG00000036568	Gltscr1l	mKIAA0240	GLTSCR1-like	protein-coding
mm_118144.1	chr13	105054783	105054792	-	1	NA	5' UTR (NM_029879, exon 1 of 6)	5' UTR (NM_029879, exon 1 of 6)	143	NM_029879	52882	Mm.100348	NM_029879	ENSMUSG00000021719	Rgs7bp	A930030I01Rik|AI842293|D13Bwg1146e|R7bp	regulator of G-protein signalling 7 binding protein	protein-coding
mm_94329.1	chr11	4266526	4266544	+	1	NA	promoter-TSS (NM_001039537)	promoter-TSS (NM_001039537)	-261	NM_001039537	16878	Mm.4964	NM_008501	ENSMUSG00000034394	Lif	-	leukemia inhibitory factor	protein-coding
mm_65880.1	chr7	29556517	29556519	-	1	NA	Intergenic	Intergenic	-51058	NM_001081028	74206	Mm.447042	NM_001081028	ENSMUSG00000030583	Sipa1l3	2610511M17Rik	signal-induced proliferation-associated 1 like 3	protein-coding
mm_152948.1	chr19	28990895	28990929	-	1	NA	intron (NM_001302382, intron 1 of 6)	intron (NM_001302382, intron 1 of 6)	560	NM_025950	67072	Mm.78875	NM_025950	ENSMUSG00000024780	Cdc37l1	2700033A15Rik|BB159850|Cdc37l|Harc	cell division cycle 37-like 1	protein-coding
mm_131382.1	chr16	14163288	14163307	+	1	NA	promoter-TSS (NM_001285504)	promoter-TSS (NM_001285504)	22	NM_001114085	67203	Mm.24105	NM_023317	ENSMUSG00000022678	Nde1	2810027M15Rik|AU042936|AW822251|Nude|mNudE	nudE neurodevelopment protein 1	protein-coding
mm_114505.1	chr13	70650142	70650149	+	1	NA	Intergenic	L2a|LINE|L2	-12511	NM_144837	218333	Mm.139738	NM_144837	ENSMUSG00000034525	Ice1	C77245|mKIAA0947	interactor of little elongation complex ELL subunit 1	protein-coding
mm_91175.1	chr10	20725024	20725048	-	1	NA	promoter-TSS (NM_013875)	promoter-TSS (NM_013875)	42	NM_013875	29863	Mm.425617	NM_013875	ENSMUSG00000019990	Pde7b	-	phosphodiesterase 7B	protein-coding
mm_22390.1	chr2	181202508	181202534	-	1	NA	5' UTR (NM_009184, exon 1 of 8)	5' UTR (NM_009184, exon 1 of 8)	268	NM_009184	20459	Mm.4497	NM_009184	ENSMUSG00000038751	Ptk6	BRK|Sik|Tksk|tks	PTK6 protein tyrosine kinase 6	protein-coding
mm_99911.1	chr11	109845865	109845870	+	1	NA	promoter-TSS (NR_045909)	promoter-TSS (NR_045909)	-11	NR_045909	73257	Mm.250442	NR_045909	ENSMUSG00000087393	1700023C21Rik	-	RIKEN cDNA 1700023C21 gene	ncRNA
mm_55484.1	chr6	69043535	69043556	-	1	NA	Intergenic	Intergenic	283629	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_40111.1	chr5	34827493	34827499	+	1	NA	intron (NM_010414, intron 24 of 66)	intron (NM_010414, intron 24 of 66)	65756	NM_010414	15194	Mm.209071	NM_010414	ENSMUSG00000029104	Htt	AI256365|C430023I11Rik|Hd|Hdh|IT15	huntingtin	protein-coding
mm_46460.1	chr5	105118351	105118361	-	1	NA	exon (NM_001256005, exon 11 of 11)	exon (NM_001256005, exon 11 of 11)	-8064	NM_172777	236573	Mm.425261	NM_172777	ENSMUSG00000029298	Gbp9	-	guanylate-binding protein 9	protein-coding
mm_136974.1	chr17	15755020	15755058	+	1	NA	exon (NM_007690, exon 24 of 36)	exon (NM_007690, exon 24 of 36)	50072	NM_007690	12648	Mm.8137	NM_007690	ENSMUSG00000023852	Chd1	4930525N21Rik|AI851787|AW555109	chromodomain helicase DNA binding protein 1	protein-coding
mm_154091.1	chr19	56815819	56815820	-	1	NA	Intergenic	Intergenic	-2136	NM_170757	213993	Mm.469677	NM_170757	ENSMUSG00000035173	Ccdc186	1810028B20Rik|A630007B06Rik|AI159700|Otg1	coiled-coil domain containing 186	protein-coding
mm_147515.1	chr18	52518489	52518502	-	1	NA	3' UTR (NM_010728, exon 7 of 7)	3' UTR (NM_010728, exon 7 of 7)	11226	NM_001286181	16948	Mm.172	NM_010728	ENSMUSG00000024529	Lox	AI893619|TSC-160|rrg	lysyl oxidase	protein-coding
mm_95416.1	chr11	50039041	50039041	+	1	NA	intron (NM_001290750, intron 1 of 7)	intron (NM_001290750, intron 1 of 7)	13710	NM_001290750	59044	Mm.359004	NM_021540	ENSMUSG00000020376	Rnf130	2510042A13Rik|G1RZFP|G1rp|GOLIATH|GP	ring finger protein 130	protein-coding
mm_74230.1	chr8	124231462	124231530	+	1	NA	5' UTR (NM_139272, exon 1 of 16)	5' UTR (NM_139272, exon 1 of 16)	102	NM_139272	108148	Mm.33808	NM_139272	ENSMUSG00000089704	Galnt2	AI480629	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2	protein-coding
mm_15941.1	chr2	165810252	165810294	+	1	NA	intron (NM_027230, intron 15 of 23)	intron (NM_027230, intron 15 of 23)	47900	NM_001252585	228880	Mm.227598	NM_027230	ENSMUSG00000039671	Zmynd8	1110013E22Rik|2010005I16Rik|3632413B07Rik|AI316811|AL024039|Prkcbp1|RACK7	zinc finger, MYND-type containing 8	protein-coding
mm_100206.1	chr11	116852185	116852220	+	1	NA	exon (NM_011358, exon 2 of 3)	exon (NM_011358, exon 2 of 3)	892	NM_011358	20382	Mm.21841	NM_011358	ENSMUSG00000034120	Srsf2	D11Wsu175e|MRF-1|Pr264|SC35|Sfrs10|Sfrs2	serine/arginine-rich splicing factor 2	protein-coding
mm_153553.1	chr19	42128947	42128967	-	1	NA	promoter-TSS (NM_027106)	promoter-TSS (NM_027106)	36	NM_027106	69534	Mm.30060	NM_027106	ENSMUSG00000018821	Avpi1	2310008N12Rik|AA410041|VIT32|esu|mVIT32	arginine vasopressin-induced 1	protein-coding
mm_128872.1	chr15	73030823	73030829	-	1	NA	intron (NM_029640, intron 5 of 21)	MTC|LTR|ERVL-MaLR	24986	NM_029640	76510	Mm.158902	NM_029640	ENSMUSG00000047921	Trappc9	1810044A24Rik|2900005P22Rik|4632408O18Rik|Ibp|Nibp|TRS130|mKIAA1882	trafficking protein particle complex 9	protein-coding
mm_94491.1	chr11	6680356	6680391	+	1	NA	Intergenic	Intergenic	-20137	NR_028586	100041311	Mm.388018	NR_028586	ENSMUSG00000086373	Gm11978	OTTMUSG00000005125|OTTMUSG00000005127	predicted gene 11978	pseudo
mm_91795.1	chr10	53379865	53379899	-	1	NA	promoter-TSS (NM_001204983)	promoter-TSS (NM_001204983)	-31	NM_001204983	100038725	Mm.441403	NM_001204983	ENSMUSG00000038594	Cep85l	ENSMUSG00000038594|Gm9766	centrosomal protein 85-like	protein-coding
mm_86913.1	chr10	23787417	23787437	+	1	NA	promoter-TSS (NM_011295)	promoter-TSS (NM_011295)	-218	NM_011295	20042	Mm.371846	NM_011295	ENSMUSG00000061983	Rps12	-	ribosomal protein S12	protein-coding
mm_42448.1	chr5	115434975	115434986	+	1	NA	intron (NM_008629, intron 5 of 14)	intron (NM_008629, intron 5 of 14)	5295	NM_008629	17690	Mm.5077	NM_008629	ENSMUSG00000054256	Msi1	Msi1h|Musahi1|m-Msi-1	musashi RNA-binding protein 1	protein-coding
mm_123449.1	chr14	65174947	65174963	-	1	NA	Intergenic	MLTR73|LTR|ERV1	-76849	NM_018788	54616	Mm.103748	NM_018788	ENSMUSG00000021978	Extl3	2900009G18Rik|AU040105|Ext1l|mKIAA0519	exostoses (multiple)-like 3	protein-coding
mm_108922.1	chr12	100779141	100779156	+	1	NA	promoter-TSS (NM_145448)	promoter-TSS (NM_145448)	25	NM_145448	217830	Mm.218590	NM_145448	ENSMUSG00000021185	9030617O03Rik	-	RIKEN cDNA 9030617O03 gene	protein-coding
mm_98113.1	chr11	87109253	87109274	+	1	NA	promoter-TSS (NM_175563)	promoter-TSS (NM_175563)	2	NM_025377	66140	Mm.45008	NM_025377	ENSMUSG00000020492	Ska2	1110001A07Rik|C78640|Fam33a	spindle and kinetochore associated complex subunit 2	protein-coding
mm_35793.1	chr4	46534583	46534615	-	1	NA	intron (NM_029077, intron 1 of 5)	intron (NM_029077, intron 1 of 5)	1542	NM_029077	74735	Mm.240252	NM_029077	ENSMUSG00000039853	Trim14	5830400N10Rik|pub	tripartite motif-containing 14	protein-coding
mm_44697.1	chr5	30408083	30408091	-	1	NA	intron (NM_001313767, intron 5 of 45)	intron (NM_001313767, intron 5 of 45)	53845	NM_001286421	83762	Mm.244502	NM_031875	ENSMUSG00000062372	Otof	-	otoferlin	protein-coding
mm_3244.1	chr1	136052772	136052796	+	1	NA	promoter-TSS (NM_014193)	promoter-TSS (NM_014193)	-117	NM_001081023	12292	Mm.4418	NM_014193	ENSMUSG00000026407	Cacna1s	AW493108|Cav1.1|Cchl1a3|fmd|mdg|sj	calcium channel, voltage-dependent, L type, alpha 1S subunit	protein-coding
mm_104011.1	chr11	85234808	85234840	-	1	NA	promoter-TSS (NR_028329)	promoter-TSS (NR_028329)	296	NM_025825	66884	Mm.271997	NM_025825	ENSMUSG00000018481	Appbp2	1300003O07Rik|AI465480|PAT1	amyloid beta precursor protein (cytoplasmic tail) binding protein 2	protein-coding
mm_121905.1	chr14	21987494	21987509	-	1	NA	exon (NM_145459, exon 2 of 3)	exon (NM_145459, exon 2 of 3)	2100	NM_145459	218820	Mm.292401	NM_145459	ENSMUSG00000039081	Zfp503	AI181838|B830002A16Rik|Nolz-1|Nolz1|Znf503	zinc finger protein 503	protein-coding
mm_48555.1	chr5	143104867	143104892	-	1	NA	intron (NM_080561, intron 1 of 16)	intron (NM_080561, intron 1 of 16)	8141	NM_207110	108086	Mm.381440	NM_080561	ENSMUSG00000045078	Rnf216	2810055G22Rik|AI647468|AU019462|C86502|F830018F18Rik|TRIAD3|UIP83|Ubce7ip1	ring finger protein 216	protein-coding
mm_136532.1	chr16	97514796	97514802	-	1	NA	Intergenic	Intergenic	-9863	NM_020622	52793	Mm.327932	NM_020622	ENSMUSG00000022938	Fam3b	2-21|9030624C24Rik|D16Jhu19e|ORF9|Pander	family with sequence similarity 3, member B	protein-coding
mm_156721.1	chrX	159708656	159708660	+	1	NA	promoter-TSS (NM_021389)	promoter-TSS (NM_021389)	57	NR_110970	58194	Mm.286495	NM_021389	ENSMUSG00000040990	Sh3kbp1	1200007H22Rik|1700125L08Rik|5830464D22Rik|AI447724|Cin85|IN85|Ruk|Seta	SH3-domain kinase binding protein 1	protein-coding
mm_3677.1	chr1	153667671	153667676	+	1	NA	intron (NM_001347115, intron 2 of 5)	intron (NM_001347115, intron 2 of 5)	2000	NM_001347115	67792	Mm.379143	NM_026380	ENSMUSG00000042671	Rgs8	6530413N01Rik	regulator of G-protein signaling 8	protein-coding
mm_62387.1	chr7	100894502	100894503	+	1	NA	intron (NM_001081116, intron 1 of 20)	CpG	-12093	NR_037289	100526508		NR_037289	ENSMUSG00000093296	Mir3102	mmu-mir-3102	microRNA 3102	ncRNA
mm_53814.1	chr6	147032610	147032625	+	1	NA	promoter-TSS (NM_025620)	promoter-TSS (NM_025620)	80	NM_025620	66532	Mm.45888	NM_025620	ENSMUSG00000040121	Rep15	2210417D09Rik	RAB15 effector protein	protein-coding
mm_136133.1	chr16	86806359	86806368	-	1	NA	Intergenic	LTR10_RN|LTR|ERVK	-547822	NM_001159331	67768	Mm.296532	NM_026366	ENSMUSG00000044442	N6amt1	5830445C04Rik|Hemk2|Pred28	N-6 adenine-specific DNA methyltransferase 1 (putative)	protein-coding
mm_88073.1	chr10	67910060	67910061	+	1	NA	intron (NM_178679, intron 1 of 4)	intron (NM_178679, intron 1 of 4)	2602	NM_178679	216049	Mm.268346	NM_178679	ENSMUSG00000037855	Zfp365	AI839779|AV340892|DBZ|Su48|Znf365|talanin	zinc finger protein 365	protein-coding
mm_99558.1	chr11	103649579	103649585	+	1	NA	promoter-TSS (NM_001033212)	promoter-TSS (NM_001033212)	73	NM_001033212	104582	Mm.44618	NM_001033212	ENSMUSG00000046215	Rprml	AW049332	reprimo-like	protein-coding
mm_162205.1	chrX	135589102	135589102	-	1	NA	intron (NM_130888, intron 3 of 21)	intron (NM_130888, intron 3 of 21)	4753	NM_130888	170722	Mm.103373	NM_130888	ENSMUSG00000031410	Nxf7	Nx7|Nxf6|nfx-a1|nxf-a|nxf-a2	nuclear RNA export factor 7	protein-coding
mm_130645.1	chr15	100599984	100600039	-	1	NA	promoter-TSS (NM_001304965)	promoter-TSS (NM_001304965)	-27	NM_001304965	19009	Mm.28825	NM_010127	ENSMUSG00000009739	Pou6f1	2310038G18Rik|C79593|Emb|cns-1	POU domain, class 6, transcription factor 1	protein-coding
mm_2725.1	chr1	128193731	128193733	+	1	NA	exon (NM_181750, exon 18 of 27)	exon (NM_181750, exon 18 of 27)	-8629	NR_029543	387147		NR_029543	ENSMUSG00000065520	Mir128-1	Mirn128|Mirn128-1|Mirn128a|mir-128-1	microRNA 128-1	ncRNA
mm_172787.1	chr9	105819550	105819551	-	1	NA	intron (NM_001102607, intron 1 of 36)	LSU-rRNA_Hsa|rRNA|rRNA	8535	NM_001102607	245026	Mm.482507	NM_172927	ENSMUSG00000043719	Col6a6	E330019B14|E330026B02Rik	collagen, type VI, alpha 6	protein-coding
mm_108298.1	chr12	79255299	79255326	+	1	NA	exon (NM_001008550, exon 29 of 42)	exon (NM_001008550, exon 29 of 42)	40970	NM_001008550	211978	Mm.297919	NM_001008550	ENSMUSG00000066440	Zfyve26	4930465A13|9330197E15Rik|A630028O16Rik|Gm893|mKIAA0321	zinc finger, FYVE domain containing 26	protein-coding
mm_130721.1	chr15	101078411	101078419	-	1	NA	Intergenic	CpG	-24016	NM_001214911	668225	Mm.385011	NM_001214911	ENSMUSG00000095440	Fignl2	EG668225	fidgetin-like 2	protein-coding
mm_163105.1	chr11	69921210	69921218	-	1	NA	promoter-TSS (NM_001166592)	promoter-TSS (NM_001166592)	61	NM_001166595	276770	Mm.18026	NM_181582	ENSMUSG00000078812	Eif5a	AA410058|D19Wsu54e|Eif4d|Eif5a1|eIF-4D|eIF-5A|eIF-5A-1|eIF-5A1	eukaryotic translation initiation factor 5A	protein-coding
mm_146988.1	chr18	34007027	34007057	-	1	NA	5' UTR (NM_013512, exon 1 of 24)	5' UTR (NM_013512, exon 1 of 24)	164	NM_013512	13824	Mm.3465	NM_013512	ENSMUSG00000024376	Epb41l4a	Epb4.1l4|Epb4.1l4a|NBL4	erythrocyte membrane protein band 4.1 like 4a	protein-coding
mm_37714.1	chr4	129500771	129500784	-	1	NA	Intergenic	CpG	9587	NM_001085491	68233	Mm.424983	NM_001085491	ENSMUSG00000078554	Fam229a	1700125D06Rik	family with sequence similarity 229, member A	protein-coding
mm_49360.1	chr6	22875497	22875512	+	1	NA	promoter-TSS (NM_001311064)	promoter-TSS (NM_001311064)	2	NM_001081306	19283	Mm.41639	NM_011219	ENSMUSG00000068748	Ptprz1	AI850339|DSD-1-PG|PTPbeta|PTPzeta|Ptprz|Ptpz|R-PTP-zeta|RPTPz|Rptpbeta	protein tyrosine phosphatase, receptor type Z, polypeptide 1	protein-coding
mm_133374.1	chr16	84710445	84710456	+	1	NA	Intergenic	Intergenic	-2573	NR_132106	100653389	Mm.261808	NR_132106	ENSMUSG00000097418	Mir155hg	Bic|Gm26667	Mir155 host gene (non-protein coding)	ncRNA
mm_165179.1	chr2	29189177	29189185	+	1	NA	Intergenic	RLTR6_Mm|LTR|ERV1	58918	NM_001305805	171171	Mm.442448	NM_133500	ENSMUSG00000035513	Ntng2	2610016D08Rik|Lmnt2	netrin G2	protein-coding
mm_124741.1	chr15	6597860	6597870	+	1	NA	intron (NM_011815, intron 1 of 17)	(T)n|Simple_repeat|Simple_repeat	18018	NM_011815	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_35919.1	chr4	53031651	53031662	-	1	NA	3' UTR (NM_013454, exon 50 of 50)	3' UTR (NM_013454, exon 50 of 50)	19776	NM_025623	66536	Mm.38244	NM_025623	ENSMUSG00000015247	Nipsnap3b	2700063N13Rik|Nipsnap3a	nipsnap homolog 3B (C. elegans)	protein-coding
mm_24844.1	chr3	95662078	95662150	+	1	NA	3' UTR (NM_008562, exon 3 of 3)	3' UTR (NM_008562, exon 3 of 3)	3393	NM_008562	17210	Mm.1639	NM_008562	ENSMUSG00000038612	Mcl1	AW556805|Mcl-1	myeloid cell leukemia sequence 1	protein-coding
mm_80978.1	chr9	103183366	103183377	+	1	NA	3' UTR (NM_173781, exon 8 of 8)	3' UTR (NM_173781, exon 8 of 8)	18694	NM_009275	20818	Mm.273053	NM_009275	ENSMUSG00000032553	Srprb	AA409543	signal recognition particle receptor, B subunit	protein-coding
mm_150809.1	chr19	44378370	44378372	+	1	NA	Intergenic	Intergenic	29338	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_46587.1	chr5	107723955	107723974	-	1	NA	5' UTR (NM_010278, exon 1 of 6)	5' UTR (NM_010278, exon 1 of 6)	379	NM_010278	14581	Mm.2078	NM_010278	ENSMUSG00000029275	Gfi1	AW495828|Gfi-1|Pal-1|Pal1	growth factor independent 1	protein-coding
mm_137197.1	chr17	23853753	23853780	+	1	NA	promoter-TSS (NM_027220)	promoter-TSS (NM_027220)	-6	NM_027220	69814	Mm.244143	NM_027220	ENSMUSG00000048992	Prss32	2010001P08Rik|mT5|tryptase-5	protease, serine 32	protein-coding
mm_61773.1	chr7	83631965	83631969	+	1	NA	promoter-TSS (NM_023377)	promoter-TSS (NM_023377)	-50	NM_023377	170460	Mm.357953	NM_023377	ENSMUSG00000046027	Stard5	2310058G22Rik|AI607880|D7Ertd152e	StAR-related lipid transfer (START) domain containing 5	protein-coding
mm_4570.1	chr1	177729844	177729869	+	1	NA	promoter-TSS (NM_027077)	promoter-TSS (NM_027077)	42	NM_027077	69428	Mm.84467	NM_027077	ENSMUSG00000015962	1700016C15Rik	-	RIKEN cDNA 1700016C15 gene	protein-coding
mm_172418.1	chr7	25395993	25396010	-	1	NA	promoter-TSS (NM_010719)	promoter-TSS (NM_010719)	-14	NM_010719	16890	Mm.158548	NM_010719	ENSMUSG00000003123	Lipe	4933403G17Rik|HSL	lipase, hormone sensitive	protein-coding
mm_94222.1	chr11	3202877	3202904	+	1	NA	promoter-TSS (NM_001166549)	promoter-TSS (NM_001166549)	-105	NM_001166547	74203	Mm.255649	NM_023743	ENSMUSG00000020454	Eif4enif1	2610509L04Rik|A930019J01Rik|AA410001|AU021239|Clast4|D11Ertd166e	eukaryotic translation initiation factor 4E nuclear import factor 1	protein-coding
mm_159768.1	chr5	98329425	98329425	+	1	NA	exon (NM_001024614, exon 1 of 6)	exon (NM_001024614, exon 1 of 6)	121	NM_001024614	75784	Mm.443240	NM_001024614	ENSMUSG00000057816	1700007G11Rik	4930428O21Rik	RIKEN cDNA 1700007G11 gene	protein-coding
mm_92694.1	chr10	80668685	80668695	-	1	NA	exon (NM_021462, exon 11 of 14)	exon (NM_021462, exon 11 of 14)	7603	NM_021462	17347	Mm.42126	NM_021462	ENSMUSG00000020190	Mknk2	2010016G11Rik|Gprk7|Mnk2	MAP kinase-interacting serine/threonine kinase 2	protein-coding
mm_129276.1	chr15	77134929	77134931	-	1	NA	intron (NM_053104, intron 2 of 13)	MTD|LTR|ERVL-MaLR	18882	NM_001110830	93686	Mm.202774	NM_053104	ENSMUSG00000033565	Rbfox2	Fbm2|Fxh|Hrnbp2|Rbm9	RNA binding protein, fox-1 homolog (C. elegans) 2	protein-coding
mm_20877.1	chr2	148732379	148732455	-	1	NA	promoter-TSS (NM_019632)	promoter-TSS (NM_019632)	3	NM_019632	17957	Mm.274308	NM_019632	ENSMUSG00000027438	Napb	Brp14|E161|I47|SNARE|b-SNAP	N-ethylmaleimide sensitive fusion protein attachment protein beta	protein-coding
mm_157552.1	chrX	51801079	51801083	-	1	NA	5' UTR (NM_031388, exon 2 of 9)	5' UTR (NM_031388, exon 2 of 9)	152	NM_031388	83563	Mm.242827	NM_031388	ENSMUSG00000055780	Usp26	-	ubiquitin specific peptidase 26	protein-coding
mm_125590.1	chr15	59648298	59648307	+	1	NA	promoter-TSS (NM_144549)	promoter-TSS (NM_144549)	-352	NM_144549	211770	Mm.40298	NM_144549	ENSMUSG00000032501	Trib1	A530090O15Rik|TRB-1|Trb1	tribbles pseudokinase 1	protein-coding
mm_106373.1	chr11	118415801	118415824	-	1	NA	promoter-TSS (NM_001267591)	promoter-TSS (NM_001267591)	-12	NM_001267591	76025	Mm.177551	NM_029502	ENSMUSG00000025575	Cant1	5830420C20Rik|Apy1h|D11Bwg0554e|Entpd8|SCAN-1|Shapy	calcium activated nucleotidase 1	protein-coding
mm_138046.1	chr17	33925696	33925710	+	1	NA	exon (NM_009318, exon 4 of 8)	exon (NM_009318, exon 4 of 8)	-4191	NM_009059	19732	Mm.43777	NM_009059	ENSMUSG00000041354	Rgl2	KE1.5|Rab2l|Rgt2|Rlf	ral guanine nucleotide dissociation stimulator-like 2	protein-coding
mm_123700.1	chr14	69716645	69716656	-	1	NA	TTS (NM_134078)	TTS (NM_134078)	-1841	NM_001301651	71843	Mm.27738	NM_001146012	ENSMUSG00000034194	R3hcc1	1700020M16Rik|AA407796	R3H domain and coiled-coil containing 1	protein-coding
mm_59366.1	chr7	25687839	25687882	+	1	NA	5' UTR (NM_011577, exon 1 of 7)	5' UTR (NM_011577, exon 1 of 7)	858	NM_011577	21803	Mm.248380	NM_011577	ENSMUSG00000002603	Tgfb1	TGF-beta1|TGFbeta1|Tgfb|Tgfb-1	transforming growth factor, beta 1	protein-coding
mm_142511.1	chr17	46202451	46202473	-	1	NA	promoter-TSS (NM_028198)	promoter-TSS (NM_028198)	163	NM_030715	80905	Mm.311585	NM_030715	ENSMUSG00000023953	Polh	RAD30A|XPV	polymerase (DNA directed), eta (RAD 30 related)	protein-coding
mm_169858.1	chr16	3345970	3345971	+	1	NA	Intergenic	Intergenic	-246428	NM_146860	258859	Mm.377723	NM_146860	ENSMUSG00000051003	Olfr161	MOR131-1|OR912-47M6	olfactory receptor 161	protein-coding
mm_147064.1	chr18	35087594	35087625	-	1	NA	Intergenic	Intergenic	-31303	NM_009818	12385	Mm.18962	NM_009818	ENSMUSG00000037815	Ctnna1	2010010M04Rik|AA517462|AI988031|Catna1	catenin (cadherin associated protein), alpha 1	protein-coding
mm_98665.1	chr11	96282353	96282411	+	1	NA	5' UTR (NM_010461, exon 1 of 2)	5' UTR (NM_010461, exon 1 of 2)	477	NM_010461	15416	Mm.4822	NM_010461	ENSMUSG00000056648	Hoxb8	Hox-2.4	homeobox B8	protein-coding
mm_57716.1	chr6	128788539	128788559	-	1	NA	promoter-TSS (NM_001159904)	promoter-TSS (NM_001159904)	92	NM_008527	17059	Mm.480764	NM_008527	ENSMUSG00000030325	Klrb1c	AI462337|CD161|Ly-59|Ly55c|Ly59|NK-RP1|NK1.1|NKR-P1.9|NKRP1|NKRP140|Nk-1|Nk-1.2|Nk1|Nk1.2|Nkrp1c|ly-55c	killer cell lectin-like receptor subfamily B member 1C	protein-coding
mm_119517.1	chr14	47472548	47472625	+	1	NA	promoter-TSS (NM_030236)	promoter-TSS (NM_030236)	25	NM_001146085	78938	Mm.11935	NM_030236	ENSMUSG00000037536	Fbxo34	2900057B08Rik|5830426G16Rik	F-box protein 34	protein-coding
mm_133120.1	chr16	65815199	65815268	+	1	NA	promoter-TSS (NM_028572)	promoter-TSS (NM_028572)	-400	NM_028572	73569	Mm.25670	NM_028572	ENSMUSG00000091243	Vgll3	1700110N18Rik|4832416J22|C80713|Vgl-3|Vito-2	vestigial like family member 3	protein-coding
mm_36023.1	chr4	56990403	56990413	-	1	NA	promoter-TSS (NM_001142965)	promoter-TSS (NM_001142965)	-17	NM_001142965	230235	Mm.207654	NM_001142965	ENSMUSG00000045589	Frrs1l	6430704M03Rik	ferric-chelate reductase 1 like	protein-coding
mm_42252.1	chr5	114003726	114003737	+	1	NA	promoter-TSS (NM_001286397)	promoter-TSS (NM_001286397)	-4	NM_010018	13142	Mm.20115	NM_010018	ENSMUSG00000042096	Dao	AI987963|DAAO|DAMOX|Dao-1|Dao1	D-amino acid oxidase	protein-coding
mm_51373.1	chr6	72955104	72955128	+	1	NA	Intergenic	Intergenic	3116	NM_001039392	19240	Mm.3532	NM_025284	ENSMUSG00000079523	Tmsb10	Ptmb10|Tb10	thymosin, beta 10	protein-coding
mm_133812.1	chr16	95703197	95703200	+	1	NA	intron (NM_011809, intron 1 of 9)	intron (NM_011809, intron 1 of 9)	791	NM_011809	23872	Mm.290207	NM_011809	ENSMUSG00000022895	Ets2	AU022856|Ets-2	E26 avian leukemia oncogene 2, 3' domain	protein-coding
mm_118250.1	chr13	112001241	112001252	-	1	NA	Intergenic	Intergenic	133310	NR_130345	102636620	Mm.402328	NR_130345	ENSMUSG00000086111	Gm15326	OTTMUSG00000020187	predicted gene 15326	ncRNA
mm_63755.1	chr7	131106911	131106926	+	1	NA	intron (NM_001347632, intron 40 of 47)	intron (NM_001347632, intron 40 of 47)	39365	NM_173409	233918	Mm.78341	NM_173409	ENSMUSG00000013668	4933402N03Rik	4930412O05	RIKEN cDNA 4933402N03 gene	protein-coding
mm_141751.1	chr17	34239721	34239735	-	1	NA	intron (NM_010389, intron 1 of 5)	intron (NM_010389, intron 1 of 5)	823	NM_010389	15002	Mm.327358	NM_010389	ENSMUSG00000041538	H2-Ob	A-beta-2|A-beta2|H-2Ab|H-2I|H-2Ob|H2-Ab|H2-Ab2|H2-IAb2|Ob	histocompatibility 2, O region beta locus	protein-coding
mm_79606.1	chr9	58599386	58599389	+	1	NA	intron (NM_001293673, intron 1 of 7)	intron (NM_001293673, intron 1 of 7)	17147	NM_009145	20320	Mm.15125	NM_009145	ENSMUSG00000032336	Nptn	AW554172|SDR-1|Sdfr1	neuroplastin	protein-coding
mm_113144.1	chr13	24721674	24721683	+	1	NA	exon (NM_029679, exon 20 of 23)	exon (NM_029679, exon 20 of 23)	40259	NM_020567	57441	Mm.12239	NM_020567	ENSMUSG00000006715	Gmnn	AW546347|Gem	geminin	protein-coding
mm_5535.1	chr1	38106831	38106831	-	1	NA	intron (NM_019570, intron 3 of 22)	URR1B|DNA|hAT-Charlie	22831	NM_019570	56210	Mm.389103	NM_019570	ENSMUSG00000026082	Rev1	1110027I23Rik|AU022044|Rev1l	REV1, DNA directed polymerase	protein-coding
mm_22998.1	chr3	34041093	34041107	+	1	NA	exon (NM_001113188, exon 3 of 17)	exon (NM_001113188, exon 3 of 17)	21021	NM_001113188	14359	Mm.259021	NM_008053	ENSMUSG00000027680	Fxr1	1110050J02Rik|9530073J07Rik|AI851072|Fxr1h|Fxr1p	fragile X mental retardation gene 1, autosomal homolog	protein-coding
mm_145879.1	chr18	65476518	65476530	+	1	NA	3' UTR (NM_172833, exon 16 of 16)	3' UTR (NM_172833, exon 16 of 16)	45527	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_13465.1	chr2	105675670	105675680	+	1	NA	promoter-TSS (NM_013627)	promoter-TSS (NM_013627)	-69	NM_001244200	18508	Mm.3608	NM_013627	ENSMUSG00000027168	Pax6	1500038E17Rik|AEY11|Dey|Gsfaey11|Pax-6|Sey	paired box 6	protein-coding
mm_93737.1	chr10	120140613	120140617	-	1	NA	Intergenic	Intergenic	-27650	NM_080446	117599	Mm.214703	NM_080446	ENSMUSG00000020228	Helb	AI447783|D10Ertd664e	helicase (DNA) B	protein-coding
mm_11548.1	chr2	32715090	32715112	+	1	NA	Intergenic	Intergenic	-2129	NR_039536	100628606		NR_039536	ENSMUSG00000105841	Mir3960	mmu-mir-3960	microRNA 3960	ncRNA
mm_114321.1	chr13	60601775	60601788	+	1	NA	promoter-TSS (NM_134062)	promoter-TSS (NM_134062)	-166	NM_001285917	69635	Mm.24103	NM_029653	ENSMUSG00000021559	Dapk1	D13Ucla1|DAP-Kinase	death associated protein kinase 1	protein-coding
mm_19264.1	chr2	84822547	84822593	-	1	NA	promoter-TSS (NM_024230)	promoter-TSS (NM_024230)	82	NM_024230	68678	Mm.33452	NM_024230	ENSMUSG00000027077	Smtnl1	1110030K22Rik|CHASM	smoothelin-like 1	protein-coding
mm_20153.1	chr2	121569517	121569518	-	1	NA	intron (NM_172673, intron 6 of 14)	intron (NM_172673, intron 6 of 14)	62794	NM_001290986	241627	Mm.293284	NM_030234	ENSMUSG00000027242	Wdr76	5830411K18Rik|6030457D09|AA517836	WD repeat domain 76	protein-coding
mm_134662.1	chr16	22163722	22163749	-	1	NA	promoter-TSS (NM_183029)	promoter-TSS (NM_183029)	-436	NM_183029	319765	Mm.489442	NM_183029	ENSMUSG00000033581	Igf2bp2	C330012H03Rik|IMP-2|Imp2|Neilsen	insulin-like growth factor 2 mRNA binding protein 2	protein-coding
mm_116641.1	chr13	49062440	49062443	-	1	NA	intron (NM_029361, intron 19 of 27)	intron (NM_029361, intron 19 of 27)	85887	NM_029361	75607	Mm.342723	NM_029361	ENSMUSG00000037989	Wnk2	1810073P09Rik|AW122246|ESTM15|X83337|mKIAA1760	WNK lysine deficient protein kinase 2	protein-coding
mm_81561.1	chr9	110415496	110415499	+	1	NA	Intergenic	Intergenic	-4311	NM_008694	18054	Mm.236225	NM_008694	ENSMUSG00000032484	Ngp	bectenecin	neutrophilic granule protein	protein-coding
mm_118605.1	chr14	20836654	20836669	+	1	NA	promoter-TSS (NM_008873)	promoter-TSS (NM_008873)	-1	NM_008873	18792	Mm.4183	NM_008873	ENSMUSG00000021822	Plau	u-PA|uPA	plasminogen activator, urokinase	protein-coding
mm_2208.1	chr1	89580316	89580326	+	1	NA	intron (NM_001037136, intron 1 of 16)	CpG	103571	NR_015540	74403	Mm.444291	NR_015540		4933400F21Rik	1700091C04Rik|4930565K10Rik	RIKEN cDNA 4933400F21 gene	ncRNA
mm_18780.1	chr2	73625732	73625744	-	1	NA	promoter-TSS (NM_029716)	promoter-TSS (NM_029716)	2	NM_029716	108699	Mm.257073	NM_029716	ENSMUSG00000056486	Chn1	0610007I19Rik|0710001E19Rik|1700112L09Rik|2900046J01Rik|AI413815|ARHGAP2	chimerin 1	protein-coding
mm_3630.1	chr1	152807820	152807826	+	1	NA	5' UTR (NM_010877, exon 2 of 16)	5' UTR (NM_010877, exon 2 of 16)	7670	NM_010877	17970	Mm.270307	NM_010877	ENSMUSG00000026480	Ncf2	NOXA2|Ncf-2|p67phox	neutrophil cytosolic factor 2	protein-coding
mm_93526.1	chr10	115315508	115315522	-	1	NA	promoter-TSS (NM_024454)	promoter-TSS (NM_024454)	76	NM_024454	216344	Mm.21936	NM_024454	ENSMUSG00000020132	Rab21	9630024B22	RAB21, member RAS oncogene family	protein-coding
mm_63721.1	chr7	130834429	130834457	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-31281	NM_001346515	101476	Mm.323554	NM_133942	ENSMUSG00000040268	Plekha1	AA960558|C920009D07Rik|TAPP1	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 1	protein-coding
mm_67327.1	chr7	79732756	79732847	-	1	NA	promoter-TSS (NM_175640)	promoter-TSS (NM_175640)	-25	NM_001113471	103968	Mm.254917	NM_175640	ENSMUSG00000030546	Plin1	6030432J05Rik|Peri|Plin	perilipin 1	protein-coding
mm_65617.1	chr7	27533722	27533734	-	1	NA	exon (NM_011116, exon 12 of 14)	exon (NM_011116, exon 12 of 14)	10467	NM_001033315	233020	Mm.429716	NM_001033315	ENSMUSG00000040424	Hipk4	Gm162	homeodomain interacting protein kinase 4	protein-coding
mm_29399.1	chr3	108904595	108904603	-	1	NA	exon (NM_025845, exon 6 of 6)	exon (NM_025845, exon 6 of 6)	7105	NM_025845	66921	Mm.51049	NM_025845	ENSMUSG00000027881	Prpf38b	1110021E09Rik|AU018955	PRP38 pre-mRNA processing factor 38 (yeast) domain containing B	protein-coding
mm_170059.1	chr17	30624353	30624354	+	1	NA	non-coding (NR_045287, exon 3 of 4)	non-coding (NR_045287, exon 3 of 4)	2552	NR_045287	67522	Mm.254797	NR_045287	ENSMUSG00000099474	1700097N02Rik	-	RIKEN cDNA 1700097N02 gene	ncRNA
mm_90024.1	chr10	115393493	115393499	+	1	NA	intron (NM_001033261, intron 2 of 34)	intron (NM_001033261, intron 2 of 34)	8537	NM_001033261	216345	Mm.207621	NM_001033261	ENSMUSG00000034163	Zfc3h1	BC033596|Ccdc131|Psrc2	zinc finger, C3H1-type containing	protein-coding
mm_111529.1	chr12	100447291	100447291	-	1	NA	intron (NM_001033213, intron 4 of 19)	intron (NM_001033213, intron 4 of 19)	73531	NM_001033213	104718	Mm.295441	NM_001033213	ENSMUSG00000033530	Ttc7b	AA408451|Ttc7l1	tetratricopeptide repeat domain 7B	protein-coding
mm_104005.1	chr11	84944790	84944800	-	1	NA	Intergenic	RMER17C|LTR|ERVK	-12959	NM_007607	12351	Mm.1641	NM_007607	ENSMUSG00000000805	Car4	AW456718|Ca4	carbonic anhydrase 4	protein-coding
mm_138598.1	chr17	35533195	35533208	+	1	NA	promoter-TSS (NM_020576)	promoter-TSS (NM_020576)	0	NM_020576	57390	Mm.34201	NM_020576	ENSMUSG00000024409	Psors1c2	AI448740|Pcg|SPR1	psoriasis susceptibility 1 candidate 2 (human)	protein-coding
mm_52650.1	chr6	117180896	117180907	+	1	NA	3' UTR (NM_001012477, exon 4 of 4)	3' UTR (NM_001012477, exon 4 of 4)	12366	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_60139.1	chr7	38094596	38094610	+	1	NA	Intergenic	Intergenic	12887	NM_007633	12447	Mm.16110	NM_007633	ENSMUSG00000002068	Ccne1	AW538188|CycE1	cyclin E1	protein-coding
mm_155005.1	chrX	41400717	41400729	+	1	NA	promoter-TSS (NM_001290451)	promoter-TSS (NM_001290451)	-578	NM_016886	53623	Mm.327681	NM_016886	ENSMUSG00000001986	Gria3	2900064I19Rik|GluA3|GluR-C|GluR-K3|Glur-3|Glur3|Gluralpha3	glutamate receptor, ionotropic, AMPA3 (alpha 3)	protein-coding
mm_19149.1	chr2	80580889	80580899	-	1	NA	exon (NM_001290745, exon 1 of 32)	exon (NM_001290745, exon 1 of 32)	288	NM_001290745	50884	Mm.25203	NM_016965	ENSMUSG00000027002	Nckap1	C79304|H19|Hem-2|Hem2|Nap1|mKIAA0587|mh19|p125Nap1	NCK-associated protein 1	protein-coding
mm_58952.1	chr7	18786283	18786323	+	1	NA	promoter-TSS (NR_024208)	promoter-TSS (NR_024208)	1	NR_024208	20958	Mm.423480	NR_024208	ENSMUSG00000109116	Sycp1-ps1	Sycp1-rs	synaptonemal complex protein 1, pseudogene 1	pseudo
mm_132804.1	chr16	45158821	45158839	+	1	NA	promoter-TSS (NM_028756)	promoter-TSS (NM_028756)	1	NM_026402	67841	Mm.41775	NM_026402	ENSMUSG00000022663	Atg3	2610016C12Rik|APG3|Apg3l|Atg3l|PC3-96	autophagy related 3	protein-coding
mm_74496.1	chr8	5105348	5105358	-	1	NA	promoter-TSS (NM_011388)	promoter-TSS (NM_011388)	-66	NM_011388	20494	Mm.3500	NM_011388	ENSMUSG00000023073	Slc10a2	9130221J18Rik|AI605518|ASBT|IBAT|ISBT	solute carrier family 10, member 2	protein-coding
mm_72399.1	chr8	81768525	81768532	+	1	NA	intron (NM_001024617, intron 6 of 24)	intron (NM_001024617, intron 6 of 24)	425966	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_54775.1	chr6	41539282	41539294	-	1	NA	Intergenic	Intergenic	17512	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_164838.1	chr18	41916565	41916569	+	1	NA	intron (NM_029942, intron 4 of 6)	B4A|SINE|B4	34627	NM_029942	77619	Mm.30649	NM_029942	ENSMUSG00000056671	Prelid2	1700003A01Rik|C330008K14Rik	PRELI domain containing 2	protein-coding
mm_68135.1	chr7	102239574	102239587	-	1	NA	3' UTR (NM_019566, exon 2 of 2)	3' UTR (NM_019566, exon 2 of 2)	10538	NM_019566	56212	Mm.259795	NM_019566	ENSMUSG00000073982	Rhog	2810426G09Rik|Arhg|Sid10750	ras homolog family member G	protein-coding
mm_146385.1	chr18	82692518	82692550	+	1	NA	intron (NM_177832, intron 1 of 29)	C-rich|Low_complexity|Low_complexity	200	NM_177832	329002	Mm.34438	NM_177832	ENSMUSG00000041258	Zfp236	AI447957|Gm335	zinc finger protein 236	protein-coding
mm_63382.1	chr7	127213157	127213189	+	1	NA	exon (NM_016754, exon 3 of 7)	exon (NM_016754, exon 3 of 7)	1565	NM_016754	17907	Mm.14526	NM_016754	ENSMUSG00000030672	Mylpf	2410014J02Rik|MLC-2|Mlc2	myosin light chain, phosphorylatable, fast skeletal muscle	protein-coding
mm_59061.1	chr7	19415463	19415476	+	1	NA	exon (NM_007710, exon 4 of 8)	exon (NM_007710, exon 4 of 8)	4375	NM_007710	12715	Mm.2375	NM_007710	ENSMUSG00000030399	Ckm	Ckmm|M-CK|MCK	creatine kinase, muscle	protein-coding
mm_165069.1	chr19	44407516	44407518	-	1	NA	5' UTR (NM_009127, exon 1 of 6)	5' UTR (NM_009127, exon 1 of 6)	192	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_130955.1	chr15	103260141	103260187	-	1	NA	Intergenic	Intergenic	-1761	NM_001302341	18022	Mm.457989	NM_008685	ENSMUSG00000058794	Nfe2	NF-E2|NF-E2/P45|p45|p45NFE2|p45nf-e2	nuclear factor, erythroid derived 2	protein-coding
mm_132649.1	chr16	41532914	41532972	+	1	NA	promoter-TSS (NM_175548)	promoter-TSS (NM_175548)	117	NM_001347236	268890	Mm.310524	NM_175548	ENSMUSG00000061080	Lsamp	5430428I19|AW046674|B130007O04Rik|D930023J12Rik|Lam|Lamp	limbic system-associated membrane protein	protein-coding
mm_99945.1	chr11	111073779	111073792	+	1	NA	3' UTR (NM_008425, exon 2 of 2)	3' UTR (NM_008425, exon 2 of 2)	7621	NM_008425	16518	Mm.4951	NM_008425	ENSMUSG00000041695	Kcnj2	IRK1|Kcnf1|Kir2.1	potassium inwardly-rectifying channel, subfamily J, member 2	protein-coding
mm_12948.1	chr2	87526023	87526044	+	1	NA	Intergenic	CpG	-6002	NM_206823	110511	Mm.424751	NM_206823	ENSMUSG00000061520	Olfr153	GA_x6K02T2Q125-49033418-49034341|MOR177-5|Olfr4-2|V5	olfactory receptor 153	protein-coding
mm_155735.1	chrX	96166091	96166105	+	1	NA	exon (NM_010833, exon 12 of 13)	exon (NM_010833, exon 12 of 13)	70053	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_87459.1	chr10	51484647	51484668	+	1	NA	intron (NM_001291892, intron 7 of 8)	intron (NM_001291892, intron 7 of 8)	4045	NM_001291892	14727	Mm.439661	NM_008147	ENSMUSG00000062593	Lilr4b	Gp49a|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4B	protein-coding
mm_3498.1	chr1	150106931	150106946	+	1	NA	3' UTR (NM_011198, exon 10 of 10)	3' UTR (NM_011198, exon 10 of 10)	6907	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_72985.1	chr8	92960601	92960616	+	1	NA	promoter-TSS (NM_009209)	promoter-TSS (NM_009209)	-439	NM_009209	20538	Mm.57040	NM_009209	ENSMUSG00000055368	Slc6a2	NE-T|NET|Slc6a5	solute carrier family 6 (neurotransmitter transporter, noradrenalin), member 2	protein-coding
mm_151559.1	chr19	60144592	60144602	+	1	NA	promoter-TSS (NR_026942)	promoter-TSS (NR_026942)	-78	NR_026942	107376	Mm.245813	NR_026942	ENSMUSG00000053117	E330013P04Rik	9930018I18Rik|AW492152	RIKEN cDNA E330013P04 gene	ncRNA
mm_138465.1	chr17	35171535	35171548	+	1	NA	exon (NM_019467, exon 7 of 8)	exon (NM_019467, exon 7 of 8)	4460	NM_019467	11629	Mm.10747	NM_019467	ENSMUSG00000024397	Aif1	AI607846|AIF-1|D17H6S50E|G1|Iba1	allograft inflammatory factor 1	protein-coding
mm_147288.1	chr18	39489777	39489868	-	1	NA	Intergenic	CpG	-2577	NM_008173	14815	Mm.129481	NM_008173	ENSMUSG00000024431	Nr3c1	GR|Grl-1|Grl1	nuclear receptor subfamily 3, group C, member 1	protein-coding
mm_132230.1	chr16	32673145	32673188	+	1	NA	promoter-TSS (NM_001289443)	promoter-TSS (NM_001289443)	12	NM_001289443	51789	Mm.251115	NM_016788	ENSMUSG00000022791	Tnk2	Ack|Ack-1|Ack1|Cdgip|Pyk1	tyrosine kinase, non-receptor, 2	protein-coding
mm_132019.1	chr16	26463074	26463087	+	1	NA	promoter-TSS (NM_053241)	promoter-TSS (NM_053241)	-55	NM_053241	114141	Mm.275205	NM_053241	ENSMUSG00000038148	Cldn16	PCLN1|claudin-16	claudin 16	protein-coding
mm_22598.1	chr3	13946386	13946416	+	1	NA	promoter-TSS (NM_001163330)	promoter-TSS (NM_001163330)	29	NM_001163330	76897	Mm.422625	NM_178631	ENSMUSG00000039717	Ralyl	0710005M24Rik	RALY RNA binding protein-like	protein-coding
mm_134064.1	chr16	8471080	8471107	-	1	NA	intron (NM_146247, intron 1 of 10)	intron (NM_146247, intron 1 of 10)	280	NM_146247	239706	Mm.214953	NM_146247	ENSMUSG00000039345	Mettl22	-	methyltransferase like 22	protein-coding
mm_125839.1	chr15	74958634	74958654	+	1	NA	exon (NM_001164036, exon 4 of 4)	exon (NM_001164036, exon 4 of 4)	3538	NM_001164040	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_102124.1	chr11	53351987	53351993	-	1	NA	intron (NM_033565, intron 1 of 20)	intron (NM_033565, intron 1 of 20)	1223	NM_033565	93736	Mm.395281	NM_033565	ENSMUSG00000049470	Aff4	AF5Q31|Alf4|Laf4l|MCEF	AF4/FMR2 family, member 4	protein-coding
mm_9332.1	chr1	171919346	171919372	-	1	NA	intron (NM_001347187, intron 1 of 7)	intron (NM_001347187, intron 1 of 7)	1822	NM_030710	30925	Mm.486404	NM_030710	ENSMUSG00000015314	Slamf6	KAL1|KAL1b|Ly108|NTB-A|NTBA|SF2000	SLAM family member 6	protein-coding
mm_105423.1	chr11	103697780	103697790	-	1	NA	promoter-TSS (NM_019650)	promoter-TSS (NM_019650)	61	NR_102396	399609	Mm.351922	NR_102388		C130046K22Rik	-	RIKEN cDNA C130046K22 gene	ncRNA
mm_150390.1	chr19	36409631	36409662	+	1	NA	intron (NM_029508, intron 1 of 8)	CpG	30579	NM_029508	76073	Mm.259180	NM_029508	ENSMUSG00000024805	Pcgf5	0610009F02Rik|1110054A01Rik|5830406C17Rik|5830443C21Rik|9530023M17Rik|AI324127	polycomb group ring finger 5	protein-coding
mm_92770.1	chr10	81151730	81151775	-	1	NA	TTS (NM_010731)	TTS (NM_010731)	15481	NM_010731	16969	Mm.20920	NM_010731	ENSMUSG00000035011	Zbtb7a	9030619K07Rik|9130006G12Rik|AI452336|FBI-1|Lrf|Pokemon|Zbtb7	zinc finger and BTB domain containing 7a	protein-coding
mm_112055.1	chr12	111813835	111813858	-	1	NA	promoter-TSS (NM_028875)	promoter-TSS (NM_028875)	33	NM_028875	74335	Mm.19082	NM_028875	ENSMUSG00000021287	Xrcc3	-	X-ray repair complementing defective repair in Chinese hamster cells 3	protein-coding
mm_149718.1	chr19	21713841	21713861	+	1	NA	Intergenic	RLTR20D|LTR|ERVK	60542	NM_146096	226016	Mm.28796	NM_146096	ENSMUSG00000047368	Abhd17b	5730446C15Rik|Cgi67|Fam108b|Fam108b1	abhydrolase domain containing 17B	protein-coding
mm_97026.1	chr11	72207522	72207532	+	1	NA	promoter-TSS (NM_026559)	promoter-TSS (NM_026559)	-27	NM_026559	52700	Mm.27670	NM_026559	ENSMUSG00000020803	Txndc17	4831443O22Rik|D11Ertd672e|TRP14|Txnl5	thioredoxin domain containing 17	protein-coding
mm_42950.1	chr5	123015145	123015153	+	1	NA	promoter-TSS (NM_175423)	promoter-TSS (NM_175423)	75	NM_175423	109305	Mm.218582	NM_175423	ENSMUSG00000049686	Orai1	D730049H07Rik|Tmem142a|orai-1	ORAI calcium release-activated calcium modulator 1	protein-coding
mm_139137.1	chr17	47509449	47509457	+	1	NA	intron (NM_001081635, intron 1 of 6)	intron (NM_001081635, intron 1 of 6)	4402	NM_001081635	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_22716.1	chr3	19310693	19310705	+	1	NA	intron (NM_001122759, intron 1 of 12)	CpG	623	NM_001122759	18583	Mm.355614	NM_008802	ENSMUSG00000069094	Pde7a	AU015378|AW047537	phosphodiesterase 7A	protein-coding
mm_24132.1	chr3	88214475	88214491	+	1	NA	promoter-TSS (NR_037276)	promoter-TSS (NR_037276)	-688	NR_037276	100526540		NR_037276	ENSMUSG00000092988	Mir3093	mir-3093|mmu-mir-3093	microRNA 3093	ncRNA
mm_103374.1	chr11	75341064	75341108	-	1	NA	exon (NM_026653, exon 3 of 17)	exon (NM_026653, exon 3 of 17)	7297	NM_001164223	68275	Mm.102574	NM_026653	ENSMUSG00000000751	Rpa1	5031405K23Rik|70kDa|AA589576|AW557552|RF-A|RP-A|Rpa	replication protein A1	protein-coding
mm_20475.1	chr2	129581728	129581732	-	1	NA	Intergenic	Intergenic	-11109	NM_001291020	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_49895.1	chr6	38919043	38919054	+	1	NA	promoter-TSS (NM_011539)	promoter-TSS (NM_011539)	62	NM_011539	21391	Mm.4054	NM_011539	ENSMUSG00000029925	Tbxas1	CYP5|CYP5A1|THAS|TS|TXAS|TXS	thromboxane A synthase 1, platelet	protein-coding
mm_87915.1	chr10	62432650	62432656	+	1	NA	intron (NM_181423, intron 12 of 14)	B1_Mus2|SINE|Alu	-10196	NM_145419	216019	Mm.213213	NM_145419	ENSMUSG00000020080	Hkdc1	BC016235	hexokinase domain containing 1	protein-coding
mm_168913.1	chr12	55502176	55502181	-	1	NA	Intergenic	RLTR27|LTR|ERVK	-9531	NM_010907	18035	Mm.170515	NM_010907	ENSMUSG00000021025	Nfkbia	AI462015|Nfkbi	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, alpha	protein-coding
mm_4936.1	chr1	191121050	191121078	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	22650	NM_030060	381319	Mm.6922	NM_030060	ENSMUSG00000026630	Batf3	9130211I03Rik|Snft	basic leucine zipper transcription factor, ATF-like 3	protein-coding
mm_98045.1	chr11	85683853	85683867	+	1	NA	intron (NM_138681, intron 24 of 25)	intron (NM_138681, intron 24 of 25)	35884	NR_045875	71489	Mm.442482	NR_045875	ENSMUSG00000086199	Bcas3os1	8430403D17Rik	breast carcinoma amplified sequence 3, opposite strand 1	ncRNA
mm_67051.1	chr7	67337407	67337436	-	1	NA	intron (NM_001033713, intron 2 of 11)	Lx9|LINE|L1	35437	NM_001291192	17258	Mm.132788	NM_001033713	ENSMUSG00000030557	Mef2a	A430079H05Rik	myocyte enhancer factor 2A	protein-coding
mm_144171.1	chr18	6603628	6603633	+	1	NA	promoter-TSS (NM_027598)	promoter-TSS (NM_027598)	-3	NM_027598	70901	Mm.158484	NM_027598	ENSMUSG00000039540	4921524L21Rik	-	RIKEN cDNA 4921524L21 gene	protein-coding
mm_146620.1	chr18	10106444	10106462	-	1	NA	exon (NM_009071, exon 14 of 33)	exon (NM_009071, exon 14 of 33)	75339	NM_009071	19877	Mm.6710	NM_009071	ENSMUSG00000024290	Rock1	1110055K06Rik|Rock-I	Rho-associated coiled-coil containing protein kinase 1	protein-coding
mm_148917.1	chr19	6975213	6975231	+	1	NA	5' UTR (NM_008889, exon 1 of 4)	5' UTR (NM_008889, exon 1 of 4)	174	NM_008889	18938	Mm.140	NM_008889	ENSMUSG00000056612	Ppp1r14b	AOM172|PHI-1|PLCB3N|Png	protein phosphatase 1, regulatory (inhibitor) subunit 14B	protein-coding
mm_170864.1	chr2	181953184	181953199	-	1	NA	Intergenic	Intergenic	-38035	NM_001205282	672125	Mm.489571	NM_001205282	ENSMUSG00000098505	Gm14496	OTTMUSG00000016837	predicted gene 14496	protein-coding
mm_17010.1	chr2	18872367	18872389	-	1	NA	exon (NM_008845, exon 5 of 10)	exon (NM_008845, exon 5 of 10)	-70560	NR_131254	66774	Mm.87075	NR_131254	ENSMUSG00000097638	Carlr	4933439G12Rik|Carl	cardiac and apoptosis-related long non-coding RNA	ncRNA
mm_105216.1	chr11	102177719	102177721	-	1	NA	intron (NM_172947, intron 2 of 4)	ID_B1|SINE|B4	7536	NM_172947	268490	Mm.259079	NM_172947	ENSMUSG00000020922	Lsm12	1110032E16Rik|1110059P07|2600001B17Rik	LSM12 homolog	protein-coding
mm_149960.1	chr19	28990348	28990373	+	1	NA	promoter-TSS (NM_025950)	promoter-TSS (NM_025950)	8	NM_025950	67072	Mm.78875	NM_025950	ENSMUSG00000024780	Cdc37l1	2700033A15Rik|BB159850|Cdc37l|Harc	cell division cycle 37-like 1	protein-coding
mm_56673.1	chr6	113690494	113690501	-	1	NA	intron (NM_001113553, intron 10 of 11)	RLTR35B_MM|LTR|ERVL	-6553	NM_001347356	381801	Mm.333322	NM_001033463	ENSMUSG00000056952	Tatdn2	AI646012|mKIAA0218	TatD DNase domain containing 2	protein-coding
mm_144785.1	chr18	35854735	35854750	+	1	NA	intron (NM_133687, intron 1 of 2)	intron (NM_133687, intron 1 of 2)	24924	NM_133687	67393	Mm.94560	NM_133687	ENSMUSG00000046668	Cxxc5	4930415K17Rik	CXXC finger 5	protein-coding
mm_124936.1	chr15	12230482	12230484	+	1	NA	intron (NM_172958, intron 2 of 15)	intron (NM_172958, intron 2 of 15)	25389	NM_172958	268783	Mm.54460	NM_172958	ENSMUSG00000039458	Mtmr12	3Pap|4932703C11|C730015A02Rik|Pip3ap|mKIAA1682	myotubularin related protein 12	protein-coding
mm_21966.1	chr2	167300776	167300779	-	1	NA	3' UTR (NM_019835, exon 9 of 9)	3' UTR (NM_019835, exon 9 of 9)	48401	NM_019835	56336	Mm.200886	NM_019835	ENSMUSG00000017929	B4galt5	9430078I07Rik|AW049941|AW539721	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 5	protein-coding
mm_62645.1	chr7	107666187	107666204	+	1	NA	intron (NM_001163557, intron 3 of 25)	intron (NM_001163557, intron 3 of 25)	59351	NM_001163557	19024	Mm.2817	NM_008905	ENSMUSG00000036528	Ppfibp2	Cclp1	PTPRF interacting protein, binding protein 2 (liprin beta 2)	protein-coding
mm_144252.1	chr18	10920923	10920942	+	1	NA	Intergenic	Intergenic	-131578	NM_010258	14465	Mm.329287	NM_010258	ENSMUSG00000005836	Gata6	AA410133|GATA-6	GATA binding protein 6	protein-coding
mm_134330.1	chr16	16439486	16439517	-	1	NA	intron (NM_001301817, intron 11 of 16)	Lx9|LINE|L1	-80470	NM_001276340	74006	Mm.218820	NM_152816	ENSMUSG00000022789	Dnm1l	6330417M19Rik|AI450666|Dlp1|Dnmlp1|Drp1|python	dynamin 1-like	protein-coding
mm_25541.1	chr3	115801113	115801120	+	1	NA	Intergenic	Intergenic	-86061	NM_007901	13609	Mm.982	NM_007901	ENSMUSG00000045092	S1pr1	AI849002|Edg1|Lpb1|S1p|S1p1	sphingosine-1-phosphate receptor 1	protein-coding
mm_82352.1	chr9	14275973	14275985	-	1	NA	promoter-TSS (NM_030261)	promoter-TSS (NM_030261)	-322	NM_030261	75747	Mm.325126	NM_030261	ENSMUSG00000032009	Sesn3	5630400E15Rik|BC003348|SEST3	sestrin 3	protein-coding
mm_75092.1	chr8	34093162	34093172	-	1	NA	intron (NM_001293759, intron 6 of 7)	intron (NM_001293759, intron 6 of 7)	14647	NM_001293758	22428	Mm.150373	NM_011722	ENSMUSG00000031516	Dctn6	AU044699|WS-3|p27	dynactin 6	protein-coding
mm_129249.1	chr15	76669800	76669804	-	1	NA	exon (NM_007989, exon 1 of 3)	exon (NM_007989, exon 1 of 3)	146	NM_007989	14106	Mm.42011	NM_007989	ENSMUSG00000033837	Foxh1	Fast1|Fast2|fast-1|fast-2	forkhead box H1	protein-coding
mm_154349.1	chrM	5804	5815	+	1	NA	NA	Intergenic	NA	NA								
mm_98798.1	chr11	97018820	97018827	+	1	NA	intron (NM_031183, intron 1 of 1)	CpG	5254	NM_031183	83395	Mm.156282	NM_031183	ENSMUSG00000038560	Sp6	1110025J03Rik|AA591031|AI592962|Epfn|Klf14	trans-acting transcription factor 6	protein-coding
mm_104553.1	chr11	96798601	96798636	-	1	NA	promoter-TSS (NR_033523)	promoter-TSS (NR_033523)	-462	NR_033523	629750	Mm.390396	NR_033523		Gm11517	OTTMUSG00000001634	ubiquitin A-52 residue ribosomal protein fusion product 1 pseudogene	pseudo
mm_68031.1	chr7	101293480	101293483	-	1	NA	intron (NM_001111111, intron 9 of 17)	intron (NM_001111111, intron 9 of 17)	8607	NM_001111111	73683	Mm.275744	NM_001111111	ENSMUSG00000047767	Atg16l2	2410118P20Rik	autophagy related 16-like 2 (S. cerevisiae)	protein-coding
mm_166611.1	chr6	70031684	70031688	-	1	NA	Intergenic	Intergenic	-704512	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_132648.1	chr16	41532852	41532865	+	1	NA	promoter-TSS (NM_175548)	promoter-TSS (NM_175548)	32	NM_001347236	268890	Mm.310524	NM_175548	ENSMUSG00000061080	Lsamp	5430428I19|AW046674|B130007O04Rik|D930023J12Rik|Lam|Lamp	limbic system-associated membrane protein	protein-coding
mm_64712.1	chr7	4630275	4630333	-	1	NA	5' UTR (NM_023440, exon 1 of 3)	5' UTR (NM_023440, exon 1 of 3)	178	NM_023440	68255	Mm.389784	NM_023440	ENSMUSG00000045282	Tmem86b	C330014O21Rik	transmembrane protein 86B	protein-coding
mm_108716.1	chr12	87157581	87157599	+	1	NA	intron (NM_001252555, intron 2 of 9)	intron (NM_001252555, intron 2 of 9)	-2105	NR_136901	625237	Mm.390529	NR_136901		Gm6566	EG625237	predicted gene 6566	ncRNA
mm_109685.1	chr12	113140567	113140577	+	1	NA	promoter-TSS (NM_001347443)	promoter-TSS (NM_001347443)	-33	NM_001347443	68337	Mm.133825	NM_024223	ENSMUSG00000006356	Crip2	0610010I23Rik|AW743261|C77570|CRP2|CRP4|Crp|ESP1|Hlp	cysteine rich protein 2	protein-coding
mm_113091.1	chr13	24104299	24104342	+	1	NA	intron (NM_026825, intron 17 of 37)	intron (NM_026825, intron 17 of 37)	-113106	NM_145399	214189	Mm.255667	NM_145399	ENSMUSG00000021337	Scgn	-	secretagogin, EF-hand calcium binding protein	protein-coding
mm_16221.1	chr2	173110821	173110834	+	1	NA	intron (NM_001081387, intron 5 of 10)	intron (NM_001081387, intron 5 of 10)	8698	NM_001081387	664799	Mm.389396	NM_001081387	ENSMUSG00000070495	Ctcfl	Boris|OTTMUSG00000016680	CCCTC-binding factor (zinc finger protein)-like	protein-coding
mm_158741.1	chrX	164246731	164246745	-	1	NA	intron (NM_009759, intron 3 of 18)	intron (NM_009759, intron 3 of 18)	11455	NM_009759	12169	Mm.504	NM_009759	ENSMUSG00000031377	Bmx	Etk|Etk/Bmx|Tyro8	BMX non-receptor tyrosine kinase	protein-coding
mm_158717.1	chrX	162643630	162643665	-	1	NA	promoter-TSS (NM_001290633)	promoter-TSS (NM_001290633)	11	NM_001290633	194590	Mm.442441	NM_178256	ENSMUSG00000040855	Reps2	POB1	RALBP1 associated Eps domain containing protein 2	protein-coding
mm_90246.1	chr10	121494434	121494434	+	1	NA	Intergenic	Intergenic	-18184	NM_138956	192678	Mm.41265	NM_138956	ENSMUSG00000025795	Rassf3	AW212023|AW322379	Ras association (RalGDS/AF-6) domain family member 3	protein-coding
mm_72597.1	chr8	84414686	84414725	+	1	NA	promoter-TSS (NM_001252060)	promoter-TSS (NM_001252060)	-659	NM_001252060	12286	Mm.334658	NM_007578	ENSMUSG00000034656	Cacna1a	APCA|BI|Caca1a|Cacnl1a4|Cav2.1|Ccha1a|EA2|FHM|HPCA|MHP|MHP1|SCA6|alpha1A|la|nmf352|rkr|smrl|tg	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	protein-coding
mm_90192.1	chr10	120208740	120208781	+	1	NA	promoter-TSS (NM_026617)	promoter-TSS (NM_026617)	-66	NM_026617	68212	Mm.157426	NM_026617	ENSMUSG00000020225	Tmbim4	0610007H07Rik|AU022431	transmembrane BAX inhibitor motif containing 4	protein-coding
mm_132845.1	chr16	46009095	46009105	+	1	NA	intron (NM_001134480, intron 1 of 3)	intron (NM_001134480, intron 1 of 3)	1313	NM_001134480	433022	Mm.380993	NM_001134480	ENSMUSG00000087141	Plcxd2	AW494639|EG433022	phosphatidylinositol-specific phospholipase C, X domain containing 2	protein-coding
mm_148671.1	chr19	5637709	5637730	+	1	NA	5' UTR (NM_009045, exon 1 of 11)	5' UTR (NM_009045, exon 1 of 11)	229	NM_009045	19697	Mm.249966	NM_009045	ENSMUSG00000024927	Rela	p65	v-rel reticuloendotheliosis viral oncogene homolog A (avian)	protein-coding
mm_40957.1	chr5	76951326	76951363	+	1	NA	promoter-TSS (NM_025939)	promoter-TSS (NM_025939)	-67	NM_025939	67054	Mm.182931	NM_025939	ENSMUSG00000029247	Paics	2610511I09Rik|ADE2H1|AIRC|PAIS	phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoribosylaminoimidazole, succinocarboxamide synthetase	protein-coding
mm_105490.1	chr11	106084145	106084157	-	1	NA	promoter-TSS (NM_011947)	promoter-TSS (NM_011947)	-751	NM_011947	26406	Mm.27041	NM_011947	ENSMUSG00000020700	Map3k3	AW548911|MAPKKK3|Mekk3|mKIAA4031	mitogen-activated protein kinase kinase kinase 3	protein-coding
mm_137789.1	chr17	29614849	29614928	+	1	NA	promoter-TSS (NM_021419)	promoter-TSS (NM_021419)	99	NM_021419	58230	Mm.305994	NM_021419	ENSMUSG00000090083	Rnf8	3830404E21Rik|AIP37|laXp180	ring finger protein 8	protein-coding
mm_138597.1	chr17	35532942	35532948	+	1	NA	promoter-TSS (NM_020576)	promoter-TSS (NM_020576)	-256	NM_020576	57390	Mm.34201	NM_020576	ENSMUSG00000024409	Psors1c2	AI448740|Pcg|SPR1	psoriasis susceptibility 1 candidate 2 (human)	protein-coding
mm_76508.1	chr8	86885223	86885282	-	1	NA	promoter-TSS (NM_030563)	promoter-TSS (NM_030563)	6	NM_030563	80750	Mm.25117	NM_030563	ENSMUSG00000031652	N4bp1	AI481586|C81621	NEDD4 binding protein 1	protein-coding
mm_134423.1	chr16	17894087	17894106	-	1	NA	promoter-TSS (NM_009435)	promoter-TSS (NM_009435)	-107	NM_009435	22114	Mm.439725	NM_009435	ENSMUSG00000041566	Tssk1	Stk22a|TSK-1|Tsk1|Tssk|Tssk1b	testis-specific serine kinase 1	protein-coding
mm_24278.1	chr3	89215193	89215243	+	1	NA	promoter-TSS (NM_013604)	promoter-TSS (NM_013604)	31	NM_013691	21827	Mm.2114	NM_013691	ENSMUSG00000028047	Thbs3	TSP3|Thbs-3	thrombospondin 3	protein-coding
mm_171072.1	chr3	115942459	115942478	+	1	NA	3' UTR (NM_023214, exon 11 of 11)	3' UTR (NM_023214, exon 11 of 11)	-37434	NR_130332	100316705		NR_130332	ENSMUSG00000089261	Mir669n	mmu-mir-669n	microRNA 669n	ncRNA
mm_120398.1	chr14	64690688	64690691	+	1	NA	intron (NM_001081177, intron 2 of 39)	intron (NM_001081177, intron 2 of 39)	38158	NM_001081177	16554	Mm.23611	NM_001081177	ENSMUSG00000060012	Kif13b	5330429L19Rik|6030414C01|AI429803|C130021D12Rik|GAKIN	kinesin family member 13B	protein-coding
mm_110775.1	chr12	70347537	70347556	-	1	NA	promoter-TSS (NM_001110203)	promoter-TSS (NM_001110203)	68	NM_001286386	94090	Mm.184012	NM_053167	ENSMUSG00000021071	Trim9	-	tripartite motif-containing 9	protein-coding
mm_5713.1	chr1	43933838	43933914	-	1	NA	promoter-TSS (NM_009418)	promoter-TSS (NM_009418)	-118	NM_001310540	22019	Mm.401675	NM_009418	ENSMUSG00000041763	Tpp2	TPP-2|TppII	tripeptidyl peptidase II	protein-coding
mm_161053.1	chr12	55492557	55492557	-	1	NA	promoter-TSS (NM_010907)	promoter-TSS (NM_010907)	90	NM_010907	18035	Mm.170515	NM_010907	ENSMUSG00000021025	Nfkbia	AI462015|Nfkbi	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, alpha	protein-coding
mm_54801.1	chr6	41699930	41699930	-	1	NA	intron (NM_032540, intron 6 of 18)	MER96B|DNA|hAT-Tip100	4395	NM_032540	23925	Mm.19958	NM_032540	ENSMUSG00000029866	Kel	CD238|Ece3	Kell blood group	protein-coding
mm_164337.1	chr16	11022149	11022151	-	1	NA	Intergenic	Intergenic	13252	NR_040518	100043147	Mm.489001	NR_040518	ENSMUSG00000097056	Gm4262	-	predicted gene 4262	ncRNA
mm_95246.1	chr11	44617929	44617935	+	1	NA	promoter-TSS (NM_001290711)	promoter-TSS (NM_001290711)	-168	NM_001290711	13591	Mm.439662	NM_007897	ENSMUSG00000057098	Ebf1	Ebf|O/E-1|OE-1|Olf-1|Olf1	early B cell factor 1	protein-coding
mm_145267.1	chr18	52767696	52767737	+	1	NA	promoter-TSS (NM_001199153)	promoter-TSS (NM_001199153)	-95	NM_026408	67847	Mm.292168	NM_026408	ENSMUSG00000024534	Sncaip	2810407O15Rik|4933427B05Rik|BB104594|SYPH1	synuclein, alpha interacting protein (synphilin)	protein-coding
mm_79547.1	chr9	57922471	57922502	+	1	NA	exon (NM_027086, exon 9 of 11)	exon (NM_027086, exon 9 of 11)	11500	NM_001122873	69459	Mm.41735	NM_027086	ENSMUSG00000055720	Ubl7	2300004C15Rik	ubiquitin-like 7 (bone marrow stromal cell-derived)	protein-coding
mm_155264.1	chrX	58030651	58030661	+	1	NA	promoter-TSS (NM_009575)	promoter-TSS (NM_009575)	28	NM_009575	22773	Mm.255890	NM_009575	ENSMUSG00000067860	Zic3	Bn|Ka	zinc finger protein of the cerebellum 3	protein-coding
mm_123334.1	chr14	63104000	63104029	-	1	NA	Intergenic	Intergenic	-18448	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_99569.1	chr11	103954148	103954175	+	1	NA	promoter-TSS (NM_008740)	promoter-TSS (NM_008740)	-105	NM_008740	18195	Mm.260117	NM_008740	ENSMUSG00000034187	Nsf	AI316878|AU020090|AU067812|SKD2	N-ethylmaleimide sensitive fusion protein	protein-coding
mm_16980.1	chr2	18028821	18028840	-	1	NA	non-coding (NR_028378, exon 1 of 1)	non-coding (NR_028378, exon 1 of 1)	1581	NR_028378	100034739	Mm.401643	NR_028378		Gm17762	-	predicted gene, 17762	ncRNA
mm_166617.1	chr6	72109786	72109796	+	1	NA	intron (NM_011375, intron 1 of 6)	intron (NM_011375, intron 1 of 6)	12183	NM_011375	20454	Mm.38248	NM_011375	ENSMUSG00000056091	St3gal5	3S-T|Siat9|[a]2	ST3 beta-galactoside alpha-2,3-sialyltransferase 5	protein-coding
mm_140460.1	chr17	90088462	90088508	+	1	NA	promoter-TSS (NM_001347419)	promoter-TSS (NM_001347419)	-117	NM_001347419	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_91273.1	chr10	24590607	24590613	-	1	NA	Intergenic	Intergenic	-4832	NM_010217	14219	Mm.390287	NM_010217	ENSMUSG00000019997	Ctgf	Ccn2|Fisp12|Hcs24|fisp-12	connective tissue growth factor	protein-coding
mm_77640.1	chr8	124369964	124369972	-	1	NA	3' UTR (NM_171824, exon 7 of 7)	3' UTR (NM_171824, exon 7 of 7)	63968	NM_171824	209966	Mm.234233	NM_171824	ENSMUSG00000050751	Pgbd5	2900019M05Rik|AI854313	piggyBac transposable element derived 5	protein-coding
mm_108300.1	chr12	79297312	79297327	+	1	NA	promoter-TSS (NM_009014)	promoter-TSS (NM_009014)	-32	NM_001252562	19363	Mm.341756	NM_009014	ENSMUSG00000059060	Rad51b	AI553500|R51H2|Rad51l1|mREC2	RAD51 paralog B	protein-coding
mm_149125.1	chr19	8990601	8990616	+	1	NA	intron (NR_104460, intron 1 of 6)	intron (NR_104460, intron 1 of 6)	1324	NM_001286518	66395	Mm.203866	NM_009643	ENSMUSG00000069833	Ahnak	DY6	AHNAK nucleoprotein (desmoyokin)	protein-coding
mm_43222.1	chr5	129787366	129787388	+	1	NA	promoter-TSS (NM_009838)	promoter-TSS (NM_009838)	21	NM_009838	12466	Mm.153159	NM_009838		Cct6a	CCT-zeta|CCT-zeta-1|Cct6|Cctz-1|TCP-1-zeta	chaperonin containing Tcp1, subunit 6a (zeta)	protein-coding
mm_73780.1	chr8	116943388	116943424	+	1	NA	promoter-TSS (NM_177700)	promoter-TSS (NM_177700)	13	NM_177700	234776	Mm.259736	NM_177700	ENSMUSG00000047388	Atmin	Asciz|gpg6|mKIAA0431	ATM interactor	protein-coding
mm_9006.1	chr1	165849054	165849073	-	1	NA	intron (NM_001113391, intron 1 of 7)	intron (NM_001113391, intron 1 of 7)	60382	NM_001113392	12503	Mm.217308	NM_031162	ENSMUSG00000005763	Cd247	4930549J05Rik|A430104F18Rik|AW552088|Cd3|Cd3-eta|Cd3-zeta|Cd3h|Cd3z|Cd3zeta|T3z|Tcrk|Tcrz	CD247 antigen	protein-coding
mm_68047.1	chr7	101538182	101538197	-	1	NA	Intergenic	LTR16E2|LTR|ERVL	17613	NM_007490	11871	Mm.439746	NM_007490	ENSMUSG00000092517	Art2a-ps	ARTC2|Art2a|Ly92a|Rt-6|Rt6|Rt6-1	ADP-ribosyltransferase 2a, pseudogene	protein-coding
mm_116812.1	chr13	54380219	54380227	-	1	NA	3' UTR (NM_009946, exon 4 of 4)	3' UTR (NM_009946, exon 4 of 4)	8874	NM_009946	12890	Mm.268902	NM_009946	ENSMUSG00000025867	Cplx2	921-L|AI413745|AW492120	complexin 2	protein-coding
mm_22640.1	chr3	14863496	14863521	+	1	NA	promoter-TSS (NM_007606)	promoter-TSS (NM_007606)	-30	NM_007606	12350	Mm.300	NM_007606	ENSMUSG00000027559	Car3	BB219044|Ca3|Car-3	carbonic anhydrase 3	protein-coding
mm_74967.1	chr8	27042727	27042741	-	1	NA	intron (NM_001039077, intron 1 of 4)	CpG	179	NM_054057	114863	Mm.277501	NM_054057	ENSMUSG00000031485	Prosc	1700024N20Rik|2200002F22Rik	proline synthetase co-transcribed	protein-coding
mm_81430.1	chr9	109094507	109094515	+	1	NA	promoter-TSS (NM_172775)	promoter-TSS (NM_172775)	-925	NM_172775	235611	Mm.53862	NM_172775	ENSMUSG00000053646	Plxnb1	2900002G15Rik|AU042020|mKIAA0407	plexin B1	protein-coding
mm_67271.1	chr7	75780772	75780794	-	1	NA	Intergenic	Intergenic	-67555	NM_001122780	207952	Mm.206223	NM_029652	ENSMUSG00000055652	Klhl25	2810402K13Rik|BC027373|Enc-1	kelch-like 25	protein-coding
mm_151477.1	chr19	58675057	58675065	+	1	NA	exon (NM_026925, exon 6 of 13)	exon (NM_026925, exon 6 of 13)	4696	NM_026925	69060	Mm.20407	NM_026925	ENSMUSG00000046008	Pnlip	1810007A24Rik|PL|PTL	pancreatic lipase	protein-coding
mm_20631.1	chr2	131994316	131994336	-	1	NA	3' UTR (NM_175445, exon 11 of 11)	3' UTR (NM_175445, exon 11 of 11)	35662	NM_175445	215653	Mm.204737	NM_175445	ENSMUSG00000027339	Rassf2	3830431H01Rik|9030412M04Rik|AI852669|AW495050	Ras association (RalGDS/AF-6) domain family member 2	protein-coding
mm_109604.1	chr12	112719238	112719256	+	1	NA	Intergenic	Intergenic	-2927	NM_001024602	217882	Mm.23689	NM_001024602	ENSMUSG00000072825	Cep170b	AI466840|AW555464|Kiaa0284|mKIAA0284	centrosomal protein 170B	protein-coding
mm_99694.1	chr11	106090974	106091006	+	1	NA	intron (NM_011947, intron 1 of 15)	intron (NM_011947, intron 1 of 15)	6088	NM_011947	26406	Mm.27041	NM_011947	ENSMUSG00000020700	Map3k3	AW548911|MAPKKK3|Mekk3|mKIAA4031	mitogen-activated protein kinase kinase kinase 3	protein-coding
mm_2277.1	chr1	91298355	91298391	+	1	NA	promoter-TSS (NM_016717)	promoter-TSS (NM_016717)	35	NM_016717	50880	Mm.25724	NM_016717	ENSMUSG00000026307	Scly	9830169H08|A930015N15Rik|SCL|Scly1|Scly2	selenocysteine lyase	protein-coding
mm_3676.1	chr1	153667636	153667640	+	1	NA	intron (NM_001347115, intron 2 of 5)	intron (NM_001347115, intron 2 of 5)	1965	NM_001347115	67792	Mm.379143	NM_026380	ENSMUSG00000042671	Rgs8	6530413N01Rik	regulator of G-protein signaling 8	protein-coding
mm_85852.1	chr9	110656383	110656419	-	1	NA	promoter-TSS (NM_028312)	promoter-TSS (NM_028312)	-102	NM_028312	72654	Mm.249115	NM_028312	ENSMUSG00000019659	Ccdc12	2700094L05Rik|C76605	coiled-coil domain containing 12	protein-coding
mm_68219.1	chr7	104411076	104411095	-	1	NA	exon (NM_009099, exon 8 of 8)	exon (NM_009099, exon 8 of 8)	-52439	NM_175648	244183	Mm.347647	NM_175648	ENSMUSG00000052749	Trim30b	A530023O14Rik|Trim30-1	tripartite motif-containing 30B	protein-coding
mm_3094.1	chr1	134415511	134415534	+	1	NA	promoter-TSS (NM_001306069)	promoter-TSS (NM_001306069)	-142	NM_001306069	72674	Mm.259976	NM_028320	ENSMUSG00000026457	Adipor1	2810031L11Rik|ACDCR1|CGI-45|Paqr1	adiponectin receptor 1	protein-coding
mm_6745.1	chr1	83277333	83277344	-	1	NA	exon (NM_172430, exon 7 of 11)	exon (NM_172430, exon 7 of 11)	117576	NM_027725	71227	Mm.256482	NM_027725	ENSMUSG00000053161	Daw1	4930563E19Rik|4933429D11Rik|Wdr69|b2b1116Clo|b2b1584Clo	dynein assembly factor with WDR repeat domains 1	protein-coding
mm_2081.1	chr1	87675641	87675671	+	1	NA	intron (NM_010566, intron 5 of 26)	B4A|SINE|B4	55344	NM_001110193	16331	Mm.15105	NM_010566	ENSMUSG00000026288	Inpp5d	SHIP|SHIP-1|SHIP1|SIP-145|p150Ship|s-SHIP	inositol polyphosphate-5-phosphatase D	protein-coding
mm_140723.1	chr17	15434820	15434850	-	1	NA	Intergenic	L1M4c|LINE|L1	38589	NM_024203	67544	Mm.35039	NM_024203	ENSMUSG00000014763	Fam120b	4932442K08Rik|AW049283|AW413338|CCPG|Pgcc1|mKIAA1838	family with sequence similarity 120, member B	protein-coding
mm_41468.1	chr5	91139592	91139607	+	1	NA	promoter-TSS (NM_009704)	promoter-TSS (NM_009704)	0	NM_009704	11839	Mm.8039	NM_009704	ENSMUSG00000029378	Areg	AR|Mcub|Sdgf	amphiregulin	protein-coding
mm_73367.1	chr8	105605221	105605306	+	1	NA	promoter-TSS (NM_001081241)	promoter-TSS (NM_001081241)	34	NM_001081241	75687	Mm.41261	NM_001081241	ENSMUSG00000038604	Fam65a	2310066E14Rik|AI837433	family with sequence similarity 65, member A	protein-coding
mm_155316.1	chrX	61830198	61830210	+	1	NA	Intergenic	Intergenic	120588	NM_001018087	434784	Mm.23468	NM_001018087	ENSMUSG00000057615	Ldoc1	Gm366|Mar7|Mart7|Sirh7	leucine zipper, down-regulated in cancer 1	protein-coding
mm_94549.1	chr11	11171326	11171327	+	1	NA	intron (NM_177033, intron 3 of 3)	intron (NM_177033, intron 3 of 3)	57310	NM_177033	319922	Mm.337851	NM_177033	ENSMUSG00000050830	Vwc2	A930041G11Rik|G11|PSST739|UNQ739|cradin	von Willebrand factor C domain containing 2	protein-coding
mm_108202.1	chr12	76902171	76902182	+	1	NA	intron (NM_145927, intron 7 of 11)	ORR1C2|LTR|ERVL-MaLR	60072	NM_008558	17187	Mm.268548	NM_008558	ENSMUSG00000059436	Max	AA960152|AI875693|bHLHd4|bHLHd5|bHLHd6|bHLHd7|bHLHd8	Max protein	protein-coding
mm_50362.1	chr6	48647413	48647423	+	1	NA	promoter-TSS (NM_001286629)	promoter-TSS (NM_001286629)	57	NM_212486	243374	Mm.86514	NM_212486	ENSMUSG00000064262	Gimap8	Gm457|IAN9|IMAP8	GTPase, IMAP family member 8	protein-coding
mm_31936.1	chr4	86575721	86575731	+	1	NA	promoter-TSS (NM_178376)	promoter-TSS (NM_178376)	53	NM_178376	68441	Mm.31178	NM_178376	ENSMUSG00000070934	Rraga	1300010C19Rik|AI255374|FIP-1|RAGA	Ras-related GTP binding A	protein-coding
mm_12842.1	chr2	82507113	82507127	+	1	NA	Intergenic	Intergenic	453462	NM_175513	241514	Mm.119383	NM_175513	ENSMUSG00000070866	Zfp804a	C630007C17Rik|Znf804a	zinc finger protein 804A	protein-coding
mm_55014.1	chr6	48840721	48840731	-	1	NA	promoter-TSS (NM_025326)	promoter-TSS (NM_025326)	262	NM_023056	65963	Mm.28385	NM_023056	ENSMUSG00000029810	Tmem176b	1810009M01Rik|Clast1|Lr8	transmembrane protein 176B	protein-coding
mm_83472.1	chr9	45787652	45787666	-	1	NA	intron (NM_001081373, intron 10 of 29)	intron (NM_001081373, intron 10 of 29)	40979	NM_001081373	214552	Mm.260103	NM_172531	ENSMUSG00000043987	Cep164	AI450905|BC027092|D030051D21|mKIAA1052	centrosomal protein 164	protein-coding
mm_79893.1	chr9	65312815	65312835	+	1	NA	intron (NM_011802, intron 6 of 13)	B1_Mus2|SINE|Alu	18565	NM_011802	270166	Mm.30088	NM_011802	ENSMUSG00000015357	Clpx	AU014732|E330029I21	caseinolytic mitochondrial matrix peptidase chaperone subunit	protein-coding
mm_97629.1	chr11	78959683	78959694	+	1	NA	exon (NM_010927, exon 27 of 27)	exon (NM_010927, exon 27 of 27)	25236	NM_001159301	16859	Mm.341434	NM_010708	ENSMUSG00000001123	Lgals9	AA407335|AI194909|AI265545|LGALS35|Lgals5|gal-9|galectin-9	lectin, galactose binding, soluble 9	protein-coding
mm_116601.1	chr13	48593364	48593400	-	1	NA	intron (NM_207232, intron 2 of 9)	intron (NM_207232, intron 2 of 9)	32290	NM_207232	218232	Mm.315089	NM_207232	ENSMUSG00000038042	Ptpdc1	AI843923|AW456874|Naa-1|Ptpcd1	protein tyrosine phosphatase domain containing 1	protein-coding
mm_143643.1	chr17	79354944	79354949	-	1	NA	5' UTR (NM_026514, exon 1 of 2)	5' UTR (NM_026514, exon 1 of 2)	145	NM_026514	260409	Mm.140601	NM_026514	ENSMUSG00000036533	Cdc42ep3	3200001F04Rik|AA986861|Borg2|Cep3|UB1	CDC42 effector protein (Rho GTPase binding) 3	protein-coding
mm_35303.1	chr4	24430556	24430586	-	1	NA	Intergenic	Intergenic	-65891	NM_199467	212377	Mm.120919	NM_199467	ENSMUSG00000045751	Mms22l	F730047E07Rik|Gm134	MMS22-like, DNA repair protein	protein-coding
mm_113769.1	chr13	44840687	44840697	+	1	NA	intron (NM_001205044, intron 3 of 18)	intron (NM_001205044, intron 3 of 18)	109421	NM_001205043	16468	Mm.25059	NM_021878	ENSMUSG00000038518	Jarid2	Jmj|jumonji	jumonji, AT rich interactive domain 2	protein-coding
mm_27183.1	chr3	34649725	34649735	-	1	NA	promoter-TSS (NM_011443)	promoter-TSS (NM_011443)	-265	NM_011443	20674	Mm.65396	NM_011443	ENSMUSG00000074637	Sox2	Sox-2|lcc|ysb	SRY (sex determining region Y)-box 2	protein-coding
mm_85666.1	chr9	107675653	107675673	-	1	NA	intron (NM_008140, intron 8 of 8)	intron (NM_008140, intron 8 of 8)	3929	NM_008140	14685	Mm.284853	NM_008140	ENSMUSG00000034837	Gnat1	Gnat-1|Ird1|Ird2|Tralpha|irdc|irdr|transducin	guanine nucleotide binding protein, alpha transducing 1	protein-coding
mm_19580.1	chr2	101649524	101649539	-	1	NA	promoter-TSS (NM_009019)	promoter-TSS (NM_009019)	1	NM_009019	19373	Mm.828	NM_009019	ENSMUSG00000061311	Rag1	Rag-1	recombination activating gene 1	protein-coding
mm_5027.1	chr1	193207709	193207730	+	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-6173	NM_153137	215243	Mm.261259	NM_153137	ENSMUSG00000037318	Traf3ip3	6030423D04Rik|AI115021|T3jam	TRAF3 interacting protein 3	protein-coding
mm_142393.1	chr17	44880872	44880874	-	1	NA	promoter-TSS (NM_029257)	promoter-TSS (NM_029257)	12	NM_029257	75341	Mm.386821	NM_029257		4930564C03Rik	-	RIKEN cDNA 4930564C03 gene	protein-coding
mm_31763.1	chr4	63395158	63395167	+	1	NA	exon (NM_001045514, exon 3 of 22)	exon (NM_001045514, exon 3 of 22)	3078	NM_001305432	100182	Mm.387725	NM_001045514	ENSMUSG00000039158	Akna	AI597013	AT-hook transcription factor	protein-coding
mm_131370.1	chr16	13830567	13830577	+	1	NA	intron (NR_144374, intron 4 of 7)	B3|SINE|B2	11321	NM_001346111	18203	Mm.380410	NM_010946	ENSMUSG00000022681	Ntan1	PNAA|PNAD	N-terminal Asn amidase	protein-coding
mm_74782.1	chr8	22039608	22039625	-	1	NA	intron (NM_007511, intron 1 of 20)	intron (NM_007511, intron 1 of 20)	20458	NM_007511	11979	Mm.87854	NM_007511	ENSMUSG00000006567	Atp7b	Atp7a|WND|tx	ATPase, Cu++ transporting, beta polypeptide	protein-coding
mm_5082.1	chr1	4409279	4409290	-	1	NA	promoter-TSS (NM_001195662)	promoter-TSS (NM_001195662)	-43	NM_001195662	19888	Mm.294263	NM_011283	ENSMUSG00000025900	Rp1	Dcdc3|Orp1|Rp1h|mG145	retinitis pigmentosa 1 (human)	protein-coding
mm_90779.1	chr10	6980297	6980320	-	1	NA	promoter-TSS (NM_001347225)	promoter-TSS (NM_001347225)	-27	NM_001347225	320495	Mm.331674	NM_001033391	ENSMUSG00000064065	Ipcef1	A130090K04Rik	interaction protein for cytohesin exchange factors 1	protein-coding
mm_60104.1	chr7	35353544	35353554	+	1	NA	intron (NM_027897, intron 1 of 14)	Lx9|LINE|L1	19312	NM_027897	52428	Mm.286600	NM_027897	ENSMUSG00000030494	Rhpn2	1300002E07Rik|AA536890|C85860|D7Ertd784e	rhophilin, Rho GTPase binding protein 2	protein-coding
mm_3146.1	chr1	135146708	135146718	+	1	NA	promoter-TSS (NM_026823)	promoter-TSS (NM_026823)	-121	NM_026823	68724	Mm.174998	NM_026823	ENSMUSG00000026426	Arl8a	1110033P22Rik|Arl10b|gie2	ADP-ribosylation factor-like 8A	protein-coding
mm_38862.1	chr4	149445588	149445601	-	1	NA	Intergenic	CpG	9374	NM_022020	63954	Mm.46023	NM_022020	ENSMUSG00000028996	Rbp7	1110002J23Rik|CRBP-III	retinol binding protein 7, cellular	protein-coding
mm_121341.1	chr14	115623066	115623070	+	1	NA	intron (NM_175500, intron 6 of 7)	intron (NM_175500, intron 6 of 7)	-213516	NR_045761	75088	Mm.444706	NR_045761	ENSMUSG00000093551	4930505G20Rik	-	RIKEN cDNA 4930505G20 gene	ncRNA
mm_146441.1	chr18	84935016	84935031	+	1	NA	promoter-TSS (NM_015798)	promoter-TSS (NM_015798)	-2	NM_015798	50764	Mm.28369	NM_015798	ENSMUSG00000034391	Fbxo15	AU019763|Fbx15|ecat3	F-box protein 15	protein-coding
mm_104838.1	chr11	99170830	99170839	-	1	NA	Intergenic	Intergenic	-15757	NM_007719	12775	Mm.2932	NM_007719	ENSMUSG00000037944	Ccr7	CC-CKR-7|CCR-7|CD197|Cdw197|Cmkbr7|EBI1|Ebi1h	chemokine (C-C motif) receptor 7	protein-coding
mm_143252.1	chr17	65510049	65510051	-	1	NA	intron (NM_001008973, intron 2 of 14)	RMER19B2|LTR|ERVK	30732	NM_001008973	381107	Mm.141275	NM_001008973	ENSMUSG00000045036	Tmem232	E130009J12Rik|Gm940|Tes13-L|Tes13-S	transmembrane protein 232	protein-coding
mm_80921.1	chr9	101053515	101053534	+	1	NA	Intergenic	Intergenic	-18640	NM_025835	66904	Mm.335385	NM_025835	ENSMUSG00000032527	Pccb	1300012P06Rik|AI314687|R74805	propionyl Coenzyme A carboxylase, beta polypeptide	protein-coding
mm_78560.1	chr9	35740903	35740907	+	1	NA	promoter-TSS (NM_001167588)	promoter-TSS (NM_001167588)	-144	NM_001167588	100312949	Mm.475848	NM_001167588	ENSMUSG00000091174	Gm17677	Pate-n|Pate10	predicted gene, 17677	protein-coding
mm_38875.1	chr4	149683144	149683146	-	1	NA	intron (NM_001029837, intron 1 of 23)	MTB_Mm|LTR|ERVL-MaLR	-7056	NM_001164051	18707	Mm.229108	NM_008840	ENSMUSG00000039936	Pik3cd	2410099E07Rik|2610208K16Rik|AW545373|p110delta	phosphatidylinositol 3-kinase catalytic delta polypeptide	protein-coding
mm_44097.1	chr5	149287691	149287722	+	1	NA	exon (NM_009663, exon 5 of 5)	exon (NM_009663, exon 5 of 5)	22702	NM_009663	11690	Mm.19844	NM_009663	ENSMUSG00000060063	Alox5ap	Flap	arachidonate 5-lipoxygenase activating protein	protein-coding
mm_83111.1	chr9	40376214	40376263	-	1	NA	intron (NM_172768, intron 2 of 19)	intron (NM_172768, intron 2 of 19)	42766	NR_040728	73558	Mm.398307	NR_040728		1700110K17Rik	-	RIKEN cDNA 1700110K17 gene	ncRNA
mm_142204.1	chr17	36973258	36973273	-	1	NA	Intergenic	RLTR41|LTR|ERV1	7972	NM_029747	76797	Mm.159787	NM_029747	ENSMUSG00000064308	2410137M14Rik	-	RIKEN cDNA 2410137M14 gene	protein-coding
mm_9173.1	chr1	171018710	171018753	-	1	NA	promoter-TSS (NM_144559)	promoter-TSS (NM_144559)	-195	NM_144559	246256	Mm.251254	NM_144559	ENSMUSG00000059089	Fcgr4	4833442P21Rik|CD16-2|FcgRIV|FcgammaRIV|Fcgr3a|Fcrl3	Fc receptor, IgG, low affinity IV	protein-coding
mm_19646.1	chr2	102865334	102865355	-	1	NA	exon (NM_009851, exon 2 of 19)	exon (NM_009851, exon 2 of 19)	36321	NM_001177785	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_122052.1	chr14	30177416	30177420	-	1	NA	intron (NM_001302637, intron 7 of 48)	intron (NM_001302637, intron 7 of 48)	154785	NM_175343	218865	Mm.259916	NM_172264	ENSMUSG00000015970	Chdh	AU041472|D630034H06Rik	choline dehydrogenase	protein-coding
mm_18056.1	chr2	39226273	39226332	-	1	NA	promoter-TSS (NM_024209)	promoter-TSS (NM_024209)	36	NM_024209	67857	Mm.389242	NM_024209	ENSMUSG00000026753	Ppp6c	2310003C10Rik	protein phosphatase 6, catalytic subunit	protein-coding
mm_40298.1	chr5	43662374	43662384	+	1	NA	promoter-TSS (NM_172274)	promoter-TSS (NM_172274)	0	NM_172274	231214	Mm.44434	NM_172274	ENSMUSG00000039765	Cc2d2a	5730509K17Rik|b2b1035Clo	coiled-coil and C2 domain containing 2A	protein-coding
mm_71239.1	chr8	40908669	40908679	+	1	NA	intron (NM_007514, intron 7 of 11)	intron (NM_007514, intron 7 of 11)	-17559	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_96911.1	chr11	70459780	70459799	+	1	NA	5' UTR (NM_001029929, exon 1 of 14)	5' UTR (NM_001029929, exon 1 of 14)	167	NM_001029929	574428	Mm.472771	NM_001029929	ENSMUSG00000040829	Zmynd15	-	zinc finger, MYND-type containing 15	protein-coding
mm_72424.1	chr8	82774768	82774776	+	1	NA	promoter-TSS (NM_145600)	promoter-TSS (NM_145600)	-646	NM_145600	30932	Mm.269248	NM_145600	ENSMUSG00000031711	Zfp330	BC008086|Noa36|Znf330	zinc finger protein 330	protein-coding
mm_50794.1	chr6	54041379	54041382	+	1	NA	intron (NM_001163640, intron 1 of 12)	intron (NM_001163640, intron 1 of 12)	1448	NM_001163640	69993	Mm.321147	NM_023543	ENSMUSG00000004633	Chn2	1700026N20Rik|4930557O16Rik|ARHGAP3|Bch	chimerin 2	protein-coding
mm_77440.1	chr8	121602255	121602258	-	1	NA	3' UTR (NM_080855, exon 13 of 13)	3' UTR (NM_080855, exon 13 of 13)	11788	NM_026160	67443	Mm.28357	NM_026160	ENSMUSG00000031812	Map1lc3b	1010001C15Rik|Atg8|LC3b|Map1lc3	microtubule-associated protein 1 light chain 3 beta	protein-coding
mm_58082.1	chr6	136941846	136941856	-	1	NA	promoter-TSS (NM_007486)	promoter-TSS (NM_007486)	48	NM_001301301	11857	Mm.2241	NM_007486	ENSMUSG00000030220	Arhgdib	D4|Gdid4|Ly-GDI	Rho, GDP dissociation inhibitor (GDI) beta	protein-coding
mm_17763.1	chr2	32788329	32788348	-	1	NA	3' UTR (NM_001113569, exon 20 of 20)	3' UTR (NM_001113569, exon 20 of 20)	-3933	NM_025619	227736	Mm.441499	NM_025619	ENSMUSG00000038987	Cfap157	1700019L03Rik	cilia and flagella associated protein 157	protein-coding
mm_81104.1	chr9	106448630	106448655	+	1	NA	promoter-TSS (NM_145919)	promoter-TSS (NM_145919)	2	NM_029631	76491	Mm.335427	NM_029631	ENSMUSG00000042073	Abhd14b	1810013B01Rik	abhydrolase domain containing 14b	protein-coding
mm_144489.1	chr18	24205304	24205348	+	1	NA	promoter-TSS (NM_013814)	promoter-TSS (NM_013814)	-18	NM_013814	14423	Mm.30249	NM_013814	ENSMUSG00000000420	Galnt1	-	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 1	protein-coding
mm_109492.1	chr12	111446002	111446018	+	1	NA	exon (NM_009396, exon 3 of 12)	exon (NM_009396, exon 3 of 12)	3349	NM_009396	21928	Mm.255332	NM_009396	ENSMUSG00000021281	Tnfaip2	B94|Exoc3l3|M-sec|Tnfip2|tnfb94	tumor necrosis factor, alpha-induced protein 2	protein-coding
mm_84149.1	chr9	59472248	59472257	-	1	NA	intron (NM_019927, intron 1 of 13)	intron (NM_019927, intron 1 of 13)	9489	NR_045640	100504377	Mm.446631	NR_045640		Gm20199	-	predicted gene, 20199	ncRNA
mm_151488.1	chr19	58679543	58679557	+	1	NA	exon (NM_026925, exon 10 of 13)	exon (NM_026925, exon 10 of 13)	9185	NM_026925	69060	Mm.20407	NM_026925	ENSMUSG00000046008	Pnlip	1810007A24Rik|PL|PTL	pancreatic lipase	protein-coding
mm_103524.1	chr11	77009169	77009183	-	1	NA	intron (NM_010484, intron 1 of 13)	intron (NM_010484, intron 1 of 13)	10579	NM_010484	15567	Mm.300318	NM_010484	ENSMUSG00000020838	Slc6a4	5-HTT|AI323329|Htt|Sert	solute carrier family 6 (neurotransmitter transporter, serotonin), member 4	protein-coding
mm_64636.1	chr7	3715712	3715734	-	1	NA	exon (NM_011095, exon 9 of 15)	exon (NM_011095, exon 9 of 15)	4659	NM_011095	18733	Mm.326531	NM_011095	ENSMUSG00000058818	Pirb	Gp91|LIR-3|Lilrb3|PIR-B	paired Ig-like receptor B	protein-coding
mm_63625.1	chr7	128314781	128314799	+	1	NA	Intergenic	Intergenic	-16659	NM_145590	233913	Mm.220880	NM_145590	ENSMUSG00000030780	BC017158	-	cDNA sequence BC017158	protein-coding
mm_17199.1	chr2	25468882	25468896	-	1	NA	exon (NM_008963, exon 3 of 7)	exon (NM_008963, exon 3 of 7)	860	NM_008963	19215	Mm.1008	NM_008963	ENSMUSG00000015090	Ptgds	21kDa|L-PGDS|PGD2|PGDS|PGDS2|Ptgs3	prostaglandin D2 synthase (brain)	protein-coding
mm_63011.1	chr7	120982481	120982489	+	1	NA	promoter-TSS (NM_007672)	promoter-TSS (NM_007672)	-24	NM_028955	74466	Mm.189707	NM_028955	ENSMUSG00000030877	Mfsd13b	4933427G17Rik	major facilitator superfamily domain containing 13B	protein-coding
mm_155806.1	chrX	99136091	99136107	+	1	NA	promoter-TSS (NM_010110)	promoter-TSS (NM_010110)	38	NM_010110	13641	Mm.3374	NM_010110	ENSMUSG00000031217	Efnb1	Cek5-L|EFL-3|Elk-L|Epl2|Eplg2|LERK-2|Lerk2|Stra1	ephrin B1	protein-coding
mm_21468.1	chr2	160981677	160981687	-	1	NA	intron (NR_126509, intron 23 of 35)	intron (NR_126509, intron 23 of 35)	-69343	NM_182840	280635	Mm.330747	NM_182840	ENSMUSG00000050700	Emilin3	1110013O17Rik|EMILIN-3|EMILIN-5|EMILIN-T|Emilin5	elastin microfibril interfacer 3	protein-coding
mm_159991.1	chr6	116107793	116107793	-	1	NA	intron (NM_177412, intron 3 of 5)	intron (NM_177412, intron 3 of 5)	85581	NM_177412	330401	Mm.425352	NM_177412	ENSMUSG00000030126	Tmcc1	3632431M01Rik|mKIAA0779	transmembrane and coiled coil domains 1	protein-coding
mm_102698.1	chr11	65807020	65807034	-	1	NA	promoter-TSS (NM_026107)	promoter-TSS (NM_026107)	-148	NM_001302374	52712	Mm.340052	NM_026107	ENSMUSG00000018347	Zkscan6	1700128E15Rik|D11Ertd714e|KOX11|Zfp535|Znf18	zinc finger with KRAB and SCAN domains 6	protein-coding
mm_71079.1	chr8	34622454	34622458	+	1	NA	intron (NR_040706, intron 1 of 4)	intron (NR_040706, intron 1 of 4)	17860	NR_040706	330734	Mm.149998	NR_040706	ENSMUSG00000109819	B930018H19Rik	B930018H19	RIKEN cDNA B930018H19 gene	ncRNA
mm_16242.1	chr2	173157082	173157095	+	1	NA	exon (NM_011044, exon 7 of 10)	exon (NM_011044, exon 7 of 10)	4015	NM_011044	18534	Mm.266867	NM_011044	ENSMUSG00000027513	Pck1	AI265463|PEPCK|Pck-1	phosphoenolpyruvate carboxykinase 1, cytosolic	protein-coding
mm_93110.1	chr10	91082784	91082807	-	1	NA	promoter-TSS (NM_026166)	promoter-TSS (NM_026166)	-52	NM_009684	11783	Mm.220289	NM_009684	ENSMUSG00000019979	Apaf1	6230400I06Rik|Apaf-1|Apaf1l|fog|mKIAA0413	apoptotic peptidase activating factor 1	protein-coding
mm_108856.1	chr12	98746936	98747046	+	1	NA	promoter-TSS (NR_027648)	promoter-TSS (NR_027648)	23	NM_029334	75553	Mm.25549	NM_029334	ENSMUSG00000021012	Zc3h14	1010001P15Rik|1700016A15Rik|2700069A02Rik|AU014748	zinc finger CCCH type containing 14	protein-coding
mm_49368.1	chr6	23248829	23248837	+	1	NA	promoter-TSS (NM_028462)	promoter-TSS (NM_028462)	-569	NM_028462	73191	Mm.55115	NM_028462	ENSMUSG00000029697	Fezf1	3110069A13Rik|Fez|Zfp312-like|fez-like	Fez family zinc finger 1	protein-coding
mm_86198.1	chr9	119977613	119977624	-	1	NA	intron (NM_153287, intron 1 of 4)	(CAGA)n|Simple_repeat|Simple_repeat	7040	NM_153287	215418	Mm.491094	NM_153287	ENSMUSG00000032515	Csrnp1	4931429D10Rik|Axud1|CSRNP-1|URAX1|taip-3	cysteine-serine-rich nuclear protein 1	protein-coding
mm_43558.1	chr5	137625194	137625204	+	1	NA	promoter-TSS (NM_027708)	promoter-TSS (NM_027708)	-121	NM_027708	71176	Mm.474695	NM_027708	ENSMUSG00000089984	Fbxo24	4933422D21Rik|Fbx24	F-box protein 24	protein-coding
mm_144959.1	chr18	37815445	37815467	+	1	NA	5' UTR (NM_033582, exon 1 of 4)	5' UTR (NM_033582, exon 1 of 4)	377	NM_033582	93707	Mm.247203	NM_033582	ENSMUSG00000023036	Pcdhgc4	-	protocadherin gamma subfamily C, 4	protein-coding
mm_91269.1	chr10	24132479	24132497	-	1	NA	Intergenic	Intergenic	-16829	NM_016797	53331	Mm.248042	NM_016797	ENSMUSG00000019998	Stx7	AI315064|AI317144|AW107239|Syn7	syntaxin 7	protein-coding
mm_162233.1	chrX	151890782	151890782	+	1	NA	exon (NM_021523, exon 39 of 83)	exon (NM_021523, exon 39 of 83)	-21564	NR_029732	387253		NR_029732	ENSMUSG00000065602	Mirlet7f-2	Mirlet7f2|Mirnlet7f2|let-7f-2	microRNA let7f-2	ncRNA
mm_101039.1	chr11	8605240	8605257	-	1	NA	intron (NM_001083587, intron 2 of 30)	intron (NM_001083587, intron 2 of 30)	59287	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_151434.1	chr19	57273931	57273962	+	1	NA	promoter-TSS (NR_045319)	promoter-TSS (NR_045319)	-14	NR_045319	78120	Mm.445892	NR_045319		4930449E18Rik	-	RIKEN cDNA 4930449E18 gene	ncRNA
mm_142478.1	chr17	45686793	45686806	-	1	NA	promoter-TSS (NM_198167)	promoter-TSS (NM_198167)	427	NM_026732	68463	Mm.379158	NM_026732	ENSMUSG00000023939	Mrpl14	1110006I11Rik|AI846816|MRP-L32|Rpml32	mitochondrial ribosomal protein L14	protein-coding
mm_1085.1	chr1	59548863	59548871	+	1	NA	intron (NM_001013771, intron 4 of 19)	intron (NM_001013771, intron 4 of 19)	32603	NM_001013771	381260	Mm.486706	NM_001013771	ENSMUSG00000047361	Gm973	AW554518	predicted gene 973	protein-coding
mm_171009.1	chr2	82851286	82851305	-	1	NA	Intergenic	ERVB7_1-LTR_MM|LTR|ERVK	-793283	NM_026934	69082	Mm.27804	NM_026934	ENSMUSG00000027091	Zc3h15	1700006A17Rik|1810012H02Rik|2610312B22Rik|FM22|Ierepo4	zinc finger CCCH-type containing 15	protein-coding
mm_94739.1	chr11	21092550	21092560	+	1	NA	intron (NM_023324, intron 1 of 6)	intron (NM_023324, intron 1 of 6)	1231	NM_023324	67245	Mm.28957	NM_023324	ENSMUSG00000020134	Peli1	2810468L03Rik|A930031K15Rik|AA409794|AI586297|D11Ertd676e	pellino 1	protein-coding
mm_170954.1	chr2	5379317	5379318	-	1	NA	promoter-TSS (NR_030601)	promoter-TSS (NR_030601)	-73	NR_030601	100124465		NR_030601	ENSMUSG00000078031	Mir466d	Mirn466d	microRNA 466d	ncRNA
mm_11762.1	chr2	38522325	38522339	+	1	NA	intron (NM_001159631, intron 1 of 9)	intron (NM_001159631, intron 1 of 9)	10456	NM_001159631	59126	Mm.143818	NM_021606	ENSMUSG00000026749	Nek6	1300007C09Rik	NIMA (never in mitosis gene a)-related expressed kinase 6	protein-coding
mm_54559.1	chr6	37355292	37355292	-	1	NA	intron (NM_178661, intron 6 of 11)	intron (NM_178661, intron 6 of 11)	-55316	NM_001347104	320127	Mm.119469	NM_001081206	ENSMUSG00000038665	Dgki	C130010K08Rik	diacylglycerol kinase, iota	protein-coding
mm_144668.1	chr18	34409416	34409458	+	1	NA	promoter-TSS (NM_016927)	promoter-TSS (NM_016927)	14	NM_016927	53871	Mm.445792	NM_016927	ENSMUSG00000014503	Pkd2l2	TRPP5	polycystic kidney disease 2-like 2	protein-coding
mm_101986.1	chr11	50758168	50758198	-	1	NA	intron (NM_175643, intron 5 of 21)	intron (NM_175643, intron 5 of 21)	69548	NM_013922	30944	Mm.103674	NM_013922	ENSMUSG00000044807	Zfp354c	5330421P20Rik|AJ18|AW743325|Kid3|Tcf17l2|Znf354c|mKIAA4218	zinc finger protein 354C	protein-coding
mm_38570.1	chr4	141790900	141790941	-	1	NA	promoter-TSS (NM_172338)	promoter-TSS (NM_172338)	-276	NM_172338	214063	Mm.39102	NM_172338	ENSMUSG00000040697	Dnajc16	2900037O03Rik|4732437J24Rik|D030060M24|mKIAA0962	DnaJ heat shock protein family (Hsp40) member C16	protein-coding
mm_77898.1	chr9	7348655	7348670	+	1	NA	exon (NM_008605, exon 2 of 10)	exon (NM_008605, exon 2 of 10)	1288	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_129260.1	chr15	76723815	76723853	-	1	NA	promoter-TSS (NM_176828)	promoter-TSS (NM_176828)	11	NM_145472	223665	Mm.291713	NM_145472	ENSMUSG00000033707	C030006K11Rik	1110033I13Rik	RIKEN cDNA C030006K11 gene	protein-coding
mm_113808.1	chr13	46502142	46502187	+	1	NA	5' UTR (NM_026056, exon 1 of 13)	5' UTR (NM_026056, exon 1 of 13)	261	NM_026056	67252	Mm.44529	NM_026056	ENSMUSG00000021373	Cap2	2810452G09Rik|AV045235	CAP, adenylate cyclase-associated protein, 2 (yeast)	protein-coding
mm_49098.1	chr6	7845252	7845299	+	1	NA	promoter-TSS (NM_052993)	promoter-TSS (NM_052993)	51	NM_052993	94192	Mm.102752	NM_052993	ENSMUSG00000042460	C1galt1	2210410E06Rik|AV284120|T-synthase	core 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase, 1	protein-coding
mm_116333.1	chr13	38037920	38037932	-	1	NA	promoter-TSS (NM_027724)	promoter-TSS (NM_027724)	937	NM_024242	71340	Mm.297130	NM_024242	ENSMUSG00000021428	Riok1	3110046C13Rik|5430416A05Rik|Ad034	RIO kinase 1 (yeast)	protein-coding
mm_143162.1	chr17	57224353	57224366	-	1	NA	exon (NM_009778, exon 9 of 41)	exon (NM_009778, exon 9 of 41)	3777	NM_009778	12266	Mm.19131	NM_009778	ENSMUSG00000024164	C3	AI255234|ASP|HSE-MSF|Plp	complement component 3	protein-coding
mm_111086.1	chr12	80260380	80260400	-	1	NA	promoter-TSS (NM_134156)	promoter-TSS (NM_134156)	-9	NM_001346669	109711	Mm.253564	NM_134156	ENSMUSG00000015143	Actn1	3110023F10Rik|Actn1a	actinin, alpha 1	protein-coding
mm_154013.1	chr19	53188365	53188375	-	1	NA	intron (NM_013758, intron 1 of 15)	B3A|SINE|B2	44373	NM_013758	27360	Mm.426080	NM_013758	ENSMUSG00000025026	Add3	AI463285|R75380	adducin 3 (gamma)	protein-coding
mm_170076.1	chr17	33677384	33677390	-	1	NA	exon (NM_001109913, exon 2 of 17)	exon (NM_001109913, exon 2 of 17)	8071	NM_001109913	76936	Mm.311439	NM_029804	ENSMUSG00000059208	Hnrnpm	2610023M21Rik|AA409009|Hnrpm|mKIAA4193	heterogeneous nuclear ribonucleoprotein M	protein-coding
mm_136089.1	chr16	84977945	84977957	-	1	NA	intron (NR_045889, intron 3 of 3)	intron (NR_045889, intron 3 of 3)	5740	NR_045889	100038614	Mm.441351	NR_045889		Gm10791	ENSMUSG00000074933	predicted gene 10791	ncRNA
mm_105933.1	chr11	115133929	115133949	-	1	NA	promoter-TSS (NM_001169153)	promoter-TSS (NM_001169153)	53	NM_001347648	246746	Mm.277387	NM_145634	ENSMUSG00000047798	Cd300lf	CLIM1|CLM-1|CLM1|Digr2|F730004D16Rik|IREM1|IgSF13|LMIR3|Pigr3	CD300 molecule like family member F	protein-coding
mm_159593.1	chr4	126148077	126148077	+	1	NA	promoter-TSS (NM_172145)	promoter-TSS (NM_172145)	74	NM_172145	230752	Mm.41569	NM_172145	ENSMUSG00000050212	Eva1b	2610027C15Rik|Fam176b	eva-1 homolog B (C. elegans)	protein-coding
mm_161169.1	chr13	37827360	37827360	+	1	NA	promoter-TSS (NM_001039188)	promoter-TSS (NM_001039188)	-33	NM_001039188	68750	Mm.491109	NM_026830	ENSMUSG00000039087	Rreb1	1110037N09Rik|AA414966|B930013M22Rik	ras responsive element binding protein 1	protein-coding
mm_7118.1	chr1	90153427	90153442	-	1	NA	promoter-TSS (NM_029122)	promoter-TSS (NM_029122)	-33	NM_029122	74918	Mm.317517	NM_029122	ENSMUSG00000026301	Iqca	4930465P12Rik|4930585L22Rik|BB288505|Iqca1	IQ motif containing with AAA domain	protein-coding
mm_33501.1	chr4	130826188	130826203	+	1	NA	3' UTR (NM_011520, exon 5 of 5)	3' UTR (NM_011520, exon 5 of 5)	33658	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_57935.1	chr6	134645938	134645947	-	1	NA	intron (NM_026371, intron 2 of 3)	MLT1A|LTR|ERVL-MaLR	5002	NM_026371	67774	Mm.41892	NM_026371	ENSMUSG00000042992	Borcs5	5830457J20Rik|AW124643|Loh12cr1	BLOC-1 related complex subunit 5	protein-coding
mm_47022.1	chr5	115490345	115490378	-	1	NA	Intergenic	U4|snRNA|snRNA	-5877	NM_133760	75387	Mm.332616	NM_133760	ENSMUSG00000029524	Sirt4	4930596O17Rik	sirtuin 4	protein-coding
mm_70582.1	chr8	13167821	13167874	+	1	NA	exon (NM_010684, exon 4 of 9)	exon (NM_010684, exon 4 of 9)	8686	NM_010684	16783	Mm.16716	NM_010684	ENSMUSG00000031447	Lamp1	CD107a|LGP-120|LGP-A|Lamp-1|P2B	lysosomal-associated membrane protein 1	protein-coding
mm_64654.1	chr7	4149782	4149829	-	1	NA	promoter-TSS (NM_175529)	promoter-TSS (NM_175529)	67	NM_175529	243813	Mm.347643	NM_175529	ENSMUSG00000043432	Leng9	9530024C23Rik|F630035L11Rik	leukocyte receptor cluster (LRC) member 9	protein-coding
mm_91753.1	chr10	50589580	50589586	-	1	NA	Intergenic	RMER6A|LTR|ERVK	-3086	NM_198007	77987	Mm.222497	NM_198007	ENSMUSG00000038774	Ascc3	ASC1p200|B630009I04Rik|BC023451|D430001L07Rik|D630041L21|Helic1|RNAH	activating signal cointegrator 1 complex subunit 3	protein-coding
mm_54957.1	chr6	48701959	48701963	-	1	NA	3' UTR (NM_153175, exon 3 of 3)	3' UTR (NM_153175, exon 3 of 3)	6283	NM_153175	231931	Mm.321047	NM_153175	ENSMUSG00000047867	Gimap6	4833419H03Rik|Ian6|mFLJ00102	GTPase, IMAP family member 6	protein-coding
mm_23962.1	chr3	84952334	84952409	+	1	NA	5' UTR (NM_080428, exon 1 of 11)	5' UTR (NM_080428, exon 1 of 11)	160	NM_080428	50754	Mm.196475	NM_080428	ENSMUSG00000028086	Fbxw7	1110001A17Rik|AGO|Cdc4|Fbw7|Fbwd6|Fbx30|Fbxo30|Fbxw6|SEL-10	F-box and WD-40 domain protein 7	protein-coding
mm_27705.1	chr3	67463799	67463825	-	1	NA	promoter-TSS (NM_016753)	promoter-TSS (NM_016753)	95	NM_016753	17035	Mm.2632	NM_016753	ENSMUSG00000047557	Lxn	-	latexin	protein-coding
mm_166106.1	chr4	146909565	146909586	-	1	NA	Intergenic	Intergenic	-112275	NM_001177767	100043034	Mm.422606	NM_001177767	ENSMUSG00000067919	Rex2	Gm13138|OTTMUSG00000010655	reduced expression 2	protein-coding
mm_129030.1	chr15	74958922	74958956	-	1	NA	3' UTR (NM_001164036, exon 4 of 4)	3' UTR (NM_001164036, exon 4 of 4)	3833	NM_001164040	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_155055.1	chrX	42275267	42275281	+	1	NA	exon (NM_021465, exon 33 of 33)	exon (NM_021465, exon 33 of 33)	73419	NM_001290713	20843	Mm.290422	NM_021465	ENSMUSG00000025862	Stag2	9230105L23Rik|B230112I07Rik|SA-2|SAP2	stromal antigen 2	protein-coding
mm_101152.1	chr11	16791302	16791319	-	1	NA	intron (NM_207655, intron 1 of 27)	intron (NM_207655, intron 1 of 27)	39107	NM_007912	13649	Mm.8534	NM_007912	ENSMUSG00000020122	Egfr	9030024J15Rik|AI552599|Erbb|Errb1|Errp|Wa5|wa-2|wa2	epidermal growth factor receptor	protein-coding
mm_101543.1	chr11	33537206	33537224	-	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	-23469	NM_023146	66011	Mm.383775	NM_023146	ENSMUSG00000040594	Ranbp17	-	RAN binding protein 17	protein-coding
mm_146063.1	chr18	69686773	69686784	+	1	NA	3' UTR (NM_001083967, exon 20 of 20)	3' UTR (NM_001083967, exon 20 of 20)	-238781	NM_201362	381175	Mm.266831	NM_201362	ENSMUSG00000038903	Ccdc68	BC046343	coiled-coil domain containing 68	protein-coding
mm_166922.1	chr7	30981889	30981893	+	1	NA	promoter-TSS (NM_001242647)	promoter-TSS (NM_001242647)	-30	NM_001242647	76415	Mm.259739	NM_175240	ENSMUSG00000046826	Fam187b	1700020B09Rik|Tmem162	family with sequence similarity 187, member B	protein-coding
mm_159509.1	chr4	55378333	55378333	+	1	NA	intron (NM_009011, intron 5 of 9)	intron (NM_009011, intron 5 of 9)	28291	NM_009011	19359	Mm.196846	NM_009011	ENSMUSG00000028426	Rad23b	0610007D13Rik|AV001138|HR23B|mHR23B|p58	RAD23 homolog B, nucleotide excision repair protein	protein-coding
mm_25276.1	chr3	105451968	105451974	+	1	NA	promoter-TSS (NM_001039347)	promoter-TSS (NM_001039347)	-359	NM_001039347	56543	Mm.44530	NM_019931	ENSMUSG00000040896	Kcnd3	AW045978|Kncd3|Kv4.3	potassium voltage-gated channel, Shal-related family, member 3	protein-coding
mm_22395.1	chr2	181228344	181228354	-	1	NA	3' UTR (NM_183162, exon 19 of 19)	3' UTR (NM_183162, exon 19 of 19)	8333	NM_199312	332713	Mm.23349	NM_199312	ENSMUSG00000047841	BC051628	1700026M20Rik|Fndc11	cDNA sequence BC051628	protein-coding
mm_158563.1	chrX	150440888	150440937	-	1	NA	promoter-TSS (NM_001164686)	promoter-TSS (NM_001164686)	-7	NM_001164686	382245	Mm.277309	NM_001164683	ENSMUSG00000041353	Tmem29	2700081K05Rik|6330540D07Rik|CXorf44-like	transmembrane protein 29	protein-coding
mm_108352.1	chr12	80519008	80519087	+	1	NA	promoter-TSS (NM_001081421)	promoter-TSS (NM_001081421)	57	NM_001081421	108760	Mm.308296	NM_001081421	ENSMUSG00000021130	Galnt16	5730405L21Rik|AI415388|Galntl1|mpp-GalNAc-T16	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 16	protein-coding
mm_67906.1	chr7	99695641	99695653	-	1	NA	5' UTR (NM_001252531, exon 1 of 14)	5' UTR (NM_001252531, exon 1 of 14)	162	NM_001252531	101488	Mm.11249	NM_175316	ENSMUSG00000030737	Slco2b1	AI060904|AI852653|OATP-B|Slc21a9	solute carrier organic anion transporter family, member 2b1	protein-coding
mm_100495.1	chr11	120467774	120467799	+	1	NA	promoter-TSS (NM_197995)	promoter-TSS (NM_197995)	151	NM_001159328	15239	Mm.7919	NM_008244	ENSMUSG00000025793	Hgs	Hgr|Hrs|ZFYVE8|tn	HGF-regulated tyrosine kinase substrate	protein-coding
mm_78153.1	chr9	21019101	21019111	+	1	NA	exon (NM_010493, exon 2 of 7)	exon (NM_010493, exon 2 of 7)	3166	NM_010493	15894	Mm.435508	NM_010493	ENSMUSG00000037405	Icam1	CD54|Icam-1|Ly-47|MALA-2	intercellular adhesion molecule 1	protein-coding
mm_120260.1	chr14	63046989	63047013	+	1	NA	promoter-TSS (NM_001034910)	promoter-TSS (NM_001034910)	10	NM_001034910	619548	Mm.387101	NM_001034910	ENSMUSG00000054763	Defb42	BD-42|Defb44|mBD-42	defensin beta 42	protein-coding
mm_132569.1	chr16	38132000	38132036	+	1	NA	intron (NM_001347232, intron 1 of 11)	intron (NM_001347232, intron 1 of 11)	-42758	NR_033221	414072	Mm.483602	NR_033221		BC031361	-	cDNA sequence BC031361	ncRNA
mm_118535.1	chr14	16224994	16224998	+	1	NA	Intergenic	Intergenic	-24318	NM_021504	59007	Mm.258381	NM_021504	ENSMUSG00000021785	Ngly1	1110002C09Rik|PNGase|Png1	N-glycanase 1	protein-coding
mm_122418.1	chr14	41185159	41185171	-	1	NA	promoter-TSS (NM_009160)	promoter-TSS (NM_009160)	33	NM_009160	20390	Mm.1321	NM_009160	ENSMUSG00000021795	Sftpd	AI573415|SP-D|Sfpd|Sftp4	surfactant associated protein D	protein-coding
mm_87608.1	chr10	57784961	57784973	+	1	NA	promoter-TSS (NM_021272)	promoter-TSS (NM_021272)	44	NM_021272	12140	Mm.3644	NM_021272	ENSMUSG00000019874	Fabp7	B-FABP|BFABP|Blbp|MRG	fatty acid binding protein 7, brain	protein-coding
mm_140227.1	chr17	83986394	83986400	+	1	NA	Intergenic	Intergenic	-12155	NR_130994	78148	Mm.243918	NR_130994		8430430B14Rik	-	RIKEN cDNA 8430430B14 gene	ncRNA
mm_42494.1	chr5	115474649	115474662	+	1	NA	TTS (NM_011107)	TTS (NM_011107)	8389	NM_011107	18778	Mm.20190	NM_011107	ENSMUSG00000029522	Pla2g1b	Pla2a|sPLA2IB	phospholipase A2, group IB, pancreas	protein-coding
mm_129238.1	chr15	76626008	76626089	-	1	NA	promoter-TSS (NM_025842)	promoter-TSS (NM_025842)	36	NM_025842	66914	Mm.30028	NM_025842	ENSMUSG00000059323	Vps28	1110014J03Rik|CIIA|D730005C08Rik	vacuolar protein sorting 28	protein-coding
mm_99833.1	chr11	109011716	109011755	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	91386	NM_015732	12006	Mm.71710	NM_015732	ENSMUSG00000000142	Axin2	Axi1|Axil|Conductin	axin 2	protein-coding
mm_90043.1	chr10	115817500	115817514	+	1	NA	5' UTR (NM_001168680, exon 2 of 9)	5' UTR (NM_001168680, exon 2 of 9)	223	NM_001168679	216350	Mm.22270	NM_146010	ENSMUSG00000034127	Tspan8	C76990|E330007O21Rik|Tm4sf3	tetraspanin 8	protein-coding
mm_8897.1	chr1	162898756	162898760	-	1	NA	promoter-TSS (NM_018881)	promoter-TSS (NM_018881)	-46	NM_018881	55990	Mm.10929	NM_018881	ENSMUSG00000040170	Fmo2	2310008D08Rik|2310042I22Rik|AW107733	flavin containing monooxygenase 2	protein-coding
mm_103572.1	chr11	77893860	77893870	-	1	NA	promoter-TSS (NM_008952)	promoter-TSS (NM_008952)	7	NM_008952	19193	Mm.8543	NM_008952	ENSMUSG00000017453	Pipox	LPIPOX|Pso	pipecolic acid oxidase	protein-coding
mm_14864.1	chr2	148798813	148798844	+	1	NA	promoter-TSS (NM_009978)	promoter-TSS (NM_009978)	-11	NM_009978	13012	Mm.20435	NM_009978	ENSMUSG00000027442	Cst8	Cres|Cst-rs1	cystatin 8 (cystatin-related epididymal spermatogenic)	protein-coding
mm_126069.1	chr15	77357953	77357954	+	1	NA	Intergenic	B4A|SINE|B4	41157	NM_029419	75761	Mm.232636	NM_029419	ENSMUSG00000010601	Apol7a	9130022K13Rik|Apol3	apolipoprotein L 7a	protein-coding
mm_135862.1	chr16	60605244	60605254	-	1	NA	5' UTR (NM_007938, exon 1 of 18)	5' UTR (NM_007938, exon 1 of 18)	282	NM_007938	13840	Mm.455790	NM_007938	ENSMUSG00000055540	Epha6	Ehk2|Hek12|m-ehk2	Eph receptor A6	protein-coding
mm_165705.1	chr3	96824085	96824089	+	1	NA	intron (NM_001163496, intron 1 of 4)	intron (NM_001163496, intron 1 of 4)	5264	NM_001163497	54215	Mm.34693	NM_018767	ENSMUSG00000038304	Cd160	AU045688|By55	CD160 antigen	protein-coding
mm_132756.1	chr16	44347397	44347479	+	1	NA	promoter-TSS (NM_144550)	promoter-TSS (NM_144550)	37	NM_144550	212514	Mm.24035	NM_144550	ENSMUSG00000043065	Spice1	Ccdc52|D16Ertd480e	spindle and centriole associated protein 1	protein-coding
mm_76655.1	chr8	93197733	93197759	-	1	NA	promoter-TSS (NM_053200)	promoter-TSS (NM_053200)	58	NM_053200	104158	Mm.292803	NM_053200	ENSMUSG00000056973	Ces1d	Ces3|TGH	carboxylesterase 1D	protein-coding
mm_70737.1	chr8	19140752	19140767	+	1	NA	promoter-TSS (NM_001034905)	promoter-TSS (NM_001034905)	0	NM_001034905	546038	Mm.99206	NM_001034905	ENSMUSG00000059463	Spag11b	EG546038|Ep2c/h|Spag11c/h	sperm associated antigen 11B	protein-coding
mm_27010.1	chr3	25872604	25872613	-	1	NA	intron (NM_001163387, intron 3 of 5)	intron (NM_001163387, intron 3 of 5)	280699	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_65469.1	chr7	25476643	25476654	-	1	NA	exon (NM_001039186, exon 2 of 8)	exon (NM_001039186, exon 2 of 8)	977	NM_001039185	26365	Mm.322502	NM_011926	ENSMUSG00000074272	Ceacam1	Bgp|Bgp1|C-CAM|CD66a|Cc1|Cea-1|Cea-7|Cea1|Cea7|Hv-2|Hv2|MHVR|MHVR1|Mhv-1|bb-1|mCEA1|mmCGM1|mmCGM1a|mmCGM2	carcinoembryonic antigen-related cell adhesion molecule 1	protein-coding
mm_106663.1	chr11	121354338	121354436	-	1	NA	promoter-TSS (NM_025793)	promoter-TSS (NM_025793)	60	NM_025793	66840	Mm.103986	NM_025793	ENSMUSG00000025173	Wdr45b	0610008N23Rik|AA408735|D16Bwg0193e|WIPI-3|Wdr45l	WD repeat domain 45B	protein-coding
mm_120477.1	chr14	65975601	65975620	+	1	NA	exon (NM_013492, exon 5 of 9)	exon (NM_013492, exon 5 of 9)	7127	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_96492.1	chr11	67798291	67798298	+	1	NA	promoter-TSS (NM_001013013)	promoter-TSS (NM_001013013)	23	NM_001013013	68460	Mm.22167	NM_001013013	ENSMUSG00000033044	Dhrs7c	1110001P11Rik|AI120487|SRP-35	dehydrogenase/reductase (SDR family) member 7C	protein-coding
mm_145300.1	chr18	53323376	53323384	+	1	NA	intron (NM_029394, intron 1 of 6)	intron (NM_029394, intron 1 of 6)	77718	NM_029394	69226	Mm.32414	NM_029394	ENSMUSG00000024535	Snx24	2810011K15Rik|5730433I16Rik|AI451341	sorting nexing 24	protein-coding
mm_3928.1	chr1	162710346	162710505	+	1	NA	exon (NM_001081290, exon 12 of 35)	exon (NM_001081290, exon 12 of 35)	30131	NM_001081290	226562	Mm.245446	NM_001081290	ENSMUSG00000040225	Prrc2c	1810043M20Rik|9630039I18Rik|A630006J20|Bat2d|Bat2d1|Bat2l2|E130112L15Rik|Prrc3|mKIAA1096	proline-rich coiled-coil 2C	protein-coding
mm_141915.1	chr17	34999235	34999255	-	1	NA	exon (NM_033075, exon 2 of 2)	exon (NM_033075, exon 2 of 2)	1501	NM_033075	110956	Mm.22506	NM_033075		D17H6S56E-5	G7e	DNA segment, Chr 17, human D6S56E 5	protein-coding
mm_138124.1	chr17	34153166	34153239	+	1	NA	promoter-TSS (NM_010387)	promoter-TSS (NM_010387)	11	NM_010387	14999	Mm.460938	NM_010387	ENSMUSG00000079547	H2-DMb1	AI385589|H-2Mb1|H2-Mb1	histocompatibility 2, class II, locus Mb1	protein-coding
mm_28102.1	chr3	86547022	86547032	-	1	NA	exon (NM_011839, exon 1 of 1)	exon (NM_011839, exon 1 of 1)	1256	NM_011839	23937	Mm.389466	NM_011839	ENSMUSG00000057777	Mab21l2	-	mab-21-like 2 (C. elegans)	protein-coding
mm_82826.1	chr9	31131781	31131814	-	1	NA	promoter-TSS (NM_011176)	promoter-TSS (NM_011176)	2	NM_011176	19143	Mm.243926	NM_011176	ENSMUSG00000031995	St14	Epithin|MT-SP1|Prss14|Tmprss14|mCAP3|matriptase	suppression of tumorigenicity 14 (colon carcinoma)	protein-coding
mm_88521.1	chr10	78054881	78054912	+	1	NA	promoter-TSS (NM_001284200)	promoter-TSS (NM_001284200)	-439	NM_001284198	54427	Mm.13433	NM_019448	ENSMUSG00000000730	Dnmt3l	D6Ertd14e|ecat7	DNA (cytosine-5-)-methyltransferase 3-like	protein-coding
mm_171655.1	chr4	41275131	41275133	-	1	NA	promoter-TSS (NM_026872)	promoter-TSS (NM_026872)	3	NM_026872	68926	Mm.41864	NM_026872	ENSMUSG00000028433	Ubap2	1190005K07Rik|AA408600|AU045235|UBAP-2|mKIAA1491	ubiquitin-associated protein 2	protein-coding
mm_34537.1	chr4	149496971	149496985	+	1	NA	TTS (NM_026963)	TTS (NM_026963)	11645	NM_026963	69151	Mm.464434	NM_026963	ENSMUSG00000028990	Lzic	1810030J04Rik|AW047580	leucine zipper and CTNNBIP1 domain containing	protein-coding
mm_65150.1	chr7	19604428	19604438	-	1	NA	promoter-TSS (NR_125836)	promoter-TSS (NR_125836)	53	NR_125832	53609	Mm.20913	NM_016680	ENSMUSG00000061028	Clasrp	Clasp|Sfrs16|Srsf16|Swap2	CLK4-associating serine/arginine rich protein	protein-coding
mm_119194.1	chr14	32513562	32513571	+	1	NA	promoter-TSS (NM_001081221)	promoter-TSS (NM_001081221)	45	NM_001081221	319955	Mm.318310	NM_177043	ENSMUSG00000054051	Ercc6	4732403I04|C130058G22Rik|CSB	excision repair cross-complementing rodent repair deficiency, complementation group 6	protein-coding
mm_35136.1	chr4	11386569	11386598	-	1	NA	5' UTR (NM_001290383, exon 1 of 16)	5' UTR (NM_001290383, exon 1 of 16)	195	NM_001347052	207920	Mm.387719	NM_194055	ENSMUSG00000040728	Esrp1	2210008M09Rik|A630065D16|BC031468|Rbm35a	epithelial splicing regulatory protein 1	protein-coding
mm_99583.1	chr11	104282372	104282392	+	1	NA	exon (NM_010838, exon 2 of 10)	exon (NM_010838, exon 2 of 10)	50946	NM_001285454	17762	Mm.1287	NM_010838	ENSMUSG00000018411	Mapt	AI413597|AW045860|Mtapt|Tau	microtubule-associated protein tau	protein-coding
mm_80496.1	chr9	78482062	78482077	+	1	NA	promoter-TSS (NM_010106)	promoter-TSS (NM_010106)	-345	NM_010106	13627	Mm.138471	NM_010106	ENSMUSG00000037742	Eef1a1	-	eukaryotic translation elongation factor 1 alpha 1	protein-coding
mm_109737.1	chr12	117154027	117154056	+	1	NA	intron (NM_011215, intron 12 of 22)	CpG	-2772	NR_033538	100038689	Mm.445351	NR_033538	ENSMUSG00000099907	Gm10421	ENSMUSG00000072792	predicted gene 10421	ncRNA
mm_150750.1	chr19	43792384	43792398	+	1	NA	intron (NM_013806, intron 2 of 31)	intron (NM_013806, intron 2 of 31)	10083	NM_013806	12780	Mm.39054	NM_013806	ENSMUSG00000025194	Abcc2	AI173996|Abc30|Cmoat|Mrp2|cMRP	ATP-binding cassette, sub-family C (CFTR/MRP), member 2	protein-coding
mm_27750.1	chr3	69319257	69319293	-	1	NA	intron (NM_178726, intron 1 of 3)	intron (NM_178726, intron 1 of 3)	2357	NM_178726	242083	Mm.40577	NM_178726	ENSMUSG00000027784	Ppm1l	3222401G13|5930404J21Rik|AI481720|AW045850|PP2C|PP2Cepsilon|Pp2ce|Ppp2ce|mKIAA4175	protein phosphatase 1 (formerly 2C)-like	protein-coding
mm_96000.1	chr11	59306921	59306935	+	1	NA	promoter-TSS (NM_139298)	promoter-TSS (NM_139298)	-2	NM_139298	216795	Mm.218794	NM_139298	ENSMUSG00000000126	Wnt9a	Wnt14	wingless-type MMTV integration site family, member 9A	protein-coding
mm_9107.1	chr1	170110724	170110729	-	1	NA	Intergenic	Intergenic	-21782	NM_022563	18214	Mm.229249	NM_022563	ENSMUSG00000026674	Ddr2	AW495251|Ntrkr3|tyro10	discoidin domain receptor family, member 2	protein-coding
mm_39741.1	chr5	29569209	29569267	+	1	NA	promoter-TSS (NM_133907)	promoter-TSS (NM_133907)	-4	NM_133907	100763	Mm.137746	NM_133907	ENSMUSG00000039000	Ube3c	AI853514|mKIAA0010	ubiquitin protein ligase E3C	protein-coding
mm_6394.1	chr1	72859039	72859074	-	1	NA	3' UTR (NM_010518, exon 4 of 4)	3' UTR (NM_010518, exon 4 of 4)	15809	NM_010518	16011	Mm.405761	NM_010518	ENSMUSG00000026185	Igfbp5	AI256729|AW208790|IGFBP-5|IGFBP-5P	insulin-like growth factor binding protein 5	protein-coding
mm_37300.1	chr4	119232662	119232717	-	1	NA	promoter-TSS (NM_019782)	promoter-TSS (NM_019782)	35	NM_001012400	230696	Mm.473722	NM_001012400	ENSMUSG00000078584	AU022252	AI450326	expressed sequence AU022252	protein-coding
mm_96410.1	chr11	67254456	67254466	+	1	NA	exon (NM_010855, exon 29 of 40)	exon (NM_010855, exon 29 of 40)	16649	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_146724.1	chr18	15064364	15064374	-	1	NA	promoter-TSS (NM_001142731)	promoter-TSS (NM_001142731)	-787	NM_001142731	106931	Mm.329299	NM_134112	ENSMUSG00000036225	Kctd1	4933402K10Rik|AI661543|AW553000	potassium channel tetramerisation domain containing 1	protein-coding
mm_63293.1	chr7	126807715	126807723	+	1	NA	Intergenic	Intergenic	-7272	NM_001177308	11674	Mm.275831	NM_007438	ENSMUSG00000030695	Aldoa	Aldo-1|Aldo1	aldolase A, fructose-bisphosphate	protein-coding
mm_5910.1	chr1	55010336	55010336	-	1	NA	intron (NM_031179, intron 6 of 24)	intron (NM_031179, intron 6 of 24)	17142	NM_031179	81898	Mm.279736	NM_031179	ENSMUSG00000025982	Sf3b1	155kDa|2810001M05Rik|AA409119|Prp10|SAP155|SF3b155|TA-8|Targ4	splicing factor 3b, subunit 1	protein-coding
mm_39426.1	chr5	16296821	16296824	+	1	NA	intron (NM_001110846, intron 10 of 37)	intron (NM_001110846, intron 10 of 37)	-256673	NM_001289460	15234	Mm.267078	NM_010427	ENSMUSG00000028864	Hgf	C230052L06Rik|HGF/SF|NK1|NK2|SF|SF/HGF	hepatocyte growth factor	protein-coding
mm_108831.1	chr12	95750420	95750432	+	1	NA	intron (NM_201518, intron 1 of 1)	intron (NM_201518, intron 1 of 1)	58200	NM_201518	399558	Mm.341948	NM_201518	ENSMUSG00000047414	Flrt2	-	fibronectin leucine rich transmembrane protein 2	protein-coding
mm_21192.1	chr2	155407735	155407753	-	1	NA	exon (NM_019825, exon 10 of 14)	exon (NM_019825, exon 10 of 14)	25888	NM_178111	68728	Mm.293605	NM_178111	ENSMUSG00000038375	Trp53inp2	1110029F20Rik|Tp53inp2	transformation related protein 53 inducible nuclear protein 2	protein-coding
mm_167117.1	chr7	118974764	118974787	-	1	NA	3' UTR (NM_022420, exon 4 of 4)	3' UTR (NM_022420, exon 4 of 4)	20436	NM_022420	64297	Mm.103439	NM_022420	ENSMUSG00000008734	Gprc5b	AW125761|Raig2	G protein-coupled receptor, family C, group 5, member B	protein-coding
mm_71511.1	chr8	46846123	46846133	+	1	NA	exon (NM_008391, exon 9 of 9)	exon (NM_008391, exon 9 of 9)	106383	NM_008391	16363	Mm.1149	NM_008391	ENSMUSG00000031627	Irf2	9830146E22Rik|AI646973|Irf-2	interferon regulatory factor 2	protein-coding
mm_64686.1	chr7	4514559	4514567	-	1	NA	intron (NM_011618, intron 1 of 13)	intron (NM_011618, intron 1 of 13)	1412	NM_001277903	21955	Mm.358643	NM_011618	ENSMUSG00000064179	Tnnt1	AW146156|Tnt|sTnT|ssTnT	troponin T1, skeletal, slow	protein-coding
mm_30696.1	chr4	11694783	11694798	+	1	NA	Intergenic	Intergenic	-9657	NM_010276	14579	Mm.247486	NM_010276	ENSMUSG00000028214	Gem	AV020497	GTP binding protein (gene overexpressed in skeletal muscle)	protein-coding
mm_136103.1	chr16	85141233	85141269	-	1	NA	intron (NM_007471, intron 1 of 15)	GA-rich|Low_complexity|Low_complexity	32456	NM_001198825	11820	Mm.277585	NM_007471	ENSMUSG00000022892	App	Abeta|Abpp|Adap|Ag|Cvap|E030013M08Rik|betaApp	amyloid beta (A4) precursor protein	protein-coding
mm_107000.1	chr12	11279702	11279715	+	1	NA	exon (NM_025695, exon 5 of 27)	exon (NM_025695, exon 5 of 27)	13822	NM_025695	67241	Mm.173953	NM_025695	ENSMUSG00000020608	Smc6	2810489L22Rik|3830418C19Rik|AA990493|AU018782|AW742439|SMC-6|Smc6l1|mKIAA4103	structural maintenance of chromosomes 6	protein-coding
mm_46151.1	chr5	93306451	93306458	-	1	NA	Intergenic	Intergenic	38881	NM_007635	12452	Mm.3527	NM_007635	ENSMUSG00000029385	Ccng2	-	cyclin G2	protein-coding
mm_32604.1	chr4	112006246	112006273	+	1	NA	promoter-TSS (NM_001102662)	promoter-TSS (NM_001102662)	-10	NM_001102662	639781	Mm.398873	NM_001102662	ENSMUSG00000089773	Skint1	OTTMUSG00000008542|Skint-1	selection and upkeep of intraepithelial T cells 1	protein-coding
mm_166064.1	chr4	134470099	134470111	+	1	NA	5' UTR (NM_019641, exon 2 of 5)	5' UTR (NM_019641, exon 2 of 5)	1785	NM_019641	16765	Mm.378957	NM_019641	ENSMUSG00000028832	Stmn1	19k|Lag|Lap18|Op18|P18|P19|Pig|Pp17|Pp18|Pp19|Pr22|Smn	stathmin 1	protein-coding
mm_31275.1	chr4	45798886	45798925	+	1	NA	promoter-TSS (NM_028270)	promoter-TSS (NM_028270)	-117	NM_028270	72535	Mm.331583	NM_028270	ENSMUSG00000035561	Aldh1b1	2700007F14Rik	aldehyde dehydrogenase 1 family, member B1	protein-coding
mm_66758.1	chr7	46715693	46715708	-	1	NA	promoter-TSS (NM_011315)	promoter-TSS (NM_011315)	-24	NM_011315	20210	Mm.14277	NM_011315	ENSMUSG00000040026	Saa3	AV098916|Saa-3|l7R3	serum amyloid A 3	protein-coding
mm_120272.1	chr14	63124535	63124589	+	1	NA	intron (NM_007798, intron 1 of 9)	intron (NM_007798, intron 1 of 9)	2100	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_4868.1	chr1	187742533	187742544	+	1	NA	intron (NM_001243792, intron 1 of 7)	intron (NM_001243792, intron 1 of 7)	133532	NM_001243792	26381	Mm.89989	NM_011935	ENSMUSG00000026610	Esrrg	ERR3|Errg|NR3B3|mKIAA0832	estrogen-related receptor gamma	protein-coding
mm_161733.1	chr17	30954607	30954607	+	1	NA	promoter-TSS (NM_177465)	promoter-TSS (NM_177465)	-76	NM_177465	52020	Mm.25923	NM_177465	ENSMUSG00000054134	Umodl1	D17Ertd488e	uromodulin-like 1	protein-coding
mm_99196.1	chr11	101011994	101011997	+	1	NA	intron (NM_001243050, intron 2 of 20)	intron (NM_001243050, intron 2 of 20)	2543	NM_001243051	11975	Mm.340818	NM_016920	ENSMUSG00000019302	Atp6v0a1	AA959968|ATP6a1|Atp6n1|Atp6n1a|Atpv0a1|Vpp-1|Vpp1	ATPase, H+ transporting, lysosomal V0 subunit A1	protein-coding
mm_70990.1	chr8	27343982	27343992	+	1	NA	promoter-TSS (NM_001013609)	promoter-TSS (NM_001013609)	-407	NM_001013609	541463	Mm.84066	NM_001013609	ENSMUSG00000071138	Tex24	1700108N07Rik|TESF-1	testis expressed gene 24	protein-coding
mm_31048.1	chr4	41135986	41135992	+	1	NA	promoter-TSS (NM_026275)	promoter-TSS (NM_026275)	-32	NM_026275	67615	Mm.389540	NM_026275	ENSMUSG00000036241	Ube2r2	1200003M11Rik|Cdc34b|Ubc3b	ubiquitin-conjugating enzyme E2R 2	protein-coding
mm_3977.1	chr1	164249053	164249096	+	1	NA	promoter-TSS (NM_054087)	promoter-TSS (NM_054087)	28	NM_001276455	116914	Mm.35444	NM_054087	ENSMUSG00000040918	Slc19a2	AV276020|AW322295|DDA1|THTR1|TRMA	solute carrier family 19 (thiamine transporter), member 2	protein-coding
mm_171443.1	chr4	143522204	143522213	+	1	NA	Intergenic	MT2_Mm|LTR|ERVL	10865	NM_001039595	545693	Mm.441388	NM_001039595	ENSMUSG00000095409	Gm13043	OTTMUSG00000010136	predicted gene 13043	protein-coding
mm_130988.1	chr15	103366771	103366798	-	1	NA	promoter-TSS (NM_010577)	promoter-TSS (NM_010577)	7	NM_010577	16402	Mm.16234	NM_010577	ENSMUSG00000000555	Itga5	Cd49e|Fnra|VLA5	integrin alpha 5 (fibronectin receptor alpha)	protein-coding
mm_118277.1	chr13	112652270	112652276	-	1	NA	promoter-TSS (NM_010029)	promoter-TSS (NM_010029)	37	NM_010029	13206	Mm.12818	NM_010029	ENSMUSG00000021758	Ddx4	AV206478|Mvh|VASA	DEAD (Asp-Glu-Ala-Asp) box polypeptide 4	protein-coding
mm_115665.1	chr13	12464952	12464959	-	1	NA	Intergenic	Intergenic	-3217	NM_001291057	56048	Mm.474138	NM_018886	ENSMUSG00000057554	Lgals8	1200015E08Rik|AI326142|D13Ertd524e|Lgals-8	lectin, galactose binding, soluble 8	protein-coding
mm_148326.1	chr18	84085971	84085991	-	1	NA	5' UTR (NM_001081300, exon 1 of 2)	5' UTR (NM_001081300, exon 1 of 2)	581	NM_001081300	110796	Mm.102136	NM_001081300	ENSMUSG00000046982	Tshz1	5730407I04Rik|D18Bwg1409e|Mtsh1|NY-CO-33|Sdccag33|Tsh1|mKIAA4206|teashirt1	teashirt zinc finger family member 1	protein-coding
mm_135972.1	chr16	75016142	75016161	-	1	NA	Intergenic	Intergenic	569910	NM_001252513	320355	Mm.99517	NM_177142	ENSMUSG00000032948	Lipi	D930038D03Rik|lpd1	lipase, member I	protein-coding
mm_166665.1	chr6	90552400	90552410	+	1	NA	intron (NM_027406, intron 1 of 22)	intron (NM_027406, intron 1 of 22)	1557	NM_027406	107747	Mm.30035	NM_027406	ENSMUSG00000030088	Aldh1l1	1810048F20Rik|FDH|Fthfd|Neut2	aldehyde dehydrogenase 1 family, member L1	protein-coding
mm_77062.1	chr8	109693236	109693289	-	1	NA	promoter-TSS (NM_028018)	promoter-TSS (NM_028018)	32	NM_028018	71955	Mm.290036	NM_028018	ENSMUSG00000031729	Ist1	2400003C14Rik|AW536298|mKIAA0174	increased sodium tolerance 1 homolog (yeast)	protein-coding
mm_22504.1	chr3	7429049	7429062	+	1	NA	intron (NM_008862, intron 1 of 2)	intron (NM_008862, intron 1 of 2)	62451	NM_008862	18767	Mm.3193	NM_008862	ENSMUSG00000027499	Pkia	AI415001|PKIalpha	protein kinase inhibitor, alpha	protein-coding
mm_30159.1	chr3	142882441	142882457	-	1	NA	promoter-TSS (NM_178654)	promoter-TSS (NM_178654)	-445	NM_178654	109333	Mm.244236	NM_178654	ENSMUSG00000004591	Pkn2	6030436C20Rik|AI507382|PRK2|Prkcl2|Stk7	protein kinase N2	protein-coding
mm_118197.1	chr13	107871234	107871238	-	1	NA	intron (NM_145456, intron 2 of 14)	AT_rich|Low_complexity|Low_complexity	18828	NM_145456	67263	Mm.490418	NM_145456	ENSMUSG00000032846	Zswim6	2900036G02Rik|mKIAA1577	zinc finger SWIM-type containing 6	protein-coding
mm_91564.1	chr10	40025254	40025286	-	1	NA	promoter-TSS (NM_144821)	promoter-TSS (NM_144821)	-2	NM_144821	215929	Mm.55513	NM_144821	ENSMUSG00000038522	Mfsd4b1	AI317395|AI482555|Naglt1a	major facilitator superfamily domain containing 4B1	protein-coding
mm_166501.1	chr6	4537972	4537980	+	1	NA	exon (NM_007743, exon 49 of 52)	exon (NM_007743, exon 49 of 52)	32358	NM_007743	12843	Mm.277792	NM_007743	ENSMUSG00000029661	Col1a2	AA960264|AI325291|Col1a-2|Cola-2|Cola2|oim	collagen, type I, alpha 2	protein-coding
mm_6904.1	chr1	84824919	84824920	-	1	NA	intron (NM_133975, intron 1 of 40)	intron (NM_133975, intron 1 of 40)	14385	NM_133975	14897	Mm.209265	NM_133975	ENSMUSG00000026219	Trip12	1110036I07Rik|6720416K24Rik|AA410158|Gtl6|TRIP-12	thyroid hormone receptor interactor 12	protein-coding
mm_138447.1	chr17	35135464	35135539	+	1	NA	promoter-TSS (NM_001252469)	promoter-TSS (NM_001252469)	-213	NM_001252469	224727	Mm.203962	NM_057171	ENSMUSG00000024392	Bag6	2410045D21Rik|AA408914|BAG-6|Bat3|D17H6S52E|G3|Scythe	BCL2-associated athanogene 6	protein-coding
mm_53573.1	chr6	137410721	137410723	+	1	NA	promoter-TSS (NM_001164403)	promoter-TSS (NM_001164403)	1	NM_001164403	19277	Mm.186361	NM_011216	ENSMUSG00000030223	Ptpro	D28|GLEPP1|PTPBK|PTPROt|PTPU2|PTPoc|PTPphi|Ptpn15|R-PTP-O	protein tyrosine phosphatase, receptor type, O	protein-coding
mm_49604.1	chr6	30742531	30742576	+	1	NA	exon (NM_001252293, exon 4 of 12)	exon (NM_001252293, exon 4 of 12)	1254	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_96926.1	chr11	70510246	70510255	+	1	NA	exon (NM_029360, exon 3 of 5)	exon (NM_029360, exon 3 of 5)	4366	NM_001013607	327956	Mm.244514	NM_001013607	ENSMUSG00000020830	Vmo1	Gm741	vitelline membrane outer layer 1 homolog (chicken)	protein-coding
mm_35483.1	chr4	40854521	40854565	-	1	NA	promoter-TSS (NM_022305)	promoter-TSS (NM_022305)	-6	NM_022305	14595	Mm.15622	NM_022305	ENSMUSG00000028413	B4galt1	B-1,4-GalT|B-1,4-GalT1|GalT|Ggtb|Ggtb2|b4Gal-T1|beta-1,4-GalT|beta-1,4-GalT1|beta4Gal-T1	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1	protein-coding
mm_157344.1	chrX	36903455	36903482	-	1	NA	promoter-TSS (NM_029891)	promoter-TSS (NM_029891)	-569	NM_029891	77286	Mm.21649	NM_029891	ENSMUSG00000044149	Nkrf	9430034D17Rik|AW124770|C80287	NF-kappaB repressing factor	protein-coding
mm_20071.1	chr2	120534879	120534912	-	1	NA	exon (NM_011743, exon 5 of 22)	exon (NM_011743, exon 5 of 22)	28936	NM_011743	20402	Mm.485295	NM_011743	ENSMUSG00000027288	Zfp106	Cd-1|D2Dcr28|H3a|Sh3bp3|Znf106|sirm	zinc finger protein 106	protein-coding
mm_132027.1	chr16	27388849	27388859	+	1	NA	promoter-TSS (NM_001289436)	promoter-TSS (NM_001289436)	-102	NM_001025615	67501	Mm.258985	NM_026202	ENSMUSG00000038127	Ccdc50	C3orf6	coiled-coil domain containing 50	protein-coding
mm_37372.1	chr4	120965836	120965846	-	1	NA	Intergenic	Intergenic	7481	NR_105982	102465614		NR_105982	ENSMUSG00000106436	Mir7015	mmu-mir-7015	microRNA 7015	ncRNA
mm_123629.1	chr14	68491673	68491676	-	1	NA	Intergenic	(TTAGGG)n|Simple_repeat|Simple_repeat	42015	NM_007402	11500	Mm.261495	NM_007402	ENSMUSG00000022056	Adam7	ADAM 7|EAP1|EAPI	a disintegrin and metallopeptidase domain 7	protein-coding
mm_99763.1	chr11	106788679	106788706	+	1	NA	promoter-TSS (NM_177088)	promoter-TSS (NM_177088)	-198	NM_007840	13207	Mm.491096	NM_007840	ENSMUSG00000020719	Ddx5	2600009A06Rik|G17P1|HUMP68|Hlr1|p68	DEAD (Asp-Glu-Ala-Asp) box polypeptide 5	protein-coding
mm_94840.1	chr11	23666206	23666225	+	1	NA	promoter-TSS (NM_023651)	promoter-TSS (NM_023651)	239	NM_028304	74467	Mm.29536	NM_028304	ENSMUSG00000020280	Pus10	2810013G11Rik|4933435A13Rik|AU014648|C77560|Ccdc139	pseudouridylate synthase 10	protein-coding
mm_25946.1	chr3	131564840	131564849	+	1	NA	promoter-TSS (NM_001289478)	promoter-TSS (NM_001289478)	76	NM_011863	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_155327.1	chrX	65047623	65047629	+	1	NA	promoter-TSS (NM_027302)	promoter-TSS (NM_027302)	-18	NM_027302	70062	Mm.45791	NM_027302	ENSMUSG00000031181	Ctag2	1700030B21Rik	cancer/testis antigen 2	protein-coding
mm_28561.1	chr3	93444034	93444038	-	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	1706	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_99097.1	chr11	99932946	99932954	+	1	NA	Intergenic	Intergenic	-3341	NM_001025244	432602	Mm.246878	NM_001025244	ENSMUSG00000051481	Krtap31-2	OTTMUSG00000002177	keratin associated protein 31-2	protein-coding
mm_22190.1	chr2	173276145	173276184	-	1	NA	exon (NM_022995, exon 1 of 4)	exon (NM_022995, exon 1 of 4)	369	NM_022995	65112	Mm.73682	NM_022995	ENSMUSG00000038400	Pmepa1	2210418I02Rik|AW455466|Erg1.2|N4wbp4|Stag1|Tmepai	prostate transmembrane protein, androgen induced 1	protein-coding
mm_164482.1	chr16	75909148	75909151	-	1	NA	exon (NM_023380, exon 1 of 8)	exon (NM_023380, exon 1 of 8)	117	NM_023380	67742	Mm.131406	NM_023380	ENSMUSG00000022876	Samsn1	4930571B16Rik|930571B16Rik|Hacs1|SLy2	SAM domain, SH3 domain and nuclear localization signals, 1	protein-coding
mm_10934.1	chr2	25468099	25468113	+	1	NA	exon (NM_008963, exon 4 of 7)	exon (NM_008963, exon 4 of 7)	1643	NM_008963	19215	Mm.1008	NM_008963	ENSMUSG00000015090	Ptgds	21kDa|L-PGDS|PGD2|PGDS|PGDS2|Ptgs3	prostaglandin D2 synthase (brain)	protein-coding
mm_133839.1	chr16	96200489	96200491	+	1	NA	promoter-TSS (NM_015825)	promoter-TSS (NM_015825)	20	NM_015825	50795	Mm.28638	NM_015825	ENSMUSG00000040666	Sh3bgr	5430437A18Rik	SH3-binding domain glutamic acid-rich protein	protein-coding
mm_28481.1	chr3	92456858	92456884	-	1	NA	exon (NM_011478, exon 2 of 2)	exon (NM_011478, exon 2 of 2)	1849	NM_001204427	20766	Mm.57092	NM_011478	ENSMUSG00000045539	Sprr3	SPR3	small proline-rich protein 3	protein-coding
mm_63704.1	chr7	130646184	130646248	+	1	NA	intron (NM_001004468, intron 3 of 21)	CpG	-46340	NM_001347637	57752	Mm.86322	NM_021314	ENSMUSG00000030852	Tacc2	mKIAA4180	transforming, acidic coiled-coil containing protein 2	protein-coding
mm_82751.1	chr9	26829511	26829525	-	1	NA	intron (NM_001113323, intron 10 of 19)	intron (NM_001113323, intron 10 of 19)	-23050	NM_001310768	244757	Mm.293696	NM_153803	ENSMUSG00000036395	Glb1l2	-	galactosidase, beta 1-like 2	protein-coding
mm_130823.1	chr15	101845762	101845772	-	1	NA	3' UTR (NM_008473, exon 9 of 9)	3' UTR (NM_008473, exon 9 of 9)	5019	NM_008473	16678	Mm.183137	NM_008473	ENSMUSG00000046834	Krt1	Krt-2.1|Krt2-1|Krt86	keratin 1	protein-coding
mm_27117.1	chr3	31095828	31095844	-	1	NA	intron (NM_001271772, intron 1 of 8)	intron (NM_001271772, intron 1 of 8)	778	NM_001039090	20482	Mm.15406	NM_011386	ENSMUSG00000027660	Skil	Skir|SnoN|sno	SKI-like	protein-coding
mm_23676.1	chr3	68584185	68584207	+	1	NA	intron (NM_013928, intron 1 of 6)	intron (NM_013928, intron 1 of 6)	11828	NM_013928	30953	Mm.331064	NM_013928	ENSMUSG00000027777	Schip1	Nf2ip|Schip-1	schwannomin interacting protein 1	protein-coding
mm_84871.1	chr9	79691338	79691341	-	1	NA	intron (NM_001290308, intron 13 of 65)	intron (NM_001290308, intron 13 of 65)	27383	NM_001290308	12816	Mm.3819	NM_007730	ENSMUSG00000032332	Col12a1	-	collagen, type XII, alpha 1	protein-coding
mm_83289.1	chr9	43116515	43116572	-	1	NA	promoter-TSS (NM_001034863)	promoter-TSS (NM_001034863)	27	NM_001034863	235300	Mm.261326	NM_001034863	ENSMUSG00000048503	Tmem136	AA396355|Gm184	transmembrane protein 136	protein-coding
mm_163804.1	chr14	19415933	19415949	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	186646	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_161237.1	chr13	95478434	95478434	-	1	NA	intron (NM_001081159, intron 1 of 1)	intron (NM_001081159, intron 1 of 1)	221	NM_001081159	268686	Mm.291249	NM_001081159	ENSMUSG00000021679	S100z	Gm625	S100 calcium binding protein, zeta	protein-coding
mm_90266.1	chr10	122678981	122678991	+	1	NA	promoter-TSS (NR_106182)	promoter-TSS (NR_106182)	224	NM_001110218	319468	Mm.489703	NM_176919	ENSMUSG00000034613	Ppm1h	A430075L18Rik|ARHCL1|C030002B11Rik	protein phosphatase 1H (PP2C domain containing)	protein-coding
mm_12704.1	chr2	76539724	76539745	+	1	NA	intron (NM_001290733, intron 4 of 26)	intron (NM_001290733, intron 4 of 26)	40728	NM_001290735	99031	Mm.240435	NM_145525	ENSMUSG00000042359	Osbpl6	1110062M20Rik|AI596402|ORP-6|mKIAA4128	oxysterol binding protein-like 6	protein-coding
mm_38539.1	chr4	141581390	141581395	-	1	NA	intron (NM_001163256, intron 7 of 8)	AT_rich|Low_complexity|Low_complexity	18532	NM_001163256	74202	Mm.490327	NM_133754	ENSMUSG00000006219	Fblim1	2410043F08Rik|Cal|Fblp1|Gt10|migfilin|migfilin(s)	filamin binding LIM protein 1	protein-coding
mm_51950.1	chr6	91739171	91739181	+	1	NA	intron (NM_009320, intron 6 of 14)	PB1D7|SINE|Alu	55109	NM_009320	21366	Mm.395650	NM_009320	ENSMUSG00000030096	Slc6a6	AA589629|C80501|Taut	solute carrier family 6 (neurotransmitter transporter, taurine), member 6	protein-coding
mm_127143.1	chr15	98398437	98398450	+	1	NA	promoter-TSS (NR_015496)	promoter-TSS (NR_015496)	-2	NR_015496	73302	Mm.272760	NR_015496	ENSMUSG00000099353	1700031M16Rik	4930413L20Rik	RIKEN cDNA 1700031M16 gene	ncRNA
mm_100813.1	chr11	5099224	5099242	-	1	NA	promoter-TSS (NM_177370)	promoter-TSS (NM_177370)	-40	NM_001290492	279766	Mm.260866	NM_177370	ENSMUSG00000034175	Rhbdd3	Ptag	rhomboid domain containing 3	protein-coding
mm_165814.1	chr3	145758825	145758840	+	1	NA	5' UTR (NM_026993, exon 1 of 6)	5' UTR (NM_026993, exon 1 of 6)	140	NM_026993	69219	Mm.234247	NM_026993	ENSMUSG00000028194	Ddah1	2410006N07Rik|2510015N06Rik|AI987801|AW050362	dimethylarginine dimethylaminohydrolase 1	protein-coding
mm_133857.1	chr16	96273586	96273602	+	1	NA	intron (NM_001122993, intron 2 of 3)	intron (NM_001122993, intron 2 of 3)	-7438	NM_033149	93961	Mm.154783	NM_033149	ENSMUSG00000074892	B3galt5	1190002B21Rik|AU045265|b3Galt-V	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 5	protein-coding
mm_171810.1	chr5	13121483	13121500	+	1	NA	Intergenic	Intergenic	-275293	NM_001243072	20346	Mm.372039	NM_009152	ENSMUSG00000028883	Sema3a	Hsema-I|SEMA1|SemD|Semad|coll-1	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	protein-coding
mm_58857.1	chr7	16893110	16893123	+	1	NA	intron (NM_010320, intron 2 of 3)	intron (NM_010320, intron 2 of 3)	1330	NM_010320	14709	Mm.103770	NM_010320	ENSMUSG00000063594	Gng8	G(y)8	guanine nucleotide binding protein (G protein), gamma 8	protein-coding
mm_173116.1	chrX	160132156	160132158	-	1	NA	exon (NM_008810, exon 3 of 11)	exon (NM_008810, exon 3 of 11)	6273	NM_008810	18597	Mm.34775	NM_008810	ENSMUSG00000031299	Pdha1	Pdha-1	pyruvate dehydrogenase E1 alpha 1	protein-coding
mm_126121.1	chr15	78325842	78325862	+	1	NA	promoter-TSS (NM_007780)	promoter-TSS (NM_007780)	-138	NM_007780	12983	Mm.235324	NM_007780	ENSMUSG00000071713	Csf2rb	AI848964|AIC2B|Bc|CDw131|Csf2rb1|Csfgmrb|Il3r|Il3rb|Il3rb1|Il5rb	colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage)	protein-coding
mm_64141.1	chr7	141216184	141216198	+	1	NA	intron (NM_025886, intron 1 of 5)	CpG	331	NM_025886	66985	Mm.21202	NM_025886	ENSMUSG00000038618	Rassf7	2400009B11Rik|AW210608	Ras association (RalGDS/AF-6) domain family (N-terminal) member 7	protein-coding
mm_85994.1	chr9	112211752	112211753	-	1	NA	intron (NM_001177619, intron 1 of 10)	B1_Mus1|SINE|Alu	5509	NM_001177617	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_23473.1	chr3	60480798	60480808	+	1	NA	intron (NM_001253713, intron 2 of 9)	intron (NM_001253713, intron 2 of 9)	7973	NM_001253713	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_46877.1	chr5	113843946	113843975	-	1	NA	3' UTR (NM_011779, exon 11 of 11)	3' UTR (NM_011779, exon 11 of 11)	-13459	NM_009151	20345	Mm.332590	NM_009151	ENSMUSG00000048163	Selplg	CD162|Psgl-1|Psgl1|Selp1|Selpl	selectin, platelet (p-selectin) ligand	protein-coding
mm_47854.1	chr5	134552382	134552413	-	1	NA	promoter-TSS (NM_001039162)	promoter-TSS (NM_001039162)	37	NM_001039162	269713	Mm.255138	NM_009990	ENSMUSG00000063146	Clip2	B230327O20|CLIP-115|Clip1|Cyln2|WSCR4|mKIAA0291|wbscr4	CAP-GLY domain containing linker protein 2	protein-coding
mm_149070.1	chr19	8871561	8871598	+	1	NA	promoter-TSS (NM_146093)	promoter-TSS (NM_146093)	20	NM_146093	225896	Mm.27839	NM_146093	ENSMUSG00000071655	Ubxn1	2B28|4930455J02Rik|D19Ertd721e|T25529	UBX domain protein 1	protein-coding
mm_17833.1	chr2	34278317	34278320	-	1	NA	intron (NM_016768, intron 2 of 8)	intron (NM_016768, intron 2 of 8)	93727	NM_001290576	18516	Mm.239941	NM_016768	ENSMUSG00000038718	Pbx3	-	pre B cell leukemia homeobox 3	protein-coding
mm_76459.1	chr8	85328015	85328019	-	1	NA	intron (NM_001297612, intron 11 of 12)	MTC|LTR|ERVL-MaLR	28385	NR_028268	56452	Mm.29709	NM_019716	ENSMUSG00000031697	Orc6	6720420I10Rik|Orc6l	origin recognition complex, subunit 6	protein-coding
mm_75886.1	chr8	70839527	70839542	-	1	NA	5' UTR (NM_027560, exon 1 of 8)	5' UTR (NM_027560, exon 1 of 8)	186	NM_027560	70807	Mm.24215	NM_027560	ENSMUSG00000002910	Arrdc2	4632416I05Rik|Ilad1	arrestin domain containing 2	protein-coding
mm_42229.1	chr5	113510900	113510905	+	1	NA	Intergenic	Intergenic	-39518	NM_177292	320916	Mm.102783	NM_177292	ENSMUSG00000063430	Wscd2	4933413A10Rik|C530024P05Rik|Gm450	WSC domain containing 2	protein-coding
mm_106846.1	chr12	8007855	8007861	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	30181	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_169767.1	chr15	99820045	99820050	-	1	NA	5' UTR (NM_023063, exon 1 of 8)	5' UTR (NM_023063, exon 1 of 8)	102	NM_023063	65970	Mm.33207	NM_023063	ENSMUSG00000023022	Lima1	Eplin	LIM domain and actin binding 1	protein-coding
mm_113694.1	chr13	43125847	43125853	+	1	NA	intron (NM_001005740, intron 9 of 12)	intron (NM_001005740, intron 9 of 12)	3011	NM_001005748	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding
mm_163222.1	chr11	102097310	102097310	+	1	NA	Intergenic	Intergenic	3990	NM_008918	19064	Mm.1269	NM_008918	ENSMUSG00000017316	Ppy	AV061413|IGSPP|PP	pancreatic polypeptide	protein-coding
mm_146099.1	chr18	73878542	73878543	+	1	NA	3' UTR (NM_001305882, exon 9 of 9)	3' UTR (NM_001305882, exon 9 of 9)	19157	NM_001305882	71263	Mm.126220	NM_027741	ENSMUSG00000064036	Mro	4930507C04Rik|4933435E20Rik	maestro	protein-coding
mm_172572.1	chr8	112321129	112321129	+	1	NA	Intergenic	LTRIS2|LTR|ERV1	248446	NR_132433	102640845	Mm.405615	NR_132433	ENSMUSG00000098075	Gm26994	-	predicted gene, 26994	ncRNA
mm_28040.1	chr3	83841556	83841568	-	1	NA	promoter-TSS (NM_011905)	promoter-TSS (NM_011905)	46	NM_011905	24088	Mm.87596	NM_011905	ENSMUSG00000027995	Tlr2	Ly105	toll-like receptor 2	protein-coding
mm_107324.1	chr12	31447007	31447009	+	1	NA	intron (NM_021353, intron 1 of 20)	intron (NM_021353, intron 1 of 20)	8789	NM_021353	13487	Mm.490454	NM_021353	ENSMUSG00000001225	Slc26a3	9030623B18Rik|9130013M11Rik|AV376035|Dra	solute carrier family 26, member 3	protein-coding
mm_72265.1	chr8	75097227	75097231	+	1	NA	exon (NM_010442, exon 3 of 5)	exon (NM_010442, exon 3 of 5)	3611	NM_010442	15368	Mm.276389	NM_010442	ENSMUSG00000005413	Hmox1	D8Wsu38e|HO-1|HO1|Hemox|Hmox|Hsp32	heme oxygenase 1	protein-coding
mm_150752.1	chr19	43808765	43808779	+	1	NA	intron (NM_013806, intron 11 of 31)	intron (NM_013806, intron 11 of 31)	26464	NM_013806	12780	Mm.39054	NM_013806	ENSMUSG00000025194	Abcc2	AI173996|Abc30|Cmoat|Mrp2|cMRP	ATP-binding cassette, sub-family C (CFTR/MRP), member 2	protein-coding
mm_154211.1	chr19	59170386	59170405	-	1	NA	promoter-TSS (NM_009501)	promoter-TSS (NM_009501)	-366	NM_009501	22326	Mm.23801	NM_009501	ENSMUSG00000006270	Vax1	-	ventral anterior homeobox 1	protein-coding
mm_2601.1	chr1	120007073	120007083	+	1	NA	promoter-TSS (NM_001012322)	promoter-TSS (NM_001012322)	98	NM_001311077	319229	Mm.189223	NM_001012322	ENSMUSG00000026387	Sctr	6530402O03Rik	secretin receptor	protein-coding
mm_115720.1	chr13	15980399	15980403	-	1	NA	Intergenic	Intergenic	-31450	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_153709.1	chr19	44397902	44397947	-	1	NA	exon (NM_009127, exon 6 of 6)	exon (NM_009127, exon 6 of 6)	9785	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_68158.1	chr7	102565426	102565474	-	1	NA	promoter-TSS (NM_009277)	promoter-TSS (NM_009277)	32	NM_001082552	20821	Mm.321227	NM_009277	ENSMUSG00000030966	Trim21	Ro52|Ssa1	tripartite motif-containing 21	protein-coding
mm_169157.1	chr13	64152498	64152502	-	1	NA	intron (NM_175494, intron 1 of 4)	CpG	699	NM_175494	238673	Mm.300065	NM_175494	ENSMUSG00000044934	Zfp367	8030486J21Rik|ZFF29a|ZFF29b|Znf367	zinc finger protein 367	protein-coding
mm_108642.1	chr12	85824919	85825009	+	1	NA	promoter-TSS (NM_001081423)	promoter-TSS (NM_001081423)	14	NM_001081423	320244	Mm.132172	NM_177114	ENSMUSG00000012609	Ttll5	1700048H13Rik|2310009M18Rik|4930556H18Rik|AI428864|D630041K24Rik|R75373|Stamp|mKIAA0998	tubulin tyrosine ligase-like family, member 5	protein-coding
mm_135865.1	chr16	60605592	60605609	-	1	NA	promoter-TSS (NM_007938)	promoter-TSS (NM_007938)	-69	NM_007938	13840	Mm.455790	NM_007938	ENSMUSG00000055540	Epha6	Ehk2|Hek12|m-ehk2	Eph receptor A6	protein-coding
mm_101703.1	chr11	40755476	40755486	-	1	NA	promoter-TSS (NM_009831)	promoter-TSS (NM_009831)	-195	NM_009831	12450	Mm.2103	NM_009831	ENSMUSG00000020326	Ccng1	AI314029	cyclin G1	protein-coding
mm_157221.1	chrX	13345307	13345322	-	1	NA	Intergenic	Intergenic	64292	NM_010028	13205	Mm.289662	NM_010028	ENSMUSG00000000787	Ddx3x	D1Pas1-rs2|Ddx3|Fin14	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 3, X-linked	protein-coding
mm_89526.1	chr10	94463837	94463841	+	1	NA	Intergenic	B3A|SINE|B2	-51018	NM_172051	319880	Mm.23047	NM_172051	ENSMUSG00000020023	Tmcc3	AW488095|C630016B22Rik|C88213|Tmcc1	transmembrane and coiled coil domains 3	protein-coding
mm_84669.1	chr9	72008012	72008016	-	1	NA	intron (NM_001253862, intron 4 of 19)	PB1D11|SINE|Alu	44573	NR_029879	723889		NR_029879	ENSMUSG00000105200	Mir378a	Mir378|Mirn378|mmu-mir-378|mmu-mir-378a	microRNA 378a	ncRNA
mm_97131.1	chr11	74981767	74981802	+	1	NA	intron (NM_001002764, intron 8 of 18)	intron (NM_001002764, intron 8 of 18)	55912	NM_001002764	103677	Mm.288460	NM_001002764	ENSMUSG00000038290	Smg6	AI317223|AU041178	Smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans)	protein-coding
mm_40072.1	chr5	34336385	34336395	+	1	NA	promoter-TSS (NM_001304270)	promoter-TSS (NM_001304270)	10	NM_001304269	19822	Mm.21281	NM_011278	ENSMUSG00000029110	Rnf4	AU018689|Gtrgeo8|SNURF	ring finger protein 4	protein-coding
mm_24521.1	chr3	92957387	92957389	+	1	NA	promoter-TSS (NM_001270426)	promoter-TSS (NM_001270426)	-2	NM_001270426	630994	Mm.455176	NM_001270426	ENSMUSG00000043472	Lce3d	ENSMUSG00000043472|Gm9782	late cornified envelope 3D	protein-coding
mm_32591.1	chr4	111720054	111720073	+	1	NA	promoter-TSS (NM_026470)	promoter-TSS (NM_026470)	53	NM_026470	67946	Mm.275526	NM_026470	ENSMUSG00000034401	Spata6	1700062C23Rik|AI790763|Hash|KRP|Mash	spermatogenesis associated 6	protein-coding
mm_92069.1	chr10	62578388	62578450	-	1	NA	promoter-TSS (NM_028197)	promoter-TSS (NM_028197)	38	NM_028197	72320	Mm.258955	NM_028197	ENSMUSG00000036955	Kif1bp	0710007C18Rik|2510003E04Rik|KBP|mKIAA1279	KIF1 binding protein	protein-coding
mm_165746.1	chr3	107760173	107760182	-	1	NA	5' UTR (NM_007778, exon 1 of 9)	5' UTR (NM_007778, exon 1 of 9)	292	NM_001113530	12977	Mm.795	NM_007778	ENSMUSG00000014599	Csf1	C87615|Csfm|MCSF|op	colony stimulating factor 1 (macrophage)	protein-coding
mm_116539.1	chr13	45923421	45923440	-	1	NA	intron (NM_001199304, intron 2 of 6)	(TG)n|Simple_repeat|Simple_repeat	41561	NM_001199304	20238	Mm.342683	NM_009124	ENSMUSG00000046876	Atxn1	2900016G23Rik|Atx1|C85907|ENSMUSG00000074917|Gm10786|Sca1	ataxin 1	protein-coding
mm_114808.1	chr13	91461200	91461204	+	1	NA	exon (NM_024186, exon 1 of 16)	exon (NM_024186, exon 1 of 16)	105	NM_024186	66970	Mm.343095	NM_024186	ENSMUSG00000003992	Ssbp2	1500004K09Rik|2310079I02Rik|9330163K02Rik|A830008M03Rik|AU067692|AW558684|Hspc116|SSDP2	single-stranded DNA binding protein 2	protein-coding
mm_115722.1	chr13	16023402	16023437	-	1	NA	intron (NM_008380, intron 4 of 4)	intron (NM_008380, intron 4 of 4)	11568	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_70345.1	chr8	4678447	4678486	+	1	NA	Intergenic	CpG	65296	NM_145591	233987	Mm.102799	NM_145591	ENSMUSG00000058748	Zfp958	-	zinc finger protein 958	protein-coding
mm_106982.1	chr12	9580820	9580832	+	1	NA	3' UTR (NM_011859, exon 3 of 3)	3' UTR (NM_011859, exon 3 of 3)	6384	NM_011859	23967	Mm.45055	NM_011859	ENSMUSG00000048387	Osr1	Odd1|Osr	odd-skipped related 1 (Drosophila)	protein-coding
mm_136330.1	chr16	92398814	92398842	-	1	NA	intron (NM_001081549, intron 1 of 3)	intron (NM_001081549, intron 1 of 3)	1250	NM_019466	54720	Mm.265744	NM_019466	ENSMUSG00000022951	Rcan1	Adapt78|CALP1L|CSP1|DSC1|Dscr1|MCIP1|RCN1	regulator of calcineurin 1	protein-coding
mm_154890.1	chrX	20842328	20842350	+	1	NA	Intergenic	Intergenic	-6204	NM_009703	11836	Mm.220946	NM_009703	ENSMUSG00000001127	Araf	1200013E08Rik|A-Raf|AW495444|Araf1	Araf proto-oncogene, serine/threonine kinase	protein-coding
mm_18662.1	chr2	70746024	70746043	-	1	NA	exon (NM_172664, exon 9 of 20)	exon (NM_172664, exon 9 of 20)	79447	NM_172664	228012	Mm.136511	NM_172664	ENSMUSG00000041997	Tlk1	4930545J15Rik	tousled-like kinase 1	protein-coding
mm_167536.1	chr9	21798063	21798078	+	1	NA	intron (NM_145611, intron 1 of 11)	intron (NM_145611, intron 1 of 11)	476	NM_145611	235041	Mm.257371	NM_145611	ENSMUSG00000032194	Kank2	AI504612|Ankrd25|BC010245	KN motif and ankyrin repeat domains 2	protein-coding
mm_60317.1	chr7	44207308	44207329	+	1	NA	promoter-TSS (NM_010915)	promoter-TSS (NM_010915)	-115	NM_010915	18048	Mm.440886	NM_010915	ENSMUSG00000066513	Klk1b4	Ngfa|alpha-NGF|mGk-4	kallikrein 1-related pepidase b4	protein-coding
mm_94118.1	chr10	128626724	128626740	-	1	NA	promoter-TSS (NM_013765)	promoter-TSS (NM_013765)	-226	NM_013765	27370	Mm.32118	NM_013765	ENSMUSG00000025362	Rps26	-	ribosomal protein S26	protein-coding
mm_172268.1	chr6	78155538	78155551	+	1	NA	Intergenic	L1Md_T|LINE|L1	-175877	NM_009819	12386	Mm.34637	NM_009819	ENSMUSG00000063063	Ctnna2	AI481747|Catna|Catna2|cdf|chp	catenin (cadherin associated protein), alpha 2	protein-coding
mm_29093.1	chr3	104777232	104777235	-	1	NA	5' UTR (NM_183224, exon 1 of 7)	5' UTR (NM_183224, exon 1 of 7)	314	NM_183224	329731	Mm.389494	NM_183224	ENSMUSG00000055865	Fam19a3	7530404M11Rik|TAFA3|Tafa-3	family with sequence similarity 19, member A3	protein-coding
mm_14224.1	chr2	127363261	127363271	+	1	NA	promoter-TSS (NM_009633)	promoter-TSS (NM_009633)	-20	NM_009633	11552	Mm.347390	NM_009633	ENSMUSG00000058620	Adra2b	Adra-2b|[a]2B|a2b-AR|alpha2-C2|alpha2B	adrenergic receptor, alpha 2b	protein-coding
mm_158628.1	chrX	153037475	153037485	-	1	NA	promoter-TSS (NM_023788)	promoter-TSS (NM_023788)	83	NM_023788	75625	Mm.6890	NM_023788	ENSMUSG00000047238	Mageh1	2010107K23Rik|APR-1|APR1	melanoma antigen, family H, 1	protein-coding
mm_72967.1	chr8	92855320	92855400	+	1	NA	promoter-TSS (NM_173014)	promoter-TSS (NM_173014)	10	NM_173014	270084	Mm.21463	NM_173014	ENSMUSG00000033192	Lpcat2	A330042H22|Aytl1|Aytl1a|lpafat1	lysophosphatidylcholine acyltransferase 2	protein-coding
mm_80192.1	chr9	72395960	72395975	+	1	NA	Intergenic	Intergenic	-42562	NM_008613	17427	Mm.387671	NM_008613	ENSMUSG00000032221	Mns1	AW546487	meiosis-specific nuclear structural protein 1	protein-coding
mm_110328.1	chr12	35021428	35021443	-	1	NA	Intergenic	Intergenic	-25754	NM_001014973	217463	Mm.213991	NM_001014973	ENSMUSG00000020590	Snx13	Rgs-px1|mKIAA0713	sorting nexin 13	protein-coding
mm_13491.1	chr2	106693503	106693520	+	1	NA	promoter-TSS (NM_001143683)	promoter-TSS (NM_001143683)	52	NM_001143683	77015	Mm.45628	NM_029837	ENSMUSG00000016386	Mpped2	239Fb|2700082O15Rik|AV354767|AW060960	metallophosphoesterase domain containing 2	protein-coding
mm_61625.1	chr7	80213941	80213957	+	1	NA	intron (NM_013659, intron 4 of 14)	ID_B1|SINE|B4	18856	NM_001291276	23991	Mm.30217	NM_011870	ENSMUSG00000030538	Cib1	Cibkip|Kip|Prkdcip	calcium and integrin binding 1 (calmyrin)	protein-coding
mm_139290.1	chr17	48300449	48300458	+	1	NA	5' UTR (NM_001033405, exon 1 of 5)	5' UTR (NM_001033405, exon 1 of 5)	415	NM_001033405	328833	Mm.329104	NM_001033405	ENSMUSG00000071068	Treml2	AW049306|Gm750|Tlt2	triggering receptor expressed on myeloid cells-like 2	protein-coding
mm_43164.1	chr5	127170550	127170579	+	1	NA	promoter-TSS (NR_045371)	promoter-TSS (NR_045371)	-1	NR_045371	75916	Mm.394659	NR_045371	ENSMUSG00000105308	4930572K03Rik	-	RIKEN cDNA 4930572K03 gene	ncRNA
mm_96805.1	chr11	69981523	69981533	+	1	NA	promoter-TSS (NM_018740)	promoter-TSS (NM_018740)	-293	NM_018740	54351	Mm.13430	NM_018740	ENSMUSG00000018565	Elp5	Derp6|Rai12	elongator acetyltransferase complex subunit 5	protein-coding
mm_47388.1	chr5	123012877	123012880	-	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-2196	NM_175423	109305	Mm.218582	NM_175423	ENSMUSG00000049686	Orai1	D730049H07Rik|Tmem142a|orai-1	ORAI calcium release-activated calcium modulator 1	protein-coding
mm_95799.1	chr11	55109014	55109056	+	1	NA	exon (NM_010299, exon 3 of 4)	exon (NM_010299, exon 3 of 4)	11050	NM_010299	14667	Mm.287807	NM_010299	ENSMUSG00000000594	Gm2a	AA408702|AW215435|GM2-AP|SAP-3	GM2 ganglioside activator protein	protein-coding
mm_157651.1	chrX	57326274	57326312	-	1	NA	intron (NM_152801, intron 2 of 21)	intron (NM_152801, intron 2 of 21)	12436	NM_152801	73341	Mm.261443	NM_152801	ENSMUSG00000031133	Arhgef6	1600028C08Rik|1700038J06Rik|4930592P22Rik|alpha-PIX	Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_43577.1	chr5	137746239	137746249	+	1	NA	5' UTR (NM_023910, exon 1 of 5)	5' UTR (NM_023910, exon 1 of 5)	275	NM_029805	78829	Mm.286399	NM_023910	ENSMUSG00000029723	Tsc22d4	0610009M14Rik|1700023B23Rik|AI415410|Thg-1pit|Tilz2	TSC22 domain family, member 4	protein-coding
mm_42476.1	chr5	115466176	115466189	+	1	NA	promoter-TSS (NM_011107)	promoter-TSS (NM_011107)	-84	NM_011107	18778	Mm.20190	NM_011107	ENSMUSG00000029522	Pla2g1b	Pla2a|sPLA2IB	phospholipase A2, group IB, pancreas	protein-coding
mm_56254.1	chr6	90781283	90781286	-	1	NA	intron (NM_001134384, intron 1 of 13)	intron (NM_001134384, intron 1 of 13)	28839	NM_001134384	232227	Mm.196943	NM_182784	ENSMUSG00000034312	Iqsec1	AW561907|BC026481|BRAG2|D6Ertd349e|cI-43	IQ motif and Sec7 domain 1	protein-coding
mm_102956.1	chr11	69664468	69664488	-	1	NA	non-coding (NR_110993, exon 5 of 5)	non-coding (NR_110993, exon 5 of 5)	1435	NR_035455	100316840		NR_035455	ENSMUSG00000088752	Mir1934	mir-1934|mmu-mir-1934	microRNA 1934	ncRNA
mm_122276.1	chr14	34403742	34403745	-	1	NA	3' UTR (NM_153127, exon 7 of 7)	3' UTR (NM_153127, exon 7 of 7)	28239	NM_153127	105450	Mm.272673	NM_153127	ENSMUSG00000041445	Mmrn2	AA986839|ENDOGLYX1|Emilin3|EndoGlyx-1	multimerin 2	protein-coding
mm_81345.1	chr9	108560013	108560044	+	1	NA	promoter-TSS (NM_011830)	promoter-TSS (NM_011830)	-473	NM_011830	23918	Mm.6065	NM_011830	ENSMUSG00000062867	Impdh2	IMPD	inosine 5'-phosphate dehydrogenase 2	protein-coding
mm_109473.1	chr12	111421464	111421485	+	1	NA	intron (NM_001289487, intron 2 of 13)	intron (NM_001289487, intron 2 of 13)	4029	NM_001289488	74190	Mm.248640	NM_028807	ENSMUSG00000021280	Exoc3l4	1200009I06Rik|1600013K19Rik	exocyst complex component 3-like 4	protein-coding
mm_132434.1	chr16	35871617	35871631	+	1	NA	promoter-TSS (NM_001039530)	promoter-TSS (NM_001039530)	-242	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_155053.1	chrX	42238593	42238604	+	1	NA	intron (NM_001077712, intron 16 of 32)	L1M2|LINE|L1	36743	NM_001290713	20843	Mm.290422	NM_021465	ENSMUSG00000025862	Stag2	9230105L23Rik|B230112I07Rik|SA-2|SAP2	stromal antigen 2	protein-coding
mm_24483.1	chr3	92024529	92024539	+	1	NA	intron (NM_207247, intron 2 of 6)	CpG	9951	NM_207247	242100	Mm.297406	NM_207247	ENSMUSG00000042244	Pglyrp3	Gm420	peptidoglycan recognition protein 3	protein-coding
mm_18814.1	chr2	74562798	74562803	-	1	NA	intron (NM_001110209, intron 4 of 13)	(A)n|Simple_repeat|Simple_repeat	16148	NM_001110209	69605	Mm.156113	NM_027133	ENSMUSG00000009207	Lnpk	2310011O18Rik|4921514L11Rik|9530051D01Rik|AI666268|Lnp|Lnpk1|Ul|ulnaless	lunapark, ER junction formation factor	protein-coding
mm_52398.1	chr6	113307842	113307861	+	1	NA	intron (NM_001282128, intron 1 of 13)	intron (NM_001282128, intron 1 of 13)	714	NM_001282126	78783	Mm.356059	NM_030178	ENSMUSG00000001632	Brpf1	4833438B11Rik|4930540D11Rik|Brpf2	bromodomain and PHD finger containing, 1	protein-coding
mm_50480.1	chr6	48988246	48988253	+	1	NA	exon (NM_172888, exon 1 of 5)	exon (NM_172888, exon 1 of 5)	1388	NM_172888	243377	Mm.446302	NM_172888	ENSMUSG00000039215	Svs1	9530003A11	seminal vesicle secretory protein 1	protein-coding
mm_53022.1	chr6	124279798	124279811	+	1	NA	Intergenic	Intergenic	-24847	NM_001170395	93671	Mm.37426	NM_053094	ENSMUSG00000008845	Cd163	CD163v2|CD163v3	CD163 antigen	protein-coding
mm_60364.1	chr7	44441990	44442022	+	1	NA	promoter-TSS (NM_198250)	promoter-TSS (NM_198250)	-481	NM_198250	272381	Mm.44173	NM_198250	ENSMUSG00000047085	Lrrc4b	A830007M12|Lrig4	leucine rich repeat containing 4B	protein-coding
mm_96775.1	chr11	69935936	69935965	+	1	NA	promoter-TSS (NM_016875)	promoter-TSS (NM_016875)	51	NM_016875	53422	Mm.29286	NM_016875	ENSMUSG00000018554	Ybx2	Msy2	Y box protein 2	protein-coding
mm_28677.1	chr3	95315087	95315103	-	1	NA	promoter-TSS (NM_029789)	promoter-TSS (NM_029789)	-95	NM_029789	76893	Mm.181009	NM_029789	ENSMUSG00000015714	Cers2	0610013I17Rik|AI225939|Lass2|TRH3	ceramide synthase 2	protein-coding
mm_84665.1	chr9	71976120	71976121	-	1	NA	intron (NM_001253862, intron 5 of 19)	intron (NM_001253862, intron 5 of 19)	12679	NR_029879	723889		NR_029879	ENSMUSG00000105200	Mir378a	Mir378|Mirn378|mmu-mir-378|mmu-mir-378a	microRNA 378a	ncRNA
mm_23869.1	chr3	83028604	83028614	+	1	NA	exon (NM_010196, exon 2 of 5)	exon (NM_010196, exon 2 of 5)	2456	NM_001111048	14161	Mm.88793	NM_010196	ENSMUSG00000028001	Fga	ENSMUSG00000059807|Fib	fibrinogen alpha chain	protein-coding
mm_110510.1	chr12	54695886	54695893	-	1	NA	promoter-TSS (NM_001331162)	promoter-TSS (NM_001331162)	5	NM_001331162	66266	Mm.156440	NM_025456	ENSMUSG00000054302	Eapp	1810011O16Rik	E2F-associated phosphoprotein	protein-coding
mm_47124.1	chr5	119807632	119807632	-	1	NA	Intergenic	Intergenic	-27031	NM_011537	21388	Mm.103636	NM_011537	ENSMUSG00000018263	Tbx5	-	T-box 5	protein-coding
mm_36430.1	chr4	82294374	82294386	-	1	NA	3' UTR (NM_001113209, exon 12 of 12)	3' UTR (NM_001113209, exon 12 of 12)	211399	NM_001286127	18028	Mm.317947	NM_008687	ENSMUSG00000008575	Nfib	6720429L07Rik|CTF|E030026I10Rik|NF-I/B|NF1-B|NFI-B	nuclear factor I/B	protein-coding
mm_5724.1	chr1	44102434	44102448	-	1	NA	promoter-TSS (NM_029368)	promoter-TSS (NM_029368)	-53	NM_029368	75623	Mm.348017	NM_029368	ENSMUSG00000026049	Tex30	1700029F09Rik|3110030D08Rik	testis expressed 30	protein-coding
mm_24833.1	chr3	95658772	95658787	+	1	NA	promoter-TSS (NM_008562)	promoter-TSS (NM_008562)	58	NM_008562	17210	Mm.1639	NM_008562	ENSMUSG00000038612	Mcl1	AW556805|Mcl-1	myeloid cell leukemia sequence 1	protein-coding
mm_43918.1	chr5	144768117	144768123	+	1	NA	promoter-TSS (NM_001081362)	promoter-TSS (NM_001081362)	-672	NM_001081362	100683	Mm.273570	NM_001081362	ENSMUSG00000045482	Trrap	AI481500	transformation/transcription domain-associated protein	protein-coding
mm_103794.1	chr11	82871107	82871121	-	1	NA	promoter-TSS (NM_001007465)	promoter-TSS (NM_001007465)	96	NM_001007465	67338	Mm.341608	NM_026097	ENSMUSG00000020696	Rffl	1700051E09Rik|4930516L10Rik|BG080975|Carp2	ring finger and FYVE like domain containing protein	protein-coding
mm_158805.1	chrX	167264218	167264266	-	1	NA	promoter-TSS (NM_001313760)	promoter-TSS (NM_001313760)	87	NM_001313761	170744	Mm.196676	NM_133212	ENSMUSG00000040522	Tlr8	-	toll-like receptor 8	protein-coding
mm_166247.1	chr5	77261687	77261687	+	1	NA	Intergenic	Intergenic	-3807	NM_011263	19712	Mm.28840	NM_011263	ENSMUSG00000029249	Rest	2610008J04Rik|AA407358|NRSF|REST4	RE1-silencing transcription factor	protein-coding
mm_94090.1	chr10	128518534	128518535	-	1	NA	intron (NM_011843, intron 15 of 30)	PB1D9|SINE|Alu	-6504	NR_105881	102465552		NR_105881	ENSMUSG00000099292	Mir6916	Gm27721|mmu-mir-6916	microRNA 6916	ncRNA
mm_7971.1	chr1	134060911	134060959	-	1	NA	Intergenic	Intergenic	18220	NM_007570	12227	Mm.392646	NM_007570	ENSMUSG00000020423	Btg2	AA959598|APRO1|Pc3|TIS21	B cell translocation gene 2, anti-proliferative	protein-coding
mm_103163.1	chr11	70455299	70455317	-	1	NA	3' UTR (NM_023158, exon 5 of 5)	3' UTR (NM_023158, exon 5 of 5)	3377	NM_025397	66172	Mm.46424	NM_025397	ENSMUSG00000018923	Med11	1110030J09Rik|AI465144|AW545069	mediator complex subunit 11	protein-coding
mm_27992.1	chr3	82145866	82145883	-	1	NA	promoter-TSS (NM_021896)	promoter-TSS (NM_021896)	3	NM_021896	60596	Mm.143831	NM_021896	ENSMUSG00000033910	Gucy1a3	1200016O07Rik|sGC-alpha1	guanylate cyclase 1, soluble, alpha 3	protein-coding
mm_42826.1	chr5	122100817	122100851	+	1	NA	promoter-TSS (NM_010861)	promoter-TSS (NM_010861)	-146	NM_010861	17906	Mm.1529	NM_010861	ENSMUSG00000013936	Myl2	MLC-2|MLC-2s/v|MLC-2v|Mlc2v|Mylpc	myosin, light polypeptide 2, regulatory, cardiac, slow	protein-coding
mm_7924.1	chr1	133801184	133801185	-	1	NA	Intergenic	Intergenic	-47437	NM_213616	381290	Mm.188617	NM_213616	ENSMUSG00000026463	Atp2b4	Pmca4	ATPase, Ca++ transporting, plasma membrane 4	protein-coding
mm_87617.1	chr10	57794549	57794569	+	1	NA	promoter-TSS (NM_020561)	promoter-TSS (NM_020561)	15	NM_020561	57319	Mm.2379	NM_020561	ENSMUSG00000019872	Smpdl3a	0610010C24Rik|AI529588|ASM3A|ASML3|ASML3A	sphingomyelin phosphodiesterase, acid-like 3A	protein-coding
mm_56576.1	chr6	106748935	106748958	-	1	NA	promoter-TSS (NM_008370)	promoter-TSS (NM_008370)	91	NM_008370	16192	Mm.3448	NM_008370	ENSMUSG00000005364	Il5ra	CD125|CDw125|Il5r	interleukin 5 receptor, alpha	protein-coding
mm_152537.1	chr19	11327238	11327248	-	1	NA	intron (NM_027836, intron 3 of 6)	intron (NM_027836, intron 3 of 6)	7452	NM_001276398	109225	Mm.491251	NM_027836	ENSMUSG00000024672	Ms4a7	9130422I10Rik|A430103C15Rik|CD20l4|CFFMA	membrane-spanning 4-domains, subfamily A, member 7	protein-coding
mm_37240.1	chr4	118134802	118134812	-	1	NA	5' UTR (NM_001285521, exon 1 of 11)	5' UTR (NM_001285521, exon 1 of 11)	139	NM_001285520	20441	Mm.251002	NM_009176	ENSMUSG00000028538	St3gal3	ST3GalIII|ST3N|Siat3|Siat6	ST3 beta-galactoside alpha-2,3-sialyltransferase 3	protein-coding
mm_32896.1	chr4	118968157	118968169	+	1	NA	exon (NM_133892, exon 7 of 7)	exon (NM_133892, exon 7 of 7)	6196	NM_133892	100470	Mm.26698	NM_133892	ENSMUSG00000024903	Lao1	AW990848	L-amino acid oxidase 1	protein-coding
mm_159698.1	chr5	26105315	26105315	-	1	NA	promoter-TSS (NM_207657)	promoter-TSS (NM_207657)	-1	NM_207657	381622	Mm.226878	NM_207657	ENSMUSG00000051940	5031410I06Rik	-	RIKEN cDNA 5031410I06 gene	protein-coding
mm_59957.1	chr7	30427423	30427441	+	1	NA	exon (NM_172142, exon 10 of 11)	exon (NM_172142, exon 10 of 11)	4128	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_5174.1	chr1	10233112	10233122	-	1	NA	promoter-TSS (NM_001102430)	promoter-TSS (NM_001102430)	-447	NM_001102430	211673	Mm.229141	NM_001102430	ENSMUSG00000067851	Arfgef1	ARFGEP1|BIG1|D130059B05Rik|D730028O18Rik|P200	ADP-ribosylation factor guanine nucleotide-exchange factor 1(brefeldin A-inhibited)	protein-coding
mm_153982.1	chr19	47913883	47913886	-	1	NA	intron (NM_001001738, intron 1 of 1)	AT_rich|Low_complexity|Low_complexity	5415	NM_001001738	414801	Mm.29457	NM_001001738	ENSMUSG00000044948	Itprip	4833424O12Rik|DANGER|mKIAA1754	inositol 1,4,5-triphosphate receptor interacting protein	protein-coding
mm_25296.1	chr3	105907562	105907566	+	1	NA	exon (NM_001174169, exon 2 of 2)	exon (NM_001174169, exon 2 of 2)	3143	NM_009631	11542	Mm.235024	NM_009631	ENSMUSG00000000562	Adora3	A3AR|A3R|AA3R|ARA3|Gpcr2	adenosine A3 receptor	protein-coding
mm_143066.1	chr17	57021451	57021475	-	1	NA	3' UTR (NM_010613, exon 18 of 18)	3' UTR (NM_010613, exon 18 of 18)	10044	NM_010613	16549	Mm.34296	NM_010613	ENSMUSG00000007670	Khsrp	6330409F21Rik|Fbp2|Fubp2|Ksrp	KH-type splicing regulatory protein	protein-coding
mm_17393.1	chr2	27112018	27112034	-	1	NA	3' UTR (NM_175427, exon 3 of 3)	3' UTR (NM_175427, exon 3 of 3)	30451	NM_175427	109349	Mm.314080	NM_175427	ENSMUSG00000009216	Fam163b	C630035N08Rik	family with sequence similarity 163, member B	protein-coding
mm_108781.1	chr12	89870712	89870720	+	1	NA	intron (NM_001252074, intron 1 of 6)	Lx8|LINE|L1	58233	NM_001252074	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding
mm_50675.1	chr6	51544668	51544687	+	1	NA	5' UTR (NM_028035, exon 1 of 7)	5' UTR (NM_028035, exon 1 of 7)	154	NM_001127348	71982	Mm.294166	NM_028035	ENSMUSG00000038301	Snx10	2410004M09Rik	sorting nexin 10	protein-coding
mm_47506.1	chr5	124035791	124035802	-	1	NA	Intergenic	Intergenic	-3536	NM_177876	330192	Mm.4079	NM_177876	ENSMUSG00000066278	Vps37b	2300007F24Rik|AI415429|BC026744	vacuolar protein sorting 37B	protein-coding
mm_50386.1	chr6	48691059	48691069	+	1	NA	exon (NM_001243200, exon 4 of 4)	exon (NM_001243200, exon 4 of 4)	6486	NM_174990	107526	Mm.333048	NM_174990	ENSMUSG00000054435	Gimap4	AU019574|E430007K16Rik|Ian-1|Ian1|Imap4	GTPase, IMAP family member 4	protein-coding
mm_117341.1	chr13	69594971	69594977	-	1	NA	exon (NM_175283, exon 3 of 5)	exon (NM_175283, exon 3 of 5)	16489	NM_175283	78925	Mm.451912	NM_175283	ENSMUSG00000021594	Srd5a1	0610031P22Rik|4930435F02Rik|S5AR 1|Srd5a-1	steroid 5 alpha-reductase 1	protein-coding
mm_99345.1	chr11	101552850	101552874	+	1	NA	promoter-TSS (NM_009764)	promoter-TSS (NM_009764)	208	NM_001252223	17966	Mm.784	NM_008676	ENSMUSG00000017119	Nbr1	mKIAA0049	neighbor of Brca1 gene 1	protein-coding
mm_89190.1	chr10	86347331	86347357	+	1	NA	3' UTR (NM_011595, exon 5 of 5)	3' UTR (NM_011595, exon 5 of 5)	46932	NM_011595	21859	Mm.4871	NM_011595	ENSMUSG00000020044	Timp3	Timp-3	tissue inhibitor of metalloproteinase 3	protein-coding
mm_68246.1	chr7	105482201	105482216	-	1	NA	promoter-TSS (NM_028444)	promoter-TSS (NM_028444)	-11	NM_028444	109042	Mm.3124	NM_028444	ENSMUSG00000037060	Prkcdbp	3110015B12Rik|6330514M23Rik|SRBC	protein kinase C, delta binding protein	protein-coding
mm_90440.1	chr10	127643143	127643158	+	1	NA	5' UTR (NM_009284, exon 1 of 22)	5' UTR (NM_009284, exon 1 of 22)	164	NM_009284	20852	Mm.121721	NM_009284	ENSMUSG00000002147	Stat6	-	signal transducer and activator of transcription 6	protein-coding
mm_169686.1	chr1	57377565	57377569	-	1	NA	promoter-TSS (NM_028546)	promoter-TSS (NM_028546)	-23	NR_037999	75323	Mm.362968	NR_037999	ENSMUSG00000097519	4930558J18Rik	-	RIKEN cDNA 4930558J18 gene	ncRNA
mm_49732.1	chr6	34709611	34709635	+	1	NA	5' UTR (NM_145575, exon 1 of 12)	5' UTR (NM_145575, exon 1 of 12)	179	NM_145575	109624	Mm.308134	NM_145575	ENSMUSG00000029761	Cald1	4833423D12Rik|AI195384|AV071549|AW536160|C920027I18Rik	caldesmon 1	protein-coding
mm_79854.1	chr9	64960815	64960843	+	1	NA	promoter-TSS (NM_001077631)	promoter-TSS (NM_001077631)	-3	NM_001077631	69882	Mm.272616	NM_175153	ENSMUSG00000034263	Vwa9	2010321M09Rik	von Willebrand factor A domain containing 9	protein-coding
mm_63413.1	chr7	127448627	127448644	+	1	NA	intron (NM_175163, intron 1 of 2)	CpG	523	NM_175163	71131	Mm.474533	NM_175163	ENSMUSG00000048921	Zfp689	4933416E05Rik|Znf689	zinc finger protein 689	protein-coding
mm_61429.1	chr7	73740336	73740402	+	1	NA	promoter-TSS (NM_001162532)	promoter-TSS (NM_001162532)	62	NM_001162532	100038347	Mm.425464	NM_001162532	ENSMUSG00000078670	Fam174b	-	family with sequence similarity 174, member B	protein-coding
mm_86850.1	chr10	21593152	21593181	+	1	NA	promoter-TSS (NR_027968)	promoter-TSS (NR_027968)	21	NR_027968	67692	Mm.54306	NM_183266	ENSMUSG00000050844	1700020N01Rik	-	RIKEN cDNA 1700020N01 gene	ncRNA
mm_163353.1	chr12	24830893	24830914	+	1	NA	promoter-TSS (NM_026037)	promoter-TSS (NM_026037)	-696	NM_026037	67216	Mm.167671	NM_026037	ENSMUSG00000020646	Mboat2	2810049G06Rik|AU022889|AW547221|LPCAT4|Moact2|Oact2	membrane bound O-acyltransferase domain containing 2	protein-coding
mm_170145.1	chr17	4403907	4403912	-	1	NA	Intergenic	RLTR10A|LTR|ERVK	-231071	NR_130984	75117	Mm.429393	NR_130984		4930517M08Rik	-	RIKEN cDNA 4930517M08 gene	ncRNA
mm_70680.1	chr8	14994648	14994658	+	1	NA	intron (NM_172751, intron 27 of 28)	intron (NM_172751, intron 27 of 28)	-16372	NM_029116	74901	Mm.46675	NM_029116	ENSMUSG00000055675	Kbtbd11	2900016B01Rik|4930465M17Rik|mKIAA0711	kelch repeat and BTB (POZ) domain containing 11	protein-coding
mm_48471.1	chr5	140936141	140936141	-	1	NA	intron (NM_175362, intron 1 of 24)	intron (NM_175362, intron 1 of 24)	64455	NM_175362	108723	Mm.46187	NM_175362	ENSMUSG00000036526	Card11	0610008L17Rik|2410011D02Rik|BIMP3|CARMA1	caspase recruitment domain family, member 11	protein-coding
mm_65134.1	chr7	19562123	19562166	-	1	NA	5' UTR (NM_199149, exon 1 of 13)	5' UTR (NM_199149, exon 1 of 13)	254	NM_199149	232947	Mm.219662	NM_199149	ENSMUSG00000051403	Ppp1r37	Gm158|Lrrc68	protein phosphatase 1, regulatory subunit 37	protein-coding
mm_42434.1	chr5	115429506	115429517	+	1	NA	promoter-TSS (NM_008629)	promoter-TSS (NM_008629)	-174	NM_008629	17690	Mm.5077	NM_008629	ENSMUSG00000054256	Msi1	Msi1h|Musahi1|m-Msi-1	musashi RNA-binding protein 1	protein-coding
mm_68294.1	chr7	105737239	105737275	-	1	NA	promoter-TSS (NM_025897)	promoter-TSS (NM_025897)	128	NM_133951	101867	Mm.231400	NM_025897	ENSMUSG00000030888	Rrp8	1500003O22Rik|2900001K19Rik|AW538116	ribosomal RNA processing 8, methyltransferase, homolog (yeast)	protein-coding
mm_119892.1	chr14	54937756	54937785	+	1	NA	intron (NM_029390, intron 1 of 3)	intron (NM_029390, intron 1 of 3)	1273	NM_029390	67272	Mm.41614	NM_026066	ENSMUSG00000040759	Cmtm5	1500005P16Rik|2900052H21Rik|Cklfsf5	CKLF-like MARVEL transmembrane domain containing 5	protein-coding
mm_97858.1	chr11	83116681	83116689	+	1	NA	promoter-TSS (NM_011407)	promoter-TSS (NM_011407)	-160	NM_011407	20555	Mm.10948	NM_011407	ENSMUSG00000078763	Slfn1	AV316259	schlafen 1	protein-coding
mm_119933.1	chr14	54970226	54970234	+	1	NA	TTS (NM_080728)	TTS (NM_080728)	1443	NR_033497	791403	Mm.319176	NR_033497	ENSMUSG00000097652	Mhrt	D830015G02Rik|ENSMUSG00000053118|Myheart	myosin heavy chain associated RNA transcript	ncRNA
mm_138620.1	chr17	35829969	35829991	+	1	NA	exon (NM_008027, exon 9 of 13)	exon (NM_008027, exon 9 of 13)	6623	NM_008027	14251	Mm.2931	NM_008027	ENSMUSG00000059714	Flot1	reggie-2	flotillin 1	protein-coding
mm_82661.1	chr9	22108228	22108244	-	1	NA	3' UTR (NM_009922, exon 7 of 7)	3' UTR (NM_009922, exon 7 of 7)	5777	NR_106052	102466221		NR_106052	ENSMUSG00000098646	Mir7084	Gm27978|mmu-mir-7084	microRNA 7084	ncRNA
mm_76691.1	chr8	94154145	94154146	-	1	NA	TTS (NM_013603)	TTS (NM_013603)	1538	NM_013603	17751	Mm.2064	NM_013603	ENSMUSG00000031760	Mt3	Mt-3	metallothionein 3	protein-coding
mm_9864.1	chr1	184845839	184845854	-	1	NA	promoter-TSS (NM_133684)	promoter-TSS (NM_133684)	1	NM_133684	67247	Mm.177724	NM_133684	ENSMUSG00000073481	Marc2	2810484M10Rik|Mosc2|mARC1	mitochondrial amidoxime reducing component 2	protein-coding
mm_163404.1	chr12	75308549	75308562	+	1	NA	5' UTR (NM_023275, exon 1 of 5)	5' UTR (NM_023275, exon 1 of 5)	242	NM_023275	80837	Mm.27467	NM_023275	ENSMUSG00000046768	Rhoj	1110005O19Rik|AW210585|Arhj|TC10L|TCL	ras homolog family member J	protein-coding
mm_114782.1	chr13	88824215	88824218	+	1	NA	intron (NM_010103, intron 1 of 9)	intron (NM_010103, intron 1 of 9)	2744	NM_001037987	13612	Mm.125580	NM_010103	ENSMUSG00000034488	Edil3	Del-1|Del1	EGF-like repeats and discoidin I-like domains 3	protein-coding
mm_25404.1	chr3	107278870	107278892	+	1	NA	promoter-TSS (NM_026774)	promoter-TSS (NM_026774)	23	NM_026774	68576	Mm.290035	NM_026774	ENSMUSG00000087260	Lamtor5	1110003H18Rik|Hbxip|XIP	late endosomal/lysosomal adaptor, MAPK and MTOR activator 5	protein-coding
mm_22633.1	chr3	14776220	14776238	+	1	NA	exon (NM_001083957, exon 3 of 7)	exon (NM_001083957, exon 3 of 7)	2231	NM_001083957	12346	Mm.273195	NM_009799	ENSMUSG00000027556	Car1	AW555628|Ca1|Car-1	carbonic anhydrase 1	protein-coding
mm_172050.1	chr6	128760290	128760298	+	1	NA	Intergenic	CpG	28347	NM_008527	17059	Mm.480764	NM_008527	ENSMUSG00000030325	Klrb1c	AI462337|CD161|Ly-59|Ly55c|Ly59|NK-RP1|NK1.1|NKR-P1.9|NKRP1|NKRP140|Nk-1|Nk-1.2|Nk1|Nk1.2|Nkrp1c|ly-55c	killer cell lectin-like receptor subfamily B member 1C	protein-coding
mm_132268.1	chr16	32877886	32877894	+	1	NA	5' UTR (NM_001159349, exon 1 of 8)	5' UTR (NM_001159349, exon 1 of 8)	106	NM_001159349	69823	Mm.12831	NM_027226	ENSMUSG00000022800	Fyttd1	2010005M05Rik|3830411L18Rik|3830421F13Rik|4933423A17Rik|AI098218|AW539567|C85190	forty-two-three domain containing 1	protein-coding
mm_80606.1	chr9	86743617	86743638	+	1	NA	promoter-TSS (NM_178738)	promoter-TSS (NM_178738)	-6	NM_178738	244954	Mm.257629	NM_178738	ENSMUSG00000033491	Prss35	6030424L22Rik|P3D9	protease, serine 35	protein-coding
mm_101676.1	chr11	39767832	39767837	-	1	NA	Intergenic	Intergenic	-377609	NR_126439	75315	Mm.461295	NR_126439		4930553C11Rik	-	RIKEN cDNA 4930553C11 gene	ncRNA
mm_15933.1	chr2	165595010	165595080	+	1	NA	promoter-TSS (NM_001271963)	promoter-TSS (NM_001271963)	17	NM_001271963	14049	Mm.282719	NM_010165	ENSMUSG00000017897	Eya2	Eab1	EYA transcriptional coactivator and phosphatase 2	protein-coding
mm_91653.1	chr10	42583580	42583595	-	1	NA	promoter-TSS (NM_152229)	promoter-TSS (NM_152229)	1	NM_152229	21907	Mm.287100	NM_152229	ENSMUSG00000019803	Nr2e1	Mtl1|Mtll|TLL|Tlx|XTLL|fierce|frc|tailless	nuclear receptor subfamily 2, group E, member 1	protein-coding
mm_26098.1	chr3	136935518	136935544	+	1	NA	3' UTR (NM_001293622, exon 13 of 13)	3' UTR (NM_001293622, exon 13 of 13)	265465	NM_001293622	19055	Mm.331389	NM_008913	ENSMUSG00000028161	Ppp3ca	2900074D19Rik|CN|Caln|Calna|CnA	protein phosphatase 3, catalytic subunit, alpha isoform	protein-coding
mm_10636.1	chr2	20355761	20355768	+	1	NA	intron (NM_001081006, intron 2 of 21)	intron (NM_001081006, intron 2 of 21)	65851	NM_001081006	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding
mm_1008.1	chr1	58726096	58726106	+	1	NA	intron (NM_009805, intron 1 of 4)	intron (NM_009805, intron 1 of 4)	-4451	NM_001293805	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_162990.1	chr11	23961608	23961609	+	1	NA	Intergenic	MERVL-int|LTR|ERVL	-66338	NM_172555	216578	Mm.470599	NM_172555	ENSMUSG00000020273	Papolg	9630006B20Rik	poly(A) polymerase gamma	protein-coding
mm_20875.1	chr2	148701206	148701216	-	1	NA	intron (NM_019632, intron 7 of 10)	intron (NM_019632, intron 7 of 10)	20091	NM_028986	74533	Mm.136913	NM_028986	ENSMUSG00000027439	Gzf1	8430437G08Rik|Zfp336|mGZF1	GDNF-inducible zinc finger protein 1	protein-coding
mm_113860.1	chr13	48031840	48031856	+	1	NA	Intergenic	Intergenic	-13240	NR_038004	70971	Mm.158514	NR_038004	ENSMUSG00000047324	4931429P17Rik	-	RIKEN cDNA 4931429P17 gene	ncRNA
mm_18060.1	chr2	39421124	39421144	-	1	NA	Intergenic	Intergenic	-194796	NM_024209	67857	Mm.389242	NM_024209	ENSMUSG00000026753	Ppp6c	2310003C10Rik	protein phosphatase 6, catalytic subunit	protein-coding
mm_147089.1	chr18	35648417	35648430	-	1	NA	intron (NM_027222, intron 1 of 3)	intron (NM_027222, intron 1 of 3)	944	NM_027222	69816	Mm.27252	NM_027222	ENSMUSG00000024353	Mzb1	2010001M09Rik|AV064572|PACAP|pERp1	marginal zone B and B1 cell-specific protein 1	protein-coding
mm_108610.1	chr12	85476488	85476495	+	1	NA	3' UTR (NM_010234, exon 4 of 4)	3' UTR (NM_010234, exon 4 of 4)	2590	NM_010234	14281	Mm.246513	NM_010234	ENSMUSG00000021250	Fos	D12Rfj1|c-fos|cFos	FBJ osteosarcoma oncogene	protein-coding
mm_79451.1	chr9	56119646	56119649	+	1	NA	intron (NM_011193, intron 3 of 14)	intron (NM_011193, intron 3 of 14)	29671	NM_011193	19200	Mm.2534	NM_011193	ENSMUSG00000032322	Pstpip1	CD2BP1|def-2	proline-serine-threonine phosphatase-interacting protein 1	protein-coding
mm_42239.1	chr5	113819390	113819457	+	1	NA	exon (NM_009151, exon 2 of 2)	exon (NM_009151, exon 2 of 2)	11078	NM_009151	20345	Mm.332590	NM_009151	ENSMUSG00000048163	Selplg	CD162|Psgl-1|Psgl1|Selp1|Selpl	selectin, platelet (p-selectin) ligand	protein-coding
mm_17457.1	chr2	28556747	28556758	-	1	NA	exon (NM_009885, exon 10 of 11)	exon (NM_009885, exon 10 of 11)	6651	NM_009885	12613	Mm.236017	NM_009885	ENSMUSG00000026818	Cel	1810036E18Rik|BAL	carboxyl ester lipase	protein-coding
mm_49556.1	chr6	30544987	30544997	+	1	NA	exon (NM_001024698, exon 3 of 11)	exon (NM_001024698, exon 3 of 11)	3350	NM_001024698	232680	Mm.268855	NM_001024698	ENSMUSG00000071553	Cpa2	-	carboxypeptidase A2, pancreatic	protein-coding
mm_151034.1	chr19	47015318	47015335	+	1	NA	promoter-TSS (NM_001164363)	promoter-TSS (NM_001164363)	-137	NM_001164363	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_66822.1	chr7	48658074	48658113	-	1	NA	Intergenic	Intergenic	-14292	NM_207537	404238	Mm.377926	NM_207537	ENSMUSG00000070546	Mrgprb3	MrgB3	MAS-related GPR, member B3	protein-coding
mm_104870.1	chr11	99405836	99405840	-	1	NA	Intergenic	Intergenic	16421	NM_010661	268482	Mm.436651	NM_010661	ENSMUSG00000020912	Krt12	AI835216|K12|Krt-12|Krt1-12	keratin 12	protein-coding
mm_70174.1	chr7	143649597	143649605	-	1	NA	promoter-TSS (NM_001311145)	promoter-TSS (NM_001311145)	63	NM_001311145	79202	Mm.261384	NM_023680	ENSMUSG00000010751	Tnfrsf22	2810028K06Rik|C130035G06Rik|SOBa|Tnfrh2|Tnfrsf1al2|mDcTrailr2	tumor necrosis factor receptor superfamily, member 22	protein-coding
mm_25167.1	chr3	103071196	103071199	+	1	NA	Intergenic	B1_Mur4|SINE|Alu	-2817	NM_001033303	229665	Mm.331272	NM_001033303	ENSMUSG00000070385	Ampd1	AI553520|Ampd-1	adenosine monophosphate deaminase 1	protein-coding
mm_62429.1	chr7	101361251	101361287	+	1	NA	intron (NM_001040111, intron 1 of 33)	intron (NM_001040111, intron 1 of 33)	13200	NM_001040111	69710	Mm.277687	NM_027180	ENSMUSG00000032812	Arap1	2410002L19Rik|Centd2|mKIAA0782	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	protein-coding
mm_131743.1	chr16	22096002	22096012	+	1	NA	intron (NM_183029, intron 2 of 15)	ORR1F|LTR|ERVL-MaLR	67292	NM_183029	319765	Mm.489442	NM_183029	ENSMUSG00000033581	Igf2bp2	C330012H03Rik|IMP-2|Imp2|Neilsen	insulin-like growth factor 2 mRNA binding protein 2	protein-coding
mm_65412.1	chr7	25245177	25245207	-	1	NA	exon (NM_010155, exon 4 of 4)	exon (NM_010155, exon 4 of 4)	5566	NM_010155	13875	Mm.8068	NM_010155	ENSMUSG00000040857	Erf	-	Ets2 repressor factor	protein-coding
mm_65255.1	chr7	19880285	19880327	-	1	NA	intron (NM_177036, intron 5 of 6)	B3A|SINE|B2	7659	NM_177036	319930	Mm.215839	NM_177036	ENSMUSG00000049848	Ceacam19	C130022P09Rik|CEAL1	carcinoembryonic antigen-related cell adhesion molecule 19	protein-coding
mm_79849.1	chr9	64822067	64822070	+	1	NA	intron (NM_001162917, intron 2 of 34)	intron (NM_001162917, intron 2 of 34)	11057	NM_001162917	102442	Mm.222473	NM_176935	ENSMUSG00000053641	Dennd4a	AI115600|AI851943|F730015K02Rik	DENN/MADD domain containing 4A	protein-coding
mm_167509.1	chr9	13324033	13324055	+	1	NA	Intergenic	Intergenic	77088	NM_025534	66396	Mm.290620	NM_025534	ENSMUSG00000079084	Ccdc82	2310043N13Rik	coiled-coil domain containing 82	protein-coding
mm_97732.1	chr11	80395536	80395548	+	1	NA	non-coding (NR_045038, exon 11 of 17)	non-coding (NR_045038, exon 11 of 17)	12263	NM_001130171	22680	Mm.401332	NM_011751	ENSMUSG00000017421	Zfp207	8430401D15Rik|BuGZ|Zep|Znf207	zinc finger protein 207	protein-coding
mm_16543.1	chr2	181689114	181689140	+	1	NA	exon (NM_026446, exon 6 of 6)	exon (NM_026446, exon 6 of 6)	2690	NM_001291205	56470	Mm.274366	NM_026446	ENSMUSG00000002458	Rgs19	2610042F04Rik|AI324841|AW547781|GAIP	regulator of G-protein signaling 19	protein-coding
mm_137022.1	chr17	17867056	17867062	+	1	NA	Intergenic	Intergenic	-11871	NM_008215	15116	Mm.255701	NM_008215	ENSMUSG00000003665	Has1	HAS	hyaluronan synthase1	protein-coding
mm_112372.1	chr12	119197701	119197706	-	1	NA	intron (NM_177290, intron 3 of 13)	intron (NM_177290, intron 3 of 13)	40573	NM_177290	320910	Mm.217000	NM_177290	ENSMUSG00000025321	Itgb8	4832412O06Rik	integrin beta 8	protein-coding
mm_53770.1	chr6	145934114	145934136	+	1	NA	promoter-TSS (NM_010656)	promoter-TSS (NM_010656)	-22	NM_010656	16651	Mm.49689	NM_010656	ENSMUSG00000030255	Sspn	Krag	sarcospan	protein-coding
mm_51462.1	chr6	82070731	82070751	+	1	NA	intron (NM_145570, intron 1 of 2)	intron (NM_145570, intron 1 of 2)	29113	NM_145570	232146	Mm.489683	NM_145570	ENSMUSG00000035104	Eva1a	BC014699|Fam176a|Tmem166	eva-1 homolog A (C. elegans)	protein-coding
mm_122158.1	chr14	31374595	31374607	-	1	NA	3' UTR (NM_001347585, exon 8 of 8)	3' UTR (NM_001347585, exon 8 of 8)	37877	NM_009796	12339	Mm.201535	NM_009796	ENSMUSG00000021893	Capn7	AU022319|PalBH	calpain 7	protein-coding
mm_599.1	chr1	39650728	39650738	+	1	NA	exon (NM_170597, exon 1 of 4)	exon (NM_170597, exon 1 of 4)	449	NM_170597	263764	Mm.122091	NM_170597	ENSMUSG00000050967	Creg2	A830098L22Rik	cellular repressor of E1A-stimulated genes 2	protein-coding
mm_136390.1	chr16	93142152	93142163	-	1	NA	Intergenic	Intergenic	211032	NR_040486	69857	Mm.81192	NR_040486	ENSMUSG00000100277	1810053B23Rik	1810008L18Rik|1810056K14Rik	RIKEN cDNA 1810053B23 gene	ncRNA
mm_137947.1	chr17	32878045	32878051	+	1	NA	Intergenic	Intergenic	13555	NM_207245	240066	Mm.26636	NM_207245	ENSMUSG00000095325	Zfp870	AI173952	zinc finger protein 870	protein-coding
mm_38610.1	chr4	141874880	141874953	-	1	NA	promoter-TSS (NM_025994)	promoter-TSS (NM_025994)	4	NM_025994	27984	Mm.395598	NM_025994	ENSMUSG00000040659	Efhd2	2600015J22Rik|AA408606|D4Wsu27e	EF hand domain containing 2	protein-coding
mm_47248.1	chr5	121572710	121572720	-	1	NA	exon (NM_001308450, exon 9 of 11)	exon (NM_001308450, exon 9 of 11)	21109	NM_009656	11669	Mm.284446	NM_009656	ENSMUSG00000029455	Aldh2	AHD-M1|ALDH-E2|ALDHI|Ahd-5|Ahd5	aldehyde dehydrogenase 2, mitochondrial	protein-coding
mm_92950.1	chr10	85184664	85184688	-	1	NA	5' UTR (NM_007771, exon 1 of 13)	5' UTR (NM_007771, exon 1 of 13)	378	NM_007771	12952	Mm.26237	NM_007771	ENSMUSG00000020038	Cry1	AU020726|AU021000|Phll1	cryptochrome 1 (photolyase-like)	protein-coding
mm_22352.1	chr2	180921016	180921022	-	1	NA	promoter-TSS (NM_173761)	promoter-TSS (NM_173761)	-83	NM_173761	228994	Mm.30205	NM_173761	ENSMUSG00000038848	Ythdf1	2210410K23Rik|8030473O16	YTH domain family 1	protein-coding
mm_46294.1	chr5	100416116	100416282	-	1	NA	promoter-TSS (NM_026969)	promoter-TSS (NM_026969)	35	NM_026969	69162	Mm.18634	NM_026969	ENSMUSG00000035325	Sec31a	1810024J13Rik|ABP125|ABP130|AU042160|HSPC275|Sec31l1	Sec31 homolog A (S. cerevisiae)	protein-coding
mm_91110.1	chr10	19185858	19185876	-	1	NA	intron (NR_038022, intron 1 of 1)	intron (NR_038022, intron 1 of 1)	18629	NR_038022	100504265	Mm.383417	NR_038021		Gm20139	-	predicted gene, 20139	ncRNA
mm_126258.1	chr15	79085576	79085595	+	1	NA	exon (NM_145139, exon 9 of 13)	exon (NM_145139, exon 9 of 13)	10362	NM_145139	223691	Mm.206404	NM_145139	ENSMUSG00000033047	Eif3l	0610011H21Rik|D15N1e|Eif3eip|Eif3ip|Eif3s6ip|HSP-66Y|PAF67	eukaryotic translation initiation factor 3, subunit L	protein-coding
mm_67066.1	chr7	67736525	67736547	-	1	NA	exon (NM_207663, exon 4 of 5)	exon (NM_207663, exon 4 of 5)	23206	NM_183312	233335	Mm.60526	NM_183312	ENSMUSG00000030554	Synm	4930412K21Rik|AI852401|Dmn|E130104F11|Syn|Synemin	synemin, intermediate filament protein	protein-coding
mm_168165.1	chr10	51490958	51490973	+	1	NA	promoter-TSS (NM_013532)	promoter-TSS (NM_013532)	67	NM_013532	14728	Mm.34408	NM_013532	ENSMUSG00000062593	Lilrb4a	CD85K|Gp49b|HM18|ILT3|LIR-5|Lilrb4|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4A	protein-coding
mm_136576.1	chr17	3482245	3482255	+	1	NA	promoter-TSS (NM_001286758)	promoter-TSS (NM_001286758)	-65	NM_001286758	24001	Mm.137134	NM_011878	ENSMUSG00000023800	Tiam2	3000002F19Rik|STEF|mKIAA2016	T cell lymphoma invasion and metastasis 2	protein-coding
mm_34672.1	chr4	150928020	150928035	+	1	NA	promoter-TSS (NM_001077509)	promoter-TSS (NM_001077509)	28	NM_001077509	21942	Mm.244187	NM_011612	ENSMUSG00000028965	Tnfrsf9	4-1BB|A930040I11Rik|AA408498|AI325004|CDw137|Cd137|ILA|Ly63	tumor necrosis factor receptor superfamily, member 9	protein-coding
mm_138863.1	chr17	43016510	43016518	+	1	NA	promoter-TSS (NM_178589)	promoter-TSS (NM_178589)	-41	NM_178589	94185	Mm.200792	NM_178589	ENSMUSG00000023915	Tnfrsf21	AA959878|DR6|R74815|TR7	tumor necrosis factor receptor superfamily, member 21	protein-coding
mm_65837.1	chr7	29232452	29232471	-	1	NA	promoter-TSS (NM_001033525)	promoter-TSS (NM_001033525)	61	NM_001033525	52150	Mm.24877	NM_001033525	ENSMUSG00000046410	Kcnk6	D7Ertd764e|Toss|Twik2	potassium inwardly-rectifying channel, subfamily K, member 6	protein-coding
mm_73810.1	chr8	117342671	117342673	+	1	NA	intron (NM_001163262, intron 1 of 20)	intron (NM_001163262, intron 1 of 20)	-6498	NM_028941	74440	Mm.233181	NM_028941	ENSMUSG00000034390	Cmip	4933407C03Rik|5830471E12Rik|AI314065|AI464126	c-Maf inducing protein	protein-coding
mm_169431.1	chr14	53763105	53763109	+	1	NA	Intergenic	Intergenic	490822	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_147227.1	chr18	38209643	38209670	-	1	NA	5' UTR (NM_029357, exon 1 of 3)	5' UTR (NM_029357, exon 1 of 3)	106	NM_029357	75599	Mm.36560	NM_029357	ENSMUSG00000051375	Pcdh1	2010005A06Rik|AI585920	protocadherin 1	protein-coding
mm_12232.1	chr2	68568578	68568584	+	1	NA	Intergenic	Intergenic	-13832	NM_177651	227998	Mm.67562	NM_177651	ENSMUSG00000053896	4933409G03Rik	-	RIKEN cDNA 4933409G03 gene	protein-coding
mm_31049.1	chr4	41135995	41136069	+	1	NA	promoter-TSS (NM_026275)	promoter-TSS (NM_026275)	11	NM_026275	67615	Mm.389540	NM_026275	ENSMUSG00000036241	Ube2r2	1200003M11Rik|Cdc34b|Ubc3b	ubiquitin-conjugating enzyme E2R 2	protein-coding
mm_123754.1	chr14	70196028	70196034	-	1	NA	intron (NM_001271408, intron 5 of 20)	intron (NM_001271408, intron 5 of 20)	-3785	NM_001271409	20410	Mm.5068	NM_011366	ENSMUSG00000022091	Sorbs3	SCAM-1|SH3P3|Sh3d4|vinexin-g	sorbin and SH3 domain containing 3	protein-coding
mm_149466.1	chr19	11536770	11536846	+	1	NA	promoter-TSS (NM_025658)	promoter-TSS (NM_025658)	-41	NM_025658	66607	Mm.441056	NM_025658	ENSMUSG00000024678	Ms4a4d	2210417J23Rik	membrane-spanning 4-domains, subfamily A, member 4D	protein-coding
mm_134308.1	chr16	15863224	15863238	-	1	NA	promoter-TSS (NM_029354)	promoter-TSS (NM_029354)	91	NM_029354	72083	Mm.22351	NM_029354	ENSMUSG00000022671	Mzt2	2410018G20Rik|2610001E06Rik|Fam128|Fam128b	mitotic spindle organizing protein 2	protein-coding
mm_156713.1	chrX	159627548	159627558	+	1	NA	5' UTR (NM_001135727, exon 1 of 18)	5' UTR (NM_001135727, exon 1 of 18)	281	NM_001135727	58194	Mm.286495	NM_021389	ENSMUSG00000040990	Sh3kbp1	1200007H22Rik|1700125L08Rik|5830464D22Rik|AI447724|Cin85|IN85|Ruk|Seta	SH3-domain kinase binding protein 1	protein-coding
mm_32217.1	chr4	101647743	101647762	+	1	NA	promoter-TSS (NM_175036)	promoter-TSS (NM_175036)	-31	NM_175036	230514	Mm.4756	NM_175036	ENSMUSG00000035212	Leprot	LEPR|OB-RGRP|Obrgrp|VPS55	leptin receptor overlapping transcript	protein-coding
mm_148144.1	chr18	77047283	77047313	-	1	NA	promoter-TSS (NM_027721)	promoter-TSS (NM_027721)	-2	NM_027721	71206	Mm.35803	NM_027721	ENSMUSG00000025420	Katnal2	3110023G01Rik|4933439B08Rik	katanin p60 subunit A-like 2	protein-coding
mm_9509.1	chr1	173738895	173738919	-	1	NA	intron (NM_001204910, intron 1 of 7)	L1MA4|LINE|L1	2902	NM_001204910	226691	Mm.440876	NM_001204910	ENSMUSG00000073490	Ifi207	AI607873|Pyhin-A	interferon activated gene 207	protein-coding
mm_149844.1	chr19	25044587	25044598	+	1	NA	intron (NM_028785, intron 1 of 47)	MTD|LTR|ERVL-MaLR	45063	NM_028785	76088	Mm.102485	NM_028785	ENSMUSG00000052085	Dock8	1200017A24Rik|5830472H07Rik|A130095G14Rik|AI461977	dedicator of cytokinesis 8	protein-coding
mm_30810.1	chr4	20042135	20042141	+	1	NA	promoter-TSS (NM_010281)	promoter-TSS (NM_010281)	86	NM_010281	14590	Mm.20461	NM_010281	ENSMUSG00000073987	Ggh	gamma-GH	gamma-glutamyl hydrolase	protein-coding
mm_139072.1	chr17	46650576	46650589	+	1	NA	TTS (NM_001316742)	TTS (NM_001316742)	244	NM_025611	66515	Mm.329078	NM_025611	ENSMUSG00000038545	Cul7	2510004L20Rik|AA409809|C230011P08Rik|p185|p193	cullin 7	protein-coding
mm_165308.1	chr2	101797649	101797653	-	1	NA	promoter-TSS (NM_001083810)	promoter-TSS (NM_001083810)	56	NM_175181	72446	Mm.24138	NM_175181	ENSMUSG00000032841	Prr5l	2600010E01Rik|4833411O04Rik|Protor-2|Protor2	proline rich 5 like	protein-coding
mm_104493.1	chr11	95835346	95835352	-	1	NA	intron (NM_025659, intron 3 of 7)	intron (NM_025659, intron 3 of 7)	-6946	NM_023121	14710	Mm.46299	NM_023121	ENSMUSG00000038811	Gngt2	AV096488	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 2	protein-coding
mm_64107.1	chr7	141051647	141051676	+	1	NA	Intergenic	Intergenic	-9613	NM_177897	330671	Mm.133741	NM_177897	ENSMUSG00000055629	B4galnt4	BC038881|Gm1095|beta4GalNAcT4	beta-1,4-N-acetyl-galactosaminyl transferase 4	protein-coding
mm_170729.1	chr2	15125335	15125340	+	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	69975	NM_029466	75869	Mm.174068	NM_029466	ENSMUSG00000017418	Arl5b	4930587A11Rik|AW146430|Arl8	ADP-ribosylation factor-like 5B	protein-coding
mm_21919.1	chr2	166825112	166825118	-	1	NA	intron (NM_001085495, intron 1 of 38)	intron (NM_001085495, intron 1 of 38)	19534	NM_001085495	99371	Mm.297192	NM_001085495	ENSMUSG00000074582	Arfgef2	AI463430|AW493672|BIG2|E230011G24Rik	ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited)	protein-coding
mm_5986.1	chr1	58424043	58424064	-	1	NA	promoter-TSS (NM_001042634)	promoter-TSS (NM_001042634)	35	NR_027853	12747	Mm.1761	NM_009905	ENSMUSG00000026034	Clk1	STY	CDC-like kinase 1	protein-coding
mm_56996.1	chr6	120971610	120971638	-	1	NA	intron (NM_001270475, intron 21 of 31)	intron (NM_001270475, intron 21 of 31)	12780	NR_138099	215458	Mm.122399	NR_138099		LOC215458	-	uncharacterized LOC215458	ncRNA
mm_164380.1	chr16	31234388	31234403	+	1	NA	intron (NR_035427, intron 1 of 2)	intron (NR_035427, intron 1 of 2)	-33157	NM_030138	78618	Mm.274646	NM_030138	ENSMUSG00000049076	Acap2	4832442G16|9530039J15Rik|CNT-B2|Centb2|mKIAA0041	ArfGAP with coiled-coil, ankyrin repeat and PH domains 2	protein-coding
mm_62469.1	chr7	101765493	101765493	+	1	NA	intron (NM_009191, intron 7 of 15)	intron (NM_009191, intron 7 of 15)	-52820	NM_008887	11859	Mm.5028	NM_008887	ENSMUSG00000007946	Phox2a	Arix|Phox2|Pmx2|Pmx2a|Px2a	paired-like homeobox 2a	protein-coding
mm_166956.1	chr7	44477377	44477379	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	7031	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_114015.1	chr13	52610931	52610957	+	1	NA	exon (NM_011518, exon 2 of 14)	exon (NM_011518, exon 2 of 14)	14062	NM_011518	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_9396.1	chr1	172219833	172219876	-	1	NA	promoter-TSS (NM_009813)	promoter-TSS (NM_009813)	41	NM_009813	12372	Mm.12829	NM_009813	ENSMUSG00000007122	Casq1	CSQ|CSQ-1|CSQ1|sCSQ	calsequestrin 1	protein-coding
mm_114390.1	chr13	63272597	63272600	+	1	NA	intron (NR_110520, intron 2 of 5)	intron (NR_110520, intron 2 of 5)	24549	NR_045794	100504114	Mm.437070	NR_045794	ENSMUSG00000097242	Gm16907	-	predicted gene, 16907	ncRNA
mm_4604.1	chr1	178448607	178448615	+	1	NA	intron (NM_026626, intron 2 of 6)	L2a|LINE|L2	42730	NM_026626	68226	Mm.252132	NM_026626	ENSMUSG00000026495	Efcab2	1700073K01Rik|D830011E08Rik	EF-hand calcium binding domain 2	protein-coding
mm_91236.1	chr10	22302825	22302856	-	1	NA	intron (NM_009018, intron 5 of 5)	intron (NM_009018, intron 5 of 5)	-3880	NR_015465	606736	Mm.387042	NR_015465	ENSMUSG00000097352	C920009B18Rik	-	RIKEN cDNA C920009B18 gene	ncRNA
mm_23974.1	chr3	85914604	85914604	+	1	NA	Intergenic	Intergenic	-27086	NM_177130	320302	Mm.482978	NM_177130	ENSMUSG00000031286	Glt28d2	4732486J07Rik|Glt28d1l	glycosyltransferase 28 domain containing 2	protein-coding
mm_165823.1	chr3	149423771	149423775	+	1	NA	Intergenic	Intergenic	149036	NR_040591	381482	Mm.393866	NR_040591		Gm1653	-	predicted gene 1653	ncRNA
mm_36754.1	chr4	101265215	101265231	-	1	NA	promoter-TSS (NM_146145)	promoter-TSS (NM_146145)	59	NM_146145	16451	Mm.289657	NM_146145	ENSMUSG00000028530	Jak1	AA960307|BAP004|C130039L05Rik	Janus kinase 1	protein-coding
mm_54464.1	chr6	34903364	34903368	-	1	NA	intron (NM_001013366, intron 6 of 14)	intron (NM_001013366, intron 6 of 14)	7465	NM_001013366	101240	Mm.152120	NM_001013366	ENSMUSG00000058486	Wdr91	9530020G05Rik|AI987683|AU018665	WD repeat domain 91	protein-coding
mm_131040.1	chr16	3884688	3884709	+	1	NA	promoter-TSS (NM_001290689)	promoter-TSS (NM_001290689)	79	NM_001290689	74763	Mm.28403	NM_029090	ENSMUSG00000005982	Naa60	1200013P24Rik|AI315146|Nat15	N(alpha)-acetyltransferase 60, NatF catalytic subunit	protein-coding
mm_21691.1	chr2	164444075	164444085	-	1	NA	promoter-TSS (NM_011521)	promoter-TSS (NM_011521)	-892	NM_011521	20971	Mm.3815	NM_011521	ENSMUSG00000017009	Sdc4	AA959608|AW108331|S4|Synd4|ryudocan|syndecan-4	syndecan 4	protein-coding
mm_69363.1	chr7	130547257	130547270	-	1	NA	exon (NM_001162855, exon 1 of 11)	exon (NM_001162855, exon 1 of 11)	118	NM_001162855	67872	Mm.21714	NM_001162855	ENSMUSG00000040331	Nsmce4a	2410003A14Rik	NSE4 homolog A, SMC5-SMC6 complex component	protein-coding
mm_105892.1	chr11	114934352	114934377	-	1	NA	promoter-TSS (NM_199221)	promoter-TSS (NM_199221)	22	NM_001347651	217304	Mm.185355	NM_199221	ENSMUSG00000063193	Cd300lb	CLM-7|Clm7|Gm253|LMIR5	CD300 molecule like family member B	protein-coding
mm_154803.1	chrX	13297590	13297600	+	1	NA	Intergenic	RLTR9A|LTR|ERVK	16573	NM_010028	13205	Mm.289662	NM_010028	ENSMUSG00000000787	Ddx3x	D1Pas1-rs2|Ddx3|Fin14	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 3, X-linked	protein-coding
mm_135384.1	chr16	44140522	44140556	-	1	NA	intron (NM_028108, intron 1 of 4)	intron (NM_028108, intron 1 of 4)	730	NM_028108	72117	Mm.278726	NM_028108	ENSMUSG00000022698	Naa50	2600005K24Rik|2810441M03Rik|AW112078|Mak3|Mak3p|Nat13|Nat5|San	N(alpha)-acetyltransferase 50, NatE catalytic subunit	protein-coding
mm_145557.1	chr18	60812168	60812178	+	1	NA	promoter-TSS (NR_039567)	promoter-TSS (NR_039567)	97	NR_039567	100628611		NR_039567	ENSMUSG00000093327	Mir5107	mir-5107|mmu-mir-5107|mu-mir-5107	microRNA 5107	ncRNA
mm_34093.1	chr4	138834921	138834938	+	1	NA	non-coding (NR_002926, exon 5 of 5)	non-coding (NR_002926, exon 5 of 5)	3053	NM_001082531	18780	Mm.4675	NM_011108	ENSMUSG00000058908	Pla2g2a	EF|Mom1|Pla2|sPLA2|sPla2-IIA	phospholipase A2, group IIA (platelets, synovial fluid)	protein-coding
mm_125454.1	chr15	52039956	52039965	+	1	NA	promoter-TSS (NM_175503)	promoter-TSS (NM_175503)	-147	NM_175503	239435	Mm.24204	NM_175503	ENSMUSG00000068522	Aard	A5D3|AV328152	alanine and arginine rich domain containing protein	protein-coding
mm_870.1	chr1	52152352	52152358	+	1	NA	exon (NM_001205314, exon 21 of 25)	exon (NM_001205314, exon 21 of 25)	32733	NM_001205313	20846	Mm.277406	NM_009283	ENSMUSG00000026104	Stat1	2010005J02Rik|AA408197	signal transducer and activator of transcription 1	protein-coding
mm_130970.1	chr15	103323430	103323446	-	1	NA	intron (NM_013866, intron 2 of 7)	CpG	-13000	NM_030720	80910	Mm.160369	NM_030720	ENSMUSG00000063234	Gpr84	EX33	G protein-coupled receptor 84	protein-coding
mm_81987.1	chr9	121415953	121415961	+	1	NA	intron (NM_175114, intron 2 of 15)	intron (NM_175114, intron 2 of 15)	48999	NM_175114	67095	Mm.491112	NM_175114	ENSMUSG00000032536	Trak1	2310001H13Rik|AI413908|AI467545|hyrt|mKIAA1042	trafficking protein, kinesin binding 1	protein-coding
mm_112070.1	chr12	112511104	112511135	-	1	NA	promoter-TSS (NM_178915)	promoter-TSS (NM_178915)	41	NM_178915	104885	Mm.37751	NM_178915	ENSMUSG00000054013	Tmem179	AI839735	transmembrane protein 179	protein-coding
mm_119607.1	chr14	51096416	51096423	+	1	NA	5' UTR (NM_201239, exon 1 of 2)	5' UTR (NM_201239, exon 1 of 2)	419	NM_201239	58809	Mm.202665	NM_021472	ENSMUSG00000021876	Rnase4	C730049F20Rik|Rab1	ribonuclease, RNase A family 4	protein-coding
mm_30804.1	chr4	20028713	20028720	+	1	NA	3' UTR (NM_015767, exon 5 of 5)	3' UTR (NM_015767, exon 5 of 5)	-13336	NM_010281	14590	Mm.20461	NM_010281	ENSMUSG00000073987	Ggh	gamma-GH	gamma-glutamyl hydrolase	protein-coding
mm_40780.1	chr5	67306942	67306977	+	1	NA	promoter-TSS (NM_178651)	promoter-TSS (NM_178651)	4	NM_001310629	109108	Mm.234455	NM_178651	ENSMUSG00000029221	Slc30a9	2310024J23Rik|AL024256|GAC63|HUEL|znT-9	solute carrier family 30 (zinc transporter), member 9	protein-coding
mm_15864.1	chr2	164832960	164832970	+	1	NA	promoter-TSS (NM_008906)	promoter-TSS (NM_008906)	93	NM_001038492	19025	Mm.359633	NM_008906	ENSMUSG00000017760	Ctsa	AU019505|PPCA|Ppgb	cathepsin A	protein-coding
mm_79378.1	chr9	54764558	54764583	+	1	NA	promoter-TSS (NM_001284507)	promoter-TSS (NM_001284507)	-178	NM_001284507	12903	Mm.34797	NM_013496	ENSMUSG00000032291	Crabp1	AI326249|CRABP-I|Crabp-1|CrabpI|Rbp-5	cellular retinoic acid binding protein I	protein-coding
mm_106786.1	chr12	4769152	4769165	+	1	NA	promoter-TSS (NM_028376)	promoter-TSS (NM_028376)	109	NM_175431	207921	Mm.184898	NM_175431	ENSMUSG00000050545	Fam228b	A830093I24Rik	family with sequence similarity 228, member B	protein-coding
mm_8182.1	chr1	138080877	138080893	-	1	NA	exon (NM_001268286, exon 20 of 29)	exon (NM_001268286, exon 20 of 29)	94241	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_14553.1	chr2	133552219	133552237	+	1	NA	promoter-TSS (NM_007553)	promoter-TSS (NM_007553)	69	NM_007553	12156	Mm.103205	NM_007553	ENSMUSG00000027358	Bmp2	AI467020|Bmp2a	bone morphogenetic protein 2	protein-coding
mm_41965.1	chr5	107055175	107055201	+	1	NA	Intergenic	Intergenic	90627	NM_001271566	12545	Mm.20842	NM_009863	ENSMUSG00000029283	Cdc7	AI597260|Cdc7l1|muCdc7	cell division cycle 7 (S. cerevisiae)	protein-coding
mm_104233.1	chr11	88689915	88689956	-	1	NA	intron (NM_001201341, intron 5 of 7)	intron (NM_001201341, intron 5 of 7)	28294	NM_054043	76626	Mm.400451	NM_054043	ENSMUSG00000069769	Msi2	1700105C15Rik|AI451722|AI563628|AW489193|Msi2h	musashi RNA-binding protein 2	protein-coding
mm_156914.1	chrX	169082608	169082646	+	1	NA	intron (NR_109847, intron 1 of 14)	intron (NR_109847, intron 1 of 14)	-30251	NM_001287530	11856	Mm.441810	NM_009707	ENSMUSG00000031355	Arhgap6	AI504284|RhoGAPX-1	Rho GTPase activating protein 6	protein-coding
mm_158648.1	chrX	155504939	155504947	-	1	NA	Intergenic	Intergenic	118384	NM_001093750	211612	Mm.218811	NM_001093750	ENSMUSG00000041552	Ptchd1	9630036J22Rik|AI848149|Gm387	patched domain containing 1	protein-coding
mm_155317.1	chrX	62222511	62222519	+	1	NA	Intergenic	Intergenic	-60984	NM_001199997	74437	Mm.85792	NM_001199996	ENSMUSG00000045330	4933402E13Rik	-	RIKEN cDNA 4933402E13 gene	protein-coding
mm_11934.1	chr2	52619736	52619746	+	1	NA	intron (NM_001285426, intron 2 of 13)	intron (NM_001285426, intron 2 of 13)	56118	NM_001285428	12298	Mm.330223	NM_146123	ENSMUSG00000017412	Cacnb4	3110038O15Rik|Cchb4|lh	calcium channel, voltage-dependent, beta 4 subunit	protein-coding
mm_75078.1	chr8	33886751	33886752	-	1	NA	intron (NM_001042674, intron 1 of 7)	intron (NM_001042674, intron 1 of 7)	43112	NM_019733	19663	Mm.323997	NM_019733	ENSMUSG00000031586	Rbpms	2010300K22Rik|2700019M19Rik|AU017537|RBP-MS|hermes	RNA binding protein gene with multiple splicing	protein-coding
mm_121690.1	chr14	13961187	13961199	-	1	NA	exon (NM_025435, exon 1 of 8)	exon (NM_025435, exon 1 of 8)	120	NM_001285780	66231	Mm.295875	NM_025435	ENSMUSG00000053453	Thoc7	Nif3l1bp1	THO complex 7	protein-coding
mm_115126.1	chr13	104287453	104287466	+	1	NA	promoter-TSS (NM_001081020)	promoter-TSS (NM_001081020)	-376	NR_136938	108154	Mm.208125	NM_175496	ENSMUSG00000046169	Adamts6	A930019D11Rik|ADAM-TS6|b2b1879.1Clo|b2b2029Clo|b2b2182Clo|b2b2187.1Clo|b2b2228Clo	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 6	protein-coding
mm_110641.1	chr12	58268841	58268906	-	1	NA	5' UTR (NM_025809, exon 1 of 1)	5' UTR (NM_025809, exon 1 of 1)	385	NM_025809	66864	Mm.280563	NM_025809	ENSMUSG00000045930	Clec14a	1200003C23Rik|AI642649	C-type lectin domain family 14, member a	protein-coding
mm_154943.1	chrX	36195951	36195959	+	1	NA	promoter-TSS (NM_028325)	promoter-TSS (NM_028325)	51	NM_028325	72693	Mm.297698	NM_028325	ENSMUSG00000036699	Zcchc12	2810028A01Rik|AV136720|Sizn1	zinc finger, CCHC domain containing 12	protein-coding
mm_127109.1	chr15	97869647	97869684	+	1	NA	exon (NM_009504, exon 5 of 10)	exon (NM_009504, exon 5 of 10)	-25163	NM_001204278	56233	Mm.384027	NM_019572	ENSMUSG00000022475	Hdac7	5830434K02Rik|HD7|HD7a|Hdac7a|mFLJ00062	histone deacetylase 7	protein-coding
mm_65721.1	chr7	28379248	28379263	-	1	NA	promoter-TSS (NM_011756)	promoter-TSS (NM_011756)	-27	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_65889.1	chr7	29953871	29953900	-	1	NA	Intergenic	CpG	-1992	NM_178384	72723	Mm.371648	NM_178384	ENSMUSG00000059975	Zfp74	2810054M15Rik|KRAB8|Zfp66|Znf569|mszf21|mszf77	zinc finger protein 74	protein-coding
mm_15854.1	chr2	164777943	164777965	+	1	NA	exon (NM_009394, exon 3 of 6)	exon (NM_009394, exon 3 of 6)	1780	NM_009394	21925	Mm.1716	NM_009394	ENSMUSG00000017300	Tnnc2	Tncs	troponin C2, fast	protein-coding
mm_167490.1	chr9	6953272	6953280	+	1	NA	intron (NM_029851, intron 85 of 88)	Lx8b|LINE|L1	223770	NM_029851	110350	Mm.237596	NM_029851	ENSMUSG00000047193	Dync2h1	4432416O06Rik|AI448217|D030010H02Rik|D330044F14Rik|DHC1b|DHC2|Dnchc2|b2b414Clo|mKIAA1997	dynein cytoplasmic 2 heavy chain 1	protein-coding
mm_93573.1	chr10	116581517	116581525	-	1	NA	promoter-TSS (NM_028082)	promoter-TSS (NM_028082)	-10	NM_001037846	72068	Mm.351553	NM_028082	ENSMUSG00000020166	Cnot2	2600016M12Rik|2810470K03Rik|AA537049|AA959607|AW557563|C79650	CCR4-NOT transcription complex, subunit 2	protein-coding
mm_92543.1	chr10	79711529	79711553	-	1	NA	exon (NM_001077184, exon 7 of 7)	exon (NM_001077184, exon 7 of 7)	-5093	NM_008226	15166	Mm.12956	NM_008226	ENSMUSG00000020331	Hcn2	BCNG2|HAC1|trls	hyperpolarization-activated, cyclic nucleotide-gated K+ 2	protein-coding
mm_76930.1	chr8	105937027	105937042	-	1	NA	intron (NM_013640, intron 4 of 7)	intron (NM_013640, intron 4 of 7)	1358	NM_013640	19171	Mm.787	NM_013640	ENSMUSG00000031897	Psmb10	Mecl-1|Mecl1	proteasome (prosome, macropain) subunit, beta type 10	protein-coding
mm_1419.1	chr1	67165445	67165493	+	1	NA	exon (NM_001080809, exon 14 of 38)	exon (NM_001080809, exon 14 of 38)	42442	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_68812.1	chr7	125605810	125605835	-	1	NA	intron (NM_021887, intron 1 of 8)	intron (NM_021887, intron 1 of 8)	2393	NM_021887	60504	Mm.155643	NM_021887	ENSMUSG00000030745	Il21r	NILR	interleukin 21 receptor	protein-coding
mm_66218.1	chr7	34389700	34389720	-	1	NA	promoter-TSS (NM_025948)	promoter-TSS (NM_025948)	-170	NM_025948	67070	Mm.276503	NM_025948	ENSMUSG00000066568	Lsm14a	2700023B17Rik|AA407828|AU017544|Tral	LSM14A mRNA processing body assembly factor	protein-coding
mm_109315.1	chr12	109561202	109561212	+	1	NA	non-coding (NR_003633, exon 5 of 5)	non-coding (NR_003633, exon 5 of 5)	-2485	NR_030427	791079		NR_030427	ENSMUSG00000076451	Mir770	Mirn770|mir-770|mmu-mir-770	microRNA 770	ncRNA
mm_417.1	chr1	34238095	34238106	+	1	NA	intron (NM_001276764, intron 60 of 102)	intron (NM_001276764, intron 60 of 102)	77770	NM_010081	13518	Mm.336625	NM_010081	ENSMUSG00000026131	Dst	2310001O04Rik|A830042E19Rik|AW554249|BP230|BPAG1-n|Bpag|Bpag1|Macf2|ah|athetoid|dt|mKIAA0728|nmf203|nmf339	dystonin	protein-coding
mm_153116.1	chr19	33177181	33177182	-	1	NA	intron (NM_001167818, intron 5 of 6)	intron (NM_001167818, intron 5 of 6)	215114	NM_001167818	67795	Mm.204591	NM_001146342	ENSMUSG00000071573	Rnls	6530404N21Rik|AI452315|AW060440|C10orf59	renalase, FAD-dependent amine oxidase	protein-coding
mm_60106.1	chr7	35416343	35416370	+	1	NA	intron (NM_028120, intron 6 of 18)	intron (NM_028120, intron 6 of 18)	19263	NM_028120	72140	Mm.133263	NM_028120	ENSMUSG00000023072	Cep89	2610507L03Rik|Ccdc123	centrosomal protein 89	protein-coding
mm_32976.1	chr4	120097901	120097947	+	1	NA	exon (NM_010657, exon 4 of 9)	exon (NM_010657, exon 4 of 9)	-63282	NM_007902	13615	Mm.284855	NM_007902	ENSMUSG00000028635	Edn2	ET-2|PPET2|VIC	endothelin 2	protein-coding
mm_99455.1	chr11	102434445	102434471	+	1	NA	exon (NM_008175, exon 7 of 13)	exon (NM_008175, exon 7 of 13)	4136	NM_008175	14824	Mm.1568	NM_008175	ENSMUSG00000034708	Grn	Pgrn|epithelin	granulin	protein-coding
mm_96469.1	chr11	67646595	67646607	+	1	NA	intron (NM_001109657, intron 4 of 13)	B4A|SINE|B4	-48725	NM_009038	19674	Mm.439726	NM_009038	ENSMUSG00000020907	Rcvrn	CAR|S-modulin	recoverin	protein-coding
mm_96958.1	chr11	70639119	70639175	+	1	NA	promoter-TSS (NM_010326)	promoter-TSS (NM_010326)	25	NM_010326	14723	Mm.377085	NM_010326	ENSMUSG00000050675	Gp1ba	GPIba|GPIbalpha	glycoprotein 1b, alpha polypeptide	protein-coding
mm_55210.1	chr6	52218687	52218716	-	1	NA	promoter-TSS (NM_010455)	promoter-TSS (NM_010455)	-128	NM_010455	15404	Mm.294826	NM_010455	ENSMUSG00000038236	Hoxa7	AV118143|Hox-1.1|M6	homeobox A7	protein-coding
mm_38270.1	chr4	136880781	136880800	-	1	NA	exon (NM_009777, exon 3 of 3)	exon (NM_009777, exon 3 of 3)	5387	NM_009777	12260	Mm.2570	NM_009777	ENSMUSG00000036905	C1qb	-	complement component 1, q subcomponent, beta polypeptide	protein-coding
mm_82507.1	chr9	20481722	20481755	-	1	NA	intron (NM_146221, intron 1 of 6)	intron (NM_146221, intron 1 of 6)	11008	NM_146221	235028	Mm.297660	NM_146221	ENSMUSG00000059475	Zfp426	2900057C04Rik|KRAB1|Zfo61|Zfp68-rs1|Znf426|mKIAA4237	zinc finger protein 426	protein-coding
mm_59861.1	chr7	30095151	30095192	+	1	NA	promoter-TSS (NM_011981)	promoter-TSS (NM_011981)	95	NM_011981	26466	Mm.195092	NM_011981	ENSMUSG00000049421	Zfp260	AI480997|Ozrf1|PEX1|Zfp63|Znf260	zinc finger protein 260	protein-coding
mm_49034.1	chr6	4759876	4759886	+	1	NA	3' UTR (NM_130877, exon 2 of 2)	3' UTR (NM_130877, exon 2 of 2)	12575	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_72769.1	chr8	85730811	85730828	+	1	NA	intron (NM_028007, intron 14 of 17)	intron (NM_028007, intron 14 of 17)	29914	NR_106189	102465898		NR_106189	ENSMUSG00000098388	Mir8109	Gm27495|mmu-mir-8109	microRNA 8109	ncRNA
mm_28806.1	chr3	96245218	96245222	-	1	NA	promoter-TSS (NM_178212).2	promoter-TSS (NM_178212).2	-237	NM_178212	319192	Mm.5220	NM_178212	ENSMUSG00000063954	Hist2h2aa2	H2a-614|H2a-615	histone cluster 2, H2aa2	protein-coding
mm_127700.1	chr15	102990936	102990940	+	1	NA	exon (NM_010466, exon 1 of 2)	exon (NM_010466, exon 1 of 2)	399	NM_010466	15426	Mm.6167	NM_010466	ENSMUSG00000001657	Hoxc8	D130011F21Rik|Hox-3.1	homeobox C8	protein-coding
mm_120475.1	chr14	65974924	65974978	+	1	NA	exon (NM_013492, exon 4 of 9)	exon (NM_013492, exon 4 of 9)	6468	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_17887.1	chr2	34963745	34963751	-	1	NA	Intergenic	Intergenic	-1976	NM_001326601	22029	Mm.239514	NM_009421	ENSMUSG00000026875	Traf1	4732496E14Rik	TNF receptor-associated factor 1	protein-coding
mm_100479.1	chr11	120230076	120230098	+	1	NA	Intergenic	Intergenic	-2860	NM_001347621	268515	Mm.309498	NM_198423	ENSMUSG00000039741	Bahcc1	B930044J06|BC060615	BAH domain and coiled-coil containing 1	protein-coding
mm_135970.1	chr16	74961140	74961143	-	1	NA	Intergenic	Intergenic	-550229	NM_175549	268902	Mm.171736	NM_175549	ENSMUSG00000052516	Robo2	2600013A04Rik|9430089E08Rik|BB097918|D230004I22Rik|mKIAA1568	roundabout guidance receptor 2	protein-coding
mm_36306.1	chr4	68954430	68954438	-	1	NA	promoter-TSS (NM_019967)	promoter-TSS (NM_019967)	-37	NM_019967	56710	Mm.248788	NM_019967	ENSMUSG00000028351	Brinp1	BRINP|Dbc1|Dbccr1|Fam5a	bone morphogenic protein/retinoic acid inducible neural specific 1	protein-coding
mm_33789.1	chr4	134923980	134923999	+	1	NA	exon (NM_023665, exon 2 of 5)	exon (NM_023665, exon 2 of 5)	364	NM_023665	27981	Mm.331964	NM_023665	ENSMUSG00000037266	Rsrp1	2700043I21Rik|D4Ucla2|D4Wsu53e	arginine/serine rich protein 1	protein-coding
mm_86265.1	chr9	121705297	121705322	-	1	NA	promoter-TSS (NM_178677)	promoter-TSS (NM_178677)	-280	NM_178677	215474	Mm.31421	NM_178677	ENSMUSG00000061536	Sec22c	4932412K21|5930407I15Rik|C530046H07|Sec22l3	SEC22 homolog C, vesicle trafficking protein	protein-coding
mm_43625.1	chr5	138171998	138172021	+	1	NA	promoter-TSS (NM_008568)	promoter-TSS (NM_008568)	-12	NM_021392	11781	Mm.113205	NM_021392	ENSMUSG00000019518	Ap4m1	4930443L05Rik|Ap4m4	adaptor-related protein complex AP-4, mu 1	protein-coding
mm_53114.1	chr6	125096170	125096189	+	1	NA	promoter-TSS (NR_106012)	promoter-TSS (NR_106012)	16	NM_145979	107932	Mm.333388	NM_145979	ENSMUSG00000063870	Chd4	9530019N15Rik|AA617397|BC005710|D6Ertd380e|Mi-2beta|mKIAA4075	chromodomain helicase DNA binding protein 4	protein-coding
mm_98591.1	chr11	95778020	95778046	+	1	NA	Intergenic	MLT1F1|LTR|ERVL-MaLR	28966	NM_201609	268469	Mm.389038	NM_201609	ENSMUSG00000075595	Zfp652	9530033F24Rik|ZNF652	zinc finger protein 652	protein-coding
mm_101346.1	chr11	23633622	23633638	-	1	NA	promoter-TSS (NM_001347242)	promoter-TSS (NM_001347242)	1	NM_001347242	71675	Mm.48031	NM_027860	ENSMUSG00000042208	0610010F05Rik	Kiaa1841|mKIAA1841	RIKEN cDNA 0610010F05 gene	protein-coding
mm_133397.1	chr16	84783719	84783723	+	1	NA	intron (NM_023844, intron 1 of 9)	intron (NM_023844, intron 1 of 9)	9598	NM_023844	67374	Mm.41758	NM_023844	ENSMUSG00000053062	Jam2	1110002N23Rik|2410030G21Rik|2410167M24Rik|JAM-2|JAM-B|Jcam2|VE-JAM	junction adhesion molecule 2	protein-coding
mm_127942.1	chr15	10713553	10713570	-	1	NA	promoter-TSS (NM_030690)	promoter-TSS (NM_030690)	-21	NM_030690	75646	Mm.212395	NM_030690	ENSMUSG00000022246	Rai14	1700008J19Rik|1700020L11Rik|Ankycorbin|Norpeg|mKIAA1334	retinoic acid induced 14	protein-coding
mm_56831.1	chr6	117174560	117174597	-	1	NA	3' UTR (NM_021704, exon 3 of 3)	3' UTR (NM_021704, exon 3 of 3)	6043	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_67787.1	chr7	97578765	97578767	-	1	NA	intron (NM_001177945, intron 1 of 4)	RMER15|LTR|ERVL	731	NM_001177945	66273	Mm.41583	NM_183251	ENSMUSG00000035642	Aamdc	1810020D17Rik|1810037D19Rik|LI2	adipogenesis associated Mth938 domain containing	protein-coding
mm_116727.1	chr13	51714817	51714846	-	1	NA	exon (NM_001281880, exon 8 of 17)	exon (NM_001281880, exon 8 of 17)	63123	NM_029279	75420	Mm.275981	NM_029279	ENSMUSG00000035139	Secisbp2	2210413N07Rik|2810012K13Rik|SBP2	SECIS binding protein 2	protein-coding
mm_2782.1	chr1	130841547	130841559	+	1	NA	exon (NM_011082, exon 3 of 11)	exon (NM_011082, exon 3 of 11)	14869	NM_011082	18703	Mm.276414	NM_011082	ENSMUSG00000026417	Pigr	-	polymeric immunoglobulin receptor	protein-coding
mm_134286.1	chr16	14215836	14215851	-	1	NA	exon (NM_013607, exon 25 of 42)	exon (NM_013607, exon 25 of 42)	52568	NM_001114085	67203	Mm.24105	NM_023317	ENSMUSG00000022678	Nde1	2810027M15Rik|AU042936|AW822251|Nude|mNudE	nudE neurodevelopment protein 1	protein-coding
mm_87487.1	chr10	51494622	51494640	+	1	NA	intron (NM_001291894, intron 6 of 8)	intron (NM_001291894, intron 6 of 8)	3733	NM_013532	14728	Mm.34408	NM_013532	ENSMUSG00000062593	Lilrb4a	CD85K|Gp49b|HM18|ILT3|LIR-5|Lilrb4|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4A	protein-coding
mm_145296.1	chr18	53275830	53275835	+	1	NA	intron (NM_029394, intron 1 of 6)	B3|SINE|B2	30170	NM_029394	69226	Mm.32414	NM_029394	ENSMUSG00000024535	Snx24	2810011K15Rik|5730433I16Rik|AI451341	sorting nexing 24	protein-coding
mm_126798.1	chr15	86704161	86704174	+	1	NA	Intergenic	Intergenic	489708	NM_145476	223754	Mm.28904	NM_145476	ENSMUSG00000051864	Tbc1d22a	BC023106|D15Ertd781e	TBC1 domain family, member 22a	protein-coding
mm_16664.1	chr2	6721638	6721648	-	1	NA	promoter-TSS (NM_001310447)	promoter-TSS (NM_001310447)	19	NM_001310447	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_126858.1	chr15	89286551	89286551	+	1	NA	TTS (NM_026813)	TTS (NM_026813)	19181	NR_105924	102465981		NR_105924	ENSMUSG00000098442	Mir6959	Gm27807|mmu-mir-6959	microRNA 6959	ncRNA
mm_33401.1	chr4	129821548	129821563	+	1	NA	intron (NM_001164745, intron 1 of 5)	intron (NM_001164745, intron 1 of 5)	847	NM_001164745	19244	Mm.193688	NM_008974	ENSMUSG00000028788	Ptp4a2	Prl-2	protein tyrosine phosphatase 4a2	protein-coding
mm_64363.1	chr7	142399644	142399671	+	1	NA	Intergenic	Intergenic	-11787	NM_009983	13033	Mm.231395	NM_009983	ENSMUSG00000007891	Ctsd	CD|CatD	cathepsin D	protein-coding
mm_148939.1	chr19	7056732	7056773	+	1	NA	promoter-TSS (NM_134147)	promoter-TSS (NM_134147)	-16	NM_134147	107227	Mm.439977	NM_134147	ENSMUSG00000036278	Macrod1	AI604841|AW743046|D930010J01Rik|Lrp16	MACRO domain containing 1	protein-coding
mm_119172.1	chr14	32159333	32159353	+	1	NA	promoter-TSS (NM_001033988)	promoter-TSS (NM_001033988)	-544	NM_001033988	27057	Mm.371598	NM_019744	ENSMUSG00000056234	Ncoa4	ARA70|Rfg	nuclear receptor coactivator 4	protein-coding
mm_114822.1	chr13	91750203	91750235	+	1	NA	exon (NM_028790, exon 2 of 15)	exon (NM_028790, exon 2 of 15)	-8347	NR_028313	373852	Mm.466817	NR_015501	ENSMUSG00000074782	4833422C13Rik	-	RIKEN cDNA 4833422C13 gene	ncRNA
mm_142117.1	chr17	35865705	35865707	-	1	NA	promoter-TSS (NM_001146710)	promoter-TSS (NM_001146710)	111	NM_001146711	76448	Mm.359982	NM_175242	ENSMUSG00000034595	Ppp1r18	2310014H01Rik|AA407849|AI450394	protein phosphatase 1, regulatory subunit 18	protein-coding
mm_109871.1	chr12	4916178	4916184	-	1	NA	Intergenic	Intergenic	-1172	NM_001099628	320817	Mm.210966	NM_001099628	ENSMUSG00000052812	Atad2b	1110014E10Rik|BC032887|C79189|D530031C13Rik	ATPase family, AAA domain containing 2B	protein-coding
mm_100683.1	chr11	3502637	3502667	-	1	NA	exon (NM_172439, exon 2 of 13)	exon (NM_172439, exon 2 of 13)	2169	NM_172439	170835	Mm.24313	NM_172439	ENSMUSG00000034570	Inpp5j	Pib5pa|Pipp	inositol polyphosphate 5-phosphatase J	protein-coding
mm_62580.1	chr7	105375026	105375044	+	1	NA	promoter-TSS (NM_001195727)	promoter-TSS (NM_001195727)	-3	NM_001195727	100503879	Mm.380109	NM_001195727	ENSMUSG00000078611	Gm5901	EG545989	predicted gene 5901	protein-coding
mm_25735.1	chr3	122860270	122860270	+	1	NA	TTS (NM_153422)	TTS (NM_153422)	-34802	NM_007980	14079	Mm.28398	NM_007980	ENSMUSG00000023057	Fabp2	Fabpi|I-FABP	fatty acid binding protein 2, intestinal	protein-coding
mm_170742.1	chr2	154892793	154892793	-	1	NA	5' UTR (NM_026030, exon 1 of 9)	5' UTR (NM_026030, exon 1 of 9)	113	NM_026030	67204	Mm.377134	NM_026030	ENSMUSG00000074656	Eif2s2	2810026E11Rik|38kDa|AA408636|AA571381|AA986487|AW822225|D2Ertd303e|EIF2|EIF2B	eukaryotic translation initiation factor 2, subunit 2 (beta)	protein-coding
mm_90719.1	chr10	4432286	4432302	-	1	NA	promoter-TSS (NM_024261)	promoter-TSS (NM_024261)	58	NM_025343	66084	Mm.153111	NM_025343	ENSMUSG00000019763	Rmnd1	0610042C05Rik|AA408137|AI462664|AW536662	required for meiotic nuclear division 1 homolog	protein-coding
mm_73764.1	chr8	115707617	115707634	+	1	NA	promoter-TSS (NM_001025577)	promoter-TSS (NM_001025577)	-731	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_150122.1	chr19	29959068	29959072	+	1	NA	3' UTR (NM_001164724, exon 8 of 8)	3' UTR (NM_001164724, exon 8 of 8)	13280	NM_001164724	77125	Mm.182359	NM_133775	ENSMUSG00000024810	Il33	9230117N10Rik|Il-33|Il1f11|NF-HEV	interleukin 33	protein-coding
mm_94978.1	chr11	31733320	31733326	+	1	NA	Intergenic	Intergenic	-61461	NM_001024919	69556	Mm.34183	NM_001024919	ENSMUSG00000044502	Bod1	2310022M17Rik|BOD2.1|Fam44b	biorientation of chromosomes in cell division 1	protein-coding
mm_93594.1	chr10	117087128	117087130	-	1	NA	intron (NM_177798, intron 4 of 9)	intron (NM_177798, intron 4 of 9)	-23315	NM_007636	12461	Mm.247788	NM_007636	ENSMUSG00000034024	Cct2	Cctb	chaperonin containing Tcp1, subunit 2 (beta)	protein-coding
mm_113878.1	chr13	48968325	48968355	+	1	NA	promoter-TSS (NM_001033268)	promoter-TSS (NM_001033268)	228	NR_015601	68128	Mm.426304	NR_015601		Fam120aos	C030044B11Rik	family with sequence similarity 120A, opposite strand	ncRNA
mm_92712.1	chr10	80796360	80796373	-	1	NA	3' UTR (NM_023900, exon 6 of 6)	3' UTR (NM_023900, exon 6 of 6)	2260	NM_023900	78670	Mm.41479	NM_023900	ENSMUSG00000035278	Plekhj1	9530063M10Rik	pleckstrin homology domain containing, family J member 1	protein-coding
mm_129880.1	chr15	83464535	83464563	-	1	NA	promoter-TSS (NM_001159509)	promoter-TSS (NM_001159509)	57	NM_001159509	23970	Mm.23978	NM_011862	ENSMUSG00000016664	Pacsin2	AI197433	protein kinase C and casein kinase substrate in neurons 2	protein-coding
mm_172880.1	chr9	48303628	48303629	-	1	NA	Intergenic	RLTR9E|LTR|ERVK	37270	NM_030069	78252	Mm.31626	NM_030069	ENSMUSG00000032028	Nxpe2	4432416J03Rik|AI323362|Fam55b	neurexophilin and PC-esterase domain family, member 2	protein-coding
mm_145089.1	chr18	42524220	42524243	+	1	NA	exon (NM_001289526, exon 4 of 22)	exon (NM_001289526, exon 4 of 22)	12744	NR_110344	56070	Mm.270511	NM_001039474	ENSMUSG00000024498	Tcerg1	2410022J09Rik|2900090C16Rik|AI428505|CA150b|FBP23|FBP28|Taf2s|ca150|p144	transcription elongation regulator 1 (CA150)	protein-coding
mm_149971.1	chr19	29048199	29048207	+	1	NA	promoter-TSS (NM_021299)	promoter-TSS (NM_021299)	-301	NM_021299	56248	Mm.196067	NM_021299	ENSMUSG00000024782	Ak3	AA407498|AI506714|AK-3|Ak3l|Ak3l1|Akl3l	adenylate kinase 3	protein-coding
mm_65427.1	chr7	25297733	25297752	-	1	NA	intron (NM_008776, intron 1 of 5)	CpG-12842	213	NM_008776	18476	Mm.597	NM_008776	ENSMUSG00000005447	Pafah1b3	Pafahg|mus[g]	platelet-activating factor acetylhydrolase, isoform 1b, subunit 3	protein-coding
mm_101819.1	chr11	46451341	46451367	-	1	NA	intron (NR_105955, intron 2 of 4)	intron (NR_105955, intron 2 of 4)	-3577	NM_134250	171285	Mm.72168	NM_134250	ENSMUSG00000020399	Havcr2	TIM-3|Tim3|Timd3	hepatitis A virus cellular receptor 2	protein-coding
mm_25865.1	chr3	129878790	129878812	+	1	NA	non-coding (NR_104611, exon 1 of 5)	non-coding (NR_104611, exon 1 of 5)	195	NR_104611	66350	Mm.151951	NM_023196	ENSMUSG00000027999	Pla2g12a	2310004B05Rik|GXII|GXII-1|GXII-1-PLA2|Pla2g12|Rossy|mGXII-1	phospholipase A2, group XIIA	protein-coding
mm_40217.1	chr5	37091484	37091523	+	1	NA	exon (NM_178394, exon 3 of 13)	exon (NM_178394, exon 3 of 13)	6267	NM_001347348	76071	Mm.85280	NM_178394	ENSMUSG00000063646	Jakmip1	5830437M04Rik|C330021K24Rik|Gababrbp|Marlin-1	janus kinase and microtubule interacting protein 1	protein-coding
mm_140146.1	chr17	80062480	80062518	+	1	NA	promoter-TSS (NM_144802)	promoter-TSS (NM_144802)	-231	NM_144802	72692	Mm.64579	NM_144802	ENSMUSG00000024095	Hnrnpll	2510028H02Rik|2810036L13Rik|AI256697|AI852082|Hnrpll	heterogeneous nuclear ribonucleoprotein L-like	protein-coding
mm_35403.1	chr4	34687458	34687464	-	1	NA	promoter-TSS (NM_011895)	promoter-TSS (NM_011895)	-23	NM_011895	24060	Mm.281885	NM_011895	ENSMUSG00000028293	Slc35a1	AA408150|AI314851	solute carrier family 35 (CMP-sialic acid transporter), member 1	protein-coding
mm_95375.1	chr11	49089584	49089605	+	1	NA	intron (NM_010999, intron 2 of 5)	RSINE1|SINE|B4	2577	NM_008330	15953	Mm.24769	NM_008330	ENSMUSG00000078920	Ifi47	47kDa|IRG-47|Ifggc1|Igrd|Iigp4|Iipg4|Irgd	interferon gamma inducible protein 47	protein-coding
mm_39115.1	chr4	154936579	154936599	-	1	NA	Intergenic	Intergenic	-8512	NM_178931	230979	Mm.215147	NM_178931	ENSMUSG00000042333	Tnfrsf14	Atar|HveA|Hvem|Tnfrs14	tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)	protein-coding
mm_76778.1	chr8	96403881	96403892	-	1	NA	Intergenic	Intergenic	142087	NR_039538	100628567		NR_039538	ENSMUSG00000104794	Mir28c	mmu-mir-28c	microRNA 28c	ncRNA
mm_163151.1	chr11	83437727	83437727	+	1	NA	promoter-TSS (NM_025492)	promoter-TSS (NM_025492)	33	NM_025492	66330	Mm.44800	NM_025492	ENSMUSG00000035085	1700020L24Rik	-	RIKEN cDNA 1700020L24 gene	protein-coding
mm_144950.1	chr18	37808046	37808119	+	1	NA	exon (NM_033581, exon 1 of 4)	exon (NM_033581, exon 1 of 4)	1672	NM_033581	93706	Mm.247203	NM_033581	ENSMUSG00000102918	Pcdhgc3	PC43|Pcdh2	protocadherin gamma subfamily C, 3	protein-coding
mm_172357.1	chr7	116084618	116084619	-	1	NA	intron (NR_029433, intron 3 of 3)	intron (NR_029433, intron 3 of 3)	8531	NR_029433	69350	Mm.440425	NR_029433	ENSMUSG00000087621	1700003G18Rik	2610312K03Rik	RIKEN cDNA 1700003G18 gene	ncRNA
mm_143484.1	chr17	71270313	71270354	-	1	NA	intron (NM_145158, intron 4 of 7)	RLTR11A|LTR|ERVK	40632	NM_145158	246707	Mm.23462	NM_145158	ENSMUSG00000024053	Emilin2	FOAP-10	elastin microfibril interfacer 2	protein-coding
mm_13699.1	chr2	117123539	117123542	+	1	NA	intron (NM_033524, intron 1 of 6)	intron (NM_033524, intron 1 of 6)	2469	NM_033524	114715	Mm.245890	NM_033524	ENSMUSG00000027351	Spred1	5730461F13Rik|AL024345|AW047647	sprouty protein with EVH-1 domain 1, related sequence	protein-coding
mm_63880.1	chr7	137316900	137316904	+	1	NA	Intergenic	Intergenic	-2457	NM_010096	13593	Mm.258708	NM_010096	ENSMUSG00000010476	Ebf3	3110018A08Rik|O/E-2|mKIAA4201	early B cell factor 3	protein-coding
mm_95996.1	chr11	59208358	59208419	+	1	NA	promoter-TSS (NM_024210)	promoter-TSS (NM_024210)	27	NM_024210	67862	Mm.358708	NM_024210	ENSMUSG00000020441	2310033P09Rik	Mmtag2	RIKEN cDNA 2310033P09 gene	protein-coding
mm_138444.1	chr17	35132164	35132170	+	1	NA	promoter-TSS (NM_018816)	promoter-TSS (NM_018816)	-415	NM_018816	55938	Mm.2161	NM_018816	ENSMUSG00000024391	Apom	1190010O19Rik|G3a|NG20	apolipoprotein M	protein-coding
mm_19510.1	chr2	93869360	93869375	-	1	NA	promoter-TSS (NM_001033452)	promoter-TSS (NM_001033452)	-210	NM_001033452	381411	Mm.9889	NM_001033452	ENSMUSG00000075023	Accsl	Gm1967	1-aminocyclopropane-1-carboxylate synthase (non-functional)-like	protein-coding
mm_114030.1	chr13	52646920	52646950	+	1	NA	3' UTR (NM_011518, exon 14 of 14)	3' UTR (NM_011518, exon 14 of 14)	50053	NM_011518	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_82550.1	chr9	20952803	20952834	-	1	NA	promoter-TSS (NM_001199433)	promoter-TSS (NM_001199433)	161	NM_010066	13433	Mm.128580	NM_010066	ENSMUSG00000004099	Dnmt1	Cxxc9|Dnmt|Dnmt1o|MCMT|MTase|Met-1|Met1|MommeD2|m.MmuI	DNA methyltransferase (cytosine-5) 1	protein-coding
mm_93074.1	chr10	89434055	89434091	-	1	NA	intron (NM_001033331, intron 3 of 10)	intron (NM_001033331, intron 3 of 10)	9894	NM_001284344	237436	Mm.11982	NM_001033331	ENSMUSG00000074802	Gas2l3	8430435B07Rik|Gm240	growth arrest-specific 2 like 3	protein-coding
mm_132304.1	chr16	33594392	33594400	+	1	NA	intron (NM_001083902, intron 5 of 11)	intron (NM_001083902, intron 5 of 11)	75801	NM_001083902	171286	Mm.35253	NM_134251	ENSMUSG00000035506	Slc12a8	CCC9|E330020C02Rik	solute carrier family 12 (potassium/chloride transporters), member 8	protein-coding
mm_97304.1	chr11	76672457	76672461	+	1	NA	promoter-TSS (NM_177182)	promoter-TSS (NM_177182)	-11	NM_177182	320522	Mm.131585	NM_177182	ENSMUSG00000044243	Bhlha9	A830053O21Rik|Fingerin	basic helix-loop-helix family, member a9	protein-coding
mm_87415.1	chr10	50252982	50252983	+	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	-339687	NM_198007	77987	Mm.222497	NM_198007	ENSMUSG00000038774	Ascc3	ASC1p200|B630009I04Rik|BC023451|D430001L07Rik|D630041L21|Helic1|RNAH	activating signal cointegrator 1 complex subunit 3	protein-coding
mm_157146.1	chrX	9461428	9461431	-	1	NA	intron (NM_007807, intron 3 of 12)	intron (NM_007807, intron 3 of 12)	7895	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_82150.1	chr9	123774963	123774973	+	1	NA	intron (NM_009913, intron 2 of 2)	intron (NM_009913, intron 2 of 2)	7757	NM_001166625	12769	Mm.440604	NM_009913	ENSMUSG00000029530	Ccr9	A130091K22Rik|Cmkbr10|GPR-9-6	chemokine (C-C motif) receptor 9	protein-coding
mm_103452.1	chr11	76243657	76243685	-	1	NA	promoter-TSS (NM_183263)	promoter-TSS (NM_183263)	28	NM_026029	67201	Mm.482113	NM_026029	ENSMUSG00000017286	Glod4	1700082G03Rik|2700085E05Rik|C81254	glyoxalase domain containing 4	protein-coding
mm_158405.1	chrX	136837894	136837903	-	1	NA	3' UTR (NM_011123, exon 7 of 7)	3' UTR (NM_011123, exon 7 of 7)	15152	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_137325.1	chr17	25016069	25016124	+	1	NA	promoter-TSS (NM_020608)	promoter-TSS (NM_020608)	10	NM_134126	106633	Mm.32802	NM_134126	ENSMUSG00000024169	Ift140	AI661311|Tce5|Wdtc2|mKIAA0590	intraflagellar transport 140	protein-coding
mm_63574.1	chr7	128117819	128117821	+	1	NA	3' UTR (NM_008401, exon 30 of 30)	3' UTR (NM_008401, exon 30 of 30)	-11748	NM_021334	16411	Mm.22378	NM_021334	ENSMUSG00000030789	Itgax	AI449405|Cd11c|Cr4|N418	integrin alpha X	protein-coding
mm_105179.1	chr11	101785226	101785241	-	1	NA	promoter-TSS (NM_001316366)	promoter-TSS (NM_001316366)	77	NM_008815	18612	Mm.5025	NM_008815	ENSMUSG00000017724	Etv4	AW414408|Pea-3|Pea3	ets variant 4	protein-coding
mm_129132.1	chr15	76195713	76195717	-	1	NA	promoter-TSS (NM_201394)	promoter-TSS (NM_201394)	-5	NM_201394	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
mm_4718.1	chr1	181051250	181051266	+	1	NA	promoter-TSS (NM_001033819)	promoter-TSS (NM_001033819)	21	NM_001033819	619326	Mm.355174	NM_001033819	ENSMUSG00000038768	9130409I23Rik	-	RIKEN cDNA 9130409I23 gene	protein-coding
mm_133110.1	chr16	65520687	65520697	+	1	NA	promoter-TSS (NM_008849)	promoter-TSS (NM_008849)	63	NM_008849	18736	Mm.355440	NM_008849	ENSMUSG00000004842	Pou1f1	GHF-1|Hmp1|Pit-1|Pit1|Pit1-rs1|dw|dwarf	POU domain, class 1, transcription factor 1	protein-coding
mm_5601.1	chr1	39570925	39570974	-	1	NA	intron (NM_001033135, intron 1 of 6)	B3|SINE|B2	6398	NM_001033135	67702	Mm.28614	NM_001033135	ENSMUSG00000048234	Rnf149	1600023E10Rik|AV037261|C76763|Gm15832|Greul4|OTTMUSG00000026591	ring finger protein 149	protein-coding
mm_143090.1	chr17	57080531	57080577	-	1	NA	3' UTR (NM_009451, exon 4 of 4)	3' UTR (NM_009451, exon 4 of 4)	-2044	NM_153551	70785	Mm.284447	NM_153551	ENSMUSG00000002668	Dennd1c	4432409M07Rik	DENN/MADD domain containing 1C	protein-coding
mm_71691.1	chr8	61327948	61327963	+	1	NA	intron (NM_021506, intron 2 of 11)	MTD|LTR|ERVL-MaLR	-39083	NR_045475	69279	Mm.417857	NR_045475	ENSMUSG00000099419	1700001D01Rik	-	RIKEN cDNA 1700001D01 gene	ncRNA
mm_169087.1	chr13	37837670	37837671	+	1	NA	intron (NM_001039188, intron 1 of 9)	intron (NM_001039188, intron 1 of 9)	10277	NM_001039188	68750	Mm.491109	NM_026830	ENSMUSG00000039087	Rreb1	1110037N09Rik|AA414966|B930013M22Rik	ras responsive element binding protein 1	protein-coding
mm_150354.1	chr19	34648264	34648272	+	1	NA	exon (NM_008331, exon 2 of 2)	exon (NM_008331, exon 2 of 2)	7379	NM_008331	15957	Mm.439751	NM_008331	ENSMUSG00000034459	Ifit1	ISG56|Ifi56|P56	interferon-induced protein with tetratricopeptide repeats 1	protein-coding
mm_13597.1	chr2	112618387	112618406	+	1	NA	intron (NM_001165935, intron 1 of 4)	intron (NM_001165935, intron 1 of 4)	58714	NM_001165935	74268	Mm.315125	NM_028844	ENSMUSG00000003604	Aven	1700013A01Rik|1700056A21Rik|mAven-L|mAven-S	apoptosis, caspase activation inhibitor	protein-coding
mm_14073.1	chr2	122771690	122771702	+	1	NA	promoter-TSS (NR_027888)	promoter-TSS (NR_027888)	-17	NR_027888	59010	Mm.28986	NM_021507	ENSMUSG00000005803	Sqrdl	0610039J17Rik|4930557M22Rik|SQOR	sulfide quinone reductase-like (yeast)	protein-coding
mm_4892.1	chr1	188727012	188727012	+	1	NA	intron (NM_021408, intron 39 of 70)	intron (NM_021408, intron 39 of 70)	280828	NM_172650	226823	Mm.209880	NM_172650	ENSMUSG00000026608	Kctd3	4930438A20Rik|9330185B06|E330032J19Rik|NY-REN-45	potassium channel tetramerisation domain containing 3	protein-coding
mm_41224.1	chr5	88593679	88593713	+	1	NA	intron (NM_027530, intron 1 of 12)	intron (NM_027530, intron 1 of 12)	10183	NM_027530	52822	Mm.270469	NM_027530	ENSMUSG00000029291	Rufy3	2810428M05Rik|6330416M07Rik|AW455998|AW538594|D5Bwg0860e|Ripx|Rpipx	RUN and FYVE domain containing 3	protein-coding
mm_24038.1	chr3	87845296	87845299	+	1	NA	Intergenic	RMER19A|LTR|ERVK	-1458	NM_001025571	27371	Mm.86361	NM_021309	ENSMUSG00000028071	Sh2d2a	Lad|Ribp|Tsad	SH2 domain containing 2A	protein-coding
mm_109240.1	chr12	109375396	109375396	+	1	NA	Intergenic	Intergenic	-77427	NR_033813	13386	Mm.157069	NM_010052	ENSMUSG00000040856	Dlk1	AW742678|DLK-1|DlkI|FA1|Ly107|Peg9|SCP1|ZOG|pG2|pref-1	delta-like 1 homolog (Drosophila)	protein-coding
mm_88801.1	chr10	80702650	80702761	+	1	NA	promoter-TSS (NM_027829)	promoter-TSS (NM_027829)	12	NM_027829	71564	Mm.35802	NM_027829	ENSMUSG00000055862	Izumo4	9030607L17Rik|AI550407	IZUMO family member 4	protein-coding
mm_87710.1	chr10	60003322	60003343	+	1	NA	promoter-TSS (NM_001199187)	promoter-TSS (NM_001199187)	5	NM_001199187	69090	Mm.155839	NM_026937	ENSMUSG00000044475	Ascc1	1810015P09Rik|AI550520|ASC1p50|CGI-18	activating signal cointegrator 1 complex subunit 1	protein-coding
mm_143235.1	chr17	63499984	63500075	-	1	NA	5' UTR (NM_015794, exon 1 of 9)	5' UTR (NM_015794, exon 1 of 9)	551	NM_015794	50758	Mm.136366	NM_015794	ENSMUSG00000023965	Fbxl17	6330576B01Rik|AI452053|BB073797|C130023C01Rik|Fbx13|Fbxo13	F-box and leucine-rich repeat protein 17	protein-coding
mm_29735.1	chr3	126921811	126921813	-	1	NA	3' UTR (NM_178655, exon 25 of 25)	3' UTR (NM_178655, exon 25 of 25)	21574	NM_001034168	109676	Mm.220242	NM_178655	ENSMUSG00000032826	Ank2	100043364|AI835472|AW491075|Ank-2|Gm4392	ankyrin 2, brain	protein-coding
mm_86622.1	chr10	13966207	13966222	+	1	NA	promoter-TSS (NM_010437)	promoter-TSS (NM_010437)	-165	NM_010437	15273	Mm.42157	NM_010437	ENSMUSG00000015501	Hivep2	Gm20114|MIBP1|Schnurri-2|Shn-2	human immunodeficiency virus type I enhancer binding protein 2	protein-coding
mm_24002.1	chr3	86986563	86986584	+	1	NA	promoter-TSS (NM_001289449)	promoter-TSS (NM_001289449)	-13	NM_007640	12480	Mm.389465	NM_007640	ENSMUSG00000041750	Cd1d2	CD1.2|Cd1b|Ly-38	CD1d2 antigen	protein-coding
mm_3318.1	chr1	137907027	137907027	+	1	NA	Intergenic	Intergenic	-59428	NR_029795	735252		NR_029795	ENSMUSG00000065565	Mir181a-1	Mirn181a-1|Mirn213|miR-213|mir-181a-1|mmu-mir-213	microRNA 181a-1	ncRNA
mm_151946.1	chr19	5801060	5801064	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	1610	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_44500.1	chr5	23783613	23783697	-	1	NA	promoter-TSS (NM_001289780)	promoter-TSS (NM_001289780)	56	NM_001289780	78697	Mm.58660	NM_178403	ENSMUSG00000057541	Pus7	C330017I15Rik	pseudouridylate synthase 7	protein-coding
mm_149813.1	chr19	23893542	23893553	+	1	NA	exon (NM_177034, exon 2 of 13)	exon (NM_177034, exon 2 of 13)	134671	NM_177034	319924	Mm.22879	NM_177034	ENSMUSG00000024897	Apba1	6430513E09Rik|Lin-10|Mint|Mint1|Urop11|X11|X11alpha	amyloid beta (A4) precursor protein binding, family A, member 1	protein-coding
mm_10845.1	chr2	24976028	24976043	+	1	NA	promoter-TSS (NM_001031808)	promoter-TSS (NM_001031808)	2	NM_146251	241274	Mm.389243	NM_146251	ENSMUSG00000036833	Pnpla7	BC027342|E430013P11Rik|Nre	patatin-like phospholipase domain containing 7	protein-coding
mm_8913.1	chr1	163313249	163313271	-	1	NA	5' UTR (NM_175686, exon 1 of 5)	5' UTR (NM_175686, exon 1 of 5)	390	NM_011127	18933	Mm.288642	NM_011127	ENSMUSG00000026586	Prrx1	A230024N07Rik|AA755424|AI385634|AI843499|K-2|Pmx|Pmx1|Prx1|mHox	paired related homeobox 1	protein-coding
mm_150462.1	chr19	38348695	38348722	+	1	NA	Intergenic	Intergenic	-47272	NM_175507	240660	Mm.262085	NM_175507	ENSMUSG00000044026	Slc35g1	AA590464|D330039I19Rik|Tmem20	solute carrier family 35, member G1	protein-coding
mm_78788.1	chr9	44043212	44043253	+	1	NA	promoter-TSS (NM_009382)	promoter-TSS (NM_009382)	-152	NM_009382	21838	Mm.3951	NM_009382	ENSMUSG00000032011	Thy1	CD90|T25|Thy-1|Thy-1.2|Thy1.1|Thy1.2	thymus cell antigen 1, theta	protein-coding
mm_59348.1	chr7	25644898	25644900	+	1	NA	intron (NM_007533, intron 1 of 8)	intron (NM_007533, intron 1 of 8)	13862	NM_007533	12039	Mm.25848	NM_007533	ENSMUSG00000060376	Bckdha	-	branched chain ketoacid dehydrogenase E1, alpha polypeptide	protein-coding
mm_70738.1	chr8	19141372	19141383	+	1	NA	exon (NM_001034905, exon 2 of 2)	exon (NM_001034905, exon 2 of 2)	618	NM_001286493	546038	Mm.99206	NM_001034905	ENSMUSG00000059463	Spag11b	EG546038|Ep2c/h|Spag11c/h	sperm associated antigen 11B	protein-coding
mm_18313.1	chr2	54085563	54085573	-	1	NA	promoter-TSS (NM_023396)	promoter-TSS (NM_023396)	-16	NM_023396	67874	Mm.27086	NM_023396	ENSMUSG00000075334	Rprm	2410012A13Rik|Reprimo	reprimo, TP53 dependent G2 arrest mediator candidate	protein-coding
mm_44091.1	chr5	149244942	149244951	+	1	NA	Intergenic	Intergenic	-20058	NM_001308462	11690	Mm.19844	NM_009663	ENSMUSG00000060063	Alox5ap	Flap	arachidonate 5-lipoxygenase activating protein	protein-coding
mm_81723.1	chr9	112234234	112234251	+	1	NA	promoter-TSS (NR_015468)	promoter-TSS (NR_015468)	-35	NR_033432	620760	Mm.259863	NR_015468	ENSMUSG00000087038	2900079G21Rik	C130083B14|Gm6179	RIKEN cDNA 2900079G21 gene	ncRNA
mm_167459.1	chr8	123418086	123418092	+	1	NA	intron (NM_023279, intron 1 of 3)	intron (NM_023279, intron 1 of 3)	6525	NM_023279	22152	Mm.40068	NM_023279	ENSMUSG00000062380	Tubb3	3200002H15Rik|M(beta)3|M(beta)6	tubulin, beta 3 class III	protein-coding
mm_6441.1	chr1	73998450	73998498	-	1	NA	intron (NM_027884, intron 6 of 34)	intron (NM_027884, intron 6 of 34)	125973	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_42291.1	chr5	114408085	114408097	+	1	NA	intron (NM_001331219, intron 17 of 26)	intron (NM_001331219, intron 17 of 26)	3623	NR_105994	102465621		NR_105994	ENSMUSG00000098731	Mir7027	Gm27831|mmu-mir-7027	microRNA 7027	ncRNA
mm_4538.1	chr1	176814853	176814910	+	1	NA	5' UTR (NM_029756, exon 1 of 18)	5' UTR (NM_029756, exon 1 of 18)	221	NM_029756	76816	Mm.171399	NM_029756	ENSMUSG00000026504	Sdccag8	2700048G21Rik|5730470G24Rik|Cccap	serologically defined colon cancer antigen 8	protein-coding
mm_109204.1	chr12	108675454	108675492	+	1	NA	exon (NM_007965, exon 6 of 13)	exon (NM_007965, exon 6 of 13)	16853	NR_029771	723909		NR_029771	ENSMUSG00000065436	Mir342	Mirn342|mmu-mir-342	microRNA 342	ncRNA
mm_161192.1	chr13	51567228	51567228	-	1	NA	promoter-TSS (NM_009167)	promoter-TSS (NM_009167)	-144	NM_009167	20418	Mm.131870	NM_009167	ENSMUSG00000021448	Shc3	N-Shc|Rai|ShcC	src homology 2 domain-containing transforming protein C3	protein-coding
mm_135073.1	chr16	34262879	34262888	-	1	NA	intron (NM_001164268, intron 10 of 33)	intron (NM_001164268, intron 10 of 33)	251144	NM_001164268	545156	Mm.82274	NM_177357	ENSMUSG00000061751	Kalrn	2210407G14Rik|AV235988|DUET|E530005C20Rik|Gm539|Hapip|TRAD	kalirin, RhoGEF kinase	protein-coding
mm_169714.1	chr15	77113775	77113780	-	1	NA	intron (NM_053104, intron 4 of 13)	intron (NM_053104, intron 4 of 13)	29379	NR_108037	74303	Mm.444304	NR_108037	ENSMUSG00000097267	1700109K24Rik	4933425G21Rik	RIKEN cDNA 1700109K24 gene	ncRNA
mm_101744.1	chr11	43379298	43379322	-	1	NA	Intergenic	Intergenic	-4849	NR_029558	387164		NR_029558	ENSMUSG00000065601	Mir146	Mirn146|miR-146a|mmu-mir-146	microRNA 146	ncRNA
mm_70202.1	chr7	144678776	144678839	-	1	NA	intron (NM_178642, intron 1 of 25)	CpG-13775	59785	NM_178642	101772	Mm.26700	NM_178642	ENSMUSG00000031075	Ano1	Tmem16a	anoctamin 1, calcium activated chloride channel	protein-coding
mm_127639.1	chr15	102473511	102473518	+	1	NA	intron (NM_001103165, intron 2 of 14)	intron (NM_001103165, intron 2 of 14)	2882	NM_001174073	18521	Mm.236513	NM_011042	ENSMUSG00000056851	Pcbp2	AW412548|Hnrpx|alphaCP-2	poly(rC) binding protein 2	protein-coding
mm_13212.1	chr2	96317752	96317781	+	1	NA	promoter-TSS (NM_001289742)	promoter-TSS (NM_001289742)	-403	NM_001289742	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_42994.1	chr5	123344583	123344629	+	1	NA	5' UTR (NM_029850, exon 1 of 6)	5' UTR (NM_029850, exon 1 of 6)	158	NM_029850	77045	Mm.151960	NM_029850	ENSMUSG00000029438	Bcl7a	4432415N06Rik|AI448316	B cell CLL/lymphoma 7A	protein-coding
mm_25422.1	chr3	107873881	107873887	+	1	NA	Intergenic	Intergenic	-3346	NM_133867	99662	Mm.108491	NM_133867	ENSMUSG00000040600	Eps8l3	AI504489|Eps8r3	EPS8-like 3	protein-coding
mm_135975.1	chr16	75047401	75047437	-	1	NA	Intergenic	Lx2|LINE|L1	538642	NM_001252513	320355	Mm.99517	NM_177142	ENSMUSG00000032948	Lipi	D930038D03Rik|lpd1	lipase, member I	protein-coding
mm_94412.1	chr11	5849317	5849326	+	1	NA	Intergenic	Intergenic	-11305	NM_017401	54125	Mm.260194	NM_017401	ENSMUSG00000020474	Polm	AI462166|B230309I03Rik|Tdt-N	polymerase (DNA directed), mu	protein-coding
mm_159636.1	chr4	139575374	139575374	+	1	NA	exon (NM_001205173, exon 1 of 9)	exon (NM_001205173, exon 1 of 9)	654	NM_001205173	212632	Mm.30464	NM_183148	ENSMUSG00000041025	Iffo2	C79267	intermediate filament family orphan 2	protein-coding
mm_75098.1	chr8	34108512	34108522	-	1	NA	promoter-TSS (NM_001293758)	promoter-TSS (NM_001293758)	195	NM_001293759	22428	Mm.150373	NM_011722	ENSMUSG00000031516	Dctn6	AU044699|WS-3|p27	dynactin 6	protein-coding
mm_52315.1	chr6	108836093	108836101	+	1	NA	intron (NM_138677, intron 1 of 11)	intron (NM_138677, intron 1 of 11)	7456	NM_138677	192193	Mm.21596	NM_138677	ENSMUSG00000030104	Edem1	A130059K23Rik|EDEM|mKIAA0212	ER degradation enhancer, mannosidase alpha-like 1	protein-coding
mm_51889.1	chr6	90604909	90604959	+	1	NA	promoter-TSS (NM_027868)	promoter-TSS (NM_027868)	54	NM_027868	71699	Mm.272633	NM_027868	ENSMUSG00000030089	Slc41a3	1010001P06Rik|AI480742|SLC41A1-L2	solute carrier family 41, member 3	protein-coding
mm_129400.1	chr15	78284165	78284189	-	1	NA	TTS (NR_106137).2	TTS (NR_106137).2	672	NR_106138	102466845		NR_106138	ENSMUSG00000099059	Mir7676-2	Gm27790|mmu-mir-7676-2	microRNA 7676-2	ncRNA
mm_36872.1	chr4	107177700	107177712	-	1	NA	promoter-TSS (NM_029565)	promoter-TSS (NM_029565)	660	NM_025617	66526	Mm.246956	NM_025617	ENSMUSG00000028619	Tceanc2	2210010B22Rik|2210012G02Rik|6330404A07Rik|AU015593|Tdeanc2	transcription elongation factor A (SII) N-terminal and central domain containing 2	protein-coding
mm_23656.1	chr3	67892129	67892155	+	1	NA	promoter-TSS (NM_177585)	promoter-TSS (NM_177585)	-78	NM_001113419	100505386	Mm.331064	NM_001113419	ENSMUSG00000102422	Gm21949	Iqcj-schip1|Schip-1-iqcj|Schip1	predicted gene, 21949	protein-coding
mm_62662.1	chr7	108934406	108934430	+	1	NA	promoter-TSS (NM_025344)	promoter-TSS (NM_025344)	3	NM_025344	66085	Mm.182962	NM_025344	ENSMUSG00000031029	Eif3f	0610037M02Rik|AA409853|Eif3s5	eukaryotic translation initiation factor 3, subunit F	protein-coding
mm_107742.1	chr12	58212427	58212443	+	1	NA	5' UTR (NM_009216, exon 2 of 2)	5' UTR (NM_009216, exon 2 of 2)	631	NM_009216	20605	Mm.278336	NM_009216	ENSMUSG00000035431	Sstr1	SRIF-2|SS-1-R|SS1-R|SS1R|Smstr-1|Smstr1|sst1	somatostatin receptor 1	protein-coding
mm_77726.1	chr8	126849951	126849980	-	1	NA	Intergenic	Intergenic	95956	NM_024214	67952	Mm.6932	NM_024214	ENSMUSG00000093904	Tomm20	1810060K07Rik|BB284719|Gm19268|MAS20|MOM19|TOM20|mKIAA0016	translocase of outer mitochondrial membrane 20 homolog (yeast)	protein-coding
mm_149264.1	chr19	10577181	10577196	+	1	NA	promoter-TSS (NM_201351)	promoter-TSS (NM_201351)	31	NM_001282067	225912	Mm.252701	NM_201351	ENSMUSG00000034445	Cyb561a3	2310004G04Rik|Cybasc3|Lcytb	cytochrome b561 family, member A3	protein-coding
mm_24682.1	chr3	94933042	94933073	+	1	NA	promoter-TSS (NM_009150)	promoter-TSS (NM_009150)	-26	NM_009150	20341	Mm.196558	NM_009150	ENSMUSG00000068874	Selenbp1	Lp56|Lpsb|SBP56	selenium binding protein 1	protein-coding
mm_44998.1	chr5	38159725	38159743	-	1	NA	promoter-TSS (NM_010942)	promoter-TSS (NM_010942)	-267	NM_010942	18196	Mm.7414	NM_010942	ENSMUSG00000029126	Nsg1	Neep21|m234|p21	neuron specific gene family member 1	protein-coding
mm_112696.1	chr13	17695260	17695270	+	1	NA	promoter-TSS (NM_138654)	promoter-TSS (NM_138654)	-148	NM_025479	66308	Mm.291109	NM_025479	ENSMUSG00000012429	Mplkip	2810021B07Rik|C330007M08Rik|Ttdn1	M-phase specific PLK1 intereacting protein	protein-coding
mm_95253.1	chr11	44621197	44621205	+	1	NA	exon (NM_001290710, exon 3 of 15)	exon (NM_001290710, exon 3 of 15)	3101	NM_001290710	13591	Mm.439662	NM_007897	ENSMUSG00000057098	Ebf1	Ebf|O/E-1|OE-1|Olf-1|Olf1	early B cell factor 1	protein-coding
mm_135211.1	chr16	36621590	36621600	-	1	NA	intron (NM_019388, intron 2 of 7)	intron (NM_019388, intron 2 of 7)	44482	NM_019388	12524	Mm.1452	NM_019388	ENSMUSG00000022901	Cd86	B7|B7-2|B7.2|B70|CLS1|Cd28l2|ETC-1|Ly-58|Ly58|MB7|MB7-2|TS/A-2	CD86 antigen	protein-coding
mm_76770.1	chr8	95817681	95817703	-	1	NA	intron (NR_015574, intron 3 of 3)	intron (NR_015574, intron 3 of 3)	-10230	NM_001205226	234594	Mm.259220	NM_153164	ENSMUSG00000036550	Cnot1	6030411K04Rik|AA815922|D830048B13	CCR4-NOT transcription complex, subunit 1	protein-coding
mm_160208.1	chr7	92661869	92661869	-	1	NA	exon (NM_029078, exon 5 of 16)	exon (NM_029078, exon 5 of 16)	8043	NM_029078	74737	Mm.288645	NM_029078	ENSMUSG00000041328	Pcf11	2500001H09Rik|5730417B17Rik|C77803	PCF11 cleavage and polyadenylation factor subunit	protein-coding
mm_7288.1	chr1	97769406	97769423	-	1	NA	promoter-TSS (NM_001310773)	promoter-TSS (NM_001310773)	678	NM_173760	227399	Mm.220817	NM_173760	ENSMUSG00000040648	Ppip5k2	AW555814|Cfap160|D330021B20|Hisppd1|Vip2|mKIAA0433	diphosphoinositol pentakisphosphate kinase 2	protein-coding
mm_69822.1	chr7	141265858	141265881	-	1	NA	5' UTR (NM_001252601, exon 2 of 10)	5' UTR (NM_001252601, exon 2 of 10)	555	NM_001252601	54123	Mm.3233	NM_016850	ENSMUSG00000025498	Irf7	-	interferon regulatory factor 7	protein-coding
mm_56335.1	chr6	92677854	92677856	-	1	NA	intron (NM_001081146, intron 2 of 8)	intron (NM_001081146, intron 2 of 8)	28329	NM_001081146	243548	Mm.248820	NM_001081146	ENSMUSG00000030020	Prickle2	6230400G14Rik|6720451F06Rik|mpk2	prickle planar cell polarity protein 2	protein-coding
mm_104694.1	chr11	97884123	97884139	-	1	NA	promoter-TSS (NM_001081435)	promoter-TSS (NM_001081435)	23	NM_001081435	72973	Mm.245939	NM_001081435	ENSMUSG00000070336	Fbxo47	2900052P03Rik|Gm1562	F-box protein 47	protein-coding
mm_62569.1	chr7	104244466	104244491	+	1	NA	promoter-TSS (NM_030684)	promoter-TSS (NM_030684)	21	NM_030684	94094	Mm.326945	NM_030684	ENSMUSG00000056144	Trim34a	Trim34|Trim34-1	tripartite motif-containing 34A	protein-coding
mm_64716.1	chr7	4655554	4655566	-	1	NA	intron (NM_172894, intron 1 of 23)	L2b|LINE|L2	3390	NM_172894	243819	Mm.258670	NM_172894	ENSMUSG00000052296	Ppp6r1	2010309P17Rik|AI836219|B430201G11Rik|D030074N20Rik|Pp6r1|Saps1|mKIAA1115	protein phosphatase 6, regulatory subunit 1	protein-coding
mm_108837.1	chr12	96662311	96662317	+	1	NA	Intergenic	Lx5|LINE|L1	-615092	NR_103800	69423	Mm.46121	NM_027076		1700019M22Rik	-	NFX-like protein	pseudo
mm_105567.1	chr11	106579075	106579087	-	1	NA	intron (NM_198292, intron 1 of 11)	intron (NM_198292, intron 1 of 11)	33849	NM_198292	21763	Mm.102407	NM_198292	ENSMUSG00000040548	Tex2	4930568E07Rik|AI553404|Def-5|Taz4	testis expressed gene 2	protein-coding
mm_17346.1	chr2	26604399	26604430	-	1	NA	promoter-TSS (NM_026212)	promoter-TSS (NM_026212)	3	NM_026212	67512	Mm.24244	NM_026212	ENSMUSG00000026922	Agpat2	2510002J07Rik|AV000834|BSCL|BSCL1|LPAAB|LPAAT-beta	1-acylglycerol-3-phosphate O-acyltransferase 2 (lysophosphatidic acid acyltransferase, beta)	protein-coding
mm_89989.1	chr10	112002346	112002386	+	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-5102	NM_028608	73690	Mm.173790	NM_028608	ENSMUSG00000056888	Glipr1	2410114O14Rik|RTVP-1|RTVP1|mRTVP-1	GLI pathogenesis-related 1 (glioma)	protein-coding
mm_110526.1	chr12	54937679	54937685	-	1	NA	intron (NM_013815, intron 7 of 26)	ORR1A2|LTR|ERVL-MaLR	48654	NM_013815	217578	Mm.479583	NM_013815	ENSMUSG00000035021	Baz1a	Acf1|B930060C03|BC065123|Gtl5|Wcrf180|cbp146	bromodomain adjacent to zinc finger domain 1A	protein-coding
mm_31524.1	chr4	54947842	54947855	+	1	NA	promoter-TSS (NM_172867)	promoter-TSS (NM_172867)	-97	NM_172867	242466	Mm.102904	NM_172867	ENSMUSG00000060206	Zfp462	6030417H05|9430078C22Rik|Gt4-2|Zfpip	zinc finger protein 462	protein-coding
mm_160040.1	chr6	137170630	137170630	-	1	NA	promoter-TSS (NM_001164214)	promoter-TSS (NM_001164214)	-134	NM_181988	232441	Mm.46233	NM_181988	ENSMUSG00000030222	Rerg	-	RAS-like, estrogen-regulated, growth-inhibitor	protein-coding
mm_52777.1	chr6	121245904	121245908	+	1	NA	promoter-TSS (NM_011909)	promoter-TSS (NM_011909)	0	NM_011909	24110	Mm.326911	NM_011909	ENSMUSG00000030107	Usp18	1110058H21Rik|AW047653|UBP43|Ubp15	ubiquitin specific peptidase 18	protein-coding
mm_105025.1	chr11	100472763	100472767	-	1	NA	promoter-TSS (NM_172565)	promoter-TSS (NM_172565)	17	NM_172565	217194	Mm.183320	NM_172565	ENSMUSG00000048732	Klhl11	BC011167	kelch-like 11	protein-coding
mm_53453.1	chr6	134641100	134641117	+	1	NA	5' UTR (NM_026371, exon 1 of 4)	5' UTR (NM_026371, exon 1 of 4)	168	NM_026371	67774	Mm.41892	NM_026371	ENSMUSG00000042992	Borcs5	5830457J20Rik|AW124643|Loh12cr1	BLOC-1 related complex subunit 5	protein-coding
mm_104125.1	chr11	86757426	86757436	-	1	NA	promoter-TSS (NM_001003908)	promoter-TSS (NM_001003908)	61	NM_001003908	67300	Mm.254588	NM_001003908	ENSMUSG00000047126	Cltc	3110065L21Rik|CHC|R74732	clathrin, heavy polypeptide (Hc)	protein-coding
mm_161898.1	chr18	46198845	46198845	+	1	NA	promoter-TSS (NM_001170855)	promoter-TSS (NM_001170855)	-27	NM_001170855	28105	Mm.277382	NM_178872	ENSMUSG00000033949	Trim36	D18Wsu100e|haprin	tripartite motif-containing 36	protein-coding
mm_125529.1	chr15	57919235	57919255	+	1	NA	intron (NM_001167679, intron 2 of 17)	RMER1C|Other|Other	7046	NM_001167679	210544	Mm.390835	NM_199300	ENSMUSG00000022364	Tbc1d31	4B3|D330013L20Rik|Gm85|Wdr67	TBC1 domain family, member 31	protein-coding
mm_141200.1	chr17	27028611	27028615	-	1	NA	promoter-TSS (NM_027544)	promoter-TSS (NM_027544)	13	NM_007523	12018	Mm.2443	NM_007523	ENSMUSG00000057789	Bak1	Bak|N-BAK1|N-Bak	BCL2-antagonist/killer 1	protein-coding
mm_104768.1	chr11	98535673	98535676	-	1	NA	intron (NM_011771, intron 1 of 7)	intron (NM_011771, intron 1 of 7)	10357	NM_011771	22780	Mm.133367	NM_011771	ENSMUSG00000018168	Ikzf3	5830411O07Rik|Aiolos|Zfpn1a3|Znfn1a3	IKAROS family zinc finger 3	protein-coding
mm_7044.1	chr1	87125719	87125730	-	1	NA	exon (NM_007432, exon 4 of 11)	exon (NM_007432, exon 4 of 11)	716	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_163411.1	chr12	77238707	77238735	+	1	NA	promoter-TSS (NR_045554)	promoter-TSS (NR_045554)	-18	NR_045554	53618	Mm.35628	NM_016893	ENSMUSG00000021065	Fut8	-	fucosyltransferase 8	protein-coding
mm_58993.1	chr7	19131713	19131729	+	1	NA	intron (NM_175530, intron 1 of 1)	CpG	11862	NM_175530	243867	Mm.230830	NM_175530	ENSMUSG00000050428	Fbxo46	20D7-FC4|4932704E22Rik|Fbxo34l	F-box protein 46	protein-coding
mm_162810.1	chr10	79664375	79664383	+	1	NA	promoter-TSS (NM_013591)	promoter-TSS (NM_013591)	-195	NM_013591	17123	Mm.391556	NM_013591	ENSMUSG00000020310	Madcam1	AV211525	mucosal vascular addressin cell adhesion molecule 1	protein-coding
mm_31311.1	chr4	46082871	46082891	+	1	NA	intron (NM_021883, intron 3 of 9)	MLT1A|LTR|ERVL-MaLR	43659	NM_021883	21916	Mm.249594	NM_021883	ENSMUSG00000028328	Tmod1	E-Tmod|Tmod	tropomodulin 1	protein-coding
mm_104643.1	chr11	97537158	97537165	-	1	NA	exon (NM_018873, exon 5 of 20)	exon (NM_018873, exon 5 of 20)	-36821	NM_001289118	100141474	Mm.482426	NM_001289118	ENSMUSG00000047988	4933428G20Rik	-	RIKEN cDNA 4933428G20 gene	protein-coding
mm_170932.1	chr2	42956172	42956187	-	1	NA	Intergenic	L1Md_T|LINE|L1	-302581	NM_053011	94217	Mm.441398	NM_053011	ENSMUSG00000049252	Lrp1b	9630004P12Rik|LRP-DIT	low density lipoprotein-related protein 1B (deleted in tumors)	protein-coding
mm_23055.1	chr3	35754122	35754135	+	1	NA	promoter-TSS (NM_029570)	promoter-TSS (NM_029570)	-10	NM_029570	76295	Mm.239416	NM_029570	ENSMUSG00000037400	Atp11b	1110019I14Rik|ATPIF|ATPIR|mKIAA0956	ATPase, class VI, type 11B	protein-coding
mm_53011.1	chr6	123275010	123275024	+	1	NA	3' UTR (NM_010819, exon 6 of 6)	3' UTR (NM_010819, exon 6 of 6)	12910	NM_010819	17474	Mm.441101	NM_010819	ENSMUSG00000030144	Clec4d	Clecsf8|Mpcl|mcl	C-type lectin domain family 4, member d	protein-coding
mm_35792.1	chr4	46528372	46528384	-	1	NA	intron (NM_029077, intron 2 of 5)	intron (NM_029077, intron 2 of 5)	7763	NM_029077	74735	Mm.240252	NM_029077	ENSMUSG00000039853	Trim14	5830400N10Rik|pub	tripartite motif-containing 14	protein-coding
mm_59672.1	chr7	28381260	28381281	+	1	NA	Intergenic	Intergenic	-2042	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_112428.1	chr13	4233787	4233797	+	1	NA	promoter-TSS (NM_001013785)	promoter-TSS (NM_001013785)	52	NM_001013785	432720	Mm.22832	NM_001013785	ENSMUSG00000071551	Akr1c19	1810010N06Rik	aldo-keto reductase family 1, member C19	protein-coding
mm_3458.1	chr1	150103962	150103990	+	1	NA	exon (NM_011198, exon 7 of 10)	exon (NM_011198, exon 7 of 10)	3945	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_148014.1	chr18	68300241	68300259	-	1	NA	promoter-TSS (NM_026440)	promoter-TSS (NM_026440)	83	NM_153794	108654	Mm.125857	NM_153794	ENSMUSG00000038121	Fam210a	4933403F05Rik|AA987140|AV134576|AW491926	family with sequence similarity 210, member A	protein-coding
mm_136397.1	chr16	93358711	93358730	-	1	NA	promoter-TSS (NR_040489)	promoter-TSS (NR_040489)	-8	NR_040489	69857	Mm.81192	NR_040486	ENSMUSG00000100277	1810053B23Rik	1810008L18Rik|1810056K14Rik	RIKEN cDNA 1810053B23 gene	ncRNA
mm_154764.1	chrX	12089033	12089055	+	1	NA	intron (NM_001168321, intron 1 of 13)	CpG	-8491	NM_029510	71458	Mm.196328	NM_029510	ENSMUSG00000040363	Bcor	2900008C10Rik|5830466J11Rik|8430401K06Rik|BcorR|D930024N20Rik|mKIAA1575	BCL6 interacting corepressor	protein-coding
mm_53732.1	chr6	145121728	145121748	+	1	NA	promoter-TSS (NM_008511)	promoter-TSS (NM_008511)	-1	NM_008511	16970	Mm.843	NM_008511	ENSMUSG00000030263	Lrmp	D6Int3|D6Int4|D6Int5|D6Int7|D6Int8|Jaw1	lymphoid-restricted membrane protein	protein-coding
mm_25002.1	chr3	97651823	97651830	+	1	NA	exon (NM_001161763, exon 9 of 9)	exon (NM_001161763, exon 9 of 9)	-6386	NM_182997	108097	Mm.31175	NM_182997	ENSMUSG00000038205	Prkab2	5730553K21Rik|AW049591|BB124140	protein kinase, AMP-activated, beta 2 non-catalytic subunit	protein-coding
mm_32944.1	chr4	119539141	119539151	+	1	NA	promoter-TSS (NM_001290696)	promoter-TSS (NM_001290696)	-377	NM_001004178	433752	Mm.425205	NM_001004178	ENSMUSG00000087385	AA415398	-	expressed sequence AA415398	protein-coding
mm_173217.1	chrX	74170621	74170637	+	1	NA	Intergenic	Intergenic	-2791	NM_001126488	385380	Mm.475616	NM_001126488	ENSMUSG00000062564	Tex28	Gm1538|Gm1811	testis expressed 28	protein-coding
mm_32837.1	chr4	117835236	117835275	+	1	NA	promoter-TSS (NM_008135)	promoter-TSS (NM_008135)	-3	NM_008135	14664	Mm.244549	NM_008135	ENSMUSG00000028542	Slc6a9	Glyt-1|Glyt1	solute carrier family 6 (neurotransmitter transporter, glycine), member 9	protein-coding
mm_76108.1	chr8	80395215	80395228	-	1	NA	Intergenic	Intergenic	-98824	NM_010369	14934	Mm.13123	NM_010369	ENSMUSG00000051839	Gypa	AI853584|CD235a|GPA	glycophorin A	protein-coding
mm_52992.1	chr6	123266160	123266184	+	1	NA	intron (NM_001163161, intron 2 of 5)	L1ME3A|LINE|L1	4065	NM_010819	17474	Mm.441101	NM_010819	ENSMUSG00000030144	Clec4d	Clecsf8|Mpcl|mcl	C-type lectin domain family 4, member d	protein-coding
mm_133032.1	chr16	57352814	57352825	+	1	NA	promoter-TSS (NM_001040397)	promoter-TSS (NM_001040397)	-458	NM_001040397	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding
mm_120633.1	chr14	70466821	70466848	+	1	NA	exon (NM_145981, exon 5 of 5)	exon (NM_145981, exon 5 of 5)	9317	NM_145981	105653	Mm.192598	NM_145981	ENSMUSG00000003469	Phyhip	AW049870|C630010D02Rik|Lnap1ip|PAHX-AP#1|PAHX-AP1	phytanoyl-CoA hydroxylase interacting protein	protein-coding
mm_116020.1	chr13	24831354	24831408	-	1	NA	promoter-TSS (NM_019551)	promoter-TSS (NM_019551)	108	NM_025790	66834	Mm.2125	NM_025790	ENSMUSG00000006717	Acot13	0610006O17Rik|Them2	acyl-CoA thioesterase 13	protein-coding
mm_94554.1	chr11	11522214	11522251	+	1	NA	Intergenic	Intergenic	32966	NM_028669	73862	Mm.159077	NM_028669	ENSMUSG00000020191	4930415F15Rik	-	RIKEN cDNA 4930415F15 gene	protein-coding
mm_134413.1	chr16	17704401	17704409	-	1	NA	intron (NM_001285886, intron 2 of 16)	intron (NM_001285886, intron 2 of 16)	18495	NM_001285886	94112	Mm.208970	NM_033609	ENSMUSG00000012114	Med15	A230074L19Rik|AW536074|Pcqap|mPcqap	mediator complex subunit 15	protein-coding
mm_54692.1	chr6	39445805	39445820	-	1	NA	Intergenic	MLTR14|LTR|ERV1	-25443	NM_018810	54484	Mm.270484	NM_018810	ENSMUSG00000029922	Mkrn1	RFP	makorin, ring finger protein, 1	protein-coding
mm_17885.1	chr2	34962928	34962954	-	1	NA	Intergenic	Intergenic	-1169	NM_001326601	22029	Mm.239514	NM_009421	ENSMUSG00000026875	Traf1	4732496E14Rik	TNF receptor-associated factor 1	protein-coding
mm_88460.1	chr10	77561020	77561036	+	1	NA	exon (NM_008404, exon 14 of 16)	exon (NM_008404, exon 14 of 16)	-20739	NM_145925	108705	Mm.28853	NM_145925	ENSMUSG00000009291	Pttg1ip	1810010L20Rik|AI314311|AU018448|C79540	pituitary tumor-transforming 1 interacting protein	protein-coding
mm_133354.1	chr16	84606491	84606502	+	1	NA	Intergenic	Intergenic	-73293	NR_040537	78023	Mm.243853	NR_040537		4930529L06Rik	-	RIKEN cDNA 4930529L06 gene	ncRNA
mm_15282.1	chr2	155276504	155276553	+	1	NA	non-coding (NR_046364, exon 1 of 3)	non-coding (NR_046364, exon 1 of 3)	164	NR_046364	66734	Mm.196239	NM_025735	ENSMUSG00000027602	Map1lc3a	1010001H21Rik|4922501H04Rik|LC3|LC3a	microtubule-associated protein 1 light chain 3 alpha	protein-coding
mm_81920.1	chr9	120116508	120116526	+	1	NA	exon (NM_144793, exon 2 of 7)	exon (NM_144793, exon 2 of 7)	6118	NM_144793	208638	Mm.236656	NM_144793	ENSMUSG00000032519	Slc25a38	AV019094|BC010801|appoptosin	solute carrier family 25, member 38	protein-coding
mm_125276.1	chr15	36210498	36210523	+	1	NA	intron (NM_012031, intron 10 of 18)	CpG	29654	NR_106173	102465888		NR_106173	ENSMUSG00000098457	Mir8097	Gm27497|mmu-mir-8097	microRNA 8097	ncRNA
mm_1368.1	chr1	66439769	66439777	+	1	NA	3' UTR (NM_008632, exon 14 of 14)	3' UTR (NM_008632, exon 14 of 14)	-28674	NM_175510	329178	Mm.44798	NM_175510	ENSMUSG00000055567	Unc80	C030018G13Rik|C230061B10Rik|UNC-80	unc-80, NALCN activator	protein-coding
mm_145956.1	chr18	67700637	67700643	+	1	NA	intron (NM_008977, intron 2 of 9)	intron (NM_008977, intron 2 of 9)	23981	NM_001127177	19255	Mm.260433	NM_008977	ENSMUSG00000024539	Ptpn2	AI325124|Ptpt|TC-PTP	protein tyrosine phosphatase, non-receptor type 2	protein-coding
mm_41040.1	chr5	86086266	86086281	+	1	NA	intron (NM_001310639, intron 3 of 7)	B1_Mur3|SINE|Alu	14527	NM_001310639	56792	Mm.131237	NM_019992	ENSMUSG00000029254	Stap1	AI586015|Brdg1|STAP-1	signal transducing adaptor family member 1	protein-coding
mm_111469.1	chr12	98574729	98574741	-	1	NA	promoter-TSS (NM_001316665)	promoter-TSS (NM_001316665)	-23	NM_001316665	72258	Mm.196158	NM_029911	ENSMUSG00000033854	Kcnk10	1700024D23Rik|3010005K24Rik|Trek2	potassium channel, subfamily K, member 10	protein-coding
mm_136258.1	chr16	91011030	91011069	-	1	NA	promoter-TSS (NM_001045515)	promoter-TSS (NM_001045515)	46	NM_001045515	104015	Mm.187079	NM_001045515	ENSMUSG00000022973	Synj1	A930006D20Rik|AA675315|mKIAA0910	synaptojanin 1	protein-coding
mm_120508.1	chr14	66297091	66297101	+	1	NA	promoter-TSS (NM_029979)	promoter-TSS (NM_029979)	33	NR_038077	69303	Mm.352258	NR_038077	ENSMUSG00000085984	1700001G11Rik	-	RIKEN cDNA 1700001G11 gene	ncRNA
mm_133211.1	chr16	75592902	75592928	+	1	NA	promoter-TSS (NM_198302)	promoter-TSS (NM_198302)	24	NM_198302	224344	Mm.273214	NM_198302	ENSMUSG00000032940	Rbm11	A330018F01	RNA binding motif protein 11	protein-coding
mm_67797.1	chr7	97738223	97738317	-	1	NA	promoter-TSS (NM_175105)	promoter-TSS (NM_175105)	-23	NM_175105	66333	Mm.29756	NM_175105	ENSMUSG00000042797	Aqp11	1700015P13Rik|AI648923|sjds	aquaporin 11	protein-coding
mm_123685.1	chr14	69555382	69555392	-	1	NA	promoter-TSS (NM_026174)	promoter-TSS (NM_026174)	0	NR_045091	100504477	Mm.396396	NR_045091		Gm16677	-	predicted gene, 16677	ncRNA
mm_27086.1	chr3	30013328	30013340	-	1	NA	promoter-TSS (NM_007963)	promoter-TSS (NM_007963)	-130	NM_007963	14013	Mm.56965	NM_007963	ENSMUSG00000027684	Mecom	D630039M04Rik|Evi-1|Evi1|Jbo|Mds|Mds1|Mds1-Evi1|Prdm3|Znfpr1b1	MDS1 and EVI1 complex locus	protein-coding
mm_32561.1	chr4	109666845	109666877	+	1	NA	promoter-TSS (NM_001301368)	promoter-TSS (NM_001301368)	-105	NM_001301368	12580	Mm.1912	NM_007671	ENSMUSG00000028551	Cdkn2c	C77269|INK4c|p18|p18-INK4c|p18-INK6|p18INK4c	cyclin-dependent kinase inhibitor 2C (p18, inhibits CDK4)	protein-coding
mm_61259.1	chr7	66060775	66060787	+	1	NA	intron (NM_021336, intron 1 of 8)	CpG	445	NM_021336	68981	Mm.22362	NM_021336	ENSMUSG00000030512	Snrpa1	1500015N06Rik	small nuclear ribonucleoprotein polypeptide A'	protein-coding
mm_171371.1	chr4	119282346	119282348	-	1	NA	exon (NM_011732, exon 5 of 8)	exon (NM_011732, exon 5 of 8)	12166	NM_011732	22608	Mm.258204	NM_011732	ENSMUSG00000028639	Ybx1	1700102N10Rik|C79409|EF1A|MSY1|Nsep1|YB-1|dbpB|mYB-1a	Y box protein 1	protein-coding
mm_112773.1	chr13	19623301	19623313	+	1	NA	5' UTR (NM_016687, exon 1 of 6)	5' UTR (NM_016687, exon 1 of 6)	132	NM_016687	20379	Mm.42095	NM_016687	ENSMUSG00000021319	Sfrp4	-	secreted frizzled-related protein 4	protein-coding
mm_16297.1	chr2	174285353	174285364	+	1	NA	exon (NM_022000, exon 2 of 13)	exon (NM_022000, exon 2 of 13)	1038	NM_022000	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_162715.1	chr10	33461690	33461690	+	1	NA	intron (NM_029726, intron 33 of 37)	intron (NM_029726, intron 33 of 37)	162910	NM_175448	215890	Mm.94461	NM_175448	ENSMUSG00000019785	Clvs2	A330019N05Rik|Rlbp1l2	clavesin 2	protein-coding
mm_33098.1	chr4	124700672	124700698	+	1	NA	promoter-TSS (NM_010213)	promoter-TSS (NM_010213)	-14	NM_010213	14201	Mm.331856	NM_010213	ENSMUSG00000032643	Fhl3	SLIM2	four and a half LIM domains 3	protein-coding
mm_84959.1	chr9	83587243	83587259	-	1	NA	intron (NM_172507, intron 2 of 3)	intron (NM_172507, intron 2 of 3)	38913	NM_172507	212531	Mm.491246	NM_172507	ENSMUSG00000032261	Sh3bgrl2	A930014C21Rik|AA408038|B930089I21	SH3 domain binding glutamic acid-rich protein like 2	protein-coding
mm_38108.1	chr4	134532171	134532186	-	1	NA	exon (NM_001256112, exon 3 of 7)	exon (NM_001256112, exon 3 of 7)	3090	NM_001256112	76824	Mm.30153	NM_029759	ENSMUSG00000046671	Mtfr1l	2410166I05Rik|AI480750|Fam54b	mitochondrial fission regulator 1-like	protein-coding
mm_23486.1	chr3	60501215	60501242	+	1	NA	promoter-TSS (NM_001253711)	promoter-TSS (NM_001253711)	49	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_80355.1	chr9	75190236	75190248	+	1	NA	intron (NM_010864, intron 30 of 40)	intron (NM_010864, intron 30 of 40)	-41772	NM_001081322	208943	Mm.41339	NM_001081322	ENSMUSG00000033590	Myo5c	9130003O20Rik|BB085560|C330029I24	myosin VC	protein-coding
mm_75782.1	chr8	70018619	70018621	-	1	NA	3' UTR (NM_001167939, exon 19 of 19)	3' UTR (NM_001167939, exon 19 of 19)	-22236	NM_145596	234366	Mm.270044	NM_145596	ENSMUSG00000036180	Gatad2a	1110066C11Rik|BC031407|C80248	GATA zinc finger domain containing 2A	protein-coding
mm_168999.1	chr13	100786473	100786476	-	1	NA	promoter-TSS (NM_172301)	promoter-TSS (NM_172301)	12	NM_172301	268697	Mm.260114	NM_172301	ENSMUSG00000041431	Ccnb1	Ccnb1-rs1|Ccnb1-rs13|CycB1|Cycb-4|Cycb-5|Cycb1-rs1	cyclin B1	protein-coding
mm_147337.1	chr18	42899453	42899463	-	1	NA	promoter-TSS (NR_073583)	promoter-TSS (NR_073583)	48	NR_073583	72930	Mm.26134	NM_027531	ENSMUSG00000024500	Ppp2r2b	2900026H06Rik|6330404L05Rik|E130009M08Rik|PP2A-PR55B|PR55-BETA|SCA12	protein phosphatase 2, regulatory subunit B, beta	protein-coding
mm_65264.1	chr7	19921140	19921146	-	1	NA	promoter-TSS (NM_027514)	promoter-TSS (NM_027514)	0	NM_027514	52118	Mm.227506	NM_027514	ENSMUSG00000040511	Pvr	3830421F03Rik|CD155|D7Ertd458e|HVED|PVS|Taa1|Tage4|mE4|necl-5	poliovirus receptor	protein-coding
mm_172668.1	chr8	43306955	43306956	-	1	NA	promoter-TSS (NM_009556)	promoter-TSS (NM_009556)	54	NM_009556	22702	Mm.285848	NM_009556	ENSMUSG00000051176	Zfp42	Rex-1|Rex1|Zfp-42	zinc finger protein 42	protein-coding
mm_166092.1	chr4	140750515	140750521	-	1	NA	intron (NM_011061, intron 12 of 15)	intron (NM_011061, intron 12 of 15)	-7875	NM_153106	242726	Mm.271661	NM_153106	ENSMUSG00000040935	Padi6	Pad6|Padi5|ePAD	peptidyl arginine deiminase, type VI	protein-coding
mm_95233.1	chr11	44538055	44538058	+	1	NA	intron (NM_028862, intron 3 of 10)	intron (NM_028862, intron 3 of 10)	18679	NM_001166553	74315	Mm.156771	NM_028862	ENSMUSG00000019189	Rnf145	3732413I11Rik|TMRF1	ring finger protein 145	protein-coding
mm_30024.1	chr3	135665514	135665524	-	1	NA	intron (NM_008689, intron 3 of 24)	intron (NM_008689, intron 3 of 24)	26028	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_79808.1	chr9	64177442	64177452	+	1	NA	exon (NM_024212, exon 7 of 10)	exon (NM_024212, exon 7 of 10)	-1850	NM_183316	330959	Mm.24082	NM_183316	ENSMUSG00000032398	Snapc5	2010103A03Rik	small nuclear RNA activating complex, polypeptide 5	protein-coding
mm_90629.1	chr10	128459735	128459763	+	1	NA	TTS (NR_106183)	TTS (NR_106183)	513	NM_001114097	68094	Mm.417338	NM_198160	ENSMUSG00000025369	Smarcc2	5930405J04Rik	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2	protein-coding
mm_131957.1	chr16	24486949	24486986	+	1	NA	intron (NM_001145952, intron 2 of 11)	(CA)n|Simple_repeat|Simple_repeat	38876	NM_001145952	210126	Mm.209385	NM_178665	ENSMUSG00000033306	Lpp	9430020K16Rik|AA959454|AU024130|B130055L10Rik|C79715|D630048H16	LIM domain containing preferred translocation partner in lipoma	protein-coding
mm_49765.1	chr6	34863102	34863112	+	1	NA	promoter-TSS (NM_197986)	promoter-TSS (NM_197986)	-39	NM_197986	68487	Mm.248440	NM_197986	ENSMUSG00000057137	Tmem140	1110007F12Rik	transmembrane protein 140	protein-coding
mm_94009.1	chr10	127620961	127621031	-	1	NA	5' UTR (NM_008512, exon 1 of 89)	5' UTR (NM_008512, exon 1 of 89)	152	NM_008512	16971	Mm.271854	NM_008512	ENSMUSG00000040249	Lrp1	A2mr|AI316852|CD91|Lrp|b2b1554Clo	low density lipoprotein receptor-related protein 1	protein-coding
mm_28827.1	chr3	96293997	96294001	-	1	NA	promoter-TSS (NM_010186)	promoter-TSS (NM_010186)	-30	NM_010186	14129	Mm.150	NM_010186	ENSMUSG00000015947	Fcgr1	AI323638|AV092959|CD64|FcgammaRI|IGGHAFC	Fc receptor, IgG, high affinity I	protein-coding
mm_28185.1	chr3	88058233	88058245	-	1	NA	intron (NM_144897, intron 1 of 5)	intron (NM_144897, intron 1 of 5)	256	NM_144897	246703	Mm.205996	NM_144897	ENSMUSG00000028070	Apoa1bp	AA087124|AI-BP|AIBP|Apoa1ip|ESTM37|Naxe	apolipoprotein A-I binding protein	protein-coding
mm_131237.1	chr16	10484139	10484166	+	1	NA	intron (NM_001302618, intron 1 of 18)	intron (NM_001302618, intron 1 of 18)	-4026	NM_007575	12265	Mm.249560	NM_007575	ENSMUSG00000022504	Ciita	C2ta|EG669998|Gm9475|Mhc2ta	class II transactivator	protein-coding
mm_118849.1	chr14	25666190	25666210	+	1	NA	3' UTR (NM_183208, exon 24 of 24)	3' UTR (NM_183208, exon 24 of 24)	-27970	NM_134084	105675	Mm.41656	NM_134084	ENSMUSG00000021868	Ppif	AW457192|CyP-D|CyP-F|CypD|PPIase	peptidylprolyl isomerase F (cyclophilin F)	protein-coding
mm_15842.1	chr2	164746029	164746039	+	1	NA	promoter-TSS (NM_133763)	promoter-TSS (NM_133763)	19	NM_133763	76233	Mm.440009	NM_133763	ENSMUSG00000017299	Dnttip1	6430706C13Rik	deoxynucleotidyltransferase, terminal, interacting protein 1	protein-coding
mm_125559.1	chr15	58889072	58889151	+	1	NA	promoter-TSS (NM_175226)	promoter-TSS (NM_175226)	-118	NM_175226	75841	Mm.4537	NM_175226	ENSMUSG00000037075	Rnf139	4930555P18Rik	ring finger protein 139	protein-coding
mm_123532.1	chr14	66804897	66804906	-	1	NA	3' UTR (NM_009955, exon 14 of 14)	3' UTR (NM_009955, exon 14 of 14)	63699	NM_009955	12934	Mm.352648	NM_009955	ENSMUSG00000022048	Dpysl2	AI851130|Crmp2|DRP2|Musunc33|TOAD-64|Ulip2	dihydropyrimidinase-like 2	protein-coding
mm_73581.1	chr8	109838769	109838782	+	1	NA	promoter-TSS (NR_028532)	promoter-TSS (NR_028532)	-537	NR_028532	100217432		NR_028532		Snord71	MBII-239	small nucleolar RNA, C/D box 71	snoRNA
mm_17119.1	chr2	24475597	24475605	-	1	NA	promoter-TSS (NM_011040)	promoter-TSS (NM_011040)	-2	NM_011040	18510	Mm.2533	NM_011040	ENSMUSG00000026976	Pax8	Pax-8	paired box 8	protein-coding
mm_71349.1	chr8	45628156	45628170	+	1	NA	5' UTR (NM_001310707, exon 1 of 24)	5' UTR (NM_001310707, exon 1 of 24)	412	NM_001310707	234214	Mm.211096	NM_172752	ENSMUSG00000031626	Sorbs2	2010203O03Rik|9430041O17Rik|A530071H08|Argbp2|mKIAA0777|nArgBP2	sorbin and SH3 domain containing 2	protein-coding
mm_84016.1	chr9	57653432	57653455	-	1	NA	5' UTR (NM_001304761, exon 1 of 15)	5' UTR (NM_001304761, exon 1 of 15)	188	NM_001304761	12988	Mm.21974	NM_007783	ENSMUSG00000032312	Csk	AW212630|p50CSK	c-src tyrosine kinase	protein-coding
mm_38812.1	chr4	148444734	148444739	-	1	NA	promoter-TSS (NM_027873)	promoter-TSS (NM_027873)	15	NM_027873	71707	Mm.292503	NM_027873	ENSMUSG00000047719	Ubiad1	1200002M06Rik|AI426463|AW320947|Tere1	UbiA prenyltransferase domain containing 1	protein-coding
mm_140766.1	chr17	17624624	17624634	-	1	NA	promoter-TSS (NM_172827)	promoter-TSS (NM_172827)	-140	NM_172827	240028	Mm.328807	NM_172827	ENSMUSG00000023845	Lnpep	2010309L07Rik|4732490P18Rik|CAP|IRAP|PLAP|gp160|vp165	leucyl/cystinyl aminopeptidase	protein-coding
mm_128484.1	chr15	50890071	50890086	-	1	NA	promoter-TSS (NR_035444)	promoter-TSS (NR_035444)	-37	NM_032000	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_33570.1	chr4	132274370	132274383	+	1	NA	promoter-TSS (NM_025579)	promoter-TSS (NM_025579)	1	NM_025579	66464	Mm.331926	NM_025579	ENSMUSG00000028899	Taf12	20kDa|2810422D08Rik|AW557038|Taf2J	TATA-box binding protein associated factor 12	protein-coding
mm_129414.1	chr15	78336417	78336428	-	1	NA	exon (NM_007780, exon 3 of 14)	exon (NM_007780, exon 3 of 14)	10432	NM_007780	12983	Mm.235324	NM_007780	ENSMUSG00000071713	Csf2rb	AI848964|AIC2B|Bc|CDw131|Csf2rb1|Csfgmrb|Il3r|Il3rb|Il3rb1|Il5rb	colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage)	protein-coding
mm_19161.1	chr2	83725420	83725456	-	1	NA	intron (NM_008402, intron 1 of 29)	intron (NM_008402, intron 1 of 29)	1041	NM_008402	16410	Mm.227	NM_008402	ENSMUSG00000027087	Itgav	1110004F14Rik|2610028E01Rik|CD51|D430040G12Rik	integrin alpha V	protein-coding
mm_121115.1	chr14	101840324	101840328	+	1	NA	promoter-TSS (NM_001347628)	promoter-TSS (NM_001347628)	-297	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_107439.1	chr12	36314138	36314148	+	1	NA	promoter-TSS (NM_025312)	promoter-TSS (NM_025312)	-26	NM_025312	66042	Mm.43375	NM_025312	ENSMUSG00000036169	Sostdc1	0610006G05Rik|Sostl|USAG-1|Wise|ectodin	sclerostin domain containing 1	protein-coding
mm_74731.1	chr8	18296489	18296489	-	1	NA	Intergenic	U2|snRNA|snRNA	-298684	NM_173189	244329	Mm.235296	NM_173189	ENSMUSG00000039842	Mcph1	5430437K10Rik|BRIT1|D030046N04Rik|MCT	microcephaly, primary autosomal recessive 1	protein-coding
mm_125429.1	chr15	44064198	44064203	+	1	NA	Intergenic	RMER17A2|LTR|ERVK	-131935	NM_013696	22045	Mm.309350	NM_013696	ENSMUSG00000038760	Trhr	TRH-R1	thyrotropin releasing hormone receptor	protein-coding
mm_146648.1	chr18	11051330	11051369	-	1	NA	non-coding (NR_105023, exon 2 of 6)	non-coding (NR_105023, exon 2 of 6)	-1161	NM_010258	14465	Mm.329287	NM_010258	ENSMUSG00000005836	Gata6	AA410133|GATA-6	GATA binding protein 6	protein-coding
mm_40782.1	chr5	67307025	67307033	+	1	NA	promoter-TSS (NM_178651)	promoter-TSS (NM_178651)	74	NM_001310629	109108	Mm.234455	NM_178651	ENSMUSG00000029221	Slc30a9	2310024J23Rik|AL024256|GAC63|HUEL|znT-9	solute carrier family 30 (zinc transporter), member 9	protein-coding
mm_106672.1	chr11	121673104	121673146	-	1	NA	promoter-TSS (NM_178664)	promoter-TSS (NM_178664)	26	NM_178664	210004	Mm.386847	NM_178664	ENSMUSG00000046605	B3gntl1	6030413G23Rik	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase-like 1	protein-coding
mm_155648.1	chrX	85716541	85716551	+	1	NA	intron (NM_001331046, intron 13 of 19)	intron (NM_001331046, intron 13 of 19)	60273	NM_001294140	14933	Mm.246682	NM_008194	ENSMUSG00000025059	Gk	D930012N15Rik|Gyk	glycerol kinase	protein-coding
mm_116644.1	chr13	49147932	49148037	-	1	NA	5' UTR (NM_001290311, exon 1 of 29)	5' UTR (NM_001290311, exon 1 of 29)	344	NM_029361	75607	Mm.342723	NM_029361	ENSMUSG00000037989	Wnk2	1810073P09Rik|AW122246|ESTM15|X83337|mKIAA1760	WNK lysine deficient protein kinase 2	protein-coding
mm_2756.1	chr1	129273492	129273498	+	1	NA	5' UTR (NM_172485, exon 1 of 28)	5' UTR (NM_172485, exon 1 of 28)	191	NM_172485	210417	Mm.380518	NM_172485	ENSMUSG00000042581	Thsd7b	1700074E13Rik|B930082A18|D130067I03Rik	thrombospondin, type I, domain containing 7B	protein-coding
mm_152396.1	chr19	10525702	10525732	-	1	NA	promoter-TSS (NM_025333)	promoter-TSS (NM_025333)	473	NM_172302	269061	Mm.490260	NM_172302	ENSMUSG00000034820	Cpsf7	5730453I16Rik|AL022757|C330017N18Rik	cleavage and polyadenylation specific factor 7	protein-coding
mm_116612.1	chr13	48871007	48871020	-	1	NA	promoter-TSS (NM_011078)	promoter-TSS (NM_011078)	-128	NM_011078	18676	Mm.486213	NM_011078	ENSMUSG00000038025	Phf2	GRC5	PHD finger protein 2	protein-coding
mm_97251.1	chr11	75755566	75755628	+	1	NA	exon (NM_009536, exon 3 of 6)	exon (NM_009536, exon 3 of 6)	22710	NM_009536	22627	Mm.234700	NM_009536	ENSMUSG00000020849	Ywhae	AU019196	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide	protein-coding
mm_164441.1	chr16	49855107	49855116	+	1	NA	promoter-TSS (NM_010581)	promoter-TSS (NM_010581)	-543	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_97988.1	chr11	83942216	83942218	+	1	NA	exon (NM_030096, exon 1 of 15)	exon (NM_030096, exon 1 of 15)	127	NM_030096	78394	Mm.280544	NM_030096	ENSMUSG00000020677	Ddx52	2700029C06Rik|ROK1	DEAD (Asp-Glu-Ala-Asp) box polypeptide 52	protein-coding
mm_16342.1	chr2	174344380	174344403	+	1	NA	intron (NM_001310085, intron 7 of 12)	intron (NM_001310085, intron 7 of 12)	14302	NM_001077510	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_65579.1	chr7	27228287	27228304	-	1	NA	exon (NM_181593, exon 1 of 7)	exon (NM_181593, exon 1 of 7)	302	NM_181593	233011	Mm.30963	NM_181593	ENSMUSG00000003752	Itpkc	9130023N17Rik	inositol 1,4,5-trisphosphate 3-kinase C	protein-coding
mm_41239.1	chr5	88765150	88765160	+	1	NA	5' UTR (NM_007832, exon 1 of 7)	5' UTR (NM_007832, exon 1 of 7)	142	NM_007832	13178	Mm.298892	NM_007832	ENSMUSG00000029366	Dck	-	deoxycytidine kinase	protein-coding
mm_14380.1	chr2	129630733	129630914	+	1	NA	3' UTR (NM_001291022, exon 5 of 5)	3' UTR (NM_001291022, exon 5 of 5)	37654	NM_001291022	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_116837.1	chr13	54688066	54688093	-	1	NA	promoter-TSS (NM_001146025)	promoter-TSS (NM_001146025)	121	NM_001146027	105239	Mm.25366	NM_134064	ENSMUSG00000034928	Rnf44	AI854545|mKIAA1100	ring finger protein 44	protein-coding
mm_9974.1	chr1	191201250	191201279	-	1	NA	Intergenic	Intergenic	-17931	NM_007498	11910	Mm.2706	NM_007498	ENSMUSG00000026628	Atf3	LRG-21	activating transcription factor 3	protein-coding
mm_25546.1	chr3	115888099	115888103	+	1	NA	promoter-TSS (NR_027895)	promoter-TSS (NR_027895)	19	NR_027895	68161	Mm.392043	NR_015487	ENSMUSG00000054426	A930005H10Rik	-	RIKEN cDNA A930005H10 gene	ncRNA
mm_109983.1	chr12	13249139	13249191	-	1	NA	promoter-TSS (NM_134040)	promoter-TSS (NM_134040)	9	NM_134040	104721	Mm.251255	NM_134040	ENSMUSG00000037149	Ddx1	AA409185|DBP-RB	DEAD (Asp-Glu-Ala-Asp) box polypeptide 1	protein-coding
mm_81362.1	chr9	108692203	108692212	+	1	NA	promoter-TSS (NM_008924)	promoter-TSS (NM_008924)	64	NM_008924	19087	Mm.253102	NM_008924	ENSMUSG00000032601	Prkar2a	1110061A24Rik|AI317181|AI836829|RII(alpha)	protein kinase, cAMP dependent regulatory, type II alpha	protein-coding
mm_140726.1	chr17	15498264	15498274	-	1	NA	promoter-TSS (NM_011185)	promoter-TSS (NM_011185)	7	NM_011185	19170	Mm.32912	NM_011185	ENSMUSG00000014769	Psmb1	AA409053|C81484|Lmpc5	proteasome (prosome, macropain) subunit, beta type 1	protein-coding
mm_144952.1	chr18	37808714	37808719	+	1	NA	exon (NM_033581, exon 1 of 4)	exon (NM_033581, exon 1 of 4)	2306	NM_033581	93706	Mm.247203	NM_033581	ENSMUSG00000102918	Pcdhgc3	PC43|Pcdh2	protocadherin gamma subfamily C, 3	protein-coding
mm_1106.1	chr1	59763754	59763764	+	1	NA	promoter-TSS (NM_007561)	promoter-TSS (NM_007561)	-520	NM_007561	12168	Mm.7106	NM_007561	ENSMUSG00000067336	Bmpr2	2610024H22Rik|AL117858|AW546137|BB189135|BMP-2|BMPR-2|BMPR-II|BMPRII|BRK-3|Gm20272	bone morphogenetic protein receptor, type II (serine/threonine kinase)	protein-coding
mm_36855.1	chr4	106855137	106855162	-	1	NA	Intergenic	Intergenic	-50142	NM_001347159	329910	Mm.222956	NM_025590	ENSMUSG00000034853	Acot11	1110020M10Rik|2010309H15Rik|AW060409|BFIT|BFIT1|Thea|Them1|mKIAA0707	acyl-CoA thioesterase 11	protein-coding
mm_99649.1	chr11	105589759	105589808	+	1	NA	promoter-TSS (NM_181071)	promoter-TSS (NM_181071)	-203	NM_181071	77097	Mm.22501	NM_175492	ENSMUSG00000053580	Tanc2	3526402J09Rik|5730590C14Rik	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2	protein-coding
mm_135570.1	chr16	50330974	50330978	-	1	NA	intron (NM_001347240, intron 3 of 16)	intron (NM_001347240, intron 3 of 16)	101413	NM_027444	70508	Mm.28940	NM_027444	ENSMUSG00000022641	Bbx	5530401J07Rik|5730403O13Rik	bobby sox HMG box containing	protein-coding
mm_14326.1	chr2	129367269	129367290	+	1	NA	exon (NM_008361, exon 5 of 7)	exon (NM_008361, exon 5 of 7)	-2623	NR_015474	329514	Mm.207315	NM_177848	ENSMUSG00000074805	Il1bos	9430083I22|Gm14047|OTTMUSG00000015529	interleukin 1 beta, opposite strand	ncRNA
mm_16365.1	chr2	174760753	174760780	+	1	NA	5' UTR (NM_007903, exon 1 of 5)	5' UTR (NM_007903, exon 1 of 5)	147	NM_007903	13616	Mm.9478	NM_007903	ENSMUSG00000027524	Edn3	ET-3|PPET3|ls|tmgc48	endothelin 3	protein-coding
mm_36965.1	chr4	109202226	109202246	-	1	NA	promoter-TSS (NM_133885)	promoter-TSS (NM_133885)	36	NM_133885	100273	Mm.366315	NM_133885	ENSMUSG00000028559	Osbpl9	2600011I06Rik|AU015843|Orp-9	oxysterol binding protein-like 9	protein-coding
mm_55085.1	chr6	49215014	49215022	-	1	NA	promoter-TSS (NM_023670)	promoter-TSS (NM_023670)	-64	NM_023670	140488	Mm.281018	NM_023670	ENSMUSG00000029814	Igf2bp3	2610101N11Rik|AA522010|AL022933|AU045931|IMP-3|IMP3|Koc13|Neilsen|mimp3	insulin-like growth factor 2 mRNA binding protein 3	protein-coding
mm_158709.1	chrX	162415282	162415304	-	1	NA	3' UTR (NM_001290633, exon 18 of 18)	3' UTR (NM_001290633, exon 18 of 18)	228365	NM_001290633	194590	Mm.442441	NM_178256	ENSMUSG00000040855	Reps2	POB1	RALBP1 associated Eps domain containing protein 2	protein-coding
mm_69672.1	chr7	139983980	139984001	-	1	NA	exon (NM_001291066, exon 20 of 24)	exon (NM_001291066, exon 20 of 24)	2884	NR_106029	102465643		NR_106029	ENSMUSG00000099092	Mir7062	Gm27339|mmu-mir-7062	microRNA 7062	ncRNA
mm_58167.1	chr6	142571626	142571631	-	1	NA	promoter-TSS (NM_008428)	promoter-TSS (NM_008428)	-14	NM_008428	16523	Mm.1482	NM_008428	ENSMUSG00000030247	Kcnj8	AI448900|Kir6.1|gnite|slmbr|sltr|uKATP-1	potassium inwardly-rectifying channel, subfamily J, member 8	protein-coding
mm_50508.1	chr6	49036668	49036705	+	1	NA	5' UTR (NM_053110, exon 1 of 11)	5' UTR (NM_053110, exon 1 of 11)	168	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_25885.1	chr3	130874103	130874133	+	1	NA	Intergenic	Intergenic	-143720	NM_001005859	68436	Mm.140568	NM_026724	ENSMUSG00000062006	Rpl34	1100001I22Rik	ribosomal protein L34	protein-coding
mm_142643.1	chr17	47437221	47437247	-	1	NA	5' UTR (NM_029296, exon 1 of 4)	5' UTR (NM_029296, exon 1 of 4)	141	NM_029296	75462	Mm.46129	NM_029296	ENSMUSG00000047150	1700001C19Rik	-	RIKEN cDNA 1700001C19 gene	protein-coding
mm_162418.1	chr1	91296004	91296011	+	1	NA	Intergenic	Intergenic	-2331	NM_016717	50880	Mm.25724	NM_016717	ENSMUSG00000026307	Scly	9830169H08|A930015N15Rik|SCL|Scly1|Scly2	selenocysteine lyase	protein-coding
mm_103429.1	chr11	75751907	75751945	-	1	NA	exon (NM_009536, exon 2 of 6)	exon (NM_009536, exon 2 of 6)	19039	NM_009536	22627	Mm.234700	NM_009536	ENSMUSG00000020849	Ywhae	AU019196	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide	protein-coding
mm_87081.1	chr10	29313228	29313238	+	1	NA	promoter-TSS (NM_001110195)	promoter-TSS (NM_001110195)	67	NM_001110195	52665	Mm.28930	NM_025855	ENSMUSG00000019883	Echdc1	1700028A24Rik|AI314462|AI930038|D10Ertd667e|MMCD	enoyl Coenzyme A hydratase domain containing 1	protein-coding
mm_100997.1	chr11	8468468	8468477	-	1	NA	intron (NM_001083587, intron 20 of 30)	intron (NM_001083587, intron 20 of 30)	196063	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_11448.1	chr2	32081584	32081621	+	1	NA	intron (NM_175511, intron 1 of 1)	intron (NM_175511, intron 1 of 1)	2103	NM_175511	241303	Mm.250441	NM_175511	ENSMUSG00000050592	Fam78a	A130092J06Rik	family with sequence similarity 78, member A	protein-coding
mm_142850.1	chr17	51804260	51804270	-	1	NA	intron (NM_009122, intron 4 of 10)	intron (NM_009122, intron 4 of 10)	7789	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_8594.1	chr1	156007709	156007722	-	1	NA	intron (NM_144791, intron 6 of 6)	intron (NM_144791, intron 6 of 6)	27102	NM_001160019	208263	Mm.211654	NM_144791	ENSMUSG00000026466	Tor1aip1	LAP1|Lap1B	torsin A interacting protein 1	protein-coding
mm_79104.1	chr9	46256897	46256937	+	1	NA	Intergenic	Intergenic	-11691	NM_080434	66113	Mm.29738	NM_080434	ENSMUSG00000032079	Apoa5	1300007O05Rik|Apoav|RAP3	apolipoprotein A-V	protein-coding
mm_129127.1	chr15	76188967	76188978	-	1	NA	exon (NM_201393, exon 14 of 32)	exon (NM_201393, exon 14 of 32)	6738	NM_201394	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
mm_8315.1	chr1	144249135	144249146	-	1	NA	promoter-TSS (NM_015811)	promoter-TSS (NM_015811)	-36	NM_015811	50778	Mm.103701	NM_015811	ENSMUSG00000026358	Rgs1	BL34	regulator of G-protein signaling 1	protein-coding
mm_95470.1	chr11	50772214	50772214	+	1	NA	intron (NM_175643, intron 5 of 21)	intron (NM_175643, intron 5 of 21)	55517	NM_013922	30944	Mm.103674	NM_013922	ENSMUSG00000044807	Zfp354c	5330421P20Rik|AJ18|AW743325|Kid3|Tcf17l2|Znf354c|mKIAA4218	zinc finger protein 354C	protein-coding
mm_81915.1	chr9	120110498	120110508	+	1	NA	exon (NM_144793, exon 1 of 7)	exon (NM_144793, exon 1 of 7)	104	NM_144793	208638	Mm.236656	NM_144793	ENSMUSG00000032519	Slc25a38	AV019094|BC010801|appoptosin	solute carrier family 25, member 38	protein-coding
mm_167326.1	chr8	69901769	69901796	+	1	NA	promoter-TSS (NM_032004)	promoter-TSS (NM_032004)	-402	NM_032004	83984	Mm.432504	NM_032004	ENSMUSG00000047654	Tssk6	Sstk|TSK-6|TSSK-6	testis-specific serine kinase 6	protein-coding
mm_143757.1	chr17	81604268	81604286	-	1	NA	intron (NR_104580, intron 2 of 8)	intron (NR_104580, intron 2 of 8)	134110	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_27148.1	chr3	32985077	32985085	-	1	NA	promoter-TSS (NM_001163517)	promoter-TSS (NM_001163517)	-2	NM_001163517	58869	Mm.151332	NM_021483	ENSMUSG00000027674	Pex5l	1700016J08Rik|PXR2|Pex2|TRIP8b|pex5Rp	peroxisomal biogenesis factor 5-like	protein-coding
mm_16510.1	chr2	181365418	181365438	+	1	NA	promoter-TSS (NM_001165995)	promoter-TSS (NM_001165995)	5	NM_001048148	229007	Mm.87720	NM_144894	ENSMUSG00000027582	Zgpat	1500006I01Rik|BC021513	zinc finger, CCCH-type with G patch domain	protein-coding
mm_17137.1	chr2	24975850	24975857	-	1	NA	promoter-TSS (NM_001031808)	promoter-TSS (NM_001031808)	-180	NM_146251	241274	Mm.389243	NM_146251	ENSMUSG00000036833	Pnpla7	BC027342|E430013P11Rik|Nre	patatin-like phospholipase domain containing 7	protein-coding
mm_102241.1	chr11	54985165	54985178	-	1	NA	exon (NM_013472, exon 23 of 26)	exon (NM_013472, exon 23 of 26)	-22231	NM_001271455	57783	Mm.259671	NM_021327	ENSMUSG00000020400	Tnip1	ABIN|ABIN-1|ABIN1|AU018810|Naf1|Nef|VAN	TNFAIP3 interacting protein 1	protein-coding
mm_92351.1	chr10	75893062	75893082	-	1	NA	promoter-TSS (NM_024440)	promoter-TSS (NM_024440)	-326	NM_024440	70377	Mm.275878	NM_024440	ENSMUSG00000009092	Derl3	1810006I20Rik|1810063P04Rik|IZP6|derlin-3	Der1-like domain family, member 3	protein-coding
mm_47099.1	chr5	118169586	118169589	-	1	NA	promoter-TSS (NM_007545)	promoter-TSS (NM_007545)	-177	NM_007545	12123	Mm.384468	NM_007545	ENSMUSG00000046607	Hrk	AI838259|Bid3|DP5|harakiri	harakiri, BCL2 interacting protein (contains only BH3 domain)	protein-coding
mm_99661.1	chr11	105901897	105901910	+	1	NA	intron (NM_181071, intron 17 of 25)	intron (NM_181071, intron 17 of 25)	42244	NM_007805	13056	Mm.149403	NM_007805	ENSMUSG00000019590	Cyb561	-	cytochrome b-561	protein-coding
mm_93435.1	chr10	109010923	109010952	-	1	NA	promoter-TSS (NM_001252342)	promoter-TSS (NM_001252342)	38	NM_009306	20979	Mm.289702	NM_009306	ENSMUSG00000035864	Syt1	AW124717|G630098F17Rik|SytI	synaptotagmin I	protein-coding
mm_62994.1	chr7	120635201	120635251	+	1	NA	promoter-TSS (NM_025899)	promoter-TSS (NM_025899)	37	NM_025899	67003	Mm.334206	NM_025899	ENSMUSG00000030884	Uqcrc2	1500004O06Rik	ubiquinol cytochrome c reductase core protein 2	protein-coding
mm_156121.1	chrX	115683703	115683703	+	1	NA	Intergenic	Intergenic	756714	NR_130989	78086		NR_130989	ENSMUSG00000085619	4930555B12Rik	-	RIKEN cDNA 4930555B12 gene	ncRNA
mm_91484.1	chr10	35485354	35485363	-	1	NA	Intergenic	RLTR44A|LTR|ERVK	1001958	NM_010237	14302	Mm.332432	NM_010237	ENSMUSG00000019779	Frk	BSK|BSK/IYK|C85044|GTK|RAK	fyn-related kinase	protein-coding
mm_18254.1	chr2	52263609	52263619	-	1	NA	exon (NM_010889, exon 54 of 157)	exon (NM_010889, exon 54 of 157)	-27388	NR_040620	78049	Mm.243883	NR_040620		4930573O16Rik	-	RIKEN cDNA 4930573O16 gene	ncRNA
mm_55124.1	chr6	50566536	50566558	-	1	NA	promoter-TSS (NM_007808)	promoter-TSS (NM_007808)	-73	NM_007808	13063	Mm.35389	NM_007808	ENSMUSG00000063694	Cycs	-	cytochrome c, somatic	protein-coding
mm_75061.1	chr8	33666372	33666377	-	1	NA	intron (NM_010344, intron 1 of 12)	intron (NM_010344, intron 1 of 12)	13136	NM_010344	14782	Mm.283573	NM_010344	ENSMUSG00000031584	Gsr	AI325518|D8Ertd238e|Gr-1|Gr1	glutathione reductase	protein-coding
mm_40855.1	chr5	73502660	73502675	+	1	NA	intron (NM_001190733, intron 1 of 9)	intron (NM_001190733, intron 1 of 9)	11641	NM_178896	100737	Mm.220312	NM_178896	ENSMUSG00000051674	Dcun1d4	AI836376	DCN1, defective in cullin neddylation 1, domain containing 4 (S. cerevisiae)	protein-coding
mm_172575.1	chr8	11313019	11313032	+	1	NA	promoter-TSS (NM_009931)	promoter-TSS (NM_009931)	-199	NM_009931	12826	Mm.738	NM_009931	ENSMUSG00000031502	Col4a1	Bru|Col4a-1|Raw|Svc	collagen, type IV, alpha 1	protein-coding
mm_34530.1	chr4	149334651	149334679	+	1	NA	promoter-TSS (NR_131918)	promoter-TSS (NR_131918)	26	NR_131918	74310	Mm.440455	NR_131918	ENSMUSG00000085286	Ube4bos3	1700121F15Rik	ubiquitination factor E4B, opposite strand 3	ncRNA
mm_29933.1	chr3	131504945	131504954	-	1	NA	Intergenic	Intergenic	-59819	NM_001289479	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_34024.1	chr4	138045348	138045354	+	1	NA	5' UTR (NM_001256198, exon 3 of 33)	5' UTR (NM_001256198, exon 3 of 33)	51895	NM_172703	230861	Mm.268903	NM_172703	ENSMUSG00000028760	Eif4g3	1500002J22Rik|4930523M17Rik|G1-419-52|eIF4GII|repro8	eukaryotic translation initiation factor 4 gamma, 3	protein-coding
mm_118862.1	chr14	25842224	25842234	+	1	NA	promoter-TSS (NM_013469)	promoter-TSS (NM_013469)	74	NM_013469	11744	Mm.294083	NM_013469	ENSMUSG00000021866	Anxa11	A830099O17Rik|Anx11	annexin A11	protein-coding
mm_46245.1	chr5	99243215	99243252	-	1	NA	exon (NM_181318, exon 2 of 14)	exon (NM_181318, exon 2 of 14)	9694	NM_181318	320292	Mm.259074	NM_145839	ENSMUSG00000089809	Rasgef1b	4732452O09Rik|GPIgamma4|Gpig4	RasGEF domain family, member 1B	protein-coding
mm_125190.1	chr15	32489686	32489689	+	1	NA	intron (NM_009154, intron 5 of 22)	intron (NM_009154, intron 5 of 22)	244874	NM_009154	20356	Mm.260374	NM_009154	ENSMUSG00000022231	Sema5a	5930434A13|9130201M22Rik|AI464145|Semaf|semF	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A	protein-coding
mm_166043.1	chr4	130520509	130520556	+	1	NA	Intergenic	Intergenic	53504	NM_025998	67149	Mm.423029	NM_025998	ENSMUSG00000078532	Nkain1	2610200G18Rik|2810426C15Rik	Na+/K+ transporting ATPase interacting 1	protein-coding
mm_105789.1	chr11	109828067	109828070	-	1	NA	promoter-TSS (NM_001162428)	promoter-TSS (NM_001162428)	-22	NM_001162428	69324	Mm.31700	NM_027038	ENSMUSG00000020617	1700012B07Rik	1700069D21Rik	RIKEN cDNA 1700012B07 gene	protein-coding
mm_139156.1	chr17	47540726	47540737	+	1	NA	intron (NM_001081635, intron 1 of 6)	PB1D10|SINE|Alu	35680	NM_001081635	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_162439.1	chr1	109983752	109983762	+	1	NA	promoter-TSS (NM_172853)	promoter-TSS (NM_172853)	34	NM_172853	241201	Mm.213407	NM_172853	ENSMUSG00000026312	Cdh7	9330156F07Rik|CDH7L1	cadherin 7, type 2	protein-coding
mm_172426.1	chr7	28259508	28259519	-	1	NA	Intergenic	MMVL30-int|LTR|ERV1	-8368	NM_198425	386655	Mm.258201	NM_198425	ENSMUSG00000046058	Eid2	Cri2|EID-2	EP300 interacting inhibitor of differentiation 2	protein-coding
mm_53772.1	chr6	145953578	145953584	+	1	NA	intron (NM_010656, intron 1 of 2)	intron (NM_010656, intron 1 of 2)	19434	NM_010656	16651	Mm.49689	NM_010656	ENSMUSG00000030255	Sspn	Krag	sarcospan	protein-coding
mm_62010.1	chr7	91262724	91262735	+	1	NA	intron (NM_011807, intron 1 of 22)	intron (NM_011807, intron 1 of 22)	171943	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_150861.1	chr19	45016938	45016942	+	1	NA	intron (NM_145503, intron 1 of 4)	intron (NM_145503, intron 1 of 4)	-1195	NM_001130526	226154	Mm.28204	NM_145503	ENSMUSG00000035342	Lzts2	BC014695|LAPSER1|mKIAA1813	leucine zipper, putative tumor suppressor 2	protein-coding
mm_43299.1	chr5	134583087	134583094	+	1	NA	intron (NM_020022, intron 1 of 10)	ID_B1|SINE|B4	400	NM_020022	19718	Mm.332739	NM_020022	ENSMUSG00000023104	Rfc2	2610008M13Rik|40kDa|AI326953|Recc2	replication factor C (activator 1) 2	protein-coding
mm_83445.1	chr9	45009600	45009645	-	1	NA	promoter-TSS (NM_007648)	promoter-TSS (NM_007648)	-32	NM_007648	12501	Mm.210361	NM_007648	ENSMUSG00000032093	Cd3e	AI504783|CD3|CD3epsilon|T3e	CD3 antigen, epsilon polypeptide	protein-coding
mm_30130.1	chr3	141982225	141982237	-	1	NA	promoter-TSS (NM_007560)	promoter-TSS (NM_007560)	33	NM_007560	12167	Mm.39089	NM_007560	ENSMUSG00000052430	Bmpr1b	AI385617|ALK-6|AV355320|Acvrlk6|Alk6|BMPR-1B|BMPR-IB|CFK-43a|SKR6	bone morphogenetic protein receptor, type 1B	protein-coding
mm_135516.1	chr16	48772103	48772143	-	1	NA	promoter-TSS (NM_198297)	promoter-TSS (NM_198297)	-167	NM_198297	77647	Mm.167298	NM_198297	ENSMUSG00000030775	Trat1	C030046M14Rik|Tcrim|Trim	T cell receptor associated transmembrane adaptor 1	protein-coding
mm_87449.1	chr10	51482579	51482613	+	1	NA	intron (NM_001291892, intron 4 of 8)	intron (NM_001291892, intron 4 of 8)	1984	NM_001291892	14727	Mm.439661	NM_008147	ENSMUSG00000062593	Lilr4b	Gp49a|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4B	protein-coding
mm_144381.1	chr18	20666481	20666517	+	1	NA	exon (NM_013697, exon 2 of 4)	exon (NM_013697, exon 2 of 4)	1249	NM_013697	22139	Mm.2108	NM_013697	ENSMUSG00000061808	Ttr	AA408768|AI787086|D17860|prealbumin	transthyretin	protein-coding
mm_167429.1	chr8	117343259	117343307	+	1	NA	intron (NM_001163262, intron 1 of 20)	intron (NM_001163262, intron 1 of 20)	-5887	NM_028941	74440	Mm.233181	NM_028941	ENSMUSG00000034390	Cmip	4933407C03Rik|5830471E12Rik|AI314065|AI464126	c-Maf inducing protein	protein-coding
mm_1433.1	chr1	67193763	67193774	+	1	NA	intron (NM_001080809, intron 21 of 37)	B3|SINE|B2	70741	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_169575.1	chr15	22705010	22705010	-	1	NA	Intergenic	LTRIS2|LTR|ERV1	9974	NM_001165971	545091	Mm.475598	NM_001165971		Gm5803	EG545091	predicted gene 5803	protein-coding
mm_134722.1	chr16	22898196	22898221	-	1	NA	exon (NM_001276450, exon 6 of 7)	exon (NM_001276450, exon 6 of 7)	-3822	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_117462.1	chr13	75942295	75942298	-	1	NA	intron (NM_028493, intron 2 of 11)	intron (NM_028493, intron 2 of 11)	1528	NM_028493	73296	Mm.276200	NM_028493	ENSMUSG00000021589	Rhobtb3	1700040C17Rik|2610033K01Rik|4930503C18Rik|AI317148|AW208826|mKIAA0878	Rho-related BTB domain containing 3	protein-coding
mm_57222.1	chr6	123263311	123263321	-	1	NA	intron (NM_001163161, intron 1 of 5)	intron (NM_001163161, intron 1 of 5)	1209	NM_010819	17474	Mm.441101	NM_010819	ENSMUSG00000030144	Clec4d	Clecsf8|Mpcl|mcl	C-type lectin domain family 4, member d	protein-coding
mm_121935.1	chr14	24004119	24004144	-	1	NA	promoter-TSS (NM_001253365)	promoter-TSS (NM_001253365)	74	NM_001253375	16531	Mm.343607	NM_010610	ENSMUSG00000063142	Kcnma1	5730414M22Rik|BKCa|MaxiK|Slo|Slo1|mSlo|mSlo1	potassium large conductance calcium-activated channel, subfamily M, alpha member 1	protein-coding
mm_110312.1	chr12	33315242	33315262	-	1	NA	intron (NM_001033436, intron 1 of 7)	intron (NM_001033436, intron 1 of 7)	12737	NM_001033436	380753	Mm.41540	NM_028139	ENSMUSG00000020564	Atxn7l1	2810423G08Rik|Atxn7l4	ataxin 7-like 1	protein-coding
mm_9381.1	chr1	172211984	172212022	-	1	NA	exon (NM_009813, exon 10 of 11)	exon (NM_009813, exon 10 of 11)	-5199	NM_011063	18611	Mm.544	NM_011063	ENSMUSG00000013698	Pea15a	Mat1|PEA-15|Pea15|Pkcs15	phosphoprotein enriched in astrocytes 15A	protein-coding
mm_41864.1	chr5	104440709	104440720	+	1	NA	3' UTR (NM_001204203, exon 7 of 7)	3' UTR (NM_001204203, exon 7 of 7)	4522	NM_001204233	20750	Mm.288474	NM_009263	ENSMUSG00000029304	Spp1	2AR|Apl-1|BNSP|BSPI|Bsp|ETA-1|Eta|OP|Opn|Opnl|Ric|Spp-1	secreted phosphoprotein 1	protein-coding
mm_139183.1	chr17	47594582	47594599	+	1	NA	intron (NM_001081635, intron 3 of 6)	intron (NM_001081635, intron 3 of 6)	1123	NM_007632	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_117132.1	chr13	60936783	60936787	-	1	NA	promoter-TSS (NM_001145799)	promoter-TSS (NM_001145799)	-160	NM_007796	13024	Mm.482089	NM_007796	ENSMUSG00000044258	Ctla2a	Ctla-2a	cytotoxic T lymphocyte-associated protein 2 alpha	protein-coding
mm_110310.1	chr12	33147592	33147617	-	1	NA	promoter-TSS (NM_028139)	promoter-TSS (NM_028139)	-18	NR_015602	320046	Mm.208337	NR_015602	ENSMUSG00000052125	F730043M19Rik	-	RIKEN cDNA F730043M19 gene	ncRNA
mm_75155.1	chr8	36223113	36223115	-	1	NA	intron (NM_001081150, intron 8 of 11)	intron (NM_001081150, intron 8 of 11)	26402	NM_001081150	244421	Mm.324032	NM_001081150	ENSMUSG00000039633	Lonrf1	-	LON peptidase N-terminal domain and ring finger 1	protein-coding
mm_143825.1	chr17	83990473	83990480	-	1	NA	Intergenic	MIRb|SINE|MIR	-8076	NR_130994	78148	Mm.243918	NR_130994		8430430B14Rik	-	RIKEN cDNA 8430430B14 gene	ncRNA
mm_148478.1	chr19	4104422	4104423	+	1	NA	intron (NR_075078, intron 5 of 23)	intron (NR_075078, intron 5 of 23)	3800	NM_008851	18739	Mm.1860	NM_008851	ENSMUSG00000024851	Pitpnm1	DRES9|Mpt-1|Nir-2|PITPnm 1|Pitpnm|R75447|Rd9|RdgB|RdgB1	phosphatidylinositol transfer protein, membrane-associated 1	protein-coding
mm_59664.1	chr7	28350741	28350762	+	1	NA	promoter-TSS (NM_013647)	promoter-TSS (NM_013647)	62	NM_013647	20055	Mm.702	NM_013647	ENSMUSG00000037563	Rps16	AA420385|AI317031	ribosomal protein S16	protein-coding
mm_163448.1	chr12	87373905	87373905	+	1	NA	intron (NM_011479, intron 1 of 11)	intron (NM_011479, intron 1 of 11)	14450	NM_011479	20773	Mm.565	NM_011479	ENSMUSG00000021036	Sptlc2	LCB2|LCB2a|Spt2	serine palmitoyltransferase, long chain base subunit 2	protein-coding
mm_163571.1	chr13	30659955	30659977	+	1	NA	promoter-TSS (NM_134068)	promoter-TSS (NM_134068)	-93	NM_001037955	105352	Mm.289646	NM_134068	ENSMUSG00000069255	Dusp22	JKAP|JSP1|LMW-DSP2|MKPX	dual specificity phosphatase 22	protein-coding
mm_77713.1	chr8	126592236	126592261	-	1	NA	intron (NM_001164598, intron 1 of 1)	intron (NM_001164598, intron 1 of 1)	1188	NM_001164598	270110	Mm.334918	NM_001164598	ENSMUSG00000051495	Irf2bp2	E130305N23Rik|IRF-2BP2	interferon regulatory factor 2 binding protein 2	protein-coding
mm_21391.1	chr2	157561853	157561884	-	1	NA	3' UTR (NM_010923, exon 3 of 3)	3' UTR (NM_010923, exon 3 of 3)	1790	NM_180960	18111	Mm.34330	NM_010923	ENSMUSG00000067786	Nnat	5730414I02Rik|AW107673|Peg5	neuronatin	protein-coding
mm_30078.1	chr3	138090231	138090243	-	1	NA	3' UTR (NM_001163457, exon 20 of 20)	3' UTR (NM_001163457, exon 20 of 20)	-22849	NR_037975	329763	Mm.169710	NM_177860	ENSMUSG00000049349	Gm5105	D830013H12|EG329763	predicted gene 5105	ncRNA
mm_134303.1	chr16	15636730	15636748	-	1	NA	exon (NM_008565, exon 2 of 16)	exon (NM_008565, exon 2 of 16)	661	NM_008565	17217	Mm.1500	NM_008565	ENSMUSG00000022673	Mcm4	19G|AI325074|AU045576|Cdc21|Mcmd4|mKIAA4003|mcdc21	minichromosome maintenance complex component 4	protein-coding
mm_115901.1	chr13	23368970	23369011	-	1	NA	5' UTR (NM_001286156, exon 1 of 4)	5' UTR (NM_001286156, exon 1 of 4)	218	NM_001286156	218100	Mm.286454	NM_172586	ENSMUSG00000046351	Zfp322a	Znf322|Znf322a	zinc finger protein 322A	protein-coding
mm_103119.1	chr11	70153582	70153582	-	1	NA	Intergenic	L1M4|LINE|L1	-13041	NM_001204252	17312	Mm.252405	NM_010796	ENSMUSG00000000318	Clec10a	CD301a|M-ASGP-BP-1|Mgl|Mgl1	C-type lectin domain family 10, member A	protein-coding
mm_51914.1	chr6	91233497	91233507	+	1	NA	exon (NM_001081437, exon 2 of 17)	exon (NM_001081437, exon 2 of 17)	20738	NM_007992	14115	Mm.249146	NM_007992	ENSMUSG00000064080	Fbln2	5730577E14Rik|FIBL-2	fibulin 2	protein-coding
mm_138361.1	chr17	34982587	34982652	+	1	NA	intron (NM_001204273, intron 1 of 5)	intron (NM_001204273, intron 1 of 5)	489	NM_030597	27756	Mm.165735	NM_030597	ENSMUSG00000007050	Lsm2	D17H6S56E-2|D17H6S56E2|Dmapl|Dmpkap|G7b|Sm-X5|SmX5|snRNP	LSM2 homolog, U6 small nuclear RNA and mRNA degradation associated	protein-coding
mm_117820.1	chr13	98016176	98016184	-	1	NA	intron (NM_012026, intron 9 of 35)	intron (NM_012026, intron 9 of 35)	189985	NM_012026	110596	Mm.252718	NM_012026	ENSMUSG00000021662	Arhgef28	9230110L08Rik|AI323540|D13Bwg1089e|RIP2|Rgnef|RhoGEF|Rhoip2|p190RhoGEF	Rho guanine nucleotide exchange factor (GEF) 28	protein-coding
mm_36432.1	chr4	82294664	82294685	-	1	NA	3' UTR (NM_001113209, exon 12 of 12)	3' UTR (NM_001113209, exon 12 of 12)	211105	NM_001286127	18028	Mm.317947	NM_008687	ENSMUSG00000008575	Nfib	6720429L07Rik|CTF|E030026I10Rik|NF-I/B|NF1-B|NFI-B	nuclear factor I/B	protein-coding
mm_66947.1	chr7	61989650	61989653	-	1	NA	Intergenic	L1_Mur1|LINE|L1	-7292	NR_037287	100526507		NR_037287	ENSMUSG00000092850	Mir344g	mir-344g|mmu-mir-344g	microRNA 344g	ncRNA
mm_168229.1	chr10	80107195	80107195	+	1	NA	intron (NR_038088, intron 1 of 4)	B1_Mm|SINE|Alu	-4493	NM_183426	216161	Mm.262102	NM_183426	ENSMUSG00000035673	Sbno2	BC019206|F730040C21|Sno|Stno	strawberry notch homolog 2 (Drosophila)	protein-coding
mm_111833.1	chr12	107911610	107911615	-	1	NA	3' UTR (NM_021399, exon 3 of 3)	3' UTR (NM_021399, exon 3 of 3)	91802	NM_001079883	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_128157.1	chr15	32623502	32623508	-	1	NA	intron (NM_009154, intron 13 of 22)	intron (NM_009154, intron 13 of 22)	-297218	NM_008304	15529	Mm.234266	NM_008304	ENSMUSG00000022261	Sdc2	4833414L08Rik|AA960457|Hspg1|Synd2|syndecan-2	syndecan 2	protein-coding
mm_15261.1	chr2	155018911	155018921	+	1	NA	intron (NM_015770, intron 1 of 3)	ERVB4_1-I_MM-int|LTR|ERVK	5346	NM_015770	50518	Mm.315593	NM_015770	ENSMUSG00000027596	a	A<y>|ASIP|ASP|As	nonagouti	protein-coding
mm_66306.1	chr7	39264451	39264459	-	1	NA	Intergenic	Intergenic	148705	NM_177890	330513	Mm.67238	NM_177890	ENSMUSG00000053742	Gm5114	4921507A12|EG330513	predicted gene 5114	protein-coding
mm_49386.1	chr6	24791216	24791223	+	1	NA	promoter-TSS (NM_001079875)	promoter-TSS (NM_001079875)	31	NM_001079875	20690	Mm.4688	NM_009241	ENSMUSG00000029682	Spam1	AV039194|Ph-20	sperm adhesion molecule 1	protein-coding
mm_142341.1	chr17	43591485	43591489	-	1	NA	promoter-TSS (NR_045445)	promoter-TSS (NR_045445)	22	NR_045445	73504	Mm.9277	NR_045444	ENSMUSG00000090307	1700071M16Rik	-	RIKEN cDNA 1700071M16 gene	ncRNA
mm_61221.1	chr7	64439604	64439604	+	1	NA	Intergenic	Intergenic	46833	NM_028626	73724	Mm.10093	NM_028626	ENSMUSG00000033429	Mcee	1110007A04Rik	methylmalonyl CoA epimerase	protein-coding
mm_19322.1	chr2	90568634	90568652	-	1	NA	intron (NM_008982, intron 1 of 23)	B3|SINE|B2	12004	NM_008982	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_87905.1	chr10	62252326	62252357	+	1	NA	promoter-TSS (NM_009314)	promoter-TSS (NM_009314)	-97	NM_009314	21337	Mm.8054	NM_009314	ENSMUSG00000020081	Tacr2	Nk2r|Skr|Tac2r	tachykinin receptor 2	protein-coding
mm_135612.1	chr16	52268412	52268460	-	1	NA	exon (NM_001331110, exon 13 of 15)	exon (NM_001331110, exon 13 of 15)	184645	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_127025.1	chr15	96287249	96287265	+	1	NA	promoter-TSS (NM_175251)	promoter-TSS (NM_175251)	-265	NM_175251	77044	Mm.17166	NM_175251	ENSMUSG00000033237	Arid2	1700124K17Rik|4432409D24Rik|zipzap/p200	AT rich interactive domain 2 (ARID, RFX-like)	protein-coding
mm_88729.1	chr10	80226756	80226762	+	1	NA	intron (NM_023431, intron 1 of 13)	CpG	161	NM_023431	68114	Mm.273418	NM_023431	ENSMUSG00000020156	Mum1	2610019J09|9430059D04Rik|UBE-1C2	melanoma associated antigen (mutated) 1	protein-coding
mm_14168.1	chr2	126673650	126673659	+	1	NA	intron (NM_001271470, intron 1 of 8)	intron (NM_001271470, intron 1 of 8)	1938	NM_001271469	14391	Mm.293266	NM_010249	ENSMUSG00000027361	Gabpb1	BABPB2|E4TF1|E4TF1-47|E4TF1-53|E4Tf1B|GABPB|GABPB-1|GABPB-2|GABPB1-1|GABPB1-2|NRF2B1|NRF2B2	GA repeat binding protein, beta 1	protein-coding
mm_23325.1	chr3	53488643	53488661	+	1	NA	promoter-TSS (NM_153156)	promoter-TSS (NM_153156)	-141	NM_153156	229277	Mm.222810	NM_153156	ENSMUSG00000027744	Stoml3	Epb7.2l|SLP3|sro	stomatin (Epb7.2)-like 3	protein-coding
mm_81171.1	chr9	107300021	107300031	+	1	NA	exon (NM_009895, exon 2 of 3)	exon (NM_009895, exon 2 of 3)	3367	NM_009895	12700	Mm.4592	NM_009895	ENSMUSG00000032578	Cish	CIS-1|CIS1|Cis|F17|F23|SOCS	cytokine inducible SH2-containing protein	protein-coding
mm_25529.1	chr3	114904267	114904291	+	1	NA	promoter-TSS (NM_001286750)	promoter-TSS (NM_001286750)	201	NM_153458	229759	Mm.54183	NM_153157	ENSMUSG00000027965	Olfm3	B230206G02Rik	olfactomedin 3	protein-coding
mm_118405.1	chr13	119409185	119409246	-	1	NA	promoter-TSS (NM_008710)	promoter-TSS (NM_008710)	42	NM_001308506	18115	Mm.132584	NM_008710	ENSMUSG00000025453	Nnt	4930423F13Rik|AI323702|BB168308	nicotinamide nucleotide transhydrogenase	protein-coding
mm_155912.1	chrX	101849376	101849393	+	1	NA	promoter-TSS (NM_001163610)	promoter-TSS (NM_001163610)	-1	NM_001163610	100042480	Mm.232	NM_001163610	ENSMUSG00000079481	Nhsl2	1110062M06Rik|6430511F03|AI225852|AW488865|EG621083|ENSMUSG00000073037|Gm10456	NHS-like 2	protein-coding
mm_77629.1	chr8	124021044	124021106	-	1	NA	intron (NM_133966, intron 1 of 4)	CpG	234	NM_133966	102162	Mm.291777	NM_133966	ENSMUSG00000038697	Taf5l	1110005N04Rik|AI849020	TATA-box binding protein associated factor 5 like	protein-coding
mm_49553.1	chr6	30541636	30541650	+	1	NA	promoter-TSS (NM_001024698)	promoter-TSS (NM_001024698)	1	NM_001024698	232680	Mm.268855	NM_001024698	ENSMUSG00000071553	Cpa2	-	carboxypeptidase A2, pancreatic	protein-coding
mm_67352.1	chr7	79836289	79836301	-	1	NA	exon (NM_008486, exon 10 of 20)	exon (NM_008486, exon 10 of 20)	6057	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_20712.1	chr2	134634469	134634472	-	1	NA	intron (NM_029148, intron 2 of 7)	RMER15-int|LTR|ERVL	9651	NM_029148	52837	Mm.264096	NM_029148	ENSMUSG00000034723	Tmx4	2810417D04Rik|4930500L08Rik|AI843224|AW046784|D2Bwg1356e|Txndc13|mKIAA1162	thioredoxin-related transmembrane protein 4	protein-coding
mm_124773.1	chr15	7129598	7129608	+	1	NA	promoter-TSS (NM_001113386)	promoter-TSS (NM_001113386)	31	NM_001113386	16880	Mm.149720	NM_013584	ENSMUSG00000054263	Lifr	A230075M04Rik|AW061234|LIF	leukemia inhibitory factor receptor	protein-coding
mm_145190.1	chr18	49832623	49832686	+	1	NA	promoter-TSS (NM_001081371)	promoter-TSS (NM_001081371)	-343	NM_001081371	240283	Mm.257790	NM_001081371	ENSMUSG00000037416	Dmxl1	C630007L23Rik|D030030C22	Dmx-like 1	protein-coding
mm_127217.1	chr15	99392890	99392903	+	1	NA	promoter-TSS (NM_026669)	promoter-TSS (NM_026669)	-51	NM_026669	110213	Mm.16769	NM_026669	ENSMUSG00000023010	Tmbim6	5031406P05Rik|Bi1|Tegt	transmembrane BAX inhibitor motif containing 6	protein-coding
mm_110006.1	chr12	16221245	16221251	-	1	NA	Intergenic	Intergenic	368522	NM_015763	14245	Mm.153625	NM_015763	ENSMUSG00000020593	Lpin1	4631420P06|Kiaa0188|Lipin1|fld|mKIAA0188	lipin 1	protein-coding
mm_153144.1	chr19	34248669	34248685	-	1	NA	intron (NM_007392, intron 3 of 8)	intron (NM_007392, intron 3 of 8)	6696	NM_007392	11475	Mm.213025	NM_007392	ENSMUSG00000035783	Acta2	0610041G09Rik|Actvs|SMalphaA|a-SMA|alphaSMA	actin, alpha 2, smooth muscle, aorta	protein-coding
mm_23077.1	chr3	36475933	36475959	+	1	NA	promoter-TSS (NR_105976)	promoter-TSS (NR_105976)	9	NM_028183	72282	Mm.55317	NM_028183	ENSMUSG00000027713	1810062G17Rik	-	RIKEN cDNA 1810062G17 gene	protein-coding
mm_35482.1	chr4	40854025	40854041	-	1	NA	5' UTR (NM_022305, exon 1 of 6)	5' UTR (NM_022305, exon 1 of 6)	504	NM_022305	14595	Mm.15622	NM_022305	ENSMUSG00000028413	B4galt1	B-1,4-GalT|B-1,4-GalT1|GalT|Ggtb|Ggtb2|b4Gal-T1|beta-1,4-GalT|beta-1,4-GalT1|beta4Gal-T1	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1	protein-coding
mm_163876.1	chr14	19419451	19419494	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	183115	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_137132.1	chr17	23600833	23600839	+	1	NA	promoter-TSS (NM_001033425)	promoter-TSS (NM_001033425)	10	NM_001289482	332221	Mm.270315	NM_001033425	ENSMUSG00000023902	Zscan10	BC068284|Zfp206|Zkscan10|Znf206	zinc finger and SCAN domain containing 10	protein-coding
mm_98476.1	chr11	94950482	94950496	+	1	NA	exon (NM_007742, exon 48 of 51)	exon (NM_007742, exon 48 of 51)	14265	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_153317.1	chr19	38116774	38116801	-	1	NA	3' UTR (NM_011255, exon 6 of 6)	3' UTR (NM_011255, exon 6 of 6)	8024	NM_011255	19662	Mm.2605	NM_011255	ENSMUSG00000024990	Rbp4	Rbp-4	retinol binding protein 4, plasma	protein-coding
mm_16166.1	chr2	172472556	172472567	+	1	NA	promoter-TSS (NM_029608)	promoter-TSS (NM_029608)	7	NM_029608	76426	Mm.46148	NM_029608	ENSMUSG00000027505	Fam209	1700029J11Rik	family with sequence similarity 209	protein-coding
mm_73709.1	chr8	111688537	111688585	+	1	NA	exon (NM_025583, exon 5 of 7)	exon (NM_025583, exon 5 of 7)	1113	NR_106044	102466993		NR_106044	ENSMUSG00000099129	Mir7076	Gm27318|mmu-mir-7076	microRNA 7076	ncRNA
mm_52975.1	chr6	123260455	123260461	+	1	NA	Intergenic	Intergenic	-1649	NM_001163161	17474	Mm.441101	NM_010819	ENSMUSG00000030144	Clec4d	Clecsf8|Mpcl|mcl	C-type lectin domain family 4, member d	protein-coding
mm_36288.1	chr4	63987827	63987835	-	1	NA	intron (NM_011607, intron 14 of 25)	intron (NM_011607, intron 14 of 25)	59184	NM_011607	21923	Mm.980	NM_011607	ENSMUSG00000028364	Tnc	AI528729|C130033P17Rik|Hxb|TN|TN-C|Ten|cytotactin|tenascin-C	tenascin C	protein-coding
mm_148560.1	chr19	4731149	4731154	+	1	NA	intron (NM_021287, intron 9 of 36)	intron (NM_021287, intron 9 of 36)	19928	NM_021287	20743	Mm.329668	NM_021287	ENSMUSG00000067889	Sptbn2	Spnb3|mKIAA0302	spectrin beta, non-erythrocytic 2	protein-coding
mm_32179.1	chr4	100819287	100819307	+	1	NA	intron (NM_198037, intron 1 of 26)	(CA)n|Simple_repeat|Simple_repeat	42618	NM_198037	320508	Mm.151962	NM_198037	ENSMUSG00000028532	Cachd1	1190007F10Rik|AI852726|B430218L07Rik|Vwcd1|mKIAA1573	cache domain containing 1	protein-coding
mm_106057.1	chr11	116110718	116110739	-	1	NA	promoter-TSS (NM_001205081)	promoter-TSS (NM_001205081)	-493	NM_172570	217333	Mm.347770	NM_172570	ENSMUSG00000020773	Trim47	2210023F24Rik	tripartite motif-containing 47	protein-coding
mm_22289.1	chr2	180227702	180227737	-	1	NA	Intergenic	Intergenic	-1860	NM_001081171	16776	Mm.4339	NM_001081171	ENSMUSG00000015647	Lama5	AA408760|AA408762|AI853660|[a]5|laminin-511|mKIAA0533	laminin, alpha 5	protein-coding
mm_66152.1	chr7	31148835	31148857	-	1	NA	intron (NM_027898, intron 1 of 18)	intron (NM_027898, intron 1 of 18)	2204	NM_027898	52857	Mm.27366	NM_027898	ENSMUSG00000001248	Gramd1a	1300003M23Rik|AI415002|AW547240|D7Bwg0611e	GRAM domain containing 1A	protein-coding
mm_168279.1	chr1	107208943	107208953	-	1	NA	Intergenic	L1Md_T|LINE|L1	-47834	NM_198680	383548	Mm.483991	NM_198680	ENSMUSG00000073602	Serpinb3b	Scca2-rs|Scca2-rs1	serine (or cysteine) peptidase inhibitor, clade B (ovalbumin), member 3B	protein-coding
mm_19212.1	chr2	84601517	84601547	-	1	NA	3' UTR (NM_001085449, exon 17 of 17)	3' UTR (NM_001085449, exon 17 of 17)	48978	NM_001085453	12388	Mm.35738	NM_007615	ENSMUSG00000034101	Ctnnd1	AA409437|AU019353|Catns|Ctnnd|P120|mKIAA0384	catenin (cadherin associated protein), delta 1	protein-coding
mm_63172.1	chr7	125349864	125349877	+	1	NA	promoter-TSS (NR_045804)	promoter-TSS (NR_045804)	-84	NR_045803	71208	Mm.159465	NM_172408	ENSMUSG00000045928	4933440M02Rik	-	RIKEN cDNA 4933440M02 gene	ncRNA
mm_106089.1	chr11	116193539	116193561	-	1	NA	intron (NM_001271898, intron 2 of 13)	intron (NM_001271898, intron 2 of 13)	-5305	NM_027107	69535	Mm.390347	NM_027107	ENSMUSG00000020778	Ten1	2310004N24Rik	TEN1 telomerase capping complex subunit	protein-coding
mm_87802.1	chr10	60300239	60300280	+	1	NA	exon (NM_011179, exon 12 of 15)	exon (NM_011179, exon 12 of 15)	15798	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_117325.1	chr13	67830935	67830958	-	1	NA	promoter-TSS (NR_045194)	promoter-TSS (NR_045194)	39	NR_045194	320163	Mm.444711	NR_045194	ENSMUSG00000097276	4930525G20Rik	-	RIKEN cDNA 4930525G20 gene	ncRNA
mm_102046.1	chr11	52000411	52000428	-	1	NA	promoter-TSS (NM_009458)	promoter-TSS (NM_009458)	47	NM_009458	22210	Mm.384918	NM_009458	ENSMUSG00000020390	Ube2b	2610301N02Rik|E2-14k|HR6B|Rad6b|mHR6B	ubiquitin-conjugating enzyme E2B	protein-coding
mm_23240.1	chr3	51210368	51210374	+	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	-14076	NM_009834	12457	Mm.86541	NM_009834	ENSMUSG00000023087	Noct	AU043840|Ccr4|Ccrn4l	nocturnin	protein-coding
mm_113477.1	chr13	36734857	36734867	+	1	NA	promoter-TSS (NM_153529)	promoter-TSS (NM_153529)	-385	NM_153529	68404	Mm.232930	NM_153529	ENSMUSG00000039114	Nrn1	0710008J23Rik|Cpg15|Nrn	neuritin 1	protein-coding
mm_52417.1	chr6	113434893	113434906	+	1	NA	intron (NM_178373, intron 1 of 5)	intron (NM_178373, intron 1 of 5)	856	NM_178373	14311	Mm.10026	NM_178373	ENSMUSG00000030278	Cidec	CIDE-3|Fsp27	cell death-inducing DFFA-like effector c	protein-coding
mm_132749.1	chr16	44159750	44159765	+	1	NA	3' UTR (NM_028108, exon 5 of 5)	3' UTR (NM_028108, exon 5 of 5)	-13640	NM_001029889	207806	Mm.310566	NM_001029889	ENSMUSG00000068284	Usf3	5530400K22Rik|Gm1779|Gm608|mKIAA2018	upstream transcription factor family member 3	protein-coding
mm_97076.1	chr11	73009105	73009117	+	1	NA	intron (NM_008771, intron 4 of 11)	intron (NM_008771, intron 4 of 11)	-9897	NM_018883	55984	Mm.9998	NM_018883	ENSMUSG00000020785	Camkk1	AI846603|CaMKKalpha|Camkk	calcium/calmodulin-dependent protein kinase kinase 1, alpha	protein-coding
mm_33619.1	chr4	132656684	132656705	+	1	NA	5' UTR (NM_010166, exon 2 of 18)	5' UTR (NM_010166, exon 2 of 18)	17648	NM_010166	14050	Mm.227733	NM_010166	ENSMUSG00000028886	Eya3	AI844637	EYA transcriptional coactivator and phosphatase 3	protein-coding
mm_156758.1	chrX	160502419	160502485	+	1	NA	promoter-TSS (NM_001177878)	promoter-TSS (NM_001177878)	18	NM_001177878	110094	Mm.350712	NM_172783	ENSMUSG00000031295	Phka2	6330505C01Rik|D330034O08|Phk	phosphorylase kinase alpha 2	protein-coding
mm_79271.1	chr9	50754225	50754240	+	1	NA	intron (NM_009964, intron 1 of 2)	intron (NM_009964, intron 1 of 2)	1261	NM_009964	12955	Mm.178	NM_009964	ENSMUSG00000032060	Cryab	Crya-2|Crya2|HspB5|P23	crystallin, alpha B	protein-coding
mm_59793.1	chr7	29000785	29000822	+	1	NA	intron (NM_008279, intron 26 of 31)	intron (NM_008279, intron 26 of 31)	17949	NM_008279	26411	Mm.148278	NM_008279	ENSMUSG00000037337	Map4k1	Hpk1|mHPK1	mitogen-activated protein kinase kinase kinase kinase 1	protein-coding
mm_135739.1	chr16	55838781	55838789	-	1	NA	promoter-TSS (NM_030612)	promoter-TSS (NM_030612)	-144	NM_001159395	80859	Mm.247272	NM_030612	ENSMUSG00000035356	Nfkbiz	AA408868|INAP|Mail	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, zeta	protein-coding
mm_29490.1	chr3	115801157	115801171	-	1	NA	Intergenic	Intergenic	-86109	NM_007901	13609	Mm.982	NM_007901	ENSMUSG00000045092	S1pr1	AI849002|Edg1|Lpb1|S1p|S1p1	sphingosine-1-phosphate receptor 1	protein-coding
mm_84603.1	chr9	70103076	70103110	-	1	NA	intron (NM_029784, intron 4 of 8)	RSINE1|SINE|B4	38464	NM_029784	76886	Mm.44355	NM_029784	ENSMUSG00000032224	Fam81a	6430514L14Rik	family with sequence similarity 81, member A	protein-coding
mm_78443.1	chr9	32159553	32159556	+	1	NA	intron (NM_001195632, intron 4 of 21)	intron (NM_001195632, intron 4 of 21)	43418	NM_001195632	330914	Mm.46683	NM_177379	ENSMUSG00000041444	Arhgap32	3426406O18Rik|Gc-gap|Grit|Px-rics|Rics|mKIAA0712|p200Rhogap|p250Gap	Rho GTPase activating protein 32	protein-coding
mm_158081.1	chrX	101265664	101265676	-	1	NA	exon (NM_001308535, exon 6 of 8)	exon (NM_001308535, exon 6 of 8)	-1678	NM_001317221	245536	Mm.212463	NM_001033362	ENSMUSG00000090141	Gm614	-	predicted gene 614	protein-coding
mm_92270.1	chr10	71159677	71159708	-	1	NA	promoter-TSS (NM_001347189)	promoter-TSS (NM_001347189)	-2	NM_001347189	83675	Mm.286834	NM_031397	ENSMUSG00000014329	Bicc1	Bic-C|bpk|jcpk	BicC family RNA binding protein 1	protein-coding
mm_38952.1	chr4	150570067	150570074	-	1	NA	intron (NM_001085492, intron 11 of 22)	intron (NM_001085492, intron 11 of 22)	82104	NM_173774	242773	Mm.29280	NM_173774	ENSMUSG00000039838	Slc45a1	C230078B22|Dnb5	solute carrier family 45, member 1	protein-coding
mm_147725.1	chr18	60877329	60877337	-	1	NA	Intergenic	Intergenic	-28369	NM_001198984	21453	Mm.486251	NM_011552	ENSMUSG00000024613	Tcof1	AA408847|AW209012|treacle	treacle ribosome biogenesis factor 1	protein-coding
mm_130219.1	chr15	95887505	95887537	-	1	NA	intron (NM_175344, intron 2 of 19)	intron (NM_175344, intron 2 of 19)	96678	NM_001253813	105722	Mm.38087	NM_175344	ENSMUSG00000064210	Ano6	2900059G15Rik|AA407480|AW554778|F730003B03Rik|Tmem16f	anoctamin 6	protein-coding
mm_134165.1	chr16	10796048	10796056	-	1	NA	TTS (NM_013637)	TTS (NM_013637)	771	NM_013637	19118	Mm.42733	NM_013637	ENSMUSG00000022501	Prm1	Prm-1	protamine 1	protein-coding
mm_77662.1	chr8	124663386	124663409	-	1	NA	promoter-TSS (NM_175149)	promoter-TSS (NM_175149)	-28	NM_175149	69551	Mm.261920	NM_175149	ENSMUSG00000031983	2310022B05Rik	-	RIKEN cDNA 2310022B05 gene	protein-coding
mm_108895.1	chr12	100156521	100156537	+	1	NA	intron (NM_183155, intron 1 of 13)	intron (NM_183155, intron 1 of 13)	3124	NM_001290303	217827	Mm.224076	NM_183155	ENSMUSG00000021179	Nrde2	6720454P05Rik	nrde-2 necessary for RNA interference, domain containing	protein-coding
mm_54096.1	chr6	16837085	16837117	-	1	NA	intron (NM_031198, intron 5 of 6)	intron (NM_031198, intron 5 of 6)	61340	NM_031198	21426	Mm.36217	NM_031198	ENSMUSG00000029553	Tfec	BB107417|Tcfec|bHLHe34	transcription factor EC	protein-coding
mm_33282.1	chr4	128745050	128745067	+	1	NA	exon (NM_018774, exon 11 of 15)	exon (NM_018774, exon 11 of 15)	-14200	NM_001009819	215493	Mm.300900	NM_001009819	ENSMUSG00000028794	A3galt2	Gm433|iGb3|iGb3S	alpha 1,3-galactosyltransferase 2 (isoglobotriaosylceramide synthase)	protein-coding
mm_73093.1	chr8	94544173	94544185	+	1	NA	intron (NM_153507, intron 1 of 15)	intron (NM_153507, intron 1 of 15)	11151	NM_153507	234577	Mm.291815	NM_153507	ENSMUSG00000034361	Cpne2	3322401K10Rik	copine II	protein-coding
mm_70546.1	chr8	13055833	13055843	+	1	NA	exon (NM_007972, exon 9 of 9)	exon (NM_007972, exon 9 of 9)	-5070	NM_025834	66901	Mm.441140	NM_025834	ENSMUSG00000031445	Proz	1300015B06Rik	protein Z, vitamin K-dependent plasma glycoprotein	protein-coding
mm_50318.1	chr6	47943142	47943215	+	1	NA	promoter-TSS (NR_027963)	promoter-TSS (NR_027963)	3	NR_027963	232785	Mm.482185	NR_027963	ENSMUSG00000072653	Zfp783	A230106D06Rik|ENSMUSG00000072653|Gm20494	zinc finger protein 783	ncRNA
mm_3640.1	chr1	152812506	152812517	+	1	NA	intron (NM_010877, intron 3 of 15)	B2_Mm2|SINE|B2	12358	NM_010877	17970	Mm.270307	NM_010877	ENSMUSG00000026480	Ncf2	NOXA2|Ncf-2|p67phox	neutrophil cytosolic factor 2	protein-coding
mm_109824.1	chr12	3862306	3862316	-	1	NA	promoter-TSS (NR_045884)	promoter-TSS (NR_045884)	-67	NR_045884	100038522	Mm.417270	NR_045884	ENSMUSG00000073242	Dnmt3aos	ENSMUSG00000073242|Gm10485	DNA methyltransferase 3A, opposite strand	ncRNA
mm_99319.1	chr11	101442413	101442439	+	1	NA	5' UTR (NM_011289, exon 1 of 5)	5' UTR (NM_011289, exon 1 of 5)	181	NM_011289	19942	Mm.340658	NM_011289	ENSMUSG00000063316	Rpl27	-	ribosomal protein L27	protein-coding
mm_35468.1	chr4	40805847	40805863	-	1	NA	3' UTR (NM_022305, exon 6 of 6)	3' UTR (NM_022305, exon 6 of 6)	44283	NR_039584	100628614		NR_039584	ENSMUSG00000096377	Mir5123	mmu-mir-5123|mu-mir-5123	microRNA 5123	ncRNA
mm_72984.1	chr8	92960573	92960584	+	1	NA	promoter-TSS (NM_009209)	promoter-TSS (NM_009209)	-469	NM_009209	20538	Mm.57040	NM_009209	ENSMUSG00000055368	Slc6a2	NE-T|NET|Slc6a5	solute carrier family 6 (neurotransmitter transporter, noradrenalin), member 2	protein-coding
mm_119215.1	chr14	33203967	33203973	+	1	NA	Intergenic	RMER19B|LTR|ERVK	-12853	NM_153800	239027	Mm.318350	NM_153800	ENSMUSG00000063506	Arhgap22	B230341L19Rik|RHOGAP2|p68RacGAP	Rho GTPase activating protein 22	protein-coding
mm_145880.1	chr18	65476893	65476905	+	1	NA	3' UTR (NM_172833, exon 16 of 16)	3' UTR (NM_172833, exon 16 of 16)	45902	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_79579.1	chr9	58135016	58135029	+	1	NA	intron (NM_001162479, intron 1 of 18)	T-rich|Low_complexity|Low_complexity	357	NM_001162479	20897	Mm.10801	NM_009291	ENSMUSG00000032327	Stra6	AI891933	stimulated by retinoic acid gene 6	protein-coding
mm_131317.1	chr16	11778449	11778465	+	1	NA	Intergenic	Intergenic	-1245	NR_126430	73761	Mm.39183	NR_126430		4833415N18Rik	-	RIKEN cDNA 4833415N18 gene	ncRNA
mm_141334.1	chr17	28507515	28507529	-	1	NA	Intergenic	Intergenic	-21373	NM_010220	14229	Mm.276405	NM_010220	ENSMUSG00000024222	Fkbp5	D17Ertd592e|Dit1|FKBP-5|FKBP51	FK506 binding protein 5	protein-coding
mm_81489.1	chr9	110003639	110003642	+	1	NA	3' UTR (NM_001205331, exon 4 of 4)	3' UTR (NM_001205331, exon 4 of 4)	-48381	NM_001311163	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_172016.1	chr6	111513968	111513968	+	1	NA	intron (NM_001346640, intron 10 of 10)	B1_Mus2|SINE|Alu	-696740	NR_027865	67336	Mm.378014	NR_027865	ENSMUSG00000100219	1700054K19Rik	-	RIKEN cDNA 1700054K19 gene	ncRNA
mm_6491.1	chr1	74150653	74150696	-	1	NA	Intergenic	Intergenic	-3320	NM_009909	12765	Mm.234466	NM_009909	ENSMUSG00000026180	Cxcr2	CD128|CDw128|Cmkar2|Gpcr16|IL-8Rh|IL-8rb|IL8RA|Il8rb|mIL-8RH	chemokine (C-X-C motif) receptor 2	protein-coding
mm_85786.1	chr9	109071715	109071718	-	1	NA	intron (NM_172774, intron 3 of 12)	intron (NM_172774, intron 3 of 12)	2408	NM_172774	235610	Mm.100622	NM_172774	ENSMUSG00000025646	Atrip	6620401K05Rik	ATR interacting protein	protein-coding
mm_57094.1	chr6	122587894	122587927	-	1	NA	intron (NM_001134391, intron 5 of 7)	intron (NM_001134391, intron 5 of 7)	14534	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_103446.1	chr11	76154958	76154989	-	1	NA	intron (NM_026664, intron 4 of 21)	intron (NM_026664, intron 4 of 21)	24657	NM_026664	68299	Mm.46397	NM_026664	ENSMUSG00000017288	Vps53	2010002A08Rik|2310040I21Rik|3100002B05Rik|Hccs1	VPS53 GARP complex subunit	protein-coding
mm_2619.1	chr1	120495463	120495468	+	1	NA	intron (NM_010766, intron 1 of 16)	G-rich|Low_complexity|Low_complexity	9619	NM_010766	17167	Mm.1856	NM_010766	ENSMUSG00000026390	Marco	AI323439|Ly112|Scara2	macrophage receptor with collagenous structure	protein-coding
mm_12165.1	chr2	62395187	62395197	+	1	NA	intron (NM_001159543, intron 2 of 24)	Lx6|LINE|L1	17039	NM_010074	13482	Mm.1151	NM_010074	ENSMUSG00000035000	Dpp4	Cd26|Dpp-4|THAM	dipeptidylpeptidase 4	protein-coding
mm_166908.1	chr7	28962513	28962533	+	1	NA	promoter-TSS (NM_021895)	promoter-TSS (NM_021895)	-243	NM_021895	60595	Mm.81144	NM_021895	ENSMUSG00000054808	Actn4	C77391	actinin alpha 4	protein-coding
mm_123563.1	chr14	66869019	66869067	-	1	NA	promoter-TSS (NM_009955)	promoter-TSS (NM_009955)	193	NM_001034881	432870	Mm.425890	NM_001034881	ENSMUSG00000075553	Gm5464	EG432870	predicted gene 5464	protein-coding
mm_21637.1	chr2	164317567	164317569	-	1	NA	exon (NM_013679, exon 3 of 4)	exon (NM_013679, exon 3 of 4)	817	NM_013679	20945	Mm.439686	NM_013679	ENSMUSG00000017000	Svs6	MSVSP99|Svp6	seminal vesicle secretory protein 6	protein-coding
mm_165533.1	chr2	180104401	180104426	-	1	NA	promoter-TSS (NM_133849)	promoter-TSS (NM_133849)	-6	NM_133849	99296	Mm.285360	NM_133849	ENSMUSG00000039059	Hrh3	AW049250|H3R|HH3R	histamine receptor H3	protein-coding
mm_8079.1	chr1	135585518	135585546	-	1	NA	promoter-TSS (NM_173437)	promoter-TSS (NM_173437)	-177	NM_173437	215690	Mm.34977	NM_173437	ENSMUSG00000009418	Nav1	9530089B19|9930003A20Rik|C230080M11Rik|Pomfil3|Unc53h1|mKIAA1151|steerin-1	neuron navigator 1	protein-coding
mm_105098.1	chr11	100939458	100939484	-	1	NA	promoter-TSS (NM_011486)	promoter-TSS (NM_011486)	69	NM_213660	20848	Mm.249934	NM_011486	ENSMUSG00000004040	Stat3	1110034C02Rik|AW109958|Aprf	signal transducer and activator of transcription 3	protein-coding
mm_102300.1	chr11	55469146	55469185	-	1	NA	promoter-TSS (NM_013716)	promoter-TSS (NM_013716)	-587	NM_013716	27041	Mm.39631	NM_013716	ENSMUSG00000018583	G3bp1	AI849976|B430204O07|C87777|G3bp|mKIAA4115	GTPase activating protein (SH3 domain) binding protein 1	protein-coding
mm_106322.1	chr11	118303638	118303659	-	1	NA	3' UTR (NM_011594, exon 5 of 5)	3' UTR (NM_011594, exon 5 of 5)	-13404	NM_001033528	72344	Mm.232293	NM_001033528	ENSMUSG00000033909	Usp36	2700002L06Rik|mKIAA1453	ubiquitin specific peptidase 36	protein-coding
mm_26076.1	chr3	136670457	136670474	+	1	NA	5' UTR (NM_001293622, exon 1 of 13)	5' UTR (NM_001293622, exon 1 of 13)	399	NM_001293622	19055	Mm.331389	NM_008913	ENSMUSG00000028161	Ppp3ca	2900074D19Rik|CN|Caln|Calna|CnA	protein phosphatase 3, catalytic subunit, alpha isoform	protein-coding
mm_120690.1	chr14	70774602	70774610	+	1	NA	intron (NM_010071, intron 1 of 4)	intron (NM_010071, intron 1 of 4)	225	NM_010071	13449	Mm.243323	NM_010071	ENSMUSG00000022102	Dok2	DokR|Frip	docking protein 2	protein-coding
mm_92415.1	chr10	76822819	76822831	-	1	NA	intron (NM_001347216, intron 3 of 15)	intron (NM_001347216, intron 3 of 15)	-96781	NM_009933	12833	Mm.2509	NM_009933	ENSMUSG00000001119	Col6a1	AI747156|Col6a-1	collagen, type VI, alpha 1	protein-coding
mm_74622.1	chr8	13104960	13104990	-	1	NA	promoter-TSS (NM_146207)	promoter-TSS (NM_146207)	368	NM_178708	234069	Mm.103427	NM_178708	ENSMUSG00000038542	Pcid2	A730042J05Rik	PCI domain containing 2	protein-coding
mm_111768.1	chr12	104013780	104013788	-	1	NA	promoter-TSS (NM_027997)	promoter-TSS (NM_027997)	-132	NM_027997	71907	Mm.326723	NM_027997	ENSMUSG00000058260	Serpina9	2310014L03Rik|AW049635|Centerin	serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9	protein-coding
mm_35964.1	chr4	53144025	53144037	-	1	NA	5' UTR (NM_013454, exon 2 of 50)	5' UTR (NM_013454, exon 2 of 50)	15864	NM_013454	11303	Mm.277376	NM_013454	ENSMUSG00000015243	Abca1	ABC-1|Abc1	ATP-binding cassette, sub-family A (ABC1), member 1	protein-coding
mm_86277.1	chr9	121809812	121809824	-	1	NA	intron (NM_028384, intron 11 of 15)	intron (NM_028384, intron 11 of 15)	-17311	NM_029095	74770	Mm.44195	NM_029095	ENSMUSG00000032523	Hhatl	1110011D13Rik|Gup1|Mg56	hedgehog acyltransferase-like	protein-coding
mm_74466.1	chr8	4217180	4217252	-	1	NA	promoter-TSS (NM_207203)	promoter-TSS (NM_207203)	96	NM_207203	73072	Mm.477379	NM_207203	ENSMUSG00000064125	Prr36	-	proline rich 36	protein-coding
mm_43637.1	chr5	138229813	138229819	+	1	NA	5' UTR (NM_001013773, exon 2 of 6)	5' UTR (NM_001013773, exon 2 of 6)	3912	NM_001013773	381680	Mm.156846	NM_001013773	ENSMUSG00000047592	Nxpe5	-	neurexophilin and PC-esterase domain family, member 5	protein-coding
mm_70637.1	chr8	13896465	13896477	+	1	NA	Intergenic	Intergenic	-6200	NM_025556	66423	Mm.29063	NM_025556	ENSMUSG00000031458	Coprs	1700029I03Rik|2410022L05Rik|AA409325|AI256813|C85432|Copr5	coordinator of PRMT5, differentiation stimulator	protein-coding
mm_117063.1	chr13	58668744	58668779	-	1	NA	Intergenic	Intergenic	-57884	NM_022317	114304	Mm.18188	NM_022317	ENSMUSG00000021553	Slc28a3	Cnt3	solute carrier family 28 (sodium-coupled nucleoside transporter), member 3	protein-coding
mm_147947.1	chr18	66471515	66471521	-	1	NA	Intergenic	Intergenic	12914	NM_021451	58801	Mm.271878	NM_021451	ENSMUSG00000024521	Pmaip1	Noxa	phorbol-12-myristate-13-acetate-induced protein 1	protein-coding
mm_103880.1	chr11	83530481	83530500	-	1	NA	promoter-TSS (NM_013653)	promoter-TSS (NM_013653)	28	NM_013653	20304	Mm.284248	NM_013653	ENSMUSG00000035042	Ccl5	MuRantes|RANTES|SISd|Scya5|TCP228	chemokine (C-C motif) ligand 5	protein-coding
mm_21848.1	chr2	165858134	165858187	-	1	NA	promoter-TSS (NM_001252585)	promoter-TSS (NM_001252585)	13	NM_001252585	228880	Mm.227598	NM_027230	ENSMUSG00000039671	Zmynd8	1110013E22Rik|2010005I16Rik|3632413B07Rik|AI316811|AL024039|Prkcbp1|RACK7	zinc finger, MYND-type containing 8	protein-coding
mm_36842.1	chr4	106678656	106678678	-	1	NA	promoter-TSS (NM_001172073)	promoter-TSS (NM_001172073)	19	NM_001172073	72354	Mm.25806	NM_028209	ENSMUSG00000025413	Ttc4	2810002P21Rik|AF007005|L62	tetratricopeptide repeat domain 4	protein-coding
mm_172259.1	chr6	73454444	73454445	-	1	NA	intron (NR_108032, intron 2 of 4)	intron (NR_108032, intron 2 of 4)	15223	NM_025737	66740	Mm.440760	NM_025737	ENSMUSG00000056197	4931417E11Rik	-	RIKEN cDNA 4931417E11 gene	protein-coding
mm_44766.1	chr5	31698246	31698256	-	1	NA	promoter-TSS (NM_153196)	promoter-TSS (NM_153196)	201	NM_144541	107976	Mm.482126	NM_144541	ENSMUSG00000052139	Bre	6030405P19Rik|AI429776|B830038C02Rik	brain and reproductive organ-expressed protein	protein-coding
mm_138573.1	chr17	35424843	35424856	+	1	NA	promoter-TSS (NM_207648)	promoter-TSS (NM_207648)	2	NM_023124	15019	Mm.486287	NM_023124		H2-Q8	H-2Q8|MMS10-T|Ms10t|Qa-2|Qa-8|Qa8	histocompatibility 2, Q region locus 8	protein-coding
mm_45055.1	chr5	41810080	41810105	-	1	NA	exon (NM_001081422, exon 13 of 27)	exon (NM_001081422, exon 13 of 27)	34223	NM_001310601	665775	Mm.158726	NM_001081422	ENSMUSG00000061755	Bod1l	A230054D04Rik|AI853319|FAM44A|mKIAA1327	biorientation of chromosomes in cell division 1-like	protein-coding
mm_96582.1	chr11	69073425	69073429	+	1	NA	TTS (NM_025838)	TTS (NM_025838)	2618	NM_028336	66910	Mm.33964	NM_025838	ENSMUSG00000020895	Tmem107	1110004B13Rik|2810049P21Rik	transmembrane protein 107	protein-coding
mm_26214.1	chr3	138758123	138758137	+	1	NA	intron (NM_019571, intron 1 of 7)	intron (NM_019571, intron 1 of 7)	15922	NM_019571	56224	Mm.31927	NM_019571	ENSMUSG00000028152	Tspan5	2810455A09Rik|4930505M03Rik|NET-4|Tm4sf9	tetraspanin 5	protein-coding
mm_48668.1	chr5	145997150	145997159	-	1	NA	intron (NR_030782, intron 4 of 11)	intron (NR_030782, intron 4 of 11)	12463	NM_019792	56388	Mm.301900	NM_019792	ENSMUSG00000029630	Cyp3a25	AI327008	cytochrome P450, family 3, subfamily a, polypeptide 25	protein-coding
mm_81312.1	chr9	108392909	108392918	+	1	NA	promoter-TSS (NM_053216)	promoter-TSS (NM_053216)	79	NM_053216	112418	Mm.78287	NM_053216	ENSMUSG00000032611	1700102P08Rik	AI593206	RIKEN cDNA 1700102P08 gene	protein-coding
mm_69151.1	chr7	127137357	127137401	-	1	NA	intron (NR_110337, intron 1 of 3)	intron (NR_110337, intron 1 of 3)	444	NR_110337	20737	Mm.283714	NM_009259	ENSMUSG00000051457	Spn	A630014B01Rik|Cd43|Galgp|Ly-48|Ly48	sialophorin	protein-coding
mm_66088.1	chr7	30972170	30972197	-	1	NA	exon (NM_017405, exon 2 of 10)	exon (NM_017405, exon 2 of 10)	1286	NM_001164185	54135	Mm.4067	NM_017405	ENSMUSG00000001247	Lsr	ILDR3|Lisch7	lipolysis stimulated lipoprotein receptor	protein-coding
mm_130277.1	chr15	96699699	96699717	-	1	NA	promoter-TSS (NM_175121)	promoter-TSS (NM_175121)	-10	NM_175121	67760	Mm.46754	NM_175121	ENSMUSG00000022462	Slc38a2	5033402L14Rik|AI316867|ATA2|SAT2|mKIAA1382	solute carrier family 38, member 2	protein-coding
mm_137335.1	chr17	25120788	25120803	+	1	NA	promoter-TSS (NM_001163416)	promoter-TSS (NM_001163416)	35	NM_001163416	68509	Mm.328855	NM_026747	ENSMUSG00000044172	Ptx4	1110018H23Rik	pentraxin 4	protein-coding
mm_50410.1	chr6	48739040	48739096	+	1	NA	promoter-TSS (NM_008376)	promoter-TSS (NM_008376)	21	NM_008376	16205	Mm.252599	NM_008376	ENSMUSG00000090019	Gimap1	IAP38|Imap38|imap	GTPase, IMAP family member 1	protein-coding
mm_136714.1	chr17	7929379	7929394	+	1	NA	exon (NM_145968, exon 6 of 10)	exon (NM_145968, exon 6 of 10)	3386	NM_145968	72536	Mm.119680	NM_145968	ENSMUSG00000033450	Tagap	2610315E15Rik	T cell activation Rho GTPase activating protein	protein-coding
mm_37562.1	chr4	126201151	126201165	-	1	NA	intron (NM_146153, intron 1 of 10)	B1F2|SINE|Alu	1552	NM_146153	230753	Mm.29813	NM_146153	ENSMUSG00000043962	Thrap3	9330151F09Rik|B230333E16Rik|Trap150	thyroid hormone receptor associated protein 3	protein-coding
mm_105666.1	chr11	107419882	107419885	-	1	NA	intron (NM_145823, intron 1 of 9)	intron (NM_145823, intron 1 of 9)	50837	NM_145823	71795	Mm.397413	NM_145823	ENSMUSG00000040430	Pitpnc1	1110020B03Rik|5830436L09Rik|AI662802|AI851387|C330017I21Rik|Dnr411|RDGBB|RDGBB1|rdgB-beta	phosphatidylinositol transfer protein, cytoplasmic 1	protein-coding
mm_166037.1	chr4	129189459	129189483	-	1	NA	promoter-TSS (NM_029036)	promoter-TSS (NM_029036)	11	NM_029036	74648	Mm.172064	NM_029036	ENSMUSG00000040928	S100pbp	4930429A08Rik|AI851343|S100pbpr	S100P binding protein	protein-coding
mm_81186.1	chr9	107534031	107534136	+	1	NA	5' UTR (NM_019704, exon 1 of 2)	5' UTR (NM_019704, exon 1 of 2)	138	NM_019704	56395	Mm.260153	NM_019704	ENSMUSG00000010045	Tmem115	C78915|Pl6|Pp6	transmembrane protein 115	protein-coding
mm_77672.1	chr8	124897686	124897757	-	1	NA	promoter-TSS (NM_198103)	promoter-TSS (NM_198103)	-16	NM_198103	102058	Mm.347360	NM_198103	ENSMUSG00000074030	Exoc8	AI414418|EXO84|Exo84p|R74783|SEC84	exocyst complex component 8	protein-coding
mm_172552.1	chr8	102785062	102785062	-	1	NA	promoter-TSS (NM_009866)	promoter-TSS (NM_009866)	49	NM_009866	12552	Mm.1571	NM_009866	ENSMUSG00000031673	Cdh11	Cad11|OSF-4	cadherin 11	protein-coding
mm_75311.1	chr8	41209850	41209857	-	1	NA	exon (NM_145594, exon 3 of 8)	exon (NM_145594, exon 3 of 8)	5303	NM_145594	234199	Mm.277955	NM_145594	ENSMUSG00000031594	Fgl1	Mfire1	fibrinogen-like protein 1	protein-coding
mm_10967.1	chr2	25702541	25702547	+	1	NA	intron (NM_153558, intron 5 of 6)	intron (NM_153558, intron 5 of 6)	2470	NM_153558	227627	Mm.44630	NM_153558	ENSMUSG00000062061	Obp2a	BC027556|Lcn13	odorant binding protein 2A	protein-coding
mm_51955.1	chr6	91756144	91756157	+	1	NA	3' UTR (NM_009320, exon 15 of 15)	3' UTR (NM_009320, exon 15 of 15)	51243	NM_001159507	243547	Mm.333264	NM_001033353	ENSMUSG00000030098	Grip2	-	glutamate receptor interacting protein 2	protein-coding
mm_117407.1	chr13	73937762	73937787	-	1	NA	promoter-TSS (NM_027182)	promoter-TSS (NM_027182)	-7	NM_027182	69716	Mm.275095	NM_027182	ENSMUSG00000021569	Trip13	2410002G23Rik|D13Ertd328e	thyroid hormone receptor interactor 13	protein-coding
mm_122577.1	chr14	50830039	50830075	-	1	NA	intron (NM_009351, intron 45 of 54)	ID2|SINE|ID	22111	NM_009632	11546	Mm.281482	NM_009632	ENSMUSG00000036023	Parp2	ARTD2|Adprt2|Adprtl2|Aspartl2|C78626|PARP-2	poly (ADP-ribose) polymerase family, member 2	protein-coding
mm_173250.1	chrX	92662930	92662947	-	1	NA	Intergenic	RLTR9F|LTR|ERVK	-63366	NM_173783	215641	Mm.327999	NM_173783	ENSMUSG00000067649	Mageb18	B430216B18Rik	melanoma antigen family B, 18	protein-coding
mm_133738.1	chr16	93929362	93929367	+	1	NA	5' UTR (NM_001165925, exon 1 of 2)	5' UTR (NM_001165925, exon 1 of 2)	203	NM_001165925	56173	Mm.328716	NM_019500	ENSMUSG00000047109	Cldn14	AI851731	claudin 14	protein-coding
mm_51009.1	chr6	64734699	64734703	+	1	NA	Intergenic	CpG	5555	NM_007500	11921	Mm.57229	NM_007500	ENSMUSG00000073043	Atoh1	Hath1|MATH-1|Math1|bHLHa14	atonal bHLH transcription factor 1	protein-coding
mm_166011.1	chr4	118409386	118409392	+	1	NA	promoter-TSS (NM_198170)	promoter-TSS (NM_198170)	52	NM_020000	80509	Mm.259567	NM_020000	ENSMUSG00000006392	Med8	2210021A15Rik|AB041805|ARC32	mediator complex subunit 8	protein-coding
mm_63323.1	chr7	126942061	126942074	+	1	NA	intron (NM_172747, intron 4 of 5)	intron (NM_172747, intron 4 of 5)	7514	NM_001347657	233879	Mm.444143	NM_001039645	ENSMUSG00000046378	Asphd1	A830007L07Rik|Gm168	aspartate beta-hydroxylase domain containing 1	protein-coding
mm_138933.1	chr17	43804022	43804041	+	1	NA	promoter-TSS (NM_001286653)	promoter-TSS (NM_001286653)	28	NM_001286653	53901	Mm.251242	NM_030598	ENSMUSG00000039601	Rcan2	Csp2|Dscr1l1|MCIP2|ZAKI-4	regulator of calcineurin 2	protein-coding
mm_148187.1	chr18	78867869	78867871	-	1	NA	intron (NM_053099, intron 3 of 5)	intron (NM_053099, intron 3 of 5)	241521	NM_053099	240427	Mm.312871	NM_053099	ENSMUSG00000024548	Setbp1	C130092E12|Seb|mKIAA0437	SET binding protein 1	protein-coding
mm_49550.1	chr6	30512295	30512319	+	1	NA	promoter-TSS (NM_029373)	promoter-TSS (NM_029373)	21	NM_029373	75647	Mm.46117	NM_027073	ENSMUSG00000029784	Ssmem1	1700016K02Rik|1700025E21Rik	serine-rich single-pass membrane protein 1	protein-coding
mm_140948.1	chr17	24527897	24527907	-	1	NA	promoter-TSS (NR_045289)	promoter-TSS (NR_045289)	36	NM_153792	224619	Mm.275150	NM_153792	ENSMUSG00000052752	Traf7	RFWD1	TNF receptor-associated factor 7	protein-coding
mm_72353.1	chr8	79711742	79711789	+	1	NA	promoter-TSS (NM_026904)	promoter-TSS (NM_026904)	-25	NM_015751	24015	Mm.5831	NM_015751	ENSMUSG00000058355	Abce1	C79080|Oabp|RLI|RNS41|Rnaseli	ATP-binding cassette, sub-family E (OABP), member 1	protein-coding
mm_72341.1	chr8	79458875	79458875	+	1	NA	Intergenic	Intergenic	-59407	NM_008539	17125	Mm.223717	NM_008539	ENSMUSG00000031681	Smad1	AI528653|Madh1|Madr1|Mlp1|MusMLP	SMAD family member 1	protein-coding
mm_158375.1	chrX	135210641	135210661	-	1	NA	promoter-TSS (NM_025355)	promoter-TSS (NM_025355)	36	NM_025355	66104	Mm.336239	NM_025355	ENSMUSG00000031409	Tceal6	1500026B10Rik	transcription elongation factor A (SII)-like 6	protein-coding
mm_61474.1	chr7	75612540	75612543	+	1	NA	intron (NM_029332, intron 7 of 36)	intron (NM_029332, intron 7 of 36)	157007	NM_029332	75547	Mm.216107	NM_029332	ENSMUSG00000066406	Akap13	1700026G02Rik|5730522G15Rik|5830460E08Rik|AKAP-13|AKAP-Lbc|BRX|Ht31|LBC|PROTO-LB|PROTO-LBC	A kinase (PRKA) anchor protein 13	protein-coding
mm_9394.1	chr1	172219528	172219532	-	1	NA	exon (NM_009813, exon 1 of 11)	exon (NM_009813, exon 1 of 11)	365	NM_009813	12372	Mm.12829	NM_009813	ENSMUSG00000007122	Casq1	CSQ|CSQ-1|CSQ1|sCSQ	calsequestrin 1	protein-coding
mm_157997.1	chrX	94540432	94540444	-	1	NA	exon (NM_019791, exon 3 of 13)	exon (NM_019791, exon 3 of 13)	1636	NM_019791	94275	Mm.27578	NM_019791	ENSMUSG00000025151	Maged1	2810433C11Rik|5430405L04Rik|DXBwg1492e|Dlixin|Dlxin-1|Dlxin1|MAGE-D1|NRAGE|mFLJ00163	melanoma antigen, family D, 1	protein-coding
mm_114738.1	chr13	83732564	83732574	+	1	NA	intron (NR_015561, intron 2 of 3)	intron (NR_015561, intron 2 of 3)	4463	NR_015561	320203	Mm.245636	NM_177100	ENSMUSG00000050334	C130071C03Rik	2810449C10Rik	RIKEN cDNA C130071C03 gene	ncRNA
mm_35494.1	chr4	41033669	41033674	-	1	NA	3' UTR (NM_007473, exon 8 of 8)	3' UTR (NM_007473, exon 8 of 8)	14465	NM_007473	11832	Mm.8728	NM_007473	ENSMUSG00000028427	Aqp7	AQP7L|AQPap	aquaporin 7	protein-coding
mm_99188.1	chr11	100884375	100884390	+	1	NA	3' UTR (NM_011488, exon 20 of 20)	3' UTR (NM_011488, exon 20 of 20)	23898	NM_001164062	20850	Mm.277403	NM_011488	ENSMUSG00000004043	Stat5a	AA959963|STAT5	signal transducer and activator of transcription 5A	protein-coding
mm_92386.1	chr10	76595920	76595945	-	1	NA	3' UTR (NM_146007, exon 28 of 28)	3' UTR (NM_146007, exon 28 of 28)	20284	NM_080845	14317	Mm.36278	NM_080845	ENSMUSG00000001155	Ftcd	-	formiminotransferase cyclodeaminase	protein-coding
mm_147413.1	chr18	45895587	45895590	-	1	NA	intron (NR_040342, intron 2 of 3)	intron (NR_040342, intron 2 of 3)	149672	NR_040342	107003	Mm.395148	NR_040342		A330093E20Rik	AU043608	RIKEN cDNA A330093E20 gene	ncRNA
mm_68570.1	chr7	115722739	115722741	-	1	NA	intron (NM_001025560, intron 4 of 15)	intron (NM_001025560, intron 4 of 15)	78869	NM_001277328	20679	Mm.323365	NM_011445	ENSMUSG00000051910	Sox6	AI987981|SOX-LZ	SRY (sex determining region Y)-box 6	protein-coding
mm_126177.1	chr15	78597134	78597152	+	1	NA	promoter-TSS (NM_028195)	promoter-TSS (NM_028195)	96	NM_028195	72318	Mm.32911	NM_028195	ENSMUSG00000018008	Cyth4	2510004M07Rik|5830469K17Rik|AI467541|Pscd4|mFLJ00017	cytohesin 4	protein-coding
mm_168190.1	chr10	62602307	62602325	-	1	NA	promoter-TSS (NM_019553)	promoter-TSS (NM_019553)	-18	NM_019553	56200	Mm.413275	NM_019553	ENSMUSG00000020075	Ddx21	AI255159|AL022742|D10Ertd645e|D10Wsu42e	DEAD (Asp-Glu-Ala-Asp) box polypeptide 21	protein-coding
mm_63855.1	chr7	135667518	135667557	+	1	NA	intron (NM_001316681, intron 7 of 17)	intron (NM_001316681, intron 7 of 17)	-15223	NR_015548	67765	Mm.445272	NR_015548	ENSMUSG00000097471	5830432E09Rik	-	RIKEN cDNA 5830432E09 gene	ncRNA
mm_85984.1	chr9	112185782	112185791	-	1	NA	intron (NM_001177617, intron 2 of 14)	intron (NM_001177617, intron 2 of 14)	163	NM_001177618	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_109911.1	chr12	8480201	8480208	-	1	NA	Intergenic	Intergenic	19781	NM_007483	11852	Mm.687	NM_007483	ENSMUSG00000054364	Rhob	AA017882|Arh6|Arhb	ras homolog family member B	protein-coding
mm_45561.1	chr5	73191928	73191932	-	1	NA	intron (NM_028194, intron 3 of 62)	intron (NM_028194, intron 3 of 62)	64688	NM_028194	72313	Mm.260594	NM_028194	ENSMUSG00000070733	Fryl	2010313D22Rik|2310004H21Rik|2510002A14Rik|9030227G01Rik|mKIAA0826	FRY like transcription coactivator	protein-coding
mm_89225.1	chr10	87206012	87206037	+	1	NA	intron (NM_029685, intron 4 of 5)	intron (NM_029685, intron 4 of 5)	147978	NM_029685	76640	Mm.78423	NM_029685	ENSMUSG00000047129	1700113H08Rik	-	RIKEN cDNA 1700113H08 gene	protein-coding
mm_88633.1	chr10	79887918	79887925	+	1	NA	exon (NM_015779, exon 5 of 5)	exon (NM_015779, exon 5 of 5)	1609	NM_015779	50701	Mm.262194	NM_015779	ENSMUSG00000020125	Elane	Ela2|F430011M15Rik|NE	elastase, neutrophil expressed	protein-coding
mm_158685.1	chrX	160735748	160735758	-	1	NA	Intergenic	Intergenic	-15781	NM_011147	237178	Mm.296779	NM_011147	ENSMUSG00000062168	Ppef1	PPEF-1	protein phosphatase with EF hand calcium-binding domain 1	protein-coding
mm_137038.1	chr17	17890742	17890752	+	1	NA	intron (NM_008039, intron 1 of 1)	PB1D10|SINE|Alu	2923	NM_008039	14289	Mm.378918	NM_008039	ENSMUSG00000052270	Fpr2	E330010I07Rik|Fpr-rs2	formyl peptide receptor 2	protein-coding
mm_25116.1	chr3	101667602	101667624	+	1	NA	Intergenic	Intergenic	-62906	NM_144900	11928	Mm.193670	NM_144900	ENSMUSG00000033161	Atp1a1	Atpa-1|BC010319	ATPase, Na+/K+ transporting, alpha 1 polypeptide	protein-coding
mm_37453.1	chr4	123411983	123411987	-	1	NA	promoter-TSS (NM_001167918)	promoter-TSS (NM_001167918)	-74	NM_001167918	442834	Mm.483803	NM_001167918		D830031N03Rik	Kiaa0754|mKIAA0754	RIKEN cDNA D830031N03 gene	protein-coding
mm_69854.1	chr7	141429434	141429455	-	1	NA	promoter-TSS (NM_021316)	promoter-TSS (NM_021316)	-24	NM_021316	57754	Mm.87027	NM_021316	ENSMUSG00000060240	Cend1	1500001H12Rik|AI415214|BM88	cell cycle exit and neuronal differentiation 1	protein-coding
mm_103370.1	chr11	75195310	75195319	-	1	NA	intron (NM_177708, intron 1 of 1)	CpG	1321	NM_177708	237847	Mm.82661	NM_177708	ENSMUSG00000045287	Rtn4rl1	Ngr3|Ngrh2|Ngrl2	reticulon 4 receptor-like 1	protein-coding
mm_123031.1	chr14	55524917	55524930	-	1	NA	promoter-TSS (NM_008736)	promoter-TSS (NM_008736)	58	NM_001271916	18185	Mm.20422	NM_008736	ENSMUSG00000040632	Nrl	D14H14S46E	neural retina leucine zipper gene	protein-coding
mm_125115.1	chr15	28203800	28203811	+	1	NA	promoter-TSS (NM_133365)	promoter-TSS (NM_133365)	39	NM_133365	110082	Mm.248464	NM_133365	ENSMUSG00000022262	Dnah5	AU022615|Dnahc5|Mdnah5|b2b1134Clo|b2b1154Clo|b2b1537Clo|b2b1565Clo|b2b601Clo|mKIAA1603	dynein, axonemal, heavy chain 5	protein-coding
mm_51212.1	chr6	71352939	71352947	+	1	NA	Intergenic	Intergenic	-20484	NM_009857	12525	Mm.1858	NM_009857	ENSMUSG00000053977	Cd8a	BB154331|Ly-2|Ly-35|Ly-B|Lyt-2	CD8 antigen, alpha chain	protein-coding
mm_135176.1	chr16	35939053	35939074	-	1	NA	promoter-TSS (NM_001013371)	promoter-TSS (NM_001013371)	-36	NM_001013371	209200	Mm.390852	NM_001013371	ENSMUSG00000049502	Dtx3l	AU042200|BC023741	deltex 3-like, E3 ubiquitin ligase	protein-coding
mm_10151.1	chr2	4300774	4300797	+	1	NA	intron (NM_172475, intron 1 of 22)	intron (NM_172475, intron 1 of 22)	-100191	NM_001177843	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding
mm_72142.1	chr8	72135280	72135294	+	1	NA	promoter-TSS (NM_001001491)	promoter-TSS (NM_001001491)	-5	NM_001001491	326618	Mm.295124	NM_001001491	ENSMUSG00000031799	Tpm4	2610528G24Rik|Tpm4.2|Tpm4.2cy	tropomyosin 4	protein-coding
mm_88137.1	chr10	69398951	69398977	+	1	NA	Intergenic	CpG	-46052	NM_007659	12534	Mm.281367	NM_007659	ENSMUSG00000019942	Cdk1	Cdc2|Cdc2a|p34<CDC2>	cyclin-dependent kinase 1	protein-coding
mm_140527.1	chr17	6743839	6743846	-	1	NA	intron (NM_009510, intron 7 of 12)	intron (NM_009510, intron 7 of 12)	38012	NM_183368	83672	Mm.442201	NM_031395	ENSMUSG00000041831	Sytl3	A430092N21|Slp3|Slp3-a|Slp3-b|mFLJ00307	synaptotagmin-like 3	protein-coding
mm_60598.1	chr7	44516928	44516940	+	1	NA	exon (NM_146189, exon 8 of 28)	exon (NM_146189, exon 8 of 28)	7735	NM_146189	233199	Mm.358888	NM_146189	ENSMUSG00000038670	Mybpc2	-	myosin binding protein C, fast-type	protein-coding
mm_61926.1	chr7	90163062	90163074	+	1	NA	intron (NM_001252520, intron 3 of 20)	intron (NM_001252520, intron 3 of 20)	32836	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_108478.1	chr12	83659517	83659527	+	1	NA	exon (NM_027349, exon 7 of 19)	exon (NM_027349, exon 7 of 19)	27288	NM_027349	67039	Mm.46005	NM_027349	ENSMUSG00000010608	Rbm25	2600011C06Rik|2610015J01Rik|A130095G20Rik|AI159652|AL023075|AU043498|RNPC7	RNA binding motif protein 25	protein-coding
mm_100698.1	chr11	3531560	3531572	-	1	NA	intron (NM_001159284, intron 7 of 21)	intron (NM_001159284, intron 7 of 21)	7726	NM_013870	29856	Mm.188516	NM_013870	ENSMUSG00000020439	Smtn	smsmo	smoothelin	protein-coding
mm_89034.1	chr10	82771311	82771352	+	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-7190	NM_010914	18045	Mm.245998	NM_010914	ENSMUSG00000020248	Nfyb	AA985999|Cbf-A	nuclear transcription factor-Y beta	protein-coding
mm_27175.1	chr3	34079038	34079052	-	1	NA	intron (NM_001026211, intron 4 of 5)	intron (NM_001026211, intron 4 of 5)	2309	NM_001286972	67713	Mm.274266	NM_026332	ENSMUSG00000027679	Dnajc19	1810055D05Rik|AA959924|Tim14	DnaJ heat shock protein family (Hsp40) member C19	protein-coding
mm_2905.1	chr1	131970590	131970601	+	1	NA	promoter-TSS (NM_145977)	promoter-TSS (NM_145977)	-14	NM_145977	212980	Mm.200307	NM_145977	ENSMUSG00000026435	Slc45a3	2210413P12Rik|AU023994|AU043764|IPCA-6|PRST|Pcanap6	solute carrier family 45, member 3	protein-coding
mm_139247.1	chr17	47734240	47734247	+	1	NA	exon (NM_025973, exon 9 of 9)	exon (NM_025973, exon 9 of 9)	-2794	NM_001161722	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_73561.1	chr8	109493983	109494026	+	1	NA	promoter-TSS (NM_019938)	promoter-TSS (NM_019938)	-23	NM_019938	56523	Mm.42166	NM_019938	ENSMUSG00000031727	Pmfbp1	1700016D22Rik|F77|Stap	polyamine modulated factor 1 binding protein 1	protein-coding
mm_100455.1	chr11	119729527	119729548	+	1	NA	intron (NM_028898, intron 4 of 33)	intron (NM_028898, intron 4 of 33)	104828	NR_045313	319454	Mm.442144	NR_045312	ENSMUSG00000085081	Rptoros	A430071A18Rik	regulatory associated protein of MTOR, complex 1, opposite strand	ncRNA
mm_1900.1	chr1	85780069	85780084	+	1	NA	intron (NR_108086, intron 2 of 3)	ORR1B2|LTR|ERVL-MaLR	4805	NR_108086	77762	Mm.434298	NR_108086	ENSMUSG00000100217	9930111H07Rik	-	RIKEN cDNA 9930111H07 gene	ncRNA
mm_148776.1	chr19	6106880	6106904	+	1	NA	exon (NM_001009546, exon 4 of 18)	exon (NM_001009546, exon 4 of 18)	1094	NM_001009546	381204	Mm.359041	NM_001009546	ENSMUSG00000054999	Naaladl1	Gm964|Naaladasel	N-acetylated alpha-linked acidic dipeptidase-like 1	protein-coding
mm_133476.1	chr16	89511980	89511985	+	1	NA	Intergenic	Intergenic	-3659	NM_027771	71363	Mm.158680	NM_027771	ENSMUSG00000056706	Krtap7-1	5430433J05Rik	keratin associated protein 7-1	protein-coding
mm_121002.1	chr14	79515619	79515694	+	1	NA	promoter-TSS (NM_001286412)	promoter-TSS (NM_001286412)	-18	NM_001286412	13709	Mm.20938	NM_007920	ENSMUSG00000036461	Elf1	Elf-1|Sts1|mElf-1|p70	E74-like factor 1	protein-coding
mm_113514.1	chr13	37778523	37778531	+	1	NA	Intergenic	CpG	-47511	NM_026830	68750	Mm.491109	NM_026830	ENSMUSG00000039087	Rreb1	1110037N09Rik|AA414966|B930013M22Rik	ras responsive element binding protein 1	protein-coding
mm_115286.1	chr13	111868005	111868019	+	1	NA	promoter-TSS (NR_130345)	promoter-TSS (NR_130345)	76	NR_130345	102636620	Mm.402328	NR_130345	ENSMUSG00000086111	Gm15326	OTTMUSG00000020187	predicted gene 15326	ncRNA
mm_1908.1	chr1	85903097	85903116	+	1	NA	exon (NM_022417, exon 2 of 6)	exon (NM_022417, exon 2 of 6)	8596	NM_022417	64294	Mm.29870	NM_022417	ENSMUSG00000026223	Itm2c	3110038L02Rik|BRI3|Bricd2c|E25|E25C|ITM3	integral membrane protein 2C	protein-coding
mm_23239.1	chr3	51210353	51210357	+	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	-14092	NM_009834	12457	Mm.86541	NM_009834	ENSMUSG00000023087	Noct	AU043840|Ccr4|Ccrn4l	nocturnin	protein-coding
mm_83402.1	chr9	44735217	44735240	-	1	NA	promoter-TSS (NM_153537)	promoter-TSS (NM_153537)	-30	NM_153537	102693	Mm.28639	NM_153537	ENSMUSG00000048537	Phldb1	AU041016|D330037A14Rik|Ll5a	pleckstrin homology like domain, family B, member 1	protein-coding
mm_17548.1	chr2	29914833	29914846	-	1	NA	exon (NM_001113213, exon 12 of 21)	exon (NM_001113213, exon 12 of 21)	-20570	NM_028923	74412	Mm.275121	NM_028923	ENSMUSG00000019715	Gle1	4933405K21Rik|AA553313|Gle1l	GLE1 RNA export mediator (yeast)	protein-coding
mm_22917.1	chr3	31094938	31094948	+	1	NA	promoter-TSS (NM_001039090)	promoter-TSS (NM_001039090)	-115	NM_011386	20482	Mm.15406	NM_011386	ENSMUSG00000027660	Skil	Skir|SnoN|sno	SKI-like	protein-coding
mm_96728.1	chr11	69684490	69684507	+	1	NA	exon (NM_001159503, exon 10 of 13)	exon (NM_001159503, exon 10 of 13)	1056	NM_001159505	69583	Mm.8983	NM_023517	ENSMUSG00000089669	Tnfsf13	2310026N09Rik|April|Tall2|Tnlg7b|Trdl1	tumor necrosis factor (ligand) superfamily, member 13	protein-coding
mm_143675.1	chr17	80006265	80006269	-	1	NA	Intergenic	Intergenic	56001	NM_144802	72692	Mm.64579	NM_144802	ENSMUSG00000024095	Hnrnpll	2510028H02Rik|2810036L13Rik|AI256697|AI852082|Hnrpll	heterogeneous nuclear ribonucleoprotein L-like	protein-coding
mm_37571.1	chr4	126242179	126242193	-	1	NA	exon (NM_144941, exon 2 of 17)	exon (NM_144941, exon 2 of 17)	14133	NM_144941	245877	Mm.266716	NM_144941	ENSMUSG00000028849	Map7d1	AV028413|BC019977|Mtap7d1|Parcc1|Rprc1|mKIAA1187	MAP7 domain containing 1	protein-coding
mm_42200.1	chr5	112309821	112309863	+	1	NA	exon (NM_009419, exon 4 of 7)	exon (NM_009419, exon 4 of 7)	-16527	NM_018783	54723	Mm.172947	NM_018783	ENSMUSG00000029345	Tfip11	2810002G02Rik|AF097181|AW046167|Srr1|TIP33|Tip39	tuftelin interacting protein 11	protein-coding
mm_59999.1	chr7	30589776	30589798	+	1	NA	TTS (NR_106134)	TTS (NR_106134)	407	NR_106134	102465774		NR_106134	ENSMUSG00000098553	Mir3569	Gm27279|mmu-mir-3569	microRNA 3569	ncRNA
mm_65472.1	chr7	25477598	25477602	-	1	NA	promoter-TSS (NM_001039186)	promoter-TSS (NM_001039186)	25	NM_001039185	26365	Mm.322502	NM_011926	ENSMUSG00000074272	Ceacam1	Bgp|Bgp1|C-CAM|CD66a|Cc1|Cea-1|Cea-7|Cea1|Cea7|Hv-2|Hv2|MHVR|MHVR1|Mhv-1|bb-1|mCEA1|mmCGM1|mmCGM1a|mmCGM2	carcinoembryonic antigen-related cell adhesion molecule 1	protein-coding
mm_141867.1	chr17	34810558	34810596	-	1	NA	exon (NM_011413, exon 36 of 41)	exon (NM_011413, exon 36 of 41)	-6151	NM_009995	13079	Mm.440407	NM_009995	ENSMUSG00000024365	Cyp21a1	21-OH|21OH|21OHA|21OHB|CYP21OH-A|Cyp21|Cyp21-ps1|Cyp21B|Cyp21a2-ps|Cyp21a2ps|Oh21-1|Oh21-2	cytochrome P450, family 21, subfamily a, polypeptide 1	protein-coding
mm_13206.1	chr2	93642270	93642277	+	1	NA	promoter-TSS (NM_007442)	promoter-TSS (NM_007442)	-161	NM_007442	11695	Mm.389389	NM_007442	ENSMUSG00000040310	Alx4	lst	aristaless-like homeobox 4	protein-coding
mm_129119.1	chr15	76091655	76091671	-	1	NA	Intergenic	CpG	-1650	NM_144847	223649	Mm.101946	NM_144847	ENSMUSG00000075590	Nrbp2	BC011468	nuclear receptor binding protein 2	protein-coding
mm_65470.1	chr7	25476697	25476701	-	1	NA	exon (NM_001039186, exon 2 of 8)	exon (NM_001039186, exon 2 of 8)	926	NM_001039185	26365	Mm.322502	NM_011926	ENSMUSG00000074272	Ceacam1	Bgp|Bgp1|C-CAM|CD66a|Cc1|Cea-1|Cea-7|Cea1|Cea7|Hv-2|Hv2|MHVR|MHVR1|Mhv-1|bb-1|mCEA1|mmCGM1|mmCGM1a|mmCGM2	carcinoembryonic antigen-related cell adhesion molecule 1	protein-coding
mm_44278.1	chr5	5783444	5783477	-	1	NA	Intergenic	Intergenic	-34143	NM_027399	70358	Mm.85429	NM_027399	ENSMUSG00000015652	Steap1	2410007B19Rik|Prss24|Steap	six transmembrane epithelial antigen of the prostate 1	protein-coding
mm_166219.1	chr5	64264294	64264302	+	1	NA	intron (NM_001310611, intron 5 of 21)	intron (NM_001310611, intron 5 of 21)	33941	NM_001289514	57915	Mm.286353	NM_019636	ENSMUSG00000029174	Tbc1d1	1110062G02Rik|AI385682|AW555803|Nob1|Nobq1|Tbc1|mKIAA1108	TBC1 domain family, member 1	protein-coding
mm_105197.1	chr11	102088541	102088554	-	1	NA	promoter-TSS (NM_016695)	promoter-TSS (NM_016695)	-32	NM_016695	50997	Mm.36242	NM_016695	ENSMUSG00000017314	Mpp2	D11Bwg0652e|Dlg2|Dlgh2|Pals4	membrane protein, palmitoylated 2 (MAGUK p55 subfamily member 2)	protein-coding
mm_97213.1	chr11	75630760	75630770	+	1	NA	promoter-TSS (NM_008916)	promoter-TSS (NM_008916)	-255	NM_008916	19062	Mm.1458	NM_008916	ENSMUSG00000006127	Inpp5k	C62|Pps|SKIP	inositol polyphosphate 5-phosphatase K	protein-coding
mm_171834.1	chr5	148176822	148176824	+	1	NA	intron (NM_029920, intron 4 of 14)	LTRIS2|LTR|ERV1	215992	NM_001301424	11987	Mm.275489	NM_007513	ENSMUSG00000041313	Slc7a1	4831426K01Rik|AI447493|Atrc-1|Atrc1|Cat1|Rec-1|Rev-1|mCAT-1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 1	protein-coding
mm_24422.1	chr3	90527740	90527753	+	1	NA	exon (NM_001163525, exon 3 of 4)	exon (NM_001163525, exon 3 of 4)	897	NM_001163526	66166	Mm.24006	NM_025393	ENSMUSG00000042306	S100a14	1110013O05Rik|S100a15|S114	S100 calcium binding protein A14	protein-coding
mm_73518.1	chr8	107457778	107457790	+	1	NA	intron (NM_025830, intron 3 of 23)	intron (NM_025830, intron 3 of 23)	21386	NM_025830	66894	Mm.390058	NM_025830	ENSMUSG00000031930	Wwp2	1300010O06Rik|AA690238|AIP2|AW554328	WW domain containing E3 ubiquitin protein ligase 2	protein-coding
mm_66852.1	chr7	51772749	51772770	-	1	NA	Intergenic	Intergenic	-89256	NM_001330608	14453	Mm.207360	NM_008087	ENSMUSG00000030498	Gas2	Gas-2	growth arrest specific 2	protein-coding
mm_60110.1	chr7	35449117	35449131	+	1	NA	promoter-TSS (NM_001199016)	promoter-TSS (NM_001199016)	26	NM_001199016	30962	Mm.45874	NM_021291	ENSMUSG00000030492	Slc7a9	CSNU3	solute carrier family 7 (cationic amino acid transporter, y+ system), member 9	protein-coding
mm_26577.1	chr3	146899178	146899192	+	1	NA	intron (NM_001302957, intron 5 of 21)	B4A|SINE|B4	46818	NM_001302958	70892	Mm.187793	NM_027594	ENSMUSG00000036745	Ttll7	1110049N09Rik|4921517B04Rik|C630030B20|mTTLL7	tubulin tyrosine ligase-like family, member 7	protein-coding
mm_74774.1	chr8	21756840	21756863	-	1	NA	Intergenic	Intergenic	-19704	NM_007843	13214	Mm.431316	NM_007843	ENSMUSG00000044748	Defb1	AW260221|BD-1	defensin beta 1	protein-coding
mm_58260.1	chr6	145250178	145250259	-	1	NA	promoter-TSS (NM_021284)	promoter-TSS (NM_021284)	13	NM_021284	16653	Mm.383182	NM_021284	ENSMUSG00000030265	Kras	AI929937|K-Ras|K-Ras 2|K-ras|Ki-ras|Kras-2|Kras2|c-K-ras|c-Ki-ras|p21B|ras	Kirsten rat sarcoma viral oncogene homolog	protein-coding
mm_168928.1	chr12	63692352	63692356	+	1	NA	Intergenic	L1Md_T|LINE|L1	782544	NM_001163271	623046	Mm.189552	NM_001163271	ENSMUSG00000043060	Fscb	EG623046	fibrous sheath CABYR binding protein	protein-coding
mm_23928.1	chr3	83766629	83766639	+	1	NA	exon (NM_009144, exon 1 of 3)	exon (NM_009144, exon 1 of 3)	313	NM_009144	20319	Mm.19155	NM_009144	ENSMUSG00000027996	Sfrp2	AI851596|Sdf5	secreted frizzled-related protein 2	protein-coding
mm_43938.1	chr5	145123562	145123615	+	1	NA	exon (NM_023142, exon 4 of 10)	exon (NM_023142, exon 4 of 10)	9332	NM_023142	11867	Mm.30010	NM_023142	ENSMUSG00000029622	Arpc1b	41kDa|AA408064|AA408534|AA571392|AF007010|AW208418|L72|SOP2Hs|p41-ARC	actin related protein 2/3 complex, subunit 1B	protein-coding
mm_71326.1	chr8	44951348	44951384	+	1	NA	exon (NM_001081286, exon 1 of 26)	exon (NM_001081286, exon 1 of 26)	1158	NM_001081286	14107	Mm.27365	NM_001081286	ENSMUSG00000070047	Fat1	2310038E12Rik|AU023433|Fath|mFat1	FAT atypical cadherin 1	protein-coding
mm_3044.1	chr1	134040401	134040406	+	1	NA	exon (NM_021355, exon 2 of 3)	exon (NM_021355, exon 2 of 3)	2888	NM_021355	14264	Mm.287146	NM_021355	ENSMUSG00000041559	Fmod	AI131919|AU041740|SLRR2E	fibromodulin	protein-coding
mm_62033.1	chr7	92062393	92062425	+	1	NA	promoter-TSS (NM_001243046)	promoter-TSS (NM_001243046)	15	NM_001243046	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_95171.1	chr11	40733937	40733947	+	1	NA	promoter-TSS (NM_013552)	promoter-TSS (NM_013552)	281	NM_001290697	52653	Mm.276504	NM_026023	ENSMUSG00000020328	Nudcd2	-	NudC domain containing 2	protein-coding
mm_33438.1	chr4	130108405	130108407	+	1	NA	intron (NM_026441, intron 1 of 4)	MIRc|SINE|MIR	850	NM_026441	67898	Mm.20818	NM_026441	ENSMUSG00000028779	Pef1	2600002E23Rik|Peflin	penta-EF hand domain containing 1	protein-coding
mm_22181.1	chr2	173216991	173217013	-	1	NA	exon (NM_021394, exon 2 of 8)	exon (NM_021394, exon 2 of 8)	1920	NM_021394	58203	Mm.116687	NM_021394	ENSMUSG00000027514	Zbp1	2010010H03Rik|Dai|Dlm1|mZaDLM	Z-DNA binding protein 1	protein-coding
mm_97548.1	chr11	78927403	78927412	+	1	NA	intron (NM_001313922, intron 1 of 25)	B1_Mm|SINE|Alu	2116	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_102322.1	chr11	57507130	57507134	-	1	NA	intron (NM_001168667, intron 6 of 13)	intron (NM_001168667, intron 6 of 13)	11512	NM_001168667	67726	Mm.25632	NM_026342	ENSMUSG00000020523	Fam114a2	1810073G14Rik|9030624B09Rik	family with sequence similarity 114, member A2	protein-coding
mm_47470.1	chr5	123684290	123684379	-	1	NA	promoter-TSS (NM_019765)	promoter-TSS (NM_019765)	27	NM_019765	56430	Mm.241109	NM_019765	ENSMUSG00000049550	Clip1	1110007I12Rik|4631429H07Rik|AV017631|C81039|CLIP-170|CLIP170|CYLN1|Clip50|Rsn|mKIAA4046|restin	CAP-GLY domain containing linker protein 1	protein-coding
mm_48610.1	chr5	144358046	144358101	-	1	NA	promoter-TSS (NM_025833)	promoter-TSS (NM_025833)	39	NM_025833	66898	Mm.18814	NM_025833	ENSMUSG00000038859	Baiap2l1	1300006M19Rik|AI585895|IRTKS	BAI1-associated protein 2-like 1	protein-coding
mm_111069.1	chr12	80116920	80116941	-	1	NA	Intergenic	Intergenic	-3917	NM_007564	12192	Mm.235132	NM_007564	ENSMUSG00000021127	Zfp36l1	AW742437|AW743212|Berg36|Brf1|D530020L18Rik|ERF1|TIS11b|cMG1	zinc finger protein 36, C3H type-like 1	protein-coding
mm_168200.1	chr10	66582804	66582807	+	1	NA	Intergenic	L1Md_T|LINE|L1	337579	NR_138560	68488	Mm.338835	NR_138560		1110002J07Rik	-	RIKEN cDNA 1110002J07 gene	ncRNA
mm_6227.1	chr1	66937462	66937482	-	1	NA	intron (NM_021285, intron 1 of 6)	intron (NM_021285, intron 1 of 6)	-2106	NM_001113387	17901	Mm.1000	NM_021285	ENSMUSG00000061816	Myl1	AI325107|MLC1f|MLC3f|Mylf	myosin, light polypeptide 1	protein-coding
mm_73149.1	chr8	94992921	94992937	+	1	NA	intron (NM_018882, intron 1 of 13)	intron (NM_018882, intron 1 of 13)	8530	NM_018882	14766	Mm.290834	NM_018882	ENSMUSG00000031785	Adgrg1	Cyt28|Gpr56|TM7LN4|TM7XN1	adhesion G protein-coupled receptor G1	protein-coding
mm_6930.1	chr1	84935090	84935108	-	1	NA	promoter-TSS (NM_027921)	promoter-TSS (NM_027921)	-16	NM_027921	71781	Mm.158754	NM_027921	ENSMUSG00000026220	Slc16a14	1110004H10Rik	solute carrier family 16 (monocarboxylic acid transporters), member 14	protein-coding
mm_164559.1	chr17	15577494	15577497	-	1	NA	Intergenic	Intergenic	-14172	NM_144809	213389	Mm.215162	NM_144809	ENSMUSG00000051977	Prdm9	BC012016|Dsbc1|G1-419-29|Meisetz|PRDM9-B|Rcr1|repro7	PR domain containing 9	protein-coding
mm_50323.1	chr6	48289217	48289227	+	1	NA	Intergenic	Intergenic	-106364	NM_001347152	77827	Mm.107646	NM_133922	ENSMUSG00000042810	Krba1	A930040G15Rik|AI448780	KRAB-A domain containing 1	protein-coding
mm_69358.1	chr7	130488760	130488769	-	1	NA	intron (NM_001029895, intron 7 of 11)	(A)n|Simple_repeat|Simple_repeat	30816	NM_001136054	11907	Mm.216321	NM_013799	ENSMUSG00000030850	Ate1	AI225793|AW547406	arginyltransferase 1	protein-coding
mm_109986.1	chr12	14147102	14147105	-	1	NA	TTS (NM_029007)	TTS (NM_029007)	4935	NM_029007	105005	Mm.227253	NM_029007	ENSMUSG00000020607	Fam84a	2310003N02Rik|4731402F03Rik|AW125753|Nse1	family with sequence similarity 84, member A	protein-coding
mm_49740.1	chr6	34745842	34745854	+	1	NA	exon (NM_145575, exon 3 of 12)	exon (NM_145575, exon 3 of 12)	-34584	NM_001289657	76223	Mm.150047	NM_178630	ENSMUSG00000038836	Agbl3	2900053G10Rik|4930431N21Rik|6530406M24Rik|CCP3	ATP/GTP binding protein-like 3	protein-coding
mm_101307.1	chr11	22610382	22610396	-	1	NA	Intergenic	Intergenic	98106	NM_153596	103765	Mm.221274	NM_153596	ENSMUSG00000049904	Tmem17	AI503894|AW049890	transmembrane protein 17	protein-coding
mm_37575.1	chr4	126256074	126256101	-	1	NA	5' UTR (NM_144941, exon 1 of 17)	5' UTR (NM_144941, exon 1 of 17)	232	NM_144941	245877	Mm.266716	NM_144941	ENSMUSG00000028849	Map7d1	AV028413|BC019977|Mtap7d1|Parcc1|Rprc1|mKIAA1187	MAP7 domain containing 1	protein-coding
mm_130105.1	chr15	89429803	89429820	-	1	NA	non-coding (NR_004843, exon 1 of 27)	non-coding (NR_004843, exon 1 of 27)	116	NR_037154	12651	Mm.485045	NM_007692	ENSMUSG00000022617	Chkb	Chetk|Chkl|Ck|Ck/Ek|Ck/Ek-beta|Ckb|Ckekb|Ek	choline kinase beta	protein-coding
mm_2834.1	chr1	131525423	131525453	+	1	NA	5' UTR (NM_001081011, exon 2 of 23)	5' UTR (NM_001081011, exon 2 of 23)	1923	NM_001081011	14270	Mm.276259	NM_019520	ENSMUSG00000026425	Srgap2	9930124L22Rik|AI448945|FBP2|Fnbp2|srGAP3	SLIT-ROBO Rho GTPase activating protein 2	protein-coding
mm_155745.1	chrX	96166881	96166906	+	1	NA	3' UTR (NM_010833, exon 13 of 13)	3' UTR (NM_010833, exon 13 of 13)	70848	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_3017.1	chr1	133363817	133363821	+	1	NA	exon (NM_175443, exon 1 of 8)	exon (NM_175443, exon 1 of 8)	247	NM_175443	214253	Mm.52111	NM_175443	ENSMUSG00000070644	Etnk2	4933417N20Rik|AI197444|EKI 2|Eki2|Tuc1	ethanolamine kinase 2	protein-coding
mm_82275.1	chr9	7353476	7353505	-	1	NA	exon (NM_008605, exon 6 of 10)	exon (NM_008605, exon 6 of 10)	6116	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_5125.1	chr1	9631102	9631116	-	1	NA	promoter-TSS (NR_015470)	promoter-TSS (NR_015470)	-17	NR_015470	72481	Mm.279818	NR_015470	ENSMUSG00000079671	2610203C22Rik	2310007M24Rik	RIKEN cDNA 2610203C22 gene	ncRNA
mm_85633.1	chr9	107635381	107635385	-	1	NA	promoter-TSS (NM_008138)	promoter-TSS (NM_008138)	-41	NM_008138	14678	Mm.196464	NM_008138	ENSMUSG00000032562	Gnai2	C76432|Galphai2|Gia|Gnai-2	guanine nucleotide binding protein (G protein), alpha inhibiting 2	protein-coding
mm_140603.1	chr17	10319382	10319392	-	1	NA	promoter-TSS (NM_001159517)	promoter-TSS (NM_001159517)	-26	NM_001159517	19317	Mm.130694	NM_021881	ENSMUSG00000062078	Qk	1110003F05Rik|1500005P18|QkI|l(17)-1Wis|l17Wis1	quaking	protein-coding
mm_117720.1	chr13	95444764	95444777	-	1	NA	promoter-TSS (NM_198408)	promoter-TSS (NM_198408)	61	NM_198408	12919	Mm.316614	NM_198408	ENSMUSG00000021680	Crhbp	CRH-BP	corticotropin releasing hormone binding protein	protein-coding
mm_11918.1	chr2	52071878	52071883	+	1	NA	promoter-TSS (NM_175238)	promoter-TSS (NM_175238)	-957	NM_175238	51869	Mm.254530	NM_175238	ENSMUSG00000036202	Rif1	5730435J01Rik|6530403D07Rik|AU016181|AW549474|D2Ertd145e	replication timing regulatory factor 1	protein-coding
mm_7357.1	chr1	106695712	106695725	-	1	NA	intron (NM_009741, intron 1 of 1)	intron (NM_009741, intron 1 of 1)	18572	NM_009741	12043	Mm.257460	NM_009741	ENSMUSG00000057329	Bcl2	AW986256|Bcl-2|C430015F12Rik|D630044D05Rik|D830018M01Rik	B cell leukemia/lymphoma 2	protein-coding
mm_83659.1	chr9	49554513	49554529	-	1	NA	intron (NM_001081445, intron 8 of 17)	intron (NM_001081445, intron 8 of 17)	36233	NR_029465	100036537	Mm.437541	NR_029465	ENSMUSG00000079564	Gm11149	ENSMUSG00000060603|ENSMUSG00000079564	predicted gene 11149	ncRNA
mm_58856.1	chr7	16891825	16891851	+	1	NA	promoter-TSS (NM_010320)	promoter-TSS (NM_010320)	52	NM_010320	14709	Mm.103770	NM_010320	ENSMUSG00000063594	Gng8	G(y)8	guanine nucleotide binding protein (G protein), gamma 8	protein-coding
mm_105481.1	chr11	105939955	105939961	-	1	NA	intron (NM_007805, intron 1 of 5)	intron (NM_007805, intron 1 of 5)	4189	NM_007805	13056	Mm.149403	NM_007805	ENSMUSG00000019590	Cyb561	-	cytochrome b-561	protein-coding
mm_165521.1	chr2	174284229	174284237	+	1	NA	promoter-TSS (NM_022000)	promoter-TSS (NM_022000)	-87	NM_019690	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_12768.1	chr2	79289231	79289252	+	1	NA	exon (NM_010576, exon 14 of 28)	exon (NM_010576, exon 14 of 28)	33815	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D|Itga4B	integrin alpha 4	protein-coding
mm_108569.1	chr12	84807053	84807066	+	1	NA	intron (NM_013589, intron 14 of 34)	intron (NM_013589, intron 14 of 34)	33789	NM_028863	74316	Mm.25719	NM_028863	ENSMUSG00000021241	Isca2	0710001C05Rik|5730594E03Rik|Hbld1	iron-sulfur cluster assembly 2	protein-coding
mm_106100.1	chr11	116247199	116247216	-	1	NA	intron (NM_146032, intron 13 of 15)	intron (NM_146032, intron 13 of 15)	-9116	NM_025276	14027	Mm.293683	NM_025276	ENSMUSG00000034282	Evpl	-	envoplakin	protein-coding
mm_99857.1	chr11	109365063	109365063	+	1	NA	intron (NM_010303, intron 1 of 3)	intron (NM_010303, intron 1 of 3)	-1409	NR_038097	100036768	Mm.467767	NR_038097	ENSMUSG00000056687	Gm11696	OTTMUSG00000003456	predicted gene 11696	ncRNA
mm_67358.1	chr7	79837694	79837710	-	1	NA	intron (NM_008486, intron 9 of 19)	intron (NM_008486, intron 9 of 19)	4650	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_20718.1	chr2	134644178	134644188	-	1	NA	promoter-TSS (NM_029148)	promoter-TSS (NM_029148)	-62	NM_029148	52837	Mm.264096	NM_029148	ENSMUSG00000034723	Tmx4	2810417D04Rik|4930500L08Rik|AI843224|AW046784|D2Bwg1356e|Txndc13|mKIAA1162	thioredoxin-related transmembrane protein 4	protein-coding
mm_113851.1	chr13	47209024	47209027	+	1	NA	intron (NM_001170643, intron 2 of 7)	intron (NM_001170643, intron 2 of 7)	15022	NM_001170643	218215	Mm.287609	NM_146042	ENSMUSG00000038068	Rnf144b	BC025007|E130105P19Rik|Ibrdc2|Pir2	ring finger protein 144B	protein-coding
mm_75369.1	chr8	45306807	45306822	-	1	NA	3' UTR (NM_133969, exon 11 of 11)	3' UTR (NM_133969, exon 11 of 11)	-11979	NM_008455	16621	Mm.482691	NM_008455	ENSMUSG00000109764	Klkb1	APS|Kal-3|Kal3|Klk3|PSA	kallikrein B, plasma 1	protein-coding
mm_7453.1	chr1	120265373	120265377	-	1	NA	promoter-TSS (NM_133186)	promoter-TSS (NM_133186)	-95	NM_133186	68428	Mm.181033	NM_133186	ENSMUSG00000026389	Steap3	1010001D01Rik|Tsap6|pHyde	STEAP family member 3	protein-coding
mm_40063.1	chr5	33996771	33996781	+	1	NA	5' UTR (NM_001001985, exon 1 of 3)	5' UTR (NM_001001985, exon 1 of 3)	792	NM_001001985	269642	Mm.274610	NM_001001985	ENSMUSG00000048142	Nat8l	1110038O08Rik|Shati	N-acetyltransferase 8-like	protein-coding
mm_114635.1	chr13	76384354	76384392	+	1	NA	promoter-TSS (NM_030174)	promoter-TSS (NM_030174)	-588	NM_030174	78771	Mm.316249	NM_030174	ENSMUSG00000021596	Mctp1	2810465F10Rik	multiple C2 domains, transmembrane 1	protein-coding
mm_15223.1	chr2	154472278	154472279	+	1	NA	intron (NM_009823, intron 1 of 10)	B1_Mur4|SINE|Alu	35794	NM_009823	12396	Mm.29914	NM_009823	ENSMUSG00000038533	Cbfa2t2	A430091M07|C330013D05Rik|Cbfa2t2h|MTGR1	core-binding factor, runt domain, alpha subunit 2, translocated to, 2 (human)	protein-coding
mm_163856.1	chr14	19418519	19418547	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	184054	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_121669.1	chr14	12437535	12437555	-	1	NA	intron (NM_012061, intron 25 of 28)	intron (NM_012061, intron 25 of 28)	-91680	NM_080433	54713	Mm.34644	NM_080433	ENSMUSG00000021743	Fezf2	AI451466|AI852056|Fez|Fezl|Zfp312	Fez family zinc finger 2	protein-coding
mm_123834.1	chr14	70629051	70629061	-	1	NA	promoter-TSS (NM_001252665)	promoter-TSS (NM_001252665)	-9	NM_001252665	13829	Mm.210863	NM_013514	ENSMUSG00000022099	Dmtn	AI325486|Epb4.9|Epb49|dematin	dematin actin binding protein	protein-coding
mm_44694.1	chr5	30355229	30355275	-	1	NA	exon (NM_001033460, exon 7 of 16)	exon (NM_001033460, exon 7 of 16)	13589	NM_001033460	381738	Mm.389604	NM_001033460	ENSMUSG00000073102	Drc1	Ccdc164|Gm1060|b2b1654Clo	dynein regulatory complex subunit 1	protein-coding
mm_113645.1	chr13	42301447	42301491	+	1	NA	promoter-TSS (NM_010104)	promoter-TSS (NM_010104)	-7	NM_010104	13614	Mm.14543	NM_010104	ENSMUSG00000021367	Edn1	ET-1|PPET1|preproET	endothelin 1	protein-coding
mm_15079.1	chr2	153161293	153161307	+	1	NA	promoter-TSS (NM_133847)	promoter-TSS (NM_133847)	-1	NM_133847	99237	Mm.330674	NM_133847	ENSMUSG00000068040	Tm9sf4	AA986553|AU045326|B930079E06|mKIAA0255	transmembrane 9 superfamily protein member 4	protein-coding
mm_75358.1	chr8	45262076	45262084	-	1	NA	promoter-TSS (NM_028066)	promoter-TSS (NM_028066)	-49	NM_028066	109821	Mm.33326	NM_028066	ENSMUSG00000031645	F11	1600027G01Rik|AI503996|Cf11|FXI|PTA	coagulation factor XI	protein-coding
mm_70016.1	chr7	142512128	142512152	-	1	NA	exon (NM_001163669, exon 13 of 17)	exon (NM_001163669, exon 13 of 17)	-5369	NR_033261	677289	Mm.350054	NR_033261	ENSMUSG00000043795	Prr33	ENSMUSG00000043795|Gm14492|OTTMUSG00000016823	proline rich 33	ncRNA
mm_166286.1	chr5	98030953	98030962	-	1	NA	promoter-TSS (NM_133738)	promoter-TSS (NM_133738)	5	NM_133738	71914	Mm.24842	NM_133738	ENSMUSG00000029338	Antxr2	2310046B19Rik|AW561899|CMG-2|CMG2|cI-35	anthrax toxin receptor 2	protein-coding
mm_128465.1	chr15	50814267	50814278	-	1	NA	intron (NM_001310485, intron 5 of 7)	intron (NM_001310485, intron 5 of 7)	74777	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_25944.1	chr3	131496905	131496910	+	1	NA	Intergenic	Intergenic	-67861	NM_001289479	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_111669.1	chr12	103338200	103338206	-	1	NA	intron (NM_023049, intron 2 of 9)	intron (NM_023049, intron 2 of 9)	17798	NM_023049	65256	Mm.27159	NM_023049	ENSMUSG00000021200	Asb2	1110008E15Rik	ankyrin repeat and SOCS box-containing 2	protein-coding
mm_45907.1	chr5	89416279	89416283	-	1	NA	Intergenic	Intergenic	41617	NM_008096	14473	Mm.196595	NM_008096	ENSMUSG00000035540	Gc	DBP|VDB	group specific component	protein-coding
mm_167143.1	chr7	127981934	127981966	+	1	NA	TTS (NM_139149)	TTS (NM_139149)	11917	NM_023258	66824	Mm.24163	NM_023258	ENSMUSG00000030793	Pycard	9130417A21Rik|Asc|CARD5|TMS-1|TNS1|masc	PYD and CARD domain containing	protein-coding
mm_29545.1	chr3	116712697	116712723	-	1	NA	promoter-TSS (NM_144902)	promoter-TSS (NM_144902)	-430	NM_144902	229782	Mm.190758	NM_144902	ENSMUSG00000027957	Slc35a3	2310050P13Rik	solute carrier family 35 (UDP-N-acetylglucosamine (UDP-GlcNAc) transporter), member 3	protein-coding
mm_105737.1	chr11	109298122	109298142	-	1	NA	promoter-TSS (NM_011268)	promoter-TSS (NM_011268)	49	NM_001165934	19739	Mm.38548	NM_011268	ENSMUSG00000020599	Rgs9	RGS9-1|Rgs9-2	regulator of G-protein signaling 9	protein-coding
mm_42655.1	chr5	119326010	119326041	+	1	NA	Intergenic	Intergenic	-126007	NR_046033	665194	Mm.491047	NR_046033	ENSMUSG00000107334	Gm7538	EG665194	predicted gene 7538	ncRNA
mm_63010.1	chr7	120940666	120940685	+	1	NA	exon (NM_001164096, exon 17 of 20)	exon (NM_001164096, exon 17 of 20)	22931	NM_001164096	26939	Mm.193632	NM_025298	ENSMUSG00000030880	Polr3e	RPC5|Sin	polymerase (RNA) III (DNA directed) polypeptide E	protein-coding
mm_121049.1	chr14	84443554	84443568	+	1	NA	promoter-TSS (NM_001013753)	promoter-TSS (NM_001013753)	-2	NM_001013753	219228	Mm.153643	NM_001013753	ENSMUSG00000035566	Pcdh17	C030033F14Rik|Gm78	protocadherin 17	protein-coding
mm_101817.1	chr11	46389587	46389591	-	1	NA	promoter-TSS (NM_001281968)	promoter-TSS (NM_001281968)	-74	NM_001281965	16428	Mm.339927	NM_010583	ENSMUSG00000020395	Itk	Emt|Tcsk|Tsk	IL2 inducible T cell kinase	protein-coding
mm_86049.1	chr9	114520615	114520620	-	1	NA	intron (NM_001042503, intron 2 of 3)	B1_Mur4|SINE|Alu	-24073	NM_009916	12773	Mm.1337	NM_009916	ENSMUSG00000047898	Ccr4	C-C CKR-4|CHEMR1|Cmkbr4|LESTR|Sdf1r	chemokine (C-C motif) receptor 4	protein-coding
mm_149364.1	chr19	11321407	11321418	+	1	NA	3' UTR (NM_001276398, exon 7 of 7)	3' UTR (NM_001276398, exon 7 of 7)	13283	NM_001276398	109225	Mm.491251	NM_027836	ENSMUSG00000024672	Ms4a7	9130422I10Rik|A430103C15Rik|CD20l4|CFFMA	membrane-spanning 4-domains, subfamily A, member 7	protein-coding
mm_43409.1	chr5	135887989	135888011	+	1	NA	promoter-TSS (NM_013560)	promoter-TSS (NM_013560)	81	NM_013560	15507	Mm.13849	NM_013560	ENSMUSG00000004951	Hspb1	27kDa|Hsp25	heat shock protein 1	protein-coding
mm_160769.1	chr10	110000103	110000103	-	1	NA	exon (NM_001081035, exon 1 of 39)	exon (NM_001081035, exon 1 of 39)	116	NM_001081035	260315	Mm.225050	NM_177797	ENSMUSG00000020181	Nav3	4732483H20Rik|9630020C08Rik|POMFIL1|Pomfil1p|mKIAA0938|unc53H3	neuron navigator 3	protein-coding
mm_114495.1	chr13	69959830	69959836	+	1	NA	promoter-TSS (NR_138559)	promoter-TSS (NR_138559)	0	NR_138559	67550	Mm.158159	NR_138559		4933416O17Rik	-	RIKEN cDNA 4933416O17 gene	ncRNA
mm_97719.1	chr11	80209715	80209718	+	1	NA	intron (NM_021536, intron 1 of 18)	intron (NM_021536, intron 1 of 18)	661	NM_021536	59040	Mm.489674	NM_021536	ENSMUSG00000017686	Rhot1	2210403N23Rik|AA415293|AF244542|AI834919|Arht1|C430039G08Rik|Miro1	ras homolog family member T1	protein-coding
mm_84062.1	chr9	58199762	58199772	-	1	NA	exon (NM_177193, exon 3 of 3)	exon (NM_177193, exon 3 of 3)	1948	NM_001161535	320563	Mm.186499	NM_177193	ENSMUSG00000051243	Islr2	B930052A04Rik|Linx|Mbu-3|mKIAA1465	immunoglobulin superfamily containing leucine-rich repeat 2	protein-coding
mm_93845.1	chr10	121628764	121628776	-	1	NA	Intergenic	RMER6B|LTR|ERVK	-2454	NM_001081056	73192	Mm.25042	NM_001081056	ENSMUSG00000034667	Xpot	1110004L07Rik|3110065H13Rik|AI452076|C79645|EXPORTIN-T	exportin, tRNA (nuclear export receptor for tRNAs)	protein-coding
mm_144008.1	chr17	88305386	88305398	-	1	NA	Intergenic	RLTR51A_Mm|LTR|ERVK?	-135320	NM_180974	14236	Mm.112824	NM_180974	ENSMUSG00000034998	Foxn2	3230402J05Rik|6030465J18Rik|Fkh19|Foxn1|HTLF	forkhead box N2	protein-coding
mm_35243.1	chr4	19877476	19877483	-	1	NA	3' UTR (NM_175406, exon 8 of 8)	3' UTR (NM_175406, exon 8 of 8)	45087	NM_175406	242341	Mm.19298	NM_175406	ENSMUSG00000028238	Atp6v0d2	1620401A02Rik|AI324824|V-ATPase	ATPase, H+ transporting, lysosomal V0 subunit D2	protein-coding
mm_91320.1	chr10	24959902	24959913	-	1	NA	Intergenic	MT2B1|LTR|ERVL	-32437	NM_007482	11846	Mm.154144	NM_007482	ENSMUSG00000019987	Arg1	AI|AI256583|Arg-1|PGIF	arginase, liver	protein-coding
mm_165985.1	chr4	107253229	107253242	+	1	NA	promoter-TSS (NM_028394)	promoter-TSS (NM_028394)	298	NM_029985	77809	Mm.29681	NM_029985	ENSMUSG00000028617	Lrrc42	A930011F22Rik|AA536996	leucine rich repeat containing 42	protein-coding
mm_84146.1	chr9	59410628	59410632	-	1	NA	intron (NM_019927, intron 7 of 13)	PB1D9|SINE|Alu	-57122	NM_175325	102774	Mm.200714	NM_175325	ENSMUSG00000025235	Bbs4	AW537059|AW742241|D9Ertd464e	Bardet-Biedl syndrome 4 (human)	protein-coding
mm_169801.1	chr16	17222459	17222473	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-11121	NM_178922	58180	Mm.261602	NM_178922	ENSMUSG00000050240	Hic2	AA409108|HRG22|mKIAA1020	hypermethylated in cancer 2	protein-coding
mm_22401.1	chr2	181241053	181241101	-	1	NA	intron (NM_183162, intron 1 of 18)	intron (NM_183162, intron 1 of 18)	950	NM_183162	229003	Mm.315872	NM_183162	ENSMUSG00000027580	Helz2	PDIP1|Pric285|mKIAA1769|mPDIP1	helicase with zinc finger 2, transcriptional coactivator	protein-coding
mm_43866.1	chr5	143482005	143482008	+	1	NA	intron (NM_144915, intron 6 of 14)	B1_Mur1|SINE|Alu	17513	NM_144915	231871	Mm.469963	NM_144915	ENSMUSG00000039206	Daglb	E330036I19Rik	diacylglycerol lipase, beta	protein-coding
mm_135710.1	chr16	55523681	55523701	-	1	NA	Intergenic	Intergenic	28960	NR_039578	100628589		NR_039578	ENSMUSG00000093292	Mir5118	mmu-mir-5118|mu-mir-5118	microRNA 5118	ncRNA
mm_30529.1	chr4	3090672	3090687	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	-81404	NM_001167534	100312470	Mm.480297	NM_001167534	ENSMUSG00000094798	Vmn1r2	Gm11776|OTTMUSG00000004179	vomeronasal 1 receptor 2	protein-coding
mm_35213.1	chr4	19635307	19635343	-	1	NA	exon (NM_177327, exon 17 of 25)	exon (NM_177327, exon 17 of 25)	60259	NM_025476	66302	Mm.440686	NM_025476	ENSMUSG00000028229	Rmdn1	Fam82b|RMD-1	regulator of microtubule dynamics 1	protein-coding
mm_33288.1	chr4	128883550	128883611	+	1	NA	promoter-TSS (NM_178110)	promoter-TSS (NM_178110)	-560	NM_178110	67525	Mm.30653	NM_178110	ENSMUSG00000041000	Trim62	6330414G21Rik|AI450348|Dear1	tripartite motif-containing 62	protein-coding
mm_162392.1	chr1	76596652	76596652	+	1	NA	Intergenic	Intergenic	87092	NR_105761	102465175		NR_105761	ENSMUSG00000098611	Mir6343	Gm27304|mmu-mir-6343	microRNA 6343	ncRNA
mm_122348.1	chr14	38701911	38701914	-	1	NA	intron (NM_001190187, intron 2 of 9)	intron (NM_001190187, intron 2 of 9)	-196390	NR_045713	75170	Mm.372967	NR_045713	ENSMUSG00000093528	Nrg3os	4930529F24Rik	neuregulin 3, opposite strand	ncRNA
mm_108168.1	chr12	76404169	76404264	+	1	NA	promoter-TSS (NM_001002012)	promoter-TSS (NM_001002012)	40	NM_001002012	15512	Mm.296181	NM_008301	ENSMUSG00000059970	Hspa2	70kDa|HSP70.2|HSP70A2|Hsp70-2	heat shock protein 2	protein-coding
mm_167725.1	chr9	101074584	101074675	+	1	NA	promoter-TSS (NM_001100451)	promoter-TSS (NM_001100451)	-133	NM_001100451	77853	Mm.326206	NM_001100451	ENSMUSG00000066415	Msl2	E130103E02Rik|Msl2l1|Rnf184	male-specific lethal 2 homolog (Drosophila)	protein-coding
mm_37098.1	chr4	116615278	116615301	-	1	NA	intron (NM_001081475, intron 3 of 13)	B3|SINE|B2	12208	NM_001081475	50927	Mm.257181	NM_016777	ENSMUSG00000028693	Nasp	5033430J04Rik|AI131596|AI317140|D4Ertd767e|Epcs32|Nasp-T	nuclear autoantigenic sperm protein (histone-binding)	protein-coding
mm_166261.1	chr5	87694555	87694561	+	1	NA	exon (NM_001286023, exon 5 of 7)	exon (NM_001286023, exon 5 of 7)	4867	NM_001286020	12991	Mm.268737	NM_009972	ENSMUSG00000063157	Csn2	Csnb	casein beta	protein-coding
mm_128180.1	chr15	34495168	34495171	-	1	NA	promoter-TSS (NM_008287)	promoter-TSS (NM_008287)	77	NM_008287	15473	Mm.491154	NM_008287	ENSMUSG00000022323	Rida	HR12|HRP12|Hrsp12	reactive intermediate imine deaminase A homolog	protein-coding
mm_157400.1	chrX	38424298	38424308	-	1	NA	exon (NM_001017959, exon 8 of 9)	exon (NM_001017959, exon 8 of 9)	32157	NM_010685	16784	Mm.486	NM_010685	ENSMUSG00000016534	Lamp2	CD107b|LGP-B|Lamp II|Lamp-2|Lamp-2a|Lamp-2b|Lamp-2c|Mac3	lysosomal-associated membrane protein 2	protein-coding
mm_80423.1	chr9	77917376	77917386	+	1	NA	promoter-TSS (NM_134255)	promoter-TSS (NM_134255)	16	NM_134255	68801	Mm.430736	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	ELOVL family member 5, elongation of long chain fatty acids (yeast)	protein-coding
mm_143405.1	chr17	70805986	70806005	-	1	NA	intron (NM_001347411, intron 12 of 14)	ORR1A4|LTR|ERVL-MaLR	40782	NM_001164077	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_1335.1	chr1	66032998	66033012	+	1	NA	Intergenic	Intergenic	106483	NM_027010	12969	Mm.275362	NM_027010	ENSMUSG00000025945	Crygf	3110001K11Rik|Cryg-2|DGcry-2|Len-2	crystallin, gamma F	protein-coding
mm_62454.1	chr7	101421692	101421726	+	1	NA	promoter-TSS (NM_001143848)	promoter-TSS (NM_001143848)	18	NM_001143848	207728	Mm.247564	NM_001008548	ENSMUSG00000030653	Pde2a	CGS-PDE|cGSPDE	phosphodiesterase 2A, cGMP-stimulated	protein-coding
mm_159017.1	chr1	171252176	171252176	+	1	NA	intron (NM_172845, intron 1 of 8)	intron (NM_172845, intron 1 of 8)	2047	NM_172845	240913	Mm.491147	NM_172845	ENSMUSG00000006403	Adamts4	ADAM-TS4|ADAMTS-2|ADMP-1	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 4	protein-coding
mm_83349.1	chr9	44342297	44342312	-	1	NA	promoter-TSS (NM_001110251)	promoter-TSS (NM_001110251)	77	NM_001110251	15288	Mm.247676	NM_013551	ENSMUSG00000032126	Hmbs	PBGD|T25658|Ups|Uros1	hydroxymethylbilane synthase	protein-coding
mm_46077.1	chr5	92323870	92323881	-	1	NA	exon (NM_008599, exon 4 of 4)	exon (NM_008599, exon 4 of 4)	4204	NM_008599	17329	Mm.766	NM_008599	ENSMUSG00000029417	Cxcl9	BB139920|CMK|Mig|MuMIG|Scyb9|crg-10	chemokine (C-X-C motif) ligand 9	protein-coding
mm_74606.1	chr8	12439172	12439213	-	1	NA	Intergenic	Intergenic	43673	NM_009233	20664	Mm.39088	NM_009233	ENSMUSG00000096014	Sox1	BB176347|Sox-1	SRY (sex determining region Y)-box 1	protein-coding
mm_150885.1	chr19	45150660	45150696	+	1	NA	promoter-TSS (NM_021901)	promoter-TSS (NM_021901)	-37	NM_021901	21908	Mm.391203	NM_021901	ENSMUSG00000025215	Tlx1	Hox-11|Hox11|Tlx-1	T cell leukemia, homeobox 1	protein-coding
mm_40743.1	chr5	66686885	66686893	+	1	NA	exon (NM_011670, exon 9 of 9)	exon (NM_011670, exon 9 of 9)	-10392	NR_102714	101202684	Mm.381468	NR_102714	ENSMUSG00000087601	Uchl1os	Gm16832|Uchl1as	ubiquitin carboxy-terminal hydrolase L1, opposite strand	ncRNA
mm_116435.1	chr13	42241748	42241755	-	1	NA	Intergenic	Intergenic	-59725	NM_010104	13614	Mm.14543	NM_010104	ENSMUSG00000021367	Edn1	ET-1|PPET1|preproET	endothelin 1	protein-coding
mm_166076.1	chr4	136943213	136943214	+	1	NA	intron (NM_007939, intron 3 of 16)	intron (NM_007939, intron 3 of 16)	13603	NM_007939	13842	Mm.1390	NM_007939	ENSMUSG00000028661	Epha8	AW047546|Eek|Hek3|mKIAA1459	Eph receptor A8	protein-coding
mm_49150.1	chr6	11933381	11933405	+	1	NA	exon (NM_001168382, exon 3 of 18)	exon (NM_001168382, exon 3 of 18)	7512	NM_001168382	75725	Mm.212411	NM_029404	ENSMUSG00000029629	Phf14	1110001C23Rik|4932409F11Rik|5730446A07Rik|AA623952|AV297001|mKIAA0783	PHD finger protein 14	protein-coding
mm_3424.1	chr1	146495699	146495707	+	1	NA	promoter-TSS (NM_153539)	promoter-TSS (NM_153539)	37	NM_153539	215378	Mm.441817	NM_153539	ENSMUSG00000035131	Brinp3	B830045N13Rik|Fam5c	bone morphogenetic protein/retinoic acid inducible neural specific 3	protein-coding
mm_13035.1	chr2	91054585	91054604	+	1	NA	exon (NM_008948, exon 2 of 12)	exon (NM_008948, exon 2 of 12)	578	NM_008948	19182	Mm.289832	NM_008948	ENSMUSG00000002102	Psmc3	TBP-1	proteasome (prosome, macropain) 26S subunit, ATPase 3	protein-coding
mm_34975.1	chr4	156012809	156012819	+	1	NA	promoter-TSS (NM_011659)	promoter-TSS (NM_011659)	-881	NM_011659	22163	Mm.13885	NM_011659	ENSMUSG00000029075	Tnfrsf4	ACT35|CD134|Ly-70|Ox40|TXGP1L|Txgp1	tumor necrosis factor receptor superfamily, member 4	protein-coding
mm_57475.1	chr6	125233125	125233138	-	1	NA	3' UTR (NM_001042564, exon 4 of 4)	3' UTR (NM_001042564, exon 4 of 4)	-1271	NM_145391	213233	Mm.296902	NM_145391	ENSMUSG00000038213	Tapbpl	BC017613|TAPBPL-R|Tapbplr	TAP binding protein-like	protein-coding
mm_60402.1	chr7	44475759	44475787	+	1	NA	Intergenic	Intergenic	5426	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_127769.1	chr15	3279190	3279237	-	1	NA	exon (NM_009155, exon 5 of 5)	exon (NM_009155, exon 5 of 5)	8236	NM_009155	20363	Mm.392203	NM_009155	ENSMUSG00000064373	Selenop	AU018766|D15Ucla1|Se-P|Sepp1|selp	selenoprotein P	protein-coding
mm_13106.1	chr2	91526757	91526763	+	1	NA	Intergenic	CpG	-19562	NM_001165989	75786	Mm.168478	NM_029437	ENSMUSG00000040549	Ckap5	3110043H24Rik|4930432B04Rik|D730027C18Rik|T25636|mKIAA0097	cytoskeleton associated protein 5	protein-coding
mm_63589.1	chr7	128134779	128134817	+	1	NA	intron (NM_021334, intron 8 of 29)	intron (NM_021334, intron 8 of 29)	5230	NM_021334	16411	Mm.22378	NM_021334	ENSMUSG00000030789	Itgax	AI449405|Cd11c|Cr4|N418	integrin alpha X	protein-coding
mm_117388.1	chr13	73347287	73347297	-	1	NA	promoter-TSS (NR_045293)	promoter-TSS (NR_045293)	92	NR_045293	432777	Mm.415319	NR_045293		D630045M09Rik	AU019512	RIKEN cDNA D630045M09 gene	ncRNA
mm_154040.1	chr19	53789698	53789706	-	1	NA	intron (NM_001170847, intron 1 of 13)	intron (NM_001170847, intron 1 of 13)	-102529	NM_011050	18569	Mm.1605	NM_011050	ENSMUSG00000024975	Pdcd4	D19Ucla1|Ma3|Tis	programmed cell death 4	protein-coding
mm_66831.1	chr7	48845239	48845255	-	1	NA	intron (NM_001198841, intron 1 of 5)	intron (NM_001198841, intron 1 of 5)	-1576	NM_013808	13009	Mm.17235	NM_013808	ENSMUSG00000030470	Csrp3	CRP3|MLP|MMLP	cysteine and glycine-rich protein 3	protein-coding
mm_172958.1	chr9	88482164	88482164	-	1	NA	5' UTR (NM_001284328, exon 1 of 12)	5' UTR (NM_001284328, exon 1 of 12)	233	NM_019666	56403	Mm.260545	NM_019666	ENSMUSG00000032423	Syncrip	2610109K23Rik|4632417O19Rik|GRY-RBP|Nsap1|Nsap1l|hnRNP Q|pp68	synaptotagmin binding, cytoplasmic RNA interacting protein	protein-coding
mm_10317.1	chr2	11206026	11206035	+	1	NA	intron (NM_008859, intron 1 of 17)	intron (NM_008859, intron 1 of 17)	33648	NM_008859	18761	Mm.329993	NM_008859	ENSMUSG00000026778	Prkcq	A130035A12Rik|AW494342|PKC-0|PKC-theta|PKCtheta|Pkcq	protein kinase C, theta	protein-coding
mm_72042.1	chr8	71026589	71026630	+	1	NA	intron (NR_045487, intron 1 of 2)	intron (NR_045487, intron 1 of 2)	146	NR_045487	69419	Mm.188688	NR_045487	ENSMUSG00000101854	1700026F02Rik	-	RIKEN cDNA 1700026F02 gene	ncRNA
mm_142302.1	chr17	42692303	42692322	-	1	NA	promoter-TSS (NM_001289499)	promoter-TSS (NM_001289499)	-28	NM_030067	78249	Mm.66217	NM_030067	ENSMUSG00000023918	Adgrf4	4632435A09Rik|AV239010|Gpr115	adhesion G protein-coupled receptor F4	protein-coding
mm_116134.1	chr13	28953440	28953449	-	1	NA	5' UTR (NM_009238, exon 1 of 1)	5' UTR (NM_009238, exon 1 of 1)	238	NM_009238	20677	Mm.240627	NM_009238	ENSMUSG00000076431	Sox4	AA682046|Sox-4	SRY (sex determining region Y)-box 4	protein-coding
mm_99769.1	chr11	107022737	107022743	+	1	NA	Intergenic	Intergenic	-5483	NM_001163473	69066	Mm.40679	NM_001163473	ENSMUSG00000078607	1810010H24Rik	OTTMUSG00000003581	RIKEN cDNA 1810010H24 gene	protein-coding
mm_22273.1	chr2	178594359	178594366	-	1	NA	Intergenic	Intergenic	163847	NM_198656	381409	Mm.330860	NM_198656	ENSMUSG00000039155	Cdh26	Gm1010	cadherin-like 26	protein-coding
mm_127016.1	chr15	95959184	95959193	+	1	NA	intron (NM_175344, intron 16 of 19)	intron (NM_175344, intron 16 of 19)	120365	NR_126493	402773	Mm.210567	NM_001033483	ENSMUSG00000078925	D030018L15Rik	-	nuclear receptor coactivator 2 pseudogene	pseudo
mm_43995.1	chr5	146832965	146832983	+	1	NA	promoter-TSS (NM_019647)	promoter-TSS (NM_019647)	84	NM_019647	19933	Mm.316592	NM_019647	ENSMUSG00000041453	Rpl21	8430440E03Rik|L21	ribosomal protein L21	protein-coding
mm_46820.1	chr5	113138955	113138966	-	1	NA	promoter-TSS (NM_001347397)	promoter-TSS (NM_001347397)	-375	NM_001347397	243219	Mm.160131	NM_172884	ENSMUSG00000051339	2900026A02Rik	8430408O14Rik|A530094D01|AW539426|Gm449|Kiaa1671|mKIAA1671	RIKEN cDNA 2900026A02 gene	protein-coding
mm_123462.1	chr14	65833913	65833931	-	1	NA	promoter-TSS (NM_028039)	promoter-TSS (NM_028039)	47	NM_028039	71988	Mm.249280	NM_028039	ENSMUSG00000022034	Esco2	2410004I17Rik|D030072L07Rik	establishment of sister chromatid cohesion N-acetyltransferase 2	protein-coding
mm_152385.1	chr19	10457546	10457557	-	1	NA	promoter-TSS (NM_001111140)	promoter-TSS (NM_001111140)	-104	NM_001111140	278795	Mm.490638	NM_001111140	ENSMUSG00000090291	Lrrc10b	Gm705|SerdinR	leucine rich repeat containing 10B	protein-coding
mm_100795.1	chr11	4940042	4940050	-	1	NA	exon (NM_010904, exon 4 of 4)	exon (NM_010904, exon 4 of 4)	-7475	NM_001243043	11764	Mm.274816	NM_007454	ENSMUSG00000009090	Ap1b1	Adtb1|b2b1660Clo	adaptor protein complex AP-1, beta 1 subunit	protein-coding
mm_79485.1	chr9	56995379	56995464	+	1	NA	5' UTR (NM_019651, exon 1 of 13)	5' UTR (NM_019651, exon 1 of 13)	453	NM_019651	56294	Mm.325643	NM_019651	ENSMUSG00000032290	Ptpn9	MEG2	protein tyrosine phosphatase, non-receptor type 9	protein-coding
mm_135392.1	chr16	44333011	44333026	-	1	NA	promoter-TSS (NM_001159419)	promoter-TSS (NM_001159419)	-180	NM_001159419	320007	Mm.242144	NM_198034	ENSMUSG00000022696	Sidt1	AW045928|B830021E24Rik	SID1 transmembrane family, member 1	protein-coding
mm_117125.1	chr13	60902589	60902602	-	1	NA	exon (NM_026429, exon 2 of 5)	exon (NM_026429, exon 2 of 5)	2252	NM_026429	116913	Mm.443229	NM_026429	ENSMUSG00000062705	Tpbpb	1600012N09Rik	trophoblast specific protein beta	protein-coding
mm_157149.1	chrX	9461930	9461942	-	1	NA	intron (NM_007807, intron 3 of 12)	intron (NM_007807, intron 3 of 12)	7388	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_8549.1	chr1	155159294	155159339	-	1	NA	intron (NM_021433, intron 1 of 7)	intron (NM_021433, intron 1 of 7)	613	NM_021433	58244	Mm.66264	NM_021433	ENSMUSG00000026470	Stx6	2310039E05Rik|2410005I16Rik|AA437559|AI415714|AI845861	syntaxin 6	protein-coding
mm_132954.1	chr16	49955809	49955834	+	1	NA	Intergenic	LTR33B|LTR|ERVL	-24639	NR_045001	628951	Mm.428032	NR_045001		Gm6936	-	predicted gene 6936	ncRNA
mm_17530.1	chr2	29621211	29621255	-	1	NA	intron (NM_001039087, intron 1 of 25)	intron (NM_001039087, intron 1 of 25)	1513	NM_001039086	107746	Mm.298274	NM_054050	ENSMUSG00000039844	Rapgef1	4932418O06Rik|C3G|Grf2	Rap guanine nucleotide exchange factor (GEF) 1	protein-coding
mm_61168.1	chr7	59231129	59231132	+	1	NA	intron (NM_173010, intron 1 of 8)	AT_rich|Low_complexity|Low_complexity	2378	NM_011668	22215	Mm.9002	NM_011668	ENSMUSG00000025326	Ube3a	4732496B02|5830462N02Rik|A130086L21Rik|Hpve6a|mKIAA4216	ubiquitin protein ligase E3A	protein-coding
mm_8868.1	chr1	162859557	162859572	-	1	NA	intron (NM_010231, intron 1 of 8)	intron (NM_010231, intron 1 of 8)	436	NM_001330291	14261	Mm.976	NM_010231	ENSMUSG00000040181	Fmo1	-	flavin containing monooxygenase 1	protein-coding
mm_26282.1	chr3	142505693	142505714	+	1	NA	intron (NM_153564, intron 7 of 10)	intron (NM_153564, intron 7 of 10)	8769	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_152204.1	chr19	7610466	7610483	-	1	NA	Intergenic	MT2A|LTR|ERVL	-2095	NM_025731	66727	Mm.116803	NM_025731	ENSMUSG00000024973	Hrasls5	1700055A14Rik|1700086E08Rik|4921526K24Rik|HRSL5|iNAT	HRAS-like suppressor family, member 5	protein-coding
mm_166598.1	chr6	67376237	67376250	-	1	NA	promoter-TSS (NM_008354)	promoter-TSS (NM_008354)	-106	NM_008354	16162	Mm.188337	NM_008354	ENSMUSG00000018341	Il12rb2	A930027I18Rik|IL-12RB2|Ifnm	interleukin 12 receptor, beta 2	protein-coding
mm_124362.1	chr14	105177281	105177334	-	1	NA	promoter-TSS (NM_134077)	promoter-TSS (NM_134077)	20	NM_134077	74213	Mm.474531	NM_134077	ENSMUSG00000022119	Rbm26	1700009P03Rik|AI447318|C230097K14Rik|C86225|MLZ-393|Pro1777|Se70-2	RNA binding motif protein 26	protein-coding
mm_14643.1	chr2	136892209	136892241	+	1	NA	promoter-TSS (NM_001286983)	promoter-TSS (NM_001286983)	-38	NM_028834	74243	Mm.330612	NM_028201	ENSMUSG00000027281	Slx4ip	2210009G21Rik|2410004I22Rik|C85661|Slxip	SLX4 interacting protein	protein-coding
mm_115231.1	chr13	109903054	109903064	+	1	NA	promoter-TSS (NR_035442)	promoter-TSS (NR_035442)	-750	NR_035442	100316683		NR_035442	ENSMUSG00000084651	Mir1904	Mirn1904|mmu-mir-1904	microRNA 1904	ncRNA
mm_40158.1	chr5	35588019	35588042	+	1	NA	intron (NR_045807, intron 2 of 3)	intron (NR_045807, intron 2 of 3)	733	NR_045807	74364	Mm.473123	NM_175208	ENSMUSG00000055061	4931431C16Rik	-	RIKEN cDNA 4931431C16 gene	ncRNA
mm_38433.1	chr4	139352318	139352346	-	1	NA	promoter-TSS (NM_146157)	promoter-TSS (NM_146157)	244	NM_001290810	69902	Mm.27871	NM_023536	ENSMUSG00000028741	Mrto4	2610012O22Rik|Mg684|Mrt4	mRNA turnover 4, ribosome maturation factor	protein-coding
mm_165727.1	chr3	104511750	104511758	-	1	NA	5' UTR (NM_001025067, exon 1 of 18)	5' UTR (NM_001025067, exon 1 of 18)	164	NM_001310698	269473	Mm.34855	NM_001025067	ENSMUSG00000032913	Lrig2	4632419I10Rik|BB096938|LIG-2	leucine-rich repeats and immunoglobulin-like domains 2	protein-coding
mm_48065.1	chr5	136567938	136567984	-	1	NA	promoter-TSS (NM_009986)	promoter-TSS (NM_009986)	-471	NM_001291238	13047	Mm.320317	NM_009986	ENSMUSG00000029705	Cux1	CDP|Cutl1|Cux|Cux-1	cut-like homeobox 1	protein-coding
mm_158495.1	chrX	142358330	142358346	-	1	NA	intron (NM_207625, intron 2 of 15)	intron (NM_207625, intron 2 of 15)	32197	NM_001033600	50790	Mm.391337	NM_019477	ENSMUSG00000031278	Acsl4	9430020A05Rik|ACS4|AU018108|Facl4|Lacs4	acyl-CoA synthetase long-chain family member 4	protein-coding
mm_65204.1	chr7	19697044	19697055	-	1	NA	exon (NM_009696, exon 4 of 4)	exon (NM_009696, exon 4 of 4)	1349	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_150624.1	chr19	41273596	41273630	+	1	NA	TTS (NM_031376)	TTS (NM_031376)	-9609	NM_133352	107358	Mm.246440	NM_133352	ENSMUSG00000025016	Tm9sf3	1810073M23Rik|2810031D16Rik|AI115521|AI413748|AW146116|AW549777|Smbp|mKIAA4036	transmembrane 9 superfamily member 3	protein-coding
mm_56509.1	chr6	99364283	99364286	-	1	NA	intron (NM_001347345, intron 2 of 19)	intron (NM_001347345, intron 2 of 19)	71061	NM_053202	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_50372.1	chr6	48677674	48677689	+	1	NA	exon (NM_174960, exon 2 of 2)	exon (NM_174960, exon 2 of 2)	1546	NM_174960	317758	Mm.116971	NM_174960	ENSMUSG00000051124	Gimap9	A630002K24|BB145400	GTPase, IMAP family member 9	protein-coding
mm_87704.1	chr10	59916830	59916844	+	1	NA	Intergenic	Intergenic	34933	NM_029083	74747	Mm.21697	NM_029083	ENSMUSG00000020108	Ddit4	5830413E08Rik|AA415483|REDD1|Rtp801|dig2	DNA-damage-inducible transcript 4	protein-coding
mm_123585.1	chr14	67063071	67063104	-	1	NA	intron (NM_001205188, intron 2 of 9)	B1_Mur4|SINE|Alu	9384	NM_028032	71978	Mm.273997	NM_028032	ENSMUSG00000022052	Ppp2r2a	2410004D02Rik|mKIAA1541	protein phosphatase 2, regulatory subunit B, alpha	protein-coding
mm_139148.1	chr17	47529314	47529324	+	1	NA	intron (NM_001081635, intron 1 of 6)	Tigger17a|DNA|TcMar-Tigger	24268	NM_001081635	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_23379.1	chr3	55707544	55707548	+	1	NA	intron (NM_030595, intron 45 of 57)	intron (NM_030595, intron 45 of 57)	-74964	NM_010750	17116	Mm.440209	NM_010750	ENSMUSG00000056947	Mab21l1	AW047968	mab-21-like 1 (C. elegans)	protein-coding
mm_28682.1	chr3	95357187	95357211	-	1	NA	promoter-TSS (NM_001163642)	promoter-TSS (NM_001163642)	3	NM_001163641	84505	Mm.490259	NM_018877	ENSMUSG00000015697	Setdb1	AU022152|ESET|KMT1E|mKIAA0067	SET domain, bifurcated 1	protein-coding
mm_2787.1	chr1	130848435	130848446	+	1	NA	exon (NM_011082, exon 7 of 11)	exon (NM_011082, exon 7 of 11)	-17337	NM_026976	69169	Mm.46042	NM_026976	ENSMUSG00000042474	Fcmr	1810037B05Rik|Faim3|FcmuR|Toso	Fc fragment of IgM receptor	protein-coding
mm_121902.1	chr14	21889764	21889791	-	1	NA	Intergenic	Intergenic	-40867	NM_026965	69156	Mm.11827	NM_026965	ENSMUSG00000021773	Comtd1	1810030M08Rik|MT773	catechol-O-methyltransferase domain containing 1	protein-coding
mm_42513.1	chr5	115544083	115544100	+	1	NA	intron (NM_133915, intron 1 of 11)	intron (NM_133915, intron 1 of 11)	-15376	NM_007475	11837	Mm.5286	NM_007475	ENSMUSG00000067274	Rplp0	36B4|Arbp|L10E	ribosomal protein, large, P0	protein-coding
mm_27469.1	chr3	52856355	52856365	-	1	NA	Intergenic	Intergenic	71306	NR_040555	622124	Mm.389434	NR_040555	ENSMUSG00000104401	Gm20750	-	predicted gene, 20750	ncRNA
mm_111427.1	chr12	91686106	91686149	-	1	NA	intron (NM_175367, intron 4 of 6)	intron (NM_175367, intron 4 of 6)	-95640	NM_175335	83602	Mm.275728	NM_031391	ENSMUSG00000020962	Gtf2a1	6330549H03Rik|AA536742|AA959775|AW060250|TfIIAa/b|Tfiia1	general transcription factor II A, 1	protein-coding
mm_165098.1	chr19	55183789	55183800	-	1	NA	exon (NM_009348, exon 3 of 10)	exon (NM_009348, exon 3 of 10)	2909	NM_009348	21684	Mm.42139	NM_009348	ENSMUSG00000024979	Tectb	Tctnb	tectorin beta	protein-coding
mm_6617.1	chr1	75506435	75506459	-	1	NA	promoter-TSS (NM_178884)	promoter-TSS (NM_178884)	5	NM_178884	98733	Mm.236454	NM_178884	ENSMUSG00000026211	Obsl1	AW822216	obscurin-like 1	protein-coding
mm_97591.1	chr11	78945904	78945918	+	1	NA	exon (NM_010927, exon 15 of 27)	exon (NM_010927, exon 15 of 27)	20620	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_2206.1	chr1	89580263	89580286	+	1	NA	intron (NM_001037136, intron 1 of 16)	CpG	103618	NR_015540	74403	Mm.444291	NR_015540		4933400F21Rik	1700091C04Rik|4930565K10Rik	RIKEN cDNA 4933400F21 gene	ncRNA
mm_8127.1	chr1	136212816	136212828	-	1	NA	promoter-TSS (NM_001329610)	promoter-TSS (NM_001329610)	6	NM_001329610	76422	Mm.159735	NM_001329610		Mroh3	2310006M14Rik	maestro heat-like repeat family member 3	protein-coding
mm_72755.1	chr8	85421573	85421585	+	1	NA	intron (NR_033144, intron 1 of 2)	RLTR17|LTR|ERVK	11262	NR_033144	66714	Mm.272748	NM_025722	ENSMUSG00000036934	4921524J17Rik	-	RIKEN cDNA 4921524J17 gene	protein-coding
mm_79947.1	chr9	66032508	66032511	+	1	NA	intron (NM_173185, intron 13 of 13)	intron (NM_173185, intron 13 of 13)	-27660	NM_011149	19035	Mm.335249	NM_011149	ENSMUSG00000032383	Ppib	AA408962|AA553318|AI844835|Cphn-2|Cphn2|CyP-20b	peptidylprolyl isomerase B	protein-coding
mm_65621.1	chr7	27537751	27537779	-	1	NA	exon (NM_011116, exon 10 of 14)	exon (NM_011116, exon 10 of 14)	14504	NM_001033315	233020	Mm.429716	NM_001033315	ENSMUSG00000040424	Hipk4	Gm162	homeodomain interacting protein kinase 4	protein-coding
mm_642.1	chr1	40404940	40404950	+	1	NA	Intergenic	Intergenic	-24625	NM_001294171	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_6446.1	chr1	74001565	74001585	-	1	NA	intron (NM_027884, intron 6 of 34)	intron (NM_027884, intron 6 of 34)	122872	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_169846.1	chr16	3120681	3120687	-	1	NA	Intergenic	Intergenic	-471714	NM_146860	258859	Mm.377723	NM_146860	ENSMUSG00000051003	Olfr161	MOR131-1|OR912-47M6	olfactory receptor 161	protein-coding
mm_18128.1	chr2	45004566	45004602	-	1	NA	intron (NM_001289521, intron 3 of 8)	intron (NM_001289521, intron 3 of 8)	18593	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_130047.1	chr15	89140665	89140696	-	1	NA	promoter-TSS (NM_013871)	promoter-TSS (NM_013871)	23	NM_013871	29857	Mm.38343	NM_013871	ENSMUSG00000022610	Mapk12	AW123708|Erk6|P38gamma|Prkm12|Sapk3	mitogen-activated protein kinase 12	protein-coding
mm_91036.1	chr10	18234931	18235008	-	1	NA	promoter-TSS (NM_144820)	promoter-TSS (NM_144820)	12	NM_001346751	215814	Mm.296565	NM_144820	ENSMUSG00000059554	Ccdc28a	1700009P13Rik|AI480677	coiled-coil domain containing 28A	protein-coding
mm_98334.1	chr11	90676004	90676015	+	1	NA	intron (NM_028011, intron 3 of 15)	intron (NM_028011, intron 3 of 15)	11592	NM_028011	71943	Mm.167868	NM_028011	ENSMUSG00000020541	Tom1l1	2310045L10Rik|C80573|Srcasm	target of myb1-like 1 (chicken)	protein-coding
mm_18969.1	chr2	76811400	76811402	-	1	NA	exon (NM_011652, exon 181 of 313)	exon (NM_011652, exon 181 of 313)	136086	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_148942.1	chr19	7056950	7056950	+	1	NA	exon (NM_134147, exon 1 of 11)	exon (NM_134147, exon 1 of 11)	182	NM_134147	107227	Mm.439977	NM_134147	ENSMUSG00000036278	Macrod1	AI604841|AW743046|D930010J01Rik|Lrp16	MACRO domain containing 1	protein-coding
mm_74681.1	chr8	14090311	14090334	-	1	NA	promoter-TSS (NM_001034862)	promoter-TSS (NM_001034862)	5	NM_001034862	234086	Mm.268896	NM_001034862	ENSMUSG00000051978	Erich1	-	glutamate rich 1	protein-coding
mm_58472.1	chr7	3390880	3390899	+	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	-3153	NM_133190	81905	Mm.357990	NM_133190	ENSMUSG00000053395	Cacng8	-	calcium channel, voltage-dependent, gamma subunit 8	protein-coding
mm_126451.1	chr15	80820404	80820415	+	1	NA	intron (NM_177124, intron 1 of 21)	intron (NM_177124, intron 1 of 21)	21799	NM_177124	213988	Mm.131328	NM_144812	ENSMUSG00000047888	Tnrc6b	2700090M07Rik|A730065C02Rik|AI848765|D230019K20Rik	trinucleotide repeat containing 6b	protein-coding
mm_64786.1	chr7	5129416	5129422	-	1	NA	Intergenic	Intergenic	-3469	NM_009028	19428	Mm.322186	NM_009028	ENSMUSG00000083649	Rasl2-9	M2|Ran|Ran/M2|Rasl2-9-ps	RAS-like, family 2, locus 9	protein-coding
mm_82589.1	chr9	21238835	21238849	-	1	NA	5' UTR (NM_016679, exon 1 of 5)	5' UTR (NM_016679, exon 1 of 5)	490	NM_016679	50868	Mm.248266	NM_016679	ENSMUSG00000003308	Keap1	INRF2|mKIAA0132	kelch-like ECH-associated protein 1	protein-coding
mm_2823.1	chr1	131138432	131138456	+	1	NA	promoter-TSS (NM_145508)	promoter-TSS (NM_145508)	-210	NM_145508	226419	Mm.39299	NM_145508	ENSMUSG00000016526	Dyrk3	BC006704	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 3	protein-coding
mm_158350.1	chrX	134541848	134541900	-	1	NA	promoter-TSS (NM_013898).2	promoter-TSS (NM_013898).2	-204	NM_013898	30058	Mm.214504	NM_013898	ENSMUSG00000048007	Timm8a1	DXHXS1274E|Ddp1|Fci-12|Tim8a|Timm8a	translocase of inner mitochondrial membrane 8A1	protein-coding
mm_150276.1	chr19	34248425	34248449	+	1	NA	exon (NM_007392, exon 4 of 9)	exon (NM_007392, exon 4 of 9)	6936	NM_007392	11475	Mm.213025	NM_007392	ENSMUSG00000035783	Acta2	0610041G09Rik|Actvs|SMalphaA|a-SMA|alphaSMA	actin, alpha 2, smooth muscle, aorta	protein-coding
mm_49822.1	chr6	37530205	37530240	+	1	NA	promoter-TSS (NM_145364)	promoter-TSS (NM_145364)	49	NM_145364	208665	Mm.262635	NM_145364	ENSMUSG00000038641	Akr1d1	-	aldo-keto reductase family 1, member D1	protein-coding
mm_111227.1	chr12	84756681	84756729	-	1	NA	3' UTR (NM_023409, exon 4 of 4)	3' UTR (NM_023409, exon 4 of 4)	16407	NM_023409	67963	Mm.282556	NM_023409	ENSMUSG00000021242	Npc2	2700012J19Rik|AA408070|AU045843|HE1	Niemann-Pick type C2	protein-coding
mm_112817.1	chr13	20796510	20796526	+	1	NA	intron (NM_012054, intron 1 of 20)	(CA)n|Simple_repeat|Simple_repeat	2405	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_89313.1	chr10	87925263	87925266	+	1	NA	intron (NM_001111274, intron 4 of 4)	LTR16B2|LTR|ERVL	-41407	NR_000040	22172	Mm.391420	NR_000040		Tyms-ps	-	thymidylate synthase, pseudogene	pseudo
mm_70627.1	chr8	13686774	13686785	+	1	NA	Intergenic	Intergenic	-9192	NM_009025	19414	Mm.18517	NM_009025	ENSMUSG00000031453	Rasa3	AI326412|C86362|E130011G04|GAPIII|hlb381|scat	RAS p21 protein activator 3	protein-coding
mm_69910.1	chr7	141640310	141640323	-	1	NA	intron (NM_001330001, intron 31 of 33)	intron (NM_001330001, intron 31 of 33)	15003	NM_001330001	353328	Mm.246621	NM_181729	ENSMUSG00000048191	Muc6	-	mucin 6, gastric	protein-coding
mm_89043.1	chr10	82859222	82859232	+	1	NA	promoter-TSS (NM_015762)	promoter-TSS (NM_015762)	21	NM_015762	50493	Mm.210155	NM_015762	ENSMUSG00000020250	Txnrd1	TR|TR1|TrxR1	thioredoxin reductase 1	protein-coding
mm_36836.1	chr4	106492224	106492251	-	1	NA	promoter-TSS (NM_080458)	promoter-TSS (NM_080458)	6	NM_080458	140475	Mm.135448	NM_080458	ENSMUSG00000025418	Bsnd	-	Bartter syndrome, infantile, with sensorineural deafness (Barttin)	protein-coding
mm_158159.1	chrX	103480884	103480935	-	1	NA	non-coding (NR_001570, exon 1 of 8)	non-coding (NR_001570, exon 1 of 8)	2324	NR_001570	213742	Mm.274770	NR_001463	ENSMUSG00000086503	Xist	A430022B11|AI314753	inactive X specific transcripts	ncRNA
mm_135869.1	chr16	61056368	61056380	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-450843	NM_007938	13840	Mm.455790	NM_007938	ENSMUSG00000055540	Epha6	Ehk2|Hek12|m-ehk2	Eph receptor A6	protein-coding
mm_91531.1	chr10	37233312	37233321	-	1	NA	Intergenic	Intergenic	-94390	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_9551.1	chr1	173923843	173923845	-	1	NA	intron (NM_001302649, intron 9 of 9)	intron (NM_001302649, intron 9 of 9)	-10798	NM_001033450	381308	Mm.490248	NM_001033450	ENSMUSG00000026536	Ifi211	A730048F03|Ifi205b|Mnda|ifi-205-B	interferon activated gene 211	protein-coding
mm_112326.1	chr12	115508015	115508034	-	1	NA	Intergenic	Intergenic	187770	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
mm_78370.1	chr9	27299206	27299254	+	1	NA	promoter-TSS (NM_001129787)	promoter-TSS (NM_001129787)	2	NM_001129787	235086	Mm.48719	NM_001033323	ENSMUSG00000034275	Igsf9b	AI414108|AI854107|Gm508|mKIAA1030	immunoglobulin superfamily, member 9B	protein-coding
mm_121939.1	chr14	24004877	24004906	-	1	NA	promoter-TSS (NM_001253365)	promoter-TSS (NM_001253365)	-100	NR_131107	78019	Mm.243845	NR_131107		4930519K11Rik	-	RIKEN cDNA 4930519K11 gene	ncRNA
mm_72316.1	chr8	78066336	78066348	+	1	NA	Intergenic	Intergenic	-147000	NM_183096	73301	Mm.61243	NM_183096	ENSMUSG00000037101	Ttc29	1700031F13Rik	tetratricopeptide repeat domain 29	protein-coding
mm_25044.1	chr3	98299109	98299131	+	1	NA	exon (NM_008256, exon 6 of 10)	exon (NM_008256, exon 6 of 10)	18689	NM_008256	15360	Mm.289131	NM_008256	ENSMUSG00000027875	Hmgcs2	1300002P16|mHS	3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2	protein-coding
mm_49414.1	chr6	28773295	28773297	+	1	NA	intron (NM_019776, intron 15 of 23)	intron (NM_019776, intron 15 of 23)	58451	NM_138682	192198	Mm.443660	NM_138682	ENSMUSG00000049939	Lrrc4	MBAG1|NGL-2|NGL2|NLG-2|Nag14	leucine rich repeat containing 4	protein-coding
mm_68465.1	chr7	110464635	110464667	-	1	NA	exon (NM_177324, exon 4 of 41)	exon (NM_177324, exon 4 of 41)	150269	NM_177324	319934	Mm.102970	NM_177324	ENSMUSG00000038371	Sbf2	4833411B01Rik|AA414977|AI317167|B430219L04Rik|Mtmr13|mMTMH1	SET binding factor 2	protein-coding
mm_131683.1	chr16	20677615	20677634	+	1	NA	intron (NM_001304432, intron 5 of 31)	intron (NM_001304432, intron 5 of 31)	4897	NM_001304432	208643	Mm.260256	NM_145941	ENSMUSG00000045983	Eif4g1	E030015G23Rik|eIF-4-gamma 1|eIF-4G 1|eIF-4G1|eIF4GI	eukaryotic translation initiation factor 4, gamma 1	protein-coding
mm_85944.1	chr9	112101687	112101689	-	1	NA	intron (NM_001177618, intron 17 of 18)	intron (NM_001177618, intron 17 of 18)	17023	NR_029823	723815		NR_029823	ENSMUSG00000065441	Mir128-2	Mirn128-2|Mirn128b|mir-128-2|mir-128b	microRNA 128-2	ncRNA
mm_55573.1	chr6	71395025	71395034	-	1	NA	intron (NM_024288, intron 7 of 8)	intron (NM_024288, intron 7 of 8)	21602	NM_001081110	12525	Mm.1858	NM_009857	ENSMUSG00000053977	Cd8a	BB154331|Ly-2|Ly-35|Ly-B|Lyt-2	CD8 antigen, alpha chain	protein-coding
mm_104201.1	chr11	87987496	87987512	-	1	NA	promoter-TSS (NM_001168472)	promoter-TSS (NM_001168472)	29	NM_026556	68097	Mm.246436	NM_026556	ENSMUSG00000020483	Dynll2	1700064A15Rik|6720463E02Rik|C87222|DLC8|DLC8b|Dlc2	dynein light chain LC8-type 2	protein-coding
mm_75873.1	chr8	70764630	70764644	-	1	NA	exon (NM_023065, exon 5 of 8)	exon (NM_023065, exon 5 of 8)	2026	NM_023065	65972	Mm.30241	NM_023065	ENSMUSG00000031838	Ifi30	GILT|IP30	interferon gamma inducible protein 30	protein-coding
mm_82630.1	chr9	21927516	21927563	-	1	NA	promoter-TSS (NM_178577)	promoter-TSS (NM_178577)	-4	NM_001253870	235043	Mm.253329	NM_178577	ENSMUSG00000040883	Tmem205	-	transmembrane protein 205	protein-coding
mm_91686.1	chr10	43971960	43971970	-	1	NA	intron (NM_172393, intron 11 of 19)	intron (NM_172393, intron 11 of 19)	32881	NM_172393	11630	Mm.292082	NM_172393	ENSMUSG00000019866	Aim1	AI462491|AI463325	absent in melanoma 1	protein-coding
mm_150915.1	chr19	46075843	46075859	+	1	NA	promoter-TSS (NM_001039352)	promoter-TSS (NM_001039352)	4	NM_001039351	70769	Mm.402190	NM_053086	ENSMUSG00000015176	Nolc1	NOPP130|NOPP140|P130	nucleolar and coiled-body phosphoprotein 1	protein-coding
mm_68572.1	chr7	115737935	115737936	-	1	NA	intron (NM_001025560, intron 4 of 15)	intron (NM_001025560, intron 4 of 15)	63674	NM_001277328	20679	Mm.323365	NM_011445	ENSMUSG00000051910	Sox6	AI987981|SOX-LZ	SRY (sex determining region Y)-box 6	protein-coding
mm_127164.1	chr15	98644053	98644086	+	1	NA	3' UTR (NM_001044741, exon 13 of 13)	3' UTR (NM_001044741, exon 13 of 13)	9302	NM_001286226	12297	Mm.3544	NM_007581	ENSMUSG00000003352	Cacnb3	Beta3|CAB3|Ca(v)beta3|Cchb3	calcium channel, voltage-dependent, beta 3 subunit	protein-coding
mm_112615.1	chr13	15463723	15463741	+	1	NA	promoter-TSS (NM_008130)	promoter-TSS (NM_008130)	9	NM_008130	14634	Mm.5098	NM_008130	ENSMUSG00000021318	Gli3	AI854843|AU023367|Bph|GLI3-190|GLI3FL|Pdn|Xt|add	GLI-Kruppel family member GLI3	protein-coding
mm_10091.1	chr2	3284203	3284220	+	1	NA	promoter-TSS (NM_008708)	promoter-TSS (NM_008708)	-1	NM_008708	18108	Mm.65021	NM_008708	ENSMUSG00000026643	Nmt2	A930001K02Rik|AI605445|AU044698|hNMT-2	N-myristoyltransferase 2	protein-coding
mm_50647.1	chr6	51464451	51464460	+	1	NA	exon (NM_016806, exon 8 of 11)	exon (NM_016806, exon 8 of 11)	5439	NM_182650	53379	Mm.155896	NM_016806	ENSMUSG00000004980	Hnrnpa2b1	9130414A06Rik|Hnrpa2|Hnrpa2b1|hnrnp-A	heterogeneous nuclear ribonucleoprotein A2/B1	protein-coding
mm_52590.1	chr6	116669424	116669467	+	1	NA	intron (NM_178045, intron 1 of 10)	MLTR14|LTR|ERV1	4391	NM_178045	213391	Mm.257931	NM_178045	ENSMUSG00000042129	Rassf4	3830411C14Rik|AD037|AI586137	Ras association (RalGDS/AF-6) domain family member 4	protein-coding
mm_150375.1	chr19	34961834	34961868	+	1	NA	intron (NM_183046, intron 25 of 31)	intron (NM_183046, intron 25 of 31)	39493	NM_183046	240641	Mm.278471	NM_183046	ENSMUSG00000024795	Kif20b	33cex|B130024C23|C330014J10Rik|Mphosph1|magoo	kinesin family member 20B	protein-coding
mm_108748.1	chr12	88795012	88795034	+	1	NA	5' UTR (NM_001198587, exon 1 of 20)	5' UTR (NM_001198587, exon 1 of 20)	519	NM_001198587	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding
mm_170495.1	chr19	23135928	23135942	+	1	NA	Intergenic	CpG	-5291	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_52681.1	chr6	117926560	117926563	+	1	NA	TTS (NM_001166432)	TTS (NM_001166432)	9267	NM_001166427	98758	Mm.422979	NM_133834	ENSMUSG00000042079	Hnrnpf	4833420I20Rik|AA407306|Hnrpf	heterogeneous nuclear ribonucleoprotein F	protein-coding
mm_79831.1	chr9	64794597	64794606	+	1	NA	Intergenic	Intergenic	-16410	NM_001162917	102442	Mm.222473	NM_176935	ENSMUSG00000053641	Dennd4a	AI115600|AI851943|F730015K02Rik	DENN/MADD domain containing 4A	protein-coding
mm_60725.1	chr7	45361566	45361579	+	1	NA	exon (NM_029741, exon 2 of 30)	exon (NM_029741, exon 2 of 30)	-4591	NR_015480	50994	Mm.389897	NM_016664	ENSMUSG00000091510	Mtag2	MAG	metastasis associated gene 2	ncRNA
mm_93020.1	chr10	87860201	87860202	-	1	NA	promoter-TSS (NM_001111276)	promoter-TSS (NM_001111276)	-910	NM_001111274	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_136366.1	chr16	92801442	92801490	-	1	NA	intron (NM_001111022, intron 2 of 6)	intron (NM_001111022, intron 2 of 6)	24608	NM_001111021	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_106035.1	chr11	116077928	116077952	-	1	NA	promoter-TSS (NM_001009573)	promoter-TSS (NM_001009573)	21	NM_001009573	70450	Mm.259460	NM_001009573	ENSMUSG00000057948	Unc13d	2610108D09Rik|Jinx|Munc13-4|mFLJ00067	unc-13 homolog D (C. elegans)	protein-coding
mm_125674.1	chr15	66577523	66577533	+	1	NA	promoter-TSS (NM_001081409)	promoter-TSS (NM_001081409)	-44	NM_001081409	239510	Mm.267473	NM_178718	ENSMUSG00000072501	Phf20l1	CGI-72|E130113K22Rik	PHD finger protein 20-like 1	protein-coding
mm_102965.1	chr11	69665837	69665843	-	1	NA	exon (NM_001291058, exon 2 of 6)	exon (NM_001291058, exon 2 of 6)	330	NM_001291058	12514	Mm.15819	NM_009853	ENSMUSG00000018774	Cd68	Lamp4|Scard1|gp110	CD68 antigen	protein-coding
mm_148503.1	chr19	4201798	4201816	+	1	NA	promoter-TSS (NM_011237)	promoter-TSS (NM_011237)	-204	NM_011237	19367	Mm.277629	NM_011237	ENSMUSG00000024824	Rad9a	Rad9	RAD9 checkpoint clamp component A	protein-coding
mm_76504.1	chr8	86883278	86883295	-	1	NA	intron (NM_030563, intron 1 of 6)	intron (NM_030563, intron 1 of 6)	1972	NM_030563	80750	Mm.25117	NM_030563	ENSMUSG00000031652	N4bp1	AI481586|C81621	NEDD4 binding protein 1	protein-coding
mm_139447.1	chr17	55445747	55445755	+	1	NA	promoter-TSS (NM_172829)	promoter-TSS (NM_172829)	34	NM_172829	240119	Mm.311687	NM_172829	ENSMUSG00000024172	St6gal2	C230064G14Rik|St6galII|mKIAA1877	beta galactoside alpha 2,6 sialyltransferase 2	protein-coding
mm_138397.1	chr17	35052806	35052853	+	1	NA	exon (NM_033444, exon 3 of 6)	exon (NM_033444, exon 3 of 6)	2586	NM_033444	114584	Mm.29524	NM_033444	ENSMUSG00000007041	Clic1	Clcp|G6	chloride intracellular channel 1	protein-coding
mm_93179.1	chr10	93589622	93589681	-	1	NA	promoter-TSS (NM_027246)	promoter-TSS (NM_027246)	7	NM_027246	69878	Mm.259642	NM_027246	ENSMUSG00000020018	Snrpf	2010013O18Rik|SMF|sm-F|snRNP-F	small nuclear ribonucleoprotein polypeptide F	protein-coding
mm_171676.1	chr4	53057987	53057998	-	1	NA	intron (NM_013454, intron 34 of 49)	L1Md_T|LINE|L1	46112	NM_025623	66536	Mm.38244	NM_025623	ENSMUSG00000015247	Nipsnap3b	2700063N13Rik|Nipsnap3a	nipsnap homolog 3B (C. elegans)	protein-coding
mm_2577.1	chr1	118482005	118482024	+	1	NA	intron (NM_001293300, intron 8 of 40)	intron (NM_001293300, intron 8 of 40)	-22749	NR_027901	68204	Mm.443536	NR_027901	ENSMUSG00000107722	2900060B14Rik	-	RIKEN cDNA 2900060B14 gene	ncRNA
mm_171791.1	chr5	115802183	115802188	-	1	NA	Intergenic	Intergenic	-43471	NM_007708	12704	Mm.8321	NM_007708	ENSMUSG00000029516	Cit	C030025P15Rik|CRIK|CRIK-SK|Cit-k	citron	protein-coding
mm_167803.1	chr9	123928220	123928260	+	1	NA	Intergenic	MLT1F|LTR|ERVL-MaLR	40452	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_51440.1	chr6	80068043	80068045	+	1	NA	intron (NM_001347261, intron 2 of 2)	intron (NM_001347261, intron 2 of 2)	48401	NM_178731	243499	Mm.483425	NM_178731	ENSMUSG00000052581	Lrrtm4	7530419J18Rik|A230052N11	leucine rich repeat transmembrane neuronal 4	protein-coding
mm_98365.1	chr11	93995361	93995384	+	1	NA	promoter-TSS (NM_001199204)	promoter-TSS (NM_001199204)	-719	NM_001199203	70834	Mm.260737	NM_027569	ENSMUSG00000020859	Spag9	3110018C07Rik|4733401I23Rik|4831406C20Rik|AW552012|JLP|JSAP2|JSAP2a|Jip4|Mapk8ip4|syd1	sperm associated antigen 9	protein-coding
mm_85740.1	chr9	108566928	108566978	-	1	NA	5' UTR (NM_023247, exon 1 of 5)	5' UTR (NM_023247, exon 1 of 5)	389	NM_023247	66706	Mm.29471	NM_023247	ENSMUSG00000070283	Ndufaf3	4733401H18Rik	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, assembly factor 3	protein-coding
mm_82385.1	chr9	14662962	14662974	-	1	NA	Intergenic	Intergenic	-47968	NM_001081395	75723	Mm.159552	NM_001081395	ENSMUSG00000013076	Amotl1	2310010G08Rik|2310067L22Rik|4932416D09Rik|JEAP|mFLJ00155	angiomotin-like 1	protein-coding
mm_114594.1	chr13	75763890	75763911	+	1	NA	exon (NM_138953, exon 8 of 12)	exon (NM_138953, exon 8 of 12)	56416	NM_138953	192657	Mm.21288	NM_138953	ENSMUSG00000001542	Ell2	-	elongation factor RNA polymerase II 2	protein-coding
mm_92455.1	chr10	77811885	77811890	-	1	NA	intron (NM_001287074, intron 1 of 11)	intron (NM_001287074, intron 1 of 11)	-2795	NM_001205009	100040299	Mm.486155	NM_001205009		Gm2696	-	predicted gene 2696	protein-coding
mm_172416.1	chr7	24702994	24702999	+	1	NA	Intergenic	RLTR9F|LTR|ERVK	-6263	NM_199150	232972	Mm.293074	NM_199150	ENSMUSG00000045587	BC049730	Lypd10	cDNA sequence BC049730	protein-coding
mm_145392.1	chr18	57142706	57142710	+	1	NA	intron (NM_001001979, intron 1 of 24)	intron (NM_001001979, intron 1 of 24)	9618	NM_001001979	70417	Mm.297863	NM_001001979	ENSMUSG00000024593	Megf10	3000002B06Rik|Gm331	multiple EGF-like-domains 10	protein-coding
mm_85017.1	chr9	88273366	88273376	-	1	NA	Intergenic	Intergenic	-54238	NM_011851	23959	Mm.244235	NM_011851	ENSMUSG00000032420	Nt5e	2210401F01Rik|5'-NT|AI447961|CD73|NT|Nt5|eNT	5' nucleotidase, ecto	protein-coding
mm_165977.1	chr4	102955812	102955818	+	1	NA	intron (NM_001285852, intron 19 of 25)	intron (NM_001285852, intron 19 of 25)	-30564	NM_001163767	67344	Mm.111346	NM_026100	ENSMUSG00000028523	Tctex1d1	1700055O19Rik	Tctex1 domain containing 1	protein-coding
mm_55147.1	chr6	51466623	51466688	-	1	NA	exon (NM_182650, exon 4 of 10)	exon (NM_182650, exon 4 of 10)	3239	NM_182650	53379	Mm.155896	NM_016806	ENSMUSG00000004980	Hnrnpa2b1	9130414A06Rik|Hnrpa2|Hnrpa2b1|hnrnp-A	heterogeneous nuclear ribonucleoprotein A2/B1	protein-coding
mm_169089.1	chr1	33839010	33839023	-	1	NA	promoter-TSS (NM_001161816)	promoter-TSS (NM_001161816)	-102	NM_001161816	433287	Mm.383632	NM_001161816		Gm15455	AA692849|OTTMUSG00000022109	predicted gene 15455	protein-coding
mm_11799.1	chr2	43635285	43635290	+	1	NA	3' UTR (NM_001289594, exon 11 of 11)	3' UTR (NM_001289594, exon 11 of 11)	79962	NM_027552	70789	Mm.105278	NM_027552	ENSMUSG00000026866	Kynu	4432411A05Rik	kynureninase (L-kynurenine hydrolase)	protein-coding
mm_80455.1	chr9	77982722	77982730	+	1	NA	exon (NM_134255, exon 8 of 8)	exon (NM_134255, exon 8 of 8)	65361	NM_134255	68801	Mm.430736	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	ELOVL family member 5, elongation of long chain fatty acids (yeast)	protein-coding
mm_113539.1	chr13	37857415	37857421	+	1	NA	intron (NM_001039188, intron 1 of 9)	CpG	30025	NM_001039188	68750	Mm.491109	NM_026830	ENSMUSG00000039087	Rreb1	1110037N09Rik|AA414966|B930013M22Rik	ras responsive element binding protein 1	protein-coding
mm_62621.1	chr7	107422667	107422670	+	1	NA	intron (NM_021889, intron 1 of 6)	ID_B1|SINE|B4	51878	NM_021889	60510	Mm.302793	NM_021889	ENSMUSG00000062542	Syt9	-	synaptotagmin IX	protein-coding
mm_146323.1	chr18	80705025	80705029	+	1	NA	intron (NM_198429, intron 1 of 9)	intron (NM_198429, intron 1 of 9)	3146	NM_001164111	18018	Mm.329560	NM_016791	ENSMUSG00000033016	Nfatc1	2210017P03Rik|AI449492|AV076380|NF-ATc|NFAT2|NFATc|Nfatcb	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 1	protein-coding
mm_34046.1	chr4	138217236	138217310	+	1	NA	5' UTR (NM_001122897, exon 1 of 13)	5' UTR (NM_001122897, exon 1 of 13)	146	NM_001122897	15441	Mm.348429	NM_010470	ENSMUSG00000028759	Hp1bp3	Hp1bp74	heterochromatin protein 1, binding protein 3	protein-coding
mm_82123.1	chr9	123509168	123509178	+	1	NA	intron (NM_013860, intron 2 of 7)	intron (NM_013860, intron 2 of 7)	-20709	NM_030692	83493	Mm.273671	NM_030692	ENSMUSG00000025240	Sacm1l	SAC1|Sac1p|mKIAA0851	SAC1 suppressor of actin mutations 1-like (yeast)	protein-coding
mm_51456.1	chr6	82041646	82041698	+	1	NA	promoter-TSS (NM_145570)	promoter-TSS (NM_145570)	44	NM_145570	232146	Mm.489683	NM_145570	ENSMUSG00000035104	Eva1a	BC014699|Fam176a|Tmem166	eva-1 homolog A (C. elegans)	protein-coding
mm_106340.1	chr11	118393171	118393180	-	1	NA	exon (NM_011150, exon 6 of 6)	exon (NM_011150, exon 6 of 6)	8756	NM_011150	19039	Mm.3152	NM_011150	ENSMUSG00000033880	Lgals3bp	90K|CyCAP|MAC-2BP|Ppicap|Tango10b	lectin, galactoside-binding, soluble, 3 binding protein	protein-coding
mm_124952.1	chr15	12824885	12824907	+	1	NA	promoter-TSS (NM_029998)	promoter-TSS (NM_029998)	81	NM_001130149	14000	Mm.293142	NM_026799	ENSMUSG00000022191	Drosha	1110013A17Rik|AI874853|Etohi2|Rn3|Rnasen	drosha, ribonuclease type III	protein-coding
mm_92398.1	chr10	76614589	76614597	-	1	NA	exon (NM_146007, exon 3 of 28)	exon (NM_146007, exon 3 of 28)	8811	NM_146007	12834	Mm.1949	NM_146007	ENSMUSG00000020241	Col6a2	Col6a-2	collagen, type VI, alpha 2	protein-coding
mm_72653.1	chr8	84842566	84842586	+	1	NA	3' UTR (NM_007591, exon 9 of 9)	3' UTR (NM_007591, exon 9 of 9)	-1911	NM_009010	19358	Mm.255539	NM_009010	ENSMUSG00000003813	Rad23a	2310040P19Rik|AL024030|HR23A|mHR23A	RAD23 homolog A, nucleotide excision repair protein	protein-coding
mm_62361.1	chr7	100537053	100537139	+	1	NA	promoter-TSS (NM_183270)	promoter-TSS (NM_183270)	-4	NM_183270	68185	Mm.228995	NM_183270	ENSMUSG00000044881	Coa4	5330414O08Rik|AI115477|AW047259|Chchd8|E2ig2	cytochrome c oxidase assembly factor 4	protein-coding
mm_60515.1	chr7	44479772	44479808	+	1	NA	Intergenic	Intergenic	-4727	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_143882.1	chr17	84306325	84306335	-	1	NA	intron (NM_183021, intron 29 of 37)	intron (NM_183021, intron 29 of 37)	-118383	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_153920.1	chr19	47314376	47314383	-	1	NA	intron (NM_001164717, intron 7 of 13)	G-rich|Low_complexity|Low_complexity	-40790	NR_105961	102466782		NR_105961	ENSMUSG00000098786	Mir6995	Gm27576|mmu-mir-6995	microRNA 6995	ncRNA
mm_147863.1	chr18	64339789	64339791	-	1	NA	promoter-TSS (NM_194268)	promoter-TSS (NM_194268)	-574	NM_194268	225631	Mm.234723	NM_194268	ENSMUSG00000045991	Onecut2	C730009D12|OC-2|Oc2	one cut domain, family member 2	protein-coding
mm_93245.1	chr10	95416851	95416861	-	1	NA	promoter-TSS (NM_007706)	promoter-TSS (NM_007706)	1	NM_007706	216233	Mm.474283	NM_007706	ENSMUSG00000020027	Socs2	8030460M17|AI527257|AW108012|CIS2|Cish2|D130043N08Rik|JAB|SOCS-2|SSI-2|hg	suppressor of cytokine signaling 2	protein-coding
mm_44828.1	chr5	33936231	33936296	-	1	NA	promoter-TSS (NM_011914)	promoter-TSS (NM_011914)	-5	NM_011914	24116	Mm.332320	NM_011914	ENSMUSG00000029111	Nelfa	Whsc2|Whsc2h	negative elongation factor complex member A, Whsc2	protein-coding
mm_107208.1	chr12	26444411	26444430	+	1	NA	3' UTR (NM_021384, exon 6 of 6)	3' UTR (NM_021384, exon 6 of 6)	12032	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_57163.1	chr6	122800826	122800827	-	1	NA	Intergenic	BC1_Mm|scRNA|scRNA	-19358	NM_021899	60611	Mm.87142	NM_021899	ENSMUSG00000003154	Foxj2	Fhx	forkhead box J2	protein-coding
mm_2674.1	chr1	127228610	127228617	+	1	NA	intron (NM_145128, intron 1 of 17)	intron (NM_145128, intron 1 of 17)	23627	NM_145128	107895	Mm.214682	NM_145128	ENSMUSG00000036155	Mgat5	4930471A21Rik|5330407H02Rik|AI480971|GlcNAc-TV	mannoside acetylglucosaminyltransferase 5	protein-coding
mm_137159.1	chr17	23749361	23749384	+	1	NA	non-coding (NR_015472, exon 1 of 3)	non-coding (NR_015472, exon 1 of 3)	136	NR_015472	638247	Mm.382600	NR_015472	ENSMUSG00000097006	9530082P21Rik	E030034P13Rik	RIKEN cDNA 9530082P21 gene	ncRNA
mm_79645.1	chr9	59561979	59561995	+	1	NA	exon (NM_010421, exon 9 of 14)	exon (NM_010421, exon 9 of 14)	-16350	NM_175235	76183	Mm.265415	NM_175235	ENSMUSG00000032297	Celf6	6330569O16Rik|Brunol6	CUGBP, Elav-like family member 6	protein-coding
mm_106137.1	chr11	116490162	116490168	-	1	NA	exon (NM_026364, exon 1 of 10)	exon (NM_026364, exon 1 of 10)	181	NM_026364	67763	Mm.25125	NM_026364	ENSMUSG00000015869	Prpsap1	5730409F23Rik|PAP39	phosphoribosyl pyrophosphate synthetase-associated protein 1	protein-coding
mm_64255.1	chr7	141744678	141744691	+	1	NA	exon (NM_023566, exon 28 of 46)	exon (NM_023566, exon 28 of 46)	-44327	NM_010844	17833	Mm.334332	NM_010844	ENSMUSG00000037974	Muc5ac	2210005L13Rik|MGM	mucin 5, subtypes A and C, tracheobronchial/gastric	protein-coding
mm_154664.1	chrX	7874475	7874485	+	1	NA	3' UTR (NM_001290536, exon 9 of 9)	3' UTR (NM_001290536, exon 9 of 9)	-3826	NM_138606	18715	Mm.347478	NM_138606	ENSMUSG00000031155	Pim2	DXCch3|Pim-2	proviral integration site 2	protein-coding
mm_10502.1	chr2	15526528	15526528	+	1	NA	promoter-TSS (NM_001310455)	promoter-TSS (NM_001310455)	49	NM_001310455	102635496		NM_001310455	ENSMUSG00000075520	Malrd1	-	MAM and LDL receptor class A domain containing 1	protein-coding
mm_121450.1	chr14	120431264	120431308	+	1	NA	3' UTR (NM_207515, exon 8 of 8)	3' UTR (NM_207515, exon 8 of 8)	-47175	NM_029519	76108	Mm.261448	NM_029519	ENSMUSG00000051615	Rap2a	5830461H18Rik	RAS related protein 2a	protein-coding
mm_169007.1	chr13	105974299	105974299	-	1	NA	Intergenic	L1_Mus3|LINE|L1	530606	NM_008308	15550	Mm.4716	NM_008308	ENSMUSG00000021721	Htr1a	Gpcr18	5-hydroxytryptamine (serotonin) receptor 1A	protein-coding
mm_7958.1	chr1	133929892	133929904	-	1	NA	Intergenic	Intergenic	-8497	NM_054077	116847	Mm.214514	NM_054077	ENSMUSG00000041577	Prelp	7330409J17Rik|SLRR2A	proline arginine-rich end leucine-rich repeat	protein-coding
mm_169279.1	chr13	94418071	94418082	+	1	NA	exon (NM_009680, exon 7 of 27)	exon (NM_009680, exon 7 of 27)	59116	NM_009680	11774	Mm.21185	NM_009680	ENSMUSG00000021686	Ap3b1	AP-3|AU015684|C78395|Hps2|beta3A|pe|pearl|rim2	adaptor-related protein complex 3, beta 1 subunit	protein-coding
mm_80075.1	chr9	69989417	69989450	+	1	NA	promoter-TSS (NM_016787)	promoter-TSS (NM_016787)	-33	NM_016787	12175	Mm.159777	NM_016787	ENSMUSG00000011958	Bnip2	5730523P12Rik|BNIP2beta|Nip21	BCL2/adenovirus E1B interacting protein 2	protein-coding
mm_50840.1	chr6	54816891	54816903	+	1	NA	promoter-TSS (NM_199143)	promoter-TSS (NM_199143)	-19	NM_199143	387524	Mm.286149	NM_199143	ENSMUSG00000058446	Znrf2	1190002C14Rik|AU044205|D6Ertd365e	zinc and ring finger 2	protein-coding
mm_65737.1	chr7	28386117	28386138	-	1	NA	3' UTR (NM_026042, exon 4 of 4)	3' UTR (NM_026042, exon 4 of 4)	6563	NM_026042	67224	Mm.41647	NM_026042	ENSMUSG00000003444	Med29	2810405O22Rik|AU020902|Ixl	mediator complex subunit 29	protein-coding
mm_144206.1	chr18	9505517	9505527	+	1	NA	Intergenic	Intergenic	-55372	NM_026484	67974	Mm.86523	NM_026484	ENSMUSG00000024286	Ccny	1700025H17Rik|3110050L10Rik|4631402G10Rik|5730405I09Rik	cyclin Y	protein-coding
mm_130528.1	chr15	98898484	98898558	-	1	NA	promoter-TSS (NM_007857)	promoter-TSS (NM_007857)	19	NM_007857	13363	Mm.324688	NM_007857	ENSMUSG00000023000	Dhh	C78960	desert hedgehog	protein-coding
mm_10485.1	chr2	14763250	14763259	+	1	NA	intron (NM_023116, intron 2 of 13)	intron (NM_023116, intron 2 of 13)	42612	NR_028497	625342	Mm.484784	NR_028497		Gm13315	OTTMUSG00000011384	lactate dehydrogenase A pseudogene	pseudo
mm_91326.1	chr10	25215746	25215754	-	1	NA	intron (NM_018747, intron 7 of 7)	B4|SINE|B4	-15580	NM_001347460	432442	Mm.485937	NM_018747	ENSMUSG00000039166	Akap7	6430401D08|AI662165|AKAP15|Akap18|BB170514	A kinase (PRKA) anchor protein 7	protein-coding
mm_138332.1	chr17	34894645	34894685	+	1	NA	5' UTR (NM_198886, exon 1 of 2)	5' UTR (NM_198886, exon 1 of 2)	106	NM_198886	193736	Mm.161119	NM_198886	ENSMUSG00000049823	Zbtb12	BC020447|Bat-9|Bat9|G10|NG35	zinc finger and BTB domain containing 12	protein-coding
mm_156184.1	chrX	133859692	133859706	+	1	NA	intron (NM_022322, intron 2 of 6)	intron (NM_022322, intron 2 of 6)	8691	NM_022322	64103	Mm.46221	NM_022322	ENSMUSG00000031250	Tnmd	1110017I01Rik|Bricd4|ChM1L|TeM	tenomodulin	protein-coding
mm_51232.1	chr6	71374578	71374586	+	1	NA	exon (NM_009857, exon 2 of 4)	exon (NM_009857, exon 2 of 4)	1155	NM_001081110	12525	Mm.1858	NM_009857	ENSMUSG00000053977	Cd8a	BB154331|Ly-2|Ly-35|Ly-B|Lyt-2	CD8 antigen, alpha chain	protein-coding
mm_134805.1	chr16	24393619	24393697	-	1	NA	promoter-TSS (NR_037954)	promoter-TSS (NR_037954)	-3	NR_037954	68841	Mm.361995	NR_037954		Lppos	1110054M08Rik|AI481106	LIM domain containing preferred translocation partner in lipoma, opposite strand	ncRNA
mm_89921.1	chr10	111211564	111211606	+	1	NA	intron (NM_001003717, intron 2 of 22)	B1_Mur2|SINE|Alu	46783	NM_175489	237542	Mm.220204	NM_175489	ENSMUSG00000020189	Osbpl8	AA536976|AA536995|C730029P18Rik|D330025H14Rik|ORP-8	oxysterol binding protein-like 8	protein-coding
mm_123279.1	chr14	61411067	61411104	-	1	NA	intron (NM_008466, intron 1 of 16)	B1_Mur3|SINE|Alu	28862	NM_008466	16648	Mm.25548	NM_008466	ENSMUSG00000021929	Kpna3	IPOA4	karyopherin (importin) alpha 3	protein-coding
mm_48590.1	chr5	143895026	143895075	-	1	NA	promoter-TSS (NM_001310772)	promoter-TSS (NM_001310772)	17	NM_025732	66729	Mm.439817	NM_025732	ENSMUSG00000029607	Ankrd61	4921520G13Rik	ankyrin repeat domain 61	protein-coding
mm_157515.1	chrX	49787634	49787648	-	1	NA	exon (NM_177591, exon 12 of 20)	exon (NM_177591, exon 12 of 20)	602	NM_183336	209268	Mm.110505	NM_177591	ENSMUSG00000031111	Igsf1	5330413N23|5530402E03|AI747649|InhBP/p120|mKIAA0364	immunoglobulin superfamily, member 1	protein-coding
mm_133656.1	chr16	91818285	91818289	+	1	NA	intron (NM_001110275, intron 11 of 28)	intron (NM_001110275, intron 11 of 28)	88916	NM_010587	16443	Mm.40546	NM_010587	ENSMUSG00000022957	Itsn1	AA517634|AA545208|AI316805|AI839402|AI848451|Ehsh1|Ese1|Itsn|Sh3p17	intersectin 1 (SH3 domain protein 1A)	protein-coding
mm_158122.1	chrX	102505101	102505129	-	1	NA	promoter-TSS (NM_001313742)	promoter-TSS (NM_001313742)	43	NM_001313742	70315	Mm.328128	NM_027382	ENSMUSG00000067567	Hdac8	2610007D20Rik	histone deacetylase 8	protein-coding
mm_79260.1	chr9	50753100	50753105	+	1	NA	promoter-TSS (NM_024441)	promoter-TSS (NM_024441)	131	NM_009964	12955	Mm.178	NM_009964	ENSMUSG00000032060	Cryab	Crya-2|Crya2|HspB5|P23	crystallin, alpha B	protein-coding
mm_154721.1	chrX	9272761	9272805	+	1	NA	promoter-TSS (NM_023500)	promoter-TSS (NM_023500)	-1	NM_023500	22439	Mm.56468	NM_023500	ENSMUSG00000015342	Xk	1810038K19Rik|XRG1|Xkh	X-linked Kx blood group	protein-coding
mm_78267.1	chr9	22002788	22002817	+	1	NA	promoter-TSS (NM_029939)	promoter-TSS (NM_029939)	-168	NM_029939	77609	Mm.159953	NM_029939	ENSMUSG00000039632	Ccdc151	AI644415|C330001K17Rik|b2b1885Clo	coiled-coil domain containing 151	protein-coding
mm_5786.1	chr1	51852821	51852824	-	1	NA	intron (NM_001290982, intron 3 of 28)	intron (NM_001290982, intron 3 of 28)	63156	NM_001290982	17912	Mm.3390	NM_010863	ENSMUSG00000018417	Myo1b	AA406997|MIH-L|MMIa	myosin IB	protein-coding
mm_20304.1	chr2	127143314	127143330	-	1	NA	promoter-TSS (NM_001163528)	promoter-TSS (NM_001163528)	135	NM_001163527	73338	Mm.57559	NM_001163527	ENSMUSG00000074825	Itpripl1	1700041B20Rik	inositol 1,4,5-triphosphate receptor interacting protein-like 1	protein-coding
mm_122021.1	chr14	28308721	28308731	-	1	NA	intron (NM_177814, intron 15 of 15)	intron (NM_177814, intron 15 of 15)	-196747	NM_009524	22418	Mm.287544	NM_009524	ENSMUSG00000021994	Wnt5a	8030457G12Rik|Wnt-5a	wingless-type MMTV integration site family, member 5A	protein-coding
mm_18766.1	chr2	73463915	73463925	-	1	NA	intron (NM_153138, intron 1 of 7)	intron (NM_153138, intron 1 of 7)	-10031	NM_001289722	215280	Mm.223504	NM_153138	ENSMUSG00000075284	Wipf1	AI115543|D2Ertd120e|WIP|Waspip	WAS/WASL interacting protein family, member 1	protein-coding
mm_158227.1	chrX	106219631	106219658	-	1	NA	exon (NM_001167988, exon 2 of 8)	exon (NM_001167988, exon 2 of 8)	198	NM_001001176	407786	Mm.19440	NM_001001176	ENSMUSG00000047242	Taf9b	BC066223|Taf9l	TATA-box binding protein associated factor 9B	protein-coding
mm_137289.1	chr17	24740058	24740067	+	1	NA	intron (NM_013759, intron 2 of 4)	intron (NM_013759, intron 2 of 4)	3469	NM_001346668	27361	Mm.28212	NM_013759	ENSMUSG00000075705	Msrb1	D17Wsu82e|SELX|SelR|Sepr|Sepx1	methionine sulfoxide reductase B1	protein-coding
mm_58912.1	chr7	17672269	17672279	+	1	NA	promoter-TSS (NR_002857)	promoter-TSS (NR_002857)	-39	NR_002857	232919	Mm.153893	NR_002857	ENSMUSG00000108558	Psg-ps1	AV036018|Cea-6|Cea6	pregnancy specific glycoprotein pseudogene 1	pseudo
mm_80627.1	chr9	89066971	89066976	+	1	NA	Intergenic	Intergenic	25862	NM_001170884	666747	Mm.425592	NM_001170884	ENSMUSG00000079162	Trim43b	EG666747|Gm8269	tripartite motif-containing 43B	protein-coding
mm_100048.1	chr11	115163401	115163413	+	1	NA	promoter-TSS (NM_012030)	promoter-TSS (NM_012030)	66	NM_012030	26941	Mm.27842	NM_012030	ENSMUSG00000020733	Slc9a3r1	EBP-50|NHE-RF|NHERF-1|NHERF1	solute carrier family 9 (sodium/hydrogen exchanger), member 3 regulator 1	protein-coding
mm_158026.1	chrX	96166991	96167015	-	1	NA	3' UTR (NM_010833, exon 13 of 13)	3' UTR (NM_010833, exon 13 of 13)	70958	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_99198.1	chr11	101016046	101016059	+	1	NA	intron (NM_001243050, intron 2 of 20)	intron (NM_001243050, intron 2 of 20)	6600	NM_001243051	11975	Mm.340818	NM_016920	ENSMUSG00000019302	Atp6v0a1	AA959968|ATP6a1|Atp6n1|Atp6n1a|Atpv0a1|Vpp-1|Vpp1	ATPase, H+ transporting, lysosomal V0 subunit A1	protein-coding
mm_64168.1	chr7	141447816	141447836	+	1	NA	promoter-TSS (NR_034049)	promoter-TSS (NR_034049)	176	NM_026020	67186	Mm.380435	NM_026020	ENSMUSG00000025508	Rplp2	2700049I22Rik	ribosomal protein, large P2	protein-coding
mm_113266.1	chr13	28951567	28951577	+	1	NA	3' UTR (NM_009238, exon 1 of 1)	3' UTR (NM_009238, exon 1 of 1)	2110	NM_009238	20677	Mm.240627	NM_009238	ENSMUSG00000076431	Sox4	AA682046|Sox-4	SRY (sex determining region Y)-box 4	protein-coding
mm_27044.1	chr3	27153866	27153876	-	1	NA	promoter-TSS (NM_001177626)	promoter-TSS (NM_001177626)	7	NM_001177626	13605	Mm.261453	NM_007900	ENSMUSG00000027699	Ect2	AI528536|mKIAA4037	ect2 oncogene	protein-coding
mm_114893.1	chr13	94359481	94359500	+	1	NA	promoter-TSS (NR_045619)	promoter-TSS (NR_045619)	530	NM_009680	11774	Mm.21185	NM_009680	ENSMUSG00000021686	Ap3b1	AP-3|AU015684|C78395|Hps2|beta3A|pe|pearl|rim2	adaptor-related protein complex 3, beta 1 subunit	protein-coding
mm_131958.1	chr16	24487073	24487109	+	1	NA	intron (NM_001145952, intron 2 of 11)	(CA)n|Simple_repeat|Simple_repeat	39000	NM_001145952	210126	Mm.209385	NM_178665	ENSMUSG00000033306	Lpp	9430020K16Rik|AA959454|AU024130|B130055L10Rik|C79715|D630048H16	LIM domain containing preferred translocation partner in lipoma	protein-coding
mm_2389.1	chr1	93509126	93509157	+	1	NA	3' UTR (NM_010891, exon 13 of 13)	3' UTR (NM_010891, exon 13 of 13)	-2963	NM_145519	227377	Mm.243091	NM_145519	ENSMUSG00000034066	Farp2	AI465173|BC009153|D030026M03Rik|Fir|mKIAA0793	FERM, RhoGEF and pleckstrin domain protein 2	protein-coding
mm_7923.1	chr1	133801058	133801066	-	1	NA	Intergenic	Intergenic	-47315	NM_213616	381290	Mm.188617	NM_213616	ENSMUSG00000026463	Atp2b4	Pmca4	ATPase, Ca++ transporting, plasma membrane 4	protein-coding
mm_71166.1	chr8	40546350	40546400	+	1	NA	3' UTR (NM_033560, exon 12 of 12)	3' UTR (NM_033560, exon 12 of 12)	-30528	NM_001271542	18983	Mm.272551	NM_011135	ENSMUSG00000031601	Cnot7	AU022737|CAF-1|Caf1|Pop2	CCR4-NOT transcription complex, subunit 7	protein-coding
mm_9737.1	chr1	180245928	180245955	-	1	NA	promoter-TSS (NM_011183)	promoter-TSS (NM_011183)	9	NM_011183	19165	Mm.330850	NM_011183	ENSMUSG00000010609	Psen2	ALG-3|Ad4h|Alg3|PS-2|PS2|Psnl2|STM2	presenilin 2	protein-coding
mm_146719.1	chr18	15064119	15064140	-	1	NA	promoter-TSS (NM_001142731)	promoter-TSS (NM_001142731)	-547	NM_001142731	106931	Mm.329299	NM_134112	ENSMUSG00000036225	Kctd1	4933402K10Rik|AI661543|AW553000	potassium channel tetramerisation domain containing 1	protein-coding
mm_50467.1	chr6	48977159	48977163	+	1	NA	intron (NM_001029987, intron 1 of 3)	intron (NM_001029987, intron 1 of 3)	2018	NM_001029987	243376	Mm.244112	NM_001029987	ENSMUSG00000068536	Doxl2	-	diamine oxidase-like protein 2	protein-coding
mm_70879.1	chr8	25198852	25198856	+	1	NA	intron (NM_177089, intron 2 of 12)	ORR1A4|LTR|ERVL-MaLR	2688	NM_199323	320165	Mm.308452	NM_177089	ENSMUSG00000065954	Tacc1	4833447E04Rik|AA960202|B230378H13Rik	transforming, acidic coiled-coil containing protein 1	protein-coding
mm_113111.1	chr13	24416879	24416951	+	1	NA	5' UTR (NM_001111110, exon 3 of 17)	5' UTR (NM_001111110, exon 3 of 17)	1793	NM_001284520	12763	Mm.8396	NM_007717	ENSMUSG00000016756	Cmah	-	cytidine monophospho-N-acetylneuraminic acid hydroxylase	protein-coding
mm_105634.1	chr11	106998442	106998446	-	1	NA	intron (NM_010655, intron 1 of 10)	MER33|DNA|hAT-Charlie	1081	NM_010655	16647	Mm.12508	NM_010655	ENSMUSG00000018362	Kpna2	2410044B12Rik|IPOA1|PTAC58|Rch1	karyopherin (importin) alpha 2	protein-coding
mm_67643.1	chr7	84444532	84444539	-	1	NA	Intergenic	Intergenic	-34497	NM_007488	11864	Mm.38594	NM_007488	ENSMUSG00000015709	Arnt2	Hif-2b|bHLHe1|mKIAA0307	aryl hydrocarbon receptor nuclear translocator 2	protein-coding
mm_28938.1	chr3	98882241	98882268	-	1	NA	intron (NM_019545, intron 4 of 8)	intron (NM_019545, intron 4 of 8)	10976	NM_019545	56185	Mm.281874	NM_019545	ENSMUSG00000027870	Hao2	AI325478|Hao-2|Hao3|Haox3	hydroxyacid oxidase 2	protein-coding
mm_48552.1	chr5	142929089	142929127	-	1	NA	Intergenic	Intergenic	-22354	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_7939.1	chr1	133914753	133914766	-	1	NA	exon (NM_054077, exon 2 of 3)	exon (NM_054077, exon 2 of 3)	6642	NM_054077	116847	Mm.214514	NM_054077	ENSMUSG00000041577	Prelp	7330409J17Rik|SLRR2A	proline arginine-rich end leucine-rich repeat	protein-coding
mm_44903.1	chr5	35652608	35652627	-	1	NA	3' UTR (NM_030127, exon 9 of 9)	3' UTR (NM_030127, exon 9 of 9)	27163	NM_001042615	78558	Mm.274255	NM_030127	ENSMUSG00000029096	Htra3	2210021K23Rik|9530081K03Rik|Prsp|Tasp	HtrA serine peptidase 3	protein-coding
mm_154557.1	chrM	16054	16095	-	1	NA	NA	Intergenic	NA	NA								
mm_110626.1	chr12	57197263	57197275	-	1	NA	5' UTR (NM_172577, exon 1 of 10)	5' UTR (NM_172577, exon 1 of 10)	203	NM_172577	217593	Mm.32835	NM_172577	ENSMUSG00000035472	Slc25a21	9930033G19Rik|A630030I10|BB158148	solute carrier family 25 (mitochondrial oxodicarboxylate carrier), member 21	protein-coding
mm_64366.1	chr7	142434933	142434970	+	1	NA	promoter-TSS (NM_001285857)	promoter-TSS (NM_001285857)	-26	NM_001285857	55925	Mm.213002	NM_018802	ENSMUSG00000031098	Syt8	-	synaptotagmin VIII	protein-coding
mm_141344.1	chr17	28558421	28558452	-	1	NA	promoter-TSS (NR_105935)	promoter-TSS (NR_105935)	65	NR_105935	102465585		NR_105935	ENSMUSG00000099152	Mir6969	Gm27305|mmu-mir-6969	microRNA 6969	ncRNA
mm_75895.1	chr8	70897408	70897423	-	1	NA	promoter-TSS (NM_029751)	promoter-TSS (NM_029751)	28	NM_029751	76808	Mm.379251	NM_029751	ENSMUSG00000045128	Rpl18a	2510019J09Rik	ribosomal protein L18A	protein-coding
mm_49613.1	chr6	30747363	30747383	+	1	NA	TTS (NM_017478)	TTS (NM_017478)	6074	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_62728.1	chr7	110777654	110777697	+	1	NA	intron (NM_009667, intron 1 of 14)	intron (NM_009667, intron 1 of 14)	5071	NM_009667	11717	Mm.3238	NM_009667	ENSMUSG00000005686	Ampd3	-	adenosine monophosphate deaminase 3	protein-coding
mm_11860.1	chr2	48814125	48814173	+	1	NA	promoter-TSS (NM_007396)	promoter-TSS (NM_007396)	40	NM_007396	11480	Mm.314338	NM_007396	ENSMUSG00000052155	Acvr2a	ActrIIa|Acvr2|TactrII	activin receptor IIA	protein-coding
mm_54850.1	chr6	42591036	42591045	-	1	NA	intron (NM_203396, intron 5 of 6)	RLTR12B|LTR|ERVK	6332	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_22447.1	chr2	181697838	181697844	-	1	NA	intron (NM_199023, intron 1 of 3)	intron (NM_199023, intron 1 of 3)	601	NM_199023	277496	Mm.212749	NM_199023	ENSMUSG00000045794	Lkaaear1	4930526D03Rik|Gm692	LKAAEAR motif containing 1 (IKAAEAR murine motif)	protein-coding
mm_57381.1	chr6	124814289	124814296	-	1	NA	promoter-TSS (NM_009415)	promoter-TSS (NM_009415)	4	NM_009415	21991	Mm.4222	NM_009415	ENSMUSG00000023456	Tpi1	AI255506|Tpi|Tpi-1	triosephosphate isomerase 1	protein-coding
mm_69058.1	chr7	126897234	126897244	-	1	NA	intron (NM_026827, intron 1 of 5)	intron (NM_026827, intron 1 of 5)	1039	NM_026827	68742	Mm.248646	NM_026827	ENSMUSG00000060538	Tmem219	1110032O16Rik|2900045G02Rik|IGFBP-3R	transmembrane protein 219	protein-coding
mm_16152.1	chr2	172345629	172345647	+	1	NA	promoter-TSS (NM_025912)	promoter-TSS (NM_025912)	61	NM_025912	67017	Mm.30013	NM_025912	ENSMUSG00000027495	Fam210b	2010011I20Rik|AI430961|AV108736	family with sequence similarity 210, member B	protein-coding
mm_105073.1	chr11	100759996	100760011	-	1	NA	promoter-TSS (NM_001081194)	promoter-TSS (NM_001081194)	-225	NM_001081194	380728	Mm.297539	NM_001081194	ENSMUSG00000035355	Kcnh4	BEC2	potassium voltage-gated channel, subfamily H (eag-related), member 4	protein-coding
mm_33391.1	chr4	129811644	129811684	+	1	NA	Intergenic	Intergenic	-8815	NM_008974	19244	Mm.193688	NM_008974	ENSMUSG00000028788	Ptp4a2	Prl-2	protein tyrosine phosphatase 4a2	protein-coding
mm_74255.1	chr8	124863033	124863089	+	1	NA	promoter-TSS (NM_025615)	promoter-TSS (NM_025615)	28	NM_010322	14712	Mm.29114	NM_010322	ENSMUSG00000031985	Gnpat	AU019525|D1Ertd819e|DHAPAT	glyceronephosphate O-acyltransferase	protein-coding
mm_128876.1	chr15	73040767	73040773	-	1	NA	intron (NM_180662, intron 4 of 21)	intron (NM_180662, intron 4 of 21)	15042	NM_029640	76510	Mm.158902	NM_029640	ENSMUSG00000047921	Trappc9	1810044A24Rik|2900005P22Rik|4632408O18Rik|Ibp|Nibp|TRS130|mKIAA1882	trafficking protein particle complex 9	protein-coding
mm_155433.1	chrX	73493281	73493315	+	1	NA	exon (NM_007542, exon 7 of 8)	exon (NM_007542, exon 7 of 8)	9697	NM_007542	12111	Mm.2608	NM_007542	ENSMUSG00000031375	Bgn	BG|DSPG1|PG-S1|PGI|SLRR1A	biglycan	protein-coding
mm_168735.1	chr12	115120220	115120236	-	1	NA	Intergenic	Intergenic	575566	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
mm_51348.1	chr6	72555774	72555803	+	1	NA	exon (NM_001042534, exon 4 of 10)	exon (NM_001042534, exon 4 of 10)	6141	NM_001271395	12332	Mm.18626	NM_007599	ENSMUSG00000056737	Capg	gCap39|mbh1	capping protein (actin filament), gelsolin-like	protein-coding
mm_116599.1	chr13	48552320	48552330	-	1	NA	Intergenic	Intergenic	-14053	NR_029725	387244		NR_029725	ENSMUSG00000065421	Mirlet7a-1	Let-7a|Mirnlet7a|Mirnlet7a-1|let-7a-1	microRNA let7a-1	ncRNA
mm_163954.1	chr14	54476247	54476259	+	1	NA	5' UTR (NM_080726, exon 1 of 5)	5' UTR (NM_080726, exon 1 of 5)	153	NM_080726	140743	Mm.274727	NM_080726	ENSMUSG00000022176	Rem2	AW411893	rad and gem related GTP binding protein 2	protein-coding
mm_119490.1	chr14	47376348	47376358	+	1	NA	intron (NM_001145953, intron 1 of 5)	B1F2|SINE|Alu	2493	NM_001145953	16854	Mm.248615	NM_010705	ENSMUSG00000050335	Lgals3	GBP|L-34|Mac-2|gal3	lectin, galactose binding, soluble 3	protein-coding
mm_70228.1	chr7	145283983	145283993	-	1	NA	promoter-TSS (NM_146206)	promoter-TSS (NM_146206)	23	NR_132644	233979	Mm.102235	NM_146206	ENSMUSG00000048677	Tpcn2	D830047E22Rik|Gm35086	two pore segment channel 2	protein-coding
mm_143344.1	chr17	66594593	66594654	-	1	NA	promoter-TSS (NM_028998)	promoter-TSS (NM_028998)	-1	NM_028998	74556	Mm.218634	NM_028998	ENSMUSG00000024105	Themis3	9130404H23Rik	thymocyte selection associated family member 3	protein-coding
mm_12132.1	chr2	61653509	61653520	+	1	NA	exon (NM_001164072, exon 8 of 8)	exon (NM_001164072, exon 8 of 8)	-58180	NM_021526	59029	Mm.218198	NM_021526	ENSMUSG00000026914	Psmd14	2610312C03Rik|3200001M20Rik|AA986732|Pad1|Poh1|rpm11	proteasome (prosome, macropain) 26S subunit, non-ATPase, 14	protein-coding
mm_40650.1	chr5	65107614	65107616	+	1	NA	promoter-TSS (NM_001347355)	promoter-TSS (NM_001347355)	47	NM_001347355	71778	Mm.10281	NM_175174	ENSMUSG00000054920	Klhl5	1300013C10Rik	kelch-like 5	protein-coding
mm_49812.1	chr6	36389390	36389407	+	1	NA	intron (NM_203491, intron 2 of 2)	intron (NM_203491, intron 2 of 2)	-1164	NR_015589	319472	Mm.226434	NR_015589	ENSMUSG00000073154	9330158H04Rik	-	RIKEN cDNA 9330158H04 gene	ncRNA
mm_94347.1	chr11	4887762	4887767	+	1	NA	intron (NM_008698, intron 4 of 9)	ID_B1|SINE|B4	-3581	NR_105883	102466764		NR_105883	ENSMUSG00000098296	Mir6918	Gm27968|mmu-mir-6918	microRNA 6918	ncRNA
mm_11230.1	chr2	29802698	29802720	+	1	NA	promoter-TSS (NM_011989)	promoter-TSS (NM_011989)	29	NM_011989	26569	Mm.330113	NM_011989	ENSMUSG00000059316	Slc27a4	BB144259|FATP4	solute carrier family 27 (fatty acid transporter), member 4	protein-coding
mm_109789.1	chr12	3249296	3249310	-	1	NA	3' UTR (NM_016676, exon 6 of 6)	3' UTR (NM_016676, exon 6 of 6)	13512	NR_015551	74173	Mm.309774	NM_028796	ENSMUSG00000079179	Rab10os	1700012B15Rik|1810036A22Rik	RAB10, member RAS oncogene family, opposite strand	ncRNA
mm_47935.1	chr5	135251210	135251242	-	1	NA	promoter-TSS (NM_010246)	promoter-TSS (NM_010246)	-179	NM_010246	14371	Mm.6256	NM_010246	ENSMUSG00000049551	Fzd9	mfz9	frizzled class receptor 9	protein-coding
mm_158181.1	chrX	103981230	103981238	-	1	NA	promoter-TSS (NM_011276)	promoter-TSS (NM_011276)	50	NM_011276	19820	Mm.427762	NM_011276	ENSMUSG00000056537	Rlim	AL022832|AW743871|Ha1r|Rlim1|Rnf12	ring finger protein, LIM domain interacting	protein-coding
mm_102206.1	chr11	54787598	54787711	-	1	NA	promoter-TSS (NM_178626)	promoter-TSS (NM_178626)	49	NM_178626	72729	Mm.29476	NM_178626	ENSMUSG00000052298	Cdc42se2	2810404F18Rik|AA408783|AA536669|SPEC2	CDC42 small effector 2	protein-coding
mm_66230.1	chr7	35067825	35067830	-	1	NA	Intergenic	MTC|LTR|ERVL-MaLR	-11261	NM_009884	12611	Mm.273090	NM_009884	ENSMUSG00000056216	Cebpg	C/EBP[g]|C/EBPgamma|GPE1-BP|Gpe1bp|Ig/EBP	CCAAT/enhancer binding protein (C/EBP), gamma	protein-coding
mm_150251.1	chr19	34101115	34101125	+	1	NA	5' UTR (NM_023903, exon 2 of 10)	5' UTR (NM_023903, exon 2 of 10)	177	NM_023903	78753	Mm.195937	NM_023903	ENSMUSG00000056078	Lipm	4632427C23Rik|AW227514|Lipl3	lipase, family member M	protein-coding
mm_29148.1	chr3	105932688	105932711	-	1	NA	promoter-TSS (NM_001033780)	promoter-TSS (NM_001033780)	-35	NM_001033780	433638	Mm.239081	NM_001033780	ENSMUSG00000074342	I830077J02Rik	-	RIKEN cDNA I830077J02 gene	protein-coding
mm_31705.1	chr4	62583569	62583585	+	1	NA	intron (NM_019492, intron 3 of 19)	CpG	23730	NM_019492	50780	Mm.286753	NM_019492	ENSMUSG00000059810	Rgs3	4930506N09Rik|C2PA-RGS3|C2pa|PDZ-RGS3|RGS3S	regulator of G-protein signaling 3	protein-coding
mm_89051.1	chr10	82874655	82874685	+	1	NA	exon (NM_001042523, exon 3 of 15)	exon (NM_001042523, exon 3 of 15)	8044	NM_025499	66341	Mm.443284	NM_025499	ENSMUSG00000109864	Eid3	1700027M21Rik|NS4EB	EP300 interacting inhibitor of differentiation 3	protein-coding
mm_147891.1	chr18	65040731	65040741	-	1	NA	intron (NM_031881, intron 1 of 29)	MTD|LTR|ERVL-MaLR	17209	NM_031881	83814	Mm.98668	NM_031881	ENSMUSG00000024589	Nedd4l	1300012C07Rik|Nedd4-2|Nedd4b	neural precursor cell expressed, developmentally down-regulated gene 4-like	protein-coding
mm_12382.1	chr2	69862176	69862178	+	1	NA	intron (NM_009278, intron 1 of 11)	intron (NM_009278, intron 1 of 11)	615	NM_009278	20823	Mm.10508	NM_009278	ENSMUSG00000068882	Ssb	SS-B	Sjogren syndrome antigen B	protein-coding
mm_9555.1	chr1	173940630	173940638	-	1	NA	intron (NM_001302649, intron 2 of 9)	intron (NM_001302649, intron 2 of 9)	1858	NM_001302649	15950	Mm.463437	NM_008328	ENSMUSG00000039997	Ifi203	Mndal	interferon activated gene 203	protein-coding
mm_57463.1	chr6	125191536	125191620	-	1	NA	promoter-TSS (NM_025595)	promoter-TSS (NM_025595)	8	NM_146171	68298	Mm.257590	NM_146171	ENSMUSG00000038252	Ncapd2	2810406C15Rik|2810465G24Rik|CAP-D2|CNAP1|mKIAA0159	non-SMC condensin I complex, subunit D2	protein-coding
mm_134204.1	chr16	11134625	11134659	-	1	NA	promoter-TSS (NM_029582)	promoter-TSS (NM_029582)	-110	NM_029582	106200	Mm.291015	NM_029582	ENSMUSG00000022498	Txndc11	2810408E11Rik|AI427833|EFP1|Txdc11	thioredoxin domain containing 11	protein-coding
mm_163674.1	chr13	83572059	83572078	-	1	NA	intron (NM_001347566, intron 1 of 10)	intron (NM_001347566, intron 1 of 10)	-1539	NM_001347577	17260	Mm.24001	NM_025282	ENSMUSG00000005583	Mef2c	5430401D19Rik|9930028G15Rik|AV011172|Mef2	myocyte enhancer factor 2C	protein-coding
mm_83597.1	chr9	48494410	48494427	-	1	NA	promoter-TSS (NM_001004191)	promoter-TSS (NM_001004191)	912	NM_001326355	67010	Mm.76911	NM_144948	ENSMUSG00000042396	Rbm7	1200007M24Rik|1500011D06Rik|AU041934|AW554393	RNA binding motif protein 7	protein-coding
mm_111656.1	chr12	102878409	102878449	-	1	NA	promoter-TSS (NM_172806)	promoter-TSS (NM_172806)	-23	NM_172806	238386	Mm.63456	NM_172806	ENSMUSG00000041702	Btbd7	5730507E09Rik|8030448M07|E130118E17Rik|FUP1|mKIAA1525	BTB (POZ) domain containing 7	protein-coding
mm_24854.1	chr3	95871586	95871635	+	1	NA	promoter-TSS (NR_040446)	promoter-TSS (NR_040446)	88	NR_040446	100042889	Mm.440109	NR_040446	ENSMUSG00000080727	C920021L13Rik	-	RIKEN cDNA C920021L13 gene	ncRNA
mm_29772.1	chr3	127240791	127240798	-	1	NA	intron (NM_001327938, intron 1 of 47)	intron (NM_001327938, intron 1 of 47)	79489	NR_105029	100862268	Mm.444603	NR_105029	ENSMUSG00000097456	LOC100862268	-	uncharacterized LOC100862268	ncRNA
mm_59742.1	chr7	28818458	28818478	+	1	NA	exon (NM_177301, exon 7 of 13)	exon (NM_177301, exon 7 of 13)	-6870	NM_016772	51798	Mm.291776	NM_016772	ENSMUSG00000053898	Ech1	AA617331	enoyl coenzyme A hydratase 1, peroxisomal	protein-coding
mm_66971.1	chr7	63887646	63887649	-	1	NA	3' UTR (NM_021366, exon 2 of 2)	3' UTR (NM_021366, exon 2 of 2)	-29210	NM_001256311	381994	Mm.425466	NM_001256311	ENSMUSG00000095061	E030018B13Rik	Gm1697	RIKEN cDNA E030018B13 gene	protein-coding
mm_139628.1	chr17	57367292	57367314	+	1	NA	intron (NM_010130, intron 2 of 21)	Lx8b|LINE|L1	8617	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_100180.1	chr11	116624409	116624430	+	1	NA	promoter-TSS (NM_001167680)	promoter-TSS (NM_001167680)	-167	NM_001167680	217344	Mm.89695	NM_172572	ENSMUSG00000020806	Rhbdf2	4732465I17Rik|Rhbdl6|cub	rhomboid 5 homolog 2	protein-coding
mm_110198.1	chr12	27340619	27340642	-	1	NA	3' UTR (NM_009234, exon 1 of 1)	3' UTR (NM_009234, exon 1 of 1)	2088	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding
mm_145238.1	chr18	50278372	50278403	+	1	NA	promoter-TSS (NM_001004061)	promoter-TSS (NM_001004061)	18	NM_001004061	225497	Mm.329435	NM_001004061	ENSMUSG00000035420	Fam170a	Gm93|Znfd	family with sequence similarity 170, member A	protein-coding
mm_47465.1	chr5	123671078	123671091	-	1	NA	intron (NM_001347468, intron 1 of 24)	intron (NM_001347468, intron 1 of 24)	13277	NM_019765	56430	Mm.241109	NM_019765	ENSMUSG00000049550	Clip1	1110007I12Rik|4631429H07Rik|AV017631|C81039|CLIP-170|CLIP170|CYLN1|Clip50|Rsn|mKIAA4046|restin	CAP-GLY domain containing linker protein 1	protein-coding
mm_47391.1	chr5	123015947	123015957	-	1	NA	intron (NM_175423, intron 1 of 1)	intron (NM_175423, intron 1 of 1)	878	NM_175423	109305	Mm.218582	NM_175423	ENSMUSG00000049686	Orai1	D730049H07Rik|Tmem142a|orai-1	ORAI calcium release-activated calcium modulator 1	protein-coding
mm_84874.1	chr9	79718588	79718592	-	1	NA	5' UTR (NM_001290308, exon 1 of 66)	5' UTR (NM_001290308, exon 1 of 66)	132	NM_001290308	12816	Mm.3819	NM_007730	ENSMUSG00000032332	Col12a1	-	collagen, type XII, alpha 1	protein-coding
mm_137365.1	chr17	25453720	25453742	+	1	NA	Intergenic	Intergenic	-17859	NM_027951	71840	Mm.282330	NM_027951	ENSMUSG00000024175	Tekt4	1700010L19Rik	tektin 4	protein-coding
mm_146198.1	chr18	76241661	76241741	+	1	NA	promoter-TSS (NM_010754)	promoter-TSS (NM_010754)	0	NM_010754	17126	Mm.152699	NM_010754	ENSMUSG00000024563	Smad2	7120426M23Rik|Madh2|Madr2|Smad-2|mMad2	SMAD family member 2	protein-coding
mm_57006.1	chr6	121103523	121103530	-	1	NA	intron (NM_001270475, intron 1 of 31)	intron (NM_001270475, intron 1 of 31)	-21899	NR_138097	194401	Mm.122399	NM_153396	ENSMUSG00000051586	Mical3	C130040D16Rik|Mical-3|mKIAA1364	microtubule associated monooxygenase, calponin and LIM domain containing 3	protein-coding
mm_107044.1	chr12	15811342	15811348	+	1	NA	intron (NM_144551, intron 1 of 2)	intron (NM_144551, intron 1 of 2)	5440	NM_144551	217410	Mm.491136	NM_144551	ENSMUSG00000020601	Trib2	AW319517|TRB-2|TRB2	tribbles pseudokinase 2	protein-coding
mm_165214.1	chr2	38166075	38166081	-	1	NA	intron (NM_146122, intron 2 of 21)	intron (NM_146122, intron 2 of 21)	121306	NM_146122	227801	Mm.314245	NM_146122	ENSMUSG00000035392	Dennd1a	6030446I19Rik|connecdenn	DENN/MADD domain containing 1A	protein-coding
mm_42695.1	chr5	119836860	119836879	+	1	NA	intron (NM_011537, intron 1 of 8)	intron (NM_011537, intron 1 of 8)	2206	NM_011537	21388	Mm.103636	NM_011537	ENSMUSG00000018263	Tbx5	-	T-box 5	protein-coding
mm_53186.1	chr6	125434328	125434332	+	1	NA	Intergenic	B1_Mus1|SINE|Alu	-53826	NM_198604	213522	Mm.333396	NM_198604	ENSMUSG00000038167	Plekhg6	BC026778|Gm155	pleckstrin homology domain containing, family G (with RhoGef domain) member 6	protein-coding
mm_39950.1	chr5	32055248	32055251	+	1	NA	intron (NM_144541, intron 10 of 11)	intron (NM_144541, intron 10 of 11)	-81223	NM_008037	14284	Mm.24684	NM_008037	ENSMUSG00000029135	Fosl2	Fra-2	fos-like antigen 2	protein-coding
mm_136411.1	chr16	93795025	93795065	-	1	NA	intron (NM_027293, intron 27 of 36)	intron (NM_027293, intron 27 of 36)	-37076	NM_001045529	338467	Mm.287329	NM_001045529	ENSMUSG00000039456	Morc3	1110051N18Rik|AI452146|BF318192|D16Jhu32e|NXP2|Zcwcc3	microrchidia 3	protein-coding
mm_111400.1	chr12	90969782	90969790	-	1	NA	Intergenic	RMER1C|Other|Other	-76062	NR_045858	71349	Mm.442093	NR_045858		5430427M07Rik	-	RIKEN cDNA 5430427M07 gene	ncRNA
mm_82765.1	chr9	26920091	26920096	-	1	NA	intron (NM_001281475, intron 3 of 20)	MT2A|LTR|ERVL	2988	NM_001281475	382064	Mm.335028	NM_001177509	ENSMUSG00000079644	Gm1110	-	predicted gene 1110	protein-coding
mm_99910.1	chr11	109845829	109845838	+	1	NA	promoter-TSS (NR_045909)	promoter-TSS (NR_045909)	-45	NR_045909	73257	Mm.250442	NR_045909	ENSMUSG00000087393	1700023C21Rik	-	RIKEN cDNA 1700023C21 gene	ncRNA
mm_21922.1	chr2	166905882	166905909	-	1	NA	promoter-TSS (NM_023565)	promoter-TSS (NM_023565)	-201	NM_023565	110750	Mm.22417	NM_023565	ENSMUSG00000002718	Cse1l	2610100P18Rik|AA407533|Capts|Cas|Xpo2	chromosome segregation 1-like (S. cerevisiae)	protein-coding
mm_70458.1	chr8	11822307	11822310	+	1	NA	intron (NM_017402, intron 17 of 19)	intron (NM_017402, intron 17 of 19)	-18213	NM_029326	75528	Mm.440342	NM_029326	ENSMUSG00000031512	Tex29	1700018L24Rik	testis expressed 29	protein-coding
mm_11861.1	chr2	48814177	48814219	+	1	NA	promoter-TSS (NM_007396)	promoter-TSS (NM_007396)	89	NM_007396	11480	Mm.314338	NM_007396	ENSMUSG00000052155	Acvr2a	ActrIIa|Acvr2|TactrII	activin receptor IIA	protein-coding
mm_170383.1	chr18	60212075	60212086	+	1	NA	promoter-TSS (NM_001033767)	promoter-TSS (NM_001033767)	3	NM_001033767	240327	Mm.357104	NM_001033767	ENSMUSG00000073555	Gm4951	EG240327|Ifgga2	predicted gene 4951	protein-coding
mm_107713.1	chr12	55836366	55836408	+	1	NA	promoter-TSS (NM_001037756)	promoter-TSS (NM_001037756)	21	NM_001037756	52592	Mm.24761	NM_027867	ENSMUSG00000012076	Brms1l	0710008O11Rik|AI159718|BRMS1|D12Ertd407e	breast cancer metastasis-suppressor 1-like	protein-coding
mm_48412.1	chr5	140262556	140262579	-	1	NA	intron (NM_010752, intron 9 of 17)	intron (NM_010752, intron 9 of 17)	58985	NM_010752	17120	Mm.27250	NM_010752	ENSMUSG00000029554	Mad1l1	AI173502|AW550425|Mad1	MAD1 mitotic arrest deficient 1-like 1	protein-coding
mm_100027.1	chr11	114908603	114908620	+	1	NA	Intergenic	MLT1D|LTR|ERVL-MaLR	18570	NM_170758	217303	Mm.294439	NM_170758	ENSMUSG00000034652	Cd300a	B230315M08Rik|Clm8|LMIR1|MAIR-I|MAIR-Ia|MMAC8|Pigr4|mcpir1	CD300A molecule	protein-coding
mm_156977.1	chrX	7188637	7188650	-	1	NA	promoter-TSS (NM_016691)	promoter-TSS (NM_016691)	71	NM_016691	12728	Mm.486257	NM_016691	ENSMUSG00000004317	Clcn5	5430408K11Rik|ClC-5|Clc4-1|Clc5|Clcn4-1|D930009B12Rik|DXImx42e|Sfc13|T25545	chloride channel, voltage-sensitive 5	protein-coding
mm_55638.1	chr6	72333467	72333471	-	1	NA	intron (NM_138592, intron 6 of 12)	intron (NM_138592, intron 6 of 12)	11706	NM_138592	28035	Mm.281900	NM_138592	ENSMUSG00000056305	Usp39	AA408960|AI894154|CGI-21|D6Wsu157e|SAD1	ubiquitin specific peptidase 39	protein-coding
mm_98783.1	chr11	96849864	96849897	+	1	NA	promoter-TSS (NR_029562)	promoter-TSS (NR_029562)	4	NM_019877	56358	Mm.22144	NM_019877	ENSMUSG00000018672	Copz2	1110012D12Rik|zeta2-COP	coatomer protein complex, subunit zeta 2	protein-coding
mm_2646.1	chr1	125438223	125438256	+	1	NA	Intergenic	Intergenic	-2512	NM_001205386	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding
mm_152769.1	chr19	20954250	20954295	-	1	NA	promoter-TSS (NM_028953)	promoter-TSS (NM_028953)	-70	NM_028953	13409	Mm.219585	NM_028953	ENSMUSG00000024749	Tmc1	4933416G09Rik|Beethoven|Bth|CWEA1|dn	transmembrane channel-like gene family 1	protein-coding
mm_44311.1	chr5	9161609	9161619	-	1	NA	5' UTR (NM_001110327, exon 1 of 17)	5' UTR (NM_001110327, exon 1 of 17)	162	NM_001110327	23857	Mm.22480	NM_011806	ENSMUSG00000042508	Dmtf1	Dimp|Dmp1	cyclin D binding myb-like transcription factor 1	protein-coding
mm_45104.1	chr5	44782528	44782556	-	1	NA	intron (NM_001347349, intron 1 of 7)	intron (NM_001347349, intron 1 of 7)	17204	NM_001347349	16826	Mm.25785	NM_010698	ENSMUSG00000039706	Ldb2	AI035351|AW146358|CLIM1|CLP-36|Ldb3	LIM domain binding 2	protein-coding
mm_33603.1	chr4	132579411	132579427	+	1	NA	exon (NM_001081211, exon 2 of 2)	exon (NM_001081211, exon 2 of 2)	15352	NM_001081211	19204	Mm.89389	NM_001081211	ENSMUSG00000056529	Ptafr	PAFR	platelet-activating factor receptor	protein-coding
mm_56636.1	chr6	113077238	113077250	-	1	NA	promoter-TSS (NR_027008)	promoter-TSS (NR_027008)	0	NR_027010	14910	Mm.280950	NR_027008	ENSMUSG00000086429	Gt(ROSA)26Sor	AV258896|Gtrgeo26|Gtrosa26|R26|ROSA26|Thumpd3as1	gene trap ROSA 26, Philippe Soriano	ncRNA
mm_34475.1	chr4	148332308	148332311	+	1	NA	Intergenic	Intergenic	-44344	NM_001083342	242748	Mm.33873	NM_001083342	ENSMUSG00000041544	Ptchd2	Disp3|G630052C06Rik|RNDEu-2	patched domain containing 2	protein-coding
mm_61577.1	chr7	79841830	79841839	+	1	NA	exon (NM_008486, exon 1 of 20)	exon (NM_008486, exon 1 of 20)	518	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_68191.1	chr7	104353329	104353394	-	1	NA	promoter-TSS (NM_175677)	promoter-TSS (NM_175677)	-3	NM_001146007	319236	Mm.425502	NM_175677	ENSMUSG00000057143	Trim12c	9230105E10Rik|Trim12-2	tripartite motif-containing 12C	protein-coding
mm_105743.1	chr11	109366978	109367012	-	1	NA	intron (NM_010303, intron 2 of 3)	intron (NM_010303, intron 2 of 3)	-3341	NR_038097	100036768	Mm.467767	NR_038097	ENSMUSG00000056687	Gm11696	OTTMUSG00000003456	predicted gene 11696	ncRNA
mm_48140.1	chr5	137150355	137150365	-	1	NA	Intergenic	Intergenic	-34153	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_127241.1	chr15	99591137	99591150	+	1	NA	5' UTR (NM_009701, exon 1 of 4)	5' UTR (NM_009701, exon 1 of 4)	115	NM_009701	11830	Mm.45580	NM_009701	ENSMUSG00000044217	Aqp5	-	aquaporin 5	protein-coding
mm_63496.1	chr7	127777377	127777413	+	1	NA	promoter-TSS (NM_178029)	promoter-TSS (NM_178029)	6	NM_178029	233904	Mm.435494	NM_010940	ENSMUSG00000042308	Setd1a	BC010250|KMT2F|Nsccn1|mKIAA0339|mNSC1	SET domain containing 1A	protein-coding
mm_21322.1	chr2	157099474	157099535	-	1	NA	intron (NM_018851, intron 15 of 15)	intron (NM_018851, intron 15 of 15)	12449	NM_001177439	383766	Mm.480305	NM_001177439	ENSMUSG00000074628	Tldc2	Gm1332	TBC/LysM associated domain containing 2	protein-coding
mm_79592.1	chr9	58280071	58280087	+	1	NA	Intergenic	ID_B1|SINE|B4	26915	NM_026942	69106	Mm.216502	NM_026942	ENSMUSG00000032333	Stoml1	1810015E19Rik|AI847431|SLP1|STORP|UNC24|WPB72	stomatin-like 1	protein-coding
mm_104461.1	chr11	95076644	95076655	-	1	NA	promoter-TSS (NM_013565)	promoter-TSS (NM_013565)	65	NM_013565	16400	Mm.57035	NM_013565	ENSMUSG00000001507	Itga3	AA407068|CD49C|GAPB3	integrin alpha 3	protein-coding
mm_91176.1	chr10	20725052	20725062	-	1	NA	promoter-TSS (NM_013875)	promoter-TSS (NM_013875)	21	NM_013875	29863	Mm.425617	NM_013875	ENSMUSG00000019990	Pde7b	-	phosphodiesterase 7B	protein-coding
mm_130847.1	chr15	101929277	101929281	-	1	NA	TTS (NM_146063)	TTS (NM_146063)	-4544	NM_008475	16682	Mm.46425	NM_008475	ENSMUSG00000059668	Krt4	AW108092|K4|Krt-2.4|Krt2-4	keratin 4	protein-coding
mm_125862.1	chr15	75222538	75222548	+	1	NA	Intergenic	RMER1B|Other|Other	-45878	NM_008530	17071	Mm.377095	NM_008530	ENSMUSG00000022583	Ly6f	-	lymphocyte antigen 6 complex, locus F	protein-coding
mm_123606.1	chr14	68087337	68087372	-	1	NA	exon (NM_010910, exon 4 of 4)	exon (NM_010910, exon 4 of 4)	3470	NM_010910	18039	Mm.1956	NM_010910	ENSMUSG00000022055	Nefl	AI847934|CMT2E|NF-L|NF68|Nfl	neurofilament, light polypeptide	protein-coding
mm_91348.1	chr10	27134012	27134015	-	1	NA	exon (NM_008481, exon 34 of 64)	exon (NM_008481, exon 34 of 64)	-255853	NR_131034	75855	Mm.402080	NR_131034	ENSMUSG00000101636	4930579H20Rik	-	RIKEN cDNA 4930579H20 gene	ncRNA
mm_43281.1	chr5	131753687	131753697	+	1	NA	intron (NM_177047, intron 5 of 18)	intron (NM_177047, intron 5 of 18)	-126577	NR_040704	75369	Mm.389696	NR_040704	ENSMUSG00000105773	4930563F08Rik	-	RIKEN cDNA 4930563F08 gene	ncRNA
mm_151681.1	chr19	4269079	4269126	-	1	NA	promoter-TSS (NM_198113)	promoter-TSS (NM_198113)	70	NM_198113	245857	Mm.248388	NM_198113	ENSMUSG00000034616	Ssh3	BC028922|SSH-3|mSSH-3L	slingshot homolog 3 (Drosophila)	protein-coding
mm_33492.1	chr4	130823451	130823466	+	1	NA	3' UTR (NM_011520, exon 5 of 5)	3' UTR (NM_011520, exon 5 of 5)	30921	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_56914.1	chr6	119330807	119330817	-	1	NA	promoter-TSS (NM_172492)	promoter-TSS (NM_172492)	-46	NM_172492	211187	Mm.121498	NM_172492	ENSMUSG00000055003	Lrtm2	A230084J22|AI841794	leucine-rich repeats and transmembrane domains 2	protein-coding
mm_17076.1	chr2	22775266	22775279	-	1	NA	intron (NM_019456, intron 1 of 13)	intron (NM_019456, intron 1 of 13)	945	NM_019456	54519	Mm.14255	NM_019456	ENSMUSG00000026786	Apbb1ip	9930118P07Rik|Prp48	amyloid beta (A4) precursor protein-binding, family B, member 1 interacting protein	protein-coding
mm_150032.1	chr19	29375711	29375730	+	1	NA	intron (NM_021893, intron 3 of 6)	intron (NM_021893, intron 3 of 6)	8282	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_114009.1	chr13	52606915	52606933	+	1	NA	intron (NM_011518, intron 1 of 13)	B4|SINE|B4	10042	NM_011518	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_28811.1	chr3	96259728	96259738	-	1	NA	Intergenic	Intergenic	3584	NM_033596	97122	Mm.227295	NM_033596	ENSMUSG00000091405	Hist2h4	H4|X04652	histone cluster 2, H4	protein-coding
mm_88541.1	chr10	78542661	78542662	+	1	NA	Intergenic	RLTR21|LTR|ERVK	-31839	NM_173751	216136	Mm.2644	NM_173751	ENSMUSG00000032763	Ilvbl	5830463I21|AI415009	ilvB (bacterial acetolactate synthase)-like	protein-coding
mm_90327.1	chr10	127078887	127078918	+	1	NA	promoter-TSS (NM_001301014)	promoter-TSS (NM_001301014)	-5	NM_001301014	216439	Mm.336761	NM_001033263	ENSMUSG00000025422	Agap2	AGAP-2|Centg1|PIKE|cnt-g1|mKIAA0167	ArfGAP with GTPase domain, ankyrin repeat and PH domain 2	protein-coding
mm_19073.1	chr2	77816711	77816727	-	1	NA	promoter-TSS (NM_178723)	promoter-TSS (NM_178723)	97	NM_178723	241494	Mm.490320	NM_178723	ENSMUSG00000027016	Zfp385b	B830010L13Rik|C130013B13Rik|Zfp533|Znf385b	zinc finger protein 385B	protein-coding
mm_85246.1	chr9	99035734	99035751	-	1	NA	promoter-TSS (NM_001080776)	promoter-TSS (NM_001080776)	-52	NM_001080776	382097	Mm.293727	NM_001080776	ENSMUSG00000044860	Gm1123	AV052824|CLSP	predicted gene 1123	protein-coding
mm_46371.1	chr5	103647494	103647505	-	1	NA	Intergenic	B3|SINE|B2	8225	NM_028824	74218	Mm.159141	NM_028824	ENSMUSG00000029320	1700016H13Rik	-	RIKEN cDNA 1700016H13 gene	protein-coding
mm_85077.1	chr9	91362614	91362622	-	1	NA	exon (NM_009573, exon 2 of 3)	exon (NM_009573, exon 2 of 3)	3181	NM_009573	22771	Mm.335350	NM_009573	ENSMUSG00000032368	Zic1	ZIC|ZNF201	zinc finger protein of the cerebellum 1	protein-coding
mm_156254.1	chrX	136708045	136708064	+	1	NA	promoter-TSS (NM_146236)	promoter-TSS (NM_146236)	-11	NM_146236	237052	Mm.40713	NM_146236	ENSMUSG00000049536	Tceal1	0610011M09Rik|BC011290|P21|SIIR|pp21	transcription elongation factor A (SII)-like 1	protein-coding
mm_103075.1	chr11	69894788	69894812	-	1	NA	intron (NM_153788, intron 1 of 21)	intron (NM_153788, intron 1 of 21)	739	NM_153788	216859	Mm.288671	NM_153788	ENSMUSG00000001588	Acap1	Centb1	ArfGAP with coiled-coil, ankyrin repeat and PH domains 1	protein-coding
mm_143031.1	chr17	56609824	56609834	-	1	NA	promoter-TSS (NM_153152)	promoter-TSS (NM_153152)	-58	NM_153152	224904	Mm.34002	NM_153152	ENSMUSG00000049760	2410015M20Rik	Mic13|QIL1|sr104	RIKEN cDNA 2410015M20 gene	protein-coding
mm_14127.1	chr2	126034638	126034646	+	1	NA	promoter-TSS (NM_008008)	promoter-TSS (NM_008008)	-16	NM_008008	14178	Mm.330557	NM_008008	ENSMUSG00000027208	Fgf7	Kgf	fibroblast growth factor 7	protein-coding
mm_86930.1	chr10	24151142	24151171	+	1	NA	intron (NM_016797, intron 1 of 9)	intron (NM_016797, intron 1 of 9)	1839	NM_016797	53331	Mm.248042	NM_016797	ENSMUSG00000019998	Stx7	AI315064|AI317144|AW107239|Syn7	syntaxin 7	protein-coding
mm_45768.1	chr5	86917316	86917328	-	1	NA	3' UTR (NM_152811, exon 6 of 6)	3' UTR (NM_152811, exon 6 of 6)	9181	NM_152811	71773	Mm.26741	NM_152811	ENSMUSG00000035836	Ugt2b1	1300012D20Rik	UDP glucuronosyltransferase 2 family, polypeptide B1	protein-coding
mm_46491.1	chr5	105132343	105132351	-	1	NA	intron (NM_008620, intron 3 of 10)	L1M2|LINE|L1	7205	NM_008620	17472	Mm.440525	NM_008620	ENSMUSG00000079363	Gbp4	AW228052|Mag-2|Mpa-2|Mpa2	guanylate binding protein 4	protein-coding
mm_42084.1	chr5	110176965	110176973	+	1	NA	promoter-TSS (NR_040431)	promoter-TSS (NR_040431)	268	NM_008146	269682	Mm.9392	NM_008146	ENSMUSG00000029502	Golga3	5330413L04|5430416E01Rik|AI449376|AW490576|G1-499-14|Mea-2|Mea2|repro27	golgi autoantigen, golgin subfamily a, 3	protein-coding
mm_123028.1	chr14	55511217	55511220	-	1	NA	promoter-TSS (NM_009947)	promoter-TSS (NM_009947)	-142	NM_009947	12891	Mm.5249	NM_009947	ENSMUSG00000022212	Cpne6	AU067659|BB076446	copine VI	protein-coding
mm_167970.1	chrX	152584212	152584212	+	1	NA	Intergenic	Intergenic	20878	NM_001199311	635396	Mm.485766	NM_001199311	ENSMUSG00000091863	Cldn34a	Gm7157	claudin 34A	protein-coding
mm_65141.1	chr7	19573380	19573403	-	1	NA	promoter-TSS (NM_027189)	promoter-TSS (NM_027189)	-48	NM_027189	69731	Mm.24540	NM_027189	ENSMUSG00000044709	Gemin7	2400008I04Rik|AI120175|AI461688	gem (nuclear organelle) associated protein 7	protein-coding
mm_5221.1	chr1	14299707	14299714	-	1	NA	intron (NM_001252192, intron 2 of 16)	B3|SINE|B2	10489	NM_001310459	14048	Mm.250185	NM_010164	ENSMUSG00000025932	Eya1	bor	EYA transcriptional coactivator and phosphatase 1	protein-coding
mm_60430.1	chr7	44476792	44476813	+	1	NA	Intergenic	L1MEd|LINE|L1	6455	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_134496.1	chr16	18811616	18811635	-	1	NA	promoter-TSS (NM_001161623)	promoter-TSS (NM_001161623)	14	NM_001161623	12544	Mm.1248	NM_009862	ENSMUSG00000000028	Cdc45	Cdc45l	cell division cycle 45	protein-coding
mm_122906.1	chr14	54953830	54953838	-	1	NA	exon (NM_010856, exon 21 of 39)	exon (NM_010856, exon 21 of 39)	-4692	NR_029724	387204		NR_029724	ENSMUSG00000065432	Mir208a	Mirn208|Mirn208a|mir-208|mir-208a|mmu-mir-208	microRNA 208a	ncRNA
mm_11936.1	chr2	52857745	52857798	+	1	NA	promoter-TSS (NM_172409)	promoter-TSS (NM_172409)	-97	NM_172409	71409	Mm.394427	NM_172409	ENSMUSG00000036053	Fmnl2	5430425K04Rik|Man	formin-like 2	protein-coding
mm_9085.1	chr1	168432112	168432125	-	1	NA	promoter-TSS (NM_001291509)	promoter-TSS (NM_001291509)	51	NM_001291508	18514	Mm.43358	NM_008783	ENSMUSG00000052534	Pbx1	2310056B04Rik|D230003C07Rik|Pbx-1	pre B cell leukemia homeobox 1	protein-coding
mm_134297.1	chr16	14317320	14317370	-	1	NA	promoter-TSS (NM_025345)	promoter-TSS (NM_025345)	-13	NM_025345	66086	Mm.42072	NM_025345	ENSMUSG00000022677	Fopnl	0610037P05Rik	Fgfr1op N-terminal like	protein-coding
mm_21721.1	chr2	164638813	164638833	-	1	NA	promoter-TSS (NM_001012723)	promoter-TSS (NM_001012723)	-21	NM_001012723	277345	Mm.247244	NM_001012723	ENSMUSG00000070530	Wfdc16	BC043944|WAP16	WAP four-disulfide core domain 16	protein-coding
mm_24999.1	chr3	97651675	97651694	+	1	NA	exon (NM_001161763, exon 9 of 9)	exon (NM_001161763, exon 9 of 9)	-6528	NM_182997	108097	Mm.31175	NM_182997	ENSMUSG00000038205	Prkab2	5730553K21Rik|AW049591|BB124140	protein kinase, AMP-activated, beta 2 non-catalytic subunit	protein-coding
mm_67538.1	chr7	81454752	81454764	-	1	NA	promoter-TSS (NM_001252526)	promoter-TSS (NM_001252526)	0	NM_001252525	12877	Mm.273122	NM_007755	ENSMUSG00000025586	Cpeb1	AU024112|Cpeb|mCPEB	cytoplasmic polyadenylation element binding protein 1	protein-coding
mm_157351.1	chrX	36989684	36989704	-	1	NA	promoter-TSS (NM_001253706)	promoter-TSS (NM_001253706)	1	NM_001177324	56526	Mm.260036	NM_019942	ENSMUSG00000050379	Sept6	2810035H17Rik|C920001C06Rik|Sep6|mKIAA0128	septin 6	protein-coding
mm_118282.1	chr13	112753487	112753494	-	1	NA	Intergenic	Intergenic	-47287	NM_008903	19012	Mm.291029	NM_008247	ENSMUSG00000021759	Plpp1	Hic53|Hpic53|LPP-1|LPP1|PAP-2a|PAP2-alpha|PAP2a|Ppap2a|mPAP	phospholipid phosphatase 1	protein-coding
mm_72267.1	chr8	75097307	75097318	+	1	NA	exon (NM_010442, exon 3 of 5)	exon (NM_010442, exon 3 of 5)	3694	NM_010442	15368	Mm.276389	NM_010442	ENSMUSG00000005413	Hmox1	D8Wsu38e|HO-1|HO1|Hemox|Hmox|Hsp32	heme oxygenase 1	protein-coding
mm_130288.1	chr15	97008701	97008716	-	1	NA	exon (NM_027052, exon 11 of 16)	exon (NM_027052, exon 11 of 16)	47248	NM_027052	69354	Mm.250980	NM_027052	ENSMUSG00000022464	Slc38a4	1110012E16Rik|1700012A18Rik|Ata3|mATA3|mNAT3	solute carrier family 38, member 4	protein-coding
mm_94745.1	chr11	21101025	21101058	+	1	NA	intron (NM_023324, intron 1 of 6)	intron (NM_023324, intron 1 of 6)	9717	NM_023324	67245	Mm.28957	NM_023324	ENSMUSG00000020134	Peli1	2810468L03Rik|A930031K15Rik|AA409794|AI586297|D11Ertd676e	pellino 1	protein-coding
mm_93978.1	chr10	127341861	127341918	-	1	NA	promoter-TSS (NM_010296)	promoter-TSS (NM_010296)	-310	NM_010296	14632	Mm.391450	NM_010296	ENSMUSG00000025407	Gli1	AV235269|Zfp-5|Zfp5	GLI-Kruppel family member GLI1	protein-coding
mm_144859.1	chr18	36709207	36709224	+	1	NA	Intergenic	Intergenic	-13290	NM_172831	240216	Mm.252323	NM_172831	ENSMUSG00000044719	E230025N22Rik	EG240216	Riken cDNA E230025N22 gene	protein-coding
mm_43926.1	chr5	144855214	144855217	+	1	NA	intron (NM_001081362, intron 68 of 70)	intron (NM_001081362, intron 68 of 70)	41601	NR_106006	102465629		NR_106006	ENSMUSG00000098822	Mir7039	Gm27824|mmu-mir-7039	microRNA 7039	ncRNA
mm_100578.1	chr11	120767322	120767351	+	1	NA	Intergenic	Intergenic	16868	NM_009053	19719	Mm.871	NM_009053	ENSMUSG00000025158	Rfng	-	RFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	protein-coding
mm_110855.1	chr12	73287191	73287204	-	1	NA	promoter-TSS (NM_029580)	promoter-TSS (NM_029580)	349	NM_001037717	625098	Mm.32075	NM_001037717	ENSMUSG00000044712	Slc38a6	AW322671|EG625098	solute carrier family 38, member 6	protein-coding
mm_94488.1	chr11	6658511	6658574	+	1	NA	promoter-TSS (NM_019511)	promoter-TSS (NM_019511)	9	NM_019511	56089	Mm.39884	NM_019511	ENSMUSG00000041046	Ramp3	AI850306	receptor (calcitonin) activity modifying protein 3	protein-coding
mm_110333.1	chr12	35534974	35535058	-	1	NA	promoter-TSS (NM_013464)	promoter-TSS (NM_013464)	-27	NM_001314027	11622	Mm.341377	NM_013464	ENSMUSG00000019256	Ahr	Ah|Ahh|Ahre|In|bHLHe76	aryl-hydrocarbon receptor	protein-coding
mm_133156.1	chr16	70352259	70352274	+	1	NA	intron (NM_028803, intron 1 of 15)	intron (NM_028803, intron 1 of 15)	38317	NM_028803	74185	Mm.396102	NM_028803	ENSMUSG00000022707	Gbe1	2310045H19Rik|2810426P10Rik|D16Ertd536e	glucan (1,4-alpha-), branching enzyme 1	protein-coding
mm_123738.1	chr14	70184868	70184899	-	1	NA	exon (NM_001271407, exon 18 of 21)	exon (NM_001271407, exon 18 of 21)	-7211	NM_145978	213019	Mm.283968	NM_145978	ENSMUSG00000022090	Pdlim2	4732462F18Rik|Slim	PDZ and LIM domain 2	protein-coding
mm_90599.1	chr10	128322444	128322476	+	1	NA	promoter-TSS (NM_019953)	promoter-TSS (NM_019953)	1	NM_019953	56530	Mm.44220	NM_019953	ENSMUSG00000025381	Cnpy2	5330432A10Rik|AW229003|D10Bwg1546e|Tmem4|Zsig9	canopy FGF signaling regulator 2	protein-coding
mm_45487.1	chr5	71095928	71095965	-	1	NA	promoter-TSS (NM_008066)	promoter-TSS (NM_008066)	-97	NM_008066	14395	Mm.5304	NM_008066	ENSMUSG00000000560	Gabra2	C630048P16Rik|Gabra-2	gamma-aminobutyric acid (GABA) A receptor, subunit alpha 2	protein-coding
mm_116125.1	chr13	28951855	28951868	-	1	NA	exon (NM_009238, exon 1 of 1)	exon (NM_009238, exon 1 of 1)	1821	NM_009238	20677	Mm.240627	NM_009238	ENSMUSG00000076431	Sox4	AA682046|Sox-4	SRY (sex determining region Y)-box 4	protein-coding
mm_93265.1	chr10	95673465	95673485	-	1	NA	Intergenic	Intergenic	-109308	NM_027722	71207	Mm.24397	NM_027722	ENSMUSG00000020029	Nudt4	4933436C10Rik|DIPP2|DIPP2alpha|DIPP2beta|HDCMB47P	nudix (nucleoside diphosphate linked moiety X)-type motif 4	protein-coding
mm_168431.1	chr11	33755000	33755018	-	1	NA	intron (NM_001190885, intron 1 of 8)	LSU-rRNA_Hsa|rRNA|rRNA	88576	NM_027398	70357	Mm.252514	NM_027398	ENSMUSG00000053519	Kcnip1	KCHIP1|Kchip1.2	Kv channel-interacting protein 1	protein-coding
mm_38046.1	chr4	133967954	133968005	-	1	NA	promoter-TSS (NM_016957)	promoter-TSS (NM_016957)	12	NM_016957	15331	Mm.319660	NM_016957	ENSMUSG00000003038	Hmgn2	HMG-17|Hmg17	high mobility group nucleosomal binding domain 2	protein-coding
mm_137017.1	chr17	17838309	17838333	+	1	NA	exon (NM_001162909, exon 8 of 9)	exon (NM_001162909, exon 8 of 9)	7346	NM_001162909	75202	Mm.227456	NM_029205	ENSMUSG00000080316	Spaca6	4930546H06Rik|9530079D04Rik|B230206P06Rik|Ncrna00085|SPACA6A|let-7e|mir-125a|mir-99b	sperm acrosome associated 6	protein-coding
mm_103668.1	chr11	79087009	79087012	-	1	NA	intron (NM_013571, intron 1 of 17)	intron (NM_013571, intron 1 of 17)	59344	NM_013571	16706	Mm.4745	NM_013571	ENSMUSG00000018334	Ksr1	AW492498|B-KSR1|D11Bhm183e|D11Bhm184e|Ksr|RSU2|hb	kinase suppressor of ras 1	protein-coding
mm_59594.1	chr7	28137531	28137542	+	1	NA	exon (NM_001164655, exon 4 of 20)	exon (NM_001164655, exon 4 of 20)	8070	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_124537.1	chr14	122451264	122451270	-	1	NA	promoter-TSS (NR_033325)	promoter-TSS (NR_033325)	-121	NR_033326	328479	Mm.86095	NR_033325	ENSMUSG00000064052	Gm5089	6530402A20|C030005G22Rik|EG328479	predicted gene 5089	ncRNA
mm_163519.1	chr12	114896722	114896725	-	1	NA	Intergenic	Intergenic	-383029	NR_106063	102465664		NR_106063	ENSMUSG00000098357	Mir7094-2	Gm27508|mmu-mir-7094-2	microRNA 7094-2	ncRNA
mm_102031.1	chr11	51693463	51693466	-	1	NA	3' UTR (NM_175255, exon 23 of 23)	3' UTR (NM_175255, exon 23 of 23)	-4830	NM_025319	66050	Mm.35693	NM_025319	ENSMUSG00000007777	0610009B22Rik	-	RIKEN cDNA 0610009B22 gene	protein-coding
mm_51389.1	chr6	77245246	77245249	+	1	NA	3' UTR (NM_028880, exon 2 of 2)	3' UTR (NM_028880, exon 2 of 2)	2530	NM_028880	74342	Mm.292568	NM_028880	ENSMUSG00000060780	Lrrtm1	4632401D06Rik|AW125451	leucine rich repeat transmembrane neuronal 1	protein-coding
mm_55039.1	chr6	48987732	48987741	-	1	NA	exon (NM_172888, exon 1 of 5)	exon (NM_172888, exon 1 of 5)	875	NM_172888	243377	Mm.446302	NM_172888	ENSMUSG00000039215	Svs1	9530003A11	seminal vesicle secretory protein 1	protein-coding
mm_105474.1	chr11	105936483	105936490	-	1	NA	intron (NM_007805, intron 3 of 5)	intron (NM_007805, intron 3 of 5)	7661	NM_007805	13056	Mm.149403	NM_007805	ENSMUSG00000019590	Cyb561	-	cytochrome b-561	protein-coding
mm_23020.1	chr3	34590028	34590031	+	1	NA	intron (NR_015580, intron 2 of 4)	intron (NR_015580, intron 2 of 4)	29648	NR_015580	320478	Mm.444063	NR_015580	ENSMUSG00000105265	Sox2ot	B230215L15Rik	SOX2 overlapping transcript (non-protein coding)	ncRNA
mm_121456.1	chr14	120480203	120480208	+	1	NA	intron (NM_029519, intron 1 of 1)	intron (NM_029519, intron 1 of 1)	1744	NM_029519	76108	Mm.261448	NM_029519	ENSMUSG00000051615	Rap2a	5830461H18Rik	RAS related protein 2a	protein-coding
mm_57797.1	chr6	129284437	129284441	-	1	NA	Intergenic	MIRc|SINE|MIR	-9070	NM_001033122	12515	Mm.74745	NM_001033122	ENSMUSG00000030156	Cd69	5830438K24Rik|AI452015|AIM|VEA	CD69 antigen	protein-coding
mm_96555.1	chr11	68901539	68901633	+	1	NA	promoter-TSS (NM_009080)	promoter-TSS (NM_009080)	-3	NR_003373	100034726	Mm.3229	NR_003373	ENSMUSG00000062353	Gm15772	ENSMUSG00000062353|OTTMUSG00000026108	ribosomal protein L26 pseudogene	pseudo
mm_152408.1	chr19	10604354	10604367	-	1	NA	promoter-TSS (NM_145496)	promoter-TSS (NM_145496)	-102	NM_145496	225913	Mm.374868	NM_145496	ENSMUSG00000034371	Tkfc	BC021917|Dak	triokinase, FMN cyclase	protein-coding
mm_9752.1	chr1	180808674	180808676	-	1	NA	intron (NM_008210, intron 3 of 3)	intron (NM_008210, intron 3 of 3)	4930	NM_008210	15078	Mm.138832	NM_008210	ENSMUSG00000060743	H3f3a	H3.3A	H3 histone, family 3A	protein-coding
mm_84409.1	chr9	65556626	65556659	-	1	NA	exon (NM_153119, exon 6 of 6)	exon (NM_153119, exon 6 of 6)	23445	NM_153119	102595	Mm.247303	NM_153119	ENSMUSG00000050721	Plekho2	AI840980|Plekhq1	pleckstrin homology domain containing, family O member 2	protein-coding
mm_106624.1	chr11	120825156	120825183	-	1	NA	promoter-TSS (NM_007988)	promoter-TSS (NM_007988)	-622	NM_007988	14104	Mm.236443	NM_007988	ENSMUSG00000025153	Fasn	A630082H08Rik|FAS	fatty acid synthase	protein-coding
mm_153956.1	chr19	47692008	47692027	-	1	NA	promoter-TSS (NM_007732)	promoter-TSS (NM_007732)	25	NM_007732	12821	Mm.1225	NM_007732	ENSMUSG00000025064	Col17a1	BP180|Bpag|Bpag2	collagen, type XVII, alpha 1	protein-coding
mm_147902.1	chr18	65381658	65381680	-	1	NA	intron (NM_001037294, intron 1 of 12)	intron (NM_001037294, intron 1 of 12)	12219	NM_001037294	225638	Mm.296528	NM_001037294	ENSMUSG00000032845	Alpk2	Gm549|Hak	alpha-kinase 2	protein-coding
mm_143646.1	chr17	79355083	79355103	-	1	NA	promoter-TSS (NM_026514)	promoter-TSS (NM_026514)	-2	NM_026514	260409	Mm.140601	NM_026514	ENSMUSG00000036533	Cdc42ep3	3200001F04Rik|AA986861|Borg2|Cep3|UB1	CDC42 effector protein (Rho GTPase binding) 3	protein-coding
mm_117259.1	chr13	64368234	64368244	-	1	NA	intron (NM_009984, intron 2 of 7)	intron (NM_009984, intron 2 of 7)	2281	NM_009984	13039	Mm.930	NM_009984	ENSMUSG00000021477	Ctsl	1190035F06Rik|CatL|Ctsl1|MEP|fs|nkt	cathepsin L	protein-coding
mm_59115.1	chr7	19822959	19822967	+	1	NA	promoter-TSS (NM_033601)	promoter-TSS (NM_033601)	-208	NM_033601	12051	Mm.439658	NM_033601	ENSMUSG00000053175	Bcl3	AI528691|Bcl-3	B cell leukemia/lymphoma 3	protein-coding
mm_169785.1	chr16	11403384	11403387	+	1	NA	intron (NM_028964, intron 7 of 20)	intron (NM_028964, intron 7 of 20)	-2263	NM_001290148	74478	Mm.325831	NM_028964	ENSMUSG00000071669	Snx29	4933437K13Rik|ENSMUSG00000079738|Gm11170|Gm1737|Gm930|Rundc2a	sorting nexin 29	protein-coding
mm_38767.1	chr4	147904786	147904799	-	1	NA	promoter-TSS (NM_001285923)	promoter-TSS (NM_001285923)	-94	NM_001285923	170731	Mm.154312	NM_133201	ENSMUSG00000029020	Mfn2	D630023P19Rik|Fzo	mitofusin 2	protein-coding
mm_42668.1	chr5	119671254	119671273	+	1	NA	promoter-TSS (NM_011535)	promoter-TSS (NM_011535)	30	NM_011535	21386	Mm.219139	NM_011535	ENSMUSG00000018604	Tbx3	D5Ertd189e	T-box 3	protein-coding
mm_88558.1	chr10	79497157	79497164	+	1	NA	Intergenic	RLTR9E|LTR|ERVK	28202	NM_001104537	625029	Mm.469865	NM_001104537	ENSMUSG00000091381	Vmn2r83	EG625029	vomeronasal 2, receptor 83	protein-coding
mm_72639.1	chr8	84701431	84701497	+	1	NA	promoter-TSS (NM_008535)	promoter-TSS (NM_008535)	7	NM_008535	17095	Mm.4925	NM_008535	ENSMUSG00000034041	Lyl1	Lyl-1|bHLHa18	lymphoblastomic leukemia 1	protein-coding
mm_150306.1	chr19	34570640	34570644	+	1	NA	intron (NM_008332, intron 2 of 2)	intron (NM_008332, intron 2 of 2)	-12887	NM_010501	15959	Mm.426079	NM_010501	ENSMUSG00000074896	Ifit3	Ifi49|P49	interferon-induced protein with tetratricopeptide repeats 3	protein-coding
mm_108760.1	chr12	89089455	89089456	+	1	NA	intron (NM_172544, intron 2 of 19)	intron (NM_172544, intron 2 of 19)	136065	NM_172544	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding
mm_94965.1	chr11	30831290	30831298	+	1	NA	intron (NM_134013, intron 21 of 46)	intron (NM_134013, intron 21 of 46)	-54064	NM_175490	237716	Mm.338361	NM_175490	ENSMUSG00000043999	Gpr75	-	G protein-coupled receptor 75	protein-coding
mm_50667.1	chr6	51531374	51531377	+	1	NA	intron (NM_001127349, intron 1 of 6)	intron (NM_001127349, intron 1 of 6)	7472	NM_001127349	71982	Mm.294166	NM_028035	ENSMUSG00000038301	Snx10	2410004M09Rik	sorting nexin 10	protein-coding
mm_94580.1	chr11	11690314	11690329	+	1	NA	5' UTR (NM_001301865, exon 1 of 7)	5' UTR (NM_001301865, exon 1 of 7)	144	NM_001301863	22778	Mm.103545	NM_009578	ENSMUSG00000018654	Ikzf1	5832432G11Rik|Ikaros|LyF-1|Zfpn1a1|Znfn1a1|hlk-1|mKIAA4227	IKAROS family zinc finger 1	protein-coding
mm_48244.1	chr5	137786240	137786263	-	1	NA	5' UTR (NM_144913, exon 1 of 4)	5' UTR (NM_144913, exon 1 of 4)	450	NM_144913	231803	Mm.61193	NM_144913	ENSMUSG00000029726	Mepce	Bcdin3|D5Wsu46e	methylphosphate capping enzyme	protein-coding
mm_161159.1	chr13	27156776	27156776	+	1	NA	promoter-TSS (NM_172156)	promoter-TSS (NM_172156)	-23	NM_172156	215029	Mm.461202	NM_172156	ENSMUSG00000062201	Prl3d3	Ghd6|PL-Ig|Plig	prolactin family 3, subfamily d, member 3	protein-coding
mm_127310.1	chr15	100228314	100228341	+	1	NA	intron (NM_007497, intron 1 of 6)	CpG	468	NM_007497	11908	Mm.676	NM_007497	ENSMUSG00000023027	Atf1	-	activating transcription factor 1	protein-coding
mm_140501.1	chr17	4281604	4281612	-	1	NA	Intergenic	Intergenic	-159506	NR_045462	78043	Mm.398313	NR_045462		4930548J01Rik	1700113K09Rik	RIKEN cDNA 4930548J01 gene	ncRNA
mm_35552.1	chr4	41517281	41517292	-	1	NA	promoter-TSS (NM_001048005)	promoter-TSS (NM_001048005)	47	NM_001048005	73721	Mm.45614	NM_028624	ENSMUSG00000028441	1110017D15Rik	Cbe1|Smrp1	RIKEN cDNA 1110017D15 gene	protein-coding
mm_81608.1	chr9	110665434	110665442	+	1	NA	intron (NM_028312, intron 1 of 6)	RSINE1|SINE|B4	8935	NM_028312	72654	Mm.249115	NM_028312	ENSMUSG00000019659	Ccdc12	2700094L05Rik|C76605	coiled-coil domain containing 12	protein-coding
mm_59686.1	chr7	28441027	28441035	+	1	NA	promoter-TSS (NM_001039192)	promoter-TSS (NM_001039192)	94	NM_001039192	63986	Mm.194536	NM_022024	ENSMUSG00000060791	Gmfg	0610039G16Rik|2310057N07Rik|AI324845	glia maturation factor, gamma	protein-coding
mm_136989.1	chr17	17374520	17374541	+	1	NA	5' UTR (NM_025934, exon 1 of 10)	5' UTR (NM_025934, exon 1 of 10)	198	NM_025934	67045	Mm.35117	NM_025934	ENSMUSG00000023852	Riok2	2010110K24Rik|2410085M17Rik	RIO kinase 2 (yeast)	protein-coding
mm_57036.1	chr6	122339406	122339443	-	1	NA	intron (NM_001271579, intron 1 of 14)	CpG	233	NM_001042623	13619	Mm.6822	NM_007905	ENSMUSG00000040669	Phc1	AW557034|Edr|Edr1|Mph1|Rae-28|rae28	polyhomeotic-like 1 (Drosophila)	protein-coding
mm_142743.1	chr17	48409730	48409766	-	1	NA	promoter-TSS (NM_001289491)	promoter-TSS (NM_001289491)	72	NM_001110832	18044	Mm.4929	NM_010913	ENSMUSG00000023994	Nfya	AA407810|Cbf-b|SEZ-10|SEZ10	nuclear transcription factor-Y alpha	protein-coding
mm_10351.1	chr2	11689885	11689901	+	1	NA	3' UTR (NM_008367, exon 8 of 8)	3' UTR (NM_008367, exon 8 of 8)	-15400	NM_001271498	16169	Mm.200196	NM_008358	ENSMUSG00000023206	Il15ra	AA690181|IL-15RA	interleukin 15 receptor, alpha chain	protein-coding
mm_128870.1	chr15	72925712	72925723	-	1	NA	intron (NM_029640, intron 14 of 21)	intron (NM_029640, intron 14 of 21)	-115393	NR_002864	353342	Mm.440245	NR_002864	ENSMUSG00000106847	Peg13	-	paternally expressed 13	ncRNA
mm_34341.1	chr4	143413765	143413770	+	1	NA	intron (NM_172877, intron 1 of 4)	PB1D9|SINE|Alu	1341	NM_172877	242736	Mm.275953	NM_172877	ENSMUSG00000046862	Pramef8	4732496O08Rik|AU023234	PRAME family member 8	protein-coding
mm_77930.1	chr9	7353886	7353896	+	1	NA	intron (NM_001320077, intron 7 of 10)	B4A|SINE|B4	6517	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_172071.1	chr6	137280801	137280819	+	1	NA	intron (NM_001164401, intron 1 of 25)	GA-rich|Low_complexity|Low_complexity	28511	NM_011216	19277	Mm.186361	NM_011216	ENSMUSG00000030223	Ptpro	D28|GLEPP1|PTPBK|PTPROt|PTPU2|PTPoc|PTPphi|Ptpn15|R-PTP-O	protein tyrosine phosphatase, receptor type, O	protein-coding
mm_14638.1	chr2	136781882	136781888	+	1	NA	3' UTR (NM_001291056, exon 8 of 8)	3' UTR (NM_001291056, exon 8 of 8)	68435	NM_001291056	20614	Mm.45953	NM_011428	ENSMUSG00000027273	Snap25	Bdr|GENA70|SNAP-25|SUP|sp	synaptosomal-associated protein 25	protein-coding
mm_50899.1	chr6	57581061	57581115	+	1	NA	promoter-TSS (NM_025992)	promoter-TSS (NM_025992)	96	NM_025992	67138	Mm.297393	NM_025992	ENSMUSG00000029798	Herc6	1700121D12Rik|2510038N07Rik|4930427L17Rik|AI451296|CEB1|Herc5	hect domain and RLD 6	protein-coding
mm_119770.1	chr14	54174866	54174879	+	1	NA	Intergenic	Intergenic	79057	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_122540.1	chr14	47418222	47418232	-	1	NA	5' UTR (NM_144553, exon 1 of 19)	5' UTR (NM_144553, exon 1 of 19)	180	NM_144553	218977	Mm.240543	NM_144553	ENSMUSG00000037544	Dlgap5	C77459|C86398|Dap-5|Dlg7|Hurp|mKIAA0008	discs, large (Drosophila) homolog-associated protein 5	protein-coding
mm_137569.1	chr17	27840126	27840143	+	1	NA	promoter-TSS (NM_011432)	promoter-TSS (NM_011432)	47	NM_011432	20630	Mm.103949	NM_011432	ENSMUSG00000024217	Snrpc	Snrp1c|U1-C|U1C	U1 small nuclear ribonucleoprotein C	protein-coding
mm_93267.1	chr10	95722431	95722478	-	1	NA	Intergenic	Intergenic	-158287	NM_027722	71207	Mm.24397	NM_027722	ENSMUSG00000020029	Nudt4	4933436C10Rik|DIPP2|DIPP2alpha|DIPP2beta|HDCMB47P	nudix (nucleoside diphosphate linked moiety X)-type motif 4	protein-coding
mm_17627.1	chr2	31035517	31035551	-	1	NA	intron (NM_001038700, intron 13 of 14)	(TG)n|Simple_repeat|Simple_repeat	53255	NM_028846	74270	Mm.346654	NM_028846	ENSMUSG00000026854	Usp20	1700055M05Rik|AI467231|Vdu2	ubiquitin specific peptidase 20	protein-coding
mm_147878.1	chr18	64516548	64516565	-	1	NA	promoter-TSS (NM_027350)	promoter-TSS (NM_027350)	1	NM_027350	70223	Mm.29192	NM_027350	ENSMUSG00000024587	Nars	3010001M15Rik|AA960128|ASNRS|C78150	asparaginyl-tRNA synthetase	protein-coding
mm_34427.1	chr4	145434684	145434729	+	1	NA	Intergenic	L1_Mus3|LINE|L1	-29504	NR_002888	545700	Mm.389595	NR_002888	ENSMUSG00000052912	Smarca5-ps	9230115A19Rik|OTTMUSG00000011029	SWI/SNF related, matrix associated, actin depenent ragulator of chromatin, subfamily a, member 5, pseudogene	pseudo
mm_156820.1	chrX	164140547	164140562	+	1	NA	promoter-TSS (NM_027286)	promoter-TSS (NM_027286)	74	NM_027286	70008	Mm.13451	NM_027286	ENSMUSG00000015405	Ace2	2010305L05Rik	angiotensin I converting enzyme (peptidyl-dipeptidase A) 2	protein-coding
mm_62116.1	chr7	96644139	96644178	+	1	NA	exon (NM_001310762, exon 7 of 33)	exon (NM_001310762, exon 7 of 33)	157391	NR_045874	791381	Mm.402112	NR_045874	ENSMUSG00000053049	Gm15413	ENSMUSG00000053049|OTTMUSG00000021246	predicted gene 15413	ncRNA
mm_50487.1	chr6	48988625	48988631	+	1	NA	exon (NM_172888, exon 1 of 5)	exon (NM_172888, exon 1 of 5)	1767	NM_172888	243377	Mm.446302	NM_172888	ENSMUSG00000039215	Svs1	9530003A11	seminal vesicle secretory protein 1	protein-coding
mm_145119.1	chr18	44344429	44344433	+	1	NA	intron (NM_001033621, intron 4 of 9)	intron (NM_001033621, intron 4 of 9)	10357	NM_001033621	58916	Mm.143804	NM_001033621	ENSMUSG00000024471	Myot	5530402I04Rik|Ttid	myotilin	protein-coding
mm_61245.1	chr7	65803901	65803918	+	1	NA	promoter-TSS (NR_045301)	promoter-TSS (NR_045301)	-143	NR_045301	100503969	Mm.383527	NR_045301		1810008I18Rik	-	RIKEN cDNA 1810008I18 gene	ncRNA
mm_105343.1	chr11	102997526	102997542	-	1	NA	intron (NM_026551, intron 3 of 4)	intron (NM_026551, intron 3 of 4)	2387	NR_105896	102466988		NR_105896	ENSMUSG00000098613	Mir6931	Gm27303|mmu-mir-6931	microRNA 6931	ncRNA
mm_10435.1	chr2	14174493	14174509	+	1	NA	promoter-TSS (NM_001081310)	promoter-TSS (NM_001081310)	-23	NM_001081310	625286	Mm.158781	NM_001081310	ENSMUSG00000061531	Tmem236	2010003H20Rik|Fam23a|Gm613	transmembrane protein 236	protein-coding
mm_115300.1	chr13	112001902	112001924	+	1	NA	Intergenic	Intergenic	133977	NR_130345	102636620	Mm.402328	NR_130345	ENSMUSG00000086111	Gm15326	OTTMUSG00000020187	predicted gene 15326	ncRNA
mm_93909.1	chr10	127030790	127030812	-	1	NA	promoter-TSS (NM_025537)	promoter-TSS (NM_025537)	13	NM_025537	66399	Mm.29900	NM_025537	ENSMUSG00000040521	Tsfm	2310050B20Rik|9430024O13Rik|EF-TS|EF-Tsmt	Ts translation elongation factor, mitochondrial	protein-coding
mm_139615.1	chr17	57361160	57361172	+	1	NA	intron (NM_010130, intron 1 of 21)	intron (NM_010130, intron 1 of 21)	2480	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_72411.1	chr8	81779925	81779926	+	1	NA	intron (NM_001024617, intron 7 of 24)	RMER17B|LTR|ERVK	437363	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_56333.1	chr6	92642344	92642347	-	1	NA	intron (NM_001081146, intron 2 of 8)	(A)n|Simple_repeat|Simple_repeat	63839	NM_001081146	243548	Mm.248820	NM_001081146	ENSMUSG00000030020	Prickle2	6230400G14Rik|6720451F06Rik|mpk2	prickle planar cell polarity protein 2	protein-coding
mm_55411.1	chr6	65021922	65021935	-	1	NA	Intergenic	Intergenic	-20739	NM_007958	13990	Mm.99113	NM_007958	ENSMUSG00000029920	Smarcad1	AV081750|AW226546|D6Pas1|Etl1|mKIAA1122	SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1	protein-coding
mm_1956.1	chr1	86359639	86359692	+	1	NA	promoter-TSS (NM_010880)	promoter-TSS (NM_010880)	91	NR_015507	319336	Mm.389155	NR_015507	ENSMUSG00000073627	C130036L24Rik	ENSMUSG00000073627	RIKEN cDNA C130036L24 gene	ncRNA
mm_141520.1	chr17	31690425	31690426	-	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	12494	NM_001278570	12954	Mm.1228	NM_013501	ENSMUSG00000024041	Cryaa	Acry-1|Crya-1|Crya1|DAcry-1|lop18	crystallin, alpha A	protein-coding
mm_145500.1	chr18	60390927	60390944	+	1	NA	exon (NM_001146275, exon 3 of 3)	exon (NM_001146275, exon 3 of 3)	14906	NM_001146275	60440	Mm.261140	NM_021792	ENSMUSG00000054072	Iigp1	2900074L10Rik|AI046432|AW111922|Ifgga1|Iigp|Irga6	interferon inducible GTPase 1	protein-coding
mm_38635.1	chr4	142460399	142460412	-	1	NA	Intergenic	B3|SINE|B2	-221004	NM_001109685	71529	Mm.255986	NM_144531	ENSMUSG00000040606	Kazn	2310007B04Rik|9030409G11Rik|AI256607|AI666764|AW061099|Kaz|Kazrin	kazrin, periplakin interacting protein	protein-coding
mm_77186.1	chr8	111854239	111854266	-	1	NA	promoter-TSS (NM_011801)	promoter-TSS (NM_011801)	58	NM_011801	23837	Mm.279437	NM_011801	ENSMUSG00000031954	Cfdp1	AA408409|Bcnt|Bucentaur|Cfdp|cp27	craniofacial development protein 1	protein-coding
mm_7231.1	chr1	93428218	93428233	-	1	NA	exon (NM_133808, exon 10 of 28)	exon (NM_133808, exon 10 of 28)	17476	NM_001301364	110611	Mm.30012	NM_133808	ENSMUSG00000034088	Hdlbp	1110005P14Rik|AA960365|AI118566|D1Ertd101e	high density lipoprotein (HDL) binding protein	protein-coding
mm_152925.1	chr19	28011508	28011538	-	1	NA	promoter-TSS (NM_011265)	promoter-TSS (NM_011265)	-357	NM_011265	19726	Mm.313321	NM_011265	ENSMUSG00000040929	Rfx3	C230093O12Rik|MRFX3	regulatory factor X, 3 (influences HLA class II expression)	protein-coding
mm_12056.1	chr2	59314827	59314831	+	1	NA	intron (NM_175464, intron 9 of 20)	intron (NM_175464, intron 9 of 20)	71853	NR_040510	76676	Mm.110038	NR_040510	ENSMUSG00000087455	5330411J11Rik	-	RIKEN cDNA 5330411J11 gene	ncRNA
mm_93716.1	chr10	118889257	118889266	-	1	NA	Intergenic	Intergenic	-20358	NM_001014390	69181	Mm.45565	NM_001014390	ENSMUSG00000028630	Dyrk2	1810038L18Rik	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 2	protein-coding
mm_9026.1	chr1	166409774	166409849	-	1	NA	promoter-TSS (NM_001142948)	promoter-TSS (NM_001142948)	17	NM_175170	71592	Mm.192094	NM_175170	ENSMUSG00000040596	Pogk	9130401E23Rik|BASS2|mKIAA1513	pogo transposable element with KRAB domain	protein-coding
mm_25059.1	chr3	98852711	98852731	+	1	NA	exon (NM_001304800, exon 4 of 4)	exon (NM_001304800, exon 4 of 4)	7073	NM_001304800	15492	Mm.140811	NM_008293	ENSMUSG00000027871	Hsd3b1	3-beta-HSD I|D3Ertd383e	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1	protein-coding
mm_161921.1	chr18	73677821	73677821	-	1	NA	exon (NM_008540, exon 2 of 12)	exon (NM_008540, exon 2 of 12)	25920	NM_008540	17128	Mm.100399	NM_008540	ENSMUSG00000024515	Smad4	AW743858|D18Wsu70e|DPC4|Madh4	SMAD family member 4	protein-coding
mm_30104.1	chr3	138526228	138526254	-	1	NA	promoter-TSS (NM_007917)	promoter-TSS (NM_007917)	50	NM_007917	13684	Mm.3941	NM_007917	ENSMUSG00000028156	Eif4e	EG668879|Eif4e-ps|If4e|eIF-4E	eukaryotic translation initiation factor 4E	protein-coding
mm_37189.1	chr4	117474020	117474031	-	1	NA	intron (NM_025739, intron 2 of 14)	(A)n|Simple_repeat|Simple_repeat	23027	NM_025739	66743	Mm.318331	NM_025739	ENSMUSG00000028677	Rnf220	4732477A13|4931406I20Rik|5730503K05Rik|AV302541	ring finger protein 220	protein-coding
mm_119371.1	chr14	41122706	41122739	+	1	NA	3' UTR (NM_133653, exon 10 of 10)	3' UTR (NM_133653, exon 10 of 10)	-9066	NM_023134	20387	Mm.46062	NM_023134	ENSMUSG00000021789	Sftpa1	SP-A|Sftp-1|Sftp1	surfactant associated protein A1	protein-coding
mm_16861.1	chr2	11659793	11659809	-	1	NA	intron (NM_008367, intron 1 of 7)	ORR1B2|LTR|ERVL-MaLR	17009	NM_008367	16184	Mm.915	NM_008367	ENSMUSG00000026770	Il2ra	CD25|Il2r|Ly-43	interleukin 2 receptor, alpha chain	protein-coding
mm_127767.1	chr15	3219715	3219746	-	1	NA	Intergenic	Intergenic	-51037	NM_001042613	20363	Mm.392203	NM_009155	ENSMUSG00000064373	Selenop	AU018766|D15Ucla1|Se-P|Sepp1|selp	selenoprotein P	protein-coding
mm_46236.1	chr5	99218334	99218339	-	1	NA	3' UTR (NM_181318, exon 14 of 14)	3' UTR (NM_181318, exon 14 of 14)	34591	NM_181318	320292	Mm.259074	NM_145839	ENSMUSG00000089809	Rasgef1b	4732452O09Rik|GPIgamma4|Gpig4	RasGEF domain family, member 1B	protein-coding
mm_118648.1	chr14	21622559	21622562	+	1	NA	intron (NM_017479, intron 6 of 16)	intron (NM_017479, intron 6 of 16)	92016	NM_001013826	435391	Mm.295860	NM_001013826	ENSMUSG00000063821	Dupd1	EG435391	dual specificity phosphatase and pro isomerase domain containing 1	protein-coding
mm_27494.1	chr3	54915815	54915827	-	1	NA	promoter-TSS (NM_177854)	promoter-TSS (NM_177854)	66	NM_177854	329641	Mm.51187	NM_177854	ENSMUSG00000056306	Sertm1	6030405A18Rik	serine rich and transmembrane domain containing 1	protein-coding
mm_71106.1	chr8	35587829	35587850	+	1	NA	promoter-TSS (NM_001081279)	promoter-TSS (NM_001081279)	41	NM_001081279	52065	Mm.103246	NM_001081279	ENSMUSG00000070056	Mfhas1	2310066G09Rik|D8Ertd91e	malignant fibrous histiocytoma amplified sequence 1	protein-coding
mm_120365.1	chr14	64441095	64441096	+	1	NA	promoter-TSS (NM_001253715)	promoter-TSS (NM_001253715)	-55	NM_001253712	110265	Mm.26713	NM_026322	ENSMUSG00000054733	Msra	2310045J23Rik|6530413P12Rik|MSR-A	methionine sulfoxide reductase A	protein-coding
mm_134019.1	chr16	4880265	4880275	-	1	NA	promoter-TSS (NM_145359)	promoter-TSS (NM_145359)	-419	NM_145359	207740	Mm.268895	NM_145359	ENSMUSG00000039568	Ubald1	1500031H01Rik|BC013706|Fam100a	UBA-like domain containing 1	protein-coding
mm_95884.1	chr11	58104032	58104050	+	1	NA	promoter-TSS (NM_026949)	promoter-TSS (NM_026949)	-112	NM_026949	69125	Mm.28910	NM_026949	ENSMUSG00000020515	Cnot8	1500015I04Rik|1810022F04Rik|AA536816|AU015770|AU043059	CCR4-NOT transcription complex, subunit 8	protein-coding
mm_97743.1	chr11	80470819	80470829	+	1	NA	intron (NM_178616, intron 12 of 13)	B3A|SINE|B2	-6222	NM_009871	12569	Mm.142275	NM_009871	ENSMUSG00000048895	Cdk5r1	Cdk5r|D11Bwg0379e|p25|p35	cyclin-dependent kinase 5, regulatory subunit 1 (p35)	protein-coding
mm_61588.1	chr7	80024848	80024883	+	1	NA	promoter-TSS (NM_001146000)	promoter-TSS (NM_001146000)	51	NM_001146000	209225	Mm.290925	NM_175433	ENSMUSG00000048897	Zfp710	5430400N05Rik|9830165K13|AI324798|Znf710	zinc finger protein 710	protein-coding
mm_85782.1	chr9	109058760	109058771	-	1	NA	TTS (NM_026381)	TTS (NM_026381)	486	NM_001012236	22040	Mm.439964	NM_011637	ENSMUSG00000049734	Trex1	AU041952	three prime repair exonuclease 1	protein-coding
mm_48649.1	chr5	145856026	145856032	-	1	NA	intron (NM_007818, intron 12 of 12)	RMER17A2|LTR|ERVK	23825	NM_007818	13112	Mm.332844	NM_007818	ENSMUSG00000056035	Cyp3a11	AI256190|Cyp3a|IIIAm1|Pcn	cytochrome P450, family 3, subfamily a, polypeptide 11	protein-coding
mm_127771.1	chr15	3279310	3279312	-	1	NA	exon (NM_009155, exon 5 of 5)	exon (NM_009155, exon 5 of 5)	8334	NM_009155	20363	Mm.392203	NM_009155	ENSMUSG00000064373	Selenop	AU018766|D15Ucla1|Se-P|Sepp1|selp	selenoprotein P	protein-coding
mm_27825.1	chr3	79083597	79083616	-	1	NA	exon (NM_001099624, exon 15 of 24)	exon (NM_001099624, exon 15 of 24)	61281	NM_001310536	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_46159.1	chr5	96162079	96162097	-	1	NA	promoter-TSS (NM_178854)	promoter-TSS (NM_178854)	-98	NM_144910	231464	Mm.28374	NM_144910	ENSMUSG00000034724	Cnot6l	4932442K20Rik	CCR4-NOT transcription complex, subunit 6-like	protein-coding
mm_153831.1	chr19	46318124	46318147	-	1	NA	intron (NM_028627, intron 11 of 17)	CpG	8731	NM_001347454	73728	Mm.268532	NM_028627	ENSMUSG00000037126	Psd	1110007H17Rik|A930015K15|Efa6|Efa6a|Psdl|mKIAA2011	pleckstrin and Sec7 domain containing	protein-coding
mm_83346.1	chr9	44320230	44320290	-	1	NA	promoter-TSS (NM_027909)	promoter-TSS (NM_027909)	22	NM_027909	71764	Mm.491174	NM_027909	ENSMUSG00000032120	C2cd2l	1300006O23Rik|Tmem24	C2 calcium-dependent domain containing 2-like	protein-coding
mm_122188.1	chr14	31640892	31640980	-	1	NA	promoter-TSS (NM_019975)	promoter-TSS (NM_019975)	29	NM_019975	56794	Mm.38887	NM_019975	ENSMUSG00000021884	Hacl1	1600020H07Rik|Hpcl|Phyh2	2-hydroxyacyl-CoA lyase 1	protein-coding
mm_38292.1	chr4	136892486	136892593	-	1	NA	exon (NM_007574, exon 2 of 3)	exon (NM_007574, exon 2 of 3)	375	NM_007574	12262	Mm.439732	NM_007574	ENSMUSG00000036896	C1qc	AI385742|C1qg|Ciqc	complement component 1, q subcomponent, C chain	protein-coding
mm_33736.1	chr4	134118489	134118503	+	1	NA	intron (NR_045571, intron 8 of 13)	intron (NR_045571, intron 8 of 13)	10257	NM_080559	73723	Mm.22240	NM_080559	ENSMUSG00000028843	Sh3bgrl3	1110004L05Rik|AU022188	SH3 domain binding glutamic acid-rich protein-like 3	protein-coding
mm_124401.1	chr14	114945952	114945958	-	1	NA	promoter-TSS (NR_126551)	promoter-TSS (NR_126551)	-7	NR_126548	74982		NR_126548		1700100I10Rik	1700085D13Rik|4930481K08Rik	RIKEN cDNA 1700100I10 gene	ncRNA
mm_141304.1	chr17	28211548	28211553	-	1	NA	intron (NM_027185, intron 1 of 10)	MT2B|LTR|ERVL	3772	NM_027185	23853	Mm.204731	NM_027185	ENSMUSG00000002257	Def6	2410003F05Rik|6430538D02Rik|AV094905|Ibp|Slat|Slat2|Slat6	differentially expressed in FDCP 6	protein-coding
mm_76127.1	chr8	80879930	80879946	-	1	NA	5' UTR (NM_001301298, exon 1 of 11)	5' UTR (NM_001301298, exon 1 of 11)	541	NM_021356	14388	Mm.277409	NM_021356	ENSMUSG00000031714	Gab1	AA408973|AW107238	growth factor receptor bound protein 2-associated protein 1	protein-coding
mm_12590.1	chr2	73584836	73584891	+	1	NA	Intergenic	Intergenic	-4525	NM_007389	11435	Mm.4583	NM_007389	ENSMUSG00000027107	Chrna1	AI385656|AI608266|Achr-1|Acra	cholinergic receptor, nicotinic, alpha polypeptide 1 (muscle)	protein-coding
mm_166760.1	chr6	129236114	129236129	+	1	NA	intron (NR_040265, intron 1 of 2)	intron (NR_040265, intron 1 of 2)	1924	NR_040265	76432	Mm.261738	NR_040265	ENSMUSG00000097354	2310001H17Rik	AI646108	RIKEN cDNA 2310001H17 gene	ncRNA
mm_109616.1	chr12	112760720	112760742	+	1	NA	promoter-TSS (NM_178911)	promoter-TSS (NM_178911)	76	NM_178911	104759	Mm.203915	NM_178911	ENSMUSG00000052160	Pld4	AI132321|thss	phospholipase D family, member 4	protein-coding
mm_4241.1	chr1	171389101	171389115	+	1	NA	TTS (NM_027893)	TTS (NM_027893)	148	NM_001005508	226652	Mm.251048	NM_001005508	ENSMUSG00000048865	Arhgap30	6030405P05Rik|Gm102|mFLJ00267	Rho GTPase activating protein 30	protein-coding
mm_131419.1	chr16	14706882	14706903	+	1	NA	exon (NM_011415, exon 2 of 3)	exon (NM_011415, exon 2 of 3)	1033	NM_011415	20583	Mm.4272	NM_011415	ENSMUSG00000022676	Snai2	Slug|Slugh|Snail2	snail family zinc finger 2	protein-coding
mm_89656.1	chr10	97482391	97482404	+	1	NA	promoter-TSS (NM_007833)	promoter-TSS (NM_007833)	66	NM_007833	13179	Mm.56769	NM_007833	ENSMUSG00000019929	Dcn	DC|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding
mm_33296.1	chr4	128976984	128976986	+	1	NA	Intergenic	RMER6D|LTR|ERVK	-14530	NM_001301841	242669	Mm.215814	NM_172875	ENSMUSG00000028789	Azin2	4933429I20Rik|Adc|Azi2|B930082O19|ODC-p|Odcp	antizyme inhibitor 2	protein-coding
mm_55882.1	chr6	83527346	83527358	-	1	NA	exon (NM_009610, exon 2 of 9)	exon (NM_009610, exon 2 of 9)	8899	NM_009610	11468	Mm.292865	NM_009610	ENSMUSG00000059430	Actg2	ACTA3|Act-4|Act4|SMGA	actin, gamma 2, smooth muscle, enteric	protein-coding
mm_15346.1	chr2	156065739	156065760	+	1	NA	intron (NM_139151, intron 1 of 11)	CpG	536	NM_139151	245865	Mm.330713	NM_139151	ENSMUSG00000038180	Spag4	1700041K21Rik|MNCb-0953|Sun4|mKIAA4118	sperm associated antigen 4	protein-coding
mm_62112.1	chr7	96593362	96593377	+	1	NA	intron (NM_011858, intron 5 of 32)	B3A|SINE|B2	208180	NR_045874	791381	Mm.402112	NR_045874	ENSMUSG00000053049	Gm15413	ENSMUSG00000053049|OTTMUSG00000021246	predicted gene 15413	ncRNA
mm_123745.1	chr14	70191904	70191941	-	1	NA	intron (NM_001271409, intron 1 of 9)	CpG	324	NM_001271409	20410	Mm.5068	NM_011366	ENSMUSG00000022091	Sorbs3	SCAM-1|SH3P3|Sh3d4|vinexin-g	sorbin and SH3 domain containing 3	protein-coding
mm_73165.1	chr8	95017735	95017755	+	1	NA	promoter-TSS (NM_173036)	promoter-TSS (NM_173036)	53	NM_173036	54672	Mm.27995	NM_173036	ENSMUSG00000060470	Adgrg3	A030001G24Rik|AW214383|Gpr97|Pb1|Pb99	adhesion G protein-coupled receptor G3	protein-coding
mm_14166.1	chr2	126637096	126637098	+	1	NA	intron (NM_001271469, intron 3 of 3)	intron (NM_001271469, intron 3 of 3)	-18419	NM_008230	15186	Mm.18603	NM_008230	ENSMUSG00000027360	Hdc	AW108189|Hdc-a|Hdc-c|Hdc-e|Hdc-s	histidine decarboxylase	protein-coding
mm_157731.1	chrX	70477171	70477197	-	1	NA	promoter-TSS (NM_001033328)	promoter-TSS (NM_001033328)	-141	NM_001033328	236848	Mm.24569	NM_001033328	ENSMUSG00000073139	Tmem185a	-	transmembrane protein 185A	protein-coding
mm_110776.1	chr12	70371687	70371689	-	1	NA	intron (NR_037248, intron 2 of 4)	RLTR13B4|LTR|ERVK	-24074	NM_001110203	94090	Mm.184012	NM_053167	ENSMUSG00000021071	Trim9	-	tripartite motif-containing 9	protein-coding
mm_92475.1	chr10	78169727	78169792	-	1	NA	promoter-TSS (NM_138601)	promoter-TSS (NM_138601)	9	NM_138601	28295	Mm.268691	NM_138601	ENSMUSG00000053329	D10Jhu81e	C21orf33|ES1	DNA segment, Chr 10, Johns Hopkins University 81 expressed	protein-coding
mm_76643.1	chr8	93079937	93079946	-	1	NA	promoter-TSS (NM_001081372)	promoter-TSS (NM_001081372)	76	NM_001081372	382044	Mm.482549	NM_001081372	ENSMUSG00000078964	Ces1b	Gm5158	carboxylesterase 1B	protein-coding
mm_155075.1	chrX	46156078	46156079	+	1	NA	Intergenic	Intergenic	172833	NR_045440	75133	Mm.417818	NR_045440	ENSMUSG00000085157	4930515L19Rik	-	RIKEN cDNA 4930515L19 gene	ncRNA
mm_34321.1	chr4	141821739	141821751	+	1	NA	exon (NM_007919, exon 4 of 8)	exon (NM_007919, exon 4 of 8)	4260	NM_007919	13706	Mm.45316	NM_007919	ENSMUSG00000058579	Cela2a	Ela-2|Ela2|Ela2a	chymotrypsin-like elastase family, member 2A	protein-coding
mm_63611.1	chr7	128203599	128203607	+	1	NA	promoter-TSS (NR_045183)	promoter-TSS (NR_045183)	-275	NR_045183	70973	Mm.441564	NR_045183	ENSMUSG00000108354	4931431B13Rik	1700108I23Rik|AA536668	RIKEN cDNA 4931431B13 gene	ncRNA
mm_162351.1	chr1	55052283	55052293	+	1	NA	promoter-TSS (NM_001039710)	promoter-TSS (NM_001039710)	-482	NM_026424	67876	Mm.281019	NM_026424	ENSMUSG00000025981	Coq10b	1500041J02Rik|1700030I21Rik|9530077A17Rik|AV002237|AW742641	coenzyme Q10B	protein-coding
mm_81332.1	chr9	108517128	108517141	+	1	NA	promoter-TSS (NM_175143)	promoter-TSS (NM_175143)	47	NM_175143	69232	Mm.335449	NM_175143	ENSMUSG00000006673	Qrich1	2610028H07Rik	glutamine-rich 1	protein-coding
mm_30893.1	chr4	32291706	32291710	+	1	NA	Intergenic	Intergenic	-125727	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_4335.1	chr1	171855075	171855086	+	1	NA	TTS (NM_001252472)	TTS (NM_001252472)	15383	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_87544.1	chr10	53596937	53597004	+	1	NA	promoter-TSS (NM_025541)	promoter-TSS (NM_025541)	9	NM_025541	66403	Mm.272989	NM_025541	ENSMUSG00000019857	Asf1a	2310079C17Rik|C79052	anti-silencing function 1A histone chaperone	protein-coding
mm_86692.1	chr10	18431458	18431463	+	1	NA	intron (NM_173390, intron 1 of 6)	intron (NM_173390, intron 1 of 6)	23785	NM_173390	215819	Mm.297971	NM_173390	ENSMUSG00000039835	Nhsl1	5730409E15Rik|A630035H13Rik|A730096F01|BC013565|D10Bwg0940e|mKIAA1357	NHS-like 1	protein-coding
mm_30817.1	chr4	21776262	21776297	+	1	NA	promoter-TSS (NM_001290425)	promoter-TSS (NM_001290425)	9	NM_152825	77593	Mm.154306	NM_152825	ENSMUSG00000040455	Usp45	3110003C05Rik|4930550B20Rik|AI843191|Gcap7	ubiquitin specific petidase 45	protein-coding
mm_9697.1	chr1	178337741	178337761	-	1	NA	promoter-TSS (NM_016805)	promoter-TSS (NM_016805)	33	NM_016805	51810	Mm.86589	NM_016805	ENSMUSG00000039630	Hnrnpu	AA408410|AI256620|AL024194|AL024437|AW557595|C86794|Hnrpu|SAFA|Sp120|hnRNP U	heterogeneous nuclear ribonucleoprotein U	protein-coding
mm_137424.1	chr17	26252904	26252914	+	1	NA	promoter-TSS (NM_025881)	promoter-TSS (NM_025881)	-1	NM_025881	66978	Mm.440216	NM_025881	ENSMUSG00000024188	Luc7l	1810045C04Rik|2410018D03Rik	Luc7-like	protein-coding
mm_136015.1	chr16	76022300	76022315	-	1	NA	Intergenic	Intergenic	-100306	NR_040575	78215	Mm.243885	NR_040575		4930578N18Rik	-	RIKEN cDNA 4930578N18 gene	ncRNA
mm_12720.1	chr2	78214788	78214792	+	1	NA	Intergenic	Intergenic	-22757	NM_177843	329436	Mm.235448	NM_177843		Gm14461	A830093M07|OTTMUSG00000016703	predicted gene 14461	protein-coding
mm_116321.1	chr13	37827223	37827253	-	1	NA	promoter-TSS (NM_001039188)	promoter-TSS (NM_001039188)	-155	NM_001039188	68750	Mm.491109	NM_026830	ENSMUSG00000039087	Rreb1	1110037N09Rik|AA414966|B930013M22Rik	ras responsive element binding protein 1	protein-coding
mm_34252.1	chr4	141296264	141296267	+	1	NA	Intergenic	Intergenic	-4956	NM_010139	13836	Mm.2581	NM_010139	ENSMUSG00000006445	Epha2	AW545284|Eck|Myk2|Sek-2|Sek2	Eph receptor A2	protein-coding
mm_9740.1	chr1	180263466	180263497	-	1	NA	Intergenic	B1F2|SINE|Alu	-7181	NM_001128605	19165	Mm.330850	NM_011183	ENSMUSG00000010609	Psen2	ALG-3|Ad4h|Alg3|PS-2|PS2|Psnl2|STM2	presenilin 2	protein-coding
mm_163611.1	chr13	51833577	51833577	+	1	NA	Intergenic	Intergenic	-13098	NM_011817	23882	Mm.281298	NM_011817	ENSMUSG00000021453	Gadd45g	AI327420|C86281|CR6|DDIT2|OIG37	growth arrest and DNA-damage-inducible 45 gamma	protein-coding
mm_4584.1	chr1	178318811	178318865	+	1	NA	promoter-TSS (NM_025511)	promoter-TSS (NM_025511)	-315	NM_025511	66359	Mm.489720	NM_025511	ENSMUSG00000026500	Cox20	2310005N03Rik|Fam36a	COX20 Cox2 chaperone	protein-coding
mm_21852.1	chr2	165878933	165878949	-	1	NA	promoter-TSS (NM_001291158)	promoter-TSS (NM_001291158)	-504	NM_001291158	228880	Mm.227598	NM_027230	ENSMUSG00000039671	Zmynd8	1110013E22Rik|2010005I16Rik|3632413B07Rik|AI316811|AL024039|Prkcbp1|RACK7	zinc finger, MYND-type containing 8	protein-coding
mm_135885.1	chr16	64771126	64771136	-	1	NA	promoter-TSS (NM_026273)	promoter-TSS (NM_026273)	-192	NM_026273	67609	Mm.212157	NM_026273	ENSMUSG00000059920	4930453N24Rik	AI649104|din	RIKEN cDNA 4930453N24 gene	protein-coding
mm_1026.1	chr1	58754882	58754896	+	1	NA	3' UTR (NM_207653, exon 10 of 10)	3' UTR (NM_207653, exon 10 of 10)	24337	NM_001293805	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_152525.1	chr19	11321575	11321585	-	1	NA	exon (NM_001276398, exon 7 of 7)	exon (NM_001276398, exon 7 of 7)	13115	NM_001276398	109225	Mm.491251	NM_027836	ENSMUSG00000024672	Ms4a7	9130422I10Rik|A430103C15Rik|CD20l4|CFFMA	membrane-spanning 4-domains, subfamily A, member 7	protein-coding
mm_17126.1	chr2	24818991	24819001	-	1	NA	intron (NM_001012518, intron 16 of 26)	(TG)n|Simple_repeat|Simple_repeat	-55844	NM_007579	12287	Mm.4424	NM_007579	ENSMUSG00000004113	Cacna1b	AW050276|AW060892|AW822256|BIII|Cav2.2|Cchn1a|alpha(1B)	calcium channel, voltage-dependent, N type, alpha 1B subunit	protein-coding
mm_157577.1	chrX	52614240	52614260	-	1	NA	promoter-TSS (NM_016697)	promoter-TSS (NM_016697)	-276	NM_016697	14734	Mm.22515	NM_016697	ENSMUSG00000055653	Gpc3	OCI-5	glypican 3	protein-coding
mm_46581.1	chr5	107437764	107437781	-	1	NA	promoter-TSS (NM_001255991)	promoter-TSS (NM_001255991)	-225	NM_001255991	100503185	Mm.366650	NM_001255991	ENSMUSG00000111375	Btbd8	EG627196|Gm16115|OTTMUSG00000030610	BTB (POZ) domain containing 8	protein-coding
mm_53121.1	chr6	125113512	125113540	+	1	NA	exon (NM_145979, exon 23 of 39)	exon (NM_145979, exon 23 of 39)	16502	NR_106012	102466272		NR_106012	ENSMUSG00000098762	Mir7045	Gm27758|mmu-mir-7045	microRNA 7045	ncRNA
mm_17360.1	chr2	26640237	26640249	-	1	NA	promoter-TSS (NR_028571)	promoter-TSS (NR_028571)	1	NR_024068	72091	Mm.27103	NR_024068		Snhg7	2610002F03Rik|AI427062	small nucleolar RNA host gene 7	ncRNA
mm_70814.1	chr8	23095480	23095500	+	1	NA	intron (NR_102385, intron 11 of 45)	GSAT_MM|Satellite|Satellite	37231	NR_102385	11733	Mm.334444	NM_031158	ENSMUSG00000031543	Ank1	Ank-1|nb|pale	ankyrin 1, erythroid	protein-coding
mm_113858.1	chr13	47246982	47246990	+	1	NA	3' UTR (NM_146042, exon 8 of 8)	3' UTR (NM_146042, exon 8 of 8)	52983	NM_001170643	218215	Mm.287609	NM_146042	ENSMUSG00000038068	Rnf144b	BC025007|E130105P19Rik|Ibrdc2|Pir2	ring finger protein 144B	protein-coding
mm_123884.1	chr14	72709845	72709859	-	1	NA	5' UTR (NM_207636, exon 1 of 26)	5' UTR (NM_207636, exon 1 of 26)	151	NM_207636	319448	Mm.205421	NM_207636	ENSMUSG00000033487	Fndc3a	1700094E19Rik|D14Ertd453e|F730017H24Rik|Fndc3|sys	fibronectin type III domain containing 3A	protein-coding
mm_140695.1	chr17	13761442	13761452	-	1	NA	promoter-TSS (NM_022311)	promoter-TSS (NM_022311)	-53	NM_022311	21646	Mm.486358	NM_022311	ENSMUSG00000038347	Tcte2	AI429268|Tcte-2	t-complex-associated testis expressed 2	protein-coding
mm_54504.1	chr6	35510660	35510729	-	1	NA	3' UTR (NM_008098, exon 4 of 4)	3' UTR (NM_008098, exon 4 of 4)	29194	NM_008098	14489	Mm.182746	NM_008098	ENSMUSG00000029840	Mtpn	5033418D15Rik|Gcdp|V1	myotrophin	protein-coding
mm_106808.1	chr12	5896589	5896593	+	1	NA	Intergenic	Intergenic	520089	NR_015579	72669	Mm.10434	NM_028318		2810032G03Rik	AI461720	RIKEN cDNA 2810032G03 gene	ncRNA
mm_131311.1	chr16	11584509	11584513	+	1	NA	intron (NM_001290148, intron 8 of 13)	intron (NM_001290148, intron 8 of 13)	178863	NM_001290148	74478	Mm.325831	NM_028964	ENSMUSG00000071669	Snx29	4933437K13Rik|ENSMUSG00000079738|Gm11170|Gm1737|Gm930|Rundc2a	sorting nexin 29	protein-coding
mm_152457.1	chr19	10869758	10869798	-	1	NA	promoter-TSS (NM_133804)	promoter-TSS (NM_133804)	1	NM_133804	98170	Mm.490254	NM_133804	ENSMUSG00000024736	Tmem132a	6720481D13Rik|Hspa5bp1|Orai1|R74613	transmembrane protein 132A	protein-coding
mm_157849.1	chrX	74410217	74410233	-	1	NA	exon (NM_008062, exon 13 of 13)	exon (NM_008062, exon 13 of 13)	-14387	NM_001161421	16151	Mm.12967	NM_010547	ENSMUSG00000004221	Ikbkg	1110037D23Rik|AI848108|AI851264|AW124339|IKK[g]|NEMO	inhibitor of kappaB kinase gamma	protein-coding
mm_168481.1	chr11	49023459	49023474	+	1	NA	Intergenic	L1Md_F3|LINE|L1	-27267	NM_010999	18356	Mm.24769	NM_010999	ENSMUSG00000040328	Olfr56	IF7|MOR276-1	olfactory receptor 56	protein-coding
mm_57272.1	chr6	123289818	123289826	-	1	NA	promoter-TSS (NM_019948)	promoter-TSS (NM_019948)	49	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_131499.1	chr16	17336546	17336554	+	1	NA	exon (NM_001331047, exon 2 of 5)	exon (NM_001331047, exon 2 of 5)	5179	NM_001331047	15160	Mm.6609	NM_008223	ENSMUSG00000022766	Serpind1	AA985900|AI303446|HC-II|HCII|Hcf2	serine (or cysteine) peptidase inhibitor, clade D, member 1	protein-coding
mm_169966.1	chr17	12198999	12199013	+	1	NA	intron (NM_026644, intron 3 of 8)	intron (NM_026644, intron 3 of 8)	79722	NM_026644	68262	Mm.258300	NM_026644	ENSMUSG00000023827	Agpat4	1500003P24Rik	1-acylglycerol-3-phosphate O-acyltransferase 4 (lysophosphatidic acid acyltransferase, delta)	protein-coding
mm_148896.1	chr19	6909723	6909760	+	1	NA	promoter-TSS (NM_026306)	promoter-TSS (NM_026306)	43	NM_026306	67674	Mm.318804	NM_026306	ENSMUSG00000038812	Trmt112	0610038D11Rik|Trm112p	tRNA methyltransferase 11-2	protein-coding
mm_132661.1	chr16	41830534	41830536	+	1	NA	intron (NM_001347236, intron 1 of 6)	intron (NM_001347236, intron 1 of 6)	297193	NM_175548	268890	Mm.310524	NM_175548	ENSMUSG00000061080	Lsamp	5430428I19|AW046674|B130007O04Rik|D930023J12Rik|Lam|Lamp	limbic system-associated membrane protein	protein-coding
mm_13445.1	chr2	105162526	105162534	+	1	NA	intron (NM_144783, intron 5 of 9)	B4A|SINE|B4	36001	NM_144783	22431	Mm.389339	NM_144783	ENSMUSG00000016458	Wt1	D630046I19Rik|Wt-1	Wilms tumor 1 homolog	protein-coding
mm_121792.1	chr14	20082735	20082747	-	1	NA	intron (NM_026209, intron 1 of 1)	intron (NM_026209, intron 1 of 1)	431	NM_026209	67509	Mm.292423	NM_026209	ENSMUSG00000045107	Saysd1	1810063B07Rik|4930488P03Rik	SAYSVFN motif domain containing 1	protein-coding
mm_66615.1	chr7	45466873	45466883	-	1	NA	promoter-TSS (NM_007527)	promoter-TSS (NM_007527)	20	NM_007527	12028	Mm.19904	NM_007527	ENSMUSG00000003873	Bax	-	BCL2-associated X protein	protein-coding
mm_29390.1	chr3	108889991	108890031	-	1	NA	promoter-TSS (NM_177091)	promoter-TSS (NM_177091)	-3	NM_001165965	320181	Mm.244233	NM_177091	ENSMUSG00000045326	Fndc7	E230011A21Rik	fibronectin type III domain containing 7	protein-coding
mm_110498.1	chr12	54203823	54203838	-	1	NA	promoter-TSS (NM_028133)	promoter-TSS (NM_028133)	44	NM_028133	112407	Mm.133037	NM_028133	ENSMUSG00000035105	Egln3	2610021G09Rik|AI505553|AI648162|Hif-p4h-3|Phd3|SM-20	egl-9 family hypoxia-inducible factor 3	protein-coding
mm_37601.1	chr4	126752112	126752118	-	1	NA	intron (NM_011986, intron 1 of 6)	intron (NM_011986, intron 1 of 6)	1314	NM_011986	26562	Mm.206206	NM_011986	ENSMUSG00000028833	Ncdn	AU042419|MMS10-AE|Ms10ae|mKIAA0607|norbin	neurochondrin	protein-coding
mm_47883.1	chr5	134703338	134703353	-	1	NA	3' UTR (NM_007925, exon 37 of 37)	3' UTR (NM_007925, exon 37 of 37)	-14755	NM_010717	16885	Mm.15409	NM_010717	ENSMUSG00000029674	Limk1	KIZ-1|LIMK-1|Limk	LIM-domain containing, protein kinase	protein-coding
mm_78300.1	chr9	22475692	22475756	+	1	NA	promoter-TSS (NM_181316)	promoter-TSS (NM_181316)	9	NM_178415	319845	Mm.176725	NM_178415	ENSMUSG00000035919	Bbs9	E130103I17Rik	Bardet-Biedl syndrome 9 (human)	protein-coding
mm_140524.1	chr17	6317483	6317517	-	1	NA	promoter-TSS (NM_001166629)	promoter-TSS (NM_001166629)	-26	NM_001166629	100310872	Mm.381893	NM_001166629	ENSMUSG00000092074	Dynlt1a	-	dynein light chain Tctex-type 1A	protein-coding
mm_163041.1	chr11	54141870	54141872	+	1	NA	Intergenic	Intergenic	40947	NM_011031	18452	Mm.3705	NM_011031	ENSMUSG00000018906	P4ha2	AA407196|C76437|P4hl	procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha II polypeptide	protein-coding
mm_109035.1	chr12	104101143	104101157	+	1	NA	promoter-TSS (NM_172953)	promoter-TSS (NM_172953)	37	NM_172953	268591	Mm.73172	NM_172953	ENSMUSG00000041550	Serpina5	4933415L04|PAI-3|Pci	serine (or cysteine) peptidase inhibitor, clade A, member 5	protein-coding
mm_100150.1	chr11	116080607	116080621	+	1	NA	exon (NM_016852, exon 5 of 8)	exon (NM_016852, exon 5 of 8)	-2653	NM_001009573	70450	Mm.259460	NM_001009573	ENSMUSG00000057948	Unc13d	2610108D09Rik|Jinx|Munc13-4|mFLJ00067	unc-13 homolog D (C. elegans)	protein-coding
mm_91460.1	chr10	34096465	34096467	-	1	NA	promoter-TSS (NM_178908)	promoter-TSS (NM_178908)	53	NM_178908	103511	Mm.66334	NM_178908	ENSMUSG00000049872	Fam26e	BB146404	family with sequence similarity 26, member E	protein-coding
mm_129436.1	chr15	78495242	78495251	-	1	NA	promoter-TSS (NM_008368)	promoter-TSS (NM_008368)	-180	NM_008368	16185	Mm.35287	NM_008368	ENSMUSG00000068227	Il2rb	CD122|IL-15Rbeta|IL15Rbeta|Il-2/15Rbeta|Il-2Rbeta|p70	interleukin 2 receptor, beta chain	protein-coding
mm_122799.1	chr14	54550037	54550040	-	1	NA	intron (NM_145462, intron 2 of 9)	intron (NM_145462, intron 2 of 9)	4323	NM_145462	219072	Mm.202152	NM_145462	ENSMUSG00000022177	Haus4	9430093H08Rik|AU016300|D14Ertd500e	HAUS augmin-like complex, subunit 4	protein-coding
mm_154249.1	chr19	60766615	60766625	-	1	NA	exon (NM_010123, exon 19 of 22)	exon (NM_010123, exon 19 of 22)	7765	NR_034047	100217439		NR_034047		Snora19	MBI-51	small nucleolar RNA, H/ACA box 19	snoRNA
mm_160635.1	chr9	107710307	107710307	-	1	NA	intron (NM_011349, intron 1 of 17)	intron (NM_011349, intron 1 of 17)	168	NM_011349	20350	Mm.12903	NM_011349	ENSMUSG00000034684	Sema3f	Sema4|Semak	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F	protein-coding
mm_66151.1	chr7	31142628	31142632	-	1	NA	exon (NM_027898, exon 5 of 19)	exon (NM_027898, exon 5 of 19)	8420	NM_027898	52857	Mm.27366	NM_027898	ENSMUSG00000001248	Gramd1a	1300003M23Rik|AI415002|AW547240|D7Bwg0611e	GRAM domain containing 1A	protein-coding
mm_4956.1	chr1	191266814	191266836	+	1	NA	Intergenic	Intergenic	51293	NM_025424	66208	Mm.46444	NM_025424	ENSMUSG00000037499	Nenf	1110060M21Rik|SCIRP10|Spuf	neuron derived neurotrophic factor	protein-coding
mm_150801.1	chr19	44333319	44333333	+	1	NA	promoter-TSS (NM_183216)	promoter-TSS (NM_183216)	0	NM_183216	329065	Mm.313583	NM_183216	ENSMUSG00000050195	Scd4	ACOD4	stearoyl-coenzyme A desaturase 4	protein-coding
mm_14074.1	chr2	122771711	122771719	+	1	NA	promoter-TSS (NR_027888)	promoter-TSS (NR_027888)	2	NR_027888	59010	Mm.28986	NM_021507	ENSMUSG00000005803	Sqrdl	0610039J17Rik|4930557M22Rik|SQOR	sulfide quinone reductase-like (yeast)	protein-coding
mm_46387.1	chr5	104018432	104018434	-	1	NA	intron (NM_053262, intron 1 of 6)	intron (NM_053262, intron 1 of 6)	3363	NM_053262	114664	Mm.46019	NM_053262	ENSMUSG00000029311	Hsd17b11	Dhrs8|Pan1b|SDR2|retSDR2	hydroxysteroid (17-beta) dehydrogenase 11	protein-coding
mm_108010.1	chr12	73584838	73584851	+	1	NA	promoter-TSS (NM_008856)	promoter-TSS (NM_008856)	48	NM_008856	18755	Mm.341677	NM_008856	ENSMUSG00000021108	Prkch	Pkch	protein kinase C, eta	protein-coding
mm_37558.1	chr4	126163471	126163486	-	1	NA	promoter-TSS (NM_001162533)	promoter-TSS (NM_001162533)	-137	NM_001162533	66938	Mm.29813	NM_025856	ENSMUSG00000073758	Sh3d21	1700029G01Rik|AU019788	SH3 domain containing 21	protein-coding
mm_83731.1	chr9	51056976	51056996	-	1	NA	3' UTR (NM_001033534, exon 8 of 8)	3' UTR (NM_001033534, exon 8 of 8)	20108	NM_001033534	244864	Mm.335152	NM_001033534	ENSMUSG00000060594	Layn	E030012M19Rik|Gm511	layilin	protein-coding
mm_165140.1	chr2	14512592	14512594	+	1	NA	Intergenic	L1_Mus3|LINE|L1	-91713	NM_023116	12296	Mm.313930	NM_023116	ENSMUSG00000057914	Cacnb2	AW060387|CAB2|Cavbeta2|Cchb2	calcium channel, voltage-dependent, beta 2 subunit	protein-coding
mm_163474.1	chr12	103992391	103992393	+	1	NA	Intergenic	Intergenic	-2435	NM_001166350	380780	Mm.201338	NM_199314	ENSMUSG00000063232	Serpina11	Gm895	serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 11	protein-coding
mm_4590.1	chr1	178335907	178335923	+	1	NA	exon (NM_016805, exon 3 of 14)	exon (NM_016805, exon 3 of 14)	1869	NM_016805	51810	Mm.86589	NM_016805	ENSMUSG00000039630	Hnrnpu	AA408410|AI256620|AL024194|AL024437|AW557595|C86794|Hnrpu|SAFA|Sp120|hnRNP U	heterogeneous nuclear ribonucleoprotein U	protein-coding
mm_123050.1	chr14	55604424	55604436	-	1	NA	promoter-TSS (NM_001159418)	promoter-TSS (NM_001159418)	-149	NM_001159418	16391	Mm.2032	NM_008394	ENSMUSG00000002325	Irf9	Irf-9|Isgf3g|p48	interferon regulatory factor 9	protein-coding
mm_85899.1	chr9	111055959	111055980	-	1	NA	exon (NM_017466, exon 2 of 2)	exon (NM_017466, exon 2 of 2)	1275	NM_001302377	54199	Mm.7336	NM_017466	ENSMUSG00000043953	Ccrl2	1810047I05Rik|Ackr5|CCR11|Cmkbr1l2|E01|L-CCR	chemokine (C-C motif) receptor-like 2	protein-coding
mm_5447.1	chr1	36241086	36241089	-	1	NA	intron (NM_198899, intron 1 of 40)	intron (NM_198899, intron 1 of 40)	3215	NM_198899	320011	Mm.261022	NM_198899	ENSMUSG00000037470	Uggt1	0910001L17Rik|A930007H10Rik|AA589501|AI414429|AI448372|C820010P03Rik|GT|UGT1|Ugcgl1	UDP-glucose glycoprotein glucosyltransferase 1	protein-coding
mm_167411.1	chr8	105932612	105932635	+	1	NA	TTS (NM_173432)	TTS (NM_173432)	1239	NM_023182	109660	Mm.2745	NM_023182	ENSMUSG00000031896	Ctrl	0910001G08Rik|1810004D15Rik|AV005227|Ctra-1|Ctra1|chymopasin|mFLJ00366	chymotrypsin-like	protein-coding
mm_13183.1	chr2	93181252	93181259	+	1	NA	Intergenic	PB1D10|SINE|Alu	-6329	NM_001025246	277414	Mm.41033	NM_001025246	ENSMUSG00000068735	Trp53i11	Tp53i11	transformation related protein 53 inducible protein 11	protein-coding
mm_74590.1	chr8	11478619	11478668	-	1	NA	promoter-TSS (NM_011227)	promoter-TSS (NM_011227)	-144	NM_011227	19332	Mm.37632	NM_011227	ENSMUSG00000031504	Rab20	AA536966|D8Ertd350e	RAB20, member RAS oncogene family	protein-coding
mm_116076.1	chr13	27716730	27716741	-	1	NA	promoter-TSS (NM_011120)	promoter-TSS (NM_011120)	2	NM_011120	18814	Mm.3258	NM_011120	ENSMUSG00000021348	Prl7d1	Ghd19|PLF-RP|PRP|Plfr	prolactin family 7, subfamily d, member 1	protein-coding
mm_1216.1	chr1	62727122	62727142	+	1	NA	intron (NM_001077405, intron 2 of 15)	(CA)n|Simple_repeat|Simple_repeat	23815	NM_001077405	18187	Mm.266341	NM_010939	ENSMUSG00000025969	Nrp2	1110048P06Rik|Np-2|Np2|Npn-2|Npn2	neuropilin 2	protein-coding
mm_49475.1	chr6	29526691	29526724	+	1	NA	promoter-TSS (NM_012057)	promoter-TSS (NM_012057)	82	NM_012057	27056	Mm.6479	NM_012057	ENSMUSG00000029771	Irf5	AW491843|mirf5	interferon regulatory factor 5	protein-coding
mm_14299.1	chr2	128967779	128967811	+	1	NA	5' UTR (NM_178404, exon 1 of 12)	5' UTR (NM_178404, exon 1 of 12)	393	NM_178404	78751	Mm.26377	NM_178404	ENSMUSG00000042851	Zc3h6	4631426G04Rik|4833425H18Rik|AU024389|AW060453|Zc3hdc6|mKIAA2035	zinc finger CCCH type containing 6	protein-coding
mm_121242.1	chr14	103056325	103056335	+	1	NA	3' UTR (NM_008392, exon 5 of 5)	3' UTR (NM_008392, exon 5 of 5)	9318	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_46879.1	chr5	113844067	113844088	-	1	NA	3' UTR (NM_011779, exon 11 of 11)	3' UTR (NM_011779, exon 11 of 11)	-13576	NM_009151	20345	Mm.332590	NM_009151	ENSMUSG00000048163	Selplg	CD162|Psgl-1|Psgl1|Selp1|Selpl	selectin, platelet (p-selectin) ligand	protein-coding
mm_54406.1	chr6	31563883	31563883	-	1	NA	promoter-TSS (NM_013723)	promoter-TSS (NM_013723)	54	NM_013723	27205	Mm.89918	NM_013723	ENSMUSG00000025608	Podxl	AW121214|Ly102|PC|PCLP-1|Pclp1	podocalyxin-like	protein-coding
mm_4625.1	chr1	179546409	179546433	+	1	NA	promoter-TSS (NM_146105)	promoter-TSS (NM_146105)	-108	NM_146105	226744	Mm.87662	NM_146105	ENSMUSG00000038949	Cnst	9630058J23Rik	consortin, connexin sorting protein	protein-coding
mm_122971.1	chr14	54974720	54974732	-	1	NA	TTS (NR_030607)	TTS (NR_030607)	1050	NR_030607	100124433		NR_030607	ENSMUSG00000077928	Mir208b	Mirn208b|mir-208b	microRNA 208b	ncRNA
mm_34348.1	chr4	144529226	144529232	+	1	NA	exon (NM_198662, exon 4 of 4)	exon (NM_198662, exon 4 of 4)	9407	NM_198662	381572	Mm.184290	NM_198662	ENSMUSG00000028593	9430007A20Rik	Aadacl4|Gm1034	RIKEN cDNA 9430007A20 gene	protein-coding
mm_48671.1	chr5	146009083	146009090	-	1	NA	intron (NR_030782, intron 1 of 11)	MTD|LTR|ERVL-MaLR	531	NM_019792	56388	Mm.301900	NM_019792	ENSMUSG00000029630	Cyp3a25	AI327008	cytochrome P450, family 3, subfamily a, polypeptide 25	protein-coding
mm_97404.1	chr11	77853607	77853654	+	1	NA	intron (NM_001291214, intron 36 of 38)	intron (NM_001291214, intron 36 of 38)	40242	NM_008952	19193	Mm.8543	NM_008952	ENSMUSG00000017453	Pipox	LPIPOX|Pso	pipecolic acid oxidase	protein-coding
mm_41265.1	chr5	89028130	89028134	+	1	NA	intron (NM_001197147, intron 3 of 25)	intron (NM_001197147, intron 3 of 25)	140872	NM_018760	54403	Mm.41044	NM_018760	ENSMUSG00000060961	Slc4a4	AI835705|NBC|NBC1	solute carrier family 4 (anion exchanger), member 4	protein-coding
mm_124535.1	chr14	122451131	122451150	-	1	NA	promoter-TSS (NR_033325)	promoter-TSS (NR_033325)	6	NR_033326	328479	Mm.86095	NR_033325	ENSMUSG00000064052	Gm5089	6530402A20|C030005G22Rik|EG328479	predicted gene 5089	ncRNA
mm_83463.1	chr9	45264177	45264190	-	1	NA	intron (NR_136903, intron 4 of 5)	intron (NR_136903, intron 4 of 5)	2524	NR_106054	102466803		NR_106054	ENSMUSG00000098361	Mir7086	Gm27643|mmu-mir-7086	microRNA 7086	ncRNA
mm_166016.1	chr4	121084145	121084147	-	1	NA	intron (NM_172700, intron 3 of 9)	U1|snRNA|snRNA	14097	NM_172700	230709	Mm.34399	NM_172700	ENSMUSG00000043207	Zmpste24	A530043O15Rik|D030046F19|FACE1|Face-1|MADB|STE24|Ste24p	zinc metallopeptidase, STE24	protein-coding
mm_40828.1	chr5	72905050	72905055	+	1	NA	Intergenic	Intergenic	-9310	NM_001113423	75991	Mm.121285	NM_153567	ENSMUSG00000036087	Slain2	5033405K12Rik|8030444K12Rik|AI596370	SLAIN motif family, member 2	protein-coding
mm_57322.1	chr6	124733122	124733145	-	1	NA	promoter-TSS (NM_013545)	promoter-TSS (NM_013545)	21	NM_013545	15170	Mm.271799	NM_013545	ENSMUSG00000004266	Ptpn6	70Z-SHP|Hcph|PTPTY-42|Ptp1C|SH-PTP1|SHP-1|hcp|me	protein tyrosine phosphatase, non-receptor type 6	protein-coding
mm_129269.1	chr15	76925407	76925437	-	1	NA	promoter-TSS (NM_172817)	promoter-TSS (NM_172817)	26	NM_172817	239546	Mm.183650	NM_172817	ENSMUSG00000054967	Zfp647	6030449J21|Es492|Znf250	zinc finger protein 647	protein-coding
mm_161398.1	chr14	118676894	118676894	-	1	NA	promoter-TSS (NM_001163675)	promoter-TSS (NM_001163675)	37	NM_001163675	239273	Mm.40537	NM_001033336	ENSMUSG00000032849	Abcc4	ABCC4-N1|D630049P08Rik|MOATB|MRP4	ATP-binding cassette, sub-family C (CFTR/MRP), member 4	protein-coding
mm_126279.1	chr15	79209280	79209294	+	1	NA	intron (NR_029470, intron 2 of 4)	intron (NR_029470, intron 2 of 4)	-19886	NM_008837	18693	Mm.259464	NM_008837	ENSMUSG00000068206	Pick1	Prkcabp	protein interacting with C kinase 1	protein-coding
mm_37012.1	chr4	112774842	112774854	-	1	NA	promoter-TSS (NM_177668)	promoter-TSS (NM_177668)	13	NM_177668	230613	Mm.122553	NM_177668	ENSMUSG00000048766	Skint10	A030001H23Rik|Gm570	selection and upkeep of intraepithelial T cells 10	protein-coding
mm_45516.1	chr5	72504530	72504551	-	1	NA	promoter-TSS (NM_001122756)	promoter-TSS (NM_001122756)	0	NM_001122756	53419	Mm.332425	NM_016869	ENSMUSG00000005220	Corin	AV273130|Lrp4	corin	protein-coding
mm_168371.1	chr11	19409457	19409469	+	1	NA	Intergenic	MMETn-int|LTR|ERVK	344188	NR_046037	74059	Mm.292321	NR_046037	ENSMUSG00000086025	4933406G16Rik	-	RIKEN cDNA 4933406G16 gene	ncRNA
mm_83225.1	chr9	42264227	42264282	-	1	NA	promoter-TSS (NM_172769)	promoter-TSS (NM_172769)	46	NM_172769	235293	Mm.32700	NM_172769	ENSMUSG00000032018	Sc5d	A830037K02|A830073K23Rik|Sc5dl	sterol-C5-desaturase	protein-coding
mm_122995.1	chr14	54991600	54991646	-	1	NA	intron (NM_080728, intron 7 of 40)	intron (NM_080728, intron 7 of 40)	2926	NM_080728	140781	Mm.457983	NM_080728	ENSMUSG00000053093	Myh7	B-MHC|MyHC-I|Myhc-b|Myhcb|beta-MHC	myosin, heavy polypeptide 7, cardiac muscle, beta	protein-coding
mm_110760.1	chr12	70111966	70112039	-	1	NA	promoter-TSS (NM_001286080)	promoter-TSS (NM_001286080)	33	NM_001286080	18080	Mm.244047	NM_008697	ENSMUSG00000021068	Nin	3110068G20Rik|AI385615|AU024711|mKIAA1565	ninein	protein-coding
mm_137777.1	chr17	29492998	29493009	+	1	NA	intron (NM_008842, intron 4 of 5)	intron (NM_008842, intron 4 of 5)	1958	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_79433.1	chr9	56041863	56041880	+	1	NA	promoter-TSS (NM_001278274)	promoter-TSS (NM_001278274)	26	NM_011992	26611	Mm.1782	NM_011992	ENSMUSG00000032320	Rcn2	AA408742|Tcbp49	reticulocalbin 2	protein-coding
mm_61988.1	chr7	91090874	91090887	+	1	NA	promoter-TSS (NM_011807)	promoter-TSS (NM_011807)	94	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_99320.1	chr11	101442441	101442468	+	1	NA	5' UTR (NM_011289, exon 1 of 5)	5' UTR (NM_011289, exon 1 of 5)	209	NM_011289	19942	Mm.340658	NM_011289	ENSMUSG00000063316	Rpl27	-	ribosomal protein L27	protein-coding
mm_172445.1	chr7	3002327	3002343	+	1	NA	Intergenic	RLTR45|LTR|ERVK	-125811	NR_001583	73949	Mm.55687	NR_001583	ENSMUSG00000107956	Speer9-ps1	4930415A14Rik|SPEER-9|Speer9-ps	spermatogenesis associated glutamate (E)-rich protein 9, pseudogene 1	pseudo
mm_71022.1	chr8	33516731	33516744	+	1	NA	Intergenic	Intergenic	32426	NR_033589	628431	Mm.376526	NR_033589		Hmgb1-rs17	Hmg1-rs17	high mobility group box 1, related sequence 17	pseudo
mm_9578.1	chr1	174027300	174027324	-	1	NA	exon (NM_172648, exon 3 of 7)	exon (NM_172648, exon 3 of 7)	4443	NM_172648	226695	Mm.425061	NM_172648	ENSMUSG00000054203	Ifi205	D3|D3cDNA|Ifi205a	interferon activated gene 205	protein-coding
mm_140839.1	chr17	23670925	23670941	-	1	NA	intron (NM_001008425, intron 1 of 12)	intron (NM_001008425, intron 1 of 12)	-2675	NM_181821	353502	Mm.359030	NM_181821	ENSMUSG00000023904	Hcfc1r1	HPIP	host cell factor C1 regulator 1 (XPO1-dependent)	protein-coding
mm_136061.1	chr16	84585058	84585067	-	1	NA	Intergenic	Intergenic	-94727	NR_040537	78023	Mm.243853	NR_040537		4930529L06Rik	-	RIKEN cDNA 4930529L06 gene	ncRNA
mm_92252.1	chr10	70599272	70599282	-	1	NA	promoter-TSS (NM_178621)	promoter-TSS (NM_178621)	14	NM_178621	70911	Mm.19825	NM_178621	ENSMUSG00000037747	Phyhipl	4921522K17Rik|AI267048	phytanoyl-CoA hydroxylase interacting protein-like	protein-coding
mm_164675.1	chr17	46124228	46124230	+	1	NA	intron (NM_026768, intron 3 of 5)	intron (NM_026768, intron 3 of 5)	13225	NM_026768	68565	Mm.287443	NM_026768	ENSMUSG00000023967	Mrps18a	1110004O20Rik|C79712	mitochondrial ribosomal protein S18A	protein-coding
mm_113354.1	chr13	31884188	31884200	+	1	NA	intron (NM_146041, intron 9 of 10)	intron (NM_146041, intron 9 of 10)	77548	NM_008592	17300	Mm.12949	NM_008592	ENSMUSG00000050295	Foxc1	FREAC3|Fkh1|Mf1|Mf4|ch|fkh-1|frkhda	forkhead box C1	protein-coding
mm_31498.1	chr4	53246207	53246213	+	1	NA	promoter-TSS (NR_040665)	promoter-TSS (NR_040665)	14	NR_040665	78180	Mm.243847	NR_040665	ENSMUSG00000086947	4930522O17Rik	-	RIKEN cDNA 4930522O17 gene	ncRNA
mm_109045.1	chr12	104263118	104263129	+	1	NA	promoter-TSS (NM_001199940)	promoter-TSS (NM_001199940)	1	NM_001199940	628900	Mm.436602	NM_001199940	ENSMUSG00000079014	Serpina3i	2B2|EG628900|Gm6930	serine (or cysteine) peptidase inhibitor, clade A, member 3I	protein-coding
mm_44315.1	chr5	9300125	9300138	-	1	NA	intron (NM_172706, intron 1 of 21)	intron (NM_172706, intron 1 of 21)	33938	NM_172706	231014	Mm.130063	NM_172706	ENSMUSG00000056004	9330182L06Rik	Eig121l	RIKEN cDNA 9330182L06 gene	protein-coding
mm_89967.1	chr10	111473254	111473262	+	1	NA	promoter-TSS (NM_015781)	promoter-TSS (NM_015781)	66	NM_015781	53605	Mm.290407	NM_015781	ENSMUSG00000058799	Nap1l1	AA407126|AI256722|D10Ertd68e|NAP-1	nucleosome assembly protein 1-like 1	protein-coding
mm_87940.1	chr10	62893168	62893179	+	1	NA	Intergenic	Intergenic	-13159	NM_001253857	52463	Mm.17774	NM_027384	ENSMUSG00000047146	Tet1	2510010B09Rik|AA517754|BB001228|Cxxc6|D10Ertd17e|LCX|mKIAA1676	tet methylcytosine dioxygenase 1	protein-coding
mm_64535.1	chr7	144175514	144175527	+	1	NA	promoter-TSS (NM_001113373)	promoter-TSS (NM_001113373)	0	NM_001113373	210274	Mm.483624	NM_001081370	ENSMUSG00000037541	Shank2	ProSAP1|mKIAA1022	SH3/ankyrin domain gene 2	protein-coding
mm_110897.1	chr12	75631201	75631228	-	1	NA	non-coding (NR_038063, exon 1 of 1)	non-coding (NR_038063, exon 1 of 1)	535	NR_038063	665931	Mm.341719	NR_038063		Rplp2-ps1	Gm7852	ribosomal protein, large P2, pseudogene 1	pseudo
mm_18487.1	chr2	62601506	62601525	-	1	NA	exon (NM_027835, exon 13 of 16)	exon (NM_027835, exon 13 of 16)	-27494	NM_007986	14089	Mm.41816	NM_007986	ENSMUSG00000000392	Fap	SIMP	fibroblast activation protein	protein-coding
mm_75874.1	chr8	70764759	70764782	-	1	NA	exon (NM_023065, exon 3 of 8)	exon (NM_023065, exon 3 of 8)	1893	NM_023065	65972	Mm.30241	NM_023065	ENSMUSG00000031838	Ifi30	GILT|IP30	interferon gamma inducible protein 30	protein-coding
mm_152714.1	chr19	17394491	17394516	-	1	NA	intron (NM_019437, intron 1 of 3)	CpG	460	NM_019437	54391	Mm.7013	NM_019437	ENSMUSG00000024712	Rfk	0610038L10Rik|AF031381|KOI-4	riboflavin kinase	protein-coding
mm_31373.1	chr4	47386235	47386265	+	1	NA	promoter-TSS (NM_001312869)	promoter-TSS (NM_001312869)	34	NM_001312869	21812	Mm.197552	NM_009370	ENSMUSG00000007613	Tgfbr1	ALK5|AU017191|Alk-5|ESK2|TGFR-1|TbetaR-I|TbetaRI	transforming growth factor, beta receptor I	protein-coding
mm_97090.1	chr11	73160309	73160341	+	1	NA	promoter-TSS (NM_033321)	promoter-TSS (NM_033321)	-205	NM_033321	94045	Mm.156893	NM_033321	ENSMUSG00000005950	P2rx5	P2X5	purinergic receptor P2X, ligand-gated ion channel, 5	protein-coding
mm_153196.1	chr19	34524991	34525023	-	1	NA	intron (NM_021460, intron 1 of 9)	intron (NM_021460, intron 1 of 9)	2467	NM_001111100	16889	Mm.157545	NM_021460	ENSMUSG00000024781	Lipa	AA960673|Lal|Lip-1|Lip1	lysosomal acid lipase A	protein-coding
mm_107150.1	chr12	23903146	23903187	+	1	NA	Intergenic	Intergenic	194103	NM_001256489	66808	Mm.379124	NM_001256489	ENSMUSG00000073158	9030624G23Rik	-	RIKEN cDNA 9030624G23 gene	protein-coding
mm_21017.1	chr2	152397734	152397776	-	1	NA	5' UTR (NM_011438, exon 1 of 1)	5' UTR (NM_011438, exon 1 of 1)	291	NM_011438	20667	Mm.28424	NM_011438	ENSMUSG00000051817	Sox12	2010205A02Rik	SRY (sex determining region Y)-box 12	protein-coding
mm_87682.1	chr10	59230073	59230076	+	1	NA	Intergenic	AT_rich|Low_complexity|Low_complexity	8152	NM_172939	268301	Mm.3036	NM_172939	ENSMUSG00000098188	Sowahc	4921515A04Rik|9430099J10Rik|Ankrd57|C820004L04Rik	sosondowah ankyrin repeat domain family member C	protein-coding
mm_88294.1	chr10	75278311	75278315	+	1	NA	intron (NM_153406, intron 12 of 15)	ORR1A4|LTR|ERVL-MaLR	-38564	NM_009630	11540	Mm.333734	NM_009630	ENSMUSG00000020178	Adora2a	A2AAR|A2aR|AA2AR	adenosine A2a receptor	protein-coding
mm_49731.1	chr6	34709576	34709586	+	1	NA	5' UTR (NM_145575, exon 1 of 12)	5' UTR (NM_145575, exon 1 of 12)	137	NM_145575	109624	Mm.308134	NM_145575	ENSMUSG00000029761	Cald1	4833423D12Rik|AI195384|AV071549|AW536160|C920027I18Rik	caldesmon 1	protein-coding
mm_50717.1	chr6	52211788	52211793	+	1	NA	intron (NR_015611, intron 1 of 2)	CpG	1277	NM_010452	15400	Mm.71533	NM_010452	ENSMUSG00000079560	Hoxa3	Hox-1.5|Mo-10	homeobox A3	protein-coding
mm_19765.1	chr2	105399373	105399379	-	1	NA	promoter-TSS (NM_009037)	promoter-TSS (NM_009037)	-57	NM_009037	19672	Mm.4876	NM_009037	ENSMUSG00000005973	Rcn1	Rcn	reticulocalbin 1	protein-coding
mm_72199.1	chr8	72571180	72571226	+	1	NA	promoter-TSS (NM_172396)	promoter-TSS (NM_172396)	-155	NM_172396	66818	Mm.22565	NM_172396	ENSMUSG00000044600	Smim7	9130011J15Rik	small integral membrane protein 7	protein-coding
mm_70221.1	chr7	145110718	145110719	-	1	NA	Intergenic	B4A|SINE|B4	97401	NR_033626	100040049	Mm.102235	NR_033626	ENSMUSG00000109305	1810010D01Rik	Gm2572	RIKEN cDNA 1810010D01 gene	ncRNA
mm_1645.1	chr1	74601442	74601520	+	1	NA	promoter-TSS (NM_021313)	promoter-TSS (NM_021313)	26	NM_175031	269209	Mm.310974	NM_175031	ENSMUSG00000033276	Stk36	1700112N14Rik|B930045J24|FU|Fused|mKIAA1278	serine/threonine kinase 36	protein-coding
mm_49751.1	chr6	34746426	34746437	+	1	NA	intron (NM_001347100, intron 5 of 13)	GA-rich|Low_complexity|Low_complexity	-34001	NM_001289657	76223	Mm.150047	NM_178630	ENSMUSG00000038836	Agbl3	2900053G10Rik|4930431N21Rik|6530406M24Rik|CCP3	ATP/GTP binding protein-like 3	protein-coding
mm_166848.1	chr7	19696703	19696715	+	1	NA	exon (NM_009696, exon 4 of 4)	exon (NM_009696, exon 4 of 4)	1689	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_124506.1	chr14	121879725	121879732	-	1	NA	promoter-TSS (NR_130999)	promoter-TSS (NR_130999)	-320	NR_130999	78312	Mm.188743	NR_130999	ENSMUSG00000102112	1810041H14Rik	-	RIKEN cDNA 1810041H14 gene	ncRNA
mm_149785.1	chr19	23140823	23140841	+	1	NA	promoter-TSS (NM_010638)	promoter-TSS (NM_010638)	-394	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_64002.1	chr7	140137950	140137972	+	1	NA	intron (NM_199301, intron 1 of 10)	intron (NM_199301, intron 1 of 10)	397	NM_199301	212508	Mm.296088	NM_199301	ENSMUSG00000039018	Mtg1	Gm169|Gtpbp7	mitochondrial ribosome-associated GTPase 1	protein-coding
mm_86936.1	chr10	24223605	24223611	+	1	NA	promoter-TSS (NM_021509)	promoter-TSS (NM_021509)	91	NM_021509	59012	Mm.285934	NM_021509	ENSMUSG00000020000	Moxd1	3230402N08Rik|MNCb-5203	monooxygenase, DBH-like 1	protein-coding
mm_69449.1	chr7	133015502	133015519	-	1	NA	promoter-TSS (NM_001170744)	promoter-TSS (NM_001170744)	-263	NM_001170744	13017	Mm.246240	NM_009980	ENSMUSG00000030970	Ctbp2	AA407280|D7Ertd45e|Gtrgeo6|Ribeye	C-terminal binding protein 2	protein-coding
mm_155691.1	chrX	94234595	94234604	+	1	NA	promoter-TSS (NM_153165)	promoter-TSS (NM_153165)	-331	NM_001039059	236904	Mm.115533	NM_153165	ENSMUSG00000043929	Klhl15	6330500C13Rik	kelch-like 15	protein-coding
mm_27311.1	chr3	50366591	50366625	-	1	NA	3' UTR (NM_011990, exon 12 of 12)	3' UTR (NM_011990, exon 12 of 12)	77005	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_76981.1	chr8	106893535	106893545	-	1	NA	promoter-TSS (NM_011574)	promoter-TSS (NM_011574)	53	NM_145412	214987	Mm.490308	NM_145412	ENSMUSG00000046691	Chtf8	5830457O10Rik|Ctf8|Derpc	CTF8, chromosome transmission fidelity factor 8	protein-coding
mm_82749.1	chr9	26806385	26806461	-	1	NA	promoter-TSS (NM_153803)	promoter-TSS (NM_153803)	-6	NM_153803	244757	Mm.293696	NM_153803	ENSMUSG00000036395	Glb1l2	-	galactosidase, beta 1-like 2	protein-coding
mm_35854.1	chr4	49408043	49408045	-	1	NA	intron (NM_145368, intron 1 of 4)	intron (NM_145368, intron 1 of 4)	107	NM_145368	209186	Mm.35071	NM_145368	ENSMUSG00000060317	Acnat2	C730036D15Rik	acyl-coenzyme A amino acid N-acyltransferase 2	protein-coding
mm_125174.1	chr15	31565411	31565425	+	1	NA	Intergenic	Intergenic	-3494	NM_181588	69574	Mm.28108	NM_181588	ENSMUSG00000022235	Cmbl	2310016A09Rik	carboxymethylenebutenolidase-like (Pseudomonas)	protein-coding
mm_51196.1	chr6	71271673	71271743	+	1	NA	promoter-TSS (NM_145568)	promoter-TSS (NM_145568)	37	NR_106192	102465900		NR_106192	ENSMUSG00000098623	Mir8112	Gm27739|mmu-mir-8112	microRNA 8112	ncRNA
mm_72885.1	chr8	89041689	89041714	+	1	NA	intron (NM_021390, intron 2 of 3)	CpG	2461	NM_021390	58198	Mm.214361	NM_021390	ENSMUSG00000031665	Sall1	Msal-3	sal-like 1 (Drosophila)	protein-coding
mm_58943.1	chr7	18472386	18472388	+	1	NA	Intergenic	RMER17A|LTR|ERVK	11762	NM_001029893	574429	Mm.296754	NM_001029893	ENSMUSG00000070799	Psg26	EG574429|cea14	pregnancy-specific glycoprotein 26	protein-coding
mm_99205.1	chr11	101022934	101022937	+	1	NA	intron (NM_001243050, intron 5 of 20)	intron (NM_001243050, intron 5 of 20)	-7405	NR_105893	102466767		NR_105893	ENSMUSG00000098415	Mir6928	Gm27728|mmu-mir-6928	microRNA 6928	ncRNA
mm_33049.1	chr4	123016633	123016639	+	1	NA	promoter-TSS (NM_025873)	promoter-TSS (NM_025873)	39	NM_025873	66966	Mm.235030	NM_025873	ENSMUSG00000028653	Trit1	2310075G14Rik|AI314189|AI314635|AV099619|IPT|MOD5	tRNA isopentenyltransferase 1	protein-coding
mm_23609.1	chr3	65527802	65527844	+	1	NA	promoter-TSS (NM_178892)	promoter-TSS (NM_178892)	-624	NM_178892	99929	Mm.246398	NM_178892	ENSMUSG00000034640	Tiparp	ARTD14|AW558171|PARP7	TCDD-inducible poly(ADP-ribose) polymerase	protein-coding
mm_92555.1	chr10	79766958	79766976	-	1	NA	promoter-TSS (NM_144528)	promoter-TSS (NM_144528)	-15	NR_027505	70294	Mm.466670	NM_144528	ENSMUSG00000035890	Rnf126	2610010O19Rik	ring finger protein 126	protein-coding
mm_169875.1	chr16	37654387	37654387	-	1	NA	promoter-TSS (NM_026610)	promoter-TSS (NM_026610)	-19	NM_026610	68194	Mm.379154	NM_026610	ENSMUSG00000022820	Ndufb4	0610006N12Rik|1300010H20Rik	NADH dehydrogenase (ubiquinone) 1 beta subcomplex 4	protein-coding
mm_68162.1	chr7	103812218	103812225	-	1	NA	TTS (NM_016956)	TTS (NM_016956)	1702	NM_016956	15130	Mm.288567	NM_016956		Hbb-b2	AI036344|Hbb2|Hbbt2|beta2	hemoglobin, beta adult minor chain	protein-coding
mm_40172.1	chr5	35893431	35893473	+	1	NA	5' UTR (NM_027373, exon 1 of 17)	5' UTR (NM_027373, exon 1 of 17)	133	NM_027373	70292	Mm.125167	NM_027373	ENSMUSG00000029094	Afap1	2600003E23Rik|9630044L16Rik|AI848729|Afap|mKIAA3018	actin filament associated protein 1	protein-coding
mm_60076.1	chr7	34021480	34021483	+	1	NA	promoter-TSS (NM_009596)	promoter-TSS (NM_009596)	-86	NM_009596	11354	Mm.8025	NM_009596	ENSMUSG00000066583	Scgb1b27	Abp|Abpa|Abpa27|Sal-1|Tcp	secretoglobin, family 1B, member 27	protein-coding
mm_52560.1	chr6	116208031	116208114	+	1	NA	promoter-TSS (NM_026585)	promoter-TSS (NM_026585)	39	NM_026585	28006	Mm.28524	NM_026585	ENSMUSG00000024104	Washc2	A130095H06|C530005J20Rik|D6Wsu116e|Fam21	WASH complex subunit 2	protein-coding
mm_155834.1	chrX	100774791	100774807	+	1	NA	5' UTR (NM_001177779, exon 1 of 14)	5' UTR (NM_001177779, exon 1 of 14)	304	NM_001177779	53310	Mm.4615	NM_016747	ENSMUSG00000000881	Dlg3	Dlgh3|SAP102|mKIAA1232	discs, large homolog 3 (Drosophila)	protein-coding
mm_88499.1	chr10	77837666	77837674	+	1	NA	TTS (NM_001024709)	TTS (NM_001024709)	1723	NM_001024709	544710	Mm.441890	NM_001024709		Krtap10-10	EG544710	keratin associated protein 10-10	protein-coding
mm_45955.1	chr5	90462769	90462803	-	1	NA	exon (NM_009654, exon 3 of 15)	exon (NM_009654, exon 3 of 15)	1916	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_146024.1	chr18	69519811	69519824	+	1	NA	intron (NM_013685, intron 5 of 19)	intron (NM_013685, intron 5 of 19)	174096	NM_001083967	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding
mm_152019.1	chr19	6015515	6015528	-	1	NA	promoter-TSS (NM_007600)	promoter-TSS (NM_007600)	-274	NM_007600	12333	Mm.6221	NM_007600	ENSMUSG00000024942	Capn1	Capa-1|Capa1|mu-calpin	calpain 1	protein-coding
mm_21579.1	chr2	164237215	164237221	-	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	1123	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_115468.1	chr13	119457135	119457138	+	1	NA	3' UTR (NM_001079849, exon 11 of 11)	3' UTR (NM_001079849, exon 11 of 11)	-5623	NM_001113550	67392	Mm.390641	NM_026127	ENSMUSG00000062822	4833420G17Rik	2210017J06Rik|5730533D17Rik|AW107518|C85193	RIKEN cDNA 4833420G17 gene	protein-coding
mm_99817.1	chr11	108587132	108587136	+	1	NA	intron (NM_029606, intron 19 of 27)	intron (NM_029606, intron 19 of 27)	-95475	NM_145688	76380	Mm.344071	NM_029586	ENSMUSG00000020728	Cep112	1700001M19Rik|1700029K01Rik|8430407H02Rik|AV043680|AV207351|Ccdc46|Macoco	centrosomal protein 112	protein-coding
mm_12647.1	chr2	74729830	74729833	+	1	NA	TTS (NM_010469)	TTS (NM_010469)	3761	NR_029566	387144		NR_029566	ENSMUSG00000065500	Mir10b	Mirn10b|mir-10b|mmu-mir-10b	microRNA 10b	ncRNA
mm_23146.1	chr3	39364564	39364565	+	1	NA	Intergenic	Lx10|LINE|L1	477624	NM_183221	329628	Mm.316210	NM_183221	ENSMUSG00000046743	Fat4	6030410K14Rik|9430004M15	FAT atypical cadherin 4	protein-coding
mm_32972.1	chr4	120095114	120095154	+	1	NA	exon (NM_010657, exon 4 of 9)	exon (NM_010657, exon 4 of 9)	-66072	NM_007902	13615	Mm.284855	NM_007902	ENSMUSG00000028635	Edn2	ET-2|PPET2|VIC	endothelin 2	protein-coding
mm_2739.1	chr1	128259440	128259468	+	1	NA	exon (NM_026390, exon 6 of 13)	exon (NM_026390, exon 6 of 13)	15273	NM_026390	67812	Mm.293321	NM_026390	ENSMUSG00000026353	Ubxn4	1300013G12Rik|Ubxd2|mKIAA0242	UBX domain protein 4	protein-coding
mm_121444.1	chr14	120430315	120430379	+	1	NA	3' UTR (NM_207515, exon 8 of 8)	3' UTR (NM_207515, exon 8 of 8)	-48114	NM_029519	76108	Mm.261448	NM_029519	ENSMUSG00000051615	Rap2a	5830461H18Rik	RAS related protein 2a	protein-coding
mm_84977.1	chr9	85327290	85327304	-	1	NA	promoter-TSS (NM_001160378)	promoter-TSS (NM_001160378)	-147	NM_001160379	212943	Mm.74610	NM_001160378	ENSMUSG00000032265	Fam46a	BAP014|D930050G01Rik	family with sequence similarity 46, member A	protein-coding
mm_129985.1	chr15	86051281	86051305	-	1	NA	Intergenic	MER3|DNA|hAT-Charlie	-6402	NM_172611	223752	Mm.24442	NM_172611	ENSMUSG00000035900	Gramd4	9930016O13	GRAM domain containing 4	protein-coding
mm_121847.1	chr14	20631732	20631735	-	1	NA	Intergenic	Intergenic	-13379	NM_030180	78787	Mm.301173	NM_030180	ENSMUSG00000034235	Usp54	4930429G18Rik|AI115571|C030002J06Rik	ubiquitin specific peptidase 54	protein-coding
mm_33496.1	chr4	130823648	130823652	+	1	NA	3' UTR (NM_011520, exon 5 of 5)	3' UTR (NM_011520, exon 5 of 5)	31113	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_46835.1	chr5	113310713	113310727	-	1	NA	promoter-TSS (NM_001254731)	promoter-TSS (NM_001254731)	66	NM_001162965	52850	Mm.200203	NM_172718	ENSMUSG00000042216	Sgsm1	2410098H20Rik|AA408781|D5Bwg1524e|E130107M15|NuIP|Rutbc2	small G protein signaling modulator 1	protein-coding
mm_134651.1	chr16	21995456	21995472	-	1	NA	promoter-TSS (NM_153404)	promoter-TSS (NM_153404)	78	NM_001289582	239759	Mm.33192	NM_153404	ENSMUSG00000044626	Liph	C130037N08Rik|D16Wsu119e|H06|Lpdlr|P3|PLA1B|lpd1|lpd2|mPA-PLA1	lipase, member H	protein-coding
mm_4252.1	chr1	171408180	171408197	+	1	NA	exon (NM_001005508, exon 12 of 12)	exon (NM_001005508, exon 12 of 12)	-3125	NM_001305678	22278	Mm.8	NM_009480	ENSMUSG00000026641	Usf1	bHLHb11	upstream transcription factor 1	protein-coding
mm_171247.1	chr3	78559647	78559648	-	1	NA	Intergenic	ERVB7_1-LTR_MM|LTR|ERVK	585240	NM_001310536	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_134241.1	chr16	12945895	12945907	-	1	NA	Intergenic	Lx8|LINE|L1	134511	NR_040507	75493	Mm.396146	NR_040507	ENSMUSG00000101565	1700003L19Rik	-	RIKEN cDNA 1700003L19 gene	ncRNA
mm_128324.1	chr15	38061605	38061607	-	1	NA	intron (NM_001112721, intron 1 of 58)	intron (NM_001112721, intron 1 of 58)	17248	NM_001112721	70790	Mm.476840	NM_027553	ENSMUSG00000037487	Ubr5	Edd|Edd1	ubiquitin protein ligase E3 component n-recognin 5	protein-coding
mm_111289.1	chr12	85455208	85455218	-	1	NA	Intergenic	Intergenic	-18688	NM_010234	14281	Mm.246513	NM_010234	ENSMUSG00000021250	Fos	D12Rfj1|c-fos|cFos	FBJ osteosarcoma oncogene	protein-coding
mm_173176.1	chrX	50469084	50469084	-	1	NA	Intergenic	RLTR10|LTR|ERVK	-42590	NM_146292	258289	Mm.451653	NM_146292	ENSMUSG00000048173	Olfr1324	MOR128-2	olfactory receptor 1324	protein-coding
mm_72632.1	chr8	84664244	84664257	+	1	NA	Intergenic	CpG	-1398	NM_010499	15936	Mm.399	NM_010499	ENSMUSG00000053560	Ier2	AI317238|Ch1|Pip92	immediate early response 2	protein-coding
mm_160533.1	chr9	39019677	39019677	-	1	NA	promoter-TSS (NM_146747)	promoter-TSS (NM_146747)	-138	NM_146747	258742	Mm.271535	NM_146747	ENSMUSG00000058820	Olfr146	M15|MOR171-10	olfactory receptor 146	protein-coding
mm_88234.1	chr10	71347737	71347763	+	1	NA	promoter-TSS (NM_001347191)	promoter-TSS (NM_001347191)	-13	NM_001347191	69718	Mm.245867	NM_027184	ENSMUSG00000060733	Ipmk	2410017C19Rik|AA408208|Impk	inositol polyphosphate multikinase	protein-coding
mm_152126.1	chr19	6999431	6999441	-	1	NA	TTS (NM_153597)	TTS (NM_153597)	3305	NR_027351	107328	Mm.391161	NM_153597	ENSMUSG00000047656	Trpt1	AU079016|AW045591|Tpt1|Tpt1h	tRNA phosphotransferase 1	protein-coding
mm_137927.1	chr17	32536556	32536573	+	1	NA	promoter-TSS (NM_024442)	promoter-TSS (NM_024442)	-65	NM_024442	70101	Mm.30504	NM_024442	ENSMUSG00000048440	Cyp4f16	2310021J05Rik|AI746515	cytochrome P450, family 4, subfamily f, polypeptide 16	protein-coding
mm_26025.1	chr3	135439055	135439063	+	1	NA	promoter-TSS (NR_030689)	promoter-TSS (NR_030689)	300	NM_025356	66105	Mm.49884	NM_025356	ENSMUSG00000078578	Ube2d3	1100001F19Rik|9430029A22Rik|AA414951	ubiquitin-conjugating enzyme E2D 3	protein-coding
mm_2534.1	chr1	106998589	106998601	+	1	NA	exon (NM_172852, exon 6 of 8)	exon (NM_172852, exon 6 of 8)	17611	NM_172852	241196	Mm.110886	NM_172852	ENSMUSG00000048775	Serpinb13	5430417G24|HUR7|HURPIN|PI13|headpin	serine (or cysteine) peptidase inhibitor, clade B (ovalbumin), member 13	protein-coding
mm_149630.1	chr19	17222477	17222488	+	1	NA	3' UTR (NM_181348, exon 20 of 20)	3' UTR (NM_181348, exon 20 of 20)	117023	NM_001136484	14537	Mm.244825	NM_010265	ENSMUSG00000038843	Gcnt1	5630400D21Rik|B130048E03|C2 GlcNAcT|C2GNT|IGnT	glucosaminyl (N-acetyl) transferase 1, core 2	protein-coding
mm_48172.1	chr5	137154062	137154071	-	1	NA	Intergenic	Intergenic	-37859	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_158755.1	chrX	166457873	166457901	-	1	NA	exon (NM_019773, exon 3 of 3)	exon (NM_019773, exon 3 of 3)	17132	NM_001313722	66226	Mm.279752	NM_025432	ENSMUSG00000079317	Trappc2	1110066L09Rik|1810064C02Rik|AW496358|MIP-2A|Sedl|TRS20	trafficking protein particle complex 2	protein-coding
mm_165578.1	chr3	27317087	27317097	+	1	NA	promoter-TSS (NM_009425)	promoter-TSS (NM_009425)	15	NM_009425	22035	Mm.1062	NM_009425	ENSMUSG00000039304	Tnfsf10	A330042I21Rik|AI448571|APO-2L|Ly81|TL2|Tnlg6a|Trail	tumor necrosis factor (ligand) superfamily, member 10	protein-coding
mm_172547.1	chr8	100030486	100030503	+	1	NA	Intergenic	Intergenic	613820	NR_132435	234624	Mm.124595	NM_175479	ENSMUSG00000052479	A330008L17Rik	-	RIKEN cDNA A330008L17 gene	ncRNA
mm_23950.1	chr3	84858822	84858826	+	1	NA	intron (NM_001177773, intron 1 of 13)	L1MA6|LINE|L1	-5321	NM_001177774	50754	Mm.196475	NM_080428	ENSMUSG00000028086	Fbxw7	1110001A17Rik|AGO|Cdc4|Fbw7|Fbwd6|Fbx30|Fbxo30|Fbxw6|SEL-10	F-box and WD-40 domain protein 7	protein-coding
mm_13139.1	chr2	92183776	92183867	+	1	NA	promoter-TSS (NM_138755)	promoter-TSS (NM_138755)	-361	NM_138755	192285	Mm.330408	NM_138755	ENSMUSG00000058318	Phf21a	80kDa|Bhc|Bhc80|D030065N23Rik|PFTF1	PHD finger protein 21A	protein-coding
mm_150886.1	chr19	45150787	45150814	+	1	NA	promoter-TSS (NM_021901)	promoter-TSS (NM_021901)	85	NM_021901	21908	Mm.391203	NM_021901	ENSMUSG00000025215	Tlx1	Hox-11|Hox11|Tlx-1	T cell leukemia, homeobox 1	protein-coding
mm_144147.1	chr18	4995010	4995014	+	1	NA	Intergenic	Intergenic	-51577	NM_153153	225115	Mm.136791	NM_153153	ENSMUSG00000024236	Svil	AU024053|B430302E16Rik	supervillin	protein-coding
mm_117923.1	chr13	99434002	99434006	-	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-21178	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_107913.1	chr12	70997534	70997539	+	1	NA	intron (NR_045055, intron 3 of 3)	intron (NR_045055, intron 3 of 3)	18287	NR_045056	73204	Mm.363770	NR_045055	ENSMUSG00000085622	3110056K07Rik	4921536K06Rik	RIKEN cDNA 3110056K07 gene	ncRNA
mm_18750.1	chr2	73386364	73386382	-	1	NA	5' UTR (NM_001276443, exon 1 of 17)	5' UTR (NM_001276443, exon 1 of 17)	107	NM_001276443	68526	Mm.451014	NM_001080707	ENSMUSG00000041762	Gpr155	1110017O10Rik|DEPDC3|F730029F15Rik|PGR22	G protein-coupled receptor 155	protein-coding
mm_61763.1	chr7	82771926	82771955	+	1	NA	intron (NM_175317, intron 18 of 19)	intron (NM_175317, intron 18 of 19)	-16296	NR_046004	77800	Mm.444811	NR_046004	ENSMUSG00000086690	4933406J10Rik	A930009F24Rik	RIKEN cDNA 4933406J10 gene	ncRNA
mm_3899.1	chr1	161704866	161704871	+	1	NA	Intergenic	Intergenic	83627	NM_001205243	14103	Mm.3355	NM_010177	ENSMUSG00000000817	Fasl	APT1LG1|CD178|CD95-L|CD95L|Fas-L|Faslg|Tnfsf6|Tnlg1a|gld	Fas ligand (TNF superfamily, member 6)	protein-coding
mm_84260.1	chr9	62536968	62536986	-	1	NA	promoter-TSS (NM_175484)	promoter-TSS (NM_175484)	67	NM_175484	235431	Mm.335229	NM_175484	ENSMUSG00000041729	Coro2b	CLIPINC|E130012P22Rik	coronin, actin binding protein, 2B	protein-coding
mm_41620.1	chr5	96837478	96837526	+	1	NA	intron (NM_013470, intron 11 of 12)	intron (NM_013470, intron 11 of 12)	44117	NM_013470	11745	Mm.7214	NM_013470	ENSMUSG00000029484	Anxa3	Anx3	annexin A3	protein-coding
mm_4673.1	chr1	180402042	180402063	+	1	NA	intron (NM_001081175, intron 2 of 7)	intron (NM_001081175, intron 2 of 7)	-71503	NR_003623	277333	Mm.389223	NM_199472		Gm5069	EG277333	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_135439.1	chr16	45397130	45397145	-	1	NA	exon (NM_010818, exon 3 of 6)	exon (NM_010818, exon 3 of 6)	11916	NM_010818	17470	Mm.245851	NM_010818	ENSMUSG00000022661	Cd200	Mox2|OX2	CD200 antigen	protein-coding
mm_86170.1	chr9	119093469	119093502	-	1	NA	promoter-TSS (NM_019676)	promoter-TSS (NM_019676)	17	NR_121571	18799	Mm.23963	NM_019676	ENSMUSG00000010660	Plcd1	AW212592|C79986	phospholipase C, delta 1	protein-coding
mm_169559.1	chr15	10470335	10470335	-	1	NA	exon (NM_030046, exon 1 of 12)	exon (NM_030046, exon 1 of 12)	181	NM_030046	78244	Mm.297862	NM_030046	ENSMUSG00000044224	Dnajc21	4930461P20Rik|9930116P15Rik	DnaJ heat shock protein family (Hsp40) member C21	protein-coding
mm_43530.1	chr5	137289980	137289990	+	1	NA	intron (NM_009599, intron 1 of 4)	intron (NM_009599, intron 1 of 4)	1731	NM_001290010	11423	Mm.255464	NM_009599	ENSMUSG00000023328	Ache	-	acetylcholinesterase	protein-coding
mm_99937.1	chr11	111026930	111026950	+	1	NA	3' UTR (NM_001252208, exon 2 of 2)	3' UTR (NM_001252208, exon 2 of 2)	3080	NM_001252208	16517	Mm.30176	NM_010604	ENSMUSG00000051497	Kcnj16	6430410F18Rik|AI132396|Kir5.1	potassium inwardly-rectifying channel, subfamily J, member 16	protein-coding
mm_3218.1	chr1	135845607	135845618	+	1	NA	exon (NM_001130176, exon 3 of 13)	exon (NM_001130176, exon 3 of 13)	4751	NM_001130176	21956	Mm.247470	NM_011619	ENSMUSG00000026414	Tnnt2	Tnt|cTnT	troponin T2, cardiac	protein-coding
mm_92187.1	chr10	68098023	68098031	-	1	NA	exon (NM_023598, exon 10 of 10)	exon (NM_023598, exon 10 of 10)	118429	NM_001081346	170799	Mm.209844	NM_133244	ENSMUSG00000037846	Rtkn2	B130039D23Rik|Mbf|Plekhk1	rhotekin 2	protein-coding
mm_63781.1	chr7	131571051	131571093	+	1	NA	3' UTR (NM_009774, exon 8 of 8)	3' UTR (NM_009774, exon 8 of 8)	10578	NM_001317350	12237	Mm.927	NM_009774	ENSMUSG00000066979	Bub3	AU019800|AU021329|AU043350|AW146323|C78067	BUB3 mitotic checkpoint protein	protein-coding
mm_126012.1	chr15	76626190	76626208	+	1	NA	promoter-TSS (NM_025842)	promoter-TSS (NM_025842)	-115	NM_001305668	66914	Mm.30028	NM_025842	ENSMUSG00000059323	Vps28	1110014J03Rik|CIIA|D730005C08Rik	vacuolar protein sorting 28	protein-coding
mm_120362.1	chr14	64440158	64440179	+	1	NA	intron (NM_001253712, intron 1 of 5)	RSINE1|SINE|B4	858	NM_001253715	110265	Mm.26713	NM_026322	ENSMUSG00000054733	Msra	2310045J23Rik|6530413P12Rik|MSR-A	methionine sulfoxide reductase A	protein-coding
mm_10008.1	chr1	191791369	191791375	-	1	NA	Intergenic	Intergenic	-30101	NM_010892	18005	Mm.33773	NM_010892	ENSMUSG00000026622	Nek2	AA617254|C77054	NIMA (never in mitosis gene a)-related expressed kinase 2	protein-coding
mm_53042.1	chr6	124663190	124663212	+	1	NA	promoter-TSS (NM_145130)	promoter-TSS (NM_145130)	97	NM_145130	14792	Mm.273915	NM_145130	ENSMUSG00000004270	Lpcat3	C3f|Grcc3f|Lpcat|Lpeat|Lplat5|Lpsat|Mboat5|Moact5|Oact5|PTG	lysophosphatidylcholine acyltransferase 3	protein-coding
mm_11828.1	chr2	44988709	44988757	+	1	NA	exon (NM_015753, exon 10 of 10)	exon (NM_015753, exon 10 of 10)	34444	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_75794.1	chr8	70108447	70108458	-	1	NA	exon (NM_007789, exon 8 of 15)	exon (NM_007789, exon 8 of 15)	-5866	NR_106033	102465646		NR_106033	ENSMUSG00000099042	Mir7066	Gm27290|mmu-mir-7066	microRNA 7066	ncRNA
mm_169922.1	chr16	57391295	57391297	-	1	NA	intron (NM_001040397, intron 1 of 4)	LSU-rRNA_Hsa|rRNA|rRNA	38019	NM_001040397	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding
mm_45616.1	chr5	75835834	75835842	-	1	NA	Intergenic	Intergenic	142590	NM_010612	16542	Mm.285	NM_010612	ENSMUSG00000062960	Kdr	6130401C07|Flk-1|Flk1|Krd-1|Ly73|VEGFR-2|VEGFR2|sVEGFR-2	kinase insert domain protein receptor	protein-coding
mm_173064.1	chrX	134054476	134054479	-	1	NA	Intergenic	Intergenic	-4699	NM_001290398	108062	Mm.67938	NM_133196	ENSMUSG00000031256	Cstf2	C630034J23Rik|Cstf64|mir-3112	cleavage stimulation factor, 3' pre-RNA subunit 2	protein-coding
mm_25052.1	chr3	98382439	98382520	+	1	NA	promoter-TSS (NM_172863)	promoter-TSS (NM_172863)	-2	NM_172863	242109	Mm.358911	NM_172863	ENSMUSG00000050064	Zfp697	9430053K19|AI467503|Znf697	zinc finger protein 697	protein-coding
mm_51552.1	chr6	83326030	83326064	+	1	NA	promoter-TSS (NM_145571)	promoter-TSS (NM_145571)	8	NM_145571	232157	Mm.29500	NM_145571	ENSMUSG00000043131	Mob1a	4022402H07Rik|MOB1|MOB4B|Mobk1b|Mobkl1b	MOB kinase activator 1A	protein-coding
mm_125215.1	chr15	34082790	34082836	+	1	NA	promoter-TSS (NM_026002)	promoter-TSS (NM_026002)	94	NM_026002	67154	Mm.130883	NM_026002	ENSMUSG00000022255	Mtdh	2610103J23Rik|3D3|3D3/Lyric|AEG-1|AV353288|D8Bwg1112e|Lyric	metadherin	protein-coding
mm_116696.1	chr13	49652757	49652781	-	1	NA	promoter-TSS (NM_001271397)	promoter-TSS (NM_001271397)	-38	NM_025495	66336	Mm.440323	NM_025495	ENSMUSG00000021391	Cenpp	1700022C02Rik|4921518G09Rik	centromere protein P	protein-coding
mm_65083.1	chr7	19227982	19227998	-	1	NA	promoter-TSS (NM_207525)	promoter-TSS (NM_207525)	-399	NM_207525	403187	Mm.239583	NM_207525	ENSMUSG00000052214	Opa3	D630048P19Rik|Gm1425|Gm472	optic atrophy 3	protein-coding
mm_144446.1	chr18	22643576	22643581	+	1	NA	Intergenic	RLTR13C1|LTR|ERVK	298489	NM_001167777	211961	Mm.392310	NM_001167777	ENSMUSG00000045215	Asxl3	C230079D11Rik|D430002O22Rik|D930044O18Rik|Gm329|Gm945	additional sex combs like 3 (Drosophila)	protein-coding
mm_172177.1	chr6	48525100	48525117	-	1	NA	non-coding (NR_027808, exon 4 of 7)	non-coding (NR_027808, exon 4 of 7)	12366	NR_130985	69432		NR_130985	ENSMUSG00000097716	1700026J14Rik	-	RIKEN cDNA 1700026J14 gene	ncRNA
mm_78671.1	chr9	40774414	40774429	+	1	NA	exon (NM_133733, exon 5 of 7)	exon (NM_133733, exon 5 of 7)	-26852	NM_031165	15481	Mm.290774	NM_031165	ENSMUSG00000015656	Hspa8	2410008N15Rik|Hsc70|Hsc71|Hsc73|Hsp73|Hspa10	heat shock protein 8	protein-coding
mm_111862.1	chr12	107972037	107972038	-	1	NA	intron (NM_001079883, intron 2 of 3)	intron (NM_001079883, intron 2 of 3)	31377	NM_001079883	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_64746.1	chr7	4771344	4771345	-	1	NA	promoter-TSS (NM_172895)	promoter-TSS (NM_172895)	-74	NM_172895	243822	Mm.333542	NM_172895	ENSMUSG00000092518	Fam71e2	4930401F20Rik	family with sequence similarity 71, member E2	protein-coding
mm_66845.1	chr7	49162149	49162171	-	1	NA	intron (NM_001111016, intron 2 of 38)	intron (NM_001111016, intron 2 of 38)	-84029	NM_175272	78286	Mm.333881	NM_175272	ENSMUSG00000052512	Nav2	5330421F07Rik|AU067780|BQ960892|HELAD1|POMFIL2|RAINB1|RAINB2|Unc53H2|mKIAA3015	neuron navigator 2	protein-coding
mm_132725.1	chr16	43618989	43619038	+	1	NA	3' UTR (NM_019778, exon 9 of 9)	3' UTR (NM_019778, exon 9 of 9)	-21642	NR_030576	100124467		NR_030576	ENSMUSG00000076372	Mir568	Mirn568|mmu-mir-568	microRNA 568	ncRNA
mm_91944.1	chr10	60831572	60831588	-	1	NA	promoter-TSS (NM_029770)	promoter-TSS (NM_029770)	1	NM_029770	107449	Mm.290433	NM_029770	ENSMUSG00000020099	Unc5b	6330415E02Rik|A630020F16|D10Bwg0792e|Unc5h2	unc-5 netrin receptor B	protein-coding
mm_170465.1	chr18	9707569	9707569	+	1	NA	promoter-TSS (NM_130449)	promoter-TSS (NM_130449)	-79	NM_130449	140792	Mm.218571	NM_130449	ENSMUSG00000036103	Colec12	CL-P1|SRCL|Scara4	collectin sub-family member 12	protein-coding
mm_156234.1	chrX	135885950	135885978	+	1	NA	5' UTR (NM_198161, exon 1 of 5)	5' UTR (NM_198161, exon 1 of 5)	113	NM_198161	70237	Mm.440847	NM_198161	ENSMUSG00000072964	Bhlhb9	2700087I09Rik	basic helix-loop-helix domain containing, class B9	protein-coding
mm_58639.1	chr7	6155295	6155308	+	1	NA	intron (NM_001013012, intron 1 of 2)	CpG	670	NM_001013012	67109	Mm.3254	NM_001013012	ENSMUSG00000046792	Zfp787	2210018M03Rik|Znf787	zinc finger protein 787	protein-coding
mm_7395.1	chr1	113904075	113904081	-	1	NA	Intergenic	L1Md_F3|LINE|L1	-1781059	NM_001077425	636808	Mm.101576	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding
mm_133560.1	chr16	91391812	91391840	+	1	NA	exon (NM_010509, exon 6 of 9)	exon (NM_010509, exon 6 of 9)	-14409	NM_008349	16155	Mm.4154	NM_008349	ENSMUSG00000022969	Il10rb	6620401D04Rik|AI528744|CRF2-4|Crfb4|D16H21S58|D21S58h|IL-10R2|Il10r2	interleukin 10 receptor, beta	protein-coding
mm_144018.1	chr17	89200685	89200697	-	1	NA	promoter-TSS (NM_013523)	promoter-TSS (NM_013523)	-16	NM_013523	14309	Mm.57155	NM_013523	ENSMUSG00000032937	Fshr	-	follicle stimulating hormone receptor	protein-coding
mm_74628.1	chr8	13171229	13171250	-	1	NA	exon (NM_010684, exon 5 of 9)	exon (NM_010684, exon 5 of 9)	12078	NM_010684	16783	Mm.16716	NM_010684	ENSMUSG00000031447	Lamp1	CD107a|LGP-120|LGP-A|Lamp-1|P2B	lysosomal-associated membrane protein 1	protein-coding
mm_139039.1	chr17	46227771	46227780	+	1	NA	exon (NM_028198, exon 18 of 32)	exon (NM_028198, exon 18 of 32)	-3756	NR_030466	751553		NR_030466	ENSMUSG00000076141	Mir693	Mirn693|mir-693|mmu-mir-693	microRNA 693	ncRNA
mm_49299.1	chr6	17743583	17743593	+	1	NA	promoter-TSS (NM_001289629)	promoter-TSS (NM_001289629)	-4	NM_001289629	64213	Mm.12051	NM_022332	ENSMUSG00000029534	St7	9430001H04Rik|Fam4a2|HELG|RAY1|SEN4|TSG7	suppression of tumorigenicity 7	protein-coding
mm_70313.1	chr8	4239099	4239107	+	1	NA	intron (NM_001291777, intron 1 of 11)	CpG	363	NM_001164172	26400	Mm.3906	NM_011944	ENSMUSG00000002948	Map2k7	5930412N11Rik|JNKK 2|Jnkk2|MAPKK 7|MEK 7|Mapkk7|Mek7|Mkk7|Prkmk7|sek2	mitogen-activated protein kinase kinase 7	protein-coding
mm_86444.1	chr10	4242468	4242498	+	1	NA	Intergenic	Intergenic	-23846	NM_031185	83397	Mm.27481	NM_031185	ENSMUSG00000038587	Akap12	AI317366|SSeCKS|Srcs5|Tsga12	A kinase (PRKA) anchor protein (gravin) 12	protein-coding
mm_132132.1	chr16	31878848	31878858	+	1	NA	promoter-TSS (NM_013900)	promoter-TSS (NM_013900)	43	NM_013900	30060	Mm.30988	NM_013900	ENSMUSG00000022780	Mfi2	CD228|MTf|Meltf	antigen p97 (melanoma associated) identified by monoclonal antibodies 133.2 and 96.5	protein-coding
mm_62914.1	chr7	117670619	117670642	+	1	NA	Intergenic	IMPB_01|Satellite|Satellite	289651	NM_175645	233781	Mm.461427	NM_175645	ENSMUSG00000030657	Xylt1	8030490L12	xylosyltransferase 1	protein-coding
mm_20006.1	chr2	119156937	119156986	-	1	NA	promoter-TSS (NM_001033136)	promoter-TSS (NM_001033136)	73	NM_001033136	67809	Mm.475909	NM_001033136	ENSMUSG00000070730	Rmdn3	1200015F23Rik|AI131757|Fam82a2|Ptpip51|RMD-3|Rmd3	regulator of microtubule dynamics 3	protein-coding
mm_166113.1	chr4	149622761	149622788	+	1	NA	intron (NM_001290989, intron 2 of 17)	intron (NM_001290989, intron 2 of 17)	32793	NR_105990	102465983		NR_105990	ENSMUSG00000098580	Mir7023	Gm27912|mmu-mir-7023	microRNA 7023	ncRNA
mm_162317.1	chr1	38393973	38393975	-	1	NA	intron (NM_001290814, intron 5 of 21)	intron (NM_001290814, intron 5 of 21)	233270	NM_001290814	16764	Mm.336679	NM_010678	ENSMUSG00000037138	Aff3	3222402O04Rik|A730046J16|LAF-4|Laf4	AF4/FMR2 family, member 3	protein-coding
mm_15605.1	chr2	160731259	160731300	+	1	NA	promoter-TSS (NM_021280)	promoter-TSS (NM_021280)	-31	NM_021280	18803	Mm.44463	NM_021280	ENSMUSG00000016933	Plcg1	AI894140|Cded|Plc-1|Plc-gamma1|Plcg-1	phospholipase C, gamma 1	protein-coding
mm_112640.1	chr13	16014458	16014473	+	1	NA	5' UTR (NM_008380, exon 3 of 5)	5' UTR (NM_008380, exon 3 of 5)	2614	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_24451.1	chr3	90612901	90612979	+	1	NA	promoter-TSS (NM_011313)	promoter-TSS (NM_011313)	46	NM_011313	20200	Mm.100144	NM_011313	ENSMUSG00000001025	S100a6	2A9|5B10|CALCYCLIN|Cacy|PRA	S100 calcium binding protein A6 (calcyclin)	protein-coding
mm_135071.1	chr16	34255663	34255668	-	1	NA	intron (NM_001164268, intron 12 of 33)	MLTR11A|LTR|ERVK	258362	NM_001164268	545156	Mm.82274	NM_177357	ENSMUSG00000061751	Kalrn	2210407G14Rik|AV235988|DUET|E530005C20Rik|Gm539|Hapip|TRAD	kalirin, RhoGEF kinase	protein-coding
mm_151130.1	chr19	48206134	48206163	+	1	NA	5' UTR (NM_025696, exon 1 of 27)	5' UTR (NM_025696, exon 1 of 27)	123	NM_025696	66673	Mm.70980	NM_025696	ENSMUSG00000063434	Sorcs3	6330404A12Rik|AW045579	sortilin-related VPS10 domain containing receptor 3	protein-coding
mm_31348.1	chr4	46602027	46602035	+	1	NA	promoter-TSS (NM_001164804)	promoter-TSS (NM_001164804)	-102	NM_001164804	107684	Mm.416311	NM_178893	ENSMUSG00000028337	Coro2a	9030208C03Rik|AI563590|IR10	coronin, actin binding protein 2A	protein-coding
mm_117456.1	chr13	74808808	74808849	-	1	NA	promoter-TSS (NM_009817)	promoter-TSS (NM_009817)	-68	NM_001301153	12380	Mm.29163	NM_009817	ENSMUSG00000021585	Cast	-	calpastatin	protein-coding
mm_169772.1	chr1	60047815	60047824	+	1	NA	Intergenic	RLTR9D|LTR|ERVK	-4697	NM_001316695	70375	Mm.17834	NM_027407	ENSMUSG00000026018	Ica1l	1700030B17Rik|Als2cr15	islet cell autoantigen 1-like	protein-coding
mm_151935.1	chr19	5800602	5800612	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	2065	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_92751.1	chr10	81025364	81025402	-	1	NA	promoter-TSS (NM_145217)	promoter-TSS (NM_145217)	-6	NM_145217	208666	Mm.44995	NM_145217	ENSMUSG00000043670	Diras1	Di-Ras1|Gbts1|RIG	DIRAS family, GTP-binding RAS-like 1	protein-coding
mm_171268.1	chr3	88577850	88577864	-	1	NA	Intergenic	ORR1A0|LTR|ERVL-MaLR	-1814	NM_025448	66256	Mm.7091	NM_025448	ENSMUSG00000041355	Ssr2	1500032E05Rik|AI315033|AU020133|TLAP|TRAPB|TRAPbeta	signal sequence receptor, beta	protein-coding
mm_150830.1	chr19	44746703	44746712	+	1	NA	Intergenic	CpG	-10687	NM_011037	18504	Mm.192158	NM_011037	ENSMUSG00000004231	Pax2	Opdc|Pax-2	paired box 2	protein-coding
mm_154988.1	chrX	38189851	38189865	+	1	NA	promoter-TSS (NM_020256)	promoter-TSS (NM_020256)	65	NM_001079513	56805	Mm.391248	NM_020256	ENSMUSG00000048047	Zbtb33	AW260253|E130014G12Rik|Kaiso|Znf-kaiso	zinc finger and BTB domain containing 33	protein-coding
mm_92937.1	chr10	84533969	84534029	-	1	NA	promoter-TSS (NM_175451)	promoter-TSS (NM_175451)	-111	NM_175451	216197	Mm.334999	NM_175451	ENSMUSG00000046841	Ckap4	5630400A09Rik|CLIMP-63|P63	cytoskeleton-associated protein 4	protein-coding
mm_149782.1	chr19	23136738	23136744	+	1	NA	Intergenic	Intergenic	-4485	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_58535.1	chr7	4460739	4460749	+	1	NA	Intergenic	Intergenic	-3991	NM_026146	67425	Mm.360392	NM_026146	ENSMUSG00000006154	Eps8l1	2310051G19Rik|4632407K17Rik|AW060268|DRC3|EPS8R1	EPS8-like 1	protein-coding
mm_94261.1	chr11	3488293	3488304	+	1	NA	promoter-TSS (NM_172791)	promoter-TSS (NM_172791)	71	NM_172791	237625	Mm.100476	NM_172791	ENSMUSG00000034579	Pla2g3	-	phospholipase A2, group III	protein-coding
mm_152671.1	chr19	14598032	14598088	-	1	NA	promoter-TSS (NM_001302951)	promoter-TSS (NM_001302951)	123	NM_001302950	21888	Mm.103638	NM_011600	ENSMUSG00000024642	Tle4	5730411M05Rik|AA792082|Bce-1|Bce1|ESTM13|ESTM14|Grg4|X83332|X83333|grg-4	transducin-like enhancer of split 4	protein-coding
mm_34581.1	chr4	150139514	150139520	+	1	NA	exon (NM_019741, exon 8 of 14)	exon (NM_019741, exon 8 of 14)	-9455	NM_001085529	435818	Mm.359648	NM_001085529	ENSMUSG00000062064	Slc2a7	OTTMUSG00000010396	solute carrier family 2 (facilitated glucose transporter), member 7	protein-coding
mm_111851.1	chr12	107939091	107939123	-	1	NA	intron (NM_001286343, intron 1 of 1)	intron (NM_001286343, intron 1 of 1)	64307	NM_001079883	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_103378.1	chr11	75414966	75414978	-	1	NA	exon (NM_011340, exon 5 of 8)	exon (NM_011340, exon 5 of 8)	7651	NM_011340	20317	Mm.2044	NM_011340	ENSMUSG00000000753	Serpinf1	AI195227|EPC-1|Pedf|Pedfl|Sdf3	serine (or cysteine) peptidase inhibitor, clade F, member 1	protein-coding
mm_123363.1	chr14	63144740	63144752	-	1	NA	TTS (NM_010191)	TTS (NM_010191)	22284	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_119110.1	chr14	31001631	31001713	+	1	NA	promoter-TSS (NM_026911)	promoter-TSS (NM_026911)	-6	NM_026911	69019	Mm.28852	NM_026911	ENSMUSG00000021917	Spcs1	1810004F21Rik	signal peptidase complex subunit 1 homolog (S. cerevisiae)	protein-coding
mm_3756.1	chr1	156041081	156041108	+	1	NA	5' UTR (NM_001160182, exon 2 of 3)	5' UTR (NM_001160182, exon 2 of 3)	233	NM_022329	240832	Mm.253335	NM_022329	ENSMUSG00000050565	Tor1aip2	1110020D10Rik|15kDa|A130072J07|AA103493|AW060462|AW610675|C77739|Ifrg15|Lull1	torsin A interacting protein 2	protein-coding
mm_44968.1	chr5	36795836	36795841	-	1	NA	3' UTR (NM_026242, exon 2 of 2)	3' UTR (NM_026242, exon 2 of 2)	916	NM_026242	67568	Mm.332336	NM_026242	ENSMUSG00000055302	Mrfap1	9130413I22Rik|AL022827|Pam14	Morf4 family associated protein 1	protein-coding
mm_98568.1	chr11	95384947	95384957	+	1	NA	promoter-TSS (NM_016752)	promoter-TSS (NM_016752)	30	NM_016752	110172	Mm.4593	NM_016752	ENSMUSG00000020873	Slc35b1	Ugalt2	solute carrier family 35, member B1	protein-coding
mm_65112.1	chr7	19310198	19310228	-	1	NA	promoter-TSS (NM_008036)	promoter-TSS (NM_008036)	-168	NM_001347586	14282	Mm.248335	NM_008036	ENSMUSG00000003545	Fosb	-	FBJ osteosarcoma oncogene B	protein-coding
mm_79531.1	chr9	57764450	57764463	+	1	NA	intron (NM_007713, intron 1 of 12)	CpG	1404	NM_007713	102414	Mm.25720	NM_007713	ENSMUSG00000032316	Clk3	AI256811	CDC-like kinase 3	protein-coding
mm_131578.1	chr16	18407632	18407688	+	1	NA	TTS (NM_001272032)	TTS (NM_001272032)	5834	NM_001111063	12846	Mm.100940	NM_007744	ENSMUSG00000000326	Comt	Comt1|D16Wsu103e|D330014B15Rik	catechol-O-methyltransferase	protein-coding
mm_143560.1	chr17	74188121	74188123	-	1	NA	Intergenic	Intergenic	106741	NM_133771	76890	Mm.311874	NM_133771	ENSMUSG00000058704	Memo1	0610016J10Rik|D930048L02Rik	mediator of cell motility 1	protein-coding
mm_84170.1	chr9	59941054	59941075	-	1	NA	Intergenic	Intergenic	9015	NM_013708	23958	Mm.103641	NM_013708	ENSMUSG00000032292	Nr2e3	A930035N01Rik|PNR|RNR|rd7	nuclear receptor subfamily 2, group E, member 3	protein-coding
mm_77601.1	chr8	123892923	123892947	-	1	NA	exon (NM_009606, exon 4 of 7)	exon (NM_009606, exon 4 of 7)	1840	NM_001272041	11459	Mm.214950	NM_009606	ENSMUSG00000031972	Acta1	AA959943|Acta-2|Acts|Actsk-1	actin, alpha 1, skeletal muscle	protein-coding
mm_116623.1	chr13	48880440	48880455	-	1	NA	3' UTR (NM_001033268, exon 18 of 18)	3' UTR (NM_001033268, exon 18 of 18)	-9562	NM_011078	18676	Mm.486213	NM_011078	ENSMUSG00000038025	Phf2	GRC5	PHD finger protein 2	protein-coding
mm_20009.1	chr2	119208768	119208802	-	1	NA	promoter-TSS (NM_139139)	promoter-TSS (NM_139139)	10	NM_139139	69408	Mm.222241	NM_139139	ENSMUSG00000034278	Dnajc17	1700025B16Rik|C87112|D9Bwg1371e	DnaJ heat shock protein family (Hsp40) member C17	protein-coding
mm_142874.1	chr17	51823386	51823389	-	1	NA	intron (NM_001163632, intron 1 of 10)	intron (NM_001163632, intron 1 of 10)	3201	NM_001163631	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_11767.1	chr2	38536865	38536867	+	1	NA	intron (NM_001159631, intron 1 of 9)	intron (NM_001159631, intron 1 of 9)	24990	NM_001159631	59126	Mm.143818	NM_021606	ENSMUSG00000026749	Nek6	1300007C09Rik	NIMA (never in mitosis gene a)-related expressed kinase 6	protein-coding
mm_58139.1	chr6	141855525	141855570	-	1	NA	intron (NM_030687, intron 1 of 16)	intron (NM_030687, intron 1 of 16)	624	NM_030687	28250	Mm.255586	NM_030687	ENSMUSG00000030237	Slco1a4	AI785519|Oatp1a4|Oatp2|Slc21a5	solute carrier organic anion transporter family, member 1a4	protein-coding
mm_147372.1	chr18	43438461	43438467	-	1	NA	promoter-TSS (NM_001291455)	promoter-TSS (NM_001291455)	-178	NM_001291455	22240	Mm.8180	NM_009468	ENSMUSG00000024501	Dpysl3	CRMP-4|DRP-3|TUC4|ULIP-1|Ulip|Ulip1	dihydropyrimidinase-like 3	protein-coding
mm_131795.1	chr16	22899051	22899056	+	1	NA	exon (NM_001276450, exon 7 of 7)	exon (NM_001276450, exon 7 of 7)	-4667	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_99203.1	chr11	101022876	101022886	+	1	NA	intron (NM_001243050, intron 5 of 20)	intron (NM_001243050, intron 5 of 20)	-7459	NR_105893	102466767		NR_105893	ENSMUSG00000098415	Mir6928	Gm27728|mmu-mir-6928	microRNA 6928	ncRNA
mm_170879.1	chr2	20900068	20900070	+	1	NA	intron (NM_001128084, intron 3 of 24)	LSU-rRNA_Hsa|rRNA|rRNA	67652	NM_001081364	71435	Mm.28507	NM_001081364	ENSMUSG00000036591	Arhgap21	5530401C11Rik|AA416458|ARHGAP10	Rho GTPase activating protein 21	protein-coding
mm_107618.1	chr12	51348266	51348368	+	1	NA	promoter-TSS (NM_001015099)	promoter-TSS (NM_001015099)	87	NM_001015099	217558	Mm.253264	NM_001015099	ENSMUSG00000035293	G2e3	6030408C04Rik|9030416F18|AW046379|D930034K21Rik|mKIAA1333	G2/M-phase specific E3 ubiquitin ligase	protein-coding
mm_50859.1	chr6	55306891	55306904	+	1	NA	intron (NM_001142781, intron 15 of 17)	RMER17C|LTR|ERVK	-29402	NM_007472	11826	Mm.18625	NM_007472	ENSMUSG00000004655	Aqp1	CHIP28	aquaporin 1	protein-coding
mm_34059.1	chr4	138434648	138434748	+	1	NA	promoter-TSS (NM_026689)	promoter-TSS (NM_026689)	26	NM_026689	68350	Mm.103413	NM_026689	ENSMUSG00000041241	Mul1	0610009K11Rik|AV000801|Gide	mitochondrial ubiquitin ligase activator of NFKB 1	protein-coding
mm_74651.1	chr8	13396770	13396783	-	1	NA	promoter-TSS (NM_009724)	promoter-TSS (NM_009724)	2	NM_009724	11945	Mm.154039	NM_009724	ENSMUSG00000031449	Atp4b	AV080843	ATPase, H+/K+ exchanging, beta polypeptide	protein-coding
mm_130043.1	chr15	89106168	89106178	-	1	NA	exon (NM_001163319, exon 13 of 25)	exon (NM_001163319, exon 13 of 25)	16977	NM_001163319	328580	Mm.380934	NM_001163319	ENSMUSG00000051786	Tubgcp6	AI843275|D430023H11|GCP-6|mKIAA1669	tubulin, gamma complex associated protein 6	protein-coding
mm_137822.1	chr17	30576323	30576366	+	1	NA	promoter-TSS (NM_027060)	promoter-TSS (NM_027060)	-57	NM_027060	224671	Mm.41220	NM_027060	ENSMUSG00000062202	Btbd9	1700023F20Rik|4930402L05|AI464421	BTB (POZ) domain containing 9	protein-coding
mm_20402.1	chr2	129297149	129297201	-	1	NA	promoter-TSS (NM_181589)	promoter-TSS (NM_181589)	37	NM_181589	70466	Mm.45785	NM_181589	ENSMUSG00000048327	Ckap2l	2010016H04Rik|2610318C08Rik|AV070319|radmis|rdm	cytoskeleton associated protein 2-like	protein-coding
mm_79510.1	chr9	57504532	57504562	+	1	NA	exon (NM_133982, exon 1 of 1)	exon (NM_133982, exon 1 of 1)	445	NM_133982	102614	Mm.274421	NM_133982	ENSMUSG00000062309	Rpp25	AI851155	ribonuclease P/MRP 25 subunit	protein-coding
mm_134236.1	chr16	11909357	11909379	-	1	NA	promoter-TSS (NM_146067)	promoter-TSS (NM_146067)	55	NM_146067	223978	Mm.86360	NM_146067	ENSMUSG00000065979	Cpped1	C530044N13Rik	calcineurin-like phosphoesterase domain containing 1	protein-coding
mm_2605.1	chr1	120121162	120121183	+	1	NA	promoter-TSS (NM_001172074)	promoter-TSS (NM_001172074)	-15	NM_028439	73103	Mm.271602	NM_028439	ENSMUSG00000026388	3110009E18Rik	-	RIKEN cDNA 3110009E18 gene	protein-coding
mm_48763.1	chr5	148392811	148392816	-	1	NA	promoter-TSS (NM_001301424)	promoter-TSS (NM_001301424)	2	NM_001301424	11987	Mm.275489	NM_007513	ENSMUSG00000041313	Slc7a1	4831426K01Rik|AI447493|Atrc-1|Atrc1|Cat1|Rec-1|Rev-1|mCAT-1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 1	protein-coding
mm_69118.1	chr7	127026135	127026143	-	1	NA	exon (NM_010772, exon 2 of 5)	exon (NM_010772, exon 2 of 5)	340	NM_010772	17188	Mm.378964	NM_010772	ENSMUSG00000030678	Maz	MAZI|PUR1|Pur-1|SAF-1|SAF-2	MYC-associated zinc finger protein (purine-binding transcription factor)	protein-coding
mm_133968.1	chr16	4229112	4229120	-	1	NA	promoter-TSS (NR_003628)	promoter-TSS (NR_003628)	0	NR_040571	76397	Mm.243719	NM_183117		4930455F16Rik	1700013J11Rik	RIKEN cDNA 4930455F16 gene	ncRNA
mm_70311.1	chr8	4238734	4238767	+	1	NA	promoter-TSS (NM_001164172)	promoter-TSS (NM_001164172)	10	NM_001164172	26400	Mm.3906	NM_011944	ENSMUSG00000002948	Map2k7	5930412N11Rik|JNKK 2|Jnkk2|MAPKK 7|MEK 7|Mapkk7|Mek7|Mkk7|Prkmk7|sek2	mitogen-activated protein kinase kinase 7	protein-coding
mm_134552.1	chr16	19983032	19983037	-	1	NA	promoter-TSS (NM_183390)	promoter-TSS (NM_183390)	15	NM_183390	239743	Mm.86699	NM_183390	ENSMUSG00000043008	Klhl6	-	kelch-like 6	protein-coding
mm_42431.1	chr5	115345827	115345856	+	1	NA	3' UTR (NM_007748, exon 3 of 3)	3' UTR (NM_007748, exon 3 of 3)	3114	NM_007748	12861	Mm.43415	NM_007748	ENSMUSG00000041697	Cox6a1	VIaL	cytochrome c oxidase subunit VIa polypeptide 1	protein-coding
mm_106620.1	chr11	120821131	120821138	-	1	NA	intron (NM_007988, intron 3 of 42)	intron (NM_007988, intron 3 of 42)	3413	NM_007988	14104	Mm.236443	NM_007988	ENSMUSG00000025153	Fasn	A630082H08Rik|FAS	fatty acid synthase	protein-coding
mm_31123.1	chr4	42969946	42969951	+	1	NA	promoter-TSS (NM_026088)	promoter-TSS (NM_026088)	2	NM_026088	67317	Mm.478018	NM_026088	ENSMUSG00000028451	1700022I11Rik	-	RIKEN cDNA 1700022I11 gene	protein-coding
mm_71407.1	chr8	46471170	46471186	+	1	NA	5' UTR (NM_007981, exon 1 of 21)	5' UTR (NM_007981, exon 1 of 21)	141	NM_007981	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_5512.1	chr1	37519185	37519199	-	1	NA	intron (NM_001290801, intron 1 of 14)	intron (NM_001290801, intron 1 of 14)	17212	NM_001290801	269181	Mm.25861	NM_173870	ENSMUSG00000026110	Mgat4a	9530018I07Rik|GnT-IVa|glcNAc-T-IVa	mannoside acetylglucosaminyltransferase 4, isoenzyme A	protein-coding
mm_103518.1	chr11	76787603	76787617	-	1	NA	intron (NM_007754, intron 17 of 20)	Lx9|LINE|L1	-24055	NM_016810	53334	Mm.20931	NM_016810	ENSMUSG00000010392	Gosr1	AI414660|AI426320|BB145494|GOS-28|GOSRI|GS28	golgi SNAP receptor complex member 1	protein-coding
mm_60469.1	chr7	44478055	44478063	+	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	-6458	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_80379.1	chr9	75410204	75410217	+	1	NA	promoter-TSS (NR_040719)	promoter-TSS (NR_040719)	26	NR_040719	71274	Mm.399152	NR_040719	ENSMUSG00000097021	4933433G15Rik	4921522K19Rik	RIKEN cDNA 4933433G15 gene	ncRNA
mm_6759.1	chr1	84069081	84069104	-	1	NA	intron (NM_001003948, intron 2 of 2)	intron (NM_001003948, intron 2 of 2)	149869	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_2095.1	chr1	87702324	87702373	+	1	NA	intron (NM_010566, intron 17 of 26)	B3|SINE|B2	-53663	NM_029846	77040	Mm.272972	NM_029846	ENSMUSG00000026289	Atg16l1	1500009K01Rik|Apg16l|Atg16l|WDR30	autophagy related 16-like 1 (S. cerevisiae)	protein-coding
mm_161222.1	chr13	68582415	68582415	+	1	NA	promoter-TSS (NR_131892)	promoter-TSS (NR_131892)	205	NR_138478	69577	Mm.23670	NM_027123	ENSMUSG00000021532	Fastkd3	2310010B21Rik|AW048587	FAST kinase domains 3	protein-coding
mm_165786.1	chr3	131474617	131474617	-	1	NA	Intergenic	Intergenic	-90151	NM_001289479	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_47338.1	chr5	122502163	122502176	-	1	NA	promoter-TSS (NM_009722)	promoter-TSS (NM_009722)	56	NM_001110140	11938	Mm.227583	NM_009722	ENSMUSG00000029467	Atp2a2	9530097L16Rik|D5Wsu150e|SERCA2|SERCA2B|Serca2a|mKIAA4195	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	protein-coding
mm_80674.1	chr9	90245427	90245435	+	1	NA	intron (NM_194334, intron 2 of 12)	intron (NM_194334, intron 2 of 12)	25338	NM_194334	67016	Mm.335347	NM_194334	ENSMUSG00000037410	Tbc1d2b	1810061M12Rik|AI480956|AV021536|AV023399|AW491493|mKIAA1055	TBC1 domain family, member 2B	protein-coding
mm_42316.1	chr5	114883367	114883372	+	1	NA	3' UTR (NM_026263, exon 12 of 12)	3' UTR (NM_026263, exon 12 of 12)	-13565	NM_011854	23962	Mm.228363	NM_011854	ENSMUSG00000029561	Oasl2	M1204|Mmu-OASL|Oasl	2'-5' oligoadenylate synthetase-like 2	protein-coding
mm_104884.1	chr11	99543217	99543222	-	1	NA	promoter-TSS (NM_001039666)	promoter-TSS (NM_001039666)	-61	NM_001317213	406221	Mm.422372	NM_001039666	ENSMUSG00000059169	Krt40	CK-40|K40	keratin 40	protein-coding
mm_27529.1	chr3	57387772	57387788	-	1	NA	Intergenic	Intergenic	-37630	NM_145539	229302	Mm.26618	NM_145539	ENSMUSG00000027801	Tm4sf4	Iltmp	transmembrane 4 superfamily member 4	protein-coding
mm_51044.1	chr6	65621865	65621870	+	1	NA	intron (NM_001001495, intron 7 of 7)	intron (NM_001001495, intron 7 of 7)	31469	NM_001001495	414084	Mm.117558	NM_001001495	ENSMUSG00000044162	Tnip3	9030611K07Rik|ABIN-3|LIND	TNFAIP3 interacting protein 3	protein-coding
mm_13219.1	chr2	96341076	96341092	+	1	NA	intron (NM_001289743, intron 1 of 6)	intron (NM_001289743, intron 1 of 6)	22915	NM_001289743	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_104104.1	chr11	86705220	86705247	-	1	NA	exon (NM_001003908, exon 23 of 32)	exon (NM_001003908, exon 23 of 32)	21152	NM_001098810	217057	Mm.24868	NM_175004	ENSMUSG00000072582	Ptrh2	A230072I16Rik|Bit1|CGI-147	peptidyl-tRNA hydrolase 2	protein-coding
mm_171048.1	chr3	102436379	102436381	-	1	NA	Intergenic	L1MD2|LINE|L1	-33539	NM_001112698	18049	Mm.1259	NM_013609	ENSMUSG00000027859	Ngf	Ngfb	nerve growth factor	protein-coding
mm_94761.1	chr11	21149714	21149724	+	1	NA	3' UTR (NM_023324, exon 7 of 7)	3' UTR (NM_023324, exon 7 of 7)	58395	NM_023324	67245	Mm.28957	NM_023324	ENSMUSG00000020134	Peli1	2810468L03Rik|A930031K15Rik|AA409794|AI586297|D11Ertd676e	pellino 1	protein-coding
mm_95288.1	chr11	45980227	45980233	+	1	NA	promoter-TSS (NM_173384)	promoter-TSS (NM_173384)	-80	NM_173384	214105	Mm.66708	NM_173384	ENSMUSG00000040489	Sox30	-	SRY (sex determining region Y)-box 30	protein-coding
mm_138701.1	chr17	35998369	35998372	+	1	NA	intron (NR_015618, intron 1 of 1)	ORR1D1|LTR|ERVL-MaLR	3866	NR_015618	77810	Mm.483143	NR_015618		A930015D03Rik	-	RIKEN cDNA A930015D03 gene	ncRNA
mm_28671.1	chr3	95283494	95283541	-	1	NA	5' UTR (NM_133858, exon 1 of 10)	5' UTR (NM_133858, exon 1 of 10)	582	NM_199475	75007	Mm.279287	NM_133858	ENSMUSG00000038712	Fam63a	1810005H09Rik|4930504E06Rik|AA562754|AA960384|AW561904|cI-40|mKIAA1390|ni	family with sequence similarity 63, member A	protein-coding
mm_133572.1	chr16	91406240	91406334	+	1	NA	promoter-TSS (NM_008349)	promoter-TSS (NM_008349)	52	NM_008349	16155	Mm.4154	NM_008349	ENSMUSG00000022969	Il10rb	6620401D04Rik|AI528744|CRF2-4|Crfb4|D16H21S58|D21S58h|IL-10R2|Il10r2	interleukin 10 receptor, beta	protein-coding
mm_146053.1	chr18	69636890	69636910	+	1	NA	exon (NM_001083967, exon 10 of 20)	exon (NM_001083967, exon 10 of 20)	-288659	NM_201362	381175	Mm.266831	NM_201362	ENSMUSG00000038903	Ccdc68	BC046343	coiled-coil domain containing 68	protein-coding
mm_49310.1	chr6	18170561	18170620	+	1	NA	promoter-TSS (NM_021050)	promoter-TSS (NM_021050)	-97	NM_021050	12638	Mm.15621	NM_021050	ENSMUSG00000041301	Cftr	AW495489|Abcc7	cystic fibrosis transmembrane conductance regulator	protein-coding
mm_85102.1	chr9	94538240	94538247	-	1	NA	promoter-TSS (NM_001033145)	promoter-TSS (NM_001033145)	-162	NM_001033145	68861	Mm.258746	NM_001033145	ENSMUSG00000045414	1190002N15Rik	GoPro49|HASF	RIKEN cDNA 1190002N15 gene	protein-coding
mm_23393.1	chr3	57441369	57441371	+	1	NA	3' UTR (NM_145539, exon 5 of 5)	3' UTR (NM_145539, exon 5 of 5)	15960	NM_145539	229302	Mm.26618	NM_145539	ENSMUSG00000027801	Tm4sf4	Iltmp	transmembrane 4 superfamily member 4	protein-coding
mm_44093.1	chr5	149246342	149246356	+	1	NA	Intergenic	Intergenic	-18655	NM_001308462	11690	Mm.19844	NM_009663	ENSMUSG00000060063	Alox5ap	Flap	arachidonate 5-lipoxygenase activating protein	protein-coding
mm_48678.1	chr5	146220907	146220987	-	1	NA	promoter-TSS (NM_001256087)	promoter-TSS (NM_001256087)	24	NM_001256085	74132	Mm.26696	NM_028774	ENSMUSG00000029634	Rnf6	1200013I08Rik|5730419H05Rik|AA537053	ring finger protein (C3H2C3 type) 6	protein-coding
mm_169854.1	chr1	63303247	63303258	+	1	NA	exon (NM_001285937, exon 6 of 6)	exon (NM_001285937, exon 6 of 6)	29983	NM_001267872	73884	Mm.86986	NM_028673	ENSMUSG00000027520	Zdbf2	4930431J08Rik|9330107J05Rik	zinc finger, DBF-type containing 2	protein-coding
mm_151816.1	chr19	5503749	5503760	-	1	NA	promoter-TSS (NM_023781)	promoter-TSS (NM_023781)	33	NM_023781	75555	Mm.440432	NM_023781	ENSMUSG00000100937	1700020D05Rik	mage-g2	RIKEN cDNA 1700020D05 gene	protein-coding
mm_26103.1	chr3	137341033	137341046	+	1	NA	promoter-TSS (NM_016885)	promoter-TSS (NM_016885)	-39	NM_001163522	59308	Mm.27343	NM_016885	ENSMUSG00000054690	Emcn	0610012K22Rik|AI315669|Muc14	endomucin	protein-coding
mm_100309.1	chr11	117976321	117976360	+	1	NA	Intergenic	Intergenic	-6974	NM_007707	12702	Mm.3468	NM_007707	ENSMUSG00000053113	Socs3	Cis3|Cish3|EF-10|Ef10|SSI-3|Ssi3	suppressor of cytokine signaling 3	protein-coding
mm_64632.1	chr7	3693555	3693579	-	1	NA	promoter-TSS (NM_029934)	promoter-TSS (NM_029934)	-42	NM_029934	77582	Mm.397541	NM_029934	ENSMUSG00000035596	Mboat7	5730589L02Rik|BB1|Leng4|Lpiat|Lpiat1|mBB1	membrane bound O-acyltransferase domain containing 7	protein-coding
mm_154000.1	chr19	52264951	52264956	-	1	NA	TTS (NM_008386)	TTS (NM_008386)	656	NM_008386	16333	Mm.46269	NM_008386	ENSMUSG00000035804	Ins1	Ins-1|Ins2-rs1	insulin I	protein-coding
mm_170305.1	chr18	34945973	34945985	-	1	NA	exon (NM_010481, exon 9 of 17)	exon (NM_010481, exon 9 of 17)	8372	NM_010481	15526	Mm.209419	NM_010481	ENSMUSG00000024359	Hspa9	74kDa|Csa|Grp75|Hsc74|Hsp74|Hsp74a|Hspa9a|Mortalin|Mot-2|Mot2|Mthsp70|Pbp74	heat shock protein 9	protein-coding
mm_48042.1	chr5	136423102	136423111	-	1	NA	intron (NM_001291239, intron 2 of 22)	intron (NM_001291239, intron 2 of 22)	-47303	NR_030500	723975		NR_030500	ENSMUSG00000106479	Mir721	Mirn721|miRY|mir-721|mmu-mir-721	microRNA 721	ncRNA
mm_127410.1	chr15	101254512	101254518	+	1	NA	Intergenic	Intergenic	-12331	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_149798.1	chr19	23675840	23675863	+	1	NA	Intergenic	Intergenic	-11549	NM_028208	72351	Mm.474795	NM_028208	ENSMUSG00000074925	Ptar1	1700084D09Rik|2010013L17Rik|4930428J16Rik|AI449677	protein prenyltransferase alpha subunit repeat containing 1	protein-coding
mm_165393.1	chr2	131936815	131936826	+	1	NA	exon (NM_001278256, exon 4 of 4)	exon (NM_001278256, exon 4 of 4)	-14041	NM_001278257	26434	Mm.180750	NM_023043	ENSMUSG00000027338	Prnd	AI450264|Dpl|PrPLP|doppel	prion protein dublet	protein-coding
mm_39215.1	chr4	156186073	156186091	-	1	NA	intron (NM_021604, intron 2 of 35)	intron (NM_021604, intron 2 of 35)	11406	NM_021604	11603	Mm.273098	NM_021604	ENSMUSG00000041936	Agrn	Agrin|nmf380	agrin	protein-coding
mm_157144.1	chrX	9460703	9460718	-	1	NA	intron (NM_007807, intron 3 of 12)	intron (NM_007807, intron 3 of 12)	8614	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_44566.1	chr5	24685415	24685439	-	1	NA	promoter-TSS (NM_001305264)	promoter-TSS (NM_001305264)	-388	NM_016736	53312	Mm.5856	NM_016736	ENSMUSG00000028954	Nub1	4931404D21Rik|6330412F12Rik|BS4|NY-REN-18	negative regulator of ubiquitin-like proteins 1	protein-coding
mm_120259.1	chr14	63046966	63046984	+	1	NA	promoter-TSS (NM_001034910)	promoter-TSS (NM_001034910)	-16	NM_001034910	619548	Mm.387101	NM_001034910	ENSMUSG00000054763	Defb42	BD-42|Defb44|mBD-42	defensin beta 42	protein-coding
mm_121713.1	chr14	16173321	16173321	-	1	NA	Intergenic	Intergenic	-75993	NM_021504	59007	Mm.258381	NM_021504	ENSMUSG00000021785	Ngly1	1110002C09Rik|PNGase|Png1	N-glycanase 1	protein-coding
mm_142125.1	chr17	35897327	35897331	-	1	NA	promoter-TSS (NM_001033630)	promoter-TSS (NM_001033630)	49	NM_001033630	69662	Mm.260159	NM_001033630	ENSMUSG00000050705	2310061I04Rik	-	RIKEN cDNA 2310061I04 gene	protein-coding
mm_29891.1	chr3	131272078	131272078	-	1	NA	promoter-TSS (NM_008212)	promoter-TSS (NM_008212)	23	NM_008212	15107	Mm.260164	NM_008212	ENSMUSG00000027984	Hadh	AA409008|AU019341|AW742602|HCDH|Hadhsc|Schad	hydroxyacyl-Coenzyme A dehydrogenase	protein-coding
mm_82792.1	chr9	29411754	29411773	-	1	NA	intron (NM_172290, intron 1 of 7)	CpG	551366	NM_172290	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding
mm_29846.1	chr3	129901345	129901362	-	1	NA	promoter-TSS (NM_009811)	promoter-TSS (NM_009811)	-62	NM_009811	12368	Mm.281379	NM_009811	ENSMUSG00000027997	Casp6	CASP-6|Mch2	caspase 6	protein-coding
mm_49186.1	chr6	15185440	15185452	+	1	NA	promoter-TSS (NM_001286607)	promoter-TSS (NM_001286607)	-60	NM_212435	114142	Mm.332919	NM_053242	ENSMUSG00000029563	Foxp2	2810043D05Rik|AI449000|CAG-16|D0Kist7	forkhead box P2	protein-coding
mm_132841.1	chr16	45936308	45936317	+	1	NA	Intergenic	ID4|SINE|ID	74101	NM_001134480	433022	Mm.380993	NM_001134480	ENSMUSG00000087141	Plcxd2	AW494639|EG433022	phosphatidylinositol-specific phospholipase C, X domain containing 2	protein-coding
mm_68297.1	chr7	105739140	105739143	-	1	NA	intron (NM_010562, intron 2 of 12)	intron (NM_010562, intron 2 of 12)	-1756	NM_133951	101867	Mm.231400	NM_025897	ENSMUSG00000030888	Rrp8	1500003O22Rik|2900001K19Rik|AW538116	ribosomal RNA processing 8, methyltransferase, homolog (yeast)	protein-coding
mm_60946.1	chr7	46986815	46986831	+	1	NA	intron (NR_033461, intron 3 of 4)	intron (NR_033461, intron 3 of 4)	10191	NR_033461	629141	Mm.229259	NR_033461	ENSMUSG00000056509	Gm9999	ENSMUSG00000056509	predicted gene 9999	ncRNA
mm_54349.1	chr6	30896736	30896785	-	1	NA	promoter-TSS (NM_017478)	promoter-TSS (NM_017478)	34	NM_017478	54160	Mm.39896	NM_017478	ENSMUSG00000025607	Copg2	AW227625|gamma-2-COP	coatomer protein complex, subunit gamma 2	protein-coding
mm_146246.1	chr18	77733031	77733032	+	1	NA	Intergenic	Intergenic	18847	NR_027978	67640	Mm.482903	NM_026289		4930465K10Rik	-	RIKEN cDNA 4930465K10 gene	ncRNA
mm_171481.1	chr4	145868811	145868825	+	1	NA	Intergenic	Intergenic	31599	NR_033612	236069	Mm.276881	NR_033612	ENSMUSG00000096233	Gm13238	OTTMUSG00000011065	carnitine deficiency-associated gene expressed in ventricle 3 pseudogene	pseudo
mm_49829.1	chr6	37806685	37806709	+	1	NA	Intergenic	Intergenic	-64114	NM_001272064	21848	Mm.41063	NM_145076	ENSMUSG00000029833	Trim24	A130082H20Rik|AI447469|D430004I05Rik|TIF1|TIF1-alpha|TIF1alpha|Tif1a	tripartite motif-containing 24	protein-coding
mm_57673.1	chr6	128492188	128492196	-	1	NA	exon (NM_007376, exon 23 of 36)	exon (NM_007376, exon 23 of 36)	34528	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_124739.1	chr15	6592848	6592858	+	1	NA	intron (NM_011815, intron 1 of 17)	intron (NM_011815, intron 1 of 17)	13006	NM_011815	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_116700.1	chr13	50443851	50443860	-	1	NA	Intergenic	Intergenic	-23452	NM_001033400	328250	Mm.315205	NM_001033400	ENSMUSG00000071909	Nutm2	Fam22|Gm806	NUT family member 2	protein-coding
mm_171779.1	chr5	109996529	109996531	+	1	NA	promoter-TSS (NM_145563)	promoter-TSS (NM_145563)	3	NM_145563	69504	Mm.441438	NM_145563	ENSMUSG00000066613	Zfp932	2310001H12Rik|Znf431	zinc finger protein 932	protein-coding
mm_96908.1	chr11	70459427	70459527	+	1	NA	promoter-TSS (NM_001029929)	promoter-TSS (NM_001029929)	-145	NM_001029929	574428	Mm.472771	NM_001029929	ENSMUSG00000040829	Zmynd15	-	zinc finger, MYND-type containing 15	protein-coding
mm_120768.1	chr14	73510015	73510055	+	1	NA	promoter-TSS (NM_026119)	promoter-TSS (NM_026119)	-14	NM_026119	67381	Mm.282888	NM_026119	ENSMUSG00000022109	Med4	2410046H15Rik|DRIP36|HSPC126|TRAP36|Vdirp|Vdrip	mediator complex subunit 4	protein-coding
mm_136188.1	chr16	89010759	89010766	-	1	NA	promoter-TSS (NM_001191018)	promoter-TSS (NM_001191018)	-3	NM_001191018	68740	Mm.69020	NM_001191018	ENSMUSG00000095992	Krtap22-2	1110032D16Rik	keratin associated protein 22-2	protein-coding
mm_27625.1	chr3	59344439	59344449	-	1	NA	promoter-TSS (NM_001162884)	promoter-TSS (NM_001162884)	-188	NM_001162884	242050	Mm.228086	NM_001162884	ENSMUSG00000036334	Igsf10	6530405F15Rik|9030224D03|AA409708|AA536958|AI414626|Adlican2|CMF608	immunoglobulin superfamily, member 10	protein-coding
mm_172807.1	chr9	123461799	123461804	+	1	NA	3' UTR (NM_153168, exon 21 of 21)	3' UTR (NM_153168, exon 21 of 21)	-16900	NM_013860	29806	Mm.10987	NM_013860	ENSMUSG00000025239	Limd1	AW822033|D9Ertd192e	LIM domains containing 1	protein-coding
mm_37964.1	chr4	133417147	133417153	-	1	NA	intron (NM_016981, intron 4 of 11)	intron (NM_016981, intron 4 of 11)	47374	NR_039582	100628620		NR_039582	ENSMUSG00000092745	Mir5122	mmu-mir-5122|mu-mir-5122	microRNA 5122	ncRNA
mm_56046.1	chr6	86737702	86737715	-	1	NA	3' UTR (NM_001331120, exon 13 of 13)	3' UTR (NM_001331120, exon 13 of 13)	-4330	NM_011818	23885	Mm.321452	NM_011818	ENSMUSG00000001157	Gmcl1	2810049L19Rik|Btbd13|DIP|Gcl|Gcl-1|glc-1|mglc-1	germ cell-less, spermatogenesis associated 1	protein-coding
mm_51409.1	chr6	78380722	78380739	+	1	NA	promoter-TSS (NM_011259)	promoter-TSS (NM_011259)	21	NM_011259	19694	Mm.2552	NM_011259	ENSMUSG00000079516	Reg3a	AV063448	regenerating islet-derived 3 alpha	protein-coding
mm_81013.1	chr9	104063717	104063736	+	1	NA	promoter-TSS (NM_175324)	promoter-TSS (NM_175324)	23	NM_175324	102632	Mm.41274	NM_175324	ENSMUSG00000090150	Acad11	5730439E10Rik|AI987948	acyl-Coenzyme A dehydrogenase family, member 11	protein-coding
mm_85175.1	chr9	96525260	96525284	-	1	NA	Intergenic	Intergenic	-46597	NM_001311135	19823	Mm.28235	NM_011279	ENSMUSG00000051234	Rnf7	Rbx2|SAG	ring finger protein 7	protein-coding
mm_92203.1	chr10	68136714	68136722	-	1	NA	intron (NM_023598, intron 4 of 9)	intron (NM_023598, intron 4 of 9)	142008	NM_023598	71371	Mm.440357	NM_023598	ENSMUSG00000019947	Arid5b	4930580B11|5430435G07Rik|AI467247|Desrt|Mrf2|Mrf2alpha|Mrf2beta	AT rich interactive domain 5B (MRF1-like)	protein-coding
mm_329.1	chr1	24864310	24864313	+	1	NA	Intergenic	L1MA5A|LINE|L1	185393	NM_001310483	68421	Mm.336563	NM_026719	ENSMUSG00000073725	Lmbrd1	0910001K20Rik|AV347960	LMBR1 domain containing 1	protein-coding
mm_67357.1	chr7	79837660	79837666	-	1	NA	intron (NM_008486, intron 9 of 19)	intron (NM_008486, intron 9 of 19)	4689	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_20717.1	chr2	134644156	134644166	-	1	NA	promoter-TSS (NM_029148)	promoter-TSS (NM_029148)	-40	NM_029148	52837	Mm.264096	NM_029148	ENSMUSG00000034723	Tmx4	2810417D04Rik|4930500L08Rik|AI843224|AW046784|D2Bwg1356e|Txndc13|mKIAA1162	thioredoxin-related transmembrane protein 4	protein-coding
mm_92930.1	chr10	84526973	84526987	-	1	NA	3' UTR (NM_175451, exon 2 of 2)	3' UTR (NM_175451, exon 2 of 2)	6908	NM_175451	216197	Mm.334999	NM_175451	ENSMUSG00000046841	Ckap4	5630400A09Rik|CLIMP-63|P63	cytoskeleton-associated protein 4	protein-coding
mm_98328.1	chr11	90586548	90586558	+	1	NA	intron (NM_011505, intron 10 of 17)	intron (NM_011505, intron 10 of 17)	51555	NM_011505	20913	Mm.207203	NM_011505	ENSMUSG00000020546	Stxbp4	6030470M02Rik|Synip	syntaxin binding protein 4	protein-coding
mm_114462.1	chr13	67660371	67660375	+	1	NA	Intergenic	Intergenic	-22620	NM_183146	212281	Mm.342918	NM_183146	ENSMUSG00000021510	Zfp729a	A530054K11Rik|Rslcan3	zinc finger protein 729a	protein-coding
mm_81275.1	chr9	108145978	108145996	+	1	NA	intron (NM_007567, intron 1 of 11)	RMER10A|LTR|ERVL	9132	NR_126077	76873	Mm.436935	NR_126077	ENSMUSG00000102224	4930447F24Rik	-	RIKEN cDNA 4930447F24 gene	ncRNA
mm_100786.1	chr11	4849102	4849118	-	1	NA	5' UTR (NM_001252252, exon 1 of 16)	5' UTR (NM_001252252, exon 1 of 16)	434	NM_001252250	18016	Mm.297109	NM_010898	ENSMUSG00000009073	Nf2	merlin	neurofibromin 2	protein-coding
mm_41995.1	chr5	107830224	107830234	+	1	NA	promoter-TSS (NM_001276397)	promoter-TSS (NM_001276397)	67	NM_001276397	73318	Mm.441500	NM_028502	ENSMUSG00000063447	Ube2d2b	1700013N18Rik	ubiquitin-conjugating enzyme E2D 2B	protein-coding
mm_54945.1	chr6	48572824	48572826	-	1	NA	promoter-TSS (NM_001347168)	promoter-TSS (NM_001347168)	-23	NM_001347167	71660	Mm.28231	NM_027852	ENSMUSG00000009281	Rarres2	0610007L05Rik|AI303516	retinoic acid receptor responder (tazarotene induced) 2	protein-coding
mm_159947.1	chr6	85423886	85423886	+	1	NA	promoter-TSS (NM_001007472)	promoter-TSS (NM_001007472)	0	NM_001007472	384452	Mm.347883	NM_001007472	ENSMUSG00000068302	Noto	Flh|MmNot|Not|tc	notochord homeobox	protein-coding
mm_149230.1	chr19	10182869	10182879	+	1	NA	promoter-TSS (NM_146094)	promoter-TSS (NM_146094)	-14	NM_146094	76267	Mm.30158	NM_146094	ENSMUSG00000010663	Fads1	0710001O03Rik|A930006B21Rik|AI317215|DSD	fatty acid desaturase 1	protein-coding
mm_155164.1	chrX	53002159	53002185	+	1	NA	exon (NM_013556, exon 3 of 9)	exon (NM_013556, exon 3 of 9)	14094	NM_013556	15452	Mm.299381	NM_013556	ENSMUSG00000025630	Hprt	C81579|HPGRT|Hprt1	hypoxanthine guanine phosphoribosyl transferase	protein-coding
mm_82801.1	chr9	29468326	29468327	-	1	NA	intron (NM_172290, intron 1 of 7)	intron (NM_172290, intron 1 of 7)	494803	NM_172290	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding
mm_167589.1	chr9	46240971	46240979	+	1	NA	5' UTR (NM_007468, exon 1 of 3)	5' UTR (NM_007468, exon 1 of 3)	131	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_105446.1	chr11	104442233	104442291	-	1	NA	promoter-TSS (NM_001081045)	promoter-TSS (NM_001081045)	29	NM_001081045	76719	Mm.136418	NM_001081045	ENSMUSG00000018412	Kansl1	1700081L11Rik|9430041J06Rik|mKIAA1267	KAT8 regulatory NSL complex subunit 1	protein-coding
mm_55606.1	chr6	71831171	71831200	-	1	NA	promoter-TSS (NM_029673)	promoter-TSS (NM_029673)	-135	NM_001253681	76614	Mm.235123	NM_029673	ENSMUSG00000052337	Immt	1700082C19Rik|D830041H16Rik|HMP|P87|P87/89|P89	inner membrane protein, mitochondrial	protein-coding
mm_99469.1	chr11	102436041	102436052	+	1	NA	TTS (NM_199200)	TTS (NM_199200)	5724	NM_008175	14824	Mm.1568	NM_008175	ENSMUSG00000034708	Grn	Pgrn|epithelin	granulin	protein-coding
mm_168797.1	chr1	21961392	21961394	-	1	NA	exon (NM_023872, exon 1 of 14)	exon (NM_023872, exon 1 of 14)	549	NM_001160139	226922	Mm.336519	NM_023872	ENSMUSG00000028033	Kcnq5	7730402H11|9230107O05Rik|AA589396|D1Mgi1	potassium voltage-gated channel, subfamily Q, member 5	protein-coding
mm_145543.1	chr18	60807997	60808040	+	1	NA	exon (NM_010545, exon 2 of 8)	exon (NM_010545, exon 2 of 8)	-4058	NR_039567	100628611		NR_039567	ENSMUSG00000093327	Mir5107	mir-5107|mmu-mir-5107|mu-mir-5107	microRNA 5107	ncRNA
mm_60873.1	chr7	45942294	45942298	+	1	NA	intron (NM_001033243, intron 7 of 12)	intron (NM_001033243, intron 7 of 12)	13898	NM_001033243	211535	Mm.227539	NM_001033243	ENSMUSG00000040189	Ccdc114	-	coiled-coil domain containing 114	protein-coding
mm_47306.1	chr5	122396891	122396903	-	1	NA	exon (NM_019824, exon 2 of 7)	exon (NM_019824, exon 2 of 7)	5019	NM_019824	56378	Mm.275942	NM_019824	ENSMUSG00000029465	Arpc3	1110006A04Rik|p21-ARC|p21-Ar|p21Arc	actin related protein 2/3 complex, subunit 3	protein-coding
mm_168840.1	chr12	23427123	23427126	-	1	NA	Intergenic	CpG	-416881	NR_015504	69732	Mm.391403	NM_028362	ENSMUSG00000073164	2410018L13Rik	2810480C08Rik	RIKEN cDNA 2410018L13 gene	ncRNA
mm_134452.1	chr16	18407999	18408024	-	1	NA	TTS (NM_001272032)	TTS (NM_001272032)	5483	NM_001111063	12846	Mm.100940	NM_007744	ENSMUSG00000000326	Comt	Comt1|D16Wsu103e|D330014B15Rik	catechol-O-methyltransferase	protein-coding
mm_134598.1	chr16	20621210	20621229	-	1	NA	promoter-TSS (NM_028420)	promoter-TSS (NM_028420)	59	NM_028420	73047	Mm.425977	NM_028420	ENSMUSG00000051146	Camk2n2	2900075A18Rik	calcium/calmodulin-dependent protein kinase II inhibitor 2	protein-coding
mm_91664.1	chr10	42999149	42999161	-	1	NA	Intergenic	Intergenic	138643	NM_172938	268297	Mm.98731	NM_172938	ENSMUSG00000044770	Scml4	9330161D17|mFLJ00197	sex comb on midleg-like 4 (Drosophila)	protein-coding
mm_11380.1	chr2	31245906	31245916	+	1	NA	promoter-TSS (NM_019681)	promoter-TSS (NM_019681)	-12	NM_019681	14299	Mm.249318	NM_019681	ENSMUSG00000062661	Ncs1	9430075O15Rik|A730032G13Rik|AI836659|Freq|Mfreq|NCS-1	neuronal calcium sensor 1	protein-coding
mm_13996.1	chr2	121934824	121934842	+	1	NA	3' UTR (NM_199038, exon 8 of 8)	3' UTR (NM_199038, exon 8 of 8)	-21168	NM_001290992	329506	Mm.249405	NM_212450	ENSMUSG00000033411	Ctdspl2	D2Ertd485e	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase like 2	protein-coding
mm_144671.1	chr18	34624622	34624629	+	1	NA	promoter-TSS (NM_009004)	promoter-TSS (NM_009004)	1	NM_001166407	19348	Mm.258846	NM_009004	ENSMUSG00000003779	Kif20a	AA415432|Rab6kifl	kinesin family member 20A	protein-coding
mm_146788.1	chr18	20114703	20114713	-	1	NA	promoter-TSS (NM_001291804)	promoter-TSS (NM_001291804)	65	NM_001291804	13505	Mm.33740	NM_013504	ENSMUSG00000044322	Dsc1	1110020A10Rik|AI507491	desmocollin 1	protein-coding
mm_9374.1	chr1	172210107	172210126	-	1	NA	3' UTR (NM_009813, exon 11 of 11)	3' UTR (NM_009813, exon 11 of 11)	-3312	NM_011063	18611	Mm.544	NM_011063	ENSMUSG00000013698	Pea15a	Mat1|PEA-15|Pea15|Pkcs15	phosphoprotein enriched in astrocytes 15A	protein-coding
mm_29196.1	chr3	106762118	106762181	-	1	NA	exon (NM_007651, exon 7 of 8)	exon (NM_007651, exon 7 of 8)	28000	NM_007651	12508	Mm.316861	NM_007651	ENSMUSG00000040747	Cd53	AI323659|Ox-44|Tspan25	CD53 antigen	protein-coding
mm_18094.1	chr2	44986535	44986560	-	1	NA	3' UTR (NM_015753, exon 10 of 10)	3' UTR (NM_015753, exon 10 of 10)	36630	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_115436.1	chr13	117601828	117601832	+	1	NA	promoter-TSS (NM_010408)	promoter-TSS (NM_010408)	-490	NM_010408	15165	Mm.343429	NM_010408	ENSMUSG00000021730	Hcn1	Bcng1|C630013B14Rik|HAC2	hyperpolarization-activated, cyclic nucleotide-gated K+ 1	protein-coding
mm_30452.1	chr3	153866615	153866619	-	1	NA	intron (NM_031870, intron 16 of 19)	intron (NM_031870, intron 16 of 19)	-14193	NR_040373	72317	Mm.440147	NR_040373	ENSMUSG00000086438	Asb17os	2510003D18Rik	ankyrin repeat and SOCS box-containing 17, opposite strand	ncRNA
mm_103609.1	chr11	78512106	78512148	-	1	NA	promoter-TSS (NM_026389)	promoter-TSS (NM_026389)	41	NM_199199	195040	Mm.383431	NM_199199	ENSMUSG00000051232	Tmem199	AI316787|AI848469|R74819	transmembrane protein 199	protein-coding
mm_147139.1	chr18	36453831	36453835	-	1	NA	intron (NM_026027, intron 1 of 3)	B4|SINE|B4	662	NM_026027	67199	Mm.30184	NM_026027	ENSMUSG00000024346	Pfdn1	2700086I23Rik|AA408327|AU044714	prefoldin 1	protein-coding
mm_145650.1	chr18	61129049	61129077	+	1	NA	exon (NM_001037859, exon 18 of 22)	exon (NM_001037859, exon 18 of 22)	11595	NR_105949	102466212		NR_105949	ENSMUSG00000098389	Mir6983	Gm27496|mmu-mir-6983	microRNA 6983	ncRNA
mm_22039.1	chr2	168207006	168207014	-	1	NA	5' UTR (NM_009628, exon 1 of 4)	5' UTR (NM_009628, exon 1 of 4)	102	NM_009628	11538	Mm.201322	NM_009628	ENSMUSG00000051149	Adnp	AA589558|mKIAA0784	activity-dependent neuroprotective protein	protein-coding
mm_94331.1	chr11	4316157	4316168	+	1	NA	Intergenic	RLTR20B2|LTR|ERVK	49366	NM_001039537	16878	Mm.4964	NM_008501	ENSMUSG00000034394	Lif	-	leukemia inhibitory factor	protein-coding
mm_44470.1	chr5	23403287	23403308	-	1	NA	Intergenic	RMER10A|LTR|ERVL	31056	NR_040469	269630	Mm.425231	NR_040469	ENSMUSG00000073147	5031425E22Rik	-	RIKEN cDNA 5031425E22 gene	ncRNA
mm_85269.1	chr9	99436549	99436562	-	1	NA	5' UTR (NM_008624, exon 1 of 6)	5' UTR (NM_008624, exon 1 of 6)	157	NM_008624	17532	Mm.2045	NM_008624	ENSMUSG00000032470	Mras	2900078C09Rik|AI326250	muscle and microspikes RAS	protein-coding
mm_32132.1	chr4	99193897	99193935	+	1	NA	promoter-TSS (NM_001145967)	promoter-TSS (NM_001145967)	-18	NM_175029	242557	Mm.241663	NM_175029	ENSMUSG00000028550	Atg4c	Apg4-C|Apg4c|Atg4cl|Autl1	autophagy related 4C, cysteine peptidase	protein-coding
mm_55358.1	chr6	56923487	56923495	-	1	NA	intron (NM_026004, intron 1 of 8)	intron (NM_026004, intron 1 of 8)	441	NM_026004	107569	Mm.158936	NM_026004	ENSMUSG00000029780	Nt5c3	1600024P05Rik|2610206B05Rik|3110004A18Rik|AI842776|Nt5c3a|Nt5y|PN-1|PN-I|PSN1|UMPH|Umph-1|Umph1|cN-III|lupin|p36	5'-nucleotidase, cytosolic III	protein-coding
mm_120429.1	chr14	65731033	65731053	+	1	NA	exon (NM_001168318, exon 4 of 8)	exon (NM_001168318, exon 4 of 8)	64640	NM_001168318	71145	Mm.83840	NM_028903	ENSMUSG00000022032	Scara5	4932433F15Rik|4933425F03Rik|AV278087|Tesr	scavenger receptor class A, member 5	protein-coding
mm_122673.1	chr14	52008696	52008712	-	1	NA	exon (NM_001253694, exon 4 of 6)	exon (NM_001253694, exon 4 of 6)	5854	NM_001253695	69890	Mm.475652	NM_027248	ENSMUSG00000049295	Zfp219	2010302A17Rik	zinc finger protein 219	protein-coding
mm_18497.1	chr2	62606415	62606464	-	1	NA	exon (NM_027835, exon 10 of 16)	exon (NM_027835, exon 10 of 16)	-32418	NM_007986	14089	Mm.41816	NM_007986	ENSMUSG00000000392	Fap	SIMP	fibroblast activation protein	protein-coding
mm_110681.1	chr12	67082117	67082123	-	1	NA	intron (NM_001193266, intron 1 of 16)	intron (NM_001193266, intron 1 of 16)	140429	NM_001193266	320772	Mm.227680	NM_207010	ENSMUSG00000034912	Mdga2	6720489L24Rik|9330209L04Rik|Adp|Mamdc1	MAM domain containing glycosylphosphatidylinositol anchor 2	protein-coding
mm_64214.1	chr7	141482029	141482086	+	1	NA	intron (NM_001252588, intron 1 of 7)	CpG	5677	NM_001252588	64540	Mm.489619	NM_053082	ENSMUSG00000025511	Tspan4	AI325509|AI746565|D130042I01Rik|NAG-2|Tm4sf7|Tspan-4	tetraspanin 4	protein-coding
mm_165581.1	chr3	28581186	28581192	+	1	NA	intron (NM_026910, intron 12 of 32)	intron (NM_026910, intron 12 of 32)	-116714	NM_031197	20526	Mm.18443	NM_031197	ENSMUSG00000027690	Slc2a2	AI266973|Glut-2|Glut2	solute carrier family 2 (facilitated glucose transporter), member 2	protein-coding
mm_65984.1	chr7	30457398	30457435	-	1	NA	promoter-TSS (NM_172898)	promoter-TSS (NM_172898)	99	NM_172898	243911	Mm.113908	NM_172898	ENSMUSG00000036915	Kirrel2	C330019F22Rik|NEPH3|NLG1	kin of IRRE like 2 (Drosophila)	protein-coding
mm_27665.1	chr3	65380783	65380793	-	1	NA	3' UTR (NM_026155, exon 5 of 5)	3' UTR (NM_026155, exon 5 of 5)	11765	NM_026155	67437	Mm.232728	NM_026155	ENSMUSG00000027828	Ssr3	0610038P07Rik|AL022999|AU022074|AW553833|TRAPG	signal sequence receptor, gamma	protein-coding
mm_173011.1	chrM	423	423	+	1	NA	NA	Intergenic	NA	NA								
mm_25928.1	chr3	131206521	131206524	+	1	NA	intron (NM_001276403, intron 11 of 11)	L1MEg|LINE|L1	65579	NM_008212	15107	Mm.260164	NM_008212	ENSMUSG00000027984	Hadh	AA409008|AU019341|AW742602|HCDH|Hadhsc|Schad	hydroxyacyl-Coenzyme A dehydrogenase	protein-coding
mm_14966.1	chr2	152081811	152081825	+	1	NA	5' UTR (NM_001160410, exon 1 of 2)	5' UTR (NM_001160410, exon 1 of 2)	289	NM_001160410	545474	Mm.214317	NM_001160410	ENSMUSG00000060257	Scrt2	AW060659	scratch family zinc finger 2	protein-coding
mm_44304.1	chr5	8996903	8996922	-	1	NA	intron (NM_023733, intron 1 of 17)	intron (NM_023733, intron 1 of 17)	234	NM_023733	74114	Mm.28197	NM_023733	ENSMUSG00000003623	Crot	1200003H03Rik	carnitine O-octanoyltransferase	protein-coding
mm_122379.1	chr14	40295559	40295572	-	1	NA	Intergenic	Intergenic	597400	NM_177816	328381	Mm.235694	NM_177816	ENSMUSG00000037833	Sh2d4b	A430109M18Rik|D030001E08	SH2 domain containing 4B	protein-coding
mm_50640.1	chr6	51330702	51330716	+	1	NA	Intergenic	Intergenic	-49001	NR_110455	625167	Mm.389772	NR_110455	ENSMUSG00000107660	Gm6559	EG625167	predicted gene 6559	ncRNA
mm_66827.1	chr7	48748187	48748201	-	1	NA	Intergenic	Lx4A|LINE|L1	-40809	NM_028031	243983	Mm.279116	NM_028031	ENSMUSG00000030471	Zdhhc13	2410004E01Rik|C530010M18|HIP3RP|Hip14l|kojak|skc4	zinc finger, DHHC domain containing 13	protein-coding
mm_15016.1	chr2	152604446	152604450	+	1	NA	5' UTR (NM_001037247, exon 1 of 2)	5' UTR (NM_001037247, exon 1 of 2)	121	NM_001037247	266620	Mm.330669	NM_001037247	ENSMUSG00000044863	Defb36	BD-36|Defb123|mBD-36	defensin beta 36	protein-coding
mm_46600.1	chr5	107859211	107859212	-	1	NA	intron (NM_007964, intron 1 of 17)	intron (NM_007964, intron 1 of 17)	15896	NM_007964	14020	Mm.35796	NM_007964	ENSMUSG00000011831	Evi5	NB4S	ecotropic viral integration site 5	protein-coding
mm_152628.1	chr19	12487041	12487060	-	1	NA	intron (NM_172442, intron 2 of 8)	intron (NM_172442, intron 2 of 8)	14946	NM_172442	207521	Mm.247695	NM_172442	ENSMUSG00000039982	Dtx4	AI449438|BC044798|D930042H13|RNF155	deltex 4, E3 ubiquitin ligase	protein-coding
mm_60151.1	chr7	38379352	38379383	+	1	NA	Intergenic	Intergenic	-108019	NM_025390	66161	Mm.22284	NM_025390	ENSMUSG00000030423	Pop4	1110023P21Rik|Rpp29	processing of precursor 4, ribonuclease P/MRP family, (S. cerevisiae)	protein-coding
mm_39367.1	chr5	9266098	9266202	+	1	NA	promoter-TSS (NM_172706)	promoter-TSS (NM_172706)	-43	NM_172706	231014	Mm.130063	NM_172706	ENSMUSG00000056004	9330182L06Rik	Eig121l	RIKEN cDNA 9330182L06 gene	protein-coding
mm_52658.1	chr6	117879998	117880046	+	1	NA	Intergenic	Intergenic	16945	NM_001001792	22685	Mm.249661	NM_008616	ENSMUSG00000042097	Zfp239	Mok-2|Mok2|Znf239	zinc finger protein 239	protein-coding
mm_149170.1	chr19	9083700	9083704	+	1	NA	TTS (NM_011681)	TTS (NM_011681)	4254	NM_011681	22287	Mm.2258	NM_011681	ENSMUSG00000024653	Scgb1a1	CC10|CC16|CCSP|PCB-BP|UG|UGB|Utg	secretoglobin, family 1A, member 1 (uteroglobin)	protein-coding
mm_43188.1	chr5	128603661	128603665	+	1	NA	3' UTR (NM_175284, exon 1 of 1)	3' UTR (NM_175284, exon 1 of 1)	2557	NM_175284	93897	Mm.197628	NM_175284	ENSMUSG00000081683	Fzd10	Fz-10	frizzled class receptor 10	protein-coding
mm_160618.1	chr9	89211397	89211397	+	1	NA	intron (NM_026829, intron 1 of 2)	CpG	207	NM_026829	107885	Mm.486274	NM_026829	ENSMUSG00000066442	Mthfs	1110034I12Rik|2310020H23Rik|AI119695	5, 10-methenyltetrahydrofolate synthetase	protein-coding
mm_9020.1	chr1	166236908	166236925	-	1	NA	exon (NM_175296, exon 3 of 12)	exon (NM_175296, exon 3 of 12)	1828	NM_175296	98558	Mm.26189	NM_175296	ENSMUSG00000040629	Mael	4933405K18Rik|AU019877	maelstrom spermatogenic transposon silencer	protein-coding
mm_40515.1	chr5	57810252	57810253	+	1	NA	intron (NM_001310608, intron 1 of 3)	intron (NM_001310608, intron 1 of 3)	92171	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_57066.1	chr6	122571379	122571420	-	1	NA	Intergenic	Intergenic	17590	NM_009645	11628	Mm.391503	NM_009645	ENSMUSG00000040627	Aicda	Aid|Arp2	activation-induced cytidine deaminase	protein-coding
mm_135473.1	chr16	45910462	45910503	-	1	NA	Intergenic	B3A|SINE|B2	-66104	NM_001252442	208177	Mm.211477	NM_153412	ENSMUSG00000033149	Phldb2	AV253284|C820004H04Rik|LL5b|LL5beta	pleckstrin homology like domain, family B, member 2	protein-coding
mm_49202.1	chr6	15365213	15365216	+	1	NA	intron (NM_053242, intron 5 of 18)	intron (NM_053242, intron 5 of 18)	179708	NM_001286607	114142	Mm.332919	NM_053242	ENSMUSG00000029563	Foxp2	2810043D05Rik|AI449000|CAG-16|D0Kist7	forkhead box P2	protein-coding
mm_72924.1	chr8	91106390	91106414	+	1	NA	exon (NM_001282001, exon 15 of 22)	exon (NM_001282001, exon 15 of 22)	27625	NM_001302337	14339	Mm.324588	NM_010241	ENSMUSG00000031667	Aktip	AL023020|Fif|Ft|Ft1|Fts	thymoma viral proto-oncogene 1 interacting protein	protein-coding
mm_126184.1	chr15	78615762	78615780	+	1	NA	exon (NM_028195, exon 9 of 13)	exon (NM_028195, exon 9 of 13)	18724	NM_028195	72318	Mm.32911	NM_028195	ENSMUSG00000018008	Cyth4	2510004M07Rik|5830469K17Rik|AI467541|Pscd4|mFLJ00017	cytohesin 4	protein-coding
mm_30319.1	chr3	151731702	151731702	-	1	NA	3' UTR (NM_133871, exon 8 of 8)	3' UTR (NM_133871, exon 8 of 8)	18257	NM_133871	99899	Mm.30756	NM_133871	ENSMUSG00000028037	Ifi44	A430056A10Rik|AW261460|MTAP44|p44	interferon-induced protein 44	protein-coding
mm_113076.1	chr13	23807066	23807077	+	1	NA	promoter-TSS (NM_144836)	promoter-TSS (NM_144836)	44	NM_144836	218103	Mm.24030	NM_144836	ENSMUSG00000036110	Slc17a2	C730032N17Rik|NPT3	solute carrier family 17 (sodium phosphate), member 2	protein-coding
mm_87500.1	chr10	51677767	51677789	+	1	NA	promoter-TSS (NM_001159389)	promoter-TSS (NM_001159389)	18	NM_001159389	320995	Mm.109190	NM_177306	ENSMUSG00000019900	Rfx6	4930572O07Rik|Rfxdc1	regulatory factor X, 6	protein-coding
mm_153126.1	chr19	34165918	34165951	-	1	NA	5' UTR (NM_024204, exon 1 of 6)	5' UTR (NM_024204, exon 1 of 6)	107	NM_024204	52024	Mm.183030	NM_024204	ENSMUSG00000024774	Ankrd22	5430429D21Rik|D19Ertd675e	ankyrin repeat domain 22	protein-coding
mm_119988.1	chr14	55578543	55578561	+	1	NA	promoter-TSS (NM_011189)	promoter-TSS (NM_011189)	58	NM_011189	19186	Mm.830	NM_011189	ENSMUSG00000022216	Psme1	AW413925|PA28a	proteasome (prosome, macropain) activator subunit 1 (PA28 alpha)	protein-coding
mm_113348.1	chr13	31806861	31806892	+	1	NA	5' UTR (NM_008592, exon 1 of 1)	5' UTR (NM_008592, exon 1 of 1)	230	NM_008592	17300	Mm.12949	NM_008592	ENSMUSG00000050295	Foxc1	FREAC3|Fkh1|Mf1|Mf4|ch|fkh-1|frkhda	forkhead box C1	protein-coding
mm_160398.1	chr8	70755545	70755545	+	1	NA	intron (NM_001166399, intron 1 of 4)	intron (NM_001166399, intron 1 of 4)	866	NM_001166399	19339	Mm.5083	NM_009001	ENSMUSG00000031840	Rab3a	-	RAB3A, member RAS oncogene family	protein-coding
mm_116675.1	chr13	49237600	49237607	-	1	NA	exon (NM_028340, exon 4 of 5)	exon (NM_028340, exon 4 of 5)	10560	NM_025491	66329	Mm.34308	NM_025491	ENSMUSG00000021384	Susd3	1700017I11Rik|2810440J20Rik	sushi domain containing 3	protein-coding
mm_27863.1	chr3	79158761	79158812	-	1	NA	Intergenic	L1_Mur3|LINE|L1	-12911	NM_001099624	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_93994.1	chr10	127534541	127534566	-	1	NA	promoter-TSS (NM_183297)	promoter-TSS (NM_183297)	6	NM_183297	104080	Mm.437200	NM_183297	ENSMUSG00000040258	Nxph4	1110036M10Rik|AI851051	neurexophilin 4	protein-coding
mm_31744.1	chr4	63283505	63283517	+	1	NA	intron (NM_025685, intron 22 of 60)	Charlie1b|DNA|hAT-Charlie	26660	NR_030477	735262		NR_030477	ENSMUSG00000070102	Mir455	Mirn455|mir-455|mmu-mir-455	microRNA 455	ncRNA
mm_128458.1	chr15	50785161	50785183	-	1	NA	intron (NM_001310485, intron 5 of 7)	(GA)n|Simple_repeat|Simple_repeat	103877	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_170610.1	chr19	5845565	5845565	-	1	NA	promoter-TSS (NR_003513)	promoter-TSS (NR_003513)	-85	NR_003513	66961	Mm.281895	NR_003513	ENSMUSG00000092274	Neat1	2310043N10Rik|VINC	nuclear paraspeckle assembly transcript 1 (non-protein coding)	ncRNA
mm_24611.1	chr3	93447485	93447496	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	5160	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_5101.1	chr1	5020300	5020336	-	1	NA	promoter-TSS (NM_021374)	promoter-TSS (NM_021374)	-779	NM_021374	58175	Mm.103771	NM_021374	ENSMUSG00000002459	Rgs20	2900073E09Rik|Rgsz1	regulator of G-protein signaling 20	protein-coding
mm_144169.1	chr18	6516669	6516672	+	1	NA	promoter-TSS (NM_007935)	promoter-TSS (NM_007935)	-562	NM_007935	13831	Mm.312133	NM_007935	ENSMUSG00000024240	Epc1	2400007E14Rik|5730566F07Rik|A930032N02Rik|mir-1893	enhancer of polycomb homolog 1 (Drosophila)	protein-coding
mm_150431.1	chr19	37536610	37536635	+	1	NA	Intergenic	Intergenic	-13796	NM_175353	107371	Mm.24865	NM_175353	ENSMUSG00000053799	Exoc6	4833405E05Rik|AW413330|C430002C19|Sec15|Sec15l1|hbd|msec15	exocyst complex component 6	protein-coding
mm_150600.1	chr19	40738887	40738921	+	1	NA	exon (NM_009848, exon 10 of 10)	exon (NM_009848, exon 10 of 10)	79134	NM_009848	12495	Mm.2824	NM_009848	ENSMUSG00000048120	Entpd1	2610206B08Rik|AA408691|Cd39|NTPDase-1	ectonucleoside triphosphate diphosphohydrolase 1	protein-coding
mm_55682.1	chr6	72611017	72611037	-	1	NA	TTS (NM_009444)	TTS (NM_009444)	5721	NM_009444	22135	Mm.246563	NM_009444		Tgoln2	TGN38B|TGN41|TGN46|Ttgn2	trans-golgi network protein 2	protein-coding
mm_70713.1	chr8	15060315	15060346	+	1	NA	intron (NM_008664, intron 1 of 36)	intron (NM_008664, intron 1 of 36)	2677	NM_008664	17930	Mm.272115	NM_008664	ENSMUSG00000031461	Myom2	AW146149	myomesin 2	protein-coding
mm_91118.1	chr10	19321715	19321720	-	1	NA	Intergenic	Intergenic	-34822	NM_053008	94222	Mm.156946	NM_053008	ENSMUSG00000045591	Olig3	Bhlhb7|bHLHe20|oligo3	oligodendrocyte transcription factor 3	protein-coding
mm_27348.1	chr3	50414921	50414939	-	1	NA	intron (NM_011990, intron 6 of 11)	intron (NM_011990, intron 6 of 11)	28683	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_35697.1	chr4	44152393	44152396	-	1	NA	exon (NM_175201, exon 2 of 11)	exon (NM_175201, exon 2 of 11)	15144	NM_175201	73469	Mm.262859	NM_175201	ENSMUSG00000035696	Rnf38	1700065B19Rik|2610202O07Rik|AA673263|Oip1	ring finger protein 38	protein-coding
mm_167368.1	chr8	89130329	89130346	+	1	NA	Intergenic	Intergenic	-86175	NM_021390	58198	Mm.214361	NM_021390	ENSMUSG00000031665	Sall1	Msal-3	sal-like 1 (Drosophila)	protein-coding
mm_57483.1	chr6	125254055	125254102	-	1	NA	Intergenic	Intergenic	-11447	NR_015527	73870	Mm.440681	NR_015527	ENSMUSG00000108129	4930417O13Rik	-	RIKEN cDNA 4930417O13 gene	ncRNA
mm_142577.1	chr17	46680848	46680859	-	1	NA	promoter-TSS (NM_010787)	promoter-TSS (NM_010787)	70	NM_001277311	17256	Mm.329083	NM_010787	ENSMUSG00000002768	Mea1	Mea-1	male enhanced antigen 1	protein-coding
mm_116642.1	chr13	49127870	49127883	-	1	NA	intron (NM_029361, intron 2 of 27)	intron (NM_029361, intron 2 of 27)	20452	NM_029361	75607	Mm.342723	NM_029361	ENSMUSG00000037989	Wnk2	1810073P09Rik|AW122246|ESTM15|X83337|mKIAA1760	WNK lysine deficient protein kinase 2	protein-coding
mm_156430.1	chrX	140998306	140998316	+	1	NA	Intergenic	Intergenic	-41600	NM_001164177	53380	Mm.17640	NM_016883	ENSMUSG00000031429	Psmd10	AW554874	proteasome (prosome, macropain) 26S subunit, non-ATPase, 10	protein-coding
mm_13876.1	chr2	119897548	119897591	+	1	NA	intron (NM_001164274, intron 1 of 22)	CpG	341	NM_013720	29808	Mm.87532	NM_013720	ENSMUSG00000033943	Mga	AV312082|C130042M01Rik|C80739|D030062C11Rik|Mad5	MAX gene associated	protein-coding
mm_171444.1	chr4	143546842	143546851	+	1	NA	Intergenic	MT2_Mm|LTR|ERVL	-4854	NM_001113736	100040854	Mm.472683	NM_001113736	ENSMUSG00000070616	Gm13040	OTTMUSG00000010130	predicted gene 13040	protein-coding
mm_16018.1	chr2	167503208	167503224	+	1	NA	intron (NM_030743, intron 2 of 7)	MLT1E1A|LTR|ERVL-MaLR	-10342	NM_170756	263876	Mm.34342	NM_170756	ENSMUSG00000047030	Spata2	AI504642|mKIAA0757	spermatogenesis associated 2	protein-coding
mm_45356.1	chr5	65929246	65929258	-	1	NA	Intergenic	Intergenic	-37872	NM_001081104	231252	Mm.140015	NM_001081104	ENSMUSG00000029205	Chrna9	2410015I05Rik|Acra9|EG666827|Gm8311	cholinergic receptor, nicotinic, alpha polypeptide 9	protein-coding
mm_137865.1	chr17	31296797	31296816	+	1	NA	5' UTR (NM_001242427, exon 1 of 20)	5' UTR (NM_001242427, exon 1 of 20)	582	NM_001242427	224674	Mm.311395	NM_153062	ENSMUSG00000024036	Slc37a1	G3PP	solute carrier family 37 (glycerol-3-phosphate transporter), member 1	protein-coding
mm_17931.1	chr2	35463500	35463528	-	1	NA	Intergenic	B3|SINE|B2	-2065	NM_001145821	14594	Mm.281124	NM_010283	ENSMUSG00000035778	Ggta1	AW108479|GALT|Gal|Ggta|Ggta-1|alpha Gal|alpha3GalT	glycoprotein galactosyltransferase alpha 1, 3	protein-coding
mm_84184.1	chr9	60141119	60141140	-	1	NA	promoter-TSS (NM_172444)	promoter-TSS (NM_172444)	91	NM_172444	207596	Mm.28791	NM_172444	ENSMUSG00000032289	Thsd4	ADAMTSL-6|ADAMTSL6|AI585901|Adamtsl4|B230114P05Rik	thrombospondin, type I, domain containing 4	protein-coding
mm_55590.1	chr6	71502831	71502838	-	1	NA	intron (NM_001308303, intron 2 of 3)	intron (NM_001308303, intron 2 of 3)	8957	NM_001308303	22644	Mm.422969	NM_009543	ENSMUSG00000052656	Rnf103	AW146237|AW212918|Zfp103|kf-1	ring finger protein 103	protein-coding
mm_30454.1	chr3	153912200	153912208	-	1	NA	promoter-TSS (NR_028525)	promoter-TSS (NR_028525)	-1	NR_028095	19352	Mm.277831	NM_011231	ENSMUSG00000038975	Rabggtb	-	Rab geranylgeranyl transferase, b subunit	protein-coding
mm_155595.1	chrX	81094593	81094610	+	1	NA	exon (NM_138751, exon 3 of 3)	exon (NM_138751, exon 3 of 3)	23957	NM_138751	192216	Mm.490421	NM_138751	ENSMUSG00000025666	Tmem47	3010015F07Rik|AI115536|BCMP1|Tm4sf10	transmembrane protein 47	protein-coding
mm_131233.1	chr16	10480066	10480080	+	1	NA	promoter-TSS (NM_001243760)	promoter-TSS (NM_001243760)	1	NM_001302618	12265	Mm.249560	NM_007575	ENSMUSG00000022504	Ciita	C2ta|EG669998|Gm9475|Mhc2ta	class II transactivator	protein-coding
mm_169760.1	chr15	93679987	93679995	-	1	NA	Intergenic	Intergenic	-84100	NM_001033217	106042	Mm.150314	NM_001033217	ENSMUSG00000036158	Prickle1	1110058P22Rik|AW215793|Prickle|b2b019Clo|mpk1	prickle planar cell polarity protein 1	protein-coding
mm_161875.1	chr18	37144048	37144048	+	1	NA	promoter-TSS (NM_001003672)	promoter-TSS (NM_001003672)	79	NM_001003672	353237	Mm.308500	NM_001003672	ENSMUSG00000102697	Pcdhac2	CNRc2	protocadherin alpha subfamily C, 2	protein-coding
mm_75189.1	chr8	38359773	38359775	-	1	NA	intron (NM_145841, intron 1 of 7)	intron (NM_145841, intron 1 of 7)	-107572	NR_029884	723860		NR_029884	ENSMUSG00000065457	Mir383	Mirn383|mir-383|mmu-mir-383	microRNA 383	ncRNA
mm_148041.1	chr18	70276207	70276213	-	1	NA	Intergenic	Intergenic	-31626	NM_029346	75577	Mm.58214	NM_029346	ENSMUSG00000024512	Dynap	2310002L13Rik	dynactin associated protein	protein-coding
mm_165346.1	chr2	118728326	118728336	-	1	NA	5' UTR (NM_177568, exon 1 of 32)	5' UTR (NM_177568, exon 1 of 32)	107	NM_177568	18796	Mm.215156	NM_177568	ENSMUSG00000040061	Plcb2	AI550384|B230205M18Rik|B230399N12	phospholipase C, beta 2	protein-coding
mm_18304.1	chr2	53153079	53153095	-	1	NA	exon (NM_018785, exon 13 of 26)	exon (NM_018785, exon 13 of 26)	38100	NM_018785	56194	Mm.257474	NM_018785	ENSMUSG00000061136	Prpf40a	2810012K09Rik|FBP-11|FBP11|Fnbp11|Fnbp3	pre-mRNA processing factor 40A	protein-coding
mm_44930.1	chr5	36165013	36165021	-	1	NA	intron (NM_030889, intron 2 of 26)	intron (NM_030889, intron 2 of 26)	-39004	NM_175249	76943	Mm.44242	NM_175249	ENSMUSG00000043430	Psapl1	2310020A21Rik	prosaposin-like 1	protein-coding
mm_132470.1	chr16	36694044	36694062	+	1	NA	promoter-TSS (NM_134109)	promoter-TSS (NM_134109)	75	NM_001285791	106347	Mm.17807	NM_134109	ENSMUSG00000022900	Ildr1	AU041483|AU044638	immunoglobulin-like domain containing receptor 1	protein-coding
mm_151107.1	chr19	47863407	47863418	+	1	NA	exon (NM_010362, exon 5 of 6)	exon (NM_010362, exon 5 of 6)	-2133	NM_030051	68214	Mm.63791	NM_026619	ENSMUSG00000025069	Gsto2	1700020F09Rik|4930425C18Rik|GSTO 2-2	glutathione S-transferase omega 2	protein-coding
mm_159494.1	chr4	42950854	42950854	+	1	NA	Intergenic	Intergenic	-2240	NM_019874	56323	Mm.20437	NM_019874	ENSMUSG00000036052	Dnajb5	1110058L06Rik|AI462558|Hsc40|Hsp40-3	DnaJ heat shock protein family (Hsp40) member B5	protein-coding
mm_49939.1	chr6	39592591	39592617	+	1	NA	promoter-TSS (NM_026612)	promoter-TSS (NM_026612)	21	NM_026612	68198	Mm.29415	NM_026612	ENSMUSG00000002416	Ndufb2	1810011O01Rik|8kDa|AGGG|AI325567|CI-AGGG	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 2	protein-coding
mm_98212.1	chr11	87799890	87799900	+	1	NA	exon (NM_010824, exon 9 of 14)	exon (NM_010824, exon 9 of 14)	6111	NM_010824	17523	Mm.4668	NM_010824	ENSMUSG00000009350	Mpo	mKIAA4033	myeloperoxidase	protein-coding
mm_158415.1	chrX	137119707	137119714	-	1	NA	intron (NM_007957, intron 1 of 4)	(A)n|Simple_repeat|Simple_repeat	616	NM_007957	13984	Mm.8017	NM_007957	ENSMUSG00000023443	Esx1	Spx1	extraembryonic, spermatogenesis, homeobox 1	protein-coding
mm_110642.1	chr12	58268931	58268943	-	1	NA	5' UTR (NM_025809, exon 1 of 1)	5' UTR (NM_025809, exon 1 of 1)	321	NM_025809	66864	Mm.280563	NM_025809	ENSMUSG00000045930	Clec14a	1200003C23Rik|AI642649	C-type lectin domain family 14, member a	protein-coding
mm_157505.1	chrX	48868188	48868198	-	1	NA	intron (NM_001085499, intron 8 of 20)	intron (NM_001085499, intron 8 of 20)	9520	NM_001085499	209005	Mm.336054	NM_001085499	ENSMUSG00000079606	Gm595	-	predicted gene 595	protein-coding
mm_1755.1	chr1	75510033	75510034	+	1	NA	exon (NM_010564, exon 2 of 2)	exon (NM_010564, exon 2 of 2)	2424	NM_001329843	16322	Mm.1100	NM_010564	ENSMUSG00000032968	Inha	AW555078	inhibin alpha	protein-coding
mm_147304.1	chr18	39519416	39519425	-	1	NA	Intergenic	Intergenic	-32175	NM_008173	14815	Mm.129481	NM_008173	ENSMUSG00000024431	Nr3c1	GR|Grl-1|Grl1	nuclear receptor subfamily 3, group C, member 1	protein-coding
mm_122263.1	chr14	34310356	34310383	-	1	NA	promoter-TSS (NM_008133)	promoter-TSS (NM_008133)	134	NM_029389	75698	Mm.45406	NM_029389	ENSMUSG00000041471	Fam35a	3110001K24Rik	family with sequence similarity 35, member A	protein-coding
mm_119265.1	chr14	34052684	34052730	+	1	NA	promoter-TSS (NM_172808)	promoter-TSS (NM_172808)	-763	NM_172808	239029	Mm.477093	NM_172808	ENSMUSG00000047441	Antxrl	1700112N15Rik|4933430J11	anthrax toxin receptor-like	protein-coding
mm_70672.1	chr8	14906400	14906414	+	1	NA	Intergenic	Intergenic	-5256	NM_172751	234094	Mm.240298	NM_172751	ENSMUSG00000071176	Arhgef10	6430549H08Rik|mKIAA0294	Rho guanine nucleotide exchange factor (GEF) 10	protein-coding
mm_87815.1	chr10	60302084	60302088	+	1	NA	TTS (NM_001252635)	TTS (NM_001252635)	17625	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_56069.1	chr6	86790130	86790133	-	1	NA	intron (NM_013471, intron 1 of 12)	PB1D10|SINE|Alu	3453	NM_013471	11746	Mm.259702	NM_013471	ENSMUSG00000029994	Anxa4	AI265406|AIV|AW106930|Anx4|Xanx-4	annexin A4	protein-coding
mm_7280.1	chr1	97661345	97661434	-	1	NA	intron (NM_133825, intron 1 of 2)	CpG	629	NM_133825	52392	Mm.12309	NM_133825	ENSMUSG00000044768	D1Ertd622e	AI987691|AW047450	DNA segment, Chr 1, ERATO Doi 622, expressed	protein-coding
mm_16247.1	chr2	173158655	173158667	+	1	NA	3' UTR (NM_011044, exon 10 of 10)	3' UTR (NM_011044, exon 10 of 10)	5588	NM_011044	18534	Mm.266867	NM_011044	ENSMUSG00000027513	Pck1	AI265463|PEPCK|Pck-1	phosphoenolpyruvate carboxykinase 1, cytosolic	protein-coding
mm_89255.1	chr10	87859280	87859288	+	1	NA	5' UTR (NM_010512, exon 1 of 5)	5' UTR (NM_010512, exon 1 of 5)	232	NM_010512	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_31601.1	chr4	57894161	57894179	+	1	NA	3' UTR (NM_001035533, exon 4 of 4)	3' UTR (NM_001035533, exon 4 of 4)	22094	NM_178727	242484	Mm.23214	NM_178727	ENSMUSG00000052117	D630039A03Rik	-	RIKEN cDNA D630039A03 gene	protein-coding
mm_121486.1	chr14	121230936	121230939	+	1	NA	intron (NM_134082, intron 6 of 26)	intron (NM_134082, intron 6 of 26)	148293	NM_145465	223255	Mm.390756	NM_145465	ENSMUSG00000063410	Stk24	1810013H02Rik|C76483|MST-3|Mst3|STE20	serine/threonine kinase 24	protein-coding
mm_16957.1	chr2	17390954	17391042	-	1	NA	intron (NM_028757, intron 4 of 6)	intron (NM_028757, intron 4 of 6)	-172516	NR_105847	102465964		NR_105847	ENSMUSG00000099161	Mir6419	Gm27713|mmu-mir-6419	microRNA 6419	ncRNA
mm_51932.1	chr6	91516007	91516058	+	1	NA	promoter-TSS (NM_009531)	promoter-TSS (NM_009531)	-3	NM_026309	67678	Mm.246693	NM_026309	ENSMUSG00000034192	Lsm3	1010001J12Rik|2610005D18Rik|6030401D18Rik|SMX4|USS2	LSM3 homolog, U6 small nuclear RNA and mRNA degradation associated	protein-coding
mm_166470.1	chr5	142905993	142905999	-	1	NA	intron (NM_007393, intron 1 of 5)	CpG	758	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_11394.1	chr2	31454770	31454788	+	1	NA	Intergenic	Intergenic	-15491	NM_007494	11898	Mm.3217	NM_007494	ENSMUSG00000076441	Ass1	AA408052|ASS|Ass-1|fold	argininosuccinate synthetase 1	protein-coding
mm_107246.1	chr12	26479309	26479319	+	1	NA	3' UTR (NM_020557, exon 5 of 5)	3' UTR (NM_020557, exon 5 of 5)	10099	NM_020557	22169	Mm.271839	NM_020557	ENSMUSG00000020638	Cmpk2	1200004E04Rik|TDKI|Tyki	cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial	protein-coding
mm_90844.1	chr10	8756758	8756768	-	1	NA	intron (NM_175155, intron 8 of 19)	intron (NM_175155, intron 8 of 19)	129307	NM_175155	70097	Mm.338275	NM_175155	ENSMUSG00000015305	Sash1	1100001C18Rik|2500002E12Rik|A330076K04Rik|mKIAA0790	SAM and SH3 domain containing 1	protein-coding
mm_35009.1	chr4	3090273	3090280	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	-81807	NM_001167534	100312470	Mm.480297	NM_001167534	ENSMUSG00000094798	Vmn1r2	Gm11776|OTTMUSG00000004179	vomeronasal 1 receptor 2	protein-coding
mm_39335.1	chr5	8798645	8798654	+	1	NA	intron (NM_011075, intron 1 of 27)	intron (NM_011075, intron 1 of 27)	502	NM_011075	18669	Mm.146649	NM_011075	ENSMUSG00000028970	Abcb1b	Abcb1|Mdr1|Mdr1b|Pgy-1|Pgy1|mdr	ATP-binding cassette, sub-family B (MDR/TAP), member 1B	protein-coding
mm_83691.1	chr9	50561306	50561316	-	1	NA	promoter-TSS (NM_025687)	promoter-TSS (NM_025687)	-43	NM_025687	66654	Mm.442255	NM_025687	ENSMUSG00000032065	Tex12	5730518K06Rik	testis expressed gene 12	protein-coding
mm_121160.1	chr14	103008129	103008143	+	1	NA	intron (NR_045657, intron 2 of 2)	intron (NR_045657, intron 2 of 2)	-25499	NM_177715	239217	Mm.246466	NM_177715	ENSMUSG00000098557	Kctd12	AU046135|AW538430|Pfet1|Pfetin	potassium channel tetramerisation domain containing 12	protein-coding
mm_68274.1	chr7	105596374	105596380	-	1	NA	exon (NM_017371, exon 5 of 10)	exon (NM_017371, exon 5 of 10)	3739	NM_017371	15458	Mm.3485	NM_017371	ENSMUSG00000030895	Hpx	Hpxn|hx	hemopexin	protein-coding
mm_169346.1	chr14	18463590	18463593	+	1	NA	Intergenic	RLTR9E|LTR|ERVK	-131747	NM_009455	22194	Mm.4429	NM_009455	ENSMUSG00000021774	Ube2e1	UbcM3|Ubce5|ubcM2	ubiquitin-conjugating enzyme E2E 1	protein-coding
mm_48676.1	chr5	146185313	146185320	-	1	NA	promoter-TSS (NM_001008547)	promoter-TSS (NM_001008547)	-12	NM_001008547	69282	Mm.373573	NM_001008547	ENSMUSG00000095040	1700001J03Rik	-	RIKEN cDNA 1700001J03 gene	protein-coding
mm_112314.1	chr12	114932830	114932838	-	1	NA	Intergenic	Intergenic	-419140	NR_106063	102465664		NR_106063	ENSMUSG00000098357	Mir7094-2	Gm27508|mmu-mir-7094-2	microRNA 7094-2	ncRNA
mm_63247.1	chr7	126589396	126589427	+	1	NA	TTS (NM_138310)	TTS (NM_138310)	-3594	NM_001146311	12752	Mm.268930	NM_009907	ENSMUSG00000030720	Cln3	AI323623	ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease)	protein-coding
mm_82528.1	chr9	20667925	20667996	-	1	NA	TTS (NM_173777)	TTS (NM_173777)	15830	NM_023371	23988	Mm.7906	NM_023371	ENSMUSG00000032171	Pin1	0610025L01Rik|D9Bwg1161e	protein (peptidyl-prolyl cis/trans isomerase) NIMA-interacting 1	protein-coding
mm_60340.1	chr7	44343664	44343682	+	1	NA	exon (NM_001034115, exon 19 of 25)	exon (NM_001034115, exon 19 of 25)	31357	NM_027049	69349	Mm.358922	NM_027049	ENSMUSG00000008028	1700008O03Rik	-	RIKEN cDNA 1700008O03 gene	protein-coding
mm_11505.1	chr2	32567731	32567770	+	1	NA	3' UTR (NM_153560, exon 11 of 11)	3' UTR (NM_153560, exon 11 of 11)	-3108	NM_010073	13481	Mm.22001	NM_010073	ENSMUSG00000026810	Dpm2	AW557993|R75484	dolichol-phosphate (beta-D) mannosyltransferase 2	protein-coding
mm_104550.1	chr11	96780319	96780325	-	1	NA	Intergenic	B3A|SINE|B2	-2767	NM_001163389	74479	Mm.270781	NM_028965	ENSMUSG00000020876	Snx11	4933439F10Rik|A930041K09Rik|AI117694	sorting nexin 11	protein-coding
mm_54318.1	chr6	30245411	30245414	-	1	NA	intron (NM_009459, intron 3 of 6)	PB1D11|SINE|Alu	-1609	NM_001169577	22214	Mm.332967	NM_009459	ENSMUSG00000039159	Ube2h	1500009C23Rik|AI181839|AI326965|AI462483|AW227540|E2-20K|Gid3|N28148|Ubc8	ubiquitin-conjugating enzyme E2H	protein-coding
mm_23474.1	chr3	60480849	60480871	+	1	NA	intron (NM_001253713, intron 2 of 9)	intron (NM_001253713, intron 2 of 9)	8030	NM_001253713	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_33359.1	chr4	129487159	129487172	+	1	NA	3' UTR (NM_133889, exon 11 of 11)	3' UTR (NM_133889, exon 11 of 11)	3605	NM_080442	58864	Mm.143802	NM_080442	ENSMUSG00000000411	Tssk3	1700014N07Rik|4930594I21Rik|Stk22c|Stk22d|Tsk-3|Tssk-3|Tssk3b	testis-specific serine kinase 3	protein-coding
mm_63628.1	chr7	128373948	128373963	+	1	NA	exon (NM_026418, exon 5 of 5)	exon (NM_026418, exon 5 of 5)	44217	NM_026418	67865	Mm.18635	NM_026418	ENSMUSG00000030844	Rgs10	2310010N19Rik	regulator of G-protein signalling 10	protein-coding
mm_129142.1	chr15	76200578	76200621	-	1	NA	promoter-TSS (NM_201391)	promoter-TSS (NM_201391)	8	NM_201390	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
mm_47868.1	chr5	134639474	134639480	-	1	NA	promoter-TSS (NM_033561)	promoter-TSS (NM_033561)	-68	NM_033561	22384	Mm.27955	NM_033561	ENSMUSG00000040731	Eif4h	AU018978|D5Ertd355e|E430026L18Rik|Ef4h|Wbscr1|Wscr1|eIF-4H	eukaryotic translation initiation factor 4H	protein-coding
mm_155861.1	chrX	101377268	101377281	+	1	NA	promoter-TSS (NM_008124)	promoter-TSS (NM_008124)	39	NM_008124	14618	Mm.21198	NM_008124	ENSMUSG00000047797	Gjb1	Cnx32|Cx32|connexin-32	gap junction protein, beta 1	protein-coding
mm_29158.1	chr3	106032894	106032904	-	1	NA	promoter-TSS (NM_001080816)	promoter-TSS (NM_001080816)	-4	NM_001080816	229687	Mm.39224	NM_170594	ENSMUSG00000043873	Chil5	Bclp|Bclp1|Bclp2|Chi3l7	chitinase-like 5	protein-coding
mm_119289.1	chr14	34673868	34673884	+	1	NA	promoter-TSS (NM_001301330)	promoter-TSS (NM_001301330)	-52	NM_001004436	218914	Mm.27957	NM_001004436	ENSMUSG00000041408	Wapl	A530089A20Rik|BC037674|DIF-2|FOE|Wapal	WAPL cohesin release factor	protein-coding
mm_4220.1	chr1	171329624	171329653	+	1	NA	intron (NM_011615, intron 1 of 4)	intron (NM_011615, intron 1 of 4)	493	NM_011615	21945	Mm.270139	NM_011615	ENSMUSG00000013973	Dedd	CASP8IP1|DEFT|Dedpro1|FLDED1|KE05	death effector domain-containing	protein-coding
mm_173102.1	chrX	152910139	152910142	-	1	NA	Intergenic	Lx3B|LINE|L1	-96329	NM_001137547	635253	Mm.426169	NM_001137547	ENSMUSG00000067215	Usp51	AV136873	ubiquitin specific protease 51	protein-coding
mm_67331.1	chr7	79742968	79742976	-	1	NA	promoter-TSS (NM_001037927)	promoter-TSS (NM_001037927)	53	NM_011068	18631	Mm.20615	NM_011068	ENSMUSG00000030545	Pex11a	PEX11alpha	peroxisomal biogenesis factor 11 alpha	protein-coding
mm_104679.1	chr11	97699556	97699572	-	1	NA	promoter-TSS (NM_001163308)	promoter-TSS (NM_001163308)	84	NM_001163308	22658	Mm.2418	NM_009545	ENSMUSG00000018537	Pcgf2	Mel18|Rnf110|Zfp144|mel-18	polycomb group ring finger 2	protein-coding
mm_77257.1	chr8	115706967	115706991	-	1	NA	promoter-TSS (NM_001025577)	promoter-TSS (NM_001025577)	-85	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_165002.1	chr19	21778298	21778300	+	1	NA	promoter-TSS (NM_031997)	promoter-TSS (NM_031997)	-41	NM_001033759	83921	Mm.329776	NM_031997	ENSMUSG00000024754	Tmem2	-	transmembrane protein 2	protein-coding
mm_13193.1	chr2	93200262	93200284	+	1	NA	3' UTR (NM_001025246, exon 8 of 8)	3' UTR (NM_001025246, exon 8 of 8)	12689	NM_001025246	277414	Mm.41033	NM_001025246	ENSMUSG00000068735	Trp53i11	Tp53i11	transformation related protein 53 inducible protein 11	protein-coding
mm_37113.1	chr4	116641136	116641153	-	1	NA	intron (NM_021473, intron 3 of 8)	intron (NM_021473, intron 3 of 8)	10530	NM_021473	58810	Mm.30085	NM_021473	ENSMUSG00000028692	Akr1a1	2610201A18Rik|Akr1a4	aldo-keto reductase family 1, member A1 (aldehyde reductase)	protein-coding
mm_71935.1	chr8	70302762	70302804	+	1	NA	promoter-TSS (NM_021538)	promoter-TSS (NM_021538)	-2	NM_021538	59042	Mm.28668	NM_021538	ENSMUSG00000055681	Cope	1110005D17Rik|Cope1	coatomer protein complex, subunit epsilon	protein-coding
mm_172204.1	chr6	54177707	54177713	-	1	NA	intron (NM_001163640, intron 2 of 12)	intron (NM_001163640, intron 2 of 12)	-87148	NM_001311133	69993	Mm.321147	NM_023543	ENSMUSG00000004633	Chn2	1700026N20Rik|4930557O16Rik|ARHGAP3|Bch	chimerin 2	protein-coding
mm_170504.1	chr19	24290907	24290913	-	1	NA	Intergenic	Intergenic	-10324	NM_008044	14297	Mm.7319	NM_008044	ENSMUSG00000059363	Fxn	FA|FARR|Frda|X25	frataxin	protein-coding
mm_157704.1	chrX	62516067	62516112	-	1	NA	promoter-TSS (NR_045443)	promoter-TSS (NR_045443)	-20	NR_045443	75545	Mm.391270	NR_045442	ENSMUSG00000085757	1700019B21Rik	-	RIKEN cDNA 1700019B21 gene	ncRNA
mm_10395.1	chr2	13574033	13574075	+	1	NA	promoter-TSS (NM_011701)	promoter-TSS (NM_011701)	-257	NM_011701	22352	Mm.268000	NM_011701	ENSMUSG00000026728	Vim	-	vimentin	protein-coding
mm_88758.1	chr10	80329962	80329987	+	1	NA	promoter-TSS (NM_139292)	promoter-TSS (NM_139292)	-171	NM_001204931	70335	Mm.28147	NM_139292	ENSMUSG00000035504	Reep6	0610011M24Rik|Dp1l1	receptor accessory protein 6	protein-coding
mm_36177.1	chr4	62207914	62207926	-	1	NA	intron (NM_001290351, intron 1 of 3)	intron (NM_001290351, intron 1 of 3)	282	NM_001290353	22696	Mm.5011	NM_009554	ENSMUSG00000028389	Zfp37	Tzn|Zfp-37	zinc finger protein 37	protein-coding
mm_84110.1	chr9	58370379	58370382	-	1	NA	promoter-TSS (NR_040727)	promoter-TSS (NR_040727)	-11	NM_028854	74286	Mm.252761	NM_028854	ENSMUSG00000036244	Tbc1d21	1700095K08Rik|MgcRabGAP	TBC1 domain family, member 21	protein-coding
mm_63159.1	chr7	123462275	123462296	+	1	NA	promoter-TSS (NM_007474)	promoter-TSS (NM_007474)	-9	NM_007474	11833	Mm.273175	NM_007474	ENSMUSG00000030762	Aqp8	AI255744|AQP-8	aquaporin 8	protein-coding
mm_137642.1	chr17	28523319	28523327	+	1	NA	Intergenic	CpG	-7538	NM_026290	67645	Mm.46170	NM_026290	ENSMUSG00000024223	Armc12	4930511I11Rik|AV041658	armadillo repeat containing 12	protein-coding
mm_47274.1	chr5	122002312	122002320	-	1	NA	intron (NM_001312908, intron 2 of 22)	intron (NM_001312908, intron 2 of 22)	45509	NM_007804	13048	Mm.156172	NM_007804	ENSMUSG00000042589	Cux2	1700051K22Rik|Cutl2|Cux-2|ENSMUSG00000072641	cut-like homeobox 2	protein-coding
mm_66800.1	chr7	47133592	47133629	-	1	NA	promoter-TSS (NM_013643)	promoter-TSS (NM_013643)	74	NM_013643	19259	Mm.4654	NM_013643	ENSMUSG00000030854	Ptpn5	Step	protein tyrosine phosphatase, non-receptor type 5	protein-coding
mm_26803.1	chr3	10022561	10022594	-	1	NA	Intergenic	Intergenic	9992	NM_001272098	16592	Mm.741	NM_010634	ENSMUSG00000027533	Fabp5	E-FABP|Fabpe|Klbp|PA-FABP|mal1	fatty acid binding protein 5, epidermal	protein-coding
mm_73322.1	chr8	105269838	105269857	+	1	NA	promoter-TSS (NM_001256044)	promoter-TSS (NM_001256044)	46	NM_001256044	26386	Mm.89204	NM_011939	ENSMUSG00000033249	Hsf4	HSF 4|HSTF 4|HSTF4|ldis1|mHSF4	heat shock transcription factor 4	protein-coding
mm_165710.1	chr3	98592432	98592432	+	1	NA	Intergenic	Lx7|LINE|L1	-28394	NM_008294	15495	Mm.14309	NM_008294	ENSMUSG00000095143	Hsd3b4	-	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 4	protein-coding
mm_44802.1	chr5	32985615	32985650	-	1	NA	intron (NM_001025426, intron 41 of 42)	intron (NM_001025426, intron 41 of 42)	-33184	NM_011738	22629	Mm.332314	NM_011738	ENSMUSG00000018965	Ywhah	-	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta polypeptide	protein-coding
mm_30291.1	chr3	148989557	148989570	-	1	NA	Intergenic	CpG	-34928	NM_001081298	99633	Mm.9776	NM_001081298	ENSMUSG00000028184	Adgrl2	AI450192|CIRL-2|Gm619|Lec1|Lphh1|Lphn2|mKIAA0786	adhesion G protein-coupled receptor L2	protein-coding
mm_33990.1	chr4	137862253	137862268	+	1	NA	promoter-TSS (NM_199307)	promoter-TSS (NM_199307)	23	NM_199307	230857	Mm.401062	NM_199307	ENSMUSG00000057530	Ece1	AW322500|ECE-1|ECE-1a|ECE-1b|ECE-1d	endothelin converting enzyme 1	protein-coding
mm_148572.1	chr19	4859410	4859422	+	1	NA	exon (NM_019861, exon 10 of 14)	exon (NM_019861, exon 10 of 14)	4287	NM_019861	56464	Mm.29561	NM_019861	ENSMUSG00000083282	Ctsf	AI481912	cathepsin F	protein-coding
mm_29671.1	chr3	122801986	122801992	-	1	NA	promoter-TSS (NR_045168)	promoter-TSS (NR_045168)	-9	NR_045168	71647	Mm.449992	NR_045168	ENSMUSG00000106583	4930447N08Rik	-	RIKEN cDNA 4930447N08 gene	ncRNA
mm_153122.1	chr19	33626339	33626345	-	1	NA	Intergenic	Intergenic	-1093	NM_001323251	668106	Mm.379675	NM_001323251		Gm8978	EG668106	predicted gene 8978	protein-coding
mm_34716.1	chr4	152125124	152125133	+	1	NA	intron (NM_207688, intron 8 of 10)	CpG	3797	NM_019585	56226	Mm.264215	NM_019585	ENSMUSG00000028943	Espn	je	espin	protein-coding
mm_76720.1	chr8	94838256	94838336	-	1	NA	promoter-TSS (NM_026452)	promoter-TSS (NM_026452)	44	NM_134141	109006	Mm.27582	NM_134141	ENSMUSG00000031781	Ciapin1	2810413N20Rik|AA617265|AU021794|anamorsin	cytokine induced apoptosis inhibitor 1	protein-coding
mm_4774.1	chr1	182764195	182764316	+	1	NA	promoter-TSS (NM_144796)	promoter-TSS (NM_144796)	-651	NM_144796	96935	Mm.331052	NM_144796	ENSMUSG00000038576	Susd4	AI848994|E430021N18Rik|N28096	sushi domain containing 4	protein-coding
mm_121613.1	chr14	8258997	8259001	-	1	NA	promoter-TSS (NM_053115)	promoter-TSS (NM_053115)	20	NM_053115	93732	Mm.28700	NM_053115	ENSMUSG00000021751	Acox2	THCCox	acyl-Coenzyme A oxidase 2, branched chain	protein-coding
mm_12205.1	chr2	66021605	66021614	+	1	NA	intron (NM_178634, intron 5 of 5)	intron (NM_178634, intron 5 of 5)	89744	NM_001290665	77771	Mm.102025	NM_153409	ENSMUSG00000044647	Csrnp3	A330102K23Rik|CSRNP-3|Csnrp3|Mbu1|taip-2	cysteine-serine-rich nuclear protein 3	protein-coding
mm_169001.1	chr13	100909909	100909926	-	1	NA	Intergenic	Intergenic	-76490	NM_022885	69048	Mm.402215	NM_022885	ENSMUSG00000021629	Slc30a5	1810010K08Rik|AF233321|ZNT5|ZTL1|ZnT-5|Zntl1	solute carrier family 30 (zinc transporter), member 5	protein-coding
mm_99496.1	chr11	102881265	102881278	+	1	NA	promoter-TSS (NM_001109995)	promoter-TSS (NM_001109995)	27	NM_028492	73293	Mm.67659	NM_028492	ENSMUSG00000020930	Ccdc103	1700039D13Rik	coiled-coil domain containing 103	protein-coding
mm_6753.1	chr1	84037274	84037286	-	1	NA	3' UTR (NM_001003948, exon 3 of 3)	3' UTR (NM_001003948, exon 3 of 3)	181681	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_43324.1	chr5	134987141	134987163	+	1	NA	TTS (NR_026907)	TTS (NR_026907)	938	NM_009902	12739	Mm.158662	NM_009902	ENSMUSG00000070473	Cldn3	AI182374|Cpetr2|mRVP1	claudin 3	protein-coding
mm_50354.1	chr6	48594205	48594222	+	1	NA	intron (NM_001079905, intron 1 of 1)	CpG	330	NM_001079904	58887	Mm.219183	NM_175099	ENSMUSG00000052751	Repin1	AI425994|Ap4|E430037F08Rik|Zfp-464|Zfp464	replication initiator 1	protein-coding
mm_51615.1	chr6	85154993	85155006	+	1	NA	Intergenic	Intergenic	-17235	NM_011467	20751	Mm.28393	NM_011467	ENSMUSG00000033735	Spr	AA409688|ENSMUSG00000071345|Gm10328	sepiapterin reductase	protein-coding
mm_103287.1	chr11	72266622	72266640	-	1	NA	promoter-TSS (NM_001004148)	promoter-TSS (NM_001004148)	-27	NM_001004148	237831	Mm.340778	NM_001004148	ENSMUSG00000020805	Slc13a5	Indy|NaC2/NaCT|Nact|mINDY	solute carrier family 13 (sodium-dependent citrate transporter), member 5	protein-coding
mm_30202.1	chr3	144720316	144720336	-	1	NA	promoter-TSS (NM_019464)	promoter-TSS (NM_019464)	9	NM_001282042	54673	Mm.271775	NM_019464	ENSMUSG00000037062	Sh3glb1	AA409932|AI314629|AU015566|Bif-1|mKIAA0491	SH3-domain GRB2-like B1 (endophilin)	protein-coding
mm_102935.1	chr11	69601107	69601115	-	1	NA	3' UTR (NM_013415, exon 7 of 7)	3' UTR (NM_013415, exon 7 of 7)	4849	NM_013415	11932	Mm.235204	NM_013415	ENSMUSG00000041329	Atp1b2	Amog|Atpb-2	ATPase, Na+/K+ transporting, beta 2 polypeptide	protein-coding
mm_45424.1	chr5	66618753	66618770	-	1	NA	promoter-TSS (NM_009686)	promoter-TSS (NM_009686)	56	NM_009686	11787	Mm.5159	NM_009686	ENSMUSG00000029207	Apbb2	2310007D03Rik|FE65L1|Rirl1|TR2L|Zfra	amyloid beta (A4) precursor protein-binding, family B, member 2	protein-coding
mm_103095.1	chr11	69921245	69921323	-	1	NA	promoter-TSS (NM_001166592)	promoter-TSS (NM_001166592)	-9	NM_001166595	276770	Mm.18026	NM_181582	ENSMUSG00000078812	Eif5a	AA410058|D19Wsu54e|Eif4d|Eif5a1|eIF-4D|eIF-5A|eIF-5A-1|eIF-5A1	eukaryotic translation initiation factor 5A	protein-coding
mm_54340.1	chr6	30669379	30669412	-	1	NA	intron (NR_130781, intron 3 of 11)	intron (NR_130781, intron 3 of 11)	24354	NM_031998	83922	Mm.65389	NM_031998	ENSMUSG00000029790	Cep41	1700017E11Rik|2810431D15Rik|Tsga14	centrosomal protein 41	protein-coding
mm_101844.1	chr11	48816906	48816928	-	1	NA	5' UTR (NM_145377, exon 1 of 6)	5' UTR (NM_145377, exon 1 of 6)	474	NM_145377	211007	Mm.794	NM_145377	ENSMUSG00000040365	Trim41	AW552703|BC020156|R75223|RINCK	tripartite motif-containing 41	protein-coding
mm_26061.1	chr3	135826252	135826270	+	1	NA	5' UTR (NM_001135150, exon 2 of 9)	5' UTR (NM_001135150, exon 2 of 9)	471	NM_001135150	67547	Mm.30239	NM_026228	ENSMUSG00000053897	Slc39a8	4933419D20Rik|AA986696|BIGM103|ZIP-8|Zip8	solute carrier family 39 (metal ion transporter), member 8	protein-coding
mm_166077.1	chr4	137277483	137277485	+	1	NA	promoter-TSS (NM_009523)	promoter-TSS (NM_009523)	-151	NM_009523	22417	Mm.20355	NM_009523	ENSMUSG00000036856	Wnt4	Wnt-4	wingless-type MMTV integration site family, member 4	protein-coding
mm_70996.1	chr8	28520659	28520660	+	1	NA	Intergenic	Intergenic	-435806	NR_033590	666422	Mm.484413	NR_033590	ENSMUSG00000110372	Gm8096	EG666422	3-phosphoglycerate dehydrogenase pseudogene	pseudo
mm_16442.1	chr2	180440032	180440050	+	1	NA	Intergenic	Intergenic	-20937	NM_148933	108115	Mm.133687	NM_148933	ENSMUSG00000038963	Slco4a1	OATP-E|Slc21a12	solute carrier organic anion transporter family, member 4a1	protein-coding
mm_41037.1	chr5	86083277	86083282	+	1	NA	intron (NM_019992, intron 3 of 8)	intron (NM_019992, intron 3 of 8)	11533	NM_001310639	56792	Mm.131237	NM_019992	ENSMUSG00000029254	Stap1	AI586015|Brdg1|STAP-1	signal transducing adaptor family member 1	protein-coding
mm_62690.1	chr7	110061704	110061732	+	1	NA	promoter-TSS (NM_009281)	promoter-TSS (NM_009281)	16	NM_009281	20841	Mm.10815	NM_009281	ENSMUSG00000061079	Zfp143	AA959806|AU015869|D7Ertd805e|KRAB14|SBF|Staf|Zfp79|Zfp80-rs1|Znf143|pHZ-1	zinc finger protein 143	protein-coding
mm_83920.1	chr9	56620333	56620344	-	1	NA	exon (NM_181074, exon 4 of 4)	exon (NM_181074, exon 4 of 4)	15310	NM_001311076	235402	Mm.246605	NM_181074	ENSMUSG00000049556	Lingo1	4930471K13Rik|AV148400|LERN1|LINGO-1|Lrrn6a|UNQ201	leucine rich repeat and Ig domain containing 1	protein-coding
mm_80383.1	chr9	75441479	75441489	+	1	NA	promoter-TSS (NM_001039522)	promoter-TSS (NM_001039522)	-40	NM_001039522	235497	Mm.41508	NM_001006122	ENSMUSG00000042487	Leo1	Gm185	Leo1, Paf1/RNA polymerase II complex component	protein-coding
mm_63014.1	chr7	120982550	120982552	+	1	NA	promoter-TSS (NM_007672)	promoter-TSS (NM_007672)	42	NM_028955	74466	Mm.189707	NM_028955	ENSMUSG00000030877	Mfsd13b	4933427G17Rik	major facilitator superfamily domain containing 13B	protein-coding
mm_56416.1	chr6	97252649	97252662	-	1	NA	5' UTR (NM_001081157, exon 1 of 3)	5' UTR (NM_001081157, exon 1 of 3)	125	NM_001081157	320502	Mm.68163	NM_001081157	ENSMUSG00000044086	Lmod3	5430424A14Rik	leiomodin 3 (fetal)	protein-coding
mm_25739.1	chr3	122899338	122899383	+	1	NA	3' UTR (NM_007980, exon 4 of 4)	3' UTR (NM_007980, exon 4 of 4)	4288	NM_007980	14079	Mm.28398	NM_007980	ENSMUSG00000023057	Fabp2	Fabpi|I-FABP	fatty acid binding protein 2, intestinal	protein-coding
mm_54594.1	chr6	38254110	38254155	-	1	NA	promoter-TSS (NM_194061)	promoter-TSS (NM_194061)	-123	NM_194061	330286	Mm.277163	NM_194061	ENSMUSG00000063455	D630045J12Rik	Kiaa1549|mKIAA1549	RIKEN cDNA D630045J12 gene	protein-coding
mm_61750.1	chr7	82755751	82755761	+	1	NA	promoter-TSS (NR_046004)	promoter-TSS (NR_046004)	-112	NR_046004	77800	Mm.444811	NR_046004	ENSMUSG00000086690	4933406J10Rik	A930009F24Rik	RIKEN cDNA 4933406J10 gene	ncRNA
mm_133588.1	chr16	91424871	91424892	+	1	NA	exon (NM_008349, exon 7 of 7)	exon (NM_008349, exon 7 of 7)	18646	NM_008349	16155	Mm.4154	NM_008349	ENSMUSG00000022969	Il10rb	6620401D04Rik|AI528744|CRF2-4|Crfb4|D16H21S58|D21S58h|IL-10R2|Il10r2	interleukin 10 receptor, beta	protein-coding
mm_69303.1	chr7	128376160	128376171	-	1	NA	intron (NM_026418, intron 4 of 4)	intron (NM_026418, intron 4 of 4)	42007	NM_026418	67865	Mm.18635	NM_026418	ENSMUSG00000030844	Rgs10	2310010N19Rik	regulator of G-protein signalling 10	protein-coding
mm_102586.1	chr11	61855083	61855097	-	1	NA	promoter-TSS (NM_013881)	promoter-TSS (NM_013881)	2	NM_013881	29869	Mm.162025	NM_013881	ENSMUSG00000004798	Ulk2	A830085I22Rik|AU015340|Unc51.2|mKIAA0623	unc-51 like kinase 2	protein-coding
mm_161285.1	chr14	26042711	26042711	-	1	NA	promoter-TSS (NM_001270503).2	promoter-TSS (NM_001270503).2	26	NM_001270503	100039246	Mm.425864	NM_001270503	ENSMUSG00000072674	Plac9b	ENSMUSG00000072674|Gm10393	placenta specific 9b	protein-coding
mm_31054.1	chr4	41190920	41190976	+	1	NA	3' UTR (NM_026275, exon 5 of 5)	3' UTR (NM_026275, exon 5 of 5)	54927	NM_026275	67615	Mm.389540	NM_026275	ENSMUSG00000036241	Ube2r2	1200003M11Rik|Cdc34b|Ubc3b	ubiquitin-conjugating enzyme E2R 2	protein-coding
mm_78584.1	chr9	37348541	37348549	+	1	NA	promoter-TSS (NM_001081429)	promoter-TSS (NM_001081429)	-153	NM_001081429	245902	Mm.390150	NM_001081429	ENSMUSG00000034303	Ccdc15	A630039F14Rik|D030074L19	coiled-coil domain containing 15	protein-coding
mm_117866.1	chr13	98846803	98846810	-	1	NA	intron (NM_001048267, intron 22 of 23)	intron (NM_001048267, intron 22 of 23)	-31357	NM_172591	218503	Mm.23928	NM_172591	ENSMUSG00000041685	Fcho2	5832424M12Rik|AA387320	FCH domain only 2	protein-coding
mm_147322.1	chr18	42253762	42253768	-	1	NA	intron (NM_134137, intron 2 of 31)	AT_rich|Low_complexity|Low_complexity	8306	NM_134137	107045	Mm.312170	NM_134137	ENSMUSG00000024493	Lars	2310045K21Rik|3110009L02Rik|AW536573|mKIAA1352	leucyl-tRNA synthetase	protein-coding
mm_79607.1	chr9	58603730	58603752	+	1	NA	intron (NM_001293673, intron 1 of 7)	intron (NM_001293673, intron 1 of 7)	21501	NM_009145	20320	Mm.15125	NM_009145	ENSMUSG00000032336	Nptn	AW554172|SDR-1|Sdfr1	neuroplastin	protein-coding
mm_41247.1	chr5	88782193	88782203	+	1	NA	3' UTR (NM_007832, exon 7 of 7)	3' UTR (NM_007832, exon 7 of 7)	17185	NM_007832	13178	Mm.298892	NM_007832	ENSMUSG00000029366	Dck	-	deoxycytidine kinase	protein-coding
mm_160055.1	chr7	3845051	3845051	-	1	NA	promoter-TSS (NM_011089)	promoter-TSS (NM_011089)	0	NM_011089	18725	Mm.482470	NM_011089	ENSMUSG00000089942	Pira2	6M23	paired-Ig-like receptor A2	protein-coding
mm_65096.1	chr7	19271798	19271823	-	1	NA	promoter-TSS (NM_001282022)	promoter-TSS (NM_001282022)	44	NM_001282021	22323	Mm.9684	NM_009499	ENSMUSG00000030403	Vasp	-	vasodilator-stimulated phosphoprotein	protein-coding
mm_123119.1	chr14	56102459	56102472	-	1	NA	5' UTR (NM_007800, exon 1 of 5)	5' UTR (NM_007800, exon 1 of 5)	109	NM_007800	13035	Mm.4858	NM_007800	ENSMUSG00000040314	Ctsg	CatG|VSP	cathepsin G	protein-coding
mm_111472.1	chr12	98578037	98578046	-	1	NA	5' UTR (NM_029911, exon 1 of 7)	5' UTR (NM_029911, exon 1 of 7)	172	NM_029911	72258	Mm.196158	NM_029911	ENSMUSG00000033854	Kcnk10	1700024D23Rik|3010005K24Rik|Trek2	potassium channel, subfamily K, member 10	protein-coding
mm_90794.1	chr10	7140379	7140393	-	1	NA	exon (NM_172546, exon 6 of 13)	exon (NM_172546, exon 6 of 13)	71851	NM_172546	215748	Mm.37984	NM_172546	ENSMUSG00000015202	Cnksr3	6820402C05|BC024086|Magi1	Cnksr family member 3	protein-coding
mm_28513.1	chr3	92584363	92584390	-	1	NA	exon (NM_008574, exon 2 of 2)	exon (NM_008574, exon 2 of 2)	4648	NM_008574	17235	Mm.331192	NM_008574		Smcp	Mcs|Mcsp	sperm mitochondria-associated cysteine-rich protein	protein-coding
mm_151558.1	chr19	59837801	59837801	+	1	NA	Intergenic	Intergenic	105563	NM_001033172	74998	Mm.24167	NM_001033172	ENSMUSG00000040022	Rab11fip2	4930470G04Rik|A830046J09Rik|AW558126|Nrip11	RAB11 family interacting protein 2 (class I)	protein-coding
mm_22381.1	chr2	181156833	181156843	-	1	NA	5' UTR (NM_007906, exon 1 of 8)	5' UTR (NM_007906, exon 1 of 8)	177	NM_007906	13628	Mm.2645	NM_007906	ENSMUSG00000016349	Eef1a2	Eef1a|S1|wasted|wst	eukaryotic translation elongation factor 1 alpha 2	protein-coding
mm_72933.1	chr8	91313530	91313557	+	1	NA	promoter-TSS (NM_173431)	promoter-TSS (NM_173431)	18	NM_011936	26383	Mm.4375	NM_011936	ENSMUSG00000055932	Fto	AW743446|mKIAA1752	fat mass and obesity associated	protein-coding
mm_145573.1	chr18	60914624	60914632	+	1	NA	intron (NM_001038499, intron 1 of 1)	intron (NM_001038499, intron 1 of 1)	2388	NM_001038499	545260	Mm.20147	NM_001038499	ENSMUSG00000036412	Arsi	BC020108	arylsulfatase i	protein-coding
mm_81577.1	chr9	110422364	110422374	+	1	NA	exon (NM_008694, exon 4 of 4)	exon (NM_008694, exon 4 of 4)	2561	NM_008694	18054	Mm.236225	NM_008694	ENSMUSG00000032484	Ngp	bectenecin	neutrophilic granule protein	protein-coding
mm_141977.1	chr17	35160796	35160835	-	1	NA	exon (NM_020027, exon 8 of 31)	exon (NM_020027, exon 8 of 31)	4062	NM_001199044	53761	Mm.272462	NM_020027	ENSMUSG00000024393	Prrc2a	3110039B05Rik|Bat-2|Bat2|D17H6S51E|G2|Wbp12|mKIAA4178	proline-rich coiled-coil 2A	protein-coding
mm_43360.1	chr5	135217769	135217787	+	1	NA	exon (NM_011714, exon 7 of 19)	exon (NM_011714, exon 7 of 19)	30455	NM_011714	22385	Mm.40331	NM_011714	ENSMUSG00000002748	Baz1b	C87820|WSTF|Wbscr9	bromodomain adjacent to zinc finger domain, 1B	protein-coding
mm_32950.1	chr4	119553170	119553173	+	1	NA	intron (NM_172699, intron 1 of 12)	intron (NM_172699, intron 1 of 12)	13510	NM_172699	230700	Mm.259227	NM_172699	ENSMUSG00000032998	Foxj3	C330039G02Rik|Fhd6	forkhead box J3	protein-coding
mm_22762.1	chr3	19992776	19992793	+	1	NA	3' UTR (NM_007752, exon 19 of 19)	3' UTR (NM_007752, exon 19 of 19)	35730	NM_007752	12870	Mm.13787	NM_007752	ENSMUSG00000003617	Cp	D3Ertd555e	ceruloplasmin	protein-coding
mm_158736.1	chrX	164042327	164042340	-	1	NA	Intergenic	Intergenic	-14323	NM_181315	56078	Mm.180953	NM_181315	ENSMUSG00000031373	Car5b	7330410H16Rik|CAVB|Ca5b|CarVb|D730005F19Rik	carbonic anhydrase 5b, mitochondrial	protein-coding
mm_27249.1	chr3	36613490	36613500	-	1	NA	promoter-TSS (NM_027810)	promoter-TSS (NM_027810)	-106	NM_027810	71492	Mm.286187	NM_027810	ENSMUSG00000037325	Bbs7	8430406N16Rik	Bardet-Biedl syndrome 7 (human)	protein-coding
mm_3239.1	chr1	135852200	135852233	+	1	NA	TTS (NM_001130176)	TTS (NM_001130176)	11355	NM_001130176	21956	Mm.247470	NM_011619	ENSMUSG00000026414	Tnnt2	Tnt|cTnT	troponin T2, cardiac	protein-coding
mm_12032.1	chr2	58567361	58567408	+	1	NA	promoter-TSS (NM_001289660)	promoter-TSS (NM_001289660)	50	NM_001289660	76654	Mm.200370	NM_029692	ENSMUSG00000026839	Upp2	1700124F02Rik|AI266885|UDRPASE2|UP2|UPASE2	uridine phosphorylase 2	protein-coding
mm_45745.1	chr5	86632379	86632391	-	1	NA	promoter-TSS (NM_178730)	promoter-TSS (NM_178730)	39	NM_178730	243083	Mm.106867	NM_178730	ENSMUSG00000048764	Tmprss11f	4631408C20|4732406D01Rik	transmembrane protease, serine 11f	protein-coding
mm_119679.1	chr14	52795120	52795126	+	1	NA	Intergenic	Intergenic	-299428	NM_001170918	57269	Mm.88822	NM_020512	ENSMUSG00000059887	Olfr1507	MOR244-1|Mor28|Or28	olfactory receptor 1507	protein-coding
mm_10152.1	chr2	4300878	4300904	+	1	NA	intron (NM_172475, intron 1 of 22)	(CA)n|Simple_repeat|Simple_repeat	-100085	NM_001177843	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding
mm_52717.1	chr6	119515698	119515700	+	1	NA	intron (NM_009525, intron 1 of 4)	Lx5|LINE|L1	28648	NM_009525	22419	Mm.321818	NM_009525	ENSMUSG00000030170	Wnt5b	AW545702|Wnt-5b	wingless-type MMTV integration site family, member 5B	protein-coding
mm_108318.1	chr12	79663835	79663837	+	1	NA	intron (NM_009014, intron 8 of 10)	intron (NM_009014, intron 8 of 10)	260897	NR_131075	77290	Mm.395042	NR_131073		9430078K24Rik	-	RIKEN cDNA 9430078K24 gene	ncRNA
mm_1657.1	chr1	74713174	74713206	+	1	NA	promoter-TSS (NM_024264)	promoter-TSS (NM_024264)	-345	NM_024264	104086	Mm.85083	NM_024264	ENSMUSG00000026170	Cyp27a1	1300013A03Rik|Cyp27	cytochrome P450, family 27, subfamily a, polypeptide 1	protein-coding
mm_21344.1	chr2	157110592	157110645	-	1	NA	exon (NM_001139520, exon 10 of 17)	exon (NM_001139520, exon 10 of 17)	23563	NM_001177439	383766	Mm.480305	NM_001177439	ENSMUSG00000074628	Tldc2	Gm1332	TBC/LysM associated domain containing 2	protein-coding
mm_56367.1	chr6	93913408	93913425	-	1	NA	promoter-TSS (NR_104594)	promoter-TSS (NR_104594)	274	NM_001286788	14924	Mm.217216	NM_010367	ENSMUSG00000045095	Magi1	AIP3|BAP1|Baiap1|Gukmi1|MAGI1c|Magi-1|TNRC19|WWP3|mKIAA4129	membrane associated guanylate kinase, WW and PDZ domain containing 1	protein-coding
mm_120440.1	chr14	65837439	65837441	+	1	NA	5' UTR (NM_145944, exon 1 of 9)	5' UTR (NM_145944, exon 1 of 9)	138	NM_145944	67179	Mm.214576	NM_145944	ENSMUSG00000022035	Ccdc25	2610528H13Rik|NSrp70	coiled-coil domain containing 25	protein-coding
mm_99539.1	chr11	103197651	103197661	+	1	NA	intron (NM_019679, intron 24 of 26)	intron (NM_019679, intron 24 of 26)	10892	NM_001254724	69441	Mm.380648	NM_027082	ENSMUSG00000020940	1700023F06Rik	-	RIKEN cDNA 1700023F06 gene	protein-coding
mm_56596.1	chr6	108659404	108659422	-	1	NA	intron (NR_104577, intron 1 of 6)	CpG	-1216	NM_011498	20893	Mm.2436	NM_011498	ENSMUSG00000030103	Bhlhe40	Bhlhb2|C130042M06Rik|CR8|Clast5|Dec1|Sharp2|Stra13|Stra14	basic helix-loop-helix family, member e40	protein-coding
mm_132940.1	chr16	49856559	49856569	+	1	NA	intron (NM_010581, intron 1 of 9)	intron (NM_010581, intron 1 of 9)	910	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_66186.1	chr7	34192139	34192149	-	1	NA	intron (NM_026549, intron 4 of 6)	intron (NM_026549, intron 4 of 6)	4503	NM_026549	68079	Mm.38173	NM_026549	ENSMUSG00000002635	Pdcd2l	6030457N17Rik	programmed cell death 2-like	protein-coding
mm_7170.1	chr1	92126844	92126859	-	1	NA	intron (NM_207225, intron 2 of 26)	intron (NM_207225, intron 2 of 26)	53490	NM_207225	208727	Mm.318567	NM_207225	ENSMUSG00000026313	Hdac4	4932408F19Rik|HD4	histone deacetylase 4	protein-coding
mm_165370.1	chr2	128114377	128114379	+	1	NA	intron (NM_028765, intron 17 of 17)	intron (NM_028765, intron 17 of 17)	-11660	NM_207681	12125	Mm.141083	NM_009754	ENSMUSG00000027381	Bcl2l11	1500006F24Rik|Bim|Bod|bcl2-L-11	BCL2-like 11 (apoptosis facilitator)	protein-coding
mm_123916.1	chr14	73362924	73362967	-	1	NA	3' UTR (NM_008410, exon 6 of 6)	3' UTR (NM_008410, exon 6 of 6)	22326	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_75930.1	chr8	71511763	71511778	-	1	NA	promoter-TSS (NM_032398)	promoter-TSS (NM_032398)	-1	NM_032398	84094	Mm.260768	NM_032398	ENSMUSG00000034845	Plvap	MECA32|Pv1	plasmalemma vesicle associated protein	protein-coding
mm_86438.1	chr10	3973087	3973157	+	1	NA	promoter-TSS (NM_001170785)	promoter-TSS (NM_001170785)	47	NM_172308	270685	Mm.184752	NM_172308	ENSMUSG00000040675	Mthfd1l	2410004L15Rik|AI647056|Fthfsdc1	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1-like	protein-coding
mm_97695.1	chr11	80161341	80161353	+	1	NA	intron (NM_172133, intron 4 of 10)	ID_B1|SINE|B4	7185	NM_172133	216991	Mm.341520	NM_172133	ENSMUSG00000020709	Adap2	Centa2	ArfGAP with dual PH domains 2	protein-coding
mm_75984.1	chr8	72284999	72285009	-	1	NA	Intergenic	B4A|SINE|B4	-34058	NM_008452	16598	Mm.26938	NM_008452	ENSMUSG00000055148	Klf2	Lklf	Kruppel-like factor 2 (lung)	protein-coding
mm_161792.1	chr17	47695119	47695119	+	1	NA	promoter-TSS (NM_144939)	promoter-TSS (NM_144939)	-88	NM_144939	107971	Mm.392206	NM_144939	ENSMUSG00000023266	Frs3	4930417B13Rik|AI449674|Frs2beta|Snt2	fibroblast growth factor receptor substrate 3	protein-coding
mm_13482.1	chr2	106081028	106081035	+	1	NA	Intergenic	Intergenic	-77482	NR_033993	99349	Mm.25661	NM_026992	ENSMUSG00000027166	Dnajc24	1700030A21Rik|2610027M02Rik|AV066965|AW240712|Dph4|MmDjC7|Zcsl3	DnaJ heat shock protein family (Hsp40) member C24	protein-coding
mm_85717.1	chr9	108263707	108263819	-	1	NA	promoter-TSS (NM_001276482)	promoter-TSS (NM_001276482)	52	NM_010017	13138	Mm.7524	NM_010017	ENSMUSG00000039952	Dag1	D9Wsu13e|DG|Dp427|Dp71	dystroglycan 1	protein-coding
mm_77138.1	chr8	111393863	111393873	-	1	NA	promoter-TSS (NM_178086)	promoter-TSS (NM_178086)	-47	NM_178086	338521	Mm.41083	NM_178086	ENSMUSG00000033579	Fa2h	FAAH|Faxdc1|G630055L08Rik	fatty acid 2-hydroxylase	protein-coding
mm_24563.1	chr3	93443779	93443785	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	1452	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_165107.1	chr19	56535168	56535178	-	1	NA	intron (NM_018831, intron 8 of 9)	intron (NM_018831, intron 8 of 9)	13049	NM_018831	55947	Mm.2805	NM_018831	ENSMUSG00000025077	Dclre1a	2810043H12Rik|AU022226|Pso2|Smn1a|Snm1|mKIAA0086	DNA cross-link repair 1A	protein-coding
mm_32318.1	chr4	103619226	103619244	+	1	NA	Intergenic	Intergenic	236735	NR_040673	622167	Mm.244115	NR_040673	ENSMUSG00000086136	Gm12718	OTTMUSG00000008109	predicted gene 12718	ncRNA
mm_21473.1	chr2	161109018	161109027	-	1	NA	promoter-TSS (NM_173368)	promoter-TSS (NM_173368)	64	NM_173368	71389	Mm.122738	NM_173368	ENSMUSG00000057133	Chd6	5430439G14Rik|6330406J24Rik|CHD-6	chromodomain helicase DNA binding protein 6	protein-coding
mm_30321.1	chr3	151731730	151731764	-	1	NA	3' UTR (NM_133871, exon 8 of 8)	3' UTR (NM_133871, exon 8 of 8)	18212	NM_133871	99899	Mm.30756	NM_133871	ENSMUSG00000028037	Ifi44	A430056A10Rik|AW261460|MTAP44|p44	interferon-induced protein 44	protein-coding
mm_54134.1	chr6	21852127	21852183	-	1	NA	5' UTR (NM_173007, exon 2 of 9)	5' UTR (NM_173007, exon 2 of 9)	360	NM_173007	269831	Mm.21950	NM_173007	ENSMUSG00000029669	Tspan12	9030619E17|AI426782|AI663988|AW111457|Tm4sf12	tetraspanin 12	protein-coding
mm_157843.1	chrX	74373261	74373309	-	1	NA	promoter-TSS (NM_145406)	promoter-TSS (NM_145406)	64	NM_001256104	214601	Mm.19931	NM_145406	ENSMUSG00000032806	Slc10a3	DXHXS253E|DXS253Eh|DXSmhG28|P3	solute carrier family 10 (sodium/bile acid cotransporter family), member 3	protein-coding
mm_161236.1	chr13	94285958	94285958	-	1	NA	promoter-TSS (NM_029153)	promoter-TSS (NM_029153)	-127	NM_001346609	107767	Mm.201455	NM_029153	ENSMUSG00000021687	Scamp1	4930505M11Rik|AI415563|AW122395	secretory carrier membrane protein 1	protein-coding
mm_102657.1	chr11	63922258	63922292	-	1	NA	promoter-TSS (NM_018805)	promoter-TSS (NM_018805)	9	NM_018805	54710	Mm.274426	NM_018805	ENSMUSG00000070407	Hs3st3b1	3-OST-3B|3OST3B1|3Ost3b|AU041882|AW536289|Hs3st3b|m3-OST-3B	heparan sulfate (glucosamine) 3-O-sulfotransferase 3B1	protein-coding
mm_38549.1	chr4	141601677	141601738	-	1	NA	intron (NM_133754, intron 1 of 8)	intron (NM_133754, intron 1 of 8)	-1783	NM_001163256	74202	Mm.490327	NM_133754	ENSMUSG00000006219	Fblim1	2410043F08Rik|Cal|Fblp1|Gt10|migfilin|migfilin(s)	filamin binding LIM protein 1	protein-coding
mm_28912.1	chr3	98814435	98814449	-	1	NA	promoter-TSS (NM_013821)	promoter-TSS (NM_013821)	1	NM_013821	15497	Mm.14435	NM_013821	ENSMUSG00000027869	Hsd3b6	D19210	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 6	protein-coding
mm_139561.1	chr17	56931700	56931708	+	1	NA	intron (NM_022328, intron 1 of 11)	(CCTA)n|Simple_repeat|Simple_repeat	3684	NM_022328	64144	Mm.148748	NM_022328	ENSMUSG00000024212	Mllt1	AA407901|BAM11|ENL|LTG19	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 1	protein-coding
mm_121795.1	chr14	20083103	20083165	-	1	NA	promoter-TSS (NM_026209)	promoter-TSS (NM_026209)	38	NM_026209	67509	Mm.292423	NM_026209	ENSMUSG00000045107	Saysd1	1810063B07Rik|4930488P03Rik	SAYSVFN motif domain containing 1	protein-coding
mm_51405.1	chr6	78373354	78373364	+	1	NA	3' UTR (NM_011036, exon 6 of 6)	3' UTR (NM_011036, exon 6 of 6)	2474	NM_011036	18489	Mm.2553	NM_011036	ENSMUSG00000071356	Reg3b	HIP|PAP1|Pap|REG-III	regenerating islet-derived 3 beta	protein-coding
mm_111078.1	chr12	80168184	80168197	-	1	NA	3' UTR (NM_134156, exon 21 of 21)	3' UTR (NM_134156, exon 21 of 21)	-35346	NR_033514	69548	Mm.269712	NR_033514	ENSMUSG00000097729	2310015A10Rik	5330419I17Rik	RIKEN cDNA 2310015A10 gene	ncRNA
mm_129722.1	chr15	81960802	81960812	-	1	NA	exon (NM_001282041, exon 1 of 6)	exon (NM_001282041, exon 1 of 6)	123	NM_001282040	29858	Mm.18939	NM_013872	ENSMUSG00000022474	Pmm1	C77612	phosphomannomutase 1	protein-coding
mm_81632.1	chr9	110857959	110857987	+	1	NA	promoter-TSS (NM_146227)	promoter-TSS (NM_146227)	6	NM_146227	235631	Mm.102265	NM_146227	ENSMUSG00000048752	Prss50	79H19C|Tsp50	protease, serine 50	protein-coding
mm_92356.1	chr10	75921419	75921440	-	1	NA	5' UTR (NM_001161853, exon 1 of 9)	5' UTR (NM_001161853, exon 1 of 9)	185	NM_011418	20587	Mm.279751	NM_011418	ENSMUSG00000000902	Smarcb1	AU020204|Baf47|Ini1|SNF5/INI1|Snf5	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1	protein-coding
mm_108705.1	chr12	87021322	87021333	+	1	NA	Intergenic	Intergenic	-5237	NM_172583	217733	Mm.110032	NM_172583	ENSMUSG00000034145	Tmem63c	4932420N09|9330187M14Rik	transmembrane protein 63c	protein-coding
mm_117845.1	chr13	98694770	98694796	-	1	NA	promoter-TSS (NM_001025606)	promoter-TSS (NM_001025606)	48	NM_001025606	380863	Mm.28264	NM_001025606	ENSMUSG00000052485	Tmem171	Gm905	transmembrane protein 171	protein-coding
mm_170780.1	chr2	171083657	171083661	+	1	NA	Intergenic	Intergenic	351852	NM_001163686	76829	Mm.41633	NM_029761	ENSMUSG00000027560	Dok5	2700055C10Rik	docking protein 5	protein-coding
mm_138287.1	chr17	34612730	34612762	+	1	NA	TTS (NM_152922)	TTS (NM_152922)	3225	NM_152922	81701	Mm.231343	NM_152922	ENSMUSG00000015467	Egfl8	Ng3	EGF-like domain 8	protein-coding
mm_43158.1	chr5	125928766	125928779	+	1	NA	Intergenic	Intergenic	396354	NM_001190352	208151	Mm.40397	NM_001190352	ENSMUSG00000070498	Tmem132b	AK220418|mKIAA1786	transmembrane protein 132B	protein-coding
mm_97860.1	chr11	83116810	83116850	+	1	NA	promoter-TSS (NM_011407)	promoter-TSS (NM_011407)	-15	NM_011407	20555	Mm.10948	NM_011407	ENSMUSG00000078763	Slfn1	AV316259	schlafen 1	protein-coding
mm_27468.1	chr3	52755046	52755056	-	1	NA	intron (NR_038079, intron 1 of 3)	intron (NR_038079, intron 1 of 3)	15327	NR_038079	329639	Mm.131245	NR_038079	ENSMUSG00000102785	Gm2447	100039832|A530017F20	predicted gene 2447	ncRNA
mm_75288.1	chr8	41041829	41041851	-	1	NA	promoter-TSS (NM_001005865)	promoter-TSS (NM_001005865)	91	NM_001005865	102103	Mm.149438	NM_001005863	ENSMUSG00000045636	Mtus1	AI481402|ATBP135|Atip1|B430010I23Rik|B430305I03Rik|C85752|Cctsg1-440|MD44|MTSG1|mKIAA1288	mitochondrial tumor suppressor 1	protein-coding
mm_46043.1	chr5	92015331	92015334	-	1	NA	intron (NM_016912, intron 12 of 13)	L1_Rod|LINE|L1	27364	NM_001276315	53886	Mm.44963	NM_016912	ENSMUSG00000029403	Cdkl2	5330436L21Rik|AI505225|KKIAMRE|Kkm	cyclin-dependent kinase-like 2 (CDC2-related kinase)	protein-coding
mm_125561.1	chr15	58889270	58889311	+	1	NA	promoter-TSS (NM_175226)	promoter-TSS (NM_175226)	61	NM_175226	75841	Mm.4537	NM_175226	ENSMUSG00000037075	Rnf139	4930555P18Rik	ring finger protein 139	protein-coding
mm_16350.1	chr2	174346568	174346580	+	1	NA	non-coding (NR_003258, exon 13 of 13)	non-coding (NR_003258, exon 13 of 13)	16485	NM_001077510	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_168630.1	chr1	182182758	182182777	+	1	NA	Intergenic	RLTR9D2|LTR|ERVK	-24669	NM_001166728	625823	Mm.479992	NM_001166728	ENSMUSG00000091013	Vmn1r1	EG625823|Gm6628	vomeronasal 1 receptor 1	protein-coding
mm_65613.1	chr7	27531713	27531737	-	1	NA	TTS (NM_011116)	TTS (NM_011116)	8464	NM_001033315	233020	Mm.429716	NM_001033315	ENSMUSG00000040424	Hipk4	Gm162	homeodomain interacting protein kinase 4	protein-coding
mm_121360.1	chr14	117240679	117240720	+	1	NA	intron (NM_001079844, intron 2 of 9)	intron (NM_001079844, intron 2 of 9)	315402	NM_011821	23888	Mm.440025	NM_011821	ENSMUSG00000058571	Gpc6	-	glypican 6	protein-coding
mm_141488.1	chr17	31277258	31277325	-	1	NA	promoter-TSS (NM_025290)	promoter-TSS (NM_025290)	65	NM_025290	22092	Mm.12743	NM_025290	ENSMUSG00000024033	Rsph1	MCA|Tsga2	radial spoke head 1 homolog (Chlamydomonas)	protein-coding
mm_64422.1	chr7	142576986	142577040	+	1	NA	TTS (NR_030416)	TTS (NR_030416)	134	NR_030416	735280		NR_030416	ENSMUSG00000076275	Mir675	Mirn675|mir-675|mmu-mir-675	microRNA 675	ncRNA
mm_42836.1	chr5	122102971	122102975	+	1	NA	intron (NM_010861, intron 3 of 6)	intron (NM_010861, intron 3 of 6)	1993	NM_010861	17906	Mm.1529	NM_010861	ENSMUSG00000013936	Myl2	MLC-2|MLC-2s/v|MLC-2v|Mlc2v|Mylpc	myosin, light polypeptide 2, regulatory, cardiac, slow	protein-coding
mm_70925.1	chr8	25812975	25812986	+	1	NA	3' UTR (NM_011485, exon 7 of 7)	3' UTR (NM_011485, exon 7 of 7)	4506	NM_011485	20845	Mm.293314	NM_011485	ENSMUSG00000031574	Star	AV363654|D8Ertd419e|stARD1	steroidogenic acute regulatory protein	protein-coding
mm_74533.1	chr8	9702590	9702592	-	1	NA	intron (NM_001347127, intron 1 of 3)	intron (NM_001347127, intron 1 of 3)	68432	NM_173446	270028	Mm.268163	NM_173446	ENSMUSG00000079157	Fam155a	6430500D16|AW121567|Tmem28	family with sequence similarity 155, member A	protein-coding
mm_117242.1	chr13	64363001	64363003	-	1	NA	3' UTR (NM_009984, exon 8 of 8)	3' UTR (NM_009984, exon 8 of 8)	7518	NM_009984	13039	Mm.930	NM_009984	ENSMUSG00000021477	Ctsl	1190035F06Rik|CatL|Ctsl1|MEP|fs|nkt	cathepsin L	protein-coding
mm_118371.1	chr13	116888991	116889003	-	1	NA	intron (NM_001081009, intron 15 of 26)	L1M4|LINE|L1	136519	NM_001081009	52552	Mm.274466	NM_027272	ENSMUSG00000021725	Parp8	2810430O08Rik|ARTD16|D13Ertd275e	poly (ADP-ribose) polymerase family, member 8	protein-coding
mm_21929.1	chr2	167043495	167043523	-	1	NA	promoter-TSS (NM_001291162)	promoter-TSS (NM_001291162)	-14	NM_001291162	98999	Mm.297074	NM_001033196	ENSMUSG00000039501	Znfx1	AI481105|Astx3	zinc finger, NFX1-type containing 1	protein-coding
mm_25253.1	chr3	104655868	104655869	+	1	NA	3' UTR (NM_009196, exon 5 of 5)	3' UTR (NM_009196, exon 5 of 5)	17204	NM_009196	20501	Mm.9086	NM_009196	ENSMUSG00000032902	Slc16a1	AL022710|Mct1	solute carrier family 16 (monocarboxylic acid transporters), member 1	protein-coding
mm_30006.1	chr3	135613678	135613681	-	1	NA	exon (NM_008689, exon 11 of 25)	exon (NM_008689, exon 11 of 25)	77868	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_34575.1	chr4	150087514	150087541	+	1	NA	promoter-TSS (NM_177366)	promoter-TSS (NM_177366)	24	NM_177366	269604	Mm.219307	NM_177366	ENSMUSG00000047875	Gpr157	F730108M23Rik	G protein-coupled receptor 157	protein-coding
mm_57144.1	chr6	122635371	122635381	-	1	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	8952	NM_139218	73708	Mm.27982	NM_139218	ENSMUSG00000046323	Dppa3	2410075G02Rik|PCG7|PGC7|Stella	developmental pluripotency-associated 3	protein-coding
mm_91412.1	chr10	31608614	31608630	-	1	NA	exon (NM_001146349, exon 1 of 6)	exon (NM_001146349, exon 1 of 6)	1103	NM_001146349	268291	Mm.295212	NM_001146349	ENSMUSG00000063760	Rnf217	AU016819|Ibrdc1	ring finger protein 217	protein-coding
mm_66843.1	chr7	48887067	48887090	-	1	NA	Intergenic	MIRc|SINE|MIR	-6037	NM_001013368	108961	Mm.240566	NM_001013368	ENSMUSG00000046179	E2f8	4432406C08Rik|AA410048	E2F transcription factor 8	protein-coding
mm_144261.1	chr18	11052519	11052527	+	1	NA	promoter-TSS (NR_105023)	promoter-TSS (NR_105023)	13	NM_010258	14465	Mm.329287	NM_010258	ENSMUSG00000005836	Gata6	AA410133|GATA-6	GATA binding protein 6	protein-coding
mm_54106.1	chr6	16898419	16898436	-	1	NA	promoter-TSS (NM_031198)	promoter-TSS (NM_031198)	14	NM_031198	21426	Mm.36217	NM_031198	ENSMUSG00000029553	Tfec	BB107417|Tcfec|bHLHe34	transcription factor EC	protein-coding
mm_37702.1	chr4	129376013	129376026	-	1	NA	intron (NM_028603, intron 1 of 4)	intron (NM_028603, intron 1 of 4)	2009	NM_028603	73680	Mm.32997	NM_028603	ENSMUSG00000028807	Zbtb8a	2410081M15Rik|AI480941	zinc finger and BTB domain containing 8a	protein-coding
mm_42501.1	chr5	115490232	115490251	+	1	NA	Intergenic	CpG	-5757	NM_133760	75387	Mm.332616	NM_133760	ENSMUSG00000029524	Sirt4	4930596O17Rik	sirtuin 4	protein-coding
mm_71209.1	chr8	40890607	40890618	+	1	NA	intron (NM_007514, intron 1 of 11)	intron (NM_007514, intron 1 of 11)	28245	NM_001044740	11988	Mm.4676	NM_007514	ENSMUSG00000031596	Slc7a2	20.5|AI158848|Atrc2|CAT-2|Cat2|Tea	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	protein-coding
mm_32375.1	chr4	106315997	106316046	+	1	NA	promoter-TSS (NM_183225)	promoter-TSS (NM_183225)	-192	NM_183225	329908	Mm.234544	NM_183225	ENSMUSG00000028514	Usp24	2700066K03Rik|2810030C21Rik|AI414051|B130021E18|C79851	ubiquitin specific peptidase 24	protein-coding
mm_149197.1	chr19	9955087	9955096	+	1	NA	Intergenic	Intergenic	-25509	NR_073181	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
mm_128013.1	chr15	15175454	15175464	-	1	NA	Intergenic	RMER17A2|LTR|ERVK	-1602642	NM_009869	12565	Mm.439758	NM_009869	ENSMUSG00000025370	Cdh9	-	cadherin 9	protein-coding
mm_137493.1	chr17	26951704	26951720	+	1	NA	intron (NM_001281491, intron 3 of 18)	intron (NM_001281491, intron 3 of 18)	-3593	NR_037244	100526534		NR_037244	ENSMUSG00000093118	Mir3083	mir-3083|mmu-mir-3083	microRNA 3083	ncRNA
mm_94188.1	chr10	128960826	128960853	-	1	NA	exon (NM_027853, exon 1 of 2)	exon (NM_027853, exon 1 of 2)	149	NM_027853	71664	Mm.337232	NM_027853	ENSMUSG00000025347	Mettl7b	0610006F02Rik|AI266817	methyltransferase like 7B	protein-coding
mm_101338.1	chr11	23519238	23519245	-	1	NA	promoter-TSS (NM_026105)	promoter-TSS (NM_026105)	-46	NM_026105	67358	Mm.87328	NM_026105	ENSMUSG00000020286	1700093K21Rik	-	RIKEN cDNA 1700093K21 gene	protein-coding
mm_13733.1	chr2	118111493	118111515	+	1	NA	promoter-TSS (NM_011580)	promoter-TSS (NM_011580)	-302	NR_126479	329496	Mm.235844	NR_126479	ENSMUSG00000087203	Gm13986	C230060E24|OTTMUSG00000015236	predicted gene 13986	ncRNA
mm_130484.1	chr15	98742646	98742661	-	1	NA	exon (NM_007478, exon 2 of 5)	exon (NM_007478, exon 2 of 5)	-14455	NM_024169	66120	Mm.30729	NM_024169	ENSMUSG00000003355	Fkbp11	1110002O23Rik|FKBP-11	FK506 binding protein 11	protein-coding
mm_157356.1	chrX	37085138	37085154	-	1	NA	promoter-TSS (NM_026055)	promoter-TSS (NM_026055)	76	NM_026055	67248	Mm.30478	NM_026055	ENSMUSG00000079641	Rpl39	2810465O16Rik	ribosomal protein L39	protein-coding
mm_144751.1	chr18	35609055	35609060	+	1	NA	intron (NM_026420, intron 1 of 3)	B1_Mus1|SINE|Alu	10390	NM_026420	67869	Mm.126534	NM_026420	ENSMUSG00000037058	Paip2	2310050K10Rik|AU045972	polyadenylate-binding protein-interacting protein 2	protein-coding
mm_50719.1	chr6	52229896	52229916	+	1	NA	TTS (NR_029912)	TTS (NR_029912)	259	NR_029912	723820		NR_029912	ENSMUSG00000065443	Mir196b	Mirn196b|mir-196b	microRNA 196b	ncRNA
mm_25090.1	chr3	100920776	100920783	+	1	NA	Intergenic	Intergenic	-1714	NM_001165952	229644	Mm.189351	NM_194343	ENSMUSG00000033233	Trim45	4921530N01Rik	tripartite motif-containing 45	protein-coding
mm_100202.1	chr11	116843520	116843569	+	1	NA	promoter-TSS (NM_028865)	promoter-TSS (NM_028865)	29	NM_028865	74319	Mm.429312	NM_028865	ENSMUSG00000090266	Mettl23	1110005A03Rik|1500035B17Rik|4933424L15Rik	methyltransferase like 23	protein-coding
mm_112322.1	chr12	115294484	115294518	-	1	NA	Intergenic	Intergenic	401293	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
mm_46388.1	chr5	104021780	104021796	-	1	NA	promoter-TSS (NM_053262)	promoter-TSS (NM_053262)	8	NM_053262	114664	Mm.46019	NM_053262	ENSMUSG00000029311	Hsd17b11	Dhrs8|Pan1b|SDR2|retSDR2	hydroxysteroid (17-beta) dehydrogenase 11	protein-coding
mm_121614.1	chr14	8259008	8259024	-	1	NA	promoter-TSS (NM_053115)	promoter-TSS (NM_053115)	3	NM_053115	93732	Mm.28700	NM_053115	ENSMUSG00000021751	Acox2	THCCox	acyl-Coenzyme A oxidase 2, branched chain	protein-coding
mm_102646.1	chr11	62789446	62789478	-	1	NA	promoter-TSS (NM_138949)	promoter-TSS (NM_138949)	-45	NM_138949	192651	Mm.168530	NM_138949	ENSMUSG00000047342	Zfp286	BC027023	zinc finger protein 286	protein-coding
mm_142514.1	chr17	46247970	46248000	-	1	NA	promoter-TSS (NM_009085)	promoter-TSS (NM_009085)	60	NM_009085	20016	Mm.3458	NM_009085	ENSMUSG00000067148	Polr1c	40kDa|AA409007|AA959927|AL024089|Polr1e|RPA40|Rpo1-1	polymerase (RNA) I polypeptide C	protein-coding
mm_51896.1	chr6	90619223	90619233	+	1	NA	promoter-TSS (NM_001037493)	promoter-TSS (NM_001037493)	-18	NM_001037493	71699	Mm.272633	NM_027868	ENSMUSG00000030089	Slc41a3	1010001P06Rik|AI480742|SLC41A1-L2	solute carrier family 41, member 3	protein-coding
mm_84642.1	chr9	71215326	71215336	-	1	NA	promoter-TSS (NM_009022)	promoter-TSS (NM_009022)	55	NR_110518	100041660	Mm.487231	NR_110518		Gm3458	-	predicted gene 3458	ncRNA
mm_8179.1	chr1	138080196	138080207	-	1	NA	exon (NM_001268286, exon 21 of 29)	exon (NM_001268286, exon 21 of 29)	94925	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_134885.1	chr16	29378613	29378625	-	1	NA	5' UTR (NM_175650, exon 1 of 30)	5' UTR (NM_175650, exon 1 of 30)	113	NM_001284375	268878	Mm.9823	NM_175650	ENSMUSG00000048939	Atp13a5	C630015F21Rik	ATPase type 13A5	protein-coding
mm_149418.1	chr19	11435203	11435216	+	1	NA	Intergenic	L1VL4|LINE|L1	-8349	NM_021718	60361	Mm.33957	NM_021718	ENSMUSG00000056290	Ms4a4b	AI463180|Chandra|Ly116	membrane-spanning 4-domains, subfamily A, member 4B	protein-coding
mm_115038.1	chr13	99425372	99425402	+	1	NA	3' UTR (NM_008634, exon 7 of 7)	3' UTR (NM_008634, exon 7 of 7)	-12561	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_129789.1	chr15	82832517	82832519	-	1	NA	intron (NM_001114140, intron 2 of 5)	intron (NM_001114140, intron 2 of 5)	-38273	NM_029562	76279	Mm.439931	NM_029562	ENSMUSG00000022445	Cyp2d26	1300006E06Rik	cytochrome P450, family 2, subfamily d, polypeptide 26	protein-coding
mm_116956.1	chr13	56136083	56136087	-	1	NA	promoter-TSS (NM_001159515)	promoter-TSS (NM_001159515)	-535	NM_001159513	26914	Mm.283802	NM_012015	ENSMUSG00000015937	H2afy	H2AF12M|mH2a1|macroH2A1	H2A histone family, member Y	protein-coding
mm_68142.1	chr7	102240192	102240211	-	1	NA	exon (NM_019566, exon 2 of 2)	exon (NM_019566, exon 2 of 2)	9917	NM_019566	56212	Mm.259795	NM_019566	ENSMUSG00000073982	Rhog	2810426G09Rik|Arhg|Sid10750	ras homolog family member G	protein-coding
mm_83855.1	chr9	54642675	54642698	-	1	NA	exon (NM_053178, exon 2 of 14)	exon (NM_053178, exon 2 of 14)	19199	NM_053178	94180	Mm.20592	NM_053178	ENSMUSG00000032281	Acsbg1	BG1|Bgm|E230019G03Rik|GR-LACS|Lpd|R75185	acyl-CoA synthetase bubblegum family member 1	protein-coding
mm_143088.1	chr17	57080363	57080415	-	1	NA	3' UTR (NM_009451, exon 4 of 4)	3' UTR (NM_009451, exon 4 of 4)	-1879	NM_153551	70785	Mm.284447	NM_153551	ENSMUSG00000002668	Dennd1c	4432409M07Rik	DENN/MADD domain containing 1C	protein-coding
mm_36692.1	chr4	96635829	96635830	-	1	NA	exon (NM_010007, exon 6 of 9)	exon (NM_010007, exon 6 of 9)	28290	NM_010007	13109	Mm.12838	NM_010007	ENSMUSG00000052520	Cyp2j5	-	cytochrome P450, family 2, subfamily j, polypeptide 5	protein-coding
mm_121005.1	chr14	79516423	79516445	+	1	NA	intron (NM_001286411, intron 1 of 8)	intron (NM_001286411, intron 1 of 8)	760	NM_001286411	13709	Mm.20938	NM_007920	ENSMUSG00000036461	Elf1	Elf-1|Sts1|mElf-1|p70	E74-like factor 1	protein-coding
mm_48219.1	chr5	137613760	137613785	-	1	NA	exon (NM_027708, exon 9 of 10)	exon (NM_027708, exon 9 of 10)	-2368	NM_008788	18542	Mm.262345	NM_008788	ENSMUSG00000029718	Pcolce	Astt-2|Astt2|P14|PCPE-1	procollagen C-endopeptidase enhancer protein	protein-coding
mm_156455.1	chrX	142783206	142783211	+	1	NA	intron (NM_001199360, intron 4 of 6)	L1MB7|LINE|L1	44208	NR_030523	723976		NR_030523	ENSMUSG00000076011	Mir652	Mirn652|miRX|mmu-mir-652	microRNA 652	ncRNA
mm_88218.1	chr10	70285507	70285511	+	1	NA	3' UTR (NM_025807, exon 6 of 6)	3' UTR (NM_025807, exon 6 of 6)	40233	NM_025807	66859	Mm.19325	NM_025807	ENSMUSG00000037762	Slc16a9	1200003C15Rik|4930425B13Rik|AI552636	solute carrier family 16 (monocarboxylic acid transporters), member 9	protein-coding
mm_163020.1	chr11	46750483	46750491	+	1	NA	promoter-TSS (NM_001166631)	promoter-TSS (NM_001166631)	-24	NM_001166631	171283	Mm.17771	NM_134248	ENSMUSG00000040405	Havcr1	AI503787|KIM-1|TIM-1|Tim1|Timd1	hepatitis A virus cellular receptor 1	protein-coding
mm_141668.1	chr17	33890545	33890560	-	1	NA	promoter-TSS (NM_001195298)	promoter-TSS (NM_001195298)	81	NM_001195298	100502766	Mm.335713	NM_001195298	ENSMUSG00000079553	Kifc1	100042970|Gm4137|HSET|KNSL2|Kifc5a|Knsl2a|Tctex-7|Tctex-7A|Tctex7|Tctex7a	kinesin family member C1	protein-coding
mm_44261.1	chr5	5514878	5514891	-	1	NA	promoter-TSS (NM_001193660)	promoter-TSS (NM_001193660)	-35	NM_001193659	64945	Mm.40132	NM_022890	ENSMUSG00000046798	Cldn12	-	claudin 12	protein-coding
mm_129936.1	chr15	84855175	84855188	-	1	NA	intron (NR_030731, intron 1 of 11)	CpG-5189	948	NM_001081166	271305	Mm.101022	NM_001081166	ENSMUSG00000016624	Phf21b	A730032D07Rik	PHD finger protein 21B	protein-coding
mm_103802.1	chr11	82910784	82910803	-	1	NA	promoter-TSS (NM_178680)	promoter-TSS (NM_178680)	-460	NM_178680	217012	Mm.295205	NM_178680	ENSMUSG00000018845	Unc45b	AA445617|Cmya4|D230041A13Rik|Unc45	unc-45 myosin chaperone B	protein-coding
mm_89082.1	chr10	83544013	83544023	+	1	NA	promoter-TSS (NM_001033375)	promoter-TSS (NM_001033375)	77	NM_001033375	319277	Mm.491194	NM_001033375	ENSMUSG00000034560	Washc4	A230046K03Rik|AA589518|Kiaa1033|mKIAA1033	WASH complex subunit 4	protein-coding
mm_535.1	chr1	37997976	37997986	+	1	NA	promoter-TSS (NM_172054)	promoter-TSS (NM_172054)	-29	NM_198303	226982	Mm.260943	NM_198303	ENSMUSG00000026083	Eif5b	A030003E17Rik|BC018347|IF2	eukaryotic translation initiation factor 5B	protein-coding
mm_172507.1	chr7	68304089	68304100	+	1	NA	intron (NM_001013811, intron 2 of 8)	intron (NM_001013811, intron 2 of 8)	-27500	NR_040340	100504026	Mm.426764	NR_040340	ENSMUSG00000086628	Gm16157	OTTMUSG00000031023	predicted gene 16157	ncRNA
mm_164097.1	chr15	12599055	12599062	-	1	NA	Intergenic	Intergenic	-6502	NM_001081064	68070	Mm.423205	NM_001081064	ENSMUSG00000022197	Pdzd2	4930537L06Rik|A930022H17Rik|Gm21706|Gm82|Pdzk3|mKIAA0300	PDZ domain containing 2	protein-coding
mm_36884.1	chr4	107253364	107253377	-	1	NA	promoter-TSS (NM_028394)	promoter-TSS (NM_028394)	163	NM_029985	77809	Mm.29681	NM_029985	ENSMUSG00000028617	Lrrc42	A930011F22Rik|AA536996	leucine rich repeat containing 42	protein-coding
mm_97176.1	chr11	75532165	75532187	+	1	NA	promoter-TSS (NM_001199283)	promoter-TSS (NM_001199283)	64	NM_001199283	215113	Mm.11186	NM_173388	ENSMUSG00000038178	Slc43a2	7630402D21Rik|BC042513|Lat4	solute carrier family 43, member 2	protein-coding
mm_31068.1	chr4	41349029	41349064	+	1	NA	promoter-TSS (NM_001290454)	promoter-TSS (NM_001290454)	50	NM_023305	67123	Mm.289795	NM_023305	ENSMUSG00000028437	Ubap1	2700092A01Rik|NAG20|UBAP-1|Ubap	ubiquitin-associated protein 1	protein-coding
mm_158112.1	chrX	102189300	102189308	-	1	NA	promoter-TSS (NM_009094)	promoter-TSS (NM_009094)	87	NM_009094	20102	Mm.66	NM_009094	ENSMUSG00000031320	Rps4x	Rps4|Rps4-1	ribosomal protein S4, X-linked	protein-coding
mm_30815.1	chr4	21749704	21749707	+	1	NA	3' UTR (NM_016746, exon 12 of 12)	3' UTR (NM_016746, exon 12 of 12)	17506	NM_029840	77032	Mm.87238	NM_029840	ENSMUSG00000028251	Tstd3	2610029I01Rik	thiosulfate sulfurtransferase (rhodanese)-like domain containing 3	protein-coding
mm_67930.1	chr7	99922347	99922367	-	1	NA	3' UTR (NM_175388, exon 6 of 6)	3' UTR (NM_175388, exon 6 of 6)	58101	NM_175388	108937	Mm.323087	NM_175388	ENSMUSG00000058761	Rnf169	2900057K09Rik	ring finger protein 169	protein-coding
mm_155850.1	chrX	101274107	101274148	+	1	NA	promoter-TSS (NM_021521)	promoter-TSS (NM_021521)	36	NM_021521	59024	Mm.20873	NM_021521	ENSMUSG00000079487	Med12	230kDa|Mopa|OPA-1|Tnrc11|Trap230	mediator complex subunit 12	protein-coding
mm_55844.1	chr6	83317590	83317602	-	1	NA	promoter-TSS (NM_008638)	promoter-TSS (NM_008638)	8	NM_008638	17768	Mm.443	NM_008638	ENSMUSG00000005667	Mthfd2	AW558851|NMDMC	methylenetetrahydrofolate dehydrogenase (NAD+ dependent), methenyltetrahydrofolate cyclohydrolase	protein-coding
mm_38876.1	chr4	149685698	149685701	-	1	NA	intron (NM_001029837, intron 1 of 23)	intron (NM_001029837, intron 1 of 23)	-9610	NM_001164051	18707	Mm.229108	NM_008840	ENSMUSG00000039936	Pik3cd	2410099E07Rik|2610208K16Rik|AW545373|p110delta	phosphatidylinositol 3-kinase catalytic delta polypeptide	protein-coding
mm_75759.1	chr8	69917491	69917519	-	1	NA	exon (NM_001113346, exon 6 of 13)	exon (NM_001113346, exon 6 of 13)	-14947	NM_023312	67184	Mm.21162	NM_023312	ENSMUSG00000036199	Ndufa13	2700054G14Rik|AU022060|CDA016|CGI-39|GRIM-19|Grim19	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 13	protein-coding
mm_70547.1	chr8	13055955	13055966	+	1	NA	3' UTR (NM_007972, exon 9 of 9)	3' UTR (NM_007972, exon 9 of 9)	-4948	NM_025834	66901	Mm.441140	NM_025834	ENSMUSG00000031445	Proz	1300015B06Rik	protein Z, vitamin K-dependent plasma glycoprotein	protein-coding
mm_169054.1	chr13	22422968	22422978	+	1	NA	Intergenic	L1_Mus2|LINE|L1	-18299	NM_134211	171245	Mm.377201	NM_134211		Vmn1r-ps103	V1rh1	vomeronasal 1 receptor, pseudogene 103	protein-coding
mm_119934.1	chr14	54971034	54971042	+	1	NA	intron (NM_080728, intron 40 of 40)	intron (NM_080728, intron 40 of 40)	2251	NR_033497	791403	Mm.319176	NR_033497	ENSMUSG00000097652	Mhrt	D830015G02Rik|ENSMUSG00000053118|Myheart	myosin heavy chain associated RNA transcript	ncRNA
mm_94270.1	chr11	3648782	3648793	+	1	NA	promoter-TSS (NM_001159288)	promoter-TSS (NM_001159288)	27	NR_002321	544752	Mm.390314	NR_002321	ENSMUSG00000056579	Tug1	AI316828	taurine upregulated gene 1	ncRNA
mm_151407.1	chr19	56548554	56548572	+	1	NA	promoter-TSS (NM_018831)	promoter-TSS (NM_018831)	302	NM_025811	66866	Mm.46346	NM_025811	ENSMUSG00000025078	Nhlrc2	1200003G01Rik|AI835049|AV002846|AW496455	NHL repeat containing 2	protein-coding
mm_48708.1	chr5	147221804	147221815	-	1	NA	Intergenic	Intergenic	33113	NM_008178	14842	Mm.4797	NM_008178	ENSMUSG00000053129	Gsx1	Gsh-1|Gsh1	GS homeobox 1	protein-coding
mm_42928.1	chr5	122850136	122850142	+	1	NA	promoter-TSS (NM_030564)	promoter-TSS (NM_030564)	-49	NM_030564	80751	Mm.388529	NM_030564	ENSMUSG00000029474	Rnf34	AW061037|AW536122|BC004042|C88279|RIFF	ring finger protein 34	protein-coding
mm_78687.1	chr9	40801267	40801284	+	1	NA	promoter-TSS (NM_031165)	promoter-TSS (NM_031165)	2	NM_031165	15481	Mm.290774	NM_031165	ENSMUSG00000015656	Hspa8	2410008N15Rik|Hsc70|Hsc71|Hsc73|Hsp73|Hspa10	heat shock protein 8	protein-coding
mm_65080.1	chr7	19166120	19166134	-	1	NA	promoter-TSS (NM_001080815)	promoter-TSS (NM_001080815)	0	NM_001080815	381853	Mm.333633	NM_001080815	ENSMUSG00000030406	Gipr	GIP-R|Gm1081|Gm160	gastric inhibitory polypeptide receptor	protein-coding
mm_123181.1	chr14	57718976	57718978	-	1	NA	intron (NM_015771, intron 2 of 7)	intron (NM_015771, intron 2 of 7)	15441	NM_153382	50523	Mm.347899	NM_015771	ENSMUSG00000021959	Lats2	4932411G09Rik|AV277261|AW228608	large tumor suppressor 2	protein-coding
mm_62282.1	chr7	99818584	99818591	+	1	NA	intron (NM_016720, intron 2 of 2)	MMVL30-int|LTR|ERV1	9830	NM_016720	50877	Mm.103703	NM_016720	ENSMUSG00000035239	Neu3	-	neuraminidase 3	protein-coding
mm_105773.1	chr11	109721640	109721655	-	1	NA	exon (NM_153782, exon 1 of 11)	exon (NM_153782, exon 1 of 11)	609	NM_153782	208659	Mm.208662	NM_153782	ENSMUSG00000020614	Fam20a	AI606893	family with sequence similarity 20, member A	protein-coding
mm_162902.1	chr10	115764036	115764036	+	1	NA	Intergenic	Intergenic	-53248	NM_001168680	216350	Mm.22270	NM_146010	ENSMUSG00000034127	Tspan8	C76990|E330007O21Rik|Tm4sf3	tetraspanin 8	protein-coding
mm_90971.1	chr10	13446147	13446155	-	1	NA	intron (NM_001195065, intron 1 of 12)	intron (NM_001195065, intron 1 of 12)	28245	NM_001195065	215789	Mm.283359	NM_001033257	ENSMUSG00000062866	Phactr2	AV158170|BC012871	phosphatase and actin regulator 2	protein-coding
mm_63590.1	chr7	128134842	128134852	+	1	NA	intron (NM_021334, intron 8 of 29)	intron (NM_021334, intron 8 of 29)	5279	NM_021334	16411	Mm.22378	NM_021334	ENSMUSG00000030789	Itgax	AI449405|Cd11c|Cr4|N418	integrin alpha X	protein-coding
mm_128040.1	chr15	25364861	25364924	-	1	NA	exon (NM_027395, exon 2 of 2)	exon (NM_027395, exon 2 of 2)	48872	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	brain abundant, membrane attached signal protein 1	protein-coding
mm_13748.1	chr2	118120890	118120903	+	1	NA	exon (NM_011580, exon 15 of 22)	exon (NM_011580, exon 15 of 22)	9020	NM_001313914	21825	Mm.4159	NM_011580	ENSMUSG00000040152	Thbs1	TSP-1|TSP1|Thbs-1|tbsp1	thrombospondin 1	protein-coding
mm_21163.1	chr2	154603699	154603714	-	1	NA	promoter-TSS (NM_021534)	promoter-TSS (NM_021534)	-33	NM_021534	59038	Mm.24673	NM_021534	ENSMUSG00000000876	Pxmp4	3010018P03Rik|Pmp24	peroxisomal membrane protein 4	protein-coding
mm_119338.1	chr14	40972629	40972664	+	1	NA	Intergenic	Intergenic	-5750	NM_145928	52588	Mm.28876	NM_145928	ENSMUSG00000037824	Tspan14	AA958793|D14Ertd226e|Tm4sf14|tspan-14	tetraspanin 14	protein-coding
mm_120187.1	chr14	61492732	61492741	+	1	NA	promoter-TSS (NR_045714)	promoter-TSS (NR_045714)	48	NR_045714	75349	Mm.233613	NR_045714		4930556J02Rik	-	RIKEN cDNA 4930556J02 gene	ncRNA
mm_94692.1	chr11	19983136	19983146	+	1	NA	intron (NM_033523, intron 1 of 5)	intron (NM_033523, intron 1 of 5)	58699	NM_033523	114716	Mm.266627	NM_033523	ENSMUSG00000045671	Spred2	C79158	sprouty-related, EVH1 domain containing 2	protein-coding
mm_154654.1	chrX	7841928	7841934	+	1	NA	promoter-TSS (NM_001290536)	promoter-TSS (NM_001290536)	100	NM_138604	54644	Mm.142827	NM_138604	ENSMUSG00000031154	Otud5	AA407879|AI553596|BB114028|DUBA|DXImx46e|Sfc7	OTU domain containing 5	protein-coding
mm_148368.1	chr18	88894204	88894215	-	1	NA	promoter-TSS (NM_018821)	promoter-TSS (NM_018821)	-2	NM_018821	54607	Mm.91920	NM_018821	ENSMUSG00000056153	Socs6	1500012M23Rik|5830401B18Rik|AI447482|Cis4|Cish4|HSPC060|SOCS-4|SOCS-6|SSI4|STAI4|STATI4|Socs4	suppressor of cytokine signaling 6	protein-coding
mm_45603.1	chr5	75044414	75044424	-	1	NA	5' UTR (NM_028850, exon 1 of 6)	5' UTR (NM_028850, exon 1 of 6)	222	NM_028850	74277	Mm.239814	NM_028850	ENSMUSG00000029229	Chic2	1700081B18Rik|4930502K01Rik|BTL	cysteine-rich hydrophobic domain 2	protein-coding
mm_158117.1	chrX	102250941	102250959	-	1	NA	promoter-TSS (NM_001276474)	promoter-TSS (NM_001276474)	-174	NM_001276474	12705	Mm.2390	NM_007709	ENSMUSG00000051159	Cited1	AI316840|AU019144|Msg1	Cbp/p300-interacting transactivator with Glu/Asp-rich carboxy-terminal domain 1	protein-coding
mm_123177.1	chr14	57662217	57662224	-	1	NA	intron (NM_020506, intron 1 of 22)	intron (NM_020506, intron 1 of 22)	2736	NM_020506	57258	Mm.202747	NM_020506	ENSMUSG00000021952	Xpo4	B430309A01Rik|mKIAA1721	exportin 4	protein-coding
mm_42099.1	chr5	110344741	110344753	+	1	NA	promoter-TSS (NM_001310709)	promoter-TSS (NM_001310709)	17	NM_001310709	381667	Mm.332572	NM_001033459	ENSMUSG00000072754	Lrcol1	Clpsl3|Gm1679	leucine rich colipase-like 1	protein-coding
mm_81093.1	chr9	106370824	106370855	+	1	NA	exon (NM_153459, exon 2 of 3)	exon (NM_153459, exon 2 of 3)	2207	NM_153459	235584	Mm.275584	NM_153459	ENSMUSG00000053716	Dusp7	AU015694|Mkpx|Pyst2	dual specificity phosphatase 7	protein-coding
mm_163623.1	chr13	55449976	55450008	+	1	NA	intron (NM_001038018, intron 2 of 15)	intron (NM_001038018, intron 2 of 15)	-3114	NR_105908	102466770		NR_105908	ENSMUSG00000099058	Mir6943	Gm27791|mmu-mir-6943	microRNA 6943	ncRNA
mm_127110.1	chr15	97869767	97869775	+	1	NA	exon (NM_009504, exon 5 of 10)	exon (NM_009504, exon 5 of 10)	-25269	NM_001204278	56233	Mm.384027	NM_019572	ENSMUSG00000022475	Hdac7	5830434K02Rik|HD7|HD7a|Hdac7a|mFLJ00062	histone deacetylase 7	protein-coding
mm_163861.1	chr14	19418734	19418755	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	183843	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_144041.1	chr17	90313288	90313299	-	1	NA	intron (NM_001346959, intron 2 of 6)	L1Md_F2|LINE|L1	142587	NM_001346958	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_156742.1	chrX	159943092	159943105	+	1	NA	intron (NM_001290661, intron 1 of 6)	intron (NM_001290661, intron 1 of 6)	405	NM_001290664	58194	Mm.286495	NM_021389	ENSMUSG00000040990	Sh3kbp1	1200007H22Rik|1700125L08Rik|5830464D22Rik|AI447724|Cin85|IN85|Ruk|Seta	SH3-domain kinase binding protein 1	protein-coding
mm_63887.1	chr7	137437652	137437672	+	1	NA	promoter-TSS (NM_023140)	promoter-TSS (NM_023140)	-12	NR_033611	620016	Mm.388932	NR_033611	ENSMUSG00000100863	Gm12669	OTTMUSG00000007920	glutaredoxin 3 pseudogene	pseudo
mm_153064.1	chr19	32196424	32196442	-	1	NA	intron (NM_001168525, intron 5 of 9)	intron (NM_001168525, intron 5 of 9)	14580	NM_001168526	208449	Mm.329810	NM_144792	ENSMUSG00000040451	Sgms1	9530058O11Rik|AI841905|C80702|Mob|Sms1|Sor1|Tmem23	sphingomyelin synthase 1	protein-coding
mm_45693.1	chr5	82123337	82123347	-	1	NA	intron (NR_138557, intron 1 of 1)	intron (NR_138557, intron 1 of 1)	1371	NR_138557	67327	Mm.87058	NR_138557		1700031L13Rik	-	RIKEN cDNA 1700031L13 gene	ncRNA
mm_106573.1	chr11	120673196	120673210	-	1	NA	intron (NM_026877, intron 1 of 15)	CpG	230	NM_026877	68938	Mm.294020	NM_026877	ENSMUSG00000025142	Aspscr1	1190006K01Rik|ASPC|ASPCR1|ASPL|ASPS|RCC17|TUG	alveolar soft part sarcoma chromosome region, candidate 1 (human)	protein-coding
mm_50962.1	chr6	59208889	59208958	+	1	NA	promoter-TSS (NM_001081145)	promoter-TSS (NM_001081145)	53	NM_001081145	68140	Mm.25843	NM_001081145	ENSMUSG00000049232	Tigd2	3632410O17Rik	tigger transposable element derived 2	protein-coding
mm_128600.1	chr15	58191412	58191440	-	1	NA	exon (NM_026346, exon 6 of 9)	exon (NM_026346, exon 6 of 9)	23466	NM_026346	67731	Mm.25683	NM_026346	ENSMUSG00000022358	Fbxo32	4833442G10Rik|AI430017|ATROGIN1|Gm20361|MAFbx	F-box protein 32	protein-coding
mm_166967.1	chr7	44481668	44481672	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-2847	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_8798.1	chr1	161793249	161793252	-	1	NA	Intergenic	Intergenic	-4755	NM_010177	14103	Mm.3355	NM_010177	ENSMUSG00000000817	Fasl	APT1LG1|CD178|CD95-L|CD95L|Fas-L|Faslg|Tnfsf6|Tnlg1a|gld	Fas ligand (TNF superfamily, member 6)	protein-coding
mm_147549.1	chr18	54901120	54901122	-	1	NA	intron (NM_175751, intron 3 of 9)	intron (NM_175751, intron 3 of 9)	89059	NM_175751	269023	Mm.192984	NM_175751	ENSMUSG00000052713	Zfp608	4932417D18Rik|D430007A19Rik|Znf608	zinc finger protein 608	protein-coding
mm_41138.1	chr5	87825760	87825771	+	1	NA	promoter-TSS (NM_001163551)	promoter-TSS (NM_001163551)	68	NM_001163551	73779	Mm.263642	NM_028648	ENSMUSG00000002240	Prr27	4930432K09Rik	proline rich 27	protein-coding
mm_162092.1	chrX	37514424	37514424	+	1	NA	promoter-TSS (NM_001039695)	promoter-TSS (NM_001039695)	-111	NM_001039695	664610	Mm.381921	NM_001039695	ENSMUSG00000079633	Rhox4d	Rhox4.4|Rhox4c	reproductive homeobox 4D	protein-coding
mm_158065.1	chrX	101212892	101212912	-	1	NA	3' UTR (NM_001110310, exon 4 of 4)	3' UTR (NM_001110310, exon 4 of 4)	9661	NM_001110311	55988	Mm.206949	NM_018875	ENSMUSG00000046032	Snx12	2610001F05Rik|AW045757|SDP8	sorting nexin 12	protein-coding
mm_76885.1	chr8	105636155	105636177	-	1	NA	promoter-TSS (NM_181322)	promoter-TSS (NM_181322)	-372	NM_181322	13018	Mm.269474	NM_181322	ENSMUSG00000005698	Ctcf	AW108038	CCCTC-binding factor	protein-coding
mm_107444.1	chr12	36381549	36381594	+	1	NA	promoter-TSS (NM_001289503)	promoter-TSS (NM_001289503)	121	NM_178629	75847	Mm.261764	NM_178629	ENSMUSG00000043153	Ispd	4930579E17Rik|AV040780	isoprenoid synthase domain containing	protein-coding
mm_103554.1	chr11	77718890	77718906	-	1	NA	TTS (NM_001024205)	TTS (NM_001024205)	6395	NM_001313933	12957	Mm.22830	NM_009965	ENSMUSG00000000724	Cryba1	BA3/A1|Cryb	crystallin, beta A1	protein-coding
mm_6705.1	chr1	82281290	82281293	-	1	NA	intron (NM_010570, intron 1 of 1)	intron (NM_010570, intron 1 of 1)	10148	NM_010570	16367	Mm.4952	NM_010570	ENSMUSG00000055980	Irs1	G972R|IRS-1	insulin receptor substrate 1	protein-coding
mm_25829.1	chr3	128843779	128843781	+	1	NA	Intergenic	Intergenic	-356098	NM_001286942	18741	Mm.246804	NM_011098	ENSMUSG00000028023	Pitx2	9430085M16Rik|Brx1|Brx1b|Munc30|Otlx2|Ptx2|Rieg	paired-like homeodomain transcription factor 2	protein-coding
mm_39474.1	chr5	20085588	20085601	+	1	NA	intron (NM_001170746, intron 3 of 22)	AT_rich|Low_complexity|Low_complexity	178076	NM_015823	50791	Mm.332231	NM_015823	ENSMUSG00000040003	Magi2	AIP-1|Acvri1|Acvrinp1|Acvrip1|Magi-2|S-SCAM|mKIAA0705	membrane associated guanylate kinase, WW and PDZ domain containing 2	protein-coding
mm_69678.1	chr7	139985425	139985434	-	1	NA	exon (NM_001291066, exon 18 of 24)	exon (NM_001291066, exon 18 of 24)	1445	NR_106029	102465643		NR_106029	ENSMUSG00000099092	Mir7062	Gm27339|mmu-mir-7062	microRNA 7062	ncRNA
mm_141895.1	chr17	34862462	34862472	-	1	NA	promoter-TSS (NM_008198)	promoter-TSS (NM_008198)	47	NM_001142706	14962	Mm.653	NM_008198	ENSMUSG00000090231	Cfb	AI195813|AI255840|B|Bf|C2|Fb|H2-Bf	complement factor B	protein-coding
mm_50368.1	chr6	48676115	48676155	+	1	NA	promoter-TSS (NM_174960)	promoter-TSS (NM_174960)	0	NM_174960	317758	Mm.116971	NM_174960	ENSMUSG00000051124	Gimap9	A630002K24|BB145400	GTPase, IMAP family member 9	protein-coding
mm_53870.1	chr6	149361496	149361515	+	1	NA	Intergenic	Intergenic	-47479	NM_001112796	12121	Mm.177181	NM_009753	ENSMUSG00000003452	Bicd1	B830009D06Rik|bic-D 1	bicaudal D homolog 1 (Drosophila)	protein-coding
mm_49859.1	chr6	38534834	38534872	+	1	NA	promoter-TSS (NM_025363)	promoter-TSS (NM_025363)	-8	NM_025363	66117	Mm.158971	NM_025363	ENSMUSG00000019689	Fmc1	1110001J03Rik	formation of mitochondrial complex V assembly factor 1	protein-coding
mm_147759.1	chr18	61289714	61289715	-	1	NA	TTS (NM_146086)	TTS (NM_146086)	69215	NM_146086	225600	Mm.391106	NM_146086	ENSMUSG00000024575	Pde6a	Pdea|nmf282	phosphodiesterase 6A, cGMP-specific, rod, alpha	protein-coding
mm_134938.1	chr16	31167992	31167995	-	1	NA	intron (NM_030138, intron 1 of 22)	intron (NM_030138, intron 1 of 22)	33245	NM_030138	78618	Mm.274646	NM_030138	ENSMUSG00000049076	Acap2	4832442G16|9530039J15Rik|CNT-B2|Centb2|mKIAA0041	ArfGAP with coiled-coil, ankyrin repeat and PH domains 2	protein-coding
mm_119397.1	chr14	41151443	41151512	+	1	NA	promoter-TSS (NM_010775)	promoter-TSS (NM_010775)	21	NM_010775	17194	Mm.281805	NM_010775	ENSMUSG00000037780	Mbl1	MBL-A|MBP-A|S-MBP	mannose-binding lectin (protein A) 1	protein-coding
mm_112223.1	chr12	113429821	113429842	-	1	NA	Intergenic	Intergenic	-59734	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_132721.1	chr16	43573766	43573781	+	1	NA	intron (NM_001285805, intron 7 of 10)	intron (NM_001285805, intron 7 of 10)	-66882	NR_030576	100124467		NR_030576	ENSMUSG00000076372	Mir568	Mirn568|mmu-mir-568	microRNA 568	ncRNA
mm_153801.1	chr19	46039630	46039662	-	1	NA	promoter-TSS (NM_010697)	promoter-TSS (NM_010697)	-25	NM_010697	16825	Mm.327442	NM_010697	ENSMUSG00000025223	Ldb1	CLIM2|NLI	LIM domain binding 1	protein-coding
mm_14030.1	chr2	122152840	122152846	+	1	NA	3' UTR (NM_009735, exon 4 of 4)	3' UTR (NM_009735, exon 4 of 4)	5156	NM_009735	12010	Mm.163	NM_009735	ENSMUSG00000060802	B2m	Ly-m11|beta2-m|beta2m	beta-2 microglobulin	protein-coding
mm_170555.1	chr19	41525322	41525323	+	1	NA	promoter-TSS (NM_001326287)	promoter-TSS (NM_001326287)	70	NM_001326287	627352	Mm.395111	NM_001326287		Morf4l1b	EG627352|Gm6747	mortality factor 4 like 1B	protein-coding
mm_71849.1	chr8	68905972	68905978	+	1	NA	3' UTR (NM_008509, exon 10 of 10)	3' UTR (NM_008509, exon 10 of 10)	25420	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_63866.1	chr7	135684342	135684358	+	1	NA	3' UTR (NM_011212, exon 21 of 21)	3' UTR (NM_011212, exon 21 of 21)	32029	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_92504.1	chr10	78352470	78352515	-	1	NA	promoter-TSS (NM_053014)	promoter-TSS (NM_053014)	-792	NM_053014	28169	Mm.141230	NM_053014	ENSMUSG00000001211	Agpat3	AW061257|AW493985|D10Jhu12e|lpaat3	1-acylglycerol-3-phosphate O-acyltransferase 3	protein-coding
mm_9788.1	chr1	181257140	181257163	-	1	NA	Intergenic	Intergenic	-45173	NM_145514	226757	Mm.289082	NM_145514	ENSMUSG00000038733	Wdr26	1600024A01Rik|AA693241|AI447817|AU044014|C77982|Gid7	WD repeat domain 26	protein-coding
mm_107739.1	chr12	58002745	58002767	+	1	NA	Intergenic	Intergenic	-209048	NM_009216	20605	Mm.278336	NM_009216	ENSMUSG00000035431	Sstr1	SRIF-2|SS-1-R|SS1-R|SS1R|Smstr-1|Smstr1|sst1	somatostatin receptor 1	protein-coding
mm_159131.1	chr2	74763012	74763012	+	1	NA	promoter-TSS (NM_010467)	promoter-TSS (NM_010467)	32	NM_010467	15429	Mm.4932	NM_010467	ENSMUSG00000042448	Hoxd1	Hox-4.9	homeobox D1	protein-coding
mm_44351.1	chr5	17788296	17788331	-	1	NA	exon (NM_001159558, exon 13 of 16)	exon (NM_001159558, exon 13 of 16)	47583	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_163912.1	chr14	33510930	33510932	-	1	NA	Intergenic	Intergenic	-63773	NM_016700	26419	Mm.21495	NM_016700	ENSMUSG00000021936	Mapk8	AI849689|JNK|JNK1|Prkm8|SAPK1	mitogen-activated protein kinase 8	protein-coding
mm_39350.1	chr5	8957180	8957183	+	1	NA	intron (NM_008830, intron 26 of 27)	L1MD1|LINE|L1	39965	NM_023733	74114	Mm.28197	NM_023733	ENSMUSG00000003623	Crot	1200003H03Rik	carnitine O-octanoyltransferase	protein-coding
mm_142563.1	chr17	46645997	46646035	-	1	NA	promoter-TSS (NM_029091)	promoter-TSS (NM_029091)	-205	NM_001316742	27398	Mm.391007	NM_025302	ENSMUSG00000002767	Mrpl2	CGI-22|L2mt|MRP-L14|MRP-L2|Rpml14	mitochondrial ribosomal protein L2	protein-coding
mm_173343.1	chrY	90812962	90812962	+	1	NA	intron (NM_133362, intron 2 of 3)	(TTAGGG)n|Simple_repeat|Simple_repeat	26444	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_125993.1	chr15	76354498	76354503	+	1	NA	TTS (NM_026859)	TTS (NM_026859)	3206	NM_026859	68877	Mm.289680	NM_026859	ENSMUSG00000022553	Maf1	1110068E11Rik|AU042856	MAF1 homolog, negative regulator of RNA polymerase III	protein-coding
mm_118888.1	chr14	26590139	26590152	+	1	NA	intron (NM_001134465, intron 1 of 19)	PB1D7|SINE|Alu	10595	NM_145969	211922	Mm.260512	NM_145969	ENSMUSG00000040818	Dennd6a	Fam116a	DENN/MADD domain containing 6A	protein-coding
mm_44372.1	chr5	17814216	17814219	-	1	NA	exon (NM_001159558, exon 7 of 16)	exon (NM_001159558, exon 7 of 16)	21679	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_1630.1	chr1	74432345	74432373	+	1	NA	exon (NM_009509, exon 19 of 20)	exon (NM_009509, exon 19 of 20)	22975	NM_009509	22349	Mm.471601	NM_009509	ENSMUSG00000026175	Vil1	Vil	villin 1	protein-coding
mm_38732.1	chr4	145244051	145244056	-	1	NA	intron (NM_011610, intron 1 of 9)	ID_B1|SINE|B4	2817	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_51564.1	chr6	83575891	83575900	+	1	NA	intron (NR_078345, intron 2 of 7)	intron (NR_078345, intron 2 of 7)	-3391	NM_024239	70527	Mm.32801	NM_024239	ENSMUSG00000006906	Stambp	5330424L14Rik|5730422L11Rik|AW107289|Amsh|mKIAA4198	STAM binding protein	protein-coding
mm_40441.1	chr5	53591234	53591242	+	1	NA	intron (NM_001080927, intron 1 of 10)	intron (NM_001080927, intron 1 of 10)	752	NM_001080927	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_78217.1	chr9	21537226	21537233	+	1	NA	intron (NM_001198794, intron 3 of 6)	ID_B1|SINE|B4	-9665	NM_021531	59035	Mm.178115	NM_021531	ENSMUSG00000032185	Carm1	Prmt4	coactivator-associated arginine methyltransferase 1	protein-coding
mm_66092.1	chr7	30973441	30973453	-	1	NA	promoter-TSS (NM_017405)	promoter-TSS (NM_017405)	22	NM_001164185	54135	Mm.4067	NM_017405	ENSMUSG00000001247	Lsr	ILDR3|Lisch7	lipolysis stimulated lipoprotein receptor	protein-coding
mm_75220.1	chr8	39605946	39605958	-	1	NA	3' UTR (NM_031195, exon 9 of 9)	3' UTR (NM_031195, exon 9 of 9)	36726	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_30564.1	chr4	3790258	3790279	+	1	NA	3' UTR (NM_001111096, exon 13 of 13)	3' UTR (NM_001111096, exon 13 of 13)	45387	NM_026147	67427	Mm.21938	NM_026147	ENSMUSG00000028234	Rps20	4632426K06Rik|Dsk4	ribosomal protein S20	protein-coding
mm_119231.1	chr14	33317135	33317157	+	1	NA	intron (NM_153800, intron 4 of 10)	intron (NM_153800, intron 4 of 10)	93878	NM_001310452	26419	Mm.21495	NM_016700	ENSMUSG00000021936	Mapk8	AI849689|JNK|JNK1|Prkm8|SAPK1	mitogen-activated protein kinase 8	protein-coding
mm_150737.1	chr19	43753075	43753110	+	1	NA	promoter-TSS (NM_001113562)	promoter-TSS (NM_001113562)	69	NM_025530	66388	Mm.20257	NM_025530	ENSMUSG00000025193	Cutc	2310039I18Rik|AI326282|CGI-32	cutC copper transporter	protein-coding
mm_75197.1	chr8	39006249	39006263	-	1	NA	intron (NM_030254, intron 1 of 7)	CpG	389	NM_030254	80286	Mm.272722	NM_030254	ENSMUSG00000039530	Tusc3	AU022242|BC003311|N33	tumor suppressor candidate 3	protein-coding
mm_119462.1	chr14	47087526	47087530	+	1	NA	intron (NM_001037221, intron 9 of 12)	MIRb|SINE|MIR	18551	NM_001310544	74480	Mm.214454	NM_028966	ENSMUSG00000021838	Samd4	1700024G08Rik|1700111L17Rik|4933436G17Rik|Samd4a|Smaug|Smaug1|sunk	sterile alpha motif domain containing 4	protein-coding
mm_61041.1	chr7	49759513	49759529	+	1	NA	promoter-TSS (NM_001146052)	promoter-TSS (NM_001146052)	9	NM_001146052	53415	Mm.20801	NM_016865	ENSMUSG00000039745	Htatip2	AW111545|Cc3|Tip30	HIV-1 Tat interactive protein 2	protein-coding
mm_75761.1	chr8	69936498	69936510	-	1	NA	intron (NM_145596, intron 2 of 12)	intron (NM_145596, intron 2 of 12)	-33946	NM_023312	67184	Mm.21162	NM_023312	ENSMUSG00000036199	Ndufa13	2700054G14Rik|AU022060|CDA016|CGI-39|GRIM-19|Grim19	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 13	protein-coding
mm_161347.1	chr14	52495669	52495669	-	1	NA	promoter-TSS (NM_001170918)	promoter-TSS (NM_001170918)	26	NM_001170918	57269	Mm.88822	NM_020512	ENSMUSG00000059887	Olfr1507	MOR244-1|Mor28|Or28	olfactory receptor 1507	protein-coding
mm_7180.1	chr1	92641943	92641976	-	1	NA	promoter-TSS (NR_028108)	promoter-TSS (NR_028108)	-11	NR_028108	66915	Mm.30179	NM_001163425	ENSMUSG00000073616	Myeov2	1110002M09Rik|Cops9	myeloma overexpressed 2	protein-coding
mm_170315.1	chr18	36920303	36920322	+	1	NA	promoter-TSS (NR_076393)	promoter-TSS (NR_076393)	7	NR_076393	627427		NR_076393	ENSMUSG00000063514	Gm6756	EG627427	3-phosphoglycerate dehydrogenase pseudogene	pseudo
mm_22215.1	chr2	174295402	174295442	-	1	NA	promoter-TSS (NR_002846)	promoter-TSS (NR_002846)	14	NR_002846	56802	Mm.125770	NR_002846	ENSMUSG00000086537	Nespas	Gnas-as|Nespos	neuroendocrine secretory protein antisense	ncRNA
mm_131153.1	chr16	6840421	6840440	+	1	NA	intron (NM_021477, intron 5 of 16)	intron (NM_021477, intron 5 of 16)	-229405	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_7240.1	chr1	93621997	93622000	-	1	NA	TTS (NM_145519)	TTS (NM_145519)	13729	NM_021537	59041	Mm.28761	NM_021537	ENSMUSG00000026277	Stk25	1500019J11Rik|AU018434|C86992|Ste20-like|Ysk1	serine/threonine kinase 25 (yeast)	protein-coding
mm_9324.1	chr1	171841187	171841212	-	1	NA	intron (NM_001289470, intron 2 of 8)	intron (NM_001289470, intron 2 of 8)	1502	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_159701.1	chr5	27261896	27261896	+	1	NA	promoter-TSS (NM_001136060)	promoter-TSS (NM_001136060)	-39	NM_001136060	13483	Mm.42078	NM_010075	ENSMUSG00000061576	Dpp6	B930011P16Rik|D5Buc3|D5Buc4|D5Buc5|DPP VI|Dpp-6|Gm1377|In(5)6H-p|Peplb|Rw	dipeptidylpeptidase 6	protein-coding
mm_128835.1	chr15	68340476	68340488	-	1	NA	TTS (NR_029718)	TTS (NR_029718)	807	NR_029718	387228		NR_029718	ENSMUSG00000065437	Mir30d	Mirn30d|mir-30d|mmu-mir-30d	microRNA 30d	ncRNA
mm_137005.1	chr17	17624740	17624754	+	1	NA	promoter-TSS (NM_172827)	promoter-TSS (NM_172827)	-258	NM_172827	240028	Mm.328807	NM_172827	ENSMUSG00000023845	Lnpep	2010309L07Rik|4732490P18Rik|CAP|IRAP|PLAP|gp160|vp165	leucyl/cystinyl aminopeptidase	protein-coding
mm_138877.1	chr17	43360021	43360030	+	1	NA	Intergenic	Intergenic	-29441	NM_001081178	224792	Mm.23478	NM_001081178	ENSMUSG00000056492	Adgrf5	8430401C09Rik|9330185D23|AI528491|Gpr116|mKIAA0758	adhesion G protein-coupled receptor F5	protein-coding
mm_713.1	chr1	42261924	42261969	+	1	NA	Intergenic	Intergenic	432879	NR_027826	66297	Mm.45203	NM_183252	ENSMUSG00000060424	Pantr1	2610017I09Rik|Pou3f3os|linc-Brn1a	POU domain, class 3, transcription factor 3 adjacent noncoding transcript 1	ncRNA
mm_24805.1	chr3	95556195	95556247	+	1	NA	3' UTR (NM_021281, exon 8 of 8)	3' UTR (NM_021281, exon 8 of 8)	-3456	NM_026489	67981	Mm.179050	NM_026489	ENSMUSG00000028109	Hormad1	4921522K05Rik|Nohma	HORMA domain containing 1	protein-coding
mm_29514.1	chr3	116423931	116423993	-	1	NA	promoter-TSS (NM_001173553)	promoter-TSS (NM_001173553)	70	NM_001080818	229776	Mm.17647	NM_001080818	ENSMUSG00000033502	Cdc14a	A830059A17Rik|CDC14A2|CDC14a1|Cdc14	CDC14 cell division cycle 14A	protein-coding
mm_959.1	chr1	57901944	57901977	+	1	NA	intron (NM_001164566, intron 6 of 11)	intron (NM_001164566, intron 6 of 11)	56389	NM_001164566	67198	Mm.159989	NM_144882	ENSMUSG00000038305	Spats2l	2810022L02Rik|A230104H11Rik|AA987173|AI480531|AI842453|AW413586	spermatogenesis associated, serine-rich 2-like	protein-coding
mm_7397.1	chr1	118311164	118311221	-	1	NA	promoter-TSS (NM_011650)	promoter-TSS (NM_011650)	-60	NM_011650	22099	Mm.426637	NM_011650	ENSMUSG00000026374	Tsn	2610034C24Rik|AU040286|C3PO|TB-RBP	translin	protein-coding
mm_140101.1	chr17	78491550	78491552	+	1	NA	Intergenic	Intergenic	-16512	NM_001197028	74199	Mm.292983	NM_028813	ENSMUSG00000024076	Vit	1700052E02Rik|1700110E08Rik|2810429K11Rik	vitrin	protein-coding
mm_21742.1	chr2	164779722	164779740	-	1	NA	promoter-TSS (NM_009394)	promoter-TSS (NM_009394)	3	NM_009394	21925	Mm.1716	NM_009394	ENSMUSG00000017300	Tnnc2	Tncs	troponin C2, fast	protein-coding
mm_68786.1	chr7	123300516	123300523	-	1	NA	exon (NM_001122643, exon 14 of 20)	exon (NM_001122643, exon 14 of 20)	69396	NM_001122643	70497	Mm.403318	NM_144529	ENSMUSG00000030766	Arhgap17	5730403H17Rik|Nadrin|Nadrin2|Rich1|Wbp15	Rho GTPase activating protein 17	protein-coding
mm_98026.1	chr11	85178035	85178041	+	1	NA	intron (NM_028589, intron 4 of 5)	intron (NM_028589, intron 4 of 5)	6942	NM_028589	73634	Mm.48850	NM_028589	ENSMUSG00000018479	1700125H20Rik	-	RIKEN cDNA 1700125H20 gene	protein-coding
mm_35868.1	chr4	49506539	49506563	-	1	NA	promoter-TSS (NM_007519)	promoter-TSS (NM_007519)	7	NM_007519	12012	Mm.2859	NM_007519	ENSMUSG00000039653	Baat	AI118337|AI158864|BAT	bile acid-Coenzyme A: amino acid N-acyltransferase	protein-coding
mm_62292.1	chr7	99915790	99915792	+	1	NA	intron (NM_001164258, intron 15 of 18)	intron (NM_001164258, intron 15 of 18)	56573	NM_001164258	446101	Mm.440757	NM_001164258	ENSMUSG00000035211	Xrra1	AI449753	X-ray radiation resistance associated 1	protein-coding
mm_86632.1	chr10	14017947	14017969	+	1	NA	intron (NM_010437, intron 1 of 8)	intron (NM_010437, intron 1 of 8)	51579	NM_010437	15273	Mm.42157	NM_010437	ENSMUSG00000015501	Hivep2	Gm20114|MIBP1|Schnurri-2|Shn-2	human immunodeficiency virus type I enhancer binding protein 2	protein-coding
mm_117064.1	chr13	58762275	58762292	-	1	NA	promoter-TSS (NR_045469)	promoter-TSS (NR_045469)	28	NR_045469	67585	Mm.84751	NR_045469		4930455J16Rik	-	RIKEN cDNA 4930455J16 gene	ncRNA
mm_22281.1	chr2	180042372	180042398	-	1	NA	promoter-TSS (NM_178750)	promoter-TSS (NM_178750)	79	NM_001289476	26444	Mm.21728	NM_011969	ENSMUSG00000027566	Psma7	C6-I	proteasome (prosome, macropain) subunit, alpha type 7	protein-coding
mm_55370.1	chr6	57824634	57824663	-	1	NA	intron (NM_146168, intron 1 of 4)	CpG	477	NM_146168	232023	Mm.24642	NM_146168	ENSMUSG00000037788	Vopp1	AW146242|Ecop	vesicular, overexpressed in cancer, prosurvival protein 1	protein-coding
mm_75328.1	chr8	43143047	43143062	-	1	NA	Intergenic	Intergenic	-1568	NM_177742	244448	Mm.64542	NM_177742	ENSMUSG00000031651	Triml1	4933403D14|BC050188	tripartite motif family-like 1	protein-coding
mm_109853.1	chr12	4738376	4738388	-	1	NA	promoter-TSS (NM_029107)	promoter-TSS (NM_029107)	1	NM_029107	74855	Mm.269534	NM_029107	ENSMUSG00000079177	Fam228a	4930417G10Rik	family with sequence similarity 228, member A	protein-coding
mm_107417.1	chr12	34984777	34984814	+	1	NA	promoter-TSS (NM_029294)	promoter-TSS (NM_029294)	34	NM_029294	75456	Mm.79179	NM_029294	ENSMUSG00000092305	Prps1l1	1700011K15Rik	phosphoribosyl pyrophosphate synthetase 1-like 1	protein-coding
mm_107375.1	chr12	32953875	32953891	+	1	NA	promoter-TSS (NM_198710)	promoter-TSS (NM_198710)	-62	NM_013635	19027	Mm.246304	NM_013635	ENSMUSG00000020570	Sypl	AI314763|AI604763|D12Ertd446e|PanI|Pphn|Sypl1	synaptophysin-like protein	protein-coding
mm_10021.1	chr1	192074524	192074529	-	1	NA	intron (NM_011633, intron 1 of 9)	intron (NM_011633, intron 1 of 9)	18073	NM_011633	22033	Mm.380491	NM_011633		Traf5	-	TNF receptor-associated factor 5	protein-coding
mm_98000.1	chr11	84173451	84173460	+	1	NA	Intergenic	Intergenic	-5979	NM_001037932	628813	Mm.390389	NM_001037932	ENSMUSG00000051452	Gm11437	AI463690|OTTMUSG00000000997	predicted gene 11437	protein-coding
mm_173145.1	chrX	21922632	21922636	+	1	NA	Intergenic	RLTR13G|LTR|ERVK	207734	NM_020049	56774	Mm.253984	NM_020049	ENSMUSG00000031089	Slc6a14	1110007A17Rik|9030613J17Rik|ATB0plus|CATB0plus	solute carrier family 6 (neurotransmitter transporter), member 14	protein-coding
mm_118538.1	chr14	16365172	16365194	+	1	NA	promoter-TSS (NM_009409)	promoter-TSS (NM_009409)	-23	NM_009409	21974	Mm.130362	NM_009409	ENSMUSG00000017485	Top2b	D230016L12Rik|Top-2	topoisomerase (DNA) II beta	protein-coding
mm_8016.1	chr1	134955843	134955843	-	1	NA	promoter-TSS (NM_001081307)	promoter-TSS (NM_001081307)	97	NM_001081307	329251	Mm.188709	NM_001081307	ENSMUSG00000073557	Ppp1r12b	1810037O03Rik|9530009M10Rik|AI132431|Mypt2	protein phosphatase 1, regulatory (inhibitor) subunit 12B	protein-coding
mm_102738.1	chr11	67251737	67251758	-	1	NA	exon (NM_010855, exon 23 of 40)	exon (NM_010855, exon 23 of 40)	13935	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_73566.1	chr8	109608729	109608769	+	1	NA	promoter-TSS (NM_020046)	promoter-TSS (NM_020046)	-76	NM_020046	56749	Mm.23894	NM_020046	ENSMUSG00000031730	Dhodh	2810417D19Rik|AI834883	dihydroorotate dehydrogenase	protein-coding
mm_122699.1	chr14	52103992	52104011	-	1	NA	promoter-TSS (NM_001170982)	promoter-TSS (NM_001170982)	27	NM_001170982	15381	Mm.427321	NM_016884	ENSMUSG00000060373	Hnrnpc	AL022939|D14Wsu171e|Hnrpc|Hnrpc1|Hnrpc2|hnRNPC1|hnRNPC2|hnrnp-C	heterogeneous nuclear ribonucleoprotein C	protein-coding
mm_72564.1	chr8	84125981	84125999	+	1	NA	promoter-TSS (NM_001013384)	promoter-TSS (NM_001013384)	1	NM_001013384	244550	Mm.334654	NM_001013384	ENSMUSG00000012889	Podnl1	5832418A03Rik|Gm506	podocan-like 1	protein-coding
mm_93761.1	chr10	120193421	120193436	-	1	NA	intron (NM_028679, intron 1 of 11)	L2|LINE|L2	8109	NM_028679	73914	Mm.146194	NM_028679	ENSMUSG00000020227	Irak3	4833428C18Rik|AI563835|IRAK-M	interleukin-1 receptor-associated kinase 3	protein-coding
mm_90372.1	chr10	127181809	127181837	+	1	NA	TTS (NM_028027)	TTS (NM_028027)	-1178	NM_177615	216441	Mm.248373	NM_177615	ENSMUSG00000040441	Slc26a10	C78409|D630010I07	solute carrier family 26, member 10	protein-coding
mm_138179.1	chr17	34267366	34267383	+	1	NA	exon (NM_207105, exon 3 of 6)	exon (NM_207105, exon 3 of 6)	4147	NM_207105	14961	Mm.254067	NM_207105	ENSMUSG00000073421	H2-Ab1	AI845868|Abeta|H-2Ab|H2-Ab|I-Abeta|IAb|Ia-2|Ia2|Rmcs1	histocompatibility 2, class II antigen A, beta 1	protein-coding
mm_110326.1	chr12	34906910	34906955	-	1	NA	intron (NM_001271386, intron 2 of 27)	CpG	10163	NM_001271386	79221	Mm.310551	NM_024124	ENSMUSG00000004698	Hdac9	AV022454|D030072B18Rik|HD7B|HD9|HDRP|Hdac7b|Mitr|mKIAA0744	histone deacetylase 9	protein-coding
mm_113008.1	chr13	21897187	21897198	+	1	NA	promoter-TSS (NR_035500)	promoter-TSS (NR_035500)	-143	NR_035500	100316716		NR_035500	ENSMUSG00000088148	Mir1983	mmu-mir-1983	microRNA 1983	ncRNA
mm_100826.1	chr11	5381735	5381745	-	1	NA	promoter-TSS (NM_001290501)	promoter-TSS (NM_001290501)	0	NM_001290501	407821	Mm.216313	NM_001080924	ENSMUSG00000041961	Znrf3	Gm1167	zinc and ring finger 3	protein-coding
mm_164888.1	chr18	61315946	61315947	-	1	NA	exon (NM_133249, exon 3 of 12)	exon (NM_133249, exon 3 of 12)	84485	NM_133249	170826	Mm.415302	NM_133249	ENSMUSG00000033871	Ppargc1b	4631412G21Rik|Perc	peroxisome proliferative activated receptor, gamma, coactivator 1 beta	protein-coding
mm_164178.1	chr15	76234945	76234981	-	1	NA	intron (NM_001163576, intron 8 of 9)	intron (NM_001163576, intron 8 of 9)	-3585	NM_011117	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
mm_12554.1	chr2	72443090	72443103	+	1	NA	TTS (NM_023057)	TTS (NM_023057)	-33123	NM_025866	66953	Mm.270676	NM_025866	ENSMUSG00000055612	Cdca7	2310021G01Rik|AU044109|JPO1	cell division cycle associated 7	protein-coding
mm_163622.1	chr13	55449962	55449969	+	1	NA	intron (NM_001038018, intron 2 of 15)	intron (NM_001038018, intron 2 of 15)	-3141	NR_105908	102466770		NR_105908	ENSMUSG00000099058	Mir6943	Gm27791|mmu-mir-6943	microRNA 6943	ncRNA
mm_106125.1	chr11	116413016	116413069	-	1	NA	promoter-TSS (NM_027258)	promoter-TSS (NM_027258)	-10	NM_027258	217340	Mm.426344	NM_027258	ENSMUSG00000052949	Rnf157	2610036E23Rik|A130073L17Rik|mKIAA1917	ring finger protein 157	protein-coding
mm_88242.1	chr10	72634326	72634334	+	1	NA	Intergenic	Intergenic	-20516	NM_025635	52696	Mm.62876	NM_025635	ENSMUSG00000019923	Zwint	2010007E07Rik|2600001N01Rik|D10Ertd749e|Zwint-1	ZW10 interactor	protein-coding
mm_55652.1	chr6	72371248	72371294	-	1	NA	intron (NM_016872, intron 1 of 2)	intron (NM_016872, intron 1 of 2)	-4299	NM_001331167	66510	Mm.170023	NM_025607	ENSMUSG00000055850	Rnf181	1700047F16Rik|2500002L14Rik|6230415N01Rik|C77350	ring finger protein 181	protein-coding
mm_41300.1	chr5	90465177	90465188	+	1	NA	intron (NM_009654, intron 5 of 14)	intron (NM_009654, intron 5 of 14)	4312	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_103262.1	chr11	71033463	71033480	-	1	NA	5' UTR (NM_134022, exon 1 of 2)	5' UTR (NM_134022, exon 1 of 2)	146	NM_134022	103712	Mm.27768	NM_134022		6330403K07Rik	AI415455|AV161034|UGS148	RIKEN cDNA 6330403K07 gene	protein-coding
mm_150731.1	chr19	43731172	43731175	+	1	NA	3' UTR (NM_053103, exon 13 of 13)	3' UTR (NM_053103, exon 13 of 13)	21827	NM_144874	226139	Mm.248237	NM_144874	ENSMUSG00000040018	Cox15	2900026G05Rik	cytochrome c oxidase assembly protein 15	protein-coding
mm_50747.1	chr6	52776134	52776145	+	1	NA	intron (NM_173406, intron 4 of 4)	intron (NM_173406, intron 4 of 4)	62410	NM_025816	52440	Mm.389757	NM_025816	ENSMUSG00000004535	Tax1bp1	1200003J11Rik|1700069J21Rik|AA930106|D6Ertd404e|D6Ertd772e|T6bp|TXBP151	Tax1 (human T cell leukemia virus type I) binding protein 1	protein-coding
mm_167556.1	chr9	35908363	35908366	+	1	NA	Intergenic	Intergenic	-58484	NR_030730	100041605	Mm.99350	NR_030730	ENSMUSG00000098705	Gm3428	-	predicted gene 3428	ncRNA
mm_69307.1	chr7	128410402	128410413	-	1	NA	intron (NM_026418, intron 1 of 4)	intron (NM_026418, intron 1 of 4)	7765	NM_026418	67865	Mm.18635	NM_026418	ENSMUSG00000030844	Rgs10	2310010N19Rik	regulator of G-protein signalling 10	protein-coding
mm_167798.1	chr9	123927481	123927514	+	1	NA	Intergenic	Intergenic	41195	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_60019.1	chr7	30776395	30776410	+	1	NA	promoter-TSS (NM_028618)	promoter-TSS (NM_028618)	-3	NM_028618	73712	Mm.30138	NM_028618	ENSMUSG00000060962	Dmkn	1110014F24Rik|AW561900|C130074A08|SK30|SK89|cI-36	dermokine	protein-coding
mm_126862.1	chr15	89334454	89334472	+	1	NA	promoter-TSS (NM_019977)	promoter-TSS (NM_019977)	-10	NM_019977	56727	Mm.158200	NM_019977	ENSMUSG00000022613	Miox	0610009I10Rik|AI314022|Aldrl6|C85427|RSOR	myo-inositol oxygenase	protein-coding
mm_164029.1	chr14	76693980	76693991	-	1	NA	Intergenic	Intergenic	16417	NR_015485	73272	Mm.116804	NR_015485	ENSMUSG00000101009	1700108F19Rik	1700020I02Rik|BB065030	RIKEN cDNA 1700108F19 gene	ncRNA
mm_49566.1	chr6	30639435	30639452	+	1	NA	5' UTR (NM_025350, exon 1 of 10)	5' UTR (NM_025350, exon 1 of 10)	225	NM_025350	109697	Mm.25377	NM_025350	ENSMUSG00000054446	Cpa1	0910001L12Rik|Cpa	carboxypeptidase A1, pancreatic	protein-coding
mm_127836.1	chr15	6837598	6837600	-	1	NA	intron (NM_001310469, intron 8 of 17)	intron (NM_001310469, intron 8 of 17)	36714	NM_011019	18414	Mm.10760	NM_011019	ENSMUSG00000022146	Osmr	OSMRB	oncostatin M receptor	protein-coding
mm_109063.1	chr12	104344133	104344144	+	1	NA	exon (NM_011458, exon 4 of 5)	exon (NM_011458, exon 4 of 5)	5652	NM_011458	20714	Mm.291569	NM_011458	ENSMUSG00000058207	Serpina3k	1300001I07Rik|D12Rp54|MMCM2|MMSpi2|RP54|Spi-2|Spi2|contrapsin	serine (or cysteine) peptidase inhibitor, clade A, member 3K	protein-coding
mm_19806.1	chr2	110305771	110305781	-	1	NA	promoter-TSS (NM_130452)	promoter-TSS (NM_130452)	-51	NM_130452	170442	Mm.27335	NM_130452	ENSMUSG00000041660	Bbox1	AI874739	butyrobetaine (gamma), 2-oxoglutarate dioxygenase 1 (gamma-butyrobetaine hydroxylase)	protein-coding
mm_33744.1	chr4	134160351	134160376	+	1	NA	intron (NM_144527, intron 3 of 13)	RLTR4_MM-int|LTR|ERV1	26722	NM_144527	70012	Mm.26542	NM_144527	ENSMUSG00000037443	Cep85	2410030J07Rik|AI173272|AI173504|Ccdc21	centrosomal protein 85	protein-coding
mm_58558.1	chr7	4741353	4741370	+	1	NA	intron (NM_146177, intron 1 of 8)	intron (NM_146177, intron 1 of 8)	1234	NM_001115018	232811	Mm.247844	NM_146177	ENSMUSG00000059851	Kmt5c	BC024816|Suv4-20h2|Suv420h2	lysine methyltransferase 5C	protein-coding
mm_87219.1	chr10	40284020	40284024	+	1	NA	Intergenic	RMER19B|LTR|ERVK	18164	NM_007444	100041585	Mm.476925	NM_007444	ENSMUSG00000063953	Amd2	AdoMetDC|Amd1|Amd3|ENSMUSG00000063953	S-adenosylmethionine decarboxylase 2	protein-coding
mm_126628.1	chr15	83394117	83394123	+	1	NA	intron (NM_011862, intron 2 of 10)	intron (NM_011862, intron 2 of 10)	-26823	NR_027980	69291	Mm.66794	NM_001033147		1700001L05Rik	-	RIKEN cDNA 1700001L05 gene	ncRNA
mm_17504.1	chr2	28915861	28915893	-	1	NA	5' UTR (NM_019446, exon 1 of 3)	5' UTR (NM_019446, exon 1 of 3)	544	NM_019446	54422	Mm.21390	NM_019446	ENSMUSG00000026805	Barhl1	Dres115|MBH2	BarH-like 1 (Drosophila)	protein-coding
mm_52498.1	chr6	115134991	115134993	+	1	NA	promoter-TSS (NM_013681)	promoter-TSS (NM_013681)	90	NM_001111015	20965	Mm.441431	NM_013681	ENSMUSG00000009394	Syn2	2900074L19Rik|AI836018|AI841723	synapsin II	protein-coding
mm_85143.1	chr9	95815390	95815398	-	1	NA	intron (NM_001033210, intron 1 of 15)	intron (NM_001033210, intron 1 of 15)	29885	NM_001033210	102502	Mm.11869	NM_001033210	ENSMUSG00000049493	Pls1	AI427122	plastin 1 (I-isoform)	protein-coding
mm_163087.1	chr11	69734610	69734654	-	1	NA	exon (NM_001291068, exon 29 of 29)	exon (NM_001291068, exon 29 of 29)	24001	NM_001291068	20020	Mm.16533	NM_009089	ENSMUSG00000005198	Polr2a	220kDa|Rpb1|Rpo2-1	polymerase (RNA) II (DNA directed) polypeptide A	protein-coding
mm_110889.1	chr12	75549669	75549695	-	1	NA	intron (NM_012024, intron 2 of 13)	intron (NM_012024, intron 2 of 13)	46518	NM_012024	26932	Mm.259626	NM_012024	ENSMUSG00000021051	Ppp2r5e	4633401M22Rik|AI449017|B56beta	protein phosphatase 2, regulatory subunit B', epsilon	protein-coding
mm_152274.1	chr19	8819315	8819350	-	1	NA	promoter-TSS (NM_001081196)	promoter-TSS (NM_001081196)	-38	NM_027412	70387	Mm.261082	NM_027412	ENSMUSG00000071660	Ttc9c	2210019E14Rik|6330408J23Rik	tetratricopeptide repeat domain 9C	protein-coding
mm_129026.1	chr15	74958765	74958792	-	1	NA	3' UTR (NM_001164036, exon 4 of 4)	3' UTR (NM_001164036, exon 4 of 4)	3672	NM_001164040	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_157808.1	chrX	73930835	73930851	-	1	NA	promoter-TSS (NM_001164704)	promoter-TSS (NM_001164704)	7	NM_023132	19703	Mm.236969	NM_023132	ENSMUSG00000031387	Renbp	Age|Rnbp	renin binding protein	protein-coding
mm_68171.1	chr7	103826557	103826567	-	1	NA	TTS (NM_001278161)	TTS (NM_001278161)	1366	NM_001201391	100503605	Mm.288567	NM_001201391	ENSMUSG00000052305	Hbb-bs	Beta-s|Hbbt1|Hbbt2	hemoglobin, beta adult s chain	protein-coding
mm_146142.1	chr18	74765076	74765076	+	1	NA	intron (NM_201600, intron 38 of 38)	intron (NM_201600, intron 38 of 38)	13379	NR_028560	100217466		NR_028560		Scarna17	MBII-119	small Cajal body-specific RNA 17	ncRNA
mm_145428.1	chr18	58677922	58677939	+	1	NA	3' UTR (NM_025478, exon 5 of 5)	3' UTR (NM_025478, exon 5 of 5)	18448	NM_025478	66307	Mm.182574	NM_025478	ENSMUSG00000024601	Isoc1	2610034N03Rik	isochorismatase domain containing 1	protein-coding
mm_7381.1	chr1	107350026	107350039	-	1	NA	Intergenic	Intergenic	-12282	NM_025867	66957	Mm.12638	NM_025867	ENSMUSG00000026327	Serpinb11	2310046M08Rik|AU015399	serine (or cysteine) peptidase inhibitor, clade B (ovalbumin), member 11	protein-coding
mm_75750.1	chr8	69901633	69901657	-	1	NA	promoter-TSS (NM_032004)	promoter-TSS (NM_032004)	-539	NM_032004	83984	Mm.432504	NM_032004	ENSMUSG00000047654	Tssk6	Sstk|TSK-6|TSSK-6	testis-specific serine kinase 6	protein-coding
mm_103533.1	chr11	77386302	77386315	-	1	NA	intron (NM_001291190, intron 1 of 13)	intron (NM_001291190, intron 1 of 13)	38028	NM_001291190	237860	Mm.440381	NM_177710	ENSMUSG00000037926	Ssh2	SSH-2|SSH-2L|mSSH-2L	slingshot homolog 2 (Drosophila)	protein-coding
mm_60288.1	chr7	43987748	43987756	+	1	NA	Intergenic	Intergenic	-8125	NM_010640	16613	Mm.443378	NM_010640	ENSMUSG00000044485	Klk1b11	Klk11|mGK-11	kallikrein 1-related peptidase b11	protein-coding
mm_6590.1	chr1	75264240	75264240	-	1	NA	promoter-TSS (NM_008985)	promoter-TSS (NM_008985)	-32	NM_008985	19275	Mm.2902	NM_008985	ENSMUSG00000026204	Ptprn	IA-2|mIA-A|mKIAA4064	protein tyrosine phosphatase, receptor type, N	protein-coding
mm_150419.1	chr19	37263988	37264007	+	1	NA	promoter-TSS (NR_040299)	promoter-TSS (NR_040299)	98	NR_040299	77059	Mm.251476	NR_040298		4931408D14Rik	-	RIKEN cDNA 4931408D14 gene	ncRNA
mm_27493.1	chr3	54811403	54811404	-	1	NA	Intergenic	CpG	-3612	NM_133231	170767	Mm.185735	NM_133231	ENSMUSG00000036615	Rfxap	5730495K23Rik	regulatory factor X-associated protein	protein-coding
mm_33069.1	chr4	123624766	123624805	+	1	NA	intron (NM_001199136, intron 1 of 97)	intron (NM_001199136, intron 1 of 97)	8365	NR_105824	102465214		NR_105824	ENSMUSG00000099005	Mir6398	Gm27657|mmu-mir-6398	microRNA 6398	ncRNA
mm_94859.1	chr11	24077566	24077612	+	1	NA	promoter-TSS (NM_001242934)	promoter-TSS (NM_001242934)	-467	NM_016707	14025	Mm.53687	NM_016707	ENSMUSG00000000861	Bcl11a	2810047E18Rik|BCL-11A|Ctip1|D930021L15Rik|Evi9|Evi9a|Evi9b|Evi9c|mKIAA1809	B cell CLL/lymphoma 11A (zinc finger protein)	protein-coding
mm_18495.1	chr2	62606351	62606371	-	1	NA	exon (NM_027835, exon 10 of 16)	exon (NM_027835, exon 10 of 16)	-32340	NM_007986	14089	Mm.41816	NM_007986	ENSMUSG00000000392	Fap	SIMP	fibroblast activation protein	protein-coding
mm_77709.1	chr8	126591915	126591926	-	1	NA	intron (NM_001164598, intron 1 of 1)	intron (NM_001164598, intron 1 of 1)	1516	NM_001164598	270110	Mm.334918	NM_001164598	ENSMUSG00000051495	Irf2bp2	E130305N23Rik|IRF-2BP2	interferon regulatory factor 2 binding protein 2	protein-coding
mm_73879.1	chr8	119344491	119344536	+	1	NA	promoter-TSS (NM_024219)	promoter-TSS (NM_024219)	-25	NM_024219	68196	Mm.358714	NM_024219	ENSMUSG00000031839	Hsbp1	0610007A03Rik|AA408769|Hsp25	heat shock factor binding protein 1	protein-coding
mm_142796.1	chr17	50190414	50190489	-	1	NA	promoter-TSS (NM_181397)	promoter-TSS (NM_181397)	46	NM_181397	76438	Mm.41854	NM_181397	ENSMUSG00000039316	Rftn1	2310015N21Rik|AI853526	raftlin lipid raft linker 1	protein-coding
mm_108101.1	chr12	74804382	74804415	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	372934	NM_172805	238271	Mm.44465	NM_172805	ENSMUSG00000034402	Kcnh5	Eag2	potassium voltage-gated channel, subfamily H (eag-related), member 5	protein-coding
mm_158793.1	chrX	167229153	167229174	-	1	NA	Intergenic	Intergenic	-19945	NM_021278	19241	Mm.142729	NM_021278	ENSMUSG00000049775	Tmsb4x	Ptmb4|Tb4	thymosin, beta 4, X chromosome	protein-coding
mm_139257.1	chr17	47737175	47737207	+	1	NA	promoter-TSS (NM_001161723)	promoter-TSS (NM_001161723)	154	NM_001161722	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_66093.1	chr7	30973469	30973480	-	1	NA	promoter-TSS (NM_017405)	promoter-TSS (NM_017405)	-5	NM_001164184	54135	Mm.4067	NM_017405	ENSMUSG00000001247	Lsr	ILDR3|Lisch7	lipolysis stimulated lipoprotein receptor	protein-coding
mm_105533.1	chr11	106301178	106301193	-	1	NA	exon (NM_008117, exon 3 of 5)	exon (NM_008117, exon 3 of 5)	711	NM_008117	14599	Mm.343934	NM_008117	ENSMUSG00000020713	Gh	Gh1|Ghb1	growth hormone	protein-coding
mm_44775.1	chr5	32031064	32031074	-	1	NA	intron (NM_144541, intron 10 of 11)	intron (NM_144541, intron 10 of 11)	-105403	NM_008037	14284	Mm.24684	NM_008037	ENSMUSG00000029135	Fosl2	Fra-2	fos-like antigen 2	protein-coding
mm_40350.1	chr5	45670234	45670244	+	1	NA	promoter-TSS (NR_073433)	promoter-TSS (NR_073433)	314	NM_019438	54392	Mm.32012	NM_019438	ENSMUSG00000015880	Ncapg	5730507H05Rik|Hcapg|MFT.M05.13	non-SMC condensin I complex, subunit G	protein-coding
mm_26319.1	chr3	142521637	142521647	+	1	NA	3' UTR (NM_153564, exon 11 of 11)	3' UTR (NM_153564, exon 11 of 11)	-8694	NM_001083312	229900	Mm.45740	NM_145545	ENSMUSG00000040253	Gbp7	9830147J24Rik	guanylate binding protein 7	protein-coding
mm_46386.1	chr5	104018397	104018406	-	1	NA	intron (NM_053262, intron 1 of 6)	intron (NM_053262, intron 1 of 6)	3395	NM_053262	114664	Mm.46019	NM_053262	ENSMUSG00000029311	Hsd17b11	Dhrs8|Pan1b|SDR2|retSDR2	hydroxysteroid (17-beta) dehydrogenase 11	protein-coding
mm_145649.1	chr18	61128995	61129007	+	1	NA	exon (NM_001037859, exon 18 of 22)	exon (NM_001037859, exon 18 of 22)	11533	NR_105949	102466212		NR_105949	ENSMUSG00000098389	Mir6983	Gm27496|mmu-mir-6983	microRNA 6983	ncRNA
mm_50450.1	chr6	48905134	48905143	+	1	NA	5' UTR (NM_001161621, exon 1 of 4)	5' UTR (NM_001161621, exon 1 of 4)	152	NM_001161621	76507	Mm.213898	NM_029638	ENSMUSG00000029811	Aoc1	1600012D06Rik|Abp1|DAO	amine oxidase, copper-containing 1	protein-coding
mm_4976.1	chr1	191328145	191328186	+	1	NA	intron (NM_025864, intron 1 of 7)	intron (NM_025864, intron 1 of 7)	2200	NM_025864	66950	Mm.236300	NM_025864	ENSMUSG00000026627	Tmem206	2310028N02Rik|AI118576	transmembrane protein 206	protein-coding
mm_119755.1	chr14	54166522	54166546	+	1	NA	Intergenic	Intergenic	87395	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_1463.1	chr1	69681281	69681285	+	1	NA	intron (NM_011770, intron 3 of 7)	intron (NM_011770, intron 3 of 7)	4677	NM_011770	22779	Mm.106343	NM_011770	ENSMUSG00000025997	Ikzf2	A730095J18Rik|Helios|Zfpn1a2|Znfn1a2	IKAROS family zinc finger 2	protein-coding
mm_96403.1	chr11	67250894	67250920	+	1	NA	exon (NM_010855, exon 22 of 40)	exon (NM_010855, exon 22 of 40)	13095	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_566.1	chr1	38035741	38035749	+	1	NA	intron (NM_198303, intron 9 of 23)	intron (NM_198303, intron 9 of 23)	37735	NM_198303	226982	Mm.260943	NM_198303	ENSMUSG00000026083	Eif5b	A030003E17Rik|BC018347|IF2	eukaryotic translation initiation factor 5B	protein-coding
mm_82314.1	chr9	7872986	7873009	-	1	NA	5' UTR (NM_007464, exon 1 of 9)	5' UTR (NM_007464, exon 1 of 9)	173	NM_007464	11796	Mm.2026	NM_007464	ENSMUSG00000032000	Birc3	AW107670|Api1|Api2|Birc2|C-IAP2|HIAP2|IAP1|IAP2|MIAP1|MIAP2|MIHB|MIHC|RNF49|cIAP-1|cIAP-2|cIAP1|cIAP2	baculoviral IAP repeat-containing 3	protein-coding
mm_73997.1	chr8	120739661	120739675	+	1	NA	intron (NM_001301811, intron 1 of 8)	intron (NM_001301811, intron 1 of 8)	1029	NM_001301811	15900	Mm.334861	NM_008320	ENSMUSG00000041515	Irf8	AI893568|ICSBP|IRF-8|Icsbp1|Myls	interferon regulatory factor 8	protein-coding
mm_37165.1	chr4	117156145	117156174	-	1	NA	promoter-TSS (NR_030704)	promoter-TSS (NR_030704)	-27	NM_009098	20116	Mm.260904	NM_009098	ENSMUSG00000047675	Rps8	-	ribosomal protein S8	protein-coding
mm_42943.1	chr5	122989919	122989943	+	1	NA	promoter-TSS (NM_001003953)	promoter-TSS (NM_001003953)	577	NR_045820	109202	Mm.30769	NM_175405	ENSMUSG00000056735	A930024E05Rik	-	RIKEN cDNA A930024E05 gene	ncRNA
mm_117454.1	chr13	74808734	74808754	-	1	NA	promoter-TSS (NM_009817)	promoter-TSS (NM_009817)	16	NM_001301153	12380	Mm.29163	NM_009817	ENSMUSG00000021585	Cast	-	calpastatin	protein-coding
mm_169523.1	chr14	90078538	90078552	-	1	NA	Intergenic	ERVB4_2-LTR_MM|LTR|ERVK	-48346	NR_045712	74967	Mm.390704	NR_045712		4930474H20Rik	-	RIKEN cDNA 4930474H20 gene	ncRNA
mm_49674.1	chr6	31574982	31574991	+	1	NA	Intergenic	ID4_|SINE|ID	-11049	NM_013723	27205	Mm.89918	NM_013723	ENSMUSG00000025608	Podxl	AW121214|Ly102|PC|PCLP-1|Pclp1	podocalyxin-like	protein-coding
mm_93025.1	chr10	87930861	87930871	-	1	NA	3' UTR (NM_010512, exon 5 of 5)	3' UTR (NM_010512, exon 5 of 5)	-35805	NR_000040	22172	Mm.391420	NR_000040		Tyms-ps	-	thymidylate synthase, pseudogene	pseudo
mm_6184.1	chr1	65110087	65110094	-	1	NA	intron (NM_175293, intron 5 of 7)	intron (NM_175293, intron 5 of 7)	-6727	NM_007774	12964	Mm.26904	NM_007774	ENSMUSG00000044429	Cryga	Cryg-4|DGcry-4	crystallin, gamma A	protein-coding
mm_749.1	chr1	43561372	43561379	+	1	NA	intron (NM_010879, intron 4 of 4)	intron (NM_010879, intron 4 of 4)	115624	NM_010879	17974	Mm.389903	NM_010879	ENSMUSG00000066877	Nck2	4833426I10Rik|Grb4|NCKbeta|Nck-2	non-catalytic region of tyrosine kinase adaptor protein 2	protein-coding
mm_65241.1	chr7	19818805	19818848	-	1	NA	intron (NM_033601, intron 2 of 8)	intron (NM_033601, intron 2 of 8)	3929	NM_033601	12051	Mm.439658	NM_033601	ENSMUSG00000053175	Bcl3	AI528691|Bcl-3	B cell leukemia/lymphoma 3	protein-coding
mm_131966.1	chr16	24681748	24681757	+	1	NA	exon (NM_178665, exon 7 of 13)	exon (NM_178665, exon 7 of 13)	-40103	NM_001145954	210126	Mm.209385	NM_178665	ENSMUSG00000033306	Lpp	9430020K16Rik|AA959454|AU024130|B130055L10Rik|C79715|D630048H16	LIM domain containing preferred translocation partner in lipoma	protein-coding
mm_90691.1	chr10	128971192	128971202	+	1	NA	Intergenic	L1M4|LINE|L1	-10209	NM_027853	71664	Mm.337232	NM_027853	ENSMUSG00000025347	Mettl7b	0610006F02Rik|AI266817	methyltransferase like 7B	protein-coding
mm_46158.1	chr5	96161749	96161774	-	1	NA	promoter-TSS (NM_178854)	promoter-TSS (NM_178854)	-6	NM_001285514	231464	Mm.28374	NM_144910	ENSMUSG00000034724	Cnot6l	4932442K20Rik	CCR4-NOT transcription complex, subunit 6-like	protein-coding
mm_127823.1	chr15	5244165	5244175	-	1	NA	promoter-TSS (NM_001136079)	promoter-TSS (NM_001136079)	17	NM_001136079	19219	Mm.18509	NM_008965	ENSMUSG00000039942	Ptger4	EP4|Ptgerep4	prostaglandin E receptor 4 (subtype EP4)	protein-coding
mm_62513.1	chr7	102210593	102210620	+	1	NA	promoter-TSS (NM_001287167)	promoter-TSS (NM_001287167)	271	NM_001291358	233575	Mm.302013	NM_145583	ENSMUSG00000030990	Pgap2	1810006G21Rik|C76649|Frag1	post-GPI attachment to proteins 2	protein-coding
mm_149290.1	chr19	10675041	10675051	+	1	NA	exon (NM_021453, exon 3 of 9)	exon (NM_021453, exon 3 of 9)	3025	NM_021453	58803	Mm.34037	NM_021453	ENSMUSG00000024738	Pga5	1110035E17Rik|Pepf	pepsinogen 5, group I	protein-coding
mm_24798.1	chr3	95550049	95550060	+	1	NA	exon (NM_021281, exon 7 of 8)	exon (NM_021281, exon 7 of 8)	-9623	NM_026489	67981	Mm.179050	NM_026489	ENSMUSG00000028109	Hormad1	4921522K05Rik|Nohma	HORMA domain containing 1	protein-coding
mm_54978.1	chr6	48739460	48739463	-	1	NA	intron (NM_175860, intron 1 of 2)	intron (NM_175860, intron 1 of 2)	414	NM_008376	16205	Mm.252599	NM_008376	ENSMUSG00000090019	Gimap1	IAP38|Imap38|imap	GTPase, IMAP family member 1	protein-coding
mm_138543.1	chr17	35263088	35263100	+	1	NA	promoter-TSS (NM_001267808)	promoter-TSS (NM_001267808)	0	NM_010380	14964	Mm.439675	NM_010380	ENSMUSG00000073411	H2-D1	H-2D|H2-D	histocompatibility 2, D region locus 1	protein-coding
mm_128434.1	chr15	50682568	50682578	-	1	NA	intron (NM_001310481, intron 4 of 5)	intron (NM_001310481, intron 4 of 5)	206476	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_121671.1	chr14	12466992	12467010	-	1	NA	intron (NM_012061, intron 19 of 28)	intron (NM_012061, intron 19 of 28)	-121136	NM_080433	54713	Mm.34644	NM_080433	ENSMUSG00000021743	Fezf2	AI451466|AI852056|Fez|Fezl|Zfp312	Fez family zinc finger 2	protein-coding
mm_138731.1	chr17	36958624	36958630	+	1	NA	promoter-TSS (NM_029602)	promoter-TSS (NM_029602)	35	NM_029602	76416	Mm.26684	NM_029602	ENSMUSG00000036214	Znrd1as	1700022C21Rik|AI746295|Znrd1-as	zinc ribbon domain containing 1, antisense	protein-coding
mm_147450.1	chr18	46572929	46572941	-	1	NA	intron (NM_173394, intron 1 of 2)	L2|LINE|L2	1598	NM_173394	225471	Mm.149280	NM_173394	ENSMUSG00000056130	Ticam2	B430113A10|TICAM-2|TRAM|Tirp|Trif	toll-like receptor adaptor molecule 2	protein-coding
mm_163341.1	chr12	15010624	15010626	+	1	NA	intron (NR_045960, intron 5 of 7)	intron (NR_045960, intron 5 of 7)	39764	NR_045960	73972	Mm.107680	NR_045960		4930448C13Rik	-	RIKEN cDNA 4930448C13 gene	ncRNA
mm_97643.1	chr11	79329588	79329593	+	1	NA	Intergenic	B1_Mur1|SINE|Alu	-10302	NM_010897	18015	Mm.255596	NM_010897	ENSMUSG00000020716	Nf1	AW494271|Dsk9|E030030H24Rik|Mhdadsk9|Nf-1	neurofibromin 1	protein-coding
mm_60951.1	chr7	47050629	47050646	+	1	NA	promoter-TSS (NM_026436)	promoter-TSS (NM_026436)	-3	NM_026436	67893	Mm.27338	NM_026436	ENSMUSG00000010307	Tmem86a	1810054O13Rik|AI414959|AW742698	transmembrane protein 86A	protein-coding
mm_52045.1	chr6	97179197	97179206	+	1	NA	promoter-TSS (NM_001081111)	promoter-TSS (NM_001081111)	-77	NM_001081111	232286	Mm.30893	NM_001081111	ENSMUSG00000030059	Tmf1	7030402D04Rik|Gm153|Tmf1`	TATA element modulatory factor 1	protein-coding
mm_76764.1	chr8	95744627	95744639	-	1	NA	exon (NM_178078, exon 28 of 49)	exon (NM_178078, exon 28 of 49)	8581	NR_106041	102465650		NR_106041	ENSMUSG00000106145	Mir7073	mmu-mir-7073	microRNA 7073	ncRNA
mm_124007.1	chr14	76098537	76098546	-	1	NA	exon (NM_026177, exon 6 of 8)	exon (NM_026177, exon 6 of 8)	12274	NM_026177	67467	Mm.260767	NM_026177	ENSMUSG00000022008	Gpalpp1	1200011I18Rik|Kiaa1704	GPALPP motifs containing 1	protein-coding
mm_157080.1	chrX	9435885	9435904	-	1	NA	3' UTR (NM_007807, exon 13 of 13)	3' UTR (NM_007807, exon 13 of 13)	33430	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_149546.1	chr19	12595687	12595701	+	1	NA	intron (NR_015503, intron 1 of 1)	intron (NR_015503, intron 1 of 1)	872	NR_015503	74333	Mm.329744	NR_015503	ENSMUSG00000086213	A330040F15Rik	-	RIKEN cDNA A330040F15 gene	ncRNA
mm_162091.1	chrX	37480377	37480377	+	1	NA	promoter-TSS (NM_001039689)	promoter-TSS (NM_001039689)	40	NM_001039689	434759	Mm.296444	NM_001039689	ENSMUSG00000079635	Rhox4c	Rhox4.3|Rhox4b	reproductive homeobox 4C	protein-coding
mm_138247.1	chr17	34589833	34589913	+	1	NA	promoter-TSS (NM_134116)	promoter-TSS (NM_134116)	67	NM_134116	106512	Mm.26584	NM_134116	ENSMUSG00000034786	Gpsm3	AA960287|AGS4	G-protein signalling modulator 3 (AGS3-like, C. elegans)	protein-coding
mm_13215.1	chr2	96317936	96317947	+	1	NA	promoter-TSS (NM_001289742)	promoter-TSS (NM_001289742)	-228	NM_001289742	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_23874.1	chr3	83030199	83030209	+	1	NA	exon (NM_010196, exon 4 of 5)	exon (NM_010196, exon 4 of 5)	4051	NM_001111048	14161	Mm.88793	NM_010196	ENSMUSG00000028001	Fga	ENSMUSG00000059807|Fib	fibrinogen alpha chain	protein-coding
mm_143724.1	chr17	81376085	81376094	-	1	NA	non-coding (NR_104580, exon 9 of 9)	non-coding (NR_104580, exon 9 of 9)	-311004	NM_028138	72167	Mm.273257	NM_028138	ENSMUSG00000024246	Thumpd2	2810025A12Rik	THUMP domain containing 2	protein-coding
mm_45016.1	chr5	38540212	38540236	-	1	NA	exon (NM_011715, exon 8 of 15)	exon (NM_011715, exon 8 of 15)	21371	NM_011715	22388	Mm.2654	NM_011715	ENSMUSG00000005103	Wdr1	Aip1|D5Wsu185e|rede	WD repeat domain 1	protein-coding
mm_66779.1	chr7	46919916	46919986	-	1	NA	promoter-TSS (NM_021884)	promoter-TSS (NM_021884)	-21	NM_021884	22088	Mm.241334	NM_021884	ENSMUSG00000014402	Tsg101	AI255943|CC2	tumor susceptibility gene 101	protein-coding
mm_60897.1	chr7	46422657	46422684	+	1	NA	intron (NM_008421, intron 1 of 1)	intron (NM_008421, intron 1 of 1)	26202	NM_001112739	16502	Mm.249386	NM_008421	ENSMUSG00000058975	Kcnc1	C230009H10Rik|KShIIIB|KV4|Kcr2-1|Kv3.1|NGK2|Shaw	potassium voltage gated channel, Shaw-related subfamily, member 1	protein-coding
mm_27074.1	chr3	28781104	28781130	-	1	NA	promoter-TSS (NM_177586)	promoter-TSS (NM_177586)	-194	NM_177586	208691	Mm.193670	NM_177586	ENSMUSG00000050192	Eif5a2	9630038B20|eIF5AII	eukaryotic translation initiation factor 5A2	protein-coding
mm_171038.1	chr2	92184071	92184084	+	1	NA	promoter-TSS (NM_138755)	promoter-TSS (NM_138755)	-105	NM_138755	192285	Mm.330408	NM_138755	ENSMUSG00000058318	Phf21a	80kDa|Bhc|Bhc80|D030065N23Rik|PFTF1	PHD finger protein 21A	protein-coding
mm_154906.1	chrX	21068436	21068447	+	1	NA	promoter-TSS (NM_001085393)	promoter-TSS (NM_001085393)	-47	NM_001085393	278203		NM_001085393	ENSMUSG00000037167	Spaca5	Gm718|Lyze	sperm acrosome associated 5	protein-coding
mm_74391.1	chr8	3155249	3155252	-	1	NA	3' UTR (NM_001330056, exon 22 of 22)	3' UTR (NM_001330056, exon 22 of 22)	124367	NM_010568	16337	Mm.268003	NM_010568	ENSMUSG00000005534	Insr	4932439J01Rik|CD220|D630014A15Rik|IR|IR-A|IR-B	insulin receptor	protein-coding
mm_66240.1	chr7	35537733	35537748	-	1	NA	promoter-TSS (NM_028034)	promoter-TSS (NM_028034)	4	NM_028034	71981	Mm.47904	NM_028034	ENSMUSG00000030491	Tdrd12	2410004F06Rik|2410070K17Rik|ECAT8|EG434165|G1-476-14|repro23	tudor domain containing 12	protein-coding
mm_55428.1	chr6	65779637	65779642	-	1	NA	intron (NM_029549, intron 1 of 10)	intron (NM_029549, intron 1 of 10)	677	NM_029549	70779	Mm.263355	NM_027547	ENSMUSG00000029913	Prdm5	4432417F03Rik|6530401I24Rik|AI197291|E130112L17Rik|PFM2	PR domain containing 5	protein-coding
mm_71404.1	chr8	46433017	46433027	+	1	NA	Intergenic	Intergenic	-38015	NM_007981	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_63699.1	chr7	130645493	130645503	+	1	NA	intron (NM_001004468, intron 3 of 21)	intron (NM_001004468, intron 3 of 21)	-47058	NM_001347637	57752	Mm.86322	NM_021314	ENSMUSG00000030852	Tacc2	mKIAA4180	transforming, acidic coiled-coil containing protein 2	protein-coding
mm_153014.1	chr19	30625450	30625462	-	1	NA	intron (NM_011160, intron 9 of 17)	intron (NM_011160, intron 9 of 17)	-75960	NM_010051	13380	Mm.214717	NM_010051	ENSMUSG00000024868	Dkk1	mdkk-1	dickkopf WNT signaling pathway inhibitor 1	protein-coding
mm_15993.1	chr2	167061271	167061289	+	1	NA	intron (NM_001033196, intron 1 of 13)	intron (NM_001033196, intron 1 of 13)	-1654	NR_138563	68949	Mm.391959	NM_001081005		Zfas1	1500012F01Rik|Zfos1	zinc finger, NFX1-type containing 1, antisense RNA 1	ncRNA
mm_28033.1	chr3	83601537	83601557	-	1	NA	Intergenic	Intergenic	-27429	NR_036591	69460	Mm.389464	NR_036591	ENSMUSG00000101334	1700028M03Rik	-	RIKEN cDNA 1700028M03 gene	ncRNA
mm_160541.1	chr9	40992720	40992720	-	1	NA	intron (NM_001281954, intron 2 of 9)	intron (NM_001281954, intron 2 of 9)	11908	NM_001281954	54698	Mm.42791	NM_019465	ENSMUSG00000032021	Crtam	-	cytotoxic and regulatory T cell molecule	protein-coding
mm_56296.1	chr6	91668503	91668521	-	1	NA	Intergenic	Intergenic	-15555	NM_009320	21366	Mm.395650	NM_009320	ENSMUSG00000030096	Slc6a6	AA589629|C80501|Taut	solute carrier family 6 (neurotransmitter transporter, taurine), member 6	protein-coding
mm_116836.1	chr13	54687697	54687809	-	1	NA	promoter-TSS (NM_001146025)	promoter-TSS (NM_001146025)	55	NM_001146025	105239	Mm.25366	NM_134064	ENSMUSG00000034928	Rnf44	AI854545|mKIAA1100	ring finger protein 44	protein-coding
mm_161363.1	chr14	58072686	58072686	+	1	NA	promoter-TSS (NM_013518)	promoter-TSS (NM_013518)	0	NM_013518	14180	Mm.8846	NM_013518	ENSMUSG00000021974	Fgf9	Eks	fibroblast growth factor 9	protein-coding
mm_165687.1	chr3	90854385	90854385	-	1	NA	Intergenic	Intergenic	127479	NM_207263	384997	Mm.316644	NM_207263	ENSMUSG00000042250	Pglyrp4	Gm1478|Gm413	peptidoglycan recognition protein 4	protein-coding
mm_79668.1	chr9	59665306	59665329	+	1	NA	exon (NM_011099, exon 2 of 11)	exon (NM_011099, exon 2 of 11)	8949	NM_001253883	18746	Mm.326167	NM_011099	ENSMUSG00000032294	Pkm	AA414905|AL024370|AL024424|Pk-2|Pk-3|Pk3|Pkm2	pyruvate kinase, muscle	protein-coding
mm_146194.1	chr18	76165162	76165170	+	1	NA	Intergenic	Intergenic	-5386	NR_105776	102465184		NR_105776	ENSMUSG00000098276	Mir6358	Gm27830|mmu-mir-6358	microRNA 6358	ncRNA
mm_141592.1	chr17	32420999	32421003	-	1	NA	promoter-TSS (NM_021319)	promoter-TSS (NM_021319)	-26	NR_073184	57757	Mm.86752	NM_021319	ENSMUSG00000079563	Pglyrp2	C730002N09Rik|PGRP-L|Pglyrpl|tagL	peptidoglycan recognition protein 2	protein-coding
mm_31190.1	chr4	43562707	43562715	+	1	NA	promoter-TSS (NM_013497)	promoter-TSS (NM_013497)	77	NM_013497	12913	Mm.12407	NM_013497	ENSMUSG00000028466	Creb3	AU044960|AW538053|C80076|LZIP|LZIP-1|LZIP-2|Luman	cAMP responsive element binding protein 3	protein-coding
mm_34573.1	chr4	150063545	150063558	+	1	NA	Intergenic	Intergenic	-4903	NR_029751	723848		NR_029751	ENSMUSG00000065493	Mir34a	Mirn34a|mir-34a|mmu-mir-34a	microRNA 34a	ncRNA
mm_80540.1	chr9	80399484	80399524	+	1	NA	intron (NM_022016, intron 5 of 16)	LSU-rRNA_Hsa|rRNA|rRNA	65934	NM_022016	63859	Mm.422780	NM_022016	ENSMUSG00000032343	Impg1	A930015H12Rik|IMP150|SPACR	interphotoreceptor matrix proteoglycan 1	protein-coding
mm_113667.1	chr13	42709329	42709339	+	1	NA	promoter-TSS (NM_001005740)	promoter-TSS (NM_001005740)	-247	NM_001005740	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding
mm_113109.1	chr13	24416629	24416668	+	1	NA	intron (NM_007717, intron 1 of 15)	intron (NM_007717, intron 1 of 15)	1526	NM_001284520	12763	Mm.8396	NM_007717	ENSMUSG00000016756	Cmah	-	cytidine monophospho-N-acetylneuraminic acid hydroxylase	protein-coding
mm_117662.1	chr13	93499445	93499466	-	1	NA	5' UTR (NM_021310, exon 1 of 11)	5' UTR (NM_021310, exon 1 of 11)	353	NM_021310	57748	Mm.100273	NM_021310	ENSMUSG00000021690	Jmy	-	junction-mediating and regulatory protein	protein-coding
mm_95206.1	chr11	43587069	43587072	+	1	NA	TTS (NM_001045530)	TTS (NM_001045530)	14492	NM_008375	16204	Mm.142716	NM_008375	ENSMUSG00000020405	Fabp6	GT|I-15P|I-BABP|ILBP|ILBP3|Illbp	fatty acid binding protein 6, ileal (gastrotropin)	protein-coding
mm_126694.1	chr15	85028945	85028958	+	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	-8111	NM_133750	73225	Mm.247535	NM_133750	ENSMUSG00000022434	Fam118a	-	family with sequence similarity 118, member A	protein-coding
mm_16049.1	chr2	167753037	167753048	+	1	NA	Intergenic	Intergenic	61865	NR_015500	329562	Mm.123101	NM_177851	ENSMUSG00000006462	A530013C23Rik	-	RIKEN cDNA A530013C23 gene	ncRNA
mm_133904.1	chr16	97548720	97548734	+	1	NA	intron (NM_013606, intron 7 of 13)	L1_Mur3|LINE|L1	12644	NM_013606	17858	Mm.14157	NM_013606	ENSMUSG00000023341	Mx2	AI528743|Mx-2	MX dynamin-like GTPase 2	protein-coding
mm_107297.1	chr12	30884322	30884326	+	1	NA	promoter-TSS (NM_001159743)	promoter-TSS (NM_001159743)	0	NM_001159743	100294583	Mm.399726	NM_001159743	ENSMUSG00000054204	Fam150b	6230419C23Rik	family with sequence similarity 150, member B	protein-coding
mm_154440.1	chrM	1289	1299	-	1	NA	NA	Intergenic	NA	NA								
mm_150385.1	chr19	36348413	36348423	+	1	NA	Intergenic	(CCG)n|Simple_repeat|Simple_repeat	-30649	NM_029508	76073	Mm.259180	NM_029508	ENSMUSG00000024805	Pcgf5	0610009F02Rik|1110054A01Rik|5830406C17Rik|5830443C21Rik|9530023M17Rik|AI324127	polycomb group ring finger 5	protein-coding
mm_103505.1	chr11	76604621	76604639	-	1	NA	Intergenic	Intergenic	-26891	NM_198894	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_90821.1	chr10	7920081	7920094	-	1	NA	exon (NM_138667, exon 3 of 7)	exon (NM_138667, exon 3 of 7)	36036	NM_138667	68652	Mm.193041	NM_138667	ENSMUSG00000015755	Tab2	1110030N06Rik|A530078N03Rik|Map3k7ip2|mKIAA0733	TGF-beta activated kinase 1/MAP3K7 binding protein 2	protein-coding
mm_1785.1	chr1	78537980	78537992	+	1	NA	exon (NM_026713, exon 7 of 7)	exon (NM_026713, exon 7 of 7)	26926	NM_026713	68393	Mm.41325	NM_026713	ENSMUSG00000012187	Mogat1	0610030A14Rik|1110064N14Rik|Dgat2l|Dgat2l1|MGAT1|WI1-2612I11.1|mDC2	monoacylglycerol O-acyltransferase 1	protein-coding
mm_142954.1	chr17	56117538	56117551	-	1	NA	promoter-TSS (NM_001077348)	promoter-TSS (NM_001077348)	4	NM_025874	66968	Mm.254985	NM_025874	ENSMUSG00000011305	Plin5	2310076L09Rik|AI415325|AW109675|Lsdp5|MLDP|PAT-1	perilipin 5	protein-coding
mm_44553.1	chr5	24601859	24601904	-	1	NA	5' UTR (NM_025891, exon 1 of 13)	5' UTR (NM_025891, exon 1 of 13)	121	NM_025891	66993	Mm.436539	NM_025891	ENSMUSG00000028949	Smarcd3	1500001J14Rik|2210409C08Rik|BAF60C	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3	protein-coding
mm_171275.1	chr3	8882420	8882443	-	1	NA	intron (NM_025434, intron 2 of 2)	intron (NM_025434, intron 2 of 2)	41426	NM_025434	66230	Mm.38460	NM_025434	ENSMUSG00000040269	Mrps28	1500012D08Rik|AW061224	mitochondrial ribosomal protein S28	protein-coding
mm_65881.1	chr7	29726967	29726985	-	1	NA	promoter-TSS (NM_029714)	promoter-TSS (NM_029714)	39	NM_029714	76718	Mm.69030	NM_029714	ENSMUSG00000049123	Catsperg2	1700067C01Rik|CATSPERG	catsper channel auxiliary subunit gamma 2	protein-coding
mm_66375.1	chr7	43659765	43659773	-	1	NA	exon (NM_031181, exon 1 of 7)	exon (NM_031181, exon 1 of 7)	392	NM_031181	83382	Mm.157702	NM_031181	ENSMUSG00000030474	Siglece	Cd170|Siglec12|Siglec5|Siglec9|Siglecl1|mSiglec-E	sialic acid binding Ig-like lectin E	protein-coding
mm_5550.1	chr1	38628078	38628092	-	1	NA	promoter-TSS (NM_001290814)	promoter-TSS (NM_001290814)	-841	NM_001290814	16764	Mm.336679	NM_010678	ENSMUSG00000037138	Aff3	3222402O04Rik|A730046J16|LAF-4|Laf4	AF4/FMR2 family, member 3	protein-coding
mm_116500.1	chr13	44982814	44982842	-	1	NA	exon (NM_025772, exon 5 of 10)	exon (NM_025772, exon 5 of 10)	19268	NM_025772	94245	Mm.352311	NM_025772	ENSMUSG00000057531	Dtnbp1	5430437B18Rik|AW048963|Bloc1s8|dysbindin|sdy	dystrobrevin binding protein 1	protein-coding
mm_15802.1	chr2	164461082	164461091	+	1	NA	5' UTR (NM_025575, exon 1 of 4)	5' UTR (NM_025575, exon 1 of 4)	115	NM_025575	66460	Mm.44218	NM_025575	ENSMUSG00000045503	Sys1	2610042O14Rik|AI266964|C87389	SYS1 Golgi-localized integral membrane protein homolog (S. cerevisiae)	protein-coding
mm_12106.1	chr2	61582156	61582173	+	1	NA	intron (NM_011529, intron 1 of 7)	intron (NM_011529, intron 1 of 7)	3578	NM_011529	21353	Mm.244393	NM_011529	ENSMUSG00000064289	Tank	C86182|E430026L09Rik|I-TRAF	TRAF family member-associated Nf-kappa B activator	protein-coding
mm_16419.1	chr2	180171590	180171658	+	1	NA	promoter-TSS (NM_019822)	promoter-TSS (NM_019822)	36	NM_019822	56436	Mm.316654	NM_019822	ENSMUSG00000039041	Adrm1	1110063P18Rik|2510006J17Rik|AA408205|ARM-1|AU043535|Arm1|Gp110|Rpn13	adhesion regulating molecule 1	protein-coding
mm_171414.1	chr4	130053469	130053472	+	1	NA	exon (NM_028266, exon 6 of 70)	exon (NM_028266, exon 6 of 70)	5630	NM_028266	107581	Mm.41860	NM_028266	ENSMUSG00000040690	Col16a1	2700007F12Rik|A530052M23Rik|AI838662|CA1F	collagen, type XVI, alpha 1	protein-coding
mm_1052.1	chr1	58802650	58802656	+	1	NA	5' UTR (NM_001277926, exon 1 of 10)	5' UTR (NM_001277926, exon 1 of 10)	151	NM_001080126	12370	Mm.336851	NM_009812	ENSMUSG00000026029	Casp8	CASP-8|FLICE|MACH|Mch5	caspase 8	protein-coding
mm_65467.1	chr7	25476553	25476563	-	1	NA	exon (NM_001039186, exon 2 of 8)	exon (NM_001039186, exon 2 of 8)	1067	NM_001039185	26365	Mm.322502	NM_011926	ENSMUSG00000074272	Ceacam1	Bgp|Bgp1|C-CAM|CD66a|Cc1|Cea-1|Cea-7|Cea1|Cea7|Hv-2|Hv2|MHVR|MHVR1|Mhv-1|bb-1|mCEA1|mmCGM1|mmCGM1a|mmCGM2	carcinoembryonic antigen-related cell adhesion molecule 1	protein-coding
mm_171394.1	chr4	12233136	12233147	+	1	NA	Intergenic	Intergenic	-61126	NM_026558	68099	Mm.25340	NM_026558	ENSMUSG00000028218	Fam92a	6720467C03Rik|Fam92a1	family with sequence similarity 92, member A	protein-coding
mm_154388.1	chrM	12067	12077	+	1	NA	NA	Intergenic	NA	NA								
mm_78920.1	chr9	45040420	45040451	+	1	NA	Intergenic	Intergenic	-1909	NM_007962	14012	Mm.33240	NM_007962	ENSMUSG00000032092	Mpzl2	Eva|Eva1	myelin protein zero-like 2	protein-coding
mm_211.1	chr1	16665181	16665185	+	1	NA	promoter-TSS (NM_027415)	promoter-TSS (NM_027415)	-8	NM_027415	70397	Mm.194225	NM_026392	ENSMUSG00000025940	Tmem70	1110020A09Rik|2210416J16Rik	transmembrane protein 70	protein-coding
mm_66184.1	chr7	34189484	34189492	-	1	NA	intron (NM_026549, intron 4 of 6)	intron (NM_026549, intron 4 of 6)	7159	NM_026549	68079	Mm.38173	NM_026549	ENSMUSG00000002635	Pdcd2l	6030457N17Rik	programmed cell death 2-like	protein-coding
mm_69469.1	chr7	133709029	133709040	-	1	NA	promoter-TSS (NM_025392)	promoter-TSS (NM_025392)	261	NM_009479	22276	Mm.3160	NM_009479	ENSMUSG00000030979	Uros	AI415298|UROIIIS|Uros3	uroporphyrinogen III synthase	protein-coding
mm_46982.1	chr5	115300552	115300564	-	1	NA	promoter-TSS (NR_131932)	promoter-TSS (NR_131932)	432	NM_019682	56455	Mm.256858	NM_019682	ENSMUSG00000009013	Dynll1	Dlc8|Dnclc1|Pin	dynein light chain LC8-type 1	protein-coding
mm_34437.1	chr4	147847920	147847936	+	1	NA	intron (NM_198619, intron 1 of 3)	L1MC|LINE|L1	447	NM_198619	242747	Mm.332053	NM_198619	ENSMUSG00000059423	Zfp933	2810408P10Rik	zinc finger protein 933	protein-coding
mm_141544.1	chr17	31905851	31905870	-	1	NA	Intergenic	Intergenic	-50068	NM_010831	17691	Mm.290941	NM_010831	ENSMUSG00000024042	Sik1	Msk|Sik|Snf1lk	salt inducible kinase 1	protein-coding
mm_132119.1	chr16	31695540	31695555	+	1	NA	intron (NR_045516, intron 4 of 24)	intron (NR_045516, intron 4 of 24)	31612	NM_001252434	13383	Mm.382	NM_007862	ENSMUSG00000022770	Dlg1	B130052P05Rik|Dlgh1|E-dlg/SAP97|SAP-97|SAP97|mKIAA4187	discs, large homolog 1 (Drosophila)	protein-coding
mm_95697.1	chr11	54370617	54370623	+	1	NA	promoter-TSS (NM_029105)	promoter-TSS (NM_029105)	-32	NM_029105	74847	Mm.486538	NM_029105	ENSMUSG00000020332	Meikin	4930404A10Rik	meiotic kinetochore factor	protein-coding
mm_91610.1	chr10	41490329	41490331	-	1	NA	promoter-TSS (NM_009213)	promoter-TSS (NM_009213)	10	NM_009213	20598	Mm.953	NM_009213	ENSMUSG00000019822	Smpd2	AW108287|nSMase|nSMase1	sphingomyelin phosphodiesterase 2, neutral	protein-coding
mm_117940.1	chr13	99434637	99434648	-	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-21816	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_108695.1	chr12	86946522	86946532	+	1	NA	promoter-TSS (NM_001289430)	promoter-TSS (NM_001289430)	-514	NM_001289431	217732	Mm.22337	NM_173735	ENSMUSG00000034157	Cipc	2310044G17Rik|AI842544|AI853744|Kiaa1737|mKIAA1737	CLOCK interacting protein, circadian	protein-coding
mm_37395.1	chr4	121098191	121098250	-	1	NA	promoter-TSS (NM_172700)	promoter-TSS (NM_172700)	23	NM_172700	230709	Mm.34399	NM_172700	ENSMUSG00000043207	Zmpste24	A530043O15Rik|D030046F19|FACE1|Face-1|MADB|STE24|Ste24p	zinc metallopeptidase, STE24	protein-coding
mm_55637.1	chr6	72333373	72333383	-	1	NA	intron (NM_138592, intron 6 of 12)	intron (NM_138592, intron 6 of 12)	11797	NM_138592	28035	Mm.281900	NM_138592	ENSMUSG00000056305	Usp39	AA408960|AI894154|CGI-21|D6Wsu157e|SAD1	ubiquitin specific peptidase 39	protein-coding
mm_73363.1	chr8	105595195	105595203	+	1	NA	Intergenic	L3|LINE|CR1	-10030	NM_001081241	75687	Mm.41261	NM_001081241	ENSMUSG00000038604	Fam65a	2310066E14Rik|AI837433	family with sequence similarity 65, member A	protein-coding
mm_157163.1	chrX	9465673	9465762	-	1	NA	exon (NM_007807, exon 3 of 13)	exon (NM_007807, exon 3 of 13)	3607	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_21050.1	chr2	152622116	152622122	-	1	NA	TTS (NM_001039122)	TTS (NM_001039122)	934	NM_001039122	654459	Mm.358531	NM_001039122	ENSMUSG00000074678	Defb25	BD-25|OTTMUSG00000015862|mBD-25	defensin beta 25	protein-coding
mm_26132.1	chr3	137882663	137882665	+	1	NA	intron (NM_001033155, intron 1 of 7)	B1_Mus1|SINE|Alu	14989	NM_001033155	70604	Mm.256488	NM_001033155	ENSMUSG00000074212	Dnajb14	5730496F10Rik	DnaJ heat shock protein family (Hsp40) member B14	protein-coding
mm_28698.1	chr3	95540337	95540354	-	1	NA	intron (NM_001267695, intron 3 of 7)	intron (NM_001267695, intron 3 of 7)	13559	NM_001267695	13040	Mm.3619	NM_021281	ENSMUSG00000038642	Ctss	Cats	cathepsin S	protein-coding
mm_150779.1	chr19	44294921	44294938	+	1	NA	exon (NM_009128, exon 2 of 6)	exon (NM_009128, exon 2 of 6)	1253	NM_009128	20250	Mm.487021	NM_009128	ENSMUSG00000025203	Scd2	Mir5114|Scd-2|mir-5114|swty	stearoyl-Coenzyme A desaturase 2	protein-coding
mm_102344.1	chr11	58093092	58093109	-	1	NA	Intergenic	Intergenic	-11053	NM_026949	69125	Mm.28910	NM_026949	ENSMUSG00000020515	Cnot8	1500015I04Rik|1810022F04Rik|AA536816|AU015770|AU043059	CCR4-NOT transcription complex, subunit 8	protein-coding
mm_85622.1	chr9	107614975	107614994	-	1	NA	3' UTR (NM_008138, exon 9 of 9)	3' UTR (NM_008138, exon 9 of 9)	-5743	NM_001291539	20347	Mm.4083	NM_009153	ENSMUSG00000057969	Sema3b	SemA|Semaa|sema5|semaV	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B	protein-coding
mm_30059.1	chr3	137552658	137552665	-	1	NA	promoter-TSS (NM_177665)	promoter-TSS (NM_177665)	-39	NM_177665	229862	Mm.246591	NM_177665	ENSMUSG00000055138	Gm4861	9230109N16|EG229862	predicted gene 4861	protein-coding
mm_122643.1	chr14	51345487	51345490	-	1	NA	promoter-TSS (NR_045736)	promoter-TSS (NR_045736)	1	NR_045736	75377	Mm.402100	NR_045736		4930597G03Rik	-	RIKEN cDNA 4930597G03 gene	ncRNA
mm_160758.1	chr10	85598488	85598488	+	1	NA	promoter-TSS (NM_001017525)	promoter-TSS (NM_001017525)	77	NM_001017525	74007	Mm.36544	NM_028709	ENSMUSG00000020042	Btbd11	6330404E16Rik	BTB (POZ) domain containing 11	protein-coding
mm_2688.1	chr1	127483030	127483033	+	1	NA	TTS (NM_145128)	TTS (NM_145128)	194990	NM_028135	72160	Mm.281287	NM_028135	ENSMUSG00000026347	Tmem163	2610024A01Rik|SV31	transmembrane protein 163	protein-coding
mm_34215.1	chr4	140971838	140971856	+	1	NA	intron (NM_023374, intron 3 of 7)	intron (NM_023374, intron 3 of 7)	10576	NM_023374	67680	Mm.246965	NM_023374	ENSMUSG00000009863	Sdhb	0710008N11Rik	succinate dehydrogenase complex, subunit B, iron sulfur (Ip)	protein-coding
mm_65052.1	chr7	18656612	18656621	-	1	NA	5' UTR (NM_027403, exon 1 of 5)	5' UTR (NM_027403, exon 1 of 5)	109	NM_027403	72242	Mm.326858	NM_027403	ENSMUSG00000070796	Psg21	1600019C01Rik|1600025N01Rik|1600026N13Rik|cea8	pregnancy-specific glycoprotein 21	protein-coding
mm_114354.1	chr13	60940182	60940190	+	1	NA	exon (NM_009411, exon 3 of 5)	exon (NM_009411, exon 3 of 5)	1749	NM_009411	21984	Mm.2372	NM_009411	ENSMUSG00000033834	Tpbpa	AV033951|Tb-1|Tb1|Tpbp|b2b1247Clo	trophoblast specific protein alpha	protein-coding
mm_166568.1	chr6	48988382	48988384	+	1	NA	exon (NM_172888, exon 1 of 5)	exon (NM_172888, exon 1 of 5)	1522	NM_172888	243377	Mm.446302	NM_172888	ENSMUSG00000039215	Svs1	9530003A11	seminal vesicle secretory protein 1	protein-coding
mm_64576.1	chr7	144930637	144930640	+	1	NA	3' UTR (NM_007631, exon 5 of 5)	3' UTR (NM_007631, exon 5 of 5)	1497	NR_039539	100628615		NR_039539	ENSMUSG00000092633	Mir3962	mmu-mir-3962|mu-mir-3962	microRNA 3962	ncRNA
mm_137010.1	chr17	17830877	17830880	+	1	NA	promoter-TSS (NR_029539)	promoter-TSS (NR_029539)	66	NR_029539	387235		NR_029539	ENSMUSG00000065479	Mir125a	Mirn125a	microRNA 125a	ncRNA
mm_166173.1	chr5	29636697	29636708	+	1	NA	intron (NM_133907, intron 16 of 22)	LTR10_RN|LTR|ERVK	67460	NM_133907	100763	Mm.137746	NM_133907	ENSMUSG00000039000	Ube3c	AI853514|mKIAA0010	ubiquitin protein ligase E3C	protein-coding
mm_143874.1	chr17	84187172	84187190	-	1	NA	intron (NM_001001806, intron 1 of 1)	CpG	766	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_165042.1	chr19	39031404	39031405	+	1	NA	exon (NM_028089, exon 5 of 9)	exon (NM_028089, exon 5 of 9)	24385	NM_028089	72082	Mm.142581	NM_028089	ENSMUSG00000025002	Cyp2c55	2010318C06Rik	cytochrome P450, family 2, subfamily c, polypeptide 55	protein-coding
mm_154926.1	chrX	24008646	24008696	+	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	115908	NM_001034864	236749	Mm.296422	NM_001034864	ENSMUSG00000068113	Gm4907	EG236749	predicted gene 4907	protein-coding
mm_98194.1	chr11	87794522	87794536	+	1	NA	intron (NM_010824, intron 1 of 13)	intron (NM_010824, intron 1 of 13)	745	NM_010824	17523	Mm.4668	NM_010824	ENSMUSG00000009350	Mpo	mKIAA4033	myeloperoxidase	protein-coding
mm_13968.1	chr2	121430872	121430873	+	1	NA	intron (NM_007952, intron 5 of 12)	B1_Mm|SINE|Alu	11729	NM_145973	269344	Mm.330522	NM_145973	ENSMUSG00000027246	Ell3	A930015D22Rik	elongation factor RNA polymerase II-like 3	protein-coding
mm_66272.1	chr7	37366701	37366702	-	1	NA	Intergenic	Intergenic	403051	NM_172385	243937	Mm.322505	NM_172385	ENSMUSG00000043456	Zfp536	9630010P11Rik|Znf536|mKIAA0390	zinc finger protein 536	protein-coding
mm_112026.1	chr12	111458644	111458654	-	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	15988	NM_009396	21928	Mm.255332	NM_009396	ENSMUSG00000021281	Tnfaip2	B94|Exoc3l3|M-sec|Tnfip2|tnfb94	tumor necrosis factor, alpha-induced protein 2	protein-coding
mm_92621.1	chr10	80259017	80259021	-	1	NA	exon (NM_001347119, exon 5 of 6)	exon (NM_001347119, exon 5 of 6)	1993	NM_001347119	14431	Mm.7329	NM_010255	ENSMUSG00000020150	Gamt	AA571402|Spintz1	guanidinoacetate methyltransferase	protein-coding
mm_33178.1	chr4	126058558	126058613	+	1	NA	promoter-TSS (NM_172701)	promoter-TSS (NM_172701)	20	NM_172701	230751	Mm.38907	NM_172701	ENSMUSG00000042616	Oscp1	1810007P19Rik|5730415O04|6030436A01Rik	organic solute carrier partner 1	protein-coding
mm_38405.1	chr4	139075558	139075575	-	1	NA	promoter-TSS (NM_021358)	promoter-TSS (NM_021358)	-777	NM_021358	15565	Mm.291096	NM_021358	ENSMUSG00000028747	Htr6	5-HT6	5-hydroxytryptamine (serotonin) receptor 6	protein-coding
mm_158786.1	chrX	167207960	167207967	-	1	NA	exon (NM_021278, exon 2 of 3)	exon (NM_021278, exon 2 of 3)	1255	NM_021278	19241	Mm.142729	NM_021278	ENSMUSG00000049775	Tmsb4x	Ptmb4|Tb4	thymosin, beta 4, X chromosome	protein-coding
mm_17571.1	chr2	30359191	30359272	-	1	NA	promoter-TSS (NM_001289709)	promoter-TSS (NM_001289709)	85	NM_139302	227700	Mm.33343	NM_139302	ENSMUSG00000026860	Sh3glb2	SPAS-1	SH3-domain GRB2-like endophilin B2	protein-coding
mm_135464.1	chr16	45799770	45799773	-	1	NA	intron (NM_001252442, intron 5 of 18)	intron (NM_001252442, intron 5 of 18)	44607	NM_153412	208177	Mm.211477	NM_153412	ENSMUSG00000033149	Phldb2	AV253284|C820004H04Rik|LL5b|LL5beta	pleckstrin homology like domain, family B, member 2	protein-coding
mm_110787.1	chr12	72014530	72014530	-	1	NA	Intergenic	Intergenic	56461	NM_181752	238252	Mm.390508	NM_181752	ENSMUSG00000043398	Gpr135	PAFR	G protein-coupled receptor 135	protein-coding
mm_2426.1	chr1	95498582	95498607	+	1	NA	Intergenic	Intergenic	169000	NM_009183	20452	Mm.306228	NM_009183	ENSMUSG00000040710	St8sia4	PST|PST-1|SIAT8-D|ST8SiaIV|Siat8d	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4	protein-coding
mm_153912.1	chr19	47138305	47138309	-	1	NA	promoter-TSS (NM_133746)	promoter-TSS (NM_133746)	-13	NM_133746	72691	Mm.31663	NM_133746	ENSMUSG00000033033	Calhm2	2810048G17Rik|Fam26b	calcium homeostasis modulator 2	protein-coding
mm_45276.1	chr5	64812784	64812796	-	1	NA	intron (NM_008453, intron 1 of 5)	intron (NM_008453, intron 1 of 5)	9267	NM_008453	16599	Mm.392759	NM_008453	ENSMUSG00000029178	Klf3	9930027G08Rik|AL024007|Bklf|Tef-2	Kruppel-like factor 3 (basic)	protein-coding
mm_49480.1	chr6	29531152	29531172	+	1	NA	exon (NM_001252382, exon 2 of 9)	exon (NM_001252382, exon 2 of 9)	1880	NM_001252382	27056	Mm.6479	NM_012057	ENSMUSG00000029771	Irf5	AW491843|mirf5	interferon regulatory factor 5	protein-coding
mm_72818.1	chr8	88118780	88118816	+	1	NA	promoter-TSS (NM_029074)	promoter-TSS (NM_029074)	39	NM_029074	382030	Mm.216574	NM_029074	ENSMUSG00000036810	Cnep1r1	5033428A16Rik|NEP1-R1|Tmem188	CTD nuclear envelope phosphatase 1 regulatory subunit 1	protein-coding
mm_25644.1	chr3	121369583	121369598	+	1	NA	Intergenic	Intergenic	-56951	NM_028044	71994	Mm.275555	NM_028044	ENSMUSG00000053931	Cnn3	1600014M03Rik|C85854|Calpo3	calponin 3, acidic	protein-coding
mm_72942.1	chr8	91631063	91631070	+	1	NA	intron (NM_011936, intron 8 of 8)	intron (NM_011936, intron 8 of 8)	170588	NM_001253822	16373	Mm.238044	NM_008393	ENSMUSG00000031734	Irx3	AI894186	Iroquois related homeobox 3	protein-coding
mm_158910.1	chr1	39538000	39538000	+	1	NA	intron (NM_028043, intron 2 of 6)	intron (NM_028043, intron 2 of 6)	2198	NM_028043	52846	Mm.259421	NM_028043	ENSMUSG00000003135	Cnot11	2410015L18Rik|C40|D1Bwg0212e	CCR4-NOT transcription complex, subunit 11	protein-coding
mm_166536.1	chr6	30680504	30680515	-	1	NA	intron (NR_130775, intron 1 of 2)	intron (NR_130775, intron 1 of 2)	13240	NM_031998	83922	Mm.65389	NM_031998	ENSMUSG00000029790	Cep41	1700017E11Rik|2810431D15Rik|Tsga14	centrosomal protein 41	protein-coding
mm_163619.1	chr13	55322139	55322150	+	1	NA	promoter-TSS (NM_025596)	promoter-TSS (NM_025596)	89	NM_025596	66494	Mm.439805	NM_025596	ENSMUSG00000021486	Prelid1	2610524G07Rik|Preli	PRELI domain containing 1	protein-coding
mm_104990.1	chr11	100269946	100269957	-	1	NA	promoter-TSS (NM_212483)	promoter-TSS (NM_212483)	-80	NM_212483	68239	Mm.158190	NM_212483	ENSMUSG00000053654	Krt42	2410039E07Rik|K17n|Ka22|ecat6	keratin 42	protein-coding
mm_145936.1	chr18	67289228	67289234	+	1	NA	promoter-TSS (NM_053261)	promoter-TSS (NM_053261)	8	NM_053261	114663	Mm.34079	NM_053261	ENSMUSG00000024525	Impa2	2210415D20Rik|AI326924|AW259601	inositol (myo)-1(or 4)-monophosphatase 2	protein-coding
mm_154489.1	chrM	5859	5875	-	1	NA	NA	Intergenic	NA	NA								
mm_143712.1	chr17	80727997	80728019	-	1	NA	promoter-TSS (NM_001290345)	promoter-TSS (NM_001290345)	17	NM_001290345	225028	Mm.311948	NM_001081357	ENSMUSG00000024242	Map4k3	4833416M01Rik|4833416M07Rik|9530052P13Rik|Glk|MAPKKKK3|MEKKK 3|MEKKK3|RAB8IPL1	mitogen-activated protein kinase kinase kinase kinase 3	protein-coding
mm_35197.1	chr4	16163513	16163533	-	1	NA	promoter-TSS (NR_045765)	promoter-TSS (NR_045765)	120	NM_138952	192656	Mm.112765	NM_138952	ENSMUSG00000041135	Ripk2	2210420D18Rik|CARD3|CARDIAK|CCK|D4Bwg0615e|RICK|RIP2	receptor (TNFRSF)-interacting serine-threonine kinase 2	protein-coding
mm_169891.1	chr16	4798226	4798226	-	1	NA	Intergenic	LTRIS2|LTR|ERV1	-8291	NM_025670	66626	Mm.157648	NM_025670	ENSMUSG00000004071	Cdip1	2700048O17Rik|5730403B10Rik|AU018521|AW742692|CDIP	cell death inducing Trp53 target 1	protein-coding
mm_1434.1	chr1	67193815	67193824	+	1	NA	intron (NM_001080809, intron 21 of 37)	intron (NM_001080809, intron 21 of 37)	70792	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_139428.1	chr17	53566977	53567023	+	1	NA	promoter-TSS (NM_020005)	promoter-TSS (NM_020005)	29	NM_020005	18519	Mm.255025	NM_020005	ENSMUSG00000000708	Kat2b	A930006P13Rik|AI461839|AW536563|Pcaf|p/CAF	K(lysine) acetyltransferase 2B	protein-coding
mm_115559.1	chr13	9173478	9173485	-	1	NA	3' UTR (NM_172585, exon 18 of 18)	3' UTR (NM_172585, exon 18 of 18)	79600	NM_172585	217980	Mm.234944	NM_172585	ENSMUSG00000033499	Larp4b	A630096F19|AI256361|D13Wsu64e|Larp5	La ribonucleoprotein domain family, member 4B	protein-coding
mm_9789.1	chr1	181257662	181257674	-	1	NA	Intergenic	Intergenic	-45690	NM_145514	226757	Mm.289082	NM_145514	ENSMUSG00000038733	Wdr26	1600024A01Rik|AA693241|AI447817|AU044014|C77982|Gid7	WD repeat domain 26	protein-coding
mm_15707.1	chr2	164017246	164017261	+	1	NA	3' UTR (NM_018753, exon 6 of 6)	3' UTR (NM_018753, exon 6 of 6)	-7971	NM_001114079	381404	Mm.82301	NM_001114079	ENSMUSG00000054582	Pabpc1l	1810053B01Rik|Epab	poly(A) binding protein, cytoplasmic 1-like	protein-coding
mm_86067.1	chr9	114775415	114775425	-	1	NA	intron (NM_001252479, intron 1 of 3)	intron (NM_001252479, intron 1 of 3)	6573	NM_133978	102545	Mm.35600	NM_133978	ENSMUSG00000032436	Cmtm7	AI481279|Cklfsf7|LNV	CKLF-like MARVEL transmembrane domain containing 7	protein-coding
mm_43427.1	chr5	136057349	136057362	+	1	NA	promoter-TSS (NM_027158)	promoter-TSS (NM_027158)	88	NM_027158	69665	Mm.75713	NM_027158	ENSMUSG00000006143	Upk3bl	2310043J07Rik	uroplakin 3B-like	protein-coding
mm_62537.1	chr7	102266792	102266844	+	1	NA	Intergenic	Intergenic	-1006	NM_009287	20866	Mm.645	NM_009287	ENSMUSG00000030987	Stim1	SIM	stromal interaction molecule 1	protein-coding
mm_122330.1	chr14	37110026	37110061	-	1	NA	promoter-TSS (NM_001206684)	promoter-TSS (NM_001206684)	58	NM_001206684	70045	Mm.271619	NM_001206684	ENSMUSG00000096001	2610528A11Rik	AW494830	RIKEN cDNA 2610528A11 gene	protein-coding
mm_167412.1	chr8	107031274	107031291	+	1	NA	promoter-TSS (NM_126165)	promoter-TSS (NM_126165)	-44	NM_126165	116733	Mm.236004	NM_126165	ENSMUSG00000031913	Vps4a	4930589C15Rik|AI325971|AW553189	vacuolar protein sorting 4A	protein-coding
mm_87073.1	chr10	29200598	29200614	+	1	NA	TTS (NM_026138)	TTS (NM_026138)	-11037	NM_001162537	212448	Mm.132789	NM_001162537	ENSMUSG00000004360	9330159F19Rik	-	RIKEN cDNA 9330159F19 gene	protein-coding
mm_167636.1	chr9	63221017	63221020	+	1	NA	intron (NM_011840, intron 17 of 21)	intron (NM_011840, intron 17 of 21)	-72057	NM_001163758	207667	Mm.36349	NM_172446	ENSMUSG00000022245	Skor1	AV273001|C230094B15Rik|Corl1|Lbxcor1	SKI family transcriptional corepressor 1	protein-coding
mm_104995.1	chr11	100355401	100355416	-	1	NA	intron (NM_010404, intron 1 of 10)	CpG	733	NM_177981	15114	Mm.281700	NM_010404	ENSMUSG00000006930	Hap1	HAP-1	huntingtin-associated protein 1	protein-coding
mm_730.1	chr1	43196995	43197010	+	1	NA	promoter-TSS (NM_001289533)	promoter-TSS (NM_001289533)	-241	NM_001289533	14200	Mm.6799	NM_010212	ENSMUSG00000008136	Fhl2	FHL-2|SLIM-3|SLIM3	four and a half LIM domains 2	protein-coding
mm_138910.1	chr17	43594782	43594829	+	1	NA	exon (NM_013737, exon 4 of 12)	exon (NM_013737, exon 4 of 12)	-3296	NR_045444	73504	Mm.9277	NR_045444	ENSMUSG00000090307	1700071M16Rik	-	RIKEN cDNA 1700071M16 gene	ncRNA
mm_48998.1	chr6	4756712	4756725	+	1	NA	exon (NM_130877, exon 2 of 2)	exon (NM_130877, exon 2 of 2)	9412	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_88036.1	chr10	67535466	67535492	+	1	NA	Intergenic	CpG	-2390	NM_010118	13654	Mm.290421	NM_010118	ENSMUSG00000037868	Egr2	Egr-2|Krox-20|Krox20|NGF1-B|Zfp-25|Zfp-6	early growth response 2	protein-coding
mm_22938.1	chr3	31686419	31686438	+	1	NA	Intergenic	(CAGAGA)n|Simple_repeat|Simple_repeat	-216275	NM_028231	72413	Mm.64790	NM_028231	ENSMUSG00000037610	Kcnmb2	2700049B16Rik|3110031N04Rik	potassium large conductance calcium-activated channel, subfamily M, beta member 2	protein-coding
mm_70463.1	chr8	11912973	11913001	+	1	NA	Intergenic	Intergenic	72466	NM_029326	75528	Mm.440342	NM_029326	ENSMUSG00000031512	Tex29	1700018L24Rik	testis expressed 29	protein-coding
mm_147499.1	chr18	49755549	49755591	-	1	NA	promoter-TSS (NM_001170960)	promoter-TSS (NM_001170960)	31	NM_026854	68857	Mm.96010	NM_026854	ENSMUSG00000024505	Dtwd2	1190002H09Rik|8030470C17Rik|AI414673|BB115449	DTW domain containing 2	protein-coding
mm_52525.1	chr6	115666953	115666970	+	1	NA	intron (NM_029780, intron 1 of 16)	intron (NM_029780, intron 1 of 16)	9674	NM_029780	110157	Mm.184163	NM_029780	ENSMUSG00000000441	Raf1	6430402F14Rik|AA990557|BB129353|Craf1|D830050J10Rik|Raf-1|c-Raf|v-Raf	v-raf-leukemia viral oncogene 1	protein-coding
mm_159266.1	chr2	156700406	156700406	+	1	NA	intron (NM_001277186, intron 2 of 12)	intron (NM_001277186, intron 2 of 12)	20503	NR_040505	74846	Mm.443946	NR_040505	ENSMUSG00000086638	4930405A21Rik	-	RIKEN cDNA 4930405A21 gene	ncRNA
mm_112228.1	chr12	113430622	113430632	-	1	NA	Intergenic	Intergenic	-58938	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_165278.1	chr2	80316967	80316983	+	1	NA	intron (NM_024181, intron 1 of 22)	RLTR31D_MM|LTR|ERVK	1509	NM_024181	66861	Mm.21762	NM_024181	ENSMUSG00000027006	Dnajc10	1200006L06Rik|D2Ertd706e|ERdj5|JPDI	DnaJ heat shock protein family (Hsp40) member C10	protein-coding
mm_156695.1	chrX	159472868	159472881	+	1	NA	exon (NM_001081124, exon 8 of 17)	exon (NM_001081124, exon 8 of 17)	13749	NM_001313753	78283	Mm.160079	NM_001081124	ENSMUSG00000041020	Map7d2	1600028E09Rik|2900002G04Rik|5330432J06Rik|C030036K04Rik|Mtap7d2	MAP7 domain containing 2	protein-coding
mm_152865.1	chr19	24224981	24224994	-	1	NA	promoter-TSS (NM_011597)	promoter-TSS (NM_011597)	39	NM_011597	21873	Mm.104744	NM_011597	ENSMUSG00000024812	Tjp2	ZO-2	tight junction protein 2	protein-coding
mm_97876.1	chr11	83191327	83191339	+	1	NA	promoter-TSS (NM_011409)	promoter-TSS (NM_011409)	3	NM_011409	20557	Mm.290922	NM_011409	ENSMUSG00000018986	Slfn3	-	schlafen 3	protein-coding
mm_40665.1	chr5	65386456	65386457	+	1	NA	Intergenic	B1F1|SINE|Alu	4975	NM_011292	20005	Mm.300271	NM_011292	ENSMUSG00000047215	Rpl9	-	ribosomal protein L9	protein-coding
mm_133011.1	chr16	56075509	56075518	+	1	NA	promoter-TSS (NM_001304503)	promoter-TSS (NM_001304503)	33	NM_001304503	66315	Mm.255784	NM_025483	ENSMUSG00000052917	Senp7	2410152H17Rik|2810413I22Rik|2900036C23Rik|6030449K19Rik|AI790676	SUMO1/sentrin specific peptidase 7	protein-coding
mm_152419.1	chr19	10673668	10673681	-	1	NA	exon (NM_021453, exon 5 of 9)	exon (NM_021453, exon 5 of 9)	4397	NM_021453	58803	Mm.34037	NM_021453	ENSMUSG00000024738	Pga5	1110035E17Rik|Pepf	pepsinogen 5, group I	protein-coding
mm_54541.1	chr6	36743372	36743400	-	1	NA	exon (NM_008973, exon 3 of 5)	exon (NM_008973, exon 3 of 5)	67975	NM_008973	19242	Mm.279690	NM_008973	ENSMUSG00000029838	Ptn	HARP|HB-GAM|HBBN|HBGF-8|HBNF|OSF|Osf-1|Osf1	pleiotrophin	protein-coding
mm_139555.1	chr17	56875499	56875507	+	1	NA	promoter-TSS (NM_030141)	promoter-TSS (NM_030141)	-130	NM_030141	78625	Mm.160106	NM_030141	ENSMUSG00000024209	1700061G19Rik	1700026H02|AI507598	RIKEN cDNA 1700061G19 gene	protein-coding
mm_76846.1	chr8	105296045	105296110	-	1	NA	promoter-TSS (NM_177788)	promoter-TSS (NM_177788)	21	NM_177788	277978	Mm.40228	NM_177788	ENSMUSG00000043251	Exoc3l	C730015A04Rik|Exoc3l1	exocyst complex component 3-like	protein-coding
mm_102003.1	chr11	51584642	51584687	-	1	NA	promoter-TSS (NM_028398)	promoter-TSS (NM_028398)	-93	NM_028398	72947	Mm.256875	NM_028398	ENSMUSG00000020359	Phykpl	2900006B13Rik|Agxt2l2	5-phosphohydroxy-L-lysine phospholyase	protein-coding
mm_3749.1	chr1	156005395	156005420	+	1	NA	3' UTR (NM_144791, exon 7 of 7)	3' UTR (NM_144791, exon 7 of 7)	29410	NM_001160019	208263	Mm.211654	NM_144791	ENSMUSG00000026466	Tor1aip1	LAP1|Lap1B	torsin A interacting protein 1	protein-coding
mm_127661.1	chr15	102518715	102518778	+	1	NA	intron (NM_001253795, intron 1 of 6)	intron (NM_001253795, intron 1 of 6)	554	NM_009319	21357	Mm.291485	NM_009319	ENSMUSG00000023051	Tarbp2	Prbp|TRBP	TARBP2, RISC loading complex RNA binding subunit	protein-coding
mm_112691.1	chr13	17310879	17310882	+	1	NA	intron (NM_138654, intron 10 of 13)	RMER15-int|LTR|ERVL	383885	NM_138654	192136	Mm.364180	NM_138654	ENSMUSG00000055137	Sugct	5033411D12Rik|D17907	succinyl-CoA glutarate-CoA transferase	protein-coding
mm_142675.1	chr17	47730751	47730763	-	1	NA	exon (NM_025973, exon 5 of 9)	exon (NM_025973, exon 5 of 9)	3915	NM_025973	109820	Mm.22957	NM_025973	ENSMUSG00000023987	Pgc	2210410L06Rik|Upg-1|Upg1	progastricsin (pepsinogen C)	protein-coding
mm_58237.1	chr6	145047531	145047554	-	1	NA	intron (NM_007532, intron 1 of 10)	intron (NM_007532, intron 1 of 10)	1270	NM_001024468	12035	Mm.4606	NM_007532	ENSMUSG00000030268	Bcat1	BCATc|Eca39	branched chain aminotransferase 1, cytosolic	protein-coding
mm_23531.1	chr3	60626910	60626927	+	1	NA	3' UTR (NM_001253711, exon 8 of 8)	3' UTR (NM_001253711, exon 8 of 8)	125739	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_59477.1	chr7	27459347	27459370	+	1	NA	exon (NM_144923, exon 2 of 5)	exon (NM_144923, exon 2 of 5)	6940	NM_001290525	233016	Mm.24021	NM_144923	ENSMUSG00000040466	Blvrb	-	biliverdin reductase B (flavin reductase (NADPH))	protein-coding
mm_109798.1	chr12	3309311	3309341	-	1	NA	exon (NM_016676, exon 1 of 6)	exon (NM_016676, exon 1 of 6)	643	NM_016676	19325	Mm.378993	NM_016676	ENSMUSG00000020671	Rab10	AW107754	RAB10, member RAS oncogene family	protein-coding
mm_109192.1	chr12	108554952	108554980	+	1	NA	5' UTR (NM_007965, exon 1 of 13)	5' UTR (NM_007965, exon 1 of 13)	246	NM_007965	14026	Mm.238841	NM_007965	ENSMUSG00000021262	Evl	AI528774	Ena-vasodilator stimulated phosphoprotein	protein-coding
mm_66968.1	chr7	62823739	62823747	-	1	NA	Intergenic	Intergenic	-359233	NM_013788	27412	Mm.422745	NM_013788	ENSMUSG00000070526	Peg12	Frat3	paternally expressed 12	protein-coding
mm_97130.1	chr11	74927727	74927731	+	1	NA	intron (NM_001002764, intron 1 of 18)	intron (NM_001002764, intron 1 of 18)	1857	NM_001002764	103677	Mm.288460	NM_001002764	ENSMUSG00000038290	Smg6	AI317223|AU041178	Smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans)	protein-coding
mm_81953.1	chr9	120555600	120555623	+	1	NA	intron (NM_178676, intron 4 of 10)	intron (NM_178676, intron 4 of 10)	15793	NM_178676	215446	Mm.76648	NM_178676	ENSMUSG00000041608	Entpd3	Cd39l3|HB6|NTPDase-3	ectonucleoside triphosphate diphosphohydrolase 3	protein-coding
mm_130778.1	chr15	101488296	101488313	-	1	NA	intron (NM_001201323, intron 3 of 8)	intron (NM_001201323, intron 3 of 8)	2999	NM_016879	53622	Mm.347934	NM_016879		Krt85	AA589597|BB007925|Hb5|Krt2-18	keratin 85	protein-coding
mm_69255.1	chr7	127875614	127875623	-	1	NA	intron (NM_146259, intron 1 of 2)	CpG	1205	NM_146259	244219	Mm.207872	NM_146259	ENSMUSG00000049728	Zfp668	BC030314|E130018B19Rik|Znf668	zinc finger protein 668	protein-coding
mm_122929.1	chr14	54961668	54961682	-	1	NA	intron (NM_001164171, intron 10 of 38)	intron (NM_001164171, intron 10 of 38)	4932	NM_001164171	17888	Mm.290003	NM_010856	ENSMUSG00000040752	Myh6	A830009F23Rik|AA517445|Myhc-a|Myhca|alpha-MHC	myosin, heavy polypeptide 6, cardiac muscle, alpha	protein-coding
mm_120068.1	chr14	56938559	56938563	+	1	NA	intron (NM_029498, intron 13 of 23)	intron (NM_029498, intron 13 of 23)	50766	NM_029498	76007	Mm.31417	NM_029498	ENSMUSG00000021945	Zmym2	5830413P05Rik|FIM|MYM|RAMP|SCLL|Zfp198|Znf198	zinc finger, MYM-type 2	protein-coding
mm_117620.1	chr13	91861311	91861313	-	1	NA	exon (NM_198415, exon 5 of 10)	exon (NM_198415, exon 5 of 10)	15573	NM_198415	76722	Mm.316438	NM_198415	ENSMUSG00000021622	Ckmt2	2300008A19Rik|ScCKmit	creatine kinase, mitochondrial 2	protein-coding
mm_49060.1	chr6	5390344	5390365	+	1	NA	intron (NM_023048, intron 1 of 5)	intron (NM_023048, intron 1 of 5)	6968	NM_023048	65255	Mm.51340	NM_023048	ENSMUSG00000042607	Asb4	8430401O13Rik|AV117194|AW060255	ankyrin repeat and SOCS box-containing 4	protein-coding
mm_42896.1	chr5	122404141	122404195	+	1	NA	exon (NM_019824, exon 5 of 7)	exon (NM_019824, exon 5 of 7)	12290	NM_019824	56378	Mm.275942	NM_019824	ENSMUSG00000029465	Arpc3	1110006A04Rik|p21-ARC|p21-Ar|p21Arc	actin related protein 2/3 complex, subunit 3	protein-coding
mm_49759.1	chr6	34773895	34773932	+	1	NA	3' UTR (NM_145575, exon 12 of 12)	3' UTR (NM_145575, exon 12 of 12)	-6519	NM_001289657	76223	Mm.150047	NM_178630	ENSMUSG00000038836	Agbl3	2900053G10Rik|4930431N21Rik|6530406M24Rik|CCP3	ATP/GTP binding protein-like 3	protein-coding
mm_121153.1	chr14	102515253	102515255	+	1	NA	Intergenic	Lx10|LINE|L1	467378	NR_039592	100628599		NR_039592	ENSMUSG00000092901	Mir5130	mir-5130|mmu-mir-5130|mu-mir-5130	microRNA 5130	ncRNA
mm_10832.1	chr2	24386639	24386652	+	1	NA	intron (NM_177611, intron 1 of 16)	intron (NM_177611, intron 1 of 16)	1248	NM_177611	215632	Mm.490434	NM_177611	ENSMUSG00000026979	Psd4	BC046518|EFA6B	pleckstrin and Sec7 domain containing 4	protein-coding
mm_117390.1	chr13	73347374	73347385	-	1	NA	promoter-TSS (NR_045293)	promoter-TSS (NR_045293)	5	NR_045293	432777	Mm.415319	NR_045293		D630045M09Rik	AU019512	RIKEN cDNA D630045M09 gene	ncRNA
mm_96005.1	chr11	59541579	59541591	+	1	NA	Intergenic	Intergenic	-1101	NM_145827	216799	Mm.54174	NM_145827	ENSMUSG00000032691	Nlrp3	AGTAVPRL|AII/AVP|Cias1|FCAS|FCU|MWS|Mmig1|NALP3|Pypaf1	NLR family, pyrin domain containing 3	protein-coding
mm_65580.1	chr7	27228503	27228517	-	1	NA	promoter-TSS (NM_181593)	promoter-TSS (NM_181593)	87	NM_181593	233011	Mm.30963	NM_181593	ENSMUSG00000003752	Itpkc	9130023N17Rik	inositol 1,4,5-trisphosphate 3-kinase C	protein-coding
mm_123624.1	chr14	68121320	68121334	-	1	NA	exon (NM_008691, exon 3 of 3)	exon (NM_008691, exon 3 of 3)	-2425	NR_045897	100043072	Mm.242832	NR_045897		A230070E04Rik	Gm4210	RIKEN cDNA A230070E04 gene	ncRNA
mm_109226.1	chr12	108793419	108793431	+	1	NA	exon (NM_009537, exon 1 of 5)	exon (NM_009537, exon 1 of 5)	114	NM_009537	22632	Mm.3868	NM_009537	ENSMUSG00000021264	Yy1	AW488674|NF-E1	YY1 transcription factor	protein-coding
mm_76214.1	chr8	83458353	83458365	-	1	NA	promoter-TSS (NM_001039137)	promoter-TSS (NM_001039137)	37	NM_001039137	56367	Mm.246911	NM_019708	ENSMUSG00000063253	Scoc	0610011C06Rik|2810002J11Rik|AA415030|SCOCO	short coiled-coil protein	protein-coding
mm_134873.1	chr16	28902594	28902615	-	1	NA	intron (NM_177718, intron 1 of 1)	intron (NM_177718, intron 1 of 1)	27094	NM_177718	239796	Mm.155887	NM_177718	ENSMUSG00000051065	Mb21d2	1600021P15Rik|A430031N04|C87006	Mab-21 domain containing 2	protein-coding
mm_64392.1	chr7	142489177	142489195	+	1	NA	intron (NM_001271508, intron 6 of 10)	intron (NM_001271508, intron 6 of 10)	-9650	NM_001347549	21957	Mm.389992	NM_011620	ENSMUSG00000061723	Tnnt3	fTnT	troponin T3, skeletal, fast	protein-coding
mm_31798.1	chr4	63979958	63979966	+	1	NA	intron (NM_011607, intron 15 of 25)	intron (NM_011607, intron 15 of 25)	67053	NM_011607	21923	Mm.980	NM_011607	ENSMUSG00000028364	Tnc	AI528729|C130033P17Rik|Hxb|TN|TN-C|Ten|cytotactin|tenascin-C	tenascin C	protein-coding
mm_94115.1	chr10	128626555	128626556	-	1	NA	promoter-TSS (NM_013765)	promoter-TSS (NM_013765)	-49	NM_013765	27370	Mm.32118	NM_013765	ENSMUSG00000025362	Rps26	-	ribosomal protein S26	protein-coding
mm_77764.1	chr9	3002479	3002500	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	36254	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_59711.1	chr7	28741976	28742013	+	1	NA	promoter-TSS (NM_023637)	promoter-TSS (NM_023637)	26	NM_023637	71984	Mm.333725	NM_023637	ENSMUSG00000070699	Sars2	2410015F05Rik|D7Ertd353e|SerRS|SerRSmt	seryl-aminoacyl-tRNA synthetase 2	protein-coding
mm_38946.1	chr4	150315519	150315561	-	1	NA	intron (NM_001085492, intron 1 of 22)	intron (NM_001085492, intron 1 of 22)	33624	NM_001085492	68703	Mm.291274	NM_001085492	ENSMUSG00000039852	Rere	1110033A15Rik|AI414665|ARG|ARP|ATN1L|AW742570|Atr2|DNB1|eye<m03Jus>|eyes3|mKIAA0458	arginine glutamic acid dipeptide (RE) repeats	protein-coding
mm_5575.1	chr1	39550035	39550038	-	1	NA	Intergenic	Intergenic	-1196	NR_028555	100217461		NR_028555	ENSMUSG00000077704	Snord89	MBII-289	small nucleolar RNA, C/D box 89	snoRNA
mm_170384.1	chr18	6030101	6030112	-	1	NA	intron (NM_029277, intron 14 of 17)	intron (NM_029277, intron 14 of 17)	105992	NM_029277	75415	Mm.239675	NM_029277	ENSMUSG00000041225	Arhgap12	2810011M08Rik	Rho GTPase activating protein 12	protein-coding
mm_124057.1	chr14	77875128	77875134	-	1	NA	promoter-TSS (NM_025384)	promoter-TSS (NM_025384)	-214	NM_025384	66148	Mm.248046	NM_025384	ENSMUSG00000022013	Dnajc15	1110003P16Rik|Dnajd1	DnaJ heat shock protein family (Hsp40) member C15	protein-coding
mm_22339.1	chr2	180711612	180711647	-	1	NA	promoter-TSS (NM_029607)	promoter-TSS (NM_029607)	-917	NM_029607	76425	Mm.41464	NM_029607	ENSMUSG00000027573	Gid8	2310003C23Rik|4833420G11Rik|AI451474|Twa1	GID complex subunit 8	protein-coding
mm_88345.1	chr10	75837468	75837476	+	1	NA	Intergenic	CpG	-2591	NM_010361	14872	Mm.24118	NM_010361	ENSMUSG00000033318	Gstt2	AI266894|Yrs|mGSTT2	glutathione S-transferase, theta 2	protein-coding
mm_87049.1	chr10	28808889	28808893	+	1	NA	intron (NM_001305663, intron 5 of 5)	intron (NM_001305663, intron 5 of 5)	114616	NR_033601	114676	Mm.390292	NR_033601		4930519F09Rik	-	pyruvate dehydrogenase E1 alpha 1 pseudogene	pseudo
mm_103806.1	chr11	82979976	82979979	-	1	NA	TTS (NM_172796)	TTS (NM_172796)	5088	NR_106144	102466846		NR_106144	ENSMUSG00000098840	Mir7679	Gm27908|mmu-mir-7679	microRNA 7679	ncRNA
mm_165238.1	chr2	62046599	62046611	+	1	NA	promoter-TSS (NM_001242379)	promoter-TSS (NM_001242379)	90	NM_033552	94229	Mm.314497	NM_033552	ENSMUSG00000026904	Slc4a10	NCBE|mKIAA4136	solute carrier family 4, sodium bicarbonate cotransporter-like, member 10	protein-coding
mm_167542.1	chr9	25263208	25263220	+	1	NA	intron (NM_001205367, intron 1 of 12)	L2|LINE|L2	10775	NM_001205367	235072	Mm.270259	NM_009859	ENSMUSG00000001833	Sept7	Cdc10|E430034N22	septin 7	protein-coding
mm_141157.1	chr17	26507629	26507659	-	1	NA	exon (NM_013642, exon 2 of 4)	exon (NM_013642, exon 2 of 4)	828	NM_013642	19252	Mm.239041	NM_013642	ENSMUSG00000024190	Dusp1	3CH134|MKP1|Ptpn16|U19515|erp|mkp-1	dual specificity phosphatase 1	protein-coding
mm_114146.1	chr13	55322884	55322898	+	1	NA	promoter-TSS (NM_009000)	promoter-TSS (NM_009000)	836	NM_025596	66494	Mm.439805	NM_025596	ENSMUSG00000021486	Prelid1	2610524G07Rik|Preli	PRELI domain containing 1	protein-coding
mm_154681.1	chrX	7922050	7922067	+	1	NA	exon (NM_013892, exon 2 of 3)	exon (NM_013892, exon 2 of 3)	2236	NM_013892	30052	Mm.4881	NM_013892	ENSMUSG00000039278	Pcsk1n	AI848336|KEP|PEN|PEN19|PEN20|Pan3|SAAS|SAASCT|bLEN|lLEN|proSAAS	proprotein convertase subtilisin/kexin type 1 inhibitor	protein-coding
mm_113267.1	chr13	28951645	28951648	+	1	NA	3' UTR (NM_009238, exon 1 of 1)	3' UTR (NM_009238, exon 1 of 1)	2036	NM_009238	20677	Mm.240627	NM_009238	ENSMUSG00000076431	Sox4	AA682046|Sox-4	SRY (sex determining region Y)-box 4	protein-coding
mm_30507.1	chr3	158024686	158024695	-	1	NA	intron (NM_001093752, intron 3 of 12)	intron (NM_001093752, intron 3 of 12)	7064	NM_001093753	69207	Mm.223946	NM_026989	ENSMUSG00000055436	Srsf11	0610009J05Rik|2610019N13Rik|BF642805|Sfrs11	serine/arginine-rich splicing factor 11	protein-coding
mm_167527.1	chr9	21288280	21288298	+	1	NA	promoter-TSS (NM_145416)	promoter-TSS (NM_145416)	-320	NM_145416	215194	Mm.290690	NM_145416	ENSMUSG00000035047	Kri1	-	KRI1 homolog	protein-coding
mm_149621.1	chr19	16955961	16955980	+	1	NA	promoter-TSS (NM_181348)	promoter-TSS (NM_181348)	-148	NM_181348	353211	Mm.257354	NM_181348	ENSMUSG00000039126	Prune2	6330414G02Rik|A230083H22Rik|A330102H22Rik|Bmcc1|mKIAA0367	prune homolog 2	protein-coding
mm_86037.1	chr9	114365662	114365686	-	1	NA	Intergenic	Intergenic	-1047	NR_040738	75100	Mm.78599	NR_040738		4930525D18Rik	-	RIKEN cDNA 4930525D18 gene	ncRNA
mm_166995.1	chr7	46715421	46715440	-	1	NA	intron (NM_011315, intron 1 of 3)	intron (NM_011315, intron 1 of 3)	246	NM_011315	20210	Mm.14277	NM_011315	ENSMUSG00000040026	Saa3	AV098916|Saa-3|l7R3	serum amyloid A 3	protein-coding
mm_104186.1	chr11	87797614	87797622	-	1	NA	exon (NM_010824, exon 8 of 14)	exon (NM_010824, exon 8 of 14)	3834	NM_010824	17523	Mm.4668	NM_010824	ENSMUSG00000009350	Mpo	mKIAA4033	myeloperoxidase	protein-coding
mm_15392.1	chr2	156721275	156721290	+	1	NA	promoter-TSS (NM_001042487)	promoter-TSS (NM_001042487)	3	NM_001042487	228836	Mm.22094	NM_146128	ENSMUSG00000061689	Dlgap4	AI225853|BC024558|DAP-4|DAP4|SAPAP-4|Sapap4|WBP16	discs, large homolog-associated protein 4 (Drosophila)	protein-coding
mm_156795.1	chrX	162901568	162901677	+	1	NA	promoter-TSS (NM_001168569)	promoter-TSS (NM_001168569)	27	NM_018737	55936	Mm.2065	NM_018737	ENSMUSG00000031360	Ctps2	A830031M15Rik|AI326475|Ctpsh	cytidine 5'-triphosphate synthase 2	protein-coding
mm_68879.1	chr7	126447643	126447651	-	1	NA	exon (NM_007504, exon 18 of 23)	exon (NM_007504, exon 18 of 23)	15426	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_95478.1	chr11	51238412	51238418	+	1	NA	Intergenic	Lx5c|LINE|L1	-17997	NR_110444	71297	Mm.390420	NR_110444	ENSMUSG00000086646	Platr20	5133400J02Rik	pluripotency associated transcript 20	ncRNA
mm_3773.1	chr1	156468884	156468932	+	1	NA	intron (NM_009230, intron 1 of 15)	intron (NM_009230, intron 1 of 15)	5420	NM_009230	20652	Mm.28099	NM_009230	ENSMUSG00000026600	Soat1	8430426K15Rik|ACAT-1|AW550831|Acact|ald|hid	sterol O-acyltransferase 1	protein-coding
mm_102926.1	chr11	69600659	69600671	-	1	NA	3' UTR (NM_013415, exon 7 of 7)	3' UTR (NM_013415, exon 7 of 7)	5295	NM_013415	11932	Mm.235204	NM_013415	ENSMUSG00000041329	Atp1b2	Amog|Atpb-2	ATPase, Na+/K+ transporting, beta 2 polypeptide	protein-coding
mm_25139.1	chr3	102513983	102513994	+	1	NA	exon (NM_013609, exon 3 of 4)	exon (NM_013609, exon 3 of 4)	44069	NM_013609	18049	Mm.1259	NM_013609	ENSMUSG00000027859	Ngf	Ngfb	nerve growth factor	protein-coding
mm_83716.1	chr9	50752548	50752558	-	1	NA	promoter-TSS (NM_001289784)	promoter-TSS (NM_001289784)	-199	NM_024441	69253	Mm.1980	NM_024441	ENSMUSG00000038086	Hspb2	27kDa|2810021G24Rik|HSP27|MKBP	heat shock protein 2	protein-coding
mm_13176.1	chr2	92952127	92952131	+	1	NA	intron (NM_030725, intron 5 of 5)	intron (NM_030725, intron 5 of 5)	37028	NM_030725	80976	Mm.33490	NM_030725	ENSMUSG00000027220	Syt13	5730409J20Rik|AI549909|mKIAA1427	synaptotagmin XIII	protein-coding
mm_169467.1	chr1	46649975	46649986	-	1	NA	intron (NM_001310335, intron 35 of 64)	RLTR9D|LTR|ERVK	203529	NM_172653	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|mKIAA1265	solute carrier family 39 (zinc transporter), member 10	protein-coding
mm_164164.1	chr15	73487885	73487894	+	1	NA	Intergenic	Intergenic	-24671	NM_001081066	105841	Mm.322557	NM_001081066	ENSMUSG00000036661	Dennd3	AI447457|E030003N15Rik	DENN/MADD domain containing 3	protein-coding
mm_162534.1	chr1	166003345	166003391	-	1	NA	promoter-TSS (NM_198932)	promoter-TSS (NM_198932)	-734	NM_011137	18986	Mm.245261	NM_011137	ENSMUSG00000026565	Pou2f1	2810482H01Rik|NF-A1|Oct-1|Oct1|Otf-1|Otf1	POU domain, class 2, transcription factor 1	protein-coding
mm_77212.1	chr8	114130997	114131010	-	1	NA	Intergenic	Intergenic	-2571	NM_024446	67528	Mm.27889	NM_024437	ENSMUSG00000031767	Nudt7	1300007B24Rik|2210404C19Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 7	protein-coding
mm_81056.1	chr9	106147943	106147955	+	1	NA	Intergenic	Intergenic	-6175	NR_029549	387153		NR_029549	ENSMUSG00000065407	Mir135a-1	Mir135a01|Mirn135|Mirn135a-1|mir-135a-1	microRNA 135a-1	ncRNA
mm_131747.1	chr16	22265559	22265565	+	1	NA	intron (NM_001330555, intron 1 of 9)	CpG	443	NM_001330554	20462	Mm.210352	NM_009186	ENSMUSG00000022858	Tra2b	5730405G21Rik|D16Ertd266e|SIG-41|Sfrs10|Silg41|TRA2beta	transformer 2 beta homolog (Drosophila)	protein-coding
mm_28084.1	chr3	84875519	84875529	-	1	NA	intron (NM_001177773, intron 3 of 13)	intron (NM_001177773, intron 3 of 13)	11379	NM_001177774	50754	Mm.196475	NM_080428	ENSMUSG00000028086	Fbxw7	1110001A17Rik|AGO|Cdc4|Fbw7|Fbwd6|Fbx30|Fbxo30|Fbxw6|SEL-10	F-box and WD-40 domain protein 7	protein-coding
mm_156339.1	chrX	139009937	139009941	+	1	NA	TTS (NM_013724)	TTS (NM_013724)	75297	NM_177920	331535	Mm.211704	NM_177920	ENSMUSG00000031271	Serpina7	C730040N12Rik|Tbg	serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 7	protein-coding
mm_78779.1	chr9	43804133	43804154	+	1	NA	3' UTR (NM_021424, exon 6 of 6)	3' UTR (NM_021424, exon 6 of 6)	59567	NM_021424	58235	Mm.335096	NM_021424	ENSMUSG00000032012	Nectin1	AI835281|AW549174|Cd111|HIgR|HveC|PRR|PRR1|Pvrl1|nectin-1	nectin cell adhesion molecule 1	protein-coding
mm_24646.1	chr3	94386918	94386928	+	1	NA	intron (NR_121656, intron 1 of 9)	intron (NR_121656, intron 1 of 9)	9491	NR_121656	19885	Mm.4372	NM_011281	ENSMUSG00000028150	Rorc	Nr1f3|RORgamma|TOR|Thor	RAR-related orphan receptor gamma	protein-coding
mm_41168.1	chr5	87969456	87969461	+	1	NA	intron (NR_045924, intron 1 of 4)	intron (NR_045924, intron 1 of 4)	9893	NR_045924	73471	Mm.396240	NR_045924	ENSMUSG00000099605	1700066N21Rik	-	RIKEN cDNA 1700066N21 gene	ncRNA
mm_53618.1	chr6	140424047	140424082	+	1	NA	promoter-TSS (NM_144920)	promoter-TSS (NM_144920)	-35	NM_144920	109135	Mm.247670	NM_144920	ENSMUSG00000030231	Plekha5	2810431N21Rik|AI428202|AK129423|AMH-Cre|Ayu21-9|Gt(pU21)9Imeg|Pepp2|Tg(AMH-cre)1Flor	pleckstrin homology domain containing, family A member 5	protein-coding
mm_67095.1	chr7	69756900	69756901	-	1	NA	Intergenic	Intergenic	260806	NR_045940	73796	Mm.410832	NR_045940	ENSMUSG00000108885	4930402F11Rik	-	RIKEN cDNA 4930402F11 gene	ncRNA
mm_2494.1	chr1	106002844	106002848	+	1	NA	intron (NM_001122676, intron 2 of 13)	intron (NM_001122676, intron 2 of 13)	12440	NM_001122675	227449	Mm.210188	NM_001122675	ENSMUSG00000038866	Zcchc2	9930114B20Rik|AW212015	zinc finger, CCHC domain containing 2	protein-coding
mm_7762.1	chr1	131138269	131138326	-	1	NA	promoter-TSS (NM_145508)	promoter-TSS (NM_145508)	-63	NM_145508	226419	Mm.39299	NM_145508	ENSMUSG00000016526	Dyrk3	BC006704	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 3	protein-coding
mm_21633.1	chr2	164278255	164278260	-	1	NA	promoter-TSS (NM_009300)	promoter-TSS (NM_009300)	50	NM_009300	20941	Mm.1286	NM_009300	ENSMUSG00000016998	Svs4	SVS-IV|Svp-2|Svp-4|Svp2|Svp4	seminal vesicle secretory protein 4	protein-coding
mm_82711.1	chr9	24503276	24503292	-	1	NA	promoter-TSS (NM_172920)	promoter-TSS (NM_172920)	-144	NM_172920	244745	Mm.38526	NM_172920	ENSMUSG00000043067	Dpy19l1	1100001I19Rik|6030402K12|AI225861|AW558481	dpy-19-like 1 (C. elegans)	protein-coding
mm_63848.1	chr7	135652539	135652549	+	1	NA	promoter-TSS (NR_015548)	promoter-TSS (NR_015548)	-230	NR_015548	67765	Mm.445272	NR_015548	ENSMUSG00000097471	5830432E09Rik	-	RIKEN cDNA 5830432E09 gene	ncRNA
mm_44354.1	chr5	17795602	17795608	-	1	NA	exon (NM_001159558, exon 12 of 16)	exon (NM_001159558, exon 12 of 16)	40291	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_6074.1	chr1	60974373	60974397	-	1	NA	Intergenic	Intergenic	-3529	NM_017480	54167	Mm.42044	NM_017480	ENSMUSG00000026009	Icos	AILIM|CCLP|CRP-1|H4|Ly115	inducible T cell co-stimulator	protein-coding
mm_171674.1	chr4	5006895	5006895	-	1	NA	Intergenic	L1_Mus3|LINE|L1	-213589	NM_177730	242291	Mm.218889	NM_177730	ENSMUSG00000066324	Impad1	1110001C20Rik|AA408880|AI451589|AL022796|B230207P20|Jaws|gPAPP	inositol monophosphatase domain containing 1	protein-coding
mm_74430.1	chr8	3717563	3717582	-	1	NA	intron (NM_029465, intron 6 of 8)	intron (NM_029465, intron 6 of 8)	3079	NM_029465	75863	Mm.109183	NM_029465	ENSMUSG00000074491	Clec4g	4930572L20Rik	C-type lectin domain family 4, member g	protein-coding
mm_103482.1	chr11	76495365	76495403	-	1	NA	promoter-TSS (NM_001346670)	promoter-TSS (NM_001346670)	-889	NM_001346670	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_133519.1	chr16	90830117	90830133	+	1	NA	promoter-TSS (NM_001316761)	promoter-TSS (NM_001316761)	-734	NR_133572	70967	Mm.253077	NM_027627	ENSMUSG00000039903	Eva1c	1700092M14Rik|4931408A02Rik|Fam176c	eva-1 homolog C (C. elegans)	protein-coding
mm_106823.1	chr12	7987741	7987782	+	1	NA	exon (NM_009693, exon 9 of 29)	exon (NM_009693, exon 9 of 29)	10084	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_26372.1	chr3	142560958	142560966	+	1	NA	intron (NM_001289492, intron 2 of 11)	intron (NM_001289492, intron 2 of 11)	466	NM_001289493	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_140468.1	chr17	93199163	93199173	+	1	NA	promoter-TSS (NM_009625)	promoter-TSS (NM_009625)	0	NM_001315504	11516	Mm.3407	NM_009625	ENSMUSG00000024256	Adcyap1	PACAP	adenylate cyclase activating polypeptide 1	protein-coding
mm_116756.1	chr13	52530690	52530807	-	1	NA	promoter-TSS (NM_001024474)	promoter-TSS (NM_001024474)	88	NM_001024474	68203	Mm.29362	NM_001024474	ENSMUSG00000047842	Diras2	2900052J15Rik|AI414999	DIRAS family, GTP-binding RAS-like 2	protein-coding
mm_30751.1	chr4	14929861	14929871	+	1	NA	promoter-TSS (NM_001243100)	promoter-TSS (NM_001243100)	-775	NM_001243100	100038514	Mm.331495	NM_001243100		Gm11837	OTTMUSG00000004551	predicted gene 11837	protein-coding
mm_158867.1	chrY	1197439	1197452	-	1	NA	intron (NM_009484, intron 5 of 26)	intron (NM_009484, intron 5 of 26)	48314	NM_001326683	22290	Mm.20477	NM_009484	ENSMUSG00000068457	Uty	Hydb|mKIAA4057	ubiquitously transcribed tetratricopeptide repeat gene, Y chromosome	protein-coding
mm_18145.1	chr2	45065265	45065285	-	1	NA	intron (NM_001289521, intron 1 of 8)	intron (NM_001289521, intron 1 of 8)	-42098	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_136154.1	chr16	87736901	87736926	-	1	NA	Intergenic	Intergenic	37959	NM_007520	12013	Mm.26147	NM_007520	ENSMUSG00000025612	Bach1	6230421P05Rik|AI323795	BTB and CNC homology 1, basic leucine zipper transcription factor 1	protein-coding
mm_74320.1	chr8	126848987	126849002	+	1	NA	Intergenic	Intergenic	96927	NM_024214	67952	Mm.6932	NM_024214	ENSMUSG00000093904	Tomm20	1810060K07Rik|BB284719|Gm19268|MAS20|MOM19|TOM20|mKIAA0016	translocase of outer mitochondrial membrane 20 homolog (yeast)	protein-coding
mm_76346.1	chr8	84727215	84727232	-	1	NA	exon (NM_010906, exon 5 of 9)	exon (NM_010906, exon 5 of 9)	25766	NM_008535	17095	Mm.4925	NM_008535	ENSMUSG00000034041	Lyl1	Lyl-1|bHLHa18	lymphoblastomic leukemia 1	protein-coding
mm_33346.1	chr4	129327185	129327189	+	1	NA	intron (NM_009030, intron 3 of 11)	intron (NM_009030, intron 3 of 11)	8183	NM_009030	19646	Mm.12145	NM_009030	ENSMUSG00000057236	Rbbp4	RBAP48|mRbAp48	retinoblastoma binding protein 4	protein-coding
mm_163823.1	chr14	19416804	19416866	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	185752	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_116918.1	chr13	55528446	55528449	-	1	NA	promoter-TSS (NM_013739)	promoter-TSS (NM_013739)	91	NM_013739	27261	Mm.33910	NM_013739	ENSMUSG00000035711	Dok3	AI450713|Dokl	docking protein 3	protein-coding
mm_24329.1	chr3	89459277	89459289	+	1	NA	promoter-TSS (NM_027348)	promoter-TSS (NM_027348)	165	NM_026784	68603	Mm.34242	NM_026784	ENSMUSG00000027952	Pmvk	1110011E12Rik|2900002L22Rik|AV001327|PMK|PMKA|PMKASE	phosphomevalonate kinase	protein-coding
mm_37091.1	chr4	116557048	116557057	-	1	NA	promoter-TSS (NM_029868)	promoter-TSS (NM_029868)	-675	NM_029868	77110	Mm.41715	NM_029868	ENSMUSG00000034042	Gpbp1l1	5330440M15Rik|BC002292	GC-rich promoter binding protein 1-like 1	protein-coding
mm_123835.1	chr14	70630150	70630185	-	1	NA	promoter-TSS (NM_013514)	promoter-TSS (NM_013514)	-13	NM_013514	13829	Mm.210863	NM_013514	ENSMUSG00000022099	Dmtn	AI325486|Epb4.9|Epb49|dematin	dematin actin binding protein	protein-coding
mm_31040.1	chr4	41067846	41067853	+	1	NA	Intergenic	RMER19C|LTR|ERVK	-19713	NM_007473	11832	Mm.8728	NM_007473	ENSMUSG00000028427	Aqp7	AQP7L|AQPap	aquaporin 7	protein-coding
mm_78424.1	chr9	31211335	31211367	+	1	NA	intron (NM_001102455, intron 1 of 16)	CpG	464	NM_001102455	11804	Mm.19133	NM_009691	ENSMUSG00000031996	Aplp2	AI790698|APLP-2	amyloid beta (A4) precursor-like protein 2	protein-coding
mm_61235.1	chr7	64754075	64754085	+	1	NA	TTS (NM_001291167)	TTS (NM_001291167)	118960	NM_023239	66647	Mm.19944	NM_023239	ENSMUSG00000070520	Ndnl2	5730494G16Rik|AI642138|BB044375|HCA4|Mageg1|Nsmce3|mage-g1	necdin-like 2	protein-coding
mm_119907.1	chr14	54950106	54950128	+	1	NA	promoter-TSS (NR_029724)	promoter-TSS (NR_029724)	-975	NR_029724	387204		NR_029724	ENSMUSG00000065432	Mir208a	Mirn208|Mirn208a|mir-208|mir-208a|mmu-mir-208	microRNA 208a	ncRNA
mm_162885.1	chr10	105574382	105574382	-	1	NA	promoter-TSS (NM_177368)	promoter-TSS (NM_177368)	97	NM_177368	278279	Mm.25225	NM_177368	ENSMUSG00000036019	Tmtc2	8430438D04Rik|D330034A10Rik	transmembrane and tetratricopeptide repeat containing 2	protein-coding
mm_141835.1	chr17	34637973	34637981	-	1	NA	Intergenic	Intergenic	-6906	NM_019873	56299	Mm.10025	NM_019873	ENSMUSG00000033739	Fkbpl	DIR1|NG7|Ppiase-X|Wisp39	FK506 binding protein-like	protein-coding
mm_23951.1	chr3	84869479	84869485	+	1	NA	intron (NM_001177773, intron 3 of 13)	MLT1-int|LTR|ERVL-MaLR	5337	NM_001177774	50754	Mm.196475	NM_080428	ENSMUSG00000028086	Fbxw7	1110001A17Rik|AGO|Cdc4|Fbw7|Fbwd6|Fbx30|Fbxo30|Fbxw6|SEL-10	F-box and WD-40 domain protein 7	protein-coding
mm_137892.1	chr17	31681144	31681152	+	1	NA	exon (NM_001278570, exon 3 of 3)	exon (NM_001278570, exon 3 of 3)	3217	NM_001278570	12954	Mm.1228	NM_013501	ENSMUSG00000024041	Cryaa	Acry-1|Crya-1|Crya1|DAcry-1|lop18	crystallin, alpha A	protein-coding
mm_111286.1	chr12	85394081	85394106	-	1	NA	Intergenic	Intergenic	-19376	NM_026775	68581	Mm.379159	NM_026775	ENSMUSG00000021248	Tmed10	1110014C03Rik|Tmp21|p23|p24delta1	transmembrane p24 trafficking protein 10	protein-coding
mm_98876.1	chr11	97801918	97801955	+	1	NA	intron (NM_010688, intron 1 of 6)	intron (NM_010688, intron 1 of 6)	2264	NM_010688	16796	Mm.271967	NM_010688	ENSMUSG00000038366	Lasp1	AA408629|Def-4|SH3P6|Tg(Col1a1-lacZ)1Ngma	LIM and SH3 protein 1	protein-coding
mm_111493.1	chr12	99162662	99162669	-	1	NA	non-coding (NR_038130, exon 1 of 2)	non-coding (NR_038130, exon 1 of 2)	143	NR_038130	67639	Mm.87374	NR_038130		4930474N09Rik	-	RIKEN cDNA 4930474N09 gene	ncRNA
mm_410.1	chr1	34215302	34215313	+	1	NA	intron (NM_001276764, intron 53 of 102)	intron (NM_001276764, intron 53 of 102)	54977	NM_010081	13518	Mm.336625	NM_010081	ENSMUSG00000026131	Dst	2310001O04Rik|A830042E19Rik|AW554249|BP230|BPAG1-n|Bpag|Bpag1|Macf2|ah|athetoid|dt|mKIAA0728|nmf203|nmf339	dystonin	protein-coding
mm_68326.1	chr7	106503978	106503988	-	1	NA	Intergenic	Intergenic	-62910	NR_003967	209380	Mm.461779	NM_001001318		Gm4759	EG209380	GTPase, very large interferon inducible 1 pseudogene	pseudo
mm_54485.1	chr6	35256799	35256815	-	1	NA	intron (NR_027875, intron 1 of 2)	B3A|SINE|B2	4075	NR_027875	67705	Mm.228046	NR_015608	ENSMUSG00000073155	1810058I24Rik	AI414869|AI848234	RIKEN cDNA 1810058I24 gene	ncRNA
mm_164031.1	chr14	77176920	77176920	+	1	NA	intron (NM_001253759, intron 1 of 19)	intron (NM_001253759, intron 1 of 19)	20157	NM_172813	239188	Mm.441158	NM_172813	ENSMUSG00000022012	Enox1	B230207J08|D230005D02Rik	ecto-NOX disulfide-thiol exchanger 1	protein-coding
mm_14671.1	chr2	139493977	139494015	+	1	NA	promoter-TSS (NM_175467)	promoter-TSS (NM_175467)	76	NM_175467	228677	Mm.100450	NM_175467	ENSMUSG00000039092	Sptlc3	C130053K05Rik	serine palmitoyltransferase, long chain base subunit 3	protein-coding
mm_171592.1	chr4	147642531	147642537	-	1	NA	promoter-TSS (NM_145078)	promoter-TSS (NM_145078)	-26	NM_145078	112422	Mm.327194	NM_145078	ENSMUSG00000066000	Zfp979	2610305D13Rik|Ssm1b	zinc finger protein 979	protein-coding
mm_12441.1	chr2	70843541	70843551	+	1	NA	Intergenic	RMER19C|LTR|ERVK	-18066	NM_172664	228012	Mm.136511	NM_172664	ENSMUSG00000041997	Tlk1	4930545J15Rik	tousled-like kinase 1	protein-coding
mm_102143.1	chr11	53618660	53618668	-	1	NA	promoter-TSS (NM_021283)	promoter-TSS (NM_021283)	1	NM_021283	16189	Mm.276360	NM_021283	ENSMUSG00000000869	Il4	BSF-1|Il-4	interleukin 4	protein-coding
mm_96381.1	chr11	67243260	67243289	+	1	NA	exon (NM_010855, exon 10 of 40)	exon (NM_010855, exon 10 of 40)	5462	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_29041.1	chr3	102936094	102936107	-	1	NA	promoter-TSS (NM_011516)	promoter-TSS (NM_011516)	0	NM_011516	20957	Mm.243849	NM_011516	ENSMUSG00000027855	Sycp1	SCP1	synaptonemal complex protein 1	protein-coding
mm_104518.1	chr11	96064998	96065029	-	1	NA	exon (NM_172300, exon 1 of 7)	exon (NM_172300, exon 1 of 7)	351	NM_172300	268470	Mm.38802	NM_172300	ENSMUSG00000014349	Ube2z	AW049199|C030047H17Rik|D11Moh35	ubiquitin-conjugating enzyme E2Z	protein-coding
mm_58307.1	chr6	146212914	146212922	-	1	NA	intron (NM_010586, intron 44 of 55)	(TG)n|Simple_repeat|Simple_repeat	278771	NM_010656	16651	Mm.49689	NM_010656	ENSMUSG00000030255	Sspn	Krag	sarcospan	protein-coding
mm_37454.1	chr4	123412003	123412017	-	1	NA	promoter-TSS (NM_001167918)	promoter-TSS (NM_001167918)	-99	NM_001167918	442834	Mm.483803	NM_001167918		D830031N03Rik	Kiaa0754|mKIAA0754	RIKEN cDNA D830031N03 gene	protein-coding
mm_39273.1	chr5	3803196	3803206	+	1	NA	promoter-TSS (NM_001003909)	promoter-TSS (NM_001003909)	20	NR_033173	79264	Mm.32368	NM_030675	ENSMUSG00000000600	Krit1	2010007K12Rik|A630036P20Rik|AA432855|AI450393|AI643869|BB155247|BB235701|Ccm1	KRIT1, ankyrin repeat containing	protein-coding
mm_38575.1	chr4	141817886	141817897	-	1	NA	exon (NM_007919, exon 7 of 8)	exon (NM_007919, exon 7 of 8)	8114	NM_007919	13706	Mm.45316	NM_007919	ENSMUSG00000058579	Cela2a	Ela-2|Ela2|Ela2a	chymotrypsin-like elastase family, member 2A	protein-coding
mm_131120.1	chr16	5393695	5393708	+	1	NA	Intergenic	Intergenic	-137745	NM_027446	70511	Mm.45780	NM_027446	ENSMUSG00000022544	Eef2kmt	5730409G15Rik|Fam86|Fam86a|eEF2-KMT	eukaryotic elongation factor 2 lysine methyltransferase	protein-coding
mm_163965.1	chr14	54966493	54966499	-	1	NA	intron (NM_001164171, intron 1 of 38)	intron (NM_001164171, intron 1 of 38)	111	NM_001164171	17888	Mm.290003	NM_010856	ENSMUSG00000040752	Myh6	A830009F23Rik|AA517445|Myhc-a|Myhca|alpha-MHC	myosin, heavy polypeptide 6, cardiac muscle, alpha	protein-coding
mm_5140.1	chr1	9736595	9736597	-	1	NA	intron (NM_173443, intron 2 of 2)	PB1|SINE|Alu	-11052	NR_040462	73331	Mm.460470	NR_040462		1700034P13Rik	-	RIKEN cDNA 1700034P13 gene	ncRNA
mm_36367.1	chr4	76435864	76435878	-	1	NA	intron (NM_011211, intron 10 of 39)	intron (NM_011211, intron 10 of 39)	-1157585	NM_025849	66928	Mm.24332	NM_025849	ENSMUSG00000028398	Tmem261	1700027K24Rik|3110001D03Rik	transmembrane protein 261	protein-coding
mm_49443.1	chr6	29319262	29319272	+	1	NA	exon (NM_001289664, exon 1 of 7)	exon (NM_001289664, exon 1 of 7)	127	NM_001289664	330277	Mm.87624	NM_207258	ENSMUSG00000039742	Fam71f1	GARI-L1|Gm764|NYD-SP18	family with sequence similarity 71, member F1	protein-coding
mm_153804.1	chr19	46044993	46045127	-	1	NA	5' UTR (NM_001113408, exon 1 of 11)	5' UTR (NM_001113408, exon 1 of 11)	151	NM_001113408	16825	Mm.327442	NM_010697	ENSMUSG00000025223	Ldb1	CLIM2|NLI	LIM domain binding 1	protein-coding
mm_68850.1	chr7	126369422	126369422	-	1	NA	TTS (NM_023712)	TTS (NM_023712)	146	NM_010689	16797	Mm.10280	NM_010689	ENSMUSG00000030742	Lat	p36-38|pp36	linker for activation of T cells	protein-coding
mm_42074.1	chr5	110110117	110110140	+	1	NA	promoter-TSS (NM_001163996)	promoter-TSS (NM_001163996)	36	NM_001163996	675812	Mm.442122	NM_001163996	ENSMUSG00000023284	Zfp605	A830023I12Rik	zinc finger protein 605	protein-coding
mm_25755.1	chr3	123429802	123429813	+	1	NA	Intergenic	Intergenic	-17106	NM_008939	19142	Mm.9431	NM_008939	ENSMUSG00000027978	Prss12	Bssp-3|motopsin	protease, serine 12 neurotrypsin (motopsin)	protein-coding
mm_101720.1	chr11	42182340	42182350	-	1	NA	5' UTR (NM_010250, exon 1 of 10)	5' UTR (NM_010250, exon 1 of 10)	585	NM_010250	14394	Mm.439668	NM_010250	ENSMUSG00000010803	Gabra1	Gabra-1	gamma-aminobutyric acid (GABA) A receptor, subunit alpha 1	protein-coding
mm_140442.1	chr17	88530253	88530273	+	1	NA	exon (NM_028658, exon 1 of 22)	exon (NM_028658, exon 1 of 22)	139	NM_028658	73825	Mm.271817	NM_028658	ENSMUSG00000034709	Ppp1r21	1110018J12Rik|AI426045|AW550781|Ccdc128|Klraq1	protein phosphatase 1, regulatory subunit 21	protein-coding
mm_62875.1	chr7	114745940	114745950	+	1	NA	5' UTR (NM_173767, exon 1 of 13)	5' UTR (NM_173767, exon 1 of 13)	179	NM_173767	233752	Mm.83037	NM_173767	ENSMUSG00000048782	Insc	3830422K02Rik|C730020D23	inscuteable homolog (Drosophila)	protein-coding
mm_58262.1	chr6	145267861	145267864	-	1	NA	Intergenic	Intergenic	17310	NR_045598	100039495	Mm.121014	NR_045598	ENSMUSG00000086013	Gm15706	OTTMUSG00000025463	predicted gene 15706	ncRNA
mm_35475.1	chr4	40846609	40846639	-	1	NA	intron (NM_022305, intron 1 of 5)	MTD|LTR|ERVL-MaLR	3514	NR_039584	100628614		NR_039584	ENSMUSG00000096377	Mir5123	mmu-mir-5123|mu-mir-5123	microRNA 5123	ncRNA
mm_137527.1	chr17	27398213	27398215	+	1	NA	Intergenic	Intergenic	40117	NR_106077	102466228		NR_106077	ENSMUSG00000106215	Mir7218	mmu-mir-7218	microRNA 7218	ncRNA
mm_4317.1	chr1	171848384	171848406	+	1	NA	intron (NM_001289470, intron 2 of 8)	intron (NM_001289470, intron 2 of 8)	8698	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_39705.1	chr5	27262201	27262210	+	1	NA	5' UTR (NM_001136060, exon 1 of 26)	5' UTR (NM_001136060, exon 1 of 26)	270	NM_001136060	13483	Mm.42078	NM_010075	ENSMUSG00000061576	Dpp6	B930011P16Rik|D5Buc3|D5Buc4|D5Buc5|DPP VI|Dpp-6|Gm1377|In(5)6H-p|Peplb|Rw	dipeptidylpeptidase 6	protein-coding
mm_1992.1	chr1	87125998	87126004	+	1	NA	exon (NM_007432, exon 5 of 11)	exon (NM_007432, exon 5 of 11)	993	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_126429.1	chr15	80572683	80572692	+	1	NA	promoter-TSS (NM_001289442)	promoter-TSS (NM_001289442)	90	NM_001289442	17444	Mm.12947	NM_010815	ENSMUSG00000042351	Grap2	GRAP-2|GRB2L|GRBLG|GRID|Gads|GrbX|Grf40|GrpL|Mona|P38	GRB2-related adaptor protein 2	protein-coding
mm_132075.1	chr16	30067020	30067030	+	1	NA	exon (NM_008235, exon 4 of 4)	exon (NM_008235, exon 4 of 4)	1668	NM_008235	15205	Mm.390859	NM_008235	ENSMUSG00000022528	Hes1	Hry|bHLHb39	hairy and enhancer of split 1 (Drosophila)	protein-coding
mm_143201.1	chr17	62780324	62780346	-	1	NA	intron (NM_010109, intron 1 of 3)	intron (NM_010109, intron 1 of 3)	100982	NM_207654	13640	Mm.7978	NM_010109	ENSMUSG00000048915	Efna5	AL-1|AV158822|EFL-5|Ephrin-A5|Epl7|LERK-7|RAGS	ephrin A5	protein-coding
mm_31758.1	chr4	63377107	63377142	+	1	NA	intron (NM_001305432, intron 13 of 20)	B3A|SINE|B2	14675	NM_011016	18406	Mm.14173	NM_011016	ENSMUSG00000061540	Orm2	Agp1|Orm-2	orosomucoid 2	protein-coding
mm_147016.1	chr18	34579042	34579052	-	1	NA	promoter-TSS (NM_080637)	promoter-TSS (NM_080637)	59	NM_080637	75533	Mm.275430	NM_080637	ENSMUSG00000035984	Nme5	1700019D05Rik|Nm23-M5	NME/NM23 family member 5	protein-coding
mm_121210.1	chr14	103054036	103054048	+	1	NA	intron (NM_008392, intron 4 of 4)	intron (NM_008392, intron 4 of 4)	7030	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_117113.1	chr13	60480363	60480371	-	1	NA	Intergenic	Intergenic	-121580	NM_001285917	69635	Mm.24103	NM_029653	ENSMUSG00000021559	Dapk1	D13Ucla1|DAP-Kinase	death associated protein kinase 1	protein-coding
mm_12538.1	chr2	72297802	72297831	+	1	NA	intron (NM_023057, intron 1 of 19)	intron (NM_023057, intron 1 of 19)	12115	NM_178084	65964	Mm.304143	NM_023057	ENSMUSG00000004085	Map3k20	AV006891|B230120H23Rik|MLTK|MLTKalpha|MLTKbeta|Zak	mitogen-activated protein kinase kinase kinase 20	protein-coding
mm_55497.1	chr6	69727149	69727163	-	1	NA	Intergenic	Intergenic	-399982	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_59948.1	chr7	30425721	30425726	+	1	NA	exon (NM_172142, exon 6 of 11)	exon (NM_172142, exon 6 of 11)	2419	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_128745.1	chr15	64382737	64382845	-	1	NA	5' UTR (NM_001276467, exon 1 of 30)	5' UTR (NM_001276467, exon 1 of 30)	128	NM_001276461	13196	Mm.277236	NM_010026	ENSMUSG00000022377	Asap1	AV239055|DEF-1|Ddef1|PAP|mKIAA1249|s19	ArfGAP with SH3 domain, ankyrin repeat and PH domain1	protein-coding
mm_117878.1	chr13	98926637	98926688	-	1	NA	promoter-TSS (NM_178716)	promoter-TSS (NM_178716)	-278	NM_178716	238799	Mm.173286	NM_178716	ENSMUSG00000009470	Tnpo1	AU021749|D13Ertd688e|IPO2|Kpnb2|MIP|MIP1|TRN	transportin 1	protein-coding
mm_115289.1	chr13	111958358	111958360	+	1	NA	Intergenic	B1F|SINE|Alu	90423	NR_130345	102636620	Mm.402328	NR_130345	ENSMUSG00000086111	Gm15326	OTTMUSG00000020187	predicted gene 15326	ncRNA
mm_129308.1	chr15	77584901	77584905	-	1	NA	3' UTR (NM_177820, exon 4 of 4)	3' UTR (NM_177820, exon 4 of 4)	11222	NM_177820	328561	Mm.379486	NM_177820	ENSMUSG00000050014	Apol10b	9130218O11Rik	apolipoprotein L 10B	protein-coding
mm_14220.1	chr2	127362812	127362818	+	1	NA	promoter-TSS (NM_009633)	promoter-TSS (NM_009633)	-471	NM_009633	11552	Mm.347390	NM_009633	ENSMUSG00000058620	Adra2b	Adra-2b|[a]2B|a2b-AR|alpha2-C2|alpha2B	adrenergic receptor, alpha 2b	protein-coding
mm_163273.1	chr11	115297502	115297508	-	1	NA	promoter-TSS (NM_178035)	promoter-TSS (NM_178035)	41	NM_178035	328035	Mm.21995	NM_178035	ENSMUSG00000044788	Fads6	BC044804|OTTMUSG00000021749	fatty acid desaturase domain family, member 6	protein-coding
mm_24623.1	chr3	93526055	93526090	+	1	NA	exon (NM_016740, exon 3 of 3)	exon (NM_016740, exon 3 of 3)	5576	NM_016740	20195	Mm.280038	NM_016740	ENSMUSG00000027907	S100a11	EMAPI|Emap1|S100a14|S100c|cal	S100 calcium binding protein A11	protein-coding
mm_150579.1	chr19	40640056	40640058	+	1	NA	intron (NM_001304721, intron 1 of 9)	intron (NM_001304721, intron 1 of 9)	-19713	NM_009848	12495	Mm.2824	NM_009848	ENSMUSG00000048120	Entpd1	2610206B08Rik|AA408691|Cd39|NTPDase-1	ectonucleoside triphosphate diphosphohydrolase 1	protein-coding
mm_99298.1	chr11	101338238	101338266	+	1	NA	3' UTR (NM_009675, exon 4 of 4)	3' UTR (NM_009675, exon 4 of 4)	7646	NM_009675	11754	Mm.67281	NM_009675	ENSMUSG00000019326	Aoc3	SSAO|VAP1	amine oxidase, copper containing 3	protein-coding
mm_78623.1	chr9	38718264	38718277	+	1	NA	promoter-TSS (NM_001145957)	promoter-TSS (NM_001145957)	2	NM_172767	67776	Mm.290950	NM_172767	ENSMUSG00000023186	Vwa5a	5830475I06Rik|AW552491|BCSC-1|E130119J22|Loh11cr2a	von Willebrand factor A domain containing 5A	protein-coding
mm_64846.1	chr7	13014283	13014301	-	1	NA	Intergenic	Intergenic	-4492	NM_001024699	232879	Mm.279272	NM_001024699	ENSMUSG00000049600	Zbtb45	BB161562|Gm157|Zfp499	zinc finger and BTB domain containing 45	protein-coding
mm_74017.1	chr8	121544379	121544387	+	1	NA	promoter-TSS (NR_045903)	promoter-TSS (NR_045903)	-5	NR_045903	72259	Mm.396206	NR_045903	ENSMUSG00000097424	1700030M09Rik	-	RIKEN cDNA 1700030M09 gene	ncRNA
mm_16009.1	chr2	167381853	167381898	+	1	NA	Intergenic	Intergenic	-32697	NM_019835	56336	Mm.200886	NM_019835	ENSMUSG00000017929	B4galt5	9430078I07Rik|AW049941|AW539721	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 5	protein-coding
mm_77234.1	chr8	115704734	115704768	-	1	NA	3' UTR (NM_001025577, exon 1 of 1)	3' UTR (NM_001025577, exon 1 of 1)	2143	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_64665.1	chr7	4397706	4397728	-	1	NA	promoter-TSS (NM_001163014)	promoter-TSS (NM_001163014)	27	NM_001163014	243816	Mm.248662	NM_001163014	ENSMUSG00000078810	Gp6	9830166G18Rik|Gm469|Gpvi	glycoprotein 6 (platelet)	protein-coding
mm_27483.1	chr3	53863765	53863830	-	1	NA	promoter-TSS (NM_026435)	promoter-TSS (NM_026435)	10	NM_026435	67890	Mm.23067	NM_026435	ENSMUSG00000027746	Ufm1	1810045K17Rik|AI132708|AI463323|ENSMUSG00000074598|Gm10726	ubiquitin-fold modifier 1	protein-coding
mm_6239.1	chr1	66945462	66945483	-	1	NA	promoter-TSS (NM_021285)	promoter-TSS (NM_021285)	-416	NM_021285	17901	Mm.1000	NM_021285	ENSMUSG00000061816	Myl1	AI325107|MLC1f|MLC3f|Mylf	myosin, light polypeptide 1	protein-coding
mm_57853.1	chr6	129472776	129472792	-	1	NA	promoter-TSS (NM_020008)	promoter-TSS (NM_020008)	-5	NR_132130	56644	Mm.239516	NM_020008	ENSMUSG00000079293	Clec7a	BGR|Clecsf12|beta-GR	C-type lectin domain family 7, member a	protein-coding
mm_65468.1	chr7	25476567	25476590	-	1	NA	exon (NM_001039186, exon 2 of 8)	exon (NM_001039186, exon 2 of 8)	1047	NM_001039185	26365	Mm.322502	NM_011926	ENSMUSG00000074272	Ceacam1	Bgp|Bgp1|C-CAM|CD66a|Cc1|Cea-1|Cea-7|Cea1|Cea7|Hv-2|Hv2|MHVR|MHVR1|Mhv-1|bb-1|mCEA1|mmCGM1|mmCGM1a|mmCGM2	carcinoembryonic antigen-related cell adhesion molecule 1	protein-coding
mm_80142.1	chr9	70779119	70779144	+	1	NA	3' UTR (NM_007399, exon 16 of 16)	3' UTR (NM_007399, exon 16 of 16)	100149	NM_007399	11487	Mm.3037	NM_007399	ENSMUSG00000054693	Adam10	1700031C13Rik|MADM|kuz|kuzbanian	a disintegrin and metallopeptidase domain 10	protein-coding
mm_5998.1	chr1	58804783	58804792	-	1	NA	intron (NM_001277926, intron 2 of 9)	intron (NM_001277926, intron 2 of 9)	2285	NM_001080126	12370	Mm.336851	NM_009812	ENSMUSG00000026029	Casp8	CASP-8|FLICE|MACH|Mch5	caspase 8	protein-coding
mm_125921.1	chr15	76199524	76199536	+	1	NA	promoter-TSS (NM_201392)	promoter-TSS (NM_201392)	-124	NM_201392	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
mm_119884.1	chr14	54897163	54897189	+	1	NA	exon (NM_019402, exon 6 of 7)	exon (NM_019402, exon 6 of 7)	3033	NM_019402	54196	Mm.7723	NM_019402	ENSMUSG00000022194	Pabpn1	PAB2|Pabp3|mPABII	poly(A) binding protein, nuclear 1	protein-coding
mm_91230.1	chr10	22301686	22301711	-	1	NA	intron (NM_009018, intron 5 of 5)	ORR1C1|LTR|ERVL-MaLR	-5022	NR_015465	606736	Mm.387042	NR_015465	ENSMUSG00000097352	C920009B18Rik	-	RIKEN cDNA C920009B18 gene	ncRNA
mm_170738.1	chr2	154285556	154285565	-	1	NA	Intergenic	Intergenic	-21684	NM_001025574	433492	Mm.330682	NM_001025574	ENSMUSG00000067996	Bpifb9b	5430413K10Rik|AI413838|OTTMUSG00000015915	BPI fold containing family B, member 9B	protein-coding
mm_50668.1	chr6	51537430	51537436	+	1	NA	intron (NM_001127349, intron 1 of 6)	B2_Mm2|SINE|B2	-7090	NM_028035	71982	Mm.294166	NM_028035	ENSMUSG00000038301	Snx10	2410004M09Rik	sorting nexin 10	protein-coding
mm_83098.1	chr9	40321313	40321317	-	1	NA	intron (NM_172768, intron 4 of 19)	intron (NM_172768, intron 4 of 19)	-12157	NR_040728	73558	Mm.398307	NR_040728		1700110K17Rik	-	RIKEN cDNA 1700110K17 gene	ncRNA
mm_161241.1	chr13	96519139	96519139	-	1	NA	promoter-TSS (NM_001347604)	promoter-TSS (NM_001347604)	48	NR_144623	27015	Mm.89926	NM_012048	ENSMUSG00000021668	Polk	DINP|Dinb1	polymerase (DNA directed), kappa	protein-coding
mm_69793.1	chr7	141117773	141117797	-	1	NA	promoter-TSS (NM_178381)	promoter-TSS (NM_178381)	21	NM_178381	71345	Mm.235813	NM_178381	ENSMUSG00000054662	Ano9	5430425C04Rik|Tmem16j|Tp53i5|Trp53i5	anoctamin 9	protein-coding
mm_130217.1	chr15	95772624	95772638	-	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-18212	NM_175344	105722	Mm.38087	NM_175344	ENSMUSG00000064210	Ano6	2900059G15Rik|AA407480|AW554778|F730003B03Rik|Tmem16f	anoctamin 6	protein-coding
mm_159207.1	chr2	121443073	121443073	-	1	NA	promoter-TSS (NM_145973)	promoter-TSS (NM_145973)	-472	NM_145973	269344	Mm.330522	NM_145973	ENSMUSG00000027246	Ell3	A930015D22Rik	elongation factor RNA polymerase II-like 3	protein-coding
mm_153772.1	chr19	45683526	45683546	-	1	NA	Intergenic	Intergenic	-23343	NM_013907	30838	Mm.254739	NM_013907	ENSMUSG00000040913	Fbxw4	Dac|Fbw4|SHFM3|SHSF3|dactylin|dactylyn	F-box and WD-40 domain protein 4	protein-coding
mm_76933.1	chr8	105938385	105938421	-	1	NA	promoter-TSS (NM_013640)	promoter-TSS (NM_013640)	-11	NM_013640	19171	Mm.787	NM_013640	ENSMUSG00000031897	Psmb10	Mecl-1|Mecl1	proteasome (prosome, macropain) subunit, beta type 10	protein-coding
mm_67613.1	chr7	83884263	83884286	-	1	NA	promoter-TSS (NM_030705)	promoter-TSS (NM_030705)	67	NM_030705	80889	Mm.272998	NM_030705	ENSMUSG00000070462	Mesdc1	AW061151	mesoderm development candidate 1	protein-coding
mm_90233.1	chr10	121376454	121376478	+	1	NA	intron (NM_029364, intron 4 of 13)	intron (NM_029364, intron 4 of 13)	11376	NM_029364	75612	Mm.207683	NM_029364	ENSMUSG00000034707	Gns	2610016K11Rik|AU042285|C87209|G6S|N28088	glucosamine (N-acetyl)-6-sulfatase	protein-coding
mm_38098.1	chr4	134245580	134245604	-	1	NA	promoter-TSS (NM_024215)	promoter-TSS (NM_024215)	-1	NM_024215	68040	Mm.300404	NM_024215	ENSMUSG00000028840	Zfp593	3110024A21Rik|AV062409|E130106C14Rik|ZNF593	zinc finger protein 593	protein-coding
mm_136391.1	chr16	93142193	93142254	-	1	NA	Intergenic	Intergenic	210966	NR_040486	69857	Mm.81192	NR_040486	ENSMUSG00000100277	1810053B23Rik	1810008L18Rik|1810056K14Rik	RIKEN cDNA 1810053B23 gene	ncRNA
mm_111567.1	chr12	101809854	101809865	-	1	NA	exon (NM_011812, exon 4 of 11)	exon (NM_011812, exon 4 of 11)	9260	NM_011812	23876	Mm.288381	NM_011812	ENSMUSG00000021186	Fbln5	A55|DANCE|EVEC	fibulin 5	protein-coding
mm_40120.1	chr5	34975245	34975256	+	1	NA	exon (NM_173402, exon 3 of 17)	exon (NM_173402, exon 3 of 17)	-23828	NM_001163512	71729	Mm.196208	NM_173402	ENSMUSG00000029101	Rgs12	1200016K18Rik|4632412M04Rik|AI481290|E130309H11	regulator of G-protein signaling 12	protein-coding
mm_18165.1	chr2	45102130	45102155	-	1	NA	intron (NM_001289521, intron 1 of 8)	(TG)n|Simple_repeat|Simple_repeat	8135	NM_001289521	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_139429.1	chr17	53567260	53567286	+	1	NA	5' UTR (NM_020005, exon 1 of 18)	5' UTR (NM_020005, exon 1 of 18)	302	NM_020005	18519	Mm.255025	NM_020005	ENSMUSG00000000708	Kat2b	A930006P13Rik|AI461839|AW536563|Pcaf|p/CAF	K(lysine) acetyltransferase 2B	protein-coding
mm_105418.1	chr11	103686838	103686848	-	1	NA	intron (NM_019650, intron 3 of 5)	intron (NM_019650, intron 3 of 5)	10867	NM_019650	56494	Mm.195451	NM_019650	ENSMUSG00000020946	Gosr2	2310032N09Rik|C76855|Gs27|SNARE|membrin	golgi SNAP receptor complex member 2	protein-coding
mm_24035.1	chr3	87650961	87650963	+	1	NA	intron (NM_001003912, intron 1 of 39)	intron (NM_001003912, intron 1 of 39)	32211	NM_001003912	213498	Mm.287267	NM_001003912	ENSMUSG00000041977	Arhgef11	B930073M02|E130307F09|PDZ-RhoGEF|Prg|RhoGEF|mKIAA0380	Rho guanine nucleotide exchange factor (GEF) 11	protein-coding
mm_64838.1	chr7	12998111	12998125	-	1	NA	promoter-TSS (NM_009512)	promoter-TSS (NM_009512)	74	NM_009512	26459	Mm.10984	NM_009512	ENSMUSG00000030382	Slc27a5	FACVL3|FATP5|VLCS-H2|VLCSH2|Vlacsr	solute carrier family 27 (fatty acid transporter), member 5	protein-coding
mm_108776.1	chr12	89812926	89812930	+	1	NA	5' UTR (NM_001252074, exon 1 of 7)	5' UTR (NM_001252074, exon 1 of 7)	445	NM_001252074	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding
mm_60798.1	chr7	45621784	45621796	+	1	NA	promoter-TSS (NM_001018013)	promoter-TSS (NM_001018013)	-21	NM_001018013	73456	Mm.380445	NM_001018013	ENSMUSG00000064158	Izumo1	1700058F15Rik|Izumo	izumo sperm-egg fusion 1	protein-coding
mm_40965.1	chr5	76995829	76995842	+	1	NA	exon (NM_025691, exon 16 of 19)	exon (NM_025691, exon 16 of 19)	-8220	NM_206935	384185	Mm.451858	NM_206935	ENSMUSG00000063820	Arl9	1700110A09Rik	ADP-ribosylation factor-like 9	protein-coding
mm_158561.1	chrX	150435511	150435541	-	1	NA	intron (NM_001164683, intron 1 of 2)	intron (NM_001164683, intron 1 of 2)	5379	NM_001164686	382245	Mm.277309	NM_001164683	ENSMUSG00000041353	Tmem29	2700081K05Rik|6330540D07Rik|CXorf44-like	transmembrane protein 29	protein-coding
mm_29017.1	chr3	101924197	101924215	-	1	NA	5' UTR (NM_001039371, exon 1 of 12)	5' UTR (NM_001039371, exon 1 of 12)	247	NM_001039371	242126	Mm.90204	NM_001039371	ENSMUSG00000033147	Slc22a15	2610034P21Rik|4930477M19|A530052I06Rik|BB219042	solute carrier family 22 (organic anion/cation transporter), member 15	protein-coding
mm_14936.1	chr2	151543670	151543711	+	1	NA	intron (NR_126058, intron 2 of 3)	intron (NR_126058, intron 2 of 3)	1207	NM_001302078	14225	Mm.278458	NM_008019	ENSMUSG00000032966	Fkbp1a	FKBP12|Fkbp|Fkbp1	FK506 binding protein 1a	protein-coding
mm_161741.1	chr17	33089317	33089317	+	1	NA	promoter-TSS (NM_001024950)	promoter-TSS (NM_001024950)	-50	NM_001024950	240068	Mm.121392	NM_001024950	ENSMUSG00000067424	Zfp563	D10628|D130054H01|NTfin7|Zfp413	zinc finger protein 563	protein-coding
mm_2178.1	chr1	88472385	88472388	+	1	NA	Intergenic	Intergenic	37680	NM_008132	14659	Mm.5187	NM_008132	ENSMUSG00000062310	Glrp1	GRP-1	glutamine repeat protein 1	protein-coding
mm_166975.1	chr7	44858066	44858074	-	1	NA	intron (NM_001290766, intron 1 of 14)	intron (NM_001290766, intron 1 of 14)	667	NM_001290767	59047	Mm.238254	NM_021549	ENSMUSG00000002963	Pnkp	1810009G08Rik|PNK	polynucleotide kinase 3'- phosphatase	protein-coding
mm_32339.1	chr4	104486538	104486539	+	1	NA	intron (NM_010014, intron 2 of 6)	T-rich|Low_complexity|Low_complexity	119000	NM_177259	13131	Mm.289682	NM_010014	ENSMUSG00000028519	Dab1	AI956902|C630028C02Rik|scm|scr|scrambler|yot	disabled 1	protein-coding
mm_31808.1	chr4	65605055	65605061	+	1	NA	promoter-TSS (NM_053084)	promoter-TSS (NM_053084)	72	NM_001161782	69807	Mm.22786	NM_053084	ENSMUSG00000051675	Trim32	1810045E12Rik|3f3|BBS11|Zfp117	tripartite motif-containing 32	protein-coding
mm_109765.1	chr12	118301621	118301648	+	1	NA	promoter-TSS (NM_009239)	promoter-TSS (NM_009239)	-194	NM_001166385	20688	Mm.34699	NM_009239	ENSMUSG00000025323	Sp4	5730497N03Rik|HF-1b|HF1-b	trans-acting transcription factor 4	protein-coding
mm_172391.1	chr7	139867451	139867462	-	1	NA	intron (NM_177469, intron 6 of 7)	MTD|LTR|ERVL-MaLR	-27240	NM_177261	76484	Mm.44442	NM_177261	ENSMUSG00000066129	Kndc1	2410012C07Rik|B830014K08Rik|VKIND|very-kind	kinase non-catalytic C-lobe domain (KIND) containing 1	protein-coding
mm_168285.1	chr11	100494221	100494223	-	1	NA	intron (NM_001199296, intron 17 of 28)	IAPLTR2a|LTR|ERVK	-15742	NR_130343	102465671		NR_130343	ENSMUSG00000104854	Mir7116	mmu-mir-7116	microRNA 7116	ncRNA
mm_107026.1	chr12	12993208	12993214	+	1	NA	Intergenic	Intergenic	-51375	NM_008709	18109	Mm.16469	NM_008709	ENSMUSG00000037169	Mycn	N-myc|Nmyc|Nmyc-1|Nmyc1|bHLHe37|c-nmyc	v-myc avian myelocytomatosis viral related oncogene, neuroblastoma derived	protein-coding
mm_152893.1	chr19	24862163	24862173	-	1	NA	promoter-TSS (NM_175013)	promoter-TSS (NM_175013)	-326	NM_175013	226041	Mm.105222	NM_175013	ENSMUSG00000041731	Pgm5	4833423B07|9530034F03Rik|D830025G17|aciculin	phosphoglucomutase 5	protein-coding
mm_111512.1	chr12	99627928	99627936	-	1	NA	promoter-TSS (NR_045288)	promoter-TSS (NR_045288)	42	NR_045288	73457	Mm.383439	NR_045288	ENSMUSG00000100211	1700064M15Rik	-	RIKEN cDNA 1700064M15 gene	ncRNA
mm_3125.1	chr1	134709294	134709318	+	1	NA	intron (NM_009307, intron 2 of 9)	CpG	62625	NM_009307	20980	Mm.5102	NM_009307	ENSMUSG00000026452	Syt2	IP4BP|R74640|mKIAA4194	synaptotagmin II	protein-coding
mm_71143.1	chr8	39119127	39119139	+	1	NA	intron (NM_030254, intron 6 of 7)	MTC|LTR|ERVL-MaLR	113266	NM_030254	80286	Mm.272722	NM_030254	ENSMUSG00000039530	Tusc3	AU022242|BC003311|N33	tumor suppressor candidate 3	protein-coding
mm_86858.1	chr10	21884173	21884175	+	1	NA	intron (NM_001161845, intron 1 of 13)	PB1|SINE|Alu	1990	NM_001161845	20393	Mm.28405	NM_011361	ENSMUSG00000019970	Sgk1	Sgk	serum/glucocorticoid regulated kinase 1	protein-coding
mm_18855.1	chr2	75677579	75677593	-	1	NA	exon (NM_010902, exon 4 of 5)	exon (NM_010902, exon 4 of 5)	18296	NR_033513	627828	Mm.459502	NR_033513	ENSMUSG00000092086	Gm6793	EG627828	heterogeneous nuclear ribonucleoprotein A3 pseudogene	pseudo
mm_111779.1	chr12	104194860	104194865	-	1	NA	Intergenic	Intergenic	-19682	NM_001168294	238393	Mm.483584	NM_001033335	ENSMUSG00000066363	Serpina3f	2A1|BC049975	serine (or cysteine) peptidase inhibitor, clade A, member 3F	protein-coding
mm_133391.1	chr16	84774230	84774238	+	1	NA	5' UTR (NM_023844, exon 1 of 10)	5' UTR (NM_023844, exon 1 of 10)	111	NM_023844	67374	Mm.41758	NM_023844	ENSMUSG00000053062	Jam2	1110002N23Rik|2410030G21Rik|2410167M24Rik|JAM-2|JAM-B|Jcam2|VE-JAM	junction adhesion molecule 2	protein-coding
mm_132511.1	chr16	37011759	37011791	+	1	NA	promoter-TSS (NM_001159369)	promoter-TSS (NM_001159369)	-11	NM_029977	77782	Mm.259114	NM_029977	ENSMUSG00000034206	Polq	A430110D14Rik	polymerase (DNA directed), theta	protein-coding
mm_143170.1	chr17	57226286	57226298	-	1	NA	exon (NM_009778, exon 3 of 41)	exon (NM_009778, exon 3 of 41)	1844	NM_009778	12266	Mm.19131	NM_009778	ENSMUSG00000024164	C3	AI255234|ASP|HSE-MSF|Plp	complement component 3	protein-coding
mm_164483.1	chr16	75909173	75909182	-	1	NA	promoter-TSS (NM_023380)	promoter-TSS (NM_023380)	89	NM_023380	67742	Mm.131406	NM_023380	ENSMUSG00000022876	Samsn1	4930571B16Rik|930571B16Rik|Hacs1|SLy2	SAM domain, SH3 domain and nuclear localization signals, 1	protein-coding
mm_39999.1	chr5	32637264	32637268	+	1	NA	intron (NM_009535, intron 1 of 11)	intron (NM_009535, intron 1 of 11)	26095	NM_009535	22612	Mm.4558	NM_009535	ENSMUSG00000014932	Yes1	Yes|p61-Yes	YES proto-oncogene 1, Src family tyrosine kinase	protein-coding
mm_63910.1	chr7	139214711	139214722	+	1	NA	5' UTR (NM_027164, exon 2 of 11)	5' UTR (NM_027164, exon 2 of 11)	-1409	NM_001162540	57740	Mm.65336	NM_021302	ENSMUSG00000015981	Stk32c	PKE|Pkek|YANK3	serine/threonine kinase 32C	protein-coding
mm_103460.1	chr11	76399064	76399072	-	1	NA	promoter-TSS (NM_008750)	promoter-TSS (NM_008750)	73	NM_008750	18230	Mm.27915	NM_008750	ENSMUSG00000020844	Nxn	l11Jus13	nucleoredoxin	protein-coding
mm_35202.1	chr4	19122537	19122555	-	1	NA	Intergenic	Intergenic	-158304	NM_013927	30952	Mm.445778	NM_013927	ENSMUSG00000056494	Cngb3	CCNC2|CNG6|Cngbeta2	cyclic nucleotide gated channel beta 3	protein-coding
mm_117226.1	chr13	64153150	64153189	-	1	NA	promoter-TSS (NM_175494)	promoter-TSS (NM_175494)	30	NM_175494	238673	Mm.300065	NM_175494	ENSMUSG00000044934	Zfp367	8030486J21Rik|ZFF29a|ZFF29b|Znf367	zinc finger protein 367	protein-coding
mm_89753.1	chr10	99267199	99267202	+	1	NA	3' UTR (NM_026268, exon 3 of 3)	3' UTR (NM_026268, exon 3 of 3)	3969	NM_026268	67603	Mm.1791	NM_026268	ENSMUSG00000019960	Dusp6	1300019I03Rik|MKP-3|MKP3|PYST1	dual specificity phosphatase 6	protein-coding
mm_84002.1	chr9	57552761	57552771	-	1	NA	promoter-TSS (NM_025837)	promoter-TSS (NM_025837)	-14	NM_025837	110119	Mm.247218	NM_025837	ENSMUSG00000032306	Mpi	1110002E17Rik|AI315153|Mpi-1|Mpi1	mannose phosphate isomerase	protein-coding
mm_55432.1	chr6	65779774	65779778	-	1	NA	intron (NM_029549, intron 1 of 10)	intron (NM_029549, intron 1 of 10)	814	NM_029549	70779	Mm.263355	NM_027547	ENSMUSG00000029913	Prdm5	4432417F03Rik|6530401I24Rik|AI197291|E130112L17Rik|PFM2	PR domain containing 5	protein-coding
mm_152984.1	chr19	29522193	29522216	-	1	NA	promoter-TSS (NM_001081319)	promoter-TSS (NM_001081319)	-78	NM_001081319	226089	Mm.353838	NM_177641	ENSMUSG00000038658	Ric1	C030046E11Rik|C130057E09Rik|Kiaa1432	RAB6A GEF complex partner 1	protein-coding
mm_94918.1	chr11	29482285	29482314	+	1	NA	exon (NM_176841, exon 20 of 32)	exon (NM_176841, exon 20 of 32)	32734	NM_026465	67939	Mm.251087	NM_026465	ENSMUSG00000032673	Prorsd1	2010316F05Rik|Ncrna00117|Prdxdd1	prolyl-tRNA synthetase domain containing 1	protein-coding
mm_60436.1	chr7	44476914	44476923	+	1	NA	Intergenic	L1MEd|LINE|L1	6571	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_24850.1	chr3	95736121	95736143	+	1	NA	exon (NM_007899, exon 8 of 11)	exon (NM_007899, exon 8 of 11)	-1159	NR_105981	102466787		NR_105981	ENSMUSG00000098737	Mir7014	Gm27837|mmu-mir-7014	microRNA 7014	ncRNA
mm_42962.1	chr5	123128620	123128634	+	1	NA	intron (NM_175092, intron 2 of 4)	intron (NM_175092, intron 2 of 4)	4002	NM_175092	23912	Mm.253876	NM_175092	ENSMUSG00000029449	Rhof	AI845056|AV026554|Arhf|Ifld1|Rif	ras homolog family member F (in filopodia)	protein-coding
mm_112478.1	chr13	5868873	5868898	+	1	NA	3' UTR (NM_011803, exon 4 of 4)	3' UTR (NM_011803, exon 4 of 4)	7396	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_73954.1	chr8	120335183	120335226	+	1	NA	Intergenic	Intergenic	-106974	NR_110496	434353	Mm.411793	NR_110496	ENSMUSG00000097960	A330074K22Rik	-	RIKEN cDNA A330074K22 gene	ncRNA
mm_155086.1	chrX	48108892	48108906	+	1	NA	5' UTR (NM_001289729, exon 1 of 21)	5' UTR (NM_001289729, exon 1 of 21)	174	NM_133213	170745	Mm.129279	NM_133213	ENSMUSG00000037005	Xpnpep2	9030008G12Rik|mAPP	X-prolyl aminopeptidase (aminopeptidase P) 2, membrane-bound	protein-coding
mm_164290.1	chr15	103861157	103861164	-	1	NA	intron (NM_009268, intron 2 of 4)	intron (NM_009268, intron 2 of 4)	38140	NM_009268	20771	Mm.30276	NM_009268		Mucl1	Spt-2|Spt2	mucin-like 1	protein-coding
mm_124396.1	chr14	111778222	111778229	-	1	NA	Intergenic	Lx6|LINE|L1	103110	NM_198865	75409	Mm.235097	NM_029273	ENSMUSG00000033214	Slitrk5	2610019D03Rik	SLIT and NTRK-like family, member 5	protein-coding
mm_26051.1	chr3	135689235	135689243	+	1	NA	intron (NM_008689, intron 1 of 24)	intron (NM_008689, intron 1 of 24)	2308	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_59842.1	chr7	29535031	29535063	+	1	NA	Intergenic	Intergenic	-29587	NM_001081028	74206	Mm.447042	NM_001081028	ENSMUSG00000030583	Sipa1l3	2610511M17Rik	signal-induced proliferation-associated 1 like 3	protein-coding
mm_157341.1	chrX	36902848	36902871	-	1	NA	promoter-TSS (NM_029891)	promoter-TSS (NM_029891)	40	NM_029891	77286	Mm.21649	NM_029891	ENSMUSG00000044149	Nkrf	9430034D17Rik|AW124770|C80287	NF-kappaB repressing factor	protein-coding
mm_65660.1	chr7	28139817	28139836	-	1	NA	exon (NM_001164655, exon 5 of 20)	exon (NM_001164655, exon 5 of 20)	10360	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_107469.1	chr12	37242066	37242098	+	1	NA	exon (NM_178767, exon 1 of 13)	exon (NM_178767, exon 1 of 13)	443	NM_178767	319660	Mm.485540	NM_178767	ENSMUSG00000050103	Agmo	A530016O06Rik|AI790538|Tmem195	alkylglycerol monooxygenase	protein-coding
mm_128287.1	chr15	37080400	37080408	-	1	NA	Intergenic	Intergenic	-73002	NM_026521	68036	Mm.371631	NM_026521	ENSMUSG00000062397	Zfp706	3110006P09Rik|AA793007|AW536850|C77232|Znf706	zinc finger protein 706	protein-coding
mm_145932.1	chr18	67205434	67205452	+	1	NA	promoter-TSS (NM_024190)	promoter-TSS (NM_024190)	84	NM_024190	67064	Mm.73777	NM_024190	ENSMUSG00000109901	Chmp1b	2810405I11Rik|Chmp1b1	charged multivesicular body protein 1B	protein-coding
mm_13351.1	chr2	103009584	103009628	+	1	NA	Intergenic	Intergenic	63907	NM_175094	27402	Mm.315011	NM_175094	ENSMUSG00000010914	Pdhx	AI481367|E3bp|Pdx1	pyruvate dehydrogenase complex, component X	protein-coding
mm_4476.1	chr1	173420568	173420622	+	1	NA	promoter-TSS (NM_001013779)	promoter-TSS (NM_001013779)	-9	NM_001013779	383619	Mm.131453	NM_001013779	ENSMUSG00000037860	Aim2	Gm1313|Ifi210	absent in melanoma 2	protein-coding
mm_12486.1	chr2	71530759	71530779	+	1	NA	non-coding (NR_002854, exon 2 of 2)	non-coding (NR_002854, exon 2 of 2)	1324	NM_010053	13390	Mm.475101	NM_010053	ENSMUSG00000041911	Dlx1	Dlx|Dlx-1	distal-less homeobox 1	protein-coding
mm_10084.1	chr2	3114200	3114206	+	1	NA	promoter-TSS (NM_001310434)	promoter-TSS (NM_001310434)	-21	NM_001310434	269233	Mm.23044	NM_001081161	ENSMUSG00000050530	Fam171a1	9630050M13Rik|AA409679	family with sequence similarity 171, member A1	protein-coding
mm_12358.1	chr2	69749729	69749742	+	1	NA	exon (NM_001081086, exon 14 of 14)	exon (NM_001081086, exon 14 of 14)	26647	NM_001081086	228005	Mm.11815	NM_001081086	ENSMUSG00000042133	Ppig	AU019516|AU022200|B230312B02Rik|CYP|SRCyp	peptidyl-prolyl isomerase G (cyclophilin G)	protein-coding
mm_151661.1	chr19	4139563	4139580	-	1	NA	promoter-TSS (NM_206973)	promoter-TSS (NM_206973)	38	NM_144532	73660	Mm.379226	NM_144532	ENSMUSG00000024842	Cabp4	2410038D05Rik	calcium binding protein 4	protein-coding
mm_162849.1	chr10	87456137	87456161	+	1	NA	Intergenic	Intergenic	37511	NM_008553	17172	Mm.136217	NM_008553	ENSMUSG00000020052	Ascl1	AI225900|ASH1|Mash1|bHLHa46	achaete-scute family bHLH transcription factor 1	protein-coding
mm_51093.1	chr6	67236768	67236775	+	1	NA	Intergenic	Intergenic	-30208	NM_001113564	66870	Mm.240490	NM_025814	ENSMUSG00000036371	Serbp1	1200009K13Rik|9330147J08Rik|AL022786|Pairbp1	serpine1 mRNA binding protein 1	protein-coding
mm_42546.1	chr5	116009324	116009330	+	1	NA	Intergenic	Intergenic	15101	NM_031869	19079	Mm.458152	NM_031869	ENSMUSG00000029513	Prkab1	1300015D22Rik|AU021155|E430008F22	protein kinase, AMP-activated, beta 1 non-catalytic subunit	protein-coding
mm_37732.1	chr4	129573600	129573629	-	1	NA	promoter-TSS (NM_001162433)	promoter-TSS (NM_001162433)	27	NM_001162433	16818	Mm.293753	NM_010693	ENSMUSG00000000409	Lck	Hck-3|Lsk|Lskt|p56<lck>|p56Lck	lymphocyte protein tyrosine kinase	protein-coding
mm_88189.1	chr10	70025688	70025700	+	1	NA	3' UTR (NM_170688, exon 43 of 43)	3' UTR (NM_170688, exon 43 of 43)	-71427	NM_001111121	76551	Mm.281741	NM_001111121	ENSMUSG00000048701	Ccdc6	2810012H18Rik|AA536681|AA960498|AW061011	coiled-coil domain containing 6	protein-coding
mm_172690.1	chr8	60056306	60056308	+	1	NA	Intergenic	Intergenic	230658	NR_126087	75017	Mm.60775	NR_126087	ENSMUSG00000110406	4930470O06Rik	-	RIKEN cDNA 4930470O06 gene	ncRNA
mm_41590.1	chr5	93268503	93268522	+	1	NA	intron (NM_007635, intron 1 of 7)	CpG	939	NM_007635	12452	Mm.3527	NM_007635	ENSMUSG00000029385	Ccng2	-	cyclin G2	protein-coding
mm_142031.1	chr17	35235736	35235742	-	1	NA	promoter-TSS (NM_010909)	promoter-TSS (NM_010909)	76	NM_010909	18038	Mm.300795	NM_010909	ENSMUSG00000042419	Nfkbil1	Def-7|IKBL	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor like 1	protein-coding
mm_170566.1	chr19	47092811	47092812	+	1	NA	exon (NM_011053, exon 2 of 36)	exon (NM_011053, exon 2 of 36)	2045	NM_011053	18572	Mm.41166	NM_011053	ENSMUSG00000025047	Pdcd11	1110021I22Rik|ALG-4|Pdcd7|mKIAA0185	programmed cell death 11	protein-coding
mm_87856.1	chr10	61175207	61175222	+	1	NA	promoter-TSS (NM_001017407)	promoter-TSS (NM_001017407)	-48	NM_001017409	65971	Mm.30227	NM_023064	ENSMUSG00000020096	Tbata	1700021K02Rik|AI428928|Spatial|Titest	thymus, brain and testes associated	protein-coding
mm_89268.1	chr10	87860167	87860179	+	1	NA	promoter-TSS (NM_001111276)	promoter-TSS (NM_001111276)	-938	NM_001111274	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_14514.1	chr2	132490698	132490707	+	1	NA	promoter-TSS (NR_028286)	promoter-TSS (NR_028286)	-26	NR_028286	70371	Mm.394667	NR_028286	ENSMUSG00000086379	1700026D11Rik	-	RIKEN cDNA 1700026D11 gene	ncRNA
mm_40429.1	chr5	53555796	53555819	+	1	NA	promoter-TSS (NM_001080928)	promoter-TSS (NM_001080928)	28	NM_001080928	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_42927.1	chr5	122820999	122821009	+	1	NA	exon (NM_021505, exon 1 of 17)	exon (NM_021505, exon 1 of 17)	338	NM_021505	59008	Mm.332667	NM_021505	ENSMUSG00000029472	Anapc5	2510006G12Rik|AA408751|AA536819|AA986414|APC5|Anpc5	anaphase-promoting complex subunit 5	protein-coding
mm_19265.1	chr2	84886440	84886441	-	1	NA	intron (NM_199223, intron 1 of 2)	CpG	252	NM_199223	269295	Mm.86447	NM_199223	ENSMUSG00000050896	Rtn4rl2	Ngr2|Ngrh1|Ngrl3	reticulon 4 receptor-like 2	protein-coding
mm_94855.1	chr11	24076530	24076563	+	1	NA	Intergenic	CpG	-1510	NM_016707	14025	Mm.53687	NM_016707	ENSMUSG00000000861	Bcl11a	2810047E18Rik|BCL-11A|Ctip1|D930021L15Rik|Evi9|Evi9a|Evi9b|Evi9c|mKIAA1809	B cell CLL/lymphoma 11A (zinc finger protein)	protein-coding
mm_5467.1	chr1	36547195	36547233	-	1	NA	promoter-TSS (NM_026241)	promoter-TSS (NM_026241)	38	NM_001310533	109346	Mm.247537	NM_026241	ENSMUSG00000079610	Ankrd39	9130416N05Rik|C030004B10Rik	ankyrin repeat domain 39	protein-coding
mm_47696.1	chr5	129779176	129779186	-	1	NA	5' UTR (NM_133900, exon 3 of 8)	5' UTR (NM_133900, exon 3 of 8)	8072	NM_133900	100678	Mm.271784	NM_133900	ENSMUSG00000029446	Psph	AI480570|PSP|PSPase	phosphoserine phosphatase	protein-coding
mm_150816.1	chr19	44401868	44401882	+	1	NA	exon (NM_009127, exon 4 of 6)	exon (NM_009127, exon 4 of 6)	5834	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_102526.1	chr11	60931827	60931853	-	1	NA	promoter-TSS (NR_027800)	promoter-TSS (NR_027800)	27	NR_027800	24082	Mm.46270	NM_025293	ENSMUSG00000042549	Map2k3os	F3-1|Gm16516|Gtlf3a	mitogen-activated protein kinase kinase 3, opposite strand	ncRNA
mm_20562.1	chr2	131079441	131079444	-	1	NA	exon (NM_011426, exon 8 of 21)	exon (NM_011426, exon 8 of 21)	7323	NM_011426	20612	Mm.1374	NM_011426	ENSMUSG00000027322	Siglec1	Cd169|Siglec-1|Sn	sialic acid binding Ig-like lectin 1, sialoadhesin	protein-coding
mm_24936.1	chr3	96560281	96560293	+	1	NA	exon (NM_023719, exon 7 of 8)	exon (NM_023719, exon 7 of 8)	2330	NM_023719	56338	Mm.410189	NM_023719	ENSMUSG00000038393	Txnip	1200008J08Rik|AA682105|Hyplip1|THIF|Tbp-2|VDUP1	thioredoxin interacting protein	protein-coding
mm_169535.1	chr1	4947298	4947301	+	1	NA	intron (NM_001177795, intron 2 of 5)	L1Md_F3|LINE|L1	71435	NM_001290372	58175	Mm.103771	NM_021374	ENSMUSG00000002459	Rgs20	2900073E09Rik|Rgsz1	regulator of G-protein signaling 20	protein-coding
mm_35945.1	chr4	53112526	53112559	-	1	NA	intron (NM_013454, intron 5 of 49)	B1_Mus2|SINE|Alu	47353	NM_013454	11303	Mm.277376	NM_013454	ENSMUSG00000015243	Abca1	ABC-1|Abc1	ATP-binding cassette, sub-family A (ABC1), member 1	protein-coding
mm_11897.1	chr2	49890358	49890361	+	1	NA	intron (NM_027990, intron 3 of 9)	intron (NM_027990, intron 3 of 9)	102673	NM_027990	71897	Mm.41381	NM_027990	ENSMUSG00000026765	Lypd6b	2310010M24Rik|AW049525	LY6/PLAUR domain containing 6B	protein-coding
mm_159927.1	chr6	58596628	58596628	+	1	NA	promoter-TSS (NM_011920)	promoter-TSS (NM_011920)	-44	NM_011920	26357	Mm.333096	NM_011920	ENSMUSG00000029802	Abcg2	ABC15|ABCP|AI428558|BCRP|Bcrp1|MXR|MXR1	ATP-binding cassette, sub-family G (WHITE), member 2	protein-coding
mm_127288.1	chr15	100038748	100038808	+	1	NA	5' UTR (NM_001159361, exon 1 of 38)	5' UTR (NM_001159361, exon 1 of 38)	114	NM_001159361	239667	Mm.243658	NM_172819	ENSMUSG00000023026	Dip2b	4932422C22|AI317237|AI854602|mKIAA1463	disco interacting protein 2 homolog B	protein-coding
mm_89379.1	chr10	88886016	88886031	+	1	NA	promoter-TSS (NM_145423)	promoter-TSS (NM_145423)	31	NM_145423	216225	Mm.77381	NM_145423	ENSMUSG00000020062	Slc5a8	Ait|SMCT	solute carrier family 5 (iodide transporter), member 8	protein-coding
mm_145148.1	chr18	46176592	46176594	+	1	NA	intron (NM_178872, intron 5 of 9)	intron (NM_178872, intron 5 of 9)	22225	NM_001170855	28105	Mm.277382	NM_178872	ENSMUSG00000033949	Trim36	D18Wsu100e|haprin	tripartite motif-containing 36	protein-coding
mm_17001.1	chr2	18392722	18392726	-	1	NA	5' UTR (NM_001190817, exon 1 of 13)	5' UTR (NM_001190817, exon 1 of 13)	106	NM_001190817	13418	Mm.246674	NM_007869	ENSMUSG00000026740	Dnajc1	4733401K02Rik|AA960110|D230036H06Rik|Dnajl1|ERdj1|ERj1p|MTJ1	DnaJ heat shock protein family (Hsp40) member C1	protein-coding
mm_128815.1	chr15	67105137	67105178	-	1	NA	3' UTR (NM_009177, exon 9 of 9)	3' UTR (NM_009177, exon 9 of 9)	71725	NM_009177	20442	Mm.248334	NM_009177	ENSMUSG00000013846	St3gal1	5330418N22Rik|AI467004|ST3GalI|Siat4|Siat4a|St3gal-1	ST3 beta-galactoside alpha-2,3-sialyltransferase 1	protein-coding
mm_142914.1	chr17	53539467	53539467	-	1	NA	promoter-TSS (NM_173449)	promoter-TSS (NM_173449)	-16	NM_173449	110332	Mm.444633	NM_173449	ENSMUSG00000044957	Pp2d1	4921523A10Rik	protein phosphatase 2C-like domain containing 1	protein-coding
mm_135704.1	chr16	52468758	52468774	-	1	NA	Intergenic	Intergenic	-15685	NM_001331110	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_144203.1	chr18	9487588	9487595	+	1	NA	Intergenic	Intergenic	-37441	NM_026484	67974	Mm.86523	NM_026484	ENSMUSG00000024286	Ccny	1700025H17Rik|3110050L10Rik|4631402G10Rik|5730405I09Rik	cyclin Y	protein-coding
mm_23759.1	chr3	70007685	70007694	+	1	NA	promoter-TSS (NM_001018031)	promoter-TSS (NM_001018031)	76	NM_001018031	229389	Mm.331071	NM_001018031	ENSMUSG00000027788	Otol1	Gm414	otolin 1	protein-coding
mm_57655.1	chr6	128485645	128485667	-	1	NA	exon (NM_007376, exon 34 of 36)	exon (NM_007376, exon 34 of 36)	41064	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_71659.1	chr8	60524319	60524324	+	1	NA	intron (NM_011834, intron 4 of 12)	L1VL4|LINE|L1	18197	NM_011834	23923	Mm.35020	NM_011834	ENSMUSG00000057228	Aadat	AI875679|Aadt|KATII|Kat2|Kyat2|mKat-2	aminoadipate aminotransferase	protein-coding
mm_151592.1	chr19	3388653	3388665	-	1	NA	promoter-TSS (NM_001286558)	promoter-TSS (NM_001286558)	-198	NM_001039658	17771	Mm.209941	NM_010841	ENSMUSG00000024905	Mtl5	tesmin	metallothionein-like 5, testis-specific (tesmin)	protein-coding
mm_110404.1	chr12	45074295	45074306	-	1	NA	5' UTR (NM_144552, exon 1 of 6)	5' UTR (NM_144552, exon 1 of 6)	183	NM_144552	217517	Mm.285400	NM_144552	ENSMUSG00000046314	Stxbp6	BC024598|C85317	syntaxin binding protein 6 (amisyn)	protein-coding
mm_172720.1	chr8	71742019	71742022	+	1	NA	Intergenic	Intergenic	-16339	NM_028715	74015	Mm.22025	NM_028715	ENSMUSG00000070000	Fcho1	3322402E17Rik|N28152	FCH domain only 1	protein-coding
mm_96017.1	chr11	59543015	59543031	+	1	NA	intron (NM_145827, intron 1 of 9)	intron (NM_145827, intron 1 of 9)	337	NM_145827	216799	Mm.54174	NM_145827	ENSMUSG00000032691	Nlrp3	AGTAVPRL|AII/AVP|Cias1|FCAS|FCU|MWS|Mmig1|NALP3|Pypaf1	NLR family, pyrin domain containing 3	protein-coding
mm_169299.1	chr14	101670440	101670457	-	1	NA	intron (NM_016723, intron 6 of 8)	BGLII|LTR|ERVK	16481	NM_016723	50933	Mm.275970	NM_016723	ENSMUSG00000022111	Uchl3	-	ubiquitin carboxyl-terminal esterase L3 (ubiquitin thiolesterase)	protein-coding
mm_44990.1	chr5	37824581	37824584	-	1	NA	promoter-TSS (NM_010835)	promoter-TSS (NM_010835)	3	NM_010835	17701	Mm.256509	NM_010835	ENSMUSG00000048450	Msx1	AA675338|AI324650|Hox-7|Hox7|Hox7.1|msh	msh homeobox 1	protein-coding
mm_38857.1	chr4	149426263	149426271	-	1	NA	5' UTR (NM_022022, exon 1 of 27)	5' UTR (NM_022022, exon 1 of 27)	364	NM_022022	63958	Mm.415260	NM_022022	ENSMUSG00000028960	Ube4b	4930551I19Rik|4933406G05Rik|AU014668|D4Bwg0973e|UFD2|UFD2a|Ufd2p|mKIAA0684	ubiquitination factor E4B	protein-coding
mm_116241.1	chr13	33905721	33905731	-	1	NA	promoter-TSS (NM_148942)	promoter-TSS (NM_148942)	-18	NM_148942	97848	Mm.272188	NM_148942	ENSMUSG00000052180	Serpinb6c	C76171|C76174|SPI3C|SPIC|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 6c	protein-coding
mm_52927.1	chr6	122922745	122922756	+	1	NA	intron (NM_199311, intron 1 of 5)	intron (NM_199311, intron 1 of 5)	902	NM_199311	269799	Mm.297275	NM_199311	ENSMUSG00000049037	Clec4a1	BC049354|Dcir4	C-type lectin domain family 4, member a1	protein-coding
mm_46055.1	chr5	92140966	92140977	-	1	NA	intron (NM_019490, intron 1 of 23)	intron (NM_019490, intron 1 of 23)	3033	NM_019490	56041	Mm.15868	NM_019490	ENSMUSG00000029407	Uso1	115kDa|TAP|Vdp	USO1 vesicle docking factor	protein-coding
mm_125877.1	chr15	75632277	75632306	+	1	NA	Intergenic	Intergenic	15607	NM_011759	22701	Mm.87210	NM_011759	ENSMUSG00000047003	Zfp41	CTfin92|Zfp-41	zinc finger protein 41	protein-coding
mm_23390.1	chr3	57425646	57425660	+	1	NA	exon (NM_145539, exon 1 of 5)	exon (NM_145539, exon 1 of 5)	243	NM_145539	229302	Mm.26618	NM_145539	ENSMUSG00000027801	Tm4sf4	Iltmp	transmembrane 4 superfamily member 4	protein-coding
mm_58292.1	chr6	145864888	145864891	-	1	NA	intron (NM_024469, intron 2 of 4)	intron (NM_024469, intron 2 of 4)	531	NM_001271768	79362	Mm.154529	NM_024469	ENSMUSG00000030256	Bhlhe41	6430520M22Rik|Bhlhb2l|Bhlhb3|DEC2|Sharp1	basic helix-loop-helix family, member e41	protein-coding
mm_15795.1	chr2	164443371	164443405	+	1	NA	promoter-TSS (NM_011521)	promoter-TSS (NM_011521)	-200	NM_011521	20971	Mm.3815	NM_011521	ENSMUSG00000017009	Sdc4	AA959608|AW108331|S4|Synd4|ryudocan|syndecan-4	syndecan 4	protein-coding
mm_100429.1	chr11	119456941	119456951	+	1	NA	Intergenic	B3A|SINE|B2	-34401	NM_001164636	338371	Mm.271946	NM_177394	ENSMUSG00000039850	Endov	A730011L01Rik	endonuclease V	protein-coding
mm_90674.1	chr10	128900965	128900975	+	1	NA	Intergenic	Intergenic	-7949	NM_001042580	12512	Mm.371552	NM_007653	ENSMUSG00000025351	Cd63	C75951|ME491|Tspan30	CD63 antigen	protein-coding
mm_164963.1	chr19	5992088	5992105	-	1	NA	intron (NM_001110504, intron 17 of 21)	intron (NM_001110504, intron 17 of 21)	-5953	NM_198650	381203	Mm.329638	NM_198650	ENSMUSG00000037451	Slc22a20	Gm963|OAT1-L|mOAT6	solute carrier family 22 (organic anion transporter), member 20	protein-coding
mm_151443.1	chr19	57477544	57477558	+	1	NA	intron (NM_028115, intron 4 of 7)	intron (NM_028115, intron 4 of 7)	24645	NM_028115	72133	Mm.258404	NM_028115	ENSMUSG00000025086	Trub1	2610009I02Rik|9030425C13Rik|AI448235|BB118943|C76870	TruB pseudouridine (psi) synthase family member 1	protein-coding
mm_46549.1	chr5	106574707	106574727	-	1	NA	Intergenic	CpG	-116551	NM_001005477	104382	Mm.271593	NM_001005477	ENSMUSG00000034384	Barhl2	E130309B19Rik|MBH1	BarH-like 2 (Drosophila)	protein-coding
mm_149664.1	chr19	18732741	18732743	+	1	NA	Intergenic	U1|snRNA|snRNA	-17241	NM_153417	225997	Mm.215171	NM_153417	ENSMUSG00000024727	Trpm6	CHAK2|TRPM6/CHAK2	transient receptor potential cation channel, subfamily M, member 6	protein-coding
mm_145024.1	chr18	38993274	38993286	+	1	NA	5' UTR (NM_175164, exon 1 of 23)	5' UTR (NM_175164, exon 1 of 23)	135	NM_175164	71302	Mm.329396	NM_175164	ENSMUSG00000036452	Arhgap26	1810044B20Rik|2610010G17Rik|4933432P15Rik|AI853435|mKIAA0621	Rho GTPase activating protein 26	protein-coding
mm_136772.1	chr17	9864602	9864628	+	1	NA	Intergenic	Intergenic	-88749	NR_045433	71092	Mm.243827	NR_045433		4930452A19Rik	4933424P20Rik	RIKEN cDNA 4930452A19 gene	ncRNA
mm_47036.1	chr5	116021685	116021696	-	1	NA	intron (NM_031869, intron 1 of 6)	intron (NM_031869, intron 1 of 6)	2738	NM_031869	19079	Mm.458152	NM_031869	ENSMUSG00000029513	Prkab1	1300015D22Rik|AU021155|E430008F22	protein kinase, AMP-activated, beta 1 non-catalytic subunit	protein-coding
mm_62245.1	chr7	98895929	98895933	+	1	NA	intron (NM_178635, intron 14 of 14)	intron (NM_178635, intron 14 of 14)	57086	NM_001285795	22411	Mm.22182	NM_009519	ENSMUSG00000015957	Wnt11	-	wingless-type MMTV integration site family, member 11	protein-coding
mm_67409.1	chr7	80075266	80075268	-	1	NA	promoter-TSS (NR_045695)	promoter-TSS (NR_045695)	-10	NR_045695	100859962	Mm.392575	NR_045695	ENSMUSG00000108714	Gm21057	-	predicted gene, 21057	ncRNA
mm_86730.1	chr10	19065506	19065510	+	1	NA	Intergenic	Intergenic	-50098	NM_009397	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_161564.1	chr16	18498823	18498823	+	1	NA	promoter-TSS (NM_001285494)	promoter-TSS (NM_001285494)	-48	NM_001285494	13972	Mm.236139	NM_023120	ENSMUSG00000000884	Gnb1l	ESTM55|Gm16314|Me49f07|OTTMUSG00000033458|Wdr14|Wdvcf	guanine nucleotide binding protein (G protein), beta polypeptide 1-like	protein-coding
mm_123241.1	chr14	60197174	60197185	-	1	NA	Intergenic	Intergenic	31736	NR_030458	751526		NR_030458	ENSMUSG00000076270	Mir719	Mirn719|mmu-mir-719	microRNA 719	ncRNA
mm_6129.1	chr1	64532421	64532439	-	1	NA	promoter-TSS (NM_009952)	promoter-TSS (NM_009952)	-374	NM_133828	12912	Mm.422634	NM_009952	ENSMUSG00000025958	Creb1	2310001E10Rik|3526402H21Rik|AV083133|Creb|Creb-1	cAMP responsive element binding protein 1	protein-coding
mm_16705.1	chr2	7081234	7081248	-	1	NA	promoter-TSS (NM_001160292)	promoter-TSS (NM_001160292)	61	NM_001110230	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_76298.1	chr8	84223446	84223462	-	1	NA	intron (NM_172503, intron 9 of 13)	intron (NM_172503, intron 9 of 13)	13588	NM_172503	212168	Mm.117094	NM_172503	ENSMUSG00000035671	Zswim4	D330002I24|E130119J17Rik	zinc finger SWIM-type containing 4	protein-coding
mm_153976.1	chr19	47864438	47864462	-	1	NA	exon (NM_010362, exon 6 of 6)	exon (NM_010362, exon 6 of 6)	-1095	NM_030051	68214	Mm.63791	NM_026619	ENSMUSG00000025069	Gsto2	1700020F09Rik|4930425C18Rik|GSTO 2-2	glutathione S-transferase omega 2	protein-coding
mm_146500.1	chr18	3281753	3281778	-	1	NA	promoter-TSS (NM_001110855)	promoter-TSS (NM_001110855)	-18	NM_001110855	12916	Mm.5244	NM_013498	ENSMUSG00000063889	Crem	ICER|ICERI	cAMP responsive element modulator	protein-coding
mm_59385.1	chr7	26215340	26215342	+	1	NA	Intergenic	Lx|LINE|L1	41932	NM_010000	13094	Mm.14413	NM_010000	ENSMUSG00000040660	Cyp2b9	Cyp2b	cytochrome P450, family 2, subfamily b, polypeptide 9	protein-coding
mm_68659.1	chr7	118707348	118707352	-	1	NA	Intergenic	RMER17C|LTR|ERVK	-1612	NM_019580	56209	Mm.273142	NM_019580	ENSMUSG00000033917	Gde1	1200003M13Rik|Mir16|RGS16	glycerophosphodiester phosphodiesterase 1	protein-coding
mm_99561.1	chr11	103697322	103697340	+	1	NA	promoter-TSS (NR_102389)	promoter-TSS (NR_102389)	379	NM_019650	56494	Mm.195451	NM_019650	ENSMUSG00000020946	Gosr2	2310032N09Rik|C76855|Gs27|SNARE|membrin	golgi SNAP receptor complex member 2	protein-coding
mm_144120.1	chr18	4634913	4634974	+	1	NA	promoter-TSS (NM_001081963)	promoter-TSS (NM_001081963)	14	NM_001081963	240185	Mm.33179	NM_001081963	ENSMUSG00000033960	9430020K01Rik	1110056P05Rik|Gm328|Jcad|mKIAA1462	RIKEN cDNA 9430020K01 gene	protein-coding
mm_139712.1	chr17	57460710	57460730	+	1	NA	exon (NM_010130, exon 18 of 22)	exon (NM_010130, exon 18 of 22)	84594	NM_001104591	224916	Mm.469889	NM_001104591	ENSMUSG00000090655	Vmn2r120	EG224916	vomeronasal 2, receptor 120	protein-coding
mm_76942.1	chr8	105943278	105943288	-	1	NA	TTS (NM_001253804)	TTS (NM_001253804)	119	NM_008490	16816	Mm.1593	NM_008490	ENSMUSG00000035237	Lcat	AI046659|D8Wsu61e	lecithin cholesterol acyltransferase	protein-coding
mm_158778.1	chrX	167174356	167174368	-	1	NA	Intergenic	Intergenic	34856	NM_021278	19241	Mm.142729	NM_021278	ENSMUSG00000049775	Tmsb4x	Ptmb4|Tb4	thymosin, beta 4, X chromosome	protein-coding
mm_102357.1	chr11	58307689	58307701	-	1	NA	exon (NM_001040686, exon 2 of 12)	exon (NM_001040686, exon 2 of 12)	626	NM_001040686	103836	Mm.41440	NM_182996	ENSMUSG00000037243	Zfp692	AI746306|AI839920|Zfp692-ps|Znf692	zinc finger protein 692	protein-coding
mm_34741.1	chr4	152242015	152242023	+	1	NA	intron (NM_001146057, intron 6 of 8)	intron (NM_001146057, intron 6 of 8)	-32343	NM_178406	100129	Mm.23235	NM_178406	ENSMUSG00000042804	Gpr153	1110065N12Rik|AI449320|PGR1	G protein-coupled receptor 153	protein-coding
mm_26775.1	chr3	9001397	9001399	-	1	NA	intron (NM_001025263, intron 1 of 6)	intron (NM_001025263, intron 1 of 6)	3117	NM_009412	21985	Mm.371590	NM_009412	ENSMUSG00000027506	Tpd52	AI043038|mD52	tumor protein D52	protein-coding
mm_28916.1	chr3	98853331	98853347	-	1	NA	exon (NM_001304800, exon 4 of 4)	exon (NM_001304800, exon 4 of 4)	6455	NM_001304800	15492	Mm.140811	NM_008293	ENSMUSG00000027871	Hsd3b1	3-beta-HSD I|D3Ertd383e	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1	protein-coding
mm_24.1	chr1	5115206	5115211	+	1	NA	intron (NM_133826, intron 7 of 13)	B1_Mur4|SINE|Alu	32122	NM_001310442	108664	Mm.27082	NM_133826	ENSMUSG00000033793	Atp6v1h	0710001F19Rik|AU022349|CGI-11|SFD|SFDalpha|SFDbeta|VMA13	ATPase, H+ transporting, lysosomal V1 subunit H	protein-coding
mm_3398.1	chr1	143681925	143681933	+	1	NA	intron (NM_145991, intron 6 of 16)	intron (NM_145991, intron 6 of 16)	20964	NM_145991	214498	Mm.156727	NM_145991	ENSMUSG00000026361	Cdc73	8430414L16Rik|C130030P16Rik|C81219|Hrpt2	cell division cycle 73, Paf1/RNA polymerase II complex component	protein-coding
mm_108648.1	chr12	85987965	85987970	+	1	NA	intron (NM_001347395, intron 29 of 32)	PB1D10|SINE|Alu	91074	NM_009368	21809	Mm.3992	NM_009368	ENSMUSG00000021253	Tgfb3	TGF-beta-3|Tgfb-3	transforming growth factor, beta 3	protein-coding
mm_124763.1	chr15	6663350	6663364	+	1	NA	3' UTR (NM_001278269, exon 17 of 17)	3' UTR (NM_001278269, exon 17 of 17)	-45024	NM_030168	78757	Mm.275811	NM_030168	ENSMUSG00000050310	Rictor	4921505C17Rik|6030405M08Rik|AVO3|AW492497|D530039E11Rik	RPTOR independent companion of MTOR, complex 2	protein-coding
mm_152318.1	chr19	9928365	9928385	-	1	NA	Intergenic	Intergenic	-28842	NM_016692	16319	Mm.29755	NM_016692	ENSMUSG00000024660	Incenp	2700067E22Rik|AU019509|C130081E20|C77457	inner centromere protein	protein-coding
mm_121012.1	chr14	79535597	79535607	+	1	NA	intron (NM_001286411, intron 1 of 8)	intron (NM_001286411, intron 1 of 8)	19928	NM_001286411	13709	Mm.20938	NM_007920	ENSMUSG00000036461	Elf1	Elf-1|Sts1|mElf-1|p70	E74-like factor 1	protein-coding
mm_24664.1	chr3	94486333	94486333	+	1	NA	intron (NR_110353, intron 4 of 11)	L1MEc|LINE|L1	3611	NR_110353	78784	Mm.44292	NM_172434	ENSMUSG00000028137	Celf3	4930415M08Rik|BRUNOL1|CAGH4|ERDA4|Tnrc4	CUGBP, Elav-like family member 3	protein-coding
mm_69614.1	chr7	137303226	137303230	-	1	NA	intron (NM_001113415, intron 6 of 15)	intron (NM_001113415, intron 6 of 15)	11217	NM_001113415	13593	Mm.258708	NM_010096	ENSMUSG00000010476	Ebf3	3110018A08Rik|O/E-2|mKIAA4201	early B cell factor 3	protein-coding
mm_172369.1	chr7	123224868	123224882	+	1	NA	intron (NM_146198, intron 1 of 16)	MLT1A0|LTR|ERVL-MaLR	10009	NM_146198	233836	Mm.211838	NM_146198	ENSMUSG00000030769	Slc5a11	2010013B02Rik|Kst1|RKST2|SMIT2|Slc5a10	solute carrier family 5 (sodium/glucose cotransporter), member 11	protein-coding
mm_97759.1	chr11	80858359	80858367	+	1	NA	promoter-TSS (NM_029367)	promoter-TSS (NM_029367)	-26	NM_029367	75622	Mm.26988	NM_029367	ENSMUSG00000053184	Spaca3	1700025M08Rik|ALLP17|Lyc3|SLLP1|mSLLP1	sperm acrosome associated 3	protein-coding
mm_693.1	chr1	40580313	40580334	+	1	NA	promoter-TSS (NM_177084)	promoter-TSS (NM_177084)	96	NM_177084	110895	Mm.108602	NM_177084	ENSMUSG00000026065	Slc9a4	AW990558|D730009J23Rik|NHE4	solute carrier family 9 (sodium/hydrogen exchanger), member 4	protein-coding
mm_130762.1	chr15	101364532	101364566	-	1	NA	intron (NM_028770, intron 1 of 8)	intron (NM_028770, intron 1 of 8)	-4803	NR_035462	100316694		NR_035462	ENSMUSG00000088459	Mir1941	mmu-mir-1941	microRNA 1941	ncRNA
mm_19879.1	chr2	114049349	114049353	-	1	NA	exon (NM_009608, exon 5 of 7)	exon (NM_009608, exon 5 of 7)	3524	NM_009608	11464	Mm.686	NM_009608	ENSMUSG00000068614	Actc1	Actc-1	actin, alpha, cardiac muscle 1	protein-coding
mm_127218.1	chr15	99392949	99392987	+	1	NA	promoter-TSS (NM_026669)	promoter-TSS (NM_026669)	21	NM_001171034	110213	Mm.16769	NM_026669	ENSMUSG00000023010	Tmbim6	5031406P05Rik|Bi1|Tegt	transmembrane BAX inhibitor motif containing 6	protein-coding
mm_162063.1	chrX	9350635	9350635	+	1	NA	promoter-TSS (NM_001085537)	promoter-TSS (NM_001085537)	36	NM_001085537	547154	Mm.327545	NM_001085537	ENSMUSG00000100448	H2al1k	Gm14501|OTTMUSG00000016887	H2A histone family member L1K	protein-coding
mm_61215.1	chr7	64287666	64287676	+	1	NA	promoter-TSS (NM_172742)	promoter-TSS (NM_172742)	1	NM_172742	233315	Mm.214959	NM_172742	ENSMUSG00000030522	Mtmr10	BB128963|C79734	myotubularin related protein 10	protein-coding
mm_164344.1	chr16	16409585	16409587	+	1	NA	Intergenic	Lx8|LINE|L1	-50555	NM_001276340	74006	Mm.218820	NM_152816	ENSMUSG00000022789	Dnm1l	6330417M19Rik|AI450666|Dlp1|Dnmlp1|Drp1|python	dynamin 1-like	protein-coding
mm_64575.1	chr7	144915212	144915222	+	1	NA	promoter-TSS (NM_028184)	promoter-TSS (NM_028184)	23	NM_028184	72284	Mm.273049	NM_028184	ENSMUSG00000031072	Oraov1	2210010N10Rik|TAOS1	oral cancer overexpressed 1	protein-coding
mm_91100.1	chr10	19065261	19065269	-	1	NA	Intergenic	Intergenic	-49855	NM_009397	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_162240.1	chrX	154995863	154995863	-	1	NA	promoter-TSS (NM_020020)	promoter-TSS (NM_020020)	-13	NM_020020	17144	Mm.196415	NM_020020	ENSMUSG00000079350	Magea8	Mage-a8	melanoma antigen, family A, 8	protein-coding
mm_144865.1	chr18	36725919	36725994	+	1	NA	exon (NM_009841, exon 2 of 2)	exon (NM_009841, exon 2 of 2)	859	NM_009841	12475	Mm.3460	NM_009841	ENSMUSG00000051439	Cd14	-	CD14 antigen	protein-coding
mm_1164.1	chr1	60909351	60909356	+	1	NA	intron (NM_001281976, intron 1 of 2)	intron (NM_001281976, intron 1 of 2)	328	NM_001281976	12477	Mm.390	NM_009843	ENSMUSG00000026011	Ctla4	Cd152|Ctla-4|Ly-56	cytotoxic T-lymphocyte-associated protein 4	protein-coding
mm_81291.1	chr9	108327668	108327693	+	1	NA	exon (NM_016802, exon 3 of 6)	exon (NM_016802, exon 3 of 6)	-11400	NM_008160	14775	Mm.1090	NM_008160	ENSMUSG00000063856	Gpx1	AI195024|AL033363|CGPx|GPx-1|GSHPx-1|Gpx	glutathione peroxidase 1	protein-coding
mm_128998.1	chr15	74841802	74841816	-	1	NA	promoter-TSS (NM_001033229)	promoter-TSS (NM_001033229)	-166	NM_001033229	110115	Mm.322606	NM_001033229	ENSMUSG00000075604	Cyp11b1	AA389061|CPN1|Cyp11b|Cyp11b-1|FHI	cytochrome P450, family 11, subfamily b, polypeptide 1	protein-coding
mm_30231.1	chr3	145924874	145924895	-	1	NA	intron (NM_009740, intron 1 of 2)	CpG	622	NM_009740	12042	Mm.239141	NM_009740	ENSMUSG00000028191	Bcl10	AI132454|BCL-10|C81403|CARMEN|CIPER|CLAP|ME10|cE10	B cell leukemia/lymphoma 10	protein-coding
mm_171419.1	chr4	133601552	133601558	-	1	NA	exon (NM_018754, exon 1 of 1)	exon (NM_018754, exon 1 of 1)	613	NM_018754	55948	Mm.44482	NM_018754	ENSMUSG00000047281	Sfn	Er|Mme1|Ywhas	stratifin	protein-coding
mm_44624.1	chr5	25713193	25713203	-	1	NA	Intergenic	ORR1C1|LTR|ERVL-MaLR	-7401	NM_020570	57434	Mm.143767	NM_020570	ENSMUSG00000028933	Xrcc2	4921524O04Rik|8030409M04Rik|RAD51|RecA	X-ray repair complementing defective repair in Chinese hamster cells 2	protein-coding
mm_41543.1	chr5	92897783	92897793	+	1	NA	promoter-TSS (NM_001077596)	promoter-TSS (NM_001077596)	-205	NM_001077596	27428	Mm.46014	NM_015756	ENSMUSG00000029381	Shroom3	AL022960|D5Ertd287e|Shrm|Shrm3	shroom family member 3	protein-coding
mm_148952.1	chr19	7274443	7274453	+	1	NA	TTS (NM_001080388)	TTS (NM_001080388)	6169	NM_001320554	104383	Mm.283859	NM_054048	ENSMUSG00000024968	Rcor2	1A13|AW122124|CoREST|Rcor|Rcor1	REST corepressor 2	protein-coding
mm_168580.1	chr1	171728994	171729000	+	1	NA	Intergenic	RLTR10C|LTR|ERVK	-38135	NM_013730	27218	Mm.103648	NM_013730	ENSMUSG00000015316	Slamf1	4933415F16|AA177906|CD150|CDw150|ESTM51|IPO-3|Slam	signaling lymphocytic activation molecule family member 1	protein-coding
mm_123504.1	chr14	66232354	66232360	-	1	NA	intron (NM_001162365, intron 1 of 30)	intron (NM_001162365, intron 1 of 30)	-18805	NM_001162366	19229	Mm.21613	NM_172498	ENSMUSG00000059456	Ptk2b	CADTK|CAKB|CAKbeta|E430023O05Rik|FADK2|FAK2|PYK2|Raftk	PTK2 protein tyrosine kinase 2 beta	protein-coding
mm_10452.1	chr2	14278922	14278926	+	1	NA	intron (NM_008625, intron 10 of 29)	intron (NM_008625, intron 10 of 29)	17921	NR_030609	100124488		NR_030609	ENSMUSG00000077897	Mir511	Mirn511|mir-511|mmu-mir-511	microRNA 511	ncRNA
mm_84903.1	chr9	79961984	79962001	-	1	NA	intron (NM_001081243, intron 1 of 5)	intron (NM_001081243, intron 1 of 5)	15890	NM_001081243	70598	Mm.23049	NM_001081243	ENSMUSG00000034898	Filip1	5730485H21Rik|AI843021	filamin A interacting protein 1	protein-coding
mm_134875.1	chr16	28929659	28929698	-	1	NA	promoter-TSS (NM_177718)	promoter-TSS (NM_177718)	20	NM_177718	239796	Mm.155887	NM_177718	ENSMUSG00000051065	Mb21d2	1600021P15Rik|A430031N04|C87006	Mab-21 domain containing 2	protein-coding
mm_121279.1	chr14	103719857	103719877	+	1	NA	Intergenic	(T)n|Simple_repeat|Simple_repeat	-20435	NR_045148	70898	Mm.27548	NR_045148	ENSMUSG00000089707	Slain1os	4921525B02Rik	SLAIN motif family, member 1, opposite strand	ncRNA
mm_145515.1	chr18	60443194	60443204	+	1	NA	Intergenic	Intergenic	58784	NM_134133	106878	Mm.273197	NM_134133	ENSMUSG00000038059	Smim3	2010002N04Rik|AI195350|AW561905|Nid67|cI-41	small integral membrane protein 3	protein-coding
mm_16571.1	chr2	3422577	3422600	-	1	NA	promoter-TSS (NM_008579)	promoter-TSS (NM_008579)	60	NM_008579	104362	Mm.2688	NM_008579	ENSMUSG00000026650	Meig1	MLZ-278|Meg1	meiosis expressed gene 1	protein-coding
mm_72681.1	chr8	84949866	84949872	+	1	NA	intron (NM_144929, intron 1 of 5)	intron (NM_144929, intron 1 of 5)	2878	NM_144929	234542	Mm.461701	NM_144929	ENSMUSG00000048617	Rtbdn	A330096I21Rik|BC022744|Rtbnd	retbindin	protein-coding
mm_23929.1	chr3	83766662	83766672	+	1	NA	exon (NM_009144, exon 1 of 3)	exon (NM_009144, exon 1 of 3)	346	NM_009144	20319	Mm.19155	NM_009144	ENSMUSG00000027996	Sfrp2	AI851596|Sdf5	secreted frizzled-related protein 2	protein-coding
mm_13078.1	chr2	91205813	91205829	+	1	NA	exon (NM_007387, exon 4 of 11)	exon (NM_007387, exon 4 of 11)	2909	NM_007387	11432	Mm.45570	NM_007387	ENSMUSG00000002103	Acp2	Acp-2|LAP	acid phosphatase 2, lysosomal	protein-coding
mm_31438.1	chr4	48540348	48540368	+	1	NA	promoter-TSS (NM_028137)	promoter-TSS (NM_028137)	-141	NM_028137	66665	Mm.140749	NM_028137	ENSMUSG00000039693	Msantd3	2410046L14Rik|2810429P03Rik|5730528L13Rik|Mysantd3	Myb/SANT-like DNA-binding domain containing 3	protein-coding
mm_112338.1	chr12	116200206	116200227	-	1	NA	Intergenic	Intergenic	62809	NM_146039	217935	Mm.31382	NM_146039	ENSMUSG00000042050	Wdr60	D430033N04Rik	WD repeat domain 60	protein-coding
mm_21316.1	chr2	157098989	157099015	-	1	NA	3' UTR (NM_001139520, exon 17 of 17)	3' UTR (NM_001139520, exon 17 of 17)	11947	NM_001177439	383766	Mm.480305	NM_001177439	ENSMUSG00000074628	Tldc2	Gm1332	TBC/LysM associated domain containing 2	protein-coding
mm_12651.1	chr2	74752977	74752989	+	1	NA	non-coding (NR_110447, exon 1 of 2)	non-coding (NR_110447, exon 1 of 2)	299	NR_110447	102634401	Mm.235021	NR_110447	ENSMUSG00000085015	LOC102634401	-	uncharacterized LOC102634401	ncRNA
mm_44781.1	chr5	32133046	32133053	-	1	NA	Intergenic	CpG	-3423	NM_008037	14284	Mm.24684	NM_008037	ENSMUSG00000029135	Fosl2	Fra-2	fos-like antigen 2	protein-coding
mm_65787.1	chr7	28810495	28810522	-	1	NA	promoter-TSS (NM_177301)	promoter-TSS (NM_177301)	-382	NM_177301	15388	Mm.9043	NM_177301	ENSMUSG00000015165	Hnrnpl	C79783|D830027H13Rik|Hnrpl	heterogeneous nuclear ribonucleoprotein L	protein-coding
mm_28188.1	chr3	88072047	88072068	-	1	NA	intron (NM_172526, intron 6 of 9)	intron (NM_172526, intron 6 of 9)	6247	NM_172526	214191	Mm.229191	NM_172526	ENSMUSG00000051036	Ttc24	A430025D11Rik	tetratricopeptide repeat domain 24	protein-coding
mm_75682.1	chr8	68062445	68062504	-	1	NA	Intergenic	CpG	-87900	NM_177698	234353	Mm.32525	NM_027626	ENSMUSG00000030465	Psd3	4931420C21Rik|AI661273|BC003498|D430018P08|EFA6D	pleckstrin and Sec7 domain containing 3	protein-coding
mm_67735.1	chr7	90131117	90131127	-	1	NA	intron (NM_001252520, intron 1 of 20)	intron (NM_001252520, intron 1 of 20)	890	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_140275.1	chr17	84956719	84956745	+	1	NA	promoter-TSS (NM_001159497)	promoter-TSS (NM_001159497)	-9	NM_001159497	19043	Mm.249695	NM_011151	ENSMUSG00000061130	Ppm1b	PP2CB	protein phosphatase 1B, magnesium dependent, beta isoform	protein-coding
mm_98988.1	chr11	98753384	98753393	+	1	NA	5' UTR (NM_001313983, exon 2 of 10)	5' UTR (NM_001313983, exon 2 of 10)	11603	NM_001313983	21833	Mm.265917	NM_178060	ENSMUSG00000058756	Thra	6430529J03Rik|AW259572|Erba|Nr1a1|Rvr|T3R[a]|T3Ralpha|Thra1|Thra2|c-erbA-1|c-erbA-alpha|c-erbAalpha	thyroid hormone receptor alpha	protein-coding
mm_145223.1	chr18	50057106	50057118	+	1	NA	intron (NM_134131, intron 1 of 1)	intron (NM_134131, intron 1 of 1)	3830	NM_134131	106869	Mm.27740	NM_134131	ENSMUSG00000062210	Tnfaip8	AA987150|E130304C20Rik|ENSMUSG00000073567|Gg2-1|Gm10539|Nded|Ssc-2|Tipe	tumor necrosis factor, alpha-induced protein 8	protein-coding
mm_86873.1	chr10	21996924	21996936	+	1	NA	intron (NM_001161848, intron 7 of 11)	intron (NM_001161848, intron 7 of 11)	2264	NM_011361	20393	Mm.28405	NM_011361	ENSMUSG00000019970	Sgk1	Sgk	serum/glucocorticoid regulated kinase 1	protein-coding
mm_86486.1	chr10	5003431	5003435	+	1	NA	3' UTR (NM_007956, exon 9 of 9)	3' UTR (NM_007956, exon 9 of 9)	65630	NM_022027	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_97087.1	chr11	73138314	73138356	+	1	NA	promoter-TSS (NM_010353)	promoter-TSS (NM_010353)	-41	NM_010353	14841	Mm.42045	NM_010353	ENSMUSG00000050107	Gsg2	Haspin	germ cell associated 2, haspin	protein-coding
mm_61136.1	chr7	56050342	56050352	+	1	NA	intron (NM_010418, intron 1 of 92)	CpG	192	NM_010418	15204	Mm.20929	NM_010418	ENSMUSG00000030451	Herc2	D15F32S1h|D7H15F32S1|D7H15F37S1|jdf2|mKIAA0393|rjs	HECT and RLD domain containing E3 ubiquitin protein ligase 2	protein-coding
mm_168409.1	chr1	131158033	131158035	-	1	NA	intron (NM_001136070, intron 4 of 14)	intron (NM_001136070, intron 4 of 14)	4827	NM_010709	16865	Mm.276294	NM_010709	ENSMUSG00000026427	Eif2d	D1Ertd5e|Lgtn	eukaryotic translation initiation factor 2D	protein-coding
mm_153120.1	chr19	33392256	33392300	-	1	NA	promoter-TSS (NM_001146342)	promoter-TSS (NM_001146342)	17	NM_001167818	67795	Mm.204591	NM_001146342	ENSMUSG00000071573	Rnls	6530404N21Rik|AI452315|AW060440|C10orf59	renalase, FAD-dependent amine oxidase	protein-coding
mm_31111.1	chr4	42921911	42921919	+	1	NA	intron (NM_001346526, intron 1 of 8)	intron (NM_001346526, intron 1 of 8)	4664	NM_172690	230085	Mm.240965	NM_172690	ENSMUSG00000036062	Phf24	GINIP|N28178	PHD finger protein 24	protein-coding
mm_75891.1	chr8	70887835	70887894	-	1	NA	exon (NM_053248, exon 12 of 15)	exon (NM_053248, exon 12 of 15)	4893	NM_053248	114479	Mm.172923	NM_053248	ENSMUSG00000000792	Slc5a5	NIS	solute carrier family 5 (sodium iodide symporter), member 5	protein-coding
mm_133238.1	chr16	77071740	77071756	+	1	NA	exon (NM_013918, exon 10 of 24)	exon (NM_013918, exon 10 of 24)	57679	NM_013918	30940	Mm.40986	NM_013918	ENSMUSG00000022867	Usp25	-	ubiquitin specific peptidase 25	protein-coding
mm_134815.1	chr16	25059265	25059280	-	1	NA	promoter-TSS (NR_040374)	promoter-TSS (NR_040374)	-367	NR_040374	319487	Mm.137341	NR_040374	ENSMUSG00000096960	A230028O05Rik	-	RIKEN cDNA A230028O05 gene	ncRNA
mm_87121.1	chr10	33305031	33305045	+	1	NA	exon (NM_029726, exon 13 of 38)	exon (NM_029726, exon 13 of 38)	-48681	NR_040657	442820	Mm.490725	NR_040657		D830005E20Rik	-	RIKEN cDNA D830005E20 gene	ncRNA
mm_162907.1	chr10	117361077	117361115	-	1	NA	exon (NM_001013391, exon 6 of 10)	exon (NM_001013391, exon 6 of 10)	15877	NM_001013391	432508	Mm.478881	NM_001013391	ENSMUSG00000055531	Cpsf6	4733401N12Rik|AI256641|CFIM|CFIM68|HPBRII-4|HPBRII-7	cleavage and polyadenylation specific factor 6	protein-coding
mm_36140.1	chr4	59438346	59438426	-	1	NA	5' UTR (NM_001163288, exon 1 of 17)	5' UTR (NM_001163288, exon 1 of 17)	247	NM_001163288	634731	Mm.483589	NM_001163288	ENSMUSG00000038578	Susd1	A530080P10|Gm12528|OTTMUSG00000007332	sushi domain containing 1	protein-coding
mm_31166.1	chr4	43443158	43443169	+	1	NA	5' UTR (NM_011571, exon 1 of 10)	5' UTR (NM_011571, exon 1 of 10)	886	NM_011571	21754	Mm.485441	NM_011571	ENSMUSG00000028458	Tesk1	AI326901	testis specific protein kinase 1	protein-coding
mm_26480.1	chr3	144677712	144677732	+	1	NA	Intergenic	Intergenic	42613	NM_001282042	54673	Mm.271775	NM_019464	ENSMUSG00000037062	Sh3glb1	AA409932|AI314629|AU015566|Bif-1|mKIAA0491	SH3-domain GRB2-like B1 (endophilin)	protein-coding
mm_138147.1	chr17	34204832	34204864	+	1	NA	intron (NM_011530, intron 1 of 11)	CpG	369	NM_011530	21355	Mm.14814	NM_011530	ENSMUSG00000024339	Tap2	ABC18|AI462429|APT2|Abcb3|Ham-2|Ham2|MTP2|PSF2|RING11|Tap-2|Y1|jas	transporter 2, ATP-binding cassette, sub-family B (MDR/TAP)	protein-coding
mm_59614.1	chr7	28143858	28143864	+	1	NA	exon (NM_001164655, exon 7 of 20)	exon (NM_001164655, exon 7 of 20)	14395	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_165804.1	chr3	144324857	144324863	+	1	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	-119605	NM_010723	16911	Mm.29187	NM_010723	ENSMUSG00000028266	Lmo4	A730077C12Rik|Crp3|Etohi4	LIM domain only 4	protein-coding
mm_32427.1	chr4	107135132	107135135	+	1	NA	3' UTR (NM_025617, exon 5 of 5)	3' UTR (NM_025617, exon 5 of 5)	38242	NM_172873	242603	Mm.257231	NM_172873	ENSMUSG00000047636	Cdcp2	D030010E02Rik	CUB domain containing protein 2	protein-coding
mm_42464.1	chr5	115448885	115448890	+	1	NA	intron (NM_008629, intron 11 of 14)	PB1D10|SINE|Alu	-17379	NM_011107	18778	Mm.20190	NM_011107	ENSMUSG00000029522	Pla2g1b	Pla2a|sPLA2IB	phospholipase A2, group IB, pancreas	protein-coding
mm_119195.1	chr14	32573641	32573645	+	1	NA	intron (NM_001081221, intron 18 of 20)	intron (NM_001081221, intron 18 of 20)	-25765	NM_001347590	107751	Mm.119274	NM_001001796	ENSMUSG00000041730	Prrxl1	Drg11|Drgx	paired related homeobox protein-like 1	protein-coding
mm_57632.1	chr6	128300553	128300562	-	1	NA	5' UTR (NM_001080979, exon 1 of 11)	5' UTR (NM_001080979, exon 1 of 11)	256	NM_001080979	21679	Mm.14774	NM_011567	ENSMUSG00000030353	Tead4	ETFR-2|Etfr2|FR-19|Rtef1|TEAD-4|TEF-3|Tcf13r1|Tef3|Tefr|Tefr1|Tefr1a	TEA domain family member 4	protein-coding
mm_127849.1	chr15	7398387	7398400	-	1	NA	promoter-TSS (NM_001289498)	promoter-TSS (NM_001289498)	2	NM_001289498	268780	Mm.203208	NM_178748	ENSMUSG00000042961	Egflam	5930412K08|AU040377	EGF-like, fibronectin type III and laminin G domains	protein-coding
mm_119054.1	chr14	30677274	30677278	+	1	NA	intron (NM_177815, intron 8 of 12)	L1MD1|LINE|L1	22901	NM_177815	328370	Mm.259657	NM_177815	ENSMUSG00000052395	Rft1	D930025H04	RFT1 homolog	protein-coding
mm_22769.1	chr3	20223102	20223145	+	1	NA	promoter-TSS (NR_105974)	promoter-TSS (NR_105974)	-764	NR_105974	102465609		NR_105974	ENSMUSG00000099105	Mir7007	Gm27897|mmu-mir-7007	microRNA 7007	ncRNA
mm_44159.1	chr5	150566510	150566542	+	1	NA	intron (NM_001081001, intron 24 of 26)	L1MC5a|LINE|L1	27999	NM_133898	100637	Mm.279932	NM_133898	ENSMUSG00000041132	N4bp2l1	2410024N18Rik|AI428195|B230342M21Rik	NEDD4 binding protein 2-like 1	protein-coding
mm_109793.1	chr12	3256936	3256956	-	1	NA	exon (NM_016676, exon 3 of 6)	exon (NM_016676, exon 3 of 6)	21155	NR_015551	74173	Mm.309774	NM_028796	ENSMUSG00000079179	Rab10os	1700012B15Rik|1810036A22Rik	RAB10, member RAS oncogene family, opposite strand	ncRNA
mm_149021.1	chr19	8757080	8757093	+	1	NA	promoter-TSS (NM_001276704)	promoter-TSS (NM_001276704)	-17	NM_016813	53319	Mm.7271	NM_016813	ENSMUSG00000010097	Nxf1	Mex67|Mvb1|Tap	nuclear RNA export factor 1	protein-coding
mm_153349.1	chr19	39741094	39741114	-	1	NA	promoter-TSS (NM_001039555)	promoter-TSS (NM_001039555)	-3	NM_001039555	433247	Mm.335660	NM_001039555	ENSMUSG00000074882	Cyp2c68	9030012A22Rik	cytochrome P450, family 2, subfamily c, polypeptide 68	protein-coding
mm_115570.1	chr13	10360916	10360941	-	1	NA	promoter-TSS (NM_033269)	promoter-TSS (NM_033269)	-125	NM_033269	12671	Mm.342315	NM_033269	ENSMUSG00000046159	Chrm3	Chrm-3|M3|M3R	cholinergic receptor, muscarinic 3, cardiac	protein-coding
mm_93372.1	chr10	105456227	105456235	-	1	NA	intron (NM_177368, intron 1 of 11)	intron (NM_177368, intron 1 of 11)	118248	NM_177368	278279	Mm.25225	NM_177368	ENSMUSG00000036019	Tmtc2	8430438D04Rik|D330034A10Rik	transmembrane and tetratricopeptide repeat containing 2	protein-coding
mm_127435.1	chr15	101270189	101270225	+	1	NA	exon (NM_010444, exon 2 of 7)	exon (NM_010444, exon 2 of 7)	3361	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_3936.1	chr1	163762203	163762207	+	1	NA	Intergenic	Intergenic	-17378	NM_001305643	16579	Mm.4651	NM_010629	ENSMUSG00000026585	Kifap3	KAP-3|KAP3|SMAP	kinesin-associated protein 3	protein-coding
mm_22546.1	chr3	9034091	9034117	+	1	NA	Intergenic	Intergenic	-27860	NR_040597	75149	Mm.399324	NR_040597	ENSMUSG00000103116	4930539M17Rik	-	RIKEN cDNA 4930539M17 gene	ncRNA
mm_142708.1	chr17	47888169	47888173	-	1	NA	exon (NM_028767, exon 3 of 17)	exon (NM_028767, exon 3 of 17)	36461	NM_028767	74123	Mm.240062	NM_028767	ENSMUSG00000023991	Foxp4	1200010K03Rik|2310007G05Rik|mFKHLA	forkhead box P4	protein-coding
mm_73358.1	chr8	105518930	105518947	+	1	NA	exon (NM_008289, exon 1 of 5)	exon (NM_008289, exon 1 of 5)	192	NM_008289	15484	Mm.5079	NM_008289	ENSMUSG00000031891	Hsd11b2	11HSD2	hydroxysteroid 11-beta dehydrogenase 2	protein-coding
mm_3246.1	chr1	136052947	136052958	+	1	NA	promoter-TSS (NM_014193)	promoter-TSS (NM_014193)	51	NM_014193	12292	Mm.4418	NM_014193	ENSMUSG00000026407	Cacna1s	AW493108|Cav1.1|Cchl1a3|fmd|mdg|sj	calcium channel, voltage-dependent, L type, alpha 1S subunit	protein-coding
mm_134816.1	chr16	25059723	25059755	-	1	NA	promoter-TSS (NR_040374)	promoter-TSS (NR_040374)	100	NR_040374	319487	Mm.137341	NR_040374	ENSMUSG00000096960	A230028O05Rik	-	RIKEN cDNA A230028O05 gene	ncRNA
mm_163708.1	chr13	108465802	108465802	+	1	NA	Intergenic	Intergenic	149465	NM_178683	218581	Mm.32318	NM_178683	ENSMUSG00000021697	Depdc1b	9830132O03|AW260467|XTP1	DEP domain containing 1B	protein-coding
mm_54675.1	chr6	39377642	39377678	-	1	NA	promoter-TSS (NM_028123)	promoter-TSS (NM_028123)	47	NM_028123	72144	Mm.482167	NM_028123	ENSMUSG00000029924	Slc37a3	2610507O21Rik|AU044904	solute carrier family 37 (glycerol-3-phosphate transporter), member 3	protein-coding
mm_117189.1	chr13	63563088	63563131	-	1	NA	intron (NM_001328514, intron 2 of 23)	GC_rich|Low_complexity|Low_complexity	2626	NM_008957	19206	Mm.228798	NM_008957	ENSMUSG00000021466	Ptch1	A230106A15Rik|Ptc|Ptc1|Ptch|mes	patched 1	protein-coding
mm_117080.1	chr13	59640154	59640172	-	1	NA	exon (NM_001035122, exon 8 of 10)	exon (NM_001035122, exon 8 of 10)	35621	NM_001035122	105348	Mm.171335	NM_027307	ENSMUSG00000021556	Golm1	2310001L02Rik|AW125446|D030064E01Rik|GP73|Golph2|PSEC0257	golgi membrane protein 1	protein-coding
mm_120312.1	chr14	63142403	63142440	+	1	NA	3' UTR (NM_007798, exon 10 of 10)	3' UTR (NM_007798, exon 10 of 10)	19959	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_117262.1	chr13	64369017	64369029	-	1	NA	intron (NM_009984, intron 2 of 7)	intron (NM_009984, intron 2 of 7)	1497	NM_009984	13039	Mm.930	NM_009984	ENSMUSG00000021477	Ctsl	1190035F06Rik|CatL|Ctsl1|MEP|fs|nkt	cathepsin L	protein-coding
mm_143034.1	chr17	56609989	56610005	-	1	NA	promoter-TSS (NM_153152)	promoter-TSS (NM_153152)	-226	NM_153152	224904	Mm.34002	NM_153152	ENSMUSG00000049760	2410015M20Rik	Mic13|QIL1|sr104	RIKEN cDNA 2410015M20 gene	protein-coding
mm_121894.1	chr14	21748611	21748650	-	1	NA	promoter-TSS (NM_001007268)	promoter-TSS (NM_001007268)	-8	NM_001007268	27389	Mm.390674	NM_013849	ENSMUSG00000021768	Dusp13	DUSP13A|DUSP13B|Gm1203|LMW-DSP6|MDSP|TMDP|TS-DSP6	dual specificity phosphatase 13	protein-coding
mm_116535.1	chr13	45875948	45875956	-	1	NA	intron (NM_001199304, intron 2 of 6)	B4|SINE|B4	89039	NM_001199304	20238	Mm.342683	NM_009124	ENSMUSG00000046876	Atxn1	2900016G23Rik|Atx1|C85907|ENSMUSG00000074917|Gm10786|Sca1	ataxin 1	protein-coding
mm_147800.1	chr18	61658049	61658135	-	1	NA	intron (NR_045402, intron 1 of 4)	intron (NR_045402, intron 1 of 4)	7446	NR_045402	328968	Mm.392305	NR_045402		Carmn	Carmen|E330013P06|Gm16908|Mir143hg	cardiac mesoderm enhancer-associated non-coding RNA	ncRNA
mm_81195.1	chr9	107554634	107554651	+	1	NA	promoter-TSS (NM_019713)	promoter-TSS (NM_019713)	59	NM_019713	56289	Mm.12091	NM_019713	ENSMUSG00000010067	Rassf1	123F2|AA536941|AU044980|NORE2A|RDA32|REH3P21|Rassf1A|Rassf1B|Rassf1C	Ras association (RalGDS/AF-6) domain family member 1	protein-coding
mm_73842.1	chr8	117498273	117498291	+	1	NA	promoter-TSS (NM_172285)	promoter-TSS (NM_172285)	7	NM_172285	234779	Mm.192699	NM_172285	ENSMUSG00000034330	Plcg2	PLC-gamma-2|PLCgamma2|Plcg-2	phospholipase C, gamma 2	protein-coding
mm_66993.1	chr7	64373596	64373599	-	1	NA	5' UTR (NM_177893, exon 2 of 14)	5' UTR (NM_177893, exon 2 of 14)	498	NM_177893	330554	Mm.236510	NM_177893	ENSMUSG00000033458	Fan1	6030441H18Rik|Mtmr15|mFAN1	FANCD2/FANCI-associated nuclease 1	protein-coding
mm_110176.1	chr12	27336945	27336967	-	1	NA	3' UTR (NM_009234, exon 1 of 1)	3' UTR (NM_009234, exon 1 of 1)	5762	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding
mm_56728.1	chr6	115675872	115675887	-	1	NA	intron (NM_029780, intron 1 of 16)	intron (NM_029780, intron 1 of 16)	756	NM_029780	110157	Mm.184163	NM_029780	ENSMUSG00000000441	Raf1	6430402F14Rik|AA990557|BB129353|Craf1|D830050J10Rik|Raf-1|c-Raf|v-Raf	v-raf-leukemia viral oncogene 1	protein-coding
mm_54988.1	chr6	48747742	48747755	-	1	NA	intron (NM_175035, intron 1 of 2)	intron (NM_175035, intron 1 of 2)	1551	NM_175035	317757	Mm.455917	NM_175035	ENSMUSG00000043505	Gimap5	D630024P16|E230026N22Rik	GTPase, IMAP family member 5	protein-coding
mm_21041.1	chr2	152511794	152511800	-	1	NA	promoter-TSS (NM_001039120)	promoter-TSS (NM_001039120)	-61	NM_001039120	654457	Mm.389363	NM_001039120	ENSMUSG00000074680	Defb26	EG654457	defensin beta 26	protein-coding
mm_136279.1	chr16	91069127	91069139	-	1	NA	promoter-TSS (NM_028905)	promoter-TSS (NM_028905)	12	NM_001163695	74387	Mm.236220	NM_028905	ENSMUSG00000039851	4932438H23Rik	4931406G06Rik|AI550392	RIKEN cDNA 4932438H23 gene	protein-coding
mm_32569.1	chr4	109836369	109836394	+	1	NA	intron (NM_007983, intron 9 of 18)	intron (NM_007983, intron 9 of 18)	-141644	NM_172296	242620	Mm.32825	NM_172296	ENSMUSG00000047143	Dmrta2	Dmrt5	doublesex and mab-3 related transcription factor like family A2	protein-coding
mm_132771.1	chr16	44766106	44766113	+	1	NA	intron (NM_021325, intron 1 of 6)	intron (NM_021325, intron 1 of 6)	373	NM_021325	57781	Mm.416152	NM_021325	ENSMUSG00000022667	Cd200r1	CD200R|Mox2r|OX2R	CD200 receptor 1	protein-coding
mm_62919.1	chr7	118329454	118329465	+	1	NA	Intergenic	Intergenic	85552	NR_027879	67745	Mm.483404	NM_183267	ENSMUSG00000055159	4930583K01Rik	-	RIKEN cDNA 4930583K01 gene	ncRNA
mm_134476.1	chr16	18588819	18588832	-	1	NA	intron (NM_001285472, intron 1 of 8)	CpG	1846	NM_001285472	21380	Mm.295194	NM_011532	ENSMUSG00000009097	Tbx1	-	T-box 1	protein-coding
mm_88849.1	chr10	80930257	80930266	+	1	NA	5' UTR (NM_008655, exon 1 of 4)	5' UTR (NM_008655, exon 1 of 4)	170	NM_008655	17873	Mm.1360	NM_008655	ENSMUSG00000015312	Gadd45b	AI323528|Myd118	growth arrest and DNA-damage-inducible 45 beta	protein-coding
mm_147993.1	chr18	67641360	67641378	-	1	NA	promoter-TSS (NM_001081073)	promoter-TSS (NM_001081073)	-33	NM_001081073	225659	Mm.111928	NM_001081073	ENSMUSG00000073542	Cep76	6230425F05Rik|9630013E05	centrosomal protein 76	protein-coding
mm_18525.1	chr2	63184185	63184195	-	1	NA	promoter-TSS (NM_133207)	promoter-TSS (NM_133207)	97	NM_133207	170738	Mm.242532	NM_133207	ENSMUSG00000059742	Kcnh7	9330137I11Rik|Kv11.3|erg3	potassium voltage-gated channel, subfamily H (eag-related), member 7	protein-coding
mm_20476.1	chr2	129592602	129592605	-	1	NA	promoter-TSS (NM_001291022)	promoter-TSS (NM_001291022)	-236	NM_001291020	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_3942.1	chr1	163779746	163779763	+	1	NA	5' UTR (NM_010629, exon 1 of 21)	5' UTR (NM_010629, exon 1 of 21)	171	NM_010629	16579	Mm.4651	NM_010629	ENSMUSG00000026585	Kifap3	KAP-3|KAP3|SMAP	kinesin-associated protein 3	protein-coding
mm_94653.1	chr11	17051824	17051899	+	1	NA	promoter-TSS (NM_029861)	promoter-TSS (NM_029861)	-73	NM_029861	380686	Mm.425666	NM_029861	ENSMUSG00000044629	Cnrip1	1500041B16Rik|3110054C06Rik|5330437A18Rik|AI854501|C2orf32	cannabinoid receptor interacting protein 1	protein-coding
mm_154129.1	chr19	57274796	57274800	-	1	NA	intron (NR_045319, intron 1 of 2)	RMER17C|LTR|ERVK	838	NR_045319	78120	Mm.445892	NR_045319		4930449E18Rik	-	RIKEN cDNA 4930449E18 gene	ncRNA
mm_164778.1	chr18	3531897	3531902	+	1	NA	Intergenic	Intergenic	23942	NM_026505	68010	Mm.284863	NM_026505	ENSMUSG00000024232	Bambi	2610003H06Rik	BMP and activin membrane-bound inhibitor	protein-coding
mm_119252.1	chr14	33923644	33923685	+	1	NA	promoter-TSS (NM_145741)	promoter-TSS (NM_145741)	77	NM_145741	14560	Mm.432071	NM_145741	ENSMUSG00000021943	Gdf10	Bmp3b	growth differentiation factor 10	protein-coding
mm_50725.1	chr6	52245966	52245987	+	1	NA	promoter-TSS (NM_010450)	promoter-TSS (NM_010450)	-166	NM_010450	15396	Mm.26954	NM_010450	ENSMUSG00000038210	Hoxa11	Hox-1.9|Hoxa-11	homeobox A11	protein-coding
mm_172242.1	chr6	69035520	69035535	-	1	NA	Intergenic	L1Md_T|LINE|L1	291647	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_138687.1	chr17	35947162	35947170	+	1	NA	promoter-TSS (NR_028278)	promoter-TSS (NR_028278)	12	NR_028278	667766	Mm.29385	NR_028278		Gm8801	-	protein phosphatase 1, regulatory subunit 10 pseudogene	pseudo
mm_81371.1	chr9	108854025	108854065	+	1	NA	promoter-TSS (NM_134420)	promoter-TSS (NM_134420)	2	NM_134420	171429	Mm.45201	NM_134420	ENSMUSG00000023259	Slc26a6	B930010B04Rik|CFEX|Pat-1|Pat1	solute carrier family 26, member 6	protein-coding
mm_167036.1	chr7	75455536	75455542	+	1	NA	promoter-TSS (NM_029332)	promoter-TSS (NM_029332)	5	NM_029332	75547	Mm.216107	NM_029332	ENSMUSG00000066406	Akap13	1700026G02Rik|5730522G15Rik|5830460E08Rik|AKAP-13|AKAP-Lbc|BRX|Ht31|LBC|PROTO-LB|PROTO-LBC	A kinase (PRKA) anchor protein 13	protein-coding
mm_129942.1	chr15	84856542	84856546	-	1	NA	promoter-TSS (NM_001081166)	promoter-TSS (NM_001081166)	-415	NR_030731	271305	Mm.101022	NM_001081166	ENSMUSG00000016624	Phf21b	A730032D07Rik	PHD finger protein 21B	protein-coding
mm_95019.1	chr11	32001271	32001278	+	1	NA	promoter-TSS (NM_001290681)	promoter-TSS (NM_001290681)	-3	NM_001290681	18197	Mm.3304	NM_008741	ENSMUSG00000020297	Nsg2	-	neuron specific gene family member 2	protein-coding
mm_11928.1	chr2	52121464	52121477	+	1	NA	3' UTR (NM_175238, exon 36 of 36)	3' UTR (NM_175238, exon 36 of 36)	48633	NM_175238	51869	Mm.254530	NM_175238	ENSMUSG00000036202	Rif1	5730435J01Rik|6530403D07Rik|AU016181|AW549474|D2Ertd145e	replication timing regulatory factor 1	protein-coding
mm_173205.1	chrX	69606181	69606195	-	1	NA	intron (NM_008032, intron 3 of 19)	intron (NM_008032, intron 3 of 19)	245857	NM_008032	14266	Mm.466576	NM_008032	ENSMUSG00000031189	Aff2	FMR2P|Fmr2|Ox19|Oxh	AF4/FMR2 family, member 2	protein-coding
mm_148584.1	chr19	5041516	5041533	+	1	NA	TTS (NM_175383)	TTS (NM_175383)	120	NM_134155	107392	Mm.29628	NM_134155	ENSMUSG00000080268	Brms1	AV003220|AW554636	breast cancer metastasis-suppressor 1	protein-coding
mm_3588.1	chr1	151354986	151354991	+	1	NA	intron (NM_054102, intron 7 of 14)	T-rich|Low_complexity|Low_complexity	10490	NM_001039511	117198	Mm.33764	NM_028582	ENSMUSG00000023150	Ivns1abp	1190004M08Rik|1700126I16Rik|AA960440|HSPC068|ND1|NS-1|NS1-BP|Nd1-L|Nd1-S|mKIAA0850	influenza virus NS1A binding protein	protein-coding
mm_135287.1	chr16	38452684	38452704	-	1	NA	promoter-TSS (NM_007414)	promoter-TSS (NM_007414)	-5	NM_007414	11544	Mm.20047	NM_007414	ENSMUSG00000002844	Adprh	Arh1	ADP-ribosylarginine hydrolase	protein-coding
mm_39145.1	chr4	155345697	155345799	-	1	NA	promoter-TSS (NM_001039079)	promoter-TSS (NM_001039079)	41	NM_001039079	18762	Mm.28561	NM_008860	ENSMUSG00000029053	Prkcz	AI098070|C80388|Pkcz|R74924|aPKCzeta|nPKC-zeta|zetaPKC	protein kinase C, zeta	protein-coding
mm_83973.1	chr9	57261577	57261585	-	1	NA	intron (NM_028820, intron 1 of 2)	CpG	1018	NM_028820	74211	Mm.428905	NM_028820	ENSMUSG00000032300	1700017B05Rik	AA682102|D9Ertd278e	RIKEN cDNA 1700017B05 gene	protein-coding
mm_18064.1	chr2	42079634	42079637	-	1	NA	intron (NM_053011, intron 2 of 90)	intron (NM_053011, intron 2 of 90)	367933	NR_105754	102465171		NR_105754	ENSMUSG00000098660	Mir6336	Gm27584|mmu-mir-6336	microRNA 6336	ncRNA
mm_90845.1	chr10	8760603	8760626	-	1	NA	intron (NM_175155, intron 8 of 19)	intron (NM_175155, intron 8 of 19)	125456	NM_175155	70097	Mm.338275	NM_175155	ENSMUSG00000015305	Sash1	1100001C18Rik|2500002E12Rik|A330076K04Rik|mKIAA0790	SAM and SH3 domain containing 1	protein-coding
mm_7647.1	chr1	128299590	128299634	-	1	NA	intron (NM_001081078, intron 8 of 16)	B4|SINE|B4	28706	NM_001081078	226413	Mm.26930	NM_001081078	ENSMUSG00000026354	Lct	Gm100|LAC|LPH|Lphl	lactase	protein-coding
mm_117550.1	chr13	84056438	84056468	-	1	NA	intron (NR_131220, intron 1 of 1)	intron (NR_131220, intron 1 of 1)	8321	NR_131220	553095	Mm.39702	NR_131220	ENSMUSG00000098087	Gm17750	-	predicted gene, 17750	ncRNA
mm_107328.1	chr12	31735692	31735714	+	1	NA	intron (NM_001163126, intron 6 of 22)	(T)n|Simple_repeat|Simple_repeat	-21777	NM_175191	73010	Mm.441517	NM_175191	ENSMUSG00000044067	Gpr22	2900068K05Rik|AW061316	G protein-coupled receptor 22	protein-coding
mm_53093.1	chr6	125009114	125009142	+	1	NA	promoter-TSS (NM_175557)	promoter-TSS (NM_175557)	-110	NM_001252083	269800	Mm.108677	NM_175557	ENSMUSG00000038346	Zfp384	BB163993|C130073D16Rik|Ciz|NP|Nmp4	zinc finger protein 384	protein-coding
mm_92121.1	chr10	63339058	63339068	-	1	NA	promoter-TSS (NM_001159589)	promoter-TSS (NM_001159589)	-28	NM_001159589	93759	Mm.351459	NM_019812	ENSMUSG00000020063	Sirt1	AA673258|SIR2L1|Sir2|Sir2a|Sir2alpha	sirtuin 1	protein-coding
mm_13168.1	chr2	92609568	92609588	+	1	NA	intron (NM_023850, intron 1 of 2)	MLTR31C_MM|LTR|ERVK	9871	NM_023850	76969	Mm.38021	NM_023850	ENSMUSG00000027221	Chst1	2610008E20Rik|AW125896|C6ST|GST-1|Gst1|KSGAL6ST	carbohydrate (keratan sulfate Gal-6) sulfotransferase 1	protein-coding
mm_58699.1	chr7	12927342	12927350	+	1	NA	promoter-TSS (NM_029809)	promoter-TSS (NM_029809)	-70	NM_029809	381845	Mm.439896	NM_029809	ENSMUSG00000033967	Rnf225	2310014L17Rik|AV237412|C77118	ring finger protein 225	protein-coding
mm_79548.1	chr9	57922521	57922538	+	1	NA	exon (NM_027086, exon 9 of 11)	exon (NM_027086, exon 9 of 11)	11543	NM_001122873	69459	Mm.41735	NM_027086	ENSMUSG00000055720	Ubl7	2300004C15Rik	ubiquitin-like 7 (bone marrow stromal cell-derived)	protein-coding
mm_50874.1	chr6	55452271	55452281	+	1	NA	5' UTR (NM_001025372, exon 1 of 16)	5' UTR (NM_001025372, exon 1 of 16)	298	NM_007407	11517	Mm.44245	NM_007407	ENSMUSG00000029778	Adcyap1r1	2900024I10Rik|AI846590|PAC1|PAC1R|PACAP1-R	adenylate cyclase activating polypeptide 1 receptor 1	protein-coding
mm_11306.1	chr2	30263060	30263106	+	1	NA	3' UTR (NM_177725, exon 4 of 4)	3' UTR (NM_177725, exon 4 of 4)	-3120	NM_001252568	227696	Mm.297949	NM_172267	ENSMUSG00000079484	Phyhd1	-	phytanoyl-CoA dioxygenase domain containing 1	protein-coding
mm_13442.1	chr2	105127201	105127222	+	1	NA	promoter-TSS (NR_015462)	promoter-TSS (NR_015462)	682	NM_144783	22431	Mm.389339	NM_144783	ENSMUSG00000016458	Wt1	D630046I19Rik|Wt-1	Wilms tumor 1 homolog	protein-coding
mm_26482.1	chr3	144691938	144691979	+	1	NA	exon (NM_019464, exon 8 of 9)	exon (NM_019464, exon 8 of 9)	28377	NM_001282042	54673	Mm.271775	NM_019464	ENSMUSG00000037062	Sh3glb1	AA409932|AI314629|AU015566|Bif-1|mKIAA0491	SH3-domain GRB2-like B1 (endophilin)	protein-coding
mm_141578.1	chr17	32364416	32364426	-	1	NA	intron (NR_033525, intron 4 of 10)	intron (NR_033525, intron 4 of 10)	-13844	NM_017476	54194	Mm.281005	NM_017476	ENSMUSG00000002625	Akap8l	HAP95|Nakap95	A kinase (PRKA) anchor protein 8-like	protein-coding
mm_162954.1	chr11	4233054	4233064	+	1	NA	Intergenic	Intergenic	-3726	NM_001013365	18413	Mm.131422	NM_001013365	ENSMUSG00000058755	Osm	OncoM	oncostatin M	protein-coding
mm_47790.1	chr5	132250802	132250825	-	1	NA	intron (NM_177047, intron 2 of 18)	L1_Mur3|LINE|L1	291530	NM_177047	319974	Mm.409595	NM_177047	ENSMUSG00000029673	Auts2	2700063G02Rik|A730011F23Rik|D830032G16Rik	autism susceptibility candidate 2	protein-coding
mm_51369.1	chr6	72744021	72744058	+	1	NA	intron (NM_001079822, intron 3 of 12)	intron (NM_001079822, intron 3 of 12)	45006	NM_001079822	21415	Mm.440067	NM_009332	ENSMUSG00000055799	Tcf7l1	Tcf-3|Tcf3|bHLHb21	transcription factor 7 like 1 (T cell specific, HMG box)	protein-coding
mm_119301.1	chr14	34709869	34709872	+	1	NA	intron (NM_001004436, intron 4 of 18)	intron (NM_001004436, intron 4 of 18)	35942	NM_001301330	218914	Mm.27957	NM_001004436	ENSMUSG00000041408	Wapl	A530089A20Rik|BC037674|DIF-2|FOE|Wapal	WAPL cohesin release factor	protein-coding
mm_91968.1	chr10	61416701	61416707	-	1	NA	Intergenic	Intergenic	-1268	NM_013611	18119	Mm.57195	NM_013611	ENSMUSG00000037171	Nodal	Tg.413d	nodal	protein-coding
mm_8815.1	chr1	161979685	161979687	-	1	NA	promoter-TSS (NM_001204904)	promoter-TSS (NM_001204904)	-50	NM_001204904	75368	Mm.108728	NM_001204904	ENSMUSG00000086277	4930558K02Rik	-	RIKEN cDNA 4930558K02 gene	protein-coding
mm_28589.1	chr3	94412888	94412890	-	1	NA	promoter-TSS (NM_028307)	promoter-TSS (NM_028307)	-429	NM_028307	72634	Mm.331198	NM_028307	ENSMUSG00000041912	Tdrkh	2700091C21Rik|Tdrd2	tudor and KH domain containing protein	protein-coding
mm_168226.1	chr10	79960174	79960176	+	1	NA	promoter-TSS (NM_175450)	promoter-TSS (NM_175450)	23	NM_175450	216156	Mm.35828	NM_175450	ENSMUSG00000035754	Wdr18	2310012I10Rik|AU044733|AW122032	WD repeat domain 18	protein-coding
mm_22380.1	chr2	181156817	181156829	-	1	NA	5' UTR (NM_007906, exon 1 of 8)	5' UTR (NM_007906, exon 1 of 8)	192	NM_007906	13628	Mm.2645	NM_007906	ENSMUSG00000016349	Eef1a2	Eef1a|S1|wasted|wst	eukaryotic translation elongation factor 1 alpha 2	protein-coding
mm_64127.1	chr7	141145128	141145130	+	1	NA	intron (NM_013782, intron 3 of 11)	B1_Mur2|SINE|Alu	13843	NM_013782	27388	Mm.293591	NM_013782	ENSMUSG00000025495	Ptdss2	AI481134|AI988017|PSS2	phosphatidylserine synthase 2	protein-coding
mm_98276.1	chr11	89016934	89016948	+	1	NA	3' UTR (NM_009546, exon 9 of 9)	3' UTR (NM_009546, exon 9 of 9)	17538	NM_009546	217069	Mm.248445	NM_009546	ENSMUSG00000000275	Trim25	AA960166|AL022677|EFP|Zfp147	tripartite motif-containing 25	protein-coding
mm_5443.1	chr1	36010999	36011005	-	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	-57398	NM_015818	50785	Mm.213566	NM_015818	ENSMUSG00000045216	Hs6st1	6Ost1	heparan sulfate 6-O-sulfotransferase 1	protein-coding
mm_158392.1	chrX	136271431	136271453	-	1	NA	exon (NM_009750, exon 3 of 3)	exon (NM_009750, exon 3 of 3)	1189	NM_001110234	12070	Mm.90787	NM_009750	ENSMUSG00000046432	Bex3	AL033356|DXWsu67e|Gcap27|Nade|Ngfrap1	brain expressed X-linked 3	protein-coding
mm_137260.1	chr17	24632726	24632746	+	1	NA	promoter-TSS (NM_008743)	promoter-TSS (NM_008743)	54	NM_008743	18207	Mm.148315	NM_008743	ENSMUSG00000041429	Nthl1	Nth1|Octs3	nth (endonuclease III)-like 1 (E.coli)	protein-coding
mm_51063.1	chr6	65818310	65818318	+	1	NA	intron (NM_029549, intron 2 of 10)	intron (NM_029549, intron 2 of 10)	39352	NM_029549	70779	Mm.263355	NM_027547	ENSMUSG00000029913	Prdm5	4432417F03Rik|6530401I24Rik|AI197291|E130112L17Rik|PFM2	PR domain containing 5	protein-coding
mm_108652.1	chr12	86275804	86275808	+	1	NA	intron (NM_001324488, intron 8 of 8)	intron (NM_001324488, intron 8 of 8)	33948	NM_001324488	70373	Mm.252967	NM_027405	ENSMUSG00000021254	Gpatch2l	1700020O03Rik|4732487G21Rik|A630090I05Rik|Kiaa1152	G patch domain containing 2 like	protein-coding
mm_82152.1	chr9	123775031	123775041	+	1	NA	intron (NM_009913, intron 2 of 2)	intron (NM_009913, intron 2 of 2)	7825	NM_001166625	12769	Mm.440604	NM_009913	ENSMUSG00000029530	Ccr9	A130091K22Rik|Cmkbr10|GPR-9-6	chemokine (C-C motif) receptor 9	protein-coding
mm_12499.1	chr2	71867755	71867759	+	1	NA	intron (NR_039557, intron 3 of 3).2	intron (NR_039557, intron 3 of 3).2	-5467	NM_172665	228026	Mm.34411	NM_172665	ENSMUSG00000006494	Pdk1	B830012B01|D530020C15Rik	pyruvate dehydrogenase kinase, isoenzyme 1	protein-coding
mm_97868.1	chr11	83122278	83122289	+	1	NA	3' UTR (NM_011407, exon 2 of 2)	3' UTR (NM_011407, exon 2 of 2)	5438	NM_011407	20555	Mm.10948	NM_011407	ENSMUSG00000078763	Slfn1	AV316259	schlafen 1	protein-coding
mm_166715.1	chr6	118277521	118277522	-	1	NA	Intergenic	Lx8|LINE|L1	-29067	NR_040527	73531	Mm.396245	NR_040527	ENSMUSG00000107637	1700069P05Rik	-	RIKEN cDNA 1700069P05 gene	ncRNA
mm_102957.1	chr11	69664501	69664517	-	1	NA	intron (NM_001291058, intron 5 of 5)	intron (NM_001291058, intron 5 of 5)	1466	NR_035455	100316840		NR_035455	ENSMUSG00000088752	Mir1934	mir-1934|mmu-mir-1934	microRNA 1934	ncRNA
mm_45992.1	chr5	90504971	90504978	-	1	NA	exon (NM_007423, exon 11 of 15)	exon (NM_007423, exon 11 of 15)	-13975	NM_145146	280662	Mm.348786	NM_145146	ENSMUSG00000029369	Afm	Alf|alpha-Alb	afamin	protein-coding
mm_5237.1	chr1	15892658	15892729	-	1	NA	promoter-TSS (NM_001033288)	promoter-TSS (NM_001033288)	29	NM_001033288	226866	Mm.131665	NM_001033288	ENSMUSG00000032719	Sbspon	Gm106|Rpesp	somatomedin B and thrombospondin, type 1 domain containing	protein-coding
mm_82343.1	chr9	13105852	13105858	-	1	NA	promoter-TSS (NR_040755)	promoter-TSS (NR_040755)	0	NR_040755	78219	Mm.414868	NR_040755	ENSMUSG00000111830	4930568E12Rik	-	RIKEN cDNA 4930568E12 gene	ncRNA
mm_63826.1	chr7	134800705	134800709	+	1	NA	intron (NM_001033420, intron 22 of 51)	intron (NM_001033420, intron 22 of 51)	130020	NM_001033420	330662	Mm.436572	NM_001033420	ENSMUSG00000058325	Dock1	9130006G06Rik|AI854900|D630004B07Rik	dedicator of cytokinesis 1	protein-coding
mm_132551.1	chr16	37883631	37883641	+	1	NA	3' UTR (NM_177093, exon 4 of 4)	3' UTR (NM_177093, exon 4 of 4)	15236	NM_177093	320184	Mm.390882	NM_177093	ENSMUSG00000034158	Lrrc58	1810012N18Rik|C330018J07Rik	leucine rich repeat containing 58	protein-coding
mm_80553.1	chr9	83014856	83014864	+	1	NA	Intergenic	RMER15|LTR|ERVL	-39371	NM_001081216	83946	Mm.221688	NM_031879	ENSMUSG00000032253	Phip	2810004D21Rik|4632404O06Rik|Ndrp|Wdr11	pleckstrin homology domain interacting protein	protein-coding
mm_133437.1	chr16	87699055	87699058	+	1	NA	5' UTR (NM_007520, exon 1 of 5)	5' UTR (NM_007520, exon 1 of 5)	102	NM_007520	12013	Mm.26147	NM_007520	ENSMUSG00000025612	Bach1	6230421P05Rik|AI323795	BTB and CNC homology 1, basic leucine zipper transcription factor 1	protein-coding
mm_93549.1	chr10	116113945	116113949	-	1	NA	promoter-TSS (NM_001161855)	promoter-TSS (NM_001161855)	-30	NM_001161855	619332	Mm.391427	NM_001033821	ENSMUSG00000074734	4933416C03Rik	-	RIKEN cDNA 4933416C03 gene	protein-coding
mm_137973.1	chr17	33557758	33557806	+	1	NA	intron (NM_053214, intron 1 of 27)	intron (NM_053214, intron 1 of 27)	2075	NM_053214	17916	Mm.42019	NM_053214	ENSMUSG00000024300	Myo1f	C330006B10Rik	myosin IF	protein-coding
mm_89459.1	chr10	93188180	93188214	+	1	NA	intron (NM_146239, intron 1 of 16)	intron (NM_146239, intron 1 of 16)	25412	NR_035452	100316689		NR_035452	ENSMUSG00000089214	Mir1931	mir-1931|mmu-mir-1931	microRNA 1931	ncRNA
mm_66465.1	chr7	44929392	44929402	-	1	NA	promoter-TSS (NM_001077264)	promoter-TSS (NM_001077264)	93	NM_007458	11771	Mm.6877	NM_007458	ENSMUSG00000060279	Ap2a1	Adtaa	adaptor-related protein complex 2, alpha 1 subunit	protein-coding
mm_128737.1	chr15	64304953	64304970	-	1	NA	intron (NM_010026, intron 3 of 30)	RMER4B|LTR|ERVK	7712	NM_001276462	13196	Mm.277236	NM_010026	ENSMUSG00000022377	Asap1	AV239055|DEF-1|Ddef1|PAP|mKIAA1249|s19	ArfGAP with SH3 domain, ankyrin repeat and PH domain1	protein-coding
mm_135433.1	chr16	45382906	45382917	-	1	NA	3' UTR (NM_010818, exon 6 of 6)	3' UTR (NM_010818, exon 6 of 6)	26142	NM_010818	17470	Mm.245851	NM_010818	ENSMUSG00000022661	Cd200	Mox2|OX2	CD200 antigen	protein-coding
mm_11598.1	chr2	33641251	33641263	+	1	NA	promoter-TSS (NM_010725)	promoter-TSS (NM_010725)	64	NR_046275	100504399	Mm.72070	NM_177842		C130021I20Rik	-	Riken cDNA C130021I20 gene	ncRNA
mm_52314.1	chr6	108834553	108834563	+	1	NA	intron (NM_138677, intron 1 of 11)	intron (NM_138677, intron 1 of 11)	5917	NM_138677	192193	Mm.21596	NM_138677	ENSMUSG00000030104	Edem1	A130059K23Rik|EDEM|mKIAA0212	ER degradation enhancer, mannosidase alpha-like 1	protein-coding
mm_55775.1	chr6	78468864	78468878	-	1	NA	promoter-TSS (NM_011260)	promoter-TSS (NM_011260)	3	NM_011260	19695	Mm.252385	NM_011260	ENSMUSG00000030017	Reg3g	AI449515|REG-3-gamma|reg III-gamma	regenerating islet-derived 3 gamma	protein-coding
mm_161336.1	chr14	51096011	51096011	+	1	NA	promoter-TSS (NM_201239)	promoter-TSS (NM_201239)	11	NM_201239	58809	Mm.202665	NM_021472	ENSMUSG00000021876	Rnase4	C730049F20Rik|Rab1	ribonuclease, RNase A family 4	protein-coding
mm_31235.1	chr4	44664440	44664445	+	1	NA	intron (NM_008782, intron 5 of 9)	CpG	-38358	NR_073462	70602	Mm.491142	NR_073462	ENSMUSG00000103995	5730488B01Rik	-	RIKEN cDNA 5730488B01 gene	ncRNA
mm_128515.1	chr15	53346097	53346110	-	1	NA	promoter-TSS (NM_010162)	promoter-TSS (NM_010162)	80	NM_010162	14042	Mm.309395	NM_010162	ENSMUSG00000061731	Ext1	AA409028	exostoses (multiple) 1	protein-coding
mm_108119.1	chr12	75750073	75750117	+	1	NA	Intergenic	Intergenic	-14366	NM_030750	81535	Mm.280199	NM_030750	ENSMUSG00000021054	Sgpp1	AI463453|SPP|SPP1|Spph1	sphingosine-1-phosphate phosphatase 1	protein-coding
mm_147481.1	chr18	47248120	47248152	-	1	NA	3' UTR (NM_018744, exon 19 of 19)	3' UTR (NM_018744, exon 19 of 19)	120732	NM_018744	20358	Mm.40909	NM_018744	ENSMUSG00000019647	Sema6a	A730020P05Rik|AI851735|Sema6A-1|Semaq|VIa	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A	protein-coding
mm_49007.1	chr6	4758299	4758301	+	1	NA	3' UTR (NM_130877, exon 2 of 2)	3' UTR (NM_130877, exon 2 of 2)	10994	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_127571.1	chr15	102279482	102279488	+	1	NA	promoter-TSS (NM_134100)	promoter-TSS (NM_134100)	29	NM_134100	106073	Mm.287740	NM_134100	ENSMUSG00000045665	Mfsd5	AA409375|AW556797|D15Mgi27	major facilitator superfamily domain containing 5	protein-coding
mm_27921.1	chr3	79532165	79532175	-	1	NA	intron (NM_001162999, intron 1 of 16)	intron (NM_001162999, intron 1 of 16)	35509	NM_001162999	329679	Mm.244005	NM_001162999	ENSMUSG00000061175	Fnip2	D630023B12Rik|mKIAA1450	folliculin interacting protein 2	protein-coding
mm_77616.1	chr8	123925866	123925874	-	1	NA	intron (NM_172288, intron 12 of 25)	intron (NM_172288, intron 12 of 25)	23395	NM_172288	234865	Mm.267812	NM_172288	ENSMUSG00000039509	Nup133	mermaid	nucleoporin 133	protein-coding
mm_48137.1	chr5	137150269	137150275	-	1	NA	Intergenic	(TGG)n|Simple_repeat|Simple_repeat	-34065	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_37749.1	chr4	129621393	129621427	-	1	NA	intron (NM_025455, intron 2 of 5)	intron (NM_025455, intron 2 of 5)	-2317	NM_198026	230767	Mm.441132	NM_198026	ENSMUSG00000040795	Iqcc	BC026978	IQ motif containing C	protein-coding
mm_156123.1	chrX	116448940	116448948	+	1	NA	promoter-TSS (NM_001033471)	promoter-TSS (NM_001033471)	0	NM_001033471	382239	Mm.336224	NM_001033471	ENSMUSG00000072995	Cpxcr1	Gm1143	CPX chromosome region, candidate 1	protein-coding
mm_54677.1	chr6	39412222	39412223	-	1	NA	intron (NM_018810, intron 1 of 7)	intron (NM_018810, intron 1 of 7)	7554	NM_001311109	54484	Mm.270484	NM_018810	ENSMUSG00000029922	Mkrn1	RFP	makorin, ring finger protein, 1	protein-coding
mm_24633.1	chr3	94310238	94310270	+	1	NA	exon (NM_029431, exon 1 of 6)	exon (NM_029431, exon 1 of 6)	122	NM_029431	75778	Mm.45092	NM_029431	ENSMUSG00000028145	Them4	2700077M13Rik|4921507I02Rik	thioesterase superfamily member 4	protein-coding
mm_167516.1	chr9	14643610	14643616	+	1	NA	Intergenic	Intergenic	-28613	NM_001081395	75723	Mm.159552	NM_001081395	ENSMUSG00000013076	Amotl1	2310010G08Rik|2310067L22Rik|4932416D09Rik|JEAP|mFLJ00155	angiomotin-like 1	protein-coding
mm_124342.1	chr14	103844345	103844359	-	1	NA	promoter-TSS (NM_001276296)	promoter-TSS (NM_001276296)	124	NM_001136061	13618	Mm.229532	NM_007904	ENSMUSG00000022122	Ednrb	ET-B|ET-BR|ETR-b|ETb|Sox10m1	endothelin receptor type B	protein-coding
mm_165013.1	chr19	28402406	28402409	+	1	NA	intron (NM_001305671, intron 3 of 9)	intron (NM_001305671, intron 3 of 9)	-275817	NR_045330	320176	Mm.406716	NR_045330	ENSMUSG00000097735	D930032P07Rik	-	RIKEN cDNA D930032P07 gene	ncRNA
mm_18107.1	chr2	44988915	44988937	-	1	NA	exon (NM_015753, exon 10 of 10)	exon (NM_015753, exon 10 of 10)	34251	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_137153.1	chr17	23681543	23681553	+	1	NA	exon (NM_018777, exon 3 of 3)	exon (NM_018777, exon 3 of 3)	2183	NM_018777	54419	Mm.86421	NM_018777	ENSMUSG00000023906	Cldn6	AL024037	claudin 6	protein-coding
mm_170215.1	chr17	74528840	74528854	+	1	NA	intron (NM_007566, intron 1 of 72)	CpG	552	NM_007566	12211	Mm.442564	NM_007566	ENSMUSG00000024073	Birc6	A430032G04Rik|A430040A19Rik|AA501170|Bruce|D630005A10Rik|mKIAA1289	baculoviral IAP repeat-containing 6	protein-coding
mm_145366.1	chr18	56732672	56732676	+	1	NA	intron (NM_010721, intron 4 of 10)	RLTR51A_Mm|LTR|ERVK?	24861	NM_010721	16906	Mm.4105	NM_010721	ENSMUSG00000024590	Lmnb1	-	lamin B1	protein-coding
mm_90507.1	chr10	128039594	128039606	+	1	NA	exon (NM_001113199, exon 3 of 9)	exon (NM_001113199, exon 3 of 9)	4254	NM_001113199	17938	Mm.3746	NM_013608	ENSMUSG00000061315	Naca	AL022831|AL024382|Gm1878|mKIAA0363|skNAC	nascent polypeptide-associated complex alpha polypeptide	protein-coding
mm_99890.1	chr11	109525314	109525343	+	1	NA	intron (NM_028710, intron 6 of 13)	intron (NM_028710, intron 6 of 13)	-18383	NM_001166177	74008	Mm.482224	NM_028710	ENSMUSG00000020604	Arsg	6330406P08Rik|AI846872	arylsulfatase G	protein-coding
mm_127742.1	chr15	103308368	103308406	+	1	NA	3' UTR (NM_030720, exon 2 of 2)	3' UTR (NM_030720, exon 2 of 2)	2051	NM_030720	80910	Mm.160369	NM_030720	ENSMUSG00000063234	Gpr84	EX33	G protein-coupled receptor 84	protein-coding
mm_54272.1	chr6	29026179	29026182	-	1	NA	Intergenic	Intergenic	3561	NR_029567	387237		NR_029567	ENSMUSG00000065469	Mir129-1	Mirn129-1|Mirn129b|miR-129b|mir-129-1	microRNA 129-1	ncRNA
mm_53330.1	chr6	129233059	129233112	+	1	NA	non-coding (NR_040268, exon 3 of 4)	non-coding (NR_040268, exon 3 of 4)	4960	NR_040265	76432	Mm.261738	NR_040265	ENSMUSG00000097354	2310001H17Rik	AI646108	RIKEN cDNA 2310001H17 gene	ncRNA
mm_52550.1	chr6	115944937	115944943	+	1	NA	promoter-TSS (NM_138311)	promoter-TSS (NM_138311)	9	NM_138311	171506	Mm.21899	NM_138311	ENSMUSG00000042279	H1foo	C86609|H1.8|H1fo|H1oo	H1 histone family, member O, oocyte-specific	protein-coding
mm_35900.1	chr4	49597426	49597493	-	1	NA	intron (NM_025944, intron 1 of 1)	CpG	411	NM_025944	67063	Mm.490285	NM_025944	ENSMUSG00000039611	Tmem246	2810432L12Rik|9330170P15Rik|AI835809	transmembrane protein 246	protein-coding
mm_128191.1	chr15	34983345	34983356	-	1	NA	intron (NM_019635, intron 8 of 10)	intron (NM_019635, intron 8 of 10)	145301	NM_001271704	16539	Mm.71045	NM_181317	ENSMUSG00000050963	Kcns2	E130006J24Rik|Kv9.2	K+ voltage-gated channel, subfamily S, 2	protein-coding
mm_89130.1	chr10	85102738	85102748	+	1	NA	promoter-TSS (NM_010214)	promoter-TSS (NM_010214)	116	NM_001013028	103266	Mm.335025	NM_001013028	ENSMUSG00000060935	Tmem263	AI597468	transmembrane protein 263	protein-coding
mm_145219.1	chr18	50053437	50053457	+	1	NA	5' UTR (NM_134131, exon 1 of 2)	5' UTR (NM_134131, exon 1 of 2)	165	NM_134131	106869	Mm.27740	NM_134131	ENSMUSG00000062210	Tnfaip8	AA987150|E130304C20Rik|ENSMUSG00000073567|Gg2-1|Gm10539|Nded|Ssc-2|Tipe	tumor necrosis factor, alpha-induced protein 8	protein-coding
mm_129588.1	chr15	79786878	79786885	-	1	NA	3' UTR (NM_001013360, exon 8 of 8)	3' UTR (NM_001013360, exon 8 of 8)	-12414	NM_017470	54152	Mm.288159	NM_017470	ENSMUSG00000022420	Dnal4	D15Ertd424e|Dnalc4	dynein, axonemal, light chain 4	protein-coding
mm_90086.1	chr10	116914119	116914128	+	1	NA	exon (NM_001003950, exon 7 of 10)	exon (NM_001003950, exon 7 of 10)	-17244	NM_001033333	237558	Mm.336386	NM_001033333	ENSMUSG00000034057	Myrfl	Gm239	myelin regulatory factor-like	protein-coding
mm_87654.1	chr10	58446846	58446928	+	1	NA	promoter-TSS (NM_011240)	promoter-TSS (NM_011240)	35	NM_011240	19386	Mm.431695	NM_011240	ENSMUSG00000003226	Ranbp2	A430087B05Rik|AI256741|NUP358	RAN binding protein 2	protein-coding
mm_115576.1	chr13	11573304	11573314	-	1	NA	intron (NM_023868, intron 97 of 104)	B3|SINE|B2	51257	NR_027813	664793	Mm.410565	NR_027813		Zp4-ps	EG664793|Zp4|Zpb	zona pellucida glycoprotein 4, pseudogene	pseudo
mm_69800.1	chr7	141172810	141172862	-	1	NA	promoter-TSS (NM_001172100)	promoter-TSS (NM_001172100)	15	NM_001172100	107702	Mm.197493	NM_145135	ENSMUSG00000038650	Rnh1	AW546468|C80305|RNH	ribonuclease/angiogenin inhibitor 1	protein-coding
mm_163703.1	chr13	104377054	104377057	+	1	NA	intron (NR_136938, intron 12 of 26)	intron (NR_136938, intron 12 of 26)	89220	NM_001081020	108154	Mm.208125	NM_175496	ENSMUSG00000046169	Adamts6	A930019D11Rik|ADAM-TS6|b2b1879.1Clo|b2b2029Clo|b2b2182Clo|b2b2187.1Clo|b2b2228Clo	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 6	protein-coding
mm_118319.1	chr13	113593693	113593741	-	1	NA	3' UTR (NM_130796, exon 2 of 2)	3' UTR (NM_130796, exon 2 of 2)	24847	NM_130796	170625	Mm.33721	NM_130796	ENSMUSG00000042364	Snx18	Snag1	sorting nexin 18	protein-coding
mm_25503.1	chr3	109524242	109524255	+	1	NA	intron (NM_020505, intron 12 of 26)	intron (NM_020505, intron 12 of 26)	-49759	NM_146139	57257	Mm.282257	NM_020505	ENSMUSG00000033721	Vav3	A530094I06Rik|AA986410|Idd18.1	vav 3 oncogene	protein-coding
mm_124955.1	chr15	12918393	12918407	+	1	NA	intron (NM_001130149, intron 29 of 34)	intron (NM_001130149, intron 29 of 34)	93585	NM_001130149	14000	Mm.293142	NM_026799	ENSMUSG00000022191	Drosha	1110013A17Rik|AI874853|Etohi2|Rn3|Rnasen	drosha, ribonuclease type III	protein-coding
mm_113029.1	chr13	23493820	23493830	+	1	NA	Intergenic	MER34|LTR|ERV1	-4968	NM_001289614	238555	Mm.129668	NM_175938	ENSMUSG00000053216	Btn2a2	Btn2|D030063K05	butyrophilin, subfamily 2, member A2	protein-coding
mm_78998.1	chr9	45406115	45406118	+	1	NA	promoter-TSS (NM_007503)	promoter-TSS (NM_007503)	39	NM_007503	11936	Mm.22742	NM_007503	ENSMUSG00000059412	Fxyd2	Atp1g1	FXYD domain-containing ion transport regulator 2	protein-coding
mm_87706.1	chr10	60002586	60002629	+	1	NA	promoter-TSS (NM_001199187)	promoter-TSS (NM_001199187)	-198	NM_026937	69090	Mm.155839	NM_026937	ENSMUSG00000044475	Ascc1	1810015P09Rik|AI550520|ASC1p50|CGI-18	activating signal cointegrator 1 complex subunit 1	protein-coding
mm_143799.1	chr17	83181630	83181633	-	1	NA	Intergenic	Intergenic	-33652	NM_134117	106522	Mm.311974	NM_134117	ENSMUSG00000024247	Pkdcc	AI115348|AW548124|Adtk1|ESTM17|MAd1|Sgk493|Vlk|X83346	protein kinase domain containing, cytoplasmic	protein-coding
mm_28526.1	chr3	92621174	92621188	-	1	NA	5' UTR (NM_001166172, exon 2 of 3)	5' UTR (NM_001166172, exon 2 of 3)	479	NM_001166172	78382	Mm.235474	NM_001166172	ENSMUSG00000086848	Lce6a	2210420J11Rik	late cornified envelope 6A	protein-coding
mm_74024.1	chr8	121730080	121730164	+	1	NA	promoter-TSS (NM_020605)	promoter-TSS (NM_020605)	-437	NM_020605	57340	Mm.306870	NM_020605	ENSMUSG00000025318	Jph3	JP-3|Jp3	junctophilin 3	protein-coding
mm_13347.1	chr2	102948773	102948778	+	1	NA	Intergenic	Intergenic	-47110	NM_001039150	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_151087.1	chr19	47636430	47636442	+	1	NA	exon (NM_001164639, exon 14 of 18)	exon (NM_001164639, exon 14 of 18)	55606	NM_007732	12821	Mm.1225	NM_007732	ENSMUSG00000025064	Col17a1	BP180|Bpag|Bpag2	collagen, type XVII, alpha 1	protein-coding
mm_104166.1	chr11	87359087	87359093	-	1	NA	promoter-TSS (NM_177167)	promoter-TSS (NM_177167)	-96	NM_177167	320472	Mm.341988	NM_177167	ENSMUSG00000046442	Ppm1e	AW049266|B930008A12Rik|POPX1|PP2CH|mKIAA1072	protein phosphatase 1E (PP2C domain containing)	protein-coding
mm_150367.1	chr19	34649808	34649832	+	1	NA	3' UTR (NM_008331, exon 2 of 2)	3' UTR (NM_008331, exon 2 of 2)	8931	NM_008331	15957	Mm.439751	NM_008331	ENSMUSG00000034459	Ifit1	ISG56|Ifi56|P56	interferon-induced protein with tetratricopeptide repeats 1	protein-coding
mm_40537.1	chr5	57963597	57963638	+	1	NA	intron (NM_001310608, intron 3 of 3)	intron (NM_001310608, intron 3 of 3)	245536	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_124994.1	chr15	22789657	22789681	+	1	NA	Intergenic	Intergenic	-74685	NM_001165971	545091	Mm.475598	NM_001165971		Gm5803	EG545091	predicted gene 5803	protein-coding
mm_127837.1	chr15	6853126	6853129	-	1	NA	intron (NM_001310469, intron 2 of 17)	intron (NM_001310469, intron 2 of 17)	21186	NM_011019	18414	Mm.10760	NM_011019	ENSMUSG00000022146	Osmr	OSMRB	oncostatin M receptor	protein-coding
mm_64816.1	chr7	7278030	7278045	-	1	NA	intron (NR_003555, intron 1 of 6)	CpG	252	NR_003555	76229	Mm.387947	NM_001113468	ENSMUSG00000095730	Vmn2r29	6430701C03Rik	vomeronasal 2, receptor 29	protein-coding
mm_102677.1	chr11	65261709	65261725	-	1	NA	intron (NM_146386, intron 1 of 12)	intron (NM_146386, intron 1 of 12)	8272	NM_145136	214384	Mm.32257	NM_145136	ENSMUSG00000020542	Myocd	BSAC2A|Srfcp	myocardin	protein-coding
mm_158937.1	chr1	74362406	74362406	+	1	NA	5' UTR (NM_001033345, exon 2 of 10)	5' UTR (NM_001033345, exon 2 of 10)	298	NM_001033345	241112	Mm.310460	NM_001033345	ENSMUSG00000073650	Catip	Gm216	ciliogenesis associated TTC17 interacting protein	protein-coding
mm_160190.1	chr7	55806385	55806385	+	1	NA	intron (NM_146190, intron 9 of 22)	intron (NM_146190, intron 9 of 22)	12237	NM_146190	233276	Mm.284306	NM_146190	ENSMUSG00000033790	Tubgcp5	B130010C12Rik|GCP5|mKIAA1899	tubulin, gamma complex associated protein 5	protein-coding
mm_10733.1	chr2	22971117	22971137	+	1	NA	exon (NM_001077190, exon 3 of 11)	exon (NM_001077190, exon 3 of 11)	69114	NM_001077192	11308	Mm.205647	NM_007380	ENSMUSG00000058835	Abi1	E3B1|NAP1|Ssh3bp1|abi-1	abl-interactor 1	protein-coding
mm_51911.1	chr6	91212860	91212870	+	1	NA	5' UTR (NM_001081437, exon 1 of 17)	5' UTR (NM_001081437, exon 1 of 17)	101	NM_007992	14115	Mm.249146	NM_007992	ENSMUSG00000064080	Fbln2	5730577E14Rik|FIBL-2	fibulin 2	protein-coding
mm_70776.1	chr8	22192859	22192869	+	1	NA	promoter-TSS (NM_027338)	promoter-TSS (NM_027338)	4	NM_027338	70160	Mm.41453	NM_027338	ENSMUSG00000031479	Vps36	1700010A24Rik|2210415M20Rik|2810408E15Rik|Eap45	vacuolar protein sorting 36	protein-coding
mm_129958.1	chr15	85156127	85156137	-	1	NA	promoter-TSS (NR_040360)	promoter-TSS (NR_040360)	0	NR_040360	100502602	Mm.390830	NR_040360		Gm19277	-	predicted gene, 19277	ncRNA
mm_42760.1	chr5	121204478	121204499	+	1	NA	promoter-TSS (NM_011290)	promoter-TSS (NM_011290)	-13	NM_011290	19988	Mm.262021	NM_011290	ENSMUSG00000029614	Rpl6	Taxreb107	ribosomal protein L6	protein-coding
mm_111128.1	chr12	81472265	81472276	-	1	NA	exon (NM_025461, exon 4 of 4)	exon (NM_025461, exon 4 of 4)	12581	NR_132135	66272	Mm.439970	NM_025461	ENSMUSG00000091803	Cox16	1810020G14Rik|1810055I05Rik|BB388670	cytochrome c oxidase assembly protein 16	protein-coding
mm_95071.1	chr11	32611047	32611060	+	1	NA	intron (NM_009288, intron 13 of 18)	intron (NM_009288, intron 13 of 18)	-31502	NM_001271348	103583	Mm.28017	NM_134015	ENSMUSG00000020271	Fbxw11	2310065A07Rik|AA536858|BTRC2|BTRCP2|Fbxw1b|HOS	F-box and WD-40 domain protein 11	protein-coding
mm_146242.1	chr18	77281657	77281664	+	1	NA	promoter-TSS (NM_172834)	promoter-TSS (NM_172834)	-298	NM_172834	240411	Mm.380247	NM_172834	ENSMUSG00000032818	Loxhd1	1700096C21Rik|4932417K07|sba	lipoxygenase homology domains 1	protein-coding
mm_120291.1	chr14	63135606	63135643	+	1	NA	exon (NM_007798, exon 4 of 10)	exon (NM_007798, exon 4 of 10)	13162	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_120361.1	chr14	64434372	64434391	+	1	NA	intron (NM_001253712, intron 1 of 5)	intron (NM_001253712, intron 1 of 5)	6645	NM_001253715	110265	Mm.26713	NM_026322	ENSMUSG00000054733	Msra	2310045J23Rik|6530413P12Rik|MSR-A	methionine sulfoxide reductase A	protein-coding
mm_32182.1	chr4	100994607	100994633	+	1	NA	intron (NM_198037, intron 25 of 26)	intron (NM_198037, intron 25 of 26)	-74418	NM_183024	242570	Mm.185636	NM_183024	ENSMUSG00000035275	Raver2	A430091O22Rik	ribonucleoprotein, PTB-binding 2	protein-coding
mm_123562.1	chr14	66868920	66868948	-	1	NA	promoter-TSS (NM_001034881)	promoter-TSS (NM_001034881)	84	NM_001034881	432870	Mm.425890	NM_001034881	ENSMUSG00000075553	Gm5464	EG432870	predicted gene 5464	protein-coding
mm_79444.1	chr9	56090343	56090358	+	1	NA	5' UTR (NM_011193, exon 1 of 15)	5' UTR (NM_011193, exon 1 of 15)	374	NM_011193	19200	Mm.2534	NM_011193	ENSMUSG00000032322	Pstpip1	CD2BP1|def-2	proline-serine-threonine phosphatase-interacting protein 1	protein-coding
mm_40488.1	chr5	56896482	56896484	+	1	NA	Intergenic	Intergenic	821436	NR_015588	319216	Mm.332387	NR_015588	ENSMUSG00000097216	4932441J04Rik	-	RIKEN cDNA 4932441J04 gene	ncRNA
mm_5333.1	chr1	23922253	23922281	-	1	NA	5' UTR (NM_028534, exon 1 of 10)	5' UTR (NM_028534, exon 1 of 10)	114	NM_028534	98366	Mm.329963	NM_028534	ENSMUSG00000026155	Smap1	1700056O10Rik|4921514B13Rik|4921525H11Rik|AI462175	small ArfGAP 1	protein-coding
mm_56868.1	chr6	118479238	118479318	-	1	NA	promoter-TSS (NM_011763)	promoter-TSS (NM_011763)	-5	NM_011763	22750	Mm.106970	NM_011763	ENSMUSG00000072623	Zfp9	1810048F22Rik|AU016736|Krox-4|Zfp-9|mszf79-2	zinc finger protein 9	protein-coding
mm_81512.1	chr9	110034957	110034968	+	1	NA	exon (NM_008633, exon 7 of 19)	exon (NM_008633, exon 7 of 19)	-17059	NM_001311163	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_105885.1	chr11	114930700	114930714	-	1	NA	intron (NM_199221, intron 1 of 3)	intron (NM_199221, intron 1 of 3)	3679	NM_001347651	217304	Mm.185355	NM_199221	ENSMUSG00000063193	Cd300lb	CLM-7|Clm7|Gm253|LMIR5	CD300 molecule like family member B	protein-coding
mm_29659.1	chr3	122552339	122552341	-	1	NA	intron (NM_001114665, intron 10 of 15)	intron (NM_001114665, intron 10 of 15)	-10659	NR_106117	102465764		NR_106117	ENSMUSG00000104773	Mir7657	mmu-mir-7657	microRNA 7657	ncRNA
mm_49437.1	chr6	29313476	29313491	+	1	NA	Intergenic	L1M6|LINE|L1	-5657	NM_001289663	330277	Mm.87624	NM_207258	ENSMUSG00000039742	Fam71f1	GARI-L1|Gm764|NYD-SP18	family with sequence similarity 71, member F1	protein-coding
mm_87918.1	chr10	62504102	62504108	+	1	NA	intron (NM_011157, intron 1 of 2)	intron (NM_011157, intron 1 of 2)	3650	NM_011157	19073	Mm.338790	NM_011157	ENSMUSG00000020077	Srgn	Prg|Prg1|Sgc	serglycin	protein-coding
mm_68996.1	chr7	126675585	126675593	-	1	NA	intron (NM_133670, intron 1 of 6)	intron (NM_133670, intron 1 of 6)	768	NM_133670	20887	Mm.368982	NM_133670	ENSMUSG00000030711	Sult1a1	AI266890|PST|ST1A1|Stp|Stp1	sulfotransferase family 1A, phenol-preferring, member 1	protein-coding
mm_105994.1	chr11	115645061	115645065	-	1	NA	3' UTR (NM_008163, exon 6 of 6)	3' UTR (NM_008163, exon 6 of 6)	-16768	NM_001252395	67283	Mm.383426	NM_026071	ENSMUSG00000020744	Slc25a19	2900089E13Rik|DNC|MUP1|TPC	solute carrier family 25 (mitochondrial thiamine pyrophosphate carrier), member 19	protein-coding
mm_100863.1	chr11	5896740	5896765	-	1	NA	exon (NM_022879, exon 7 of 7)	exon (NM_022879, exon 7 of 7)	2030	NM_022879	17898	Mm.46514	NM_022879	ENSMUSG00000020469	Myl7	MLC-2alpha|MLC2a|MYL2A|Mylc2a|RLC-A	myosin, light polypeptide 7, regulatory	protein-coding
mm_152129.1	chr19	7019329	7019339	-	1	NA	5' UTR (NM_153795, exon 1 of 15)	5' UTR (NM_153795, exon 1 of 15)	135	NM_153795	108101	Mm.157591	NM_153795	ENSMUSG00000024965	Fermt3	C79673|Kindlin3	fermitin family member 3	protein-coding
mm_124585.1	chr15	3251264	3251268	+	1	NA	Intergenic	Intergenic	-19501	NM_001042613	20363	Mm.392203	NM_009155	ENSMUSG00000064373	Selenop	AU018766|D15Ucla1|Se-P|Sepp1|selp	selenoprotein P	protein-coding
mm_31416.1	chr4	48050778	48050781	+	1	NA	promoter-TSS (NM_001307989)	promoter-TSS (NM_001307989)	-467	NM_001307989	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_159290.1	chr2	173578300	173578300	-	1	NA	promoter-TSS (NM_001199955)	promoter-TSS (NM_001199955)	41	NM_001199955	70065	Mm.425115	NM_027303	ENSMUSG00000027517	Ankrd60	1700019A24Rik|1700030G11Rik	ankyrin repeat domain 60	protein-coding
mm_22367.1	chr2	181135199	181135213	-	1	NA	promoter-TSS (NM_010611)	promoter-TSS (NM_010611)	83	NM_001006668	16536	Mm.40615	NM_010611	ENSMUSG00000016346	Kcnq2	HNSPC|KQT2|Nmf134	potassium voltage-gated channel, subfamily Q, member 2	protein-coding
mm_113590.1	chr13	40918527	40918538	+	1	NA	exon (NM_133219, exon 1 of 3)	exon (NM_133219, exon 1 of 3)	898	NM_133219	14538	Mm.314757	NM_008105	ENSMUSG00000021360	Gcnt2	5330430K10Rik|IGnT|IGnTA|IGnTB|IGnTC	glucosaminyl (N-acetyl) transferase 2, I-branching enzyme	protein-coding
mm_15234.1	chr2	154604018	154604029	+	1	NA	promoter-TSS (NM_021534)	promoter-TSS (NM_021534)	-350	NM_021534	59038	Mm.24673	NM_021534	ENSMUSG00000000876	Pxmp4	3010018P03Rik|Pmp24	peroxisomal membrane protein 4	protein-coding
mm_8033.1	chr1	135160774	135160782	-	1	NA	3' UTR (NM_134438, exon 2 of 2)	3' UTR (NM_134438, exon 2 of 2)	6903	NM_134438	171469	Mm.272290	NM_134438	ENSMUSG00000026424	Gpr37l1	AW047233|CAG-18|D0Kist8	G protein-coupled receptor 37-like 1	protein-coding
mm_64742.1	chr7	4770624	4770636	-	1	NA	exon (NM_172895, exon 2 of 11)	exon (NM_172895, exon 2 of 11)	640	NM_172895	243822	Mm.333542	NM_172895	ENSMUSG00000092518	Fam71e2	4930401F20Rik	family with sequence similarity 71, member E2	protein-coding
mm_107837.1	chr12	69296832	69296904	+	1	NA	5' UTR (NM_027117, exon 1 of 13)	5' UTR (NM_027117, exon 1 of 13)	187	NM_027117	69554	Mm.234368	NM_027117	ENSMUSG00000020978	Klhdc2	2310022K15Rik|D12Ertd522e|HCLP-1|LCP	kelch domain containing 2	protein-coding
mm_147228.1	chr18	38209677	38209728	-	1	NA	promoter-TSS (NM_029357)	promoter-TSS (NM_029357)	60	NM_029357	75599	Mm.36560	NM_029357	ENSMUSG00000051375	Pcdh1	2010005A06Rik|AI585920	protocadherin 1	protein-coding
mm_166428.1	chr5	137152419	137152429	+	1	NA	Intergenic	Intergenic	-36217	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_78885.1	chr9	44581715	44581726	+	1	NA	Intergenic	Intergenic	-23172	NM_001110826	13209	Mm.267061	NM_007841	ENSMUSG00000032097	Ddx6	1110001P04Rik|E230023J21Rik|HLR2|mRCK/P54|p54|rck	DEAD (Asp-Glu-Ala-Asp) box polypeptide 6	protein-coding
mm_81142.1	chr9	106822000	106822016	+	1	NA	promoter-TSS (NM_001015507)	promoter-TSS (NM_001015507)	32	NM_001015507	321006	Mm.440089	NM_001015507	ENSMUSG00000040325	Vprbp	AI447437|B930007L02Rik|mKIAA0800	Vpr (HIV-1) binding protein	protein-coding
mm_50393.1	chr6	48708341	48708351	+	1	NA	promoter-TSS (NM_153175)	promoter-TSS (NM_153175)	-102	NM_153175	231931	Mm.321047	NM_153175	ENSMUSG00000047867	Gimap6	4833419H03Rik|Ian6|mFLJ00102	GTPase, IMAP family member 6	protein-coding
mm_98382.1	chr11	94137672	94137682	+	1	NA	Intergenic	B1_Mur1|SINE|Alu	-73777	NM_009427	22057	Mm.259673	NM_009427	ENSMUSG00000037573	Tob1	Tob|Trob	transducer of ErbB-2.1	protein-coding
mm_158586.1	chrX	150814253	150814263	-	1	NA	promoter-TSS (NM_030700)	promoter-TSS (NM_030700)	81	NM_030700	80884	Mm.22575	NM_030700	ENSMUSG00000025268	Maged2	4833439A22Rik|Mage-d2|ORF1	melanoma antigen, family D, 2	protein-coding
mm_122402.1	chr14	41004395	41004412	-	1	NA	intron (NM_001316735, intron 1 of 5)	intron (NM_001316735, intron 1 of 5)	2517	NM_001316739	70564	Mm.27227	NM_027464	ENSMUSG00000021792	Fam213a	5730469M10Rik|AU040822|Adrx|Pamm	family with sequence similarity 213, member A	protein-coding
mm_54573.1	chr6	38096950	38096973	-	1	NA	intron (NM_080467, intron 1 of 20)	intron (NM_080467, intron 1 of 20)	-12392	NM_029921	77522	Mm.387207	NM_029921	ENSMUSG00000029829	Tmem213	D630002J15Rik	transmembrane protein 213	protein-coding
mm_119130.1	chr14	31139016	31139024	+	1	NA	TTS (NM_138672)	TTS (NM_138672)	4167	NM_027289	70021	Mm.261681	NM_027289	ENSMUSG00000071547	Nt5dc2	2510015F01Rik	5'-nucleotidase domain containing 2	protein-coding
mm_164531.1	chr17	6241215	6241215	-	1	NA	TTS (NM_001103181)	TTS (NM_001103181)	-29255	NM_001033178	77106	Mm.381893	NM_001033178	ENSMUSG00000038141	Tmem181a	5930418K15Rik|C76977|Gpr178|Tmem181|mKIAA1423	transmembrane protein 181A	protein-coding
mm_17855.1	chr2	34774060	34774081	-	1	NA	exon (NM_001163434, exon 6 of 9)	exon (NM_001163434, exon 6 of 9)	1980	NM_022310	14828	Mm.330160	NM_022310	ENSMUSG00000026864	Hspa5	AL022860|AU019543|Bip|D2Wsu141e|D2Wsu17e|Grp78|Hsce70|SEZ-7|Sez7|baffled|mBiP	heat shock protein 5	protein-coding
mm_140523.1	chr17	6317418	6317441	-	1	NA	promoter-TSS (NM_001166629)	promoter-TSS (NM_001166629)	45	NM_001166629	100310872	Mm.381893	NM_001166629	ENSMUSG00000092074	Dynlt1a	-	dynein light chain Tctex-type 1A	protein-coding
mm_137562.1	chr17	27702523	27702525	+	1	NA	intron (NM_011861, intron 2 of 9)	intron (NM_011861, intron 2 of 9)	17285	NM_178365	23969	Mm.4926	NM_011861	ENSMUSG00000040276	Pacsin1	A830061D09Rik|H74|mKIAA1379|syndapin	protein kinase C and casein kinase substrate in neurons 1	protein-coding
mm_144037.1	chr17	90144033	90144054	-	1	NA	intron (NM_001346959, intron 5 of 6)	intron (NM_001346959, intron 5 of 6)	-55675	NM_001347419	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_72722.1	chr8	85037152	85037210	+	1	NA	promoter-TSS (NM_001122843)	promoter-TSS (NM_001122843)	13	NM_001122843	212999	Mm.220357	NM_145390	ENSMUSG00000031691	Tnpo2	1110034O24Rik|AA414969|AI464345|AI852433|IPO3|Knpb2b|Kpnb2b|TRN2	transportin 2 (importin 3, karyopherin beta 2b)	protein-coding
mm_165080.1	chr19	46558775	46558800	-	1	NA	intron (NM_019718, intron 1 of 5)	intron (NM_019718, intron 1 of 5)	14298	NM_019718	56350	Mm.22085	NM_019718	ENSMUSG00000025035	Arl3	-	ADP-ribosylation factor-like 3	protein-coding
mm_75104.1	chr8	34146718	34146718	-	1	NA	promoter-TSS (NM_026609)	promoter-TSS (NM_026609)	21	NM_026609	68192	Mm.34212	NM_026609	ENSMUSG00000031513	Leprotl1	1110067H13Rik|1520402O14Rik|AI854296	leptin receptor overlapping transcript-like 1	protein-coding
mm_123796.1	chr14	70443443	70443476	-	1	NA	promoter-TSS (NM_025945)	promoter-TSS (NM_025945)	12	NM_025945	67065	Mm.20420	NM_025945	ENSMUSG00000000776	Polr3d	2810426M17Rik|44kDa|AI326118|AW489084|BN51T|RPC4|TSBN51	polymerase (RNA) III (DNA directed) polypeptide D	protein-coding
mm_14581.1	chr2	135674248	135674275	+	1	NA	Intergenic	Intergenic	-67569	NM_013829	18798	Mm.38009	NM_013829	ENSMUSG00000039943	Plcb4	A930039J07Rik|AI854601|C230058B11Rik	phospholipase C, beta 4	protein-coding
mm_122685.1	chr14	52019657	52019706	-	1	NA	promoter-TSS (NM_001253694)	promoter-TSS (NM_001253694)	32	NM_001253694	69890	Mm.475652	NM_027248	ENSMUSG00000049295	Zfp219	2010302A17Rik	zinc finger protein 219	protein-coding
mm_18448.1	chr2	60937856	60937868	-	1	NA	intron (NM_020296, intron 1 of 13)	intron (NM_020296, intron 1 of 13)	25342	NM_020296	56878	Mm.259667	NM_020296	ENSMUSG00000026970	Rbms1	2600014B10Rik|AI255215|MSSP-1|MSSP-2|MSSP-3|YC1	RNA binding motif, single stranded interacting protein 1	protein-coding
mm_127020.1	chr15	96286006	96286024	+	1	NA	Intergenic	CpG	-1507	NM_175251	77044	Mm.17166	NM_175251	ENSMUSG00000033237	Arid2	1700124K17Rik|4432409D24Rik|zipzap/p200	AT rich interactive domain 2 (ARID, RFX-like)	protein-coding
mm_167927.1	chrX	103466616	103466632	-	1	NA	non-coding (NR_001570, exon 7 of 8)	non-coding (NR_001570, exon 7 of 8)	16609	NR_001570	213742	Mm.274770	NR_001463	ENSMUSG00000086503	Xist	A430022B11|AI314753	inactive X specific transcripts	ncRNA
mm_47033.1	chr5	115732482	115732496	-	1	NA	promoter-TSS (NM_001080808)	promoter-TSS (NM_001080808)	-930	NM_001080808	75665	Mm.233914	NM_001080808	ENSMUSG00000041609	Ccdc64	2210403N09Rik|BICDR-1|Bicdl1	coiled-coil domain containing 64	protein-coding
mm_142615.1	chr17	46858455	46858515	-	1	NA	Intergenic	Intergenic	-27072	NM_001100452	210982	Mm.37642	NM_001100452	ENSMUSG00000036568	Gltscr1l	mKIAA0240	GLTSCR1-like	protein-coding
mm_164893.1	chr18	63692463	63692473	+	1	NA	promoter-TSS (NM_016792)	promoter-TSS (NM_016792)	-109	NM_016792	53382	Mm.19169	NM_016792	ENSMUSG00000024583	Txnl1	32kDa|TRP32|Txnl	thioredoxin-like 1	protein-coding
mm_70305.1	chr8	4134719	4134725	+	1	NA	promoter-TSS (NM_027343)	promoter-TSS (NM_027343)	-14	NM_027343	70192	Mm.390006	NM_027343	ENSMUSG00000079168	Cd209g	2310066I10Rik|AI481039|SIGNR7	CD209g antigen	protein-coding
mm_122165.1	chr14	31417667	31417678	-	1	NA	promoter-TSS (NM_001347585)	promoter-TSS (NM_001347585)	5	NM_001347585	24056	Mm.383198	NM_011894	ENSMUSG00000021892	Sh3bp5	AI606498|SH3BP-5|Sab	SH3-domain binding protein 5 (BTK-associated)	protein-coding
mm_141677.1	chr17	33920471	33920500	-	1	NA	exon (NM_009318, exon 3 of 8)	exon (NM_009318, exon 3 of 8)	1007	NM_009318	21356	Mm.154457	NM_009318	ENSMUSG00000024308	Tapbp	D17Wsu91e|TPN	TAP binding protein	protein-coding
mm_144658.1	chr18	34312799	34312826	+	1	NA	exon (NM_007462, exon 16 of 16)	exon (NM_007462, exon 16 of 16)	-18333	NM_025527	66384	Mm.29452	NM_025527	ENSMUSG00000014504	Srp19	2310020D23Rik	signal recognition particle 19	protein-coding
mm_45169.1	chr5	51479281	51479304	-	1	NA	intron (NR_132764, intron 7 of 12)	intron (NR_132764, intron 7 of 12)	74629	NR_027710	19017	Mm.259072	NM_008904	ENSMUSG00000029167	Ppargc1a	A830037N07Rik|ENSMUSG00000079510|Gm11133|PGC-1|PPARGC-1-alpha|Pgc-1alpha|Pgc1|Pgco1|Ppargc1	peroxisome proliferative activated receptor, gamma, coactivator 1 alpha	protein-coding
mm_152208.1	chr19	7802186	7802200	-	1	NA	exon (NM_146232, exon 1 of 10)	exon (NM_146232, exon 1 of 10)	474	NM_146232	236149	Mm.207060	NM_146232	ENSMUSG00000053303	Slc22a26	-	solute carrier family 22 (organic cation transporter), member 26	protein-coding
mm_16893.1	chr2	13224352	13224370	-	1	NA	exon (NM_009105, exon 4 of 9)	exon (NM_009105, exon 4 of 9)	47054	NM_009105	20163	Mm.905	NM_009105	ENSMUSG00000026727	Rsu1	RsuI|rsp-1	Ras suppressor protein 1	protein-coding
mm_88456.1	chr10	77560196	77560206	+	1	NA	exon (NM_008404, exon 13 of 16)	exon (NM_008404, exon 13 of 16)	-21566	NM_145925	108705	Mm.28853	NM_145925	ENSMUSG00000009291	Pttg1ip	1810010L20Rik|AI314311|AU018448|C79540	pituitary tumor-transforming 1 interacting protein	protein-coding
mm_75620.1	chr8	64609125	64609139	-	1	NA	exon (NM_013494, exon 5 of 9)	exon (NM_013494, exon 5 of 9)	83977	NM_013494	12876	Mm.31395	NM_013494	ENSMUSG00000037852	Cpe	CPH|Cph-1|Cph1|R74677|fat	carboxypeptidase E	protein-coding
mm_93870.1	chr10	123171788	123171838	-	1	NA	intron (NM_001301628, intron 3 of 20)	intron (NM_001301628, intron 3 of 20)	25206	NM_027604	14479	Mm.244209	NM_027604	ENSMUSG00000020124	Usp15	4921514G19Rik|AI327321|E430033I05Rik|Gcap18	ubiquitin specific peptidase 15	protein-coding
mm_69209.1	chr7	127449061	127449077	-	1	NA	promoter-TSS (NM_175163)	promoter-TSS (NM_175163)	89	NM_175163	71131	Mm.474533	NM_175163	ENSMUSG00000048921	Zfp689	4933416E05Rik|Znf689	zinc finger protein 689	protein-coding
mm_133300.1	chr16	77545839	77545841	+	1	NA	intron (NR_015543, intron 4 of 4)	intron (NR_015543, intron 4 of 4)	-53096	NR_029535	387229		NR_029535	ENSMUSG00000065530	Mir99a	Mirn99a|mir-99a|mmu-mir-99a	microRNA 99a	ncRNA
mm_23383.1	chr3	55890303	55890313	+	1	NA	intron (NM_030595, intron 35 of 57)	intron (NM_030595, intron 35 of 57)	43203	NR_033592	71182	Mm.195603	NR_033592	ENSMUSG00000106572	4933417G07Rik	-	SEC13 homolog pseudogene	pseudo
mm_91463.1	chr10	34127920	34127930	-	1	NA	promoter-TSS (NM_175449)	promoter-TSS (NM_175449)	47	NM_175449	215900	Mm.34479	NM_175449	ENSMUSG00000046031	Fam26f	A630077B13Rik	family with sequence similarity 26, member F	protein-coding
mm_164094.1	chr15	10996429	10996431	+	1	NA	3' UTR (NM_008537, exon 5 of 5)	3' UTR (NM_008537, exon 5 of 5)	-4291	NM_053077	22293	Mm.138278	NM_053077	ENSMUSG00000022243	Slc45a2	Aim-1|Aim1|Dbr|Matp|Oca4|blanc-sale|bls|uw	solute carrier family 45, member 2	protein-coding
mm_2253.1	chr1	91083484	91083487	+	1	NA	intron (NM_001310732, intron 7 of 24)	intron (NM_001310732, intron 7 of 24)	30041	NM_008515	16978	Mm.45039	NM_008515	ENSMUSG00000026305	Lrrfip1	AU024550|Fliiap1	leucine rich repeat (in FLII) interacting protein 1	protein-coding
mm_155835.1	chrX	100777244	100777268	+	1	NA	promoter-TSS (NM_001177780)	promoter-TSS (NM_001177780)	-15	NM_001177780	53310	Mm.4615	NM_016747	ENSMUSG00000000881	Dlg3	Dlgh3|SAP102|mKIAA1232	discs, large homolog 3 (Drosophila)	protein-coding
mm_161626.1	chr16	75567691	75567691	-	1	NA	intron (NM_001252513, intron 4 of 10)	L1Md_T|LINE|L1	18370	NM_001252513	320355	Mm.99517	NM_177142	ENSMUSG00000032948	Lipi	D930038D03Rik|lpd1	lipase, member I	protein-coding
mm_128532.1	chr15	54847429	54847440	-	1	NA	intron (NM_001136077, intron 22 of 25)	intron (NM_001136077, intron 22 of 25)	72712	NM_015744	18606	Mm.250256	NM_015744	ENSMUSG00000022425	Enpp2	ATX|E-NPP 2|Npps2|PD-Ialpha|Pdnp2|lysoPLD	ectonucleotide pyrophosphatase/phosphodiesterase 2	protein-coding
mm_14576.1	chr2	135659294	135659357	+	1	NA	Intergenic	CpG	-76105	NR_015544	320684	Mm.421433	NR_015544	ENSMUSG00000085631	9630028H03Rik	-	RIKEN cDNA 9630028H03 gene	ncRNA
mm_8746.1	chr1	160287377	160287379	-	1	NA	intron (NM_001038621, intron 2 of 8)	intron (NM_001038621, intron 2 of 8)	8594	NR_035448	100316784		NR_035448	ENSMUSG00000089204	Mir1927	mmu-mir-1927	microRNA 1927	ncRNA
mm_56730.1	chr6	115676602	115676618	-	1	NA	promoter-TSS (NM_029780)	promoter-TSS (NM_029780)	25	NM_029780	110157	Mm.184163	NM_029780	ENSMUSG00000000441	Raf1	6430402F14Rik|AA990557|BB129353|Craf1|D830050J10Rik|Raf-1|c-Raf|v-Raf	v-raf-leukemia viral oncogene 1	protein-coding
mm_93773.1	chr10	120408323	120408327	-	1	NA	intron (NM_001347170, intron 3 of 5)	A-rich|Low_complexity|Low_complexity	18802	NR_040626	320626	Mm.446091	NR_040626	ENSMUSG00000090191	9230105E05Rik	-	RIKEN cDNA 9230105E05 gene	ncRNA
mm_86511.1	chr10	7663369	7663395	+	1	NA	promoter-TSS (NR_030698)	promoter-TSS (NR_030698)	11	NR_030698	320642	Mm.398806	NR_030698		A630066F11Rik	-	RIKEN cDNA A630066F11 gene	ncRNA
mm_2243.1	chr1	91053974	91053992	+	1	NA	intron (NM_001310732, intron 1 of 24)	intron (NM_001310732, intron 1 of 24)	539	NM_008515	16978	Mm.45039	NM_008515	ENSMUSG00000026305	Lrrfip1	AU024550|Fliiap1	leucine rich repeat (in FLII) interacting protein 1	protein-coding
mm_118486.1	chr14	12190043	12190047	+	1	NA	exon (NM_001347593, exon 1 of 17)	exon (NM_001347593, exon 1 of 17)	102	NM_001347593	19270	Mm.431266	NM_008981	ENSMUSG00000021745	Ptprg	5430405N12Rik|AW046354|AW549872|RPTPgamma	protein tyrosine phosphatase, receptor type, G	protein-coding
mm_116806.1	chr13	54190050	54190063	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-2073	NM_001010973	15466	Mm.57243	NM_008286	ENSMUSG00000034987	Hrh2	-	histamine receptor H2	protein-coding
mm_84468.1	chr9	66593080	66593099	-	1	NA	promoter-TSS (NM_144937)	promoter-TSS (NM_144937)	26	NM_144937	235441	Mm.32465	NM_144937	ENSMUSG00000032376	Usp3	AA409661|BC017156	ubiquitin specific peptidase 3	protein-coding
mm_41828.1	chr5	104047065	104047073	+	1	NA	promoter-TSS (NR_049192)	promoter-TSS (NR_049192)	205	NM_028794	74167	Mm.241484	NM_028794	ENSMUSG00000029310	Nudt9	1190002C07Rik|ADPR-PPase|AI462474	nudix (nucleoside diphosphate linked moiety X)-type motif 9	protein-coding
mm_88209.1	chr10	70194872	70194885	+	1	NA	Intergenic	7SLRNA|srpRNA|srpRNA	-9786	NM_001304739	69563	Mm.64672	NM_001304739	ENSMUSG00000019933	Mrln	2310015B20Rik|Mln	myoregulin	protein-coding
mm_18893.1	chr2	76711730	76711741	-	1	NA	exon (NM_011652, exon 307 of 313)	exon (NM_011652, exon 307 of 313)	36420	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_105681.1	chr11	107716451	107716453	-	1	NA	promoter-TSS (NM_007582)	promoter-TSS (NM_007582)	24	NM_007582	12299	Mm.57093	NM_007582	ENSMUSG00000020722	Cacng1	-	calcium channel, voltage-dependent, gamma subunit 1	protein-coding
mm_93414.1	chr10	108500454	108500465	-	1	NA	3' UTR (NM_001252342, exon 11 of 11)	3' UTR (NM_001252342, exon 11 of 11)	168270	NM_054056	114774	Mm.391419	NM_054056	ENSMUSG00000035873	Pawr	2310001G03Rik|PAR4|Par-4	PRKC, apoptosis, WT1, regulator	protein-coding
mm_71316.1	chr8	43703447	43703458	+	1	NA	Intergenic	Intergenic	-3961	NM_001079931	384814	Mm.491652	NM_001079931		Gm5347	EG384814	predicted gene 5347	protein-coding
mm_29974.1	chr3	133545130	133545155	-	1	NA	promoter-TSS (NM_001346736)	promoter-TSS (NM_001346736)	-752	NM_001040400	214133	Mm.347816	NM_145989	ENSMUSG00000040943	Tet2	Ayu17-449|E130014J05Rik|mKIAA1546	tet methylcytosine dioxygenase 2	protein-coding
mm_102991.1	chr11	69686724	69686739	-	1	NA	3' UTR (NM_011614, exon 7 of 7)	3' UTR (NM_011614, exon 7 of 7)	-1177	NM_023517	69583	Mm.8983	NM_023517	ENSMUSG00000089669	Tnfsf13	2310026N09Rik|April|Tall2|Tnlg7b|Trdl1	tumor necrosis factor (ligand) superfamily, member 13	protein-coding
mm_88837.1	chr10	80855290	80855322	+	1	NA	promoter-TSS (NM_025349)	promoter-TSS (NM_025349)	31	NM_175195	73218	Mm.3285	NM_175195	ENSMUSG00000035206	Sppl2b	3110056O03Rik|AW550292|PSL1	signal peptide peptidase like 2B	protein-coding
mm_168597.1	chr1	173942485	173942485	-	1	NA	promoter-TSS (NM_001302651)	promoter-TSS (NM_001302651)	7	NM_001302649	15950	Mm.463437	NM_008328	ENSMUSG00000039997	Ifi203	Mndal	interferon activated gene 203	protein-coding
mm_2009.1	chr1	87127597	87127601	+	1	NA	exon (NM_007432, exon 11 of 11)	exon (NM_007432, exon 11 of 11)	2591	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_139306.1	chr17	48348510	48348525	+	1	NA	exon (NM_031254, exon 2 of 5)	exon (NM_031254, exon 2 of 5)	2116	NM_001272078	83433	Mm.261623	NM_031254	ENSMUSG00000023992	Trem2	TREM-2|Trem2a|Trem2b|Trem2c	triggering receptor expressed on myeloid cells 2	protein-coding
mm_55282.1	chr6	54473155	54473174	-	1	NA	intron (NM_001167860, intron 1 of 7)	intron (NM_001167860, intron 1 of 7)	20281	NM_001167861	330319	Mm.434326	NM_001167860	ENSMUSG00000086040	Wipf3	9030621G03|BQ952480	WAS/WASL interacting protein family, member 3	protein-coding
mm_172566.1	chr8	111029774	111029775	+	1	NA	intron (NM_001190786, intron 1 of 11)	RLTR31_Mm|LTR|ERVK	1977	NM_001190786	234733	Mm.482176	NM_172284	ENSMUSG00000033658	Ddx19b	2810457M08Rik|4921519L13Rik|AW260119	DEAD (Asp-Glu-Ala-Asp) box polypeptide 19b	protein-coding
mm_55025.1	chr6	48841438	48841451	-	1	NA	promoter-TSS (NM_001164209)	promoter-TSS (NM_001164209)	-39	NM_025326	66058	Mm.27061	NM_025326	ENSMUSG00000023367	Tmem176a	0610011I04Rik|AU040201|AU041743|Keg2	transmembrane protein 176A	protein-coding
mm_70719.1	chr8	15519903	15519925	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	462261	NM_008664	17930	Mm.272115	NM_008664	ENSMUSG00000031461	Myom2	AW146149	myomesin 2	protein-coding
mm_57650.1	chr6	128438594	128438606	-	1	NA	promoter-TSS (NM_010219)	promoter-TSS (NM_010219)	31	NM_010219	14228	Mm.12758	NM_010219	ENSMUSG00000030357	Fkbp4	59kDa|AL022792|AW208983|FKBP-4|FKBP-52|FKBP52|FKPB52|p59	FK506 binding protein 4	protein-coding
mm_33232.1	chr4	126968428	126968436	+	1	NA	promoter-TSS (NM_001114399)	promoter-TSS (NM_001114399)	-509	NM_001114399	67785	Mm.165401	NM_001114399	ENSMUSG00000042446	Zmym4	6330503C17Rik|AI480785|AW493829|CDIR|D630001M21|MYM|Zfp262|Znf262|mKIAA0425	zinc finger, MYM-type 4	protein-coding
mm_133796.1	chr16	95278559	95278567	+	1	NA	intron (NM_001271687, intron 3 of 4)	B4A|SINE|B4	21005	NM_001271690	16516	Mm.272239	NM_019664	ENSMUSG00000062609	Kcnj15	4930414N08Rik|AI182284|AI267127|IRKK|Kir4.2	potassium inwardly-rectifying channel, subfamily J, member 15	protein-coding
mm_104496.1	chr11	95842152	95842168	-	1	NA	promoter-TSS (NM_001284393)	promoter-TSS (NM_001284393)	-135	NM_023121	14710	Mm.46299	NM_023121	ENSMUSG00000038811	Gngt2	AV096488	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 2	protein-coding
mm_168681.1	chr11	95414337	95414349	+	1	NA	5' UTR (NM_025287, exon 2 of 11)	5' UTR (NM_025287, exon 2 of 11)	260	NM_025287	20747	Mm.285454	NM_025287	ENSMUSG00000057522	Spop	AI315626|Pcif1|TEF2	speckle-type POZ protein	protein-coding
mm_137579.1	chr17	27979067	27979090	+	1	NA	intron (NM_001286040, intron 4 of 24)	intron (NM_001286040, intron 4 of 24)	69772	NM_181413	224650	Mm.32556	NM_181413	ENSMUSG00000024219	Anks1	Anks1a|mKIAA0229	ankyrin repeat and SAM domain containing 1	protein-coding
mm_164746.1	chr17	73952287	73952299	-	1	NA	Intergenic	Intergenic	-2097	NM_011723	22436	Mm.11223	NM_011723	ENSMUSG00000024066	Xdh	XO|Xor|Xox-1|Xox1	xanthine dehydrogenase	protein-coding
mm_46457.1	chr5	105118010	105118016	-	1	NA	3' UTR (NM_001256005, exon 11 of 11)	3' UTR (NM_001256005, exon 11 of 11)	-7721	NM_172777	236573	Mm.425261	NM_172777	ENSMUSG00000029298	Gbp9	-	guanylate-binding protein 9	protein-coding
mm_114452.1	chr13	66989297	66989300	+	1	NA	intron (NM_008959, intron 10 of 12)	intron (NM_008959, intron 10 of 12)	43107	NR_045851	71226	Mm.399574	NR_045851		4933433G19Rik	-	RIKEN cDNA 4933433G19 gene	ncRNA
mm_162139.1	chrX	73950551	73950551	-	1	NA	exon (NM_008224, exon 17 of 26)	exon (NM_008224, exon 17 of 26)	15806	NM_008224	15161	Mm.491126	NM_008224	ENSMUSG00000031386	Hcfc1	AW060991|HCF|HCF1	host cell factor C1	protein-coding
mm_9475.1	chr1	173336811	173336820	-	1	NA	3' UTR (NM_053199, exon 9 of 9)	3' UTR (NM_053199, exon 9 of 9)	-3312	NM_010045	13349	Mm.6393	NM_010045	ENSMUSG00000037872	Ackr1	AA162249|CCBP1|CD234|Darc|Dfy|ESTM35|FY|GPD	atypical chemokine receptor 1 (Duffy blood group)	protein-coding
mm_148852.1	chr19	6389541	6389555	+	1	NA	exon (NM_011224, exon 10 of 20)	exon (NM_011224, exon 10 of 20)	5140	NM_011224	19309	Mm.27806	NM_011224	ENSMUSG00000032648	Pygm	AI115133|PG	muscle glycogen phosphorylase	protein-coding
mm_56732.1	chr6	115685451	115685498	-	1	NA	Intergenic	RLTR17|LTR|ERVK	-8839	NM_029780	110157	Mm.184163	NM_029780	ENSMUSG00000000441	Raf1	6430402F14Rik|AA990557|BB129353|Craf1|D830050J10Rik|Raf-1|c-Raf|v-Raf	v-raf-leukemia viral oncogene 1	protein-coding
mm_132069.1	chr16	30064438	30064444	+	1	NA	promoter-TSS (NM_008235)	promoter-TSS (NM_008235)	-916	NM_008235	15205	Mm.390859	NM_008235	ENSMUSG00000022528	Hes1	Hry|bHLHb39	hairy and enhancer of split 1 (Drosophila)	protein-coding
mm_119932.1	chr14	54970193	54970207	+	1	NA	TTS (NM_080728)	TTS (NM_080728)	1413	NR_033497	791403	Mm.319176	NR_033497	ENSMUSG00000097652	Mhrt	D830015G02Rik|ENSMUSG00000053118|Myheart	myosin heavy chain associated RNA transcript	ncRNA
mm_103130.1	chr11	70230217	70230241	-	1	NA	promoter-TSS (NM_007528)	promoter-TSS (NM_007528)	-431	NM_007528	12029	Mm.12930	NM_007528	ENSMUSG00000000317	Bcl6b	Bazf	B cell CLL/lymphoma 6, member B	protein-coding
mm_145221.1	chr18	50053542	50053544	+	1	NA	5' UTR (NM_134131, exon 1 of 2)	5' UTR (NM_134131, exon 1 of 2)	261	NM_134131	106869	Mm.27740	NM_134131	ENSMUSG00000062210	Tnfaip8	AA987150|E130304C20Rik|ENSMUSG00000073567|Gg2-1|Gm10539|Nded|Ssc-2|Tipe	tumor necrosis factor, alpha-induced protein 8	protein-coding
mm_16240.1	chr2	173156392	173156400	+	1	NA	intron (NM_011044, intron 6 of 9)	RSINE1|SINE|B4	3323	NM_011044	18534	Mm.266867	NM_011044	ENSMUSG00000027513	Pck1	AI265463|PEPCK|Pck-1	phosphoenolpyruvate carboxykinase 1, cytosolic	protein-coding
mm_171367.1	chr4	118943444	118943450	-	1	NA	Intergenic	Intergenic	-8607	NM_146399	258394	Mm.434316	NM_146399	ENSMUSG00000111259	Olfr1328	MOR259-1|MOR259-13|Olfr1519	olfactory receptor 1328	protein-coding
mm_102467.1	chr11	59964937	59964951	-	1	NA	promoter-TSS (NM_009026)	promoter-TSS (NM_009026)	0	NM_009026	19416	Mm.3903	NM_009026	ENSMUSG00000049892	Rasd1	Dexras1	RAS, dexamethasone-induced 1	protein-coding
mm_46592.1	chr5	107725484	107725512	-	1	NA	intron (NM_001267621, intron 1 of 6)	CpG	307	NM_001267621	14581	Mm.2078	NM_010278	ENSMUSG00000029275	Gfi1	AW495828|Gfi-1|Pal-1|Pal1	growth factor independent 1	protein-coding
mm_135605.1	chr16	52147499	52147514	-	1	NA	intron (NM_001033238, intron 9 of 17)	intron (NM_001033238, intron 9 of 17)	115957	NM_001033238	208650	Mm.328206	NM_001033238	ENSMUSG00000022637	Cblb	AI429560|AI851073|Cbl-b	Casitas B-lineage lymphoma b	protein-coding
mm_87311.1	chr10	42761610	42761663	+	1	NA	5' UTR (NM_153055, exon 1 of 21)	5' UTR (NM_153055, exon 1 of 21)	140	NM_153055	140740	Mm.214344	NM_153055	ENSMUSG00000019802	Sec63	5730478J10Rik|AI649014|AW319215	SEC63-like (S. cerevisiae)	protein-coding
mm_62382.1	chr7	100816151	100816169	+	1	NA	intron (NM_178764, intron 4 of 8)	intron (NM_178764, intron 4 of 8)	47253	NM_177073	320100	Mm.40336	NM_177073	ENSMUSG00000008318	Relt	E430021K24Rik|Tnfrsf19l	RELT tumor necrosis factor receptor	protein-coding
mm_113918.1	chr13	49544626	49544636	+	1	NA	5' UTR (NM_025711, exon 1 of 8)	5' UTR (NM_025711, exon 1 of 8)	188	NM_025711	66695	Mm.383216	NM_025711	ENSMUSG00000021388	Aspn	4631401G09Rik|AA986886|Plap1|Slrr1c	asporin	protein-coding
mm_77145.1	chr8	111562054	111562059	-	1	NA	intron (NM_001168623, intron 1 of 4)	intron (NM_001168623, intron 1 of 4)	23713	NM_001168623	170737	Mm.271578	NM_133206	ENSMUSG00000033545	Znrf1	B830022L21Rik|Rnf42|Zrfp1|nin283	zinc and ring finger 1	protein-coding
mm_89528.1	chr10	94476611	94476621	+	1	NA	Intergenic	RLTR20D|LTR|ERVK	-38241	NM_172051	319880	Mm.23047	NM_172051	ENSMUSG00000020023	Tmcc3	AW488095|C630016B22Rik|C88213|Tmcc1	transmembrane and coiled coil domains 3	protein-coding
mm_80585.1	chr9	84652708	84652711	+	1	NA	Intergenic	Intergenic	-121689	NR_040739	75253	Mm.401984	NR_040739	ENSMUSG00000099724	4930554C24Rik	-	RIKEN cDNA 4930554C24 gene	ncRNA
mm_164536.1	chr17	6741236	6741257	-	1	NA	intron (NM_009510, intron 10 of 12)	intron (NM_009510, intron 10 of 12)	35416	NM_183368	83672	Mm.442201	NM_031395	ENSMUSG00000041831	Sytl3	A430092N21|Slp3|Slp3-a|Slp3-b|mFLJ00307	synaptotagmin-like 3	protein-coding
mm_99253.1	chr11	101120159	101120173	+	1	NA	promoter-TSS (NM_134024)	promoter-TSS (NM_134024)	35	NM_134024	103733	Mm.479145	NM_134024	ENSMUSG00000035198	Tubg1	1500010O08Rik|AI451582|AI503389|Tubg	tubulin, gamma 1	protein-coding
mm_120089.1	chr14	57826372	57826417	+	1	NA	promoter-TSS (NM_198605)	promoter-TSS (NM_198605)	155	NM_026401	67840	Mm.319530	NM_026401	ENSMUSG00000021967	Mrpl57	2610025P17Rik|AV005697|Mrp63	mitochondrial ribosomal protein L57	protein-coding
mm_127930.1	chr15	10470531	10470605	-	1	NA	promoter-TSS (NM_030046)	promoter-TSS (NM_030046)	-52	NM_030046	78244	Mm.297862	NM_030046	ENSMUSG00000044224	Dnajc21	4930461P20Rik|9930116P15Rik	DnaJ heat shock protein family (Hsp40) member C21	protein-coding
mm_96920.1	chr11	70497799	70497850	+	1	NA	Intergenic	Intergenic	-7450	NM_029360	75604	Mm.24400	NM_029360	ENSMUSG00000018919	Tm4sf5	2010003F10Rik|AI323987	transmembrane 4 superfamily member 5	protein-coding
mm_81668.1	chr9	111025121	111025131	+	1	NA	exon (NM_008522, exon 8 of 17)	exon (NM_008522, exon 8 of 17)	5834	NM_008522	17002	Mm.282359	NM_008522	ENSMUSG00000032496	Ltf	Csp82|Lf|MMS10R|Ms10r	lactotransferrin	protein-coding
mm_84673.1	chr9	72034990	72034993	-	1	NA	intron (NM_001253862, intron 3 of 19)	intron (NM_001253862, intron 3 of 19)	71550	NR_029879	723889		NR_029879	ENSMUSG00000105200	Mir378a	Mir378|Mirn378|mmu-mir-378|mmu-mir-378a	microRNA 378a	ncRNA
mm_111277.1	chr12	85344453	85344458	-	1	NA	intron (NM_026775, intron 3 of 4)	intron (NM_026775, intron 3 of 4)	-5093	NM_145138	217718	Mm.29071	NM_145138	ENSMUSG00000034290	Nek9	C130021H08Rik	NIMA (never in mitosis gene a)-related expressed kinase 9	protein-coding
mm_81946.1	chr9	120492678	120492686	+	1	NA	promoter-TSS (NM_026892)	promoter-TSS (NM_026892)	76	NM_026892	68969	Mm.28753	NM_026892	ENSMUSG00000006941	Eif1b	1500010M16Rik|3110001N14Rik|Gc20	eukaryotic translation initiation factor 1B	protein-coding
mm_12169.1	chr2	62610525	62610553	+	1	NA	exon (NM_027835, exon 7 of 16)	exon (NM_027835, exon 7 of 16)	35716	NM_027835	71586	Mm.136224	NM_027835	ENSMUSG00000026896	Ifih1	9130009C22Rik|Helicard|Hlcd|MDA5|RLR-2	interferon induced with helicase C domain 1	protein-coding
mm_2803.1	chr1	130851736	130851763	+	1	NA	3' UTR (NM_011082, exon 11 of 11)	3' UTR (NM_011082, exon 11 of 11)	-14028	NM_026976	69169	Mm.46042	NM_026976	ENSMUSG00000042474	Fcmr	1810037B05Rik|Faim3|FcmuR|Toso	Fc fragment of IgM receptor	protein-coding
mm_84382.1	chr9	65422835	65422848	-	1	NA	promoter-TSS (NM_178933)	promoter-TSS (NM_178933)	-68	NM_178933	330962	Mm.335247	NM_178933	ENSMUSG00000053862	Slc51b	Ostb	solute carrier family 51, beta subunit	protein-coding
mm_41742.1	chr5	102768805	102768815	+	1	NA	promoter-TSS (NM_001286468)	promoter-TSS (NM_001286468)	0	NM_001286468	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding
mm_6597.1	chr1	75316947	75316982	-	1	NA	promoter-TSS (NM_016878)	promoter-TSS (NM_016878)	53	NM_016878	13437	Mm.24680	NM_016878	ENSMUSG00000026209	Dnpep	AA407814	aspartyl aminopeptidase	protein-coding
mm_65738.1	chr7	28392689	28392708	-	1	NA	promoter-TSS (NM_019458)	promoter-TSS (NM_019458)	-8	NM_026042	67224	Mm.41647	NM_026042	ENSMUSG00000003444	Med29	2810405O22Rik|AU020902|Ixl	mediator complex subunit 29	protein-coding
mm_155785.1	chrX	96456491	96456502	+	1	NA	promoter-TSS (NM_172931)	promoter-TSS (NM_172931)	150	NM_001159627	15203	Mm.277092	NM_010417	ENSMUSG00000031209	Heph	C130006F04Rik|Cpl|mKIAA0698|sla	hephaestin	protein-coding
mm_109387.1	chr12	109738892	109738905	+	1	NA	promoter-TSS (NR_030437)	promoter-TSS (NR_030437)	-221	NR_030437	751524		NR_030437	ENSMUSG00000070136	Mir496a	Mir496|Mirn496|mir-496a|mmu-mir-496|mmu-mir-496a	microRNA 496a	ncRNA
mm_28223.1	chr3	88452369	88452401	-	1	NA	intron (NM_001163491, intron 3 of 14)	intron (NM_001163491, intron 3 of 14)	3376	NM_013658	20351	Mm.439752	NM_013658	ENSMUSG00000028064	Sema4a	AI132332|SemB|Semab	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A	protein-coding
mm_10145.1	chr2	4300538	4300568	+	1	NA	intron (NM_172475, intron 1 of 22)	intron (NM_172475, intron 1 of 22)	-100423	NM_001177843	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding
mm_166510.1	chr6	8728999	8729012	-	1	NA	intron (NM_001252266, intron 5 of 11)	LSU-rRNA_Hsa|rRNA|rRNA	29453	NM_001252266	15893	Mm.275683	NM_010492	ENSMUSG00000062995	Ica1	69kDa|ICA69	islet cell autoantigen 1	protein-coding
mm_63354.1	chr7	126976611	126976619	+	1	NA	5' UTR (NM_026638, exon 1 of 6)	5' UTR (NM_026638, exon 1 of 6)	701	NM_001347656	52858	Mm.28219	NM_026638	ENSMUSG00000030682	Cdipt	9530042F15Rik|D7Bwg0575e|Pis|Pis1	CDP-diacylglycerol--inositol 3-phosphatidyltransferase (phosphatidylinositol synthase)	protein-coding
mm_117542.1	chr13	83721150	83721155	-	1	NA	Intergenic	CpG	-6954	NR_015561	320203	Mm.245636	NM_177100	ENSMUSG00000050334	C130071C03Rik	2810449C10Rik	RIKEN cDNA C130071C03 gene	ncRNA
mm_51904.1	chr6	91156741	91156765	+	1	NA	promoter-TSS (NM_144919)	promoter-TSS (NM_144919)	-62	NM_144919	232232	Mm.206218	NM_144919	ENSMUSG00000034245	Hdac11	-	histone deacetylase 11	protein-coding
mm_31784.1	chr4	63634409	63634420	+	1	NA	Intergenic	MER2|DNA|TcMar-Tigger	-11985	NM_029324	75524	Mm.38543	NM_029324	ENSMUSG00000058935	1700018C11Rik	bM230C2.3	RIKEN cDNA 1700018C11 gene	protein-coding
mm_5746.1	chr1	45927969	45927985	-	1	NA	Intergenic	Intergenic	-2383	NM_016917	53945	Mm.28756	NM_016917	ENSMUSG00000025993	Slc40a1	Dusg|Fpn1|IREG1|MTP|MTP1|Ol5|Pcm|Slc11a3|Slc39a1	solute carrier family 40 (iron-regulated transporter), member 1	protein-coding
mm_16085.1	chr2	168670494	168670541	+	1	NA	intron (NM_001289446, intron 13 of 27)	ID_B1|SINE|B4	-29758	NR_105971	102466784		NR_105971	ENSMUSG00000105496	Mir7004	mmu-mir-7004	microRNA 7004	ncRNA
mm_129576.1	chr15	79735970	79735984	-	1	NA	intron (NM_001205345, intron 6 of 17)	intron (NM_001205345, intron 6 of 17)	6559	NM_194342	223697	Mm.202715	NM_194342	ENSMUSG00000042524	Sun2	B230369L08Rik|C030011B15|Unc84b	Sad1 and UNC84 domain containing 2	protein-coding
mm_109773.1	chr12	118847573	118847584	+	1	NA	5' UTR (NM_177082, exon 2 of 3)	5' UTR (NM_177082, exon 2 of 3)	1249	NM_177082	320145	Mm.51682	NM_177082	ENSMUSG00000048562	Sp8	D930049B17Rik|mBtd	trans-acting transcription factor 8	protein-coding
mm_12328.1	chr2	69394487	69394502	+	1	NA	exon (NM_175512, exon 3 of 5)	exon (NM_175512, exon 3 of 5)	14032	NM_175512	241452	Mm.211655	NM_175512	ENSMUSG00000027068	Dhrs9	C730025I08Rik|Rdh15	dehydrogenase/reductase (SDR family) member 9	protein-coding
mm_156377.1	chrX	139672011	139672025	+	1	NA	3' UTR (NM_023270, exon 7 of 7)	3' UTR (NM_023270, exon 7 of 7)	-12978	NM_001081499	245638	Mm.275869	NM_001081499	ENSMUSG00000042473	Tbc1d8b	4921505D17Rik|9030605E16Rik	TBC1 domain family, member 8B	protein-coding
mm_131187.1	chr16	7217729	7217733	+	1	NA	intron (NM_183188, intron 1 of 12)	intron (NM_183188, intron 1 of 12)	147896	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_104968.1	chr11	100203189	100203201	-	1	NA	TTS (NM_016958)	TTS (NM_016958)	2835	NM_001313957	16664	Mm.439898	NM_016958	ENSMUSG00000045545	Krt14	AI626930|CK-14|K14|Krt-1.14|Krt1-14	keratin 14	protein-coding
mm_92632.1	chr10	80323757	80323795	-	1	NA	exon (NM_008793, exon 10 of 15)	exon (NM_008793, exon 10 of 15)	-3228	NM_025521	66374	Mm.383824	NM_025521	ENSMUSG00000020133	2310011J03Rik	AI452186|AW545358	RIKEN cDNA 2310011J03 gene	protein-coding
mm_10356.1	chr2	11690141	11690191	+	1	NA	3' UTR (NM_008367, exon 8 of 8)	3' UTR (NM_008367, exon 8 of 8)	-15127	NM_001271498	16169	Mm.200196	NM_008358	ENSMUSG00000023206	Il15ra	AA690181|IL-15RA	interleukin 15 receptor, alpha chain	protein-coding
mm_171326.1	chr3	96486721	96486722	-	1	NA	Intergenic	Intergenic	-34415	NM_001256180	329716	Mm.275223	NM_183223	ENSMUSG00000046317	BC107364	D730018G16	cDNA sequence BC107364	protein-coding
mm_131868.1	chr16	23175178	23175193	+	1	NA	Intergenic	Intergenic	28649	NM_009605	11450	Mm.3969	NM_009605	ENSMUSG00000022878	Adipoq	30kDa|APN|Acdc|Acrp30|Ad|GBP28|adipo|apM1	adiponectin, C1Q and collagen domain containing	protein-coding
mm_159708.1	chr5	30461782	30461782	-	1	NA	exon (NM_001100395, exon 1 of 47)	exon (NM_001100395, exon 1 of 47)	150	NM_001286421	83762	Mm.244502	NM_031875	ENSMUSG00000062372	Otof	-	otoferlin	protein-coding
mm_92725.1	chr10	80818515	80818518	-	1	NA	Intergenic	Intergenic	-5018	NM_028001	71912	Mm.45137	NM_028001	ENSMUSG00000020216	Jsrp1	2300003C06Rik|2310032K21Rik|JP-45|JP45	junctional sarcoplasmic reticulum protein 1	protein-coding
mm_167630.1	chr9	62026854	62026858	-	1	NA	promoter-TSS (NM_028748)	promoter-TSS (NM_028748)	-66	NM_028748	74090	Mm.273267	NM_028748	ENSMUSG00000032278	Paqr5	0610010I15Rik|AV002411|BB115488|mPRg	progestin and adipoQ receptor family member V	protein-coding
mm_24870.1	chr3	95951308	95951367	+	1	NA	Intergenic	CpG	22080	NM_023210	66471	Mm.218657	NM_023210	ENSMUSG00000015749	Anp32e	2810018A15Rik|AI047746|AI326868|CPD1|LANP-L|LANPL|mLANP-L	acidic (leucine-rich) nuclear phosphoprotein 32 family, member E	protein-coding
mm_94096.1	chr10	128549104	128549121	-	1	NA	promoter-TSS (NM_018860)	promoter-TSS (NM_018860)	56	NM_018860	67945	Mm.290786	NM_018860	ENSMUSG00000093674	Rpl41	1810055P16Rik|2210411K19Rik	ribosomal protein L41	protein-coding
mm_149502.1	chr19	11921423	11921433	+	1	NA	exon (NM_172635, exon 5 of 19)	exon (NM_172635, exon 5 of 19)	-2300	NR_105960	102465601		NR_105960	ENSMUSG00000104979	Mir6994	mmu-mir-6994	microRNA 6994	ncRNA
mm_5139.1	chr1	9725931	9725934	-	1	NA	intron (NM_173443, intron 2 of 2)	intron (NM_173443, intron 2 of 2)	-21716	NR_040462	73331	Mm.460470	NR_040462		1700034P13Rik	-	RIKEN cDNA 1700034P13 gene	ncRNA
mm_10259.1	chr2	9369065	9369075	+	1	NA	Intergenic	Intergenic	179555	NR_038180	73438	Mm.23558	NR_038180	ENSMUSG00000085580	1700061F12Rik	-	RIKEN cDNA 1700061F12 gene	ncRNA
mm_107937.1	chr12	71832467	71832504	+	1	NA	intron (NM_026102, intron 1 of 25)	intron (NM_026102, intron 1 of 25)	1417	NM_172464	208846	Mm.87417	NM_026102	ENSMUSG00000034574	Daam1	-	dishevelled associated activator of morphogenesis 1	protein-coding
mm_101270.1	chr11	21370453	21370485	-	1	NA	5' UTR (NM_139297, exon 1 of 10)	5' UTR (NM_139297, exon 1 of 10)	160	NM_139297	216558	Mm.28877	NM_139297	ENSMUSG00000001891	Ugp2	UDPGP|UGPase	UDP-glucose pyrophosphorylase 2	protein-coding
mm_136823.1	chr17	12466842	12466855	+	1	NA	promoter-TSS (NR_077217)	promoter-TSS (NR_077217)	4	NR_077217	77414	Mm.417145	NR_077216		C030013G03Rik	-	RIKEN cDNA C030013G03 gene	ncRNA
mm_40240.1	chr5	37735613	37735630	+	1	NA	exon (NM_001081106, exon 1 of 4)	exon (NM_001081106, exon 1 of 4)	102	NM_001081106	231162	Mm.76407	NM_001081106	ENSMUSG00000062329	Cytl1	4930443F05Rik|4Cytl1|C17|Cyt1|Gm147	cytokine-like 1	protein-coding
mm_4197.1	chr1	171226161	171226182	+	1	NA	exon (NM_013474, exon 4 of 4)	exon (NM_013474, exon 4 of 4)	1117	NM_013474	11807	Mm.389209	NM_013474	ENSMUSG00000005681	Apoa2	Alp-2|Apo-AII|ApoA-II|ApoAII|Apoa-2|Hdl-1	apolipoprotein A-II	protein-coding
mm_36132.1	chr4	59331732	59331743	-	1	NA	intron (NM_001163288, intron 13 of 16)	intron (NM_001163288, intron 13 of 16)	71686	NR_105031	101055769	Mm.421401	NR_105031		Gm12596	OTTMUSG00000007649	predicted gene 12596	ncRNA
mm_130634.1	chr15	100425099	100425105	-	1	NA	intron (NR_040351, intron 1 of 2)	intron (NR_040351, intron 1 of 2)	1909	NR_040351	432982	Mm.234608	NM_001034883	ENSMUSG00000087444	Gm5475	EG432982	predicted gene 5475	ncRNA
mm_107679.1	chr12	54343747	54343765	+	1	NA	Intergenic	L1MA5|LINE|L1	47562	NR_033689	665239	Mm.26856	NR_033689		Gm7550	EG665239|Gm666	predicted gene 7550	ncRNA
mm_47550.1	chr5	124352258	124352302	-	1	NA	intron (NM_013812, intron 1 of 3)	intron (NM_013812, intron 1 of 3)	2348	NM_013812	13445	Mm.391838	NM_013812	ENSMUSG00000029394	Cdk2ap1	Apc10|Cdkap1|DORC1|Doc1|ST19|doc-1|p12	CDK2 (cyclin-dependent kinase 2)-associated protein 1	protein-coding
mm_159221.1	chr2	127656810	127656810	-	1	NA	promoter-TSS (NM_001171187)	promoter-TSS (NM_001171187)	-115	NM_001171187	17153	Mm.39040	NM_010762	ENSMUSG00000027375	Mal	Mpv17|Vip17	myelin and lymphocyte protein, T cell differentiation protein	protein-coding
mm_51291.1	chr6	72305853	72305897	+	1	NA	exon (NM_001282071, exon 4 of 11)	exon (NM_001282071, exon 4 of 11)	1265	NM_147779	20388	Mm.46033	NM_147779	ENSMUSG00000056370	Sftpb	AI562151|SF-B|SP-B|Sftp-3|Sftp3	surfactant associated protein B	protein-coding
mm_167768.1	chr9	110880108	110880119	-	1	NA	promoter-TSS (NM_001146059)	promoter-TSS (NM_001146059)	-30	NM_146260	20776	Mm.390229	NM_146260	ENSMUSG00000049555	Tmie	5131400L21Rik|Mm.87012|sr	transmembrane inner ear	protein-coding
mm_136605.1	chr17	5227898	5227898	+	1	NA	intron (NM_001085355, intron 4 of 19)	intron (NM_001085355, intron 4 of 19)	190869	NM_175349	106557	Mm.432764	NM_175349	ENSMUSG00000101959	Ldhal6b	4933402O15Rik|AI326310|LDHL|Ldhal	lactate dehydrogenase A-like 6B	protein-coding
mm_2240.1	chr1	91053523	91053532	+	1	NA	promoter-TSS (NM_008515)	promoter-TSS (NM_008515)	83	NM_008515	16978	Mm.45039	NM_008515	ENSMUSG00000026305	Lrrfip1	AU024550|Fliiap1	leucine rich repeat (in FLII) interacting protein 1	protein-coding
mm_29612.1	chr3	121263315	121263347	-	1	NA	promoter-TSS (NM_178936)	promoter-TSS (NM_178936)	-15	NM_178936	99887	Mm.26088	NM_178936	ENSMUSG00000028132	Tmem56	4930577M16Rik|AU018104|AW109744|C730036B01Rik	transmembrane protein 56	protein-coding
mm_7304.1	chr1	97977234	97977279	-	1	NA	5' UTR (NM_013626, exon 2 of 26)	5' UTR (NM_013626, exon 2 of 26)	70537	NR_037993	78603	Mm.442597	NR_037993	ENSMUSG00000089706	B230216N24Rik	-	RIKEN cDNA B230216N24 gene	ncRNA
mm_39236.1	chr4	156255328	156255344	-	1	NA	promoter-TSS (NM_001110516)	promoter-TSS (NM_001110516)	2	NM_001110516	231004	Mm.406833	NM_173736	ENSMUSG00000096351	Samd11	BC026991|mr-s	sterile alpha motif domain containing 11	protein-coding
mm_153342.1	chr19	38809968	38809972	-	1	NA	intron (NM_021315, intron 8 of 20)	B1_Mur2|SINE|Alu	9267	NM_021315	57753	Mm.86482	NM_021315	ENSMUSG00000024999	Noc3l	AF233884|Fad24	NOC3 like DNA replication regulator	protein-coding
mm_139926.1	chr17	71019504	71019523	+	1	NA	promoter-TSS (NM_001083934)	promoter-TSS (NM_001083934)	-44	NM_010867	17929	Mm.4103	NM_010867	ENSMUSG00000024049	Myom1	D430047A17Rik	myomesin 1	protein-coding
mm_101348.1	chr11	23646050	23646063	-	1	NA	TTS (NM_023651)	TTS (NM_023651)	-12425	NM_027860	71675	Mm.48031	NM_027860	ENSMUSG00000042208	0610010F05Rik	Kiaa1841|mKIAA1841	RIKEN cDNA 0610010F05 gene	protein-coding
mm_160281.1	chr7	122970381	122970381	+	1	NA	promoter-TSS (NM_175023)	promoter-TSS (NM_175023)	78	NR_045614	73951	Mm.389936	NR_045614		4930413G21Rik	-	RIKEN cDNA 4930413G21 gene	ncRNA
mm_18642.1	chr2	69491521	69491532	-	1	NA	intron (NM_001081088, intron 35 of 78)	intron (NM_001081088, intron 35 of 78)	94541	NM_001081088	14725	Mm.23847	NM_001081088	ENSMUSG00000027070	Lrp2	AI315343|AW536255|D230004K18Rik|Gp330|Megalin|b2b1625.2Clo	low density lipoprotein receptor-related protein 2	protein-coding
mm_66364.1	chr7	43533082	43533131	-	1	NA	promoter-TSS (NM_001111058)	promoter-TSS (NM_001111058)	65	NM_001111058	12489	Mm.140157	NM_021293	ENSMUSG00000004609	Cd33	Siglec-3|gp67	CD33 antigen	protein-coding
mm_90249.1	chr10	121586218	121586242	+	1	NA	intron (NM_019786, intron 1 of 20)	intron (NM_019786, intron 1 of 20)	564	NM_019786	56480	Mm.34580	NM_019786	ENSMUSG00000020115	Tbk1	1200008B05Rik|AI462036|AW048562	TANK-binding kinase 1	protein-coding
mm_170192.1	chr17	6601769	6601778	+	1	NA	promoter-TSS (NM_001166630)	promoter-TSS (NM_001166630)	-6	NM_001166630	100040563	Mm.457381	NM_001166630	ENSMUSG00000000579	Dynlt1c	100040603|Dynlt1d	dynein light chain Tctex-type 1C	protein-coding
mm_122306.1	chr14	35811966	35811999	-	1	NA	promoter-TSS (NM_001033766)	promoter-TSS (NM_001033766)	-4	NM_001033766	239036	Mm.239970	NM_001033766	ENSMUSG00000041068	4930596D02Rik	-	RIKEN cDNA 4930596D02 gene	protein-coding
mm_40672.1	chr5	65536842	65536846	+	1	NA	promoter-TSS (NM_016786)	promoter-TSS (NM_016786)	-401	NM_016786	53323	Mm.319512	NM_016786	ENSMUSG00000029203	Ube2k	AW492011|D5Ertd601e|E2-25k|HIP-2|Hip2|Hypg|Lig	ubiquitin-conjugating enzyme E2K	protein-coding
mm_162952.1	chr11	3530000	3530009	+	1	NA	exon (NM_001284429, exon 11 of 22)	exon (NM_001284429, exon 11 of 22)	9288	NM_013870	29856	Mm.188516	NM_013870	ENSMUSG00000020439	Smtn	smsmo	smoothelin	protein-coding
mm_145030.1	chr18	39291433	39291440	+	1	NA	intron (NM_175164, intron 18 of 22)	intron (NM_175164, intron 18 of 22)	195809	NM_008173	14815	Mm.129481	NM_008173	ENSMUSG00000024431	Nr3c1	GR|Grl-1|Grl1	nuclear receptor subfamily 3, group C, member 1	protein-coding
mm_166432.1	chr5	137180060	137180070	-	1	NA	Intergenic	Intergenic	-63858	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_69365.1	chr7	130547359	130547386	-	1	NA	promoter-TSS (NM_001162855)	promoter-TSS (NM_001162855)	9	NM_001162855	67872	Mm.21714	NM_001162855	ENSMUSG00000040331	Nsmce4a	2410003A14Rik	NSE4 homolog A, SMC5-SMC6 complex component	protein-coding
mm_169158.1	chr13	65313714	65313718	+	1	NA	Intergenic	Intergenic	34862	NM_178364	170936	Mm.151546	NM_178364	ENSMUSG00000021514	Zfp369	B930030B22Rik|D230020H11Rik|NRIF2	zinc finger protein 369	protein-coding
mm_45960.1	chr5	90464168	90464170	-	1	NA	exon (NM_009654, exon 4 of 15)	exon (NM_009654, exon 4 of 15)	3299	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_26865.1	chr3	16006345	16006361	-	1	NA	promoter-TSS (NM_001081687)	promoter-TSS (NM_001081687)	-21	NM_001081687	381484	Mm.217376	NM_001081687	ENSMUSG00000078780	Gm5150	-	predicted gene 5150	protein-coding
mm_151395.1	chr19	56441192	56441205	+	1	NA	3' UTR (NM_007611, exon 7 of 7)	3' UTR (NM_007611, exon 7 of 7)	-20439	NM_001164263	226245	Mm.156742	NM_172641	ENSMUSG00000035818	Plekhs1	9930023K05Rik	pleckstrin homology domain containing, family S member 1	protein-coding
mm_3795.1	chr1	157412702	157412774	+	1	NA	promoter-TSS (NM_177644)	promoter-TSS (NM_177644)	-143	NM_177644	226525	Mm.235028	NM_177644	ENSMUSG00000070565	Rasal2	6530401P13|A330066M24Rik	RAS protein activator like 2	protein-coding
mm_61319.1	chr7	68148584	68148594	+	1	NA	intron (NM_010513, intron 2 of 20)	intron (NM_010513, intron 2 of 20)	115644	NM_030101	78444	Mm.425468	NM_030101	ENSMUSG00000030553	Pgpep1l	C330024D12Rik	pyroglutamyl-peptidase I-like	protein-coding
mm_137774.1	chr17	29491726	29491738	+	1	NA	exon (NM_008842, exon 4 of 6)	exon (NM_008842, exon 4 of 6)	687	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_161023.1	chr11	121631096	121631096	-	1	NA	intron (NM_178664, intron 6 of 12)	intron (NM_178664, intron 6 of 12)	42055	NM_178664	210004	Mm.386847	NM_178664	ENSMUSG00000046605	B3gntl1	6030413G23Rik	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase-like 1	protein-coding
mm_173349.1	chrY	90813274	90813275	+	1	NA	intron (NM_133362, intron 2 of 3)	IMPB_01|Satellite|Satellite	26132	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_5689.1	chr1	43183921	43183933	-	1	NA	intron (NM_001289533, intron 1 of 5)	ORR1A4|LTR|ERVL-MaLR	12834	NM_001289533	14200	Mm.6799	NM_010212	ENSMUSG00000008136	Fhl2	FHL-2|SLIM-3|SLIM3	four and a half LIM domains 2	protein-coding
mm_95675.1	chr11	54101035	54101043	+	1	NA	5' UTR (NM_001136076, exon 1 of 16)	5' UTR (NM_001136076, exon 1 of 16)	115	NM_011031	18452	Mm.3705	NM_011031	ENSMUSG00000018906	P4ha2	AA407196|C76437|P4hl	procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha II polypeptide	protein-coding
mm_88726.1	chr10	80179494	80179531	+	1	NA	promoter-TSS (NM_007909)	promoter-TSS (NM_007909)	30	NM_007909	13637	Mm.1478	NM_007909	ENSMUSG00000003070	Efna2	CEK7L|Elf1|Epl6|Eplg6|Lerk6	ephrin A2	protein-coding
mm_87594.1	chr10	57632047	57632060	+	1	NA	promoter-TSS (NM_008863)	promoter-TSS (NM_008863)	72	NM_001039051	18768	Mm.262135	NM_008863	ENSMUSG00000019876	Pkib	Pkibeta|Prkacn2	protein kinase inhibitor beta, cAMP dependent, testis specific	protein-coding
mm_31697.1	chr4	62409845	62409847	+	1	NA	intron (NM_027297, intron 2 of 13)	ID_B1|SINE|B4	1063	NM_027297	70052	Mm.30660	NM_027297	ENSMUSG00000066148	Prpf4	1600015H11Rik|AI874830|AW047464|bN189G18.1	pre-mRNA processing factor 4	protein-coding
mm_67285.1	chr7	78628002	78628002	-	1	NA	intron (NR_015542, intron 8 of 10)	intron (NR_015542, intron 8 of 10)	-50164	NM_182809	18213	Mm.33496	NM_008746	ENSMUSG00000059146	Ntrk3	AW125844|Ntrk3_tv3|TrkC	neurotrophic tyrosine kinase, receptor, type 3	protein-coding
mm_11356.1	chr2	30913461	30913493	+	1	NA	Intergenic	Intergenic	-10180	NM_022415	64292	Mm.28768	NM_022415	ENSMUSG00000050737	Ptges	2410099E23Rik|D2Ertd369e|Pges|mPGES|mPGES-1	prostaglandin E synthase	protein-coding
mm_20645.1	chr2	132029809	132029813	-	1	NA	5' UTR (NM_175445, exon 1 of 11)	5' UTR (NM_175445, exon 1 of 11)	177	NM_175445	215653	Mm.204737	NM_175445	ENSMUSG00000027339	Rassf2	3830431H01Rik|9030412M04Rik|AI852669|AW495050	Ras association (RalGDS/AF-6) domain family member 2	protein-coding
mm_33245.1	chr4	127035100	127035115	+	1	NA	intron (NR_045010, intron 9 of 11)	intron (NR_045010, intron 9 of 11)	13806	NM_023603	71514	Mm.257276	NM_023603	ENSMUSG00000028820	Sfpq	1110004P21Rik|2810416M14Rik|5730453G22Rik|9030402K04Rik|AU021830|D4Ertd314e|Gm12940|OTTMUSG00000009329|PSF|REP1	splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)	protein-coding
mm_95893.1	chr11	58183887	58183897	+	1	NA	promoter-TSS (NM_001135115)	promoter-TSS (NM_001135115)	49	NM_001135115	631323	Mm.394103	NM_001135115		Gm12250	Irgb10|OTTMUSG00000005723	predicted gene 12250	protein-coding
mm_89852.1	chr10	107271869	107271888	+	1	NA	promoter-TSS (NM_001039354)	promoter-TSS (NM_001039354)	47	NM_001033223	108030	Mm.268025	NM_001033223	ENSMUSG00000019906	Lin7a	AI848705|LIN-7A|MALS-1|TIP-33|Veli|Veli1	lin-7 homolog A (C. elegans)	protein-coding
mm_171758.1	chr5	105093742	105093744	-	1	NA	intron (NM_172777, intron 5 of 10)	L1Md_T|LINE|L1	16549	NM_172777	236573	Mm.425261	NM_172777	ENSMUSG00000029298	Gbp9	-	guanylate-binding protein 9	protein-coding
mm_20128.1	chr2	121301266	121301298	-	1	NA	exon (NM_001173506, exon 4 of 6)	exon (NM_001173506, exon 4 of 6)	5828	NM_001173506	17754	Mm.36501	NM_032393	ENSMUSG00000027254	Map1a	6330416M19Rik|AI853608|Mtap-1|Mtap1|Mtap1a|moth1	microtubule-associated protein 1 A	protein-coding
mm_8906.1	chr1	163312571	163312585	-	1	NA	exon (NM_175686, exon 1 of 5)	exon (NM_175686, exon 1 of 5)	1072	NM_011127	18933	Mm.288642	NM_011127	ENSMUSG00000026586	Prrx1	A230024N07Rik|AA755424|AI385634|AI843499|K-2|Pmx|Pmx1|Prx1|mHox	paired related homeobox 1	protein-coding
mm_153832.1	chr19	46324698	46324728	-	1	NA	exon (NM_001347454, exon 3 of 18)	exon (NM_001347454, exon 3 of 18)	2153	NM_001347454	73728	Mm.268532	NM_028627	ENSMUSG00000037126	Psd	1110007H17Rik|A930015K15|Efa6|Efa6a|Psdl|mKIAA2011	pleckstrin and Sec7 domain containing	protein-coding
mm_158297.1	chrX	114981388	114981390	-	1	NA	Intergenic	Intergenic	54400	NR_130989	78086		NR_130989	ENSMUSG00000085619	4930555B12Rik	-	RIKEN cDNA 4930555B12 gene	ncRNA
mm_15593.1	chr2	160583397	160583400	+	1	NA	Intergenic	RLTR27|LTR|ERVK	-62499	NM_009408	21969	Mm.217233	NM_009408	ENSMUSG00000070544	Top1	AI467334|D130064I21Rik|Top-1	topoisomerase (DNA) I	protein-coding
mm_53743.1	chr6	145163127	145163130	+	1	NA	intron (NM_008511, intron 11 of 18)	L1M3|LINE|L1	41389	NM_008511	16970	Mm.843	NM_008511	ENSMUSG00000030263	Lrmp	D6Int3|D6Int4|D6Int5|D6Int7|D6Int8|Jaw1	lymphoid-restricted membrane protein	protein-coding
mm_34708.1	chr4	152116037	152116080	+	1	NA	promoter-TSS (NM_033042)	promoter-TSS (NM_033042)	124	NM_001291010	85030	Mm.101198	NM_033042	ENSMUSG00000024793	Tnfrsf25	APO-3|DDR3|DR3|LARD|TR3|TRAMP|Tnfrsf12|WSL-1|WSL-LR|Wsl	tumor necrosis factor receptor superfamily, member 25	protein-coding
mm_68596.1	chr7	116093312	116093320	-	1	NA	promoter-TSS (NM_019772)	promoter-TSS (NM_019772)	-64	NM_019772	56372	Mm.24231	NM_019772	ENSMUSG00000030663	1110004F10Rik	Smacp|Smap|sid2057|sid2057p	RIKEN cDNA 1110004F10 gene	protein-coding
mm_136766.1	chr17	8849975	8850001	+	1	NA	promoter-TSS (NM_001347321)	promoter-TSS (NM_001347321)	3	NM_001347321	23984	Mm.87161	NM_011866	ENSMUSG00000023868	Pde10a	-	phosphodiesterase 10A	protein-coding
mm_47436.1	chr5	123181448	123181458	-	1	NA	exon (NM_008277, exon 4 of 14)	exon (NM_008277, exon 4 of 14)	1233	NM_008277	15445	Mm.439709	NM_008277	ENSMUSG00000029445	Hpd	Fla|Flp|Hppd|Laf	4-hydroxyphenylpyruvic acid dioxygenase	protein-coding
mm_150289.1	chr19	34492819	34492838	+	1	NA	3' UTR (NM_021460, exon 10 of 10)	3' UTR (NM_021460, exon 10 of 10)	-17693	NM_009890	12642	Mm.30824	NM_009890	ENSMUSG00000050370	Ch25h	AI462618|m25OH	cholesterol 25-hydroxylase	protein-coding
mm_74732.1	chr8	18334319	18334321	-	1	NA	Intergenic	Intergenic	-260853	NM_173189	244329	Mm.235296	NM_173189	ENSMUSG00000039842	Mcph1	5430437K10Rik|BRIT1|D030046N04Rik|MCT	microcephaly, primary autosomal recessive 1	protein-coding
mm_129054.1	chr15	75566569	75566604	-	1	NA	promoter-TSS (NM_001135689)	promoter-TSS (NM_001135689)	62	NM_001135689	23934	Mm.22154	NM_011837	ENSMUSG00000022577	Ly6h	-	lymphocyte antigen 6 complex, locus H	protein-coding
mm_81836.1	chr9	118478816	118478824	+	1	NA	exon (NM_010136, exon 1 of 6)	exon (NM_010136, exon 1 of 6)	631	NM_010136	13813	Mm.200692	NM_010136	ENSMUSG00000032446	Eomes	C77258|TBR-2|Tbr2	eomesodermin	protein-coding
mm_548.1	chr1	38019099	38019109	+	1	NA	exon (NM_198303, exon 4 of 24)	exon (NM_198303, exon 4 of 24)	21094	NM_198303	226982	Mm.260943	NM_198303	ENSMUSG00000026083	Eif5b	A030003E17Rik|BC018347|IF2	eukaryotic translation initiation factor 5B	protein-coding
mm_45778.1	chr5	87127857	87127858	-	1	NA	exon (NM_009467, exon 5 of 6)	exon (NM_009467, exon 5 of 6)	12483	NM_009467	22238	Mm.291575	NM_009467	ENSMUSG00000054630	Ugt2b5	AI118071|M-1|Udpgt-3|Udpgt2b5|Ugt2b17	UDP glucuronosyltransferase 2 family, polypeptide B5	protein-coding
mm_134972.1	chr16	32019491	32019501	-	1	NA	3' UTR (NM_177326, exon 15 of 15)	3' UTR (NM_177326, exon 15 of 15)	-16209	NM_177103	320213	Mm.152890	NM_023801	ENSMUSG00000022772	Senp5	6230429P13Rik|A730063F07Rik|AI851888|BB189556|SMT3IP3	SUMO/sentrin specific peptidase 5	protein-coding
mm_121526.1	chr14	122155338	122155356	+	1	NA	exon (NM_080556, exon 16 of 17)	exon (NM_080556, exon 16 of 17)	-26347	NM_029556	69634	Mm.34608	NM_029556	ENSMUSG00000025545	Clybl	0610033J05Rik|2310014M14Rik|AI256068|Clb	citrate lyase beta like	protein-coding
mm_39179.1	chr4	155784937	155784954	-	1	NA	intron (NM_001033394, intron 1 of 1)	G-rich|Low_complexity|Low_complexity	929	NM_001033394	320587	Mm.384382	NM_001033394	ENSMUSG00000073680	Tmem88b	A230069A22Rik	transmembrane protein 88B	protein-coding
mm_6827.1	chr1	84200552	84200565	-	1	NA	intron (NM_001003948, intron 1 of 2)	intron (NM_001003948, intron 1 of 2)	18403	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_3984.1	chr1	164275690	164275702	+	1	NA	promoter-TSS (NM_029115)	promoter-TSS (NM_029115)	98	NM_029115	74895	Mm.167258	NM_029115	ENSMUSG00000026578	Ccdc181	4930455F23Rik|AI427889	coiled-coil domain containing 181	protein-coding
mm_143829.1	chr17	84025967	84026004	-	1	NA	Intergenic	Intergenic	27433	NR_130994	78148	Mm.243918	NR_130994		8430430B14Rik	-	RIKEN cDNA 8430430B14 gene	ncRNA
mm_134449.1	chr16	18348014	18348088	-	1	NA	promoter-TSS (NM_001272029)	promoter-TSS (NM_001272029)	-131	NM_033474	11877	Mm.293599	NM_033474	ENSMUSG00000000325	Arvcf	-	armadillo repeat gene deleted in velo-cardio-facial syndrome	protein-coding
mm_139443.1	chr17	55445376	55445388	+	1	NA	promoter-TSS (NM_172829)	promoter-TSS (NM_172829)	0	NM_001347403	240119	Mm.311687	NM_172829	ENSMUSG00000024172	St6gal2	C230064G14Rik|St6galII|mKIAA1877	beta galactoside alpha 2,6 sialyltransferase 2	protein-coding
mm_145834.1	chr18	65442327	65442345	+	1	NA	intron (NM_172833, intron 2 of 15)	intron (NM_172833, intron 2 of 15)	11339	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_30978.1	chr4	34614941	34614996	+	1	NA	promoter-TSS (NM_015824)	promoter-TSS (NM_015824)	10	NM_181406	109093	Mm.22363	NM_181406	ENSMUSG00000028292	Rars2	1500002I10Rik|PRO1992|Rarsl	arginyl-tRNA synthetase 2, mitochondrial	protein-coding
mm_79159.1	chr9	47810096	47810109	+	1	NA	exon (NM_018770, exon 6 of 10)	exon (NM_018770, exon 6 of 10)	8106	NR_046048	100038460	Mm.447649	NR_046048		Gm10677	ENSMUSG00000074363	predicted gene 10677	ncRNA
mm_97104.1	chr11	73663003	73663005	+	1	NA	Intergenic	Intergenic	-25774	NM_001126489	76390	Mm.267142	NM_001126489	ENSMUSG00000060630	Zfp735	1700012C15Rik	zinc finger protein 735	protein-coding
mm_29678.1	chr3	122924104	122924145	-	1	NA	promoter-TSS (NM_024461)	promoter-TSS (NM_024461)	-8	NR_046036	74057	Mm.159123	NR_046036	ENSMUSG00000097852	4933405D12Rik	-	RIKEN cDNA 4933405D12 gene	ncRNA
mm_26501.1	chr3	145758675	145758685	+	1	NA	promoter-TSS (NM_026993)	promoter-TSS (NM_026993)	-12	NM_026993	69219	Mm.234247	NM_026993	ENSMUSG00000028194	Ddah1	2410006N07Rik|2510015N06Rik|AI987801|AW050362	dimethylarginine dimethylaminohydrolase 1	protein-coding
mm_100847.1	chr11	5788359	5788434	-	1	NA	promoter-TSS (NM_001146309)	promoter-TSS (NM_001146309)	-87	NM_001146309	13169	Mm.256925	NM_013810	ENSMUSG00000020476	Dbnl	Abp1|SH3P7|mAbp1	drebrin-like	protein-coding
mm_141486.1	chr17	31265869	31265878	-	1	NA	exon (NM_025290, exon 5 of 9)	exon (NM_025290, exon 5 of 9)	11483	NM_025290	22092	Mm.12743	NM_025290	ENSMUSG00000024033	Rsph1	MCA|Tsga2	radial spoke head 1 homolog (Chlamydomonas)	protein-coding
mm_126296.1	chr15	79348130	79348154	+	1	NA	promoter-TSS (NM_001304832)	promoter-TSS (NM_001304832)	81	NM_001304831	17133	Mm.86646	NM_010755	ENSMUSG00000042622	Maff	-	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein F (avian)	protein-coding
mm_97505.1	chr11	78465698	78465735	+	1	NA	promoter-TSS (NM_026740)	promoter-TSS (NM_026740)	15	NM_026740	52466	Mm.131618	NM_026740	ENSMUSG00000020829	Slc46a1	1110002C08Rik|D11Ertd18e|HCP1|Pcft	solute carrier family 46, member 1	protein-coding
mm_2455.1	chr1	101487663	101487663	+	1	NA	Intergenic	B1_Mur1|SINE|Alu	331895	NR_037989	100504525	Mm.87065	NR_037989	ENSMUSG00000100684	Gm20268	-	predicted gene, 20268	ncRNA
mm_10523.1	chr2	16384625	16384636	+	1	NA	intron (NM_026162, intron 1 of 13)	intron (NM_026162, intron 1 of 13)	28326	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding
mm_38728.1	chr4	145237083	145237091	-	1	NA	intron (NM_011610, intron 1 of 9)	intron (NM_011610, intron 1 of 9)	9783	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_118372.1	chr13	116923923	116923939	-	1	NA	intron (NM_001081009, intron 7 of 26)	intron (NM_001081009, intron 7 of 26)	101585	NM_001081009	52552	Mm.274466	NM_027272	ENSMUSG00000021725	Parp8	2810430O08Rik|ARTD16|D13Ertd275e	poly (ADP-ribose) polymerase family, member 8	protein-coding
mm_14269.1	chr2	128704802	128704819	+	1	NA	intron (NM_008587, intron 1 of 18)	intron (NM_008587, intron 1 of 18)	5813	NM_008587	17289	Mm.239655	NM_008587	ENSMUSG00000014361	Mertk	Eyk|Mer|Nyk|nmf12	c-mer proto-oncogene tyrosine kinase	protein-coding
mm_171980.1	chr5	89690185	89690193	-	1	NA	intron (NM_001081401, intron 18 of 21)	intron (NM_001081401, intron 18 of 21)	73753	NR_037571	631105	Mm.7732	NR_037571		Gm7056	Gm149	predicted gene 7056	ncRNA
mm_46781.1	chr5	112522588	112522589	-	1	NA	intron (NM_001253917, intron 1 of 15)	intron (NM_001253917, intron 1 of 15)	54610	NM_001253917	56747	Mm.143742	NM_019982	ENSMUSG00000058153	Sez6l	AI843918|AIG1|AW539724|Acig1|BSRP-B|mKIAA0927	seizure related 6 homolog like	protein-coding
mm_4386.1	chr1	172219484	172219497	+	1	NA	exon (NM_009813, exon 1 of 11)	exon (NM_009813, exon 1 of 11)	405	NM_009813	12372	Mm.12829	NM_009813	ENSMUSG00000007122	Casq1	CSQ|CSQ-1|CSQ1|sCSQ	calsequestrin 1	protein-coding
mm_26481.1	chr3	144689499	144689540	+	1	NA	3' UTR (NM_019464, exon 9 of 9)	3' UTR (NM_019464, exon 9 of 9)	30816	NM_001282042	54673	Mm.271775	NM_019464	ENSMUSG00000037062	Sh3glb1	AA409932|AI314629|AU015566|Bif-1|mKIAA0491	SH3-domain GRB2-like B1 (endophilin)	protein-coding
mm_54782.1	chr6	41544270	41544279	-	1	NA	Intergenic	Intergenic	22498	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_59697.1	chr7	28543983	28544013	+	1	NA	3' UTR (NM_001081115, exon 6 of 6)	3' UTR (NM_001081115, exon 6 of 6)	3113	NM_026716	68416	Mm.25210	NM_026716	ENSMUSG00000084174	Sycn	0910001K16Rik|1810038B08Rik|SYL	syncollin	protein-coding
mm_144855.1	chr18	36665322	36665347	+	1	NA	exon (NM_201256, exon 2 of 3)	exon (NM_201256, exon 2 of 3)	1274	NM_201256	108112	Mm.24790	NM_201256	ENSMUSG00000090264	Eif4ebp3	4e-bp3	eukaryotic translation initiation factor 4E binding protein 3	protein-coding
mm_47925.1	chr5	135012813	135012823	-	1	NA	TTS (NM_001190437)	TTS (NM_001190437)	339	NR_026688	69812	Mm.18422	NR_026688	ENSMUSG00000085042	Abhd11os	2010001M06Rik|AI462243|Wbscr26|Wnscr26	abhydrolase domain containing 11, opposite strand	ncRNA
mm_115437.1	chr13	117602310	117602325	+	1	NA	promoter-TSS (NM_010408)	promoter-TSS (NM_010408)	-3	NM_010408	15165	Mm.343429	NM_010408	ENSMUSG00000021730	Hcn1	Bcng1|C630013B14Rik|HAC2	hyperpolarization-activated, cyclic nucleotide-gated K+ 1	protein-coding
mm_19490.1	chr2	93203655	93203673	-	1	NA	3' UTR (NM_183180, exon 10 of 10)	3' UTR (NM_183180, exon 10 of 10)	16080	NM_001025246	277414	Mm.41033	NM_001025246	ENSMUSG00000068735	Trp53i11	Tp53i11	transformation related protein 53 inducible protein 11	protein-coding
mm_29849.1	chr3	129970058	129970130	-	1	NA	5' UTR (NM_025779, exon 1 of 8)	5' UTR (NM_025779, exon 1 of 8)	112	NM_025779	66815	Mm.31056	NM_025779	ENSMUSG00000027994	Ccdc109b	9030408N13Rik|MCUb	coiled-coil domain containing 109B	protein-coding
mm_71883.1	chr8	69812650	69812664	+	1	NA	intron (NM_198101, intron 7 of 20)	ID4_|SINE|ID	3970	NM_198101	78816	Mm.324305	NM_198101	ENSMUSG00000036246	Gmip	5031419I10Rik	Gem-interacting protein	protein-coding
mm_123667.1	chr14	69245261	69245276	-	1	NA	exon (NM_026331, exon 4 of 4)	exon (NM_026331, exon 4 of 4)	39835	NM_026331	67712	Mm.293635	NM_026331	ENSMUSG00000034248	Slc25a37	1700020E22Rik|4930513O14Rik|4930526G11Rik|AI848481|C330015G08Rik|Mfrn|Mfrn1|Mscp|frascati|mitoferrin	solute carrier family 25, member 37	protein-coding
mm_9270.1	chr1	171633313	171633331	-	1	NA	3' UTR (NM_144539, exon 8 of 8)	3' UTR (NM_144539, exon 8 of 8)	8578	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_2598.1	chr1	119837171	119837177	+	1	NA	promoter-TSS (NM_019933)	promoter-TSS (NM_019933)	-103	NM_019933	19258	Mm.458796	NM_019933	ENSMUSG00000026384	Ptpn4	PTPMEG|Ptn4|TEP|TEP/mPTPMEG|hPTP-MEG	protein tyrosine phosphatase, non-receptor type 4	protein-coding
mm_35729.1	chr4	44714322	44714352	-	1	NA	Intergenic	Intergenic	-3897	NM_008782	18507	Mm.439659	NM_008782	ENSMUSG00000014030	Pax5	BSAP|EBB-1|KLP|Pax-5	paired box 5	protein-coding
mm_50820.1	chr6	54440516	54440518	+	1	NA	Intergenic	Intergenic	-10296	NR_033635	100042056	Mm.448157	NM_198118	ENSMUSG00000073067	9130019P16Rik	6430501H15Rik|OTTMUSG00000023151	RIKEN cDNA 9130019P16 gene	ncRNA
mm_37037.1	chr4	115491145	115491155	-	1	NA	exon (NM_007822, exon 9 of 12)	exon (NM_007822, exon 9 of 12)	4991	NM_007822	13119	Mm.250901	NM_007822	ENSMUSG00000028715	Cyp4a14	AI314743	cytochrome P450, family 4, subfamily a, polypeptide 14	protein-coding
mm_118503.1	chr14	13670932	13670940	+	1	NA	promoter-TSS (NM_177624)	promoter-TSS (NM_177624)	60	NM_177624	218739	Mm.39919	NM_177624	ENSMUSG00000044772	Sntn	A430083B19Rik	sentan, cilia apical structure protein	protein-coding
mm_99381.1	chr11	102041533	102041581	+	1	NA	promoter-TSS (NM_001160713)	promoter-TSS (NM_001160713)	46	NM_001160713	52685	Mm.266885	NM_027987	ENSMUSG00000017309	Cd300lg	2310016B05Rik|Clm9|D11Ertd736e	CD300 molecule like family member G	protein-coding
mm_19168.1	chr2	84342546	84342557	-	1	NA	intron (NM_018782, intron 13 of 15)	Lx10|LINE|L1	82715	NM_018782	54598	Mm.75467	NM_018782	ENSMUSG00000059588	Calcrl	AV071593|CRLR	calcitonin receptor-like	protein-coding
mm_168723.1	chr12	110694680	110694697	-	1	NA	exon (NM_010480, exon 4 of 11)	exon (NM_010480, exon 4 of 11)	1707	NM_010480	15519	Mm.1843	NM_010480	ENSMUSG00000021270	Hsp90aa1	86kDa|89kDa|AL024080|AL024147|Hsp86-1|Hsp89|Hsp90|Hspca|hsp4	heat shock protein 90, alpha (cytosolic), class A member 1	protein-coding
mm_151275.1	chr19	55251926	55251944	+	1	NA	Intergenic	Intergenic	-1434	NM_027976	433256	Mm.292056	NM_027976	ENSMUSG00000024981	Acsl5	1700030F05Rik|ACS2|ACS5|Facl5	acyl-CoA synthetase long-chain family member 5	protein-coding
mm_102799.1	chr11	68854054	68854056	-	1	NA	promoter-TSS (NM_023668)	promoter-TSS (NM_023668)	-924	NM_023668	83431	Mm.31979	NM_023668	ENSMUSG00000018736	Ndel1	2600006O07Rik|MITAP1|NUDEL|mNudel	nudE neurodevelopment protein 1 like 1	protein-coding
mm_121857.1	chr14	20668257	20668267	-	1	NA	promoter-TSS (NM_175132)	promoter-TSS (NM_175132)	92	NM_175132	68760	Mm.35789	NM_175132	ENSMUSG00000039376	Synpo2l	1110054M18Rik|Chap	synaptopodin 2-like	protein-coding
mm_138428.1	chr17	35076934	35076961	+	1	NA	promoter-TSS (NM_027366)	promoter-TSS (NM_027366)	5	NM_027366	70274	Mm.250491	NM_027366	ENSMUSG00000013766	Ly6g6e	2310011I02Rik|G6e	lymphocyte antigen 6 complex, locus G6E	protein-coding
mm_135763.1	chr16	56717287	56717412	-	1	NA	5' UTR (NM_001252443, exon 1 of 7)	5' UTR (NM_001252443, exon 1 of 7)	101	NM_001252443	21787	Mm.425970	NM_019678	ENSMUSG00000022757	Tfg	AI173908	Trk-fused gene	protein-coding
mm_151300.1	chr19	55741789	55741797	+	1	NA	promoter-TSS (NM_001142918)	promoter-TSS (NM_001142918)	-17	NM_001331147	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_44586.1	chr5	24908672	24908683	-	1	NA	promoter-TSS (NM_001170556)	promoter-TSS (NM_001170556)	-168	NM_001170555	108099	Mm.33649	NM_145401	ENSMUSG00000028944	Prkag2	2410051C13Rik|AAKG|AAKG2|AI854673|H91620p|WPWS	protein kinase, AMP-activated, gamma 2 non-catalytic subunit	protein-coding
mm_52599.1	chr6	117171489	117171506	+	1	NA	exon (NM_021704, exon 2 of 3)	exon (NM_021704, exon 2 of 3)	2962	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_138959.1	chr17	44188690	44188702	+	1	NA	5' UTR (NM_172621, exon 1 of 6)	5' UTR (NM_172621, exon 1 of 6)	124	NM_172621	224796	Mm.37666	NM_172621	ENSMUSG00000023959	Clic5	5730531E12Rik|B330005L24|Gm322|jbg	chloride intracellular channel 5	protein-coding
mm_52918.1	chr6	122850576	122850590	+	1	NA	exon (NM_009779, exon 2 of 2)	exon (NM_009779, exon 2 of 2)	5574	NM_009779	12267	Mm.2408	NM_009779	ENSMUSG00000040552	C3ar1	AZ3B|C3AR|HNFAG09	complement component 3a receptor 1	protein-coding
mm_128132.1	chr15	31367732	31367791	-	1	NA	promoter-TSS (NM_001164441)	promoter-TSS (NM_001164441)	-2	NM_027496	67434	Mm.102470	NM_026153	ENSMUSG00000022237	Ankrd33b	0610012A05Rik|3021401C12Rik|5730557B15Rik	ankyrin repeat domain 33B	protein-coding
mm_154941.1	chrX	36195929	36195932	+	1	NA	promoter-TSS (NM_028325)	promoter-TSS (NM_028325)	26	NM_028325	72693	Mm.297698	NM_028325	ENSMUSG00000036699	Zcchc12	2810028A01Rik|AV136720|Sizn1	zinc finger, CCHC domain containing 12	protein-coding
mm_132453.1	chr16	36041199	36041234	+	1	NA	promoter-TSS (NM_027113)	promoter-TSS (NM_027113)	26	NM_027113	69544	Mm.37802	NM_027113	ENSMUSG00000034379	Wdr5b	2310009C03Rik|AI606931	WD repeat domain 5B	protein-coding
mm_22624.1	chr3	14704604	14704612	+	1	NA	Intergenic	Intergenic	62881	NM_024495	71934	Mm.158776	NM_024495	ENSMUSG00000027555	Car13	2310075C21Rik|Ca13	carbonic anhydrase 13	protein-coding
mm_128085.1	chr15	27697776	27697794	-	1	NA	Intergenic	Intergenic	-16243	NM_001242423	223433	Mm.266485	NM_198301	ENSMUSG00000056069	Fam105a	9830126M18	family with sequence similarity 105, member A	protein-coding
mm_68014.1	chr7	100954719	100954734	-	1	NA	intron (NM_183168, intron 1 of 2)	intron (NM_183168, intron 1 of 2)	9640	NM_183168	233571	Mm.235193	NM_183168	ENSMUSG00000048779	P2ry6	2010204J23Rik|P2Y6	pyrimidinergic receptor P2Y, G-protein coupled, 6	protein-coding
mm_167825.1	chr9	124423299	124423310	+	1	NA	promoter-TSS (NR_015516)	promoter-TSS (NR_015516)	53	NR_027950	75135	Mm.476814	NR_015516		4930526I15Rik	1600027J15Rik	RIKEN cDNA 4930526I15 gene	ncRNA
mm_163100.1	chr11	69735342	69735355	-	1	NA	exon (NM_001291068, exon 29 of 29)	exon (NM_001291068, exon 29 of 29)	23285	NM_001291068	20020	Mm.16533	NM_009089	ENSMUSG00000005198	Polr2a	220kDa|Rpb1|Rpo2-1	polymerase (RNA) II (DNA directed) polypeptide A	protein-coding
mm_29640.1	chr3	121815213	121815225	-	1	NA	promoter-TSS (NM_008991)	promoter-TSS (NM_008991)	-4	NM_008991	19299	Mm.399042	NM_008991	ENSMUSG00000028127	Abcd3	AI313901|AU018866|AW146054|PMP68|PMP70|Pxmp1	ATP-binding cassette, sub-family D (ALD), member 3	protein-coding
mm_44342.1	chr5	17780578	17780608	-	1	NA	Intergenic	Intergenic	55303	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_105586.1	chr11	106715237	106715247	-	1	NA	promoter-TSS (NM_008816)	promoter-TSS (NM_008816)	39	NM_001305158	18613	Mm.343951	NM_008816	ENSMUSG00000020717	Pecam1	C85791|Cd31|PECAM-1|Pecam	platelet/endothelial cell adhesion molecule 1	protein-coding
mm_59157.1	chr7	24370446	24370459	+	1	NA	exon (NM_001163510, exon 1 of 9)	exon (NM_001163510, exon 1 of 9)	189	NM_008433	16534	Mm.9911	NM_008433	ENSMUSG00000054342	Kcnn4	IK1|IKCA1|KCA4|KCa3.1|SK4|SKCas|mIKCa1	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4	protein-coding
mm_3406.1	chr1	143917828	143917842	+	1	NA	Intergenic	Intergenic	86314	NM_009061	19735	Mm.28262	NM_009061	ENSMUSG00000026360	Rgs2	GOS8	regulator of G-protein signaling 2	protein-coding
mm_11242.1	chr2	29889743	29889753	+	1	NA	promoter-TSS (NM_001113213)	promoter-TSS (NM_001113213)	28	NM_001177659	18286	Mm.330116	NM_013615	ENSMUSG00000026790	Odf2	AI848335|MMTEST29	outer dense fiber of sperm tails 2	protein-coding
mm_869.1	chr1	52152326	52152343	+	1	NA	exon (NM_001205314, exon 21 of 25)	exon (NM_001205314, exon 21 of 25)	32712	NM_001205313	20846	Mm.277406	NM_009283	ENSMUSG00000026104	Stat1	2010005J02Rik|AA408197	signal transducer and activator of transcription 1	protein-coding
mm_2907.1	chr1	132007379	132007392	+	1	NA	promoter-TSS (NM_007923)	promoter-TSS (NM_007923)	-220	NM_007923	13714	Mm.254233	NM_007923	ENSMUSG00000026436	Elk4	2310011G17Rik|A130026I01Rik|BB162516|SAP-1|Sap1	ELK4, member of ETS oncogene family	protein-coding
mm_105675.1	chr11	107470741	107470755	-	1	NA	promoter-TSS (NM_145823)	promoter-TSS (NM_145823)	-28	NM_145823	71795	Mm.397413	NM_145823	ENSMUSG00000040430	Pitpnc1	1110020B03Rik|5830436L09Rik|AI662802|AI851387|C330017I21Rik|Dnr411|RDGBB|RDGBB1|rdgB-beta	phosphatidylinositol transfer protein, cytoplasmic 1	protein-coding
mm_110331.1	chr12	35533881	35533881	-	1	NA	intron (NM_001314027, intron 1 of 9)	intron (NM_001314027, intron 1 of 9)	1108	NM_013464	11622	Mm.341377	NM_013464	ENSMUSG00000019256	Ahr	Ah|Ahh|Ahre|In|bHLHe76	aryl-hydrocarbon receptor	protein-coding
mm_148299.1	chr18	82692874	82692933	-	1	NA	promoter-TSS (NM_177832)	promoter-TSS (NM_177832)	-169	NM_177832	329002	Mm.34438	NM_177832	ENSMUSG00000041258	Zfp236	AI447957|Gm335	zinc finger protein 236	protein-coding
mm_13089.1	chr2	91219573	91219576	+	1	NA	intron (NM_028119, intron 3 of 9)	B3A|SINE|B2	16662	NM_007387	11432	Mm.45570	NM_007387	ENSMUSG00000002103	Acp2	Acp-2|LAP	acid phosphatase 2, lysosomal	protein-coding
mm_111675.1	chr12	103346892	103346923	-	1	NA	intron (NM_023049, intron 1 of 9)	intron (NM_023049, intron 1 of 9)	9094	NM_023049	65256	Mm.27159	NM_023049	ENSMUSG00000021200	Asb2	1110008E15Rik	ankyrin repeat and SOCS box-containing 2	protein-coding
mm_160718.1	chr10	63100184	63100184	+	1	NA	promoter-TSS (NM_016864)	promoter-TSS (NM_016864)	28	NM_016864	53404	Mm.228661	NM_016864	ENSMUSG00000036816	Atoh7	Math5|bHLHa13	atonal bHLH transcription factor 7	protein-coding
mm_95368.1	chr11	49086772	49086806	+	1	NA	promoter-TSS (NM_008330)	promoter-TSS (NM_008330)	-228	NM_001271676	15953	Mm.24769	NM_008330	ENSMUSG00000078920	Ifi47	47kDa|IRG-47|Ifggc1|Igrd|Iigp4|Iipg4|Irgd	interferon gamma inducible protein 47	protein-coding
mm_2418.1	chr1	94075189	94075196	+	1	NA	Intergenic	RLTR19B|LTR|ERVK	-22639	NM_008798	18566	Mm.5024	NM_008798	ENSMUSG00000026285	Pdcd1	Ly101|PD-1|Pdc1	programmed cell death 1	protein-coding
mm_47584.1	chr5	124861855	124861862	-	1	NA	promoter-TSS (NM_001081750)	promoter-TSS (NM_001081750)	363	NM_144819	215707	Mm.389693	NM_144819	ENSMUSG00000037979	Ccdc92	AW050178|D5Bwg0834e	coiled-coil domain containing 92	protein-coding
mm_101594.1	chr11	34683733	34683743	-	1	NA	intron (NM_033374, intron 22 of 51)	MTD|LTR|ERVL-MaLR	100167	NM_033374	94176	Mm.380679	NM_033374	ENSMUSG00000020143	Dock2	AI662014|AW122239|CED-5|Hch|MBC	dedicator of cyto-kinesis 2	protein-coding
mm_95648.1	chr11	53723996	53724024	+	1	NA	exon (NM_010558, exon 4 of 4)	exon (NM_010558, exon 4 of 4)	3216	NM_010558	16191	Mm.4461	NM_010558	ENSMUSG00000036117	Il5	Il-5	interleukin 5	protein-coding
mm_3240.1	chr1	136015327	136015331	+	1	NA	intron (NM_001160145, intron 1 of 5)	ORR1A2|LTR|ERVL-MaLR	-2672	NM_025439	66241	Mm.41773	NM_025439	ENSMUSG00000026411	Tmem9	1500015G18Rik|AW545782	transmembrane protein 9	protein-coding
mm_147251.1	chr18	38601337	38601355	-	1	NA	promoter-TSS (NM_011898)	promoter-TSS (NM_011898)	-78	NM_011898	24066	Mm.42038	NM_011898	ENSMUSG00000024427	Spry4	A030006O18Rik|sprouty4	sprouty homolog 4 (Drosophila)	protein-coding
mm_81792.1	chr9	115039530	115039534	+	1	NA	Intergenic	RMER17C|LTR|ERVK	-27747	NM_148958	74486	Mm.458474	NM_148958	ENSMUSG00000040875	Osbpl10	4933433D06Rik|C820004B04Rik|OPR-10|ORP-10	oxysterol binding protein-like 10	protein-coding
mm_108681.1	chr12	86734366	86734377	+	1	NA	promoter-TSS (NM_001195767)	promoter-TSS (NM_001195767)	2	NM_001195767	627607	Mm.341880	NM_001195767	ENSMUSG00000059114	Lrrc74a	EG627607|Gm6772|Lrrc74	leucine rich repeat containing 74A	protein-coding
mm_84258.1	chr9	62536901	62536911	-	1	NA	5' UTR (NM_175484, exon 1 of 12)	5' UTR (NM_175484, exon 1 of 12)	138	NM_175484	235431	Mm.335229	NM_175484	ENSMUSG00000041729	Coro2b	CLIPINC|E130012P22Rik	coronin, actin binding protein, 2B	protein-coding
mm_114975.1	chr13	97242031	97242077	+	1	NA	intron (NM_007930, intron 1 of 2)	intron (NM_007930, intron 1 of 2)	949	NM_007930	13803	Mm.241073	NM_007930	ENSMUSG00000041773	Enc1	Nrpb|PIG10	ectodermal-neural cortex 1	protein-coding
mm_95269.1	chr11	45006830	45006869	+	1	NA	3' UTR (NM_001290711, exon 16 of 16)	3' UTR (NM_001290711, exon 16 of 16)	110079	NR_045100	100504255	Mm.123608	NR_045100	ENSMUSG00000084773	Gm12159	OTTMUSG00000005475	predicted gene 12159	ncRNA
mm_41618.1	chr5	96827578	96827583	+	1	NA	intron (NM_013470, intron 7 of 12)	L1MC2|LINE|L1	34195	NM_013470	11745	Mm.7214	NM_013470	ENSMUSG00000029484	Anxa3	Anx3	annexin A3	protein-coding
mm_46536.1	chr5	105701530	105701569	-	1	NA	intron (NM_178701, intron 1 of 2)	intron (NM_178701, intron 1 of 2)	739	NM_178701	231549	Mm.23837	NM_178701	ENSMUSG00000046079	Lrrc8d	2810473G09Rik|4930525N13Rik|A930019F03|Lrrc5	leucine rich repeat containing 8D	protein-coding
mm_132207.1	chr16	32608936	32608945	+	1	NA	promoter-TSS (NM_011638)	promoter-TSS (NM_011638)	44	NM_011638	22042	Mm.28683	NM_011638	ENSMUSG00000022797	Tfrc	2610028K12Rik|CD71|E430033M20Rik|Mtvr1|TFR|TFR1|TR|Trfr|p90	transferrin receptor	protein-coding
mm_91446.1	chr10	33936628	33936651	-	1	NA	intron (NM_028287, intron 5 of 9)	MTEa-int|LTR|ERVL-MaLR	14573	NM_028287	72580	Mm.248081	NM_028287	ENSMUSG00000039531	Zufsp	2700019D07Rik	zinc finger with UFM1-specific peptidase domain	protein-coding
mm_20764.1	chr2	142758049	142758056	-	1	NA	intron (NM_001081133, intron 13 of 25)	intron (NM_001081133, intron 13 of 25)	143412	NM_001081133	16558	Mm.251934	NM_001081133	ENSMUSG00000038844	Kif16b	8430434E15Rik|AA623607|AI789011|C80253|C80902|mKIAA1590	kinesin family member 16B	protein-coding
mm_130359.1	chr15	97767709	97767719	-	1	NA	promoter-TSS (NM_001177811)	promoter-TSS (NM_001177811)	-48	NM_001177811	223864	Mm.24028	NM_144850	ENSMUSG00000022469	Rapgef3	2310016P22Rik|9330170P05Rik|Epac|Epac1	Rap guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_124998.1	chr15	23038379	23038386	+	1	NA	intron (NM_001081299, intron 1 of 11)	intron (NM_001081299, intron 1 of 11)	1919	NM_001081299	320865	Mm.241965	NM_001081299	ENSMUSG00000040420	Cdh18	B230220E17Rik|Cdh14l	cadherin 18	protein-coding
mm_64053.1	chr7	140845563	140845567	+	1	NA	promoter-TSS (NM_001099742)	promoter-TSS (NM_001099742)	0	NM_001099742	338417	Mm.270960	NM_001099742	ENSMUSG00000038801	Scgb1c1	Ryd5	secretoglobin, family 1C, member 1	protein-coding
mm_169484.1	chr14	73797152	73797159	-	1	NA	Intergenic	Intergenic	244369	NM_011506	20916	Mm.38951	NM_011506	ENSMUSG00000022110	Sucla2	4930547K18Rik|A-SCS	succinate-Coenzyme A ligase, ADP-forming, beta subunit	protein-coding
mm_70608.1	chr8	13405081	13405098	+	1	NA	promoter-TSS (NM_011881)	promoter-TSS (NM_011881)	8	NM_011881	24013	Mm.257501	NM_011881	ENSMUSG00000031450	Grk1	Gprk1|Rhok|Rk	G protein-coupled receptor kinase 1	protein-coding
mm_29895.1	chr3	131322469	131322472	-	1	NA	3' UTR (NM_028943, exon 6 of 6)	3' UTR (NM_028943, exon 6 of 6)	-19243	NM_027816	71519	Mm.473179	NM_027816	ENSMUSG00000027983	Cyp2u1	8430436A10Rik	cytochrome P450, family 2, subfamily u, polypeptide 1	protein-coding
mm_159821.1	chr5	122823968	122823968	+	1	NA	Intergenic	Intergenic	-2626	NM_001289519	59008	Mm.332667	NM_021505	ENSMUSG00000029472	Anapc5	2510006G12Rik|AA408751|AA536819|AA986414|APC5|Anpc5	anaphase-promoting complex subunit 5	protein-coding
mm_118024.1	chr13	100833370	100833445	-	1	NA	promoter-TSS (NM_022885)	promoter-TSS (NM_022885)	20	NM_022885	69048	Mm.402215	NM_022885	ENSMUSG00000021629	Slc30a5	1810010K08Rik|AF233321|ZNT5|ZTL1|ZnT-5|Zntl1	solute carrier family 30 (zinc transporter), member 5	protein-coding
mm_129316.1	chr15	77760991	77761013	-	1	NA	3' UTR (NM_022410, exon 41 of 41)	3' UTR (NM_022410, exon 41 of 41)	-5773	NM_001081970	239552	Mm.125650	NM_001081970	ENSMUSG00000056656	Apol8	9830006J20Rik|APOL-II|Apol2	apolipoprotein L 8	protein-coding
mm_14980.1	chr2	152110832	152110838	+	1	NA	3' UTR (NM_029688, exon 2 of 2)	3' UTR (NM_029688, exon 2 of 2)	5311	NM_029688	76650	Mm.218639	NM_029688	ENSMUSG00000032802	Srxn1	1700127B04Rik|AI854065|AW488194|Npn3|Srx|Srx1|TX01	sulfiredoxin 1 homolog (S. cerevisiae)	protein-coding
mm_119806.1	chr14	54220697	54220710	+	1	NA	Intergenic	Intergenic	33226	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_20151.1	chr2	121551354	121551376	-	1	NA	intron (NM_172673, intron 13 of 14)	intron (NM_172673, intron 13 of 14)	44642	NM_001290986	241627	Mm.293284	NM_030234	ENSMUSG00000027242	Wdr76	5830411K18Rik|6030457D09|AA517836	WD repeat domain 76	protein-coding
mm_156043.1	chrX	108484393	108484420	+	1	NA	Intergenic	Intergenic	349949	NM_001081477	382236	Mm.100112	NM_001081477	ENSMUSG00000063663	Brwd3	Brodl|D030064D06Rik|Gm596	bromodomain and WD repeat domain containing 3	protein-coding
mm_12788.1	chr2	79606296	79606302	+	1	NA	Intergenic	Intergenic	-29126	NM_080558	70599	Mm.272881	NM_080558	ENSMUSG00000027007	Ssfa2	5730488C15Rik|CS-1|CS1|KRAP|SPAG13|mKIAA1927	sperm specific antigen 2	protein-coding
mm_84028.1	chr9	57761969	57761980	-	1	NA	intron (NM_007713, intron 1 of 12)	intron (NM_007713, intron 1 of 12)	3886	NM_007713	102414	Mm.25720	NM_007713	ENSMUSG00000032316	Clk3	AI256811	CDC-like kinase 3	protein-coding
mm_31306.1	chr4	46077153	46077168	+	1	NA	intron (NM_021883, intron 2 of 9)	intron (NM_021883, intron 2 of 9)	37938	NM_021883	21916	Mm.249594	NM_021883	ENSMUSG00000028328	Tmod1	E-Tmod|Tmod	tropomodulin 1	protein-coding
mm_109048.1	chr12	104338373	104338416	+	1	NA	promoter-TSS (NM_011458)	promoter-TSS (NM_011458)	-92	NM_011458	20714	Mm.291569	NM_011458	ENSMUSG00000058207	Serpina3k	1300001I07Rik|D12Rp54|MMCM2|MMSpi2|RP54|Spi-2|Spi2|contrapsin	serine (or cysteine) peptidase inhibitor, clade A, member 3K	protein-coding
mm_64597.1	chr7	3204069	3204082	-	1	NA	Intergenic	Intergenic	-14551	NR_029640	100049710		NR_029640	ENSMUSG00000077815	Mir290a	Mir290|Mirn290|mir-290a|mmu-miR-290|mmu-mir-290a	microRNA 290a	ncRNA
mm_161977.1	chr19	13500525	13500525	+	1	NA	promoter-TSS (NM_146696)	promoter-TSS (NM_146696)	-21	NM_146696	258691	Mm.271532	NM_146696	ENSMUSG00000071629	Olfr1477	MOR202-10	olfactory receptor 1477	protein-coding
mm_114050.1	chr13	54302785	54302800	+	1	NA	Intergenic	CpG	-68557	NM_009946	12890	Mm.268902	NM_009946	ENSMUSG00000025867	Cplx2	921-L|AI413745|AW492120	complexin 2	protein-coding
mm_25301.1	chr3	105973791	105973809	+	1	NA	promoter-TSS (NM_007696)	promoter-TSS (NM_007696)	-2	NM_007696	12659	Mm.431947	NM_007696	ENSMUSG00000074340	Ovgp1	120kDa|AU016433|AU019448|Chit5|MOGP|OGP|muc9	oviductal glycoprotein 1	protein-coding
mm_11759.1	chr2	38511874	38511884	+	1	NA	promoter-TSS (NM_001159631)	promoter-TSS (NM_001159631)	3	NM_001159631	59126	Mm.143818	NM_021606	ENSMUSG00000026749	Nek6	1300007C09Rik	NIMA (never in mitosis gene a)-related expressed kinase 6	protein-coding
mm_82638.1	chr9	21989428	21989456	-	1	NA	promoter-TSS (NM_023622)	promoter-TSS (NM_023622)	11	NM_023622	71746	Mm.110594	NM_023622	ENSMUSG00000040146	Rgl3	1300003D20Rik|mFLJ00153	ral guanine nucleotide dissociation stimulator-like 3	protein-coding
mm_50509.1	chr6	49036715	49036718	+	1	NA	5' UTR (NM_053110, exon 1 of 11)	5' UTR (NM_053110, exon 1 of 11)	198	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_65160.1	chr7	19671790	19671828	-	1	NA	exon (NM_001309795, exon 4 of 4)	exon (NM_001309795, exon 4 of 4)	2111	NM_001309795	11813	Mm.28394	NM_001277944	ENSMUSG00000002992	Apoc2	apo-CII|apoC-II	apolipoprotein C-II	protein-coding
mm_43490.1	chr5	136932939	136932958	+	1	NA	intron (NR_015555, intron 3 of 3)	intron (NR_015555, intron 3 of 3)	13802	NR_015555	66752	Mm.135764	NR_015555	ENSMUSG00000097908	4933404O12Rik	AW494809	RIKEN cDNA 4933404O12 gene	ncRNA
mm_13178.1	chr2	92954568	92954578	+	1	NA	3' UTR (NM_030725, exon 6 of 6)	3' UTR (NM_030725, exon 6 of 6)	39472	NM_030725	80976	Mm.33490	NM_030725	ENSMUSG00000027220	Syt13	5730409J20Rik|AI549909|mKIAA1427	synaptotagmin XIII	protein-coding
mm_143989.1	chr17	87644721	87644744	-	1	NA	intron (NM_008532, intron 7 of 9)	intron (NM_008532, intron 7 of 9)	8753	NM_008532	17075	Mm.4259	NM_008532	ENSMUSG00000045394	Epcam	CD326|EGP|EGP-2|Egp314|Ep-CAM|EpCAM1|GA733-2|Ly74|TROP1|Tacsd1|Tacstd1|gp40	epithelial cell adhesion molecule	protein-coding
mm_151937.1	chr19	5800755	5800766	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	1912	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_33046.1	chr4	122996036	122996093	+	1	NA	5' UTR (NM_008506, exon 1 of 2)	5' UTR (NM_008506, exon 1 of 2)	133	NM_008506	16918	Mm.1055	NM_008506	ENSMUSG00000028654	Mycl	AW536278|L-myc|Lmyc-1|Lmyc1|Mycl1|bHLHe38	v-myc avian myelocytomatosis viral oncogene lung carcinoma derived	protein-coding
mm_114059.1	chr13	54371468	54371498	+	1	NA	5' UTR (NM_009946, exon 1 of 4)	5' UTR (NM_009946, exon 1 of 4)	134	NM_009946	12890	Mm.268902	NM_009946	ENSMUSG00000025867	Cplx2	921-L|AI413745|AW492120	complexin 2	protein-coding
mm_45000.1	chr5	38220401	38220459	-	1	NA	promoter-TSS (NM_029162)	promoter-TSS (NM_029162)	-2	NM_029162	75079	Mm.258741	NM_029162	ENSMUSG00000029127	Zbtb49	4930518A03Rik|Zfp509|Znf509	zinc finger and BTB domain containing 49	protein-coding
mm_94896.1	chr11	29131653	29131678	+	1	NA	intron (NM_027869, intron 1 of 27)	intron (NM_027869, intron 1 of 27)	914	NM_027869	71701	Mm.211131	NM_027869	ENSMUSG00000020464	Pnpt1	1200003F12Rik|Old35|PNPase|Pnptl1	polyribonucleotide nucleotidyltransferase 1	protein-coding
mm_113913.1	chr13	49504775	49504816	+	1	NA	promoter-TSS (NM_001012324)	promoter-TSS (NM_001012324)	-15	NM_001012324	407800	Mm.386931	NM_001012324	ENSMUSG00000043631	Ecm2	9030618O22Rik|BC065151|tenonectin	extracellular matrix protein 2, female organ and adipocyte specific	protein-coding
mm_45797.1	chr5	87567349	87567365	-	1	NA	intron (NM_016771, intron 1 of 7)	intron (NM_016771, intron 1 of 7)	1649	NM_016771	53315	Mm.6824	NM_016771	ENSMUSG00000029273	Sult1d1	5033411P13Rik|AI987815|ST1d1|SULT-N|Sultn	sulfotransferase family 1D, member 1	protein-coding
mm_112018.1	chr12	111377605	111377696	-	1	NA	promoter-TSS (NM_183016)	promoter-TSS (NM_183016)	68	NM_183016	217866	Mm.27397	NM_183016	ENSMUSG00000021279	Cdc42bpb	MRCKb	CDC42 binding protein kinase beta	protein-coding
mm_81700.1	chr9	111224580	111224585	+	1	NA	3' UTR (NM_001164838, exon 15 of 15)	3' UTR (NM_001164838, exon 15 of 15)	47026	NM_026810	17350	Mm.486383	NM_026810	ENSMUSG00000032498	Mlh1	1110035C23Rik|AI317206|AI325952|AI561766	mutL homolog 1	protein-coding
mm_35404.1	chr4	34730143	34730153	-	1	NA	promoter-TSS (NM_027041)	promoter-TSS (NM_027041)	58	NM_027041	69329	Mm.389548	NM_027041	ENSMUSG00000028294	Cfap206	1700003M02Rik|AU024269	cilia and flagella associated protein 206	protein-coding
mm_146301.1	chr18	80207172	80207218	+	1	NA	exon (NM_025299, exon 2 of 4)	exon (NM_025299, exon 2 of 4)	328	NM_001042408	27366	Mm.172411	NM_025299	ENSMUSG00000057130	Txnl4a	D18Wsu98e|Dim1|ENSMUSG00000057130|Txnl4|U5-15kD|U5-15kDa	thioredoxin-like 4A	protein-coding
mm_17279.1	chr2	26097252	26097259	-	1	NA	intron (NM_026495, intron 1 of 5)	intron (NM_026495, intron 1 of 5)	-4859	NM_001037098	67991	Mm.131074	NM_026495	ENSMUSG00000026932	Nacc2	0610020I02Rik|AI448087|Btbd14a|C030048H19Rik	nucleus accumbens associated 2, BEN and BTB (POZ) domain containing	protein-coding
mm_67354.1	chr7	79836343	79836353	-	1	NA	exon (NM_008486, exon 10 of 20)	exon (NM_008486, exon 10 of 20)	6004	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_20714.1	chr2	134644052	134644058	-	1	NA	promoter-TSS (NM_029148)	promoter-TSS (NM_029148)	66	NM_029148	52837	Mm.264096	NM_029148	ENSMUSG00000034723	Tmx4	2810417D04Rik|4930500L08Rik|AI843224|AW046784|D2Bwg1356e|Txndc13|mKIAA1162	thioredoxin-related transmembrane protein 4	protein-coding
mm_165546.1	chr3	7366658	7366666	+	1	NA	promoter-TSS (NM_008862)	promoter-TSS (NM_008862)	58	NM_008862	18767	Mm.3193	NM_008862	ENSMUSG00000027499	Pkia	AI415001|PKIalpha	protein kinase inhibitor, alpha	protein-coding
mm_53227.1	chr6	127150237	127150243	+	1	NA	intron (NR_040275, intron 1 of 1)	intron (NR_040275, intron 1 of 1)	614	NR_040273	77558	Mm.358918	NR_040273	ENSMUSG00000097166	9330179D12Rik	-	RIKEN cDNA 9330179D12 gene	ncRNA
mm_36801.1	chr4	103173369	103173386	-	1	NA	3' UTR (NM_177732, exon 10 of 10)	3' UTR (NM_177732, exon 10 of 10)	41507	NM_177732	242585	Mm.281800	NM_177732	ENSMUSG00000028521	Slc35d1	AI834976|C330011J09|UGTREL7|mKIAA0260	solute carrier family 35 (UDP-glucuronic acid/UDP-N-acetylgalactosamine dual transporter), member D1	protein-coding
mm_67054.1	chr7	67370026	67370029	-	1	NA	intron (NM_001291191, intron 1 of 10)	intron (NM_001291191, intron 1 of 10)	2831	NM_001291192	17258	Mm.132788	NM_001033713	ENSMUSG00000030557	Mef2a	A430079H05Rik	myocyte enhancer factor 2A	protein-coding
mm_130945.1	chr15	103251658	103251705	-	1	NA	promoter-TSS (NM_001302340)	promoter-TSS (NM_001302340)	-5	NM_001302338	18022	Mm.457989	NM_008685	ENSMUSG00000058794	Nfe2	NF-E2|NF-E2/P45|p45|p45NFE2|p45nf-e2	nuclear factor, erythroid derived 2	protein-coding
mm_91029.1	chr10	17947998	17948098	-	1	NA	promoter-TSS (NM_001033432)	promoter-TSS (NM_001033432)	19	NM_001033432	380629	Mm.276430	NM_001033432	ENSMUSG00000039879	Heca	Gm869|HDC|HDCL	hdc homolog, cell cycle regulator	protein-coding
mm_95674.1	chr11	54100970	54101025	+	1	NA	promoter-TSS (NM_001136076)	promoter-TSS (NM_001136076)	73	NM_011031	18452	Mm.3705	NM_011031	ENSMUSG00000018906	P4ha2	AA407196|C76437|P4hl	procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha II polypeptide	protein-coding
mm_67557.1	chr7	81706906	81706964	-	1	NA	promoter-TSS (NM_001164086)	promoter-TSS (NM_001164086)	-10	NM_001164086	26557	Mm.228	NM_011983	ENSMUSG00000025813	Homer2	9330120H11Rik|AW539445|CPD|Vesl-2	homer scaffolding protein 2	protein-coding
mm_96427.1	chr11	67277169	67277183	+	1	NA	promoter-TSS (NM_177369)	promoter-TSS (NM_177369)	52	NM_177369	17885	Mm.340163	NM_177369	ENSMUSG00000055775	Myh8	4832426G23Rik|AI327267|MHCp|MyHC-pn|Myhs-p|Myhsp	myosin, heavy polypeptide 8, skeletal muscle, perinatal	protein-coding
mm_20917.1	chr2	150638096	150638107	-	1	NA	intron (NM_080575, intron 4 of 13)	intron (NM_080575, intron 4 of 13)	-29393	NR_040331	109344	Mm.440012	NR_040331	ENSMUSG00000087406	E130215H24Rik	-	RIKEN cDNA E130215H24 gene	ncRNA
mm_61006.1	chr7	49348211	49348216	+	1	NA	intron (NM_175272, intron 1 of 37)	intron (NM_175272, intron 1 of 37)	102024	NM_175272	78286	Mm.333881	NM_175272	ENSMUSG00000052512	Nav2	5330421F07Rik|AU067780|BQ960892|HELAD1|POMFIL2|RAINB1|RAINB2|Unc53H2|mKIAA3015	neuron navigator 2	protein-coding
mm_104743.1	chr11	98438942	98439008	-	1	NA	promoter-TSS (NM_025559)	promoter-TSS (NM_025559)	13	NM_025559	103742	Mm.259614	NM_025559	ENSMUSG00000002580	Mien1	1810046J19Rik|AI463380|Rdx12	migration and invasion enhancer 1	protein-coding
mm_149014.1	chr19	8740713	8740723	+	1	NA	promoter-TSS (NM_001177347)	promoter-TSS (NM_001177347)	0	NM_001177347	74307	Mm.48791	NM_001177347	ENSMUSG00000090840	1700092M07Rik	-	RIKEN cDNA 1700092M07 gene	protein-coding
mm_53232.1	chr6	127434428	127434439	+	1	NA	Intergenic	L3|LINE|CR1	-12407	NM_001346513	101187	Mm.110818	NM_181402	ENSMUSG00000037997	Parp11	5330431N24Rik|AI851877|ARTD11|HIN1L|PARP-11	poly (ADP-ribose) polymerase family, member 11	protein-coding
mm_109683.1	chr12	113140474	113140482	+	1	NA	promoter-TSS (NM_001347443)	promoter-TSS (NM_001347443)	-127	NM_001347443	68337	Mm.133825	NM_024223	ENSMUSG00000006356	Crip2	0610010I23Rik|AW743261|C77570|CRP2|CRP4|Crp|ESP1|Hlp	cysteine rich protein 2	protein-coding
mm_54013.1	chr6	8193675	8193706	-	1	NA	Intergenic	Intergenic	-1073	NM_001037865	213945	Mm.297404	NM_001037865	ENSMUSG00000068794	Col28a1	Col28|Gm466	collagen, type XXVIII, alpha 1	protein-coding
mm_51871.1	chr6	90552205	90552206	+	1	NA	intron (NM_027406, intron 1 of 22)	intron (NM_027406, intron 1 of 22)	1357	NM_027406	107747	Mm.30035	NM_027406	ENSMUSG00000030088	Aldh1l1	1810048F20Rik|FDH|Fthfd|Neut2	aldehyde dehydrogenase 1 family, member L1	protein-coding
mm_166260.1	chr5	87682342	87682342	+	1	NA	3' UTR (NM_007784, exon 34 of 34)	3' UTR (NM_007784, exon 34 of 34)	16134	NM_001286016	12990	Mm.427467	NM_007784	ENSMUSG00000070702	Csn1s1	AA959832|AW212882|Csna	casein alpha s1	protein-coding
mm_122395.1	chr14	40994066	40994081	-	1	NA	3' UTR (NM_001316734, exon 6 of 6)	3' UTR (NM_001316734, exon 6 of 6)	12847	NM_001316739	70564	Mm.27227	NM_027464	ENSMUSG00000021792	Fam213a	5730469M10Rik|AU040822|Adrx|Pamm	family with sequence similarity 213, member A	protein-coding
mm_88174.1	chr10	69787432	69787458	+	1	NA	intron (NM_170730, intron 1 of 17)	intron (NM_170730, intron 1 of 17)	-138087	NM_170687	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_151285.1	chr19	55284326	55284347	+	1	NA	intron (NM_027976, intron 11 of 21)	intron (NM_027976, intron 11 of 21)	30967	NM_027976	433256	Mm.292056	NM_027976	ENSMUSG00000024981	Acsl5	1700030F05Rik|ACS2|ACS5|Facl5	acyl-CoA synthetase long-chain family member 5	protein-coding
mm_92600.1	chr10	80104302	80104312	-	1	NA	intron (NR_038088, intron 1 of 4)	intron (NR_038088, intron 1 of 4)	-1605	NM_183426	216161	Mm.262102	NM_183426	ENSMUSG00000035673	Sbno2	BC019206|F730040C21|Sno|Stno	strawberry notch homolog 2 (Drosophila)	protein-coding
mm_165594.1	chr3	38258858	38258860	+	1	NA	Intergenic	Intergenic	-50740	NR_040541	71342	Mm.410782	NR_040541	ENSMUSG00000106002	5430434I15Rik	-	RIKEN cDNA 5430434I15 gene	ncRNA
mm_5099.1	chr1	4972391	4972416	-	1	NA	intron (NM_001177795, intron 2 of 5)	intron (NM_001177795, intron 2 of 5)	46331	NM_001290372	58175	Mm.103771	NM_021374	ENSMUSG00000002459	Rgs20	2900073E09Rik|Rgsz1	regulator of G-protein signaling 20	protein-coding
mm_155628.1	chrX	84076618	84076653	+	1	NA	intron (NM_007868, intron 44 of 78)	intron (NM_007868, intron 44 of 78)	-588711	NM_021898	100502723	Mm.383210	NM_021898	ENSMUSG00000035522	Tsga8	Halap-X|Halapx	testis specific gene A8	protein-coding
mm_42813.1	chr5	121837259	121837275	+	1	NA	promoter-TSS (NM_001306128)	promoter-TSS (NM_001306128)	-408	NM_008507	16923	Mm.65493	NM_008507	ENSMUSG00000042594	Sh2b3	AI429800|Lnk	SH2B adaptor protein 3	protein-coding
mm_171803.1	chr5	124618967	124618986	+	1	NA	intron (NM_026486, intron 11 of 18)	ORR1A4|LTR|ERVL-MaLR	-10076	NM_011596	21871	Mm.1158	NM_011596	ENSMUSG00000038023	Atp6v0a2	8430408C20Rik|AI385560|ATP6a2|AW489264|Atp6n1d|Atp6n2|C76904|ISF|J6B7|SHIF|Stv1|TJ6M|TJ6s|Tj6|V-ATPase 116 kDa|V-ATPase a2	ATPase, H+ transporting, lysosomal V0 subunit A2	protein-coding
mm_43211.1	chr5	129363544	129363581	+	1	NA	Intergenic	Intergenic	-137669	NM_172276	231769	Mm.288714	NM_172276	ENSMUSG00000029439	Sfswap	1190005N23Rik|6330437E22Rik|AI197402|AW212079|SWAP|Sfrs8|Srsf8	splicing factor, suppressor of white-apricot homolog (Drosophila)	protein-coding
mm_37527.1	chr4	124850616	124850640	-	1	NA	promoter-TSS (NM_153566)	promoter-TSS (NM_153566)	-64	NM_001347196	68920	Mm.272397	NM_001142727	ENSMUSG00000078570	1110065P20Rik	C530005M16Rik	RIKEN cDNA 1110065P20 gene	protein-coding
mm_117171.1	chr13	62888154	62888168	-	1	NA	5' UTR (NM_019395, exon 1 of 7)	5' UTR (NM_019395, exon 1 of 7)	121	NM_019395	14121	Mm.423078	NM_019395	ENSMUSG00000069805	Fbp1	Fbp-2|Fbp2|Fbp3	fructose bisphosphatase 1	protein-coding
mm_56469.1	chr6	99025213	99025215	-	1	NA	intron (NM_001347345, intron 6 of 19)	intron (NM_001347345, intron 6 of 19)	3084	NM_001197322	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_124092.1	chr14	79151794	79151817	-	1	NA	intron (NM_027906, intron 37 of 44)	intron (NM_027906, intron 37 of 44)	95562	NM_001033215	105590	Mm.486536	NM_001033215	ENSMUSG00000071262	Zfp957	AU017455	zinc finger protein 957	protein-coding
mm_113703.1	chr13	43183979	43183997	+	1	NA	Intergenic	ORR1C1|LTR|ERVL-MaLR	-12487	NM_001252640	67046	Mm.269213	NM_025935	ENSMUSG00000021368	Tbc1d7	2610009C09Rik	TBC1 domain family, member 7	protein-coding
mm_137903.1	chr17	31912658	31912673	+	1	NA	Intergenic	Intergenic	-56873	NM_010831	17691	Mm.290941	NM_010831	ENSMUSG00000024042	Sik1	Msk|Sik|Snf1lk	salt inducible kinase 1	protein-coding
mm_26951.1	chr3	20275449	20275503	-	1	NA	exon (NM_029706, exon 2 of 11)	exon (NM_029706, exon 2 of 11)	257	NM_029706	76703	Mm.34692	NM_029706	ENSMUSG00000011463	Cpb1	0910001A18Rik|1810063F02Rik|2210008M23Rik|AI504870	carboxypeptidase B1 (tissue)	protein-coding
mm_29365.1	chr3	108704441	108704453	-	1	NA	intron (NM_029522, intron 2 of 14)	Lx8|LINE|L1	17852	NM_029522	76123	Mm.226941	NM_029522	ENSMUSG00000027883	Gpsm2	6230410J09Rik|LGN|Pins	G-protein signalling modulator 2 (AGS3-like, C. elegans)	protein-coding
mm_27471.1	chr3	52856398	52856422	-	1	NA	Intergenic	Intergenic	71256	NR_040555	622124	Mm.389434	NR_040555	ENSMUSG00000104401	Gm20750	-	predicted gene, 20750	ncRNA
mm_122686.1	chr14	52019787	52019813	-	1	NA	promoter-TSS (NM_001253694)	promoter-TSS (NM_001253694)	-87	NM_001253694	69890	Mm.475652	NM_027248	ENSMUSG00000049295	Zfp219	2010302A17Rik	zinc finger protein 219	protein-coding
mm_58213.1	chr6	144204071	144204082	-	1	NA	intron (NM_001113559, intron 1 of 13)	intron (NM_001113559, intron 1 of 13)	5492	NM_001113559	20678	Mm.1752	NM_011444	ENSMUSG00000041540	Sox5	A730017D01Rik|AI528773	SRY (sex determining region Y)-box 5	protein-coding
mm_159320.1	chr3	15542363	15542363	-	1	NA	exon (NM_001173460, exon 4 of 6)	exon (NM_001173460, exon 4 of 6)	32702	NM_001173460	668101	Mm.423523	NM_001173460	ENSMUSG00000095028	Sirpb1b	-	signal-regulatory protein beta 1B	protein-coding
mm_29791.1	chr3	127553234	127553364	-	1	NA	promoter-TSS (NM_138593)	promoter-TSS (NM_138593)	50	NM_138593	28036	Mm.291032	NM_138593	ENSMUSG00000027968	Larp7	C330027G06Rik|D3Wsu161e	La ribonucleoprotein domain family, member 7	protein-coding
mm_15069.1	chr2	153107657	153107673	+	1	NA	promoter-TSS (NM_010407)	promoter-TSS (NM_010407)	-803	NM_001172117	15162	Mm.715	NM_010407	ENSMUSG00000003283	Hck	AI849071|Bmk	hemopoietic cell kinase	protein-coding
mm_26384.1	chr3	142569163	142569195	+	1	NA	exon (NM_018734, exon 8 of 11)	exon (NM_018734, exon 8 of 11)	8683	NM_001289493	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_151633.1	chr19	3929768	3929783	-	1	NA	promoter-TSS (NM_026316)	promoter-TSS (NM_026316)	-59	NM_026316	67689	Mm.109341	NM_026316	ENSMUSG00000024885	Aldh3b1	1700001N19Rik|ALDH4|ALDH7	aldehyde dehydrogenase 3 family, member B1	protein-coding
mm_148466.1	chr19	4082540	4082545	+	1	NA	promoter-TSS (NM_001160252)	promoter-TSS (NM_001160252)	54	NM_001160253	29866	Mm.46268	NM_013878	ENSMUSG00000024857	Cabp2	-	calcium binding protein 2	protein-coding
mm_47173.1	chr5	120744324	120744349	-	1	NA	intron (NM_001347448, intron 3 of 11)	L1M5|LINE|L1	5512	NM_145227	246728	Mm.260926	NM_145227	ENSMUSG00000032690	Oas2	Oasl11	2'-5' oligoadenylate synthetase 2	protein-coding
mm_108123.1	chr12	75880120	75880152	+	1	NA	exon (NM_001005510, exon 4 of 116)	exon (NM_001005510, exon 4 of 116)	-28967	NR_039560	100628610		NR_039560	ENSMUSG00000092922	Mir5101	mmu-mir-5101|mu-mir-5101	microRNA 5101	ncRNA
mm_123655.1	chr14	69243084	69243095	-	1	NA	3' UTR (NM_026331, exon 4 of 4)	3' UTR (NM_026331, exon 4 of 4)	42014	NM_026331	67712	Mm.293635	NM_026331	ENSMUSG00000034248	Slc25a37	1700020E22Rik|4930513O14Rik|4930526G11Rik|AI848481|C330015G08Rik|Mfrn|Mfrn1|Mscp|frascati|mitoferrin	solute carrier family 25, member 37	protein-coding
mm_17369.1	chr2	26910575	26910650	-	1	NA	promoter-TSS (NM_001033908)	promoter-TSS (NM_001033908)	30	NM_011513	20933	Mm.397932	NM_011513	ENSMUSG00000015776	Med22	AW212655|AW558812|Surf-5|Surf5	mediator complex subunit 22	protein-coding
mm_58210.1	chr6	144020107	144020112	-	1	NA	intron (NM_001113559, intron 6 of 13)	intron (NM_001113559, intron 6 of 13)	-73003	NM_001347506	20678	Mm.1752	NM_011444	ENSMUSG00000041540	Sox5	A730017D01Rik|AI528773	SRY (sex determining region Y)-box 5	protein-coding
mm_61187.1	chr7	63444742	63444762	+	1	NA	promoter-TSS (NM_130880)	promoter-TSS (NM_130880)	-20	NM_130880	170711	Mm.156872	NM_130880	ENSMUSG00000033510	Otud7a	AJ430384|Otud7	OTU domain containing 7A	protein-coding
mm_34855.1	chr4	155522561	155522591	+	1	NA	intron (NM_001160016, intron 2 of 11)	intron (NM_001160016, intron 2 of 11)	31215	NM_001160016	14688	Mm.2344	NM_008142	ENSMUSG00000029064	Gnb1	AA409223|C77571|Gnb-1	guanine nucleotide binding protein (G protein), beta 1	protein-coding
mm_166537.1	chr6	30805011	30805015	+	1	NA	intron (NM_017478, intron 20 of 23)	intron (NM_017478, intron 20 of 23)	63714	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_64785.1	chr7	5125994	5125999	-	1	NA	promoter-TSS (NM_009028)	promoter-TSS (NM_009028)	-46	NM_009028	19428	Mm.322186	NM_009028	ENSMUSG00000083649	Rasl2-9	M2|Ran|Ran/M2|Rasl2-9-ps	RAS-like, family 2, locus 9	protein-coding
mm_137109.1	chr17	21976398	21976405	+	1	NA	intron (NM_001025373, intron 1 of 3)	intron (NM_001025373, intron 1 of 3)	13842	NM_001025373	74670	Mm.26540	NM_001025373	ENSMUSG00000053347	Zfp943	4930432O21Rik	zinc finger prtoein 943	protein-coding
mm_128184.1	chr15	34678806	34678827	-	1	NA	promoter-TSS (NM_145469)	promoter-TSS (NM_145469)	-110	NM_145469	223473	Mm.258402	NM_145469	ENSMUSG00000038879	Nipal2	9330161F08Rik|Npal2	NIPA-like domain containing 2	protein-coding
mm_172241.1	chr6	68970475	68970475	+	1	NA	Intergenic	L1Md_T|LINE|L1	356699	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_88908.1	chr10	81179572	81179583	+	1	NA	TTS (NR_028549)	TTS (NR_028549)	616	NR_028549	100217454		NR_028549	ENSMUSG00000064441	Snord37	MBII-376	small nucleolar RNA, C/D box 37	snoRNA
mm_148893.1	chr19	6906889	6906930	+	1	NA	TTS (NM_012021)	TTS (NM_012021)	2736	NM_012021	54683	Mm.279782	NM_012021	ENSMUSG00000024953	Prdx5	AOEB166|AOPP|Pmp20|Prdx6|PrxV	peroxiredoxin 5	protein-coding
mm_148958.1	chr19	7417128	7417229	+	1	NA	promoter-TSS (NM_175381)	promoter-TSS (NM_175381)	-447	NM_175381	108899	Mm.386838	NM_175381	ENSMUSG00000053080	2700081O15Rik	AI255177|AI848741|AW742297	RIKEN cDNA 2700081O15 gene	protein-coding
mm_74106.1	chr8	122870570	122870600	+	1	NA	Intergenic	CpG	22211	NM_007662	12555	Mm.1976	NM_007662	ENSMUSG00000031962	Cdh15	AI323380|Cdh14|Mcad	cadherin 15	protein-coding
mm_135992.1	chr16	75141902	75141904	-	1	NA	Intergenic	Intergenic	444158	NM_001252513	320355	Mm.99517	NM_177142	ENSMUSG00000032948	Lipi	D930038D03Rik|lpd1	lipase, member I	protein-coding
mm_10176.1	chr2	4560051	4560063	+	1	NA	5' UTR (NM_001177844, exon 1 of 12)	5' UTR (NM_001177844, exon 1 of 12)	303	NM_001177844	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding
mm_140268.1	chr17	84683134	84683141	+	1	NA	promoter-TSS (NM_031884)	promoter-TSS (NM_031884)	16	NM_026180	67470	Mm.26581	NM_026180	ENSMUSG00000024254	Abcg8	1300003C16Rik|AI114946|sterolin-2	ATP-binding cassette, sub-family G (WHITE), member 8	protein-coding
mm_133371.1	chr16	84709350	84709370	+	1	NA	Intergenic	Intergenic	-3663	NR_132106	100653389	Mm.261808	NR_132106	ENSMUSG00000097418	Mir155hg	Bic|Gm26667	Mir155 host gene (non-protein coding)	ncRNA
mm_46252.1	chr5	99251510	99251529	-	1	NA	intron (NM_145839, intron 1 of 13)	intron (NM_145839, intron 1 of 13)	1408	NM_181318	320292	Mm.259074	NM_145839	ENSMUSG00000089809	Rasgef1b	4732452O09Rik|GPIgamma4|Gpig4	RasGEF domain family, member 1B	protein-coding
mm_91257.1	chr10	23185528	23185536	-	1	NA	intron (NM_010167, intron 3 of 18)	intron (NM_010167, intron 3 of 18)	164358	NM_001347372	14051	Mm.332128	NM_010167	ENSMUSG00000010461	Eya4	B130023L16Rik	EYA transcriptional coactivator and phosphatase 4	protein-coding
mm_143003.1	chr17	56423329	56423344	-	1	NA	exon (NM_001252453, exon 14 of 29)	exon (NM_001252453, exon 14 of 29)	-4427	NR_105943	102465590		NR_105943	ENSMUSG00000098339	Mir6977	Gm27922|mmu-mir-6977	microRNA 6977	ncRNA
mm_65021.1	chr7	18069390	18069397	-	1	NA	exon (NM_001162524, exon 3 of 3)	exon (NM_001162524, exon 3 of 3)	3464	NM_001162523	67315	Mm.46089	NM_026087	ENSMUSG00000030366	Ceacam12	1600031J20Rik|Ceacam12-C1|Ceacam12-C3|Ceacam12C1|Ceacam12C3	carcinoembryonic antigen-related cell adhesion molecule 12	protein-coding
mm_74272.1	chr8	125012987	125013006	+	1	NA	promoter-TSS (NM_016909)	promoter-TSS (NM_016909)	-1	NM_016909	53424	Mm.5248	NM_016909	ENSMUSG00000056820	Tsnax	R74833|Trax	translin-associated factor X	protein-coding
mm_1333.1	chr1	65311454	65311457	+	1	NA	5' UTR (NM_139270, exon 1 of 13)	5' UTR (NM_139270, exon 1 of 13)	198	NM_139270	213527	Mm.294225	NM_139270	ENSMUSG00000025946	Pth2r	Pthr2	parathyroid hormone 2 receptor	protein-coding
mm_209.1	chr1	16661533	16661545	+	1	NA	intron (NR_037998, intron 3 of 3)	RLTR30D2_MM|LTR|ERV1	-3652	NM_027415	70397	Mm.194225	NM_026392	ENSMUSG00000025940	Tmem70	1110020A09Rik|2210416J16Rik	transmembrane protein 70	protein-coding
mm_136768.1	chr17	8988341	8988347	+	1	NA	promoter-TSS (NM_025851)	promoter-TSS (NM_025851)	11	NM_001347544	66931	Mm.67591	NM_025851	ENSMUSG00000023873	1700010I14Rik	-	RIKEN cDNA 1700010I14 gene	protein-coding
mm_32847.1	chr4	117883598	117883610	+	1	NA	promoter-TSS (NM_001253381)	promoter-TSS (NM_001253381)	-128	NM_001253381	53418	Mm.123843	NM_017377	ENSMUSG00000028541	B4galt2	Ggtb2	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 2	protein-coding
mm_32255.1	chr4	102570587	102570618	+	1	NA	5' UTR (NM_001177980, exon 1 of 10)	5' UTR (NM_001177980, exon 1 of 10)	542	NM_001177980	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_6677.1	chr1	80405497	80405498	-	1	NA	Intergenic	RMER6C|LTR|ERVK	-40435	NR_040460	72208	Mm.396181	NR_040460	ENSMUSG00000101483	1700016L21Rik	Jr3	RIKEN cDNA 1700016L21 gene	ncRNA
mm_55765.1	chr6	78466857	78466866	-	1	NA	exon (NM_011260, exon 5 of 6)	exon (NM_011260, exon 5 of 6)	2013	NM_011260	19695	Mm.252385	NM_011260	ENSMUSG00000030017	Reg3g	AI449515|REG-3-gamma|reg III-gamma	regenerating islet-derived 3 gamma	protein-coding
mm_23400.1	chr3	57977025	57977028	+	1	NA	Intergenic	Intergenic	-129269	NM_019410	18645	Mm.271744	NM_019410	ENSMUSG00000027805	Pfn2	Pfn	profilin 2	protein-coding
mm_152926.1	chr19	28011556	28011590	-	1	NA	promoter-TSS (NM_011265)	promoter-TSS (NM_011265)	-407	NM_011265	19726	Mm.313321	NM_011265	ENSMUSG00000040929	Rfx3	C230093O12Rik|MRFX3	regulatory factor X, 3 (influences HLA class II expression)	protein-coding
mm_93832.1	chr10	121586711	121586721	-	1	NA	promoter-TSS (NM_019786)	promoter-TSS (NM_019786)	78	NM_019786	56480	Mm.34580	NM_019786	ENSMUSG00000020115	Tbk1	1200008B05Rik|AI462036|AW048562	TANK-binding kinase 1	protein-coding
mm_69155.1	chr7	127144552	127144565	-	1	NA	Intergenic	MTE2b|LTR|ERVL-MaLR	-6735	NM_001037810	20737	Mm.283714	NM_009259	ENSMUSG00000051457	Spn	A630014B01Rik|Cd43|Galgp|Ly-48|Ly48	sialophorin	protein-coding
mm_167628.1	chr9	61356043	61356045	+	1	NA	Intergenic	B4A|SINE|B4	-16322	NM_001083928	21887	Mm.24255	NM_009389	ENSMUSG00000032280	Tle3	2610103N05Rik|ESG|Grg3a|Grg3b|mKIAA1547	transducin-like enhancer of split 3	protein-coding
mm_142240.1	chr17	37482419	37482423	-	1	NA	intron (NM_001347387, intron 3 of 4)	intron (NM_001347387, intron 3 of 4)	1108	NM_008204	14990	Mm.329041	NM_008204	ENSMUSG00000016283	H2-M2	H-2M2|Thy19.4	histocompatibility 2, M region locus 2	protein-coding
mm_85348.1	chr9	103209078	103209091	-	1	NA	intron (NM_133977, intron 16 of 16)	intron (NM_133977, intron 16 of 16)	-7019	NM_009275	20818	Mm.273053	NM_009275	ENSMUSG00000032553	Srprb	AA409543	signal recognition particle receptor, B subunit	protein-coding
mm_111049.1	chr12	80108848	80108871	-	1	NA	3' UTR (NM_007564, exon 2 of 2)	3' UTR (NM_007564, exon 2 of 2)	4154	NM_007564	12192	Mm.235132	NM_007564	ENSMUSG00000021127	Zfp36l1	AW742437|AW743212|Berg36|Brf1|D530020L18Rik|ERF1|TIS11b|cMG1	zinc finger protein 36, C3H type-like 1	protein-coding
mm_138905.1	chr17	43588559	43588596	+	1	NA	non-coding (NR_045445, exon 4 of 4)	non-coding (NR_045445, exon 4 of 4)	2932	NR_045445	73504	Mm.9277	NR_045444	ENSMUSG00000090307	1700071M16Rik	-	RIKEN cDNA 1700071M16 gene	ncRNA
mm_99285.1	chr11	101321884	101321916	+	1	NA	3' UTR (NM_011192, exon 11 of 11)	3' UTR (NM_011192, exon 11 of 11)	-3163	NM_178932	237940	Mm.302277	NM_178932	ENSMUSG00000078651	Aoc2	RAO	amine oxidase, copper containing 2 (retina-specific)	protein-coding
mm_4755.1	chr1	182288038	182288054	+	1	NA	Intergenic	LTR33A_|LTR|ERVL	-5287	NM_007853	13244	Mm.29648	NM_007853	ENSMUSG00000038633	Degs1	AA536663|Degs|Des1|Mdes	delta(4)-desaturase, sphingolipid 1	protein-coding
mm_122008.1	chr14	26970821	26970843	-	1	NA	promoter-TSS (NM_145221)	promoter-TSS (NM_145221)	-281	NM_145221	72993	Mm.202322	NM_145221	ENSMUSG00000040760	Appl1	2900057D21Rik|7330406P05Rik|AI585782|AW209077|BB022931|C88264|DIP13	adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 1	protein-coding
mm_35802.1	chr4	46601872	46601911	-	1	NA	promoter-TSS (NM_001164804)	promoter-TSS (NM_001164804)	38	NM_001164804	107684	Mm.416311	NM_178893	ENSMUSG00000028337	Coro2a	9030208C03Rik|AI563590|IR10	coronin, actin binding protein 2A	protein-coding
mm_33014.1	chr4	120925111	120925178	+	1	NA	promoter-TSS (NM_001160043)	promoter-TSS (NM_001160043)	-139	NM_001160043	73172	Mm.151436	NM_028457	ENSMUSG00000028629	Exo5	3110037I16Rik|AV297100|Dem1|Exo V|mExo5	exonuclease 5	protein-coding
mm_94799.1	chr11	22973836	22973868	+	1	NA	exon (NM_011663, exon 1 of 1)	exon (NM_011663, exon 1 of 1)	1847	NM_011663	22183	Mm.29542	NM_011663	ENSMUSG00000044068	Zrsr1	D11Ncvs75|Irlgs2|SP2|U2af1-rs1|U2afbp-rs	zinc finger (CCCH type), RNA binding motif and serine/arginine rich 1	protein-coding
mm_101445.1	chr11	30197830	30197850	-	1	NA	5' UTR (NM_009260, exon 1 of 31)	5' UTR (NM_009260, exon 1 of 31)	417	NM_009260	20742	Mm.123110	NM_009260	ENSMUSG00000020315	Sptbn1	9930031C03Rik|AL033301|SPTB2|Spnb-2|Spnb2|elf1|elf3|mKIAA4049	spectrin beta, non-erythrocytic 1	protein-coding
mm_2622.1	chr1	120602429	120602437	+	1	NA	promoter-TSS (NM_010133)	promoter-TSS (NM_010133)	-54	NM_010133	13798	Mm.2657	NM_010133	ENSMUSG00000058665	En1	En-1|Mo-en.1|engrailed-1	engrailed 1	protein-coding
mm_35982.1	chr4	54945854	54945864	-	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-2086	NM_172867	242466	Mm.102904	NM_172867	ENSMUSG00000060206	Zfp462	6030417H05|9430078C22Rik|Gt4-2|Zfpip	zinc finger protein 462	protein-coding
mm_64106.1	chr7	141048016	141048034	+	1	NA	Intergenic	Intergenic	-13249	NM_177897	330671	Mm.133741	NM_177897	ENSMUSG00000055629	B4galnt4	BC038881|Gm1095|beta4GalNAcT4	beta-1,4-N-acetyl-galactosaminyl transferase 4	protein-coding
mm_272.1	chr1	21218799	21218824	+	1	NA	5' UTR (NM_001290679, exon 1 of 5)	5' UTR (NM_001290679, exon 1 of 5)	236	NM_029398	75712	Mm.304763	NM_029398	ENSMUSG00000025933	Tmem14a	5730496E24Rik|C85783|PTD011	transmembrane protein 14A	protein-coding
mm_84264.1	chr9	62537372	62537380	-	1	NA	promoter-TSS (NM_175484)	promoter-TSS (NM_175484)	-332	NM_175484	235431	Mm.335229	NM_175484	ENSMUSG00000041729	Coro2b	CLIPINC|E130012P22Rik	coronin, actin binding protein, 2B	protein-coding
mm_67615.1	chr7	83884325	83884336	-	1	NA	promoter-TSS (NM_030705)	promoter-TSS (NM_030705)	11	NM_030705	80889	Mm.272998	NM_030705	ENSMUSG00000070462	Mesdc1	AW061151	mesoderm development candidate 1	protein-coding
mm_41624.1	chr5	96917997	96918014	+	1	NA	Intergenic	Intergenic	-3267	NR_131152	666266	Mm.32442	NR_131152	ENSMUSG00000106357	Gm8013	EG666266	predicted gene 8013	ncRNA
mm_119858.1	chr14	54464481	54464515	+	1	NA	5' UTR (NM_022993, exon 1 of 7)	5' UTR (NM_022993, exon 1 of 7)	351	NM_022993	65107	Mm.472719	NM_022993	ENSMUSG00000022175	Lrp10	Lrp9	low-density lipoprotein receptor-related protein 10	protein-coding
mm_139301.1	chr17	48346466	48346493	+	1	NA	promoter-TSS (NM_031254)	promoter-TSS (NM_031254)	78	NM_001272078	83433	Mm.261623	NM_031254	ENSMUSG00000023992	Trem2	TREM-2|Trem2a|Trem2b|Trem2c	triggering receptor expressed on myeloid cells 2	protein-coding
mm_21180.1	chr2	154899150	154899154	-	1	NA	Intergenic	RLTR13B2|LTR|ERVK	-6246	NM_026030	67204	Mm.377134	NM_026030	ENSMUSG00000074656	Eif2s2	2810026E11Rik|38kDa|AA408636|AA571381|AA986487|AW822225|D2Ertd303e|EIF2|EIF2B	eukaryotic translation initiation factor 2, subunit 2 (beta)	protein-coding
mm_17924.1	chr2	35461248	35461271	-	1	NA	5' UTR (NM_001145821, exon 1 of 8)	5' UTR (NM_001145821, exon 1 of 8)	190	NM_001308299	14594	Mm.281124	NM_010283	ENSMUSG00000035778	Ggta1	AW108479|GALT|Gal|Ggta|Ggta-1|alpha Gal|alpha3GalT	glycoprotein galactosyltransferase alpha 1, 3	protein-coding
mm_59415.1	chr7	27121641	27121660	+	1	NA	exon (NM_007817, exon 2 of 10)	exon (NM_007817, exon 2 of 10)	1695	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_40013.1	chr5	33019049	33019054	+	1	NA	5' UTR (NM_011738, exon 1 of 2)	5' UTR (NM_011738, exon 1 of 2)	235	NM_011738	22629	Mm.332314	NM_011738	ENSMUSG00000018965	Ywhah	-	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta polypeptide	protein-coding
mm_32264.1	chr4	102596112	102596120	+	1	NA	intron (NM_001177982, intron 3 of 9)	intron (NM_001177982, intron 3 of 9)	6273	NM_001177981	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_133441.1	chr16	87720901	87720905	+	1	NA	intron (NM_007520, intron 3 of 4)	intron (NM_007520, intron 3 of 4)	21949	NM_007520	12013	Mm.26147	NM_007520	ENSMUSG00000025612	Bach1	6230421P05Rik|AI323795	BTB and CNC homology 1, basic leucine zipper transcription factor 1	protein-coding
mm_73331.1	chr8	105300236	105300277	+	1	NA	intron (NM_148952, intron 5 of 9)	intron (NM_148952, intron 5 of 9)	2593	NM_148952	104394	Mm.34554	NM_148952	ENSMUSG00000014859	E2f4	2010111M04Rik|AI427446	E2F transcription factor 4	protein-coding
mm_74759.1	chr8	19158635	19158666	-	1	NA	intron (NM_153115, intron 1 of 1)	intron (NM_153115, intron 1 of 1)	763	NM_153115	78128	Mm.229357	NM_153115	ENSMUSG00000079842	Spag11a	9230111C08Rik|Bin1b|EP2Q|EP2e|Spag11	sperm associated antigen 11A	protein-coding
mm_136943.1	chr17	14279532	14279550	+	1	NA	promoter-TSS (NM_022315)	promoter-TSS (NM_022315)	35	NM_022315	64074	Mm.30162	NM_022315	ENSMUSG00000023886	Smoc2	1700056C05Rik|5430426J21Rik|Smoc2l	SPARC related modular calcium binding 2	protein-coding
mm_50797.1	chr6	54267136	54267145	+	1	NA	intron (NM_001311133, intron 1 of 7)	intron (NM_001311133, intron 1 of 7)	-2016	NM_001311134	69993	Mm.321147	NM_023543	ENSMUSG00000004633	Chn2	1700026N20Rik|4930557O16Rik|ARHGAP3|Bch	chimerin 2	protein-coding
mm_48450.1	chr5	140702221	140702236	-	1	NA	5' UTR (NM_028833, exon 1 of 23)	5' UTR (NM_028833, exon 1 of 23)	150	NM_028833	74239	Mm.179704	NM_028833	ENSMUSG00000036555	Iqce	1700028P05Rik|mKIAA1023	IQ motif containing E	protein-coding
mm_155639.1	chrX	85202733	85202752	+	1	NA	3' UTR (NM_007868, exon 79 of 79)	3' UTR (NM_007868, exon 79 of 79)	-46935	NM_028046	71996	Mm.20201	NM_028046	ENSMUSG00000035491	Fthl17a	1600014K23Rik|AI324104	ferritin, heavy polypeptide-like 17, member A	protein-coding
mm_94526.1	chr11	9049070	9049082	+	1	NA	promoter-TSS (NM_001290520)	promoter-TSS (NM_001290520)	-85	NM_177576	194974	Mm.79210	NM_177576	ENSMUSG00000040985	Sun3	Sunc1	Sad1 and UNC84 domain containing 3	protein-coding
mm_136613.1	chr17	5336671	5336684	+	1	NA	exon (NM_001085355, exon 18 of 20)	exon (NM_001085355, exon 18 of 20)	82090	NM_175349	106557	Mm.432764	NM_175349	ENSMUSG00000101959	Ldhal6b	4933402O15Rik|AI326310|LDHL|Ldhal	lactate dehydrogenase A-like 6B	protein-coding
mm_147665.1	chr18	60613502	60613527	-	1	NA	intron (NM_177340, intron 1 of 2)	intron (NM_177340, intron 1 of 2)	-3410	NM_001109975	104027	Mm.252321	NM_177340	ENSMUSG00000043079	Synpo	9030217H17Rik|9130229N11|9330140I15Rik|AW046661	synaptopodin	protein-coding
mm_72889.1	chr8	90493056	90493066	+	1	NA	Intergenic	Intergenic	-144809	NM_172913	244579	Mm.302755	NM_172913	ENSMUSG00000043668	Tox3	500-9|BC052044|C230068E13|CAGF9|Tnrc9	TOX high mobility group box family member 3	protein-coding
mm_131155.1	chr16	6863001	6863002	+	1	NA	intron (NM_021477, intron 5 of 16)	intron (NM_021477, intron 5 of 16)	-206834	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_117886.1	chr13	99421724	99421740	-	1	NA	3' UTR (NM_008634, exon 7 of 7)	3' UTR (NM_008634, exon 7 of 7)	-8906	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_40916.1	chr5	75642467	75642467	+	1	NA	intron (NM_021099, intron 13 of 20)	L1M5|LINE|L1	67476	NM_021099	16590	Mm.247073	NM_021099	ENSMUSG00000005672	Kit	Bs|CD117|Fdc|Gsfsco1|Gsfsco5|Gsfsow3|SCO1|SCO5|SOW3|Ssm|Tr-kit|W|c-KIT	KIT proto-oncogene receptor tyrosine kinase	protein-coding
mm_99984.1	chr11	114675509	114675522	+	1	NA	promoter-TSS (NM_053273)	promoter-TSS (NM_053273)	47	NM_053273	117160	Mm.271934	NM_053273	ENSMUSG00000034714	Ttyh2	1110001A03Rik	tweety family member 2	protein-coding
mm_25035.1	chr3	98279931	98279952	+	1	NA	promoter-TSS (NM_008256)	promoter-TSS (NM_008256)	-490	NM_008256	15360	Mm.289131	NM_008256	ENSMUSG00000027875	Hmgcs2	1300002P16|mHS	3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2	protein-coding
mm_58073.1	chr6	136924214	136924232	-	1	NA	exon (NM_007486, exon 6 of 6)	exon (NM_007486, exon 6 of 6)	-2043	NM_026983	69187	Mm.33692	NM_026983	ENSMUSG00000030219	Erp27	1810033M07Rik|1810047B09Rik	endoplasmic reticulum protein 27	protein-coding
mm_146183.1	chr18	75562759	75562768	+	1	NA	intron (NM_201354, intron 7 of 11)	intron (NM_201354, intron 7 of 11)	48118	NR_045879	100038353	Mm.440724	NR_045879	ENSMUSG00000097712	Gm10532	ENSMUSG00000073534	predicted gene 10532	ncRNA
mm_169252.1	chr13	78261701	78261701	+	1	NA	Intergenic	L1Md_T|LINE|L1	-62828	NM_010151	13865	Mm.439653	NM_010151	ENSMUSG00000069171	Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR-3|EAR3|Erbal3|SVP44|Tcfcoup1	nuclear receptor subfamily 2, group F, member 1	protein-coding
mm_136805.1	chr17	12378653	12378665	+	1	NA	promoter-TSS (NM_008877)	promoter-TSS (NM_008877)	50	NM_008877	18815	Mm.971	NM_008877	ENSMUSG00000059481	Plg	AI649309|Pg	plasminogen	protein-coding
mm_97951.1	chr11	83677508	83677511	+	1	NA	Intergenic	Intergenic	14925	NM_013652	20303	Mm.244263	NM_013652	ENSMUSG00000018930	Ccl4	AT744.1|Act-2|MIP-1B|Mip1b|Scya4	chemokine (C-C motif) ligand 4	protein-coding
mm_96090.1	chr11	60388191	60388213	+	1	NA	intron (NM_029044, intron 11 of 13)	intron (NM_029044, intron 11 of 13)	28897	NM_145427	246782	Mm.41651	NM_145427	ENSMUSG00000042709	Atpaf2	ATP12|ATP12p	ATP synthase mitochondrial F1 complex assembly factor 2	protein-coding
mm_67675.1	chr7	88530927	88530928	-	1	NA	Intergenic	Intergenic	100654	NM_028238	72433	Mm.276669	NM_028238	ENSMUSG00000030559	Rab38	2310011F14Rik|AU043391|cht	RAB38, member RAS oncogene family	protein-coding
mm_170391.1	chr1	86356706	86356715	-	1	NA	promoter-TSS (NR_002851)	promoter-TSS (NR_002851)	-383	NR_002851	80828		NR_002851	ENSMUSG00000064823	Snord82	Rnu82|U82|Z25	small nucleolar RNA, C/D box 82	snoRNA
mm_142466.1	chr17	45601886	45601928	-	1	NA	promoter-TSS (NM_001177470)	promoter-TSS (NM_001177470)	8	NM_001177470	653016	Mm.45676	NM_001177468	ENSMUSG00000079471	Gm7325	EG653016|Esgp	predicted gene 7325	protein-coding
mm_123574.1	chr14	66999902	66999926	-	1	NA	intron (NM_009761, intron 1 of 5)	intron (NM_009761, intron 1 of 5)	8963	NM_009761	12177	Mm.29820	NM_009761	ENSMUSG00000022051	Bnip3l	C86132|D14Ertd719e|Nip3L|Nix	BCL2/adenovirus E1B interacting protein 3-like	protein-coding
mm_115210.1	chr13	109260387	109260401	+	1	NA	intron (NM_011056, intron 3 of 16)	intron (NM_011056, intron 3 of 16)	-64350	NR_030644	100124489		NR_030644	ENSMUSG00000076946	Mir582	Mirn582|mir-582|mmu-mir-582	microRNA 582	ncRNA
mm_127253.1	chr15	99702098	99702119	+	1	NA	promoter-TSS (NM_031842)	promoter-TSS (NM_031842)	-179	NM_031842	83797	Mm.273756	NM_031842	ENSMUSG00000023018	Smarcd1	AA407987|Baf60a|D15Kz1	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1	protein-coding
mm_163874.1	chr14	19419417	19419435	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	183161	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_131071.1	chr16	4684100	4684137	+	1	NA	promoter-TSS (NM_023646)	promoter-TSS (NM_023646)	48	NM_001135112	83945	Mm.248337	NM_023646	ENSMUSG00000004069	Dnaja3	1200003J13Rik|1810053A11Rik|C81173|Tid-1|Tid1l	DnaJ heat shock protein family (Hsp40) member A3	protein-coding
mm_77.1	chr1	6730125	6730134	+	1	NA	promoter-TSS (NR_045189)	promoter-TSS (NR_045189)	78	NR_045188	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding
mm_94034.1	chr10	127991268	127991284	-	1	NA	exon (NM_013786, exon 6 of 6)	exon (NM_013786, exon 6 of 6)	16232	NM_013786	27400	Mm.26719	NM_013786	ENSMUSG00000025396	Hsd17b6	17betaHSD9|Hsd17b9|Rdh8	hydroxysteroid (17-beta) dehydrogenase 6	protein-coding
mm_141571.1	chr17	32315760	32315776	-	1	NA	exon (NM_019774, exon 6 of 14)	exon (NM_019774, exon 6 of 14)	5470	NM_019774	56399	Mm.328945	NM_019774	ENSMUSG00000024045	Akap8	1200016A02Rik|AA673585|AKAP-8|AKAP95|AU015639	A kinase (PRKA) anchor protein 8	protein-coding
mm_52237.1	chr6	104493221	104493230	+	1	NA	5' UTR (NM_017383, exon 1 of 23)	5' UTR (NM_017383, exon 1 of 23)	181	NM_017383	53870	Mm.321671	NM_017383	ENSMUSG00000030092	Cntn6	NB-3	contactin 6	protein-coding
mm_74724.1	chr8	17535191	17535197	-	1	NA	5' UTR (NM_053171, exon 1 of 70)	5' UTR (NM_053171, exon 1 of 70)	191	NM_053171	94109	Mm.436988	NM_053171	ENSMUSG00000060924	Csmd1	B930082H09|mKIAA1890	CUB and Sushi multiple domains 1	protein-coding
mm_74711.1	chr8	17214842	17214860	-	1	NA	intron (NM_053171, intron 2 of 69)	intron (NM_053171, intron 2 of 69)	320534	NM_053171	94109	Mm.436988	NM_053171	ENSMUSG00000060924	Csmd1	B930082H09|mKIAA1890	CUB and Sushi multiple domains 1	protein-coding
mm_102536.1	chr11	61175021	61175060	-	1	NA	promoter-TSS (NM_001004143)	promoter-TSS (NM_001004143)	19	NM_001004143	216825	Mm.30602	NM_001004143	ENSMUSG00000042506	Usp22	AI427806	ubiquitin specific peptidase 22	protein-coding
mm_131576.1	chr16	18392555	18392622	+	1	NA	promoter-TSS (NM_001272032)	promoter-TSS (NM_001272032)	25	NM_001272032	11877	Mm.293599	NM_033474	ENSMUSG00000000325	Arvcf	-	armadillo repeat gene deleted in velo-cardio-facial syndrome	protein-coding
mm_111100.1	chr12	80780497	80780506	-	1	NA	Intergenic	RMER6A|LTR|ERVK	-10031	NM_178682	217684	Mm.341776	NM_178682	ENSMUSG00000021133	Susd6	4933426M11Rik|mKIAA0247	sushi domain containing 6	protein-coding
mm_67714.1	chr7	89980884	89980908	-	1	NA	promoter-TSS (NM_021876)	promoter-TSS (NM_021876)	80	NM_021876	13626	Mm.380914	NM_021876	ENSMUSG00000030619	Eed	ENSMUSG00000039373|l(7)5Rn|l7Rn5|lusk	embryonic ectoderm development	protein-coding
mm_152843.1	chr19	23448394	23448406	-	1	NA	promoter-TSS (NM_174857)	promoter-TSS (NM_174857)	-78	NM_174857	71738	Mm.50841	NM_174857	ENSMUSG00000033207	Mamdc2	1200015L10Rik|AI591564|mamcan	MAM domain containing 2	protein-coding
mm_99361.1	chr11	101642784	101642788	+	1	NA	Intergenic	AT_rich|Low_complexity|Low_complexity	14837	NM_025654	66599	Mm.41449	NM_025654	ENSMUSG00000010362	Rdm1	2410008M22Rik|AW212028|Rad52b	RAD52 motif 1	protein-coding
mm_69538.1	chr7	135695530	135695538	-	1	NA	exon (NM_001081117, exon 12 of 14)	exon (NM_001081117, exon 12 of 14)	20845	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_158351.1	chrX	134556133	134556133	-	1	NA	intron (NM_013482, intron 9 of 18)	intron (NM_013482, intron 9 of 18)	-14463	NM_013898	30058	Mm.214504	NM_013898	ENSMUSG00000048007	Timm8a1	DXHXS1274E|Ddp1|Fci-12|Tim8a|Timm8a	translocase of inner mitochondrial membrane 8A1	protein-coding
mm_80056.1	chr9	69363854	69363867	+	1	NA	intron (NM_013646, intron 4 of 10)	PB1D11|SINE|Alu	387	NR_136934	102642202	Mm.415363	NR_136934	ENSMUSG00000086648	Gm15511	OTTMUSG00000023029	predicted gene 15511	ncRNA
mm_84363.1	chr9	64790823	64790828	-	1	NA	Intergenic	MIRb|SINE|MIR	-20186	NM_001162917	102442	Mm.222473	NM_176935	ENSMUSG00000053641	Dennd4a	AI115600|AI851943|F730015K02Rik	DENN/MADD domain containing 4A	protein-coding
mm_129752.1	chr15	82354195	82354208	-	1	NA	promoter-TSS (NM_025987)	promoter-TSS (NM_025987)	90	NM_025987	67130	Mm.27570	NM_025987	ENSMUSG00000022450	Ndufa6	14kDa|2700038D15Rik|B230217P19Rik	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 6 (B14)	protein-coding
mm_2397.1	chr1	93685739	93685807	+	1	NA	5' UTR (NM_016778, exon 1 of 5)	5' UTR (NM_016778, exon 1 of 5)	198	NM_016778	51800	Mm.3295	NM_016778	ENSMUSG00000026278	Bok	matador|mtd	BCL2-related ovarian killer	protein-coding
mm_41723.1	chr5	102481423	102481495	+	1	NA	promoter-TSS (NM_029270)	promoter-TSS (NM_029270)	68	NM_029270	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding
mm_1304.1	chr1	64690792	64690803	+	1	NA	promoter-TSS (NM_001097644)	promoter-TSS (NM_001097644)	-138	NR_038009	69941	Mm.69044	NR_038009	ENSMUSG00000087213	2810408I11Rik	-	RIKEN cDNA 2810408I11 gene	ncRNA
mm_96572.1	chr11	69045887	69045897	+	1	NA	5' UTR (NM_011496, exon 1 of 8)	5' UTR (NM_011496, exon 1 of 8)	255	NM_011496	20877	Mm.3488	NM_011496	ENSMUSG00000020897	Aurkb	AIM-1|AIRK2|AL022959|Aik2|Aim1|Ark2|AurB|IPL1|STK-1|Stk12|Stk5	aurora kinase B	protein-coding
mm_91554.1	chr10	39960145	39960162	-	1	NA	promoter-TSS (NM_001173500)	promoter-TSS (NM_001173500)	0	NM_001173500	100041085	Mm.332530	NM_001173500	ENSMUSG00000071335	Mfsd4b3	G630090E17Rik|Naglt1c	major facilitator superfamily domain containing 4B3	protein-coding
mm_77880.1	chr9	7277911	7277938	+	1	NA	exon (NM_008607, exon 6 of 10)	exon (NM_008607, exon 6 of 10)	5410	NM_008607	17386	Mm.5022	NM_008607	ENSMUSG00000050578	Mmp13	Clg|MMP-13|Mmp1	matrix metallopeptidase 13	protein-coding
mm_102413.1	chr11	59201713	59201739	-	1	NA	promoter-TSS (NM_026035)	promoter-TSS (NM_026035)	705	NR_037964	72203	Mm.339566	NR_037964		2610507I01Rik	5033414D05Rik	RIKEN cDNA 2610507I01 gene	ncRNA
mm_141904.1	chr17	34956820	34956828	-	1	NA	3' UTR (NM_010478, exon 1 of 1)	3' UTR (NM_010478, exon 1 of 1)	2414	NM_010478	15511	Mm.372314	NM_010478	ENSMUSG00000090877	Hspa1b	Hsp70|Hsp70-1|Hsp70.1|hsp68	heat shock protein 1B	protein-coding
mm_164632.1	chr17	34039298	34039306	+	1	NA	TTS (NM_001205216)	TTS (NM_001205216)	164	NM_001317722	12815	Mm.20230	NM_009926	ENSMUSG00000024330	Col11a2	-	collagen, type XI, alpha 2	protein-coding
mm_161632.1	chr16	89015271	89015271	+	1	NA	promoter-TSS (NM_001199334)	promoter-TSS (NM_001199334)	-6	NM_001199334	100040201	Mm.436873	NM_001199334	ENSMUSG00000068075	Gm10229	ENSMUSG00000068075	predicted gene 10229	protein-coding
mm_99334.1	chr11	101468139	101468149	+	1	NA	promoter-TSS (NM_009708)	promoter-TSS (NM_009708)	-194	NM_009708	11858	Mm.378883	NM_009708	ENSMUSG00000001313	Rnd2	Arhn|Rohn	Rho family GTPase 2	protein-coding
mm_90384.1	chr10	127288529	127288551	+	1	NA	intron (NM_033072, intron 1 of 12)	intron (NM_033072, intron 1 of 12)	478	NM_001347171	110962	Mm.372826	NM_033072	ENSMUSG00000025409	Mbd6	D10Wsu93e	methyl-CpG binding domain protein 6	protein-coding
mm_11352.1	chr2	30845537	30845541	+	1	NA	exon (NM_009116, exon 1 of 4)	exon (NM_009116, exon 1 of 4)	172	NM_009116	20204	Mm.1802	NM_009116	ENSMUSG00000039476	Prrx2	Prx2|S8	paired related homeobox 2	protein-coding
mm_60785.1	chr7	45566792	45566805	+	1	NA	TTS (NR_038166)	TTS (NR_038166)	-3355	NM_009737	12036	Mm.24210	NM_009737	ENSMUSG00000030826	Bcat2	Bcat-2|Eca40	branched chain aminotransferase 2, mitochondrial	protein-coding
mm_108605.1	chr12	85473884	85473896	+	1	NA	promoter-TSS (NM_010234)	promoter-TSS (NM_010234)	-11	NM_010234	14281	Mm.246513	NM_010234	ENSMUSG00000021250	Fos	D12Rfj1|c-fos|cFos	FBJ osteosarcoma oncogene	protein-coding
mm_19325.1	chr2	90572117	90572144	-	1	NA	intron (NM_008982, intron 1 of 23)	L1ME4b|LINE|L1	8517	NM_008982	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_110128.1	chr12	26444630	26444641	-	1	NA	3' UTR (NM_021384, exon 6 of 6)	3' UTR (NM_021384, exon 6 of 6)	11817	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_106133.1	chr11	116466220	116466241	-	1	NA	Intergenic	Intergenic	-11883	NM_001033267	217341	Mm.387352	NM_001033267	ENSMUSG00000070331	Qrich2	Gm66	glutamine rich 2	protein-coding
mm_95801.1	chr11	55109614	55109622	+	1	NA	3' UTR (NM_010299, exon 4 of 4)	3' UTR (NM_010299, exon 4 of 4)	11633	NM_010299	14667	Mm.287807	NM_010299	ENSMUSG00000000594	Gm2a	AA408702|AW215435|GM2-AP|SAP-3	GM2 ganglioside activator protein	protein-coding
mm_2729.1	chr1	128244123	128244175	+	1	NA	promoter-TSS (NM_026390)	promoter-TSS (NM_026390)	-32	NM_026390	67812	Mm.293321	NM_026390	ENSMUSG00000026353	Ubxn4	1300013G12Rik|Ubxd2|mKIAA0242	UBX domain protein 4	protein-coding
mm_59494.1	chr7	27523277	27523285	+	1	NA	promoter-TSS (NM_001033315)	promoter-TSS (NM_001033315)	20	NM_001033315	233020	Mm.429716	NM_001033315	ENSMUSG00000040424	Hipk4	Gm162	homeodomain interacting protein kinase 4	protein-coding
mm_29171.1	chr3	106513537	106513540	-	1	NA	intron (NM_133869, intron 4 of 8)	A-rich|Low_complexity|Low_complexity	27498	NM_028110	72121	Mm.14816	NM_028110	ENSMUSG00000027901	Dennd2d	2010308M01Rik|AI451421	DENN/MADD domain containing 2D	protein-coding
mm_148549.1	chr19	4711394	4711414	+	1	NA	5' UTR (NM_021287, exon 1 of 37)	5' UTR (NM_021287, exon 1 of 37)	181	NM_021287	20743	Mm.329668	NM_021287	ENSMUSG00000067889	Sptbn2	Spnb3|mKIAA0302	spectrin beta, non-erythrocytic 2	protein-coding
mm_16841.1	chr2	11502051	11502061	-	1	NA	promoter-TSS (NM_001177754)	promoter-TSS (NM_001177754)	34	NM_001177754	170768	Mm.19669	NM_133232	ENSMUSG00000026773	Pfkfb3	E330010H22Rik|iPFK-2|uPFK-2	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	protein-coding
mm_15302.1	chr2	155386805	155386824	+	1	NA	3' UTR (NM_178111, exon 4 of 4)	3' UTR (NM_178111, exon 4 of 4)	4958	NM_178111	68728	Mm.293605	NM_178111	ENSMUSG00000038375	Trp53inp2	1110029F20Rik|Tp53inp2	transformation related protein 53 inducible nuclear protein 2	protein-coding
mm_134408.1	chr16	17673186	17673284	-	1	NA	exon (NM_001040683, exon 7 of 17)	exon (NM_001040683, exon 7 of 17)	26765	NM_001166164	72315	Mm.297777	NM_001166164	ENSMUSG00000041617	Ccdc74a	2310015A05Rik	coiled-coil domain containing 74A	protein-coding
mm_98359.1	chr11	93886158	93886210	+	1	NA	promoter-TSS (NM_134012)	promoter-TSS (NM_134012)	-23	NM_001346525	103537	Mm.210334	NM_134012	ENSMUSG00000059474	Mbtd1	AA408199|AI194990|hemp	mbt domain containing 1	protein-coding
mm_153580.1	chr19	43420666	43420692	-	1	NA	Intergenic	LFSINE_Vert|SINE|tRNA	-19757	NM_031396	83674	Mm.329864	NM_031396	ENSMUSG00000025189	Cnnm1	AI846314|Acdp1|CLP-1	cyclin M1	protein-coding
mm_95187.1	chr11	42421259	42421284	+	1	NA	promoter-TSS (NM_001347314)	promoter-TSS (NM_001347314)	-79	NM_001347314	14401	Mm.338723	NM_008070	ENSMUSG00000007653	Gabrb2	AI834970|C030002O17Rik|C030021G16Rik|Gabrab2|Gabrb-2	gamma-aminobutyric acid (GABA) A receptor, subunit beta 2	protein-coding
mm_55356.1	chr6	56901871	56901891	-	1	NA	promoter-TSS (NM_001252374)	promoter-TSS (NM_001252374)	5	NM_001252374	107569	Mm.158936	NM_026004	ENSMUSG00000029780	Nt5c3	1600024P05Rik|2610206B05Rik|3110004A18Rik|AI842776|Nt5c3a|Nt5y|PN-1|PN-I|PSN1|UMPH|Umph-1|Umph1|cN-III|lupin|p36	5'-nucleotidase, cytosolic III	protein-coding
mm_12397.1	chr2	70094972	70094984	+	1	NA	intron (NM_177376, intron 2 of 34)	intron (NM_177376, intron 2 of 34)	55852	NM_177376	329421	Mm.99648	NM_177376	ENSMUSG00000042064	Myo3b	A430065P19Rik	myosin IIIB	protein-coding
mm_7769.1	chr1	131200167	131200177	-	1	NA	promoter-TSS (NM_001311094)	promoter-TSS (NM_001311094)	13	NM_001311094	54354	Mm.248291	NM_018750	ENSMUSG00000026430	Rassf5	1300019G20Rik|Maxp1|Nore1|Nore1A|Nore1B|Rapl	Ras association (RalGDS/AF-6) domain family member 5	protein-coding
mm_98188.1	chr11	87793810	87793828	+	1	NA	promoter-TSS (NM_010824)	promoter-TSS (NM_010824)	35	NM_010824	17523	Mm.4668	NM_010824	ENSMUSG00000009350	Mpo	mKIAA4033	myeloperoxidase	protein-coding
mm_11374.1	chr2	31082874	31082876	+	1	NA	intron (NM_001038700, intron 6 of 14)	intron (NM_001038700, intron 6 of 14)	13625	NM_001177650	14269	Mm.52297	NM_019406	ENSMUSG00000075415	Fnbp1	1110057E06Rik|2210010H06Rik|FBP1|Fbp17	formin binding protein 1	protein-coding
mm_140683.1	chr17	13007709	13007734	-	1	NA	promoter-TSS (NM_013671)	promoter-TSS (NM_013671)	-118	NM_013671	20656	Mm.290876	NM_013671	ENSMUSG00000006818	Sod2	MnSOD|Sod-2	superoxide dismutase 2, mitochondrial	protein-coding
mm_163613.1	chr13	51843850	51843860	-	1	NA	Intergenic	Intergenic	-2820	NM_011817	23882	Mm.281298	NM_011817	ENSMUSG00000021453	Gadd45g	AI327420|C86281|CR6|DDIT2|OIG37	growth arrest and DNA-damage-inducible 45 gamma	protein-coding
mm_171417.1	chr4	132310233	132310238	+	1	NA	promoter-TSS (NR_034046)	promoter-TSS (NR_034046)	-72	NR_034046	100217440		NR_034046		Snora61	MBI-164	small nucleolar RNA, H/ACA box 61	snoRNA
mm_152249.1	chr19	8714441	8714450	-	1	NA	promoter-TSS (NM_008577)	promoter-TSS (NM_008577)	-548	NM_008577	17254	Mm.4114	NM_008577	ENSMUSG00000010095	Slc3a2	4F2|4F2HC|AI314110|Cd98|Ly-10|Ly-m10|Ly10|Mdu1|Mgp-2hc|NACAE	solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2	protein-coding
mm_140038.1	chr17	74395608	74395639	+	1	NA	promoter-TSS (NM_144798)	promoter-TSS (NM_144798)	15	NM_144798	210148	Mm.243943	NM_144798	ENSMUSG00000024069	Slc30a6	9530029F08Rik|ZnT6	solute carrier family 30 (zinc transporter), member 6	protein-coding
mm_124665.1	chr15	6380616	6380624	+	1	NA	intron (NM_001008702, intron 1 of 13)	intron (NM_001008702, intron 1 of 13)	-6128	NM_023118	13132	Mm.240830	NM_023118	ENSMUSG00000022150	Dab2	5730435J12Rik|AA960054|AI957090|D15Wsu122e|D630005B22Rik|Doc-2|Doc2|p96	disabled 2, mitogen-responsive phosphoprotein	protein-coding
mm_132058.1	chr16	29839350	29839385	+	1	NA	Intergenic	Intergenic	139757	NR_037689	328657	Mm.425982	NM_001033403		Gm1968	-	predicted gene 1968	ncRNA
mm_14830.1	chr2	147072597	147072600	+	1	NA	intron (NM_011917, intron 28 of 29)	B1_Mur1|SINE|Alu	12747	NM_023504	228731	Mm.315498	NM_023504	ENSMUSG00000054160	Nkx2-4	1700001P03Rik|Nkx-2.4|tinman	NK2 homeobox 4	protein-coding
mm_72344.1	chr8	79639400	79639424	+	1	NA	promoter-TSS (NM_001256033)	promoter-TSS (NM_001256033)	-264	NM_001256033	73945	Mm.34348	NM_001081164	ENSMUSG00000036990	Otud4	4930431L18Rik|AI449692|D8Ertd69e|mKIAA1046	OTU domain containing 4	protein-coding
mm_93512.1	chr10	115222705	115222712	-	1	NA	intron (NM_025706, intron 5 of 16)	intron (NM_025706, intron 5 of 16)	28785	NM_025706	66687	Mm.22252	NM_025706	ENSMUSG00000020130	Tbc1d15	4432405K22Rik|AU022358|AU023730|AW557774|Ly6dl|Rab7-GAP	TBC1 domain family, member 15	protein-coding
mm_129152.1	chr15	76232047	76232054	-	1	NA	promoter-TSS (NM_001163542)	promoter-TSS (NM_001163542)	-672	NM_011117	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
mm_157605.1	chrX	53643772	53643778	-	1	NA	promoter-TSS (NM_024170)	promoter-TSS (NM_024170)	-12	NM_024170	66158	Mm.391252	NM_024170	ENSMUSG00000067925	Cxx1a	1110012O05Rik|Mar8.2A/B|Mart8b	CAAX box 1A	protein-coding
mm_106855.1	chr12	8009087	8009097	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	31415	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_66256.1	chr7	35647116	35647124	-	1	NA	intron (NM_019746, intron 1 of 5)	CpG	362	NM_019746	56330	Mm.371609	NM_019746	ENSMUSG00000030417	Pdcd5	2200003D22Rik|AA408513|Tfar19	programmed cell death 5	protein-coding
mm_115292.1	chr13	111978018	111978024	+	1	NA	Intergenic	CpG	110085	NR_130345	102636620	Mm.402328	NR_130345	ENSMUSG00000086111	Gm15326	OTTMUSG00000020187	predicted gene 15326	ncRNA
mm_84589.1	chr9	70036682	70036704	-	1	NA	5' UTR (NM_028087, exon 2 of 3)	5' UTR (NM_028087, exon 2 of 3)	1395	NM_028087	72077	Mm.195555	NM_028087	ENSMUSG00000032226	Gcnt3	2010013H22Rik|2210021I22Rik|2210401J11Rik	glucosaminyl (N-acetyl) transferase 3, mucin type	protein-coding
mm_10631.1	chr2	19909798	19909829	+	1	NA	Intergenic	CpG	251751	NM_027715	71198	Mm.83981	NM_027715	ENSMUSG00000043415	Otud1	4933428L19Rik	OTU domain containing 1	protein-coding
mm_41949.1	chr5	105734511	105734530	+	1	NA	intron (NM_001122768, intron 2 of 2)	AT_rich|Low_complexity|Low_complexity	33710	NM_178701	231549	Mm.23837	NM_178701	ENSMUSG00000046079	Lrrc8d	2810473G09Rik|4930525N13Rik|A930019F03|Lrrc5	leucine rich repeat containing 8D	protein-coding
mm_152658.1	chr19	12795482	12795497	-	1	NA	non-coding (NR_024093, exon 1 of 13)	non-coding (NR_024093, exon 1 of 13)	634	NR_024093	664779	Mm.290924	NM_001039718	ENSMUSG00000024695	Gm44505	Zfp91-Cntf|Zfp91Cntf	predicted readthrough transcript (NMD candidate), 44505	ncRNA
mm_171694.1	chr4	6649186	6649186	+	1	NA	Intergenic	RMER16-int|LTR|ERVK	-194915	NM_010945	18201	Mm.3059	NM_010945	ENSMUSG00000028245	Nsmaf	AA959567|C630007J05|Fan	neutral sphingomyelinase (N-SMase) activation associated factor	protein-coding
mm_73982.1	chr8	120537506	120537512	+	1	NA	promoter-TSS (NM_001145896)	promoter-TSS (NM_001145896)	100	NM_001145896	382034	Mm.334856	NM_198671	ENSMUSG00000031822	Gse1	2210013I18Rik|mKIAA0182	genetic suppressor element 1, coiled-coil protein	protein-coding
mm_146945.1	chr18	32462463	32462468	-	1	NA	Intergenic	Intergenic	-84181	NR_045403	402767	Mm.385109	NR_045403	ENSMUSG00000097413	A830052D11Rik	-	RIKEN cDNA A830052D11 gene	ncRNA
mm_97299.1	chr11	76494721	76494737	+	1	NA	promoter-TSS (NM_001346670)	promoter-TSS (NM_001346670)	-234	NM_001346670	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_116884.1	chr13	55190187	55190236	-	1	NA	Intergenic	Intergenic	-19571	NM_008739	18193	Mm.12964	NM_008739	ENSMUSG00000021488	Nsd1	AI528500|KMT3B	nuclear receptor-binding SET-domain protein 1	protein-coding
mm_119691.1	chr14	53553988	53554003	+	1	NA	Intergenic	Intergenic	699934	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_46569.1	chr5	107178387	107178390	-	1	NA	intron (NM_011578, intron 3 of 16)	intron (NM_011578, intron 3 of 16)	111207	NM_011578	21814	Mm.200775	NM_011578	ENSMUSG00000029287	Tgfbr3	1110036H20Rik|AU015626|AW215636|TBRIII	transforming growth factor, beta receptor III	protein-coding
mm_136918.1	chr17	13760503	13760600	+	1	NA	promoter-TSS (NM_010806)	promoter-TSS (NM_010806)	10	NM_010806	17356	Mm.59167	NM_010806	ENSMUSG00000068036	Afdn	5033403D15Rik|AF6|Af-6|Afadin|Gm314|I-afadin|Mllt4|S-afadin	afadin, adherens junction formation factor	protein-coding
mm_149025.1	chr19	8765031	8765034	+	1	NA	exon (NM_001276704, exon 10 of 20)	exon (NM_001276704, exon 10 of 20)	-5964	NM_025791	66836	Mm.440071	NM_025791	ENSMUSG00000010097	Tmem223	0610006I08Rik	transmembrane protein 223	protein-coding
mm_149486.1	chr19	11810653	11810705	+	1	NA	intron (NM_001025307, intron 1 of 10)	intron (NM_001025307, intron 1 of 10)	8724	NM_001286543	20908	Mm.272264	NM_011502	ENSMUSG00000041488	Stx3	Syn-3	syntaxin 3	protein-coding
mm_136479.1	chr16	96001711	96001720	-	1	NA	3' UTR (NM_001103179, exon 41 of 41)	3' UTR (NM_001103179, exon 41 of 41)	-10812	NM_019537	56088	Mm.396248	NM_019537	ENSMUSG00000022913	Psmg1	AW552102|Dscr2	proteasome (prosome, macropain) assembly chaperone 1	protein-coding
mm_66570.1	chr7	45321734	45321747	-	1	NA	intron (NM_175130, intron 9 of 24)	intron (NM_175130, intron 9 of 24)	-3218	NR_110499	100040970	Mm.289810	NR_110499	ENSMUSG00000046721	Rpl14-ps1	ENSMUSG00000046721|Gm9811	ribosomal protein L14, pseudogene 1	pseudo
mm_17149.1	chr2	25211345	25211357	-	1	NA	5' UTR (NM_021393, exon 1 of 13)	5' UTR (NM_021393, exon 1 of 13)	138	NM_021393	58202	Mm.116418	NM_021393	ENSMUSG00000013465	Nelfb	A730008L03Rik|AB041607|AI663983|Cobra1|Nelf-b	negative elongation factor complex member B	protein-coding
mm_17219.1	chr2	25493969	25493972	-	1	NA	promoter-TSS (NM_029958)	promoter-TSS (NM_029958)	-59	NM_029958	77701	Mm.99123	NM_029958	ENSMUSG00000026943	Lcn12	9230102M18Rik	lipocalin 12	protein-coding
mm_961.1	chr1	57996062	57996072	+	1	NA	promoter-TSS (NM_199007)	promoter-TSS (NM_199007)	93	NM_199007	68549	Mm.32800	NM_199007	ENSMUSG00000026039	Sgol2a	1110007N04Rik|4932411A20Rik|5730576N04Rik|AU018846|AV008062|D1Ertd8e|Sgol2|Tripin	shugoshin-like 2a (S. pombe)	protein-coding
mm_164845.1	chr18	44073574	44073585	+	1	NA	intron (NM_001013797, intron 1 of 4)	intron (NM_001013797, intron 1 of 4)	2186	NM_001013797	433180	Mm.57302	NM_001013797	ENSMUSG00000055095	Spink6	EG433180	serine peptidase inhibitor, Kazal type 6	protein-coding
mm_42217.1	chr5	113137290	113137324	+	1	NA	intron (NM_172884, intron 1 of 7)	intron (NM_172884, intron 1 of 7)	1278	NM_001347397	243219	Mm.160131	NM_172884	ENSMUSG00000051339	2900026A02Rik	8430408O14Rik|A530094D01|AW539426|Gm449|Kiaa1671|mKIAA1671	RIKEN cDNA 2900026A02 gene	protein-coding
mm_16786.1	chr2	9952630	9952661	-	1	NA	exon (NM_027748, exon 3 of 7)	exon (NM_027748, exon 3 of 7)	-63105	NR_040511	77682	Mm.488621	NR_040511	ENSMUSG00000079602	9230102O04Rik	-	RIKEN cDNA 9230102O04 gene	ncRNA
mm_164481.1	chr16	74306529	74306537	-	1	NA	intron (NM_175549, intron 2 of 27)	intron (NM_175549, intron 2 of 27)	35534	NR_030464	751561		NR_030464	ENSMUSG00000104758	Mir691	Mirn691|mir-691|mmu-mir-691	microRNA 691	ncRNA
mm_34170.1	chr4	140038352	140038361	+	1	NA	intron (NM_198610, intron 4 of 9)	RMER17C|LTR|ERVK	-70330	NM_173427	242721	Mm.60400	NM_173427	ENSMUSG00000078234	Klhdc7a	B230308G19Rik	kelch domain containing 7A	protein-coding
mm_73778.1	chr8	116921736	116921752	+	1	NA	promoter-TSS (NM_028131)	promoter-TSS (NM_028131)	4	NM_028131	72155	Mm.23185	NM_028131	ENSMUSG00000031756	Cenpn	2610510J17Rik|AI426416|AW545024	centromere protein N	protein-coding
mm_73181.1	chr8	95081188	95081205	+	1	NA	promoter-TSS (NM_028805)	promoter-TSS (NM_028805)	-5	NM_028805	74187	Mm.28382	NM_028805	ENSMUSG00000031787	Katnb1	2410003J24Rik|KAT	katanin p80 (WD40-containing) subunit B 1	protein-coding
mm_101303.1	chr11	22342267	22342273	-	1	NA	Intergenic	Intergenic	-55475	NM_001252515	216565	Mm.491265	NM_153078	ENSMUSG00000042302	Ehbp1	AF424697|Flj21950|NACSIN	EH domain binding protein 1	protein-coding
mm_139845.1	chr17	69382798	69382813	+	1	NA	Intergenic	CpG	-1173	NM_009547	22666	Mm.29434	NM_009547	ENSMUSG00000049672	Zbtb14	ZF5|Zfp161|b2b1982Clo	zinc finger and BTB domain containing 14	protein-coding
mm_170871.1	chr2	20651762	20651771	+	1	NA	intron (NM_029895, intron 3 of 18)	RLTR11A2|LTR|ERVK	132253	NM_001177631	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding
mm_80854.1	chr9	98424923	98424935	+	1	NA	5' UTR (NM_011254, exon 1 of 4)	5' UTR (NM_011254, exon 1 of 4)	1968	NM_011254	19659	Mm.279741	NM_011254	ENSMUSG00000046402	Rbp1	CRBPI|Crbp|Rbp-1	retinol binding protein 1, cellular	protein-coding
mm_47754.1	chr5	131290047	131290050	-	1	NA	intron (NM_145218, intron 1 of 10)	ID_B1|SINE|B4	17474	NM_145218	212996	Mm.299204	NM_145218	ENSMUSG00000034040	Wbscr17	AA388321|E330012B09Rik	Williams-Beuren syndrome chromosome region 17 homolog (human)	protein-coding
mm_56816.1	chr6	116716627	116716662	-	1	NA	5' UTR (NM_178768, exon 1 of 5)	5' UTR (NM_178768, exon 1 of 5)	114	NM_178768	319776	Mm.133120	NM_178768	ENSMUSG00000048108	Tmem72	C230095G01Rik	transmembrane protein 72	protein-coding
mm_107227.1	chr12	26476209	26476219	+	1	NA	intron (NM_020557, intron 3 of 4)	intron (NM_020557, intron 3 of 4)	6999	NM_020557	22169	Mm.271839	NM_020557	ENSMUSG00000020638	Cmpk2	1200004E04Rik|TDKI|Tyki	cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial	protein-coding
mm_4962.1	chr1	191267126	191267137	+	1	NA	Intergenic	Intergenic	50987	NM_025424	66208	Mm.46444	NM_025424	ENSMUSG00000037499	Nenf	1110060M21Rik|SCIRP10|Spuf	neuron derived neurotrophic factor	protein-coding
mm_46097.1	chr5	92347302	92347317	-	1	NA	3' UTR (NM_021274, exon 4 of 4)	3' UTR (NM_021274, exon 4 of 4)	1580	NM_021274	15945	Mm.877	NM_021274	ENSMUSG00000034855	Cxcl10	C7|CRG-2|INP10|IP-10|IP10|Ifi10|Scyb10|gIP-10|mob-1	chemokine (C-X-C motif) ligand 10	protein-coding
mm_43135.1	chr5	125389341	125389357	+	1	NA	intron (NM_019639, intron 1 of 1)	CpG	668	NM_019639	22190	Mm.331	NM_019639	ENSMUSG00000008348	Ubc	2700054O04Rik|AI194771|Rps27a|TI-225|Uba52|Ubb	ubiquitin C	protein-coding
mm_18202.1	chr2	46360442	46360442	-	1	NA	Intergenic	Intergenic	663837	NR_040497	69405	Mm.396184	NR_040497	ENSMUSG00000086202	1700019E08Rik	-	RIKEN cDNA 1700019E08 gene	ncRNA
mm_48015.1	chr5	136169994	136169997	-	1	NA	intron (NM_178751, intron 1 of 2)	intron (NM_178751, intron 1 of 2)	661	NM_178751	269717	Mm.308396	NM_178751	ENSMUSG00000039747	Orai2	A730041O15Rik|Tmem142b	ORAI calcium release-activated calcium modulator 2	protein-coding
mm_62723.1	chr7	110773659	110773685	+	1	NA	intron (NM_009667, intron 1 of 14)	intron (NM_009667, intron 1 of 14)	1068	NM_009667	11717	Mm.3238	NM_009667	ENSMUSG00000005686	Ampd3	-	adenosine monophosphate deaminase 3	protein-coding
mm_128502.1	chr15	52753419	52753456	-	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	40992	NM_027212	69790	Mm.195562	NM_027212	ENSMUSG00000038622	Med30	1810038N03Rik|2510044J04Rik|TRAP25|Thrap6	mediator complex subunit 30	protein-coding
mm_146638.1	chr18	10610302	10610312	-	1	NA	promoter-TSS (NM_001081222)	promoter-TSS (NM_001081222)	45	NM_001081222	77805	Mm.210996	NM_144542	ENSMUSG00000024293	Esco1	A930014I12Rik	establishment of sister chromatid cohesion N-acetyltransferase 1	protein-coding
mm_11321.1	chr2	30415619	30415683	+	1	NA	promoter-TSS (NM_007760)	promoter-TSS (NM_007760)	97	NM_007760	12908	Mm.20396	NM_007760	ENSMUSG00000026853	Crat	AW107812|CARAT	carnitine acetyltransferase	protein-coding
mm_154265.1	chr19	60771674	60771690	-	1	NA	exon (NM_010123, exon 14 of 22)	exon (NM_010123, exon 14 of 22)	2703	NR_034047	100217439		NR_034047		Snora19	MBI-51	small nucleolar RNA, H/ACA box 19	snoRNA
mm_64611.1	chr7	3297051	3297083	-	1	NA	exon (NM_016969, exon 3 of 3)	exon (NM_016969, exon 3 of 3)	4039	NM_001093766	50918	Mm.29874	NM_016969	ENSMUSG00000068566	Myadm	D7Wsu62e	myeloid-associated differentiation marker	protein-coding
mm_161920.1	chr18	70530338	70530338	-	1	NA	promoter-TSS (NM_001136090)	promoter-TSS (NM_001136090)	-17	NM_001289515	26447	Mm.244352	NM_011972	ENSMUSG00000038425	Poli	Rad30b	polymerase (DNA directed), iota	protein-coding
mm_44893.1	chr5	35102422	35102432	-	1	NA	exon (NM_013587, exon 2 of 8)	exon (NM_013587, exon 2 of 8)	3270	NM_013587	16976	Mm.277661	NM_013587	ENSMUSG00000029103	Lrpap1	AA617339|AI790446|AU042172|C77774|HBP44|RAP	low density lipoprotein receptor-related protein associated protein 1	protein-coding
mm_150033.1	chr19	29376169	29376178	+	1	NA	intron (NM_021893, intron 3 of 6)	intron (NM_021893, intron 3 of 6)	8735	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_10423.1	chr2	13581638	13581648	+	1	NA	exon (NM_011701, exon 8 of 9)	exon (NM_011701, exon 8 of 9)	7332	NM_011701	22352	Mm.268000	NM_011701	ENSMUSG00000026728	Vim	-	vimentin	protein-coding
mm_11290.1	chr2	30067160	30067187	+	1	NA	intron (NM_001204875, intron 1 of 7)	CpG	699	NM_001204875	56086	Mm.326055	NM_023871	ENSMUSG00000054766	Set	2610030F17Rik|5730420M11Rik|AA407739|I-2PP2A|StF-IT-1|TAF-I	SET nuclear oncogene	protein-coding
mm_117615.1	chr13	91741747	91741766	-	1	NA	non-coding (NR_028314, exon 1 of 2)	non-coding (NR_028314, exon 1 of 2)	116	NR_015501	373852	Mm.466817	NR_015501	ENSMUSG00000074782	4833422C13Rik	-	RIKEN cDNA 4833422C13 gene	ncRNA
mm_108829.1	chr12	95750244	95750257	+	1	NA	intron (NM_201518, intron 1 of 1)	intron (NM_201518, intron 1 of 1)	58024	NM_201518	399558	Mm.341948	NM_201518	ENSMUSG00000047414	Flrt2	-	fibronectin leucine rich transmembrane protein 2	protein-coding
mm_106480.1	chr11	120164658	120164659	-	1	NA	Intergenic	Intergenic	-13307	NM_001164798	72055	Mm.253403	NM_024249	ENSMUSG00000061306	Slc38a10	1810073N04Rik	solute carrier family 38, member 10	protein-coding
mm_135620.1	chr16	52272054	52272081	-	1	NA	intron (NM_009655, intron 11 of 15)	intron (NM_009655, intron 11 of 15)	181014	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_125709.1	chr15	68395328	68395338	+	1	NA	Intergenic	Intergenic	-54044	NR_029718	387228		NR_029718	ENSMUSG00000065437	Mir30d	Mirn30d|mir-30d|mmu-mir-30d	microRNA 30d	ncRNA
mm_51222.1	chr6	71371356	71371369	+	1	NA	Intergenic	B4A|SINE|B4	-2065	NM_009857	12525	Mm.1858	NM_009857	ENSMUSG00000053977	Cd8a	BB154331|Ly-2|Ly-35|Ly-B|Lyt-2	CD8 antigen, alpha chain	protein-coding
mm_141921.1	chr17	35000809	35000836	-	1	NA	promoter-TSS (NM_011690)	promoter-TSS (NM_011690)	-76	NM_033075	110956	Mm.22506	NM_033075		D17H6S56E-5	G7e	DNA segment, Chr 17, human D6S56E 5	protein-coding
mm_79132.1	chr9	47550373	47550385	+	1	NA	intron (NM_001025600, intron 1 of 8)	intron (NM_001025600, intron 1 of 8)	20027	NM_018770	54725	Mm.234832	NM_018770	ENSMUSG00000032076	Cadm1	2900073G06Rik|3100001I08Rik|AI987920|Bl2|Igsf4|Igsf4a|Necl2|RA175|RA175A|RA175B|RA175C|RA175N|ST17|SgIGSF|SynCam|Tslc1	cell adhesion molecule 1	protein-coding
mm_58511.1	chr7	4129176	4129186	+	1	NA	intron (NR_033548, intron 2 of 2)	intron (NR_033548, intron 2 of 2)	7745	NR_033548	100037396	Mm.447887	NR_033548	ENSMUSG00000085886	D030047H15Rik	Gm15924|OTTMUSG00000027889	RIKEN cDNA D030047H15 gene	ncRNA
mm_139714.1	chr17	57462899	57462913	+	1	NA	intron (NM_010130, intron 18 of 21)	L1M2|LINE|L1	82408	NM_001104591	224916	Mm.469889	NM_001104591	ENSMUSG00000090655	Vmn2r120	EG224916	vomeronasal 2, receptor 120	protein-coding
mm_8317.1	chr1	144330351	144330362	-	1	NA	Intergenic	Intergenic	-81252	NM_015811	50778	Mm.103701	NM_015811	ENSMUSG00000026358	Rgs1	BL34	regulator of G-protein signaling 1	protein-coding
mm_84719.1	chr9	73968902	73968999	-	1	NA	Intergenic	Intergenic	-35383	NM_001081153	208898	Mm.41035	NM_001081153	ENSMUSG00000062151	Unc13c	1500037O19Rik|AU019458|D9Ertd414e|Munc13-3|Unc13h3	unc-13 homolog C (C. elegans)	protein-coding
mm_120059.1	chr14	56811976	56812002	+	1	NA	promoter-TSS (NM_001253752)	promoter-TSS (NM_001253752)	-273	NM_144842	219105	Mm.473172	NM_144842	ENSMUSG00000040123	Zmym5	9830124H08Rik	zinc finger, MYM-type 5	protein-coding
mm_97738.1	chr11	80442699	80442703	+	1	NA	intron (NM_178616, intron 3 of 13)	intron (NM_178616, intron 3 of 13)	14086	NM_178616	69077	Mm.260539	NM_178616	ENSMUSG00000017428	Psmd11	1700089D09Rik|1810019E17Rik|2610024G20Rik|2810055C24Rik|C78232|P44.5|S9	proteasome (prosome, macropain) 26S subunit, non-ATPase, 11	protein-coding
mm_102013.1	chr11	51606868	51606885	-	1	NA	promoter-TSS (NM_010448)	promoter-TSS (NM_010448)	5	NM_001048061	15384	Mm.256875	NM_010448	ENSMUSG00000020358	Hnrnpab	3010025C11Rik|CBF-A|Cgbfa|Hnrpab	heterogeneous nuclear ribonucleoprotein A/B	protein-coding
mm_150686.1	chr19	42091545	42091557	+	1	NA	intron (NM_145501, intron 1 of 8)	intron (NM_145501, intron 1 of 8)	1116	NM_145501	84095	Mm.117037	NM_145501	ENSMUSG00000025178	Pi4k2a	Pi4k2	phosphatidylinositol 4-kinase type 2 alpha	protein-coding
mm_59844.1	chr7	29768547	29768559	+	1	NA	promoter-TSS (NM_023750)	promoter-TSS (NM_023750)	1	NM_023750	74352	Mm.251083	NM_023750	ENSMUSG00000046185	Zfp84	2210410P13Rik|4633401C23Rik|AI415447|BB081605|C86188|KRAB18|Zfp69	zinc finger protein 84	protein-coding
mm_94664.1	chr11	17211878	17211886	+	1	NA	promoter-TSS (NM_178909)	promoter-TSS (NM_178909)	-11	NM_178909	103784	Mm.298132	NM_178909	ENSMUSG00000078970	Wdr92	AI553587|HZGJ	WD repeat domain 92	protein-coding
mm_45761.1	chr5	86891182	86891196	-	1	NA	3' UTR (NM_153598, exon 6 of 6)	3' UTR (NM_153598, exon 6 of 6)	15748	NM_153598	100727	Mm.281844	NM_153598	ENSMUSG00000029260	Ugt2b34	AI788959	UDP glucuronosyltransferase 2 family, polypeptide B34	protein-coding
mm_48908.1	chr6	3989054	3989077	+	1	NA	promoter-TSS (NR_138566)	promoter-TSS (NR_138566)	-207	NR_138566	21789	Mm.25612	NM_009364	ENSMUSG00000029664	Tfpi2	AV000670|PP5/TFPI-2	tissue factor pathway inhibitor 2	protein-coding
mm_135911.1	chr16	67584136	67584140	-	1	NA	intron (NM_178721, intron 1 of 9)	intron (NM_178721, intron 1 of 9)	36770	NM_001347247	239857	Mm.394300	NM_178721	ENSMUSG00000064115	Cadm2	2900078E11Rik|9330131D06|A830029E02Rik|Igdf4d|Igsf4d|NECL3|SynCAM 2|SynCAM2	cell adhesion molecule 2	protein-coding
mm_102636.1	chr11	62550941	62550980	-	1	NA	promoter-TSS (NR_002875).2	promoter-TSS (NR_002875).2	-211	NM_011664	22187	Mm.371592	NM_011664	ENSMUSG00000019505	Ubb	AL033289|Rps27a|Uba52|Ubb2|Ubc	ubiquitin B	protein-coding
mm_61557.1	chr7	79500046	79500066	+	1	NA	promoter-TSS (NR_040314)	promoter-TSS (NR_040314)	30	NR_040313	101694	Mm.41661	NR_040311	ENSMUSG00000097023	Mir9-3hg	AI854517	Mir9-3 host gene	ncRNA
mm_161476.1	chr15	82059014	82059014	+	1	NA	promoter-TSS (NM_001166475)	promoter-TSS (NM_001166475)	-137	NM_001166475	328573	Mm.399189	NM_001166475	ENSMUSG00000075524	4930407I10Rik	Gm747	RIKEN cDNA 4930407I10 gene	protein-coding
mm_153725.1	chr19	44407611	44407623	-	1	NA	promoter-TSS (NM_009127)	promoter-TSS (NM_009127)	92	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_13439.1	chr2	105126753	105126763	+	1	NA	promoter-TSS (NR_015462)	promoter-TSS (NR_015462)	229	NM_144783	22431	Mm.389339	NM_144783	ENSMUSG00000016458	Wt1	D630046I19Rik|Wt-1	Wilms tumor 1 homolog	protein-coding
mm_142335.1	chr17	43557937	43557947	-	1	NA	Intergenic	Intergenic	-10509	NM_013737	27226	Mm.9277	NM_013737	ENSMUSG00000023913	Pla2g7	PAF-AH|R75400	phospholipase A2, group VII (platelet-activating factor acetylhydrolase, plasma)	protein-coding
mm_17718.1	chr2	32387134	32387163	-	1	NA	exon (NM_008491, exon 2 of 6)	exon (NM_008491, exon 2 of 6)	591	NM_008491	16819	Mm.9537	NM_008491	ENSMUSG00000026822	Lcn2	24p3|AW212229|NRL|Sip24	lipocalin 2	protein-coding
mm_136936.1	chr17	14226552	14226569	+	1	NA	Intergenic	Intergenic	-22729	NM_172826	240025	Mm.79993	NM_172826	ENSMUSG00000048826	Dact2	2900084M21Rik|A630024E20|Dpr2|Frd2|dapper2	dishevelled-binding antagonist of beta-catenin 2	protein-coding
mm_105658.1	chr11	107337557	107337598	-	1	NA	intron (NM_145823, intron 1 of 9)	intron (NM_145823, intron 1 of 9)	133143	NM_145823	71795	Mm.397413	NM_145823	ENSMUSG00000040430	Pitpnc1	1110020B03Rik|5830436L09Rik|AI662802|AI851387|C330017I21Rik|Dnr411|RDGBB|RDGBB1|rdgB-beta	phosphatidylinositol transfer protein, cytoplasmic 1	protein-coding
mm_79053.1	chr9	46229823	46229908	+	1	NA	exon (NM_009692, exon 4 of 4)	exon (NM_009692, exon 4 of 4)	1235	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2|apo-AI|apoA-I	apolipoprotein A-I	protein-coding
mm_170177.1	chr17	5798681	5798694	+	1	NA	promoter-TSS (NR_045081)	promoter-TSS (NR_045081)	30	NR_045081	78512	Mm.23696	NR_045079	ENSMUSG00000096965	3300005D01Rik	-	RIKEN cDNA 3300005D01 gene	ncRNA
mm_81898.1	chr9	119895156	119895211	+	1	NA	intron (NM_026236, intron 1 of 18)	CpG	288	NM_026236	67561	Mm.104789	NM_026236	ENSMUSG00000032512	Wdr48	8430408H12Rik|Uaf1|mKIAA1449	WD repeat domain 48	protein-coding
mm_31090.1	chr4	41639359	41639405	+	1	NA	intron (NM_027147, intron 1 of 1)	intron (NM_027147, intron 1 of 1)	920	NM_027147	69638	Mm.372459	NM_027147	ENSMUSG00000028445	Enho	1110065P19Rik|2310040A07Rik	energy homeostasis associated	protein-coding
mm_111835.1	chr12	107912221	107912231	-	1	NA	3' UTR (NM_021399, exon 3 of 3)	3' UTR (NM_021399, exon 3 of 3)	91188	NM_001079883	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_38899.1	chr4	149856467	149856480	-	1	NA	Intergenic	Intergenic	-82206	NM_027460	70556	Mm.41877	NM_027460	ENSMUSG00000028982	Slc25a33	5730438N18Rik|Pnc1	solute carrier family 25, member 33	protein-coding
mm_134186.1	chr16	10963612	10963655	-	1	NA	intron (NM_019980, intron 2 of 3)	L1MB3|LINE|L1	29488	NM_019980	56722	Mm.294753	NM_019980	ENSMUSG00000022500	Litaf	3222402J11Rik|C85531|N4WBP3|TBX1	LPS-induced TN factor	protein-coding
mm_35762.1	chr4	46129347	46129368	-	1	NA	intron (NM_173033, intron 3 of 9)	intron (NM_173033, intron 3 of 9)	9118	NM_173033	272027	Mm.331588	NM_173033	ENSMUSG00000035495	Tstd2	3010020C06	thiosulfate sulfurtransferase (rhodanese)-like domain containing 2	protein-coding
mm_167010.1	chr7	58308227	58308230	-	1	NA	Intergenic	Intergenic	-349974	NM_009728	11982	Mm.135129	NM_009728	ENSMUSG00000025324	Atp10a	Atp10c|pfatp	ATPase, class V, type 10A	protein-coding
mm_42068.1	chr5	109923634	109923664	+	1	NA	Intergenic	Intergenic	-9914	NR_040366	100642166		NR_040366	ENSMUSG00000090015	Gm15446	OTTMUSG00000022004	predicted gene 15446	ncRNA
mm_102307.1	chr11	55608548	55608559	-	1	NA	promoter-TSS (NM_020492)	promoter-TSS (NM_020492)	-355	NM_020492	14654	Mm.89320	NM_020492	ENSMUSG00000000263	Glra1	nmf11|oscillator|ot|spasmodic|spd	glycine receptor, alpha 1 subunit	protein-coding
mm_2938.1	chr1	132299337	132299349	+	1	NA	exon (NM_144810, exon 1 of 5)	exon (NM_144810, exon 1 of 5)	717	NM_144810	213417	Mm.39723	NM_144810	ENSMUSG00000042115	Klhdc8a	A630065K24Rik	kelch domain containing 8A	protein-coding
mm_94492.1	chr11	6688018	6688022	+	1	NA	Intergenic	RMER15|LTR|ERVL	-27784	NR_028586	100041311	Mm.388018	NR_028586	ENSMUSG00000086373	Gm11978	OTTMUSG00000005125|OTTMUSG00000005127	predicted gene 11978	pseudo
mm_757.1	chr1	43933681	43933694	+	1	NA	promoter-TSS (NM_009418)	promoter-TSS (NM_009418)	-307	NM_001310540	22019	Mm.401675	NM_009418	ENSMUSG00000041763	Tpp2	TPP-2|TppII	tripeptidyl peptidase II	protein-coding
mm_43906.1	chr5	144255781	144255802	+	1	NA	intron (NM_018772, intron 1 of 2)	CpG	566	NM_018772	55950	Mm.38011	NM_018772	ENSMUSG00000047843	Bri3	I3	brain protein I3	protein-coding
mm_163652.1	chr13	69534550	69534567	-	1	NA	promoter-TSS (NM_198600)	promoter-TSS (NM_198600)	-694	NM_001169131	210106	Mm.315959	NM_198600	ENSMUSG00000034575	Papd7	LAK-1|POLK|Pols|TRF4|TRF4-1	PAP associated domain containing 7	protein-coding
mm_41676.1	chr5	99687736	99687736	+	1	NA	intron (NR_030692, intron 1 of 3)	intron (NR_030692, intron 1 of 3)	41324	NR_030692	319818	Mm.295233	NR_030692	ENSMUSG00000089809	A930011G23Rik	-	RIKEN cDNA A930011G23 gene	ncRNA
mm_56722.1	chr6	115592544	115592570	-	1	NA	promoter-TSS (NM_001101431)	promoter-TSS (NM_001101431)	19	NM_001101431	70291	Mm.133694	NM_001101431	ENSMUSG00000068011	Mkrn2os	2510049J12Rik	makorin, ring finger protein 2, opposite strand	protein-coding
mm_19795.1	chr2	109913298	109913324	-	1	NA	promoter-TSS (NR_033473)	promoter-TSS (NR_033473)	8	NR_033473	100038454	Mm.365649	NR_033473	ENSMUSG00000063751	Platr8	Gm13939|OTTMUSG00000015136	pluripotency associated transcript 8	ncRNA
mm_156753.1	chrX	160391545	160391572	+	1	NA	intron (NM_001079847, intron 1 of 26)	MER5A1|DNA|hAT-Charlie	868	NM_001290445	237175	Mm.213016	NM_178712	ENSMUSG00000031298	Adgrg2	AW212196|B830041D06Rik|Gpr64|Me6	adhesion G protein-coupled receptor G2	protein-coding
mm_52873.1	chr6	122342676	122342687	+	1	NA	Intergenic	Intergenic	-2454	NM_001271579	13619	Mm.6822	NM_007905	ENSMUSG00000040669	Phc1	AW557034|Edr|Edr1|Mph1|Rae-28|rae28	polyhomeotic-like 1 (Drosophila)	protein-coding
mm_51759.1	chr6	87810968	87810982	+	1	NA	intron (NR_104478, intron 1 of 2)	intron (NR_104478, intron 1 of 2)	804	NM_001039394	69834	Mm.37380	NM_133717	ENSMUSG00000030055	Rab43	1810048P08Rik|2500004H21Rik|AW490415	RAB43, member RAS oncogene family	protein-coding
mm_56658.1	chr6	113435749	113435764	-	1	NA	promoter-TSS (NM_178373)	promoter-TSS (NM_178373)	-1	NM_178373	14311	Mm.10026	NM_178373	ENSMUSG00000030278	Cidec	CIDE-3|Fsp27	cell death-inducing DFFA-like effector c	protein-coding
mm_63688.1	chr7	130574956	130574973	+	1	NA	Intergenic	Intergenic	-2520	NM_001004468	57752	Mm.86322	NM_021314	ENSMUSG00000030852	Tacc2	mKIAA4180	transforming, acidic coiled-coil containing protein 2	protein-coding
mm_103636.1	chr11	78951165	78951185	-	1	NA	exon (NM_010927, exon 21 of 27)	exon (NM_010927, exon 21 of 27)	25884	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_10225.1	chr2	6294344	6294349	+	1	NA	intron (NR_040333, intron 4 of 6)	intron (NR_040333, intron 4 of 6)	-28411	NM_001080548	98910	Mm.40673	NM_181399	ENSMUSG00000039046	Usp6nl	AI316785|RNTRE|TRE2NL|mKIAA0019	USP6 N-terminal like	protein-coding
mm_35664.1	chr4	43562262	43562272	-	1	NA	promoter-TSS (NM_013497)	promoter-TSS (NM_013497)	316	NM_011602	21894	Mm.208601	NM_011602	ENSMUSG00000028465	Tln1	Tln	talin 1	protein-coding
mm_19126.1	chr2	80129161	80129173	-	1	NA	promoter-TSS (NM_016744)	promoter-TSS (NM_016744)	-196	NM_016744	18573	Mm.40678	NM_016744	ENSMUSG00000059173	Pde1a	AI987702|AW125737	phosphodiesterase 1A, calmodulin-dependent	protein-coding
mm_45833.1	chr5	87694699	87694720	-	1	NA	exon (NM_001286023, exon 5 of 7)	exon (NM_001286023, exon 5 of 7)	4716	NM_001286020	12991	Mm.268737	NM_009972	ENSMUSG00000063157	Csn2	Csnb	casein beta	protein-coding
mm_127409.1	chr15	101254487	101254497	+	1	NA	Intergenic	Intergenic	-12354	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_82932.1	chr9	35185464	35185467	-	1	NA	3' UTR (NM_001177847, exon 7 of 7)	3' UTR (NM_001177847, exon 7 of 7)	-9478	NM_027030	69305	Mm.229110	NM_027030	ENSMUSG00000032040	Dcps	1700001E16Rik|AA408441	decapping enzyme, scavenger	protein-coding
mm_45141.1	chr5	49112590	49112600	-	1	NA	intron (NM_001199244, intron 1 of 7)	intron (NM_001199244, intron 1 of 7)	173064	NM_001199244	80334	Mm.160172	NM_030265	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding
mm_146706.1	chr18	13972186	13972188	-	1	NA	intron (NM_145492, intron 1 of 7)	intron (NM_145492, intron 1 of 7)	546	NM_145492	225207	Mm.40325	NM_145492	ENSMUSG00000024420	Zfp521	B930086A16Rik|Evi3|Znf521	zinc finger protein 521	protein-coding
mm_78109.1	chr9	20581425	20581458	+	1	NA	5' UTR (NM_172919, exon 1 of 6)	5' UTR (NM_172919, exon 1 of 6)	113	NM_172919	244721	Mm.86627	NM_172919	ENSMUSG00000058192	Zfp846	2210010B09Rik|9130221F13|Znf846	zinc finger protein 846	protein-coding
mm_95735.1	chr11	54645081	54645083	+	1	NA	intron (NM_175258, intron 16 of 27)	B1F1|SINE|Alu	48936	NM_001252497	192786	Mm.254404	NM_175258	ENSMUSG00000037533	Rapgef6	A530068K01|AI844632|BB085664|C030018K18Rik|PDZ-GEF2|Pdzgef2|RA-GEF-2|Ragef2|mKIAA4052	Rap guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_148192.1	chr18	79021161	79021162	-	1	NA	intron (NM_053099, intron 2 of 5)	intron (NM_053099, intron 2 of 5)	88230	NM_053099	240427	Mm.312871	NM_053099	ENSMUSG00000024548	Setbp1	C130092E12|Seb|mKIAA0437	SET binding protein 1	protein-coding
mm_60769.1	chr7	45554949	45554961	+	1	NA	promoter-TSS (NM_025330)	promoter-TSS (NM_025330)	27	NM_025330	66065	Mm.285710	NM_025330	ENSMUSG00000030825	Hsd17b14	0610039E24Rik|Dhrs10|retSDR3	hydroxysteroid (17-beta) dehydrogenase 14	protein-coding
mm_68787.1	chr7	123312477	123312500	-	1	NA	intron (NM_001316713, intron 8 of 19)	B2_Mm2|SINE|B2	57427	NM_001122643	70497	Mm.403318	NM_144529	ENSMUSG00000030766	Arhgap17	5730403H17Rik|Nadrin|Nadrin2|Rich1|Wbp15	Rho GTPase activating protein 17	protein-coding
mm_53597.1	chr6	138141570	138141617	+	1	NA	promoter-TSS (NM_001347489)	promoter-TSS (NM_001347489)	-1	NM_001347489	56615	Mm.14796	NM_019946	ENSMUSG00000008540	Mgst1	1500002K10Rik|Gst	microsomal glutathione S-transferase 1	protein-coding
mm_22062.1	chr2	168670053	168670084	-	1	NA	intron (NM_001289446, intron 13 of 27)	intron (NM_001289446, intron 13 of 27)	-29309	NR_105971	102466784		NR_105971	ENSMUSG00000105496	Mir7004	mmu-mir-7004	microRNA 7004	ncRNA
mm_23050.1	chr3	35545881	35545883	+	1	NA	Intergenic	Intergenic	120281	NR_040748	625963	Mm.251506	NR_040748	ENSMUSG00000105662	Gm6639	-	predicted gene 6639	ncRNA
mm_168333.1	chr11	118304480	118304481	+	1	NA	intron (NM_011594, intron 4 of 4)	MMERVK9C_I-int|LTR|ERVK	-14236	NM_001033528	72344	Mm.232293	NM_001033528	ENSMUSG00000033909	Usp36	2700002L06Rik|mKIAA1453	ubiquitin specific peptidase 36	protein-coding
mm_49473.1	chr6	29526666	29526676	+	1	NA	promoter-TSS (NM_012057)	promoter-TSS (NM_012057)	46	NM_012057	27056	Mm.6479	NM_012057	ENSMUSG00000029771	Irf5	AW491843|mirf5	interferon regulatory factor 5	protein-coding
mm_145592.1	chr18	60986063	60986071	+	1	NA	3' UTR (NM_001286809, exon 6 of 6)	3' UTR (NM_001286809, exon 6 of 6)	22513	NM_001286809	12322	Mm.131530	NM_009792	ENSMUSG00000024617	Camk2a	CaMKII|R74975|mKIAA0968	calcium/calmodulin-dependent protein kinase II alpha	protein-coding
mm_144939.1	chr18	37751602	37751652	+	1	NA	promoter-TSS (NM_033579)	promoter-TSS (NM_033579)	-152	NM_033579	93704	Mm.247203	NM_033579	ENSMUSG00000104063	Pcdhgb7	-	protocadherin gamma subfamily B, 7	protein-coding
mm_136631.1	chr17	5685678	5685689	+	1	NA	exon (NM_146073, exon 3 of 9)	exon (NM_146073, exon 3 of 9)	-112974	NR_045081	78512	Mm.23696	NR_045079	ENSMUSG00000096965	3300005D01Rik	-	RIKEN cDNA 3300005D01 gene	ncRNA
mm_140796.1	chr17	21463453	21463457	-	1	NA	exon (NM_009558, exon 5 of 5)	exon (NM_009558, exon 5 of 5)	13081	NM_009558	22709	Mm.293030	NM_009558	ENSMUSG00000023892	Zfp51	Zfp-51|zfec12	zinc finger protein 51	protein-coding
mm_149144.1	chr19	9004420	9004446	+	1	NA	exon (NM_009643, exon 5 of 5)	exon (NM_009643, exon 5 of 5)	-13471	NR_105786	102465190		NR_105786	ENSMUSG00000099308	Mir6367	Gm27467|mmu-mir-6367	microRNA 6367	ncRNA
mm_51845.1	chr6	90333271	90333306	+	1	NA	promoter-TSS (NM_144940)	promoter-TSS (NM_144940)	-1	NM_001347329	243537	Mm.335669	NM_144940	ENSMUSG00000034456	Uroc1	AI265605|BC022133	urocanase domain containing 1	protein-coding
mm_58283.1	chr6	145862786	145862827	-	1	NA	3' UTR (NM_001271768, exon 5 of 5)	3' UTR (NM_001271768, exon 5 of 5)	2614	NM_001271768	79362	Mm.154529	NM_024469	ENSMUSG00000030256	Bhlhe41	6430520M22Rik|Bhlhb2l|Bhlhb3|DEC2|Sharp1	basic helix-loop-helix family, member e41	protein-coding
mm_55863.1	chr6	83456532	83456569	-	1	NA	promoter-TSS (NM_001347313)	promoter-TSS (NM_001347313)	-158	NM_001347313	194388	Mm.211030	NM_183138	ENSMUSG00000034832	Tet3	B430006D22Rik|BC037432|D230004J03Rik	tet methylcytosine dioxygenase 3	protein-coding
mm_111280.1	chr12	85350581	85350585	-	1	NA	intron (NM_026775, intron 3 of 4)	intron (NM_026775, intron 3 of 4)	-11221	NM_145138	217718	Mm.29071	NM_145138	ENSMUSG00000034290	Nek9	C130021H08Rik	NIMA (never in mitosis gene a)-related expressed kinase 9	protein-coding
mm_37258.1	chr4	118437232	118437240	-	1	NA	5' UTR (NM_023223, exon 1 of 10)	5' UTR (NM_023223, exon 1 of 10)	107	NM_023223	107995	Mm.261764	NM_023223	ENSMUSG00000006398	Cdc20	2310042N09Rik|C87100|p55CDC	cell division cycle 20	protein-coding
mm_160473.1	chr8	117349167	117349167	+	1	NA	promoter-TSS (NM_028941)	promoter-TSS (NM_028941)	-3	NM_028941	74440	Mm.233181	NM_028941	ENSMUSG00000034390	Cmip	4933407C03Rik|5830471E12Rik|AI314065|AI464126	c-Maf inducing protein	protein-coding
mm_158292.1	chrX	112698643	112698657	-	1	NA	promoter-TSS (NM_181579)	promoter-TSS (NM_181579)	1	NM_181579	69693	Mm.34964	NM_181579	ENSMUSG00000034607	Pof1b	2310066B14Rik	premature ovarian failure 1B	protein-coding
mm_70584.1	chr8	13167900	13167927	+	1	NA	exon (NM_010684, exon 4 of 9)	exon (NM_010684, exon 4 of 9)	8752	NM_010684	16783	Mm.16716	NM_010684	ENSMUSG00000031447	Lamp1	CD107a|LGP-120|LGP-A|Lamp-1|P2B	lysosomal-associated membrane protein 1	protein-coding
mm_59518.1	chr7	27592777	27592790	+	1	NA	intron (NM_001110208, intron 1 of 13)	intron (NM_001110208, intron 1 of 13)	1231	NM_001110208	11652	Mm.177194	NM_007434	ENSMUSG00000004056	Akt2	2410016A19Rik|AW554154|PKB|PKBbeta	thymoma viral proto-oncogene 2	protein-coding
mm_86338.1	chr9	123215943	123216016	-	1	NA	promoter-TSS (NM_133974)	promoter-TSS (NM_133974)	59	NM_133974	109332	Mm.27519	NM_133974	ENSMUSG00000035498	Cdcp1	9030022E12Rik|AA409659|E030027H19Rik	CUB domain containing protein 1	protein-coding
mm_106908.1	chr12	8015815	8015826	+	1	NA	exon (NM_009693, exon 29 of 29)	exon (NM_009693, exon 29 of 29)	38143	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_136606.1	chr17	5242991	5242999	+	1	NA	exon (NM_001085355, exon 5 of 20)	exon (NM_001085355, exon 5 of 20)	175772	NM_175349	106557	Mm.432764	NM_175349	ENSMUSG00000101959	Ldhal6b	4933402O15Rik|AI326310|LDHL|Ldhal	lactate dehydrogenase A-like 6B	protein-coding
mm_34.1	chr1	6249703	6249714	+	1	NA	exon (NM_009826, exon 15 of 24)	exon (NM_009826, exon 15 of 24)	35046	NM_009826	12421	Mm.293811	NM_009826	ENSMUSG00000025907	Rb1cc1	2900055E04Rik|5930404L04Rik|Cc1|FIP200|LaXp180	RB1-inducible coiled-coil 1	protein-coding
mm_158695.1	chrX	161777848	161777855	-	1	NA	exon (NM_198409, exon 2 of 2)	exon (NM_198409, exon 2 of 2)	60298	NM_198409	24004	Mm.328503	NM_198409	ENSMUSG00000043518	Rai2	3f8	retinoic acid induced 2	protein-coding
mm_84399.1	chr9	65552356	65552366	-	1	NA	TTS (NM_153119)	TTS (NM_153119)	27726	NM_153119	102595	Mm.247303	NM_153119	ENSMUSG00000050721	Plekho2	AI840980|Plekhq1	pleckstrin homology domain containing, family O member 2	protein-coding
mm_37298.1	chr4	119218166	119218183	-	1	NA	promoter-TSS (NM_029198)	promoter-TSS (NM_029198)	43	NM_029198	75180	Mm.179335	NM_029198	ENSMUSG00000028642	Tmem269	4930538K18Rik	transmembrane protein 269	protein-coding
mm_41759.1	chr5	102860046	102860054	+	1	NA	intron (NM_001346585, intron 1 of 6)	intron (NM_001346585, intron 1 of 6)	15043	NM_001346585	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding
mm_167862.1	chrX	19704021	19704023	+	1	NA	Intergenic	Lx|LINE|L1	-355548	NM_021715	60322	Mm.44827	NM_021715	ENSMUSG00000037347	Chst7	2600013M07Rik|C6ST-2|GST5|Gn6st-4|glcNAc6ST-4	carbohydrate (N-acetylglucosamino) sulfotransferase 7	protein-coding
mm_21610.1	chr2	164254711	164254721	-	1	NA	3' UTR (NM_173377, exon 3 of 3)	3' UTR (NM_173377, exon 3 of 3)	1927	NM_173377	329557	Mm.118769	NM_173377	ENSMUSG00000050383	Svs3b	9530004A22Rik	seminal vesicle secretory protein 3B	protein-coding
mm_153305.1	chr19	38022735	38022752	-	1	NA	intron (NM_001302140, intron 2 of 53)	intron (NM_001302140, intron 2 of 53)	20834	NM_001099634	226101	Mm.34674	NM_177035	ENSMUSG00000048612	Myof	2310004N10Rik|2310051D19Rik|E030042N20Rik|Fer1l3	myoferlin	protein-coding
mm_117561.1	chr13	85258358	85258376	-	1	NA	exon (NM_145452, exon 2 of 25)	exon (NM_145452, exon 2 of 25)	31119	NM_145452	218397	Mm.259653	NM_145452	ENSMUSG00000021549	Rasa1	Gap|RasGAP|Rasa	RAS p21 protein activator 1	protein-coding
mm_81972.1	chr9	121128508	121128511	+	1	NA	intron (NM_177589, intron 30 of 36)	intron (NM_177589, intron 30 of 36)	148663	NM_177589	209012	Mm.371804	NM_177589	ENSMUSG00000040936	Ulk4	4932415A06Rik|A730098P15	unc-51-like kinase 4	protein-coding
mm_136435.1	chr16	94370995	94371019	-	1	NA	promoter-TSS (NM_001159620)	promoter-TSS (NM_001159620)	8	NM_019543	56176	Mm.474449	NM_019543	ENSMUSG00000022940	Pigp	Dcrc|Dscr5	phosphatidylinositol glycan anchor biosynthesis, class P	protein-coding
mm_127440.1	chr15	101270364	101270384	+	1	NA	exon (NM_010444, exon 2 of 7)	exon (NM_010444, exon 2 of 7)	3528	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_104593.1	chr11	97048368	97048385	-	1	NA	3' UTR (NM_026154, exon 5 of 5)	3' UTR (NM_026154, exon 5 of 5)	-2252	NM_001310509	71240	Mm.190450	NM_001081434	ENSMUSG00000038534	Osbpl7	4933437E18Rik	oxysterol binding protein-like 7	protein-coding
mm_157699.1	chrX	60727490	60727501	-	1	NA	Intergenic	Intergenic	165935	NM_009237	20675	Mm.35784	NM_009237	ENSMUSG00000045179	Sox3	Sox-3	SRY (sex determining region Y)-box 3	protein-coding
mm_18648.1	chr2	69586022	69586037	-	1	NA	promoter-TSS (NM_001081088)	promoter-TSS (NM_001081088)	38	NM_001081088	14725	Mm.23847	NM_001081088	ENSMUSG00000027070	Lrp2	AI315343|AW536255|D230004K18Rik|Gp330|Megalin|b2b1625.2Clo	low density lipoprotein receptor-related protein 2	protein-coding
mm_81450.1	chr9	109816619	109816639	+	1	NA	promoter-TSS (NM_183136)	promoter-TSS (NM_183136)	2	NM_183136	78709	Mm.99613	NM_183136	ENSMUSG00000050074	Spink8	C630041L24Rik	serine peptidase inhibitor, Kazal type 8	protein-coding
mm_57930.1	chr6	134566862	134566875	-	1	NA	promoter-TSS (NM_008514)	promoter-TSS (NM_008514)	45	NM_008514	16974	Mm.321990	NM_008514	ENSMUSG00000030201	Lrp6	C030016K15Rik|Cd|Gw|ska26|ska<m26Jus>|skax26	low density lipoprotein receptor-related protein 6	protein-coding
mm_169153.1	chr13	63222907	63222923	-	1	NA	intron (NM_001289926, intron 11 of 15)	IAPLTR1_Mm|LTR|ERVK	-17114	NR_110520	72061	Mm.188105	NM_028079	ENSMUSG00000021458	2010111I01Rik	2300006M17Rik|AP-O|AW742919|Aopep|ApO|mir-23b|mir-24-1|mir-27b	RIKEN cDNA 2010111I01 gene	protein-coding
mm_115337.1	chr13	112488574	112488610	+	1	NA	exon (NM_010560, exon 7 of 17)	exon (NM_010560, exon 7 of 17)	24522	NM_010560	16195	Mm.4364	NM_010560	ENSMUSG00000021756	Il6st	5133400A03Rik|AA389424|BB405851|CD130|D13Ertd699e|gp130	interleukin 6 signal transducer	protein-coding
mm_34688.1	chr4	151933707	151933715	+	1	NA	promoter-TSS (NM_172704)	promoter-TSS (NM_172704)	-9	NM_172704	230935	Mm.21353	NM_172704	ENSMUSG00000039768	Dnajc11	E030019A03Rik	DnaJ heat shock protein family (Hsp40) member C11	protein-coding
mm_152919.1	chr19	28010019	28010028	-	1	NA	intron (NM_011265, intron 1 of 16)	intron (NM_011265, intron 1 of 16)	1143	NM_011265	19726	Mm.313321	NM_011265	ENSMUSG00000040929	Rfx3	C230093O12Rik|MRFX3	regulatory factor X, 3 (influences HLA class II expression)	protein-coding
mm_56180.1	chr6	88225677	88225688	-	1	NA	Intergenic	Intergenic	3414	NM_019964	56691	Mm.272871	NM_019964	ENSMUSG00000048206	Dnajb8	1700016F14Rik|1700031F10Rik|AI326313|mDj6	DnaJ heat shock protein family (Hsp40) member B8	protein-coding
mm_83711.1	chr9	50746476	50746494	-	1	NA	promoter-TSS (NM_025865)	promoter-TSS (NM_025865)	36	NM_025865	66952	Mm.273375	NM_025865	ENSMUSG00000032062	2310030G06Rik	2610024D04Rik|AV017521	RIKEN cDNA 2310030G06 gene	protein-coding
mm_1538.1	chr1	72852025	72852060	+	1	NA	exon (NM_008342, exon 4 of 4)	exon (NM_008342, exon 4 of 4)	22823	NM_010518	16011	Mm.405761	NM_010518	ENSMUSG00000026185	Igfbp5	AI256729|AW208790|IGFBP-5|IGFBP-5P	insulin-like growth factor binding protein 5	protein-coding
mm_26141.1	chr3	138000870	138000909	+	1	NA	Intergenic	Intergenic	-19340	NM_001310753	26377	Mm.254835	NM_011932	ENSMUSG00000028159	Dapp1	Bam32	dual adaptor for phosphotyrosine and 3-phosphoinositides 1	protein-coding
mm_35549.1	chr4	41507742	41507775	-	1	NA	promoter-TSS (NM_001253780)	promoter-TSS (NM_001253780)	6	NM_028624	73721	Mm.45614	NM_028624	ENSMUSG00000028441	1110017D15Rik	Cbe1|Smrp1	RIKEN cDNA 1110017D15 gene	protein-coding
mm_120831.1	chr14	75176793	75176797	+	1	NA	intron (NM_008879, intron 1 of 16)	intron (NM_008879, intron 1 of 16)	40370	NM_008879	18826	Mm.153911	NM_008879	ENSMUSG00000021998	Lcp1	AW536232|D14Ertd310e|LCP-1|Pls2|pp65	lymphocyte cytosolic protein 1	protein-coding
mm_161171.1	chr13	38036967	38036967	-	1	NA	promoter-TSS (NM_027724)	promoter-TSS (NM_027724)	-22	NM_024242	71340	Mm.297130	NM_024242	ENSMUSG00000021428	Riok1	3110046C13Rik|5430416A05Rik|Ad034	RIO kinase 1 (yeast)	protein-coding
mm_106795.1	chr12	4843317	4843419	+	1	NA	promoter-TSS (NM_001170858)	promoter-TSS (NM_001170858)	65	NM_001170858	238037	Mm.146087	NM_173416	ENSMUSG00000051721	BC068281	A430092C04|Wdcp	cDNA sequence BC068281	protein-coding
mm_168314.1	chr11	109011987	109011987	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	91638	NM_015732	12006	Mm.71710	NM_015732	ENSMUSG00000000142	Axin2	Axi1|Axil|Conductin	axin 2	protein-coding
mm_49303.1	chr6	17749173	17749265	+	1	NA	promoter-TSS (NM_001083315)	promoter-TSS (NM_001083315)	49	NM_022332	64213	Mm.12051	NM_022332	ENSMUSG00000029534	St7	9430001H04Rik|Fam4a2|HELG|RAY1|SEN4|TSG7	suppression of tumorigenicity 7	protein-coding
mm_91632.1	chr10	42182448	42182451	-	1	NA	Intergenic	AT_rich|Low_complexity|Low_complexity	94293	NM_019740	56484	Mm.338613	NM_019740	ENSMUSG00000048756	Foxo3	1110048B16Rik|2010203A17Rik|C76856|FKHRL1|Fkhr2|Foxo3a	forkhead box O3	protein-coding
mm_65454.1	chr7	25463483	25463517	-	1	NA	3' UTR (NM_001039186, exon 8 of 8)	3' UTR (NM_001039186, exon 8 of 8)	14125	NM_001039185	26365	Mm.322502	NM_011926	ENSMUSG00000074272	Ceacam1	Bgp|Bgp1|C-CAM|CD66a|Cc1|Cea-1|Cea-7|Cea1|Cea7|Hv-2|Hv2|MHVR|MHVR1|Mhv-1|bb-1|mCEA1|mmCGM1|mmCGM1a|mmCGM2	carcinoembryonic antigen-related cell adhesion molecule 1	protein-coding
mm_97321.1	chr11	76904514	76904569	+	1	NA	promoter-TSS (NM_025655)	promoter-TSS (NM_025655)	-4	NM_025655	66601	Mm.25138	NM_025655	ENSMUSG00000020839	Tmigd1	2010002A20Rik|Tmigd	transmembrane and immunoglobulin domain containing 1	protein-coding
mm_164231.1	chr15	89384861	89384867	+	1	NA	Intergenic	Intergenic	-2027	NM_001160178	546648	Mm.478787	NM_001160178	ENSMUSG00000091680	Klhdc7b	EG546648|Gm306	kelch domain containing 7B	protein-coding
mm_114831.1	chr13	92355213	92355217	+	1	NA	promoter-TSS (NM_010829)	promoter-TSS (NM_010829)	-212	NM_010829	17686	Mm.343101	NM_010829	ENSMUSG00000014850	Msh3	D13Em1|Rep-3|Rep3	mutS homolog 3	protein-coding
mm_120614.1	chr14	70242447	70242460	+	1	NA	intron (NM_001304991, intron 6 of 14)	intron (NM_001304991, intron 6 of 14)	-34782	NM_011366	20410	Mm.5068	NM_011366	ENSMUSG00000022091	Sorbs3	SCAM-1|SH3P3|Sh3d4|vinexin-g	sorbin and SH3 domain containing 3	protein-coding
mm_23717.1	chr3	69005441	69005485	+	1	NA	promoter-TSS (NM_026641)	promoter-TSS (NM_026641)	491	NM_133786	70099	Mm.206841	NM_133786	ENSMUSG00000034349	Smc4	2500002A22Rik|C79747|SMC-4|Smc4l1	structural maintenance of chromosomes 4	protein-coding
mm_46586.1	chr5	107721117	107721120	-	1	NA	intron (NM_001267621, intron 5 of 6)	CpG	3225	NM_010278	14581	Mm.2078	NM_010278	ENSMUSG00000029275	Gfi1	AW495828|Gfi-1|Pal-1|Pal1	growth factor independent 1	protein-coding
mm_131577.1	chr16	18392632	18392643	+	1	NA	promoter-TSS (NM_001272032)	promoter-TSS (NM_001272032)	74	NM_001272032	11877	Mm.293599	NM_033474	ENSMUSG00000000325	Arvcf	-	armadillo repeat gene deleted in velo-cardio-facial syndrome	protein-coding
mm_123412.1	chr14	64085401	64085415	-	1	NA	promoter-TSS (NM_001081063)	promoter-TSS (NM_001081063)	-19	NM_001081063	71037	Mm.19977	NM_001081063	ENSMUSG00000034623	Prss55	4933401F05Rik	protease, serine 55	protein-coding
mm_122853.1	chr14	54781935	54781952	-	1	NA	promoter-TSS (NM_016972)	promoter-TSS (NM_016972)	-57	NM_016972	50934	Mm.276831	NM_016972	ENSMUSG00000022180	Slc7a8	AA408822|LAT2	solute carrier family 7 (cationic amino acid transporter, y+ system), member 8	protein-coding
mm_124744.1	chr15	6599722	6599724	+	1	NA	intron (NM_011815, intron 1 of 17)	intron (NM_011815, intron 1 of 17)	19876	NM_011815	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_60814.1	chr7	45699797	45699814	+	1	NA	promoter-TSS (NM_009800)	promoter-TSS (NM_009800)	-162	NM_009800	12348	Mm.27736	NM_009800	ENSMUSG00000003273	Car11	Ca11	carbonic anhydrase 11	protein-coding
mm_42310.1	chr5	114853661	114853667	+	1	NA	promoter-TSS (NM_026263)	promoter-TSS (NM_026263)	-50	NM_026263	67593	Mm.251409	NM_026263	ENSMUSG00000029564	4930519G04Rik	1700014B12Rik	RIKEN cDNA 4930519G04 gene	protein-coding
mm_101723.1	chr11	42182448	42182466	-	1	NA	5' UTR (NM_010250, exon 1 of 10)	5' UTR (NM_010250, exon 1 of 10)	473	NM_010250	14394	Mm.439668	NM_010250	ENSMUSG00000010803	Gabra1	Gabra-1	gamma-aminobutyric acid (GABA) A receptor, subunit alpha 1	protein-coding
mm_123058.1	chr14	55660274	55660314	-	1	NA	intron (NM_023397, intron 1 of 5)	CpG	214	NM_023397	67881	Mm.24601	NM_023397	ENSMUSG00000002329	Mdp1	1810034K20Rik|AI035604	magnesium-dependent phosphatase 1	protein-coding
mm_33246.1	chr4	127035669	127035678	+	1	NA	intron (NR_045010, intron 9 of 11)	(T)n|Simple_repeat|Simple_repeat	14372	NM_023603	71514	Mm.257276	NM_023603	ENSMUSG00000028820	Sfpq	1110004P21Rik|2810416M14Rik|5730453G22Rik|9030402K04Rik|AU021830|D4Ertd314e|Gm12940|OTTMUSG00000009329|PSF|REP1	splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)	protein-coding
mm_34050.1	chr4	138250426	138250461	+	1	NA	promoter-TSS (NM_001099631)	promoter-TSS (NM_001099631)	32	NM_001099631	230863	Mm.482408	NM_001099631	ENSMUSG00000045349	Sh2d5	BC036961	SH2 domain containing 5	protein-coding
mm_135837.1	chr16	58523759	58523810	-	1	NA	promoter-TSS (NM_018784)	promoter-TSS (NM_018784)	-472	NM_018784	54613	Mm.212742	NM_018784	ENSMUSG00000022747	St3gal6	1700023B24Rik|AI930218|AW552396|Siat10|St3galVI	ST3 beta-galactoside alpha-2,3-sialyltransferase 6	protein-coding
mm_35805.1	chr4	46648781	46648792	-	1	NA	intron (NM_198664, intron 1 of 12)	intron (NM_198664, intron 1 of 12)	1413	NM_198664	381605	Mm.331595	NM_198664	ENSMUSG00000039813	Tbc1d2	A630005A06Rik|BC022630|Gm1037|PARIS-1|PARIS1	TBC1 domain family, member 2	protein-coding
mm_86122.1	chr9	116173103	116173106	-	1	NA	intron (NM_009371, intron 1 of 7)	intron (NM_009371, intron 1 of 7)	2259	NM_029575	21813	Mm.172346	NM_009371	ENSMUSG00000032440	Tgfbr2	1110020H15Rik|AU042018|DNIIR|RIIDN|TBR-II|TbetaR-II|TbetaRII	transforming growth factor, beta receptor II	protein-coding
mm_145531.1	chr18	60774676	60774686	+	1	NA	promoter-TSS (NM_020600)	promoter-TSS (NM_020600)	85	NM_020600	20044	Mm.43778	NM_020600	ENSMUSG00000024608	Rps14	2600014J02Rik|AL023078	ribosomal protein S14	protein-coding
mm_70991.1	chr8	27368794	27368807	+	1	NA	promoter-TSS (NM_027454)	promoter-TSS (NM_027454)	89	NM_173212	108043	Mm.110444	NM_027454	ENSMUSG00000031492	Chrnb3	5730417K16Rik|Acrb3	cholinergic receptor, nicotinic, beta polypeptide 3	protein-coding
mm_27658.1	chr3	64844718	64844728	-	1	NA	promoter-TSS (NR_003962)	promoter-TSS (NR_003962)	20	NR_003962	319210	Mm.246646	NM_175670	ENSMUSG00000097538	Vmn2r-ps11	4930518C23Rik	vomeronasal 2, receptor, pseudogene 11	pseudo
mm_106722.1	chr12	3861005	3861028	+	1	NA	intron (NR_045884, intron 3 of 3)	ID_B1|SINE|B4	1228	NR_045884	100038522	Mm.417270	NR_045884	ENSMUSG00000073242	Dnmt3aos	ENSMUSG00000073242|Gm10485	DNA methyltransferase 3A, opposite strand	ncRNA
mm_151349.1	chr19	55897914	55897931	+	1	NA	intron (NM_001142924, intron 1 of 11)	intron (NM_001142924, intron 1 of 11)	2601	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_109628.1	chr12	112767485	112767514	+	1	NA	exon (NM_178911, exon 8 of 11)	exon (NM_178911, exon 8 of 11)	6844	NM_178911	104759	Mm.203915	NM_178911	ENSMUSG00000052160	Pld4	AI132321|thss	phospholipase D family, member 4	protein-coding
mm_84454.1	chr9	66518645	66518653	-	1	NA	intron (NM_001302122, intron 12 of 12)	intron (NM_001302122, intron 12 of 12)	-4056	NM_175206	74165	Mm.297998	NM_175206	ENSMUSG00000050503	Fbxl22	1110004B15Rik	F-box and leucine-rich repeat protein 22	protein-coding
mm_41814.1	chr5	103784234	103784275	+	1	NA	exon (NM_133919, exon 3 of 20)	exon (NM_133919, exon 3 of 20)	29681	NM_001080798	17355	Mm.6949	NM_133919	ENSMUSG00000029313	Aff1	9630032B01Rik|AW319193|Af4|Mllt2h|Rob	AF4/FMR2 family, member 1	protein-coding
mm_38750.1	chr4	145315144	145315169	-	1	NA	promoter-TSS (NM_009401)	promoter-TSS (NM_009401)	-9	NM_009401	21941	Mm.12810	NM_009401	ENSMUSG00000028602	Tnfrsf8	Cd30|D1S166E|Ki|Ki-1	tumor necrosis factor receptor superfamily, member 8	protein-coding
mm_119191.1	chr14	32492864	32492885	+	1	NA	Intergenic	Intergenic	-20647	NM_001081221	319955	Mm.318310	NM_177043	ENSMUSG00000054051	Ercc6	4732403I04|C130058G22Rik|CSB	excision repair cross-complementing rodent repair deficiency, complementation group 6	protein-coding
mm_151847.1	chr19	5771344	5771371	-	1	NA	promoter-TSS (NM_023912)	promoter-TSS (NM_023912)	44	NM_023912	78891	Mm.276063	NM_023912	ENSMUSG00000024941	Scyl1	2810011O19Rik|C85140|Ntkl|mdf|mfd|p105	SCY1-like 1 (S. cerevisiae)	protein-coding
mm_32020.1	chr4	95054092	95054092	+	1	NA	Intergenic	Intergenic	-1870	NM_010591	16476	Mm.275071	NM_010591	ENSMUSG00000052684	Jun	AP-1|Junc|c-jun	jun proto-oncogene	protein-coding
mm_80458.1	chr9	77983155	77983165	+	1	NA	3' UTR (NM_134255, exon 8 of 8)	3' UTR (NM_134255, exon 8 of 8)	65795	NM_134255	68801	Mm.430736	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	ELOVL family member 5, elongation of long chain fatty acids (yeast)	protein-coding
mm_124979.1	chr15	20538381	20538400	+	1	NA	Intergenic	Intergenic	128360	NM_022816	64833	Mm.352763	NM_022816	ENSMUSG00000047565	Acot10	Acate3|MT-ACT48|p48	acyl-CoA thioesterase 10	protein-coding
mm_118922.1	chr14	26969911	26969964	+	1	NA	intron (NM_145221, intron 1 of 21)	CpG	614	NM_145221	72993	Mm.202322	NM_145221	ENSMUSG00000040760	Appl1	2900057D21Rik|7330406P05Rik|AI585782|AW209077|BB022931|C88264|DIP13	adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 1	protein-coding
mm_86958.1	chr10	25000007	25000029	+	1	NA	Intergenic	Intergenic	-72548	NM_007482	11846	Mm.154144	NM_007482	ENSMUSG00000019987	Arg1	AI|AI256583|Arg-1|PGIF	arginase, liver	protein-coding
mm_128615.1	chr15	58823632	58823643	-	1	NA	promoter-TSS (NM_175212)	promoter-TSS (NM_175212)	-210	NM_175212	74868	Mm.293754	NM_175212	ENSMUSG00000062373	Tmem65	2610029O13Rik|4930438D12Rik	transmembrane protein 65	protein-coding
mm_80710.1	chr9	92250196	92250274	+	1	NA	promoter-TSS (NM_011636)	promoter-TSS (NM_011636)	41	NM_011636	22038	Mm.421956	NM_011636	ENSMUSG00000032369	Plscr1	MmTRA1a|MmTRA1b|Nor1|Tra1|Tra1a|Tra1b|Tras1|Tras2	phospholipid scramblase 1	protein-coding
mm_160472.1	chr8	117256771	117256771	+	1	NA	promoter-TSS (NM_001163262)	promoter-TSS (NM_001163262)	-248	NM_001163262	74440	Mm.233181	NM_028941	ENSMUSG00000034390	Cmip	4933407C03Rik|5830471E12Rik|AI314065|AI464126	c-Maf inducing protein	protein-coding
mm_51422.1	chr6	78426193	78426201	+	1	NA	intron (NM_009042, intron 1 of 5)	intron (NM_009042, intron 1 of 5)	214	NM_009042	19692	Mm.142731	NM_009042	ENSMUSG00000059654	Reg1	-	regenerating islet-derived 1	protein-coding
mm_113479.1	chr13	37333700	37333710	+	1	NA	Intergenic	Intergenic	-11640	NM_010745	17084	Mm.2639	NM_010745	ENSMUSG00000021423	Ly86	MD-1|MD1|ly86_tv2	lymphocyte antigen 86	protein-coding
mm_170436.1	chr18	80015990	80015997	+	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	-30902	NM_053117	93737	Mm.24678	NM_053117	ENSMUSG00000056214	Pard6g	2410049N21Rik|Par6a	par-6 family cell polarity regulator gamma	protein-coding
mm_11539.1	chr2	32634204	32634218	+	1	NA	3' UTR (NM_001198792, exon 6 of 6)	3' UTR (NM_001198792, exon 6 of 6)	4711	NM_021515	11636	Mm.29189	NM_021515	ENSMUSG00000026817	Ak1	Ak-1|B430205N08Rik	adenylate kinase 1	protein-coding
mm_100294.1	chr11	117825934	117825969	+	1	NA	promoter-TSS (NM_027827)	promoter-TSS (NM_027827)	32	NM_027827	71562	Mm.273958	NM_027827	ENSMUSG00000017718	Afmid	9030621K19Rik|Ammd|FKF|KFA|Kf|formylase	arylformamidase	protein-coding
mm_171568.1	chr4	147310558	147310572	+	1	NA	intron (NM_001039209, intron 1 of 2)	intron (NM_001039209, intron 1 of 2)	134699	NM_001039209	195531	Mm.270762	NM_001039209	ENSMUSG00000078496	Zfp982	Gm13152|OTTMUSG00000010671	zinc finger protein 982	protein-coding
mm_13330.1	chr2	102785399	102785405	+	1	NA	3' UTR (NM_001077514, exon 11 of 11)	3' UTR (NM_001077514, exon 11 of 11)	78964	NM_001077515	20511	Mm.267547	NM_011393	ENSMUSG00000005089	Slc1a2	1700091C19Rik|2900019G14Rik|AI159670|Eaat2|GLT-1|GLT1|MGLT1	solute carrier family 1 (glial high affinity glutamate transporter), member 2	protein-coding
mm_130779.1	chr15	101491510	101491514	-	1	NA	promoter-TSS (NM_016879)	promoter-TSS (NM_016879)	0	NM_001201323	100126226	Mm.347934	NM_001201323	ENSMUSG00000067613	Krt83	5430421N21Rik	keratin 83	protein-coding
mm_141741.1	chr17	34122573	34122632	-	1	NA	promoter-TSS (NM_001204973)	promoter-TSS (NM_001204973)	5	NM_001204973	14312	Mm.3444	NM_010238	ENSMUSG00000024335	Brd2	AW228947|D17H6S113E|Frg-1|Fsrg-1|Fsrg1|Nat|Ring3|Rnf3|mKIAA4005	bromodomain containing 2	protein-coding
mm_105818.1	chr11	112515629	112515651	-	1	NA	Intergenic	Intergenic	195716	NR_024085	217294	Mm.297761	NM_146031	ENSMUSG00000041674	BC006965	-	cDNA sequence BC006965	ncRNA
mm_158840.1	chrX	169182526	169182526	-	1	NA	exon (NM_001081978, exon 4 of 7)	exon (NM_001081978, exon 4 of 7)	4683	NM_001290371	11704	Mm.391342	NM_009666	ENSMUSG00000031354	Amelx	ALGN|AMGL|AMGX|Amel|Amg|LRAP|Rgsc888	amelogenin, X-linked	protein-coding
mm_79352.1	chr9	53771676	53771687	+	1	NA	5' UTR (NM_028060, exon 1 of 8)	5' UTR (NM_028060, exon 1 of 8)	146	NM_028060	72022	Mm.26159	NM_028060	ENSMUSG00000042195	Slc35f2	1500009K05Rik|AU019213	solute carrier family 35, member F2	protein-coding
mm_76099.1	chr8	80325303	80325328	-	1	NA	Intergenic	Intergenic	-168730	NM_010369	14934	Mm.13123	NM_010369	ENSMUSG00000051839	Gypa	AI853584|CD235a|GPA	glycophorin A	protein-coding
mm_169131.1	chr13	58402086	58402086	-	1	NA	promoter-TSS (NR_031761)	promoter-TSS (NR_031761)	83	NM_001301343	15387	Mm.142872	NM_025279	ENSMUSG00000021546	Hnrnpk	Hnrpk|KBBP|NOVA	heterogeneous nuclear ribonucleoprotein K	protein-coding
mm_23345.1	chr3	54735537	54735586	+	1	NA	promoter-TSS (NM_025442)	promoter-TSS (NM_025442)	22	NM_025442	66248	Mm.144218	NM_025442	ENSMUSG00000036632	Alg5	1500026A19Rik|2600005J22Rik|AV009521|AV170001|AW545564	asparagine-linked glycosylation 5 (dolichyl-phosphate beta-glucosyltransferase)	protein-coding
mm_141152.1	chr17	26506503	26506516	-	1	NA	exon (NM_013642, exon 4 of 4)	exon (NM_013642, exon 4 of 4)	1963	NM_013642	19252	Mm.239041	NM_013642	ENSMUSG00000024190	Dusp1	3CH134|MKP1|Ptpn16|U19515|erp|mkp-1	dual specificity phosphatase 1	protein-coding
mm_5127.1	chr1	9631176	9631189	-	1	NA	promoter-TSS (NR_015470)	promoter-TSS (NR_015470)	-90	NR_015470	72481	Mm.279818	NR_015470	ENSMUSG00000079671	2610203C22Rik	2310007M24Rik	RIKEN cDNA 2610203C22 gene	ncRNA
mm_2152.1	chr1	88166747	88166762	+	1	NA	exon (NM_201643, exon 1 of 5)	exon (NM_201643, exon 1 of 5)	742	NM_201643	394433	Mm.300095	NM_201643	ENSMUSG00000089943	Ugt1a5	-	UDP glucuronosyltransferase 1 family, polypeptide A5	protein-coding
mm_158080.1	chrX	101265405	101265446	-	1	NA	exon (NM_001308535, exon 7 of 8)	exon (NM_001308535, exon 7 of 8)	-1433	NM_001317221	245536	Mm.212463	NM_001033362	ENSMUSG00000090141	Gm614	-	predicted gene 614	protein-coding
mm_66303.1	chr7	38271179	38271219	-	1	NA	5' UTR (NM_025390, exon 1 of 7)	5' UTR (NM_025390, exon 1 of 7)	149	NM_025390	66161	Mm.22284	NM_025390	ENSMUSG00000030423	Pop4	1110023P21Rik|Rpp29	processing of precursor 4, ribonuclease P/MRP family, (S. cerevisiae)	protein-coding
mm_9818.1	chr1	182282219	182282239	-	1	NA	intron (NM_007853, intron 1 of 2)	CpG	530	NM_007853	13244	Mm.29648	NM_007853	ENSMUSG00000038633	Degs1	AA536663|Degs|Des1|Mdes	delta(4)-desaturase, sphingolipid 1	protein-coding
mm_132947.1	chr16	49908992	49908995	+	1	NA	intron (NM_010581, intron 9 of 9)	intron (NM_010581, intron 9 of 9)	53339	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_85872.1	chr9	110916892	110916900	-	1	NA	promoter-TSS (NM_001195437)	promoter-TSS (NM_001195437)	-35	NM_001195437	235634	Mm.31788	NM_001195437	ENSMUSG00000096393	Gm590	-	predicted gene 590	protein-coding
mm_95389.1	chr11	49247463	49247512	+	1	NA	promoter-TSS (NM_001110149)	promoter-TSS (NM_001110149)	10	NM_001110149	17308	Mm.196933	NM_010794	ENSMUSG00000020346	Mgat1	Mgat-1	mannoside acetylglucosaminyltransferase 1	protein-coding
mm_64878.1	chr7	14446571	14446587	-	1	NA	promoter-TSS (NM_175250)	promoter-TSS (NM_175250)	8	NM_175250	76971	Mm.290727	NM_175250	ENSMUSG00000030378	Sult2a8	2810007J24Rik	sulfotransferase family 2A, dehydroepiandrosterone (DHEA)-preferring, member 8	protein-coding
mm_81674.1	chr9	111038730	111038736	+	1	NA	intron (NM_008522, intron 14 of 16)	intron (NM_008522, intron 14 of 16)	18511	NM_001302377	54199	Mm.7336	NM_017466	ENSMUSG00000043953	Ccrl2	1810047I05Rik|Ackr5|CCR11|Cmkbr1l2|E01|L-CCR	chemokine (C-C motif) receptor-like 2	protein-coding
mm_51598.1	chr6	84008516	84008533	+	1	NA	promoter-TSS (NM_001077694)	promoter-TSS (NM_001077694)	-74	NM_001077694	26903	Mm.220982	NM_021469	ENSMUSG00000033788	Dysf	2310004N10Rik|AI604795|D6Pas3	dysferlin	protein-coding
mm_136540.1	chr16	97851776	97851788	-	1	NA	promoter-TSS (NM_144789)	promoter-TSS (NM_144789)	-555	NM_144789	114604	Mm.328741	NM_144789	ENSMUSG00000014039	Prdm15	C21orf83|E130018M06Rik|ORF62|Zfp298	PR domain containing 15	protein-coding
mm_6529.1	chr1	74747355	74747363	-	1	NA	exon (NM_153744, exon 4 of 14)	exon (NM_153744, exon 4 of 14)	1596	NM_153744	241113	Mm.166501	NM_153744	ENSMUSG00000006542	Prkag3	AMPKg3L|AMPKg3S|Amkg3|Ampkg3	protein kinase, AMP-activated, gamma 3 non-catatlytic subunit	protein-coding
mm_62471.1	chr7	101820736	101820755	+	1	NA	intron (NM_008887, intron 1 of 2)	intron (NM_008887, intron 1 of 2)	2432	NM_008887	11859	Mm.5028	NM_008887	ENSMUSG00000007946	Phox2a	Arix|Phox2|Pmx2|Pmx2a|Px2a	paired-like homeobox 2a	protein-coding
mm_9856.1	chr1	184810981	184810991	-	1	NA	exon (NM_001290273, exon 1 of 7)	exon (NM_001290273, exon 1 of 7)	314	NM_001290273	66112	Mm.272457	NM_001081361	ENSMUSG00000026621	Marc1	1300013F15Rik|Mosc1	mitochondrial amidoxime reducing component 1	protein-coding
mm_123999.1	chr14	75834842	75834872	-	1	NA	Intergenic	Intergenic	10107	NR_045294	100043189	Mm.426329	NR_045294		Gm4285	-	predicted gene 4285	ncRNA
mm_73116.1	chr8	94750007	94750017	+	1	NA	3' UTR (NM_009137, exon 3 of 3)	3' UTR (NM_009137, exon 3 of 3)	4328	NM_009137	20299	Mm.12895	NM_009137	ENSMUSG00000031779	Ccl22	ABCD-1|DCBCK|MDC|Scya22	chemokine (C-C motif) ligand 22	protein-coding
mm_65387.1	chr7	25091740	25091754	-	1	NA	3' UTR (NM_001163556, exon 14 of 14)	3' UTR (NM_001163556, exon 14 of 14)	5428	NR_105855	102465968		NR_105855	ENSMUSG00000098441	Mir6537	Gm27808|mmu-mir-6537	microRNA 6537	ncRNA
mm_102640.1	chr11	62648035	62648050	-	1	NA	promoter-TSS (NM_175002)	promoter-TSS (NM_175002)	481	NM_198861	192976	Mm.339972	NM_198861	ENSMUSG00000046417	Lrrc75a	Fam211a	leucine rich repeat containing 75A	protein-coding
mm_65518.1	chr7	25756079	25756097	-	1	NA	TTS (NM_001190974)	TTS (NM_001190974)	-1368	NM_144922	232989	Mm.254223	NM_144922	ENSMUSG00000040725	Hnrnpul1	E130317O14Rik|E1B-AP5|E1BAP5|Hnrnpul|Hnrpul1	heterogeneous nuclear ribonucleoprotein U-like 1	protein-coding
mm_97265.1	chr11	75764967	75764984	+	1	NA	3' UTR (NM_009536, exon 6 of 6)	3' UTR (NM_009536, exon 6 of 6)	-30834	NR_136933	102641247	Mm.411386	NR_136932		Gm12339	OTTMUSG00000006218	predicted gene 12339	ncRNA
mm_59912.1	chr7	30415510	30415534	+	1	NA	intron (NM_011662, intron 3 of 4)	RMER17C|LTR|ERVK	1734	NM_011662	22177	Mm.46301	NM_011662	ENSMUSG00000030579	Tyrobp	DAP12|KARAP|Ly83	TYRO protein tyrosine kinase binding protein	protein-coding
mm_146428.1	chr18	84851408	84851429	+	1	NA	promoter-TSS (NM_025797)	promoter-TSS (NM_025797)	4	NM_025797	109672	Mm.31018	NM_025797	ENSMUSG00000024646	Cyb5a	0610009N12Rik|Cyb5	cytochrome b5 type A (microsomal)	protein-coding
mm_157879.1	chrX	75842947	75842963	-	1	NA	promoter-TSS (NM_001166454)	promoter-TSS (NM_001166454)	66	NM_001166454	102866	Mm.28777	NM_145629	ENSMUSG00000016382	Pls3	AI115446|AL024105	plastin 3 (T-isoform)	protein-coding
mm_158916.1	chr1	53187577	53187577	-	1	NA	promoter-TSS (NM_027070)	promoter-TSS (NM_027070)	40	NM_027070	69397	Mm.307084	NM_027070	ENSMUSG00000060715	1700019A02Rik	-	RIKEN cDNA 1700019A02 gene	protein-coding
mm_160241.1	chr7	104465190	104465190	-	1	NA	promoter-TSS (NM_009099)	promoter-TSS (NM_009099)	3	NM_009099	20128	Mm.295578	NM_009099	ENSMUSG00000030921	Trim30a	Rpt-1|Rpt1|Trim30	tripartite motif-containing 30A	protein-coding
mm_124130.1	chr14	83497109	83497117	-	1	NA	Intergenic	MT2B1|LTR|ERVL	-946450	NM_001013753	219228	Mm.153643	NM_001013753	ENSMUSG00000035566	Pcdh17	C030033F14Rik|Gm78	protocadherin 17	protein-coding
mm_30338.1	chr3	151732494	151732504	-	1	NA	exon (NM_133871, exon 8 of 8)	exon (NM_133871, exon 8 of 8)	17460	NM_133871	99899	Mm.30756	NM_133871	ENSMUSG00000028037	Ifi44	A430056A10Rik|AW261460|MTAP44|p44	interferon-induced protein 44	protein-coding
mm_95212.1	chr11	43632830	43632851	+	1	NA	Intergenic	Intergenic	-31278	NM_008375	16204	Mm.142716	NM_008375	ENSMUSG00000020405	Fabp6	GT|I-15P|I-BABP|ILBP|ILBP3|Illbp	fatty acid binding protein 6, ileal (gastrotropin)	protein-coding
mm_166114.1	chr4	149702898	149702931	+	1	NA	Intergenic	Intergenic	-1285	NM_001029837	18707	Mm.229108	NM_008840	ENSMUSG00000039936	Pik3cd	2410099E07Rik|2610208K16Rik|AW545373|p110delta	phosphatidylinositol 3-kinase catalytic delta polypeptide	protein-coding
mm_60279.1	chr7	43954041	43954082	+	1	NA	exon (NM_008457, exon 3 of 5)	exon (NM_008457, exon 3 of 5)	3395	NM_008457	16624	Mm.435488	NM_008457	ENSMUSG00000063089	Klk1b8	Klk8|Nrpn|TADG14|kallikrein|mGK-8	kallikrein 1-related peptidase b8	protein-coding
mm_73650.1	chr8	110940910	110940926	+	1	NA	intron (NM_009179, intron 1 of 6)	intron (NM_009179, intron 1 of 6)	21053	NM_009179	20444	Mm.200388	NM_009179	ENSMUSG00000031749	St3gal2	AI429591|AW822065|ST3GalII|Siat5	ST3 beta-galactoside alpha-2,3-sialyltransferase 2	protein-coding
mm_40698.1	chr5	65858160	65858174	+	1	NA	Intergenic	Intergenic	-5402	NM_001081105	74734	Mm.20323	NM_001081105	ENSMUSG00000029204	Rhoh	5830400A04Rik|AU019774|Arhh	ras homolog family member H	protein-coding
mm_67965.1	chr7	100589946	100589993	-	1	NA	intron (NR_003559, intron 1 of 7)	intron (NR_003559, intron 1 of 7)	-6839	NM_198831	52443	Mm.473730	NM_198831	ENSMUSG00000030706	Mrpl48	1810030E20Rik|2610028L11Rik|CGI-118|D4Ertd786e	mitochondrial ribosomal protein L48	protein-coding
mm_47771.1	chr5	131594880	131594880	-	1	NA	intron (NM_177047, intron 5 of 18)	intron (NM_177047, intron 5 of 18)	-285389	NR_040704	75369	Mm.389696	NR_040704	ENSMUSG00000105773	4930563F08Rik	-	RIKEN cDNA 4930563F08 gene	ncRNA
mm_155941.1	chrX	104482775	104482858	+	1	NA	promoter-TSS (NM_001081189)	promoter-TSS (NM_001081189)	34	NM_001081189	331487	Mm.438275	NM_001081189	ENSMUSG00000073016	Uprt	Gm774	uracil phosphoribosyltransferase	protein-coding
mm_126591.1	chr15	82346118	82346122	+	1	NA	promoter-TSS (NM_026914)	promoter-TSS (NM_026914)	74	NM_026914	69029	Mm.260042	NM_026914	ENSMUSG00000022452	Smdt1	1500032L24Rik|Emre	single-pass membrane protein with aspartate rich tail 1	protein-coding
mm_54291.1	chr6	29272541	29272550	-	1	NA	promoter-TSS (NM_001190461)	promoter-TSS (NM_001190461)	57	NM_001190461	69573	Mm.45161	NM_023516	ENSMUSG00000043421	Hilpda	2310016C08Rik|AW049004|Hig2	hypoxia inducible lipid droplet associated	protein-coding
mm_134511.1	chr16	19067184	19067195	-	1	NA	Intergenic	Intergenic	190439	NM_010435	15260	Mm.15694	NM_010435	ENSMUSG00000022702	Hira	AA138857|D16Ertd95e|Gm15797|N28177|OTTMUSG00000026264|Tuple1	histone cell cycle regulator	protein-coding
mm_42007.1	chr5	108060734	108060749	+	1	NA	Intergenic	MERV1_LTR|LTR|ERV1	-4933	NM_001253877	17765	Mm.257149	NM_013827	ENSMUSG00000029267	Mtf2	9230112N11Rik|AA537621|C76717|M96|Pcl2	metal response element binding transcription factor 2	protein-coding
mm_172570.1	chr8	111854365	111854370	-	1	NA	promoter-TSS (NM_011801)	promoter-TSS (NM_011801)	-57	NM_011801	23837	Mm.279437	NM_011801	ENSMUSG00000031954	Cfdp1	AA408409|Bcnt|Bucentaur|Cfdp|cp27	craniofacial development protein 1	protein-coding
mm_31043.1	chr4	41135570	41135638	+	1	NA	promoter-TSS (NM_026275)	promoter-TSS (NM_026275)	-417	NM_026275	67615	Mm.389540	NM_026275	ENSMUSG00000036241	Ube2r2	1200003M11Rik|Cdc34b|Ubc3b	ubiquitin-conjugating enzyme E2R 2	protein-coding
mm_85045.1	chr9	89704894	89704904	-	1	NA	exon (NM_025360, exon 1 of 3)	exon (NM_025360, exon 1 of 3)	144	NM_025360	66111	Mm.27606	NM_025360	ENSMUSG00000032353	Tmed3	1200002G13Rik|AW546672|P24b	transmembrane p24 trafficking protein 3	protein-coding
mm_5588.1	chr1	39552404	39552412	-	1	NA	3' UTR (NM_001033135, exon 7 of 7)	3' UTR (NM_001033135, exon 7 of 7)	-3568	NR_028555	100217461		NR_028555	ENSMUSG00000077704	Snord89	MBII-289	small nucleolar RNA, C/D box 89	snoRNA
mm_138878.1	chr17	43360323	43360336	+	1	NA	Intergenic	Intergenic	-29137	NM_001081178	224792	Mm.23478	NM_001081178	ENSMUSG00000056492	Adgrf5	8430401C09Rik|9330185D23|AI528491|Gpr116|mKIAA0758	adhesion G protein-coupled receptor F5	protein-coding
mm_105421.1	chr11	103697662	103697718	-	1	NA	promoter-TSS (NM_019650)	promoter-TSS (NM_019650)	20	NM_019650	56494	Mm.195451	NM_019650	ENSMUSG00000020946	Gosr2	2310032N09Rik|C76855|Gs27|SNARE|membrin	golgi SNAP receptor complex member 2	protein-coding
mm_148402.1	chr19	3851856	3851860	+	1	NA	promoter-TSS (NM_001271496)	promoter-TSS (NM_001271496)	85	NR_073190	12660	Mm.225505	NM_013490	ENSMUSG00000024843	Chka	CK|CK/EK-alpha|Chetk-alpha|Chk|ChoK|EK|EtnK-alpha	choline kinase alpha	protein-coding
mm_11381.1	chr2	31246043	31246055	+	1	NA	5' UTR (NM_019681, exon 1 of 8)	5' UTR (NM_019681, exon 1 of 8)	126	NM_019681	14299	Mm.249318	NM_019681	ENSMUSG00000062661	Ncs1	9430075O15Rik|A730032G13Rik|AI836659|Freq|Mfreq|NCS-1	neuronal calcium sensor 1	protein-coding
mm_163493.1	chr12	109636075	109636085	+	1	NA	promoter-TSS (NR_046302)	promoter-TSS (NR_046302)	68	NR_046302	449562		NR_046302	ENSMUSG00000088294	AF357425	MBII-48	snoRNA AF357425	snoRNA
mm_1568.1	chr1	74236603	74236628	+	1	NA	promoter-TSS (NM_029711)	promoter-TSS (NM_029711)	65	NM_029711	76709	Mm.337038	NM_029711	ENSMUSG00000006304	Arpc2	2210023N03Rik|34kDa|p34-Arc	actin related protein 2/3 complex, subunit 2	protein-coding
mm_24791.1	chr3	95545399	95545430	+	1	NA	exon (NM_021281, exon 5 of 8)	exon (NM_021281, exon 5 of 8)	-14263	NM_026489	67981	Mm.179050	NM_026489	ENSMUSG00000028109	Hormad1	4921522K05Rik|Nohma	HORMA domain containing 1	protein-coding
mm_58146.1	chr6	142278847	142278855	-	1	NA	promoter-TSS (NM_001267707)	promoter-TSS (NM_001267707)	23	NM_001267707	108096	Mm.206599	NM_130861	ENSMUSG00000063975	Slco1a5	Oatp-3|Oatp3|Slc21a7	solute carrier organic anion transporter family, member 1a5	protein-coding
mm_13665.1	chr2	114103328	114103333	+	1	NA	intron (NM_009702, intron 34 of 34)	intron (NM_009702, intron 34 of 34)	47240	NR_105968	102465982		NR_105968	ENSMUSG00000098464	Mir7002	Gm27429|mmu-mir-7002	microRNA 7002	ncRNA
mm_161805.1	chr17	56597769	56597769	+	1	NA	intron (NM_001163300, intron 5 of 20)	intron (NM_001163300, intron 5 of 20)	12002	NM_153152	224904	Mm.34002	NM_153152	ENSMUSG00000049760	2410015M20Rik	Mic13|QIL1|sr104	RIKEN cDNA 2410015M20 gene	protein-coding
mm_69489.1	chr7	134197774	134197776	-	1	NA	intron (NM_007400, intron 1 of 22)	AT_rich|Low_complexity|Low_complexity	27322	NM_007400	11489	Mm.439714	NM_007400	ENSMUSG00000054555	Adam12	Mltna	a disintegrin and metallopeptidase domain 12 (meltrin alpha)	protein-coding
mm_167266.1	chr8	28585931	28585936	+	1	NA	Intergenic	Intergenic	-501080	NR_033590	666422	Mm.484413	NR_033590	ENSMUSG00000110372	Gm8096	EG666422	3-phosphoglycerate dehydrogenase pseudogene	pseudo
mm_34624.1	chr4	150569218	150569242	+	1	NA	intron (NM_001085492, intron 11 of 22)	intron (NM_001085492, intron 11 of 22)	82944	NM_173774	242773	Mm.29280	NM_173774	ENSMUSG00000039838	Slc45a1	C230078B22|Dnb5	solute carrier family 45, member 1	protein-coding
mm_26829.1	chr3	10439996	10440006	-	1	NA	5' UTR (NM_001127191, exon 1 of 7)	5' UTR (NM_001127191, exon 1 of 7)	129	NM_029068	74718	Mm.440548	NM_029068	ENSMUSG00000027534	Snx16	4930522N22Rik|AI117577|AI747675	sorting nexin 16	protein-coding
mm_89758.1	chr10	99913130	99913145	+	1	NA	Intergenic	Intergenic	-102684	NM_001347156	17311	Mm.45124	NM_013598	ENSMUSG00000019966	Kitl	Clo|Con|Gb|Kitlg|Mgf|SCF|SF|SLF|Sl|blz|contrasted	kit ligand	protein-coding
mm_128645.1	chr15	59524624	59524662	-	1	NA	intron (NM_026746, intron 4 of 6)	intron (NM_026746, intron 4 of 6)	-124011	NM_144549	211770	Mm.40298	NM_144549	ENSMUSG00000032501	Trib1	A530090O15Rik|TRB-1|Trb1	tribbles pseudokinase 1	protein-coding
mm_101146.1	chr11	16591512	16591530	-	1	NA	Intergenic	Intergenic	-83037	NM_001109971	20335	Mm.325350	NM_011343	ENSMUSG00000078974	Sec61g	-	SEC61, gamma subunit	protein-coding
mm_131948.1	chr16	24393535	24393545	+	1	NA	non-coding (NR_037954, exon 1 of 2)	non-coding (NR_037954, exon 1 of 2)	115	NR_037954	68841	Mm.361995	NR_037954		Lppos	1110054M08Rik|AI481106	LIM domain containing preferred translocation partner in lipoma, opposite strand	ncRNA
mm_128350.1	chr15	39943630	39943640	-	1	NA	exon (NM_172814, exon 1 of 7)	exon (NM_172814, exon 1 of 7)	122	NM_172814	239393	Mm.39874	NM_172814	ENSMUSG00000022305	Lrp12	AI848829|C820005L12Rik|LRP-12	low density lipoprotein-related protein 12	protein-coding
mm_802.1	chr1	45348631	45348665	+	1	NA	exon (NM_009930, exon 51 of 51)	exon (NM_009930, exon 51 of 51)	37110	NM_009930	12825	Mm.249555	NM_009930	ENSMUSG00000026043	Col3a1	AW550625|Col3a-1|Tsk-2|Tsk2	collagen, type III, alpha 1	protein-coding
mm_29131.1	chr3	105687553	105687591	-	1	NA	promoter-TSS (NM_017397)	promoter-TSS (NM_017397)	-1	NM_017397	53975	Mm.272826	NM_017397	ENSMUSG00000027905	Ddx20	GEMIN3|dp103	DEAD (Asp-Glu-Ala-Asp) box polypeptide 20	protein-coding
mm_126602.1	chr15	82452545	82452558	+	1	NA	exon (NM_010006, exon 1 of 9)	exon (NM_010006, exon 1 of 9)	174	NM_010006	13105	Mm.226708	NM_010006	ENSMUSG00000068086	Cyp2d9	Cyp2d|P450-2D	cytochrome P450, family 2, subfamily d, polypeptide 9	protein-coding
mm_92469.1	chr10	78038256	78038263	-	1	NA	intron (NM_001271558, intron 7 of 11)	RMER20A|LTR|ERVK	-4028	NM_001081695	54427	Mm.13433	NM_019448	ENSMUSG00000000730	Dnmt3l	D6Ertd14e|ecat7	DNA (cytosine-5-)-methyltransferase 3-like	protein-coding
mm_139352.1	chr17	50509519	50509553	+	1	NA	promoter-TSS (NM_013880)	promoter-TSS (NM_013880)	-11	NM_013880	224860	Mm.217362	NM_013880	ENSMUSG00000038910	Plcl2	PLC-L2|PRIP-2|Plce2|mKIAA1092	phospholipase C-like 2	protein-coding
mm_128602.1	chr15	58214883	58214926	-	1	NA	promoter-TSS (NM_026346)	promoter-TSS (NM_026346)	-12	NM_026346	67731	Mm.25683	NM_026346	ENSMUSG00000022358	Fbxo32	4833442G10Rik|AI430017|ATROGIN1|Gm20361|MAFbx	F-box protein 32	protein-coding
mm_11859.1	chr2	48814017	48814040	+	1	NA	promoter-TSS (NM_007396)	promoter-TSS (NM_007396)	-81	NM_007396	11480	Mm.314338	NM_007396	ENSMUSG00000052155	Acvr2a	ActrIIa|Acvr2|TactrII	activin receptor IIA	protein-coding
mm_33981.1	chr4	137712024	137712041	+	1	NA	exon (NM_001331215, exon 5 of 23)	exon (NM_001331215, exon 5 of 23)	4527	NM_001331215	110351	Mm.180763	NM_029563	ENSMUSG00000041351	Rap1gap	1300019I11Rik|2310004O14Rik|AI427470|ARPP-90|Gap|Rap1GAP1|Rap1ga1	Rap1 GTPase-activating protein	protein-coding
mm_136007.1	chr16	75870802	75870814	-	1	NA	exon (NM_023380, exon 7 of 8)	exon (NM_023380, exon 7 of 8)	38458	NM_023380	67742	Mm.131406	NM_023380	ENSMUSG00000022876	Samsn1	4930571B16Rik|930571B16Rik|Hacs1|SLy2	SAM domain, SH3 domain and nuclear localization signals, 1	protein-coding
mm_131851.1	chr16	23061637	23061653	+	1	NA	exon (NM_001102411, exon 3 of 10)	exon (NM_001102411, exon 3 of 10)	3345	NM_001102412	16644	Mm.2160	NM_023125	ENSMUSG00000022875	Kng1	Kng	kininogen 1	protein-coding
mm_40435.1	chr5	53590423	53590433	+	1	NA	promoter-TSS (NM_001277116)	promoter-TSS (NM_001277116)	-58	NM_001080927	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_64493.1	chr7	143306365	143306367	+	1	NA	intron (NM_008434, intron 11 of 15)	L1MB7|LINE|L1	-9819	NR_001461	63830	Mm.356096	NR_001461	ENSMUSG00000101609	Kcnq1ot1	Kvlqt1-as|Lit1|Tssc8	KCNQ1 overlapping transcript 1	ncRNA
mm_110364.1	chr12	40105005	40105018	-	1	NA	exon (NM_001146196, exon 4 of 16)	exon (NM_001146196, exon 4 of 16)	29217	NM_009132	20259	Mm.2416	NM_009132	ENSMUSG00000002565	Scin	AW545522|adseverin	scinderin	protein-coding
mm_108279.1	chr12	79029151	79029193	+	1	NA	promoter-TSS (NM_181073)	promoter-TSS (NM_181073)	9	NM_181073	211945	Mm.478321	NM_181073	ENSMUSG00000060716	Plekhh1	AV308913|C77772|D630024D12Rik|mKIAA1200	pleckstrin homology domain containing, family H (with MyTH4 domain) member 1	protein-coding
mm_161949.1	chr19	5366163	5366163	-	1	NA	promoter-TSS (NM_027236)	promoter-TSS (NM_027236)	200	NM_001038231	23825	Mm.358649	NM_011793	ENSMUSG00000024844	Banf1	Baf|Bcrp1|L2bp1/Baf	barrier to autointegration factor 1	protein-coding
mm_32853.1	chr4	118076991	118077019	+	1	NA	intron (NM_009176, intron 2 of 11)	MTD|LTR|ERVL-MaLR	57941	NM_001285520	20441	Mm.251002	NM_009176	ENSMUSG00000028538	St3gal3	ST3GalIII|ST3N|Siat3|Siat6	ST3 beta-galactoside alpha-2,3-sialyltransferase 3	protein-coding
mm_145519.1	chr18	60526195	60526234	+	1	NA	promoter-TSS (NM_026302)	promoter-TSS (NM_026302)	-7	NM_026302	67665	Mm.272801	NM_026302	ENSMUSG00000024603	Dctn4	1110001K06Rik|4930547K17Rik|C130039E17Rik|p62	dynactin 4	protein-coding
mm_78456.1	chr9	32372448	32372454	+	1	NA	promoter-TSS (NM_019659)	promoter-TSS (NM_019659)	33	NM_019659	56379	Mm.390168	NM_019659	ENSMUSG00000041248	Kcnj1	Kir1.1|ROMK|Romk2	potassium inwardly-rectifying channel, subfamily J, member 1	protein-coding
mm_13509.1	chr2	109890847	109890882	+	1	NA	promoter-TSS (NM_011699)	promoter-TSS (NM_011699)	-14	NM_011699	22343	Mm.235300	NM_011699	ENSMUSG00000027162	Lin7c	9130007B12Rik|AI303698|AU019331|AW125731|D2Ertd520e|LIN-7-C|LIN-7C|MALS-3|Veli3	lin-7 homolog C (C. elegans)	protein-coding
mm_130425.1	chr15	98093531	98093543	-	1	NA	promoter-TSS (NM_144851)	promoter-TSS (NM_144851)	32	NM_144851	223870	Mm.384023	NM_144851	ENSMUSG00000033075	Senp1	2310046A20Rik|D15Ertd528e|E330036L07Rik|suPr-2	SUMO1/sentrin specific peptidase 1	protein-coding
mm_101053.1	chr11	8664500	8664551	-	1	NA	promoter-TSS (NM_001083587)	promoter-TSS (NM_001083587)	10	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_5937.1	chr1	55363735	55363756	-	1	NA	promoter-TSS (NM_029267)	promoter-TSS (NM_029267)	-276	NM_029267	75388	Mm.483408	NM_029267	ENSMUSG00000025977	Boll	4930554P13Rik|4930597B14Rik	bol, boule-like (Drosophila)	protein-coding
mm_25792.1	chr3	127512812	127512817	+	1	NA	Intergenic	Intergenic	-13699	NM_001327938	109676	Mm.220242	NM_178655	ENSMUSG00000032826	Ank2	100043364|AI835472|AW491075|Ank-2|Gm4392	ankyrin 2, brain	protein-coding
mm_48927.1	chr6	4516392	4516413	+	1	NA	exon (NM_007743, exon 11 of 52)	exon (NM_007743, exon 11 of 52)	10784	NM_007743	12843	Mm.277792	NM_007743	ENSMUSG00000029661	Col1a2	AA960264|AI325291|Col1a-2|Cola-2|Cola2|oim	collagen, type I, alpha 2	protein-coding
mm_82722.1	chr9	24774277	24774291	-	1	NA	promoter-TSS (NM_020496)	promoter-TSS (NM_020496)	19	NM_020496	57246	Mm.31452	NM_020496	ENSMUSG00000031965	Tbx20	9430010M06Rik|AL022859|Tbx12	T-box 20	protein-coding
mm_84238.1	chr9	62282146	62282154	-	1	NA	promoter-TSS (NM_025721)	promoter-TSS (NM_025721)	29	NM_025721	66712	Mm.263615	NM_025721	ENSMUSG00000046846	Spesp1	4921508E09Rik|AI428149	sperm equatorial segment protein 1	protein-coding
mm_132258.1	chr16	32755376	32755398	+	1	NA	exon (NM_080457, exon 4 of 27)	exon (NM_080457, exon 4 of 27)	19501	NM_080457	140474	Mm.214599	NM_080457	ENSMUSG00000079620	Muc4	4933405I11Rik|Asgp	mucin 4	protein-coding
mm_149083.1	chr19	8915757	8915783	+	1	NA	3' UTR (NM_008060, exon 25 of 25)	3' UTR (NM_008060, exon 25 of 25)	-4623	NM_024256	72727	Mm.259	NM_024256	ENSMUSG00000071649	B3gat3	2810405M13Rik	beta-1,3-glucuronyltransferase 3 (glucuronosyltransferase I)	protein-coding
mm_125613.1	chr15	61987039	61987059	+	1	NA	intron (NM_001177353, intron 1 of 2)	CpG	1708	NM_001177352	17869	Mm.2444	NM_010849	ENSMUSG00000022346	Myc	AU016757|Myc2|Niard|Nird|bHLHe39	myelocytomatosis oncogene	protein-coding
mm_112116.1	chr12	112803585	112803585	-	1	NA	Intergenic	Intergenic	-5390	NM_145450	217887	Mm.186678	NM_145450	ENSMUSG00000037594	BC022687	AW050009|C130001I08Rik|Flj20080	cDNA sequence BC022687	protein-coding
mm_44026.1	chr5	147430223	147430244	+	1	NA	promoter-TSS (NM_028291)	promoter-TSS (NM_028291)	-347	NM_028291	72587	Mm.320469	NM_028291	ENSMUSG00000029647	Pan3	2700050F09Rik|A430027N15Rik|AU014670	PAN3 poly(A) specific ribonuclease subunit	protein-coding
mm_153302.1	chr19	37989535	37989545	-	1	NA	intron (NM_001302140, intron 5 of 53)	B1F|SINE|Alu	54037	NM_001099634	226101	Mm.34674	NM_177035	ENSMUSG00000048612	Myof	2310004N10Rik|2310051D19Rik|E030042N20Rik|Fer1l3	myoferlin	protein-coding
mm_72312.1	chr8	77744535	77744541	+	1	NA	Intergenic	RMER1A|Other|Other	-20086	NM_010332	13617	Mm.283168	NM_010332	ENSMUSG00000031616	Ednra	ET-AR|ETa|Gpcr10	endothelin receptor type A	protein-coding
mm_35733.1	chr4	45012094	45012159	-	1	NA	5' UTR (NM_001163284, exon 1 of 2)	5' UTR (NM_001163284, exon 1 of 2)	286	NM_001163284	230119	Mm.44222	NM_173399	ENSMUSG00000049657	Zbtb5	5930421I10|9430083K24Rik|AI646847|mKIAA0354	zinc finger and BTB domain containing 5	protein-coding
mm_171777.1	chr5	109900678	109900692	-	1	NA	Intergenic	RLTR4_Mm|LTR|ERV1	-32878	NR_040366	100642166		NR_040366	ENSMUSG00000090015	Gm15446	OTTMUSG00000022004	predicted gene 15446	ncRNA
mm_129322.1	chr15	77767568	77767593	-	1	NA	exon (NM_022410, exon 32 of 41)	exon (NM_022410, exon 32 of 41)	-12351	NM_001081970	239552	Mm.125650	NM_001081970	ENSMUSG00000056656	Apol8	9830006J20Rik|APOL-II|Apol2	apolipoprotein L 8	protein-coding
mm_118540.1	chr14	16398725	16398730	+	1	NA	exon (NM_009409, exon 12 of 36)	exon (NM_009409, exon 12 of 36)	33521	NM_009409	21974	Mm.130362	NM_009409	ENSMUSG00000017485	Top2b	D230016L12Rik|Top-2	topoisomerase (DNA) II beta	protein-coding
mm_159137.1	chr2	82053675	82053675	+	1	NA	promoter-TSS (NM_175513)	promoter-TSS (NM_175513)	17	NM_175513	241514	Mm.119383	NM_175513	ENSMUSG00000070866	Zfp804a	C630007C17Rik|Znf804a	zinc finger protein 804A	protein-coding
mm_36157.1	chr4	59914257	59914259	-	1	NA	exon (NM_021053, exon 1 of 4)	exon (NM_021053, exon 1 of 4)	798	NM_021053	30936	Mm.284433	NM_021053	ENSMUSG00000028386	Slc46a2	5430429N04Rik|Ly110|TSO-1C12|Tscot	solute carrier family 46, member 2	protein-coding
mm_134434.1	chr16	18073718	18073741	-	1	NA	intron (NM_011172, intron 11 of 13)	intron (NM_011172, intron 11 of 13)	7326	NM_001289813	13353	Mm.27155	NM_010047	ENSMUSG00000003531	Dgcr6	-	DiGeorge syndrome critical region gene 6	protein-coding
mm_125971.1	chr15	76294358	76294380	+	1	NA	promoter-TSS (NM_001195537)	promoter-TSS (NM_001195537)	-65	NM_001195537	100503915	Mm.393455	NM_001195537	ENSMUSG00000071724	Smpd5	ENSMUSG00000071724|Gm10345|MA-nSMase	sphingomyelin phosphodiesterase 5	protein-coding
mm_10534.1	chr2	16410551	16410566	+	1	NA	intron (NM_026162, intron 1 of 13)	L1_Mus3|LINE|L1	54254	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding
mm_27624.1	chr3	59344371	59344422	-	1	NA	promoter-TSS (NM_001162884)	promoter-TSS (NM_001162884)	-140	NM_001162884	242050	Mm.228086	NM_001162884	ENSMUSG00000036334	Igsf10	6530405F15Rik|9030224D03|AA409708|AA536958|AI414626|Adlican2|CMF608	immunoglobulin superfamily, member 10	protein-coding
mm_96145.1	chr11	61022561	61022570	+	1	NA	promoter-TSS (NM_001267593)	promoter-TSS (NM_001267593)	1	NM_001267593	16515	Mm.4970	NM_010603	ENSMUSG00000042529	Kcnj12	IRK-2|IRK2|Kir2.2|MB-IRK2	potassium inwardly-rectifying channel, subfamily J, member 12	protein-coding
mm_91486.1	chr10	37135245	37135418	-	1	NA	3' UTR (NM_008538, exon 2 of 2)	3' UTR (NM_008538, exon 2 of 2)	3595	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_86415.1	chr10	3395783	3395814	+	1	NA	intron (NM_133485, intron 1 of 3)	intron (NM_133485, intron 1 of 3)	29648	NM_133485	76142	Mm.308126	NM_133485	ENSMUSG00000040653	Ppp1r14c	6330514J04Rik|KEPI	protein phosphatase 1, regulatory (inhibitor) subunit 14c	protein-coding
mm_88448.1	chr10	77549634	77549650	+	1	NA	intron (NM_008404, intron 6 of 15)	IMPB_01|Satellite|Satellite	19294	NM_008404	16414	Mm.1137	NM_008404	ENSMUSG00000000290	Itgb2	2E6|AI528527|Cd18|LAD|LCAMB|Lfa1|MF17	integrin beta 2	protein-coding
mm_172559.1	chr8	106573430	106573432	-	1	NA	Intergenic	Intergenic	-13712	NR_045470	68692	Mm.416843	NR_045470	ENSMUSG00000099139	1110028F18Rik	-	RIKEN cDNA 1110028F18 gene	ncRNA
mm_87394.1	chr10	45335724	45335744	+	1	NA	promoter-TSS (NM_024285)	promoter-TSS (NM_024285)	-28	NM_024285	23828	Mm.332793	NM_024285	ENSMUSG00000071317	Bves	Pop1|Popdc1|mBVES	blood vessel epicardial substance	protein-coding
mm_136673.1	chr17	6107135	6107162	+	1	NA	intron (NM_001103181, intron 1 of 13)	CpG	318	NM_001103181	68842	Mm.449307	NM_054040	ENSMUSG00000034377	Tulp4	1110057P05Rik|2210038L17Rik|Tusp	tubby like protein 4	protein-coding
mm_16238.1	chr2	173156364	173156374	+	1	NA	intron (NM_011044, intron 6 of 9)	RSINE1|SINE|B4	3296	NM_011044	18534	Mm.266867	NM_011044	ENSMUSG00000027513	Pck1	AI265463|PEPCK|Pck-1	phosphoenolpyruvate carboxykinase 1, cytosolic	protein-coding
mm_173239.1	chrX	86822028	86822037	+	1	NA	intron (NM_001160403, intron 6 of 10)	L1Md_A|LINE|L1	-467038	NR_036689	245502	Mm.490821	NR_036689		Gm41	-	melanoma antigen, family B, 4 pseudogene	pseudo
mm_93643.1	chr10	117348242	117348246	-	1	NA	3' UTR (NM_001013391, exon 10 of 10)	3' UTR (NM_001013391, exon 10 of 10)	28729	NM_001013391	432508	Mm.478881	NM_001013391	ENSMUSG00000055531	Cpsf6	4733401N12Rik|AI256641|CFIM|CFIM68|HPBRII-4|HPBRII-7	cleavage and polyadenylation specific factor 6	protein-coding
mm_58009.1	chr6	136518499	136518501	-	1	NA	promoter-TSS (NM_019426)	promoter-TSS (NM_019426)	-351	NM_019426	54343	Mm.173271	NM_019426	ENSMUSG00000030213	Atf7ip	2610204M12Rik|AM|Mcaf1	activating transcription factor 7 interacting protein	protein-coding
mm_27638.1	chr3	62506971	62507027	-	1	NA	promoter-TSS (NM_028136)	promoter-TSS (NM_028136)	-11	NM_028136	72162	Mm.224233	NM_028136	ENSMUSG00000027770	Dhx36	2810407E23Rik|AI452301|AU022184|Ddx36|mKIAA1488	DEAH (Asp-Glu-Ala-His) box polypeptide 36	protein-coding
mm_125368.1	chr15	39729238	39729245	+	1	NA	Intergenic	RMER17A2|LTR|ERVK	-16689	NM_001289506	75766	Mm.159563	NM_029422	ENSMUSG00000022303	Dcstamp	4833414I07Rik|DC-STAMP|FIND|Tm7sf4|mDC-STAMP	dendrocyte expressed seven transmembrane protein	protein-coding
mm_141029.1	chr17	25248133	25248150	-	1	NA	exon (NM_001163270, exon 15 of 34)	exon (NM_001163270, exon 15 of 34)	-2503	NR_105931	102465583		NR_105931	ENSMUSG00000093202	Mir3547	Gm22410|mmu-mir-3547	microRNA 3547	ncRNA
mm_68414.1	chr7	109671941	109671961	-	1	NA	Intergenic	Intergenic	-31786	NM_020616	57373	Mm.334138	NM_020616	ENSMUSG00000031023	Akip1	BCA3|C11orf17|D7H11orf17|D930014E17Rik|ICRFP703B1614Q5.6|ORF27	A kinase (PRKA) interacting protein 1	protein-coding
mm_125935.1	chr15	76247824	76247836	+	1	NA	promoter-TSS (NR_105918)	promoter-TSS (NR_105918)	-361	NR_105918	102465575		NR_105918	ENSMUSG00000098625	Mir6953	Gm27738|mmu-mir-6953	microRNA 6953	ncRNA
mm_120730.1	chr14	73143107	73143166	+	1	NA	non-coding (NR_033185, exon 1 of 16)	non-coding (NR_033185, exon 1 of 16)	351	NR_033185	105670	Mm.280068	NM_134083	ENSMUSG00000022106	Rcbtb2	2610028E02Rik|2810420M18Rik|AI448345|AW240694|Chc1l|RC/BTB2	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 2	protein-coding
mm_171587.1	chr4	147642108	147642124	-	1	NA	intron (NM_145078, intron 1 of 4)	intron (NM_145078, intron 1 of 4)	392	NM_145078	112422	Mm.327194	NM_145078	ENSMUSG00000066000	Zfp979	2610305D13Rik|Ssm1b	zinc finger protein 979	protein-coding
mm_31283.1	chr4	45848921	45848950	+	1	NA	promoter-TSS (NM_028788)	promoter-TSS (NM_028788)	-12	NM_028788	74152	Mm.63645	NM_028788	ENSMUSG00000028327	Stra6l	1300002K09Rik|Rbpr2	STRA6-like	protein-coding
mm_63691.1	chr7	130577335	130577351	+	1	NA	promoter-TSS (NM_206856)	promoter-TSS (NM_206856)	-141	NM_001004468	57752	Mm.86322	NM_021314	ENSMUSG00000030852	Tacc2	mKIAA4180	transforming, acidic coiled-coil containing protein 2	protein-coding
mm_142873.1	chr17	51822404	51822406	-	1	NA	intron (NM_001163632, intron 1 of 10)	intron (NM_001163632, intron 1 of 10)	4183	NM_001163631	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_13456.1	chr2	105668889	105668914	+	1	NA	promoter-TSS (NM_001244198)	promoter-TSS (NM_001244198)	5	NM_001244201	18508	Mm.3608	NM_013627	ENSMUSG00000027168	Pax6	1500038E17Rik|AEY11|Dey|Gsfaey11|Pax-6|Sey	paired box 6	protein-coding
mm_69081.1	chr7	127014536	127014583	-	1	NA	promoter-TSS (NM_080638)	promoter-TSS (NM_080638)	35	NM_080638	78388	Mm.228797	NM_080638	ENSMUSG00000030681	Mvp	2310009M24Rik|LRP|VAULT1	major vault protein	protein-coding
mm_112352.1	chr12	118301923	118301942	-	1	NA	promoter-TSS (NM_009239)	promoter-TSS (NM_009239)	-492	NM_001166385	20688	Mm.34699	NM_009239	ENSMUSG00000025323	Sp4	5730497N03Rik|HF-1b|HF1-b	trans-acting transcription factor 4	protein-coding
mm_172257.1	chr6	71124571	71124589	+	1	NA	Intergenic	Intergenic	19800	NM_001033929	232078	Mm.37547	NM_178413	ENSMUSG00000054474	Thnsl2	BC051244|TSH2	threonine synthase-like 2 (bacterial)	protein-coding
mm_155045.1	chrX	42150756	42150767	+	1	NA	promoter-TSS (NM_021465)	promoter-TSS (NM_021465)	60	NM_021465	20843	Mm.290422	NM_021465	ENSMUSG00000025862	Stag2	9230105L23Rik|B230112I07Rik|SA-2|SAP2	stromal antigen 2	protein-coding
mm_72637.1	chr8	84689309	84689318	+	1	NA	promoter-TSS (NM_198020)	promoter-TSS (NM_198020)	66	NM_198020	212528	Mm.275720	NM_198020	ENSMUSG00000001909	Trmt1	6720406L13Rik|6720477L24|D8Ertd812e	tRNA methyltransferase 1	protein-coding
mm_161635.1	chr16	89974670	89974670	-	1	NA	promoter-TSS (NM_001145886)	promoter-TSS (NM_001145886)	29	NM_001145886	21844	Mm.310902	NM_009384	ENSMUSG00000002489	Tiam1	AI847750|D16Ium10|D16Ium10e	T cell lymphoma invasion and metastasis 1	protein-coding
mm_96356.1	chr11	67025145	67025179	+	1	NA	promoter-TSS (NM_001291043)	promoter-TSS (NM_001291043)	8	NM_001291043	338369	Mm.128138	NM_177392	ENSMUSG00000050270	Tmem220	-	transmembrane protein 220	protein-coding
mm_156850.1	chrX	164400928	164400948	+	1	NA	TTS (NM_001308489)	TTS (NM_001308489)	-18849	NM_011081	18700	Mm.3781	NM_011081	ENSMUSG00000031381	Piga	AI194334|Pig-a	phosphatidylinositol glycan anchor biosynthesis, class A	protein-coding
mm_116965.1	chr13	56176265	56176281	-	1	NA	exon (NM_001168615, exon 3 of 3)	exon (NM_001168615, exon 3 of 3)	2612	NM_145976	212937	Mm.116697	NM_145976	ENSMUSG00000049625	Tifab	-	TRAF-interacting protein with forkhead-associated domain, family member B	protein-coding
mm_16331.1	chr2	174328201	174328211	+	1	NA	5' UTR (NM_001310083, exon 2 of 13)	5' UTR (NM_001310083, exon 2 of 13)	292	NR_003258	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_129162.1	chr15	76243171	76243181	-	1	NA	exon (NM_001163575, exon 2 of 11)	exon (NM_001163575, exon 2 of 11)	264	NM_001163576	671535	Mm.373750	NM_001163575	ENSMUSG00000063268	Parp10	-	poly (ADP-ribose) polymerase family, member 10	protein-coding
mm_66384.1	chr7	43998919	43998931	-	1	NA	exon (NM_010640, exon 3 of 5)	exon (NM_010640, exon 3 of 5)	3048	NM_010640	16613	Mm.443378	NM_010640	ENSMUSG00000044485	Klk1b11	Klk11|mGK-11	kallikrein 1-related peptidase b11	protein-coding
mm_59856.1	chr7	29982123	29982133	+	1	NA	Intergenic	RLTR53B_Mm|LTR|ERVK	-1827	NM_001167873	243905	Mm.322432	NM_001033355	ENSMUSG00000074221	Zfp568	C80731|Gm1691|Znf568|chato	zinc finger protein 568	protein-coding
mm_34607.1	chr4	150248590	150248597	+	1	NA	3' UTR (NM_001025388, exon 12 of 12)	3' UTR (NM_001025388, exon 12 of 12)	11269	NM_001025388	433182	Mm.70666	NM_001025388	ENSMUSG00000059040	Eno1b	EG433182|Eno1|Gm5506	enolase 1B, retrotransposed	protein-coding
mm_9484.1	chr1	173526231	173526241	-	1	NA	intron (NM_001024721, intron 4 of 4)	MTD|LTR|ERVL-MaLR	9721	NM_001024721	545384	Mm.371698	NM_001024721	ENSMUSG00000070501	Ifi214	Pyhin-B|p214	interferon activated gene 214	protein-coding
mm_45112.1	chr5	45450222	45450230	-	1	NA	promoter-TSS (NM_024236)	promoter-TSS (NM_024236)	3	NM_024236	110391	Mm.30204	NM_024236	ENSMUSG00000015806	Qdpr	2610008L04Rik|D5Ertd371e|Dhpr|PKU2	quinoid dihydropteridine reductase	protein-coding
mm_148796.1	chr19	6184340	6184352	+	1	NA	promoter-TSS (NM_001165919)	promoter-TSS (NM_001165919)	-64	NM_001165919	622554	Mm.159757	NM_001165919	ENSMUSG00000024786	Majin	1700123I01Rik	membrane anchored junction protein	protein-coding
mm_31586.1	chr4	57821082	57821101	+	1	NA	intron (NM_001304544, intron 6 of 8)	intron (NM_001304544, intron 6 of 8)	-24157	NM_009649	11641	Mm.467752	NM_009649	ENSMUSG00000038729	Akap2	AA959716|AI649048|Akap-2|Akap-kl|B230340M18Rik|Prka2	A kinase (PRKA) anchor protein 2	protein-coding
mm_167997.1	chrX	170017430	170017436	+	1	NA	Intergenic	B2_Mm1t|SINE|B2	-38516	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_5548.1	chr1	38627570	38627582	-	1	NA	promoter-TSS (NM_001290814)	promoter-TSS (NM_001290814)	-332	NM_001290814	16764	Mm.336679	NM_010678	ENSMUSG00000037138	Aff3	3222402O04Rik|A730046J16|LAF-4|Laf4	AF4/FMR2 family, member 3	protein-coding
mm_165156.1	chr2	22774293	22774333	-	1	NA	promoter-TSS (NM_019456)	promoter-TSS (NM_019456)	-14	NM_019456	54519	Mm.14255	NM_019456	ENSMUSG00000026786	Apbb1ip	9930118P07Rik|Prp48	amyloid beta (A4) precursor protein-binding, family B, member 1 interacting protein	protein-coding
mm_21245.1	chr2	156174524	156174536	-	1	NA	intron (NM_133242, intron 3 of 16)	intron (NM_133242, intron 3 of 16)	5050	NM_001291115	170791	Mm.392436	NM_133242	ENSMUSG00000027620	Rbm39	1500012C14Rik|2310040E03Rik|B330012G18Rik|C79248|R75070|Rnpc2|caper	RNA binding motif protein 39	protein-coding
mm_68233.1	chr7	104465178	104465188	-	1	NA	promoter-TSS (NM_009099)	promoter-TSS (NM_009099)	10	NM_009099	20128	Mm.295578	NM_009099	ENSMUSG00000030921	Trim30a	Rpt-1|Rpt1|Trim30	tripartite motif-containing 30A	protein-coding
mm_117343.1	chr13	69611265	69611279	-	1	NA	promoter-TSS (NM_145354)	promoter-TSS (NM_145354)	191	NM_175283	78925	Mm.451912	NM_175283	ENSMUSG00000021594	Srd5a1	0610031P22Rik|4930435F02Rik|S5AR 1|Srd5a-1	steroid 5 alpha-reductase 1	protein-coding
mm_123425.1	chr14	64434183	64434226	-	1	NA	intron (NM_001253712, intron 1 of 5)	intron (NM_001253712, intron 1 of 5)	6822	NM_001253715	110265	Mm.26713	NM_026322	ENSMUSG00000054733	Msra	2310045J23Rik|6530413P12Rik|MSR-A	methionine sulfoxide reductase A	protein-coding
mm_23767.1	chr3	74984618	74984619	+	1	NA	Intergenic	Lx8|LINE|L1	159154	NM_001310529	213234	Mm.80075	NM_172515	ENSMUSG00000034151	Zbbx	4931432L23	zinc finger, B-box domain containing	protein-coding
mm_66956.1	chr7	62420143	62420157	-	1	NA	promoter-TSS (NM_011746)	promoter-TSS (NM_011746)	-11	NM_011746	22652	Mm.146	NM_011746	ENSMUSG00000070527	Mkrn3	D7H15S9-1|Zfp127	makorin, ring finger protein, 3	protein-coding
mm_29012.1	chr3	101604694	101604715	-	1	NA	promoter-TSS (NM_144900)	promoter-TSS (NM_144900)	3	NM_144900	11928	Mm.193670	NM_144900	ENSMUSG00000033161	Atp1a1	Atpa-1|BC010319	ATPase, Na+/K+ transporting, alpha 1 polypeptide	protein-coding
mm_43115.1	chr5	124598753	124598798	+	1	NA	promoter-TSS (NM_026486)	promoter-TSS (NM_026486)	26	NM_026486	67978	Mm.1158	NM_026486		Tctn2	4432405B04Rik|Tect2	tectonic family member 2	protein-coding
mm_43934.1	chr5	145104557	145104567	+	1	NA	intron (NM_019767, intron 7 of 9)	intron (NM_019767, intron 7 of 9)	-9694	NM_023142	11867	Mm.30010	NM_023142	ENSMUSG00000029622	Arpc1b	41kDa|AA408064|AA408534|AA571392|AF007010|AW208418|L72|SOP2Hs|p41-ARC	actin related protein 2/3 complex, subunit 1B	protein-coding
mm_103750.1	chr11	80505078	80505093	-	1	NA	intron (NM_177390, intron 21 of 21)	intron (NM_177390, intron 21 of 21)	4021	NR_126552	77417	Mm.437510	NR_126552	ENSMUSG00000085078	C030013C21Rik	-	RIKEN cDNA C030013C21 gene	ncRNA
mm_51325.1	chr6	72347711	72347714	+	1	NA	intron (NM_026696, intron 2 of 3)	CpG-12156	395	NM_026696	68364	Mm.52711	NM_026696	ENSMUSG00000058706	0610030E20Rik	1500031N04Rik|2810411C16Rik|AI461894	RIKEN cDNA 0610030E20 gene	protein-coding
mm_151048.1	chr19	47024979	47024986	+	1	NA	TTS (NM_146100)	TTS (NM_146100)	-9793	NM_001164363	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_32935.1	chr4	119255466	119255493	+	1	NA	promoter-TSS (NM_153105)	promoter-TSS (NM_153105)	10	NM_001038590	242653	Mm.130701	NM_153105	ENSMUSG00000066058	Cldn19	-	claudin 19	protein-coding
mm_70710.1	chr8	15059084	15059090	+	1	NA	intron (NM_008664, intron 1 of 36)	intron (NM_008664, intron 1 of 36)	1434	NM_008664	17930	Mm.272115	NM_008664	ENSMUSG00000031461	Myom2	AW146149	myomesin 2	protein-coding
mm_164139.1	chr15	57347685	57347695	+	1	NA	intron (NM_172378, intron 2 of 11)	intron (NM_172378, intron 2 of 11)	129935	NM_172378	210463	Mm.26555	NM_172378	ENSMUSG00000022366	Slc22a22	oat-pg	solute carrier family 22 (organic cation transporter), member 22	protein-coding
mm_50494.1	chr6	48990203	48990216	+	1	NA	exon (NM_172888, exon 2 of 5)	exon (NM_172888, exon 2 of 5)	3348	NM_172888	243377	Mm.446302	NM_172888	ENSMUSG00000039215	Svs1	9530003A11	seminal vesicle secretory protein 1	protein-coding
mm_164659.1	chr17	37481287	37481287	-	1	NA	exon (NM_001347387, exon 5 of 5)	exon (NM_001347387, exon 5 of 5)	2242	NM_008204	14990	Mm.329041	NM_008204	ENSMUSG00000016283	H2-M2	H-2M2|Thy19.4	histocompatibility 2, M region locus 2	protein-coding
mm_16322.1	chr2	174304602	174304606	+	1	NA	intron (NM_001310085, intron 2 of 12)	(CA)n|Simple_repeat|Simple_repeat	6745	NM_001310085	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_98626.1	chr11	96007323	96007343	+	1	NA	Intergenic	CpG-2488	-1389	NM_009951	140486	Mm.294769	NM_009951	ENSMUSG00000013415	Igf2bp1	AL024068|AW549074|CRD-BP|Crdbp|D030026A21Rik|D11Moh40e|D11Moh45|IMP-1|IMP1|Neilsen|ZBP-1|Zbp1|mir-3063	insulin-like growth factor 2 mRNA binding protein 1	protein-coding
mm_43578.1	chr5	137746356	137746374	+	1	NA	5' UTR (NM_023910, exon 1 of 5)	5' UTR (NM_023910, exon 1 of 5)	396	NM_029805	78829	Mm.286399	NM_023910	ENSMUSG00000029723	Tsc22d4	0610009M14Rik|1700023B23Rik|AI415410|Thg-1pit|Tilz2	TSC22 domain family, member 4	protein-coding
mm_94939.1	chr11	29707734	29707758	+	1	NA	exon (NM_194051, exon 3 of 9)	exon (NM_194051, exon 3 of 9)	-10817	NM_024226	68585	Mm.192580	NM_024226	ENSMUSG00000020458	Rtn4	1110020G17Rik|AA407876|AA409940|AA960376|ASY|C130026I10Rik|NOGO|NSP-CL|NgA|Nogo-A|Nogo-B|Nogo-C|mKIAA0886|mKIAA4153	reticulon 4	protein-coding
mm_95894.1	chr11	58183919	58183931	+	1	NA	promoter-TSS (NM_001135115)	promoter-TSS (NM_001135115)	82	NM_001135115	631323	Mm.394103	NM_001135115		Gm12250	Irgb10|OTTMUSG00000005723	predicted gene 12250	protein-coding
mm_159278.1	chr2	165317000	165317000	-	1	NA	promoter-TSS (NM_001302754)	promoter-TSS (NM_001302754)	-649	NM_001302754	140579	Mm.35064	NM_080287	ENSMUSG00000017670	Elmo2	1190002F24Rik|CED-12	engulfment and cell motility 2	protein-coding
mm_156696.1	chrX	159482276	159482294	+	1	NA	exon (NM_001081124, exon 9 of 17)	exon (NM_001081124, exon 9 of 17)	23160	NM_001313753	78283	Mm.160079	NM_001081124	ENSMUSG00000041020	Map7d2	1600028E09Rik|2900002G04Rik|5330432J06Rik|C030036K04Rik|Mtap7d2	MAP7 domain containing 2	protein-coding
mm_124909.1	chr15	11000717	11000736	+	1	NA	promoter-TSS (NM_053077)	promoter-TSS (NM_053077)	5	NM_053077	22293	Mm.138278	NM_053077	ENSMUSG00000022243	Slc45a2	Aim-1|Aim1|Dbr|Matp|Oca4|blanc-sale|bls|uw	solute carrier family 45, member 2	protein-coding
mm_92146.1	chr10	67069096	67069103	-	1	NA	intron (NM_178606, intron 1 of 7)	intron (NM_178606, intron 1 of 7)	27889	NM_001204915	28193	Mm.41272	NM_178606	ENSMUSG00000019873	Reep3	D10Ucla1	receptor accessory protein 3	protein-coding
mm_131638.1	chr16	20498794	20498804	+	1	NA	promoter-TSS (NM_172265)	promoter-TSS (NM_172265)	-18	NM_172265	224045	Mm.233855	NM_172265	ENSMUSG00000003235	Eif2b5	C81315	eukaryotic translation initiation factor 2B, subunit 5 epsilon	protein-coding
mm_54375.1	chr6	31196603	31196623	-	1	NA	intron (NR_110470, intron 1 of 2)	intron (NR_110470, intron 1 of 2)	21861	NR_110470	232685	Mm.443019	NM_144555	ENSMUSG00000044471	Lncpint	Lincpint|MNCb-1768|Pint|linc-Pint	long non-protein coding RNA, Trp53 induced transcript	ncRNA
mm_70999.1	chr8	31089576	31089593	+	1	NA	promoter-TSS (NM_025869)	promoter-TSS (NM_025869)	-78	NM_025869	66959	Mm.23916	NM_025869	ENSMUSG00000039661	Dusp26	2310043K02Rik|Skrp3	dual specificity phosphatase 26 (putative)	protein-coding
mm_113517.1	chr13	37801535	37801538	+	1	NA	Intergenic	BC1_Mm|scRNA|scRNA	-24502	NM_026830	68750	Mm.491109	NM_026830	ENSMUSG00000039087	Rreb1	1110037N09Rik|AA414966|B930013M22Rik	ras responsive element binding protein 1	protein-coding
mm_3421.1	chr1	146495622	146495636	+	1	NA	promoter-TSS (NM_153539)	promoter-TSS (NM_153539)	-37	NM_153539	215378	Mm.441817	NM_153539	ENSMUSG00000035131	Brinp3	B830045N13Rik|Fam5c	bone morphogenetic protein/retinoic acid inducible neural specific 3	protein-coding
mm_136143.1	chr16	87443217	87443220	-	1	NA	Intergenic	RMER16B|LTR|ERVK	-2626	NM_016924	53858	Mm.162406	NM_016924	ENSMUSG00000041079	Rwdd2b	ORF5	RWD domain containing 2B	protein-coding
mm_124029.1	chr14	76821741	76821753	-	1	NA	Intergenic	Intergenic	144179	NR_015485	73272	Mm.116804	NR_015485	ENSMUSG00000101009	1700108F19Rik	1700020I02Rik|BB065030	RIKEN cDNA 1700108F19 gene	ncRNA
mm_146013.1	chr18	69347601	69347607	+	1	NA	intron (NM_013685, intron 2 of 19)	intron (NM_013685, intron 2 of 19)	1883	NM_001083967	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding
mm_24659.1	chr3	94479129	94479149	+	1	NA	exon (NM_001289613, exon 1 of 13)	exon (NM_001289613, exon 1 of 13)	590	NM_172434	78784	Mm.44292	NM_172434	ENSMUSG00000028137	Celf3	4930415M08Rik|BRUNOL1|CAGH4|ERDA4|Tnrc4	CUGBP, Elav-like family member 3	protein-coding
mm_1884.1	chr1	85670079	85670090	+	1	NA	intron (NM_001313713, intron 7 of 15)	intron (NM_001313713, intron 7 of 15)	20096	NM_001313714	20684	Mm.290906	NM_013673	ENSMUSG00000026222	Sp100	A430075G10Rik	nuclear antigen Sp100	protein-coding
mm_34527.1	chr4	149261120	149261134	+	1	NA	intron (NM_001290995, intron 14 of 48)	intron (NM_001290995, intron 14 of 48)	46571	NM_207682	16561	Mm.402393	NM_008441	ENSMUSG00000063077	Kif1b	A530096N05Rik|AI448212|AI506502|D4Mil1e|KIF1Bp130|KIF1Bp204	kinesin family member 1B	protein-coding
mm_16043.1	chr2	167698163	167698199	+	1	NA	TTS (NR_015500)	TTS (NR_015500)	7004	NR_015500	329562	Mm.123101	NM_177851	ENSMUSG00000006462	A530013C23Rik	-	RIKEN cDNA A530013C23 gene	ncRNA
mm_101826.1	chr11	47105735	47105737	-	1	NA	intron (NM_011891, intron 5 of 7)	intron (NM_011891, intron 5 of 7)	273566	NM_011891	24052	Mm.338890	NM_011891	ENSMUSG00000020354	Sgcd	35kDa|delta-SG	sarcoglycan, delta (dystrophin-associated glycoprotein)	protein-coding
mm_165213.1	chr2	35964930	35964930	+	1	NA	intron (NM_029774, intron 1 of 9)	intron (NM_029774, intron 1 of 9)	14694	NM_029774	74410	Mm.21591	NM_028921	ENSMUSG00000026885	Ttll11	4932702F08Rik|4933424A20Rik|AU043211|D2Ertd624e	tubulin tyrosine ligase-like family, member 11	protein-coding
mm_17663.1	chr2	32083622	32083634	-	1	NA	promoter-TSS (NM_175511)	promoter-TSS (NM_175511)	77	NM_175511	241303	Mm.250441	NM_175511	ENSMUSG00000050592	Fam78a	A130092J06Rik	family with sequence similarity 78, member A	protein-coding
mm_81499.1	chr9	110034381	110034414	+	1	NA	exon (NM_008633, exon 7 of 19)	exon (NM_008633, exon 7 of 19)	-17624	NM_001311163	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_72559.1	chr8	84073901	84073919	+	1	NA	exon (NM_009055, exon 2 of 21)	exon (NM_009055, exon 2 of 21)	7074	NM_009055	19724	Mm.7892	NM_009055	ENSMUSG00000031706	Rfx1	AI047719|AI385641	regulatory factor X, 1 (influences HLA class II expression)	protein-coding
mm_24867.1	chr3	95937144	95937157	+	1	NA	exon (NM_001253757, exon 4 of 7)	exon (NM_001253757, exon 4 of 7)	7893	NM_023210	66471	Mm.218657	NM_023210	ENSMUSG00000015749	Anp32e	2810018A15Rik|AI047746|AI326868|CPD1|LANP-L|LANPL|mLANP-L	acidic (leucine-rich) nuclear phosphoprotein 32 family, member E	protein-coding
mm_82097.1	chr9	123056643	123056653	+	1	NA	exon (NM_177911, exon 10 of 14)	exon (NM_177911, exon 10 of 14)	21907	NM_177911	331046	Mm.195309	NM_177911	ENSMUSG00000025787	Tgm4	9530008N10Rik|Eapa1|TGP	transglutaminase 4 (prostate)	protein-coding
mm_2375.1	chr1	93343619	93343672	+	1	NA	promoter-TSS (NM_080850)	promoter-TSS (NM_080850)	0	NM_023200	66385	Mm.88704	NM_023200	ENSMUSG00000026275	Ppp1r7	2310014J01Rik|SDS22	protein phosphatase 1, regulatory (inhibitor) subunit 7	protein-coding
mm_126162.1	chr15	78437113	78437145	+	1	NA	intron (NR_110357, intron 6 of 6)	intron (NR_110357, intron 6 of 6)	8565	NR_110357	72844	Mm.390816	NM_001081367	ENSMUSG00000033287	Kctd17	2900008M13Rik|AA414907|AW742389|N28155	potassium channel tetramerisation domain containing 17	protein-coding
mm_143961.1	chr17	87025540	87025548	-	1	NA	promoter-TSS (NM_008838)	promoter-TSS (NM_008838)	-17	NM_019936	56724	Mm.109329	NM_019936	ENSMUSG00000024146	Cript	1200020A08Rik|AA589469	cysteine-rich PDZ-binding protein	protein-coding
mm_166348.1	chr5	119670727	119670730	+	1	NA	promoter-TSS (NM_011535)	promoter-TSS (NM_011535)	-134	NM_198052	21386	Mm.219139	NM_011535	ENSMUSG00000018604	Tbx3	D5Ertd189e	T-box 3	protein-coding
mm_141299.1	chr17	28080273	28080279	-	1	NA	exon (NM_013687, exon 2 of 10)	exon (NM_013687, exon 2 of 10)	308	NM_013687	21463	Mm.29758	NM_013687	ENSMUSG00000062859	Tcp11	D17Ken1|Tcp-11	t-complex protein 11	protein-coding
mm_119946.1	chr14	54991099	54991113	+	1	NA	exon (NM_080728, exon 8 of 41)	exon (NM_080728, exon 8 of 41)	3443	NM_080728	140781	Mm.457983	NM_080728	ENSMUSG00000053093	Myh7	B-MHC|MyHC-I|Myhc-b|Myhcb|beta-MHC	myosin, heavy polypeptide 7, cardiac muscle, beta	protein-coding
mm_52500.1	chr6	115212907	115212915	+	1	NA	intron (NM_001111015, intron 1 of 12)	intron (NM_001111015, intron 1 of 12)	-26083	NM_001326560	20965	Mm.441431	NM_013681	ENSMUSG00000009394	Syn2	2900074L19Rik|AI836018|AI841723	synapsin II	protein-coding
mm_132519.1	chr16	37592082	37592085	+	1	NA	intron (NM_013547, intron 3 of 13)	intron (NM_013547, intron 3 of 13)	11930	NM_013547	15233	Mm.157442	NM_013547	ENSMUSG00000022821	Hgd	Hgo|aku	homogentisate 1, 2-dioxygenase	protein-coding
mm_18891.1	chr2	76709903	76709915	-	1	NA	exon (NM_011652, exon 307 of 313)	exon (NM_011652, exon 307 of 313)	34594	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_29457.1	chr3	113545560	113545585	-	1	NA	Intergenic	Intergenic	29190	NM_007446	11722	Mm.439727	NM_007446	ENSMUSG00000074264	Amy1	Amy-1|Amy1a|C030014B17Rik	amylase 1, salivary	protein-coding
mm_111132.1	chr12	81511059	81511083	-	1	NA	intron (NM_001309814, intron 1 of 2)	intron (NM_001309814, intron 1 of 2)	21840	NM_001309847	105940408		NM_001309847	ENSMUSG00000021139	Synj2bp-cox16	ARIP2a	Synj2bp-cox16 readthrough	protein-coding
mm_119805.1	chr14	54220567	54220585	+	1	NA	Intergenic	Intergenic	33353	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_161512.1	chr15	98604671	98604671	-	1	NA	exon (NM_007405, exon 2 of 22)	exon (NM_007405, exon 2 of 22)	2962	NM_007405	11512	Mm.157091	NM_007405	ENSMUSG00000022994	Adcy6	AC6|mKIAA0422	adenylate cyclase 6	protein-coding
mm_7794.1	chr1	131520707	131520710	-	1	NA	intron (NM_001081011, intron 2 of 22)	B1_Mur2|SINE|Alu	6653	NM_001081011	14270	Mm.276259	NM_019520	ENSMUSG00000026425	Srgap2	9930124L22Rik|AI448945|FBP2|Fnbp2|srGAP3	SLIT-ROBO Rho GTPase activating protein 2	protein-coding
mm_148338.1	chr18	84468646	84468648	-	1	NA	intron (NM_001033341, intron 3 of 8)	PB1D10|SINE|Alu	120857	NM_001033341	240476	Mm.329575	NM_001033341	ENSMUSG00000048410	Zfp407	6430585N13Rik|Gm333|Gm334|Gm948|ZNF407	zinc finger protein 407	protein-coding
mm_63981.1	chr7	139983834	139983883	+	1	NA	exon (NM_001291066, exon 20 of 24)	exon (NM_001291066, exon 20 of 24)	3016	NR_106029	102465643		NR_106029	ENSMUSG00000099092	Mir7062	Gm27339|mmu-mir-7062	microRNA 7062	ncRNA
mm_67970.1	chr7	100644919	100644931	-	1	NA	3' UTR (NM_001163182, exon 8 of 8)	3' UTR (NM_001163182, exon 8 of 8)	12040	NM_001163187	27276	Mm.491216	NM_013746	ENSMUSG00000030701	Plekhb1	AI315628|PHR1|Phret1|evt-1	pleckstrin homology domain containing, family B (evectins) member 1	protein-coding
mm_143869.1	chr17	84186873	84186889	-	1	NA	exon (NM_001001806, exon 2 of 2)	exon (NM_001001806, exon 2 of 2)	1066	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_91692.1	chr10	43997365	43997375	-	1	NA	exon (NM_172393, exon 2 of 20)	exon (NM_172393, exon 2 of 20)	7476	NM_172393	11630	Mm.292082	NM_172393	ENSMUSG00000019866	Aim1	AI462491|AI463325	absent in melanoma 1	protein-coding
mm_103898.1	chr11	83575359	83575366	-	1	NA	3' UTR (NM_011338, exon 4 of 4)	3' UTR (NM_011338, exon 4 of 4)	3274	NM_011338	20308	Mm.416125	NM_011338	ENSMUSG00000019122	Ccl9	CCF18|MRP-2|Scya10|Scya9	chemokine (C-C motif) ligand 9	protein-coding
mm_7776.1	chr1	131275278	131275305	-	1	NA	intron (NM_019777, intron 4 of 21)	intron (NM_019777, intron 4 of 21)	4272	NM_019777	56489	Mm.386783	NM_019777	ENSMUSG00000042349	Ikbke	AW558201|IKK-i|IKKepsilon|Ikki	inhibitor of kappaB kinase epsilon	protein-coding
mm_172413.1	chr7	19903247	19903251	+	1	NA	TTS (NM_027514)	TTS (NM_027514)	-15284	NM_177036	319930	Mm.215839	NM_177036	ENSMUSG00000049848	Ceacam19	C130022P09Rik|CEAL1	carcinoembryonic antigen-related cell adhesion molecule 19	protein-coding
mm_156342.1	chrX	139010098	139010113	+	1	NA	Intergenic	B4|SINE|B4	75131	NM_177920	331535	Mm.211704	NM_177920	ENSMUSG00000031271	Serpina7	C730040N12Rik|Tbg	serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 7	protein-coding
mm_15901.1	chr2	164960847	164960863	+	1	NA	Intergenic	CpG	-7133	NM_020333	57138	Mm.252987	NM_020333	ENSMUSG00000017740	Slc12a5	KCC2|mKIAA1176	solute carrier family 12, member 5	protein-coding
mm_115056.1	chr13	100655283	100655313	+	1	NA	exon (NM_001015889, exon 3 of 3)	exon (NM_001015889, exon 3 of 3)	3691	NM_001015889	108143	Mm.301148	NM_027139	ENSMUSG00000052293	Taf9	2310012M09Rik|AA673500|AU045423|TAFII31|TAFII32|Taf2g	TATA-box binding protein associated factor 9	protein-coding
mm_34637.1	chr4	150615078	150615118	+	1	NA	exon (NM_001085492, exon 18 of 23)	exon (NM_001085492, exon 18 of 23)	37076	NM_173774	242773	Mm.29280	NM_173774	ENSMUSG00000039838	Slc45a1	C230078B22|Dnb5	solute carrier family 45, member 1	protein-coding
mm_47335.1	chr5	122501272	122501281	-	1	NA	intron (NM_001110140, intron 1 of 19)	CpG	949	NM_001110140	11938	Mm.227583	NM_009722	ENSMUSG00000029467	Atp2a2	9530097L16Rik|D5Wsu150e|SERCA2|SERCA2B|Serca2a|mKIAA4195	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	protein-coding
mm_156673.1	chrX	159255904	159255912	+	1	NA	5' UTR (NM_148945, exon 1 of 22)	5' UTR (NM_148945, exon 1 of 22)	126	NM_001346675	110651	Mm.328476	NM_148945	ENSMUSG00000031309	Rps6ka3	MAPKAPK-1b|MPK-9|Rsk2|S6K-alpha3|p90RSK3|pp90RSK2	ribosomal protein S6 kinase polypeptide 3	protein-coding
mm_92131.1	chr10	64090299	64090309	-	1	NA	promoter-TSS (NM_178678)	promoter-TSS (NM_178678)	-49	NM_178678	216028	Mm.431318	NM_178678	ENSMUSG00000042846	Lrrtm3	9630044H04Rik	leucine rich repeat transmembrane neuronal 3	protein-coding
mm_113123.1	chr13	24575558	24575569	+	1	NA	Intergenic	Intergenic	-6626	NM_001286100	193385	Mm.217319	NM_029679	ENSMUSG00000036006	Fam65b	-	family with sequence similarity 65, member B	protein-coding
mm_29949.1	chr3	132977208	132977211	-	1	NA	Intergenic	Intergenic	-26918	NM_033525	114249	Mm.279310	NM_033525	ENSMUSG00000040998	Npnt	1110009H02Rik|AA682063|AI314031|Nctn|POEM	nephronectin	protein-coding
mm_80013.1	chr9	67854307	67854323	+	1	NA	intron (NM_177184, intron 3 of 84)	intron (NM_177184, intron 3 of 84)	13919	NM_177184	320528	Mm.241454	NM_177184	ENSMUSG00000035284	Vps13c	AI552542|AV026040|C230055H22Rik|W51662|chorein	vacuolar protein sorting 13C	protein-coding
mm_67547.1	chr7	81493865	81493871	-	1	NA	promoter-TSS (NM_021492)	promoter-TSS (NM_021492)	57	NM_021492	11775	Mm.322894	NM_021492	ENSMUSG00000062444	Ap3b2	AI549966|AU042881|Naptb|[b]-NAP|beta-NAP|beta3B	adaptor-related protein complex 3, beta 2 subunit	protein-coding
mm_12135.1	chr2	61660990	61661012	+	1	NA	Intergenic	Intergenic	-50693	NM_021526	59029	Mm.218198	NM_021526	ENSMUSG00000026914	Psmd14	2610312C03Rik|3200001M20Rik|AA986732|Pad1|Poh1|rpm11	proteasome (prosome, macropain) 26S subunit, non-ATPase, 14	protein-coding
mm_20907.1	chr2	150362689	150362698	-	1	NA	promoter-TSS (NM_027017)	promoter-TSS (NM_027017)	72	NM_027017	69277	Mm.272470	NM_027017	ENSMUSG00000063364	3300002I08Rik	2900016H11Rik	RIKEN cDNA 3300002I08 gene	protein-coding
mm_46271.1	chr5	99978903	99978913	-	1	NA	promoter-TSS (NM_007516)	promoter-TSS (NM_007516)	30	NM_001077266	11991	Mm.150231	NM_007516	ENSMUSG00000000568	Hnrnpd	Auf1|Hnrpd	heterogeneous nuclear ribonucleoprotein D	protein-coding
mm_88611.1	chr10	79824674	79824695	+	1	NA	intron (NM_030218, intron 1 of 4)	intron (NM_030218, intron 1 of 4)	3663	NM_030218	78906	Mm.33087	NM_030218	ENSMUSG00000035852	Misp	9130017N09Rik	mitotic spindle positioning	protein-coding
mm_134228.1	chr16	11343406	11343450	-	1	NA	intron (NM_028964, intron 1 of 20)	intron (NM_028964, intron 1 of 20)	20524	NM_028964	74478	Mm.325831	NM_028964	ENSMUSG00000071669	Snx29	4933437K13Rik|ENSMUSG00000079738|Gm11170|Gm1737|Gm930|Rundc2a	sorting nexin 29	protein-coding
mm_769.1	chr1	44120089	44120102	+	1	NA	5' UTR (NM_144558, exon 1 of 10)	5' UTR (NM_144558, exon 1 of 10)	127	NM_144558	246229	Mm.386883	NM_144558	ENSMUSG00000041684	Bivm	AI854267	basic, immunoglobulin-like variable motif containing	protein-coding
mm_67014.1	chr7	65452909	65452911	-	1	NA	Intergenic	B1_Mur2|SINE|Alu	-81666	NM_009386	21872	Mm.4342	NM_009386	ENSMUSG00000030516	Tjp1	ZO1	tight junction protein 1	protein-coding
mm_170813.1	chr2	176226536	176226548	+	1	NA	promoter-TSS (NM_001305136)	promoter-TSS (NM_001305136)	-23	NM_001305137	100504263	Mm.379980	NM_001305136	ENSMUSG00000078894	2210418O10Rik	Gm6182	predicted gene 2210418O10Rik	protein-coding
mm_43180.1	chr5	127896242	127896248	+	1	NA	intron (NM_172885, intron 4 of 8)	ORR1A2|LTR|ERVL-MaLR	263983	NM_177005	319804	Mm.237888	NM_177005	ENSMUSG00000049971	Glt1d1	5730455A04Rik	glycosyltransferase 1 domain containing 1	protein-coding
mm_23490.1	chr3	60501978	60502000	+	1	NA	intron (NM_001253710, intron 1 of 7)	intron (NM_001253710, intron 1 of 7)	810	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_104936.1	chr11	100096274	100096279	-	1	NA	promoter-TSS (NM_016880)	promoter-TSS (NM_016880)	-52	NM_016880	53617	Mm.37952	NM_016880	ENSMUSG00000048013	Krt35	AI662400|Ha5|Krt1-24|Krtha5	keratin 35	protein-coding
mm_12918.1	chr2	84937615	84937634	+	1	NA	5' UTR (NM_021398, exon 2 of 13)	5' UTR (NM_021398, exon 2 of 13)	978	NM_021398	58207	Mm.290729	NM_021398	ENSMUSG00000027074	Slc43a3	Eeg1|SEEEG-1	solute carrier family 43, member 3	protein-coding
mm_34747.1	chr4	152297251	152297255	+	1	NA	promoter-TSS (NM_133788)	promoter-TSS (NM_133788)	39	NM_133788	57295	Mm.277464	NM_133788	ENSMUSG00000039662	Icmt	1700008E11Rik|C80758|Gm13095|HSTE14|OTTMUSG00000010406|PPMT|STE14|pcCMT	isoprenylcysteine carboxyl methyltransferase	protein-coding
mm_57903.1	chr6	131388418	131388464	-	1	NA	promoter-TSS (NM_011733)	promoter-TSS (NM_011733)	9	NM_139117	56449	Mm.458000	NM_011733	ENSMUSG00000030189	Ybx3	Csda|Dpba|MSY3|MSY4|Yb2|dbpA|oxyR	Y box protein 3	protein-coding
mm_98817.1	chr11	97310217	97310225	+	1	NA	Intergenic	Intergenic	-5495	NM_025927	67036	Mm.5381	NM_025927	ENSMUSG00000018882	Mrpl45	2600005P05Rik|AU043542|R75241	mitochondrial ribosomal protein L45	protein-coding
mm_23399.1	chr3	57942889	57942899	+	1	NA	Intergenic	Intergenic	-95137	NM_019410	18645	Mm.271744	NM_019410	ENSMUSG00000027805	Pfn2	Pfn	profilin 2	protein-coding
mm_86081.1	chr9	114781946	114781956	-	1	NA	promoter-TSS (NM_133978)	promoter-TSS (NM_133978)	42	NM_133978	102545	Mm.35600	NM_133978	ENSMUSG00000032436	Cmtm7	AI481279|Cklfsf7|LNV	CKLF-like MARVEL transmembrane domain containing 7	protein-coding
mm_43441.1	chr5	136096871	136096884	+	1	NA	intron (NM_001039103, intron 7 of 19)	intron (NM_001039103, intron 7 of 19)	-8645	NR_106002	102465626		NR_106002	ENSMUSG00000099003	Mir7035	Gm27661|mmu-mir-7035	microRNA 7035	ncRNA
mm_12761.1	chr2	79255747	79255760	+	1	NA	exon (NM_010576, exon 1 of 28)	exon (NM_010576, exon 1 of 28)	327	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D|Itga4B	integrin alpha 4	protein-coding
mm_26055.1	chr3	135825649	135825664	+	1	NA	promoter-TSS (NM_001135150)	promoter-TSS (NM_001135150)	-1	NM_001135149	67547	Mm.30239	NM_026228	ENSMUSG00000053897	Slc39a8	4933419D20Rik|AA986696|BIGM103|ZIP-8|Zip8	solute carrier family 39 (metal ion transporter), member 8	protein-coding
mm_32644.1	chr4	115057411	115057437	+	1	NA	promoter-TSS (NM_001287388)	promoter-TSS (NM_001287388)	-387	NM_001287388	21349	Mm.239869	NM_011527	ENSMUSG00000028717	Tal1	Hpt|SCL/tal-1|Scl|bHLHa17|tal-1	T cell acute lymphocytic leukemia 1	protein-coding
mm_150308.1	chr19	34570986	34570994	+	1	NA	intron (NM_008332, intron 2 of 2)	RMER17C|LTR|ERVK	-12539	NM_010501	15959	Mm.426079	NM_010501	ENSMUSG00000074896	Ifit3	Ifi49|P49	interferon-induced protein with tetratricopeptide repeats 3	protein-coding
mm_121881.1	chr14	21500284	21500299	-	1	NA	intron (NM_017479, intron 1 of 16)	CpG	506	NM_017479	54169	Mm.248967	NM_017479	ENSMUSG00000021767	Kat6b	AI507552|B130044K16Rik|MYST-4|Morf|Myst4|mKIAA0383|qkf|querkopf	K(lysine) acetyltransferase 6B	protein-coding
mm_63473.1	chr7	127652126	127652130	+	1	NA	Intergenic	RLTR26_Mus|LTR|ERVK	-37695	NM_177226	320683	Mm.156718	NM_177226	ENSMUSG00000045639	Zfp629	9330199A09Rik|Znf629	zinc finger protein 629	protein-coding
mm_120611.1	chr14	70205226	70205237	+	1	NA	promoter-TSS (NM_001271408)	promoter-TSS (NM_001271408)	-608	NM_001271408	20410	Mm.5068	NM_011366	ENSMUSG00000022091	Sorbs3	SCAM-1|SH3P3|Sh3d4|vinexin-g	sorbin and SH3 domain containing 3	protein-coding
mm_153848.1	chr19	46338590	46338630	-	1	NA	promoter-TSS (NM_001164295)	promoter-TSS (NM_001164295)	50	NM_001164294	67116	Mm.218848	NM_024192	ENSMUSG00000036748	Cuedc2	3010002G01Rik	CUE domain containing 2	protein-coding
mm_98624.1	chr11	95918892	95918901	+	1	NA	Intergenic	RMER2|LTR|ERV1	-4025	NM_008081	14422	Mm.340702	NM_008081	ENSMUSG00000013418	B4galnt2	AI593864|Dlb-1|Dlb1|Galg2|Galgt2|Ggm3|Igf2bp1	beta-1,4-N-acetyl-galactosaminyl transferase 2	protein-coding
mm_126384.1	chr15	80173553	80173580	+	1	NA	promoter-TSS (NM_010795)	promoter-TSS (NM_010795)	-155	NM_010795	17309	Mm.299693	NM_010795	ENSMUSG00000042428	Mgat3	1110038J12Rik|AI848272|GnT-III	mannoside acetylglucosaminyltransferase 3	protein-coding
mm_163169.1	chr11	86807659	86807661	-	1	NA	promoter-TSS (NM_026191)	promoter-TSS (NM_026191)	0	NM_026191	67487	Mm.260627	NM_026191	ENSMUSG00000018425	Dhx40	2410016C14Rik|ARG147|DDX40|PAD	DEAH (Asp-Glu-Ala-His) box polypeptide 40	protein-coding
mm_103046.1	chr11	69799938	69799966	-	1	NA	intron (NM_001291104, intron 1 of 5)	intron (NM_001291104, intron 1 of 5)	1764	NM_001291104	14166	Mm.269011	NM_010198	ENSMUSG00000042826	Fgf11	Fgf-11|Fhf-3|Fhf3	fibroblast growth factor 11	protein-coding
mm_88706.1	chr10	80150449	80150482	+	1	NA	intron (NM_001347117, intron 2 of 7)	CpG-1261	783	NM_001305799	59090	Mm.143813	NM_021565	ENSMUSG00000035621	Midn	3000003C15Rik	midnolin	protein-coding
mm_46509.1	chr5	105136328	105136342	-	1	NA	intron (NM_008620, intron 2 of 10)	B3|SINE|B2	3217	NM_008620	17472	Mm.440525	NM_008620	ENSMUSG00000079363	Gbp4	AW228052|Mag-2|Mpa-2|Mpa2	guanylate binding protein 4	protein-coding
mm_128072.1	chr15	27661551	27661551	-	1	NA	intron (NM_198301, intron 4 of 6)	L1ME1|LINE|L1	19991	NM_001242424	223433	Mm.266485	NM_198301	ENSMUSG00000056069	Fam105a	9830126M18	family with sequence similarity 105, member A	protein-coding
mm_143190.1	chr17	59013265	59013343	-	1	NA	promoter-TSS (NM_026497)	promoter-TSS (NM_026497)	18	NM_026497	67993	Mm.36507	NM_026497	ENSMUSG00000024228	Nudt12	0610016O18Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 12	protein-coding
mm_39976.1	chr5	32353523	32353536	+	1	NA	promoter-TSS (NM_172147)	promoter-TSS (NM_172147)	-51	NM_172147	665270	Mm.160067	NM_030072	ENSMUSG00000029134	Plb1	4632413E21Rik|4930433E17Rik|4930539A06Rik|BC033606	phospholipase B1	protein-coding
mm_49644.1	chr6	30805611	30805624	+	1	NA	intron (NM_017478, intron 20 of 23)	intron (NM_017478, intron 20 of 23)	64318	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_133575.1	chr16	91406439	91406460	+	1	NA	TTS (NM_010509)	TTS (NM_010509)	214	NM_008349	16155	Mm.4154	NM_008349	ENSMUSG00000022969	Il10rb	6620401D04Rik|AI528744|CRF2-4|Crfb4|D16H21S58|D21S58h|IL-10R2|Il10r2	interleukin 10 receptor, beta	protein-coding
mm_102811.1	chr11	68947541	68947574	-	1	NA	intron (NM_177566, intron 11 of 15)	intron (NM_177566, intron 11 of 15)	9301	NM_177566	442801	Mm.376147	NM_177566	ENSMUSG00000052921	Arhgef15	D130071N09|D530030K12Rik|E5	Rho guanine nucleotide exchange factor (GEF) 15	protein-coding
mm_53674.1	chr6	141866359	141866365	+	1	NA	Intergenic	Intergenic	-10191	NM_030687	28250	Mm.255586	NM_030687	ENSMUSG00000030237	Slco1a4	AI785519|Oatp1a4|Oatp2|Slc21a5	solute carrier organic anion transporter family, member 1a4	protein-coding
mm_117128.1	chr13	60934801	60934811	-	1	NA	3' UTR (NM_001145799, exon 5 of 5)	3' UTR (NM_001145799, exon 5 of 5)	1760	NM_001145799	13024	Mm.482089	NM_007796	ENSMUSG00000044258	Ctla2a	Ctla-2a	cytotoxic T lymphocyte-associated protein 2 alpha	protein-coding
mm_164948.1	chr19	4262517	4262517	+	1	NA	exon (NM_198113, exon 14 of 14)	exon (NM_198113, exon 14 of 14)	1361	NR_105951	102465595		NR_105951	ENSMUSG00000099290	Mir6985	Gm27719|mmu-mir-6985	microRNA 6985	ncRNA
mm_101722.1	chr11	42182442	42182442	-	1	NA	5' UTR (NM_010250, exon 1 of 10)	5' UTR (NM_010250, exon 1 of 10)	488	NM_010250	14394	Mm.439668	NM_010250	ENSMUSG00000010803	Gabra1	Gabra-1	gamma-aminobutyric acid (GABA) A receptor, subunit alpha 1	protein-coding
mm_76017.1	chr8	73353478	73353551	-	1	NA	promoter-TSS (NM_010687)	promoter-TSS (NM_010687)	26	NM_001317391	16795	Mm.324371	NM_010687	ENSMUSG00000004383	Large1	BPFD#36|Gyltl1a|Large|Mbp-1|Mbp1|enr|fg|froggy|myd	LARGE xylosyl- and glucuronyltransferase 1	protein-coding
mm_162483.1	chr1	135105235	135105237	-	1	NA	promoter-TSS (NM_001033409)	promoter-TSS (NM_001033409)	40	NM_001033409	329252	Mm.279594	NM_001033409	ENSMUSG00000042793	Lgr6	A530037C04Rik|D830026M09	leucine-rich repeat-containing G protein-coupled receptor 6	protein-coding
mm_153195.1	chr19	34524593	34524619	-	1	NA	intron (NM_001111100, intron 2 of 9)	intron (NM_001111100, intron 2 of 9)	2868	NM_001111100	16889	Mm.157545	NM_021460	ENSMUSG00000024781	Lipa	AA960673|Lal|Lip-1|Lip1	lysosomal acid lipase A	protein-coding
mm_70359.1	chr8	8335066	8335080	+	1	NA	Intergenic	Intergenic	325700	NM_010111	13642	Mm.209813	NM_010111	ENSMUSG00000001300	Efnb2	ELF-2|Epl5|Eplg5|Htk-L|LERK-5|Lerk5|NLERK-1	ephrin B2	protein-coding
mm_33170.1	chr4	126025521	126025531	+	1	NA	intron (NR_045561, intron 1 of 15)	B1F|SINE|Alu	867	NM_001252651	12986	Mm.271701	NM_007782	ENSMUSG00000028859	Csf3r	Cd114|Csfgr|G-CSF-R|G-CSFR	colony stimulating factor 3 receptor (granulocyte)	protein-coding
mm_122878.1	chr14	54926564	54926572	-	1	NA	5' UTR (NM_010112, exon 1 of 6)	5' UTR (NM_010112, exon 1 of 6)	220	NM_010112	13644	Mm.236438	NM_010112	ENSMUSG00000022203	Efs	-	embryonal Fyn-associated substrate	protein-coding
mm_27139.1	chr3	32616464	32616473	-	1	NA	promoter-TSS (NM_013531)	promoter-TSS (NM_013531)	67	NM_013531	14696	Mm.139192	NM_013531	ENSMUSG00000027669	Gnb4	6720453A21Rik|G(beta)4	guanine nucleotide binding protein (G protein), beta 4	protein-coding
mm_37102.1	chr4	116627897	116627908	-	1	NA	promoter-TSS (NM_016777)	promoter-TSS (NM_016777)	49	NM_016777	50927	Mm.257181	NM_016777	ENSMUSG00000028693	Nasp	5033430J04Rik|AI131596|AI317140|D4Ertd767e|Epcs32|Nasp-T	nuclear autoantigenic sperm protein (histone-binding)	protein-coding
mm_81935.1	chr9	120180263	120180277	+	1	NA	Intergenic	Intergenic	30528	NM_001039364	17433	Mm.486167	NM_008614	ENSMUSG00000032517	Mobp	AI835053|AI839848|MOBP155|MOBP170|MOBP69|MOBP73|MOBP81|R74645	myelin-associated oligodendrocytic basic protein	protein-coding
mm_73230.1	chr8	104111389	104111401	+	1	NA	intron (NM_009868, intron 1 of 11)	intron (NM_009868, intron 1 of 11)	-5522	NR_131138	546096	Mm.252264	NR_131138	ENSMUSG00000110053	Gm29682	-	predicted gene, 29682	ncRNA
mm_72289.1	chr8	75213260	75213285	+	1	NA	promoter-TSS (NM_029182)	promoter-TSS (NM_029182)	-672	NM_029182	75141	Mm.179267	NM_029182	ENSMUSG00000034472	Rasd2	4930526B11Rik|AU045414|Rhes|TEM-2|TEM2	RASD family, member 2	protein-coding
mm_11503.1	chr2	32536049	32536055	+	1	NA	5' UTR (NM_153560, exon 1 of 11)	5' UTR (NM_153560, exon 1 of 11)	693	NM_153560	98952	Mm.4065	NM_153560	ENSMUSG00000039157	Fam102a	AI426465|C230093N12Rik|Eeig1	family with sequence similarity 102, member A	protein-coding
mm_6574.1	chr1	75210733	75210807	-	1	NA	promoter-TSS (NM_011494)	promoter-TSS (NM_011494)	8	NM_029010	74577	Mm.458319	NM_029010	ENSMUSG00000026200	Glb1l	4833408P15Rik	galactosidase, beta 1-like	protein-coding
mm_5212.1	chr1	13626206	13626210	-	1	NA	3' UTR (NM_145381, exon 7 of 7)	3' UTR (NM_145381, exon 7 of 7)	34301	NM_145381	212442	Mm.89572	NM_145381	ENSMUSG00000025937	Lactb2	Cgi-83|E430032H21Rik	lactamase, beta 2	protein-coding
mm_107668.1	chr12	53248400	53248421	+	1	NA	promoter-TSS (NM_013780)	promoter-TSS (NM_013780)	-267	NM_013780	27386	Mm.247044	NM_013780	ENSMUSG00000021010	Npas3	4930423H22Rik|bHLHe12	neuronal PAS domain protein 3	protein-coding
mm_85860.1	chr9	110747126	110747132	-	1	NA	promoter-TSS (NM_011199)	promoter-TSS (NM_011199)	16	NM_011199	19228	Mm.3542	NM_011199	ENSMUSG00000032492	Pth1r	PPR|Pthr|Pthr1	parathyroid hormone 1 receptor	protein-coding
mm_68928.1	chr7	126475083	126475120	-	1	NA	promoter-TSS (NM_001289538)	promoter-TSS (NM_001289538)	29	NM_001289538	20399	Mm.8538	NM_011363	ENSMUSG00000030733	Sh2b1	AI425885|C530001K22Rik|Irip|Psm|SH2-B|SH2-Bb|Sh2bpsm1|mKIAA1299	SH2B adaptor protein 1	protein-coding
mm_144275.1	chr18	11657490	11657502	+	1	NA	non-coding (NR_045526, exon 1 of 18)	non-coding (NR_045526, exon 1 of 18)	147	NM_001081223	225182	Mm.154275	NM_175458	ENSMUSG00000041238	Rbbp8	9930104E21Rik|CtIP|RBBP-8|RIM|SAE2	retinoblastoma binding protein 8	protein-coding
mm_38186.1	chr4	135325318	135325327	-	1	NA	intron (NM_016799, intron 14 of 17)	intron (NM_016799, intron 14 of 17)	27892	NM_016799	51796	Mm.1963	NM_016799	ENSMUSG00000028809	Srrm1	AA407769|POP101|Srm160	serine/arginine repetitive matrix 1	protein-coding
mm_29898.1	chr3	131364735	131364740	-	1	NA	Intergenic	Intergenic	-19814	NM_028943	74442	Mm.273360	NM_028943	ENSMUSG00000050931	Sgms2	4933405A16Rik|5133401H06Rik|AI854299	sphingomyelin synthase 2	protein-coding
mm_158979.1	chr1	125435694	125435694	-	1	NA	promoter-TSS (NM_023735)	promoter-TSS (NM_023735)	33	NM_023735	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding
mm_124575.1	chr14	124557543	124557555	-	1	NA	intron (NM_207667, intron 1 of 4)	intron (NM_207667, intron 1 of 4)	119578	NM_207667	14169	Mm.206362	NM_010201	ENSMUSG00000025551	Fgf14	FHF-4|Fhf4|mFHF-4(1B)	fibroblast growth factor 14	protein-coding
mm_69287.1	chr7	128205972	128206005	-	1	NA	TTS (NM_001029872)	TTS (NM_001029872)	378	NM_009943	12862	Mm.43824	NM_009943	ENSMUSG00000030785	Cox6a2	CoxVIaH|VIaH	cytochrome c oxidase subunit VIa polypeptide 2	protein-coding
mm_81.1	chr1	6749238	6749238	+	1	NA	intron (NM_001244692, intron 3 of 23)	intron (NM_001244692, intron 3 of 23)	19187	NR_045188	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding
mm_136618.1	chr17	5492915	5492954	+	1	NA	5' UTR (NM_146073, exon 1 of 9)	5' UTR (NM_146073, exon 1 of 9)	334	NM_146073	224454	Mm.487663	NM_146073	ENSMUSG00000034265	Zdhhc14	B530001K09Rik|New1cp	zinc finger, DHHC domain containing 14	protein-coding
mm_99827.1	chr11	108920812	108920841	+	1	NA	intron (NM_015732, intron 1 of 10)	CpG	477	NM_015732	12006	Mm.71710	NM_015732	ENSMUSG00000000142	Axin2	Axi1|Axil|Conductin	axin 2	protein-coding
mm_136691.1	chr17	6895953	6895963	+	1	NA	promoter-TSS (NR_030465)	promoter-TSS (NR_030465)	-621	NR_030465	751529		NR_030465	ENSMUSG00000076218	Mir692-1	Mirn692-1|mir-692-1	microRNA 692-1	ncRNA
mm_67680.1	chr7	89338606	89338632	-	1	NA	5' UTR (NM_028343, exon 1 of 15)	5' UTR (NM_028343, exon 1 of 15)	168	NM_028343	72759	Mm.208477	NM_028343	ENSMUSG00000039428	Tmem135	2810439K08Rik|AW319712|PMP52	transmembrane protein 135	protein-coding
mm_127762.1	chr15	103538067	103538088	+	1	NA	promoter-TSS (NM_021391)	promoter-TSS (NM_021391)	-85	NM_021391	58200	Mm.143788	NM_021391	ENSMUSG00000022490	Ppp1r1a	0610038N18Rik|I-1	protein phosphatase 1, regulatory (inhibitor) subunit 1A	protein-coding
mm_92524.1	chr10	78712977	78712978	-	1	NA	3' UTR (NM_009809, exon 7 of 7)	3' UTR (NM_009809, exon 7 of 7)	5316	NM_009809	12365	Mm.20940	NM_009809	ENSMUSG00000005355	Casp14	MICE|mini-ICE	caspase 14	protein-coding
mm_122609.1	chr14	51057596	51057606	-	1	NA	promoter-TSS (NM_001011875)	promoter-TSS (NM_001011875)	-359	NM_001011875	497106	Mm.379740	NM_001011875	ENSMUSG00000068407	Rnase12	Rai1	ribonuclease, RNase A family, 12 (non-active)	protein-coding
mm_62448.1	chr7	101384873	101384887	+	1	NA	promoter-TSS (NM_027180)	promoter-TSS (NM_027180)	-646	NM_027180	69710	Mm.277687	NM_027180	ENSMUSG00000032812	Arap1	2410002L19Rik|Centd2|mKIAA0782	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	protein-coding
mm_121866.1	chr14	20734303	20734313	-	1	NA	TTS (NM_178597)	TTS (NM_178597)	254	NM_010811	17423	Mm.4084	NM_010811	ENSMUSG00000039308	Ndst2	Mndns|NDST-2	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 2	protein-coding
mm_101798.1	chr11	46237215	46237216	-	1	NA	intron (NM_177075, intron 1 of 1)	intron (NM_177075, intron 1 of 1)	1658	NM_177075	320116	Mm.39600	NM_177075	ENSMUSG00000048721	Fndc9	C030019I05Rik	fibronectin type III domain containing 9	protein-coding
mm_71884.1	chr8	69816799	69816831	+	1	NA	exon (NM_198101, exon 16 of 21)	exon (NM_198101, exon 16 of 21)	-5750	NM_020028	53978	Mm.23253	NM_020028	ENSMUSG00000031861	Lpar2	Edg4|IPA2|LPA2	lysophosphatidic acid receptor 2	protein-coding
mm_94582.1	chr11	11690450	11690468	+	1	NA	intron (NM_001301866, intron 1 of 5)	intron (NM_001301866, intron 1 of 5)	282	NM_001301863	22778	Mm.103545	NM_009578	ENSMUSG00000018654	Ikzf1	5832432G11Rik|Ikaros|LyF-1|Zfpn1a1|Znfn1a1|hlk-1|mKIAA4227	IKAROS family zinc finger 1	protein-coding
mm_139497.1	chr17	56241753	56241786	+	1	NA	Intergenic	Intergenic	-1219	NR_029827	723883		NR_029827	ENSMUSG00000065491	Mir7b	Mirn7b|mir-7b|mmu-mir-7b	microRNA 7b	ncRNA
mm_46973.1	chr5	115194215	115194225	-	1	NA	exon (NM_001310712, exon 1 of 6)	exon (NM_001310712, exon 1 of 6)	161	NM_001310712	29867	Mm.38551	NM_013879	ENSMUSG00000029544	Cabp1	caldendrin	calcium binding protein 1	protein-coding
mm_140198.1	chr17	83705892	83705913	+	1	NA	promoter-TSS (NM_001171052)	promoter-TSS (NM_001171052)	-261	NM_001171054	116871	Mm.277668	NM_054082	ENSMUSG00000055817	Mta3	1110002J22Rik|mKIAA1266	metastasis associated 3	protein-coding
mm_70142.1	chr7	143458491	143458517	-	1	NA	3' UTR (NM_001161624, exon 4 of 4)	3' UTR (NM_001161624, exon 4 of 4)	2546	NM_009876	12577	Mm.168789	NM_009876	ENSMUSG00000037664	Cdkn1c	AL024410|CDKI|Kip2|p57(kip2)|p57Kip2	cyclin-dependent kinase inhibitor 1C (P57)	protein-coding
mm_32011.1	chr4	94739463	94739484	+	1	NA	5' UTR (NM_001290551, exon 1 of 22)	5' UTR (NM_001290551, exon 1 of 22)	184	NM_001290551	21687	Mm.14313	NM_013690	ENSMUSG00000006386	Tek	AA517024|Cd202b|Hyk|STK1|Tie-2|Tie2	endothelial-specific receptor tyrosine kinase	protein-coding
mm_130584.1	chr15	99590855	99590899	-	1	NA	promoter-TSS (NM_009701)	promoter-TSS (NM_009701)	-151	NM_009701	11830	Mm.45580	NM_009701	ENSMUSG00000044217	Aqp5	-	aquaporin 5	protein-coding
mm_1258.1	chr1	63114734	63114765	+	1	NA	promoter-TSS (NM_001114609)	promoter-TSS (NM_001114609)	9	NR_045914	100380944	Mm.392955	NR_045914	ENSMUSG00000084799	Ino80dos	Gm11602|OTTMUSG00000002611	INO80 complex subunit D, opposite strand	ncRNA
mm_12190.1	chr2	65553850	65553856	+	1	NA	intron (NM_018732, intron 1 of 26)	intron (NM_018732, intron 1 of 26)	13639	NM_018732	20269	Mm.330256	NM_018732	ENSMUSG00000057182	Scn3a	Gm1000|Nav1.3	sodium channel, voltage-gated, type III, alpha	protein-coding
mm_108560.1	chr12	84641395	84641409	+	1	NA	intron (NM_001168589, intron 1 of 1)	intron (NM_001168589, intron 1 of 1)	383	NM_001168589	432677	Mm.311913	NM_001033776	ENSMUSG00000071235	Vrtn	7420416P09Rik	vertebrae development associated	protein-coding
mm_89383.1	chr10	89465404	89465407	+	1	NA	intron (NM_009108, intron 7 of 8)	RLTR48A|LTR|ERV1	-21438	NM_001033331	237436	Mm.11982	NM_001033331	ENSMUSG00000074802	Gas2l3	8430435B07Rik|Gm240	growth arrest-specific 2 like 3	protein-coding
mm_119572.1	chr14	50357905	50357916	+	1	NA	promoter-TSS (NM_205819)	promoter-TSS (NM_205819)	-4	NM_205819	239081	Mm.291512	NM_205819	ENSMUSG00000051969	Tlr11	Gm287	toll-like receptor 11	protein-coding
mm_46769.1	chr5	112273766	112273788	-	1	NA	Intergenic	B4|SINE|B4	-2914	NM_001326590	22022	Mm.250631	NM_009419	ENSMUSG00000029344	Tpst2	AI448750|D5Ucla3|Tango13b|grm|grt	protein-tyrosine sulfotransferase 2	protein-coding
mm_158219.1	chrX	105929334	105929382	-	1	NA	promoter-TSS (NM_009530)	promoter-TSS (NM_009530)	14	NM_009530	22589	Mm.10141	NM_009530	ENSMUSG00000031229	Atrx	4833408C14Rik|AI447451|ATR2|DXHXS6677E|HP1-BP38|Hp1bp2|Hp1bp38|MRXS3|RAD54L|Rad54|XH2|Xnp|ZNF-HX	alpha thalassemia/mental retardation syndrome X-linked	protein-coding
mm_157054.1	chrX	8090436	8090439	-	1	NA	promoter-TSS (NM_009515)	promoter-TSS (NM_009515)	54	NM_009515	22376	Mm.4735	NM_009515	ENSMUSG00000031165	Was	U42471|Wasp	Wiskott-Aldrich syndrome	protein-coding
mm_60952.1	chr7	47050659	47050680	+	1	NA	promoter-TSS (NM_026436)	promoter-TSS (NM_026436)	29	NM_026436	67893	Mm.27338	NM_026436	ENSMUSG00000010307	Tmem86a	1810054O13Rik|AI414959|AW742698	transmembrane protein 86A	protein-coding
mm_89897.1	chr10	110933885	110933885	+	1	NA	intron (NM_007792, intron 2 of 5)	ID2|SINE|ID	13709	NM_007792	13008	Mm.2020	NM_007792	ENSMUSG00000020186	Csrp2	AW551867|Crp2|SmLim	cysteine and glycine-rich protein 2	protein-coding
mm_15887.1	chr2	164841539	164841557	+	1	NA	TTS (NM_008906)	TTS (NM_008906)	7775	NM_008906	19025	Mm.359633	NM_008906	ENSMUSG00000017760	Ctsa	AU019505|PPCA|Ppgb	cathepsin A	protein-coding
mm_29760.1	chr3	127162366	127162385	-	1	NA	intron (NR_105029, intron 2 of 3)	(CCG)n|Simple_repeat|Simple_repeat	1070	NR_105029	100862268	Mm.444603	NR_105029	ENSMUSG00000097456	LOC100862268	-	uncharacterized LOC100862268	ncRNA
mm_127826.1	chr15	6435196	6435239	-	1	NA	exon (NM_001102400, exon 10 of 13)	exon (NM_001102400, exon 10 of 13)	-10116	NM_013485	12279	Mm.29095	NM_013485	ENSMUSG00000022149	C9	-	complement component 9	protein-coding
mm_75234.1	chr8	39629399	39629409	-	1	NA	intron (NM_001113326, intron 3 of 9)	intron (NM_001113326, intron 3 of 9)	13274	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_61639.1	chr7	80294542	80294550	+	1	NA	promoter-TSS (NM_145150)	promoter-TSS (NM_145150)	95	NM_001285998	233406	Mm.227274	NM_145150	ENSMUSG00000038943	Prc1	D7Ertd348e	protein regulator of cytokinesis 1	protein-coding
mm_44815.1	chr5	33629578	33629649	-	1	NA	promoter-TSS (NM_178390)	promoter-TSS (NM_178390)	22	NM_178390	74504	Mm.294695	NM_178390	ENSMUSG00000037339	Fam53a	2410018C17Rik|5430419M09Rik|Dntnp	family with sequence similarity 53, member A	protein-coding
mm_150180.1	chr19	32620049	32620060	+	1	NA	promoter-TSS (NM_011864)	promoter-TSS (NM_011864)	49	NM_011864	23972	Mm.203916	NM_011864	ENSMUSG00000024899	Papss2	1810018P12Rik|AI159688|AtpsU2|Atpsk2|Sk2|bm	3'-phosphoadenosine 5'-phosphosulfate synthase 2	protein-coding
mm_16490.1	chr2	180985033	180985071	+	1	NA	Intergenic	Intergenic	-1483	NM_028518	73368	Mm.345095	NM_028518	ENSMUSG00000016356	Col20a1	1700051I12Rik	collagen, type XX, alpha 1	protein-coding
mm_118512.1	chr14	14346401	14346477	+	1	NA	promoter-TSS (NM_008369)	promoter-TSS (NM_008369)	-56	NM_008369	16188	Mm.425857	NM_008369	ENSMUSG00000068758	Il3ra	CD123|CDw123|SUT-1	interleukin 3 receptor, alpha chain	protein-coding
mm_87770.1	chr10	60294526	60294534	+	1	NA	intron (NM_001146120, intron 4 of 13)	intron (NM_001146120, intron 4 of 13)	10069	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_31152.1	chr4	43406491	43406615	+	1	NA	promoter-TSS (NM_199057)	promoter-TSS (NM_199057)	51	NM_199057	100213	Mm.235730	NM_199057	ENSMUSG00000035969	Rusc2	AI840675|mKIAA0375	RUN and SH3 domain containing 2	protein-coding
mm_52811.1	chr6	121343330	121343341	+	1	NA	intron (NM_001347433, intron 1 of 14)	intron (NM_001347433, intron 1 of 14)	259	NM_001347433	14411	Mm.274506	NM_133661	ENSMUSG00000030109	Slc6a12	BGT1|GAT-2|GAT2|Gabt2	solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12	protein-coding
mm_46028.1	chr5	91402906	91402922	-	1	NA	promoter-TSS (NM_007568)	promoter-TSS (NM_007568)	80	NM_007568	12223	Mm.2024	NM_007568	ENSMUSG00000082361	Btc	Bcn	betacellulin, epidermal growth factor family member	protein-coding
mm_151888.1	chr19	5798709	5798709	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	-2728	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_86628.1	chr10	13967822	13967841	+	1	NA	intron (NM_010437, intron 1 of 8)	intron (NM_010437, intron 1 of 8)	1452	NM_010437	15273	Mm.42157	NM_010437	ENSMUSG00000015501	Hivep2	Gm20114|MIBP1|Schnurri-2|Shn-2	human immunodeficiency virus type I enhancer binding protein 2	protein-coding
mm_26993.1	chr3	25790398	25790409	-	1	NA	intron (NM_001163387, intron 3 of 5)	RMER17C|LTR|ERVK	362904	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_9822.1	chr1	182468615	182468620	-	1	NA	intron (NM_009794, intron 20 of 20)	B1_Mur2|SINE|Alu	48866	NM_009794	12334	Mm.19306	NM_009794	ENSMUSG00000026509	Capn2	AI326419|Capa-2|Capa2|m-calpain|m-calpin	calpain 2	protein-coding
mm_119595.1	chr14	50956135	50956169	+	1	NA	promoter-TSS (NM_001123371)	promoter-TSS (NM_001123371)	11	NM_001123371	667034	Mm.482171	NM_001123371	ENSMUSG00000068417	Pnp2	-	purine-nucleoside phosphorylase 2	protein-coding
mm_27482.1	chr3	53692909	53692916	-	1	NA	Intergenic	Intergenic	-35557	NM_172862	242022	Mm.38378	NM_172862	ENSMUSG00000037016	Frem2	6030440P17Rik|8430406N05Rik|Gm409|b2b1562Clo|my|ne|nv1	Fras1 related extracellular matrix protein 2	protein-coding
mm_25573.1	chr3	116844544	116844547	+	1	NA	Intergenic	Intergenic	-15022	NM_001113478	20321	Mm.66293	NM_009146	ENSMUSG00000033386	Frrs1	AI131732|Sdfr2	ferric-chelate reductase 1	protein-coding
mm_12857.1	chr2	83724430	83724515	+	1	NA	promoter-TSS (NM_008402)	promoter-TSS (NM_008402)	75	NM_008402	16410	Mm.227	NM_008402	ENSMUSG00000027087	Itgav	1110004F14Rik|2610028E01Rik|CD51|D430040G12Rik	integrin alpha V	protein-coding
mm_70786.1	chr8	22506408	22506449	+	1	NA	intron (NM_011394, intron 1 of 10)	intron (NM_011394, intron 1 of 10)	-29549	NM_001146117	102032	Mm.378231	NM_001012667	ENSMUSG00000031534	Smim19	AI316807|BG694986|EST-c39	small integral membrane protein 19	protein-coding
mm_101858.1	chr11	48871206	48871210	-	1	NA	5' UTR (NM_008326, exon 1 of 3)	5' UTR (NM_008326, exon 1 of 3)	138	NM_008326	15944	Mm.29938	NM_008326	ENSMUSG00000046879	Irgm1	Ifggd3|Ifi1|Iigp3|Iipg3|Irgm|LRG-47	immunity-related GTPase family M member 1	protein-coding
mm_25233.1	chr3	103864074	103864076	+	1	NA	intron (NR_104070, intron 3 of 22)	intron (NR_104070, intron 3 of 22)	3798	NM_008979	19260	Mm.395	NM_008979	ENSMUSG00000027843	Ptpn22	70zpep|PEP|Ptpn8	protein tyrosine phosphatase, non-receptor type 22 (lymphoid)	protein-coding
mm_33165.1	chr4	126023450	126023470	+	1	NA	Intergenic	MT2A|LTR|ERVL	-1199	NR_045561	12986	Mm.271701	NM_007782	ENSMUSG00000028859	Csf3r	Cd114|Csfgr|G-CSF-R|G-CSFR	colony stimulating factor 3 receptor (granulocyte)	protein-coding
mm_93677.1	chr10	117746332	117746350	-	1	NA	promoter-TSS (NM_029875)	promoter-TSS (NM_029875)	17	NM_029875	215436	Mm.256753	NM_029875	ENSMUSG00000060181	Slc35e3	9330166G04Rik|AI481200	solute carrier family 35, member E3	protein-coding
mm_14262.1	chr2	128364417	128364439	+	1	NA	intron (NR_028589, intron 1 of 2)	intron (NR_028589, intron 1 of 2)	64923	NR_028591	100043424	Mm.297222	NR_028589		Gm14005	OTTMUSG00000015351	predicted gene 14005	ncRNA
mm_133756.1	chr16	94448109	94448119	+	1	NA	exon (NM_009441, exon 35 of 46)	exon (NM_009441, exon 35 of 46)	-77099	NM_001159617	56176	Mm.474449	NM_019543	ENSMUSG00000022940	Pigp	Dcrc|Dscr5	phosphatidylinositol glycan anchor biosynthesis, class P	protein-coding
mm_153141.1	chr19	34246703	34246731	-	1	NA	exon (NM_007392, exon 5 of 9)	exon (NM_007392, exon 5 of 9)	8656	NM_007392	11475	Mm.213025	NM_007392	ENSMUSG00000035783	Acta2	0610041G09Rik|Actvs|SMalphaA|a-SMA|alphaSMA	actin, alpha 2, smooth muscle, aorta	protein-coding
mm_66909.1	chr7	60003062	60003090	-	1	NA	intron (NM_001082962, intron 2 of 10)	intron (NM_001082962, intron 2 of 10)	2080	NM_013670	20646	Mm.274995	NM_013670	ENSMUSG00000102252	Snrpn	2410045I01Rik|HCERN3|Peg4|Pwcr1|SMN	small nuclear ribonucleoprotein N	protein-coding
mm_29279.1	chr3	107664372	107664399	-	1	NA	3' UTR (NM_145542, exon 17 of 17)	3' UTR (NM_145542, exon 17 of 17)	32163	NM_145542	229709	Mm.220328	NM_145542	ENSMUSG00000027893	Ahcyl1	1110034F20Rik|AA409031|AA414901|Ahcy-rs3|DCAL|Irbit	S-adenosylhomocysteine hydrolase-like 1	protein-coding
mm_47446.1	chr5	123482570	123482598	-	1	NA	promoter-TSS (NM_029594)	promoter-TSS (NM_029594)	-483	NM_029594	76399	Mm.75049	NM_029594	ENSMUSG00000029437	Il31	1700013B14Rik	interleukin 31	protein-coding
mm_76947.1	chr8	105979414	105979444	-	1	NA	promoter-TSS (NM_027960)	promoter-TSS (NM_027960)	-10	NM_027960	71854	Mm.173395	NM_027960	ENSMUSG00000031898	Dpep3	1700018F16Rik|AI507039|MBD-3|MLZ-136	dipeptidase 3	protein-coding
mm_74637.1	chr8	13254069	13254085	-	1	NA	promoter-TSS (NM_172750)	promoter-TSS (NM_172750)	85	NM_172750	234072	Mm.132785	NM_172750	ENSMUSG00000031448	Adprhl1	Arh2|D330008N11Rik	ADP-ribosylhydrolase like 1	protein-coding
mm_35424.1	chr4	35211283	35211295	-	1	NA	intron (NM_001081343, intron 6 of 10)	intron (NM_001081343, intron 6 of 10)	14591	NM_001081343	73205	Mm.331544	NM_001081343	ENSMUSG00000028300	3110043O21Rik	AI840585	RIKEN cDNA 3110043O21 gene	protein-coding
mm_60012.1	chr7	30737887	30737913	+	1	NA	exon (NM_001290631, exon 2 of 11)	exon (NM_001290631, exon 2 of 11)	1507	NM_008085	14447	Mm.436562	NM_008085	ENSMUSG00000061099	Gapdhs	Gapd-s|Gapds	glyceraldehyde-3-phosphate dehydrogenase, spermatogenic	protein-coding
mm_106928.1	chr12	8433148	8433151	+	1	NA	Intergenic	Intergenic	66836	NM_007483	11852	Mm.687	NM_007483	ENSMUSG00000054364	Rhob	AA017882|Arh6|Arhb	ras homolog family member B	protein-coding
mm_169903.1	chr16	52084169	52084174	+	1	NA	intron (NM_001033238, intron 3 of 17)	(AGGTG)n|Simple_repeat|Simple_repeat	52622	NM_001033238	208650	Mm.328206	NM_001033238	ENSMUSG00000022637	Cblb	AI429560|AI851073|Cbl-b	Casitas B-lineage lymphoma b	protein-coding
mm_138429.1	chr17	35077061	35077073	+	1	NA	5' UTR (NM_027366, exon 1 of 3)	5' UTR (NM_027366, exon 1 of 3)	125	NM_027366	70274	Mm.250491	NM_027366	ENSMUSG00000013766	Ly6g6e	2310011I02Rik|G6e	lymphocyte antigen 6 complex, locus G6E	protein-coding
mm_132159.1	chr16	32179839	32179850	+	1	NA	promoter-TSS (NM_001033539)	promoter-TSS (NM_001033539)	44	NM_001033539	328660	Mm.441006	NM_001033539	ENSMUSG00000075269	Bex6	B020003O03Rik	brain expressed family member 6	protein-coding
mm_120432.1	chr14	65805913	65805930	+	1	NA	promoter-TSS (NM_023209)	promoter-TSS (NM_023209)	10	NM_023209	52033	Mm.24337	NM_023209	ENSMUSG00000022033	Pbk	2810434B10Rik|AW538537|D14Ertd732e|TOPK	PDZ binding kinase	protein-coding
mm_41520.1	chr5	92398052	92398057	+	1	NA	intron (NM_001310665, intron 2 of 6)	intron (NM_001310665, intron 2 of 6)	9920	NM_001310665	109979	Mm.263514	NM_181728	ENSMUSG00000034842	Art3	4930569O04Rik|ARTC3	ADP-ribosyltransferase 3	protein-coding
mm_142839.1	chr17	51794244	51794252	-	1	NA	intron (NM_009122, intron 5 of 10)	intron (NM_009122, intron 5 of 10)	17806	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_92446.1	chr10	77690808	77690812	-	1	NA	promoter-TSS (NM_001205032)	promoter-TSS (NM_001205032)	-53	NM_001205032	100502831	Mm.486158	NM_001205032	ENSMUSG00000095970	Gm19402	-	predicted gene, 19402	protein-coding
mm_122270.1	chr14	34362298	34362320	-	1	NA	Intergenic	L1MC4|LINE|L1	-6916	NM_183278	69134	Mm.27156	NM_183278	ENSMUSG00000043681	Fam25c	2200001I15Rik|Fam25	family with sequence similarity 25, member C	protein-coding
mm_134057.1	chr16	6745483	6745495	-	1	NA	intron (NM_021477, intron 4 of 16)	intron (NM_021477, intron 4 of 16)	-324346	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_4172.1	chr1	171121672	171121678	+	1	NA	promoter-TSS (NM_001081275)	promoter-TSS (NM_001081275)	14	NM_001081275	75472	Mm.32760	NM_029301	ENSMUSG00000026649	Cfap126	1700009P17Rik|AV282292|Flattop|Fltp	cilia and flagella associated protein 126	protein-coding
mm_8436.1	chr1	152625213	152625220	-	1	NA	promoter-TSS (NM_016846)	promoter-TSS (NM_016846)	1	NM_016846	19731	Mm.245270	NM_016846	ENSMUSG00000026482	Rgl1	Rgl|mKIAA0959	ral guanine nucleotide dissociation stimulator,-like 1	protein-coding
mm_241.1	chr1	19209071	19209089	+	1	NA	5' UTR (NM_009334, exon 1 of 7)	5' UTR (NM_009334, exon 1 of 7)	166	NM_001286340	21419	Mm.137021	NM_009334	ENSMUSG00000025927	Tfap2b	AI606113|AP-2(beta)|E130018K07Rik|Tcfap2b	transcription factor AP-2 beta	protein-coding
mm_15614.1	chr2	160880643	160880650	+	1	NA	promoter-TSS (NM_022883)	promoter-TSS (NM_022883)	-24	NM_022883	64899	Mm.292111	NM_022883	ENSMUSG00000027412	Lpin3	9130206L11Rik|AA438110|AV236139|mKIAA4023	lipin 3	protein-coding
mm_160648.1	chr9	110388512	110388512	-	1	NA	exon (NM_001081043, exon 20 of 25)	exon (NM_001081043, exon 20 of 25)	19698	NM_001081043	104831	Mm.335477	NM_001081043	ENSMUSG00000036057	Ptpn23	AI462446|PTP-TD14	protein tyrosine phosphatase, non-receptor type 23	protein-coding
mm_10650.1	chr2	20668084	20668094	+	1	NA	intron (NM_029895, intron 4 of 18)	ORR1A3|LTR|ERVL-MaLR	148576	NM_001177631	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding
mm_115376.1	chr13	113087917	113087944	+	1	NA	intron (NM_001281487, intron 11 of 11)	intron (NM_001281487, intron 11 of 11)	13051	NM_010370	14938	Mm.15510	NM_010370	ENSMUSG00000023132	Gzma	AW494114|Ctla-3|Ctla3|Hf|Hf1|SE1|TSP-1|TSP1	granzyme A	protein-coding
mm_81826.1	chr9	118050227	118050231	+	1	NA	intron (NM_001286508, intron 4 of 7)	intron (NM_001286508, intron 4 of 7)	9707	NM_013727	27215	Mm.92705	NM_013727	ENSMUSG00000039285	Azi2	AA410145|AZ2	5-azacytidine induced gene 2	protein-coding
mm_5275.1	chr1	18265131	18265141	-	1	NA	promoter-TSS (NM_183124)	promoter-TSS (NM_183124)	2	NM_183124	77673	Mm.99530	NM_183124	ENSMUSG00000067773	Defb41	9230102D03Rik|BD-17|Bd-41|Defb16|Defb17|Gm15386|OTTMUSG00000020946|OTTMUSG00000020948	defensin beta 41	protein-coding
mm_115058.1	chr13	100676104	100676136	+	1	NA	intron (NM_183115, intron 1 of 11)	intron (NM_183115, intron 1 of 11)	6639	NM_001168386	76041	Mm.23977	NM_183115	ENSMUSG00000048924	Ccdc125	5830436D01Rik|AL023012	coiled-coil domain containing 125	protein-coding
mm_127937.1	chr15	10558645	10558697	-	1	NA	promoter-TSS (NM_029430)	promoter-TSS (NM_029430)	-3	NM_029430	75777	Mm.48812	NM_029430	ENSMUSG00000022249	Ttc23l	4930401A09Rik	tetratricopeptide repeat domain 23-like	protein-coding
mm_71087.1	chr8	34807315	34807350	+	1	NA	promoter-TSS (NM_176933)	promoter-TSS (NM_176933)	-278	NM_176933	319520	Mm.170276	NM_176933	ENSMUSG00000031530	Dusp4	2700078F24Rik|AI844617|BB104621|E130306H24Rik|MKP2	dual specificity phosphatase 4	protein-coding
mm_85007.1	chr9	87209908	87209929	-	1	NA	intron (NM_199316, intron 21 of 26)	intron (NM_199316, intron 21 of 26)	45614	NM_199316	382090	Mm.335338	NM_199316	ENSMUSG00000056919	Cep162	4922501C03Rik|mKIAA1009	centrosomal protein 162	protein-coding
mm_81558.1	chr9	110344252	110344262	+	1	NA	intron (NM_001001144, intron 1 of 22)	RSINE1|SINE|B4	10901	NM_001001144	235623	Mm.288741	NM_001001144	ENSMUSG00000032485	Scap	9530044G19|mKIAA0199	SREBF chaperone	protein-coding
mm_69635.1	chr7	137564698	137564706	-	1	NA	Intergenic	Intergenic	127028	NR_033611	620016	Mm.388932	NR_033611	ENSMUSG00000100863	Gm12669	OTTMUSG00000007920	glutaredoxin 3 pseudogene	pseudo
mm_24736.1	chr3	95283210	95283222	+	1	NA	5' UTR (NM_133858, exon 1 of 10)	5' UTR (NM_133858, exon 1 of 10)	281	NM_199475	75007	Mm.279287	NM_133858	ENSMUSG00000038712	Fam63a	1810005H09Rik|4930504E06Rik|AA562754|AA960384|AW561904|cI-40|mKIAA1390|ni	family with sequence similarity 63, member A	protein-coding
mm_26594.1	chr3	151438161	151438168	+	1	NA	intron (NM_133222, intron 1 of 15)	intron (NM_133222, intron 1 of 15)	282	NM_133222	170757	Mm.317261	NM_133222	ENSMUSG00000039167	Adgrl4	1110033N21Rik|ETL1|Eltd1|Etl	adhesion G protein-coupled receptor L4	protein-coding
mm_151497.1	chr19	58728007	58728015	+	1	NA	promoter-TSS (NM_018874)	promoter-TSS (NM_018874)	-876	NM_018874	18946	Mm.10753	NM_018874	ENSMUSG00000042179	Pnliprp1	Plrp1	pancreatic lipase related protein 1	protein-coding
mm_164476.1	chr16	71868952	71868953	+	1	NA	Intergenic	Lx9|LINE|L1	365375	NR_131116	319533	Mm.373754	NR_131115		8030451O07Rik	-	RIKEN cDNA 8030451O07 gene	ncRNA
mm_167442.1	chr8	121571366	121571368	-	1	NA	intron (NM_133765, intron 1 of 8)	intron (NM_133765, intron 1 of 8)	7439	NM_133765	76454	Mm.24829	NM_133765	ENSMUSG00000052934	Fbxo31	1110003O08Rik|2310046N15Rik|Fbx14|Fbxo14	F-box protein 31	protein-coding
mm_112745.1	chr13	19341693	19341698	+	1	NA	Intergenic	Intergenic	54118	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_19502.1	chr2	93462458	93462494	-	1	NA	promoter-TSS (NM_007656)	promoter-TSS (NM_007656)	26	NM_001271430	12521	Mm.4261	NM_007656	ENSMUSG00000027215	Cd82	AA682076|AL023070|C33|IA4|Kai1|Tspan27	CD82 antigen	protein-coding
mm_38032.1	chr4	133874683	133874722	-	1	NA	promoter-TSS (NM_001285506)	promoter-TSS (NM_001285506)	29	NM_001285506	20111	Mm.301827	NM_009097	ENSMUSG00000003644	Rps6ka1	Mapkapk-1a|Rsk|Rsk-1|Rsk1|S6K-alpha-1|p90-Rsk1|p90Rsk1|p90S6K|p90rsk	ribosomal protein S6 kinase polypeptide 1	protein-coding
mm_82890.1	chr9	32541467	32541476	-	1	NA	promoter-TSS (NM_008026)	promoter-TSS (NM_008026)	-19	NM_008026	14247	Mm.258908	NM_008026	ENSMUSG00000016087	Fli1	EWSR2|Fli-1|SIC-1|Sic1	Friend leukemia integration 1	protein-coding
mm_113953.1	chr13	51100782	51100799	+	1	NA	promoter-TSS (NM_001283028)	promoter-TSS (NM_001283028)	-63	NR_029463	77428	Mm.405630	NR_029463		9430083A17Rik	-	RIKEN cDNA 9430083A17 gene	ncRNA
mm_16144.1	chr2	171640836	171640871	+	1	NA	Intergenic	Intergenic	321946	NR_040509	75655	Mm.396203	NR_040509	ENSMUSG00000086823	1700028P15Rik	-	RIKEN cDNA 1700028P15 gene	ncRNA
mm_3394.1	chr1	143640705	143640751	+	1	NA	promoter-TSS (NM_020025)	promoter-TSS (NM_020025)	31	NM_020025	26878	Mm.285580	NM_020025	ENSMUSG00000033849	B3galt2	-	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 2	protein-coding
mm_160788.1	chr10	128989674	128989674	+	1	NA	promoter-TSS (NM_146861)	promoter-TSS (NM_146861)	-240	NM_146861	18373	Mm.377111	NM_146861	ENSMUSG00000069430	Olfr9	MOR269-3	olfactory receptor 9	protein-coding
mm_56463.1	chr6	98928924	98928925	-	1	NA	3' UTR (NM_053202, exon 19 of 19)	3' UTR (NM_053202, exon 19 of 19)	99374	NM_001197322	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_96038.1	chr11	59556422	59556432	+	1	NA	intron (NM_145827, intron 6 of 9)	ID_B1|SINE|B4	13741	NM_145827	216799	Mm.54174	NM_145827	ENSMUSG00000032691	Nlrp3	AGTAVPRL|AII/AVP|Cias1|FCAS|FCU|MWS|Mmig1|NALP3|Pypaf1	NLR family, pyrin domain containing 3	protein-coding
mm_166320.1	chr5	110867931	110867938	+	1	NA	intron (NM_016681, intron 12 of 14)	intron (NM_016681, intron 12 of 14)	-11869	NM_001267622	209683	Mm.295660	NM_024477	ENSMUSG00000033209	Ttc28	2310015L07Rik|6030435N04|AI428795|AI851761|BC002262|TPRBK	tetratricopeptide repeat domain 28	protein-coding
mm_144159.1	chr18	5603763	5603776	+	1	NA	intron (NM_011546, intron 1 of 7)	intron (NM_011546, intron 1 of 7)	-11332	NR_033552	791318	Mm.84339	NR_033552	ENSMUSG00000063087	Gm10125	ENSMUSG00000063087|Zeb1os	predicted gene 10125	ncRNA
mm_171107.1	chr3	134545769	134545770	+	1	NA	Intergenic	Intergenic	-122134	NR_040600	75208	Mm.84580	NR_040600	ENSMUSG00000105765	4930539C22Rik	-	RIKEN cDNA 4930539C22 gene	ncRNA
mm_161138.1	chr13	14170032	14170032	+	1	NA	exon (NM_194262, exon 17 of 24)	exon (NM_194262, exon 17 of 24)	106248	NM_198122	94246	Mm.439784	NM_194262	ENSMUSG00000039219	Arid4b	BCAA|BRCAA1|RBBP1L1|Rbp1l1|SAP180	AT rich interactive domain 4B (RBP1-like)	protein-coding
mm_13392.1	chr2	103969670	103969680	+	1	NA	promoter-TSS (NM_008505)	promoter-TSS (NM_008505)	118	NM_001142336	16909	Mm.29266	NM_008505	ENSMUSG00000032698	Lmo2	Rbtn-2|Rbtn2|Rhom-2|Ttg2	LIM domain only 2	protein-coding
mm_138188.1	chr17	34269078	34269104	+	1	NA	intron (NM_207105, intron 5 of 5)	intron (NM_207105, intron 5 of 5)	5864	NM_207105	14961	Mm.254067	NM_207105	ENSMUSG00000073421	H2-Ab1	AI845868|Abeta|H-2Ab|H2-Ab|I-Abeta|IAb|Ia-2|Ia2|Rmcs1	histocompatibility 2, class II antigen A, beta 1	protein-coding
mm_18162.1	chr2	45099397	45099419	-	1	NA	intron (NM_001289521, intron 1 of 8)	intron (NM_001289521, intron 1 of 8)	10869	NM_001289521	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_36473.1	chr4	82800260	82800279	-	1	NA	3' UTR (NM_026647, exon 9 of 9)	3' UTR (NM_026647, exon 9 of 9)	59392	NM_026647	68268	Mm.32047	NM_026647	ENSMUSG00000028403	Zdhhc21	9130404H11Rik|AL024349|D130004H04Rik|dep	zinc finger, DHHC domain containing 21	protein-coding
mm_70740.1	chr8	19141448	19141469	+	1	NA	exon (NM_001034905, exon 2 of 2)	exon (NM_001034905, exon 2 of 2)	699	NM_001286493	546038	Mm.99206	NM_001034905	ENSMUSG00000059463	Spag11b	EG546038|Ep2c/h|Spag11c/h	sperm associated antigen 11B	protein-coding
mm_123742.1	chr14	70191466	70191471	-	1	NA	exon (NM_001271407, exon 13 of 21)	exon (NM_001271407, exon 13 of 21)	778	NM_001271409	20410	Mm.5068	NM_011366	ENSMUSG00000022091	Sorbs3	SCAM-1|SH3P3|Sh3d4|vinexin-g	sorbin and SH3 domain containing 3	protein-coding
mm_2940.1	chr1	132316087	132316093	+	1	NA	promoter-TSS (NM_028778)	promoter-TSS (NM_028778)	-35	NM_028778	74137	Mm.100666	NM_028778	ENSMUSG00000009772	Nuak2	1200013B22Rik|Omphk2|Snark|mKIAA0537	NUAK family, SNF1-like kinase, 2	protein-coding
mm_157467.1	chrX	47892406	47892414	-	1	NA	5' UTR (NM_001290708, exon 1 of 24)	5' UTR (NM_001290708, exon 1 of 24)	142	NM_053123	93761	Mm.229151	NM_053123	ENSMUSG00000031099	Smarca1	5730494M04Rik|Snf2l	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1	protein-coding
mm_94439.1	chr11	6292855	6292870	+	1	NA	intron (NM_001252288, intron 1 of 22)	intron (NM_001252288, intron 1 of 22)	304	NM_001252288	18293	Mm.276348	NM_010956	ENSMUSG00000020456	Ogdh	2210403E04Rik|2210412K19Rik|AA409584|d1401|mKIAA4192	oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)	protein-coding
mm_24899.1	chr3	96173983	96173996	+	1	NA	exon (NM_153053, exon 3 of 6)	exon (NM_153053, exon 3 of 6)	1483	NM_153053	107701	Mm.219671	NM_153053	ENSMUSG00000068856	Sf3b4	SF3b49|SF3b50|Sap49	splicing factor 3b, subunit 4	protein-coding
mm_50515.1	chr6	49039879	49039907	+	1	NA	intron (NM_053110, intron 1 of 10)	intron (NM_053110, intron 1 of 10)	3375	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_95990.1	chr11	59002975	59002981	+	1	NA	intron (NM_001171512, intron 89 of 103)	intron (NM_001171512, intron 89 of 103)	24885	NM_053168	94091	Mm.248049	NM_053168	ENSMUSG00000020455	Trim11	-	tripartite motif-containing 11	protein-coding
mm_93669.1	chr10	117710089	117710099	-	1	NA	intron (NM_001288586, intron 1 of 10)	CpG-1528	664	NM_010786	17246	Mm.22670	NM_010786	ENSMUSG00000020184	Mdm2	1700007J15Rik|AA415488|Mdm-2	transformed mouse 3T3 cell double minute 2	protein-coding
mm_159894.1	chr6	29560109	29560109	-	1	NA	exon (NM_177296, exon 16 of 23)	exon (NM_177296, exon 16 of 23)	30827	NM_001252382	27056	Mm.6479	NM_012057	ENSMUSG00000029771	Irf5	AW491843|mirf5	interferon regulatory factor 5	protein-coding
mm_131143.1	chr16	6349162	6349172	+	1	NA	intron (NM_021477, intron 2 of 16)	intron (NM_021477, intron 2 of 16)	373580	NR_045799	68238	Mm.434605	NR_045799	ENSMUSG00000101481	1700123O21Rik	-	RIKEN cDNA 1700123O21 gene	ncRNA
mm_148835.1	chr19	6346412	6346425	+	1	NA	exon (NM_001291787, exon 22 of 32)	exon (NM_001291787, exon 22 of 32)	5258	NR_117093	26412	Mm.25860	NM_009006	ENSMUSG00000024948	Map4k2	AI385662|BL44|GCK|Rab8ip	mitogen-activated protein kinase kinase kinase kinase 2	protein-coding
mm_90651.1	chr10	128747851	128747895	+	1	NA	promoter-TSS (NM_001170869)	promoter-TSS (NM_001170869)	-6	NM_030100	78428	Mm.27358	NM_030100	ENSMUSG00000064030	Pym1	A030010B05Rik|Pym|Wibg	PYM homolog 1, exon junction complex associated factor	protein-coding
mm_149111.1	chr19	8966722	8966735	+	1	NA	promoter-TSS (NM_026007)	promoter-TSS (NM_026007)	-313	NM_026007	67160	Mm.247762	NM_026007	ENSMUSG00000071644	Eef1g	2610301D06Rik|AA407312|EF1G	eukaryotic translation elongation factor 1 gamma	protein-coding
mm_78404.1	chr9	28944372	28944375	+	1	NA	Intergenic	Intergenic	1018756	NM_172290	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding
mm_126281.1	chr15	79209355	79209376	+	1	NA	intron (NR_029470, intron 2 of 4)	intron (NR_029470, intron 2 of 4)	-19808	NM_008837	18693	Mm.259464	NM_008837	ENSMUSG00000068206	Pick1	Prkcabp	protein interacting with C kinase 1	protein-coding
mm_49082.1	chr6	6862963	6862979	+	1	NA	promoter-TSS (NM_010057)	promoter-TSS (NM_010057)	-363	NM_010057	13396	Mm.439763	NM_010057	ENSMUSG00000029754	Dlx6	-	distal-less homeobox 6	protein-coding
mm_138519.1	chr17	35237986	35238010	+	1	NA	3' UTR (NM_023179, exon 3 of 3)	3' UTR (NM_023179, exon 3 of 3)	1402	NM_023179	66237	Mm.396107	NM_023179	ENSMUSG00000024403	Atp6v1g2	1500002D01Rik|Atp6g2|NG38|VAG2	ATPase, H+ transporting, lysosomal V1 subunit G2	protein-coding
mm_6287.1	chr1	69687168	69687193	-	1	NA	Intergenic	Intergenic	-1220	NM_011770	22779	Mm.106343	NM_011770	ENSMUSG00000025997	Ikzf2	A730095J18Rik|Helios|Zfpn1a2|Znfn1a2	IKAROS family zinc finger 2	protein-coding
mm_5391.1	chr1	31222645	31222677	-	1	NA	promoter-TSS (NM_029062)	promoter-TSS (NM_029062)	-5	NR_033445	70988	Mm.161414	NM_027637	ENSMUSG00000086727	4931428L18Rik	4930563O14Rik	RIKEN cDNA 4931428L18 gene	ncRNA
mm_82066.1	chr9	122805592	122805625	+	1	NA	promoter-TSS (NM_001013405)	promoter-TSS (NM_001013405)	61	NM_001013405	382117	Mm.215892	NM_001013405	ENSMUSG00000046603	Tcaim	D9Ertd402e|Gm1129|TOAG-1	T cell activation inhibitor, mitochondrial	protein-coding
mm_59702.1	chr7	28693004	28693010	+	1	NA	promoter-TSS (NM_001163702)	promoter-TSS (NM_001163702)	-137	NM_001163702	233040	Mm.116116	NM_207238	ENSMUSG00000037463	Fbxo27	E130008B10Rik|FBG5|Gm161	F-box protein 27	protein-coding
mm_17997.1	chr2	38190680	38190693	-	1	NA	intron (NM_146122, intron 2 of 21)	L1MEg|LINE|L1	96698	NM_146122	227801	Mm.314245	NM_146122	ENSMUSG00000035392	Dennd1a	6030446I19Rik|connecdenn	DENN/MADD domain containing 1A	protein-coding
mm_117694.1	chr13	94295020	94295036	-	1	NA	Intergenic	MTC|LTR|ERVL-MaLR	-9197	NM_001346609	107767	Mm.201455	NM_029153	ENSMUSG00000021687	Scamp1	4930505M11Rik|AI415563|AW122395	secretory carrier membrane protein 1	protein-coding
mm_107114.1	chr12	18135932	18135945	+	1	NA	Intergenic	CpG	-378572	NM_001033157	236366	Mm.352227	NM_001033157	ENSMUSG00000073197	5730507C01Rik	-	RIKEN cDNA 5730507C01 gene	protein-coding
mm_68891.1	chr7	126448363	126448382	-	1	NA	exon (NM_007504, exon 16 of 23)	exon (NM_007504, exon 16 of 23)	14701	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_146120.1	chr18	74442399	74442409	+	1	NA	promoter-TSS (NM_201600)	promoter-TSS (NM_201600)	-215	NM_201600	17919	Mm.260098	NM_008661	ENSMUSG00000025885	Myo5b	AI661750|mKIAA1119	myosin VB	protein-coding
mm_63324.1	chr7	126942082	126942092	+	1	NA	intron (NM_172747, intron 4 of 5)	intron (NM_172747, intron 4 of 5)	7494	NM_001347657	233879	Mm.444143	NM_001039645	ENSMUSG00000046378	Asphd1	A830007L07Rik|Gm168	aspartate beta-hydroxylase domain containing 1	protein-coding
mm_163724.1	chr13	117909212	117909216	+	1	NA	intron (NM_010408, intron 5 of 7)	Lx|LINE|L1	-189203	NR_045508	71100	Mm.414841	NR_045508	ENSMUSG00000079048	4933413L06Rik	-	RIKEN cDNA 4933413L06 gene	ncRNA
mm_108285.1	chr12	79135654	79135657	+	1	NA	intron (NM_009705, intron 2 of 7)	B1F2|SINE|Alu	4867	NM_009705	11847	Mm.3506	NM_009705	ENSMUSG00000021125	Arg2	AII|AU022422	arginase type II	protein-coding
mm_81706.1	chr9	111289899	111289907	+	1	NA	Intergenic	Intergenic	18058	NM_175266	77781	Mm.209005	NM_175266	ENSMUSG00000046785	Epm2aip1	A930003G21Rik|mKIAA0766	EPM2A (laforin) interacting protein 1	protein-coding
mm_74078.1	chr8	122470228	122470232	+	1	NA	exon (NM_001033142, exon 2 of 6)	exon (NM_001033142, exon 2 of 6)	5834	NM_001033142	68718	Mm.34356	NM_001033142	ENSMUSG00000014470	Rnf166	1110031E24Rik|AW555115|Zfp313l	ring finger protein 166	protein-coding
mm_21034.1	chr2	152490150	152490180	-	1	NA	promoter-TSS (NM_001002791)	promoter-TSS (NM_001002791)	-27	NM_001002791	442835	Mm.99065	NM_001002791	ENSMUSG00000027468	Defb22	9230002F21Rik	defensin beta 22	protein-coding
mm_122572.1	chr14	50807726	50807732	-	1	NA	promoter-TSS (NR_002142)	promoter-TSS (NR_002142)	42	NR_002142	85029		NR_002142	ENSMUSG00000092837	Rpph1	Gm24821|H1RNA|Rmrp5|Rpr	ribonuclease P RNA component H1	ncRNA
mm_168096.1	chr10	128821918	128821932	+	1	NA	promoter-TSS (NM_024180)	promoter-TSS (NM_024180)	154	NM_025364	66118	Mm.235562	NM_025364	ENSMUSG00000078427	Sarnp	1110005A23Rik|Cip29	SAP domain containing ribonucleoprotein	protein-coding
mm_24404.1	chr3	90359627	90359639	+	1	NA	Intergenic	Intergenic	17979	NM_139304	229542	Mm.270999	NM_139304	ENSMUSG00000042390	Gatad2b	AL118180|C430014D17Rik|P66beta|mKIAA1150	GATA zinc finger domain containing 2B	protein-coding
mm_138090.1	chr17	34032072	34032123	+	1	NA	promoter-TSS (NM_001205216)	promoter-TSS (NM_001205216)	-253	NM_001205216	20182	Mm.1243	NM_011306	ENSMUSG00000039656	Rxrb	AL023085|H-2RIIBP|Nr2b2|RCoR-1|Rub	retinoid X receptor beta	protein-coding
mm_73811.1	chr8	117365041	117365054	+	1	NA	intron (NM_028941, intron 1 of 20)	intron (NM_028941, intron 1 of 20)	15877	NM_028941	74440	Mm.233181	NM_028941	ENSMUSG00000034390	Cmip	4933407C03Rik|5830471E12Rik|AI314065|AI464126	c-Maf inducing protein	protein-coding
mm_136597.1	chr17	5089897	5089901	+	1	NA	intron (NM_001085355, intron 2 of 19)	intron (NM_001085355, intron 2 of 19)	94825	NM_001085355	239985	Mm.133401	NM_001085355	ENSMUSG00000069729	Arid1b	8030481M12|9330189K18Rik|AI836955|Ardi1b|B230217J03Rik|mKIAA1235	AT rich interactive domain 1B (SWI-like)	protein-coding
mm_14511.1	chr2	132263437	132263445	+	1	NA	5' UTR (NM_001291040, exon 1 of 4)	5' UTR (NM_001291040, exon 1 of 4)	293	NM_138651	110911	Mm.284503	NM_138651	ENSMUSG00000058793	Cds2	5730450N06Rik|5730460C18Rik|AI854580|D2Wsu127e	CDP-diacylglycerol synthase (phosphatidate cytidylyltransferase) 2	protein-coding
mm_83721.1	chr9	50765928	50765935	-	1	NA	promoter-TSS (NM_001311073)	promoter-TSS (NM_001311073)	2	NM_001311073	68721	Mm.171374	NM_023483	ENSMUSG00000037971	1110032A03Rik	4930500N06Rik|c11orf1	RIKEN cDNA 1110032A03 gene	protein-coding
mm_73929.1	chr8	119910793	119910848	+	1	NA	5' UTR (NM_009462, exon 1 of 14)	5' UTR (NM_009462, exon 1 of 14)	460	NM_001310630	22224	Mm.256910	NM_009462	ENSMUSG00000031826	Usp10	2610014N07Rik|UBPO|Uchrp|mKIAA0190	ubiquitin specific peptidase 10	protein-coding
mm_132358.1	chr16	34651227	34651235	+	1	NA	promoter-TSS (NM_030744)	promoter-TSS (NM_030744)	20	NM_030744	76378	Mm.23515	NM_030744	ENSMUSG00000022832	Ropn1	1700008N21Rik|ODF6|RHPNAP1|Rppn|ropporin	ropporin, rhophilin associated protein 1	protein-coding
mm_108355.1	chr12	80644471	80644496	+	1	NA	promoter-TSS (NM_007951)	promoter-TSS (NM_007951)	268	NM_026244	328133	Mm.238279	NM_026244	ENSMUSG00000048833	Slc39a9	2010002A02Rik|2610511I23Rik|4833420E20Rik|AW209151	solute carrier family 39 (zinc transporter), member 9	protein-coding
mm_109818.1	chr12	3834579	3834589	-	1	NA	intron (NM_001271753, intron 1 of 22)	intron (NM_001271753, intron 1 of 22)	27424	NM_001271753	13435	Mm.5001	NM_007872	ENSMUSG00000020661	Dnmt3a	MmuIIIA	DNA methyltransferase 3A	protein-coding
mm_64765.1	chr7	4964396	4964411	-	1	NA	promoter-TSS (NM_001146329)	promoter-TSS (NM_001146329)	-55	NM_001146329	381836	Mm.297829	NM_001146329	ENSMUSG00000030433	Sbk2	Gm1079|Sgk069	SH3-binding domain kinase family, member 2	protein-coding
mm_97518.1	chr11	78499844	78499856	+	1	NA	exon (NM_011707, exon 3 of 8)	exon (NM_011707, exon 3 of 8)	730	NM_011707	22370	Mm.3667	NM_011707	ENSMUSG00000017344	Vtn	AI256434|Vn	vitronectin	protein-coding
mm_89149.1	chr10	86022019	86022027	+	1	NA	promoter-TSS (NM_153195)	promoter-TSS (NM_153195)	94	NM_153195	69754	Mm.44236	NM_153195	ENSMUSG00000001786	Fbxo7	2410015K21Rik|A230052G17Rik|AI117679|AW260462|C85118	F-box protein 7	protein-coding
mm_58657.1	chr7	6415165	6415206	+	1	NA	promoter-TSS (NM_001134752)	promoter-TSS (NM_001134752)	10	NM_001134752	100042450	Mm.416919	NM_001134752	ENSMUSG00000093536	Smim17	Gm16532	small integral membrane protein 17	protein-coding
mm_80045.1	chr9	69288380	69288404	+	1	NA	intron (NM_013646, intron 2 of 10)	intron (NM_013646, intron 2 of 10)	-1449	NM_001289916	19883	Mm.378450	NM_013646	ENSMUSG00000032238	Rora	9530021D13Rik|Nr1f1|ROR1|ROR2|ROR3|nmf267|sg|staggerer|tmgc26	RAR-related orphan receptor alpha	protein-coding
mm_118546.1	chr14	17659250	17659277	+	1	NA	Intergenic	Intergenic	-1697	NM_001113417	21834	Mm.32563	NM_009380	ENSMUSG00000021779	Thrb	Nr1a2|T3R[b]|T3Rbeta|Thrb1|Thrb2|c-erbAbeta	thyroid hormone receptor beta	protein-coding
mm_76609.1	chr8	90817396	90817402	-	1	NA	Intergenic	Intergenic	-11436	NM_177224	109151	Mm.100615	NM_177224	ENSMUSG00000056608	Chd9	1810014J18Rik|9030205D12Rik|A330063D19Rik|AD013|PRIC320|mKIAA0308	chromodomain helicase DNA binding protein 9	protein-coding
mm_63519.1	chr7	127877131	127877145	+	1	NA	promoter-TSS (NM_146259)	promoter-TSS (NM_146259)	-315	NM_146259	244219	Mm.207872	NM_146259	ENSMUSG00000049728	Zfp668	BC030314|E130018B19Rik|Znf668	zinc finger protein 668	protein-coding
mm_137291.1	chr17	24742449	24742466	+	1	NA	3' UTR (NM_001346668, exon 4 of 4)	3' UTR (NM_001346668, exon 4 of 4)	5864	NM_001346668	27361	Mm.28212	NM_013759	ENSMUSG00000075705	Msrb1	D17Wsu82e|SELX|SelR|Sepr|Sepx1	methionine sulfoxide reductase B1	protein-coding
mm_105673.1	chr11	107470062	107470076	-	1	NA	5' UTR (NM_145823, exon 1 of 10)	5' UTR (NM_145823, exon 1 of 10)	651	NM_145823	71795	Mm.397413	NM_145823	ENSMUSG00000040430	Pitpnc1	1110020B03Rik|5830436L09Rik|AI662802|AI851387|C330017I21Rik|Dnr411|RDGBB|RDGBB1|rdgB-beta	phosphatidylinositol transfer protein, cytoplasmic 1	protein-coding
mm_982.1	chr1	58431399	58431400	+	1	NA	intron (NM_001285826, intron 6 of 6)	intron (NM_001285826, intron 6 of 6)	-7311	NR_027854	12747	Mm.1761	NM_009905	ENSMUSG00000026034	Clk1	STY	CDC-like kinase 1	protein-coding
mm_83918.1	chr9	56506598	56506604	-	1	NA	Intergenic	Intergenic	87755	NM_025812	66867	Mm.150856	NM_025812	ENSMUSG00000032329	Hmg20a	1200004E06Rik|5730490E10Rik|Hmgxb1|Ibraf	high mobility group 20A	protein-coding
mm_90535.1	chr10	128088314	128088365	+	1	NA	exon (NM_016774, exon 8 of 10)	exon (NM_016774, exon 8 of 10)	3053	NR_030442	751518		NR_030442	ENSMUSG00000093245	Mir677	Mirn677|mir-677|mmu-mir-677	microRNA 677	ncRNA
mm_104346.1	chr11	94242940	94242956	-	1	NA	promoter-TSS (NM_181819)	promoter-TSS (NM_181819)	-369	NM_181819	278507	Mm.342216	NM_181819	ENSMUSG00000044177	Wfikkn2	2610304F08Rik|AY100450|Gasp1|WFIKKNRP	WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 2	protein-coding
mm_161882.1	chr18	37513630	37513630	+	1	NA	promoter-TSS (NM_053146)	promoter-TSS (NM_053146)	-22	NM_053146	93892	Mm.348053	NM_053146	ENSMUSG00000044022	Pcdhb21	Pcdhb18|PcdhbU	protocadherin beta 21	protein-coding
mm_147246.1	chr18	38381174	38381176	-	1	NA	Intergenic	Intergenic	-37800	NM_022996	65113	Mm.102496	NM_022996	ENSMUSG00000024425	Ndfip1	0610010M22Rik|N4wbp5	Nedd4 family interacting protein 1	protein-coding
mm_132282.1	chr16	33056545	33056570	+	1	NA	promoter-TSS (NM_021338)	promoter-TSS (NM_021338)	43	NM_021338	57808	Mm.19355	NM_021338	ENSMUSG00000060636	Rpl35a	2810431L15Rik|Rpl35	ribosomal protein L35A	protein-coding
mm_6386.1	chr1	72849223	72849236	-	1	NA	exon (NM_008342, exon 2 of 4)	exon (NM_008342, exon 2 of 4)	23842	NM_001310659	16008	Mm.141936	NM_008342	ENSMUSG00000039323	Igfbp2	AI255832|IBP-2|Igfbp-2|mIGFBP-2	insulin-like growth factor binding protein 2	protein-coding
mm_166074.1	chr4	135958570	135958604	+	1	NA	intron (NM_008254, intron 5 of 8)	intron (NM_008254, intron 5 of 8)	-6578	NM_178389	74246	Mm.247946	NM_178389	ENSMUSG00000028671	Gale	2310002A12Rik|AI323962	galactose-4-epimerase, UDP	protein-coding
mm_167618.1	chr9	57521378	57521378	+	1	NA	exon (NM_007747, exon 1 of 5)	exon (NM_007747, exon 1 of 5)	146	NM_007747	12858	Mm.273403	NM_007747	ENSMUSG00000000088	Cox5a	AA959768|CcOX	cytochrome c oxidase subunit Va	protein-coding
mm_132317.1	chr16	33754776	33754779	+	1	NA	intron (NM_175256, intron 12 of 14)	intron (NM_175256, intron 12 of 14)	-39260	NM_010739	17063	Mm.3177	NM_010739	ENSMUSG00000022824	Muc13	114/A10|14/A10|AI159736|Lrrp|Ly64|NJ-1	mucin 13, epithelial transmembrane	protein-coding
mm_111550.1	chr12	101028845	101028913	-	1	NA	5' UTR (NM_026681, exon 1 of 30)	5' UTR (NM_026681, exon 1 of 30)	104	NM_026681	68339	Mm.156217	NM_026681	ENSMUSG00000021182	Ccdc88c	0610010D24Rik|AV000935|AW324073|Daple|mKIAA1509	coiled-coil domain containing 88C	protein-coding
mm_23775.1	chr3	76074606	76074614	+	1	NA	promoter-TSS (NM_178673)	promoter-TSS (NM_178673)	49	NM_178673	213262	Mm.379337	NM_178673	ENSMUSG00000034098	Fstl5	9130207J01Rik	follistatin-like 5	protein-coding
mm_136139.1	chr16	87432485	87432548	-	1	NA	promoter-TSS (NM_001081068)	promoter-TSS (NM_001081068)	90	NM_001081068	78913	Mm.249005	NM_001081068	ENSMUSG00000052299	Ltn1	4930528H02Rik|AV266914|C87237|Listerin|Rnf160|Zfp294	listerin E3 ubiquitin protein ligase 1	protein-coding
mm_142623.1	chr17	47043058	47043090	-	1	NA	Intergenic	Intergenic	-32542	NM_001177374	224826	Mm.28234	NM_146078	ENSMUSG00000023977	Ubr2	9930021A08Rik|AI462103|AW540746|E130209G04Rik|ENSMUSG00000043296|mKIAA0349	ubiquitin protein ligase E3 component n-recognin 2	protein-coding
mm_89748.1	chr10	99261552	99261617	+	1	NA	Intergenic	CpG	-1647	NM_026268	67603	Mm.1791	NM_026268	ENSMUSG00000019960	Dusp6	1300019I03Rik|MKP-3|MKP3|PYST1	dual specificity phosphatase 6	protein-coding
mm_26764.1	chr3	8829697	8829707	-	1	NA	intron (NM_025434, intron 2 of 2)	Lx8|LINE|L1	94155	NM_025434	66230	Mm.38460	NM_025434	ENSMUSG00000040269	Mrps28	1500012D08Rik|AW061224	mitochondrial ribosomal protein S28	protein-coding
mm_42751.1	chr5	120812626	120812668	+	1	NA	promoter-TSS (NR_003507)	promoter-TSS (NR_003507)	9	NM_001083925	23961	Mm.233471	NM_001083925	ENSMUSG00000029605	Oas1b	Flv|L1|Mmu-L1|Oas1|Oias-2|Oias2|Wnv	2'-5' oligoadenylate synthetase 1B	protein-coding
mm_76683.1	chr8	94037008	94037027	-	1	NA	promoter-TSS (NM_026623)	promoter-TSS (NM_026623)	22	NM_026623	68219	Mm.354445	NM_026623	ENSMUSG00000031754	Nudt21	25kDa|3110048P04Rik|5730530J16Rik|AU014860|AW549947|Cpsf5	nudix (nucleoside diphosphate linked moiety X)-type motif 21	protein-coding
mm_82163.1	chr9	123782031	123782037	+	1	NA	3' UTR (NM_001166625, exon 4 of 4)	3' UTR (NM_001166625, exon 4 of 4)	14823	NM_001166625	12769	Mm.440604	NM_009913	ENSMUSG00000029530	Ccr9	A130091K22Rik|Cmkbr10|GPR-9-6	chemokine (C-C motif) receptor 9	protein-coding
mm_169225.1	chr13	66862378	66862397	+	1	NA	Intergenic	Intergenic	42963	NM_026219	67530	Mm.379136	NM_026219	ENSMUSG00000021520	Uqcrb	2210415M14Rik|QP-C|QPC|UQBC|UQBP|UQPC	ubiquinol-cytochrome c reductase binding protein	protein-coding
mm_78451.1	chr9	32239147	32239178	+	1	NA	intron (NM_177379, intron 1 of 12)	intron (NM_177379, intron 1 of 12)	14913	NM_177379	330914	Mm.46683	NM_177379	ENSMUSG00000041444	Arhgap32	3426406O18Rik|Gc-gap|Grit|Px-rics|Rics|mKIAA0712|p200Rhogap|p250Gap	Rho GTPase activating protein 32	protein-coding
mm_56227.1	chr6	90428402	90428455	-	1	NA	promoter-TSS (NM_173775)	promoter-TSS (NM_173775)	52	NM_173775	243538	Mm.386876	NM_173775	ENSMUSG00000048794	Cfap100	AW048498|C030041G11Rik|C230069K22Rik|Ccdc37	cilia and flagella associated protein 100	protein-coding
mm_9142.1	chr1	170868606	170868639	-	1	NA	promoter-TSS (NM_001081304)	promoter-TSS (NM_001081304)	-851	NM_001081304	226641	Mm.377046	NM_001081304	ENSMUSG00000026663	Atf6	9130025P16Rik|9630036G24|AA789574|Atf6alpha|ESTM49	activating transcription factor 6	protein-coding
mm_44025.1	chr5	147430154	147430217	+	1	NA	promoter-TSS (NM_028291)	promoter-TSS (NM_028291)	-395	NM_028291	72587	Mm.320469	NM_028291	ENSMUSG00000029647	Pan3	2700050F09Rik|A430027N15Rik|AU014670	PAN3 poly(A) specific ribonuclease subunit	protein-coding
mm_129918.1	chr15	84192107	84192157	-	1	NA	promoter-TSS (NM_178614)	promoter-TSS (NM_178614)	-101	NM_178614	68653	Mm.290725	NM_178614	ENSMUSG00000022437	Samm50	1110030L07Rik	SAMM50 sorting and assembly machinery component	protein-coding
mm_116251.1	chr13	33965721	33965727	-	1	NA	intron (NM_001163239, intron 1 of 5)	intron (NM_001163239, intron 1 of 5)	1065	NM_001163241	18105	Mm.264036	NM_020282	ENSMUSG00000046949	Nqo2	NMO2|Nmor2|Ox2	NAD(P)H dehydrogenase, quinone 2	protein-coding
mm_111759.1	chr12	103958925	103958935	-	1	NA	Intergenic	Intergenic	-2033	NM_009247	20704	Mm.312593	NM_009247	ENSMUSG00000072849	Serpina1e	Dom5|PI5|Spi1-5	serine (or cysteine) peptidase inhibitor, clade A, member 1E	protein-coding
mm_166942.1	chr7	43437009	43437019	+	1	NA	promoter-TSS (NM_024253)	promoter-TSS (NM_024253)	-124	NM_024253	72310	Mm.34613	NM_024253	ENSMUSG00000004612	Nkg7	2500004F03Rik	natural killer cell group 7 sequence	protein-coding
mm_11397.1	chr2	31470255	31470282	+	1	NA	promoter-TSS (NM_007494)	promoter-TSS (NM_007494)	-2	NM_007494	11898	Mm.3217	NM_007494	ENSMUSG00000076441	Ass1	AA408052|ASS|Ass-1|fold	argininosuccinate synthetase 1	protein-coding
mm_100509.1	chr11	120529188	120529198	+	1	NA	Intergenic	Intergenic	-1534	NM_008101	14527	Mm.22329	NM_008101	ENSMUSG00000025127	Gcgr	GR	glucagon receptor	protein-coding
mm_42264.1	chr5	114131158	114131178	+	1	NA	promoter-TSS (NM_011677)	promoter-TSS (NM_011677)	12	NM_011677	22256	Mm.1393	NM_011677	ENSMUSG00000029591	Ung	UNG1|UNG2	uracil DNA glycosylase	protein-coding
mm_149578.1	chr19	14664372	14664407	+	1	NA	Intergenic	ORR1C1|LTR|ERVL-MaLR	-66206	NM_001302947	21888	Mm.103638	NM_011600	ENSMUSG00000024642	Tle4	5730411M05Rik|AA792082|Bce-1|Bce1|ESTM13|ESTM14|Grg4|X83332|X83333|grg-4	transducin-like enhancer of split 4	protein-coding
mm_33725.1	chr4	134068430	134068442	+	1	NA	promoter-TSS (NM_001162970)	promoter-TSS (NM_001162970)	-16	NM_001162970	230806	Mm.240080	NM_001162970	ENSMUSG00000012123	Aim1l	-	absent in melanoma 1-like	protein-coding
mm_161194.1	chr13	54766478	54766478	-	1	NA	promoter-TSS (NM_033610)	promoter-TSS (NM_033610)	-38	NM_033610	104069	Mm.200843	NM_033610	ENSMUSG00000034891	Sncb	AI838531|betaSYN	synuclein, beta	protein-coding
mm_88831.1	chr10	80806129	80806141	+	1	NA	exon (NM_007445, exon 2 of 5)	exon (NM_007445, exon 2 of 5)	887	NM_007445	11705	Mm.376094	NM_007445	ENSMUSG00000035262	Amh	MIS	anti-Mullerian hormone	protein-coding
mm_87906.1	chr10	62252732	62252766	+	1	NA	5' UTR (NM_009314, exon 1 of 5)	5' UTR (NM_009314, exon 1 of 5)	311	NM_009314	21337	Mm.8054	NM_009314	ENSMUSG00000020081	Tacr2	Nk2r|Skr|Tac2r	tachykinin receptor 2	protein-coding
mm_81961.1	chr9	120929259	120929268	+	1	NA	intron (NR_040753, intron 2 of 2)	intron (NR_040753, intron 2 of 2)	1539	NR_040753	78060	Mm.463884	NR_040753	ENSMUSG00000086365	4930593C16Rik	-	RIKEN cDNA 4930593C16 gene	ncRNA
mm_163423.1	chr12	81421932	81421936	-	1	NA	5' UTR (NM_009620, exon 1 of 1)	5' UTR (NM_009620, exon 1 of 1)	105	NM_009620	11498	Mm.408462	NM_009620	ENSMUSG00000072972	Adam4	AV274654|tMDCV	a disintegrin and metallopeptidase domain 4	protein-coding
mm_144376.1	chr18	20558222	20558232	+	1	NA	5' UTR (NM_007883, exon 1 of 15)	5' UTR (NM_007883, exon 1 of 15)	153	NM_007883	13511	Mm.345891	NM_007883	ENSMUSG00000044393	Dsg2	AA408168|D18Ertd293e	desmoglein 2	protein-coding
mm_159191.1	chr2	118400579	118400579	+	1	NA	exon (NM_013719, exon 2 of 39)	exon (NM_013719, exon 2 of 39)	11467	NM_001177806	27103	Mm.217616	NM_013719	ENSMUSG00000005102	Eif2ak4	2610011M03|GCN2|MGCN2	eukaryotic translation initiation factor 2 alpha kinase 4	protein-coding
mm_163043.1	chr11	54860768	54860778	+	1	NA	promoter-TSS (NM_029327)	promoter-TSS (NM_029327)	-182	NM_029327	75530	Mm.83578	NM_029327	ENSMUSG00000020268	Lyrm7	1700024C24Rik|9330147L21Rik	LYR motif containing 7	protein-coding
mm_158890.1	chr1	15312556	15312556	+	1	NA	exon (NM_001098528, exon 1 of 2)	exon (NM_001098528, exon 1 of 2)	104	NM_001098528	98741	Mm.156081	NM_001033195	ENSMUSG00000092083	Kcnb2	9630047L19Rik|BB130875|Kv2.2	potassium voltage gated channel, Shab-related subfamily, member 2	protein-coding
mm_77274.1	chr8	116573963	116573965	-	1	NA	3' UTR (NM_029441, exon 7 of 7)	3' UTR (NM_029441, exon 7 of 7)	68949	NM_029297	75465	Mm.23114	NM_029297	ENSMUSG00000034467	Dynlrb2	1700009A04Rik|DNLC2B|Dncl2b	dynein light chain roadblock-type 2	protein-coding
mm_147887.1	chr18	64888732	64888752	-	1	NA	intron (NM_001114386, intron 1 of 30)	intron (NM_001114386, intron 1 of 30)	986	NM_001114386	83814	Mm.98668	NM_031881	ENSMUSG00000024589	Nedd4l	1300012C07Rik|Nedd4-2|Nedd4b	neural precursor cell expressed, developmentally down-regulated gene 4-like	protein-coding
mm_14843.1	chr2	147515981	147515981	+	1	NA	Intergenic	Intergenic	150987	NM_008780	18503	Mm.315502	NM_008780	ENSMUSG00000037034	Pax1	Pax-1|hbs|hunchback|un|undulated|wt	paired box 1	protein-coding
mm_32097.1	chr4	98546747	98546763	+	1	NA	5' UTR (NM_007704, exon 1 of 18)	5' UTR (NM_007704, exon 1 of 18)	121	NM_001005787	12695	Mm.90218	NM_007704	ENSMUSG00000061859	Patj	Cipp|Inadl	PATJ, crumbs cell polarity complex component	protein-coding
mm_153818.1	chr19	46267675	46267702	-	1	NA	intron (NM_178930, intron 18 of 39)	intron (NM_178930, intron 18 of 39)	-37049	NM_001177369	18034	Mm.102365	NM_019408	ENSMUSG00000025225	Nfkb2	NF-kappaB2|lyt|p49|p49/p100|p50B|p52	nuclear factor of kappa light polypeptide gene enhancer in B cells 2, p49/p100	protein-coding
mm_151321.1	chr19	55892741	55892744	+	1	NA	intron (NR_138565, intron 4 of 15)	intron (NR_138565, intron 4 of 15)	-2579	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_130538.1	chr15	98937389	98937413	-	1	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	-3011	NM_011654	22143	Mm.392113	NM_011654	ENSMUSG00000023004	Tuba1b	Tuba2	tubulin, alpha 1B	protein-coding
mm_86474.1	chr10	4611972	4612015	+	1	NA	promoter-TSS (NR_126357)	promoter-TSS (NR_126357)	4	NM_007956	13982	Mm.9213	NM_007956	ENSMUSG00000019768	Esr1	ER|ER-alpha|ERa|ERalpha|ESR|Estr|Estra|Nr3a1	estrogen receptor 1 (alpha)	protein-coding
mm_9209.1	chr1	171229864	171229874	-	1	NA	exon (NM_010185, exon 5 of 5)	exon (NM_010185, exon 5 of 5)	4480	NM_010185	14127	Mm.22673	NM_010185	ENSMUSG00000058715	Fcer1g	AI573376|CD23|FcR-gamma|FcR[g]|FcRgamma|Fce1g|FcepsilonRI|Ly-50	Fc receptor, IgE, high affinity I, gamma polypeptide	protein-coding
mm_36665.1	chr4	95052171	95052181	-	1	NA	promoter-TSS (NM_010591)	promoter-TSS (NM_010591)	46	NM_010591	16476	Mm.275071	NM_010591	ENSMUSG00000052684	Jun	AP-1|Junc|c-jun	jun proto-oncogene	protein-coding
mm_78236.1	chr9	21616301	21616311	+	1	NA	5' UTR (NM_001174078, exon 1 of 34)	5' UTR (NM_001174078, exon 1 of 34)	137	NM_001174078	20586	Mm.286593	NM_011417	ENSMUSG00000032187	Smarca4	Brg1|HP1-BP72|SNF2beta|SW1/SNF|b2b508.1Clo|b2b692Clo	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	protein-coding
mm_12756.1	chr2	79255438	79255448	+	1	NA	promoter-TSS (NM_010576)	promoter-TSS (NM_010576)	17	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D|Itga4B	integrin alpha 4	protein-coding
mm_133858.1	chr16	96273604	96273616	+	1	NA	intron (NM_001122993, intron 2 of 3)	intron (NM_001122993, intron 2 of 3)	-7422	NM_033149	93961	Mm.154783	NM_033149	ENSMUSG00000074892	B3galt5	1190002B21Rik|AU045265|b3Galt-V	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 5	protein-coding
mm_167799.1	chr9	123927538	123927548	+	1	NA	Intergenic	Intergenic	41149	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_132269.1	chr16	32878086	32878095	+	1	NA	intron (NM_027226, intron 1 of 8)	CpG	306	NM_001159349	69823	Mm.12831	NM_027226	ENSMUSG00000022800	Fyttd1	2010005M05Rik|3830411L18Rik|3830421F13Rik|4933423A17Rik|AI098218|AW539567|C85190	forty-two-three domain containing 1	protein-coding
mm_92885.1	chr10	82763965	82763975	-	1	NA	intron (NM_010914, intron 1 of 7)	CpG	171	NM_010914	18045	Mm.245998	NM_010914	ENSMUSG00000020248	Nfyb	AA985999|Cbf-A	nuclear transcription factor-Y beta	protein-coding
mm_152125.1	chr19	6996026	6996096	-	1	NA	promoter-TSS (NM_153597)	promoter-TSS (NM_153597)	-24	NM_026675	68323	Mm.49041	NM_026675	ENSMUSG00000037349	Nudt22	0610006K04Rik|AI851793|AW545547	nudix (nucleoside diphosphate linked moiety X)-type motif 22	protein-coding
mm_62738.1	chr7	111028766	111028785	+	1	NA	promoter-TSS (NM_009431)	promoter-TSS (NM_009431)	-176	NM_009431	22083	Mm.255858	NM_009431	ENSMUSG00000005609	Ctr9	AA409336|Sh2bp1|Tsbp|Tsp|mKIAA0155	CTR9 homolog, Paf1/RNA polymerase II complex component	protein-coding
mm_133534.1	chr16	91046945	91046946	+	1	NA	Intergenic	Intergenic	-2566	NM_026110	67367	Mm.347	NM_026110	ENSMUSG00000022974	Paxbp1	1810007M14Rik|C21orf66|Gcfc|Gcfc1|Pax3/7bp	PAX3 and PAX7 binding protein 1	protein-coding
mm_144953.1	chr18	37812661	37812687	+	1	NA	intron (NM_033581, intron 1 of 3)	intron (NM_033581, intron 1 of 3)	-2405	NM_033582	93707	Mm.247203	NM_033582	ENSMUSG00000023036	Pcdhgc4	-	protocadherin gamma subfamily C, 4	protein-coding
mm_148172.1	chr18	78101409	78101422	-	1	NA	3' UTR (NM_028122, exon 9 of 9)	3' UTR (NM_028122, exon 9 of 9)	22011	NM_001171010	108052	Mm.33832	NM_028122	ENSMUSG00000059336	Slc14a1	2610507K20Rik|3021401A05Rik|UT-B|Utb1	solute carrier family 14 (urea transporter), member 1	protein-coding
mm_162821.1	chr10	80752344	80752362	+	1	NA	Intergenic	Intergenic	-2853	NM_199322	208266	Mm.152371	NM_199322	ENSMUSG00000061589	Dot1l	A630076O07|AW907654|Dot1|KMT4|mDot1	DOT1-like, histone H3 methyltransferase (S. cerevisiae)	protein-coding
mm_128739.1	chr15	64312493	64312508	-	1	NA	5' UTR (NM_001276463, exon 1 of 28)	5' UTR (NM_001276463, exon 1 of 28)	173	NM_001276462	13196	Mm.277236	NM_010026	ENSMUSG00000022377	Asap1	AV239055|DEF-1|Ddef1|PAP|mKIAA1249|s19	ArfGAP with SH3 domain, ankyrin repeat and PH domain1	protein-coding
mm_100096.1	chr11	115612603	115612611	+	1	NA	promoter-TSS (NM_027162)	promoter-TSS (NM_027162)	-104	NM_001243586	69674	Mm.390387	NM_027162	ENSMUSG00000020743	Mif4gd	1110014L05Rik|2310075G12Rik	MIF4G domain containing	protein-coding
mm_140230.1	chr17	84086612	84086621	+	1	NA	non-coding (NR_045458, exon 4 of 6)	non-coding (NR_045458, exon 4 of 6)	7956	NR_045458	74473	Mm.399575	NR_045458		4933433H22Rik	-	RIKEN cDNA 4933433H22 gene	ncRNA
mm_47163.1	chr5	120711698	120711708	-	1	NA	promoter-TSS (NM_008052)	promoter-TSS (NM_008052)	-34	NM_008052	14357	Mm.1645	NM_008052	ENSMUSG00000029603	Dtx1	Fxit1|mKIAA4160	deltex 1, E3 ubiquitin ligase	protein-coding
mm_170026.1	chr17	21679962	21679963	+	1	NA	Intergenic	Intergenic	-10250	NR_045766	100310809	Mm.293030	NR_045766		Gm10509	ENSMUSG00000073448	zinc finger protein 51 pseudogene	pseudo
mm_171411.1	chr4	129542650	129542667	-	1	NA	promoter-TSS (NM_008228)	promoter-TSS (NM_008228)	-12	NM_008228	433759	Mm.202504	NM_008228	ENSMUSG00000028800	Hdac1	HD1|Hdac1-ps|MommeD5|RPD3	histone deacetylase 1	protein-coding
mm_171923.1	chr5	58726569	58726586	+	1	NA	Intergenic	L1Md_T|LINE|L1	-273579	NR_046190	78163	Mm.243828	NR_046190	ENSMUSG00000105234	4930459L07Rik	-	RIKEN cDNA 4930459L07 gene	ncRNA
mm_164042.1	chr14	92053187	92053192	-	1	NA	Intergenic	Intergenic	1835699	NM_001271800	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding
mm_29269.1	chr3	107459692	107459716	-	1	NA	promoter-TSS (NM_145922)	promoter-TSS (NM_145922)	-806	NM_145922	99738	Mm.101976	NM_145922	ENSMUSG00000027895	Kcnc4	AI850292|KSHIIIC|Kcr2-4|Kv3.4	potassium voltage gated channel, Shaw-related subfamily, member 4	protein-coding
mm_106132.1	chr11	116466199	116466202	-	1	NA	Intergenic	Intergenic	-11853	NM_001033267	217341	Mm.387352	NM_001033267	ENSMUSG00000070331	Qrich2	Gm66	glutamine rich 2	protein-coding
mm_139370.1	chr17	51826723	51826741	+	1	NA	promoter-TSS (NM_001163631)	promoter-TSS (NM_001163631)	-144	NM_001163631	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_9393.1	chr1	172219463	172219498	-	1	NA	exon (NM_009813, exon 1 of 11)	exon (NM_009813, exon 1 of 11)	415	NM_009813	12372	Mm.12829	NM_009813	ENSMUSG00000007122	Casq1	CSQ|CSQ-1|CSQ1|sCSQ	calsequestrin 1	protein-coding
mm_124931.1	chr15	12205050	12205064	+	1	NA	promoter-TSS (NM_172958)	promoter-TSS (NM_172958)	-37	NM_172958	268783	Mm.54460	NM_172958	ENSMUSG00000039458	Mtmr12	3Pap|4932703C11|C730015A02Rik|Pip3ap|mKIAA1682	myotubularin related protein 12	protein-coding
mm_140710.1	chr17	14943101	14943111	-	1	NA	promoter-TSS (NM_001083881)	promoter-TSS (NM_001083881)	18	NM_175173	71682	Mm.122698	NM_175173	ENSMUSG00000046991	Wdr27	0610012K18Rik	WD repeat domain 27	protein-coding
mm_139799.1	chr17	66101700	66101714	+	1	NA	promoter-TSS (NM_028388)	promoter-TSS (NM_028388)	-148	NM_028388	72900	Mm.2206	NM_028388	ENSMUSG00000024099	Ndufv2	2900010C23Rik	NADH dehydrogenase (ubiquinone) flavoprotein 2	protein-coding
mm_164137.1	chr15	52387147	52387150	+	1	NA	Intergenic	Lx5c|LINE|L1	91595	NM_172816	239436	Mm.208831	NM_172816	ENSMUSG00000022315	Slc30a8	C820002P14Rik|ZnT-8|ZnT8	solute carrier family 30 (zinc transporter), member 8	protein-coding
mm_51481.1	chr6	83034189	83034252	+	1	NA	promoter-TSS (NM_013586)	promoter-TSS (NM_013586)	-4	NM_013586	16950	Mm.380433	NM_013586	ENSMUSG00000000693	Loxl3	Lor2|Loxl2	lysyl oxidase-like 3	protein-coding
mm_156522.1	chrX	150594326	150594336	+	1	NA	intron (NM_008824, intron 1 of 13)	intron (NM_008824, intron 1 of 13)	4410	NM_008824	18639	Mm.249131	NM_008824	ENSMUSG00000025271	Pfkfb1	PFK/FBPase 1	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1	protein-coding
mm_20795.1	chr2	144255395	144255412	-	1	NA	exon (NM_024225, exon 8 of 13)	exon (NM_024225, exon 8 of 13)	10799	NR_030762	100313519	Mm.453538	NR_030762	ENSMUSG00000077714	Snord17	MBI-43	small nucleolar RNA, C/D box 17	snoRNA
mm_10352.1	chr2	11689942	11689975	+	1	NA	3' UTR (NM_008367, exon 8 of 8)	3' UTR (NM_008367, exon 8 of 8)	-15335	NM_001271498	16169	Mm.200196	NM_008358	ENSMUSG00000023206	Il15ra	AA690181|IL-15RA	interleukin 15 receptor, alpha chain	protein-coding
mm_139707.1	chr17	57458886	57458897	+	1	NA	intron (NM_010130, intron 17 of 21)	Lx3A|LINE|L1	86423	NM_001104591	224916	Mm.469889	NM_001104591	ENSMUSG00000090655	Vmn2r120	EG224916	vomeronasal 2, receptor 120	protein-coding
mm_117457.1	chr13	74808853	74808887	-	1	NA	promoter-TSS (NM_009817)	promoter-TSS (NM_009817)	-110	NM_001301153	12380	Mm.29163	NM_009817	ENSMUSG00000021585	Cast	-	calpastatin	protein-coding
mm_104369.1	chr11	94352145	94352153	-	1	NA	exon (NM_029600, exon 27 of 31)	exon (NM_029600, exon 27 of 31)	24148	NM_146024	71452	Mm.141054	NM_027799	ENSMUSG00000020864	Ankrd40	1110011C06Rik|5530600A18Rik|Gcap15	ankyrin repeat domain 40	protein-coding
mm_10703.1	chr2	22774020	22774042	+	1	NA	promoter-TSS (NM_019456)	promoter-TSS (NM_019456)	-296	NM_019456	54519	Mm.14255	NM_019456	ENSMUSG00000026786	Apbb1ip	9930118P07Rik|Prp48	amyloid beta (A4) precursor protein-binding, family B, member 1 interacting protein	protein-coding
mm_23796.1	chr3	79629140	79629176	+	1	NA	promoter-TSS (NM_025794)	promoter-TSS (NM_025794)	79	NM_029482	75939	Mm.221520	NM_029482	ENSMUSG00000027811	4930579G24Rik	-	RIKEN cDNA 4930579G24 gene	protein-coding
mm_58945.1	chr7	18565084	18565090	+	1	NA	exon (NM_001037168, exon 2 of 5)	exon (NM_001037168, exon 2 of 5)	2218	NM_001037168	545925	Mm.440302	NM_001037168	ENSMUSG00000070797	Psg27	EG545925|cea15	pregnancy-specific glycoprotein 27	protein-coding
mm_14824.1	chr2	147013014	147013083	+	1	NA	promoter-TSS (NM_011917)	promoter-TSS (NM_011917)	-12	NM_011917	24128	Mm.3065	NM_011917	ENSMUSG00000027433	Xrn2	-	5'-3' exoribonuclease 2	protein-coding
mm_45390.1	chr5	66150673	66150707	-	1	NA	5' UTR (NM_001291226, exon 1 of 6)	5' UTR (NM_001291226, exon 1 of 6)	288	NM_001291226	245945	Mm.36863	NM_139065	ENSMUSG00000070780	Rbm47	9530077J19Rik	RNA binding motif protein 47	protein-coding
mm_75970.1	chr8	72002582	72002588	-	1	NA	intron (NM_024444, intron 2 of 12)	intron (NM_024444, intron 2 of 12)	7041	NM_024444	72054	Mm.160020	NM_024444	ENSMUSG00000003484	Cyp4f18	1810054N16Rik|Cyp4f3|Cypf18	cytochrome P450, family 4, subfamily f, polypeptide 18	protein-coding
mm_127073.1	chr15	97377159	97377175	+	1	NA	intron (NM_172293, intron 5 of 5)	intron (NM_172293, intron 5 of 5)	-129880	NM_001164602	105827	Mm.24005	NM_178114	ENSMUSG00000048218	Amigo2	AI415330|AMIGO-2|AW208913|Ali1	adhesion molecule with Ig like domain 2	protein-coding
mm_112058.1	chr12	111908056	111908125	-	1	NA	promoter-TSS (NM_011625)	promoter-TSS (NM_011625)	-35	NM_011625	21981	Mm.313076	NM_011625	ENSMUSG00000021285	Ppp1r13b	AI449786|ASPP1|AW545810|Tp53bp2|Trp53bp2|p85	protein phosphatase 1, regulatory (inhibitor) subunit 13B	protein-coding
mm_157195.1	chrX	12080576	12080582	-	1	NA	promoter-TSS (NM_029510)	promoter-TSS (NM_029510)	-26	NM_029510	71458	Mm.196328	NM_029510	ENSMUSG00000040363	Bcor	2900008C10Rik|5830466J11Rik|8430401K06Rik|BcorR|D930024N20Rik|mKIAA1575	BCL6 interacting corepressor	protein-coding
mm_113508.1	chr13	37598761	37598773	+	1	NA	Intergenic	PB1D11|SINE|Alu	-227271	NM_026830	68750	Mm.491109	NM_026830	ENSMUSG00000039087	Rreb1	1110037N09Rik|AA414966|B930013M22Rik	ras responsive element binding protein 1	protein-coding
mm_5457.1	chr1	36296665	36296672	-	1	NA	Intergenic	Intergenic	-11065	NM_001290727	214855	Mm.34316	NM_145996	ENSMUSG00000037447	Arid5a	D430024K22Rik|Mrf1	AT rich interactive domain 5A (MRF1-like)	protein-coding
mm_129139.1	chr15	76199959	76199972	-	1	NA	promoter-TSS (NM_201392)	promoter-TSS (NM_201392)	-130	NM_001163549	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
mm_53312.1	chr6	129182703	129182725	+	1	NA	intron (NM_053109, intron 1 of 4)	B3A|SINE|B2	2099	NM_053109	93694	Mm.197536	NM_053109	ENSMUSG00000030157	Clec2d	Clr-b|Clrb|Ocil	C-type lectin domain family 2, member d	protein-coding
mm_59791.1	chr7	28982911	28982921	+	1	NA	promoter-TSS (NM_008279)	promoter-TSS (NM_008279)	62	NM_008279	26411	Mm.148278	NM_008279	ENSMUSG00000037337	Map4k1	Hpk1|mHPK1	mitogen-activated protein kinase kinase kinase kinase 1	protein-coding
mm_35878.1	chr4	49536883	49536901	-	1	NA	intron (NM_144903, intron 8 of 8)	intron (NM_144903, intron 8 of 8)	12654	NM_144903	230163	Mm.482116	NM_144903	ENSMUSG00000028307	Aldob	Aldo-2|Aldo2|BC016435	aldolase B, fructose-bisphosphate	protein-coding
mm_83210.1	chr9	42022420	42022430	-	1	NA	exon (NM_011436, exon 23 of 48)	exon (NM_011436, exon 23 of 48)	101864	NM_011436	20660	Mm.121920	NM_011436	ENSMUSG00000049313	Sorl1	2900010L19Rik|AI596264|AW261561|LR11|SorLA|gp250|mSorLA	sortilin-related receptor, LDLR class A repeats-containing	protein-coding
mm_141352.1	chr17	28622480	28622502	-	1	NA	promoter-TSS (NM_016795)	promoter-TSS (NM_016795)	-37	NM_016795	20815	Mm.15252	NM_016795	ENSMUSG00000004865	Srpk1	AU017960	serine/arginine-rich protein specific kinase 1	protein-coding
mm_154063.1	chr19	55217567	55217577	-	1	NA	intron (NM_001081076, intron 12 of 20)	intron (NM_001081076, intron 12 of 20)	23664	NM_001081076	73707	Mm.489987	NM_001081076	ENSMUSG00000055523	Gucy2g	2410077I05Rik|GC-G	guanylate cyclase 2g	protein-coding
mm_158485.1	chrX	142318657	142318673	-	1	NA	3' UTR (NM_207625, exon 16 of 16)	3' UTR (NM_207625, exon 16 of 16)	-12467	NM_021487	66240	Mm.58507	NM_021487	ENSMUSG00000090122	Kcne1l	1500015C14Rik|Kcne5|Mink	potassium voltage-gated channel, Isk-related family, member 1-like, pseudogene	protein-coding
mm_101610.1	chr11	35817439	35817446	-	1	NA	exon (NM_025936, exon 10 of 15)	exon (NM_025936, exon 10 of 15)	17086	NM_025936	104458	Mm.284906	NM_025936	ENSMUSG00000018848	Rars	2610011N19Rik|2610037E21Rik|AL033339|AW985894	arginyl-tRNA synthetase	protein-coding
mm_85977.1	chr9	112164544	112164559	-	1	NA	intron (NM_001177623, intron 9 of 9)	intron (NM_001177623, intron 9 of 9)	21398	NM_001177618	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_133470.1	chr16	89250998	89251003	+	1	NA	Intergenic	Intergenic	45139	NM_001163615	622935	Mm.459837	NM_001163615	ENSMUSG00000091039	Krtap20-2	1190004K03Rik|EG622935|Gm6371	keratin associated protein 20-2	protein-coding
mm_129893.1	chr15	83563023	83563042	-	1	NA	promoter-TSS (NM_009775)	promoter-TSS (NM_009775)	-541	NM_009775	12257	Mm.1508	NM_009775	ENSMUSG00000041736	Tspo	Bzrp|IBP|PBR|Tspo1	translocator protein	protein-coding
mm_117953.1	chr13	99444423	99444441	-	1	NA	intron (NM_008634, intron 2 of 6)	intron (NM_008634, intron 2 of 6)	-31606	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_96626.1	chr11	69156914	69156916	+	1	NA	promoter-TSS (NM_009659)	promoter-TSS (NM_009659)	-157	NM_009659	11686	Mm.340329	NM_009659	ENSMUSG00000032807	Alox12b	12R-LOX|Aloxe2|e-LOX2	arachidonate 12-lipoxygenase, 12R type	protein-coding
mm_140231.1	chr17	84100803	84100818	+	1	NA	Intergenic	Intergenic	22150	NR_045458	74473	Mm.399575	NR_045458		4933433H22Rik	-	RIKEN cDNA 4933433H22 gene	ncRNA
mm_50663.1	chr6	51523946	51523976	+	1	NA	promoter-TSS (NM_001127349)	promoter-TSS (NM_001127349)	58	NM_001127349	71982	Mm.294166	NM_028035	ENSMUSG00000038301	Snx10	2410004M09Rik	sorting nexin 10	protein-coding
mm_67351.1	chr7	79836251	79836262	-	1	NA	exon (NM_008486, exon 10 of 20)	exon (NM_008486, exon 10 of 20)	6096	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_20711.1	chr2	134596653	134596671	-	1	NA	3' UTR (NM_029148, exon 8 of 8)	3' UTR (NM_029148, exon 8 of 8)	-42310	NM_010403	15112	Mm.26634	NM_010403	ENSMUSG00000027261	Hao1	GOX|Gox1|Hao-1	hydroxyacid oxidase 1, liver	protein-coding
mm_27765.1	chr3	69861375	69861395	-	1	NA	Intergenic	Intergenic	-1491	NM_001286959	66183	Mm.45481	NM_133675	ENSMUSG00000043461	Sptssb	1110032A04Rik|ADMP|Sssptb	serine palmitoyltransferase, small subunit B	protein-coding
mm_161712.1	chr17	25162342	25162342	+	1	NA	promoter-TSS (NM_001079929)	promoter-TSS (NM_001079929)	-119	NM_001079929	207209	Mm.207121	NM_001079929	ENSMUSG00000059562	Ccdc154	Ccdc157|Gm317	coiled-coil domain containing 154	protein-coding
mm_170234.1	chr17	87435846	87435848	-	1	NA	exon (NM_007589, exon 3 of 6)	exon (NM_007589, exon 3 of 6)	-8106	NM_029298	75467	Mm.50108	NM_029298	ENSMUSG00000036557	Stpg4	1700011E24Rik|GSE	sperm tail PG rich repeat containing 4	protein-coding
mm_9961.1	chr1	191098226	191098290	-	1	NA	promoter-TSS (NM_030060)	promoter-TSS (NM_030060)	-156	NM_030060	381319	Mm.6922	NM_030060	ENSMUSG00000026630	Batf3	9130211I03Rik|Snft	basic leucine zipper transcription factor, ATF-like 3	protein-coding
mm_147087.1	chr18	35648380	35648395	-	1	NA	intron (NM_027222, intron 1 of 3)	intron (NM_027222, intron 1 of 3)	980	NM_027222	69816	Mm.27252	NM_027222	ENSMUSG00000024353	Mzb1	2010001M09Rik|AV064572|PACAP|pERp1	marginal zone B and B1 cell-specific protein 1	protein-coding
mm_115336.1	chr13	112482160	112482191	+	1	NA	intron (NM_010560, intron 5 of 16)	ORR1B1|LTR|ERVL-MaLR	18105	NM_010560	16195	Mm.4364	NM_010560	ENSMUSG00000021756	Il6st	5133400A03Rik|AA389424|BB405851|CD130|D13Ertd699e|gp130	interleukin 6 signal transducer	protein-coding
mm_151943.1	chr19	5800970	5800974	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	1700	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_120240.1	chr14	62935056	62935064	+	1	NA	intron (NM_175546, intron 6 of 11)	intron (NM_175546, intron 6 of 11)	49450	NM_001037751	432867	Mm.99387	NM_001037751	ENSMUSG00000075574	Defb48	Defb42|EG432867	defensin beta 48	protein-coding
mm_92090.1	chr10	62865243	62865277	-	1	NA	intron (NM_027384, intron 1 of 10)	intron (NM_027384, intron 1 of 10)	14754	NM_027384	52463	Mm.17774	NM_027384	ENSMUSG00000047146	Tet1	2510010B09Rik|AA517754|BB001228|Cxxc6|D10Ertd17e|LCX|mKIAA1676	tet methylcytosine dioxygenase 1	protein-coding
mm_166339.1	chr5	114853576	114853588	-	1	NA	promoter-TSS (NM_026263)	promoter-TSS (NM_026263)	-132	NM_026263	67593	Mm.251409	NM_026263	ENSMUSG00000029564	4930519G04Rik	1700014B12Rik	RIKEN cDNA 4930519G04 gene	protein-coding
mm_79635.1	chr9	59542773	59542804	+	1	NA	intron (NM_010421, intron 1 of 13)	intron (NM_010421, intron 1 of 13)	3248	NM_010421	15211	Mm.2284	NM_010421	ENSMUSG00000025232	Hexa	Hex-1	hexosaminidase A	protein-coding
mm_58428.1	chr7	3297377	3297420	+	1	NA	exon (NM_016969, exon 3 of 3)	exon (NM_016969, exon 3 of 3)	4370	NM_001093766	50918	Mm.29874	NM_016969	ENSMUSG00000068566	Myadm	D7Wsu62e	myeloid-associated differentiation marker	protein-coding
mm_25628.1	chr3	119084916	119084921	+	1	NA	intron (NM_170778, intron 14 of 22)	MYSERV-int|LTR|ERVK	522740	NM_170778	99586	Mm.27907	NM_170778	ENSMUSG00000033308	Dpyd	AI315208|DPD|E330028L06Rik	dihydropyrimidine dehydrogenase	protein-coding
mm_123280.1	chr14	61419702	61419707	-	1	NA	intron (NM_008466, intron 1 of 16)	intron (NM_008466, intron 1 of 16)	20243	NM_008466	16648	Mm.25548	NM_008466	ENSMUSG00000021929	Kpna3	IPOA4	karyopherin (importin) alpha 3	protein-coding
mm_46621.1	chr5	108369407	108369431	-	1	NA	Intergenic	Intergenic	-18954	NM_008806	18587	Mm.1372	NM_008806	ENSMUSG00000029491	Pde6b	Pdeb|r|rd|rd-1|rd1|rd10	phosphodiesterase 6B, cGMP, rod receptor, beta polypeptide	protein-coding
mm_74670.1	chr8	13785483	13785502	-	1	NA	promoter-TSS (NM_025924)	promoter-TSS (NM_025924)	-123	NM_025924	67031	Mm.44858	NM_025924	ENSMUSG00000038398	Upf3a	2600001C03Rik|4930546M19Rik|RENT3A|UPF3	UPF3 regulator of nonsense transcripts homolog A (yeast)	protein-coding
mm_25990.1	chr3	134200065	134200090	+	1	NA	Intergenic	Intergenic	-36418	NM_001004367	319478	Mm.224814	NM_001004367	ENSMUSG00000044365	Cxxc4	9330210J02Rik|C030003J12Rik|Idax	CXXC finger 4	protein-coding
mm_89486.1	chr10	93678731	93678733	+	1	NA	intron (NR_038017, intron 4 of 5)	intron (NR_038017, intron 4 of 5)	4590	NR_038017	100504069	Mm.391412	NR_038017	ENSMUSG00000085723	Gm15915	OTTMUSG00000027787	predicted gene 15915	ncRNA
mm_133611.1	chr16	91545674	91545694	+	1	NA	Intergenic	Intergenic	-1410	NM_008338	15980	Mm.249364	NM_008338	ENSMUSG00000022965	Ifngr2	Ifgr2|Ifgt	interferon gamma receptor 2	protein-coding
mm_111633.1	chr12	102495521	102495546	-	1	NA	intron (NM_001199004, intron 11 of 12)	intron (NM_001199004, intron 11 of 12)	25623	NM_013747	27277	Mm.273370	NM_013747	ENSMUSG00000021192	Golga5	Ret-II	golgi autoantigen, golgin subfamily a, 5	protein-coding
mm_93069.1	chr10	89257697	89257712	-	1	NA	promoter-TSS (NM_001277188)	promoter-TSS (NM_001277188)	86	NM_001277188	320091	Mm.236464	NM_178773	ENSMUSG00000035189	Ano4	A330096O15Rik|Gm65|Tmem16d	anoctamin 4	protein-coding
mm_93715.1	chr10	118889242	118889255	-	1	NA	Intergenic	ERVL-int|LTR|ERVL	-20345	NM_001014390	69181	Mm.45565	NM_001014390	ENSMUSG00000028630	Dyrk2	1810038L18Rik	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 2	protein-coding
mm_87636.1	chr10	58351945	58351971	+	1	NA	intron (NM_026148, intron 1 of 9)	intron (NM_026148, intron 1 of 9)	-19496	NM_201242	110829	Mm.57734	NM_026148	ENSMUSG00000019920	Lims1	2310016J22Rik|4921524A02Rik|AI507642|AU021743|AW551584|C430041B13Rik|Lims1l|PINCH|PINCH1	LIM and senescent cell antigen-like domains 1	protein-coding
mm_17682.1	chr2	32309013	32309021	-	1	NA	non-coding (NR_125959, exon 22 of 22)	non-coding (NR_125959, exon 22 of 22)	-9248	NR_128563	104795665		NR_128563	ENSMUSG00000092765	Gm23363	Mir3154|mir-3154|mmu-mir-3154	predicted gene, 23363	ncRNA
mm_156042.1	chrX	108109977	108109978	+	1	NA	Intergenic	Intergenic	-161541	NM_001033252	213450	Mm.300779	NM_001033252	ENSMUSG00000073006	Gm732	-	predicted gene 732	protein-coding
mm_84773.1	chr9	75643222	75643237	-	1	NA	TTS (NM_001164790)	TTS (NM_001164790)	17497	NM_027309	70082	Mm.19119	NM_027309	ENSMUSG00000032184	Lysmd2	2210402C18Rik|AV033872|AW538442	LysM, putative peptidoglycan-binding, domain containing 2	protein-coding
mm_71545.1	chr8	47824460	47824471	+	1	NA	promoter-TSS (NM_029383)	promoter-TSS (NM_029383)	-17	NM_029383	75677	Mm.390033	NM_029383	ENSMUSG00000038064	Cldn22	2210404A22Rik|5330431C14Rik|9530051B05Rik	claudin 22	protein-coding
mm_48616.1	chr5	144761566	144761576	-	1	NA	promoter-TSS (NM_177735)	promoter-TSS (NM_177735)	7	NM_177735	243339	Mm.126793	NM_177735	ENSMUSG00000043388	Tmem130	BC067004|C130036G08	transmembrane protein 130	protein-coding
mm_36415.1	chr4	78211733	78211754	-	1	NA	5' UTR (NM_011211, exon 1 of 40)	5' UTR (NM_011211, exon 1 of 40)	152	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding
mm_155003.1	chrX	41400658	41400668	+	1	NA	promoter-TSS (NM_001290451)	promoter-TSS (NM_001290451)	-638	NM_016886	53623	Mm.327681	NM_016886	ENSMUSG00000001986	Gria3	2900064I19Rik|GluA3|GluR-C|GluR-K3|Glur-3|Glur3|Gluralpha3	glutamate receptor, ionotropic, AMPA3 (alpha 3)	protein-coding
mm_139693.1	chr17	57438377	57438425	+	1	NA	intron (NM_010130, intron 12 of 21)	ORR1F|LTR|ERVL-MaLR	79715	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_146102.1	chr18	73963599	73963603	+	1	NA	intron (NM_172632, intron 2 of 5)	intron (NM_172632, intron 2 of 5)	-54306	NR_045390	77855	Mm.410760	NR_045390	ENSMUSG00000090263	D730045A05Rik	-	RIKEN cDNA D730045A05 gene	ncRNA
mm_153359.1	chr19	40180394	40180405	-	1	NA	exon (NM_145499, exon 3 of 9)	exon (NM_145499, exon 3 of 9)	6887	NM_145499	226105	Mm.29119	NM_145499	ENSMUSG00000060613	Cyp2c70	-	cytochrome P450, family 2, subfamily c, polypeptide 70	protein-coding
mm_14407.1	chr2	130274438	130274454	+	1	NA	promoter-TSS (NM_024193)	promoter-TSS (NM_024193)	34	NM_024193	67134	Mm.29363	NM_024193	ENSMUSG00000027405	Nop56	2310044F10Rik|Nol5a	NOP56 ribonucleoprotein	protein-coding
mm_18085.1	chr2	44927195	44927205	-	1	NA	Intergenic	CpG	-65578	NM_172662	227835	Mm.314312	NM_172662	ENSMUSG00000036890	Gtdc1	E330008O22Rik	glycosyltransferase-like domain containing 1	protein-coding
mm_50863.1	chr6	55336425	55336438	+	1	NA	5' UTR (NM_007472, exon 1 of 4)	5' UTR (NM_007472, exon 1 of 4)	132	NM_007472	11826	Mm.18625	NM_007472	ENSMUSG00000004655	Aqp1	CHIP28	aquaporin 1	protein-coding
mm_53177.1	chr6	125349808	125349820	+	1	NA	promoter-TSS (NM_011609)	promoter-TSS (NM_011609)	91	NM_011609	21937	Mm.1258	NM_011609	ENSMUSG00000030341	Tnfrsf1a	CD120a|FPF|TNF-R|TNF-R-I|TNF-R1|TNF-R55|TNF-alphaR1|TNFAR|TNFR60|TNFRI|TNFRp55|TNFalpha-R1|Tnfr-2|Tnfr1|p55|p55-R	tumor necrosis factor receptor superfamily, member 1a	protein-coding
mm_100818.1	chr11	5152219	5152272	-	1	NA	promoter-TSS (NM_080595)	promoter-TSS (NM_080595)	-23	NM_080595	140703	Mm.840	NM_080595	ENSMUSG00000034164	Emid1	AW122071|CO-5|Emu1	EMI domain containing 1	protein-coding
mm_126484.1	chr15	81588951	81588958	+	1	NA	intron (NM_177821, intron 1 of 30)	PB1D9|SINE|Alu	2740	NM_177821	328572	Mm.258397	NM_177821	ENSMUSG00000055024	Ep300	A430090G16|A730011L11|KAT3B|p300|p300 HAT	E1A binding protein p300	protein-coding
mm_12480.1	chr2	71529590	71529601	+	1	NA	5' UTR (NM_010053, exon 1 of 3)	5' UTR (NM_010053, exon 1 of 3)	150	NM_010053	13390	Mm.475101	NM_010053	ENSMUSG00000041911	Dlx1	Dlx|Dlx-1	distal-less homeobox 1	protein-coding
mm_61162.1	chr7	59228772	59228782	+	1	NA	promoter-TSS (NM_001033962)	promoter-TSS (NM_001033962)	25	NM_011668	22215	Mm.9002	NM_011668	ENSMUSG00000025326	Ube3a	4732496B02|5830462N02Rik|A130086L21Rik|Hpve6a|mKIAA4216	ubiquitin protein ligase E3A	protein-coding
mm_114453.1	chr13	66994914	66994918	+	1	NA	intron (NM_008959, intron 11 of 12)	intron (NM_008959, intron 11 of 12)	37489	NR_045851	71226	Mm.399574	NR_045851		4933433G19Rik	-	RIKEN cDNA 4933433G19 gene	ncRNA
mm_6320.1	chr1	71605965	71605986	-	1	NA	exon (NM_001276413, exon 30 of 44)	exon (NM_001276413, exon 30 of 44)	47259	NM_010233	14268	Mm.193099	NM_010233	ENSMUSG00000026193	Fn1	E330027I09|Fn|Fn-1	fibronectin 1	protein-coding
mm_67243.1	chr7	75309027	75309052	-	1	NA	promoter-TSS (NM_001109753)	promoter-TSS (NM_001109753)	223	NM_153579	64176	Mm.273082	NM_153579	ENSMUSG00000053025	Sv2b	A830038F04Rik|AI850768|mKIAA0735	synaptic vesicle glycoprotein 2 b	protein-coding
mm_20603.1	chr2	131434390	131434396	-	1	NA	intron (NR_037281, intron 1 of 2)	intron (NR_037281, intron 1 of 2)	-57469	NM_001177834	228608	Mm.136586	NM_145533	ENSMUSG00000027333	Smox	B130066H01Rik|PAO|PAOh1|SMO	spermine oxidase	protein-coding
mm_81180.1	chr9	107399797	107399849	+	1	NA	promoter-TSS (NM_001174049)	promoter-TSS (NM_001174049)	-57	NM_001174049	56808	Mm.273084	NM_020263	ENSMUSG00000010066	Cacna2d2	Cacna2d|a2d2|du|mKIAA0558|td|torpid	calcium channel, voltage-dependent, alpha 2/delta subunit 2	protein-coding
mm_107631.1	chr12	51838539	51838539	+	1	NA	Intergenic	Intergenic	-9003	NM_144788	207304	Mm.249391	NM_144788	ENSMUSG00000035247	Hectd1	A630086P08Rik|AI844876|b2b327Clo|opm	HECT domain containing 1	protein-coding
mm_76499.1	chr8	86745951	86746054	-	1	NA	promoter-TSS (NM_009172)	promoter-TSS (NM_009172)	4	NM_009172	20437	Mm.324553	NM_009172	ENSMUSG00000036840	Siah1a	AA982064|AI853500|Sinh1a	seven in absentia 1A	protein-coding
mm_138709.1	chr17	36043048	36043056	+	1	NA	promoter-TSS (NM_001034909)	promoter-TSS (NM_001034909)	91	NM_001034909	547347	Mm.484641	NM_001034909	ENSMUSG00000073407	Gm6034	EG547347|H2-gs14-2	predicted gene 6034	protein-coding
mm_145247.1	chr18	51231928	51231931	+	1	NA	intron (NM_001081224, intron 1 of 1)	intron (NM_001081224, intron 1 of 1)	114031	NM_001081224	71373	Mm.63546	NM_001081224	ENSMUSG00000073565	Prr16	5430406M13Rik|AI607429	proline rich 16	protein-coding
mm_78237.1	chr9	21616369	21616371	+	1	NA	5' UTR (NM_001174078, exon 1 of 34)	5' UTR (NM_001174078, exon 1 of 34)	201	NM_001174078	20586	Mm.286593	NM_011417	ENSMUSG00000032187	Smarca4	Brg1|HP1-BP72|SNF2beta|SW1/SNF|b2b508.1Clo|b2b692Clo	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	protein-coding
mm_170955.1	chr2	5379363	5379363	-	1	NA	promoter-TSS (NR_030601)	promoter-TSS (NR_030601)	-27	NR_030601	100124465		NR_030601	ENSMUSG00000078031	Mir466d	Mirn466d	microRNA 466d	ncRNA
mm_116690.1	chr13	49309199	49309214	-	1	NA	promoter-TSS (NM_015759)	promoter-TSS (NM_015759)	2	NM_015759	30938	Mm.291089	NM_015759	ENSMUSG00000037946	Fgd3	5830461L01Rik|ZFYVE5	FYVE, RhoGEF and PH domain containing 3	protein-coding
mm_75144.1	chr8	35495488	35495545	-	1	NA	promoter-TSS (NM_026067)	promoter-TSS (NM_026067)	17	NM_026067	67276	Mm.207534	NM_026067	ENSMUSG00000031527	Eri1	3'hexo|3110010F15Rik|Thex1|eri-1	exoribonuclease 1	protein-coding
mm_150030.1	chr19	29373823	29373849	+	1	NA	exon (NM_021893, exon 3 of 7)	exon (NM_021893, exon 3 of 7)	6398	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_60738.1	chr7	45439896	45439908	+	1	NA	intron (NM_030678, intron 4 of 15)	intron (NM_030678, intron 4 of 15)	5063	NM_030678	14936	Mm.275654	NM_030678	ENSMUSG00000003865	Gys1	Gys3|MGS	glycogen synthase 1, muscle	protein-coding
mm_51709.1	chr6	86669608	86669646	+	1	NA	promoter-TSS (NM_010751)	promoter-TSS (NM_010751)	-468	NM_010751	17119	Mm.279580	NM_010751	ENSMUSG00000001156	Mxd1	AW122478|Mad|Mad1	MAX dimerization protein 1	protein-coding
mm_23868.1	chr3	83028562	83028597	+	1	NA	exon (NM_010196, exon 2 of 5)	exon (NM_010196, exon 2 of 5)	2426	NM_001111048	14161	Mm.88793	NM_010196	ENSMUSG00000028001	Fga	ENSMUSG00000059807|Fib	fibrinogen alpha chain	protein-coding
mm_47959.1	chr5	135586139	135586154	-	1	NA	Intergenic	Intergenic	-13103	NM_019577	56221	Mm.31505	NM_019577	ENSMUSG00000004814	Ccl24	CKb-6|MPIF-2|Scya24	chemokine (C-C motif) ligand 24	protein-coding
mm_83549.1	chr9	46242324	46242335	-	1	NA	exon (NM_007468, exon 3 of 3)	exon (NM_007468, exon 3 of 3)	1485	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_106479.1	chr11	120151195	120151354	-	1	NA	promoter-TSS (NM_001164801)	promoter-TSS (NM_001164801)	77	NM_001164799	72055	Mm.253403	NM_024249	ENSMUSG00000061306	Slc38a10	1810073N04Rik	solute carrier family 38, member 10	protein-coding
mm_110962.1	chr12	76822387	76822414	-	1	NA	5' UTR (NM_134050, exon 1 of 7)	5' UTR (NM_134050, exon 1 of 7)	124	NM_134050	104886	Mm.172847	NM_134050	ENSMUSG00000021062	Rab15	2310012G06Rik|AI840042	RAB15, member RAS oncogene family	protein-coding
mm_56196.1	chr6	88841852	88841905	-	1	NA	promoter-TSS (NM_030251)	promoter-TSS (NM_030251)	57	NM_030251	80283	Mm.166858	NM_030251	ENSMUSG00000030083	Abtb1	AI847549|BC003234|BPOZ|EF1ABP	ankyrin repeat and BTB (POZ) domain containing 1	protein-coding
mm_90732.1	chr10	5289457	5289467	-	1	NA	exon (NM_001347711, exon 55 of 146)	exon (NM_001347711, exon 55 of 146)	-94755	NM_001079686	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_138982.1	chr17	45459249	45459268	+	1	NA	intron (NM_027649, intron 3 of 7)	intron (NM_027649, intron 3 of 7)	15680	NM_027649	71020	Mm.44257	NM_027649	ENSMUSG00000023935	Spats1	1700011H05Rik|4933400B06Rik|Daip2|Ddip|Srsp1	spermatogenesis associated, serine-rich 1	protein-coding
mm_61356.1	chr7	68418452	68418459	+	1	NA	intron (NR_046208, intron 1 of 2)	intron (NR_046208, intron 1 of 2)	1031	NR_046208	71244	Mm.410787	NR_046208	ENSMUSG00000108924	4933436H12Rik	-	RIKEN cDNA 4933436H12 gene	ncRNA
mm_172879.1	chr9	47958410	47958412	-	1	NA	Intergenic	Intergenic	-140203	NR_046048	100038460	Mm.447649	NR_046048		Gm10677	ENSMUSG00000074363	predicted gene 10677	ncRNA
mm_25069.1	chr3	99296521	99296531	+	1	NA	intron (NM_009323, intron 1 of 7)	intron (NM_009323, intron 1 of 7)	42766	NM_009323	21384	Mm.88761	NM_009323	ENSMUSG00000027868	Tbx15	Tbx14|Tbx8|de	T-box 15	protein-coding
mm_7622.1	chr1	127207267	127207272	-	1	NA	intron (NM_145128, intron 1 of 17)	intron (NM_145128, intron 1 of 17)	2283	NM_145128	107895	Mm.214682	NM_145128	ENSMUSG00000036155	Mgat5	4930471A21Rik|5330407H02Rik|AI480971|GlcNAc-TV	mannoside acetylglucosaminyltransferase 5	protein-coding
mm_56184.1	chr6	88465265	88465304	-	1	NA	promoter-TSS (NM_019685)	promoter-TSS (NM_019685)	-125	NM_019685	56505	Mm.42195	NM_019685	ENSMUSG00000030079	Ruvbl1	2510009G06Rik|Pontin52|Tip49a	RuvB-like protein 1	protein-coding
mm_136655.1	chr17	5975803	5975830	+	1	NA	exon (NM_001113353, exon 2 of 27)	exon (NM_001113353, exon 2 of 27)	230	NM_011523	20975	Mm.236068	NM_011523	ENSMUSG00000023805	Synj2	AI481647|SJ2|mKIAA0348	synaptojanin 2	protein-coding
mm_2319.1	chr1	92049119	92049121	+	1	NA	intron (NM_207225, intron 3 of 26)	intron (NM_207225, intron 3 of 26)	131221	NM_207225	208727	Mm.318567	NM_207225	ENSMUSG00000026313	Hdac4	4932408F19Rik|HD4	histone deacetylase 4	protein-coding
mm_74580.1	chr8	11239176	11239178	-	1	NA	exon (NM_009931, exon 16 of 52)	exon (NM_009931, exon 16 of 52)	-73628	NM_009932	12827	Mm.181021	NM_009932	ENSMUSG00000031503	Col4a2	Col4a-2	collagen, type IV, alpha 2	protein-coding
mm_53214.1	chr6	126808340	126808351	+	1	NA	Intergenic	Intergenic	40799	NM_025358	66108	Mm.29939	NM_025358	ENSMUSG00000000399	Ndufa9	1010001N11Rik	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 9	protein-coding
mm_139486.1	chr17	56079653	56079667	+	1	NA	promoter-TSS (NM_001304785)	promoter-TSS (NM_001304785)	29	NM_001304785	15193	Mm.12966	NM_008233	ENSMUSG00000002833	Hdgfrp2	HRP-2	hepatoma-derived growth factor, related protein 2	protein-coding
mm_19784.1	chr2	106974434	106974465	-	1	NA	promoter-TSS (NM_001025102)	promoter-TSS (NM_001025102)	-52	NM_001025102	212772	Mm.381231	NM_173750	ENSMUSG00000027122	Arl14ep	2700007P21Rik|4930448O08Rik|ARF7EP	ADP-ribosylation factor-like 14 effector protein	protein-coding
mm_3787.1	chr1	156939658	156939689	+	1	NA	promoter-TSS (NM_001159968)	promoter-TSS (NM_001159968)	-47	NM_023884	78255	Mm.28376	NM_023884	ENSMUSG00000026594	Ralgps2	1810020P17Rik|2210408F11Rik|4921528G01Rik|9130014M22Rik|AU043409|AW046161	Ral GEF with PH domain and SH3 binding motif 2	protein-coding
mm_141687.1	chr17	33951717	33951728	-	1	NA	promoter-TSS (NM_019420)	promoter-TSS (NM_019420)	-234	NM_019420	54218	Mm.11132	NM_019420	ENSMUSG00000067370	B3galt4	Gal-T2|Galt2	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 4	protein-coding
mm_145643.1	chr18	61118946	61119014	+	1	NA	exon (NM_001037859, exon 11 of 22)	exon (NM_001037859, exon 11 of 22)	1512	NR_105949	102466212		NR_105949	ENSMUSG00000098389	Mir6983	Gm27496|mmu-mir-6983	microRNA 6983	ncRNA
mm_124536.1	chr14	122451157	122451186	-	1	NA	promoter-TSS (NR_033325)	promoter-TSS (NR_033325)	-25	NR_033326	328479	Mm.86095	NR_033325	ENSMUSG00000064052	Gm5089	6530402A20|C030005G22Rik|EG328479	predicted gene 5089	ncRNA
mm_172350.1	chr7	11397912	11397924	+	1	NA	promoter-TSS (NM_001110316)	promoter-TSS (NM_001110316)	3	NM_001110316	665902	Mm.425380	NM_001110316	ENSMUSG00000070828	Zscan4f	C330039H09Rik	zinc finger and SCAN domain containing 4F	protein-coding
mm_67752.1	chr7	92654017	92654020	-	1	NA	intron (NM_029078, intron 8 of 15)	PB1D10|SINE|Alu	15894	NM_029078	74737	Mm.288645	NM_029078	ENSMUSG00000041328	Pcf11	2500001H09Rik|5730417B17Rik|C77803	PCF11 cleavage and polyadenylation factor subunit	protein-coding
mm_55472.1	chr6	68769147	68769159	-	1	NA	Intergenic	Intergenic	558021	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_117035.1	chr13	58274505	58274518	-	1	NA	promoter-TSS (NM_019832)	promoter-TSS (NM_019832)	-323	NM_019832	56278	Mm.296625	NM_019832	ENSMUSG00000021552	Gkap1	42kDa|4933400B15Rik|D13Ertd340e|Gkap42	G kinase anchoring protein 1	protein-coding
mm_144555.1	chr18	31634369	31634371	+	1	NA	promoter-TSS (NM_172965)	promoter-TSS (NM_172965)	-13	NM_172965	269003	Mm.194538	NM_172965	ENSMUSG00000024260	Sap130	2610304F09Rik|6720406D06	Sin3A associated protein	protein-coding
mm_129604.1	chr15	79893053	79893063	-	1	NA	promoter-TSS (NR_030675)	promoter-TSS (NR_030675)	80	NR_030675	109361	Mm.394656	NR_030675		D730005E14Rik	-	RIKEN cDNA D730005E14 gene	ncRNA
mm_126321.1	chr15	79733966	79733968	+	1	NA	intron (NM_001205346, intron 8 of 17)	intron (NM_001205346, intron 8 of 17)	8569	NM_194342	223697	Mm.202715	NM_194342	ENSMUSG00000042524	Sun2	B230369L08Rik|C030011B15|Unc84b	Sad1 and UNC84 domain containing 2	protein-coding
mm_2964.1	chr1	133019656	133019668	+	1	NA	intron (NM_008575, intron 1 of 11)	intron (NM_008575, intron 1 of 11)	5754	NR_126506	17248	Mm.426531	NM_008575	ENSMUSG00000054387	Mdm4	4933417N07Rik|AA414968|AL023055|AU018793|AU021806|C85810|Mdmx	transformed mouse 3T3 cell double minute 4	protein-coding
mm_23384.1	chr3	56325287	56325288	+	1	NA	Intergenic	RMER1A|Other|Other	-141586	NM_030595	26422	Mm.384353	NM_030595	ENSMUSG00000027799	Nbea	Lyst2|mKIAA1544	neurobeachin	protein-coding
mm_172063.1	chr6	132941192	132941192	-	1	NA	Intergenic	LTRIS2|LTR|ERV1	-9910	NM_207029	387354	Mm.377915	NM_207029	ENSMUSG00000063762	Tas2r129	T2R29|Tas2r29|mGR29|mt2r60	taste receptor, type 2, member 129	protein-coding
mm_108773.1	chr12	89812468	89812488	+	1	NA	promoter-TSS (NM_001252074)	promoter-TSS (NM_001252074)	-5	NM_001252074	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding
mm_134266.1	chr16	13902969	13902985	-	1	NA	promoter-TSS (NM_001289562)	promoter-TSS (NM_001289562)	168	NM_001039533	94184	Mm.171484	NM_053181	ENSMUSG00000022680	Pdxdc1	2210010A19Rik|AA415817|Kiaa0251-hp	pyridoxal-dependent decarboxylase domain containing 1	protein-coding
mm_47600.1	chr5	125042795	125042818	-	1	NA	exon (NM_001253904, exon 22 of 48)	exon (NM_001253904, exon 22 of 48)	39331	NM_028443	73121	Mm.296138	NM_028443	ENSMUSG00000037962	Rflna	3110032G18Rik|Fam101a|cfm|cfm2	refilin A	protein-coding
mm_53068.1	chr6	124914627	124914669	+	1	NA	exon (NM_026988, exon 3 of 5)	exon (NM_026988, exon 3 of 5)	-2943	NM_008479	16768	Mm.4528	NM_008479	ENSMUSG00000030124	Lag3	CD223|LAG-3|Ly66	lymphocyte-activation gene 3	protein-coding
mm_127472.1	chr15	101273052	101273058	+	1	NA	exon (NM_010444, exon 6 of 7)	exon (NM_010444, exon 6 of 7)	6209	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_163591.1	chr13	41137086	41137095	-	1	NA	intron (NM_001324525, intron 8 of 27)	G-rich|Low_complexity|Low_complexity	19079	NM_001324525	637277		NM_001324525		Sycp2l	EG621792|Gm268|Gm40956	synaptonemal complex protein 2-like	protein-coding
mm_7302.1	chr1	97977139	97977202	-	1	NA	5' UTR (NM_013626, exon 2 of 26)	5' UTR (NM_013626, exon 2 of 26)	70623	NR_037993	78603	Mm.442597	NR_037993	ENSMUSG00000089706	B230216N24Rik	-	RIKEN cDNA B230216N24 gene	ncRNA
mm_45681.1	chr5	77351065	77351079	-	1	NA	intron (NM_001159518, intron 5 of 5)	intron (NM_001159518, intron 5 of 5)	40588	NM_153798	231329	Mm.273217	NM_153798	ENSMUSG00000029250	Polr2b	Pol2rb|Rpb140|Rpb2	polymerase (RNA) II (DNA directed) polypeptide B	protein-coding
mm_45640.1	chr5	76905442	76905459	-	1	NA	promoter-TSS (NM_173765)	promoter-TSS (NM_173765)	64	NM_173765	231326	Mm.39271	NM_173765	ENSMUSG00000055923	Aasdh	A230062G08Rik|A830035E16|Acsf4|U26	aminoadipate-semialdehyde dehydrogenase	protein-coding
mm_129776.1	chr15	82792615	82792622	-	1	NA	exon (NM_029562, exon 4 of 9)	exon (NM_029562, exon 4 of 9)	1627	NM_029562	76279	Mm.439931	NM_029562	ENSMUSG00000022445	Cyp2d26	1300006E06Rik	cytochrome P450, family 2, subfamily d, polypeptide 26	protein-coding
mm_30147.1	chr3	142503090	142503118	-	1	NA	exon (NM_153564, exon 4 of 11)	exon (NM_153564, exon 4 of 11)	6170	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_4205.1	chr1	171232128	171232160	+	1	NA	intron (NM_010185, intron 1 of 4)	intron (NM_010185, intron 1 of 4)	2205	NM_010185	14127	Mm.22673	NM_010185	ENSMUSG00000058715	Fcer1g	AI573376|CD23|FcR-gamma|FcR[g]|FcRgamma|Fce1g|FcepsilonRI|Ly-50	Fc receptor, IgE, high affinity I, gamma polypeptide	protein-coding
mm_77059.1	chr8	109682194	109682208	-	1	NA	intron (NM_028018, intron 3 of 9)	intron (NM_028018, intron 3 of 9)	11093	NM_028018	71955	Mm.290036	NM_028018	ENSMUSG00000031729	Ist1	2400003C14Rik|AW536298|mKIAA0174	increased sodium tolerance 1 homolog (yeast)	protein-coding
mm_92181.1	chr10	67912595	67912617	-	1	NA	promoter-TSS (NM_178679)	promoter-TSS (NM_178679)	56	NM_178679	216049	Mm.268346	NM_178679	ENSMUSG00000037855	Zfp365	AI839779|AV340892|DBZ|Su48|Znf365|talanin	zinc finger protein 365	protein-coding
mm_145178.1	chr18	47112138	47112149	+	1	NA	Intergenic	Intergenic	153267	NM_178377	69456	Mm.210734	NM_178377	ENSMUSG00000042705	Commd10	2310003A05Rik|AU019438|DRWMS2	COMM domain containing 10	protein-coding
mm_1487.1	chr1	71714140	71714140	+	1	NA	Intergenic	Intergenic	60805	NR_040308	100042814	Mm.405775	NR_040308	ENSMUSG00000073652	Apol7d	ENSMUSG00000073652|Gm15456|OTTMUSG00000022136	apolipoprotein L 7d	ncRNA
mm_171860.1	chr5	21721376	21721380	+	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	-15782	NM_028431	73078	Mm.301655	NM_028431	ENSMUSG00000029017	Pmpcb	3110004O18Rik|MPP11|MPPB|MPPP52	peptidase (mitochondrial processing) beta	protein-coding
mm_24356.1	chr3	90052922	90052936	+	1	NA	promoter-TSS (NM_001165987)	promoter-TSS (NM_001165987)	127	NM_027500	99650	Mm.300083	NM_025762	ENSMUSG00000027942	4933434E20Rik	5730552F22Rik|AI462154|NICE-3|NS5ATP4	RIKEN cDNA 4933434E20 gene	protein-coding
mm_65451.1	chr7	25412846	25412856	-	1	NA	promoter-TSS (NM_153576)	promoter-TSS (NM_153576)	35	NM_153576	232983	Mm.10545	NM_153576	ENSMUSG00000060188	Cxcl17	VCC-1|Vcc1	chemokine (C-X-C motif) ligand 17	protein-coding
mm_74920.1	chr8	25556162	25556184	-	1	NA	promoter-TSS (NR_110510)	promoter-TSS (NR_110510)	-90	NR_110510	102633315	Mm.437828	NR_110510	ENSMUSG00000086134	Gm16159	OTTMUSG00000031030	predicted gene 16159	ncRNA
mm_25332.1	chr3	106573784	106573795	+	1	NA	3' UTR (NM_026013, exon 9 of 9)	3' UTR (NM_026013, exon 9 of 9)	-25987	NM_133869	99712	Mm.429443	NM_133869	ENSMUSG00000040774	Cept1	9930118K05Rik|mCEPT1	choline/ethanolaminephosphotransferase 1	protein-coding
mm_126412.1	chr15	80257083	80257135	+	1	NA	exon (NM_009716, exon 3 of 3)	exon (NM_009716, exon 3 of 3)	1925	NM_009716	11911	Mm.641	NM_009716	ENSMUSG00000042406	Atf4	Atf-4|C/ATF|CREB2|TAXREB67	activating transcription factor 4	protein-coding
mm_119414.1	chr14	45155819	45155843	+	1	NA	intron (NM_001310534, intron 14 of 20)	MT2A|LTR|ERVL	63594	NM_172597	70561	Mm.28129	NM_172597	ENSMUSG00000021830	Txndc16	5730420B22Rik|C77647	thioredoxin domain containing 16	protein-coding
mm_67516.1	chr7	80826002	80826023	-	1	NA	Intergenic	Intergenic	-22681	NM_016721	29875	Mm.207619	NM_016721	ENSMUSG00000030536	Iqgap1	AA682088|D7Ertd237e|D7Ertd257e|mKIAA0051	IQ motif containing GTPase activating protein 1	protein-coding
mm_73875.1	chr8	119277369	119277392	+	1	NA	intron (NM_019707, intron 10 of 13)	intron (NM_019707, intron 10 of 13)	-67158	NM_024219	68196	Mm.358714	NM_024219	ENSMUSG00000031839	Hsbp1	0610007A03Rik|AA408769|Hsp25	heat shock factor binding protein 1	protein-coding
mm_14007.1	chr2	122028602	122028664	+	1	NA	promoter-TSS (NM_001256055)	promoter-TSS (NM_001256055)	50	NM_001256055	100042807	Mm.329403	NM_001256055	ENSMUSG00000043424	Eif3j2	ENSMUSG00000043424|Eif3j-2|Gm9781|eIF3 p35|eIF3j-B	eukaryotic translation initiation factor 3, subunit J2	protein-coding
mm_88354.1	chr10	75933357	75933377	+	1	NA	promoter-TSS (NM_008606)	promoter-TSS (NM_008606)	-865	NM_008606	17385	Mm.4561	NM_008606	ENSMUSG00000000901	Mmp11	MMP-11|SL-3|ST3|Stmy3	matrix metallopeptidase 11	protein-coding
mm_106003.1	chr11	115699462	115699514	-	1	NA	promoter-TSS (NM_001313937)	promoter-TSS (NM_001313937)	46	NM_001313937	14784	Mm.439649	NM_008163	ENSMUSG00000059923	Grb2	AA408164|Ash	growth factor receptor bound protein 2	protein-coding
mm_24455.1	chr3	90613520	90613536	+	1	NA	intron (NM_011313, intron 1 of 2)	intron (NM_011313, intron 1 of 2)	634	NM_011313	20200	Mm.100144	NM_011313	ENSMUSG00000001025	S100a6	2A9|5B10|CALCYCLIN|Cacy|PRA	S100 calcium binding protein A6 (calcyclin)	protein-coding
mm_50750.1	chr6	52912662	52912671	+	1	NA	intron (NM_173406, intron 1 of 4)	intron (NM_173406, intron 1 of 4)	-3046	NM_001168277	231986	Mm.386865	NM_173406	ENSMUSG00000063568	Jazf1	AI591476|C820002C15|Jaz1|Tip27	JAZF zinc finger 1	protein-coding
mm_8847.1	chr1	162706131	162706145	-	1	NA	exon (NM_001081290, exon 16 of 35)	exon (NM_001081290, exon 16 of 35)	34418	NM_001081290	226562	Mm.245446	NM_001081290	ENSMUSG00000040225	Prrc2c	1810043M20Rik|9630039I18Rik|A630006J20|Bat2d|Bat2d1|Bat2l2|E130112L15Rik|Prrc3|mKIAA1096	proline-rich coiled-coil 2C	protein-coding
mm_94240.1	chr11	3293139	3293160	+	1	NA	intron (NM_019574, intron 1 of 3)	intron (NM_019574, intron 1 of 3)	2692	NM_019574	56218	Mm.275563	NM_019574	ENSMUSG00000020453	Patz1	8430401L15Rik|AI447519|Mazr|Patz|Zfp278	POZ (BTB) and AT hook containing zinc finger 1	protein-coding
mm_159303.1	chr2	178175455	178175455	+	1	NA	exon (NM_001177791, exon 1 of 13)	exon (NM_001177791, exon 1 of 13)	106	NM_001177791	74189	Mm.44413	NM_028806	ENSMUSG00000027525	Phactr3	1500003N10Rik|4930415A02Rik|H17739|Scapin1|Scapinin|mKIAA4224	phosphatase and actin regulator 3	protein-coding
mm_61428.1	chr7	73740278	73740333	+	1	NA	promoter-TSS (NM_001162532)	promoter-TSS (NM_001162532)	-2	NM_001162532	100038347	Mm.425464	NM_001162532	ENSMUSG00000078670	Fam174b	-	family with sequence similarity 174, member B	protein-coding
mm_156183.1	chrX	133851116	133851129	+	1	NA	5' UTR (NM_022322, exon 1 of 7)	5' UTR (NM_022322, exon 1 of 7)	114	NM_022322	64103	Mm.46221	NM_022322	ENSMUSG00000031250	Tnmd	1110017I01Rik|Bricd4|ChM1L|TeM	tenomodulin	protein-coding
mm_35486.1	chr4	40898553	40898560	-	1	NA	Intergenic	RMER17C|LTR|ERVK	-21500	NM_011463	20731	Mm.25246	NM_011463	ENSMUSG00000028415	Spink4	MPGC60	serine peptidase inhibitor, Kazal type 4	protein-coding
mm_51834.1	chr6	90301214	90301220	+	1	NA	promoter-TSS (NM_177738)	promoter-TSS (NM_177738)	-53	NM_177738	243535	Mm.233854	NM_177738	ENSMUSG00000049694	BC048671	-	cDNA sequence BC048671	protein-coding
mm_11338.1	chr2	30712346	30712349	+	1	NA	Intergenic	CpG	-8863	NR_037272	100526499		NR_037272	ENSMUSG00000093091	Mir3089	mir-3089|mmu-mir-3089	microRNA 3089	ncRNA
mm_160400.1	chr8	70797035	70797035	-	1	NA	Intergenic	CpG	-1100	NR_106099	102466823		NR_106099	ENSMUSG00000099031	Mir7240	Gm27487|mmu-mir-7240	microRNA 7240	ncRNA
mm_69524.1	chr7	135651893	135651910	-	1	NA	promoter-TSS (NM_001316681)	promoter-TSS (NM_001316681)	2	NM_001316681	19267	Mm.945	NM_011212	ENSMUSG00000041836	Ptpre	PTPe|PTPepsilon|RPTPepsilon	protein tyrosine phosphatase, receptor type, E	protein-coding
mm_17295.1	chr2	26237369	26237386	-	1	NA	promoter-TSS (NM_153559)	promoter-TSS (NM_153559)	22	NM_153559	227638	Mm.116769	NM_153559	ENSMUSG00000036327	Qsox2	BC030934|Qscn6l1|Soxn	quiescin Q6 sulfhydryl oxidase 2	protein-coding
mm_58083.1	chr6	136941860	136941884	-	1	NA	promoter-TSS (NM_007486)	promoter-TSS (NM_007486)	27	NM_001301301	11857	Mm.2241	NM_007486	ENSMUSG00000030220	Arhgdib	D4|Gdid4|Ly-GDI	Rho, GDP dissociation inhibitor (GDI) beta	protein-coding
mm_33872.1	chr4	136081986	136082007	+	1	NA	Intergenic	CpG	-28625	NM_025919	67025	Mm.276856	NM_025919	ENSMUSG00000059291	Rpl11	2010203J19Rik	ribosomal protein L11	protein-coding
mm_5508.1	chr1	37475456	37475458	-	1	NA	intron (NM_001290801, intron 4 of 14)	PB1D9|SINE|Alu	13148	NR_024017	77633	Mm.483177	NR_024017	ENSMUSG00000103948	4930594C11Rik	-	G1 to S phase transition pseudogene	pseudo
mm_139871.1	chr17	70657451	70657475	+	1	NA	exon (NM_177639, exon 4 of 12)	exon (NM_177639, exon 4 of 12)	95716	NM_001128181	224997	Mm.311840	NM_027712	ENSMUSG00000003279	Dlgap1	4933422O14Rik|9630002F18|AI845682|AI848168|BB075781|D17Bwg0511e|GKAP/SAPAP|GKPA/SAPAP|Gkap|Sapap1|mKIAA4162	discs, large (Drosophila) homolog-associated protein 1	protein-coding
mm_110062.1	chr12	21373482	21373492	-	1	NA	non-coding (NR_102380, exon 1 of 16)	non-coding (NR_102380, exon 1 of 16)	145	NR_102380	11491	Mm.27681	NM_009615	ENSMUSG00000052593	Adam17	CD156b|Tace	a disintegrin and metallopeptidase domain 17	protein-coding
mm_91783.1	chr10	52381957	52381978	-	1	NA	5' UTR (NM_053187, exon 1 of 8)	5' UTR (NM_053187, exon 1 of 8)	157	NM_053187	94221	Mm.390258	NM_053187	ENSMUSG00000019861	Gopc	2210402P09Rik|AI844555|CAL|FIG|GOPC1|PIST	golgi associated PDZ and coiled-coil motif containing	protein-coding
mm_11072.1	chr2	27677141	27677175	+	1	NA	promoter-TSS (NM_011305)	promoter-TSS (NM_011305)	-43	NM_011305	20181	Mm.24624	NM_011305	ENSMUSG00000015846	Rxra	9530071D11Rik|Nr2b1|RXRalpha1	retinoid X receptor alpha	protein-coding
mm_6134.1	chr1	64690651	64690666	-	1	NA	promoter-TSS (NM_001097644)	promoter-TSS (NM_001097644)	1	NR_038009	69941	Mm.69044	NR_038009	ENSMUSG00000087213	2810408I11Rik	-	RIKEN cDNA 2810408I11 gene	ncRNA
mm_169703.1	chr15	75086900	75086904	+	1	NA	Intergenic	Intergenic	25047	NM_001099217	100041546	Mm.482110	NM_001099217	ENSMUSG00000022584	Ly6c2	Ly-6C.2|Ly-6C2	lymphocyte antigen 6 complex, locus C2	protein-coding
mm_144368.1	chr18	20510224	20510234	+	1	NA	promoter-TSS (NM_030596)	promoter-TSS (NM_030596)	-45	NM_030596	13512	Mm.106811	NM_030596	ENSMUSG00000056632	Dsg3	bal	desmoglein 3	protein-coding
mm_113823.1	chr13	46966670	46966679	+	1	NA	Intergenic	MTEa-int|LTR|ERVL-MaLR	-36956	NM_010617	16553	Mm.342703	NM_010617	ENSMUSG00000021375	Kif13a	4930505I07Rik|mKIAA4109	kinesin family member 13A	protein-coding
mm_39152.1	chr4	155411314	155411318	-	1	NA	non-coding (NR_102283, exon 4 of 5)	non-coding (NR_102283, exon 4 of 5)	2126	NM_001166029	544678	Mm.472798	NM_177674	ENSMUSG00000078490	Cfap74	2010015L04Rik|A530045M11	cilia and flagella associated protein 74	protein-coding
mm_77931.1	chr9	7354010	7354033	+	1	NA	intron (NM_001320077, intron 7 of 10)	B4A|SINE|B4	6647	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_134811.1	chr16	25041231	25041246	-	1	NA	Intergenic	Intergenic	-18401	NR_040374	319487	Mm.137341	NR_040374	ENSMUSG00000096960	A230028O05Rik	-	RIKEN cDNA A230028O05 gene	ncRNA
mm_131566.1	chr16	18213952	18213961	+	1	NA	promoter-TSS (NR_027843)	promoter-TSS (NR_027843)	-93	NR_015575	66779	Mm.387525	NR_015575		4933432I09Rik	-	RIKEN cDNA 4933432I09 gene	ncRNA
mm_78518.1	chr9	32928715	32928720	+	1	NA	intron (NR_131058, intron 1 of 3)	intron (NR_131058, intron 1 of 3)	249	NR_131058	330917	Mm.488283	NR_131058		Gm27162	A430016B06	predicted gene 27162	ncRNA
mm_47394.1	chr5	123018945	123018949	-	1	NA	intron (NM_175423, intron 1 of 1)	intron (NM_175423, intron 1 of 1)	3873	NM_175423	109305	Mm.218582	NM_175423	ENSMUSG00000049686	Orai1	D730049H07Rik|Tmem142a|orai-1	ORAI calcium release-activated calcium modulator 1	protein-coding
mm_27734.1	chr3	69068466	69068481	-	1	NA	Intergenic	Intergenic	-23731	NM_025863	66949	Mm.176695	NM_025863	ENSMUSG00000034317	Trim59	2310035M22Rik|2700022F13Rik|Mrf1|TSBF1	tripartite motif-containing 59	protein-coding
mm_110998.1	chr12	78842577	78842592	-	1	NA	TTS (NM_023721)	TTS (NM_023721)	19054	NM_023721	73834	Mm.311549	NM_023721	ENSMUSG00000021114	Atp6v1d	1110004P10Rik|Atp6m|VATD|Vma8	ATPase, H+ transporting, lysosomal V1 subunit D	protein-coding
mm_139047.1	chr17	46253918	46253978	+	1	NA	promoter-TSS (NM_001111142)	promoter-TSS (NM_001111142)	-217	NM_001111142	224813	Mm.70999	NM_001111142	ENSMUSG00000071073	Lrrc73	Gm88	leucine rich repeat containing 73	protein-coding
mm_131945.1	chr16	24327533	24327538	+	1	NA	Intergenic	Intergenic	-65815	NM_178665	210126	Mm.209385	NM_178665	ENSMUSG00000033306	Lpp	9430020K16Rik|AA959454|AU024130|B130055L10Rik|C79715|D630048H16	LIM domain containing preferred translocation partner in lipoma	protein-coding
mm_158723.1	chrX	162964229	162964237	-	1	NA	intron (NM_009789, intron 1 of 2)	intron (NM_009789, intron 1 of 2)	366	NM_009789	12309	Mm.6891	NM_009789	ENSMUSG00000040808	S100g	AU042539|CABP1|CaBP-D9K|Cabp9k|Calb3	S100 calcium binding protein G	protein-coding
mm_61482.1	chr7	75678641	75678650	+	1	NA	intron (NM_029332, intron 11 of 36)	L2b|LINE|L2	-169693	NM_001122780	207952	Mm.206223	NM_029652	ENSMUSG00000055652	Klhl25	2810402K13Rik|BC027373|Enc-1	kelch-like 25	protein-coding
mm_134584.1	chr16	20423482	20423504	-	1	NA	intron (NM_176839, intron 1 of 6)	ID_B1|SINE|B4	2901	NM_013790	27416	Mm.20845	NM_013790	ENSMUSG00000022822	Abcc5	2900011L11Rik|AI132311|Abcc5a|Abcc5b|Mrp5	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	protein-coding
mm_68943.1	chr7	126503584	126503594	-	1	NA	promoter-TSS (NM_183020)	promoter-TSS (NM_183020)	-287	NM_183020	233871	Mm.231450	NM_183020	ENSMUSG00000032637	Atxn2l	A2D|A2LG|A2RP|A2lp|Atxnl2	ataxin 2-like	protein-coding
mm_48338.1	chr5	139130045	139130063	-	1	NA	promoter-TSS (NM_008923)	promoter-TSS (NM_008923)	-302	NM_008923	19085	Mm.306163	NM_008923	ENSMUSG00000025855	Prkar1b	AI385716|RIbeta	protein kinase, cAMP dependent regulatory, type I beta	protein-coding
mm_22104.1	chr2	169888024	169888040	-	1	NA	3' UTR (NM_080455, exon 2 of 2)	3' UTR (NM_080455, exon 2 of 2)	75155	NR_131974	446211	Mm.266854	NR_131974	ENSMUSG00000103935	AY702102	STDP1	cDNA sequence AY702102	ncRNA
mm_86975.1	chr10	25414589	25414590	+	1	NA	intron (NM_013511, intron 1 of 19)	Lx10|LINE|L1	6221	NM_013511	13822	Mm.306026	NM_013511	ENSMUSG00000019978	Epb41l2	4.1G|AW555191|D10Ertd398e|Epb4.1l2|NBL2	erythrocyte membrane protein band 4.1 like 2	protein-coding
mm_149020.1	chr19	8756724	8756744	+	1	NA	promoter-TSS (NM_001276704)	promoter-TSS (NM_001276704)	235	NR_132423	102640359	Mm.440831	NR_132423		LOC102640359	-	uncharacterized LOC102640359	ncRNA
mm_90906.1	chr10	11280361	11280361	-	1	NA	promoter-TSS (NM_027968)	promoter-TSS (NM_027968)	-969	NM_027968	71865	Mm.276229	NM_027968	ENSMUSG00000047648	Fbxo30	1700026A16Rik|MUSA1	F-box protein 30	protein-coding
mm_168596.1	chr1	173942479	173942479	-	1	NA	promoter-TSS (NM_001302651)	promoter-TSS (NM_001302651)	13	NM_001302649	15950	Mm.463437	NM_008328	ENSMUSG00000039997	Ifi203	Mndal	interferon activated gene 203	protein-coding
mm_171372.1	chr4	119282415	119282417	-	1	NA	exon (NM_011732, exon 5 of 8)	exon (NM_011732, exon 5 of 8)	12097	NM_011732	22608	Mm.258204	NM_011732	ENSMUSG00000028639	Ybx1	1700102N10Rik|C79409|EF1A|MSY1|Nsep1|YB-1|dbpB|mYB-1a	Y box protein 1	protein-coding
mm_47403.1	chr5	123130856	123130868	-	1	NA	intron (NM_175092, intron 2 of 4)	intron (NM_175092, intron 2 of 4)	1767	NM_175092	23912	Mm.253876	NM_175092	ENSMUSG00000029449	Rhof	AI845056|AV026554|Arhf|Ifld1|Rif	ras homolog family member F (in filopodia)	protein-coding
mm_158299.1	chrX	116287284	116287302	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-161651	NM_001033471	382239	Mm.336224	NM_001033471	ENSMUSG00000072995	Cpxcr1	Gm1143	CPX chromosome region, candidate 1	protein-coding
mm_24233.1	chr3	88950672	88950692	+	1	NA	promoter-TSS (NM_022994)	promoter-TSS (NM_022994)	-400	NM_001164533	65111	Mm.29028	NM_022994	ENSMUSG00000068921	Dap3	4921514D13Rik|DAP-3|MRP-S29|S29mt	death associated protein 3	protein-coding
mm_20021.1	chr2	119346752	119346756	-	1	NA	Intergenic	RMER4B|LTR|ERVK	-4488	NM_026929	69065	Mm.35083	NM_026929	ENSMUSG00000027313	Chac1	1810008K03Rik	ChaC, cation transport regulator 1	protein-coding
mm_36218.1	chr4	62516669	62516703	-	1	NA	intron (NM_008525, intron 1 of 11)	intron (NM_008525, intron 1 of 11)	3223	NM_001276446	17025	Mm.6988	NM_008525	ENSMUSG00000028393	Alad	ALADH|Lv	aminolevulinate, delta-, dehydratase	protein-coding
mm_135348.1	chr16	43664133	43664141	-	1	NA	promoter-TSS (NM_001146325)	promoter-TSS (NM_001146325)	47	NM_001146325	100043314	Mm.390896	NM_001146325	ENSMUSG00000071552	Tigit	ENSMUSG00000071552|Vstm3	T cell immunoreceptor with Ig and ITIM domains	protein-coding
mm_131314.1	chr16	11644709	11644749	+	1	NA	intron (NM_001290148, intron 9 of 13)	intron (NM_001290148, intron 9 of 13)	-134973	NR_126430	73761	Mm.39183	NR_126430		4833415N18Rik	-	RIKEN cDNA 4833415N18 gene	ncRNA
mm_79562.1	chr9	58129063	58129068	+	1	NA	promoter-TSS (NM_009291)	promoter-TSS (NM_009291)	-23	NM_001162475	20897	Mm.10801	NM_009291	ENSMUSG00000032327	Stra6	AI891933	stimulated by retinoic acid gene 6	protein-coding
mm_134276.1	chr16	14110069	14110069	-	1	NA	3' UTR (NM_001081154, exon 27 of 27)	3' UTR (NM_001081154, exon 27 of 27)	49205	NM_001081154	223989	Mm.85442	NM_001081154	ENSMUSG00000060657	Marf1	4921513D23Rik|BC031575|C87306|E030019O05|Lkap|mKIAA0430	meiosis arrest female 1	protein-coding
mm_63099.1	chr7	122438651	122438652	+	1	NA	intron (NM_001316672, intron 3 of 16)	intron (NM_001316672, intron 3 of 16)	149526	NM_008855	18751	Mm.207496	NM_008855	ENSMUSG00000052889	Prkcb	PKC-B|PKC-Beta|Pkcb|Prkcb1|Prkcb2	protein kinase C, beta	protein-coding
mm_98913.1	chr11	98203308	98203348	+	1	NA	promoter-TSS (NM_026952)	promoter-TSS (NM_026952)	23	NM_001109626	69131	Mm.260516	NM_026952	ENSMUSG00000003119	Cdk12	1810022J16Rik|AI646528|Crk7|Crkrs|D11Ertd752e|Pksc	cyclin-dependent kinase 12	protein-coding
mm_67061.1	chr7	67619978	67619997	-	1	NA	intron (NR_028144, intron 2 of 8)	intron (NR_028144, intron 2 of 8)	25249	NM_175124	67867	Mm.31247	NM_027413	ENSMUSG00000030556	Lrrc28	1300004K21Rik|2210012C09Rik|2310058O11Rik	leucine rich repeat containing 28	protein-coding
mm_10372.1	chr2	11725002	11725014	+	1	NA	intron (NR_073191, intron 4 of 5)	B3A|SINE|B2	19296	NM_001271500	16169	Mm.200196	NM_008358	ENSMUSG00000023206	Il15ra	AA690181|IL-15RA	interleukin 15 receptor, alpha chain	protein-coding
mm_108582.1	chr12	85110874	85110890	+	1	NA	promoter-TSS (NM_030225)	promoter-TSS (NM_030225)	49	NM_030225	78920	Mm.296221	NM_030225	ENSMUSG00000004789	Dlst	1600017E01Rik|4632413C10Rik|4930529O08Rik|DLTS	dihydrolipoamide S-succinyltransferase (E2 component of 2-oxo-glutarate complex)	protein-coding
mm_6993.1	chr1	86358477	86358481	-	1	NA	intron (NM_010880, intron 1 of 13)	intron (NM_010880, intron 1 of 13)	976	NM_010880	17975	Mm.154378	NM_010880	ENSMUSG00000026234	Ncl	B530004O11Rik|C23|D0Nds28|D1Nds28|Nucl	nucleolin	protein-coding
mm_124830.1	chr15	9155515	9155537	+	1	NA	promoter-TSS (NM_001285980)	promoter-TSS (NM_001285980)	-101	NM_001285980	27401	Mm.35584	NM_013787	ENSMUSG00000054115	Skp2	4930500A04Rik|FBXL1|FWD1|p45	S-phase kinase-associated protein 2 (p45)	protein-coding
mm_3168.1	chr1	135673719	135673738	+	1	NA	Intergenic	Intergenic	-55469	NM_007791	13007	Mm.196484	NM_007791	ENSMUSG00000026421	Csrp1	AA408841|AA959891|AW545626|CRP1|Csrp	cysteine and glycine-rich protein 1	protein-coding
mm_17667.1	chr2	32085321	32085329	-	1	NA	Intergenic	Intergenic	-1620	NM_175511	241303	Mm.250441	NM_175511	ENSMUSG00000050592	Fam78a	A130092J06Rik	family with sequence similarity 78, member A	protein-coding
mm_135669.1	chr16	52411573	52411583	-	1	NA	intron (NM_009655, intron 1 of 15)	L1MA7|LINE|L1	41503	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_157557.1	chrX	52053102	52053125	-	1	NA	TTS (NM_008150)	TTS (NM_008150)	-80341	NM_028851	74279	Mm.159154	NM_028851	ENSMUSG00000031118	1700080O16Rik	-	RIKEN cDNA 1700080O16 gene	protein-coding
mm_145548.1	chr18	60808963	60808981	+	1	NA	intron (NM_001042605, intron 3 of 8)	intron (NM_001042605, intron 3 of 8)	-3104	NR_039567	100628611		NR_039567	ENSMUSG00000093327	Mir5107	mir-5107|mmu-mir-5107|mu-mir-5107	microRNA 5107	ncRNA
mm_146271.1	chr18	77879532	77879541	+	1	NA	intron (NM_013831, intron 14 of 14)	intron (NM_013831, intron 14 of 14)	-58931	NM_001195633	100502841	Mm.297782	NM_001195633	ENSMUSG00000039840	Epg5	4732475F16|5430411K18Rik|AI661957|AW456499|mKIAA1632	ectopic P-granules autophagy protein 5 homolog (C. elegans)	protein-coding
mm_38177.1	chr4	135266775	135266787	-	1	NA	intron (NM_013885, intron 1 of 5)	intron (NM_013885, intron 1 of 5)	5979	NM_013885	29876	Mm.257765	NM_013885	ENSMUSG00000037242	Clic4	D0Jmb3|TU-74|mc3s5|mtCLIC	chloride intracellular channel 4 (mitochondrial)	protein-coding
mm_60544.1	chr7	44480577	44480613	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-3922	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_92016.1	chr10	62342727	62342733	-	1	NA	intron (NR_038038, intron 1 of 1)	intron (NR_038038, intron 1 of 1)	2123	NR_038038	70162	Mm.441212	NR_038038		Hk1os	2210417K05Rik	hexokinase 1, opposite strand	ncRNA
mm_99576.1	chr11	104132865	104132876	+	1	NA	promoter-TSS (NM_007762)	promoter-TSS (NM_007762)	89	NM_001313929	12921	Mm.1892	NM_007762	ENSMUSG00000018634	Crhr1	CRF1R|CRFR1|Crhr	corticotropin releasing hormone receptor 1	protein-coding
mm_110753.1	chr12	70044413	70044420	-	1	NA	intron (NM_001081453, intron 15 of 28)	intron (NM_001081453, intron 15 of 28)	-57414	NM_022028	64010	Mm.390480	NM_022028	ENSMUSG00000021067	Sav1	1700040G09Rik|Salv|Sav|WW45|Wwp3|Wwp4	salvador family WW domain containing 1	protein-coding
mm_38817.1	chr4	148599108	148599116	-	1	NA	Intergenic	RLTR1A2_MM|LTR|ERV1	-3432	NM_010767	17175	Mm.378962	NM_010767	ENSMUSG00000028979	Masp2	MASP-2|MAp19	mannan-binding lectin serine peptidase 2	protein-coding
mm_63140.1	chr7	123124267	123124277	+	1	NA	5' UTR (NM_144925, exon 1 of 24)	5' UTR (NM_144925, exon 1 of 24)	387	NM_144925	233833	Mm.102305	NM_144925	ENSMUSG00000052707	Tnrc6a	2010321I05Rik|3110054G10Rik|AW557223|CAGH26|D130023A07Rik|GW182|Tnrc6	trinucleotide repeat containing 6a	protein-coding
mm_165984.1	chr4	107178370	107178417	+	1	NA	promoter-TSS (NM_029565)	promoter-TSS (NM_029565)	-27	NM_025617	66526	Mm.246956	NM_025617	ENSMUSG00000028619	Tceanc2	2210010B22Rik|2210012G02Rik|6330404A07Rik|AU015593|Tdeanc2	transcription elongation factor A (SII) N-terminal and central domain containing 2	protein-coding
mm_37507.1	chr4	123841988	123841995	-	1	NA	Intergenic	Intergenic	54116	NM_183163	230726	Mm.37334	NM_183163	ENSMUSG00000043333	Rhbdl2	9130416B15|RRP2	rhomboid, veinlet-like 2 (Drosophila)	protein-coding
mm_159212.1	chr2	122439782	122439782	+	1	NA	intron (NM_172980, intron 1 of 18)	MERVL_2A-int|LTR|ERVL	13305	NM_172980	269346	Mm.29510	NM_172980	ENSMUSG00000027219	Slc28a2	2010208B10Rik|B430217P18|BB152493|Cnt2	solute carrier family 28 (sodium-coupled nucleoside transporter), member 2	protein-coding
mm_69119.1	chr7	127026228	127026246	-	1	NA	exon (NM_010772, exon 1 of 5)	exon (NM_010772, exon 1 of 5)	242	NM_010772	17188	Mm.378964	NM_010772	ENSMUSG00000030678	Maz	MAZI|PUR1|Pur-1|SAF-1|SAF-2	MYC-associated zinc finger protein (purine-binding transcription factor)	protein-coding
mm_100555.1	chr11	120722245	120722265	+	1	NA	exon (NM_133223, exon 2 of 6)	exon (NM_133223, exon 2 of 6)	787	NM_133223	170758	Mm.34008	NM_133223	ENSMUSG00000018012	Rac3	Rac1B	RAS-related C3 botulinum substrate 3	protein-coding
mm_159844.1	chr5	135435142	135435142	-	1	NA	exon (NM_146001, exon 14 of 31)	exon (NM_146001, exon 14 of 31)	-40596	NM_148932	107939	Mm.28399	NM_148932	ENSMUSG00000053293	Pom121	2610027A18Rik|C80273|mKIAA0618	nuclear pore membrane protein 121	protein-coding
mm_63032.1	chr7	121074652	121074662	+	1	NA	promoter-TSS (NM_030691)	promoter-TSS (NM_030691)	-127	NM_030691	80719	Mm.160384	NM_030691	ENSMUSG00000035004	Igsf6	-	immunoglobulin superfamily, member 6	protein-coding
mm_9208.1	chr1	171229835	171229851	-	1	NA	3' UTR (NM_010185, exon 5 of 5)	3' UTR (NM_010185, exon 5 of 5)	4506	NM_010185	14127	Mm.22673	NM_010185	ENSMUSG00000058715	Fcer1g	AI573376|CD23|FcR-gamma|FcR[g]|FcRgamma|Fce1g|FcepsilonRI|Ly-50	Fc receptor, IgE, high affinity I, gamma polypeptide	protein-coding
mm_19291.1	chr2	90457166	90457196	-	1	NA	intron (NM_001135657, intron 10 of 25)	L1MEg|LINE|L1	21993	NM_001135657	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_85038.1	chr9	88719322	88719327	-	1	NA	intron (NM_001128601, intron 1 of 2)	intron (NM_001128601, intron 1 of 2)	474	NM_001128601	100039707	Mm.347377	NM_001128601	ENSMUSG00000079427	Mthfsl	Gm2382	5, 10-methenyltetrahydrofolate synthetase-like	protein-coding
mm_118128.1	chr13	104610626	104610636	-	1	NA	Intergenic	Intergenic	206322	NM_026072	67285	Mm.235398	NM_026072	ENSMUSG00000021715	Cwc27	3110009E13Rik|NY-CO-10|Sdccag10	CWC27 spliceosome-associated protein	protein-coding
mm_105854.1	chr11	113750882	113750901	-	1	NA	5' UTR (NM_020006, exon 1 of 2)	5' UTR (NM_020006, exon 1 of 2)	269	NM_020006	56699	Mm.293378	NM_020006	ENSMUSG00000041598	Cdc42ep4	1500041M20Rik|Borg4|CEP4	CDC42 effector protein (Rho GTPase binding) 4	protein-coding
mm_77216.1	chr8	114978923	114978923	-	1	NA	intron (NM_019573, intron 8 of 8)	(TCTG)n|Simple_repeat|Simple_repeat	539271	NM_019573	80707	Mm.440420	NM_019573	ENSMUSG00000004637	Wwox	5330426P09Rik|9030416C10Rik|WOX1	WW domain-containing oxidoreductase	protein-coding
mm_154150.1	chr19	58454526	58454552	-	1	NA	non-coding (NR_104342, exon 2 of 12)	non-coding (NR_104342, exon 2 of 12)	859	NM_001285457	14585	Mm.88367	NM_010279	ENSMUSG00000025089	Gfra1	AU042498	glial cell line derived neurotrophic factor family receptor alpha 1	protein-coding
mm_109380.1	chr12	109709124	109709126	+	1	NA	promoter-TSS (NR_029880)	promoter-TSS (NR_029880)	65	NR_029880	723858		NR_029880	ENSMUSG00000065498	Mir379	Mirn379|mir-379|mmu-mir-379	microRNA 379	ncRNA
mm_49010.1	chr6	4758434	4758438	+	1	NA	3' UTR (NM_130877, exon 2 of 2)	3' UTR (NM_130877, exon 2 of 2)	11130	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_11667.1	chr2	35282322	35282329	+	1	NA	promoter-TSS (NM_146120)	promoter-TSS (NM_146120)	-55	NM_146120	227753	Mm.443	NM_146120	ENSMUSG00000026879	Gsn	ADF	gelsolin	protein-coding
mm_59548.1	chr7	28070999	28071029	+	1	NA	promoter-TSS (NM_001122603)	promoter-TSS (NM_001122603)	-222	NM_001122603	215384	Mm.292276	NM_175444	ENSMUSG00000047730	Fcgbp	A430096B05Rik	Fc fragment of IgG binding protein	protein-coding
mm_111797.1	chr12	104926837	104926839	-	1	NA	Intergenic	Intergenic	-61762	NR_104435	94040	Mm.244078	NM_053155	ENSMUSG00000021097	Clmn	9330188N17Rik|AI428889|AI788815|mKIAA1188	calmin	protein-coding
mm_81325.1	chr9	108490835	108490874	+	1	NA	TTS (NM_008483)	TTS (NM_008483)	178	NM_027804	71472	Mm.289706	NM_027804	ENSMUSG00000006676	Usp19	8430421I07Rik|AI047774|Zmynd9	ubiquitin specific peptidase 19	protein-coding
mm_163075.1	chr11	68118005	68118006	+	1	NA	intron (NM_018768, intron 7 of 7)	intron (NM_018768, intron 7 of 7)	-102887	NR_105833	102465219		NR_105833	ENSMUSG00000099174	Mir6406	Gm27981|mmu-mir-6406	microRNA 6406	ncRNA
mm_20784.1	chr2	143989335	143989344	-	1	NA	exon (NM_133626, exon 2 of 3)	exon (NM_133626, exon 2 of 3)	21924	NM_133626	81910	Mm.13705	NM_024281	ENSMUSG00000027422	Rrbp1	1700087N07Rik|5730465C04Rik|ES/130|mKIAA1398|mRRp0|mRRp1.8|mRRp10|mRRp15a|mRRp15b|mRRp16.8|mRRp2|mRRp41|mRRp47|mRRp5.4|p180	ribosome binding protein 1	protein-coding
mm_51226.1	chr6	71373401	71373465	+	1	NA	promoter-TSS (NM_009857)	promoter-TSS (NM_009857)	6	NM_001081110	12525	Mm.1858	NM_009857	ENSMUSG00000053977	Cd8a	BB154331|Ly-2|Ly-35|Ly-B|Lyt-2	CD8 antigen, alpha chain	protein-coding
mm_17572.1	chr2	30359279	30359341	-	1	NA	promoter-TSS (NM_001289709)	promoter-TSS (NM_001289709)	6	NM_139302	227700	Mm.33343	NM_139302	ENSMUSG00000026860	Sh3glb2	SPAS-1	SH3-domain GRB2-like endophilin B2	protein-coding
mm_85336.1	chr9	102626096	102626147	-	1	NA	promoter-TSS (NM_181394)	promoter-TSS (NM_181394)	3	NM_001301689	28135	Mm.38910	NM_001081122	ENSMUSG00000032534	Cep63	4921501M07|AL450317.13gm1|AW107703|CD20R|D9Mgc41|D9Mgc48e|ET2	centrosomal protein 63	protein-coding
mm_78292.1	chr9	22388869	22388890	+	1	NA	intron (NM_028390, intron 1 of 23)	CpG	327	NM_028390	68743	Mm.282751	NM_028390	ENSMUSG00000036777	Anln	1110037A17Rik|2900037I21Rik|C78101|Scraps	anillin, actin binding protein	protein-coding
mm_88427.1	chr10	77259355	77259364	+	1	NA	promoter-TSS (NM_030262)	promoter-TSS (NM_030262)	59	NM_030262	80294	Mm.203556	NM_030262	ENSMUSG00000020260	Pofut2	2310011G23Rik|AI256847|BC003494|C21orf80|FUT13	protein O-fucosyltransferase 2	protein-coding
mm_14433.1	chr2	130589432	130589451	+	1	NA	TTS (NM_001255994)	TTS (NM_001255994)	-6853	NM_009732	11998	Mm.6190	NM_009732	ENSMUSG00000037727	Avp	Vp|Vsp	arginine vasopressin	protein-coding
mm_77813.1	chr9	3199889	3199899	+	1	NA	promoter-TSS (NR_027988)	promoter-TSS (NR_027988)	-81	NR_027988	114673	Mm.422774	NM_053265	ENSMUSG00000042360	4930433N12Rik	-	RIKEN cDNA 4930433N12 gene	ncRNA
mm_56064.1	chr6	86781019	86781028	-	1	NA	intron (NM_013471, intron 1 of 12)	B3|SINE|B2	-5909	NM_001331120	11746	Mm.259702	NM_013471	ENSMUSG00000029994	Anxa4	AI265406|AIV|AW106930|Anx4|Xanx-4	annexin A4	protein-coding
mm_60761.1	chr7	45526532	45526534	+	1	NA	promoter-TSS (NM_008654)	promoter-TSS (NM_008654)	203	NM_148927	69217	Mm.274158	NM_148927	ENSMUSG00000040428	Plekha4	2410005C22Rik|C88169|Pepp1	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 4	protein-coding
mm_129602.1	chr15	79892316	79892349	-	1	NA	promoter-TSS (NM_001160415)	promoter-TSS (NM_001160415)	-76	NM_001160415	80287	Mm.284059	NM_030255	ENSMUSG00000009585	Apobec3	Apobec|Arp3|BC003314|Cem15|Rfv3	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 3	protein-coding
mm_101111.1	chr11	11944907	11944921	-	1	NA	exon (NM_010345, exon 10 of 17)	exon (NM_010345, exon 10 of 17)	-46770	NM_001190448	13195	Mm.12906	NM_016672	ENSMUSG00000020182	Ddc	Aadc	dopa decarboxylase	protein-coding
mm_123516.1	chr14	66279615	66279626	-	1	NA	intron (NM_001162365, intron 1 of 30)	intron (NM_001162365, intron 1 of 30)	1432	NM_172498	19229	Mm.21613	NM_172498	ENSMUSG00000059456	Ptk2b	CADTK|CAKB|CAKbeta|E430023O05Rik|FADK2|FAK2|PYK2|Raftk	PTK2 protein tyrosine kinase 2 beta	protein-coding
mm_88581.1	chr10	79693863	79693869	+	1	NA	promoter-TSS (NM_001302499)	promoter-TSS (NM_001302499)	40	NM_001302499	16904	Mm.378960	NM_008504	ENSMUSG00000054206	Gzmm	Lmet1|MMET-1	granzyme M (lymphocyte met-ase 1)	protein-coding
mm_135242.1	chr16	36990510	36990540	-	1	NA	Intergenic	Intergenic	-11389	NM_001037321	207215	Mm.211899	NM_001037321	ENSMUSG00000047746	Fbxo40	9830003A13Rik|mKIAA1195	F-box protein 40	protein-coding
mm_115014.1	chr13	98354803	98354809	+	1	NA	exon (NM_008242, exon 1 of 1)	exon (NM_008242, exon 1 of 1)	561	NM_008242	15229	Mm.347441	NM_008242	ENSMUSG00000078302	Foxd1	AI385632|BF-2|FREAC4|Hfh10|Hfhbf2	forkhead box D1	protein-coding
mm_94631.1	chr11	16842411	16842421	+	1	NA	intron (NM_207655, intron 1 of 27)	intron (NM_207655, intron 1 of 27)	90213	NM_007912	13649	Mm.8534	NM_007912	ENSMUSG00000020122	Egfr	9030024J15Rik|AI552599|Erbb|Errb1|Errp|Wa5|wa-2|wa2	epidermal growth factor receptor	protein-coding
mm_10838.1	chr2	24934849	24934881	+	1	NA	intron (NR_027876, intron 1 of 6)	CpG	416	NR_027876	215705	Mm.45275	NM_178408	ENSMUSG00000026972	Arrdc1	AI957342|BC004091	arrestin domain containing 1	protein-coding
mm_125762.1	chr15	74044161	74044162	+	1	NA	Intergenic	Intergenic	-204490	NM_001033365	268816	Mm.440635	NM_001033365	ENSMUSG00000072487	Mroh5	Gm628	maestro heat-like repeat family member 5	protein-coding
mm_63744.1	chr7	130936258	130936268	+	1	NA	promoter-TSS (NM_019564)	promoter-TSS (NM_019564)	60	NM_019564	56213	Mm.30156	NM_019564	ENSMUSG00000006205	Htra1	AI429470|HTRA|L56|Prss11|RSPP11	HtrA serine peptidase 1	protein-coding
mm_118504.1	chr14	13932588	13932593	+	1	NA	Intergenic	RLTR1B|LTR|ERV1	28723	NM_001285780	66231	Mm.295875	NM_025435	ENSMUSG00000053453	Thoc7	Nif3l1bp1	THO complex 7	protein-coding
mm_152166.1	chr19	7297597	7297603	-	1	NA	intron (NM_007928, intron 1 of 17)	intron (NM_007928, intron 1 of 17)	-2153	NM_001080390	13728	Mm.258986	NM_007928	ENSMUSG00000024969	Mark2	EMK-1|Emk|Par-1|Par-1b	MAP/microtubule affinity regulating kinase 2	protein-coding
mm_167500.1	chr9	13296840	13296852	+	1	NA	Intergenic	Intergenic	49890	NM_025534	66396	Mm.290620	NM_025534	ENSMUSG00000079084	Ccdc82	2310043N13Rik	coiled-coil domain containing 82	protein-coding
mm_37055.1	chr4	116018154	116018176	-	1	NA	promoter-TSS (NM_010173)	promoter-TSS (NM_010173)	-263	NM_010173	14073	Mm.256025	NM_010173	ENSMUSG00000034171	Faah	AW412498	fatty acid amide hydrolase	protein-coding
mm_50338.1	chr6	48523447	48523455	+	1	NA	intron (NR_015597, intron 4 of 6)	intron (NR_015597, intron 4 of 6)	14023	NR_130985	69432		NR_130985	ENSMUSG00000097716	1700026J14Rik	-	RIKEN cDNA 1700026J14 gene	ncRNA
mm_118349.1	chr13	114932036	114932066	-	1	NA	promoter-TSS (NM_008396)	promoter-TSS (NM_008396)	-10	NM_008396	16398	Mm.5007	NM_008396	ENSMUSG00000015533	Itga2	CD49B|DX5	integrin alpha 2	protein-coding
mm_154973.1	chrX	37179599	37179607	+	1	NA	Intergenic	RMER19B|LTR|ERVK	-10761	NM_001033785	434756	Mm.471848	NM_001033785	ENSMUSG00000036551	Akap14	-	A kinase (PRKA) anchor protein 14	protein-coding
mm_121172.1	chr14	103025193	103025196	+	1	NA	intron (NR_045657, intron 2 of 2)	intron (NR_045657, intron 2 of 2)	8609	NR_045657	71264	Mm.399572	NR_045657		4933432I03Rik	-	RIKEN cDNA 4933432I03 gene	ncRNA
mm_114423.1	chr13	64432348	64432419	+	1	NA	promoter-TSS (NM_053180)	promoter-TSS (NM_053180)	-170	NM_053180	105278	Mm.74982	NM_053180	ENSMUSG00000021483	Cdk20	4932702G04Rik|AU019450|AW558027|CDCH|Ccrk|PNQLARE|p42	cyclin-dependent kinase 20	protein-coding
mm_71642.1	chr8	57512846	57512894	+	1	NA	intron (NM_008252, intron 2 of 4)	CpG-14025	1027	NM_008252	97165	Mm.276881	NM_008252	ENSMUSG00000054717	Hmgb2	C80539|HMG-2|Hmg2	high mobility group box 2	protein-coding
mm_15520.1	chr2	158328360	158328369	+	1	NA	exon (NM_008489, exon 14 of 15)	exon (NM_008489, exon 14 of 15)	21871	NM_008489	16803	Mm.218846	NM_008489	ENSMUSG00000016024	Lbp	Bpifd2|Ly88	lipopolysaccharide binding protein	protein-coding
mm_36346.1	chr4	73771144	73771146	-	1	NA	intron (NM_001017427, intron 3 of 17)	intron (NM_001017427, intron 3 of 17)	19457	NM_001017427	242505	Mm.389582	NM_001017427	ENSMUSG00000043003	Rasef	BC030882|RAB45	RAS and EF hand domain containing	protein-coding
mm_73286.1	chr8	104926216	104926227	+	1	NA	promoter-TSS (NM_001163756)	promoter-TSS (NM_001163756)	-39	NM_001163756	234673	Mm.441134	NM_172759	ENSMUSG00000031886	Ces2e	9030624L02Rik|Ces5	carboxylesterase 2E	protein-coding
mm_17490.1	chr2	28583240	28583274	-	1	NA	promoter-TSS (NM_001290484)	promoter-TSS (NM_001290484)	22	NM_148928	70239	Mm.274120	NM_148928	ENSMUSG00000026816	Gtf3c5	2700084A09Rik|TFIIIC63|TFiiiC2-63	general transcription factor IIIC, polypeptide 5	protein-coding
mm_158483.1	chrX	142196997	142197001	-	1	NA	promoter-TSS (NM_001007576)	promoter-TSS (NM_001007576)	-63	NM_001007576	245650	Mm.208511	NM_001007576	ENSMUSG00000042282	Gucy2f	A930002I06|GC-F|GC2	guanylate cyclase 2f	protein-coding
mm_7818.1	chr1	132007171	132007175	-	1	NA	promoter-TSS (NM_007923)	promoter-TSS (NM_007923)	-432	NM_007923	13714	Mm.254233	NM_007923	ENSMUSG00000026436	Elk4	2310011G17Rik|A130026I01Rik|BB162516|SAP-1|Sap1	ELK4, member of ETS oncogene family	protein-coding
mm_138760.1	chr17	37050864	37050869	+	1	NA	intron (NM_019439, intron 5 of 22)	CpG	4900	NM_019439	54393	Mm.32191	NM_019439	ENSMUSG00000024462	Gabbr1	GABAB1|GABAbR1|bM573K1.1	gamma-aminobutyric acid (GABA) B receptor, 1	protein-coding
mm_67214.1	chr7	74428163	74428167	-	1	NA	intron (NM_001038643, intron 2 of 10)	intron (NM_001038643, intron 2 of 10)	126615	NM_023908	108116	Mm.425467	NM_023908	ENSMUSG00000025790	Slco3a1	5830414C08Rik|Anr1|MJAM|OATP-D|R75096|Slc21a11	solute carrier organic anion transporter family, member 3a1	protein-coding
mm_76642.1	chr8	92855257	92855298	-	1	NA	promoter-TSS (NM_173014)	promoter-TSS (NM_173014)	-73	NM_173014	270084	Mm.21463	NM_173014	ENSMUSG00000033192	Lpcat2	A330042H22|Aytl1|Aytl1a|lpafat1	lysophosphatidylcholine acyltransferase 2	protein-coding
mm_94787.1	chr11	22287399	22287421	+	1	NA	promoter-TSS (NM_153078)	promoter-TSS (NM_153078)	-615	NM_001252515	216565	Mm.491265	NM_153078	ENSMUSG00000042302	Ehbp1	AF424697|Flj21950|NACSIN	EH domain binding protein 1	protein-coding
mm_45465.1	chr5	67847401	67847439	-	1	NA	promoter-TSS (NM_009727)	promoter-TSS (NM_009727)	11	NM_009727	11980	Mm.153230	NM_009727	ENSMUSG00000037685	Atp8a1	AI481521|AI853962|APLT|AW743152|AW822227|Atp3a2|B230107D19Rik|ClassI	ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1	protein-coding
mm_70005.1	chr7	142387920	142387935	-	1	NA	promoter-TSS (NM_009983)	promoter-TSS (NM_009983)	-57	NM_009983	13033	Mm.231395	NM_009983	ENSMUSG00000007891	Ctsd	CD|CatD	cathepsin D	protein-coding
mm_4047.1	chr1	165780756	165780771	+	1	NA	Intergenic	Intergenic	-7918	NM_031162	12503	Mm.217308	NM_031162	ENSMUSG00000005763	Cd247	4930549J05Rik|A430104F18Rik|AW552088|Cd3|Cd3-eta|Cd3-zeta|Cd3h|Cd3z|Cd3zeta|T3z|Tcrk|Tcrz	CD247 antigen	protein-coding
mm_574.1	chr1	38987785	38987805	+	1	NA	promoter-TSS (NM_026850)	promoter-TSS (NM_026850)	-19	NM_026850	68833	Mm.28121	NM_026850	ENSMUSG00000026078	Pdcl3	1110061A19Rik|C80025|Viaf1	phosducin-like 3	protein-coding
mm_47245.1	chr5	121567800	121567814	-	1	NA	3' UTR (NM_009656, exon 13 of 13)	3' UTR (NM_009656, exon 13 of 13)	-21915	NM_010765	17165	Mm.272206	NM_010765	ENSMUSG00000029454	Mapkapk5	MK5|PRAK	MAP kinase-activated protein kinase 5	protein-coding
mm_97658.1	chr11	79540646	79540654	+	1	NA	intron (NM_010897, intron 39 of 57)	intron (NM_010897, intron 39 of 57)	-10041	NM_010161	14017	Mm.439665	NM_010161	ENSMUSG00000078771	Evi2a	AW491894|Evi-2|Evi2	ecotropic viral integration site 2a	protein-coding
mm_170266.1	chr18	18947140	18947144	-	1	NA	Intergenic	RLTR9F|LTR|ERVK	1054955	NM_007882	13507	Mm.89935	NM_007882	ENSMUSG00000059898	Dsc3	5430426I24Rik	desmocollin 3	protein-coding
mm_16581.1	chr2	3517791	3517796	-	1	NA	intron (NM_177647, intron 1 of 3)	intron (NM_177647, intron 1 of 3)	4728	NM_177647	227526	Mm.211455	NM_177647	ENSMUSG00000039496	Cdnf	9330140G23|Armetl1	cerebral dopamine neurotrophic factor	protein-coding
mm_26595.1	chr3	151439244	151439260	+	1	NA	exon (NM_133222, exon 2 of 16)	exon (NM_133222, exon 2 of 16)	1370	NM_133222	170757	Mm.317261	NM_133222	ENSMUSG00000039167	Adgrl4	1110033N21Rik|ETL1|Eltd1|Etl	adhesion G protein-coupled receptor L4	protein-coding
mm_142905.1	chr17	52312166	52312181	-	1	NA	Intergenic	Intergenic	-290536	NM_001031811	211468	Mm.399068	NM_001031811	ENSMUSG00000035580	Kcnh8	C130090D05Rik|ELK|ELK1|ELK3|Kv12.1	potassium voltage-gated channel, subfamily H (eag-related), member 8	protein-coding
mm_32238.1	chr4	102255165	102255178	+	1	NA	5' UTR (NM_001177983, exon 1 of 6)	5' UTR (NM_001177983, exon 1 of 6)	232	NM_019840	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_46105.1	chr5	92347840	92347874	-	1	NA	exon (NM_021274, exon 3 of 4)	exon (NM_021274, exon 3 of 4)	1032	NM_021274	15945	Mm.877	NM_021274	ENSMUSG00000034855	Cxcl10	C7|CRG-2|INP10|IP-10|IP10|Ifi10|Scyb10|gIP-10|mob-1	chemokine (C-X-C motif) ligand 10	protein-coding
mm_21453.1	chr2	160769955	160769957	-	1	NA	TTS (NM_177263)	TTS (NM_177263)	38646	NM_021280	18803	Mm.44463	NM_021280	ENSMUSG00000016933	Plcg1	AI894140|Cded|Plc-1|Plc-gamma1|Plcg-1	phospholipase C, gamma 1	protein-coding
mm_132978.1	chr16	52074326	52074349	+	1	NA	intron (NM_001033238, intron 3 of 17)	intron (NM_001033238, intron 3 of 17)	42788	NM_001033238	208650	Mm.328206	NM_001033238	ENSMUSG00000022637	Cblb	AI429560|AI851073|Cbl-b	Casitas B-lineage lymphoma b	protein-coding
mm_66221.1	chr7	34655501	34655515	-	1	NA	Intergenic	CpG	-2667	NM_146188	233107	Mm.486198	NM_146188	ENSMUSG00000030499	Kctd15	BC031749	potassium channel tetramerisation domain containing 15	protein-coding
mm_2384.1	chr1	93479088	93479098	+	1	NA	promoter-TSS (NM_010891)	promoter-TSS (NM_010891)	32	NM_001159719	18000	Mm.428652	NM_010891	ENSMUSG00000026276	Sept2	AW208991|Nedd-5|Nedd5|mKIAA0158	septin 2	protein-coding
mm_33068.1	chr4	123283799	123283810	+	1	NA	exon (NM_130881, exon 1 of 15)	exon (NM_130881, exon 1 of 15)	519	NM_148917	230721	Mm.277091	NM_130881	ENSMUSG00000011257	Pabpc4	-	poly(A) binding protein, cytoplasmic 4	protein-coding
mm_15567.1	chr2	158611072	158611074	+	1	NA	promoter-TSS (NR_040359)	promoter-TSS (NR_040359)	315	NM_009508	22348	Mm.143404	NM_009508	ENSMUSG00000037771	Slc32a1	R75019|VGAT|Viaat	solute carrier family 32 (GABA vesicular transporter), member 1	protein-coding
mm_77101.1	chr8	111027753	111027791	-	1	NA	promoter-TSS (NM_001190800)	promoter-TSS (NM_001190800)	-2	NM_001190800	234733	Mm.482176	NM_172284	ENSMUSG00000033658	Ddx19b	2810457M08Rik|4921519L13Rik|AW260119	DEAD (Asp-Glu-Ala-Asp) box polypeptide 19b	protein-coding
mm_143385.1	chr17	67993087	67993095	-	1	NA	intron (NM_172964, intron 1 of 17)	RCHARR1|DNA|hAT-Charlie	11017	NM_172964	268970	Mm.9935	NM_172964	ENSMUSG00000024043	Arhgap28	AU044757|AW550892|E130310N06	Rho GTPase activating protein 28	protein-coding
mm_157079.1	chrX	9435610	9435648	-	1	NA	3' UTR (NM_007807, exon 13 of 13)	3' UTR (NM_007807, exon 13 of 13)	33695	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_157016.1	chrX	7681216	7681229	-	1	NA	promoter-TSS (NR_037581)	promoter-TSS (NR_037581)	29	NR_037581	54634	Mm.67912	NM_018832	ENSMUSG00000031147	Magix	Pdzx|Sfc18	MAGI family member, X-linked	protein-coding
mm_140492.1	chr17	3314178	3314221	-	1	NA	Intergenic	CpG	-12374	NM_001122998	24001	Mm.137134	NM_011878	ENSMUSG00000023800	Tiam2	3000002F19Rik|STEF|mKIAA2016	T cell lymphoma invasion and metastasis 2	protein-coding
mm_130708.1	chr15	100720234	100720246	-	1	NA	intron (NM_172451, intron 1 of 11)	intron (NM_172451, intron 1 of 11)	237	NM_001161768	207839	Mm.22969	NM_172451	ENSMUSG00000037280	Galnt6	4632410F13|AW047994|GalNAc-T6	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 6	protein-coding
mm_170219.1	chr17	77829058	77829058	+	1	NA	Intergenic	Intergenic	-371190	NM_015800	50766	Mm.311912	NM_015800	ENSMUSG00000024074	Crim1	AU015004	cysteine rich transmembrane BMP regulator 1 (chordin like)	protein-coding
mm_69170.1	chr7	127215086	127215103	-	1	NA	TTS (NM_016754)	TTS (NM_016754)	3351	NM_017461	54204	Mm.18	NM_017461	ENSMUSG00000000486	Sept1	Diff6|Pnutl3	septin 1	protein-coding
mm_101766.1	chr11	43835979	43836005	-	1	NA	exon (NM_001284381, exon 4 of 5)	exon (NM_001284381, exon 4 of 5)	497	NM_007416	11548	Mm.39086	NM_007416	ENSMUSG00000050541	Adra1b	[a]1b	adrenergic receptor, alpha 1b	protein-coding
mm_82902.1	chr9	32747600	32747612	-	1	NA	intron (NM_011808, intron 6 of 7)	intron (NM_011808, intron 6 of 7)	51564	NM_001038642	23871	Mm.292415	NM_011808	ENSMUSG00000032035	Ets1	AI196000|AI448617|D230050P06|Ets-1|Tpl1|vs	E26 avian leukemia oncogene 1, 5' domain	protein-coding
mm_37804.1	chr4	130812447	130812478	-	1	NA	intron (NM_011520, intron 1 of 4)	intron (NM_011520, intron 1 of 4)	19925	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_48307.1	chr5	138619665	138619683	-	1	NA	promoter-TSS (NM_001163797)	promoter-TSS (NM_001163797)	69	NM_001163797	24135	Mm.27575	NM_013844	ENSMUSG00000058291	Zfp68	KRAB3|KRAZ2|Zfp70|mszf22|mszf49	zinc finger protein 68	protein-coding
mm_139149.1	chr17	47538437	47538448	+	1	NA	intron (NM_001081635, intron 1 of 6)	B4A|SINE|B4	33391	NM_001081635	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_163310.1	chr12	4769101	4769107	+	1	NA	promoter-TSS (NM_028376)	promoter-TSS (NM_028376)	163	NM_175431	207921	Mm.184898	NM_175431	ENSMUSG00000050545	Fam228b	A830093I24Rik	family with sequence similarity 228, member B	protein-coding
mm_111763.1	chr12	104002727	104002734	-	1	NA	intron (NM_027997, intron 2 of 4)	L1M4|LINE|L1	10922	NM_027997	71907	Mm.326723	NM_027997	ENSMUSG00000058260	Serpina9	2310014L03Rik|AW049635|Centerin	serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9	protein-coding
mm_135337.1	chr16	42292139	42292153	-	1	NA	exon (NM_008083, exon 2 of 3)	exon (NM_008083, exon 2 of 3)	11323	NR_105858	102466172		NR_105858	ENSMUSG00000098300	Mir6540	Gm27780|mir-6540|mmu-mir-6540	microRNA 6540	ncRNA
mm_129916.1	chr15	84185153	84185156	-	1	NA	intron (NM_054088, intron 7 of 7)	intron (NM_054088, intron 7 of 7)	-7079	NM_178614	68653	Mm.290725	NM_178614	ENSMUSG00000022437	Samm50	1110030L07Rik	SAMM50 sorting and assembly machinery component	protein-coding
mm_2590.1	chr1	119290103	119290110	+	1	NA	Intergenic	Intergenic	132142	NM_008381	16324	Mm.3092	NM_008381	ENSMUSG00000037035	Inhbb	-	inhibin beta-B	protein-coding
mm_73653.1	chr8	110940981	110940981	+	1	NA	intron (NM_009179, intron 1 of 6)	intron (NM_009179, intron 1 of 6)	21116	NM_009179	20444	Mm.200388	NM_009179	ENSMUSG00000031749	St3gal2	AI429591|AW822065|ST3GalII|Siat5	ST3 beta-galactoside alpha-2,3-sialyltransferase 2	protein-coding
mm_5229.1	chr1	14309985	14310006	-	1	NA	5' UTR (NM_001252192, exon 1 of 17)	5' UTR (NM_001252192, exon 1 of 17)	204	NM_001310459	14048	Mm.250185	NM_010164	ENSMUSG00000025932	Eya1	bor	EYA transcriptional coactivator and phosphatase 1	protein-coding
mm_76328.1	chr8	84706050	84706060	-	1	NA	3' UTR (NM_010906, exon 9 of 9)	3' UTR (NM_010906, exon 9 of 9)	4598	NM_008535	17095	Mm.4925	NM_008535	ENSMUSG00000034041	Lyl1	Lyl-1|bHLHa18	lymphoblastomic leukemia 1	protein-coding
mm_60205.1	chr7	43436967	43436981	+	1	NA	promoter-TSS (NM_024253)	promoter-TSS (NM_024253)	-164	NM_024253	72310	Mm.34613	NM_024253	ENSMUSG00000004612	Nkg7	2500004F03Rik	natural killer cell group 7 sequence	protein-coding
mm_34421.1	chr4	145274216	145274230	+	1	NA	intron (NM_009401, intron 12 of 12)	intron (NM_009401, intron 12 of 12)	-27353	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_28957.1	chr3	100489330	100489354	-	1	NA	promoter-TSS (NM_001142952)	promoter-TSS (NM_001142952)	-150	NM_001142952	74645	Mm.226900	NM_001142952	ENSMUSG00000044468	Fam46c	4930431B09Rik|AI449797	family with sequence similarity 46, member C	protein-coding
mm_12118.1	chr2	61604451	61604469	+	1	NA	intron (NM_001164071, intron 2 of 8)	intron (NM_001164071, intron 2 of 8)	11363	NM_001164071	21353	Mm.244393	NM_011529	ENSMUSG00000064289	Tank	C86182|E430026L09Rik|I-TRAF	TRAF family member-associated Nf-kappa B activator	protein-coding
mm_152161.1	chr19	7275860	7275889	-	1	NA	TTS (NM_054048)	TTS (NM_054048)	7595	NM_001320554	104383	Mm.283859	NM_054048	ENSMUSG00000024968	Rcor2	1A13|AW122124|CoREST|Rcor|Rcor1	REST corepressor 2	protein-coding
mm_123709.1	chr14	69805564	69805578	-	1	NA	promoter-TSS (NM_153514)	promoter-TSS (NM_153514)	-26	NM_153514	246710	Mm.102367	NM_153514	ENSMUSG00000022075	Rhobtb2	Dbc2|E130206H14Rik|mKIAA0717	Rho-related BTB domain containing 2	protein-coding
mm_18334.1	chr2	57297634	57297646	-	1	NA	intron (NM_001145820, intron 3 of 16)	intron (NM_001145820, intron 3 of 16)	59258	NM_010274	14571	Mm.3711	NM_010274	ENSMUSG00000026827	Gpd2	AA408484|AI448216|AU021455|AW494132|GPDH|Gdm1|Gpd-m|Gpdh-m|TISP38	glycerol phosphate dehydrogenase 2, mitochondrial	protein-coding
mm_153897.1	chr19	47050327	47050374	-	1	NA	intron (NR_133574, intron 1 of 9)	CpG	556	NM_027654	71041	Mm.35413	NM_027654	ENSMUSG00000025050	Pcgf6	4933407A11Rik|AI604840|MBLR|Rnf134	polycomb group ring finger 6	protein-coding
mm_11685.1	chr2	35622000	35622004	+	1	NA	promoter-TSS (NM_001114124)	promoter-TSS (NM_001114124)	21	NM_001114124	69601	Mm.29629	NM_001001602	ENSMUSG00000026883	Dab2ip	2310011D08Rik|AI480459|Aip1|mKIAA1743	disabled 2 interacting protein	protein-coding
mm_16056.1	chr2	167777476	167777513	+	1	NA	Intergenic	CpG	86317	NR_015500	329562	Mm.123101	NM_177851	ENSMUSG00000006462	A530013C23Rik	-	RIKEN cDNA A530013C23 gene	ncRNA
mm_154927.1	chrX	24008707	24008717	+	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	115949	NM_001034864	236749	Mm.296422	NM_001034864	ENSMUSG00000068113	Gm4907	EG236749	predicted gene 4907	protein-coding
mm_107074.1	chr12	16942834	16942887	+	1	NA	exon (NM_009072, exon 5 of 33)	exon (NM_009072, exon 5 of 33)	47882	NM_009072	19878	Mm.276024	NM_009072	ENSMUSG00000020580	Rock2	B230113H15Rik|ROKalpha|Rho-kinase|Rock-II|Rock2m|mKIAA0619	Rho-associated coiled-coil containing protein kinase 2	protein-coding
mm_63884.1	chr7	137437572	137437580	+	1	NA	promoter-TSS (NM_023140)	promoter-TSS (NM_023140)	-72	NM_023140	30926	Mm.267692	NM_023140	ENSMUSG00000031068	Glrx3	PICOT|Txnl2	glutaredoxin 3	protein-coding
mm_143855.1	chr17	84183562	84183592	-	1	NA	TTS (NM_001001806)	TTS (NM_001001806)	4370	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_167900.1	chrX	73863034	73863037	-	1	NA	intron (NM_008478, intron 8 of 28)	intron (NM_008478, intron 8 of 28)	17799	NM_008478	16728	Mm.260568	NM_008478	ENSMUSG00000031391	L1cam	CD171|L1|N-CAM-L1|NCAM-L1	L1 cell adhesion molecule	protein-coding
mm_76485.1	chr8	85700886	85700900	-	1	NA	promoter-TSS (NR_106189)	promoter-TSS (NR_106189)	-12	NR_106189	102465898		NR_106189	ENSMUSG00000098388	Mir8109	Gm27495|mmu-mir-8109	microRNA 8109	ncRNA
mm_125597.1	chr15	59648695	59648705	+	1	NA	promoter-TSS (NM_144549)	promoter-TSS (NM_144549)	46	NM_144549	211770	Mm.40298	NM_144549	ENSMUSG00000032501	Trib1	A530090O15Rik|TRB-1|Trb1	tribbles pseudokinase 1	protein-coding
mm_146403.1	chr18	82972772	82972793	+	1	NA	intron (NM_183033, intron 2 of 5)	intron (NM_183033, intron 2 of 5)	-52222	NR_033307	75853	Mm.420737	NR_033307		4930592I03Rik	-	RIKEN cDNA 4930592I03 gene	ncRNA
mm_62693.1	chr7	110122034	110122135	+	1	NA	promoter-TSS (NM_009516)	promoter-TSS (NM_009516)	25	NM_009516	22390	Mm.287173	NM_009516	ENSMUSG00000031016	Wee1	Wee1A	WEE 1 homolog 1 (S. pombe)	protein-coding
mm_52875.1	chr6	122345975	122345984	+	1	NA	Intergenic	Intergenic	-5752	NM_001271579	13619	Mm.6822	NM_007905	ENSMUSG00000040669	Phc1	AW557034|Edr|Edr1|Mph1|Rae-28|rae28	polyhomeotic-like 1 (Drosophila)	protein-coding
mm_79985.1	chr9	66974990	66975003	+	1	NA	intron (NM_030717, intron 1 of 5)	CpG	488	NM_030717	80907	Mm.157882	NM_030717	ENSMUSG00000032370	Lactb	LACT-1|Lact1|Mrpl56	lactamase, beta	protein-coding
mm_94543.1	chr11	9191935	9191948	+	1	NA	promoter-TSS (NM_178259)	promoter-TSS (NM_178259)	-1	NM_178259	268379	Mm.39270	NM_178259	ENSMUSG00000004668	Abca13	9830132L24|A930002G16Rik|AI956815	ATP-binding cassette, sub-family A (ABC1), member 13	protein-coding
mm_163572.1	chr13	30760985	30760986	+	1	NA	intron (NM_001347508, intron 7 of 8)	intron (NM_001347508, intron 7 of 8)	11752	NM_013674	16364	Mm.4677	NM_013674	ENSMUSG00000021356	Irf4	AI385587|IRF-4|LSIRF|NF-EM5|Spip	interferon regulatory factor 4	protein-coding
mm_12218.1	chr2	67628723	67628746	+	1	NA	Intergenic	Intergenic	-46723	NR_106083	102465706		NR_106083	ENSMUSG00000098299	Mir7224	Gm27971|mmu-mir-7224	microRNA 7224	ncRNA
mm_136657.1	chr17	5996839	5996864	+	1	NA	intron (NM_001113352, intron 4 of 25)	intron (NM_001113352, intron 4 of 25)	-10729	NM_001290698	20975	Mm.236068	NM_011523	ENSMUSG00000023805	Synj2	AI481647|SJ2|mKIAA0348	synaptojanin 2	protein-coding
mm_135067.1	chr16	34204832	34204833	-	1	NA	intron (NM_001164268, intron 22 of 33)	intron (NM_001164268, intron 22 of 33)	-237829	NM_009471	22247	Mm.13145	NM_009471	ENSMUSG00000022814	Umps	1700095D23Rik|AA408257|AL033308|BB164745	uridine monophosphate synthetase	protein-coding
mm_101370.1	chr11	23770737	23770748	-	1	NA	5' UTR (NM_009044, exon 1 of 10)	5' UTR (NM_009044, exon 1 of 10)	228	NM_009044	19696	Mm.4869	NM_009044	ENSMUSG00000020275	Rel	c-Rel	reticuloendotheliosis oncogene	protein-coding
mm_35834.1	chr4	48042527	48042532	-	1	NA	Intergenic	Intergenic	-2776	NM_015743	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_62732.1	chr7	110808804	110808821	+	1	NA	intron (NM_001276301, intron 13 of 14)	PB1D7|SINE|Alu	35569	NM_025999	67150	Mm.96867	NM_025999	ENSMUSG00000030788	Rnf141	2610110L04Rik|AA792898|AU022812|ZFP36|ZNF230	ring finger protein 141	protein-coding
mm_88082.1	chr10	68043844	68043849	+	1	NA	TTS (NM_001081346)	TTS (NM_001081346)	64248	NM_001081346	170799	Mm.209844	NM_133244	ENSMUSG00000037846	Rtkn2	B130039D23Rik|Mbf|Plekhk1	rhotekin 2	protein-coding
mm_140956.1	chr17	24614514	24614528	-	1	NA	intron (NM_001286718, intron 18 of 39)	intron (NM_001286718, intron 18 of 39)	18106	NM_011647	22084	Mm.30435	NM_011647	ENSMUSG00000002496	Tsc2	Nafld|Tcs2	tuberous sclerosis 2	protein-coding
mm_17610.1	chr2	30921907	30921920	-	1	NA	Intergenic	Intergenic	-18616	NM_022415	64292	Mm.28768	NM_022415	ENSMUSG00000050737	Ptges	2410099E23Rik|D2Ertd369e|Pges|mPGES|mPGES-1	prostaglandin E synthase	protein-coding
mm_33234.1	chr4	127021295	127021299	+	1	NA	promoter-TSS (NM_023603)	promoter-TSS (NM_023603)	-4	NR_045010	71514	Mm.257276	NM_023603	ENSMUSG00000028820	Sfpq	1110004P21Rik|2810416M14Rik|5730453G22Rik|9030402K04Rik|AU021830|D4Ertd314e|Gm12940|OTTMUSG00000009329|PSF|REP1	splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)	protein-coding
mm_88697.1	chr10	80142359	80142404	+	1	NA	promoter-TSS (NM_025313)	promoter-TSS (NM_025313)	66	NM_025313	66043	Mm.278560	NM_025313	ENSMUSG00000003072	Atp5d	0610008F14Rik|1500000I11Rik|AA960090|AI876556|AU020773|C85518	ATP synthase, H+ transporting, mitochondrial F1 complex, delta subunit	protein-coding
mm_101979.1	chr11	50408008	50408022	-	1	NA	intron (NM_172557, intron 8 of 17)	intron (NM_172557, intron 8 of 17)	23096	NM_172557	216724	Mm.390400	NM_172557	ENSMUSG00000020375	Rufy1	3000002E04Rik|Rabip4|ZFYVE12	RUN and FYVE domain containing 1	protein-coding
mm_53052.1	chr6	124808659	124808704	+	1	NA	promoter-TSS (NM_001306053)	promoter-TSS (NM_001306053)	20	NM_001306050	14794	Mm.261906	NM_013539	ENSMUSG00000038451	Spsb2	AI461677|C9|Grcc9|SSB2	splA/ryanodine receptor domain and SOCS box containing 2	protein-coding
mm_1757.1	chr1	75521758	75521801	+	1	NA	5' UTR (NM_027886, exon 2 of 25)	5' UTR (NM_027886, exon 2 of 25)	250	NM_027886	71728	Mm.312650	NM_027886	ENSMUSG00000026213	Stk11ip	1200014D22Rik|BB131189|LIP1|LKB1IP	serine/threonine kinase 11 interacting protein	protein-coding
mm_92727.1	chr10	80826989	80827018	-	1	NA	intron (NM_001301034, intron 1 of 4)	CpG	307	NR_027656	100041965	Mm.328806	NR_027656		Oaz1-ps	ENSMUSG00000043801|Gm1823|Gm9786|Oaz-ps	ornithine decarboxylase antizyme 1, pseudogene	pseudo
mm_26021.1	chr3	135438527	135438540	+	1	NA	promoter-TSS (NM_025356)	promoter-TSS (NM_025356)	132	NR_030689	319587	Mm.358971	NR_030689	ENSMUSG00000097032	4930539J05Rik	8030475D13Rik	RIKEN cDNA 4930539J05 gene	ncRNA
mm_173007.1	chrM	227	235	+	1	NA	NA	Intergenic	NA	NA								
mm_145621.1	chr18	61108862	61108872	+	1	NA	intron (NM_001037859, intron 2 of 21)	intron (NM_001037859, intron 2 of 21)	3295	NM_001037859	12978	Mm.22574	NM_007779	ENSMUSG00000024621	Csf1r	AI323359|CD115|CSF-1R|Csfmr|Fim-2|Fim2|Fms|M-CSF-R|M-CSFR	colony stimulating factor 1 receptor	protein-coding
mm_66302.1	chr7	38227976	38228000	-	1	NA	promoter-TSS (NM_024413)	promoter-TSS (NM_024413)	6	NM_024413	72287	Mm.333798	NM_024413	ENSMUSG00000074170	Plekhf1	1810013P09Rik|APPD|LAPF|PHAFIN1|ZFYVE15	pleckstrin homology domain containing, family F (with FYVE domain) member 1	protein-coding
mm_164949.1	chr19	4601666	4601681	+	1	NA	exon (NM_001162946, exon 3 of 21)	exon (NM_001162946, exon 3 of 21)	7354	NM_008797	18563	Mm.1845	NM_008797	ENSMUSG00000024892	Pcx	Pc|Pcb	pyruvate carboxylase	protein-coding
mm_76919.1	chr8	105933229	105933259	-	1	NA	exon (NM_023182, exon 2 of 7)	exon (NM_023182, exon 2 of 7)	618	NM_023182	109660	Mm.2745	NM_023182	ENSMUSG00000031896	Ctrl	0910001G08Rik|1810004D15Rik|AV005227|Ctra-1|Ctra1|chymopasin|mFLJ00366	chymotrypsin-like	protein-coding
mm_49205.1	chr6	15720655	15720747	+	1	NA	promoter-TSS (NM_175088)	promoter-TSS (NM_175088)	40	NM_175088	16543	Mm.1314	NM_175088	ENSMUSG00000041390	Mdfic	Kdt1|Mdfid	MyoD family inhibitor domain containing	protein-coding
mm_70198.1	chr7	144553658	144553757	-	1	NA	promoter-TSS (NM_001195086)	promoter-TSS (NM_001195086)	22	NM_001033319	233977	Mm.490347	NM_001033319	ENSMUSG00000037519	Ppfia1	C030014K08Rik|C87158|LIP.1|LIP1	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1	protein-coding
mm_165089.1	chr19	49144735	49144738	-	1	NA	Intergenic	L3|LINE|CR1	938711	NM_025696	66673	Mm.70980	NM_025696	ENSMUSG00000063434	Sorcs3	6330404A12Rik|AW045579	sortilin-related VPS10 domain containing receptor 3	protein-coding
mm_104528.1	chr11	96124459	96124478	-	1	NA	Intergenic	CpG	-9318	NM_172799	237930	Mm.249912	NM_172799	ENSMUSG00000038756	Ttll6	4932418K24Rik|D11Moh43e|D11Moh44e|t8130b59	tubulin tyrosine ligase-like family, member 6	protein-coding
mm_164205.1	chr15	81969320	81969365	-	1	NA	Intergenic	ERVB7_2-LTR_MM|LTR|ERVK	-8412	NM_001282041	29858	Mm.18939	NM_013872	ENSMUSG00000022474	Pmm1	C77612	phosphomannomutase 1	protein-coding
mm_135104.1	chr16	35490874	35490891	-	1	NA	promoter-TSS (NM_028295)	promoter-TSS (NM_028295)	-9	NM_028295	72599	Mm.71015	NM_028295	ENSMUSG00000022844	Pdia5	2700053F16Rik|AU015525|Pdir	protein disulfide isomerase associated 5	protein-coding
mm_9914.1	chr1	189007857	189007869	-	1	NA	promoter-TSS (NM_172650)	promoter-TSS (NM_172650)	-23	NM_172650	226823	Mm.209880	NM_172650	ENSMUSG00000026608	Kctd3	4930438A20Rik|9330185B06|E330032J19Rik|NY-REN-45	potassium channel tetramerisation domain containing 3	protein-coding
mm_72038.1	chr8	70808432	70808474	+	1	NA	promoter-TSS (NM_008353)	promoter-TSS (NM_008353)	4	NM_008353	16161	Mm.731	NM_008353	ENSMUSG00000000791	Il12rb1	CD212|IL-12R[b]	interleukin 12 receptor, beta 1	protein-coding
mm_54585.1	chr6	38128078	38128080	-	1	NA	3' UTR (NM_194061, exon 20 of 20)	3' UTR (NM_194061, exon 20 of 20)	-3493	NM_080467	140494	Mm.462308	NM_080467	ENSMUSG00000038600	Atp6v0a4	Atp6n1b|a4	ATPase, H+ transporting, lysosomal V0 subunit A4	protein-coding
mm_108782.1	chr12	90169036	90169040	+	1	NA	exon (NM_001198587, exon 16 of 20)	exon (NM_001198587, exon 16 of 20)	356555	NM_001252074	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding
mm_140624.1	chr17	12318673	12318684	-	1	NA	promoter-TSS (NR_045290)	promoter-TSS (NR_045290)	-18	NM_011948	26407	Mm.28587	NM_011948	ENSMUSG00000014426	Map3k4	D17Rp17|D17Rp17e|MAPKKK4|MEKK 4|MTK1|Mek4b|Mekk4|RP17|Rp17a|Tas|mKIAA0213	mitogen-activated protein kinase kinase kinase 4	protein-coding
mm_148276.1	chr18	81927670	81927672	-	1	NA	Intergenic	Intergenic	64409	NR_039589	100628596		NR_039589	ENSMUSG00000093036	Mir5127	mmu-mir-5127|mu-mir-5127	microRNA 5127	ncRNA
mm_55359.1	chr6	56923805	56923815	-	1	NA	5' UTR (NM_026004, exon 1 of 9)	5' UTR (NM_026004, exon 1 of 9)	122	NM_026004	107569	Mm.158936	NM_026004	ENSMUSG00000029780	Nt5c3	1600024P05Rik|2610206B05Rik|3110004A18Rik|AI842776|Nt5c3a|Nt5y|PN-1|PN-I|PSN1|UMPH|Umph-1|Umph1|cN-III|lupin|p36	5'-nucleotidase, cytosolic III	protein-coding
mm_166243.1	chr5	74647681	74647731	+	1	NA	intron (NM_001159577, intron 2 of 10)	intron (NM_001159577, intron 2 of 10)	30166	NM_001159580	16924	Mm.440403	NM_010727	ENSMUSG00000029228	Lnx1	Lnx	ligand of numb-protein X 1	protein-coding
mm_1964.1	chr1	86487747	86487770	+	1	NA	Intergenic	CpG	-38978	NM_008972	19231	Mm.19187	NM_008972	ENSMUSG00000026238	Ptma	Thym	prothymosin alpha	protein-coding
mm_124440.1	chr14	118706424	118706435	-	1	NA	promoter-TSS (NM_001163676)	promoter-TSS (NM_001163676)	-210	NM_001033336	239273	Mm.40537	NM_001033336	ENSMUSG00000032849	Abcc4	ABCC4-N1|D630049P08Rik|MOATB|MRP4	ATP-binding cassette, sub-family C (CFTR/MRP), member 4	protein-coding
mm_60554.1	chr7	44481125	44481145	+	1	NA	Intergenic	Intergenic	-3382	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_134033.1	chr16	5013506	5013558	-	1	NA	promoter-TSS (NM_133185)	promoter-TSS (NM_133185)	21	NM_133185	66049	Mm.27792	NM_133185	ENSMUSG00000022540	Rogdi	0610011C19Rik|AU020118|C76152|Lzf	rogdi homolog	protein-coding
mm_147420.1	chr18	46198811	46198824	-	1	NA	promoter-TSS (NM_001170855)	promoter-TSS (NM_001170855)	1	NM_001170855	28105	Mm.277382	NM_178872	ENSMUSG00000033949	Trim36	D18Wsu100e|haprin	tripartite motif-containing 36	protein-coding
mm_92461.1	chr10	77924182	77924204	-	1	NA	intron (NM_138301, intron 22 of 33)	intron (NM_138301, intron 22 of 33)	-21657	NM_145152	237387	Mm.133301	NM_145152	ENSMUSG00000051652	Lrrc3	1300011L04Rik|C21orf102	leucine rich repeat containing 3	protein-coding
mm_58325.1	chr6	146502142	146502230	-	1	NA	promoter-TSS (NM_019923)	promoter-TSS (NM_019923)	37	NM_010586	16439	Mm.7800	NM_010586	ENSMUSG00000030287	Itpr2	AI649341|InsP3R-2|InsP3R-5|Ip3r2|Itpr5|insP3R2	inositol 1,4,5-triphosphate receptor 2	protein-coding
mm_55367.1	chr6	57541089	57541092	-	1	NA	Intergenic	RMER2|LTR|ERV1	-5664	NM_175523	243382	Mm.396893	NM_175523	ENSMUSG00000037826	Ppm1k	2900063A19Rik|A930026L03Rik|PP2Cm	protein phosphatase 1K (PP2C domain containing)	protein-coding
mm_122649.1	chr14	51908622	51908648	-	1	NA	exon (NM_001145959, exon 7 of 15)	exon (NM_001145959, exon 7 of 15)	4853	NM_001145959	29811	Mm.26722	NM_013864	ENSMUSG00000004558	Ndrg2	AI182517|AU040374|Ndr2|SYLD	N-myc downstream regulated gene 2	protein-coding
mm_135923.1	chr16	69861791	69861799	-	1	NA	intron (NM_173069, intron 1 of 5)	intron (NM_173069, intron 1 of 5)	1949	NM_173069	224318	Mm.212743	NM_173069	ENSMUSG00000063163	Speer2	SPEER-2	spermatogenesis associated glutamate (E)-rich protein 2	protein-coding
mm_26253.1	chr3	142496773	142496789	+	1	NA	promoter-TSS (NM_153564)	promoter-TSS (NM_153564)	-153	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_196.1	chr1	15805640	15805675	+	1	NA	promoter-TSS (NM_001286628)	promoter-TSS (NM_001286628)	11	NM_001286628	21749	Mm.4306	NM_009352	ENSMUSG00000025925	Terf1	Pin2|Trbf1|Trf1	telomeric repeat binding factor 1	protein-coding
mm_11970.1	chr2	54436375	54436422	+	1	NA	promoter-TSS (NM_173030)	promoter-TSS (NM_173030)	11	NM_173030	271786	Mm.330227	NM_173030	ENSMUSG00000060988	Galnt13	A230002A12|A230020F20|BB182356	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13	protein-coding
mm_67743.1	chr7	90442625	90442650	-	1	NA	promoter-TSS (NR_073438)	promoter-TSS (NR_073438)	-144	NR_073436	233490	Mm.29496	NM_145151	ENSMUSG00000051451	Crebzf	1110034C16Rik|6330417B10Rik|LAZip|LAZipII|SMILE|Zf	CREB/ATF bZIP transcription factor	protein-coding
mm_151630.1	chr19	3914686	3914718	-	1	NA	intron (NM_026316, intron 9 of 9)	intron (NM_026316, intron 9 of 9)	-1928	NM_001271444	225887	Mm.44227	NM_144870	ENSMUSG00000059734	Ndufs8	BC021616|CI-23kD|TYKY	NADH dehydrogenase (ubiquinone) Fe-S protein 8	protein-coding
mm_109400.1	chr12	109948891	109948901	+	1	NA	Intergenic	Intergenic	201018	NR_037233	100499517		NR_037233	ENSMUSG00000093351	Mir3072	mir-3072|mmu-mir-3072	microRNA 3072	ncRNA
mm_135013.1	chr16	32487153	32487161	-	1	NA	intron (NM_145932, intron 1 of 8)	intron (NM_145932, intron 1 of 8)	722	NM_145932	106407	Mm.476915	NM_145932	ENSMUSG00000035699	Slc51a	AV001382|AW261577|D630035O19Rik|OSTalpha|Osta	solute carrier family 51, alpha subunit	protein-coding
mm_58160.1	chr6	142472961	142472985	-	1	NA	5' UTR (NM_145572, exon 1 of 17)	5' UTR (NM_145572, exon 1 of 17)	136	NM_145572	232493	Mm.275975	NM_145572	ENSMUSG00000030244	Gys2	BC021322|LGS	glycogen synthase 2	protein-coding
mm_117762.1	chr13	96132569	96132628	-	1	NA	promoter-TSS (NM_029210)	promoter-TSS (NM_029210)	-21	NM_029210	75209	Mm.40436	NM_029210	ENSMUSG00000051111	Sv2c	4930527L09Rik|AI841971	synaptic vesicle glycoprotein 2c	protein-coding
mm_58813.1	chr7	16400258	16400301	+	1	NA	promoter-TSS (NM_198631)	promoter-TSS (NM_198631)	-917	NM_198631	330474	Mm.333594	NM_198631	ENSMUSG00000059273	Zc3h4	Bwq1|Gm768|Kiaa1064-hp|mKIAA1064	zinc finger CCCH-type containing 4	protein-coding
mm_58110.1	chr6	138422531	138422543	-	1	NA	promoter-TSS (NR_126073)	promoter-TSS (NR_126073)	-568	NR_126073	319702	Mm.403785	NR_126072	ENSMUSG00000089957	A830011K09Rik	-	RIKEN cDNA A830011K09 gene	ncRNA
mm_172678.1	chr8	51347415	51347415	+	1	NA	Intergenic	L1Md_T|LINE|L1	979303	NR_046067	100039954	Mm.400419	NR_046067	ENSMUSG00000110281	Gm2516	-	predicted gene 2516	ncRNA
mm_130146.1	chr15	90980991	90981002	-	1	NA	exon (NM_001109041, exon 11 of 36)	exon (NM_001109041, exon 11 of 36)	68955	NM_001109041	16564	Mm.41379	NM_016705	ENSMUSG00000022629	Kif21a	-	kinesin family member 21A	protein-coding
mm_170718.1	chr2	14739148	14739148	+	1	NA	intron (NM_023116, intron 2 of 13)	intron (NM_023116, intron 2 of 13)	18506	NR_028497	625342	Mm.484784	NR_028497		Gm13315	OTTMUSG00000011384	lactate dehydrogenase A pseudogene	pseudo
mm_167613.1	chr9	56146120	56146120	+	1	NA	intron (NM_019793, intron 4 of 6)	MER3|DNA|hAT-Charlie	14950	NM_019793	56434	Mm.28484	NM_019793	ENSMUSG00000032324	Tspan3	1700055K04Rik|TM4-A|Tm4sf8	tetraspanin 3	protein-coding
mm_87135.1	chr10	34297433	34297513	+	1	NA	promoter-TSS (NM_030203)	promoter-TSS (NM_030203)	52	NM_030203	72480	Mm.21485	NM_030203	ENSMUSG00000039485	Tspyl4	2610102M01Rik|B230210I21Rik|D10Bwg0791e	TSPY-like 4	protein-coding
mm_43160.1	chr5	127027382	127027388	+	1	NA	Intergenic	Intergenic	-3404	NR_040685	71247	Mm.399586	NR_040685	ENSMUSG00000105490	4933438B17Rik	-	RIKEN cDNA 4933438B17 gene	ncRNA
mm_145827.1	chr18	65438187	65438208	+	1	NA	intron (NM_172833, intron 2 of 15)	B1_Mus2|SINE|Alu	7200	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_131254.1	chr16	10716165	10716169	+	1	NA	intron (NM_001204229, intron 21 of 22)	intron (NM_001204229, intron 21 of 22)	69369	NM_009896	12703	Mm.130	NM_009896	ENSMUSG00000038037	Socs1	Cish1|Cish7|JAB|SOCS-1|SSI-1	suppressor of cytokine signaling 1	protein-coding
mm_96644.1	chr11	69331438	69331451	+	1	NA	intron (NM_010599, intron 11 of 13)	intron (NM_010599, intron 11 of 13)	5186	NM_010599	16499	Mm.232472	NM_010599	ENSMUSG00000018470	Kcnab3	C330022D06Rik|Kcnab4|mKv(beta)4	potassium voltage-gated channel, shaker-related subfamily, beta member 3	protein-coding
mm_146661.1	chr18	12121461	12121492	-	1	NA	promoter-TSS (NM_001289667)	promoter-TSS (NM_001289667)	61	NR_110356	338363	Mm.271567	NM_178801	ENSMUSG00000049411	Tmem241	6030446N20Rik	transmembrane protein 241	protein-coding
mm_82824.1	chr9	31120876	31120901	-	1	NA	intron (NM_011176, intron 1 of 18)	intron (NM_011176, intron 1 of 18)	10911	NM_011176	19143	Mm.243926	NM_011176	ENSMUSG00000031995	St14	Epithin|MT-SP1|Prss14|Tmprss14|mCAP3|matriptase	suppression of tumorigenicity 14 (colon carcinoma)	protein-coding
mm_36215.1	chr4	62502201	62502226	-	1	NA	promoter-TSS (NM_024257)	promoter-TSS (NM_024257)	-13	NM_024257	72748	Mm.41506	NM_024257	ENSMUSG00000038422	Hdhd3	2810435D12Rik	haloacid dehalogenase-like hydrolase domain containing 3	protein-coding
mm_4.1	chr1	4722856	4722893	+	1	NA	Intergenic	Intergenic	62852	NR_033530	27395	Mm.182927	NM_025300	ENSMUSG00000033845	Mrpl15	HSPC145|MRP-L7|Rpml7	mitochondrial ribosomal protein L15	protein-coding
mm_122638.1	chr14	51185714	51185730	-	1	NA	Intergenic	RLTR25B|LTR|ERVK	10201	NM_007449	11731	Mm.377077	NM_007449	ENSMUSG00000047894	Ang2	Angrp|Raa3|Rnase5b	angiogenin, ribonuclease A family, member 2	protein-coding
mm_13621.1	chr2	113440979	113441000	+	1	NA	promoter-TSS (NM_001285459)	promoter-TSS (NM_001285459)	-75	NM_001285459	14260	Mm.4938	NM_010230	ENSMUSG00000044042	Fmn1	Fmn|formin-1|ld	formin 1	protein-coding
mm_15238.1	chr2	154656886	154656894	+	1	NA	promoter-TSS (NM_029362)	promoter-TSS (NM_029362)	-136	NM_029362	75608	Mm.262480	NM_029362	ENSMUSG00000038467	Chmp4b	2010012F05Rik|C76846|Snf7-2	charged multivesicular body protein 4B	protein-coding
mm_56849.1	chr6	117937329	117937343	-	1	NA	promoter-TSS (NM_001173372)	promoter-TSS (NM_001173372)	-1	NM_001173372	108017	Mm.250392	NM_033648	ENSMUSG00000004988	Fxyd4	0610008I02Rik|AI267073|Chif	FXYD domain-containing ion transport regulator 4	protein-coding
mm_94479.1	chr11	6561134	6561149	+	1	NA	5' UTR (NM_001190344, exon 2 of 10)	5' UTR (NM_001190344, exon 2 of 10)	958	NM_001190344	216527	Mm.221271	NM_146014	ENSMUSG00000000378	Ccm2	BC029157	cerebral cavernous malformation 2	protein-coding
mm_131416.1	chr16	14705654	14705668	+	1	NA	promoter-TSS (NM_011415)	promoter-TSS (NM_011415)	-198	NM_011415	20583	Mm.4272	NM_011415	ENSMUSG00000022676	Snai2	Slug|Slugh|Snail2	snail family zinc finger 2	protein-coding
mm_28280.1	chr3	88950282	88950321	-	1	NA	promoter-TSS (NM_022994)	promoter-TSS (NM_022994)	-19	NM_001164533	65111	Mm.29028	NM_022994	ENSMUSG00000068921	Dap3	4921514D13Rik|DAP-3|MRP-S29|S29mt	death associated protein 3	protein-coding
mm_107380.1	chr12	32954560	32954573	+	1	NA	promoter-TSS (NR_044986)	promoter-TSS (NR_044986)	380	NM_198710	19027	Mm.246304	NM_013635	ENSMUSG00000020570	Sypl	AI314763|AI604763|D12Ertd446e|PanI|Pphn|Sypl1	synaptophysin-like protein	protein-coding
mm_147848.1	chr18	63682274	63682312	-	1	NA	exon (NM_016792, exon 2 of 8)	exon (NM_016792, exon 2 of 8)	10066	NM_016792	53382	Mm.19169	NM_016792	ENSMUSG00000024583	Txnl1	32kDa|TRP32|Txnl	thioredoxin-like 1	protein-coding
mm_9641.1	chr1	177193933	177193953	-	1	NA	intron (NM_011785, intron 1 of 12)	intron (NM_011785, intron 1 of 12)	54824	NM_011785	23797	Mm.235194	NM_011785	ENSMUSG00000019699	Akt3	AI851531|D930002M15Rik|Nmf350	thymoma viral proto-oncogene 3	protein-coding
mm_86193.1	chr9	119578982	119579031	-	1	NA	promoter-TSS (NM_021544)	promoter-TSS (NM_021544)	10	NM_021544	20271	Mm.103584	NM_021544	ENSMUSG00000032511	Scn5a	Nav1.5|Nav1.5c|SkM1|SkM2|mH1	sodium channel, voltage-gated, type V, alpha	protein-coding
mm_43553.1	chr5	137601194	137601250	+	1	NA	promoter-TSS (NM_030037)	promoter-TSS (NM_030037)	-163	NM_030037	68929	Mm.41355	NM_030037	ENSMUSG00000037221	Mospd3	1190005J19Rik|5133401H10Rik|Gtig2|R124	motile sperm domain containing 3	protein-coding
mm_51627.1	chr6	85452042	85452087	+	1	NA	promoter-TSS (NM_001163427)	promoter-TSS (NM_001163427)	-94	NR_028081	73327	Mm.379221	NM_028505	ENSMUSG00000030008	Pradc1	1700040I03Rik|Pap21	protease-associated domain containing 1	protein-coding
mm_85539.1	chr9	106663247	106663270	-	1	NA	intron (NR_104459, intron 3 of 4)	intron (NR_104459, intron 3 of 4)	-7149	NM_001160353	108068	Mm.410822	NM_001160353	ENSMUSG00000023192	Grm2	4930441L02Rik|Gprc1b|mGluR2|mGluR7	glutamate receptor, metabotropic 2	protein-coding
mm_121844.1	chr14	20618314	20618334	-	1	NA	promoter-TSS (NM_030180)	promoter-TSS (NM_030180)	30	NM_030180	78787	Mm.301173	NM_030180	ENSMUSG00000034235	Usp54	4930429G18Rik|AI115571|C030002J06Rik	ubiquitin specific peptidase 54	protein-coding
mm_43171.1	chr5	127554722	127554732	+	1	NA	exon (NM_175432, exon 8 of 9)	exon (NM_175432, exon 8 of 9)	62665	NM_133895	100561	Mm.28506	NM_133895	ENSMUSG00000029416	Slc15a4	AA987064|AW742963|C130069N12Rik|PHT1|PTR4	solute carrier family 15, member 4	protein-coding
mm_168129.1	chr10	25237278	25237292	-	1	NA	intron (NM_018747, intron 6 of 7)	BGLII|LTR|ERVK	-37115	NM_001347460	432442	Mm.485937	NM_018747	ENSMUSG00000039166	Akap7	6430401D08|AI662165|AKAP15|Akap18|BB170514	A kinase (PRKA) anchor protein 7	protein-coding
mm_58609.1	chr7	5059652	5059676	+	1	NA	exon (NM_001290429, exon 5 of 6)	exon (NM_001290429, exon 5 of 6)	-2479	NM_133671	22185	Mm.360389	NM_133671	ENSMUSG00000030435	U2af2	65kDa	U2 small nuclear ribonucleoprotein auxiliary factor (U2AF) 2	protein-coding
mm_18198.1	chr2	45117427	45117516	-	1	NA	Intergenic	Intergenic	-4192	NM_015753	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_123631.1	chr14	68504633	68504639	-	1	NA	exon (NM_007402, exon 20 of 23)	exon (NM_007402, exon 20 of 23)	29053	NM_007402	11500	Mm.261495	NM_007402	ENSMUSG00000022056	Adam7	ADAM 7|EAP1|EAPI	a disintegrin and metallopeptidase domain 7	protein-coding
mm_69490.1	chr7	134215030	134215038	-	1	NA	intron (NM_007400, intron 1 of 22)	intron (NM_007400, intron 1 of 22)	10063	NM_007400	11489	Mm.439714	NM_007400	ENSMUSG00000054555	Adam12	Mltna	a disintegrin and metallopeptidase domain 12 (meltrin alpha)	protein-coding
mm_26879.1	chr3	17785527	17785557	-	1	NA	Intergenic	Intergenic	-4379	NR_033490	70441	Mm.458192	NR_033490	ENSMUSG00000100252	Mir124-2hg	100040120|2610100L16Rik|6430547I21Rik|A930005K07Rik|AW125202|Gm2612	Mir124-2 host gene (non-protein coding)	ncRNA
mm_23291.1	chr3	52102824	52102837	+	1	NA	intron (NM_001004176, intron 1 of 4)	CpG	2176	NM_001004176	433586	Mm.234972	NM_001004176	ENSMUSG00000061143	Maml3	AV234550|BC049812|Mam-2|mKIAA1816	mastermind like 3 (Drosophila)	protein-coding
mm_53572.1	chr6	137386592	137386594	+	1	NA	intron (NM_001164401, intron 7 of 25)	intron (NM_001164401, intron 7 of 25)	-24128	NM_001164402	19277	Mm.186361	NM_011216	ENSMUSG00000030223	Ptpro	D28|GLEPP1|PTPBK|PTPROt|PTPU2|PTPoc|PTPphi|Ptpn15|R-PTP-O	protein tyrosine phosphatase, receptor type, O	protein-coding
mm_102367.1	chr11	58390230	58390257	-	1	NA	exon (NM_001083884, exon 7 of 7)	exon (NM_001083884, exon 7 of 7)	9597	NM_001330197	70163	Mm.24119	NM_027339	ENSMUSG00000013643	Lypd8	2210415F13Rik	LY6/PLAUR domain containing 8	protein-coding
mm_93421.1	chr10	108710820	108710832	-	1	NA	intron (NM_001252341, intron 4 of 11)	intron (NM_001252341, intron 4 of 11)	-10666	NM_203660	368203	Mm.452758	NM_203660		Gm5136	C6.1AL|EG368203	predicted gene 5136	protein-coding
mm_156554.1	chrX	151800874	151800912	+	1	NA	Intergenic	Intergenic	-2389	NM_021523	59026	Mm.27372	NM_021523	ENSMUSG00000025261	Huwe1	5430439H10Rik|AU041296|Arf-bp1|C430014N20Rik|C80292|Gm1718|Ib772|LASU1|Mule|Ureb1	HECT, UBA and WWE domain containing 1	protein-coding
mm_42817.1	chr5	121849022	121849037	+	1	NA	promoter-TSS (NM_175474)	promoter-TSS (NM_175474)	1	NM_175474	231717	Mm.12654	NM_175474	ENSMUSG00000044134	Fam109a	A230106M15Rik|AU017694|IPIP27A|Ses1	family with sequence similarity 109, member A	protein-coding
mm_136452.1	chr16	94997471	94997486	-	1	NA	5' UTR (NM_010606, exon 1 of 4)	5' UTR (NM_010606, exon 1 of 4)	218	NM_001025584	16522	Mm.328720	NM_010606	ENSMUSG00000043301	Kcnj6	BIR1|GIRK2|KATP2|KCNJ7|Kir3.2|weaver|wv	potassium inwardly-rectifying channel, subfamily J, member 6	protein-coding
mm_112330.1	chr12	115869227	115869254	-	1	NA	Intergenic	Intergenic	-173446	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
mm_112904.1	chr13	20902891	20902901	+	1	NA	intron (NM_012054, intron 5 of 20)	intron (NM_012054, intron 5 of 20)	108783	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_44422.1	chr5	20855275	20855301	-	1	NA	intron (NM_172992, intron 1 of 17)	intron (NM_172992, intron 1 of 17)	26836	NM_172992	68770	Mm.86410	NM_172992	ENSMUSG00000039987	Phtf2	1110054G21Rik|9530062N20Rik|AI447096|C77923	putative homeodomain transcription factor 2	protein-coding
mm_16445.1	chr2	180444042	180444053	+	1	NA	Intergenic	Intergenic	-16931	NM_148933	108115	Mm.133687	NM_148933	ENSMUSG00000038963	Slco4a1	OATP-E|Slc21a12	solute carrier organic anion transporter family, member 4a1	protein-coding
mm_156852.1	chrX	164401138	164401144	+	1	NA	TTS (NM_001308489)	TTS (NM_001308489)	-18646	NM_011081	18700	Mm.3781	NM_011081	ENSMUSG00000031381	Piga	AI194334|Pig-a	phosphatidylinositol glycan anchor biosynthesis, class A	protein-coding
mm_152384.1	chr19	10304868	10304954	-	1	NA	promoter-TSS (NM_198114)	promoter-TSS (NM_198114)	-34	NM_198114	269060	Mm.329718	NM_198114	ENSMUSG00000035735	Dagla	Nsddr	diacylglycerol lipase, alpha	protein-coding
mm_11019.1	chr2	26609763	26609773	+	1	NA	Intergenic	Intergenic	-5351	NM_026212	67512	Mm.24244	NM_026212	ENSMUSG00000026922	Agpat2	2510002J07Rik|AV000834|BSCL|BSCL1|LPAAB|LPAAT-beta	1-acylglycerol-3-phosphate O-acyltransferase 2 (lysophosphatidic acid acyltransferase, beta)	protein-coding
mm_81179.1	chr9	107340594	107340648	+	1	NA	promoter-TSS (NM_175486)	promoter-TSS (NM_175486)	-19	NM_175486	235599	Mm.71039	NM_175486	ENSMUSG00000037977	6430571L13Rik	-	RIKEN cDNA 6430571L13 gene	protein-coding
mm_120088.1	chr14	57826211	57826272	+	1	NA	promoter-TSS (NM_198605)	promoter-TSS (NM_198605)	2	NM_026401	67840	Mm.319530	NM_026401	ENSMUSG00000021967	Mrpl57	2610025P17Rik|AV005697|Mrp63	mitochondrial ribosomal protein L57	protein-coding
mm_108965.1	chr12	102401875	102401911	+	1	NA	exon (NM_011175, exon 8 of 14)	exon (NM_011175, exon 8 of 14)	37920	NM_011175	19141	Mm.17185	NM_011175	ENSMUSG00000021190	Lgmn	AEP|AI746452|AU022324|Prsc1	legumain	protein-coding
mm_77785.1	chr9	3025496	3025532	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	13229	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_122423.1	chr14	44772462	44772466	-	1	NA	Intergenic	RodERV21-int|LTR|ERV1	-47477	NM_001162954	666744	Mm.387002	NM_001162954	ENSMUSG00000091923	Gm8267	EG666744	predicted gene 8267	protein-coding
mm_94349.1	chr11	4895317	4895327	+	1	NA	promoter-TSS (NM_172438)	promoter-TSS (NM_172438)	-21	NM_172438	107829	Mm.28969	NM_172438	ENSMUSG00000034274	Thoc5	1700060C24Rik|A430085L24Rik|Fmip|PK1.3|Sgk2	THO complex 5	protein-coding
mm_160608.1	chr9	80136604	80136604	+	1	NA	exon (NM_146003, exon 18 of 23)	exon (NM_146003, exon 18 of 23)	-28430	NM_001039546	17920	Mm.4040	NM_008662	ENSMUSG00000033577	Myo6	BC029719|Tlc|sv	myosin VI	protein-coding
mm_95630.1	chr11	53631942	53631954	+	1	NA	3' UTR (NM_008355, exon 4 of 4)	3' UTR (NM_008355, exon 4 of 4)	2754	NM_008355	16163	Mm.1284	NM_008355	ENSMUSG00000020383	Il13	Il-13	interleukin 13	protein-coding
mm_89550.1	chr10	94688740	94688808	+	1	NA	promoter-TSS (NM_029852)	promoter-TSS (NM_029852)	-16	NM_029852	77048	Mm.296971	NM_029852	ENSMUSG00000020024	Cep83	2600001G24Rik|4921537D05Rik|5730513H21Rik|Ccdc41	centrosomal protein 83	protein-coding
mm_19947.1	chr2	117298153	117298195	-	1	NA	intron (NM_011246, intron 6 of 16)	intron (NM_011246, intron 6 of 16)	44703	NM_011246	19419	Mm.42150	NM_011246	ENSMUSG00000027347	Rasgrp1	Rasgrp	RAS guanyl releasing protein 1	protein-coding
mm_86425.1	chr10	3789378	3789378	+	1	NA	intron (NM_001159942, intron 1 of 16)	intron (NM_001159942, intron 1 of 16)	49001	NM_001159942	213783	Mm.150831	NM_001033253	ENSMUSG00000040624	Plekhg1	D10Ertd733e|Gm521|mKIAA1209	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	protein-coding
mm_48485.1	chr5	142501798	142501822	-	1	NA	intron (NM_001289588, intron 5 of 14)	B4|SINE|B4	28266	NM_019943	56522	Mm.441372	NM_019943	ENSMUSG00000074817	Papolb	PAP|Paplob|Papola-ps|Papt|Plap-ps|Tpap	poly (A) polymerase beta (testis specific)	protein-coding
mm_163790.1	chr14	9955749	9955752	-	1	NA	intron (NM_001308286, intron 2 of 6)	intron (NM_001308286, intron 2 of 6)	71655	NR_030680	100042415	Mm.235938	NR_030680		Mnd1-ps	Gm3833	Mnd1 retrotransposed pseudogene	pseudo
mm_155425.1	chrX	73492122	73492135	+	1	NA	exon (NM_007542, exon 4 of 8)	exon (NM_007542, exon 4 of 8)	8527	NM_007542	12111	Mm.2608	NM_007542	ENSMUSG00000031375	Bgn	BG|DSPG1|PG-S1|PGI|SLRR1A	biglycan	protein-coding
mm_69434.1	chr7	132845931	132845934	-	1	NA	intron (NM_028095, intron 3 of 5)	intron (NM_028095, intron 3 of 5)	6715	NM_028095	72096	Mm.28631	NM_028095	ENSMUSG00000030960	Mettl10	2010208K18Rik	methyltransferase like 10	protein-coding
mm_51018.1	chr6	65042576	65042662	+	1	NA	promoter-TSS (NM_007958)	promoter-TSS (NM_007958)	-48	NM_007958	13990	Mm.99113	NM_007958	ENSMUSG00000029920	Smarcad1	AV081750|AW226546|D6Pas1|Etl1|mKIAA1122	SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1	protein-coding
mm_84950.1	chr9	83146529	83146588	-	1	NA	promoter-TSS (NM_026122)	promoter-TSS (NM_026122)	49	NM_175074	94353	Mm.244426	NM_026122	ENSMUSG00000066456	Hmgn3	1110002A15Rik|6330514M13Rik|BB071015|TRIP7	high mobility group nucleosomal binding domain 3	protein-coding
mm_63686.1	chr7	130574886	130574896	+	1	NA	Intergenic	Intergenic	-2593	NM_001004468	57752	Mm.86322	NM_021314	ENSMUSG00000030852	Tacc2	mKIAA4180	transforming, acidic coiled-coil containing protein 2	protein-coding
mm_139839.1	chr17	69159998	69160014	+	1	NA	intron (NM_013813, intron 1 of 21)	intron (NM_013813, intron 1 of 21)	3196	NM_013813	13823	Mm.131135	NM_013813	ENSMUSG00000024044	Epb41l3	4.1B|DAL1P|Dal1|Epb4.1l3|NBL3	erythrocyte membrane protein band 4.1 like 3	protein-coding
mm_144086.1	chr17	94834411	94834443	-	1	NA	intron (NR_045963, intron 1 of 4)	intron (NR_045963, intron 1 of 4)	372	NR_045964	100038746	Mm.456686	NR_045963	ENSMUSG00000066057	Gm1976	100038868	predicted gene 1976	ncRNA
mm_100780.1	chr11	4808354	4808356	-	1	NA	intron (NM_001252251, intron 4 of 16)	intron (NM_001252251, intron 4 of 16)	24780	NM_001252253	18016	Mm.297109	NM_010898	ENSMUSG00000009073	Nf2	merlin	neurofibromin 2	protein-coding
mm_71416.1	chr8	46478727	46478729	+	1	NA	intron (NM_007981, intron 1 of 20)	intron (NM_007981, intron 1 of 20)	7691	NM_007981	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_113288.1	chr13	30166987	30167003	+	1	NA	intron (NM_153546, intron 1 of 12)	intron (NM_153546, intron 1 of 12)	30505	NM_153546	218121	Mm.89682	NM_153546	ENSMUSG00000038732	Mboat1	9130215M02Rik|BC023845|LPEAT1|Moact1|Oact1	membrane bound O-acyltransferase domain containing 1	protein-coding
mm_76001.1	chr8	72475213	72475244	-	1	NA	promoter-TSS (NM_138585)	promoter-TSS (NM_138585)	5	NM_138585	27967	Mm.30136	NM_138585	ENSMUSG00000052488	Cherp	5730408I11Rik|D8Wsu96e|DAN16|Scaf6	calcium homeostasis endoplasmic reticulum protein	protein-coding
mm_68019.1	chr7	100964275	100964288	-	1	NA	promoter-TSS (NM_183168)	promoter-TSS (NM_183168)	85	NM_183168	233571	Mm.235193	NM_183168	ENSMUSG00000048779	P2ry6	2010204J23Rik|P2Y6	pyrimidinergic receptor P2Y, G-protein coupled, 6	protein-coding
mm_66343.1	chr7	43473540	43473577	-	1	NA	3' UTR (NM_001164518, exon 8 of 8)	3' UTR (NM_001164518, exon 8 of 8)	10325	NM_001290316	75690	Mm.30200	NM_001290316	ENSMUSG00000070604	Vsig10l	-	V-set and immunoglobulin domain containing 10 like	protein-coding
mm_151670.1	chr19	4188757	4188761	-	1	NA	intron (NM_178650, intron 6 of 9)	intron (NM_178650, intron 6 of 9)	2288	NM_178650	108995	Mm.288312	NM_178650	ENSMUSG00000040247	Tbc1d10c	1810062O14Rik|AI428527	TBC1 domain family, member 10c	protein-coding
mm_52899.1	chr6	122695972	122695976	+	1	NA	Intergenic	Intergenic	-11515	NM_001289831	71950	Mm.6047	NM_028016	ENSMUSG00000012396	Nanog	2410002E02Rik|ENK|ecat4	Nanog homeobox	protein-coding
mm_130098.1	chr15	89425819	89425851	-	1	NA	promoter-TSS (NM_009948)	promoter-TSS (NM_009948)	27	NM_009948	12895	Mm.227738	NM_009948	ENSMUSG00000078937	Cpt1b	Cpt1|Cpt1-m|Cpti|Cpti-m|M-cpti	carnitine palmitoyltransferase 1b, muscle	protein-coding
mm_4201.1	chr1	171229655	171229717	+	1	NA	3' UTR (NM_010185, exon 5 of 5)	3' UTR (NM_010185, exon 5 of 5)	4632	NM_013474	11807	Mm.389209	NM_013474	ENSMUSG00000005681	Apoa2	Alp-2|Apo-AII|ApoA-II|ApoAII|Apoa-2|Hdl-1	apolipoprotein A-II	protein-coding
mm_153824.1	chr19	46305565	46305575	-	1	NA	promoter-TSS (NM_001177370)	promoter-TSS (NM_001177370)	-125	NM_019408	18034	Mm.102365	NM_019408	ENSMUSG00000025225	Nfkb2	NF-kappaB2|lyt|p49|p49/p100|p50B|p52	nuclear factor of kappa light polypeptide gene enhancer in B cells 2, p49/p100	protein-coding
mm_32197.1	chr4	101419360	101419378	+	1	NA	promoter-TSS (NM_009647)	promoter-TSS (NM_009647)	48	NM_001177604	11639	Mm.42040	NM_009647	ENSMUSG00000028527	Ak4	AK 4|Ak-3|Ak-4|Ak3|Ak3l1|D4Ertd274e	adenylate kinase 4	protein-coding
mm_27154.1	chr3	33083017	33083046	-	1	NA	promoter-TSS (NM_021483)	promoter-TSS (NM_021483)	29	NM_021483	58869	Mm.151332	NM_021483	ENSMUSG00000027674	Pex5l	1700016J08Rik|PXR2|Pex2|TRIP8b|pex5Rp	peroxisomal biogenesis factor 5-like	protein-coding
mm_49628.1	chr6	30804796	30804817	+	1	NA	intron (NM_017478, intron 20 of 23)	intron (NM_017478, intron 20 of 23)	63507	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_66549.1	chr7	45211797	45211808	-	1	NA	promoter-TSS (NM_015789)	promoter-TSS (NM_015789)	81	NM_015789	50722	Mm.27287	NM_015789	ENSMUSG00000030792	Dkkl1	AI414495|SGY|SGY-1|SGY1|Soggy|mSgy	dickkopf-like 1	protein-coding
mm_75645.1	chr8	65037177	65037191	-	1	NA	intron (NM_001297554, intron 1 of 3)	intron (NM_001297554, intron 1 of 3)	152	NM_001297554	100038489	Mm.58847	NM_001297554	ENSMUSG00000079042	Apela	ENSMUSG00000074303|Ela|Ende|Gm10664	apelin receptor early endogenous ligand	protein-coding
mm_141098.1	chr17	26004855	26004873	-	1	NA	intron (NM_153140, intron 4 of 11)	intron (NM_153140, intron 4 of 11)	16996	NM_153140	215445	Mm.41191	NM_153140	ENSMUSG00000037098	Rab11fip3	Cart1|D030060O14Rik|Rab11-FIP3|mKIAA0665	RAB11 family interacting protein 3 (class II)	protein-coding
mm_84207.1	chr9	60688035	60688053	-	1	NA	promoter-TSS (NM_001146047)	promoter-TSS (NM_001146047)	90	NM_145616	102747	Mm.269413	NM_145616	ENSMUSG00000047766	Lrrc49	AI430817|AW050057|D430025H09Rik|PGs4|p79	leucine rich repeat containing 49	protein-coding
mm_71629.1	chr8	57455978	57455997	+	1	NA	promoter-TSS (NM_009136)	promoter-TSS (NM_009136)	64	NM_009136	20284	Mm.12886	NM_009136	ENSMUSG00000031610	Scrg1	AW124307	scrapie responsive gene 1	protein-coding
mm_144799.1	chr18	36109628	36109629	+	1	NA	non-coding (NR_015571, exon 2 of 2)	non-coding (NR_015571, exon 2 of 2)	3425	NR_015571	74966	Mm.379238	NM_030089		4930471G03Rik	1700007N01Rik	RIKEN cDNA 4930471G03 gene	ncRNA
mm_145139.1	chr18	45559489	45559503	+	1	NA	promoter-TSS (NM_080465)	promoter-TSS (NM_080465)	-658	NM_080465	140492	Mm.411614	NM_080465	ENSMUSG00000054477	Kcnn2	KCa2.2|SK2|SKCA2|bc|fri	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2	protein-coding
mm_71189.1	chr8	40866717	40866735	+	1	NA	intron (NM_007514, intron 1 of 11)	intron (NM_007514, intron 1 of 11)	4359	NM_001044740	11988	Mm.4676	NM_007514	ENSMUSG00000031596	Slc7a2	20.5|AI158848|Atrc2|CAT-2|Cat2|Tea	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	protein-coding
mm_51172.1	chr6	70726622	70726627	+	1	NA	Intergenic	Intergenic	65551	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_102668.1	chr11	65032433	65032447	-	1	NA	intron (NM_175003, intron 10 of 20)	intron (NM_175003, intron 10 of 20)	53405	NM_023479	68626	Mm.157711	NM_023479	ENSMUSG00000020549	Elac2	1110017O07Rik|D11Wsu80e|Hpc2	elaC ribonuclease Z 2	protein-coding
mm_144319.1	chr18	12662004	12662013	+	1	NA	intron (NM_028341, intron 1 of 13)	intron (NM_028341, intron 1 of 13)	18475	NM_028341	72747	Mm.52526	NM_028341	ENSMUSG00000024424	Ttc39c	1700008N02Rik|2810439F02Rik	tetratricopeptide repeat domain 39C	protein-coding
mm_19654.1	chr2	102901450	102901465	-	1	NA	5' UTR (NM_009851, exon 1 of 19)	5' UTR (NM_009851, exon 1 of 19)	208	NM_001177785	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_81719.1	chr9	111641816	111641817	+	1	NA	intron (NM_016853, intron 1 of 10)	intron (NM_016853, intron 1 of 10)	48532	NM_016853	20840	Mm.1414	NM_016853	ENSMUSG00000032502	Stac	-	src homology three (SH3) and cysteine rich domain	protein-coding
mm_15483.1	chr2	157561903	157561914	+	1	NA	3' UTR (NM_010923, exon 3 of 3)	3' UTR (NM_010923, exon 3 of 3)	1830	NM_180960	18111	Mm.34330	NM_010923	ENSMUSG00000067786	Nnat	5730414I02Rik|AW107673|Peg5	neuronatin	protein-coding
mm_59266.1	chr7	24898369	24898371	+	1	NA	intron (NM_007655, intron 1 of 4)	intron (NM_007655, intron 1 of 4)	859	NM_007655	12518	Mm.1355	NM_007655	ENSMUSG00000003379	Cd79a	Ig-alpha|Iga|Igalpha|Ly-54|Ly54|mb-1	CD79A antigen (immunoglobulin-associated alpha)	protein-coding
mm_134352.1	chr16	16600098	16600110	-	1	NA	promoter-TSS (NM_001301817)	promoter-TSS (NM_001301817)	-126	NM_001301817	224014	Mm.256131	NM_139232	ENSMUSG00000022788	Fgd4	9030023J02Rik|9330209B17Rik|Frabp|ZFYVE6	FYVE, RhoGEF and PH domain containing 4	protein-coding
mm_54933.1	chr6	48445428	48445505	-	1	NA	promoter-TSS (NM_001085415)	promoter-TSS (NM_001085415)	359	NM_020589	68910	Mm.2464	NM_020589	ENSMUSG00000068551	Zfp467	1190001I08Rik|AB041616|AI426952|AV017623|EZI|MNCb-3350|Znf467	zinc finger protein 467	protein-coding
mm_74966.1	chr8	27042683	27042704	-	1	NA	exon (NM_001039078, exon 1 of 4)	exon (NM_001039078, exon 1 of 4)	138	NM_054057	114863	Mm.277501	NM_054057	ENSMUSG00000031485	Prosc	1700024N20Rik|2200002F22Rik	proline synthetase co-transcribed	protein-coding
mm_166939.1	chr7	42430651	42430652	-	1	NA	promoter-TSS (NR_028441)	promoter-TSS (NR_028441)	-282	NR_028441	628490	Mm.246518	NR_028441		Vmn2r-ps60	Casr-rs4|Gprc2a-rs4	vomeronasal 2, receptor, pseudogene 60	pseudo
mm_125386.1	chr15	40682087	40682095	+	1	NA	intron (NM_011766, intron 1 of 7)	intron (NM_011766, intron 1 of 7)	27049	NM_011766	22762	Mm.39496	NM_011766	ENSMUSG00000022306	Zfpm2	B330005D23Rik|FOG-2|FOG2	zinc finger protein, multitype 2	protein-coding
mm_48907.1	chr6	3763847	3763857	+	1	NA	promoter-TSS (NM_001042725)	promoter-TSS (NM_001042725)	-229	NM_001042725	12311	Mm.4642	NM_007588	ENSMUSG00000023964	Calcr	Clr	calcitonin receptor	protein-coding
mm_114614.1	chr13	75849317	75849327	+	1	NA	3' UTR (NM_053108, exon 3 of 3)	3' UTR (NM_053108, exon 3 of 3)	9436	NM_053108	93692	Mm.25844	NM_053108	ENSMUSG00000021591	Glrx	C86710|D13Wsu156e|Glrx1|Grx1|TTase	glutaredoxin	protein-coding
mm_12624.1	chr2	74697994	74698008	+	1	NA	5' UTR (NM_013555, exon 1 of 2)	5' UTR (NM_013555, exon 1 of 2)	238	NM_013555	15438	Mm.26544	NM_013555	ENSMUSG00000043342	Hoxd9	Hox-4.4|Hox-5.2	homeobox D9	protein-coding
mm_26029.1	chr3	135439443	135439469	+	1	NA	promoter-TSS (NR_030689)	promoter-TSS (NR_030689)	697	NM_025356	66105	Mm.49884	NM_025356	ENSMUSG00000078578	Ube2d3	1100001F19Rik|9430029A22Rik|AA414951	ubiquitin-conjugating enzyme E2D 3	protein-coding
mm_96463.1	chr11	67596615	67596621	+	1	NA	promoter-TSS (NM_001277080)	promoter-TSS (NM_001277080)	63	NM_001277079	14457	Mm.40338	NM_008088	ENSMUSG00000033066	Gas7	AW124766|B230343A10Rik|Gas7-cb	growth arrest specific 7	protein-coding
mm_119340.1	chr14	41072861	41072903	+	1	NA	promoter-TSS (NM_027094)	promoter-TSS (NM_027094)	-29	NM_027094	69496	Mm.55734	NM_027094	ENSMUSG00000021790	Dydc1	1700029M23Rik	DPY30 domain containing 1	protein-coding
mm_147077.1	chr18	35562523	35562533	-	1	NA	intron (NM_010771, intron 1 of 14)	CpG	370	NM_010771	17184	Mm.215034	NM_010771	ENSMUSG00000037236	Matr3	1110061A14Rik|2810017I02Rik|AI841759|AW555618|D030046F20Rik|mKIAA0723	matrin 3	protein-coding
mm_36287.1	chr4	63861327	63861355	-	1	NA	promoter-TSS (NM_009403)	promoter-TSS (NM_009403)	-57	NM_009403	21949	Mm.4664	NM_009403	ENSMUSG00000028362	Tnfsf8	CD153|CD30LG|Cd30l|Tnlg3a	tumor necrosis factor (ligand) superfamily, member 8	protein-coding
mm_102098.1	chr11	52336080	52336094	-	1	NA	Intergenic	Intergenic	-24775	NM_011694	22333	Mm.3555	NM_011694	ENSMUSG00000020402	Vdac1	AL033343|Vdac5|mVDAC1|mVDAC5	voltage-dependent anion channel 1	protein-coding
mm_90597.1	chr10	128303359	128303418	+	1	NA	promoter-TSS (NM_001252327)	promoter-TSS (NM_001252327)	53	NM_001252326	103135	Mm.244183	NM_133992	ENSMUSG00000005682	Pan2	1200014O24Rik|AI047843|AW742773|Usp52|mKIAA0710	PAN2 poly(A) specific ribonuclease subunit	protein-coding
mm_118618.1	chr14	21052595	21052633	+	1	NA	promoter-TSS (NM_134079)	promoter-TSS (NM_134079)	40	NM_134079	11534	Mm.188734	NM_134079	ENSMUSG00000039197	Adk	2310026J05Rik|5033405D03Rik|AI255373|AI987814|Ak	adenosine kinase	protein-coding
mm_110601.1	chr12	56535973	56535989	-	1	NA	intron (NM_009385, intron 1 of 2)	CpG	927	NM_009385	21869	Mm.89972	NM_009385	ENSMUSG00000001496	Nkx2-1	AV026640|Nkx2.1|T/EBP|Titf1|Ttf-1	NK2 homeobox 1	protein-coding
mm_88094.1	chr10	68723828	68723841	+	1	NA	promoter-TSS (NM_177794)	promoter-TSS (NM_177794)	88	NM_177794	327766	Mm.2479	NM_177794	ENSMUSG00000060044	Tmem26	3230401A06|AI195372	transmembrane protein 26	protein-coding
mm_37081.1	chr4	116371749	116371759	-	1	NA	intron (NM_008641, intron 4 of 28)	intron (NM_008641, intron 4 of 28)	92427	NM_001042743	17776	Mm.9287	NM_008641	ENSMUSG00000003810	Mast2	MAST205|Mtssk	microtubule associated serine/threonine kinase 2	protein-coding
mm_159971.1	chr6	99692577	99692577	+	1	NA	promoter-TSS (NM_008158)	promoter-TSS (NM_008158)	-102	NM_008158	14761	Mm.35009	NM_008158	ENSMUSG00000072875	Gpr27	-	G protein-coupled receptor 27	protein-coding
mm_46128.1	chr5	92505474	92505489	-	1	NA	5' UTR (NM_007644, exon 1 of 12)	5' UTR (NM_007644, exon 1 of 12)	176	NM_007644	12492	Mm.297964	NM_007644	ENSMUSG00000029426	Scarb2	9330185J12Rik|Cd36l2|LGP85|LIMP II|LIMP-2|MLGP85	scavenger receptor class B, member 2	protein-coding
mm_127260.1	chr15	99704309	99704322	+	1	NA	intron (NM_031842, intron 4 of 12)	intron (NM_031842, intron 4 of 12)	2028	NM_031842	83797	Mm.273756	NM_031842	ENSMUSG00000023018	Smarcd1	AA407987|Baf60a|D15Kz1	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1	protein-coding
mm_52707.1	chr6	119388891	119388920	+	1	NA	intron (NM_197985, intron 1 of 7)	CpG	28578	NM_197985	68465	Mm.291826	NM_197985	ENSMUSG00000030168	Adipor2	1110001I14Rik|ADCR2|AI115388|AW554121|D6Ucla1e|Paqr2	adiponectin receptor 2	protein-coding
mm_11771.1	chr2	38823338	38823350	+	1	NA	intron (NM_010264, intron 3 of 10)	intron (NM_010264, intron 3 of 10)	-29391	NR_029568	387176		NR_029568	ENSMUSG00000065423	Mir181a-2	Mirn181|Mirn181a|Mirn181a-2|miR-181|mir-181a|mir-181a-2	microRNA 181a-2	ncRNA
mm_132545.1	chr16	37883012	37883014	+	1	NA	3' UTR (NM_177093, exon 4 of 4)	3' UTR (NM_177093, exon 4 of 4)	14613	NM_177093	320184	Mm.390882	NM_177093	ENSMUSG00000034158	Lrrc58	1810012N18Rik|C330018J07Rik	leucine rich repeat containing 58	protein-coding
mm_134817.1	chr16	25178089	25178099	-	1	NA	Intergenic	Lx8|LINE|L1	-108723	NM_175165	71338	Mm.126851	NM_175165	ENSMUSG00000048399	Tprg	5430420C16Rik|Tprg1	transformation related protein 63 regulated	protein-coding
mm_172731.1	chr8	78081401	78081416	-	1	NA	Intergenic	RLTR9E|LTR|ERVK	-131934	NM_183096	73301	Mm.61243	NM_183096	ENSMUSG00000037101	Ttc29	1700031F13Rik	tetratricopeptide repeat domain 29	protein-coding
mm_34788.1	chr4	154191319	154191336	+	1	NA	intron (NM_001162977, intron 3 of 36)	(CA)n|Simple_repeat|Simple_repeat	20614	NM_001162977	230971	Mm.275216	NM_172273	ENSMUSG00000057751	Megf6	2600001P17Rik|Egfl3	multiple EGF-like-domains 6	protein-coding
mm_42690.1	chr5	119835136	119835151	+	1	NA	5' UTR (NM_011537, exon 1 of 9)	5' UTR (NM_011537, exon 1 of 9)	480	NM_011537	21388	Mm.103636	NM_011537	ENSMUSG00000018263	Tbx5	-	T-box 5	protein-coding
mm_107748.1	chr12	59013412	59013462	+	1	NA	promoter-TSS (NM_025656)	promoter-TSS (NM_025656)	46	NM_025656	66603	Mm.35353	NM_025656	ENSMUSG00000060121	Gemin2	Sip1|gemin-2	gem (nuclear organelle) associated protein 2	protein-coding
mm_129422.1	chr15	78405986	78405993	-	1	NA	promoter-TSS (NM_009437)	promoter-TSS (NM_009437)	-130	NM_009437	22117	Mm.15312	NM_009437	ENSMUSG00000044986	Tst	Rhodanese	thiosulfate sulfurtransferase, mitochondrial	protein-coding
mm_73761.1	chr8	115190249	115190251	+	1	NA	intron (NM_019573, intron 8 of 8)	intron (NM_019573, intron 8 of 8)	516644	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_59756.1	chr7	28825319	28825363	+	1	NA	promoter-TSS (NM_016772)	promoter-TSS (NM_016772)	3	NM_016772	51798	Mm.291776	NM_016772	ENSMUSG00000053898	Ech1	AA617331	enoyl coenzyme A hydratase 1, peroxisomal	protein-coding
mm_7725.1	chr1	130715828	130715848	-	1	NA	promoter-TSS (NM_008825)	promoter-TSS (NM_008825)	-17	NM_008825	18640	Mm.249861	NM_008825	ENSMUSG00000026409	Pfkfb2	4930568D07Rik	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2	protein-coding
mm_87494.1	chr10	51496018	51496038	+	1	NA	exon (NM_013532, exon 8 of 9)	exon (NM_013532, exon 8 of 9)	5130	NM_013532	14728	Mm.34408	NM_013532	ENSMUSG00000062593	Lilrb4a	CD85K|Gp49b|HM18|ILT3|LIR-5|Lilrb4|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4A	protein-coding
mm_54577.1	chr6	38110421	38110425	-	1	NA	intron (NM_029921, intron 1 of 2)	MIR|SINE|MIR	1070	NM_029921	77522	Mm.387207	NM_029921	ENSMUSG00000029829	Tmem213	D630002J15Rik	transmembrane protein 213	protein-coding
mm_169248.1	chr13	74865158	74865161	+	1	NA	Intergenic	(TGG)n|Simple_repeat|Simple_repeat	-56399	NM_001301153	12380	Mm.29163	NM_009817	ENSMUSG00000021585	Cast	-	calpastatin	protein-coding
mm_72992.1	chr8	93012440	93012482	+	1	NA	Intergenic	Intergenic	35731	NM_001013764	244595	Mm.390089	NM_001013764	ENSMUSG00000071047	Ces1a	Ces1l|EG244595|Gm4976	carboxylesterase 1A	protein-coding
mm_144858.1	chr18	36702434	36702452	+	1	NA	Intergenic	RMER19C|LTR|ERVK	-6518	NM_172831	240216	Mm.252323	NM_172831	ENSMUSG00000044719	E230025N22Rik	EG240216	Riken cDNA E230025N22 gene	protein-coding
mm_141594.1	chr17	32424140	32424153	-	1	NA	promoter-TSS (NM_001271478)	promoter-TSS (NM_001271478)	21	NM_001271476	57757	Mm.86752	NM_021319	ENSMUSG00000079563	Pglyrp2	C730002N09Rik|PGRP-L|Pglyrpl|tagL	peptidoglycan recognition protein 2	protein-coding
mm_142139.1	chr17	35969698	35969711	-	1	NA	promoter-TSS (NM_013854)	promoter-TSS (NM_013854)	46	NM_013854	224742	Mm.329022	NM_013854	ENSMUSG00000038762	Abcf1	AU041969|Abc50|D17Wsu166e|GCN20	ATP-binding cassette, sub-family F (GCN20), member 1	protein-coding
mm_69325.1	chr7	128540068	128540112	-	1	NA	exon (NM_013863, exon 2 of 4)	exon (NM_013863, exon 2 of 4)	16507	NM_013863	29810	Mm.84073	NM_013863	ENSMUSG00000030847	Bag3	AA407278|Bis|mg638	BCL2-associated athanogene 3	protein-coding
mm_66041.1	chr7	30664942	30664984	-	1	NA	promoter-TSS (NM_027999)	promoter-TSS (NM_027999)	31	NM_027999	71909	Mm.290410	NM_027999	ENSMUSG00000078762	Haus5	2310022K01Rik	HAUS augmin-like complex, subunit 5	protein-coding
mm_129192.1	chr15	76374916	76374925	-	1	NA	promoter-TSS (NM_183099)	promoter-TSS (NM_183099)	18	NM_183099	73542	Mm.159026	NM_183099	ENSMUSG00000060794	Tssk5	1700091F14Rik	testis-specific serine kinase 5	protein-coding
mm_84494.1	chr9	66879062	66879072	-	1	NA	intron (NM_173413, intron 1 of 7)	intron (NM_173413, intron 1 of 7)	40638	NM_173413	235442	Mm.260376	NM_173413	ENSMUSG00000036943	Rab8b	5930437D16|D330025I23Rik	RAB8B, member RAS oncogene family	protein-coding
mm_41854.1	chr5	104440218	104440227	+	1	NA	intron (NM_001204233, intron 5 of 5)	intron (NM_001204233, intron 5 of 5)	4030	NM_001204233	20750	Mm.288474	NM_009263	ENSMUSG00000029304	Spp1	2AR|Apl-1|BNSP|BSPI|Bsp|ETA-1|Eta|OP|Opn|Opnl|Ric|Spp-1	secreted phosphoprotein 1	protein-coding
mm_100212.1	chr11	116918795	116918803	+	1	NA	promoter-TSS (NM_172948)	promoter-TSS (NM_172948)	-64	NM_172948	268510	Mm.35141	NM_172948	ENSMUSG00000043857	Mgat5b	C330018B01|GnT-IX|mGnTVB	mannoside acetylglucosaminyltransferase 5, isoenzyme B	protein-coding
mm_128919.1	chr15	73751972	73752009	-	1	NA	exon (NM_008975, exon 2 of 6)	exon (NM_008975, exon 2 of 6)	3964	NM_008975	19245	Mm.390807	NM_008975	ENSMUSG00000059895	Ptp4a3	AV088979|Prl-3|pPtp4a3	protein tyrosine phosphatase 4a3	protein-coding
mm_37937.1	chr4	132922621	132922626	-	1	NA	promoter-TSS (NM_145553)	promoter-TSS (NM_145553)	-72	NM_001163792	230789	Mm.11473	NM_145553	ENSMUSG00000028878	Fam76a	-	family with sequence similarity 76, member A	protein-coding
mm_141577.1	chr17	32350570	32350600	-	1	NA	promoter-TSS (NM_017476)	promoter-TSS (NM_017476)	-8	NM_017476	54194	Mm.281005	NM_017476	ENSMUSG00000002625	Akap8l	HAP95|Nakap95	A kinase (PRKA) anchor protein 8-like	protein-coding
mm_50006.1	chr6	41058553	41058564	+	1	NA	Intergenic	Intergenic	-23049	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_61597.1	chr7	80026196	80026215	+	1	NA	promoter-TSS (NM_175433)	promoter-TSS (NM_175433)	-23	NM_175433	209225	Mm.290925	NM_175433	ENSMUSG00000048897	Zfp710	5430400N05Rik|9830165K13|AI324798|Znf710	zinc finger protein 710	protein-coding
mm_11324.1	chr2	30416097	30416147	+	1	NA	promoter-TSS (NM_007760)	promoter-TSS (NM_007760)	72	NM_138748	110854	Mm.275393	NM_138748	ENSMUSG00000039515	Ptpa	2610042B21Rik|C77440|N28142|PR53|Ppp2r4	protein phosphatase 2 protein activator	protein-coding
mm_27553.1	chr3	58372441	58372470	-	1	NA	Intergenic	Intergenic	-42265	NM_001347233	72033	Mm.218409	NM_001081229	ENSMUSG00000027806	Tsc22d2	1810043J12Rik|5530402M19Rik	TSC22 domain family, member 2	protein-coding
mm_54167.1	chr6	23132982	23132992	-	1	NA	promoter-TSS (NM_013930)	promoter-TSS (NM_013930)	-1	NM_013930	30956	Mm.18651	NM_013930	ENSMUSG00000029695	Aass	LKR|LKR/SDH|LOR|LOR/SDH|Lorsdh|SDH	aminoadipate-semialdehyde synthase	protein-coding
mm_164082.1	chr15	4119960	4119967	+	1	NA	intron (NM_024188, intron 13 of 16)	intron (NM_024188, intron 13 of 16)	-92557	NR_028266	414066	Mm.394461	NR_028266		BC037032	-	cDNA Sequence BC037032	ncRNA
mm_106366.1	chr11	118396693	118396741	-	1	NA	exon (NM_011150, exon 5 of 6)	exon (NM_011150, exon 5 of 6)	5214	NM_011150	19039	Mm.3152	NM_011150	ENSMUSG00000033880	Lgals3bp	90K|CyCAP|MAC-2BP|Ppicap|Tango10b	lectin, galactoside-binding, soluble, 3 binding protein	protein-coding
mm_3771.1	chr1	156439696	156439714	+	1	NA	exon (NM_009230, exon 9 of 16)	exon (NM_009230, exon 9 of 16)	-18790	NM_001346967	77352	Mm.428709	NM_001033180	ENSMUSG00000026601	Axdnd1	9430070O13Rik|Gm979	axonemal dynein light chain domain containing 1	protein-coding
mm_153357.1	chr19	40166978	40166981	-	1	NA	intron (NM_145499, intron 4 of 8)	intron (NM_145499, intron 4 of 8)	20307	NM_145499	226105	Mm.29119	NM_145499	ENSMUSG00000060613	Cyp2c70	-	cytochrome P450, family 2, subfamily c, polypeptide 70	protein-coding
mm_122422.1	chr14	43923593	43923598	-	1	NA	promoter-TSS (NM_053112)	promoter-TSS (NM_053112)	-227	NM_053112	93725	Mm.429087	NM_053112	ENSMUSG00000090166	Ear10	Raf2	eosinophil-associated, ribonuclease A family, member 10	protein-coding
mm_20173.1	chr2	122369131	122369154	-	1	NA	promoter-TSS (NM_001013829)	promoter-TSS (NM_001013829)	-224	NM_001013829	435684	Mm.458215	NM_001013829	ENSMUSG00000033256	Shf	-	Src homology 2 domain containing F	protein-coding
mm_40487.1	chr5	56157306	56157306	+	1	NA	Intergenic	Intergenic	1560613	NR_015588	319216	Mm.332387	NR_015588	ENSMUSG00000097216	4932441J04Rik	-	RIKEN cDNA 4932441J04 gene	ncRNA
mm_63345.1	chr7	126967570	126967597	+	1	NA	intron (NM_001252566, intron 14 of 16)	intron (NM_001252566, intron 14 of 16)	-8331	NM_026638	52858	Mm.28219	NM_026638	ENSMUSG00000030682	Cdipt	9530042F15Rik|D7Bwg0575e|Pis|Pis1	CDP-diacylglycerol--inositol 3-phosphatidyltransferase (phosphatidylinositol synthase)	protein-coding
mm_558.1	chr1	38021731	38021743	+	1	NA	exon (NM_198303, exon 5 of 24)	exon (NM_198303, exon 5 of 24)	23727	NM_198303	226982	Mm.260943	NM_198303	ENSMUSG00000026083	Eif5b	A030003E17Rik|BC018347|IF2	eukaryotic translation initiation factor 5B	protein-coding
mm_92068.1	chr10	62578198	62578229	-	1	NA	exon (NM_028197, exon 1 of 7)	exon (NM_028197, exon 1 of 7)	244	NM_028197	72320	Mm.258955	NM_028197	ENSMUSG00000036955	Kif1bp	0710007C18Rik|2510003E04Rik|KBP|mKIAA1279	KIF1 binding protein	protein-coding
mm_131127.1	chr16	5884970	5885048	+	1	NA	5' UTR (NM_021477, exon 1 of 17)	5' UTR (NM_021477, exon 1 of 17)	216	NM_021477	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_125914.1	chr15	76034698	76034714	+	1	NA	Intergenic	CpG	-20370	NM_134087	105732	Mm.267178	NM_134087	ENSMUSG00000046761	Fam83h	AA409316	family with sequence similarity 83, member H	protein-coding
mm_97119.1	chr11	74830936	74831005	+	1	NA	promoter-TSS (NM_010813)	promoter-TSS (NM_010813)	46	NM_010813	17428	Mm.3759	NM_010813	ENSMUSG00000000282	Mnt	Rox|bHLHd3	max binding protein	protein-coding
mm_3123.1	chr1	134646770	134646776	+	1	NA	promoter-TSS (NM_009307)	promoter-TSS (NM_009307)	92	NM_009307	20980	Mm.5102	NM_009307	ENSMUSG00000026452	Syt2	IP4BP|R74640|mKIAA4194	synaptotagmin II	protein-coding
mm_139266.1	chr17	47785704	47785720	+	1	NA	promoter-TSS (NM_011549)	promoter-TSS (NM_011549)	-32	NM_011549	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_58446.1	chr7	3303504	3303565	+	1	NA	promoter-TSS (NM_011102)	promoter-TSS (NM_011102)	2	NM_011102	18752	Mm.7980	NM_011102	ENSMUSG00000078816	Prkcg	PKCgamma|Pkcc|Prkcc	protein kinase C, gamma	protein-coding
mm_74504.1	chr8	8484702	8484731	-	1	NA	Intergenic	Intergenic	176057	NM_010111	13642	Mm.209813	NM_010111	ENSMUSG00000001300	Efnb2	ELF-2|Epl5|Eplg5|Htk-L|LERK-5|Lerk5|NLERK-1	ephrin B2	protein-coding
mm_134941.1	chr16	31191951	31191987	-	1	NA	intron (NM_030138, intron 1 of 22)	intron (NM_030138, intron 1 of 22)	9269	NM_030138	78618	Mm.274646	NM_030138	ENSMUSG00000049076	Acap2	4832442G16|9530039J15Rik|CNT-B2|Centb2|mKIAA0041	ArfGAP with coiled-coil, ankyrin repeat and PH domains 2	protein-coding
mm_122999.1	chr14	54992724	54992740	-	1	NA	exon (NM_080728, exon 4 of 41)	exon (NM_080728, exon 4 of 41)	1817	NM_080728	140781	Mm.457983	NM_080728	ENSMUSG00000053093	Myh7	B-MHC|MyHC-I|Myhc-b|Myhcb|beta-MHC	myosin, heavy polypeptide 7, cardiac muscle, beta	protein-coding
mm_133284.1	chr16	77432838	77432841	+	1	NA	intron (NR_015543, intron 2 of 4)	L1Md_F3|LINE|L1	103511	NR_015543	77994	Mm.394688	NR_015543	ENSMUSG00000090386	Mir99ahg	2810055G20Rik|D730043B02Rik	Mir99a and Mirlet7c-1 host gene (non-protein coding)	ncRNA
mm_46885.1	chr5	113952351	113952392	-	1	NA	intron (NM_198109, intron 11 of 14)	intron (NM_198109, intron 11 of 14)	41386	NM_198109	231637	Mm.389682	NM_198109	ENSMUSG00000042121	Ssh1	AW551225|Gm1394|Gm1395|SSH-1|SSH-1L	slingshot homolog 1 (Drosophila)	protein-coding
mm_52971.1	chr6	123229923	123229927	+	1	NA	promoter-TSS (NM_001190321)	promoter-TSS (NM_001190321)	82	NM_001190321	56620	Mm.271782	NM_020001	ENSMUSG00000023349	Clec4n	Clec6a|Clecsf10|Nkcl	C-type lectin domain family 4, member n	protein-coding
mm_43873.1	chr5	143622467	143622548	+	1	NA	promoter-TSS (NM_011182)	promoter-TSS (NM_011182)	60	NM_011182	19159	Mm.281003	NM_011182	ENSMUSG00000018001	Cyth3	AI648983|ARNO3|CLM3|Grp1|Pscd3	cytohesin 3	protein-coding
mm_55789.1	chr6	82705268	82705284	-	1	NA	Intergenic	Intergenic	-52411	NM_025882	66979	Mm.195753	NM_025882	ENSMUSG00000030042	Pole4	2400007P05Rik|5830430F06Rik	polymerase (DNA-directed), epsilon 4 (p12 subunit)	protein-coding
mm_45699.1	chr5	82124729	82124740	-	1	NA	promoter-TSS (NR_138557)	promoter-TSS (NR_138557)	-21	NR_138557	67327	Mm.87058	NR_138557		1700031L13Rik	-	RIKEN cDNA 1700031L13 gene	ncRNA
mm_157902.1	chrX	77848096	77848109	-	1	NA	exon (NM_017471, exon 2 of 7)	exon (NM_017471, exon 2 of 7)	5398	NM_017471	54192	Mm.8034	NM_017471	ENSMUSG00000000003	Pbsn	PB|Prbs	probasin	protein-coding
mm_60245.1	chr7	43768950	43768961	+	1	NA	promoter-TSS (NM_027097)	promoter-TSS (NM_027097)	-145	NM_027097	69511	Mm.20163	NM_027097	ENSMUSG00000044430	Klk12	2310008B01Rik|AI324852|KLK-L5	kallikrein related-peptidase 12	protein-coding
mm_52680.1	chr6	117922651	117922660	+	1	NA	intron (NM_133834, intron 3 of 3)	PB1D9|SINE|Alu	5361	NM_001166427	98758	Mm.422979	NM_133834	ENSMUSG00000042079	Hnrnpf	4833420I20Rik|AA407306|Hnrpf	heterogeneous nuclear ribonucleoprotein F	protein-coding
mm_89509.1	chr10	94141299	94141328	+	1	NA	intron (NM_053072, intron 20 of 20)	intron (NM_053072, intron 20 of 20)	-6618	NM_011629	22025	Mm.107483	NM_011629	ENSMUSG00000005897	Nr2c1	4831444H07Rik|80.3|Eenr|TR2|Tr2-11	nuclear receptor subfamily 2, group C, member 1	protein-coding
mm_61791.1	chr7	83891984	83892033	+	1	NA	promoter-TSS (NM_023403)	promoter-TSS (NM_023403)	8	NM_023403	67943	Mm.117365	NM_023403	ENSMUSG00000038503	Mesdc2	2210015O11Rik|AW537813|mKIAA0081|mesd|msd	mesoderm development candidate 2	protein-coding
mm_31914.1	chr4	85205210	85205228	+	1	NA	promoter-TSS (NM_019535)	promoter-TSS (NM_019535)	-237	NM_019535	20404	Mm.143603	NM_019535	ENSMUSG00000028488	Sh3gl2	9530001L19Rik|AI120490|AW555077|B930049H17Rik|EEN-B1|SH3PA|Sh3d2a	SH3-domain GRB2-like 2	protein-coding
mm_124624.1	chr15	3290848	3290862	+	1	NA	intron (NM_001166063, intron 5 of 8)	ORR1E|LTR|ERVL-MaLR	12671	NM_001166063	100039139	Mm.455610	NM_001166063	ENSMUSG00000091119	Ccdc152	ENSMUSG00000071814	coiled-coil domain containing 152	protein-coding
mm_14029.1	chr2	122152785	122152835	+	1	NA	3' UTR (NM_009735, exon 4 of 4)	3' UTR (NM_009735, exon 4 of 4)	5123	NM_009735	12010	Mm.163	NM_009735	ENSMUSG00000060802	B2m	Ly-m11|beta2-m|beta2m	beta-2 microglobulin	protein-coding
mm_163758.1	chr13	119791194	119791215	+	1	NA	promoter-TSS (NM_028245)	promoter-TSS (NM_028245)	-82	NM_001302550	72465	Mm.139115	NM_028245	ENSMUSG00000094870	Zfp131	2610109I01Rik|AW558871|Znf131	zinc finger protein 131	protein-coding
mm_170685.1	chr2	129315472	129315480	-	1	NA	Intergenic	Intergenic	-5504	NM_010554	16175	Mm.15534	NM_010554	ENSMUSG00000027399	Il1a	Il-1a	interleukin 1 alpha	protein-coding
mm_49121.1	chr6	8517810	8517849	+	1	NA	intron (NM_133236, intron 1 of 7)	RLTR16|LTR|ERVK	-2229	NM_001286728	170772	Mm.210787	NM_133236	ENSMUSG00000029638	Glcci1	2310047L21Rik|A130036A18Rik|Fam117c|Gig18|Tssn1	glucocorticoid induced transcript 1	protein-coding
mm_41178.1	chr5	88008186	88008207	+	1	NA	exon (NM_011422, exon 3 of 3)	exon (NM_011422, exon 3 of 3)	5671	NM_011422	20599	Mm.261199	NM_011422	ENSMUSG00000029280	Smr3a	AA589601|MSG1|MSG3|Smr1|Smr3	submaxillary gland androgen regulated protein 3A	protein-coding
mm_85745.1	chr9	108567581	108567595	-	1	NA	promoter-TSS (NR_029577)	promoter-TSS (NR_029577)	-246	NM_023247	66706	Mm.29471	NM_023247	ENSMUSG00000070283	Ndufaf3	4733401H18Rik	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, assembly factor 3	protein-coding
mm_101756.1	chr11	43385173	43385186	-	1	NA	Intergenic	Intergenic	-10718	NR_029558	387164		NR_029558	ENSMUSG00000065601	Mir146	Mirn146|miR-146a|mmu-mir-146	microRNA 146	ncRNA
mm_6914.1	chr1	84839480	84839490	-	1	NA	promoter-TSS (NM_025386)	promoter-TSS (NM_025386)	-181	NM_133975	14897	Mm.209265	NM_133975	ENSMUSG00000026219	Trip12	1110036I07Rik|6720416K24Rik|AA410158|Gtl6|TRIP-12	thyroid hormone receptor interactor 12	protein-coding
mm_116747.1	chr13	51793616	51793624	-	1	NA	5' UTR (NM_001281880, exon 1 of 17)	5' UTR (NM_001281880, exon 1 of 17)	127	NM_001281880	20354	Mm.33903	NM_013660	ENSMUSG00000021451	Sema4d	CD100|Semacl2|Semaj|Semcl2|coll-4	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D	protein-coding
mm_163471.1	chr12	103895082	103895087	+	1	NA	exon (NM_009245, exon 5 of 5)	exon (NM_009245, exon 5 of 5)	9866	NM_009245	20702	Mm.439692	NM_009245	ENSMUSG00000079015	Serpina1c	Pi3|Pi6|Skalp|Spi1-3|Spi1-6|Wap3	serine (or cysteine) peptidase inhibitor, clade A, member 1C	protein-coding
mm_17586.1	chr2	30415768	30415774	-	1	NA	promoter-TSS (NM_007760)	promoter-TSS (NM_007760)	-23	NM_007760	12908	Mm.20396	NM_007760	ENSMUSG00000026853	Crat	AW107812|CARAT	carnitine acetyltransferase	protein-coding
mm_47065.1	chr5	116422793	116422807	-	1	NA	promoter-TSS (NM_030704)	promoter-TSS (NM_030704)	64	NM_030704	80888	Mm.21549	NM_030704	ENSMUSG00000041548	Hspb8	AU018630|AW413033|Cryac|D5Ucla4|E2IG1|H11|H11K|HSP20-like|HSP22	heat shock protein 8	protein-coding
mm_75576.1	chr8	60983216	60983319	-	1	NA	promoter-TSS (NM_173873)	promoter-TSS (NM_173873)	44	NM_173873	12725	Mm.25263	NM_007711	ENSMUSG00000004319	Clcn3	Clc3	chloride channel, voltage-sensitive 3	protein-coding
mm_124173.1	chr14	93812279	93812312	-	1	NA	intron (NM_001346722, intron 2 of 4)	B1_Mur2|SINE|Alu	76593	NM_001271800	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding
mm_129295.1	chr15	77257669	77257672	-	1	NA	intron (NM_053104, intron 1 of 13)	intron (NM_053104, intron 1 of 13)	49383	NM_001110827	93686	Mm.202774	NM_053104	ENSMUSG00000033565	Rbfox2	Fbm2|Fxh|Hrnbp2|Rbm9	RNA binding protein, fox-1 homolog (C. elegans) 2	protein-coding
mm_121951.1	chr14	24369421	24369425	-	1	NA	Intergenic	PB1D10|SINE|Alu	76059	NM_001033214	105418	Mm.2077	NM_001033214	ENSMUSG00000038925	E330034G19Rik	AA415275|Zpac	RIKEN cDNA E330034G19 gene	protein-coding
mm_9896.1	chr1	186705564	186705598	-	1	NA	5' UTR (NM_009367, exon 1 of 7)	5' UTR (NM_009367, exon 1 of 7)	408	NM_009367	21808	Mm.18213	NM_009367	ENSMUSG00000039239	Tgfb2	BB105277|Tgf-beta2|Tgfb-2	transforming growth factor, beta 2	protein-coding
mm_102194.1	chr11	54353287	54353296	-	1	NA	intron (NM_001033597, intron 20 of 20)	intron (NM_001033597, intron 20 of 20)	-17361	NM_029105	74847	Mm.486538	NM_029105	ENSMUSG00000020332	Meikin	4930404A10Rik	meiotic kinetochore factor	protein-coding
mm_1274.1	chr1	63445716	63445765	+	1	NA	promoter-TSS (NM_011780)	promoter-TSS (NM_011780)	-151	NM_011780	23792	Mm.124892	NM_011780	ENSMUSG00000025964	Adam23	AW046396|MDC3	a disintegrin and metallopeptidase domain 23	protein-coding
mm_82325.1	chr9	8134352	8134364	-	1	NA	promoter-TSS (NM_001045524)	promoter-TSS (NM_001045524)	-64	NM_001045524	234915	Mm.101341	NM_001045524	ENSMUSG00000040729	Cep126	Kiaa1377|mKIAA1377	centrosomal protein 126	protein-coding
mm_103976.1	chr11	84823541	84823553	-	1	NA	intron (NM_177564, intron 2 of 6)	intron (NM_177564, intron 2 of 6)	-4032	NM_145433	217038	Mm.280825	NM_145433	ENSMUSG00000018405	Mrm1	A530065E19Rik|ENSMUSG00000054212	mitochondrial rRNA methyltransferase 1	protein-coding
mm_4065.1	chr1	166130216	166130231	+	1	NA	promoter-TSS (NM_021610)	promoter-TSS (NM_021610)	-237	NM_021610	59290	Mm.46357	NM_021610	ENSMUSG00000000544	Gpa33	2010310L10Rik|2210401D16Rik|BB116197	glycoprotein A33 (transmembrane)	protein-coding
mm_11755.1	chr2	38490023	38490025	+	1	NA	Intergenic	Intergenic	-21673	NM_021606	59126	Mm.143818	NM_021606	ENSMUSG00000026749	Nek6	1300007C09Rik	NIMA (never in mitosis gene a)-related expressed kinase 6	protein-coding
mm_47875.1	chr5	134688569	134688587	-	1	NA	promoter-TSS (NM_010717)	promoter-TSS (NM_010717)	12	NM_010717	16885	Mm.15409	NM_010717	ENSMUSG00000029674	Limk1	KIZ-1|LIMK-1|Limk	LIM-domain containing, protein kinase	protein-coding
mm_45388.1	chr5	66146804	66146814	-	1	NA	intron (NM_001127382, intron 2 of 7)	B2_Mm2|SINE|B2	4169	NM_001291226	245945	Mm.36863	NM_139065	ENSMUSG00000070780	Rbm47	9530077J19Rik	RNA binding motif protein 47	protein-coding
mm_68150.1	chr7	102250087	102250123	-	1	NA	promoter-TSS (NM_019566)	promoter-TSS (NM_019566)	13	NM_019566	56212	Mm.259795	NM_019566	ENSMUSG00000073982	Rhog	2810426G09Rik|Arhg|Sid10750	ras homolog family member G	protein-coding
mm_130030.1	chr15	88954401	88954446	-	1	NA	promoter-TSS (NM_172818)	promoter-TSS (NM_172818)	-5	NM_172818	239591	Mm.86807	NM_172818	ENSMUSG00000022388	Ttll8	1700019P01Rik|4933401B17	tubulin tyrosine ligase-like family, member 8	protein-coding
mm_21974.1	chr2	167349143	167349157	-	1	NA	promoter-TSS (NM_019835)	promoter-TSS (NM_019835)	28	NM_019835	56336	Mm.200886	NM_019835	ENSMUSG00000017929	B4galt5	9430078I07Rik|AW049941|AW539721	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 5	protein-coding
mm_826.1	chr1	50927512	50927543	+	1	NA	promoter-TSS (NM_019790)	promoter-TSS (NM_019790)	4	NM_019790	56363	Mm.245154	NM_019790	ENSMUSG00000026109	Tmeff2	4832418D20Rik|7630402F16Rik|TR-2	transmembrane protein with EGF-like and two follistatin-like domains 2	protein-coding
mm_36069.1	chr4	57951843	57951860	-	1	NA	exon (NM_011660, exon 2 of 5)	exon (NM_011660, exon 2 of 5)	4560	NM_011660	22166	Mm.260618	NM_011660	ENSMUSG00000028367	Txn1	ADF|AW550880|Trx1|Txn	thioredoxin 1	protein-coding
mm_118111.1	chr13	103921479	103921491	-	1	NA	promoter-TSS (NM_001289475)	promoter-TSS (NM_001289475)	-899	NM_001005868	59079	Mm.277354	NM_021563	ENSMUSG00000021709	Erbin	1700028E05Rik|Erbb2ip|mKIAA1225	Erbb2 interacting protein	protein-coding
mm_107714.1	chr12	55847728	55847731	+	1	NA	intron (NM_001037756, intron 4 of 9)	intron (NM_001037756, intron 4 of 9)	11363	NM_001037756	52592	Mm.24761	NM_027867	ENSMUSG00000012076	Brms1l	0710008O11Rik|AI159718|BRMS1|D12Ertd407e	breast cancer metastasis-suppressor 1-like	protein-coding
mm_26949.1	chr3	20270329	20270365	-	1	NA	exon (NM_029706, exon 3 of 11)	exon (NM_029706, exon 3 of 11)	5386	NM_029706	76703	Mm.34692	NM_029706	ENSMUSG00000011463	Cpb1	0910001A18Rik|1810063F02Rik|2210008M23Rik|AI504870	carboxypeptidase B1 (tissue)	protein-coding
mm_84514.1	chr9	67033904	67033960	-	1	NA	exon (NM_001164251, exon 4 of 10)	exon (NM_001164251, exon 4 of 10)	9939	NM_001164252	22003	Mm.121878	NM_024427	ENSMUSG00000032366	Tpm1	AA986836|AI854628|TM2|Tm3|Tmpa|Tpm-1|alpha-TM	tropomyosin 1, alpha	protein-coding
mm_17541.1	chr2	29787629	29787680	-	1	NA	promoter-TSS (NM_178693)	promoter-TSS (NM_178693)	17	NM_001290496	227682	Mm.245739	NM_145520	ENSMUSG00000039826	Trub2	G430055L02Rik	TruB pseudouridine (psi) synthase family member 2	protein-coding
mm_71837.1	chr8	68902322	68902334	+	1	NA	exon (NM_008509, exon 9 of 10)	exon (NM_008509, exon 9 of 10)	21773	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_126406.1	chr15	80255249	80255263	+	1	NA	promoter-TSS (NM_009716)	promoter-TSS (NM_009716)	72	NM_009716	11911	Mm.641	NM_009716	ENSMUSG00000042406	Atf4	Atf-4|C/ATF|CREB2|TAXREB67	activating transcription factor 4	protein-coding
mm_102434.1	chr11	59506393	59506408	-	1	NA	non-coding (NR_135273, exon 1 of 4)	non-coding (NR_135273, exon 1 of 4)	240	NM_001291014	268417	Mm.239793	NM_172941	ENSMUSG00000020472	Zkscan17	Nizp1|Zfp496|Znf496	zinc finger with KRAB and SCAN domains 17	protein-coding
mm_3491.1	chr1	150105880	150105890	+	1	NA	3' UTR (NM_011198, exon 10 of 10)	3' UTR (NM_011198, exon 10 of 10)	5854	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_144576.1	chr18	31881242	31881251	+	1	NA	exon (NM_028866, exon 11 of 22)	exon (NM_028866, exon 11 of 22)	30657	NM_026006	67158	Mm.31537	NM_026006	ENSMUSG00000044982	Sft2d3	2610206C24Rik|AI847965|AW046173	SFT2 domain containing 3	protein-coding
mm_153117.1	chr19	33224308	33224314	-	1	NA	intron (NM_001167818, intron 4 of 6)	intron (NM_001167818, intron 4 of 6)	167984	NM_001167818	67795	Mm.204591	NM_001146342	ENSMUSG00000071573	Rnls	6530404N21Rik|AI452315|AW060440|C10orf59	renalase, FAD-dependent amine oxidase	protein-coding
mm_38980.1	chr4	150915282	150915290	-	1	NA	Intergenic	Intergenic	-4869	NM_011612	21942	Mm.244187	NM_011612	ENSMUSG00000028965	Tnfrsf9	4-1BB|A930040I11Rik|AA408498|AI325004|CDw137|Cd137|ILA|Ly63	tumor necrosis factor receptor superfamily, member 9	protein-coding
mm_167158.1	chr7	132317393	132317403	-	1	NA	promoter-TSS (NM_029935)	promoter-TSS (NM_029935)	-243	NM_029935	77590	Mm.213582	NM_029935	ENSMUSG00000030930	Chst15	4631426J05Rik|BRAG|GalNAcS-6ST|MAd5|mKIAA0598	carbohydrate (N-acetylgalactosamine 4-sulfate 6-O) sulfotransferase 15	protein-coding
mm_59834.1	chr7	29304011	29304013	+	1	NA	promoter-TSS (NM_013874)	promoter-TSS (NM_013874)	7	NM_013874	29861	Mm.101885	NM_013874	ENSMUSG00000030584	Dpf1	Neud4	D4, zinc and double PHD fingers family 1	protein-coding
mm_57469.1	chr6	125231649	125231689	-	1	NA	TTS (NM_001042564)	TTS (NM_001042564)	191	NM_145391	213233	Mm.296902	NM_145391	ENSMUSG00000038213	Tapbpl	BC017613|TAPBPL-R|Tapbplr	TAP binding protein-like	protein-coding
mm_64369.1	chr7	142442300	142442310	+	1	NA	promoter-TSS (NM_009405)	promoter-TSS (NM_009405)	-163	NM_009405	21953	Mm.39469	NM_009405	ENSMUSG00000031097	Tnni2	-	troponin I, skeletal, fast 2	protein-coding
mm_119339.1	chr14	40972686	40972688	+	1	NA	Intergenic	Intergenic	-5791	NM_145928	52588	Mm.28876	NM_145928	ENSMUSG00000037824	Tspan14	AA958793|D14Ertd226e|Tm4sf14|tspan-14	tetraspanin 14	protein-coding
mm_114989.1	chr13	97495932	97495945	+	1	NA	non-coding (NR_110432, exon 2 of 2)	non-coding (NR_110432, exon 2 of 2)	13237	NR_110431	100039691	Mm.219358	NR_110430	ENSMUSG00000078952	Lncenc1	ENSMUSG00000078952|Gm11019|Gm2373|Lincenc1|Platr18|linc-Enc1	long non-coding RNA, embryonic stem cells expressed 1	ncRNA
mm_154279.1	chr19	60790693	60790700	-	1	NA	promoter-TSS (NM_010123)	promoter-TSS (NM_010123)	-3	NM_010123	13669	Mm.2238	NM_010123	ENSMUSG00000024991	Eif3a	A830012B05Rik|Csma|Eif3|Eif3s10|mKIAA0139	eukaryotic translation initiation factor 3, subunit A	protein-coding
mm_108639.1	chr12	85774816	85774830	+	1	NA	intron (NM_145447, intron 1 of 9)	intron (NM_145447, intron 1 of 9)	28284	NM_145447	217721	Mm.301076	NM_145447	ENSMUSG00000034258	Mfsd7c	CCT|Flvcr2	major facilitator superfamily domain containing 7C	protein-coding
mm_16862.1	chr2	11671121	11671126	-	1	NA	intron (NM_008367, intron 1 of 7)	intron (NM_008367, intron 1 of 7)	28331	NM_008367	16184	Mm.915	NM_008367	ENSMUSG00000026770	Il2ra	CD25|Il2r|Ly-43	interleukin 2 receptor, alpha chain	protein-coding
mm_68120.1	chr7	102116744	102116755	-	1	NA	promoter-TSS (NM_001081424)	promoter-TSS (NM_001081424)	-36	NM_001081424	504186	Mm.334074	NM_001081424	ENSMUSG00000066279	Chrna10	-	cholinergic receptor, nicotinic, alpha polypeptide 10	protein-coding
mm_68590.1	chr7	116034464	116034543	-	1	NA	intron (NM_001025559, intron 1 of 15)	intron (NM_001025559, intron 1 of 15)	-3456	NM_001025560	20679	Mm.323365	NM_011445	ENSMUSG00000051910	Sox6	AI987981|SOX-LZ	SRY (sex determining region Y)-box 6	protein-coding
mm_138580.1	chr17	35470760	35470762	+	1	NA	intron (NM_010391, intron 2 of 6)	CpG-6324	672	NM_010391	15007	Mm.88795	NM_010391	ENSMUSG00000067235	H2-Q10	H-2Q10|Q10|Qa10	histocompatibility 2, Q region locus 10	protein-coding
mm_151741.1	chr19	4993711	4993725	-	1	NA	Intergenic	Intergenic	-3747	NM_153553	225872	Mm.287867	NM_153553	ENSMUSG00000045903	Npas4	LE-PAS|Nxf	neuronal PAS domain protein 4	protein-coding
mm_101774.1	chr11	44496294	44496311	-	1	NA	Intergenic	Intergenic	-22662	NM_028862	74315	Mm.156771	NM_028862	ENSMUSG00000019189	Rnf145	3732413I11Rik|TMRF1	ring finger protein 145	protein-coding
mm_57850.1	chr6	129470944	129470960	-	1	NA	exon (NM_020008, exon 2 of 6)	exon (NM_020008, exon 2 of 6)	1827	NM_001309637	56644	Mm.239516	NM_020008	ENSMUSG00000079293	Clec7a	BGR|Clecsf12|beta-GR	C-type lectin domain family 7, member a	protein-coding
mm_159012.1	chr1	165916834	165916834	-	1	NA	intron (NM_198934, intron 3 of 16)	intron (NM_198934, intron 3 of 16)	18114	NM_198933	18986	Mm.245261	NM_011137	ENSMUSG00000026565	Pou2f1	2810482H01Rik|NF-A1|Oct-1|Oct1|Otf-1|Otf1	POU domain, class 2, transcription factor 1	protein-coding
mm_36672.1	chr4	96077510	96077547	-	1	NA	promoter-TSS (NM_145548)	promoter-TSS (NM_145548)	12	NM_145548	230459	Mm.268175	NM_145548	ENSMUSG00000028571	Cyp2j13	-	cytochrome P450, family 2, subfamily j, polypeptide 13	protein-coding
mm_110955.1	chr12	76710096	76710107	-	1	NA	5' UTR (NM_013675, exon 1 of 36)	5' UTR (NM_013675, exon 1 of 36)	446	NM_013675	20741	Mm.32881	NM_013675	ENSMUSG00000021061	Sptb	AI842465|D330027P03Rik|Gm1301|Spnb-1|Spnb1|ja|jaundiced|mKIAA4219	spectrin beta, erythrocytic	protein-coding
mm_69031.1	chr7	126797749	126797794	-	1	NA	exon (NM_001177307, exon 3 of 10)	exon (NM_001177307, exon 3 of 10)	1407	NM_001177307	11674	Mm.275831	NM_007438	ENSMUSG00000030695	Aldoa	Aldo-1|Aldo1	aldolase A, fructose-bisphosphate	protein-coding
mm_70909.1	chr8	25677003	25677007	+	1	NA	3' UTR (NM_001308481, exon 10 of 10)	3' UTR (NM_001308481, exon 10 of 10)	36428	NM_001081269	234135	Mm.217337	NM_001001735	ENSMUSG00000054823	Whsc1l1	6720429E03|A530023P05|AI528490|NSD3|WHISTLE	Wolf-Hirschhorn syndrome candidate 1-like 1 (human)	protein-coding
mm_114371.1	chr13	63108894	63108904	+	1	NA	intron (NM_001289926, intron 5 of 15)	intron (NM_001289926, intron 5 of 15)	-131130	NR_110520	72061	Mm.188105	NM_028079	ENSMUSG00000021458	2010111I01Rik	2300006M17Rik|AP-O|AW742919|Aopep|ApO|mir-23b|mir-24-1|mir-27b	RIKEN cDNA 2010111I01 gene	protein-coding
mm_160776.1	chr10	123263978	123263978	+	1	NA	promoter-TSS (NM_182807)	promoter-TSS (NM_182807)	-98	NM_182807	268354	Mm.51939	NM_182807	ENSMUSG00000044071	Fam19a2	6330575M02|FAM19A2 TAFA-2|TAFA2|Tafa-2	family with sequence similarity 19, member A2	protein-coding
mm_103108.1	chr11	69980275	69980290	-	1	NA	promoter-TSS (NM_026017)	promoter-TSS (NM_026017)	48	NM_001253700	54351	Mm.13430	NM_018740	ENSMUSG00000018565	Elp5	Derp6|Rai12	elongator acetyltransferase complex subunit 5	protein-coding
mm_44157.1	chr5	150522600	150522637	+	1	NA	promoter-TSS (NM_009765)	promoter-TSS (NM_009765)	-3	NM_009765	12190	Mm.236256	NM_009765	ENSMUSG00000041147	Brca2	Fancd1|RAB163	breast cancer 2, early onset	protein-coding
mm_74758.1	chr8	19142834	19142840	-	1	NA	3' UTR (NM_001034905, exon 2 of 2)	3' UTR (NM_001034905, exon 2 of 2)	2078	NM_001286493	546038	Mm.99206	NM_001034905	ENSMUSG00000059463	Spag11b	EG546038|Ep2c/h|Spag11c/h	sperm associated antigen 11B	protein-coding
mm_58235.1	chr6	145034602	145034628	-	1	NA	exon (NM_001024468, exon 4 of 11)	exon (NM_001024468, exon 4 of 11)	14197	NM_001024468	12035	Mm.4606	NM_007532	ENSMUSG00000030268	Bcat1	BCATc|Eca39	branched chain aminotransferase 1, cytosolic	protein-coding
mm_119990.1	chr14	55590986	55591006	+	1	NA	promoter-TSS (NM_011190)	promoter-TSS (NM_011190)	25	NM_011190	19188	Mm.371573	NM_011190	ENSMUSG00000079197	Psme2	AA589371|AI788882|PA28b	proteasome (prosome, macropain) activator subunit 2 (PA28 beta)	protein-coding
mm_28004.1	chr3	83010405	83010416	-	1	NA	intron (NM_001317105, intron 5 of 8)	intron (NM_001317105, intron 5 of 8)	2686	NM_001317105	99571	Mm.16422	NM_133862	ENSMUSG00000033860	Fgg	3010002H13Rik|AI256424	fibrinogen gamma chain	protein-coding
mm_20148.1	chr2	121549615	121549621	-	1	NA	intron (NM_172673, intron 13 of 14)	intron (NM_172673, intron 13 of 14)	42895	NM_001290986	241627	Mm.293284	NM_030234	ENSMUSG00000027242	Wdr76	5830411K18Rik|6030457D09|AA517836	WD repeat domain 76	protein-coding
mm_82736.1	chr9	25252372	25252387	-	1	NA	promoter-TSS (NM_001205367)	promoter-TSS (NM_001205367)	-60	NM_009859	235072	Mm.270259	NM_009859	ENSMUSG00000001833	Sept7	Cdc10|E430034N22	septin 7	protein-coding
mm_133676.1	chr16	92292381	92292397	+	1	NA	promoter-TSS (NM_134110)	promoter-TSS (NM_134110)	0	NM_134110	246133	Mm.156736	NM_134110	ENSMUSG00000039672	Kcne2	2200002I16Rik|AW048273|MiRP1	potassium voltage-gated channel, Isk-related subfamily, gene 2	protein-coding
mm_164432.1	chr16	48818660	48818666	-	1	NA	exon (NM_023881, exon 4 of 4)	exon (NM_023881, exon 4 of 4)	1807	NM_023881	57263	Mm.21123	NM_023881	ENSMUSG00000022650	Retnlb	9030012B21Rik|Fizz2|RELMbeta|Relmb|Xcp3	resistin like beta	protein-coding
mm_872.1	chr1	52155098	52155112	+	1	NA	intron (NM_001205313, intron 23 of 24)	intron (NM_001205313, intron 23 of 24)	35483	NM_001205313	20846	Mm.277406	NM_009283	ENSMUSG00000026104	Stat1	2010005J02Rik|AA408197	signal transducer and activator of transcription 1	protein-coding
mm_847.1	chr1	52008263	52008280	+	1	NA	promoter-TSS (NM_011487)	promoter-TSS (NM_011487)	31	NM_011487	20849	Mm.1550	NM_011487	ENSMUSG00000062939	Stat4	-	signal transducer and activator of transcription 4	protein-coding
mm_83186.1	chr9	40994592	40994617	-	1	NA	intron (NM_001281954, intron 1 of 9)	intron (NM_001281954, intron 1 of 9)	10024	NM_001281954	54698	Mm.42791	NM_019465	ENSMUSG00000032021	Crtam	-	cytotoxic and regulatory T cell molecule	protein-coding
mm_54638.1	chr6	38819195	38819220	-	1	NA	exon (NM_010433, exon 2 of 15)	exon (NM_010433, exon 2 of 15)	18104	NM_001136065	15258	Mm.23790	NM_010433	ENSMUSG00000061436	Hipk2	1110014O20Rik|B230339E18Rik|Stank	homeodomain interacting protein kinase 2	protein-coding
mm_78936.1	chr9	45117887	45117897	+	1	NA	promoter-TSS (NM_001014761)	promoter-TSS (NM_001014761)	16	NM_001014761	72821	Mm.229373	NM_001014761	ENSMUSG00000070304	Scn2b	2810451E09Rik|AI840361|Gm183	sodium channel, voltage-gated, type II, beta	protein-coding
mm_107936.1	chr12	71831065	71831178	+	1	NA	promoter-TSS (NM_026102)	promoter-TSS (NM_026102)	53	NM_172464	208846	Mm.87417	NM_026102	ENSMUSG00000034574	Daam1	-	dishevelled associated activator of morphogenesis 1	protein-coding
mm_145727.1	chr18	64190503	64190520	+	1	NA	intron (NR_045366, intron 2 of 5)	intron (NR_045366, intron 2 of 5)	-63848	NM_009182	20451	Mm.252110	NM_009182	ENSMUSG00000056812	St8sia3	AI847333|ST8SiaIII|Siat8c	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3	protein-coding
mm_65552.1	chr7	27133269	27133288	-	1	NA	exon (NM_007817, exon 10 of 10)	exon (NM_007817, exon 10 of 10)	13323	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_15635.1	chr2	163007461	163007463	+	1	NA	intron (NM_001291154, intron 12 of 12)	intron (NM_001291154, intron 12 of 12)	-10010	NM_172150	245866	Mm.34034	NM_172150	ENSMUSG00000017858	Ift52	BC037708|NGD5	intraflagellar transport 52	protein-coding
mm_22487.1	chr3	5575880	5575913	+	1	NA	intron (NM_001163305, intron 1 of 4)	CpG	352	NM_001163301	19302	Mm.132336	NM_008994	ENSMUSG00000040374	Pex2	D3Ertd138e|PAF-1|PMP35|Pxmp3	peroxisomal biogenesis factor 2	protein-coding
mm_65550.1	chr7	27131292	27131322	-	1	NA	exon (NM_007817, exon 8 of 10)	exon (NM_007817, exon 8 of 10)	11352	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_62194.1	chr7	97724132	97724140	+	1	NA	Intergenic	ORR1D2|LTR|ERVL-MaLR	14111	NM_175105	66333	Mm.29756	NM_175105	ENSMUSG00000042797	Aqp11	1700015P13Rik|AI648923|sjds	aquaporin 11	protein-coding
mm_11781.1	chr2	39008044	39008071	+	1	NA	promoter-TSS (NM_028809)	promoter-TSS (NM_028809)	-82	NM_028809	74192	Mm.38155	NM_028809	ENSMUSG00000026755	Arpc5l	2010015J01Rik|AI852867|ARC16-2|AW555592|AW742746	actin related protein 2/3 complex, subunit 5-like	protein-coding
mm_123433.1	chr14	64440965	64440981	-	1	NA	promoter-TSS (NM_001253715)	promoter-TSS (NM_001253715)	53	NM_001253715	110265	Mm.26713	NM_026322	ENSMUSG00000054733	Msra	2310045J23Rik|6530413P12Rik|MSR-A	methionine sulfoxide reductase A	protein-coding
mm_105116.1	chr11	101095368	101095439	-	1	NA	promoter-TSS (NM_008949)	promoter-TSS (NM_008949)	32	NM_008949	19183	Mm.18344	NM_008949	ENSMUSG00000019303	Psmc3ip	C79099|GT198|HOP2|Tbpip	proteasome (prosome, macropain) 26S subunit, ATPase 3, interacting protein	protein-coding
mm_19218.1	chr2	84650491	84650544	-	1	NA	promoter-TSS (NM_001085453)	promoter-TSS (NM_001085453)	-7	NM_001085453	12388	Mm.35738	NM_007615	ENSMUSG00000034101	Ctnnd1	AA409437|AU019353|Catns|Ctnnd|P120|mKIAA0384	catenin (cadherin associated protein), delta 1	protein-coding
mm_62560.1	chr7	103826530	103826540	+	1	NA	TTS (NM_001278161)	TTS (NM_001278161)	1393	NM_001201391	100503605	Mm.288567	NM_001201391	ENSMUSG00000052305	Hbb-bs	Beta-s|Hbbt1|Hbbt2	hemoglobin, beta adult s chain	protein-coding
mm_25494.1	chr3	109340732	109340743	+	1	NA	promoter-TSS (NM_020505)	promoter-TSS (NM_020505)	54	NM_020505	57257	Mm.282257	NM_020505	ENSMUSG00000033721	Vav3	A530094I06Rik|AA986410|Idd18.1	vav 3 oncogene	protein-coding
mm_156995.1	chrX	7422978	7422996	-	1	NA	promoter-TSS (NR_027924)	promoter-TSS (NR_027924)	1	NR_027924	68355	Mm.45111	NR_027924		2010204K13Rik	0610010M13Rik|Cip7	RIKEN cDNA 2010204K13 gene	ncRNA
mm_52228.1	chr6	103512063	103512084	+	1	NA	intron (NM_007697, intron 1 of 26)	intron (NM_007697, intron 1 of 26)	1197	NM_007697	12661	Mm.251288	NM_007697	ENSMUSG00000030077	Chl1	A530023M13Rik|AI465420|CALL|LICAM2	cell adhesion molecule L1-like	protein-coding
mm_29852.1	chr3	129995641	129995653	-	1	NA	intron (NM_207209, intron 14 of 23)	intron (NM_207209, intron 14 of 23)	-25441	NM_001293644	66815	Mm.31056	NM_025779	ENSMUSG00000027994	Ccdc109b	9030408N13Rik|MCUb	coiled-coil domain containing 109B	protein-coding
mm_62813.1	chr7	113237319	113237323	+	1	NA	intron (NM_001243048, intron 2 of 16)	intron (NM_001243048, intron 2 of 16)	29856	NM_007489	11865	Mm.33970	NM_007489	ENSMUSG00000055116	Arntl	Arnt3|BMAL1b|Bmal1|MOP3|bHLHe5|bmal1b'	aryl hydrocarbon receptor nuclear translocator-like	protein-coding
mm_99178.1	chr11	100860112	100860116	+	1	NA	promoter-TSS (NM_001164062)	promoter-TSS (NM_001164062)	-370	NM_001164062	20850	Mm.277403	NM_011488	ENSMUSG00000004043	Stat5a	AA959963|STAT5	signal transducer and activator of transcription 5A	protein-coding
mm_62260.1	chr7	99334812	99334812	+	1	NA	intron (NM_010837, intron 3 of 3)	intron (NM_010837, intron 3 of 3)	18427	NM_009825	12406	Mm.22708	NM_009825	ENSMUSG00000070436	Serpinh1	BERF-1|Cbp1|Cbp2|Hsp47|J6|Serpinh2|gp46	serine (or cysteine) peptidase inhibitor, clade H, member 1	protein-coding
mm_115309.1	chr13	112318390	112318405	+	1	NA	intron (NM_001168403, intron 2 of 11)	intron (NM_001168403, intron 2 of 11)	29879	NM_001168404	77318	Mm.159895	NM_029898	ENSMUSG00000049985	Ankrd55	C030011J08Rik	ankyrin repeat domain 55	protein-coding
mm_77643.1	chr8	124434324	124434372	-	1	NA	promoter-TSS (NM_171824)	promoter-TSS (NM_171824)	-412	NM_171824	209966	Mm.234233	NM_171824	ENSMUSG00000050751	Pgbd5	2900019M05Rik|AI854313	piggyBac transposable element derived 5	protein-coding
mm_107331.1	chr12	32017904	32017917	+	1	NA	intron (NM_011158, intron 2 of 10)	intron (NM_011158, intron 2 of 10)	43369	NM_011158	19088	Mm.25594	NM_011158	ENSMUSG00000002997	Prkar2b	AI451071|AW061005|PKARIIbeta|Pkarb2|RII(beta)	protein kinase, cAMP dependent regulatory, type II beta	protein-coding
mm_151052.1	chr19	47090811	47090813	+	1	NA	promoter-TSS (NM_011053)	promoter-TSS (NM_011053)	46	NM_011053	18572	Mm.41166	NM_011053	ENSMUSG00000025047	Pdcd11	1110021I22Rik|ALG-4|Pdcd7|mKIAA0185	programmed cell death 11	protein-coding
mm_30623.1	chr4	8711765	8711767	+	1	NA	intron (NM_001277149, intron 1 of 37)	intron (NM_001277149, intron 1 of 37)	21360	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_130413.1	chr15	97977903	97977920	-	1	NA	exon (NM_001113515, exon 50 of 53)	exon (NM_001113515, exon 50 of 53)	13682	NM_001252153	380967	Mm.196630	NM_201359	ENSMUSG00000052369	Tmem106c	AI046681|BC046621|D15Ertd405e	transmembrane protein 106C	protein-coding
mm_63619.1	chr7	128246954	128246993	+	1	NA	5' UTR (NM_001289552, exon 1 of 10)	5' UTR (NM_001289552, exon 1 of 10)	161	NM_001289552	21804	Mm.3248	NM_009365	ENSMUSG00000030782	Tgfb1i1	ARA55|Hic5|TSC-5|hic-5	transforming growth factor beta 1 induced transcript 1	protein-coding
mm_65309.1	chr7	24765931	24765938	-	1	NA	Intergenic	Intergenic	-5623	NM_026862	68891	Mm.292848	NM_026862	ENSMUSG00000052212	Cd177	1190003K14Rik|Pdp3	CD177 antigen	protein-coding
mm_143143.1	chr17	57221082	57221094	-	1	NA	exon (NM_009778, exon 17 of 41)	exon (NM_009778, exon 17 of 41)	-3860	NR_105944	102465591		NR_105944	ENSMUSG00000099066	Mir6978	Gm27858|mmu-mir-6978	microRNA 6978	ncRNA
mm_138524.1	chr17	35241786	35241837	+	1	NA	promoter-TSS (NM_019693)	promoter-TSS (NM_019693)	65	NM_019693	53817	Mm.439827	NM_019693	ENSMUSG00000019432	Ddx39b	0610030D10Rik|AI428441|Bat-1|Bat1|Bat1a|D17H6S81E|D17H6S81E-1|D6S81Eh	DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B	protein-coding
mm_13987.1	chr2	121621418	121621426	+	1	NA	intron (NM_172673, intron 1 of 14)	intron (NM_172673, intron 1 of 14)	114699	NM_001290986	241627	Mm.293284	NM_030234	ENSMUSG00000027242	Wdr76	5830411K18Rik|6030457D09|AA517836	WD repeat domain 76	protein-coding
mm_168774.1	chr12	17464331	17464334	-	1	NA	Intergenic	MMERVK9E_I-int|LTR|ERVK	-80541	NM_013614	18263	Mm.34102	NM_013614	ENSMUSG00000011179	Odc1	ODC	ornithine decarboxylase, structural 1	protein-coding
mm_27011.1	chr3	25893544	25893554	-	1	NA	intron (NM_001163387, intron 3 of 5)	intron (NM_001163387, intron 3 of 5)	259758	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_65770.1	chr7	28761706	28761728	-	1	NA	exon (NM_010908, exon 3 of 7)	exon (NM_010908, exon 3 of 7)	4927	NM_001306222	18036	Mm.220333	NM_010908	ENSMUSG00000030595	Nfkbib	I(Kappa)B(beta)|I-kappa-B-beta|IKB-beta|IKappaBbeta|IkB|IkBb|NF-kappa-BIB|ikB-B	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, beta	protein-coding
mm_110773.1	chr12	70347301	70347360	-	1	NA	5' UTR (NM_001110203, exon 1 of 9)	5' UTR (NM_001110203, exon 1 of 9)	284	NM_001286386	94090	Mm.184012	NM_053167	ENSMUSG00000021071	Trim9	-	tripartite motif-containing 9	protein-coding
mm_77034.1	chr8	109565693	109565703	-	1	NA	promoter-TSS (NM_178380)	promoter-TSS (NM_178380)	-97	NM_178380	64340	Mm.23705	NM_178380	ENSMUSG00000037993	Dhx38	5730550P09Rik|AI325984|AW540902|Ddx38|Prp16|mKIAA0224	DEAH (Asp-Glu-Ala-His) box polypeptide 38	protein-coding
mm_172432.1	chr7	28981786	28981786	-	1	NA	5' UTR (NM_028659, exon 1 of 8)	5' UTR (NM_028659, exon 1 of 8)	102	NM_001285943	73830	Mm.29714	NM_028659	ENSMUSG00000053565	Eif3k	1200009C21Rik|Eif3s12	eukaryotic translation initiation factor 3, subunit K	protein-coding
mm_39255.1	chr5	3522261	3522265	+	1	NA	3' UTR (NM_009873, exon 8 of 8)	3' UTR (NM_009873, exon 8 of 8)	-21570	NM_001042501	68152	Mm.240265	NM_026583	ENSMUSG00000058503	Fam133b	2900022K02Rik|5830415L20Rik	family with sequence similarity 133, member B	protein-coding
mm_151531.1	chr19	58759686	58759698	+	1	NA	promoter-TSS (NM_011128)	promoter-TSS (NM_011128)	-31	NM_011128	18947	Mm.212333	NM_011128	ENSMUSG00000025091	Pnliprp2	PLRP2	pancreatic lipase-related protein 2	protein-coding
mm_29077.1	chr3	103914179	103914186	-	1	NA	promoter-TSS (NM_172684)	promoter-TSS (NM_172684)	62	NM_172684	229675	Mm.29366	NM_172684	ENSMUSG00000044098	Rsbn1	C230004D03Rik|E330004N01|Rosbin|Rsbn|Rsbp|mKIAA3002	rosbin, round spermatid basic protein 1	protein-coding
mm_116782.1	chr13	53184119	53184123	-	1	NA	intron (NM_013846, intron 1 of 8)	RLTR41|LTR|ERV1	101988	NM_013846	26564	Mm.342774	NM_013846	ENSMUSG00000021464	Ror2	Ntrkr2|mRor2	receptor tyrosine kinase-like orphan receptor 2	protein-coding
mm_46263.1	chr5	99729040	99729112	-	1	NA	promoter-TSS (NR_030692)	promoter-TSS (NR_030692)	-16	NR_030692	319818	Mm.295233	NR_030692	ENSMUSG00000089809	A930011G23Rik	-	RIKEN cDNA A930011G23 gene	ncRNA
mm_54161.1	chr6	23098068	23098077	-	1	NA	intron (NM_013930, intron 11 of 23)	intron (NM_013930, intron 11 of 23)	34914	NM_013930	30956	Mm.18651	NM_013930	ENSMUSG00000029695	Aass	LKR|LKR/SDH|LOR|LOR/SDH|Lorsdh|SDH	aminoadipate-semialdehyde synthase	protein-coding
mm_39074.1	chr4	154299852	154299919	-	1	NA	promoter-TSS (NM_001112744)	promoter-TSS (NM_001112744)	10	NM_001112744	230972	Mm.38481	NM_001112744	ENSMUSG00000029032	Arhgef16	-	Rho guanine nucleotide exchange factor (GEF) 16	protein-coding
mm_17551.1	chr2	30093562	30093603	-	1	NA	promoter-TSS (NM_025428)	promoter-TSS (NM_025428)	53	NM_025428	66220	Mm.22538	NM_025428	ENSMUSG00000015335	Zdhhc12	1190004A01Rik	zinc finger, DHHC domain containing 12	protein-coding
mm_14279.1	chr2	128796918	128796935	+	1	NA	intron (NM_008587, intron 18 of 18)	intron (NM_008587, intron 18 of 18)	-21377	NM_028248	72477	Mm.259688	NM_028248	ENSMUSG00000014353	Tmem87b	2610301K12Rik|2810431I02Rik|AU014804	transmembrane protein 87B	protein-coding
mm_74259.1	chr8	124897274	124897297	+	1	NA	promoter-TSS (NM_001111141)	promoter-TSS (NM_001111141)	420	NM_198103	102058	Mm.347360	NM_198103	ENSMUSG00000074030	Exoc8	AI414418|EXO84|Exo84p|R74783|SEC84	exocyst complex component 8	protein-coding
mm_87813.1	chr10	60302016	60302024	+	1	NA	TTS (NM_001252635)	TTS (NM_001252635)	17559	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_60961.1	chr7	47699965	47699968	+	1	NA	Intergenic	Intergenic	-98594	NM_153067	233222	Mm.240142	NM_153067	ENSMUSG00000078698	Mrgpra3	Mrga3	MAS-related GPR, member A3	protein-coding
mm_97986.1	chr11	83942112	83942132	+	1	NA	promoter-TSS (NM_030096)	promoter-TSS (NM_030096)	32	NM_030096	78394	Mm.280544	NM_030096	ENSMUSG00000020677	Ddx52	2700029C06Rik|ROK1	DEAD (Asp-Glu-Ala-Asp) box polypeptide 52	protein-coding
mm_1695.1	chr1	75142763	75142773	+	1	NA	promoter-TSS (NM_026977)	promoter-TSS (NM_026977)	-18	NM_170755	227298	Mm.273062	NM_170755	ENSMUSG00000049339	Fam134a	-	family with sequence similarity 134, member A	protein-coding
mm_170582.1	chr19	5742434	5742434	+	1	NA	exon (NM_008520, exon 2 of 28)	exon (NM_008520, exon 2 of 28)	1530	NM_008520	16998	Mm.182396	NM_008520	ENSMUSG00000024940	Ltbp3	Ltbp2|mFLJ00070	latent transforming growth factor beta binding protein 3	protein-coding
mm_162282.1	chr1	20606081	20606084	+	1	NA	intron (NM_153179, intron 5 of 66)	intron (NM_153179, intron 5 of 66)	11975	NM_153179	241035	Mm.249253	NM_153179	ENSMUSG00000043760	Pkhd1	AI118496|AI182499|FPC|Tigm1	polycystic kidney and hepatic disease 1	protein-coding
mm_86423.1	chr10	3740645	3740671	+	1	NA	intron (NM_001159942, intron 1 of 16)	CpG	281	NM_001159942	213783	Mm.150831	NM_001033253	ENSMUSG00000040624	Plekhg1	D10Ertd733e|Gm521|mKIAA1209	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	protein-coding
mm_50355.1	chr6	48598684	48598688	+	1	NA	3' UTR (NM_001079905, exon 2 of 2)	3' UTR (NM_001079905, exon 2 of 2)	4803	NM_001079904	58887	Mm.219183	NM_175099	ENSMUSG00000052751	Repin1	AI425994|Ap4|E430037F08Rik|Zfp-464|Zfp464	replication initiator 1	protein-coding
mm_42609.1	chr5	117842114	117842167	+	1	NA	Intergenic	CpG	-24699	NM_008712	18125	Mm.44249	NM_008712	ENSMUSG00000029361	Nos1	2310005C01Rik|N-NOS|NC-NOS|NO|NOS|NOS-I|Nos-1|bNOS|nNOS	nitric oxide synthase 1, neuronal	protein-coding
mm_167568.1	chr9	42296823	42296831	+	1	NA	Intergenic	Intergenic	-32527	NM_172769	235293	Mm.32700	NM_172769	ENSMUSG00000032018	Sc5d	A830037K02|A830073K23Rik|Sc5dl	sterol-C5-desaturase	protein-coding
mm_134718.1	chr16	22896558	22896566	-	1	NA	exon (NM_001276450, exon 5 of 7)	exon (NM_001276450, exon 5 of 7)	-2176	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_55031.1	chr6	48951455	48951458	-	1	NA	Intergenic	Lx8b|LINE|L1	21560	NM_001081273	69761	Mm.333053	NM_001081273	ENSMUSG00000029813	1600015I10Rik	AI429442|Doxl1	RIKEN cDNA 1600015I10 gene	protein-coding
mm_155616.1	chrX	83087800	83087800	+	1	NA	intron (NM_007868, intron 1 of 78)	MER31A|LTR|ERV1	138930	NM_007868	13405	Mm.275608	NM_007868	ENSMUSG00000045103	Dmd	DXSmh7|DXSmh9|Dp427|Dp71|dys|mdx|pke	dystrophin, muscular dystrophy	protein-coding
mm_15726.1	chr2	164084607	164084619	+	1	NA	intron (NM_021420, intron 3 of 10)	intron (NM_021420, intron 3 of 10)	10435	NM_021420	58231	Mm.234472	NM_021420	ENSMUSG00000018209	Stk4	AI447339|AU020804|Kas-2|Mst1|Ysk3	serine/threonine kinase 4	protein-coding
mm_111611.1	chr12	102401561	102401571	-	1	NA	intron (NM_011175, intron 8 of 13)	B3A|SINE|B2	38247	NM_011175	19141	Mm.17185	NM_011175	ENSMUSG00000021190	Lgmn	AEP|AI746452|AU022324|Prsc1	legumain	protein-coding
mm_88235.1	chr10	71347779	71347813	+	1	NA	promoter-TSS (NM_001347191)	promoter-TSS (NM_001347191)	33	NM_027184	69718	Mm.245867	NM_027184	ENSMUSG00000060733	Ipmk	2410017C19Rik|AA408208|Impk	inositol polyphosphate multikinase	protein-coding
mm_32929.1	chr4	119195513	119195515	+	1	NA	promoter-TSS (NM_001038998)	promoter-TSS (NM_001038998)	-11	NM_001038998	69216	Mm.36697	NM_024462	ENSMUSG00000028643	Svbp	2410005K17Rik|AI851162|Ccdc23	small vasohibin binding protein	protein-coding
mm_150495.1	chr19	39016751	39016761	+	1	NA	intron (NM_028089, intron 3 of 8)	MER74B|LTR|ERVL	9737	NM_028089	72082	Mm.142581	NM_028089	ENSMUSG00000025002	Cyp2c55	2010318C06Rik	cytochrome P450, family 2, subfamily c, polypeptide 55	protein-coding
mm_165374.1	chr2	128307006	128307010	+	1	NA	intron (NR_028589, intron 2 of 2)	intron (NR_028589, intron 2 of 2)	122343	NR_028591	100043424	Mm.297222	NR_028589		Gm14005	OTTMUSG00000015351	predicted gene 14005	ncRNA
mm_135916.1	chr16	67606000	67606005	-	1	NA	intron (NM_178721, intron 1 of 9)	intron (NM_178721, intron 1 of 9)	14906	NM_001347247	239857	Mm.394300	NM_178721	ENSMUSG00000064115	Cadm2	2900078E11Rik|9330131D06|A830029E02Rik|Igdf4d|Igsf4d|NECL3|SynCAM 2|SynCAM2	cell adhesion molecule 2	protein-coding
mm_167206.1	chr7	144284413	144284424	+	1	NA	promoter-TSS (NM_001081370)	promoter-TSS (NM_001081370)	33	NM_001081370	210274	Mm.483624	NM_001081370	ENSMUSG00000037541	Shank2	ProSAP1|mKIAA1022	SH3/ankyrin domain gene 2	protein-coding
mm_161573.1	chr16	22163282	22163282	-	1	NA	promoter-TSS (NM_183029)	promoter-TSS (NM_183029)	17	NM_183029	319765	Mm.489442	NM_183029	ENSMUSG00000033581	Igf2bp2	C330012H03Rik|IMP-2|Imp2|Neilsen	insulin-like growth factor 2 mRNA binding protein 2	protein-coding
mm_156376.1	chrX	139671922	139671933	+	1	NA	3' UTR (NM_023270, exon 7 of 7)	3' UTR (NM_023270, exon 7 of 7)	-13069	NM_001081499	245638	Mm.275869	NM_001081499	ENSMUSG00000042473	Tbc1d8b	4921505D17Rik|9030605E16Rik	TBC1 domain family, member 8B	protein-coding
mm_137292.1	chr17	24752942	24752954	+	1	NA	promoter-TSS (NM_001012402)	promoter-TSS (NM_001012402)	-55	NM_001012402	328779	Mm.328848	NM_001012402	ENSMUSG00000039628	Hs3st6	3-OST-6	heparan sulfate (glucosamine) 3-O-sulfotransferase 6	protein-coding
mm_117806.1	chr13	97482577	97482598	-	1	NA	promoter-TSS (NR_110431)	promoter-TSS (NR_110431)	-114	NR_110430	100039691	Mm.219358	NR_110430	ENSMUSG00000078952	Lncenc1	ENSMUSG00000078952|Gm11019|Gm2373|Lincenc1|Platr18|linc-Enc1	long non-coding RNA, embryonic stem cells expressed 1	ncRNA
mm_13484.1	chr2	106304738	106304754	+	1	NA	Intergenic	(CAGT)n|Simple_repeat|Simple_repeat	218357	NR_040637	329483	Mm.246777	NR_040637	ENSMUSG00000087226	Gm14015	9330126M15|OTTMUSG00000015366	predicted gene 14015	ncRNA
mm_152807.1	chr19	22340716	22340719	-	1	NA	intron (NM_001035243, intron 1 of 23)	intron (NM_001035243, intron 1 of 23)	-107491	NM_177341	226025	Mm.131943	NM_177341	ENSMUSG00000052387	Trpm3	6330504P12Rik|9330180E14|AU018608|B930001P07Rik|LTRPC3|MLSN2	transient receptor potential cation channel, subfamily M, member 3	protein-coding
mm_159819.1	chr5	122138062	122138062	-	1	NA	promoter-TSS (NM_183307)	promoter-TSS (NM_183307)	0	NM_183307	330188	Mm.386907	NM_183307	ENSMUSG00000043036	Ccdc63	4921511C16Rik	coiled-coil domain containing 63	protein-coding
mm_121437.1	chr14	120418880	120418895	+	1	NA	intron (NM_175341, intron 8 of 8)	intron (NM_175341, intron 8 of 8)	-59574	NM_029519	76108	Mm.261448	NM_029519	ENSMUSG00000051615	Rap2a	5830461H18Rik	RAS related protein 2a	protein-coding
mm_130122.1	chr15	89568243	89568257	-	1	NA	promoter-TSS (NM_013455)	promoter-TSS (NM_013455)	-76	NM_013455	11434	Mm.57	NM_013455	ENSMUSG00000022622	Acr	-	acrosin prepropeptide	protein-coding
mm_160680.1	chr10	14545056	14545056	-	1	NA	promoter-TSS (NM_001002268)	promoter-TSS (NM_001002268)	-20	NM_001002268	215798	Mm.440142	NM_001002268	ENSMUSG00000039116	Adgrg6	1190004A11Rik|AI449247|AW045736|DREG|Gm222|Gpr126	adhesion G protein-coupled receptor G6	protein-coding
mm_132427.1	chr16	35661111	35661112	+	1	NA	intron (NM_013661, intron 17 of 21)	intron (NM_013661, intron 17 of 21)	108245	NM_153550	224132	Mm.24094	NM_153550	ENSMUSG00000022848	Dirc2	RCC4	disrupted in renal carcinoma 2 (human)	protein-coding
mm_32372.1	chr4	105718907	105718928	+	1	NA	Intergenic	Intergenic	561570	NM_080555	67916	Mm.348326	NM_080555	ENSMUSG00000028517	Plpp3	1110003O22Rik|2610002D05Rik|AV025606|D4Bwg0538e|D4Bwg1535e|Lpp3|Ppab2b|Ppap2b	phospholipid phosphatase 3	protein-coding
mm_58629.1	chr7	5083704	5083740	+	1	NA	5' UTR (NM_010147, exon 3 of 12)	5' UTR (NM_010147, exon 3 of 12)	3487	NM_001252454	13854	Mm.3091	NM_010147	ENSMUSG00000035203	Epn1	AA269831|Ibp1	epsin 1	protein-coding
mm_29374.1	chr3	108722143	108722201	-	1	NA	5' UTR (NM_029522, exon 1 of 15)	5' UTR (NM_029522, exon 1 of 15)	127	NM_029522	76123	Mm.226941	NM_029522	ENSMUSG00000027883	Gpsm2	6230410J09Rik|LGN|Pins	G-protein signalling modulator 2 (AGS3-like, C. elegans)	protein-coding
mm_80046.1	chr9	69289842	69289849	+	1	NA	promoter-TSS (NM_001289916)	promoter-TSS (NM_001289916)	4	NM_001289916	19883	Mm.378450	NM_013646	ENSMUSG00000032238	Rora	9530021D13Rik|Nr1f1|ROR1|ROR2|ROR3|nmf267|sg|staggerer|tmgc26	RAR-related orphan receptor alpha	protein-coding
mm_70407.1	chr8	11354319	11354330	+	1	NA	exon (NM_009932, exon 4 of 48)	exon (NM_009932, exon 4 of 48)	-41498	NM_009931	12826	Mm.738	NM_009931	ENSMUSG00000031502	Col4a1	Bru|Col4a-1|Raw|Svc	collagen, type IV, alpha 1	protein-coding
mm_127957.1	chr15	11720559	11720564	-	1	NA	Intergenic	Intergenic	185113	NM_008728	18162	Mm.25259	NM_008728	ENSMUSG00000022206	Npr3	ANP-C|ANPR-C|EF-2|NPR-C|lgj|stri	natriuretic peptide receptor 3	protein-coding
mm_90476.1	chr10	127866458	127866496	+	1	NA	promoter-TSS (NM_145424)	promoter-TSS (NM_145424)	1	NM_145424	216454	Mm.214923	NM_145424	ENSMUSG00000074639	BC089597	CRAD-L	cDNA sequence BC089597	protein-coding
mm_129298.1	chr15	77306880	77306927	-	1	NA	5' UTR (NM_175387, exon 1 of 13)	5' UTR (NM_175387, exon 1 of 13)	150	NM_001110827	93686	Mm.202774	NM_053104	ENSMUSG00000033565	Rbfox2	Fbm2|Fxh|Hrnbp2|Rbm9	RNA binding protein, fox-1 homolog (C. elegans) 2	protein-coding
mm_26238.1	chr3	141465180	141465223	+	1	NA	promoter-TSS (NM_009472)	promoter-TSS (NM_009472)	-363	NM_009472	22253	Mm.24430	NM_009472	ENSMUSG00000059921	Unc5c	B130051O18Rik|Unc5h3|rcm	unc-5 netrin receptor C	protein-coding
mm_88316.1	chr10	75532009	75532026	+	1	NA	intron (NM_026095, intron 2 of 3)	intron (NM_026095, intron 2 of 3)	13975	NM_026095	67332	Mm.45151	NM_026095	ENSMUSG00000020180	Snrpd3	1700043E15Rik|2310009E13Rik|AW046420|SMD3	small nuclear ribonucleoprotein D3	protein-coding
mm_6905.1	chr1	84837797	84837809	-	1	NA	intron (NM_133975, intron 1 of 40)	intron (NM_133975, intron 1 of 40)	1501	NM_133975	14897	Mm.209265	NM_133975	ENSMUSG00000026219	Trip12	1110036I07Rik|6720416K24Rik|AA410158|Gtl6|TRIP-12	thyroid hormone receptor interactor 12	protein-coding
mm_33179.1	chr4	126058616	126058624	+	1	NA	promoter-TSS (NM_172701)	promoter-TSS (NM_172701)	55	NM_172701	230751	Mm.38907	NM_172701	ENSMUSG00000042616	Oscp1	1810007P19Rik|5730415O04|6030436A01Rik	organic solute carrier partner 1	protein-coding
mm_52894.1	chr6	122626419	122626420	+	1	NA	promoter-TSS (NM_139218)	promoter-TSS (NM_139218)	-5	NM_139218	73708	Mm.27982	NM_139218	ENSMUSG00000046323	Dppa3	2410075G02Rik|PCG7|PGC7|Stella	developmental pluripotency-associated 3	protein-coding
mm_110943.1	chr12	76612663	76612669	-	1	NA	exon (NM_013675, exon 16 of 36)	exon (NM_013675, exon 16 of 36)	-64741	NR_046044	100504549	Mm.440349	NR_046044		AI463170	-	expressed sequence AI463170	ncRNA
mm_80679.1	chr9	90351993	90351998	+	1	NA	Intergenic	Intergenic	-81226	NM_194334	67016	Mm.335347	NM_194334	ENSMUSG00000037410	Tbc1d2b	1810061M12Rik|AI480956|AV021536|AV023399|AW491493|mKIAA1055	TBC1 domain family, member 2B	protein-coding
mm_156148.1	chrX	129869819	129869823	+	1	NA	intron (NM_172493, intron 4 of 26)	MTE2b|LTR|ERVL-MaLR	120079	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diaph2	Dia3|Diap2|Drf2|E430022I22Rik	diaphanous related formin 2	protein-coding
mm_91130.1	chr10	19594689	19594701	-	1	NA	intron (NM_010511, intron 1 of 6)	intron (NM_010511, intron 1 of 6)	2746	NM_010511	15979	Mm.549	NM_010511	ENSMUSG00000020009	Ifngr1	CD119|IFN-gammaR|Ifgr|Ifngr|Nktar	interferon gamma receptor 1	protein-coding
mm_134516.1	chr16	19200351	19200354	-	1	NA	Intergenic	Intergenic	86389	NM_146451	258443	Mm.377506	NM_146451	ENSMUSG00000050742	Olfr164	MOR279-2	olfactory receptor 164	protein-coding
mm_87101.1	chr10	33157066	33157112	+	1	NA	exon (NM_029726, exon 3 of 38)	exon (NM_029726, exon 3 of 38)	73606	NM_029726	76757	Mm.338508	NM_029726	ENSMUSG00000019787	Trdn	2310045H21Rik|EG432451|TDN	triadin	protein-coding
mm_92346.1	chr10	75859966	75860039	-	1	NA	intron (NM_010798, intron 1 of 2)	CpG-1170	248	NM_010798	17319	Mm.2326	NM_010798	ENSMUSG00000033307	Mif	GIF|Glif	macrophage migration inhibitory factor	protein-coding
mm_57023.1	chr6	122282589	122282628	-	1	NA	intron (NM_016970, intron 1 of 4)	intron (NM_016970, intron 1 of 4)	225	NM_016970	50928	Mm.20434	NM_016970	ENSMUSG00000030114	Klrg1	2F1-Ag|MAFA|MAFA-L	killer cell lectin-like receptor subfamily G, member 1	protein-coding
mm_153044.1	chr19	32068736	32068757	-	1	NA	intron (NM_018830, intron 2 of 23)	intron (NM_018830, intron 2 of 23)	34394	NM_018830	54447	Mm.491229	NM_018830	ENSMUSG00000024887	Asah2	AI585898	N-acylsphingosine amidohydrolase 2	protein-coding
mm_44889.1	chr5	35093106	35093122	-	1	NA	3' UTR (NM_013587, exon 8 of 8)	3' UTR (NM_013587, exon 8 of 8)	12583	NM_013587	16976	Mm.277661	NM_013587	ENSMUSG00000029103	Lrpap1	AA617339|AI790446|AU042172|C77774|HBP44|RAP	low density lipoprotein receptor-related protein associated protein 1	protein-coding
mm_45920.1	chr5	89441636	89441647	-	1	NA	exon (NM_008096, exon 5 of 13)	exon (NM_008096, exon 5 of 13)	16257	NM_008096	14473	Mm.196595	NM_008096	ENSMUSG00000035540	Gc	DBP|VDB	group specific component	protein-coding
mm_70009.1	chr7	142443359	142443385	-	1	NA	exon (NM_009405, exon 3 of 6)	exon (NM_009405, exon 3 of 6)	904	NM_009405	21953	Mm.39469	NM_009405	ENSMUSG00000031097	Tnni2	-	troponin I, skeletal, fast 2	protein-coding
mm_76486.1	chr8	85700924	85700924	-	1	NA	promoter-TSS (NR_106189)	promoter-TSS (NR_106189)	19	NR_106189	102465898		NR_106189	ENSMUSG00000098388	Mir8109	Gm27495|mmu-mir-8109	microRNA 8109	ncRNA
mm_121533.1	chr14	122280769	122280779	+	1	NA	intron (NM_029556, intron 1 of 7)	intron (NM_029556, intron 1 of 7)	-47136	NR_015532	68245	Mm.443285	NR_015532	ENSMUSG00000100585	1700108J01Rik	-	RIKEN cDNA 1700108J01 gene	ncRNA
mm_102996.1	chr11	69686940	69686953	-	1	NA	exon (NM_011614, exon 7 of 7)	exon (NM_011614, exon 7 of 7)	-1392	NM_023517	69583	Mm.8983	NM_023517	ENSMUSG00000089669	Tnfsf13	2310026N09Rik|April|Tall2|Tnlg7b|Trdl1	tumor necrosis factor (ligand) superfamily, member 13	protein-coding
mm_99895.1	chr11	109649377	109649437	+	1	NA	promoter-TSS (NM_001313974)	promoter-TSS (NM_001313974)	2	NM_001313974	19084	Mm.30039	NM_021880	ENSMUSG00000020612	Prkar1a	1300018C22Rik|RIalpha|Tse-1|Tse1	protein kinase, cAMP dependent regulatory, type I, alpha	protein-coding
mm_102748.1	chr11	67255597	67255619	-	1	NA	exon (NM_010855, exon 32 of 40)	exon (NM_010855, exon 32 of 40)	17796	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_162955.1	chr11	4236780	4236790	+	1	NA	promoter-TSS (NM_001013365)	promoter-TSS (NM_001013365)	0	NM_001013365	18413	Mm.131422	NM_001013365	ENSMUSG00000058755	Osm	OncoM	oncostatin M	protein-coding
mm_18272.1	chr2	52335753	52335767	-	1	NA	intron (NM_010889, intron 1 of 156)	intron (NM_010889, intron 1 of 156)	3038	NM_010889	17996	Mm.389247	NM_010889	ENSMUSG00000026950	Neb	AI595938	nebulin	protein-coding
mm_1779.1	chr1	78511837	78511847	+	1	NA	intron (NM_026713, intron 1 of 6)	CpG	782	NM_026713	68393	Mm.41325	NM_026713	ENSMUSG00000012187	Mogat1	0610030A14Rik|1110064N14Rik|Dgat2l|Dgat2l1|MGAT1|WI1-2612I11.1|mDC2	monoacylglycerol O-acyltransferase 1	protein-coding
mm_106024.1	chr11	116027850	116027858	-	1	NA	Intergenic	Intergenic	-2462	NM_001286006	217331	Mm.297706	NM_172569	ENSMUSG00000020770	Unk	B230379M23Rik|Zc3h5|Zc3hdc5|mKIAA1753	unkempt family zinc finger	protein-coding
mm_19394.1	chr2	91629242	91629250	-	1	NA	exon (NM_010168, exon 10 of 14)	exon (NM_010168, exon 10 of 14)	7211	NM_010168	14061	Mm.89048	NM_010168	ENSMUSG00000027249	F2	Cf-2|Cf2|FII	coagulation factor II	protein-coding
mm_655.1	chr1	40431416	40431429	+	1	NA	intron (NM_001294171, intron 1 of 7)	intron (NM_001294171, intron 1 of 7)	1852	NM_001294171	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_158715.1	chrX	162643547	162643573	-	1	NA	promoter-TSS (NM_001290633)	promoter-TSS (NM_001290633)	98	NM_001290633	194590	Mm.442441	NM_178256	ENSMUSG00000040855	Reps2	POB1	RALBP1 associated Eps domain containing protein 2	protein-coding
mm_110618.1	chr12	57007825	57007825	-	1	NA	intron (NM_172577, intron 1 of 9)	intron (NM_172577, intron 1 of 9)	152818	NM_001167976	217593	Mm.32835	NM_172577	ENSMUSG00000035472	Slc25a21	9930033G19Rik|A630030I10|BB158148	solute carrier family 25 (mitochondrial oxodicarboxylate carrier), member 21	protein-coding
mm_29505.1	chr3	116129616	116129624	-	1	NA	promoter-TSS (NM_011693)	promoter-TSS (NM_011693)	68	NM_011693	22329	Mm.76649	NM_011693	ENSMUSG00000027962	Vcam1	CD106|Vcam-1	vascular cell adhesion molecule 1	protein-coding
mm_58337.1	chr6	146647612	146647613	-	1	NA	non-coding (NR_038089, exon 1 of 1)	non-coding (NR_038089, exon 1 of 1)	190	NR_038089	626175	Mm.391544	NM_001178001		Gm6654	EG626175	predicted pseudogene 6654	pseudo
mm_109509.1	chr12	111452446	111452486	+	1	NA	intron (NM_009396, intron 11 of 11)	(TCCA)n|Simple_repeat|Simple_repeat	9805	NM_009396	21928	Mm.255332	NM_009396	ENSMUSG00000021281	Tnfaip2	B94|Exoc3l3|M-sec|Tnfip2|tnfb94	tumor necrosis factor, alpha-induced protein 2	protein-coding
mm_50877.1	chr6	55484609	55484613	+	1	NA	intron (NM_007407, intron 12 of 16)	PB1D10|SINE|Alu	32633	NM_007407	11517	Mm.44245	NM_007407	ENSMUSG00000029778	Adcyap1r1	2900024I10Rik|AI846590|PAC1|PAC1R|PACAP1-R	adenylate cyclase activating polypeptide 1 receptor 1	protein-coding
mm_121818.1	chr14	20452188	20452208	-	1	NA	promoter-TSS (NM_001163638)	promoter-TSS (NM_001163638)	27	NM_001163638	76670	Mm.159759	NM_029698	ENSMUSG00000039543	Cfap70	Ttc18	cilia and flagella associated protein 70	protein-coding
mm_68447.1	chr7	110006609	110006651	-	1	NA	promoter-TSS (NR_037959)	promoter-TSS (NR_037959)	16	NR_037959	69781	Mm.440728	NR_037959	ENSMUSG00000101585	1600010M07Rik	-	RIKEN cDNA 1600010M07 gene	ncRNA
mm_123564.1	chr14	66869078	66869103	-	1	NA	promoter-TSS (NM_009955)	promoter-TSS (NM_009955)	240	NM_001034881	432870	Mm.425890	NM_001034881	ENSMUSG00000075553	Gm5464	EG432870	predicted gene 5464	protein-coding
mm_104932.1	chr11	100050543	100050557	-	1	NA	promoter-TSS (NM_010659)	promoter-TSS (NM_010659)	1	NM_010659	16660	Mm.439673	NM_010659	ENSMUSG00000048981	Krt31	Ha1|Kha1|Krt1-1|MKHA-1	keratin 31	protein-coding
mm_77345.1	chr8	119574822	119574833	-	1	NA	promoter-TSS (NM_026648)	promoter-TSS (NM_026648)	373	NM_175185	72552	Mm.36756	NM_175185	ENSMUSG00000034189	Hsdl1	2700067E09Rik	hydroxysteroid dehydrogenase like 1	protein-coding
mm_76761.1	chr8	95576335	95576340	-	1	NA	promoter-TSS (NM_001310539)	promoter-TSS (NM_001310539)	-730	NM_001310539	70993	Mm.486561	NM_027640	ENSMUSG00000048400	Prss54	4931432M23Rik|Klkbl4	protease, serine 54	protein-coding
mm_170910.1	chr2	32961739	32961743	+	1	NA	promoter-TSS (NM_009076)	promoter-TSS (NM_009076)	29	NM_009076	269261	Mm.250030	NM_009076	ENSMUSG00000038900	Rpl12	E430018F03	ribosomal protein L12	protein-coding
mm_151388.1	chr19	56397216	56397226	+	1	NA	promoter-TSS (NM_007611)	promoter-TSS (NM_007611)	92	NM_007611	12369	Mm.35687	NM_007611	ENSMUSG00000025076	Casp7	AI314680|CMH-1|ICE-IAP3|Mch3|caspase-7|mCASP-7	caspase 7	protein-coding
mm_152608.1	chr19	11869041	11869090	-	1	NA	Intergenic	CpG	2149	NM_001011775	257938	Mm.377309	NM_001011775	ENSMUSG00000067545	Olfr1419	MOR266-10	olfactory receptor 1419	protein-coding
mm_123996.1	chr14	75786992	75787011	-	1	NA	promoter-TSS (NM_026232)	promoter-TSS (NM_026232)	36	NM_026232	67554	Mm.46067	NM_026232	ENSMUSG00000022003	Slc25a30	4933433D23Rik|AV025504|AV221431|AW319655|KMCP1	solute carrier family 25, member 30	protein-coding
mm_160159.1	chr7	44250068	44250068	+	1	NA	promoter-TSS (NR_028533)	promoter-TSS (NR_028533)	-82	NR_028533	100217433		NR_028533	ENSMUSG00000095472	Snord88a	MBII-211	small nucleolar RNA, C/D box 88A	snoRNA
mm_125707.1	chr15	68259279	68259282	+	1	NA	promoter-TSS (NM_198644)	promoter-TSS (NM_198644)	-424	NM_198644	380993	Mm.309526	NM_198644	ENSMUSG00000022335	Zfat	Gm922|Zfat1|Zfp406	zinc finger and AT hook domain containing	protein-coding
mm_123342.1	chr14	63138068	63138092	-	1	NA	exon (NM_007798, exon 6 of 10)	exon (NM_007798, exon 6 of 10)	15618	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_13907.1	chr2	120490084	120490113	+	1	NA	intron (NM_001109761, intron 7 of 20)	intron (NM_001109761, intron 7 of 20)	13189	NM_001109761	12335	Mm.458021	NM_007601	ENSMUSG00000079110	Capn3	AI323605|Capa-3|Capa3|Lp82|p94	calpain 3	protein-coding
mm_97901.1	chr11	83409737	83409749	+	1	NA	promoter-TSS (NM_001013386)	promoter-TSS (NM_001013386)	-329	NM_001013386	276952	Mm.66275	NM_001013386	ENSMUSG00000020684	Rasl10b	B230331P10Rik|Gm729|VTS58635	RAS-like, family 10, member B	protein-coding
mm_37516.1	chr4	124120521	124120542	-	1	NA	Intergenic	RSINE1|SINE|B4	203098	NM_017475	54170	Mm.220922	NM_017475	ENSMUSG00000028646	Rragc	AU041672|Gtr2|RAGC|TIB929|YGR163W	Ras-related GTP binding C	protein-coding
mm_163219.1	chr11	101396182	101396195	+	1	NA	Intergenic	RMER16|LTR|ERVK	21245	NM_144829	69684	Mm.146283	NM_144829	ENSMUSG00000075528	Aarsd1	1110069E20Rik|2310044P18Rik|AA589600|AlaX|AlaXp-II	alanyl-tRNA synthetase domain containing 1	protein-coding
mm_66811.1	chr7	47252997	47253004	-	1	NA	promoter-TSS (NM_001288801)	promoter-TSS (NM_001288801)	-152	NM_001288801	668725	Mm.436563	NM_001177566	ENSMUSG00000074111	Mrgpra9	EG668725|MrgA9	MAS-related GPR, member A9	protein-coding
mm_66236.1	chr7	35318409	35318437	-	1	NA	promoter-TSS (NM_026181)	promoter-TSS (NM_026181)	17	NM_026181	67471	Mm.358705	NM_026181	ENSMUSG00000063808	Gpatch1	1300003A17Rik|ECGP|Gpatc1	G patch domain containing 1	protein-coding
mm_21907.1	chr2	166567202	166567232	-	1	NA	3' UTR (NM_177782, exon 40 of 40)	3' UTR (NM_177782, exon 40 of 40)	-105501	NR_105783	102465188		NR_105783	ENSMUSG00000098675	Mir6364	Gm27327|mmu-mir-6364	microRNA 6364	ncRNA
mm_126158.1	chr15	78428448	78428457	+	1	NA	promoter-TSS (NM_001289671)	promoter-TSS (NM_001289671)	-112	NM_001289672	72844	Mm.390816	NM_001081367	ENSMUSG00000033287	Kctd17	2900008M13Rik|AA414907|AW742389|N28155	potassium channel tetramerisation domain containing 17	protein-coding
mm_106909.1	chr12	8015956	8015970	+	1	NA	exon (NM_009693, exon 29 of 29)	exon (NM_009693, exon 29 of 29)	38286	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_120984.1	chr14	78849233	78849243	+	1	NA	promoter-TSS (NM_027906)	promoter-TSS (NM_027906)	60	NM_173758	219189	Mm.159651	NM_027906	ENSMUSG00000058997	Vwa8	1300010F03Rik|4932416F07Rik|AI957255|Kiaa0564|mKIAA0564	von Willebrand factor A domain containing 8	protein-coding
mm_88301.1	chr10	75317055	75317073	+	1	NA	promoter-TSS (NM_001331095)	promoter-TSS (NM_001331095)	187	NM_009630	11540	Mm.333734	NM_009630	ENSMUSG00000020178	Adora2a	A2AAR|A2aR|AA2AR	adenosine A2a receptor	protein-coding
mm_21947.1	chr2	167062608	167062724	-	1	NA	promoter-TSS (NR_138563)	promoter-TSS (NR_138563)	-268	NR_138563	68949	Mm.391959	NM_001081005		Zfas1	1500012F01Rik|Zfos1	zinc finger, NFX1-type containing 1, antisense RNA 1	ncRNA
mm_157286.1	chrX	20861177	20861198	-	1	NA	TTS (NM_009703)	TTS (NM_009703)	1995	NR_049190	100885829		NR_049190	ENSMUSG00000093408	Mir5617	Gm25192|mir-5617|mmu-mir-5617	microRNA 5617	ncRNA
mm_150449.1	chr19	38097066	38097104	+	1	NA	promoter-TSS (NM_181748)	promoter-TSS (NM_181748)	6	NM_181748	107221	Mm.35288	NM_181748	ENSMUSG00000054200	Ffar4	AI552415|GT01|Gpr120|Gpr129|KPG_013|O3far1|Pgr4	free fatty acid receptor 4	protein-coding
mm_7475.1	chr1	120496023	120496046	-	1	NA	intron (NM_010766, intron 1 of 16)	intron (NM_010766, intron 1 of 16)	9050	NM_010766	17167	Mm.1856	NM_010766	ENSMUSG00000026390	Marco	AI323439|Ly112|Scara2	macrophage receptor with collagenous structure	protein-coding
mm_138055.1	chr17	33926620	33926637	+	1	NA	exon (NM_001025313, exon 7 of 8)	exon (NM_001025313, exon 7 of 8)	-3266	NM_009059	19732	Mm.43777	NM_009059	ENSMUSG00000041354	Rgl2	KE1.5|Rab2l|Rgt2|Rlf	ral guanine nucleotide dissociation stimulator-like 2	protein-coding
mm_38651.1	chr4	143276150	143276166	-	1	NA	exon (NM_010329, exon 2 of 6)	exon (NM_010329, exon 2 of 6)	23406	NM_010329	14726	Mm.2976	NM_010329	ENSMUSG00000028583	Pdpn	Gp38|OTS-8|RANDAM-2|T1-alpha|T1a|T1alpha	podoplanin	protein-coding
mm_22462.1	chr3	3508025	3508069	+	1	NA	promoter-TSS (NM_013920)	promoter-TSS (NM_013920)	17	NM_013920	30942	Mm.330897	NM_013920	ENSMUSG00000017688	Hnf4g	NR2A2	hepatocyte nuclear factor 4, gamma	protein-coding
mm_57722.1	chr6	128890960	128890962	-	1	NA	exon (NM_001254946, exon 1 of 3)	exon (NM_001254946, exon 1 of 3)	163	NM_001254946	232406	Mm.30745	NM_001254946	ENSMUSG00000090164	BC035044	-	cDNA sequence BC035044	protein-coding
mm_58612.1	chr7	5061673	5061752	+	1	NA	promoter-TSS (NM_001205231)	promoter-TSS (NM_001205231)	-431	NM_133671	22185	Mm.360389	NM_133671	ENSMUSG00000030435	U2af2	65kDa	U2 small nuclear ribonucleoprotein auxiliary factor (U2AF) 2	protein-coding
mm_138939.1	chr17	43953359	43953369	+	1	NA	5' UTR (NM_030598, exon 1 of 4)	5' UTR (NM_030598, exon 1 of 4)	173	NM_030598	53901	Mm.251242	NM_030598	ENSMUSG00000039601	Rcan2	Csp2|Dscr1l1|MCIP2|ZAKI-4	regulator of calcineurin 2	protein-coding
mm_84528.1	chr9	67047829	67047923	-	1	NA	exon (NM_001164251, exon 2 of 10)	exon (NM_001164251, exon 2 of 10)	1337	NM_001164255	22003	Mm.121878	NM_024427	ENSMUSG00000032366	Tpm1	AA986836|AI854628|TM2|Tm3|Tmpa|Tpm-1|alpha-TM	tropomyosin 1, alpha	protein-coding
mm_125299.1	chr15	37135902	37135914	+	1	NA	Intergenic	CpG	-97128	NM_026496	252973	Mm.244612	NM_026496	ENSMUSG00000022286	Grhl2	0610015A08Rik|BOM|Tcfcp2l3|clft3	grainyhead-like 2 (Drosophila)	protein-coding
mm_74641.1	chr8	13254177	13254188	-	1	NA	promoter-TSS (NM_172750)	promoter-TSS (NM_172750)	-20	NM_172750	234072	Mm.132785	NM_172750	ENSMUSG00000031448	Adprhl1	Arh2|D330008N11Rik	ADP-ribosylhydrolase like 1	protein-coding
mm_67093.1	chr7	68768329	68768332	-	1	NA	Intergenic	MTEa-int|LTR|ERVL-MaLR	-19092	NM_025549	66412	Mm.251199	NM_025549	ENSMUSG00000042659	Arrdc4	2410003C09Rik|AV216361	arrestin domain containing 4	protein-coding
mm_142282.1	chr17	40222336	40222344	-	1	NA	3' UTR (NM_009639, exon 8 of 8)	3' UTR (NM_009639, exon 8 of 8)	-13731	NM_031190	18663	Mm.717	NM_031190	ENSMUSG00000031233	Pgk2	Pgk-2|Tcp-2	phosphoglycerate kinase 2	protein-coding
mm_149284.1	chr19	10629307	10629326	+	1	NA	3' UTR (NM_015735, exon 27 of 27)	3' UTR (NM_015735, exon 27 of 27)	-4917	NM_027913	71768	Mm.169261	NM_027913	ENSMUSG00000043789	Vwce	1300015B04Rik	von Willebrand factor C and EGF domains	protein-coding
mm_58053.1	chr6	136857419	136857451	-	1	NA	5' UTR (NM_026639, exon 1 of 3)	5' UTR (NM_026639, exon 1 of 3)	165	NM_026639	109978	Mm.31840	NM_026639	ENSMUSG00000030217	Art4	4432404K01Rik|ARTC4|DO|DOK1	ADP-ribosyltransferase 4	protein-coding
mm_5298.1	chr1	21291554	21291562	-	1	NA	intron (NR_002858, intron 3 of 5)	intron (NR_002858, intron 3 of 5)	6754	NR_002858	241041	Mm.290634	NR_002858	ENSMUSG00000025936	Gm4956	EG241041	predicted gene 4956	pseudo
mm_5740.1	chr1	45442718	45442752	-	1	NA	exon (NM_007737, exon 2 of 54)	exon (NM_007737, exon 2 of 54)	60547	NM_007737	12832	Mm.10299	NM_007737	ENSMUSG00000026042	Col5a2	1110014L14Rik	collagen, type V, alpha 2	protein-coding
mm_5053.1	chr1	194943854	194943866	+	1	NA	intron (NM_001111059, intron 1 of 7)	intron (NM_001111059, intron 1 of 7)	5039	NM_001111059	12490	Mm.29798	NM_133654	ENSMUSG00000016494	Cd34	AU040960	CD34 antigen	protein-coding
mm_157650.1	chrX	57326228	57326249	-	1	NA	intron (NM_152801, intron 2 of 21)	intron (NM_152801, intron 2 of 21)	12491	NM_152801	73341	Mm.261443	NM_152801	ENSMUSG00000031133	Arhgef6	1600028C08Rik|1700038J06Rik|4930592P22Rik|alpha-PIX	Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_84455.1	chr9	66520311	66520342	-	1	NA	exon (NM_144937, exon 13 of 15)	exon (NM_144937, exon 13 of 15)	-5733	NM_175206	74165	Mm.297998	NM_175206	ENSMUSG00000050503	Fbxl22	1110004B15Rik	F-box and leucine-rich repeat protein 22	protein-coding
mm_41815.1	chr5	103784417	103784429	+	1	NA	exon (NM_133919, exon 3 of 20)	exon (NM_133919, exon 3 of 20)	29850	NM_001080798	17355	Mm.6949	NM_133919	ENSMUSG00000029313	Aff1	9630032B01Rik|AW319193|Af4|Mllt2h|Rob	AF4/FMR2 family, member 1	protein-coding
mm_79642.1	chr9	59558103	59558112	+	1	NA	exon (NM_010421, exon 6 of 14)	exon (NM_010421, exon 6 of 14)	18567	NM_010421	15211	Mm.2284	NM_010421	ENSMUSG00000025232	Hexa	Hex-1	hexosaminidase A	protein-coding
mm_74404.1	chr8	3354599	3354601	-	1	NA	intron (NM_001033378, intron 1 of 10)	intron (NM_001033378, intron 1 of 10)	1185	NM_001033378	319493	Mm.234565	NM_001033378	ENSMUSG00000074497	A430078G23Rik	-	RIKEN cDNA A430078G23 gene	protein-coding
mm_164802.1	chr18	23917055	23917084	+	1	NA	Intergenic	Intergenic	-37619	NM_027007	69256	Mm.218343	NM_027007	ENSMUSG00000024276	Zfp397	2810411K16Rik|6720480F11Rik|AI461664	zinc finger protein 397	protein-coding
mm_130042.1	chr15	89075894	89075951	-	1	NA	promoter-TSS (NM_026485)	promoter-TSS (NM_026485)	-68	NR_040417	69120	Mm.276391	NR_040417	ENSMUSG00000087331	1810021B22Rik	-	RIKEN cDNA 1810021B22 gene	ncRNA
mm_78128.1	chr9	20653980	20653997	+	1	NA	intron (NM_023371, intron 1 of 3)	B3|SINE|B2	1858	NM_023371	23988	Mm.7906	NM_023371	ENSMUSG00000032171	Pin1	0610025L01Rik|D9Bwg1161e	protein (peptidyl-prolyl cis/trans isomerase) NIMA-interacting 1	protein-coding
mm_110805.1	chr12	72212516	72212524	-	1	NA	non-coding (NR_104446, exon 7 of 7)	non-coding (NR_104446, exon 7 of 7)	23226	NR_104446	104001	Mm.221275	NM_153457	ENSMUSG00000021087	Rtn1	Nsp	reticulon 1	protein-coding
mm_17202.1	chr2	25469112	25469122	-	1	NA	exon (NM_008963, exon 2 of 7)	exon (NM_008963, exon 2 of 7)	632	NM_008963	19215	Mm.1008	NM_008963	ENSMUSG00000015090	Ptgds	21kDa|L-PGDS|PGD2|PGDS|PGDS2|Ptgs3	prostaglandin D2 synthase (brain)	protein-coding
mm_56593.1	chr6	108532626	108532646	-	1	NA	intron (NM_010585, intron 60 of 61)	intron (NM_010585, intron 60 of 61)	42893	NR_106121	102465766		NR_106121	ENSMUSG00000105697	Mir7661	mmu-mir-7661	microRNA 7661	ncRNA
mm_111648.1	chr12	102730415	102730428	-	1	NA	Intergenic	Intergenic	13240	NM_001142937	64113	Mm.291222	NM_022323	ENSMUSG00000096458	Moap1	AA987038|Map-1|Pnma4	modulator of apoptosis 1	protein-coding
mm_112693.1	chr13	17694915	17694929	+	1	NA	promoter-TSS (NM_138654)	promoter-TSS (NM_138654)	-157	NM_138654	192136	Mm.364180	NM_138654	ENSMUSG00000055137	Sugct	5033411D12Rik|D17907	succinyl-CoA glutarate-CoA transferase	protein-coding
mm_547.1	chr1	38019069	38019081	+	1	NA	exon (NM_198303, exon 4 of 24)	exon (NM_198303, exon 4 of 24)	21065	NM_198303	226982	Mm.260943	NM_198303	ENSMUSG00000026083	Eif5b	A030003E17Rik|BC018347|IF2	eukaryotic translation initiation factor 5B	protein-coding
mm_167810.1	chr9	123929191	123929205	-	1	NA	Intergenic	Intergenic	39494	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_116186.1	chr13	31079874	31079876	-	1	NA	Intergenic	Intergenic	-105828	NM_025588	66482	Mm.293510	NM_025588	ENSMUSG00000021357	Exoc2	2410030I24Rik|AI648199|Sec5|Sec5l1	exocyst complex component 2	protein-coding
mm_142782.1	chr17	50154893	50154906	-	1	NA	intron (NM_181397, intron 2 of 9)	Lx8|LINE|L1	35598	NM_181397	76438	Mm.41854	NM_181397	ENSMUSG00000039316	Rftn1	2310015N21Rik|AI853526	raftlin lipid raft linker 1	protein-coding
mm_117551.1	chr13	84064706	84064724	-	1	NA	promoter-TSS (NR_131220)	promoter-TSS (NR_131220)	59	NR_131220	553095	Mm.39702	NR_131220	ENSMUSG00000098087	Gm17750	-	predicted gene, 17750	ncRNA
mm_73988.1	chr8	120668282	120668299	+	1	NA	promoter-TSS (NM_009941)	promoter-TSS (NM_009941)	-30	NM_001293559	12857	Mm.386758	NM_009941	ENSMUSG00000031818	Cox4i1	AL024441|COX|COX IV-1|COXIV|Cox4|Cox4a|IV-1	cytochrome c oxidase subunit IV isoform 1	protein-coding
mm_170318.1	chr18	37761717	37761726	+	1	NA	promoter-TSS (NM_033580)	promoter-TSS (NM_033580)	-80	NM_033580	93705	Mm.247203	NM_033580	ENSMUSG00000103081	Pcdhgb8	-	protocadherin gamma subfamily B, 8	protein-coding
mm_69909.1	chr7	141640105	141640117	-	1	NA	intron (NM_001330001, intron 31 of 33)	intron (NM_001330001, intron 31 of 33)	15208	NM_001330001	353328	Mm.246621	NM_181729	ENSMUSG00000048191	Muc6	-	mucin 6, gastric	protein-coding
mm_129329.1	chr15	77775210	77775224	-	1	NA	exon (NM_022410, exon 22 of 41)	exon (NM_022410, exon 22 of 41)	-19988	NM_001081970	239552	Mm.125650	NM_001081970	ENSMUSG00000056656	Apol8	9830006J20Rik|APOL-II|Apol2	apolipoprotein L 8	protein-coding
mm_64039.1	chr7	140773078	140773111	+	1	NA	exon (NM_021282, exon 7 of 9)	exon (NM_021282, exon 7 of 9)	9262	NM_021282	13106	Mm.21758	NM_021282	ENSMUSG00000025479	Cyp2e1	Cyp2e	cytochrome P450, family 2, subfamily e, polypeptide 1	protein-coding
mm_85589.1	chr9	107313372	107313379	-	1	NA	Intergenic	Intergenic	16716	NM_009895	12700	Mm.4592	NM_009895	ENSMUSG00000032578	Cish	CIS-1|CIS1|Cis|F17|F23|SOCS	cytokine inducible SH2-containing protein	protein-coding
mm_124778.1	chr15	7198705	7198707	+	1	NA	Intergenic	Intergenic	58164	NM_013584	16880	Mm.149720	NM_013584	ENSMUSG00000054263	Lifr	A230075M04Rik|AW061234|LIF	leukemia inhibitory factor receptor	protein-coding
mm_11613.1	chr2	34589651	34589656	+	1	NA	intron (NM_001290626, intron 8 of 10)	intron (NM_001290626, intron 8 of 10)	165579	NM_025709	66691	Mm.156452	NM_025709	ENSMUSG00000026867	Gapvd1	2010005B09Rik|4432404J10Rik|AW108497|Gapex-5|RAP6|RME-6|mKIAA1521	GTPase activating protein and VPS9 domains 1	protein-coding
mm_156760.1	chrX	160502632	160502706	+	1	NA	5' UTR (NM_001177878, exon 1 of 33)	5' UTR (NM_001177878, exon 1 of 33)	235	NM_001177878	110094	Mm.350712	NM_172783	ENSMUSG00000031295	Phka2	6330505C01Rik|D330034O08|Phk	phosphorylase kinase alpha 2	protein-coding
mm_92482.1	chr10	78295420	78295422	-	1	NA	intron (NM_053014, intron 2 of 9)	intron (NM_053014, intron 2 of 9)	44786	NR_106119	102465765		NR_106119	ENSMUSG00000098885	Mir7659	Gm27433|mmu-mir-7659	microRNA 7659	ncRNA
mm_162212.1	chrX	136741278	136741278	-	1	NA	promoter-TSS (NM_001168229)	promoter-TSS (NM_001168229)	74	NM_001168229	56397	Mm.27218	NM_019768	ENSMUSG00000031422	Morf4l2	2410017O14Rik|Mrgx|Sid393p|mKIAA0026	mortality factor 4 like 2	protein-coding
mm_32509.1	chr4	108479212	108479224	+	1	NA	exon (NM_175472, exon 3 of 31)	exon (NM_175472, exon 3 of 31)	19792	NM_175472	230594	Mm.25181	NM_175472	ENSMUSG00000034610	Zcchc11	6030404K05Rik|9230115F04Rik|PPAPD3|mKIAA0191	zinc finger, CCHC domain containing 11	protein-coding
mm_141391.1	chr17	29167443	29167461	-	1	NA	intron (NM_153166, intron 13 of 20)	intron (NM_153166, intron 13 of 20)	32396	NM_001002786	442827	Mm.440341	NM_001002786	ENSMUSG00000064147	Rab44	9830134C10Rik	RAB44, member RAS oncogene family	protein-coding
mm_116602.1	chr13	48625505	48625564	-	1	NA	5' UTR (NM_207232, exon 1 of 10)	5' UTR (NM_207232, exon 1 of 10)	138	NM_207232	218232	Mm.315089	NM_207232	ENSMUSG00000038042	Ptpdc1	AI843923|AW456874|Naa-1|Ptpcd1	protein tyrosine phosphatase domain containing 1	protein-coding
mm_16293.1	chr2	174284313	174284326	+	1	NA	promoter-TSS (NM_022000)	promoter-TSS (NM_022000)	-1	NM_019690	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_151613.1	chr19	3899047	3899069	-	1	NA	exon (NM_001136091, exon 11 of 20)	exon (NM_001136091, exon 11 of 20)	6172	NM_016921	27060	Mm.271689	NM_016921	ENSMUSG00000001750	Tcirg1	ATP6N1C|ATP6a3|Atp6i|OC-116|OPTB1|Stv1|TIRC7|Vph1|oc	T cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 protein A3	protein-coding
mm_104925.1	chr11	99979098	99979103	-	1	NA	Intergenic	Intergenic	7493	NM_001256057	100504183	Mm.426560	NM_001256057	ENSMUSG00000078253	Krtap16-1	Gm11570|OTTMUSG00000002209	keratin associated protein 16-1	protein-coding
mm_37868.1	chr4	132348130	132348135	-	1	NA	Intergenic	Intergenic	-2382	NM_133878	100088	Mm.255045	NM_133878	ENSMUSG00000028896	Rcc1	4931417M11Rik|AI326872|Chc1	regulator of chromosome condensation 1	protein-coding
mm_101548.1	chr11	33578889	33578896	-	1	NA	promoter-TSS (NM_146017)	promoter-TSS (NM_146017)	65	NM_146017	216643	Mm.99989	NM_146017	ENSMUSG00000020159	Gabrp	-	gamma-aminobutyric acid (GABA) A receptor, pi	protein-coding
mm_147674.1	chr18	60648947	60648969	-	1	NA	Intergenic	Intergenic	-14452	NR_045401	328963	Mm.417203	NR_045401		G630071F17Rik	G630071F17	RIKEN cDNA G630071F17 gene	ncRNA
mm_106048.1	chr11	116080281	116080316	-	1	NA	exon (NM_016852, exon 6 of 8)	exon (NM_016852, exon 6 of 8)	-2337	NM_001009573	70450	Mm.259460	NM_001009573	ENSMUSG00000057948	Unc13d	2610108D09Rik|Jinx|Munc13-4|mFLJ00067	unc-13 homolog D (C. elegans)	protein-coding
mm_159199.1	chr2	119758508	119758508	-	1	NA	promoter-TSS (NM_008523)	promoter-TSS (NM_008523)	17	NM_206941	17005	Mm.1740	NM_008523	ENSMUSG00000027297	Ltk	-	leukocyte tyrosine kinase	protein-coding
mm_40722.1	chr5	65967347	65967381	+	1	NA	5' UTR (NM_001081104, exon 1 of 5)	5' UTR (NM_001081104, exon 1 of 5)	240	NM_001081104	231252	Mm.140015	NM_001081104	ENSMUSG00000029205	Chrna9	2410015I05Rik|Acra9|EG666827|Gm8311	cholinergic receptor, nicotinic, alpha polypeptide 9	protein-coding
mm_115084.1	chr13	102693597	102693607	+	1	NA	promoter-TSS (NM_008533)	promoter-TSS (NM_008533)	44	NM_008533	17079	Mm.373974	NM_008533	ENSMUSG00000021624	Cd180	F630107B15|Ly78|RP105	CD180 antigen	protein-coding
mm_72468.1	chr8	83348738	83348745	+	1	NA	intron (NM_026233, intron 1 of 10)	intron (NM_026233, intron 1 of 10)	269	NM_026233	67555	Mm.84115	NM_026233	ENSMUSG00000035057	Mgat4d	4933434I20Rik|GnT1IP|GnT1IP-L	MGAT4 family, member C	protein-coding
mm_49228.1	chr6	15800970	15800977	+	1	NA	3' UTR (NM_175088, exon 5 of 5)	3' UTR (NM_175088, exon 5 of 5)	80312	NM_175088	16543	Mm.1314	NM_175088	ENSMUSG00000041390	Mdfic	Kdt1|Mdfid	MyoD family inhibitor domain containing	protein-coding
mm_65608.1	chr7	27465736	27465775	-	1	NA	exon (NM_144923, exon 5 of 5)	exon (NM_144923, exon 5 of 5)	-8085	NM_133210	170742	Mm.200120	NM_133210	ENSMUSG00000055200	Sertad3	AW124805|D1Mgi51|Rbt1|Sei3	SERTA domain containing 3	protein-coding
mm_127355.1	chr15	100619965	100620007	+	1	NA	3' UTR (NM_011873, exon 4 of 4)	3' UTR (NM_011873, exon 4 of 4)	4324	NM_011873	23994	Mm.486175	NM_011873	ENSMUSG00000000346	Dazap2	AI314727|Brbp|Gcap28|Prtb|gt6-12|mKIAA0058	DAZ associated protein 2	protein-coding
mm_42625.1	chr5	118245302	118245358	+	1	NA	promoter-TSS (NM_001109902)	promoter-TSS (NM_001109902)	103	NM_001081236	76792	Mm.103428	NM_001081236	ENSMUSG00000032840	2410131K14Rik	-	RIKEN cDNA 2410131K14 gene	protein-coding
mm_110041.1	chr12	17176955	17176965	-	1	NA	promoter-TSS (NM_201531)	promoter-TSS (NM_201531)	-72	NM_201531	382571	Mm.40173	NM_201531	ENSMUSG00000051726	Kcnf1	Gm1182|Kv5.1	potassium voltage-gated channel, subfamily F, member 1	protein-coding
mm_9807.1	chr1	181929063	181929067	-	1	NA	intron (NM_001083121, intron 4 of 13)	intron (NM_001083121, intron 4 of 13)	-86664	NM_133815	98386	Mm.4538	NM_133815	ENSMUSG00000004880	Lbr	AI505894|ic	lamin B receptor	protein-coding
mm_110976.1	chr12	76982824	76982826	-	1	NA	Intergenic	MER115|DNA|hAT-Tip100	-20577	NM_001146176	17187	Mm.268548	NM_008558	ENSMUSG00000059436	Max	AA960152|AI875693|bHLHd4|bHLHd5|bHLHd6|bHLHd7|bHLHd8	Max protein	protein-coding
mm_91773.1	chr10	51757190	51757201	-	1	NA	promoter-TSS (NR_045158)	promoter-TSS (NR_045158)	-1	NR_045158	71090	Mm.72588	NM_027670	ENSMUSG00000062224	4933411G06Rik	-	Sumo1 pseudogene	pseudo
mm_23723.1	chr3	69009982	69009986	+	1	NA	promoter-TSS (NR_029735)	promoter-TSS (NR_029735)	82	NR_029735	723949		NR_029735	ENSMUSG00000065606	Mir16-2	Mirn16-2|mir-16-2	microRNA 16-2	ncRNA
mm_156992.1	chrX	7421124	7421132	-	1	NA	promoter-TSS (NR_027925)	promoter-TSS (NR_027925)	-81	NR_027925	68355	Mm.45111	NR_027924		2010204K13Rik	0610010M13Rik|Cip7	RIKEN cDNA 2010204K13 gene	ncRNA
mm_4645.1	chr1	180256391	180256435	+	1	NA	promoter-TSS (NM_001128605)	promoter-TSS (NM_001128605)	-113	NM_001128605	19165	Mm.330850	NM_011183	ENSMUSG00000010609	Psen2	ALG-3|Ad4h|Alg3|PS-2|PS2|Psnl2|STM2	presenilin 2	protein-coding
mm_79256.1	chr9	50751874	50751902	+	1	NA	intron (NM_024441, intron 1 of 1)	intron (NM_024441, intron 1 of 1)	466	NM_001164708	69253	Mm.1980	NM_024441	ENSMUSG00000038086	Hspb2	27kDa|2810021G24Rik|HSP27|MKBP	heat shock protein 2	protein-coding
mm_53136.1	chr6	125215377	125215390	+	1	NA	promoter-TSS (NM_001080557)	promoter-TSS (NM_001080557)	-198	NM_009496	22317	Mm.32321	NM_009496	ENSMUSG00000030337	Vamp1	Syb-1|Syb1|VAMP-1|lew	vesicle-associated membrane protein 1	protein-coding
mm_77929.1	chr9	7353565	7353577	+	1	NA	intron (NM_001320077, intron 7 of 10)	intron (NM_001320077, intron 7 of 10)	6197	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_168010.1	chrY	15198558	15198558	+	1	NA	Intergenic	B1_Mus1|SINE|Alu	684687	NM_001199331	100040022	Mm.485767	NM_001199331	ENSMUSG00000095172	Gm20822	-	predicted gene, 20822	protein-coding
mm_88525.1	chr10	78069321	78069346	+	1	NA	promoter-TSS (NM_015790)	promoter-TSS (NM_015790)	-35	NM_015790	50723	Mm.17819	NM_015790	ENSMUSG00000000732	Icosl	AU044799|B7-H2|B7RP-1|B7h|BG071784|GI50|GL50|GL50-B|ICOS-L|Icoslg|LICOS|Ly115l|mKIAA0653	icos ligand	protein-coding
mm_139326.1	chr17	48462356	48462409	+	1	NA	exon (NM_152823, exon 4 of 9)	exon (NM_152823, exon 4 of 9)	7481	NM_152823	76589	Mm.311629	NM_152823	ENSMUSG00000043592	Unc5cl	2510009H09Rik|BB155270|Zud	unc-5 family C-terminal like	protein-coding
mm_63478.1	chr7	127745533	127745544	+	1	NA	Intergenic	Intergenic	-1237	NM_172748	233902	Mm.259353	NM_172748	ENSMUSG00000030811	Fbxl19	6030430O11|BC059812|Fbl19	F-box and leucine-rich repeat protein 19	protein-coding
mm_122122.1	chr14	31019346	31019411	-	1	NA	promoter-TSS (NM_153547)	promoter-TSS (NM_153547)	240	NM_001081251	66923	Mm.27913	NM_025847	ENSMUSG00000042323	Pbrm1	2610016F04Rik|AI507524|BAF180|Pb1	polybromo 1	protein-coding
mm_121521.1	chr14	122107030	122107044	+	1	NA	promoter-TSS (NM_080556)	promoter-TSS (NM_080556)	-45	NM_080556	68059	Mm.275191	NM_080556	ENSMUSG00000025544	Tm9sf2	1500001N15Rik|AA536814|D14Ertd64e|P76	transmembrane 9 superfamily member 2	protein-coding
mm_133518.1	chr16	90830082	90830102	+	1	NA	promoter-TSS (NM_001316761)	promoter-TSS (NM_001316761)	-767	NR_133572	70967	Mm.253077	NM_027627	ENSMUSG00000039903	Eva1c	1700092M14Rik|4931408A02Rik|Fam176c	eva-1 homolog C (C. elegans)	protein-coding
mm_598.1	chr1	39650601	39650609	+	1	NA	exon (NM_170597, exon 1 of 4)	exon (NM_170597, exon 1 of 4)	577	NM_170597	263764	Mm.122091	NM_170597	ENSMUSG00000050967	Creg2	A830098L22Rik	cellular repressor of E1A-stimulated genes 2	protein-coding
mm_133824.1	chr16	95824880	95824896	+	1	NA	Intergenic	Intergenic	73825	NR_040485	69776	Mm.120470	NR_040484	ENSMUSG00000086899	1600002D24Rik	-	RIKEN cDNA 1600002D24 gene	ncRNA
mm_21722.1	chr2	164654928	164654956	-	1	NA	promoter-TSS (NM_001160414)	promoter-TSS (NM_001160414)	24	NM_001160414	629754	Mm.190489	NM_001160414	ENSMUSG00000074594	Wfdc9	OTTMUSG00000001088	WAP four-disulfide core domain 9	protein-coding
mm_158394.1	chrX	136741095	136741115	-	1	NA	promoter-TSS (NM_001168225)	promoter-TSS (NM_001168225)	50	NM_001168225	56397	Mm.27218	NM_019768	ENSMUSG00000031422	Morf4l2	2410017O14Rik|Mrgx|Sid393p|mKIAA0026	mortality factor 4 like 2	protein-coding
mm_99104.1	chr11	100119087	100119097	+	1	NA	exon (NM_010662, exon 5 of 8)	exon (NM_010662, exon 5 of 8)	1485	NM_001313949	16663	Mm.4646	NM_010662	ENSMUSG00000044041	Krt13	CK13|K13|Krt-1.13|Krt1-13	keratin 13	protein-coding
mm_150914.1	chr19	46064422	46064425	+	1	NA	exon (NM_001081214, exon 5 of 14)	exon (NM_001081214, exon 5 of 14)	7884	NM_001081214	226169	Mm.2415	NM_145504	ENSMUSG00000055491	Pprc1	A930018M19|BC013720|PRC|mKIAA0595	peroxisome proliferative activated receptor, gamma, coactivator-related 1	protein-coding
mm_16378.1	chr2	178193103	178193118	+	1	NA	promoter-TSS (NM_001007154)	promoter-TSS (NM_001007154)	26	NM_001007154	74189	Mm.44413	NM_028806	ENSMUSG00000027525	Phactr3	1500003N10Rik|4930415A02Rik|H17739|Scapin1|Scapinin|mKIAA4224	phosphatase and actin regulator 3	protein-coding
mm_120806.1	chr14	74922157	74922161	+	1	NA	intron (NM_001252132, intron 1 of 18)	intron (NM_001252132, intron 1 of 18)	25718	NM_001252132	380916	Mm.288868	NM_001033439	ENSMUSG00000068015	Lrch1	4832412D13Rik|AI552548|AW215503|Chdc1|mKIAA1016	leucine-rich repeats and calponin homology (CH) domain containing 1	protein-coding
mm_54970.1	chr6	48737901	48737931	-	1	NA	Intergenic	LTR16A|LTR|ERVL	-1131	NM_175860	16205	Mm.252599	NM_008376	ENSMUSG00000090019	Gimap1	IAP38|Imap38|imap	GTPase, IMAP family member 1	protein-coding
mm_24888.1	chr3	96108535	96108566	+	1	NA	intron (NM_001025614, intron 1 of 11)	intron (NM_001025614, intron 1 of 11)	4023	NM_001025614	229603	Mm.272336	NM_001025613	ENSMUSG00000038495	Otud7b	2900060B22Rik|4930463P07Rik|AI462125|CEZANNE|Trabid2|Za20d1	OTU domain containing 7B	protein-coding
mm_20080.1	chr2	120609494	120609496	-	1	NA	promoter-TSS (NM_025657)	promoter-TSS (NM_025657)	13	NR_027510	66606	Mm.428639	NM_025657	ENSMUSG00000027286	Lrrc57	2810002D13Rik|AA407405	leucine rich repeat containing 57	protein-coding
mm_128463.1	chr15	50806780	50806793	-	1	NA	intron (NM_001310485, intron 5 of 7)	intron (NM_001310485, intron 5 of 7)	82263	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_104420.1	chr11	94761180	94761183	-	1	NA	promoter-TSS (NM_001105561)	promoter-TSS (NM_001105561)	1	NM_001105561	217122	Mm.24063	NM_183153		Gm11545	A430060F13Rik|C86086|OTTMUSG00000002043	predicted gene 11545	protein-coding
mm_95374.1	chr11	49088907	49088913	+	1	NA	intron (NM_010999, intron 2 of 5)	intron (NM_010999, intron 2 of 5)	1893	NM_008330	15953	Mm.24769	NM_008330	ENSMUSG00000078920	Ifi47	47kDa|IRG-47|Ifggc1|Igrd|Iigp4|Iipg4|Irgd	interferon gamma inducible protein 47	protein-coding
mm_81080.1	chr9	106224089	106224112	+	1	NA	exon (NM_031178, exon 2 of 2)	exon (NM_031178, exon 2 of 2)	1502	NM_031178	81897	Mm.44889	NM_031178	ENSMUSG00000045322	Tlr9	-	toll-like receptor 9	protein-coding
mm_100829.1	chr11	5401277	5401282	-	1	NA	intron (NM_001080924, intron 1 of 8)	B2_Mm1a|SINE|B2	-19539	NM_001290501	407821	Mm.216313	NM_001080924	ENSMUSG00000041961	Znrf3	Gm1167	zinc and ring finger 3	protein-coding
mm_60792.1	chr7	45570343	45570371	+	1	NA	promoter-TSS (NM_001243052)	promoter-TSS (NM_001243052)	204	NM_009737	12036	Mm.24210	NM_009737	ENSMUSG00000030826	Bcat2	Bcat-2|Eca40	branched chain aminotransferase 2, mitochondrial	protein-coding
mm_11614.1	chr2	34608407	34608464	+	1	NA	intron (NM_001290626, intron 9 of 10)	MLT1F2|LTR|ERVL-MaLR	146797	NM_025709	66691	Mm.156452	NM_025709	ENSMUSG00000026867	Gapvd1	2010005B09Rik|4432404J10Rik|AW108497|Gapex-5|RAP6|RME-6|mKIAA1521	GTPase activating protein and VPS9 domains 1	protein-coding
mm_46394.1	chr5	104022191	104022210	-	1	NA	promoter-TSS (NM_053262)	promoter-TSS (NM_053262)	-404	NM_053262	114664	Mm.46019	NM_053262	ENSMUSG00000029311	Hsd17b11	Dhrs8|Pan1b|SDR2|retSDR2	hydroxysteroid (17-beta) dehydrogenase 11	protein-coding
mm_72576.1	chr8	84192266	84192285	+	1	NA	Intergenic	Intergenic	-13314	NR_029821	723819		NR_029821	ENSMUSG00000065483	Mir181c	Mirn181c|mir-181c	microRNA 181c	ncRNA
mm_74276.1	chr8	125200602	125200607	+	1	NA	intron (NM_174854, intron 9 of 12)	intron (NM_174854, intron 9 of 12)	146409	NM_174854	244667	Mm.233504	NM_170596	ENSMUSG00000043051	Disc1	-	disrupted in schizophrenia 1	protein-coding
mm_35343.1	chr4	32239993	32239998	-	1	NA	Intergenic	CpG	-177440	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_28470.1	chr3	90889126	90889131	-	1	NA	Intergenic	Intergenic	162222	NM_207263	384997	Mm.316644	NM_207263	ENSMUSG00000042250	Pglyrp4	Gm1478|Gm413	peptidoglycan recognition protein 4	protein-coding
mm_157444.1	chrX	41796806	41796826	-	1	NA	3' UTR (NM_001033422, exon 39 of 39)	3' UTR (NM_001033422, exon 39 of 39)	115085	NM_001033422	331401	Mm.259498	NM_001033422	ENSMUSG00000037475	Thoc2	6330441O12Rik|D130005M13Rik|Gm1139|Gm1793|Tho2	THO complex 2	protein-coding
mm_135190.1	chr16	36359498	36359510	-	1	NA	exon (NM_001082546, exon 3 of 3)	exon (NM_001082546, exon 3 of 3)	8066	NM_001082546	100034684	Mm.383561	NM_001082546	ENSMUSG00000071561	BC100530	-	cDNA sequence BC100530	protein-coding
mm_78866.1	chr9	44400524	44400535	+	1	NA	TTS (NR_106053)	TTS (NR_106053)	106	NR_106053	102465658		NR_106053	ENSMUSG00000099309	Mir7085	Gm27423|mmu-mir-7085	microRNA 7085	ncRNA
mm_8339.1	chr1	150164850	150164874	-	1	NA	promoter-TSS (NR_110420)	promoter-TSS (NR_110420)	86	NR_110420	102639566	Mm.417208	NR_110420	ENSMUSG00000097754	Ptgs2os2	Gm26687|Linc-cox2|Lincrna-cox2	prostaglandin-endoperoxide synthase 2, opposite strand 2	ncRNA
mm_82179.1	chr9	123853361	123853366	+	1	NA	3' UTR (NM_011798, exon 2 of 2)	3' UTR (NM_011798, exon 2 of 2)	-1464	NM_001110253	17281	Mm.252941	NM_148925	ENSMUSG00000025241	Fyco1	2810409M01Rik|Mem2|RUFY3|ZFYVE7	FYVE and coiled-coil domain containing 1	protein-coding
mm_64865.1	chr7	13278662	13278708	-	1	NA	promoter-TSS (NM_010715)	promoter-TSS (NM_010715)	36	NM_177312	321008	Mm.458832	NM_177312	ENSMUSG00000070814	6330408A02Rik	-	RIKEN cDNA 6330408A02 gene	protein-coding
mm_22021.1	chr2	168003493	168003503	-	1	NA	intron (NM_001080708, intron 2 of 21)	intron (NM_001080708, intron 2 of 21)	7095	NM_001080708	69553	Mm.68454	NM_001080708	ENSMUSG00000074577	Fam65c	2310033K02Rik|Gm124	family with sequence similarity 65, member C	protein-coding
mm_161407.1	chr15	3471615	3471615	-	1	NA	intron (NM_001048178, intron 1 of 8)	intron (NM_001048178, intron 1 of 8)	110227	NM_001286370	14600	Mm.3986	NM_010284	ENSMUSG00000055737	Ghr	GHBP|GHR/BP	growth hormone receptor	protein-coding
mm_9279.1	chr1	171634445	171634455	-	1	NA	3' UTR (NM_144539, exon 8 of 8)	3' UTR (NM_144539, exon 8 of 8)	7450	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_141918.1	chr17	35000028	35000037	-	1	NA	promoter-TSS (NM_011690)	promoter-TSS (NM_011690)	714	NM_033075	110956	Mm.22506	NM_033075		D17H6S56E-5	G7e	DNA segment, Chr 17, human D6S56E 5	protein-coding
mm_75702.1	chr8	68735059	68735147	-	1	NA	promoter-TSS (NM_001252623)	promoter-TSS (NM_001252623)	43	NM_001252623	234356	Mm.334569	NM_172753	ENSMUSG00000036356	Csgalnact1	4732435N03Rik|CSGalNAcT-1	chondroitin sulfate N-acetylgalactosaminyltransferase 1	protein-coding
mm_33912.1	chr4	136357424	136357432	+	1	NA	Intergenic	Intergenic	46486	NM_001277123	74326	Mm.31051	NM_028871	ENSMUSG00000066037	Hnrnpr	2610003J05Rik|2610528B01Rik|Hnrpr	heterogeneous nuclear ribonucleoprotein R	protein-coding
mm_103325.1	chr11	74457259	74457296	-	1	NA	intron (NM_001015046, intron 3 of 24)	intron (NM_001015046, intron 3 of 24)	92606	NM_001011851	258153	Mm.376124	NM_001011851	ENSMUSG00000058275	Olfr412	MOR127-5P	olfactory receptor 412	protein-coding
mm_171377.1	chr4	119282846	119282846	-	1	NA	exon (NM_011732, exon 4 of 8)	exon (NM_011732, exon 4 of 8)	11667	NM_011732	22608	Mm.258204	NM_011732	ENSMUSG00000028639	Ybx1	1700102N10Rik|C79409|EF1A|MSY1|Nsep1|YB-1|dbpB|mYB-1a	Y box protein 1	protein-coding
mm_157603.1	chrX	53370554	53370564	-	1	NA	promoter-TSS (NM_027409)	promoter-TSS (NM_027409)	0	NM_027409	70380	Mm.491083	NM_027409	ENSMUSG00000023074	Mospd1	1810018L05Rik	motile sperm domain containing 1	protein-coding
mm_22127.1	chr2	170357123	170357129	-	1	NA	intron (NR_040610, intron 2 of 7)	intron (NR_040610, intron 2 of 7)	765	NR_040610	73303	Mm.443297	NR_040610	ENSMUSG00000086999	Bcas1os2	1700040N02Rik	breast carcinoma amplified sequence 1, opposite strand 2	ncRNA
mm_7016.1	chr1	86526206	86526247	-	1	NA	promoter-TSS (NM_008972)	promoter-TSS (NM_008972)	-510	NM_008972	19231	Mm.19187	NM_008972	ENSMUSG00000026238	Ptma	Thym	prothymosin alpha	protein-coding
mm_14850.1	chr2	148440152	148440153	+	1	NA	3' UTR (NM_010740, exon 2 of 2)	3' UTR (NM_010740, exon 2 of 2)	3383	NM_010740	17064	Mm.681	NM_010740	ENSMUSG00000027435	Cd93	6030404G09Rik|AA145088|AA4.1|AW555904|C1qr1|C1qrp|Ly68	CD93 antigen	protein-coding
mm_148230.1	chr18	80440807	80440835	-	1	NA	intron (NM_026295, intron 10 of 12)	intron (NM_026295, intron 10 of 12)	28846	NM_026295	67655	Mm.312893	NM_026295	ENSMUSG00000033323	Ctdp1	4930563P03Rik|AW553592	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) phosphatase, subunit 1	protein-coding
mm_153849.1	chr19	46338633	46338670	-	1	NA	promoter-TSS (NM_001164295)	promoter-TSS (NM_001164295)	9	NM_001164294	67116	Mm.218848	NM_024192	ENSMUSG00000036748	Cuedc2	3010002G01Rik	CUE domain containing 2	protein-coding
mm_57335.1	chr6	124742644	124742670	-	1	NA	3' UTR (NM_007881, exon 10 of 10)	3' UTR (NM_007881, exon 10 of 10)	-1578	NM_013535	14790	Mm.439877	NM_013535	ENSMUSG00000072772	Grcc10	2310033H05Rik|C10	gene rich cluster, C10 gene	protein-coding
mm_25858.1	chr3	129797564	129797572	+	1	NA	intron (NM_001287224, intron 2 of 3)	intron (NM_001287224, intron 2 of 3)	6462	NM_001287224	242235	Mm.302549	NM_001205102	ENSMUSG00000093865	Lrit3	Gm421	leucine-rich repeat, immunoglobulin-like and transmembrane domains 3	protein-coding
mm_41767.1	chr5	103501366	103501425	+	1	NA	exon (NM_011204, exon 7 of 48)	exon (NM_011204, exon 7 of 48)	76203	NM_011204	19249	Mm.3414	NM_011204	ENSMUSG00000034573	Ptpn13	AI324989|PTP-BL|PTPL1|Ptpri|RIP	protein tyrosine phosphatase, non-receptor type 13	protein-coding
mm_47262.1	chr5	121836754	121836764	-	1	NA	promoter-TSS (NM_001306128)	promoter-TSS (NM_001306128)	100	NM_001306128	16923	Mm.65493	NM_008507	ENSMUSG00000042594	Sh2b3	AI429800|Lnk	SH2B adaptor protein 3	protein-coding
mm_42716.1	chr5	120476523	120476538	+	1	NA	promoter-TSS (NM_145565)	promoter-TSS (NM_145565)	-17	NM_145565	231691	Mm.28685	NM_145565	ENSMUSG00000029597	Sds	4432411H13Rik|SDH	serine dehydratase	protein-coding
mm_71952.1	chr8	70498622	70498625	+	1	NA	exon (NM_018827, exon 2 of 9)	exon (NM_018827, exon 2 of 9)	5492	NM_018827	12931	Mm.335584	NM_018827	ENSMUSG00000007888	Crlf1	CLF-1|CRLM-3|CRLM3|NR6|NR6.1	cytokine receptor-like factor 1	protein-coding
mm_147698.1	chr18	60804003	60804014	-	1	NA	exon (NM_010545, exon 1 of 8)	exon (NM_010545, exon 1 of 8)	159	NM_010545	16149	Mm.439737	NM_010545	ENSMUSG00000024610	Cd74	CLIP|DHLAG|HLADG|Ia-GAMMA|Ii	CD74 antigen (invariant polypeptide of major histocompatibility complex, class II antigen-associated)	protein-coding
mm_24273.1	chr3	89203978	89203994	+	1	NA	exon (NM_001077411, exon 3 of 11)	exon (NM_001077411, exon 3 of 11)	1061	NR_122037	14466	Mm.5031	NM_008094	ENSMUSG00000028048	Gba	GBA1|GC|GCase|GLUC|betaGC	glucosidase, beta, acid	protein-coding
mm_124001.1	chr14	75844953	75844998	-	1	NA	promoter-TSS (NM_009429)	promoter-TSS (NM_009429)	-11	NR_045294	100043189	Mm.426329	NR_045294		Gm4285	-	predicted gene 4285	ncRNA
mm_140826.1	chr17	23644954	23644958	-	1	NA	5' UTR (NM_001033339, exon 1 of 10)	5' UTR (NM_001033339, exon 1 of 10)	313	NM_001033339	240047	Mm.235343	NM_001033339	ENSMUSG00000023903	Mmp25	F730048C11Rik|Leukolysin|MMP20|MT6-MMP	matrix metallopeptidase 25	protein-coding
mm_436.1	chr1	34678150	34678175	+	1	NA	Intergenic	CpG	-41952	NR_033627	241051	Mm.282827	NR_033627		AA619741	-	PHD finger protein 19 pseudogene	pseudo
mm_3353.1	chr1	138164935	138164941	+	1	NA	intron (NM_001111316, intron 1 of 31)	intron (NM_001111316, intron 1 of 31)	10188	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_99580.1	chr11	104231466	104231507	+	1	NA	promoter-TSS (NM_010838)	promoter-TSS (NM_010838)	50	NM_001285454	17762	Mm.1287	NM_010838	ENSMUSG00000018411	Mapt	AI413597|AW045860|Mtapt|Tau	microtubule-associated protein tau	protein-coding
mm_162548.1	chr1	170959895	170959899	-	1	NA	TTS (NM_001077189)	TTS (NM_001077189)	16174	NM_001077189	14130	Mm.425062	NM_010187	ENSMUSG00000026656	Fcgr2b	AI528646|CD32|F630109E10Rik|Fc[g]RII|FcgRII|Fcgr2|Fcgr2a|Fcr-2|Fcr-3|Ly-17|Ly-m20|LyM-1|Lym-1|fcRII	Fc receptor, IgG, low affinity IIb	protein-coding
mm_155708.1	chrX	96095993	96096003	+	1	NA	promoter-TSS (NM_010833)	promoter-TSS (NM_010833)	-47	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_107745.1	chr12	58813883	58813901	+	1	NA	Intergenic	Intergenic	198125	NM_009147	20334	Mm.491137	NM_009147	ENSMUSG00000020986	Sec23a	Msec23|Sec23r	SEC23 homolog A, COPII coat complex component	protein-coding
mm_59304.1	chr7	25221418	25221469	+	1	NA	promoter-TSS (NM_175436)	promoter-TSS (NM_175436)	18	NM_175436	210172	Mm.129371	NM_175436	ENSMUSG00000046541	Zfp526	D030024H03Rik|Znf526	zinc finger protein 526	protein-coding
mm_6097.1	chr1	63442244	63442257	-	1	NA	Intergenic	MLTR25A|LTR|ERVK	-3641	NM_011780	23792	Mm.124892	NM_011780	ENSMUSG00000025964	Adam23	AW046396|MDC3	a disintegrin and metallopeptidase domain 23	protein-coding
mm_43314.1	chr5	134945269	134945307	+	1	NA	3' UTR (NM_009903, exon 1 of 1)	3' UTR (NM_009903, exon 1 of 1)	1646	NM_009903	12740	Mm.7339	NM_009903	ENSMUSG00000047501	Cldn4	Cep-r|Cpetr|Cpetr1	claudin 4	protein-coding
mm_17128.1	chr2	24819095	24819114	-	1	NA	intron (NM_001012518, intron 16 of 26)	Lx9|LINE|L1	-55952	NM_007579	12287	Mm.4424	NM_007579	ENSMUSG00000004113	Cacna1b	AW050276|AW060892|AW822256|BIII|Cav2.2|Cchn1a|alpha(1B)	calcium channel, voltage-dependent, N type, alpha 1B subunit	protein-coding
mm_143229.1	chr17	63428060	63428068	-	1	NA	intron (NM_015794, intron 4 of 8)	(A)n|Simple_repeat|Simple_repeat	72516	NM_015794	50758	Mm.136366	NM_015794	ENSMUSG00000023965	Fbxl17	6330576B01Rik|AI452053|BB073797|C130023C01Rik|Fbx13|Fbxo13	F-box and leucine-rich repeat protein 17	protein-coding
mm_60857.1	chr7	45870457	45870473	+	1	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	-2375	NM_133950	68137	Mm.298433	NM_133950	ENSMUSG00000002778	Kdelr1	8030486F04Rik|AW215843|Erd2.1	KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 1	protein-coding
mm_59745.1	chr7	28818681	28818705	+	1	NA	exon (NM_177301, exon 8 of 13)	exon (NM_177301, exon 8 of 13)	-6645	NM_016772	51798	Mm.291776	NM_016772	ENSMUSG00000053898	Ech1	AA617331	enoyl coenzyme A hydratase 1, peroxisomal	protein-coding
mm_84628.1	chr9	70692014	70692040	-	1	NA	intron (NM_007399, intron 1 of 15)	intron (NM_007399, intron 1 of 15)	13045	NM_007399	11487	Mm.3037	NM_007399	ENSMUSG00000054693	Adam10	1700031C13Rik|MADM|kuz|kuzbanian	a disintegrin and metallopeptidase domain 10	protein-coding
mm_139285.1	chr17	48299953	48299965	+	1	NA	promoter-TSS (NM_001033405)	promoter-TSS (NM_001033405)	-79	NM_001033405	328833	Mm.329104	NM_001033405	ENSMUSG00000071068	Treml2	AW049306|Gm750|Tlt2	triggering receptor expressed on myeloid cells-like 2	protein-coding
mm_90247.1	chr10	121496977	121496995	+	1	NA	Intergenic	Intergenic	-20736	NM_138956	192678	Mm.41265	NM_138956	ENSMUSG00000025795	Rassf3	AW212023|AW322379	Ras association (RalGDS/AF-6) domain family member 3	protein-coding
mm_56994.1	chr6	120933806	120933809	-	1	NA	3' UTR (NM_001270475, exon 32 of 32)	3' UTR (NM_001270475, exon 32 of 32)	-16987	NM_007544	12122	Mm.235081	NM_007544	ENSMUSG00000004446	Bid	2700049M22Rik|AI875481|AU022477	BH3 interacting domain death agonist	protein-coding
mm_92416.1	chr10	76874481	76874498	-	1	NA	intron (NM_001347216, intron 2 of 15)	intron (NM_001347216, intron 2 of 15)	87458	NM_001347216	59093	Mm.272803	NM_021568	ENSMUSG00000001120	Pcbp3	AlphaCP-3	poly(rC) binding protein 3	protein-coding
mm_96035.1	chr11	59556311	59556326	+	1	NA	intron (NM_145827, intron 6 of 9)	intron (NM_145827, intron 6 of 9)	13632	NM_145827	216799	Mm.54174	NM_145827	ENSMUSG00000032691	Nlrp3	AGTAVPRL|AII/AVP|Cias1|FCAS|FCU|MWS|Mmig1|NALP3|Pypaf1	NLR family, pyrin domain containing 3	protein-coding
mm_167467.1	chr8	126029299	126029301	+	1	NA	intron (NM_008430, intron 2 of 2)	intron (NM_008430, intron 2 of 2)	34198	NM_008430	16525	Mm.10800	NM_008430	ENSMUSG00000033998	Kcnk1	AI788889|TWIK-1	potassium channel, subfamily K, member 1	protein-coding
mm_129723.1	chr15	81960819	81960846	-	1	NA	promoter-TSS (NM_001282040)	promoter-TSS (NM_001282040)	98	NM_001282040	29858	Mm.18939	NM_013872	ENSMUSG00000022474	Pmm1	C77612	phosphomannomutase 1	protein-coding
mm_75808.1	chr8	70234402	70234459	-	1	NA	promoter-TSS (NM_133972)	promoter-TSS (NM_133972)	-8	NM_133972	76813	Mm.383251	NM_133972	ENSMUSG00000002343	Armc6	2410153K17Rik|AW554412	armadillo repeat containing 6	protein-coding
mm_152373.1	chr19	10204391	10204413	-	1	NA	promoter-TSS (NM_001271614)	promoter-TSS (NM_001271614)	200	NM_026919	69038	Mm.375100	NM_026919	ENSMUSG00000036372	Tmem258	1810006K21Rik	transmembrane protein 258	protein-coding
mm_126025.1	chr15	76696726	76696747	+	1	NA	promoter-TSS (NM_182805)	promoter-TSS (NM_182805)	10	NM_182805	76282	Mm.30130	NM_182805	ENSMUSG00000022546	Gpt	1300007J06Rik|2310022B03Rik|ALT|ALT1|Gpt-1|Gpt1	glutamic pyruvic transaminase, soluble	protein-coding
mm_23139.1	chr3	38885743	38885764	+	1	NA	Intergenic	CpG	-1187	NM_183221	329628	Mm.316210	NM_183221	ENSMUSG00000046743	Fat4	6030410K14Rik|9430004M15	FAT atypical cadherin 4	protein-coding
mm_58972.1	chr7	19004360	19004377	+	1	NA	5' UTR (NM_178757, exon 1 of 1)	5' UTR (NM_178757, exon 1 of 1)	303	NM_178757	272359	Mm.274237	NM_178757	ENSMUSG00000044030	Irf2bp1	6330414O09Rik|C530033F24	interferon regulatory factor 2 binding protein 1	protein-coding
mm_159444.1	chr3	129203836	129203836	+	1	NA	intron (NM_011098, intron 1 of 4)	intron (NM_011098, intron 1 of 4)	3958	NM_001042504	18741	Mm.246804	NM_011098	ENSMUSG00000028023	Pitx2	9430085M16Rik|Brx1|Brx1b|Munc30|Otlx2|Ptx2|Rieg	paired-like homeodomain transcription factor 2	protein-coding
mm_46671.1	chr5	108795353	108795374	-	1	NA	promoter-TSS (NM_026109)	promoter-TSS (NM_026109)	0	NM_026109	67366	Mm.46274	NM_026109	ENSMUSG00000004821	Tmed11	1810008K16Rik	transmembrane p24 trafficking protein 11	protein-coding
mm_73318.1	chr8	105225337	105225345	+	1	NA	5' UTR (NM_145604, exon 1 of 16)	5' UTR (NM_145604, exon 1 of 16)	153	NM_145604	234678	Mm.27186	NM_145604	ENSMUSG00000031889	D230025D16Rik	BC006874|Lin10	RIKEN cDNA D230025D16 gene	protein-coding
mm_164541.1	chr17	8283836	8283846	+	1	NA	promoter-TSS (NM_018819)	promoter-TSS (NM_018819)	28	NM_018819	55951	Mm.288510	NM_018819	ENSMUSG00000023861	Mpc1	0610006G08Rik|3830411I18Rik|Brp44l	mitochondrial pyruvate carrier 1	protein-coding
mm_146725.1	chr18	15064422	15064443	-	1	NA	promoter-TSS (NM_001142731)	promoter-TSS (NM_001142731)	-850	NM_001142731	106931	Mm.329299	NM_134112	ENSMUSG00000036225	Kctd1	4933402K10Rik|AI661543|AW553000	potassium channel tetramerisation domain containing 1	protein-coding
mm_42357.1	chr5	114911701	114911735	+	1	NA	3' UTR (NM_011854, exon 6 of 6)	3' UTR (NM_011854, exon 6 of 6)	-11522	NM_145209	231655	Mm.95479	NM_145209	ENSMUSG00000041827	Oasl1	7530414C13Rik|oasl9	2'-5' oligoadenylate synthetase-like 1	protein-coding
mm_152022.1	chr19	6044891	6044901	-	1	NA	Intergenic	Intergenic	-1680	NM_028769	74126	Mm.149870	NM_028769	ENSMUSG00000024807	Syvn1	1200010C09Rik|AW211966|C85322|D530017H19Rik|Hrd1	synovial apoptosis inhibitor 1, synoviolin	protein-coding
mm_167238.1	chr8	19123715	19123715	+	1	NA	promoter-TSS (NM_183035)	promoter-TSS (NM_183035)	-37	NM_183035	360211	Mm.271557	NM_183035	ENSMUSG00000052554	Defb34	BD-34	defensin beta 34	protein-coding
mm_136096.1	chr16	85079884	85079898	-	1	NA	exon (NM_001198823, exon 5 of 18)	exon (NM_001198823, exon 5 of 18)	93816	NM_001198825	11820	Mm.277585	NM_007471	ENSMUSG00000022892	App	Abeta|Abpp|Adap|Ag|Cvap|E030013M08Rik|betaApp	amyloid beta (A4) precursor protein	protein-coding
mm_85287.1	chr9	99717260	99717274	-	1	NA	promoter-TSS (NM_001194921)	promoter-TSS (NM_001194921)	0	NM_001194923	56492	Mm.386784	NM_019815	ENSMUSG00000032473	Cldn18	-	claudin 18	protein-coding
mm_18388.1	chr2	60125608	60125618	-	1	NA	5' UTR (NM_001001182, exon 1 of 36)	5' UTR (NM_001001182, exon 1 of 36)	127	NM_001001182	407823	Mm.228071	NM_001001182	ENSMUSG00000026987	Baz2b	5830435C13Rik|BC053917|D2Ertd794e	bromodomain adjacent to zinc finger domain, 2B	protein-coding
mm_18799.1	chr2	73892299	73892368	-	1	NA	intron (NM_001284374, intron 1 of 11)	CpG	306	NM_001284371	11909	Mm.209903	NM_009715	ENSMUSG00000027104	Atf2	Atf-2|CRE-BP|Creb2|D130078H02Rik|D18875|Tg(Gzma-Klra1)7Wum|mXBP	activating transcription factor 2	protein-coding
mm_19312.1	chr2	90546940	90546943	-	1	NA	intron (NM_008982, intron 1 of 23)	(TTCA)n|Simple_repeat|Simple_repeat	33706	NM_008982	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_33928.1	chr4	136880496	136880554	+	1	NA	exon (NM_009777, exon 3 of 3)	exon (NM_009777, exon 3 of 3)	5652	NM_009777	12260	Mm.2570	NM_009777	ENSMUSG00000036905	C1qb	-	complement component 1, q subcomponent, beta polypeptide	protein-coding
mm_12594.1	chr2	74579040	74579048	+	1	NA	promoter-TSS (NM_027133)	promoter-TSS (NM_027133)	-96	NM_027133	69605	Mm.156113	NM_027133	ENSMUSG00000009207	Lnpk	2310011O18Rik|4921514L11Rik|9530051D01Rik|AI666268|Lnp|Lnpk1|Ul|ulnaless	lunapark, ER junction formation factor	protein-coding
mm_90881.1	chr10	9782829	9782831	-	1	NA	intron (NM_001081344, intron 19 of 25)	intron (NM_001081344, intron 19 of 25)	98108	NR_038036	620417	Mm.378085	NR_038036		Gm6150	-	predicted gene 6150	ncRNA
mm_100746.1	chr11	4135355	4135357	-	1	NA	exon (NM_027859, exon 1 of 9)	exon (NM_027859, exon 1 of 9)	196	NM_027859	71673	Mm.240586	NM_027859	ENSMUSG00000003581	Rnf215	0610009J22Rik|AW557025|C77903	ring finger protein 215	protein-coding
mm_76003.1	chr8	72491673	72491685	-	1	NA	intron (NM_177766, intron 2 of 5)	intron (NM_177766, intron 2 of 5)	935	NM_177766	270066	Mm.291461	NM_177766	ENSMUSG00000019731	Slc35e1	6030458H05|AA408278	solute carrier family 35, member E1	protein-coding
mm_14644.1	chr2	136892250	136892272	+	1	NA	promoter-TSS (NM_001286983)	promoter-TSS (NM_001286983)	-2	NM_028834	74243	Mm.330612	NM_028201	ENSMUSG00000027281	Slx4ip	2210009G21Rik|2410004I22Rik|C85661|Slxip	SLX4 interacting protein	protein-coding
mm_18651.1	chr2	69722748	69722783	-	1	NA	promoter-TSS (NM_001081086)	promoter-TSS (NM_001081086)	-323	NM_001081086	228005	Mm.11815	NM_001081086	ENSMUSG00000042133	Ppig	AU019516|AU022200|B230312B02Rik|CYP|SRCyp	peptidyl-prolyl isomerase G (cyclophilin G)	protein-coding
mm_38963.1	chr4	150866853	150866875	-	1	NA	exon (NM_133753, exon 4 of 4)	exon (NM_133753, exon 4 of 4)	11773	NM_133753	74155	Mm.318841	NM_133753	ENSMUSG00000028967	Errfi1	1300002F13Rik|AI788755|Mig-6|Mig6|RALT	ERBB receptor feedback inhibitor 1	protein-coding
mm_121350.1	chr14	116925380	116925394	+	1	NA	promoter-TSS (NM_011821)	promoter-TSS (NM_011821)	90	NM_011821	23888	Mm.440025	NM_011821	ENSMUSG00000058571	Gpc6	-	glypican 6	protein-coding
mm_61355.1	chr7	68364105	68364110	+	1	NA	Intergenic	L1MB7|LINE|L1	-53317	NR_046208	71244	Mm.410787	NR_046208	ENSMUSG00000108924	4933436H12Rik	-	RIKEN cDNA 4933436H12 gene	ncRNA
mm_130063.1	chr15	89187438	89187446	-	1	NA	exon (NM_027081, exon 10 of 20)	exon (NM_027081, exon 10 of 20)	-1905	NR_105923	102465578		NR_105923	ENSMUSG00000098663	Mir6958	Gm27581|mmu-mir-6958	microRNA 6958	ncRNA
mm_82027.1	chr9	121898410	121898423	+	1	NA	promoter-TSS (NM_021609)	promoter-TSS (NM_021609)	61	NM_021609	59289	Mm.258105	NM_021609	ENSMUSG00000044534	Ackr2	AI464239|CCR10|CCR9|Ccbp2|Cmkbr9|D6	atypical chemokine receptor 2	protein-coding
mm_132882.1	chr16	48790270	48790281	+	1	NA	Intergenic	Intergenic	-18319	NM_198297	77647	Mm.167298	NM_198297	ENSMUSG00000030775	Trat1	C030046M14Rik|Tcrim|Trim	T cell receptor associated transmembrane adaptor 1	protein-coding
mm_169122.1	chr13	51817661	51817672	+	1	NA	Intergenic	(CCTG)n|Simple_repeat|Simple_repeat	-23919	NM_013660	20354	Mm.33903	NM_013660	ENSMUSG00000021451	Sema4d	CD100|Semacl2|Semaj|Semcl2|coll-4	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D	protein-coding
mm_64480.1	chr7	143064970	143064977	+	1	NA	intron (NM_133655, intron 2 of 7)	intron (NM_133655, intron 2 of 7)	-4395	NM_020285	56844	Mm.139675	NM_020285	ENSMUSG00000045752	Tssc4	AA241958|ESTM671070	tumor-suppressing subchromosomal transferable fragment 4	protein-coding
mm_146554.1	chr18	6223688	6223698	-	1	NA	intron (NM_008448, intron 9 of 25)	intron (NM_008448, intron 9 of 25)	17831	NM_008448	16573	Mm.223744	NM_008448	ENSMUSG00000006740	Kif5b	AL022807|Khc|Khcs|Kns1|Ukhc	kinesin family member 5B	protein-coding
mm_132630.1	chr16	38910111	38910115	+	1	NA	intron (NM_170599, intron 1 of 6)	intron (NM_170599, intron 1 of 6)	7768	NM_170599	207683	Mm.245564	NM_170599	ENSMUSG00000022790	Igsf11	1700025L02Rik|BT-IgSF|Igsf13	immunoglobulin superfamily, member 11	protein-coding
mm_73644.1	chr8	110847016	110847049	+	1	NA	promoter-TSS (NM_133973)	promoter-TSS (NM_133973)	8	NM_133973	102339	Mm.272930	NM_133973	ENSMUSG00000031753	Cog4	AW554810|D8Ertd515e	component of oligomeric golgi complex 4	protein-coding
mm_43344.1	chr5	135126421	135126427	+	1	NA	intron (NM_021455, intron 7 of 16)	intron (NM_021455, intron 7 of 16)	19533	NM_021455	58805	Mm.34213	NM_021455	ENSMUSG00000005373	Mlxipl	ChREBP|Mlx|WS-bHLH|Wbscr14|bHLHd14	MLX interacting protein-like	protein-coding
mm_88449.1	chr10	77550489	77550507	+	1	NA	intron (NM_008404, intron 7 of 15)	intron (NM_008404, intron 7 of 15)	20150	NM_008404	16414	Mm.1137	NM_008404	ENSMUSG00000000290	Itgb2	2E6|AI528527|Cd18|LAD|LCAMB|Lfa1|MF17	integrin beta 2	protein-coding
mm_72257.1	chr8	75096909	75096938	+	1	NA	exon (NM_010442, exon 3 of 5)	exon (NM_010442, exon 3 of 5)	3305	NM_010442	15368	Mm.276389	NM_010442	ENSMUSG00000005413	Hmox1	D8Wsu38e|HO-1|HO1|Hemox|Hmox|Hsp32	heme oxygenase 1	protein-coding
mm_78845.1	chr9	44327577	44327603	+	1	NA	exon (NM_007875, exon 2 of 9)	exon (NM_007875, exon 2 of 9)	745	NM_007875	13478	Mm.18353	NM_007875	ENSMUSG00000032123	Dpagt1	AU021132|Dpagt2|GPT|Gnpta	dolichyl-phosphate (UDP-N-acetylglucosamine) acetylglucosaminephosphotransferase 1 (GlcNAc-1-P transferase)	protein-coding
mm_135437.1	chr16	45383211	45383227	-	1	NA	3' UTR (NM_010818, exon 6 of 6)	3' UTR (NM_010818, exon 6 of 6)	25834	NM_010818	17470	Mm.245851	NM_010818	ENSMUSG00000022661	Cd200	Mox2|OX2	CD200 antigen	protein-coding
mm_169109.1	chr13	44869896	44869896	-	1	NA	intron (NM_001205044, intron 4 of 18)	LSU-rRNA_Hsa|rRNA|rRNA	132200	NM_025772	94245	Mm.352311	NM_025772	ENSMUSG00000057531	Dtnbp1	5430437B18Rik|AW048963|Bloc1s8|dysbindin|sdy	dystrobrevin binding protein 1	protein-coding
mm_8585.1	chr1	155973356	155973372	-	1	NA	promoter-TSS (NM_001039184)	promoter-TSS (NM_001039184)	-109	NM_001039184	74081	Mm.260247	NM_001039184	ENSMUSG00000033671	Cep350	4933409L06Rik|6430546F08Rik	centrosomal protein 350	protein-coding
mm_114153.1	chr13	55401098	55401102	+	1	NA	intron (NM_011392, intron 4 of 12)	intron (NM_011392, intron 4 of 12)	1452	NM_011392	20505	Mm.276355	NM_011392	ENSMUSG00000021490	Slc34a1	NaPi-IIa|Npt2|Npt2a|Slc17a2	solute carrier family 34 (sodium phosphate), member 1	protein-coding
mm_95025.1	chr11	32024713	32024739	+	1	NA	intron (NM_001290680, intron 3 of 4)	intron (NM_001290680, intron 3 of 4)	23449	NM_001290681	18197	Mm.3304	NM_008741	ENSMUSG00000020297	Nsg2	-	neuron specific gene family member 2	protein-coding
mm_162369.1	chr1	66816033	66816048	-	1	NA	intron (NM_177645, intron 1 of 13)	intron (NM_177645, intron 1 of 13)	1555	NM_177645	68691	Mm.240912	NM_177645	ENSMUSG00000026004	Kansl1l	1110028C15Rik|1190030G24|AI427598|C430010P07Rik|mKIAA4189	KAT8 regulatory NSL complex subunit 1-like	protein-coding
mm_9600.1	chr1	175492540	175492556	-	1	NA	promoter-TSS (NM_011880)	promoter-TSS (NM_011880)	-3	NM_001347195	24012	Mm.7956	NM_011880	ENSMUSG00000026527	Rgs7	-	regulator of G protein signaling 7	protein-coding
mm_160826.1	chr11	36944285	36944285	-	1	NA	promoter-TSS (NM_001290702)	promoter-TSS (NM_001290702)	-44	NM_011856	23964	Mm.439889	NM_011856	ENSMUSG00000049336	Tenm2	Odz2|Odz3|Ten-2|Ten-m2	teneurin transmembrane protein 2	protein-coding
mm_18053.1	chr2	39196865	39196880	-	1	NA	TTS (NM_024209)	TTS (NM_024209)	-6142	NM_178778	320271	Mm.204836	NM_178778	ENSMUSG00000035236	Scai	9330112M16|A930041I02Rik|AI662729	suppressor of cancer cell invasion	protein-coding
mm_103945.1	chr11	84067064	84067095	-	1	NA	intron (NM_019819, intron 1 of 2)	intron (NM_019819, intron 1 of 2)	1278	NM_019819	56405	Mm.240885	NM_019819	ENSMUSG00000018648	Dusp14	1110014C10Rik|2310042C07Rik|D11Ertd395e|MKP-L|Mkp6	dual specificity phosphatase 14	protein-coding
mm_72162.1	chr8	72219727	72219785	+	1	NA	promoter-TSS (NM_026455)	promoter-TSS (NM_026455)	26	NM_026455	67922	Mm.28327	NM_026455	ENSMUSG00000003039	Fam32a	2510049I19Rik|AW822030|OTAG-12|Otag12	family with sequence similarity 32, member A	protein-coding
mm_84406.1	chr9	65555460	65555475	-	1	NA	3' UTR (NM_153119, exon 6 of 6)	3' UTR (NM_153119, exon 6 of 6)	24620	NM_153119	102595	Mm.247303	NM_153119	ENSMUSG00000050721	Plekho2	AI840980|Plekhq1	pleckstrin homology domain containing, family O member 2	protein-coding
mm_32083.1	chr4	98395892	98395908	+	1	NA	promoter-TSS (NM_172696)	promoter-TSS (NM_172696)	74	NM_172696	12695	Mm.90218	NM_007704	ENSMUSG00000061859	Patj	Cipp|Inadl	PATJ, crumbs cell polarity complex component	protein-coding
mm_78814.1	chr9	44072197	44072211	+	1	NA	intron (NM_016808, intron 1 of 12)	intron (NM_016808, intron 1 of 12)	2775	NM_016808	53376	Mm.272770	NM_016808	ENSMUSG00000032010	Usp2	B930035K21Rik|Ubp41	ubiquitin specific peptidase 2	protein-coding
mm_129834.1	chr15	83149358	83149364	-	1	NA	promoter-TSS (NM_178627)	promoter-TSS (NM_178627)	17	NM_001347082	73826	Mm.23758	NM_178627	ENSMUSG00000041815	Poldip3	1110008P04Rik|AA408269|AL022852|C77954|PDIP46|SKAR|mKIAA1649	polymerase (DNA-directed), delta interacting protein 3	protein-coding
mm_167135.1	chr7	127052681	127052694	-	1	NA	promoter-TSS (NM_026918)	promoter-TSS (NM_026918)	-710	NM_026918	69036	Mm.21835	NM_026918	ENSMUSG00000049350	Zg16	1810010M01Rik|AI593689|ZG16p	zymogen granule protein 16	protein-coding
mm_28663.1	chr3	95251149	95251160	-	1	NA	promoter-TSS (NM_001168356)	promoter-TSS (NM_001168356)	39	NM_001168356	171388	Mm.331209	NM_134253	ENSMUSG00000028115	Bnipl	1700128A13Rik|BNIP-S|BNIPL1|BNIPL2|PP73|PP753	BCL2/adenovirus E1B 19kD interacting protein like	protein-coding
mm_36221.1	chr4	62519886	62519967	-	1	NA	promoter-TSS (NM_001276446)	promoter-TSS (NM_001276446)	-17	NM_001276446	17025	Mm.6988	NM_008525	ENSMUSG00000028393	Alad	ALADH|Lv	aminolevulinate, delta-, dehydratase	protein-coding
mm_4461.1	chr1	172705912	172705947	+	1	NA	Intergenic	Intergenic	7873	NM_007768	12944	Mm.28767	NM_007768	ENSMUSG00000037942	Crp	AI255847	C-reactive protein, pentraxin-related	protein-coding
mm_94857.1	chr11	24076907	24076924	+	1	NA	Intergenic	CpG	-1141	NM_016707	14025	Mm.53687	NM_016707	ENSMUSG00000000861	Bcl11a	2810047E18Rik|BCL-11A|Ctip1|D930021L15Rik|Evi9|Evi9a|Evi9b|Evi9c|mKIAA1809	B cell CLL/lymphoma 11A (zinc finger protein)	protein-coding
mm_149250.1	chr19	10389219	10389233	+	1	NA	5' UTR (NM_018801, exon 1 of 9)	5' UTR (NM_018801, exon 1 of 9)	136	NM_173068	54525	Mm.182654	NM_018801	ENSMUSG00000024743	Syt7	AI851541|B230112P13Rik	synaptotagmin VII	protein-coding
mm_45919.1	chr5	89441615	89441632	-	1	NA	exon (NM_008096, exon 5 of 13)	exon (NM_008096, exon 5 of 13)	16275	NM_008096	14473	Mm.196595	NM_008096	ENSMUSG00000035540	Gc	DBP|VDB	group specific component	protein-coding
mm_92897.1	chr10	83239345	83239381	-	1	NA	intron (NM_177388, intron 10 of 10)	intron (NM_177388, intron 10 of 10)	98454	NM_177388	338365	Mm.67073	NM_177388	ENSMUSG00000034591	Slc41a2	A230035L05Rik|SLC41A1-L1	solute carrier family 41, member 2	protein-coding
mm_131330.1	chr16	13247076	13247109	+	1	NA	Intergenic	Intergenic	-9389	NM_001122667	239719	Mm.270643	NM_153588	ENSMUSG00000009569	Mkl2	ENSMUSG00000075401|Gt4-1|MRTF-B|Mrtfb|mKIAA1243	MKL/myocardin-like 2	protein-coding
mm_138924.1	chr17	43667514	43667537	+	1	NA	promoter-TSS (NM_028711)	promoter-TSS (NM_028711)	153	NM_018887	56050	Mm.17991	NM_018887	ENSMUSG00000023963	Cyp39a1	mCYP39A1	cytochrome P450, family 39, subfamily a, polypeptide 1	protein-coding
mm_15248.1	chr2	154689649	154689673	+	1	NA	exon (NM_029362, exon 2 of 5)	exon (NM_029362, exon 2 of 5)	32635	NM_029362	75608	Mm.262480	NM_029362	ENSMUSG00000038467	Chmp4b	2010012F05Rik|C76846|Snf7-2	charged multivesicular body protein 4B	protein-coding
mm_34260.1	chr4	141421660	141421676	+	1	NA	5' UTR (NM_013868, exon 1 of 3)	5' UTR (NM_013868, exon 1 of 3)	889	NM_013868	29818	Mm.46181	NM_013868	ENSMUSG00000006221	Hspb7	27kDa|Hsp25-2|cvHsp	heat shock protein family, member 7 (cardiovascular)	protein-coding
mm_26050.1	chr3	135689174	135689203	+	1	NA	intron (NM_008689, intron 1 of 24)	intron (NM_008689, intron 1 of 24)	2359	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_48248.1	chr5	137786682	137786706	-	1	NA	promoter-TSS (NM_144913)	promoter-TSS (NM_144913)	7	NM_144913	231803	Mm.61193	NM_144913	ENSMUSG00000029726	Mepce	Bcdin3|D5Wsu46e	methylphosphate capping enzyme	protein-coding
mm_52326.1	chr6	108839214	108839222	+	1	NA	intron (NM_138677, intron 2 of 11)	intron (NM_138677, intron 2 of 11)	10577	NM_138677	192193	Mm.21596	NM_138677	ENSMUSG00000030104	Edem1	A130059K23Rik|EDEM|mKIAA0212	ER degradation enhancer, mannosidase alpha-like 1	protein-coding
mm_99240.1	chr11	101078364	101078408	+	1	NA	promoter-TSS (NM_010475)	promoter-TSS (NM_010475)	-25	NM_010475	15485	Mm.188939	NM_010475	ENSMUSG00000019301	Hsd17b1	17HSDB1|17beta-HSD|E2DH|Hsd17ba	hydroxysteroid (17-beta) dehydrogenase 1	protein-coding
mm_26837.1	chr3	13933884	13933906	-	1	NA	intron (NM_178631, intron 3 of 9)	intron (NM_178631, intron 3 of 9)	-12477	NM_001163329	76897	Mm.422625	NM_178631	ENSMUSG00000039717	Ralyl	0710005M24Rik	RALY RNA binding protein-like	protein-coding
mm_116018.1	chr13	24831323	24831333	-	1	NA	promoter-TSS (NM_019551)	promoter-TSS (NM_019551)	161	NM_025790	66834	Mm.2125	NM_025790	ENSMUSG00000006717	Acot13	0610006O17Rik|Them2	acyl-CoA thioesterase 13	protein-coding
mm_31133.1	chr4	43249444	43249500	+	1	NA	exon (NM_021468, exon 25 of 40)	exon (NM_021468, exon 25 of 40)	-17687	NM_177195	320571	Mm.74465	NM_177195	ENSMUSG00000028457	Atp8b5	4930417M19Rik|Feta	ATPase, class I, type 8B, member 5	protein-coding
mm_136342.1	chr16	92603221	92603229	-	1	NA	3' UTR (NM_001111021, exon 8 of 8)	3' UTR (NM_001111021, exon 8 of 8)	94104	NM_001111023	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_6601.1	chr1	75317361	75317491	-	1	NA	promoter-TSS (NM_016878)	promoter-TSS (NM_016878)	211	NM_001110831	13437	Mm.24680	NM_016878	ENSMUSG00000026209	Dnpep	AA407814	aspartyl aminopeptidase	protein-coding
mm_142066.1	chr17	35685421	35685431	-	1	NA	exon (NM_001198833, exon 13 of 18)	exon (NM_001198833, exon 13 of 18)	-11683	NM_010364	14885	Mm.10182	NM_010364	ENSMUSG00000001524	Gtf2h4	AW545633|BTF2 p52|p52	general transcription factor II H, polypeptide 4	protein-coding
mm_76743.1	chr8	95203029	95203056	-	1	NA	Intergenic	Intergenic	-60502	NM_001145831	16582	Mm.378951	NM_010631	ENSMUSG00000031788	Kifc3	AI325457|BB123200	kinesin family member C3	protein-coding
mm_141625.1	chr17	32917018	32917022	-	1	NA	promoter-TSS (NM_022434)	promoter-TSS (NM_022434)	67	NM_022434	64385	Mm.486449	NM_022434	ENSMUSG00000024292	Cyp4f14	1300014O15Rik|cyp4f-14	cytochrome P450, family 4, subfamily f, polypeptide 14	protein-coding
mm_94477.1	chr11	6560227	6560240	+	1	NA	promoter-TSS (NM_001190344)	promoter-TSS (NM_001190344)	50	NM_001190344	216527	Mm.221271	NM_146014	ENSMUSG00000000378	Ccm2	BC029157	cerebral cavernous malformation 2	protein-coding
mm_119038.1	chr14	30565510	30565561	+	1	NA	exon (NM_009388, exon 5 of 14)	exon (NM_009388, exon 5 of 14)	-6614	NR_037237	100526475		NR_037237	ENSMUSG00000093156	Mir3076	mir-3076|mmu-mir-3076	microRNA 3076	ncRNA
mm_105138.1	chr11	101459524	101459534	-	1	NA	TTS (NM_027320)	TTS (NM_027320)	6670	NM_012037	26949	Mm.29210	NM_012037	ENSMUSG00000034993	Vat1	VAT-1	vesicle amine transport 1	protein-coding
mm_113946.1	chr13	50417857	50417872	+	1	NA	promoter-TSS (NM_175401)	promoter-TSS (NM_175401)	-13	NM_175401	109082	Mm.18638	NM_175401	ENSMUSG00000037816	Fbxw17	1110064L07Rik|C85886	F-box and WD-40 domain protein 17	protein-coding
mm_22991.1	chr3	34019870	34019883	+	1	NA	promoter-TSS (NM_001113188)	promoter-TSS (NM_001113188)	-203	NM_001113189	14359	Mm.259021	NM_008053	ENSMUSG00000027680	Fxr1	1110050J02Rik|9530073J07Rik|AI851072|Fxr1h|Fxr1p	fragile X mental retardation gene 1, autosomal homolog	protein-coding
mm_171932.1	chr5	6407988	6407988	-	1	NA	Intergenic	RLTR9E|LTR|ERVK	-658671	NM_027399	70358	Mm.85429	NM_027399	ENSMUSG00000015652	Steap1	2410007B19Rik|Prss24|Steap	six transmembrane epithelial antigen of the prostate 1	protein-coding
mm_86499.1	chr10	6788831	6788843	+	1	NA	5' UTR (NM_001304950, exon 1 of 5)	5' UTR (NM_001304950, exon 1 of 5)	261	NM_001039652	18390	Mm.438000	NM_011013	ENSMUSG00000000766	Oprm1	M-OR-1|MOP-R|MOR-1|MOR-1O|Oprm|mor|muOR	opioid receptor, mu 1	protein-coding
mm_59095.1	chr7	19696875	19696897	+	1	NA	exon (NM_009696, exon 4 of 4)	exon (NM_009696, exon 4 of 4)	1512	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_131197.1	chr16	8513473	8513497	+	1	NA	promoter-TSS (NM_001170978)	promoter-TSS (NM_001170978)	56	NM_172961	268860	Mm.259315	NM_172961	ENSMUSG00000057880	Abat	9630038C02Rik|AI255750|ENSMUSG00000051226|Gabaat|Gabat|Gm9851|I54|Laibat|X61497	4-aminobutyrate aminotransferase	protein-coding
mm_59731.1	chr7	28808796	28808832	+	1	NA	Intergenic	Intergenic	-2076	NM_177301	15388	Mm.9043	NM_177301	ENSMUSG00000015165	Hnrnpl	C79783|D830027H13Rik|Hnrpl	heterogeneous nuclear ribonucleoprotein L	protein-coding
mm_23629.1	chr3	66219943	66219951	+	1	NA	promoter-TSS (NM_008987)	promoter-TSS (NM_008987)	60	NM_008987	19288	Mm.276776	NM_008987	ENSMUSG00000027832	Ptx3	AI607804|TSG-14	pentraxin related gene	protein-coding
mm_421.1	chr1	34439856	34439910	+	1	NA	promoter-TSS (NM_178601)	promoter-TSS (NM_178601)	54	NM_178601	27993	Mm.289667	NM_178601	ENSMUSG00000026127	Imp4	AA409888|AV031295|D1Wsu40e	IMP4, U3 small nucleolar ribonucleoprotein	protein-coding
mm_91373.1	chr10	29699380	29699382	-	1	NA	Intergenic	Lx6|LINE|L1	-163514	NM_028351	72780	Mm.45191	NM_028351	ENSMUSG00000019880	Rspo3	2810459H04Rik|AW742308|Cristin1|Thsd2	R-spondin 3	protein-coding
mm_171952.1	chr5	77409642	77409642	+	1	NA	Intergenic	L1Md_T|LINE|L1	-1597	NM_008048	29817	Mm.233470	NM_008048	ENSMUSG00000036256	Igfbp7	AGM|Fstl2|Mac25	insulin-like growth factor binding protein 7	protein-coding
mm_117638.1	chr13	92483952	92483986	-	1	NA	promoter-TSS (NM_001163627)	promoter-TSS (NM_001163627)	62	NM_001163627	73942	Mm.85935	NM_001163627	ENSMUSG00000034334	Fam151b	4930405M20Rik	family with sequence similarity 151, member B	protein-coding
mm_117437.1	chr13	74725454	74725467	-	1	NA	exon (NM_009817, exon 20 of 31)	exon (NM_009817, exon 20 of 31)	8801	NM_001301158	12380	Mm.29163	NM_009817	ENSMUSG00000021585	Cast	-	calpastatin	protein-coding
mm_120197.1	chr14	61607456	61607458	+	1	NA	promoter-TSS (NM_001039105)	promoter-TSS (NM_001039105)	0	NM_206974	328424	Mm.224464	NM_206974	ENSMUSG00000046168	Kcnrg	Clld4|E030012H22Rik|Gm745	potassium channel regulator	protein-coding
mm_41891.1	chr5	105499620	105499623	+	1	NA	Intergenic	ORR1B2|LTR|ERVL-MaLR	-19850	NM_133897	100604	Mm.319847	NM_133897	ENSMUSG00000054720	Lrrc8c	AD158|AI326115|E430036I04Rik|fad158	leucine rich repeat containing 8 family, member C	protein-coding
mm_62434.1	chr7	101362055	101362069	+	1	NA	intron (NM_001040111, intron 1 of 33)	intron (NM_001040111, intron 1 of 33)	13993	NM_001040111	69710	Mm.277687	NM_027180	ENSMUSG00000032812	Arap1	2410002L19Rik|Centd2|mKIAA0782	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	protein-coding
mm_137389.1	chr17	25814143	25814147	+	1	NA	intron (NM_001164225, intron 1 of 5)	intron (NM_001164225, intron 1 of 5)	5060	NM_001164225	214931	Mm.152289	NM_001164225	ENSMUSG00000025738	Fbxl16	BC042620|Scirr1	F-box and leucine-rich repeat protein 16	protein-coding
mm_81027.1	chr9	104566769	104566773	+	1	NA	Intergenic	Intergenic	-3017	NM_028719	74020	Mm.326240	NM_028719	ENSMUSG00000032564	Cpne4	3632411M23Rik|4933406O10Rik	copine IV	protein-coding
mm_33490.1	chr4	130823314	130823335	+	1	NA	3' UTR (NM_011520, exon 5 of 5)	3' UTR (NM_011520, exon 5 of 5)	30787	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_1410.1	chr1	67154323	67154337	+	1	NA	intron (NM_001080809, intron 7 of 37)	intron (NM_001080809, intron 7 of 37)	31303	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_55409.1	chr6	63031015	63031015	-	1	NA	Intergenic	Lx9|LINE|L1	-225842	NM_008167	14804	Mm.439651	NM_008167	ENSMUSG00000071424	Grid2	B230104L07Rik|GluD2|GluRdelta2|Lc|Lc<J>|MMS10-AC|Ms10ac|cpr|ho|nmf408|tpr	glutamate receptor, ionotropic, delta 2	protein-coding
mm_108858.1	chr12	98755007	98755011	+	1	NA	intron (NM_001008506, intron 3 of 14)	intron (NM_001008506, intron 3 of 14)	8041	NM_029334	75553	Mm.25549	NM_029334	ENSMUSG00000021012	Zc3h14	1010001P15Rik|1700016A15Rik|2700069A02Rik|AU014748	zinc finger CCCH type containing 14	protein-coding
mm_89295.1	chr10	87913627	87913639	+	1	NA	exon (NM_010512, exon 3 of 5)	exon (NM_010512, exon 3 of 5)	52522	NM_001111276	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_125477.1	chr15	54571341	54571357	+	1	NA	promoter-TSS (NM_178920)	promoter-TSS (NM_178920)	-17	NM_178920	105853	Mm.410994	NM_178920	ENSMUSG00000024479	Mal2	AI461653	mal, T cell differentiation protein 2	protein-coding
mm_149908.1	chr19	25610924	25610947	+	1	NA	exon (NM_177360, exon 1 of 2)	exon (NM_177360, exon 1 of 2)	398	NM_177360	240590	Mm.62785	NM_177360	ENSMUSG00000042372	Dmrt3	-	doublesex and mab-3 related transcription factor 3	protein-coding
mm_87140.1	chr10	34456488	34456488	+	1	NA	Intergenic	Intergenic	-26912	NM_001159544	14302	Mm.332432	NM_010237	ENSMUSG00000019779	Frk	BSK|BSK/IYK|C85044|GTK|RAK	fyn-related kinase	protein-coding
mm_54648.1	chr6	38876275	38876350	-	1	NA	promoter-TSS (NM_010433)	promoter-TSS (NM_010433)	-122	NM_001294143	15258	Mm.23790	NM_010433	ENSMUSG00000061436	Hipk2	1110014O20Rik|B230339E18Rik|Stank	homeodomain interacting protein kinase 2	protein-coding
mm_105522.1	chr11	106300401	106300409	-	1	NA	exon (NM_008117, exon 5 of 5)	exon (NM_008117, exon 5 of 5)	1491	NM_008117	14599	Mm.343934	NM_008117	ENSMUSG00000020713	Gh	Gh1|Ghb1	growth hormone	protein-coding
mm_53648.1	chr6	140651084	140651117	+	1	NA	3' UTR (NM_178803, exon 8 of 8)	3' UTR (NM_178803, exon 8 of 8)	24215	NM_001309436	11569	Mm.86453	NM_009637	ENSMUSG00000030232	Aebp2	AU023766|B230313N05Rik	AE binding protein 2	protein-coding
mm_25393.1	chr3	107218693	107218697	+	1	NA	exon (NM_001111143, exon 3 of 9)	exon (NM_001111143, exon 3 of 9)	3037	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_116840.1	chr13	54688247	54688263	-	1	NA	promoter-TSS (NM_001146025)	promoter-TSS (NM_001146025)	-55	NM_001146027	105239	Mm.25366	NM_134064	ENSMUSG00000034928	Rnf44	AI854545|mKIAA1100	ring finger protein 44	protein-coding
mm_37431.1	chr4	122933943	122933954	-	1	NA	Intergenic	B1F2|SINE|Alu	27240	NM_029662	76574	Mm.331842	NM_029662	ENSMUSG00000028655	Mfsd2a	1700018O18Rik|Mfsd2|NLS1	major facilitator superfamily domain containing 2A	protein-coding
mm_129890.1	chr15	83510862	83510906	-	1	NA	promoter-TSS (NM_178869)	promoter-TSS (NM_178869)	23	NM_178869	319953	Mm.235007	NM_178869	ENSMUSG00000022442	Ttll1	6330444E16Rik|AV014541	tubulin tyrosine ligase-like 1	protein-coding
mm_143000.1	chr17	56417348	56417357	-	1	NA	exon (NM_001252453, exon 23 of 29)	exon (NM_001252453, exon 23 of 29)	1557	NR_105943	102465590		NR_105943	ENSMUSG00000098339	Mir6977	Gm27922|mmu-mir-6977	microRNA 6977	ncRNA
mm_143354.1	chr17	67143603	67143613	-	1	NA	intron (NM_008984, intron 2 of 30)	ORR1B1|LTR|ERVL-MaLR	-117373	NR_049205	100885844		NR_049205	ENSMUSG00000093508	Mir5709	Gm22041|mir-5709|mmu-mir-5709	microRNA 5709	ncRNA
mm_131889.1	chr16	23226118	23226128	+	1	NA	5' UTR (NM_001252505, exon 1 of 8)	5' UTR (NM_001252505, exon 1 of 8)	102	NM_001252505	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_72746.1	chr8	85090918	85090952	+	1	NA	exon (NM_010764, exon 8 of 24)	exon (NM_010764, exon 8 of 24)	7666	NM_010764	17159	Mm.4219	NM_010764	ENSMUSG00000005142	Man2b1	AW107687|LAMAN	mannosidase 2, alpha B1	protein-coding
mm_96687.1	chr11	69587495	69587533	+	1	NA	exon (NM_011640, exon 4 of 11)	exon (NM_011640, exon 4 of 11)	7155	NM_001127233	22059	Mm.222	NM_011640	ENSMUSG00000059552	Trp53	Tp53|bbl|bfy|bhy|p44|p53	transformation related protein 53	protein-coding
mm_137127.1	chr17	22876455	22876478	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-9332	NM_001110254	240041	Mm.328828	NM_177358	ENSMUSG00000059142	Zfp945	A630033E08Rik|C730040L01Rik	zinc finger protein 945	protein-coding
mm_150065.1	chr19	29386339	29386349	+	1	NA	3' UTR (NM_021893, exon 7 of 7)	3' UTR (NM_021893, exon 7 of 7)	18906	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_110961.1	chr12	76818390	76818395	-	1	NA	promoter-TSS (NM_001347406)	promoter-TSS (NM_001347406)	-18	NM_001347406	104886	Mm.172847	NM_134050	ENSMUSG00000021062	Rab15	2310012G06Rik|AI840042	RAB15, member RAS oncogene family	protein-coding
mm_156001.1	chrX	106188006	106188023	+	1	NA	intron (NM_008828, intron 1 of 10)	intron (NM_008828, intron 1 of 10)	914	NM_008828	18655	Mm.316355	NM_008828	ENSMUSG00000062070	Pgk1	Pgk-1	phosphoglycerate kinase 1	protein-coding
mm_142906.1	chr17	52312205	52312220	-	1	NA	Intergenic	Intergenic	-290497	NM_001031811	211468	Mm.399068	NM_001031811	ENSMUSG00000035580	Kcnh8	C130090D05Rik|ELK|ELK1|ELK3|Kv12.1	potassium voltage-gated channel, subfamily H (eag-related), member 8	protein-coding
mm_145772.1	chr18	65025909	65025957	+	1	NA	intron (NM_031881, intron 1 of 29)	intron (NM_031881, intron 1 of 29)	2406	NM_031881	83814	Mm.98668	NM_031881	ENSMUSG00000024589	Nedd4l	1300012C07Rik|Nedd4-2|Nedd4b	neural precursor cell expressed, developmentally down-regulated gene 4-like	protein-coding
mm_120804.1	chr14	74922120	74922136	+	1	NA	intron (NM_001252132, intron 1 of 18)	intron (NM_001252132, intron 1 of 18)	25749	NM_001252132	380916	Mm.288868	NM_001033439	ENSMUSG00000068015	Lrch1	4832412D13Rik|AI552548|AW215503|Chdc1|mKIAA1016	leucine-rich repeats and calponin homology (CH) domain containing 1	protein-coding
mm_119744.1	chr14	54122231	54122248	+	1	NA	Intergenic	Intergenic	131690	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_55065.1	chr6	49050482	49050491	-	1	NA	exon (NM_053110, exon 7 of 11)	exon (NM_053110, exon 7 of 11)	13968	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_65571.1	chr7	27189470	27189489	-	1	NA	exon (NM_015782, exon 5 of 7)	exon (NM_015782, exon 5 of 7)	6281	NM_001046637	53607	Mm.386890	NM_015782	ENSMUSG00000061479	Snrpa	C430021M15Rik|Rnu1a-1|Rnu1a1|U1-A|U1A	small nuclear ribonucleoprotein polypeptide A	protein-coding
mm_58296.1	chr6	145865433	145865435	-	1	NA	promoter-TSS (NM_001271768)	promoter-TSS (NM_001271768)	-14	NM_024469	79362	Mm.154529	NM_024469	ENSMUSG00000030256	Bhlhe41	6430520M22Rik|Bhlhb2l|Bhlhb3|DEC2|Sharp1	basic helix-loop-helix family, member e41	protein-coding
mm_67180.1	chr7	73686597	73686600	-	1	NA	promoter-TSS (NR_033604)	promoter-TSS (NR_033604)	-35	NR_033604	244061	Mm.484605	NR_033604	ENSMUSG00000108337	Gm4971	EG244061	Smad nuclear interacting protein 1 pseudogene	pseudo
mm_20540.1	chr2	131056582	131056610	-	1	NA	intron (NR_136922, intron 4 of 21)	intron (NR_136922, intron 4 of 21)	7218	NR_136922	110751	Mm.108550	NM_033615	ENSMUSG00000027318	Adam33	Adaml	a disintegrin and metallopeptidase domain 33	protein-coding
mm_105223.1	chr11	102230092	102230122	-	1	NA	promoter-TSS (NM_001284249)	promoter-TSS (NM_001284249)	43	NR_106179	102465892		NR_106179	ENSMUSG00000098863	Mir8101	Gm27705|mmu-mir-8101	microRNA 8101	ncRNA
mm_98403.1	chr11	94328221	94328238	+	1	NA	5' UTR (NM_027799, exon 1 of 5)	5' UTR (NM_027799, exon 1 of 5)	228	NM_146024	71452	Mm.141054	NM_027799	ENSMUSG00000020864	Ankrd40	1110011C06Rik|5530600A18Rik|Gcap15	ankyrin repeat domain 40	protein-coding
mm_31489.1	chr4	52900609	52900620	+	1	NA	Intergenic	Intergenic	11178	NM_146839	258836	Mm.331617	NM_146839	ENSMUSG00000051593	Olfr272	MOR262-7	olfactory receptor 272	protein-coding
mm_53690.1	chr6	142537168	142537172	+	1	NA	Intergenic	(CAG)n|Simple_repeat|Simple_repeat	-29213	NM_001302765	16832	Mm.9745	NM_008492	ENSMUSG00000030246	Ldhb	AI790582|H-Ldh|LDH-B|LDH-H|Ldh-2|Ldh2	lactate dehydrogenase B	protein-coding
mm_131075.1	chr16	4726285	4726290	+	1	NA	promoter-TSS (NM_001136066)	promoter-TSS (NM_001136066)	-74	NM_001136066	15369	Mm.272866	NM_010443	ENSMUSG00000004070	Hmox2	HO-2|HO2	heme oxygenase 2	protein-coding
mm_50560.1	chr6	49047903	49047914	+	1	NA	exon (NM_053110, exon 6 of 11)	exon (NM_053110, exon 6 of 11)	11390	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_81178.1	chr9	107335737	107335760	+	1	NA	intron (NM_133984, intron 4 of 10)	intron (NM_133984, intron 4 of 10)	2602	NM_133984	69536	Mm.259467	NM_133984	ENSMUSG00000032579	Hemk1	2310008M14Rik|AW049265	HemK methyltransferase family member 1	protein-coding
mm_64579.1	chr7	145216259	145216259	+	1	NA	intron (NR_132644, intron 24 of 24)	intron (NR_132644, intron 24 of 24)	-8140	NR_033626	100040049	Mm.102235	NR_033626	ENSMUSG00000109305	1810010D01Rik	Gm2572	RIKEN cDNA 1810010D01 gene	ncRNA
mm_160312.1	chr7	141338799	141338799	-	1	NA	promoter-TSS (NM_001282073)	promoter-TSS (NM_001282073)	-16	NM_001282073	54006	Mm.28392	NM_016874	ENSMUSG00000058886	Deaf1	AU042387|C230009B13Rik|NUDR	deformed epidermal autoregulatory factor 1 (Drosophila)	protein-coding
mm_34890.1	chr4	155601855	155601940	+	1	NA	intron (NM_177186, intron 1 of 8)	CpG	481	NM_177186	320541	Mm.306018	NM_177186	ENSMUSG00000042202	Slc35e2	A530082C11Rik|AI957035	solute carrier family 35, member E2	protein-coding
mm_60870.1	chr7	45942237	45942241	+	1	NA	intron (NM_001033243, intron 7 of 12)	intron (NM_001033243, intron 7 of 12)	13841	NM_001033243	211535	Mm.227539	NM_001033243	ENSMUSG00000040189	Ccdc114	-	coiled-coil domain containing 114	protein-coding
mm_173245.1	chrX	89422509	89422522	+	1	NA	Intergenic	L1Md_A|LINE|L1	-12826	NM_008821	18630	Mm.3086	NM_008821	ENSMUSG00000035395	Pet2	PC231|PC326|Pex3	plasmacytoma expressed transcript 2	protein-coding
mm_19512.1	chr2	93957097	93957107	-	1	NA	promoter-TSS (NM_001145034)	promoter-TSS (NM_001145034)	-2	NM_001145034	620695	Mm.482106	NM_001145034	ENSMUSG00000087006	Gm13889	Ag2|OTTMUSG00000014994	predicted gene 13889	protein-coding
mm_77942.1	chr9	7357802	7357860	+	1	NA	exon (NM_008605, exon 9 of 10)	exon (NM_008605, exon 9 of 10)	10457	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_120995.1	chr14	79426455	79426478	+	1	NA	promoter-TSS (NM_001024135)	promoter-TSS (NM_001024135)	-45	NM_001024135	211255	Mm.284526	NM_001024135	ENSMUSG00000043881	Kbtbd7	1110008P08Rik|AU045792|Gm295	kelch repeat and BTB (POZ) domain containing 7	protein-coding
mm_169706.1	chr15	75155331	75155331	+	1	NA	promoter-TSS (NM_001310438)	promoter-TSS (NM_001310438)	70	NM_001310438	546644		NM_008531	ENSMUSG00000022582	Ly6g	Gr-1|Gr1|Ly-6G	lymphocyte antigen 6 complex, locus G	protein-coding
mm_164437.1	chr16	48874354	48874376	-	1	NA	3' UTR (NM_181596, exon 4 of 4)	3' UTR (NM_181596, exon 4 of 4)	1757	NM_181596	245195	Mm.231288	NM_181596	ENSMUSG00000022651	Retnlg	Fizz3|Relmg|Xcp1	resistin like gamma	protein-coding
mm_83181.1	chr9	40984461	40984474	-	1	NA	intron (NM_001281954, intron 5 of 9)	intron (NM_001281954, intron 5 of 9)	20161	NM_001281954	54698	Mm.42791	NM_019465	ENSMUSG00000032021	Crtam	-	cytotoxic and regulatory T cell molecule	protein-coding
mm_50721.1	chr6	52230010	52230024	+	1	NA	TTS (NR_029912)	TTS (NR_029912)	148	NR_029912	723820		NR_029912	ENSMUSG00000065443	Mir196b	Mirn196b|mir-196b	microRNA 196b	ncRNA
mm_16549.1	chr2	181767006	181767037	+	1	NA	promoter-TSS (NM_008665)	promoter-TSS (NM_008665)	-8	NM_008665	17932	Mm.458718	NM_008665	ENSMUSG00000010505	Myt1	Nzf2|Nzf2a|Nzf2b|Nztf2	myelin transcription factor 1	protein-coding
mm_120943.1	chr14	76677574	76677594	+	1	NA	promoter-TSS (NR_015485)	promoter-TSS (NR_015485)	16	NR_015485	73272	Mm.116804	NR_015485	ENSMUSG00000101009	1700108F19Rik	1700020I02Rik|BB065030	RIKEN cDNA 1700108F19 gene	ncRNA
mm_117065.1	chr13	58762301	58762318	-	1	NA	promoter-TSS (NR_045469)	promoter-TSS (NR_045469)	2	NR_045469	67585	Mm.84751	NR_045469		4930455J16Rik	-	RIKEN cDNA 4930455J16 gene	ncRNA
mm_78223.1	chr9	21587296	21587327	+	1	NA	exon (NM_021531, exon 13 of 16)	exon (NM_021531, exon 13 of 16)	-5411	NM_178619	69773	Mm.39704	NM_178619	ENSMUSG00000048429	Timm29	1810026J23Rik	translocase of inner mitochondrial membrane 29	protein-coding
mm_52242.1	chr6	105677644	105677738	+	1	NA	promoter-TSS (NM_173004)	promoter-TSS (NM_173004)	-54	NM_001109749	269784	Mm.321683	NM_173004	ENSMUSG00000064293	Cntn4	9630050B05|Axcam|BIG-2	contactin 4	protein-coding
mm_172038.1	chr6	126740580	126740587	+	1	NA	promoter-TSS (NM_013568)	promoter-TSS (NM_013568)	91	NM_013568	16494	Mm.62535	NM_013568	ENSMUSG00000038077	Kcna6	Kv1.6|MK1.6	potassium voltage-gated channel, shaker-related, subfamily, member 6	protein-coding
mm_158911.1	chr1	42697072	42697072	+	1	NA	promoter-TSS (NM_008900)	promoter-TSS (NM_008900)	-74	NM_008900	18993	Mm.440553	NM_008900	ENSMUSG00000045515	Pou3f3	Brn-1|Brn1|Otf8|Skin1	POU domain, class 3, transcription factor 3	protein-coding
mm_129075.1	chr15	75748319	75748322	-	1	NA	promoter-TSS (NM_194350)	promoter-TSS (NM_194350)	-398	NM_194350	378435	Mm.309589	NM_194350	ENSMUSG00000047591	Mafa	RIPE3b1	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein A (avian)	protein-coding
mm_115141.1	chr13	104816583	104816590	+	1	NA	promoter-TSS (NM_026075)	promoter-TSS (NM_026075)	367	NM_026072	67285	Mm.235398	NM_026072	ENSMUSG00000021715	Cwc27	3110009E13Rik|NY-CO-10|Sdccag10	CWC27 spliceosome-associated protein	protein-coding
mm_166528.1	chr6	28522227	28522229	+	1	NA	intron (NM_019776, intron 3 of 23)	MTEa|LTR|ERVL-MaLR	41880	NM_019776	56463	Mm.439987	NM_019776	ENSMUSG00000001424	Snd1	AL033314|Tudor-SN	staphylococcal nuclease and tudor domain containing 1	protein-coding
mm_58208.1	chr6	143947062	143947084	-	1	NA	promoter-TSS (NM_001347506)	promoter-TSS (NM_001347506)	33	NM_001347506	20678	Mm.1752	NM_011444	ENSMUSG00000041540	Sox5	A730017D01Rik|AI528773	SRY (sex determining region Y)-box 5	protein-coding
mm_30496.1	chr3	157534078	157534094	-	1	NA	promoter-TSS (NM_017381)	promoter-TSS (NM_017381)	-311	NM_017381	53861	Mm.259036	NM_017381	ENSMUSG00000028180	Zranb2	AI227013|Zfp265|Zis|Znf265	zinc finger, RAN-binding domain containing 2	protein-coding
mm_42833.1	chr5	122102671	122102734	+	1	NA	exon (NM_010861, exon 3 of 7)	exon (NM_010861, exon 3 of 7)	1722	NM_010861	17906	Mm.1529	NM_010861	ENSMUSG00000013936	Myl2	MLC-2|MLC-2s/v|MLC-2v|Mlc2v|Mylpc	myosin, light polypeptide 2, regulatory, cardiac, slow	protein-coding
mm_75372.1	chr8	45310281	45310285	-	1	NA	exon (NM_133969, exon 8 of 11)	exon (NM_133969, exon 8 of 11)	-15448	NM_008455	16621	Mm.482691	NM_008455	ENSMUSG00000109764	Klkb1	APS|Kal-3|Kal3|Klk3|PSA	kallikrein B, plasma 1	protein-coding
mm_122709.1	chr14	52197406	52197465	-	1	NA	promoter-TSS (NM_033618)	promoter-TSS (NM_033618)	-196	NM_033618	114741	Mm.21662	NM_033618	ENSMUSG00000035726	Supt16	Cdc68|Fact140|Spt16|Supt16h	suppressor of Ty 16	protein-coding
mm_98310.1	chr11	90034750	90034761	+	1	NA	intron (NM_026433, intron 2 of 2)	intron (NM_026433, intron 2 of 2)	4407	NM_026433	67888	Mm.212428	NM_026433	ENSMUSG00000069763	Tmem100	1810057C19Rik|AV011897	transmembrane protein 100	protein-coding
mm_143862.1	chr17	84186362	84186382	-	1	NA	exon (NM_001001806, exon 2 of 2)	exon (NM_001001806, exon 2 of 2)	1575	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_938.1	chr1	56018955	56018993	+	1	NA	promoter-TSS (NR_126076)	promoter-TSS (NR_126076)	-4	NR_126075	69356	Mm.393775	NR_126075	ENSMUSG00000100372	1700003I22Rik	-	RIKEN cDNA 1700003I22 gene	ncRNA
mm_85164.1	chr9	96364432	96364451	-	1	NA	promoter-TSS (NM_007502)	promoter-TSS (NM_007502)	-142	NM_007502	11933	Mm.424	NM_007502	ENSMUSG00000032412	Atp1b3	AA409958|AI664000|AW212096	ATPase, Na+/K+ transporting, beta 3 polypeptide	protein-coding
mm_7356.1	chr1	106664270	106664273	-	1	NA	intron (NM_009741, intron 1 of 1)	intron (NM_009741, intron 1 of 1)	50019	NM_009741	12043	Mm.257460	NM_009741	ENSMUSG00000057329	Bcl2	AW986256|Bcl-2|C430015F12Rik|D630044D05Rik|D830018M01Rik	B cell leukemia/lymphoma 2	protein-coding
mm_81846.1	chr9	118558029	118558041	+	1	NA	exon (NM_018748, exon 15 of 24)	exon (NM_018748, exon 15 of 24)	-48674	NM_133721	104099	Mm.335520	NM_133721	ENSMUSG00000039115	Itga9	(alpha)9|2610002H11Rik|6720458D17Rik|AI461869|D130073C02|D9Ertd428e	integrin alpha 9	protein-coding
mm_153819.1	chr19	46267709	46267715	-	1	NA	intron (NM_178930, intron 18 of 39)	intron (NM_178930, intron 18 of 39)	-37025	NM_001177369	18034	Mm.102365	NM_019408	ENSMUSG00000025225	Nfkb2	NF-kappaB2|lyt|p49|p49/p100|p50B|p52	nuclear factor of kappa light polypeptide gene enhancer in B cells 2, p49/p100	protein-coding
mm_72958.1	chr8	92826258	92826274	+	1	NA	Intergenic	Intergenic	-1031	NM_008610	17390	Mm.29564	NM_008610	ENSMUSG00000031740	Mmp2	Clg4a|GelA|MMP-2	matrix metallopeptidase 2	protein-coding
mm_81691.1	chr9	111152096	111152096	+	1	NA	intron (NM_027742, intron 3 of 13)	intron (NM_027742, intron 3 of 13)	33985	NM_001164838	71268	Mm.302287	NM_027742	ENSMUSG00000032497	Lrrfip2	5133400F20Rik|AI850587	leucine rich repeat (in FLII) interacting protein 2	protein-coding
mm_149107.1	chr19	8953827	8953856	+	1	NA	promoter-TSS (NM_197993)	promoter-TSS (NM_197993)	9	NM_197993	70044	Mm.165979	NM_197993	ENSMUSG00000071645	Tut1	2700038E08Rik|PAPD2|Rbm21|TUTase6|U6-TUTase|star-PAP	terminal uridylyl transferase 1, U6 snRNA-specific	protein-coding
mm_21694.1	chr2	164473715	164473730	-	1	NA	promoter-TSS (NM_001271575)	promoter-TSS (NM_001271575)	2	NM_001271575	73603	Mm.472883	NM_001271575	ENSMUSG00000017720	Trp53tg5	1700126L10Rik	transformation related protein 53 target 5	protein-coding
mm_146626.1	chr18	10182011	10182032	-	1	NA	promoter-TSS (NM_009071)	promoter-TSS (NM_009071)	-229	NM_009071	19877	Mm.6710	NM_009071	ENSMUSG00000024290	Rock1	1110055K06Rik|Rock-I	Rho-associated coiled-coil containing protein kinase 1	protein-coding
mm_19796.1	chr2	110032371	110032381	-	1	NA	exon (NM_026613, exon 3 of 6)	exon (NM_026613, exon 3 of 6)	14559	NM_026613	68201	Mm.181767	NM_026613	ENSMUSG00000027160	Ccdc34	2810027O19Rik|4930522P10Rik|AI596202	coiled-coil domain containing 34	protein-coding
mm_20997.1	chr2	152332432	152332447	-	1	NA	promoter-TSS (NM_001083921)	promoter-TSS (NM_001083921)	-14	NM_001083921	24105	Mm.182145	NM_019705	ENSMUSG00000027466	Rbck1	AL033326|HOIL-1|HOIL-1L|UIP28|Ubce7ip3	RanBP-type and C3HC4-type zinc finger containing 1	protein-coding
mm_64180.1	chr7	141459401	141459409	+	1	NA	non-coding (NR_028142, exon 10 of 10)	non-coding (NR_028142, exon 10 of 10)	-1689	NM_001025103	213573	Mm.386851	NM_001025103	ENSMUSG00000048200	Cracr2b	6330520A15Rik|BC026645|Cracr2a|Efcab4|Efcab4a	calcium release activated channel regulator 2B	protein-coding
mm_123114.1	chr14	55900189	55900235	-	1	NA	promoter-TSS (NM_001082975)	promoter-TSS (NM_001082975)	20	NM_001082975	654795	Mm.486218	NM_001082975	ENSMUSG00000022223	Sdr39u1	2310014G06Rik	short chain dehydrogenase/reductase family 39U, member 1	protein-coding
mm_35564.1	chr4	41640101	41640137	-	1	NA	5' UTR (NM_027147, exon 1 of 2)	5' UTR (NM_027147, exon 1 of 2)	183	NM_027147	69638	Mm.372459	NM_027147	ENSMUSG00000028445	Enho	1110065P19Rik|2310040A07Rik	energy homeostasis associated	protein-coding
mm_46038.1	chr5	91962716	91962740	-	1	NA	promoter-TSS (NR_028429)	promoter-TSS (NR_028429)	-154	NR_028429	381650	Mm.159453	NR_028429	ENSMUSG00000102644	Thap6	4930534K21Rik|AI448650	THAP domain containing 6	pseudo
mm_166050.1	chr4	131572922	131572924	+	1	NA	Intergenic	Intergenic	265355	NM_011214	19273	Mm.4860	NM_011214	ENSMUSG00000028909	Ptpru	Ftp-1|PCP-2|PTP|PTP-lambda|PTPlambda|Pcp2|Ptpf|Ptprl|R-PTP-U|R-PTP-psi|RPTPlambda	protein tyrosine phosphatase, receptor type, U	protein-coding
mm_158489.1	chrX	142326769	142326771	-	1	NA	intron (NM_019477, intron 15 of 15)	intron (NM_019477, intron 15 of 15)	-20572	NM_021487	66240	Mm.58507	NM_021487	ENSMUSG00000090122	Kcne1l	1500015C14Rik|Kcne5|Mink	potassium voltage-gated channel, Isk-related family, member 1-like, pseudogene	protein-coding
mm_147086.1	chr18	35629860	35629870	-	1	NA	Intergenic	Intergenic	-2638	NM_011397	20522	Mm.22702	NM_011397	ENSMUSG00000024354	Slc23a1	D18Ucla2|SVCT1|Slc23a2|YSPL3	solute carrier family 23 (nucleobase transporters), member 1	protein-coding
mm_28054.1	chr3	84191183	84191193	-	1	NA	exon (NM_030706, exon 6 of 12)	exon (NM_030706, exon 6 of 12)	16550	NR_036654	624713	Mm.442604	NR_036654		Gm6525	EG624713	ribosomal protein L36a pseudogene	pseudo
mm_121741.1	chr14	18665141	18665156	-	1	NA	intron (NM_144839, intron 3 of 5)	intron (NM_144839, intron 3 of 5)	228479	NM_144839	218793	Mm.23551	NM_144839	ENSMUSG00000058317	Ube2e2	BC016265	ubiquitin-conjugating enzyme E2E 2	protein-coding
mm_33289.1	chr4	128884040	128884050	+	1	NA	promoter-TSS (NM_178110)	promoter-TSS (NM_178110)	-95	NM_178110	67525	Mm.30653	NM_178110	ENSMUSG00000041000	Trim62	6330414G21Rik|AI450348|Dear1	tripartite motif-containing 62	protein-coding
mm_70556.1	chr8	13060983	13061027	+	1	NA	promoter-TSS (NM_025834)	promoter-TSS (NM_025834)	97	NM_025834	66901	Mm.441140	NM_025834	ENSMUSG00000031445	Proz	1300015B06Rik	protein Z, vitamin K-dependent plasma glycoprotein	protein-coding
mm_95935.1	chr11	58382281	58382299	+	1	NA	5' UTR (NM_001083884, exon 3 of 7)	5' UTR (NM_001083884, exon 3 of 7)	1644	NM_001330197	70163	Mm.24119	NM_027339	ENSMUSG00000013643	Lypd8	2210415F13Rik	LY6/PLAUR domain containing 8	protein-coding
mm_38357.1	chr4	137862090	137862109	-	1	NA	promoter-TSS (NM_199307)	promoter-TSS (NM_199307)	-138	NM_199307	230857	Mm.401062	NM_199307	ENSMUSG00000057530	Ece1	AW322500|ECE-1|ECE-1a|ECE-1b|ECE-1d	endothelin converting enzyme 1	protein-coding
mm_116973.1	chr13	56178865	56178897	-	1	NA	promoter-TSS (NM_001168615)	promoter-TSS (NM_001168615)	4	NM_145976	212937	Mm.116697	NM_145976	ENSMUSG00000049625	Tifab	-	TRAF-interacting protein with forkhead-associated domain, family member B	protein-coding
mm_82592.1	chr9	21239229	21239308	-	1	NA	promoter-TSS (NM_016679)	promoter-TSS (NM_016679)	64	NM_016679	50868	Mm.248266	NM_016679	ENSMUSG00000003308	Keap1	INRF2|mKIAA0132	kelch-like ECH-associated protein 1	protein-coding
mm_108537.1	chr12	84236572	84236591	+	1	NA	Intergenic	Intergenic	-17700	NM_001163501	238317	Mm.31256	NM_001163501	ENSMUSG00000042507	Elmsan1	9430029N19Rik|C130039O16Rik|Gm260	ELM2 and Myb/SANT-like domain containing 1	protein-coding
mm_63048.1	chr7	121739402	121739405	+	1	NA	intron (NM_011326, intron 2 of 12)	intron (NM_011326, intron 2 of 12)	4924	NM_011326	20278	Mm.35247	NM_011326	ENSMUSG00000000216	Scnn1g	SCNEG	sodium channel, nonvoltage-gated 1 gamma	protein-coding
mm_52577.1	chr6	116358957	116358973	+	1	NA	intron (NM_001302385, intron 2 of 6)	intron (NM_001302385, intron 2 of 6)	20943	NM_027920	71779	Mm.27064	NM_027920	ENSMUSG00000025702	March8	1300017E09Rik|MARCH-VIII|Mir	membrane-associated ring finger (C3HC4) 8	protein-coding
mm_77597.1	chr8	123892389	123892399	-	1	NA	exon (NM_009606, exon 6 of 7)	exon (NM_009606, exon 6 of 7)	2381	NM_001272041	11459	Mm.214950	NM_009606	ENSMUSG00000031972	Acta1	AA959943|Acta-2|Acts|Actsk-1	actin, alpha 1, skeletal muscle	protein-coding
mm_92056.1	chr10	62507217	62507257	-	1	NA	intron (NM_011157, intron 1 of 2)	ID_B1|SINE|B4	518	NM_011157	19073	Mm.338790	NM_011157	ENSMUSG00000020077	Srgn	Prg|Prg1|Sgc	serglycin	protein-coding
mm_153876.1	chr19	46864234	46864280	-	1	NA	intron (NM_033569, intron 4 of 7)	intron (NM_033569, intron 4 of 7)	98094	NM_029810	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_75435.1	chr8	47289414	47289461	-	1	NA	promoter-TSS (NM_001286376)	promoter-TSS (NM_001286376)	-35	NM_001114311	71069	Mm.23973	NM_175162	ENSMUSG00000038143	Stox2	4933409N07Rik|AI449080|AI835114|mKIAA1392	storkhead box 2	protein-coding
mm_119097.1	chr14	30895465	30895484	+	1	NA	exon (NM_001289633, exon 13 of 22)	exon (NM_001289633, exon 13 of 22)	8998	NM_001289632	16427	Mm.34819	NM_018746	ENSMUSG00000021922	Itih4	ITI-HC4|Itih-4|PK-120	inter alpha-trypsin inhibitor, heavy chain 4	protein-coding
mm_159891.1	chr6	29179654	29179654	-	1	NA	promoter-TSS (NM_001101443)	promoter-TSS (NM_001101443)	-70	NM_001101443	101359	Mm.22818	NM_001101443	ENSMUSG00000079654	Prrt4	AW455481|D330027H18Rik	proline-rich transmembrane protein 4	protein-coding
mm_4970.1	chr1	191281498	191281502	+	1	NA	Intergenic	Intergenic	36618	NM_025424	66208	Mm.46444	NM_025424	ENSMUSG00000037499	Nenf	1110060M21Rik|SCIRP10|Spuf	neuron derived neurotrophic factor	protein-coding
mm_29347.1	chr3	108284614	108284622	-	1	NA	intron (NM_001271599, intron 1 of 20)	intron (NM_001271599, intron 1 of 20)	554	NM_019972	20661	Mm.157119	NM_019972	ENSMUSG00000068747	Sort1	2900053A11Rik|AI852375|Ntr3|Ntsr3	sortilin 1	protein-coding
mm_151703.1	chr19	4498400	4498410	-	1	NA	exon (NM_027237, exon 1 of 2)	exon (NM_027237, exon 1 of 2)	178	NM_027237	69861	Mm.282978	NM_027237	ENSMUSG00000042041	2010003K11Rik	-	RIKEN cDNA 2010003K11 gene	protein-coding
mm_114552.1	chr13	74009461	74009483	+	1	NA	promoter-TSS (NM_182839)	promoter-TSS (NM_182839)	53	NM_182839	72948	Mm.39752	NM_182839	ENSMUSG00000021573	Tppp	2900041A09Rik|AI849835	tubulin polymerization promoting protein	protein-coding
mm_24688.1	chr3	94974912	94974964	+	1	NA	5' UTR (NM_001293716, exon 1 of 10)	5' UTR (NM_001293716, exon 1 of 10)	207	NM_001293716	107650	Mm.217222	NM_175356	ENSMUSG00000038861	Pi4kb	ESTM41|PI4K-beta|PI4Kbeta|Pik4cb	phosphatidylinositol 4-kinase, catalytic, beta polypeptide	protein-coding
mm_34098.1	chr4	138967113	138967127	+	1	NA	promoter-TSS (NM_025786)	promoter-TSS (NM_025786)	8	NM_025786	66825	Mm.252312	NM_025786	ENSMUSG00000070661	Rnf186	9130020G10Rik	ring finger protein 186	protein-coding
mm_2642.1	chr1	125174926	125174932	+	1	NA	Intergenic	Intergenic	260798	NM_023735	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding
mm_149989.1	chr19	29251893	29251901	+	1	NA	promoter-TSS (NM_008413)	promoter-TSS (NM_008413)	94	NM_008413	16452	Mm.275839	NM_008413	ENSMUSG00000024789	Jak2	Fd17	Janus kinase 2	protein-coding
mm_24528.1	chr3	93277545	93277560	+	1	NA	Intergenic	Intergenic	-42197	NM_133698	68723	Mm.208047	NM_133698	ENSMUSG00000041991	Hrnr	1110033K19Rik|A530063N20Rik|S100a18	hornerin	protein-coding
mm_165094.1	chr19	53903346	53903366	+	1	NA	promoter-TSS (NM_001168492)	promoter-TSS (NM_001168492)	5	NM_001168491	18569	Mm.1605	NM_011050	ENSMUSG00000024975	Pdcd4	D19Ucla1|Ma3|Tis	programmed cell death 4	protein-coding
mm_39173.1	chr4	155735977	155735987	-	1	NA	intron (NM_001101506, intron 2 of 3)	intron (NM_001101506, intron 2 of 3)	1178	NM_001101506	381582	Mm.379515	NM_001101506	ENSMUSG00000084845	Tmem240	EG381582|Gm5151	transmembrane protein 240	protein-coding
mm_145347.1	chr18	56471084	56471094	+	1	NA	intron (NM_026240, intron 2 of 13)	intron (NM_026240, intron 2 of 13)	38957	NM_026240	107022	Mm.24356	NM_026240	ENSMUSG00000001700	Gramd3	9030613F08Rik|9130427A09Rik|AW061306|NS3TP2	GRAM domain containing 3	protein-coding
mm_25058.1	chr3	98852556	98852566	+	1	NA	exon (NM_001304800, exon 4 of 4)	exon (NM_001304800, exon 4 of 4)	7233	NM_001304800	15492	Mm.140811	NM_008293	ENSMUSG00000027871	Hsd3b1	3-beta-HSD I|D3Ertd383e	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1	protein-coding
mm_22107.1	chr2	169970577	169970585	-	1	NA	Intergenic	RLTR17|LTR|ERVK	-7394	NR_131974	446211	Mm.266854	NR_131974	ENSMUSG00000103935	AY702102	STDP1	cDNA sequence AY702102	ncRNA
mm_119846.1	chr14	54440666	54440681	+	1	NA	3' UTR (NM_008608, exon 10 of 10)	3' UTR (NM_008608, exon 10 of 10)	9075	NM_008608	17387	Mm.280175	NM_008608	ENSMUSG00000000957	Mmp14	AI325305|MMP-X1|MT-MMP-1|MT1-MMP|sabe	matrix metallopeptidase 14 (membrane-inserted)	protein-coding
mm_114530.1	chr13	73603956	73603966	+	1	NA	promoter-TSS (NM_146047)	promoter-TSS (NM_146047)	-41	NM_146047	218335	Mm.30099	NM_146047	ENSMUSG00000021610	Clptm1l	C130052I12Rik|Crr9	CLPTM1-like	protein-coding
mm_90021.1	chr10	115384952	115385021	+	1	NA	promoter-TSS (NM_025780)	promoter-TSS (NM_025780)	27	NM_001033261	216345	Mm.207621	NM_001033261	ENSMUSG00000034163	Zfc3h1	BC033596|Ccdc131|Psrc2	zinc finger, C3H1-type containing	protein-coding
mm_173297.1	chrY	43043853	43043866	-	1	NA	Intergenic	RLTR4_Mm|LTR|ERV1	113536	NR_038299	100041346	Mm.426191	NR_038299	ENSMUSG00000101005	Gm20871	-	Sycp3 like Y-linked pseudogene	pseudo
mm_29483.1	chr3	115713794	115713806	-	1	NA	intron (NM_007901, intron 1 of 1)	intron (NM_007901, intron 1 of 1)	1255	NM_007901	13609	Mm.982	NM_007901	ENSMUSG00000045092	S1pr1	AI849002|Edg1|Lpb1|S1p|S1p1	sphingosine-1-phosphate receptor 1	protein-coding
mm_63586.1	chr7	128131491	128131514	+	1	NA	exon (NM_021334, exon 5 of 30)	exon (NM_021334, exon 5 of 30)	1934	NM_021334	16411	Mm.22378	NM_021334	ENSMUSG00000030789	Itgax	AI449405|Cd11c|Cr4|N418	integrin alpha X	protein-coding
mm_170388.1	chr18	60439391	60439401	+	1	NA	Intergenic	Intergenic	62587	NM_134133	106878	Mm.273197	NM_134133	ENSMUSG00000038059	Smim3	2010002N04Rik|AI195350|AW561905|Nid67|cI-41	small integral membrane protein 3	protein-coding
mm_132690.1	chr16	43235925	43235937	+	1	NA	intron (NM_001285805, intron 3 of 10)	intron (NM_001285805, intron 3 of 10)	-11353	NM_181058	56490	Mm.136238	NM_019778	ENSMUSG00000022708	Zbtb20	1300017A20Rik|7330412A13Rik|A930017C21Rik|D16Wsu73e|DPZF|HOF|ODA-8S|Oda8|Zfp288	zinc finger and BTB domain containing 20	protein-coding
mm_24008.1	chr3	87376397	87376410	+	1	NA	promoter-TSS (NM_178165)	promoter-TSS (NM_178165)	16	NM_001136236	229499	Mm.255203	NM_153090	ENSMUSG00000059994	Fcrl1	A230020G22Rik|Bxmas1|Bxmh1|Bxmh1b|Fcrh1|Fcrh1l|Fcrh1s|Ifgp1	Fc receptor-like 1	protein-coding
mm_37366.1	chr4	120825166	120825212	-	1	NA	intron (NM_001048168, intron 1 of 9)	CpG	552	NM_001277095	18046	Mm.435590	NM_008692	ENSMUSG00000032897	Nfyc	-	nuclear transcription factor-Y gamma	protein-coding
mm_54488.1	chr6	35326000	35326047	-	1	NA	5' UTR (NM_173375, exon 1 of 3)	5' UTR (NM_173375, exon 1 of 3)	118	NM_173375	208164	Mm.257766	NM_173375	ENSMUSG00000047420	Fam180a	B230314O19	family with sequence similarity 180, member A	protein-coding
mm_22866.1	chr3	28781346	28781374	+	1	NA	promoter-TSS (NM_177586)	promoter-TSS (NM_177586)	49	NM_177586	208691	Mm.193670	NM_177586	ENSMUSG00000050192	Eif5a2	9630038B20|eIF5AII	eukaryotic translation initiation factor 5A2	protein-coding
mm_54725.1	chr6	40577421	40577434	-	1	NA	3' UTR (NM_021364, exon 6 of 6)	3' UTR (NM_021364, exon 6 of 6)	6039	NM_146383	258381	Mm.377469	NM_146383	ENSMUSG00000045514	Olfr460	MOR120-2	olfactory receptor 460	protein-coding
mm_71274.1	chr8	40919582	40919599	+	1	NA	3' UTR (NM_001044740, exon 12 of 12)	3' UTR (NM_001044740, exon 12 of 12)	-6643	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_85112.1	chr9	95407202	95407212	-	1	NA	promoter-TSS (NM_018763)	promoter-TSS (NM_018763)	63	NM_018763	54371	Mm.212446	NM_018763	ENSMUSG00000033350	Chst2	AI428561|AW121776|C130041E03Rik|Chts2|GST-2|GlcNAc6ST|Gn6st	carbohydrate sulfotransferase 2	protein-coding
mm_37181.1	chr4	117277657	117277669	-	1	NA	intron (NM_025739, intron 10 of 14)	intron (NM_025739, intron 10 of 14)	11792	NM_001310730	66743	Mm.318331	NM_025739	ENSMUSG00000028677	Rnf220	4732477A13|4931406I20Rik|5730503K05Rik|AV302541	ring finger protein 220	protein-coding
mm_82221.1	chr9	3022910	3022917	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	15830	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_155127.1	chrX	48967980	48967982	+	1	NA	Intergenic	RLTR6-int|LTR|ERV1	-90268	NM_001085499	209005	Mm.336054	NM_001085499	ENSMUSG00000079606	Gm595	-	predicted gene 595	protein-coding
mm_26336.1	chr3	142546981	142546992	+	1	NA	3' UTR (NM_001083312, exon 11 of 11)	3' UTR (NM_001083312, exon 11 of 11)	-13066	NM_018734	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_160436.1	chr8	94268665	94268665	+	1	NA	intron (NM_172410, intron 4 of 22)	intron (NM_172410, intron 4 of 22)	54064	NM_172410	71805	Mm.458170	NM_172410	ENSMUSG00000032939	Nup93	2410008G02Rik	nucleoporin 93	protein-coding
mm_117183.1	chr13	63431738	63431755	-	1	NA	promoter-TSS (NM_007985)	promoter-TSS (NM_007985)	-1	NM_001282942	14088	Mm.126106	NM_007985	ENSMUSG00000021461	Fancc	Facc	Fanconi anemia, complementation group C	protein-coding
mm_97291.1	chr11	76217672	76217676	+	1	NA	promoter-TSS (NM_177367)	promoter-TSS (NM_177367)	61	NM_021294	13168	Mm.347413	NM_021294	ENSMUSG00000038057	Dbil5	ELP	diazepam binding inhibitor-like 5	protein-coding
mm_100574.1	chr11	120765285	120765300	+	1	NA	Intergenic	Intergenic	18912	NM_009053	19719	Mm.871	NM_009053	ENSMUSG00000025158	Rfng	-	RFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	protein-coding
mm_40831.1	chr5	72914353	72914383	+	1	NA	promoter-TSS (NM_001113423)	promoter-TSS (NM_001113423)	6	NM_153567	75991	Mm.121285	NM_153567	ENSMUSG00000036087	Slain2	5033405K12Rik|8030444K12Rik|AI596370	SLAIN motif family, member 2	protein-coding
mm_52455.1	chr6	113690755	113690769	+	1	NA	intron (NM_001113553, intron 10 of 11)	intron (NM_001113553, intron 10 of 11)	-6288	NM_001347356	381801	Mm.333322	NM_001033463	ENSMUSG00000056952	Tatdn2	AI646012|mKIAA0218	TatD DNase domain containing 2	protein-coding
mm_8528.1	chr1	154884501	154884513	-	1	NA	Intergenic	Intergenic	-158587	NM_009782	12290	Mm.267517	NM_009782	ENSMUSG00000004110	Cacna1e	A430040I15|BII|Cach6|Cacnl1a6|Cav2.3|Cchra1|alpha1E	calcium channel, voltage-dependent, R type, alpha 1E subunit	protein-coding
mm_35933.1	chr4	53032479	53032497	-	1	NA	3' UTR (NM_013454, exon 50 of 50)	3' UTR (NM_013454, exon 50 of 50)	20608	NM_025623	66536	Mm.38244	NM_025623	ENSMUSG00000015247	Nipsnap3b	2700063N13Rik|Nipsnap3a	nipsnap homolog 3B (C. elegans)	protein-coding
mm_34821.1	chr4	154961399	154961418	+	1	NA	exon (NM_010419, exon 3 of 3)	exon (NM_010419, exon 3 of 3)	485	NM_010419	15208	Mm.137268	NM_010419	ENSMUSG00000048001	Hes5	bHLHb38	hairy and enhancer of split 5 (Drosophila)	protein-coding
mm_162104.1	chrX	38772737	38772737	+	1	NA	promoter-TSS (NM_183126)	promoter-TSS (NM_183126)	-43	NM_183126	77883	Mm.113311	NM_183126	ENSMUSG00000051361	6030498E09Rik	-	RIKEN cDNA 6030498E09 gene	protein-coding
mm_68430.1	chr7	109840889	109840896	-	1	NA	intron (NM_020052, intron 7 of 21)	ID_B1|SINE|B4	24787	NM_020052	56788	Mm.40447	NM_020052	ENSMUSG00000007279	Scube2	4932442O19Rik|Cegf1|Cegp1	signal peptide, CUB domain, EGF-like 2	protein-coding
mm_35088.1	chr4	7912058	7912071	-	1	NA	Intergenic	Intergenic	326977	NM_007592	12319	Mm.119320	NM_007592	ENSMUSG00000041261	Car8	AW546993|Ca8|Cals|Cals1|Carp|wdl	carbonic anhydrase 8	protein-coding
mm_84761.1	chr9	75599090	75599104	-	1	NA	promoter-TSS (NM_001038710)	promoter-TSS (NM_001038710)	36	NM_001038710	50876	Mm.291880	NM_016711	ENSMUSG00000032186	Tmod2	N-Tmod|NTMOD	tropomodulin 2	protein-coding
mm_95868.1	chr11	58040414	58040422	+	1	NA	exon (NM_028451, exon 2 of 19)	exon (NM_028451, exon 2 of 19)	31354	NM_028451	73158	Mm.248843	NM_028451	ENSMUSG00000037331	Larp1	1810024J12Rik|3110040D16Rik|Larp|mKIAA0731	La ribonucleoprotein domain family, member 1	protein-coding
mm_67726.1	chr7	90129340	90129356	-	1	NA	promoter-TSS (NM_001252521)	promoter-TSS (NM_001252521)	126	NR_046006	78329	Mm.389940	NR_046006	ENSMUSG00000097162	2310010J17Rik	-	RIKEN cDNA 2310010J17 gene	ncRNA
mm_25982.1	chr3	133310182	133310218	+	1	NA	promoter-TSS (NM_001293641)	promoter-TSS (NM_001293641)	90	NM_146141	74776	Mm.210305	NM_146141	ENSMUSG00000028013	Ppa2	1110013G13Rik|Sid6306	pyrophosphatase (inorganic) 2	protein-coding
mm_151440.1	chr19	57361221	57361238	+	1	NA	promoter-TSS (NR_040316)	promoter-TSS (NR_040316)	220	NM_145505	226252	Mm.358870	NM_145505	ENSMUSG00000033478	Fam160b1	AI450540|mKIAA1600	family with sequence similarity 160, member B1	protein-coding
mm_162067.1	chrX	11327726	11327726	+	1	NA	promoter-TSS (NM_001114529)	promoter-TSS (NM_001114529)	-96	NM_001114529	236663	Mm.473680	NM_001114529	ENSMUSG00000069038	H2al1j	EG236663|Gm4906	H2A histone family member L1J	protein-coding
mm_16621.1	chr2	5672968	5672969	-	1	NA	intron (NM_001290374, intron 1 of 9)	intron (NM_001290374, intron 1 of 9)	3078	NM_001290376	227541	Mm.191949	NM_177343	ENSMUSG00000039145	Camk1d	A630059D12Rik|CKLiK|CaMKIdelta|E030025C11Rik|mCKLiK	calcium/calmodulin-dependent protein kinase ID	protein-coding
mm_37411.1	chr4	122859313	122859329	-	1	NA	TTS (NM_008917)	TTS (NM_008917)	23094	NM_008917	19063	Mm.277719	NM_008917	ENSMUSG00000028657	Ppt1	9530043G02Rik|AA960502|C77813|CLN1|D4Ertd184e|INCL|PPT	palmitoyl-protein thioesterase 1	protein-coding
mm_156821.1	chrX	164140596	164140639	+	1	NA	5' UTR (NM_027286, exon 1 of 18)	5' UTR (NM_027286, exon 1 of 18)	137	NM_027286	70008	Mm.13451	NM_027286	ENSMUSG00000015405	Ace2	2010305L05Rik	angiotensin I converting enzyme (peptidyl-dipeptidase A) 2	protein-coding
mm_68016.1	chr7	100956119	100956132	-	1	NA	intron (NM_183168, intron 1 of 2)	intron (NM_183168, intron 1 of 2)	8241	NM_183168	233571	Mm.235193	NM_183168	ENSMUSG00000048779	P2ry6	2010204J23Rik|P2Y6	pyrimidinergic receptor P2Y, G-protein coupled, 6	protein-coding
mm_112011.1	chr12	110978965	110978979	-	1	NA	promoter-TSS (NM_175207)	promoter-TSS (NM_175207)	49	NM_175207	74251	Mm.250989	NM_175207	ENSMUSG00000037904	Ankrd9	2500003O20Rik	ankyrin repeat domain 9	protein-coding
mm_123764.1	chr14	70206112	70206129	-	1	NA	promoter-TSS (NM_001271407)	promoter-TSS (NM_001271407)	-98	NM_001271407	20410	Mm.5068	NM_011366	ENSMUSG00000022091	Sorbs3	SCAM-1|SH3P3|Sh3d4|vinexin-g	sorbin and SH3 domain containing 3	protein-coding
mm_2278.1	chr1	91306172	91306174	+	1	NA	intron (NM_016717, intron 4 of 11)	ID4_|SINE|ID	7835	NM_016717	50880	Mm.25724	NM_016717	ENSMUSG00000026307	Scly	9830169H08|A930015N15Rik|SCL|Scly1|Scly2	selenocysteine lyase	protein-coding
mm_12409.1	chr2	70509345	70509382	+	1	NA	exon (NM_025744, exon 1 of 13)	exon (NM_025744, exon 1 of 13)	544	NM_025744	66748	Mm.423014	NM_025744	ENSMUSG00000075302	Erich2	4933404M02Rik	glutamate rich 2	protein-coding
mm_134005.1	chr16	4790206	4790216	-	1	NA	promoter-TSS (NM_025670)	promoter-TSS (NM_025670)	-276	NM_025670	66626	Mm.157648	NM_025670	ENSMUSG00000004071	Cdip1	2700048O17Rik|5730403B10Rik|AU018521|AW742692|CDIP	cell death inducing Trp53 target 1	protein-coding
mm_89959.1	chr10	111296203	111296210	+	1	NA	3' UTR (NM_001003717, exon 23 of 23)	3' UTR (NM_001003717, exon 23 of 23)	-2473	NM_027914	71769	Mm.45256	NM_027914	ENSMUSG00000035759	Bbs10	1300007O09Rik|AI452285	Bardet-Biedl syndrome 10 (human)	protein-coding
mm_117507.1	chr13	78200445	78200459	-	1	NA	intron (NR_045195, intron 1 of 2)	intron (NR_045195, intron 1 of 2)	-1579	NM_010151	13865	Mm.439653	NM_010151	ENSMUSG00000069171	Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR-3|EAR3|Erbal3|SVP44|Tcfcoup1	nuclear receptor subfamily 2, group F, member 1	protein-coding
mm_71867.1	chr8	69105901	69105926	+	1	NA	exon (NM_007509, exon 10 of 14)	exon (NM_007509, exon 10 of 14)	-16691	NM_153054	110877	Mm.19301	NM_153054	ENSMUSG00000036330	Slc18a1	4832416I10Rik|Vat1|Vmat1	solute carrier family 18 (vesicular monoamine), member 1	protein-coding
mm_70684.1	chr8	15011066	15011083	+	1	NA	promoter-TSS (NM_029116)	promoter-TSS (NM_029116)	49	NM_029116	74901	Mm.46675	NM_029116	ENSMUSG00000055675	Kbtbd11	2900016B01Rik|4930465M17Rik|mKIAA0711	kelch repeat and BTB (POZ) domain containing 11	protein-coding
mm_27834.1	chr3	79138470	79138473	-	1	NA	intron (NM_001099624, intron 1 of 23)	B1_Mur4|SINE|Alu	6416	NM_001310536	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_126373.1	chr15	80148710	80148724	+	1	NA	exon (NM_025609, exon 3 of 11)	exon (NM_025609, exon 3 of 11)	15563	NM_025609	66513	Mm.288245	NM_025609	ENSMUSG00000022414	Tab1	2310012M03Rik|Map3k7ip1|b2b449Clo	TGF-beta activated kinase 1/MAP3K7 binding protein 1	protein-coding
mm_28731.1	chr3	95736021	95736052	-	1	NA	exon (NM_007899, exon 8 of 11)	exon (NM_007899, exon 8 of 11)	-1063	NR_105981	102466787		NR_105981	ENSMUSG00000098737	Mir7014	Gm27837|mmu-mir-7014	microRNA 7014	ncRNA
mm_57713.1	chr6	128707781	128707788	-	1	NA	intron (NM_001099918, intron 5 of 5)	intron (NM_001099918, intron 5 of 5)	15262	NM_001099918	100043861	Mm.66911	NM_001099918	ENSMUSG00000079299	Klrb1	4930431A04Rik|Gm4696|Klrb1g|Klrb6|Ly-55|Ly55|NKR-P1G|Nkrp-1e|Nkrp1g	killer cell lectin-like receptor subfamily B member 1	protein-coding
mm_34800.1	chr4	154810497	154810503	+	1	NA	Intergenic	Intergenic	-45700	NM_172878	242800	Mm.72944	NM_172878	ENSMUSG00000046637	Ttc34	4932418L02|B230396O12Rik	tetratricopeptide repeat domain 34	protein-coding
mm_76119.1	chr8	80859260	80859269	-	1	NA	intron (NM_021356, intron 1 of 9)	RLTR15|LTR|ERVK	21215	NM_021356	14388	Mm.277409	NM_021356	ENSMUSG00000031714	Gab1	AA408973|AW107238	growth factor receptor bound protein 2-associated protein 1	protein-coding
mm_93375.1	chr10	105521767	105521795	-	1	NA	intron (NM_177368, intron 1 of 11)	intron (NM_177368, intron 1 of 11)	52698	NM_177368	278279	Mm.25225	NM_177368	ENSMUSG00000036019	Tmtc2	8430438D04Rik|D330034A10Rik	transmembrane and tetratricopeptide repeat containing 2	protein-coding
mm_19372.1	chr2	91183955	91183961	-	1	NA	promoter-TSS (NM_145527)	promoter-TSS (NM_145527)	-911	NM_145527	228355	Mm.36410	NM_145527	ENSMUSG00000040687	Madd	9630059K23Rik|IG20	MAP-kinase activating death domain	protein-coding
mm_38790.1	chr4	148100840	148100885	-	1	NA	3' UTR (NM_027426, exon 7 of 7)	3' UTR (NM_027426, exon 7 of 7)	-12798	NM_001301281	11610	Mm.46247	NM_009642	ENSMUSG00000029007	Agtrap	3300002E14Rik|AT1R|Atrap|D4Wsu124e	angiotensin II, type I receptor-associated protein	protein-coding
mm_117904.1	chr13	99430213	99430242	-	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-17401	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_150292.1	chr19	34493088	34493107	+	1	NA	3' UTR (NM_021460, exon 10 of 10)	3' UTR (NM_021460, exon 10 of 10)	-17962	NM_009890	12642	Mm.30824	NM_009890	ENSMUSG00000050370	Ch25h	AI462618|m25OH	cholesterol 25-hydroxylase	protein-coding
mm_133251.1	chr16	77301985	77301992	+	1	NA	Intergenic	Intergenic	-27340	NR_015543	77994	Mm.394688	NR_015543	ENSMUSG00000090386	Mir99ahg	2810055G20Rik|D730043B02Rik	Mir99a and Mirlet7c-1 host gene (non-protein coding)	ncRNA
mm_6596.1	chr1	75316915	75316937	-	1	NA	promoter-TSS (NM_016878)	promoter-TSS (NM_016878)	91	NM_016878	13437	Mm.24680	NM_016878	ENSMUSG00000026209	Dnpep	AA407814	aspartyl aminopeptidase	protein-coding
mm_77846.1	chr9	5301145	5301172	+	1	NA	intron (NM_009807, intron 3 of 9)	intron (NM_009807, intron 3 of 9)	2641	NM_009807	12362	Mm.1051	NM_009807	ENSMUSG00000025888	Casp1	ICE|Il1bc	caspase 1	protein-coding
mm_165493.1	chr2	165792814	165792816	-	1	NA	exon (NM_001281926, exon 20 of 23)	exon (NM_001281926, exon 20 of 23)	65358	NM_001252585	228880	Mm.227598	NM_027230	ENSMUSG00000039671	Zmynd8	1110013E22Rik|2010005I16Rik|3632413B07Rik|AI316811|AL024039|Prkcbp1|RACK7	zinc finger, MYND-type containing 8	protein-coding
mm_80093.1	chr9	70235870	70235901	+	1	NA	intron (NM_181072, intron 1 of 27)	RSINE1|SINE|B4	28535	NM_181072	71602	Mm.249311	NM_181072	ENSMUSG00000032220	Myo1e	2310020N23Rik|9130023P14Rik|AA407778|myosin-1e|myr 3	myosin IE	protein-coding
mm_17130.1	chr2	24919573	24919616	-	1	NA	promoter-TSS (NM_001109687)	promoter-TSS (NM_001109687)	15	NM_172545	77683	Mm.24176	NM_172545	ENSMUSG00000036893	Ehmt1	9230102N17Rik|D330003E03|Eu-HMTase1|GLP|GLP1|KMT1D|mKIAA1876	euchromatic histone methyltransferase 1	protein-coding
mm_26669.1	chr3	154711152	154711162	+	1	NA	promoter-TSS (NM_175176)	promoter-TSS (NM_175176)	24	NM_175176	209601	Mm.331454	NM_175176	ENSMUSG00000078161	Erich3	1700013E18Rik|4922501L14Rik|5031409G23Rik|AI596448|Gm133	glutamate rich 3	protein-coding
mm_72948.1	chr8	92193363	92193367	+	1	NA	Intergenic	Intergenic	162755	NR_110452	71296	Mm.86664	NR_033641	ENSMUSG00000031736	Crnde	4933436C20Rik	colorectal neoplasia differentially expressed (non-protein coding)	ncRNA
mm_75034.1	chr8	32264247	32264251	-	1	NA	Intergenic	L1MD3|LINE|L1	112354	NR_046039	666589	Mm.367675	NR_046039		Gm8179	EG666589	predicted gene 8179	ncRNA
mm_160917.1	chr11	83429360	83429360	-	1	NA	exon (NM_001013759, exon 1 of 6)	exon (NM_001013759, exon 1 of 6)	161	NM_001013759	237891	Mm.340523	NM_001013759	ENSMUSG00000020686	Gas2l2	-	growth arrest-specific 2 like 2	protein-coding
mm_154377.1	chrM	11173	11190	+	1	NA	NA	Intergenic	NA	NA								
mm_5805.1	chr1	52232982	52232998	-	1	NA	exon (NM_001113383, exon 1 of 15)	exon (NM_001113383, exon 1 of 15)	242	NM_001081081	14660	Mm.398608	NM_001081081	ENSMUSG00000026103	Gls	6330442B14|AI314027|B230365M23Rik	glutaminase	protein-coding
mm_9504.1	chr1	173732709	173732716	-	1	NA	intron (NM_001204910, intron 3 of 7)	ORR1C2|LTR|ERVL-MaLR	9097	NM_001204910	226691	Mm.440876	NM_001204910	ENSMUSG00000073490	Ifi207	AI607873|Pyhin-A	interferon activated gene 207	protein-coding
mm_137989.1	chr17	33629512	33629554	+	1	NA	intron (NM_026712, intron 1 of 5)	intron (NM_026712, intron 1 of 5)	441	NM_026712	328801	Mm.181488	NM_026712	ENSMUSG00000073423	Zfp414	0610030H11Rik|Znf414	zinc finger protein 414	protein-coding
mm_39663.1	chr5	25181492	25181512	+	1	NA	promoter-TSS (NM_026449)	promoter-TSS (NM_026449)	22	NM_026449	67909	Mm.141471	NM_026449	ENSMUSG00000028938	Galntl5	1700021B12Rik|Galnt15	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 5	protein-coding
mm_88734.1	chr10	80249442	80249468	+	1	NA	promoter-TSS (NM_029272)	promoter-TSS (NM_029272)	3	NM_029272	75406	Mm.28712	NM_029272	ENSMUSG00000020153	Ndufs7	1010001M04Rik	NADH dehydrogenase (ubiquinone) Fe-S protein 7	protein-coding
mm_49857.1	chr6	38501827	38501830	+	1	NA	intron (NM_177185, intron 16 of 16)	intron (NM_177185, intron 16 of 16)	-5497	NR_106130	102466843		NR_106130	ENSMUSG00000098285	Mir7670	Gm27707|mmu-mir-7670	microRNA 7670	ncRNA
mm_149753.1	chr19	22692716	22692724	+	1	NA	5' UTR (NM_001035246, exon 1 of 8)	5' UTR (NM_001035246, exon 1 of 8)	101	NM_001035244	226025	Mm.131943	NM_177341	ENSMUSG00000052387	Trpm3	6330504P12Rik|9330180E14|AU018608|B930001P07Rik|LTRPC3|MLSN2	transient receptor potential cation channel, subfamily M, member 3	protein-coding
mm_20666.1	chr2	132128699	132128704	-	1	NA	intron (NM_018824, intron 1 of 15)	intron (NM_018824, intron 1 of 15)	16407	NM_018824	54338	Mm.103581	NM_018824	ENSMUSG00000027340	Slc23a2	AI844736|NBTL1|SVCT2|Slc23a1|YSPL2|YSPL3|mKIAA0238	solute carrier family 23 (nucleobase transporters), member 2	protein-coding
mm_158174.1	chrX	103821941	103821992	-	1	NA	promoter-TSS (NM_009197)	promoter-TSS (NM_009197)	22	NM_009197	20502	Mm.388973	NM_009197	ENSMUSG00000033965	Slc16a2	AW105741|Mct8|Xpct	solute carrier family 16 (monocarboxylic acid transporters), member 2	protein-coding
mm_160677.1	chr10	13091785	13091785	+	1	NA	non-coding (NR_131912, exon 1 of 1)	non-coding (NR_131912, exon 1 of 1)	940	NR_131912	338438		NR_131912		Hymai	-	hydatidiform mole associated and imprinted transcript	ncRNA
mm_155589.1	chrX	81070638	81070644	+	1	NA	promoter-TSS (NM_138751)	promoter-TSS (NM_138751)	-3	NM_138751	192216	Mm.490421	NM_138751	ENSMUSG00000025666	Tmem47	3010015F07Rik|AI115536|BCMP1|Tm4sf10	transmembrane protein 47	protein-coding
mm_136663.1	chr17	6079929	6079939	+	1	NA	promoter-TSS (NM_001111017)	promoter-TSS (NM_001111017)	106	NM_181392	66467	Mm.303441	NM_181392	ENSMUSG00000034345	Gtf2h5	2700017P07Rik|2810432H05Rik|D17Wsu155e	general transcription factor IIH, polypeptide 5	protein-coding
mm_125266.1	chr15	35501908	35501912	+	1	NA	intron (NM_177151, intron 17 of 61)	intron (NM_177151, intron 17 of 61)	130364	NM_177151	666173	Mm.309250	NM_177151	ENSMUSG00000037646	Vps13b	1810042B05Rik|2310042E16Rik|4732488H20|C330002D13Rik|C87206|Coh1|D230005K13|mKIAA0532|mKIAA5032	vacuolar protein sorting 13B	protein-coding
mm_18157.1	chr2	45094251	45094267	-	1	NA	intron (NM_001289521, intron 1 of 8)	intron (NM_001289521, intron 1 of 8)	16018	NM_001289521	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_23268.1	chr3	51484320	51484346	+	1	NA	exon (NM_016858, exon 1 of 2)	exon (NM_016858, exon 1 of 2)	367	NM_016858	19338	Mm.1664	NM_016858	ENSMUSG00000027739	Rab33b	-	RAB33B, member RAS oncogene family	protein-coding
mm_22977.1	chr3	32817521	32817576	+	1	NA	promoter-TSS (NM_001013024)	promoter-TSS (NM_001013024)	-78	NM_001013024	72607	Mm.316153	NM_001013024	ENSMUSG00000056900	Usp13	2700071E21Rik|AI848077|ISOT3|IsoT-3	ubiquitin specific peptidase 13 (isopeptidase T-3)	protein-coding
mm_39722.1	chr5	28210123	28210133	+	1	NA	promoter-TSS (NM_001310511)	promoter-TSS (NM_001310511)	40	NM_001310511	269637	Mm.68286	NM_175651	ENSMUSG00000044681	Cnpy1	1500012D20Rik|9630008K15Rik|AI853839	canopy FGF signaling regulator 1	protein-coding
mm_98832.1	chr11	97435312	97435334	+	1	NA	Intergenic	Intergenic	-14837	NM_021493	58996	Mm.394118	NM_021493	ENSMUSG00000049807	Arhgap23	A330041B18Rik	Rho GTPase activating protein 23	protein-coding
mm_91908.1	chr10	60245179	60245219	-	1	NA	Intergenic	Intergenic	-25939	NM_016803	53374	Mm.12866	NM_016803	ENSMUSG00000057337	Chst3	C6ST|C6ST-1|GST-0	carbohydrate (chondroitin 6/keratan) sulfotransferase 3	protein-coding
mm_94157.1	chr10	128745070	128745081	-	1	NA	Intergenic	Intergenic	-1019	NM_016811	13139	Mm.291235	NM_016811	ENSMUSG00000025357	Dgka	80kDa|AW146112|Dagk1	diacylglycerol kinase, alpha	protein-coding
mm_3695.1	chr1	153752853	153752868	+	1	NA	5' UTR (NM_011882, exon 3 of 9)	5' UTR (NM_011882, exon 3 of 9)	3434	NM_011882	24014	Mm.259254	NM_011882	ENSMUSG00000066800	Rnasel	E230029I04Rik	ribonuclease L (2', 5'-oligoisoadenylate synthetase-dependent)	protein-coding
mm_149238.1	chr19	10183523	10183546	+	1	NA	intron (NM_146094, intron 1 of 11)	intron (NM_146094, intron 1 of 11)	646	NM_146094	76267	Mm.30158	NM_146094	ENSMUSG00000010663	Fads1	0710001O03Rik|A930006B21Rik|AI317215|DSD	fatty acid desaturase 1	protein-coding
mm_165824.1	chr3	149954588	149954594	+	1	NA	Intergenic	Intergenic	679854	NR_040591	381482	Mm.393866	NR_040591		Gm1653	-	predicted gene 1653	ncRNA
mm_50754.1	chr6	53287361	53287365	+	1	NA	promoter-TSS (NM_001327821)	promoter-TSS (NM_001327821)	60	NM_001327821	231991	Mm.227444	NM_172728	ENSMUSG00000053007	Creb5	9430076C15Rik|CRE-BPa|Crebpa|D430026C09Rik	cAMP responsive element binding protein 5	protein-coding
mm_103540.1	chr11	77506786	77506799	-	1	NA	3' UTR (NM_001004144, exon 20 of 20)	3' UTR (NM_001004144, exon 20 of 20)	6481	NM_001024920	216964	Mm.341211	NM_001024920	ENSMUSG00000044328	Trp53i13	2410019G02Rik|Tp53i13	transformation related protein 53 inducible protein 13	protein-coding
mm_171183.1	chr3	37481575	37481594	+	1	NA	intron (NM_001310473, intron 14 of 16)	LSU-rRNA_Hsa|rRNA|rRNA	61634	NM_021343	57815	Mm.172679	NM_021343	ENSMUSG00000027722	Spata5	2510048F20Rik|C78064|Spaf	spermatogenesis associated 5	protein-coding
mm_19129.1	chr2	80129245	80129278	-	1	NA	promoter-TSS (NM_016744)	promoter-TSS (NM_016744)	151	NM_001159582	18573	Mm.40678	NM_016744	ENSMUSG00000059173	Pde1a	AI987702|AW125737	phosphodiesterase 1A, calmodulin-dependent	protein-coding
mm_22976.1	chr3	32737046	32737082	+	1	NA	promoter-TSS (NM_025316)	promoter-TSS (NM_025316)	1	NM_025316	66046	Mm.28058	NM_025316	ENSMUSG00000027673	Ndufb5	0610007D05Rik|AU015782|CI-SGDH|SGDH	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 5	protein-coding
mm_41244.1	chr5	88765850	88765852	+	1	NA	intron (NM_007832, intron 1 of 6)	B1_Mur2|SINE|Alu	838	NM_007832	13178	Mm.298892	NM_007832	ENSMUSG00000029366	Dck	-	deoxycytidine kinase	protein-coding
mm_128.1	chr1	9908680	9908686	+	1	NA	promoter-TSS (NM_177722)	promoter-TSS (NM_177722)	45	NM_177722	240697	Mm.259800	NM_177722	ENSMUSG00000046101	Mcmdc2	6030422M02Rik	minichromosome maintenance domain containing 2	protein-coding
mm_39527.1	chr5	21269893	21269898	+	1	NA	intron (NM_175437, intron 19 of 30)	intron (NM_175437, intron 19 of 30)	83628	NM_175437	212167	Mm.121705	NM_175437	ENSMUSG00000039934	Gsap	A530088I07Rik|Pion	gamma-secretase activating protein	protein-coding
mm_129350.1	chr15	77915633	77915651	-	1	NA	3' UTR (NM_019913, exon 4 of 4)	3' UTR (NM_019913, exon 4 of 4)	13352	NM_019913	56551	Mm.291917	NM_019913	ENSMUSG00000005354	Txn2	2510006J11Rik|AI788873|Trx2	thioredoxin 2	protein-coding
mm_173325.1	chrY	90738032	90738046	+	1	NA	Intergenic	IMPB_01|Satellite|Satellite	17011	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_66783.1	chr7	47008216	47008231	-	1	NA	5' UTR (NM_175318, exon 1 of 6)	5' UTR (NM_175318, exon 1 of 6)	191	NM_175318	101685	Mm.155687	NM_175318	ENSMUSG00000049516	Spty2d1	5830435K17Rik|AI852426|P16H6	SPT2, Suppressor of Ty, domain containing 1 (S. cerevisiae)	protein-coding
mm_107730.1	chr12	57501214	57501221	+	1	NA	Intergenic	Intergenic	44904	NM_008259	15375	Mm.4578	NM_008259	ENSMUSG00000035451	Foxa1	Hnf-3a|Hnf3a|Tcf-3a|Tcf3a	forkhead box A1	protein-coding
mm_38156.1	chr4	135131215	135131246	-	1	NA	intron (NM_019732, intron 1 of 5)	intron (NM_019732, intron 1 of 5)	10585	NM_019732	12399	Mm.378894	NM_019732	ENSMUSG00000070691	Runx3	AML2|Cbfa3|Pebp2a3	runt related transcription factor 3	protein-coding
mm_13613.1	chr2	113405132	113405157	+	1	NA	intron (NM_001285458, intron 2 of 16)	intron (NM_001285458, intron 2 of 16)	-35920	NM_001285459	14260	Mm.4938	NM_010230	ENSMUSG00000044042	Fmn1	Fmn|formin-1|ld	formin 1	protein-coding
mm_34918.1	chr4	155734826	155734846	+	1	NA	promoter-TSS (NM_001101506)	promoter-TSS (NM_001101506)	32	NM_001101506	381582	Mm.379515	NM_001101506	ENSMUSG00000084845	Tmem240	EG381582|Gm5151	transmembrane protein 240	protein-coding
mm_16356.1	chr2	174438202	174438262	+	1	NA	exon (NM_022325, exon 2 of 6)	exon (NM_022325, exon 2 of 6)	807	NM_022325	64138	Mm.156919	NM_022325	ENSMUSG00000016256	Ctsz	AI787083|AU019819|CTSX|D2Wsu143e	cathepsin Z	protein-coding
mm_17042.1	chr2	20804309	20804312	-	1	NA	intron (NM_029895, intron 17 of 18)	U2|snRNA|snRNA	163411	NM_001081364	71435	Mm.28507	NM_001081364	ENSMUSG00000036591	Arhgap21	5530401C11Rik|AA416458|ARHGAP10	Rho GTPase activating protein 21	protein-coding
mm_132395.1	chr16	35000918	35000940	+	1	NA	3' UTR (NM_139300, exon 32 of 32)	3' UTR (NM_139300, exon 32 of 32)	-21492	NM_023587	70757	Mm.27286	NM_023587	ENSMUSG00000035376	Hacd2	6330408J20Rik|AI255777|AI481689|Hcad2|Ptplb	3-hydroxyacyl-CoA dehydratase 2	protein-coding
mm_134944.1	chr16	31275251	31275267	-	1	NA	promoter-TSS (NM_025800)	promoter-TSS (NM_025800)	18	NM_025800	66849	Mm.291593	NM_025800	ENSMUSG00000047714	Ppp1r2	0610025N14Rik|2310007G06Rik|4930440J04Rik|5430408E15Rik|D16Ertd248e|IPP-2	protein phosphatase 1, regulatory (inhibitor) subunit 2	protein-coding
mm_131534.1	chr16	17722555	17722600	+	1	NA	intron (NM_001285886, intron 1 of 16)	intron (NM_001285886, intron 1 of 16)	323	NM_001285886	94112	Mm.208970	NM_033609	ENSMUSG00000012114	Med15	A230074L19Rik|AW536074|Pcqap|mPcqap	mediator complex subunit 15	protein-coding
mm_40819.1	chr5	72261433	72261437	+	1	NA	intron (NM_153389, intron 11 of 22)	Lx5b|LINE|L1	58092	NM_153389	231287	Mm.32775	NM_153389	ENSMUSG00000046808	Atp10d	9830145H18Rik|ATPVD|D5Buc24e	ATPase, class V, type 10D	protein-coding
mm_43294.1	chr5	134313980	134313991	+	1	NA	intron (NM_001080746, intron 1 of 34)	CpG	775	NM_001080746	14886	Mm.261570	NM_010365	ENSMUSG00000060261	Gtf2i	6030441I21Rik|BAP-135|Diws1t|GtfII-I|Spin|TFII-I|WBSCR6	general transcription factor II I	protein-coding
mm_97511.1	chr11	78499128	78499131	+	1	NA	promoter-TSS (NM_011707)	promoter-TSS (NM_011707)	9	NM_011707	22370	Mm.3667	NM_011707	ENSMUSG00000017344	Vtn	AI256434|Vn	vitronectin	protein-coding
mm_18417.1	chr2	60705596	60705609	-	1	NA	intron (NM_001159564, intron 1 of 17)	intron (NM_001159564, intron 1 of 17)	17001	NM_001159564	16420	Mm.98193	NM_021359	ENSMUSG00000026971	Itgb6	2210409C20Rik|4831415H04Rik	integrin beta 6	protein-coding
mm_63967.1	chr7	139944614	139944623	+	1	NA	exon (NM_009482, exon 2 of 2)	exon (NM_009482, exon 2 of 2)	762	NM_009482	22286	Mm.10205	NM_009482	ENSMUSG00000047751	Utf1	AI505934	undifferentiated embryonic cell transcription factor 1	protein-coding
mm_20105.1	chr2	121085836	121085846	-	1	NA	promoter-TSS (NM_028799)	promoter-TSS (NM_028799)	-82	NM_028799	74176	Mm.20187	NM_028799	ENSMUSG00000053675	Tgm5	2310007C07Rik|TGMX|TGx	transglutaminase 5	protein-coding
mm_165359.1	chr2	122369166	122369166	-	1	NA	promoter-TSS (NM_001013829)	promoter-TSS (NM_001013829)	-248	NM_001013829	435684	Mm.458215	NM_001013829	ENSMUSG00000033256	Shf	-	Src homology 2 domain containing F	protein-coding
mm_74977.1	chr8	27141521	27141531	-	1	NA	3' UTR (NM_001080813, exon 6 of 6)	3' UTR (NM_001080813, exon 6 of 6)	-1384	NR_045840	71082	Mm.395259	NR_045840		4933416M07Rik	-	RIKEN cDNA 4933416M07 gene	ncRNA
mm_138786.1	chr17	37270959	37271024	+	1	NA	intron (NM_013819, intron 2 of 7)	intron (NM_013819, intron 2 of 7)	757	NM_013819	14991	Mm.14437	NM_013819	ENSMUSG00000016206	H2-M3	H-2M3|Hmt|M3a|MuprM3|MuprM301|MuprM302|R4B2	histocompatibility 2, M region locus 3	protein-coding
mm_108935.1	chr12	101975367	101975371	+	1	NA	promoter-TSS (NM_016856)	promoter-TSS (NM_016856)	-605	NM_016856	51786	Mm.716	NM_016856	ENSMUSG00000041781	Cpsf2	100kDa|2610024B04Rik|AI662483|Cpsf|MCPSF|mKIAA1367	cleavage and polyadenylation specific factor 2	protein-coding
mm_157411.1	chrX	38440308	38440318	-	1	NA	exon (NM_001017959, exon 3 of 9)	exon (NM_001017959, exon 3 of 9)	16147	NM_010685	16784	Mm.486	NM_010685	ENSMUSG00000016534	Lamp2	CD107b|LGP-B|Lamp II|Lamp-2|Lamp-2a|Lamp-2b|Lamp-2c|Mac3	lysosomal-associated membrane protein 2	protein-coding
mm_132521.1	chr16	37624346	37624351	+	1	NA	non-coding (NR_027778, exon 11 of 13)	non-coding (NR_027778, exon 11 of 13)	30020	NM_026610	68194	Mm.379154	NM_026610	ENSMUSG00000022820	Ndufb4	0610006N12Rik|1300010H20Rik	NADH dehydrogenase (ubiquinone) 1 beta subcomplex 4	protein-coding
mm_12874.1	chr2	84549934	84549945	+	1	NA	Intergenic	L2c|LINE|L2	-43066	NR_046046	672763	Mm.491046	NR_046046	ENSMUSG00000087362	Gm13710	OTTMUSG00000013441	predicted gene 13710	ncRNA
mm_17941.1	chr2	36104022	36104028	-	1	NA	promoter-TSS (NM_001083127)	promoter-TSS (NM_001083127)	35	NM_001083126	16874	Mm.12881	NM_008500	ENSMUSG00000026890	Lhx6	Lhx6.1	LIM homeobox protein 6	protein-coding
mm_125027.1	chr15	25751788	25751799	+	1	NA	intron (NM_019472, intron 19 of 40)	intron (NM_019472, intron 19 of 40)	-91505	NM_001034851	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_54064.1	chr6	13872285	13872298	-	1	NA	promoter-TSS (NR_024619)	promoter-TSS (NR_024619)	722	NR_045995	76311	Mm.367129	NR_045995	ENSMUSG00000097616	1110019D14Rik	-	RIKEN cDNA 1110019D14 gene	ncRNA
mm_20449.1	chr2	129364812	129364816	-	1	NA	3' UTR (NM_008361, exon 7 of 7)	3' UTR (NM_008361, exon 7 of 7)	-5088	NR_015474	329514	Mm.207315	NM_177848	ENSMUSG00000074805	Il1bos	9430083I22|Gm14047|OTTMUSG00000015529	interleukin 1 beta, opposite strand	ncRNA
mm_167270.1	chr8	32712502	32712505	+	1	NA	Intergenic	Intergenic	237523	NM_001177589	100042715	Mm.291093	NM_001177589		Gm3985	-	predicted gene 3985	protein-coding
mm_123438.1	chr14	64942281	64942285	-	1	NA	intron (NM_001347627, intron 1 of 10)	intron (NM_001347627, intron 1 of 10)	7574	NM_177338	219150	Mm.344074	NM_177338	ENSMUSG00000021972	Hmbox1	AI451877|AI604847|F830020C16Rik	homeobox containing 1	protein-coding
mm_147558.1	chr18	54987675	54987725	-	1	NA	exon (NM_175751, exon 2 of 10)	exon (NM_175751, exon 2 of 10)	2480	NM_175751	269023	Mm.192984	NM_175751	ENSMUSG00000052713	Zfp608	4932417D18Rik|D430007A19Rik|Znf608	zinc finger protein 608	protein-coding
mm_71415.1	chr8	46476558	46476563	+	1	NA	intron (NM_007981, intron 1 of 20)	intron (NM_007981, intron 1 of 20)	5523	NM_007981	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_139915.1	chr17	70963774	70963803	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	26728	NM_023402	67938	Mm.261329	NM_023402	ENSMUSG00000034868	Myl12b	1500001M02Rik|C77744|Mylc2b|RLC-B	myosin, light chain 12B, regulatory	protein-coding
mm_7146.1	chr1	91398714	91398724	-	1	NA	promoter-TSS (NM_023343)	promoter-TSS (NM_023343)	64	NM_023343	67444	Mm.337240	NM_023343	ENSMUSG00000026309	Ilkap	0710007A14Rik|1600009O09Rik|PP2C-DELTA	integrin-linked kinase-associated serine/threonine phosphatase 2C	protein-coding
mm_53827.1	chr6	147531393	147531438	+	1	NA	intron (NM_025911, intron 3 of 12)	intron (NM_025911, intron 3 of 12)	55544	NM_025911	67015	Mm.209774	NM_025911	ENSMUSG00000030301	Ccdc91	1700086G08Rik|1810060J02Rik|AU045683|AW555238|p56	coiled-coil domain containing 91	protein-coding
mm_50597.1	chr6	49087143	49087146	+	1	NA	3' UTR (NM_023670, exon 15 of 15)	3' UTR (NM_023670, exon 15 of 15)	13349	NM_029353	75593	Mm.439947	NM_029353	ENSMUSG00000029815	Malsu1	2410003K15Rik|Matsu1	mitochondrial assembly of ribosomal large subunit 1	protein-coding
mm_173366.1	chrY	90819905	90819919	+	1	NA	Intergenic	IMPB_01|Satellite|Satellite	19494	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_96444.1	chr11	67455069	67455156	+	1	NA	Intergenic	CpG	-77886	NM_008088	14457	Mm.40338	NM_008088	ENSMUSG00000033066	Gas7	AW124766|B230343A10Rik|Gas7-cb	growth arrest specific 7	protein-coding
mm_100807.1	chr11	5074879	5074882	-	1	NA	intron (NM_001283061, intron 11 of 16)	B2_Mm2|SINE|B2	-9553	NM_001190406	78926	Mm.44591	NM_030228	ENSMUSG00000034201	Gas2l1	4930500E24Rik|D0Jmb1|Gar22|TU-71.1	growth arrest-specific 2 like 1	protein-coding
mm_21614.1	chr2	164256706	164256711	-	1	NA	promoter-TSS (NM_173377)	promoter-TSS (NM_173377)	-65	NM_173377	329557	Mm.118769	NM_173377	ENSMUSG00000050383	Svs3b	9530004A22Rik	seminal vesicle secretory protein 3B	protein-coding
mm_145532.1	chr18	60803839	60803856	+	1	NA	promoter-TSS (NM_010545)	promoter-TSS (NM_010545)	-2	NM_001042605	16149	Mm.439737	NM_010545	ENSMUSG00000024610	Cd74	CLIP|DHLAG|HLADG|Ia-GAMMA|Ii	CD74 antigen (invariant polypeptide of major histocompatibility complex, class II antigen-associated)	protein-coding
mm_5062.1	chr1	194991249	194991257	+	1	NA	Intergenic	Intergenic	-14294	NR_033564	320400	Mm.417608	NR_033564	ENSMUSG00000097325	Gm16897	C030002c11rik	predicted gene, 16897	ncRNA
mm_142122.1	chr17	35896023	35896061	-	1	NA	exon (NM_001033630, exon 2 of 6)	exon (NM_001033630, exon 2 of 6)	1336	NM_001033630	69662	Mm.260159	NM_001033630	ENSMUSG00000050705	2310061I04Rik	-	RIKEN cDNA 2310061I04 gene	protein-coding
mm_82367.1	chr9	14596520	14596535	-	1	NA	exon (NM_001081395, exon 2 of 13)	exon (NM_001081395, exon 2 of 13)	18473	NM_001081395	75723	Mm.159552	NM_001081395	ENSMUSG00000013076	Amotl1	2310010G08Rik|2310067L22Rik|4932416D09Rik|JEAP|mFLJ00155	angiomotin-like 1	protein-coding
mm_133814.1	chr16	95703957	95703960	+	1	NA	intron (NM_011809, intron 1 of 9)	intron (NM_011809, intron 1 of 9)	1551	NM_011809	23872	Mm.290207	NM_011809	ENSMUSG00000022895	Ets2	AU022856|Ets-2	E26 avian leukemia oncogene 2, 3' domain	protein-coding
mm_81742.1	chr9	113803382	113803403	+	1	NA	intron (NM_001286603, intron 1 of 4)	AT_rich|Low_complexity|Low_complexity	-9194	NM_001286601	76499	Mm.222272	NM_029633	ENSMUSG00000033392	Clasp2	1500004F14Rik|8030404L10Rik|C77448|CLASP2beta|mKIAA0627	CLIP associating protein 2	protein-coding
mm_129924.1	chr15	84444320	84444330	-	1	NA	intron (NM_001347543, intron 1 of 5)	intron (NM_001347543, intron 1 of 5)	2285	NM_001347543	72301	Mm.275387	NM_001163145	ENSMUSG00000062760	1810041L15Rik	Kiaa1644	RIKEN cDNA 1810041L15 gene	protein-coding
mm_59478.1	chr7	27459372	27459391	+	1	NA	exon (NM_144923, exon 2 of 5)	exon (NM_144923, exon 2 of 5)	6963	NM_001290525	233016	Mm.24021	NM_144923	ENSMUSG00000040466	Blvrb	-	biliverdin reductase B (flavin reductase (NADPH))	protein-coding
mm_168685.1	chr11	96032671	96032683	+	1	NA	Intergenic	Intergenic	-2240	NM_033568	27681	Mm.372235	NM_033568	ENSMUSG00000006058	Snf8	D11Moh34	SNF8, ESCRT-II complex subunit, homolog (S. cerevisiae)	protein-coding
mm_102711.1	chr11	67051743	67051775	-	1	NA	promoter-TSS (NM_001040026)	promoter-TSS (NM_001040026)	859	NM_025510	66358	Mm.22511	NM_025510	ENSMUSG00000020910	Adprm	2310004I24Rik|MDS006	ADP-ribose/CDP-alcohol diphosphatase, manganese dependent	protein-coding
mm_162288.1	chr1	25830085	25830089	-	1	NA	promoter-TSS (NM_175642)	promoter-TSS (NM_175642)	-380	NM_175642	210933	Mm.336569	NM_175642	ENSMUSG00000033569	Adgrb3	A830096D10Rik|Bai3	adhesion G protein-coupled receptor B3	protein-coding
mm_67560.1	chr7	81829444	81829514	-	1	NA	promoter-TSS (NM_146193)	promoter-TSS (NM_146193)	-48	NM_146193	83962	Mm.439893	NM_146193	ENSMUSG00000025103	Btbd1	1190005H08Rik	BTB (POZ) domain containing 1	protein-coding
mm_113822.1	chr13	46944822	46944856	+	1	NA	Intergenic	RMER17A|LTR|ERVK	-15121	NM_010617	16553	Mm.342703	NM_010617	ENSMUSG00000021375	Kif13a	4930505I07Rik|mKIAA4109	kinesin family member 13A	protein-coding
mm_20920.1	chr2	150822536	150822577	-	1	NA	intron (NM_153781, intron 14 of 19)	PB1|SINE|Alu	35760	NM_153781	110078	Mm.222584	NM_153781	ENSMUSG00000033059	Pygb	-	brain glycogen phosphorylase	protein-coding
mm_113458.1	chr13	35963128	35963131	+	1	NA	Intergenic	B1_Mur1|SINE|Alu	-4777	NM_029628	76487	Mm.44745	NM_029628	ENSMUSG00000050423	Ppp1r3g	1600032L17Rik	protein phosphatase 1, regulatory (inhibitor) subunit 3G	protein-coding
mm_98947.1	chr11	98447014	98447062	+	1	NA	5' UTR (NM_010346, exon 1 of 15)	5' UTR (NM_010346, exon 1 of 15)	204	NM_010346	14786	Mm.276702	NM_010346	ENSMUSG00000019312	Grb7	mKIAA4028	growth factor receptor bound protein 7	protein-coding
mm_19619.1	chr2	102812511	102812529	-	1	NA	3' UTR (NM_009851, exon 19 of 19)	3' UTR (NM_009851, exon 19 of 19)	89145	NM_001177785	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_133737.1	chr16	93912360	93912403	+	1	NA	Intergenic	Intergenic	17186	NM_001165925	56173	Mm.328716	NM_019500	ENSMUSG00000047109	Cldn14	AI851731	claudin 14	protein-coding
mm_104687.1	chr11	97766481	97766487	-	1	NA	5' UTR (NM_026186, exon 1 of 10)	5' UTR (NM_026186, exon 1 of 10)	129	NM_026186	67480	Mm.33206	NM_026186	ENSMUSG00000018541	Cwc25	1300013D05Rik|AA473636|Ccdc49|R75228	CWC25 spliceosome-associated protein	protein-coding
mm_79247.1	chr9	50565383	50565427	+	1	NA	promoter-TSS (NM_008360)	promoter-TSS (NM_008360)	37	NM_008360	16173	Mm.1410	NM_008360	ENSMUSG00000039217	Il18	Igif|Il-18	interleukin 18	protein-coding
mm_138017.1	chr17	33909604	33909612	+	1	NA	promoter-TSS (NM_001199733)	promoter-TSS (NM_001199733)	7	NM_001199733	13163	Mm.271809	NM_007829	ENSMUSG00000002307	Daxx	-	Fas death domain-associated protein	protein-coding
mm_54327.1	chr6	30509739	30509757	-	1	NA	promoter-TSS (NM_027073)	promoter-TSS (NM_027073)	25	NM_001347087	72649	Mm.45418	NM_178625	ENSMUSG00000029782	Tmem209	2700094F01Rik|AI428435	transmembrane protein 209	protein-coding
mm_130026.1	chr15	88891482	88891518	-	1	NA	Intergenic	Intergenic	29306	NM_145478	223775	Mm.400129	NM_145478	ENSMUSG00000035828	Pim3	BC026639|Kid1	proviral integration site 3	protein-coding
mm_99194.1	chr11	101009530	101009538	+	1	NA	promoter-TSS (NM_001243049)	promoter-TSS (NM_001243049)	82	NM_001243051	11975	Mm.340818	NM_016920	ENSMUSG00000019302	Atp6v0a1	AA959968|ATP6a1|Atp6n1|Atp6n1a|Atpv0a1|Vpp-1|Vpp1	ATPase, H+ transporting, lysosomal V0 subunit A1	protein-coding
mm_68291.1	chr7	105736427	105736441	-	1	NA	promoter-TSS (NM_001161724)	promoter-TSS (NM_001161724)	150	NM_025897	101867	Mm.231400	NM_025897	ENSMUSG00000030888	Rrp8	1500003O22Rik|2900001K19Rik|AW538116	ribosomal RNA processing 8, methyltransferase, homolog (yeast)	protein-coding
mm_91364.1	chr10	29035460	29035463	-	1	NA	Intergenic	Intergenic	-49155	NM_026336	67719	Mm.440480	NM_026336	ENSMUSG00000015519	2310057J18Rik	2210414P04Rik|Leg1	RIKEN cDNA 2310057J18 gene	protein-coding
mm_132890.1	chr16	48842672	48842695	+	1	NA	intron (NM_020509, intron 1 of 3)	intron (NM_020509, intron 1 of 3)	131	NM_020509	57262	Mm.441868	NM_020509	ENSMUSG00000061100	Retnla	1810019L16Rik|Fizz-1|Fizz1|HIMF|RELM-alpha|RELMa|RELMalpha|Xcp2	resistin like alpha	protein-coding
mm_167456.1	chr8	123254320	123254330	+	1	NA	promoter-TSS (NM_028200)	promoter-TSS (NM_028200)	-103	NM_028200	72325	Mm.276193	NM_028200	ENSMUSG00000001062	Vps9d1	1300018I17Rik|2410004N05Rik|5DOS1|Vsp9d1	VPS9 domain containing 1	protein-coding
mm_92423.1	chr10	77059943	77059978	-	1	NA	exon (NM_001109991, exon 33 of 41)	exon (NM_001109991, exon 33 of 41)	26748	NM_031196	20509	Mm.265060	NM_031196	ENSMUSG00000001436	Slc19a1	AI323572|RFC|RFC-1|RFC1	solute carrier family 19 (folate transporter), member 1	protein-coding
mm_110517.1	chr12	54862467	54862488	-	1	NA	intron (NM_007688, intron 1 of 3)	CpG	400	NM_007688	12632	Mm.276826	NM_007688	ENSMUSG00000062929	Cfl2	-	cofilin 2, muscle	protein-coding
mm_97294.1	chr11	76261475	76261501	+	1	NA	intron (NM_008750, intron 7 of 7)	intron (NM_008750, intron 7 of 7)	17752	NM_183263	67390	Mm.24886	NM_183263	ENSMUSG00000038046	Rnmtl1	4833420N02Rik|AI255153|HC90|Mrm3	RNA methyltransferase like 1	protein-coding
mm_163484.1	chr12	108875535	108875539	-	1	NA	intron (NM_011710, intron 5 of 10)	intron (NM_011710, intron 5 of 10)	17661	NM_001164488	22375	Mm.38433	NM_011710	ENSMUSG00000021266	Wars	TrpRS|WRS	tryptophanyl-tRNA synthetase	protein-coding
mm_172306.1	chr7	104353235	104353242	-	1	NA	5' UTR (NM_001146007, exon 1 of 8)	5' UTR (NM_001146007, exon 1 of 8)	111	NM_175677	319236	Mm.425502	NM_175677	ENSMUSG00000057143	Trim12c	9230105E10Rik|Trim12-2	tripartite motif-containing 12C	protein-coding
mm_140048.1	chr17	74528325	74528370	+	1	NA	promoter-TSS (NM_007566)	promoter-TSS (NM_007566)	52	NM_007566	12211	Mm.442564	NM_007566	ENSMUSG00000024073	Birc6	A430032G04Rik|A430040A19Rik|AA501170|Bruce|D630005A10Rik|mKIAA1289	baculoviral IAP repeat-containing 6	protein-coding
mm_56544.1	chr6	99726402	99726414	-	1	NA	promoter-TSS (NM_001170419)	promoter-TSS (NM_001170419)	-16	NM_001170419	50501	Mm.87365	NM_015768	ENSMUSG00000030069	Prok2	Bv8|PK2|Prok1	prokineticin 2	protein-coding
mm_23597.1	chr3	65108997	65109037	+	1	NA	promoter-TSS (NM_010597)	promoter-TSS (NM_010597)	-351	NM_010597	16497	Mm.316402	NM_010597	ENSMUSG00000027827	Kcnab1	Akr8a8|Kvbeta1.1|mKv(beta)1	potassium voltage-gated channel, shaker-related subfamily, beta member 1	protein-coding
mm_37064.1	chr4	116075001	116075017	-	1	NA	promoter-TSS (NM_153521)	promoter-TSS (NM_153521)	61	NM_025641	66576	Mm.181721	NM_025641	ENSMUSG00000063882	Uqcrh	2210416J04Rik|2310021J10Rik|2610041P16Rik	ubiquinol-cytochrome c reductase hinge protein	protein-coding
mm_8486.1	chr1	153550046	153550081	-	1	NA	promoter-TSS (NM_028749)	promoter-TSS (NM_028749)	-349	NM_028749	74091	Mm.24887	NM_028749	ENSMUSG00000042684	Npl	0610033B02Rik	N-acetylneuraminate pyruvate lyase	protein-coding
mm_123238.1	chr14	60177483	60177559	-	1	NA	Intergenic	CpG	51394	NR_030458	751526		NR_030458	ENSMUSG00000076270	Mir719	Mirn719|mmu-mir-719	microRNA 719	ncRNA
mm_65317.1	chr7	24897242	24897274	-	1	NA	promoter-TSS (NM_007655)	promoter-TSS (NM_007655)	-253	NM_007655	12518	Mm.1355	NM_007655	ENSMUSG00000003379	Cd79a	Ig-alpha|Iga|Igalpha|Ly-54|Ly54|mb-1	CD79A antigen (immunoglobulin-associated alpha)	protein-coding
mm_36448.1	chr4	82498390	82498401	-	1	NA	exon (NM_001113209, exon 2 of 12)	exon (NM_001113209, exon 2 of 12)	7384	NM_001286127	18028	Mm.317947	NM_008687	ENSMUSG00000008575	Nfib	6720429L07Rik|CTF|E030026I10Rik|NF-I/B|NF1-B|NFI-B	nuclear factor I/B	protein-coding
mm_25110.1	chr3	101460615	101460624	+	1	NA	3' UTR (NM_207205, exon 11 of 11)	3' UTR (NM_207205, exon 11 of 11)	83494	NM_207205	78908	Mm.257997	NM_207205	ENSMUSG00000042035	Igsf3	1700016K10Rik|2810035F16Rik|4833439O17Rik|mKIAA0466	immunoglobulin superfamily, member 3	protein-coding
mm_77434.1	chr8	121570331	121570332	-	1	NA	intron (NM_133765, intron 1 of 8)	intron (NM_133765, intron 1 of 8)	8475	NM_133765	76454	Mm.24829	NM_133765	ENSMUSG00000052934	Fbxo31	1110003O08Rik|2310046N15Rik|Fbx14|Fbxo14	F-box protein 31	protein-coding
mm_62273.1	chr7	99579576	99579604	+	1	NA	intron (NM_177231, intron 1 of 15)	MLT1O|LTR|ERVL-MaLR	27321	NR_029760	723840		NR_029760	ENSMUSG00000065571	Mir326	Mirn326|mir-326|mmu-mir-326	microRNA 326	ncRNA
mm_88996.1	chr10	81575258	81575269	+	1	NA	promoter-TSS (NM_019725)	promoter-TSS (NM_019725)	-24	NM_019725	21886	Mm.38608	NM_019725	ENSMUSG00000034771	Tle2	Grg2|mKIAA4188	transducin-like enhancer of split 2	protein-coding
mm_135385.1	chr16	44140571	44140584	-	1	NA	intron (NM_028108, intron 1 of 4)	intron (NM_028108, intron 1 of 4)	768	NM_028108	72117	Mm.278726	NM_028108	ENSMUSG00000022698	Naa50	2600005K24Rik|2810441M03Rik|AW112078|Mak3|Mak3p|Nat13|Nat5|San	N(alpha)-acetyltransferase 50, NatE catalytic subunit	protein-coding
mm_31173.1	chr4	43473401	43473429	+	1	NA	Intergenic	L1MEj|LINE|L1	10294	NM_019436	54390	Mm.31775	NM_019436	ENSMUSG00000028460	Sit1	Sit	suppression inducing transmembrane adaptor 1	protein-coding
mm_47493.1	chr5	124006552	124006569	-	1	NA	exon (NM_177876, exon 4 of 4)	exon (NM_177876, exon 4 of 4)	9708	NR_105999	102465625		NR_105999	ENSMUSG00000098454	Mir7032	Gm27309|mmu-mir-7032	microRNA 7032	ncRNA
mm_111987.1	chr12	110486180	110486190	-	1	NA	intron (NM_012023, intron 1 of 13)	intron (NM_012023, intron 1 of 13)	446	NM_012023	26931	Mm.240396	NM_012023	ENSMUSG00000017843	Ppp2r5c	2610043M05Rik|2700063L20Rik|AI060890|AW545884|C85228|D12Bwg0916e|mKIAA0044	protein phosphatase 2, regulatory subunit B', gamma	protein-coding
mm_135827.1	chr16	58507902	58507918	-	1	NA	intron (NM_018784, intron 1 of 10)	intron (NM_018784, intron 1 of 10)	15402	NM_018784	54613	Mm.212742	NM_018784	ENSMUSG00000022747	St3gal6	1700023B24Rik|AI930218|AW552396|Siat10|St3galVI	ST3 beta-galactoside alpha-2,3-sialyltransferase 6	protein-coding
mm_137469.1	chr17	26676391	26676401	+	1	NA	promoter-TSS (NM_025272)	promoter-TSS (NM_025272)	0	NM_025272	11974	Mm.22602	NM_025272	ENSMUSG00000015575	Atp6v0e	Atp6k|Atp6v0e1|M9.2	ATPase, H+ transporting, lysosomal V0 subunit E	protein-coding
mm_160344.1	chr8	19447620	19447620	-	1	NA	promoter-TSS (NM_153108)	promoter-TSS (NM_153108)	-14	NM_153108	244334	Mm.390008	NM_153108	ENSMUSG00000031471	Defb8	BD-8|Defr1	defensin beta 8	protein-coding
mm_128017.1	chr15	23437399	23437425	-	1	NA	intron (NM_001081299, intron 9 of 11)	intron (NM_001081299, intron 9 of 11)	400949	NM_001081299	320865	Mm.241965	NM_001081299	ENSMUSG00000040420	Cdh18	B230220E17Rik|Cdh14l	cadherin 18	protein-coding
mm_88568.1	chr10	79669414	79669459	+	1	NA	promoter-TSS (NM_148934)	promoter-TSS (NM_148934)	26	NM_148934	110012	Mm.22623	NM_148934	ENSMUSG00000020308	Tpgs1	AV005629|Gm16517|Gtrgeo22|PGs1	tubulin polyglutamylase complex subunit 1	protein-coding
mm_130153.1	chr15	91191386	91191401	-	1	NA	exon (NM_011994, exon 1 of 10)	exon (NM_011994, exon 1 of 10)	414	NM_011994	26874	Mm.295456	NM_011994	ENSMUSG00000055782	Abcd2	ABC39|ALDL1|ALDR|ALDRP	ATP-binding cassette, sub-family D (ALD), member 2	protein-coding
mm_110393.1	chr12	41485981	41485995	-	1	NA	promoter-TSS (NM_001271709)	promoter-TSS (NM_001271709)	69	NM_001271708	16981	Mm.404786	NM_010733	ENSMUSG00000036295	Lrrn3	NLRR-3	leucine rich repeat protein 3, neuronal	protein-coding
mm_94907.1	chr11	29373727	29373737	+	1	NA	promoter-TSS (NM_176841)	promoter-TSS (NM_176841)	-440	NM_176841	108686	Mm.338284	NM_176841	ENSMUSG00000032740	Ccdc88a	A430106J12Rik|AI848406|Ape|C130096N06Rik|C330012F17Rik|D130005J21Rik|Girdin|Giv|Grdn|Hkrp1	coiled coil domain containing 88A	protein-coding
mm_89401.1	chr10	90576660	90576668	+	1	NA	promoter-TSS (NM_181398)	promoter-TSS (NM_181398)	-27	NM_001177396	77531	Mm.440605	NM_181398	ENSMUSG00000058589	Anks1b	AIDA-1b|C030032C09Rik|E530015N03Rik|ENSMUSG00000078431|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding
mm_37177.1	chr4	117251840	117251874	-	1	NA	promoter-TSS (NM_001033774)	promoter-TSS (NM_001033774)	60	NM_001145637	381544	Mm.23504	NM_001033774	ENSMUSG00000060268	Gm1661	Gm1662|Ncrna00082	predicted gene 1661	protein-coding
mm_32987.1	chr4	120161420	120161425	+	1	NA	5' UTR (NM_007902, exon 1 of 5)	5' UTR (NM_007902, exon 1 of 5)	216	NM_007902	13615	Mm.284855	NM_007902	ENSMUSG00000028635	Edn2	ET-2|PPET2|VIC	endothelin 2	protein-coding
mm_38154.1	chr4	135073571	135073574	-	1	NA	Intergenic	Intergenic	-47073	NM_019732	12399	Mm.378894	NM_019732	ENSMUSG00000070691	Runx3	AML2|Cbfa3|Pebp2a3	runt related transcription factor 3	protein-coding
mm_39312.1	chr5	8055086	8055114	+	1	NA	intron (NM_025618, intron 1 of 7)	intron (NM_025618, intron 1 of 7)	-1442	NM_001080974	109552	Mm.96211	NM_025618	ENSMUSG00000003161	Sri	2210417O06Rik|2900070H08Rik|Sor	sorcin	protein-coding
mm_169976.1	chr17	14978783	14978790	-	1	NA	promoter-TSS (NM_001123370)	promoter-TSS (NM_001123370)	26	NM_001123368	100041586	Mm.440445	NM_001123368	ENSMUSG00000079710	Gm3417	-	predicted gene 3417	protein-coding
mm_96613.1	chr11	69098724	69098728	+	1	NA	promoter-TSS (NM_011065)	promoter-TSS (NM_011065)	-230	NM_011065	18626	Mm.7373	NM_011065	ENSMUSG00000020893	Per1	Hftm|Per|m-rigui|mPer1	period circadian clock 1	protein-coding
mm_37255.1	chr4	118409220	118409282	-	1	NA	promoter-TSS (NM_198170)	promoter-TSS (NM_198170)	12	NM_198170	230676	Mm.415218	NM_198170	ENSMUSG00000033253	Szt2	6430407N22|ENSMUSG00000058432|TIGR	seizure threshold 2	protein-coding
mm_121301.1	chr14	105681825	105681831	+	1	NA	Intergenic	Intergenic	-58058	NR_105814	102465207		NR_105814	ENSMUSG00000098780	Mir6390	Gm27562|mmu-mir-6390	microRNA 6390	ncRNA
mm_46741.1	chr5	110839721	110839734	-	1	NA	promoter-TSS (NM_016681)	promoter-TSS (NM_016681)	50	NM_153571	100900	Mm.200231	NM_153571	ENSMUSG00000043510	Hscb	AI325508|AW049829|Hsc20	HscB iron-sulfur cluster co-chaperone	protein-coding
mm_53451.1	chr6	134640980	134641014	+	1	NA	promoter-TSS (NM_026371)	promoter-TSS (NM_026371)	57	NM_026371	67774	Mm.41892	NM_026371	ENSMUSG00000042992	Borcs5	5830457J20Rik|AW124643|Loh12cr1	BLOC-1 related complex subunit 5	protein-coding
mm_158557.1	chrX	150336290	150336292	-	1	NA	Intergenic	Intergenic	-22927	NM_001101501	333588	Mm.159296	NM_001101501		Gm15104	OTTMUSG00000018998	predicted gene 15104	protein-coding
mm_42227.1	chr5	113490736	113490760	+	1	NA	Intergenic	CpG	-59672	NM_177292	320916	Mm.102783	NM_177292	ENSMUSG00000063430	Wscd2	4933413A10Rik|C530024P05Rik|Gm450	WSC domain containing 2	protein-coding
mm_59071.1	chr7	19508744	19508754	+	1	NA	promoter-TSS (NM_177692)	promoter-TSS (NM_177692)	79	NM_025960	67091	Mm.44213	NM_025960	ENSMUSG00000002043	Trappc6a	1810073E21Rik|4930519D19Rik|AI480686|TRS33|mhyp	trafficking protein particle complex 6A	protein-coding
mm_56803.1	chr6	116657199	116657223	-	1	NA	intron (NM_178045, intron 3 of 10)	(TG)n|Simple_repeat|Simple_repeat	6527	NM_001166580	213393	Mm.38231	NM_145980	ENSMUSG00000048489	8430408G22Rik	Depp|Fseg	RIKEN cDNA 8430408G22 gene	protein-coding
mm_24880.1	chr3	95995986	95996004	+	1	NA	promoter-TSS (NM_023320)	promoter-TSS (NM_023320)	-156	NM_023320	67220	Mm.458147	NM_023320	ENSMUSG00000015745	Plekho1	2810052M02Rik|CKIP-1|Ckip1|JZA-20|Jza2	pleckstrin homology domain containing, family O member 1	protein-coding
mm_49852.1	chr6	38433852	38433863	+	1	NA	promoter-TSS (NM_177185)	promoter-TSS (NM_177185)	-68	NM_177185	320538	Mm.302831	NM_177185	ENSMUSG00000038538	Ubn2	2900060J04Rik|6030408G03Rik|BC060116|D130059P03Rik|mKIAA2030	ubinuclein 2	protein-coding
mm_125077.1	chr15	25984463	25984477	+	1	NA	5' UTR (NM_144523, exon 1 of 6)	5' UTR (NM_144523, exon 1 of 6)	104	NM_144523	52521	Mm.29145	NM_144523	ENSMUSG00000052253	Zfp622	1110033B05Rik|D15Ertd806e|ZPR9|Znf622	zinc finger protein 622	protein-coding
mm_168573.1	chr1	171050528	171050537	+	1	NA	TTS (NM_010188)	TTS (NM_010188)	8871	NM_010188	14131	Mm.22119	NM_010188	ENSMUSG00000059498	Fcgr3	CD16	Fc receptor, IgG, low affinity III	protein-coding
mm_51150.1	chr6	70698419	70698427	+	1	NA	Intergenic	Intergenic	93752	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_49439.1	chr6	29319134	29319153	+	1	NA	promoter-TSS (NM_001289664)	promoter-TSS (NM_001289664)	3	NM_001289664	330277	Mm.87624	NM_207258	ENSMUSG00000039742	Fam71f1	GARI-L1|Gm764|NYD-SP18	family with sequence similarity 71, member F1	protein-coding
mm_49957.1	chr6	40628825	40628839	+	1	NA	promoter-TSS (NM_001171003)	promoter-TSS (NM_001171003)	1	NM_001171003	232714	Mm.33401	NM_001171003	ENSMUSG00000068587	Mgam	6030407P20Rik|MGA	maltase-glucoamylase	protein-coding
mm_70225.1	chr7	145236562	145236602	-	1	NA	intron (NR_132644, intron 24 of 24)	intron (NR_132644, intron 24 of 24)	-28463	NR_033626	100040049	Mm.102235	NR_033626	ENSMUSG00000109305	1810010D01Rik	Gm2572	RIKEN cDNA 1810010D01 gene	ncRNA
mm_50312.1	chr6	47869983	47869985	+	1	NA	Intergenic	Intergenic	-7571	NM_146175	101095	Mm.440186	NM_146175	ENSMUSG00000025821	Zfp282	AI449432|C81429|E430019K09Rik|HUB1	zinc finger protein 282	protein-coding
mm_18068.1	chr2	42245067	42245071	-	1	NA	intron (NM_053011, intron 2 of 90)	Lx5c|LINE|L1	202499	NR_105754	102465171		NR_105754	ENSMUSG00000098660	Mir6336	Gm27584|mmu-mir-6336	microRNA 6336	ncRNA
mm_6845.1	chr1	84237722	84237743	-	1	NA	intron (NM_001003948, intron 1 of 2)	intron (NM_001003948, intron 1 of 2)	-18771	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_20660.1	chr2	132112339	132112354	-	1	NA	intron (NM_018824, intron 1 of 15)	intron (NM_018824, intron 1 of 15)	32762	NM_018824	54338	Mm.103581	NM_018824	ENSMUSG00000027340	Slc23a2	AI844736|NBTL1|SVCT2|Slc23a1|YSPL2|YSPL3|mKIAA0238	solute carrier family 23 (nucleobase transporters), member 2	protein-coding
mm_128756.1	chr15	64922326	64922341	-	1	NA	promoter-TSS (NM_009623)	promoter-TSS (NM_009623)	-37	NM_009623	11514	Mm.1425	NM_009623	ENSMUSG00000022376	Adcy8	AC8|AW060868	adenylate cyclase 8	protein-coding
mm_8647.1	chr1	156430904	156430928	-	1	NA	3' UTR (NM_009230, exon 16 of 16)	3' UTR (NM_009230, exon 16 of 16)	-10001	NM_001346967	77352	Mm.428709	NM_001033180	ENSMUSG00000026601	Axdnd1	9430070O13Rik|Gm979	axonemal dynein light chain domain containing 1	protein-coding
mm_118351.1	chr13	115052730	115052736	-	1	NA	intron (NM_001033228, intron 1 of 28)	intron (NM_001033228, intron 1 of 28)	37425	NM_134058	105083	Mm.486295	NM_134058	ENSMUSG00000042275	Pelo	AA409897|AI852218	pelota homolog (Drosophila)	protein-coding
mm_80036.1	chr9	68906884	68906885	+	1	NA	intron (NM_013646, intron 1 of 10)	intron (NM_013646, intron 1 of 10)	141538	NR_033299	320440	Mm.483129	NM_177159		9530091C08Rik	-	RIKEN cDNA 9530091C08 gene	ncRNA
mm_147730.1	chr18	61014201	61014261	-	1	NA	promoter-TSS (NM_201353)	promoter-TSS (NM_201353)	-32	NM_201353	240332	Mm.39846	NM_201353	ENSMUSG00000052026	Slc6a7	AW455934|PROT	solute carrier family 6 (neurotransmitter transporter, L-proline), member 7	protein-coding
mm_148119.1	chr18	75278777	75278797	-	1	NA	intron (NM_027727, intron 16 of 16)	intron (NM_027727, intron 16 of 16)	18530	NR_045394	100503117	Mm.250517	NR_045393	ENSMUSG00000102047	2010010A06Rik	5033420E22Rik	RIKEN cDNA 2010010A06 gene	ncRNA
mm_32990.1	chr4	120405174	120405221	+	1	NA	promoter-TSS (NM_013883)	promoter-TSS (NM_013883)	-84	NM_001159630	29871	Mm.427014	NM_013883	ENSMUSG00000000085	Scmh1	AI315320|AI851618|Scml1|Scml3	sex comb on midleg homolog 1	protein-coding
mm_108724.1	chr12	87200503	87200522	+	1	NA	promoter-TSS (NM_001290288)	promoter-TSS (NM_001290288)	-31	NM_001290288	238333	Mm.302304	NM_001290288	ENSMUSG00000090812	Samd15	Gm263	sterile alpha motif domain containing 15	protein-coding
mm_68061.1	chr7	101845301	101845339	-	1	NA	promoter-TSS (NM_008035)	promoter-TSS (NM_008035)	11	NM_001303231	14276	Mm.439666	NM_008035	ENSMUSG00000032725	Folr2	FBP2|FR-P3|FR-beta|Folbp-2|Folbp2	folate receptor 2 (fetal)	protein-coding
mm_59790.1	chr7	28982833	28982892	+	1	NA	promoter-TSS (NM_028659)	promoter-TSS (NM_028659)	8	NM_008279	26411	Mm.148278	NM_008279	ENSMUSG00000037337	Map4k1	Hpk1|mHPK1	mitogen-activated protein kinase kinase kinase kinase 1	protein-coding
mm_151054.1	chr19	47178948	47178997	+	1	NA	5' UTR (NM_021360, exon 1 of 6)	5' UTR (NM_021360, exon 1 of 6)	152	NM_021360	18011	Mm.313651	NM_021360	ENSMUSG00000006435	Neurl1a	2410129E16Rik|AI450910|AI481072|Neu1|Neur1|Neurl|Neurl1|Nlz|Rnf67	neuralized E3 ubiquitin protein ligase 1A	protein-coding
mm_68861.1	chr7	126414793	126414801	-	1	NA	promoter-TSS (NM_009844)	promoter-TSS (NM_009844)	73	NM_009844	12478	Mm.4360	NM_009844	ENSMUSG00000030724	Cd19	AW495831	CD19 antigen	protein-coding
mm_47970.1	chr5	135909235	135909250	-	1	NA	3' UTR (NM_018871, exon 2 of 2)	3' UTR (NM_018871, exon 2 of 2)	21323	NM_013560	15507	Mm.13849	NM_013560	ENSMUSG00000004951	Hspb1	27kDa|Hsp25	heat shock protein 1	protein-coding
mm_64435.1	chr7	142652945	142653017	+	1	NA	3' UTR (NM_010514, exon 4 of 4)	3' UTR (NM_010514, exon 4 of 4)	2015	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_14197.1	chr2	127142738	127142749	+	1	NA	promoter-TSS (NM_001163528)	promoter-TSS (NM_001163528)	-153	NM_001163528	73338	Mm.57559	NM_001163527	ENSMUSG00000074825	Itpripl1	1700041B20Rik	inositol 1,4,5-triphosphate receptor interacting protein-like 1	protein-coding
mm_171872.1	chr5	28852601	28852609	+	1	NA	Intergenic	(GA)n|Simple_repeat|Simple_repeat	-343388	NM_001289757	56874	Mm.87352	NM_021470	ENSMUSG00000029130	Rnf32	1700009J01Rik|2700025B22Rik|4930542N22Rik|Lmbr2	ring finger protein 32	protein-coding
mm_130590.1	chr15	99637806	99637816	-	1	NA	intron (NM_012025, intron 4 of 17)	intron (NM_012025, intron 4 of 17)	13845	NM_001253808	26934	Mm.273804	NM_012025	ENSMUSG00000023015	Racgap1	AI227039|AI327394|Band25|GTPase|MgcRacGAP|gtl11|mKIAA1478	Rac GTPase-activating protein 1	protein-coding
mm_78403.1	chr9	28921117	28921121	+	1	NA	3' UTR (NM_177906, exon 8 of 8)	3' UTR (NM_177906, exon 8 of 8)	1042010	NM_172290	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding
mm_13028.1	chr2	91054055	91054114	+	1	NA	promoter-TSS (NM_008948)	promoter-TSS (NM_008948)	68	NM_008948	19182	Mm.289832	NM_008948	ENSMUSG00000002102	Psmc3	TBP-1	proteasome (prosome, macropain) 26S subunit, ATPase 3	protein-coding
mm_158060.1	chrX	101081980	101082024	-	1	NA	exon (NM_007515, exon 8 of 13)	exon (NM_007515, exon 8 of 13)	3403	NM_001301840	11989	Mm.5140	NM_007515	ENSMUSG00000031297	Slc7a3	Atrc3|CAT-3|CAT3|SLC7A1|SLC7A2	solute carrier family 7 (cationic amino acid transporter, y+ system), member 3	protein-coding
mm_97494.1	chr11	78343476	78343526	+	1	NA	promoter-TSS (NM_011676)	promoter-TSS (NM_011676)	6	NM_011676	22248	Mm.284811	NM_011676	ENSMUSG00000002058	Unc119	D11Bhm52|HRG4|MRG4|Rg4|Rtg4|Unc119h	unc-119 lipid binding chaperone	protein-coding
mm_51387.1	chr6	77243270	77243285	+	1	NA	intron (NM_028880, intron 1 of 1)	intron (NM_028880, intron 1 of 1)	560	NM_028880	74342	Mm.292568	NM_028880	ENSMUSG00000060780	Lrrtm1	4632401D06Rik|AW125451	leucine rich repeat transmembrane neuronal 1	protein-coding
mm_138614.1	chr17	35821676	35821693	+	1	NA	promoter-TSS (NM_133662)	promoter-TSS (NM_133662)	-29	NM_133662	15937	Mm.25613	NM_133662	ENSMUSG00000003541	Ier3	AI663993|IEX-1|cI-3|gly96	immediate early response 3	protein-coding
mm_19787.1	chr2	107058980	107058980	-	1	NA	5' UTR (NM_008045, exon 2 of 3)	5' UTR (NM_008045, exon 2 of 3)	671	NM_008045	14308	Mm.249525	NM_008045	ENSMUSG00000027120	Fshb	FSH|FSH-B|FSH-beta|Fshbeta	follicle stimulating hormone beta	protein-coding
mm_96327.1	chr11	64741595	64741600	+	1	NA	Intergenic	MT2A|LTR|ERVL	-237438	NM_023479	68626	Mm.157711	NM_023479	ENSMUSG00000020549	Elac2	1110017O07Rik|D11Wsu80e|Hpc2	elaC ribonuclease Z 2	protein-coding
mm_3751.1	chr1	156035706	156035763	+	1	NA	promoter-TSS (NM_001160182)	promoter-TSS (NM_001160182)	7	NM_001160180	240832	Mm.253335	NM_022329	ENSMUSG00000050565	Tor1aip2	1110020D10Rik|15kDa|A130072J07|AA103493|AW060462|AW610675|C77739|Ifrg15|Lull1	torsin A interacting protein 2	protein-coding
mm_138926.1	chr17	43801325	43801354	+	1	NA	promoter-TSS (NM_207649)	promoter-TSS (NM_207649)	-512	NM_207649	53901	Mm.251242	NM_030598	ENSMUSG00000039601	Rcan2	Csp2|Dscr1l1|MCIP2|ZAKI-4	regulator of calcineurin 2	protein-coding
mm_30774.1	chr4	17872093	17872098	+	1	NA	intron (NM_019724, intron 1 of 9)	L1_Mus1|LINE|L1	18637	NM_019724	17389	Mm.187315	NM_019724	ENSMUSG00000028226	Mmp16	MT-MMP 3|MT3-MMP|Mt3mmp	matrix metallopeptidase 16	protein-coding
mm_107615.1	chr12	49389860	49389894	+	1	NA	non-coding (NR_026733, exon 1 of 3)	non-coding (NR_026733, exon 1 of 3)	225	NR_026733	67293	Mm.185800	NR_026733	ENSMUSG00000104861	3110039M20Rik	-	RIKEN cDNA 3110039M20 gene	ncRNA
mm_127706.1	chr15	102998212	102998222	+	1	NA	Intergenic	Intergenic	7678	NM_010466	15426	Mm.6167	NM_010466	ENSMUSG00000001657	Hoxc8	D130011F21Rik|Hox-3.1	homeobox C8	protein-coding
mm_114891.1	chr13	94359105	94359115	+	1	NA	promoter-TSS (NR_045619)	promoter-TSS (NR_045619)	150	NM_009680	11774	Mm.21185	NM_009680	ENSMUSG00000021686	Ap3b1	AP-3|AU015684|C78395|Hps2|beta3A|pe|pearl|rim2	adaptor-related protein complex 3, beta 1 subunit	protein-coding
mm_80166.1	chr9	71451204	71451229	+	1	NA	Intergenic	Intergenic	33742	NM_001164793	28015	Mm.21094	NM_178602	ENSMUSG00000032199	Polr2m	AA407243|AA408799|AI303746|AW553238|D9Wsu138e|Grinl1a|mKIAA4185	polymerase (RNA) II (DNA directed) polypeptide M	protein-coding
mm_72061.1	chr8	71406004	71406050	+	1	NA	promoter-TSS (NM_172756)	promoter-TSS (NM_172756)	15	NM_172756	234396	Mm.216549	NM_172756	ENSMUSG00000046295	Ankle1	8430438L13Rik|Ankrd41|C430003I23|Lem3	ankyrin repeat and LEM domain containing 1	protein-coding
mm_35513.1	chr4	41098175	41098190	-	1	NA	promoter-TSS (NM_016689)	promoter-TSS (NM_016689)	1	NM_016689	11828	Mm.34043	NM_016689	ENSMUSG00000028435	Aqp3	AQP-2	aquaporin 3	protein-coding
mm_138545.1	chr17	35263426	35263457	+	1	NA	exon (NM_001267808, exon 5 of 11)	exon (NM_001267808, exon 5 of 11)	318	NM_001267808	14980	Mm.439675	NM_001267808		H2-L	H-2L	histocompatibility 2, D region locus L	protein-coding
mm_114580.1	chr13	75707389	75707399	+	1	NA	promoter-TSS (NM_138953)	promoter-TSS (NM_138953)	-90	NM_138953	192657	Mm.21288	NM_138953	ENSMUSG00000001542	Ell2	-	elongation factor RNA polymerase II 2	protein-coding
mm_2775.1	chr1	130764972	130764988	+	1	NA	Intergenic	Intergenic	33004	NM_177604	212439	Mm.268547	NM_177604	ENSMUSG00000042510	AA986860	E030025M07|Sarg	expressed sequence AA986860	protein-coding
mm_113569.1	chr13	38345109	38345140	+	1	NA	promoter-TSS (NM_007556)	promoter-TSS (NM_007556)	-592	NM_007556	12161	Mm.385759	NM_007556	ENSMUSG00000039004	Bmp6	D13Wsu115e|Vgr1	bone morphogenetic protein 6	protein-coding
mm_7204.1	chr1	93068680	93068719	-	1	NA	intron (NM_001294150, intron 9 of 46)	intron (NM_001294150, intron 9 of 46)	13781	NM_001294150	16560	Mm.276408	NM_008440	ENSMUSG00000014602	Kif1a	ATSV|C630002N23Rik|Gm1626|Kns1	kinesin family member 1A	protein-coding
mm_58841.1	chr7	16838177	16838193	+	1	NA	intron (NM_133789, intron 14 of 17)	intron (NM_133789, intron 14 of 17)	-4717	NM_001252458	101540	Mm.1881	NM_178900	ENSMUSG00000041187	Prkd2	AI325941|PKD2	protein kinase D2	protein-coding
mm_172275.1	chr6	85588001	85588006	+	1	NA	exon (NM_145223, exon 1 of 23)	exon (NM_145223, exon 1 of 23)	472	NM_145223	236266	Mm.246967	NM_145223	ENSMUSG00000063810	Alms1	bbb	Alstrom syndrome 1	protein-coding
mm_12964.1	chr2	90674913	90674919	+	1	NA	Intergenic	B3|SINE|B2	-2299	NM_021512	59015	Mm.24532	NM_021512	ENSMUSG00000051329	Nup160	160kDa|2810011M03Rik|AA414952|AU020188|Gtl-13|Gtl1-13|Gtl13|mKIAA0197	nucleoporin 160	protein-coding
mm_105430.1	chr11	103938212	103938217	-	1	NA	intron (NM_008740, intron 1 of 20)	intron (NM_008740, intron 1 of 20)	15842	NM_008740	18195	Mm.260117	NM_008740	ENSMUSG00000034187	Nsf	AI316878|AU020090|AU067812|SKD2	N-ethylmaleimide sensitive fusion protein	protein-coding
mm_169473.1	chr14	69284982	69284989	-	1	NA	5' UTR (NM_026331, exon 1 of 4)	5' UTR (NM_026331, exon 1 of 4)	118	NM_026331	67712	Mm.293635	NM_026331	ENSMUSG00000034248	Slc25a37	1700020E22Rik|4930513O14Rik|4930526G11Rik|AI848481|C330015G08Rik|Mfrn|Mfrn1|Mscp|frascati|mitoferrin	solute carrier family 25, member 37	protein-coding
mm_151067.1	chr19	47509210	47509241	+	1	NA	intron (NM_175360, intron 8 of 9)	intron (NM_175360, intron 8 of 9)	-3757	NR_045322	100503104	Mm.442735	NR_045322	ENSMUSG00000097990	Gm19557	-	predicted gene, 19557	ncRNA
mm_106939.1	chr12	8674702	8674746	+	1	NA	promoter-TSS (NM_030723)	promoter-TSS (NM_030723)	43	NM_030723	80913	Mm.341243	NM_030723	ENSMUSG00000020594	Pum2	5730503J23Rik|Pumm2	pumilio RNA-binding family member 2	protein-coding
mm_155665.1	chrX	88580384	88580387	+	1	NA	Intergenic	RLTR9E|LTR|ERVK	179168	NR_035440	100316809		NR_035440	ENSMUSG00000084535	Mir1906-1	Mir1906|Mirn1906|mmu-mir-1906|mmu-mir-1906-1	microRNA 1906-1	ncRNA
mm_141948.1	chr17	35074486	35074497	-	1	NA	promoter-TSS (NM_033478)	promoter-TSS (NM_033478)	-27	NM_033478	114654	Mm.246697	NM_033478	ENSMUSG00000073413	Ly6g6d	A930024F17Rik|G6d|G6f|MEGT1|NG25|NG32	lymphocyte antigen 6 complex, locus G6D	protein-coding
mm_108792.1	chr12	91400467	91400477	+	1	NA	promoter-TSS (NM_001113404)	promoter-TSS (NM_001113404)	-521	NM_001113404	22095	Mm.173847	NM_011648	ENSMUSG00000020963	Tshr	AI481368|hypothroid|hyt|pet	thyroid stimulating hormone receptor	protein-coding
mm_138993.1	chr17	45555637	45555673	+	1	NA	promoter-TSS (NM_008690)	promoter-TSS (NM_008690)	-45	NM_008690	18037	Mm.57043	NM_008690	ENSMUSG00000023947	Nfkbie	I-kappa-B-epsilon|IKBE|IkB-E|NF-kappa-BIE|ikB-epsilon	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, epsilon	protein-coding
mm_162452.1	chr1	125434585	125434609	-	1	NA	intron (NM_001205385, intron 2 of 12)	intron (NM_001205385, intron 2 of 12)	1130	NM_023735	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding
mm_73011.1	chr8	93947013	93947025	+	1	NA	intron (NM_001113384, intron 4 of 7)	intron (NM_001113384, intron 4 of 7)	65621	NM_011787	23802	Mm.34641	NM_011787	ENSMUSG00000031751	Amfr	gp78	autocrine motility factor receptor	protein-coding
mm_57047.1	chr6	122344926	122344936	-	1	NA	Intergenic	Intergenic	-4704	NM_001271579	13619	Mm.6822	NM_007905	ENSMUSG00000040669	Phc1	AW557034|Edr|Edr1|Mph1|Rae-28|rae28	polyhomeotic-like 1 (Drosophila)	protein-coding
mm_167041.1	chr7	79891102	79891105	+	1	NA	intron (NM_009682, intron 4 of 5)	intron (NM_009682, intron 4 of 5)	29537	NM_009682	11778	Mm.220173	NM_009682	ENSMUSG00000063801	Ap3s2	[s]3B	adaptor-related protein complex 3, sigma 2 subunit	protein-coding
mm_3068.1	chr1	134183542	134183562	+	1	NA	exon (NM_007695, exon 3 of 10)	exon (NM_007695, exon 3 of 10)	1148	NM_007695	12654	Mm.38274	NM_007695	ENSMUSG00000064246	Chil1	AW208766|Brp39|Chi3l1|Gp39	chitinase-like 1	protein-coding
mm_140094.1	chr17	78200191	78200228	+	1	NA	promoter-TSS (NM_015800)	promoter-TSS (NM_015800)	-39	NM_015800	50766	Mm.311912	NM_015800	ENSMUSG00000024074	Crim1	AU015004	cysteine rich transmembrane BMP regulator 1 (chordin like)	protein-coding
mm_123900.1	chr14	73170256	73170291	-	1	NA	intron (NR_033185, intron 11 of 15)	intron (NR_033185, intron 11 of 15)	27488	NR_033185	105670	Mm.280068	NM_134083	ENSMUSG00000022106	Rcbtb2	2610028E02Rik|2810420M18Rik|AI448345|AW240694|Chc1l|RC/BTB2	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 2	protein-coding
mm_152657.1	chr19	12795425	12795465	-	1	NA	non-coding (NR_024093, exon 1 of 13)	non-coding (NR_024093, exon 1 of 13)	678	NR_024093	664779	Mm.290924	NM_001039718	ENSMUSG00000024695	Gm44505	Zfp91-Cntf|Zfp91Cntf	predicted readthrough transcript (NMD candidate), 44505	ncRNA
mm_12999.1	chr2	90889907	90889954	+	1	NA	exon (NM_026161, exon 2 of 2)	exon (NM_026161, exon 2 of 2)	4144	NM_026161	67445	Mm.258993	NM_026161	ENSMUSG00000040794	C1qtnf4	0710001E10Rik|9430004J15Rik|CTRP4	C1q and tumor necrosis factor related protein 4	protein-coding
mm_122383.1	chr14	40899275	40899301	-	1	NA	Intergenic	Intergenic	-6323	NM_177816	328381	Mm.235694	NM_177816	ENSMUSG00000037833	Sh2d4b	A430109M18Rik|D030001E08	SH2 domain containing 4B	protein-coding
mm_19184.1	chr2	84407578	84407588	-	1	NA	5' UTR (NM_018782, exon 2 of 16)	5' UTR (NM_018782, exon 2 of 16)	17683	NM_018782	54598	Mm.75467	NM_018782	ENSMUSG00000059588	Calcrl	AV071593|CRLR	calcitonin receptor-like	protein-coding
mm_74862.1	chr8	24824050	24824059	-	1	NA	5' UTR (NM_007401, exon 1 of 21)	5' UTR (NM_007401, exon 1 of 21)	315	NM_001272058	11499	Mm.143889	NM_007401	ENSMUSG00000031554	Adam5	tMDC II|tMDCII	a disintegrin and metallopeptidase domain 5	protein-coding
mm_91403.1	chr10	30842766	30842791	-	1	NA	promoter-TSS (NM_013904)	promoter-TSS (NM_013904)	5	NM_013904	15214	Mm.103573	NM_013904	ENSMUSG00000019789	Hey2	CHF1|Herp1|Hrt2|bHLHb32|hesr2	hairy/enhancer-of-split related with YRPW motif 2	protein-coding
mm_24629.1	chr3	93820925	93820928	+	1	NA	Intergenic	MT2B1|LTR|ERVL	-5094	NM_207271	399674	Mm.377923	NM_207271	ENSMUSG00000058005	Tdpoz3	-	TD and POZ domain containing 3	protein-coding
mm_138630.1	chr17	35854833	35854841	+	1	NA	intron (NM_001010833, intron 13 of 15)	intron (NM_001010833, intron 13 of 15)	-6481	NM_134122	106582	Mm.390992	NM_134122	ENSMUSG00000059791	Nrm	2610307M02Rik|AI429796	nurim (nuclear envelope membrane protein)	protein-coding
mm_80617.1	chr9	88390802	88390802	+	1	NA	intron (NM_172926, intron 18 of 27)	intron (NM_172926, intron 18 of 27)	48149	NM_172926	244962	Mm.439873	NM_172926	ENSMUSG00000032422	Snx14	B830022K16|C330035N22Rik|YR-14	sorting nexin 14	protein-coding
mm_128683.1	chr15	60824904	60824917	-	1	NA	5' UTR (NM_001162926, exon 1 of 2)	5' UTR (NM_001162926, exon 1 of 2)	170	NM_001162926	399603	Mm.411968	NM_207269	ENSMUSG00000072568	Fam84b	BF642811|D330050I23Rik	family with sequence similarity 84, member B	protein-coding
mm_156501.1	chrX	144455951	144455961	+	1	NA	promoter-TSS (NM_001195579)	promoter-TSS (NM_001195579)	-626	NM_001195579	100503240	Mm.387258	NM_001195579	ENSMUSG00000072934	Trpc5os	ENSMUSG00000072934|Gm15070|OTTMUSG00000018931	transient receptor potential cation channel, subfamily C, member 5, opposite strand	protein-coding
mm_31286.1	chr4	45890308	45890340	+	1	NA	promoter-TSS (NM_198660)	promoter-TSS (NM_198660)	21	NM_198660	381522	Mm.54220	NM_198660	ENSMUSG00000035539	Ccdc180	E230008N13Rik|Gm1025	coiled-coil domain containing 180	protein-coding
mm_114720.1	chr13	83665972	83665984	+	1	NA	3' UTR (NM_025282, exon 11 of 11)	3' UTR (NM_025282, exon 11 of 11)	-62128	NR_015561	320203	Mm.245636	NM_177100	ENSMUSG00000050334	C130071C03Rik	2810449C10Rik	RIKEN cDNA C130071C03 gene	ncRNA
mm_62237.1	chr7	98656902	98656946	+	1	NA	promoter-TSS (NM_172280)	promoter-TSS (NM_172280)	-355	NM_172280	233545	Mm.387819	NM_172280	ENSMUSG00000035401	Emsy	2210018M11Rik|2310016L09Rik|AU019521|AU019557	EMSY, BRCA2-interacting transcriptional repressor	protein-coding
mm_112981.1	chr13	21317209	21317247	+	1	NA	intron (NM_145451, intron 3 of 4)	intron (NM_145451, intron 3 of 4)	5025	NM_145451	75512	Mm.46195	NM_145451	ENSMUSG00000004341	Gpx6	1700020G18Rik|Ry2d1|olfactory	glutathione peroxidase 6	protein-coding
mm_121331.1	chr14	115040278	115040288	+	1	NA	Intergenic	Intergenic	-3388	NR_029785	723905		NR_029785	ENSMUSG00000065508	Mir17	Mirn17|mir-17|mmu-mir-17	microRNA 17	ncRNA
mm_118576.1	chr14	19750938	19750954	+	1	NA	promoter-TSS (NM_008695)	promoter-TSS (NM_008695)	-311	NM_008695	18074	Mm.20348	NM_008695	ENSMUSG00000021806	Nid2	AW547149|Ly111|NID-2|entactin-2|nidogen-2	nidogen 2	protein-coding
mm_117385.1	chr13	73346932	73346940	-	1	NA	non-coding (NR_045293, exon 2 of 3)	non-coding (NR_045293, exon 2 of 3)	448	NR_045293	432777	Mm.415319	NR_045293		D630045M09Rik	AU019512	RIKEN cDNA D630045M09 gene	ncRNA
mm_29637.1	chr3	121814920	121814951	-	1	NA	intron (NM_008991, intron 1 of 22)	CpG	280	NM_008991	19299	Mm.399042	NM_008991	ENSMUSG00000028127	Abcd3	AI313901|AU018866|AW146054|PMP68|PMP70|Pxmp1	ATP-binding cassette, sub-family D (ALD), member 3	protein-coding
mm_57184.1	chr6	122848794	122848812	-	1	NA	3' UTR (NM_009779, exon 2 of 2)	3' UTR (NM_009779, exon 2 of 2)	7354	NM_009779	12267	Mm.2408	NM_009779	ENSMUSG00000040552	C3ar1	AZ3B|C3AR|HNFAG09	complement component 3a receptor 1	protein-coding
mm_50292.1	chr6	47454703	47454719	+	1	NA	intron (NM_012042, intron 1 of 21)	CpG	387	NM_012042	26965	Mm.87611	NM_012042	ENSMUSG00000029686	Cul1	-	cullin 1	protein-coding
mm_91235.1	chr10	22302772	22302819	-	1	NA	intron (NM_009018, intron 5 of 5)	intron (NM_009018, intron 5 of 5)	-3925	NR_015465	606736	Mm.387042	NR_015465	ENSMUSG00000097352	C920009B18Rik	-	RIKEN cDNA C920009B18 gene	ncRNA
mm_13583.1	chr2	112379205	112379253	+	1	NA	promoter-TSS (NM_024254)	promoter-TSS (NM_024254)	18	NM_024254	72425	Mm.425091	NM_024254	ENSMUSG00000027132	Katnbl1	2410042D21Rik|AA166487|AA473307|AI467442	katanin p80 subunit B like 1	protein-coding
mm_32829.1	chr4	117564808	117564825	+	1	NA	exon (NM_080469, exon 3 of 9)	exon (NM_080469, exon 3 of 9)	14451	NM_080469	140546	Mm.235891	NM_080469	ENSMUSG00000033423	Eri3	PINT1|Prnpip1	exoribonuclease 3	protein-coding
mm_126526.1	chr15	81972366	81972379	+	1	NA	Intergenic	MMERVK9C_I-int|LTR|ERVK	-8168	NM_025503	66346	Mm.54292	NM_025503	ENSMUSG00000061633	1700029P11Rik	-	RIKEN cDNA 1700029P11 gene	protein-coding
mm_91395.1	chr10	30771843	30771851	-	1	NA	intron (NM_172495, intron 1 of 15)	intron (NM_172495, intron 1 of 15)	31260	NM_172495	211329	Mm.297903	NM_172495	ENSMUSG00000039697	Ncoa7	9030406N13Rik	nuclear receptor coactivator 7	protein-coding
mm_104190.1	chr11	87825939	87825941	-	1	NA	5' UTR (NM_080420, exon 1 of 13)	5' UTR (NM_080420, exon 1 of 13)	174	NM_080420	76113	Mm.41236	NM_080420	ENSMUSG00000009356	Lpo	5830499B15Rik	lactoperoxidase	protein-coding
mm_64892.1	chr7	15946024	15946034	-	1	NA	promoter-TSS (NM_133831)	promoter-TSS (NM_133831)	79	NM_133831	68077	Mm.277634	NM_133831	ENSMUSG00000041560	Gltscr2	5330430H08Rik|9430097C02Rik|AU041936|AW536441|PICT-1|R74911	glioma tumor suppressor candidate region gene 2	protein-coding
mm_105201.1	chr11	102097542	102097557	-	1	NA	Intergenic	Intergenic	3751	NM_008918	19064	Mm.1269	NM_008918	ENSMUSG00000017316	Ppy	AV061413|IGSPP|PP	pancreatic polypeptide	protein-coding
mm_72894.1	chr8	90828821	90828842	+	1	NA	promoter-TSS (NM_177224)	promoter-TSS (NM_177224)	-4	NM_177224	109151	Mm.100615	NM_177224	ENSMUSG00000056608	Chd9	1810014J18Rik|9030205D12Rik|A330063D19Rik|AD013|PRIC320|mKIAA0308	chromodomain helicase DNA binding protein 9	protein-coding
mm_95383.1	chr11	49203315	49203344	+	1	NA	promoter-TSS (NM_001024846)	promoter-TSS (NM_001024846)	-171	NM_001024846	22720	Mm.16650	NM_009562	ENSMUSG00000046311	Zfp62	-	zinc finger protein 62	protein-coding
mm_78429.1	chr9	31354317	31354340	+	1	NA	intron (NM_001080817, intron 12 of 20)	intron (NM_001080817, intron 12 of 20)	-31864	NM_172766	235134	Mm.238146	NM_172766	ENSMUSG00000042185	Nfrkb	A530090G11Rik	nuclear factor related to kappa B binding protein	protein-coding
mm_132060.1	chr16	29843875	29843923	+	1	NA	Intergenic	MLT1H2|LTR|ERVL-MaLR	135225	NR_037689	328657	Mm.425982	NM_001033403		Gm1968	-	predicted gene 1968	ncRNA
mm_32846.1	chr4	117883543	117883579	+	1	NA	promoter-TSS (NM_001253381)	promoter-TSS (NM_001253381)	-85	NM_001253381	53418	Mm.123843	NM_017377	ENSMUSG00000028541	B4galt2	Ggtb2	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 2	protein-coding
mm_173042.1	chrX	114981368	114981386	-	1	NA	Intergenic	Intergenic	54388	NR_130989	78086		NR_130989	ENSMUSG00000085619	4930555B12Rik	-	RIKEN cDNA 4930555B12 gene	ncRNA
mm_3692.1	chr1	153752003	153752034	+	1	NA	5' UTR (NM_011882, exon 2 of 9)	5' UTR (NM_011882, exon 2 of 9)	2592	NM_011882	24014	Mm.259254	NM_011882	ENSMUSG00000066800	Rnasel	E230029I04Rik	ribonuclease L (2', 5'-oligoisoadenylate synthetase-dependent)	protein-coding
mm_149128.1	chr19	8997886	8997905	+	1	NA	intron (NR_104460, intron 1 of 6)	intron (NR_104460, intron 1 of 6)	8611	NM_001286518	66395	Mm.203866	NM_009643	ENSMUSG00000069833	Ahnak	DY6	AHNAK nucleoprotein (desmoyokin)	protein-coding
mm_94966.1	chr11	30855756	30855762	+	1	NA	intron (NM_134013, intron 40 of 46)	intron (NM_134013, intron 40 of 46)	-29599	NM_175490	237716	Mm.338361	NM_175490	ENSMUSG00000043999	Gpr75	-	G protein-coupled receptor 75	protein-coding
mm_71009.1	chr8	31129403	31129412	+	1	NA	3' UTR (NM_175136, exon 6 of 6)	3' UTR (NM_175136, exon 6 of 6)	17561	NM_175136	68867	Mm.29532	NM_175136	ENSMUSG00000039328	Rnf122	1110063C11Rik	ring finger protein 122	protein-coding
mm_82540.1	chr9	20815049	20815069	-	1	NA	promoter-TSS (NM_001317388)	promoter-TSS (NM_001317388)	8	NM_001317388	53867	Mm.334994	NM_016919	ENSMUSG00000004098	Col5a3	-	collagen, type V, alpha 3	protein-coding
mm_10249.1	chr2	9189547	9189557	+	1	NA	promoter-TSS (NR_038180)	promoter-TSS (NR_038180)	37	NR_038180	73438	Mm.23558	NR_038180	ENSMUSG00000085580	1700061F12Rik	-	RIKEN cDNA 1700061F12 gene	ncRNA
mm_38989.1	chr4	151062814	151062839	-	1	NA	exon (NM_001081557, exon 24 of 24)	exon (NM_001081557, exon 24 of 24)	-4873	NM_009498	22319	Mm.273930	NM_009498	ENSMUSG00000028955	Vamp3	D130027G05Rik|VAMP-3|ceb	vesicle-associated membrane protein 3	protein-coding
mm_7413.1	chr1	119422240	119422291	-	1	NA	promoter-TSS (NM_008381)	promoter-TSS (NM_008381)	-17	NM_008381	16324	Mm.3092	NM_008381	ENSMUSG00000037035	Inhbb	-	inhibin beta-B	protein-coding
mm_8554.1	chr1	155232598	155232606	-	1	NA	Intergenic	Intergenic	73899	NM_021433	58244	Mm.66264	NM_021433	ENSMUSG00000026470	Stx6	2310039E05Rik|2410005I16Rik|AA437559|AI415714|AI845861	syntaxin 6	protein-coding
mm_10486.1	chr2	14763446	14763457	+	1	NA	intron (NM_023116, intron 2 of 13)	intron (NM_023116, intron 2 of 13)	42809	NR_028497	625342	Mm.484784	NR_028497		Gm13315	OTTMUSG00000011384	lactate dehydrogenase A pseudogene	pseudo
mm_126367.1	chr15	80110446	80110485	+	1	NA	exon (NM_009303, exon 2 of 4)	exon (NM_009303, exon 2 of 4)	19131	NM_207708	20972	Mm.230301	NM_009303	ENSMUSG00000022415	Syngr1	R75468|Syngr1b|p29	synaptogyrin 1	protein-coding
mm_10353.1	chr2	11690002	11690023	+	1	NA	3' UTR (NM_008367, exon 8 of 8)	3' UTR (NM_008367, exon 8 of 8)	-15281	NM_001271498	16169	Mm.200196	NM_008358	ENSMUSG00000023206	Il15ra	AA690181|IL-15RA	interleukin 15 receptor, alpha chain	protein-coding
mm_37649.1	chr4	128786457	128786485	-	1	NA	intron (NM_001081098, intron 5 of 8)	intron (NM_001081098, intron 5 of 8)	19641	NM_001081098	230761	Mm.22616	NM_001081098	ENSMUSG00000028799	Zfp362	-	zinc finger protein 362	protein-coding
mm_131312.1	chr16	11615881	11615902	+	1	NA	intron (NM_001290148, intron 8 of 13)	MIRb|SINE|MIR	-163811	NR_126430	73761	Mm.39183	NR_126430		4833415N18Rik	-	RIKEN cDNA 4833415N18 gene	ncRNA
mm_100137.1	chr11	115974984	115975051	+	1	NA	5' UTR (NM_133663, exon 1 of 39)	5' UTR (NM_133663, exon 1 of 39)	292	NM_133663	192897	Mm.213873	NM_133663	ENSMUSG00000020758	Itgb4	AA407042|C230078O20|CD104	integrin beta 4	protein-coding
mm_64758.1	chr7	4844795	4844869	-	1	NA	promoter-TSS (NM_172737)	promoter-TSS (NM_172737)	-136	NM_172737	232813	Mm.44666	NM_172737	ENSMUSG00000053550	Shisa7	ckamp59	shisa family member 7	protein-coding
mm_109597.1	chr12	112674413	112674423	+	1	NA	promoter-TSS (NM_001165894)	promoter-TSS (NM_001165894)	-142	NM_009652	11651	Mm.6645	NM_009652	ENSMUSG00000001729	Akt1	Akt|LTR-akt|PKB|PKB/Akt|PKBalpha|Rac	thymoma viral proto-oncogene 1	protein-coding
mm_116639.1	chr13	49015478	49015497	-	1	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	47375	NR_015601	68128	Mm.426304	NR_015601		Fam120aos	C030044B11Rik	family with sequence similarity 120A, opposite strand	ncRNA
mm_9526.1	chr1	173775299	173775312	-	1	NA	Intergenic	Intergenic	-8386	NM_008329	15951	Mm.261270	NM_008329	ENSMUSG00000073489	Ifi204	Ifi16|p204	interferon activated gene 204	protein-coding
mm_36319.1	chr4	70260337	70260337	-	1	NA	intron (NM_145990, intron 25 of 36)	intron (NM_145990, intron 25 of 36)	150098	NM_001313762	214444	Mm.370777	NM_145990	ENSMUSG00000039298	Cdk5rap2	2900018K03Rik|an|mKIAA1633	CDK5 regulatory subunit associated protein 2	protein-coding
mm_73501.1	chr8	107293464	107293483	+	1	NA	promoter-TSS (NM_018823)	promoter-TSS (NM_018823)	3	NM_133957	54446	Mm.390057	NM_018823	ENSMUSG00000003847	Nfat5	AI225870|B130038B15Rik|CAG-8|CAG80|NFATL1|OREBP|TonEBP|mKIAA0827|nfatz	nuclear factor of activated T cells 5	protein-coding
mm_102339.1	chr11	57832143	57832147	-	1	NA	promoter-TSS (NM_008213)	promoter-TSS (NM_008213)	2	NM_008213	15110	Mm.4746	NM_008213	ENSMUSG00000037335	Hand1	Ehand1|Hxt|Th1|Thing1|bHLHa27|eHAND	heart and neural crest derivatives expressed transcript 1	protein-coding
mm_33902.1	chr4	136284709	136284717	+	1	NA	Intergenic	Intergenic	-1356	NM_009557	22704	Mm.1504	NM_009557	ENSMUSG00000051351	Zfp46	AI426962|Mlz-4|Zfp-46|Znf436	zinc finger protein 46	protein-coding
mm_87756.1	chr10	60278560	60278564	+	1	NA	intron (NM_001146120, intron 1 of 13)	intron (NM_001146120, intron 1 of 13)	934	NM_001146121	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_139766.1	chr17	64601396	64601415	+	1	NA	promoter-TSS (NM_008549)	promoter-TSS (NM_008549)	-244	NM_008549	17158	Mm.2433	NM_008549	ENSMUSG00000024085	Man2a1	Mana-2|Mana2|Map-2	mannosidase 2, alpha 1	protein-coding
mm_11636.1	chr2	34802337	34802391	+	1	NA	Intergenic	CpG	-2452	NM_145522	227746	Mm.158705	NM_145522	ENSMUSG00000070953	Rabepk	8430412M01Rik|9530020D24Rik|AV073337|C87311|Rab9p40	Rab9 effector protein with kelch motifs	protein-coding
mm_152363.1	chr19	10092206	10092217	-	1	NA	intron (NM_019699, intron 1 of 11)	intron (NM_019699, intron 1 of 11)	9292	NM_019699	56473	Mm.38901	NM_019699	ENSMUSG00000024665	Fads2	2900042M13Rik|Fadsd2	fatty acid desaturase 2	protein-coding
mm_156876.1	chrX	166238769	166238782	+	1	NA	promoter-TSS (NM_001177961)	promoter-TSS (NM_001177961)	-168	NM_001177961	14758	Mm.222320	NM_023122	ENSMUSG00000031342	Gpm6b	AI593561|Gpm6|M6B	glycoprotein m6b	protein-coding
mm_158008.1	chrX	95444790	95444829	-	1	NA	promoter-TSS (NM_175179)	promoter-TSS (NM_175179)	31	NM_175179	72345	Mm.182867	NM_175179	ENSMUSG00000050332	Amer1	2810002O09Rik|AW492303|Fam123b|Wtx	APC membrane recruitment 1	protein-coding
mm_28143.1	chr3	87263655	87263662	-	1	NA	promoter-TSS (NM_030707)	promoter-TSS (NM_030707)	-134	NM_030707	80891	Mm.45173	NM_030707	ENSMUSG00000015852	Fcrls	2810439C17Rik|9330158F12|FcRH2sc|Fcrh2|IFGP2|IgSR|MMAN-g|Msr2|moFcRH2sc	Fc receptor-like S, scavenger receptor	protein-coding
mm_12013.1	chr2	57368418	57368432	+	1	NA	3' UTR (NM_010274, exon 17 of 17)	3' UTR (NM_010274, exon 17 of 17)	130043	NM_010274	14571	Mm.3711	NM_010274	ENSMUSG00000026827	Gpd2	AA408484|AI448216|AU021455|AW494132|GPDH|Gdm1|Gpd-m|Gpdh-m|TISP38	glycerol phosphate dehydrogenase 2, mitochondrial	protein-coding
mm_20331.1	chr2	127521307	127521322	-	1	NA	promoter-TSS (NM_019789)	promoter-TSS (NM_019789)	78	NM_001291005	56461	Mm.315292	NM_019789	ENSMUSG00000079056	Kcnip3	4933407H12Rik|AI413860|Csen|DREAM|KChIP3|R74849	Kv channel interacting protein 3, calsenilin	protein-coding
mm_35800.1	chr4	46566485	46566489	-	1	NA	promoter-TSS (NM_178893)	promoter-TSS (NM_178893)	-47	NM_178893	107684	Mm.416311	NM_178893	ENSMUSG00000028337	Coro2a	9030208C03Rik|AI563590|IR10	coronin, actin binding protein 2A	protein-coding
mm_143883.1	chr17	84313620	84313631	-	1	NA	intron (NM_183021, intron 28 of 37)	intron (NM_183021, intron 28 of 37)	-125678	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_21885.1	chr2	166155178	166155188	-	1	NA	5' UTR (NM_001252578, exon 1 of 21)	5' UTR (NM_001252578, exon 1 of 21)	102	NM_001252578	72043	Mm.1011	NM_028072	ENSMUSG00000006800	Sulf2	2010004N24Rik|AU020235|MSulf-2|mKIAA1247	sulfatase 2	protein-coding
mm_60219.1	chr7	43553564	43553574	+	1	NA	Intergenic	Intergenic	-8801	NM_001008549	210104	Mm.333821	NM_001008549	ENSMUSG00000056592	Zfp658	-	zinc finger protein 658	protein-coding
mm_52240.1	chr6	105334489	105334490	+	1	NA	Intergenic	Intergenic	158179	NR_040297	100503536	Mm.366960	NR_040297	ENSMUSG00000108237	Gm19757	-	predicted gene, 19757	ncRNA
mm_139479.1	chr17	56009306	56009320	+	1	NA	intron (NM_026530, intron 1 of 12)	CpG	112	NM_026530	68047	Mm.358710	NM_026530	ENSMUSG00000003199	Mpnd	E130307M08Rik	MPN domain containing	protein-coding
mm_107893.1	chr12	70466116	70466135	+	1	NA	exon (NM_028339, exon 8 of 8)	exon (NM_028339, exon 8 of 8)	12971	NM_028339	72736	Mm.204670	NM_028339	ENSMUSG00000021072	Tmx1	2810425A04Rik|AI465319|Txndc1	thioredoxin-related transmembrane protein 1	protein-coding
mm_147091.1	chr18	35648484	35648502	-	1	NA	intron (NM_027222, intron 1 of 3)	intron (NM_027222, intron 1 of 3)	874	NM_027222	69816	Mm.27252	NM_027222	ENSMUSG00000024353	Mzb1	2010001M09Rik|AV064572|PACAP|pERp1	marginal zone B and B1 cell-specific protein 1	protein-coding
mm_73643.1	chr8	110805433	110805452	+	1	NA	intron (NM_029646, intron 1 of 7)	intron (NM_029646, intron 1 of 7)	482	NM_029646	76527	Mm.77697	NM_029646	ENSMUSG00000031750	Il34	2010004A03Rik|AI593503	interleukin 34	protein-coding
mm_10796.1	chr2	24349548	24349558	+	1	NA	exon (NM_031167, exon 5 of 5)	exon (NM_031167, exon 5 of 5)	4182	NM_001039701	16181	Mm.882	NM_031167	ENSMUSG00000026981	Il1rn	F630041P17Rik|IL-1ra	interleukin 1 receptor antagonist	protein-coding
mm_171865.1	chr5	24010414	24010434	-	1	NA	intron (NM_053090, intron 1 of 10)	intron (NM_053090, intron 1 of 10)	19888	NM_001310471	84652	Mm.304976	NM_053090	ENSMUSG00000028995	Fam126a	AB030242|Drctnnb1a	family with sequence similarity 126, member A	protein-coding
mm_124172.1	chr14	93809813	93809835	-	1	NA	intron (NM_001346722, intron 2 of 4)	intron (NM_001346722, intron 2 of 4)	79064	NM_001271800	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding
mm_164213.1	chr15	82662299	82662302	-	1	NA	Intergenic	ORR1A1-int|LTR|ERVL-MaLR	-20255	NR_003552	68444	Mm.443212	NR_003552		Cyp2d13	1300007K12Rik	cytochrome P450, family 2, subfamily d, polypeptide 13	pseudo
mm_99955.1	chr11	113061236	113061273	+	1	NA	intron (NR_015556, intron 2 of 2)	intron (NR_015556, intron 2 of 2)	140584	NR_015556	72386	Mm.266961	NR_015556	ENSMUSG00000087259	2610035D17Rik	-	RIKEN cDNA 2610035D17 gene	ncRNA
mm_58271.1	chr6	145433994	145434013	-	1	NA	intron (NM_028742, intron 1 of 9)	intron (NM_028742, intron 1 of 9)	922	NM_028742	74071	Mm.441497	NM_028742	ENSMUSG00000054966	Lmntd1	4933403M22Rik|AI482300|Ifltd1|Lmna-rs1|Lmna1|OTTMUSG00000022798	lamin tail domain containing 1	protein-coding
mm_68236.1	chr7	105395559	105395577	-	1	NA	intron (NM_001242363, intron 1 of 12)	intron (NM_001242363, intron 1 of 12)	4486	NM_001242364	74349	Mm.30254	NM_199009	ENSMUSG00000044465	Fam160a2	4632419K20Rik|6530415H11Rik|FHIP	family with sequence similarity 160, member A2	protein-coding
mm_96594.1	chr11	69090861	69090872	+	1	NA	3' UTR (NM_009497, exon 5 of 5)	3' UTR (NM_009497, exon 5 of 5)	2338	NM_009497	22318	Mm.28643	NM_009497	ENSMUSG00000020894	Vamp2	Syb-2|Syb2|sybII	vesicle-associated membrane protein 2	protein-coding
mm_10058.1	chr1	193264007	193264079	-	1	NA	promoter-TSS (NM_008288)	promoter-TSS (NM_008288)	2	NM_008288	15483	Mm.28328	NM_008288	ENSMUSG00000016194	Hsd11b1	-	hydroxysteroid 11-beta dehydrogenase 1	protein-coding
mm_89943.1	chr10	111280312	111280332	+	1	NA	exon (NM_001003717, exon 15 of 23)	exon (NM_001003717, exon 15 of 23)	-18357	NM_027914	71769	Mm.45256	NM_027914	ENSMUSG00000035759	Bbs10	1300007O09Rik|AI452285	Bardet-Biedl syndrome 10 (human)	protein-coding
mm_3080.1	chr1	134385939	134385943	+	1	NA	promoter-TSS (NM_173771)	promoter-TSS (NM_173771)	1	NM_173771	240755	Mm.67133	NM_173771	ENSMUSG00000050526	4933406M09Rik	-	RIKEN cDNA 4933406M09 gene	protein-coding
mm_93899.1	chr10	125389575	125389594	-	1	NA	Intergenic	Intergenic	-61049	NM_011391	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|Mct2	solute carrier family 16 (monocarboxylic acid transporters), member 7	protein-coding
mm_106056.1	chr11	116110407	116110417	-	1	NA	promoter-TSS (NM_001205081)	promoter-TSS (NM_001205081)	-177	NM_172570	217333	Mm.347770	NM_172570	ENSMUSG00000020773	Trim47	2210023F24Rik	tripartite motif-containing 47	protein-coding
mm_13034.1	chr2	91054264	91054303	+	1	NA	exon (NM_008948, exon 1 of 12)	exon (NM_008948, exon 1 of 12)	267	NM_008948	19182	Mm.289832	NM_008948	ENSMUSG00000002102	Psmc3	TBP-1	proteasome (prosome, macropain) 26S subunit, ATPase 3	protein-coding
mm_14492.1	chr2	131937006	131937018	+	1	NA	exon (NM_001278256, exon 4 of 4)	exon (NM_001278256, exon 4 of 4)	-13849	NM_001278257	26434	Mm.180750	NM_023043	ENSMUSG00000027338	Prnd	AI450264|Dpl|PrPLP|doppel	prion protein dublet	protein-coding
mm_49314.1	chr6	18335750	18335759	+	1	NA	Intergenic	Intergenic	165067	NM_021050	12638	Mm.15621	NM_021050	ENSMUSG00000041301	Cftr	AW495489|Abcc7	cystic fibrosis transmembrane conductance regulator	protein-coding
mm_150896.1	chr19	45472796	45472813	+	1	NA	intron (NM_001286466, intron 4 of 13)	intron (NM_001286466, intron 4 of 13)	87760	NM_001330506	56626	Mm.46509	NM_020032	ENSMUSG00000025218	Poll	1110003P06Rik|AV007317	polymerase (DNA directed), lambda	protein-coding
mm_35531.1	chr4	41313903	41313914	-	1	NA	intron (NM_026893, intron 1 of 8)	intron (NM_026893, intron 1 of 8)	993	NM_026893	68970	Mm.28891	NM_026893	ENSMUSG00000028436	Dcaf12	1500001L20Rik|5830424K06Rik|AA420338|AI851081|Wdr40a	DDB1 and CUL4 associated factor 12	protein-coding
mm_114248.1	chr13	56632912	56632926	+	1	NA	exon (NM_009369, exon 12 of 17)	exon (NM_009369, exon 12 of 17)	23316	NM_009369	21810	Mm.14455	NM_009369	ENSMUSG00000035493	Tgfbi	68kDa|AI181842|AI747162|Beta-ig|big-h3	transforming growth factor, beta induced	protein-coding
mm_39004.1	chr4	151989015	151989025	-	1	NA	promoter-TSS (NM_001145929)	promoter-TSS (NM_001145929)	-34	NM_001145929	69876	Mm.226820	NM_175152	ENSMUSG00000039759	Thap3	2010013E08Rik|2210418H06Rik	THAP domain containing, apoptosis associated protein 3	protein-coding
mm_17935.1	chr2	35979757	35979800	-	1	NA	promoter-TSS (NM_029774)	promoter-TSS (NM_029774)	-154	NM_029774	74410	Mm.21591	NM_028921	ENSMUSG00000026885	Ttll11	4932702F08Rik|4933424A20Rik|AU043211|D2Ertd624e	tubulin tyrosine ligase-like family, member 11	protein-coding
mm_86658.1	chr10	17724775	17724810	+	1	NA	3' UTR (NM_010828, exon 2 of 2)	3' UTR (NM_010828, exon 2 of 2)	1564	NM_010828	17684	Mm.272321	NM_010828	ENSMUSG00000039910	Cited2	AI835299|ER154-like|Mrg1|Msg2|p35srj	Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 2	protein-coding
mm_83749.1	chr9	51165427	51165449	-	1	NA	Intergenic	Intergenic	-48252	NM_011136	18985	Mm.897	NM_011136	ENSMUSG00000032053	Pou2af1	BOB.1|Bob-1|Bob1|OBF-1|OBF.1|OCA-B|OCAB	POU domain, class 2, associating factor 1	protein-coding
mm_152260.1	chr19	8786409	8786422	-	1	NA	promoter-TSS (NM_001177798)	promoter-TSS (NM_001177798)	2	NM_001177798	225895	Mm.220886	NM_146092	ENSMUSG00000003680	Taf6l	2810417N14Rik|BB223262|C530024J06Rik|Paf65a	TATA-box binding protein associated factor 6 like	protein-coding
mm_17052.1	chr2	20969253	20969282	-	1	NA	non-coding (NR_033225, exon 1 of 2)	non-coding (NR_033225, exon 1 of 2)	393	NR_033225	433408	Mm.386941	NR_033225		Gm13375	OTTMUSG00000011664	predicted gene 13375	ncRNA
mm_48525.1	chr5	142903527	142903575	-	1	NA	3' UTR (NM_007393, exon 6 of 6)	3' UTR (NM_007393, exon 6 of 6)	3203	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_82666.1	chr9	22129903	22129936	-	1	NA	exon (NM_001102404, exon 2 of 5)	exon (NM_001102404, exon 2 of 5)	679	NM_007388	11433	Mm.46354	NM_007388	ENSMUSG00000001348	Acp5	TRACP|TRAP	acid phosphatase 5, tartrate resistant	protein-coding
mm_150479.1	chr19	38930949	38930968	+	1	NA	promoter-TSS (NM_008234)	promoter-TSS (NM_008234)	-32	NM_008234	15201	Mm.57223	NM_008234	ENSMUSG00000025001	Hells	AI323785|E130115I21Rik|LSH|Lysh|PASG|YFK8	helicase, lymphoid specific	protein-coding
mm_107556.1	chr12	41261055	41261058	+	1	NA	intron (NM_053122, intron 4 of 6)	Lx2B|LINE|L1	225001	NM_001271708	16981	Mm.404786	NM_010733	ENSMUSG00000036295	Lrrn3	NLRR-3	leucine rich repeat protein 3, neuronal	protein-coding
mm_83646.1	chr9	49505374	49505414	-	1	NA	3' UTR (NM_001311065, exon 18 of 18)	3' UTR (NM_001311065, exon 18 of 18)	-12894	NR_029465	100036537	Mm.437541	NR_029465	ENSMUSG00000079564	Gm11149	ENSMUSG00000060603|ENSMUSG00000079564	predicted gene 11149	ncRNA
mm_47870.1	chr5	134639542	134639546	-	1	NA	promoter-TSS (NM_033561)	promoter-TSS (NM_033561)	-135	NM_033561	22384	Mm.27955	NM_033561	ENSMUSG00000040731	Eif4h	AU018978|D5Ertd355e|E430026L18Rik|Ef4h|Wbscr1|Wscr1|eIF-4H	eukaryotic translation initiation factor 4H	protein-coding
mm_57397.1	chr6	124863699	124863724	-	1	NA	TTS (NM_013488)	TTS (NM_013488)	206	NM_013533	14788	Mm.2514	NM_013533	ENSMUSG00000038390	Gpr162	A-2|BC031437|Grca	G protein-coupled receptor 162	protein-coding
mm_142046.1	chr17	35516781	35516835	-	1	NA	promoter-TSS (NM_001163763)	promoter-TSS (NM_001163763)	16	NM_001163764	106795	Mm.11434	NM_025674	ENSMUSG00000050410	Tcf19	5730403J10Rik|AW495861	transcription factor 19	protein-coding
mm_36505.1	chr4	83485787	83485824	-	1	NA	5' UTR (NM_001290527, exon 2 of 11)	5' UTR (NM_001290527, exon 2 of 11)	643	NM_001290527	101739	Mm.105331	NM_133948	ENSMUSG00000028484	Psip1	AA408851|AU015605|Dfs70|Ledgfa|Ledgfb|Psip2	PC4 and SFRS1 interacting protein 1	protein-coding
mm_166949.1	chr7	43979154	43979156	+	1	NA	intron (NM_010116, intron 2 of 4)	intron (NM_010116, intron 2 of 4)	3094	NM_010116	13648	Mm.440884	NM_010116	ENSMUSG00000059042	Klk1b9	EGF-BP C|Egfbp-3|Egfbp3|KAL|Klk9|kallikrein|mGk-9	kallikrein 1-related peptidase b9	protein-coding
mm_160150.1	chr7	41499682	41499682	-	1	NA	5' UTR (NM_001033530, exon 1 of 4)	5' UTR (NM_001033530, exon 1 of 4)	208	NM_001033530	101835	Mm.370336	NM_001033530	ENSMUSG00000074166	AW146154	AI451288	expressed sequence AW146154	protein-coding
mm_42506.1	chr5	115500643	115500649	+	1	NA	Intergenic	MLT1E1|LTR|ERVL-MaLR	-6030	NM_011223	19303	Mm.18714	NM_011223	ENSMUSG00000029528	Pxn	AW108311|AW123232|Pax	paxillin	protein-coding
mm_12373.1	chr2	69822442	69822511	+	1	NA	5' UTR (NM_177784, exon 1 of 4)	5' UTR (NM_177784, exon 1 of 4)	106	NM_177784	277396	Mm.138073	NM_177784	ENSMUSG00000042155	Klhl23	C130068N17Rik	kelch-like 23	protein-coding
mm_46610.1	chr5	107972865	107972879	-	1	NA	intron (NM_026062, intron 1 of 4)	intron (NM_026062, intron 1 of 4)	14205	NM_026062	67266	Mm.277897	NM_026062	ENSMUSG00000029270	Fam69a	2900024C23Rik|AI315274	family with sequence similarity 69, member A	protein-coding
mm_61263.1	chr7	66079806	66079817	+	1	NA	intron (NM_024439, intron 1 of 5)	CpG	162	NM_024439	109815	Mm.482127	NM_024439	ENSMUSG00000075701	Selenos	1500011E07Rik|C78786|H-4|H-47|H4|H47|Sels|Vimp	selenoprotein S	protein-coding
mm_101311.1	chr11	22779308	22779312	-	1	NA	Intergenic	Intergenic	80425	NM_016888	53625	Mm.395495	NM_016888	ENSMUSG00000051650	B3gnt2	AA408337|AA409404|AW260308|B3Galt6|B3gnt1|BGnT-1|BGnT-2|BGnT1|BGnT2|Beta3gnt	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 2	protein-coding
mm_153328.1	chr19	38124411	38124435	-	1	NA	exon (NM_011255, exon 3 of 6)	exon (NM_011255, exon 3 of 6)	388	NM_011255	19662	Mm.2605	NM_011255	ENSMUSG00000024990	Rbp4	Rbp-4	retinol binding protein 4, plasma	protein-coding
mm_32653.1	chr4	115088780	115088790	+	1	NA	promoter-TSS (NM_001164557)	promoter-TSS (NM_001164557)	77	NM_001164557	67182	Mm.30181	NM_026018	ENSMUSG00000028716	Pdzk1ip1	0610007F13Rik|2700030M23Rik|AU046042|Map17	PDZK1 interacting protein 1	protein-coding
mm_42719.1	chr5	120513103	120513123	+	1	NA	intron (NM_001177594, intron 1 of 14)	intron (NM_001177594, intron 1 of 14)	1921	NM_001177594	170756	Mm.291070	NM_133221	ENSMUSG00000032754	Slc8b1	AF261233|NCKX6|NCLX|Slc24a6	solute carrier family 8 (sodium/lithium/calcium exchanger), member B1	protein-coding
mm_152378.1	chr19	10237960	10237972	-	1	NA	intron (NM_001033481, intron 1 of 25)	intron (NM_001033481, intron 1 of 25)	2782	NM_001033481	225908	Mm.329716	NM_001033481	ENSMUSG00000036098	Myrf	6030439E18|Gm1804|Gm98|Mrf	myelin regulatory factor	protein-coding
mm_171693.1	chr4	66078721	66078741	+	1	NA	intron (NM_019514, intron 3 of 21)	L1Md_T|LINE|L1	325752	NM_019514	56079	Mm.445312	NM_019514	ENSMUSG00000028373	Astn2	1d8|Astnl|bM452J22.1	astrotactin 2	protein-coding
mm_70077.1	chr7	142653266	142653279	-	1	NA	3' UTR (NM_010514, exon 4 of 4)	3' UTR (NM_010514, exon 4 of 4)	1724	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_60408.1	chr7	44476025	44476029	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	5680	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_151473.1	chr19	58673087	58673104	+	1	NA	exon (NM_026925, exon 4 of 13)	exon (NM_026925, exon 4 of 13)	2730	NM_026925	69060	Mm.20407	NM_026925	ENSMUSG00000046008	Pnlip	1810007A24Rik|PL|PTL	pancreatic lipase	protein-coding
mm_85780.1	chr9	109058624	109058638	-	1	NA	TTS (NM_026381)	TTS (NM_026381)	620	NM_001012236	22040	Mm.439964	NM_011637	ENSMUSG00000049734	Trex1	AU041952	three prime repair exonuclease 1	protein-coding
mm_56209.1	chr6	89316684	89316687	-	1	NA	3' UTR (NM_008881, exon 32 of 32)	3' UTR (NM_008881, exon 32 of 32)	-30960	NR_131021	75131	Mm.391482	NR_131021	ENSMUSG00000107622	4930512J16Rik	-	RIKEN cDNA 4930512J16 gene	ncRNA
mm_93298.1	chr10	96616635	96616666	-	1	NA	promoter-TSS (NM_007569)	promoter-TSS (NM_007569)	-351	NM_007569	12226	Mm.23811	NM_007569	ENSMUSG00000036478	Btg1	AI426953|AW546738	B cell translocation gene 1, anti-proliferative	protein-coding
mm_34501.1	chr4	148603756	148603762	+	1	NA	exon (NM_010767, exon 4 of 5)	exon (NM_010767, exon 4 of 5)	1215	NM_001003893	17175	Mm.378962	NM_010767	ENSMUSG00000028979	Masp2	MASP-2|MAp19	mannan-binding lectin serine peptidase 2	protein-coding
mm_11842.1	chr2	45117232	45117284	+	1	NA	Intergenic	CpG	-3979	NM_015753	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_120920.1	chr14	76427314	76427321	+	1	NA	intron (NM_001310646, intron 3 of 4)	intron (NM_001310646, intron 3 of 4)	11496	NM_207652	21807	Mm.153272	NM_009366	ENSMUSG00000022010	Tsc22d1	AA589566|AW105905|Egr5|TSC-22|Tgfb1i4|Tsc|Tsc22	TSC22 domain family, member 1	protein-coding
mm_100171.1	chr11	116532423	116532425	+	1	NA	promoter-TSS (NM_001172472)	promoter-TSS (NM_001172472)	-20	NM_001172472	20698	Mm.20944	NM_011451	ENSMUSG00000061878	Sphk1	1110006G24Rik|Sk1|Spk1	sphingosine kinase 1	protein-coding
mm_284.1	chr1	21264837	21264867	+	1	NA	exon (NM_010356, exon 7 of 7)	exon (NM_010356, exon 7 of 7)	24267	NM_010356	14859	Mm.394593	NM_010356	ENSMUSG00000025934	Gsta3	Gst2-3	glutathione S-transferase, alpha 3	protein-coding
mm_166211.1	chr5	49760412	49760412	+	1	NA	Intergenic	Intergenic	298584	NM_133911	70693	Mm.272974	NM_133911	ENSMUSG00000029090	Adgra3	3830613O22Rik|AU044632|Gpr125|Tem5-like	adhesion G protein-coupled receptor A3	protein-coding
mm_132832.1	chr16	45434854	45434854	+	1	NA	intron (NM_001005854, intron 3 of 4)	intron (NM_001005854, intron 3 of 4)	-25801	NM_010818	17470	Mm.245851	NM_010818	ENSMUSG00000022661	Cd200	Mox2|OX2	CD200 antigen	protein-coding
mm_118132.1	chr13	104816869	104816886	-	1	NA	promoter-TSS (NM_026072)	promoter-TSS (NM_026072)	76	NM_026072	67285	Mm.235398	NM_026072	ENSMUSG00000021715	Cwc27	3110009E13Rik|NY-CO-10|Sdccag10	CWC27 spliceosome-associated protein	protein-coding
mm_115706.1	chr13	14523027	14523037	-	1	NA	5' UTR (NM_001081348, exon 1 of 29)	5' UTR (NM_001081348, exon 1 of 29)	194	NM_001081348	94253	Mm.125298	NM_153130	ENSMUSG00000021301	Hecw1	9330116H24Rik|AV273951|E130207I19Rik|Nedl1	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	protein-coding
mm_7277.1	chr1	97128324	97128328	-	1	NA	promoter-TSS (NM_028942)	promoter-TSS (NM_028942)	-23	NM_028942	74441	Mm.60362	NM_028942	ENSMUSG00000026331	Slco6c1	4933404A18Rik|C79179	solute carrier organic anion transporter family, member 6c1	protein-coding
mm_32952.1	chr4	119619295	119619321	+	1	NA	exon (NM_001290696, exon 7 of 12)	exon (NM_001290696, exon 7 of 12)	-18424	NM_008190	14915	Mm.2614	NM_008190	ENSMUSG00000023247	Guca2a	Guca2	guanylate cyclase activator 2a (guanylin)	protein-coding
mm_71669.1	chr8	60674355	60674376	+	1	NA	3' UTR (NM_001177882, exon 3 of 3)	3' UTR (NM_001177882, exon 3 of 3)	18808	NM_001177882	71306	Mm.23242	NM_027756	ENSMUSG00000031647	Mfap3l	4933428A15Rik|5430405D20Rik|AI461995|AW125052|NYD-sp9|mKIAA0626	microfibrillar-associated protein 3-like	protein-coding
mm_102721.1	chr11	67116832	67116845	-	1	NA	intron (NR_038055, intron 2 of 4)	intron (NR_038055, intron 2 of 4)	3242	NR_038055	74184	Mm.162554	NR_038055	ENSMUSG00000087410	2310065F04Rik	linc-Myh	RIKEN cDNA 2310065F04 gene	ncRNA
mm_50201.1	chr6	42040088	42040098	+	1	NA	exon (NM_009299, exon 2 of 4)	exon (NM_009299, exon 2 of 4)	1699	NM_009299	20939	Mm.4119	NM_009299	ENSMUSG00000023289	Sva	-	seminal vesicle antigen	protein-coding
mm_17207.1	chr2	25470112	25470112	-	1	NA	promoter-TSS (NM_008963)	promoter-TSS (NM_008963)	-363	NM_008963	19215	Mm.1008	NM_008963	ENSMUSG00000015090	Ptgds	21kDa|L-PGDS|PGD2|PGDS|PGDS2|Ptgs3	prostaglandin D2 synthase (brain)	protein-coding
mm_118296.1	chr13	113079121	113079127	-	1	NA	intron (NM_001281487, intron 7 of 11)	intron (NM_001281487, intron 7 of 11)	21857	NM_010370	14938	Mm.15510	NM_010370	ENSMUSG00000023132	Gzma	AW494114|Ctla-3|Ctla3|Hf|Hf1|SE1|TSP-1|TSP1	granzyme A	protein-coding
mm_13708.1	chr2	117157591	117157610	+	1	NA	intron (NM_033524, intron 2 of 6)	intron (NM_033524, intron 2 of 6)	-27527	NR_030440	732489		NR_030440	ENSMUSG00000076376	Mir674	Mirn674|mir-674|mmu-mir-674	microRNA 674	ncRNA
mm_70066.1	chr7	142652417	142652429	-	1	NA	3' UTR (NM_010514, exon 4 of 4)	3' UTR (NM_010514, exon 4 of 4)	2573	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_62908.1	chr7	117390136	117390147	+	1	NA	intron (NM_175645, intron 1 of 11)	intron (NM_175645, intron 1 of 11)	9162	NM_175645	233781	Mm.461427	NM_175645	ENSMUSG00000030657	Xylt1	8030490L12	xylosyltransferase 1	protein-coding
mm_24249.1	chr3	89164791	89164863	+	1	NA	promoter-TSS (NM_007712)	promoter-TSS (NM_007712)	32	NM_001163432	12748	Mm.288098	NM_007712	ENSMUSG00000068917	Clk2	AU041688	CDC-like kinase 2	protein-coding
mm_80927.1	chr9	102172732	102172764	+	1	NA	intron (NM_001168296, intron 3 of 14)	MLT1G|LTR|ERVL-MaLR	132227	NR_106163	102466241		NR_106163	ENSMUSG00000098521	Mir7243	Gm27363|mmu-mir-7243	microRNA 7243	ncRNA
mm_48168.1	chr5	137153090	137153098	-	1	NA	Intergenic	Intergenic	-36887	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_80498.1	chr9	78503936	78503960	+	1	NA	Intergenic	Intergenic	-22224	NM_010106	13627	Mm.138471	NM_010106	ENSMUSG00000037742	Eef1a1	-	eukaryotic translation elongation factor 1 alpha 1	protein-coding
mm_164122.1	chr15	38322203	38322209	+	1	NA	Intergenic	Intergenic	-21495	NM_001289471	21847	Mm.4292	NM_013692	ENSMUSG00000037465	Klf10	AI115143|EGR[a]|Egral|Gdnfif|TIEG-1|Tieg|Tieg1|mGIF	Kruppel-like factor 10	protein-coding
mm_22521.1	chr3	7644569	7644607	+	1	NA	Intergenic	Intergenic	-30828	NM_001313888	16196	Mm.3825	NM_008371	ENSMUSG00000040329	Il7	A630026I06Rik|Il-7|hlb368	interleukin 7	protein-coding
mm_153398.1	chr19	40487569	40487591	-	1	NA	intron (NM_178362, intron 1 of 28)	intron (NM_178362, intron 1 of 28)	26156	NM_178362	20411	Mm.210815	NM_009166	ENSMUSG00000025006	Sorbs1	2310065E01Rik|9530001P15Rik|CAP|SH3P12|Sh3d5|mKIAA1296	sorbin and SH3 domain containing 1	protein-coding
mm_33555.1	chr4	130936049	130936069	+	1	NA	TTS (NM_010686)	TTS (NM_010686)	-8326	NM_010769	17180	Mm.271796	NM_010769	ENSMUSG00000040533	Matn1	CMP|Crtm|Mat1|matrilin-1	matrilin 1, cartilage matrix protein	protein-coding
mm_12170.1	chr2	62646295	62646304	+	1	NA	promoter-TSS (NM_027835)	promoter-TSS (NM_027835)	-44	NM_001164477	71586	Mm.136224	NM_027835	ENSMUSG00000026896	Ifih1	9130009C22Rik|Helicard|Hlcd|MDA5|RLR-2	interferon induced with helicase C domain 1	protein-coding
mm_33699.1	chr4	133584420	133584426	+	1	NA	promoter-TSS (NM_001290742)	promoter-TSS (NM_001290742)	50	NM_133884	100210	Mm.274001	NM_133884	ENSMUSG00000028848	Gpn2	AI838661|Atpbd1b|R74630	GPN-loop GTPase 2	protein-coding
mm_124424.1	chr14	118211671	118211679	-	1	NA	Intergenic	Intergenic	-24557	NR_131969	105245869	Mm.460408	NR_131969	ENSMUSG00000090534	LOC105245869	-	uncharacterized LOC105245869	ncRNA
mm_78034.1	chr9	13827819	13827828	+	1	NA	promoter-TSS (NM_001310721)	promoter-TSS (NM_001310721)	96	NM_176836	72826	Mm.246174	NM_176836	ENSMUSG00000037808	Fam76b	2810485I05Rik|C78303	family with sequence similarity 76, member B	protein-coding
mm_35240.1	chr4	19877292	19877319	-	1	NA	3' UTR (NM_175406, exon 8 of 8)	3' UTR (NM_175406, exon 8 of 8)	45261	NM_175406	242341	Mm.19298	NM_175406	ENSMUSG00000028238	Atp6v0d2	1620401A02Rik|AI324824|V-ATPase	ATPase, H+ transporting, lysosomal V0 subunit D2	protein-coding
mm_104583.1	chr11	96977291	96977328	-	1	NA	intron (NM_030220, intron 1 of 6)	CpG	379	NM_030220	78912	Mm.491183	NM_030220	ENSMUSG00000018678	Sp2	4930480I16Rik|mKIAA0048	Sp2 transcription factor	protein-coding
mm_95558.1	chr11	52311166	52311194	+	1	NA	Intergenic	Intergenic	-28166	NM_001313981	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_65029.1	chr7	18521109	18521133	-	1	NA	3' UTR (NM_054060, exon 5 of 5)	3' UTR (NM_054060, exon 5 of 5)	11106	NM_054060	114868	Mm.389809	NM_054060	ENSMUSG00000070798	Psg25	cea13	pregnancy-specific glycoprotein 25	protein-coding
mm_53987.1	chr6	6871534	6871538	-	1	NA	Intergenic	Intergenic	-2003	NR_015388	320038	Mm.94021	NR_015388		Dlx6os1	A230055N17Rik|Dlx6as1|Evf-1|Evf-2|Evf1|Evf1/2|Evf2|Shhrs|mEvf-1	distal-less homeobox 6, opposite strand 1	ncRNA
mm_63149.1	chr7	123369765	123369769	+	1	NA	exon (NM_001122643, exon 1 of 20)	exon (NM_001122643, exon 1 of 20)	148	NM_001122643	70497	Mm.403318	NM_144529	ENSMUSG00000030766	Arhgap17	5730403H17Rik|Nadrin|Nadrin2|Rich1|Wbp15	Rho GTPase activating protein 17	protein-coding
mm_23617.1	chr3	65666224	65666259	+	1	NA	promoter-TSS (NM_001037923)	promoter-TSS (NM_001037923)	13	NM_001166659	624866	Mm.296317	NM_001037923	ENSMUSG00000074579	Lekr1	EG546798|EG624866|Gm6534	leucine, glutamate and lysine rich 1	protein-coding
mm_127451.1	chr15	101270751	101270763	+	1	NA	exon (NM_010444, exon 2 of 7)	exon (NM_010444, exon 2 of 7)	3911	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_94596.1	chr11	11809520	11809526	+	1	NA	promoter-TSS (NM_021891)	promoter-TSS (NM_021891)	-561	NM_001163360	60530	Mm.236114	NM_021891	ENSMUSG00000035455	Fignl1	-	fidgetin-like 1	protein-coding
mm_30637.1	chr4	8811347	8811357	+	1	NA	intron (NM_001277149, intron 6 of 37)	intron (NM_001277149, intron 6 of 37)	120946	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_159386.1	chr3	91090803	91090803	-	1	NA	promoter-TSS (NM_001101461)	promoter-TSS (NM_001101461)	2	NM_001101461	229550	Mm.98335	NM_001101461	ENSMUSG00000091175	9130204L05Rik	Gm127	RIKEN cDNA 9130204L05 gene	protein-coding
mm_102782.1	chr11	68400467	68400482	-	1	NA	Intergenic	CpG	-13648	NM_008744	18208	Mm.39095	NM_008744	ENSMUSG00000020902	Ntn1	AI561871|BC019633|Netrin-1	netrin 1	protein-coding
mm_48887.1	chr5	151234021	151234034	-	1	NA	Intergenic	Intergenic	-43834	NM_146258	243362	Mm.209272	NM_146258	ENSMUSG00000016128	Stard13	DLC2|GT650	StAR-related lipid transfer (START) domain containing 13	protein-coding
mm_103685.1	chr11	79482384	79482400	-	1	NA	non-coding (NR_045305, exon 4 of 4)	non-coding (NR_045305, exon 4 of 4)	1639	NR_045305	104522	Mm.436987	NR_045305	ENSMUSG00000091523	AU040972	AU040954	expressed sequence AU040972	ncRNA
mm_87017.1	chr10	26917434	26917446	+	1	NA	3' UTR (NM_176837, exon 15 of 15)	3' UTR (NM_176837, exon 15 of 15)	144928	NM_176837	73910	Mm.356496	NM_176837	ENSMUSG00000039031	Arhgap18	4833419J07Rik|AI314906|AI843501	Rho GTPase activating protein 18	protein-coding
mm_164600.1	chr17	28952682	28952697	+	1	NA	promoter-TSS (NM_025888)	promoter-TSS (NM_025888)	-527	NM_025888	66989	Mm.435	NM_025888	ENSMUSG00000005936	Kctd20	2410004N11Rik|AI451943|AW541186|D17Ertd562e	potassium channel tetramerisation domain containing 20	protein-coding
mm_140372.1	chr17	86964316	86964323	+	1	NA	exon (NM_145491, exon 2 of 5)	exon (NM_145491, exon 2 of 5)	1208	NM_145491	104215	Mm.826	NM_145491	ENSMUSG00000024143	Rhoq	Arhq|TC10A|Tc10	ras homolog family member Q	protein-coding
mm_77837.1	chr9	5298670	5298694	+	1	NA	5' UTR (NM_009807, exon 1 of 10)	5' UTR (NM_009807, exon 1 of 10)	165	NM_009807	12362	Mm.1051	NM_009807	ENSMUSG00000025888	Casp1	ICE|Il1bc	caspase 1	protein-coding
mm_92147.1	chr10	67096837	67096866	-	1	NA	5' UTR (NM_001204915, exon 1 of 9)	5' UTR (NM_001204915, exon 1 of 9)	137	NM_001204915	28193	Mm.41272	NM_178606	ENSMUSG00000019873	Reep3	D10Ucla1	receptor accessory protein 3	protein-coding
mm_12217.1	chr2	67602052	67602066	+	1	NA	Intergenic	Intergenic	-73398	NR_106083	102465706		NR_106083	ENSMUSG00000098299	Mir7224	Gm27971|mmu-mir-7224	microRNA 7224	ncRNA
mm_57530.1	chr6	126535366	126535376	-	1	NA	5' UTR (NM_145983, exon 1 of 1)	5' UTR (NM_145983, exon 1 of 1)	184	NM_145983	16493	Mm.222831	NM_145983	ENSMUSG00000045534	Kcna5	Kv1.5	potassium voltage-gated channel, shaker-related subfamily, member 5	protein-coding
mm_92225.1	chr10	68321076	68321089	-	1	NA	promoter-TSS (NR_045357)	promoter-TSS (NR_045357)	60	NR_045357	75148	Mm.23505	NR_045357		4930545H06Rik	-	RIKEN cDNA 4930545H06 gene	ncRNA
mm_40248.1	chr5	38076564	38076572	+	1	NA	intron (NM_001289536, intron 1 of 9)	intron (NM_001289536, intron 1 of 9)	37338	NM_026959	71116	Mm.18959	NM_026959	ENSMUSG00000029125	Stx18	1810035L21Rik|4933425D03Rik|AU041562	syntaxin 18	protein-coding
mm_127163.1	chr15	98634988	98635075	+	1	NA	5' UTR (NM_007581, exon 1 of 13)	5' UTR (NM_007581, exon 1 of 13)	264	NM_001286226	12297	Mm.3544	NM_007581	ENSMUSG00000003352	Cacnb3	Beta3|CAB3|Ca(v)beta3|Cchb3	calcium channel, voltage-dependent, beta 3 subunit	protein-coding
mm_90235.1	chr10	121381168	121381183	+	1	NA	exon (NM_029364, exon 8 of 14)	exon (NM_029364, exon 8 of 14)	16085	NM_029364	75612	Mm.207683	NM_029364	ENSMUSG00000034707	Gns	2610016K11Rik|AU042285|C87209|G6S|N28088	glucosamine (N-acetyl)-6-sulfatase	protein-coding
mm_109813.1	chr12	3426701	3426782	-	1	NA	promoter-TSS (NM_172421)	promoter-TSS (NM_172421)	6	NR_030694	100043040	Mm.415417	NR_030694	ENSMUSG00000071456	1110002L01Rik	-	RIKEN cDNA 1110002L01 gene	ncRNA
mm_130575.1	chr15	99499499	99499511	-	1	NA	3' UTR (NM_028224, exon 12 of 12)	3' UTR (NM_028224, exon 12 of 12)	-24775	NM_029236	75284	Mm.32826	NM_029236	ENSMUSG00000037525	Bcdin3d	4930556P03Rik|AV138748	BCDIN3 domain containing	protein-coding
mm_137787.1	chr17	29614787	29614797	+	1	NA	promoter-TSS (NM_021419)	promoter-TSS (NM_021419)	3	NM_021419	58230	Mm.305994	NM_021419	ENSMUSG00000090083	Rnf8	3830404E21Rik|AIP37|laXp180	ring finger protein 8	protein-coding
mm_80463.1	chr9	78109189	78109285	+	1	NA	promoter-TSS (NM_001081490)	promoter-TSS (NM_001081490)	45	NM_001163780	56542	Mm.288719	NM_019987	ENSMUSG00000009828	Ick	2210420N10Rik|AI848300|Mrk	intestinal cell kinase	protein-coding
mm_120888.1	chr14	75455958	75455996	+	1	NA	promoter-TSS (NM_001128093)	promoter-TSS (NM_001128093)	-5	NM_001128093	380918	Mm.484360	NM_001128093	ENSMUSG00000091722	Siah3	Gm912	seven in absentia homolog 3 (Drosophila)	protein-coding
mm_33586.1	chr4	132553364	132553384	+	1	NA	3' UTR (NM_172400, exon 9 of 9)	3' UTR (NM_172400, exon 9 of 9)	-10693	NM_001081211	19204	Mm.89389	NM_001081211	ENSMUSG00000056529	Ptafr	PAFR	platelet-activating factor receptor	protein-coding
mm_99249.1	chr11	101082718	101082726	+	1	NA	intron (NM_001305982, intron 1 of 9)	CpG	157	NM_001305982	71743	Mm.182271	NM_027896	ENSMUSG00000001755	Coasy	1300003G02Rik|Dpck|Ppat|Ukr1	Coenzyme A synthase	protein-coding
mm_11431.1	chr2	31962181	31962197	+	1	NA	intron (NM_145144, intron 2 of 5)	intron (NM_145144, intron 2 of 5)	11886	NM_145144	108897	Mm.24838	NM_145144	ENSMUSG00000001864	Aif1l	2810003C17Rik|AI043124|C87647|Iba2	allograft inflammatory factor 1-like	protein-coding
mm_92641.1	chr10	80348433	80348458	-	1	NA	promoter-TSS (NM_001285435)	promoter-TSS (NM_001285435)	3	NM_001285435	66548	Mm.71891	NM_025629	ENSMUSG00000043822	Adamtsl5	2010109H09Rik|Thsd6	ADAMTS-like 5	protein-coding
mm_77241.1	chr8	115705266	115705276	-	1	NA	3' UTR (NM_001025577, exon 1 of 1)	3' UTR (NM_001025577, exon 1 of 1)	1623	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_162541.1	chr1	169930095	169930136	+	1	NA	exon (NM_001033185, exon 2 of 4)	exon (NM_001033185, exon 2 of 4)	196	NM_001347138	78465	Mm.291078	NM_001033185	ENSMUSG00000070532	Ccdc190	1700084C01Rik	coiled-coil domain containing 190	protein-coding
mm_79794.1	chr9	64084908	64084918	+	1	NA	intron (NR_040743, intron 1 of 2)	CpG	4152	NR_040743	76814	Mm.243771	NR_040743		Scarletltr	2600006L11Rik	Scarletltr, erythroid developmental long intergenic non-protein coding transcript	ncRNA
mm_92381.1	chr10	76442680	76442697	-	1	NA	5' UTR (NM_001282992, exon 1 of 42)	5' UTR (NM_001282992, exon 1 of 42)	224	NM_008787	18541	Mm.251794	NM_008787	ENSMUSG00000001151	Pcnt	AW476095|C86676|KEN|Pcnt2|kendrin|m239Asp|m275Asp	pericentrin (kendrin)	protein-coding
mm_8863.1	chr1	162740541	162740551	-	1	NA	promoter-TSS (NM_001081290)	promoter-TSS (NM_001081290)	10	NM_001081290	226562	Mm.245446	NM_001081290	ENSMUSG00000040225	Prrc2c	1810043M20Rik|9630039I18Rik|A630006J20|Bat2d|Bat2d1|Bat2l2|E130112L15Rik|Prrc3|mKIAA1096	proline-rich coiled-coil 2C	protein-coding
mm_104767.1	chr11	98508874	98508888	-	1	NA	intron (NM_011771, intron 3 of 7)	B1F|SINE|Alu	37150	NM_011771	22780	Mm.133367	NM_011771	ENSMUSG00000018168	Ikzf3	5830411O07Rik|Aiolos|Zfpn1a3|Znfn1a3	IKAROS family zinc finger 3	protein-coding
mm_39971.1	chr5	32192409	32192442	+	1	NA	Intergenic	Intergenic	-40283	NM_030072	665270	Mm.160067	NM_030072	ENSMUSG00000029134	Plb1	4632413E21Rik|4930433E17Rik|4930539A06Rik|BC033606	phospholipase B1	protein-coding
mm_22775.1	chr3	20275446	20275456	+	1	NA	exon (NM_029706, exon 2 of 11)	exon (NM_029706, exon 2 of 11)	282	NM_029706	76703	Mm.34692	NM_029706	ENSMUSG00000011463	Cpb1	0910001A18Rik|1810063F02Rik|2210008M23Rik|AI504870	carboxypeptidase B1 (tissue)	protein-coding
mm_10583.1	chr2	18172270	18172281	+	1	NA	intron (NR_045539, intron 15 of 24)	intron (NR_045539, intron 15 of 24)	107690	NM_001252561	17354	Mm.209175	NM_010804	ENSMUSG00000026743	Mllt10	Af10|B130021D15Rik|D630001B22Rik|mKIAA4140	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 10	protein-coding
mm_89558.1	chr10	95265195	95265209	+	1	NA	intron (NM_009950, intron 2 of 2)	intron (NM_009950, intron 2 of 2)	58507	NM_001330138	12905	Mm.473739	NM_009950	ENSMUSG00000045867	Cradd	RAIDD	CASP2 and RIPK1 domain containing adaptor with death domain	protein-coding
mm_114019.1	chr13	52618664	52618682	+	1	NA	intron (NM_001198977, intron 3 of 13)	intron (NM_001198977, intron 3 of 13)	21791	NM_011518	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_154201.1	chr19	58991712	58991737	-	1	NA	intron (NM_001114312, intron 15 of 16)	intron (NM_001114312, intron 15 of 16)	-48052	NM_001327998	73442	Mm.39739	NM_175199	ENSMUSG00000025092	Hspa12a	1700063D12Rik|AI118035|AI840429|AW048913|AW556406|D5Mgi40|Gm19925|mKIAA0417	heat shock protein 12A	protein-coding
mm_87480.1	chr10	51493645	51493718	+	1	NA	intron (NM_001291894, intron 5 of 8)	intron (NM_001291894, intron 5 of 8)	2783	NM_013532	14728	Mm.34408	NM_013532	ENSMUSG00000062593	Lilrb4a	CD85K|Gp49b|HM18|ILT3|LIR-5|Lilrb4|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4A	protein-coding
mm_237.1	chr1	19208984	19208994	+	1	NA	promoter-TSS (NM_009334)	promoter-TSS (NM_009334)	75	NM_001286340	21419	Mm.137021	NM_009334	ENSMUSG00000025927	Tfap2b	AI606113|AP-2(beta)|E130018K07Rik|Tcfap2b	transcription factor AP-2 beta	protein-coding
mm_7548.1	chr1	124507742	124507752	-	1	NA	Intergenic	Lx4A|LINE|L1	-462188	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_2405.1	chr1	93755175	93755193	+	1	NA	promoter-TSS (NM_025920)	promoter-TSS (NM_025920)	151	NM_174874	66615	Mm.29087	NM_174874	ENSMUSG00000026280	Atg4b	2510009N07Rik|AW048066|Apg4b|Atg4bl|Autl1	autophagy related 4B, cysteine peptidase	protein-coding
mm_118290.1	chr13	113046317	113046327	-	1	NA	promoter-TSS (NM_027127)	promoter-TSS (NM_027127)	66	NM_027127	69590	Mm.12715	NM_027127	ENSMUSG00000021760	Gpx8	2310016C16Rik|AU017063	glutathione peroxidase 8 (putative)	protein-coding
mm_145601.1	chr18	61045304	61045313	+	1	NA	5' UTR (NM_001146268, exon 1 of 23)	5' UTR (NM_001146268, exon 1 of 23)	158	NM_008809	18596	Mm.4146	NM_008809	ENSMUSG00000024620	Pdgfrb	AI528809|CD140b|PDGFR-1|Pdgfr	platelet derived growth factor receptor, beta polypeptide	protein-coding
mm_11165.1	chr2	28557780	28557797	+	1	NA	exon (NM_009885, exon 9 of 11)	exon (NM_009885, exon 9 of 11)	5615	NM_009885	12613	Mm.236017	NM_009885	ENSMUSG00000026818	Cel	1810036E18Rik|BAL	carboxyl ester lipase	protein-coding
mm_22232.1	chr2	174437775	174437776	-	1	NA	intron (NM_022325, intron 2 of 5)	intron (NM_022325, intron 2 of 5)	1264	NM_022325	64138	Mm.156919	NM_022325	ENSMUSG00000016256	Ctsz	AI787083|AU019819|CTSX|D2Wsu143e	cathepsin Z	protein-coding
mm_78622.1	chr9	38470311	38470324	+	1	NA	Intergenic	Intergenic	-2432	NM_146804	258800	Mm.377697	NM_146804	ENSMUSG00000096794	Olfr905	MOR167-1	olfactory receptor 905	protein-coding
mm_37769.1	chr4	129742276	129742312	-	1	NA	promoter-TSS (NR_045036)	promoter-TSS (NR_045036)	9	NM_011317	20218	Mm.8256	NM_011317	ENSMUSG00000028790	Khdrbs1	Sam68|p62|p68	KH domain containing, RNA binding, signal transduction associated 1	protein-coding
mm_39274.1	chr5	3806059	3806062	+	1	NA	intron (NR_033173, intron 1 of 17)	(T)n|Simple_repeat|Simple_repeat	2879	NR_033173	79264	Mm.32368	NM_030675	ENSMUSG00000000600	Krit1	2010007K12Rik|A630036P20Rik|AA432855|AI450393|AI643869|BB155247|BB235701|Ccm1	KRIT1, ankyrin repeat containing	protein-coding
mm_62324.1	chr7	100372389	100372424	+	1	NA	promoter-TSS (NM_028292)	promoter-TSS (NM_028292)	173	NM_001017985	277939	Mm.276374	NM_001017985	ENSMUSG00000047248	C2cd3	AU020772	C2 calcium-dependent domain containing 3	protein-coding
mm_40511.1	chr5	57785982	57786003	+	1	NA	intron (NM_001310608, intron 1 of 3)	intron (NM_001310608, intron 1 of 3)	67911	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_101960.1	chr11	50300928	50300943	-	1	NA	exon (NM_001110500, exon 10 of 15)	exon (NM_001110500, exon 10 of 15)	-8599	NM_175334	103806	Mm.51116	NM_175334	ENSMUSG00000050567	Maml1	AI644666|AW743257|D930008C07Rik|Mam-1|Mam1|mKIAA0200	mastermind like 1 (Drosophila)	protein-coding
mm_141771.1	chr17	34283671	34283723	-	1	NA	exon (NM_010378, exon 3 of 5)	exon (NM_010378, exon 3 of 5)	4074	NM_010378	14960	Mm.235338	NM_010378	ENSMUSG00000036594	H2-Aa	Aalpha|H-2Aa|H2Aa|I-Aalpha|IAalpha|Ia-1|Ia1	histocompatibility 2, class II antigen A, alpha	protein-coding
mm_150075.1	chr19	29386863	29386893	+	1	NA	3' UTR (NM_021893, exon 7 of 7)	3' UTR (NM_021893, exon 7 of 7)	19440	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_87472.1	chr10	51491952	51491964	+	1	NA	exon (NM_013532, exon 4 of 9)	exon (NM_013532, exon 4 of 9)	1060	NM_013532	14728	Mm.34408	NM_013532	ENSMUSG00000062593	Lilrb4a	CD85K|Gp49b|HM18|ILT3|LIR-5|Lilrb4|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4A	protein-coding
mm_15169.1	chr2	154013709	154013729	+	1	NA	exon (NM_008953, exon 6 of 9)	exon (NM_008953, exon 6 of 9)	5443	NM_008953	19194	Mm.29197	NM_008953	ENSMUSG00000042459	Bpifa2	Bpifa2e|Psp	BPI fold containing family A, member 2	protein-coding
mm_84627.1	chr9	70657236	70657248	-	1	NA	promoter-TSS (NM_172772)	promoter-TSS (NM_172772)	-68	NM_172772	235461	Mm.170855	NM_172772	ENSMUSG00000042444	Fam63b	AI465301|B230380D07Rik|mKIAA1164	family with sequence similarity 63, member B	protein-coding
mm_122887.1	chr14	54947002	54947010	-	1	NA	exon (NM_010856, exon 33 of 39)	exon (NM_010856, exon 33 of 39)	2136	NR_029724	387204		NR_029724	ENSMUSG00000065432	Mir208a	Mirn208|Mirn208a|mir-208|mir-208a|mmu-mir-208	microRNA 208a	ncRNA
mm_117647.1	chr13	92755143	92755176	-	1	NA	exon (NM_011582, exon 19 of 22)	exon (NM_011582, exon 19 of 22)	39659	NM_011582	21828	Mm.20865	NM_011582	ENSMUSG00000021702	Thbs4	TSP4	thrombospondin 4	protein-coding
mm_19310.1	chr2	90540808	90540811	-	1	NA	intron (NM_008982, intron 1 of 23)	ID_B1|SINE|B4	39838	NM_008982	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_121764.1	chr14	19823772	19823797	-	1	NA	promoter-TSS (NM_026528)	promoter-TSS (NM_026528)	39	NM_026528	68045	Mm.21932	NM_026528	ENSMUSG00000021807	2700060E02Rik	-	RIKEN cDNA 2700060E02 gene	protein-coding
mm_29606.1	chr3	121249966	121249966	-	1	NA	intron (NM_178936, intron 1 of 7)	LSU-rRNA_Hsa|rRNA|rRNA	13350	NM_178936	99887	Mm.26088	NM_178936	ENSMUSG00000028132	Tmem56	4930577M16Rik|AU018104|AW109744|C730036B01Rik	transmembrane protein 56	protein-coding
mm_49291.1	chr6	17693608	17693618	+	1	NA	promoter-TSS (NM_001289625)	promoter-TSS (NM_001289625)	-381	NM_001289624	64213	Mm.12051	NM_022332	ENSMUSG00000029534	St7	9430001H04Rik|Fam4a2|HELG|RAY1|SEN4|TSG7	suppression of tumorigenicity 7	protein-coding
mm_74561.1	chr8	11006243	11006246	-	1	NA	exon (NM_001081212, exon 1 of 2)	exon (NM_001081212, exon 1 of 2)	-1606	NR_046017	619321	Mm.403007	NR_046017	ENSMUSG00000096938	9530052E02Rik	-	RIKEN cDNA 9530052E02 gene	ncRNA
mm_53242.1	chr6	127561208	127561241	+	1	NA	Intergenic	CpG	-16751	NM_001033464	381812	Mm.296093	NM_001033464	ENSMUSG00000061414	Cracr2a	Efcab4b|Gm1073|Gm462	calcium release activated channel regulator 2A	protein-coding
mm_136621.1	chr17	5497458	5497465	+	1	NA	intron (NM_146073, intron 1 of 8)	(G)n|Simple_repeat|Simple_repeat	4861	NM_146073	224454	Mm.487663	NM_146073	ENSMUSG00000034265	Zdhhc14	B530001K09Rik|New1cp	zinc finger, DHHC domain containing 14	protein-coding
mm_151950.1	chr19	5801218	5801233	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	1447	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_36266.1	chr4	63605076	63605099	-	1	NA	intron (NR_028583, intron 1 of 1)	intron (NR_028583, intron 1 of 1)	174	NR_028583	670833	Mm.32213	NR_028583	ENSMUSG00000084782	Gm11213	OTTMUSG00000000252	predicted gene 11213	ncRNA
mm_49565.1	chr6	30611030	30611040	+	1	NA	promoter-TSS (NM_144537)	promoter-TSS (NM_144537)	25	NM_144537	74649	Mm.159276	NM_144537	ENSMUSG00000029788	Cpa5	4930430M09Rik	carboxypeptidase A5	protein-coding
mm_149967.1	chr19	29047530	29047534	+	1	NA	promoter-TSS (NR_028360)	promoter-TSS (NR_028360)	49	NR_028360	67329	Mm.394933	NR_028360		1700018L02Rik	-	RIKEN cDNA 1700018L02 gene	ncRNA
mm_6409.1	chr1	72874248	72874262	-	1	NA	5' UTR (NM_010518, exon 1 of 4)	5' UTR (NM_010518, exon 1 of 4)	610	NM_010518	16011	Mm.405761	NM_010518	ENSMUSG00000026185	Igfbp5	AI256729|AW208790|IGFBP-5|IGFBP-5P	insulin-like growth factor binding protein 5	protein-coding
mm_138285.1	chr17	34612595	34612630	+	1	NA	TTS (NM_152922)	TTS (NM_152922)	3359	NM_152922	81701	Mm.231343	NM_152922	ENSMUSG00000015467	Egfl8	Ng3	EGF-like domain 8	protein-coding
mm_13417.1	chr2	104122818	104122827	+	1	NA	promoter-TSS (NM_026634)	promoter-TSS (NM_026634)	53	NM_026634	68243	Mm.158191	NM_026634	ENSMUSG00000032671	A930018P22Rik	-	RIKEN cDNA A930018P22 gene	protein-coding
mm_47602.1	chr5	125043042	125043050	-	1	NA	intron (NM_011424, intron 21 of 46)	intron (NM_011424, intron 21 of 46)	39571	NM_028443	73121	Mm.296138	NM_028443	ENSMUSG00000037962	Rflna	3110032G18Rik|Fam101a|cfm|cfm2	refilin A	protein-coding
mm_104403.1	chr11	94521300	94521323	-	1	NA	intron (NM_170671, intron 1 of 18)	CpG	191	NM_170671	104601	Mm.84725	NM_170671	ENSMUSG00000039110	Mycbpap	4932408B01Rik|AMAP-1|AW125474	MYCBP associated protein	protein-coding
mm_126556.1	chr15	82147373	82147398	+	1	NA	5' UTR (NM_033218, exon 1 of 19)	5' UTR (NM_033218, exon 1 of 19)	116	NM_033218	20788	Mm.9002	NM_033218	ENSMUSG00000022463	Srebf2	AI608257|SREBP-2|SREBP2|SREBP2gc|bHLHd2|lop13|nuc	sterol regulatory element binding factor 2	protein-coding
mm_1963.1	chr1	86473528	86473568	+	1	NA	Intergenic	Intergenic	47219	NM_027966	71863	Mm.179627	NM_027966	ENSMUSG00000036574	1700019O17Rik	-	RIKEN cDNA 1700019O17 gene	protein-coding
mm_52175.1	chr6	99262887	99262891	+	1	NA	intron (NM_001347345, intron 3 of 19)	intron (NM_001347345, intron 3 of 19)	3626	NM_001197321	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_14207.1	chr2	127258610	127258627	+	1	NA	3' UTR (NM_175145, exon 4 of 4)	3' UTR (NM_175145, exon 4 of 4)	10643	NM_175145	69470	Mm.200889	NM_175145	ENSMUSG00000034850	Tmem127	2310003P10Rik|AI314202|AI317350	transmembrane protein 127	protein-coding
mm_146740.1	chr18	15403659	15403667	-	1	NA	promoter-TSS (NM_009700)	promoter-TSS (NM_009700)	95	NM_001317729	11829	Mm.250786	NM_009700	ENSMUSG00000024411	Aqp4	WCH4	aquaporin 4	protein-coding
mm_119156.1	chr14	31575523	31575532	+	1	NA	intron (NM_009937, intron 1 of 16)	L2b|LINE|L2	1856	NM_009937	382864	Mm.239821	NM_009937	ENSMUSG00000057606	Colq	A130034K24Rik	collagen-like tail subunit (single strand of homotrimer) of asymmetric acetylcholinesterase	protein-coding
mm_31584.1	chr4	57792383	57792386	+	1	NA	intron (NM_001304544, intron 6 of 8)	PB1|SINE|Alu	-52864	NM_009649	11641	Mm.467752	NM_009649	ENSMUSG00000038729	Akap2	AA959716|AI649048|Akap-2|Akap-kl|B230340M18Rik|Prka2	A kinase (PRKA) anchor protein 2	protein-coding
mm_74322.1	chr8	126854674	126854677	+	1	NA	Intergenic	Intergenic	91246	NM_024214	67952	Mm.6932	NM_024214	ENSMUSG00000093904	Tomm20	1810060K07Rik|BB284719|Gm19268|MAS20|MOM19|TOM20|mKIAA0016	translocase of outer mitochondrial membrane 20 homolog (yeast)	protein-coding
mm_144064.1	chr17	90834236	90834240	-	1	NA	intron (NM_001346957, intron 3 of 18)	intron (NM_001346957, intron 3 of 18)	-26931	NR_045463	78800	Mm.410772	NR_045463	ENSMUSG00000090160	4930480K15Rik	-	RIKEN cDNA 4930480K15 gene	ncRNA
mm_110981.1	chr12	77060190	77060202	-	1	NA	Intergenic	Intergenic	-97948	NM_001146176	17187	Mm.268548	NM_008558	ENSMUSG00000059436	Max	AA960152|AI875693|bHLHd4|bHLHd5|bHLHd6|bHLHd7|bHLHd8	Max protein	protein-coding
mm_92559.1	chr10	79807111	79807135	-	1	NA	intron (NM_023128, intron 3 of 8)	intron (NM_023128, intron 3 of 8)	13551	NM_001161747	18483	Mm.34650	NM_023128	ENSMUSG00000035863	Palm	-	paralemmin	protein-coding
mm_105879.1	chr11	114928094	114928105	-	1	NA	intron (NM_001347651, intron 2 of 3)	(TCCC)n|Simple_repeat|Simple_repeat	6287	NM_001347651	217304	Mm.185355	NM_199221	ENSMUSG00000063193	Cd300lb	CLM-7|Clm7|Gm253|LMIR5	CD300 molecule like family member B	protein-coding
mm_170543.1	chr19	40119778	40119781	+	1	NA	Intergenic	Lx2|LINE|L1	30100	NM_001167875	107141	Mm.474575	NM_134144	ENSMUSG00000054827	Cyp2c50	AI266900	cytochrome P450, family 2, subfamily c, polypeptide 50	protein-coding
mm_158783.1	chrX	167207331	167207343	-	1	NA	3' UTR (NM_021278, exon 3 of 3)	3' UTR (NM_021278, exon 3 of 3)	1881	NM_021278	19241	Mm.142729	NM_021278	ENSMUSG00000049775	Tmsb4x	Ptmb4|Tb4	thymosin, beta 4, X chromosome	protein-coding
mm_23765.1	chr3	73310614	73310614	+	1	NA	intron (NR_040557, intron 2 of 4)	Lx5c|LINE|L1	171037	NR_040547	74693	Mm.292227	NR_040547	ENSMUSG00000102362	4930509J09Rik	-	RIKEN cDNA 4930509J09 gene	ncRNA
mm_169236.1	chr1	37205953	37205961	+	1	NA	Intergenic	RLTR9E|LTR|ERVK	-12321	NM_001282010	12790	Mm.214224	NM_009918	ENSMUSG00000026114	Cnga3	CNG3	cyclic nucleotide gated channel alpha 3	protein-coding
mm_151486.1	chr19	58677170	58677217	+	1	NA	exon (NM_026925, exon 9 of 13)	exon (NM_026925, exon 9 of 13)	6828	NM_026925	69060	Mm.20407	NM_026925	ENSMUSG00000046008	Pnlip	1810007A24Rik|PL|PTL	pancreatic lipase	protein-coding
mm_87541.1	chr10	53596845	53596853	+	1	NA	promoter-TSS (NM_025541)	promoter-TSS (NM_025541)	-112	NM_025541	66403	Mm.272989	NM_025541	ENSMUSG00000019857	Asf1a	2310079C17Rik|C79052	anti-silencing function 1A histone chaperone	protein-coding
mm_141665.1	chr17	33799328	33799335	-	1	NA	Intergenic	B2_Mm2|SINE|B2	-11192	NM_030697	80880	Mm.196330	NM_030697	ENSMUSG00000042099	Kank3	0610013D04Rik|Ankrd47|D17Ertd288e|NG28	KN motif and ankyrin repeat domains 3	protein-coding
mm_126077.1	chr15	77733611	77733654	+	1	NA	intron (NM_001168660, intron 1 of 2)	intron (NM_001168660, intron 1 of 2)	4511	NM_001168660	71898	Mm.422856	NM_173743	ENSMUSG00000068246	Apol9b	2310016F22Rik	apolipoprotein L 9b	protein-coding
mm_114345.1	chr13	60902128	60902142	+	1	NA	exon (NM_026429, exon 3 of 5)	exon (NM_026429, exon 3 of 5)	2712	NM_026429	116913	Mm.443229	NM_026429	ENSMUSG00000062705	Tpbpb	1600012N09Rik	trophoblast specific protein beta	protein-coding
mm_84564.1	chr9	68558607	68558607	-	1	NA	Intergenic	Intergenic	-38407	NR_040737	74951	Mm.60678	NR_040737	ENSMUSG00000111303	4930502A04Rik	-	RIKEN cDNA 4930502A04 gene	ncRNA
mm_89348.1	chr10	88146996	88147037	+	1	NA	promoter-TSS (NM_027191)	promoter-TSS (NM_027191)	24	NM_027191	69736	Mm.222184	NM_027191	ENSMUSG00000035351	Nup37	2410003L22Rik|2810039M17Rik	nucleoporin 37	protein-coding
mm_41924.1	chr5	105621038	105621046	+	1	NA	Intergenic	LTR85b|LTR|Gypsy?	-78927	NM_001122768	231549	Mm.23837	NM_178701	ENSMUSG00000046079	Lrrc8d	2810473G09Rik|4930525N13Rik|A930019F03|Lrrc5	leucine rich repeat containing 8D	protein-coding
mm_138636.1	chr17	35861344	35861380	+	1	NA	promoter-TSS (NM_134122)	promoter-TSS (NM_134122)	44	NM_134122	106582	Mm.390992	NM_134122	ENSMUSG00000059791	Nrm	2610307M02Rik|AI429796	nurim (nuclear envelope membrane protein)	protein-coding
mm_10731.1	chr2	22914664	22914682	+	1	NA	intron (NM_019501, intron 5 of 10)	ID_B1|SINE|B4	19151	NM_019501	56075	Mm.249752	NM_019501	ENSMUSG00000026784	Pdss1	2610203G20Rik|2700031G06Rik|TPT|TPT 1|Tprt|mDLP1|mSPS1	prenyl (solanesyl) diphosphate synthase, subunit 1	protein-coding
mm_141557.1	chr17	32213696	32213727	-	1	NA	exon (NM_001286630, exon 10 of 20)	exon (NM_001286630, exon 10 of 20)	-24162	NM_001347341	71932	Mm.176240	NM_001033163	ENSMUSG00000037577	Ephx3	2310063B19Rik|Abhd9	epoxide hydrolase 3	protein-coding
mm_30640.1	chr4	8821772	8821780	+	1	NA	intron (NM_001277149, intron 7 of 37)	intron (NM_001277149, intron 7 of 37)	131370	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_6838.1	chr1	84232981	84233031	-	1	NA	intron (NM_001003948, intron 1 of 2)	GA-rich|Low_complexity|Low_complexity	-14045	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_43297.1	chr5	134582733	134582784	+	1	NA	promoter-TSS (NM_020022)	promoter-TSS (NM_020022)	68	NM_020022	19718	Mm.332739	NM_020022	ENSMUSG00000023104	Rfc2	2610008M13Rik|40kDa|AI326953|Recc2	replication factor C (activator 1) 2	protein-coding
mm_78414.1	chr9	30942542	30942546	+	1	NA	promoter-TSS (NM_001326292)	promoter-TSS (NM_001326292)	-18	NM_013906	30806	Mm.100582	NM_013906	ENSMUSG00000031994	Adamts8	METH-2|METH2	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 8	protein-coding
mm_77033.1	chr8	109565602	109565639	-	1	NA	promoter-TSS (NM_178380)	promoter-TSS (NM_178380)	-19	NM_178380	64340	Mm.23705	NM_178380	ENSMUSG00000037993	Dhx38	5730550P09Rik|AI325984|AW540902|Ddx38|Prp16|mKIAA0224	DEAH (Asp-Glu-Ala-His) box polypeptide 38	protein-coding
mm_156019.1	chrX	107148905	107148963	+	1	NA	promoter-TSS (NM_175442)	promoter-TSS (NM_175442)	7	NM_001122596	213438	Mm.265244	NM_175442	ENSMUSG00000054293	A630033H20Rik	AI662791|P2ry10	RIKEN cDNA A630033H20 gene	protein-coding
mm_126165.1	chr15	78493870	78493882	+	1	NA	intron (NM_008368, intron 1 of 9)	intron (NM_008368, intron 1 of 9)	1190	NM_008368	16185	Mm.35287	NM_008368	ENSMUSG00000068227	Il2rb	CD122|IL-15Rbeta|IL15Rbeta|Il-2/15Rbeta|Il-2Rbeta|p70	interleukin 2 receptor, beta chain	protein-coding
mm_34885.1	chr4	155587909	155587920	+	1	NA	exon (NM_001159637, exon 10 of 12)	exon (NM_001159637, exon 10 of 12)	-13502	NM_177186	320541	Mm.306018	NM_177186	ENSMUSG00000042202	Slc35e2	A530082C11Rik|AI957035	solute carrier family 35, member E2	protein-coding
mm_67141.1	chr7	73310945	73310956	-	1	NA	non-coding (NR_105062, exon 1 of 3)	non-coding (NR_105062, exon 1 of 3)	570	NR_105062	100505025	Mm.445959	NR_105062	ENSMUSG00000108530	LOC100505025	-	uncharacterized LOC100505025	ncRNA
mm_20501.1	chr2	130424243	130424293	-	1	NA	promoter-TSS (NM_178762)	promoter-TSS (NM_178762)	20	NM_178762	319513	Mm.482539	NM_178762	ENSMUSG00000037773	Pced1a	A930025D01Rik|AI480484|Fam113a	PC-esterase domain containing 1A	protein-coding
mm_58591.1	chr7	5015467	5015509	+	1	NA	promoter-TSS (NM_001110329)	promoter-TSS (NM_001110329)	-20	NM_025324	66056	Mm.19974	NM_025324	ENSMUSG00000051184	Zfp524	0610012F07Rik|2300009P13Rik|Znf524	zinc finger protein 524	protein-coding
mm_79383.1	chr9	54772869	54772877	+	1	NA	exon (NM_001284507, exon 3 of 3)	exon (NM_001284507, exon 3 of 3)	8125	NM_013496	12903	Mm.34797	NM_013496	ENSMUSG00000032291	Crabp1	AI326249|CRABP-I|Crabp-1|CrabpI|Rbp-5	cellular retinoic acid binding protein I	protein-coding
mm_127893.1	chr15	9155382	9155398	-	1	NA	promoter-TSS (NM_001285980)	promoter-TSS (NM_001285980)	35	NM_001285980	27401	Mm.35584	NM_013787	ENSMUSG00000054115	Skp2	4930500A04Rik|FBXL1|FWD1|p45	S-phase kinase-associated protein 2 (p45)	protein-coding
mm_14228.1	chr2	127483628	127483633	+	1	NA	intron (NM_019789, intron 2 of 8)	intron (NM_019789, intron 2 of 8)	-1131	NM_001111331	56461	Mm.315292	NM_019789	ENSMUSG00000079056	Kcnip3	4933407H12Rik|AI413860|Csen|DREAM|KChIP3|R74849	Kv channel interacting protein 3, calsenilin	protein-coding
mm_11627.1	chr2	34775144	34775199	+	1	NA	exon (NM_001163434, exon 8 of 9)	exon (NM_001163434, exon 8 of 9)	3081	NM_022310	14828	Mm.330160	NM_022310	ENSMUSG00000026864	Hspa5	AL022860|AU019543|Bip|D2Wsu141e|D2Wsu17e|Grp78|Hsce70|SEZ-7|Sez7|baffled|mBiP	heat shock protein 5	protein-coding
mm_97515.1	chr11	78499760	78499778	+	1	NA	exon (NM_011707, exon 3 of 8)	exon (NM_011707, exon 3 of 8)	649	NM_011707	22370	Mm.3667	NM_011707	ENSMUSG00000017344	Vtn	AI256434|Vn	vitronectin	protein-coding
mm_156577.1	chrX	152016436	152016518	+	1	NA	promoter-TSS (NM_025660)	promoter-TSS (NM_025660)	49	NM_019710	24061	Mm.482095	NM_019710	ENSMUSG00000041133	Smc1a	5830426I24Rik|SMC-1A|Sb1.8|Smc1|Smc1alpha|Smc1l1|Smcb|mKIAA0178	structural maintenance of chromosomes 1A	protein-coding
mm_122969.1	chr14	54974231	54974266	-	1	NA	non-coding (NR_033497, exon 5 of 5)	non-coding (NR_033497, exon 5 of 5)	1528	NR_030607	100124433		NR_030607	ENSMUSG00000077928	Mir208b	Mirn208b|mir-208b	microRNA 208b	ncRNA
mm_125476.1	chr15	54571180	54571213	+	1	NA	promoter-TSS (NM_178920)	promoter-TSS (NM_178920)	-170	NM_178920	105853	Mm.410994	NM_178920	ENSMUSG00000024479	Mal2	AI461653	mal, T cell differentiation protein 2	protein-coding
mm_89810.1	chr10	103367653	103367669	+	1	NA	promoter-TSS (NM_175328)	promoter-TSS (NM_175328)	-147	NM_001252330	103098	Mm.458408	NM_175328	ENSMUSG00000019894	Slc6a15	AA536730|AI326450|AI326451|v7-3	solute carrier family 6 (neurotransmitter transporter), member 15	protein-coding
mm_30661.1	chr4	9770626	9770689	+	1	NA	promoter-TSS (NR_030693)	promoter-TSS (NR_030693)	72	NR_030693	320152	Mm.159946	NR_030693		4930412C18Rik	5730591J02Rik	RIKEN cDNA 4930412C18 gene	ncRNA
mm_43956.1	chr5	145233180	145233186	+	1	NA	intron (NM_001347533, intron 1 of 2)	AT_rich|Low_complexity|Low_complexity	1424	NM_028298	72611	Mm.206555	NM_028298	ENSMUSG00000007812	Zfp655	2700038I16Rik|9030409O18Rik|mKIAA4222	zinc finger protein 655	protein-coding
mm_166318.1	chr5	110447968	110447969	+	1	NA	exon (NM_001142642, exon 1 of 19)	exon (NM_001142642, exon 1 of 19)	535	NM_001317042	381668	Mm.348782	NM_028596	ENSMUSG00000043323	Fbrsl1	2410025L10Rik|AI467568|Gm1049|Gm29766|mKIAA1545	fibrosin-like 1	protein-coding
mm_34006.1	chr4	137939370	137939375	+	1	NA	intron (NM_199307, intron 9 of 19)	ID_B1|SINE|B4	-54084	NM_001256198	230861	Mm.268903	NM_172703	ENSMUSG00000028760	Eif4g3	1500002J22Rik|4930523M17Rik|G1-419-52|eIF4GII|repro8	eukaryotic translation initiation factor 4 gamma, 3	protein-coding
mm_47345.1	chr5	122560704	122560716	-	1	NA	exon (NM_009879, exon 15 of 19)	exon (NM_009879, exon 15 of 19)	53808	NM_009879	12589	Mm.10125	NM_009879	ENSMUSG00000029469	Ift81	AW060663|Cdv-1|Cdv-1r|Cdv1	intraflagellar transport 81	protein-coding
mm_34732.1	chr4	152186055	152186094	+	1	NA	promoter-TSS (NM_001146057)	promoter-TSS (NM_001146057)	-60	NM_001146057	70025	Mm.296191	NM_133348	ENSMUSG00000028937	Acot7	2410041A17Rik|Ach1|Act|Bach|CTE-IIa|Cte-II|Lach1	acyl-CoA thioesterase 7	protein-coding
mm_71776.1	chr8	66471511	66471539	+	1	NA	3' UTR (NM_001293784, exon 9 of 9)	3' UTR (NM_001293784, exon 9 of 9)	14982	NM_025465	66282	Mm.294985	NM_025465	ENSMUSG00000025591	Tma16	1810029B16Rik	translation machinery associated 16	protein-coding
mm_112982.1	chr13	21317255	21317261	+	1	NA	intron (NM_145451, intron 3 of 4)	intron (NM_145451, intron 3 of 4)	5055	NM_145451	75512	Mm.46195	NM_145451	ENSMUSG00000004341	Gpx6	1700020G18Rik|Ry2d1|olfactory	glutathione peroxidase 6	protein-coding
mm_172587.1	chr8	123961589	123961595	-	1	NA	intron (NM_019552, intron 8 of 12)	(CCCTAA)n|Simple_repeat|Simple_repeat	-12327	NM_172288	234865	Mm.267812	NM_172288	ENSMUSG00000039509	Nup133	mermaid	nucleoporin 133	protein-coding
mm_88590.1	chr10	79716589	79716666	+	1	NA	promoter-TSS (NM_008226)	promoter-TSS (NM_008226)	-7	NM_008226	15166	Mm.12956	NM_008226	ENSMUSG00000020331	Hcn2	BCNG2|HAC1|trls	hyperpolarization-activated, cyclic nucleotide-gated K+ 2	protein-coding
mm_99030.1	chr11	98943474	98943505	+	1	NA	intron (NM_001177303, intron 1 of 8)	intron (NM_001177303, intron 1 of 8)	3778	NM_001177303	19401	Mm.439744	NM_009024	ENSMUSG00000037992	Rara	Nr1b1|RAR|RARalpha1	retinoic acid receptor, alpha	protein-coding
mm_105802.1	chr11	110190777	110190777	-	1	NA	intron (NM_147218, intron 26 of 38)	intron (NM_147218, intron 26 of 38)	-22624	NM_147220	217262	Mm.291459	NM_147220	ENSMUSG00000041797	Abca9	D630040K07Rik	ATP-binding cassette, sub-family A (ABC1), member 9	protein-coding
mm_57260.1	chr6	123285465	123285473	-	1	NA	exon (NM_019948, exon 5 of 6)	exon (NM_019948, exon 5 of 6)	4402	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_108128.1	chr12	76005210	76005249	+	1	NA	intron (NM_001005510, intron 62 of 115)	intron (NM_001005510, intron 62 of 115)	96126	NR_039560	100628610		NR_039560	ENSMUSG00000092922	Mir5101	mmu-mir-5101|mu-mir-5101	microRNA 5101	ncRNA
mm_170336.1	chr18	45161681	45161687	+	1	NA	Intergenic	L1Md_F2|LINE|L1	-107176	NM_001312905	140492	Mm.411614	NM_080465	ENSMUSG00000054477	Kcnn2	KCa2.2|SK2|SKCA2|bc|fri	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2	protein-coding
mm_13153.1	chr2	92422860	92422893	+	1	NA	non-coding (NR_040621, exon 3 of 4)	non-coding (NR_040621, exon 3 of 4)	11193	NM_009963	12953	Mm.254181	NM_009963	ENSMUSG00000068742	Cry2	AV006279|D130054K12Rik	cryptochrome 2 (photolyase-like)	protein-coding
mm_172043.1	chr6	127561311	127561311	+	1	NA	Intergenic	CpG	-16664	NM_001033464	381812	Mm.296093	NM_001033464	ENSMUSG00000061414	Cracr2a	Efcab4b|Gm1073|Gm462	calcium release activated channel regulator 2A	protein-coding
mm_39278.1	chr5	3909311	3909321	+	1	NA	Intergenic	Intergenic	-15383	NM_172135	545725	Mm.99593	NM_172135	ENSMUSG00000040429	Mterf1a	4931431L11Rik|9230106K09Rik|Mterf|Mterf1|mTERF1b	mitochondrial transcription termination factor 1a	protein-coding
mm_47326.1	chr5	122486289	122486309	-	1	NA	intron (NM_001110140, intron 5 of 19)	intron (NM_001110140, intron 5 of 19)	15926	NM_001110140	11938	Mm.227583	NM_009722	ENSMUSG00000029467	Atp2a2	9530097L16Rik|D5Wsu150e|SERCA2|SERCA2B|Serca2a|mKIAA4195	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	protein-coding
mm_48935.1	chr6	4537991	4538010	+	1	NA	exon (NM_007743, exon 49 of 52)	exon (NM_007743, exon 49 of 52)	32382	NM_007743	12843	Mm.277792	NM_007743	ENSMUSG00000029661	Col1a2	AA960264|AI325291|Col1a-2|Cola-2|Cola2|oim	collagen, type I, alpha 2	protein-coding
mm_154700.1	chrX	8271474	8271484	+	1	NA	promoter-TSS (NM_172479)	promoter-TSS (NM_172479)	98	NM_172479	209837	Mm.6055	NM_172479	ENSMUSG00000031170	Slc38a5	C81234|E330031E14|JM24|SN2	solute carrier family 38, member 5	protein-coding
mm_65353.1	chr7	24998699	24998734	-	1	NA	exon (NM_001290469, exon 6 of 23)	exon (NM_001290469, exon 6 of 23)	7221	NM_001290469	232975	Mm.44101	NM_144921	ENSMUSG00000040907	Atp1a3	Atpa-2	ATPase, Na+/K+ transporting, alpha 3 polypeptide	protein-coding
mm_85198.1	chr9	96732218	96732230	-	1	NA	promoter-TSS (NM_175537)	promoter-TSS (NM_175537)	-549	NM_175537	245007	Mm.485954	NM_175537	ENSMUSG00000040433	Zbtb38	A930014K01Rik|CIBZ	zinc finger and BTB domain containing 38	protein-coding
mm_91549.1	chr10	39752902	39752917	-	1	NA	intron (NM_011264, intron 1 of 31)	intron (NM_011264, intron 1 of 31)	20749	NM_011264	19714	Mm.439723	NM_011264	ENSMUSG00000019841	Rev3l	Rev|Rev3|Sez4	REV3 like, DNA directed polymerase zeta catalytic subunit	protein-coding
mm_48037.1	chr5	136302502	136302511	-	1	NA	intron (NM_001291233, intron 20 of 23)	intron (NM_001291233, intron 20 of 23)	-57566	NM_018825	23921	Mm.425294	NM_018825	ENSMUSG00000005057	Sh2b2	Aps	SH2B adaptor protein 2	protein-coding
mm_85421.1	chr9	103480367	103480373	-	1	NA	promoter-TSS (NM_001002896)	promoter-TSS (NM_001002896)	-42	NM_001002896	107993	Mm.335403	NM_001002896	ENSMUSG00000032556	Bfsp2	AI448593|CP49	beaded filament structural protein 2, phakinin	protein-coding
mm_52356.1	chr6	112459716	112459749	+	1	NA	5' UTR (NM_007617, exon 1 of 2)	5' UTR (NM_007617, exon 1 of 2)	227	NM_007617	12391	Mm.3924	NM_007617	ENSMUSG00000062694	Cav3	AI385751|Cav-3|M-cav	caveolin 3	protein-coding
mm_53377.1	chr6	129486589	129486602	+	1	NA	3' UTR (NM_138648, exon 8 of 8)	3' UTR (NM_138648, exon 8 of 8)	-13816	NR_132130	56644	Mm.239516	NM_020008	ENSMUSG00000079293	Clec7a	BGR|Clecsf12|beta-GR	C-type lectin domain family 7, member a	protein-coding
mm_37644.1	chr4	128618573	128618597	-	1	NA	promoter-TSS (NM_205823)	promoter-TSS (NM_205823)	34	NM_205823	384059	Mm.331901	NM_205823	ENSMUSG00000062545	Tlr12	Gm1365|Tlr11	toll-like receptor 12	protein-coding
mm_38741.1	chr4	145254437	145254460	-	1	NA	Intergenic	Intergenic	-7578	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_37701.1	chr4	129374286	129374327	-	1	NA	intron (NM_028603, intron 1 of 4)	RLTR28B|LTR|ERVL	3722	NM_028603	73680	Mm.32997	NM_028603	ENSMUSG00000028807	Zbtb8a	2410081M15Rik|AI480941	zinc finger and BTB domain containing 8a	protein-coding
mm_116710.1	chr13	51567751	51567773	-	1	NA	promoter-TSS (NM_009167)	promoter-TSS (NM_009167)	-678	NM_009167	20418	Mm.131870	NM_009167	ENSMUSG00000021448	Shc3	N-Shc|Rai|ShcC	src homology 2 domain-containing transforming protein C3	protein-coding
mm_143817.1	chr17	83846730	83846742	-	1	NA	promoter-TSS (NM_025325)	promoter-TSS (NM_025325)	54	NM_025325	107766	Mm.30100	NM_025325	ENSMUSG00000000673	Haao	0610007K21Rik|0610012J07Rik|3-HAO|3-HAOxase|3HAO	3-hydroxyanthranilate 3,4-dioxygenase	protein-coding
mm_168084.1	chr10	12386074	12386074	+	1	NA	intron (NM_011682, intron 72 of 73)	L1Md_T|LINE|L1	475661	NM_011682	22288	Mm.331784	NM_011682	ENSMUSG00000019820	Utrn	AA589569|DRP|Dmdl	utrophin	protein-coding
mm_12354.1	chr2	69749568	69749586	+	1	NA	exon (NM_001081086, exon 14 of 14)	exon (NM_001081086, exon 14 of 14)	26489	NM_001081086	228005	Mm.11815	NM_001081086	ENSMUSG00000042133	Ppig	AU019516|AU022200|B230312B02Rik|CYP|SRCyp	peptidyl-prolyl isomerase G (cyclophilin G)	protein-coding
mm_27056.1	chr3	27556154	27556168	-	1	NA	exon (NM_173182, exon 4 of 26)	exon (NM_173182, exon 4 of 26)	28834	NR_037275	100526525		NR_037275	ENSMUSG00000092695	Mir3092	mir-3092|mmu-mir-3092	microRNA 3092	ncRNA
mm_60142.1	chr7	38183225	38183278	+	1	NA	promoter-TSS (NM_028166)	promoter-TSS (NM_028166)	34	NM_001085385	72244	Mm.187554	NM_028166		1600014C10Rik	AI428873	RIKEN cDNA 1600014C10 gene	protein-coding
mm_117710.1	chr13	95223046	95223080	-	1	NA	promoter-TSS (NM_001170669)	promoter-TSS (NM_001170669)	-13	NM_001170669	218461	Mm.100167	NM_172263	ENSMUSG00000021684	Pde8b	B230331L10Rik|C030047E14Rik	phosphodiesterase 8B	protein-coding
mm_23666.1	chr3	68496121	68496122	+	1	NA	intron (NM_001113419, intron 5 of 10)	intron (NM_001113419, intron 5 of 10)	1940	NM_001282044	30953	Mm.331064	NM_013928	ENSMUSG00000027777	Schip1	Nf2ip|Schip-1	schwannomin interacting protein 1	protein-coding
mm_84850.1	chr9	78479049	78479068	-	1	NA	exon (NM_010106, exon 7 of 8)	exon (NM_010106, exon 7 of 8)	2666	NM_010106	13627	Mm.138471	NM_010106	ENSMUSG00000037742	Eef1a1	-	eukaryotic translation elongation factor 1 alpha 1	protein-coding
mm_107814.1	chr12	65225484	65225494	+	1	NA	promoter-TSS (NM_027614)	promoter-TSS (NM_027614)	-28	NM_027614	70948	Mm.219475	NM_027614	ENSMUSG00000035560	Wdr20rt	4921538B03Rik|4930427E19Rik|Wdr20|Wdr20b	WD repeat domain 20, retrogene	protein-coding
mm_74408.1	chr8	3621284	3621323	-	1	NA	promoter-TSS (NM_026156)	promoter-TSS (NM_026156)	-7	NM_026156	67439	Mm.23739	NM_026156	ENSMUSG00000019470	Xab2	0610041O14Rik|AV025587	XPA binding protein 2	protein-coding
mm_122528.1	chr14	47380408	47380423	-	1	NA	exon (NM_010705, exon 3 of 6)	exon (NM_010705, exon 3 of 6)	6555	NM_001145953	16854	Mm.248615	NM_010705	ENSMUSG00000050335	Lgals3	GBP|L-34|Mac-2|gal3	lectin, galactose binding, soluble 3	protein-coding
mm_112256.1	chr12	113839030	113839045	-	1	NA	Intergenic	Intergenic	295129	NM_174885	238406	Mm.188683	NM_174885	ENSMUSG00000043945	Adam6a	Adam6|tMDCIV	a disintegrin and metallopeptidase domain 6A	protein-coding
mm_90036.1	chr10	115570042	115570055	+	1	NA	promoter-TSS (NM_029982)	promoter-TSS (NM_029982)	62	NM_029982	77798	Mm.446685	NM_029982	ENSMUSG00000092210	A930009A15Rik	-	RIKEN cDNA A930009A15 gene	protein-coding
mm_170424.1	chr18	72507060	72507060	+	1	NA	Intergenic	L1Md_T|LINE|L1	-155991	NM_007831	13176	Mm.167882	NM_007831	ENSMUSG00000060534	Dcc	C030036D22Rik|Igdcc1	deleted in colorectal carcinoma	protein-coding
mm_101866.1	chr11	48891541	48891565	-	1	NA	intron (NM_001024230, intron 4 of 4)	RMER17C|LTR|ERVK	10599	NM_001024230	432555	Mm.338931	NM_001024230	ENSMUSG00000058163	Gm5431	EG432555|Irgb9b8	predicted gene 5431	protein-coding
mm_117755.1	chr13	95961578	95961587	-	1	NA	intron (NM_029210, intron 12 of 12)	intron (NM_029210, intron 12 of 12)	-69660	NM_027711	544963	Mm.38878	NM_027711	ENSMUSG00000021676	Iqgap2	4933417J23Rik|A630053O10|AI788777	IQ motif containing GTPase activating protein 2	protein-coding
mm_128108.1	chr15	28024458	28024473	-	1	NA	intron (NM_001081302, intron 1 of 56)	CpG	1383	NM_001081302	223435	Mm.485422	NM_001081302	ENSMUSG00000022263	Trio	6720464I07Rik|AA408740|Solo	triple functional domain (PTPRF interacting)	protein-coding
mm_62685.1	chr7	110018302	110018326	+	1	NA	promoter-TSS (NM_181517)	promoter-TSS (NM_181517)	-111	NM_181517	233726	Mm.222328	NM_181517	ENSMUSG00000066232	Ipo7	A330055O14Rik|C330016G14|Imp7|Ranbp7	importin 7	protein-coding
mm_99985.1	chr11	114702546	114702549	+	1	NA	intron (NM_053273, intron 6 of 13)	intron (NM_053273, intron 6 of 13)	-24865	NM_001034878	432611	Mm.212764	NM_001034878	ENSMUSG00000034706	Dnaic2	C030015H18Rik|Dnai2|Gm728	dynein, axonemal, intermediate chain 2	protein-coding
mm_33350.1	chr4	129375329	129375346	+	1	NA	intron (NM_028603, intron 1 of 4)	MLT1A1|LTR|ERVL-MaLR	2691	NM_028603	73680	Mm.32997	NM_028603	ENSMUSG00000028807	Zbtb8a	2410081M15Rik|AI480941	zinc finger and BTB domain containing 8a	protein-coding
mm_8346.1	chr1	150197192	150197210	-	1	NA	Intergenic	Lx|LINE|L1	-32253	NR_110420	102639566	Mm.417208	NR_110420	ENSMUSG00000097754	Ptgs2os2	Gm26687|Linc-cox2|Lincrna-cox2	prostaglandin-endoperoxide synthase 2, opposite strand 2	ncRNA
mm_96331.1	chr11	65159958	65159984	+	1	NA	intron (NM_175003, intron 1 of 20)	intron (NM_175003, intron 1 of 20)	2990	NM_001099288	216831	Mm.134338	NM_175003	ENSMUSG00000033389	Arhgap44	6330543G20|AI840762|AU040829|AW493732|Rich2	Rho GTPase activating protein 44	protein-coding
mm_169605.1	chr15	36760427	36760432	+	1	NA	Intergenic	BGLII|LTR|ERVK	30503	NM_001253807	22631	Mm.3360	NM_011740	ENSMUSG00000022285	Ywhaz	1110013I11Rik|14-3-3zeta|AI596267|AL022924|AU020854	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide	protein-coding
mm_34200.1	chr4	140721169	140721193	+	1	NA	exon (NM_173867, exon 13 of 13)	exon (NM_173867, exon 13 of 13)	19708	NM_173867	108911	Mm.253	NM_173867	ENSMUSG00000040945	Rcc2	2610510H01Rik|2610529N02Rik|AA536646|AA675016|Td60|mKIAA1470	regulator of chromosome condensation 2	protein-coding
mm_47626.1	chr5	125283938	125283954	-	1	NA	exon (NM_001205082, exon 11 of 12)	exon (NM_001205082, exon 11 of 12)	57148	NM_016741	20778	Mm.282242	NM_016741	ENSMUSG00000037936	Scarb1	AI120173|CD36|Cd36l1|Chohd1|Cla-1|Cla1|D5Ertd460e|Hdlq1|Hlb398|SR-B1|SR-BI|SRBI|Srb1|mSR-BI	scavenger receptor class B, member 1	protein-coding
mm_128526.1	chr15	54818985	54818987	-	1	NA	Intergenic	RLTR31D_MM|LTR|ERVK	73058	NM_010930	18133	Mm.5167	NM_010930	ENSMUSG00000037362	Nov	C130088N23Rik|CCN3	nephroblastoma overexpressed gene	protein-coding
mm_164035.1	chr14	79703739	79703749	+	1	NA	intron (NR_045060, intron 1 of 3)	intron (NR_045060, intron 1 of 3)	824	NR_045060	73989	Mm.107775	NR_045060		4930452G13Rik	-	RIKEN cDNA 4930452G13 gene	ncRNA
mm_6487.1	chr1	74108373	74108381	-	1	NA	intron (NM_027884, intron 1 of 34)	intron (NM_027884, intron 1 of 34)	16070	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_62697.1	chr7	110122720	110122778	+	1	NA	exon (NM_009516, exon 1 of 11)	exon (NM_009516, exon 1 of 11)	690	NM_009516	22390	Mm.287173	NM_009516	ENSMUSG00000031016	Wee1	Wee1A	WEE 1 homolog 1 (S. pombe)	protein-coding
mm_154574.1	chrX	7068209	7068219	+	1	NA	promoter-TSS (NM_001042542)	promoter-TSS (NM_001042542)	4	NM_001042542	11643	Mm.1498	NM_009651	ENSMUSG00000050089	Akap4	AKAP-4|AKAP82|Fsc1|PRKA4|mAKAP82|p82	A kinase (PRKA) anchor protein 4	protein-coding
mm_169097.1	chr1	34113900	34113901	+	1	NA	intron (NM_001276764, intron 5 of 102)	intron (NM_001276764, intron 5 of 102)	-3459	NR_105861	102466987		NR_105861	ENSMUSG00000105982	Mir6896	mmu-mir-6896	microRNA 6896	ncRNA
mm_1722.1	chr1	75362016	75362044	+	1	NA	intron (NM_010043, intron 1 of 8)	intron (NM_010043, intron 1 of 8)	1738	NM_010043	13346	Mm.6712	NM_010043	ENSMUSG00000026208	Des	-	desmin	protein-coding
mm_45396.1	chr5	66151392	66151400	-	1	NA	promoter-TSS (NM_001291226)	promoter-TSS (NM_001291226)	-418	NM_178446	245945	Mm.36863	NM_139065	ENSMUSG00000070780	Rbm47	9530077J19Rik	RNA binding motif protein 47	protein-coding
mm_62771.1	chr7	112342400	112342403	+	1	NA	intron (NM_001193305, intron 21 of 25)	intron (NM_001193305, intron 21 of 25)	-25907	NM_027587	100504195	Mm.291129	NM_027587	ENSMUSG00000030771	Micalcl	4921517J23Rik	MICAL C-terminal like	protein-coding
mm_50024.1	chr6	41121324	41121334	+	1	NA	Intergenic	Intergenic	-85820	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_14391.1	chr2	129800712	129800728	+	1	NA	exon (NM_183262, exon 1 of 4)	exon (NM_183262, exon 1 of 4)	203	NM_001038635	67333	Mm.389329	NM_183262	ENSMUSG00000037885	Stk35	1700054C12Rik|CLIK1|Stk35l1	serine/threonine kinase 35	protein-coding
mm_91998.1	chr10	62190861	62190873	-	1	NA	intron (NM_197996, intron 5 of 7)	intron (NM_197996, intron 5 of 7)	3360	NR_106122	102465767		NR_106122	ENSMUSG00000099185	Mir7662	Gm27876|mmu-mir-7662	microRNA 7662	ncRNA
mm_39479.1	chr5	20677681	20677687	+	1	NA	intron (NM_001170746, intron 22 of 22)	intron (NM_001170746, intron 22 of 22)	204440	NM_172992	68770	Mm.86410	NM_172992	ENSMUSG00000039987	Phtf2	1110054G21Rik|9530062N20Rik|AI447096|C77923	putative homeodomain transcription factor 2	protein-coding
mm_62845.1	chr7	114291612	114291626	+	1	NA	Intergenic	Intergenic	-15503	NM_011965	26440	Mm.121265	NM_011965	ENSMUSG00000030751	Psma1	C2|HC2|Pros-30|alpha-type	proteasome (prosome, macropain) subunit, alpha type 1	protein-coding
mm_130564.1	chr15	99370428	99370489	-	1	NA	promoter-TSS (NM_011711)	promoter-TSS (NM_011711)	24	NM_001310623	22379	Mm.29043	NM_011711	ENSMUSG00000023008	Fmnl3	2700073B04Rik|FBP11|Wbp3|mKIAA2014	formin-like 3	protein-coding
mm_78621.1	chr9	37613807	37613858	+	1	NA	promoter-TSS (NM_011734)	promoter-TSS (NM_011734)	-15	NM_011734	22619	Mm.196345	NM_011734	ENSMUSG00000001942	Siae	LSE|Ysg2	sialic acid acetylesterase	protein-coding
mm_6813.1	chr1	84158264	84158273	-	1	NA	intron (NM_001003948, intron 2 of 2)	AT_rich|Low_complexity|Low_complexity	60693	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_149589.1	chr19	16133123	16133145	+	1	NA	5' UTR (NM_008139, exon 1 of 7)	5' UTR (NM_008139, exon 1 of 7)	303	NM_008139	14682	Mm.439701	NM_008139	ENSMUSG00000024639	Gnaq	1110005L02Rik|6230401I02Rik|AA408290|AW060788|Dsk1|Dsk10|Galphaq|Gq|GqI	guanine nucleotide binding protein, alpha q polypeptide	protein-coding
mm_75517.1	chr8	54724318	54724373	-	1	NA	promoter-TSS (NM_001172152)	promoter-TSS (NM_001172152)	23	NM_001172152	244484	Mm.95281	NM_028220	ENSMUSG00000039375	Wdr17	3010002I12Rik|B230207L18Rik	WD repeat domain 17	protein-coding
mm_407.1	chr1	34197240	34197254	+	1	NA	exon (NM_134448, exon 41 of 98)	exon (NM_134448, exon 41 of 98)	36917	NM_010081	13518	Mm.336625	NM_010081	ENSMUSG00000026131	Dst	2310001O04Rik|A830042E19Rik|AW554249|BP230|BPAG1-n|Bpag|Bpag1|Macf2|ah|athetoid|dt|mKIAA0728|nmf203|nmf339	dystonin	protein-coding
mm_149283.1	chr19	10622338	10622386	+	1	NA	exon (NM_015735, exon 16 of 27)	exon (NM_015735, exon 16 of 27)	-11871	NM_027913	71768	Mm.169261	NM_027913	ENSMUSG00000043789	Vwce	1300015B04Rik	von Willebrand factor C and EGF domains	protein-coding
mm_69913.1	chr7	141692694	141692703	-	1	NA	exon (NM_023566, exon 3 of 46)	exon (NM_023566, exon 3 of 46)	2358	NM_023566	17831	Mm.2041	NM_023566		Muc2	2010015E03Rik|MCM|wnn	mucin 2	protein-coding
mm_162871.1	chr10	95409030	95409032	+	1	NA	Intergenic	Intergenic	6252	NM_001168657	216233	Mm.474283	NM_007706	ENSMUSG00000020027	Socs2	8030460M17|AI527257|AW108012|CIS2|Cish2|D130043N08Rik|JAB|SOCS-2|SSI-2|hg	suppressor of cytokine signaling 2	protein-coding
mm_134605.1	chr16	20701857	20701867	-	1	NA	exon (NM_133778, exon 6 of 6)	exon (NM_133778, exon 6 of 6)	6805	NM_133778	78408	Mm.196512	NM_133778	ENSMUSG00000050821	Fam131a	2900046G09Rik	family with sequence similarity 131, member A	protein-coding
mm_128845.1	chr15	71671422	71671441	-	1	NA	intron (NM_177819, intron 1 of 19)	intron (NM_177819, intron 1 of 19)	56407	NM_177819	70363	Mm.126450	NM_177819	ENSMUSG00000036800	Fam135b	1700010C24Rik|A830008O07Rik	family with sequence similarity 135, member B	protein-coding
mm_85163.1	chr9	96364408	96364425	-	1	NA	promoter-TSS (NM_007502)	promoter-TSS (NM_007502)	-117	NM_007502	11933	Mm.424	NM_007502	ENSMUSG00000032412	Atp1b3	AA409958|AI664000|AW212096	ATPase, Na+/K+ transporting, beta 3 polypeptide	protein-coding
mm_99486.1	chr11	102665567	102665595	+	1	NA	promoter-TSS (NM_001127576)	promoter-TSS (NM_001127576)	-4	NM_001127576	268491	Mm.447643	NM_001127576	ENSMUSG00000051455	Meioc	Gm1564|Gm663	meiosis specific with coiled-coil domain	protein-coding
mm_81151.1	chr9	106892477	106892487	+	1	NA	promoter-TSS (NM_029103)	promoter-TSS (NM_029103)	-544	NM_029103	74840	Mm.29778	NM_029103	ENSMUSG00000032575	Manf	3230402M22Rik|AA407711|AA408789|AA673178|Armet|D17914|D18Mgi17	mesencephalic astrocyte-derived neurotrophic factor	protein-coding
mm_75864.1	chr8	70760846	70760854	-	1	NA	promoter-TSS (NM_183170)	promoter-TSS (NM_183170)	71	NM_183170	234384	Mm.213010	NM_183170	ENSMUSG00000035559	Mpv17l2	Fksg24	MPV17 mitochondrial membrane protein-like 2	protein-coding
mm_166347.1	chr5	119670713	119670721	+	1	NA	promoter-TSS (NM_011535)	promoter-TSS (NM_011535)	-145	NM_198052	21386	Mm.219139	NM_011535	ENSMUSG00000018604	Tbx3	D5Ertd189e	T-box 3	protein-coding
mm_59966.1	chr7	30428387	30428397	+	1	NA	3' UTR (NM_172142, exon 11 of 11)	3' UTR (NM_172142, exon 11 of 11)	5088	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_37336.1	chr4	119656767	119656777	-	1	NA	3' UTR (NM_008191, exon 3 of 3)	3' UTR (NM_008191, exon 3 of 3)	2173	NM_008191	14916	Mm.278	NM_008191	ENSMUSG00000032978	Guca2b	AV066530|Gcap2|Ugn	guanylate cyclase activator 2b (retina)	protein-coding
mm_167404.1	chr8	104101599	104101613	+	1	NA	promoter-TSS (NM_009868)	promoter-TSS (NM_009868)	-19	NM_009868	12562	Mm.21767	NM_009868	ENSMUSG00000031871	Cdh5	7B4|AA408225|Cd144|VE-Cad|VECD|VEcad|Vec	cadherin 5	protein-coding
mm_155275.1	chrX	61120296	61120310	+	1	NA	intron (NR_030706, intron 4 of 7)	intron (NR_030706, intron 4 of 7)	3925	NR_030706	331424	Mm.127263	NM_177916	ENSMUSG00000071753	C230004F18Rik	-	RIKEN cDNA C230004F18 gene	ncRNA
mm_130605.1	chr15	99819933	99819939	-	1	NA	exon (NM_001113545, exon 4 of 11)	exon (NM_001113545, exon 4 of 11)	213	NM_023063	65970	Mm.33207	NM_023063	ENSMUSG00000023022	Lima1	Eplin	LIM domain and actin binding 1	protein-coding
mm_110587.1	chr12	56529457	56529463	-	1	NA	promoter-TSS (NR_045082)	promoter-TSS (NR_045082)	-40	NR_045082	104798	Mm.310950	NR_045082		E030019B13Rik	AI413669	RIKEN cDNA E030019B13 gene	ncRNA
mm_93031.1	chr10	88146805	88146820	-	1	NA	promoter-TSS (NM_027191)	promoter-TSS (NM_027191)	129	NM_029249	75317	Mm.179378	NM_029249	ENSMUSG00000035365	Parpbp	4930547N16Rik|AI503644|PARI	PARP1 binding protein	protein-coding
mm_44871.1	chr5	34513893	34513984	-	1	NA	promoter-TSS (NM_139064)	promoter-TSS (NM_139064)	41	NM_139064	231130	Mm.28615	NM_139064	ENSMUSG00000059866	Tnip2	1810020H16Rik|ABIN-2|AI428870	TNFAIP3 interacting protein 2	protein-coding
mm_115153.1	chr13	106260623	106260627	+	1	NA	Intergenic	U2|snRNA|snRNA	676290	NM_029665	76582	Mm.132208	NM_029665	ENSMUSG00000042590	Ipo11	1700081H05Rik|2510001A17Rik|AI314624|AW555235|E330021B14Rik|Ranbp11	importin 11	protein-coding
mm_118996.1	chr14	28509791	28509820	+	1	NA	intron (NM_009524, intron 1 of 4)	intron (NM_009524, intron 1 of 4)	-1600	NM_001256224	22418	Mm.287544	NM_009524	ENSMUSG00000021994	Wnt5a	8030457G12Rik|Wnt-5a	wingless-type MMTV integration site family, member 5A	protein-coding
mm_116999.1	chr13	56753815	56753854	-	1	NA	Intergenic	Intergenic	50166	NM_001164042	17129	Mm.272920	NM_008541	ENSMUSG00000021540	Smad5	1110051M15Rik|AI451355|Dwf-C|Madh5|MusMLP	SMAD family member 5	protein-coding
mm_113026.1	chr13	23260916	23260919	+	1	NA	Intergenic	RLTR10C|LTR|ERVK	11679	NM_001083311	100036518	Mm.455332	NM_001083311	ENSMUSG00000069280	Vmn1r223	Gm11330|OTTMUSG00000000541	vomeronasal 1 receptor 223	protein-coding
mm_2477.1	chr1	105845254	105845264	+	1	NA	3' UTR (NM_009399, exon 10 of 10)	3' UTR (NM_009399, exon 10 of 10)	64536	NM_009399	21934	Mm.6251	NM_009399	ENSMUSG00000026321	Tnfrsf11a	Ly109|ODFR|OFE|Rank|TRANCE-R|mRANK	tumor necrosis factor receptor superfamily, member 11a, NFKB activator	protein-coding
mm_23524.1	chr3	60617381	60617403	+	1	NA	intron (NM_001310514, intron 7 of 8)	intron (NM_001310514, intron 7 of 8)	116213	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_83624.1	chr9	48836202	48836259	-	1	NA	promoter-TSS (NM_001033324)	promoter-TSS (NM_001033324)	-285	NM_001033324	235320	Mm.457803	NM_001033324	ENSMUSG00000066687	Zbtb16	AI467657|PLZF|Zfp145|lu	zinc finger and BTB domain containing 16	protein-coding
mm_26064.1	chr3	135826424	135826449	+	1	NA	5' UTR (NM_001135150, exon 2 of 9)	5' UTR (NM_001135150, exon 2 of 9)	646	NM_001135150	67547	Mm.30239	NM_026228	ENSMUSG00000053897	Slc39a8	4933419D20Rik|AA986696|BIGM103|ZIP-8|Zip8	solute carrier family 39 (metal ion transporter), member 8	protein-coding
mm_87120.1	chr10	33257096	33257110	+	1	NA	promoter-TSS (NR_040657)	promoter-TSS (NR_040657)	-746	NR_040657	442820	Mm.490725	NR_040657		D830005E20Rik	-	RIKEN cDNA D830005E20 gene	ncRNA
mm_30899.1	chr4	32335964	32335974	+	1	NA	Intergenic	Intergenic	-81466	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_19877.1	chr2	114049245	114049305	-	1	NA	exon (NM_009608, exon 5 of 7)	exon (NM_009608, exon 5 of 7)	3600	NM_009608	11464	Mm.686	NM_009608	ENSMUSG00000068614	Actc1	Actc-1	actin, alpha, cardiac muscle 1	protein-coding
mm_123762.1	chr14	70206039	70206060	-	1	NA	promoter-TSS (NM_001271407)	promoter-TSS (NM_001271407)	-27	NM_001271407	20410	Mm.5068	NM_011366	ENSMUSG00000022091	Sorbs3	SCAM-1|SH3P3|Sh3d4|vinexin-g	sorbin and SH3 domain containing 3	protein-coding
mm_140083.1	chr17	75390961	75390964	+	1	NA	3' UTR (NM_019919, exon 34 of 34)	3' UTR (NM_019919, exon 34 of 34)	-44943	NM_001166493	240168	Mm.329203	NM_207246	ENSMUSG00000071042	Rasgrp3	BC066069|Gm327	RAS, guanyl releasing protein 3	protein-coding
mm_149295.1	chr19	10689229	10689243	+	1	NA	intron (NM_181403, intron 1 of 4)	intron (NM_181403, intron 1 of 4)	421	NM_181403	107305	Mm.19091	NM_181403	ENSMUSG00000048832	Vps37c	5730409F24Rik|AU042646	vacuolar protein sorting 37C	protein-coding
mm_165252.1	chr2	71873346	71873346	+	1	NA	5' UTR (NM_172665, exon 1 of 11)	5' UTR (NM_172665, exon 1 of 11)	122	NM_172665	228026	Mm.34411	NM_172665	ENSMUSG00000006494	Pdk1	B830012B01|D530020C15Rik	pyruvate dehydrogenase kinase, isoenzyme 1	protein-coding
mm_96551.1	chr11	68888546	68888562	+	1	NA	promoter-TSS (NM_177060)	promoter-TSS (NM_177060)	1	NM_177060	320040	Mm.305696	NM_177060	ENSMUSG00000046490	Rnf222	9930039A11Rik	ring finger protein 222	protein-coding
mm_81146.1	chr9	106880110	106880131	+	1	NA	3' UTR (NM_001015507, exon 23 of 23)	3' UTR (NM_001015507, exon 23 of 23)	6880	NM_175402	109095	Mm.431589	NM_175402	ENSMUSG00000074102	Rbm15b	1810017N16Rik	RNA binding motif protein 15B	protein-coding
mm_60177.1	chr7	41633546	41633603	+	1	NA	promoter-TSS (NM_023363)	promoter-TSS (NM_023363)	43	NM_023363	67607	Mm.384626	NM_023363	ENSMUSG00000074165	Zfp788	2810426N06Rik|AI256342|AI605193	zinc finger protein 788	protein-coding
mm_36707.1	chr4	97584581	97584601	-	1	NA	promoter-TSS (NR_015513)	promoter-TSS (NR_015513)	0	NR_015513	319865	Mm.373807	NM_177023		E130114P18Rik	-	RIKEN cDNA E130114P18 gene	ncRNA
mm_48857.1	chr5	149636664	149636695	-	1	NA	promoter-TSS (NM_013559)	promoter-TSS (NM_013559)	-343	NM_001347534	15505	Mm.270681	NM_013559	ENSMUSG00000029657	Hsph1	105kDa|AI790491|Hsp105|Hsp110|hsp-E7I|hsp110/105	heat shock 105kDa/110kDa protein 1	protein-coding
mm_3939.1	chr1	163779595	163779631	+	1	NA	promoter-TSS (NM_010629)	promoter-TSS (NM_010629)	30	NM_010629	16579	Mm.4651	NM_010629	ENSMUSG00000026585	Kifap3	KAP-3|KAP3|SMAP	kinesin-associated protein 3	protein-coding
mm_32674.1	chr4	115775523	115775533	+	1	NA	3' UTR (NM_172698, exon 12 of 12)	3' UTR (NM_172698, exon 12 of 12)	5506	NM_029196	75173	Mm.331798	NM_029196	ENSMUSG00000044556	Tex38	4930544O15Rik|Theg4	testis expressed 38	protein-coding
mm_136144.1	chr16	87490547	87490576	-	1	NA	exon (NM_009840, exon 5 of 15)	exon (NM_009840, exon 5 of 15)	5308	NM_009840	12469	Mm.328673	NM_009840	ENSMUSG00000025613	Cct8	AI132397|Cctq|Tcpq	chaperonin containing Tcp1, subunit 8 (theta)	protein-coding
mm_37953.1	chr4	133277684	133277712	-	1	NA	promoter-TSS (NR_110978)	promoter-TSS (NR_110978)	92	NM_025667	52174	Mm.244748	NM_025667	ENSMUSG00000028857	Tmem222	5730406H10Rik|AA409341|D4Ertd196e	transmembrane protein 222	protein-coding
mm_153280.1	chr19	37207586	37207622	-	1	NA	promoter-TSS (NM_027314)	promoter-TSS (NM_027314)	59	NM_001164336	69104	Mm.175989	NM_027314	ENSMUSG00000023307	March5	1810015H18Rik|2310008I22Rik|2700055A20Rik|5730499H23Rik|E130202O05Rik|MARCH-V|MITOL|Marchv|Rnf153	membrane-associated ring finger (C3HC4) 5	protein-coding
mm_9052.1	chr1	167285157	167285167	-	1	NA	promoter-TSS (NM_030724)	promoter-TSS (NM_030724)	-35	NM_030724	80914	Mm.280895	NM_030724	ENSMUSG00000026558	Uck2	AA407809|AI481316|AU018180|AU020720|TSA903|UK|UMK|Umpk	uridine-cytidine kinase 2	protein-coding
mm_40227.1	chr5	37282906	37282925	+	1	NA	exon (NM_001136058, exon 10 of 14)	exon (NM_001136058, exon 10 of 14)	37151	NM_007765	12933	Mm.290995	NM_007765	ENSMUSG00000029121	Crmp1	CRMP-1|DRP-1|Dpysl1|ULIP-3|Ulip3	collapsin response mediator protein 1	protein-coding
mm_90702.1	chr10	130361093	130361095	+	1	NA	intron (NM_183264, intron 8 of 8)	RMER4B|LTR|ERVK	33147	NM_001081448	625068	Mm.359168	NM_001081448	ENSMUSG00000070601	Vmn2r84	EG625068	vomeronasal 2, receptor 84	protein-coding
mm_36329.1	chr4	70534871	70534885	-	1	NA	promoter-TSS (NM_172694)	promoter-TSS (NM_172694)	50	NM_172694	230316	Mm.251188	NM_172694	ENSMUSG00000039270	Megf9	4933405H16Rik|9630025C07|Egfl5|mKIAA0818	multiple EGF-like-domains 9	protein-coding
mm_10758.1	chr2	23259987	23259990	+	1	NA	intron (NM_027635, intron 9 of 10)	L1_Mus4|LINE|L1	52512	NM_027635	70981	Mm.314026	NM_027635	ENSMUSG00000026774	4931423N10Rik	-	RIKEN cDNA 4931423N10 gene	protein-coding
mm_63571.1	chr7	128117441	128117474	+	1	NA	3' UTR (NM_008401, exon 30 of 30)	3' UTR (NM_008401, exon 30 of 30)	-12111	NM_021334	16411	Mm.22378	NM_021334	ENSMUSG00000030789	Itgax	AI449405|Cd11c|Cr4|N418	integrin alpha X	protein-coding
mm_120075.1	chr14	57424095	57424111	+	1	NA	promoter-TSS (NM_009376)	promoter-TSS (NM_009376)	32	NM_009376	21821	Mm.4653	NM_009376	ENSMUSG00000040040	Ift88	AW552028|Tg737|Tg737Rpw|TgN737Rpw|Ttc10|flexo|fxo|orpk|polaris	intraflagellar transport 88	protein-coding
mm_143277.1	chr17	65675089	65675093	-	1	NA	intron (NM_133685, intron 5 of 6)	intron (NM_133685, intron 5 of 6)	-32887	NM_001146002	213272	Mm.255732	NM_153519	ENSMUSG00000050612	Txndc2	AU021712|Sptrx-1|Sptrx1|Trx4	thioredoxin domain containing 2 (spermatozoa)	protein-coding
mm_15396.1	chr2	156721365	156721386	+	1	NA	promoter-TSS (NM_001042487)	promoter-TSS (NM_001042487)	96	NM_001042487	228836	Mm.22094	NM_146128	ENSMUSG00000061689	Dlgap4	AI225853|BC024558|DAP-4|DAP4|SAPAP-4|Sapap4|WBP16	discs, large homolog-associated protein 4 (Drosophila)	protein-coding
mm_104634.1	chr11	97511026	97511040	-	1	NA	3' UTR (NM_018873, exon 20 of 20)	3' UTR (NM_018873, exon 20 of 20)	-10693	NM_001289118	100141474	Mm.482426	NM_001289118	ENSMUSG00000047988	4933428G20Rik	-	RIKEN cDNA 4933428G20 gene	protein-coding
mm_110686.1	chr12	67222551	67222578	-	1	NA	promoter-TSS (NM_207010)	promoter-TSS (NM_207010)	-15	NM_207010	320772	Mm.227680	NM_207010	ENSMUSG00000034912	Mdga2	6720489L24Rik|9330209L04Rik|Adp|Mamdc1	MAM domain containing glycosylphosphatidylinositol anchor 2	protein-coding
mm_95851.1	chr11	57807331	57807332	+	1	NA	intron (NM_001081168, intron 2 of 3)	intron (NM_001081168, intron 2 of 3)	5694	NM_001081168	50724	Mm.340083	NM_001081168	ENSMUSG00000020519	Sap30l	2310079P12Rik|AF006998|L55	SAP30-like	protein-coding
mm_32093.1	chr4	98546632	98546655	+	1	NA	promoter-TSS (NM_007704)	promoter-TSS (NM_007704)	9	NM_001005787	12695	Mm.90218	NM_007704	ENSMUSG00000061859	Patj	Cipp|Inadl	PATJ, crumbs cell polarity complex component	protein-coding
mm_17507.1	chr2	29055052	29055079	-	1	NA	promoter-TSS (NM_001166705)	promoter-TSS (NM_001166705)	1	NM_001166705	329375	Mm.425079	NM_001085514	ENSMUSG00000079502	Cfap77	1700101E01Rik|Gm823	cilia and flagella associated protein 77	protein-coding
mm_169946.1	chr16	69893569	69893584	+	1	NA	Intergenic	L1Md_T|LINE|L1	-29832	NM_173069	224318	Mm.212743	NM_173069	ENSMUSG00000063163	Speer2	SPEER-2	spermatogenesis associated glutamate (E)-rich protein 2	protein-coding
mm_74424.1	chr8	3665622	3665655	-	1	NA	promoter-TSS (NM_026985)	promoter-TSS (NM_026985)	-124	NM_026985	69189	Mm.175176	NM_026985	ENSMUSG00000013974	Mcemp1	1810033B17Rik	mast cell expressed membrane protein 1	protein-coding
mm_65246.1	chr7	19831941	19831958	-	1	NA	Intergenic	Intergenic	-9194	NM_033601	12051	Mm.439658	NM_033601	ENSMUSG00000053175	Bcl3	AI528691|Bcl-3	B cell leukemia/lymphoma 3	protein-coding
mm_126666.1	chr15	84324467	84324483	+	1	NA	promoter-TSS (NM_022321)	promoter-TSS (NM_022321)	-245	NM_022321	64099	Mm.251356	NM_022321	ENSMUSG00000022439	Parvg	AI413459	parvin, gamma	protein-coding
mm_96197.1	chr11	62005775	62005783	+	1	NA	intron (NM_001310526, intron 1 of 7)	intron (NM_001310526, intron 1 of 7)	49016	NM_001310526	432572	Mm.438022	NM_001029936	ENSMUSG00000042331	Specc1	2810012G08Rik|B230396K10Rik|Cytsb	sperm antigen with calponin homology and coiled-coil domains 1	protein-coding
mm_95176.1	chr11	41498674	41498687	+	1	NA	Intergenic	Intergenic	502034	NM_177408	14406	Mm.5309	NM_008073	ENSMUSG00000020436	Gabrg2	GABAA-R|Gabrg-2|gamma2	gamma-aminobutyric acid (GABA) A receptor, subunit gamma 2	protein-coding
mm_173035.1	chrX	106545990	106545992	-	1	NA	Intergenic	LTRIS2|LTR|ERV1	-37195	NM_001033541	331493	Mm.249319	NM_001033541	ENSMUSG00000073010	Gm5127	B130007I08|EG331493	predicted gene 5127	protein-coding
mm_162905.1	chr10	116896896	116896906	-	1	NA	promoter-TSS (NM_001033333)	promoter-TSS (NM_001033333)	-22	NM_001033333	237558	Mm.336386	NM_001033333	ENSMUSG00000034057	Myrfl	Gm239	myelin regulatory factor-like	protein-coding
mm_29344.1	chr3	108256981	108257030	-	1	NA	promoter-TSS (NM_011967)	promoter-TSS (NM_011967)	79	NM_011967	26442	Mm.208883	NM_011967	ENSMUSG00000068749	Psma5	ZETA	proteasome (prosome, macropain) subunit, alpha type 5	protein-coding
mm_139717.1	chr17	57466309	57466323	+	1	NA	intron (NM_010130, intron 18 of 21)	Lx|LINE|L1	78998	NM_001104591	224916	Mm.469889	NM_001104591	ENSMUSG00000090655	Vmn2r120	EG224916	vomeronasal 2, receptor 120	protein-coding
mm_84419.1	chr9	65580082	65580086	-	1	NA	promoter-TSS (NM_153119)	promoter-TSS (NM_153119)	3	NM_153119	102595	Mm.247303	NM_153119	ENSMUSG00000050721	Plekho2	AI840980|Plekhq1	pleckstrin homology domain containing, family O member 2	protein-coding
mm_123823.1	chr14	70618541	70618574	-	1	NA	promoter-TSS (NM_001252666)	promoter-TSS (NM_001252666)	12	NM_001252666	13829	Mm.210863	NM_013514	ENSMUSG00000022099	Dmtn	AI325486|Epb4.9|Epb49|dematin	dematin actin binding protein	protein-coding
mm_68520.1	chr7	111780055	111780068	-	1	NA	promoter-TSS (NM_173739)	promoter-TSS (NM_173739)	-84	NM_173739	233733	Mm.323322	NM_173739	ENSMUSG00000038296	Galnt18	2900011G21Rik|BC024988|Galntl4	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 18	protein-coding
mm_138928.1	chr17	43801824	43801863	+	1	NA	promoter-TSS (NM_207649)	promoter-TSS (NM_207649)	-8	NM_207649	53901	Mm.251242	NM_030598	ENSMUSG00000039601	Rcan2	Csp2|Dscr1l1|MCIP2|ZAKI-4	regulator of calcineurin 2	protein-coding
mm_156292.1	chrX	136837502	136837514	+	1	NA	3' UTR (NM_011123, exon 7 of 7)	3' UTR (NM_011123, exon 7 of 7)	14762	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_12595.1	chr2	74667268	74667273	+	1	NA	Intergenic	Intergenic	-1040	NM_008275	15433	Mm.57227	NM_008275	ENSMUSG00000001819	Hoxd13	Hox-4.8|spdh	homeobox D13	protein-coding
mm_72661.1	chr8	84872106	84872112	+	1	NA	promoter-TSS (NR_031759)	promoter-TSS (NR_031759)	-2	NR_031759	71846	Mm.229128	NM_027954	ENSMUSG00000003824	Syce2	1700013H19Rik|AA407907|Cesc1	synaptonemal complex central element protein 2	protein-coding
mm_61802.1	chr7	84333314	84333319	+	1	NA	intron (NM_007488, intron 5 of 18)	intron (NM_007488, intron 5 of 18)	76722	NM_007488	11864	Mm.38594	NM_007488	ENSMUSG00000015709	Arnt2	Hif-2b|bHLHe1|mKIAA0307	aryl hydrocarbon receptor nuclear translocator 2	protein-coding
mm_53514.1	chr6	136328518	136328527	+	1	NA	5' UTR (NM_001142734, exon 2 of 2)	5' UTR (NM_001142734, exon 2 of 2)	983	NM_001142734	668137	Mm.417085	NM_001142734	ENSMUSG00000094973	Gm8994	B020013A22Rik|EG668137	predicted gene 8994	protein-coding
mm_163760.1	chr13	119791410	119791496	-	1	NA	promoter-TSS (NM_028245)	promoter-TSS (NM_028245)	-331	NM_001302550	72465	Mm.139115	NM_028245	ENSMUSG00000094870	Zfp131	2610109I01Rik|AW558871|Znf131	zinc finger protein 131	protein-coding
mm_131352.1	chr16	13702537	13702558	+	1	NA	3' UTR (NM_001177552, exon 6 of 6)	3' UTR (NM_001177552, exon 6 of 6)	-27289	NR_040574	76684	Mm.491043	NR_040574		Pla2g10os	1810007I06Rik	phospholipase A2, group X, opposite strand	ncRNA
mm_136619.1	chr17	5492983	5492989	+	1	NA	5' UTR (NM_146073, exon 1 of 9)	5' UTR (NM_146073, exon 1 of 9)	386	NM_146073	224454	Mm.487663	NM_146073	ENSMUSG00000034265	Zdhhc14	B530001K09Rik|New1cp	zinc finger, DHHC domain containing 14	protein-coding
mm_78975.1	chr9	45370200	45370208	+	1	NA	promoter-TSS (NM_022004)	promoter-TSS (NM_022004)	19	NM_022004	59095	Mm.208287	NM_022004	ENSMUSG00000066705	Fxyd6	0610030I18Rik|Php	FXYD domain-containing ion transport regulator 6	protein-coding
mm_144780.1	chr18	35830180	35830208	+	1	NA	intron (NM_133687, intron 1 of 2)	CpG	376	NM_133687	67393	Mm.94560	NM_133687	ENSMUSG00000046668	Cxxc5	4930415K17Rik	CXXC finger 5	protein-coding
mm_169880.1	chr16	37883417	37883421	+	1	NA	3' UTR (NM_177093, exon 4 of 4)	3' UTR (NM_177093, exon 4 of 4)	15019	NM_177093	320184	Mm.390882	NM_177093	ENSMUSG00000034158	Lrrc58	1810012N18Rik|C330018J07Rik	leucine rich repeat containing 58	protein-coding
mm_158003.1	chrX	95166344	95166426	-	1	NA	5' UTR (NM_001290385, exon 1 of 10)	5' UTR (NM_001290385, exon 1 of 10)	154	NM_001290385	236915	Mm.44841	NM_001033329	ENSMUSG00000025656	Arhgef9	9630036L12Rik	CDC42 guanine nucleotide exchange factor (GEF) 9	protein-coding
mm_59542.1	chr7	27860553	27860564	+	1	NA	promoter-TSS (NM_001024726)	promoter-TSS (NM_001024726)	-27	NM_001024726	545938	Mm.458180	NM_001024726	ENSMUSG00000020420	Zfp607a	4732475C15Rik|Zfp607	zinc finger protein 607A	protein-coding
mm_106193.1	chr11	116828001	116828071	-	1	NA	promoter-TSS (NM_026280)	promoter-TSS (NM_026280)	10	NM_026280	67622	Mm.64962	NM_026280	ENSMUSG00000020814	Mxra7	1810057P16Rik|E130302J09Rik	matrix-remodelling associated 7	protein-coding
mm_56829.1	chr6	117174294	117174312	-	1	NA	3' UTR (NM_021704, exon 3 of 3)	3' UTR (NM_021704, exon 3 of 3)	5768	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_157781.1	chrX	73787080	73787098	-	1	NA	promoter-TSS (NM_008323)	promoter-TSS (NM_008323)	-54	NM_009279	20832	Mm.831	NM_009279	ENSMUSG00000002014	Ssr4	AW743063|C78062|Trap	signal sequence receptor, delta	protein-coding
mm_69896.1	chr7	141637860	141637876	-	1	NA	intron (NM_001330001, intron 31 of 33)	intron (NM_001330001, intron 31 of 33)	17167	NR_106030	102466798		NR_106030	ENSMUSG00000098759	Mir7063	Gm27654|mmu-mir-7063	microRNA 7063	ncRNA
mm_148249.1	chr18	80708185	80708194	-	1	NA	promoter-TSS (NM_016791)	promoter-TSS (NM_016791)	-16	NM_001164112	18018	Mm.329560	NM_016791	ENSMUSG00000033016	Nfatc1	2210017P03Rik|AI449492|AV076380|NF-ATc|NFAT2|NFATc|Nfatcb	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 1	protein-coding
mm_130555.1	chr15	99096861	99096861	-	1	NA	Intergenic	CpG	-2623	NM_176835	72778	Mm.30544	NM_176835	ENSMUSG00000038009	Dnajc22	2810451A06Rik|AI506245	DnaJ heat shock protein family (Hsp40) member C22	protein-coding
mm_91063.1	chr10	19001571	19001610	-	1	NA	3' UTR (NM_009397, exon 9 of 9)	3' UTR (NM_009397, exon 9 of 9)	10373	NM_001166402	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_118030.1	chr13	101548144	101548157	-	1	NA	Intergenic	LTR33B|LTR|ERVL	144480	NM_001024955	18708	Mm.259333	NM_001024955	ENSMUSG00000041417	Pik3r1	PI3K|p50alpha|p55alpha|p85alpha	phosphatidylinositol 3-kinase, regulatory subunit, polypeptide 1 (p85 alpha)	protein-coding
mm_62820.1	chr7	113369469	113369509	+	1	NA	promoter-TSS (NM_133700)	promoter-TSS (NM_133700)	-150	NM_133700	68815	Mm.238034	NM_133700	ENSMUSG00000038187	Btbd10	1110056N09Rik|Gmrp1	BTB (POZ) domain containing 10	protein-coding
mm_52420.1	chr6	113458766	113458836	+	1	NA	promoter-TSS (NM_001034029)	promoter-TSS (NM_001034029)	-94	NM_001034031	57890	Mm.131781	NM_145826	ENSMUSG00000043088	Il17re	AA589509|IL-17RE|Il25r	interleukin 17 receptor E	protein-coding
mm_11662.1	chr2	35224517	35224548	+	1	NA	Intergenic	MLTR18D_MM|LTR|ERVK	-23412	NM_026697	68365	Mm.198264	NM_026697	ENSMUSG00000026878	Rab14	0610030G24Rik|2810475J17Rik|A830021G03Rik|AI314285|AI649155|D030017L14Rik	RAB14, member RAS oncogene family	protein-coding
mm_59347.1	chr7	25627605	25627652	+	1	NA	promoter-TSS (NM_146184)	promoter-TSS (NM_146184)	4	NM_146184	232984	Mm.192369	NM_146184	ENSMUSG00000059479	B3gnt8	B3galt7|B7galt7|BC025206	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 8	protein-coding
mm_134908.1	chr16	30260314	30260324	-	1	NA	exon (NM_027904, exon 2 of 2)	exon (NM_027904, exon 2 of 2)	7213	NM_027904	71756	Mm.290614	NM_027904	ENSMUSG00000023176	Cpn2	1300018K11Rik	carboxypeptidase N, polypeptide 2	protein-coding
mm_40767.1	chr5	67028800	67028821	+	1	NA	exon (NM_001001980, exon 19 of 26)	exon (NM_001001980, exon 19 of 26)	60394	NM_001256122	77569	Mm.374778	NM_001001980	ENSMUSG00000037736	Limch1	3732412D22Rik|mKIAA1102	LIM and calponin homology domains 1	protein-coding
mm_115420.1	chr13	117211931	117211934	+	1	NA	Intergenic	Intergenic	-8641	NM_010330	13723	Mm.274926	NM_010330	ENSMUSG00000021728	Emb	AL022799|Gp70	embigin	protein-coding
mm_145061.1	chr18	40512987	40513003	+	1	NA	intron (NM_026135, intron 1 of 1)	intron (NM_026135, intron 1 of 1)	254634	NM_026135	383348	Mm.76366	NM_026135	ENSMUSG00000051401	Kctd16	4930434H12Rik|Gm1267	potassium channel tetramerisation domain containing 16	protein-coding
mm_142790.1	chr17	50164310	50164325	-	1	NA	intron (NM_181397, intron 2 of 9)	B4A|SINE|B4	26180	NM_181397	76438	Mm.41854	NM_181397	ENSMUSG00000039316	Rftn1	2310015N21Rik|AI853526	raftlin lipid raft linker 1	protein-coding
mm_163071.1	chr11	67254790	67254799	+	1	NA	exon (NM_010855, exon 30 of 40)	exon (NM_010855, exon 30 of 40)	16982	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_33034.1	chr4	122689433	122689437	+	1	NA	exon (NM_023865, exon 1 of 5)	exon (NM_023865, exon 1 of 5)	176	NM_023865	77432	Mm.491436	NM_023865	ENSMUSG00000023263	9530002B09Rik	Aump|Vpp1|Vppl	RIKEN cDNA 9530002B09 gene	protein-coding
mm_71201.1	chr8	40887853	40887863	+	1	NA	intron (NM_007514, intron 1 of 11)	intron (NM_007514, intron 1 of 11)	25491	NM_001044740	11988	Mm.4676	NM_007514	ENSMUSG00000031596	Slc7a2	20.5|AI158848|Atrc2|CAT-2|Cat2|Tea	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	protein-coding
mm_18084.1	chr2	44926892	44926899	-	1	NA	Intergenic	CpG	-65273	NM_172662	227835	Mm.314312	NM_172662	ENSMUSG00000036890	Gtdc1	E330008O22Rik	glycosyltransferase-like domain containing 1	protein-coding
mm_5665.1	chr1	42694814	42694877	-	1	NA	promoter-TSS (NR_027826)	promoter-TSS (NR_027826)	-20	NR_027826	66297	Mm.45203	NM_183252	ENSMUSG00000060424	Pantr1	2610017I09Rik|Pou3f3os|linc-Brn1a	POU domain, class 3, transcription factor 3 adjacent noncoding transcript 1	ncRNA
mm_133114.1	chr16	65534003	65534011	+	1	NA	TTS (NM_008849)	TTS (NM_008849)	13378	NM_008849	18736	Mm.355440	NM_008849	ENSMUSG00000004842	Pou1f1	GHF-1|Hmp1|Pit-1|Pit1|Pit1-rs1|dw|dwarf	POU domain, class 1, transcription factor 1	protein-coding
mm_28306.1	chr3	89237838	89237845	-	1	NA	exon (NM_183037, exon 8 of 10)	exon (NM_183037, exon 8 of 10)	7172	NR_121683	360213	Mm.331156	NM_183037	ENSMUSG00000042766	Trim46	TRIFIC	tripartite motif-containing 46	protein-coding
mm_67855.1	chr7	98702900	98702934	-	1	NA	promoter-TSS (NM_028410)	promoter-TSS (NM_028410)	11	NR_144495	100040769	Mm.126401	NR_144495		Gm15506	OTTMUSG00000023003	predicted gene 15506	ncRNA
mm_147612.1	chr18	56981182	56981221	-	1	NA	Intergenic	L2b|LINE|L2	-5822	NM_029909	77422	Mm.256874	NM_029909	ENSMUSG00000024592	C330018D20Rik	AU018666	RIKEN cDNA C330018D20 gene	protein-coding
mm_149462.1	chr19	11528594	11528602	+	1	NA	exon (NM_027209, exon 6 of 7)	exon (NM_027209, exon 6 of 7)	-8251	NM_025658	66607	Mm.441056	NM_025658	ENSMUSG00000024678	Ms4a4d	2210417J23Rik	membrane-spanning 4-domains, subfamily A, member 4D	protein-coding
mm_12320.1	chr2	69382029	69382035	+	1	NA	intron (NM_175512, intron 1 of 4)	intron (NM_175512, intron 1 of 4)	1570	NM_175512	241452	Mm.211655	NM_175512	ENSMUSG00000027068	Dhrs9	C730025I08Rik|Rdh15	dehydrogenase/reductase (SDR family) member 9	protein-coding
mm_71957.1	chr8	70514062	70514090	+	1	NA	exon (NM_029366, exon 5 of 5)	exon (NM_029366, exon 5 of 5)	-3709	NM_019883	22186	Mm.297372	NM_019883	ENSMUSG00000090137	Uba52	D8Ertd21e|Gm1863|Rps27a|Ubb|Ubc	ubiquitin A-52 residue ribosomal protein fusion product 1	protein-coding
mm_64267.1	chr7	141751456	141751467	+	1	NA	exon (NM_023566, exon 38 of 46)	exon (NM_023566, exon 38 of 46)	-37550	NM_010844	17833	Mm.334332	NM_010844	ENSMUSG00000037974	Muc5ac	2210005L13Rik|MGM	mucin 5, subtypes A and C, tracheobronchial/gastric	protein-coding
mm_27261.1	chr3	37707414	37707415	-	1	NA	Intergenic	Intergenic	16946	NM_198657	381438	Mm.490549	NM_198657	ENSMUSG00000058174	Gm5148	EG381438	predicted gene 5148	protein-coding
mm_19731.1	chr2	104494401	104494463	-	1	NA	promoter-TSS (NM_001145824)	promoter-TSS (NM_001145824)	57	NM_010434	15259	Mm.257925	NM_010434	ENSMUSG00000027177	Hipk3	DYRK6|FIST3|PKY|mir-1902	homeodomain interacting protein kinase 3	protein-coding
mm_112876.1	chr13	20853920	20853946	+	1	NA	intron (NM_012054, intron 4 of 20)	intron (NM_012054, intron 4 of 20)	59820	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_90877.1	chr10	9675164	9675243	-	1	NA	promoter-TSS (NM_177271)	promoter-TSS (NM_177271)	5	NM_177271	320825	Mm.101115	NM_177271	ENSMUSG00000060487	Samd5	E130306M17Rik	sterile alpha motif domain containing 5	protein-coding
mm_31435.1	chr4	48540068	48540086	+	1	NA	promoter-TSS (NM_028137)	promoter-TSS (NM_028137)	-4	NM_001145924	66665	Mm.140749	NM_028137	ENSMUSG00000039693	Msantd3	2410046L14Rik|2810429P03Rik|5730528L13Rik|Mysantd3	Myb/SANT-like DNA-binding domain containing 3	protein-coding
mm_81445.1	chr9	109812250	109812269	+	1	NA	Intergenic	Intergenic	-4368	NM_183136	78709	Mm.99613	NM_183136	ENSMUSG00000050074	Spink8	C630041L24Rik	serine peptidase inhibitor, Kazal type 8	protein-coding
mm_18066.1	chr2	42165286	42165293	-	1	NA	intron (NM_053011, intron 2 of 90)	intron (NM_053011, intron 2 of 90)	282279	NR_105754	102465171		NR_105754	ENSMUSG00000098660	Mir6336	Gm27584|mmu-mir-6336	microRNA 6336	ncRNA
mm_133548.1	chr16	91269847	91269898	+	1	NA	5' UTR (NM_016968, exon 1 of 1)	5' UTR (NM_016968, exon 1 of 1)	103	NM_016968	50914	Mm.39300	NM_016968	ENSMUSG00000046160	Olig1	AI836478|AW494459|Bhlhb6|Olg-1|Oligo1|bHLHe21	oligodendrocyte transcription factor 1	protein-coding
mm_49626.1	chr6	30804186	30804209	+	1	NA	intron (NM_017478, intron 20 of 23)	intron (NM_017478, intron 20 of 23)	62898	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_67976.1	chr7	100656917	100656942	-	1	NA	promoter-TSS (NM_001163187)	promoter-TSS (NM_001163187)	36	NM_001163187	27276	Mm.491216	NM_013746	ENSMUSG00000030701	Plekhb1	AI315628|PHR1|Phret1|evt-1	pleckstrin homology domain containing, family B (evectins) member 1	protein-coding
mm_115545.1	chr13	8852005	8852030	-	1	NA	3' UTR (NM_001039389, exon 5 of 5)	3' UTR (NM_001039389, exon 5 of 5)	19027	NM_001039389	207615	Mm.284654	NM_172445	ENSMUSG00000021147	Wdr37	-	WD repeat domain 37	protein-coding
mm_144521.1	chr18	24941458	24941466	+	1	NA	intron (NM_175276, intron 5 of 26)	intron (NM_175276, intron 5 of 26)	224503	NM_001142697	66648	Mm.263189	NM_001004361	ENSMUSG00000024269	Tpgs2	5730437P09Rik|5730494M16Rik|AI666318|Pgs2	tubulin polyglutamylase complex subunit 2	protein-coding
mm_108096.1	chr12	74803866	74803875	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	373462	NM_172805	238271	Mm.44465	NM_172805	ENSMUSG00000034402	Kcnh5	Eag2	potassium voltage-gated channel, subfamily H (eag-related), member 5	protein-coding
mm_47343.1	chr5	122502732	122502742	-	1	NA	promoter-TSS (NM_009722)	promoter-TSS (NM_009722)	-512	NR_027838	11938	Mm.227583	NM_009722	ENSMUSG00000029467	Atp2a2	9530097L16Rik|D5Wsu150e|SERCA2|SERCA2B|Serca2a|mKIAA4195	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	protein-coding
mm_26394.1	chr3	142587625	142587634	+	1	NA	Intergenic	Intergenic	-7218	NM_010259	14468	Mm.457978	NM_010259	ENSMUSG00000040264	Gbp2b	Gbp-1|Gbp1|Mag-1|Mpa-1|Mpa1	guanylate binding protein 2b	protein-coding
mm_12868.1	chr2	83812786	83812796	+	1	NA	promoter-TSS (NM_175514)	promoter-TSS (NM_175514)	63	NM_175514	241520	Mm.330351	NM_175514	ENSMUSG00000048388	Fam171b	D430039N05Rik	family with sequence similarity 171, member B	protein-coding
mm_114071.1	chr13	54382643	54382653	+	1	NA	3' UTR (NM_009946, exon 4 of 4)	3' UTR (NM_009946, exon 4 of 4)	11299	NM_009946	12890	Mm.268902	NM_009946	ENSMUSG00000025867	Cplx2	921-L|AI413745|AW492120	complexin 2	protein-coding
mm_169773.1	chr1	60704166	60704173	+	1	NA	Intergenic	Intergenic	-42219	NM_007642	12487	Mm.255003	NM_007642	ENSMUSG00000026012	Cd28	-	CD28 antigen	protein-coding
mm_163846.1	chr14	19418113	19418136	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	184463	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_117234.1	chr13	64274963	64275004	-	1	NA	promoter-TSS (NM_172587)	promoter-TSS (NM_172587)	5	NM_172587	218294	Mm.25335	NM_172587	ENSMUSG00000033102	Cdc14b	2810432N10Rik|A530086E13Rik|AA472821|CDC14B3|Cdc14B1	CDC14 cell division cycle 14B	protein-coding
mm_81878.1	chr9	119323140	119323153	+	1	NA	promoter-TSS (NM_133985)	promoter-TSS (NM_133985)	-719	NM_133985	108737	Mm.293565	NM_133985	ENSMUSG00000036737	Oxsr1	2210022N24Rik|2810422B09Rik|AI462649|AW209236|Osr1|mKIAA1101	oxidative-stress responsive 1	protein-coding
mm_67956.1	chr7	100511781	100511801	-	1	NA	exon (NM_153527, exon 2 of 8)	exon (NM_153527, exon 2 of 8)	3024	NM_153527	69387	Mm.278554	NM_153527	ENSMUSG00000030708	Dnajb13	1700014P03Rik|Tsarg	DnaJ heat shock protein family (Hsp40) member B13	protein-coding
mm_162090.1	chrX	37469964	37469964	+	1	NA	promoter-TSS (NM_001102457)	promoter-TSS (NM_001102457)	96	NM_001102457	100135654	Mm.359489	NM_001102457	ENSMUSG00000079636	Rhox3c	EG665203|Rhox3.3|Rhox3b	reproductive homeobox 3C	protein-coding
mm_76366.1	chr8	84774122	84774142	-	1	NA	5' UTR (NM_001081981, exon 1 of 11)	5' UTR (NM_001081981, exon 1 of 11)	237	NM_001081981	18032	Mm.9394	NM_010906	ENSMUSG00000001911	Nfix	CTF|NF-I/X|NF1-X|NFI-X	nuclear factor I/X	protein-coding
mm_158720.1	chrX	162888375	162888401	-	1	NA	promoter-TSS (NM_025932)	promoter-TSS (NM_025932)	74	NM_025932	67043	Mm.44207	NM_025932	ENSMUSG00000031357	Syap1	2010110O17Rik|AW011796	synapse associated protein 1	protein-coding
mm_88334.1	chr10	75573493	75573501	+	1	NA	promoter-TSS (NM_008116)	promoter-TSS (NM_008116)	2	NM_008116	14598	Mm.4559	NM_008116	ENSMUSG00000006345	Ggt1	CD224|GGT|GGT 1|GGT-1|Ggtp|dwg	gamma-glutamyltransferase 1	protein-coding
mm_27083.1	chr3	30013158	30013174	-	1	NA	promoter-TSS (NM_007963)	promoter-TSS (NM_007963)	38	NM_007963	14013	Mm.56965	NM_007963	ENSMUSG00000027684	Mecom	D630039M04Rik|Evi-1|Evi1|Jbo|Mds|Mds1|Mds1-Evi1|Prdm3|Znfpr1b1	MDS1 and EVI1 complex locus	protein-coding
mm_96252.1	chr11	62576026	62576032	+	1	NA	5' UTR (NM_011706, exon 2 of 16)	5' UTR (NM_011706, exon 2 of 16)	1543	NM_011706	22368	Mm.288064	NM_011706	ENSMUSG00000018507	Trpv2	GRC|OTRPC2|VRL-1|Vrl1	transient receptor potential cation channel, subfamily V, member 2	protein-coding
mm_102310.1	chr11	55608623	55608627	-	1	NA	promoter-TSS (NM_020492)	promoter-TSS (NM_020492)	-427	NM_020492	14654	Mm.89320	NM_020492	ENSMUSG00000000263	Glra1	nmf11|oscillator|ot|spasmodic|spd	glycine receptor, alpha 1 subunit	protein-coding
mm_11302.1	chr2	30184826	30184831	+	1	NA	TTS (NM_172404)	TTS (NM_172404)	-6369	NM_172660	227695	Mm.4449	NM_172660	ENSMUSG00000039660	Spout1	9930028P05|AL033358|D2Wsu81e	SPOUT domain containing methyltransferase 1	protein-coding
mm_74371.1	chr8	128493888	128493908	+	1	NA	intron (NM_008737, intron 13 of 16)	intron (NM_008737, intron 13 of 16)	134657	NR_035436	100316680		NR_035436	ENSMUSG00000084523	Mir1903	Mirn1903|mmu-mir-1903	microRNA 1903	ncRNA
mm_33576.1	chr4	132311517	132311519	+	1	NA	TTS (NM_027925)	TTS (NM_027925)	815	NR_028537	100217437		NR_028537		Snord99	MBII-420	small nucleolar RNA, C/D box 99	snoRNA
mm_111485.1	chr12	98822236	98822238	-	1	NA	intron (NM_001081191, intron 27 of 43)	intron (NM_001081191, intron 27 of 43)	51215	NM_001160108	75553	Mm.25549	NM_029334	ENSMUSG00000021012	Zc3h14	1010001P15Rik|1700016A15Rik|2700069A02Rik|AU014748	zinc finger CCCH type containing 14	protein-coding
mm_27893.1	chr3	79287270	79287294	-	1	NA	Intergenic	CpG	-58094	NM_001142953	100233207	Mm.373801	NM_001142953	ENSMUSG00000091685	Gm17359	-	predicted gene, 17359	protein-coding
mm_120400.1	chr14	64950038	64950056	+	1	NA	promoter-TSS (NM_001253731)	promoter-TSS (NM_001253731)	2	NM_001253731	210925	Mm.71332	NM_153414	ENSMUSG00000021975	Ints9	BC028953|D14Ertd231e	integrator complex subunit 9	protein-coding
mm_8977.1	chr1	165601958	165601960	-	1	NA	intron (NM_001083897, intron 4 of 5)	intron (NM_001083897, intron 4 of 5)	32582	NM_001001880	68481	Mm.46438	NM_001001880	ENSMUSG00000026566	Mpzl1	1110007A10Rik|PZR	myelin protein zero-like 1	protein-coding
mm_155543.1	chrX	74309090	74309105	+	1	NA	exon (NM_010273, exon 7 of 11)	exon (NM_010273, exon 7 of 11)	-3936	NM_138607	108160	Mm.4370	NM_138607	ENSMUSG00000001962	Fam50a	D0HXS9928E|XAP-5	family with sequence similarity 50, member A	protein-coding
mm_143674.1	chr17	79981629	79981636	-	1	NA	Intergenic	Intergenic	80636	NM_144802	72692	Mm.64579	NM_144802	ENSMUSG00000024095	Hnrnpll	2510028H02Rik|2810036L13Rik|AI256697|AI852082|Hnrpll	heterogeneous nuclear ribonucleoprotein L-like	protein-coding
mm_12824.1	chr2	80318017	80318024	+	1	NA	intron (NM_024181, intron 2 of 22)	intron (NM_024181, intron 2 of 22)	2554	NM_024181	66861	Mm.21762	NM_024181	ENSMUSG00000027006	Dnajc10	1200006L06Rik|D2Ertd706e|ERdj5|JPDI	DnaJ heat shock protein family (Hsp40) member C10	protein-coding
mm_71742.1	chr8	64543850	64543854	+	1	NA	Intergenic	Intergenic	-29411	NR_030491	735270		NR_030491	ENSMUSG00000076042	Mir710	Mirn710|mmu-mir-710	microRNA 710	ncRNA
mm_163204.1	chr11	97728360	97728408	-	1	NA	intron (NM_054051, intron 3 of 9)	intron (NM_054051, intron 3 of 9)	16320	NM_054051	108083	Mm.39700	NM_054051	ENSMUSG00000018547	Pip4k2b	AI848124|PI5P4Kbeta|Pip5k2b|c11	phosphatidylinositol-5-phosphate 4-kinase, type II, beta	protein-coding
mm_50426.1	chr6	48841634	48841644	+	1	NA	promoter-TSS (NM_001164209)	promoter-TSS (NM_001164209)	-17	NM_001098271	66058	Mm.27061	NM_025326	ENSMUSG00000023367	Tmem176a	0610011I04Rik|AU040201|AU041743|Keg2	transmembrane protein 176A	protein-coding
mm_33963.1	chr4	137560699	137560719	+	1	NA	intron (NM_008305, intron 81 of 96)	intron (NM_008305, intron 81 of 96)	14471	NM_001033979	435811	Mm.359646	NM_001033979	ENSMUSG00000094035	Ldlrad2	-	low density lipoprotein receptor A domain containing 2	protein-coding
mm_15235.1	chr2	154613328	154613369	+	1	NA	promoter-TSS (NM_199304)	promoter-TSS (NM_199304)	-20	NM_199304	228807	Mm.103555	NM_199304	ENSMUSG00000059842	Zfp341	Znf341	zinc finger protein 341	protein-coding
mm_30524.1	chr4	3089541	3089542	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	-82542	NM_001167534	100312470	Mm.480297	NM_001167534	ENSMUSG00000094798	Vmn1r2	Gm11776|OTTMUSG00000004179	vomeronasal 1 receptor 2	protein-coding
mm_159932.1	chr6	71373220	71373220	+	1	NA	promoter-TSS (NM_009857)	promoter-TSS (NM_009857)	-207	NM_009857	12525	Mm.1858	NM_009857	ENSMUSG00000053977	Cd8a	BB154331|Ly-2|Ly-35|Ly-B|Lyt-2	CD8 antigen, alpha chain	protein-coding
mm_142018.1	chr17	35200924	35200935	-	1	NA	intron (NM_013693, intron 2 of 3)	intron (NM_013693, intron 2 of 3)	1078	NM_013693	21926	Mm.1293	NM_013693	ENSMUSG00000024401	Tnf	DIF|TNF-a|TNF-alpha|TNFSF2|TNFalpha|Tnfa|Tnfsf1a|Tnlg1f	tumor necrosis factor	protein-coding
mm_69918.1	chr7	141704579	141704600	-	1	NA	intron (NM_023566, intron 27 of 45)	intron (NM_023566, intron 27 of 45)	14249	NM_023566	17831	Mm.2041	NM_023566		Muc2	2010015E03Rik|MCM|wnn	mucin 2	protein-coding
mm_80786.1	chr9	95954745	95954783	+	1	NA	promoter-TSS (NM_001311130)	promoter-TSS (NM_001311130)	4	NM_001311130	24127	Mm.291179	NM_011916	ENSMUSG00000032410	Xrn1	Dhm2|exo|mXrn1	5'-3' exoribonuclease 1	protein-coding
mm_60829.1	chr7	45707900	45707935	+	1	NA	intron (NM_016974, intron 2 of 3)	intron (NM_016974, intron 2 of 3)	2670	NM_016974	13170	Mm.24222	NM_016974	ENSMUSG00000059824	Dbp	-	D site albumin promoter binding protein	protein-coding
mm_171906.1	chr5	47287297	47287301	-	1	NA	Intergenic	L1Md_T|LINE|L1	-695856	NR_111900	20563	Mm.289739	NM_178804	ENSMUSG00000031558	Slit2	Drad-1|E030015M03Rik|E130320P19Rik|Slil3|mKIAA4141|slit-2	slit homolog 2 (Drosophila)	protein-coding
mm_94967.1	chr11	30863668	30863671	+	1	NA	intron (NM_134013, intron 42 of 46)	intron (NM_134013, intron 42 of 46)	-21689	NM_175490	237716	Mm.338361	NM_175490	ENSMUSG00000043999	Gpr75	-	G protein-coupled receptor 75	protein-coding
mm_3536.1	chr1	150393254	150393265	+	1	NA	promoter-TSS (NM_145511)	promoter-TSS (NM_145511)	-204	NM_145511	226499	Mm.222093	NM_145511	ENSMUSG00000006010	BC003331	1810053E15Rik|Odr4|odr-4	cDNA sequence BC003331	protein-coding
mm_93293.1	chr10	96374208	96374231	-	1	NA	Intergenic	Intergenic	148012	NR_110448	74881	Mm.410819	NR_110448		4930459C07Rik	-	RIKEN cDNA 4930459C07 gene	ncRNA
mm_122595.1	chr14	50930312	50930329	-	1	NA	exon (NM_001033271, exon 2 of 7)	exon (NM_001033271, exon 2 of 7)	529	NM_001310506	219024	Mm.239117	NM_001033271	ENSMUSG00000035953	Tmem55b	BC039161	transmembrane protein 55b	protein-coding
mm_153473.1	chr19	41273651	41273662	-	1	NA	TTS (NM_031376)	TTS (NM_031376)	-9652	NM_133352	107358	Mm.246440	NM_133352	ENSMUSG00000025016	Tm9sf3	1810073M23Rik|2810031D16Rik|AI115521|AI413748|AW146116|AW549777|Smbp|mKIAA4036	transmembrane 9 superfamily member 3	protein-coding
mm_14270.1	chr2	128708717	128708734	+	1	NA	intron (NM_008587, intron 1 of 18)	ORR1B1|LTR|ERVL-MaLR	9728	NM_008587	17289	Mm.239655	NM_008587	ENSMUSG00000014361	Mertk	Eyk|Mer|Nyk|nmf12	c-mer proto-oncogene tyrosine kinase	protein-coding
mm_35504.1	chr4	41093357	41093368	-	1	NA	3' UTR (NM_016689, exon 6 of 6)	3' UTR (NM_016689, exon 6 of 6)	4821	NM_016689	11828	Mm.34043	NM_016689	ENSMUSG00000028435	Aqp3	AQP-2	aquaporin 3	protein-coding
mm_170967.1	chr2	60021262	60021265	-	1	NA	intron (NM_001001182, intron 2 of 35)	ID_B1|SINE|B4	104477	NM_001001182	407823	Mm.228071	NM_001001182	ENSMUSG00000026987	Baz2b	5830435C13Rik|BC053917|D2Ertd794e	bromodomain adjacent to zinc finger domain, 2B	protein-coding
mm_45935.1	chr5	89883346	89883378	-	1	NA	promoter-TSS (NM_177872)	promoter-TSS (NM_177872)	-28	NM_001081401	330119	Mm.133062	NM_177872	ENSMUSG00000043635	Adamts3	1100001H14Rik|6330442E02Rik	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 3	protein-coding
mm_149761.1	chr19	22851982	22852022	+	1	NA	intron (NM_001035243, intron 8 of 23)	LSU-rRNA_Hsa|rRNA|rRNA	101397	NR_029591	387200		NR_029591	ENSMUSG00000065507	Mir204	Mirn204|mir-204|mmu-mir-204	microRNA 204	ncRNA
mm_65749.1	chr7	28547110	28547120	-	1	NA	exon (NM_001081115, exon 1 of 6)	exon (NM_001081115, exon 1 of 6)	139	NM_001081115	233038	Mm.224815	NM_001081115	ENSMUSG00000047586	Nccrp1	1190020J12Rik|Gm163|NCCRP-1	non-specific cytotoxic cell receptor protein 1 homolog (zebrafish)	protein-coding
mm_155895.1	chrX	101652607	101652645	+	1	NA	intron (NM_139144, intron 4 of 21)	intron (NM_139144, intron 4 of 21)	12408	NM_001290535	108155	Mm.487332	NM_139144	ENSMUSG00000034160	Ogt	1110038P24Rik|4831420N21Rik|AI115525|Ogtl	O-linked N-acetylglucosamine (GlcNAc) transferase (UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase)	protein-coding
mm_83539.1	chr9	46234453	46234471	-	1	NA	exon (NM_001289755, exon 3 of 4)	exon (NM_001289755, exon 3 of 4)	837	NM_001289833	11814	Mm.390161	NM_023114	ENSMUSG00000032081	Apoc3	apo-CIII|apoC-III	apolipoprotein C-III	protein-coding
mm_91002.1	chr10	14545317	14545344	-	1	NA	promoter-TSS (NM_001002268)	promoter-TSS (NM_001002268)	-294	NM_001002268	215798	Mm.440142	NM_001002268	ENSMUSG00000039116	Adgrg6	1190004A11Rik|AI449247|AW045736|DREG|Gm222|Gpr126	adhesion G protein-coupled receptor G6	protein-coding
mm_138919.1	chr17	43611265	43611311	+	1	NA	exon (NM_013737, exon 11 of 12)	exon (NM_013737, exon 11 of 12)	19011	NM_001161366	210510	Mm.329058	NM_198418	ENSMUSG00000040140	Tdrd6	AB097085|Tdr2	tudor domain containing 6	protein-coding
mm_136013.1	chr16	75909273	75909301	-	1	NA	promoter-TSS (NM_023380)	promoter-TSS (NM_023380)	-21	NM_023380	67742	Mm.131406	NM_023380	ENSMUSG00000022876	Samsn1	4930571B16Rik|930571B16Rik|Hacs1|SLy2	SAM domain, SH3 domain and nuclear localization signals, 1	protein-coding
mm_71265.1	chr8	40918763	40918776	+	1	NA	3' UTR (NM_001044740, exon 12 of 12)	3' UTR (NM_001044740, exon 12 of 12)	-7464	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_132893.1	chr16	48842885	48842897	+	1	NA	exon (NM_020509, exon 2 of 4)	exon (NM_020509, exon 2 of 4)	339	NM_020509	57262	Mm.441868	NM_020509	ENSMUSG00000061100	Retnla	1810019L16Rik|Fizz-1|Fizz1|HIMF|RELM-alpha|RELMa|RELMalpha|Xcp2	resistin like alpha	protein-coding
mm_143039.1	chr17	56718031	56718042	-	1	NA	promoter-TSS (NM_001166474)	promoter-TSS (NM_001166474)	274	NM_027244	69875	Mm.279823	NM_027244	ENSMUSG00000002379	Ndufa11	2010012C24Rik|AV006275|B14.7	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex 11	protein-coding
mm_47536.1	chr5	124248374	124248399	-	1	NA	intron (NM_011256, intron 1 of 24)	intron (NM_011256, intron 1 of 24)	1374	NM_011256	19679	Mm.44261	NM_011256	ENSMUSG00000029406	Pitpnm2	NIR3|RDGBA2|Rdgb2|mKIAA1457	phosphatidylinositol transfer protein, membrane-associated 2	protein-coding
mm_162689.1	chr10	18953379	18953379	+	1	NA	Intergenic	Intergenic	58584	NM_001166402	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_94023.1	chr10	127667584	127667610	-	1	NA	promoter-TSS (NM_008668)	promoter-TSS (NM_008668)	474	NR_045171	72243	Mm.482902	NR_045171	ENSMUSG00000040195	1700012D01Rik	-	RIKEN cDNA 1700012D01 gene	ncRNA
mm_68284.1	chr7	105610915	105610931	-	1	NA	3' UTR (NM_001285871, exon 12 of 12)	3' UTR (NM_001285871, exon 12 of 12)	-10807	NM_017371	15458	Mm.3485	NM_017371	ENSMUSG00000030895	Hpx	Hpxn|hx	hemopexin	protein-coding
mm_15629.1	chr2	162987443	162987449	+	1	NA	promoter-TSS (NM_013731)	promoter-TSS (NM_013731)	-35	NM_001291154	27219	Mm.26462	NM_013731	ENSMUSG00000017868	Sgk2	AI098171|AW146006|Sgkl	serum/glucocorticoid regulated kinase 2	protein-coding
mm_43161.1	chr5	127027390	127027399	+	1	NA	Intergenic	Intergenic	-3395	NR_040685	71247	Mm.399586	NR_040685	ENSMUSG00000105490	4933438B17Rik	-	RIKEN cDNA 4933438B17 gene	ncRNA
mm_87375.1	chr10	44358393	44358398	+	1	NA	intron (NM_001314013, intron 6 of 6)	B1_Mur4|SINE|Alu	-1281	NR_035450	100316688		NR_035450	ENSMUSG00000089260	Mir1929	mir-1929|mmu-mir-1929	microRNA 1929	ncRNA
mm_26601.1	chr3	152122975	152122981	+	1	NA	intron (NM_016867, intron 3 of 5)	ORR1C1|LTR|ERVL-MaLR	42922	NM_016867	54120	Mm.97	NM_016867	ENSMUSG00000039131	Gipc2	2200002N01Rik|AU021850|Semcap2	GIPC PDZ domain containing family, member 2	protein-coding
mm_84897.1	chr9	79811153	79811158	-	1	NA	Intergenic	Intergenic	17514	NR_040734	74633	Mm.262175	NR_040734	ENSMUSG00000086918	4930429F24Rik	-	RIKEN cDNA 4930429F24 gene	ncRNA
mm_47393.1	chr5	123017558	123017575	-	1	NA	intron (NM_175423, intron 1 of 1)	intron (NM_175423, intron 1 of 1)	2492	NM_175423	109305	Mm.218582	NM_175423	ENSMUSG00000049686	Orai1	D730049H07Rik|Tmem142a|orai-1	ORAI calcium release-activated calcium modulator 1	protein-coding
mm_15409.1	chr2	156775392	156775402	+	1	NA	promoter-TSS (NM_172118)	promoter-TSS (NM_172118)	-67	NM_172118	98932	Mm.271770	NM_172118	ENSMUSG00000067818	Myl9	AI327049|MLC20|Mylc2c|RLC-C	myosin, light polypeptide 9, regulatory	protein-coding
mm_65286.1	chr7	24435492	24435554	-	1	NA	intron (NM_199013, intron 2 of 2)	intron (NM_199013, intron 2 of 2)	10159	NM_199013	210145	Mm.33811	NM_199013	ENSMUSG00000062028	Irgc1	F630044M05Rik|Gm1102|Gm474|Ifgge|Iigp5|Irgc	immunity-related GTPase family, cinema 1	protein-coding
mm_89686.1	chr10	97565437	97565546	+	1	NA	promoter-TSS (NM_008524)	promoter-TSS (NM_008524)	-10	NM_008524	17022	Mm.18888	NM_008524	ENSMUSG00000036446	Lum	Ldc|SLRR2D	lumican	protein-coding
mm_148113.1	chr18	74347602	74347630	-	1	NA	intron (NR_029424, intron 8 of 8)	RMER20C_Mm|LTR|ERVK	64516	NM_028948	74453	Mm.182293	NM_028948	ENSMUSG00000035394	Cfap53	4933415I03Rik|Ccdc11	cilia and flagella associated protein 53	protein-coding
mm_86341.1	chr9	123260777	123260803	-	1	NA	promoter-TSS (NM_001002267)	promoter-TSS (NM_001002267)	-1	NM_001002267	72309	Mm.8569	NM_001002267	ENSMUSG00000054871	Tmem158	2310037P21Rik|Ris1	transmembrane protein 158	protein-coding
mm_43701.1	chr5	139252344	139252455	+	1	NA	promoter-TSS (NM_026269)	promoter-TSS (NM_026269)	75	NM_026269	67604	Mm.270137	NM_026269	ENSMUSG00000025858	Get4	1110007L15Rik|AW412535|Cee	golgi to ER traffic protein 4	protein-coding
mm_25620.1	chr3	118562146	118562156	+	1	NA	promoter-TSS (NM_170778)	promoter-TSS (NM_170778)	-27	NM_170778	99586	Mm.27907	NM_170778	ENSMUSG00000033308	Dpyd	AI315208|DPD|E330028L06Rik	dihydropyrimidine dehydrogenase	protein-coding
mm_80656.1	chr9	90054488	90054499	+	1	NA	5' UTR (NM_007801, exon 1 of 12)	5' UTR (NM_007801, exon 1 of 12)	226	NM_001312649	13036	Mm.2277	NM_007801	ENSMUSG00000032359	Ctsh	AL022844	cathepsin H	protein-coding
mm_46035.1	chr5	91961608	91961612	-	1	NA	intron (NR_073442, intron 1 of 9)	intron (NR_073442, intron 1 of 9)	946	NR_073442	68098	Mm.159453	NM_026557	ENSMUSG00000029397	Rchy1	ARNIP|CHIMP|Pirh2|Zfp363|Znf363	ring finger and CHY zinc finger domain containing 1	protein-coding
mm_121244.1	chr14	103057204	103057214	+	1	NA	TTS (NM_008392)	TTS (NM_008392)	10197	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_98399.1	chr11	94328068	94328077	+	1	NA	promoter-TSS (NM_027799)	promoter-TSS (NM_027799)	71	NM_146024	71452	Mm.141054	NM_027799	ENSMUSG00000020864	Ankrd40	1110011C06Rik|5530600A18Rik|Gcap15	ankyrin repeat domain 40	protein-coding
mm_89323.1	chr10	87931343	87931354	+	1	NA	3' UTR (NM_010512, exon 5 of 5)	3' UTR (NM_010512, exon 5 of 5)	-35323	NR_000040	22172	Mm.391420	NR_000040		Tyms-ps	-	thymidylate synthase, pseudogene	pseudo
mm_52302.1	chr6	108821572	108821610	+	1	NA	3' UTR (NM_026011, exon 7 of 7)	3' UTR (NM_026011, exon 7 of 7)	-7050	NM_138677	192193	Mm.21596	NM_138677	ENSMUSG00000030104	Edem1	A130059K23Rik|EDEM|mKIAA0212	ER degradation enhancer, mannosidase alpha-like 1	protein-coding
mm_106729.1	chr12	3886009	3886013	+	1	NA	intron (NM_007872, intron 6 of 22)	intron (NM_007872, intron 6 of 22)	-5733	NM_153743	13435	Mm.5001	NM_007872	ENSMUSG00000020661	Dnmt3a	MmuIIIA	DNA methyltransferase 3A	protein-coding
mm_129440.1	chr15	78529581	78529605	-	1	NA	promoter-TSS (NM_001204153)	promoter-TSS (NM_001204153)	58	NM_001204153	72709	Mm.34776	NM_028331	ENSMUSG00000022440	C1qtnf6	2810036M19Rik|CTRP6	C1q and tumor necrosis factor related protein 6	protein-coding
mm_124991.1	chr15	22018944	22018945	+	1	NA	Intergenic	Lx6|LINE|L1	696040	NM_001165971	545091	Mm.475598	NM_001165971		Gm5803	EG545091	predicted gene 5803	protein-coding
mm_16887.1	chr2	13011631	13011657	-	1	NA	promoter-TSS (NM_153155)	promoter-TSS (NM_153155)	-780	NM_153155	227580	Mm.229322	NM_153155	ENSMUSG00000049630	C1ql3	1110065A22Rik|AI661623|C1ql|C1qtnf13|CTRP13|K100	C1q-like 3	protein-coding
mm_136843.1	chr17	12760179	12760183	+	1	NA	intron (NM_010515, intron 1 of 47)	PB1D10|SINE|Alu	9525	NM_010515	16004	Mm.26553	NM_010515	ENSMUSG00000023830	Igf2r	AI661837|CD222|CI-MPR|M6P/IGF2R|Mpr300	insulin-like growth factor 2 receptor	protein-coding
mm_47523.1	chr5	124112220	124112246	-	1	NA	promoter-TSS (NM_001347478)	promoter-TSS (NM_001347478)	-67	NM_001347478	66627	Mm.7050	NM_025671	ENSMUSG00000023707	Ogfod2	1300006G11Rik|5730405M13Rik|AU041636|AW552395	2-oxoglutarate and iron-dependent oxygenase domain containing 2	protein-coding
mm_140747.1	chr17	15831173	15831195	-	1	NA	Intergenic	CpG	-4598	NM_178615	68799	Mm.293466	NM_178615	ENSMUSG00000048027	Rgmb	1110059F19Rik|DRAGON	repulsive guidance molecule family member B	protein-coding
mm_48335.1	chr5	139129874	139129880	-	1	NA	promoter-TSS (NM_008923)	promoter-TSS (NM_008923)	-125	NM_008923	19085	Mm.306163	NM_008923	ENSMUSG00000025855	Prkar1b	AI385716|RIbeta	protein kinase, cAMP dependent regulatory, type I beta	protein-coding
mm_154530.1	chrM	13684	13710	-	1	NA	NA	Intergenic	NA	NA								
mm_5826.1	chr1	52799520	52799533	-	1	NA	5' UTR (NM_008384, exon 2 of 6)	5' UTR (NM_008384, exon 2 of 6)	18162	NM_008384	16329	Mm.917	NM_008384	ENSMUSG00000026102	Inpp1	2300002C06Rik|AV137389	inositol polyphosphate-1-phosphatase	protein-coding
mm_64491.1	chr7	143107301	143107314	+	1	NA	promoter-TSS (NM_008434)	promoter-TSS (NM_008434)	53	NM_008434	16535	Mm.439769	NM_008434	ENSMUSG00000009545	Kcnq1	AW559127|KVLQT1|Kcna9	potassium voltage-gated channel, subfamily Q, member 1	protein-coding
mm_6037.1	chr1	59668974	59668977	-	1	NA	intron (NM_009460, intron 1 of 4)	intron (NM_009460, intron 1 of 4)	1859	NM_009460	22218	Mm.362118	NM_009460	ENSMUSG00000026021	Sumo1	GMP1|PIC1|SENTRIN|SMT3|SMT3H3|SMTP3|SUMO-1|Smt3C|Ubl1	small ubiquitin-like modifier 1	protein-coding
mm_6735.1	chr1	82832589	82832597	-	1	NA	Intergenic	Intergenic	-6867	NM_001310713	15463	Mm.392569	NM_010472	ENSMUSG00000026159	Agfg1	AU045498|C130049H11Rik|C85612|D730048C23Rik|Hrb|RAB|Rip	ArfGAP with FG repeats 1	protein-coding
mm_2071.1	chr1	87635963	87635978	+	1	NA	intron (NM_010566, intron 2 of 26)	RSINE1|SINE|B4	15658	NM_001110193	16331	Mm.15105	NM_010566	ENSMUSG00000026288	Inpp5d	SHIP|SHIP-1|SHIP1|SIP-145|p150Ship|s-SHIP	inositol polyphosphate-5-phosphatase D	protein-coding
mm_22589.1	chr3	13473206	13473218	+	1	NA	intron (NM_178631, intron 2 of 9)	CpG	1557	NM_001163328	76897	Mm.422625	NM_178631	ENSMUSG00000039717	Ralyl	0710005M24Rik	RALY RNA binding protein-like	protein-coding
mm_148666.1	chr19	5610066	5610108	+	1	NA	promoter-TSS (NM_178637)	promoter-TSS (NM_178637)	7	NM_001199249	81601	Mm.228930	NM_178637	ENSMUSG00000024926	Kat5	AI839539|CPLA2|Htatip|Htatip1|PLIP|Tip55|Tip60	K(lysine) acetyltransferase 5	protein-coding
mm_42480.1	chr5	115470782	115470793	+	1	NA	exon (NM_011107, exon 2 of 4)	exon (NM_011107, exon 2 of 4)	4521	NM_011107	18778	Mm.20190	NM_011107	ENSMUSG00000029522	Pla2g1b	Pla2a|sPLA2IB	phospholipase A2, group IB, pancreas	protein-coding
mm_73660.1	chr8	111033891	111033932	+	1	NA	promoter-TSS (NM_146217)	promoter-TSS (NM_146217)	69	NM_146217	234734	Mm.24174	NM_146217	ENSMUSG00000031960	Aars	AI316495|C76919|sti	alanyl-tRNA synthetase	protein-coding
mm_134011.1	chr16	4878311	4878313	-	1	NA	intron (NM_145359, intron 1 of 2)	intron (NM_145359, intron 1 of 2)	1539	NM_145359	207740	Mm.268895	NM_145359	ENSMUSG00000039568	Ubald1	1500031H01Rik|BC013706|Fam100a	UBA-like domain containing 1	protein-coding
mm_90282.1	chr10	122941976	122941979	+	1	NA	3' UTR (NM_001110218, exon 10 of 10)	3' UTR (NM_001110218, exon 10 of 10)	43747	NR_029527	387251		NR_029527	ENSMUSG00000065406	Mirlet7i	Mirnlet7i|let-7i|mmu-let-7i	microRNA let7i	ncRNA
mm_107256.1	chr12	28675221	28675239	+	1	NA	promoter-TSS (NM_134052)	promoter-TSS (NM_134052)	23	NM_134052	104923	Mm.291504	NM_134052	ENSMUSG00000020629	Adi1	AL024210|Fe-ARD|MTCBP-1|Ni-ARD	acireductone dioxygenase 1	protein-coding
mm_100617.1	chr11	121556220	121556223	+	1	NA	intron (NM_029878, intron 15 of 38)	intron (NM_029878, intron 15 of 38)	-36879	NM_178763	319530	Mm.11395	NM_178763	ENSMUSG00000039238	Zfp750	A030007D23Rik|Znf750	zinc finger protein 750	protein-coding
mm_31862.1	chr4	80002656	80002669	+	1	NA	Intergenic	Intergenic	-831551	NM_031202	22178	Mm.30438	NM_031202	ENSMUSG00000005994	Tyrp1	Oca3|TRP-1|TRP1|Tyrp|b|brown|isa	tyrosinase-related protein 1	protein-coding
mm_39183.1	chr4	155785060	155785074	-	1	NA	intron (NM_001033394, intron 1 of 1)	intron (NM_001033394, intron 1 of 1)	807	NM_001033394	320587	Mm.384382	NM_001033394	ENSMUSG00000073680	Tmem88b	A230069A22Rik	transmembrane protein 88B	protein-coding
mm_104967.1	chr11	100193254	100193256	-	1	NA	promoter-TSS (NM_201255)	promoter-TSS (NM_201255)	-9	NM_201255	107656	Mm.445335	NM_201255	ENSMUSG00000051617	Krt9	EPPK|K9|Krt1-9	keratin 9	protein-coding
mm_94338.1	chr11	4704643	4704702	+	1	NA	promoter-TSS (NM_026015)	promoter-TSS (NM_026015)	-6	NM_026015	67178	Mm.271056	NM_026015	ENSMUSG00000009076	Zmat5	2610510L01Rik|D11Bwg0572e|D11Bwg1548e	zinc finger, matrin type 5	protein-coding
mm_23692.1	chr3	68691946	68691957	+	1	NA	intron (NM_001159424, intron 2 of 7)	intron (NM_001159424, intron 2 of 7)	527	NM_008351	16159	Mm.103783	NM_008351	ENSMUSG00000027776	Il12a	IL-12p35|Il-12a|Ll12a|p35	interleukin 12a	protein-coding
mm_73666.1	chr8	111056320	111056384	+	1	NA	promoter-TSS (NM_028274)	promoter-TSS (NM_028274)	13	NM_028274	72544	Mm.24174	NM_028274	ENSMUSG00000109941	Exosc6	2610510N21Rik|C76919|Mtr3	exosome component 6	protein-coding
mm_39281.1	chr5	3928034	3928103	+	1	NA	promoter-TSS (NM_194462)	promoter-TSS (NM_194462)	-118	NM_194462	100986	Mm.46044	NM_194462	ENSMUSG00000040407	Akap9	5730481H23Rik|AKAP-9|AKAP450|AW545847|C79026|G1-448-15|PRKA9|mKIAA0803|mei2-5|repro12	A kinase (PRKA) anchor protein (yotiao) 9	protein-coding
mm_65919.1	chr7	30216927	30216933	-	1	NA	Intergenic	Intergenic	15099	NM_025548	66411	Mm.27947	NM_025548	ENSMUSG00000006095	Tbcb	2410007D12Rik|AU041393|CG22|CKAPI|Ckap1	tubulin folding cofactor B	protein-coding
mm_9144.1	chr1	170885389	170885446	-	1	NA	5' UTR (NM_023173, exon 1 of 6)	5' UTR (NM_023173, exon 1 of 6)	123	NM_023173	80915	Mm.34365	NM_023173	ENSMUSG00000026659	Dusp12	1190004O14Rik|AA027408|AW049275|ENSMUSG00000045460|ESTM36|LMW-DSP4|T-DSP4|VH1|mVH1	dual specificity phosphatase 12	protein-coding
mm_29430.1	chr3	109027601	109027646	-	1	NA	promoter-TSS (NM_001163567)	promoter-TSS (NM_001163567)	-16	NM_001163567	329739	Mm.69013	NM_001163567	ENSMUSG00000040339	Fam102b	1600010D10Rik|B430201A12Rik	family with sequence similarity 102, member B	protein-coding
mm_156639.1	chrX	157598194	157598215	+	1	NA	intron (NM_172307, intron 1 of 10)	CpG	511	NM_172307	270669	Mm.37577	NM_172307	ENSMUSG00000046873	Mbtps2	9630032G22Rik|AI662535	membrane-bound transcription factor peptidase, site 2	protein-coding
mm_42694.1	chr5	119836790	119836806	+	1	NA	intron (NM_011537, intron 1 of 8)	intron (NM_011537, intron 1 of 8)	2135	NM_011537	21388	Mm.103636	NM_011537	ENSMUSG00000018263	Tbx5	-	T-box 5	protein-coding
mm_42091.1	chr5	110286327	110286391	+	1	NA	promoter-TSS (NM_011132)	promoter-TSS (NM_011132)	40	NM_011132	18973	Mm.35061	NM_011132	ENSMUSG00000007080	Pole	-	polymerase (DNA directed), epsilon	protein-coding
mm_161621.1	chr16	58729156	58729156	+	1	NA	intron (NR_045517, intron 1 of 4)	intron (NR_045517, intron 1 of 4)	1246	NM_001252451	224250	Mm.29482	NM_171826	ENSMUSG00000022744	Cldnd1	1110019C08Rik|AA407103|AI849195|AW489850|Cldn25	claudin domain containing 1	protein-coding
mm_132103.1	chr16	31428758	31428762	+	1	NA	promoter-TSS (NM_001122683)	promoter-TSS (NM_001122683)	7	NM_001122683	71911	Mm.293470	NM_175177	ENSMUSG00000046598	Bdh1	2310032J20Rik|AI327223|Bdh	3-hydroxybutyrate dehydrogenase, type 1	protein-coding
mm_63522.1	chr7	127904080	127904125	+	1	NA	promoter-TSS (NM_009739)	promoter-TSS (NM_009739)	29	NM_009739	12041	Mm.425495	NM_009739	ENSMUSG00000030802	Bckdk	AI327402	branched chain ketoacid dehydrogenase kinase	protein-coding
mm_27774.1	chr3	72967965	72967970	-	1	NA	Intergenic	Intergenic	-1101	NM_001081137	69983	Mm.261054	NM_001081137	ENSMUSG00000027790	Sis	2010204N08Rik|SI|Si-s	sucrase isomaltase (alpha-glucosidase)	protein-coding
mm_11020.1	chr2	26609802	26609812	+	1	NA	Intergenic	Intergenic	-5390	NM_026212	67512	Mm.24244	NM_026212	ENSMUSG00000026922	Agpat2	2510002J07Rik|AV000834|BSCL|BSCL1|LPAAB|LPAAT-beta	1-acylglycerol-3-phosphate O-acyltransferase 2 (lysophosphatidic acid acyltransferase, beta)	protein-coding
mm_165611.1	chr3	53614761	53614761	+	1	NA	intron (NM_172862, intron 2 of 23)	intron (NM_172862, intron 2 of 23)	42594	NM_172862	242022	Mm.38378	NM_172862	ENSMUSG00000037016	Frem2	6030440P17Rik|8430406N05Rik|Gm409|b2b1562Clo|my|ne|nv1	Fras1 related extracellular matrix protein 2	protein-coding
mm_46064.1	chr5	92278156	92278171	-	1	NA	promoter-TSS (NM_001163687)	promoter-TSS (NM_001163687)	18	NM_001163687	67111	Mm.28890	NM_025972	ENSMUSG00000029413	Naaa	2210023K21Rik|3830414F09Rik|Asahl	N-acylethanolamine acid amidase	protein-coding
mm_68523.1	chr7	112024112	112024154	-	1	NA	intron (NM_133758, intron 1 of 27)	CpG	627	NM_177249	74996	Mm.16974	NM_133758	ENSMUSG00000059263	Usp47	4930502N04Rik|A630020C16Rik	ubiquitin specific peptidase 47	protein-coding
mm_169948.1	chr16	73554131	73554133	-	1	NA	Intergenic	MIRc|SINE|MIR	787935	NR_030464	751561		NR_030464	ENSMUSG00000104758	Mir691	Mirn691|mir-691|mmu-mir-691	microRNA 691	ncRNA
mm_6058.1	chr1	60489819	60489835	-	1	NA	exon (NM_001045513, exon 14 of 14)	exon (NM_001045513, exon 14 of 14)	76938	NM_001045513	77300	Mm.440325	NM_001045513	ENSMUSG00000026014	Raph1	9430025M21Rik|C730009O10Rik|Lpd	Ras association (RalGDS/AF-6) and pleckstrin homology domains 1	protein-coding
mm_107092.1	chr12	17544895	17544951	+	1	NA	promoter-TSS (NM_013614)	promoter-TSS (NM_013614)	50	NM_013614	18263	Mm.34102	NM_013614	ENSMUSG00000011179	Odc1	ODC	ornithine decarboxylase, structural 1	protein-coding
mm_8661.1	chr1	156654238	156654272	-	1	NA	3' UTR (NM_023141, exon 6 of 6)	3' UTR (NM_023141, exon 6 of 6)	20084	NM_023141	30935	Mm.206737	NM_023141	ENSMUSG00000060519	Tor3a	Adir	torsin family 3, member A	protein-coding
mm_77380.1	chr8	119840568	119840570	-	1	NA	promoter-TSS (NM_028071)	promoter-TSS (NM_028071)	10	NM_028071	72042	Mm.393405	NM_028071	ENSMUSG00000031827	Cotl1	1810074P22Rik|2010004C08Rik|Clp	coactosin-like 1 (Dictyostelium)	protein-coding
mm_64488.1	chr7	143069398	143069500	+	1	NA	promoter-TSS (NM_020285)	promoter-TSS (NM_020285)	81	NM_001115085	56844	Mm.139675	NM_020285	ENSMUSG00000045752	Tssc4	AA241958|ESTM671070	tumor-suppressing subchromosomal transferable fragment 4	protein-coding
mm_32102.1	chr4	98726745	98726766	+	1	NA	promoter-TSS (NM_001081202)	promoter-TSS (NM_001081202)	1	NM_001081202	381591	Mm.34340	NM_001081202	ENSMUSG00000087166	L1td1	AA546746|AB211064|D76865|ECAT11	LINE-1 type transposase domain containing 1	protein-coding
mm_52084.1	chr6	97829305	97829316	+	1	NA	intron (NM_001113198, intron 1 of 9)	intron (NM_001113198, intron 1 of 9)	22252	NM_001113198	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_13839.1	chr2	119356321	119356326	+	1	NA	Intergenic	RSINE1|SINE|B4	5081	NM_026929	69065	Mm.35083	NM_026929	ENSMUSG00000027313	Chac1	1810008K03Rik	ChaC, cation transport regulator 1	protein-coding
mm_18925.1	chr2	76745118	76745134	-	1	NA	exon (NM_011652, exon 275 of 313)	exon (NM_011652, exon 275 of 313)	69811	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_97025.1	chr11	72042493	72042508	+	1	NA	promoter-TSS (NM_144526)	promoter-TSS (NM_144526)	-2	NM_144526	109212	Mm.33118	NM_144526	ENSMUSG00000020808	Fam64a	2610008F03Rik|6720460F02Rik|AI115087|CATS	family with sequence similarity 64, member A	protein-coding
mm_57753.1	chr6	129216344	129216364	-	1	NA	Intergenic	Intergenic	21691	NR_040265	76432	Mm.261738	NR_040265	ENSMUSG00000097354	2310001H17Rik	AI646108	RIKEN cDNA 2310001H17 gene	ncRNA
mm_16117.1	chr2	169915090	169915098	+	1	NA	Intergenic	ORR1A3|LTR|ERVL-MaLR	48093	NR_131974	446211	Mm.266854	NR_131974	ENSMUSG00000103935	AY702102	STDP1	cDNA sequence AY702102	ncRNA
mm_42757.1	chr5	120854311	120854312	+	1	NA	intron (NM_145153, intron 3 of 5)	MTD-int|LTR|ERVL-MaLR	6944	NM_145153	243262	Mm.105369	NM_145153	ENSMUSG00000053765	Oas1f	-	2'-5' oligoadenylate synthetase 1F	protein-coding
mm_89009.1	chr10	81628703	81628719	+	1	NA	intron (NM_027480, intron 1 of 19)	intron (NM_027480, intron 1 of 19)	171	NM_027480	70615	Mm.304382	NM_027480	ENSMUSG00000054708	Ankrd24	4631433D01Rik|5730519E19Rik|D10Bur2e	ankyrin repeat domain 24	protein-coding
mm_20086.1	chr2	120731504	120731534	-	1	NA	promoter-TSS (NM_026891)	promoter-TSS (NM_026891)	-2	NM_026891	68968	Mm.2289	NM_026891	ENSMUSG00000027284	Cdan1	1500015A01Rik|AI448026|AW492297|CDA-I|CDA1|CDAI	congenital dyserythropoietic anemia, type I (human)	protein-coding
mm_104322.1	chr11	93955934	93955944	-	1	NA	promoter-TSS (NM_001077529)	promoter-TSS (NM_001077529)	-156	NM_001077529	18103	Mm.1260	NM_008705	ENSMUSG00000020857	Nme2	NM23-H2|NM23B|nm23-M2	NME/NM23 nucleoside diphosphate kinase 2	protein-coding
mm_70807.1	chr8	23021970	23021972	+	1	NA	intron (NM_001277280, intron 1 of 42)	intron (NM_001277280, intron 1 of 42)	-13128	NM_001277281	11733	Mm.334444	NM_031158	ENSMUSG00000031543	Ank1	Ank-1|nb|pale	ankyrin 1, erythroid	protein-coding
mm_162089.1	chrX	37453659	37453659	+	1	NA	promoter-TSS (NM_001099318)	promoter-TSS (NM_001099318)	0	NM_001099318	100039948	Mm.477362	NM_001099318	ENSMUSG00000079637	Rhox2c	OTTMUSG00000017149|Rhox2.3|Rhox2b	reproductive homeobox 2C	protein-coding
mm_108656.1	chr12	86361490	86361499	+	1	NA	5' UTR (NM_001159500, exon 1 of 7)	5' UTR (NM_001159500, exon 1 of 7)	377	NM_001159500	26380	Mm.235550	NM_011934	ENSMUSG00000021255	Esrrb	Err2|Errb|Estrrb|Nr3b2	estrogen related receptor, beta	protein-coding
mm_80040.1	chr9	68970384	68970403	+	1	NA	intron (NM_013646, intron 1 of 10)	MER119|DNA|hAT-Charlie	205047	NR_033299	320440	Mm.483129	NM_177159		9530091C08Rik	-	RIKEN cDNA 9530091C08 gene	ncRNA
mm_121180.1	chr14	103049256	103049262	+	1	NA	intron (NM_008392, intron 1 of 4)	intron (NM_008392, intron 1 of 4)	2247	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_50406.1	chr6	48728185	48728192	+	1	NA	Intergenic	Intergenic	9567	NM_146167	231932	Mm.30479	NM_146167	ENSMUSG00000043931	Gimap7	IAN7|Ian3	GTPase, IMAP family member 7	protein-coding
mm_172780.1	chr8	97592862	97592867	+	1	NA	Intergenic	BGLII|LTR|ERVK	-1046891	NR_039538	100628567		NR_039538	ENSMUSG00000104794	Mir28c	mmu-mir-28c	microRNA 28c	ncRNA
mm_163282.1	chr11	116615908	116615909	-	1	NA	intron (NM_172572, intron 1 of 18)	intron (NM_172572, intron 1 of 18)	8344	NM_001167680	217344	Mm.89695	NM_172572	ENSMUSG00000020806	Rhbdf2	4732465I17Rik|Rhbdl6|cub	rhomboid 5 homolog 2	protein-coding
mm_101066.1	chr11	11404927	11404930	-	1	NA	intron (NM_001185153, intron 5 of 7)	intron (NM_001185153, intron 5 of 7)	57491	NM_015785	53604	Mm.9500	NM_015785	ENSMUSG00000020193	Zpbp	4930486K01Rik|Iam38|Sp38	zona pellucida binding protein	protein-coding
mm_138601.1	chr17	35556048	35556054	+	1	NA	exon (NM_001008424, exon 2 of 2)	exon (NM_001008424, exon 2 of 2)	3923	NM_001008424	386463	Mm.426664	NM_001008424	ENSMUSG00000039518	Cdsn	AI747712	corneodesmosin	protein-coding
mm_60827.1	chr7	45707129	45707142	+	1	NA	intron (NM_016974, intron 2 of 3)	intron (NM_016974, intron 2 of 3)	1888	NM_016974	13170	Mm.24222	NM_016974	ENSMUSG00000059824	Dbp	-	D site albumin promoter binding protein	protein-coding
mm_162244.1	chrX	157818205	157818205	+	1	NA	promoter-TSS (NM_001081667)	promoter-TSS (NM_001081667)	-230	NM_001081667	245683	Mm.295846	NM_001081667	ENSMUSG00000047485	Klhl34	Gm388	kelch-like 34	protein-coding
mm_36551.1	chr4	86691465	86691480	-	1	NA	Intergenic	Intergenic	-21413	NM_007408	11520	Mm.381	NM_007408	ENSMUSG00000028494	Plin2	AA407157|ADPH|Adfp|Adrp	perilipin 2	protein-coding
mm_91602.1	chr10	41221321	41221332	-	1	NA	intron (NM_133999, intron 21 of 22)	intron (NM_133999, intron 21 of 22)	81915	NM_133999	103199	Mm.277242	NM_133999	ENSMUSG00000038417	Fig4	A530089I17Rik|AI326867|Sac3	FIG4 phosphoinositide 5-phosphatase	protein-coding
mm_127197.1	chr15	99075007	99075022	+	1	NA	promoter-TSS (NM_030159)	promoter-TSS (NM_030159)	41	NM_030159	78733	Mm.124905	NM_030159	ENSMUSG00000032783	Troap	AW476063|E130301L11Rik|tastin	trophinin associated protein	protein-coding
mm_37569.1	chr4	126242082	126242096	-	1	NA	exon (NM_144941, exon 2 of 17)	exon (NM_144941, exon 2 of 17)	14230	NM_144941	245877	Mm.266716	NM_144941	ENSMUSG00000028849	Map7d1	AV028413|BC019977|Mtap7d1|Parcc1|Rprc1|mKIAA1187	MAP7 domain containing 1	protein-coding
mm_103047.1	chr11	69802891	69802941	-	1	NA	promoter-TSS (NR_027913)	promoter-TSS (NR_027913)	-753	NR_027913	74341	Mm.280165	NR_027913		G630025P09Rik	4632403M07Rik	RIKEN cDNA G630025P09 gene	ncRNA
mm_141256.1	chr17	27596912	27596919	-	1	NA	intron (NM_019837, intron 1 of 4)	intron (NM_019837, intron 1 of 4)	26049	NM_001291046	56409	Mm.144699	NM_019837	ENSMUSG00000024213	Nudt3	1110011B09Rik|AA960325|Dipp|Dipp1	nudix (nucleotide diphosphate linked moiety X)-type motif 3	protein-coding
mm_149505.1	chr19	11958634	11958646	+	1	NA	Intergenic	Intergenic	-7204	NM_001033174	76303	Mm.291279	NM_001033174	ENSMUSG00000024687	Osbp	1110018F06Rik|AW559088|mKIAA4220	oxysterol binding protein	protein-coding
mm_118212.1	chr13	110127792	110127804	-	1	NA	intron (NM_023852, intron 3 of 4)	intron (NM_023852, intron 3 of 4)	152408	NM_023852	67295	Mm.151600	NM_023852	ENSMUSG00000021700	Rab3c	2700062I01Rik|3110015B08Rik|3110037E15Rik|AI850886	RAB3C, member RAS oncogene family	protein-coding
mm_103797.1	chr11	82890022	82890032	-	1	NA	exon (NM_001277939, exon 2 of 10)	exon (NM_001277939, exon 2 of 10)	597	NR_102719	19364	Mm.9286	NM_011235	ENSMUSG00000018841	Rad51d	R51H3|Rad51l3|TRAD|Trad-d5	RAD51 paralog D	protein-coding
mm_26685.1	chr3	156562142	156562196	+	1	NA	promoter-TSS (NR_040400)	promoter-TSS (NR_040400)	375	NM_001039094	320840	Mm.317293	NM_177274	ENSMUSG00000040037	Negr1	5330422G01Rik|KILON|Ntra	neuronal growth regulator 1	protein-coding
mm_28864.1	chr3	97297922	97297938	-	1	NA	Intergenic	Intergenic	-11326	NR_105813	102465206		NR_105813	ENSMUSG00000099036	Mir378c	Gm27930|mmu-mir-378c	microRNA 378c	ncRNA
mm_25308.1	chr3	106034662	106034692	+	1	NA	Intergenic	Intergenic	-1782	NM_001080816	229687	Mm.39224	NM_170594	ENSMUSG00000043873	Chil5	Bclp|Bclp1|Bclp2|Chi3l7	chitinase-like 5	protein-coding
mm_109354.1	chr12	109615771	109615772	+	1	NA	intron (NR_028261, intron 2 of 20)	intron (NR_028261, intron 2 of 20)	-2487	NR_029918	723854		NR_029918	ENSMUSG00000065433	Mir370	Mirn370|mir-370|mmu-mir-370	microRNA 370	ncRNA
mm_96082.1	chr11	60105053	60105078	+	1	NA	promoter-TSS (NM_009021)	promoter-TSS (NM_009021)	52	NM_009021	19377	Mm.296366	NM_009021	ENSMUSG00000062115	Rai1	Gt1	retinoic acid induced 1	protein-coding
mm_58299.1	chr6	145865549	145865557	-	1	NA	promoter-TSS (NM_001271768)	promoter-TSS (NM_001271768)	-133	NM_024469	79362	Mm.154529	NM_024469	ENSMUSG00000030256	Bhlhe41	6430520M22Rik|Bhlhb2l|Bhlhb3|DEC2|Sharp1	basic helix-loop-helix family, member e41	protein-coding
mm_64807.1	chr7	6706411	6706422	-	1	NA	promoter-TSS (NR_023846)	promoter-TSS (NR_023846)	-344	NR_023846	100169889	Mm.491213	NR_023846		Peg3os	Apeg3|Peg3as	Peg3 opposite strand	ncRNA
mm_84859.1	chr9	78583232	78583249	-	1	NA	intron (NM_001276452, intron 1 of 10)	intron (NM_001276452, intron 1 of 10)	4805	NM_172773	235504	Mm.46932	NM_172773	ENSMUSG00000049624	Slc17a5	4631416G20Rik|4732491M05|AST|ISSD|NSD|SD|SIALIN|SIASD|SLD	solute carrier family 17 (anion/sugar transporter), member 5	protein-coding
mm_25100.1	chr3	101284137	101284157	+	1	NA	intron (NM_013486, intron 2 of 4)	intron (NM_013486, intron 2 of 4)	3792	NM_013486	12481	Mm.22842	NM_013486	ENSMUSG00000027863	Cd2	LFA-2|Ly-37|Ly37	CD2 antigen	protein-coding
mm_135955.1	chr16	74644232	74644237	-	1	NA	Intergenic	Lx2|LINE|L1	-233322	NM_175549	268902	Mm.171736	NM_175549	ENSMUSG00000052516	Robo2	2600013A04Rik|9430089E08Rik|BB097918|D230004I22Rik|mKIAA1568	roundabout guidance receptor 2	protein-coding
mm_112708.1	chr13	18842142	18842163	+	1	NA	intron (NM_172120, intron 17 of 28)	intron (NM_172120, intron 17 of 28)	-106199	NM_175007	218038	Mm.101650	NM_175007	ENSMUSG00000021314	Amph	-	amphiphysin	protein-coding
mm_32749.1	chr4	116685591	116685608	+	1	NA	promoter-TSS (NM_011034)	promoter-TSS (NM_011034)	0	NM_011034	18477	Mm.30929	NM_011034	ENSMUSG00000028691	Prdx1	MSP23|NkefA|OSF-3|OSF3|PAG|Paga|PrdxI|PrxI|TDX2|TPxA|Tdpx2|prx1	peroxiredoxin 1	protein-coding
mm_167983.1	chrX	166217265	166217265	+	1	NA	Intergenic	Intergenic	-21678	NM_001177961	14758	Mm.222320	NM_023122	ENSMUSG00000031342	Gpm6b	AI593561|Gpm6|M6B	glycoprotein m6b	protein-coding
mm_131012.1	chr15	103563273	103563275	-	1	NA	exon (NM_008134, exon 3 of 4)	exon (NM_008134, exon 3 of 4)	1807	NM_001289587	14663	Mm.219621	NM_008134	ENSMUSG00000022491	Glycam1	MC26|Sgp50|glyCAM-1	glycosylation dependent cell adhesion molecule 1	protein-coding
mm_102154.1	chr11	53705685	53705725	-	1	NA	intron (NM_009012, intron 2 of 24)	intron (NM_009012, intron 2 of 24)	1614	NM_009012	19360	Mm.4888	NM_009012	ENSMUSG00000020380	Rad50	Mrell|Rad50l	RAD50 double strand break repair protein	protein-coding
mm_119461.1	chr14	47069041	47069049	+	1	NA	promoter-TSS (NM_001310544)	promoter-TSS (NM_001310544)	68	NM_001310544	74480	Mm.214454	NM_028966	ENSMUSG00000021838	Samd4	1700024G08Rik|1700111L17Rik|4933436G17Rik|Samd4a|Smaug|Smaug1|sunk	sterile alpha motif domain containing 4	protein-coding
mm_125708.1	chr15	68309777	68309784	+	1	NA	Intergenic	Intergenic	27730	NR_029534	387226		NR_029534	ENSMUSG00000065476	Mir30b	Mirn30b|mir-30b|mmu-mir-30b	microRNA 30b	ncRNA
mm_569.1	chr1	38042778	38042791	+	1	NA	intron (NM_198303, intron 14 of 23)	intron (NM_198303, intron 14 of 23)	44774	NM_198303	226982	Mm.260943	NM_198303	ENSMUSG00000026083	Eif5b	A030003E17Rik|BC018347|IF2	eukaryotic translation initiation factor 5B	protein-coding
mm_91758.1	chr10	51454014	51454038	-	1	NA	Intergenic	Intergenic	-26586	NM_008147	14727	Mm.439661	NM_008147	ENSMUSG00000062593	Lilr4b	Gp49a|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4B	protein-coding
mm_64578.1	chr7	144941682	144941721	+	1	NA	Intergenic	CpG	-1776	NM_007631	12443	Mm.273049	NM_007631	ENSMUSG00000070348	Ccnd1	AI327039|CycD1|Cyl-1|PRAD1|bcl-1|cD1	cyclin D1	protein-coding
mm_72420.1	chr8	82054106	82054111	+	1	NA	intron (NM_001024617, intron 22 of 24)	intron (NM_001024617, intron 22 of 24)	348478	NM_001254747	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_67031.1	chr7	66689501	66689525	-	1	NA	promoter-TSS (NR_003961)	promoter-TSS (NR_003961)	48	NM_080443	117589	Mm.34785	NM_080443	ENSMUSG00000030509	Asb7	AI449039|Asb-7|D030055C23Rik	ankyrin repeat and SOCS box-containing 7	protein-coding
mm_52517.1	chr6	115422041	115422067	+	1	NA	promoter-TSS (NM_011146)	promoter-TSS (NM_011146)	-12	NM_011146	19016	Mm.3020	NM_011146	ENSMUSG00000000440	Pparg	Nr1c3|PPAR-gamma|PPAR-gamma2|PPARgamma|PPARgamma2	peroxisome proliferator activated receptor gamma	protein-coding
mm_105458.1	chr11	104550461	104550560	-	1	NA	promoter-TSS (NM_010858)	promoter-TSS (NM_010858)	110	NM_001285990	217232	Mm.89845	NM_145436	ENSMUSG00000020687	Cdc27	AI452358|APC3|BC023187	cell division cycle 27	protein-coding
mm_68073.1	chr7	101869207	101869230	-	1	NA	5' UTR (NM_008034, exon 2 of 7)	5' UTR (NM_008034, exon 2 of 7)	1570	NM_001252554	14275	Mm.2135	NM_008034	ENSMUSG00000001827	Folr1	FBP1|Folbp-1|Folbp1	folate receptor 1 (adult)	protein-coding
mm_119144.1	chr14	31255581	31255628	+	1	NA	exon (NM_027088, exon 10 of 17)	exon (NM_027088, exon 10 of 17)	4115	NM_027088	104416	Mm.3779	NM_027088	ENSMUSG00000021901	Bap1	2300006C11Rik|AA989761|AW553466|mKIAA0272|uch-x4	Brca1 associated protein 1	protein-coding
mm_94142.1	chr10	128734448	128734452	-	1	NA	intron (NM_016811, intron 5 of 23)	B2_Mm2|SINE|B2	9606	NM_016811	13139	Mm.291235	NM_016811	ENSMUSG00000025357	Dgka	80kDa|AW146112|Dagk1	diacylglycerol kinase, alpha	protein-coding
mm_69697.1	chr7	140036364	140036400	-	1	NA	promoter-TSS (NM_001286011)	promoter-TSS (NM_001286011)	-9	NM_027201	69752	Mm.200818	NM_027201	ENSMUSG00000025470	Zfp511	2410004P19Rik|C86579|Znf511	zinc finger protein 511	protein-coding
mm_10129.1	chr2	3780091	3780114	+	1	NA	3' UTR (NM_025626, exon 4 of 4)	3' UTR (NM_025626, exon 4 of 4)	66644	NM_025626	66540	Mm.277864	NM_025626	ENSMUSG00000026655	Fam107b	3110001A13Rik|AA589595|AA959793|AI132312	family with sequence similarity 107, member B	protein-coding
mm_35862.1	chr4	49481118	49481128	-	1	NA	Intergenic	RLTR9C|LTR|ERVK	25435	NM_007519	12012	Mm.2859	NM_007519	ENSMUSG00000039653	Baat	AI118337|AI158864|BAT	bile acid-Coenzyme A: amino acid N-acyltransferase	protein-coding
mm_99643.1	chr11	105292678	105292692	+	1	NA	promoter-TSS (NM_008626)	promoter-TSS (NM_008626)	39	NM_008626	17534	Mm.235616	NM_008626	ENSMUSG00000020695	Mrc2	Endo180|mKIAA0709|uPARAP	mannose receptor, C type 2	protein-coding
mm_154634.1	chrX	7762883	7762898	+	1	NA	5' UTR (NM_001271489, exon 1 of 10)	5' UTR (NM_001271489, exon 1 of 10)	229	NM_172472	209446	Mm.249142	NM_172472	ENSMUSG00000000134	Tfe3	F830016E06Rik|Tcfe3|Tfe-3|bHLHe33	transcription factor E3	protein-coding
mm_2551.1	chr1	107917280	107917302	+	1	NA	promoter-TSS (NR_102307)	promoter-TSS (NR_102307)	32	NR_102307	319596	Mm.136054	NR_102306	ENSMUSG00000100457	D830032E09Rik	-	RIKEN cDNA D830032E09 gene	ncRNA
mm_165324.1	chr2	110419634	110419643	-	1	NA	Intergenic	Intergenic	-56645	NM_026271	67606	Mm.291809	NM_026271	ENSMUSG00000074971	Fibin	1110018M03Rik	fin bud initiation factor homolog (zebrafish)	protein-coding
mm_112073.1	chr12	112581178	112581203	-	1	NA	Intergenic	Intergenic	-7594	NM_198411	70435	Mm.250193	NM_198411	ENSMUSG00000037679	Inf2	2610204M08Rik|AA589465|AW125550|EG629699	inverted formin, FH2 and WH2 domain containing	protein-coding
mm_2020.1	chr1	87128079	87128092	+	1	NA	TTS (NM_007432)	TTS (NM_007432)	3077	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_39060.1	chr4	154025624	154025634	-	1	NA	intron (NM_001163721, intron 1 of 3)	intron (NM_001163721, intron 1 of 3)	415	NM_001163722	68859	Mm.477488	NM_001033144	ENSMUSG00000078350	Smim1	0610011H04Rik|1190007F08Rik|2700009I11Rik	small integral membrane protein 1	protein-coding
mm_15444.1	chr2	157367177	157367200	+	1	NA	promoter-TSS (NM_026968)	promoter-TSS (NM_026968)	-406	NM_026968	69161	Mm.228619	NM_026968	ENSMUSG00000063019	Manbal	1810024K12Rik|AI836500	mannosidase, beta A, lysosomal-like	protein-coding
mm_72244.1	chr8	75033674	75033702	+	1	NA	promoter-TSS (NM_011622)	promoter-TSS (NM_011622)	2	NM_011622	21968	Mm.1967	NM_011622	ENSMUSG00000042870	Tom1	-	target of myb1 trafficking protein	protein-coding
mm_71564.1	chr8	53511775	53511808	+	1	NA	promoter-TSS (NM_001205054)	promoter-TSS (NM_001205054)	89	NM_001005847	11593	Mm.334535	NM_001005847	ENSMUSG00000031521	Aga	AW060726	aspartylglucosaminidase	protein-coding
mm_111632.1	chr12	102439824	102439836	-	1	NA	promoter-TSS (NM_011175)	promoter-TSS (NM_011175)	-17	NM_011175	19141	Mm.17185	NM_011175	ENSMUSG00000021190	Lgmn	AEP|AI746452|AU022324|Prsc1	legumain	protein-coding
mm_107920.1	chr12	71059383	71059383	+	1	NA	intron (NM_001081195, intron 11 of 23)	intron (NM_001081195, intron 11 of 23)	43416	NM_001081195	238247	Mm.241601	NM_001081195	ENSMUSG00000048118	Arid4a	A630009N03|A630067N03Rik|MmRBBP1|Rbbp1	AT rich interactive domain 4A (RBP1-like)	protein-coding
mm_36897.1	chr4	107683531	107683574	-	1	NA	intron (NM_019872, intron 1 of 3)	CpG	610	NM_019872	56296	Mm.141324	NM_019872	ENSMUSG00000028610	Dmrtb1	Dmrt6|Prp13	DMRT-like family B with proline-rich C-terminal, 1	protein-coding
mm_9567.1	chr1	173979489	173979503	-	1	NA	intron (NM_008327, intron 1 of 6)	L1_Mur3|LINE|L1	3348	NM_008327	26388	Mm.218770	NM_008327	ENSMUSG00000026535	Ifi202b	Ifbip-1|Ifi202|Ifi202a|p202	interferon activated gene 202B	protein-coding
mm_155725.1	chrX	96155452	96155501	+	1	NA	exon (NM_010833, exon 6 of 13)	exon (NM_010833, exon 6 of 13)	59431	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_121373.1	chr14	118137102	118137178	+	1	NA	promoter-TSS (NM_021434)	promoter-TSS (NM_021434)	13	NM_021434	58245	Mm.275411	NM_021434	ENSMUSG00000022131	Gpr180	AB041545|E130016I23Rik|Itr	G protein-coupled receptor 180	protein-coding
mm_28601.1	chr3	94582549	94582573	-	1	NA	5' UTR (NM_029721, exon 1 of 12)	5' UTR (NM_029721, exon 1 of 12)	155	NM_001082484	76742	Mm.28160	NM_029721	ENSMUSG00000028136	Snx27	5730552M22Rik|ESTM45|ESTM47|R75405	sorting nexin family member 27	protein-coding
mm_113063.1	chr13	23740127	23740175	+	1	NA	TTS (NM_015786)	TTS (NM_015786)	1344	NM_015786	50708	Mm.193539	NM_015786	ENSMUSG00000036181	Hist1h1c	0610008C09Rik|H1.2|H1c|H1f2|H1var1|His1a	histone cluster 1, H1c	protein-coding
mm_13580.1	chr2	112377156	112377175	+	1	NA	Intergenic	RLTR12D|LTR|ERVK	-2046	NM_024254	72425	Mm.425091	NM_024254	ENSMUSG00000027132	Katnbl1	2410042D21Rik|AA166487|AA473307|AI467442	katanin p80 subunit B like 1	protein-coding
mm_132623.1	chr16	38892503	38892534	+	1	NA	Intergenic	Intergenic	-9827	NM_170599	207683	Mm.245564	NM_170599	ENSMUSG00000022790	Igsf11	1700025L02Rik|BT-IgSF|Igsf13	immunoglobulin superfamily, member 11	protein-coding
mm_165598.1	chr3	49051271	49051272	+	1	NA	Intergenic	Intergenic	-442171	NR_003617	66332	Mm.46124	NM_025493		1700018B24Rik	-	enhancer of rudimentary homolog pseudogene	pseudo
mm_45449.1	chr5	67428101	67428138	-	1	NA	promoter-TSS (NM_001164806)	promoter-TSS (NM_001164806)	-320	NM_001164806	666938	Mm.101339	NM_001164806	ENSMUSG00000092060	Bend4	D330027G24Rik|EG666938	BEN domain containing 4	protein-coding
mm_103510.1	chr11	76623297	76623309	-	1	NA	Intergenic	CpG	-45564	NM_198894	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_146940.1	chr18	32240228	32240274	-	1	NA	promoter-TSS (NM_133658)	promoter-TSS (NM_133658)	-80	NM_133658	13872	Mm.282335	NM_133658	ENSMUSG00000024382	Ercc3	BTF2 p89|Ercc-3|XPB	excision repair cross-complementing rodent repair deficiency, complementation group 3	protein-coding
mm_39542.1	chr5	21543505	21543521	+	1	NA	promoter-TSS (NM_028977)	promoter-TSS (NM_028977)	-14	NM_028977	74511	Mm.439963	NM_028977	ENSMUSG00000039883	Lrrc17	37kDa|4833425M04Rik|6130400C22Rik|P37nb	leucine rich repeat containing 17	protein-coding
mm_90029.1	chr10	115427320	115427332	+	1	NA	intron (NM_001033261, intron 28 of 34)	intron (NM_001033261, intron 28 of 34)	42367	NM_001033261	216345	Mm.207621	NM_001033261	ENSMUSG00000034163	Zfc3h1	BC033596|Ccdc131|Psrc2	zinc finger, C3H1-type containing	protein-coding
mm_39137.1	chr4	155217206	155217212	-	1	NA	intron (NM_011385, intron 1 of 6)	intron (NM_011385, intron 1 of 6)	5326	NM_011385	20481	Mm.28520	NM_011385	ENSMUSG00000029050	Ski	2310012I02Rik|2610001A11Rik|AA062172|AA589460|BC004088	ski sarcoma viral oncogene homolog (avian)	protein-coding
mm_25451.1	chr3	108364977	108364988	+	1	NA	promoter-TSS (NM_026831)	promoter-TSS (NM_026831)	71	NM_026831	68753	Mm.75201	NM_026831	ENSMUSG00000068745	Mybphl	1110037P11Rik	myosin binding protein H-like	protein-coding
mm_139711.1	chr17	57460043	57460082	+	1	NA	intron (NM_010130, intron 17 of 21)	Lx9|LINE|L1	85252	NM_001104591	224916	Mm.469889	NM_001104591	ENSMUSG00000090655	Vmn2r120	EG224916	vomeronasal 2, receptor 120	protein-coding
mm_42774.1	chr5	121367093	121367110	+	1	NA	3' UTR (NM_181421, exon 76 of 76)	3' UTR (NM_181421, exon 76 of 76)	18514	NM_001163470	231712	Mm.20488	NM_172275	ENSMUSG00000042726	Trafd1	1110008K06Rik|Fln29	TRAF type zinc finger domain containing 1	protein-coding
mm_74414.1	chr8	3624990	3625014	-	1	NA	promoter-TSS (NM_001129804)	promoter-TSS (NM_001129804)	47	NM_001129804	18545	Mm.440882	NM_008790	ENSMUSG00000004630	Pcp2	L7|Pcp-2	Purkinje cell protein 2 (L7)	protein-coding
mm_161554.1	chr16	11405747	11405747	+	1	NA	promoter-TSS (NM_001290148)	promoter-TSS (NM_001290148)	99	NM_001290148	74478	Mm.325831	NM_028964	ENSMUSG00000071669	Snx29	4933437K13Rik|ENSMUSG00000079738|Gm11170|Gm1737|Gm930|Rundc2a	sorting nexin 29	protein-coding
mm_14574.1	chr2	135646518	135646529	+	1	NA	Intergenic	RLTR17|LTR|ERVK	-63303	NR_015544	320684	Mm.421433	NR_015544	ENSMUSG00000085631	9630028H03Rik	-	RIKEN cDNA 9630028H03 gene	ncRNA
mm_118010.1	chr13	100724545	100724547	-	1	NA	intron (NM_009874, intron 2 of 11)	MERVK26-int|LTR|ERVK	6396	NM_009874	12572	Mm.259718	NM_009874	ENSMUSG00000069089	Cdk7	AI323415|AI528512|C230069N13|Cdkn7|Crk4	cyclin-dependent kinase 7	protein-coding
mm_5997.1	chr1	58727093	58727112	-	1	NA	intron (NM_001293804, intron 3 of 9)	intron (NM_001293804, intron 3 of 9)	-3450	NM_001293805	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_124269.1	chr14	102982696	102982704	-	1	NA	promoter-TSS (NR_039592)	promoter-TSS (NR_039592)	-63	NM_177715	239217	Mm.246466	NM_177715	ENSMUSG00000098557	Kctd12	AU046135|AW538430|Pfet1|Pfetin	potassium channel tetramerisation domain containing 12	protein-coding
mm_33664.1	chr4	133174540	133174572	+	1	NA	intron (NM_153423, intron 1 of 8)	intron (NM_153423, intron 1 of 8)	-21099	NR_105984	102466215		NR_105984	ENSMUSG00000099202	Mir7017	Gm27945|mmu-mir-7017	microRNA 7017	ncRNA
mm_13218.1	chr2	96318360	96318403	+	1	NA	5' UTR (NM_001289742, exon 1 of 8)	5' UTR (NM_001289742, exon 1 of 8)	212	NM_001289743	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_97862.1	chr11	83116914	83116918	+	1	NA	promoter-TSS (NM_011407)	promoter-TSS (NM_011407)	71	NM_011407	20555	Mm.10948	NM_011407	ENSMUSG00000078763	Slfn1	AV316259	schlafen 1	protein-coding
mm_57878.1	chr6	131245250	131245283	-	1	NA	exon (NM_001170851, exon 2 of 9)	exon (NM_001170851, exon 2 of 9)	2096	NM_001170851	16633	Mm.4783	NM_008462	ENSMUSG00000030187	Klra2	Klra30|Ly49b	killer cell lectin-like receptor, subfamily A, member 2	protein-coding
mm_12729.1	chr2	78869010	78869109	+	1	NA	promoter-TSS (NM_009454)	promoter-TSS (NM_009454)	12	NM_009454	22193	Mm.1485	NM_009454	ENSMUSG00000027011	Ube2e3	Ubce4|ubcM2	ubiquitin-conjugating enzyme E2E 3	protein-coding
mm_91026.1	chr10	17920195	17920209	-	1	NA	intron (NM_001033432, intron 1 of 3)	B4A|SINE|B4	27865	NM_001033432	380629	Mm.276430	NM_001033432	ENSMUSG00000039879	Heca	Gm869|HDC|HDCL	hdc homolog, cell cycle regulator	protein-coding
mm_62083.1	chr7	92934315	92934325	+	1	NA	3' UTR (NM_028243, exon 9 of 9)	3' UTR (NM_028243, exon 9 of 9)	59067	NM_028243	72461	Mm.389969	NM_028243	ENSMUSG00000061119	Prcp	2510048K03Rik|2610104A14Rik|AI451719|HUMPCP|PCP	prolylcarboxypeptidase (angiotensinase C)	protein-coding
mm_28327.1	chr3	89349969	89350001	-	1	NA	promoter-TSS (NM_001037722)	promoter-TSS (NM_001037722)	43	NM_001037722	11490	Mm.274049	NM_009614	ENSMUSG00000028041	Adam15	AD56|MDC15	a disintegrin and metallopeptidase domain 15 (metargidin)	protein-coding
mm_134708.1	chr16	22892224	22892295	-	1	NA	exon (NM_001276450, exon 1 of 7)	exon (NM_001276450, exon 1 of 7)	244	NM_001276449	11625	Mm.197554	NM_013465	ENSMUSG00000022868	Ahsg	-	alpha-2-HS-glycoprotein	protein-coding
mm_74462.1	chr8	4216980	4217003	-	1	NA	intron (NM_207203, intron 1 of 6)	intron (NM_207203, intron 1 of 6)	321	NM_207203	73072	Mm.477379	NM_207203	ENSMUSG00000064125	Prr36	-	proline rich 36	protein-coding
mm_96419.1	chr11	67255829	67255840	+	1	NA	exon (NM_010855, exon 33 of 40)	exon (NM_010855, exon 33 of 40)	18022	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_78037.1	chr9	13894847	13894852	+	1	NA	Intergenic	Intergenic	67122	NM_176836	72826	Mm.246174	NM_176836	ENSMUSG00000037808	Fam76b	2810485I05Rik|C78303	family with sequence similarity 76, member B	protein-coding
mm_165101.1	chr19	55318025	55318025	+	1	NA	intron (NM_001293685, intron 1 of 8)	intron (NM_001293685, intron 1 of 8)	1968	NM_001293686	53611	Mm.258637	NM_016862	ENSMUSG00000024983	Vti1a	1110014F16Rik|1110018K19Rik|4921537J05Rik|MVti1|MVti1a|Vti1|Vti1-rp2	vesicle transport through interaction with t-SNAREs 1A	protein-coding
mm_38821.1	chr4	148723353	148723363	-	1	NA	Intergenic	Intergenic	80041	NM_001085505	230909	Mm.332067	NM_001085505	ENSMUSG00000070577	Gm572	b2b1167Clo	predicted gene 572	protein-coding
mm_89974.1	chr10	111553992	111554025	+	1	NA	Intergenic	Intergenic	40265	NR_045344	71321	Mm.410785	NR_045344	ENSMUSG00000097082	4933440J02Rik	-	RIKEN cDNA 4933440J02 gene	ncRNA
mm_139506.1	chr17	56304229	56304247	+	1	NA	promoter-TSS (NM_001111080)	promoter-TSS (NM_001111080)	-75	NM_001111078	18140	Mm.42196	NM_010931	ENSMUSG00000001228	Uhrf1	AL022808|ICBP90|Np95|RNF106	ubiquitin-like, containing PHD and RING finger domains, 1	protein-coding
mm_91126.1	chr10	19591702	19591712	-	1	NA	promoter-TSS (NM_010511)	promoter-TSS (NM_010511)	-242	NM_010511	15979	Mm.549	NM_010511	ENSMUSG00000020009	Ifngr1	CD119|IFN-gammaR|Ifgr|Ifngr|Nktar	interferon gamma receptor 1	protein-coding
mm_26299.1	chr3	142508045	142508056	+	1	NA	exon (NM_153564, exon 10 of 11)	exon (NM_153564, exon 10 of 11)	11116	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_126407.1	chr15	80255302	80255321	+	1	NA	5' UTR (NM_009716, exon 1 of 3)	5' UTR (NM_009716, exon 1 of 3)	127	NM_009716	11911	Mm.641	NM_009716	ENSMUSG00000042406	Atf4	Atf-4|C/ATF|CREB2|TAXREB67	activating transcription factor 4	protein-coding
mm_112512.1	chr13	8995592	8995611	+	1	NA	intron (NM_027000, intron 1 of 16)	intron (NM_027000, intron 1 of 16)	411	NM_027000	69237	Mm.41800	NM_027000	ENSMUSG00000021149	Gtpbp4	2610028C09Rik|Crfg|Gtpbp3|NGB|Nog1	GTP binding protein 4	protein-coding
mm_138280.1	chr17	34608987	34608989	+	1	NA	promoter-TSS (NM_018862)	promoter-TSS (NM_018862)	-26	NM_018862	55979	Mm.8684	NM_018862	ENSMUSG00000034254	Agpat1	1-AGP|1-AGPAT|AW047140	1-acylglycerol-3-phosphate O-acyltransferase 1 (lysophosphatidic acid acyltransferase, alpha)	protein-coding
mm_144390.1	chr18	20670049	20670067	+	1	NA	exon (NM_013697, exon 3 of 4)	exon (NM_013697, exon 3 of 4)	4808	NM_013697	22139	Mm.2108	NM_013697	ENSMUSG00000061808	Ttr	AA408768|AI787086|D17860|prealbumin	transthyretin	protein-coding
mm_146265.1	chr18	77847490	77847498	+	1	NA	intron (NM_013831, intron 3 of 14)	ID_B1|SINE|B4	52944	NM_013831	19201	Mm.57174	NM_013831	ENSMUSG00000025429	Pstpip2	MAYP|cmo	proline-serine-threonine phosphatase-interacting protein 2	protein-coding
mm_161941.1	chr19	4100780	4100780	+	1	NA	5' UTR (NM_008851, exon 1 of 23)	5' UTR (NM_008851, exon 1 of 23)	158	NM_008851	18739	Mm.1860	NM_008851	ENSMUSG00000024851	Pitpnm1	DRES9|Mpt-1|Nir-2|PITPnm 1|Pitpnm|R75447|Rd9|RdgB|RdgB1	phosphatidylinositol transfer protein, membrane-associated 1	protein-coding
mm_53659.1	chr6	141296977	141296981	+	1	NA	intron (NM_018779, intron 1 of 15)	intron (NM_018779, intron 1 of 15)	-43574	NR_033555	100093700	Mm.483778	NR_033555	ENSMUSG00000107456	Gm10400	ENSMUSG00000072690	predicted gene 10400	ncRNA
mm_119961.1	chr14	55478754	55478767	+	1	NA	promoter-TSS (NM_030686)	promoter-TSS (NM_030686)	2	NM_030686	28200	Mm.27427	NM_030686	ENSMUSG00000022210	Dhrs4	AI043103|AI790593|CR|D14Ucla2|NDRD|PHCR|PSCD|RRD|mouNRDR	dehydrogenase/reductase (SDR family) member 4	protein-coding
mm_142350.1	chr17	43628572	43628579	-	1	NA	exon (NM_198418, exon 1 of 5)	exon (NM_198418, exon 1 of 5)	1724	NM_001161366	210510	Mm.329058	NM_198418	ENSMUSG00000040140	Tdrd6	AB097085|Tdr2	tudor domain containing 6	protein-coding
mm_63694.1	chr7	130624583	130624601	+	1	NA	exon (NM_001004468, exon 3 of 22)	exon (NM_001004468, exon 3 of 22)	47108	NM_206856	57752	Mm.86322	NM_021314	ENSMUSG00000030852	Tacc2	mKIAA4180	transforming, acidic coiled-coil containing protein 2	protein-coding
mm_149414.1	chr19	11426192	11426218	+	1	NA	exon (NM_029499, exon 7 of 7)	exon (NM_029499, exon 7 of 7)	-17353	NM_021718	60361	Mm.33957	NM_021718	ENSMUSG00000056290	Ms4a4b	AI463180|Chandra|Ly116	membrane-spanning 4-domains, subfamily A, member 4B	protein-coding
mm_42674.1	chr5	119680222	119680236	+	1	NA	intron (NM_198052, intron 6 of 7)	intron (NM_198052, intron 6 of 7)	8996	NM_011535	21386	Mm.219139	NM_011535	ENSMUSG00000018604	Tbx3	D5Ertd189e	T-box 3	protein-coding
mm_158097.1	chrX	101734111	101734123	-	1	NA	promoter-TSS (NM_009910)	promoter-TSS (NM_009910)	30	NM_009910	12766	Mm.12876	NM_009910	ENSMUSG00000050232	Cxcr3	Cd183|Cmkar3	chemokine (C-X-C motif) receptor 3	protein-coding
mm_117320.1	chr13	67724265	67724340	-	1	NA	intron (NM_145622, intron 1 of 3)	intron (NM_145622, intron 1 of 3)	4871	NM_145622	235907	Mm.440123	NM_145622	ENSMUSG00000071281	Zfp65	KRAB5|Zfp71-rs1|pz114	zinc finger protein 65	protein-coding
mm_121452.1	chr14	120478355	120478392	+	1	NA	promoter-TSS (NM_029519)	promoter-TSS (NM_029519)	-88	NM_029519	76108	Mm.261448	NM_029519	ENSMUSG00000051615	Rap2a	5830461H18Rik	RAS related protein 2a	protein-coding
mm_164880.1	chr18	58210523	58210569	-	1	NA	promoter-TSS (NM_010181)	promoter-TSS (NM_010181)	-620	NM_010181	14119	Mm.20271	NM_010181	ENSMUSG00000024598	Fbn2	BC063774|Fib-2|mKIAA4226|sne|sy	fibrillin 2	protein-coding
mm_26961.1	chr3	21988258	21988279	-	1	NA	Intergenic	Intergenic	-88384	NM_030732	81004	Mm.202966	NM_030732	ENSMUSG00000027630	Tbl1xr1	8030499H02Rik|A630076E03Rik|AW539987|C21|C230089I12Rik|DC42|Ira1|TBLR1	transducin (beta)-like 1X-linked receptor 1	protein-coding
mm_56833.1	chr6	117174687	117174707	-	1	NA	3' UTR (NM_021704, exon 3 of 3)	3' UTR (NM_021704, exon 3 of 3)	6162	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_7254.1	chr1	93754691	93754707	-	1	NA	promoter-TSS (NM_174874)	promoter-TSS (NM_174874)	139	NM_025920	67026	Mm.272356	NM_025920	ENSMUSG00000026279	Thap4	2010320B01Rik	THAP domain containing 4	protein-coding
mm_64009.1	chr7	140203824	140203849	+	1	NA	Intergenic	Intergenic	-1068	NM_001011814	258055	Mm.377339	NM_001011814	ENSMUSG00000050366	Olfr524	MOR103-14P	olfactory receptor 524	protein-coding
mm_123573.1	chr14	66986028	66986040	-	1	NA	3' UTR (NM_009761, exon 6 of 6)	3' UTR (NM_009761, exon 6 of 6)	22843	NM_009761	12177	Mm.29820	NM_009761	ENSMUSG00000022051	Bnip3l	C86132|D14Ertd719e|Nip3L|Nix	BCL2/adenovirus E1B interacting protein 3-like	protein-coding
mm_107072.1	chr12	16909483	16909485	+	1	NA	intron (NM_009072, intron 1 of 32)	intron (NM_009072, intron 1 of 32)	14506	NM_009072	19878	Mm.276024	NM_009072	ENSMUSG00000020580	Rock2	B230113H15Rik|ROKalpha|Rho-kinase|Rock-II|Rock2m|mKIAA0619	Rho-associated coiled-coil containing protein kinase 2	protein-coding
mm_171441.1	chr4	141743498	141743498	-	1	NA	Intergenic	RLTR1B|LTR|ERV1	-3177	NM_001081408	75986	Mm.30032	NM_001081408	ENSMUSG00000040706	Agmat	5033405N08Rik	agmatine ureohydrolase (agmatinase)	protein-coding
mm_98740.1	chr11	96365755	96365761	+	1	NA	promoter-TSS (NM_008266)	promoter-TSS (NM_008266)	0	NM_008266	15407	Mm.890	NM_008266	ENSMUSG00000018973	Hoxb1	Hox-2.9	homeobox B1	protein-coding
mm_118717.1	chr14	22202193	22202208	+	1	NA	intron (NM_028275, intron 2 of 6)	Lx7|LINE|L1	182488	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_4138.1	chr1	170644590	170644602	+	1	NA	promoter-TSS (NM_177068)	promoter-TSS (NM_177068)	64	NM_177068	320078	Mm.287131	NM_177068	ENSMUSG00000038463	Olfml2b	1110018N05Rik|4832415H08Rik|AI467542	olfactomedin-like 2B	protein-coding
mm_123720.1	chr14	70152748	70152757	-	1	NA	5' UTR (NM_146055, exon 2 of 21)	5' UTR (NM_146055, exon 2 of 21)	1039	NM_146055	219158	Mm.218284	NM_146055	ENSMUSG00000033712	Ccar2	2610301G19Rik|Dbc1|mKIAA1967	cell cycle activator and apoptosis regulator 2	protein-coding
mm_80866.1	chr9	98509728	98509738	+	1	NA	TTS (NM_009034)	TTS (NM_009034)	19196	NM_009034	19660	Mm.12825	NM_009034	ENSMUSG00000032454	Rbp2	Crbp-2|CrbpII|Rbp-2	retinol binding protein 2, cellular	protein-coding
mm_93543.1	chr10	115569747	115569750	-	1	NA	promoter-TSS (NM_029982)	promoter-TSS (NM_029982)	-238	NM_029982	77798	Mm.446685	NM_029982	ENSMUSG00000092210	A930009A15Rik	-	RIKEN cDNA A930009A15 gene	protein-coding
mm_147703.1	chr18	60810032	60810074	-	1	NA	exon (NM_010545, exon 5 of 8)	exon (NM_010545, exon 5 of 8)	-2023	NR_039567	100628611		NR_039567	ENSMUSG00000093327	Mir5107	mir-5107|mmu-mir-5107|mu-mir-5107	microRNA 5107	ncRNA
mm_123812.1	chr14	70522770	70522782	-	1	NA	intron (NM_011359, intron 1 of 5)	intron (NM_011359, intron 1 of 5)	1305	NM_011359	20389	Mm.24040	NM_011359	ENSMUSG00000022097	Sftpc	Bricd6|SP-C|SP5|SPC|Sftp-2|Sftp2|pro-SpC	surfactant associated protein C	protein-coding
mm_1947.1	chr1	86312606	86312609	+	1	NA	Intergenic	B1_Mur1|SINE|Alu	9386	NM_145222	227327	Mm.86467	NM_145222	ENSMUSG00000079445	B3gnt7	C330001H22Rik|beta-3GnT7	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 7	protein-coding
mm_116821.1	chr13	54590014	54590034	-	1	NA	promoter-TSS (NM_025933)	promoter-TSS (NM_025933)	50	NM_178605	28126	Mm.439993	NM_178605	ENSMUSG00000025869	Nop16	AA409471|D13Wsu177e	NOP16 nucleolar protein	protein-coding
mm_51243.1	chr6	71683269	71683270	+	1	NA	Intergenic	Intergenic	-24412	NM_178608	52250	Mm.146332	NM_178608	ENSMUSG00000052852	Reep1	D6Ertd253e	receptor accessory protein 1	protein-coding
mm_6311.1	chr1	71593122	71593137	-	1	NA	exon (NM_001276413, exon 40 of 44)	exon (NM_001276413, exon 40 of 44)	35973	NM_026195	108147	Mm.38010	NM_026195	ENSMUSG00000026192	Atic	2610509C24Rik|AA536954|AW212393	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	protein-coding
mm_31979.1	chr4	89050274	89050280	+	1	NA	promoter-TSS (NR_033533)	promoter-TSS (NR_033533)	-30	NR_033533	100040617	Mm.171720	NR_033533	ENSMUSG00000085183	Gm12603	OTTMUSG00000007693	predicted gene 12603	ncRNA
mm_94622.1	chr11	16778147	16778148	+	1	NA	intron (NM_207655, intron 1 of 27)	intron (NM_207655, intron 1 of 27)	25944	NM_007912	13649	Mm.8534	NM_007912	ENSMUSG00000020122	Egfr	9030024J15Rik|AI552599|Erbb|Errb1|Errp|Wa5|wa-2|wa2	epidermal growth factor receptor	protein-coding
mm_87554.1	chr10	54118074	54118084	+	1	NA	Intergenic	Intergenic	42157	NR_038016	100502920	Mm.403982	NR_038016	ENSMUSG00000097069	Gm16998	-	predicted gene, 16998	ncRNA
mm_149597.1	chr19	16315763	16315775	+	1	NA	promoter-TSS (NR_105832)	promoter-TSS (NR_105832)	-765	NR_105832	102465218		NR_105832	ENSMUSG00000098718	Mir496b	Gm28028|mmu-mir-496b	microRNA 496b	ncRNA
mm_38606.1	chr4	141860676	141860689	-	1	NA	exon (NM_025994, exon 3 of 4)	exon (NM_025994, exon 3 of 4)	14238	NM_025994	27984	Mm.395598	NM_025994	ENSMUSG00000040659	Efhd2	2600015J22Rik|AA408606|D4Wsu27e	EF hand domain containing 2	protein-coding
mm_100660.1	chr11	3266323	3266333	-	1	NA	promoter-TSS (NM_007879)	promoter-TSS (NM_007879)	58	NM_007879	13494	Mm.3250	NM_007879	ENSMUSG00000020457	Drg1	AA408859|AI132520|Nedd3	developmentally regulated GTP binding protein 1	protein-coding
mm_3691.1	chr1	153751947	153752000	+	1	NA	5' UTR (NM_011882, exon 2 of 9)	5' UTR (NM_011882, exon 2 of 9)	2547	NM_011882	24014	Mm.259254	NM_011882	ENSMUSG00000066800	Rnasel	E230029I04Rik	ribonuclease L (2', 5'-oligoisoadenylate synthetase-dependent)	protein-coding
mm_48191.1	chr5	137529136	137529173	-	1	NA	TTS (NR_105846)	TTS (NR_105846)	440	NR_105846	102465227		NR_105846	ENSMUSG00000098597	Mir6418	Gm27629|mir-6418|mmu-mir-6418	microRNA 6418	ncRNA
mm_61914.1	chr7	90146983	90147005	+	1	NA	intron (NM_001252520, intron 1 of 20)	intron (NM_001252520, intron 1 of 20)	16762	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_104469.1	chr11	95309558	95309586	-	1	NA	intron (NM_177619, intron 1 of 12)	CpG	674	NM_001195004	217127	Mm.90213	NM_177619	ENSMUSG00000038909	Kat7	Hbo1|Hboa|Myst2	K(lysine) acetyltransferase 7	protein-coding
mm_32559.1	chr4	109475879	109475901	+	1	NA	intron (NM_013876, intron 1 of 2)	intron (NM_013876, intron 1 of 2)	615	NM_013876	29864	Mm.392580	NM_013876	ENSMUSG00000028557	Rnf11	-	ring finger protein 11	protein-coding
mm_4907.1	chr1	190159793	190159817	+	1	NA	intron (NM_008937, intron 2 of 4)	intron (NM_008937, intron 2 of 4)	10875	NM_008937	19130	Mm.132579	NM_008937	ENSMUSG00000010175	Prox1	A230003G05Rik	prospero homeobox 1	protein-coding
mm_54815.1	chr6	42349693	42349717	-	1	NA	promoter-TSS (NM_001289618)	promoter-TSS (NM_001289618)	-123	NM_011777	22793	Mm.282303	NM_011777	ENSMUSG00000029860	Zyx	9530098H06Rik|R75157	zyxin	protein-coding
mm_77506.1	chr8	122699460	122699465	-	1	NA	promoter-TSS (NM_009824)	promoter-TSS (NM_009824)	-353	NM_009824	12398	Mm.194339	NM_009824	ENSMUSG00000006362	Cbfa2t3	A630044F12Rik|AI465270|AW229127|Cbfa2t3h|ETO-2|Eto2|MTGR2	core-binding factor, runt domain, alpha subunit 2, translocated to, 3 (human)	protein-coding
mm_48802.1	chr5	148959281	148959309	-	1	NA	Intergenic	Intergenic	9045	NR_040686	71473	Mm.90306	NR_040686	ENSMUSG00000079069	8430423G03Rik	-	RIKEN cDNA 8430423G03 gene	ncRNA
mm_96001.1	chr11	59319681	59319685	+	1	NA	intron (NM_139298, intron 1 of 3)	B1_Mur3|SINE|Alu	12753	NM_139298	216795	Mm.218794	NM_139298	ENSMUSG00000000126	Wnt9a	Wnt14	wingless-type MMTV integration site family, member 9A	protein-coding
mm_68389.1	chr7	109494038	109494067	-	1	NA	promoter-TSS (NM_001170913)	promoter-TSS (NM_001170913)	-314	NM_001170913	330627	Mm.183528	NM_181853	ENSMUSG00000031026	Trim66	Kiaa0298-hp|Tif1d	tripartite motif-containing 66	protein-coding
mm_89804.1	chr10	102546714	102546718	+	1	NA	TTS (NM_146240)	TTS (NM_146240)	34494	NM_146240	237504	Mm.282672	NM_146240	ENSMUSG00000044921	Rassf9	AW322107|Pamci	Ras association (RalGDS/AF-6) domain family (N-terminal) member 9	protein-coding
mm_94744.1	chr11	21097359	21097377	+	1	NA	intron (NM_023324, intron 1 of 6)	intron (NM_023324, intron 1 of 6)	6044	NM_023324	67245	Mm.28957	NM_023324	ENSMUSG00000020134	Peli1	2810468L03Rik|A930031K15Rik|AA409794|AI586297|D11Ertd676e	pellino 1	protein-coding
mm_80797.1	chr9	96258729	96258785	+	1	NA	promoter-TSS (NM_001184710)	promoter-TSS (NM_001184710)	52	NM_001184709	211586	Mm.17977	NM_178667	ENSMUSG00000032411	Tfdp2	1110029I05Rik|A330080J22Rik|DP-3|DP3	transcription factor Dp 2	protein-coding
mm_12437.1	chr2	70678039	70678052	+	1	NA	exon (NM_027352, exon 3 of 10)	exon (NM_027352, exon 3 of 10)	16536	NM_027352	70231	Mm.271950	NM_027352	ENSMUSG00000014959	Gorasp2	0610011A07Rik|2410043M02Rik|5730520M13Rik|9430094F20Rik|AW552058|ENSMUSG00000075299|GOLPH2|GRASP55|GRS2|p59	golgi reassembly stacking protein 2	protein-coding
mm_146195.1	chr18	76241304	76241314	+	1	NA	promoter-TSS (NM_010754)	promoter-TSS (NM_010754)	-392	NM_010754	17126	Mm.152699	NM_010754	ENSMUSG00000024563	Smad2	7120426M23Rik|Madh2|Madr2|Smad-2|mMad2	SMAD family member 2	protein-coding
mm_3488.1	chr1	150105841	150105849	+	1	NA	3' UTR (NM_011198, exon 10 of 10)	3' UTR (NM_011198, exon 10 of 10)	5814	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_166707.1	chr6	116458866	116458902	-	1	NA	intron (NM_009662, intron 1 of 13)	intron (NM_009662, intron 1 of 13)	2294	NM_009662	11689	Mm.41072	NM_009662	ENSMUSG00000025701	Alox5	5-LO|5-LOX|5LO|5LX|AI850497|F730011J02	arachidonate 5-lipoxygenase	protein-coding
mm_125932.1	chr15	76247599	76247609	+	1	NA	promoter-TSS (NR_105918)	promoter-TSS (NR_105918)	-587	NR_105918	102465575		NR_105918	ENSMUSG00000098625	Mir6953	Gm27738|mmu-mir-6953	microRNA 6953	ncRNA
mm_116609.1	chr13	48819750	48819753	-	1	NA	intron (NM_011078, intron 9 of 21)	intron (NM_011078, intron 9 of 21)	51134	NM_011078	18676	Mm.486213	NM_011078	ENSMUSG00000038025	Phf2	GRC5	PHD finger protein 2	protein-coding
mm_150694.1	chr19	42170563	42170600	+	1	NA	promoter-TSS (NM_001164531)	promoter-TSS (NM_001164531)	14	NM_001164531	319740	Mm.287359	NM_177319	ENSMUSG00000018820	Zfyve27	2210011N02Rik|9530077C24Rik|AI426636|AI593546|AI835681	zinc finger, FYVE domain containing 27	protein-coding
mm_74837.1	chr8	23231541	23231545	-	1	NA	intron (NM_024240, intron 4 of 7)	ID_B1|SINE|B4	6125	NM_024240	109145	Mm.27945	NM_024240	ENSMUSG00000031546	Gins4	2810037C03Rik|4933405K01Rik|Sld5	GINS complex subunit 4 (Sld5 homolog)	protein-coding
mm_102688.1	chr11	65365867	65365872	-	1	NA	Intergenic	Intergenic	-78036	NR_040280	327946	Mm.383301	NR_040280	ENSMUSG00000085162	Gm12295	A730013G04|OTTMUSG00000005904	predicted gene 12295	ncRNA
mm_155609.1	chrX	83043229	83043240	+	1	NA	intron (NM_007868, intron 1 of 78)	intron (NM_007868, intron 1 of 78)	94364	NM_007868	13405	Mm.275608	NM_007868	ENSMUSG00000045103	Dmd	DXSmh7|DXSmh9|Dp427|Dp71|dys|mdx|pke	dystrophin, muscular dystrophy	protein-coding
mm_63754.1	chr7	131106384	131106394	+	1	NA	exon (NM_007769, exon 39 of 47)	exon (NM_007769, exon 39 of 47)	39894	NM_173409	233918	Mm.78341	NM_173409	ENSMUSG00000013668	4933402N03Rik	4930412O05	RIKEN cDNA 4933402N03 gene	protein-coding
mm_46213.1	chr5	98186015	98186021	-	1	NA	exon (NM_029947, exon 4 of 4)	exon (NM_029947, exon 4 of 4)	5149	NM_029947	77630	Mm.332511	NM_029947	ENSMUSG00000035456	Prdm8	4930565F05Rik|PFM5	PR domain containing 8	protein-coding
mm_134961.1	chr16	31421369	31421378	-	1	NA	promoter-TSS (NM_175177)	promoter-TSS (NM_175177)	-924	NM_175177	71911	Mm.293470	NM_175177	ENSMUSG00000046598	Bdh1	2310032J20Rik|AI327223|Bdh	3-hydroxybutyrate dehydrogenase, type 1	protein-coding
mm_144494.1	chr18	24205723	24205762	+	1	NA	promoter-TSS (NM_001160404)	promoter-TSS (NM_001160404)	-252	NM_001160404	14423	Mm.30249	NM_013814	ENSMUSG00000000420	Galnt1	-	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 1	protein-coding
mm_38500.1	chr4	141078303	141078338	-	1	NA	promoter-TSS (NM_025383)	promoter-TSS (NM_025383)	25	NM_025383	66147	Mm.21187	NM_025383	ENSMUSG00000028923	Necap2	1110005F07Rik|AA409105|C78898	NECAP endocytosis associated 2	protein-coding
mm_52653.1	chr6	117841175	117841251	+	1	NA	promoter-TSS (NM_001346650)	promoter-TSS (NM_001346650)	32	NM_001346648	232337	Mm.290847	NM_177684	ENSMUSG00000059689	Zfp637	AI646709|BC021601|Znf32	zinc finger protein 637	protein-coding
mm_140518.1	chr17	6079694	6079760	-	1	NA	promoter-TSS (NM_001111017)	promoter-TSS (NM_001111017)	12	NM_001111017	321007	Mm.5548	NM_177311	ENSMUSG00000015659	Serac1	4930511N22Rik|D17Ertd141e	serine active site containing 1	protein-coding
mm_101748.1	chr11	43379431	43379448	-	1	NA	Intergenic	Intergenic	-4978	NR_029558	387164		NR_029558	ENSMUSG00000065601	Mir146	Mirn146|miR-146a|mmu-mir-146	microRNA 146	ncRNA
mm_168144.1	chr10	33797873	33797886	+	1	NA	Intergenic	RLTR9E|LTR|ERVK	-15764	NM_001101452	215895	Mm.473684	NM_001101452	ENSMUSG00000090298	Sult3a2	EG215895|Gm4794	sulfotransferase family 3A, member 2	protein-coding
mm_32322.1	chr4	103676807	103676811	+	1	NA	Intergenic	RMER12B|LTR|ERVK	294309	NR_040673	622167	Mm.244115	NR_040673	ENSMUSG00000086136	Gm12718	OTTMUSG00000008109	predicted gene 12718	ncRNA
mm_153672.1	chr19	44396141	44396149	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	11564	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_136419.1	chr16	93971081	93971092	-	1	NA	intron (NM_019500, intron 1 of 2)	intron (NM_019500, intron 1 of 2)	37751	NM_019500	56173	Mm.328716	NM_019500	ENSMUSG00000047109	Cldn14	AI851731	claudin 14	protein-coding
mm_121150.1	chr14	101910818	101910822	+	1	NA	exon (NM_201529, exon 16 of 31)	exon (NM_201529, exon 16 of 31)	70197	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_46954.1	chr5	114970874	114970887	-	1	NA	5' UTR (NM_009327, exon 1 of 10)	5' UTR (NM_009327, exon 1 of 10)	182	NM_009327	21405	Mm.332607	NM_009327	ENSMUSG00000029556	Hnf1a	AI323641|HNF1|HNF1-alpha|HNF1[a]|Hnf-1|Hnf1alpha|LFB1|Tcf-1|Tcf1	HNF1 homeobox A	protein-coding
mm_76997.1	chr8	107096511	107096562	-	1	NA	promoter-TSS (NM_001286200)	promoter-TSS (NM_001286200)	9	NM_001286200	21750	Mm.6402	NM_009353	ENSMUSG00000031921	Terf2	TRF2	telomeric repeat binding factor 2	protein-coding
mm_172305.1	chr7	104315634	104315642	+	1	NA	promoter-TSS (NM_023835)	promoter-TSS (NM_023835)	-143	NM_023835	76681	Mm.458309	NM_023835	ENSMUSG00000066258	Trim12a	2310043C01Rik|Trim12	tripartite motif-containing 12A	protein-coding
mm_159611.1	chr4	132007250	132007250	-	1	NA	exon (NM_183428, exon 2 of 21)	exon (NM_183428, exon 2 of 21)	41828	NM_001128606	269587	Mm.30038	NM_183428	ENSMUSG00000028906	Epb41	4.1R|AI415518|D4Ertd442e|Elp-1|Elp1|Epb4.1|mKIAA4056	erythrocyte membrane protein band 4.1	protein-coding
mm_104929.1	chr11	100029884	100029887	-	1	NA	promoter-TSS (NM_013570)	promoter-TSS (NM_013570)	-17	NM_013570	16671	Mm.439738	NM_013570	ENSMUSG00000057723	Krt33b	Ha3|Ha4|Krt1-3|mHa3	keratin 33B	protein-coding
mm_98639.1	chr11	96194300	96194314	+	1	NA	promoter-TSS (NM_008267)	promoter-TSS (NM_008267)	-54	NM_008267	15408	Mm.57221	NM_008267	ENSMUSG00000049604	Hoxb13	-	homeobox B13	protein-coding
mm_108324.1	chr12	79770046	79770059	+	1	NA	intron (NM_009014, intron 9 of 10)	intron (NM_009014, intron 9 of 10)	154681	NR_131075	77290	Mm.395042	NR_131073		9430078K24Rik	-	RIKEN cDNA 9430078K24 gene	ncRNA
mm_163094.1	chr11	69734832	69734835	-	1	NA	exon (NM_001291068, exon 29 of 29)	exon (NM_001291068, exon 29 of 29)	23800	NM_001291068	20020	Mm.16533	NM_009089	ENSMUSG00000005198	Polr2a	220kDa|Rpb1|Rpo2-1	polymerase (RNA) II (DNA directed) polypeptide A	protein-coding
mm_35511.1	chr4	41094817	41094844	-	1	NA	exon (NM_016689, exon 3 of 6)	exon (NM_016689, exon 3 of 6)	3353	NM_016689	11828	Mm.34043	NM_016689	ENSMUSG00000028435	Aqp3	AQP-2	aquaporin 3	protein-coding
mm_162274.1	chr1	12615769	12615770	+	1	NA	Intergenic	Intergenic	-51794	NR_045297	329096	Mm.417782	NR_045297	ENSMUSG00000097171	Gm17644	4932411L15	predicted gene, 17644	ncRNA
mm_58180.1	chr6	142867917	142867937	-	1	NA	exon (NM_011374, exon 4 of 5)	exon (NM_011374, exon 4 of 5)	53696	NR_045707	665037	Mm.401493	NR_045707	ENSMUSG00000072683	Gm7457	EG665037|ENSMUSG00000072683	predicted gene 7457	ncRNA
mm_42710.1	chr5	120431931	120431937	+	1	NA	promoter-TSS (NM_008499)	promoter-TSS (NM_008499)	48	NM_008499	16873	Mm.5151	NM_008499	ENSMUSG00000029595	Lhx5	Lim2	LIM homeobox protein 5	protein-coding
mm_118047.1	chr13	101702080	101702116	-	1	NA	intron (NM_001077495, intron 5 of 15)	intron (NM_001077495, intron 5 of 15)	-9468	NM_001024955	18708	Mm.259333	NM_001024955	ENSMUSG00000041417	Pik3r1	PI3K|p50alpha|p55alpha|p85alpha	phosphatidylinositol 3-kinase, regulatory subunit, polypeptide 1 (p85 alpha)	protein-coding
mm_7744.1	chr1	131054881	131054903	-	1	NA	3' UTR (NM_008551, exon 10 of 10)	3' UTR (NM_008551, exon 10 of 10)	35047	NM_010548	16153	Mm.874	NM_010548	ENSMUSG00000016529	Il10	CSIF|Il-10	interleukin 10	protein-coding
mm_70436.1	chr8	11558451	11558468	+	1	NA	promoter-TSS (NM_001302459)	promoter-TSS (NM_001302459)	49	NM_001302459	26356	Mm.25709	NM_011919	ENSMUSG00000045969	Ing1	2610028J21Rik|AA407184|AI875420|mING1h|p33Ing1|p37Ing1b	inhibitor of growth family, member 1	protein-coding
mm_26995.1	chr3	25818839	25818842	-	1	NA	intron (NM_001163387, intron 3 of 5)	intron (NM_001163387, intron 3 of 5)	334467	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_91434.1	chr10	33624151	33624175	-	1	NA	5' UTR (NM_175448, exon 1 of 6)	5' UTR (NM_175448, exon 1 of 6)	437	NM_175448	215890	Mm.94461	NM_175448	ENSMUSG00000019785	Clvs2	A330019N05Rik|Rlbp1l2	clavesin 2	protein-coding
mm_21187.1	chr2	155299650	155299677	-	1	NA	intron (NM_001004721, intron 8 of 11)	intron (NM_001004721, intron 8 of 11)	23299	NR_046364	66734	Mm.196239	NM_025735	ENSMUSG00000027602	Map1lc3a	1010001H21Rik|4922501H04Rik|LC3|LC3a	microtubule-associated protein 1 light chain 3 alpha	protein-coding
mm_84372.1	chr9	64951600	64951635	-	1	NA	promoter-TSS (NM_144813)	promoter-TSS (NM_144813)	-10	NM_144813	214111	Mm.156124	NM_144813	ENSMUSG00000034452	Slc24a1	-	solute carrier family 24 (sodium/potassium/calcium exchanger), member 1	protein-coding
mm_41732.1	chr5	102669572	102669574	+	1	NA	intron (NM_146161, intron 2 of 8)	intron (NM_146161, intron 2 of 8)	-99237	NM_001286468	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding
mm_83339.1	chr9	44279340	44279351	-	1	NA	exon (NM_138955, exon 8 of 15)	exon (NM_138955, exon 8 of 15)	8899	NM_138955	192663	Mm.101876	NM_138955	ENSMUSG00000032131	Abcg4	6430517O04Rik	ATP-binding cassette, sub-family G (WHITE), member 4	protein-coding
mm_32825.1	chr4	117552953	117552967	+	1	NA	exon (NM_001285899, exon 2 of 9)	exon (NM_001285899, exon 2 of 9)	2595	NM_080469	140546	Mm.235891	NM_080469	ENSMUSG00000033423	Eri3	PINT1|Prnpip1	exoribonuclease 3	protein-coding
mm_168651.1	chr11	8623825	8623838	-	1	NA	intron (NM_001083587, intron 1 of 30)	intron (NM_001083587, intron 1 of 30)	40704	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_21995.1	chr2	167661515	167661591	-	1	NA	promoter-TSS (NM_145538)	promoter-TSS (NM_145538)	-9	NM_145538	407243	Mm.4863	NM_145538	ENSMUSG00000090213	Tmem189	AI840826|Kua	transmembrane protein 189	protein-coding
mm_103604.1	chr11	78422224	78422240	-	1	NA	promoter-TSS (NM_022411)	promoter-TSS (NM_022411)	-47	NM_022411	20500	Mm.274058	NM_022411	ENSMUSG00000001095	Slc13a2	Nadc1|mNaDC-1	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 2	protein-coding
mm_728.1	chr1	43098713	43098760	+	1	NA	promoter-TSS (NM_001013025)	promoter-TSS (NM_001013025)	26	NM_133818	98404	Mm.28817	NM_133818	ENSMUSG00000010290	AI597479	-	expressed sequence AI597479	protein-coding
mm_74503.1	chr8	8457436	8457437	-	1	NA	Intergenic	Intergenic	203337	NM_010111	13642	Mm.209813	NM_010111	ENSMUSG00000001300	Efnb2	ELF-2|Epl5|Eplg5|Htk-L|LERK-5|Lerk5|NLERK-1	ephrin B2	protein-coding
mm_103165.1	chr11	70455932	70455997	-	1	NA	exon (NM_023158, exon 4 of 5)	exon (NM_023158, exon 4 of 5)	-3658	NM_001029929	574428	Mm.472771	NM_001029929	ENSMUSG00000040829	Zmynd15	-	zinc finger, MYND-type containing 15	protein-coding
mm_90855.1	chr10	8819820	8819830	-	1	NA	intron (NM_175155, intron 2 of 19)	MTEa|LTR|ERVL-MaLR	66245	NM_175155	70097	Mm.338275	NM_175155	ENSMUSG00000015305	Sash1	1100001C18Rik|2500002E12Rik|A330076K04Rik|mKIAA0790	SAM and SH3 domain containing 1	protein-coding
mm_41227.1	chr5	88657436	88657479	+	1	NA	Intergenic	Intergenic	18123	NM_001098476	231413	Mm.332474	NM_178700	ENSMUSG00000044221	Grsf1	BB232551|C80280|D5Wsu31e	G-rich RNA sequence binding factor 1	protein-coding
mm_94403.1	chr11	5784791	5784794	+	1	NA	TTS (NR_015577)	TTS (NR_015577)	-3691	NM_001146309	13169	Mm.256925	NM_013810	ENSMUSG00000020476	Dbnl	Abp1|SH3P7|mAbp1	drebrin-like	protein-coding
mm_92486.1	chr10	78297994	78297998	-	1	NA	intron (NM_053014, intron 2 of 9)	intron (NM_053014, intron 2 of 9)	42211	NR_106119	102465765		NR_106119	ENSMUSG00000098885	Mir7659	Gm27433|mmu-mir-7659	microRNA 7659	ncRNA
mm_146123.1	chr18	74442501	74442532	+	1	NA	promoter-TSS (NM_201600)	promoter-TSS (NM_201600)	-103	NM_201600	17919	Mm.260098	NM_008661	ENSMUSG00000025885	Myo5b	AI661750|mKIAA1119	myosin VB	protein-coding
mm_109229.1	chr12	108836028	108836088	+	1	NA	promoter-TSS (NM_181328)	promoter-TSS (NM_181328)	-182	NM_181328	214663	Mm.266264	NM_181328	ENSMUSG00000021265	Slc25a29	C030003J19Rik|CACL|mCACL	solute carrier family 25 (mitochondrial carrier, palmitoylcarnitine transporter), member 29	protein-coding
mm_46496.1	chr5	105132589	105132597	-	1	NA	intron (NM_008620, intron 3 of 10)	L1M2|LINE|L1	6959	NM_008620	17472	Mm.440525	NM_008620	ENSMUSG00000079363	Gbp4	AW228052|Mag-2|Mpa-2|Mpa2	guanylate binding protein 4	protein-coding
mm_19336.1	chr2	90580469	90580496	-	1	NA	exon (NM_008982, exon 1 of 24)	exon (NM_008982, exon 1 of 24)	165	NM_008982	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_111065.1	chr12	80115204	80115225	-	1	NA	Intergenic	Intergenic	-2201	NM_007564	12192	Mm.235132	NM_007564	ENSMUSG00000021127	Zfp36l1	AW742437|AW743212|Berg36|Brf1|D530020L18Rik|ERF1|TIS11b|cMG1	zinc finger protein 36, C3H type-like 1	protein-coding
mm_89620.1	chr10	96181691	96181716	+	1	NA	Intergenic	Intergenic	-44504	NR_110448	74881	Mm.410819	NR_110448		4930459C07Rik	-	RIKEN cDNA 4930459C07 gene	ncRNA
mm_96602.1	chr11	69091129	69091133	+	1	NA	3' UTR (NM_009497, exon 5 of 5)	3' UTR (NM_009497, exon 5 of 5)	2603	NM_009497	22318	Mm.28643	NM_009497	ENSMUSG00000020894	Vamp2	Syb-2|Syb2|sybII	vesicle-associated membrane protein 2	protein-coding
mm_168398.1	chr1	129308236	129308237	+	1	NA	intron (NM_172485, intron 1 of 27)	intron (NM_172485, intron 1 of 27)	34932	NM_172485	210417	Mm.380518	NM_172485	ENSMUSG00000042581	Thsd7b	1700074E13Rik|B930082A18|D130067I03Rik	thrombospondin, type I, domain containing 7B	protein-coding
mm_63249.1	chr7	126595200	126595204	+	1	NA	promoter-TSS (NM_145636)	promoter-TSS (NM_145636)	-292	NM_145636	246779	Mm.222632	NM_145636	ENSMUSG00000044701	Il27	IL-27|IL-27p28|Il30|p28	interleukin 27	protein-coding
mm_57235.1	chr6	123282903	123282918	-	1	NA	3' UTR (NM_019948, exon 6 of 6)	3' UTR (NM_019948, exon 6 of 6)	6961	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_147136.1	chr18	36286975	36286996	-	1	NA	intron (NM_008989, intron 1 of 1)	intron (NM_008989, intron 1 of 1)	5823	NM_008989	19290	Mm.231802	NM_008989	ENSMUSG00000043991	Pura	CAGER-1|Pur-alpha|ssCRE-BP	purine rich element binding protein A	protein-coding
mm_20583.1	chr2	131148468	131148480	-	1	NA	intron (NM_001311138, intron 3 of 5)	intron (NM_001311138, intron 3 of 5)	11546	NM_026091	67326	Mm.27711	NM_026091	ENSMUSG00000027327	1700037H04Rik	-	RIKEN cDNA 1700037H04 gene	protein-coding
mm_146916.1	chr18	31597780	31597795	-	1	NA	intron (NM_026165, intron 5 of 7)	(GAAA)n|Simple_repeat|Simple_repeat	12115	NM_026165	67453	Mm.23896	NM_026165	ENSMUSG00000024259	Slc25a46	1200007B05Rik|AI325987	solute carrier family 25, member 46	protein-coding
mm_60072.1	chr7	33653454	33653493	+	1	NA	promoter-TSS (NR_045685)	promoter-TSS (NR_045685)	-192	NR_045685	353109	Mm.63867	NR_045685	ENSMUSG00000083896	Scgb2b23-ps	1700028O08Rik|Abpbg23-ps|C2y|Scgb2b1|Scgb2b1-ps	secretoglobin, family 2B, member 23, pseudogene	pseudo
mm_13179.1	chr2	93027944	93027957	+	1	NA	intron (NM_001177536, intron 1 of 6)	intron (NM_001177536, intron 1 of 6)	-1398	NR_110333	433456	Mm.235231	NM_001002794	ENSMUSG00000075027	4631405J19Rik	-	RIKEN cDNA 4631405J19 gene	ncRNA
mm_91851.1	chr10	59164542	59164542	-	1	NA	3' UTR (NM_001024911, exon 10 of 10)	3' UTR (NM_001024911, exon 10 of 10)	57305	NM_001024911	103080	Mm.346842	NM_001024910	ENSMUSG00000019917	Sept10	4921515A04Rik|9430099J10Rik|AA408298|AI874685	septin 10	protein-coding
mm_68446.1	chr7	109991430	109991441	-	1	NA	Intergenic	B4A|SINE|B4	-5205	NM_153525	233724	Mm.43212	NM_153525	ENSMUSG00000047554	Tmem41b	1500015G02Rik|1500031M19Rik|AU018901|D7Ertd70e|D7Ertd743e	transmembrane protein 41B	protein-coding
mm_91658.1	chr10	42762341	42762351	-	1	NA	intron (NM_153055, intron 1 of 20)	intron (NM_153055, intron 1 of 20)	850	NM_153055	140740	Mm.214344	NM_153055	ENSMUSG00000019802	Sec63	5730478J10Rik|AI649014|AW319215	SEC63-like (S. cerevisiae)	protein-coding
mm_127786.1	chr15	3542545	3542574	-	1	NA	intron (NM_001048178, intron 1 of 8)	intron (NM_001048178, intron 1 of 8)	39283	NM_001286370	14600	Mm.3986	NM_010284	ENSMUSG00000055737	Ghr	GHBP|GHR/BP	growth hormone receptor	protein-coding
mm_102396.1	chr11	59002199	59002231	-	1	NA	intron (NM_001171512, intron 89 of 103)	intron (NM_001171512, intron 89 of 103)	24122	NM_053168	94091	Mm.248049	NM_053168	ENSMUSG00000020455	Trim11	-	tripartite motif-containing 11	protein-coding
mm_93514.1	chr10	115250532	115250540	-	1	NA	intron (NM_025706, intron 1 of 16)	intron (NM_025706, intron 1 of 16)	957	NM_025706	66687	Mm.22252	NM_025706	ENSMUSG00000020130	Tbc1d15	4432405K22Rik|AU022358|AU023730|AW557774|Ly6dl|Rab7-GAP	TBC1 domain family, member 15	protein-coding
mm_160449.1	chr8	105375179	105375179	+	1	NA	promoter-TSS (NM_001081333)	promoter-TSS (NM_001081333)	-202	NM_001081333	102075	Mm.32034	NM_175321	ENSMUSG00000014782	Plekhg4	4931414L13Rik|AI448583|mFLJ00068	pleckstrin homology domain containing, family G (with RhoGef domain) member 4	protein-coding
mm_41424.1	chr5	90892502	90892518	+	1	NA	exon (NM_008176, exon 4 of 4)	exon (NM_008176, exon 4 of 4)	1265	NM_008176	14825	Mm.21013	NM_008176	ENSMUSG00000029380	Cxcl1	Fsp|Gro1|KC|Mgsa|N51|Scyb1|gro	chemokine (C-X-C motif) ligand 1	protein-coding
mm_31776.1	chr4	63560189	63560199	+	1	NA	promoter-TSS (NM_144905)	promoter-TSS (NM_144905)	-166	NM_144905	230279	Mm.41523	NM_144905	ENSMUSG00000045917	Tmem268	6330416G13Rik|AW492431|bM230C2.2	transmembrane protein 268	protein-coding
mm_69457.1	chr7	133123329	133123339	-	1	NA	5' UTR (NM_009980, exon 1 of 11)	5' UTR (NM_009980, exon 1 of 11)	149	NM_009980	13017	Mm.246240	NM_009980	ENSMUSG00000030970	Ctbp2	AA407280|D7Ertd45e|Gtrgeo6|Ribeye	C-terminal binding protein 2	protein-coding
mm_65056.1	chr7	18746653	18746667	-	1	NA	Intergenic	MMERVK9C_I-int|LTR|ERVK	28570	NM_001004152	243862	Mm.389833	NM_001004152	ENSMUSG00000044903	Psg22	AA408604|cea9	pregnancy-specific glycoprotein 22	protein-coding
mm_54509.1	chr6	35511482	35511492	-	1	NA	3' UTR (NM_008098, exon 4 of 4)	3' UTR (NM_008098, exon 4 of 4)	28401	NM_008098	14489	Mm.182746	NM_008098	ENSMUSG00000029840	Mtpn	5033418D15Rik|Gcdp|V1	myotrophin	protein-coding
mm_160263.1	chr7	109782005	109782005	-	1	NA	promoter-TSS (NM_020610)	promoter-TSS (NM_020610)	-460	NM_020610	78593	Mm.275374	NM_020610	ENSMUSG00000034825	Nrip3	A330103B05Rik|D7H11orf14|ICRFP703B1614Q5.2	nuclear receptor interacting protein 3	protein-coding
mm_46949.1	chr5	114923754	114923790	-	1	NA	intron (NM_145209, intron 2 of 6)	intron (NM_145209, intron 2 of 6)	532	NM_145209	231655	Mm.95479	NM_145209	ENSMUSG00000041827	Oasl1	7530414C13Rik|oasl9	2'-5' oligoadenylate synthetase-like 1	protein-coding
mm_2602.1	chr1	120055234	120055236	+	1	NA	intron (NM_001311077, intron 9 of 12)	intron (NM_001311077, intron 9 of 12)	18545	NM_019432	170706	Mm.24750	NM_019432	ENSMUSG00000050777	Tmem37	AI173373|AW540203|Pr|Pr1	transmembrane protein 37	protein-coding
mm_50851.1	chr6	54888816	54888850	+	1	NA	3' UTR (NM_199143, exon 5 of 5)	3' UTR (NM_199143, exon 5 of 5)	71917	NM_199143	387524	Mm.286149	NM_199143	ENSMUSG00000058446	Znrf2	1190002C14Rik|AU044205|D6Ertd365e	zinc and ring finger 2	protein-coding
mm_15980.1	chr2	166792526	166792536	+	1	NA	Intergenic	Intergenic	-1236	NM_023815	76367	Mm.330796	NM_023815	ENSMUSG00000042854	Trp53rkb	2810408M09Rik|4933401B08Rik|5630401H01Rik|Nori-2|PRPK|Tp53rk|Trp53rk|Trp53tk|mNori-2p	transformation related protein 53 regulating kinase B	protein-coding
mm_35401.1	chr4	34687348	34687375	-	1	NA	promoter-TSS (NM_011895)	promoter-TSS (NM_011895)	77	NM_011895	24060	Mm.281885	NM_011895	ENSMUSG00000028293	Slc35a1	AA408150|AI314851	solute carrier family 35 (CMP-sialic acid transporter), member 1	protein-coding
mm_157297.1	chrX	20928058	20928075	-	1	NA	exon (NM_008823, exon 6 of 9)	exon (NM_008823, exon 6 of 9)	3489	NM_008823	18636	Mm.3064	NM_008823	ENSMUSG00000001128	Cfp	BCFG|Pfc	complement factor properdin	protein-coding
mm_69986.1	chr7	142380937	142380950	-	1	NA	exon (NM_009983, exon 5 of 9)	exon (NM_009983, exon 5 of 9)	6927	NM_009983	13033	Mm.231395	NM_009983	ENSMUSG00000007891	Ctsd	CD|CatD	cathepsin D	protein-coding
mm_162562.1	chr1	172317564	172317581	+	1	NA	exon (NM_080419, exon 3 of 7)	exon (NM_080419, exon 3 of 7)	5205	NM_080419	140559	Mm.271717	NM_080419	ENSMUSG00000038034	Igsf8	ESTM34|EWI-2|KCT-4|PGRL	immunoglobulin superfamily, member 8	protein-coding
mm_59397.1	chr7	26764657	26764668	+	1	NA	intron (NM_007814, intron 6 of 8)	(TCCA)n|Simple_repeat|Simple_repeat	7520	NM_007814	13090	Mm.14098	NM_007814	ENSMUSG00000066704	Cyp2b19	CYPIIB19	cytochrome P450, family 2, subfamily b, polypeptide 19	protein-coding
mm_143475.1	chr17	71256835	71256845	-	1	NA	intron (NM_145158, intron 4 of 7)	intron (NM_145158, intron 4 of 7)	52186	NM_001164885	64898	Mm.227924	NM_022882	ENSMUSG00000024052	Lpin2	2610511G02Rik|AI481352|AW742896	lipin 2	protein-coding
mm_115180.1	chr13	108446675	108446675	+	1	NA	Intergenic	Intergenic	130338	NM_178683	218581	Mm.32318	NM_178683	ENSMUSG00000021697	Depdc1b	9830132O03|AW260467|XTP1	DEP domain containing 1B	protein-coding
mm_47733.1	chr5	130172463	130172471	-	1	NA	intron (NM_001199059, intron 1 of 8)	intron (NM_001199059, intron 1 of 8)	648	NM_001199059	56715	Mm.288639	NM_019983	ENSMUSG00000025340	Rabgef1	Rab5ef|Rabex5|Rin2	RAB guanine nucleotide exchange factor (GEF) 1	protein-coding
mm_165579.1	chr3	28431530	28431532	+	1	NA	intron (NM_026910, intron 2 of 32)	intron (NM_026910, intron 2 of 32)	11588	NR_130342	100628591		NR_130342	ENSMUSG00000092990	Mir466q	Mir446q|mmu-mir-466q|mu-mir-446q	microRNA 466q	ncRNA
mm_170278.1	chr18	27463145	27463145	-	1	NA	Intergenic	Intergenic	-1097019	NR_045398	320624	Mm.50107	NR_045398		4930474G06Rik	-	RIKEN cDNA 4930474G06 gene	ncRNA
mm_148741.1	chr19	5953619	5953632	+	1	NA	intron (NM_001164057, intron 6 of 17)	intron (NM_001164057, intron 6 of 17)	10581	NM_001164057	18969	Mm.209931	NM_008893	ENSMUSG00000024833	Pola2	AI573378	polymerase (DNA directed), alpha 2	protein-coding
mm_70252.1	chr8	3493136	3493212	+	1	NA	promoter-TSS (NM_080461)	promoter-TSS (NM_080461)	36	NM_080461	140482	Mm.299073	NM_080461	ENSMUSG00000047264	Zfp358	Zfend	zinc finger protein 358	protein-coding
mm_16359.1	chr2	174442232	174442238	+	1	NA	Intergenic	Intergenic	-3196	NM_022325	64138	Mm.156919	NM_022325	ENSMUSG00000016256	Ctsz	AI787083|AU019819|CTSX|D2Wsu143e	cathepsin Z	protein-coding
mm_25330.1	chr3	106569608	106569621	+	1	NA	intron (NM_001025582, intron 5 of 6)	intron (NM_001025582, intron 5 of 6)	-21812	NM_133869	99712	Mm.429443	NM_133869	ENSMUSG00000040774	Cept1	9930118K05Rik|mCEPT1	choline/ethanolaminephosphotransferase 1	protein-coding
mm_80196.1	chr9	72396353	72396363	+	1	NA	Intergenic	Intergenic	-42171	NM_008613	17427	Mm.387671	NM_008613	ENSMUSG00000032221	Mns1	AW546487	meiosis-specific nuclear structural protein 1	protein-coding
mm_128927.1	chr15	74636242	74636267	-	1	NA	promoter-TSS (NM_001177437)	promoter-TSS (NM_001177437)	64	NM_001177437	69439	Mm.263708	NM_001177437	ENSMUSG00000022603	Mroh4	1700016M24Rik	maestro heat-like repeat family member 4	protein-coding
mm_164818.1	chr18	34954655	34954690	+	1	NA	promoter-TSS (NM_010481)	promoter-TSS (NM_010481)	-321	NM_010481	15526	Mm.209419	NM_010481	ENSMUSG00000024359	Hspa9	74kDa|Csa|Grp75|Hsc74|Hsp74|Hsp74a|Hspa9a|Mortalin|Mot-2|Mot2|Mthsp70|Pbp74	heat shock protein 9	protein-coding
mm_125277.1	chr15	36210528	36210544	+	1	NA	intron (NM_012031, intron 10 of 18)	CpG	29628	NR_106173	102465888		NR_106173	ENSMUSG00000098457	Mir8097	Gm27497|mmu-mir-8097	microRNA 8097	ncRNA
mm_86464.1	chr10	4429266	4429279	+	1	NA	promoter-TSS (NR_002891)	promoter-TSS (NR_002891)	-106	NR_002891	433224	Mm.153111	NR_002891		Gm5512	EG433224	required for meiotic nuclear division 1 pseudogene	pseudo
mm_79863.1	chr9	65032734	65032759	+	1	NA	intron (NM_028906, intron 1 of 20)	CpG	288	NM_028906	74388	Mm.202749	NM_028906	ENSMUSG00000032393	Dpp8	2310004I03Rik|4932434F09Rik|AI666706|DPP VIII	dipeptidylpeptidase 8	protein-coding
mm_117775.1	chr13	96666710	96666727	-	1	NA	intron (NM_008255, intron 1 of 19)	intron (NM_008255, intron 1 of 19)	4218	NM_008255	15357	Mm.316652	NM_008255	ENSMUSG00000021670	Hmgcr	HMG-CoAR|Red	3-hydroxy-3-methylglutaryl-Coenzyme A reductase	protein-coding
mm_54598.1	chr6	38299237	38299290	-	1	NA	promoter-TSS (NM_172467)	promoter-TSS (NM_172467)	-4	NM_172467	209032	Mm.101389	NM_172467	ENSMUSG00000047749	Zc3hav1l	B130055L09Rik|E430016P22Rik	zinc finger CCCH-type, antiviral 1-like	protein-coding
mm_38006.1	chr4	133722897	133722909	-	1	NA	exon (NM_001080819, exon 2 of 20)	exon (NM_001080819, exon 2 of 20)	-5795	NR_106086	102465707		NR_106086	ENSMUSG00000104566	Mir7227	mmu-mir-7227	microRNA 7227	ncRNA
mm_163033.1	chr11	52230873	52230884	+	1	NA	Intergenic	Intergenic	-1117	NM_011543	21402	Mm.42944	NM_011543	ENSMUSG00000036309	Skp1a	15kDa|2610043E24Rik|2610206H23Rik|EMC19|OCP-II|OCP2|SKP1|Tceb1l|p19A|p19Skp1	S-phase kinase-associated protein 1A	protein-coding
mm_30569.1	chr4	3791989	3792008	+	1	NA	TTS (NM_001111096)	TTS (NM_001111096)	43657	NM_026147	67427	Mm.21938	NM_026147	ENSMUSG00000028234	Rps20	4632426K06Rik|Dsk4	ribosomal protein S20	protein-coding
mm_69436.1	chr7	132852658	132852668	-	1	NA	promoter-TSS (NM_028095)	promoter-TSS (NM_028095)	-16	NM_001347629	72096	Mm.28631	NM_028095	ENSMUSG00000030960	Mettl10	2010208K18Rik	methyltransferase like 10	protein-coding
mm_8588.1	chr1	156005740	156005785	-	1	NA	3' UTR (NM_144791, exon 7 of 7)	3' UTR (NM_144791, exon 7 of 7)	29055	NM_001160019	208263	Mm.211654	NM_144791	ENSMUSG00000026466	Tor1aip1	LAP1|Lap1B	torsin A interacting protein 1	protein-coding
mm_41405.1	chr5	90786577	90786587	+	1	NA	intron (NM_203320, intron 2 of 3)	intron (NM_203320, intron 2 of 3)	481	NM_203320	330122	Mm.244289	NM_203320	ENSMUSG00000029379	Cxcl3	Dcip1|Gm1960	chemokine (C-X-C motif) ligand 3	protein-coding
mm_113745.1	chr13	44730595	44730598	+	1	NA	promoter-TSS (NM_001205043)	promoter-TSS (NM_001205043)	-178	NM_021878	16468	Mm.25059	NM_021878	ENSMUSG00000038518	Jarid2	Jmj|jumonji	jumonji, AT rich interactive domain 2	protein-coding
mm_50841.1	chr6	54816907	54816920	+	1	NA	promoter-TSS (NM_199143)	promoter-TSS (NM_199143)	-3	NM_199143	387524	Mm.286149	NM_199143	ENSMUSG00000058446	Znrf2	1190002C14Rik|AU044205|D6Ertd365e	zinc and ring finger 2	protein-coding
mm_169850.1	chr1	63200232	63200237	+	1	NA	promoter-TSS (NM_001285937)	promoter-TSS (NM_001285937)	-124	NM_001285937	73884	Mm.86986	NM_028673	ENSMUSG00000027520	Zdbf2	4930431J08Rik|9330107J05Rik	zinc finger, DBF-type containing 2	protein-coding
mm_160883.1	chr11	69655447	69655447	+	1	NA	exon (NM_009235, exon 1 of 2)	exon (NM_009235, exon 1 of 2)	410	NM_009235	20670	Mm.347499	NM_009235	ENSMUSG00000041287	Sox15	-	SRY (sex determining region Y)-box 15	protein-coding
mm_163461.1	chr12	100134458	100134470	-	1	NA	exon (NM_001290303, exon 9 of 14)	exon (NM_001290303, exon 9 of 14)	22133	NM_008947	19179	Mm.157105	NM_008947	ENSMUSG00000021178	Psmc1	AI325227|P26s4|Rpt2/S4|S4|rpt2	protease (prosome, macropain) 26S subunit, ATPase 1	protein-coding
mm_34387.1	chr4	144923979	144923993	+	1	NA	exon (NM_001172424, exon 6 of 7)	exon (NM_001172424, exon 6 of 7)	30849	NM_011303	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding
mm_166731.1	chr6	122578189	122578191	-	1	NA	3' UTR (NM_031159, exon 8 of 8)	3' UTR (NM_031159, exon 8 of 8)	24254	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_18051.1	chr2	39190688	39190746	-	1	NA	promoter-TSS (NM_178778)	promoter-TSS (NM_178778)	13	NM_178778	320271	Mm.204836	NM_178778	ENSMUSG00000035236	Scai	9330112M16|A930041I02Rik|AI662729	suppressor of cancer cell invasion	protein-coding
mm_102533.1	chr11	61174959	61174961	-	1	NA	promoter-TSS (NM_001004143)	promoter-TSS (NM_001004143)	99	NM_001004143	216825	Mm.30602	NM_001004143	ENSMUSG00000042506	Usp22	AI427806	ubiquitin specific peptidase 22	protein-coding
mm_144967.1	chr18	37824947	37824972	+	1	NA	intron (NM_033583, intron 1 of 3)	intron (NM_033583, intron 1 of 3)	5413	NM_033583	93708	Mm.247203	NM_033583	ENSMUSG00000102543	Pcdhgc5	-	protocadherin gamma subfamily C, 5	protein-coding
mm_42486.1	chr5	115471692	115471693	+	1	NA	intron (NM_011107, intron 2 of 3)	BC1_Mm|scRNA|scRNA	5426	NM_011107	18778	Mm.20190	NM_011107	ENSMUSG00000029522	Pla2g1b	Pla2a|sPLA2IB	phospholipase A2, group IB, pancreas	protein-coding
mm_80364.1	chr9	75314134	75314210	+	1	NA	non-coding (NR_073186, exon 1 of 12)	non-coding (NR_073186, exon 1 of 12)	104	NM_138719	14697	Mm.17604	NM_010313	ENSMUSG00000032192	Gnb5	GBS|Gbeta5|flr	guanine nucleotide binding protein (G protein), beta 5	protein-coding
mm_39941.1	chr5	31814316	31814340	+	1	NA	intron (NM_144541, intron 4 of 11)	intron (NM_144541, intron 4 of 11)	116278	NM_144541	107976	Mm.482126	NM_144541	ENSMUSG00000052139	Bre	6030405P19Rik|AI429776|B830038C02Rik	brain and reproductive organ-expressed protein	protein-coding
mm_98219.1	chr11	88047661	88047690	+	1	NA	5' UTR (NM_001078167, exon 1 of 3)	5' UTR (NM_001078167, exon 1 of 3)	302	NM_173374	110809	Mm.391719	NM_173374	ENSMUSG00000018379	Srsf1	1110054N12Rik|5730507C05Rik|6330415C05Rik|AI482334|AW491331|Asf|Sf2|Sfrs1	serine/arginine-rich splicing factor 1	protein-coding
mm_97814.1	chr11	82962870	82962880	+	1	NA	3' UTR (NM_183201, exon 6 of 6)	3' UTR (NM_183201, exon 6 of 6)	-2194	NR_045932	76392	Mm.295205	NR_045932	ENSMUSG00000086327	Slfn5os	1700003F17Rik	schlafen 5, opposite strand	ncRNA
mm_92496.1	chr10	78320705	78320707	-	1	NA	intron (NM_053014, intron 2 of 9)	intron (NM_053014, intron 2 of 9)	19501	NR_106119	102465765		NR_106119	ENSMUSG00000098885	Mir7659	Gm27433|mmu-mir-7659	microRNA 7659	ncRNA
mm_59816.1	chr7	29179541	29179547	+	1	NA	intron (NM_026545, intron 1 of 6)	PB1D10|SINE|Alu	1129	NM_026545	57296	Mm.273152	NM_026545	ENSMUSG00000030591	Psmd8	6720456J22Rik|AA407360|AL033291|AL033322|AL033323|C76433	proteasome (prosome, macropain) 26S subunit, non-ATPase, 8	protein-coding
mm_12605.1	chr2	74681992	74682007	+	1	NA	promoter-TSS (NM_008273)	promoter-TSS (NM_008273)	-324	NM_008273	15431	Mm.207763	NM_008273	ENSMUSG00000042499	Hoxd11	E230017H14Rik|Hox-4.6|Hox-5.4|Hox-5.5	homeobox D11	protein-coding
mm_171842.1	chr5	15670987	15670989	+	1	NA	Intergenic	L1Md_T|LINE|L1	-9722	NR_001585	75858	Mm.359463	NR_001585	ENSMUSG00000089871	Speer4cos	4930568L21Rik|SPEER-7|Speer7-ps|Speer7-ps1	spermatogenesis associated glutamate (E)-rich protein 4C, opposite strand transcript	pseudo
mm_155688.1	chrX	93968683	93968689	+	1	NA	promoter-TSS (NR_028320)	promoter-TSS (NR_028320)	30	NR_028320	385493	Mm.328014	NM_001033480	ENSMUSG00000081044	AU015836	-	expressed sequence AU015836	ncRNA
mm_152487.1	chr19	11050437	11050441	-	1	NA	non-coding (NR_102366, exon 1 of 3)	non-coding (NR_102366, exon 1 of 3)	127	NR_102366	107350	Mm.6381	NM_001177351	ENSMUSG00000075010	AW112010	-	expressed sequence AW112010	ncRNA
mm_25893.1	chr3	131110640	131110664	+	1	NA	5' UTR (NM_001276402, exon 1 of 10)	5' UTR (NM_001276402, exon 1 of 10)	355	NM_001276402	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_45426.1	chr5	66689918	66689966	-	1	NA	Intergenic	RLTR31D_MM|LTR|ERVK	-13445	NR_102714	101202684	Mm.381468	NR_102714	ENSMUSG00000087601	Uchl1os	Gm16832|Uchl1as	ubiquitin carboxy-terminal hydrolase L1, opposite strand	ncRNA
mm_55621.1	chr6	72235217	72235234	-	1	NA	5' UTR (NM_153778, exon 1 of 3)	5' UTR (NM_153778, exon 1 of 3)	352	NM_153778	71093	Mm.87449	NM_153778	ENSMUSG00000037621	Atoh8	4933425C05Rik|Hath6|Math6|bHLHa21|okadin	atonal bHLH transcription factor 8	protein-coding
mm_51120.1	chr6	68016708	68016714	+	1	NA	Intergenic	Intergenic	-451012	NR_003100	75070	Mm.463364	NR_003100		4930515G16Rik	-	myc induced nuclear antigen pseudogene	pseudo
mm_38143.1	chr4	134853229	134853272	-	1	NA	promoter-TSS (NM_025382)	promoter-TSS (NM_025382)	95	NM_025382	66146	Mm.99793	NM_025382	ENSMUSG00000028826	Tmem57	1110007C24Rik|9230118A01Rik|AI317300|AI606104|C61	transmembrane protein 57	protein-coding
mm_124456.1	chr14	119099400	119099445	-	1	NA	promoter-TSS (NM_001081252)	promoter-TSS (NM_001081252)	12	NM_001081252	66435	Mm.213406	NM_025561	ENSMUSG00000042104	Uggt2	1810064L21Rik|3110001A05Rik|3110027P15Rik|A230065J02Rik|AW047562|Ugcgl2	UDP-glucose glycoprotein glucosyltransferase 2	protein-coding
mm_30460.1	chr3	153944633	153944681	-	1	NA	promoter-TSS (NM_007382)	promoter-TSS (NM_007382)	-14	NM_007382	11364	Mm.10530	NM_007382	ENSMUSG00000062908	Acadm	AU018656|MCAD	acyl-Coenzyme A dehydrogenase, medium chain	protein-coding
mm_72209.1	chr8	72646442	72646452	+	1	NA	promoter-TSS (NM_176940)	promoter-TSS (NM_176940)	-264	NM_176940	319555	Mm.212927	NM_176940	ENSMUSG00000048148	Nwd1	A230063L24Rik	NACHT and WD repeat domain containing 1	protein-coding
mm_97960.1	chr11	83740675	83740677	+	1	NA	Intergenic	Intergenic	-6264	NM_183249	66107	Mm.902	NM_183249	ENSMUSG00000051748	Wfdc21	1100001G20Rik|Wdnm1-like	WAP four-disulfide core domain 21	protein-coding
mm_8270.1	chr1	139494685	139494696	-	1	NA	TTS (NM_009791)	TTS (NM_009791)	-7017	NM_031164	14060	Mm.30105	NM_031164	ENSMUSG00000026368	F13b	Cf-13b|Cf13b	coagulation factor XIII, beta subunit	protein-coding
mm_83190.1	chr9	41012905	41012908	-	1	NA	TTS (NM_176860)	TTS (NM_176860)	-8278	NM_019465	54698	Mm.42791	NM_019465	ENSMUSG00000032021	Crtam	-	cytotoxic and regulatory T cell molecule	protein-coding
mm_70357.1	chr8	5640201	5640241	+	1	NA	Intergenic	Intergenic	-534934	NM_011388	20494	Mm.3500	NM_011388	ENSMUSG00000023073	Slc10a2	9130221J18Rik|AI605518|ASBT|IBAT|ISBT	solute carrier family 10, member 2	protein-coding
mm_141252.1	chr17	27580217	27580219	-	1	NA	3' UTR (NM_001291046, exon 5 of 5)	3' UTR (NM_001291046, exon 5 of 5)	-14491	NM_001002895	106672	Mm.61488	NM_001002895	ENSMUSG00000062753	AI413582	AI854251	expressed sequence AI413582	protein-coding
mm_79588.1	chr9	58275439	58275448	+	1	NA	Intergenic	Intergenic	22279	NM_026942	69106	Mm.216502	NM_026942	ENSMUSG00000032333	Stoml1	1810015E19Rik|AI847431|SLP1|STORP|UNC24|WPB72	stomatin-like 1	protein-coding
mm_3122.1	chr1	134646748	134646758	+	1	NA	promoter-TSS (NM_009307)	promoter-TSS (NM_009307)	72	NM_009307	20980	Mm.5102	NM_009307	ENSMUSG00000026452	Syt2	IP4BP|R74640|mKIAA4194	synaptotagmin II	protein-coding
mm_122480.1	chr14	45658095	45658128	-	1	NA	promoter-TSS (NM_001042719)	promoter-TSS (NM_001042719)	32	NM_001039106	114874	Mm.121918	NM_176845	ENSMUSG00000037697	Ddhd1	Mir5131|PA-PLA1	DDHD domain containing 1	protein-coding
mm_146046.1	chr18	69593455	69593485	+	1	NA	intron (NM_013685, intron 8 of 19)	intron (NM_013685, intron 8 of 19)	247749	NM_001083967	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding
mm_52699.1	chr6	119236508	119236532	+	1	NA	promoter-TSS (NM_001033382)	promoter-TSS (NM_001033382)	-6	NM_001033382	319734	Mm.440773	NM_001033382	ENSMUSG00000041460	Cacna2d4	5730412N02Rik|BE686333	calcium channel, voltage-dependent, alpha 2/delta subunit 4	protein-coding
mm_91536.1	chr10	39133915	39133927	-	1	NA	promoter-TSS (NM_028006)	promoter-TSS (NM_028006)	-26	NM_183254	66337	Mm.45187	NM_183254	ENSMUSG00000051736	Fam229b	1700025K23Rik	family with sequence similarity 229, member B	protein-coding
mm_160664.1	chr9	119977120	119977120	-	1	NA	exon (NM_153287, exon 2 of 5)	exon (NM_153287, exon 2 of 5)	7538	NM_153287	215418	Mm.491094	NM_153287	ENSMUSG00000032515	Csrnp1	4931429D10Rik|Axud1|CSRNP-1|URAX1|taip-3	cysteine-serine-rich nuclear protein 1	protein-coding
mm_46883.1	chr5	113945263	113945277	-	1	NA	intron (NM_198109, intron 14 of 14)	intron (NM_198109, intron 14 of 14)	-36564	NM_011779	23790	Mm.260158	NM_011779	ENSMUSG00000004530	Coro1c	AL022675|AW455561|AW548837	coronin, actin binding protein 1C	protein-coding
mm_171207.1	chr3	58104282	58104299	-	1	NA	Intergenic	Intergenic	59517	NR_040538	67850	Mm.416968	NR_040538	ENSMUSG00000100666	1700007F19Rik	-	RIKEN cDNA 1700007F19 gene	ncRNA
mm_82791.1	chr9	29368232	29368234	-	1	NA	intron (NM_172290, intron 2 of 7)	intron (NM_172290, intron 2 of 7)	594896	NM_172290	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding
mm_8405.1	chr1	151520776	151520776	-	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-19953	NM_011277	19821	Mm.474038	NM_011277	ENSMUSG00000026484	Rnf2	AI326319|AI450156|AU019207|Ring1B|dinG	ring finger protein 2	protein-coding
mm_96115.1	chr11	60699851	60699897	+	1	NA	exon (NM_001159405, exon 1 of 22)	exon (NM_001159405, exon 1 of 22)	184	NM_008502	16897	Mm.285453	NM_008502	ENSMUSG00000020536	Llgl1	AI325176|Lgl1|Llglh|Mgl1	lethal giant larvae homolog 1 (Drosophila)	protein-coding
mm_77718.1	chr8	126594563	126594568	-	1	NA	Intergenic	CpG-14677	-1129	NM_001164598	270110	Mm.334918	NM_001164598	ENSMUSG00000051495	Irf2bp2	E130305N23Rik|IRF-2BP2	interferon regulatory factor 2 binding protein 2	protein-coding
mm_118289.1	chr13	112927599	112927640	-	1	NA	promoter-TSS (NM_172594)	promoter-TSS (NM_172594)	-174	NM_172594	218629	Mm.35094	NM_172594	ENSMUSG00000042426	Dhx29	3732415M03|AU043276|Ddxx|E130202M19Rik	DEAH (Asp-Glu-Ala-His) box polypeptide 29	protein-coding
mm_106163.1	chr11	116654003	116654023	-	1	NA	5' UTR (NM_030206, exon 1 of 4)	5' UTR (NM_030206, exon 1 of 4)	300	NM_030206	114886	Mm.34598	NM_030206	ENSMUSG00000020810	Cygb	3110001K20Rik|HGb|Staap	cytoglobin	protein-coding
mm_156330.1	chrX	138975493	138975539	+	1	NA	exon (NM_013724, exon 13 of 28)	exon (NM_013724, exon 13 of 28)	61086	NM_013724	27206	Mm.482319	NM_013724	ENSMUSG00000052854	Nrk	AA407323|AA409510|AI225895|AV168563|AW538185|Nesk	Nik related kinase	protein-coding
mm_65159.1	chr7	19671694	19671703	-	1	NA	3' UTR (NM_001309795, exon 4 of 4)	3' UTR (NM_001309795, exon 4 of 4)	2222	NM_001309795	11813	Mm.28394	NM_001277944	ENSMUSG00000002992	Apoc2	apo-CII|apoC-II	apolipoprotein C-II	protein-coding
mm_120685.1	chr14	70773263	70773301	+	1	NA	Intergenic	MLTR25A|LTR|ERVK	-1099	NM_010071	13449	Mm.243323	NM_010071	ENSMUSG00000022102	Dok2	DokR|Frip	docking protein 2	protein-coding
mm_139095.1	chr17	46893916	46893921	+	1	NA	Intergenic	Intergenic	3297	NM_178385	72726	Mm.33780	NM_178385	ENSMUSG00000036430	Tbcc	2810055C19Rik	tubulin-specific chaperone C	protein-coding
mm_165081.1	chr19	46635824	46635831	+	1	NA	intron (NM_001177813, intron 1 of 3)	L1MEd|LINE|L1	12426	NM_001177813	226178	Mm.329895	NM_146099	ENSMUSG00000047731	Wbp1l	D19Wsu162e|Opal1	WW domain binding protein 1 like	protein-coding
mm_158015.1	chrX	95956891	95956918	-	1	NA	promoter-TSS (NM_152822)	promoter-TSS (NM_152822)	70	NM_152822	76130	Mm.274318	NM_152822	ENSMUSG00000057421	Las1l	1810030A06Rik|5830482G23Rik	LAS1-like (S. cerevisiae)	protein-coding
mm_12950.1	chr2	87769564	87769580	+	1	NA	Intergenic	IAPLTR1_Mm|LTR|ERVK	-12964	NM_146646	258640	Mm.377607	NM_146646	ENSMUSG00000068816	Olfr152	MOR181-1|Olfr4-1|V1	olfactory receptor 152	protein-coding
mm_50151.1	chr6	41544510	41544520	+	1	NA	Intergenic	Intergenic	22739	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_64605.1	chr7	3228531	3228541	-	1	NA	exon (NM_001033431, exon 8 of 10)	exon (NM_001033431, exon 8 of 10)	7763	NR_029645	100049713		NR_029645	ENSMUSG00000077886	Mir295	Mirn295|mir-295|mmu-miR-295	microRNA 295	ncRNA
mm_53362.1	chr6	129366548	129366558	+	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	16309	NM_177686	232413	Mm.90241	NM_177686	ENSMUSG00000053063	Clec12a	CLL-1|D230024O04|KLRL1|Micl	C-type lectin domain family 12, member a	protein-coding
mm_103934.1	chr11	83649047	83649056	-	1	NA	intron (NM_011337, intron 1 of 2)	intron (NM_011337, intron 1 of 2)	327	NM_011337	20302	Mm.1282	NM_011337	ENSMUSG00000000982	Ccl3	AI323804|G0S19-1|LD78alpha|MIP-1alpha|MIP1-(a)|MIP1-alpha|Mip1a|Scya3	chemokine (C-C motif) ligand 3	protein-coding
mm_72288.1	chr8	75213180	75213257	+	1	NA	promoter-TSS (NM_029182)	promoter-TSS (NM_029182)	-726	NM_029182	75141	Mm.179267	NM_029182	ENSMUSG00000034472	Rasd2	4930526B11Rik|AU045414|Rhes|TEM-2|TEM2	RASD family, member 2	protein-coding
mm_132708.1	chr16	43474227	43474241	+	1	NA	intron (NM_181058, intron 3 of 6)	intron (NM_181058, intron 3 of 6)	-54038	NR_046026	626693	Mm.447083	NR_046026	ENSMUSG00000085499	Gm15713	OTTMUSG00000025617	predicted gene 15713	ncRNA
mm_140882.1	chr17	23829148	23829156	-	1	NA	promoter-TSS (NM_026305)	promoter-TSS (NM_026305)	-43	NM_026305	67673	Mm.153758	NM_026305	ENSMUSG00000055839	Elob	0610040H15Rik|Tceb2	elongin B	protein-coding
mm_89262.1	chr10	87859536	87859572	+	1	NA	intron (NM_001314010, intron 2 of 4)	intron (NM_001314010, intron 2 of 4)	502	NM_010512	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_36827.1	chr4	105268447	105268474	-	1	NA	Intergenic	RSINE1|SINE|B4	111113	NM_080555	67916	Mm.348326	NM_080555	ENSMUSG00000028517	Plpp3	1110003O22Rik|2610002D05Rik|AV025606|D4Bwg0538e|D4Bwg1535e|Lpp3|Ppab2b|Ppap2b	phospholipid phosphatase 3	protein-coding
mm_146239.1	chr18	77194770	77194773	+	1	NA	intron (NM_153124, intron 1 of 6)	(T)n|Simple_repeat|Simple_repeat	8924	NM_013666	225742	Mm.365178	NM_013666	ENSMUSG00000025425	St8sia5	ST8SiaV|Siat8e	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 5	protein-coding
mm_32379.1	chr4	106316188	106316243	+	1	NA	promoter-TSS (NM_183225)	promoter-TSS (NM_183225)	2	NM_183225	329908	Mm.234544	NM_183225	ENSMUSG00000028514	Usp24	2700066K03Rik|2810030C21Rik|AI414051|B130021E18|C79851	ubiquitin specific peptidase 24	protein-coding
mm_117079.1	chr13	59557355	59557372	-	1	NA	promoter-TSS (NM_001284219)	promoter-TSS (NM_001284219)	-16	NM_023328	67269	Mm.153008	NM_023328	ENSMUSG00000021557	Agtpbp1	1700020N17Rik|2310001G17Rik|2900054O13Rik|4930445M19Rik|5730402G09Rik|CCP1|Nna1|nmf243|pcd	ATP/GTP binding protein 1	protein-coding
mm_60127.1	chr7	36729488	36729498	+	1	NA	intron (NM_172298, intron 1 of 1)	intron (NM_172298, intron 1 of 1)	31375	NM_172298	243931	Mm.44141	NM_172298	ENSMUSG00000021217	Tshz3	A630038G13Rik|Tsh3|Zfp537|mKIAA1474|teashirt3	teashirt zinc finger family member 3	protein-coding
mm_103252.1	chr11	70971077	70971087	-	1	NA	intron (NM_001252413, intron 1 of 5)	MER20|DNA|hAT-Charlie	882	NM_001252415	69723	Mm.275691	NM_027186	ENSMUSG00000018449	Rpain	2400006N03Rik|Rip	RPA interacting protein	protein-coding
mm_27556.1	chr3	58525718	58525728	-	1	NA	promoter-TSS (NM_001005509)	promoter-TSS (NM_001005509)	-98	NM_001005509	229317	Mm.21617	NM_001005509	ENSMUSG00000027810	Eif2a	D030048D22|D3Ertd194e	eukaryotic translation initiation factor 2A	protein-coding
mm_87247.1	chr10	41303926	41303966	+	1	NA	promoter-TSS (NM_133999)	promoter-TSS (NM_133999)	-705	NM_133999	103199	Mm.277242	NM_133999	ENSMUSG00000038417	Fig4	A530089I17Rik|AI326867|Sac3	FIG4 phosphoinositide 5-phosphatase	protein-coding
mm_93211.1	chr10	94944791	94944831	-	1	NA	promoter-TSS (NM_018797)	promoter-TSS (NM_018797)	-233	NM_018797	54712	Mm.256712	NM_018797	ENSMUSG00000074785	Plxnc1	2510048K12Rik|AW742158|CD232|Vespr	plexin C1	protein-coding
mm_37289.1	chr4	119174179	119174221	-	1	NA	promoter-TSS (NM_001145936)	promoter-TSS (NM_001145936)	-5	NM_001145936	195522	Mm.169620	NM_183140	ENSMUSG00000045268	Zfp691	6430544H17Rik|Znf691	zinc finger protein 691	protein-coding
mm_91217.1	chr10	21846501	21846507	-	1	NA	Intergenic	Intergenic	-35680	NM_001161845	20393	Mm.28405	NM_011361	ENSMUSG00000019970	Sgk1	Sgk	serum/glucocorticoid regulated kinase 1	protein-coding
mm_100322.1	chr11	118014592	118014594	+	1	NA	exon (NM_133757, exon 8 of 10)	exon (NM_133757, exon 8 of 10)	12323	NR_105898	102466768		NR_105898	ENSMUSG00000098958	Mir6933	Gm27856|mmu-mir-6933	microRNA 6933	ncRNA
mm_137840.1	chr17	30984091	30984100	+	1	NA	exon (NM_177465, exon 9 of 22)	exon (NM_177465, exon 9 of 22)	29412	NM_177465	52020	Mm.25923	NM_177465	ENSMUSG00000054134	Umodl1	D17Ertd488e	uromodulin-like 1	protein-coding
mm_140743.1	chr17	15830787	15830797	-	1	NA	Intergenic	CpG	-4206	NM_178615	68799	Mm.293466	NM_178615	ENSMUSG00000048027	Rgmb	1110059F19Rik|DRAGON	repulsive guidance molecule family member B	protein-coding
mm_29036.1	chr3	102204577	102204647	-	1	NA	promoter-TSS (NM_177545)	promoter-TSS (NM_177545)	81	NM_177545	229658	Mm.118004	NM_177545	ENSMUSG00000027860	Vangl1	Kitenin|Lpp2|Stb2|Stbm	vang-like 1 (van gogh, Drosophila)	protein-coding
mm_35773.1	chr4	46404013	46404023	-	1	NA	5' UTR (NM_053149, exon 1 of 4)	5' UTR (NM_053149, exon 1 of 4)	165	NM_053149	93966	Mm.25793	NM_053149	ENSMUSG00000028332	Hemgn	4921524M03Rik|AI317176|EDAG|Hgn|mNDR	hemogen	protein-coding
mm_116192.1	chr13	31439767	31439775	-	1	NA	Intergenic	Intergenic	-118399	NM_008239	15220	Mm.44235	NM_008239	ENSMUSG00000038415	Foxq1	HFH-1|Hfh1|Hfh1l|sa	forkhead box Q1	protein-coding
mm_72950.1	chr8	92357741	92357751	+	1	NA	promoter-TSS (NM_018826)	promoter-TSS (NM_018826)	-50	NM_018826	54352	Mm.101153	NM_018826	ENSMUSG00000031737	Irx5	-	Iroquois related homeobox 5 (Drosophila)	protein-coding
mm_151195.1	chr19	53533902	53533912	+	1	NA	exon (NM_001085390, exon 2 of 4)	exon (NM_001085390, exon 2 of 4)	4589	NM_001085390	240672	Mm.482424	NM_001085390	ENSMUSG00000034765	Dusp5	Gm337	dual specificity phosphatase 5	protein-coding
mm_152947.1	chr19	28975655	28975667	-	1	NA	Intergenic	Intergenic	-11507	NM_198651	381218	Mm.280653	NM_198651	ENSMUSG00000064202	4430402I18Rik	AW122618|Spata6l	RIKEN cDNA 4430402I18 gene	protein-coding
mm_56500.1	chr6	99300300	99300313	-	1	NA	intron (NM_001347345, intron 3 of 19)	PB1D10|SINE|Alu	-33791	NM_001197321	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_135469.1	chr16	45844971	45844987	-	1	NA	promoter-TSS (NM_153412)	promoter-TSS (NM_153412)	-601	NM_001252442	208177	Mm.211477	NM_153412	ENSMUSG00000033149	Phldb2	AV253284|C820004H04Rik|LL5b|LL5beta	pleckstrin homology like domain, family B, member 2	protein-coding
mm_96870.1	chr11	70198873	70198877	+	1	NA	Intergenic	RLTR19B|LTR|ERVK	-15035	NM_153081	216867	Mm.289238	NM_153081	ENSMUSG00000040938	Slc16a11	AB041591|MCT 11|MNCb-2717	solute carrier family 16 (monocarboxylic acid transporters), member 11	protein-coding
mm_101431.1	chr11	30078914	30078915	-	1	NA	Intergenic	RMER17D|LTR|ERVK	-52881	NM_146016	237711	Mm.445271	NM_146016	ENSMUSG00000044072	Eml6	2900083P10Rik|C230094A16Rik|EMAP-6	echinoderm microtubule associated protein like 6	protein-coding
mm_50864.1	chr6	55336831	55336835	+	1	NA	exon (NM_007472, exon 1 of 4)	exon (NM_007472, exon 1 of 4)	534	NM_007472	11826	Mm.18625	NM_007472	ENSMUSG00000004655	Aqp1	CHIP28	aquaporin 1	protein-coding
mm_48141.1	chr5	137150406	137150418	-	1	NA	Intergenic	Intergenic	-34205	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_73213.1	chr8	95806992	95807018	+	1	NA	non-coding (NR_015574, exon 1 of 4)	non-coding (NR_015574, exon 1 of 4)	175	NR_015574	319960	Mm.386996	NR_015574	ENSMUSG00000074136	4930513N10Rik	-	RIKEN cDNA 4930513N10 gene	ncRNA
mm_128353.1	chr15	39943964	39944029	-	1	NA	promoter-TSS (NM_172814)	promoter-TSS (NM_172814)	-2	NM_001347036	239393	Mm.39874	NM_172814	ENSMUSG00000022305	Lrp12	AI848829|C820005L12Rik|LRP-12	low density lipoprotein-related protein 12	protein-coding
mm_106912.1	chr12	8208165	8208172	+	1	NA	promoter-TSS (NM_001167768)	promoter-TSS (NM_001167768)	41	NM_001167767	68832	Mm.25608	NM_172401	ENSMUSG00000037669	Ldah	1110057K04Rik|mLDAH	lipid droplet associated hydrolase	protein-coding
mm_30520.1	chr3	158561542	158561550	-	1	NA	5' UTR (NM_001291453, exon 1 of 26)	5' UTR (NM_001291453, exon 1 of 26)	675	NM_001291453	242274	Mm.132162	NM_001081358	ENSMUSG00000028176	Lrrc7	AK122498|densin|mKIAA1365	leucine rich repeat containing 7	protein-coding
mm_80468.1	chr9	78113359	78113373	+	1	NA	5' UTR (NM_019987, exon 1 of 14)	5' UTR (NM_019987, exon 1 of 14)	128	NM_019987	56542	Mm.288719	NM_019987	ENSMUSG00000009828	Ick	2210420N10Rik|AI848300|Mrk	intestinal cell kinase	protein-coding
mm_79405.1	chr9	55149365	55149395	+	1	NA	promoter-TSS (NM_180600)	promoter-TSS (NM_180600)	11	NM_001346657	109161	Mm.207894	NM_180600	ENSMUSG00000032307	Ube2q2	3010021M21Rik	ubiquitin-conjugating enzyme E2Q family member 2	protein-coding
mm_71067.1	chr8	34145245	34145249	+	1	NA	intron (NM_026609, intron 1 of 3)	intron (NM_026609, intron 1 of 3)	1492	NM_026609	68192	Mm.34212	NM_026609	ENSMUSG00000031513	Leprotl1	1110067H13Rik|1520402O14Rik|AI854296	leptin receptor overlapping transcript-like 1	protein-coding
mm_87427.1	chr10	50797990	50798005	+	1	NA	intron (NM_198007, intron 36 of 41)	intron (NM_198007, intron 36 of 41)	-97654	NM_011376	20464	Mm.4774	NM_011376	ENSMUSG00000019913	Sim1	bHLHe14|mSIM1	single-minded homolog 1 (Drosophila)	protein-coding
mm_125850.1	chr15	74959206	74959214	+	1	NA	3' UTR (NM_001164036, exon 4 of 4)	3' UTR (NM_001164036, exon 4 of 4)	4104	NM_001164040	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_41171.1	chr5	88002487	88002497	+	1	NA	promoter-TSS (NM_011422)	promoter-TSS (NM_011422)	-33	NM_011422	20599	Mm.261199	NM_011422	ENSMUSG00000029280	Smr3a	AA589601|MSG1|MSG3|Smr1|Smr3	submaxillary gland androgen regulated protein 3A	protein-coding
mm_113402.1	chr13	33936028	33936075	+	1	NA	promoter-TSS (NM_009254)	promoter-TSS (NM_009254)	19	NR_040707	68808	Mm.443347	NR_040707	ENSMUSG00000085457	1110046J04Rik	-	RIKEN cDNA 1110046J04 gene	ncRNA
mm_150155.1	chr19	32172701	32172747	+	1	NA	intron (NM_001168525, intron 5 of 9)	ORR1C2|LTR|ERVL-MaLR	38289	NM_001168526	208449	Mm.329810	NM_144792	ENSMUSG00000040451	Sgms1	9530058O11Rik|AI841905|C80702|Mob|Sms1|Sor1|Tmem23	sphingomyelin synthase 1	protein-coding
mm_114386.1	chr13	63251379	63251392	+	1	NA	intron (NR_110520, intron 2 of 5)	intron (NR_110520, intron 2 of 5)	11356	NR_110521	72061	Mm.188105	NM_028079	ENSMUSG00000021458	2010111I01Rik	2300006M17Rik|AP-O|AW742919|Aopep|ApO|mir-23b|mir-24-1|mir-27b	RIKEN cDNA 2010111I01 gene	protein-coding
mm_157837.1	chrX	74281708	74281737	-	1	NA	promoter-TSS (NM_001242616)	promoter-TSS (NM_001242616)	14	NM_027109	69537	Mm.20169	NM_027109	ENSMUSG00000019088	Dnase1l1	2310005K03Rik|AI324885|Dnase1ll|Dnasex|Dnl1ll|G4.8	deoxyribonuclease 1-like 1	protein-coding
mm_93695.1	chr10	117845939	117845949	-	1	NA	promoter-TSS (NM_024457)	promoter-TSS (NM_024457)	30	NM_024457	215449	Mm.233009	NM_024457	ENSMUSG00000052681	Rap1b	2810443E11Rik	RAS related protein 1b	protein-coding
mm_5883.1	chr1	53978512	53978530	-	1	NA	intron (NM_001001883, intron 2 of 28)	intron (NM_001001883, intron 2 of 28)	129097	NR_106149	102465783		NR_106149	ENSMUSG00000098443	Mir7681	Gm27806|mmu-mir-7681	microRNA 7681	ncRNA
mm_161699.1	chr17	23868050	23868050	+	1	NA	promoter-TSS (NM_020487)	promoter-TSS (NM_020487)	-22	NM_020487	57256	Mm.386785	NM_020487	ENSMUSG00000024116	Prss21	1700023E12Rik|TESP5|mT4|testisin	protease, serine 21	protein-coding
mm_108820.1	chr12	95695457	95695508	+	1	NA	intron (NM_201518, intron 1 of 1)	CpG	3256	NM_201518	399558	Mm.341948	NM_201518	ENSMUSG00000047414	Flrt2	-	fibronectin leucine rich transmembrane protein 2	protein-coding
mm_108861.1	chr12	98920532	98920553	+	1	NA	promoter-TSS (NM_198311)	promoter-TSS (NM_198311)	-32	NM_029553	76260	Mm.282660	NM_029553	ENSMUSG00000021013	Ttc8	0610012F22Rik|AV001447|BBS8	tetratricopeptide repeat domain 8	protein-coding
mm_59401.1	chr7	26784891	26784891	+	1	NA	Intergenic	Intergenic	-24036	NM_013809	13108	Mm.102312	NM_013809	ENSMUSG00000049685	Cyp2g1	-	cytochrome P450, family 2, subfamily g, polypeptide 1	protein-coding
mm_115312.1	chr13	112335930	112335942	+	1	NA	intron (NM_001168405, intron 4 of 5)	intron (NM_001168405, intron 4 of 5)	47418	NM_001168404	77318	Mm.159895	NM_029898	ENSMUSG00000049985	Ankrd55	C030011J08Rik	ankyrin repeat domain 55	protein-coding
mm_55249.1	chr6	52714331	52714349	-	1	NA	intron (NM_025816, intron 1 of 17)	intron (NM_025816, intron 1 of 17)	611	NM_025816	52440	Mm.389757	NM_025816	ENSMUSG00000004535	Tax1bp1	1200003J11Rik|1700069J21Rik|AA930106|D6Ertd404e|D6Ertd772e|T6bp|TXBP151	Tax1 (human T cell leukemia virus type I) binding protein 1	protein-coding
mm_165732.1	chr3	106465026	106465034	+	1	NA	Intergenic	Intergenic	-17401	NM_001093754	72121	Mm.14816	NM_028110	ENSMUSG00000027901	Dennd2d	2010308M01Rik|AI451421	DENN/MADD domain containing 2D	protein-coding
mm_137404.1	chr17	25961739	25961767	+	1	NA	exon (NM_015830, exon 6 of 11)	exon (NM_015830, exon 6 of 11)	3752	NM_015830	50817	Mm.216072	NM_015830	ENSMUSG00000037326	Capn15	Solh	calpain 15	protein-coding
mm_94253.1	chr11	3330917	3330934	+	1	NA	5' UTR (NM_178149, exon 1 of 6)	5' UTR (NM_178149, exon 1 of 6)	194	NM_178149	216505	Mm.390323	NM_178149	ENSMUSG00000034614	Pik3ip1	1500004A08Rik|5830455E04Rik|Crkd|Hgfl	phosphoinositide-3-kinase interacting protein 1	protein-coding
mm_167208.1	chr7	144939768	144939778	-	1	NA	5' UTR (NM_007631, exon 1 of 5)	5' UTR (NM_007631, exon 1 of 5)	152	NM_007631	12443	Mm.273049	NM_007631	ENSMUSG00000070348	Ccnd1	AI327039|CycD1|Cyl-1|PRAD1|bcl-1|cD1	cyclin D1	protein-coding
mm_165529.1	chr2	178416618	178416622	-	1	NA	intron (NM_001081289, intron 1 of 3)	intron (NM_001081289, intron 1 of 3)	2086	NM_001081289	71532	Mm.40216	NM_001081289	ENSMUSG00000070476	Fam217b	9030418K01Rik|AI851938	family with sequence similarity 217, member B	protein-coding
mm_104745.1	chr11	98457999	98458019	-	1	NA	Intergenic	CpG	11175	NM_010346	14786	Mm.276702	NM_010346	ENSMUSG00000019312	Grb7	mKIAA4028	growth factor receptor bound protein 7	protein-coding
mm_100326.1	chr11	118153210	118153239	+	1	NA	Intergenic	MLT1B|LTR|ERVL-MaLR	-24005	NM_001167746	69926	Mm.473893	NM_001167746	ENSMUSG00000033987	Dnah17	2810003K23Rik|Dnahc17|Dnahcl1|Gm1178|mKIAA3028	dynein, axonemal, heavy chain 17	protein-coding
mm_57357.1	chr6	124760508	124760522	-	1	NA	3' UTR (NM_013509, exon 12 of 12)	3' UTR (NM_013509, exon 12 of 12)	-4028	NM_007881	13498	Mm.333380	NM_007881	ENSMUSG00000004263	Atn1	Atr1|Drpla|atrophin-1	atrophin 1	protein-coding
mm_160175.1	chr7	45438062	45438062	-	1	NA	intron (NM_030678, intron 2 of 15)	intron (NM_030678, intron 2 of 15)	3223	NM_030678	14936	Mm.275654	NM_030678	ENSMUSG00000003865	Gys1	Gys3|MGS	glycogen synthase 1, muscle	protein-coding
mm_46037.1	chr5	91962316	91962324	-	1	NA	promoter-TSS (NR_028429)	promoter-TSS (NR_028429)	236	NR_073442	68098	Mm.159453	NM_026557	ENSMUSG00000029397	Rchy1	ARNIP|CHIMP|Pirh2|Zfp363|Znf363	ring finger and CHY zinc finger domain containing 1	protein-coding
mm_122554.1	chr14	49066316	49066324	-	1	NA	promoter-TSS (NM_144535)	promoter-TSS (NM_144535)	-175	NM_144535	74385	Mm.379235	NM_144535	ENSMUSG00000036291	Ap5m1	4932432K03Rik|Mu5|Mudeng	adaptor-related protein complex 5, mu 1 subunit	protein-coding
mm_3804.1	chr1	158362090	158362102	+	1	NA	promoter-TSS (NM_001205204)	promoter-TSS (NM_001205204)	-208	NM_007495	11899	Mm.329586	NM_007495	ENSMUSG00000026587	Astn1	Astn|GC14|mKIAA0289	astrotactin 1	protein-coding
mm_147608.1	chr18	56925510	56925522	-	1	NA	promoter-TSS (NM_177115)	promoter-TSS (NM_177115)	32	NM_177115	320253	Mm.312623	NM_177115	ENSMUSG00000032656	March3	6330411I15Rik|A530081L18Rik|AI843639|MARCH-III	membrane-associated ring finger (C3HC4) 3	protein-coding
mm_38430.1	chr4	139310666	139310702	-	1	NA	promoter-TSS (NM_025337)	promoter-TSS (NM_025337)	16	NM_145384	212555	Mm.45131	NM_145384	ENSMUSG00000028744	Pqlc2	BC019216	PQ loop repeat containing 2	protein-coding
mm_67440.1	chr7	80387409	80387426	-	1	NA	intron (NM_010194, intron 1 of 18)	intron (NM_010194, intron 1 of 18)	529	NM_010194	14159	Mm.48757	NM_010194	ENSMUSG00000053158	Fes	AI586313|BB137047|FPS|c-fes	feline sarcoma oncogene	protein-coding
mm_20800.1	chr2	144270067	144270068	-	1	NA	promoter-TSS (NM_028984)	promoter-TSS (NM_028984)	505	NM_024225	69178	Mm.273379	NM_024225	ENSMUSG00000027423	Snx5	0910001N05Rik|1810032P22Rik|AU019504|D2Ertd52e	sorting nexin 5	protein-coding
mm_169485.1	chr14	73797226	73797240	-	1	NA	Intergenic	Intergenic	244447	NM_011506	20916	Mm.38951	NM_011506	ENSMUSG00000022110	Sucla2	4930547K18Rik|A-SCS	succinate-Coenzyme A ligase, ADP-forming, beta subunit	protein-coding
mm_113618.1	chr13	41605822	41605863	+	1	NA	promoter-TSS (NM_001163572)	promoter-TSS (NM_001163572)	-374	NM_001163572	621976	Mm.259830	NM_001163572	ENSMUSG00000087370	Tmem170b	EG621976	transmembrane protein 170B	protein-coding
mm_21109.1	chr2	153411422	153411429	-	1	NA	3' UTR (NM_001134300, exon 11 of 11)	3' UTR (NM_001134300, exon 11 of 11)	33054	NM_001001986	329540	Mm.50600	NM_001001986	ENSMUSG00000061411	Nol4l	4931410H15|8430427H17Rik|AI429157|Gm1636	nucleolar protein 4-like	protein-coding
mm_34405.1	chr4	145234233	145234253	+	1	NA	intron (NM_011610, intron 1 of 9)	B1_Mur4|SINE|Alu	12627	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_125488.1	chr15	54745871	54745881	+	1	NA	promoter-TSS (NM_010930)	promoter-TSS (NM_010930)	-52	NM_010930	18133	Mm.5167	NM_010930	ENSMUSG00000037362	Nov	C130088N23Rik|CCN3	nephroblastoma overexpressed gene	protein-coding
mm_129200.1	chr15	76511857	76511868	-	1	NA	promoter-TSS (NM_010046)	promoter-TSS (NM_010046)	-44	NM_010046	13350	Mm.22633	NM_010046	ENSMUSG00000022555	Dgat1	ARAT|C75990|D15Ertd23e|Dgat	diacylglycerol O-acyltransferase 1	protein-coding
mm_124197.1	chr14	98169284	98169297	-	1	NA	exon (NM_001038610, exon 1 of 11)	exon (NM_001038610, exon 1 of 11)	475	NM_001038610	13134	Mm.320593	NM_007826	ENSMUSG00000055639	Dach1	Dac|Dach	dachshund 1 (Drosophila)	protein-coding
mm_62997.1	chr7	120739885	120739908	+	1	NA	5' UTR (NM_177697, exon 1 of 34)	5' UTR (NM_177697, exon 1 of 34)	339	NM_177697	233813	Mm.389939	NM_177697	ENSMUSG00000030889	Vwa3a	E030013G06Rik	von Willebrand factor A domain containing 3A	protein-coding
mm_162068.1	chrX	13554931	13554931	-	1	NA	exon (NM_001284505, exon 17 of 26)	exon (NM_001284505, exon 17 of 26)	-77838	NM_011823	23890	Mm.487326	NM_011823	ENSMUSG00000040229	Gpr34	Lypsr1	G protein-coupled receptor 34	protein-coding
mm_25351.1	chr3	106788859	106788882	+	1	NA	intron (NM_007651, intron 1 of 7)	intron (NM_007651, intron 1 of 7)	1279	NM_007651	12508	Mm.316861	NM_007651	ENSMUSG00000040747	Cd53	AI323659|Ox-44|Tspan25	CD53 antigen	protein-coding
mm_13167.1	chr2	92609542	92609560	+	1	NA	intron (NM_023850, intron 1 of 2)	intron (NM_023850, intron 1 of 2)	9844	NM_023850	76969	Mm.38021	NM_023850	ENSMUSG00000027221	Chst1	2610008E20Rik|AW125896|C6ST|GST-1|Gst1|KSGAL6ST	carbohydrate (keratan sulfate Gal-6) sulfotransferase 1	protein-coding
mm_161310.1	chr14	40892994	40892994	-	1	NA	promoter-TSS (NM_177816)	promoter-TSS (NM_177816)	-29	NM_177816	328381	Mm.235694	NM_177816	ENSMUSG00000037833	Sh2d4b	A430109M18Rik|D030001E08	SH2 domain containing 4B	protein-coding
mm_45981.1	chr5	90475300	90475336	-	1	NA	3' UTR (NM_009654, exon 14 of 15)	3' UTR (NM_009654, exon 14 of 15)	14448	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_84742.1	chr9	75387888	75387898	-	1	NA	3' UTR (NM_015806, exon 6 of 6)	3' UTR (NM_015806, exon 6 of 6)	21466	NM_027418	50772	Mm.480076	NM_015806	ENSMUSG00000042688	Mapk6	2610021I23Rik|D130053K17Rik|Erk3|Mapk4|Mapk63|Prkm4|Prkm6	mitogen-activated protein kinase 6	protein-coding
mm_128476.1	chr15	50889267	50889346	-	1	NA	promoter-TSS (NR_035444)	promoter-TSS (NR_035444)	-192	NR_035444	100316685		NR_035444	ENSMUSG00000084458	Mir1907	Mirn1907|mmu-mir-1907	microRNA 1907	ncRNA
mm_163935.1	chr14	50381285	50381294	-	1	NA	Intergenic	Intergenic	-11469	NM_146666	258660	Mm.377623	NM_146666	ENSMUSG00000047716	Olfr736	MOR106-5	olfactory receptor 736	protein-coding
mm_159354.1	chr3	80741112	80741112	-	1	NA	exon (NM_013540, exon 3 of 16)	exon (NM_013540, exon 3 of 16)	61679	NM_013540	14800	Mm.220224	NM_013540	ENSMUSG00000033981	Gria2	GluA2|GluR-B|Glur-2|Glur2	glutamate receptor, ionotropic, AMPA2 (alpha 2)	protein-coding
mm_164102.1	chr15	22548940	22548950	+	1	NA	Intergenic	Intergenic	166039	NM_001165971	545091	Mm.475598	NM_001165971		Gm5803	EG545091	predicted gene 5803	protein-coding
mm_119052.1	chr14	30654343	30654364	+	1	NA	promoter-TSS (NM_177815)	promoter-TSS (NM_177815)	-22	NM_177815	328370	Mm.259657	NM_177815	ENSMUSG00000052395	Rft1	D930025H04	RFT1 homolog	protein-coding
mm_12701.1	chr2	76537363	76537375	+	1	NA	intron (NM_001290733, intron 4 of 26)	intron (NM_001290733, intron 4 of 26)	38363	NM_001290735	99031	Mm.240435	NM_145525	ENSMUSG00000042359	Osbpl6	1110062M20Rik|AI596402|ORP-6|mKIAA4128	oxysterol binding protein-like 6	protein-coding
mm_26113.1	chr3	137624204	137624210	+	1	NA	exon (NM_030143, exon 2 of 3)	exon (NM_030143, exon 2 of 3)	535	NM_030143	73284	Mm.250841	NM_030143	ENSMUSG00000046818	Ddit4l	1700037B15Rik|1700108M02Rik|REDD2|RTP801L|Smhs1	DNA-damage-inducible transcript 4-like	protein-coding
mm_116101.1	chr13	28884683	28884691	-	1	NA	intron (NR_045053, intron 1 of 8)	intron (NR_045053, intron 1 of 8)	735	NR_045054	72518	Mm.37454	NR_045053		2610307P16Rik	AI666457	RIKEN cDNA 2610307P16 gene	ncRNA
mm_19152.1	chr2	80581216	80581228	-	1	NA	promoter-TSS (NM_001290745)	promoter-TSS (NM_001290745)	-40	NM_016965	50884	Mm.25203	NM_016965	ENSMUSG00000027002	Nckap1	C79304|H19|Hem-2|Hem2|Nap1|mKIAA0587|mh19|p125Nap1	NCK-associated protein 1	protein-coding
mm_79201.1	chr9	48670449	48670497	+	1	NA	intron (NM_001033324, intron 4 of 6)	intron (NM_001033324, intron 4 of 6)	-65350	NM_010924	18113	Mm.8362	NM_010924	ENSMUSG00000032271	Nnmt	-	nicotinamide N-methyltransferase	protein-coding
mm_172388.1	chr7	135651889	135651892	+	1	NA	promoter-TSS (NM_001316681)	promoter-TSS (NM_001316681)	-9	NM_001316681	19267	Mm.945	NM_011212	ENSMUSG00000041836	Ptpre	PTPe|PTPepsilon|RPTPepsilon	protein tyrosine phosphatase, receptor type, E	protein-coding
mm_60070.1	chr7	31375588	31375596	+	1	NA	promoter-TSS (NM_001256073)	promoter-TSS (NM_001256073)	0	NM_001256073	384585	Mm.305164	NM_001256073	ENSMUSG00000095257	Scgb1b3	Abpa21|Abpa3|EG384585|Gm5325	secretoglobin, family 1B, member 3	protein-coding
mm_92823.1	chr10	81461723	81461733	-	1	NA	3' UTR (NM_176954, exon 12 of 12)	3' UTR (NM_176954, exon 12 of 12)	11403	NM_001311127	319586	Mm.152689	NM_176954	ENSMUSG00000034818	Celf5	4930565A21Rik|Brunol5	CUGBP, Elav-like family member 5	protein-coding
mm_57681.1	chr6	128503548	128503570	-	1	NA	TTS (NR_028593)	TTS (NR_028593)	23161	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_148101.1	chr18	73971448	73971487	-	1	NA	intron (NM_172632, intron 1 of 5)	intron (NM_172632, intron 1 of 5)	-46440	NR_045390	77855	Mm.410760	NR_045390	ENSMUSG00000090263	D730045A05Rik	-	RIKEN cDNA D730045A05 gene	ncRNA
mm_62979.1	chr7	120173848	120173893	+	1	NA	promoter-TSS (NM_028085)	promoter-TSS (NM_028085)	12	NM_028085	72074	Mm.23165	NM_028085	ENSMUSG00000030909	Anks4b	2010013E14Rik|AI956809|Harp	ankyrin repeat and sterile alpha motif domain containing 4B	protein-coding
mm_119995.1	chr14	55604174	55604230	+	1	NA	promoter-TSS (NM_001159418)	promoter-TSS (NM_001159418)	217	NM_001159417	16391	Mm.2032	NM_008394	ENSMUSG00000002325	Irf9	Irf-9|Isgf3g|p48	interferon regulatory factor 9	protein-coding
mm_145358.1	chr18	56676622	56676624	+	1	NA	Intergenic	RMER17C2|LTR|ERVK	-31190	NM_010721	16906	Mm.4105	NM_010721	ENSMUSG00000024590	Lmnb1	-	lamin B1	protein-coding
mm_85100.1	chr9	94538005	94538053	-	1	NA	promoter-TSS (NM_001033145)	promoter-TSS (NM_001033145)	52	NM_001033145	68861	Mm.258746	NM_001033145	ENSMUSG00000045414	1190002N15Rik	GoPro49|HASF	RIKEN cDNA 1190002N15 gene	protein-coding
mm_65765.1	chr7	28741737	28741745	-	1	NA	promoter-TSS (NM_023637)	promoter-TSS (NM_023637)	40	NM_011885	24030	Mm.358650	NM_011885	ENSMUSG00000045948	Mrps12	AI327385|Rpms12|rps12	mitochondrial ribosomal protein S12	protein-coding
mm_170442.1	chr18	80186323	80186324	+	1	NA	promoter-TSS (NR_131039)	promoter-TSS (NR_131039)	84	NR_131039	105246506	Mm.392326	NR_131039		LOC105246506	-	uncharacterized LOC105246506	ncRNA
mm_52.1	chr1	6528006	6528017	+	1	NA	intron (NM_001244693, intron 2 of 22)	intron (NM_001244693, intron 2 of 22)	40780	NM_001244692	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding
mm_90947.1	chr10	12975596	12975604	-	1	NA	Intergenic	Intergenic	-11341	NM_001163591	74732	Mm.248648	NM_029075	ENSMUSG00000039232	Stx11	5830405C08Rik	syntaxin 11	protein-coding
mm_172883.1	chr9	49483122	49483125	+	1	NA	intron (NM_172770, intron 2 of 21)	ORR1A3|LTR|ERVL-MaLR	3102	NM_172770	235330	Mm.177413	NM_172770	ENSMUSG00000040219	Ttc12	E330017O07Rik	tetratricopeptide repeat domain 12	protein-coding
mm_66153.1	chr7	31148937	31148947	-	1	NA	intron (NM_027898, intron 1 of 18)	intron (NM_027898, intron 1 of 18)	2108	NM_027898	52857	Mm.27366	NM_027898	ENSMUSG00000001248	Gramd1a	1300003M23Rik|AI415002|AW547240|D7Bwg0611e	GRAM domain containing 1A	protein-coding
mm_120643.1	chr14	70522201	70522245	+	1	NA	exon (NM_011359, exon 3 of 6)	exon (NM_011359, exon 3 of 6)	1858	NM_011359	20389	Mm.24040	NM_011359	ENSMUSG00000022097	Sftpc	Bricd6|SP-C|SP5|SPC|Sftp-2|Sftp2|pro-SpC	surfactant associated protein C	protein-coding
mm_126657.1	chr15	84232031	84232041	+	1	NA	promoter-TSS (NM_133167)	promoter-TSS (NM_133167)	-7	NM_133167	170736	Mm.323892	NM_133167	ENSMUSG00000022438	Parvb	AI595373|AW742462|D15Gsk1|affixin	parvin, beta	protein-coding
mm_114087.1	chr13	54590222	54590267	+	1	NA	promoter-TSS (NM_025933)	promoter-TSS (NM_025933)	13	NM_025933	67044	Mm.29353	NM_025933	ENSMUSG00000025868	Higd2a	2010110M21Rik|AA690237	HIG1 domain family, member 2A	protein-coding
mm_18269.1	chr2	52335183	52335200	-	1	NA	intron (NM_010889, intron 1 of 156)	intron (NM_010889, intron 1 of 156)	3607	NM_010889	17996	Mm.389247	NM_010889	ENSMUSG00000026950	Neb	AI595938	nebulin	protein-coding
mm_104451.1	chr11	95040580	95040610	-	1	NA	intron (NM_133667, intron 1 of 10)	intron (NM_133667, intron 1 of 10)	776	NM_133667	18604	Mm.29768	NM_133667	ENSMUSG00000038967	Pdk2	-	pyruvate dehydrogenase kinase, isoenzyme 2	protein-coding
mm_128078.1	chr15	27664368	27664380	-	1	NA	exon (NM_198301, exon 4 of 7)	exon (NM_198301, exon 4 of 7)	17168	NM_001242424	223433	Mm.266485	NM_198301	ENSMUSG00000056069	Fam105a	9830126M18	family with sequence similarity 105, member A	protein-coding
mm_45049.1	chr5	41708136	41708170	-	1	NA	promoter-TSS (NM_001310589)	promoter-TSS (NM_001310589)	26	NR_132325	100972	Mm.41555	NM_027295	ENSMUSG00000029128	Rab28	2700023P08Rik|AW496496	RAB28, member RAS oncogene family	protein-coding
mm_75910.1	chr8	71382069	71382079	-	1	NA	promoter-TSS (NM_010150)	promoter-TSS (NM_010150)	-122	NM_010150	13864	Mm.28989	NM_010150	ENSMUSG00000002393	Nr2f6	AV090102|COUP-TF3|EAR2|Erbal2	nuclear receptor subfamily 2, group F, member 6	protein-coding
mm_116468.1	chr13	43481057	43481067	-	1	NA	promoter-TSS (NM_019930)	promoter-TSS (NM_019930)	-89	NM_019930	56705	Mm.148781	NM_019930	ENSMUSG00000038546	Ranbp9	IBAP-1|Ibap1|RanBPM	RAN binding protein 9	protein-coding
mm_111936.1	chr12	108893384	108893397	-	1	NA	promoter-TSS (NM_177602)	promoter-TSS (NM_177602)	-179	NM_011710	22375	Mm.38433	NM_011710	ENSMUSG00000021266	Wars	TrpRS|WRS	tryptophanyl-tRNA synthetase	protein-coding
mm_54698.1	chr6	39557799	39557827	-	1	NA	promoter-TSS (NM_172477)	promoter-TSS (NM_172477)	21	NM_172477	209773	Mm.440021	NM_172477	ENSMUSG00000038456	Dennd2a	B930096L08Rik|C130031G22|mKIAA1277	DENN/MADD domain containing 2A	protein-coding
mm_71303.1	chr8	41299131	41299133	+	1	NA	intron (NM_023662, intron 22 of 37)	intron (NM_023662, intron 22 of 37)	59373	NM_023662	18536	Mm.117896	NM_023662	ENSMUSG00000031592	Pcm1	2600002H09Rik|9430077F19Rik|C030044G17Rik	pericentriolar material 1	protein-coding
mm_102276.1	chr11	55395509	55395517	-	1	NA	3' UTR (NM_009242, exon 10 of 10)	3' UTR (NM_009242, exon 10 of 10)	24567	NM_009242	20692	Mm.291442	NM_009242	ENSMUSG00000018593	Sparc	BM-40|ON	secreted acidic cysteine rich glycoprotein	protein-coding
mm_153250.1	chr19	36349402	36349417	-	1	NA	Intergenic	CpG	-29658	NM_029508	76073	Mm.259180	NM_029508	ENSMUSG00000024805	Pcgf5	0610009F02Rik|1110054A01Rik|5830406C17Rik|5830443C21Rik|9530023M17Rik|AI324127	polycomb group ring finger 5	protein-coding
mm_29867.1	chr3	130709393	130709417	-	1	NA	promoter-TSS (NM_025509)	promoter-TSS (NM_025509)	39	NM_025509	66357	Mm.300697	NM_025509	ENSMUSG00000041084	Ostc	2310008M10Rik|5730557H03Rik	oligosaccharyltransferase complex subunit (non-catalytic)	protein-coding
mm_82305.1	chr9	7868108	7868155	-	1	NA	intron (NM_007464, intron 1 of 8)	intron (NM_007464, intron 1 of 8)	5039	NM_007464	11796	Mm.2026	NM_007464	ENSMUSG00000032000	Birc3	AW107670|Api1|Api2|Birc2|C-IAP2|HIAP2|IAP1|IAP2|MIAP1|MIAP2|MIHB|MIHC|RNF49|cIAP-1|cIAP-2|cIAP1|cIAP2	baculoviral IAP repeat-containing 3	protein-coding
mm_161764.1	chr17	36111446	36111446	-	1	NA	intron (NM_001271005, intron 1 of 6)	CpG	230	NM_001271005	667803	Mm.477808	NM_001271005		H2-T-ps	C920025E04Rik|H2-T11	histocompatibility 2, T region locus, pseudogene	protein-coding
mm_91533.1	chr10	39122214	39122260	-	1	NA	5' UTR (NM_183254, exon 3 of 5)	5' UTR (NM_183254, exon 3 of 5)	11658	NM_183254	66337	Mm.45187	NM_183254	ENSMUSG00000051736	Fam229b	1700025K23Rik	family with sequence similarity 229, member B	protein-coding
mm_103990.1	chr11	84840302	84840330	-	1	NA	exon (NM_153144, exon 8 of 14)	exon (NM_153144, exon 8 of 14)	11138	NR_046281	74995	Mm.84413	NR_046281	ENSMUSG00000086799	4930502E09Rik	-	RIKEN cDNA 4930502E09 gene	ncRNA
mm_100189.1	chr11	116725434	116725437	+	1	NA	Intergenic	Intergenic	-26732	NR_003364	193217	Mm.100084	NR_003364		BC018473	-	cDNA sequence BC018473	ncRNA
mm_42377.1	chr5	114929830	114929847	+	1	NA	intron (NM_145209, intron 3 of 6)	intron (NM_145209, intron 3 of 6)	6598	NM_145209	231655	Mm.95479	NM_145209	ENSMUSG00000041827	Oasl1	7530414C13Rik|oasl9	2'-5' oligoadenylate synthetase-like 1	protein-coding
mm_85760.1	chr9	108649661	108649671	-	1	NA	promoter-TSS (NM_011790)	promoter-TSS (NM_011790)	-286	NM_011790	23807	Mm.290447	NM_011790	ENSMUSG00000064145	Arih2	AI843547|ARI2|TRIAD1|UIP48	ariadne RBR E3 ubiquitin protein ligase 2	protein-coding
mm_133785.1	chr16	95257618	95257644	+	1	NA	promoter-TSS (NM_001271695)	promoter-TSS (NM_001271695)	73	NM_001271690	16516	Mm.272239	NM_019664	ENSMUSG00000062609	Kcnj15	4930414N08Rik|AI182284|AI267127|IRKK|Kir4.2	potassium inwardly-rectifying channel, subfamily J, member 15	protein-coding
mm_140347.1	chr17	86831060	86831073	+	1	NA	exon (NM_010137, exon 16 of 16)	exon (NM_010137, exon 16 of 16)	77202	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_154223.1	chr19	59879224	59879245	-	1	NA	Intergenic	Intergenic	64130	NM_001033172	74998	Mm.24167	NM_001033172	ENSMUSG00000040022	Rab11fip2	4930470G04Rik|A830046J09Rik|AW558126|Nrip11	RAB11 family interacting protein 2 (class I)	protein-coding
mm_21834.1	chr2	165493299	165493330	-	1	NA	promoter-TSS (NM_001007581)	promoter-TSS (NM_001007581)	0	NM_001007581	381406	Mm.330785	NM_001007581	ENSMUSG00000039725	Trp53rka	2810408M09Rik	transformation related protein 53 regulating kinase A	protein-coding
mm_53422.1	chr6	134035773	134035783	+	1	NA	promoter-TSS (NM_007961)	promoter-TSS (NM_007961)	78	NM_007961	14011	Mm.269995	NM_007961	ENSMUSG00000030199	Etv6	AW123102|AW557856|Tel	ets variant 6	protein-coding
mm_31781.1	chr4	63560704	63560710	+	1	NA	intron (NM_144905, intron 1 of 9)	intron (NM_144905, intron 1 of 9)	347	NM_144905	230279	Mm.41523	NM_144905	ENSMUSG00000045917	Tmem268	6330416G13Rik|AW492431|bM230C2.2	transmembrane protein 268	protein-coding
mm_112521.1	chr13	9171328	9171332	+	1	NA	3' UTR (NM_172585, exon 18 of 18)	3' UTR (NM_172585, exon 18 of 18)	77449	NM_172585	217980	Mm.234944	NM_172585	ENSMUSG00000033499	Larp4b	A630096F19|AI256361|D13Wsu64e|Larp5	La ribonucleoprotein domain family, member 4B	protein-coding
mm_100169.1	chr11	116531887	116531896	+	1	NA	promoter-TSS (NM_001172472)	promoter-TSS (NM_001172472)	-20	NM_001172475	20698	Mm.20944	NM_011451	ENSMUSG00000061878	Sphk1	1110006G24Rik|Sk1|Spk1	sphingosine kinase 1	protein-coding
mm_122264.1	chr14	34310389	34310400	-	1	NA	promoter-TSS (NM_008133)	promoter-TSS (NM_008133)	109	NM_029389	75698	Mm.45406	NM_029389	ENSMUSG00000041471	Fam35a	3110001K24Rik	family with sequence similarity 35, member A	protein-coding
mm_2117.1	chr1	87878186	87878198	+	1	NA	intron (NM_177646, intron 1 of 29)	intron (NM_177646, intron 1 of 29)	-23893	NR_136921	100503175	Mm.426422	NR_136921	ENSMUSG00000101942	Gm19582	-	predicted gene, 19582	ncRNA
mm_43138.1	chr5	125391847	125391878	+	1	NA	Intergenic	Intergenic	-1845	NM_019639	22190	Mm.331	NM_019639	ENSMUSG00000008348	Ubc	2700054O04Rik|AI194771|Rps27a|TI-225|Uba52|Ubb	ubiquitin C	protein-coding
mm_105980.1	chr11	115603867	115603921	-	1	NA	promoter-TSS (NM_173048)	promoter-TSS (NM_173048)	22	NM_001252067	260302	Mm.119479	NM_173048	ENSMUSG00000020740	Gga3	C230037M19Rik|mKIAA0154	golgi associated, gamma adaptin ear containing, ARF binding protein 3	protein-coding
mm_79842.1	chr9	64811427	64811437	+	1	NA	5' UTR (NM_001162917, exon 2 of 35)	5' UTR (NM_001162917, exon 2 of 35)	421	NM_001162917	102442	Mm.222473	NM_176935	ENSMUSG00000053641	Dennd4a	AI115600|AI851943|F730015K02Rik	DENN/MADD domain containing 4A	protein-coding
mm_38898.1	chr4	149856286	149856289	-	1	NA	Intergenic	Intergenic	-82020	NM_027460	70556	Mm.41877	NM_027460	ENSMUSG00000028982	Slc25a33	5730438N18Rik|Pnc1	solute carrier family 25, member 33	protein-coding
mm_52939.1	chr6	122934143	122934157	+	1	NA	3' UTR (NM_199311, exon 6 of 6)	3' UTR (NM_199311, exon 6 of 6)	12302	NM_199311	269799	Mm.297275	NM_199311	ENSMUSG00000049037	Clec4a1	BC049354|Dcir4	C-type lectin domain family 4, member a1	protein-coding
mm_107694.1	chr12	55384757	55384766	+	1	NA	intron (NM_001310583, intron 1 of 6)	RMER21B|LTR|ERV1	539	NM_001310583	26443	Mm.30210	NM_011968	ENSMUSG00000021024	Psma6	IOTA	proteasome (prosome, macropain) subunit, alpha type 6	protein-coding
mm_109810.1	chr12	3357038	3357055	-	1	NA	Intergenic	Intergenic	-8086	NM_008445	16570	Mm.7688	NM_008445	ENSMUSG00000020668	Kif3c	mKIAA4058	kinesin family member 3C	protein-coding
mm_156572.1	chrX	151919640	151919650	+	1	NA	exon (NM_021523, exon 67 of 83)	exon (NM_021523, exon 67 of 83)	6431	NR_029753	723947		NR_029753	ENSMUSG00000065536	Mir98	Mirn98|mir-98|mmu-mir-98	microRNA 98	ncRNA
mm_103544.1	chr11	77530275	77530277	-	1	NA	3' UTR (NM_144825, exon 20 of 20)	3' UTR (NM_144825, exon 20 of 20)	15159	NM_026185	67477	Mm.432526	NM_026185	ENSMUSG00000000686	Abhd15	1300007F04Rik	abhydrolase domain containing 15	protein-coding
mm_68350.1	chr7	106509402	106509429	-	1	NA	Intergenic	Intergenic	-68342	NR_003967	209380	Mm.461779	NM_001001318		Gm4759	EG209380	GTPase, very large interferon inducible 1 pseudogene	pseudo
mm_106310.1	chr11	118302167	118302170	-	1	NA	3' UTR (NM_011594, exon 5 of 5)	3' UTR (NM_011594, exon 5 of 5)	-11924	NM_001033528	72344	Mm.232293	NM_001033528	ENSMUSG00000033909	Usp36	2700002L06Rik|mKIAA1453	ubiquitin specific peptidase 36	protein-coding
mm_145639.1	chr18	61117284	61117292	+	1	NA	promoter-TSS (NR_105949)	promoter-TSS (NR_105949)	-180	NR_105949	102466212		NR_105949	ENSMUSG00000098389	Mir6983	Gm27496|mmu-mir-6983	microRNA 6983	ncRNA
mm_15371.1	chr2	156432959	156432987	+	1	NA	intron (NM_013510, intron 1 of 21)	intron (NM_013510, intron 1 of 21)	12064	NM_001291123	13821	Mm.20852	NM_013510	ENSMUSG00000027624	Epb41l1	4.1N|Epb4.1l1|NBL1|mKIAA0338	erythrocyte membrane protein band 4.1 like 1	protein-coding
mm_40226.1	chr5	37280550	37280573	+	1	NA	exon (NM_001136058, exon 9 of 14)	exon (NM_001136058, exon 9 of 14)	34797	NM_007765	12933	Mm.290995	NM_007765	ENSMUSG00000029121	Crmp1	CRMP-1|DRP-1|Dpysl1|ULIP-3|Ulip3	collapsin response mediator protein 1	protein-coding
mm_152379.1	chr19	10237974	10237984	-	1	NA	intron (NM_001033481, intron 1 of 25)	intron (NM_001033481, intron 1 of 25)	2769	NM_001033481	225908	Mm.329716	NM_001033481	ENSMUSG00000036098	Myrf	6030439E18|Gm1804|Gm98|Mrf	myelin regulatory factor	protein-coding
mm_23627.1	chr3	65975003	65975013	+	1	NA	Intergenic	Intergenic	-16783	NM_019937	56706	Mm.175612	NM_019937	ENSMUSG00000027829	Ccnl1	2610030E23Rik|AU018493|Ccnl|ania-6a	cyclin L1	protein-coding
mm_37857.1	chr4	132261597	132261622	-	1	NA	promoter-TSS (NM_020273)	promoter-TSS (NM_020273)	-60	NM_001122992	56809	Mm.103489	NM_020273	ENSMUSG00000028901	Gmeb1	1110050A04Rik|AI256615|AI481278	glucocorticoid modulatory element binding protein 1	protein-coding
mm_46802.1	chr5	113075872	113075896	-	1	NA	TTS (NM_021352)	TTS (NM_021352)	5700	NM_001159650	12962	Mm.378899	NM_021352	ENSMUSG00000029352	Crybb3	AI852419	crystallin, beta B3	protein-coding
mm_135094.1	chr16	34958817	34958835	-	1	NA	promoter-TSS (NR_045722)	promoter-TSS (NR_045722)	38	NR_045722	278725	Mm.436927	NR_045722		E130310I04Rik	A930019C19Rik	RIKEN cDNA E130310I04 gene	ncRNA
mm_57707.1	chr6	128581598	128581612	-	1	NA	promoter-TSS (NM_001001179)	promoter-TSS (NM_001001179)	1	NM_001001179	232400	Mm.259234	NM_001001179	ENSMUSG00000047228	BC048546	Ovos	cDNA sequence BC048546	protein-coding
mm_131564.1	chr16	18143515	18143526	+	1	NA	intron (NM_022982, intron 1 of 1)	intron (NM_022982, intron 1 of 1)	15814	NM_022982	65079	Mm.40149	NM_022982	ENSMUSG00000043811	Rtn4r	NOGOR|NgR|NgR1	reticulon 4 receptor	protein-coding
mm_89819.1	chr10	105040264	105040292	+	1	NA	Intergenic	U1|snRNA|snRNA	534201	NM_177368	278279	Mm.25225	NM_177368	ENSMUSG00000036019	Tmtc2	8430438D04Rik|D330034A10Rik	transmembrane and tetratricopeptide repeat containing 2	protein-coding
mm_114483.1	chr13	69612069	69612083	+	1	NA	promoter-TSS (NM_175283)	promoter-TSS (NM_175283)	60	NM_145354	28114	Mm.260009	NM_145354	ENSMUSG00000021595	Nsun2	D13Wsu123e|Misu	NOL1/NOP2/Sun domain family member 2	protein-coding
mm_102050.1	chr11	52000781	52000794	-	1	NA	promoter-TSS (NM_009458)	promoter-TSS (NM_009458)	-321	NM_009458	22210	Mm.384918	NM_009458	ENSMUSG00000020390	Ube2b	2610301N02Rik|E2-14k|HR6B|Rad6b|mHR6B	ubiquitin-conjugating enzyme E2B	protein-coding
mm_78149.1	chr9	21015376	21015417	+	1	NA	promoter-TSS (NM_010493)	promoter-TSS (NM_010493)	-544	NM_010493	15894	Mm.435508	NM_010493	ENSMUSG00000037405	Icam1	CD54|Icam-1|Ly-47|MALA-2	intercellular adhesion molecule 1	protein-coding
mm_44867.1	chr5	34495291	34495335	-	1	NA	TTS (NM_139064)	TTS (NM_139064)	18666	NM_139064	231130	Mm.28615	NM_139064	ENSMUSG00000059866	Tnip2	1810020H16Rik|ABIN-2|AI428870	TNFAIP3 interacting protein 2	protein-coding
mm_35333.1	chr4	27867588	27867621	-	1	NA	Intergenic	Intergenic	-945527	NM_001290434	13841	Mm.257266	NM_010141	ENSMUSG00000028289	Epha7	Cek11|Ebk|Ehk3|Hek11|Mdk1	Eph receptor A7	protein-coding
mm_156311.1	chrX	136838162	136838172	+	1	NA	3' UTR (NM_011123, exon 7 of 7)	3' UTR (NM_011123, exon 7 of 7)	15421	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_82991.1	chr9	36534024	36534024	-	1	NA	3' UTR (NM_001033783, exon 3 of 3)	3' UTR (NM_001033783, exon 3 of 3)	7939	NM_001033783	434396	Mm.118836	NM_001033783	ENSMUSG00000074448	Gm5615	EG434396|Pate-H|Pate9	predicted gene 5615	protein-coding
mm_154050.1	chr19	55099418	55099492	-	1	NA	promoter-TSS (NM_008149)	promoter-TSS (NM_008149)	-8	NM_008149	14732	Mm.210196	NM_008149	ENSMUSG00000024978	Gpam	GPAT|GPAT1	glycerol-3-phosphate acyltransferase, mitochondrial	protein-coding
mm_141633.1	chr17	32947390	32947395	-	1	NA	promoter-TSS (NM_130882)	promoter-TSS (NM_130882)	-31	NM_130882	170716	Mm.254838	NM_130882	ENSMUSG00000024055	Cyp4f13	0610030I10Rik|Cypf13	cytochrome P450, family 4, subfamily f, polypeptide 13	protein-coding
mm_118341.1	chr13	114458721	114458736	-	1	NA	5' UTR (NM_008046, exon 1 of 6)	5' UTR (NM_008046, exon 1 of 6)	223	NM_001301373	14313	Mm.4913	NM_008046	ENSMUSG00000021765	Fst	AL033346|FS	follistatin	protein-coding
mm_171259.1	chr3	83880349	83880352	+	1	NA	Intergenic	ORR1A0|LTR|ERVL-MaLR	-38742	NM_011905	24088	Mm.87596	NM_011905	ENSMUSG00000027995	Tlr2	Ly105	toll-like receptor 2	protein-coding
mm_156088.1	chrX	110814460	110814476	+	1	NA	promoter-TSS (NM_008901)	promoter-TSS (NM_008901)	89	NM_008901	18994	Mm.56946	NM_008901	ENSMUSG00000056854	Pou3f4	Brn-4|Brn4|OTF-9|Otf9|Slf|oct-9	POU domain, class 3, transcription factor 4	protein-coding
mm_51652.1	chr6	86028876	86028880	+	1	NA	5' UTR (NM_001271860, exon 1 of 13)	5' UTR (NM_001271860, exon 1 of 13)	197	NM_001271860	11519	Mm.104155	NM_013458	ENSMUSG00000030000	Add2	2900072M03Rik|add97	adducin 2 (beta)	protein-coding
mm_112619.1	chr13	15534465	15534467	+	1	NA	intron (NM_008130, intron 2 of 14)	intron (NM_008130, intron 2 of 14)	70743	NM_008130	14634	Mm.5098	NM_008130	ENSMUSG00000021318	Gli3	AI854843|AU023367|Bph|GLI3-190|GLI3FL|Pdn|Xt|add	GLI-Kruppel family member GLI3	protein-coding
mm_37744.1	chr4	129600609	129600639	-	1	NA	promoter-TSS (NM_029748)	promoter-TSS (NM_029748)	24	NM_018799	54709	Mm.250874	NM_018799	ENSMUSG00000028798	Eif3i	36kDa|D4Ertd632e|Eif3s2|Trip1	eukaryotic translation initiation factor 3, subunit I	protein-coding
mm_9840.1	chr1	184453377	184453390	-	1	NA	Intergenic	ID_B1|SINE|B4	104308	NR_040472	73590	Mm.82792	NR_040472	ENSMUSG00000101574	1700112H15Rik	-	RIKEN cDNA 1700112H15 gene	ncRNA
mm_107419.1	chr12	34984853	34984873	+	1	NA	5' UTR (NM_029294, exon 1 of 1)	5' UTR (NM_029294, exon 1 of 1)	102	NM_029294	75456	Mm.79179	NM_029294	ENSMUSG00000092305	Prps1l1	1700011K15Rik	phosphoribosyl pyrophosphate synthetase 1-like 1	protein-coding
mm_140614.1	chr17	10840274	10840284	-	1	NA	promoter-TSS (NM_016694)	promoter-TSS (NM_016694)	-80	NM_001317726	50873	Mm.311110	NM_016694	ENSMUSG00000023826	Park2	PRKN	Parkinson disease (autosomal recessive, juvenile) 2, parkin	protein-coding
mm_24390.1	chr3	90264968	90264988	+	1	NA	TTS (NM_028881)	TTS (NM_028881)	-1536	NM_201407	229541	Mm.30571	NM_201407	ENSMUSG00000042404	Dennd4b	-	DENN/MADD domain containing 4B	protein-coding
mm_130208.1	chr15	95528543	95528565	-	1	NA	promoter-TSS (NM_001289653)	promoter-TSS (NM_001289653)	-302	NM_001289653	54003	Mm.3959	NM_016743	ENSMUSG00000022454	Nell2	A330108N19Rik|R75516|mel91	NEL-like 2	protein-coding
mm_169392.1	chr14	43556442	43556447	+	1	NA	Intergenic	BGLII|LTR|ERVK	51569	NM_001098269	100042342	Mm.429750	NM_001098269	ENSMUSG00000095528	Gm10375	ENSMUSG00000072602	predicted gene 10375	protein-coding
mm_20770.1	chr2	142901435	142901474	-	1	NA	promoter-TSS (NM_001081133)	promoter-TSS (NM_001081133)	10	NM_001081133	16558	Mm.251934	NM_001081133	ENSMUSG00000038844	Kif16b	8430434E15Rik|AA623607|AI789011|C80253|C80902|mKIAA1590	kinesin family member 16B	protein-coding
mm_143282.1	chr17	65772687	65772695	-	1	NA	promoter-TSS (NM_133685)	promoter-TSS (NM_133685)	61	NM_133685	106572	Mm.29274	NM_133685	ENSMUSG00000056515	Rab31	1700093E07Rik|AI415285|Rab22B	RAB31, member RAS oncogene family	protein-coding
mm_70648.1	chr8	14303417	14303420	+	1	NA	intron (NM_172910, intron 3 of 15)	intron (NM_172910, intron 3 of 15)	207543	NM_172910	244310	Mm.404697	NM_172910	ENSMUSG00000047495	Dlgap2	6430596N04Rik|Dap-2|Dap2|Sapap2	discs, large (Drosophila) homolog-associated protein 2	protein-coding
mm_123470.1	chr14	65973455	65973480	-	1	NA	exon (NM_013492, exon 3 of 9)	exon (NM_013492, exon 3 of 9)	4984	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_21625.1	chr2	164277168	164277173	-	1	NA	exon (NM_009300, exon 2 of 3)	exon (NM_009300, exon 2 of 3)	1137	NM_009300	20941	Mm.1286	NM_009300	ENSMUSG00000016998	Svs4	SVS-IV|Svp-2|Svp-4|Svp2|Svp4	seminal vesicle secretory protein 4	protein-coding
mm_115998.1	chr13	24414962	24414980	-	1	NA	promoter-TSS (NM_001284520)	promoter-TSS (NM_001284520)	-151	NM_007717	12763	Mm.8396	NM_007717	ENSMUSG00000016756	Cmah	-	cytidine monophospho-N-acetylneuraminic acid hydroxylase	protein-coding
mm_68177.1	chr7	103851784	103851810	-	1	NA	TTS (NM_008221)	TTS (NM_008221)	1410	NM_008221	15135	Mm.440164	NM_008221	ENSMUSG00000052187	Hbb-y	Ey|Hby	hemoglobin Y, beta-like embryonic chain	protein-coding
mm_56692.1	chr6	114397756	114397777	-	1	NA	promoter-TSS (NM_008285)	promoter-TSS (NM_008285)	-170	NM_008285	15465	Mm.333327	NM_008285	ENSMUSG00000053004	Hrh1	Bphs|H1R|HH1R|Hir	histamine receptor H1	protein-coding
mm_18250.1	chr2	52206950	52206969	-	1	NA	exon (NM_010889, exon 98 of 157)	exon (NM_010889, exon 98 of 157)	-84043	NR_040620	78049	Mm.243883	NR_040620		4930573O16Rik	-	RIKEN cDNA 4930573O16 gene	ncRNA
mm_80122.1	chr9	70576738	70576760	+	1	NA	exon (NM_025690, exon 9 of 21)	exon (NM_025690, exon 9 of 21)	33879	NM_025690	66660	Mm.22379	NM_025690	ENSMUSG00000032212	Sltm	5730455C01Rik|5730555F13Rik|9130215G10Rik|Met	SAFB-like, transcription modulator	protein-coding
mm_61439.1	chr7	75455548	75455629	+	1	NA	promoter-TSS (NM_029332)	promoter-TSS (NM_029332)	54	NM_029332	75547	Mm.216107	NM_029332	ENSMUSG00000066406	Akap13	1700026G02Rik|5730522G15Rik|5830460E08Rik|AKAP-13|AKAP-Lbc|BRX|Ht31|LBC|PROTO-LB|PROTO-LBC	A kinase (PRKA) anchor protein 13	protein-coding
mm_40231.1	chr5	37288842	37288874	+	1	NA	exon (NM_001136058, exon 13 of 14)	exon (NM_001136058, exon 13 of 14)	43094	NM_007765	12933	Mm.290995	NM_007765	ENSMUSG00000029121	Crmp1	CRMP-1|DRP-1|Dpysl1|ULIP-3|Ulip3	collapsin response mediator protein 1	protein-coding
mm_7829.1	chr1	132116909	132116915	-	1	NA	exon (NM_008795, exon 11 of 16)	exon (NM_008795, exon 11 of 16)	22773	NM_008795	18557	Mm.28130	NM_008795	ENSMUSG00000026437	Cdk18	AA682070|Ctk18|Pctk3	cyclin-dependent kinase 18	protein-coding
mm_140130.1	chr17	79615256	79615296	+	1	NA	intron (NM_201361, intron 1 of 10)	CpG	376	NM_201361	381110	Mm.209801	NM_201361	ENSMUSG00000036368	Rmdn2	AW061290|Fam82a1|RMD-2|mRMD-2	regulator of microtubule dynamics 2	protein-coding
mm_57760.1	chr6	129232958	129232985	-	1	NA	intron (NR_040265, intron 2 of 2)	intron (NR_040265, intron 2 of 2)	5074	NR_040265	76432	Mm.261738	NR_040265	ENSMUSG00000097354	2310001H17Rik	AI646108	RIKEN cDNA 2310001H17 gene	ncRNA
mm_41342.1	chr5	90499593	90499641	+	1	NA	exon (NM_007423, exon 7 of 15)	exon (NM_007423, exon 7 of 15)	8903	NM_007423	11576	Mm.358570	NM_007423	ENSMUSG00000054932	Afp	-	alpha fetoprotein	protein-coding
mm_88314.1	chr10	75518031	75518041	+	1	NA	promoter-TSS (NM_026095)	promoter-TSS (NM_026095)	-6	NM_026095	67332	Mm.45151	NM_026095	ENSMUSG00000020180	Snrpd3	1700043E15Rik|2310009E13Rik|AW046420|SMD3	small nuclear ribonucleoprotein D3	protein-coding
mm_65127.1	chr7	19458780	19458800	-	1	NA	promoter-TSS (NM_172279)	promoter-TSS (NM_172279)	-296	NM_172279	232944	Mm.260504	NM_172279	ENSMUSG00000030397	Mark4	2410090P21Rik|C79806|Markl1	MAP/microtubule affinity regulating kinase 4	protein-coding
mm_91737.1	chr10	46819899	46819911	-	1	NA	Intergenic	RLTR9A|LTR|ERVK	575156	NR_028276	108637		NR_028276	ENSMUSG00000096263	Snord14c	Gm23107|Rnu14|U14	small nucleolar RNA, C/D box 14C	snoRNA
mm_70069.1	chr7	142653012	142653039	-	1	NA	3' UTR (NM_010514, exon 4 of 4)	3' UTR (NM_010514, exon 4 of 4)	1971	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_113991.1	chr13	52583065	52583077	+	1	NA	promoter-TSS (NM_001198977)	promoter-TSS (NM_001198977)	-366	NM_001198977	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_36555.1	chr4	86857313	86857349	-	1	NA	promoter-TSS (NM_009096)	promoter-TSS (NM_009096)	36	NM_009096	20104	Mm.379007	NM_009096	ENSMUSG00000028495	Rps6	S6R	ribosomal protein S6	protein-coding
mm_6264.1	chr1	69541317	69541343	-	1	NA	intron (NM_011770, intron 7 of 7)	intron (NM_011770, intron 7 of 7)	144630	NM_011770	22779	Mm.106343	NM_011770	ENSMUSG00000025997	Ikzf2	A730095J18Rik|Helios|Zfpn1a2|Znfn1a2	IKAROS family zinc finger 2	protein-coding
mm_73445.1	chr8	106211017	106211043	+	1	NA	promoter-TSS (NM_001007567)	promoter-TSS (NM_001007567)	-24	NM_145404	214572	Mm.251804	NM_145404	ENSMUSG00000060098	Prmt7	4933402B05Rik|BC006705	protein arginine N-methyltransferase 7	protein-coding
mm_60768.1	chr7	45554927	45554937	+	1	NA	promoter-TSS (NM_025330)	promoter-TSS (NM_025330)	4	NM_025330	66065	Mm.285710	NM_025330	ENSMUSG00000030825	Hsd17b14	0610039E24Rik|Dhrs10|retSDR3	hydroxysteroid (17-beta) dehydrogenase 14	protein-coding
mm_6967.1	chr1	86154621	86154634	-	1	NA	promoter-TSS (NM_027456)	promoter-TSS (NM_027456)	-153	NM_030184	78795	Mm.379264	NM_027456	ENSMUSG00000062590	Armc9	3830422A13Rik|4831423D23Rik|4930438O05Rik|5730415N24Rik	armadillo repeat containing 9	protein-coding
mm_137135.1	chr17	23601476	23601514	+	1	NA	intron (NM_001289482, intron 1 of 3)	intron (NM_001289482, intron 1 of 3)	669	NM_001289482	332221	Mm.270315	NM_001033425	ENSMUSG00000023902	Zscan10	BC068284|Zfp206|Zkscan10|Znf206	zinc finger and SCAN domain containing 10	protein-coding
mm_126863.1	chr15	89334971	89334979	+	1	NA	exon (NM_019977, exon 2 of 10)	exon (NM_019977, exon 2 of 10)	502	NM_019977	56727	Mm.158200	NM_019977	ENSMUSG00000022613	Miox	0610009I10Rik|AI314022|Aldrl6|C85427|RSOR	myo-inositol oxygenase	protein-coding
mm_42907.1	chr5	122502467	122502482	+	1	NA	promoter-TSS (NM_009722)	promoter-TSS (NM_009722)	-249	NR_027838	11938	Mm.227583	NM_009722	ENSMUSG00000029467	Atp2a2	9530097L16Rik|D5Wsu150e|SERCA2|SERCA2B|Serca2a|mKIAA4195	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	protein-coding
mm_158942.1	chr1	79671952	79671952	-	1	NA	promoter-TSS (NM_183027)	promoter-TSS (NM_183027)	20	NM_183027	252903	Mm.32409	NM_183027	ENSMUSG00000054702	Ap1s3	1190009B22|Jr2|[s]3A	adaptor-related protein complex AP-1, sigma 3	protein-coding
mm_115416.1	chr13	115089493	115089516	+	1	NA	exon (NM_134058, exon 1 of 2)	exon (NM_134058, exon 1 of 2)	654	NM_134058	105083	Mm.486295	NM_134058	ENSMUSG00000042275	Pelo	AA409897|AI852218	pelota homolog (Drosophila)	protein-coding
mm_34924.1	chr4	155812466	155812476	+	1	NA	promoter-TSS (NM_207678)	promoter-TSS (NM_207678)	-18	NM_207678	56036	Mm.23492	NM_018856	ENSMUSG00000029068	Ccnl2	1700010A01Rik|1810019L15Rik|2010319M22Rik|AA409936|AW261738|Ania-6b|HCLA-150|Pcee|SB138	cyclin L2	protein-coding
mm_54350.1	chr6	30915553	30915590	-	1	NA	promoter-TSS (NM_054073)	promoter-TSS (NM_054073)	2	NM_054073	116732	Mm.207048	NM_054073	ENSMUSG00000039032	Tsga13	1700023D02Rik|Vme1	testis specific gene A13	protein-coding
mm_63404.1	chr7	127325221	127325243	+	1	NA	exon (NM_001253873, exon 24 of 31)	exon (NM_001253873, exon 24 of 31)	20082	NM_146202	233890	Mm.23031	NM_146202	ENSMUSG00000047371	Zfp768	BC026432|Znf768	zinc finger protein 768	protein-coding
mm_126472.1	chr15	81466310	81466322	+	1	NA	promoter-TSS (NM_019712)	promoter-TSS (NM_019712)	0	NM_019712	56438	Mm.29405	NM_019712	ENSMUSG00000022400	Rbx1	1500002P15Rik|AA517855|ROC1	ring-box 1	protein-coding
mm_85223.1	chr9	97019045	97019068	-	1	NA	promoter-TSS (NM_145134)	promoter-TSS (NM_145134)	-701	NM_145134	211949	Mm.491271	NM_145134	ENSMUSG00000046997	Spsb4	D030068E18Rik|SSB-4|Ssb4	splA/ryanodine receptor domain and SOCS box containing 4	protein-coding
mm_154004.1	chr19	53032103	53032160	-	1	NA	intron (NM_133216, intron 1 of 20)	intron (NM_133216, intron 1 of 20)	6523	NM_133216	170750	Mm.99776	NM_133216	ENSMUSG00000025027	Xpnpep1	D230045I08Rik|sAMP	X-prolyl aminopeptidase (aminopeptidase P) 1, soluble	protein-coding
mm_92590.1	chr10	80075361	80075377	-	1	NA	intron (NM_183426, intron 4 of 31)	intron (NM_183426, intron 4 of 31)	21350	NM_001037741	625249	Mm.332810	NM_008162	ENSMUSG00000075706	Gpx4	GPx-4|GSHPx-4|PHGPx|mtPHGPx|snGPx	glutathione peroxidase 4	protein-coding
mm_8612.1	chr1	156036088	156036098	-	1	NA	promoter-TSS (NM_001160182)	promoter-TSS (NM_001160182)	57	NM_001160182	240832	Mm.253335	NM_022329	ENSMUSG00000050565	Tor1aip2	1110020D10Rik|15kDa|A130072J07|AA103493|AW060462|AW610675|C77739|Ifrg15|Lull1	torsin A interacting protein 2	protein-coding
mm_53222.1	chr6	126939994	126940004	+	1	NA	promoter-TSS (NM_001347455)	promoter-TSS (NM_001347455)	33	NM_138594	28040	Mm.44228	NM_138594	ENSMUSG00000030347	D6Wsu163e	C12orf4	DNA segment, Chr 6, Wayne State University 163, expressed	protein-coding
mm_159292.1	chr2	174298006	174298006	+	1	NA	exon (NM_001077507, exon 1 of 11)	exon (NM_001077507, exon 1 of 11)	147	NM_001310085	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_127132.1	chr15	98167817	98167873	+	1	NA	promoter-TSS (NM_177716)	promoter-TSS (NM_177716)	39	NM_177716	239650	Mm.54140	NM_177716	ENSMUSG00000029875	Ccdc184	5630400A08|AI836003	coiled-coil domain containing 184	protein-coding
mm_153840.1	chr19	46327165	46327173	-	1	NA	promoter-TSS (NM_001347454)	promoter-TSS (NM_001347454)	-13	NM_028627	73728	Mm.268532	NM_028627	ENSMUSG00000037126	Psd	1110007H17Rik|A930015K15|Efa6|Efa6a|Psdl|mKIAA2011	pleckstrin and Sec7 domain containing	protein-coding
mm_11712.1	chr2	36237509	36237510	+	1	NA	intron (NM_008969, intron 3 of 10)	intron (NM_008969, intron 3 of 10)	7083	NM_008969	19224	Mm.275434	NM_008969	ENSMUSG00000047250	Ptgs1	COX1|Cox-1|Cox-3|PGHS-1|PHS 1|Pghs1	prostaglandin-endoperoxide synthase 1	protein-coding
mm_74576.1	chr8	11218765	11218769	-	1	NA	exon (NM_009931, exon 36 of 52)	exon (NM_009931, exon 36 of 52)	-94038	NM_009932	12827	Mm.181021	NM_009932	ENSMUSG00000031503	Col4a2	Col4a-2	collagen, type IV, alpha 2	protein-coding
mm_164473.1	chr16	68104320	68104321	+	1	NA	Intergenic	Intergenic	-483412	NM_178721	239857	Mm.394300	NM_178721	ENSMUSG00000064115	Cadm2	2900078E11Rik|9330131D06|A830029E02Rik|Igdf4d|Igsf4d|NECL3|SynCAM 2|SynCAM2	cell adhesion molecule 2	protein-coding
mm_14875.1	chr2	148799906	148799910	+	1	NA	5' UTR (NM_009978, exon 2 of 4)	5' UTR (NM_009978, exon 2 of 4)	1069	NM_009978	13012	Mm.20435	NM_009978	ENSMUSG00000027442	Cst8	Cres|Cst-rs1	cystatin 8 (cystatin-related epididymal spermatogenic)	protein-coding
mm_96513.1	chr11	68473857	68473867	+	1	NA	exon (NM_177320, exon 2 of 19)	exon (NM_177320, exon 2 of 19)	-29157	NM_001004435	104709	Mm.234573	NM_001004435	ENSMUSG00000046207	Pik3r6	BB220380|p84|p84 PIKAP|p87(PIKAP)|p87PIKAP	phosphoinositide-3-kinase, regulatory subunit 6	protein-coding
mm_95263.1	chr11	44926209	44926213	+	1	NA	intron (NM_007897, intron 10 of 15)	intron (NM_007897, intron 10 of 15)	190717	NR_045100	100504255	Mm.123608	NR_045100	ENSMUSG00000084773	Gm12159	OTTMUSG00000005475	predicted gene 12159	ncRNA
mm_14664.1	chr2	138278470	138278480	+	1	NA	promoter-TSS (NM_145534)	promoter-TSS (NM_145534)	-18	NM_145534	228662	Mm.153405	NM_145534	ENSMUSG00000062098	Btbd3	mKIAA0952	BTB (POZ) domain containing 3	protein-coding
mm_132168.1	chr16	32277529	32277566	+	1	NA	promoter-TSS (NM_027355)	promoter-TSS (NM_027355)	86	NM_027355	70238	Mm.228263	NM_027355	ENSMUSG00000014074	Rnf168	3110001H15Rik	ring finger protein 168	protein-coding
mm_128457.1	chr15	50782016	50782055	-	1	NA	intron (NM_001310485, intron 5 of 7)	intron (NM_001310485, intron 5 of 7)	107014	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_88375.1	chr10	76253900	76253915	+	1	NA	promoter-TSS (NM_009115)	promoter-TSS (NM_009115)	71	NM_009115	20203	Mm.235998	NM_009115	ENSMUSG00000033208	S100b	AI850290|Bpb	S100 protein, beta polypeptide, neural	protein-coding
mm_15576.1	chr2	158667120	158667130	+	1	NA	promoter-TSS (NM_001159662)	promoter-TSS (NM_001159662)	-10	NM_001159662	228852	Mm.150540	NM_153089	ENSMUSG00000037754	Ppp1r16b	ANKRD4|C130078N17Rik|TIMAP|Wdt4	protein phosphatase 1, regulatory (inhibitor) subunit 16B	protein-coding
mm_83096.1	chr9	40321257	40321267	-	1	NA	intron (NM_172768, intron 4 of 19)	intron (NM_172768, intron 4 of 19)	-12210	NR_040728	73558	Mm.398307	NR_040728		1700110K17Rik	-	RIKEN cDNA 1700110K17 gene	ncRNA
mm_98372.1	chr11	94044143	94044156	+	1	NA	promoter-TSS (NM_001199205)	promoter-TSS (NM_001199205)	-56	NM_001025430	70834	Mm.260737	NM_027569	ENSMUSG00000020859	Spag9	3110018C07Rik|4733401I23Rik|4831406C20Rik|AW552012|JLP|JSAP2|JSAP2a|Jip4|Mapk8ip4|syd1	sperm associated antigen 9	protein-coding
mm_136602.1	chr17	5160947	5160950	+	1	NA	intron (NM_001085355, intron 4 of 19)	B2_Mm2|SINE|B2	165874	NM_001085355	239985	Mm.133401	NM_001085355	ENSMUSG00000069729	Arid1b	8030481M12|9330189K18Rik|AI836955|Ardi1b|B230217J03Rik|mKIAA1235	AT rich interactive domain 1B (SWI-like)	protein-coding
mm_33124.1	chr4	124802812	124802818	+	1	NA	intron (NM_008636, intron 1 of 10)	intron (NM_008636, intron 1 of 10)	266	NM_008636	17764	Mm.272397	NM_008636	ENSMUSG00000028890	Mtf1	MTF-1|Thyls	metal response element binding transcription factor 1	protein-coding
mm_172132.1	chr6	3399428	3399433	-	1	NA	5' UTR (NM_010156, exon 1 of 2)	5' UTR (NM_010156, exon 1 of 2)	141	NM_010156	209086	Mm.196013	NM_010156	ENSMUSG00000047735	Samd9l	AA175286|ESTM25|mKIAA2005	sterile alpha motif domain containing 9-like	protein-coding
mm_69212.1	chr7	127512232	127512242	-	1	NA	non-coding (NR_024331, exon 1 of 1)	non-coding (NR_024331, exon 1 of 1)	254	NM_001304266	100043597	Mm.428042	NM_175144	ENSMUSG00000053877	Srcap	B930091H02Rik|D030022P06Rik|F630004O05Rik	Snf2-related CREBBP activator protein	protein-coding
mm_162868.1	chr10	93589692	93589705	-	1	NA	promoter-TSS (NM_027246)	promoter-TSS (NM_027246)	-40	NM_027246	69878	Mm.259642	NM_027246	ENSMUSG00000020018	Snrpf	2010013O18Rik|SMF|sm-F|snRNP-F	small nuclear ribonucleoprotein polypeptide F	protein-coding
mm_72132.1	chr8	71882036	71882046	+	1	NA	promoter-TSS (NM_145624)	promoter-TSS (NM_145624)	-27	NM_145624	236193	Mm.290790	NM_145624	ENSMUSG00000056019	Zfp709	BC021921|GIOT-4|HIT-40	zinc finger protein 709	protein-coding
mm_126585.1	chr15	82298944	82298963	+	1	NA	promoter-TSS (NM_029066)	promoter-TSS (NM_029066)	-31	NM_029066	74716	Mm.159315	NM_029066	ENSMUSG00000022455	Wbp2nl	4930521I23Rik|PAWP	WBP2 N-terminal like	protein-coding
mm_34395.1	chr4	145023033	145023047	+	1	NA	intron (NM_001276502, intron 64 of 68)	intron (NM_001276502, intron 64 of 68)	129903	NM_011303	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding
mm_116531.1	chr13	45841637	45841653	-	1	NA	intron (NM_001199304, intron 3 of 6)	ID_B1|SINE|B4	123346	NM_001199304	20238	Mm.342683	NM_009124	ENSMUSG00000046876	Atxn1	2900016G23Rik|Atx1|C85907|ENSMUSG00000074917|Gm10786|Sca1	ataxin 1	protein-coding
mm_125558.1	chr15	58889015	58889028	+	1	NA	promoter-TSS (NM_175226)	promoter-TSS (NM_175226)	-208	NM_175226	75841	Mm.4537	NM_175226	ENSMUSG00000037075	Rnf139	4930555P18Rik	ring finger protein 139	protein-coding
mm_107905.1	chr12	70939938	70939958	+	1	NA	intron (NM_019785, intron 1 of 12)	B3|SINE|B2	2091	NM_019785	56444	Mm.29317	NM_019785	ENSMUSG00000021076	Actr10	Actr11|Arp11	ARP10 actin-related protein 10	protein-coding
mm_23302.1	chr3	52516952	52516997	+	1	NA	Intergenic	Intergenic	-222750	NR_038079	329639	Mm.131245	NR_038079	ENSMUSG00000102785	Gm2447	100039832|A530017F20	predicted gene 2447	ncRNA
mm_112779.1	chr13	20090539	20090633	+	1	NA	promoter-TSS (NM_080288)	promoter-TSS (NM_080288)	79	NM_080288	140580	Mm.342392	NM_080288	ENSMUSG00000041112	Elmo1	6330578D22Rik|C230095H21Rik|CED-12	engulfment and cell motility 1	protein-coding
mm_43288.1	chr5	134141613	134141627	+	1	NA	3' UTR (NM_030719, exon 9 of 9)	3' UTR (NM_030719, exon 9 of 9)	35147	NM_033572	94254	Mm.29508	NM_033572	ENSMUSG00000061979	Rcc1l	5730496C04Rik|AU019812|Wbscr16	reculator of chromosome condensation 1 like	protein-coding
mm_10479.1	chr2	14604213	14604241	+	1	NA	promoter-TSS (NM_023116)	promoter-TSS (NM_023116)	-79	NM_023116	12296	Mm.313930	NM_023116	ENSMUSG00000057914	Cacnb2	AW060387|CAB2|Cavbeta2|Cchb2	calcium channel, voltage-dependent, beta 2 subunit	protein-coding
mm_61969.1	chr7	90442903	90442921	+	1	NA	non-coding (NR_073438, exon 1 of 4)	non-coding (NR_073438, exon 1 of 4)	131	NR_073438	233490	Mm.29496	NM_145151	ENSMUSG00000051451	Crebzf	1110034C16Rik|6330417B10Rik|LAZip|LAZipII|SMILE|Zf	CREB/ATF bZIP transcription factor	protein-coding
mm_57111.1	chr6	122595687	122595749	-	1	NA	intron (NM_031159, intron 3 of 7)	PB1|SINE|Alu	6726	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_67395.1	chr7	79858326	79858351	-	1	NA	Intergenic	Intergenic	-15986	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_20755.1	chr2	140660369	140660388	-	1	NA	exon (NM_178382, exon 3 of 3)	exon (NM_178382, exon 3 of 3)	11098	NM_001172160	71436	Mm.426781	NM_178382	ENSMUSG00000051379	Flrt3	5530600M07Rik|C430047I10Rik|mKIAA1469	fibronectin leucine rich transmembrane protein 3	protein-coding
mm_88212.1	chr10	70204654	70204670	+	1	NA	promoter-TSS (NM_001304739)	promoter-TSS (NM_001304739)	-2	NM_001304739	69563	Mm.64672	NM_001304739	ENSMUSG00000019933	Mrln	2310015B20Rik|Mln	myoregulin	protein-coding
mm_77870.1	chr9	6168450	6168460	+	1	NA	promoter-TSS (NM_027924)	promoter-TSS (NM_027924)	-157	NM_027924	71785	Mm.390122	NM_027924	ENSMUSG00000032006	Pdgfd	1110003I09Rik	platelet-derived growth factor, D polypeptide	protein-coding
mm_17172.1	chr2	25316880	25316892	-	1	NA	exon (NM_001177657, exon 2 of 19)	exon (NM_001177657, exon 2 of 19)	2301	NM_008169	14810	Mm.278672	NM_008169	ENSMUSG00000026959	Grin1	GluN1|GluRdelta1|GluRzeta1|M100174|NMD-R1|NMDAR1|NR1|Nmdar|Rgsc174	glutamate receptor, ionotropic, NMDA1 (zeta 1)	protein-coding
mm_70962.1	chr8	26980471	26980481	+	1	NA	3' UTR (NM_001110508, exon 3 of 3)	3' UTR (NM_001110508, exon 3 of 3)	3140	NM_001110508	353310	Mm.212469	NM_001101502	ENSMUSG00000085795	Zfp703	1110032O19Rik|AI430822|AL022941|Csmn1|End2|Zeppo1|Znf703|Zpo1	zinc finger protein 703	protein-coding
mm_147144.1	chr18	36559832	36559851	-	1	NA	promoter-TSS (NM_175375)	promoter-TSS (NM_175375)	-762	NM_175375	108857	Mm.482287	NM_175375	ENSMUSG00000024483	Ankhd1	1110004O12Rik|4933432B13Rik|9130019P20Rik|A530027J04Rik|A630021B20Rik|AA571404|Mask|mFLJ00246|mKIAA1085	ankyrin repeat and KH domain containing 1	protein-coding
mm_117518.1	chr13	81004462	81004462	-	1	NA	intron (NR_015587, intron 1 of 1)	L2b|LINE|L2	40388	NR_015587	319983	Mm.343027	NR_015587	ENSMUSG00000097098	9330111N05Rik	-	RIKEN cDNA 9330111N05 gene	ncRNA
mm_153495.1	chr19	41332274	41332287	-	1	NA	exon (NM_031376, exon 3 of 17)	exon (NM_031376, exon 3 of 17)	52790	NM_031376	83490	Mm.222266	NM_031376	ENSMUSG00000025017	Pik3ap1	1810044J04Rik|BCAP	phosphoinositide-3-kinase adaptor protein 1	protein-coding
mm_22149.1	chr2	172398061	172398065	-	1	NA	intron (NM_001080820, intron 1 of 6)	intron (NM_001080820, intron 1 of 6)	4269	NM_001276423	320664	Mm.210195	NM_001033538	ENSMUSG00000074570	Cass4	F730031O20Rik	Cas scaffolding protein family member 4	protein-coding
mm_122547.1	chr14	48662741	48662751	-	1	NA	5' UTR (NM_144841, exon 1 of 3)	5' UTR (NM_144841, exon 1 of 3)	126	NM_144841	18424	Mm.134516	NM_144841	ENSMUSG00000021848	Otx2	E130306E05Rik	orthodenticle homeobox 2	protein-coding
mm_135830.1	chr16	58523350	58523361	-	1	NA	promoter-TSS (NM_018784)	promoter-TSS (NM_018784)	-43	NM_018784	54613	Mm.212742	NM_018784	ENSMUSG00000022747	St3gal6	1700023B24Rik|AI930218|AW552396|Siat10|St3galVI	ST3 beta-galactoside alpha-2,3-sialyltransferase 6	protein-coding
mm_93541.1	chr10	115384752	115384796	-	1	NA	promoter-TSS (NM_025780)	promoter-TSS (NM_025780)	-185	NM_001033261	216345	Mm.207621	NM_001033261	ENSMUSG00000034163	Zfc3h1	BC033596|Ccdc131|Psrc2	zinc finger, C3H1-type containing	protein-coding
mm_135031.1	chr16	32810483	32810494	-	1	NA	promoter-TSS (NM_001256309)	promoter-TSS (NM_001256309)	-42	NM_001256309	381043	Mm.303864	NM_001256309	ENSMUSG00000094430	Gm933	Gm1743	predicted gene 933	protein-coding
mm_169511.1	chr14	85379664	85379668	+	1	NA	Intergenic	BGLII|LTR|ERVK	-866304	NR_040457	75155	Mm.399239	NR_040457		4930529K09Rik	4930507G21Rik	RIKEN cDNA 4930529K09 gene	ncRNA
mm_109126.1	chr12	105761447	105761458	+	1	NA	intron (NM_030187, intron 12 of 17)	intron (NM_030187, intron 12 of 17)	-23245	NM_011112	18789	Mm.255877	NM_011112	ENSMUSG00000021111	Papola	Pap|PapIII|Plap	poly (A) polymerase alpha	protein-coding
mm_133577.1	chr16	91406995	91407015	+	1	NA	intron (NM_008349, intron 1 of 6)	intron (NM_008349, intron 1 of 6)	770	NM_008349	16155	Mm.4154	NM_008349	ENSMUSG00000022969	Il10rb	6620401D04Rik|AI528744|CRF2-4|Crfb4|D16H21S58|D21S58h|IL-10R2|Il10r2	interleukin 10 receptor, beta	protein-coding
mm_124473.1	chr14	121379196	121379200	-	1	NA	promoter-TSS (NM_145465)	promoter-TSS (NM_145465)	32	NM_145465	223255	Mm.390756	NM_145465	ENSMUSG00000063410	Stk24	1810013H02Rik|C76483|MST-3|Mst3|STE20	serine/threonine kinase 24	protein-coding
mm_110088.1	chr12	25002879	25002882	-	1	NA	intron (NM_001081378, intron 12 of 31)	intron (NM_001081378, intron 12 of 31)	27948	NM_001081378	77480	Mm.250641	NM_001081378	ENSMUSG00000036333	Kidins220	3110039L19Rik|AI194387|AI316525|C330002I19Rik|mKIAA1250	kinase D-interacting substrate 220	protein-coding
mm_165968.1	chr4	96244898	96244898	+	1	NA	Intergenic	Intergenic	-103746	NM_001100182	242546	Mm.302562	NM_001100182	ENSMUSG00000081225	Cyp2j12	BB197342|Cyp2j12-ps|OTTMUSG00000007939	cytochrome P450, family 2, subfamily j, polypeptide 12	protein-coding
mm_58388.1	chr7	3181067	3181080	+	1	NA	Intergenic	CpG	-11870	NM_001004153	245128	Mm.268551	NM_001004153	ENSMUSG00000054753	AU018091	-	expressed sequence AU018091	protein-coding
mm_100754.1	chr11	4240172	4240182	-	1	NA	3' UTR (NM_001013365, exon 3 of 3)	3' UTR (NM_001013365, exon 3 of 3)	3392	NM_001013365	18413	Mm.131422	NM_001013365	ENSMUSG00000058755	Osm	OncoM	oncostatin M	protein-coding
mm_52272.1	chr6	108549893	108549907	+	1	NA	3' UTR (NM_010585, exon 62 of 62)	3' UTR (NM_010585, exon 62 of 62)	60157	NR_106121	102465766		NR_106121	ENSMUSG00000105697	Mir7661	mmu-mir-7661	microRNA 7661	ncRNA
mm_30109.1	chr3	139002283	139002303	-	1	NA	intron (NM_001040690, intron 4 of 14)	L1_Mur3|LINE|L1	72908	NM_145544	229877	Mm.28893	NM_145544	ENSMUSG00000028149	Rap1gds1	BC011279|GDS1	RAP1, GTP-GDP dissociation stimulator 1	protein-coding
mm_39762.1	chr5	30013142	30013143	+	1	NA	promoter-TSS (NM_031168)	promoter-TSS (NM_031168)	28	NM_031168	16193	Mm.1019	NM_031168	ENSMUSG00000025746	Il6	Il-6	interleukin 6	protein-coding
mm_60904.1	chr7	46712205	46712239	+	1	NA	exon (NM_011315, exon 4 of 4)	exon (NM_011315, exon 4 of 4)	-1571	NM_030233	78935	Mm.289866	NM_030233	ENSMUSG00000006763	Saal1	5031425D22Rik|SPACIA1	serum amyloid A-like 1	protein-coding
mm_148798.1	chr19	6226379	6226381	+	1	NA	promoter-TSS (NM_130453)	promoter-TSS (NM_130453)	-21	NM_130453	170458	Mm.379306	NM_130453	ENSMUSG00000024784	Gpha2	GPA2|zsig51	glycoprotein hormone alpha 2	protein-coding
mm_85564.1	chr9	106891932	106891947	-	1	NA	promoter-TSS (NM_029103)	promoter-TSS (NM_029103)	-1	NM_029103	74840	Mm.29778	NM_029103	ENSMUSG00000032575	Manf	3230402M22Rik|AA407711|AA408789|AA673178|Armet|D17914|D18Mgi17	mesencephalic astrocyte-derived neurotrophic factor	protein-coding
mm_15932.1	chr2	165530117	165530119	+	1	NA	Intergenic	MamGypLTR2b|LTR|Gypsy	26221	NM_130451	170441	Mm.34147	NM_130451	ENSMUSG00000027661	Slc2a10	AA450473|Glut10	solute carrier family 2 (facilitated glucose transporter), member 10	protein-coding
mm_25117.1	chr3	102010115	102010123	+	1	NA	promoter-TSS (NM_178777)	promoter-TSS (NM_178777)	-26	NM_178777	18072	Mm.137286	NM_178777	ENSMUSG00000048540	Nhlh2	6230401I09Rik|Hen2|NSCL2|Nscl-2|bHLHa34	nescient helix loop helix 2	protein-coding
mm_30968.1	chr4	34124938	34124943	+	1	NA	Intergenic	Intergenic	-74873	NM_026293	67652	Mm.55848	NM_026293	ENSMUSG00000028264	Spaca1	1700124L11Rik|4930540L03Rik	sperm acrosome associated 1	protein-coding
mm_2961.1	chr1	132880401	132880454	+	1	NA	promoter-TSS (NM_010732)	promoter-TSS (NM_010732)	72	NM_010732	16980	Mm.39640	NM_010732	ENSMUSG00000026443	Lrrn2	5730406J09Rik|NLRR-2	leucine rich repeat protein 2, neuronal	protein-coding
mm_106355.1	chr11	118393622	118393633	-	1	NA	exon (NM_011150, exon 6 of 6)	exon (NM_011150, exon 6 of 6)	8304	NM_011150	19039	Mm.3152	NM_011150	ENSMUSG00000033880	Lgals3bp	90K|CyCAP|MAC-2BP|Ppicap|Tango10b	lectin, galactoside-binding, soluble, 3 binding protein	protein-coding
mm_141891.1	chr17	34861878	34861894	-	1	NA	TTS (NM_013484)	TTS (NM_013484)	628	NM_001142706	14962	Mm.653	NM_008198	ENSMUSG00000090231	Cfb	AI195813|AI255840|B|Bf|C2|Fb|H2-Bf	complement factor B	protein-coding
mm_151684.1	chr19	4269240	4269292	-	1	NA	promoter-TSS (NM_198113)	promoter-TSS (NM_198113)	-94	NM_198113	245857	Mm.248388	NM_198113	ENSMUSG00000034616	Ssh3	BC028922|SSH-3|mSSH-3L	slingshot homolog 3 (Drosophila)	protein-coding
mm_20860.1	chr2	148437205	148437218	-	1	NA	3' UTR (NM_010740, exon 2 of 2)	3' UTR (NM_010740, exon 2 of 2)	6324	NM_010740	17064	Mm.681	NM_010740	ENSMUSG00000027435	Cd93	6030404G09Rik|AA145088|AA4.1|AW555904|C1qr1|C1qrp|Ly68	CD93 antigen	protein-coding
mm_25003.1	chr3	97651854	97651865	+	1	NA	3' UTR (NM_001161763, exon 9 of 9)	3' UTR (NM_001161763, exon 9 of 9)	-6353	NM_182997	108097	Mm.31175	NM_182997	ENSMUSG00000038205	Prkab2	5730553K21Rik|AW049591|BB124140	protein kinase, AMP-activated, beta 2 non-catalytic subunit	protein-coding
mm_93286.1	chr10	96185721	96185726	-	1	NA	Intergenic	Intergenic	-40484	NR_110448	74881	Mm.410819	NR_110448		4930459C07Rik	-	RIKEN cDNA 4930459C07 gene	ncRNA
mm_22187.1	chr2	173247233	173247243	-	1	NA	intron (NM_022995, intron 1 of 3)	intron (NM_022995, intron 1 of 3)	-28316	NM_001139519	58203	Mm.116687	NM_021394	ENSMUSG00000027514	Zbp1	2010010H03Rik|Dai|Dlm1|mZaDLM	Z-DNA binding protein 1	protein-coding
mm_103662.1	chr11	79023506	79023525	-	1	NA	promoter-TSS (NR_045873)	promoter-TSS (NR_045873)	-82	NR_045873	790910	Mm.440410	NR_045873		Gm11201	ENSMUSG00000072637|OTTMUSG00000000169	predicted gene 11201	ncRNA
mm_141593.1	chr17	32424103	32424127	-	1	NA	promoter-TSS (NM_001271478)	promoter-TSS (NM_001271478)	52	NM_001271476	57757	Mm.86752	NM_021319	ENSMUSG00000079563	Pglyrp2	C730002N09Rik|PGRP-L|Pglyrpl|tagL	peptidoglycan recognition protein 2	protein-coding
mm_130550.1	chr15	98985768	98985779	-	1	NA	promoter-TSS (NR_045991)	promoter-TSS (NR_045991)	-192	NR_045991	75951	Mm.441657	NR_045991	ENSMUSG00000097587	4930578M01Rik	3010001K12Rik	RIKEN cDNA 4930578M01 gene	ncRNA
mm_153727.1	chr19	44407704	44407712	-	1	NA	promoter-TSS (NM_009127)	promoter-TSS (NM_009127)	1	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_12468.1	chr2	71421230	71421242	+	1	NA	exon (NM_026115, exon 7 of 11)	exon (NM_026115, exon 7 of 11)	6760	NR_039557	100628577		NR_039557	ENSMUSG00000093061	Mir5098	mmu-mir-5098|mu-mir-5098	microRNA 5098	ncRNA
mm_111116.1	chr12	80967633	80967641	-	1	NA	exon (NM_001177561, exon 1 of 5)	exon (NM_001177561, exon 1 of 5)	442	NM_011387	20493	Mm.486361	NM_011387	ENSMUSG00000021135	Slc10a1	Ntcp	solute carrier family 10 (sodium/bile acid cotransporter family), member 1	protein-coding
mm_128377.1	chr15	42676793	42676803	-	1	NA	5' UTR (NM_001286062, exon 1 of 9)	5' UTR (NM_001286062, exon 1 of 9)	179	NM_001286062	11600	Mm.309336	NM_009640	ENSMUSG00000022309	Angpt1	1110046O21Rik|Ang-1|Ang1	angiopoietin 1	protein-coding
mm_56935.1	chr6	119848070	119848078	-	1	NA	promoter-TSS (NM_178085)	promoter-TSS (NM_178085)	76	NM_053204	111173	Mm.288860	NM_053204	ENSMUSG00000030172	Erc1	4930404L01Rik|5033405M01Rik|9630025C19Rik|B430107L16Rik|CAST2|ELKS|Elks1|RAB6IP2A|RAB6IP2B|Rab6ip2|mKIAA1081	ELKS/RAB6-interacting/CAST family member 1	protein-coding
mm_65812.1	chr7	29042259	29042269	-	1	NA	intron (NM_009109, intron 84 of 105)	intron (NM_009109, intron 84 of 105)	41430	NR_035489	100316710		NR_035489	ENSMUSG00000089219	Mir1963	mir-1963|mmu-mir-1963	microRNA 1963	ncRNA
mm_123495.1	chr14	66179036	66179048	-	1	NA	intron (NM_001162366, intron 4 of 29)	intron (NM_001162366, intron 4 of 29)	34510	NM_001162366	19229	Mm.21613	NM_172498	ENSMUSG00000059456	Ptk2b	CADTK|CAKB|CAKbeta|E430023O05Rik|FADK2|FAK2|PYK2|Raftk	PTK2 protein tyrosine kinase 2 beta	protein-coding
mm_138185.1	chr17	34267995	34268005	+	1	NA	exon (NM_207105, exon 4 of 6)	exon (NM_207105, exon 4 of 6)	4773	NM_207105	14961	Mm.254067	NM_207105	ENSMUSG00000073421	H2-Ab1	AI845868|Abeta|H-2Ab|H2-Ab|I-Abeta|IAb|Ia-2|Ia2|Rmcs1	histocompatibility 2, class II antigen A, beta 1	protein-coding
mm_84391.1	chr9	65499912	65499915	-	1	NA	Intergenic	PB1D10|SINE|Alu	38976	NM_138584	27965	Mm.272475	NM_138584	ENSMUSG00000032388	Spg21	ACP33|BM-019|C78576|D9Wsu18e|GL010|MAST	spastic paraplegia 21 homolog (human)	protein-coding
mm_41751.1	chr5	102845234	102845249	+	1	NA	5' UTR (NM_001346585, exon 1 of 7)	5' UTR (NM_001346585, exon 1 of 7)	234	NM_001346585	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding
mm_136930.1	chr17	13874563	13874582	+	1	NA	intron (NM_010806, intron 22 of 32)	intron (NM_010806, intron 22 of 32)	-73801	NM_001122977	635895	Mm.388844	NM_001122977	ENSMUSG00000067941	Gm7168	EG635895	predicted gene 7168	protein-coding
mm_118019.1	chr13	100786601	100786612	-	1	NA	promoter-TSS (NM_172301)	promoter-TSS (NM_172301)	-120	NM_172301	268697	Mm.260114	NM_172301	ENSMUSG00000041431	Ccnb1	Ccnb1-rs1|Ccnb1-rs13|CycB1|Cycb-4|Cycb-5|Cycb1-rs1	cyclin B1	protein-coding
mm_96552.1	chr11	68888579	68888588	+	1	NA	promoter-TSS (NM_177060)	promoter-TSS (NM_177060)	30	NM_177060	320040	Mm.305696	NM_177060	ENSMUSG00000046490	Rnf222	9930039A11Rik	ring finger protein 222	protein-coding
mm_81892.1	chr9	119434755	119434758	+	1	NA	3' UTR (NM_007397, exon 10 of 10)	3' UTR (NM_007397, exon 10 of 10)	-10167	NM_001172136	208194	Mm.101578	NM_172456	ENSMUSG00000042787	Exog	AW557704|ENGL-B|ENGL-a|Endogl1|Endogl2|Engl|Engla|Englb	endo/exonuclease (5'-3'), endonuclease G-like	protein-coding
mm_122473.1	chr14	45598641	45598676	-	1	NA	intron (NM_001039106, intron 11 of 11)	intron (NM_001039106, intron 11 of 11)	54948	NR_045809	67651	Mm.55930	NR_045809		4930527F14Rik	-	RIKEN cDNA 4930527F14 gene	ncRNA
mm_90381.1	chr10	127274985	127274994	+	1	NA	intron (NM_001190453, intron 4 of 14)	intron (NM_001190453, intron 4 of 14)	8727	NM_001190453	69654	Mm.167537	NM_027151	ENSMUSG00000025410	Dctn2	2310042E05Rik|C130077D06Rik|C87049|DCTN-50|GMP23-48K|RBP50|p50	dynactin 2	protein-coding
mm_87576.1	chr10	56388400	56388408	+	1	NA	exon (NM_010288, exon 2 of 2)	exon (NM_010288, exon 2 of 2)	11104	NM_010288	14609	Mm.378921	NM_010288	ENSMUSG00000050953	Gja1	AU042049|AW546267|Cnx43|Cx43|Cx43alpha1|Gja-1|Npm1|connexin43	gap junction protein, alpha 1	protein-coding
mm_141511.1	chr17	31678110	31678124	-	1	NA	exon (NM_001278570, exon 1 of 3)	exon (NM_001278570, exon 1 of 3)	186	NM_001278570	12954	Mm.1228	NM_013501	ENSMUSG00000024041	Cryaa	Acry-1|Crya-1|Crya1|DAcry-1|lop18	crystallin, alpha A	protein-coding
mm_156301.1	chrX	136837897	136837901	+	1	NA	3' UTR (NM_011123, exon 7 of 7)	3' UTR (NM_011123, exon 7 of 7)	15153	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_109943.1	chr12	11326353	11326363	-	1	NA	exon (NM_012038, exon 4 of 4)	exon (NM_012038, exon 4 of 4)	26471	NR_106136	102465775		NR_106136	ENSMUSG00000098879	Mir7675	Gm27965|mmu-mir-7675	microRNA 7675	ncRNA
mm_6886.1	chr1	84695785	84695868	-	1	NA	promoter-TSS (NR_039588)	promoter-TSS (NR_039588)	-13	NR_039588	100628595		NR_039588	ENSMUSG00000093254	Mir5126	mir-5126|mmu-mir-5126|mu-mir-5126	microRNA 5126	ncRNA
mm_48727.1	chr5	147400389	147400389	-	1	NA	promoter-TSS (NM_010229)	promoter-TSS (NM_010229)	100	NM_010229	14255	Mm.194	NM_010229	ENSMUSG00000042817	Flt3	B230315G04|CD135|Flk-2|Flk2|Flt-3|Ly72|wmfl	FMS-like tyrosine kinase 3	protein-coding
mm_148915.1	chr19	6975123	6975125	+	1	NA	promoter-TSS (NM_008889)	promoter-TSS (NM_008889)	76	NM_008889	18938	Mm.140	NM_008889	ENSMUSG00000056612	Ppp1r14b	AOM172|PHI-1|PLCB3N|Png	protein phosphatase 1, regulatory (inhibitor) subunit 14B	protein-coding
mm_133369.1	chr16	84709051	84709058	+	1	NA	Intergenic	Intergenic	-3969	NR_132106	100653389	Mm.261808	NR_132106	ENSMUSG00000097418	Mir155hg	Bic|Gm26667	Mir155 host gene (non-protein coding)	ncRNA
mm_119190.1	chr14	32347865	32347869	+	1	NA	TTS (NM_001081130)	TTS (NM_001081130)	25848	NM_001081130	239017	Mm.318302	NM_001081130	ENSMUSG00000021913	Ogdhl	-	oxoglutarate dehydrogenase-like	protein-coding
mm_143332.1	chr17	66479389	66479407	-	1	NA	Intergenic	Intergenic	-29648	NM_001114098	68617	Mm.33421	NM_172963	ENSMUSG00000052105	Mtcl1	1110012J17Rik|Ccdc165|D130071O13|Kiaa0802|Soga2|mKIAA0802|t8219b25	microtubule crosslinking factor 1	protein-coding
mm_116181.1	chr13	30950315	30950325	-	1	NA	intron (NM_025588, intron 1 of 27)	intron (NM_025588, intron 1 of 27)	-2559	NM_153072	210554	Mm.450571	NM_153072	ENSMUSG00000076430	Hus1b	-	HUS1 checkpoint clamp component B	protein-coding
mm_25149.1	chr3	102760896	102760906	+	1	NA	exon (NM_001243132, exon 6 of 8)	exon (NM_001243132, exon 6 of 8)	21813	NM_009432	22094	Mm.110730	NM_009432	ENSMUSG00000027857	Tshb	-	thyroid stimulating hormone, beta subunit	protein-coding
mm_72269.1	chr8	75099878	75099888	+	1	NA	intron (NM_010442, intron 4 of 4)	intron (NM_010442, intron 4 of 4)	6265	NM_010442	15368	Mm.276389	NM_010442	ENSMUSG00000005413	Hmox1	D8Wsu38e|HO-1|HO1|Hemox|Hmox|Hsp32	heme oxygenase 1	protein-coding
mm_104221.1	chr11	88428866	88428867	-	1	NA	intron (NM_054043, intron 7 of 13)	intron (NM_054043, intron 7 of 13)	76093	NR_039545	100628571		NR_039545	ENSMUSG00000092985	Mir378b	mir-378b|mmu-mir-378b	microRNA 378b	ncRNA
mm_165782.1	chr3	131111793	131111801	-	1	NA	promoter-TSS (NM_001276403)	promoter-TSS (NM_001276403)	-994	NM_001276403	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_40104.1	chr5	34660310	34660323	+	1	NA	promoter-TSS (NM_019497)	promoter-TSS (NM_019497)	-63	NM_001080743	14772	Mm.117076	NM_019497	ENSMUSG00000052783	Grk4	A830025H08Rik|GRK|Gprk2l|Gprk4	G protein-coupled receptor kinase 4	protein-coding
mm_21800.1	chr2	164911219	164911239	-	1	NA	intron (NM_199027, intron 1 of 27)	CpG	521	NM_199027	329559	Mm.330776	NM_199027	ENSMUSG00000039834	Zfp335	1810045J01Rik|NIF-1|Nif1|Znf335	zinc finger protein 335	protein-coding
mm_165204.1	chr2	33353626	33353636	-	1	NA	intron (NM_001290572, intron 1 of 17)	intron (NM_001290572, intron 1 of 17)	17863	NM_001290570	241308	Mm.274249	NM_175211	ENSMUSG00000038831	Ralgps1	5830418G11Rik|AI853783|AI854138|RALGEF2|RALGPS1A|RalGEF 2|mKIAA0351	Ral GEF with PH domain and SH3 binding motif 1	protein-coding
mm_48336.1	chr5	139130003	139130011	-	1	NA	promoter-TSS (NM_008923)	promoter-TSS (NM_008923)	-255	NM_008923	19085	Mm.306163	NM_008923	ENSMUSG00000025855	Prkar1b	AI385716|RIbeta	protein kinase, cAMP dependent regulatory, type I beta	protein-coding
mm_157871.1	chrX	75416534	75416555	-	1	NA	promoter-TSS (NM_001166459)	promoter-TSS (NM_001166459)	40	NM_010839	105886298	Mm.16366	NM_010839	ENSMUSG00000090110	Cmc4	Mtcp1nb|p8MTCP1	C-x(9)-C motif containing 4	protein-coding
mm_18797.1	chr2	73892192	73892211	-	1	NA	intron (NM_001284374, intron 1 of 11)	CpG	438	NM_001284371	11909	Mm.209903	NM_009715	ENSMUSG00000027104	Atf2	Atf-2|CRE-BP|Creb2|D130078H02Rik|D18875|Tg(Gzma-Klra1)7Wum|mXBP	activating transcription factor 2	protein-coding
mm_135515.1	chr16	48772053	48772069	-	1	NA	promoter-TSS (NM_198297)	promoter-TSS (NM_198297)	-105	NM_198297	77647	Mm.167298	NM_198297	ENSMUSG00000030775	Trat1	C030046M14Rik|Tcrim|Trim	T cell receptor associated transmembrane adaptor 1	protein-coding
mm_123897.1	chr14	73117011	73117026	-	1	NA	Intergenic	Intergenic	-25492	NM_001170694	105670	Mm.280068	NM_134083	ENSMUSG00000022106	Rcbtb2	2610028E02Rik|2810420M18Rik|AI448345|AW240694|Chc1l|RC/BTB2	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 2	protein-coding
mm_129759.1	chr15	82380273	82380281	-	1	NA	promoter-TSS (NM_019823)	promoter-TSS (NM_019823)	-17	NM_001163472	56448	Mm.474216	NM_019823	ENSMUSG00000061740	Cyp2d22	2D22	cytochrome P450, family 2, subfamily d, polypeptide 22	protein-coding
mm_136972.1	chr17	15747799	15747813	+	1	NA	exon (NM_007690, exon 19 of 36)	exon (NM_007690, exon 19 of 36)	42839	NM_007690	12648	Mm.8137	NM_007690	ENSMUSG00000023852	Chd1	4930525N21Rik|AI851787|AW555109	chromodomain helicase DNA binding protein 1	protein-coding
mm_23010.1	chr3	34196923	34196933	+	1	NA	Intergenic	Intergenic	-115574	NM_026332	67713	Mm.274266	NM_026332	ENSMUSG00000027679	Dnajc19	1810055D05Rik|AA959924|Tim14	DnaJ heat shock protein family (Hsp40) member C19	protein-coding
mm_124672.1	chr15	6407961	6407968	+	1	NA	intron (NM_001310446, intron 1 of 13)	intron (NM_001310446, intron 1 of 13)	21216	NM_001310446	13132	Mm.240830	NM_023118	ENSMUSG00000022150	Dab2	5730435J12Rik|AA960054|AI957090|D15Wsu122e|D630005B22Rik|Doc-2|Doc2|p96	disabled 2, mitogen-responsive phosphoprotein	protein-coding
mm_153433.1	chr19	40955563	40955591	-	1	NA	intron (NM_008528, intron 6 of 16)	ID_B1|SINE|B4	38958	NM_008528	17060	Mm.9749	NM_008528	ENSMUSG00000061132	Blnk	BASH|Bca|Ly-57|Ly57|Lyw-57|SLP-65	B cell linker	protein-coding
mm_24773.1	chr3	95529429	95529536	+	1	NA	exon (NM_021281, exon 2 of 8)	exon (NM_021281, exon 2 of 8)	2696	NM_001267695	13040	Mm.3619	NM_021281	ENSMUSG00000038642	Ctss	Cats	cathepsin S	protein-coding
mm_33048.1	chr4	123016591	123016613	+	1	NA	promoter-TSS (NM_025873)	promoter-TSS (NM_025873)	5	NM_025873	66966	Mm.235030	NM_025873	ENSMUSG00000028653	Trit1	2310075G14Rik|AI314189|AI314635|AV099619|IPT|MOD5	tRNA isopentenyltransferase 1	protein-coding
mm_9853.1	chr1	184732633	184732694	-	1	NA	promoter-TSS (NM_008250)	promoter-TSS (NM_008250)	-170	NM_008250	15284	Mm.1347	NM_008250	ENSMUSG00000039377	Hlx	Hlx1	H2.0-like homeobox	protein-coding
mm_126456.1	chr15	80930532	80930554	+	1	NA	3' UTR (NM_177124, exon 22 of 22)	3' UTR (NM_177124, exon 22 of 22)	-9496	NR_039573	100628612		NR_039573	ENSMUSG00000092868	Mir5113	mir-5113|mmu-mir-5113|mu-mir-5113	microRNA 5113	ncRNA
mm_95553.1	chr11	52309508	52309533	+	1	NA	Intergenic	Intergenic	-26506	NM_001313981	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_52854.1	chr6	121870581	121870595	+	1	NA	exon (NM_008645, exon 16 of 36)	exon (NM_008645, exon 16 of 36)	32047	NM_008645	17836	Mm.1311	NM_008645	ENSMUSG00000059908	Mug1	-	murinoglobulin 1	protein-coding
mm_125291.1	chr15	36771081	36771154	+	1	NA	3' UTR (NM_001253807, exon 5 of 5)	3' UTR (NM_001253807, exon 5 of 5)	19815	NM_001253807	22631	Mm.3360	NM_011740	ENSMUSG00000022285	Ywhaz	1110013I11Rik|14-3-3zeta|AI596267|AL022924|AU020854	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide	protein-coding
mm_5931.1	chr1	55362693	55362749	-	1	NA	promoter-TSS (NM_001113367)	promoter-TSS (NM_001113367)	-14	NM_001113367	75388	Mm.483408	NM_029267	ENSMUSG00000025977	Boll	4930554P13Rik|4930597B14Rik	bol, boule-like (Drosophila)	protein-coding
mm_32371.1	chr4	105578296	105578302	+	1	NA	Intergenic	Intergenic	420952	NM_080555	67916	Mm.348326	NM_080555	ENSMUSG00000028517	Plpp3	1110003O22Rik|2610002D05Rik|AV025606|D4Bwg0538e|D4Bwg1535e|Lpp3|Ppab2b|Ppap2b	phospholipid phosphatase 3	protein-coding
mm_31492.1	chr4	53011917	53011978	+	1	NA	promoter-TSS (NM_001347099)	promoter-TSS (NM_001347099)	67	NM_025623	66536	Mm.38244	NM_025623	ENSMUSG00000015247	Nipsnap3b	2700063N13Rik|Nipsnap3a	nipsnap homolog 3B (C. elegans)	protein-coding
mm_68733.1	chr7	120754092	120754135	-	1	NA	intron (NM_177697, intron 3 of 33)	LSU-rRNA_Hsa|rRNA|rRNA	14556	NM_177697	233813	Mm.389939	NM_177697	ENSMUSG00000030889	Vwa3a	E030013G06Rik	von Willebrand factor A domain containing 3A	protein-coding
mm_21461.1	chr2	160872986	160873009	-	1	NA	promoter-TSS (NM_177263)	promoter-TSS (NM_177263)	-7	NM_177263	320799	Mm.436734	NM_177263	ENSMUSG00000035877	Zhx3	1810059C13Rik|4932418O04Rik|9530010N21Rik|Tix1|mKIAA0395	zinc fingers and homeoboxes 3	protein-coding
mm_91659.1	chr10	42768233	42768233	-	1	NA	intron (NM_153055, intron 1 of 20)	intron (NM_153055, intron 1 of 20)	6737	NM_153055	140740	Mm.214344	NM_153055	ENSMUSG00000019802	Sec63	5730478J10Rik|AI649014|AW319215	SEC63-like (S. cerevisiae)	protein-coding
mm_10330.1	chr2	11521701	11521714	+	1	NA	intron (NM_001177758, intron 1 of 14)	intron (NM_001177758, intron 1 of 14)	-19617	NM_001177757	170768	Mm.19669	NM_133232	ENSMUSG00000026773	Pfkfb3	E330010H22Rik|iPFK-2|uPFK-2	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	protein-coding
mm_143299.1	chr17	65961477	65961487	-	1	NA	Intergenic	RLTR30|LTR|ERV1	-10295	NM_023053	65960	Mm.10153	NM_023053	ENSMUSG00000024098	Twsg1	1810013J15Rik|9030422N06Rik|AW552143|D17Ertd403e|Tsg|Twg	twisted gastrulation BMP signaling modulator 1	protein-coding
mm_127616.1	chr15	102460441	102460471	+	1	NA	exon (NM_025385, exon 4 of 5)	exon (NM_025385, exon 4 of 5)	1286	NM_025385	66151	Mm.393955	NM_025385	ENSMUSG00000023048	Prr13	1110020C13Rik|2010324E22Rik	proline rich 13	protein-coding
mm_19456.1	chr2	92371000	92371036	-	1	NA	promoter-TSS (NM_001290775)	promoter-TSS (NM_001290775)	39	NM_001290774	228366	Mm.31158	NM_172670	ENSMUSG00000040434	Large2	5730485C17Rik|AI891893|Gyltl1b|Largel|mKIAA4105	LARGE xylosyl- and glucuronyltransferase 2	protein-coding
mm_13628.1	chr2	113640740	113640755	+	1	NA	intron (NM_001285458, intron 13 of 16)	intron (NM_001285458, intron 13 of 16)	-44343	NM_001287818	14260	Mm.4938	NM_010230	ENSMUSG00000044042	Fmn1	Fmn|formin-1|ld	formin 1	protein-coding
mm_8925.1	chr1	163994738	163994765	-	1	NA	promoter-TSS (NM_201364)	promoter-TSS (NM_201364)	30	NM_201364	381306	Mm.28152	NM_201364	ENSMUSG00000041406	BC055324	-	cDNA sequence BC055324	protein-coding
mm_23516.1	chr3	60575838	60575839	+	1	NA	intron (NM_001310514, intron 2 of 8)	intron (NM_001310514, intron 2 of 8)	74659	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_154958.1	chrX	36795643	36795653	+	1	NA	promoter-TSS (NM_007451)	promoter-TSS (NM_007451)	51	NM_007451	11740	Mm.371544	NM_007451	ENSMUSG00000016319	Slc25a5	Ant2	solute carrier family 25 (mitochondrial carrier, adenine nucleotide translocator), member 5	protein-coding
mm_4453.1	chr1	172698990	172699011	+	1	NA	exon (NM_007768, exon 2 of 2)	exon (NM_007768, exon 2 of 2)	944	NM_007768	12944	Mm.28767	NM_007768	ENSMUSG00000037942	Crp	AI255847	C-reactive protein, pentraxin-related	protein-coding
mm_16712.1	chr2	7099307	7099325	-	1	NA	intron (NM_001110231, intron 3 of 15)	intron (NM_001110231, intron 3 of 15)	-18014	NM_001160292	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_121352.1	chr14	116925517	116925543	+	1	NA	5' UTR (NM_011821, exon 1 of 9)	5' UTR (NM_011821, exon 1 of 9)	233	NM_011821	23888	Mm.440025	NM_011821	ENSMUSG00000058571	Gpc6	-	glypican 6	protein-coding
mm_18093.1	chr2	44986496	44986506	-	1	NA	3' UTR (NM_015753, exon 10 of 10)	3' UTR (NM_015753, exon 10 of 10)	36676	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_76542.1	chr8	87960809	87960822	-	1	NA	Intergenic	CpG-14330	-1220	NM_033327	94187	Mm.23452	NM_033327	ENSMUSG00000045333	Zfp423	Ebfaz|Roaz|Zfp104|Znf423|ataxia1|mKIAA0760|nur12	zinc finger protein 423	protein-coding
mm_33575.1	chr4	132310693	132310697	+	1	NA	promoter-TSS (NR_028537)	promoter-TSS (NR_028537)	-8	NR_028537	100217437		NR_028537		Snord99	MBII-420	small nucleolar RNA, C/D box 99	snoRNA
mm_50590.1	chr6	49061042	49061054	+	1	NA	Intergenic	B3|SINE|B2	-12747	NM_029353	75593	Mm.439947	NM_029353	ENSMUSG00000029815	Malsu1	2410003K15Rik|Matsu1	mitochondrial assembly of ribosomal large subunit 1	protein-coding
mm_32787.1	chr4	116720921	116721004	+	1	NA	promoter-TSS (NM_146151)	promoter-TSS (NM_146151)	7	NM_146151	230661	Mm.482431	NM_146151	ENSMUSG00000033985	Tesk2	-	testis-specific kinase 2	protein-coding
mm_109321.1	chr12	109561911	109561923	+	1	NA	non-coding (NR_003633, exon 5 of 5)	non-coding (NR_003633, exon 5 of 5)	-1775	NR_030427	791079		NR_030427	ENSMUSG00000076451	Mir770	Mirn770|mir-770|mmu-mir-770	microRNA 770	ncRNA
mm_69313.1	chr7	128418674	128418714	-	1	NA	promoter-TSS (NM_026418)	promoter-TSS (NM_026418)	-522	NM_026418	67865	Mm.18635	NM_026418	ENSMUSG00000030844	Rgs10	2310010N19Rik	regulator of G-protein signalling 10	protein-coding
mm_21235.1	chr2	156111914	156111940	-	1	NA	promoter-TSS (NM_029397)	promoter-TSS (NM_029397)	38	NM_170598	75710	Mm.27660	NM_029397	ENSMUSG00000089824	Rbm12	5730420G12Rik|9430070C08Rik|AI852903|SWAN|mKIAA0765	RNA binding motif protein 12	protein-coding
mm_22511.1	chr3	7615994	7616003	+	1	NA	Intergenic	(GGA)n|Simple_repeat|Simple_repeat	-2238	NM_001313888	16196	Mm.3825	NM_008371	ENSMUSG00000040329	Il7	A630026I06Rik|Il-7|hlb368	interleukin 7	protein-coding
mm_2175.1	chr1	88406972	88406974	+	1	NA	promoter-TSS (NM_029269)	promoter-TSS (NM_029269)	-37	NM_029269	75396	Mm.173058	NM_029269	ENSMUSG00000026295	Spp2	0610038O04Rik|pp-24|spp24	secreted phosphoprotein 2	protein-coding
mm_18725.1	chr2	72953032	72953053	-	1	NA	intron (NM_001018042, intron 4 of 6)	PB1D10|SINE|Alu	26239	NM_001098425	20687	Mm.124328	NM_011450	ENSMUSG00000027109	Sp3	D130027J01Rik	trans-acting transcription factor 3	protein-coding
mm_24312.1	chr3	89418657	89418675	+	1	NA	promoter-TSS (NM_016904)	promoter-TSS (NM_016904)	115	NM_011368	20416	Mm.86595	NM_011368	ENSMUSG00000042626	Shc1	Shc|ShcA|p66|p66shc	src homology 2 domain-containing transforming protein C1	protein-coding
mm_7081.1	chr1	88277511	88277636	-	1	NA	promoter-TSS (NM_172505)	promoter-TSS (NM_172505)	6	NM_198652	381280	Mm.384762	NM_198652	ENSMUSG00000044783	Hjurp	6430706D22Rik|A730008H23Rik|C330011F01Rik|Gm975|Mfleg1	Holliday junction recognition protein	protein-coding
mm_28150.1	chr3	87684634	87684644	-	1	NA	intron (NM_001003912, intron 3 of 39)	intron (NM_001003912, intron 3 of 39)	63984	NM_028971	74485	Mm.474494	NM_028971	ENSMUSG00000023084	Lrrc71	4933430H15Rik	leucine rich repeat containing 71	protein-coding
mm_170771.1	chr2	162999206	162999215	+	1	NA	exon (NM_001291152, exon 9 of 13)	exon (NM_001291152, exon 9 of 13)	7795	NM_001291152	27219	Mm.26462	NM_013731	ENSMUSG00000017868	Sgk2	AI098171|AW146006|Sgkl	serum/glucocorticoid regulated kinase 2	protein-coding
mm_150194.1	chr19	32666030	32666040	+	1	NA	3' UTR (NM_011864, exon 13 of 13)	3' UTR (NM_011864, exon 13 of 13)	46030	NM_011864	23972	Mm.203916	NM_011864	ENSMUSG00000024899	Papss2	1810018P12Rik|AI159688|AtpsU2|Atpsk2|Sk2|bm	3'-phosphoadenosine 5'-phosphosulfate synthase 2	protein-coding
mm_167145.1	chr7	128266352	128266356	+	1	NA	exon (NM_133254, exon 2 of 14)	exon (NM_133254, exon 2 of 14)	657	NM_133254	246787	Mm.38870	NM_133254	ENSMUSG00000030781	Slc5a2	Sglt2	solute carrier family 5 (sodium/glucose cotransporter), member 2	protein-coding
mm_140414.1	chr17	87650453	87650466	+	1	NA	exon (NM_008532, exon 10 of 10)	exon (NM_008532, exon 10 of 10)	14480	NM_008532	17075	Mm.4259	NM_008532	ENSMUSG00000045394	Epcam	CD326|EGP|EGP-2|Egp314|Ep-CAM|EpCAM1|GA733-2|Ly74|TROP1|Tacsd1|Tacstd1|gp40	epithelial cell adhesion molecule	protein-coding
mm_70074.1	chr7	142653194	142653200	-	1	NA	3' UTR (NM_010514, exon 4 of 4)	3' UTR (NM_010514, exon 4 of 4)	1799	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_8376.1	chr1	151250225	151250227	-	1	NA	Intergenic	Intergenic	-94272	NM_001039512	117198	Mm.33764	NM_028582	ENSMUSG00000023150	Ivns1abp	1190004M08Rik|1700126I16Rik|AA960440|HSPC068|ND1|NS-1|NS1-BP|Nd1-L|Nd1-S|mKIAA0850	influenza virus NS1A binding protein	protein-coding
mm_90213.1	chr10	120787286	120787297	+	1	NA	intron (NM_177092, intron 6 of 6)	intron (NM_177092, intron 6 of 6)	21559	NR_038003	70874	Mm.427286	NR_038000	ENSMUSG00000044544	4921513I03Rik	-	RIKEN cDNA 4921513I03 gene	ncRNA
mm_87010.1	chr10	26880705	26880734	+	1	NA	exon (NM_176837, exon 10 of 15)	exon (NM_176837, exon 10 of 15)	108207	NM_176837	73910	Mm.356496	NM_176837	ENSMUSG00000039031	Arhgap18	4833419J07Rik|AI314906|AI843501	Rho GTPase activating protein 18	protein-coding
mm_80225.1	chr9	72662402	72662412	+	1	NA	promoter-TSS (NM_010890)	promoter-TSS (NM_010890)	60	NM_010890	17999	Mm.279923	NM_010890	ENSMUSG00000032216	Nedd4	AA959633|AL023035|AU019897|E430025J12Rik|Nedd4-1|Nedd4a|mKIAA0093	neural precursor cell expressed, developmentally down-regulated 4	protein-coding
mm_27103.1	chr3	30509753	30509794	-	1	NA	promoter-TSS (NM_021442)	promoter-TSS (NM_021442)	-286	NM_021442	14013	Mm.56965	NM_007963	ENSMUSG00000027684	Mecom	D630039M04Rik|Evi-1|Evi1|Jbo|Mds|Mds1|Mds1-Evi1|Prdm3|Znfpr1b1	MDS1 and EVI1 complex locus	protein-coding
mm_25454.1	chr3	108383984	108384001	+	1	NA	promoter-TSS (NR_040560)	promoter-TSS (NR_040560)	154	NM_019976	56742	Mm.389499	NM_019976	ENSMUSG00000068744	Psrc1	5430413I02Rik|AL033312|Dda3	proline/serine-rich coiled-coil 1	protein-coding
mm_135873.1	chr16	62846845	62846873	-	1	NA	5' UTR (NM_026577, exon 1 of 10)	5' UTR (NM_026577, exon 1 of 10)	181	NM_026577	68146	Mm.96833	NM_026577	ENSMUSG00000022911	Arl13b	A530097K21Rik|A930014M17Rik|Arl2l1|C530009C10Rik|hnn	ADP-ribosylation factor-like 13B	protein-coding
mm_120341.1	chr14	63606388	63606408	+	1	NA	promoter-TSS (NM_173393)	promoter-TSS (NM_173393)	-132	NM_173393	219149	Mm.32071	NM_173393	ENSMUSG00000035067	Xkr6	2700008G24Rik|BC024502|Xrg6	X-linked Kx blood group related 6	protein-coding
mm_142849.1	chr17	51798301	51798306	-	1	NA	intron (NM_009122, intron 5 of 10)	intron (NM_009122, intron 5 of 10)	13751	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_5940.1	chr1	56637426	56637429	-	1	NA	promoter-TSS (NM_027661)	promoter-TSS (NM_027661)	24	NM_027661	71066	Mm.152656	NM_027661	ENSMUSG00000045336	Hsfy2	4933413G11Rik|Hspy2l	heat shock transcription factor, Y-linked 2	protein-coding
mm_104486.1	chr11	95799815	95799816	-	1	NA	Intergenic	B1_Mur3|SINE|Alu	-24685	NM_153104	237928	Mm.133075	NM_153104	ENSMUSG00000050860	Phospho1	D11Moh36|Phospo1	phosphatase, orphan 1	protein-coding
mm_15405.1	chr2	156743769	156743773	+	1	NA	intron (NM_001042487, intron 1 of 6)	intron (NM_001042487, intron 1 of 6)	22492	NM_001042487	228836	Mm.22094	NM_146128	ENSMUSG00000061689	Dlgap4	AI225853|BC024558|DAP-4|DAP4|SAPAP-4|Sapap4|WBP16	discs, large homolog-associated protein 4 (Drosophila)	protein-coding
mm_26088.1	chr3	136702764	136702767	+	1	NA	intron (NM_008913, intron 1 of 13)	intron (NM_008913, intron 1 of 13)	32699	NM_001293622	19055	Mm.331389	NM_008913	ENSMUSG00000028161	Ppp3ca	2900074D19Rik|CN|Caln|Calna|CnA	protein phosphatase 3, catalytic subunit, alpha isoform	protein-coding
mm_75777.1	chr8	69996241	69996258	-	1	NA	5' UTR (NM_001286450, exon 1 of 13)	5' UTR (NM_001286450, exon 1 of 13)	135	NM_001286450	234366	Mm.270044	NM_145596	ENSMUSG00000036180	Gatad2a	1110066C11Rik|BC031407|C80248	GATA zinc finger domain containing 2A	protein-coding
mm_46599.1	chr5	107856936	107856938	-	1	NA	intron (NM_007964, intron 1 of 17)	B1_Mus1|SINE|Alu	18170	NM_007964	14020	Mm.35796	NM_007964	ENSMUSG00000011831	Evi5	NB4S	ecotropic viral integration site 5	protein-coding
mm_50569.1	chr6	49050398	49050469	+	1	NA	exon (NM_053110, exon 7 of 11)	exon (NM_053110, exon 7 of 11)	13915	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_129285.1	chr15	77162975	77162985	-	1	NA	intron (NM_053104, intron 2 of 13)	intron (NM_053104, intron 2 of 13)	-9168	NM_001286418	93686	Mm.202774	NM_053104	ENSMUSG00000033565	Rbfox2	Fbm2|Fxh|Hrnbp2|Rbm9	RNA binding protein, fox-1 homolog (C. elegans) 2	protein-coding
mm_99504.1	chr11	103028543	103028573	+	1	NA	promoter-TSS (NM_008707)	promoter-TSS (NM_008707)	-4	NM_008707	18107	Mm.10265	NM_008707	ENSMUSG00000020936	Nmt1	AW536594	N-myristoyltransferase 1	protein-coding
mm_42159.1	chr5	112206787	112206793	+	1	NA	promoter-TSS (NR_045378)	promoter-TSS (NR_045378)	27	NR_045378	75569	Mm.243721	NR_045377	ENSMUSG00000101683	1700028D13Rik	-	RIKEN cDNA 1700028D13 gene	ncRNA
mm_172710.1	chr8	69563459	69563464	-	1	NA	Intergenic	B3A|SINE|B2	61714	NM_001045553	234362	Mm.458487	NM_172754	ENSMUSG00000060427	Zfp868	AI449175|AW108241|C530032E20|mszf62	zinc finger protein 868	protein-coding
mm_99588.1	chr11	104306688	104306698	+	1	NA	exon (NM_010838, exon 5 of 10)	exon (NM_010838, exon 5 of 10)	75257	NM_001285454	17762	Mm.1287	NM_010838	ENSMUSG00000018411	Mapt	AI413597|AW045860|Mtapt|Tau	microtubule-associated protein tau	protein-coding
mm_45327.1	chr5	65492875	65492889	-	1	NA	promoter-TSS (NM_133697)	promoter-TSS (NM_133697)	-47	NM_133697	68552	Mm.10709	NM_133697	ENSMUSG00000037822	Smim14	1110003E01Rik|1700127H04Rik|5430439C17Rik|MAd4	small integral membrane protein 14	protein-coding
mm_100641.1	chr11	121830216	121830224	+	1	NA	promoter-TSS (NM_029049)	promoter-TSS (NM_029049)	2	NM_029049	74675	Mm.61213	NM_029049	ENSMUSG00000039198	Ptchd3	4930451E13Rik|4933440L20Rik|RNDEu-3	patched domain containing 3	protein-coding
mm_29325.1	chr3	108044686	108044738	-	1	NA	5' UTR (NM_026764, exon 1 of 8)	5' UTR (NM_026764, exon 1 of 8)	144	NM_026764	14865	Mm.31203	NM_026764	ENSMUSG00000027890	Gstm4	1110004G14Rik|GSTM7-7|Gstb-4|Gstb4	glutathione S-transferase, mu 4	protein-coding
mm_30665.1	chr4	10877337	10877339	+	1	NA	intron (NM_026005, intron 1 of 5)	intron (NM_026005, intron 1 of 5)	2840	NM_026005	67157	Mm.440552	NM_026005	ENSMUSG00000059482	2610301B20Rik	AI428449	RIKEN cDNA 2610301B20 gene	protein-coding
mm_49795.1	chr6	35261276	35261291	+	1	NA	non-coding (NR_015608, exon 3 of 3)	non-coding (NR_015608, exon 3 of 3)	8551	NR_027875	67705	Mm.228046	NR_015608	ENSMUSG00000073155	1810058I24Rik	AI414869|AI848234	RIKEN cDNA 1810058I24 gene	ncRNA
mm_117836.1	chr13	98637355	98637373	-	1	NA	promoter-TSS (NM_026685)	promoter-TSS (NM_026685)	46	NM_026685	68344	Mm.28766	NM_026685	ENSMUSG00000046082	Tmem174	0610009B10Rik|AA986094	transmembrane protein 174	protein-coding
mm_113771.1	chr13	44840738	44840752	+	1	NA	intron (NM_001205044, intron 3 of 18)	intron (NM_001205044, intron 3 of 18)	109474	NM_001205043	16468	Mm.25059	NM_021878	ENSMUSG00000038518	Jarid2	Jmj|jumonji	jumonji, AT rich interactive domain 2	protein-coding
mm_13808.1	chr2	119047377	119047388	+	1	NA	intron (NM_029617, intron 1 of 23)	CpG	263	NM_029617	76464	Mm.202518	NM_029617	ENSMUSG00000027326	Knl1	2310043D08Rik|5730505K17Rik|Casc5	kinetochore scaffold 1	protein-coding
mm_50593.1	chr6	49069532	49069558	+	1	NA	Intergenic	RMER4A|LTR|ERVK	-4250	NM_029353	75593	Mm.439947	NM_029353	ENSMUSG00000029815	Malsu1	2410003K15Rik|Matsu1	mitochondrial assembly of ribosomal large subunit 1	protein-coding
mm_71766.1	chr8	66425843	66425871	+	1	NA	intron (NM_175188, intron 6 of 7)	intron (NM_175188, intron 6 of 7)	39556	NM_001166375	72925	Mm.380457	NM_175188	ENSMUSG00000036469	March1	2900024D24Rik|BB085186	membrane-associated ring finger (C3HC4) 1	protein-coding
mm_149872.1	chr19	25155828	25155836	+	1	NA	intron (NM_028785, intron 27 of 47)	intron (NM_028785, intron 27 of 47)	-81370	NM_181404	107351	Mm.260722	NM_181404	ENSMUSG00000032702	Kank1	A930031B09Rik|AU015049|AW121052|Ankrd15|D330024H06Rik|mKIAA0172	KN motif and ankyrin repeat domains 1	protein-coding
mm_158650.1	chrX	155606299	155606300	-	1	NA	intron (NM_001093750, intron 1 of 2)	intron (NM_001093750, intron 1 of 2)	17028	NM_001093750	211612	Mm.218811	NM_001093750	ENSMUSG00000041552	Ptchd1	9630036J22Rik|AI848149|Gm387	patched domain containing 1	protein-coding
mm_74302.1	chr8	126422479	126422514	+	1	NA	promoter-TSS (NM_174987)	promoter-TSS (NM_174987)	-5	NM_174987	67892	Mm.31946	NM_174987	ENSMUSG00000051671	Coa6	1810063B05Rik|AI447995	cytochrome c oxidase assembly factor 6	protein-coding
mm_138916.1	chr17	43607126	43607138	+	1	NA	intron (NM_013737, intron 9 of 11)	intron (NM_013737, intron 9 of 11)	-15623	NR_045444	73504	Mm.9277	NR_045444	ENSMUSG00000090307	1700071M16Rik	-	RIKEN cDNA 1700071M16 gene	ncRNA
mm_80729.1	chr9	92691916	92691919	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-26799	NR_040770	331003	Mm.50805	NR_040770	ENSMUSG00000101734	4933400C23Rik	4933400C23	RIKEN cDNA 4933400C23 gene	ncRNA
mm_168989.1	chr12	99645131	99645132	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-17157	NR_045288	73457	Mm.383439	NR_045288	ENSMUSG00000100211	1700064M15Rik	-	RIKEN cDNA 1700064M15 gene	ncRNA
mm_130458.1	chr15	98567763	98567776	-	1	NA	promoter-TSS (NM_009833)	promoter-TSS (NM_009833)	-133	NM_009833	12455	Mm.29941	NM_009833	ENSMUSG00000011960	Ccnt1	2810478G24Rik|AI115585|CycT1	cyclin T1	protein-coding
mm_126092.1	chr15	77911331	77911341	+	1	NA	Intergenic	Intergenic	17658	NM_019913	56551	Mm.291917	NM_019913	ENSMUSG00000005354	Txn2	2510006J11Rik|AI788873|Trx2	thioredoxin 2	protein-coding
mm_27742.1	chr3	69125357	69125370	-	1	NA	intron (NM_008467, intron 1 of 16)	B3|SINE|B2	1729	NM_008467	16649	Mm.30601	NM_008467	ENSMUSG00000027782	Kpna4	1110058D08Rik|IPOA3	karyopherin (importin) alpha 4	protein-coding
mm_42985.1	chr5	123273749	123273751	+	1	NA	Intergenic	Intergenic	45560	NM_026000	67151	Mm.278997	NM_026000	ENSMUSG00000029440	Psmd9	1500011J20Rik|2610202L11Rik|Bridge-1|P27	proteasome (prosome, macropain) 26S subunit, non-ATPase, 9	protein-coding
mm_13973.1	chr2	121435912	121435922	+	1	NA	intron (NM_007952, intron 10 of 12)	intron (NM_007952, intron 10 of 12)	6684	NM_145973	269344	Mm.330522	NM_145973	ENSMUSG00000027246	Ell3	A930015D22Rik	elongation factor RNA polymerase II-like 3	protein-coding
mm_104110.1	chr11	86718019	86718050	-	1	NA	exon (NM_001003908, exon 14 of 32)	exon (NM_001003908, exon 14 of 32)	33953	NM_001098810	217057	Mm.24868	NM_175004	ENSMUSG00000072582	Ptrh2	A230072I16Rik|Bit1|CGI-147	peptidyl-tRNA hydrolase 2	protein-coding
mm_115208.1	chr13	109260350	109260362	+	1	NA	intron (NM_011056, intron 3 of 16)	intron (NM_011056, intron 3 of 16)	-64388	NR_030644	100124489		NR_030644	ENSMUSG00000076946	Mir582	Mirn582|mir-582|mmu-mir-582	microRNA 582	ncRNA
mm_129630.1	chr15	80228409	80228419	-	1	NA	Intergenic	Intergenic	-5666	NM_178719	239555	Mm.307163	NM_178719	ENSMUSG00000022412	Mief1	A230016E22|AI452372|Smcr7l	mitochondrial elongation factor 1	protein-coding
mm_83397.1	chr9	44721384	44721484	-	1	NA	intron (NM_153537, intron 4 of 21)	CpG	13764	NM_153537	102693	Mm.28639	NM_153537	ENSMUSG00000048537	Phldb1	AU041016|D330037A14Rik|Ll5a	pleckstrin homology like domain, family B, member 1	protein-coding
mm_60421.1	chr7	44476399	44476402	+	1	NA	Intergenic	L1MEd|LINE|L1	6053	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_33495.1	chr4	130823641	130823645	+	1	NA	3' UTR (NM_011520, exon 5 of 5)	3' UTR (NM_011520, exon 5 of 5)	31106	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_168722.1	chr12	110485780	110485783	+	1	NA	promoter-TSS (NM_001081458)	promoter-TSS (NM_001081458)	42	NM_012023	26931	Mm.240396	NM_012023	ENSMUSG00000017843	Ppp2r5c	2610043M05Rik|2700063L20Rik|AI060890|AW545884|C85228|D12Bwg0916e|mKIAA0044	protein phosphatase 2, regulatory subunit B', gamma	protein-coding
mm_24497.1	chr3	92373909	92373921	+	1	NA	promoter-TSS (NR_003548)	promoter-TSS (NR_003548)	0	NR_003548	20761	Mm.57083	NR_003548	ENSMUSG00000046203	Sprr2g	-	small proline-rich protein 2G	pseudo
mm_39438.1	chr5	16870168	16870178	+	1	NA	Intergenic	Intergenic	316272	NM_001289461	15234	Mm.267078	NM_010427	ENSMUSG00000028864	Hgf	C230052L06Rik|HGF/SF|NK1|NK2|SF|SF/HGF	hepatocyte growth factor	protein-coding
mm_51227.1	chr6	71373481	71373490	+	1	NA	promoter-TSS (NM_009857)	promoter-TSS (NM_009857)	58	NM_001081110	12525	Mm.1858	NM_009857	ENSMUSG00000053977	Cd8a	BB154331|Ly-2|Ly-35|Ly-B|Lyt-2	CD8 antigen, alpha chain	protein-coding
mm_120591.1	chr14	70075155	70075167	+	1	NA	Intergenic	CpG	-2284	NM_018781	13655	Mm.103737	NM_018781	ENSMUSG00000033730	Egr3	Pilot	early growth response 3	protein-coding
mm_163066.1	chr11	67171012	67171040	+	1	NA	promoter-TSS (NM_001039545)	promoter-TSS (NM_001039545)	-1	NM_001039545	17882	Mm.422801	NM_144961	ENSMUSG00000033196	Myh2	MHC2A|MyHC-IIa|Myh2a|Myhs-f|Myhs-f1|Myhsf1	myosin, heavy polypeptide 2, skeletal muscle, adult	protein-coding
mm_140968.1	chr17	24689881	24689887	-	1	NA	promoter-TSS (NM_011522)	promoter-TSS (NM_011522)	65	NM_011522	20974	Mm.26032	NM_011522	ENSMUSG00000007021	Syngr3	-	synaptogyrin 3	protein-coding
mm_33898.1	chr4	136248018	136248028	+	1	NA	promoter-TSS (NM_011542)	promoter-TSS (NM_011542)	66	NM_011542	21401	Mm.112	NM_011542	ENSMUSG00000001604	Tcea3	S-II|SII-K1	transcription elongation factor A (SII), 3	protein-coding
mm_134954.1	chr16	31311053	31311064	-	1	NA	exon (NM_007470, exon 3 of 6)	exon (NM_007470, exon 3 of 6)	3750	NM_001301353	11815	Mm.2082	NM_007470	ENSMUSG00000022548	Apod	-	apolipoprotein D	protein-coding
mm_68405.1	chr7	109616405	109616487	-	1	NA	non-coding (NR_037617, exon 1 of 20)	non-coding (NR_037617, exon 1 of 20)	122	NR_037617	76954	Mm.252009	NM_029811	ENSMUSG00000031024	St5	2010004M01Rik|2610305K15Rik	suppression of tumorigenicity 5	protein-coding
mm_1326.1	chr1	65110298	65110304	+	1	NA	intron (NM_175293, intron 5 of 7)	intron (NM_175293, intron 5 of 7)	-6938	NM_007774	12964	Mm.26904	NM_007774	ENSMUSG00000044429	Cryga	Cryg-4|DGcry-4	crystallin, gamma A	protein-coding
mm_143621.1	chr17	78855071	78855081	-	1	NA	3' UTR (NM_011163, exon 16 of 16)	3' UTR (NM_011163, exon 16 of 16)	-2532	NR_003363	625054	Mm.311918	NR_003363		Gm6548	EG625054	eukaryotic translation elongation factor 1 alpha 1 pseudogene	pseudo
mm_161922.1	chr18	74273543	74273543	+	1	NA	exon (NM_013594, exon 4 of 15)	exon (NM_013594, exon 4 of 15)	5255	NM_013594	17190	Mm.22522	NM_013594	ENSMUSG00000024561	Mbd1	Cxxc3|PCM1	methyl-CpG binding domain protein 1	protein-coding
mm_25999.1	chr3	134828994	134829015	+	1	NA	promoter-TSS (NM_021382)	promoter-TSS (NM_021382)	-3	NM_021382	21338	Mm.103810	NM_021382	ENSMUSG00000028172	Tacr3	Nk3r|Nkr|Tac3r	tachykinin receptor 3	protein-coding
mm_73480.1	chr8	107019392	107019398	+	1	NA	Intergenic	Intergenic	-11931	NM_126165	116733	Mm.236004	NM_126165	ENSMUSG00000031913	Vps4a	4930589C15Rik|AI325971|AW553189	vacuolar protein sorting 4A	protein-coding
mm_64453.1	chr7	142659150	142659178	+	1	NA	promoter-TSS (NM_010514)	promoter-TSS (NM_010514)	-360	NM_010514	16002	Mm.3862	NM_010514	ENSMUSG00000048583	Igf2	AL033362|Igf-2|Igf-II|M6pr|Mpr|Peg2	insulin-like growth factor 2	protein-coding
mm_74236.1	chr8	124520777	124520865	+	1	NA	promoter-TSS (NM_029746)	promoter-TSS (NM_029746)	54	NM_029746	76332	Mm.240108	NM_029746	ENSMUSG00000031979	Cog2	1190002B08Rik|2700012E02Rik|C86089|Ldlc	component of oligomeric golgi complex 2	protein-coding
mm_74436.1	chr8	3754547	3754555	-	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	-5567	NM_133238	170786	Mm.32510	NM_133238	ENSMUSG00000031494	Cd209a	CD209|CDSIGN|CIRE|DC-SIGN|DC-SIGN1|Dcsign|SIGN-R1|SIGNR5	CD209a antigen	protein-coding
mm_88983.1	chr10	81563827	81563845	+	1	NA	intron (NR_074087, intron 2 of 6)	intron (NR_074087, intron 2 of 6)	4392	NM_001276288	14797	Mm.180013	NM_010347	ENSMUSG00000054452	Aes	AL024115|Esp1|Grg|Grg-5|Grg5|Tle5	amino-terminal enhancer of split	protein-coding
mm_65850.1	chr7	29258541	29258575	-	1	NA	exon (NM_001082548, exon 4 of 6)	exon (NM_001082548, exon 4 of 6)	-10091	NM_028179	72275	Mm.441142	NM_028179	ENSMUSG00000030587	2200002D01Rik	2010005J02Rik|H2RSP|IMUP|IMUP-1|IMUP-2	RIKEN cDNA 2200002D01 gene	protein-coding
mm_9802.1	chr1	181865655	181865670	-	1	NA	Intergenic	Intergenic	-23261	NM_133815	98386	Mm.4538	NM_133815	ENSMUSG00000004880	Lbr	AI505894|ic	lamin B receptor	protein-coding
mm_104477.1	chr11	95569036	95569044	-	1	NA	3' UTR (NM_033217, exon 6 of 6)	3' UTR (NM_033217, exon 6 of 6)	18658	NM_033217	18053	Mm.283893	NM_033217	ENSMUSG00000000120	Ngfr	LNGFR|Tnfrsf16|p75|p75NGFR|p75NTR	nerve growth factor receptor (TNFR superfamily, member 16)	protein-coding
mm_96468.1	chr11	67643298	67643317	+	1	NA	exon (NM_001277079, exon 4 of 14)	exon (NM_001277079, exon 4 of 14)	46752	NM_001277079	14457	Mm.40338	NM_008088	ENSMUSG00000033066	Gas7	AW124766|B230343A10Rik|Gas7-cb	growth arrest specific 7	protein-coding
mm_87141.1	chr10	34483416	34483445	+	1	NA	promoter-TSS (NM_001159544)	promoter-TSS (NM_001159544)	30	NM_010237	14302	Mm.332432	NM_010237	ENSMUSG00000019779	Frk	BSK|BSK/IYK|C85044|GTK|RAK	fyn-related kinase	protein-coding
mm_66149.1	chr7	31137323	31137348	-	1	NA	intron (NM_027898, intron 11 of 18)	B3A|SINE|B2	-10312	NM_011322	20266	Mm.1418	NM_011322	ENSMUSG00000019194	Scn1b	-	sodium channel, voltage-gated, type I, beta	protein-coding
mm_137763.1	chr17	29490469	29490475	+	1	NA	promoter-TSS (NM_008842)	promoter-TSS (NM_008842)	-573	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_81603.1	chr9	110624515	110624533	+	1	NA	promoter-TSS (NM_026012)	promoter-TSS (NM_026012)	-131	NM_026012	67169	Mm.46680	NM_026012	ENSMUSG00000032491	Nradd	2610311B09Rik|BB104149|NRDD|NRH2|PLAIDD	neurotrophin receptor associated death domain	protein-coding
mm_159093.1	chr2	32587633	32587633	+	1	NA	5' UTR (NM_011373, exon 1 of 5)	5' UTR (NM_011373, exon 1 of 5)	555	NM_011373	20448	Mm.27446	NM_011373	ENSMUSG00000079442	St6galnac4	SIAT7-D|ST6GalNAcIV|Siat7d	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 4	protein-coding
mm_101388.1	chr11	24172767	24172773	-	1	NA	exon (NM_001159290, exon 5 of 5)	exon (NM_001159290, exon 5 of 5)	92075	NM_001159290	14025	Mm.53687	NM_016707	ENSMUSG00000000861	Bcl11a	2810047E18Rik|BCL-11A|Ctip1|D930021L15Rik|Evi9|Evi9a|Evi9b|Evi9c|mKIAA1809	B cell CLL/lymphoma 11A (zinc finger protein)	protein-coding
mm_95165.1	chr11	40429843	40429844	+	1	NA	Intergenic	Intergenic	262839	NM_134017	108645	Mm.293771	NM_134017	ENSMUSG00000042032	Mat2b	1110064C04Rik|2410018D16Rik|AI182287|AU022853|MAT-II|MATIIbeta|TGR	methionine adenosyltransferase II, beta	protein-coding
mm_1930.1	chr1	86110951	86110973	+	1	NA	5' UTR (NM_008311, exon 2 of 4)	5' UTR (NM_008311, exon 2 of 4)	1008	NM_008311	15559	Mm.439747	NM_008311	ENSMUSG00000026228	Htr2b	5-HT2B|AJ012488|AV377389	5-hydroxytryptamine (serotonin) receptor 2B	protein-coding
mm_74598.1	chr8	11635694	11635723	-	1	NA	promoter-TSS (NM_001167967)	promoter-TSS (NM_001167967)	28	NR_106097	102465714		NR_106097	ENSMUSG00000104958	Mir7238	mmu-mir-7238	microRNA 7238	ncRNA
mm_124812.1	chr15	8967997	8968011	+	1	NA	promoter-TSS (NM_198024)	promoter-TSS (NM_198024)	55	NM_198024	223332	Mm.321371	NM_198024	ENSMUSG00000048424	Ranbp3l	C130037N17Rik	RAN binding protein 3-like	protein-coding
mm_153149.1	chr19	34251834	34251840	-	1	NA	exon (NM_007392, exon 3 of 9)	exon (NM_007392, exon 3 of 9)	3536	NM_007392	11475	Mm.213025	NM_007392	ENSMUSG00000035783	Acta2	0610041G09Rik|Actvs|SMalphaA|a-SMA|alphaSMA	actin, alpha 2, smooth muscle, aorta	protein-coding
mm_61758.1	chr7	82771563	82771563	+	1	NA	intron (NM_175317, intron 18 of 19)	intron (NM_175317, intron 18 of 19)	-15919	NR_046004	77800	Mm.444811	NR_046004	ENSMUSG00000086690	4933406J10Rik	A930009F24Rik	RIKEN cDNA 4933406J10 gene	ncRNA
mm_119645.1	chr14	51984697	51984721	+	1	NA	promoter-TSS (NM_001145922)	promoter-TSS (NM_001145922)	-124	NM_001145921	268739	Mm.9239	NM_198249	ENSMUSG00000004562	Arhgef40	E130112L23Rik|Gm669|Solo	Rho guanine nucleotide exchange factor (GEF) 40	protein-coding
mm_167471.1	chr8	126807465	126807470	-	1	NA	Intergenic	Intergenic	138454	NM_024214	67952	Mm.6932	NM_024214	ENSMUSG00000093904	Tomm20	1810060K07Rik|BB284719|Gm19268|MAS20|MOM19|TOM20|mKIAA0016	translocase of outer mitochondrial membrane 20 homolog (yeast)	protein-coding
mm_118994.1	chr14	28505782	28505797	+	1	NA	5' UTR (NM_009524, exon 1 of 5)	5' UTR (NM_009524, exon 1 of 5)	316	NM_009524	22418	Mm.287544	NM_009524	ENSMUSG00000021994	Wnt5a	8030457G12Rik|Wnt-5a	wingless-type MMTV integration site family, member 5A	protein-coding
mm_3940.1	chr1	163779636	163779705	+	1	NA	promoter-TSS (NM_010629)	promoter-TSS (NM_010629)	87	NM_010629	16579	Mm.4651	NM_010629	ENSMUSG00000026585	Kifap3	KAP-3|KAP3|SMAP	kinesin-associated protein 3	protein-coding
mm_450.1	chr1	36068372	36068391	+	1	NA	promoter-TSS (NM_015818)	promoter-TSS (NM_015818)	-19	NM_015818	50785	Mm.213566	NM_015818	ENSMUSG00000045216	Hs6st1	6Ost1	heparan sulfate 6-O-sulfotransferase 1	protein-coding
mm_108765.1	chr12	89559785	89559788	+	1	NA	intron (NM_172544, intron 14 of 19)	(T)n|Simple_repeat|Simple_repeat	-252697	NM_001252074	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding
mm_122361.1	chr14	39240245	39240255	-	1	NA	intron (NM_001190187, intron 1 of 9)	intron (NM_001190187, intron 1 of 9)	-232179	NR_131973	432842	Mm.352566	NR_131973		LOC432842	-	uncharacterized LOC432842	ncRNA
mm_47727.1	chr5	130144471	130144491	-	1	NA	promoter-TSS (NM_172509)	promoter-TSS (NM_172509)	-407	NM_172509	212919	Mm.55812	NM_172509	ENSMUSG00000034110	Kctd7	4932409E18|9430010P06Rik	potassium channel tetramerisation domain containing 7	protein-coding
mm_6432.1	chr1	73962974	73962987	-	1	NA	intron (NM_027884, intron 18 of 34)	intron (NM_027884, intron 18 of 34)	-98514	NR_045311	109198	Mm.359721	NR_045311	ENSMUSG00000100301	6030407O03Rik	-	RIKEN cDNA 6030407O03 gene	ncRNA
mm_145569.1	chr18	60911758	60911779	+	1	NA	promoter-TSS (NM_001038499)	promoter-TSS (NM_001038499)	-472	NM_001038499	545260	Mm.20147	NM_001038499	ENSMUSG00000036412	Arsi	BC020108	arylsulfatase i	protein-coding
mm_78707.1	chr9	41376489	41376497	+	1	NA	promoter-TSS (NR_040725)	promoter-TSS (NR_040725)	-33	NR_040725	73144	Mm.38166	NM_001033153	ENSMUSG00000074415	3110039I08Rik	2610203C20Rik|AI848448|D230004N17Rik|D3Mgi9|Mir100hg	RIKEN cDNA 3110039I08 gene	ncRNA
mm_109745.1	chr12	117533947	117533956	+	1	NA	intron (NM_175930, intron 3 of 27)	CpG	17472	NM_175930	217944	Mm.227642	NM_175930	ENSMUSG00000041992	Rapgef5	4932413M22|C86120|D030051B22Rik|GFR|Mrgef|mKIAA0277|mmr-gef	Rap guanine nucleotide exchange factor (GEF) 5	protein-coding
mm_144373.1	chr18	20558017	20558025	+	1	NA	promoter-TSS (NM_007883)	promoter-TSS (NM_007883)	-53	NM_007883	13511	Mm.345891	NM_007883	ENSMUSG00000044393	Dsg2	AA408168|D18Ertd293e	desmoglein 2	protein-coding
mm_8779.1	chr1	161159311	161159314	-	1	NA	promoter-TSS (NM_001195189)	promoter-TSS (NM_001195189)	2	NM_001195189	100502590	Mm.449990	NM_001195189		4930469G21Rik	-	RIKEN cDNA 4930469G21 gene	protein-coding
mm_24952.1	chr3	96635618	96635686	+	1	NA	promoter-TSS (NM_001162388)	promoter-TSS (NM_001162388)	-195	NM_001162388	18632	Mm.20901	NM_011069	ENSMUSG00000028102	Pex11b	PEX11beta|Pex11pbeta	peroxisomal biogenesis factor 11 beta	protein-coding
mm_99383.1	chr11	102050172	102050192	+	1	NA	intron (NM_001160711, intron 5 of 7)	ORR1F|LTR|ERVL-MaLR	8671	NM_001160713	52685	Mm.266885	NM_027987	ENSMUSG00000017309	Cd300lg	2310016B05Rik|Clm9|D11Ertd736e	CD300 molecule like family member G	protein-coding
mm_8381.1	chr1	151250841	151250867	-	1	NA	Intergenic	MLT1H|LTR|ERVL-MaLR	-93644	NM_001039512	117198	Mm.33764	NM_028582	ENSMUSG00000023150	Ivns1abp	1190004M08Rik|1700126I16Rik|AA960440|HSPC068|ND1|NS-1|NS1-BP|Nd1-L|Nd1-S|mKIAA0850	influenza virus NS1A binding protein	protein-coding
mm_171092.1	chr3	127772229	127772230	+	1	NA	intron (NM_027808, intron 1 of 13)	L1Md_A|LINE|L1	8298	NM_027808	71481	Mm.158704	NM_027808	ENSMUSG00000028028	Alpk1	8430410J10Rik|LAK	alpha-kinase 1	protein-coding
mm_125413.1	chr15	41788980	41788988	+	1	NA	promoter-TSS (NM_001130163)	promoter-TSS (NM_001130163)	-50	NM_001130165	170719	Mm.254267	NM_130885	ENSMUSG00000022307	Oxr1	2210416C20Rik|C7|C7B	oxidation resistance 1	protein-coding
mm_16729.1	chr2	7396193	7396241	-	1	NA	promoter-TSS (NM_001110232)	promoter-TSS (NM_001110232)	-19	NM_001110231	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_48550.1	chr5	142905929	142905978	-	1	NA	intron (NM_007393, intron 1 of 5)	CpG	801	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_92577.1	chr10	79983971	79984016	-	1	NA	exon (NM_001003949, exon 1 of 11)	exon (NM_001003949, exon 1 of 11)	337	NM_001003949	216157	Mm.29442	NM_001003949	ENSMUSG00000013858	Tmem259	AC087114.7gm2|ORF61|R32184_3|mFLJ00277	transmembrane protein 259	protein-coding
mm_151421.1	chr19	56821929	56821964	+	1	NA	Intergenic	CpG	-4263	NM_001002238	83561	Mm.247541	NM_031387	ENSMUSG00000025081	Tdrd1	MTR-1	tudor domain containing 1	protein-coding
mm_16424.1	chr2	180290714	180290731	+	1	NA	promoter-TSS (NM_173031)	promoter-TSS (NM_173031)	-843	NM_173031	271887	Mm.246640	NM_173031	ENSMUSG00000038980	Rbbp8nl	4732416F18	RBBP8 N-terminal like	protein-coding
mm_36979.1	chr4	109656527	109656540	-	1	NA	Intergenic	Intergenic	8839	NM_007671	12580	Mm.1912	NM_007671	ENSMUSG00000028551	Cdkn2c	C77269|INK4c|p18|p18-INK4c|p18-INK6|p18INK4c	cyclin-dependent kinase inhibitor 2C (p18, inhibits CDK4)	protein-coding
mm_169121.1	chr13	51754816	51754827	-	1	NA	intron (NM_001281880, intron 2 of 16)	intron (NM_001281880, intron 2 of 16)	38926	NM_001281880	20354	Mm.33903	NM_013660	ENSMUSG00000021451	Sema4d	CD100|Semacl2|Semaj|Semcl2|coll-4	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D	protein-coding
mm_96847.1	chr11	70038532	70038553	+	1	NA	intron (NM_001109752, intron 8 of 19)	intron (NM_001109752, intron 8 of 19)	-15582	NM_001291131	11889	Mm.6559	NM_009714	ENSMUSG00000020884	Asgr1	ASGPR1|Asgr|Asgr-1|HL-1	asialoglycoprotein receptor 1	protein-coding
mm_141619.1	chr17	32877873	32877914	-	1	NA	Intergenic	Intergenic	13710	NM_207245	240066	Mm.26636	NM_207245	ENSMUSG00000095325	Zfp870	AI173952	zinc finger protein 870	protein-coding
mm_43235.1	chr5	129978945	129978952	+	1	NA	intron (NM_027121, intron 2 of 2)	intron (NM_027121, intron 2 of 2)	23880	NM_010368	110006	Mm.3317	NM_010368	ENSMUSG00000025534	Gusb	AI747421|Gur|Gus|Gus-r|Gus-s|Gus-t|Gus-u|Gut|asd|g	glucuronidase, beta	protein-coding
mm_48638.1	chr5	145191550	145191565	-	1	NA	promoter-TSS (NM_020582)	promoter-TSS (NM_020582)	35	NM_020582	57423	Mm.133551	NM_020582	ENSMUSG00000038690	Atp5j2	1110019H14Rik	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit F2	protein-coding
mm_42069.1	chr5	109996507	109996522	+	1	NA	promoter-TSS (NM_145563)	promoter-TSS (NM_145563)	-13	NM_145563	69504	Mm.441438	NM_145563	ENSMUSG00000066613	Zfp932	2310001H12Rik|Znf431	zinc finger protein 932	protein-coding
mm_94558.1	chr11	11558008	11558026	+	1	NA	Intergenic	Intergenic	68751	NM_028669	73862	Mm.159077	NM_028669	ENSMUSG00000020191	4930415F15Rik	-	RIKEN cDNA 4930415F15 gene	protein-coding
mm_10019.1	chr1	192074323	192074353	-	1	NA	intron (NM_011633, intron 1 of 9)	intron (NM_011633, intron 1 of 9)	18261	NM_011633	22033	Mm.380491	NM_011633		Traf5	-	TNF receptor-associated factor 5	protein-coding
mm_42941.1	chr5	122989719	122989739	+	1	NA	promoter-TSS (NM_001003953)	promoter-TSS (NM_001003953)	375	NR_045820	109202	Mm.30769	NM_175405	ENSMUSG00000056735	A930024E05Rik	-	RIKEN cDNA A930024E05 gene	ncRNA
mm_67593.1	chr7	83697458	83697463	-	1	NA	intron (NM_010551, intron 2 of 18)	B4|SINE|B4	38030	NM_010551	16170	Mm.10137	NM_010551	ENSMUSG00000001741	Il16	mKIAA4048	interleukin 16	protein-coding
mm_20953.1	chr2	151741157	151741170	-	1	NA	5' UTR (NM_001305244, exon 1 of 5)	5' UTR (NM_001305244, exon 1 of 5)	147	NM_212446	228769	Mm.146984	NM_144889	ENSMUSG00000032869	Psmf1	AW048666|BC012260|PI31	proteasome (prosome, macropain) inhibitor subunit 1	protein-coding
mm_64243.1	chr7	141702602	141702612	+	1	NA	exon (NM_023566, exon 26 of 46)	exon (NM_023566, exon 26 of 46)	12267	NM_023566	17831	Mm.2041	NM_023566		Muc2	2010015E03Rik|MCM|wnn	mucin 2	protein-coding
mm_108454.1	chr12	82617012	82617026	+	1	NA	promoter-TSS (NM_001282061)	promoter-TSS (NM_001282061)	94	NM_015812	50779	Mm.126176	NM_015812	ENSMUSG00000021219	Rgs6	-	regulator of G-protein signaling 6	protein-coding
mm_96504.1	chr11	68442790	68442826	+	1	NA	intron (NM_177320, intron 1 of 18)	intron (NM_177320, intron 1 of 18)	10683	NM_177320	320207	Mm.244960	NM_177320	ENSMUSG00000020901	Pik3r5	AV230647|F730038I15Rik	phosphoinositide-3-kinase, regulatory subunit 5, p101	protein-coding
mm_14648.1	chr2	136910626	136910638	+	1	NA	intron (NM_001038641, intron 2 of 7)	intron (NM_001038641, intron 2 of 7)	11281	NM_001038641	74243	Mm.330612	NM_028201	ENSMUSG00000027281	Slx4ip	2210009G21Rik|2410004I22Rik|C85661|Slxip	SLX4 interacting protein	protein-coding
mm_131010.1	chr15	103562952	103562960	-	1	NA	exon (NM_008134, exon 4 of 4)	exon (NM_008134, exon 4 of 4)	2125	NM_001289587	14663	Mm.219621	NM_008134	ENSMUSG00000022491	Glycam1	MC26|Sgp50|glyCAM-1	glycosylation dependent cell adhesion molecule 1	protein-coding
mm_148579.1	chr19	4962370	4962378	+	1	NA	promoter-TSS (NM_025553)	promoter-TSS (NM_025553)	68	NM_025553	66419	Mm.28494	NM_025553	ENSMUSG00000024902	Mrpl11	2410001P07Rik|L11mt	mitochondrial ribosomal protein L11	protein-coding
mm_134481.1	chr16	18621994	18622020	-	1	NA	5' UTR (NM_010327, exon 1 of 2)	5' UTR (NM_010327, exon 1 of 2)	396	NM_001001999	14724	Mm.475622	NM_010327	ENSMUSG00000050761	Gp1bb	-	glycoprotein Ib, beta polypeptide	protein-coding
mm_32075.1	chr4	98063073	98063084	+	1	NA	exon (NM_001122953, exon 7 of 10)	exon (NM_001122953, exon 7 of 10)	285452	NM_010905	18027	Mm.31274	NM_010905	ENSMUSG00000028565	Nfia	1110047K16Rik|9430022M17Rik|CTF|NF1-A|NF1A	nuclear factor I/A	protein-coding
mm_124363.1	chr14	105642031	105642068	-	1	NA	Intergenic	RMER1A|Other|Other	-18279	NR_105814	102465207		NR_105814	ENSMUSG00000098780	Mir6390	Gm27562|mmu-mir-6390	microRNA 6390	ncRNA
mm_146756.1	chr18	16808454	16808516	-	1	NA	5' UTR (NM_007664, exon 1 of 16)	5' UTR (NM_007664, exon 1 of 16)	761	NM_007664	12558	Mm.257437	NM_007664	ENSMUSG00000024304	Cdh2	CDHN|N-CAD|Ncad	cadherin 2	protein-coding
mm_148844.1	chr19	6373671	6373718	+	1	NA	non-coding (NR_122118, exon 8 of 12)	non-coding (NR_122118, exon 8 of 12)	10004	NR_122118	22668	Mm.256422	NM_011750	ENSMUSG00000024949	Sf1	BBP|MZFM|WBP4|Zfp162	splicing factor 1	protein-coding
mm_104877.1	chr11	99432951	99432963	-	1	NA	exon (NM_023256, exon 3 of 8)	exon (NM_023256, exon 3 of 8)	5196	NM_023256	66809	Mm.28042	NM_023256	ENSMUSG00000035775	Krt20	9030623C06Rik|Ck-20|Ck20|K20|Krt21	keratin 20	protein-coding
mm_163728.1	chr13	119601514	119601531	-	1	NA	intron (NM_001039244, intron 2 of 2)	B1F1|SINE|Alu	-22297	NM_020279	56838	Mm.143745	NM_020279	ENSMUSG00000074715	Ccl28	CCK1|MEC|Scya28	chemokine (C-C motif) ligand 28	protein-coding
mm_12525.1	chr2	72179818	72179841	+	1	NA	intron (NM_001204165, intron 9 of 30)	intron (NM_001204165, intron 9 of 30)	-105808	NM_023057	65964	Mm.304143	NM_023057	ENSMUSG00000004085	Map3k20	AV006891|B230120H23Rik|MLTK|MLTKalpha|MLTKbeta|Zak	mitogen-activated protein kinase kinase kinase 20	protein-coding
mm_44426.1	chr5	20945431	20945445	-	1	NA	intron (NM_001080977, intron 1 of 7)	intron (NM_001080977, intron 1 of 7)	-5551	NR_030699	320770	Mm.491217	NR_030699	ENSMUSG00000101013	A630072M18Rik	Aptr	RIKEN cDNA A630072M18 gene	ncRNA
mm_62443.1	chr7	101383948	101383962	+	1	NA	intron (NM_001040112, intron 1 of 30)	intron (NM_001040112, intron 1 of 30)	-1571	NM_027180	69710	Mm.277687	NM_027180	ENSMUSG00000032812	Arap1	2410002L19Rik|Centd2|mKIAA0782	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	protein-coding
mm_31072.1	chr4	41358886	41358899	+	1	NA	intron (NM_023305, intron 1 of 6)	B1F|SINE|Alu	9896	NM_023305	67123	Mm.289795	NM_023305	ENSMUSG00000028437	Ubap1	2700092A01Rik|NAG20|UBAP-1|Ubap	ubiquitin-associated protein 1	protein-coding
mm_91297.1	chr10	24916072	24916082	-	1	NA	exon (NM_007482, exon 7 of 8)	exon (NM_007482, exon 7 of 8)	5413	NR_105870	102465545		NR_105870	ENSMUSG00000099181	Mir6905	Gm27879|mmu-mir-6905	microRNA 6905	ncRNA
mm_160047.1	chr6	147086975	147086975	-	1	NA	promoter-TSS (NM_001034903)	promoter-TSS (NM_001034903)	57	NM_001034903	545893	Mm.224739	NM_001034903	ENSMUSG00000072662	Mansc4	A430079E08|EG545893|Gm5887	MANSC domain containing 4	protein-coding
mm_127058.1	chr15	97246959	97247004	+	1	NA	promoter-TSS (NM_172293)	promoter-TSS (NM_172293)	-126	NM_172293	239647	Mm.130036	NM_172293	ENSMUSG00000044250	Pced1b	Fam113b	PC-esterase domain containing 1B	protein-coding
mm_146590.1	chr18	9329955	9329958	-	1	NA	intron (NM_026484, intron 8 of 9)	intron (NM_026484, intron 8 of 9)	-47147	NM_153086	225152	Mm.119273	NM_153086	ENSMUSG00000036855	Gjd4	9430022F06Rik|Cx39	gap junction protein, delta 4	protein-coding
mm_145764.1	chr18	64976863	64976875	+	1	NA	intron (NM_001114386, intron 1 of 30)	intron (NM_001114386, intron 1 of 30)	-46658	NM_031881	83814	Mm.98668	NM_031881	ENSMUSG00000024589	Nedd4l	1300012C07Rik|Nedd4-2|Nedd4b	neural precursor cell expressed, developmentally down-regulated gene 4-like	protein-coding
mm_110933.1	chr12	76370376	76370394	-	1	NA	promoter-TSS (NM_001172104)	promoter-TSS (NM_001172104)	119	NM_178744	268564	Mm.77065	NM_178744	ENSMUSG00000033454	Zbtb1	9430077A12|AI256369|Bsg2|C430003J21Rik	zinc finger and BTB domain containing 1	protein-coding
mm_66722.1	chr7	46100777	46100821	-	1	NA	promoter-TSS (NM_001204411)	promoter-TSS (NM_001204411)	-35	NM_001204411	16514	Mm.333863	NM_010602	ENSMUSG00000096146	Kcnj11	Kir6.2|mBIR	potassium inwardly rectifying channel, subfamily J, member 11	protein-coding
mm_36506.1	chr4	83485846	83485890	-	1	NA	5' UTR (NM_001290527, exon 2 of 11)	5' UTR (NM_001290527, exon 2 of 11)	580	NM_001290527	101739	Mm.105331	NM_133948	ENSMUSG00000028484	Psip1	AA408851|AU015605|Dfs70|Ledgfa|Ledgfb|Psip2	PC4 and SFRS1 interacting protein 1	protein-coding
mm_138575.1	chr17	35425315	35425350	+	1	NA	exon (NM_207648, exon 2 of 5)	exon (NM_207648, exon 2 of 5)	455	NM_207648	110557	Mm.439827	NM_207648	ENSMUSG00000073409	H2-Q6	0610037M15Rik|H-2Q6|Qa-6|Qa6	histocompatibility 2, Q region locus 6	protein-coding
mm_45581.1	chr5	74009426	74009465	-	1	NA	intron (NM_177561, intron 5 of 8)	B3A|SINE|B2	58966	NM_177561	69727	Mm.48795	NM_177561	ENSMUSG00000054814	Usp46	1190009E20Rik|2410018I08Rik|AI451644	ubiquitin specific peptidase 46	protein-coding
mm_118124.1	chr13	104205342	104205345	-	1	NA	3' UTR (NM_172807, exon 11 of 11)	3' UTR (NM_172807, exon 11 of 11)	-23268	NM_181061	60411	Mm.281498	NM_021790	ENSMUSG00000021714	Cenpk	B130045K24Rik|BB232189|C530004N04Rik|Cenp-K|Solt|Solzt	centromere protein K	protein-coding
mm_131750.1	chr16	22294972	22294973	+	1	NA	Intergenic	Intergenic	-28967	NM_001330555	20462	Mm.210352	NM_009186	ENSMUSG00000022858	Tra2b	5730405G21Rik|D16Ertd266e|SIG-41|Sfrs10|Silg41|TRA2beta	transformer 2 beta homolog (Drosophila)	protein-coding
mm_154758.1	chrX	10718535	10718543	+	1	NA	exon (NM_001166635, exon 2 of 2)	exon (NM_001166635, exon 2 of 2)	1174	NM_001166635	68041	Mm.29429	NM_026524	ENSMUSG00000008035	Mid1ip1	3110038L01Rik|Mig12|S14R	Mid1 interacting protein 1 (gastrulation specific G12-like (zebrafish))	protein-coding
mm_61792.1	chr7	83892038	83892056	+	1	NA	promoter-TSS (NM_023403)	promoter-TSS (NM_023403)	47	NM_023403	67943	Mm.117365	NM_023403	ENSMUSG00000038503	Mesdc2	2210015O11Rik|AW537813|mKIAA0081|mesd|msd	mesoderm development candidate 2	protein-coding
mm_5463.1	chr1	36445232	36445242	-	1	NA	promoter-TSS (NM_001310517)	promoter-TSS (NM_001310517)	34	NM_001310517	214895	Mm.287854	NM_001013374	ENSMUSG00000001143	Lman2l	A630028F14Rik|VIP36-like|VIPL	lectin, mannose-binding 2-like	protein-coding
mm_4077.1	chr1	166254187	166254249	+	1	NA	promoter-TSS (NM_001164528)	promoter-TSS (NM_001164528)	79	NM_001164528	100039795	Mm.101743	NM_001164528	ENSMUSG00000040612	Ildr2	2810478N18Rik|3110063L10Rik|AI852300|D1Ertd471e|Dbsm1|ENSMUSG00000040612|Ll	immunoglobulin-like domain containing receptor 2	protein-coding
mm_28.1	chr1	6214788	6214801	+	1	NA	5' UTR (NM_009826, exon 1 of 24)	5' UTR (NM_009826, exon 1 of 24)	132	NM_009826	12421	Mm.293811	NM_009826	ENSMUSG00000025907	Rb1cc1	2900055E04Rik|5930404L04Rik|Cc1|FIP200|LaXp180	RB1-inducible coiled-coil 1	protein-coding
mm_8888.1	chr1	162886500	162886502	-	1	NA	intron (NM_018881, intron 4 of 8)	intron (NM_018881, intron 4 of 8)	12211	NM_018881	55990	Mm.10929	NM_018881	ENSMUSG00000040170	Fmo2	2310008D08Rik|2310042I22Rik|AW107733	flavin containing monooxygenase 2	protein-coding
mm_54071.1	chr6	14755071	14755081	-	1	NA	exon (NM_080464, exon 1 of 4)	exon (NM_080464, exon 1 of 4)	198	NM_080464	140491	Mm.209429	NM_080464	ENSMUSG00000042717	Ppp1r3a	GM|RG1|RGL	protein phosphatase 1, regulatory (inhibitor) subunit 3A	protein-coding
mm_59905.1	chr7	30322556	30322569	+	1	NA	promoter-TSS (NM_001033140)	promoter-TSS (NM_001033140)	-187	NM_001033140	68332	Mm.6844	NM_001033140	ENSMUSG00000074211	Sdhaf1	0610010E21Rik|AI430885|AW490662|Lyrm8	succinate dehydrogenase complex assembly factor 1	protein-coding
mm_162339.1	chr1	46852783	46852795	-	1	NA	intron (NM_172653, intron 1 of 9)	CpG	720	NM_172653	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|mKIAA1265	solute carrier family 39 (zinc transporter), member 10	protein-coding
mm_165442.1	chr2	154580738	154580738	+	1	NA	Intergenic	Intergenic	-10846	NM_007891	13555	Mm.18036	NM_007891	ENSMUSG00000027490	E2f1	E2F-1|mKIAA4009	E2F transcription factor 1	protein-coding
mm_160395.1	chr8	66688017	66688017	-	1	NA	promoter-TSS (NM_016708)	promoter-TSS (NM_016708)	77	NM_016708	18168	Mm.10685	NM_016708	ENSMUSG00000044014	Npy5r	NPY5-R|NPYY5-R|Y5R	neuropeptide Y receptor Y5	protein-coding
mm_76182.1	chr8	82402368	82402388	-	1	NA	5' UTR (NM_001254747, exon 1 of 8)	5' UTR (NM_001254747, exon 1 of 8)	208	NM_001254747	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_10313.1	chr2	11172330	11172350	+	1	NA	promoter-TSS (NM_008859)	promoter-TSS (NM_008859)	-42	NM_008859	18761	Mm.329993	NM_008859	ENSMUSG00000026778	Prkcq	A130035A12Rik|AW494342|PKC-0|PKC-theta|PKCtheta|Pkcq	protein kinase C, theta	protein-coding
mm_99439.1	chr11	102433001	102433027	+	1	NA	exon (NM_008175, exon 2 of 13)	exon (NM_008175, exon 2 of 13)	2692	NM_008175	14824	Mm.1568	NM_008175	ENSMUSG00000034708	Grn	Pgrn|epithelin	granulin	protein-coding
mm_93261.1	chr10	95564100	95564121	-	1	NA	promoter-TSS (NM_027722)	promoter-TSS (NM_027722)	57	NM_027722	71207	Mm.24397	NM_027722	ENSMUSG00000020029	Nudt4	4933436C10Rik|DIPP2|DIPP2alpha|DIPP2beta|HDCMB47P	nudix (nucleoside diphosphate linked moiety X)-type motif 4	protein-coding
mm_143842.1	chr17	84126299	84126316	-	1	NA	Intergenic	Intergenic	47647	NR_045458	74473	Mm.399575	NR_045458		4933433H22Rik	-	RIKEN cDNA 4933433H22 gene	ncRNA
mm_154585.1	chrX	7572738	7572750	+	1	NA	promoter-TSS (NR_029473)	promoter-TSS (NR_029473)	-856	NR_029473	78185	Mm.160055	NR_029473	ENSMUSG00000039545	Ppp1r3fos	4930524L23Rik	protein phosphatase 1, regulatory subunit 3F, opposite strand	ncRNA
mm_5537.1	chr1	38121046	38121049	-	1	NA	intron (NM_019570, intron 1 of 22)	intron (NM_019570, intron 1 of 22)	8615	NM_019570	56210	Mm.389103	NM_019570	ENSMUSG00000026082	Rev1	1110027I23Rik|AU022044|Rev1l	REV1, DNA directed polymerase	protein-coding
mm_128414.1	chr15	44752181	44752239	-	1	NA	5' UTR (NM_178765, exon 1 of 8)	5' UTR (NM_178765, exon 1 of 8)	248	NM_178765	319613	Mm.207715	NM_176998	ENSMUSG00000022340	Sybu	Golsyn	syntabulin (syntaxin-interacting)	protein-coding
mm_32701.1	chr4	116075393	116075409	+	1	NA	promoter-TSS (NM_025641)	promoter-TSS (NM_025641)	132	NM_153521	230654	Mm.3655	NM_153521	ENSMUSG00000028703	Lrrc41	AA409966|AW555107|D630045E04Rik|D730026A16Rik|MUF1	leucine rich repeat containing 41	protein-coding
mm_42778.1	chr5	121385502	121385532	+	1	NA	promoter-TSS (NM_001163470)	promoter-TSS (NM_001163470)	98	NM_001163470	231712	Mm.20488	NM_172275	ENSMUSG00000042726	Trafd1	1110008K06Rik|Fln29	TRAF type zinc finger domain containing 1	protein-coding
mm_109114.1	chr12	105488652	105488662	+	1	NA	3' UTR (NM_001252508, exon 2 of 2)	3' UTR (NM_001252508, exon 2 of 2)	-24776	NR_102381	104932	Mm.274150	NR_102381		AU015791	-	expressed sequence AU015791	ncRNA
mm_13802.1	chr2	119008133	119008149	+	1	NA	Intergenic	Intergenic	21252	NM_199310	269336	Mm.292465	NM_199310	ENSMUSG00000039983	Ccdc32	Gm631	coiled-coil domain containing 32	protein-coding
mm_924.1	chr1	55147629	55147633	+	1	NA	intron (NM_001310585, intron 2 of 6)	intron (NM_001310585, intron 2 of 6)	16386	NM_025283	19070	Mm.291037	NM_025283	ENSMUSG00000025979	Mob4	2610109B12Rik|Mobkl3|Phocn|Prei3	MOB family member 4, phocein	protein-coding
mm_38893.1	chr4	149774212	149774234	-	1	NA	promoter-TSS (NM_027460)	promoter-TSS (NM_027460)	44	NM_027460	70556	Mm.41877	NM_027460	ENSMUSG00000028982	Slc25a33	5730438N18Rik|Pnc1	solute carrier family 25, member 33	protein-coding
mm_33869.1	chr4	135963743	135963760	+	1	NA	Intergenic	CpG	-1414	NM_178389	74246	Mm.247946	NM_178389	ENSMUSG00000028671	Gale	2310002A12Rik|AI323962	galactose-4-epimerase, UDP	protein-coding
mm_79060.1	chr9	46230233	46230243	+	1	NA	exon (NM_009692, exon 4 of 4)	exon (NM_009692, exon 4 of 4)	1608	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2|apo-AI|apoA-I	apolipoprotein A-I	protein-coding
mm_127387.1	chr15	101041036	101041053	+	1	NA	3' UTR (NM_011323, exon 26 of 26)	3' UTR (NM_011323, exon 26 of 26)	13355	NM_001214911	668225	Mm.385011	NM_001214911	ENSMUSG00000095440	Fignl2	EG668225	fidgetin-like 2	protein-coding
mm_35901.1	chr4	49597709	49597777	-	1	NA	5' UTR (NM_025944, exon 1 of 2)	5' UTR (NM_025944, exon 1 of 2)	127	NM_025944	67063	Mm.490285	NM_025944	ENSMUSG00000039611	Tmem246	2810432L12Rik|9330170P15Rik|AI835809	transmembrane protein 246	protein-coding
mm_46275.1	chr5	100038875	100038885	-	1	NA	exon (NM_016690, exon 1 of 8)	exon (NM_016690, exon 1 of 8)	342	NM_016690	50926	Mm.389579	NM_016690	ENSMUSG00000029328	Hnrnpdl	AA407431|AA959857|D5Ertd650e|D5Wsu145e|Hnrnpdl1|Hnrpdl|JKTBP|hnRNP DL|hnRNP-DL	heterogeneous nuclear ribonucleoprotein D-like	protein-coding
mm_149455.1	chr19	11516446	11516454	+	1	NA	Intergenic	Lx4A|LINE|L1	-2109	NM_027209	69774	Mm.436639	NM_027209	ENSMUSG00000024677	Ms4a6b	1810027D10Rik	membrane-spanning 4-domains, subfamily A, member 6B	protein-coding
mm_17900.1	chr2	35181681	35181717	-	1	NA	3' UTR (NM_026697, exon 8 of 8)	3' UTR (NM_026697, exon 8 of 8)	19421	NM_026697	68365	Mm.198264	NM_026697	ENSMUSG00000026878	Rab14	0610030G24Rik|2810475J17Rik|A830021G03Rik|AI314285|AI649155|D030017L14Rik	RAB14, member RAS oncogene family	protein-coding
mm_47334.1	chr5	122501251	122501265	-	1	NA	intron (NM_001110140, intron 1 of 19)	CpG	967	NM_001110140	11938	Mm.227583	NM_009722	ENSMUSG00000029467	Atp2a2	9530097L16Rik|D5Wsu150e|SERCA2|SERCA2B|Serca2a|mKIAA4195	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	protein-coding
mm_108932.1	chr12	101083807	101083832	+	1	NA	promoter-TSS (NM_001160214)	promoter-TSS (NM_001160214)	-117	NM_001160214	68734	Mm.87077	NM_211355	ENSMUSG00000041846	Smek1	1110034C04Rik|BC064465|Ppp4r3a|mKIAA2010	SMEK homolog 1, suppressor of mek1 (Dictyostelium)	protein-coding
mm_145006.1	chr18	38419491	38419495	+	1	NA	intron (NM_022996, intron 1 of 7)	intron (NM_022996, intron 1 of 7)	518	NM_022996	65113	Mm.102496	NM_022996	ENSMUSG00000024425	Ndfip1	0610010M22Rik|N4wbp5	Nedd4 family interacting protein 1	protein-coding
mm_141016.1	chr17	25081139	25081201	-	1	NA	promoter-TSS (NM_001001183)	promoter-TSS (NM_001001183)	-56	NM_001001183	407831	Mm.34379	NM_001001183	ENSMUSG00000024168	Tmem204	-	transmembrane protein 204	protein-coding
mm_140405.1	chr17	87641430	87641476	+	1	NA	exon (NM_008532, exon 5 of 10)	exon (NM_008532, exon 5 of 10)	5474	NM_008532	17075	Mm.4259	NM_008532	ENSMUSG00000045394	Epcam	CD326|EGP|EGP-2|Egp314|Ep-CAM|EpCAM1|GA733-2|Ly74|TROP1|Tacsd1|Tacstd1|gp40	epithelial cell adhesion molecule	protein-coding
mm_68359.1	chr7	106511571	106511591	-	1	NA	Intergenic	Intergenic	-70508	NR_003967	209380	Mm.461779	NM_001001318		Gm4759	EG209380	GTPase, very large interferon inducible 1 pseudogene	pseudo
mm_98464.1	chr11	94948538	94948571	+	1	NA	exon (NM_007742, exon 42 of 51)	exon (NM_007742, exon 42 of 51)	12330	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_80776.1	chr9	95564469	95564472	+	1	NA	Intergenic	Intergenic	4653	NM_198414	75552	Mm.151485	NM_198414	ENSMUSG00000064225	Paqr9	1700020G04Rik	progestin and adipoQ receptor family member IX	protein-coding
mm_24739.1	chr3	95283396	95283406	+	1	NA	5' UTR (NM_133858, exon 1 of 10)	5' UTR (NM_133858, exon 1 of 10)	466	NM_199475	75007	Mm.279287	NM_133858	ENSMUSG00000038712	Fam63a	1810005H09Rik|4930504E06Rik|AA562754|AA960384|AW561904|cI-40|mKIAA1390|ni	family with sequence similarity 63, member A	protein-coding
mm_44684.1	chr5	30120226	30120238	-	1	NA	intron (NM_178878, intron 18 of 19)	intron (NM_178878, intron 18 of 19)	-14146	NM_001256263	433868	Mm.450696	NM_001256263	ENSMUSG00000086815	3110082J24Rik	ENSMUSG00000073106	RIKEN cDNA 3110082J24 gene	protein-coding
mm_89960.1	chr10	111296303	111296314	+	1	NA	3' UTR (NM_001003717, exon 23 of 23)	3' UTR (NM_001003717, exon 23 of 23)	-2371	NM_027914	71769	Mm.45256	NM_027914	ENSMUSG00000035759	Bbs10	1300007O09Rik|AI452285	Bardet-Biedl syndrome 10 (human)	protein-coding
mm_105569.1	chr11	106579112	106579141	-	1	NA	intron (NM_198292, intron 1 of 11)	intron (NM_198292, intron 1 of 11)	33804	NM_198292	21763	Mm.102407	NM_198292	ENSMUSG00000040548	Tex2	4930568E07Rik|AI553404|Def-5|Taz4	testis expressed gene 2	protein-coding
mm_115132.1	chr13	104296464	104296469	+	1	NA	intron (NR_136938, intron 2 of 26)	(TTTTC)n|Simple_repeat|Simple_repeat	8631	NM_001081020	108154	Mm.208125	NM_175496	ENSMUSG00000046169	Adamts6	A930019D11Rik|ADAM-TS6|b2b1879.1Clo|b2b2029Clo|b2b2182Clo|b2b2187.1Clo|b2b2228Clo	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 6	protein-coding
mm_151167.1	chr19	53198001	53198008	+	1	NA	intron (NM_013758, intron 1 of 15)	intron (NM_013758, intron 1 of 15)	54007	NM_013758	27360	Mm.426080	NM_013758	ENSMUSG00000025026	Add3	AI463285|R75380	adducin 3 (gamma)	protein-coding
mm_22196.1	chr2	173291138	173291168	-	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-14620	NM_022995	65112	Mm.73682	NM_022995	ENSMUSG00000038400	Pmepa1	2210418I02Rik|AW455466|Erg1.2|N4wbp4|Stag1|Tmepai	prostate transmembrane protein, androgen induced 1	protein-coding
mm_60441.1	chr7	44477029	44477042	+	1	NA	Intergenic	L1MEd|LINE|L1	6688	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_64633.1	chr7	3703901	3703931	-	1	NA	promoter-TSS (NM_029767)	promoter-TSS (NM_029767)	-125	NM_029767	76846	Mm.13944	NM_029767	ENSMUSG00000006333	Rps9	3010033P07Rik|AL022771|AL022885	ribosomal protein S9	protein-coding
mm_6803.1	chr1	84154759	84154763	-	1	NA	intron (NM_001003948, intron 2 of 2)	(TTAA)n|Simple_repeat|Simple_repeat	64200	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_150680.1	chr19	42052986	42052996	+	1	NA	exon (NM_025752, exon 1 of 1)	exon (NM_025752, exon 1 of 1)	763	NM_025752	66765	Mm.440412	NM_025752	ENSMUSG00000090369	4933411K16Rik	-	RIKEN cDNA 4933411K16 gene	protein-coding
mm_45654.1	chr5	77095207	77095220	-	1	NA	promoter-TSS (NM_001159901)	promoter-TSS (NM_001159901)	54	NM_001159901	74318	Mm.181852	NM_175606	ENSMUSG00000059325	Hopx	1110018K11Rik|1200015P04Rik|2300002F06Rik|AI848177|AW490897|Cameo|Hdop|Hod|Hop|Ob1|Obl|Toto	HOP homeobox	protein-coding
mm_126611.1	chr15	83033387	83033397	+	1	NA	promoter-TSS (NM_001271412)	promoter-TSS (NM_001271412)	5	NM_001271412	74039	Mm.32584	NM_028728	ENSMUSG00000058099	Nfam1	4921501M20Rik|Cnaip	Nfat activating molecule with ITAM motif 1	protein-coding
mm_137095.1	chr17	21535594	21535628	+	1	NA	promoter-TSS (NM_144515)	promoter-TSS (NM_144515)	72	NM_144515	22710	Mm.296100	NM_144515	ENSMUSG00000051341	Zfp52	KRAB11|Zfp-52|Zfp76|mszf23-2|mszf24|mszf34|mszf75|zfec29	zinc finger protein 52	protein-coding
mm_151331.1	chr19	55894473	55894475	+	1	NA	promoter-TSS (NM_001142924)	promoter-TSS (NM_001142924)	-847	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_56181.1	chr6	88268836	88268844	-	1	NA	intron (NM_023060, intron 6 of 6)	intron (NM_023060, intron 6 of 6)	46572	NM_019964	56691	Mm.272871	NM_019964	ENSMUSG00000048206	Dnajb8	1700016F14Rik|1700031F10Rik|AI326313|mDj6	DnaJ heat shock protein family (Hsp40) member B8	protein-coding
mm_56522.1	chr6	99520950	99521030	-	1	NA	promoter-TSS (NM_001347345)	promoter-TSS (NM_001347345)	3	NM_001347345	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_120224.1	chr14	62857181	62857193	+	1	NA	intron (NM_175546, intron 1 of 11)	intron (NM_175546, intron 1 of 11)	-8355	NR_105860	102465311		NR_105860	ENSMUSG00000098858	Mir6541	Gm27311|mmu-mir-6541	microRNA 6541	ncRNA
mm_109878.1	chr12	4918164	4918182	-	1	NA	intron (NM_001099628, intron 1 of 30)	intron (NM_001099628, intron 1 of 30)	820	NM_001099628	320817	Mm.210966	NM_001099628	ENSMUSG00000052812	Atad2b	1110014E10Rik|BC032887|C79189|D530031C13Rik	ATPase family, AAA domain containing 2B	protein-coding
mm_15780.1	chr2	164333499	164333503	+	1	NA	exon (NM_009301, exon 2 of 3)	exon (NM_009301, exon 2 of 3)	736	NM_009301	20944	Mm.140154	NM_009301	ENSMUSG00000017004	Svs5	BB115186|Semg1|Svp-1|Svp1|Svp5	seminal vesicle secretory protein 5	protein-coding
mm_115510.1	chr13	4523323	4523355	-	1	NA	promoter-TSS (NM_054080)	promoter-TSS (NM_054080)	5	NM_001311132	116852	Mm.37605	NM_054080	ENSMUSG00000054757	Akr1c20	2610528B18Rik	aldo-keto reductase family 1, member C20	protein-coding
mm_172698.1	chr8	63933271	63933271	-	1	NA	intron (NM_001195687, intron 5 of 7)	intron (NM_001195687, intron 5 of 7)	18899	NM_001195687	244495	Mm.485331	NM_001195687	ENSMUSG00000094443	Sgol2b	EG244495|Gm4975|Sgo2B	shugoshin like 2b (S. pombe)	protein-coding
mm_48929.1	chr6	4528372	4528385	+	1	NA	exon (NM_007743, exon 32 of 52)	exon (NM_007743, exon 32 of 52)	22760	NM_007743	12843	Mm.277792	NM_007743	ENSMUSG00000029661	Col1a2	AA960264|AI325291|Col1a-2|Cola-2|Cola2|oim	collagen, type I, alpha 2	protein-coding
mm_81219.1	chr9	107590925	107590945	+	1	NA	exon (NM_025903, exon 7 of 12)	exon (NM_025903, exon 7 of 12)	3217	NM_025903	15983	Mm.215335	NM_025903	ENSMUSG00000010048	Ifrd2	1810034A24Rik|AA470234|AI838527|SKMc15	interferon-related developmental regulator 2	protein-coding
mm_74051.1	chr8	122282118	122282140	+	1	NA	promoter-TSS (NM_009569)	promoter-TSS (NM_009569)	-12	NM_009569	22761	Mm.3105	NM_009569	ENSMUSG00000049577	Zfpm1	FOG|Fog1	zinc finger protein, multitype 1	protein-coding
mm_170122.1	chr17	39846917	39846921	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	3922	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_47985.1	chr5	135933701	135933705	-	1	NA	intron (NM_018871, intron 1 of 1)	intron (NM_018871, intron 1 of 1)	938	NM_018871	22628	Mm.233813	NM_018871	ENSMUSG00000051391	Ywhag	14-3-3gamma|D7Bwg1348e	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, gamma polypeptide	protein-coding
mm_116472.1	chr13	43481222	43481325	-	1	NA	promoter-TSS (NM_019930)	promoter-TSS (NM_019930)	-300	NM_019930	56705	Mm.148781	NM_019930	ENSMUSG00000038546	Ranbp9	IBAP-1|Ibap1|RanBPM	RAN binding protein 9	protein-coding
mm_145457.1	chr18	60235812	60235815	+	1	NA	intron (NM_001033767, intron 2 of 2)	intron (NM_001033767, intron 2 of 2)	23736	NM_001033767	240327	Mm.357104	NM_001033767	ENSMUSG00000073555	Gm4951	EG240327|Ifgga2	predicted gene 4951	protein-coding
mm_44860.1	chr5	34288319	34288372	-	1	NA	promoter-TSS (NM_001015039)	promoter-TSS (NM_001015039)	-21	NM_001015039	231125	Mm.113388	NM_001015039	ENSMUSG00000037224	Zfyve28	9630058O20Rik|Gm146|mKIAA1643	zinc finger, FYVE domain containing 28	protein-coding
mm_1459.1	chr1	67230921	67230925	+	1	NA	3' UTR (NM_001080809, exon 38 of 38)	3' UTR (NM_001080809, exon 38 of 38)	107896	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_157726.1	chrX	70364929	70364937	-	1	NA	5' UTR (NM_010498, exon 1 of 9)	5' UTR (NM_010498, exon 1 of 9)	152	NM_010498	15931	Mm.233083	NM_010498	ENSMUSG00000035847	Ids	AW214631	iduronate 2-sulfatase	protein-coding
mm_149833.1	chr19	24875622	24875639	+	1	NA	Intergenic	Intergenic	-13788	NM_175013	226041	Mm.105222	NM_175013	ENSMUSG00000041731	Pgm5	4833423B07|9530034F03Rik|D830025G17|aciculin	phosphoglucomutase 5	protein-coding
mm_81828.1	chr9	118054949	118054952	+	1	NA	intron (NM_001286507, intron 4 of 6)	intron (NM_001286507, intron 4 of 6)	14428	NM_013727	27215	Mm.92705	NM_013727	ENSMUSG00000039285	Azi2	AA410145|AZ2	5-azacytidine induced gene 2	protein-coding
mm_145676.1	chr18	61566141	61566146	+	1	NA	intron (NM_146087, intron 2 of 9)	RMER6A|LTR|ERVK	10561	NM_146087	93687	Mm.26908	NM_146087	ENSMUSG00000024576	Csnk1a1	2610208K14Rik|4632404G05Rik|5430427P18Rik|CK1a|Csnk1a	casein kinase 1, alpha 1	protein-coding
mm_67933.1	chr7	99980432	99980477	-	1	NA	promoter-TSS (NM_175388)	promoter-TSS (NM_175388)	4	NM_175388	108937	Mm.323087	NM_175388	ENSMUSG00000058761	Rnf169	2900057K09Rik	ring finger protein 169	protein-coding
mm_46025.1	chr5	91283046	91283057	-	1	NA	promoter-TSS (NR_040428)	promoter-TSS (NR_040428)	25	NR_040428	100503265	Mm.125059	NR_040428	ENSMUSG00000107198	Gm19619	-	predicted gene, 19619	ncRNA
mm_171896.1	chr5	39798414	39798418	+	1	NA	Intergenic	Intergenic	-153785	NM_010474	15476	Mm.12559	NM_010474	ENSMUSG00000051022	Hs3st1	3-Ost|D5Wsu110e|Hsg3ost	heparan sulfate (glucosamine) 3-O-sulfotransferase 1	protein-coding
mm_22304.1	chr2	180381202	180381210	-	1	NA	intron (NR_040745, intron 4 of 6)	intron (NR_040745, intron 4 of 6)	-4398	NR_045331	622283	Mm.447602	NR_045331		Mir1a-1hg	EG622283|Gm6307	Mir1a-1 and Mir133a-2 host gene	ncRNA
mm_67169.1	chr7	73556694	73556702	-	1	NA	intron (NR_037569, intron 1 of 4)	intron (NR_037569, intron 1 of 4)	1697	NR_037569	69170	Mm.34539	NR_037569	ENSMUSG00000101970	1810026B05Rik	-	RIKEN cDNA 1810026B05 gene	ncRNA
mm_20529.1	chr2	131012370	131012372	-	1	NA	intron (NM_009730, intron 24 of 28)	intron (NM_009730, intron 24 of 28)	28027	NR_105969	102465606		NR_105969	ENSMUSG00000098686	Mir6973b	Gm27815|mmu-mir-6973b	microRNA 6973b	ncRNA
mm_57890.1	chr6	131368424	131368436	-	1	NA	exon (NM_011733, exon 7 of 9)	exon (NM_011733, exon 7 of 9)	20020	NM_139117	56449	Mm.458000	NM_011733	ENSMUSG00000030189	Ybx3	Csda|Dpba|MSY3|MSY4|Yb2|dbpA|oxyR	Y box protein 3	protein-coding
mm_141018.1	chr17	25115917	25115935	-	1	NA	promoter-TSS (NM_001163661)	promoter-TSS (NM_001163661)	-21	NM_027880	71718	Mm.288702	NM_027880	ENSMUSG00000024170	Telo2	1200003M09Rik|AI415602|Tel2|mKIAA0683	telomere maintenance 2	protein-coding
mm_75233.1	chr8	39629349	39629355	-	1	NA	intron (NM_001113326, intron 3 of 9)	ID_B1|SINE|B4	13326	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_75817.1	chr8	70382522	70382523	-	1	NA	TTS (NM_016685)	TTS (NM_016685)	8974	NM_016685	12845	Mm.45071	NM_016685	ENSMUSG00000031849	Comp	TSP5	cartilage oligomeric matrix protein	protein-coding
mm_119025.1	chr14	30010324	30010343	+	1	NA	intron (NM_001136240, intron 1 of 7)	intron (NM_001136240, intron 1 of 7)	1333	NM_001136240	218865	Mm.259916	NM_172264	ENSMUSG00000015970	Chdh	AU041472|D630034H06Rik	choline dehydrogenase	protein-coding
mm_84841.1	chr9	78378170	78378199	-	1	NA	intron (NM_026480, intron 1 of 2)	intron (NM_026480, intron 1 of 2)	404	NM_026480	67968	Mm.26883	NM_026480	ENSMUSG00000032346	Ooep	2410146L05Rik|Floped|Moep19|Sddr	oocyte expressed protein	protein-coding
mm_127179.1	chr15	98983688	98983702	+	1	NA	Intergenic	Intergenic	-2270	NR_045991	75951	Mm.441657	NR_045991	ENSMUSG00000097587	4930578M01Rik	3010001K12Rik	RIKEN cDNA 4930578M01 gene	ncRNA
mm_46856.1	chr5	113745189	113745197	-	1	NA	exon (NM_016926, exon 17 of 19)	exon (NM_016926, exon 17 of 19)	9411	NM_001010825	231630	Mm.21926	NM_001010825	ENSMUSG00000053334	Ficd	D5Ertd40e|Hype	FIC domain containing	protein-coding
mm_107453.1	chr12	37108534	37108546	+	1	NA	promoter-TSS (NM_008584)	promoter-TSS (NM_008584)	-6	NM_008584	17286	Mm.341398	NM_008584	ENSMUSG00000036144	Meox2	AI528662|Gax|Mox-2|Mox2	mesenchyme homeobox 2	protein-coding
mm_143841.1	chr17	84126249	84126281	-	1	NA	Intergenic	Intergenic	47605	NR_045458	74473	Mm.399575	NR_045458		4933433H22Rik	-	RIKEN cDNA 4933433H22 gene	ncRNA
mm_102051.1	chr11	52098516	52098533	-	1	NA	promoter-TSS (NM_019411)	promoter-TSS (NM_019411)	-300	NM_019411	19052	Mm.260288	NM_019411	ENSMUSG00000020349	Ppp2ca	PP2A|R75353	protein phosphatase 2 (formerly 2A), catalytic subunit, alpha isoform	protein-coding
mm_108710.1	chr12	87026459	87026522	+	1	NA	promoter-TSS (NM_172583)	promoter-TSS (NM_172583)	-74	NM_172583	217733	Mm.110032	NM_172583	ENSMUSG00000034145	Tmem63c	4932420N09|9330187M14Rik	transmembrane protein 63c	protein-coding
mm_166700.1	chr6	114880539	114880541	+	1	NA	intron (NM_177683, intron 2 of 4)	intron (NM_177683, intron 2 of 4)	41212	NM_177683	232334	Mm.268357	NM_177683	ENSMUSG00000030315	Vgll4	BC048841|VGL-4	vestigial like family member 4	protein-coding
mm_101314.1	chr11	22814063	22814079	-	1	NA	Intergenic	Intergenic	45664	NM_016888	53625	Mm.395495	NM_016888	ENSMUSG00000051650	B3gnt2	AA408337|AA409404|AW260308|B3Galt6|B3gnt1|BGnT-1|BGnT-2|BGnT1|BGnT2|Beta3gnt	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 2	protein-coding
mm_147056.1	chr18	34941900	34941922	-	1	NA	exon (NM_010481, exon 11 of 17)	exon (NM_010481, exon 11 of 17)	-9908	NM_144866	225363	Mm.329353	NM_144866	ENSMUSG00000024360	Etf1	AI463371|D6Ertd109e|ERF|ERF1|SUP45L1|TB3-1	eukaryotic translation termination factor 1	protein-coding
mm_102870.1	chr11	69407814	69407831	-	1	NA	exon (NM_001017426, exon 5 of 23)	exon (NM_001017426, exon 5 of 23)	5853	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_85933.1	chr9	112097746	112097755	-	1	NA	intron (NM_001177618, intron 17 of 18)	B4A|SINE|B4	20961	NR_029823	723815		NR_029823	ENSMUSG00000065441	Mir128-2	Mirn128-2|Mirn128b|mir-128-2|mir-128b	microRNA 128-2	ncRNA
mm_155755.1	chrX	96167498	96167521	+	1	NA	3' UTR (NM_010833, exon 13 of 13)	3' UTR (NM_010833, exon 13 of 13)	71464	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_128551.1	chr15	55638693	55638712	-	1	NA	TTS (NM_016667)	TTS (NM_016667)	81294	NM_001168250	105837	Mm.390829	NM_134092	ENSMUSG00000022369	Mtbp	AI429604|MDM2BP	Mdm2, transformed 3T3 cell double minute p53 binding protein	protein-coding
mm_156568.1	chrX	151909541	151909562	+	1	NA	exon (NM_021523, exon 56 of 83)	exon (NM_021523, exon 56 of 83)	-2795	NR_029732	387253		NR_029732	ENSMUSG00000065602	Mirlet7f-2	Mirlet7f2|Mirnlet7f2|let-7f-2	microRNA let7f-2	ncRNA
mm_116377.1	chr13	40984794	40984797	-	1	NA	Intergenic	Intergenic	-16215	NM_026550	68083	Mm.24789	NM_026550	ENSMUSG00000038683	Pak1ip1	5830431I15Rik|5930415H02Rik|AA419825|AI314040|AW556169|Gdpd1|PIP1	PAK1 interacting protein 1	protein-coding
mm_152097.1	chr19	6909935	6910015	-	1	NA	promoter-TSS (NM_012021)	promoter-TSS (NM_012021)	277	NM_026306	67674	Mm.318804	NM_026306	ENSMUSG00000038812	Trmt112	0610038D11Rik|Trm112p	tRNA methyltransferase 11-2	protein-coding
mm_42904.1	chr5	122501561	122501613	+	1	NA	exon (NM_009722, exon 1 of 21)	exon (NM_009722, exon 1 of 21)	638	NM_001110140	11938	Mm.227583	NM_009722	ENSMUSG00000029467	Atp2a2	9530097L16Rik|D5Wsu150e|SERCA2|SERCA2B|Serca2a|mKIAA4195	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	protein-coding
mm_43810.1	chr5	142904451	142904470	+	1	NA	exon (NM_007393, exon 4 of 6)	exon (NM_007393, exon 4 of 6)	2294	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_24550.1	chr3	93440762	93440764	+	1	NA	Intergenic	Intergenic	-1567	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_93473.1	chr10	111507317	111507338	-	1	NA	exon (NM_009344, exon 1 of 2)	exon (NM_009344, exon 1 of 2)	1041	NM_009344	21664	Mm.3117	NM_009344	ENSMUSG00000020205	Phlda1	DT1P1B11|TDAG51|Tdag	pleckstrin homology like domain, family A, member 1	protein-coding
mm_39093.1	chr4	154872026	154872046	-	1	NA	intron (NM_013783, intron 2 of 23)	intron (NM_013783, intron 2 of 23)	2451	NM_013783	27390	Mm.116944	NM_013783	ENSMUSG00000058183	Mmel1	Mell1|NEP2|NEPII|Nl1|SEP	membrane metallo-endopeptidase-like 1	protein-coding
mm_108833.1	chr12	95779080	95779084	+	1	NA	exon (NM_201518, exon 2 of 2)	exon (NM_201518, exon 2 of 2)	86856	NM_201518	399558	Mm.341948	NM_201518	ENSMUSG00000047414	Flrt2	-	fibronectin leucine rich transmembrane protein 2	protein-coding
mm_96429.1	chr11	67278827	67278850	+	1	NA	5' UTR (NM_177369, exon 3 of 40)	5' UTR (NM_177369, exon 3 of 40)	1714	NM_177369	17885	Mm.340163	NM_177369	ENSMUSG00000055775	Myh8	4832426G23Rik|AI327267|MHCp|MyHC-pn|Myhs-p|Myhsp	myosin, heavy polypeptide 8, skeletal muscle, perinatal	protein-coding
mm_170167.1	chr1	75431561	75431561	+	1	NA	3' UTR (NM_007463, exon 41 of 41)	3' UTR (NM_007463, exon 41 of 41)	-4382	NM_133708	69080	Mm.23951	NM_133708	ENSMUSG00000033021	Gmppa	1810012N01Rik	GDP-mannose pyrophosphorylase A	protein-coding
mm_69309.1	chr7	128412278	128412324	-	1	NA	intron (NM_026418, intron 1 of 4)	intron (NM_026418, intron 1 of 4)	5871	NM_026418	67865	Mm.18635	NM_026418	ENSMUSG00000030844	Rgs10	2310010N19Rik	regulator of G-protein signalling 10	protein-coding
mm_13210.1	chr2	94406764	94406808	+	1	NA	promoter-TSS (NR_027831)	promoter-TSS (NR_027831)	79	NR_027831	66457	Mm.402557	NR_027831		2810002D19Rik	-	RIKEN cDNA 2810002D19 gene	ncRNA
mm_61594.1	chr7	80025934	80025950	+	1	NA	promoter-TSS (NM_175433)	promoter-TSS (NM_175433)	-286	NM_175433	209225	Mm.290925	NM_175433	ENSMUSG00000048897	Zfp710	5430400N05Rik|9830165K13|AI324798|Znf710	zinc finger protein 710	protein-coding
mm_3384.1	chr1	139501693	139501726	+	1	NA	promoter-TSS (NM_031164)	promoter-TSS (NM_031164)	2	NM_031164	14060	Mm.30105	NM_031164	ENSMUSG00000026368	F13b	Cf-13b|Cf13b	coagulation factor XIII, beta subunit	protein-coding
mm_24352.1	chr3	90000837	90000846	+	1	NA	3' UTR (NM_001165983, exon 28 of 28)	3' UTR (NM_001165983, exon 28 of 28)	2081	NR_045749	100503469	Mm.440636	NR_045749	ENSMUSG00000105552	Gm19710	-	predicted gene, 19710	ncRNA
mm_161926.1	chr18	77282112	77282112	+	1	NA	intron (NM_172834, intron 1 of 38)	intron (NM_172834, intron 1 of 38)	154	NM_172834	240411	Mm.380247	NM_172834	ENSMUSG00000032818	Loxhd1	1700096C21Rik|4932417K07|sba	lipoxygenase homology domains 1	protein-coding
mm_85081.1	chr9	91365144	91365153	-	1	NA	5' UTR (NM_009573, exon 1 of 3)	5' UTR (NM_009573, exon 1 of 3)	651	NM_009573	22771	Mm.335350	NM_009573	ENSMUSG00000032368	Zic1	ZIC|ZNF201	zinc finger protein of the cerebellum 1	protein-coding
mm_140426.1	chr17	88000790	88000790	+	1	NA	exon (NM_001081034, exon 13 of 23)	exon (NM_001081034, exon 13 of 23)	25740	NM_010830	17688	Mm.18210	NM_010830	ENSMUSG00000005370	Msh6	AU044881|AW550279|GTBP|Gtmbp	mutS homolog 6	protein-coding
mm_32259.1	chr4	102572818	102572838	+	1	NA	intron (NM_019840, intron 6 of 14)	intron (NM_019840, intron 6 of 14)	2768	NM_001177980	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_163764.1	chr13	120015586	120015602	+	1	NA	Intergenic	Intergenic	36610	NM_001302966	100861753	Mm.165042	NM_001302966	ENSMUSG00000095609	Gm21188	-	predicted gene, 21188	protein-coding
mm_121964.1	chr14	25461123	25461143	-	1	NA	intron (NM_001310666, intron 1 of 23)	intron (NM_001310666, intron 1 of 23)	1948	NM_183208	328365	Mm.227484	NM_183208	ENSMUSG00000007817	Zmiz1	BC065120|E330020C23|ENSMUSG00000072684|Gm10397|I920194n01|Rai17|Zimp10	zinc finger, MIZ-type containing 1	protein-coding
mm_146171.1	chr18	75366644	75366668	+	1	NA	promoter-TSS (NM_001042660)	promoter-TSS (NM_001042660)	-709	NM_001042660	17131	Mm.34407	NM_008543	ENSMUSG00000025880	Smad7	Madh7	SMAD family member 7	protein-coding
mm_154814.1	chrX	13662332	13662343	+	1	NA	5' UTR (NM_175669, exon 2 of 4)	5' UTR (NM_175669, exon 2 of 4)	974	NM_175669	319200	Mm.383294	NM_175669	ENSMUSG00000047678	Gpr82	-	G protein-coupled receptor 82	protein-coding
mm_7406.1	chr1	119053693	119053710	-	1	NA	promoter-TSS (NM_001081125)	promoter-TSS (NM_001081125)	-82	NM_001081125	14633	Mm.273292	NM_001081125	ENSMUSG00000048402	Gli2	-	GLI-Kruppel family member GLI2	protein-coding
mm_10661.1	chr2	20737307	20737321	+	1	NA	intron (NM_029895, intron 6 of 18)	intron (NM_029895, intron 6 of 18)	217801	NM_001177631	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding
mm_136298.1	chr16	91533594	91533609	-	1	NA	Intergenic	Intergenic	-13493	NM_008338	15980	Mm.249364	NM_008338	ENSMUSG00000022965	Ifngr2	Ifgr2|Ifgt	interferon gamma receptor 2	protein-coding
mm_42011.1	chr5	108066370	108066391	+	1	NA	intron (NM_001253880, intron 1 of 12)	intron (NM_001253880, intron 1 of 12)	706	NM_013827	17765	Mm.257149	NM_013827	ENSMUSG00000029267	Mtf2	9230112N11Rik|AA537621|C76717|M96|Pcl2	metal response element binding transcription factor 2	protein-coding
mm_74282.1	chr8	125584648	125584655	+	1	NA	promoter-TSS (NR_015535)	promoter-TSS (NR_015535)	13	NR_015535	75930	Mm.195663	NR_015535	ENSMUSG00000110629	4930567H12Rik	4930579P07Rik	RIKEN cDNA 4930567H12 gene	ncRNA
mm_151337.1	chr19	55895146	55895154	+	1	NA	promoter-TSS (NM_001142924)	promoter-TSS (NM_001142924)	-171	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_114895.1	chr13	94390690	94390701	+	1	NA	intron (NM_009680, intron 1 of 26)	intron (NM_009680, intron 1 of 26)	31735	NM_009680	11774	Mm.21185	NM_009680	ENSMUSG00000021686	Ap3b1	AP-3|AU015684|C78395|Hps2|beta3A|pe|pearl|rim2	adaptor-related protein complex 3, beta 1 subunit	protein-coding
mm_172273.1	chr6	85106437	85106446	+	1	NA	Intergenic	MYSERV16_I-int|LTR|ERVK	19653	NM_001034902	545861	Mm.321419	NM_001034902	ENSMUSG00000072952	Gm5878	EG545861	predicted gene 5878	protein-coding
mm_49018.1	chr6	4758900	4758906	+	1	NA	3' UTR (NM_130877, exon 2 of 2)	3' UTR (NM_130877, exon 2 of 2)	11597	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_99566.1	chr11	103810224	103810233	+	1	NA	intron (NM_009521, intron 2 of 4)	CpG	36053	NM_009521	22415	Mm.159091	NM_009521	ENSMUSG00000000125	Wnt3	Int-4|Wnt-3	wingless-type MMTV integration site family, member 3	protein-coding
mm_19904.1	chr2	114150505	114150514	-	1	NA	promoter-TSS (NR_105968)	promoter-TSS (NR_105968)	61	NR_105968	102465982		NR_105968	ENSMUSG00000098464	Mir7002	Gm27429|mmu-mir-7002	microRNA 7002	ncRNA
mm_52998.1	chr6	123268229	123268243	+	1	NA	intron (NM_001163161, intron 4 of 5)	MTD|LTR|ERVL-MaLR	6129	NM_010819	17474	Mm.441101	NM_010819	ENSMUSG00000030144	Clec4d	Clecsf8|Mpcl|mcl	C-type lectin domain family 4, member d	protein-coding
mm_82015.1	chr9	121719404	121719471	+	1	NA	intron (NM_010918, intron 1 of 16)	CpG	256	NM_010918	18087	Mm.32842	NM_010918	ENSMUSG00000032525	Nktr	5330401F18Rik|D9Wsu172e	natural killer tumor recognition sequence	protein-coding
mm_146068.1	chr18	70472560	70472575	+	1	NA	promoter-TSS (NM_001289649)	promoter-TSS (NM_001289649)	-5	NM_001289648	170461	Mm.83623	NM_029019	ENSMUSG00000079608	Stard6	1700011K09Rik|4833424I06Rik|4933429L05Rik|AI644424	StAR-related lipid transfer (START) domain containing 6	protein-coding
mm_122302.1	chr14	34674256	34674286	-	1	NA	5' UTR (NM_001301330, exon 1 of 19)	5' UTR (NM_001301330, exon 1 of 19)	343	NM_001301330	218914	Mm.27957	NM_001004436	ENSMUSG00000041408	Wapl	A530089A20Rik|BC037674|DIF-2|FOE|Wapal	WAPL cohesin release factor	protein-coding
mm_62995.1	chr7	120677580	120677630	+	1	NA	promoter-TSS (NM_001164580)	promoter-TSS (NM_001164580)	-15	NM_001164580	233812	Mm.276479	NM_001164580	ENSMUSG00000046096	BC030336	-	cDNA sequence BC030336	protein-coding
mm_171040.1	chr2	9676686	9676686	+	1	NA	Intergenic	L1Md_F2|LINE|L1	201914	NM_008091	14462	Mm.313866	NM_008091	ENSMUSG00000015619	Gata3	Gata-3|jal	GATA binding protein 3	protein-coding
mm_136355.1	chr16	92739499	92739499	-	1	NA	intron (NM_001111022, intron 2 of 6)	intron (NM_001111022, intron 2 of 6)	-42170	NM_009821	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_167617.1	chr9	57261875	57261893	-	1	NA	intron (NM_028820, intron 1 of 2)	CpG	715	NM_028820	74211	Mm.428905	NM_028820	ENSMUSG00000032300	1700017B05Rik	AA682102|D9Ertd278e	RIKEN cDNA 1700017B05 gene	protein-coding
mm_64085.1	chr7	140954991	140955014	+	1	NA	exon (NM_030694, exon 2 of 2)	exon (NM_030694, exon 2 of 2)	959	NM_030694	80876	Mm.379266	NM_030694	ENSMUSG00000060591	Ifitm2	DSPA2c|Ifitm3l|fragilis3|mil-3	interferon induced transmembrane protein 2	protein-coding
mm_83046.1	chr9	37489830	37489853	-	1	NA	intron (NM_146222, intron 1 of 3)	CpG	520	NM_146222	235184	Mm.127892	NM_146222	ENSMUSG00000042138	Msantd2	2810450G17Rik|9530092B10Rik	Myb/SANT-like DNA-binding domain containing 2	protein-coding
mm_172395.1	chr7	140955936	140955939	-	1	NA	promoter-TSS (NM_030694)	promoter-TSS (NM_030694)	24	NM_030694	80876	Mm.379266	NM_030694	ENSMUSG00000060591	Ifitm2	DSPA2c|Ifitm3l|fragilis3|mil-3	interferon induced transmembrane protein 2	protein-coding
mm_153998.1	chr19	50713636	50713649	-	1	NA	Intergenic	Intergenic	-34996	NM_001290356	58178	Mm.313672	NM_021377	ENSMUSG00000043531	Sorcs1	Sorcs|mSorCS	sortilin-related VPS10 domain containing receptor 1	protein-coding
mm_79511.1	chr9	57504567	57504596	+	1	NA	exon (NM_133982, exon 1 of 1)	exon (NM_133982, exon 1 of 1)	479	NM_133982	102614	Mm.274421	NM_133982	ENSMUSG00000062309	Rpp25	AI851155	ribonuclease P/MRP 25 subunit	protein-coding
mm_77742.1	chr8	126971063	126971076	-	1	NA	promoter-TSS (NM_172762)	promoter-TSS (NM_172762)	10	NM_172762	52202	Mm.28199	NM_172762	ENSMUSG00000033931	Rbm34	4930547K05Rik|6330444B11|D8Ertd233e	RNA binding motif protein 34	protein-coding
mm_16769.1	chr2	9879538	9879549	-	1	NA	promoter-TSS (NM_008091)	promoter-TSS (NM_008091)	-943	NM_008091	14462	Mm.313866	NM_008091	ENSMUSG00000015619	Gata3	Gata-3|jal	GATA binding protein 3	protein-coding
mm_149292.1	chr19	10688725	10688740	+	1	NA	promoter-TSS (NM_181403)	promoter-TSS (NM_181403)	-83	NM_181403	107305	Mm.19091	NM_181403	ENSMUSG00000048832	Vps37c	5730409F24Rik|AU042646	vacuolar protein sorting 37C	protein-coding
mm_3805.1	chr1	158362181	158362192	+	1	NA	promoter-TSS (NM_001205204)	promoter-TSS (NM_001205204)	-118	NM_007495	11899	Mm.329586	NM_007495	ENSMUSG00000026587	Astn1	Astn|GC14|mKIAA0289	astrotactin 1	protein-coding
mm_7459.1	chr1	120447478	120447482	-	1	NA	Intergenic	Intergenic	57604	NM_010766	17167	Mm.1856	NM_010766	ENSMUSG00000026390	Marco	AI323439|Ly112|Scara2	macrophage receptor with collagenous structure	protein-coding
mm_119309.1	chr14	35247421	35247427	+	1	NA	intron (NM_008166, intron 4 of 15)	intron (NM_008166, intron 4 of 15)	352815	NR_029774	723847		NR_029774	ENSMUSG00000065481	Mir346	Mirn346|mir-346|mmu-mir-346	microRNA 346	ncRNA
mm_136063.1	chr16	84704899	84704912	-	1	NA	Intergenic	Intergenic	-8118	NR_132106	100653389	Mm.261808	NR_132106	ENSMUSG00000097418	Mir155hg	Bic|Gm26667	Mir155 host gene (non-protein coding)	ncRNA
mm_111359.1	chr12	86990570	86990588	-	1	NA	Intergenic	Intergenic	-1903	NM_001080943	238331	Mm.185890	NM_001080943	ENSMUSG00000048483	Zdhhc22	Gm262	zinc finger, DHHC-type containing 22	protein-coding
mm_25664.1	chr3	121734621	121734628	+	1	NA	3' UTR (NM_010171, exon 6 of 6)	3' UTR (NM_010171, exon 6 of 6)	11087	NM_010171	14066	Mm.273188	NM_010171	ENSMUSG00000028128	F3	AA409063|CD142|Cf-3|Cf3|TF	coagulation factor III	protein-coding
mm_75249.1	chr8	40307898	40307936	-	1	NA	promoter-TSS (NR_106126)	promoter-TSS (NR_106126)	12	NR_106126	102466237		NR_106126	ENSMUSG00000098431	Mir7666	Gm27915|mmu-mir-7666	microRNA 7666	ncRNA
mm_137298.1	chr17	24840109	24840123	+	1	NA	TTS (NM_029197)	TTS (NM_029197)	10186	NM_023480	68636	Mm.347964	NM_023480	ENSMUSG00000045316	Fahd1	1110025H10Rik|AV002085	fumarylacetoacetate hydrolase domain containing 1	protein-coding
mm_22895.1	chr3	30793082	30793098	+	1	NA	5' UTR (NM_027016, exon 1 of 8)	5' UTR (NM_027016, exon 1 of 8)	214	NM_027016	69276	Mm.26017	NM_027016	ENSMUSG00000027706	Sec62	3100002M17Rik|AI844545|AW545092|Dtrp1|HTP1|Tloc1	SEC62 homolog (S. cerevisiae)	protein-coding
mm_152334.1	chr19	9977746	9977752	-	1	NA	Intergenic	Intergenic	-2851	NR_073181	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
mm_4413.1	chr1	172499859	172499869	+	1	NA	promoter-TSS (NM_178598)	promoter-TSS (NM_178598)	-382	NM_178598	21346	Mm.271711	NM_178598	ENSMUSG00000026547	Tagln2	2700094C18Rik|SM22beta|Sm22B|Sm22a	transgelin 2	protein-coding
mm_150053.1	chr19	29381317	29381350	+	1	NA	intron (NM_021893, intron 4 of 6)	intron (NM_021893, intron 4 of 6)	13895	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_37219.1	chr4	117915037	117915054	-	1	NA	promoter-TSS (NM_146152)	promoter-TSS (NM_146152)	-46	NM_146152	230673	Mm.287810	NM_146152	ENSMUSG00000033365	Ipo13	Imp13|Kap13|Ranbp13	importin 13	protein-coding
mm_74596.1	chr8	11635053	11635079	-	1	NA	promoter-TSS (NR_030781)	promoter-TSS (NR_030781)	-30	NR_030781	102334	Mm.12459	NM_133971	ENSMUSG00000031508	Ankrd10	4833425P12Rik|AW549277	ankyrin repeat domain 10	protein-coding
mm_152207.1	chr19	7711264	7711313	-	1	NA	promoter-TSS (NM_144785)	promoter-TSS (NM_144785)	22	NM_144785	207151	Mm.21365	NM_144785	ENSMUSG00000024757	Slc22a19	D630043A20Rik|OAT-5|Oat5|Slc22a9	solute carrier family 22 (organic anion transporter), member 19	protein-coding
mm_102311.1	chr11	55608630	55608663	-	1	NA	promoter-TSS (NM_020492)	promoter-TSS (NM_020492)	-448	NM_020492	14654	Mm.89320	NM_020492	ENSMUSG00000000263	Glra1	nmf11|oscillator|ot|spasmodic|spd	glycine receptor, alpha 1 subunit	protein-coding
mm_66201.1	chr7	34230427	34230450	-	1	NA	promoter-TSS (NM_008155)	promoter-TSS (NM_008155)	-102	NM_008155	14751	Mm.589	NM_008155	ENSMUSG00000036427	Gpi1	Amf|Gpi|Gpi-1|Gpi-1r|Gpi-1s|Gpi-1t|Gpi1-r|Gpi1-s|Gpi1-t|Gpi1s|MF|NK|NK/GPI|Nlk|Org|Pgi|Phi	glucose phosphate isomerase 1	protein-coding
mm_154394.1	chrM	13315	13335	+	1	NA	NA	Intergenic	NA	NA								
mm_32904.1	chr4	119108737	119108758	+	1	NA	promoter-TSS (NM_011400)	promoter-TSS (NM_011400)	2	NM_011400	20525	Mm.21002	NM_011400	ENSMUSG00000028645	Slc2a1	Glut-1|Glut1	solute carrier family 2 (facilitated glucose transporter), member 1	protein-coding
mm_117848.1	chr13	98694894	98694905	-	1	NA	promoter-TSS (NM_001025606)	promoter-TSS (NM_001025606)	-68	NM_001025606	380863	Mm.28264	NM_001025606	ENSMUSG00000052485	Tmem171	Gm905	transmembrane protein 171	protein-coding
mm_67365.1	chr7	79839228	79839254	-	1	NA	exon (NM_008486, exon 5 of 20)	exon (NM_008486, exon 5 of 20)	3111	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_20725.1	chr2	136387995	136388005	-	1	NA	promoter-TSS (NM_172858)	promoter-TSS (NM_172858)	-33	NM_172858	241656	Mm.131572	NM_172858	ENSMUSG00000039913	Pak7	2900083L08Rik|6430627N20|Pak5	p21 protein (Cdc42/Rac)-activated kinase 7	protein-coding
mm_74911.1	chr8	25256401	25256423	-	1	NA	Intergenic	Intergenic	49858	NR_040352	74489	Mm.256468	NR_040352	ENSMUSG00000110140	5430421F17Rik	-	RIKEN cDNA 5430421F17 gene	ncRNA
mm_117316.1	chr13	67637731	67637737	-	1	NA	promoter-TSS (NM_183146)	promoter-TSS (NM_183146)	19	NM_183146	212281	Mm.342918	NM_183146	ENSMUSG00000021510	Zfp729a	A530054K11Rik|Rslcan3	zinc finger protein 729a	protein-coding
mm_91478.1	chr10	34233560	34233573	-	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	-26015	NM_172508	212898	Mm.34557	NM_172508	ENSMUSG00000039497	Dse	6030499O08|AI480506|B130024B19Rik|DS-epi1|Sart2	dermatan sulfate epimerase	protein-coding
mm_145633.1	chr18	61111946	61111983	+	1	NA	exon (NM_001037859, exon 5 of 22)	exon (NM_001037859, exon 5 of 22)	-5504	NR_105949	102466212		NR_105949	ENSMUSG00000098389	Mir6983	Gm27496|mmu-mir-6983	microRNA 6983	ncRNA
mm_31633.1	chr4	59337989	59338007	+	1	NA	intron (NM_001163288, intron 12 of 16)	intron (NM_001163288, intron 12 of 16)	77947	NR_105031	101055769	Mm.421401	NR_105031		Gm12596	OTTMUSG00000007649	predicted gene 12596	ncRNA
mm_157451.1	chrX	42149348	42149352	-	1	NA	promoter-TSS (NM_001077712)	promoter-TSS (NM_001077712)	-62	NM_001077712	20843	Mm.290422	NM_021465	ENSMUSG00000025862	Stag2	9230105L23Rik|B230112I07Rik|SA-2|SAP2	stromal antigen 2	protein-coding
mm_62788.1	chr7	112679328	112679373	+	1	NA	promoter-TSS (NM_001166584)	promoter-TSS (NM_001166584)	30	NM_009346	21676	Mm.24685	NM_009346	ENSMUSG00000055320	Tead1	2610024B07Rik|B230114H05Rik|Gtrgeo5|TEAD-1|TEF-1|Tcf13|mTEF-1	TEA domain family member 1	protein-coding
mm_170823.1	chr2	176670562	176670568	+	1	NA	promoter-TSS (NM_001242943).2	promoter-TSS (NM_001242943).2	43	NM_001242943	545490	Mm.484023	NM_001242943	ENSMUSG00000078879	Zfp973	6230416C02Rik|Gm14306|Gm14436|OTTMUSG00000016614	zinc finger protein 973	protein-coding
mm_6299.1	chr1	71102902	71102979	-	1	NA	promoter-TSS (NM_007525)	promoter-TSS (NM_007525)	32	NM_007525	12021	Mm.10764	NM_007525	ENSMUSG00000026196	Bard1	ENSMUSG00000060893|ENSMUSG00000073653	BRCA1 associated RING domain 1	protein-coding
mm_67696.1	chr7	89518154	89518209	-	1	NA	promoter-TSS (NM_029614)	promoter-TSS (NM_029614)	-595	NM_029614	76453	Mm.250438	NM_029614	ENSMUSG00000039405	Prss23	2310046G15Rik|4930479H08Rik|AI790574|Spuve	protease, serine 23	protein-coding
mm_60508.1	chr7	44479548	44479585	+	1	NA	Intergenic	L1MC4|LINE|L1	-4951	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_95661.1	chr11	53771373	53771388	+	1	NA	intron (NM_001159393, intron 2 of 9)	intron (NM_001159393, intron 2 of 9)	907	NM_001159396	16362	Mm.105218	NM_008390	ENSMUSG00000018899	Irf1	AU020929|Irf-1	interferon regulatory factor 1	protein-coding
mm_9113.1	chr1	170174817	170174827	-	1	NA	5' UTR (NM_133806, exon 1 of 11)	5' UTR (NM_133806, exon 1 of 11)	142	NM_001305046	107652	Mm.27969	NM_133806	ENSMUSG00000026670	Uap1	AA420407|AA437972|AGX-1|AGX-2|AGX1|AgX|ESTM38|SPAG2	UDP-N-acetylglucosamine pyrophosphorylase 1	protein-coding
mm_50900.1	chr6	57581126	57581138	+	1	NA	exon (NM_025992, exon 1 of 23)	exon (NM_025992, exon 1 of 23)	140	NM_025992	67138	Mm.297393	NM_025992	ENSMUSG00000029798	Herc6	1700121D12Rik|2510038N07Rik|4930427L17Rik|AI451296|CEB1|Herc5	hect domain and RLD 6	protein-coding
mm_167884.1	chrX	53039861	53039872	+	1	NA	Intergenic	HAL1M8|LINE|L1	8212	NR_030498	751532		NR_030498	ENSMUSG00000076050	Mir450b	Mirn450b|mir-450b	microRNA 450b	ncRNA
mm_153951.1	chr19	47681488	47681498	-	1	NA	exon (NM_007732, exon 5 of 53)	exon (NM_007732, exon 5 of 53)	10549	NM_007732	12821	Mm.1225	NM_007732	ENSMUSG00000025064	Col17a1	BP180|Bpag|Bpag2	collagen, type XVII, alpha 1	protein-coding
mm_88503.1	chr10	77861952	77861956	+	1	NA	promoter-TSS (NM_001101631)	promoter-TSS (NM_001101631)	-21	NM_001101631	100041351	Mm.441672	NM_001101631		Gm3285	-	predicted gene 3285	protein-coding
mm_22599.1	chr3	14480693	14480707	+	1	NA	promoter-TSS (NM_080852)	promoter-TSS (NM_080852)	1	NM_080852	140918	Mm.215250	NM_080852	ENSMUSG00000039710	Slc7a12	Asc-2|XAT1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 12	protein-coding
mm_134610.1	chr16	20730545	20730592	-	1	NA	promoter-TSS (NM_001289896)	promoter-TSS (NM_001289896)	30	NM_001289896	21832	Mm.3943	NM_009379	ENSMUSG00000022847	Thpo	Mgdf|Ml|Mpllg|Tpo	thrombopoietin	protein-coding
mm_72006.1	chr8	70698932	70698945	+	1	NA	5' UTR (NM_001286944, exon 1 of 1)	5' UTR (NM_001286944, exon 1 of 1)	1199	NM_001286944	16478	Mm.419851	NM_010592	ENSMUSG00000071076	Jund	Jund1	jun D proto-oncogene	protein-coding
mm_172059.1	chr6	132521499	132521508	-	1	NA	Intergenic	ERVB7_1-LTR_MM|LTR|ERVK	-48339	NM_011174	19131	Mm.425348	NM_011174	ENSMUSG00000059934	Prh1	MP2|Prp	proline rich protein HaeIII subfamily 1	protein-coding
mm_87024.1	chr10	28185334	28185337	+	1	NA	intron (NM_008983, intron 1 of 31)	intron (NM_008983, intron 1 of 31)	110515	NM_008983	19272	Mm.332303	NM_008983	ENSMUSG00000019889	Ptprk	AI853699|PTPk|RPTPkappa	protein tyrosine phosphatase, receptor type, K	protein-coding
mm_142939.1	chr17	56017441	56017458	-	1	NA	TTS (NM_026530)	TTS (NM_026530)	8248	NM_026530	68047	Mm.358710	NM_026530	ENSMUSG00000003199	Mpnd	E130307M08Rik	MPN domain containing	protein-coding
mm_105403.1	chr11	103443842	103443853	-	1	NA	Intergenic	RLTR16B_MM|LTR|ERVK	-31183	NM_183034	353047	Mm.18556	NM_183034	ENSMUSG00000034247	Plekhm1	AP162|B2|BC038943|D330036J23Rik	pleckstrin homology domain containing, family M (with RUN domain) member 1	protein-coding
mm_141795.1	chr17	34343698	34343750	-	1	NA	exon (NM_010381, exon 2 of 4)	exon (NM_010381, exon 2 of 4)	921	NM_010381	100504404	Mm.15680	NM_010381		H2-Ea-ps	AI323765|E-alpha-f|H-2Ea|H2-Ea|I-Ealpha|Ia-3|Ia3|MHC-H2-Ea	histocompatibility 2, class II antigen E alpha, pseudogene	protein-coding
mm_53996.1	chr6	6882077	6882092	-	1	NA	promoter-TSS (NM_010056)	promoter-TSS (NM_010056)	-16	NM_010056	13395	Mm.4873	NM_010056	ENSMUSG00000029755	Dlx5	AI385752	distal-less homeobox 5	protein-coding
mm_8454.1	chr1	153130083	153130092	-	1	NA	exon (NM_008485, exon 20 of 24)	exon (NM_008485, exon 20 of 24)	56360	NM_008485	16782	Mm.329272	NM_008485	ENSMUSG00000026479	Lamc2	AA589349	laminin, gamma 2	protein-coding
mm_4190.1	chr1	171214014	171214045	+	1	NA	promoter-TSS (NM_001243062)	promoter-TSS (NM_001243062)	59	NM_001243063	12355	Mm.486506	NM_009803	ENSMUSG00000005677	Nr1i3	AA209988|AI551208|CAR|CAR-beta|Care2|ESTM32|MB67	nuclear receptor subfamily 1, group I, member 3	protein-coding
mm_54875.1	chr6	42645029	42645073	-	1	NA	promoter-TSS (NM_146174)	promoter-TSS (NM_146174)	-10	NM_146174	232748	Mm.279659	NM_146174	ENSMUSG00000029851	Tcaf2	Fam115c	TRPM8 channel-associated factor 2	protein-coding
mm_104054.1	chr11	86484313	86484350	-	1	NA	promoter-TSS (NM_029788)	promoter-TSS (NM_029788)	-326	NM_029788	76892	Mm.262707	NM_029788	ENSMUSG00000020521	Rnft1	0610013E23Rik|AV007605	ring finger protein, transmembrane 1	protein-coding
mm_25273.1	chr3	104908597	104908605	+	1	NA	intron (NM_001253702, intron 11 of 13)	intron (NM_001253702, intron 11 of 13)	44095	NM_153091	229681	Mm.206379	NM_153091	ENSMUSG00000045576	St7l	St7r	suppression of tumorigenicity 7-like	protein-coding
mm_114532.1	chr13	73604136	73604146	+	1	NA	5' UTR (NM_146047, exon 1 of 17)	5' UTR (NM_146047, exon 1 of 17)	139	NM_146047	218335	Mm.30099	NM_146047	ENSMUSG00000021610	Clptm1l	C130052I12Rik|Crr9	CLPTM1-like	protein-coding
mm_63135.1	chr7	123031347	123031392	+	1	NA	Intergenic	Intergenic	60805	NM_175023	19647	Mm.4480	NM_011247	ENSMUSG00000030779	Rbbp6	4933422O15Rik|AI316869|BB233631|C030034J04Rik|C77662|P2P-R|PACT	retinoblastoma binding protein 6	protein-coding
mm_124158.1	chr14	93472025	93472037	-	1	NA	intron (NM_001271798, intron 2 of 3)	intron (NM_001271798, intron 2 of 3)	416857	NM_001271800	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding
mm_101225.1	chr11	20202465	20202483	-	1	NA	intron (NM_008996, intron 1 of 5)	intron (NM_008996, intron 1 of 5)	872	NM_008996	19324	Mm.271944	NM_008996	ENSMUSG00000020149	Rab1a	Gtbp|Rab-1|Rab1|Ypt1|mKIAA3012	RAB1A, member RAS oncogene family	protein-coding
mm_12156.1	chr2	62046581	62046593	+	1	NA	promoter-TSS (NM_001242379)	promoter-TSS (NM_001242379)	72	NM_033552	94229	Mm.314497	NM_033552	ENSMUSG00000026904	Slc4a10	NCBE|mKIAA4136	solute carrier family 4, sodium bicarbonate cotransporter-like, member 10	protein-coding
mm_122356.1	chr14	39001721	39001756	-	1	NA	intron (NM_001190187, intron 2 of 9)	intron (NM_001190187, intron 2 of 9)	103436	NR_045713	75170	Mm.372967	NR_045713	ENSMUSG00000093528	Nrg3os	4930529F24Rik	neuregulin 3, opposite strand	ncRNA
mm_157006.1	chrX	7595053	7595064	-	1	NA	3' UTR (NM_054039, exon 13 of 13)	3' UTR (NM_054039, exon 13 of 13)	10362	NM_138603	54638	Mm.288192	NM_138603	ENSMUSG00000031143	Ccdc22	AI481216|DXImx40e|Ppp1r3f|Sfc22	coiled-coil domain containing 22	protein-coding
mm_149838.1	chr19	24999501	24999555	+	1	NA	promoter-TSS (NM_028785)	promoter-TSS (NM_028785)	-1	NM_028785	76088	Mm.102485	NM_028785	ENSMUSG00000052085	Dock8	1200017A24Rik|5830472H07Rik|A130095G14Rik|AI461977	dedicator of cytokinesis 8	protein-coding
mm_46770.1	chr5	112276357	112276368	-	1	NA	promoter-TSS (NM_009419)	promoter-TSS (NM_009419)	-329	NM_001326590	22022	Mm.250631	NM_009419	ENSMUSG00000029344	Tpst2	AI448750|D5Ucla3|Tango13b|grm|grt	protein-tyrosine sulfotransferase 2	protein-coding
mm_49872.1	chr6	38567528	38567531	+	1	NA	intron (NM_001331223, intron 3 of 12)	intron (NM_001331223, intron 3 of 12)	11806	NM_001331223	192196	Mm.276133	NM_138680	ENSMUSG00000029823	Luc7l2	4930471C18Rik|AA522013|AU015269|CGI59|Cgi74	LUC7-like 2 (S. cerevisiae)	protein-coding
mm_100667.1	chr11	3332278	3332301	-	1	NA	intron (NM_178149, intron 3 of 5)	CpG-1656	1558	NM_178149	216505	Mm.390323	NM_178149	ENSMUSG00000034614	Pik3ip1	1500004A08Rik|5830455E04Rik|Crkd|Hgfl	phosphoinositide-3-kinase interacting protein 1	protein-coding
mm_91583.1	chr10	40227836	40227848	-	1	NA	intron (NM_001042556, intron 7 of 9)	intron (NM_001042556, intron 7 of 9)	19137	NM_001042556	67239	Mm.11480	NM_023323	ENSMUSG00000038510	Rpf2	2810470K21Rik|AU040229|AU043242|Bxdc1	ribosome production factor 2 homolog	protein-coding
mm_38115.1	chr4	134535383	134535391	-	1	NA	promoter-TSS (NM_001256112)	promoter-TSS (NM_001256112)	0	NM_029759	76824	Mm.30153	NM_029759	ENSMUSG00000046671	Mtfr1l	2410166I05Rik|AI480750|Fam54b	mitochondrial fission regulator 1-like	protein-coding
mm_108933.1	chr12	101169768	101169810	+	1	NA	Intergenic	Intergenic	24180	NR_033653	74947	Mm.488905	NR_033653	ENSMUSG00000092054	Kif4-ps	4930463M05Rik|Kif4b	kinesin family member 4, pseudogene	pseudo
mm_94751.1	chr11	21116854	21116865	+	1	NA	intron (NM_023324, intron 1 of 6)	intron (NM_023324, intron 1 of 6)	25535	NM_023324	67245	Mm.28957	NM_023324	ENSMUSG00000020134	Peli1	2810468L03Rik|A930031K15Rik|AA409794|AI586297|D11Ertd676e	pellino 1	protein-coding
mm_126356.1	chr15	79935958	79935972	+	1	NA	Intergenic	Intergenic	-3319	NM_144811	52609	Mm.323442	NM_144811	ENSMUSG00000053411	Cbx7	1600014J01Rik|AI851678|D15Ertd417e	chromobox 7	protein-coding
mm_38895.1	chr4	149850215	149850217	-	1	NA	Intergenic	ID_B1|SINE|B4	-75949	NM_027460	70556	Mm.41877	NM_027460	ENSMUSG00000028982	Slc25a33	5730438N18Rik|Pnc1	solute carrier family 25, member 33	protein-coding
mm_110276.1	chr12	32057558	32057603	-	1	NA	intron (NM_011158, intron 1 of 10)	intron (NM_011158, intron 1 of 10)	3699	NM_011158	19088	Mm.25594	NM_011158	ENSMUSG00000002997	Prkar2b	AI451071|AW061005|PKARIIbeta|Pkarb2|RII(beta)	protein kinase, cAMP dependent regulatory, type II beta	protein-coding
mm_17045.1	chr2	20943390	20943412	-	1	NA	intron (NM_001128084, intron 1 of 24)	intron (NM_001128084, intron 1 of 24)	24320	NM_001081364	71435	Mm.28507	NM_001081364	ENSMUSG00000036591	Arhgap21	5530401C11Rik|AA416458|ARHGAP10	Rho GTPase activating protein 21	protein-coding
mm_997.1	chr1	58713321	58713332	+	1	NA	promoter-TSS (NM_207653)	promoter-TSS (NM_207653)	40	NM_207653	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_30939.1	chr4	33031528	33031556	+	1	NA	promoter-TSS (NR_036602)	promoter-TSS (NR_036602)	117	NM_019586	56228	Mm.259095	NM_019586	ENSMUSG00000028277	Ube2j1	0710008M05Rik|1110030I22Rik|NCUBE-1|Ncube|Ncube1|Ubc6p	ubiquitin-conjugating enzyme E2J 1	protein-coding
mm_45783.1	chr5	87336677	87336686	-	1	NA	exon (NM_028094, exon 1 of 6)	exon (NM_028094, exon 1 of 6)	514	NM_028094	72094	Mm.482739	NM_028094	ENSMUSG00000035780	Ugt2a3	2010321J07Rik	UDP glucuronosyltransferase 2 family, polypeptide A3	protein-coding
mm_53249.1	chr6	127582124	127582186	+	1	NA	intron (NM_001033464, intron 1 of 6)	intron (NM_001033464, intron 1 of 6)	4180	NM_001033464	381812	Mm.296093	NM_001033464	ENSMUSG00000061414	Cracr2a	Efcab4b|Gm1073|Gm462	calcium release activated channel regulator 2A	protein-coding
mm_107323.1	chr12	31438210	31438227	+	1	NA	promoter-TSS (NM_021353)	promoter-TSS (NM_021353)	-1	NM_021353	13487	Mm.490454	NM_021353	ENSMUSG00000001225	Slc26a3	9030623B18Rik|9130013M11Rik|AV376035|Dra	solute carrier family 26, member 3	protein-coding
mm_17182.1	chr2	25365640	25365668	-	1	NA	promoter-TSS (NM_001033293)	promoter-TSS (NM_001033293)	-28	NM_001033293	227620	Mm.33797	NM_001033293	ENSMUSG00000026956	Uap1l1	5730445F03Rik	UDP-N-acteylglucosamine pyrophosphorylase 1-like 1	protein-coding
mm_81357.1	chr9	108662085	108662093	+	1	NA	promoter-TSS (NM_020520)	promoter-TSS (NM_020520)	-9	NM_020520	57279	Mm.29666	NM_020520	ENSMUSG00000032602	Slc25a20	1110007P09Rik|C78826|Cact|mCAC	solute carrier family 25 (mitochondrial carnitine/acylcarnitine translocase), member 20	protein-coding
mm_67658.1	chr7	85379728	85379732	-	1	NA	Intergenic	Intergenic	35946	NM_001105182	330581	Mm.469909	NM_001105182	ENSMUSG00000091006	Vmn2r69	-	vomeronasal 2, receptor 69	protein-coding
mm_123828.1	chr14	70627009	70627070	-	1	NA	promoter-TSS (NM_001252663)	promoter-TSS (NM_001252663)	26	NM_001252662	13829	Mm.210863	NM_013514	ENSMUSG00000022099	Dmtn	AI325486|Epb4.9|Epb49|dematin	dematin actin binding protein	protein-coding
mm_140687.1	chr17	13674731	13674742	-	1	NA	Intergenic	Intergenic	-85805	NM_010806	17356	Mm.59167	NM_010806	ENSMUSG00000068036	Afdn	5033403D15Rik|AF6|Af-6|Afadin|Gm314|I-afadin|Mllt4|S-afadin	afadin, adherens junction formation factor	protein-coding
mm_102547.1	chr11	61342795	61342803	-	1	NA	promoter-TSS (NM_001033542)	promoter-TSS (NM_001033542)	61	NM_001033542	380701	Mm.340166	NM_001033542	ENSMUSG00000069855	Slc47a2	4933429E10Rik	solute carrier family 47, member 2	protein-coding
mm_97945.1	chr11	83663572	83663579	+	1	NA	intron (NM_013652, intron 2 of 2)	intron (NM_013652, intron 2 of 2)	991	NM_013652	20303	Mm.244263	NM_013652	ENSMUSG00000018930	Ccl4	AT744.1|Act-2|MIP-1B|Mip1b|Scya4	chemokine (C-C motif) ligand 4	protein-coding
mm_80240.1	chr9	72719148	72719151	+	1	NA	intron (NM_010890, intron 10 of 28)	intron (NM_010890, intron 10 of 28)	56802	NM_010890	17999	Mm.279923	NM_010890	ENSMUSG00000032216	Nedd4	AA959633|AL023035|AU019897|E430025J12Rik|Nedd4-1|Nedd4a|mKIAA0093	neural precursor cell expressed, developmentally down-regulated 4	protein-coding
mm_78686.1	chr9	40800089	40800106	+	1	NA	Intergenic	Intergenic	-1176	NM_031165	15481	Mm.290774	NM_031165	ENSMUSG00000015656	Hspa8	2410008N15Rik|Hsc70|Hsc71|Hsc73|Hsp73|Hspa10	heat shock protein 8	protein-coding
mm_93387.1	chr10	106192800	106192801	-	1	NA	Intergenic	Intergenic	-277510	NM_177373	327814	Mm.391424	NM_177373	ENSMUSG00000053825	Ppfia2	5330438O12|B230207K17Rik|E130120L08Rik|mKIAA4112	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 2	protein-coding
mm_142631.1	chr17	47400617	47400619	-	1	NA	promoter-TSS (NM_008189)	promoter-TSS (NM_008189)	-12	NM_008189	14913	Mm.16224	NM_008189	ENSMUSG00000023982	Guca1a	GC-A|Gcap1|Guca1|mGCAP1	guanylate cyclase activator 1a (retina)	protein-coding
mm_37106.1	chr4	116638464	116638477	-	1	NA	intron (NM_021473, intron 6 of 8)	PB1D9|SINE|Alu	-10519	NM_016777	50927	Mm.257181	NM_016777	ENSMUSG00000028693	Nasp	5033430J04Rik|AI131596|AI317140|D4Ertd767e|Epcs32|Nasp-T	nuclear autoantigenic sperm protein (histone-binding)	protein-coding
mm_133790.1	chr16	95258263	95258302	+	1	NA	non-coding (NR_073406, exon 2 of 6)	non-coding (NR_073406, exon 2 of 6)	724	NM_001271690	16516	Mm.272239	NM_019664	ENSMUSG00000062609	Kcnj15	4930414N08Rik|AI182284|AI267127|IRKK|Kir4.2	potassium inwardly-rectifying channel, subfamily J, member 15	protein-coding
mm_28662.1	chr3	95251121	95251144	-	1	NA	promoter-TSS (NM_001168356)	promoter-TSS (NM_001168356)	61	NM_001168356	171388	Mm.331209	NM_134253	ENSMUSG00000028115	Bnipl	1700128A13Rik|BNIP-S|BNIPL1|BNIPL2|PP73|PP753	BCL2/adenovirus E1B 19kD interacting protein like	protein-coding
mm_82665.1	chr9	22117124	22117174	-	1	NA	intron (NR_030448, intron 3 of 4)	CpG	-2980	NM_170777	66126	Mm.29801	NM_170777	ENSMUSG00000013822	Elof1	1110011K10Rik	ELF1 homolog, elongation factor 1	protein-coding
mm_18786.1	chr2	73660352	73660397	-	1	NA	promoter-TSS (NM_175752)	promoter-TSS (NM_175752)	49	NM_175752	108699	Mm.257073	NM_029716	ENSMUSG00000056486	Chn1	0610007I19Rik|0710001E19Rik|1700112L09Rik|2900046J01Rik|AI413815|ARHGAP2	chimerin 1	protein-coding
mm_45845.1	chr5	87698062	87698092	-	1	NA	exon (NM_001286023, exon 2 of 7)	exon (NM_001286023, exon 2 of 7)	1348	NM_001286020	12991	Mm.268737	NM_009972	ENSMUSG00000063157	Csn2	Csnb	casein beta	protein-coding
mm_4773.1	chr1	182763962	182764014	+	1	NA	promoter-TSS (NM_144796)	promoter-TSS (NM_144796)	-918	NM_144796	96935	Mm.331052	NM_144796	ENSMUSG00000038576	Susd4	AI848994|E430021N18Rik|N28096	sushi domain containing 4	protein-coding
mm_116902.1	chr13	55426784	55426795	-	1	NA	promoter-TSS (NM_021489)	promoter-TSS (NM_021489)	15	NM_021489	58992	Mm.42224	NM_021489	ENSMUSG00000021492	F12	FXII|HAF	coagulation factor XII (Hageman factor)	protein-coding
mm_22678.1	chr3	16099868	16099875	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-83312	NR_027375	229096	Mm.23834	NM_172677	ENSMUSG00000047213	Ythdf3	9130022A11Rik	YTH domain family 3	protein-coding
mm_136876.1	chr17	13007695	13007704	+	1	NA	promoter-TSS (NM_013671)	promoter-TSS (NM_013671)	-140	NM_013671	20656	Mm.290876	NM_013671	ENSMUSG00000006818	Sod2	MnSOD|Sod-2	superoxide dismutase 2, mitochondrial	protein-coding
mm_169441.1	chr14	56694175	56694185	-	1	NA	intron (NM_023773, intron 11 of 13)	LSU-rRNA_Hsa|rRNA|rRNA	6820	NR_046209	100503823	Mm.474486	NR_046209		Gm16973	-	predicted gene, 16973	ncRNA
mm_86114.1	chr9	115471687	115471706	-	1	NA	Intergenic	ID_B1|SINE|B4	89877	NR_130329	100316675		NR_130329	ENSMUSG00000080409	Mir467h	Mirn467h|mmu-mir-467h	microRNA 467h	ncRNA
mm_49919.1	chr6	39150922	39150932	+	1	NA	intron (NM_001033430, intron 12 of 19)	intron (NM_001033430, intron 12 of 19)	32454	NR_045813	75379	Mm.348014	NR_045813	ENSMUSG00000073144	4930599N23Rik	-	RIKEN cDNA 4930599N23 gene	ncRNA
mm_84522.1	chr9	67043845	67043862	-	1	NA	promoter-TSS (NM_001164256)	promoter-TSS (NM_001164256)	18	NM_001164252	22003	Mm.121878	NM_024427	ENSMUSG00000032366	Tpm1	AA986836|AI854628|TM2|Tm3|Tmpa|Tpm-1|alpha-TM	tropomyosin 1, alpha	protein-coding
mm_77923.1	chr9	7352912	7352918	+	1	NA	exon (NM_008605, exon 5 of 10)	exon (NM_008605, exon 5 of 10)	5541	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_2391.1	chr1	93512089	93512125	+	1	NA	promoter-TSS (NM_145519)	promoter-TSS (NM_145519)	3	NM_145519	227377	Mm.243091	NM_145519	ENSMUSG00000034066	Farp2	AI465173|BC009153|D030026M03Rik|Fir|mKIAA0793	FERM, RhoGEF and pleckstrin domain protein 2	protein-coding
mm_60746.1	chr7	45458175	45458190	+	1	NA	exon (NM_010240, exon 4 of 4)	exon (NM_010240, exon 4 of 4)	1704	NM_010240	14325	Mm.30357	NM_010240	ENSMUSG00000050708	Ftl1	Ftl|Ftl-1|L-ferritin	ferritin light polypeptide 1	protein-coding
mm_4676.1	chr1	180421047	180421063	+	1	NA	intron (NM_001081175, intron 6 of 7)	intron (NM_001081175, intron 6 of 7)	62449	NM_001081227	381310	Mm.44791	NM_001081227	ENSMUSG00000053963	Stum	6330403A02Rik|ENSMUSG00000056615|Gm10001|R75555	mechanosensory transduction mediator	protein-coding
mm_16453.1	chr2	180499894	180499919	+	1	NA	promoter-TSS (NM_018766)	promoter-TSS (NM_018766)	-70	NM_018766	18216	Mm.301712	NM_018766	ENSMUSG00000027568	Ntsr1	NT-1R|NTR-1|NTR1	neurotensin receptor 1	protein-coding
mm_167209.1	chr7	145269038	145269039	+	1	NA	intron (NR_132644, intron 8 of 24)	intron (NR_132644, intron 8 of 24)	14973	NR_132644	233979	Mm.102235	NM_146206	ENSMUSG00000048677	Tpcn2	D830047E22Rik|Gm35086	two pore segment channel 2	protein-coding
mm_86853.1	chr10	21669217	21669226	+	1	NA	Intergenic	Intergenic	-21624	NR_045843	432436	Mm.244553	NM_001004162		Gm5420	EG432436	predicted gene 5420	ncRNA
mm_97972.1	chr11	83853817	83853826	+	1	NA	intron (NM_001291269, intron 1 of 8)	(T)n|Simple_repeat|Simple_repeat	861	NM_001291269	21410	Mm.7226	NM_009330	ENSMUSG00000020679	Hnf1b	HNF-1-beta|HNF-1B|HNF-1Beta|Hnf1beta|LFB3|Tcf-2|Tcf2|vHNF1	HNF1 homeobox B	protein-coding
mm_8392.1	chr1	151345305	151345323	-	1	NA	intron (NM_001039511, intron 1 of 7)	CpG	816	NM_001039511	117198	Mm.33764	NM_028582	ENSMUSG00000023150	Ivns1abp	1190004M08Rik|1700126I16Rik|AA960440|HSPC068|ND1|NS-1|NS1-BP|Nd1-L|Nd1-S|mKIAA0850	influenza virus NS1A binding protein	protein-coding
mm_155721.1	chrX	96115837	96115860	+	1	NA	intron (NM_010833, intron 1 of 12)	intron (NM_010833, intron 1 of 12)	19803	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_166875.1	chr7	25412798	25412802	-	1	NA	promoter-TSS (NM_153576)	promoter-TSS (NM_153576)	86	NM_153576	232983	Mm.10545	NM_153576	ENSMUSG00000060188	Cxcl17	VCC-1|Vcc1	chemokine (C-X-C motif) ligand 17	protein-coding
mm_12510.1	chr2	71981185	71981285	+	1	NA	promoter-TSS (NM_001204167)	promoter-TSS (NM_001204167)	20	NM_019688	56508	Mm.196153	NM_019688	ENSMUSG00000049044	Rapgef4	1300003D15Rik|5730402K07Rik|6330581N18Rik|EPAC 2|Epac-2|Epac2|mKIAA4040	Rap guanine nucleotide exchange factor (GEF) 4	protein-coding
mm_105142.1	chr11	101459896	101459923	-	1	NA	3' UTR (NM_012037, exon 6 of 6)	3' UTR (NM_012037, exon 6 of 6)	6290	NM_012037	26949	Mm.29210	NM_012037	ENSMUSG00000034993	Vat1	VAT-1	vesicle amine transport 1	protein-coding
mm_8592.1	chr1	156005890	156005907	-	1	NA	3' UTR (NM_144791, exon 7 of 7)	3' UTR (NM_144791, exon 7 of 7)	28919	NM_001160019	208263	Mm.211654	NM_144791	ENSMUSG00000026466	Tor1aip1	LAP1|Lap1B	torsin A interacting protein 1	protein-coding
mm_87187.1	chr10	39369916	39369926	+	1	NA	5' UTR (NM_008054, exon 1 of 14)	5' UTR (NM_008054, exon 1 of 14)	122	NM_001122893	14360	Mm.4848	NM_008054	ENSMUSG00000019843	Fyn	AI448320|AW552119	Fyn proto-oncogene	protein-coding
mm_52613.1	chr6	117173830	117173838	+	1	NA	3' UTR (NM_021704, exon 3 of 3)	3' UTR (NM_021704, exon 3 of 3)	5299	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_53402.1	chr6	131380871	131380888	+	1	NA	exon (NM_011733, exon 4 of 9)	exon (NM_011733, exon 4 of 9)	7571	NM_139117	56449	Mm.458000	NM_011733	ENSMUSG00000030189	Ybx3	Csda|Dpba|MSY3|MSY4|Yb2|dbpA|oxyR	Y box protein 3	protein-coding
mm_103818.1	chr11	83003660	83003676	-	1	NA	exon (NM_181545, exon 6 of 6)	exon (NM_181545, exon 6 of 6)	-11838	NM_172796	237886	Mm.270253	NM_172796	ENSMUSG00000069793	Slfn9	9830137M10Rik	schlafen 9	protein-coding
mm_93145.1	chr10	92247080	92247080	-	1	NA	intron (NR_046027, intron 7 of 8)	intron (NR_046027, intron 7 of 8)	-81902	NR_028262	110333	Mm.429764	NR_028262		Rmst	100041799|AI853140|C230053E11Rik|D930049J19Rik|Dmt2|Gm3515|M2|Ncrms	rhabdomyosarcoma 2 associated transcript (non-coding RNA)	ncRNA
mm_61295.1	chr7	67660857	67660904	+	1	NA	intron (NM_001168476, intron 1 of 9)	intron (NM_001168476, intron 1 of 9)	13470	NM_025905	67009	Mm.249356	NM_025905	ENSMUSG00000030555	Ttc23	1600012K10Rik	tetratricopeptide repeat domain 23	protein-coding
mm_76509.1	chr8	86885284	86885307	-	1	NA	promoter-TSS (NM_030563)	promoter-TSS (NM_030563)	-37	NM_030563	80750	Mm.25117	NM_030563	ENSMUSG00000031652	N4bp1	AI481586|C81621	NEDD4 binding protein 1	protein-coding
mm_116174.1	chr13	30820063	30820071	-	1	NA	intron (NM_025588, intron 26 of 27)	intron (NM_025588, intron 26 of 27)	70834	NM_013674	16364	Mm.4677	NM_013674	ENSMUSG00000021356	Irf4	AI385587|IRF-4|LSIRF|NF-EM5|Spip	interferon regulatory factor 4	protein-coding
mm_121921.1	chr14	23464123	23464134	-	1	NA	intron (NM_001253373, intron 13 of 27)	B3A|SINE|B2	-369557	NR_033550	791307	Mm.364384	NR_033550	ENSMUSG00000068680	Gm10248	ENSMUSG00000068680	predicted gene 10248	ncRNA
mm_59801.1	chr7	29134888	29134898	+	1	NA	promoter-TSS (NM_001174155)	promoter-TSS (NM_001174155)	-40	NM_001174155	233046	Mm.465324	NM_145149	ENSMUSG00000030589	Rasgrp4	-	RAS guanyl releasing protein 4	protein-coding
mm_115122.1	chr13	104287090	104287107	+	1	NA	promoter-TSS (NM_001081020)	promoter-TSS (NM_001081020)	-737	NR_136938	108154	Mm.208125	NM_175496	ENSMUSG00000046169	Adamts6	A930019D11Rik|ADAM-TS6|b2b1879.1Clo|b2b2029Clo|b2b2182Clo|b2b2187.1Clo|b2b2228Clo	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 6	protein-coding
mm_135002.1	chr16	32179597	32179608	-	1	NA	promoter-TSS (NM_001033539)	promoter-TSS (NM_001033539)	-198	NM_001033539	328660	Mm.441006	NM_001033539	ENSMUSG00000075269	Bex6	B020003O03Rik	brain expressed family member 6	protein-coding
mm_96164.1	chr11	61488017	61488031	+	1	NA	TTS (NM_001291037)	TTS (NM_001291037)	2580	NM_029568	76293	Mm.272278	NM_029568	ENSMUSG00000042436	Mfap4	1110007F23Rik	microfibrillar-associated protein 4	protein-coding
mm_93944.1	chr10	127211529	127211626	-	1	NA	promoter-TSS (NM_054097)	promoter-TSS (NM_054097)	45	NM_054097	117150	Mm.22682	NM_054097	ENSMUSG00000025417	Pip4k2c	Pip5k2c	phosphatidylinositol-5-phosphate 4-kinase, type II, gamma	protein-coding
mm_65998.1	chr7	30558774	30558785	-	1	NA	intron (NM_001290569, intron 1 of 8)	intron (NM_001290569, intron 1 of 8)	867	NM_029377	75660	Mm.379242	NM_029377	ENSMUSG00000036845	Lin37	1810054G18Rik	lin-37 homolog (C. elegans)	protein-coding
mm_159288.1	chr2	172043531	172043531	-	1	NA	promoter-TSS (NM_175631)	promoter-TSS (NM_175631)	-65	NM_175631	228942	Mm.40555	NM_175631	ENSMUSG00000067578	Cbln4	AI848962	cerebellin 4 precursor protein	protein-coding
mm_155303.1	chrX	61185849	61185875	+	1	NA	promoter-TSS (NM_001166658)	promoter-TSS (NM_001166658)	-304	NM_001166658	631990	Mm.401324	NM_001166658	ENSMUSG00000090546	Cdr1	100039759|Cdr|Cdr34|EG631990|Gm2409|Gm7077	cerebellar degeneration related antigen 1	protein-coding
mm_104387.1	chr11	94485276	94485281	-	1	NA	promoter-TSS (NM_144827)	promoter-TSS (NM_144827)	32	NM_144827	217116	Mm.156123	NM_144827	ENSMUSG00000020867	Spata20	Tisp78	spermatogenesis associated 20	protein-coding
mm_61881.1	chr7	89632500	89632542	+	1	NA	promoter-TSS (NM_181407)	promoter-TSS (NM_181407)	-297	NM_181407	109264	Mm.334011	NM_181407	ENSMUSG00000030621	Me3	1700020C08Rik|B230207H15Rik	malic enzyme 3, NADP(+)-dependent, mitochondrial	protein-coding
mm_44756.1	chr5	31520710	31520739	-	1	NA	intron (NM_028150, intron 2 of 4)	intron (NM_028150, intron 2 of 4)	6038	NM_028150	72195	Mm.164187	NM_028150	ENSMUSG00000053134	Supt7l	2610524B01Rik|6030455L14Rik	suppressor of Ty 7-like	protein-coding
mm_30571.1	chr4	3804379	3804383	+	1	NA	Intergenic	Intergenic	31274	NM_026147	67427	Mm.21938	NM_026147	ENSMUSG00000028234	Rps20	4632426K06Rik|Dsk4	ribosomal protein S20	protein-coding
mm_37954.1	chr4	133277731	133277804	-	1	NA	promoter-TSS (NR_110978)	promoter-TSS (NR_110978)	23	NM_025667	52174	Mm.244748	NM_025667	ENSMUSG00000028857	Tmem222	5730406H10Rik|AA409341|D4Ertd196e	transmembrane protein 222	protein-coding
mm_133464.1	chr16	89174733	89174736	+	1	NA	Intergenic	Intergenic	-31127	NM_001163615	622935	Mm.459837	NM_001163615	ENSMUSG00000091039	Krtap20-2	1190004K03Rik|EG622935|Gm6371	keratin associated protein 20-2	protein-coding
mm_119651.1	chr14	52016817	52016844	+	1	NA	promoter-TSS (NM_001033805)	promoter-TSS (NM_001033805)	-35	NM_001033805	619301	Mm.475177	NM_001033805	ENSMUSG00000072571	Tmem253	G630016D24Rik	transmembrane protein 253	protein-coding
mm_64233.1	chr7	141695346	141695362	+	1	NA	exon (NM_023566, exon 12 of 46)	exon (NM_023566, exon 12 of 46)	5014	NM_023566	17831	Mm.2041	NM_023566		Muc2	2010015E03Rik|MCM|wnn	mucin 2	protein-coding
mm_47233.1	chr5	121385600	121385619	-	1	NA	promoter-TSS (NM_001163470)	promoter-TSS (NM_001163470)	6	NM_001163470	231712	Mm.20488	NM_172275	ENSMUSG00000042726	Trafd1	1110008K06Rik|Fln29	TRAF type zinc finger domain containing 1	protein-coding
mm_2321.1	chr1	92052499	92052547	+	1	NA	intron (NM_207225, intron 3 of 26)	intron (NM_207225, intron 3 of 26)	127818	NM_207225	208727	Mm.318567	NM_207225	ENSMUSG00000026313	Hdac4	4932408F19Rik|HD4	histone deacetylase 4	protein-coding
mm_49621.1	chr6	30803355	30803370	+	1	NA	intron (NM_017478, intron 20 of 23)	intron (NM_017478, intron 20 of 23)	62063	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_150741.1	chr19	43782321	43782334	+	1	NA	promoter-TSS (NM_013806)	promoter-TSS (NM_013806)	19	NM_013806	12780	Mm.39054	NM_013806	ENSMUSG00000025194	Abcc2	AI173996|Abc30|Cmoat|Mrp2|cMRP	ATP-binding cassette, sub-family C (CFTR/MRP), member 2	protein-coding
mm_12891.1	chr2	84798281	84798295	+	1	NA	promoter-TSS (NM_019949)	promoter-TSS (NM_019949)	-540	NM_019949	56791	Mm.38261	NM_019949	ENSMUSG00000027078	Ube2l6	2810489I21Rik|RIG-B|UBCH8|Ubce8|Ubcm8	ubiquitin-conjugating enzyme E2L 6	protein-coding
mm_21308.1	chr2	157079332	157079354	-	1	NA	promoter-TSS (NM_001164663)	promoter-TSS (NM_001164663)	-78	NM_001164663	320706	Mm.79466	NM_001164663	ENSMUSG00000055485	Soga1	9830001H06Rik|AI426038|D430036N24Rik|Soga	suppressor of glucose, autophagy associated 1	protein-coding
mm_68292.1	chr7	105736448	105736488	-	1	NA	promoter-TSS (NM_001161724)	promoter-TSS (NM_001161724)	116	NM_025897	101867	Mm.231400	NM_025897	ENSMUSG00000030888	Rrp8	1500003O22Rik|2900001K19Rik|AW538116	ribosomal RNA processing 8, methyltransferase, homolog (yeast)	protein-coding
mm_167253.1	chr8	24823975	24823978	-	1	NA	exon (NM_007401, exon 1 of 21)	exon (NM_007401, exon 1 of 21)	393	NM_001272058	11499	Mm.143889	NM_007401	ENSMUSG00000031554	Adam5	tMDC II|tMDCII	a disintegrin and metallopeptidase domain 5	protein-coding
mm_97550.1	chr11	78928601	78928619	+	1	NA	exon (NM_010927, exon 3 of 27)	exon (NM_010927, exon 3 of 27)	3319	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_17919.1	chr2	35432902	35432910	-	1	NA	intron (NM_001308300, intron 1 of 6)	intron (NM_001308300, intron 1 of 6)	28543	NM_001308299	14594	Mm.281124	NM_010283	ENSMUSG00000035778	Ggta1	AW108479|GALT|Gal|Ggta|Ggta-1|alpha Gal|alpha3GalT	glycoprotein galactosyltransferase alpha 1, 3	protein-coding
mm_169021.1	chr13	112578723	112578736	-	1	NA	intron (NM_139299, intron 1 of 16)	LSU-rRNA_Hsa|rRNA|rRNA	1933	NM_139299	218624	Mm.380801	NM_139299	ENSMUSG00000050377	Il31ra	CRL3|GLM-R|GPL|Glmr|NR10	interleukin 31 receptor A	protein-coding
mm_50082.1	chr6	41522864	41522892	+	1	NA	exon (NM_009430, exon 2 of 5)	exon (NM_009430, exon 2 of 5)	1102	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_33945.1	chr4	137277501	137277518	+	1	NA	promoter-TSS (NM_009523)	promoter-TSS (NM_009523)	-126	NM_009523	22417	Mm.20355	NM_009523	ENSMUSG00000036856	Wnt4	Wnt-4	wingless-type MMTV integration site family, member 4	protein-coding
mm_42462.1	chr5	115438190	115438239	+	1	NA	intron (NM_008629, intron 6 of 14)	intron (NM_008629, intron 6 of 14)	8529	NM_008629	17690	Mm.5077	NM_008629	ENSMUSG00000054256	Msi1	Msi1h|Musahi1|m-Msi-1	musashi RNA-binding protein 1	protein-coding
mm_104867.1	chr11	99387635	99387660	-	1	NA	exon (NM_010660, exon 3 of 8)	exon (NM_010660, exon 3 of 8)	1717	NM_010660	16661	Mm.22662	NM_010660	ENSMUSG00000019761	Krt10	D130054E02Rik|K10|K1C1|Krt-1.10|Krt1-10	keratin 10	protein-coding
mm_12416.1	chr2	70561507	70561526	+	1	NA	promoter-TSS (NM_008077)	promoter-TSS (NM_008077)	-613	NM_001312900	14415	Mm.272120	NM_008077	ENSMUSG00000070880	Gad1	EP10|Gad-1	glutamate decarboxylase 1	protein-coding
mm_122668.1	chr14	51922987	51922993	-	1	NA	promoter-TSS (NM_001011687)	promoter-TSS (NM_001011687)	-217	NM_001011687	497071	Mm.378602	NM_001011687	ENSMUSG00000068392	Rnase13	-	ribonuclease, RNase A family, 13 (non-active)	protein-coding
mm_53351.1	chr6	129350310	129350331	+	1	NA	promoter-TSS (NM_177686)	promoter-TSS (NM_177686)	76	NM_177686	232413	Mm.90241	NM_177686	ENSMUSG00000053063	Clec12a	CLL-1|D230024O04|KLRL1|Micl	C-type lectin domain family 12, member a	protein-coding
mm_52666.1	chr6	117906810	117906863	+	1	NA	promoter-TSS (NM_001166431)	promoter-TSS (NM_001166431)	54	NM_133834	98758	Mm.422979	NM_133834	ENSMUSG00000042079	Hnrnpf	4833420I20Rik|AA407306|Hnrpf	heterogeneous nuclear ribonucleoprotein F	protein-coding
mm_169669.1	chr15	62693775	62693776	-	1	NA	Intergenic	Intergenic	-474324	NR_003523	67552	Mm.484027	NM_026230		H2afy3	4933432H23Rik	H2A histone family, member Y3	pseudo
mm_70617.1	chr8	13435599	13435609	+	1	NA	5' UTR (NM_001143672, exon 1 of 8)	5' UTR (NM_001143672, exon 1 of 8)	145	NM_001143672	272465	Mm.250502	NM_001143671	ENSMUSG00000038457	Tmem255b	Fam70b|Gm687	transmembrane protein 255B	protein-coding
mm_6843.1	chr1	84235315	84235319	-	1	NA	intron (NM_001003948, intron 1 of 2)	intron (NM_001003948, intron 1 of 2)	-16356	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_107401.1	chr12	33337509	33337511	+	1	NA	intron (NM_001033436, intron 2 of 7)	intron (NM_001033436, intron 2 of 7)	34995	NM_001033436	380753	Mm.41540	NM_028139	ENSMUSG00000020564	Atxn7l1	2810423G08Rik|Atxn7l4	ataxin 7-like 1	protein-coding
mm_119111.1	chr14	31001844	31001920	+	1	NA	promoter-TSS (NM_026911)	promoter-TSS (NM_026911)	-216	NM_026911	69019	Mm.28852	NM_026911	ENSMUSG00000021917	Spcs1	1810004F21Rik	signal peptidase complex subunit 1 homolog (S. cerevisiae)	protein-coding
mm_105052.1	chr11	100692441	100692473	-	1	NA	Intergenic	Intergenic	11814	NM_030150	80861	Mm.271830	NM_030150	ENSMUSG00000017830	Dhx58	B430001I08Rik|D11Lgp2e|LPG2|Lgp2|RLR-3	DEXH (Asp-Glu-X-His) box polypeptide 58	protein-coding
mm_126280.1	chr15	79209306	79209317	+	1	NA	intron (NR_029470, intron 2 of 4)	intron (NR_029470, intron 2 of 4)	-19862	NM_008837	18693	Mm.259464	NM_008837	ENSMUSG00000068206	Pick1	Prkcabp	protein interacting with C kinase 1	protein-coding
mm_82896.1	chr9	32615944	32615948	-	1	NA	Intergenic	Intergenic	-74494	NM_008026	14247	Mm.258908	NM_008026	ENSMUSG00000016087	Fli1	EWSR2|Fli-1|SIC-1|Sic1	Friend leukemia integration 1	protein-coding
mm_27951.1	chr3	79825538	79825559	-	1	NA	intron (NM_027495, intron 7 of 11)	intron (NM_027495, intron 7 of 11)	17114	NM_027495	70652	Mm.46635	NM_027495	ENSMUSG00000027956	Tmem144	1110057I03Rik|5730537D05Rik	transmembrane protein 144	protein-coding
mm_38435.1	chr4	139352539	139352586	-	1	NA	promoter-TSS (NM_146157)	promoter-TSS (NM_146157)	14	NM_001290810	69902	Mm.27871	NM_023536	ENSMUSG00000028741	Mrto4	2610012O22Rik|Mg684|Mrt4	mRNA turnover 4, ribosome maturation factor	protein-coding
mm_48250.1	chr5	137787532	137787543	-	1	NA	promoter-TSS (NM_001005426)	promoter-TSS (NM_001005426)	-265	NM_001005426	381678	Mm.332765	NM_001005426	ENSMUSG00000037108	Zcwpw1	Gm1053	zinc finger, CW type with PWWP domain 1	protein-coding
mm_3892.1	chr1	161395541	161395550	+	1	NA	5' UTR (NM_009452, exon 1 of 3)	5' UTR (NM_009452, exon 1 of 3)	107	NM_009452	22164	Mm.4994	NM_009452	ENSMUSG00000026700	Tnfsf4	Ath-1|Ath1|CD134L|OX-40L|Ox40l|TXGP1|Tnlg2b|Txgp1l|gp34	tumor necrosis factor (ligand) superfamily, member 4	protein-coding
mm_29908.1	chr3	131474508	131474514	-	1	NA	Intergenic	Intergenic	-90257	NM_001289479	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_163716.1	chr13	111805940	111805975	+	1	NA	intron (NM_011945, intron 1 of 19)	intron (NM_011945, intron 1 of 19)	3026	NM_011945	26401	Mm.15918	NM_011945	ENSMUSG00000021754	Map3k1	MAPKKK1|MEKK1|Mekk	mitogen-activated protein kinase kinase kinase 1	protein-coding
mm_82648.1	chr9	22018265	22018268	-	1	NA	3' UTR (NM_010487, exon 7 of 7)	3' UTR (NM_010487, exon 7 of 7)	15278	NM_008925	19089	Mm.214593	NM_008925	ENSMUSG00000003402	Prkcsh	80K-H|PKCSH	protein kinase C substrate 80K-H	protein-coding
mm_148471.1	chr19	4097423	4097432	+	1	NA	promoter-TSS (NM_026373)	promoter-TSS (NM_026373)	76	NM_026373	52004	Mm.29609	NM_026373	ENSMUSG00000024856	Cdk2ap2	5830466O21Rik|D19Ertd144e|Doc-1r	CDK2-associated protein 2	protein-coding
mm_21783.1	chr2	164851538	164851603	-	1	NA	exon (NM_011125, exon 8 of 16)	exon (NM_011125, exon 8 of 16)	6138	NM_011125	18830	Mm.6105	NM_011125	ENSMUSG00000017754	Pltp	Bpife|OD107	phospholipid transfer protein	protein-coding
mm_84337.1	chr9	64172890	64172918	-	1	NA	promoter-TSS (NM_026507)	promoter-TSS (NM_026507)	27	NM_026507	68014	Mm.335237	NM_026507	ENSMUSG00000032400	Zwilch	2310031L18Rik	zwilch kinetochore protein	protein-coding
mm_29601.1	chr3	121159224	121159232	-	1	NA	exon (NM_025637, exon 4 of 7)	exon (NM_025637, exon 4 of 7)	12467	NM_028456	66568	Mm.263163	NM_025637	ENSMUSG00000028133	Rwdd3	2510027J23Rik|3110037C01Rik|AI035684|AI662458|Rsume|X2CR1	RWD domain containing 3	protein-coding
mm_51081.1	chr6	66970505	66970534	+	1	NA	intron (NM_001177560, intron 3 of 4)	B3A|SINE|B2	-66080	NR_040278	320172	Mm.449039	NR_040278	ENSMUSG00000087231	E230016M11Rik	-	RIKEN cDNA E230016M11 gene	ncRNA
mm_64499.1	chr7	143475121	143475162	+	1	NA	promoter-TSS (NM_001042760)	promoter-TSS (NM_001042760)	25	NM_001042760	18400	Mm.271740	NM_008767	ENSMUSG00000000154	Slc22a18	AW260131|BWR1A|BWSCR1A|HET|ITM|Impt1|Orctl2|Slc22a1l|TSSC5|p45-BWR1A	solute carrier family 22 (organic cation transporter), member 18	protein-coding
mm_156054.1	chrX	109107019	109107021	+	1	NA	intron (NM_019989, intron 1 of 3)	intron (NM_019989, intron 1 of 3)	11613	NM_019989	56726	Mm.260760	NM_019989	ENSMUSG00000031246	Sh3bgrl	1190008F14Rik	SH3-binding domain glutamic acid-rich protein like	protein-coding
mm_135282.1	chr16	38447573	38447600	-	1	NA	exon (NM_007414, exon 3 of 4)	exon (NM_007414, exon 3 of 4)	5103	NM_007414	11544	Mm.20047	NM_007414	ENSMUSG00000002844	Adprh	Arh1	ADP-ribosylarginine hydrolase	protein-coding
mm_124547.1	chr14	122475164	122475171	-	1	NA	promoter-TSS (NR_045046)	promoter-TSS (NR_045046)	32	NR_045046	69248	Mm.235369	NR_045046	ENSMUSG00000085555	2610035F20Rik	-	RIKEN cDNA 2610035F20 gene	ncRNA
mm_139349.1	chr17	50508894	50508928	+	1	NA	promoter-TSS (NM_013880)	promoter-TSS (NM_013880)	-636	NM_013880	224860	Mm.217362	NM_013880	ENSMUSG00000038910	Plcl2	PLC-L2|PRIP-2|Plce2|mKIAA1092	phospholipase C-like 2	protein-coding
mm_69260.1	chr7	127890919	127890953	-	1	NA	promoter-TSS (NM_001081268)	promoter-TSS (NM_001081268)	34	NM_001081268	330657	Mm.425491	NM_001081268	ENSMUSG00000044139	Prss53	Pol3s|mFLJ00289	protease, serine 53	protein-coding
mm_115507.1	chr13	4279391	4279409	-	1	NA	promoter-TSS (NM_013777)	promoter-TSS (NM_013777)	-1	NM_013777	622402	Mm.27447	NM_013777	ENSMUSG00000021211	Akr1c12	AI266976|Akra	aldo-keto reductase family 1, member C12	protein-coding
mm_47867.1	chr5	134639312	134639348	-	1	NA	promoter-TSS (NM_033561)	promoter-TSS (NM_033561)	79	NM_001312867	22384	Mm.27955	NM_033561	ENSMUSG00000040731	Eif4h	AU018978|D5Ertd355e|E430026L18Rik|Ef4h|Wbscr1|Wscr1|eIF-4H	eukaryotic translation initiation factor 4H	protein-coding
mm_93919.1	chr10	127069097	127069109	-	1	NA	intron (NM_025982, intron 2 of 5)	B1_Mur2|SINE|Alu	1158	NM_025982	67125	Mm.35650	NM_025982	ENSMUSG00000006736	Tspan31	2700085A14Rik|AW742554|Sas	tetraspanin 31	protein-coding
mm_170376.1	chr1	85526642	85526659	+	1	NA	Intergenic	Intergenic	72160	NM_030194	109032	Mm.335802	NM_030194	ENSMUSG00000070034	Sp110	5031415C07Rik|52kDa|5830484A20Rik|ENSMUSG00000075603|Ifi75|Ipr1	Sp110 nuclear body protein	protein-coding
mm_37830.1	chr4	132014307	132014309	-	1	NA	intron (NM_183428, intron 1 of 20)	intron (NM_183428, intron 1 of 20)	34770	NM_001128606	269587	Mm.30038	NM_183428	ENSMUSG00000028906	Epb41	4.1R|AI415518|D4Ertd442e|Elp-1|Elp1|Epb4.1|mKIAA4056	erythrocyte membrane protein band 4.1	protein-coding
mm_73396.1	chr8	105827771	105827773	+	1	NA	promoter-TSS (NM_024445)	promoter-TSS (NM_024445)	28	NM_024445	72236	Mm.386810	NM_024445	ENSMUSG00000031893	Tsnaxip1	1700016K08Rik|TXI1	translin-associated factor X (Tsnax) interacting protein 1	protein-coding
mm_148937.1	chr19	7039527	7039538	+	1	NA	intron (NM_016737, intron 1 of 13)	CpG	494	NM_016737	20867	Mm.258633	NM_016737	ENSMUSG00000024966	Stip1	Hop|Sti1|p60	stress-induced phosphoprotein 1	protein-coding
mm_161184.1	chr13	48832021	48832021	-	1	NA	exon (NM_011078, exon 3 of 22)	exon (NM_011078, exon 3 of 22)	38864	NM_011078	18676	Mm.486213	NM_011078	ENSMUSG00000038025	Phf2	GRC5	PHD finger protein 2	protein-coding
mm_148588.1	chr19	5068102	5068115	+	1	NA	promoter-TSS (NM_054042)	promoter-TSS (NM_054042)	30	NM_054042	70445	Mm.29597	NM_054042	ENSMUSG00000056481	Cd248	2610111G01Rik|AI842296|Cd164l1|Tem1	CD248 antigen, endosialin	protein-coding
mm_5996.1	chr1	58725888	58725898	-	1	NA	intron (NM_009805, intron 1 of 4)	intron (NM_009805, intron 1 of 4)	-4659	NM_001293805	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_102583.1	chr11	61854874	61854884	-	1	NA	5' UTR (NM_013881, exon 1 of 27)	5' UTR (NM_013881, exon 1 of 27)	213	NM_013881	29869	Mm.162025	NM_013881	ENSMUSG00000004798	Ulk2	A830085I22Rik|AU015340|Unc51.2|mKIAA0623	unc-51 like kinase 2	protein-coding
mm_26424.1	chr3	142618260	142618277	+	1	NA	3' UTR (NM_010259, exon 11 of 11)	3' UTR (NM_010259, exon 11 of 11)	-2395	NM_010260	14469	Mm.24038	NM_010260	ENSMUSG00000028270	Gbp2	-	guanylate binding protein 2	protein-coding
mm_107882.1	chr12	69987202	69987212	+	1	NA	promoter-TSS (NM_022028)	promoter-TSS (NM_022028)	-205	NM_022028	64010	Mm.390480	NM_022028	ENSMUSG00000021067	Sav1	1700040G09Rik|Salv|Sav|WW45|Wwp3|Wwp4	salvador family WW domain containing 1	protein-coding
mm_90283.1	chr10	122944724	122944727	+	1	NA	3' UTR (NM_001110218, exon 10 of 10)	3' UTR (NM_001110218, exon 10 of 10)	40999	NR_029527	387251		NR_029527	ENSMUSG00000065406	Mirlet7i	Mirnlet7i|let-7i|mmu-let-7i	microRNA let7i	ncRNA
mm_1558.1	chr1	74031330	74031338	+	1	NA	intron (NM_027884, intron 3 of 34)	intron (NM_027884, intron 3 of 34)	93113	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_118266.1	chr13	112562030	112562037	-	1	NA	5' UTR (NM_139299, exon 3 of 17)	5' UTR (NM_139299, exon 3 of 17)	18629	NM_139299	218624	Mm.380801	NM_139299	ENSMUSG00000050377	Il31ra	CRL3|GLM-R|GPL|Glmr|NR10	interleukin 31 receptor A	protein-coding
mm_84579.1	chr9	69440006	69440008	-	1	NA	Intergenic	Intergenic	-13676	NM_007585	12306	Mm.238343	NM_007585	ENSMUSG00000032231	Anxa2	AW215814|Cal1h	annexin A2	protein-coding
mm_65153.1	chr7	19628404	19628429	-	1	NA	intron (NM_001290457, intron 1 of 10)	intron (NM_001290457, intron 1 of 10)	1022	NM_001290457	19698	Mm.1741	NM_009046	ENSMUSG00000002983	Relb	shep	avian reticuloendotheliosis viral (v-rel) oncogene related B	protein-coding
mm_41939.1	chr5	105731630	105731639	+	1	NA	intron (NM_178701, intron 1 of 2)	intron (NM_178701, intron 1 of 2)	30824	NM_178701	231549	Mm.23837	NM_178701	ENSMUSG00000046079	Lrrc8d	2810473G09Rik|4930525N13Rik|A930019F03|Lrrc5	leucine rich repeat containing 8D	protein-coding
mm_22260.1	chr2	177957286	177957312	-	1	NA	promoter-TSS (NM_001282028)	promoter-TSS (NM_001282028)	-11	NM_001190302	665211	Mm.441314	NM_001190302	ENSMUSG00000078862	Gm14326	OTTMUSG00000016327	predicted gene 14326	protein-coding
mm_133769.1	chr16	94570013	94570052	+	1	NA	promoter-TSS (NM_001113389)	promoter-TSS (NM_001113389)	-174	NM_007890	13548	Mm.310973	NM_007890	ENSMUSG00000022897	Dyrk1a	2310043O08Rik|D16Ertd272e|D16Ertd493e|Dyrk|ENSMUSG00000074897|Gm10783|Mnbh|Mp86|mmb	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1a	protein-coding
mm_147522.1	chr18	52529631	52529643	-	1	NA	promoter-TSS (NM_001286181)	promoter-TSS (NM_001286181)	84	NM_001286181	16948	Mm.172	NM_010728	ENSMUSG00000024529	Lox	AI893619|TSC-160|rrg	lysyl oxidase	protein-coding
mm_24699.1	chr3	95126190	95126199	+	1	NA	intron (NM_016712, intron 3 of 9)	PB1D10|SINE|Alu	1680	NM_016712	50874	Mm.71935	NM_016712	ENSMUSG00000005628	Tmod4	MTMOD|Sk-Tmod	tropomodulin 4	protein-coding
mm_123304.1	chr14	61682311	61682335	-	1	NA	promoter-TSS (NR_028264)	promoter-TSS (NR_028264)	50	NR_028264	668253	Mm.32886	NR_028264	ENSMUSG00000097589	Dleu2	1810047A16Rik|4932411A06Rik|7730401J12Rik|AI197277|AI788824|Alt1|Gm9069|Leu2	deleted in lymphocytic leukemia, 2	ncRNA
mm_78238.1	chr9	21625657	21625662	+	1	NA	intron (NM_001174079, intron 1 of 33)	intron (NM_001174079, intron 1 of 33)	9490	NM_001174078	20586	Mm.286593	NM_011417	ENSMUSG00000032187	Smarca4	Brg1|HP1-BP72|SNF2beta|SW1/SNF|b2b508.1Clo|b2b692Clo	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	protein-coding
mm_110692.1	chr12	69184440	69184460	-	1	NA	promoter-TSS (NM_025589)	promoter-TSS (NM_025589)	292	NM_146035	217664	Mm.206642	NM_146035	ENSMUSG00000043998	Mgat2	AA407964|CDGS2|GLCNACTII|GNT-II|GNT2	mannoside acetylglucosaminyltransferase 2	protein-coding
mm_172712.1	chr8	69791608	69791611	-	1	NA	exon (NM_133224, exon 1 of 26)	exon (NM_133224, exon 1 of 26)	446	NM_133224	170759	Mm.186066	NM_133224	ENSMUSG00000031862	Atp13a1	Atp13a|Cgi152|catp	ATPase type 13A1	protein-coding
mm_123272.1	chr14	61366670	61366684	-	1	NA	3' UTR (NM_008466, exon 17 of 17)	3' UTR (NM_008466, exon 17 of 17)	-6232	NM_026598	68177	Mm.22758	NM_026598	ENSMUSG00000021928	Ebpl	5730442K12Rik|EBRP	emopamil binding protein-like	protein-coding
mm_50932.1	chr6	57702473	57702523	+	1	NA	promoter-TSS (NM_133737)	promoter-TSS (NM_133737)	43	NM_133737	71835	Mm.274904	NM_133737	ENSMUSG00000062190	Lancl2	1700003F10Rik	LanC (bacterial lantibiotic synthetase component C)-like 2	protein-coding
mm_54539.1	chr6	36741430	36741440	-	1	NA	exon (NM_008973, exon 4 of 5)	exon (NM_008973, exon 4 of 5)	69926	NM_008973	19242	Mm.279690	NM_008973	ENSMUSG00000029838	Ptn	HARP|HB-GAM|HBBN|HBGF-8|HBNF|OSF|Osf-1|Osf1	pleiotrophin	protein-coding
mm_56799.1	chr6	116656496	116656507	-	1	NA	intron (NM_178045, intron 3 of 10)	(TG)n|Simple_repeat|Simple_repeat	5817	NM_001166580	213393	Mm.38231	NM_145980	ENSMUSG00000048489	8430408G22Rik	Depp|Fseg	RIKEN cDNA 8430408G22 gene	protein-coding
mm_95769.1	chr11	54908610	54908616	+	1	NA	exon (NM_008161, exon 3 of 5)	exon (NM_008161, exon 3 of 5)	5759	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_25917.1	chr3	131156308	131156344	+	1	NA	intron (NM_001276403, intron 3 of 11)	intron (NM_001276403, intron 3 of 11)	43535	NM_001276403	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_150334.1	chr19	34575245	34575263	+	1	NA	3' UTR (NM_008332, exon 3 of 3)	3' UTR (NM_008332, exon 3 of 3)	-8275	NM_010501	15959	Mm.426079	NM_010501	ENSMUSG00000074896	Ifit3	Ifi49|P49	interferon-induced protein with tetratricopeptide repeats 3	protein-coding
mm_22421.1	chr2	181581975	181581990	-	1	NA	promoter-TSS (NM_026765)	promoter-TSS (NM_026765)	-9	NM_026765	68556	Mm.232400	NM_026765	ENSMUSG00000089917	Uckl1	1110007H10Rik|Urkl1	uridine-cytidine kinase 1-like 1	protein-coding
mm_94306.1	chr11	4178113	4178140	+	1	NA	exon (NM_026175, exon 13 of 16)	exon (NM_026175, exon 13 of 16)	-8707	NM_134023	103724	Mm.28140	NM_134023	ENSMUSG00000034412	Tbc1d10a	AI447804|EPI64|Tbc1d10|mFLJ00288	TBC1 domain family, member 10a	protein-coding
mm_87738.1	chr10	60218937	60218947	+	1	NA	5' UTR (NM_016803, exon 1 of 4)	5' UTR (NM_016803, exon 1 of 4)	318	NM_016803	53374	Mm.12866	NM_016803	ENSMUSG00000057337	Chst3	C6ST|C6ST-1|GST-0	carbohydrate (chondroitin 6/keratan) sulfotransferase 3	protein-coding
mm_13791.1	chr2	118862010	118862022	+	1	NA	promoter-TSS (NM_019826)	promoter-TSS (NM_019826)	16	NM_019826	56357	Mm.6635	NM_019826	ENSMUSG00000027332	Ivd	1300016K07Rik|6720455E18Rik|AI463340	isovaleryl coenzyme A dehydrogenase	protein-coding
mm_139474.1	chr17	55986495	55986531	+	1	NA	promoter-TSS (NM_183178)	promoter-TSS (NM_183178)	2	NM_183178	240121	Mm.270660	NM_183178	ENSMUSG00000011589	Fsd1	-	fibronectin type 3 and SPRY domain-containing protein	protein-coding
mm_47076.1	chr5	116591859	116591865	-	1	NA	promoter-TSS (NM_026886)	promoter-TSS (NM_026886)	-45	NM_026886	68955	Mm.146779	NM_026886	ENSMUSG00000063919	Srrm4	1500001A10Rik|B230202K19Rik|bv|mKIAA1853|nSR100	serine/arginine repetitive matrix 4	protein-coding
mm_65476.1	chr7	25539823	25539829	-	1	NA	5' UTR (NM_001113369, exon 1 of 7)	5' UTR (NM_001113369, exon 1 of 7)	178	NM_001113368	26367	Mm.439731	NM_007543	ENSMUSG00000054385	Ceacam2	AI267129|Bgp2|Ceacam2-L	carcinoembryonic antigen-related cell adhesion molecule 2	protein-coding
mm_121151.1	chr14	101919095	101919098	+	1	NA	intron (NM_001347628, intron 20 of 26)	intron (NM_001347628, intron 20 of 26)	78473	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_15579.1	chr2	158668079	158668117	+	1	NA	intron (NM_001159662, intron 1 of 10)	intron (NM_001159662, intron 1 of 10)	963	NM_001159662	228852	Mm.150540	NM_153089	ENSMUSG00000037754	Ppp1r16b	ANKRD4|C130078N17Rik|TIMAP|Wdt4	protein phosphatase 1, regulatory (inhibitor) subunit 16B	protein-coding
mm_75115.1	chr8	34529094	34529102	-	1	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	111218	NR_040706	330734	Mm.149998	NR_040706	ENSMUSG00000109819	B930018H19Rik	B930018H19	RIKEN cDNA B930018H19 gene	ncRNA
mm_86842.1	chr10	21419444	21419460	+	1	NA	Intergenic	MTEa|LTR|ERVL-MaLR	42152	NM_178713	237320	Mm.90181	NM_178713	ENSMUSG00000037542	Aldh8a1	Raldh4	aldehyde dehydrogenase 8 family, member A1	protein-coding
mm_80298.1	chr9	73122983	73123015	+	1	NA	3' UTR (NM_198609, exon 6 of 6)	3' UTR (NM_198609, exon 6 of 6)	9530	NM_198609	225215	Mm.379366	NM_198609	ENSMUSG00000032215	Rsl24d1	2410159K22Rik	ribosomal L24 domain containing 1	protein-coding
mm_69535.1	chr7	135695004	135695012	-	1	NA	exon (NM_001081117, exon 12 of 14)	exon (NM_001081117, exon 12 of 14)	21371	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_53635.1	chr6	140607499	140607521	+	1	NA	Intergenic	RMER17C2|LTR|ERVK	-15153	NM_178803	11569	Mm.86453	NM_009637	ENSMUSG00000030232	Aebp2	AU023766|B230313N05Rik	AE binding protein 2	protein-coding
mm_122325.1	chr14	36968770	36968793	-	1	NA	promoter-TSS (NM_027045)	promoter-TSS (NM_027045)	-17	NM_027045	72972	Mm.27621	NM_027045	ENSMUSG00000058690	Ccser2	1700012P13Rik|2900054P12Rik|AI035535|AW108503|Fam190b|Gcap14	coiled-coil serine rich 2	protein-coding
mm_134733.1	chr16	22899135	22899159	-	1	NA	non-coding (NR_075099, exon 6 of 6)	non-coding (NR_075099, exon 6 of 6)	-4761	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_85694.1	chr9	108079715	108079765	-	1	NA	promoter-TSS (NM_008243)	promoter-TSS (NM_008243)	-365	NM_032543	84585	Mm.379272	NM_032543	ENSMUSG00000041528	Rnf123	BC003945|Kpc1	ring finger protein 123	protein-coding
mm_122451.1	chr14	45313357	45313393	-	1	NA	intron (NM_015774, intron 1 of 15)	RMER13B|LTR|ERVK	5197	NM_015774	50527	Mm.387108	NM_015774	ENSMUSG00000021831	Ero1l	ERO1-L|Ero1a	ERO1-like (S. cerevisiae)	protein-coding
mm_138318.1	chr17	34837055	34837077	+	1	NA	promoter-TSS (NM_019442)	promoter-TSS (NM_019442)	47	NM_001163770	112403	Mm.275309	NM_033613	ENSMUSG00000040482	Dxo	Dom3z|NG6	decapping exoribonuclease	protein-coding
mm_147651.1	chr18	60501694	60501745	-	1	NA	5' UTR (NM_134133, exon 1 of 2)	5' UTR (NM_134133, exon 1 of 2)	264	NM_134133	106878	Mm.273197	NM_134133	ENSMUSG00000038059	Smim3	2010002N04Rik|AI195350|AW561905|Nid67|cI-41	small integral membrane protein 3	protein-coding
mm_36079.1	chr4	58206534	58206544	-	1	NA	promoter-TSS (NM_022814)	promoter-TSS (NM_022814)	57	NM_022814	64817	Mm.261024	NM_022814	ENSMUSG00000028369	Svep1	1110021D17Rik|4833413O10Rik|AA387071|D430029O09Rik|Polydom	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	protein-coding
mm_93813.1	chr10	121374451	121374481	-	1	NA	exon (NM_029364, exon 3 of 14)	exon (NM_029364, exon 3 of 14)	9376	NM_029364	75612	Mm.207683	NM_029364	ENSMUSG00000034707	Gns	2610016K11Rik|AU042285|C87209|G6S|N28088	glucosamine (N-acetyl)-6-sulfatase	protein-coding
mm_30576.1	chr4	3939382	3939421	+	1	NA	promoter-TSS (NM_019969)	promoter-TSS (NM_019969)	-23	NR_104356	66433	Mm.27406	NM_181391	ENSMUSG00000042198	Chchd7	1810049H20Rik	coiled-coil-helix-coiled-coil-helix domain containing 7	protein-coding
mm_32495.1	chr4	108328137	108328180	+	1	NA	promoter-TSS (NM_027250)	promoter-TSS (NM_027250)	6	NM_027250	69893	Mm.28354	NM_027250	ENSMUSG00000048351	Coa7	2010305A19Rik|AI451324|D4Ertd796e|Selrc1	cytochrome c oxidase assembly factor 7	protein-coding
mm_71848.1	chr8	68905837	68905847	+	1	NA	3' UTR (NM_008509, exon 10 of 10)	3' UTR (NM_008509, exon 10 of 10)	25287	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_130100.1	chr15	89426237	89426260	-	1	NA	promoter-TSS (NM_009948)	promoter-TSS (NM_009948)	-386	NM_009948	12895	Mm.227738	NM_009948	ENSMUSG00000078937	Cpt1b	Cpt1|Cpt1-m|Cpti|Cpti-m|M-cpti	carnitine palmitoyltransferase 1b, muscle	protein-coding
mm_44170.1	chr5	150800846	150800859	+	1	NA	exon (NM_175310, exon 32 of 35)	exon (NM_175310, exon 32 of 35)	127025	NM_001346503	100710	Mm.32959	NM_175310	ENSMUSG00000034021	Pds5b	AI646570|AS3|AW212954|Aprin|Tg(Wap-ERBB2)229Wzw|WAP-Her-2|mKIAA0979	PDS5 cohesin associated factor B	protein-coding
mm_41474.1	chr5	91517752	91517762	+	1	NA	promoter-TSS (NM_145562)	promoter-TSS (NM_145562)	57	NM_145562	231440	Mm.5002	NM_145562	ENSMUSG00000034981	Parm1	2210012L08Rik|9130213B05Rik|W91666	prostate androgen-regulated mucin-like protein 1	protein-coding
mm_137085.1	chr17	21474908	21474922	+	1	NA	Intergenic	MMVL30-int|LTR|ERV1	-14073	NM_013843	24132	Mm.42140	NM_013843	ENSMUSG00000057409	Zfp53	D030067O06Rik|KRAZ1|Zfp-53|Zfp118|zfas8	zinc finger protein 53	protein-coding
mm_11568.1	chr2	32894559	32894563	+	1	NA	intron (NM_146119, intron 1 of 13)	B1_Mus1|SINE|Alu	18427	NM_146119	227737	Mm.301646	NM_146119	ENSMUSG00000026796	Fam129b	9130404D14Rik	family with sequence similarity 129, member B	protein-coding
mm_47272.1	chr5	121895345	121895349	-	1	NA	intron (NM_001312908, intron 5 of 22)	intron (NM_001312908, intron 5 of 22)	46319	NM_175474	231717	Mm.12654	NM_175474	ENSMUSG00000044134	Fam109a	A230106M15Rik|AU017694|IPIP27A|Ses1	family with sequence similarity 109, member A	protein-coding
mm_34580.1	chr4	150120687	150120705	+	1	NA	5' UTR (NM_019741, exon 3 of 14)	5' UTR (NM_019741, exon 3 of 14)	1352	NM_019741	56485	Mm.260220	NM_019741	ENSMUSG00000028976	Slc2a5	AI526984|Glut5|Slc5a	solute carrier family 2 (facilitated glucose transporter), member 5	protein-coding
mm_63485.1	chr7	127748109	127748120	+	1	NA	intron (NM_172748, intron 1 of 10)	intron (NM_172748, intron 1 of 10)	1339	NM_172748	233902	Mm.259353	NM_172748	ENSMUSG00000030811	Fbxl19	6030430O11|BC059812|Fbl19	F-box and leucine-rich repeat protein 19	protein-coding
mm_143178.1	chr17	57247349	57247372	-	1	NA	5' UTR (NM_001308074, exon 1 of 17)	5' UTR (NM_001308074, exon 1 of 17)	110	NM_001308074	78308	Mm.28468	NM_030084	ENSMUSG00000005823	Gpr108	1810015L19Rik|AA589464|C79132|Lustr2	G protein-coupled receptor 108	protein-coding
mm_44199.1	chr5	3647839	3648009	-	1	NA	promoter-TSS (NM_026033)	promoter-TSS (NM_026033)	12	NM_026033	67210	Mm.178424	NM_026033	ENSMUSG00000007415	Gatad1	2310031E19Rik|2810047M21Rik|8430439A17Rik|9130430G15Rik|B330017N08Rik|ENSMUSG00000073241|Odag	GATA zinc finger domain containing 1	protein-coding
mm_68461.1	chr7	110288229	110288236	-	1	NA	Intergenic	Intergenic	66529	NM_009302	20947	Mm.334144	NM_009302	ENSMUSG00000031015	Swap70	70kDa|AV235546	SWA-70 protein	protein-coding
mm_700.1	chr1	40606256	40606261	+	1	NA	intron (NM_177084, intron 4 of 11)	intron (NM_177084, intron 4 of 11)	26031	NM_177084	110895	Mm.108602	NM_177084	ENSMUSG00000026065	Slc9a4	AW990558|D730009J23Rik|NHE4	solute carrier family 9 (sodium/hydrogen exchanger), member 4	protein-coding
mm_83246.1	chr9	42399916	42399926	-	1	NA	promoter-TSS (NM_001324548)	promoter-TSS (NM_001324548)	8	NM_009347	21683	Mm.42209	NM_009347	ENSMUSG00000037705	Tecta	Tctna	tectorin alpha	protein-coding
mm_61745.1	chr7	82648353	82648356	+	1	NA	promoter-TSS (NM_001159672)	promoter-TSS (NM_001159672)	174	NM_177894	330577	Mm.222812	NM_177894	ENSMUSG00000038570	Saxo2	1700129I04Rik|D030069K18|Fam154b	stabilizer of axonemal microtubules 2	protein-coding
mm_145390.1	chr18	57142619	57142628	+	1	NA	intron (NM_001001979, intron 1 of 24)	intron (NM_001001979, intron 1 of 24)	9533	NM_001001979	70417	Mm.297863	NM_001001979	ENSMUSG00000024593	Megf10	3000002B06Rik|Gm331	multiple EGF-like-domains 10	protein-coding
mm_18887.1	chr2	76709465	76709482	-	1	NA	exon (NM_011652, exon 307 of 313)	exon (NM_011652, exon 307 of 313)	34158	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_21958.1	chr2	167190088	167190108	-	1	NA	Intergenic	CpG	-1280	NM_008420	16500	Mm.205341	NM_008420	ENSMUSG00000050556	Kcnb1	Kcr1-1|Kv2.1|Shab	potassium voltage gated channel, Shab-related subfamily, member 1	protein-coding
mm_91091.1	chr10	19061882	19061892	-	1	NA	Intergenic	Intergenic	-46477	NM_009397	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_116832.1	chr13	54684083	54684114	-	1	NA	exon (NM_001146025, exon 3 of 11)	exon (NM_001146025, exon 3 of 11)	3710	NM_001146025	105239	Mm.25366	NM_134064	ENSMUSG00000034928	Rnf44	AI854545|mKIAA1100	ring finger protein 44	protein-coding
mm_151039.1	chr19	47023546	47023556	+	1	NA	exon (NM_146100, exon 3 of 3)	exon (NM_146100, exon 3 of 3)	-8362	NM_001164363	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_14997.1	chr2	152413686	152413698	+	1	NA	exon (NM_175126, exon 1 of 1)	exon (NM_175126, exon 1 of 1)	1352	NM_175126	67917	Mm.391810	NM_175126	ENSMUSG00000074682	Zcchc3	2810406K24Rik	zinc finger, CCHC domain containing 3	protein-coding
mm_164663.1	chr17	40442997	40442998	+	1	NA	Intergenic	RLTR17B_Mm|LTR|ERVK	-77025	NM_001177584	100126778	Mm.422023	NM_001177584	ENSMUSG00000090747	Esp8	Gm17495	exocrine gland secreted peptide 8	protein-coding
mm_33442.1	chr4	130360160	130360208	+	1	NA	promoter-TSS (NM_025645)	promoter-TSS (NM_025645)	52	NM_025645	66585	Mm.423019	NM_025645	ENSMUSG00000074088	Snrnp40	0610009C03Rik|Prp8bp|Wdr57	small nuclear ribonucleoprotein 40 (U5)	protein-coding
mm_9531.1	chr1	173802741	173802760	-	1	NA	Intergenic	Intergenic	-35831	NM_008329	15951	Mm.261270	NM_008329	ENSMUSG00000073489	Ifi204	Ifi16|p204	interferon activated gene 204	protein-coding
mm_70470.1	chr8	12323661	12323675	+	1	NA	Intergenic	Intergenic	-62103	NR_027975	434280	Mm.447484	NM_001013812	ENSMUSG00000047935	Gm5607	EG434280	predicted gene 5607	ncRNA
mm_117248.1	chr13	64364142	64364195	-	1	NA	exon (NM_009984, exon 8 of 8)	exon (NM_009984, exon 8 of 8)	6352	NM_009984	13039	Mm.930	NM_009984	ENSMUSG00000021477	Ctsl	1190035F06Rik|CatL|Ctsl1|MEP|fs|nkt	cathepsin L	protein-coding
mm_101050.1	chr11	8653185	8653188	-	1	NA	intron (NM_001083587, intron 1 of 30)	intron (NM_001083587, intron 1 of 30)	11349	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_171202.1	chr3	54481703	54481717	+	1	NA	Intergenic	Intergenic	120603	NM_015784	50706	Mm.236067	NM_015784	ENSMUSG00000027750	Postn	A630052E07Rik|AI747096|OSF-2|Osf2|PLF|PN	periostin, osteoblast specific factor	protein-coding
mm_41477.1	chr5	91962467	91962473	+	1	NA	promoter-TSS (NR_028429)	promoter-TSS (NR_028429)	86	NR_073442	68098	Mm.159453	NM_026557	ENSMUSG00000029397	Rchy1	ARNIP|CHIMP|Pirh2|Zfp363|Znf363	ring finger and CHY zinc finger domain containing 1	protein-coding
mm_170616.1	chr19	61199799	61199813	-	1	NA	Intergenic	Intergenic	-23497	NM_001177513	633057	Mm.426097	NM_001177513	ENSMUSG00000094649	Gm7102	EG633057	predicted gene 7102	protein-coding
mm_132184.1	chr16	32419762	32419799	+	1	NA	promoter-TSS (NM_001347183)	promoter-TSS (NM_001347183)	78	NM_001347183	66061	Mm.302693	NM_025329	ENSMUSG00000014075	Tctex1d2	0610012D17Rik|2410011K15Rik	Tctex1 domain containing 2	protein-coding
mm_5348.1	chr1	25094301	25094317	-	1	NA	exon (NM_175642, exon 28 of 31)	exon (NM_175642, exon 28 of 31)	183645	NM_001204913	100504323	Mm.484176	NM_001204913		Gm20172	-	predicted gene, 20172	protein-coding
mm_33396.1	chr4	129820674	129820685	+	1	NA	promoter-TSS (NM_001164745)	promoter-TSS (NM_001164745)	-29	NM_001164745	19244	Mm.193688	NM_008974	ENSMUSG00000028788	Ptp4a2	Prl-2	protein tyrosine phosphatase 4a2	protein-coding
mm_68498.1	chr7	111078505	111078555	-	1	NA	exon (NM_013507, exon 6 of 22)	exon (NM_013507, exon 6 of 22)	4500	NM_001040131	13690	Mm.185453	NM_013507	ENSMUSG00000005610	Eif4g2	DAP-5|E130105L11Rik|Nat1|Natm1|p97	eukaryotic translation initiation factor 4, gamma 2	protein-coding
mm_40325.1	chr5	43910429	43910432	+	1	NA	3' UTR (NM_007646, exon 8 of 8)	3' UTR (NM_007646, exon 8 of 8)	41621	NM_007646	12494	Mm.249873	NM_007646	ENSMUSG00000029084	Cd38	ADPRC 1|Cd38-rs1|I-19	CD38 antigen	protein-coding
mm_172579.1	chr8	120719945	120719945	-	1	NA	Intergenic	Intergenic	-16413	NM_008320	15900	Mm.334861	NM_008320	ENSMUSG00000041515	Irf8	AI893568|ICSBP|IRF-8|Icsbp1|Myls	interferon regulatory factor 8	protein-coding
mm_40478.1	chr5	54047512	54047524	+	1	NA	intron (NM_001081103, intron 1 of 11)	ORR1E|LTR|ERVL-MaLR	48995	NM_001081103	116873	Mm.265985	NM_054083	ENSMUSG00000039156	Stim2	-	stromal interaction molecule 2	protein-coding
mm_125222.1	chr15	34083370	34083372	+	1	NA	exon (NM_026002, exon 1 of 12)	exon (NM_026002, exon 1 of 12)	652	NM_026002	67154	Mm.130883	NM_026002	ENSMUSG00000022255	Mtdh	2610103J23Rik|3D3|3D3/Lyric|AEG-1|AV353288|D8Bwg1112e|Lyric	metadherin	protein-coding
mm_99282.1	chr11	101316837	101316890	+	1	NA	intron (NM_011192, intron 1 of 10)	intron (NM_011192, intron 1 of 10)	612	NM_011192	19192	Mm.288477	NM_011192	ENSMUSG00000078652	Psme3	AA410043|AU020960|Ki|PA28gamma|REGgamma|pa28g	proteaseome (prosome, macropain) activator subunit 3 (PA28 gamma, Ki)	protein-coding
mm_94373.1	chr11	5099627	5099646	+	1	NA	promoter-TSS (NM_007968)	promoter-TSS (NM_007968)	-112	NR_110961	279766	Mm.260866	NM_177370	ENSMUSG00000034175	Rhbdd3	Ptag	rhomboid domain containing 3	protein-coding
mm_1383.1	chr1	66926574	66926580	+	1	NA	exon (NM_001113387, exon 4 of 7)	exon (NM_001113387, exon 4 of 7)	8789	NM_001113387	17901	Mm.1000	NM_021285	ENSMUSG00000061816	Myl1	AI325107|MLC1f|MLC3f|Mylf	myosin, light polypeptide 1	protein-coding
mm_51413.1	chr6	78381069	78381079	+	1	NA	intron (NM_011259, intron 1 of 5)	intron (NM_011259, intron 1 of 5)	365	NM_011259	19694	Mm.2552	NM_011259	ENSMUSG00000079516	Reg3a	AV063448	regenerating islet-derived 3 alpha	protein-coding
mm_52226.1	chr6	103511872	103511894	+	1	NA	intron (NM_007697, intron 1 of 26)	intron (NM_007697, intron 1 of 26)	1007	NM_007697	12661	Mm.251288	NM_007697	ENSMUSG00000030077	Chl1	A530023M13Rik|AI465420|CALL|LICAM2	cell adhesion molecule L1-like	protein-coding
mm_123199.1	chr14	59260186	59260191	-	1	NA	promoter-TSS (NM_001164329)	promoter-TSS (NM_001164329)	28	NM_001164329	628693	Mm.479519	NM_001164329	ENSMUSG00000090881	Gm6904	EG628693	predicted gene 6904	protein-coding
mm_18442.1	chr2	60889021	60889050	-	1	NA	intron (NM_020296, intron 1 of 13)	intron (NM_020296, intron 1 of 13)	-7597	NM_001141931	56878	Mm.259667	NM_020296	ENSMUSG00000026970	Rbms1	2600014B10Rik|AI255215|MSSP-1|MSSP-2|MSSP-3|YC1	RNA binding motif, single stranded interacting protein 1	protein-coding
mm_8273.1	chr1	139660919	139660945	-	1	NA	Intergenic	Intergenic	-100710	NM_015780	50702	Mm.220362	NM_015780	ENSMUSG00000057037	Cfhr1	AI194696|CFHRB|Cfhl1	complement factor H-related 1	protein-coding
mm_116746.1	chr13	51793534	51793542	-	1	NA	5' UTR (NM_001281880, exon 1 of 17)	5' UTR (NM_001281880, exon 1 of 17)	209	NM_001281880	20354	Mm.33903	NM_013660	ENSMUSG00000021451	Sema4d	CD100|Semacl2|Semaj|Semcl2|coll-4	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D	protein-coding
mm_75983.1	chr8	72284962	72284980	-	1	NA	Intergenic	B4A|SINE|B4	-34091	NM_008452	16598	Mm.26938	NM_008452	ENSMUSG00000055148	Klf2	Lklf	Kruppel-like factor 2 (lung)	protein-coding
mm_136431.1	chr16	94370451	94370553	-	1	NA	promoter-TSS (NM_001159620)	promoter-TSS (NM_001159620)	48	NM_001159618	56176	Mm.474449	NM_019543	ENSMUSG00000022940	Pigp	Dcrc|Dscr5	phosphatidylinositol glycan anchor biosynthesis, class P	protein-coding
mm_111744.1	chr12	103904893	103904901	-	1	NA	promoter-TSS (NM_009245)	promoter-TSS (NM_009245)	53	NM_009245	20702	Mm.439692	NM_009245	ENSMUSG00000079015	Serpina1c	Pi3|Pi6|Skalp|Spi1-3|Spi1-6|Wap3	serine (or cysteine) peptidase inhibitor, clade A, member 1C	protein-coding
mm_134376.1	chr16	17144416	17144451	-	1	NA	promoter-TSS (NM_029779)	promoter-TSS (NM_029779)	-10	NM_029779	76872	Mm.101656	NM_029779	ENSMUSG00000022768	Ccdc116	4930432J16Rik	coiled-coil domain containing 116	protein-coding
mm_23696.1	chr3	68693740	68693751	+	1	NA	intron (NM_001159424, intron 3 of 7)	intron (NM_001159424, intron 3 of 7)	2321	NM_008351	16159	Mm.103783	NM_008351	ENSMUSG00000027776	Il12a	IL-12p35|Il-12a|Ll12a|p35	interleukin 12a	protein-coding
mm_129960.1	chr15	85409193	85409218	-	1	NA	intron (NM_016843, intron 9 of 11)	intron (NM_016843, intron 9 of 11)	72824	NM_016843	54138	Mm.248906	NM_016843	ENSMUSG00000016541	Atxn10	AI325283|C77170|E46|Sca10|TEG-169|Tex169	ataxin 10	protein-coding
mm_36823.1	chr4	105109804	105109819	-	1	NA	promoter-TSS (NM_178143)	promoter-TSS (NM_178143)	87	NM_178143	108079	Mm.48638	NM_178143	ENSMUSG00000028518	Prkaa2	2310008I11Rik|A830082D05|AMPKalpha2	protein kinase, AMP-activated, alpha 2 catalytic subunit	protein-coding
mm_118069.1	chr13	102906047	102906111	-	1	NA	intron (NM_175171, intron 4 of 28)	intron (NM_175171, intron 4 of 28)	145824	NR_130171	76624	Mm.426384	NR_130171	ENSMUSG00000091906	1700099I09Rik	-	RIKEN cDNA 1700099I09 gene	ncRNA
mm_46903.1	chr5	114271163	114271164	-	1	NA	intron (NM_148935, intron 2 of 9)	intron (NM_148935, intron 2 of 9)	2598	NM_148935	116810	Mm.17709	NM_148935	ENSMUSG00000042002	Foxn4	-	forkhead box N4	protein-coding
mm_14088.1	chr2	125152593	125152606	+	1	NA	promoter-TSS (NM_001079690)	promoter-TSS (NM_001079690)	-1	NM_183354	20495	Mm.3914	NM_011389	ENSMUSG00000027202	Slc12a1	AI788571|D630042G03Rik|Nkcc2|mBSC1|urehr3	solute carrier family 12, member 1	protein-coding
mm_159796.1	chr5	111417985	111417985	+	1	NA	promoter-TSS (NM_001081235)	promoter-TSS (NM_001081235)	-181	NM_001081235	433938	Mm.332576	NM_001081235	ENSMUSG00000070576	Mn1	AA003644|AA009236	meningioma 1	protein-coding
mm_29474.1	chr3	115711038	115711048	-	1	NA	3' UTR (NM_007901, exon 2 of 2)	3' UTR (NM_007901, exon 2 of 2)	4012	NM_007901	13609	Mm.982	NM_007901	ENSMUSG00000045092	S1pr1	AI849002|Edg1|Lpb1|S1p|S1p1	sphingosine-1-phosphate receptor 1	protein-coding
mm_127733.1	chr15	103293405	103293406	+	1	NA	intron (NM_019817, intron 4 of 8)	intron (NM_019817, intron 4 of 8)	8280	NR_029766	724064		NR_029766	ENSMUSG00000065560	Mir148b	Mirn148b|mir-148b	microRNA 148b	ncRNA
mm_118316.1	chr13	113155503	113155546	-	1	NA	Intergenic	Intergenic	19448	NR_131045	76720	Mm.54263	NR_131045		1700084D21Rik	-	RIKEN cDNA 1700084D21 gene	ncRNA
mm_69475.1	chr7	133732267	133732269	-	1	NA	intron (NM_133941, intron 7 of 11)	intron (NM_133941, intron 7 of 11)	22935	NM_025392	66165	Mm.389983	NM_025392	ENSMUSG00000030983	Bccip	1110013J05Rik|TOK-1	BRCA2 and CDKN1A interacting protein	protein-coding
mm_14392.1	chr2	129800732	129800740	+	1	NA	exon (NM_183262, exon 1 of 4)	exon (NM_183262, exon 1 of 4)	219	NM_001038635	67333	Mm.389329	NM_183262	ENSMUSG00000037885	Stk35	1700054C12Rik|CLIK1|Stk35l1	serine/threonine kinase 35	protein-coding
mm_70139.1	chr7	143296530	143296566	-	1	NA	promoter-TSS (NR_001461)	promoter-TSS (NR_001461)	-1	NR_001461	63830	Mm.356096	NR_001461	ENSMUSG00000101609	Kcnq1ot1	Kvlqt1-as|Lit1|Tssc8	KCNQ1 overlapping transcript 1	ncRNA
mm_43331.1	chr5	135009768	135009776	+	1	NA	exon (NM_145215, exon 1 of 6)	exon (NM_145215, exon 1 of 6)	316	NR_033794	68758	Mm.389700	NM_145215	ENSMUSG00000040532	Abhd11	1110054D16Rik|A630008N09Rik|Wbscr21	abhydrolase domain containing 11	protein-coding
mm_9400.1	chr1	172234624	172234632	-	1	NA	intron (NM_013734, intron 14 of 22)	intron (NM_013734, intron 14 of 22)	-14733	NM_009813	12372	Mm.12829	NM_009813	ENSMUSG00000007122	Casq1	CSQ|CSQ-1|CSQ1|sCSQ	calsequestrin 1	protein-coding
mm_152357.1	chr19	10064777	10064815	-	1	NA	exon (NM_019699, exon 11 of 12)	exon (NM_019699, exon 11 of 12)	23248	NM_021890	60527	Mm.253875	NM_021890	ENSMUSG00000024664	Fads3	AI464531	fatty acid desaturase 3	protein-coding
mm_36082.1	chr4	58206600	58206616	-	1	NA	promoter-TSS (NM_022814)	promoter-TSS (NM_022814)	-12	NM_022814	64817	Mm.261024	NM_022814	ENSMUSG00000028369	Svep1	1110021D17Rik|4833413O10Rik|AA387071|D430029O09Rik|Polydom	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	protein-coding
mm_102323.1	chr11	57518597	57518655	-	1	NA	promoter-TSS (NM_145426)	promoter-TSS (NM_145426)	18	NM_001168667	67726	Mm.25632	NM_026342	ENSMUSG00000020523	Fam114a2	1810073G14Rik|9030624B09Rik	family with sequence similarity 114, member A2	protein-coding
mm_84253.1	chr9	62497857	62497868	-	1	NA	intron (NM_175484, intron 1 of 11)	ORR1D1|LTR|ERVL-MaLR	39182	NM_175484	235431	Mm.335229	NM_175484	ENSMUSG00000041729	Coro2b	CLIPINC|E130012P22Rik	coronin, actin binding protein, 2B	protein-coding
mm_41613.1	chr5	96793427	96793431	+	1	NA	promoter-TSS (NM_013470)	promoter-TSS (NM_013470)	44	NM_013470	11745	Mm.7214	NM_013470	ENSMUSG00000029484	Anxa3	Anx3	annexin A3	protein-coding
mm_49255.1	chr6	17408334	17408351	+	1	NA	Intergenic	Intergenic	-55615	NM_008591	17295	Mm.86844	NM_008591	ENSMUSG00000009376	Met	AI838057|HGF|HGFR|Par4|c-Met	met proto-oncogene	protein-coding
mm_158289.1	chrX	112698376	112698386	-	1	NA	exon (NM_181579, exon 2 of 17)	exon (NM_181579, exon 2 of 17)	270	NM_181579	69693	Mm.34964	NM_181579	ENSMUSG00000034607	Pof1b	2310066B14Rik	premature ovarian failure 1B	protein-coding
mm_145876.1	chr18	65476187	65476201	+	1	NA	exon (NM_172833, exon 16 of 16)	exon (NM_172833, exon 16 of 16)	45197	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_60551.1	chr7	44480990	44481010	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-3517	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_125512.1	chr15	55591774	55591791	+	1	NA	intron (NM_134092, intron 13 of 21)	intron (NM_134092, intron 13 of 21)	34374	NM_001168250	105837	Mm.390829	NM_134092	ENSMUSG00000022369	Mtbp	AI429604|MDM2BP	Mdm2, transformed 3T3 cell double minute p53 binding protein	protein-coding
mm_58745.1	chr7	13278545	13278565	+	1	NA	promoter-TSS (NM_010715)	promoter-TSS (NM_010715)	166	NM_177312	321008	Mm.458832	NM_177312	ENSMUSG00000070814	6330408A02Rik	-	RIKEN cDNA 6330408A02 gene	protein-coding
mm_35080.1	chr4	6991250	6991264	-	1	NA	promoter-TSS (NM_145711)	promoter-TSS (NM_145711)	-534	NM_145711	252838	Mm.435828	NM_145711	ENSMUSG00000041272	Tox	1700007F02Rik	thymocyte selection-associated high mobility group box	protein-coding
mm_160468.1	chr8	111178001	111178001	-	1	NA	intron (NM_009149, intron 11 of 25)	RSINE1|SINE|B4	-32503	NR_040364	434350	Mm.442061	NR_040363		9430091E24Rik	-	RIKEN cDNA 9430091E24 gene	ncRNA
mm_153947.1	chr19	47580502	47580547	-	1	NA	intron (NM_009289, intron 1 of 18)	CpG	505	NM_001164639	20874	Mm.281011	NM_009289	ENSMUSG00000025060	Slk	9A2|AV021402|AW411554|Etk4|SMAK|Stk2|mKIAA0204|mSLK	STE20-like kinase	protein-coding
mm_148856.1	chr19	6397641	6397659	+	1	NA	exon (NM_011224, exon 18 of 20)	exon (NM_011224, exon 18 of 20)	-2933	NM_011242	19395	Mm.77017	NM_011242	ENSMUSG00000032946	Rasgrp2	CDC25L|Caldaggef1	RAS, guanyl releasing protein 2	protein-coding
mm_55991.1	chr6	86003577	86003588	-	1	NA	Intergenic	Intergenic	-13609	NM_012013	26910	Mm.8024	NM_012013	ENSMUSG00000030001	Figla	FIGalpha|bHLHc8	folliculogenesis specific basic helix-loop-helix	protein-coding
mm_139102.1	chr17	47141200	47141243	+	1	NA	intron (NM_001097623, intron 2 of 19)	intron (NM_001097623, intron 2 of 19)	279	NM_001097623	224829	Mm.260989	NM_172622		Trerf1	9430096I18Rik|AI429294|B830015H24|RAPA|Trep-132|Trep132	transcriptional regulating factor 1	protein-coding
mm_53830.1	chr6	148047381	148047407	+	1	NA	promoter-TSS (NM_178797)	promoter-TSS (NM_178797)	-22	NM_001347516	330450	Mm.447274	NM_178797	ENSMUSG00000030303	Far2	A230046P18|AW048109|BC055759|Mlstd1	fatty acyl CoA reductase 2	protein-coding
mm_121865.1	chr14	20733648	20733672	-	1	NA	intron (NM_010811, intron 1 of 14)	intron (NM_010811, intron 1 of 14)	902	NM_010811	17423	Mm.4084	NM_010811	ENSMUSG00000039308	Ndst2	Mndns|NDST-2	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 2	protein-coding
mm_10078.1	chr1	195131494	195131504	-	1	NA	promoter-TSS (NM_013499)	promoter-TSS (NM_013499)	71	NM_013499	12946	Mm.301652	NM_013499	ENSMUSG00000016481	Cr1l	Crry|Mcp|mCRY	complement component (3b/4b) receptor 1-like	protein-coding
mm_66610.1	chr7	45466472	45466487	-	1	NA	intron (NM_007527, intron 1 of 5)	intron (NM_007527, intron 1 of 5)	419	NM_007527	12028	Mm.19904	NM_007527	ENSMUSG00000003873	Bax	-	BCL2-associated X protein	protein-coding
mm_171158.1	chr3	22731018	22731022	-	1	NA	Intergenic	L1Md_A|LINE|L1	479650	NR_004439	19784		NR_004439		Rprl2	RPRH3|Rmrp3	ribonuclease P RNA-like 2	ncRNA
mm_59669.1	chr7	28377487	28377495	+	1	NA	3' UTR (NM_011756, exon 2 of 2)	3' UTR (NM_011756, exon 2 of 2)	1737	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_95343.1	chr11	48782585	48782588	+	1	NA	Intergenic	U4|snRNA|snRNA	-17774	NM_008143	14694	Mm.5305	NM_008143	ENSMUSG00000020372	Rack1	AL033335|GB-like|Gnb2-rs1|Gnb2l1|p205	receptor for activated C kinase 1	protein-coding
mm_78827.1	chr9	44107287	44107355	+	1	NA	promoter-TSS (NM_001040631)	promoter-TSS (NM_001040631)	12	NM_001190319	235312	Mm.227110	NM_145613	ENSMUSG00000079592	C1qtnf5	Ctrp5	C1q and tumor necrosis factor related protein 5	protein-coding
mm_36258.1	chr4	63410746	63410757	-	1	NA	Intergenic	CpG	-7306	NM_001045514	100182	Mm.387725	NM_001045514	ENSMUSG00000039158	Akna	AI597013	AT-hook transcription factor	protein-coding
mm_53563.1	chr6	137252298	137252326	+	1	NA	promoter-TSS (NM_011216)	promoter-TSS (NM_011216)	13	NM_011216	19277	Mm.186361	NM_011216	ENSMUSG00000030223	Ptpro	D28|GLEPP1|PTPBK|PTPROt|PTPU2|PTPoc|PTPphi|Ptpn15|R-PTP-O	protein tyrosine phosphatase, receptor type, O	protein-coding
mm_45108.1	chr5	45444592	45444606	-	1	NA	intron (NM_024236, intron 3 of 6)	intron (NM_024236, intron 3 of 6)	5630	NM_024236	110391	Mm.30204	NM_024236	ENSMUSG00000015806	Qdpr	2610008L04Rik|D5Ertd371e|Dhpr|PKU2	quinoid dihydropteridine reductase	protein-coding
mm_95527.1	chr11	52232184	52232228	+	1	NA	intron (NM_011543, intron 1 of 5)	CpG	211	NM_011543	21402	Mm.42944	NM_011543	ENSMUSG00000036309	Skp1a	15kDa|2610043E24Rik|2610206H23Rik|EMC19|OCP-II|OCP2|SKP1|Tceb1l|p19A|p19Skp1	S-phase kinase-associated protein 1A	protein-coding
mm_173352.1	chrY	90813895	90813896	+	1	NA	intron (NM_133362, intron 2 of 3)	(TTAGGG)n|Simple_repeat|Simple_repeat	25511	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_156887.1	chrX	166372667	166372677	+	1	NA	exon (NM_001177959, exon 2 of 7)	exon (NM_001177959, exon 2 of 7)	28119	NM_001177960	14758	Mm.222320	NM_023122	ENSMUSG00000031342	Gpm6b	AI593561|Gpm6|M6B	glycoprotein m6b	protein-coding
mm_105872.1	chr11	114890225	114890226	-	1	NA	5' UTR (NM_170758, exon 1 of 7)	5' UTR (NM_170758, exon 1 of 7)	184	NM_170758	217303	Mm.294439	NM_170758	ENSMUSG00000034652	Cd300a	B230315M08Rik|Clm8|LMIR1|MAIR-I|MAIR-Ia|MMAC8|Pigr4|mcpir1	CD300A molecule	protein-coding
mm_19089.1	chr2	79258029	79258060	-	1	NA	intron (NM_010576, intron 2 of 27)	intron (NM_010576, intron 2 of 27)	2618	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D|Itga4B	integrin alpha 4	protein-coding
mm_93954.1	chr10	127263148	127263156	-	1	NA	5' UTR (NM_001039000, exon 1 of 29)	5' UTR (NM_001039000, exon 1 of 29)	211	NM_008447	16572	Mm.30355	NM_008447	ENSMUSG00000074657	Kif5a	D10Bwg0738e|Khc|Kif5|Kns|mKIAA4086	kinesin family member 5A	protein-coding
mm_172583.1	chr8	122841573	122841589	+	1	NA	Intergenic	Intergenic	-6793	NM_007662	12555	Mm.1976	NM_007662	ENSMUSG00000031962	Cdh15	AI323380|Cdh14|Mcad	cadherin 15	protein-coding
mm_92424.1	chr10	77085343	77085361	-	1	NA	exon (NM_001109991, exon 5 of 41)	exon (NM_001109991, exon 5 of 41)	28353	NM_001109991	12822	Mm.4352	NM_009929	ENSMUSG00000001435	Col18a1	-	collagen, type XVIII, alpha 1	protein-coding
mm_17415.1	chr2	27248305	27248320	-	1	NA	Intergenic	Intergenic	-1009	NM_138665	192166	Mm.278467	NM_138665	ENSMUSG00000009614	Sardh	-	sarcosine dehydrogenase	protein-coding
mm_59361.1	chr7	25687366	25687377	+	1	NA	TTS (NM_172148)	TTS (NM_172148)	369	NM_011577	21803	Mm.248380	NM_011577	ENSMUSG00000002603	Tgfb1	TGF-beta1|TGFbeta1|Tgfb|Tgfb-1	transforming growth factor, beta 1	protein-coding
mm_56169.1	chr6	88000290	88000328	-	1	NA	3' UTR (NM_009005, exon 6 of 6)	3' UTR (NM_009005, exon 6 of 6)	18626	NR_026990	434064	Mm.371796	NR_026990	ENSMUSG00000084950	Gm5577	EG434064	predicted gene 5577	ncRNA
mm_83852.1	chr9	54560088	54560098	-	1	NA	promoter-TSS (NM_019686)	promoter-TSS (NM_019686)	-14	NM_019686	56506	Mm.42192	NM_019686	ENSMUSG00000037493	Cib2	2810434I23Rik|AI449053	calcium and integrin binding family member 2	protein-coding
mm_51146.1	chr6	70607392	70607414	+	1	NA	Intergenic	Intergenic	184772	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_127588.1	chr15	102331961	102331991	+	1	NA	TTS (NM_027044)	TTS (NM_027044)	267	NM_021713	60315	Mm.251638	NM_021713	ENSMUSG00000001285	Myg1	0610023A07Rik|2810433J21Rik|5830429P19Rik|AI325965|Gamm1	melanocyte proliferating gene 1	protein-coding
mm_148496.1	chr19	4171582	4171595	+	1	NA	exon (NM_134148, exon 5 of 10)	exon (NM_134148, exon 5 of 10)	3891	NM_134148	107239	Mm.482310	NM_134148	ENSMUSG00000075289	Carns1	AI790298|Atpgd1|mKIAA1394	carnosine synthase 1	protein-coding
mm_3878.1	chr1	161034904	161034921	+	1	NA	promoter-TSS (NM_173424)	promoter-TSS (NM_173424)	-254	NR_002840	14455	Mm.270065	NR_002840	ENSMUSG00000053332	Gas5	Gas-5|Mir5117|Snhg2	growth arrest specific 5	ncRNA
mm_425.1	chr1	34459757	34459814	+	1	NA	promoter-TSS (NM_011206)	promoter-TSS (NM_011206)	39	NM_011206	19253	Mm.361	NM_011206	ENSMUSG00000026126	Ptpn18	FLP1|HSCF|PTP-HSCF|PTP-K1|Ptpk1	protein tyrosine phosphatase, non-receptor type 18	protein-coding
mm_7465.1	chr1	120479034	120479049	-	1	NA	intron (NM_010766, intron 13 of 16)	intron (NM_010766, intron 13 of 16)	26043	NM_010766	17167	Mm.1856	NM_010766	ENSMUSG00000026390	Marco	AI323439|Ly112|Scara2	macrophage receptor with collagenous structure	protein-coding
mm_116842.1	chr13	54691787	54691793	-	1	NA	intron (NR_027395, intron 1 of 10)	Charlie8|DNA|hAT-Charlie	2170	NR_027395	105239	Mm.25366	NM_134064	ENSMUSG00000034928	Rnf44	AI854545|mKIAA1100	ring finger protein 44	protein-coding
mm_9721.1	chr1	179803855	179803892	-	1	NA	5' UTR (NM_026375, exon 1 of 36)	5' UTR (NM_026375, exon 1 of 36)	142	NM_026375	226747	Mm.128165	NM_026375	ENSMUSG00000026491	Ahctf1	6230412P20Rik|AV011447|Elys	AT hook containing transcription factor 1	protein-coding
mm_5309.1	chr1	22398683	22398686	-	1	NA	exon (NM_053270, exon 8 of 17)	exon (NM_053270, exon 8 of 17)	34159	NM_053270	116837	Mm.60061	NM_053270	ENSMUSG00000041670	Rims1	C030033M19Rik|RIM1|RIM1a|RIM1alpha|Rab3ip1|Rim|Serg1|mKIAA0340	regulating synaptic membrane exocytosis 1	protein-coding
mm_25122.1	chr3	102012431	102012441	+	1	NA	intron (NM_178777, intron 2 of 2)	CpG	2291	NM_178777	18072	Mm.137286	NM_178777	ENSMUSG00000048540	Nhlh2	6230401I09Rik|Hen2|NSCL2|Nscl-2|bHLHa34	nescient helix loop helix 2	protein-coding
mm_49747.1	chr6	34746083	34746096	+	1	NA	intron (NM_001347100, intron 5 of 13)	intron (NM_001347100, intron 5 of 13)	-34343	NM_001289657	76223	Mm.150047	NM_178630	ENSMUSG00000038836	Agbl3	2900053G10Rik|4930431N21Rik|6530406M24Rik|CCP3	ATP/GTP binding protein-like 3	protein-coding
mm_45624.1	chr5	76182491	76182498	-	1	NA	Intergenic	Intergenic	-1386	NM_011626	21982	Mm.790	NM_011626	ENSMUSG00000029234	Tmem165	AV026557|Tpardl|Tparl|pFT27	transmembrane protein 165	protein-coding
mm_44002.1	chr5	146948641	146948716	+	1	NA	promoter-TSS (NM_025652)	promoter-TSS (NM_025652)	21	NM_025652	66596	Mm.196528	NM_025652	ENSMUSG00000016503	Gtf3a	2010015D03Rik|2610111I01Rik|5330403M05Rik	general transcription factor III A	protein-coding
mm_139965.1	chr17	71673233	71673241	+	1	NA	promoter-TSS (NM_177087)	promoter-TSS (NM_177087)	-24	NM_177087	320159	Mm.187372	NM_177087	ENSMUSG00000045761	Fam179a	4632412N22Rik	family with sequence similarity 179, member A	protein-coding
mm_28071.1	chr3	84304648	84304660	-	1	NA	5' UTR (NM_001271726, exon 1 of 12)	5' UTR (NM_001271726, exon 1 of 12)	121	NM_001271726	80890	Mm.44876	NM_030706	ENSMUSG00000027993	Trim2	mKIAA0517|narf	tripartite motif-containing 2	protein-coding
mm_34582.1	chr4	150142284	150142288	+	1	NA	intron (NM_019741, intron 12 of 13)	intron (NM_019741, intron 12 of 13)	-6686	NM_001085529	435818	Mm.359648	NM_001085529	ENSMUSG00000062064	Slc2a7	OTTMUSG00000010396	solute carrier family 2 (facilitated glucose transporter), member 7	protein-coding
mm_29508.1	chr3	116253412	116253433	-	1	NA	promoter-TSS (NM_022427)	promoter-TSS (NM_022427)	62	NM_022427	64378	Mm.40025	NM_022427	ENSMUSG00000068696	Gpr88	AW061286|Strg	G-protein coupled receptor 88	protein-coding
mm_99915.1	chr11	110180162	110180173	+	1	NA	intron (NM_147218, intron 36 of 38)	intron (NM_147218, intron 36 of 38)	-12014	NM_147220	217262	Mm.291459	NM_147220	ENSMUSG00000041797	Abca9	D630040K07Rik	ATP-binding cassette, sub-family A (ABC1), member 9	protein-coding
mm_102571.1	chr11	61579301	61579347	-	1	NA	intron (NM_001252188, intron 1 of 10)	CpG	363	NM_010148	13855	Mm.139695	NM_010148	ENSMUSG00000001036	Epn2	9530051D10Rik|AA536924|Ibp2	epsin 2	protein-coding
mm_161378.1	chr14	70078957	70078957	+	1	NA	exon (NM_001289927, exon 2 of 2)	exon (NM_001289927, exon 2 of 2)	1162	NM_001289927	13655	Mm.103737	NM_018781	ENSMUSG00000033730	Egr3	Pilot	early growth response 3	protein-coding
mm_15856.1	chr2	164785995	164786071	+	1	NA	promoter-TSS (NM_133924)	promoter-TSS (NM_133924)	12	NM_133924	101113	Mm.295647	NM_133924	ENSMUSG00000050373	Snx21	5730407K14Rik|AI481716	sorting nexin family member 21	protein-coding
mm_108365.1	chr12	80793340	80793355	+	1	NA	intron (NM_001242419, intron 1 of 6)	PB1D10|SINE|Alu	2815	NM_001242419	217684	Mm.341776	NM_178682	ENSMUSG00000021133	Susd6	4933426M11Rik|mKIAA0247	sushi domain containing 6	protein-coding
mm_92536.1	chr10	79614013	79614055	-	1	NA	promoter-TSS (NM_198614)	promoter-TSS (NM_198614)	-9	NM_001168624	237397	Mm.334207	NM_198614	ENSMUSG00000045912	C2cd4c	4932409I22Rik|Fam148c|Gm238	C2 calcium-dependent domain containing 4C	protein-coding
mm_14747.1	chr2	144527739	144527773	+	1	NA	promoter-TSS (NM_029763)	promoter-TSS (NM_029763)	11	NM_029763	70408	Mm.389351	NM_029763	ENSMUSG00000027427	Polr3f	2810411G20Rik|3010019O03Rik|3110032A07Rik|RPC39|RPC6	polymerase (RNA) III (DNA directed) polypeptide F	protein-coding
mm_25443.1	chr3	108200600	108200629	+	1	NA	intron (NM_028061, intron 1 of 2)	CpG	220	NM_028061	72023	Mm.246391	NM_028061	ENSMUSG00000048796	Cyb561d1	1600010M23Rik|AI605489|AW457162	cytochrome b-561 domain containing 1	protein-coding
mm_84309.1	chr9	63666824	63666845	-	1	NA	intron (NM_016769, intron 3 of 8)	intron (NM_016769, intron 3 of 8)	64179	NM_025857	66939	Mm.34338	NM_025857	ENSMUSG00000037257	Aagab	2310007F21Rik|p34	alpha- and gamma-adaptin binding protein	protein-coding
mm_160268.1	chr7	115801509	115801509	-	1	NA	promoter-TSS (NM_001277328)	promoter-TSS (NM_001277328)	100	NM_001277328	20679	Mm.323365	NM_011445	ENSMUSG00000051910	Sox6	AI987981|SOX-LZ	SRY (sex determining region Y)-box 6	protein-coding
mm_124511.1	chr14	121915982	121915986	-	1	NA	promoter-TSS (NM_182806)	promoter-TSS (NM_182806)	-210	NM_182806	110168	Mm.37405	NM_182806	ENSMUSG00000050350	Gpr18	-	G protein-coupled receptor 18	protein-coding
mm_94897.1	chr11	29172914	29172925	+	1	NA	promoter-TSS (NM_134034)	promoter-TSS (NM_134034)	12	NM_134034	104570	Mm.276386	NM_134034	ENSMUSG00000020463	Smek2	AW011752|AW557776|Ppp4r3b|mKIAA1387	SMEK homolog 2, suppressor of mek1 (Dictyostelium)	protein-coding
mm_92648.1	chr10	80398274	80398277	-	1	NA	intron (NM_001306143, intron 1 of 6)	intron (NM_001306143, intron 1 of 6)	1256	NM_013595	17192	Mm.7142	NM_013595	ENSMUSG00000035478	Mbd3	AI181826|AU019209	methyl-CpG binding domain protein 3	protein-coding
mm_105190.1	chr11	101987005	101987013	-	1	NA	promoter-TSS (NM_029287)	promoter-TSS (NM_029287)	-47	NM_029287	75437	Mm.108632	NM_029287	ENSMUSG00000010841	1700006E09Rik	-	RIKEN cDNA 1700006E09 gene	protein-coding
mm_75113.1	chr8	34156581	34156585	-	1	NA	intron (NM_026432, intron 1 of 5)	intron (NM_026432, intron 1 of 5)	2020	NM_026432	67887	Mm.290353	NM_026432	ENSMUSG00000031532	Saraf	1810045K07Rik|Tmem66	store-operated calcium entry-associated regulatory factor	protein-coding
mm_107268.1	chr12	29528640	29528649	+	1	NA	5' UTR (NM_008666, exon 1 of 25)	5' UTR (NM_008666, exon 1 of 25)	260	NM_008666	17933	Mm.253067	NM_008666	ENSMUSG00000061911	Myt1l	2900046C06Rik|2900093J19Rik|C630034G21Rik|Nztf1|Pmng1|Png-1|mKIAA1106	myelin transcription factor 1-like	protein-coding
mm_123024.1	chr14	55116616	55116637	-	1	NA	5' UTR (NM_177049, exon 1 of 6)	5' UTR (NM_177049, exon 1 of 6)	309	NM_177049	319984	Mm.19047	NM_177049	ENSMUSG00000022208	Jph4	9330157P13Rik|JP-4|JPHL1	junctophilin 4	protein-coding
mm_164520.1	chr16	97423704	97423704	+	1	NA	intron (NM_019517, intron 7 of 8)	B1_Mur1|SINE|Alu	39201	NM_010846	17857	Mm.33996	NM_010846	ENSMUSG00000000386	Mx1	AI893580|Mx|Mx-1	MX dynamin-like GTPase 1	protein-coding
mm_120025.1	chr14	55784119	55784180	+	1	NA	promoter-TSS (NM_080435)	promoter-TSS (NM_080435)	-130	NM_080435	104110	Mm.287010	NM_080435	ENSMUSG00000022220	Adcy4	mKIAA4004	adenylate cyclase 4	protein-coding
mm_140074.1	chr17	75165179	75165179	+	1	NA	intron (NM_019919, intron 4 of 33)	intron (NM_019919, intron 4 of 33)	-13602	NM_001331236	268977	Mm.269747	NM_019919	ENSMUSG00000001870	Ltbp1	9430031G15Rik|9830146M04|Ltbp-1|Ltbp1L|TGF-beta1-BP-1|Tgfb|b2b1000Clo	latent transforming growth factor beta binding protein 1	protein-coding
mm_56369.1	chr6	93913596	93913610	-	1	NA	promoter-TSS (NR_104594)	promoter-TSS (NR_104594)	87	NM_001286788	14924	Mm.217216	NM_010367	ENSMUSG00000045095	Magi1	AIP3|BAP1|Baiap1|Gukmi1|MAGI1c|Magi-1|TNRC19|WWP3|mKIAA4129	membrane associated guanylate kinase, WW and PDZ domain containing 1	protein-coding
mm_145769.1	chr18	65023812	65023852	+	1	NA	5' UTR (NM_031881, exon 1 of 30)	5' UTR (NM_031881, exon 1 of 30)	305	NM_031881	83814	Mm.98668	NM_031881	ENSMUSG00000024589	Nedd4l	1300012C07Rik|Nedd4-2|Nedd4b	neural precursor cell expressed, developmentally down-regulated gene 4-like	protein-coding
mm_2507.1	chr1	106213662	106213685	+	1	NA	intron (NM_133821, intron 1 of 16)	intron (NM_133821, intron 1 of 16)	41804	NM_133821	98432	Mm.24115	NM_133821	ENSMUSG00000044340	Phlpp1	AI836256|Phlpp|Plekhe1|SCOP|mKIAA0606	PH domain and leucine rich repeat protein phosphatase 1	protein-coding
mm_109714.1	chr12	114932399	114932402	+	1	NA	Intergenic	Intergenic	-418706	NR_106063	102465664		NR_106063	ENSMUSG00000098357	Mir7094-2	Gm27508|mmu-mir-7094-2	microRNA 7094-2	ncRNA
mm_28439.1	chr3	90490783	90490790	-	1	NA	intron (NM_133854, intron 1 of 3)	intron (NM_133854, intron 1 of 3)	227	NM_133854	20615	Mm.331182	NM_133854	ENSMUSG00000001018	Snapin	25kDa|AA407989|AV026596|Bloc1s7|Snap25bp|Snapap	SNAP-associated protein	protein-coding
mm_133497.1	chr16	90386383	90386454	+	1	NA	promoter-TSS (NM_015755)	promoter-TSS (NM_015755)	21	NM_015755	26559	Mm.125874	NM_015755	ENSMUSG00000053414	Hunk	Bstk1|Mak-v	hormonally upregulated Neu-associated kinase	protein-coding
mm_104030.1	chr11	86232148	86232179	-	1	NA	intron (NM_027421, intron 14 of 24)	intron (NM_027421, intron 14 of 24)	25405	NM_027421	70422	Mm.171304	NM_027421	ENSMUSG00000018068	Ints2	2810417D08Rik|AA408260|AI987735|mKIAA1287	integrator complex subunit 2	protein-coding
mm_120683.1	chr14	70659361	70659386	+	1	NA	3' UTR (NM_023045, exon 28 of 28)	3' UTR (NM_023045, exon 28 of 28)	-6289	NM_181345	328440	Mm.347749	NM_181345	ENSMUSG00000047911	Npm2	-	nucleophosmin/nucleoplasmin 2	protein-coding
mm_33205.1	chr4	126412817	126412824	+	1	NA	intron (NM_153402, intron 2 of 18)	RMER19B|LTR|ERVK	16722	NM_153402	214150	Mm.440915	NM_153402	ENSMUSG00000028842	Ago3	AW048688|C130014L07Rik|Eif2c3	argonaute RISC catalytic subunit 3	protein-coding
mm_87245.1	chr10	40938192	40938200	+	1	NA	3' UTR (NM_031877, exon 9 of 9)	3' UTR (NM_031877, exon 9 of 9)	54662	NM_031877	83767	Mm.41353	NM_031877	ENSMUSG00000019831	Wasf1	AI195380|AI838537|Scar|WAVE|WAVE-1	WAS protein family, member 1	protein-coding
mm_124289.1	chr14	103054541	103054578	-	1	NA	exon (NM_008392, exon 5 of 5)	exon (NM_008392, exon 5 of 5)	7547	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_57297.1	chr6	124464674	124464682	-	1	NA	5' UTR (NM_153508, exon 1 of 18)	5' UTR (NM_153508, exon 1 of 18)	106	NM_153508	232370	Mm.193701	NM_153508	ENSMUSG00000008153	Clstn3	CSTN3|Cs3|Cst-3|alc-beta	calsyntenin 3	protein-coding
mm_134168.1	chr16	10796368	10796374	-	1	NA	TTS (NM_013637)	TTS (NM_013637)	452	NM_013637	19118	Mm.42733	NM_013637	ENSMUSG00000022501	Prm1	Prm-1	protamine 1	protein-coding
mm_15029.1	chr2	152694987	152695013	+	1	NA	intron (NM_010376, intron 9 of 11)	intron (NM_010376, intron 9 of 11)	7852	NM_025543	66405	Mm.440291	NM_025543	ENSMUSG00000042814	Mcts2	2400002F11Rik|MCT-2	malignant T cell amplified sequence 2	protein-coding
mm_28028.1	chr3	83046779	83046792	-	1	NA	exon (NM_181849, exon 2 of 8)	exon (NM_181849, exon 2 of 8)	3078	NM_181849	110135	Mm.30063	NM_181849	ENSMUSG00000033831	Fgb	2510049G14Rik	fibrinogen beta chain	protein-coding
mm_172746.1	chr8	80739474	80739484	-	1	NA	promoter-TSS (NM_053124)	promoter-TSS (NM_053124)	-20	NM_053124	93762	Mm.246803	NM_053124	ENSMUSG00000031715	Smarca5	4933427E24Rik|D030040M08Rik|D330027N15Rik|MommeD4|Snf2h	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5	protein-coding
mm_4616.1	chr1	178739991	178739991	+	1	NA	intron (NM_001161665, intron 4 of 14)	intron (NM_001161665, intron 4 of 14)	210866	NM_001161665	269152	Mm.129727	NM_177724	ENSMUSG00000026494	Kif26b	4832420M10|BC056349|D230039L06Rik	kinesin family member 26B	protein-coding
mm_137168.1	chr17	23812365	23812378	+	1	NA	intron (NM_175229, intron 8 of 13)	intron (NM_175229, intron 8 of 13)	9184	NM_175229	75956	Mm.5222	NM_175229	ENSMUSG00000039218	Srrm2	5033413A03Rik|AA410130|SRm300|mKIAA0324	serine/arginine repetitive matrix 2	protein-coding
mm_148546.1	chr19	4711346	4711354	+	1	NA	5' UTR (NM_021287, exon 1 of 37)	5' UTR (NM_021287, exon 1 of 37)	127	NM_021287	20743	Mm.329668	NM_021287	ENSMUSG00000067889	Sptbn2	Spnb3|mKIAA0302	spectrin beta, non-erythrocytic 2	protein-coding
mm_40640.1	chr5	64910287	64910311	+	1	NA	Intergenic	RSINE1|SINE|B4	22400	NM_030682	21897	Mm.273024	NM_030682	ENSMUSG00000044827	Tlr1	-	toll-like receptor 1	protein-coding
mm_64987.1	chr7	16916358	16916375	-	1	NA	3' UTR (NM_007590, exon 6 of 6)	3' UTR (NM_007590, exon 6 of 6)	7666	NM_007590	12315	Mm.288630	NM_007590	ENSMUSG00000019370	Calm3	CaMA|R75142	calmodulin 3	protein-coding
mm_115748.1	chr13	18031617	18031626	-	1	NA	Intergenic	Intergenic	-38270	NM_025904	67008	Mm.252918	NM_025904	ENSMUSG00000075054	Yae1d1	1600012F09Rik	Yae1 domain containing 1	protein-coding
mm_131871.1	chr16	23175351	23175377	+	1	NA	Intergenic	Intergenic	28828	NM_009605	11450	Mm.3969	NM_009605	ENSMUSG00000022878	Adipoq	30kDa|APN|Acdc|Acrp30|Ad|GBP28|adipo|apM1	adiponectin, C1Q and collagen domain containing	protein-coding
mm_79514.1	chr9	57521235	57521314	+	1	NA	promoter-TSS (NM_007747)	promoter-TSS (NM_007747)	42	NM_007747	12858	Mm.273403	NM_007747	ENSMUSG00000000088	Cox5a	AA959768|CcOX	cytochrome c oxidase subunit Va	protein-coding
mm_149604.1	chr19	16349614	16349630	+	1	NA	intron (NM_008139, intron 5 of 6)	L1MB3|LINE|L1	-34618	NR_105832	102465218		NR_105832	ENSMUSG00000098718	Mir496b	Gm28028|mmu-mir-496b	microRNA 496b	ncRNA
mm_70469.1	chr8	12323645	12323659	+	1	NA	Intergenic	Intergenic	-62119	NR_027975	434280	Mm.447484	NM_001013812	ENSMUSG00000047935	Gm5607	EG434280	predicted gene 5607	ncRNA
mm_148581.1	chr19	5024163	5024182	+	1	NA	5' UTR (NM_007854, exon 1 of 12)	5' UTR (NM_007854, exon 1 of 12)	166	NM_007854	13340	Mm.4930	NM_007854	ENSMUSG00000024891	Slc29a2	Der12|Ent2|Hnp36	solute carrier family 29 (nucleoside transporters), member 2	protein-coding
mm_97412.1	chr11	77977750	77977757	+	1	NA	exon (NM_021286, exon 16 of 17)	exon (NM_021286, exon 16 of 17)	-5063	NM_174852	268448	Mm.274329	NM_174852	ENSMUSG00000037791	Phf12	2410142K10Rik|F630045O13|PF1|mKIAA1523	PHD finger protein 12	protein-coding
mm_170426.1	chr1	87327068	87327069	+	1	NA	promoter-TSS (NM_001110212)	promoter-TSS (NM_001110212)	70	NM_001110212	227331	Mm.23065	NM_146112	ENSMUSG00000048000	Gigyf2	2610016F01Rik|A830080H02Rik|AI852361|AW259676|BC006835|Tnrc15|mKIAA0642	GRB10 interacting GYF protein 2	protein-coding
mm_139153.1	chr17	47540417	47540424	+	1	NA	intron (NM_001081635, intron 1 of 6)	intron (NM_001081635, intron 1 of 6)	35369	NM_001081635	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_152752.1	chr19	20116664	20116666	-	1	NA	Intergenic	Intergenic	274006	NM_010730	16952	Mm.248360	NM_010730	ENSMUSG00000024659	Anxa1	Anx-1|Anx-A1|C430014K04Rik|Lpc-1|Lpc1	annexin A1	protein-coding
mm_50586.1	chr6	49059238	49059249	+	1	NA	Intergenic	Intergenic	-14552	NM_029353	75593	Mm.439947	NM_029353	ENSMUSG00000029815	Malsu1	2410003K15Rik|Matsu1	mitochondrial assembly of ribosomal large subunit 1	protein-coding
mm_60024.1	chr7	30832799	30832841	+	1	NA	Intergenic	RLTR1B-int|LTR|ERV1	-9045	NM_146187	233079	Mm.97338	NM_146187	ENSMUSG00000051314	Ffar2	GPCR43|Gpr43	free fatty acid receptor 2	protein-coding
mm_38207.1	chr4	135873788	135873798	-	1	NA	promoter-TSS (NM_026383)	promoter-TSS (NM_026383)	53	NM_026383	52830	Mm.29159	NM_026383	ENSMUSG00000028675	Pnrc2	0610011E17Rik|D4Bwg0593e	proline-rich nuclear receptor coactivator 2	protein-coding
mm_67891.1	chr7	99478597	99478599	-	1	NA	TTS (NR_002173)	TTS (NR_002173)	1109	NR_002173	449631	Mm.236868	NR_002173	ENSMUSG00000064966	Snord15b	Gm5775|Rnu15-b|Rnu15b|U15B	small nucleolar RNA, C/D box 14B	snoRNA
mm_143095.1	chr17	57080723	57080729	-	1	NA	exon (NM_009451, exon 4 of 4)	exon (NM_009451, exon 4 of 4)	-2216	NM_153551	70785	Mm.284447	NM_153551	ENSMUSG00000002668	Dennd1c	4432409M07Rik	DENN/MADD domain containing 1C	protein-coding
mm_63436.1	chr7	127479095	127479110	+	1	NA	Intergenic	CpG	-6119	NM_010183	14123	Mm.323505	NM_010183	ENSMUSG00000042423	Fbrs	Fbs|Fbs1	fibrosin	protein-coding
mm_99659.1	chr11	105731816	105731827	+	1	NA	intron (NM_181071, intron 4 of 25)	intron (NM_181071, intron 4 of 25)	141835	NM_181071	77097	Mm.22501	NM_175492	ENSMUSG00000053580	Tanc2	3526402J09Rik|5730590C14Rik	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2	protein-coding
mm_144767.1	chr18	35772146	35772165	+	1	NA	intron (NM_019912, intron 1 of 6)	CpG	596	NM_019912	56550	Mm.180052	NM_019912	ENSMUSG00000091896	Ube2d2a	1500034D03Rik|Ubc2e|Ube2d2|ubc4	ubiquitin-conjugating enzyme E2D 2A	protein-coding
mm_80592.1	chr9	85842884	85842902	+	1	NA	promoter-TSS (NM_001164792)	promoter-TSS (NM_001164792)	41	NM_001164792	21983	Mm.20864	NM_011627	ENSMUSG00000035274	Tpbg	5T4|AW495680|WAIF1	trophoblast glycoprotein	protein-coding
mm_62389.1	chr7	100943548	100943557	+	1	NA	intron (NM_183168, intron 1 of 2)	intron (NM_183168, intron 1 of 2)	-11391	NM_001081116	207212	Mm.29954	NM_001081116	ENSMUSG00000032875	Arhgef17	8030463K16|AI428794|AW558066|BC035332|mKIAA0337	Rho guanine nucleotide exchange factor (GEF) 17	protein-coding
mm_133459.1	chr16	89132857	89132858	+	1	NA	Intergenic	Intergenic	-68855	NM_001276278	68637	Mm.384089	NM_001276278	ENSMUSG00000068073	1110025L11Rik	-	RIKEN cDNA 1110025L11 gene	protein-coding
mm_138612.1	chr17	35808388	35808390	+	1	NA	Intergenic	Intergenic	-13324	NM_133662	15937	Mm.25613	NM_133662	ENSMUSG00000003541	Ier3	AI663993|IEX-1|cI-3|gly96	immediate early response 3	protein-coding
mm_101430.1	chr11	30025916	30025955	-	1	NA	promoter-TSS (NM_146016)	promoter-TSS (NM_146016)	98	NM_146016	237711	Mm.445271	NM_146016	ENSMUSG00000044072	Eml6	2900083P10Rik|C230094A16Rik|EMAP-6	echinoderm microtubule associated protein like 6	protein-coding
mm_15446.1	chr2	157367602	157367623	+	1	NA	promoter-TSS (NM_026968)	promoter-TSS (NM_026968)	18	NM_026968	69161	Mm.228619	NM_026968	ENSMUSG00000063019	Manbal	1810024K12Rik|AI836500	mannosidase, beta A, lysosomal-like	protein-coding
mm_100983.1	chr11	7213441	7213454	-	1	NA	exon (NM_008343, exon 1 of 5)	exon (NM_008343, exon 1 of 5)	476	NM_008343	16009	Mm.29254	NM_008343	ENSMUSG00000020427	Igfbp3	AI649005|IGFBP-3|IGgfbp3	insulin-like growth factor binding protein 3	protein-coding
mm_79017.1	chr9	45841113	45841121	+	1	NA	intron (NM_011792, intron 1 of 8)	intron (NM_011792, intron 1 of 8)	2572	NM_011792	23821	Mm.24044	NM_011792	ENSMUSG00000032086	Bace1	ASP2|Bace|C76936	beta-site APP cleaving enzyme 1	protein-coding
mm_22940.1	chr3	31902667	31902680	+	1	NA	promoter-TSS (NM_028231)	promoter-TSS (NM_028231)	-30	NM_028231	72413	Mm.64790	NM_028231	ENSMUSG00000037610	Kcnmb2	2700049B16Rik|3110031N04Rik	potassium large conductance calcium-activated channel, subfamily M, beta member 2	protein-coding
mm_93655.1	chr10	117689866	117689880	-	1	NA	3' UTR (NM_010786, exon 12 of 12)	3' UTR (NM_010786, exon 12 of 12)	20885	NM_010786	17246	Mm.22670	NM_010786	ENSMUSG00000020184	Mdm2	1700007J15Rik|AA415488|Mdm-2	transformed mouse 3T3 cell double minute 2	protein-coding
mm_153115.1	chr19	33108203	33108206	-	1	NA	Intergenic	MTE2a-int|LTR|ERVL-MaLR	284091	NM_001167818	67795	Mm.204591	NM_001146342	ENSMUSG00000071573	Rnls	6530404N21Rik|AI452315|AW060440|C10orf59	renalase, FAD-dependent amine oxidase	protein-coding
mm_20782.1	chr2	143989062	143989077	-	1	NA	exon (NM_133626, exon 2 of 3)	exon (NM_133626, exon 2 of 3)	22194	NM_133626	81910	Mm.13705	NM_024281	ENSMUSG00000027422	Rrbp1	1700087N07Rik|5730465C04Rik|ES/130|mKIAA1398|mRRp0|mRRp1.8|mRRp10|mRRp15a|mRRp15b|mRRp16.8|mRRp2|mRRp41|mRRp47|mRRp5.4|p180	ribosome binding protein 1	protein-coding
mm_149338.1	chr19	10850313	10850330	+	1	NA	intron (NM_023044, intron 2 of 7)	MTD|LTR|ERVL-MaLR	7777	NM_023044	65221	Mm.27387	NM_023044	ENSMUSG00000024737	Slc15a3	Ci1|cI-1	solute carrier family 15, member 3	protein-coding
mm_30045.1	chr3	135839742	135839759	-	1	NA	non-coding (NR_040540, exon 2 of 5)	non-coding (NR_040540, exon 2 of 5)	519	NR_040540	71038	Mm.410798	NR_040540	ENSMUSG00000106306	4933401H06Rik	-	RIKEN cDNA 4933401H06 gene	ncRNA
mm_108028.1	chr12	73720597	73720601	+	1	NA	intron (NM_001313977, intron 10 of 14)	intron (NM_001313977, intron 10 of 14)	135803	NM_008856	18755	Mm.341677	NM_008856	ENSMUSG00000021108	Prkch	Pkch	protein kinase C, eta	protein-coding
mm_82794.1	chr9	29411848	29411874	-	1	NA	intron (NM_172290, intron 1 of 7)	CpG	551268	NM_172290	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding
mm_51703.1	chr6	86628226	86628241	+	1	NA	promoter-TSS (NM_026414)	promoter-TSS (NM_026414)	59	NM_026414	67855	Mm.183043	NM_026414	ENSMUSG00000033508	Asprv1	2300003P22Rik|AA986851|SASP|SASPase|Taps	aspartic peptidase, retroviral-like 1	protein-coding
mm_9232.1	chr1	171280976	171280994	-	1	NA	TTS (NM_013919)	TTS (NM_013919)	201	NM_008911	19044	Mm.266888	NM_008911	ENSMUSG00000062729	Ppox	Ppo	protoporphyrinogen oxidase	protein-coding
mm_87976.1	chr10	63638305	63638307	+	1	NA	intron (NM_177612, intron 5 of 17)	intron (NM_177612, intron 5 of 17)	180795	NM_001164376	216033	Mm.444692	NM_177612	ENSMUSG00000060843	Ctnna3	4930429L08Rik|4933408A16|Catna3|Vr22	catenin (cadherin associated protein), alpha 3	protein-coding
mm_50198.1	chr6	42038375	42038400	+	1	NA	promoter-TSS (NM_009299)	promoter-TSS (NM_009299)	-7	NM_009299	20939	Mm.4119	NM_009299	ENSMUSG00000023289	Sva	-	seminal vesicle antigen	protein-coding
mm_99248.1	chr11	101082698	101082708	+	1	NA	intron (NM_001305982, intron 1 of 9)	CpG	138	NM_001305982	71743	Mm.182271	NM_027896	ENSMUSG00000001755	Coasy	1300003G02Rik|Dpck|Ppat|Ukr1	Coenzyme A synthase	protein-coding
mm_148507.1	chr19	4214368	4214375	+	1	NA	promoter-TSS (NM_001310039)	promoter-TSS (NM_001310039)	-18	NM_001310039	56708	Mm.347919	NM_019952	ENSMUSG00000040663	Clcf1	BSF-3|Bsf3|CLC|NNT-1	cardiotrophin-like cytokine factor 1	protein-coding
mm_23183.1	chr3	40949819	40949852	+	1	NA	promoter-TSS (NM_001040399)	promoter-TSS (NM_001040399)	-796	NM_001040399	214048	Mm.46782	NM_027663	ENSMUSG00000025762	Larp1b	1700108L22Rik|4933421B21Rik|AA690246|Larp2	La ribonucleoprotein domain family, member 1B	protein-coding
mm_166091.1	chr4	140131835	140131846	+	1	NA	intron (NM_198610, intron 2 of 9)	intron (NM_198610, intron 2 of 9)	114971	NM_198610	230868	Mm.298731	NM_198610	ENSMUSG00000040972	Igsf21	BC055811|Gm141	immunoglobulin superfamily, member 21	protein-coding
mm_67854.1	chr7	98702883	98702893	-	1	NA	promoter-TSS (NM_028410)	promoter-TSS (NM_028410)	40	NR_144495	100040769	Mm.126401	NR_144495		Gm15506	OTTMUSG00000023003	predicted gene 15506	ncRNA
mm_76951.1	chr8	105991715	105991733	-	1	NA	promoter-TSS (NM_001301204)	promoter-TSS (NM_001301204)	49	NM_001301204	319446	Mm.248357	NM_176913	ENSMUSG00000053687	Dpep2	F630103D06Rik|MBD-2	dipeptidase 2	protein-coding
mm_51088.1	chr6	67052953	67052962	+	1	NA	intron (NR_040278, intron 1 of 6)	RSINE1|SINE|B4	-15550	NM_007836	13197	Mm.72235	NM_007836	ENSMUSG00000036390	Gadd45a	AA545191|Ddit1|GADD45	growth arrest and DNA-damage-inducible 45 alpha	protein-coding
mm_127320.1	chr15	100297124	100297156	+	1	NA	Intergenic	Intergenic	-7677	NM_027334	70152	Mm.488086	NM_027334	ENSMUSG00000054619	Mettl7a1	2210414H16Rik|3300001H21Rik|Aam-B|Mettl7a|UbiE1	methyltransferase like 7A1	protein-coding
mm_67505.1	chr7	80782184	80782195	-	1	NA	intron (NM_016721, intron 2 of 37)	intron (NM_016721, intron 2 of 37)	21142	NM_016721	29875	Mm.207619	NM_016721	ENSMUSG00000030536	Iqgap1	AA682088|D7Ertd237e|D7Ertd257e|mKIAA0051	IQ motif containing GTPase activating protein 1	protein-coding
mm_138480.1	chr17	35195053	35195068	+	1	NA	promoter-TSS (NR_105939)	promoter-TSS (NR_105939)	88	NR_105939	102465588		NR_105939	ENSMUSG00000098291	Mir6973a	Gm27967|mmu-mir-6973a	microRNA 6973a	ncRNA
mm_24609.1	chr3	93446236	93446242	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	3909	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_117332.1	chr13	68999407	68999457	-	1	NA	5' UTR (NM_153534, exon 1 of 25)	5' UTR (NM_153534, exon 1 of 25)	109	NM_153534	210044	Mm.390617	NM_153534	ENSMUSG00000021536	Adcy2	mKIAA1060	adenylate cyclase 2	protein-coding
mm_80176.1	chr9	72274942	72274950	+	1	NA	promoter-TSS (NM_146224)	promoter-TSS (NM_146224)	58	NM_001311105	235469	Mm.242791	NM_146224	ENSMUSG00000038535	Zfp280d	A930005F02Rik|BC027163|Suhw4|ZNF634|Znf280d	zinc finger protein 280D	protein-coding
mm_55076.1	chr6	49111119	49111137	-	1	NA	intron (NM_023670, intron 6 of 14)	intron (NM_023670, intron 6 of 14)	37333	NM_029353	75593	Mm.439947	NM_029353	ENSMUSG00000029815	Malsu1	2410003K15Rik|Matsu1	mitochondrial assembly of ribosomal large subunit 1	protein-coding
mm_73753.1	chr8	114815584	114815605	+	1	NA	intron (NM_019573, intron 8 of 8)	intron (NM_019573, intron 8 of 8)	375942	NM_019573	80707	Mm.440420	NM_019573	ENSMUSG00000004637	Wwox	5330426P09Rik|9030416C10Rik|WOX1	WW domain-containing oxidoreductase	protein-coding
mm_126483.1	chr15	81586598	81586609	+	1	NA	5' UTR (NM_177821, exon 1 of 31)	5' UTR (NM_177821, exon 1 of 31)	389	NM_177821	328572	Mm.258397	NM_177821	ENSMUSG00000055024	Ep300	A430090G16|A730011L11|KAT3B|p300|p300 HAT	E1A binding protein p300	protein-coding
mm_64583.1	chr7	145300844	145300873	+	1	NA	promoter-TSS (NM_145379)	promoter-TSS (NM_145379)	-51	NM_145379	211577	Mm.215151	NM_145379	ENSMUSG00000031070	Mrgprf	BC019711|Mgrc|MrgF	MAS-related GPR, member F	protein-coding
mm_135597.1	chr16	50732681	50732701	-	1	NA	promoter-TSS (NR_028300)	promoter-TSS (NR_028300)	82	NR_028300	68190	Mm.139089	NR_028300		Dubr	5330426P16Rik|Dum	Dppa2 upstream binding RNA	ncRNA
mm_168113.1	chr10	15063804	15063806	+	1	NA	Intergenic	Intergenic	303516	NM_008703	18101	Mm.487342	NM_008703	ENSMUSG00000019865	Nmbr	BB182387	neuromedin B receptor	protein-coding
mm_152970.1	chr19	29386696	29386711	-	1	NA	3' UTR (NM_021893, exon 7 of 7)	3' UTR (NM_021893, exon 7 of 7)	19265	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_69750.1	chr7	140955961	140955997	-	1	NA	promoter-TSS (NM_030694)	promoter-TSS (NM_030694)	-18	NM_030694	80876	Mm.379266	NM_030694	ENSMUSG00000060591	Ifitm2	DSPA2c|Ifitm3l|fragilis3|mil-3	interferon induced transmembrane protein 2	protein-coding
mm_153776.1	chr19	45749564	45749576	-	1	NA	promoter-TSS (NM_008723)	promoter-TSS (NM_008723)	-7	NM_008723	18150	Mm.1406	NM_008723	ENSMUSG00000056209	Npm3	Nub1	nucleoplasmin 3	protein-coding
mm_42322.1	chr5	114897771	114897826	+	1	NA	exon (NM_011854, exon 1 of 6)	exon (NM_011854, exon 1 of 6)	864	NM_011854	23962	Mm.228363	NM_011854	ENSMUSG00000029561	Oasl2	M1204|Mmu-OASL|Oasl	2'-5' oligoadenylate synthetase-like 2	protein-coding
mm_96059.1	chr11	59566400	59566414	+	1	NA	3' UTR (NM_145827, exon 10 of 10)	3' UTR (NM_145827, exon 10 of 10)	5331	NM_001011789	257962	Mm.377316	NM_001011789	ENSMUSG00000059610	Olfr222	MOR256-45P	olfactory receptor 222	protein-coding
mm_103837.1	chr11	83020789	83020843	-	1	NA	promoter-TSS (NM_001167743)	promoter-TSS (NM_001167743)	-6	NM_181545	276950	Mm.491599	NM_181545	ENSMUSG00000035208	Slfn8	-	schlafen 8	protein-coding
mm_19927.1	chr2	116064559	116064598	-	1	NA	promoter-TSS (NM_001346038)	promoter-TSS (NM_001346038)	41	NM_001346044	17536	Mm.247566	NM_010825	ENSMUSG00000027210	Meis2	A430109D20Rik|Mrg1|Stra10	Meis homeobox 2	protein-coding
mm_104425.1	chr11	94938250	94938260	-	1	NA	exon (NM_007742, exon 3 of 51)	exon (NM_007742, exon 3 of 51)	2031	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_112659.1	chr13	16026935	16026945	+	1	NA	exon (NM_008380, exon 5 of 5)	exon (NM_008380, exon 5 of 5)	15089	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_62879.1	chr7	114753796	114753828	+	1	NA	intron (NM_173767, intron 1 of 12)	intron (NM_173767, intron 1 of 12)	8046	NM_173767	233752	Mm.83037	NM_173767	ENSMUSG00000048782	Insc	3830422K02Rik|C730020D23	inscuteable homolog (Drosophila)	protein-coding
mm_89964.1	chr10	111298700	111298721	+	1	NA	promoter-TSS (NM_027914)	promoter-TSS (NM_027914)	31	NM_027914	71769	Mm.45256	NM_027914	ENSMUSG00000035759	Bbs10	1300007O09Rik|AI452285	Bardet-Biedl syndrome 10 (human)	protein-coding
mm_90788.1	chr10	7054961	7054979	-	1	NA	Intergenic	Intergenic	-31785	NM_001033391	320495	Mm.331674	NM_001033391	ENSMUSG00000064065	Ipcef1	A130090K04Rik	interaction protein for cytohesin exchange factors 1	protein-coding
mm_32173.1	chr4	100479151	100479170	+	1	NA	5' UTR (NM_001033773, exon 1 of 10)	5' UTR (NM_001033773, exon 1 of 10)	293	NM_001033773	381534	Mm.318133	NM_001033773	ENSMUSG00000069733	Ube2u	-	ubiquitin-conjugating enzyme E2U (putative)	protein-coding
mm_35059.1	chr4	6452612	6452622	-	1	NA	intron (NM_010945, intron 1 of 30)	intron (NM_010945, intron 1 of 30)	1654	NM_010945	18201	Mm.3059	NM_010945	ENSMUSG00000028245	Nsmaf	AA959567|C630007J05|Fan	neutral sphingomyelinase (N-SMase) activation associated factor	protein-coding
mm_44070.1	chr5	148678907	148678925	+	1	NA	Intergenic	ERVB4_3-LTR_MM|LTR|ERVK	-62924	NR_028285	70138	Mm.417834	NR_028285	ENSMUSG00000086494	2210417A02Rik	AV081004	RIKEN cDNA 2210417A02 gene	ncRNA
mm_78585.1	chr9	37367335	37367347	+	1	NA	promoter-TSS (NM_175189)	promoter-TSS (NM_175189)	-265	NM_175189	72927	Mm.266133	NM_175189	ENSMUSG00000046240	Hepacam	2900042E01Rik|Glialcam|Hepn1	hepatocyte cell adhesion molecule	protein-coding
mm_127822.1	chr15	5121175	5121194	-	1	NA	Intergenic	Intergenic	2763	NR_028091	100302529		NR_028091		Snord72	MBII-240	small nucleolar RNA, C/D box 72	snoRNA
mm_84411.1	chr9	65562150	65562163	-	1	NA	intron (NM_153119, intron 3 of 5)	intron (NM_153119, intron 3 of 5)	17931	NM_153119	102595	Mm.247303	NM_153119	ENSMUSG00000050721	Plekho2	AI840980|Plekhq1	pleckstrin homology domain containing, family O member 2	protein-coding
mm_73797.1	chr8	117266074	117266091	+	1	NA	intron (NM_001163262, intron 1 of 20)	B1_Mm|SINE|Alu	9063	NM_001163262	74440	Mm.233181	NM_028941	ENSMUSG00000034390	Cmip	4933407C03Rik|5830471E12Rik|AI314065|AI464126	c-Maf inducing protein	protein-coding
mm_101379.1	chr11	23771231	23771264	-	1	NA	promoter-TSS (NM_009044)	promoter-TSS (NM_009044)	-277	NM_009044	19696	Mm.4869	NM_009044	ENSMUSG00000020275	Rel	c-Rel	reticuloendotheliosis oncogene	protein-coding
mm_116459.1	chr13	43304154	43304213	-	1	NA	promoter-TSS (NM_001033399)	promoter-TSS (NM_001033399)	-11	NM_001033399	328232	Mm.441399	NM_001033399	ENSMUSG00000051335	Gfod1	9630032O13|AI850995	glucose-fructose oxidoreductase domain containing 1	protein-coding
mm_102474.1	chr11	60031903	60031914	-	1	NA	intron (NM_001290012, intron 1 of 6)	intron (NM_001290012, intron 1 of 6)	5097	NM_008819	18618	Mm.2731	NM_008819	ENSMUSG00000000301	Pemt	PEAMT|PEMT2|PLMT|Pempt|Pempt2	phosphatidylethanolamine N-methyltransferase	protein-coding
mm_129519.1	chr15	79109426	79109437	-	1	NA	intron (NM_177461, intron 1 of 15)	CpG	448	NM_177461	27008	Mm.196480	NM_177461	ENSMUSG00000033039	Micall1	AI448246|D15Mit260|D15N2e|EST573322|EST820961|MIRab13|mKIAA1668	microtubule associated monooxygenase, calponin and LIM domain containing -like 1	protein-coding
mm_167732.1	chr9	105316365	105316365	+	1	NA	intron (NM_172461, intron 4 of 15)	RMER15|LTR|ERVL	78922	NM_172461	208583	Mm.347509	NM_172461	ENSMUSG00000035032	Nek11	4932416N14Rik	NIMA (never in mitosis gene a)-related expressed kinase 11	protein-coding
mm_146333.1	chr18	81387699	81387699	+	1	NA	Intergenic	Intergenic	-401121	NM_178280	20689	Mm.215917	NM_178280	ENSMUSG00000024565	Sall3	B130022O04Rik|Msal|Msal-1|Sal|Salt|Spalt	sal-like 3 (Drosophila)	protein-coding
mm_119732.1	chr14	54113328	54113338	+	1	NA	Intergenic	Intergenic	140596	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_90112.1	chr10	117277448	117277462	+	1	NA	TTS (NM_017372)	TTS (NM_017372)	4817	NM_017372	17105	Mm.45436	NM_017372	ENSMUSG00000069516	Lyz2	AI326280|Lys|Lysm|Lyzf2|Lyzs|Lzm|Lzm-s1|Lzp	lysozyme 2	protein-coding
mm_32973.1	chr4	120096566	120096573	+	1	NA	exon (NM_010657, exon 4 of 9)	exon (NM_010657, exon 4 of 9)	-64637	NM_007902	13615	Mm.284855	NM_007902	ENSMUSG00000028635	Edn2	ET-2|PPET2|VIC	endothelin 2	protein-coding
mm_114898.1	chr13	94407838	94407843	+	1	NA	intron (NM_009680, intron 5 of 26)	B3|SINE|B2	48880	NM_009680	11774	Mm.21185	NM_009680	ENSMUSG00000021686	Ap3b1	AP-3|AU015684|C78395|Hps2|beta3A|pe|pearl|rim2	adaptor-related protein complex 3, beta 1 subunit	protein-coding
mm_135886.1	chr16	64771147	64771184	-	1	NA	promoter-TSS (NM_026273)	promoter-TSS (NM_026273)	-226	NM_026273	67609	Mm.212157	NM_026273	ENSMUSG00000059920	4930453N24Rik	AI649104|din	RIKEN cDNA 4930453N24 gene	protein-coding
mm_134399.1	chr16	17531133	17531143	-	1	NA	promoter-TSS (NM_026909)	promoter-TSS (NM_026909)	-86	NM_026909	69009	Mm.10174	NM_026909	ENSMUSG00000022760	Thap7	1810004B07Rik	THAP domain containing 7	protein-coding
mm_21628.1	chr2	164277230	164277263	-	1	NA	exon (NM_009300, exon 2 of 3)	exon (NM_009300, exon 2 of 3)	1061	NM_009300	20941	Mm.1286	NM_009300	ENSMUSG00000016998	Svs4	SVS-IV|Svp-2|Svp-4|Svp2|Svp4	seminal vesicle secretory protein 4	protein-coding
mm_109378.1	chr12	109705788	109705797	+	1	NA	Intergenic	(T)n|Simple_repeat|Simple_repeat	-3268	NR_029880	723858		NR_029880	ENSMUSG00000065498	Mir379	Mirn379|mir-379|mmu-mir-379	microRNA 379	ncRNA
mm_153131.1	chr19	34241656	34241684	-	1	NA	exon (NM_007392, exon 9 of 9)	exon (NM_007392, exon 9 of 9)	13703	NM_007392	11475	Mm.213025	NM_007392	ENSMUSG00000035783	Acta2	0610041G09Rik|Actvs|SMalphaA|a-SMA|alphaSMA	actin, alpha 2, smooth muscle, aorta	protein-coding
mm_114967.1	chr13	97137968	97138013	+	1	NA	promoter-TSS (NM_001271464)	promoter-TSS (NM_001271464)	53	NM_001271464	320806	Mm.219675	NM_177266	ENSMUSG00000021666	Gfm2	6530419G12Rik|A930009M04Rik|EF-G2mt|EFG2|MST027|RRF2mt	G elongation factor, mitochondrial 2	protein-coding
mm_117683.1	chr13	94246533	94246573	-	1	NA	intron (NM_001346609, intron 2 of 8)	intron (NM_001346609, intron 2 of 8)	38728	NM_029153	107767	Mm.201455	NM_029153	ENSMUSG00000021687	Scamp1	4930505M11Rik|AI415563|AW122395	secretory carrier membrane protein 1	protein-coding
mm_26876.1	chr3	17714649	17714652	-	1	NA	Intergenic	L1_Mus3|LINE|L1	-75271	NR_033490	70441	Mm.458192	NR_033490	ENSMUSG00000100252	Mir124-2hg	100040120|2610100L16Rik|6430547I21Rik|A930005K07Rik|AW125202|Gm2612	Mir124-2 host gene (non-protein coding)	ncRNA
mm_171515.1	chr4	146502015	146502025	+	1	NA	promoter-TSS (NM_001243138)	promoter-TSS (NM_001243138)	20	NM_001243138	100041433	Mm.441741	NM_001243138	ENSMUSG00000056300	Zfp981	Gm13247|OTTMUSG00000011075	zinc finger protein 981	protein-coding
mm_169776.1	chr1	60900936	60900937	+	1	NA	Intergenic	Intergenic	-8089	NM_009843	12477	Mm.390	NM_009843	ENSMUSG00000026011	Ctla4	Cd152|Ctla-4|Ly-56	cytotoxic T-lymphocyte-associated protein 4	protein-coding
mm_15180.1	chr2	154190807	154190832	+	1	NA	promoter-TSS (NM_001012392)	promoter-TSS (NM_001012392)	1	NM_001012392	228801	Mm.3783	NM_153418	ENSMUSG00000027485	Bpifb1	Lplunc1	BPI fold containing family B, member 1	protein-coding
mm_59877.1	chr7	30291772	30291779	+	1	NA	promoter-TSS (NM_001081114)	promoter-TSS (NM_001081114)	22	NM_001081114	76686	Mm.159258	NM_001081114	ENSMUSG00000013921	Clip3	1500005P14Rik|AI844915|Clipr-59	CAP-GLY domain containing linker protein 3	protein-coding
mm_2303.1	chr1	91540012	91540020	+	1	NA	promoter-TSS (NM_001039126)	promoter-TSS (NM_001039126)	-549	NM_001039126	65247	Mm.234152	NM_023046	ENSMUSG00000026311	Asb1	1700029O08Rik|1700054C17Rik|AI426616|AI851378|mKIAA1146	ankyrin repeat and SOCS box-containing 1	protein-coding
mm_167353.1	chr8	83742556	83742565	+	1	NA	Intergenic	ID|SINE|ID	-1249	NM_001163031	26364	Mm.334648	NM_011925	ENSMUSG00000002885	Adgre5	AA409984|Cd97|TM7LN1	adhesion G protein-coupled receptor E5	protein-coding
mm_121280.1	chr14	103827201	103827209	+	1	NA	intron (NM_007904, intron 1 of 6)	intron (NM_007904, intron 1 of 6)	16496	NM_007904	13618	Mm.229532	NM_007904	ENSMUSG00000022122	Ednrb	ET-B|ET-BR|ETR-b|ETb|Sox10m1	endothelin receptor type B	protein-coding
mm_172197.1	chr6	51466540	51466562	-	1	NA	exon (NM_182650, exon 4 of 10)	exon (NM_182650, exon 4 of 10)	3343	NM_182650	53379	Mm.155896	NM_016806	ENSMUSG00000004980	Hnrnpa2b1	9130414A06Rik|Hnrpa2|Hnrpa2b1|hnrnp-A	heterogeneous nuclear ribonucleoprotein A2/B1	protein-coding
mm_46197.1	chr5	98030728	98030765	-	1	NA	5' UTR (NM_133738, exon 1 of 17)	5' UTR (NM_133738, exon 1 of 17)	216	NM_133738	71914	Mm.24842	NM_133738	ENSMUSG00000029338	Antxr2	2310046B19Rik|AW561899|CMG-2|CMG2|cI-35	anthrax toxin receptor 2	protein-coding
mm_124892.1	chr15	10314119	10314129	+	1	NA	intron (NM_001253781, intron 2 of 9)	intron (NM_001253781, intron 2 of 9)	20473	NM_001253782	19116	Mm.10516	NM_011169	ENSMUSG00000005268	Prlr	AI987712|Pr-1|Pr-3|Prlr-rs1	prolactin receptor	protein-coding
mm_22427.1	chr2	181599032	181599042	-	1	NA	5' UTR (NM_172676, exon 1 of 5)	5' UTR (NM_172676, exon 1 of 5)	110	NM_172676	229011	Mm.205422	NM_172676	ENSMUSG00000038605	Samd10	D930033N23Rik|E130318E08	sterile alpha motif domain containing 10	protein-coding
mm_165482.1	chr2	164333463	164333476	+	1	NA	exon (NM_009301, exon 2 of 3)	exon (NM_009301, exon 2 of 3)	704	NM_009301	20944	Mm.140154	NM_009301	ENSMUSG00000017004	Svs5	BB115186|Semg1|Svp-1|Svp1|Svp5	seminal vesicle secretory protein 5	protein-coding
mm_91207.1	chr10	21161548	21161558	-	1	NA	promoter-TSS (NM_001198914)	promoter-TSS (NM_001198914)	-569	NM_010848	17863	Mm.52109	NM_010848	ENSMUSG00000019982	Myb	AI550390|M16449|c-myb	myeloblastosis oncogene	protein-coding
mm_66977.1	chr7	63936310	63936342	-	1	NA	intron (NM_021366, intron 1 of 1)	intron (NM_021366, intron 1 of 1)	2589	NM_021366	50794	Mm.240473	NM_021366	ENSMUSG00000052040	Klf13	0610043C13Rik|9430029L20Rik|Bteb3|FKLF-2|FKLF2|NSLP1|RFLAT-1|RFLAT1	Kruppel-like factor 13	protein-coding
mm_29056.1	chr3	103776810	103776811	-	1	NA	intron (NM_001301304, intron 2 of 15)	intron (NM_001301304, intron 2 of 15)	14465	NM_001301306	15257	Mm.20827	NM_010432	ENSMUSG00000008730	Hipk1	1110062K04Rik|Myak	homeodomain interacting protein kinase 1	protein-coding
mm_126812.1	chr15	87655029	87655035	+	1	NA	intron (NM_134096, intron 1 of 3)	intron (NM_134096, intron 1 of 3)	29802	NM_134096	106014	Mm.244319	NM_134096	ENSMUSG00000054863	Fam19a5	TAFA5|Tafa-5|Tara-5	family with sequence similarity 19, member A5	protein-coding
mm_161385.1	chr14	75198047	75198047	+	1	NA	intron (NM_008879, intron 2 of 16)	intron (NM_008879, intron 2 of 16)	-44240	NM_019775	56373	Mm.24242	NM_019775	ENSMUSG00000021999	Cpb2	1110032P04Rik|4930405E17Rik|AI255929|CPR|Cpu|TAFI	carboxypeptidase B2 (plasma)	protein-coding
mm_96653.1	chr11	69368333	69368348	+	1	NA	intron (NM_146019, intron 1 of 39)	intron (NM_146019, intron 1 of 39)	1086	NM_146019	216848	Mm.178246	NM_146019	ENSMUSG00000018474	Chd3	2600010P09Rik|AF020312|Chd7|Prp7|Prp9-1	chromodomain helicase DNA binding protein 3	protein-coding
mm_114870.1	chr13	94068552	94068556	+	1	NA	intron (NM_172589, intron 1 of 3)	intron (NM_172589, intron 1 of 3)	10758	NM_172589	218454	Mm.316553	NM_172589	ENSMUSG00000045312	Lhfpl2	6030465B15|AI447312|AW050335|mKIAA0206|vgim	lipoma HMGIC fusion partner-like 2	protein-coding
mm_95550.1	chr11	52307808	52307822	+	1	NA	Intergenic	Intergenic	-24801	NM_001313981	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_13752.1	chr2	118126516	118126526	+	1	NA	3' UTR (NM_011580, exon 22 of 22)	3' UTR (NM_011580, exon 22 of 22)	14645	NM_001313914	21825	Mm.4159	NM_011580	ENSMUSG00000040152	Thbs1	TSP-1|TSP1|Thbs-1|tbsp1	thrombospondin 1	protein-coding
mm_39449.1	chr5	17574518	17574528	+	1	NA	promoter-TSS (NM_013657)	promoter-TSS (NM_013657)	-293	NM_013657	20348	Mm.5071	NM_013657	ENSMUSG00000028780	Sema3c	1110036B02Rik|SemE|Semae	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	protein-coding
mm_91943.1	chr10	60831492	60831509	-	1	NA	promoter-TSS (NM_029770)	promoter-TSS (NM_029770)	81	NM_029770	107449	Mm.290433	NM_029770	ENSMUSG00000020099	Unc5b	6330415E02Rik|A630020F16|D10Bwg0792e|Unc5h2	unc-5 netrin receptor B	protein-coding
mm_15960.1	chr2	166009617	166009622	+	1	NA	intron (NM_008679, intron 1 of 22)	ID_B1|SINE|B4	16982	NM_008679	17979	Mm.469663	NM_008679	ENSMUSG00000027678	Ncoa3	2010305B15Rik|AW321064|Actr|Aib1|KAT13B|Rac3|Src3|Tram-1|Tram1|bHLHe42|p/Cip|pCip	nuclear receptor coactivator 3	protein-coding
mm_88225.1	chr10	70440644	70440672	+	1	NA	promoter-TSS (NM_001143777)	promoter-TSS (NM_001143777)	-10	NM_001143777	71721	Mm.477813	NM_024244	ENSMUSG00000043259	Fam13c	1200015N20Rik|C030038O19Rik|mKIAA1796	family with sequence similarity 13, member C	protein-coding
mm_31458.1	chr4	48898559	48898565	+	1	NA	Intergenic	RMER1A|Other|Other	-160900	NM_178756	272031	Mm.299460	NM_178756	ENSMUSG00000063446	Plppr1	E130309F12Rik|Lppr1|PRG-3|mKIAA4247	phospholipid phosphatase related 1	protein-coding
mm_136555.1	chr17	3114989	3115002	+	1	NA	promoter-TSS (NM_134123)	promoter-TSS (NM_134123)	23	NM_134123	106583	Mm.124373	NM_134123	ENSMUSG00000046201	Scaf8	A630086M08Rik|A930036P18Rik|AA408306|AI447644|AI448652|AU015035|Rbm16|mKIAA1116	SR-related CTD-associated factor 8	protein-coding
mm_121510.1	chr14	121962125	121962135	+	1	NA	intron (NM_183031, intron 1 of 1)	intron (NM_183031, intron 1 of 1)	3063	NM_183031	321019	Mm.265618	NM_183031	ENSMUSG00000051212	Gpr183	Ebi2	G protein-coupled receptor 183	protein-coding
mm_125484.1	chr15	54600924	54600928	+	1	NA	3' UTR (NM_178920, exon 4 of 4)	3' UTR (NM_178920, exon 4 of 4)	29560	NM_178920	105853	Mm.410994	NM_178920	ENSMUSG00000024479	Mal2	AI461653	mal, T cell differentiation protein 2	protein-coding
mm_107743.1	chr12	58413266	58413278	+	1	NA	Intergenic	Intergenic	-144014	NM_025809	66864	Mm.280563	NM_025809	ENSMUSG00000045930	Clec14a	1200003C23Rik|AI642649	C-type lectin domain family 14, member a	protein-coding
mm_13428.1	chr2	104817033	104817071	+	1	NA	promoter-TSS (NM_001123327)	promoter-TSS (NM_001123327)	-356	NM_001123327	99003	Mm.274314	NM_001123327	ENSMUSG00000074994	Qser1	4732486I23Rik|AI502974	glutamine and serine rich 1	protein-coding
mm_54348.1	chr6	30806792	30806804	-	1	NA	intron (NM_017478, intron 20 of 23)	intron (NM_017478, intron 20 of 23)	65499	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_24471.1	chr3	90669064	90669076	+	1	NA	promoter-TSS (NM_013650)	promoter-TSS (NM_013650)	-1	NM_013650	20201	Mm.21567	NM_013650	ENSMUSG00000056054	S100a8	60B8Ag|AI323541|B8Ag|CFAg|CP-10|Caga|MRP8|p8	S100 calcium binding protein A8 (calgranulin A)	protein-coding
mm_116995.1	chr13	56548503	56548518	-	1	NA	promoter-TSS (NM_010702)	promoter-TSS (NM_010702)	28	NM_010702	16841	Mm.16973	NM_010702	ENSMUSG00000021539	Lect2	-	leukocyte cell-derived chemotaxin 2	protein-coding
mm_97194.1	chr11	75577017	75577045	+	1	NA	3' UTR (NM_001199283, exon 14 of 14)	3' UTR (NM_001199283, exon 14 of 14)	-11048	NM_008850	18738	Mm.3128	NM_008850	ENSMUSG00000017781	Pitpna	Pitpn|vb|vibrator	phosphatidylinositol transfer protein, alpha	protein-coding
mm_173099.1	chrX	15263006	15263007	+	1	NA	Intergenic	PB1D9|SINE|Alu	-151517	NR_033171	67395	Mm.50369	NM_026128	ENSMUSG00000045217	Ppp1r2-ps9	4930403L05Rik	protein phosphatase 1, regulatory (inhibitor) subunit 2, pseudogene 9	pseudo
mm_84157.1	chr9	59530237	59530240	-	1	NA	Intergenic	B3|SINE|B2	-4737	NM_178388	73893	Mm.216135	NM_178388	ENSMUSG00000049526	Tmem202	4930425N13Rik	transmembrane protein 202	protein-coding
mm_60261.1	chr7	43811439	43811454	+	1	NA	5' UTR (NM_011872, exon 1 of 6)	5' UTR (NM_011872, exon 1 of 6)	152	NM_011872	23993	Mm.251227	NM_011872	ENSMUSG00000030713	Klk7	Prss6|SCCE	kallikrein related-peptidase 7 (chymotryptic, stratum corneum)	protein-coding
mm_21172.1	chr2	154691232	154691279	-	1	NA	exon (NM_029362, exon 3 of 5)	exon (NM_029362, exon 3 of 5)	34229	NM_029362	75608	Mm.262480	NM_029362	ENSMUSG00000038467	Chmp4b	2010012F05Rik|C76846|Snf7-2	charged multivesicular body protein 4B	protein-coding
mm_21690.1	chr2	164443914	164443928	-	1	NA	promoter-TSS (NM_011521)	promoter-TSS (NM_011521)	-733	NM_011521	20971	Mm.3815	NM_011521	ENSMUSG00000017009	Sdc4	AA959608|AW108331|S4|Synd4|ryudocan|syndecan-4	syndecan 4	protein-coding
mm_74392.1	chr8	3176713	3176733	-	1	NA	intron (NM_010568, intron 10 of 20)	(GCTTG)n|Simple_repeat|Simple_repeat	102894	NM_010568	16337	Mm.268003	NM_010568	ENSMUSG00000005534	Insr	4932439J01Rik|CD220|D630014A15Rik|IR|IR-A|IR-B	insulin receptor	protein-coding
mm_59356.1	chr7	25680843	25680861	+	1	NA	promoter-TSS (NM_172148)	promoter-TSS (NM_172148)	-306	NM_172148	232987	Mm.22849	NM_172148	ENSMUSG00000063439	B9d2	stumpy	B9 protein domain 2	protein-coding
mm_4521.1	chr1	175632016	175632024	+	1	NA	promoter-TSS (NM_133809)	promoter-TSS (NM_133809)	-173	NM_133809	98256	Mm.27217	NM_133809	ENSMUSG00000039783	Kmo	AI046660	kynurenine 3-monooxygenase (kynurenine 3-hydroxylase)	protein-coding
mm_167033.1	chr7	72910529	72910529	-	1	NA	Intergenic	Intergenic	191539	NR_046024	625243	Mm.261798	NR_046024	ENSMUSG00000108383	Gm6567	-	predicted gene 6567	ncRNA
mm_68811.1	chr7	125552134	125552176	-	1	NA	promoter-TSS (NM_001008700)	promoter-TSS (NM_001008700)	-127	NM_001008700	16190	Mm.233802	NM_010557	ENSMUSG00000030748	Il4ra	CD124|Il4r	interleukin 4 receptor, alpha	protein-coding
mm_157996.1	chrX	94540404	94540422	-	1	NA	exon (NM_019791, exon 3 of 13)	exon (NM_019791, exon 3 of 13)	1661	NM_019791	94275	Mm.27578	NM_019791	ENSMUSG00000025151	Maged1	2810433C11Rik|5430405L04Rik|DXBwg1492e|Dlixin|Dlxin-1|Dlxin1|MAGE-D1|NRAGE|mFLJ00163	melanoma antigen, family D, 1	protein-coding
mm_51307.1	chr6	72313609	72313611	+	1	NA	intron (NM_001282071, intron 10 of 10)	intron (NM_001282071, intron 10 of 10)	9000	NM_147779	20388	Mm.46033	NM_147779	ENSMUSG00000056370	Sftpb	AI562151|SF-B|SP-B|Sftp-3|Sftp3	surfactant associated protein B	protein-coding
mm_52868.1	chr6	122316083	122316092	+	1	NA	exon (NM_010749, exon 6 of 7)	exon (NM_010749, exon 6 of 7)	7077	NM_010749	17113	Mm.249225	NM_010749	ENSMUSG00000007458	M6pr	CD-MPR|Mpr46	mannose-6-phosphate receptor, cation dependent	protein-coding
mm_144609.1	chr18	32431970	32432017	+	1	NA	exon (NM_009668, exon 17 of 19)	exon (NM_009668, exon 17 of 19)	-53709	NR_045403	402767	Mm.385109	NR_045403	ENSMUSG00000097413	A830052D11Rik	-	RIKEN cDNA A830052D11 gene	ncRNA
mm_82262.1	chr9	6266545	6266553	-	1	NA	promoter-TSS (NM_027942)	promoter-TSS (NM_027942)	-2	NM_027942	71829	Mm.141452	NM_027942	ENSMUSG00000047619	Ddi1	1700011N24Rik	DNA-damage inducible 1	protein-coding
mm_57103.1	chr6	122591137	122591155	-	1	NA	5' UTR (NM_031159, exon 4 of 8)	5' UTR (NM_031159, exon 4 of 8)	11298	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_91103.1	chr10	19117050	19117060	-	1	NA	Intergenic	Intergenic	-24694	NR_038021	100504265	Mm.383417	NR_038021		Gm20139	-	predicted gene, 20139	ncRNA
mm_126717.1	chr15	85336351	85336387	+	1	NA	promoter-TSS (NM_016843)	promoter-TSS (NM_016843)	-12	NM_016843	54138	Mm.248906	NM_016843	ENSMUSG00000016541	Atxn10	AI325283|C77170|E46|Sca10|TEG-169|Tex169	ataxin 10	protein-coding
mm_153650.1	chr19	44378195	44378206	-	1	NA	Intergenic	Intergenic	29509	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_67878.1	chr7	99229627	99229630	-	1	NA	intron (NM_177448, intron 2 of 5)	intron (NM_177448, intron 2 of 5)	8983	NM_177448	233549	Mm.208030	NM_177448	ENSMUSG00000052396	Mogat2	DGAT2L5|MGAT2|Mgat1l	monoacylglycerol O-acyltransferase 2	protein-coding
mm_157823.1	chrX	74085587	74085652	-	1	NA	promoter-TSS (NM_010788)	promoter-TSS (NM_010788)	71	NM_010788	17257	Mm.131408	NM_010788	ENSMUSG00000031393	Mecp2	1500041B07Rik|D630021H01Rik|Mbd5|WBP10	methyl CpG binding protein 2	protein-coding
mm_114310.1	chr13	59733658	59733666	+	1	NA	promoter-TSS (NR_045977)	promoter-TSS (NR_045977)	12	NR_045977	75223	Mm.444771	NR_045977	ENSMUSG00000097502	4930528D03Rik	-	RIKEN cDNA 4930528D03 gene	ncRNA
mm_55516.1	chr6	70172290	70172306	-	1	NA	Intergenic	Intergenic	619877	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_153154.1	chr19	34252527	34252547	-	1	NA	exon (NM_007392, exon 2 of 9)	exon (NM_007392, exon 2 of 9)	2836	NM_007392	11475	Mm.213025	NM_007392	ENSMUSG00000035783	Acta2	0610041G09Rik|Actvs|SMalphaA|a-SMA|alphaSMA	actin, alpha 2, smooth muscle, aorta	protein-coding
mm_53440.1	chr6	134222936	134222940	+	1	NA	exon (NM_007961, exon 3 of 8)	exon (NM_007961, exon 3 of 8)	-173391	NM_025778	66813	Mm.474472	NM_025778	ENSMUSG00000030200	Bcl2l14	4930452K23Rik|4933405K19Rik|9030625M01Rik|AI429211|Bclg	BCL2-like 14 (apoptosis facilitator)	protein-coding
mm_96550.1	chr11	68888518	68888523	+	1	NA	promoter-TSS (NM_177060)	promoter-TSS (NM_177060)	-33	NM_177060	320040	Mm.305696	NM_177060	ENSMUSG00000046490	Rnf222	9930039A11Rik	ring finger protein 222	protein-coding
mm_144038.1	chr17	90144057	90144068	-	1	NA	intron (NM_001346959, intron 5 of 6)	intron (NM_001346959, intron 5 of 6)	-55694	NM_001347419	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_140478.1	chr17	94864938	94864946	+	1	NA	promoter-TSS (NM_001024731)	promoter-TSS (NM_001024731)	24	NM_001024731	100044193		NM_001024731	ENSMUSG00000095193	Gm20939	-	predicted gene, 20939	protein-coding
mm_27985.1	chr3	81975743	81975760	-	1	NA	promoter-TSS (NM_019911)	promoter-TSS (NM_019911)	-23	NM_019911	56720	Mm.258622	NM_019911	ENSMUSG00000028011	Tdo2	AA407491|TDO|TO|chky	tryptophan 2,3-dioxygenase	protein-coding
mm_7419.1	chr1	119526379	119526406	-	1	NA	5' UTR (NM_146103, exon 1 of 1)	5' UTR (NM_146103, exon 1 of 1)	238	NM_146103	226351	Mm.439806	NM_146103	ENSMUSG00000098923	Tmem185b	2500001K11Rik	transmembrane protein 185B	protein-coding
mm_119370.1	chr14	41122575	41122586	+	1	NA	exon (NM_133653, exon 10 of 10)	exon (NM_133653, exon 10 of 10)	-9208	NM_023134	20387	Mm.46062	NM_023134	ENSMUSG00000021789	Sftpa1	SP-A|Sftp-1|Sftp1	surfactant associated protein A1	protein-coding
mm_66698.1	chr7	45920628	45920636	-	1	NA	intron (NM_010129, intron 1 of 4)	intron (NM_010129, intron 1 of 4)	217	NM_001146346	13732	Mm.20829	NM_010129	ENSMUSG00000040212	Emp3	H-4|H4|HNMP-1|MI-35|Ymp	epithelial membrane protein 3	protein-coding
mm_129233.1	chr15	76616826	76616837	-	1	NA	promoter-TSS (NM_028064)	promoter-TSS (NM_028064)	21	NM_028064	72027	Mm.276829	NM_028064	ENSMUSG00000063354	Slc39a4	1600025H15Rik|AU041686|AWMS2|ZIP4	solute carrier family 39 (zinc transporter), member 4	protein-coding
mm_98301.1	chr11	90030711	90030737	+	1	NA	5' UTR (NM_026433, exon 1 of 3)	5' UTR (NM_026433, exon 1 of 3)	376	NM_026433	67888	Mm.212428	NM_026433	ENSMUSG00000069763	Tmem100	1810057C19Rik|AV011897	transmembrane protein 100	protein-coding
mm_81812.1	chr9	118040476	118040494	+	1	NA	promoter-TSS (NM_013727)	promoter-TSS (NM_013727)	-37	NM_001286508	27215	Mm.92705	NM_013727	ENSMUSG00000039285	Azi2	AA410145|AZ2	5-azacytidine induced gene 2	protein-coding
mm_132292.1	chr16	33380766	33380787	+	1	NA	promoter-TSS (NM_011749)	promoter-TSS (NM_011749)	1	NM_011749	22661	Mm.392667	NM_011749	ENSMUSG00000022811	Zfp148	2210405J08Rik|AI480666|AW045217|BERF-1|BFCOL1|ZBP-89|Znf148	zinc finger protein 148	protein-coding
mm_106860.1	chr12	8009284	8009292	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	31611	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_161150.1	chr13	23465175	23465175	-	1	NA	exon (NM_013483, exon 2 of 8)	exon (NM_013483, exon 2 of 8)	726	NM_013483	12231	Mm.1420	NM_013483	ENSMUSG00000000706	Btn1a1	Btn	butyrophilin, subfamily 1, member A1	protein-coding
mm_20263.1	chr2	126675196	126675217	-	1	NA	intron (NM_001271470, intron 1 of 8)	CpG	386	NM_001271469	14391	Mm.293266	NM_010249	ENSMUSG00000027361	Gabpb1	BABPB2|E4TF1|E4TF1-47|E4TF1-53|E4Tf1B|GABPB|GABPB-1|GABPB-2|GABPB1-1|GABPB1-2|NRF2B1|NRF2B2	GA repeat binding protein, beta 1	protein-coding
mm_12454.1	chr2	71214426	71214462	+	1	NA	5' UTR (NM_001198877, exon 2 of 19)	5' UTR (NM_001198877, exon 2 of 19)	2498	NM_010064	13427	Mm.249479	NM_010064	ENSMUSG00000027012	Dync1i2	3110079H08Rik|AW554389|Dncic2	dynein cytoplasmic 1 intermediate chain 2	protein-coding
mm_29029.1	chr3	102166436	102166448	-	1	NA	intron (NM_177545, intron 5 of 7)	intron (NM_177545, intron 5 of 7)	38251	NM_177545	229658	Mm.118004	NM_177545	ENSMUSG00000027860	Vangl1	Kitenin|Lpp2|Stb2|Stbm	vang-like 1 (van gogh, Drosophila)	protein-coding
mm_134149.1	chr16	10785060	10785089	-	1	NA	intron (NM_001271603, intron 1 of 1)	CpG	462	NM_009896	12703	Mm.130	NM_009896	ENSMUSG00000038037	Socs1	Cish1|Cish7|JAB|SOCS-1|SSI-1	suppressor of cytokine signaling 1	protein-coding
mm_143194.1	chr17	62609955	62609960	-	1	NA	intron (NM_010109, intron 3 of 3)	intron (NM_010109, intron 3 of 3)	271360	NM_207654	13640	Mm.7978	NM_010109	ENSMUSG00000048915	Efna5	AL-1|AV158822|EFL-5|Ephrin-A5|Epl7|LERK-7|RAGS	ephrin A5	protein-coding
mm_23895.1	chr3	83031642	83031652	+	1	NA	exon (NM_010196, exon 5 of 5)	exon (NM_010196, exon 5 of 5)	5494	NM_001111048	14161	Mm.88793	NM_010196	ENSMUSG00000028001	Fga	ENSMUSG00000059807|Fib	fibrinogen alpha chain	protein-coding
mm_45039.1	chr5	39644645	39644649	-	1	NA	promoter-TSS (NM_010474)	promoter-TSS (NM_010474)	-16	NM_010474	15476	Mm.12559	NM_010474	ENSMUSG00000051022	Hs3st1	3-Ost|D5Wsu110e|Hsg3ost	heparan sulfate (glucosamine) 3-O-sulfotransferase 1	protein-coding
mm_53146.1	chr6	125237750	125237770	+	1	NA	promoter-TSS (NM_001042564)	promoter-TSS (NM_001042564)	-733	NM_001286753	21940	Mm.367714	NM_001033126	ENSMUSG00000030336	Cd27	S152|Tnfrsf7|Tp55	CD27 antigen	protein-coding
mm_70650.1	chr8	14353753	14353753	+	1	NA	intron (NM_172910, intron 3 of 15)	intron (NM_172910, intron 3 of 15)	257878	NM_172910	244310	Mm.404697	NM_172910	ENSMUSG00000047495	Dlgap2	6430596N04Rik|Dap-2|Dap2|Sapap2	discs, large (Drosophila) homolog-associated protein 2	protein-coding
mm_163968.1	chr14	55003352	55003398	+	1	NA	Intergenic	Intergenic	-8826	NM_080728	140781	Mm.457983	NM_080728	ENSMUSG00000053093	Myh7	B-MHC|MyHC-I|Myhc-b|Myhcb|beta-MHC	myosin, heavy polypeptide 7, cardiac muscle, beta	protein-coding
mm_131899.1	chr16	23250790	23250817	+	1	NA	intron (NM_001252505, intron 1 of 7)	HAL1|LINE|L1	24782	NM_001252505	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_84316.1	chr9	63739036	63739076	-	1	NA	intron (NM_016769, intron 1 of 8)	intron (NM_016769, intron 1 of 8)	18938	NM_016769	17127	Mm.7320	NM_016769	ENSMUSG00000032402	Smad3	AU022421|Madh3	SMAD family member 3	protein-coding
mm_65357.1	chr7	25000635	25000647	-	1	NA	exon (NM_001290469, exon 4 of 23)	exon (NM_001290469, exon 4 of 23)	5296	NM_001290469	232975	Mm.44101	NM_144921	ENSMUSG00000040907	Atp1a3	Atpa-2	ATPase, Na+/K+ transporting, alpha 3 polypeptide	protein-coding
mm_76864.1	chr8	105482849	105482861	-	1	NA	intron (NM_175160, intron 5 of 13)	intron (NM_175160, intron 5 of 13)	-11433	NM_026481	67971	Mm.29358	NM_026481	ENSMUSG00000014846	Tppp3	2700055K07Rik|CGI-38|Ceacam9|mmCGM8	tubulin polymerization-promoting protein family member 3	protein-coding
mm_76086.1	chr8	79399468	79399472	-	1	NA	promoter-TSS (NM_008539)	promoter-TSS (NM_008539)	-2	NM_008539	17125	Mm.223717	NM_008539	ENSMUSG00000031681	Smad1	AI528653|Madh1|Madr1|Mlp1|MusMLP	SMAD family member 1	protein-coding
mm_12553.1	chr2	72443063	72443076	+	1	NA	TTS (NM_023057)	TTS (NM_023057)	-33150	NM_025866	66953	Mm.270676	NM_025866	ENSMUSG00000055612	Cdca7	2310021G01Rik|AU044109|JPO1	cell division cycle associated 7	protein-coding
mm_25768.1	chr3	126106692	126106710	+	1	NA	Intergenic	B4|SINE|B4	-168151	NM_011674	22239	Mm.306021	NM_011674	ENSMUSG00000032854	Ugt8a	AI850488|AW455908|Cgt|Ugt8|mCerGT	UDP galactosyltransferase 8A	protein-coding
mm_153621.1	chr19	43986534	43986544	-	1	NA	promoter-TSS (NM_030703)	promoter-TSS (NM_030703)	-19	NM_030703	93721	Mm.206774	NM_030703	ENSMUSG00000025196	Cpn1	0610011F20Rik|CPN	carboxypeptidase N, polypeptide 1	protein-coding
mm_136440.1	chr16	94570757	94570771	-	1	NA	promoter-TSS (NM_001113389)	promoter-TSS (NM_001113389)	-143	NM_001113389	13548	Mm.310973	NM_007890	ENSMUSG00000022897	Dyrk1a	2310043O08Rik|D16Ertd272e|D16Ertd493e|Dyrk|ENSMUSG00000074897|Gm10783|Mnbh|Mp86|mmb	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1a	protein-coding
mm_41364.1	chr5	90508429	90508452	+	1	NA	exon (NM_007423, exon 14 of 15)	exon (NM_007423, exon 14 of 15)	-10509	NM_145146	280662	Mm.348786	NM_145146	ENSMUSG00000029369	Afm	Alf|alpha-Alb	afamin	protein-coding
mm_172642.1	chr8	25767782	25767786	-	1	NA	3' UTR (NM_026121, exon 5 of 5)	3' UTR (NM_026121, exon 5 of 5)	-13504	NM_028102	72108	Mm.246875	NM_028102	ENSMUSG00000061313	Ddhd2	2010305K11Rik|SAMWD1|mKIAA0725	DDHD domain containing 2	protein-coding
mm_53418.1	chr6	133851929	133851948	+	1	NA	exon (NM_010594, exon 2 of 4)	exon (NM_010594, exon 2 of 4)	1729	NM_010594	16483	Mm.13052	NM_010594	ENSMUSG00000032758	Kap	AW146435|FKSG22	kidney androgen regulated protein	protein-coding
mm_40663.1	chr5	65348387	65348406	+	1	NA	promoter-TSS (NM_031180)	promoter-TSS (NM_031180)	-15	NM_031180	83379	Mm.45274	NM_031180	ENSMUSG00000029195	Klb	AV071179|betaKlotho	klotho beta	protein-coding
mm_62514.1	chr7	102222412	102222439	+	1	NA	promoter-TSS (NM_145583)	promoter-TSS (NM_145583)	-603	NR_111938	233575	Mm.302013	NM_145583	ENSMUSG00000030990	Pgap2	1810006G21Rik|C76649|Frag1	post-GPI attachment to proteins 2	protein-coding
mm_12138.1	chr2	61711819	61711832	+	1	NA	5' UTR (NM_021526, exon 1 of 12)	5' UTR (NM_021526, exon 1 of 12)	131	NM_021526	59029	Mm.218198	NM_021526	ENSMUSG00000026914	Psmd14	2610312C03Rik|3200001M20Rik|AA986732|Pad1|Poh1|rpm11	proteasome (prosome, macropain) 26S subunit, non-ATPase, 14	protein-coding
mm_38096.1	chr4	134245518	134245533	-	1	NA	promoter-TSS (NM_024215)	promoter-TSS (NM_024215)	66	NM_024215	68040	Mm.300404	NM_024215	ENSMUSG00000028840	Zfp593	3110024A21Rik|AV062409|E130106C14Rik|ZNF593	zinc finger protein 593	protein-coding
mm_153907.1	chr19	47138141	47138150	-	1	NA	5' UTR (NM_133746, exon 1 of 3)	5' UTR (NM_133746, exon 1 of 3)	149	NM_133746	72691	Mm.31663	NM_133746	ENSMUSG00000033033	Calhm2	2810048G17Rik|Fam26b	calcium homeostasis modulator 2	protein-coding
mm_49260.1	chr6	17463886	17463898	+	1	NA	promoter-TSS (NM_008591)	promoter-TSS (NM_008591)	-65	NM_008591	17295	Mm.86844	NM_008591	ENSMUSG00000009376	Met	AI838057|HGF|HGFR|Par4|c-Met	met proto-oncogene	protein-coding
mm_134697.1	chr16	22657068	22657079	-	1	NA	5' UTR (NM_138650, exon 1 of 25)	5' UTR (NM_138650, exon 1 of 25)	158	NM_138650	110197	Mm.194986	NM_138650	ENSMUSG00000022861	Dgkg	2900055E17Rik|90kDa|AI854428|Dagk3|E430001K23Rik|mKIAA4131	diacylglycerol kinase, gamma	protein-coding
mm_134788.1	chr16	24013375	24013381	-	1	NA	Intergenic	Intergenic	-24766	NM_009744	12053	Mm.347398	NM_009744	ENSMUSG00000022508	Bcl6	Bcl5	B cell leukemia/lymphoma 6	protein-coding
mm_124161.1	chr14	93635993	93635996	-	1	NA	intron (NM_001346722, intron 2 of 4)	intron (NM_001346722, intron 2 of 4)	252894	NM_001271800	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding
mm_152726.1	chr19	18631755	18631824	-	1	NA	promoter-TSS (NM_017375)	promoter-TSS (NM_017375)	24	NM_017375	20409	Mm.172222	NM_017375	ENSMUSG00000024725	Ostf1	C78236|SH3P2|Sh3d3	osteoclast stimulating factor 1	protein-coding
mm_150956.1	chr19	46369253	46369277	+	1	NA	exon (NM_029186, exon 6 of 9)	exon (NM_029186, exon 6 of 9)	12385	NM_029186	75146	Mm.159290	NM_029186	ENSMUSG00000025227	Mfsd13a	4930449A08Rik|4930538D17Rik|Tmem180	major facilitator superfamily domain containing 13a	protein-coding
mm_55464.1	chr6	67535784	67535802	-	1	NA	promoter-TSS (NM_020047)	promoter-TSS (NM_020047)	29	NM_020047	56753	Mm.439913	NM_020047	ENSMUSG00000051397	Tacstd2	C80403|EGP-1|GA733-1|Ly97|TROP2	tumor-associated calcium signal transducer 2	protein-coding
mm_112806.1	chr13	20605438	20605461	+	1	NA	3' UTR (NM_080288, exon 22 of 22)	3' UTR (NM_080288, exon 22 of 22)	132459	NM_198093	140580	Mm.342392	NM_080288	ENSMUSG00000041112	Elmo1	6330578D22Rik|C230095H21Rik|CED-12	engulfment and cell motility 1	protein-coding
mm_13601.1	chr2	112619013	112619022	+	1	NA	intron (NM_001165935, intron 1 of 4)	intron (NM_001165935, intron 1 of 4)	59335	NM_001165935	74268	Mm.315125	NM_028844	ENSMUSG00000003604	Aven	1700013A01Rik|1700056A21Rik|mAven-L|mAven-S	apoptosis, caspase activation inhibitor	protein-coding
mm_74184.1	chr8	123518844	123518928	+	1	NA	promoter-TSS (NM_018855)	promoter-TSS (NM_018855)	51	NM_018855	104346	Mm.117265	NM_018855	ENSMUSG00000040220	Gas8	Gas11	growth arrest specific 8	protein-coding
mm_91741.1	chr10	49218374	49218376	-	1	NA	intron (NM_001111268, intron 14 of 16)	intron (NM_001111268, intron 14 of 16)	-122532	NR_046212	100418235	Mm.185993	NR_046212		C130030K03Rik	-	proteasome (prosome, macropain) subunit, alpha type 6 pseudogene	pseudo
mm_92972.1	chr10	86491862	86491882	-	1	NA	intron (NM_001164495, intron 1 of 6)	intron (NM_001164495, intron 1 of 6)	7024	NM_001164495	27204	Mm.394931	NM_013722	ENSMUSG00000059602	Syn3	-	synapsin III	protein-coding
mm_82503.1	chr9	20459951	20460004	-	1	NA	5' UTR (NM_011753, exon 1 of 10)	5' UTR (NM_011753, exon 1 of 10)	183	NM_011753	22688	Mm.107441	NM_011753	ENSMUSG00000063108	Zfp26	5033428C05Rik|KRAB15|Zfp-26|Zfp70|Zfp81-rs1|mKIAA4196|mkr-3|mszf14|mszf52	zinc finger protein 26	protein-coding
mm_111968.1	chr12	109741620	109741622	-	1	NA	promoter-TSS (NR_030263)	promoter-TSS (NR_030263)	-788	NR_030263	723941		NR_030263	ENSMUSG00000076052	Mir541	Mirn541|mir-541|mmu-mir-541	microRNA 541	ncRNA
mm_22255.1	chr2	174927744	174927749	-	1	NA	Intergenic	Intergenic	140023	NM_001085546	664987		NM_001085546	ENSMUSG00000078905	Gm14393	OTTMUSG00000016546	predicted gene 14393	protein-coding
mm_62877.1	chr7	114753760	114753764	+	1	NA	intron (NM_173767, intron 1 of 12)	intron (NM_173767, intron 1 of 12)	7996	NM_173767	233752	Mm.83037	NM_173767	ENSMUSG00000048782	Insc	3830422K02Rik|C730020D23	inscuteable homolog (Drosophila)	protein-coding
mm_35268.1	chr4	19900958	19900978	-	1	NA	intron (NM_175406, intron 2 of 7)	MIR|SINE|MIR	21598	NM_175406	242341	Mm.19298	NM_175406	ENSMUSG00000028238	Atp6v0d2	1620401A02Rik|AI324824|V-ATPase	ATPase, H+ transporting, lysosomal V0 subunit D2	protein-coding
mm_45312.1	chr5	65435656	65435695	-	1	NA	5' UTR (NM_009466, exon 1 of 12)	5' UTR (NM_009466, exon 1 of 12)	167	NM_009466	22235	Mm.344831	NM_009466	ENSMUSG00000029201	Ugdh	Udpgdh	UDP-glucose dehydrogenase	protein-coding
mm_117689.1	chr13	94285353	94285441	-	1	NA	promoter-TSS (NM_029153)	promoter-TSS (NM_029153)	-116	NM_029153	107767	Mm.201455	NM_029153	ENSMUSG00000021687	Scamp1	4930505M11Rik|AI415563|AW122395	secretory carrier membrane protein 1	protein-coding
mm_28579.1	chr3	93447377	93447403	-	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	5060	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_148497.1	chr19	4180658	4180670	+	1	NA	Intergenic	Intergenic	-5185	NM_134148	107239	Mm.482310	NM_134148	ENSMUSG00000075289	Carns1	AI790298|Atpgd1|mKIAA1394	carnosine synthase 1	protein-coding
mm_95428.1	chr11	50200620	50200643	+	1	NA	TTS (NM_026543)	TTS (NM_026543)	10189	NM_001290769	18412	Mm.40828	NM_011018	ENSMUSG00000015837	Sqstm1	A170|OSF-6|Osi|STAP|STONE14|p62	sequestosome 1	protein-coding
mm_80884.1	chr9	99243422	99243474	+	1	NA	promoter-TSS (NM_023873)	promoter-TSS (NM_023873)	-20	NM_023873	68121	Mm.288739	NM_023873	ENSMUSG00000056267	Cep70	6720484E09Rik|Bite|C030018L16Rik	centrosomal protein 70	protein-coding
mm_2141.1	chr1	88095004	88095010	+	1	NA	promoter-TSS (NM_201642)	promoter-TSS (NM_201642)	6	NM_201642	394432	Mm.300095	NM_201642	ENSMUSG00000090124	Ugt1a7c	A10'|A13|Ugt1a10	UDP glucuronosyltransferase 1 family, polypeptide A7C	protein-coding
mm_123963.1	chr14	74947663	74947674	-	1	NA	5' UTR (NM_001033439, exon 1 of 20)	5' UTR (NM_001033439, exon 1 of 20)	209	NM_001252132	380916	Mm.288868	NM_001033439	ENSMUSG00000068015	Lrch1	4832412D13Rik|AI552548|AW215503|Chdc1|mKIAA1016	leucine-rich repeats and calponin homology (CH) domain containing 1	protein-coding
mm_29181.1	chr3	106529251	106529281	-	1	NA	intron (NM_001293694, intron 4 of 8)	intron (NM_001293694, intron 4 of 8)	-18532	NM_001286986	67171	Mm.290488	NM_026013	ENSMUSG00000027900	Dram2	2010305N14Rik|2610318G18Rik|AI647667|Tmem77	DNA-damage regulated autophagy modulator 2	protein-coding
mm_145075.1	chr18	42143028	42143039	+	1	NA	intron (NM_172966, intron 5 of 7)	L2a|LINE|L2	53676	NM_027072	69401	Mm.34841	NM_027072	ENSMUSG00000059455	Plac8l1	1700009N18Rik|1700015M15Rik	PLAC8-like 1	protein-coding
mm_64088.1	chr7	140968035	140968047	+	1	NA	promoter-TSS (NM_001112715)	promoter-TSS (NM_001112715)	-35	NM_001112715	68713	Mm.175661	NM_026820	ENSMUSG00000025491	Ifitm1	1110036C17Rik|DSPA2a|Mil-2|Mil2	interferon induced transmembrane protein 1	protein-coding
mm_60967.1	chr7	47772747	47772777	+	1	NA	Intergenic	Intergenic	-171390	NM_153067	233222	Mm.240142	NM_153067	ENSMUSG00000078698	Mrgpra3	Mrga3	MAS-related GPR, member A3	protein-coding
mm_135760.1	chr16	56691000	56691012	-	1	NA	TTS (NM_178790)	TTS (NM_178790)	26444	NM_001252443	21787	Mm.425970	NM_019678	ENSMUSG00000022757	Tfg	AI173908	Trk-fused gene	protein-coding
mm_52958.1	chr6	123123354	123123369	+	1	NA	promoter-TSS (NM_001170333)	promoter-TSS (NM_001170333)	45	NM_001170333	26888	Mm.47384	NM_011999	ENSMUSG00000030148	Clec4a2	Clec4a|Clecsf6|DCIR|Dcir1	C-type lectin domain family 4, member a2	protein-coding
mm_82134.1	chr9	123534299	123534311	+	1	NA	intron (NM_030692, intron 1 of 19)	B3A|SINE|B2	4423	NM_030692	83493	Mm.273671	NM_030692	ENSMUSG00000025240	Sacm1l	SAC1|Sac1p|mKIAA0851	SAC1 suppressor of actin mutations 1-like (yeast)	protein-coding
mm_131689.1	chr16	20679637	20679678	+	1	NA	exon (NM_145941, exon 10 of 33)	exon (NM_145941, exon 10 of 33)	-4599	NR_028530	100217430		NR_028530		Snord66	MBII-142|snoRNA142	small nucleolar RNA, C/D box 66	snoRNA
mm_71487.1	chr8	46740242	46740273	+	1	NA	promoter-TSS (NR_045750)	promoter-TSS (NR_045750)	512	NM_008391	16363	Mm.1149	NM_008391	ENSMUSG00000031627	Irf2	9830146E22Rik|AI646973|Irf-2	interferon regulatory factor 2	protein-coding
mm_38072.1	chr4	134127628	134127686	-	1	NA	TTS (NM_026257)	TTS (NM_026257)	1096	NM_080559	73723	Mm.22240	NM_080559	ENSMUSG00000028843	Sh3bgrl3	1110004L05Rik|AU022188	SH3 domain binding glutamic acid-rich protein-like 3	protein-coding
mm_38276.1	chr4	136886182	136886183	-	1	NA	promoter-TSS (NM_009777)	promoter-TSS (NM_009777)	-5	NM_009777	12260	Mm.2570	NM_009777	ENSMUSG00000036905	C1qb	-	complement component 1, q subcomponent, beta polypeptide	protein-coding
mm_116144.1	chr13	29855020	29855024	-	1	NA	intron (NR_131896, intron 1 of 16)	intron (NR_131896, intron 1 of 16)	651	NR_131896	68916	Mm.212227	NM_144536	ENSMUSG00000006191	Cdkal1	1190005B03Rik|6620401C13Rik	CDK5 regulatory subunit associated protein 1-like 1	protein-coding
mm_2698.1	chr1	127793480	127793481	+	1	NA	intron (NM_028399, intron 4 of 8)	intron (NM_028399, intron 4 of 8)	19316	NM_028399	72949	Mm.268672	NM_028399	ENSMUSG00000026349	Ccnt2	2900041I18Rik|C81304|CycT2|CycT2a|CycT2b	cyclin T2	protein-coding
mm_107042.1	chr12	15606336	15606353	+	1	NA	Intergenic	Intergenic	194757	NR_105809	102465204		NR_105809	ENSMUSG00000098480	Mir6387	Gm27281|mmu-mir-6387	microRNA 6387	ncRNA
mm_37238.1	chr4	118117703	118117709	-	1	NA	intron (NM_001161774, intron 1 of 11)	ORR1F|LTR|ERVL-MaLR	17240	NM_001285520	20441	Mm.251002	NM_009176	ENSMUSG00000028538	St3gal3	ST3GalIII|ST3N|Siat3|Siat6	ST3 beta-galactoside alpha-2,3-sialyltransferase 3	protein-coding
mm_80050.1	chr9	69294666	69294678	+	1	NA	intron (NM_001289916, intron 1 of 9)	intron (NM_001289916, intron 1 of 9)	4831	NM_001289916	19883	Mm.378450	NM_013646	ENSMUSG00000032238	Rora	9530021D13Rik|Nr1f1|ROR1|ROR2|ROR3|nmf267|sg|staggerer|tmgc26	RAR-related orphan receptor alpha	protein-coding
mm_53475.1	chr6	134929090	134929103	+	1	NA	promoter-TSS (NR_037955)	promoter-TSS (NR_037955)	4	NR_037955	381822	Mm.5935	NR_037955	ENSMUSG00000098318	Lockd	1190002F15Rik|AI120476|Droc	lncRNA downstream of Cdkn1b	ncRNA
mm_10590.1	chr2	18567721	18567722	+	1	NA	Intergenic	Intergenic	-104741	NM_147778	12238	Mm.249586	NM_147778	ENSMUSG00000051154	Commd3	AW550818|Bup|D2Ertd542e	COMM domain containing 3	protein-coding
mm_160783.1	chr10	127724294	127724294	+	1	NA	promoter-TSS (NM_001199971)	promoter-TSS (NM_001199971)	-184	NM_001199971	21334	Mm.2374	NM_009312	ENSMUSG00000025400	Tac2	PPT-B|Tac3	tachykinin 2	protein-coding
mm_21581.1	chr2	164237245	164237255	-	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	1091	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_9184.1	chr1	171089981	171089989	-	1	NA	Intergenic	RLTR16B_MM|LTR|ERVK	-25333	NR_106103	102466998		NR_106103	ENSMUSG00000099119	Mir6546	Gm27408|mmu-mir-6546	microRNA 6546	ncRNA
mm_137824.1	chr17	30576566	30576603	+	1	NA	promoter-TSS (NM_027060)	promoter-TSS (NM_027060)	-297	NM_027060	224671	Mm.41220	NM_027060	ENSMUSG00000062202	Btbd9	1700023F20Rik|4930402L05|AI464421	BTB (POZ) domain containing 9	protein-coding
mm_157974.1	chrX	93832107	93832199	-	1	NA	promoter-TSS (NM_145630)	promoter-TSS (NM_145630)	-58	NM_145630	236900	Mm.12775	NM_145630	ENSMUSG00000035232	Pdk3	2610001M10Rik|AI035637	pyruvate dehydrogenase kinase, isoenzyme 3	protein-coding
mm_118490.1	chr14	12301313	12301319	+	1	NA	3' UTR (NM_146051, exon 6 of 6)	3' UTR (NM_146051, exon 6 of 6)	17113	NM_001284386	218734	Mm.44068	NM_146051	ENSMUSG00000033111	3830406C13Rik	-	RIKEN cDNA 3830406C13 gene	protein-coding
mm_160847.1	chr11	50984916	50984916	+	1	NA	exon (NM_146911, exon 1 of 1)	exon (NM_146911, exon 1 of 1)	213	NM_146911	258913	Mm.451670	NM_146911	ENSMUSG00000061952	Olfr1377	MOR129-1	olfactory receptor 1377	protein-coding
mm_62226.1	chr7	98500906	98500909	+	1	NA	3' UTR (NM_001113379, exon 2 of 2)	3' UTR (NM_001113379, exon 2 of 2)	6685	NM_001113379	434215	Mm.323057	NM_001113379	ENSMUSG00000090958	Lrrc32	AI426318|D11S833Eh|D7H11S833E|EG434215|Garp	leucine rich repeat containing 32	protein-coding
mm_169650.1	chr15	53574641	53574655	+	1	NA	intron (NM_177225, intron 4 of 4)	L1Md_T|LINE|L1	-228465	NM_010162	14042	Mm.309395	NM_010162	ENSMUSG00000061731	Ext1	AA409028	exostoses (multiple) 1	protein-coding
mm_84794.1	chr9	77200417	77200420	-	1	NA	intron (NM_027150, intron 2 of 7)	Lx9|LINE|L1	147452	NM_027150	69642	Mm.35008	NM_027150	ENSMUSG00000032355	Mlip	2310046A06Rik|AI931782|CIP	muscular LMNA-interacting protein	protein-coding
mm_126192.1	chr15	78670783	78670802	+	1	NA	3' UTR (NM_183141, exon 2 of 2)	3' UTR (NM_183141, exon 2 of 2)	47321	NM_183141	207393	Mm.323188	NM_183141	ENSMUSG00000043460	Elfn2	6330514E13|AW048948|BC094219|Lrrc62|Ppp1r29	leucine rich repeat and fibronectin type III, extracellular 2	protein-coding
mm_93156.1	chr10	93124413	93124455	-	1	NA	Intergenic	Intergenic	-36442	NM_146239	237459	Mm.217404	NM_146239	ENSMUSG00000020015	Cdk17	6430598J10Rik|Pctk2	cyclin-dependent kinase 17	protein-coding
mm_28523.1	chr3	92589023	92589025	-	1	NA	promoter-TSS (NM_008574)	promoter-TSS (NM_008574)	0	NM_008574	17235	Mm.331192	NM_008574		Smcp	Mcs|Mcsp	sperm mitochondria-associated cysteine-rich protein	protein-coding
mm_90002.1	chr10	112270298	112270333	+	1	NA	promoter-TSS (NM_001025581)	promoter-TSS (NM_001025581)	-808	NM_001025581	268345	Mm.336242	NM_001025581	ENSMUSG00000035681	Kcnc2	AW047325|B230117I07|KShIIIA|Kv3.2	potassium voltage gated channel, Shaw-related subfamily, member 2	protein-coding
mm_74396.1	chr8	3232379	3232383	-	1	NA	intron (NM_010568, intron 2 of 20)	intron (NM_010568, intron 2 of 20)	47236	NM_010568	16337	Mm.268003	NM_010568	ENSMUSG00000005534	Insr	4932439J01Rik|CD220|D630014A15Rik|IR|IR-A|IR-B	insulin receptor	protein-coding
mm_164799.1	chr18	23715248	23715272	+	1	NA	Intergenic	Intergenic	37045	NR_126066	100502834	Mm.213614	NR_126066	ENSMUSG00000086287	Gm15972	OTTMUSG00000028454	predicted gene 15972	ncRNA
mm_43152.1	chr5	125532378	125532393	+	1	NA	promoter-TSS (NM_001190352)	promoter-TSS (NM_001190352)	-33	NM_001190352	208151	Mm.40397	NM_001190352	ENSMUSG00000070498	Tmem132b	AK220418|mKIAA1786	transmembrane protein 132B	protein-coding
mm_27400.1	chr3	51276027	51276060	-	1	NA	promoter-TSS (NR_073429)	promoter-TSS (NR_073429)	-718	NR_073429	67746	Mm.441177	NR_073429	ENSMUSG00000087440	4930577N17Rik	-	RIKEN cDNA 4930577N17 gene	ncRNA
mm_96221.1	chr11	62511688	62511691	+	1	NA	intron (NM_001039536, intron 5 of 6)	MLTR25A|LTR|ERVK	27572	NM_028448	73139	Mm.390409	NM_028448	ENSMUSG00000018509	Cenpv	3110013H01Rik|AA671303|Prr6	centromere protein V	protein-coding
mm_52673.1	chr6	117907777	117907786	+	1	NA	promoter-TSS (NM_001166429)	intron (NM_133834, intron 1 of 3)	-23	NM_001166428	98758	Mm.422979	NM_133834	ENSMUSG00000042079	Hnrnpf	4833420I20Rik|AA407306|Hnrpf	heterogeneous nuclear ribonucleoprotein F	protein-coding
mm_14704.1	chr2	142632049	142632060	+	1	NA	intron (NM_001081133, intron 25 of 25)	intron (NM_001081133, intron 25 of 25)	269410	NM_001081133	16558	Mm.251934	NM_001081133	ENSMUSG00000038844	Kif16b	8430434E15Rik|AA623607|AI789011|C80253|C80902|mKIAA1590	kinesin family member 16B	protein-coding
mm_118025.1	chr13	100833448	100833470	-	1	NA	promoter-TSS (NM_022885)	promoter-TSS (NM_022885)	-32	NM_022885	69048	Mm.402215	NM_022885	ENSMUSG00000021629	Slc30a5	1810010K08Rik|AF233321|ZNT5|ZTL1|ZnT-5|Zntl1	solute carrier family 30 (zinc transporter), member 5	protein-coding
mm_155108.1	chrX	48513851	48513855	+	1	NA	promoter-TSS (NM_001290364)	promoter-TSS (NM_001290364)	-290	NM_012019	26926	Mm.240434	NM_012019	ENSMUSG00000036932	Aifm1	AIF|AIFsh2|Hq|Pdcd8	apoptosis-inducing factor, mitochondrion-associated 1	protein-coding
mm_88284.1	chr10	75173845	75173852	+	1	NA	intron (NM_001081412, intron 16 of 22)	intron (NM_001081412, intron 16 of 22)	-38225	NM_153406	74392	Mm.27716	NM_153406	ENSMUSG00000033444	Specc1l	4930470P14Rik|4932439K10Rik|9530057A13Rik|AI317249|Cytsa|mKIAA0376	sperm antigen with calponin homology and coiled-coil domains 1-like	protein-coding
mm_22884.1	chr3	30012199	30012209	+	1	NA	intron (NM_007963, intron 1 of 14)	intron (NM_007963, intron 1 of 14)	1000	NM_007963	14013	Mm.56965	NM_007963	ENSMUSG00000027684	Mecom	D630039M04Rik|Evi-1|Evi1|Jbo|Mds|Mds1|Mds1-Evi1|Prdm3|Znfpr1b1	MDS1 and EVI1 complex locus	protein-coding
mm_79880.1	chr9	65215100	65215176	+	1	NA	intron (NM_177460, intron 1 of 6)	CpG	448	NM_177460	214424	Mm.31129	NM_177460	ENSMUSG00000032392	Parp16	ARTD15|BC055447|C79952|PARP-16	poly (ADP-ribose) polymerase family, member 16	protein-coding
mm_144444.1	chr18	22318992	22318999	+	1	NA	Intergenic	Intergenic	-26094	NM_001167777	211961	Mm.392310	NM_001167777	ENSMUSG00000045215	Asxl3	C230079D11Rik|D430002O22Rik|D930044O18Rik|Gm329|Gm945	additional sex combs like 3 (Drosophila)	protein-coding
mm_76387.1	chr8	84842775	84842785	-	1	NA	exon (NM_007591, exon 9 of 9)	exon (NM_007591, exon 9 of 9)	-2115	NM_009010	19358	Mm.255539	NM_009010	ENSMUSG00000003813	Rad23a	2310040P19Rik|AL024030|HR23A|mHR23A	RAD23 homolog A, nucleotide excision repair protein	protein-coding
mm_52003.1	chr6	92827726	92827747	+	1	NA	intron (NM_175314, intron 18 of 29)	intron (NM_175314, intron 18 of 29)	73705	NM_175314	101401	Mm.158235	NM_175314	ENSMUSG00000030022	Adamts9	1810011L16Rik|8430403M15Rik|AW743315|E030027K14Rik	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 9	protein-coding
mm_13840.1	chr2	119356389	119356397	+	1	NA	Intergenic	RSINE1|SINE|B4	5151	NM_026929	69065	Mm.35083	NM_026929	ENSMUSG00000027313	Chac1	1810008K03Rik	ChaC, cation transport regulator 1	protein-coding
mm_131400.1	chr16	14365725	14365743	+	1	NA	intron (NM_008576, intron 1 of 30)	intron (NM_008576, intron 1 of 30)	4176	NM_008576	17250	Mm.196634	NM_008576	ENSMUSG00000023088	Abcc1	Abcc1a|Abcc1b|MRP|Mdrap|Mrp1	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	protein-coding
mm_108533.1	chr12	84217680	84217690	+	1	NA	intron (NM_001163501, intron 1 of 12)	intron (NM_001163501, intron 1 of 12)	1196	NM_001163501	238317	Mm.31256	NM_001163501	ENSMUSG00000042507	Elmsan1	9430029N19Rik|C130039O16Rik|Gm260	ELM2 and Myb/SANT-like domain containing 1	protein-coding
mm_155611.1	chrX	83043405	83043425	+	1	NA	intron (NM_007868, intron 1 of 78)	intron (NM_007868, intron 1 of 78)	94545	NM_007868	13405	Mm.275608	NM_007868	ENSMUSG00000045103	Dmd	DXSmh7|DXSmh9|Dp427|Dp71|dys|mdx|pke	dystrophin, muscular dystrophy	protein-coding
mm_50908.1	chr6	57582625	57582635	+	1	NA	intron (NM_025992, intron 1 of 22)	MER57E1|LTR|ERV1	1638	NM_025992	67138	Mm.297393	NM_025992	ENSMUSG00000029798	Herc6	1700121D12Rik|2510038N07Rik|4930427L17Rik|AI451296|CEB1|Herc5	hect domain and RLD 6	protein-coding
mm_49505.1	chr6	29831944	29831946	+	1	NA	intron (NM_001171000, intron 1 of 16)	intron (NM_001171000, intron 1 of 16)	-21796	NM_001347084	74340	Mm.210899	NM_021414	ENSMUSG00000029772	Ahcyl2	4631427C17Rik|AI227036|Adohcyase3|mKIAA0828	S-adenosylhomocysteine hydrolase-like 2	protein-coding
mm_141601.1	chr17	32767183	32767215	-	1	NA	3' UTR (NM_172458, exon 4 of 4)	3' UTR (NM_172458, exon 4 of 4)	20348	NM_001346705	208292	Mm.38813	NM_172458	ENSMUSG00000024298	Zfp871	4732483N19|9030612M13Rik|AI118577|AI265322|mKIAA3006	zinc finger protein 871	protein-coding
mm_135915.1	chr16	67602616	67602634	-	1	NA	intron (NM_178721, intron 1 of 9)	intron (NM_178721, intron 1 of 9)	18283	NM_001347247	239857	Mm.394300	NM_178721	ENSMUSG00000064115	Cadm2	2900078E11Rik|9330131D06|A830029E02Rik|Igdf4d|Igsf4d|NECL3|SynCAM 2|SynCAM2	cell adhesion molecule 2	protein-coding
mm_88684.1	chr10	80054047	80054053	+	1	NA	promoter-TSS (NM_001037741)	promoter-TSS (NM_001037741)	31	NM_001037741	625249	Mm.332810	NM_008162	ENSMUSG00000075706	Gpx4	GPx-4|GSHPx-4|PHGPx|mtPHGPx|snGPx	glutathione peroxidase 4	protein-coding
mm_63703.1	chr7	130646106	130646110	+	1	NA	intron (NM_001004468, intron 3 of 21)	CpG	-46448	NM_001347637	57752	Mm.86322	NM_021314	ENSMUSG00000030852	Tacc2	mKIAA4180	transforming, acidic coiled-coil containing protein 2	protein-coding
mm_96637.1	chr11	69326285	69326314	+	1	NA	promoter-TSS (NM_010599)	promoter-TSS (NM_010599)	41	NM_010599	16499	Mm.232472	NM_010599	ENSMUSG00000018470	Kcnab3	C330022D06Rik|Kcnab4|mKv(beta)4	potassium voltage-gated channel, shaker-related subfamily, beta member 3	protein-coding
mm_98949.1	chr11	98447089	98447100	+	1	NA	5' UTR (NM_010346, exon 1 of 15)	5' UTR (NM_010346, exon 1 of 15)	260	NM_010346	14786	Mm.276702	NM_010346	ENSMUSG00000019312	Grb7	mKIAA4028	growth factor receptor bound protein 7	protein-coding
mm_91160.1	chr10	20554832	20554841	-	1	NA	intron (NM_013875, intron 2 of 12)	intron (NM_013875, intron 2 of 12)	-6508	NM_001347366	29863	Mm.425617	NM_013875	ENSMUSG00000019990	Pde7b	-	phosphodiesterase 7B	protein-coding
mm_15750.1	chr2	164237661	164237665	+	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	678	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_62242.1	chr7	98835105	98835119	+	1	NA	promoter-TSS (NM_001285794)	promoter-TSS (NM_001285794)	0	NM_001285794	22411	Mm.22182	NM_009519	ENSMUSG00000015957	Wnt11	-	wingless-type MMTV integration site family, member 11	protein-coding
mm_94063.1	chr10	128369083	128369101	-	1	NA	5' UTR (NM_001081040, exon 1 of 5)	5' UTR (NM_001081040, exon 1 of 5)	945	NM_001081040	210582	Mm.296876	NM_001081040	ENSMUSG00000039914	Coq10a	Gm1	coenzyme Q10A	protein-coding
mm_38375.1	chr4	138457233	138457243	-	1	NA	3' UTR (NM_025451, exon 2 of 2)	3' UTR (NM_025451, exon 2 of 2)	2090	NM_025451	66259	Mm.41603	NM_025451	ENSMUSG00000046447	Camk2n1	1810006K23Rik|AI848599|AI891706	calcium/calmodulin-dependent protein kinase II inhibitor 1	protein-coding
mm_98745.1	chr11	96467258	96467276	+	1	NA	intron (NM_001033186, intron 1 of 12)	intron (NM_001033186, intron 1 of 12)	2676	NM_001177898	78473	Mm.395840	NM_001033186	ENSMUSG00000057058	Skap1	1700091G21Rik|Scap1|Skap-55	src family associated phosphoprotein 1	protein-coding
mm_79526.1	chr9	57645794	57645797	+	1	NA	promoter-TSS (NM_007783)	promoter-TSS (NM_007783)	-142	NM_007783	12988	Mm.21974	NM_007783	ENSMUSG00000032312	Csk	AW212630|p50CSK	c-src tyrosine kinase	protein-coding
mm_61032.1	chr7	49553831	49553861	+	1	NA	intron (NM_175272, intron 16 of 37)	intron (NM_175272, intron 16 of 37)	82989	NM_001005232	13172	Mm.307176	NM_001005232	ENSMUSG00000030507	Dbx1	AI426026|Dbx	developing brain homeobox 1	protein-coding
mm_132205.1	chr16	32551855	32551870	+	1	NA	Intergenic	Lx8|LINE|L1	55581	NM_199309	245308	Mm.76859	NM_199309	ENSMUSG00000052363	Zdhhc19	Gm1744|Gm616	zinc finger, DHHC domain containing 19	protein-coding
mm_40995.1	chr5	77312544	77312560	+	1	NA	intron (NM_153798, intron 1 of 24)	PB1D9|SINE|Alu	2068	NM_153798	231329	Mm.273217	NM_153798	ENSMUSG00000029250	Polr2b	Pol2rb|Rpb140|Rpb2	polymerase (RNA) II (DNA directed) polypeptide B	protein-coding
mm_60552.1	chr7	44481046	44481082	+	1	NA	Intergenic	Intergenic	-3453	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_3339.1	chr1	137966711	137966715	+	1	NA	promoter-TSS (NR_029820)	promoter-TSS (NR_029820)	74	NR_029820	723890		NR_029820	ENSMUSG00000065458	Mir181b-1	Mirn181b-1|mir-181b-1	microRNA 181b-1	ncRNA
mm_60817.1	chr7	45700981	45701016	+	1	NA	intron (NM_009800, intron 2 of 8)	intron (NM_009800, intron 2 of 8)	1031	NM_009800	12348	Mm.27736	NM_009800	ENSMUSG00000003273	Car11	Ca11	carbonic anhydrase 11	protein-coding
mm_160127.1	chr7	28630779	28630779	-	1	NA	intron (NM_175319, intron 1 of 12)	CpG	236	NM_175319	101744	Mm.26022	NM_175319	ENSMUSG00000037469	Acp7	AU017076|C330005M16Rik|Papl	acid phosphatase 7, tartrate resistant	protein-coding
mm_26857.1	chr3	14864043	14864054	-	1	NA	intron (NM_007606, intron 1 of 6)	intron (NM_007606, intron 1 of 6)	510	NM_007606	12350	Mm.300	NM_007606	ENSMUSG00000027559	Car3	BB219044|Ca3|Car-3	carbonic anhydrase 3	protein-coding
mm_35708.1	chr4	44168268	44168289	-	1	NA	promoter-TSS (NM_175201)	promoter-TSS (NM_175201)	5	NM_001038993	73469	Mm.262859	NM_175201	ENSMUSG00000035696	Rnf38	1700065B19Rik|2610202O07Rik|AA673263|Oip1	ring finger protein 38	protein-coding
mm_74417.1	chr8	3625247	3625253	-	1	NA	promoter-TSS (NM_001129804)	promoter-TSS (NM_001129804)	32	NM_008790	18545	Mm.440882	NM_008790	ENSMUSG00000004630	Pcp2	L7|Pcp-2	Purkinje cell protein 2 (L7)	protein-coding
mm_66837.1	chr7	48880993	48881030	-	1	NA	promoter-TSS (NM_001013368)	promoter-TSS (NM_001013368)	30	NM_001013368	108961	Mm.240566	NM_001013368	ENSMUSG00000046179	E2f8	4432406C08Rik|AA410048	E2F transcription factor 8	protein-coding
mm_28576.1	chr3	93445392	93445414	-	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	3073	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_111146.1	chr12	81817282	81817287	-	1	NA	Intergenic	Intergenic	-36114	NM_001174107	338372	Mm.35284	NM_177395	ENSMUSG00000042724	Map3k9	E130314H24Rik|Mlk1|Prke1	mitogen-activated protein kinase kinase kinase 9	protein-coding
mm_80301.1	chr9	73192467	73192469	+	1	NA	Intergenic	Intergenic	78999	NM_198609	225215	Mm.379366	NM_198609	ENSMUSG00000032215	Rsl24d1	2410159K22Rik	ribosomal L24 domain containing 1	protein-coding
mm_105129.1	chr11	101338012	101338039	-	1	NA	3' UTR (NM_009675, exon 4 of 4)	3' UTR (NM_009675, exon 4 of 4)	7419	NM_009675	11754	Mm.67281	NM_009675	ENSMUSG00000019326	Aoc3	SSAO|VAP1	amine oxidase, copper containing 3	protein-coding
mm_25863.1	chr3	129852890	129852893	+	1	NA	intron (NM_001329552, intron 3 of 13)	intron (NM_001329552, intron 3 of 13)	16152	NM_007686	12630	Mm.117180	NM_007686	ENSMUSG00000058952	Cfi	-	complement component factor i	protein-coding
mm_60338.1	chr7	44335785	44335812	+	1	NA	intron (NM_001034115, intron 15 of 24)	intron (NM_001034115, intron 15 of 24)	25534	NM_001034115	243961	Mm.360368	NM_001034115	ENSMUSG00000038738	Shank1	-	SH3/ankyrin domain gene 1	protein-coding
mm_37018.1	chr4	113999501	113999511	-	1	NA	promoter-TSS (NM_001167878)	promoter-TSS (NM_001167878)	-3	NM_001167876	242627	Mm.484115	NM_001167876	ENSMUSG00000078598	Skint5	OTTMUSG00000008560|Skint-5	selection and upkeep of intraepithelial T cells 5	protein-coding
mm_112210.1	chr12	113427408	113427422	-	1	NA	Intergenic	Intergenic	-62150	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_131828.1	chr16	22951129	22951140	+	1	NA	promoter-TSS (NM_053176)	promoter-TSS (NM_053176)	62	NM_053176	94175	Mm.358794	NM_053176	ENSMUSG00000022877	Hrg	AI265597|AW413091|D16jh2|D18020|Hprg|Hrgp	histidine-rich glycoprotein	protein-coding
mm_91369.1	chr10	29362033	29362075	-	1	NA	5' UTR (NM_001110198, exon 1 of 4)	5' UTR (NM_001110198, exon 1 of 4)	388	NM_026518	68031	Mm.28930	NM_026518	ENSMUSG00000038876	Rnf146	2610509H23Rik|Iduna	ring finger protein 146	protein-coding
mm_110532.1	chr12	55014330	55014353	-	1	NA	Intergenic	Intergenic	-28005	NM_013815	217578	Mm.479583	NM_013815	ENSMUSG00000035021	Baz1a	Acf1|B930060C03|BC065123|Gtl5|Wcrf180|cbp146	bromodomain adjacent to zinc finger domain 1A	protein-coding
mm_98327.1	chr11	90548840	90548872	+	1	NA	exon (NM_011505, exon 13 of 18)	exon (NM_011505, exon 13 of 18)	89252	NM_011505	20913	Mm.207203	NM_011505	ENSMUSG00000020546	Stxbp4	6030470M02Rik|Synip	syntaxin binding protein 4	protein-coding
mm_9995.1	chr1	191396923	191396962	-	1	NA	promoter-TSS (NM_144880)	promoter-TSS (NM_144880)	99	NM_144880	226849	Mm.205569	NM_144880	ENSMUSG00000026626	Ppp2r5a	PR61alpha	protein phosphatase 2, regulatory subunit B', alpha	protein-coding
mm_120215.1	chr14	62663666	62663672	+	1	NA	promoter-TSS (NM_001199945)	promoter-TSS (NM_001199945)	2	NM_001199945	319433	Mm.483827	NM_001199945	ENSMUSG00000091155	Serpine3	E130113E03Rik	serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 3	protein-coding
mm_98213.1	chr11	87799973	87799984	+	1	NA	exon (NM_010824, exon 9 of 14)	exon (NM_010824, exon 9 of 14)	6194	NM_010824	17523	Mm.4668	NM_010824	ENSMUSG00000009350	Mpo	mKIAA4033	myeloperoxidase	protein-coding
mm_173281.1	chrY	1561168	1561177	+	1	NA	Intergenic	L1Md_T|LINE|L1	-101390	NM_148943	107868	Mm.347376	NM_148943	ENSMUSG00000069044	Usp9y	Dffry|Fafl2	ubiquitin specific peptidase 9, Y chromosome	protein-coding
mm_128440.1	chr15	50720548	50720555	-	1	NA	intron (NM_001310481, intron 4 of 5)	intron (NM_001310481, intron 4 of 5)	168498	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_21480.1	chr2	162924659	162924662	-	1	NA	Intergenic	MT2B|LTR|ERVL	-6848	NM_026499	67996	Mm.24042	NM_026499	ENSMUSG00000016921	Srsf6	1210001E11Rik|AI314910|AW146126|Sfrs6	serine/arginine-rich splicing factor 6	protein-coding
mm_118292.1	chr13	113046358	113046422	-	1	NA	promoter-TSS (NM_027127)	promoter-TSS (NM_027127)	-2	NM_027127	69590	Mm.12715	NM_027127	ENSMUSG00000021760	Gpx8	2310016C16Rik|AU017063	glutathione peroxidase 8 (putative)	protein-coding
mm_69958.1	chr7	142376070	142376080	-	1	NA	3' UTR (NM_009983, exon 9 of 9)	3' UTR (NM_009983, exon 9 of 9)	-2329	NM_001347541	320802	Mm.154486	NM_177265	ENSMUSG00000045777	Ifitm10	6330512M04Rik|AI848576|DSPA3	interferon induced transmembrane protein 10	protein-coding
mm_60932.1	chr7	46853168	46853171	+	1	NA	intron (NM_010699, intron 6 of 7)	intron (NM_010699, intron 6 of 7)	6087	NM_001136069	16828	Mm.29324	NM_010699	ENSMUSG00000063229	Ldha	Ldh1|Ldhm|l7R2	lactate dehydrogenase A	protein-coding
mm_78891.1	chr9	44604934	44604950	+	1	NA	promoter-TSS (NM_001110826)	promoter-TSS (NM_001110826)	50	NM_181324	13209	Mm.267061	NM_007841	ENSMUSG00000032097	Ddx6	1110001P04Rik|E230023J21Rik|HLR2|mRCK/P54|p54|rck	DEAD (Asp-Glu-Ala-Asp) box polypeptide 6	protein-coding
mm_160786.1	chr10	128370059	128370059	-	1	NA	promoter-TSS (NM_001081040)	promoter-TSS (NM_001081040)	-22	NM_001081040	210582	Mm.296876	NM_001081040	ENSMUSG00000039914	Coq10a	Gm1	coenzyme Q10A	protein-coding
mm_84677.1	chr9	72090255	72090287	-	1	NA	intron (NM_001253862, intron 3 of 19)	(A)n|Simple_repeat|Simple_repeat	20930	NM_001253862	21406	Mm.171615	NM_011544	ENSMUSG00000032228	Tcf12	A130037E08Rik|ALF1|HEB|HEBAlt|HTF-4|HTF4|ME1|REB|bHLHb20	transcription factor 12	protein-coding
mm_25595.1	chr3	116899838	116899859	+	1	NA	intron (NM_009146, intron 12 of 16)	intron (NM_009146, intron 12 of 16)	38168	NM_009146	20321	Mm.66293	NM_009146	ENSMUSG00000033386	Frrs1	AI131732|Sdfr2	ferric-chelate reductase 1	protein-coding
mm_11664.1	chr2	35259654	35259657	+	1	NA	intron (NM_001206368, intron 1 of 16)	intron (NM_001206368, intron 1 of 16)	3296	NM_001206368	227753	Mm.443	NM_146120	ENSMUSG00000026879	Gsn	ADF	gelsolin	protein-coding
mm_169038.1	chr13	13870363	13870367	+	1	NA	Intergenic	Intergenic	-84309	NM_178640	97884	Mm.21686	NM_178640	ENSMUSG00000039242	B3galnt2	A930105D20Rik|C80633|D230016N13Rik	UDP-GalNAc:betaGlcNAc beta 1,3-galactosaminyltransferase, polypeptide 2	protein-coding
mm_147012.1	chr18	34511969	34511999	-	1	NA	Intergenic	Intergenic	-5161	NM_146084	225358	Mm.226899	NM_146084	ENSMUSG00000036501	Fam13b	2610024E20Rik|AW060714|AW546153	family with sequence similarity 13, member B	protein-coding
mm_89116.1	chr10	84756056	84756084	+	1	NA	promoter-TSS (NM_001024918)	promoter-TSS (NM_001024918)	22	NM_001024918	71137	Mm.79070	NM_027689	ENSMUSG00000020037	Rfx4	4933412G19Rik|NYD-sp10	regulatory factor X, 4 (influences HLA class II expression)	protein-coding
mm_60255.1	chr7	43791952	43791982	+	1	NA	promoter-TSS (NM_028660)	promoter-TSS (NM_028660)	76	NM_028660	101533	Mm.19942	NM_028660	ENSMUSG00000047884	Klk9	1200016C12Rik|AI324041	kallikrein related-peptidase 9	protein-coding
mm_110095.1	chr12	25189581	25189597	-	1	NA	Intergenic	Intergenic	60415	NR_045844	432641	Mm.112955	NR_045844		Gm17746	-	predicted gene, 17746	ncRNA
mm_23812.1	chr3	79886215	79886227	+	1	NA	5' UTR (NM_133187, exon 1 of 4)	5' UTR (NM_133187, exon 1 of 4)	291	NM_133187	68659	Mm.427274	NM_133187	ENSMUSG00000027955	Fam198b	1110032E23Rik|2210419I08Rik|AV011458|Ened	family with sequence similarity 198, member B	protein-coding
mm_129223.1	chr15	76607485	76607542	-	1	NA	promoter-TSS (NM_053193)	promoter-TSS (NM_053193)	78	NM_053193	94230	Mm.45141	NM_053193	ENSMUSG00000034022	Cpsf1	-	cleavage and polyadenylation specific factor 1	protein-coding
mm_97889.1	chr11	83298934	83298958	+	1	NA	promoter-TSS (NM_134025)	promoter-TSS (NM_134025)	31	NM_134025	103737	Mm.102205	NM_134025	ENSMUSG00000018733	Pex12	AI451906	peroxisomal biogenesis factor 12	protein-coding
mm_13473.1	chr2	105682969	105682977	+	1	NA	intron (NM_001310146, intron 1 of 9)	intron (NM_001310146, intron 1 of 9)	510	NM_001310145	18508	Mm.3608	NM_013627	ENSMUSG00000027168	Pax6	1500038E17Rik|AEY11|Dey|Gsfaey11|Pax-6|Sey	paired box 6	protein-coding
mm_7290.1	chr1	97769981	97770066	-	1	NA	promoter-TSS (NM_001310773)	promoter-TSS (NM_001310773)	69	NM_173760	227399	Mm.220817	NM_173760	ENSMUSG00000040648	Ppip5k2	AW555814|Cfap160|D330021B20|Hisppd1|Vip2|mKIAA0433	diphosphoinositol pentakisphosphate kinase 2	protein-coding
mm_158115.1	chrX	102189372	102189388	-	1	NA	promoter-TSS (NM_009094)	promoter-TSS (NM_009094)	11	NM_009094	20102	Mm.66	NM_009094	ENSMUSG00000031320	Rps4x	Rps4|Rps4-1	ribosomal protein S4, X-linked	protein-coding
mm_166198.1	chr5	37419167	37419176	+	1	NA	exon (NM_145920, exon 18 of 20)	exon (NM_145920, exon 18 of 20)	80693	NM_145920	68525	Mm.25506	NM_145920	ENSMUSG00000050248	Evc2	1110017L09Rik|Lbn|limbin	Ellis van Creveld syndrome 2	protein-coding
mm_28965.1	chr3	100969645	100969676	-	1	NA	promoter-TSS (NM_001013026)	promoter-TSS (NM_001013026)	3	NM_001013026	74044	Mm.270961	NM_001013026	ENSMUSG00000033222	Ttf2	4632434F22Rik|8030447N19|AV218430	transcription termination factor, RNA polymerase II	protein-coding
mm_107207.1	chr12	26444387	26444406	+	1	NA	3' UTR (NM_021384, exon 6 of 6)	3' UTR (NM_021384, exon 6 of 6)	12056	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_4722.1	chr1	181150927	181150984	+	1	NA	promoter-TSS (NM_030131)	promoter-TSS (NM_030131)	24	NM_030131	98417	Mm.38229	NM_030131	ENSMUSG00000062169	Cnih4	AI647760|AW050376|CNIH-4|D530030D03Rik|E430023H19Rik|HSPC163	cornichon family AMPA receptor auxiliary protein 4	protein-coding
mm_26397.1	chr3	142601275	142601289	+	1	NA	intron (NM_010259, intron 4 of 10)	intron (NM_010259, intron 4 of 10)	6435	NM_010259	14468	Mm.457978	NM_010259	ENSMUSG00000040264	Gbp2b	Gbp-1|Gbp1|Mag-1|Mpa-1|Mpa1	guanylate binding protein 2b	protein-coding
mm_40835.1	chr5	73006898	73006916	+	1	NA	promoter-TSS (NM_173403)	promoter-TSS (NM_173403)	3	NM_173403	231290	Mm.491387	NM_173403	ENSMUSG00000029219	Slc10a4	E130304D01	solute carrier family 10 (sodium/bile acid cotransporter family), member 4	protein-coding
mm_117353.1	chr13	69739846	69739889	-	1	NA	promoter-TSS (NM_001145162)	promoter-TSS (NM_001145162)	30	NM_001145162	76980	Mm.23960	NM_001145162	ENSMUSG00000052981	Ube2ql1	3110006E14Rik	ubiquitin-conjugating enzyme E2Q family-like 1	protein-coding
mm_21720.1	chr2	164638790	164638810	-	1	NA	promoter-TSS (NM_001012723)	promoter-TSS (NM_001012723)	2	NM_001012723	277345	Mm.247244	NM_001012723	ENSMUSG00000070530	Wfdc16	BC043944|WAP16	WAP four-disulfide core domain 16	protein-coding
mm_68755.1	chr7	121069670	121069674	-	1	NA	intron (NM_030691, intron 2 of 5)	intron (NM_030691, intron 2 of 5)	4858	NM_030691	80719	Mm.160384	NM_030691	ENSMUSG00000035004	Igsf6	-	immunoglobulin superfamily, member 6	protein-coding
mm_105543.1	chr11	106324905	106324916	-	1	NA	intron (NM_133199, intron 18 of 23)	intron (NM_133199, intron 18 of 23)	-10348	NM_001313939	15985	Mm.2987	NM_008339	ENSMUSG00000040592	Cd79b	B29|Ig-beta|Igb|Igbeta	CD79B antigen	protein-coding
mm_124666.1	chr15	6386671	6386681	+	1	NA	promoter-TSS (NM_001102400)	promoter-TSS (NM_001102400)	-72	NM_023118	13132	Mm.240830	NM_023118	ENSMUSG00000022150	Dab2	5730435J12Rik|AA960054|AI957090|D15Wsu122e|D630005B22Rik|Doc-2|Doc2|p96	disabled 2, mitogen-responsive phosphoprotein	protein-coding
mm_127566.1	chr15	102234200	102234234	+	1	NA	TTS (NM_011244)	TTS (NM_011244)	-2282	NM_013566	16421	Mm.58	NM_013566	ENSMUSG00000001281	Itgb7	Ly69	integrin beta 7	protein-coding
mm_6362.1	chr1	72201319	72201322	-	1	NA	intron (NM_001005423, intron 1 of 4)	L1ME3B|LINE|L1	10987	NM_001005423	381269	Mm.422636	NM_001005423	ENSMUSG00000039395	Mreg	Gm974|Wdt2|dsu	melanoregulin	protein-coding
mm_137944.1	chr17	32730981	32730988	+	1	NA	Intergenic	Intergenic	45325	NM_134127	106648	Mm.26539	NM_134127	ENSMUSG00000073424	Cyp4f15	AI787289|Cyp4f-15	cytochrome P450, family 4, subfamily f, polypeptide 15	protein-coding
mm_143965.1	chr17	87264228	87264238	-	1	NA	5' UTR (NM_176808, exon 2 of 5)	5' UTR (NM_176808, exon 2 of 5)	1714	NM_176808	193813	Mm.30251	NM_139295	ENSMUSG00000024150	Mcfd2	1810021C21Rik|F5f8d|Lman1ip|Sdnsf	multiple coagulation factor deficiency 2	protein-coding
mm_45847.1	chr5	87699415	87699427	-	1	NA	promoter-TSS (NM_001286023)	promoter-TSS (NM_001286023)	4	NM_001286020	12991	Mm.268737	NM_009972	ENSMUSG00000063157	Csn2	Csnb	casein beta	protein-coding
mm_13920.1	chr2	120609398	120609400	+	1	NA	promoter-TSS (NM_025475)	promoter-TSS (NM_025475)	17	NM_025475	66296	Mm.221900	NM_025475	ENSMUSG00000027285	Haus2	1700101G24Rik|2410007P03Rik|AU020217|Cep27	HAUS augmin-like complex, subunit 2	protein-coding
mm_148829.1	chr19	6341424	6341486	+	1	NA	TTS (NM_001168489)	TTS (NM_001168489)	295	NR_117093	26412	Mm.25860	NM_009006	ENSMUSG00000024948	Map4k2	AI385662|BL44|GCK|Rab8ip	mitogen-activated protein kinase kinase kinase kinase 2	protein-coding
mm_22139.1	chr2	170673801	170673814	-	1	NA	Intergenic	RLTR34B_MM|LTR|ERVK	-58000	NM_029761	76829	Mm.41633	NM_029761	ENSMUSG00000027560	Dok5	2700055C10Rik	docking protein 5	protein-coding
mm_126368.1	chr15	80115443	80115488	+	1	NA	intron (NM_207708, intron 3 of 3)	MLT1J|LTR|ERVL-MaLR	-17689	NM_025609	66513	Mm.288245	NM_025609	ENSMUSG00000022414	Tab1	2310012M03Rik|Map3k7ip1|b2b449Clo	TGF-beta activated kinase 1/MAP3K7 binding protein 1	protein-coding
mm_170862.1	chr2	181919148	181919158	+	1	NA	Intergenic	B2_Mm2|SINE|B2	54793	NM_025901	67005	Mm.271986	NM_025901	ENSMUSG00000038628	Polr3k	12.3kDa|1500004O14Rik|AI196849|AU014893|C11|RPC10|RPC11	polymerase (RNA) III (DNA directed) polypeptide K	protein-coding
mm_96591.1	chr11	69090765	69090817	+	1	NA	3' UTR (NM_009497, exon 5 of 5)	3' UTR (NM_009497, exon 5 of 5)	2263	NM_009497	22318	Mm.28643	NM_009497	ENSMUSG00000020894	Vamp2	Syb-2|Syb2|sybII	vesicle-associated membrane protein 2	protein-coding
mm_51726.1	chr6	86955144	86955180	+	1	NA	exon (NM_177762, exon 10 of 20)	exon (NM_177762, exon 10 of 20)	-54674	NM_001170591	56748	Mm.23809	NM_020045	ENSMUSG00000029993	Nfu1	0610006G17Rik|CGI-33|Hirip5	NFU1 iron-sulfur cluster scaffold	protein-coding
mm_69311.1	chr7	128418155	128418192	-	1	NA	promoter-TSS (NM_026418)	promoter-TSS (NM_026418)	-1	NM_026418	67865	Mm.18635	NM_026418	ENSMUSG00000030844	Rgs10	2310010N19Rik	regulator of G-protein signalling 10	protein-coding
mm_92690.1	chr10	80657103	80657119	-	1	NA	promoter-TSS (NM_145361)	promoter-TSS (NM_145361)	-40	NM_145361	208198	Mm.60720	NM_145361	ENSMUSG00000003344	Btbd2	2610037C03Rik|4930512K17Rik	BTB (POZ) domain containing 2	protein-coding
mm_165721.1	chr3	101604429	101604453	+	1	NA	5' UTR (NM_144900, exon 1 of 23)	5' UTR (NM_144900, exon 1 of 23)	266	NM_144900	11928	Mm.193670	NM_144900	ENSMUSG00000033161	Atp1a1	Atpa-1|BC010319	ATPase, Na+/K+ transporting, alpha 1 polypeptide	protein-coding
mm_22115.1	chr2	170141608	170141611	-	1	NA	intron (NM_001159683, intron 1 of 6)	intron (NM_001159683, intron 1 of 6)	1066	NM_001159683	228913	Mm.22858	NM_001033299	ENSMUSG00000052056	Zfp217	4933431C08Rik|AW987152|Gm562|ZABC1|Znf217	zinc finger protein 217	protein-coding
mm_64988.1	chr7	16916729	16916836	-	1	NA	3' UTR (NM_007590, exon 6 of 6)	3' UTR (NM_007590, exon 6 of 6)	7250	NM_007590	12315	Mm.288630	NM_007590	ENSMUSG00000019370	Calm3	CaMA|R75142	calmodulin 3	protein-coding
mm_135840.1	chr16	58524215	58524227	-	1	NA	promoter-TSS (NM_018784)	promoter-TSS (NM_018784)	-909	NM_018784	54613	Mm.212742	NM_018784	ENSMUSG00000022747	St3gal6	1700023B24Rik|AI930218|AW552396|Siat10|St3galVI	ST3 beta-galactoside alpha-2,3-sialyltransferase 6	protein-coding
mm_124214.1	chr14	100165108	100165109	-	1	NA	Intergenic	MTC|LTR|ERVL-MaLR	-15312	NM_010636	16597	Mm.396499	NM_010636	ENSMUSG00000072294	Klf12	2700063E05Rik|AI225908|AI315654|AP-2rep|B130052C06Rik|D530033K05Rik	Kruppel-like factor 12	protein-coding
mm_70800.1	chr8	22938100	22938113	+	1	NA	exon (NM_001081149, exon 18 of 18)	exon (NM_001081149, exon 18 of 18)	-36730	NM_001110783	11733	Mm.334444	NM_031158	ENSMUSG00000031543	Ank1	Ank-1|nb|pale	ankyrin 1, erythroid	protein-coding
mm_91357.1	chr10	28013358	28013399	-	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	-61442	NM_008983	19272	Mm.332303	NM_008983	ENSMUSG00000019889	Ptprk	AI853699|PTPk|RPTPkappa	protein tyrosine phosphatase, receptor type, K	protein-coding
mm_109298.1	chr12	109559922	109559937	+	1	NA	non-coding (NR_003633, exon 5 of 5)	non-coding (NR_003633, exon 5 of 5)	-3763	NR_030427	791079		NR_030427	ENSMUSG00000076451	Mir770	Mirn770|mir-770|mmu-mir-770	microRNA 770	ncRNA
mm_66371.1	chr7	43656629	43656642	-	1	NA	intron (NM_031181, intron 4 of 6)	intron (NM_031181, intron 4 of 6)	3526	NM_031181	83382	Mm.157702	NM_031181	ENSMUSG00000030474	Siglece	Cd170|Siglec12|Siglec5|Siglec9|Siglecl1|mSiglec-E	sialic acid binding Ig-like lectin E	protein-coding
mm_164435.1	chr16	48874072	48874078	+	1	NA	intron (NM_181596, intron 3 of 3)	intron (NM_181596, intron 3 of 3)	1467	NM_181596	245195	Mm.231288	NM_181596	ENSMUSG00000022651	Retnlg	Fizz3|Relmg|Xcp1	resistin like gamma	protein-coding
mm_99397.1	chr11	102185381	102185398	+	1	NA	promoter-TSS (NM_172947)	promoter-TSS (NM_172947)	-133	NM_172947	268490	Mm.259079	NM_172947	ENSMUSG00000020922	Lsm12	1110032E16Rik|1110059P07|2600001B17Rik	LSM12 homolog	protein-coding
mm_172333.1	chr7	10930984	10930987	-	1	NA	Intergenic	MMERVK9E_I-int|LTR|ERVK	-25935	NM_001185173	665780	Mm.482067	NM_001185173	ENSMUSG00000095339	Zscan4b	EG665780	zinc finger and SCAN domain containing 4B	protein-coding
mm_164635.1	chr17	34197734	34197761	+	1	NA	promoter-TSS (NM_010724)	promoter-TSS (NM_010724)	-448	NM_010724	16913	Mm.180191	NM_010724	ENSMUSG00000024338	Psmb8	Lmp-7|Lmp7	proteasome (prosome, macropain) subunit, beta type 8 (large multifunctional peptidase 7)	protein-coding
mm_52703.1	chr6	119336425	119336431	+	1	NA	exon (NM_001033382, exon 27 of 38)	exon (NM_001033382, exon 27 of 38)	-5662	NM_172492	211187	Mm.121498	NM_172492	ENSMUSG00000055003	Lrtm2	A230084J22|AI841794	leucine-rich repeats and transmembrane domains 2	protein-coding
mm_7719.1	chr1	130661554	130661564	-	1	NA	promoter-TSS (NM_007576)	promoter-TSS (NM_007576)	59	NM_007576	12269	Mm.306720	NM_007576	ENSMUSG00000026405	C4bp	AI195242|C4bpa	complement component 4 binding protein	protein-coding
mm_11435.1	chr2	31991356	31991367	+	1	NA	exon (NM_172268, exon 11 of 36)	exon (NM_172268, exon 11 of 36)	16911	NM_172268	227720	Mm.289686	NM_172268	ENSMUSG00000001855	Nup214	BC039282|CAN|D2H9S46E	nucleoporin 214	protein-coding
mm_48028.1	chr5	136245984	136245986	-	1	NA	Intergenic	Intergenic	-1045	NM_018825	23921	Mm.425294	NM_018825	ENSMUSG00000005057	Sh2b2	Aps	SH2B adaptor protein 2	protein-coding
mm_59530.1	chr7	27653995	27654007	+	1	NA	promoter-TSS (NM_028417)	promoter-TSS (NM_028417)	77	NM_028417	73032	Mm.44095	NM_028417	ENSMUSG00000007944	Ttc9b	2900074C18Rik	tetratricopeptide repeat domain 9B	protein-coding
mm_92464.1	chr10	77970522	77970531	-	1	NA	promoter-TSS (NM_138301)	promoter-TSS (NM_138301)	-654	NM_138301	28240	Mm.276762	NM_138301	ENSMUSG00000009292	Trpm2	9830168K16Rik|C79133|LTRPC2|TRPC7|Trp7|Trrp7	transient receptor potential cation channel, subfamily M, member 2	protein-coding
mm_152005.1	chr19	5918509	5918520	-	1	NA	exon (NM_026772, exon 2 of 2)	exon (NM_026772, exon 2 of 2)	-5643	NM_001291078	19708	Mm.2651	NM_011262	ENSMUSG00000024826	Dpf2	2210010M07Rik|BAF45D|Req|ubi-d4	D4, zinc and double PHD fingers family 2	protein-coding
mm_108048.1	chr12	73908186	73908236	+	1	NA	5' UTR (NM_010431, exon 1 of 15)	5' UTR (NM_010431, exon 1 of 15)	344	NM_001313919	15251	Mm.3879	NM_010431	ENSMUSG00000021109	Hif1a	AA959795|HIF-1-alpha|HIF1-alpha|HIF1alpha|MOP1|bHLHe78	hypoxia inducible factor 1, alpha subunit	protein-coding
mm_76721.1	chr8	94838811	94838845	-	1	NA	promoter-TSS (NM_134141)	promoter-TSS (NM_134141)	411	NM_026452	67914	Mm.169234	NM_026452	ENSMUSG00000031782	Coq9	2310005O14Rik|C78387	coenzyme Q9	protein-coding
mm_116440.1	chr13	43077840	43077868	-	1	NA	exon (NM_001302636, exon 6 of 13)	exon (NM_001302636, exon 6 of 13)	-44985	NM_001005748	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding
mm_86591.1	chr10	13129018	13129051	+	1	NA	exon (NM_009538, exon 6 of 6)	exon (NM_009538, exon 6 of 6)	38189	NR_131912	338438		NR_131912		Hymai	-	hydatidiform mole associated and imprinted transcript	ncRNA
mm_161884.1	chr18	37720353	37720353	+	1	NA	promoter-TSS (NM_033576)	promoter-TSS (NM_033576)	-201	NM_033576	93701	Mm.247203	NM_033576	ENSMUSG00000103585	Pcdhgb4	-	protocadherin gamma subfamily B, 4	protein-coding
mm_85391.1	chr9	103230416	103230430	-	1	NA	promoter-TSS (NM_133977)	promoter-TSS (NM_133977)	-137	NM_133977	22041	Mm.37214	NM_133977	ENSMUSG00000032554	Trf	AI266983|Cd176|HP|Tf|Tfn|hpx	transferrin	protein-coding
mm_124913.1	chr15	11064864	11064877	+	1	NA	promoter-TSS (NM_175501)	promoter-TSS (NM_175501)	97	NM_175501	239337	Mm.224825	NM_175501	ENSMUSG00000047497	Adamts12	ADAMTS-12|AI605170	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 12	protein-coding
mm_2105.1	chr1	87813343	87813351	+	1	NA	intron (NM_009118, intron 4 of 15)	intron (NM_009118, intron 4 of 15)	9667	NM_009118	20215	Mm.1276	NM_009118	ENSMUSG00000056055	Sag	A930001K18Rik|Arr1|Irbp|arrestin	S-antigen, retina and pineal gland (arrestin)	protein-coding
mm_120468.1	chr14	65971818	65971835	+	1	NA	exon (NM_013492, exon 2 of 9)	exon (NM_013492, exon 2 of 9)	3343	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_57519.1	chr6	125494755	125494765	-	1	NA	promoter-TSS (NM_007657)	promoter-TSS (NM_007657)	-5	NM_007657	12527	Mm.210676	NM_007657	ENSMUSG00000030342	Cd9	Tspan29	CD9 antigen	protein-coding
mm_6586.1	chr1	75255850	75255867	-	1	NA	exon (NM_008985, exon 9 of 23)	exon (NM_008985, exon 9 of 23)	8350	NM_008985	19275	Mm.2902	NM_008985	ENSMUSG00000026204	Ptprn	IA-2|mIA-A|mKIAA4064	protein tyrosine phosphatase, receptor type, N	protein-coding
mm_92726.1	chr10	80826212	80826277	-	1	NA	promoter-TSS (NR_027656)	promoter-TSS (NR_027656)	-412	NM_001301034	18245	Mm.398119	NM_008753	ENSMUSG00000035242	Oaz1	AZ-1|AZ1|Antizyme|ODC-Az|Oaz	ornithine decarboxylase antizyme 1	protein-coding
mm_105553.1	chr11	106395804	106395814	-	1	NA	Intergenic	Intergenic	-13028	NM_010494	15896	Mm.394	NM_010494	ENSMUSG00000001029	Icam2	CD102|Icam-2|Ly-60	intercellular adhesion molecule 2	protein-coding
mm_53307.1	chr6	129181269	129181307	+	1	NA	intron (NM_053109, intron 1 of 4)	intron (NM_053109, intron 1 of 4)	673	NM_053109	93694	Mm.197536	NM_053109	ENSMUSG00000030157	Clec2d	Clr-b|Clrb|Ocil	C-type lectin domain family 2, member d	protein-coding
mm_133307.1	chr16	77598324	77598344	+	1	NA	promoter-TSS (NR_029535)	promoter-TSS (NR_029535)	-602	NR_029535	387229		NR_029535	ENSMUSG00000065530	Mir99a	Mirn99a|mir-99a|mmu-mir-99a	microRNA 99a	ncRNA
mm_133774.1	chr16	94721981	94721991	+	1	NA	Intergenic	Intergenic	110567	NM_001347731	13548	Mm.310973	NM_007890	ENSMUSG00000022897	Dyrk1a	2310043O08Rik|D16Ertd272e|D16Ertd493e|Dyrk|ENSMUSG00000074897|Gm10783|Mnbh|Mp86|mmb	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1a	protein-coding
mm_165983.1	chr4	106464454	106464466	+	1	NA	promoter-TSS (NM_153565)	promoter-TSS (NM_153565)	-135	NM_153565	100102	Mm.133268	NM_153565	ENSMUSG00000044254	Pcsk9	AI415265|AI747682|FH3|HCHOLA3|Narc1|PC9	proprotein convertase subtilisin/kexin type 9	protein-coding
mm_162512.1	chr1	155059524	155059530	-	1	NA	Intergenic	Intergenic	40109	NM_010500	15939	Mm.12246	NM_010500	ENSMUSG00000056708	Ier5	-	immediate early response 5	protein-coding
mm_150027.1	chr19	29373716	29373731	+	1	NA	exon (NM_021893, exon 3 of 7)	exon (NM_021893, exon 3 of 7)	6285	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_57703.1	chr6	128541042	128541053	-	1	NA	exon (NM_001001179, exon 34 of 36)	exon (NM_001001179, exon 34 of 36)	-14327	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_168480.1	chr11	49023263	49023278	+	1	NA	Intergenic	L1Md_F3|LINE|L1	-27463	NM_010999	18356	Mm.24769	NM_010999	ENSMUSG00000040328	Olfr56	IF7|MOR276-1	olfactory receptor 56	protein-coding
mm_88037.1	chr10	67535494	67535515	+	1	NA	Intergenic	CpG	-2365	NM_010118	13654	Mm.290421	NM_010118	ENSMUSG00000037868	Egr2	Egr-2|Krox-20|Krox20|NGF1-B|Zfp-25|Zfp-6	early growth response 2	protein-coding
mm_77926.1	chr9	7352987	7353018	+	1	NA	exon (NM_008605, exon 5 of 10)	exon (NM_008605, exon 5 of 10)	5628	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_111699.1	chr12	103657160	103657170	-	1	NA	promoter-TSS (NM_007618)	promoter-TSS (NM_007618)	53	NM_007618	12401	Mm.290079	NM_007618	ENSMUSG00000060807	Serpina6	Cbg	serine (or cysteine) peptidase inhibitor, clade A, member 6	protein-coding
mm_159170.1	chr2	104070942	104070942	+	1	NA	promoter-TSS (NM_181858)	promoter-TSS (NM_181858)	-68	NM_181858	333883	Mm.359026	NM_181858	ENSMUSG00000068686	Cd59b	-	CD59b antigen	protein-coding
mm_22698.1	chr3	18054151	18054162	+	1	NA	promoter-TSS (NM_021560)	promoter-TSS (NM_021560)	-169	NM_021560	59058	Mm.149938	NM_021560	ENSMUSG00000025128	Bhlhe22	Beta3|Beta3a|Bhlhb5	basic helix-loop-helix family, member e22	protein-coding
mm_73284.1	chr8	104842039	104842044	+	1	NA	Intergenic	Intergenic	-5027	NM_145603	234671	Mm.28191	NM_145603	ENSMUSG00000061825	Ces2c	ACH M1|CES 2|Ces2|ces2A3	carboxylesterase 2C	protein-coding
mm_6784.1	chr1	84139618	84139631	-	1	NA	intron (NM_001003948, intron 2 of 2)	L1_Mur3|LINE|L1	79337	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_25099.1	chr3	101280633	101280672	+	1	NA	intron (NM_013486, intron 3 of 4)	intron (NM_013486, intron 3 of 4)	7287	NM_013486	12481	Mm.22842	NM_013486	ENSMUSG00000027863	Cd2	LFA-2|Ly-37|Ly37	CD2 antigen	protein-coding
mm_87178.1	chr10	39043611	39043613	+	1	NA	intron (NM_010681, intron 9 of 37)	intron (NM_010681, intron 9 of 37)	78097	NM_010681	16775	Mm.258065	NM_010681	ENSMUSG00000019846	Lama4	-	laminin, alpha 4	protein-coding
mm_83904.1	chr9	56201709	56201712	-	1	NA	3' UTR (NM_172924, exon 7 of 7)	3' UTR (NM_172924, exon 7 of 7)	-40640	NM_019793	56434	Mm.28484	NM_019793	ENSMUSG00000032324	Tspan3	1700055K04Rik|TM4-A|Tm4sf8	tetraspanin 3	protein-coding
mm_6429.1	chr1	73948085	73948091	-	1	NA	intron (NM_027884, intron 19 of 34)	L2|LINE|L2	-83622	NR_045311	109198	Mm.359721	NR_045311	ENSMUSG00000100301	6030407O03Rik	-	RIKEN cDNA 6030407O03 gene	ncRNA
mm_50112.1	chr6	41533855	41533881	+	1	NA	Intergenic	Intergenic	12092	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_144985.1	chr18	38250241	38250287	+	1	NA	promoter-TSS (NM_024179)	promoter-TSS (NM_024179)	15	NM_024179	66839	Mm.281086	NM_024179	ENSMUSG00000024442	0610009O20Rik	2700004E22Rik|Dele|Kiaa0141	RIKEN cDNA 0610009O20 gene	protein-coding
mm_133953.1	chr16	4003722	4003735	-	1	NA	Intergenic	CpG	-2050	NM_177472	52864	Mm.29935	NM_177472	ENSMUSG00000039738	Slx4	AI256635|AI426760|Btbd12|D16Bwg1016e	SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)	protein-coding
mm_133636.1	chr16	91663381	91663401	+	1	NA	TTS (NM_019973)	TTS (NM_019973)	15567	NM_178880	20658	Mm.46401	NM_019973	ENSMUSG00000022961	Son	2900011L12Rik|AA409051|AU067731|C81487|mKIAA1019|nrebp	Son DNA binding protein	protein-coding
mm_81353.1	chr9	108649435	108649502	+	1	NA	promoter-TSS (NM_011790)	promoter-TSS (NM_011790)	-88	NM_011790	23807	Mm.290447	NM_011790	ENSMUSG00000064145	Arih2	AI843547|ARI2|TRIAD1|UIP48	ariadne RBR E3 ubiquitin protein ligase 2	protein-coding
mm_52152.1	chr6	98000997	98001015	+	1	NA	intron (NM_008601, intron 4 of 8)	intron (NM_008601, intron 4 of 8)	9223	NM_008601	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_54518.1	chr6	35538242	35538283	-	1	NA	intron (NM_008098, intron 1 of 3)	intron (NM_008098, intron 1 of 3)	1626	NM_008098	14489	Mm.182746	NM_008098	ENSMUSG00000029840	Mtpn	5033418D15Rik|Gcdp|V1	myotrophin	protein-coding
mm_59305.1	chr7	25267670	25267723	+	1	NA	promoter-TSS (NM_001302811)	promoter-TSS (NM_001302811)	-3	NM_001302811	71722	Mm.28833	NM_027882	ENSMUSG00000005442	Cic	1200010B10Rik|mKIAA0306	capicua transcriptional repressor	protein-coding
mm_121785.1	chr14	19977041	19977054	-	1	NA	promoter-TSS (NM_001285911)	promoter-TSS (NM_001285911)	202	NM_001038637	14702	Mm.41737	NM_010315	ENSMUSG00000043004	Gng2	-	guanine nucleotide binding protein (G protein), gamma 2	protein-coding
mm_15220.1	chr2	154428740	154428768	+	1	NA	Intergenic	PB1D10|SINE|Alu	-7730	NM_172860	12396	Mm.29914	NM_009823	ENSMUSG00000038533	Cbfa2t2	A430091M07|C330013D05Rik|Cbfa2t2h|MTGR1	core-binding factor, runt domain, alpha subunit 2, translocated to, 2 (human)	protein-coding
mm_139391.1	chr17	52280146	52280152	+	1	NA	Intergenic	Intergenic	-322560	NM_001031811	211468	Mm.399068	NM_001031811	ENSMUSG00000035580	Kcnh8	C130090D05Rik|ELK|ELK1|ELK3|Kv12.1	potassium voltage-gated channel, subfamily H (eag-related), member 8	protein-coding
mm_162589.1	chr1	181144249	181144275	+	1	NA	promoter-TSS (NM_026171)	promoter-TSS (NM_026171)	-58	NM_026171	67459	Mm.263464	NM_026171	ENSMUSG00000026516	Nvl	1200009I24Rik	nuclear VCP-like	protein-coding
mm_22557.1	chr3	9853228	9853238	+	1	NA	Intergenic	Intergenic	-19554	NM_001195031	94212	Mm.23897	NM_053182	ENSMUSG00000027508	Pag1	Cbp|F730007C19Rik|Pag	phosphoprotein associated with glycosphingolipid microdomains 1	protein-coding
mm_143521.1	chr17	73637057	73637062	-	1	NA	intron (NM_027864, intron 1 of 14)	intron (NM_027864, intron 1 of 14)	73392	NM_027864	71685	Mm.271953	NM_027864	ENSMUSG00000024064	Galnt14	0610033M06Rik	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 14	protein-coding
mm_71030.1	chr8	33599815	33599865	+	1	NA	5' UTR (NM_017374, exon 1 of 7)	5' UTR (NM_017374, exon 1 of 7)	219	NM_017374	19053	Mm.29301	NM_017374	ENSMUSG00000009630	Ppp2cb	AI115466|D8Ertd766e|PP2Ac	protein phosphatase 2 (formerly 2A), catalytic subunit, beta isoform	protein-coding
mm_117169.1	chr13	62879976	62880014	-	1	NA	intron (NM_019395, intron 1 of 6)	intron (NM_019395, intron 1 of 6)	8287	NM_019395	14121	Mm.423078	NM_019395	ENSMUSG00000069805	Fbp1	Fbp-2|Fbp2|Fbp3	fructose bisphosphatase 1	protein-coding
mm_170062.1	chr17	30626935	30626936	+	1	NA	promoter-TSS (NR_045287)	promoter-TSS (NR_045287)	-1	NM_013811	13417	Mm.426017	NM_013811	ENSMUSG00000033826	Dnah8	ATPase|Dnahc8|Hst6.7b|P1-Loop	dynein, axonemal, heavy chain 8	protein-coding
mm_45527.1	chr5	72642759	72642766	-	1	NA	promoter-TSS (NM_007723)	promoter-TSS (NM_007723)	-10	NM_007723	12788	Mm.436652	NM_007723	ENSMUSG00000067220	Cnga1	Cncg	cyclic nucleotide gated channel alpha 1	protein-coding
mm_131038.1	chr16	3884630	3884652	+	1	NA	promoter-TSS (NM_001290689)	promoter-TSS (NM_001290689)	22	NM_001290689	74763	Mm.28403	NM_029090	ENSMUSG00000005982	Naa60	1200013P24Rik|AI315146|Nat15	N(alpha)-acetyltransferase 60, NatF catalytic subunit	protein-coding
mm_40513.1	chr5	57793251	57793254	+	1	NA	intron (NM_001310608, intron 1 of 3)	intron (NM_001310608, intron 1 of 3)	75171	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_60588.1	chr7	44482800	44482824	+	1	NA	Intergenic	Intergenic	-1705	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_138540.1	chr17	35262727	35262776	+	1	NA	promoter-TSS (NM_001267808)	promoter-TSS (NM_001267808)	-343	NM_010380	14964	Mm.439675	NM_010380	ENSMUSG00000073411	H2-D1	H-2D|H2-D	histocompatibility 2, D region locus 1	protein-coding
mm_44953.1	chr5	36621268	36621279	-	1	NA	intron (NM_001081232, intron 3 of 8)	intron (NM_001081232, intron 3 of 8)	-35047	NM_001113362	100855	Mm.486203	NM_133910	ENSMUSG00000029192	Tbc1d14	2810413P16Rik|AU043625|C86258|D5Ertd110e|mKIAA1322	TBC1 domain family, member 14	protein-coding
mm_83719.1	chr9	50765881	50765887	-	1	NA	promoter-TSS (NM_001311073)	promoter-TSS (NM_001311073)	49	NM_001311073	68721	Mm.171374	NM_023483	ENSMUSG00000037971	1110032A03Rik	4930500N06Rik|c11orf1	RIKEN cDNA 1110032A03 gene	protein-coding
mm_143094.1	chr17	57080686	57080705	-	1	NA	exon (NM_009451, exon 4 of 4)	exon (NM_009451, exon 4 of 4)	-2185	NM_153551	70785	Mm.284447	NM_153551	ENSMUSG00000002668	Dennd1c	4432409M07Rik	DENN/MADD domain containing 1C	protein-coding
mm_119401.1	chr14	43857503	43857509	+	1	NA	Intergenic	Intergenic	-37867	NM_007894	13586	Mm.86948	NM_007894	ENSMUSG00000072601	Ear1	EAR-1|ECP 1|Raf1	eosinophil-associated, ribonuclease A family, member 1	protein-coding
mm_45945.1	chr5	90263337	90263369	-	1	NA	exon (NM_030886, exon 22 of 34)	exon (NM_030886, exon 22 of 34)	-39357	NM_001163456	231430	Mm.319697	NM_001033310	ENSMUSG00000035505	Cox18	BC038311	cytochrome c oxidase assembly protein 18	protein-coding
mm_71778.1	chr8	66471881	66471924	+	1	NA	TTS (NM_001293784)	TTS (NM_001293784)	14605	NM_025465	66282	Mm.294985	NM_025465	ENSMUSG00000025591	Tma16	1810029B16Rik	translation machinery associated 16	protein-coding
mm_159340.1	chr3	57847087	57847087	-	1	NA	intron (NM_019410, intron 1 of 2)	CpG	670	NM_019410	18645	Mm.271744	NM_019410	ENSMUSG00000027805	Pfn2	Pfn	profilin 2	protein-coding
mm_30256.1	chr3	146651292	146651298	-	1	NA	promoter-TSS (NM_029144)	promoter-TSS (NM_029144)	22	NM_029144	75015	Mm.250432	NM_029144	ENSMUSG00000048652	4930503B20Rik	1700013A07Rik|1700095G21Rik|4930483N21Rik|Gm1652|Samd13	RIKEN cDNA 4930503B20 gene	protein-coding
mm_16883.1	chr2	13011040	13011048	-	1	NA	promoter-TSS (NM_153155)	promoter-TSS (NM_153155)	-180	NM_153155	227580	Mm.229322	NM_153155	ENSMUSG00000049630	C1ql3	1110065A22Rik|AI661623|C1ql|C1qtnf13|CTRP13|K100	C1q-like 3	protein-coding
mm_60686.1	chr7	45154711	45154734	+	1	NA	promoter-TSS (NM_145954)	promoter-TSS (NM_145954)	-184	NM_145954	69748	Mm.82139	NM_145954	ENSMUSG00000007833	Aldh16a1	2410004H02Rik|AI452234|mFLJ00209	aldehyde dehydrogenase 16 family, member A1	protein-coding
mm_41490.1	chr5	92137850	92137870	+	1	NA	promoter-TSS (NM_019490)	promoter-TSS (NM_019490)	-78	NM_019490	56041	Mm.15868	NM_019490	ENSMUSG00000029407	Uso1	115kDa|TAP|Vdp	USO1 vesicle docking factor	protein-coding
mm_106255.1	chr11	117849079	117849131	-	1	NA	promoter-TSS (NM_009689)	promoter-TSS (NM_009689)	-132	NM_001012273	11799	Mm.8552	NM_009689	ENSMUSG00000017716	Birc5	AAC-11|Api4|TIAP|survivin40	baculoviral IAP repeat-containing 5	protein-coding
mm_158837.1	chrX	168673806	168673816	-	1	NA	promoter-TSS (NM_010832)	promoter-TSS (NM_010832)	91	NM_010832	17692	Mm.24248	NM_010832	ENSMUSG00000031358	Msl3	AU018931|Msl31|Msl3l1	male-specific lethal 3 homolog (Drosophila)	protein-coding
mm_145989.1	chr18	68300352	68300409	+	1	NA	promoter-TSS (NM_026440)	promoter-TSS (NM_026440)	25	NM_001170953	67897	Mm.27544	NM_026440	ENSMUSG00000009535	Rnmt	2610002P10Rik|AI848273|Rg7mt1|mKIAA0398	RNA (guanine-7-) methyltransferase	protein-coding
mm_38692.1	chr4	145213657	145213673	-	1	NA	3' UTR (NM_011610, exon 10 of 10)	3' UTR (NM_011610, exon 10 of 10)	-18660	NM_001276465	230895	Mm.240310	NM_001033190	ENSMUSG00000020220	Vps13d	-	vacuolar protein sorting 13D	protein-coding
mm_135583.1	chr16	50552251	50552292	-	1	NA	intron (NR_040379, intron 4 of 5)	intron (NR_040379, intron 4 of 5)	23769	NR_040379	619312	Mm.427671	NR_040379		G730013B05Rik	linc-Cblb|linc1610	RIKEN cDNA G730013B05 gene	ncRNA
mm_116518.1	chr13	45763314	45763326	-	1	NA	intron (NM_001199304, intron 4 of 6)	RSINE1|SINE|B4	201671	NM_001199304	20238	Mm.342683	NM_009124	ENSMUSG00000046876	Atxn1	2900016G23Rik|Atx1|C85907|ENSMUSG00000074917|Gm10786|Sca1	ataxin 1	protein-coding
mm_1606.1	chr1	74381767	74381777	+	1	NA	exon (NM_013612, exon 9 of 15)	exon (NM_013612, exon 9 of 15)	6569	NM_013612	18173	Mm.2913	NM_013612	ENSMUSG00000026177	Slc11a1	Bcg|Ity|Ity1|Lsh|Nramp|Nramp1|ity	solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1	protein-coding
mm_9787.1	chr1	181255306	181255310	-	1	NA	Intergenic	Intergenic	-43330	NM_145514	226757	Mm.289082	NM_145514	ENSMUSG00000038733	Wdr26	1600024A01Rik|AA693241|AI447817|AU044014|C77982|Gid7	WD repeat domain 26	protein-coding
mm_106472.1	chr11	120136699	120136707	-	1	NA	intron (NM_024249, intron 6 of 16)	intron (NM_024249, intron 6 of 16)	14648	NM_001164799	72055	Mm.253403	NM_024249	ENSMUSG00000061306	Slc38a10	1810073N04Rik	solute carrier family 38, member 10	protein-coding
mm_90178.1	chr10	119692396	119692407	+	1	NA	intron (NM_133442, intron 1 of 21)	intron (NM_133442, intron 1 of 21)	69298	NR_045359	75321	Mm.402041	NR_045359	ENSMUSG00000084764	Grip1os2	4930564G21Rik	glutamate receptor interacting protein 1, opposite strand 2	ncRNA
mm_167994.1	chrX	170010344	170010351	+	1	NA	Intergenic	B1_Mur4|SINE|Alu	-31430	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_160610.1	chr9	80465418	80465418	-	1	NA	promoter-TSS (NM_022016)	promoter-TSS (NM_022016)	20	NM_022016	63859	Mm.422780	NM_022016	ENSMUSG00000032343	Impg1	A930015H12Rik|IMP150|SPACR	interphotoreceptor matrix proteoglycan 1	protein-coding
mm_38010.1	chr4	133752705	133752756	-	1	NA	exon (NM_001080819, exon 1 of 20)	exon (NM_001080819, exon 1 of 20)	881	NM_001080819	93760	Mm.22478	NM_001080819	ENSMUSG00000007880	Arid1a	1110030E03Rik|BAF250a|Osa1|Smarcf1	AT rich interactive domain 1A (SWI-like)	protein-coding
mm_144083.1	chr17	94749507	94749509	-	1	NA	promoter-TSS (NR_024720)	promoter-TSS (NR_024720)	384	NM_176917	76781	Mm.139146	NM_176917	ENSMUSG00000055660	Mettl4	2410198H06Rik|A730091E08Rik|AV296509|HsT661	methyltransferase like 4	protein-coding
mm_2836.1	chr1	131527902	131527911	+	1	NA	promoter-TSS (NM_001081011)	promoter-TSS (NM_001081011)	3	NM_175382	108900	Mm.31278	NM_175382	ENSMUSG00000055184	Fam72a	2700049P18Rik|P17	family with sequence similarity 72, member A	protein-coding
mm_102579.1	chr11	61720813	61720831	-	1	NA	promoter-TSS (NM_001033227)	promoter-TSS (NM_001033227)	-23	NM_001033227	109342	Mm.441070	NM_001033227	ENSMUSG00000042371	Slc5a10	C330021F16Rik|SGLT5	solute carrier family 5 (sodium/glucose cotransporter), member 10	protein-coding
mm_107047.1	chr12	15929614	15929633	+	1	NA	Intergenic	Intergenic	-112838	NM_144551	217410	Mm.491136	NM_144551	ENSMUSG00000020601	Trib2	AW319517|TRB-2|TRB2	tribbles pseudokinase 2	protein-coding
mm_19741.1	chr2	104742835	104742848	-	1	NA	promoter-TSS (NM_144804)	promoter-TSS (NM_144804)	-40	NM_144804	211896	Mm.288805	NM_144804	ENSMUSG00000027173	Depdc7	AV216087	DEP domain containing 7	protein-coding
mm_57473.1	chr6	125233025	125233037	-	1	NA	3' UTR (NM_001042564, exon 4 of 4)	3' UTR (NM_001042564, exon 4 of 4)	-1171	NM_145391	213233	Mm.296902	NM_145391	ENSMUSG00000038213	Tapbpl	BC017613|TAPBPL-R|Tapbplr	TAP binding protein-like	protein-coding
mm_162959.1	chr11	5061970	5061976	-	1	NA	intron (NM_144560, intron 6 of 6)	CpG	3354	NM_144560	78926	Mm.44591	NM_030228	ENSMUSG00000034201	Gas2l1	4930500E24Rik|D0Jmb1|Gar22|TU-71.1	growth arrest-specific 2 like 1	protein-coding
mm_146615.1	chr18	10083180	10083197	-	1	NA	exon (NM_009071, exon 25 of 33)	exon (NM_009071, exon 25 of 33)	-53039	NM_001038589	59025	Mm.329277	NM_021522	ENSMUSG00000047879	Usp14	2610005K12Rik|2610037B11Rik|AW107924|C78769|ax|nmf375	ubiquitin specific peptidase 14	protein-coding
mm_73968.1	chr8	120488731	120488748	+	1	NA	promoter-TSS (NM_198671)	promoter-TSS (NM_198671)	-127	NM_198671	382034	Mm.334856	NM_198671	ENSMUSG00000031822	Gse1	2210013I18Rik|mKIAA0182	genetic suppressor element 1, coiled-coil protein	protein-coding
mm_147102.1	chr18	35655186	35655199	-	1	NA	promoter-TSS (NM_001270646)	promoter-TSS (NM_001270646)	7	NM_001270646	381148	Mm.297784	NM_001270646	ENSMUSG00000073600	Prob1	Gm1614	proline rich basic protein 1	protein-coding
mm_11738.1	chr2	37776260	37776274	+	1	NA	promoter-TSS (NM_001163566)	promoter-TSS (NM_001163566)	18	NM_001163566	241324	Mm.392369	NM_001163566	ENSMUSG00000035403	Crb2	5930402A21|BC043114	crumbs family member 2	protein-coding
mm_60880.1	chr7	46169209	46169217	+	1	NA	intron (NM_011510, intron 4 of 38)	ORR1A3|LTR|ERVL-MaLR	10820	NM_011510	20927	Mm.259076	NM_011510	ENSMUSG00000040136	Abcc8	D930031B21Rik|SUR1|Sur	ATP-binding cassette, sub-family C (CFTR/MRP), member 8	protein-coding
mm_69608.1	chr7	137194855	137194867	-	1	NA	3' UTR (NM_001113414, exon 16 of 16)	3' UTR (NM_001113414, exon 16 of 16)	-39822	NR_045885	100038555	Mm.444788	NR_045885	ENSMUSG00000109722	Gm10578	ENSMUSG00000073800	predicted gene 10578	ncRNA
mm_28357.1	chr3	89764524	89764528	-	1	NA	5' UTR (NM_009602, exon 1 of 6)	5' UTR (NM_009602, exon 1 of 6)	106	NM_009602	11444	Mm.35088	NM_009602	ENSMUSG00000027950	Chrnb2	Acrb-2|Acrb2|C030030P04Rik|[b]2-nAchR	cholinergic receptor, nicotinic, beta polypeptide 2 (neuronal)	protein-coding
mm_3712.1	chr1	153908500	153908503	+	1	NA	3' UTR (NM_008131, exon 7 of 7)	3' UTR (NM_008131, exon 7 of 7)	8572	NM_008131	14645	Mm.210745	NM_008131	ENSMUSG00000026473	Glul	GS|Glns	glutamate-ammonia ligase (glutamine synthetase)	protein-coding
mm_26039.1	chr3	135548550	135548562	+	1	NA	intron (NM_027288, intron 10 of 16)	L2|LINE|L2	62945	NM_027288	110173	Mm.280536	NM_027288	ENSMUSG00000028164	Manba	2410030O07Rik|B930014J03Rik|Bmn	mannosidase, beta A, lysosomal	protein-coding
mm_73618.1	chr8	110126489	110126507	+	1	NA	Intergenic	Intergenic	41708	NM_007586	12308	Mm.2755	NM_007586	ENSMUSG00000003657	Calb2	CR	calbindin 2	protein-coding
mm_84091.1	chr9	58229825	58229828	-	1	NA	intron (NM_001311088, intron 6 of 8)	intron (NM_001311088, intron 6 of 8)	8676	NR_105806	102466639		NR_105806	ENSMUSG00000098886	Mir6385	Gm28021|mmu-mir-6385	microRNA 6385	ncRNA
mm_4635.1	chr1	179677250	179677290	+	1	NA	intron (NM_178653, intron 3 of 11)	intron (NM_178653, intron 3 of 11)	9039	NM_178653	109232	Mm.136458	NM_178653	ENSMUSG00000038936	Sccpdh	AW214504|C330023F11Rik	saccharopine dehydrogenase (putative)	protein-coding
mm_19411.1	chr2	91705760	91705768	-	1	NA	intron (NM_145528, intron 1 of 15)	B1_Mus2|SINE|Alu	4828	NM_145528	51897	Mm.28492	NM_145528	ENSMUSG00000027244	Atg13	1110053A20Rik|D2Ertd391e|Harbi1	autophagy related 13	protein-coding
mm_55786.1	chr6	82652857	82652881	-	1	NA	promoter-TSS (NM_025882)	promoter-TSS (NM_025882)	-4	NM_025882	66979	Mm.195753	NM_025882	ENSMUSG00000030042	Pole4	2400007P05Rik|5830430F06Rik	polymerase (DNA-directed), epsilon 4 (p12 subunit)	protein-coding
mm_24141.1	chr3	88297116	88297144	+	1	NA	promoter-TSS (NM_009836)	promoter-TSS (NM_009836)	-5	NM_009836	12462	Mm.256034	NM_009836	ENSMUSG00000001416	Cct3	AL024092|Cctg|Tcp1-rs3|TriC-P5	chaperonin containing Tcp1, subunit 3 (gamma)	protein-coding
mm_60380.1	chr7	44473556	44473568	+	1	NA	Intergenic	Intergenic	3215	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_153559.1	chr19	42202117	42202130	-	1	NA	5' UTR (NM_018780, exon 1 of 3)	5' UTR (NM_018780, exon 1 of 3)	129	NM_018780	54612	Mm.470071	NM_018780	ENSMUSG00000018822	Sfrp5	AI605071|SARP3	secreted frizzled-related sequence protein 5	protein-coding
mm_100721.1	chr11	3913747	3913757	-	1	NA	5' UTR (NM_153142, exon 1 of 2)	5' UTR (NM_153142, exon 1 of 2)	912	NM_153142	103710	Mm.171514	NM_153142	ENSMUSG00000048807	Slc35e4	A330108F03Rik|AI414849|AI536442	solute carrier family 35, member E4	protein-coding
mm_8252.1	chr1	138620215	138620227	-	1	NA	promoter-TSS (NM_021605)	promoter-TSS (NM_021605)	-464	NM_001311148	59125	Mm.143817	NM_021605	ENSMUSG00000026393	Nek7	2810460C19Rik|AU020186	NIMA (never in mitosis gene a)-related expressed kinase 7	protein-coding
mm_15849.1	chr2	164771895	164771903	+	1	NA	exon (NM_026785, exon 4 of 6)	exon (NM_026785, exon 4 of 6)	1970	NM_026785	68612	Mm.89830	NM_026785	ENSMUSG00000001403	Ube2c	1110015A16Rik|D2Ertd695e	ubiquitin-conjugating enzyme E2C	protein-coding
mm_161670.1	chr17	13354601	13354601	+	1	NA	promoter-TSS (NM_001167578)	promoter-TSS (NM_001167578)	29	NM_001167578	100041352	Mm.490251	NM_001167578	ENSMUSG00000052469	Tcp10c	D17Leh66C|D17Leh66ca|Gm9880|T66C-a|Tcp-10c	t-complex protein 10c	protein-coding
mm_63481.1	chr7	127746534	127746565	+	1	NA	promoter-TSS (NM_172748)	promoter-TSS (NM_172748)	-226	NM_172748	233902	Mm.259353	NM_172748	ENSMUSG00000030811	Fbxl19	6030430O11|BC059812|Fbl19	F-box and leucine-rich repeat protein 19	protein-coding
mm_8758.1	chr1	160352014	160352075	-	1	NA	promoter-TSS (NM_001038621)	promoter-TSS (NM_001038621)	-473	NM_001038621	29809	Mm.25833	NM_013862	ENSMUSG00000026721	Rabgap1l	5830411O09Rik|8430421H08Rik|9630005B12Rik|AW049894|HHL|Hh1|mKIAA0471	RAB GTPase activating protein 1-like	protein-coding
mm_165471.1	chr2	164255986	164256011	+	1	NA	exon (NM_173377, exon 2 of 3)	exon (NM_173377, exon 2 of 3)	645	NM_173377	329557	Mm.118769	NM_173377	ENSMUSG00000050383	Svs3b	9530004A22Rik	seminal vesicle secretory protein 3B	protein-coding
mm_17306.1	chr2	26356839	26356905	-	1	NA	exon (NM_001037747, exon 6 of 12)	exon (NM_001037747, exon 6 of 12)	2675	NM_001037747	332579	Mm.330064	NM_001037747	ENSMUSG00000026928	Card9	Gm782	caspase recruitment domain family, member 9	protein-coding
mm_20422.1	chr2	129303765	129303785	-	1	NA	intron (NM_010554, intron 5 of 6)	intron (NM_010554, intron 5 of 6)	6197	NM_010554	16175	Mm.15534	NM_010554	ENSMUSG00000027399	Il1a	Il-1a	interleukin 1 alpha	protein-coding
mm_141564.1	chr17	32229635	32229654	-	1	NA	exon (NM_001286630, exon 3 of 20)	exon (NM_001286630, exon 3 of 20)	-12276	NR_102329	100043434		NR_102329		Gm4432	-	predicted gene 4432	pseudo
mm_170433.1	chr1	87784553	87784557	+	1	NA	promoter-TSS (NR_028519)	promoter-TSS (NR_028519)	-16	NR_028519	100217415	Mm.453537	NR_028519	ENSMUSG00000089281	Scarna6	MBI-46	small Cajal body-specific RNA 6	ncRNA
mm_10697.1	chr2	22622614	22622637	+	1	NA	5' UTR (NM_008078, exon 1 of 16)	5' UTR (NM_008078, exon 1 of 16)	298	NM_008078	14417	Mm.4784	NM_008078	ENSMUSG00000026787	Gad2	6330404F12Rik|GAD(65)|GAD65|Gad-2	glutamic acid decarboxylase 2	protein-coding
mm_7455.1	chr1	120271025	120271033	-	1	NA	promoter-TSS (NM_001085409)	promoter-TSS (NM_001085409)	53	NM_001085409	68428	Mm.181033	NM_133186	ENSMUSG00000026389	Steap3	1010001D01Rik|Tsap6|pHyde	STEAP family member 3	protein-coding
mm_92609.1	chr10	80121796	80121802	-	1	NA	intron (NR_126043, intron 1 of 10)	MTEb|LTR|ERVL-MaLR	5996	NM_001301854	20869	Mm.44231	NM_011492	ENSMUSG00000003068	Stk11	AA408040|Lkb1|Par-4|R75140	serine/threonine kinase 11	protein-coding
mm_143294.1	chr17	65884953	65884963	-	1	NA	promoter-TSS (NM_001198949)	promoter-TSS (NM_001198949)	-35	NM_001198949	19765	Mm.17009	NM_009067	ENSMUSG00000024096	Ralbp1	RLIP76|Rip1	ralA binding protein 1	protein-coding
mm_149595.1	chr19	16225192	16225198	+	1	NA	intron (NM_008139, intron 2 of 6)	intron (NM_008139, intron 2 of 6)	61097	NR_033228	595139	Mm.405662	NR_033228		E030024N20Rik	9030417F11Rik|Ppia-ps8	peptidylprolyl isomerase A pseudogene 8	pseudo
mm_121650.1	chr14	10204619	10204652	-	1	NA	intron (NM_001308286, intron 2 of 6)	B4A|SINE|B4	248823	NM_001308286	14198	Mm.397619	NM_010210	ENSMUSG00000060579	Fhit	AW045638|Fra14A2	fragile histidine triad gene	protein-coding
mm_99219.1	chr11	101033110	101033127	+	1	NA	intron (NM_001243050, intron 9 of 20)	B3A|SINE|B2	2778	NR_105893	102466767		NR_105893	ENSMUSG00000098415	Mir6928	Gm27728|mmu-mir-6928	microRNA 6928	ncRNA
mm_154649.1	chrX	7800470	7800494	+	1	NA	intron (NM_207670, intron 7 of 24)	intron (NM_207670, intron 7 of 24)	10489	NM_207670	54645	Mm.194811	NM_207670	ENSMUSG00000031153	Gripap1	AI854681|DXImx47e|GRASP-1|Sfc10|mKIAA1167	GRIP1 associated protein 1	protein-coding
mm_8796.1	chr1	161788490	161788496	-	1	NA	promoter-TSS (NM_001205243)	promoter-TSS (NM_001205243)	2	NM_001205243	14103	Mm.3355	NM_010177	ENSMUSG00000000817	Fasl	APT1LG1|CD178|CD95-L|CD95L|Fas-L|Faslg|Tnfsf6|Tnlg1a|gld	Fas ligand (TNF superfamily, member 6)	protein-coding
mm_56787.1	chr6	116640318	116640343	-	1	NA	exon (NM_178045, exon 9 of 11)	exon (NM_178045, exon 9 of 11)	5717	NR_106010	102466793		NR_106010	ENSMUSG00000098334	Mir7043	Gm27776|mmu-mir-7043	microRNA 7043	ncRNA
mm_57278.1	chr6	124321557	124321627	-	1	NA	intron (NM_053094, intron 11 of 16)	RLTR19-int|LTR|ERVK	16941	NM_053094	93671	Mm.37426	NM_053094	ENSMUSG00000008845	Cd163	CD163v2|CD163v3	CD163 antigen	protein-coding
mm_67309.1	chr7	79465503	79465512	-	1	NA	intron (NM_017462, intron 1 of 22)	CpG	766	NM_017462	18975	Mm.3616	NM_017462	ENSMUSG00000039176	Polg	AA409516|PolgA	polymerase (DNA directed), gamma	protein-coding
mm_144063.1	chr17	90800585	90800588	-	1	NA	intron (NM_001346957, intron 3 of 18)	intron (NM_001346957, intron 3 of 18)	-7110	NR_136930	102634634		NR_136930		Gm20491	-	enolase 1, alpha non-neuron pseudogene	pseudo
mm_161987.1	chr19	29806102	29806102	-	1	NA	promoter-TSS (NM_172836)	promoter-TSS (NM_172836)	-93	NM_172836	240613	Mm.313351	NM_172836	ENSMUSG00000046138	9930021J03Rik	ENSMUSG00000048936|Gm9832|mKIAA2026	RIKEN cDNA 9930021J03 gene	protein-coding
mm_122954.1	chr14	54968001	54968043	-	1	NA	promoter-TSS (NR_033497)	promoter-TSS (NR_033497)	-765	NR_033497	791403	Mm.319176	NR_033497	ENSMUSG00000097652	Mhrt	D830015G02Rik|ENSMUSG00000053118|Myheart	myosin heavy chain associated RNA transcript	ncRNA
mm_159330.1	chr3	40708849	40708849	+	1	NA	promoter-TSS (NM_178386)	promoter-TSS (NM_178386)	-22	NM_178386	73333	Mm.78691	NM_178386	ENSMUSG00000069041	Slc25a31	1700034J06Rik|Ant4|Sfec	solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 31	protein-coding
mm_86012.1	chr9	112234628	112234644	-	1	NA	5' UTR (NM_001177619, exon 1 of 11)	5' UTR (NM_001177619, exon 1 of 11)	205	NM_001177619	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_102907.1	chr11	69555974	69556009	-	1	NA	exon (NM_007911, exon 5 of 5)	exon (NM_007911, exon 5 of 5)	4246	NM_007911	13643	Mm.249637	NM_007911	ENSMUSG00000003934	Efnb3	EFL-6|ELF-3|Elk-L3|Epl8|LERK-8|NLERK-2	ephrin B3	protein-coding
mm_164475.1	chr16	69254163	69254185	+	1	NA	Intergenic	RLTR13C2|LTR|ERVK	546207	NR_130991	78110	Mm.211406	NR_130991	ENSMUSG00000107073	4930428D20Rik	-	RIKEN cDNA 4930428D20 gene	ncRNA
mm_23140.1	chr3	38885844	38885854	+	1	NA	Intergenic	CpG	-1091	NM_183221	329628	Mm.316210	NM_183221	ENSMUSG00000046743	Fat4	6030410K14Rik|9430004M15	FAT atypical cadherin 4	protein-coding
mm_60487.1	chr7	44478570	44478589	+	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	-5938	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_76793.1	chr8	102785094	102785114	-	1	NA	promoter-TSS (NM_009866)	promoter-TSS (NM_009866)	7	NM_009866	12552	Mm.1571	NM_009866	ENSMUSG00000031673	Cdh11	Cad11|OSF-4	cadherin 11	protein-coding
mm_111787.1	chr12	104752026	104752115	-	1	NA	promoter-TSS (NM_148948)	promoter-TSS (NM_148948)	-118	NM_148948	192119	Mm.21135	NM_148948	ENSMUSG00000041415	Dicer1	1110006F08Rik|D12Ertd7e|mKIAA0928	dicer 1, ribonuclease type III	protein-coding
mm_104468.1	chr11	95274757	95274811	-	1	NA	3' UTR (NM_001195004, exon 14 of 14)	3' UTR (NM_001195004, exon 14 of 14)	13255	NM_053093	93670	Mm.40085	NM_053093	ENSMUSG00000020872	Tac4	AW489379|PPT-C	tachykinin 4	protein-coding
mm_89106.1	chr10	84584859	84584868	+	1	NA	5' UTR (NM_146008, exon 2 of 10)	5' UTR (NM_146008, exon 2 of 10)	7916	NM_146008	216198	Mm.296142	NM_146008	ENSMUSG00000020034	Tcp11l2	E430026E19Rik	t-complex 11 (mouse) like 2	protein-coding
mm_36526.1	chr4	85373241	85373243	-	1	NA	intron (NM_019535, intron 3 of 8)	intron (NM_019535, intron 3 of 8)	167786	NM_019535	20404	Mm.143603	NM_019535	ENSMUSG00000028488	Sh3gl2	9530001L19Rik|AI120490|AW555077|B930049H17Rik|EEN-B1|SH3PA|Sh3d2a	SH3-domain GRB2-like 2	protein-coding
mm_114906.1	chr13	94875601	94875611	+	1	NA	promoter-TSS (NM_011021)	promoter-TSS (NM_011021)	-21	NM_011021	18420	Mm.42051	NM_011021	ENSMUSG00000021685	Otp	-	orthopedia homeobox	protein-coding
mm_133871.1	chr16	96372710	96372723	+	1	NA	intron (NM_001177886, intron 2 of 8)	intron (NM_001177886, intron 2 of 8)	10952	NM_028078	72058	Mm.119714	NM_028078	ENSMUSG00000000159	Igsf5	2010003D20Rik|JCAM|Jam4	immunoglobulin superfamily, member 5	protein-coding
mm_70342.1	chr8	4613183	4613207	+	1	NA	promoter-TSS (NM_145591)	promoter-TSS (NM_145591)	25	NM_145591	233987	Mm.102799	NM_145591	ENSMUSG00000058748	Zfp958	-	zinc finger protein 958	protein-coding
mm_37907.1	chr4	132747255	132747257	-	1	NA	intron (NM_133888, intron 1 of 7)	intron (NM_133888, intron 1 of 7)	9915	NM_133888	100340	Mm.287187	NM_133888	ENSMUSG00000028885	Smpdl3b	1110054A24Rik|AU045240|Asml3b	sphingomyelin phosphodiesterase, acid-like 3B	protein-coding
mm_3060.1	chr1	134093282	134093304	+	1	NA	Intergenic	Intergenic	-14138	NM_007570	12227	Mm.392646	NM_007570	ENSMUSG00000020423	Btg2	AA959598|APRO1|Pc3|TIS21	B cell translocation gene 2, anti-proliferative	protein-coding
mm_138613.1	chr17	35813866	35813892	+	1	NA	Intergenic	Intergenic	-7834	NM_133662	15937	Mm.25613	NM_133662	ENSMUSG00000003541	Ier3	AI663993|IEX-1|cI-3|gly96	immediate early response 3	protein-coding
mm_110730.1	chr12	69767288	69767292	-	1	NA	intron (NM_183294, intron 3 of 9)	intron (NM_183294, intron 3 of 9)	-3346	NR_030450	751538		NR_030450	ENSMUSG00000076065	Mir681	Mirn681|mmu-mir-681	microRNA 681	ncRNA
mm_157244.1	chrX	18461267	18461280	-	1	NA	non-coding (NR_132634, exon 1 of 9)	non-coding (NR_132634, exon 1 of 9)	124	NR_132634	75905	Mm.159617	NM_175228	ENSMUSG00000037358	4930578C19Rik	-	RIKEN cDNA 4930578C19 gene	protein-coding
mm_101955.1	chr11	50296203	50296213	-	1	NA	3' UTR (NM_001110500, exon 15 of 15)	3' UTR (NM_001110500, exon 15 of 15)	-3872	NM_175334	103806	Mm.51116	NM_175334	ENSMUSG00000050567	Maml1	AI644666|AW743257|D930008C07Rik|Mam-1|Mam1|mKIAA0200	mastermind like 1 (Drosophila)	protein-coding
mm_18897.1	chr2	76713810	76713830	-	1	NA	exon (NM_011652, exon 307 of 313)	exon (NM_011652, exon 307 of 313)	38505	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_67517.1	chr7	80901227	80901243	-	1	NA	promoter-TSS (NM_028026)	promoter-TSS (NM_028026)	34	NM_028026	71968	Mm.274226	NM_028026	ENSMUSG00000025722	Wdr73	1200011I23Rik|2410008B13Rik|AI848574|C85352	WD repeat domain 73	protein-coding
mm_96486.1	chr11	67686645	67686656	+	1	NA	3' UTR (NM_001277080, exon 13 of 13)	3' UTR (NM_001277080, exon 13 of 13)	-8676	NM_009038	19674	Mm.439726	NM_009038	ENSMUSG00000020907	Rcvrn	CAR|S-modulin	recoverin	protein-coding
mm_135194.1	chr16	36408438	36408463	-	1	NA	promoter-TSS (NM_001082545)	promoter-TSS (NM_001082545)	-87	NM_001082545	20862	Mm.359610	NM_001082545	ENSMUSG00000022902	Stfa2	Stf2	stefin A2	protein-coding
mm_56667.1	chr6	113623529	113623532	-	1	NA	promoter-TSS (NM_009507)	promoter-TSS (NM_009507)	-491	NM_009507	22346	Mm.29407	NM_009507	ENSMUSG00000033933	Vhl	Vhlh	von Hippel-Lindau tumor suppressor	protein-coding
mm_137629.1	chr17	28328617	28328621	+	1	NA	intron (NM_011287, intron 1 of 5)	CpG	148	NM_011287	19896	Mm.336955	NM_011287	ENSMUSG00000037805	Rpl10a	CsA-19|Nedd6	ribosomal protein L10A	protein-coding
mm_83163.1	chr9	40487674	40487677	-	1	NA	Intergenic	Intergenic	-31911	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_31712.1	chr4	62634280	62634294	+	1	NA	intron (NM_134257, intron 6 of 15)	intron (NM_134257, intron 6 of 15)	14615	NM_134257	50780	Mm.286753	NM_019492	ENSMUSG00000059810	Rgs3	4930506N09Rik|C2PA-RGS3|C2pa|PDZ-RGS3|RGS3S	regulator of G-protein signaling 3	protein-coding
mm_59464.1	chr7	27252257	27252266	+	1	NA	exon (NM_133770, exon 13 of 15)	exon (NM_133770, exon 13 of 15)	-6500	NM_010950	18223	Mm.458153	NM_010950	ENSMUSG00000063160	Numbl	nbl	numb-like	protein-coding
mm_129699.1	chr15	81694196	81694241	-	1	NA	exon (NM_001164320, exon 3 of 6)	exon (NM_001164320, exon 3 of 6)	3069	NM_001164320	214685	Mm.393287	NM_001164320	ENSMUSG00000063765	Chadl	AY100452|D930017K21Rik	chondroadherin-like	protein-coding
mm_81997.1	chr9	121599800	121599804	+	1	NA	intron (NR_040740, intron 2 of 3)	intron (NR_040740, intron 2 of 3)	12782	NR_040740	75384	Mm.445955	NR_040740	ENSMUSG00000084995	Lyzl4os	4930589B17Rik|4930596M17Rik	lysozyme-like 4, opposite strand	ncRNA
mm_110035.1	chr12	16999992	17000071	-	1	NA	promoter-TSS (NM_001161111)	promoter-TSS (NM_001161111)	87	NM_172574	217430	Mm.379451	NM_172574	ENSMUSG00000045679	Pqlc3	C78076|E030024M05Rik	PQ loop repeat containing	protein-coding
mm_12254.1	chr2	68911614	68911629	+	1	NA	intron (NM_172856, intron 1 of 9)	intron (NM_172856, intron 1 of 9)	50180	NM_001347161	241447	Mm.222222	NM_172856	ENSMUSG00000027035	Cers6	4732462C07Rik|AW544719|Lass6|T1L	ceramide synthase 6	protein-coding
mm_85673.1	chr9	107709644	107709681	-	1	NA	intron (NM_011349, intron 1 of 17)	CpG	813	NM_011349	20350	Mm.12903	NM_011349	ENSMUSG00000034684	Sema3f	Sema4|Semak	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F	protein-coding
mm_122801.1	chr14	54554290	54554358	-	1	NA	promoter-TSS (NM_145462)	promoter-TSS (NM_145462)	37	NM_145462	219072	Mm.202152	NM_145462	ENSMUSG00000022177	Haus4	9430093H08Rik|AU016300|D14Ertd500e	HAUS augmin-like complex, subunit 4	protein-coding
mm_149585.1	chr19	16132663	16132721	+	1	NA	promoter-TSS (NM_008139)	promoter-TSS (NM_008139)	-139	NM_008139	14682	Mm.439701	NM_008139	ENSMUSG00000024639	Gnaq	1110005L02Rik|6230401I02Rik|AA408290|AW060788|Dsk1|Dsk10|Galphaq|Gq|GqI	guanine nucleotide binding protein, alpha q polypeptide	protein-coding
mm_71311.1	chr8	43180518	43180524	+	1	NA	Intergenic	Intergenic	-2601	NM_001160412	622117	Mm.390031	NM_001160412	ENSMUSG00000091490	Triml2	EG622117|Tu4	tripartite motif family-like 2	protein-coding
mm_170873.1	chr2	20899886	20899892	+	1	NA	intron (NM_001128084, intron 3 of 24)	LSU-rRNA_Hsa|rRNA|rRNA	67832	NM_001081364	71435	Mm.28507	NM_001081364	ENSMUSG00000036591	Arhgap21	5530401C11Rik|AA416458|ARHGAP10	Rho GTPase activating protein 21	protein-coding
mm_76228.1	chr8	83573190	83573216	-	1	NA	intron (NM_134118, intron 5 of 12)	intron (NM_134118, intron 5 of 12)	6445	NM_025843	66916	Mm.29683	NM_025843	ENSMUSG00000033938	Ndufb7	1110002H15Rik	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 7	protein-coding
mm_107982.1	chr12	72945788	72945800	+	1	NA	TTS (NM_011384)	TTS (NM_011384)	5912	NM_011384	20476	Mm.57138	NM_011384	ENSMUSG00000021099	Six6	Optx2|Six9	sine oculis-related homeobox 6	protein-coding
mm_576.1	chr1	39090094	39090098	+	1	NA	Intergenic	Intergenic	96896	NR_105767	102466631		NR_105767	ENSMUSG00000098833	Mir6349	Gm27558|mmu-mir-6349	microRNA 6349	ncRNA
mm_79039.1	chr9	46208521	46208524	+	1	NA	intron (NM_027498, intron 16 of 24)	intron (NM_027498, intron 16 of 24)	-20108	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2|apo-AI|apoA-I	apolipoprotein A-I	protein-coding
mm_2239.1	chr1	91053423	91053520	+	1	NA	promoter-TSS (NM_008515)	promoter-TSS (NM_008515)	27	NM_008515	16978	Mm.45039	NM_008515	ENSMUSG00000026305	Lrrfip1	AU024550|Fliiap1	leucine rich repeat (in FLII) interacting protein 1	protein-coding
mm_167981.1	chrX	164076131	164076166	-	1	NA	promoter-TSS (NM_009173)	promoter-TSS (NM_009173)	-13	NM_009173	20438	Mm.37215	NM_009173	ENSMUSG00000040749	Siah1b	AA960570|Sinh1b|siah-1b	seven in absentia 1B	protein-coding
mm_27438.1	chr3	51750860	51750868	-	1	NA	intron (NM_001004176, intron 2 of 4)	intron (NM_001004176, intron 2 of 4)	89685	NM_001310482	211666	Mm.24679	NM_174995	ENSMUSG00000074604	Mgst2	GST2|MGST-II	microsomal glutathione S-transferase 2	protein-coding
mm_158286.1	chrX	112384536	112384543	-	1	NA	exon (NM_028655, exon 6 of 6)	exon (NM_028655, exon 6 of 6)	22240	NM_028655	73809	Mm.50508	NM_028655	ENSMUSG00000025527	Satl1	4930404K22Rik	spermidine/spermine N1-acetyl transferase-like 1	protein-coding
mm_10776.1	chr2	24316525	24316532	+	1	NA	Intergenic	MT2A|LTR|ERVL	-20332	NM_031167	16181	Mm.882	NM_031167	ENSMUSG00000026981	Il1rn	F630041P17Rik|IL-1ra	interleukin 1 receptor antagonist	protein-coding
mm_58665.1	chr7	6894249	6894251	+	1	NA	intron (NM_021323, intron 2 of 7)	BC1_Mm|scRNA|scRNA	82412	NR_036631	116811	Mm.381671	NR_036631	ENSMUSG00000108043	Zim3	1700128I23Rik	zinc finger, imprinted 3	ncRNA
mm_111206.1	chr12	84382489	84382554	-	1	NA	intron (NM_001026214, intron 12 of 15)	intron (NM_001026214, intron 12 of 15)	18413	NM_001286058	12499	Mm.10211	NM_007647	ENSMUSG00000021236	Entpd5	AI196558|AI987697|Cd39l4|ER-UDPase|NTPDase-5|NTPDase5|Pcph|mNTPase	ectonucleoside triphosphate diphosphohydrolase 5	protein-coding
mm_67651.1	chr7	84689824	84689834	-	1	NA	intron (NR_038175, intron 1 of 4)	CpG	189	NR_038175	72495	Mm.382914	NR_038175	ENSMUSG00000085236	2610206C17Rik	-	RIKEN cDNA 2610206C17 gene	ncRNA
mm_148343.1	chr18	84649925	84649953	-	1	NA	5' UTR (NM_177450, exon 1 of 12)	5' UTR (NM_177450, exon 1 of 12)	156	NM_177450	338403	Mm.23278	NM_177450	ENSMUSG00000056162	Cndp1	AI746433|Cn1	carnosine dipeptidase 1 (metallopeptidase M20 family)	protein-coding
mm_142114.1	chr17	35838220	35838243	-	1	NA	promoter-TSS (NM_011655)	promoter-TSS (NM_011655)	70	NM_011655	22154	Mm.273538	NM_011655	ENSMUSG00000001525	Tubb5	AA408537|AI596182|B130022C14Rik|M(beta)5	tubulin, beta 5 class I	protein-coding
mm_95549.1	chr11	52307798	52307806	+	1	NA	Intergenic	Intergenic	-24788	NM_001313981	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_39656.1	chr5	24842989	24843001	+	1	NA	promoter-TSS (NM_053075)	promoter-TSS (NM_053075)	-634	NM_053075	19744	Mm.319175	NM_053075	ENSMUSG00000028945	Rheb	Rheb1	Ras homolog enriched in brain	protein-coding
mm_121196.1	chr14	103051521	103051533	+	1	NA	intron (NM_008392, intron 4 of 4)	intron (NM_008392, intron 4 of 4)	4515	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_137791.1	chr17	29637006	29637047	+	1	NA	intron (NR_132314, intron 7 of 27)	intron (NR_132314, intron 7 of 27)	22237	NM_021419	58230	Mm.305994	NM_021419	ENSMUSG00000090083	Rnf8	3830404E21Rik|AIP37|laXp180	ring finger protein 8	protein-coding
mm_100297.1	chr11	117830649	117830662	+	1	NA	intron (NM_027827, intron 2 of 10)	intron (NM_027827, intron 2 of 10)	-4641	NM_009387	21877	Mm.2661	NM_009387	ENSMUSG00000025574	Tk1	D530002A18Rik|Tk-1|Tk1a|Tk1b	thymidine kinase 1	protein-coding
mm_145473.1	chr18	60358607	60358610	+	1	NA	Intergenic	Intergenic	-17421	NM_021792	60440	Mm.261140	NM_021792	ENSMUSG00000054072	Iigp1	2900074L10Rik|AI046432|AW111922|Ifgga1|Iigp|Irga6	interferon inducible GTPase 1	protein-coding
mm_67586.1	chr7	83631824	83631852	-	1	NA	promoter-TSS (NM_023377)	promoter-TSS (NM_023377)	-179	NM_023377	170460	Mm.357953	NM_023377	ENSMUSG00000046027	Stard5	2310058G22Rik|AI607880|D7Ertd152e	StAR-related lipid transfer (START) domain containing 5	protein-coding
mm_20946.1	chr2	151632518	151632599	-	1	NA	promoter-TSS (NM_198214)	promoter-TSS (NM_198214)	35	NM_198214	241727	Mm.39312	NM_198214	ENSMUSG00000027457	Snph	6430515A01|AW045671|AW556958|AW743098|mKIAA0374	syntaphilin	protein-coding
mm_19534.1	chr2	94404986	94405002	-	1	NA	intron (NM_183106, intron 1 of 24)	intron (NM_183106, intron 1 of 24)	1695	NM_183106	74569	Mm.248504	NM_183106	ENSMUSG00000027194	Ttc17	9130020K17Rik|D2Bwg1005e	tetratricopeptide repeat domain 17	protein-coding
mm_167966.1	chrX	151801209	151801226	+	1	NA	Intergenic	Intergenic	-2065	NM_021523	59026	Mm.27372	NM_021523	ENSMUSG00000025261	Huwe1	5430439H10Rik|AU041296|Arf-bp1|C430014N20Rik|C80292|Gm1718|Ib772|LASU1|Mule|Ureb1	HECT, UBA and WWE domain containing 1	protein-coding
mm_64586.1	chr7	3155374	3155376	-	1	NA	3' UTR (NM_001004153, exon 12 of 12)	3' UTR (NM_001004153, exon 12 of 12)	13828	NM_001004153	245128	Mm.268551	NM_001004153	ENSMUSG00000054753	AU018091	-	expressed sequence AU018091	protein-coding
mm_121179.1	chr14	103049002	103049032	+	1	NA	intron (NM_008392, intron 1 of 4)	intron (NM_008392, intron 1 of 4)	2005	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_31734.1	chr4	63150351	63150360	+	1	NA	exon (NM_007443, exon 4 of 10)	exon (NM_007443, exon 4 of 10)	3817	NM_007443	11699	Mm.2197	NM_007443	ENSMUSG00000028356	Ambp	AI194774|ASPI|HI-30|Intin4|Itil|UTI	alpha 1 microglobulin/bikunin	protein-coding
mm_89365.1	chr10	88570585	88570603	+	1	NA	exon (NM_001252372, exon 5 of 29)	exon (NM_001252372, exon 5 of 29)	34558	NM_001252372	109272	Mm.147208	NM_175418	ENSMUSG00000020061	Mybpc1	8030451F13Rik	myosin binding protein C, slow-type	protein-coding
mm_3755.1	chr1	156040910	156040925	+	1	NA	promoter-TSS (NM_001160181)	promoter-TSS (NM_001160181)	56	NM_022329	240832	Mm.253335	NM_022329	ENSMUSG00000050565	Tor1aip2	1110020D10Rik|15kDa|A130072J07|AA103493|AW060462|AW610675|C77739|Ifrg15|Lull1	torsin A interacting protein 2	protein-coding
mm_143608.1	chr17	78665212	78665214	-	1	NA	intron (NM_011500, intron 10 of 17)	intron (NM_011500, intron 10 of 17)	71347	NM_011500	268980	Mm.311915	NM_011500	ENSMUSG00000024077	Strn	AU022939|D130055P19	striatin, calmodulin binding protein	protein-coding
mm_22820.1	chr3	27210465	27210479	+	1	NA	intron (NM_178772, intron 1 of 4)	intron (NM_178772, intron 1 of 4)	27468	NM_178772	320024	Mm.24576	NM_178772	ENSMUSG00000027698	Nceh1	Aadacl1|B230106I24Rik|CPO-BP|Nceh	neutral cholesterol ester hydrolase 1	protein-coding
mm_134397.1	chr16	17530994	17531016	-	1	NA	promoter-TSS (NM_026909)	promoter-TSS (NM_026909)	47	NM_026909	69009	Mm.10174	NM_026909	ENSMUSG00000022760	Thap7	1810004B07Rik	THAP domain containing 7	protein-coding
mm_19762.1	chr2	105399287	105399300	-	1	NA	promoter-TSS (NM_009037)	promoter-TSS (NM_009037)	26	NM_009037	19672	Mm.4876	NM_009037	ENSMUSG00000005973	Rcn1	Rcn	reticulocalbin 1	protein-coding
mm_43499.1	chr5	136967931	136967941	+	1	NA	promoter-TSS (NM_021719)	promoter-TSS (NM_021719)	67	NM_021719	60363	Mm.87202	NM_021719	ENSMUSG00000001739	Cldn15	2210009B08Rik|BB107105	claudin 15	protein-coding
mm_23774.1	chr3	76074540	76074597	+	1	NA	promoter-TSS (NM_178673)	promoter-TSS (NM_178673)	7	NM_178673	213262	Mm.379337	NM_178673	ENSMUSG00000034098	Fstl5	9130207J01Rik	follistatin-like 5	protein-coding
mm_25624.1	chr3	118733621	118733625	+	1	NA	intron (NM_170778, intron 3 of 22)	intron (NM_170778, intron 3 of 22)	171445	NM_170778	99586	Mm.27907	NM_170778	ENSMUSG00000033308	Dpyd	AI315208|DPD|E330028L06Rik	dihydropyrimidine dehydrogenase	protein-coding
mm_77148.1	chr8	111629157	111629169	-	1	NA	intron (NM_027570, intron 4 of 10)	intron (NM_027570, intron 4 of 10)	1159	NM_027570	52815	Mm.27589	NM_027570	ENSMUSG00000031958	Ldhd	4733401P21Rik|D8Bwg1320e	lactate dehydrogenase D	protein-coding
mm_24285.1	chr3	89231785	89231798	+	1	NA	exon (NM_013605, exon 5 of 7)	exon (NM_013605, exon 5 of 7)	2735	NM_013605	17829	Mm.16193	NM_013605	ENSMUSG00000042784	Muc1	CD227|EMA|Muc-1	mucin 1, transmembrane	protein-coding
mm_125424.1	chr15	42479737	42479745	+	1	NA	intron (NM_001286062, intron 4 of 8)	intron (NM_001286062, intron 4 of 8)	197236	NM_001286062	11600	Mm.309336	NM_009640	ENSMUSG00000022309	Angpt1	1110046O21Rik|Ang-1|Ang1	angiopoietin 1	protein-coding
mm_12806.1	chr2	80292816	80292839	+	1	NA	5' UTR (NM_177256, exon 1 of 1)	5' UTR (NM_177256, exon 1 of 1)	357	NM_177256	320769	Mm.60992	NM_177256	ENSMUSG00000050114	Prdx6b	1-cysPrx-P1|4930414C22Rik|Aop2-rs1|Prdx5-rs1|Prdx6-ps1|Prdx6-rs1|Prdx6-rs1-ps	peroxiredoxin 6B	protein-coding
mm_26916.1	chr3	20155091	20155122	-	1	NA	promoter-TSS (NM_013755)	promoter-TSS (NM_013755)	10	NM_013755	27357	Mm.6375	NM_013755	ENSMUSG00000019528	Gyg	AU017667|Gyg1	glycogenin	protein-coding
mm_28761.1	chr3	95882194	95882231	-	1	NA	promoter-TSS (NM_001033302)	promoter-TSS (NM_001033302)	16	NM_001033302	229599	Mm.331218	NM_001033302	ENSMUSG00000038550	Ciart	Chrono|Gm129	circadian associated repressor of transcription	protein-coding
mm_102891.1	chr11	69416146	69416167	-	1	NA	Intergenic	Intergenic	-2481	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_125018.1	chr15	25632333	25632341	+	1	NA	intron (NM_019472, intron 1 of 40)	intron (NM_019472, intron 1 of 40)	9787	NM_019472	17909	Mm.60590	NM_019472	ENSMUSG00000022272	Myo10	AW048724|D15Ertd600e|mKIAA0799|myosin-X	myosin X	protein-coding
mm_37582.1	chr4	126325673	126325707	-	1	NA	promoter-TSS (NM_011902)	promoter-TSS (NM_011902)	-491	NM_011902	24084	Mm.23895	NM_011902	ENSMUSG00000028845	Tekt2	AU014974|tektin-t	tektin 2	protein-coding
mm_124949.1	chr15	12350657	12350676	+	1	NA	3' UTR (NM_025673, exon 4 of 4)	3' UTR (NM_025673, exon 4 of 4)	29170	NM_025673	66629	Mm.157655	NM_025673	ENSMUSG00000022200	Golph3	4733401N08Rik|5730410D03Rik|AW413496	golgi phosphoprotein 3	protein-coding
mm_172142.1	chr6	36810241	36810246	-	1	NA	5' UTR (NM_008973, exon 1 of 5)	5' UTR (NM_008973, exon 1 of 5)	1118	NM_008973	19242	Mm.279690	NM_008973	ENSMUSG00000029838	Ptn	HARP|HB-GAM|HBBN|HBGF-8|HBNF|OSF|Osf-1|Osf1	pleiotrophin	protein-coding
mm_15333.1	chr2	155826139	155826151	+	1	NA	exon (NM_010579, exon 2 of 6)	exon (NM_010579, exon 2 of 6)	780	NM_010579	16418	Mm.271674	NM_010579	ENSMUSG00000027613	Eif6	1110004P11|AA408895|CAB|Itgb4bp|eIF-6|imc-415|p27(BBP)|p27BBP	eukaryotic translation initiation factor 6	protein-coding
mm_119752.1	chr14	54157268	54157274	+	1	NA	Intergenic	Intergenic	96658	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_118697.1	chr14	22140862	22140884	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	121161	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_73570.1	chr8	109705502	109705519	+	1	NA	promoter-TSS (NM_001286391)	promoter-TSS (NM_001286391)	-36	NM_001286393	75871	Mm.180410	NM_029468	ENSMUSG00000031728	Zfp821	4930566A11Rik|Znf821	zinc finger protein 821	protein-coding
mm_157154.1	chrX	9463424	9463440	-	1	NA	intron (NM_007807, intron 3 of 12)	ID4|SINE|ID	5892	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_94334.1	chr11	4637702	4637711	+	1	NA	promoter-TSS (NM_029291)	promoter-TSS (NM_029291)	-87	NM_029291	75452	Mm.439906	NM_029291	ENSMUSG00000020412	Ascc2	1700011I11Rik|2610034L15Rik|AI482016|ASC1p100|AW046480	activating signal cointegrator 1 complex subunit 2	protein-coding
mm_156936.1	chrX	169915905	169915925	+	1	NA	intron (NM_001290506, intron 1 of 9)	intron (NM_001290506, intron 1 of 9)	36296	NM_001290505	17318	Mm.34441	NM_010797	ENSMUSG00000035299	Mid1	61B3-R|DXHXS1141|Fxy|Trim18	midline 1	protein-coding
mm_18097.1	chr2	44987419	44987490	-	1	NA	3' UTR (NM_015753, exon 10 of 10)	3' UTR (NM_015753, exon 10 of 10)	35723	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_130806.1	chr15	101709838	101709856	-	1	NA	exon (NM_027011, exon 6 of 9)	exon (NM_027011, exon 6 of 9)	3044	NM_027011	110308	Mm.451847	NM_027011	ENSMUSG00000061527	Krt5	3300001P10Rik|AW146334|CK5|K5|Krt2-5|Tfip8	keratin 5	protein-coding
mm_75715.1	chr8	68905762	68905783	-	1	NA	3' UTR (NM_008509, exon 10 of 10)	3' UTR (NM_008509, exon 10 of 10)	25217	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_32726.1	chr4	116557579	116557587	+	1	NA	promoter-TSS (NM_029868)	promoter-TSS (NM_029868)	-144	NM_029868	77110	Mm.41715	NM_029868	ENSMUSG00000034042	Gpbp1l1	5330440M15Rik|BC002292	GC-rich promoter binding protein 1-like 1	protein-coding
mm_167503.1	chr9	13298132	13298184	+	1	NA	Intergenic	Intergenic	51202	NM_025534	66396	Mm.290620	NM_025534	ENSMUSG00000079084	Ccdc82	2310043N13Rik	coiled-coil domain containing 82	protein-coding
mm_10821.1	chr2	24351062	24351074	+	1	NA	3' UTR (NM_031167, exon 5 of 5)	3' UTR (NM_031167, exon 5 of 5)	5697	NM_001039701	16181	Mm.882	NM_031167	ENSMUSG00000026981	Il1rn	F630041P17Rik|IL-1ra	interleukin 1 receptor antagonist	protein-coding
mm_87029.1	chr10	28611945	28611945	+	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	-56415	NM_001305663	210757	Mm.123021	NM_178666	ENSMUSG00000049109	Themis	E430004N04Rik|Gasp|Spot|Tsepa|thylex	thymocyte selection associated	protein-coding
mm_155007.1	chrX	41400840	41400885	+	1	NA	promoter-TSS (NM_001290451)	promoter-TSS (NM_001290451)	-439	NM_016886	53623	Mm.327681	NM_016886	ENSMUSG00000001986	Gria3	2900064I19Rik|GluA3|GluR-C|GluR-K3|Glur-3|Glur3|Gluralpha3	glutamate receptor, ionotropic, AMPA3 (alpha 3)	protein-coding
mm_104353.1	chr11	94297841	94297887	-	1	NA	exon (NM_026313, exon 7 of 11)	exon (NM_026313, exon 7 of 11)	24047	NM_026313	67684	Mm.30927	NM_026313	ENSMUSG00000020863	Luc7l3	3300001P08Rik|Luc7a	LUC7-like 3 (S. cerevisiae)	protein-coding
mm_159542.1	chr4	88827348	88827348	+	1	NA	promoter-TSS (NM_206871)	promoter-TSS (NM_206871)	-68	NM_206871	15969	Mm.377090	NM_206871	ENSMUSG00000101252	Ifna6	IFNa8/6|Ifa6|Ifa8|Ifna8	interferon alpha 6	protein-coding
mm_91988.1	chr10	61979077	61979108	-	1	NA	promoter-TSS (NM_007731)	promoter-TSS (NM_007731)	16	NM_001304757	12817	Mm.300931	NM_007731	ENSMUSG00000058806	Col13a1	-	collagen, type XIII, alpha 1	protein-coding
mm_47113.1	chr5	119580533	119580550	-	1	NA	promoter-TSS (NR_045702)	promoter-TSS (NR_045702)	-183	NR_045702	100993	Mm.381453	NR_045702	ENSMUSG00000087516	AW549542	-	expressed sequence AW549542	ncRNA
mm_120409.1	chr14	65174045	65174055	+	1	NA	Intergenic	RMER2|LTR|ERV1	-75944	NM_018788	54616	Mm.103748	NM_018788	ENSMUSG00000021978	Extl3	2900009G18Rik|AU040105|Ext1l|mKIAA0519	exostoses (multiple)-like 3	protein-coding
mm_160364.1	chr8	21969601	21969601	+	1	NA	promoter-TSS (NM_026459)	promoter-TSS (NM_026459)	-995	NM_026459	67929	Mm.60688	NM_026459	ENSMUSG00000017049	Ccdc70	1700112P19Rik	coiled-coil domain containing 70	protein-coding
mm_173170.1	chrX	43679590	43679596	-	1	NA	Intergenic	L1Md_T|LINE|L1	88604	NM_001195271	637093	Mm.368463	NM_001195271	ENSMUSG00000078320	Tex13c1	Gm362|Tex13c	TEX13 family member C1	protein-coding
mm_142294.1	chr17	40880023	40880027	-	1	NA	exon (NM_027834, exon 1 of 2)	exon (NM_027834, exon 1 of 2)	533	NM_027834	71583	Mm.158733	NM_027834	ENSMUSG00000054951	9130008F23Rik	-	RIKEN cDNA 9130008F23 gene	protein-coding
mm_170276.1	chr18	25460751	25460752	-	1	NA	intron (NM_001033532, intron 10 of 10)	RLTR10C|LTR|ERVK	291731	NM_001033532	225289	Mm.391081	NM_001033532	ENSMUSG00000033632	AW554918	4921538P22|AI461742|Kiaa1328|mKIAA1328	expressed sequence AW554918	protein-coding
mm_31087.1	chr4	41631714	41631724	+	1	NA	intron (NM_175138, intron 16 of 19)	intron (NM_175138, intron 16 of 19)	8583	NM_027147	69638	Mm.372459	NM_027147	ENSMUSG00000028445	Enho	1110065P19Rik|2310040A07Rik	energy homeostasis associated	protein-coding
mm_50228.1	chr6	42350938	42350956	+	1	NA	exon (NM_001289618, exon 3 of 10)	exon (NM_001289618, exon 3 of 10)	1119	NM_001289619	22793	Mm.282303	NM_011777	ENSMUSG00000029860	Zyx	9530098H06Rik|R75157	zyxin	protein-coding
mm_89440.1	chr10	91170820	91170864	+	1	NA	promoter-TSS (NM_001283048)	promoter-TSS (NM_001283048)	-292	NM_001283048	21917	Mm.159684	NM_011605	ENSMUSG00000019961	Tmpo	5630400D24Rik|AI195756|AI606875|AW214352|AW547477|LAP2|TP	thymopoietin	protein-coding
mm_141441.1	chr17	29691250	29691250	-	1	NA	exon (NM_028791, exon 13 of 24)	exon (NM_028791, exon 13 of 24)	25767	NM_026782	68597	Mm.390979	NM_026782	ENSMUSG00000024018	Ccdc167	1110021J02Rik	coiled-coil domain containing 167	protein-coding
mm_26618.1	chr3	152396062	152396082	+	1	NA	promoter-TSS (NM_001080755)	promoter-TSS (NM_001080755)	69	NM_001080755	108946	Mm.379292	NM_198416	ENSMUSG00000039068	Zzz3	3110065C23Rik|6430567E01Rik|AA408566|AI481057|AW556059|R75514	zinc finger, ZZ domain containing 3	protein-coding
mm_40094.1	chr5	34557311	34557324	+	1	NA	exon (NM_001145859, exon 7 of 13)	exon (NM_001145859, exon 7 of 13)	7741	NM_001145859	24055	Mm.5012	NM_011893	ENSMUSG00000054520	Sh3bp2	3BP2	SH3-domain binding protein 2	protein-coding
mm_25162.1	chr3	103058303	103058352	+	1	NA	promoter-TSS (NM_010937)	promoter-TSS (NM_010937)	42	NM_010937	18176	Mm.400954	NM_010937	ENSMUSG00000027852	Nras	AV095280|N-ras	neuroblastoma ras oncogene	protein-coding
mm_76370.1	chr8	84800305	84800307	-	1	NA	promoter-TSS (NM_010906)	promoter-TSS (NM_010906)	32	NM_010906	18032	Mm.9394	NM_010906	ENSMUSG00000001911	Nfix	CTF|NF-I/X|NF1-X|NFI-X	nuclear factor I/X	protein-coding
mm_136421.1	chr16	93971123	93971134	-	1	NA	intron (NM_019500, intron 1 of 2)	intron (NM_019500, intron 1 of 2)	37709	NM_019500	56173	Mm.328716	NM_019500	ENSMUSG00000047109	Cldn14	AI851731	claudin 14	protein-coding
mm_162734.1	chr10	52193293	52193294	+	1	NA	intron (NM_011282, intron 1 of 43)	intron (NM_011282, intron 1 of 43)	1951	NM_011282	19886	Mm.236163	NM_011282	ENSMUSG00000019893	Ros1	Ros-1|c-ros	Ros1 proto-oncogene	protein-coding
mm_9366.1	chr1	172199223	172199249	-	1	NA	exon (NM_001329871, exon 3 of 4)	exon (NM_001329871, exon 3 of 4)	7568	NM_001329871	18611	Mm.544	NM_011063	ENSMUSG00000013698	Pea15a	Mat1|PEA-15|Pea15|Pkcs15	phosphoprotein enriched in astrocytes 15A	protein-coding
mm_42920.1	chr5	122720285	122720298	+	1	NA	intron (NM_001310720, intron 5 of 10)	Lx3_Mus|LINE|L1	12747	NM_001310718	18438	Mm.290884	NM_011026	ENSMUSG00000029470	P2rx4	AI504491|AW555605|D5Ertd444e|P2X4	purinergic receptor P2X, ligand-gated ion channel 4	protein-coding
mm_113184.1	chr13	24905657	24905661	+	1	NA	promoter-TSS (NR_045182)	promoter-TSS (NR_045182)	59	NR_045182	73326	Mm.458692	NR_045182		4932702P03Rik	1700047I16Rik	RIKEN cDNA 4932702P03 gene	ncRNA
mm_6819.1	chr1	84192074	84192100	-	1	NA	intron (NM_001003948, intron 1 of 2)	L2|LINE|L2	26874	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_67873.1	chr7	99182656	99182666	-	1	NA	promoter-TSS (NM_026384)	promoter-TSS (NM_026384)	52	NM_026384	67800	Mm.180189	NM_026384	ENSMUSG00000030747	Dgat2	0610010B06Rik|ARAT|DGAT-2	diacylglycerol O-acyltransferase 2	protein-coding
mm_55438.1	chr6	67035295	67035299	-	1	NA	3' UTR (NM_007836, exon 4 of 4)	3' UTR (NM_007836, exon 4 of 4)	-1302	NR_040278	320172	Mm.449039	NR_040278	ENSMUSG00000087231	E230016M11Rik	-	RIKEN cDNA E230016M11 gene	ncRNA
mm_57151.1	chr6	122729909	122729929	-	1	NA	3' UTR (NM_011401, exon 10 of 10)	3' UTR (NM_011401, exon 10 of 10)	12826	NM_011401	20527	Mm.395108	NM_011401	ENSMUSG00000003153	Slc2a3	AA408729|AL023014|AL024341|AU040424|C78366|Glut-3|Glut3	solute carrier family 2 (facilitated glucose transporter), member 3	protein-coding
mm_152673.1	chr19	14679862	14679888	-	1	NA	Intergenic	ORR1C2|LTR|ERVL-MaLR	-81692	NM_001302947	21888	Mm.103638	NM_011600	ENSMUSG00000024642	Tle4	5730411M05Rik|AA792082|Bce-1|Bce1|ESTM13|ESTM14|Grg4|X83332|X83333|grg-4	transducin-like enhancer of split 4	protein-coding
mm_31504.1	chr4	53456897	53456898	+	1	NA	intron (NM_133891, intron 1 of 15)	intron (NM_133891, intron 1 of 15)	16484	NM_133891	100434	Mm.482207	NM_133891	ENSMUSG00000028412	Slc44a1	2210409B22Rik|4833416H08Rik|AW547365|CHTL1|CTL1|Cdw92	solute carrier family 44, member 1	protein-coding
mm_71278.1	chr8	40919733	40919762	+	1	NA	3' UTR (NM_001044740, exon 12 of 12)	3' UTR (NM_001044740, exon 12 of 12)	-6486	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_152428.1	chr19	10676778	10676832	-	1	NA	intron (NM_021453, intron 1 of 8)	intron (NM_021453, intron 1 of 8)	1266	NM_021453	58803	Mm.34037	NM_021453	ENSMUSG00000024738	Pga5	1110035E17Rik|Pepf	pepsinogen 5, group I	protein-coding
mm_92605.1	chr10	80106070	80106121	-	1	NA	intron (NR_038088, intron 1 of 4)	intron (NR_038088, intron 1 of 4)	-3393	NM_183426	216161	Mm.262102	NM_183426	ENSMUSG00000035673	Sbno2	BC019206|F730040C21|Sno|Stno	strawberry notch homolog 2 (Drosophila)	protein-coding
mm_25862.1	chr3	129836775	129836804	+	1	NA	promoter-TSS (NM_007686)	promoter-TSS (NM_007686)	50	NM_007686	12630	Mm.117180	NM_007686	ENSMUSG00000058952	Cfi	-	complement component factor i	protein-coding
mm_163142.1	chr11	80495070	80495081	+	1	NA	intron (NM_177390, intron 21 of 21)	intron (NM_177390, intron 21 of 21)	14031	NR_126552	77417	Mm.437510	NR_126552	ENSMUSG00000085078	C030013C21Rik	-	RIKEN cDNA C030013C21 gene	ncRNA
mm_94607.1	chr11	16257635	16257649	+	1	NA	promoter-TSS (NM_001290539)	promoter-TSS (NM_001290539)	-82	NM_001290539	211739	Mm.284015	NM_145967	ENSMUSG00000048834	Vstm2a	Vstm2	V-set and transmembrane domain containing 2A	protein-coding
mm_162413.1	chr1	87358376	87358379	+	1	NA	intron (NM_146112, intron 3 of 28)	intron (NM_146112, intron 3 of 28)	31379	NM_001110212	227331	Mm.23065	NM_146112	ENSMUSG00000048000	Gigyf2	2610016F01Rik|A830080H02Rik|AI852361|AW259676|BC006835|Tnrc15|mKIAA0642	GRB10 interacting GYF protein 2	protein-coding
mm_41098.1	chr5	87694769	87694794	+	1	NA	exon (NM_001286023, exon 5 of 7)	exon (NM_001286023, exon 5 of 7)	4644	NM_001286020	12991	Mm.268737	NM_009972	ENSMUSG00000063157	Csn2	Csnb	casein beta	protein-coding
mm_105181.1	chr11	101893700	101893780	-	1	NA	exon (NM_010791, exon 1 of 3)	exon (NM_010791, exon 1 of 3)	614	NM_010791	17285	Mm.3404	NM_010791	ENSMUSG00000001493	Meox1	AI385561|D330041M02Rik|Mox-1|Mox1	mesenchyme homeobox 1	protein-coding
mm_129920.1	chr15	84238886	84238887	-	1	NA	intron (NM_133167, intron 1 of 12)	intron (NM_133167, intron 1 of 12)	6843	NM_133167	170736	Mm.323892	NM_133167	ENSMUSG00000022438	Parvb	AI595373|AW742462|D15Gsk1|affixin	parvin, beta	protein-coding
mm_60651.1	chr7	44857367	44857389	+	1	NA	promoter-TSS (NM_001290767)	promoter-TSS (NM_001290767)	-25	NM_001290767	59047	Mm.238254	NM_021549	ENSMUSG00000002963	Pnkp	1810009G08Rik|PNK	polynucleotide kinase 3'- phosphatase	protein-coding
mm_110524.1	chr12	54892575	54892580	-	1	NA	TTS (NM_013815)	TTS (NM_013815)	-29700	NM_007688	12632	Mm.276826	NM_007688	ENSMUSG00000062929	Cfl2	-	cofilin 2, muscle	protein-coding
mm_165011.1	chr19	27217070	27217077	+	1	NA	promoter-TSS (NM_013703)	promoter-TSS (NM_013703)	53	NM_001161420	22359	Mm.4141	NM_013703	ENSMUSG00000024924	Vldlr	AA408956|AI451093|AW047288	very low density lipoprotein receptor	protein-coding
mm_78461.1	chr9	32393964	32393977	+	1	NA	promoter-TSS (NM_001168354)	promoter-TSS (NM_001168354)	-15	NM_001168354	56379	Mm.390168	NM_019659	ENSMUSG00000041248	Kcnj1	Kir1.1|ROMK|Romk2	potassium inwardly-rectifying channel, subfamily J, member 1	protein-coding
mm_115361.1	chr13	112927643	112927735	+	1	NA	promoter-TSS (NM_172594)	promoter-TSS (NM_172594)	-104	NM_172594	218629	Mm.35094	NM_172594	ENSMUSG00000042426	Dhx29	3732415M03|AU043276|Ddxx|E130202M19Rik	DEAH (Asp-Glu-Ala-His) box polypeptide 29	protein-coding
mm_145622.1	chr18	61108893	61108933	+	1	NA	intron (NM_001037859, intron 2 of 21)	intron (NM_001037859, intron 2 of 21)	3341	NM_001037859	12978	Mm.22574	NM_007779	ENSMUSG00000024621	Csf1r	AI323359|CD115|CSF-1R|Csfmr|Fim-2|Fim2|Fms|M-CSF-R|M-CSFR	colony stimulating factor 1 receptor	protein-coding
mm_10885.1	chr2	25262535	25262543	+	1	NA	promoter-TSS (NM_175286)	promoter-TSS (NM_175286)	-59	NM_175286	97031	Mm.308539	NM_175286	ENSMUSG00000048707	Tprn	C430004E15Rik|C87750	taperin	protein-coding
mm_92359.1	chr10	75932469	75932484	-	1	NA	promoter-TSS (NM_008606)	promoter-TSS (NM_008606)	26	NM_001306184	17385	Mm.4561	NM_008606	ENSMUSG00000000901	Mmp11	MMP-11|SL-3|ST3|Stmy3	matrix metallopeptidase 11	protein-coding
mm_173293.1	chrY	3934671	3934676	+	1	NA	Intergenic	RLTR45|LTR|ERVK	163000	NM_011253	19657	Mm.4711	NM_011253	ENSMUSG00000094658	Rbmy	RBM|Rbm1|Rbm1-rs1|Rbmy1a1|Rbmy1a1-rs1|Rbmy1b	RNA binding motif protein, Y chromosome	protein-coding
mm_127221.1	chr15	99393575	99393599	+	1	NA	intron (NM_001171035, intron 1 of 9)	intron (NM_001171035, intron 1 of 9)	368	NM_001171035	110213	Mm.16769	NM_026669	ENSMUSG00000023010	Tmbim6	5031406P05Rik|Bi1|Tegt	transmembrane BAX inhibitor motif containing 6	protein-coding
mm_106079.1	chr11	116174732	116174794	-	1	NA	exon (NM_015729, exon 12 of 14)	exon (NM_015729, exon 12 of 14)	-6585	NM_172571	217335	Mm.35241	NM_172571	ENSMUSG00000020776	Fbf1	1110033G01Rik|5930413D20|mKIAA1863	Fas (TNFRSF6) binding factor 1	protein-coding
mm_169107.1	chr13	44869681	44869684	-	1	NA	intron (NM_001205044, intron 4 of 18)	LSU-rRNA_Hsa|rRNA|rRNA	132414	NM_025772	94245	Mm.352311	NM_025772	ENSMUSG00000057531	Dtnbp1	5430437B18Rik|AW048963|Bloc1s8|dysbindin|sdy	dystrobrevin binding protein 1	protein-coding
mm_7000.1	chr1	86426215	86426232	-	1	NA	promoter-TSS (NM_027966)	promoter-TSS (NM_027966)	-106	NM_027966	71863	Mm.179627	NM_027966	ENSMUSG00000036574	1700019O17Rik	-	RIKEN cDNA 1700019O17 gene	protein-coding
mm_79233.1	chr9	50499145	50499164	+	1	NA	non-coding (NR_040714, exon 2 of 3)	non-coding (NR_040714, exon 2 of 3)	4629	NM_029639	76509	Mm.29959	NM_029639	ENSMUSG00000032068	Plet1	0610037B23Rik|1600029D21Rik|AA407923|AU043048	placenta expressed transcript 1	protein-coding
mm_23359.1	chr3	55182025	55182059	+	1	NA	promoter-TSS (NM_028937)	promoter-TSS (NM_028937)	-2	NM_028937	74434	Mm.25514	NM_028937	ENSMUSG00000027794	Sohlh2	4933406N12Rik|AI413378|Sosf2	spermatogenesis and oogenesis specific basic helix-loop-helix 2	protein-coding
mm_13927.1	chr2	120971649	120971652	+	1	NA	promoter-TSS (NM_009461)	promoter-TSS (NM_009461)	-935	NM_009461	22222	Mm.389330	NM_009461	ENSMUSG00000027272	Ubr1	AI504731	ubiquitin protein ligase E3 component n-recognin 1	protein-coding
mm_109422.1	chr12	110500805	110500808	+	1	NA	intron (NM_012023, intron 1 of 13)	intron (NM_012023, intron 1 of 13)	15067	NM_012023	26931	Mm.240396	NM_012023	ENSMUSG00000017843	Ppp2r5c	2610043M05Rik|2700063L20Rik|AI060890|AW545884|C85228|D12Bwg0916e|mKIAA0044	protein phosphatase 2, regulatory subunit B', gamma	protein-coding
mm_135222.1	chr16	36784700	36784728	-	1	NA	exon (NM_021301, exon 1 of 22)	exon (NM_021301, exon 1 of 22)	248	NM_001145899	57738	Mm.281804	NM_021301	ENSMUSG00000022899	Slc15a2	8430408C16Rik|C78862|Pept2	solute carrier family 15 (H+/peptide transporter), member 2	protein-coding
mm_119334.1	chr14	39980524	39980526	+	1	NA	Intergenic	Intergenic	324862	NR_045936	73591	Mm.65499	NR_045936	ENSMUSG00000101261	1700109I08Rik	-	RIKEN cDNA 1700109I08 gene	ncRNA
mm_2854.1	chr1	131674946	131674960	+	1	NA	3' UTR (NM_007799, exon 10 of 10)	3' UTR (NM_007799, exon 10 of 10)	-13742	NM_145509	226421	Mm.44508	NM_145509	ENSMUSG00000052688	Rab7b	5430435G22Rik	RAB7B, member RAS oncogene family	protein-coding
mm_6298.1	chr1	71101970	71101973	-	1	NA	intron (NM_007525, intron 1 of 10)	intron (NM_007525, intron 1 of 10)	1001	NM_007525	12021	Mm.10764	NM_007525	ENSMUSG00000026196	Bard1	ENSMUSG00000060893|ENSMUSG00000073653	BRCA1 associated RING domain 1	protein-coding
mm_45538.1	chr5	72774944	72774954	-	1	NA	intron (NM_001113461, intron 8 of 17)	RMER15|LTR|ERVL	-22172	NM_001122754	22165	Mm.3264	NM_013698	ENSMUSG00000054892	Txk	A130089B16Rik|Btkl|PTK-RL-18|PTK4|Rlk	TXK tyrosine kinase	protein-coding
mm_110001.1	chr12	15816596	15816607	-	1	NA	5' UTR (NM_144551, exon 1 of 3)	5' UTR (NM_144551, exon 1 of 3)	184	NM_144551	217410	Mm.491136	NM_144551	ENSMUSG00000020601	Trib2	AW319517|TRB-2|TRB2	tribbles pseudokinase 2	protein-coding
mm_6797.1	chr1	84150477	84150488	-	1	NA	intron (NM_001003948, intron 2 of 2)	intron (NM_001003948, intron 2 of 2)	68479	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_20314.1	chr2	127300842	127300847	-	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	30615	NM_139308	99138	Mm.41271	NM_139308	ENSMUSG00000027367	Stard7	AI852671|AL022671|AW544915	START domain containing 7	protein-coding
mm_36784.1	chr4	103012002	103012011	-	1	NA	promoter-TSS (NR_028391)	promoter-TSS (NR_028391)	-41	NR_028391	100473	Mm.393171	NR_028391	ENSMUSG00000085041	BB031773	-	expressed sequence BB031773	ncRNA
mm_109322.1	chr12	109561964	109561978	+	1	NA	non-coding (NR_003633, exon 5 of 5)	non-coding (NR_003633, exon 5 of 5)	-1721	NR_030427	791079		NR_030427	ENSMUSG00000076451	Mir770	Mirn770|mir-770|mmu-mir-770	microRNA 770	ncRNA
mm_567.1	chr1	38035758	38035771	+	1	NA	intron (NM_198303, intron 9 of 23)	intron (NM_198303, intron 9 of 23)	37754	NM_198303	226982	Mm.260943	NM_198303	ENSMUSG00000026083	Eif5b	A030003E17Rik|BC018347|IF2	eukaryotic translation initiation factor 5B	protein-coding
mm_114316.1	chr13	60029674	60029693	+	1	NA	promoter-TSS (NR_046142)	promoter-TSS (NR_046142)	-28	NR_046142	328263	Mm.123405	NR_046142		A530065N20Rik	A530065N20	RIKEN cDNA A530046M15 gene	ncRNA
mm_169590.1	chr15	29015563	29015572	-	1	NA	Intergenic	(A)n|Simple_repeat|Simple_repeat	811801	NM_133365	110082	Mm.248464	NM_133365	ENSMUSG00000022262	Dnah5	AU022615|Dnahc5|Mdnah5|b2b1134Clo|b2b1154Clo|b2b1537Clo|b2b1565Clo|b2b601Clo|mKIAA1603	dynein, axonemal, heavy chain 5	protein-coding
mm_165160.1	chr2	25047972	25047982	+	1	NA	intron (NM_146251, intron 26 of 34)	intron (NM_146251, intron 26 of 34)	-6402	NM_001177654	56876	Mm.42956	NM_020276	ENSMUSG00000006476	Nsmf	Jacob|Nelf	NMDA receptor synaptonuclear signaling and neuronal migration factor	protein-coding
mm_95539.1	chr11	52275612	52275662	+	1	NA	intron (NM_001313981, intron 3 of 10)	intron (NM_001313981, intron 3 of 10)	6958	NM_009331	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_52963.1	chr6	123124431	123124441	+	1	NA	intron (NM_011999, intron 1 of 5)	B1F2|SINE|Alu	1120	NM_001170333	26888	Mm.47384	NM_011999	ENSMUSG00000030148	Clec4a2	Clec4a|Clecsf6|DCIR|Dcir1	C-type lectin domain family 4, member a2	protein-coding
mm_127627.1	chr15	102462430	102462443	+	1	NA	3' UTR (NM_025385, exon 5 of 5)	3' UTR (NM_025385, exon 5 of 5)	3266	NM_025385	66151	Mm.393955	NM_025385	ENSMUSG00000023048	Prr13	1110020C13Rik|2010324E22Rik	proline rich 13	protein-coding
mm_58647.1	chr7	6260294	6260352	+	1	NA	intron (NM_001177417, intron 2 of 10)	intron (NM_001177417, intron 2 of 10)	4401	NM_001177417	627821	Mm.99441	NM_001177416	ENSMUSG00000053367	Gm6792	EG627821	predicted gene 6792	protein-coding
mm_94504.1	chr11	7197853	7197854	+	1	NA	promoter-TSS (NM_008341)	promoter-TSS (NM_008341)	66	NM_008341	16006	Mm.21300	NM_008341	ENSMUSG00000020429	Igfbp1	-	insulin-like growth factor binding protein 1	protein-coding
mm_158781.1	chrX	167207243	167207255	-	1	NA	3' UTR (NM_021278, exon 3 of 3)	3' UTR (NM_021278, exon 3 of 3)	1969	NM_021278	19241	Mm.142729	NM_021278	ENSMUSG00000049775	Tmsb4x	Ptmb4|Tb4	thymosin, beta 4, X chromosome	protein-coding
mm_107478.1	chr12	37880774	37880800	+	1	NA	promoter-TSS (NM_178681)	promoter-TSS (NM_178681)	82	NM_178681	217480	Mm.126525	NM_178681	ENSMUSG00000036095	Dgkb	6430574F24|90kda|C630029D13Rik|DAGK2|DGK|DGK-beta|mKIAA0718	diacylglycerol kinase, beta	protein-coding
mm_56629.1	chr6	112930679	112930682	-	1	NA	intron (NM_080448, intron 1 of 21)	intron (NM_080448, intron 1 of 21)	16586	NM_080448	259302	Mm.236401	NM_080448	ENSMUSG00000030257	Srgap3	AI452337|Arhgap14|D130026O08Rik|Gbi|MEGAP|WRP|mKIAA0411	SLIT-ROBO Rho GTPase activating protein 3	protein-coding
mm_133639.1	chr16	91729317	91729390	+	1	NA	promoter-TSS (NM_001110276)	promoter-TSS (NM_001110276)	-18	NM_001110275	16443	Mm.40546	NM_010587	ENSMUSG00000022957	Itsn1	AA517634|AA545208|AI316805|AI839402|AI848451|Ehsh1|Ese1|Itsn|Sh3p17	intersectin 1 (SH3 domain protein 1A)	protein-coding
mm_136318.1	chr16	91931555	91931618	-	1	NA	promoter-TSS (NM_138597)	promoter-TSS (NM_138597)	44	NM_138597	28080	Mm.41	NM_138597	ENSMUSG00000022956	Atp5o	ATPO|D12Wsu28e|OSCP	ATP synthase, H+ transporting, mitochondrial F1 complex, O subunit	protein-coding
mm_34979.1	chr4	156013899	156013909	+	1	NA	TTS (NM_011341)	TTS (NM_011341)	209	NM_011659	22163	Mm.13885	NM_011659	ENSMUSG00000029075	Tnfrsf4	ACT35|CD134|Ly-70|Ox40|TXGP1L|Txgp1	tumor necrosis factor receptor superfamily, member 4	protein-coding
mm_167451.1	chr8	122775484	122775494	+	1	NA	promoter-TSS (NM_144932)	promoter-TSS (NM_144932)	3	NM_144932	257633	Mm.334875	NM_144932	ENSMUSG00000015016	Acsf3	BB101783	acyl-CoA synthetase family member 3	protein-coding
mm_54136.1	chr6	21852510	21852520	-	1	NA	promoter-TSS (NM_173007)	promoter-TSS (NM_173007)	0	NM_173007	269831	Mm.21950	NM_173007	ENSMUSG00000029669	Tspan12	9030619E17|AI426782|AI663988|AW111457|Tm4sf12	tetraspanin 12	protein-coding
mm_155626.1	chrX	83855383	83855399	+	1	NA	intron (NM_007868, intron 29 of 78)	intron (NM_007868, intron 29 of 78)	-367467	NM_021898	100502723	Mm.383210	NM_021898	ENSMUSG00000035522	Tsga8	Halap-X|Halapx	testis specific gene A8	protein-coding
mm_133702.1	chr16	92995775	92995779	+	1	NA	Intergenic	Intergenic	-169703	NM_001111022	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_111170.1	chr12	83621174	83621179	-	1	NA	Intergenic	Intergenic	-11058	NM_027349	67039	Mm.46005	NM_027349	ENSMUSG00000010608	Rbm25	2600011C06Rik|2610015J01Rik|A130095G20Rik|AI159652|AL023075|AU043498|RNPC7	RNA binding motif protein 25	protein-coding
mm_1240.1	chr1	62796219	62796229	+	1	NA	3' UTR (NM_001077407, exon 16 of 16)	3' UTR (NM_001077407, exon 16 of 16)	-1492	NR_040601	74992	Mm.401979	NR_040601		4930487H11Rik	-	RIKEN cDNA 4930487H11 gene	ncRNA
mm_28265.1	chr3	88744987	88744999	-	1	NA	3' UTR (NM_018804, exon 4 of 4)	3' UTR (NM_018804, exon 4 of 4)	27606	NM_018804	229521	Mm.379376	NM_018804	ENSMUSG00000068923	Syt11	1500004A13Rik|3632445O20Rik|5430404N14Rik|6530420C11Rik|AI851970	synaptotagmin XI	protein-coding
mm_154663.1	chrX	7874362	7874447	+	1	NA	3' UTR (NM_001290536, exon 9 of 9)	3' UTR (NM_001290536, exon 9 of 9)	-3902	NM_138606	18715	Mm.347478	NM_138606	ENSMUSG00000031155	Pim2	DXCch3|Pim-2	proviral integration site 2	protein-coding
mm_172517.1	chr7	80098526	80098535	-	1	NA	intron (NM_173011, intron 5 of 10)	intron (NM_173011, intron 5 of 10)	16820	NM_173011	269951	Mm.246432	NM_173011	ENSMUSG00000030541	Idh2	E430004F23|IDPm|Idh-2	isocitrate dehydrogenase 2 (NADP+), mitochondrial	protein-coding
mm_70297.1	chr8	3995022	3995024	+	1	NA	Intergenic	Intergenic	-48160	NM_130903	170776	Mm.215729	NM_130903	ENSMUSG00000040165	Cd209c	SIGNR2|mSIGNR2	CD209c antigen	protein-coding
mm_106571.1	chr11	120660566	120660587	-	1	NA	intron (NM_175263, intron 1 of 11)	CpG-2953	261	NM_175263	77583	Mm.32839	NM_175263	ENSMUSG00000042988	Notum	5730593N15Rik	notum pectinacetylesterase homolog (Drosophila)	protein-coding
mm_99390.1	chr11	102097563	102097569	+	1	NA	Intergenic	Intergenic	3734	NM_008918	19064	Mm.1269	NM_008918	ENSMUSG00000017316	Ppy	AV061413|IGSPP|PP	pancreatic polypeptide	protein-coding
mm_93609.1	chr10	117238541	117238559	-	1	NA	exon (NM_029906, exon 1 of 4)	exon (NM_029906, exon 1 of 4)	131	NM_029906	77397	Mm.118350	NM_029906	ENSMUSG00000020177	9530003J23Rik	Lyzf1	RIKEN cDNA 9530003J23 gene	protein-coding
mm_77155.1	chr8	111686626	111686679	-	1	NA	exon (NM_025583, exon 7 of 7)	exon (NM_025583, exon 7 of 7)	3022	NR_106044	102466993		NR_106044	ENSMUSG00000099129	Mir7076	Gm27318|mmu-mir-7076	microRNA 7076	ncRNA
mm_10803.1	chr2	24349736	24349756	+	1	NA	3' UTR (NM_031167, exon 5 of 5)	3' UTR (NM_031167, exon 5 of 5)	4375	NM_001039701	16181	Mm.882	NM_031167	ENSMUSG00000026981	Il1rn	F630041P17Rik|IL-1ra	interleukin 1 receptor antagonist	protein-coding
mm_2106.1	chr1	87814797	87814808	+	1	NA	exon (NM_009118, exon 5 of 16)	exon (NM_009118, exon 5 of 16)	11122	NM_009118	20215	Mm.1276	NM_009118	ENSMUSG00000056055	Sag	A930001K18Rik|Arr1|Irbp|arrestin	S-antigen, retina and pineal gland (arrestin)	protein-coding
mm_65243.1	chr7	19822699	19822776	-	1	NA	promoter-TSS (NM_033601)	promoter-TSS (NM_033601)	18	NM_033601	12051	Mm.439658	NM_033601	ENSMUSG00000053175	Bcl3	AI528691|Bcl-3	B cell leukemia/lymphoma 3	protein-coding
mm_109449.1	chr12	111029103	111029105	+	1	NA	Intergenic	ID_B1|SINE|B4	-10694	NM_198023	217864	Mm.23808	NM_198023	ENSMUSG00000037896	Rcor1	5730409O11|6720480E22Rik|AU042633|D12Wsu95e|Rocr1|mKIAA0071	REST corepressor 1	protein-coding
mm_23119.1	chr3	37643267	37643280	+	1	NA	exon (NM_011896, exon 3 of 3)	exon (NM_011896, exon 3 of 3)	3326	NM_001305442	24063	Mm.330986	NM_011896	ENSMUSG00000037211	Spry1	sprouty1|spry-1	sprouty homolog 1 (Drosophila)	protein-coding
mm_6579.1	chr1	75218484	75218494	-	1	NA	intron (NM_009447, intron 1 of 3)	intron (NM_009447, intron 1 of 3)	805	NM_001313723	22145	Mm.1155	NM_009447	ENSMUSG00000026202	Tuba4a	M[a]4|Tuba4	tubulin, alpha 4A	protein-coding
mm_167814.1	chr9	124257614	124257622	-	1	NA	Intergenic	Intergenic	55076	NM_001243118	630836	Mm.458553	NM_001243117	ENSMUSG00000074829	2010315B03Rik	BC029716	RIKEN cDNA 2010315B03 gene	protein-coding
mm_132273.1	chr16	32914095	32914138	+	1	NA	promoter-TSS (NM_001310673)	promoter-TSS (NM_001310673)	16	NM_001310672	70144	Mm.491178	NM_001081255	ENSMUSG00000022801	Lrch3	2210409B11Rik|AW215594|Gm1742	leucine-rich repeats and calponin homology (CH) domain containing 3	protein-coding
mm_42659.1	chr5	119670401	119670407	+	1	NA	promoter-TSS (NM_011535)	promoter-TSS (NM_011535)	-458	NM_198052	21386	Mm.219139	NM_011535	ENSMUSG00000018604	Tbx3	D5Ertd189e	T-box 3	protein-coding
mm_131244.1	chr16	10526362	10526373	+	1	NA	3' UTR (NM_001243761, exon 19 of 19)	3' UTR (NM_001243761, exon 19 of 19)	16687	NM_021428	58239	Mm.353006	NM_021428	ENSMUSG00000038055	Dexi	1810029J14Rik|AI836170|AW413143|D16Bwg0586e|Myle	dexamethasone-induced transcript	protein-coding
mm_358.1	chr1	33719981	33719992	+	1	NA	promoter-TSS (NM_008999)	promoter-TSS (NM_008999)	90	NM_008999	19335	Mm.86744	NM_008999	ENSMUSG00000004768	Rab23	AW545388|opb|opb2	RAB23, member RAS oncogene family	protein-coding
mm_128620.1	chr15	58942804	58942812	-	1	NA	3' UTR (NM_144800, exon 15 of 15)	3' UTR (NM_144800, exon 15 of 15)	8998	NM_023172	66218	Mm.322294	NM_023172	ENSMUSG00000022354	Ndufb9	1190008J14Rik	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 9	protein-coding
mm_120319.1	chr14	63142853	63142877	+	1	NA	3' UTR (NM_007798, exon 10 of 10)	3' UTR (NM_007798, exon 10 of 10)	20403	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_21741.1	chr2	164778207	164778228	-	1	NA	exon (NM_009394, exon 2 of 6)	exon (NM_009394, exon 2 of 6)	1517	NM_009394	21925	Mm.1716	NM_009394	ENSMUSG00000017300	Tnnc2	Tncs	troponin C2, fast	protein-coding
mm_32746.1	chr4	116668487	116668505	+	1	NA	Intergenic	Intergenic	-16822	NM_021473	58810	Mm.30085	NM_021473	ENSMUSG00000028692	Akr1a1	2610201A18Rik|Akr1a4	aldo-keto reductase family 1, member A1 (aldehyde reductase)	protein-coding
mm_22282.1	chr2	180042402	180042438	-	1	NA	promoter-TSS (NM_178750)	promoter-TSS (NM_178750)	44	NM_001289476	26444	Mm.21728	NM_011969	ENSMUSG00000027566	Psma7	C6-I	proteasome (prosome, macropain) subunit, alpha type 7	protein-coding
mm_154109.1	chr19	57118982	57119026	-	1	NA	promoter-TSS (NM_001103178)	promoter-TSS (NM_001103178)	20	NM_001347459	226251	Mm.217161	NM_178688	ENSMUSG00000025085	Ablim1	2210411C18Rik|2610209L21Rik|4833406P10Rik|9330196J19Rik|AV079770|AW060987|AW215784|Limab1|mKIAA0059	actin-binding LIM protein 1	protein-coding
mm_6213.1	chr1	66838454	66838463	-	1	NA	intron (NM_007381, intron 8 of 10)	intron (NM_007381, intron 8 of 10)	-20863	NM_001122738	68691	Mm.240912	NM_177645	ENSMUSG00000026004	Kansl1l	1110028C15Rik|1190030G24|AI427598|C430010P07Rik|mKIAA4189	KAT8 regulatory NSL complex subunit 1-like	protein-coding
mm_165497.1	chr2	166509719	166509721	+	1	NA	Intergenic	Intergenic	62269	NR_015558	319684	Mm.399746	NR_015558		5031425F14Rik	-	RIKEN cDNA 5031425F14 gene	ncRNA
mm_129193.1	chr15	76374927	76374942	-	1	NA	promoter-TSS (NM_183099)	promoter-TSS (NM_183099)	4	NM_183099	73542	Mm.159026	NM_183099	ENSMUSG00000060794	Tssk5	1700091F14Rik	testis-specific serine kinase 5	protein-coding
mm_98987.1	chr11	98753022	98753035	+	1	NA	intron (NM_178060, intron 1 of 8)	intron (NM_178060, intron 1 of 8)	11243	NM_001313983	21833	Mm.265917	NM_178060	ENSMUSG00000058756	Thra	6430529J03Rik|AW259572|Erba|Nr1a1|Rvr|T3R[a]|T3Ralpha|Thra1|Thra2|c-erbA-1|c-erbA-alpha|c-erbAalpha	thyroid hormone receptor alpha	protein-coding
mm_109341.1	chr12	109595388	109595391	+	1	NA	promoter-TSS (NR_037232)	promoter-TSS (NR_037232)	8	NR_037232	100526473		NR_037232	ENSMUSG00000070129	Mir3071	mir-3071|mmu-mir-3071	microRNA 3071	ncRNA
mm_46086.1	chr5	92346935	92346939	-	1	NA	3' UTR (NM_021274, exon 4 of 4)	3' UTR (NM_021274, exon 4 of 4)	1952	NM_021274	15945	Mm.877	NM_021274	ENSMUSG00000034855	Cxcl10	C7|CRG-2|INP10|IP-10|IP10|Ifi10|Scyb10|gIP-10|mob-1	chemokine (C-X-C motif) ligand 10	protein-coding
mm_83090.1	chr9	40320955	40320979	-	1	NA	intron (NM_172768, intron 4 of 19)	intron (NM_172768, intron 4 of 19)	-12505	NR_040728	73558	Mm.398307	NR_040728		1700110K17Rik	-	RIKEN cDNA 1700110K17 gene	ncRNA
mm_39225.1	chr4	156200792	156200805	-	1	NA	promoter-TSS (NM_015783)	promoter-TSS (NM_015783)	20	NM_015783	100038882	Mm.4950	NM_015783	ENSMUSG00000035692	Isg15	G1p2|IGI15|IP17|Irfp|UCRP	ISG15 ubiquitin-like modifier	protein-coding
mm_155737.1	chrX	96166485	96166495	+	1	NA	exon (NM_010833, exon 13 of 13)	exon (NM_010833, exon 13 of 13)	70445	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_52461.1	chr6	113697191	113697232	+	1	NA	5' UTR (NM_001347356, exon 1 of 8)	5' UTR (NM_001347356, exon 1 of 8)	161	NM_001033463	381801	Mm.333322	NM_001033463	ENSMUSG00000056952	Tatdn2	AI646012|mKIAA0218	TatD DNase domain containing 2	protein-coding
mm_153490.1	chr19	41323933	41323948	-	1	NA	intron (NM_031376, intron 7 of 16)	intron (NM_031376, intron 7 of 16)	-59936	NM_133352	107358	Mm.246440	NM_133352	ENSMUSG00000025016	Tm9sf3	1810073M23Rik|2810031D16Rik|AI115521|AI413748|AW146116|AW549777|Smbp|mKIAA4036	transmembrane 9 superfamily member 3	protein-coding
mm_117177.1	chr13	63323519	63323525	-	1	NA	intron (NM_001347514, intron 11 of 15)	intron (NM_001347514, intron 11 of 15)	-22239	NR_037235	100526474		NR_037235	ENSMUSG00000092741	Mir3074-1	mmu-mir-3074-1	microRNA 3074-1	ncRNA
mm_110656.1	chr12	59061426	59061477	-	1	NA	promoter-TSS (NM_001306218)	promoter-TSS (NM_001306218)	21	NM_001306218	78232	Mm.290070	NM_030057	ENSMUSG00000020993	Trappc6b	5830498C14Rik|C79212	trafficking protein particle complex 6B	protein-coding
mm_20271.1	chr2	126783417	126783452	-	1	NA	promoter-TSS (NM_029163)	promoter-TSS (NM_029163)	26	NM_029163	75083	Mm.389373	NM_029163	ENSMUSG00000027364	Usp50	1700086G18Rik|4930511O11Rik	ubiquitin specific peptidase 50	protein-coding
mm_45765.1	chr5	86917031	86917035	-	1	NA	3' UTR (NM_152811, exon 6 of 6)	3' UTR (NM_152811, exon 6 of 6)	9470	NM_152811	71773	Mm.26741	NM_152811	ENSMUSG00000035836	Ugt2b1	1300012D20Rik	UDP glucuronosyltransferase 2 family, polypeptide B1	protein-coding
mm_130661.1	chr15	100644941	100644957	-	1	NA	exon (NM_001270537, exon 10 of 11)	exon (NM_001270537, exon 10 of 11)	4280	NR_105926	102465580		NR_105926	ENSMUSG00000098527	Mir6961	Gm27367|mmu-mir-6961	microRNA 6961	ncRNA
mm_146298.1	chr18	80186234	80186245	+	1	NA	promoter-TSS (NR_131039)	promoter-TSS (NR_131039)	0	NR_131039	105246506	Mm.392326	NR_131039		LOC105246506	-	uncharacterized LOC105246506	ncRNA
mm_105683.1	chr11	107716518	107716528	-	1	NA	promoter-TSS (NM_007582)	promoter-TSS (NM_007582)	-47	NM_007582	12299	Mm.57093	NM_007582	ENSMUSG00000020722	Cacng1	-	calcium channel, voltage-dependent, gamma subunit 1	protein-coding
mm_17795.1	chr2	33130566	33130620	-	1	NA	Intergenic	CpG	-43389	NM_178888	99326	Mm.41290	NM_178888	ENSMUSG00000038860	Garnl3	AW120551	GTPase activating RANGAP domain-like 3	protein-coding
mm_27189.1	chr3	34699451	34699456	-	1	NA	TTS (NR_038347)	TTS (NR_038347)	17209	NR_038347	100041108	Mm.24764	NR_038347	ENSMUSG00000105153	Gm3143	-	predicted gene 3143	ncRNA
mm_138718.1	chr17	36869514	36869529	+	1	NA	promoter-TSS (NM_011280)	promoter-TSS (NM_011280)	-53	NM_011280	19824	Mm.299155	NM_011280	ENSMUSG00000073400	Trim10	AI324236|BB139825|Herf1|Rnf9	tripartite motif-containing 10	protein-coding
mm_144284.1	chr18	11924956	11924959	+	1	NA	exon (NM_001146287, exon 6 of 10)	exon (NM_001146287, exon 6 of 10)	-84519	NR_035447	100316686		NR_035447	ENSMUSG00000084565	Mir1901	Mirn1901|mmu-mir-1901	microRNA 1901	ncRNA
mm_127581.1	chr15	102326156	102326171	+	1	NA	promoter-TSS (NM_027044)	promoter-TSS (NM_027044)	47	NM_027044	56612	Mm.158264	NM_020031	ENSMUSG00000001289	Pfdn5	1190001O17Rik|1700010A06Rik|D15Ertd697e|Eig1|MM-1	prefoldin 5	protein-coding
mm_135436.1	chr16	45383117	45383126	-	1	NA	3' UTR (NM_010818, exon 6 of 6)	3' UTR (NM_010818, exon 6 of 6)	25932	NM_010818	17470	Mm.245851	NM_010818	ENSMUSG00000022661	Cd200	Mox2|OX2	CD200 antigen	protein-coding
mm_17964.1	chr2	37430836	37430898	-	1	NA	promoter-TSS (NM_146253)	promoter-TSS (NM_146253)	52	NM_146253	241322	Mm.330182	NM_146253	ENSMUSG00000066798	Zbtb6	A830092L04Rik|ZID|Zfp482	zinc finger and BTB domain containing 6	protein-coding
mm_28275.1	chr3	88913886	88913948	-	1	NA	promoter-TSS (NM_144898)	promoter-TSS (NM_144898)	33	NM_144898	229524	Mm.440405	NM_144898	ENSMUSG00000068922	Msto1	BC008103|mst	misato 1, mitochondrial distribution and morphology regulator	protein-coding
mm_172281.1	chr6	90845488	90845492	-	1	NA	Intergenic	MTEb|LTR|ERVL-MaLR	-35367	NM_001134384	232227	Mm.196943	NM_182784	ENSMUSG00000034312	Iqsec1	AW561907|BC026481|BRAG2|D6Ertd349e|cI-43	IQ motif and Sec7 domain 1	protein-coding
mm_97551.1	chr11	78929747	78929770	+	1	NA	exon (NM_010927, exon 4 of 27)	exon (NM_010927, exon 4 of 27)	4467	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_27000.1	chr3	25838449	25838463	-	1	NA	intron (NM_001163387, intron 3 of 5)	B3|SINE|B2	314851	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_171725.1	chr4	88376384	88376384	+	1	NA	intron (NM_001081184, intron 35 of 43)	L1Md_T|LINE|L1	62542	NM_025760	66775	Mm.386788	NM_025760	ENSMUSG00000028497	Hacd4	4933428I03Rik|Hcad4|Ptplad2	3-hydroxyacyl-CoA dehydratase 4	protein-coding
mm_50501.1	chr6	49036069	49036082	+	1	NA	promoter-TSS (NM_053110)	promoter-TSS (NM_053110)	-443	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_127642.1	chr15	102483180	102483203	+	1	NA	exon (NM_001174073, exon 7 of 13)	exon (NM_001174073, exon 7 of 13)	12559	NM_001174073	18521	Mm.236513	NM_011042	ENSMUSG00000056851	Pcbp2	AW412548|Hnrpx|alphaCP-2	poly(rC) binding protein 2	protein-coding
mm_106364.1	chr11	118393979	118393981	-	1	NA	exon (NM_011150, exon 6 of 6)	exon (NM_011150, exon 6 of 6)	7951	NM_011150	19039	Mm.3152	NM_011150	ENSMUSG00000033880	Lgals3bp	90K|CyCAP|MAC-2BP|Ppicap|Tango10b	lectin, galactoside-binding, soluble, 3 binding protein	protein-coding
mm_146434.1	chr18	84879591	84879606	+	1	NA	3' UTR (NM_025797, exon 5 of 5)	3' UTR (NM_025797, exon 5 of 5)	28184	NM_025797	109672	Mm.31018	NM_025797	ENSMUSG00000024646	Cyb5a	0610009N12Rik|Cyb5	cytochrome b5 type A (microsomal)	protein-coding
mm_78816.1	chr9	44084915	44084933	+	1	NA	promoter-TSS (NM_198091)	promoter-TSS (NM_198091)	4	NM_198091	53376	Mm.272770	NM_016808	ENSMUSG00000032010	Usp2	B930035K21Rik|Ubp41	ubiquitin specific peptidase 2	protein-coding
mm_50649.1	chr6	51469429	51469462	+	1	NA	intron (NR_104468, intron 1 of 10)	CpG	449	NM_182650	53379	Mm.155896	NM_016806	ENSMUSG00000004980	Hnrnpa2b1	9130414A06Rik|Hnrpa2|Hnrpa2b1|hnrnp-A	heterogeneous nuclear ribonucleoprotein A2/B1	protein-coding
mm_150168.1	chr19	32485884	32485984	+	1	NA	5' UTR (NM_010799, exon 1 of 5)	5' UTR (NM_010799, exon 1 of 5)	165	NM_010799	17330	Mm.255116	NM_010799	ENSMUSG00000024896	Minpp1	AA408516	multiple inositol polyphosphate histidine phosphatase 1	protein-coding
mm_91186.1	chr10	21125255	21125264	-	1	NA	3' UTR (NM_001198914, exon 16 of 16)	3' UTR (NM_001198914, exon 16 of 16)	35725	NM_001198914	17863	Mm.52109	NM_010848	ENSMUSG00000019982	Myb	AI550390|M16449|c-myb	myeloblastosis oncogene	protein-coding
mm_30483.1	chr3	155025444	155025453	-	1	NA	intron (NM_177066, intron 5 of 24)	RMER5|LTR|ERV1	29959	NM_177066	435766	Mm.210428	NM_177066	ENSMUSG00000040086	Tnni3k	Cark|D830019J24Rik	TNNI3 interacting kinase	protein-coding
mm_159914.1	chr6	48605536	48605536	+	1	NA	Intergenic	ORR1A1|LTR|ERVL-MaLR	-7644	NM_173429	243372	Mm.435190	NM_173429	ENSMUSG00000007216	Zfp775	C130032F08Rik|Znf775	zinc finger protein 775	protein-coding
mm_143686.1	chr17	80062577	80062585	-	1	NA	promoter-TSS (NM_144802)	promoter-TSS (NM_144802)	-313	NM_144802	72692	Mm.64579	NM_144802	ENSMUSG00000024095	Hnrnpll	2510028H02Rik|2810036L13Rik|AI256697|AI852082|Hnrpll	heterogeneous nuclear ribonucleoprotein L-like	protein-coding
mm_141881.1	chr17	34860014	34860062	-	1	NA	exon (NM_008198, exon 7 of 18)	exon (NM_008198, exon 7 of 18)	-2406	NR_105938	102465587		NR_105938	ENSMUSG00000098445	Mir6972	Gm27810|mmu-mir-6972	microRNA 6972	ncRNA
mm_18555.1	chr2	65189181	65189184	-	1	NA	intron (NM_027225, intron 1 of 12)	intron (NM_027225, intron 1 of 12)	49444	NM_177025	319876	Mm.34159	NM_027225	ENSMUSG00000034903	Cobll1	1810047P18Rik|Coblr1|D430044D16Rik	Cobl-like 1	protein-coding
mm_37916.1	chr4	132783949	132783965	-	1	NA	intron (NM_001033308, intron 4 of 5)	intron (NM_001033308, intron 4 of 5)	12407	NM_001033308	230787	Mm.290912	NM_001033308	ENSMUSG00000037731	Themis2	ICB-1	thymocyte selection associated family member 2	protein-coding
mm_45452.1	chr5	67697752	67697799	-	1	NA	intron (NM_001284345, intron 24 of 36)	intron (NM_001284345, intron 24 of 36)	89892	NM_001033415	330096	Mm.442747	NM_001033415	ENSMUSG00000050010	Shisa3	D830007B15Rik	shisa family member 3	protein-coding
mm_48301.1	chr5	138271505	138271519	-	1	NA	5' UTR (NM_001033416, exon 1 of 3)	5' UTR (NM_001033416, exon 1 of 3)	1242	NM_001033416	330217	Mm.332774	NM_001033416	ENSMUSG00000075593	Gal3st4	1500031A01Rik	galactose-3-O-sulfotransferase 4	protein-coding
mm_72201.1	chr8	72572028	72572059	+	1	NA	promoter-TSS (NM_172396)	promoter-TSS (NM_172396)	-60	NM_144534	74166	Mm.212927	NM_144534	ENSMUSG00000031791	Tmem38a	1110001E17Rik|AI413399|TRIC-A|mg33a	transmembrane protein 38A	protein-coding
mm_143084.1	chr17	57078411	57078417	-	1	NA	promoter-TSS (NM_153551)	promoter-TSS (NM_153551)	96	NM_153551	70785	Mm.284447	NM_153551	ENSMUSG00000002668	Dennd1c	4432409M07Rik	DENN/MADD domain containing 1C	protein-coding
mm_34270.1	chr4	141424057	141424070	+	1	NA	3' UTR (NM_013868, exon 3 of 3)	3' UTR (NM_013868, exon 3 of 3)	3284	NM_013868	29818	Mm.46181	NM_013868	ENSMUSG00000006221	Hspb7	27kDa|Hsp25-2|cvHsp	heat shock protein family, member 7 (cardiovascular)	protein-coding
mm_8388.1	chr1	151345063	151345089	-	1	NA	intron (NM_001039511, intron 1 of 7)	CpG	578	NM_001039511	117198	Mm.33764	NM_028582	ENSMUSG00000023150	Ivns1abp	1190004M08Rik|1700126I16Rik|AA960440|HSPC068|ND1|NS-1|NS1-BP|Nd1-L|Nd1-S|mKIAA0850	influenza virus NS1A binding protein	protein-coding
mm_102960.1	chr11	69665298	69665320	-	1	NA	non-coding (NR_110993, exon 2 of 5)	non-coding (NR_110993, exon 2 of 5)	861	NM_001291058	12514	Mm.15819	NM_009853	ENSMUSG00000018774	Cd68	Lamp4|Scard1|gp110	CD68 antigen	protein-coding
mm_149205.1	chr19	9980640	9980650	+	1	NA	promoter-TSS (NR_073181)	promoter-TSS (NR_073181)	45	NR_073181	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
mm_57730.1	chr6	128954159	128954164	-	1	NA	intron (NR_045009, intron 1 of 1)	RLTR9B|LTR|ERVK	-16999	NM_001168224	70809	Mm.439891	NM_027562	ENSMUSG00000000248	Clec2g	4632413B12Rik|Clr-c|Clr-d|Clrc|Clrd|Clrx|Ddv10|Ocilrp1	C-type lectin domain family 2, member g	protein-coding
mm_103804.1	chr11	82960674	82960683	-	1	NA	promoter-TSS (NR_045932)	promoter-TSS (NR_045932)	3	NR_045932	76392	Mm.295205	NR_045932	ENSMUSG00000086327	Slfn5os	1700003F17Rik	schlafen 5, opposite strand	ncRNA
mm_161165.1	chr13	33324066	33324066	+	1	NA	promoter-TSS (NM_183197)	promoter-TSS (NM_183197)	-11	NM_183197	20709	Mm.474264	NM_183197	ENSMUSG00000038327	Serpinb9f	BC052216|NK21|NK21L1|Spi13|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 9f	protein-coding
mm_47822.1	chr5	134236891	134236926	-	1	NA	TTS (NM_010365)	TTS (NM_010365)	-7283	NR_104383	17969	Mm.425296	NM_010876	ENSMUSG00000015950	Ncf1	NCF-47K|NOXO2|Ncf-1|p47-phox|p47<phox>|p47phox	neutrophil cytosolic factor 1	protein-coding
mm_159184.1	chr2	111984307	111984307	-	1	NA	promoter-TSS (NM_146447)	promoter-TSS (NM_146447)	-211	NM_146447	258439	Mm.377502	NM_146447	ENSMUSG00000109528	Olfr1309	MOR245-5	olfactory receptor 1309	protein-coding
mm_111035.1	chr12	79191813	79191832	-	1	NA	promoter-TSS (NM_021557)	promoter-TSS (NM_021557)	-3	NM_021557	17252	Mm.291799	NM_021557	ENSMUSG00000066441	Rdh11	2610319N22Rik|AI428145|AU045252|Arsdr1|C85936|CGI-82|HCBP12|M42C60|Mdt1|Psdr1|SCALD|UBE-1c1|Ube-1c	retinol dehydrogenase 11	protein-coding
mm_3062.1	chr1	134109337	134109343	+	1	NA	Intergenic	Intergenic	-1902	NM_001284524	71884	Mm.328268	NM_027979	ENSMUSG00000026450	Chit1	2300002L19Rik	chitinase 1 (chitotriosidase)	protein-coding
mm_163527.1	chr13	6073866	6073867	+	1	NA	Intergenic	Intergenic	212377	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_4322.1	chr1	171851983	171851993	+	1	NA	exon (NM_013489, exon 3 of 9)	exon (NM_013489, exon 3 of 9)	12291	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_77869.1	chr9	5345451	5345505	+	1	NA	promoter-TSS (NM_009808)	promoter-TSS (NM_009808)	2	NM_009808	12364	Mm.42163	NM_009808	ENSMUSG00000025887	Casp12	-	caspase 12	protein-coding
mm_50848.1	chr6	54855075	54855086	+	1	NA	intron (NM_199143, intron 1 of 4)	intron (NM_199143, intron 1 of 4)	38164	NM_199143	387524	Mm.286149	NM_199143	ENSMUSG00000058446	Znrf2	1190002C14Rik|AU044205|D6Ertd365e	zinc and ring finger 2	protein-coding
mm_58772.1	chr7	15917350	15917382	+	1	NA	3' UTR (NM_009156, exon 6 of 6)	3' UTR (NM_009156, exon 6 of 6)	5005	NM_009156	20364	Mm.42829	NM_009156	ENSMUSG00000041571	Selenow	Sepw1|selW	selenoprotein W	protein-coding
mm_6750.1	chr1	83408191	83408222	-	1	NA	promoter-TSS (NM_172430)	promoter-TSS (NM_172430)	-6	NM_172430	77629	Mm.154303	NM_172430	ENSMUSG00000026163	Sphkap	4930544G21Rik|A930009L15Rik|AI852220|SKIP|mKIAA1678	SPHK1 interactor, AKAP domain containing	protein-coding
mm_145423.1	chr18	58556225	58556246	+	1	NA	promoter-TSS (NM_001081072)	promoter-TSS (NM_001081072)	-5	NM_001081072	225579	Mm.258517	NM_001081072	ENSMUSG00000024600	Slc27a6	4732438L20Rik|FACVL2|FATP6|VLCS-H1	solute carrier family 27 (fatty acid transporter), member 6	protein-coding
mm_10771.1	chr2	24263456	24263456	+	1	NA	Intergenic	MLT1J|LTR|ERVL-MaLR	-13498	NM_001146088	54450	Mm.29261	NM_019451	ENSMUSG00000026983	Il1f5	AI413231|Fil1delta|IL-36Ra|IL36RN|Il-1h3|Il1hy1	interleukin 1 family, member 5 (delta)	protein-coding
mm_36394.1	chr4	77764376	77764379	-	1	NA	intron (NM_011211, intron 2 of 39)	intron (NM_011211, intron 2 of 39)	447518	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding
mm_8480.1	chr1	153545342	153545374	-	1	NA	intron (NM_028749, intron 1 of 11)	intron (NM_028749, intron 1 of 11)	4356	NM_028749	74091	Mm.24887	NM_028749	ENSMUSG00000042684	Npl	0610033B02Rik	N-acetylneuraminate pyruvate lyase	protein-coding
mm_74035.1	chr8	121851331	121851364	+	1	NA	Intergenic	Intergenic	-21778	NM_145605	234825	Mm.209329	NM_145605	ENSMUSG00000040263	Klhdc4	AA408426|AV352552|BC012312|G430025P05Rik	kelch domain containing 4	protein-coding
mm_157741.1	chrX	72918426	72918436	-	1	NA	promoter-TSS (NM_019405)	promoter-TSS (NM_019405)	-87	NM_019405	26370	Mm.24643	NM_019405	ENSMUSG00000031347	Cetn2	1110034A02Rik|AI326150|Calt|caltractin	centrin 2	protein-coding
mm_158967.1	chr1	93861344	93861344	+	1	NA	promoter-TSS (NM_199366)	promoter-TSS (NM_199366)	0	NM_199366	381334	Mm.482878	NM_199366	ENSMUSG00000094651	Gal3st2	GP3ST|Gm988	galactose-3-O-sulfotransferase 2	protein-coding
mm_131253.1	chr16	10700335	10700341	+	1	NA	intron (NM_001204229, intron 21 of 22)	intron (NM_001204229, intron 21 of 22)	85198	NM_009896	12703	Mm.130	NM_009896	ENSMUSG00000038037	Socs1	Cish1|Cish7|JAB|SOCS-1|SSI-1	suppressor of cytokine signaling 1	protein-coding
mm_161076.1	chr12	81379452	81379452	-	1	NA	promoter-TSS (NM_001038995)	promoter-TSS (NM_001038995)	34	NM_001038995	214321	Mm.444671	NM_001038995	ENSMUSG00000072974	Gm4787	Adam4b|EG214321	predicted gene 4787	protein-coding
mm_135262.1	chr16	37956781	37956783	-	1	NA	intron (NM_153394, intron 3 of 9)	RMER17B|LTR|ERVK	40286	NM_153394	239845	Mm.228018	NM_153394	ENSMUSG00000046961	Gpr156	Gababl	G protein-coupled receptor 156	protein-coding
mm_158935.1	chr1	73942007	73942007	-	1	NA	exon (NM_001289895, exon 20 of 33)	exon (NM_001289895, exon 20 of 33)	-77541	NR_045311	109198	Mm.359721	NR_045311	ENSMUSG00000100301	6030407O03Rik	-	RIKEN cDNA 6030407O03 gene	ncRNA
mm_2497.1	chr1	106033648	106033691	+	1	NA	3' UTR (NM_001122675, exon 13 of 13)	3' UTR (NM_001122675, exon 13 of 13)	43263	NM_001122675	227449	Mm.210188	NM_001122675	ENSMUSG00000038866	Zcchc2	9930114B20Rik|AW212015	zinc finger, CCHC domain containing 2	protein-coding
mm_67346.1	chr7	79825735	79825747	-	1	NA	exon (NM_008486, exon 18 of 20)	exon (NM_008486, exon 18 of 20)	15014	NM_008589	17293	Mm.31472	NM_008589	ENSMUSG00000030543	Mesp2	bHLHc6	mesoderm posterior 2	protein-coding
mm_20706.1	chr2	132946029	132946042	-	1	NA	promoter-TSS (NM_198029)	promoter-TSS (NM_198029)	1	NM_198029	241639	Mm.209784	NM_198029	ENSMUSG00000027356	Fermt1	5830467P10Rik|Kindlin-1	fermitin family member 1	protein-coding
mm_45180.1	chr5	51723578	51723579	-	1	NA	Intergenic	Intergenic	-155853	NR_132764	19017	Mm.259072	NM_008904	ENSMUSG00000029167	Ppargc1a	A830037N07Rik|ENSMUSG00000079510|Gm11133|PGC-1|PPARGC-1-alpha|Pgc-1alpha|Pgc1|Pgco1|Ppargc1	peroxisome proliferative activated receptor, gamma, coactivator 1 alpha	protein-coding
mm_128168.1	chr15	34083241	34083263	-	1	NA	exon (NM_026002, exon 1 of 12)	exon (NM_026002, exon 1 of 12)	533	NM_026002	67154	Mm.130883	NM_026002	ENSMUSG00000022255	Mtdh	2610103J23Rik|3D3|3D3/Lyric|AEG-1|AV353288|D8Bwg1112e|Lyric	metadherin	protein-coding
mm_5380.1	chr1	30949878	30949880	-	1	NA	promoter-TSS (NR_002688)	promoter-TSS (NR_002688)	-124	NM_011200	19243	Mm.491181	NM_011200	ENSMUSG00000026064	Ptp4a1	AA415290|AU019864|C130021B01|Prl-1	protein tyrosine phosphatase 4a1	protein-coding
mm_157372.1	chrX	37878508	37878512	-	1	NA	exon (NM_001004193, exon 2 of 4)	exon (NM_001004193, exon 2 of 4)	434	NM_001004193	434768	Mm.336025	NM_001004193	ENSMUSG00000064137	Rhox8	Tox	reproductive homeobox 8	protein-coding
mm_60372.1	chr7	44465423	44465451	+	1	NA	promoter-TSS (NM_026690)	promoter-TSS (NM_026690)	2	NM_026690	68352	Mm.88478	NM_026690	ENSMUSG00000038704	Aspdh	0610012D14Rik	aspartate dehydrogenase domain containing	protein-coding
mm_151263.1	chr19	54045234	54045244	+	1	NA	promoter-TSS (NM_007417)	promoter-TSS (NM_007417)	57	NM_007417	11551	Mm.235195	NM_007417	ENSMUSG00000033717	Adra2a	AW122659|Adra-2|Adra-2a|alpha(2A)AR|alpha2-C10|alpha2A|alpha2A-AR	adrenergic receptor, alpha 2a	protein-coding
mm_2778.1	chr1	130826660	130826665	+	1	NA	promoter-TSS (NM_011082)	promoter-TSS (NM_011082)	-22	NM_011082	18703	Mm.276414	NM_011082	ENSMUSG00000026417	Pigr	-	polymeric immunoglobulin receptor	protein-coding
mm_68374.1	chr7	108930152	108930164	-	1	NA	promoter-TSS (NM_175532)	promoter-TSS (NM_175532)	0	NM_175532	244202	Mm.37991	NM_175532	ENSMUSG00000049709	Nlrp10	6430548I20Rik|Nalp10|Napl10|PAN5|Pynod	NLR family, pyrin domain containing 10	protein-coding
mm_142069.1	chr17	35697703	35697750	-	1	NA	intron (NM_007584, intron 1 of 17)	intron (NM_007584, intron 1 of 17)	2864	NM_001198833	12305	Mm.5021	NM_007584	ENSMUSG00000003534	Ddr1	6030432F18|AI323681|CD167a|Cak|Nep|PTK3A	discoidin domain receptor family, member 1	protein-coding
mm_88711.1	chr10	80151327	80151375	+	1	NA	intron (NM_001347117, intron 2 of 7)	CT-rich|Low_complexity|Low_complexity	1669	NM_001305799	59090	Mm.143813	NM_021565	ENSMUSG00000035621	Midn	3000003C15Rik	midnolin	protein-coding
mm_143494.1	chr17	71475349	71475359	-	1	NA	promoter-TSS (NM_028887)	promoter-TSS (NM_028887)	-11	NM_028887	74355	Mm.194450	NM_028887	ENSMUSG00000024054	Smchd1	4931400A14Rik|AW554188|MommeD1|mKIAA0650	SMC hinge domain containing 1	protein-coding
mm_109732.1	chr12	116485800	116485818	+	1	NA	promoter-TSS (NM_011215)	promoter-TSS (NM_011215)	89	NM_011215	19276	Mm.206054	NM_011215	ENSMUSG00000056553	Ptprn2	4930425H11Rik|IA2beta|PTP-NP|Phol|mKIAA0387|phogrin	protein tyrosine phosphatase, receptor type, N polypeptide 2	protein-coding
mm_161188.1	chr13	50250296	50250296	-	1	NA	promoter-TSS (NM_001033438)	promoter-TSS (NM_001033438)	12	NM_001033438	380882	Mm.425809	NM_001033438	ENSMUSG00000095300	Gm906	-	predicted gene 906	protein-coding
mm_129871.1	chr15	83416917	83416918	-	1	NA	intron (NM_001159509, intron 1 of 10)	intron (NM_001159509, intron 1 of 10)	15933	NM_011862	23970	Mm.23978	NM_011862	ENSMUSG00000016664	Pacsin2	AI197433	protein kinase C and casein kinase substrate in neurons 2	protein-coding
mm_93800.1	chr10	120898911	120898954	-	1	NA	promoter-TSS (NM_177092)	promoter-TSS (NM_177092)	39	NM_177092	320183	Mm.169755	NM_177092	ENSMUSG00000051236	Msrb3	D430026P16Rik|I-8-23|MsrB2	methionine sulfoxide reductase B3	protein-coding
mm_57664.1	chr6	128487922	128487931	-	1	NA	exon (NM_007376, exon 30 of 36)	exon (NM_007376, exon 30 of 36)	38794	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_46145.1	chr5	93205365	93205376	-	1	NA	intron (NM_017367, intron 1 of 6)	intron (NM_017367, intron 1 of 6)	1125	NM_017367	12453	Mm.250419	NM_017367	ENSMUSG00000063015	Ccni	-	cyclin I	protein-coding
mm_76261.1	chr8	83996864	83996891	-	1	NA	promoter-TSS (NM_001081415)	promoter-TSS (NM_001081415)	-795	NM_001081415	666704	Mm.298091	NM_001081415	ENSMUSG00000079003	Samd1	AA589507	sterile alpha motif domain containing 1	protein-coding
mm_53981.1	chr6	6861738	6861740	-	1	NA	intron (NR_015388, intron 1 of 1)	intron (NR_015388, intron 1 of 1)	-1595	NM_010057	13396	Mm.439763	NM_010057	ENSMUSG00000029754	Dlx6	-	distal-less homeobox 6	protein-coding
mm_66144.1	chr7	31126951	31126992	-	1	NA	promoter-TSS (NM_011322)	promoter-TSS (NM_011322)	52	NM_011322	20266	Mm.1418	NM_011322	ENSMUSG00000019194	Scn1b	-	sodium channel, voltage-gated, type I, beta	protein-coding
mm_172695.1	chr8	61591167	61591168	-	1	NA	promoter-TSS (NM_001293774)	promoter-TSS (NM_001293774)	2	NM_001293774	72333	Mm.29933	NM_001081390	ENSMUSG00000058056	Palld	2410003B16Rik|6030492A02	palladin, cytoskeletal associated protein	protein-coding
mm_161113.1	chr12	104722622	104722622	-	1	NA	intron (NM_148948, intron 7 of 26)	intron (NM_148948, intron 7 of 26)	29330	NM_148948	192119	Mm.21135	NM_148948	ENSMUSG00000041415	Dicer1	1110006F08Rik|D12Ertd7e|mKIAA0928	dicer 1, ribonuclease type III	protein-coding
mm_97174.1	chr11	75532100	75532125	+	1	NA	promoter-TSS (NM_001199283)	promoter-TSS (NM_001199283)	0	NM_001199283	215113	Mm.11186	NM_173388	ENSMUSG00000038178	Slc43a2	7630402D21Rik|BC042513|Lat4	solute carrier family 43, member 2	protein-coding
mm_124405.1	chr14	115477478	115477495	-	1	NA	intron (NM_175500, intron 5 of 7)	intron (NM_175500, intron 5 of 7)	-67934	NR_045761	75088	Mm.444706	NR_045761	ENSMUSG00000093551	4930505G20Rik	-	RIKEN cDNA 4930505G20 gene	ncRNA
mm_145.1	chr1	11089658	11089669	+	1	NA	intron (NM_029525, intron 5 of 39)	intron (NM_029525, intron 5 of 39)	96198	NM_029525	109294	Mm.123247	NM_029525	ENSMUSG00000048960	Prex2	6230420N16Rik|AI316880|AI553603|C030045D06Rik|D430013K02|Depdc2|P-Rex2	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	protein-coding
mm_140987.1	chr17	24737642	24737645	-	1	NA	intron (NM_013759, intron 1 of 4)	intron (NM_013759, intron 1 of 4)	1050	NM_001346668	27361	Mm.28212	NM_013759	ENSMUSG00000075705	Msrb1	D17Wsu82e|SELX|SelR|Sepr|Sepx1	methionine sulfoxide reductase B1	protein-coding
mm_121523.1	chr14	122107077	122107116	+	1	NA	promoter-TSS (NM_080556)	promoter-TSS (NM_080556)	14	NM_080556	68059	Mm.275191	NM_080556	ENSMUSG00000025544	Tm9sf2	1500001N15Rik|AA536814|D14Ertd64e|P76	transmembrane 9 superfamily member 2	protein-coding
mm_71227.1	chr8	40902545	40902590	+	1	NA	exon (NM_001044740, exon 4 of 12)	exon (NM_001044740, exon 4 of 12)	-23666	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_36096.1	chr4	58529949	58529951	-	1	NA	intron (NM_010336, intron 1 of 3)	intron (NM_010336, intron 1 of 3)	23343	NM_172989	14745	Mm.4772	NM_010336	ENSMUSG00000038668	Lpar1	AI326300|Edg2|Gpcr26|Kdt2|lpA1|vzg-1	lysophosphatidic acid receptor 1	protein-coding
mm_112415.1	chr13	3924687	3924713	+	1	NA	promoter-TSS (NM_001033879)	promoter-TSS (NM_001033879)	5	NM_001033879	238463	Mm.313659	NM_001033879	ENSMUSG00000021216	Tubal3	-	tubulin, alpha-like 3	protein-coding
mm_93197.1	chr10	94312583	94312593	-	1	NA	Intergenic	Intergenic	-13885	NR_033209	215472	Mm.255656	NM_174999	ENSMUSG00000053420	Gm4792	E130012K09|EG215472	predicted gene 4792	ncRNA
mm_19225.1	chr2	84670615	84670625	-	1	NA	promoter-TSS (NM_001033166)	promoter-TSS (NM_001033166)	88	NM_001033166	72657	Mm.259293	NM_001033166	ENSMUSG00000076437	Selenoh	2700094K13Rik|Selh	selenoprotein H	protein-coding
mm_82111.1	chr9	123150860	123150868	+	1	NA	promoter-TSS (NM_011606)	promoter-TSS (NM_011606)	-82	NM_011606	21922	Mm.34588	NM_011606	ENSMUSG00000025784	Clec3b	Tna	C-type lectin domain family 3, member b	protein-coding
mm_61478.1	chr7	75655813	75655820	+	1	NA	intron (NM_029332, intron 8 of 36)	L1M4|LINE|L1	-192522	NM_001122780	207952	Mm.206223	NM_029652	ENSMUSG00000055652	Klhl25	2810402K13Rik|BC027373|Enc-1	kelch-like 25	protein-coding
mm_46054.1	chr5	92137770	92137786	-	1	NA	promoter-TSS (NM_019490)	promoter-TSS (NM_019490)	-160	NM_019490	56041	Mm.15868	NM_019490	ENSMUSG00000029407	Uso1	115kDa|TAP|Vdp	USO1 vesicle docking factor	protein-coding
mm_127755.1	chr15	103503068	103503088	+	1	NA	promoter-TSS (NM_008800)	promoter-TSS (NM_008800)	44	NM_008800	18574	Mm.390792	NM_008800	ENSMUSG00000022489	Pde1b	Pde1b1	phosphodiesterase 1B, Ca2+-calmodulin dependent	protein-coding
mm_18149.1	chr2	45067136	45067151	-	1	NA	intron (NM_001289521, intron 1 of 8)	intron (NM_001289521, intron 1 of 8)	43134	NM_001289521	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_116594.1	chr13	48538185	48538190	-	1	NA	promoter-TSS (NR_029725)	promoter-TSS (NR_029725)	85	NR_029725	387244		NR_029725	ENSMUSG00000065421	Mirlet7a-1	Let-7a|Mirnlet7a|Mirnlet7a-1|let-7a-1	microRNA let7a-1	ncRNA
mm_164945.1	chr19	4180634	4180636	+	1	NA	Intergenic	Intergenic	-5156	NM_134148	107239	Mm.482310	NM_134148	ENSMUSG00000075289	Carns1	AI790298|Atpgd1|mKIAA1394	carnosine synthase 1	protein-coding
mm_44267.1	chr5	5664177	5664181	-	1	NA	promoter-TSS (NM_172447)	promoter-TSS (NM_172447)	53	NM_172447	207686	Mm.319007	NM_172447	ENSMUSG00000040473	Cfap69	4921525K03|A330021E22Rik|AI427898	cilia and flagella associated protein 69	protein-coding
mm_66673.1	chr7	45742325	45742341	-	1	NA	intron (NM_017465, intron 1 of 6)	intron (NM_017465, intron 1 of 6)	-16517	NM_027055	69363	Mm.45607	NM_027055	ENSMUSG00000070563	Spaca4	1700008E09Rik|AV043694|Samp14	sperm acrosome associated 4	protein-coding
mm_171198.1	chr3	51210939	51210945	+	1	NA	Intergenic	RLTR9F|LTR|ERVK	-13505	NM_009834	12457	Mm.86541	NM_009834	ENSMUSG00000023087	Noct	AU043840|Ccr4|Ccrn4l	nocturnin	protein-coding
mm_46232.1	chr5	99217760	99217760	-	1	NA	3' UTR (NM_181318, exon 14 of 14)	3' UTR (NM_181318, exon 14 of 14)	35167	NM_181318	320292	Mm.259074	NM_145839	ENSMUSG00000089809	Rasgef1b	4732452O09Rik|GPIgamma4|Gpig4	RasGEF domain family, member 1B	protein-coding
mm_57125.1	chr6	122600178	122600191	-	1	NA	intron (NM_001134391, intron 1 of 7)	MRLTR33|LTR|ERVK	2260	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_45400.1	chr5	66151720	66151728	-	1	NA	promoter-TSS (NM_001291226)	promoter-TSS (NM_001291226)	230	NM_001127382	245945	Mm.36863	NM_139065	ENSMUSG00000070780	Rbm47	9530077J19Rik	RNA binding motif protein 47	protein-coding
mm_64291.1	chr7	141857852	141857867	+	1	NA	exon (NM_028801, exon 31 of 49)	exon (NM_028801, exon 31 of 49)	18787	NM_028801	74180	Mm.200752	NM_028801	ENSMUSG00000066108	Muc5b	2300002I04Rik|A130042M24|AV085033|MUC5|MUC9|mucin 5b	mucin 5, subtype B, tracheobronchial	protein-coding
mm_8481.1	chr1	153545385	153545396	-	1	NA	intron (NM_028749, intron 1 of 11)	intron (NM_028749, intron 1 of 11)	4324	NM_028749	74091	Mm.24887	NM_028749	ENSMUSG00000042684	Npl	0610033B02Rik	N-acetylneuraminate pyruvate lyase	protein-coding
mm_167381.1	chr8	94340563	94340570	+	1	NA	exon (NM_001205311, exon 10 of 25)	exon (NM_001205311, exon 10 of 25)	11358	NM_001205311	20497	Mm.25804	NM_019415	ENSMUSG00000031766	Slc12a3	AI035291|NCC|NCCT|TSC	solute carrier family 12, member 3	protein-coding
mm_66960.1	chr7	62423420	62423426	-	1	NA	Intergenic	Intergenic	-3284	NM_011746	22652	Mm.146	NM_011746	ENSMUSG00000070527	Mkrn3	D7H15S9-1|Zfp127	makorin, ring finger protein, 3	protein-coding
mm_59463.1	chr7	27252176	27252208	+	1	NA	intron (NM_133770, intron 12 of 14)	intron (NM_133770, intron 12 of 14)	-6569	NM_010950	18223	Mm.458153	NM_010950	ENSMUSG00000063160	Numbl	nbl	numb-like	protein-coding
mm_163805.1	chr14	19416029	19416047	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	186549	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_150713.1	chr19	43280775	43280789	+	1	NA	intron (NM_001081257, intron 3 of 11)	intron (NM_001081257, intron 3 of 11)	107573	NM_001081257	545291	Mm.442200	NM_001081257	ENSMUSG00000074852	Hpse2	Gm968|Hpa2	heparanase 2	protein-coding
mm_148367.1	chr18	88867194	88867213	-	1	NA	TTS (NM_018821)	TTS (NM_018821)	27004	NM_018821	54607	Mm.91920	NM_018821	ENSMUSG00000056153	Socs6	1500012M23Rik|5830401B18Rik|AI447482|Cis4|Cish4|HSPC060|SOCS-4|SOCS-6|SSI4|STAI4|STATI4|Socs4	suppressor of cytokine signaling 6	protein-coding
mm_158601.1	chrX	151803693	151803703	-	1	NA	intron (NM_021523, intron 1 of 82)	CpG	416	NM_021523	59026	Mm.27372	NM_021523	ENSMUSG00000025261	Huwe1	5430439H10Rik|AU041296|Arf-bp1|C430014N20Rik|C80292|Gm1718|Ib772|LASU1|Mule|Ureb1	HECT, UBA and WWE domain containing 1	protein-coding
mm_59784.1	chr7	28895115	28895119	+	1	NA	intron (NM_021895, intron 19 of 20)	intron (NM_021895, intron 19 of 20)	13461	NM_001110807	60594	Mm.476990	NM_021894	ENSMUSG00000054083	Capn12	CANP 12	calpain 12	protein-coding
mm_147357.1	chr18	43373249	43373267	-	1	NA	promoter-TSS (NM_001136086)	promoter-TSS (NM_001136086)	14	NM_001136086	22240	Mm.8180	NM_009468	ENSMUSG00000024501	Dpysl3	CRMP-4|DRP-3|TUC4|ULIP-1|Ulip|Ulip1	dihydropyrimidinase-like 3	protein-coding
mm_143952.1	chr17	86827547	86827567	-	1	NA	exon (NM_010137, exon 12 of 16)	exon (NM_010137, exon 12 of 16)	73693	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_31788.1	chr4	63668074	63668076	+	1	NA	Intergenic	Intergenic	-45646	NM_029324	75524	Mm.38543	NM_029324	ENSMUSG00000058935	1700018C11Rik	bM230C2.3	RIKEN cDNA 1700018C11 gene	protein-coding
mm_134152.1	chr16	10786001	10786011	-	1	NA	promoter-TSS (NM_001271603)	promoter-TSS (NM_001271603)	-470	NM_001271603	12703	Mm.130	NM_009896	ENSMUSG00000038037	Socs1	Cish1|Cish7|JAB|SOCS-1|SSI-1	suppressor of cytokine signaling 1	protein-coding
mm_88888.1	chr10	81136504	81136516	+	1	NA	5' UTR (NM_010731, exon 1 of 3)	5' UTR (NM_010731, exon 1 of 3)	239	NM_010731	16969	Mm.20920	NM_010731	ENSMUSG00000035011	Zbtb7a	9030619K07Rik|9130006G12Rik|AI452336|FBI-1|Lrf|Pokemon|Zbtb7	zinc finger and BTB domain containing 7a	protein-coding
mm_170369.1	chr18	54698938	54698950	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	87200	NR_045400	328957	Mm.402781	NR_045400		9330117O12Rik	9330117O12	RIKEN cDNA 9330117O12 gene	ncRNA
mm_165549.1	chr3	9887461	9887466	+	1	NA	Intergenic	MLTR11B|LTR|ERVK	-53784	NM_001195031	94212	Mm.23897	NM_053182	ENSMUSG00000027508	Pag1	Cbp|F730007C19Rik|Pag	phosphoprotein associated with glycosphingolipid microdomains 1	protein-coding
mm_111099.1	chr12	80760683	80760730	-	1	NA	promoter-TSS (NM_001008423)	promoter-TSS (NM_001008423)	9	NM_001008423	380768	Mm.29367	NM_001008423	ENSMUSG00000062961	Ccdc177	Gm1568	coiled-coil domain containing 177	protein-coding
mm_103469.1	chr11	76479133	76479164	-	1	NA	exon (NM_198018, exon 3 of 22)	exon (NM_198018, exon 3 of 22)	-10683	NM_001291186	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_72285.1	chr8	75109560	75109601	+	1	NA	promoter-TSS (NM_008566)	promoter-TSS (NM_008566)	71	NM_008566	17218	Mm.5048	NM_008566	ENSMUSG00000005410	Mcm5	AA617332|AI324988|AL033333|Cdc46|Mcmd5|P1-CDC46	minichromosome maintenance complex component 5	protein-coding
mm_114149.1	chr13	55369768	55369775	+	1	NA	promoter-TSS (NM_016758)	promoter-TSS (NM_016758)	39	NM_016758	51791	Mm.1426	NM_016758	ENSMUSG00000052087	Rgs14	RPIP1	regulator of G-protein signaling 14	protein-coding
mm_82745.1	chr9	26803630	26803642	-	1	NA	intron (NM_153803, intron 1 of 19)	intron (NM_153803, intron 1 of 19)	2781	NM_153803	244757	Mm.293696	NM_153803	ENSMUSG00000036395	Glb1l2	-	galactosidase, beta 1-like 2	protein-coding
mm_83133.1	chr9	40435157	40435171	-	1	NA	intron (NM_172768, intron 1 of 19)	intron (NM_172768, intron 1 of 19)	20600	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_30139.1	chr3	142285442	142285444	-	1	NA	intron (NM_001190852, intron 7 of 15)	intron (NM_001190852, intron 7 of 15)	106407	NM_022554	56376	Mm.117709	NM_019808	ENSMUSG00000028273	Pdlim5	1110001A05Rik|AI987914|C87059|Enh|Enh1|Enh2|Enh3|LIM	PDZ and LIM domain 5	protein-coding
mm_152837.1	chr19	23357563	23357588	-	1	NA	intron (NM_174857, intron 7 of 13)	GSAT_MM|Satellite|Satellite	-83678	NM_001252684	226026	Mm.23267	NM_153808	ENSMUSG00000024943	Smc5	MLZ-453|SMC-5|Smc5l1|mKIAA0594|mSMC5	structural maintenance of chromosomes 5	protein-coding
mm_94202.1	chr11	3102274	3102276	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	-21746	NR_003517	236604	Mm.247625	NM_001004146		Pisd-ps1	-	phosphatidylserine decarboxylase, pseudogene 1	pseudo
mm_48867.1	chr5	150062152	150062177	-	1	NA	intron (NM_001289566, intron 12 of 16)	RLTR15|LTR|ERVK	43489	NM_001289566	140498	Mm.444643	NM_080468	ENSMUSG00000053368	Rxfp2	Gpr106|Great|Lgr8	relaxin/insulin-like family peptide receptor 2	protein-coding
mm_159895.1	chr6	30243756	30243756	-	1	NA	promoter-TSS (NM_001169577)	promoter-TSS (NM_001169577)	47	NM_001169577	22214	Mm.332967	NM_009459	ENSMUSG00000039159	Ube2h	1500009C23Rik|AI181839|AI326965|AI462483|AW227540|E2-20K|Gid3|N28148|Ubc8	ubiquitin-conjugating enzyme E2H	protein-coding
mm_131460.1	chr16	16983436	16983442	+	1	NA	promoter-TSS (NM_001038663)	promoter-TSS (NM_001038663)	57	NM_001038663	26413	Mm.196581	NM_011949	ENSMUSG00000063358	Mapk1	9030612K14Rik|AA407128|AU018647|C78273|ERK|Erk2|MAPK2|PRKM2|Prkm1|p41mapk|p42mapk	mitogen-activated protein kinase 1	protein-coding
mm_145263.1	chr18	52646182	52646185	+	1	NA	promoter-TSS (NM_030097)	promoter-TSS (NM_030097)	-37	NM_030097	78414	Mm.273327	NM_030097	ENSMUSG00000024532	1700034E13Rik	-	RIKEN cDNA 1700034E13 gene	protein-coding
mm_109565.1	chr12	111966795	111966830	+	1	NA	intron (NM_027360, intron 1 of 3)	CpG	165	NM_027360	70257	Mm.318	NM_027360	ENSMUSG00000021290	2010107E04Rik	9430003J03Rik|AU043134|AV124504|Mp68	RIKEN cDNA 2010107E04 gene	protein-coding
mm_144500.1	chr18	24470845	24470922	+	1	NA	promoter-TSS (NM_026529)	promoter-TSS (NM_026529)	12	NM_026529	68046	Mm.276574	NM_026529	ENSMUSG00000024273	2700062C07Rik	AI195775|C87515	RIKEN cDNA 2700062C07 gene	protein-coding
mm_75112.1	chr8	34155044	34155056	-	1	NA	intron (NM_026432, intron 1 of 5)	intron (NM_026432, intron 1 of 5)	487	NM_026432	67887	Mm.290353	NM_026432	ENSMUSG00000031532	Saraf	1810045K07Rik|Tmem66	store-operated calcium entry-associated regulatory factor	protein-coding
mm_109952.1	chr12	11436499	11436509	-	1	NA	5' UTR (NM_012038, exon 1 of 4)	5' UTR (NM_012038, exon 1 of 4)	145	NM_012038	26950	Mm.27005	NM_012038	ENSMUSG00000054459	Vsnl1	VILIP|Vnsl1	visinin-like 1	protein-coding
mm_48116.1	chr5	137138261	137138270	-	1	NA	Intergenic	Intergenic	-22058	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_146501.1	chr18	3299488	3299515	-	1	NA	promoter-TSS (NM_001110853)	promoter-TSS (NM_001110853)	55	NM_001110853	12916	Mm.5244	NM_013498	ENSMUSG00000063889	Crem	ICER|ICERI	cAMP responsive element modulator	protein-coding
mm_138978.1	chr17	45456118	45456121	+	1	NA	intron (NM_027649, intron 4 of 7)	RLTR13B2|LTR|ERVK	18819	NM_027649	71020	Mm.44257	NM_027649	ENSMUSG00000023935	Spats1	1700011H05Rik|4933400B06Rik|Daip2|Ddip|Srsp1	spermatogenesis associated, serine-rich 1	protein-coding
mm_88730.1	chr10	80226766	80226783	+	1	NA	intron (NM_023431, intron 1 of 13)	CpG	176	NM_023431	68114	Mm.273418	NM_023431	ENSMUSG00000020156	Mum1	2610019J09|9430059D04Rik|UBE-1C2	melanoma associated antigen (mutated) 1	protein-coding
mm_146439.1	chr18	84934647	84934651	+	1	NA	promoter-TSS (NM_015798)	promoter-TSS (NM_015798)	-376	NM_015798	50764	Mm.28369	NM_015798	ENSMUSG00000034391	Fbxo15	AU019763|Fbx15|ecat3	F-box protein 15	protein-coding
mm_123430.1	chr14	64440849	64440863	-	1	NA	5' UTR (NM_026322, exon 6 of 11)	5' UTR (NM_026322, exon 6 of 11)	170	NM_001253715	110265	Mm.26713	NM_026322	ENSMUSG00000054733	Msra	2310045J23Rik|6530413P12Rik|MSR-A	methionine sulfoxide reductase A	protein-coding
mm_143746.1	chr17	81520184	81520187	-	1	NA	intron (NR_104580, intron 2 of 8)	intron (NR_104580, intron 2 of 8)	218202	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_137792.1	chr17	29660615	29660706	+	1	NA	promoter-TSS (NM_028791)	promoter-TSS (NM_028791)	65	NM_028791	74157	Mm.390979	NM_028791	ENSMUSG00000024019	Cmtr1	1300018I05Rik|AI451264|Ftsjd2|MTr1	cap methyltransferase 1	protein-coding
mm_58258.1	chr6	145122715	145122741	-	1	NA	intron (NM_008511, intron 1 of 18)	intron (NM_008511, intron 1 of 18)	989	NM_008511	16970	Mm.843	NM_008511	ENSMUSG00000030263	Lrmp	D6Int3|D6Int4|D6Int5|D6Int7|D6Int8|Jaw1	lymphoid-restricted membrane protein	protein-coding
mm_85705.1	chr9	108126543	108126559	-	1	NA	exon (NM_007567, exon 3 of 12)	exon (NM_007567, exon 3 of 12)	-7167	NR_126078	76873	Mm.436935	NR_126077	ENSMUSG00000102224	4930447F24Rik	-	RIKEN cDNA 4930447F24 gene	ncRNA
mm_16691.1	chr2	6884922	6884938	-	1	NA	promoter-TSS (NM_001110228)	promoter-TSS (NM_001110228)	66	NM_010160	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_96739.1	chr11	69777600	69777612	+	1	NA	exon (NM_029348, exon 4 of 4)	exon (NM_029348, exon 4 of 4)	11694	NM_029348	75580	Mm.426361	NM_029348	ENSMUSG00000018750	Zbtb4	2310026P19Rik|9230111I22Rik|mKIAA1538	zinc finger and BTB domain containing 4	protein-coding
mm_155049.1	chrX	42152173	42152195	+	1	NA	intron (NM_021465, intron 1 of 32)	intron (NM_021465, intron 1 of 32)	1483	NM_021465	20843	Mm.290422	NM_021465	ENSMUSG00000025862	Stag2	9230105L23Rik|B230112I07Rik|SA-2|SAP2	stromal antigen 2	protein-coding
mm_60438.1	chr7	44476960	44476970	+	1	NA	Intergenic	L1MEd|LINE|L1	6618	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_68839.1	chr7	126351567	126351575	-	1	NA	Intergenic	Intergenic	16474	NR_106025	102466797		NR_106025	ENSMUSG00000099017	Mir7058	Gm27766|mmu-mir-7058	microRNA 7058	ncRNA
mm_75773.1	chr8	69995023	69995025	-	1	NA	intron (NM_145596, intron 1 of 12)	intron (NM_145596, intron 1 of 12)	1360	NM_001286450	234366	Mm.270044	NM_145596	ENSMUSG00000036180	Gatad2a	1110066C11Rik|BC031407|C80248	GATA zinc finger domain containing 2A	protein-coding
mm_165009.1	chr19	25383566	25383568	+	1	NA	intron (NM_181404, intron 4 of 13)	intron (NM_181404, intron 4 of 13)	-122139	NM_015826	50796	Mm.391208	NM_015826	ENSMUSG00000024837	Dmrt1	-	doublesex and mab-3 related transcription factor 1	protein-coding
mm_35986.1	chr4	55477383	55477402	-	1	NA	Intergenic	Intergenic	55083	NM_010637	16600	Mm.4325	NM_010637	ENSMUSG00000003032	Klf4	EZF|Gklf|Zie	Kruppel-like factor 4 (gut)	protein-coding
mm_55214.1	chr6	52225238	52225256	-	1	NA	intron (NM_001277238, intron 2 of 2)	intron (NM_001277238, intron 2 of 2)	2123	NM_010456	15405	Mm.4694	NM_010456	ENSMUSG00000038227	Hoxa9	D6a9|Hox-1.7	homeobox A9	protein-coding
mm_131620.1	chr16	19760903	19760909	+	1	NA	intron (NM_054052, intron 2 of 3)	intron (NM_054052, intron 2 of 3)	672	NM_001159407	108105	Mm.33935	NM_054052	ENSMUSG00000022686	B3gnt5	beta3GnT5	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5	protein-coding
mm_170848.1	chr2	177600355	177600370	+	1	NA	Intergenic	Intergenic	102136	NR_036450	433520	Mm.425117	NM_001024825		Gm14403	OTTMUSG00000016571	predicted gene 14403	ncRNA
mm_121006.1	chr14	79516569	79516573	+	1	NA	intron (NM_001286411, intron 1 of 8)	intron (NM_001286411, intron 1 of 8)	897	NM_001286411	13709	Mm.20938	NM_007920	ENSMUSG00000036461	Elf1	Elf-1|Sts1|mElf-1|p70	E74-like factor 1	protein-coding
mm_67959.1	chr7	100514801	100514822	-	1	NA	promoter-TSS (NM_153527)	promoter-TSS (NM_153527)	4	NM_153527	69387	Mm.278554	NM_153527	ENSMUSG00000030708	Dnajb13	1700014P03Rik|Tsarg	DnaJ heat shock protein family (Hsp40) member B13	protein-coding
mm_151114.1	chr19	47864509	47864517	+	1	NA	3' UTR (NM_010362, exon 6 of 6)	3' UTR (NM_010362, exon 6 of 6)	-1032	NM_030051	68214	Mm.63791	NM_026619	ENSMUSG00000025069	Gsto2	1700020F09Rik|4930425C18Rik|GSTO 2-2	glutathione S-transferase omega 2	protein-coding
mm_51973.1	chr6	91758618	91758638	+	1	NA	3' UTR (NM_009320, exon 15 of 15)	3' UTR (NM_009320, exon 15 of 15)	48765	NM_001159507	243547	Mm.333264	NM_001033353	ENSMUSG00000030098	Grip2	-	glutamate receptor interacting protein 2	protein-coding
mm_140776.1	chr17	17876992	17877002	-	1	NA	exon (NM_013521, exon 2 of 2)	exon (NM_013521, exon 2 of 2)	6942	NM_013521	14293	Mm.56951	NM_013521	ENSMUSG00000045551	Fpr1	FPR|LXA4R|fMLF-R	formyl peptide receptor 1	protein-coding
mm_10309.1	chr2	11172183	11172199	+	1	NA	promoter-TSS (NM_008859)	promoter-TSS (NM_008859)	-191	NM_008859	18761	Mm.329993	NM_008859	ENSMUSG00000026778	Prkcq	A130035A12Rik|AW494342|PKC-0|PKC-theta|PKCtheta|Pkcq	protein kinase C, theta	protein-coding
mm_59593.1	chr7	28137434	28137444	+	1	NA	exon (NM_001164655, exon 4 of 20)	exon (NM_001164655, exon 4 of 20)	7973	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_9032.1	chr1	166681843	166681847	-	1	NA	promoter-TSS (NM_172844)	promoter-TSS (NM_172844)	0	NM_172844	240894	Mm.246610	NM_172844	ENSMUSG00000026560	Fmo9	4831428F09Rik	flavin containing monooxygenase 9	protein-coding
mm_91556.1	chr10	39960196	39960233	-	1	NA	promoter-TSS (NM_001173500)	promoter-TSS (NM_001173500)	-61	NM_001173500	100041085	Mm.332530	NM_001173500	ENSMUSG00000071335	Mfsd4b3	G630090E17Rik|Naglt1c	major facilitator superfamily domain containing 4B3	protein-coding
mm_76565.1	chr8	88636118	88636132	-	1	NA	promoter-TSS (NM_027840)	promoter-TSS (NM_027840)	3	NM_027840	71607	Mm.270607	NM_027840	ENSMUSG00000031662	Snx20	9130017C17Rik	sorting nexin 20	protein-coding
mm_67294.1	chr7	78913867	78913895	-	1	NA	promoter-TSS (NM_001113527)	promoter-TSS (NM_001113527)	116	NM_020583	57444	Mm.322843	NM_020583	ENSMUSG00000039236	Isg20	1600023I01Rik|2010107M23Rik|20kDa|DnaQL|HEM45	interferon-stimulated protein	protein-coding
mm_20654.1	chr2	132102677	132102691	-	1	NA	intron (NM_018824, intron 1 of 15)	intron (NM_018824, intron 1 of 15)	42424	NM_018824	54338	Mm.103581	NM_018824	ENSMUSG00000027340	Slc23a2	AI844736|NBTL1|SVCT2|Slc23a1|YSPL2|YSPL3|mKIAA0238	solute carrier family 23 (nucleobase transporters), member 2	protein-coding
mm_89277.1	chr10	87861310	87861338	+	1	NA	5' UTR (NM_001111276, exon 1 of 4)	5' UTR (NM_001111276, exon 1 of 4)	213	NM_001111276	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_50067.1	chr6	41218075	41218095	+	1	NA	Intergenic	Intergenic	-84187	NM_011646	22074	Mm.383263	NM_011646	ENSMUSG00000054106	Try4	0910001B19Rik|Td	trypsin 4	protein-coding
mm_22857.1	chr3	28559156	28559160	+	1	NA	intron (NM_026910, intron 9 of 32)	MTEb|LTR|ERVL-MaLR	-138745	NM_031197	20526	Mm.18443	NM_031197	ENSMUSG00000027690	Slc2a2	AI266973|Glut-2|Glut2	solute carrier family 2 (facilitated glucose transporter), member 2	protein-coding
mm_148316.1	chr18	83768149	83768151	-	1	NA	Intergenic	Intergenic	318412	NM_001081300	110796	Mm.102136	NM_001081300	ENSMUSG00000046982	Tshz1	5730407I04Rik|D18Bwg1409e|Mtsh1|NY-CO-33|Sdccag33|Tsh1|mKIAA4206|teashirt1	teashirt zinc finger family member 1	protein-coding
mm_22920.1	chr3	31095898	31095932	+	1	NA	intron (NM_001271772, intron 1 of 8)	intron (NM_001271772, intron 1 of 8)	857	NM_001039090	20482	Mm.15406	NM_011386	ENSMUSG00000027660	Skil	Skir|SnoN|sno	SKI-like	protein-coding
mm_53488.1	chr6	135084071	135084083	+	1	NA	3' UTR (NM_181444, exon 4 of 4)	3' UTR (NM_181444, exon 4 of 4)	18415	NM_181444	232431	Mm.23575	NM_181444	ENSMUSG00000046733	Gprc5a	Rai3|Raig1	G protein-coupled receptor, family C, group 5, member A	protein-coding
mm_148512.1	chr19	4231932	4231959	+	1	NA	promoter-TSS (NM_027196)	promoter-TSS (NM_027196)	52	NM_027196	69745	Mm.32518	NM_027196	ENSMUSG00000024854	Pold4	2410012M21Rik|AI463381|AW060307|Polds|p12	polymerase (DNA-directed), delta 4	protein-coding
mm_95401.1	chr11	49722881	49722898	+	1	NA	Intergenic	L1MDb|LINE|L1	-10167	NM_212484	104625	Mm.247113	NM_212484	ENSMUSG00000020362	Cnot6	CCR4	CCR4-NOT transcription complex, subunit 6	protein-coding
mm_29448.1	chr3	110251369	110251381	-	1	NA	promoter-TSS (NM_178891)	promoter-TSS (NM_178891)	-376	NR_024139	99890	Mm.36115	NM_178891	ENSMUSG00000049300	Prmt6	AW124876|BB233495|Hrmt1l6	protein arginine N-methyltransferase 6	protein-coding
mm_1414.1	chr1	67157781	67157823	+	1	NA	exon (NM_001080809, exon 10 of 38)	exon (NM_001080809, exon 10 of 38)	34775	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_77025.1	chr8	108722758	108722773	-	1	NA	intron (NM_007496, intron 1 of 9)	intron (NM_007496, intron 1 of 9)	8121	NM_007496	11906	Mm.416972	NM_007496	ENSMUSG00000038872	Zfhx3	A230102L03Rik|Atbf1|Sci|WBP9|mKIAA4228	zinc finger homeobox 3	protein-coding
mm_157162.1	chrX	9465633	9465648	-	1	NA	intron (NM_007807, intron 3 of 12)	intron (NM_007807, intron 3 of 12)	3684	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_149325.1	chr19	10842793	10842807	+	1	NA	5' UTR (NM_023044, exon 1 of 8)	5' UTR (NM_023044, exon 1 of 8)	256	NM_023044	65221	Mm.27387	NM_023044	ENSMUSG00000024737	Slc15a3	Ci1|cI-1	solute carrier family 15, member 3	protein-coding
mm_170827.1	chr2	176831037	176831050	+	1	NA	Intergenic	Intergenic	32443	NM_001205057	100039123	Mm.389409	NM_001205057	ENSMUSG00000078877	Gm14295	OTTMUSG00000016219	predicted gene 14295	protein-coding
mm_152484.1	chr19	11049449	11049464	-	1	NA	intron (NR_102366, intron 1 of 2)	MLTR14|LTR|ERV1	1110	NR_102366	107350	Mm.6381	NM_001177351	ENSMUSG00000075010	AW112010	-	expressed sequence AW112010	ncRNA
mm_161507.1	chr15	98220991	98220991	-	1	NA	promoter-TSS (NM_001011780)	promoter-TSS (NM_001011780)	65	NM_001011780	634104	Mm.259785	NM_001011780	ENSMUSG00000090129	Olfr287	MOR286-1	olfactory receptor 287	protein-coding
mm_120086.1	chr14	57798638	57798696	+	1	NA	TTS (NR_037238)	TTS (NR_037238)	243	NR_037238	100526476		NR_037238	ENSMUSG00000092784	Mir3077	mir-3077|mmu-mir-3077	microRNA 3077	ncRNA
mm_89463.1	chr10	93310024	93310064	+	1	NA	intron (NM_013508, intron 1 of 4)	intron (NM_013508, intron 1 of 4)	1115	NM_001322268	13713	Mm.4454	NM_013508	ENSMUSG00000008398	Elk3	D430049E23Rik|Erp|Etrp|Net|Sap-2	ELK3, member of ETS oncogene family	protein-coding
mm_142181.1	chr17	36271878	36271921	-	1	NA	promoter-TSS (NM_178281)	promoter-TSS (NM_178281)	105	NM_024468	79263	Mm.40624	NM_024468	ENSMUSG00000045409	Trim39	1100001D15Rik|E130103K13Rik|RBCC-B30.2|Rnf23|mKIAA4179|tfp	tripartite motif-containing 39	protein-coding
mm_126169.1	chr15	78560989	78561019	+	1	NA	3' UTR (NM_009008, exon 7 of 7)	3' UTR (NM_009008, exon 7 of 7)	11779	NM_009008	19354	Mm.1972	NM_009008	ENSMUSG00000033220	Rac2	AI323801|AI452260	RAS-related C3 botulinum substrate 2	protein-coding
mm_145819.1	chr18	65431083	65431087	+	1	NA	promoter-TSS (NM_172833)	promoter-TSS (NM_172833)	88	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_21194.1	chr2	155414975	155415006	-	1	NA	exon (NM_019825, exon 8 of 14)	exon (NM_019825, exon 8 of 14)	25793	NM_001242558	56406	Mm.27592	NM_019825	ENSMUSG00000038369	Ncoa6	AIB3|ASC-2|ASC2|NRC|Ncoa7|PRIP|RAP250|mKIAA0181	nuclear receptor coactivator 6	protein-coding
mm_14901.1	chr2	150107600	150107602	+	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	29077	NM_023266	104348	Mm.485851	NM_023266	ENSMUSG00000068134	Zfp120	AI315103|E030042N05Rik|F80|MZF31|Zfp844	zinc finger protein 120	protein-coding
mm_84300.1	chr9	63399032	63399062	-	1	NA	exon (NM_027090, exon 1 of 2)	exon (NM_027090, exon 1 of 2)	197	NM_027090	69478	Mm.113942	NM_027090	ENSMUSG00000032403	2300009A05Rik	-	RIKEN cDNA 2300009A05 gene	protein-coding
mm_7903.1	chr1	133660824	133660844	-	1	NA	promoter-TSS (NM_001166552)	promoter-TSS (NM_001166552)	51	NM_001166552	667118	Mm.245357	NM_001166552	ENSMUSG00000094410	Zbed6	Gm8466|MGR	zinc finger, BED type containing 6	protein-coding
mm_92041.1	chr10	62494874	62494884	-	1	NA	exon (NM_011157, exon 3 of 3)	exon (NM_011157, exon 3 of 3)	-8074	NM_133672	30930	Mm.260703	NM_133672	ENSMUSG00000020078	Vps26a	AA407240|HB58|Vps26	VPS26 retromer complex component A	protein-coding
mm_6122.1	chr1	64302952	64302962	-	1	NA	Intergenic	Intergenic	-181568	NM_033563	93691	Mm.29466	NM_033563	ENSMUSG00000025959	Klf7	9830124P08Rik	Kruppel-like factor 7 (ubiquitous)	protein-coding
mm_87555.1	chr10	54118115	54118126	+	1	NA	Intergenic	Intergenic	42198	NR_038016	100502920	Mm.403982	NR_038016	ENSMUSG00000097069	Gm16998	-	predicted gene, 16998	ncRNA
mm_58316.1	chr6	146425017	146425024	-	1	NA	intron (NM_010586, intron 4 of 55)	intron (NM_010586, intron 4 of 55)	77203	NM_010586	16439	Mm.7800	NM_010586	ENSMUSG00000030287	Itpr2	AI649341|InsP3R-2|InsP3R-5|Ip3r2|Itpr5|insP3R2	inositol 1,4,5-triphosphate receptor 2	protein-coding
mm_39556.1	chr5	22746018	22746083	+	1	NA	promoter-TSS (NM_029990)	promoter-TSS (NM_029990)	-143	NM_001081231	269629	Mm.371712	NM_029990	ENSMUSG00000106379	Lhfpl3	A930031L14Rik	lipoma HMGIC fusion partner-like 3	protein-coding
mm_65611.1	chr7	27486777	27486804	-	1	NA	promoter-TSS (NM_018820)	promoter-TSS (NM_018820)	-163	NM_018820	55942	Mm.153684	NM_018820	ENSMUSG00000008384	Sertad1	1110032C13Rik|AV000455|AW456625|Sei-1|Sei1|TRIP-Br1	SERTA domain containing 1	protein-coding
mm_136308.1	chr16	91647630	91647650	-	1	NA	promoter-TSS (NM_019973)	promoter-TSS (NM_019973)	-184	NM_019973	20658	Mm.46401	NM_019973	ENSMUSG00000022961	Son	2900011L12Rik|AA409051|AU067731|C81487|mKIAA1019|nrebp	Son DNA binding protein	protein-coding
mm_169476.1	chr14	69337195	69337200	+	1	NA	promoter-TSS (NM_026174).2	promoter-TSS (NM_026174).2	46	NM_026174	67464	Mm.489765	NM_026174	ENSMUSG00000095463	Entpd4	1200014F22Rik|4930513O14Rik|A430102M06Rik|AI414893|Lysal1|mKIAA0392	ectonucleoside triphosphate diphosphohydrolase 4	protein-coding
mm_34578.1	chr4	150119276	150119331	+	1	NA	promoter-TSS (NM_019741)	promoter-TSS (NM_019741)	-41	NM_019741	56485	Mm.260220	NM_019741	ENSMUSG00000028976	Slc2a5	AI526984|Glut5|Slc5a	solute carrier family 2 (facilitated glucose transporter), member 5	protein-coding
mm_93015.1	chr10	87492797	87492834	-	1	NA	exon (NM_008553, exon 1 of 2)	exon (NM_008553, exon 1 of 2)	845	NM_008553	17172	Mm.136217	NM_008553	ENSMUSG00000020052	Ascl1	AI225900|ASH1|Mash1|bHLHa46	achaete-scute family bHLH transcription factor 1	protein-coding
mm_82053.1	chr9	122572494	122572511	+	1	NA	promoter-TSS (NR_015610)	promoter-TSS (NR_015610)	1	NR_015610	319626	Mm.186748	NR_015610	ENSMUSG00000097736	9530059O14Rik	-	RIKEN cDNA 9530059O14 gene	ncRNA
mm_54112.1	chr6	17459610	17459629	-	1	NA	Intergenic	Intergenic	-4338	NM_008591	17295	Mm.86844	NM_008591	ENSMUSG00000009376	Met	AI838057|HGF|HGFR|Par4|c-Met	met proto-oncogene	protein-coding
mm_77500.1	chr8	122629939	122629942	-	1	NA	3' UTR (NM_009824, exon 12 of 12)	3' UTR (NM_009824, exon 12 of 12)	-7205	NM_001007462	382035	Mm.25449	NM_001007462	ENSMUSG00000069867	Pabpn1l	Gm1108|Pabpnl1|ePABP2	poly(A)binding protein nuclear 1-like	protein-coding
mm_153088.1	chr19	32389679	32389702	-	1	NA	intron (NR_033198, intron 1 of 1)	CpG-7452	474	NR_033198	67188	Mm.391160	NR_033198	ENSMUSG00000097787	2700046G09Rik	-	RIKEN cDNA 2700046G09 gene	ncRNA
mm_13963.1	chr2	121414642	121414651	+	1	NA	promoter-TSS (NM_153075)	promoter-TSS (NM_153075)	744	NM_007952	14827	Mm.263177	NM_007952	ENSMUSG00000027248	Pdia3	58kDa|ERp57|ERp60|ERp61|Erp|Grp58|PDI|PDI-Q2|PI-PLC|PLC[a]|Plca	protein disulfide isomerase associated 3	protein-coding
mm_3986.1	chr1	164307665	164307680	+	1	NA	promoter-TSS (NM_001160209)	promoter-TSS (NM_001160209)	0	NM_138314	171567	Mm.219428	NM_138314	ENSMUSG00000026575	Nme7	D530024H21Rik|Nm23-M7|Nm23-r7	NME/NM23 family member 7	protein-coding
mm_53721.1	chr6	143955920	143955928	+	1	NA	intron (NM_001113559, intron 7 of 13)	ORR1E|LTR|ERVL-MaLR	-8818	NM_001347506	20678	Mm.1752	NM_011444	ENSMUSG00000041540	Sox5	A730017D01Rik|AI528773	SRY (sex determining region Y)-box 5	protein-coding
mm_97255.1	chr11	75756977	75757002	+	1	NA	exon (NM_009536, exon 4 of 6)	exon (NM_009536, exon 4 of 6)	24102	NM_009536	22627	Mm.234700	NM_009536	ENSMUSG00000020849	Ywhae	AU019196	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide	protein-coding
mm_21896.1	chr2	166155730	166155734	-	1	NA	promoter-TSS (NM_028072)	promoter-TSS (NM_028072)	-49	NM_028072	72043	Mm.1011	NM_028072	ENSMUSG00000006800	Sulf2	2010004N24Rik|AU020235|MSulf-2|mKIAA1247	sulfatase 2	protein-coding
mm_135166.1	chr16	35926952	35926955	-	1	NA	3' UTR (NM_001013371, exon 5 of 5)	3' UTR (NM_001013371, exon 5 of 5)	-11517	NM_030253	80285	Mm.49074	NM_030253	ENSMUSG00000022906	Parp9	ARTD9|AW214463|BC003281|Bagl|Bal|PARP-9	poly (ADP-ribose) polymerase family, member 9	protein-coding
mm_95679.1	chr11	54124507	54124520	+	1	NA	intron (NM_011031, intron 9 of 15)	intron (NM_011031, intron 9 of 15)	23589	NM_011031	18452	Mm.3705	NM_011031	ENSMUSG00000018906	P4ha2	AA407196|C76437|P4hl	procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha II polypeptide	protein-coding
mm_49105.1	chr6	8259296	8259312	+	1	NA	promoter-TSS (NM_026632)	promoter-TSS (NM_026632)	16	NM_001302353	100036521	Mm.446106	NM_001302353	ENSMUSG00000089862	Umad1	Gm16039|OTTMUSG00000029336	UMAP1-MVP12 associated (UMA) domain containing 1	protein-coding
mm_7817.1	chr1	131911127	131911145	-	1	NA	intron (NM_175294, intron 1 of 6)	CpG	678	NM_001145804	98415	Mm.246869	NM_175294	ENSMUSG00000026434	Nucks1	2700010L10Rik|8430423A01Rik|AI647518|C78391|Nucks	nuclear casein kinase and cyclin-dependent kinase substrate 1	protein-coding
mm_73840.1	chr8	117461184	117461230	+	1	NA	3' UTR (NM_001163262, exon 21 of 21)	3' UTR (NM_001163262, exon 21 of 21)	1942	NR_106046	102465653		NR_106046	ENSMUSG00000098483	Mir7078	Gm27386|mmu-mir-7078	microRNA 7078	ncRNA
mm_69187.1	chr7	127272484	127272489	-	1	NA	3' UTR (NM_009266, exon 1 of 1)	3' UTR (NM_009266, exon 1 of 1)	1573	NM_009266	20768	Mm.20294	NM_009266	ENSMUSG00000049091	Sephs2	Sps2|Ysg3	selenophosphate synthetase 2	protein-coding
mm_169196.1	chr13	66113450	66113452	+	1	NA	promoter-TSS (NM_001177832)	promoter-TSS (NM_001177832)	-2	NM_001177832	628709	Mm.390595	NM_001177832	ENSMUSG00000095909	Gm10324	ENSMUSG00000071302	predicted gene 10324	protein-coding
mm_172262.1	chr6	75296700	75296714	-	1	NA	Intergenic	Intergenic	-1825686	NR_108032	73408	Mm.233629	NR_108032	ENSMUSG00000107408	1700065L07Rik	-	RIKEN cDNA 1700065L07 gene	ncRNA
mm_135149.1	chr16	35857662	35857701	-	1	NA	exon (NM_001039530, exon 6 of 17)	exon (NM_001039530, exon 6 of 17)	13701	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_130942.1	chr15	103249322	103249343	-	1	NA	exon (NM_008685, exon 3 of 3)	exon (NM_008685, exon 3 of 3)	2344	NM_001302338	18022	Mm.457989	NM_008685	ENSMUSG00000058794	Nfe2	NF-E2|NF-E2/P45|p45|p45NFE2|p45nf-e2	nuclear factor, erythroid derived 2	protein-coding
mm_86379.1	chr9	123845189	123845200	-	1	NA	5' UTR (NM_148925, exon 2 of 19)	5' UTR (NM_148925, exon 2 of 19)	6467	NM_148925	17281	Mm.252941	NM_148925	ENSMUSG00000025241	Fyco1	2810409M01Rik|Mem2|RUFY3|ZFYVE7	FYVE and coiled-coil domain containing 1	protein-coding
mm_43739.1	chr5	139822347	139822377	+	1	NA	Intergenic	Intergenic	4481	NM_025604	66506	Mm.29070	NM_025604	ENSMUSG00000029551	Psmg3	1810042K04Rik|4930403H09Rik|AI303239	proteasome (prosome, macropain) assembly chaperone 3	protein-coding
mm_154488.1	chrM	5796	5827	-	1	NA	NA	Intergenic	NA	NA								
mm_70488.1	chr8	12439345	12439357	+	1	NA	Intergenic	Intergenic	43832	NM_009233	20664	Mm.39088	NM_009233	ENSMUSG00000096014	Sox1	BB176347|Sox-1	SRY (sex determining region Y)-box 1	protein-coding
mm_149609.1	chr19	16385680	16385694	+	1	NA	3' UTR (NM_008139, exon 7 of 7)	3' UTR (NM_008139, exon 7 of 7)	-49980	NM_008137	14675	Mm.313181	NM_008137	ENSMUSG00000024697	Gna14	AU023208	guanine nucleotide binding protein, alpha 14	protein-coding
mm_79591.1	chr9	58279651	58279678	+	1	NA	Intergenic	MLTR25A|LTR|ERVK	26500	NM_026942	69106	Mm.216502	NM_026942	ENSMUSG00000032333	Stoml1	1810015E19Rik|AI847431|SLP1|STORP|UNC24|WPB72	stomatin-like 1	protein-coding
mm_36566.1	chr4	87806264	87806274	-	1	NA	promoter-TSS (NM_029931)	promoter-TSS (NM_029931)	54	NM_001286158	70122	Mm.288898	NM_027326	ENSMUSG00000028496	Mllt3	2210011H10Rik|2610012I03Rik|3830408D16Rik|Af9|D4Ertd321e	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 3	protein-coding
mm_139571.1	chr17	57060736	57060757	+	1	NA	promoter-TSS (NM_025877)	promoter-TSS (NM_025877)	-883	NM_025877	66972	Mm.23720	NM_025877	ENSMUSG00000046329	Slc25a23	2310067G05Rik|SCaMC-3	solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 23	protein-coding
mm_168779.1	chr12	17873865	17873875	-	1	NA	Intergenic	MMVL30-int|LTR|ERV1	183056	NM_016677	53602	Mm.313619	NM_016677	ENSMUSG00000071379	Hpcal1	NVP-3|Nvp3|VILIP3|Vnsl3|Vsnl3	hippocalcin-like 1	protein-coding
mm_52959.1	chr6	123123386	123123416	+	1	NA	promoter-TSS (NM_001170333)	promoter-TSS (NM_001170333)	85	NM_001170333	26888	Mm.47384	NM_011999	ENSMUSG00000030148	Clec4a2	Clec4a|Clecsf6|DCIR|Dcir1	C-type lectin domain family 4, member a2	protein-coding
mm_161307.1	chr14	34460493	34460493	-	1	NA	intron (NM_009758, intron 2 of 12)	intron (NM_009758, intron 2 of 12)	42053	NM_009758	12166	Mm.237825	NM_009758	ENSMUSG00000021796	Bmpr1a	1110037I22Rik|ALK3|AU045487|BMPR-IA|Bmpr	bone morphogenetic protein receptor, type 1A	protein-coding
mm_91303.1	chr10	24916685	24916688	-	1	NA	intron (NM_007482, intron 5 of 7)	intron (NM_007482, intron 5 of 7)	6022	NR_105870	102465545		NR_105870	ENSMUSG00000099181	Mir6905	Gm27879|mmu-mir-6905	microRNA 6905	ncRNA
mm_124278.1	chr14	103037117	103037151	-	1	NA	Intergenic	Intergenic	-3331	NR_045657	71264	Mm.399572	NR_045657		4933432I03Rik	-	RIKEN cDNA 4933432I03 gene	ncRNA
mm_149805.1	chr19	23758793	23758807	+	1	NA	promoter-TSS (NM_177034)	promoter-TSS (NM_177034)	-76	NM_177034	319924	Mm.22879	NM_177034	ENSMUSG00000024897	Apba1	6430513E09Rik|Lin-10|Mint|Mint1|Urop11|X11|X11alpha	amyloid beta (A4) precursor protein binding, family A, member 1	protein-coding
mm_101516.1	chr11	32527542	32527550	-	1	NA	promoter-TSS (NM_027031)	promoter-TSS (NM_027031)	28	NM_027031	69306	Mm.288704	NM_027031	ENSMUSG00000044056	Efcab9	1700007I06Rik|4930403C08Rik	EF-hand calcium binding domain 9	protein-coding
mm_3819.1	chr1	159241305	159241319	+	1	NA	intron (NM_011931, intron 2 of 19)	intron (NM_011931, intron 2 of 19)	8986	NM_011931	26374	Mm.328135	NM_011931	ENSMUSG00000040782	Rfwd2	AI316802|C80879|Cop1	ring finger and WD repeat domain 2	protein-coding
mm_172218.1	chr6	6351630	6351647	-	1	NA	intron (NR_136905, intron 3 of 3)	(CCA)n|Simple_repeat|Simple_repeat	102979	NR_136905	101056138	Mm.389085	NR_136904	ENSMUSG00000093482	Gm20619	-	predicted gene 20619	ncRNA
mm_130808.1	chr15	101712898	101712911	-	1	NA	promoter-TSS (NM_027011)	promoter-TSS (NM_027011)	-13	NM_027011	110308	Mm.451847	NM_027011	ENSMUSG00000061527	Krt5	3300001P10Rik|AW146334|CK5|K5|Krt2-5|Tfip8	keratin 5	protein-coding
mm_46534.1	chr5	105700569	105700585	-	1	NA	promoter-TSS (NM_178701)	promoter-TSS (NM_178701)	-233	NM_178701	231549	Mm.23837	NM_178701	ENSMUSG00000046079	Lrrc8d	2810473G09Rik|4930525N13Rik|A930019F03|Lrrc5	leucine rich repeat containing 8D	protein-coding
mm_59224.1	chr7	24636545	24636564	+	1	NA	promoter-TSS (NM_133743)	promoter-TSS (NM_133743)	-16	NM_133743	72434	Mm.281093	NM_133743	ENSMUSG00000057454	Lypd3	2310061G07Rik|C4.4a	Ly6/Plaur domain containing 3	protein-coding
mm_51781.1	chr6	88198331	88198334	+	1	NA	promoter-TSS (NM_008090)	promoter-TSS (NM_008090)	-332	NM_008090	14461	Mm.491156	NM_008090	ENSMUSG00000015053	Gata2	Gata-2	GATA binding protein 2	protein-coding
mm_68525.1	chr7	112158404	112158458	-	1	NA	intron (NM_015814, intron 1 of 7)	CpG	626	NM_015814	50781	Mm.55143	NM_015814	ENSMUSG00000030772	Dkk3	AW061014|C87148	dickkopf WNT signaling pathway inhibitor 3	protein-coding
mm_67163.1	chr7	73545644	73545647	-	1	NA	intron (NR_037569, intron 4 of 4)	intron (NR_037569, intron 4 of 4)	-3899	NM_001081345	244059	Mm.34539	NM_001081345	ENSMUSG00000078671	Chd2	2810013C04Rik|2810040A01Rik|5630401D06Rik|AI851092|BC029703|CHD-2	chromodomain helicase DNA binding protein 2	protein-coding
mm_168317.1	chr11	113136112	113136112	+	1	NA	intron (NR_015556, intron 1 of 2)	intron (NR_015556, intron 1 of 2)	65726	NR_015556	72386	Mm.266961	NR_015556	ENSMUSG00000087259	2610035D17Rik	-	RIKEN cDNA 2610035D17 gene	ncRNA
mm_20523.1	chr2	130840061	130840082	-	1	NA	promoter-TSS (NM_001311147)	promoter-TSS (NM_001311147)	74	NM_029432	228602	Mm.271990	NM_028367	ENSMUSG00000027309	4930402H24Rik	2810487F15Rik|AI413763|C78926	RIKEN cDNA 4930402H24 gene	protein-coding
mm_102966.1	chr11	69665893	69665905	-	1	NA	exon (NM_001291058, exon 2 of 6)	exon (NM_001291058, exon 2 of 6)	271	NM_001291058	12514	Mm.15819	NM_009853	ENSMUSG00000018774	Cd68	Lamp4|Scard1|gp110	CD68 antigen	protein-coding
mm_8005.1	chr1	134773264	134773268	-	1	NA	intron (NM_001081307, intron 22 of 23)	intron (NM_001081307, intron 22 of 23)	30455	NR_015606	329251	Mm.188709	NM_001081307	ENSMUSG00000073557	Ppp1r12b	1810037O03Rik|9530009M10Rik|AI132431|Mypt2	protein phosphatase 1, regulatory (inhibitor) subunit 12B	protein-coding
mm_18353.1	chr2	58161073	58161110	-	1	NA	promoter-TSS (NM_139200)	promoter-TSS (NM_139200)	-969	NM_139200	227929	Mm.273905	NM_139200	ENSMUSG00000026832	Cytip	A130053M09Rik|AI462064|C80816|Cbp|Cybr|Pscdbp	cytohesin 1 interacting protein	protein-coding
mm_115546.1	chr13	8858796	8858829	-	1	NA	intron (NM_001039388, intron 2 of 13)	intron (NM_001039388, intron 2 of 13)	12232	NM_001039389	207615	Mm.284654	NM_172445	ENSMUSG00000021147	Wdr37	-	WD repeat domain 37	protein-coding
mm_73687.1	chr8	111556612	111556622	+	1	NA	intron (NM_001168623, intron 1 of 4)	RMER21B|LTR|ERV1	18274	NM_001168623	170737	Mm.271578	NM_133206	ENSMUSG00000033545	Znrf1	B830022L21Rik|Rnf42|Zrfp1|nin283	zinc and ring finger 1	protein-coding
mm_133346.1	chr16	81269706	81269714	+	1	NA	intron (NM_001113208, intron 1 of 17)	intron (NM_001113208, intron 1 of 17)	69013	NM_010954	17968	Mm.433941	NM_010954	ENSMUSG00000022762	Ncam2	Ncam-2|Ocam|RNCAM	neural cell adhesion molecule 2	protein-coding
mm_124576.1	chr14	124572370	124572393	-	1	NA	intron (NM_207667, intron 1 of 4)	intron (NM_207667, intron 1 of 4)	104746	NM_207667	14169	Mm.206362	NM_010201	ENSMUSG00000025551	Fgf14	FHF-4|Fhf4|mFHF-4(1B)	fibroblast growth factor 14	protein-coding
mm_100735.1	chr11	3983988	3983999	-	1	NA	intron (NM_001177703, intron 1 of 2)	intron (NM_001177703, intron 1 of 2)	357	NM_016922	53897	Mm.103414	NM_016922	ENSMUSG00000049721	Gal3st1	Cst|Gcst	galactose-3-O-sulfotransferase 1	protein-coding
mm_141372.1	chr17	29007926	29007962	-	1	NA	promoter-TSS (NM_134115)	promoter-TSS (NM_134115)	-7	NM_134115	106504	Mm.439986	NM_134115	ENSMUSG00000024006	Stk38	5830476G13Rik|9530097A09Rik|AA617404|Ndr1	serine/threonine kinase 38	protein-coding
mm_84050.1	chr9	58118819	58118832	-	1	NA	promoter-TSS (NM_001166282)	promoter-TSS (NM_001166282)	-2	NM_001166282	382077	Mm.335193	NM_029212	ENSMUSG00000037716	Ccdc33	4930535E21Rik|Gm1117|Tzip1	coiled-coil domain containing 33	protein-coding
mm_78896.1	chr9	44638714	44638720	+	1	NA	3' UTR (NM_001110826, exon 14 of 14)	3' UTR (NM_001110826, exon 14 of 14)	33825	NM_181324	13209	Mm.267061	NM_007841	ENSMUSG00000032097	Ddx6	1110001P04Rik|E230023J21Rik|HLR2|mRCK/P54|p54|rck	DEAD (Asp-Glu-Ala-Asp) box polypeptide 6	protein-coding
mm_160967.1	chr11	99780704	99780704	-	1	NA	promoter-TSS (NM_001085547)	promoter-TSS (NM_001085547)	-61	NM_001085547	665992	Mm.473674	NM_001085547	ENSMUSG00000089724	Krtap4-8	OTTMUSG00000002541	keratin associated protein 4-8	protein-coding
mm_142917.1	chr17	53682944	53682948	-	1	NA	intron (NM_028232, intron 5 of 8)	intron (NM_028232, intron 5 of 8)	6369	NM_028232	72415	Mm.153202	NM_028232	ENSMUSG00000023940	Sgol1	3300001M08Rik|C81037|Sgo1	shugoshin-like 1 (S. pombe)	protein-coding
mm_120904.1	chr14	75962457	75962484	+	1	NA	5' UTR (NM_026214, exon 2 of 2)	5' UTR (NM_026214, exon 2 of 2)	7467	NM_026214	67516	Mm.390712	NM_026214	ENSMUSG00000046523	Kctd4	2210017A09Rik|AU017169	potassium channel tetramerisation domain containing 4	protein-coding
mm_107045.1	chr12	15814914	15814920	+	1	NA	intron (NM_144551, intron 1 of 2)	CpG	1868	NM_144551	217410	Mm.491136	NM_144551	ENSMUSG00000020601	Trib2	AW319517|TRB-2|TRB2	tribbles pseudokinase 2	protein-coding
mm_162918.1	chr10	120462896	120462904	-	1	NA	intron (NM_001347170, intron 2 of 5)	intron (NM_001347170, intron 2 of 5)	13569	NM_001347170	15364	Mm.157190	NM_010441	ENSMUSG00000056758	Hmga2	9430083A20Rik|HMGI-C|Hmgic|pg|pygmy	high mobility group AT-hook 2	protein-coding
mm_17382.1	chr2	27021886	27021896	-	1	NA	TTS (NM_029862)	TTS (NM_029862)	6107	NM_172659	227659	Mm.41203	NM_172659	ENSMUSG00000036067	Slc2a6	A330096C23|F630103L12Rik|Glut6|Glut9	solute carrier family 2 (facilitated glucose transporter), member 6	protein-coding
mm_65107.1	chr7	19309692	19309700	-	1	NA	5' UTR (NM_008036, exon 1 of 4)	5' UTR (NM_008036, exon 1 of 4)	349	NM_008036	14282	Mm.248335	NM_008036	ENSMUSG00000003545	Fosb	-	FBJ osteosarcoma oncogene B	protein-coding
mm_19972.1	chr2	118218631	118218632	-	1	NA	intron (NM_027759, intron 10 of 10)	intron (NM_027759, intron 10 of 10)	38335	NM_027759	71313	Mm.85046	NM_027759	ENSMUSG00000027344	Fsip1	1700012M13Rik|4933432K11Rik	fibrous sheath-interacting protein 1	protein-coding
mm_130228.1	chr15	96285710	96285732	-	1	NA	Intergenic	CpG	-1801	NM_175251	77044	Mm.17166	NM_175251	ENSMUSG00000033237	Arid2	1700124K17Rik|4432409D24Rik|zipzap/p200	AT rich interactive domain 2 (ARID, RFX-like)	protein-coding
mm_114246.1	chr13	56629723	56629735	+	1	NA	exon (NM_009369, exon 8 of 17)	exon (NM_009369, exon 8 of 17)	20126	NM_009369	21810	Mm.14455	NM_009369	ENSMUSG00000035493	Tgfbi	68kDa|AI181842|AI747162|Beta-ig|big-h3	transforming growth factor, beta induced	protein-coding
mm_106073.1	chr11	116173131	116173169	-	1	NA	3' UTR (NM_015729, exon 14 of 14)	3' UTR (NM_015729, exon 14 of 14)	-4972	NM_172571	217335	Mm.35241	NM_172571	ENSMUSG00000020776	Fbf1	1110033G01Rik|5930413D20|mKIAA1863	Fas (TNFRSF6) binding factor 1	protein-coding
mm_91510.1	chr10	37137275	37137293	-	1	NA	intron (NM_008538, intron 1 of 1)	CpG	1642	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_82620.1	chr9	21795062	21795075	-	1	NA	exon (NM_145611, exon 3 of 12)	exon (NM_145611, exon 3 of 12)	3478	NM_145611	235041	Mm.257371	NM_145611	ENSMUSG00000032194	Kank2	AI504612|Ankrd25|BC010245	KN motif and ankyrin repeat domains 2	protein-coding
mm_156391.1	chrX	139800969	139800979	+	1	NA	5' UTR (NM_016675, exon 1 of 2)	5' UTR (NM_016675, exon 1 of 2)	166	NM_016675	12738	Mm.117068	NM_016675	ENSMUSG00000047230	Cldn2	AL022813	claudin 2	protein-coding
mm_117069.1	chr13	59145825	59145857	-	1	NA	Intergenic	Intergenic	338144	NM_001025074	18212	Mm.130054	NM_008745	ENSMUSG00000055254	Ntrk2	GP145-TrkB/GP95-TrkB|Tkrb|trk-B|trkB	neurotrophic tyrosine kinase, receptor, type 2	protein-coding
mm_94252.1	chr11	3330880	3330912	+	1	NA	5' UTR (NM_178149, exon 1 of 6)	5' UTR (NM_178149, exon 1 of 6)	165	NM_178149	216505	Mm.390323	NM_178149	ENSMUSG00000034614	Pik3ip1	1500004A08Rik|5830455E04Rik|Crkd|Hgfl	phosphoinositide-3-kinase interacting protein 1	protein-coding
mm_14267.1	chr2	128698866	128698897	+	1	NA	promoter-TSS (NM_008587)	promoter-TSS (NM_008587)	-116	NM_008587	17289	Mm.239655	NM_008587	ENSMUSG00000014361	Mertk	Eyk|Mer|Nyk|nmf12	c-mer proto-oncogene tyrosine kinase	protein-coding
mm_4983.1	chr1	191717994	191718030	+	1	NA	promoter-TSS (NM_001134829)	promoter-TSS (NM_001134829)	-12	NM_172266	226856	Mm.277958	NM_172266	ENSMUSG00000026623	Lpgat1	AI649174|AW112037|BC013667	lysophosphatidylglycerol acyltransferase 1	protein-coding
mm_3596.1	chr1	151500003	151500013	+	1	NA	intron (NM_011277, intron 1 of 6)	intron (NM_011277, intron 1 of 6)	815	NM_011277	19821	Mm.474038	NM_011277	ENSMUSG00000026484	Rnf2	AI326319|AI450156|AU019207|Ring1B|dinG	ring finger protein 2	protein-coding
mm_8980.1	chr1	165652582	165652590	-	1	NA	intron (NM_178593, intron 6 of 6)	intron (NM_178593, intron 6 of 6)	-18045	NM_001083897	68481	Mm.46438	NM_001001880	ENSMUSG00000026566	Mpzl1	1110007A10Rik|PZR	myelin protein zero-like 1	protein-coding
mm_139772.1	chr17	64721752	64721755	+	1	NA	intron (NM_008549, intron 16 of 21)	Charlie2b|DNA|hAT-Charlie	-45358	NR_105051	101202683	Mm.393309	NR_105051		Dreh	-	down-regulated in hepatocellular carcinoma	ncRNA
mm_168763.1	chr1	21201822	21201830	-	1	NA	Intergenic	L1Md_T|LINE|L1	-16749	NM_001290679	75712	Mm.304763	NM_029398	ENSMUSG00000025933	Tmem14a	5730496E24Rik|C85783|PTD011	transmembrane protein 14A	protein-coding
mm_127679.1	chr15	102921173	102921199	+	1	NA	promoter-TSS (NM_010464)	promoter-TSS (NM_010464)	55	NM_010464	15422	Mm.207062	NM_010464	ENSMUSG00000001655	Hoxc13	-	homeobox C13	protein-coding
mm_108539.1	chr12	84285337	84285414	+	1	NA	promoter-TSS (NM_001252625)	promoter-TSS (NM_001252625)	79	NM_001252626	77219	Mm.246127	NM_029880	ENSMUSG00000072946	Ptgr2	1810016I24Rik|9130222H03Rik|9630002F03Rik|AI838763|B830026H24Rik|PGR-2|PRG-2|Zadh1	prostaglandin reductase 2	protein-coding
mm_12374.1	chr2	69822531	69822545	+	1	NA	5' UTR (NM_177784, exon 1 of 4)	5' UTR (NM_177784, exon 1 of 4)	168	NM_177784	277396	Mm.138073	NM_177784	ENSMUSG00000042155	Klhl23	C130068N17Rik	kelch-like 23	protein-coding
mm_166196.1	chr5	37245755	37245761	+	1	NA	promoter-TSS (NM_007765)	promoter-TSS (NM_007765)	-6	NM_007765	12933	Mm.290995	NM_007765	ENSMUSG00000029121	Crmp1	CRMP-1|DRP-1|Dpysl1|ULIP-3|Ulip3	collapsin response mediator protein 1	protein-coding
mm_14882.1	chr2	148835195	148835195	+	1	NA	promoter-TSS (NM_009979)	promoter-TSS (NM_009979)	48	NM_009979	13013	Mm.21005	NM_009979	ENSMUSG00000027445	Cst9	M12|cresp|testatin	cystatin 9	protein-coding
mm_122388.1	chr14	40937475	40937476	-	1	NA	intron (NM_145928, intron 1 of 8)	intron (NM_145928, intron 1 of 8)	10734	NM_001316748	52588	Mm.28876	NM_145928	ENSMUSG00000037824	Tspan14	AA958793|D14Ertd226e|Tm4sf14|tspan-14	tetraspanin 14	protein-coding
mm_28281.1	chr3	88950402	88950432	-	1	NA	promoter-TSS (NM_022994)	promoter-TSS (NM_022994)	-135	NM_001164533	65111	Mm.29028	NM_022994	ENSMUSG00000068921	Dap3	4921514D13Rik|DAP-3|MRP-S29|S29mt	death associated protein 3	protein-coding
mm_173153.1	chrX	32487961	32487961	+	1	NA	Intergenic	RLTR1B|LTR|ERV1	-72094	NM_001168334	100040482	Mm.479861	NM_001168334	ENSMUSG00000096194	Btbd35f2	Gm2799	BTB domain containing 35, family member 2	protein-coding
mm_112980.1	chr13	21312224	21312236	+	1	NA	promoter-TSS (NM_145451)	promoter-TSS (NM_145451)	27	NM_145451	75512	Mm.46195	NM_145451	ENSMUSG00000004341	Gpx6	1700020G18Rik|Ry2d1|olfactory	glutathione peroxidase 6	protein-coding
mm_83790.1	chr9	52168889	52168903	-	1	NA	promoter-TSS (NM_001162921)	promoter-TSS (NM_001162921)	-785	NM_001162921	244871	Mm.295686	NM_001162921	ENSMUSG00000035164	Zc3h12c	A230108E06|C230027N18Rik|mKIAA1726	zinc finger CCCH type containing 12C	protein-coding
mm_111564.1	chr12	101646275	101646279	-	1	NA	3' UTR (NM_028924, exon 12 of 12)	3' UTR (NM_028924, exon 12 of 12)	65296	NM_028924	74413	Mm.275939	NM_028924	ENSMUSG00000021187	Tc2n	4933406D09Rik|Mtac2d1|Tac2-N	tandem C2 domains, nuclear	protein-coding
mm_85027.1	chr9	88461023	88461026	-	1	NA	intron (NM_001311113, intron 9 of 10)	B1_Mur1|SINE|Alu	21373	NM_019666	56403	Mm.260545	NM_019666	ENSMUSG00000032423	Syncrip	2610109K23Rik|4632417O19Rik|GRY-RBP|Nsap1|Nsap1l|hnRNP Q|pp68	synaptotagmin binding, cytoplasmic RNA interacting protein	protein-coding
mm_124408.1	chr14	115477612	115477616	-	1	NA	intron (NM_175500, intron 5 of 7)	intron (NM_175500, intron 5 of 7)	-68062	NR_045761	75088	Mm.444706	NR_045761	ENSMUSG00000093551	4930505G20Rik	-	RIKEN cDNA 4930505G20 gene	ncRNA
mm_128209.1	chr15	36140423	36140433	-	1	NA	promoter-TSS (NM_001195748)	promoter-TSS (NM_001195748)	-28	NM_001195748	626596	Mm.321798	NM_001195748	ENSMUSG00000037627	Rgs22	-	regulator of G-protein signalling 22	protein-coding
mm_43358.1	chr5	135188462	135188473	+	1	NA	intron (NM_011714, intron 1 of 18)	ID_B1|SINE|B4	1144	NM_011714	22385	Mm.40331	NM_011714	ENSMUSG00000002748	Baz1b	C87820|WSTF|Wbscr9	bromodomain adjacent to zinc finger domain, 1B	protein-coding
mm_156253.1	chrX	136707977	136708040	+	1	NA	promoter-TSS (NM_146236)	promoter-TSS (NM_146236)	-57	NM_146236	237052	Mm.40713	NM_146236	ENSMUSG00000049536	Tceal1	0610011M09Rik|BC011290|P21|SIIR|pp21	transcription elongation factor A (SII)-like 1	protein-coding
mm_115696.1	chr13	14063293	14063306	-	1	NA	promoter-TSS (NM_194262)	promoter-TSS (NM_194262)	189	NM_001331119	14593	Mm.148039	NM_010282	ENSMUSG00000021302	Ggps1	1810026C22Rik|9530089B04Rik|AI843169|C79210	geranylgeranyl diphosphate synthase 1	protein-coding
mm_137598.1	chr17	28177131	28177214	+	1	NA	promoter-TSS (NM_172617)	promoter-TSS (NM_172617)	-246	NM_172617	224656	Mm.267359	NM_172617	ENSMUSG00000024220	Zfp523	2810027J07|BC025615|Znf76	zinc finger protein 523	protein-coding
mm_66082.1	chr7	30956828	30956911	-	1	NA	promoter-TSS (NM_011680)	promoter-TSS (NM_011680)	-66	NM_011680	22282	Mm.322453	NM_011680	ENSMUSG00000058239	Usf2	Usf-2|bHLHb12	upstream transcription factor 2	protein-coding
mm_153739.1	chr19	44695304	44695318	-	1	NA	Intergenic	Intergenic	-62083	NM_011037	18504	Mm.192158	NM_011037	ENSMUSG00000004231	Pax2	Opdc|Pax-2	paired box 2	protein-coding
mm_153053.1	chr19	32103161	32103169	-	1	NA	promoter-TSS (NM_018830)	promoter-TSS (NM_018830)	-25	NM_018830	54447	Mm.491229	NM_018830	ENSMUSG00000024887	Asah2	AI585898	N-acylsphingosine amidohydrolase 2	protein-coding
mm_12413.1	chr2	70533058	70533079	+	1	NA	intron (NM_025744, intron 9 of 12)	intron (NM_025744, intron 9 of 12)	24249	NM_025744	66748	Mm.423014	NM_025744	ENSMUSG00000075302	Erich2	4933404M02Rik	glutamate rich 2	protein-coding
mm_142497.1	chr17	46030933	46030942	-	1	NA	intron (NM_001317041, intron 1 of 6)	CpG	1440	NM_001287058	22339	Mm.282184	NM_009505	ENSMUSG00000023951	Vegfa	Vegf|Vpf	vascular endothelial growth factor A	protein-coding
mm_58094.1	chr6	137519872	137519876	-	1	NA	promoter-TSS (NM_001271589)	promoter-TSS (NM_001271589)	21	NM_001271589	13860	Mm.235346	NM_007945	ENSMUSG00000015766	Eps8	AW261790	epidermal growth factor receptor pathway substrate 8	protein-coding
mm_109567.1	chr12	111971609	111971619	+	1	NA	promoter-TSS (NM_029056)	promoter-TSS (NM_029056)	55	NM_029056	74691	Mm.60648	NM_029056	ENSMUSG00000054003	Tdrd9	4930441E05Rik	tudor domain containing 9	protein-coding
mm_90039.1	chr10	115817328	115817342	+	1	NA	promoter-TSS (NM_001168680)	promoter-TSS (NM_001168680)	51	NM_001168679	216350	Mm.22270	NM_146010	ENSMUSG00000034127	Tspan8	C76990|E330007O21Rik|Tm4sf3	tetraspanin 8	protein-coding
mm_77883.1	chr9	7280854	7280875	+	1	NA	exon (NM_008607, exon 9 of 10)	exon (NM_008607, exon 9 of 10)	8350	NM_008607	17386	Mm.5022	NM_008607	ENSMUSG00000050578	Mmp13	Clg|MMP-13|Mmp1	matrix metallopeptidase 13	protein-coding
mm_36278.1	chr4	63745056	63745061	-	1	NA	promoter-TSS (NM_177371)	promoter-TSS (NM_177371)	55	NM_177371	326623	Mm.208152	NM_177371	ENSMUSG00000050395	Tnfsf15	Tl1|Tl1a|Tnlg1b|Vegi	tumor necrosis factor (ligand) superfamily, member 15	protein-coding
mm_99338.1	chr11	101468237	101468249	+	1	NA	promoter-TSS (NM_009708)	promoter-TSS (NM_009708)	-95	NM_009708	11858	Mm.378883	NM_009708	ENSMUSG00000001313	Rnd2	Arhn|Rohn	Rho family GTPase 2	protein-coding
mm_38831.1	chr4	149143460	149143467	-	1	NA	Intergenic	Intergenic	-5863	NM_027263	69928	Mm.260893	NM_027263	ENSMUSG00000073705	Apitd1	2610040C18Rik|2810407L01Rik|CENP-S	apoptosis-inducing, TAF9-like domain 1	protein-coding
mm_82565.1	chr9	21075242	21075264	-	1	NA	TTS (NR_106050)	TTS (NR_106050)	335	NR_106050	102465656		NR_106050	ENSMUSG00000098907	Mir7082	Gm27933|mmu-mir-7082	microRNA 7082	ncRNA
mm_24822.1	chr3	95650890	95650906	+	1	NA	Intergenic	PB1D11|SINE|Alu	-7823	NM_008562	17210	Mm.1639	NM_008562	ENSMUSG00000038612	Mcl1	AW556805|Mcl-1	myeloid cell leukemia sequence 1	protein-coding
mm_852.1	chr1	52119535	52119557	+	1	NA	promoter-TSS (NM_001205313)	promoter-TSS (NM_001205313)	-76	NM_001205313	20846	Mm.277406	NM_009283	ENSMUSG00000026104	Stat1	2010005J02Rik|AA408197	signal transducer and activator of transcription 1	protein-coding
mm_149092.1	chr19	8929451	8929477	+	1	NA	promoter-TSS (NM_144872)	promoter-TSS (NM_144872)	-108	NM_009073	19881	Mm.426094	NM_009073	ENSMUSG00000071648	Rom1	M101156|Rgsc1156|Rom-1|Rosp1|Tspan23	rod outer segment membrane protein 1	protein-coding
mm_133540.1	chr16	91064241	91064245	+	1	NA	intron (NM_028905, intron 1 of 2)	RMER5|LTR|ERV1	4902	NM_001163695	74387	Mm.236220	NM_028905	ENSMUSG00000039851	4932438H23Rik	4931406G06Rik|AI550392	RIKEN cDNA 4932438H23 gene	protein-coding
mm_6160.1	chr1	65048648	65048652	-	1	NA	TTS (NM_007777)	TTS (NM_007777)	2513	NM_007777	12968	Mm.258170	NM_007777	ENSMUSG00000070870	Cryge	Cryg-2|Cryg-6|DGcry-2|Elo	crystallin, gamma E	protein-coding
mm_156515.1	chrX	150565227	150565241	+	1	NA	exon (NM_009653, exon 9 of 11)	exon (NM_009653, exon 9 of 11)	-17789	NR_106147	102465782		NR_106147	ENSMUSG00000099172	Mir3620	Gm27984|mmu-mir-3620	microRNA 3620	ncRNA
mm_121562.1	chr14	122484435	122484443	+	1	NA	Intergenic	Intergenic	9055	NM_009574	22772	Mm.308936	NM_009574	ENSMUSG00000061524	Zic2	HPE5|Ku	zinc finger protein of the cerebellum 2	protein-coding
mm_20492.1	chr2	130279359	130279374	-	1	NA	TTS (NM_130884)	TTS (NM_130884)	1340	NR_028528	100217428		NR_028528	ENSMUSG00000065272	Snord57	MBII-434	small nucleolar RNA, C/D box 57	snoRNA
mm_149229.1	chr19	10177398	10177403	+	1	NA	Intergenic	MER57C2|LTR|ERV1	-5488	NM_146094	76267	Mm.30158	NM_146094	ENSMUSG00000010663	Fads1	0710001O03Rik|A930006B21Rik|AI317215|DSD	fatty acid desaturase 1	protein-coding
mm_136736.1	chr17	8340400	8340406	+	1	NA	promoter-TSS (NM_178774)	promoter-TSS (NM_178774)	-3	NR_028280	320111	Mm.442510	NM_178774	ENSMUSG00000055945	Prr18	9630019K15Rik	proline rich 18	protein-coding
mm_61772.1	chr7	83584911	83584942	+	1	NA	promoter-TSS (NM_177695)	promoter-TSS (NM_177695)	-5	NM_177695	233424	Mm.486619	NM_177695	ENSMUSG00000038540	Tmc3	9030203A06	transmembrane channel-like gene family 3	protein-coding
mm_1978.1	chr1	86528863	86528873	+	1	NA	intron (NM_008972, intron 1 of 4)	intron (NM_008972, intron 1 of 4)	2132	NM_008972	19231	Mm.19187	NM_008972	ENSMUSG00000026238	Ptma	Thym	prothymosin alpha	protein-coding
mm_161727.1	chr17	28953221	28953221	+	1	NA	promoter-TSS (NM_025888)	promoter-TSS (NM_025888)	5	NM_025888	66989	Mm.435	NM_025888	ENSMUSG00000005936	Kctd20	2410004N11Rik|AI451943|AW541186|D17Ertd562e	potassium channel tetramerisation domain containing 20	protein-coding
mm_147079.1	chr18	35619637	35619651	-	1	NA	exon (NM_011397, exon 14 of 15)	exon (NM_011397, exon 14 of 15)	7583	NM_011397	20522	Mm.22702	NM_011397	ENSMUSG00000024354	Slc23a1	D18Ucla2|SVCT1|Slc23a2|YSPL3	solute carrier family 23 (nucleobase transporters), member 1	protein-coding
mm_160685.1	chr10	20323117	20323117	+	1	NA	exon (NM_001025393, exon 4 of 12)	exon (NM_001025393, exon 4 of 12)	10648	NM_001025393	72567	Mm.294783	NM_153787	ENSMUSG00000037608	Bclaf1	2610102K23Rik|2700025J07Rik|2810454G14Rik|5730534O06Rik|AI450190|AW556225|Btf|mKIAA0164	BCL2-associated transcription factor 1	protein-coding
mm_45690.1	chr5	77408035	77408051	-	1	NA	promoter-TSS (NM_008048)	promoter-TSS (NM_008048)	2	NM_001159518	29817	Mm.233470	NM_008048	ENSMUSG00000036256	Igfbp7	AGM|Fstl2|Mac25	insulin-like growth factor binding protein 7	protein-coding
mm_167967.1	chrX	152016419	152016427	+	1	NA	promoter-TSS (NM_025660)	promoter-TSS (NM_025660)	-5	NM_019710	24061	Mm.482095	NM_019710	ENSMUSG00000041133	Smc1a	5830426I24Rik|SMC-1A|Sb1.8|Smc1|Smc1alpha|Smc1l1|Smcb|mKIAA0178	structural maintenance of chromosomes 1A	protein-coding
mm_134803.1	chr16	24382388	24382391	-	1	NA	Intergenic	RMER4B|LTR|ERVK	-10961	NM_178665	210126	Mm.209385	NM_178665	ENSMUSG00000033306	Lpp	9430020K16Rik|AA959454|AU024130|B130055L10Rik|C79715|D630048H16	LIM domain containing preferred translocation partner in lipoma	protein-coding
mm_71827.1	chr8	68896686	68896688	+	1	NA	exon (NM_008509, exon 6 of 10)	exon (NM_008509, exon 6 of 10)	16132	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_158261.1	chrX	109013373	109013388	-	1	NA	promoter-TSS (NM_016710)	promoter-TSS (NM_016710)	0	NM_016710	50887	Mm.298443	NM_016710	ENSMUSG00000031245	Hmgn5	GARP45|NBP-45|Nsbp1	high-mobility group nucleosome binding domain 5	protein-coding
mm_111711.1	chr12	103695581	103695592	-	1	NA	promoter-TSS (NM_001164742)	promoter-TSS (NM_001164742)	-57	NM_026687	68348	Mm.20149	NM_026687	ENSMUSG00000021081	Serpina1f	0610012A11Rik|AI327419|Serpina2|epserin	serine (or cysteine) peptidase inhibitor, clade A, member 1F	protein-coding
mm_47359.1	chr5	122821259	122821292	-	1	NA	promoter-TSS (NM_021505)	promoter-TSS (NM_021505)	67	NM_021505	59008	Mm.332667	NM_021505	ENSMUSG00000029472	Anapc5	2510006G12Rik|AA408751|AA536819|AA986414|APC5|Anpc5	anaphase-promoting complex subunit 5	protein-coding
mm_44050.1	chr5	147873247	147873257	+	1	NA	intron (NM_025624, intron 5 of 5)	intron (NM_025624, intron 5 of 5)	12624	NM_025624	66537	Mm.332855	NM_025624	ENSMUSG00000029649	Pomp	2510048O06Rik|Ump1	proteasome maturation protein	protein-coding
mm_62957.1	chr7	119720418	119720425	+	1	NA	intron (NM_145585, intron 1 of 3)	CpG	377	NM_145585	233802	Mm.26392	NM_145585	ENSMUSG00000030942	Thumpd1	6330575P11Rik	THUMP domain containing 1	protein-coding
mm_102604.1	chr11	62395197	62395218	-	1	NA	exon (NM_001252313, exon 10 of 45)	exon (NM_001252313, exon 10 of 45)	43308	NM_001252313	20185	Mm.271814	NM_011308	ENSMUSG00000018501	Ncor1	5730405M06Rik|A230020K14Rik|N-CoR|RIP13|Rxrip13|mKIAA1047	nuclear receptor co-repressor 1	protein-coding
mm_65054.1	chr7	18711220	18711223	-	1	NA	Intergenic	RMER2|LTR|ERV1	-6869	NM_001004152	243862	Mm.389833	NM_001004152	ENSMUSG00000044903	Psg22	AA408604|cea9	pregnancy-specific glycoprotein 22	protein-coding
mm_69339.1	chr7	129649012	129649026	-	1	NA	Intergenic	Intergenic	57156	NM_172255	207425	Mm.229323	NM_172255	ENSMUSG00000042055	Wdr11	2900055P10Rik|AW489876|Brwd2|mKIAA1351	WD repeat domain 11	protein-coding
mm_113261.1	chr13	28839391	28839398	+	1	NA	intron (NR_045053, intron 2 of 8)	intron (NR_045053, intron 2 of 8)	46028	NR_045054	72518	Mm.37454	NR_045053		2610307P16Rik	AI666457	RIKEN cDNA 2610307P16 gene	ncRNA
mm_98037.1	chr11	85339700	85339759	+	1	NA	exon (NM_016910, exon 5 of 6)	exon (NM_016910, exon 5 of 6)	-13435	NM_001166642	192197	Mm.209989	NM_138681	ENSMUSG00000059439	Bcas3	1500019F07Rik|2610028P08Rik|AU021018|BC028339|K20D4|rudhira	breast carcinoma amplified sequence 3	protein-coding
mm_53771.1	chr6	145934138	145934161	+	1	NA	promoter-TSS (NM_010656)	promoter-TSS (NM_010656)	2	NM_010656	16651	Mm.49689	NM_010656	ENSMUSG00000030255	Sspn	Krag	sarcospan	protein-coding
mm_166504.1	chr6	4747432	4747441	+	1	NA	promoter-TSS (NM_001130188)	promoter-TSS (NM_001130188)	130	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_169435.1	chr14	5501672	5501678	+	1	NA	Intergenic	CpG	-14604	NM_001256885	100041735	Mm.464176	NM_001256885	ENSMUSG00000095295	Gm3488	100041747|Gm3494	predicted gene, 3488	protein-coding
mm_79585.1	chr9	58253288	58253311	+	1	NA	exon (NM_026942, exon 1 of 7)	exon (NM_026942, exon 1 of 7)	135	NM_026942	69106	Mm.216502	NM_026942	ENSMUSG00000032333	Stoml1	1810015E19Rik|AI847431|SLP1|STORP|UNC24|WPB72	stomatin-like 1	protein-coding
mm_149885.1	chr19	25383453	25383465	+	1	NA	intron (NM_181404, intron 4 of 13)	intron (NM_181404, intron 4 of 13)	-122247	NM_015826	50796	Mm.391208	NM_015826	ENSMUSG00000024837	Dmrt1	-	doublesex and mab-3 related transcription factor 1	protein-coding
mm_105589.1	chr11	106725265	106725270	-	1	NA	Intergenic	U3|snRNA|snRNA	-9986	NM_001305157	18613	Mm.343951	NM_008816	ENSMUSG00000020717	Pecam1	C85791|Cd31|PECAM-1|Pecam	platelet/endothelial cell adhesion molecule 1	protein-coding
mm_67393.1	chr7	79848174	79848190	-	1	NA	Intergenic	Intergenic	-5830	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_20753.1	chr2	140592375	140592375	-	1	NA	intron (NM_001013802, intron 3 of 18)	intron (NM_001013802, intron 3 of 18)	79101	NM_001172160	71436	Mm.426781	NM_178382	ENSMUSG00000051379	Flrt3	5530600M07Rik|C430047I10Rik|mKIAA1469	fibronectin leucine rich transmembrane protein 3	protein-coding
mm_45975.1	chr5	90470824	90470844	-	1	NA	exon (NM_009654, exon 10 of 15)	exon (NM_009654, exon 10 of 15)	9964	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_89011.1	chr10	81643595	81643680	+	1	NA	exon (NM_027480, exon 17 of 20)	exon (NM_027480, exon 17 of 20)	-5432	NM_001142963	100233208	Mm.327168	NM_001142963	ENSMUSG00000096856	Gm10778	ENSMUSG00000074860	predicted gene 10778	protein-coding
mm_133341.1	chr16	81200748	81200766	+	1	NA	promoter-TSS (NM_010954)	promoter-TSS (NM_010954)	60	NM_010954	17968	Mm.433941	NM_010954	ENSMUSG00000022762	Ncam2	Ncam-2|Ocam|RNCAM	neural cell adhesion molecule 2	protein-coding
mm_130582.1	chr15	99534894	99534913	-	1	NA	Intergenic	Lx8|LINE|L1	-6738	NM_001038658	72393	Mm.39760	NM_028224	ENSMUSG00000023011	Faim2	2900002L20Rik|Lfg|Lfg2|NMP25|Nmp35|Tmbim2	Fas apoptotic inhibitory molecule 2	protein-coding
mm_114095.1	chr13	54701436	54701446	+	1	NA	promoter-TSS (NM_001033364)	promoter-TSS (NM_001033364)	-22	NM_001033364	268663	Mm.315382	NM_001033364	ENSMUSG00000034918	Cdhr2	Gm624|PC-LKC|Pcdh24	cadherin-related family member 2	protein-coding
mm_56085.1	chr6	87335536	87335561	-	1	NA	5' UTR (NM_054041, exon 1 of 18)	5' UTR (NM_054041, exon 1 of 18)	227	NM_054041	69538	Mm.232525	NM_054041	ENSMUSG00000033420	Antxr1	2310008J16Rik|2810405N18Rik|Antrx1|Tem8	anthrax toxin receptor 1	protein-coding
mm_151984.1	chr19	5841882	5841884	-	1	NA	TTS (NR_003513)	TTS (NR_003513)	3595	NR_131212	66961	Mm.281895	NR_003513	ENSMUSG00000092274	Neat1	2310043N10Rik|VINC	nuclear paraspeckle assembly transcript 1 (non-protein coding)	ncRNA
mm_39063.1	chr4	154025927	154025992	-	1	NA	promoter-TSS (NM_001163722)	promoter-TSS (NM_001163722)	85	NM_001163722	68859	Mm.477488	NM_001033144	ENSMUSG00000078350	Smim1	0610011H04Rik|1190007F08Rik|2700009I11Rik	small integral membrane protein 1	protein-coding
mm_80931.1	chr9	102626279	102626328	+	1	NA	promoter-TSS (NM_181394)	promoter-TSS (NM_181394)	7	NM_181394	69010	Mm.2000	NM_181394	ENSMUSG00000035048	Anapc13	1810004D07Rik|APC13|SWM1	anaphase promoting complex subunit 13	protein-coding
mm_77599.1	chr8	123892627	123892744	-	1	NA	exon (NM_009606, exon 5 of 7)	exon (NM_009606, exon 5 of 7)	2090	NM_001272041	11459	Mm.214950	NM_009606	ENSMUSG00000031972	Acta1	AA959943|Acta-2|Acts|Actsk-1	actin, alpha 1, skeletal muscle	protein-coding
mm_27706.1	chr3	67463829	67463943	-	1	NA	promoter-TSS (NM_016753)	promoter-TSS (NM_016753)	21	NM_016753	17035	Mm.2632	NM_016753	ENSMUSG00000047557	Lxn	-	latexin	protein-coding
mm_94904.1	chr11	29198870	29198884	+	1	NA	exon (NM_134034, exon 8 of 16)	exon (NM_134034, exon 8 of 16)	25970	NM_134034	104570	Mm.276386	NM_134034	ENSMUSG00000020463	Smek2	AW011752|AW557776|Ppp4r3b|mKIAA1387	SMEK homolog 2, suppressor of mek1 (Dictyostelium)	protein-coding
mm_23651.1	chr3	67582727	67582729	+	1	NA	promoter-TSS (NM_025813)	promoter-TSS (NM_025813)	-40	NM_025813	66868	Mm.491153	NM_025813	ENSMUSG00000027775	Mfsd1	1200003O06Rik	major facilitator superfamily domain containing 1	protein-coding
mm_2036.1	chr1	87214060	87214068	+	1	NA	5' UTR (NM_001039169, exon 1 of 7)	5' UTR (NM_001039169, exon 1 of 7)	125	NM_001039169	26987	Mm.227183	NM_023314	ENSMUSG00000026254	Eif4e2	2700069E09Rik|AI036339|AV129531|D0H0S6743E|Eif4el3	eukaryotic translation initiation factor 4E member 2	protein-coding
mm_149793.1	chr19	23141643	23141667	+	1	NA	5' UTR (NM_010638, exon 1 of 2)	5' UTR (NM_010638, exon 1 of 2)	429	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_38891.1	chr4	149774050	149774060	-	1	NA	exon (NM_027460, exon 1 of 7)	exon (NM_027460, exon 1 of 7)	212	NM_027460	70556	Mm.41877	NM_027460	ENSMUSG00000028982	Slc25a33	5730438N18Rik|Pnc1	solute carrier family 25, member 33	protein-coding
mm_101076.1	chr11	11685625	11685655	-	1	NA	promoter-TSS (NM_009578)	promoter-TSS (NM_009578)	-285	NM_009578	22778	Mm.103545	NM_009578	ENSMUSG00000018654	Ikzf1	5832432G11Rik|Ikaros|LyF-1|Zfpn1a1|Znfn1a1|hlk-1|mKIAA4227	IKAROS family zinc finger 1	protein-coding
mm_4135.1	chr1	170644491	170644514	+	1	NA	promoter-TSS (NM_177068)	promoter-TSS (NM_177068)	-30	NM_177068	320078	Mm.287131	NM_177068	ENSMUSG00000038463	Olfml2b	1110018N05Rik|4832415H08Rik|AI467542	olfactomedin-like 2B	protein-coding
mm_104149.1	chr11	87074121	87074131	-	1	NA	promoter-TSS (NM_025638)	promoter-TSS (NM_025638)	11	NM_025638	66569	Mm.281887	NM_025638	ENSMUSG00000061666	Gdpd1	2610020H15Rik	glycerophosphodiester phosphodiesterase domain containing 1	protein-coding
mm_131609.1	chr16	19236392	19236403	+	1	NA	Intergenic	L1_Mur2|LINE|L1	50344	NM_146451	258443	Mm.377506	NM_146451	ENSMUSG00000050742	Olfr164	MOR279-2	olfactory receptor 164	protein-coding
mm_164795.1	chr18	20059371	20059373	-	1	NA	5' UTR (NM_013505, exon 1 of 17)	5' UTR (NM_013505, exon 1 of 17)	182	NM_013505	13506	Mm.280547	NM_013505	ENSMUSG00000024331	Dsc2	AW228162	desmocollin 2	protein-coding
mm_20669.1	chr2	132146254	132146255	-	1	NA	Intergenic	PB1D10|SINE|Alu	-1146	NM_018824	54338	Mm.103581	NM_018824	ENSMUSG00000027340	Slc23a2	AI844736|NBTL1|SVCT2|Slc23a1|YSPL2|YSPL3|mKIAA0238	solute carrier family 23 (nucleobase transporters), member 2	protein-coding
mm_33920.1	chr4	136540945	136540967	+	1	NA	exon (NM_024452, exon 4 of 5)	exon (NM_024452, exon 4 of 5)	61767	NM_133872	99982	Mm.28540	NM_133872	ENSMUSG00000036940	Kdm1a	1810043O07Rik|AA408884|Aof2|D4Ertd478e|Kdm1|Lsd1|mKIAA0601	lysine (K)-specific demethylase 1A	protein-coding
mm_100435.1	chr11	119476049	119476055	+	1	NA	Intergenic	Intergenic	-15295	NM_001164636	338371	Mm.271946	NM_177394	ENSMUSG00000039850	Endov	A730011L01Rik	endonuclease V	protein-coding
mm_97204.1	chr11	75598896	75598907	+	1	NA	TTS (NR_110477)	TTS (NR_110477)	1330	NR_110477	654359	Mm.439961	NR_110477		Gm12338	OTTMUSG00000006216	cytochrome c oxidase, subunit VIIc pseudogene	pseudo
mm_65953.1	chr7	30426182	30426203	-	1	NA	exon (NM_172142, exon 8 of 11)	exon (NM_172142, exon 8 of 11)	2888	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_102253.1	chr11	55151699	55151699	-	1	NA	promoter-TSS (NM_172258)	promoter-TSS (NM_172258)	7	NM_172258	215332	Mm.87054	NM_172258	ENSMUSG00000049491	Slc36a3	PAT3|TRAMD2|tramdorin2	solute carrier family 36 (proton/amino acid symporter), member 3	protein-coding
mm_54778.1	chr6	41541754	41541777	-	1	NA	Intergenic	Intergenic	19989	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_170453.1	chr18	85382563	85382569	-	1	NA	Intergenic	IAPLTR1_Mm|LTR|ERVK	-431042	NM_025969	67105	Mm.250617	NM_025969	ENSMUSG00000024645	Timm21	1700034H14Rik|2700002I20Rik	tranlocase of inner mitochondrial membrane 21	protein-coding
mm_37172.1	chr4	117182624	117182636	-	1	NA	promoter-TSS (NM_134471)	promoter-TSS (NM_134471)	-6	NM_134471	73804	Mm.247651	NM_134471	ENSMUSG00000028678	Kif2c	4930402F02Rik|ESTM5|Knsl6|MCAK|X83316	kinesin family member 2C	protein-coding
mm_48373.1	chr5	139484392	139484408	-	1	NA	promoter-TSS (NM_001159908)	promoter-TSS (NM_001159908)	91	NM_133349	100494	Mm.24521	NM_133349	ENSMUSG00000053581	Zfand2a	AA407930|AU016206|Airap	zinc finger, AN1-type domain 2A	protein-coding
mm_23363.1	chr3	55242654	55242664	+	1	NA	5' UTR (NM_001195538, exon 1 of 17)	5' UTR (NM_001195538, exon 1 of 17)	133	NM_001195538	13175	Mm.393242	NM_019978	ENSMUSG00000027797	Dclk1	1700113D08Rik|2810480F11Rik|AI836758|Click-I|Cpg16|Dcamkl1|Dcl|Dclk|mKIAA0369	doublecortin-like kinase 1	protein-coding
mm_64010.1	chr7	140207269	140207281	+	1	NA	Intergenic	Intergenic	-4507	NM_001011814	258055	Mm.377339	NM_001011814	ENSMUSG00000050366	Olfr524	MOR103-14P	olfactory receptor 524	protein-coding
mm_98682.1	chr11	96286779	96286791	+	1	NA	exon (NM_010460, exon 1 of 2)	exon (NM_010460, exon 1 of 2)	139	NM_010460	15415	Mm.390366	NM_010460	ENSMUSG00000038721	Hoxb7	AI325018|Hox-2.3	homeobox B7	protein-coding
mm_67693.1	chr7	89517872	89517885	-	1	NA	promoter-TSS (NM_029614)	promoter-TSS (NM_029614)	-292	NM_029614	76453	Mm.250438	NM_029614	ENSMUSG00000039405	Prss23	2310046G15Rik|4930479H08Rik|AI790574|Spuve	protease, serine 23	protein-coding
mm_111350.1	chr12	86949570	86949583	-	1	NA	intron (NM_001289432, intron 1 of 4)	intron (NM_001289432, intron 1 of 4)	2233	NM_001289432	217732	Mm.22337	NM_173735	ENSMUSG00000034157	Cipc	2310044G17Rik|AI842544|AI853744|Kiaa1737|mKIAA1737	CLOCK interacting protein, circadian	protein-coding
mm_18303.1	chr2	53146140	53146156	-	1	NA	exon (NM_018785, exon 17 of 26)	exon (NM_018785, exon 17 of 26)	45039	NM_018785	56194	Mm.257474	NM_018785	ENSMUSG00000061136	Prpf40a	2810012K09Rik|FBP-11|FBP11|Fnbp11|Fnbp3	pre-mRNA processing factor 40A	protein-coding
mm_33879.1	chr4	136172429	136172442	+	1	NA	5' UTR (NM_177733, exon 1 of 7)	5' UTR (NM_177733, exon 1 of 7)	161	NM_177733	242705	Mm.307932	NM_177733	ENSMUSG00000018983	E2f2	E2F-2	E2F transcription factor 2	protein-coding
mm_73910.1	chr8	119575355	119575361	+	1	NA	promoter-TSS (NM_175185)	promoter-TSS (NM_175185)	123	NM_026648	68270	Mm.41977	NM_026648	ENSMUSG00000031831	Dnaaf1	4930457P18Rik|Lrrc50	dynein, axonemal assembly factor 1	protein-coding
mm_50445.1	chr6	48874834	48874842	+	1	NA	Intergenic	Intergenic	-20417	NM_029638	76507	Mm.213898	NM_029638	ENSMUSG00000029811	Aoc1	1600012D06Rik|Abp1|DAO	amine oxidase, copper-containing 1	protein-coding
mm_71668.1	chr8	60673361	60673366	+	1	NA	3' UTR (NM_001177882, exon 3 of 3)	3' UTR (NM_001177882, exon 3 of 3)	17806	NM_001177882	71306	Mm.23242	NM_027756	ENSMUSG00000031647	Mfap3l	4933428A15Rik|5430405D20Rik|AI461995|AW125052|NYD-sp9|mKIAA0626	microfibrillar-associated protein 3-like	protein-coding
mm_172836.1	chr9	26406775	26406793	-	1	NA	Intergenic	L1Md_T|LINE|L1	-327024	NM_001310766	76898	Mm.218788	NM_029792	ENSMUSG00000045994	B3gat1	0710007K08Rik|AI846286|GlcAT-P|Glcatp|Hnk1	beta-1,3-glucuronyltransferase 1 (glucuronosyltransferase P)	protein-coding
mm_126419.1	chr15	80320182	80320203	+	1	NA	intron (NM_001044308, intron 2 of 36)	intron (NM_001044308, intron 2 of 36)	32954	NM_001044308	239556	Mm.291058	NM_001044308	ENSMUSG00000022416	Cacna1i	Ca(V)3.3	calcium channel, voltage-dependent, alpha 1I subunit	protein-coding
mm_108087.1	chr12	74208360	74208360	+	1	NA	intron (NM_172804, intron 2 of 6)	MTC|LTR|ERVL-MaLR	-75916	NR_030734	74284	Mm.287421	NR_030733	ENSMUSG00000071265	1700086L19Rik	1700006L05Rik|AU016007	RIKEN cDNA 1700086L19 gene	ncRNA
mm_96057.1	chr11	59566348	59566356	+	1	NA	3' UTR (NM_145827, exon 10 of 10)	3' UTR (NM_145827, exon 10 of 10)	5386	NM_001011789	257962	Mm.377316	NM_001011789	ENSMUSG00000059610	Olfr222	MOR256-45P	olfactory receptor 222	protein-coding
mm_159016.1	chr1	171150710	171150710	+	1	NA	promoter-TSS (NM_025321)	promoter-TSS (NM_025321)	-3	NM_008623	17528	Mm.9986	NM_008623	ENSMUSG00000056569	Mpz	Mpp|P-zero|P0	myelin protein zero	protein-coding
mm_80547.1	chr9	82829819	82829834	+	1	NA	promoter-TSS (NM_001168240)	promoter-TSS (NM_001168240)	20	NM_022986	65099	Mm.41415	NM_022986	ENSMUSG00000032251	Irak1bp1	4921528N06Rik|AI851240|Aabp3|Aip70|Simpl	interleukin-1 receptor-associated kinase 1 binding protein 1	protein-coding
mm_65771.1	chr7	28761771	28761818	-	1	NA	exon (NM_010908, exon 3 of 7)	exon (NM_010908, exon 3 of 7)	4850	NM_001306222	18036	Mm.220333	NM_010908	ENSMUSG00000030595	Nfkbib	I(Kappa)B(beta)|I-kappa-B-beta|IKB-beta|IKappaBbeta|IkB|IkBb|NF-kappa-BIB|ikB-B	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, beta	protein-coding
mm_126328.1	chr15	79891694	79891704	+	1	NA	promoter-TSS (NM_001160415)	promoter-TSS (NM_001160415)	-709	NM_001160415	80287	Mm.284059	NM_030255	ENSMUSG00000009585	Apobec3	Apobec|Arp3|BC003314|Cem15|Rfv3	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 3	protein-coding
mm_31803.1	chr4	65123749	65123768	+	1	NA	promoter-TSS (NM_021362)	promoter-TSS (NM_021362)	-416	NM_021362	18491	Mm.317854	NM_021362	ENSMUSG00000028370	Pappa	8430414N03Rik|IGFBP-4ase|PAG1|PAPP-A	pregnancy-associated plasma protein A	protein-coding
mm_30836.1	chr4	22357545	22357618	+	1	NA	promoter-TSS (NM_172988)	promoter-TSS (NM_172988)	38	NR_104380	269514	Mm.40708	NM_172988	ENSMUSG00000040410	Fbxl4	AI836810|FBL4|FBL5	F-box and leucine-rich repeat protein 4	protein-coding
mm_31129.1	chr4	43059029	43059045	+	1	NA	promoter-TSS (NM_021468)	promoter-TSS (NM_021468)	84	NM_001310758	22249	Mm.128892	NM_021468	ENSMUSG00000028456	Unc13b	Munc13-1|Munc13-2|Unc13a|Unc13h1|Unc13h2	unc-13 homolog B (C. elegans)	protein-coding
mm_31617.1	chr4	59035494	59035501	+	1	NA	intron (NM_025277, intron 1 of 2)	CpG	341	NM_025277	14700	Mm.41780	NM_025277	ENSMUSG00000038607	Gng10	AV006524	guanine nucleotide binding protein (G protein), gamma 10	protein-coding
mm_113996.1	chr13	52583333	52583351	+	1	NA	promoter-TSS (NM_001198977)	promoter-TSS (NM_001198977)	-95	NM_001198977	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_144080.1	chr17	91093019	91093029	-	1	NA	promoter-TSS (NM_020252)	promoter-TSS (NM_020252)	-222	NM_020252	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_28048.1	chr3	84040257	84040263	-	1	NA	promoter-TSS (NM_172681)	promoter-TSS (NM_172681)	-99	NM_172681	229473	Mm.28838	NM_172681	ENSMUSG00000033767	D930015E06Rik	Kiaa0922|mKIAA0922	RIKEN cDNA D930015E06 gene	protein-coding
mm_25215.1	chr3	103846858	103846865	+	1	NA	intron (NM_001142960, intron 3 of 3)	intron (NM_001142960, intron 3 of 3)	-12934	NR_104070	19260	Mm.395	NM_008979	ENSMUSG00000027843	Ptpn22	70zpep|PEP|Ptpn8	protein tyrosine phosphatase, non-receptor type 22 (lymphoid)	protein-coding
mm_148484.1	chr19	4148617	4148666	+	1	NA	promoter-TSS (NM_011778)	promoter-TSS (NM_011778)	-22	NM_011778	23789	Mm.276859	NM_011778	ENSMUSG00000024835	Coro1b	-	coronin, actin binding protein 1B	protein-coding
mm_118536.1	chr14	16249260	16249366	+	1	NA	promoter-TSS (NM_021504)	promoter-TSS (NM_021504)	-1	NM_021504	59007	Mm.258381	NM_021504	ENSMUSG00000021785	Ngly1	1110002C09Rik|PNGase|Png1	N-glycanase 1	protein-coding
mm_129377.1	chr15	78172416	78172459	-	1	NA	intron (NM_025931, intron 1 of 6)	intron (NM_025931, intron 1 of 6)	1671	NM_025931	67042	Mm.30191	NM_025931	ENSMUSG00000016637	Ift27	2600013G09Rik|Rabl4	intraflagellar transport 27	protein-coding
mm_147996.1	chr18	67675871	67675882	-	1	NA	exon (NM_001127177, exon 8 of 9)	exon (NM_001127177, exon 8 of 9)	34277	NM_134138	107047	Mm.150701	NM_134138	ENSMUSG00000024537	Psmg2	1700017I17Rik|AW545363|Clast3|Tnfsf5ip1	proteasome (prosome, macropain) assembly chaperone 2	protein-coding
mm_146048.1	chr18	69593515	69593532	+	1	NA	intron (NM_013685, intron 8 of 19)	intron (NM_013685, intron 8 of 19)	247802	NM_001083967	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding
mm_171213.1	chr3	5860783	5860788	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-284537	NM_001163305	19302	Mm.132336	NM_008994	ENSMUSG00000040374	Pex2	D3Ertd138e|PAF-1|PMP35|Pxmp3	peroxisomal biogenesis factor 2	protein-coding
mm_82714.1	chr9	24542105	24542124	-	1	NA	Intergenic	SYNREP_MM|Satellite|Satellite	-38974	NM_172920	244745	Mm.38526	NM_172920	ENSMUSG00000043067	Dpy19l1	1100001I19Rik|6030402K12|AI225861|AW558481	dpy-19-like 1 (C. elegans)	protein-coding
mm_125260.1	chr15	35371156	35371168	+	1	NA	promoter-TSS (NM_177151)	promoter-TSS (NM_177151)	-384	NM_177151	666173	Mm.309250	NM_177151	ENSMUSG00000037646	Vps13b	1810042B05Rik|2310042E16Rik|4732488H20|C330002D13Rik|C87206|Coh1|D230005K13|mKIAA0532|mKIAA5032	vacuolar protein sorting 13B	protein-coding
mm_32227.1	chr4	102087616	102087694	+	1	NA	Intergenic	CpG	100815	NM_001085520	381536	Mm.297685	NM_001085520	ENSMUSG00000078625	Gm12789	OTTMUSG00000008445	predicted gene 12789	protein-coding
mm_28254.1	chr3	88552844	88552855	-	1	NA	promoter-TSS (NM_033526)	promoter-TSS (NM_033526)	78	NM_031248	83409	Mm.41680	NM_031248	ENSMUSG00000028062	Lamtor2	2010111E04Rik|AL022628|Mapbpip|P14|Rab25|Robld3	late endosomal/lysosomal adaptor, MAPK and MTOR activator 2	protein-coding
mm_171274.1	chr3	88775250	88775251	+	1	NA	Intergenic	CpG	-1807	NR_028359	100302730	Mm.482358	NR_028359		5830417I10Rik	3632445O20Rik|AA387005	gon-4-like pseudogene	pseudo
mm_166600.1	chr6	67532567	67532577	-	1	NA	Intergenic	Intergenic	3250	NM_020047	56753	Mm.439913	NM_020047	ENSMUSG00000051397	Tacstd2	C80403|EGP-1|GA733-1|Ly97|TROP2	tumor-associated calcium signal transducer 2	protein-coding
mm_29222.1	chr3	107212803	107212813	-	1	NA	exon (NM_001111143, exon 8 of 9)	exon (NM_001111143, exon 8 of 9)	8924	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_61470.1	chr7	75612213	75612227	+	1	NA	intron (NM_029332, intron 7 of 36)	intron (NM_029332, intron 7 of 36)	156686	NM_029332	75547	Mm.216107	NM_029332	ENSMUSG00000066406	Akap13	1700026G02Rik|5730522G15Rik|5830460E08Rik|AKAP-13|AKAP-Lbc|BRX|Ht31|LBC|PROTO-LB|PROTO-LBC	A kinase (PRKA) anchor protein 13	protein-coding
mm_120544.1	chr14	67297991	67297995	+	1	NA	intron (NM_010095, intron 7 of 16)	intron (NM_010095, intron 7 of 16)	16718	NM_001037931	628416	Mm.390723	NM_001037931		Gm6878	EG628416	predicted gene 6878	protein-coding
mm_93103.1	chr10	91001372	91001381	-	1	NA	intron (NM_009684, intron 22 of 26)	intron (NM_009684, intron 22 of 26)	81367	NM_001042558	11783	Mm.220289	NM_009684	ENSMUSG00000019979	Apaf1	6230400I06Rik|Apaf-1|Apaf1l|fog|mKIAA0413	apoptotic peptidase activating factor 1	protein-coding
mm_129448.1	chr15	78561203	78561214	-	1	NA	3' UTR (NM_009008, exon 7 of 7)	3' UTR (NM_009008, exon 7 of 7)	11575	NM_009008	19354	Mm.1972	NM_009008	ENSMUSG00000033220	Rac2	AI323801|AI452260	RAS-related C3 botulinum substrate 2	protein-coding
mm_40762.1	chr5	66969110	66969132	+	1	NA	exon (NM_001001980, exon 7 of 26)	exon (NM_001001980, exon 7 of 26)	705	NM_001256122	77569	Mm.374778	NM_001001980	ENSMUSG00000037736	Limch1	3732412D22Rik|mKIAA1102	LIM and calponin homology domains 1	protein-coding
mm_8020.1	chr1	134985019	134985025	-	1	NA	Intergenic	(A)n|Simple_repeat|Simple_repeat	22457	NM_001278115	67196	Mm.284587	NM_026024	ENSMUSG00000026429	Ube2t	2700084L22Rik|C80607	ubiquitin-conjugating enzyme E2T	protein-coding
mm_79211.1	chr9	49037282	49037283	+	1	NA	intron (NM_175482, intron 21 of 23)	intron (NM_175482, intron 21 of 23)	-18299	NM_012039	26951	Mm.24791	NM_012039	ENSMUSG00000032264	Zw10	6330566F14Rik|MmZw10	zw10 kinetochore protein	protein-coding
mm_148688.1	chr19	5724875	5724886	+	1	NA	intron (NM_001114595, intron 1 of 17)	intron (NM_001114595, intron 1 of 17)	1437	NM_001114595	114601	Mm.210447	NM_053252	ENSMUSG00000024937	Ehbp1l1	G430002G23Rik	EH domain binding protein 1-like 1	protein-coding
mm_7022.1	chr1	86909704	86909707	-	1	NA	intron (NM_153530, intron 9 of 20)	intron (NM_153530, intron 9 of 20)	180223	NM_007433	11650	Mm.195224	NM_007433	ENSMUSG00000026246	Alppl2	Akp5|C77216|D1Ertd816e|EAP	alkaline phosphatase, placental-like 2	protein-coding
mm_70113.1	chr7	142678700	142678712	-	1	NA	TTS (NM_001185083)	TTS (NM_001185083)	1020	NM_001185083	16334	Mm.4946	NM_008387	ENSMUSG00000000215	Ins2	AA986540|Ins-2|InsII|Mody|Mody4	insulin II	protein-coding
mm_52815.1	chr6	121343962	121343974	+	1	NA	intron (NM_001347433, intron 1 of 14)	intron (NM_001347433, intron 1 of 14)	892	NM_001347433	14411	Mm.274506	NM_133661	ENSMUSG00000030109	Slc6a12	BGT1|GAT-2|GAT2|Gabt2	solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12	protein-coding
mm_24417.1	chr3	90526775	90526779	+	1	NA	promoter-TSS (NM_001163526)	promoter-TSS (NM_001163526)	-72	NM_025393	66166	Mm.24006	NM_025393	ENSMUSG00000042306	S100a14	1110013O05Rik|S100a15|S114	S100 calcium binding protein A14	protein-coding
mm_55164.1	chr6	51873698	51873709	-	1	NA	intron (NM_018773, intron 11 of 12)	intron (NM_018773, intron 11 of 12)	138846	NM_018773	54353	Mm.221479	NM_018773	ENSMUSG00000059182	Skap2	2610021A10Rik|AA960083|BB137539|RA70|SKAP-HOM|Saps|Scap2|mSKAP55R	src family associated phosphoprotein 2	protein-coding
mm_13053.1	chr2	91102274	91102286	+	1	NA	intron (NM_011355, intron 2 of 4)	MIRb|SINE|MIR	5602	NM_011355	20375	Mm.1302	NM_011355	ENSMUSG00000002111	Spi1	Dis-1|Dis1|PU.1|Sfpi-1|Sfpi1|Spi-1|Tcfpu1|Tfpu.1	spleen focus forming virus (SFFV) proviral integration oncogene	protein-coding
mm_72092.1	chr8	71580517	71580526	+	1	NA	intron (NM_011977, intron 6 of 13)	intron (NM_011977, intron 6 of 13)	11594	NM_011977	26457	Mm.38165	NM_011977	ENSMUSG00000031808	Slc27a1	FATP1|Fatp	solute carrier family 27 (fatty acid transporter), member 1	protein-coding
mm_91362.1	chr10	28986281	28986313	-	1	NA	promoter-TSS (NM_026336)	promoter-TSS (NM_026336)	9	NM_026336	67719	Mm.440480	NM_026336	ENSMUSG00000015519	2310057J18Rik	2210414P04Rik|Leg1	RIKEN cDNA 2310057J18 gene	protein-coding
mm_141196.1	chr17	27021231	27021267	-	1	NA	exon (NM_007523, exon 5 of 6)	exon (NM_007523, exon 5 of 6)	3214	NM_001251881	70772	Mm.440437	NM_027544	ENSMUSG00000048731	Ggnbp1	0610031G08Rik|mdf	gametogenetin binding protein 1	protein-coding
mm_46480.1	chr5	105131896	105131913	-	1	NA	intron (NM_008620, intron 3 of 10)	intron (NM_008620, intron 3 of 10)	7648	NM_008620	17472	Mm.440525	NM_008620	ENSMUSG00000079363	Gbp4	AW228052|Mag-2|Mpa-2|Mpa2	guanylate binding protein 4	protein-coding
mm_111115.1	chr12	80960655	80960664	-	1	NA	intron (NM_011387, intron 1 of 3)	intron (NM_011387, intron 1 of 3)	7420	NM_011387	20493	Mm.486361	NM_011387	ENSMUSG00000021135	Slc10a1	Ntcp	solute carrier family 10 (sodium/bile acid cotransporter family), member 1	protein-coding
mm_107867.1	chr12	69907829	69907843	+	1	NA	5' UTR (NM_178628, exon 2 of 15)	5' UTR (NM_178628, exon 2 of 15)	-14673	NM_201519	399510	Mm.291936	NM_201519	ENSMUSG00000034761	Map4k5	4432415E19Rik|GCKR|KHS|MAPKKKK5	mitogen-activated protein kinase kinase kinase kinase 5	protein-coding
mm_21261.1	chr2	156720771	156720828	-	1	NA	promoter-TSS (NM_001042488)	promoter-TSS (NM_001042488)	110	NR_040505	74846	Mm.443946	NR_040505	ENSMUSG00000086638	4930405A21Rik	-	RIKEN cDNA 4930405A21 gene	ncRNA
mm_30628.1	chr4	8752331	8752351	+	1	NA	exon (NM_001277149, exon 2 of 38)	exon (NM_001277149, exon 2 of 38)	61935	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_80186.1	chr9	72357775	72357778	+	1	NA	intron (NM_146224, intron 20 of 21)	AT_rich|Low_complexity|Low_complexity	-80753	NM_008613	17427	Mm.387671	NM_008613	ENSMUSG00000032221	Mns1	AW546487	meiosis-specific nuclear structural protein 1	protein-coding
mm_78470.1	chr9	32636234	32636269	+	1	NA	Intergenic	Intergenic	-59791	NM_011808	23871	Mm.292415	NM_011808	ENSMUSG00000032035	Ets1	AI196000|AI448617|D230050P06|Ets-1|Tpl1|vs	E26 avian leukemia oncogene 1, 5' domain	protein-coding
mm_101902.1	chr11	49187136	49187146	-	1	NA	promoter-TSS (NM_172793)	promoter-TSS (NM_172793)	-52	NM_172793	237754	Mm.130787	NM_172793	ENSMUSG00000040283	Btnl9	B430208I01|Btn3|D330012D11Rik	butyrophilin-like 9	protein-coding
mm_12677.1	chr2	75832169	75832194	+	1	NA	promoter-TSS (NM_172666)	promoter-TSS (NM_172666)	4	NM_172666	228061	Mm.31227	NM_172666	ENSMUSG00000042410	Agps	5832437L22|9930035G10Rik|AW123847|Adaps|Adas|Adhaps|Adps|Aldhpsy|bs2	alkylglycerone phosphate synthase	protein-coding
mm_62588.1	chr7	105640464	105640514	+	1	NA	promoter-TSS (NM_019502)	promoter-TSS (NM_019502)	-51	NM_019502	14356	Mm.220330	NM_019502	ENSMUSG00000089847	Timm10b	Fxc1|Tim10b|Tim9b	translocase of inner mitochondrial membrane 10B	protein-coding
mm_92508.1	chr10	78412852	78412862	-	1	NA	exon (NM_010925, exon 1 of 13)	exon (NM_010925, exon 1 of 13)	186	NM_010925	18114	Mm.38344	NM_010925	ENSMUSG00000061032	Rrp1	AL033305|AL033306|AU018604|NNP-1|Nnp1	ribosomal RNA processing 1 homolog (S. cerevisiae)	protein-coding
mm_146791.1	chr18	20114855	20114865	-	1	NA	promoter-TSS (NM_001291804)	promoter-TSS (NM_001291804)	-87	NM_013504	13505	Mm.33740	NM_013504	ENSMUSG00000044322	Dsc1	1110020A10Rik|AI507491	desmocollin 1	protein-coding
mm_109908.1	chr12	8351382	8351403	-	1	NA	Intergenic	Intergenic	37959	NM_021429	58240	Mm.309954	NM_021429	ENSMUSG00000020605	Hs1bp3	-	HCLS1 binding protein 3	protein-coding
mm_118714.1	chr14	22186562	22186568	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	166853	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_103240.1	chr11	70687918	70687981	-	1	NA	TTS (NM_213729)	TTS (NM_213729)	156	NM_001190376	216874	Mm.473726	NM_178116	ENSMUSG00000040712	Camta2	Kiaa0909-hp|mKIAA0909	calmodulin binding transcription activator 2	protein-coding
mm_91396.1	chr10	30771885	30771921	-	1	NA	intron (NM_172495, intron 1 of 15)	intron (NM_172495, intron 1 of 15)	31204	NM_172495	211329	Mm.297903	NM_172495	ENSMUSG00000039697	Ncoa7	9030406N13Rik	nuclear receptor coactivator 7	protein-coding
mm_6816.1	chr1	84181517	84181527	-	1	NA	intron (NM_001003948, intron 1 of 2)	intron (NM_001003948, intron 1 of 2)	37439	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_161383.1	chr14	74640975	74640975	+	1	NA	5' UTR (NM_172812, exon 1 of 3)	5' UTR (NM_172812, exon 1 of 3)	135	NM_172812	15558	Mm.214351	NM_172812	ENSMUSG00000034997	Htr2a	E030013E04|Htr-2|Htr2	5-hydroxytryptamine (serotonin) receptor 2A	protein-coding
mm_99804.1	chr11	107994007	107994025	+	1	NA	intron (NM_011101, intron 8 of 16)	intron (NM_011101, intron 8 of 16)	-2832	NR_106082	102465705		NR_106082	ENSMUSG00000098989	Mir7223	Gm28009|mmu-mir-7223	microRNA 7223	ncRNA
mm_2361.1	chr1	92973202	92973213	+	1	NA	promoter-TSS (NM_001104529)	promoter-TSS (NM_001104529)	88	NM_001104529	64095	Mm.152780	NM_022320	ENSMUSG00000026271	Gpr35	KPG_007	G protein-coupled receptor 35	protein-coding
mm_75562.1	chr8	58911832	58911848	-	1	NA	promoter-TSS (NM_175032)	promoter-TSS (NM_175032)	85	NM_173411	234290	Mm.39244	NM_173411	ENSMUSG00000049946	BC030500	-	cDNA sequence BC030500	protein-coding
mm_150573.1	chr19	40119787	40119821	+	1	NA	Intergenic	Lx2|LINE|L1	30125	NM_001167875	107141	Mm.474575	NM_134144	ENSMUSG00000054827	Cyp2c50	AI266900	cytochrome P450, family 2, subfamily c, polypeptide 50	protein-coding
mm_147361.1	chr18	43393152	43393170	-	1	NA	5' UTR (NM_009468, exon 1 of 14)	5' UTR (NM_009468, exon 1 of 14)	216	NM_009468	22240	Mm.8180	NM_009468	ENSMUSG00000024501	Dpysl3	CRMP-4|DRP-3|TUC4|ULIP-1|Ulip|Ulip1	dihydropyrimidinase-like 3	protein-coding
mm_18120.1	chr2	44997129	44997147	-	1	NA	exon (NM_015753, exon 8 of 10)	exon (NM_015753, exon 8 of 10)	26039	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_46665.1	chr5	108694034	108694045	-	1	NA	promoter-TSS (NM_001164259)	promoter-TSS (NM_001164259)	-190	NM_001164259	116701	Mm.35691	NM_054071	ENSMUSG00000008090	Fgfrl1	FGFR5|FGFR5beta|FGFR5gamma	fibroblast growth factor receptor-like 1	protein-coding
mm_56965.1	chr6	120038648	120038699	-	1	NA	promoter-TSS (NM_001185020)	promoter-TSS (NM_001185020)	-18	NM_001185021	232341	Mm.333349	NM_198703	ENSMUSG00000045962	Wnk1	6430573H23Rik|EG406236|Hsn2|Prkwnk1|mKIAA0344	WNK lysine deficient protein kinase 1	protein-coding
mm_77639.1	chr8	124369900	124369918	-	1	NA	3' UTR (NM_171824, exon 7 of 7)	3' UTR (NM_171824, exon 7 of 7)	64027	NM_171824	209966	Mm.234233	NM_171824	ENSMUSG00000050751	Pgbd5	2900019M05Rik|AI854313	piggyBac transposable element derived 5	protein-coding
mm_79403.1	chr9	54981483	54981496	+	1	NA	intron (NM_176844, intron 1 of 5)	CpG	609	NM_176844	110835	Mm.103778	NM_176844	ENSMUSG00000035594	Chrna5	Acra-5|Acra5	cholinergic receptor, nicotinic, alpha polypeptide 5	protein-coding
mm_111428.1	chr12	91696381	91696384	-	1	NA	intron (NM_175367, intron 4 of 6)	intron (NM_175367, intron 4 of 6)	90054	NM_175367	108800	Mm.23125	NM_175367	ENSMUSG00000020961	Ston2	4933401N24Rik|AI425999|AW544599	stonin 2	protein-coding
mm_108711.1	chr12	87026571	87026583	+	1	NA	promoter-TSS (NM_172583)	promoter-TSS (NM_172583)	13	NM_172583	217733	Mm.110032	NM_172583	ENSMUSG00000034145	Tmem63c	4932420N09|9330187M14Rik	transmembrane protein 63c	protein-coding
mm_140371.1	chr17	86963400	86963410	+	1	NA	5' UTR (NM_145491, exon 1 of 5)	5' UTR (NM_145491, exon 1 of 5)	294	NM_145491	104215	Mm.826	NM_145491	ENSMUSG00000024143	Rhoq	Arhq|TC10A|Tc10	ras homolog family member Q	protein-coding
mm_99015.1	chr11	98863756	98863785	+	1	NA	5' UTR (NM_197940, exon 1 of 8)	5' UTR (NM_197940, exon 1 of 8)	172	NM_197940	68524	Mm.28661	NM_197940	ENSMUSG00000038013	Wipf2	1110014J05Rik|5730509C05Rik|AA407487|Gm1176|Wich|Wire	WAS/WASL interacting protein family, member 2	protein-coding
mm_142358.1	chr17	43667140	43667163	-	1	NA	promoter-TSS (NM_001285948)	promoter-TSS (NM_001285948)	-136	NM_028711	74011	Mm.288697	NM_028711	ENSMUSG00000023912	Slc25a27	3632410G24Rik|9430092A03Rik|D530043E16Rik|Ucp4	solute carrier family 25, member 27	protein-coding
mm_33503.1	chr4	130884917	130884964	+	1	NA	Intergenic	Intergenic	-28394	NM_010686	16792	Mm.271868	NM_010686	ENSMUSG00000028581	Laptm5	E3	lysosomal-associated protein transmembrane 5	protein-coding
mm_158001.1	chrX	94999008	94999018	-	1	NA	Intergenic	Intergenic	27669	NM_178753	270624	Mm.115205	NM_178753	ENSMUSG00000071722	Spin4	9630042H07Rik	spindlin family, member 4	protein-coding
mm_92711.1	chr10	80757171	80757210	-	1	NA	intron (NM_199322, intron 1 of 27)	intron (NM_199322, intron 1 of 27)	1984	NM_199322	208266	Mm.152371	NM_199322	ENSMUSG00000061589	Dot1l	A630076O07|AW907654|Dot1|KMT4|mDot1	DOT1-like, histone H3 methyltransferase (S. cerevisiae)	protein-coding
mm_32095.1	chr4	98546697	98546709	+	1	NA	promoter-TSS (NM_007704)	promoter-TSS (NM_007704)	69	NM_001005787	12695	Mm.90218	NM_007704	ENSMUSG00000061859	Patj	Cipp|Inadl	PATJ, crumbs cell polarity complex component	protein-coding
mm_161431.1	chr15	55576820	55576820	+	1	NA	intron (NM_134092, intron 10 of 21)	MTE2b|LTR|ERVL-MaLR	19412	NM_001168250	105837	Mm.390829	NM_134092	ENSMUSG00000022369	Mtbp	AI429604|MDM2BP	Mdm2, transformed 3T3 cell double minute p53 binding protein	protein-coding
mm_162766.1	chr10	63988062	63988067	+	1	NA	intron (NM_178678, intron 2 of 2)	intron (NM_178678, intron 2 of 2)	102191	NM_178678	216028	Mm.431318	NM_178678	ENSMUSG00000042846	Lrrtm3	9630044H04Rik	leucine rich repeat transmembrane neuronal 3	protein-coding
mm_21341.1	chr2	157107565	157107567	-	1	NA	intron (NM_018851, intron 11 of 15)	intron (NM_018851, intron 11 of 15)	20511	NM_001177439	383766	Mm.480305	NM_001177439	ENSMUSG00000074628	Tldc2	Gm1332	TBC/LysM associated domain containing 2	protein-coding
mm_171718.1	chr4	8461923	8461935	-	1	NA	Intergenic	RLTR9D|LTR|ERVK	-73715	NM_021518	59021	Mm.397471	NM_021518	ENSMUSG00000047187	Rab2a	9330148M11Rik|C80220|Rab2	RAB2A, member RAS oncogene family	protein-coding
mm_168571.1	chr11	70652856	70652874	+	1	NA	exon (NM_011072, exon 2 of 3)	exon (NM_011072, exon 2 of 3)	1785	NM_011072	18643	Mm.2647	NM_011072	ENSMUSG00000018293	Pfn1	Pfn	profilin 1	protein-coding
mm_162862.1	chr10	93124287	93124299	-	1	NA	Intergenic	Intergenic	-36583	NM_146239	237459	Mm.217404	NM_146239	ENSMUSG00000020015	Cdk17	6430598J10Rik|Pctk2	cyclin-dependent kinase 17	protein-coding
mm_62222.1	chr7	98490029	98490039	+	1	NA	Intergenic	CpG	-4188	NM_001113379	434215	Mm.323057	NM_001113379	ENSMUSG00000090958	Lrrc32	AI426318|D11S833Eh|D7H11S833E|EG434215|Garp	leucine rich repeat containing 32	protein-coding
mm_106599.1	chr11	120731043	120731053	-	1	NA	exon (NM_007621, exon 2 of 8)	exon (NM_007621, exon 2 of 8)	973	NM_007621	12409	Mm.21454	NM_007621	ENSMUSG00000025150	Cbr2	MLCR	carbonyl reductase 2	protein-coding
mm_104888.1	chr11	99566422	99566439	-	1	NA	exon (NM_023511, exon 1 of 1)	exon (NM_023511, exon 1 of 1)	200	NM_023511	69473	Mm.158281	NM_023511	ENSMUSG00000047564	Krtap3-1	2310003K17Rik|KAP3.1|KRTAP3.1	keratin associated protein 3-1	protein-coding
mm_60958.1	chr7	47271824	47271831	+	1	NA	Intergenic	Intergenic	-18979	NM_001288801	668725	Mm.436563	NM_001177566	ENSMUSG00000074111	Mrgpra9	EG668725|MrgA9	MAS-related GPR, member A9	protein-coding
mm_102009.1	chr11	51605487	51605508	-	1	NA	exon (NM_010448, exon 3 of 7)	exon (NM_010448, exon 3 of 7)	1384	NM_001048061	15384	Mm.256875	NM_010448	ENSMUSG00000020358	Hnrnpab	3010025C11Rik|CBF-A|Cgbfa|Hnrpab	heterogeneous nuclear ribonucleoprotein A/B	protein-coding
mm_99075.1	chr11	99387333	99387345	+	1	NA	exon (NM_010660, exon 4 of 8)	exon (NM_010660, exon 4 of 8)	2025	NM_010660	16661	Mm.22662	NM_010660	ENSMUSG00000019761	Krt10	D130054E02Rik|K10|K1C1|Krt-1.10|Krt1-10	keratin 10	protein-coding
mm_47048.1	chr5	116083196	116083217	-	1	NA	promoter-TSS (NM_001101546)	promoter-TSS (NM_001101546)	40	NM_001101546	545798	Mm.483995	NM_001101546	ENSMUSG00000079278	Tmem233	DSPB2|Gm13843|OTTMUSG00000014722	transmembrane protein 233	protein-coding
mm_124186.1	chr14	95558117	95558145	-	1	NA	Intergenic	L1_Mur2|LINE|L1	-323135	NM_025733	66732	Mm.75060	NM_025733	ENSMUSG00000034689	4921530L21Rik	-	RIKEN cDNA 4921530L21 gene	protein-coding
mm_141135.1	chr17	26206488	26206498	-	1	NA	intron (NM_001081069, intron 9 of 16)	intron (NM_001081069, intron 9 of 16)	3531	NM_001081069	50782	Mm.109840	NM_001081069	ENSMUSG00000024186	Rgs11	C78048	regulator of G-protein signaling 11	protein-coding
mm_110445.1	chr12	51030177	51030184	-	1	NA	intron (NR_126468, intron 2 of 4)	L1MEj|LINE|L1	25024	NR_126468	75494	Mm.416848	NR_126468		1700008C04Rik	-	RIKEN cDNA 1700008C04 gene	ncRNA
mm_14346.1	chr2	129593383	129593414	+	1	NA	5' UTR (NM_001291022, exon 1 of 5)	5' UTR (NM_001291022, exon 1 of 5)	229	NM_001291022	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_31650.1	chr4	59674004	59674013	+	1	NA	intron (NM_153158, intron 1 of 2)	MLT2B5|LTR|ERVL	47797	NM_153158	230259	Mm.45688	NM_153158	ENSMUSG00000045071	E130308A19Rik	-	RIKEN cDNA E130308A19 gene	protein-coding
mm_54334.1	chr6	30641852	30641877	-	1	NA	exon (NM_025350, exon 6 of 10)	exon (NM_025350, exon 6 of 10)	2646	NM_025350	109697	Mm.25377	NM_025350	ENSMUSG00000054446	Cpa1	0910001L12Rik|Cpa	carboxypeptidase A1, pancreatic	protein-coding
mm_88766.1	chr10	80335182	80335283	+	1	NA	3' UTR (NM_139292, exon 6 of 6)	3' UTR (NM_139292, exon 6 of 6)	5087	NM_139292	70335	Mm.28147	NM_139292	ENSMUSG00000035504	Reep6	0610011M24Rik|Dp1l1	receptor accessory protein 6	protein-coding
mm_117190.1	chr13	63564731	63564772	-	1	NA	intron (NM_001328514, intron 1 of 23)	CpG-3956	984	NM_008957	19206	Mm.228798	NM_008957	ENSMUSG00000021466	Ptch1	A230106A15Rik|Ptc|Ptc1|Ptch|mes	patched 1	protein-coding
mm_78197.1	chr9	21368015	21368027	+	1	NA	promoter-TSS (NM_001277322)	promoter-TSS (NM_001277322)	150	NM_001042709	16201	Mm.440026	NM_010561	ENSMUSG00000032178	Ilf3	MBII-26|MPHOSPH4|NF90|NFAR	interleukin enhancer binding factor 3	protein-coding
mm_62701.1	chr7	110221743	110221766	+	1	NA	promoter-TSS (NM_009302)	promoter-TSS (NM_009302)	51	NM_009302	20947	Mm.334144	NM_009302	ENSMUSG00000031015	Swap70	70kDa|AV235546	SWA-70 protein	protein-coding
mm_146714.1	chr18	14729348	14729358	-	1	NA	intron (NM_001163609, intron 3 of 6)	intron (NM_001163609, intron 3 of 6)	23202	NM_001163609	73677	Mm.87277	NM_001163609	ENSMUSG00000036743	Psma8	2410072D24Rik	proteasome (prosome, macropain) subunit, alpha type, 8	protein-coding
mm_85005.1	chr9	86880648	86880659	-	1	NA	promoter-TSS (NM_001277986)	promoter-TSS (NM_001277986)	-204	NM_001277983	20616	Mm.281651	NM_013669	ENSMUSG00000033419	Snap91	91kDa|AP180|F1-20|mKIAA0656	synaptosomal-associated protein 91	protein-coding
mm_14959.1	chr2	152080944	152080954	+	1	NA	promoter-TSS (NM_001160410)	promoter-TSS (NM_001160410)	-580	NM_001160410	545474	Mm.214317	NM_001160410	ENSMUSG00000060257	Scrt2	AW060659	scratch family zinc finger 2	protein-coding
mm_170653.1	chr2	10365232	10365243	-	1	NA	Intergenic	RLTR11B|LTR|ERVK	-5214	NM_001198808	353282	Mm.329991	NM_177386	ENSMUSG00000061186	Sfmbt2	D2Wsu23e|D330030P06Rik	Scm-like with four mbt domains 2	protein-coding
mm_71377.1	chr8	45827343	45827347	+	1	NA	3' UTR (NM_001205219, exon 24 of 24)	3' UTR (NM_001205219, exon 24 of 24)	-8048	NR_045739	319940	Mm.441720	NR_045739	ENSMUSG00000085440	Sorbs2os	D330022K07Rik	sorbin and SH3 domain containing 2, opposite strand	ncRNA
mm_94413.1	chr11	5861869	5861879	+	1	NA	promoter-TSS (NM_009636)	promoter-TSS (NM_009636)	8	NM_001291857	11568	Mm.3317	NM_009636	ENSMUSG00000020473	Aebp1	ACLP	AE binding protein 1	protein-coding
mm_88271.1	chr10	74967165	74967203	+	1	NA	promoter-TSS (NM_010311)	promoter-TSS (NM_010311)	-47	NM_010311	14687	Mm.32595	NM_010311	ENSMUSG00000040009	Gnaz	AI847979|Gz	guanine nucleotide binding protein, alpha z subunit	protein-coding
mm_163500.1	chr12	112369110	112369110	-	1	NA	Intergenic	Intergenic	54088	NR_036459	100504733	Mm.255309	NM_176956		A730018C14Rik	-	RIKEN cDNA A730018C14 gene	ncRNA
mm_14092.1	chr2	125161307	125161309	+	1	NA	intron (NM_001079690, intron 5 of 27)	intron (NM_001079690, intron 5 of 27)	8708	NM_001079690	20495	Mm.3914	NM_011389	ENSMUSG00000027202	Slc12a1	AI788571|D630042G03Rik|Nkcc2|mBSC1|urehr3	solute carrier family 12, member 1	protein-coding
mm_7979.1	chr1	134099139	134099145	-	1	NA	Intergenic	Intergenic	-12100	NM_001284524	71884	Mm.328268	NM_027979	ENSMUSG00000026450	Chit1	2300002L19Rik	chitinase 1 (chitotriosidase)	protein-coding
mm_41100.1	chr5	87694844	87694865	+	1	NA	exon (NM_001286023, exon 5 of 7)	exon (NM_001286023, exon 5 of 7)	4571	NM_001286020	12991	Mm.268737	NM_009972	ENSMUSG00000063157	Csn2	Csnb	casein beta	protein-coding
mm_12467.1	chr2	71389416	71389446	+	1	NA	intron (NM_026115, intron 1 of 10)	CpG	171	NM_026115	107435	Mm.272472	NM_026115	ENSMUSG00000027018	Hat1	2410071B14Rik|AA536933|Hat-1|KAT1	histone aminotransferase 1	protein-coding
mm_133186.1	chr16	72663144	72663189	+	1	NA	promoter-TSS (NM_019413)	promoter-TSS (NM_019413)	17	NM_019413	19876	Mm.310772	NM_019413	ENSMUSG00000022883	Robo1	AW494633|AW742721|DUTT1|Gm310	roundabout guidance receptor 1	protein-coding
mm_2247.1	chr1	91056674	91056696	+	1	NA	intron (NM_001310732, intron 1 of 24)	intron (NM_001310732, intron 1 of 24)	3241	NM_008515	16978	Mm.45039	NM_008515	ENSMUSG00000026305	Lrrfip1	AU024550|Fliiap1	leucine rich repeat (in FLII) interacting protein 1	protein-coding
mm_9098.1	chr1	169531448	169531460	-	1	NA	promoter-TSS (NM_023284)	promoter-TSS (NM_023284)	10	NM_023284	66977	Mm.151315	NM_023284	ENSMUSG00000026683	Nuf2	2410003C07Rik|AU044112|C85691|Cdca1|NUF2R	NUF2, NDC80 kinetochore complex component	protein-coding
mm_158184.1	chrX	104201127	104201166	-	1	NA	promoter-TSS (NM_001077354)	promoter-TSS (NM_001077354)	-29	NM_001077354	245555	Mm.381907	NM_001077354	ENSMUSG00000046449	C77370	A230051P11|C77386|KIDLIA|Kiaa2022|Xpn|mKIAA2022	expressed sequence C77370	protein-coding
mm_31903.1	chr4	84104826	84104829	+	1	NA	Intergenic	Intergenic	-59948	NR_130998	78238	Mm.243903	NR_130998	ENSMUSG00000085217	6030471H07Rik	-	RIKEN cDNA 6030471H07 gene	ncRNA
mm_53241.1	chr6	127474138	127474151	+	1	NA	intron (NM_181402, intron 4 of 8)	intron (NM_181402, intron 4 of 8)	20421	NM_181402	101187	Mm.110818	NM_181402	ENSMUSG00000037997	Parp11	5330431N24Rik|AI851877|ARTD11|HIN1L|PARP-11	poly (ADP-ribose) polymerase family, member 11	protein-coding
mm_108654.1	chr12	86361431	86361444	+	1	NA	5' UTR (NM_001159500, exon 1 of 7)	5' UTR (NM_001159500, exon 1 of 7)	320	NM_001159500	26380	Mm.235550	NM_011934	ENSMUSG00000021255	Esrrb	Err2|Errb|Estrrb|Nr3b2	estrogen related receptor, beta	protein-coding
mm_40162.1	chr5	35592077	35592088	+	1	NA	exon (NM_030721, exon 7 of 19)	exon (NM_030721, exon 7 of 19)	-3319	NR_045807	74364	Mm.473123	NM_175208	ENSMUSG00000055061	4931431C16Rik	-	RIKEN cDNA 4931431C16 gene	ncRNA
mm_122940.1	chr14	54965344	54965359	-	1	NA	exon (NM_010856, exon 3 of 39)	exon (NM_010856, exon 3 of 39)	1256	NM_001164171	17888	Mm.290003	NM_010856	ENSMUSG00000040752	Myh6	A830009F23Rik|AA517445|Myhc-a|Myhca|alpha-MHC	myosin, heavy polypeptide 6, cardiac muscle, alpha	protein-coding
mm_38308.1	chr4	136898841	136898850	-	1	NA	promoter-TSS (NM_007572)	promoter-TSS (NM_007572)	-1	NM_007572	12259	Mm.439957	NM_007572	ENSMUSG00000036887	C1qa	AI255395|C1q	complement component 1, q subcomponent, alpha polypeptide	protein-coding
mm_34507.1	chr4	148804351	148804373	+	1	NA	promoter-TSS (NM_001159344)	promoter-TSS (NM_001159344)	-30	NM_001159344	69743	Mm.233879	NM_027195	ENSMUSG00000028977	Casz1	2410019P08Rik|AV096627|BC040081|Cst|D4Ertd432e	castor zinc finger 1	protein-coding
mm_34571.1	chr4	150049174	150049191	+	1	NA	Intergenic	Intergenic	-19272	NR_029751	723848		NR_029751	ENSMUSG00000065493	Mir34a	Mirn34a|mir-34a|mmu-mir-34a	microRNA 34a	ncRNA
mm_13661.1	chr2	114055325	114055327	+	1	NA	non-coding (NR_028422, exon 1 of 3)	non-coding (NR_028422, exon 1 of 3)	930	NR_028422	100303644	Mm.330469	NR_028422	ENSMUSG00000092397	C130080G10Rik	-	RIKEN cDNA C130080G10 gene	ncRNA
mm_8452.1	chr1	152903089	152903118	-	1	NA	promoter-TSS (NM_001160256)	promoter-TSS (NM_001160256)	-457	NM_001005507	226517	Mm.270775	NM_001005507	ENSMUSG00000042772	Smg7	9430023P16Rik|mKIAA0250	Smg-7 homolog, nonsense mediated mRNA decay factor (C. elegans)	protein-coding
mm_143859.1	chr17	84186036	84186073	-	1	NA	exon (NM_001001806, exon 2 of 2)	exon (NM_001001806, exon 2 of 2)	1893	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_111202.1	chr12	84226180	84226209	-	1	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	-7313	NM_001163501	238317	Mm.31256	NM_001163501	ENSMUSG00000042507	Elmsan1	9430029N19Rik|C130039O16Rik|Gm260	ELM2 and Myb/SANT-like domain containing 1	protein-coding
mm_127766.1	chr15	103563400	103563420	+	1	NA	exon (NM_008134, exon 3 of 4)	exon (NM_008134, exon 3 of 4)	1671	NM_001289587	14663	Mm.219621	NM_008134	ENSMUSG00000022491	Glycam1	MC26|Sgp50|glyCAM-1	glycosylation dependent cell adhesion molecule 1	protein-coding
mm_76277.1	chr8	84183866	84183916	-	1	NA	Intergenic	CpG	-4930	NR_029821	723819		NR_029821	ENSMUSG00000065483	Mir181c	Mirn181c|mir-181c	microRNA 181c	ncRNA
mm_75640.1	chr8	64849923	64849981	-	1	NA	promoter-TSS (NM_178633)	promoter-TSS (NM_178633)	-28	NM_178633	77113	Mm.350347	NM_178633	ENSMUSG00000031605	Klhl2	6030411N21Rik|ABP-KELCH|AU020744|Mav	kelch-like 2, Mayven	protein-coding
mm_105096.1	chr11	100939328	100939355	-	1	NA	5' UTR (NM_011486, exon 1 of 24)	5' UTR (NM_011486, exon 1 of 24)	199	NM_213660	20848	Mm.249934	NM_011486	ENSMUSG00000004040	Stat3	1110034C02Rik|AW109958|Aprf	signal transducer and activator of transcription 3	protein-coding
mm_134780.1	chr16	23981224	23981256	-	1	NA	intron (NM_009744, intron 1 of 9)	intron (NM_009744, intron 1 of 9)	7372	NM_009744	12053	Mm.347398	NM_009744	ENSMUSG00000022508	Bcl6	Bcl5	B cell leukemia/lymphoma 6	protein-coding
mm_98560.1	chr11	95337013	95337026	+	1	NA	promoter-TSS (NM_172543)	promoter-TSS (NM_172543)	1	NM_172543	215512	Mm.262113	NM_172543	ENSMUSG00000038893	Fam117a	5730593F17Rik|AW548096	family with sequence similarity 117, member A	protein-coding
mm_19059.1	chr2	77313965	77313986	-	1	NA	Intergenic	Intergenic	-33383	NM_175465	228071	Mm.27120	NM_175465	ENSMUSG00000042272	Sestd1	1500031J16Rik|A930010O20|Solo/Trio8	SEC14 and spectrin domains 1	protein-coding
mm_38900.1	chr4	149909571	149909575	-	1	NA	intron (NM_029035, intron 1 of 2)	intron (NM_029035, intron 1 of 2)	45433	NM_029035	74646	Mm.30	NM_029035	ENSMUSG00000039911	Spsb1	1110014L01Rik|4930422J18Rik|AI596360|AI854583|SSB-1|SSB1	splA/ryanodine receptor domain and SOCS box containing 1	protein-coding
mm_57409.1	chr6	124865766	124865781	-	1	NA	3' UTR (NM_013488, exon 10 of 10)	3' UTR (NM_013488, exon 10 of 10)	-1856	NM_013533	14788	Mm.2514	NM_013533	ENSMUSG00000038390	Gpr162	A-2|BC031437|Grca	G protein-coupled receptor 162	protein-coding
mm_168890.1	chr1	24615558	24615566	-	1	NA	Intergenic	Intergenic	-28125	NM_007733	12823	Mm.329196	NM_007733	ENSMUSG00000026141	Col19a1	-	collagen, type XIX, alpha 1	protein-coding
mm_170569.1	chr19	51142510	51142513	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-463865	NM_001290356	58178	Mm.313672	NM_021377	ENSMUSG00000043531	Sorcs1	Sorcs|mSorCS	sortilin-related VPS10 domain containing receptor 1	protein-coding
mm_120160.1	chr14	60709521	60709533	+	1	NA	exon (NM_001033272, exon 4 of 13)	exon (NM_001033272, exon 4 of 13)	-23377	NM_001310594	219140	Mm.149776	NM_001033272	ENSMUSG00000021990	Spata13	C79050|ESTM11|X83327|mFLJ00298	spermatogenesis associated 13	protein-coding
mm_138857.1	chr17	42380861	42380871	+	1	NA	intron (NM_028474, intron 3 of 3)	(T)n|Simple_repeat|Simple_repeat	64919	NM_028474	627626	Mm.390999	NM_028474	ENSMUSG00000042256	Ptchd4	3110082D06Rik|Gm321	patched domain containing 4	protein-coding
mm_34147.1	chr4	139360106	139360108	+	1	NA	exon (NM_146157, exon 7 of 24)	exon (NM_146157, exon 7 of 24)	7520	NM_146157	230866	Mm.394288	NM_146157	ENSMUSG00000078517	Emc1	2700016F22Rik	ER membrane protein complex subunit 1	protein-coding
mm_96667.1	chr11	69409771	69409779	+	1	NA	intron (NM_001017426, intron 1 of 22)	intron (NM_001017426, intron 1 of 22)	3900	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_155112.1	chrX	48519525	48519538	+	1	NA	5' UTR (NM_011228, exon 1 of 2)	5' UTR (NM_011228, exon 1 of 2)	246	NM_011228	19337	Mm.2015	NM_011228	ENSMUSG00000031104	Rab33a	Rabs10	RAB33A, member RAS oncogene family	protein-coding
mm_61493.1	chr7	75730538	75730549	+	1	NA	exon (NM_029332, exon 26 of 37)	exon (NM_029332, exon 26 of 37)	-117795	NM_001122780	207952	Mm.206223	NM_029652	ENSMUSG00000055652	Klhl25	2810402K13Rik|BC027373|Enc-1	kelch-like 25	protein-coding
mm_16507.1	chr2	181319715	181319780	+	1	NA	promoter-TSS (NM_001166665)	promoter-TSS (NM_001166665)	23	NM_001001882	269400	Mm.11333	NM_001001882	ENSMUSG00000038685	Rtel1	AI451565|AW540478|Rtel	regulator of telomere elongation helicase 1	protein-coding
mm_37465.1	chr4	123486404	123486433	-	1	NA	exon (NM_001199137, exon 32 of 93)	exon (NM_001199137, exon 32 of 93)	-74507	NM_001167918	442834	Mm.483803	NM_001167918		D830031N03Rik	Kiaa0754|mKIAA0754	RIKEN cDNA D830031N03 gene	protein-coding
mm_104736.1	chr11	98358237	98358253	-	1	NA	promoter-TSS (NR_045477)	promoter-TSS (NR_045477)	38	NR_045477	69338	Mm.398308	NR_045477	ENSMUSG00000085944	1700003D09Rik	-	RIKEN cDNA 1700003D09 gene	ncRNA
mm_122978.1	chr14	54983317	54983327	-	1	NA	exon (NM_080728, exon 25 of 41)	exon (NM_080728, exon 25 of 41)	-7546	NR_030607	100124433		NR_030607	ENSMUSG00000077928	Mir208b	Mirn208b|mir-208b	microRNA 208b	ncRNA
mm_170983.1	chr2	73214334	73214334	-	1	NA	5' UTR (NM_025942, exon 1 of 11)	5' UTR (NM_025942, exon 1 of 11)	113	NM_030091	67059	Mm.22661	NM_025942	ENSMUSG00000027108	Ola1	2510025G09Rik|2810405J23Rik|2810409H07Rik|Gtpbp9|PTD004	Obg-like ATPase 1	protein-coding
mm_142310.1	chr17	42876410	42876416	-	1	NA	promoter-TSS (NM_009847)	promoter-TSS (NM_009847)	11	NM_009847	12488	Mm.218637	NM_009847	ENSMUSG00000061665	Cd2ap	AL024079|C78928|METS-1|Mets1	CD2-associated protein	protein-coding
mm_2115.1	chr1	87878141	87878155	+	1	NA	intron (NM_177646, intron 1 of 29)	intron (NM_177646, intron 1 of 29)	-23849	NR_136921	100503175	Mm.426422	NR_136921	ENSMUSG00000101942	Gm19582	-	predicted gene, 19582	ncRNA
mm_131881.1	chr16	23224835	23224845	+	1	NA	promoter-TSS (NM_145933)	promoter-TSS (NM_145933)	100	NM_145933	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_158849.1	chrX	169985212	169985240	-	1	NA	intron (NM_001290512, intron 7 of 9)	intron (NM_001290512, intron 7 of 9)	-6309	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_44142.1	chr5	150259617	150259631	+	1	NA	promoter-TSS (NM_172887)	promoter-TSS (NM_172887)	-306	NM_172887	320365	Mm.216590	NM_172887	ENSMUSG00000056602	Fry	13CDNA73|9330186A19Rik|AF346502|AI462658|C87180|D930046M03|cg003|mKIAA4143	FRY microtubule binding protein	protein-coding
mm_120504.1	chr14	66281084	66281105	+	1	NA	promoter-TSS (NM_172498)	promoter-TSS (NM_172498)	-42	NM_001162365	19229	Mm.21613	NM_172498	ENSMUSG00000059456	Ptk2b	CADTK|CAKB|CAKbeta|E430023O05Rik|FADK2|FAK2|PYK2|Raftk	PTK2 protein tyrosine kinase 2 beta	protein-coding
mm_18791.1	chr2	73775309	73775319	-	1	NA	promoter-TSS (NM_001113246)	promoter-TSS (NM_001113246)	32	NM_001166603	108699	Mm.257073	NM_029716	ENSMUSG00000056486	Chn1	0610007I19Rik|0710001E19Rik|1700112L09Rik|2900046J01Rik|AI413815|ARHGAP2	chimerin 1	protein-coding
mm_55840.1	chr6	83156394	83156400	-	1	NA	promoter-TSS (NM_023790)	promoter-TSS (NM_023790)	-7	NM_027948	71837	Mm.17621	NM_027948	ENSMUSG00000030030	1700003E16Rik	AU041756	RIKEN cDNA 1700003E16 gene	protein-coding
mm_171297.1	chr3	91127053	91127057	-	1	NA	Intergenic	L1Md_T|LINE|L1	-36250	NM_001101461	229550	Mm.98335	NM_001101461	ENSMUSG00000091175	9130204L05Rik	Gm127	RIKEN cDNA 9130204L05 gene	protein-coding
mm_30426.1	chr3	152973353	152973364	-	1	NA	intron (NM_012028, intron 2 of 4)	B4A|SINE|B4	8849	NM_012028	26938	Mm.40915	NM_012028	ENSMUSG00000039037	St6galnac5	AI851940|Siat7e	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 5	protein-coding
mm_21669.1	chr2	164425563	164425584	-	1	NA	3' UTR (NM_011521, exon 5 of 5)	3' UTR (NM_011521, exon 5 of 5)	17615	NM_011521	20971	Mm.3815	NM_011521	ENSMUSG00000017009	Sdc4	AA959608|AW108331|S4|Synd4|ryudocan|syndecan-4	syndecan 4	protein-coding
mm_121916.1	chr14	22635606	22635610	-	1	NA	intron (NM_028275, intron 5 of 6)	B1F|SINE|Alu	-92810	NR_046307	74896	Mm.444661	NR_046307		4930405A10Rik	4930456G20Rik	RIKEN cDNA 4930405A10 gene	ncRNA
mm_15152.1	chr2	154008228	154008244	+	1	NA	promoter-TSS (NM_008953)	promoter-TSS (NM_008953)	-40	NM_008953	19194	Mm.29197	NM_008953	ENSMUSG00000042459	Bpifa2	Bpifa2e|Psp	BPI fold containing family A, member 2	protein-coding
mm_78717.1	chr9	41531999	41532021	+	1	NA	TTS (NR_029790)	TTS (NR_029790)	585	NR_029790	723892		NR_029790	ENSMUSG00000093011	Mir100	Mirn100|mir-100|mmu-mir-100	microRNA 100	ncRNA
mm_88382.1	chr10	76449058	76449068	+	1	NA	promoter-TSS (NM_029816)	promoter-TSS (NM_029816)	-18	NM_029816	76964	Mm.472489	NM_029816	ENSMUSG00000009114	2610028H24Rik	ORF67	RIKEN cDNA 2610028H24 gene	protein-coding
mm_10149.1	chr2	4300728	4300741	+	1	NA	intron (NM_172475, intron 1 of 22)	intron (NM_172475, intron 1 of 22)	-100242	NM_001177843	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding
mm_84025.1	chr9	57756289	57756292	-	1	NA	intron (NM_007713, intron 5 of 12)	AT_rich|Low_complexity|Low_complexity	9570	NM_007713	102414	Mm.25720	NM_007713	ENSMUSG00000032316	Clk3	AI256811	CDC-like kinase 3	protein-coding
mm_154776.1	chrX	12762467	12762470	+	1	NA	promoter-TSS (NM_001048208)	promoter-TSS (NM_001048208)	190	NR_045852	552913	Mm.216846	NR_045852	ENSMUSG00000085891	Gm14634	OTTMUSG00000017535	predicted gene 14634	ncRNA
mm_81442.1	chr9	109537047	109537081	+	1	NA	Intergenic	B1_Mur1|SINE|Alu	31198	NM_199036	382105	Mm.335468	NM_199036	ENSMUSG00000074060	Fbxw15	Fbxo12J	F-box and WD-40 domain protein 15	protein-coding
mm_118445.1	chr14	8125244	8125245	+	1	NA	intron (NM_178279, intron 3 of 18)	intron (NM_178279, intron 3 of 18)	27031	NM_178279	218699	Mm.29515	NM_145458	ENSMUSG00000033885	Pxk	C230080L11Rik|D14Ertd813e|MONaKA	PX domain containing serine/threonine kinase	protein-coding
mm_19966.1	chr2	117977162	117977174	-	1	NA	intron (NR_126479, intron 8 of 9)	intron (NR_126479, intron 8 of 9)	134034	NR_126479	329496	Mm.235844	NR_126479	ENSMUSG00000087203	Gm13986	C230060E24|OTTMUSG00000015236	predicted gene 13986	ncRNA
mm_64509.1	chr7	143628070	143628121	+	1	NA	promoter-TSS (NM_175649)	promoter-TSS (NM_175649)	-250	NM_175649	244237	Mm.247498	NM_175649	ENSMUSG00000045362	Tnfrsf26	Tnfrh3|Tnfrsf24	tumor necrosis factor receptor superfamily, member 26	protein-coding
mm_37965.1	chr4	133417165	133417173	-	1	NA	intron (NM_016981, intron 4 of 11)	intron (NM_016981, intron 4 of 11)	47393	NR_039582	100628620		NR_039582	ENSMUSG00000092745	Mir5122	mmu-mir-5122|mu-mir-5122	microRNA 5122	ncRNA
mm_132283.1	chr16	33057013	33057038	+	1	NA	promoter-TSS (NM_178378)	promoter-TSS (NM_178378)	511	NM_021338	57808	Mm.19355	NM_021338	ENSMUSG00000060636	Rpl35a	2810431L15Rik|Rpl35	ribosomal protein L35A	protein-coding
mm_6194.1	chr1	65161083	65161103	-	1	NA	exon (NM_010497, exon 8 of 9)	exon (NM_010497, exon 8 of 9)	18049	NM_010497	15926	Mm.9925	NM_010497	ENSMUSG00000025950	Idh1	AI314845|AI788952|E030024J03Rik|Id-1|Idh-1|Idpc	isocitrate dehydrogenase 1 (NADP+), soluble	protein-coding
mm_61859.1	chr7	88309807	88309823	+	1	NA	exon (NM_009982, exon 7 of 7)	exon (NM_009982, exon 7 of 7)	31730	NM_001311790	13032	Mm.89295	NM_009982	ENSMUSG00000030560	Ctsc	AI047818|CatC|DPP1|DPPI	cathepsin C	protein-coding
mm_169993.1	chr17	15731005	15731014	+	1	NA	exon (NM_007690, exon 7 of 36)	exon (NM_007690, exon 7 of 36)	26042	NM_007690	12648	Mm.8137	NM_007690	ENSMUSG00000023852	Chd1	4930525N21Rik|AI851787|AW555109	chromodomain helicase DNA binding protein 1	protein-coding
mm_127048.1	chr15	96643226	96643272	+	1	NA	promoter-TSS (NM_001166456)	promoter-TSS (NM_001166456)	-336	NM_001166458	105727	Mm.103568	NM_134086	ENSMUSG00000023169	Slc38a1	AA408026|AA409865|AL022800|AU015942|NAT2	solute carrier family 38, member 1	protein-coding
mm_19304.1	chr2	90490797	90490809	-	1	NA	intron (NM_008982, intron 1 of 23)	intron (NM_008982, intron 1 of 23)	-11629	NM_001135657	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_81072.1	chr9	106211600	106211620	+	1	NA	intron (NM_011876, intron 2 of 8)	intron (NM_011876, intron 2 of 8)	8502	NM_011876	23999	Mm.274346	NM_011876	ENSMUSG00000023277	Twf2	A6-related|AU014993|Ptk9l|Ptk9r	twinfilin actin binding protein 2	protein-coding
mm_152717.1	chr19	17511416	17511420	-	1	NA	exon (NM_001190483, exon 23 of 38)	exon (NM_001190483, exon 23 of 38)	117375	NM_019437	54391	Mm.7013	NM_019437	ENSMUSG00000024712	Rfk	0610038L10Rik|AF031381|KOI-4	riboflavin kinase	protein-coding
mm_124962.1	chr15	13481326	13481328	+	1	NA	Intergenic	Intergenic	-307652	NM_007666	12563	Mm.57048	NM_007666	ENSMUSG00000039385	Cdh6	cad6	cadherin 6	protein-coding
mm_95730.1	chr11	54626453	54626457	+	1	NA	intron (NM_175258, intron 10 of 27)	intron (NM_175258, intron 10 of 27)	30309	NM_001252497	192786	Mm.254404	NM_175258	ENSMUSG00000037533	Rapgef6	A530068K01|AI844632|BB085664|C030018K18Rik|PDZ-GEF2|Pdzgef2|RA-GEF-2|Ragef2|mKIAA4052	Rap guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_82977.1	chr9	35849901	35849905	-	1	NA	promoter-TSS (NR_030730)	promoter-TSS (NR_030730)	-23	NR_030730	100041605	Mm.99350	NR_030730	ENSMUSG00000098705	Gm3428	-	predicted gene 3428	ncRNA
mm_155146.1	chrX	52791079	52791099	+	1	NA	promoter-TSS (NM_001034059)	promoter-TSS (NM_001034059)	-111	NM_001034059	434778	Mm.23411	NM_001034059	ENSMUSG00000073207	Ccdc160	6330534C20Rik	coiled-coil domain containing 160	protein-coding
mm_66491.1	chr7	45053305	45053342	-	1	NA	promoter-TSS (NM_175022)	promoter-TSS (NM_175022)	-442	NM_175022	233210	Mm.219137	NM_175022	ENSMUSG00000046574	Prr12	6720469B10|BC058674	proline rich 12	protein-coding
mm_85008.1	chr9	87209938	87209945	-	1	NA	intron (NM_199316, intron 21 of 26)	intron (NM_199316, intron 21 of 26)	45591	NM_199316	382090	Mm.335338	NM_199316	ENSMUSG00000056919	Cep162	4922501C03Rik|mKIAA1009	centrosomal protein 162	protein-coding
mm_71637.1	chr8	57490318	57490328	+	1	NA	intron (NR_126553, intron 1 of 3)	ORR1A2|LTR|ERVL-MaLR	2360	NR_126555	78353	Mm.426240	NR_126553	ENSMUSG00000096917	2500002B13Rik	-	RIKEN cDNA 2500002B13 gene	ncRNA
mm_33077.1	chr4	123904908	123904916	+	1	NA	promoter-TSS (NM_019660)	promoter-TSS (NM_019660)	-101	NM_019660	56309	Mm.446553	NM_019660	ENSMUSG00000028647	Mycbp	5730488M09Rik|AW552132|AW742590|Amy-1	MYC binding protein	protein-coding
mm_108842.1	chr12	97354550	97354550	+	1	NA	Intergenic	PB1D10|SINE|Alu	904909	NM_008079	14420	Mm.5120	NM_008079	ENSMUSG00000021003	Galc	2310068B06Rik|A930008M05Rik|AW212969|AW413532|Gacy|twi|twitcher	galactosylceramidase	protein-coding
mm_6202.1	chr1	66349045	66349047	-	1	NA	intron (NM_001310634, intron 2 of 14)	intron (NM_001310634, intron 2 of 14)	27322	NM_001310634	17756	Mm.256966	NM_008632	ENSMUSG00000015222	Map2	G1-397-34|MAP-2|Mtap-2|Mtap2|repro4	microtubule-associated protein 2	protein-coding
mm_116107.1	chr13	28949381	28949392	-	1	NA	Intergenic	Intergenic	4296	NM_009238	20677	Mm.240627	NM_009238	ENSMUSG00000076431	Sox4	AA682046|Sox-4	SRY (sex determining region Y)-box 4	protein-coding
mm_86363.1	chr9	123792055	123792066	-	1	NA	3' UTR (NM_001110253, exon 18 of 18)	3' UTR (NM_001110253, exon 18 of 18)	-14417	NM_030712	80901	Mm.124289	NM_030712	ENSMUSG00000048521	Cxcr6	BB217514|BONZO|STRL33	chemokine (C-X-C motif) receptor 6	protein-coding
mm_80532.1	chr9	80274728	80274733	+	1	NA	intron (NM_001039546, intron 19 of 32)	ID4_|SINE|ID	109696	NM_001039546	17920	Mm.4040	NM_008662	ENSMUSG00000033577	Myo6	BC029719|Tlc|sv	myosin VI	protein-coding
mm_43723.1	chr5	139543863	139543871	+	1	NA	promoter-TSS (NM_013702)	promoter-TSS (NM_013702)	-31	NM_013702	22255	Mm.42190	NM_013702	ENSMUSG00000029546	Uncx	Chx4|Uncx4.1	UNC homeobox	protein-coding
mm_16178.1	chr2	172577637	172577662	+	1	NA	Intergenic	Intergenic	26658	NM_001159696	21420	Mm.3629	NM_009335	ENSMUSG00000028640	Tfap2c	AA409384|AP2gamma|Ap-2.2|Stra2|Tcfap2c	transcription factor AP-2, gamma	protein-coding
mm_113247.1	chr13	27354127	27354131	+	1	NA	TTS (NM_010088)	TTS (NM_010088)	8456	NM_001289919	13529	Mm.291450	NM_010088	ENSMUSG00000018259	Prl8a2	D/tPRP|DPRP|Dtprp|Ghd11|mdPRP	prolactin family 8, subfamily a, member 2	protein-coding
mm_100004.1	chr11	114851658	114851666	+	1	NA	promoter-TSS (NM_147217)	promoter-TSS (NM_147217)	122	NM_001110338	70355	Mm.242413	NM_147217	ENSMUSG00000051043	Gprc5c	1110028I06Rik|3200002M13Rik|Raig3	G protein-coupled receptor, family C, group 5, member C	protein-coding
mm_26687.1	chr3	156562786	156562796	+	1	NA	intron (NM_177274, intron 1 of 6)	intron (NM_177274, intron 1 of 6)	997	NM_001039094	320840	Mm.317293	NM_177274	ENSMUSG00000040037	Negr1	5330422G01Rik|KILON|Ntra	neuronal growth regulator 1	protein-coding
mm_21759.1	chr2	164839821	164839831	-	1	NA	exon (NM_011125, exon 16 of 16)	exon (NM_011125, exon 16 of 16)	6053	NM_008906	19025	Mm.359633	NM_008906	ENSMUSG00000017760	Ctsa	AU019505|PPCA|Ppgb	cathepsin A	protein-coding
mm_944.1	chr1	56972181	56972206	+	1	NA	promoter-TSS (NM_139146)	promoter-TSS (NM_139146)	724	NR_024325	329160	Mm.419039	NR_024325	ENSMUSG00000087022	9130024F11Rik	B530002L08|EG329160	RIKEN cDNA 9130024F11 gene	ncRNA
mm_153239.1	chr19	36114283	36114316	-	1	NA	intron (NM_013468, intron 8 of 8)	intron (NM_013468, intron 8 of 8)	5545	NM_013468	107765	Mm.10279	NM_013468	ENSMUSG00000024803	Ankrd1	Alrp|CARP|Crap|MARP1	ankyrin repeat domain 1 (cardiac muscle)	protein-coding
mm_125786.1	chr15	74716667	74716676	+	1	NA	3' UTR (NM_028216, exon 3 of 3)	3' UTR (NM_028216, exon 3 of 3)	1832	NM_028216	72373	Mm.46395	NM_028216	ENSMUSG00000022598	Psca	2210408B04Rik	prostate stem cell antigen	protein-coding
mm_78317.1	chr9	24341654	24341663	+	1	NA	Intergenic	Intergenic	161482	NM_172920	244745	Mm.38526	NM_172920	ENSMUSG00000043067	Dpy19l1	1100001I19Rik|6030402K12|AI225861|AW558481	dpy-19-like 1 (C. elegans)	protein-coding
mm_141022.1	chr17	25140287	25140298	-	1	NA	intron (NM_001317404, intron 1 of 24)	intron (NM_001317404, intron 1 of 24)	3661	NM_001317404	26373	Mm.270587	NM_011930	ENSMUSG00000036636	Clcn7	ClC-7|D17Wsu51e	chloride channel, voltage-sensitive 7	protein-coding
mm_67379.1	chr7	79842121	79842131	-	1	NA	exon (NM_008486, exon 1 of 20)	exon (NM_008486, exon 1 of 20)	226	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_134371.1	chr16	17130277	17130280	-	1	NA	3' UTR (NM_022324, exon 3 of 3)	3' UTR (NM_022324, exon 3 of 3)	2105	NM_022324	64136	Mm.30222	NM_022324	ENSMUSG00000022769	Sdf2l1	-	stromal cell-derived factor 2-like 1	protein-coding
mm_20739.1	chr2	137116722	137116735	-	1	NA	promoter-TSS (NM_013822)	promoter-TSS (NM_013822)	-208	NM_013822	16449	Mm.22398	NM_013822	ENSMUSG00000027276	Jag1	ABE2|Gsfabe2|Htu|Ozz|Ser-1	jagged 1	protein-coding
mm_34082.1	chr4	138775777	138775784	+	1	NA	promoter-TSS (NM_011109)	promoter-TSS (NM_011109)	45	NM_011109	18782	Mm.71913	NM_011109	ENSMUSG00000041202	Pla2g2d	Splash|mGIID	phospholipase A2, group IID	protein-coding
mm_14481.1	chr2	131514861	131514865	+	1	NA	intron (NM_001177836, intron 2 of 7)	MTD|LTR|ERVL-MaLR	23001	NM_001177838	228608	Mm.136586	NM_145533	ENSMUSG00000027333	Smox	B130066H01Rik|PAO|PAOh1|SMO	spermine oxidase	protein-coding
mm_51317.1	chr6	72314528	72314539	+	1	NA	TTS (NM_001282071)	TTS (NM_001282071)	9923	NM_147779	20388	Mm.46033	NM_147779	ENSMUSG00000056370	Sftpb	AI562151|SF-B|SP-B|Sftp-3|Sftp3	surfactant associated protein B	protein-coding
mm_129877.1	chr15	83447861	83447876	-	1	NA	intron (NM_001159509, intron 1 of 10)	intron (NM_001159509, intron 1 of 10)	-15018	NM_001159510	23970	Mm.23978	NM_011862	ENSMUSG00000016664	Pacsin2	AI197433	protein kinase C and casein kinase substrate in neurons 2	protein-coding
mm_4753.1	chr1	182287973	182287998	+	1	NA	Intergenic	Intergenic	-5226	NM_007853	13244	Mm.29648	NM_007853	ENSMUSG00000038633	Degs1	AA536663|Degs|Des1|Mdes	delta(4)-desaturase, sphingolipid 1	protein-coding
mm_89962.1	chr10	111296816	111296838	+	1	NA	3' UTR (NM_001003717, exon 23 of 23)	3' UTR (NM_001003717, exon 23 of 23)	-1852	NM_027914	71769	Mm.45256	NM_027914	ENSMUSG00000035759	Bbs10	1300007O09Rik|AI452285	Bardet-Biedl syndrome 10 (human)	protein-coding
mm_72828.1	chr8	88251992	88252014	+	1	NA	exon (NM_001164497, exon 9 of 13)	exon (NM_001164497, exon 9 of 13)	-20400	NM_007406	11513	Mm.288206	NM_007406	ENSMUSG00000031659	Adcy7	AA407758	adenylate cyclase 7	protein-coding
mm_78215.1	chr9	21526145	21526207	+	1	NA	promoter-TSS (NM_206536)	promoter-TSS (NM_206536)	-1	NM_206536	382062	Mm.325205	NM_206536	ENSMUSG00000057191	AB124611	Gm1706	cDNA sequence AB124611	protein-coding
mm_36436.1	chr4	82295371	82295390	-	1	NA	3' UTR (NM_001113209, exon 12 of 12)	3' UTR (NM_001113209, exon 12 of 12)	210399	NM_001286127	18028	Mm.317947	NM_008687	ENSMUSG00000008575	Nfib	6720429L07Rik|CTF|E030026I10Rik|NF-I/B|NF1-B|NFI-B	nuclear factor I/B	protein-coding
mm_28495.1	chr3	92484485	92484491	-	1	NA	exon (NM_009264, exon 2 of 2)	exon (NM_009264, exon 2 of 2)	1393	NM_009264	20753	Mm.331191	NM_009264	ENSMUSG00000050359	Sprr1a	AI528815|SPR1a|mSPRR1A	small proline-rich protein 1A	protein-coding
mm_109046.1	chr12	104263134	104263158	+	1	NA	promoter-TSS (NM_001199940)	promoter-TSS (NM_001199940)	24	NM_001199940	628900	Mm.436602	NM_001199940	ENSMUSG00000079014	Serpina3i	2B2|EG628900|Gm6930	serine (or cysteine) peptidase inhibitor, clade A, member 3I	protein-coding
mm_122287.1	chr14	34503324	34503345	-	1	NA	promoter-TSS (NM_009758)	promoter-TSS (NM_009758)	-788	NM_009758	12166	Mm.237825	NM_009758	ENSMUSG00000021796	Bmpr1a	1110037I22Rik|ALK3|AU045487|BMPR-IA|Bmpr	bone morphogenetic protein receptor, type 1A	protein-coding
mm_91298.1	chr10	24916092	24916101	-	1	NA	exon (NM_007482, exon 7 of 8)	exon (NM_007482, exon 7 of 8)	5432	NR_105870	102465545		NR_105870	ENSMUSG00000099181	Mir6905	Gm27879|mmu-mir-6905	microRNA 6905	ncRNA
mm_136983.1	chr17	17005110	17005136	+	1	NA	Intergenic	Intergenic	-58980	NM_001005358	449000	Mm.483718	NM_001005358	ENSMUSG00000096696	Zfp960	-	zinc finger protein 960	protein-coding
mm_80335.1	chr9	75052092	75052136	+	1	NA	intron (NM_021548, intron 1 of 2)	intron (NM_021548, intron 1 of 2)	14382	NM_021548	59046	Mm.247837	NM_021548	ENSMUSG00000007656	Arpp19	19kDa|2700024H10Rik|ARPP-19|AW559096|Arpp12	cAMP-regulated phosphoprotein 19	protein-coding
mm_64523.1	chr7	143847878	143847904	+	1	NA	3' UTR (NM_007856, exon 9 of 9)	3' UTR (NM_007856, exon 9 of 9)	24724	NM_007856	13360	Mm.249342	NM_007856	ENSMUSG00000058454	Dhcr7	AA409147	7-dehydrocholesterol reductase	protein-coding
mm_131573.1	chr16	18348182	18348273	+	1	NA	promoter-TSS (NM_001272029)	promoter-TSS (NM_001272029)	45	NM_001272029	11877	Mm.293599	NM_033474	ENSMUSG00000000325	Arvcf	-	armadillo repeat gene deleted in velo-cardio-facial syndrome	protein-coding
mm_94623.1	chr11	16778601	16778612	+	1	NA	intron (NM_207655, intron 1 of 27)	intron (NM_207655, intron 1 of 27)	26403	NM_007912	13649	Mm.8534	NM_007912	ENSMUSG00000020122	Egfr	9030024J15Rik|AI552599|Erbb|Errb1|Errp|Wa5|wa-2|wa2	epidermal growth factor receptor	protein-coding
mm_166051.1	chr4	131844509	131844509	-	1	NA	intron (NM_025297, intron 1 of 9)	PB1D10|SINE|Alu	1038	NM_025297	26922	Mm.192706	NM_025297	ENSMUSG00000028910	Mecr	AI195831|Nrbf1	mitochondrial trans-2-enoyl-CoA reductase	protein-coding
mm_7764.1	chr1	131199920	131199928	-	1	NA	exon (NM_001311094, exon 1 of 5)	exon (NM_001311094, exon 1 of 5)	261	NM_001311094	54354	Mm.248291	NM_018750	ENSMUSG00000026430	Rassf5	1300019G20Rik|Maxp1|Nore1|Nore1A|Nore1B|Rapl	Ras association (RalGDS/AF-6) domain family member 5	protein-coding
mm_75062.1	chr8	33731765	33731785	-	1	NA	promoter-TSS (NM_001167922)	promoter-TSS (NM_001167922)	-139	NM_001167921	68153	Mm.286104	NM_026584	ENSMUSG00000031585	Gtf2e2	34kDa|AI462509|C330006J08Rik	general transcription factor II E, polypeptide 2 (beta subunit)	protein-coding
mm_158453.1	chrX	140548589	140548599	-	1	NA	intron (NM_001077364, intron 2 of 3)	intron (NM_001077364, intron 2 of 3)	-5407	NM_010286	14605	Mm.22216	NM_010286	ENSMUSG00000031431	Tsc22d3	DIP|Dsip1|Gilz|TSC-22R|Tilz3	TSC22 domain family, member 3	protein-coding
mm_19303.1	chr2	90479166	90479178	-	1	NA	promoter-TSS (NM_001135657)	promoter-TSS (NM_001135657)	2	NM_001135657	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_43099.1	chr5	124478086	124478089	+	1	NA	5' UTR (NM_030259, exon 1 of 4)	5' UTR (NM_030259, exon 1 of 4)	148	NM_030259	80291	Mm.425280	NM_030259	ENSMUSG00000029401	Rilpl2	-	Rab interacting lysosomal protein-like 2	protein-coding
mm_126182.1	chr15	78609815	78609835	+	1	NA	exon (NM_028195, exon 7 of 13)	exon (NM_028195, exon 7 of 13)	12778	NM_028195	72318	Mm.32911	NM_028195	ENSMUSG00000018008	Cyth4	2510004M07Rik|5830469K17Rik|AI467541|Pscd4|mFLJ00017	cytohesin 4	protein-coding
mm_5988.1	chr1	58445407	58445491	-	1	NA	promoter-TSS (NM_027351)	promoter-TSS (NM_027351)	37	NM_027374	70225	Mm.340195	NM_027351	ENSMUSG00000026035	Ppil3	2310076N22Rik|2510026K04Rik|Cyp10l	peptidylprolyl isomerase (cyclophilin)-like 3	protein-coding
mm_127861.1	chr15	8351534	8351551	-	1	NA	exon (NM_027707, exon 10 of 47)	exon (NM_027707, exon 10 of 47)	92921	NM_027707	71175	Mm.240329	NM_027707	ENSMUSG00000022141	Nipbl	Idn3	Nipped-B homolog (Drosophila)	protein-coding
mm_66193.1	chr7	34213451	34213470	-	1	NA	intron (NM_008155, intron 9 of 17)	intron (NM_008155, intron 9 of 17)	-16813	NM_026549	68079	Mm.38173	NM_026549	ENSMUSG00000002635	Pdcd2l	6030457N17Rik	programmed cell death 2-like	protein-coding
mm_85346.1	chr9	103209003	103209015	-	1	NA	3' UTR (NM_133977, exon 17 of 17)	3' UTR (NM_133977, exon 17 of 17)	-6944	NM_009275	20818	Mm.273053	NM_009275	ENSMUSG00000032553	Srprb	AA409543	signal recognition particle receptor, B subunit	protein-coding
mm_14331.1	chr2	129490159	129490186	+	1	NA	intron (NM_177653, intron 1 of 6)	intron (NM_177653, intron 1 of 6)	46430	NM_177653	228592	Mm.452175	NM_177653	ENSMUSG00000043727	F830045P16Rik	Sirpb3	RIKEN cDNA F830045P16 gene	protein-coding
mm_167697.1	chr9	88542418	88542418	+	1	NA	Intergenic	L2a|LINE|L2	-5602	NM_001142943	71640	Mm.259988	NM_001142943	ENSMUSG00000032425	Zfp949	4930422I07Rik	zinc finger protein 949	protein-coding
mm_37795.1	chr4	130520111	130520133	-	1	NA	Intergenic	Intergenic	53914	NM_025998	67149	Mm.423029	NM_025998	ENSMUSG00000078532	Nkain1	2610200G18Rik|2810426C15Rik	Na+/K+ transporting ATPase interacting 1	protein-coding
mm_5129.1	chr1	9667701	9667701	-	1	NA	3' UTR (NM_001290397, exon 15 of 15)	3' UTR (NM_001290397, exon 15 of 15)	32508	NM_001290397	17864	Mm.479	NM_008651	ENSMUSG00000025912	Mybl1	A-myb|G1-419-6|repro9	myeloblastosis oncogene-like 1	protein-coding
mm_128996.1	chr15	74841611	74841633	-	1	NA	promoter-TSS (NM_001033229)	promoter-TSS (NM_001033229)	21	NM_001033229	110115	Mm.322606	NM_001033229	ENSMUSG00000075604	Cyp11b1	AA389061|CPN1|Cyp11b|Cyp11b-1|FHI	cytochrome P450, family 11, subfamily b, polypeptide 1	protein-coding
mm_130447.1	chr15	98529041	98529043	-	1	NA	intron (NM_133714, intron 5 of 9)	intron (NM_133714, intron 5 of 9)	-2583	NR_034052	100217416	Mm.296240	NR_034052	ENSMUSG00000065939	Snora2b	MBI-137	small nucleolar RNA, H/ACA box 2B	snoRNA
mm_118344.1	chr13	114607098	114607106	-	1	NA	promoter-TSS (NR_045976)	promoter-TSS (NR_045976)	-126	NR_045976	75161	Mm.50406	NM_175218	ENSMUSG00000051758	4930544M13Rik	-	RIKEN cDNA 4930544M13 gene	ncRNA
mm_78274.1	chr9	22071003	22071051	+	1	NA	promoter-TSS (NR_040407)	promoter-TSS (NR_040407)	25	NR_040406	100503652	Mm.439941	NR_040406	ENSMUSG00000096981	Gm16845	-	predicted gene, 16845	ncRNA
mm_151317.1	chr19	55885886	55885901	+	1	NA	intron (NR_138565, intron 4 of 15)	L3|LINE|CR1	-9428	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_164143.1	chr15	59416623	59416640	-	1	NA	intron (NM_001164604, intron 3 of 4)	intron (NM_001164604, intron 3 of 4)	42433	NM_001164604	68501	Mm.27762	NM_026746	ENSMUSG00000059586	Nsmce2	1110014D18Rik|AI661537	NSE2/MMS21 homolog, SMC5-SMC6 complex SUMO ligase	protein-coding
mm_60781.1	chr7	45565167	45565191	+	1	NA	intron (NM_025330, intron 6 of 8)	B2_Mm2|SINE|B2	-4974	NM_009737	12036	Mm.24210	NM_009737	ENSMUSG00000030826	Bcat2	Bcat-2|Eca40	branched chain aminotransferase 2, mitochondrial	protein-coding
mm_154828.1	chrX	18145852	18145877	+	1	NA	promoter-TSS (NM_028568)	promoter-TSS (NM_028568)	-6	NM_028568	73547	Mm.159027	NM_028568	ENSMUSG00000025043	Dusp21	1700094E07Rik|DSP21	dual specificity phosphatase 21	protein-coding
mm_51995.1	chr6	92156979	92156982	+	1	NA	intron (NM_001347342, intron 7 of 14)	intron (NM_001347342, intron 7 of 14)	27043	NM_025578	64658	Mm.87062	NM_025578	ENSMUSG00000014551	Mrps25	2810429N01Rik|Rpms25	mitochondrial ribosomal protein S25	protein-coding
mm_67324.1	chr7	79721286	79721297	-	1	NA	3' UTR (NM_175640, exon 9 of 9)	3' UTR (NM_175640, exon 9 of 9)	-7105	NM_001291222	16576	Mm.101633	NM_010626	ENSMUSG00000050382	Kif7	-	kinesin family member 7	protein-coding
mm_85704.1	chr9	108111280	108111293	-	1	NA	exon (NM_007567, exon 5 of 12)	exon (NM_007567, exon 5 of 12)	-16806	NM_146226	235606	Mm.219639	NM_146226	ENSMUSG00000032590	Apeh	-	acylpeptide hydrolase	protein-coding
mm_172005.1	chr6	108708396	108708398	+	1	NA	Intergenic	ERVB7_1-LTR_MM|LTR|ERVK	-47463	NR_104577	75394	Mm.395061	NR_040757	ENSMUSG00000087341	0610040F04Rik	-	RIKEN cDNA 0610040F04 gene	ncRNA
mm_19533.1	chr2	94400413	94400424	-	1	NA	intron (NM_183106, intron 1 of 24)	MT2B2|LTR|ERVL	6271	NM_183106	74569	Mm.248504	NM_183106	ENSMUSG00000027194	Ttc17	9130020K17Rik|D2Bwg1005e	tetratricopeptide repeat domain 17	protein-coding
mm_159512.1	chr4	58912027	58912027	-	1	NA	intron (NM_172381, intron 1 of 48)	CpG	698	NM_172381	230249	Mm.234801	NM_172381	ENSMUSG00000050812	AI314180	AW558785|BB181316|mKIAA0368	expressed sequence AI314180	protein-coding
mm_158082.1	chrX	101265719	101265731	-	1	NA	exon (NM_001308535, exon 6 of 8)	exon (NM_001308535, exon 6 of 8)	-1733	NM_001317221	245536	Mm.212463	NM_001033362	ENSMUSG00000090141	Gm614	-	predicted gene 614	protein-coding
mm_108826.1	chr12	95740195	95740198	+	1	NA	intron (NM_201518, intron 1 of 1)	intron (NM_201518, intron 1 of 1)	47970	NM_201518	399558	Mm.341948	NM_201518	ENSMUSG00000047414	Flrt2	-	fibronectin leucine rich transmembrane protein 2	protein-coding
mm_72226.1	chr8	72741864	72741876	+	1	NA	exon (NM_009188, exon 8 of 19)	exon (NM_009188, exon 8 of 19)	18600	NM_009188	20467	Mm.2137	NM_009188	ENSMUSG00000031622	Sin3b	2810430C10Rik	transcriptional regulator, SIN3B (yeast)	protein-coding
mm_138530.1	chr17	35243059	35243069	+	1	NA	intron (NM_001252457, intron 1 of 10)	intron (NM_001252457, intron 1 of 10)	247	NM_001252457	53817	Mm.439827	NM_019693	ENSMUSG00000019432	Ddx39b	0610030D10Rik|AI428441|Bat-1|Bat1|Bat1a|D17H6S81E|D17H6S81E-1|D6S81Eh	DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B	protein-coding
mm_67028.1	chr7	66427470	66427483	-	1	NA	promoter-TSS (NM_053080)	promoter-TSS (NM_053080)	1	NM_053080	56847	Mm.140988	NM_053080	ENSMUSG00000015134	Aldh1a3	ALDH6|RALDH3|V1	aldehyde dehydrogenase family 1, subfamily A3	protein-coding
mm_124321.1	chr14	103346766	103346841	-	1	NA	promoter-TSS (NM_207215)	promoter-TSS (NM_207215)	-3	NM_207215	105689	Mm.6478	NM_207215	ENSMUSG00000033004	Mycbp2	AU023734|AW107953|AW546647|C130061D10Rik|Pam|Phr1|R75243	MYC binding protein 2	protein-coding
mm_162343.1	chr1	50958689	50958691	+	1	NA	intron (NM_019790, intron 4 of 9)	intron (NM_019790, intron 4 of 9)	31167	NM_019790	56363	Mm.245154	NM_019790	ENSMUSG00000026109	Tmeff2	4832418D20Rik|7630402F16Rik|TR-2	transmembrane protein with EGF-like and two follistatin-like domains 2	protein-coding
mm_75901.1	chr8	71272368	71272382	-	1	NA	promoter-TSS (NM_001142322)	promoter-TSS (NM_001142322)	215	NM_001163042	76478	Mm.27355	NM_029621	ENSMUSG00000035439	Haus8	2410004L22Rik|Hice1	4HAUS augmin-like complex, subunit 8	protein-coding
mm_37486.1	chr4	123575704	123575708	-	1	NA	intron (NM_001199136, intron 1 of 97)	(A)n|Simple_repeat|Simple_repeat	-40714	NR_105824	102465214		NR_105824	ENSMUSG00000099005	Mir6398	Gm27657|mmu-mir-6398	microRNA 6398	ncRNA
mm_59484.1	chr7	27462656	27462669	+	1	NA	exon (NM_144923, exon 4 of 5)	exon (NM_144923, exon 4 of 5)	10244	NM_001290525	233016	Mm.24021	NM_144923	ENSMUSG00000040466	Blvrb	-	biliverdin reductase B (flavin reductase (NADPH))	protein-coding
mm_56541.1	chr6	99726290	99726297	-	1	NA	promoter-TSS (NM_001170419)	promoter-TSS (NM_001170419)	99	NM_001037539	50501	Mm.87365	NM_015768	ENSMUSG00000030069	Prok2	Bv8|PK2|Prok1	prokineticin 2	protein-coding
mm_47229.1	chr5	121384534	121384560	-	1	NA	intron (NM_172275, intron 1 of 11)	intron (NM_172275, intron 1 of 11)	1068	NM_001163470	231712	Mm.20488	NM_172275	ENSMUSG00000042726	Trafd1	1110008K06Rik|Fln29	TRAF type zinc finger domain containing 1	protein-coding
mm_117482.1	chr13	77135417	77135491	-	1	NA	promoter-TSS (NM_134071)	promoter-TSS (NM_134071)	14	NM_134071	105377	Mm.209730	NM_134071	ENSMUSG00000021597	Slf1	2700017A04Rik|AW545819|Ankrd32|Brctd1|Brctx|C730024G01Rik	SMC5-SMC6 complex localization factor 1	protein-coding
mm_112061.1	chr12	111966669	111966698	-	1	NA	intron (NM_027360, intron 1 of 3)	CpG	294	NM_027360	70257	Mm.318	NM_027360	ENSMUSG00000021290	2010107E04Rik	9430003J03Rik|AU043134|AV124504|Mp68	RIKEN cDNA 2010107E04 gene	protein-coding
mm_161657.1	chr17	6985017	6985017	+	1	NA	intron (NM_026611, intron 3 of 8)	intron (NM_026611, intron 3 of 8)	6157	NM_026611	68195	Mm.181237	NM_026611	ENSMUSG00000094724	Rnaset2b	0610007O07Rik|4833423A10Rik|4930532K22Rik|C79750|RNASE6PL|Rnaset2	ribonuclease T2B	protein-coding
mm_67050.1	chr7	67335251	67335254	-	1	NA	intron (NM_001033713, intron 2 of 11)	Lx9|LINE|L1	37606	NM_001291192	17258	Mm.132788	NM_001033713	ENSMUSG00000030557	Mef2a	A430079H05Rik	myocyte enhancer factor 2A	protein-coding
mm_139771.1	chr17	64719164	64719166	+	1	NA	intron (NM_008549, intron 16 of 21)	intron (NM_008549, intron 16 of 21)	-47946	NR_105051	101202683	Mm.393309	NR_105051		Dreh	-	down-regulated in hepatocellular carcinoma	ncRNA
mm_259.1	chr1	20730904	20730908	+	1	NA	promoter-TSS (NM_010552)	promoter-TSS (NM_010552)	1	NM_010552	16171	Mm.5419	NM_010552	ENSMUSG00000025929	Il17a	Ctla-8|Ctla8|IL-17|IL-17A|Il17	interleukin 17A	protein-coding
mm_86039.1	chr9	114390634	114390687	-	1	NA	promoter-TSS (NM_019922)	promoter-TSS (NM_019922)	52	NM_019922	56693	Mm.20904	NM_019922	ENSMUSG00000032431	Crtap	5730529N23Rik|CASP|Leprel3|P3h5	cartilage associated protein	protein-coding
mm_86053.1	chr9	114564087	114564103	-	1	NA	5' UTR (NM_001042503, exon 1 of 4)	5' UTR (NM_001042503, exon 1 of 4)	274	NM_001042503	636931	Mm.17857	NM_001042503	ENSMUSG00000079259	Trim71	2610206G21Rik|AL022943|Gm1127|Lin41|lin-41|mLin41|mlin-41	tripartite motif-containing 71	protein-coding
mm_130854.1	chr15	102073590	102073611	-	1	NA	promoter-TSS (NM_145625)	promoter-TSS (NM_145625)	-173	NM_145625	75705	Mm.290022	NM_145625	ENSMUSG00000058655	Eif4b	2310046H11Rik|AL024095|C85189|Eif4a2	eukaryotic translation initiation factor 4B	protein-coding
mm_43413.1	chr5	135962920	135962932	+	1	NA	exon (NM_001160366, exon 9 of 11)	exon (NM_001160366, exon 9 of 11)	11550	NM_001160366	109267	Mm.332750	NM_001160366	ENSMUSG00000029699	Ssc4d	C330016E03Rik|S4D-SRCRB|SRCRB-S4D|Srcrb4d	scavenger receptor cysteine rich family, 4 domains	protein-coding
mm_95820.1	chr11	55217710	55217732	+	1	NA	intron (NM_153139, intron 2 of 10)	intron (NM_153139, intron 2 of 10)	13381	NM_153139	215335	Mm.35732	NM_153139	ENSMUSG00000020261	Slc36a1	5830411H19Rik|AI839897|Pat1	solute carrier family 36 (proton/amino acid symporter), member 1	protein-coding
mm_18482.1	chr2	62592192	62592202	-	1	NA	Intergenic	Intergenic	-18176	NM_007986	14089	Mm.41816	NM_007986	ENSMUSG00000000392	Fap	SIMP	fibroblast activation protein	protein-coding
mm_89954.1	chr10	111293619	111293632	+	1	NA	3' UTR (NM_001003717, exon 23 of 23)	3' UTR (NM_001003717, exon 23 of 23)	-5054	NM_027914	71769	Mm.45256	NM_027914	ENSMUSG00000035759	Bbs10	1300007O09Rik|AI452285	Bardet-Biedl syndrome 10 (human)	protein-coding
mm_50.1	chr1	6527914	6527936	+	1	NA	intron (NM_001244693, intron 2 of 22)	intron (NM_001244693, intron 2 of 22)	40694	NM_001244692	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding
mm_157740.1	chrX	72918414	72918424	-	1	NA	promoter-TSS (NM_019405)	promoter-TSS (NM_019405)	-75	NM_019405	26370	Mm.24643	NM_019405	ENSMUSG00000031347	Cetn2	1110034A02Rik|AI326150|Calt|caltractin	centrin 2	protein-coding
mm_117602.1	chr13	90089106	90089116	-	1	NA	promoter-TSS (NM_025335)	promoter-TSS (NM_025335)	497	NM_028012	108138	Mm.37531	NM_028012	ENSMUSG00000021615	Xrcc4	2310057B22Rik|AW413319|AW545101	X-ray repair complementing defective repair in Chinese hamster cells 4	protein-coding
mm_131421.1	chr16	14708138	14708161	+	1	NA	exon (NM_011415, exon 3 of 3)	exon (NM_011415, exon 3 of 3)	2290	NM_011415	20583	Mm.4272	NM_011415	ENSMUSG00000022676	Snai2	Slug|Slugh|Snail2	snail family zinc finger 2	protein-coding
mm_82273.1	chr9	7352981	7353013	-	1	NA	exon (NM_008605, exon 5 of 10)	exon (NM_008605, exon 5 of 10)	5623	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_43290.1	chr5	134183999	134184046	+	1	NA	promoter-TSS (NM_053266)	promoter-TSS (NM_053266)	-16	NM_053266	114674	Mm.218744	NM_053266	ENSMUSG00000015942	Gtf2ird2	1700012P16Rik	GTF2I repeat domain containing 2	protein-coding
mm_155796.1	chrX	98938179	98938198	+	1	NA	5' UTR (NM_207633, exon 1 of 7)	5' UTR (NM_207633, exon 1 of 7)	407	NM_207633	77929	Mm.212290	NM_207633	ENSMUSG00000047694	Yipf6	A430107J06Rik	Yip1 domain family, member 6	protein-coding
mm_100529.1	chr11	120598642	120598678	+	1	NA	promoter-TSS (NM_011568)	promoter-TSS (NM_011568)	128	NM_001038230	66156	Mm.21645	NM_025389	ENSMUSG00000025135	Anapc11	1110011I19Rik|R75218	anaphase promoting complex subunit 11	protein-coding
mm_3997.1	chr1	164488956	164488957	+	1	NA	Intergenic	Intergenic	-30601	NM_009721	11931	Mm.4550	NM_009721	ENSMUSG00000026576	Atp1b1	Atp4b|Atpb|Atpb-1|NKbeta1	ATPase, Na+/K+ transporting, beta 1 polypeptide	protein-coding
mm_159091.1	chr2	32320832	32320832	-	1	NA	intron (NM_001301737, intron 13 of 21)	L3|LINE|CR1	2372	NR_029811	387239		NR_029811	ENSMUSG00000092807	Mir199b	Mirn199b|mir-199b	microRNA 199b	ncRNA
mm_36861.1	chr4	106911352	106911354	-	1	NA	promoter-TSS (NM_198438)	promoter-TSS (NM_198438)	-117	NM_198438	72475	Mm.195635	NM_023672	ENSMUSG00000061887	Ssbp3	2610021L12Rik|2610200M23Rik|5730488C10Rik|AI854733|AW551939|LAST|SSDP1	single-stranded DNA binding protein 3	protein-coding
mm_135217.1	chr16	36656819	36656829	-	1	NA	intron (NM_019388, intron 1 of 7)	PB1|SINE|Alu	9253	NM_019388	12524	Mm.1452	NM_019388	ENSMUSG00000022901	Cd86	B7|B7-2|B7.2|B70|CLS1|Cd28l2|ETC-1|Ly-58|Ly58|MB7|MB7-2|TS/A-2	CD86 antigen	protein-coding
mm_48640.1	chr5	145201830	145201873	-	1	NA	promoter-TSS (NM_023322)	promoter-TSS (NM_023322)	31	NM_023322	67235	Mm.432480	NM_023322	ENSMUSG00000029627	Zkscan14	2310046C23Rik|2810437E14Rik|Zfp99|Znf394	zinc finger with KRAB and SCAN domains 14	protein-coding
mm_64040.1	chr7	140773136	140773150	+	1	NA	exon (NM_021282, exon 7 of 9)	exon (NM_021282, exon 7 of 9)	9311	NM_021282	13106	Mm.21758	NM_021282	ENSMUSG00000025479	Cyp2e1	Cyp2e	cytochrome P450, family 2, subfamily e, polypeptide 1	protein-coding
mm_136163.1	chr16	88563059	88563070	-	1	NA	5' UTR (NM_018778, exon 1 of 1)	5' UTR (NM_018778, exon 1 of 1)	119	NM_018778	54420	Mm.25836	NM_018778	ENSMUSG00000050520	Cldn8	AI648025	claudin 8	protein-coding
mm_20036.1	chr2	119878454	119878455	-	1	NA	Intergenic	Intergenic	-18774	NM_001164274	29808	Mm.87532	NM_013720	ENSMUSG00000033943	Mga	AV312082|C130042M01Rik|C80739|D030062C11Rik|Mad5	MAX gene associated	protein-coding
mm_23749.1	chr3	69397310	69397312	+	1	NA	intron (NM_178726, intron 1 of 3)	intron (NM_178726, intron 1 of 3)	80393	NM_178726	242083	Mm.40577	NM_178726	ENSMUSG00000027784	Ppm1l	3222401G13|5930404J21Rik|AI481720|AW045850|PP2C|PP2Cepsilon|Pp2ce|Ppp2ce|mKIAA4175	protein phosphatase 1 (formerly 2C)-like	protein-coding
mm_57371.1	chr6	124780443	124780474	-	1	NA	promoter-TSS (NM_001302555)	promoter-TSS (NM_001302555)	-731	NM_001302555	16977	Mm.3207	NM_013588	ENSMUSG00000030125	Lrrc23	4921537K05Rik|B7|Lrpb7	leucine rich repeat containing 23	protein-coding
mm_96605.1	chr11	69091446	69091450	+	1	NA	3' UTR (NM_009497, exon 5 of 5)	3' UTR (NM_009497, exon 5 of 5)	2920	NM_009497	22318	Mm.28643	NM_009497	ENSMUSG00000020894	Vamp2	Syb-2|Syb2|sybII	vesicle-associated membrane protein 2	protein-coding
mm_168323.1	chr11	115536176	115536176	-	1	NA	promoter-TSS (NM_133354)	promoter-TSS (NM_133354)	54	NM_133354	170930	Mm.29923	NM_133354	ENSMUSG00000020738	Sumo2	SUMO-2|Smt3A|Smt3b|Smt3h2	small ubiquitin-like modifier 2	protein-coding
mm_70291.1	chr8	3665748	3665763	+	1	NA	promoter-TSS (NM_026985)	promoter-TSS (NM_026985)	-7	NM_026985	69189	Mm.175176	NM_026985	ENSMUSG00000013974	Mcemp1	1810033B17Rik	mast cell expressed membrane protein 1	protein-coding
mm_124933.1	chr15	12205131	12205153	+	1	NA	promoter-TSS (NM_172958)	promoter-TSS (NM_172958)	48	NM_172958	268783	Mm.54460	NM_172958	ENSMUSG00000039458	Mtmr12	3Pap|4932703C11|C730015A02Rik|Pip3ap|mKIAA1682	myotubularin related protein 12	protein-coding
mm_48151.1	chr5	137151106	137151122	-	1	NA	Intergenic	Intergenic	-34907	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_28669.1	chr3	95281834	95281843	-	1	NA	5' UTR (NM_173347, exon 1 of 8)	5' UTR (NM_173347, exon 1 of 8)	238	NM_173347	229589	Mm.14155	NM_173347	ENSMUSG00000015711	Prune1	9230112O05Rik|C130058A12|DRES-17|HTCD37|PRUNEM1|Prune|Prune-M1	prune exopolyphosphatase	protein-coding
mm_106195.1	chr11	116842820	116842828	-	1	NA	promoter-TSS (NM_028865)	promoter-TSS (NM_028865)	625	NM_033398	107817	Mm.481684	NM_033398	ENSMUSG00000056962	Jmjd6	5730436I23Rik|D11Ertd195e|PSR|PtdSerR|Ptdsr|mKIAA0585	jumonji domain containing 6	protein-coding
mm_83382.1	chr9	44568110	44568154	-	1	NA	Intergenic	Intergenic	-36760	NM_001110826	13209	Mm.267061	NM_007841	ENSMUSG00000032097	Ddx6	1110001P04Rik|E230023J21Rik|HLR2|mRCK/P54|p54|rck	DEAD (Asp-Glu-Ala-Asp) box polypeptide 6	protein-coding
mm_111224.1	chr12	84698770	84698819	-	1	NA	promoter-TSS (NM_001033334)	promoter-TSS (NM_001033334)	13	NM_001033334	627191	Mm.152484	NM_001033334	ENSMUSG00000071234	Syndig1l	DSPC1|Gm261|Tmem90a	synapse differentiation inducing 1 like	protein-coding
mm_77279.1	chr8	116708156	116708159	-	1	NA	intron (NM_029441, intron 1 of 6)	L1M4|LINE|L1	24834	NM_029441	75796	Mm.159575	NM_029441	ENSMUSG00000031758	Cdyl2	1700029M19Rik|4930453I21Rik|Gm20194	chromodomain protein, Y chromosome-like 2	protein-coding
mm_87623.1	chr10	57802415	57802432	+	1	NA	exon (NM_020561, exon 3 of 8)	exon (NM_020561, exon 3 of 8)	7879	NM_020561	57319	Mm.2379	NM_020561	ENSMUSG00000019872	Smpdl3a	0610010C24Rik|AI529588|ASM3A|ASML3|ASML3A	sphingomyelin phosphodiesterase, acid-like 3A	protein-coding
mm_65674.1	chr7	28310388	28310417	-	1	NA	intron (NM_025616, intron 2 of 10)	intron (NM_025616, intron 2 of 10)	1644	NM_025616	66525	Mm.167913	NM_025616	ENSMUSG00000003438	Timm50	2810403L02Rik|AU015082|TIM50L	translocase of inner mitochondrial membrane 50	protein-coding
mm_19459.1	chr2	92389249	92389335	-	1	NA	intron (NM_001202445, intron 2 of 11)	CpG	-1846	NR_105966	102466783		NR_105966	ENSMUSG00000099093	Mir7000	Gm27338|mmu-mir-7000	microRNA 7000	ncRNA
mm_89731.1	chr10	98987074	98987112	+	1	NA	exon (NM_026482, exon 4 of 21)	exon (NM_026482, exon 4 of 21)	71941	NM_026482	67972	Mm.166944	NM_026482	ENSMUSG00000019943	Atp2b1	2810442I22Rik|E130111D10Rik|Pmca1	ATPase, Ca++ transporting, plasma membrane 1	protein-coding
mm_67994.1	chr7	100894685	100894729	-	1	NA	intron (NM_001081116, intron 1 of 20)	CpG	-12298	NR_037289	100526508		NR_037289	ENSMUSG00000093296	Mir3102	mmu-mir-3102	microRNA 3102	ncRNA
mm_58365.1	chr6	148814927	148814931	-	1	NA	intron (NM_001081113, intron 5 of 24)	intron (NM_001081113, intron 5 of 24)	16538	NM_001081113	320727	Mm.260105	NM_001081113	ENSMUSG00000040029	Ipo8	6230418K12Rik|Abcc10|C130009K11Rik|MRP7|OM-1|Om1|Ranbp8	importin 8	protein-coding
mm_55803.1	chr6	82824320	82824339	-	1	NA	Intergenic	Intergenic	-49875	NM_013820	15277	Mm.255848	NM_013820	ENSMUSG00000000628	Hk2	AI642394|HKII	hexokinase 2	protein-coding
mm_124254.1	chr14	101892260	101892279	-	1	NA	intron (NM_001347628, intron 8 of 26)	intron (NM_001347628, intron 8 of 26)	51646	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_89646.1	chr10	96764992	96765021	+	1	NA	Intergenic	Intergenic	148005	NM_007569	12226	Mm.23811	NM_007569	ENSMUSG00000036478	Btg1	AI426953|AW546738	B cell translocation gene 1, anti-proliferative	protein-coding
mm_166446.1	chr5	137265966	137265991	-	1	NA	Intergenic	B4A|SINE|B4	-22276	NM_009599	11423	Mm.255464	NM_009599	ENSMUSG00000023328	Ache	-	acetylcholinesterase	protein-coding
mm_116540.1	chr13	45923654	45923676	-	1	NA	intron (NM_001199304, intron 2 of 6)	B4A|SINE|B4	41326	NM_001199304	20238	Mm.342683	NM_009124	ENSMUSG00000046876	Atxn1	2900016G23Rik|Atx1|C85907|ENSMUSG00000074917|Gm10786|Sca1	ataxin 1	protein-coding
mm_116703.1	chr13	50595495	50595531	-	1	NA	Intergenic	Intergenic	5567	NR_030453	751559		NR_030453	ENSMUSG00000095697	Mir683-1	Gm26093|Mirn683|Mirn683-1|Mirn683a|mmu-mir-683|mmu-mir-683-1	microRNA 683-1	ncRNA
mm_148085.1	chr18	73662701	73662749	-	1	NA	exon (NM_008540, exon 5 of 12)	exon (NM_008540, exon 5 of 12)	41016	NM_008540	17128	Mm.100399	NM_008540	ENSMUSG00000024515	Smad4	AW743858|D18Wsu70e|DPC4|Madh4	SMAD family member 4	protein-coding
mm_39959.1	chr5	32136522	32136535	+	1	NA	promoter-TSS (NM_008037)	promoter-TSS (NM_008037)	56	NM_008037	14284	Mm.24684	NM_008037	ENSMUSG00000029135	Fosl2	Fra-2	fos-like antigen 2	protein-coding
mm_152053.1	chr19	6277725	6277766	-	1	NA	intron (NM_010119, intron 1 of 4)	intron (NM_010119, intron 1 of 4)	849	NM_010119	13660	Mm.30169	NM_010119	ENSMUSG00000024772	Ehd1	AA409636|Past1|RME-1	EH-domain containing 1	protein-coding
mm_23313.1	chr3	53175475	53175477	+	1	NA	intron (NM_175386, intron 2 of 3)	intron (NM_175386, intron 2 of 3)	133929	NM_175386	108927	Mm.118617	NM_175386	ENSMUSG00000048332	Lhfp	2810489O06Rik|AI194968	lipoma HMGIC fusion partner	protein-coding
mm_8420.1	chr1	152386590	152386610	-	1	NA	promoter-TSS (NM_025677)	promoter-TSS (NM_025677)	82	NM_025677	66637	Mm.379120	NM_025677	ENSMUSG00000014980	Tsen15	5730449L18Rik|AL023077|Sen15	tRNA splicing endonuclease subunit 15	protein-coding
mm_58526.1	chr7	4147839	4147862	+	1	NA	TTS (NM_175529)	TTS (NM_175529)	2022	NM_175529	243813	Mm.347643	NM_175529	ENSMUSG00000043432	Leng9	9530024C23Rik|F630035L11Rik	leukocyte receptor cluster (LRC) member 9	protein-coding
mm_82563.1	chr9	21073495	21073541	-	1	NA	promoter-TSS (NM_001039824)	promoter-TSS (NM_001039824)	-4	NM_001039824	68165	Mm.490294	NM_001039824	ENSMUSG00000079677	Fdx1l	B230118G17Rik|Fdx2	ferredoxin 1-like	protein-coding
mm_37759.1	chr4	129672713	129672774	-	1	NA	promoter-TSS (NM_008468)	promoter-TSS (NM_008468)	24	NM_008468	16650	Mm.202358	NM_008468	ENSMUSG00000003731	Kpna6	IPOA7|Kpna5|NPI-2	karyopherin (importin) alpha 6	protein-coding
mm_49367.1	chr6	23248767	23248778	+	1	NA	promoter-TSS (NM_028462)	promoter-TSS (NM_028462)	-508	NM_028462	73191	Mm.55115	NM_028462	ENSMUSG00000029697	Fezf1	3110069A13Rik|Fez|Zfp312-like|fez-like	Fez family zinc finger 1	protein-coding
mm_136442.1	chr16	94571118	94571141	-	1	NA	intron (NM_001113389, intron 1 of 11)	intron (NM_001113389, intron 1 of 11)	222	NM_001113389	13548	Mm.310973	NM_007890	ENSMUSG00000022897	Dyrk1a	2310043O08Rik|D16Ertd272e|D16Ertd493e|Dyrk|ENSMUSG00000074897|Gm10783|Mnbh|Mp86|mmb	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1a	protein-coding
mm_169048.1	chr13	16499840	16499858	+	1	NA	Intergenic	L1Md_Gf|LINE|L1	487998	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_59900.1	chr7	30308761	30308771	+	1	NA	promoter-TSS (NM_198027)	promoter-TSS (NM_198027)	13	NM_198027	233065	Mm.276277	NM_198027	ENSMUSG00000042831	Alkbh6	AI839550|Abh6|C130099A02	alkB homolog 6	protein-coding
mm_66623.1	chr7	45475060	45475075	-	1	NA	3' UTR (NM_027903, exon 7 of 7)	3' UTR (NM_027903, exon 7 of 7)	-8169	NM_007527	12028	Mm.19904	NM_007527	ENSMUSG00000003873	Bax	-	BCL2-associated X protein	protein-coding
mm_78599.1	chr9	37488989	37488999	+	1	NA	promoter-TSS (NM_146222)	promoter-TSS (NM_146222)	-327	NM_146222	235184	Mm.127892	NM_146222	ENSMUSG00000042138	Msantd2	2810450G17Rik|9530092B10Rik	Myb/SANT-like DNA-binding domain containing 2	protein-coding
mm_17175.1	chr2	25332482	25332495	-	1	NA	promoter-TSS (NR_027448)	promoter-TSS (NR_027448)	83	NR_027448	100272219	Mm.382103	NR_027448	ENSMUSG00000097345	AA543186	-	expressed sequence AA543186	ncRNA
mm_37523.1	chr4	124699513	124699518	-	1	NA	Intergenic	L2a|LINE|L2	-1184	NM_010213	14201	Mm.331856	NM_010213	ENSMUSG00000032643	Fhl3	SLIM2	four and a half LIM domains 3	protein-coding
mm_48104.1	chr5	137071129	137071137	-	1	NA	exon (NM_008871, exon 2 of 9)	exon (NM_008871, exon 2 of 9)	1139	NM_008871	18787	Mm.250422	NM_008871	ENSMUSG00000037411	Serpine1	PAI-1|PAI1|Planh1	serine (or cysteine) peptidase inhibitor, clade E, member 1	protein-coding
mm_141175.1	chr17	26841242	26841248	-	1	NA	exon (NM_008700, exon 1 of 2)	exon (NM_008700, exon 1 of 2)	320	NM_008700	18091	Mm.41974	NM_008700	ENSMUSG00000015579	Nkx2-5	Csx|Nkx-2.5|Nkx2.5|tinman	NK2 homeobox 5	protein-coding
mm_137781.1	chr17	29493170	29493183	+	1	NA	intron (NM_008842, intron 4 of 5)	intron (NM_008842, intron 4 of 5)	2131	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_66425.1	chr7	44553902	44553955	-	1	NA	promoter-TSS (NM_009473)	promoter-TSS (NM_009473)	37	NM_009473	22260	Mm.968	NM_009473	ENSMUSG00000060601	Nr1h2	AI194859|LXR|LXRB|LXRBSV|LXRbeta|NER1|OR-1|RIP15|UR|Unr|Unr2	nuclear receptor subfamily 1, group H, member 2	protein-coding
mm_31381.1	chr4	47943751	47943756	+	1	NA	Intergenic	Intergenic	-101552	NM_015743	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_73680.1	chr8	111537001	111537037	+	1	NA	5' UTR (NM_133206, exon 1 of 4)	5' UTR (NM_133206, exon 1 of 4)	379	NM_001168621	170737	Mm.271578	NM_133206	ENSMUSG00000033545	Znrf1	B830022L21Rik|Rnf42|Zrfp1|nin283	zinc and ring finger 1	protein-coding
mm_20463.1	chr2	129367429	129367439	-	1	NA	intron (NM_008361, intron 4 of 6)	intron (NM_008361, intron 4 of 6)	-2468	NR_015474	329514	Mm.207315	NM_177848	ENSMUSG00000074805	Il1bos	9430083I22|Gm14047|OTTMUSG00000015529	interleukin 1 beta, opposite strand	ncRNA
mm_87022.1	chr10	28074929	28074937	+	1	NA	5' UTR (NM_008983, exon 1 of 32)	5' UTR (NM_008983, exon 1 of 32)	113	NM_008983	19272	Mm.332303	NM_008983	ENSMUSG00000019889	Ptprk	AI853699|PTPk|RPTPkappa	protein tyrosine phosphatase, receptor type, K	protein-coding
mm_62020.1	chr7	91542995	91543043	+	1	NA	intron (NM_011807, intron 2 of 22)	intron (NM_011807, intron 2 of 22)	452233	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_164412.1	chr16	37836464	37836473	+	1	NA	TTS (NM_008047)	TTS (NM_008047)	-31932	NM_177093	320184	Mm.390882	NM_177093	ENSMUSG00000034158	Lrrc58	1810012N18Rik|C330018J07Rik	leucine rich repeat containing 58	protein-coding
mm_120351.1	chr14	63943933	63943952	+	1	NA	exon (NM_011446, exon 1 of 2)	exon (NM_011446, exon 1 of 2)	236	NM_011446	20680	Mm.42162	NM_011446	ENSMUSG00000063060	Sox7	-	SRY (sex determining region Y)-box 7	protein-coding
mm_99980.1	chr11	114666999	114667031	+	1	NA	intron (NR_037269, intron 2 of 4)	RMER10B|LTR|ERVL	-1528	NM_023372	67671	Mm.238817	NM_023372	ENSMUSG00000057322	Rpl38	0610025G13Rik|Rbt|Ts|Tss	ribosomal protein L38	protein-coding
mm_32368.1	chr4	105261350	105261354	+	1	NA	Intergenic	Intergenic	104005	NM_080555	67916	Mm.348326	NM_080555	ENSMUSG00000028517	Plpp3	1110003O22Rik|2610002D05Rik|AV025606|D4Bwg0538e|D4Bwg1535e|Lpp3|Ppab2b|Ppap2b	phospholipid phosphatase 3	protein-coding
mm_1685.1	chr1	74856629	74856651	+	1	NA	3' UTR (NM_009872, exon 1 of 1)	3' UTR (NM_009872, exon 1 of 1)	1611	NM_009872	12570	Mm.153833	NM_009872	ENSMUSG00000090071	Cdk5r2	B230310J22Rik|p39	cyclin-dependent kinase 5, regulatory subunit 2 (p39)	protein-coding
mm_48322.1	chr5	138994113	138994124	-	1	NA	intron (NM_008808, intron 1 of 5)	CpG-11694	835	NM_008808	18590	Mm.2675	NM_008808	ENSMUSG00000025856	Pdgfa	-	platelet derived growth factor, alpha	protein-coding
mm_39734.1	chr5	29196071	29196085	+	1	NA	promoter-TSS (NM_021470)	promoter-TSS (NM_021470)	85	NR_110371	56874	Mm.87352	NM_021470	ENSMUSG00000029130	Rnf32	1700009J01Rik|2700025B22Rik|4930542N22Rik|Lmbr2	ring finger protein 32	protein-coding
mm_167299.1	chr8	55059223	55059241	+	1	NA	3' UTR (NM_001253754, exon 7 of 7)	3' UTR (NM_001253754, exon 7 of 7)	104504	NM_001253756	234267	Mm.241700	NM_153581	ENSMUSG00000031517	Gpm6a	Gpm6|M6A	glycoprotein m6a	protein-coding
mm_56161.1	chr6	87980966	87980980	-	1	NA	promoter-TSS (NR_026990)	promoter-TSS (NR_026990)	509	NM_198622	243529	Mm.33796	NM_198622	ENSMUSG00000044927	H1fx	Gm461|H1.10|H1X	H1 histone family, member X	protein-coding
mm_77778.1	chr9	3018962	3018980	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	19772	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_63922.1	chr7	139347765	139347779	+	1	NA	Intergenic	B1_Mus2|SINE|Alu	-41337	NM_183144	212111	Mm.28308	NM_183144	ENSMUSG00000025477	Inpp5a	-	inositol polyphosphate-5-phosphatase A	protein-coding
mm_51377.1	chr6	73223042	73223058	+	1	NA	Intergenic	Intergenic	-1419	NM_001164669	330355	Mm.333166	NM_001164669	ENSMUSG00000052861	Dnah6	9830168K20|A730004I20Rik|Dnahc6|mKIAA1697|mdhc6	dynein, axonemal, heavy chain 6	protein-coding
mm_147047.1	chr18	34931799	34931812	-	1	NA	intron (NM_144866, intron 1 of 10)	CpG-6828	198	NM_144866	225363	Mm.329353	NM_144866	ENSMUSG00000024360	Etf1	AI463371|D6Ertd109e|ERF|ERF1|SUP45L1|TB3-1	eukaryotic translation termination factor 1	protein-coding
mm_158464.1	chrX	140813463	140813467	-	1	NA	promoter-TSS (NM_031381)	promoter-TSS (NM_031381)	-32	NM_031381	83555	Mm.193025	NM_031381	ENSMUSG00000042386	Tex13b	4933403J23Rik|Tex13	testis expressed 13B	protein-coding
mm_164444.1	chr16	49855486	49855497	+	1	NA	promoter-TSS (NM_010581)	promoter-TSS (NM_010581)	-163	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_59357.1	chr7	25681178	25681191	+	1	NA	promoter-TSS (NM_172148)	promoter-TSS (NM_172148)	26	NM_172148	232987	Mm.22849	NM_172148	ENSMUSG00000063439	B9d2	stumpy	B9 protein domain 2	protein-coding
mm_160665.1	chr9	120128479	120128479	+	1	NA	5' UTR (NM_011029, exon 2 of 7)	5' UTR (NM_011029, exon 2 of 7)	713	NM_011029	16785	Mm.4071	NM_011029	ENSMUSG00000032518	Rpsa	67kDa|67lr|AL022858|Lamr|Lamr1|Lamrl1|MLR|P40|P40-3|P40-8	ribosomal protein SA	protein-coding
mm_62653.1	chr7	107693157	107693167	+	1	NA	intron (NM_001163557, intron 5 of 25)	intron (NM_001163557, intron 5 of 25)	64870	NM_001205227	320635	Mm.132828	NM_177216	ENSMUSG00000048065	Cyb5r2	D630003K02Rik|b5R.2	cytochrome b5 reductase 2	protein-coding
mm_142569.1	chr17	46676748	46676774	-	1	NA	exon (NM_027910, exon 9 of 12)	exon (NM_027910, exon 9 of 12)	-2506	NM_144857	224823	Mm.45101	NM_144857	ENSMUSG00000023971	Rrp36	-	ribosomal RNA processing 36 homolog (S. cerevisiae)	protein-coding
mm_61404.1	chr7	73409572	73409578	+	1	NA	exon (NM_177740, exon 3 of 4)	exon (NM_177740, exon 3 of 4)	-33801	NR_040324	319783	Mm.349813	NR_040324	ENSMUSG00000097756	A730056A06Rik	C76391	RIKEN cDNA A730056A06 gene	ncRNA
mm_88474.1	chr10	77606579	77606653	+	1	NA	promoter-TSS (NM_001301671)	promoter-TSS (NM_001301671)	18	NM_001301671	20610	Mm.24433	NM_019929	ENSMUSG00000020265	Sumo3	2810014B19Rik|D10Ertd345e|SMT3A|SUMO-3|Smt3h1	small ubiquitin-like modifier 3	protein-coding
mm_136541.1	chr16	97851797	97851853	-	1	NA	promoter-TSS (NM_144789)	promoter-TSS (NM_144789)	-598	NM_144789	114604	Mm.328741	NM_144789	ENSMUSG00000014039	Prdm15	C21orf83|E130018M06Rik|ORF62|Zfp298	PR domain containing 15	protein-coding
mm_28472.1	chr3	92080386	92080412	-	1	NA	3' UTR (NM_008508, exon 2 of 2)	3' UTR (NM_008508, exon 2 of 2)	2743	NM_008508	16939	Mm.1121	NM_008508	ENSMUSG00000043165	Lor	AI036317|S77319	loricrin	protein-coding
mm_26388.1	chr3	142570551	142570565	+	1	NA	exon (NM_018734, exon 9 of 11)	exon (NM_018734, exon 9 of 11)	10062	NM_001289493	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_40034.1	chr5	33658568	33658616	+	1	NA	promoter-TSS (NM_026698)	promoter-TSS (NM_026698)	464	NM_001040435	21335	Mm.379024	NM_011524	ENSMUSG00000037313	Tacc3	Aint|C86661|Eric1	transforming, acidic coiled-coil containing protein 3	protein-coding
mm_67711.1	chr7	89980482	89980496	-	1	NA	exon (NM_021876, exon 1 of 12)	exon (NM_021876, exon 1 of 12)	487	NM_021876	13626	Mm.380914	NM_021876	ENSMUSG00000030619	Eed	ENSMUSG00000039373|l(7)5Rn|l7Rn5|lusk	embryonic ectoderm development	protein-coding
mm_44583.1	chr5	24908375	24908428	-	1	NA	5' UTR (NM_001170556, exon 1 of 12)	5' UTR (NM_001170556, exon 1 of 12)	108	NM_001170556	108099	Mm.33649	NM_145401	ENSMUSG00000028944	Prkag2	2410051C13Rik|AAKG|AAKG2|AI854673|H91620p|WPWS	protein kinase, AMP-activated, gamma 2 non-catalytic subunit	protein-coding
mm_157517.1	chrX	49797701	49797755	-	1	NA	promoter-TSS (NM_177591)	promoter-TSS (NM_177591)	17	NM_177915	209268	Mm.110505	NM_177591	ENSMUSG00000031111	Igsf1	5330413N23|5530402E03|AI747649|InhBP/p120|mKIAA0364	immunoglobulin superfamily, member 1	protein-coding
mm_97331.1	chr11	77216172	77216178	+	1	NA	promoter-TSS (NM_177710)	promoter-TSS (NM_177710)	-250	NM_177710	237860	Mm.440381	NM_177710	ENSMUSG00000037926	Ssh2	SSH-2|SSH-2L|mSSH-2L	slingshot homolog 2 (Drosophila)	protein-coding
mm_80579.1	chr9	84049351	84049363	+	1	NA	intron (NM_001305935, intron 8 of 10)	intron (NM_001305935, intron 8 of 10)	100576	NM_199195	12040	Mm.12819	NM_199195	ENSMUSG00000032263	Bckdhb	BCKDE1B|BCKDH E1-beta	branched chain ketoacid dehydrogenase E1, beta polypeptide	protein-coding
mm_166964.1	chr7	44480842	44480842	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-3675	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_134763.1	chr16	23449829	23449833	-	1	NA	Intergenic	ORR1C1|LTR|ERVL-MaLR	20698	NM_001004151	239766	Mm.208751	NM_001004151	ENSMUSG00000033383	Rtp1	Gm1766|Gm604	receptor transporter protein 1	protein-coding
mm_82637.1	chr9	21989408	21989424	-	1	NA	promoter-TSS (NM_023622)	promoter-TSS (NM_023622)	37	NM_023622	71746	Mm.110594	NM_023622	ENSMUSG00000040146	Rgl3	1300003D20Rik|mFLJ00153	ral guanine nucleotide dissociation stimulator-like 3	protein-coding
mm_116386.1	chr13	41184077	41184080	-	1	NA	3' UTR (NM_019423, exon 8 of 8)	3' UTR (NM_019423, exon 8 of 8)	36084	NM_001311121	54326	Mm.2567	NM_019423	ENSMUSG00000021364	Elovl2	AI317360|Ssc2	elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 2	protein-coding
mm_67925.1	chr7	99889293	99889303	-	1	NA	intron (NM_001164258, intron 8 of 18)	L1M4c|LINE|L1	30080	NM_001164258	446101	Mm.440757	NM_001164258	ENSMUSG00000035211	Xrra1	AI449753	X-ray radiation resistance associated 1	protein-coding
mm_16592.1	chr2	4652061	4652077	-	1	NA	promoter-TSS (NM_026045)	promoter-TSS (NM_026045)	17	NM_026045	67229	Mm.38529	NM_026045	ENSMUSG00000039449	Prpf18	2810441A10Rik	pre-mRNA processing factor 18	protein-coding
mm_8616.1	chr1	156036418	156036454	-	1	NA	promoter-TSS (NM_144791)	promoter-TSS (NM_144791)	44	NM_144791	208263	Mm.211654	NM_144791	ENSMUSG00000026466	Tor1aip1	LAP1|Lap1B	torsin A interacting protein 1	protein-coding
mm_4352.1	chr1	171899026	171899048	+	1	NA	Intergenic	Intergenic	-18425	NM_001347187	30925	Mm.486404	NM_030710	ENSMUSG00000015314	Slamf6	KAL1|KAL1b|Ly108|NTB-A|NTBA|SF2000	SLAM family member 6	protein-coding
mm_139123.1	chr17	47504842	47504844	+	1	NA	promoter-TSS (NM_001081636)	promoter-TSS (NM_001081636)	-208	NM_001081636	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_162018.1	chr19	45235458	45235458	-	1	NA	promoter-TSS (NM_010691)	promoter-TSS (NM_010691)	-222	NM_010691	16814	Mm.116815	NM_010691	ENSMUSG00000025216	Lbx1	Lbx1h	ladybird homeobox homolog 1 (Drosophila)	protein-coding
mm_137820.1	chr17	30155962	30155968	+	1	NA	intron (NM_148926, intron 3 of 4)	MTE-int|LTR|ERVL-MaLR	100570	NR_105839	102465223		NR_105839	ENSMUSG00000098522	Mir6412	Gm27364|mmu-mir-6412	microRNA 6412	ncRNA
mm_50601.1	chr6	49218441	49218444	+	1	NA	Intergenic	Intergenic	-3488	NM_023670	140488	Mm.281018	NM_023670	ENSMUSG00000029814	Igf2bp3	2610101N11Rik|AA522010|AL022933|AU045931|IMP-3|IMP3|Koc13|Neilsen|mimp3	insulin-like growth factor 2 mRNA binding protein 3	protein-coding
mm_72671.1	chr8	84908708	84908723	+	1	NA	promoter-TSS (NM_010062)	promoter-TSS (NM_010062)	91	NM_010062	13423	Mm.350831	NM_010062	ENSMUSG00000003812	Dnase2a	Dnase2	deoxyribonuclease II alpha	protein-coding
mm_84147.1	chr9	59465091	59465106	-	1	NA	intron (NM_019927, intron 1 of 13)	intron (NM_019927, intron 1 of 13)	16643	NR_045640	100504377	Mm.446631	NR_045640		Gm20199	-	predicted gene, 20199	ncRNA
mm_107108.1	chr12	17881860	17881935	+	1	NA	Intergenic	CpG	191083	NM_016677	53602	Mm.313619	NM_016677	ENSMUSG00000071379	Hpcal1	NVP-3|Nvp3|VILIP3|Vnsl3|Vsnl3	hippocalcin-like 1	protein-coding
mm_147581.1	chr18	56470896	56470923	-	1	NA	intron (NM_026240, intron 2 of 13)	intron (NM_026240, intron 2 of 13)	38777	NM_026240	107022	Mm.24356	NM_026240	ENSMUSG00000001700	Gramd3	9030613F08Rik|9130427A09Rik|AW061306|NS3TP2	GRAM domain containing 3	protein-coding
mm_1649.1	chr1	74661634	74661656	+	1	NA	promoter-TSS (NM_001014974)	promoter-TSS (NM_001014974)	-109	NM_001014974	67534	Mm.260714	NM_001014974	ENSMUSG00000033257	Ttll4	4632407P03Rik|AI451681|mKIAA0173	tubulin tyrosine ligase-like family, member 4	protein-coding
mm_131020.1	chr15	103564223	103564252	-	1	NA	exon (NM_008134, exon 2 of 4)	exon (NM_008134, exon 2 of 4)	844	NM_001289587	14663	Mm.219621	NM_008134	ENSMUSG00000022491	Glycam1	MC26|Sgp50|glyCAM-1	glycosylation dependent cell adhesion molecule 1	protein-coding
mm_121766.1	chr14	19860599	19860621	-	1	NA	Intergenic	LTRIS2|LTR|ERV1	21685	NR_105025	52512	Mm.483998	NR_105025		D14Ertd670e	-	DNA segment, Chr 14, ERATO Doi 670, expressed	ncRNA
mm_117597.1	chr13	89742664	89742674	-	1	NA	promoter-TSS (NM_001134474)	promoter-TSS (NM_001134474)	-157	NM_001134475	13003	Mm.158700	NM_019389	ENSMUSG00000021614	Vcan	5430420N07Rik|9430051N09|Cspg2|DPEAAE|NG2|PG-M|PG-M(V0)|PG-M(V1)|hdf	versican	protein-coding
mm_100566.1	chr11	120730769	120730815	+	1	NA	exon (NM_007621, exon 3 of 8)	exon (NM_007621, exon 3 of 8)	1229	NM_007621	12409	Mm.21454	NM_007621	ENSMUSG00000025150	Cbr2	MLCR	carbonyl reductase 2	protein-coding
mm_19219.1	chr2	84650550	84650580	-	1	NA	promoter-TSS (NM_001085453)	promoter-TSS (NM_001085453)	-55	NM_001085453	12388	Mm.35738	NM_007615	ENSMUSG00000034101	Ctnnd1	AA409437|AU019353|Catns|Ctnnd|P120|mKIAA0384	catenin (cadherin associated protein), delta 1	protein-coding
mm_64018.1	chr7	140247317	140247319	+	1	NA	promoter-TSS (NM_001128145)	promoter-TSS (NM_001128145)	17	NM_175533	244234	Mm.85125	NM_175533	ENSMUSG00000054672	5830411N06Rik	Scart2	RIKEN cDNA 5830411N06 gene	protein-coding
mm_157132.1	chrX	9450759	9450816	-	1	NA	exon (NM_007807, exon 7 of 13)	exon (NM_007807, exon 7 of 13)	18537	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_96445.1	chr11	67455340	67455403	+	1	NA	Intergenic	CpG	-77627	NM_008088	14457	Mm.40338	NM_008088	ENSMUSG00000033066	Gas7	AW124766|B230343A10Rik|Gas7-cb	growth arrest specific 7	protein-coding
mm_9223.1	chr1	171234643	171234650	-	1	NA	promoter-TSS (NM_010185)	promoter-TSS (NM_010185)	-297	NM_010185	14127	Mm.22673	NM_010185	ENSMUSG00000058715	Fcer1g	AI573376|CD23|FcR-gamma|FcR[g]|FcRgamma|Fce1g|FcepsilonRI|Ly-50	Fc receptor, IgE, high affinity I, gamma polypeptide	protein-coding
mm_100356.1	chr11	118443516	118443537	+	1	NA	promoter-TSS (NM_001204130)	promoter-TSS (NM_001204130)	-8	NM_001204130	56745	Mm.23845	NM_019959	ENSMUSG00000017446	C1qtnf1	1600017K21Rik|CTRP1|Zsig37	C1q and tumor necrosis factor related protein 1	protein-coding
mm_29520.1	chr3	116508072	116508119	-	1	NA	promoter-TSS (NM_025517)	promoter-TSS (NM_025517)	80	NM_025517	66368	Mm.251228	NM_025517	ENSMUSG00000000339	Rtca	2310009A18Rik|AI450277|RPC|Rtcd1	RNA 3'-terminal phosphate cyclase	protein-coding
mm_35905.1	chr4	49631941	49631963	-	1	NA	promoter-TSS (NM_001163263)	promoter-TSS (NM_001163263)	-108	NM_001163263	109331	Mm.24765	NM_182999	ENSMUSG00000028309	Rnf20	4833430L21Rik|AW540162|C79397|mKIAA4116	ring finger protein 20	protein-coding
mm_31183.1	chr4	43519237	43519257	+	1	NA	exon (NM_009416, exon 5 of 9)	exon (NM_009416, exon 5 of 9)	4307	NM_009416	22004	Mm.646	NM_009416	ENSMUSG00000028464	Tpm2	Tpm-2|Trop-2	tropomyosin 2, beta	protein-coding
mm_84445.1	chr9	66126560	66126603	-	1	NA	promoter-TSS (NM_026635)	promoter-TSS (NM_026635)	-30	NM_026635	68250	Mm.27107	NM_026635	ENSMUSG00000032381	Fam96a	5730536A07Rik	family with sequence similarity 96, member A	protein-coding
mm_41805.1	chr5	103754201	103754217	+	1	NA	promoter-TSS (NM_133919)	promoter-TSS (NM_133919)	47	NM_133919	17355	Mm.6949	NM_133919	ENSMUSG00000029313	Aff1	9630032B01Rik|AW319193|Af4|Mllt2h|Rob	AF4/FMR2 family, member 1	protein-coding
mm_121639.1	chr14	8378822	8378846	-	1	NA	promoter-TSS (NM_146050)	promoter-TSS (NM_146050)	-71	NM_146050	18300	Mm.25351	NM_146050	ENSMUSG00000021749	Oit1	2310076N21Rik|AV067083|EF-7|Fam3d	oncoprotein induced transcript 1	protein-coding
mm_42044.1	chr5	108461252	108461305	+	1	NA	promoter-TSS (NM_172716)	promoter-TSS (NM_172716)	-54	NM_172716	69587	Mm.261218	NM_172716	ENSMUSG00000033623	Pcgf3	2310035N15Rik|AI662857|D630042K08Rik|DONG1|E430039C14|RNF3A|Rnf3	polycomb group ring finger 3	protein-coding
mm_141738.1	chr17	34122207	34122241	-	1	NA	promoter-TSS (NM_010238)	promoter-TSS (NM_010238)	383	NM_001204973	14312	Mm.3444	NM_010238	ENSMUSG00000024335	Brd2	AW228947|D17H6S113E|Frg-1|Fsrg-1|Fsrg1|Nat|Ring3|Rnf3|mKIAA4005	bromodomain containing 2	protein-coding
mm_64534.1	chr7	144175492	144175506	+	1	NA	promoter-TSS (NM_001113373)	promoter-TSS (NM_001113373)	-21	NM_001113373	210274	Mm.483624	NM_001081370	ENSMUSG00000037541	Shank2	ProSAP1|mKIAA1022	SH3/ankyrin domain gene 2	protein-coding
mm_61371.1	chr7	69918176	69918179	+	1	NA	Intergenic	Intergenic	419645	NR_131145	624549	Mm.116344	NR_131144	ENSMUSG00000109097	Gm29683	-	predicted gene, 29683	ncRNA
mm_128710.1	chr15	63943262	63943308	-	1	NA	exon (NM_144846, exon 6 of 12)	exon (NM_144846, exon 6 of 12)	28824	NR_029414	74460	Mm.390801	NR_029414	ENSMUSG00000100127	Gsdmcl-ps	4933426G20Rik	gasdermin C-like, pseudogene	pseudo
mm_20796.1	chr2	144255593	144255606	-	1	NA	exon (NM_024225, exon 7 of 13)	exon (NM_024225, exon 7 of 13)	10603	NR_030762	100313519	Mm.453538	NR_030762	ENSMUSG00000077714	Snord17	MBI-43	small nucleolar RNA, C/D box 17	snoRNA
mm_2205.1	chr1	89580246	89580256	+	1	NA	intron (NM_001037136, intron 1 of 16)	intron (NM_001037136, intron 1 of 16)	103641	NR_015540	74403	Mm.444291	NR_015540		4933400F21Rik	1700091C04Rik|4930565K10Rik	RIKEN cDNA 4933400F21 gene	ncRNA
mm_3501.1	chr1	150106996	150107012	+	1	NA	3' UTR (NM_011198, exon 10 of 10)	3' UTR (NM_011198, exon 10 of 10)	6973	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_135994.1	chr16	75240162	75240170	-	1	NA	Intergenic	Intergenic	345895	NM_001252513	320355	Mm.99517	NM_177142	ENSMUSG00000032948	Lipi	D930038D03Rik|lpd1	lipase, member I	protein-coding
mm_34486.1	chr4	148558423	148558469	+	1	NA	promoter-TSS (NR_131062)	promoter-TSS (NR_131062)	19	NR_131061	50912	Mm.266635	NM_016699	ENSMUSG00000017264	Exosc10	PM-Scl|PM/Scl-100|Pmscl2|RRP6|p2|p3|p4	exosome component 10	protein-coding
mm_76093.1	chr8	79711632	79711695	-	1	NA	promoter-TSS (NM_026904)	promoter-TSS (NM_026904)	77	NM_015751	24015	Mm.5831	NM_015751	ENSMUSG00000058355	Abce1	C79080|Oabp|RLI|RNS41|Rnaseli	ATP-binding cassette, sub-family E (OABP), member 1	protein-coding
mm_133907.1	chr16	97550488	97550527	+	1	NA	intron (NM_013606, intron 7 of 13)	intron (NM_013606, intron 7 of 13)	14424	NM_013606	17858	Mm.14157	NM_013606	ENSMUSG00000023341	Mx2	AI528743|Mx-2	MX dynamin-like GTPase 2	protein-coding
mm_51805.1	chr6	88724877	88724924	+	1	NA	5' UTR (NM_001166251, exon 1 of 8)	5' UTR (NM_001166251, exon 1 of 8)	196	NM_001166251	23945	Mm.272197	NM_011844	ENSMUSG00000033174	Mgll	AA589436|Magl|Mgl	monoglyceride lipase	protein-coding
mm_133107.1	chr16	65473790	65473805	+	1	NA	Intergenic	(CAG)n|Simple_repeat|Simple_repeat	-46832	NM_008849	18736	Mm.355440	NM_008849	ENSMUSG00000004842	Pou1f1	GHF-1|Hmp1|Pit-1|Pit1|Pit1-rs1|dw|dwarf	POU domain, class 1, transcription factor 1	protein-coding
mm_140693.1	chr17	13761365	13761410	-	1	NA	promoter-TSS (NM_022311)	promoter-TSS (NM_022311)	7	NM_022311	21646	Mm.486358	NM_022311	ENSMUSG00000038347	Tcte2	AI429268|Tcte-2	t-complex-associated testis expressed 2	protein-coding
mm_53711.1	chr6	143204026	143204038	+	1	NA	3' UTR (NM_029250, exon 8 of 8)	3' UTR (NM_029250, exon 8 of 8)	36802	NM_029250	75320	Mm.272548	NM_029250	ENSMUSG00000030275	Etnk1	1110061E11Rik|4930555L11Rik|AI195356|AI841245|C80956|D6Ertd3e|EKI1	ethanolamine kinase 1	protein-coding
mm_41230.1	chr5	88720930	88720977	+	1	NA	promoter-TSS (NM_026735)	promoter-TSS (NM_026735)	82	NM_026735	68473	Mm.35764	NM_026735	ENSMUSG00000006262	Mob1b	1110003E08Rik|AU015450|B230364F10|Mobkl1a	MOB kinase activator 1B	protein-coding
mm_59065.1	chr7	19463268	19463292	+	1	NA	Intergenic	Intergenic	-4786	NM_172279	232944	Mm.260504	NM_172279	ENSMUSG00000030397	Mark4	2410090P21Rik|C79806|Markl1	MAP/microtubule affinity regulating kinase 4	protein-coding
mm_7101.1	chr1	88779924	88779928	-	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	25036	NR_040493	78650	Mm.243767	NR_040493	ENSMUSG00000097398	Platr5	2410088K16Rik	pluripotency associated transcript 5	ncRNA
mm_4519.1	chr1	175631969	175631978	+	1	NA	promoter-TSS (NM_133809)	promoter-TSS (NM_133809)	-220	NM_133809	98256	Mm.27217	NM_133809	ENSMUSG00000039783	Kmo	AI046660	kynurenine 3-monooxygenase (kynurenine 3-hydroxylase)	protein-coding
mm_119088.1	chr14	30891400	30891417	+	1	NA	exon (NM_001289633, exon 7 of 22)	exon (NM_001289633, exon 7 of 22)	4932	NM_001289632	16427	Mm.34819	NM_018746	ENSMUSG00000021922	Itih4	ITI-HC4|Itih-4|PK-120	inter alpha-trypsin inhibitor, heavy chain 4	protein-coding
mm_158398.1	chrX	136742057	136742076	-	1	NA	promoter-TSS (NM_019768)	promoter-TSS (NM_019768)	-457	NM_019768	56397	Mm.27218	NM_019768	ENSMUSG00000031422	Morf4l2	2410017O14Rik|Mrgx|Sid393p|mKIAA0026	mortality factor 4 like 2	protein-coding
mm_38055.1	chr4	134004451	134004484	-	1	NA	3' UTR (NM_145833, exon 4 of 4)	3' UTR (NM_145833, exon 4 of 4)	-3603	NM_026144	67422	Mm.100290	NM_026144	ENSMUSG00000012117	Dhdds	3222401G21Rik|CIT|DS|HDS|W91638	dehydrodolichyl diphosphate synthase	protein-coding
mm_150246.1	chr19	34085575	34085584	+	1	NA	TTS (NM_027340)	TTS (NM_027340)	-15364	NM_023903	78753	Mm.195937	NM_023903	ENSMUSG00000056078	Lipm	4632427C23Rik|AW227514|Lipl3	lipase, family member M	protein-coding
mm_123947.1	chr14	73383411	73383432	-	1	NA	intron (NM_008410, intron 1 of 5)	intron (NM_008410, intron 1 of 5)	1850	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_21230.1	chr2	155989194	155989232	-	1	NA	intron (NM_001130000, intron 26 of 32)	intron (NM_001130000, intron 26 of 32)	15214	NM_001145351	320095	Mm.442175	NM_001145351	ENSMUSG00000074646	6430550D23Rik	-	RIKEN cDNA 6430550D23 gene	protein-coding
mm_4575.1	chr1	177741020	177741034	+	1	NA	exon (NM_027077, exon 3 of 6)	exon (NM_027077, exon 3 of 6)	11213	NM_027077	69428	Mm.84467	NM_027077	ENSMUSG00000015962	1700016C15Rik	-	RIKEN cDNA 1700016C15 gene	protein-coding
mm_81959.1	chr9	120867071	120867096	+	1	NA	Intergenic	Intergenic	48167	NR_040742	76402	Mm.436588	NR_040742	ENSMUSG00000100146	1700020M21Rik	-	RIKEN cDNA 1700020M21 gene	ncRNA
mm_68937.1	chr7	126502313	126502351	-	1	NA	promoter-TSS (NM_001347658)	promoter-TSS (NM_001347658)	93	NM_001347658	233871	Mm.231450	NM_183020	ENSMUSG00000032637	Atxn2l	A2D|A2LG|A2RP|A2lp|Atxnl2	ataxin 2-like	protein-coding
mm_101545.1	chr11	33537433	33537452	-	1	NA	Intergenic	Intergenic	-23696	NM_023146	66011	Mm.383775	NM_023146	ENSMUSG00000040594	Ranbp17	-	RAN binding protein 17	protein-coding
mm_11516.1	chr2	32599699	32599726	+	1	NA	promoter-TSS (NM_001025311)	promoter-TSS (NM_001025311)	3	NM_001025311	50935	Mm.88831	NM_016973	ENSMUSG00000026811	St6galnac6	ST6GalNAcVI|Siat7f	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 6	protein-coding
mm_53394.1	chr6	129588075	129588083	+	1	NA	Intergenic	Intergenic	-3732	NM_010654	16643	Mm.391515	NM_010654	ENSMUSG00000030165	Klrd1	CD94	killer cell lectin-like receptor, subfamily D, member 1	protein-coding
mm_102087.1	chr11	52282320	52282334	-	1	NA	intron (NM_001313981, intron 2 of 10)	intron (NM_001313981, intron 2 of 10)	268	NM_009331	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_3269.1	chr1	136415340	136415353	+	1	NA	promoter-TSS (NM_026500)	promoter-TSS (NM_026500)	75	NM_026500	67997	Mm.385462	NM_026500	ENSMUSG00000026404	Ddx59	1210002B07Rik|4833411G06Rik	DEAD (Asp-Glu-Ala-Asp) box polypeptide 59	protein-coding
mm_161102.1	chr12	102129466	102129466	+	1	NA	promoter-TSS (NM_172152)	promoter-TSS (NM_172152)	47	NM_172152	238384	Mm.312448	NM_172152	ENSMUSG00000041771	Slc24a4	A930002M03Rik|AW492432|NCKX4	solute carrier family 24 (sodium/potassium/calcium exchanger), member 4	protein-coding
mm_126389.1	chr15	80189133	80189182	+	1	NA	intron (NM_010795, intron 1 of 1)	intron (NM_010795, intron 1 of 1)	15436	NM_010795	17309	Mm.299693	NM_010795	ENSMUSG00000042428	Mgat3	1110038J12Rik|AI848272|GnT-III	mannoside acetylglucosaminyltransferase 3	protein-coding
mm_97466.1	chr11	78266383	78266396	+	1	NA	exon (NM_001002004, exon 8 of 39)	exon (NM_001002004, exon 8 of 39)	4635	NM_001002004	72503	Mm.237103	NM_001002004	ENSMUSG00000010277	2610507B11Rik	AU022687|D11Bhm178e|D11Bhm179e|E1|Kiaa0100|mKIAA0100	RIKEN cDNA 2610507B11 gene	protein-coding
mm_66984.1	chr7	63938991	63939046	-	1	NA	promoter-TSS (NM_021366)	promoter-TSS (NM_021366)	-103	NM_021366	50794	Mm.240473	NM_021366	ENSMUSG00000052040	Klf13	0610043C13Rik|9430029L20Rik|Bteb3|FKLF-2|FKLF2|NSLP1|RFLAT-1|RFLAT1	Kruppel-like factor 13	protein-coding
mm_140528.1	chr17	6745992	6746029	-	1	NA	intron (NM_009510, intron 7 of 12)	intron (NM_009510, intron 7 of 12)	36770	NM_009510	22350	Mm.277812	NM_009510	ENSMUSG00000052397	Ezr	AW146364|R75297|Vil2|p81	ezrin	protein-coding
mm_94231.1	chr11	3290464	3290485	+	1	NA	promoter-TSS (NM_001253691)	promoter-TSS (NM_001253691)	17	NM_019574	56218	Mm.275563	NM_019574	ENSMUSG00000020453	Patz1	8430401L15Rik|AI447519|Mazr|Patz|Zfp278	POZ (BTB) and AT hook containing zinc finger 1	protein-coding
mm_17494.1	chr2	28621319	28621330	-	1	NA	intron (NM_008114, intron 1 of 6)	intron (NM_008114, intron 1 of 6)	658	NM_008114	14582	Mm.373385	NM_008114	ENSMUSG00000026815	Gfi1b	Gfi-1B	growth factor independent 1B	protein-coding
mm_28746.1	chr3	95754825	95754831	-	1	NA	exon (NM_001163617, exon 1 of 17)	exon (NM_001163617, exon 1 of 17)	149	NM_027931	71807	Mm.271754	NM_027931	ENSMUSG00000028107	Tars2	2610024N01Rik|AI429208|Tarsl1	threonyl-tRNA synthetase 2, mitochondrial (putative)	protein-coding
mm_41248.1	chr5	88782267	88782301	+	1	NA	3' UTR (NM_007832, exon 7 of 7)	3' UTR (NM_007832, exon 7 of 7)	17271	NM_007832	13178	Mm.298892	NM_007832	ENSMUSG00000029366	Dck	-	deoxycytidine kinase	protein-coding
mm_4869.1	chr1	187742593	187742616	+	1	NA	intron (NM_001243792, intron 1 of 7)	intron (NM_001243792, intron 1 of 7)	133598	NM_001243792	26381	Mm.89989	NM_011935	ENSMUSG00000026610	Esrrg	ERR3|Errg|NR3B3|mKIAA0832	estrogen-related receptor gamma	protein-coding
mm_133261.1	chr16	77338299	77338314	+	1	NA	intron (NR_015543, intron 1 of 4)	Lx8b|LINE|L1	8978	NR_015543	77994	Mm.394688	NR_015543	ENSMUSG00000090386	Mir99ahg	2810055G20Rik|D730043B02Rik	Mir99a and Mirlet7c-1 host gene (non-protein coding)	ncRNA
mm_96031.1	chr11	59553506	59553508	+	1	NA	intron (NM_145827, intron 5 of 9)	B3A|SINE|B2	10821	NM_145827	216799	Mm.54174	NM_145827	ENSMUSG00000032691	Nlrp3	AGTAVPRL|AII/AVP|Cias1|FCAS|FCU|MWS|Mmig1|NALP3|Pypaf1	NLR family, pyrin domain containing 3	protein-coding
mm_51683.1	chr6	86487443	86487493	+	1	NA	intron (NR_040292, intron 1 of 1)	intron (NR_040292, intron 1 of 1)	759	NR_040293	381792	Mm.333223	NR_040292	ENSMUSG00000101655	2310040G24Rik	-	RIKEN cDNA 2310040G24 gene	ncRNA
mm_15275.1	chr2	155236603	155236617	+	1	NA	promoter-TSS (NM_025947)	promoter-TSS (NM_025947)	2	NM_001291108	67068	Mm.23693	NM_025947	ENSMUSG00000047459	Dynlrb1	2010012N15Rik|2010320M17Rik|9430076K19Rik|AV124457|DNLC2A|Dncl2a|km23-1	dynein light chain roadblock-type 1	protein-coding
mm_61175.1	chr7	60004422	60004434	+	1	NA	intron (NM_001082962, intron 2 of 10)	intron (NM_001082962, intron 2 of 10)	728	NM_013670	20646	Mm.274995	NM_013670	ENSMUSG00000102252	Snrpn	2410045I01Rik|HCERN3|Peg4|Pwcr1|SMN	small nuclear ribonucleoprotein N	protein-coding
mm_51713.1	chr6	86785488	86785500	+	1	NA	intron (NM_013471, intron 1 of 12)	intron (NM_013471, intron 1 of 12)	8090	NM_013471	11746	Mm.259702	NM_013471	ENSMUSG00000029994	Anxa4	AI265406|AIV|AW106930|Anx4|Xanx-4	annexin A4	protein-coding
mm_1959.1	chr1	86424162	86424179	+	1	NA	Intergenic	ORR1D2|LTR|ERVL-MaLR	-2159	NM_027966	71863	Mm.179627	NM_027966	ENSMUSG00000036574	1700019O17Rik	-	RIKEN cDNA 1700019O17 gene	protein-coding
mm_142231.1	chr17	37480880	37480899	-	1	NA	TTS (NM_008204)	TTS (NM_008204)	2640	NM_008204	14990	Mm.329041	NM_008204	ENSMUSG00000016283	H2-M2	H-2M2|Thy19.4	histocompatibility 2, M region locus 2	protein-coding
mm_121141.1	chr14	101896401	101896405	+	1	NA	intron (NM_001347628, intron 8 of 26)	intron (NM_001347628, intron 8 of 26)	55780	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_14807.1	chr2	145903235	145903300	+	1	NA	promoter-TSS (NM_001141965)	promoter-TSS (NM_001141965)	26	NM_001141965	67877	Mm.151168	NM_026425	ENSMUSG00000002728	Naa20	1500004D14Rik|2900026I01Rik|AU041458|D2Ertd186e|Nat5	N(alpha)-acetyltransferase 20, NatB catalytic subunit	protein-coding
mm_120271.1	chr14	63123919	63123996	+	1	NA	intron (NM_007798, intron 1 of 9)	intron (NM_007798, intron 1 of 9)	1495	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_956.1	chr1	57777070	57777072	+	1	NA	intron (NM_144882, intron 1 of 13)	intron (NM_144882, intron 1 of 13)	2210	NM_144882	67198	Mm.159989	NM_144882	ENSMUSG00000038305	Spats2l	2810022L02Rik|A230104H11Rik|AA987173|AI480531|AI842453|AW413586	spermatogenesis associated, serine-rich 2-like	protein-coding
mm_9836.1	chr1	184034126	184034144	-	1	NA	promoter-TSS (NM_028516)	promoter-TSS (NM_028516)	-137	NM_028516	73363	Mm.50115	NM_028516	ENSMUSG00000044854	1700056E22Rik	-	RIKEN cDNA 1700056E22 gene	protein-coding
mm_19709.1	chr2	103797618	103797662	-	1	NA	promoter-TSS (NM_016739)	promoter-TSS (NM_016739)	0	NM_001111291	53872	Mm.427589	NM_016739	ENSMUSG00000027184	Caprin1	AL022980|Caprin-1|Gpiap|Gpiap1|Mmgpip137|P137|rng105	cell cycle associated protein 1	protein-coding
mm_14669.1	chr2	139493933	139493937	+	1	NA	promoter-TSS (NM_175467)	promoter-TSS (NM_175467)	15	NM_175467	228677	Mm.100450	NM_175467	ENSMUSG00000039092	Sptlc3	C130053K05Rik	serine palmitoyltransferase, long chain base subunit 3	protein-coding
mm_40397.1	chr5	52834046	52834112	+	1	NA	promoter-TSS (NM_024213)	promoter-TSS (NM_024213)	-56	NM_024213	52206	Mm.272568	NM_024213	ENSMUSG00000029176	Anapc4	2610306D21Rik|APC4|D5Ertd249e	anaphase promoting complex subunit 4	protein-coding
mm_123408.1	chr14	63544000	63544014	-	1	NA	promoter-TSS (NM_177594)	promoter-TSS (NM_177594)	-54	NM_177594	210376	Mm.441613	NM_177594	ENSMUSG00000035078	Mtmr9	9430075G12Rik|AA516943|AF073881|LIP-STYX|MTMR8|mMTMH3	myotubularin related protein 9	protein-coding
mm_70683.1	chr8	14997001	14997016	+	1	NA	intron (NM_172751, intron 27 of 28)	intron (NM_172751, intron 27 of 28)	-14017	NM_029116	74901	Mm.46675	NM_029116	ENSMUSG00000055675	Kbtbd11	2900016B01Rik|4930465M17Rik|mKIAA0711	kelch repeat and BTB (POZ) domain containing 11	protein-coding
mm_114333.1	chr13	60647757	60647771	+	1	NA	intron (NM_029653, intron 2 of 25)	intron (NM_029653, intron 2 of 25)	45553	NM_134062	69635	Mm.24103	NM_029653	ENSMUSG00000021559	Dapk1	D13Ucla1|DAP-Kinase	death associated protein kinase 1	protein-coding
mm_102038.1	chr11	51857625	51857686	-	1	NA	promoter-TSS (NM_199299)	promoter-TSS (NM_199299)	-174	NM_199299	76901	Mm.259996	NM_199299	ENSMUSG00000020387	Jade2	1200017K05Rik|AI480685|Phf15|mKIAA0239	jade family PHD finger 2	protein-coding
mm_3862.1	chr1	160987104	160987117	+	1	NA	intron (NM_080844, intron 1 of 7)	intron (NM_080844, intron 1 of 7)	8504	NM_080844	11905	Mm.260770	NM_080844	ENSMUSG00000026715	Serpinc1	AI114908|ATIII|At-3|At3	serine (or cysteine) peptidase inhibitor, clade C (antithrombin), member 1	protein-coding
mm_86238.1	chr9	120807037	120807039	-	1	NA	Intergenic	Intergenic	108212	NR_040742	76402	Mm.436588	NR_040742	ENSMUSG00000100146	1700020M21Rik	-	RIKEN cDNA 1700020M21 gene	ncRNA
mm_70721.1	chr8	15726601	15726608	+	1	NA	Intergenic	Intergenic	442234	NR_037214	100526464		NR_037214	ENSMUSG00000093142	Mir3106	mir-3106|mmu-mir-3106	microRNA 3106	ncRNA
mm_157343.1	chrX	36903345	36903353	-	1	NA	promoter-TSS (NM_029891)	promoter-TSS (NM_029891)	-450	NM_029891	77286	Mm.21649	NM_029891	ENSMUSG00000044149	Nkrf	9430034D17Rik|AW124770|C80287	NF-kappaB repressing factor	protein-coding
mm_31179.1	chr4	43507041	43507051	+	1	NA	promoter-TSS (NM_139305)	promoter-TSS (NM_139305)	20	NM_139305	230099	Mm.283682	NM_139305	ENSMUSG00000028463	Car9	CAIX|Ca9|MN/CA9	carbonic anhydrase 9	protein-coding
mm_141351.1	chr17	28622420	28622473	-	1	NA	promoter-TSS (NM_016795)	promoter-TSS (NM_016795)	8	NM_016795	20815	Mm.15252	NM_016795	ENSMUSG00000004865	Srpk1	AU017960	serine/arginine-rich protein specific kinase 1	protein-coding
mm_134052.1	chr16	5431774	5431813	-	1	NA	Intergenic	Intergenic	-175837	NM_027446	70511	Mm.45780	NM_027446	ENSMUSG00000022544	Eef2kmt	5730409G15Rik|Fam86|Fam86a|eEF2-KMT	eukaryotic elongation factor 2 lysine methyltransferase	protein-coding
mm_117124.1	chr13	60901354	60901362	-	1	NA	TTS (NM_026429)	TTS (NM_026429)	3489	NM_026429	116913	Mm.443229	NM_026429	ENSMUSG00000062705	Tpbpb	1600012N09Rik	trophoblast specific protein beta	protein-coding
mm_75361.1	chr8	45281602	45281619	-	1	NA	intron (NM_008455, intron 6 of 14)	(CAAAAA)n|Simple_repeat|Simple_repeat	13225	NM_008455	16621	Mm.482691	NM_008455	ENSMUSG00000109764	Klkb1	APS|Kal-3|Kal3|Klk3|PSA	kallikrein B, plasma 1	protein-coding
mm_58975.1	chr7	19024388	19024439	+	1	NA	promoter-TSS (NM_026605)	promoter-TSS (NM_026605)	36	NM_026605	68188	Mm.130902	NM_026605	ENSMUSG00000023118	Sympk	1500016F02Rik|4632415H16Rik|AA125406|AI449890|SPK|SYM	symplekin	protein-coding
mm_76709.1	chr8	94601615	94601630	-	1	NA	promoter-TSS (NM_026274)	promoter-TSS (NM_026274)	104	NM_028221	102122	Mm.250425	NM_028221	ENSMUSG00000031774	Fam192a	1700001O11Rik|2310065K24Rik|AI596259|Nip30	family with sequence similarity 192, member A	protein-coding
mm_6787.1	chr1	84140280	84140290	-	1	NA	intron (NM_001003948, intron 2 of 2)	L1_Mur3|LINE|L1	78676	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_128280.1	chr15	36931662	36931710	-	1	NA	Intergenic	ORR1B2|LTR|ERVL-MaLR	75716	NM_026521	68036	Mm.371631	NM_026521	ENSMUSG00000062397	Zfp706	3110006P09Rik|AA793007|AW536850|C77232|Znf706	zinc finger protein 706	protein-coding
mm_81669.1	chr9	111027331	111027339	+	1	NA	exon (NM_008522, exon 10 of 17)	exon (NM_008522, exon 10 of 17)	8043	NM_008522	17002	Mm.282359	NM_008522	ENSMUSG00000032496	Ltf	Csp82|Lf|MMS10R|Ms10r	lactotransferrin	protein-coding
mm_124887.1	chr15	10276645	10276656	+	1	NA	intron (NM_001253781, intron 1 of 9)	intron (NM_001253781, intron 1 of 9)	-17001	NM_001253782	19116	Mm.10516	NM_011169	ENSMUSG00000005268	Prlr	AI987712|Pr-1|Pr-3|Prlr-rs1	prolactin receptor	protein-coding
mm_64331.1	chr7	142283225	142283241	+	1	NA	Intergenic	ERVB4_1C-LTR_Mm|LTR|ERVK	-8870	NM_001199309	100043627	Mm.388589	NM_001199309	ENSMUSG00000056885	Gm4559	-	predicted gene 4559	protein-coding
mm_23794.1	chr3	79629075	79629115	+	1	NA	promoter-TSS (NM_025794)	promoter-TSS (NM_025794)	16	NM_029482	75939	Mm.221520	NM_029482	ENSMUSG00000027811	4930579G24Rik	-	RIKEN cDNA 4930579G24 gene	protein-coding
mm_4249.1	chr1	171408018	171408034	+	1	NA	exon (NM_001005508, exon 12 of 12)	exon (NM_001005508, exon 12 of 12)	-3287	NM_001305678	22278	Mm.8	NM_009480	ENSMUSG00000026641	Usf1	bHLHb11	upstream transcription factor 1	protein-coding
mm_18937.1	chr2	76753889	76753899	-	1	NA	exon (NM_011652, exon 273 of 313)	exon (NM_011652, exon 273 of 313)	78579	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_73690.1	chr8	111562449	111562453	+	1	NA	intron (NM_001168623, intron 1 of 4)	MIRb|SINE|MIR	24108	NM_001168623	170737	Mm.271578	NM_133206	ENSMUSG00000033545	Znrf1	B830022L21Rik|Rnf42|Zrfp1|nin283	zinc and ring finger 1	protein-coding
mm_115147.1	chr13	104918671	104918673	+	1	NA	Intergenic	Intergenic	-54779	NM_029984	77803	Mm.159995	NM_029984	ENSMUSG00000042655	Fam159b	A930021C24Rik	family with sequence similarity 159, member B	protein-coding
mm_93220.1	chr10	95145802	95145815	-	1	NA	promoter-TSS (NR_131146)	promoter-TSS (NR_131146)	17	NR_131146	628062		NR_131146		Gm29684	-	predicted gene, 29684	ncRNA
mm_82739.1	chr9	26791882	26791886	-	1	NA	exon (NM_153803, exon 6 of 20)	exon (NM_153803, exon 6 of 20)	14533	NM_153803	244757	Mm.293696	NM_153803	ENSMUSG00000036395	Glb1l2	-	galactosidase, beta 1-like 2	protein-coding
mm_151544.1	chr19	59260916	59260932	+	1	NA	promoter-TSS (NM_172523)	promoter-TSS (NM_172523)	46	NM_172523	214084	Mm.268797	NM_172523	ENSMUSG00000025094	Slc18a2	1110037L13Rik|9330105E13|Vmat2	solute carrier family 18 (vesicular monoamine), member 2	protein-coding
mm_82876.1	chr9	32451400	32451416	-	1	NA	intron (NM_008026, intron 5 of 8)	ID4_|SINE|ID	57423	NM_001168354	56379	Mm.390168	NM_019659	ENSMUSG00000041248	Kcnj1	Kir1.1|ROMK|Romk2	potassium inwardly-rectifying channel, subfamily J, member 1	protein-coding
mm_164885.1	chr18	60584709	60584711	-	1	NA	intron (NM_133363, intron 2 of 6)	B3|SINE|B2	7006	NM_133363	170947	Mm.159257	NM_133363	ENSMUSG00000049173	Myoz3	4833419K08Rik|Fatz-3	myozenin 3	protein-coding
mm_39938.1	chr5	31726120	31726169	+	1	NA	intron (NM_181281, intron 2 of 10)	intron (NM_181281, intron 2 of 10)	28094	NM_144541	107976	Mm.482126	NM_144541	ENSMUSG00000052139	Bre	6030405P19Rik|AI429776|B830038C02Rik	brain and reproductive organ-expressed protein	protein-coding
mm_166375.1	chr5	128717448	128717450	+	1	NA	Intergenic	LTR41B|LTR|ERVL	-18797	NM_021311	57749	Mm.272720	NM_021311	ENSMUSG00000029423	Piwil1	MIWI	piwi-like RNA-mediated gene silencing 1	protein-coding
mm_160696.1	chr10	34037506	34037506	+	1	NA	promoter-TSS (NM_001162937)	promoter-TSS (NM_001162937)	-91	NM_001162937	692132	Mm.383415	NM_001162937	ENSMUSG00000071340	Trappc3l	Bet3l|ENSMUSG00000071340	trafficking protein particle complex 3 like	protein-coding
mm_27947.1	chr3	79790332	79790355	-	1	NA	Intergenic	Intergenic	52319	NM_027495	70652	Mm.46635	NM_027495	ENSMUSG00000027956	Tmem144	1110057I03Rik|5730537D05Rik	transmembrane protein 144	protein-coding
mm_120467.1	chr14	65971797	65971808	+	1	NA	exon (NM_013492, exon 2 of 9)	exon (NM_013492, exon 2 of 9)	3319	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_57518.1	chr6	125494707	125494748	-	1	NA	promoter-TSS (NM_007657)	promoter-TSS (NM_007657)	28	NM_007657	12527	Mm.210676	NM_007657	ENSMUSG00000030342	Cd9	Tspan29	CD9 antigen	protein-coding
mm_87764.1	chr10	60292605	60292615	+	1	NA	intron (NM_001146120, intron 3 of 13)	intron (NM_001146120, intron 3 of 13)	8149	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_138813.1	chr17	39846728	39846758	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	3746	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_72591.1	chr8	84356741	84356754	+	1	NA	Intergenic	Intergenic	-58617	NM_001252060	12286	Mm.334658	NM_007578	ENSMUSG00000034656	Cacna1a	APCA|BI|Caca1a|Cacnl1a4|Cav2.1|Ccha1a|EA2|FHM|HPCA|MHP|MHP1|SCA6|alpha1A|la|nmf352|rkr|smrl|tg	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	protein-coding
mm_149982.1	chr19	29126747	29126763	+	1	NA	intron (NM_021525, intron 5 of 8)	intron (NM_021525, intron 5 of 8)	-8524	NR_029778	724062		NR_029778	ENSMUSG00000065556	Mir101b	Mirn101b|mir-101b	microRNA 101b	ncRNA
mm_163738.1	chr13	119695850	119695872	-	1	NA	intron (NM_145942, intron 2 of 10)	intron (NM_145942, intron 2 of 10)	5510	NM_001291439	208715	Mm.61526	NM_145942	ENSMUSG00000093930	Hmgcs1	B130032C06Rik	3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1	protein-coding
mm_127650.1	chr15	102489733	102489778	+	1	NA	exon (NM_001174073, exon 11 of 13)	exon (NM_001174073, exon 11 of 13)	19123	NM_001174073	18521	Mm.236513	NM_011042	ENSMUSG00000056851	Pcbp2	AW412548|Hnrpx|alphaCP-2	poly(rC) binding protein 2	protein-coding
mm_162569.1	chr1	173673629	173673637	+	1	NA	promoter-TSS (NM_001162938)	promoter-TSS (NM_001162938)	-47	NM_001162938	100033459	Mm.303377	NM_001162938	ENSMUSG00000066677	Ifi208	9830148g24rik|E430029J22Rik|Pydc3|Pyr-rv1	interferon activated gene 208	protein-coding
mm_50913.1	chr6	57582834	57582852	+	1	NA	intron (NM_025992, intron 1 of 22)	intron (NM_025992, intron 1 of 22)	1851	NM_025992	67138	Mm.297393	NM_025992	ENSMUSG00000029798	Herc6	1700121D12Rik|2510038N07Rik|4930427L17Rik|AI451296|CEB1|Herc5	hect domain and RLD 6	protein-coding
mm_50803.1	chr6	54272786	54272804	+	1	NA	promoter-TSS (NM_023543)	promoter-TSS (NM_023543)	-27	NM_023543	69993	Mm.321147	NM_023543	ENSMUSG00000004633	Chn2	1700026N20Rik|4930557O16Rik|ARHGAP3|Bch	chimerin 2	protein-coding
mm_50816.1	chr6	54429633	54429649	+	1	NA	non-coding (NR_033635, exon 1 of 14)	non-coding (NR_033635, exon 1 of 14)	580	NR_033635	100042056	Mm.448157	NM_198118	ENSMUSG00000073067	9130019P16Rik	6430501H15Rik|OTTMUSG00000023151	RIKEN cDNA 9130019P16 gene	ncRNA
mm_79774.1	chr9	62838832	62838886	+	1	NA	promoter-TSS (NM_001033175)	promoter-TSS (NM_001033175)	72	NM_001033175	76524	Mm.283636	NM_001033175	ENSMUSG00000032245	Cln6	1810065L06Rik|AW743417|D9Bwg1455e|nclf	ceroid-lipofuscinosis, neuronal 6	protein-coding
mm_99922.1	chr11	110479374	110479386	+	1	NA	intron (NM_011943, intron 1 of 11)	intron (NM_011943, intron 1 of 11)	80258	NM_011943	26399	Mm.14487	NM_011943	ENSMUSG00000020623	Map2k6	MEK6|MKK6|Prkmk6|SAPKK3	mitogen-activated protein kinase kinase 6	protein-coding
mm_109062.1	chr12	104344121	104344127	+	1	NA	intron (NM_011458, intron 3 of 4)	intron (NM_011458, intron 3 of 4)	5638	NM_011458	20714	Mm.291569	NM_011458	ENSMUSG00000058207	Serpina3k	1300001I07Rik|D12Rp54|MMCM2|MMSpi2|RP54|Spi-2|Spi2|contrapsin	serine (or cysteine) peptidase inhibitor, clade A, member 3K	protein-coding
mm_86406.1	chr9	123986711	123986720	-	1	NA	Intergenic	Intergenic	-8307	NM_007718	12770	Mm.423532	NM_007718	ENSMUSG00000064039	Ccr1l1	Cmkbr1l1	chemokine (C-C motif) receptor 1-like 1	protein-coding
mm_104344.1	chr11	94242734	94242759	-	1	NA	promoter-TSS (NM_181819)	promoter-TSS (NM_181819)	-167	NM_181819	278507	Mm.342216	NM_181819	ENSMUSG00000044177	Wfikkn2	2610304F08Rik|AY100450|Gasp1|WFIKKNRP	WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 2	protein-coding
mm_10235.1	chr2	6582916	6582950	+	1	NA	intron (NM_001347094, intron 9 of 12)	ORR1E|LTR|ERVL-MaLR	138729	NM_001310447	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_126264.1	chr15	79109080	79109088	+	1	NA	5' UTR (NM_177461, exon 1 of 16)	5' UTR (NM_177461, exon 1 of 16)	101	NM_177461	27008	Mm.196480	NM_177461	ENSMUSG00000033039	Micall1	AI448246|D15Mit260|D15N2e|EST573322|EST820961|MIRab13|mKIAA1668	microtubule associated monooxygenase, calponin and LIM domain containing -like 1	protein-coding
mm_13325.1	chr2	102782054	102782065	+	1	NA	3' UTR (NM_001077514, exon 11 of 11)	3' UTR (NM_001077514, exon 11 of 11)	75621	NM_001077515	20511	Mm.267547	NM_011393	ENSMUSG00000005089	Slc1a2	1700091C19Rik|2900019G14Rik|AI159670|Eaat2|GLT-1|GLT1|MGLT1	solute carrier family 1 (glial high affinity glutamate transporter), member 2	protein-coding
mm_56546.1	chr6	99878432	99878433	-	1	NA	Intergenic	CpG	-152040	NM_001170419	50501	Mm.87365	NM_015768	ENSMUSG00000030069	Prok2	Bv8|PK2|Prok1	prokineticin 2	protein-coding
mm_3603.1	chr1	151603574	151603577	+	1	NA	intron (NM_022018, intron 1 of 13)	intron (NM_022018, intron 1 of 13)	32202	NM_022018	63913	Mm.157700	NM_022018	ENSMUSG00000026483	Fam129a	AI256368|AU019833|Niban	family with sequence similarity 129, member A	protein-coding
mm_112665.1	chr13	16027143	16027163	+	1	NA	3' UTR (NM_008380, exon 5 of 5)	3' UTR (NM_008380, exon 5 of 5)	15302	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_68988.1	chr7	126594926	126594939	-	1	NA	promoter-TSS (NM_145636)	promoter-TSS (NM_145636)	-22	NM_145636	246779	Mm.222632	NM_145636	ENSMUSG00000044701	Il27	IL-27|IL-27p28|Il30|p28	interleukin 27	protein-coding
mm_147488.1	chr18	47333292	47333306	-	1	NA	intron (NM_001311097, intron 1 of 17)	intron (NM_001311097, intron 1 of 17)	35569	NM_018744	20358	Mm.40909	NM_018744	ENSMUSG00000019647	Sema6a	A730020P05Rik|AI851735|Sema6A-1|Semaq|VIa	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A	protein-coding
mm_165136.1	chr2	11332594	11332616	-	1	NA	Intergenic	Intergenic	-6884	NR_040369	100503147	Mm.91961	NR_040369	ENSMUSG00000086006	Gm13293	OTTMUSG00000011311	predicted gene 13293	ncRNA
mm_16834.1	chr2	11498381	11498400	-	1	NA	intron (NM_001177758, intron 1 of 14)	intron (NM_001177758, intron 1 of 14)	3700	NM_001177754	170768	Mm.19669	NM_133232	ENSMUSG00000026773	Pfkfb3	E330010H22Rik|iPFK-2|uPFK-2	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	protein-coding
mm_152526.1	chr19	11324089	11324100	-	1	NA	intron (NM_001025610, intron 4 of 5)	intron (NM_001025610, intron 4 of 5)	10601	NM_001276398	109225	Mm.491251	NM_027836	ENSMUSG00000024672	Ms4a7	9130422I10Rik|A430103C15Rik|CD20l4|CFFMA	membrane-spanning 4-domains, subfamily A, member 7	protein-coding
mm_133761.1	chr16	94502464	94502470	+	1	NA	intron (NM_007834, intron 5 of 7)	intron (NM_007834, intron 5 of 7)	24162	NM_007834	13185	Mm.7472	NM_007834	ENSMUSG00000022898	Dscr3	AW538125|Dcra	Down syndrome critical region gene 3	protein-coding
mm_126842.1	chr15	89060069	89060100	+	1	NA	exon (NM_001002005, exon 1 of 3)	exon (NM_001002005, exon 1 of 3)	358	NM_001002005	406218	Mm.483059	NM_001002005	ENSMUSG00000058441	Panx2	-	pannexin 2	protein-coding
mm_22032.1	chr2	168119171	168119193	-	1	NA	Intergenic	Intergenic	35331	NR_040327	77017	Mm.407822	NR_040327	ENSMUSG00000087648	E130018N17Rik	-	RIKEN cDNA E130018N17 gene	ncRNA
mm_162782.1	chr10	69980334	69980348	+	1	NA	exon (NM_170688, exon 35 of 43)	exon (NM_170688, exon 35 of 43)	54809	NM_009670	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_23603.1	chr3	65109500	65109534	+	1	NA	5' UTR (NM_010597, exon 1 of 14)	5' UTR (NM_010597, exon 1 of 14)	149	NM_010597	16497	Mm.316402	NM_010597	ENSMUSG00000027827	Kcnab1	Akr8a8|Kvbeta1.1|mKv(beta)1	potassium voltage-gated channel, shaker-related subfamily, beta member 1	protein-coding
mm_45998.1	chr5	90640418	90640425	-	1	NA	5' UTR (NM_028478, exon 1 of 11)	5' UTR (NM_028478, exon 1 of 11)	106	NM_028478	73246	Mm.30172	NM_028478	ENSMUSG00000029370	Rassf6	1600016B17Rik	Ras association (RalGDS/AF-6) domain family member 6	protein-coding
mm_15438.1	chr2	157283576	157283593	+	1	NA	exon (NM_019642, exon 2 of 17)	exon (NM_019642, exon 2 of 17)	-4035	NM_001039557	629499	Mm.384235	NM_001039557	ENSMUSG00000074627	Mroh8	4922505G16Rik	maestro heat-like repeat family member 8	protein-coding
mm_50692.1	chr6	51589998	51590000	+	1	NA	3' UTR (NM_001127349, exon 7 of 7)	3' UTR (NM_001127349, exon 7 of 7)	45476	NM_001127348	71982	Mm.294166	NM_028035	ENSMUSG00000038301	Snx10	2410004M09Rik	sorting nexin 10	protein-coding
mm_96202.1	chr11	62077019	62077101	+	1	NA	promoter-TSS (NM_001029936)	promoter-TSS (NM_001029936)	36	NM_001029936	432572	Mm.438022	NM_001029936	ENSMUSG00000042331	Specc1	2810012G08Rik|B230396K10Rik|Cytsb	sperm antigen with calponin homology and coiled-coil domains 1	protein-coding
mm_147875.1	chr18	64504999	64505008	-	1	NA	exon (NM_027350, exon 10 of 15)	exon (NM_027350, exon 10 of 15)	11554	NM_027350	70223	Mm.29192	NM_027350	ENSMUSG00000024587	Nars	3010001M15Rik|AA960128|ASNRS|C78150	asparaginyl-tRNA synthetase	protein-coding
mm_25453.1	chr3	108383888	108383898	+	1	NA	promoter-TSS (NM_001190161)	promoter-TSS (NM_001190161)	55	NM_019976	56742	Mm.389499	NM_019976	ENSMUSG00000068744	Psrc1	5430413I02Rik|AL033312|Dda3	proline/serine-rich coiled-coil 1	protein-coding
mm_114949.1	chr13	96748288	96748306	+	1	NA	Intergenic	CpG	-77361	NM_008255	15357	Mm.316652	NM_008255	ENSMUSG00000021670	Hmgcr	HMG-CoAR|Red	3-hydroxy-3-methylglutaryl-Coenzyme A reductase	protein-coding
mm_155372.1	chrX	71556026	71556041	+	1	NA	5' UTR (NM_008253, exon 1 of 5)	5' UTR (NM_008253, exon 1 of 5)	116	NM_001293625	15354	Mm.336087	NM_008253	ENSMUSG00000015217	Hmgb3	Hmg2a|Hmg4	high mobility group box 3	protein-coding
mm_35.1	chr1	6267084	6267088	+	1	NA	intron (NM_009826, intron 20 of 23)	ORR1A2-int|LTR|ERVL-MaLR	52424	NM_009826	12421	Mm.293811	NM_009826	ENSMUSG00000025907	Rb1cc1	2900055E04Rik|5930404L04Rik|Cc1|FIP200|LaXp180	RB1-inducible coiled-coil 1	protein-coding
mm_44602.1	chr5	25100597	25100614	-	1	NA	promoter-TSS (NM_145401)	promoter-TSS (NM_145401)	37	NM_145401	108099	Mm.33649	NM_145401	ENSMUSG00000028944	Prkag2	2410051C13Rik|AAKG|AAKG2|AI854673|H91620p|WPWS	protein kinase, AMP-activated, gamma 2 non-catalytic subunit	protein-coding
mm_90998.1	chr10	14544973	14545013	-	1	NA	promoter-TSS (NM_001002268)	promoter-TSS (NM_001002268)	43	NM_001002268	215798	Mm.440142	NM_001002268	ENSMUSG00000039116	Adgrg6	1190004A11Rik|AI449247|AW045736|DREG|Gm222|Gpr126	adhesion G protein-coupled receptor G6	protein-coding
mm_72318.1	chr8	78330738	78330776	+	1	NA	intron (NM_183096, intron 11 of 13)	intron (NM_183096, intron 11 of 13)	105895	NM_138944	18997	Mm.234261	NM_138944	ENSMUSG00000031688	Pou4f2	Brn-3.2|Brn-3b|Brn3b|Pou4f-rs1|mBrn3-3R	POU domain, class 4, transcription factor 2	protein-coding
mm_117379.1	chr13	72839244	72839289	-	1	NA	Intergenic	Intergenic	-22503	NR_046196	78446	Mm.244082	NR_046196		D730050B12Rik	-	RIKEN cDNA D730050B12 gene	ncRNA
mm_68797.1	chr7	124655286	124655322	-	1	NA	intron (NR_045907, intron 1 of 3)	intron (NR_045907, intron 1 of 3)	53631	NR_045907	73076	Mm.417827	NR_045907	ENSMUSG00000086254	3100003L05Rik	-	RIKEN cDNA 3100003L05 gene	ncRNA
mm_7463.1	chr1	120477286	120477287	-	1	NA	intron (NM_010766, intron 15 of 16)	intron (NM_010766, intron 15 of 16)	27798	NM_010766	17167	Mm.1856	NM_010766	ENSMUSG00000026390	Marco	AI323439|Ly112|Scara2	macrophage receptor with collagenous structure	protein-coding
mm_39385.1	chr5	13125614	13125635	+	1	NA	Intergenic	Intergenic	-271160	NM_001243072	20346	Mm.372039	NM_009152	ENSMUSG00000028883	Sema3a	Hsema-I|SEMA1|SemD|Semad|coll-1	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	protein-coding
mm_86024.1	chr9	112235920	112235933	-	1	NA	TTS (NR_015468)	TTS (NR_015468)	-1085	NM_001177619	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_27490.1	chr3	54807753	54807768	-	1	NA	promoter-TSS (NM_133231)	promoter-TSS (NM_133231)	31	NM_133231	170767	Mm.185735	NM_133231	ENSMUSG00000036615	Rfxap	5730495K23Rik	regulatory factor X-associated protein	protein-coding
mm_172462.1	chr7	42592544	42592549	-	1	NA	Intergenic	Intergenic	50058	NM_001242388	208111	Mm.387841	NM_001034857	ENSMUSG00000074158	Zfp976	9830147E19Rik|C330019L16Rik	zinc finger protein 976	protein-coding
mm_145607.1	chr18	61096700	61096718	+	1	NA	Intergenic	Intergenic	-8863	NM_001037859	12978	Mm.22574	NM_007779	ENSMUSG00000024621	Csf1r	AI323359|CD115|CSF-1R|Csfmr|Fim-2|Fim2|Fms|M-CSF-R|M-CSFR	colony stimulating factor 1 receptor	protein-coding
mm_72409.1	chr8	81775796	81775811	+	1	NA	intron (NM_001024617, intron 7 of 24)	intron (NM_001024617, intron 7 of 24)	433241	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_14002.1	chr2	122000659	122000663	+	1	NA	intron (NM_212450, intron 8 of 12)	intron (NM_212450, intron 8 of 12)	-27919	NM_144545	78655	Mm.458184	NM_144545	ENSMUSG00000027236	Eif3j1	1810016I04Rik|2700079K05Rik|AA409117|AA409446|C78575|Eif3j|Eif3j-1|Eif3j-2|Eif3j2|Eif3s1|eIF-3-alpha-A|eIF-3-alpha-B|eIF3-alpha|eIF3-p35|eIF3j-A|eIF3j-B	eukaryotic translation initiation factor 3, subunit J1	protein-coding
mm_136005.1	chr16	75766759	75766797	-	1	NA	promoter-TSS (NM_030201)	promoter-TSS (NM_030201)	40	NR_027492	110920	Mm.26704	NM_030201	ENSMUSG00000032932	Hspa13	1600002I10Rik|AV006182|B230217N24Rik|Stch	heat shock protein 70 family, member 13	protein-coding
mm_98529.1	chr11	94993575	94993592	+	1	NA	intron (NM_172261, intron 1 of 9)	intron (NM_172261, intron 1 of 9)	2371	NM_172261	217124	Mm.229087	NM_172261	ENSMUSG00000038976	Ppp1r9b	SPL|Spn	protein phosphatase 1, regulatory subunit 9B	protein-coding
mm_36687.1	chr4	96553618	96553664	-	1	NA	promoter-TSS (NM_010008)	promoter-TSS (NM_010008)	10	NM_010008	13110	Mm.98200	NM_010008	ENSMUSG00000052914	Cyp2j6	-	cytochrome P450, family 2, subfamily j, polypeptide 6	protein-coding
mm_137698.1	chr17	29047216	29047218	+	1	NA	Intergenic	B1F2|SINE|Alu	14557	NR_036613	20383	Mm.6787	NM_013663	ENSMUSG00000071172	Srsf3	AL024116|Sfrs3|X16	serine/arginine-rich splicing factor 3	protein-coding
mm_95050.1	chr11	32297533	32297564	+	1	NA	TTS (NM_008218).2	TTS (NM_008218).2	1056	NM_001083955	110257	Mm.196110	NM_001083955	ENSMUSG00000069917	Hba-a2	-	hemoglobin alpha, adult chain 2	protein-coding
mm_162398.1	chr1	82796254	82796258	-	1	NA	Intergenic	Intergenic	-27800	NM_025453	66261	Mm.46325	NM_025453	ENSMUSG00000026149	Tm4sf20	1810018L02Rik	transmembrane 4 L six family member 20	protein-coding
mm_16585.1	chr2	3718096	3718108	-	1	NA	intron (NM_025626, intron 1 of 3)	L1MB1|LINE|L1	4644	NM_025626	66540	Mm.277864	NM_025626	ENSMUSG00000026655	Fam107b	3110001A13Rik|AA589595|AA959793|AI132312	family with sequence similarity 107, member B	protein-coding
mm_74015.1	chr8	121542100	121542106	+	1	NA	promoter-TSS (NM_029597)	promoter-TSS (NM_029597)	-149	NM_029597	76405	Mm.165697	NM_029597	ENSMUSG00000031809	1700018B08Rik	1700084O22Rik	RIKEN cDNA 1700018B08 gene	protein-coding
mm_134993.1	chr16	32163373	32163438	-	1	NA	intron (NM_146069, intron 1 of 3)	intron (NM_146069, intron 1 of 3)	2071	NM_146069	224109	Mm.33498	NM_146069	ENSMUSG00000052384	Nrros	E430025L02Rik|Lrcc33|Lrrc33	negative regulator of reactive oxygen species	protein-coding
mm_44395.1	chr5	17835650	17835709	-	1	NA	5' UTR (NM_001159555, exon 1 of 15)	5' UTR (NM_001159555, exon 1 of 15)	217	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_19668.1	chr2	103372694	103372702	-	1	NA	promoter-TSS (NR_040332)	promoter-TSS (NR_040332)	66	NR_040332	319854	Mm.403818	NR_040332	ENSMUSG00000087278	A930006I01Rik	-	RIKEN cDNA A930006I01 gene	ncRNA
mm_117398.1	chr13	73689144	73689166	-	1	NA	exon (NM_028878, exon 6 of 12)	exon (NM_028878, exon 6 of 12)	-10671	NM_027780	71390	Mm.105251	NM_027780		Slc6a19os	5430425J12Rik	solute carrier family 6 (neurotransmitter transporter), member 19, opposite strand	protein-coding
mm_382.1	chr1	34053658	34053688	+	1	NA	intron (NM_133833, intron 1 of 92)	intron (NM_133833, intron 1 of 92)	41848	NM_134448	13518	Mm.336625	NM_010081	ENSMUSG00000026131	Dst	2310001O04Rik|A830042E19Rik|AW554249|BP230|BPAG1-n|Bpag|Bpag1|Macf2|ah|athetoid|dt|mKIAA0728|nmf203|nmf339	dystonin	protein-coding
mm_126844.1	chr15	89076059	89076105	+	1	NA	promoter-TSS (NM_026485)	promoter-TSS (NM_026485)	18	NM_026485	67976	Mm.284710	NM_026485	ENSMUSG00000015363	Trabd	5730502D15Rik|AL023039	TraB domain containing	protein-coding
mm_122470.1	chr14	45530252	45530282	-	1	NA	promoter-TSS (NM_146054)	promoter-TSS (NM_146054)	-202	NM_146054	218952	Mm.210018	NM_146054	ENSMUSG00000037712	Fermt2	AA960555|Kindlin-2|Mig2|Plekhc1	fermitin family member 2	protein-coding
mm_16439.1	chr2	180397309	180397333	+	1	NA	intron (NR_045331, intron 3 of 3)	intron (NR_045331, intron 3 of 3)	-1058	NR_029901	723954		NR_029901	ENSMUSG00000065460	Mir133a-2	Mirn133a-2|mir-133a-2	microRNA 133a-2	ncRNA
mm_146136.1	chr18	74714784	74714796	+	1	NA	intron (NM_201600, intron 23 of 38)	intron (NM_201600, intron 23 of 38)	63665	NR_028560	100217466		NR_028560		Scarna17	MBII-119	small Cajal body-specific RNA 17	ncRNA
mm_73078.1	chr8	94460777	94460779	+	1	NA	Intergenic	RMER4B|LTR|ERVK	-11985	NM_001033207	434341	Mm.334720	NM_001033207	ENSMUSG00000074151	Nlrc5	AI451557|AK220210|NOD27	NLR family, CARD domain containing 5	protein-coding
mm_101200.1	chr11	19018432	19018486	-	1	NA	5' UTR (NM_010789, exon 1 of 12)	5' UTR (NM_010789, exon 1 of 12)	510	NM_001193271	17268	Mm.356578	NM_010789	ENSMUSG00000020160	Meis1	C530044H18Rik|Evi8	Meis homeobox 1	protein-coding
mm_32967.1	chr4	120032490	120032524	+	1	NA	intron (NM_010657, intron 2 of 8)	intron (NM_010657, intron 2 of 8)	-128699	NM_007902	13615	Mm.284855	NM_007902	ENSMUSG00000028635	Edn2	ET-2|PPET2|VIC	endothelin 2	protein-coding
mm_90294.1	chr10	125387952	125387976	+	1	NA	Intergenic	Intergenic	-59429	NM_011391	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|Mct2	solute carrier family 16 (monocarboxylic acid transporters), member 7	protein-coding
mm_69777.1	chr7	141017592	141017600	-	1	NA	promoter-TSS (NM_001033632)	promoter-TSS (NM_001033632)	-704	NM_001033632	213002	Mm.276440	NM_001033632	ENSMUSG00000059108	Ifitm6	A330075D07|Dspa2f|Fgls5|fragilis5	interferon induced transmembrane protein 6	protein-coding
mm_5339.1	chr1	24100196	24100296	-	1	NA	promoter-TSS (NM_026604)	promoter-TSS (NM_026604)	95	NM_026604	68187	Mm.87130	NM_026604	ENSMUSG00000026153	Fam135a	4921533L14Rik|AI256732|AI835491	family with sequence similarity 135, member A	protein-coding
mm_39002.1	chr4	151861763	151861773	-	1	NA	promoter-TSS (NM_001195565)	promoter-TSS (NM_001195565)	0	NM_001081557	100072	Mm.318846	NM_001081557	ENSMUSG00000014592	Camta1	1810059M14Rik|2310058O09Rik|AI316882|AW987475|mKIAA0833	calmodulin binding transcription activator 1	protein-coding
mm_20374.1	chr2	128429318	128429362	-	1	NA	promoter-TSS (NR_028591)	promoter-TSS (NR_028591)	11	NR_028591	100043424	Mm.297222	NR_028589		Gm14005	OTTMUSG00000015351	predicted gene 14005	ncRNA
mm_15577.1	chr2	158667132	158667186	+	1	NA	promoter-TSS (NM_001159662)	promoter-TSS (NM_001159662)	24	NM_001159662	228852	Mm.150540	NM_153089	ENSMUSG00000037754	Ppp1r16b	ANKRD4|C130078N17Rik|TIMAP|Wdt4	protein phosphatase 1, regulatory (inhibitor) subunit 16B	protein-coding
mm_118238.1	chr13	111748428	111748438	-	1	NA	3' UTR (NM_011945, exon 20 of 20)	3' UTR (NM_011945, exon 20 of 20)	60550	NM_011945	26401	Mm.15918	NM_011945	ENSMUSG00000021754	Map3k1	MAPKKK1|MEKK1|Mekk	mitogen-activated protein kinase kinase kinase 1	protein-coding
mm_49548.1	chr6	30509850	30509889	+	1	NA	promoter-TSS (NM_027073)	promoter-TSS (NM_027073)	20	NM_027073	75647	Mm.46117	NM_027073	ENSMUSG00000029784	Ssmem1	1700016K02Rik|1700025E21Rik	serine-rich single-pass membrane protein 1	protein-coding
mm_152224.1	chr19	8663319	8663339	-	1	NA	promoter-TSS (NM_007698)	promoter-TSS (NM_007698)	6	NR_045314	402757	Mm.150255	NR_045314		9830166K06Rik	-	RIKEN cDNA 9830166K06 gene	ncRNA
mm_156135.1	chrX	123104036	123104065	+	1	NA	intron (NM_001310652, intron 1 of 1)	MMERVK10C-int|LTR|ERVK	527	NM_028426	73061	Mm.292979	NM_028426	ENSMUSG00000079450	Cldn34c1	3110007F17Rik	claudin 34C1	protein-coding
mm_21709.1	chr2	164593534	164593537	-	1	NA	promoter-TSS (NM_029325)	promoter-TSS (NM_029325)	36	NM_029325	75526	Mm.159533	NM_029325	ENSMUSG00000017733	Eppin	1700024E17Rik|Spinlw1	epididymal peptidase inhibitor	protein-coding
mm_82708.1	chr9	24412470	24412474	-	1	NA	3' UTR (NM_172920, exon 22 of 22)	3' UTR (NM_172920, exon 22 of 22)	90668	NM_172920	244745	Mm.38526	NM_172920	ENSMUSG00000043067	Dpy19l1	1100001I19Rik|6030402K12|AI225861|AW558481	dpy-19-like 1 (C. elegans)	protein-coding
mm_32464.1	chr4	107468612	107468643	+	1	NA	intron (NM_147221, intron 2 of 10)	intron (NM_147221, intron 2 of 10)	33908	NM_147221	230587	Mm.331757	NM_147221	ENSMUSG00000034762	Glis1	Gli5|Gli6|GliH1	GLIS family zinc finger 1	protein-coding
mm_70079.1	chr7	142653689	142653699	-	1	NA	3' UTR (NM_010514, exon 4 of 4)	3' UTR (NM_010514, exon 4 of 4)	1302	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_112318.1	chr12	115024471	115024474	-	1	NA	Intergenic	Intergenic	-510778	NR_106063	102465664		NR_106063	ENSMUSG00000098357	Mir7094-2	Gm27508|mmu-mir-7094-2	microRNA 7094-2	ncRNA
mm_91727.1	chr10	45048697	45048705	-	1	NA	Intergenic	Intergenic	-18513	NM_011156	19072	Mm.10281	NM_011156	ENSMUSG00000019849	Prep	AI047692|AI450383|D10Wsu136e|PEP|Pop	prolyl endopeptidase	protein-coding
mm_138037.1	chr17	33919828	33919833	+	1	NA	TTS (NM_020625)	TTS (NM_020625)	352	NM_009318	21356	Mm.154457	NM_009318	ENSMUSG00000024308	Tapbp	D17Wsu91e|TPN	TAP binding protein	protein-coding
mm_19100.1	chr2	79454254	79454275	-	1	NA	exon (NM_010894, exon 2 of 2)	exon (NM_010894, exon 2 of 2)	2372	NM_010894	18012	Mm.4636	NM_010894	ENSMUSG00000034701	Neurod1	BETA2|BHF-1|Nd1|Neurod|bHLHa3	neurogenic differentiation 1	protein-coding
mm_156938.1	chrX	169916095	169916117	+	1	NA	intron (NM_001290506, intron 1 of 9)	intron (NM_001290506, intron 1 of 9)	36487	NM_001290505	17318	Mm.34441	NM_010797	ENSMUSG00000035299	Mid1	61B3-R|DXHXS1141|Fxy|Trim18	midline 1	protein-coding
mm_54616.1	chr6	38355521	38355531	-	1	NA	promoter-TSS (NM_028421)	promoter-TSS (NM_028421)	-923	NM_028421	78781	Mm.25243	NM_028421	ENSMUSG00000029826	Zc3hav1	1200014N16Rik|2900058M19Rik|9130009D18Rik|9830115L13Rik|ARTD13|D6Bwg1452e|ZAP	zinc finger CCCH type, antiviral 1	protein-coding
mm_23414.1	chr3	58525816	58525844	+	1	NA	promoter-TSS (NM_030685)	promoter-TSS (NM_030685)	9	NM_001005509	229317	Mm.21617	NM_001005509	ENSMUSG00000027810	Eif2a	D030048D22|D3Ertd194e	eukaryotic translation initiation factor 2A	protein-coding
mm_54727.1	chr6	40585757	40585763	-	1	NA	promoter-TSS (NM_021364)	promoter-TSS (NM_021364)	45	NM_021364	23845	Mm.103765	NM_021364	ENSMUSG00000029915	Clec5a	Clecsf5|Ly100|MDL-1|Mdl1	C-type lectin domain family 5, member a	protein-coding
mm_49341.1	chr6	21516571	21516573	+	1	NA	intron (NM_019697, intron 1 of 5)	Lx4A|LINE|L1	300463	NM_019697	16508	Mm.425316	NM_019697	ENSMUSG00000060882	Kcnd2	AI839615|AW555701|Kv4.2|R75121|mKIAA1044	potassium voltage-gated channel, Shal-related family, member 2	protein-coding
mm_83036.1	chr9	37255686	37255711	-	1	NA	promoter-TSS (NM_001145960)	promoter-TSS (NM_001145960)	40	NM_020258	56857	Mm.440037	NM_020258	ENSMUSG00000032122	Slc37a2	G3PP|Slc37a1|cI-2|ci2	solute carrier family 37 (glycerol-3-phosphate transporter), member 2	protein-coding
mm_77966.1	chr9	7767773	7767801	+	1	NA	intron (NM_133739, intron 1 of 4)	intron (NM_133739, intron 1 of 4)	3710	NM_133739	71929	Mm.283293	NM_133739	ENSMUSG00000050912	Tmem123	2310075C12Rik	transmembrane protein 123	protein-coding
mm_131617.1	chr16	19760628	19760644	+	1	NA	intron (NM_054052, intron 1 of 3)	intron (NM_054052, intron 1 of 3)	402	NM_001159407	108105	Mm.33935	NM_054052	ENSMUSG00000022686	B3gnt5	beta3GnT5	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5	protein-coding
mm_152259.1	chr19	8786273	8786297	-	1	NA	promoter-TSS (NM_146092)	promoter-TSS (NM_146092)	31	NM_146092	225895	Mm.220886	NM_146092	ENSMUSG00000003680	Taf6l	2810417N14Rik|BB223262|C530024J06Rik|Paf65a	TATA-box binding protein associated factor 6 like	protein-coding
mm_151205.1	chr19	53547930	53547941	+	1	NA	Intergenic	Intergenic	18617	NM_001085390	240672	Mm.482424	NM_001085390	ENSMUSG00000034765	Dusp5	Gm337	dual specificity phosphatase 5	protein-coding
mm_45757.1	chr5	86804785	86804813	-	1	NA	intron (NM_001347376, intron 1 of 15)	CpG	309	NM_177680	231386	Mm.196325	NM_177680	ENSMUSG00000035851	Ythdc1	A730098D12Rik|C80342|mKIAA1966	YTH domain containing 1	protein-coding
mm_60836.1	chr7	45718122	45718147	+	1	NA	promoter-TSS (NM_001172561)	promoter-TSS (NM_001172561)	63	NM_009077	19899	Mm.3459	NM_009077	ENSMUSG00000059070	Rpl18	L18|Rpl18a	ribosomal protein L18	protein-coding
mm_32451.1	chr4	107367730	107367754	+	1	NA	promoter-TSS (NM_028355)	promoter-TSS (NM_028355)	-42	NM_028355	72787	Mm.28478	NM_028355	ENSMUSG00000028614	Ndc1	2810475A17Rik|AI450313|Tmem48|sks	NDC1 transmembrane nucleoporin	protein-coding
mm_158361.1	chrX	134601509	134601513	-	1	NA	promoter-TSS (NM_013463)	promoter-TSS (NM_013463)	332	NM_001313717	56258	Mm.315909	NM_019868	ENSMUSG00000045427	Hnrnph2	DXHXS1271E|Ftp-3|Ftp3|H'|HNRNP|Hnrph2	heterogeneous nuclear ribonucleoprotein H2	protein-coding
mm_74579.1	chr8	11231428	11231472	-	1	NA	exon (NM_009931, exon 24 of 52)	exon (NM_009931, exon 24 of 52)	-81355	NM_009932	12827	Mm.181021	NM_009932	ENSMUSG00000031503	Col4a2	Col4a-2	collagen, type IV, alpha 2	protein-coding
mm_95260.1	chr11	44675666	44675672	+	1	NA	intron (NM_007897, intron 6 of 15)	intron (NM_007897, intron 6 of 15)	57569	NM_001290710	13591	Mm.439662	NM_007897	ENSMUSG00000057098	Ebf1	Ebf|O/E-1|OE-1|Olf-1|Olf1	early B cell factor 1	protein-coding
mm_65144.1	chr7	19578045	19578059	-	1	NA	intron (NM_022409, intron 2 of 2)	intron (NM_022409, intron 2 of 2)	765	NM_022409	63872	Mm.23310	NM_022409	ENSMUSG00000011267	Zfp296	2210018A16Rik|Znf296	zinc finger protein 296	protein-coding
mm_48073.1	chr5	136581850	136581870	-	1	NA	Intergenic	Intergenic	-14370	NM_001291238	13047	Mm.320317	NM_009986	ENSMUSG00000029705	Cux1	CDP|Cutl1|Cux|Cux-1	cut-like homeobox 1	protein-coding
mm_127827.1	chr15	6435333	6435355	-	1	NA	exon (NM_001102400, exon 10 of 13)	exon (NM_001102400, exon 10 of 13)	-9989	NM_013485	12279	Mm.29095	NM_013485	ENSMUSG00000022149	C9	-	complement component 9	protein-coding
mm_2002.1	chr1	87127041	87127050	+	1	NA	exon (NM_007432, exon 9 of 11)	exon (NM_007432, exon 9 of 11)	2037	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_10447.1	chr2	14273463	14273466	+	1	NA	intron (NM_008625, intron 9 of 29)	B4|SINE|B4	12461	NR_030609	100124488		NR_030609	ENSMUSG00000077897	Mir511	Mirn511|mir-511|mmu-mir-511	microRNA 511	ncRNA
mm_8468.1	chr1	153332917	153332927	-	1	NA	promoter-TSS (NM_010683)	promoter-TSS (NM_010683)	-136	NM_010683	226519	Mm.1249	NM_010683	ENSMUSG00000026478	Lamc1	Lamb2	laminin, gamma 1	protein-coding
mm_167824.1	chr9	124423267	124423290	+	1	NA	promoter-TSS (NR_015516)	promoter-TSS (NR_015516)	27	NR_027950	75135	Mm.476814	NR_015516		4930526I15Rik	1600027J15Rik	RIKEN cDNA 4930526I15 gene	ncRNA
mm_6411.1	chr1	72874413	72874451	-	1	NA	5' UTR (NM_010518, exon 1 of 4)	5' UTR (NM_010518, exon 1 of 4)	433	NM_010518	16011	Mm.405761	NM_010518	ENSMUSG00000026185	Igfbp5	AI256729|AW208790|IGFBP-5|IGFBP-5P	insulin-like growth factor binding protein 5	protein-coding
mm_122717.1	chr14	52269175	52269195	-	1	NA	intron (NM_172601, intron 3 of 7)	intron (NM_172601, intron 3 of 7)	-9961	NM_023434	268741	Mm.246237	NM_023434	ENSMUSG00000016831	Tox4	5730589K01Rik|A630040M18|AA410149|LCP1	TOX high mobility group box family member 4	protein-coding
mm_6912.1	chr1	84839421	84839441	-	1	NA	promoter-TSS (NM_025386)	promoter-TSS (NM_025386)	-127	NM_133975	14897	Mm.209265	NM_133975	ENSMUSG00000026219	Trip12	1110036I07Rik|6720416K24Rik|AA410158|Gtl6|TRIP-12	thyroid hormone receptor interactor 12	protein-coding
mm_136669.1	chr17	6106825	6106838	+	1	NA	promoter-TSS (NM_001103181)	promoter-TSS (NM_001103181)	1	NM_001103181	68842	Mm.449307	NM_054040	ENSMUSG00000034377	Tulp4	1110057P05Rik|2210038L17Rik|Tusp	tubby like protein 4	protein-coding
mm_156265.1	chrX	136832019	136832041	+	1	NA	exon (NM_011123, exon 3 of 7)	exon (NM_011123, exon 3 of 7)	9284	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_128529.1	chr15	54847361	54847367	-	1	NA	intron (NM_001136077, intron 22 of 25)	intron (NM_001136077, intron 22 of 25)	72782	NM_015744	18606	Mm.250256	NM_015744	ENSMUSG00000022425	Enpp2	ATX|E-NPP 2|Npps2|PD-Ialpha|Pdnp2|lysoPLD	ectonucleotide pyrophosphatase/phosphodiesterase 2	protein-coding
mm_1173.1	chr1	60977899	60977937	+	1	NA	promoter-TSS (NM_017480)	promoter-TSS (NM_017480)	4	NM_017480	54167	Mm.42044	NM_017480	ENSMUSG00000026009	Icos	AILIM|CCLP|CRP-1|H4|Ly115	inducible T cell co-stimulator	protein-coding
mm_94143.1	chr10	128737577	128737589	-	1	NA	intron (NM_016811, intron 1 of 23)	intron (NM_016811, intron 1 of 23)	6473	NM_016811	13139	Mm.291235	NM_016811	ENSMUSG00000025357	Dgka	80kDa|AW146112|Dagk1	diacylglycerol kinase, alpha	protein-coding
mm_110940.1	chr12	76597591	76597619	-	1	NA	intron (NM_013675, intron 32 of 35)	intron (NM_013675, intron 32 of 35)	-49680	NR_046044	100504549	Mm.440349	NR_046044		AI463170	-	expressed sequence AI463170	ncRNA
mm_70177.1	chr7	143713587	143713613	-	1	NA	intron (NM_024289, intron 2 of 21)	intron (NM_024289, intron 2 of 21)	26760	NM_001199227	79196	Mm.21199	NM_024289	ENSMUSG00000037606	Osbpl5	1110006M06Rik|AI462538|ORP5|Obph1|Osbp2	oxysterol binding protein-like 5	protein-coding
mm_128251.1	chr15	36770604	36770626	-	1	NA	3' UTR (NM_001253807, exon 5 of 5)	3' UTR (NM_001253807, exon 5 of 5)	20317	NM_001253807	22631	Mm.3360	NM_011740	ENSMUSG00000022285	Ywhaz	1110013I11Rik|14-3-3zeta|AI596267|AL022924|AU020854	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide	protein-coding
mm_68015.1	chr7	100955040	100955050	-	1	NA	intron (NM_183168, intron 1 of 2)	B1_Mus2|SINE|Alu	9321	NM_183168	233571	Mm.235193	NM_183168	ENSMUSG00000048779	P2ry6	2010204J23Rik|P2Y6	pyrimidinergic receptor P2Y, G-protein coupled, 6	protein-coding
mm_7965.1	chr1	133930170	133930178	-	1	NA	Intergenic	MamGypLTR1c|LTR|Gypsy	-8773	NM_054077	116847	Mm.214514	NM_054077	ENSMUSG00000041577	Prelp	7330409J17Rik|SLRR2A	proline arginine-rich end leucine-rich repeat	protein-coding
mm_103180.1	chr11	70460007	70460013	-	1	NA	promoter-TSS (NM_023158)	promoter-TSS (NM_023158)	-26	NM_023158	66102	Mm.425692	NM_023158	ENSMUSG00000018920	Cxcl16	0910001K24Rik|AV290116|BB024863|CXCL16v1|CXCL16v2|SR-PSOX|Zmynd15|b2b498Clo	chemokine (C-X-C motif) ligand 16	protein-coding
mm_142666.1	chr17	47728818	47728853	-	1	NA	exon (NM_025973, exon 2 of 9)	exon (NM_025973, exon 2 of 9)	1993	NM_025973	109820	Mm.22957	NM_025973	ENSMUSG00000023987	Pgc	2210410L06Rik|Upg-1|Upg1	progastricsin (pepsinogen C)	protein-coding
mm_80303.1	chr9	73192498	73192514	+	1	NA	Intergenic	Intergenic	79037	NM_198609	225215	Mm.379366	NM_198609	ENSMUSG00000032215	Rsl24d1	2410159K22Rik	ribosomal L24 domain containing 1	protein-coding
mm_114100.1	chr13	54726792	54726802	+	1	NA	exon (NM_001033364, exon 19 of 32)	exon (NM_001033364, exon 19 of 32)	23077	NM_001316710	26913	Mm.41812	NM_012014	ENSMUSG00000069227	Gprin1	GRIN1|Z16	G protein-regulated inducer of neurite outgrowth 1	protein-coding
mm_98022.1	chr11	84957818	84957835	+	1	NA	promoter-TSS (NM_007607)	promoter-TSS (NM_007607)	72	NM_007607	12351	Mm.1641	NM_007607	ENSMUSG00000000805	Car4	AW456718|Ca4	carbonic anhydrase 4	protein-coding
mm_116223.1	chr13	32940587	32940622	-	1	NA	Intergenic	Intergenic	-24909	NM_011454	20708	Mm.36526	NM_011454	ENSMUSG00000042842	Serpinb6b	NK13|Spi12|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 6b	protein-coding
mm_164607.1	chr17	30794199	30794202	+	1	NA	intron (NM_013811, intron 75 of 92)	intron (NM_013811, intron 75 of 92)	-107667	NM_021332	14652	Mm.390969	NM_021332	ENSMUSG00000024027	Glp1r	GLP-1R|GLP1Rc	glucagon-like peptide 1 receptor	protein-coding
mm_14528.1	chr2	132724292	132724300	+	1	NA	intron (NM_028637, intron 2 of 2)	intron (NM_028637, intron 2 of 2)	34013	NM_028637	73747	Mm.284114	NM_028637	ENSMUSG00000044991	1110034G24Rik	-	RIKEN cDNA 1110034G24 gene	protein-coding
mm_29619.1	chr3	121343328	121343337	-	1	NA	intron (NM_024178, intron 3 of 3)	intron (NM_024178, intron 3 of 3)	51515	NM_024178	66789	Mm.269881	NM_024178	ENSMUSG00000039887	Alg14	5430428G01Rik|AI854024	asparagine-linked glycosylation 14	protein-coding
mm_70843.1	chr8	23446573	23446581	+	1	NA	3' UTR (NM_013834, exon 3 of 3)	3' UTR (NM_013834, exon 3 of 3)	35075	NM_013834	20377	Mm.281691	NM_013834	ENSMUSG00000031548	Sfrp1	2210415K03Rik|AW011917|AW107218|AW742929|sFRP-1	secreted frizzled-related protein 1	protein-coding
mm_105644.1	chr11	107131498	107131540	-	1	NA	exon (NM_176850, exon 1 of 28)	exon (NM_176850, exon 1 of 28)	403	NM_176850	207165	Mm.343986	NM_176850	ENSMUSG00000040481	Bptf	9430093H17Rik|Falz	bromodomain PHD finger transcription factor	protein-coding
mm_130855.1	chr15	102118947	102118975	-	1	NA	exon (NM_001033277, exon 8 of 11)	exon (NM_001033277, exon 8 of 11)	15973	NM_153533	209039	Mm.29389	NM_153533	ENSMUSG00000037003	Tns2	C1-ten|Tenc1|nep|nph	tensin 2	protein-coding
mm_59610.1	chr7	28142447	28142456	+	1	NA	exon (NM_001164655, exon 6 of 20)	exon (NM_001164655, exon 6 of 20)	12985	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_8336.1	chr1	150101243	150101262	-	1	NA	exon (NM_011198, exon 3 of 10)	exon (NM_011198, exon 3 of 10)	1221	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_31687.1	chr4	62314034	62314050	+	1	NA	intron (NM_001045528, intron 20 of 27)	intron (NM_001045528, intron 20 of 27)	22495	NM_001290518	20530	Mm.292539	NM_025286	ENSMUSG00000066152	Slc31a2	AI604396|CTR2	solute carrier family 31, member 2	protein-coding
mm_89444.1	chr10	92825723	92825725	+	1	NA	intron (NM_001347060, intron 64 of 67)	intron (NM_001347060, intron 64 of 67)	-103306	NM_008682	17997	Mm.2998	NM_008682	ENSMUSG00000019988	Nedd1	-	neural precursor cell expressed, developmentally down-regulated gene 1	protein-coding
mm_121626.1	chr14	8317614	8317627	-	1	NA	Intergenic	Intergenic	-7844	NM_183187	268709	Mm.256058	NM_183187	ENSMUSG00000021750	Fam107a	DRR1	family with sequence similarity 107, member A	protein-coding
mm_146449.1	chr18	86394794	86394803	+	1	NA	promoter-TSS (NM_144946)	promoter-TSS (NM_144946)	-154	NM_144946	246317	Mm.329578	NM_144946	ENSMUSG00000050321	Neto1	AI851453|Btcl1|C130005O10Rik	neuropilin (NRP) and tolloid (TLL)-like 1	protein-coding
mm_20993.1	chr2	152332228	152332236	-	1	NA	5' UTR (NM_001083921, exon 1 of 12)	5' UTR (NM_001083921, exon 1 of 12)	193	NM_001083921	24105	Mm.182145	NM_019705	ENSMUSG00000027466	Rbck1	AL033326|HOIL-1|HOIL-1L|UIP28|Ubce7ip3	RanBP-type and C3HC4-type zinc finger containing 1	protein-coding
mm_80332.1	chr9	75037839	75037852	+	1	NA	5' UTR (NM_021548, exon 1 of 3)	5' UTR (NM_021548, exon 1 of 3)	113	NM_021548	59046	Mm.247837	NM_021548	ENSMUSG00000007656	Arpp19	19kDa|2700024H10Rik|ARPP-19|AW559096|Arpp12	cAMP-regulated phosphoprotein 19	protein-coding
mm_132605.1	chr16	38562871	38562875	+	1	NA	promoter-TSS (NM_026407)	promoter-TSS (NM_026407)	59	NM_026407	67846	Mm.310476	NM_026407	ENSMUSG00000002845	Tmem39a	2610033C09Rik	transmembrane protein 39a	protein-coding
mm_168691.1	chr11	97114282	97114292	-	1	NA	intron (NM_019507, intron 1 of 5)	intron (NM_019507, intron 1 of 5)	1044	NM_019507	57765	Mm.94519	NM_019507	ENSMUSG00000001444	Tbx21	TBT1|Tbet|Tblym	T-box 21	protein-coding
mm_86556.1	chr10	11149388	11149400	+	1	NA	promoter-TSS (NM_001077707)	promoter-TSS (NM_001077707)	-36	NM_001077707	268281	Mm.133101	NM_172937	ENSMUSG00000090112	Shprh	2610103K11Rik|AA450458|AU024614|BC006883|D230017O13Rik|E130018M05	SNF2 histone linker PHD RING helicase	protein-coding
mm_134625.1	chr16	21650112	21650123	-	1	NA	3' UTR (NM_001001881, exon 2 of 2)	3' UTR (NM_001001881, exon 2 of 2)	44548	NM_001001881	72190	Mm.131606	NM_001001881	ENSMUSG00000043391	2510009E07Rik	AI194952	RIKEN cDNA 2510009E07 gene	protein-coding
mm_149162.1	chr19	9018261	9018271	+	1	NA	TTS (NR_105786)	TTS (NR_105786)	362	NR_105786	102465190		NR_105786	ENSMUSG00000099308	Mir6367	Gm27467|mmu-mir-6367	microRNA 6367	ncRNA
mm_109750.1	chr12	117658077	117658087	+	1	NA	intron (NM_175930, intron 10 of 27)	intron (NM_175930, intron 10 of 27)	141603	NM_175930	217944	Mm.227642	NM_175930	ENSMUSG00000041992	Rapgef5	4932413M22|C86120|D030051B22Rik|GFR|Mrgef|mKIAA0277|mmr-gef	Rap guanine nucleotide exchange factor (GEF) 5	protein-coding
mm_103068.1	chr11	69858724	69858737	-	1	NA	promoter-TSS (NM_031880)	promoter-TSS (NM_031880)	0	NM_031880	83813	Mm.28874	NM_031880	ENSMUSG00000001583	Tnk1	Kos1|Tnk1a|Tnk1b	tyrosine kinase, non-receptor, 1	protein-coding
mm_90020.1	chr10	115384922	115384949	+	1	NA	promoter-TSS (NM_025780)	promoter-TSS (NM_025780)	-24	NM_001033261	216345	Mm.207621	NM_001033261	ENSMUSG00000034163	Zfc3h1	BC033596|Ccdc131|Psrc2	zinc finger, C3H1-type containing	protein-coding
mm_11223.1	chr2	29772596	29772611	+	1	NA	Intergenic	B1_Mur3|SINE|Alu	11075	NM_001177392	433416	Mm.330112	NM_001034887	ENSMUSG00000075425	Gm13547	OTTMUSG00000012686	predicted gene 13547	protein-coding
mm_89375.1	chr10	88826850	88826882	+	1	NA	promoter-TSS (NM_175158)	promoter-TSS (NM_175158)	-52	NM_175158	70683	Mm.29631	NM_175158	ENSMUSG00000004356	Utp20	3830408P06Rik|AA617408|Drim|mDRIM|mDRIN	UTP20 small subunit processome component	protein-coding
mm_81693.1	chr9	111174211	111174219	+	1	NA	intron (NM_001164838, intron 5 of 14)	intron (NM_001164838, intron 5 of 14)	56104	NM_001164838	71268	Mm.302287	NM_027742	ENSMUSG00000032497	Lrrfip2	5133400F20Rik|AI850587	leucine rich repeat (in FLII) interacting protein 2	protein-coding
mm_53318.1	chr6	129187309	129187320	+	1	NA	TTS (NM_053109)	TTS (NM_053109)	6699	NM_053109	93694	Mm.197536	NM_053109	ENSMUSG00000030157	Clec2d	Clr-b|Clrb|Ocil	C-type lectin domain family 2, member d	protein-coding
mm_48876.1	chr5	150665561	150665606	-	1	NA	promoter-TSS (NM_201369)	promoter-TSS (NM_201369)	29	NM_201369	381695	Mm.246934	NM_201369	ENSMUSG00000029655	N4bp2l2	2700092H06Rik|zag1	NEDD4 binding protein 2-like 2	protein-coding
mm_59556.1	chr7	28075312	28075328	+	1	NA	exon (NM_001122603, exon 3 of 20)	exon (NM_001122603, exon 3 of 20)	4084	NM_001122603	215384	Mm.292276	NM_175444	ENSMUSG00000047730	Fcgbp	A430096B05Rik	Fc fragment of IgG binding protein	protein-coding
mm_92290.1	chr10	71344934	71344948	-	1	NA	promoter-TSS (NM_134007)	promoter-TSS (NM_134007)	-92	NM_134007	52637	Mm.254114	NM_134007	ENSMUSG00000037710	Cisd1	AU043990|AW743335|D10Ertd214e|Zcd1|mitoNEET	CDGSH iron sulfur domain 1	protein-coding
mm_43045.1	chr5	124075345	124075375	+	1	NA	intron (NM_019875, intron 9 of 11)	intron (NM_019875, intron 9 of 11)	20438	NM_019875	56325	Mm.254839	NM_019875	ENSMUSG00000029408	Abcb9	TAPL|mKIAA1520	ATP-binding cassette, sub-family B (MDR/TAP), member 9	protein-coding
mm_162704.1	chr10	22704648	22704648	+	1	NA	TTS (NM_178934)	TTS (NM_178934)	24784	NR_106123	102465768		NR_106123	ENSMUSG00000098714	Mir7663	Gm28034|mmu-mir-7663	microRNA 7663	ncRNA
mm_148206.1	chr18	79519756	79519763	-	1	NA	Intergenic	Intergenic	-410368	NM_053099	240427	Mm.312871	NM_053099	ENSMUSG00000024548	Setbp1	C130092E12|Seb|mKIAA0437	SET binding protein 1	protein-coding
mm_34429.1	chr4	145585141	145585158	+	1	NA	promoter-TSS (NM_001324416)	promoter-TSS (NM_001324416)	-51	NM_001324416	433801	Mm.276881	NM_001013808	ENSMUSG00000078502	Gm13212	OTTMUSG00000010965	predicted gene 13212	protein-coding
mm_40295.1	chr5	43515752	43515794	+	1	NA	5' UTR (NM_001135172, exon 1 of 3)	5' UTR (NM_001135172, exon 1 of 3)	204	NM_001135172	109323	Mm.275553	NM_175425	ENSMUSG00000061535	C1qtnf7	5530401N20Rik|8430425G24Rik|Ctrp7	C1q and tumor necrosis factor related protein 7	protein-coding
mm_49084.1	chr6	6863270	6863272	+	1	NA	promoter-TSS (NM_010057)	promoter-TSS (NM_010057)	-63	NM_010057	13396	Mm.439763	NM_010057	ENSMUSG00000029754	Dlx6	-	distal-less homeobox 6	protein-coding
mm_69609.1	chr7	137194871	137194891	-	1	NA	3' UTR (NM_001113414, exon 16 of 16)	3' UTR (NM_001113414, exon 16 of 16)	-39802	NR_045885	100038555	Mm.444788	NR_045885	ENSMUSG00000109722	Gm10578	ENSMUSG00000073800	predicted gene 10578	ncRNA
mm_95607.1	chr11	53430454	53430464	+	1	NA	intron (NM_001326614, intron 2 of 2)	intron (NM_001326614, intron 2 of 2)	372	NM_025352	22272	Mm.251621	NM_025352	ENSMUSG00000044894	Uqcrq	1100001F06Rik|1500040F11Rik|5830407L17Rik|9.5kDa|AA959903|QP-C|Qpc|Uqcrb|c1502	ubiquinol-cytochrome c reductase, complex III subunit VII	protein-coding
mm_94507.1	chr11	7201973	7201983	+	1	NA	exon (NM_008341, exon 4 of 4)	exon (NM_008341, exon 4 of 4)	4191	NM_008341	16006	Mm.21300	NM_008341	ENSMUSG00000020429	Igfbp1	-	insulin-like growth factor binding protein 1	protein-coding
mm_40003.1	chr5	32863701	32863776	+	1	NA	promoter-TSS (NM_001170567)	promoter-TSS (NM_001170567)	17	NM_001170567	277854	Mm.101524	NM_177786	ENSMUSG00000037426	Depdc5	AV016528	DEP domain containing 5	protein-coding
mm_136958.1	chr17	15396241	15396317	+	1	NA	promoter-TSS (NM_024203)	promoter-TSS (NM_024203)	33	NM_024203	67544	Mm.35039	NM_024203	ENSMUSG00000014763	Fam120b	4932442K08Rik|AW049283|AW413338|CCPG|Pgcc1|mKIAA1838	family with sequence similarity 120, member B	protein-coding
mm_54018.1	chr6	8647782	8647792	-	1	NA	intron (NM_001252266, intron 10 of 11)	intron (NM_001252266, intron 10 of 11)	110671	NM_001252266	15893	Mm.275683	NM_010492	ENSMUSG00000062995	Ica1	69kDa|ICA69	islet cell autoantigen 1	protein-coding
mm_130067.1	chr15	89196458	89196478	-	1	NA	promoter-TSS (NM_027081)	promoter-TSS (NM_027081)	6	NM_027081	69440	Mm.482128	NM_027081	ENSMUSG00000015377	Dennd6b	1700027J05Rik|AI414881|Fam116b	DENN/MADD domain containing 6B	protein-coding
mm_89597.1	chr10	95970915	95970923	+	1	NA	intron (NM_001001932, intron 1 of 28)	intron (NM_001001932, intron 1 of 28)	30256	NM_001001932	216238	Mm.210035	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding
mm_164301.1	chr15	103897371	103897393	+	1	NA	exon (NM_009267, exon 3 of 4)	exon (NM_009267, exon 3 of 4)	1918	NM_009268	20771	Mm.30276	NM_009268		Mucl1	Spt-2|Spt2	mucin-like 1	protein-coding
mm_113553.1	chr13	38151254	38151278	+	1	NA	promoter-TSS (NM_023842)	promoter-TSS (NM_023842)	-28	NM_023842	109620	Mm.355327	NM_023842	ENSMUSG00000054889	Dsp	2300002E22Rik|5730453H04Rik|AA407887|AA407888|AW109828|DP|rul	desmoplakin	protein-coding
mm_108559.1	chr12	84640948	84640995	+	1	NA	promoter-TSS (NM_001168589)	promoter-TSS (NM_001168589)	-48	NM_001168589	432677	Mm.311913	NM_001033776	ENSMUSG00000071235	Vrtn	7420416P09Rik	vertebrae development associated	protein-coding
mm_48597.1	chr5	144026597	144026607	-	1	NA	intron (NM_033039, intron 1 of 4)	intron (NM_033039, intron 1 of 4)	-11749	NM_177682	231874	Mm.320432	NM_177682	ENSMUSG00000029617	Ccz1	AU022870	CCZ1 vacuolar protein trafficking and biogenesis associated	protein-coding
mm_153109.1	chr19	32957019	32957035	-	1	NA	Intergenic	Intergenic	199450	NM_008960	19211	Mm.245395	NM_008960	ENSMUSG00000013663	Pten	2310035O07Rik|A130070J02Rik|AI463227|B430203M17Rik|MMAC1|TEP1	phosphatase and tensin homolog	protein-coding
mm_61837.1	chr7	88288751	88288761	+	1	NA	3' UTR (NM_001311790, exon 4 of 4)	3' UTR (NM_001311790, exon 4 of 4)	10671	NM_001311790	13032	Mm.89295	NM_009982	ENSMUSG00000030560	Ctsc	AI047818|CatC|DPP1|DPPI	cathepsin C	protein-coding
mm_25166.1	chr3	103065373	103065394	+	1	NA	3' UTR (NM_010937, exon 7 of 7)	3' UTR (NM_010937, exon 7 of 7)	7098	NM_010937	18176	Mm.400954	NM_010937	ENSMUSG00000027852	Nras	AV095280|N-ras	neuroblastoma ras oncogene	protein-coding
mm_106504.1	chr11	120437657	120437731	-	1	NA	promoter-TSS (NM_001195023)	promoter-TSS (NM_001195023)	6	NM_001195023	217365	Mm.309520	NM_199469	ENSMUSG00000039703	Nploc4	AK129375|Npl4|mKIAA1499	NPL4 homolog, ubiquitin recognition factor	protein-coding
mm_10427.1	chr2	13582771	13582790	+	1	NA	TTS (NM_011701)	TTS (NM_011701)	8469	NM_011701	22352	Mm.268000	NM_011701	ENSMUSG00000026728	Vim	-	vimentin	protein-coding
mm_93347.1	chr10	100487292	100487311	-	1	NA	promoter-TSS (NM_001110013)	promoter-TSS (NM_001110013)	46	NM_001033332	237500	Mm.296805	NM_001033332	ENSMUSG00000036676	Tmtc3	9130014E20Rik|B130008E12Rik|mSmile	transmembrane and tetratricopeptide repeat containing 3	protein-coding
mm_82302.1	chr9	7865053	7865064	-	1	NA	intron (NM_007464, intron 1 of 8)	intron (NM_007464, intron 1 of 8)	8112	NM_007464	11796	Mm.2026	NM_007464	ENSMUSG00000032000	Birc3	AW107670|Api1|Api2|Birc2|C-IAP2|HIAP2|IAP1|IAP2|MIAP1|MIAP2|MIHB|MIHC|RNF49|cIAP-1|cIAP-2|cIAP1|cIAP2	baculoviral IAP repeat-containing 3	protein-coding
mm_131853.1	chr16	23067687	23067710	+	1	NA	exon (NM_001102411, exon 4 of 10)	exon (NM_001102411, exon 4 of 10)	9398	NM_001102412	16644	Mm.2160	NM_023125	ENSMUSG00000022875	Kng1	Kng	kininogen 1	protein-coding
mm_38135.1	chr4	134704099	134704110	-	1	NA	5' UTR (NM_207237, exon 1 of 12)	5' UTR (NM_207237, exon 1 of 12)	186	NM_207237	230815	Mm.18905	NM_207237	ENSMUSG00000037306	Man1c1	AI593348	mannosidase, alpha, class 1C, member 1	protein-coding
mm_43585.1	chr5	137747512	137747533	+	1	NA	exon (NM_023910, exon 2 of 5)	exon (NM_023910, exon 2 of 5)	1553	NM_029805	78829	Mm.286399	NM_023910	ENSMUSG00000029723	Tsc22d4	0610009M14Rik|1700023B23Rik|AI415410|Thg-1pit|Tilz2	TSC22 domain family, member 4	protein-coding
mm_134291.1	chr16	14226510	14226532	-	1	NA	exon (NM_013607, exon 16 of 42)	exon (NM_013607, exon 16 of 42)	63246	NM_001114085	67203	Mm.24105	NM_023317	ENSMUSG00000022678	Nde1	2810027M15Rik|AU042936|AW822251|Nude|mNudE	nudE neurodevelopment protein 1	protein-coding
mm_158543.1	chrX	145348933	145348944	-	1	NA	promoter-TSS (NM_178358)	promoter-TSS (NM_178358)	-44	NM_178358	237091	Mm.135547	NM_178358	ENSMUSG00000041700	Lhfpl1	Lhfp	lipoma HMGIC fusion partner-like 1	protein-coding
mm_116394.1	chr13	41217080	41217083	-	1	NA	intron (NM_019423, intron 1 of 7)	intron (NM_019423, intron 1 of 7)	3081	NM_001311121	54326	Mm.2567	NM_019423	ENSMUSG00000021364	Elovl2	AI317360|Ssc2	elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 2	protein-coding
mm_44076.1	chr5	149006949	149006966	+	1	NA	promoter-TSS (NR_040429)	promoter-TSS (NR_040429)	-5	NR_040429	100503307	Mm.188008	NR_040429	ENSMUSG00000086610	Gm15408	OTTMUSG00000021225	predicted gene 15408	ncRNA
mm_64936.1	chr7	16309341	16309370	-	1	NA	promoter-TSS (NM_133234)	promoter-TSS (NM_133234)	-228	NM_133234	170770	Mm.7660	NM_133234	ENSMUSG00000002083	Bbc3	PUMA|PUMA/JFY1	BCL2 binding component 3	protein-coding
mm_57533.1	chr6	126535515	126535532	-	1	NA	promoter-TSS (NM_145983)	promoter-TSS (NM_145983)	32	NM_145983	16493	Mm.222831	NM_145983	ENSMUSG00000045534	Kcna5	Kv1.5	potassium voltage-gated channel, shaker-related subfamily, member 5	protein-coding
mm_23413.1	chr3	58525114	58525128	+	1	NA	promoter-TSS (NM_001005509)	promoter-TSS (NM_001005509)	-700	NM_001005509	229317	Mm.21617	NM_001005509	ENSMUSG00000027810	Eif2a	D030048D22|D3Ertd194e	eukaryotic translation initiation factor 2A	protein-coding
mm_127943.1	chr15	10714580	10714610	-	1	NA	promoter-TSS (NM_001166408)	promoter-TSS (NM_001166408)	36	NM_001166408	75646	Mm.212395	NM_030690	ENSMUSG00000022246	Rai14	1700008J19Rik|1700020L11Rik|Ankycorbin|Norpeg|mKIAA1334	retinoic acid induced 14	protein-coding
mm_12985.1	chr2	90847493	90847504	+	1	NA	intron (NM_001317242, intron 1 of 12)	CpG	343	NM_001317242	56428	Mm.28023	NM_019758	ENSMUSG00000027282	Mtch2	2310034D24Rik|4930539J07Rik|HSPC032	mitochondrial carrier 2	protein-coding
mm_32025.1	chr4	95161464	95161490	+	1	NA	Intergenic	CpG	-109255	NM_010591	16476	Mm.275071	NM_010591	ENSMUSG00000052684	Jun	AP-1|Junc|c-jun	jun proto-oncogene	protein-coding
mm_14093.1	chr2	125162993	125163001	+	1	NA	intron (NM_001079690, intron 5 of 27)	intron (NM_001079690, intron 5 of 27)	10397	NM_001079690	20495	Mm.3914	NM_011389	ENSMUSG00000027202	Slc12a1	AI788571|D630042G03Rik|Nkcc2|mBSC1|urehr3	solute carrier family 12, member 1	protein-coding
mm_123466.1	chr14	65973352	65973359	-	1	NA	exon (NM_013492, exon 3 of 9)	exon (NM_013492, exon 3 of 9)	4872	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_150629.1	chr19	41344933	41344947	+	1	NA	intron (NM_031376, intron 2 of 16)	intron (NM_031376, intron 2 of 16)	40130	NM_031376	83490	Mm.222266	NM_031376	ENSMUSG00000025017	Pik3ap1	1810044J04Rik|BCAP	phosphoinositide-3-kinase adaptor protein 1	protein-coding
mm_11854.1	chr2	45774857	45774859	+	1	NA	Intergenic	Intergenic	78253	NR_040497	69405	Mm.396184	NR_040497	ENSMUSG00000086202	1700019E08Rik	-	RIKEN cDNA 1700019E08 gene	ncRNA
mm_53026.1	chr6	124476467	124476467	+	1	NA	Intergenic	Intergenic	-11683	NM_153508	232370	Mm.193701	NM_153508	ENSMUSG00000008153	Clstn3	CSTN3|Cs3|Cst-3|alc-beta	calsyntenin 3	protein-coding
mm_126316.1	chr15	79687967	79687993	+	1	NA	promoter-TSS (NM_028792)	promoter-TSS (NM_028792)	-108	NM_028792	74158	Mm.323393	NM_028792	ENSMUSG00000022426	Josd1	1300006C06Rik|mKIAA0063	Josephin domain containing 1	protein-coding
mm_42096.1	chr5	110344562	110344570	+	1	NA	promoter-TSS (NM_001310709)	promoter-TSS (NM_001310709)	-164	NR_132326	381667	Mm.332572	NM_001033459	ENSMUSG00000072754	Lrcol1	Clpsl3|Gm1679	leucine rich colipase-like 1	protein-coding
mm_135303.1	chr16	38709709	38709718	-	1	NA	intron (NM_020260, intron 1 of 11)	intron (NM_020260, intron 1 of 11)	3322	NM_020260	12549	Mm.370848	NM_020260	ENSMUSG00000022799	Arhgap31	5830477L08Rik|AU041750|Cdgap|D330026I07Rik	Rho GTPase activating protein 31	protein-coding
mm_13875.1	chr2	119897213	119897292	+	1	NA	promoter-TSS (NM_013720)	promoter-TSS (NM_013720)	24	NM_013720	29808	Mm.87532	NM_013720	ENSMUSG00000033943	Mga	AV312082|C130042M01Rik|C80739|D030062C11Rik|Mad5	MAX gene associated	protein-coding
mm_145303.1	chr18	53349521	53349532	+	1	NA	intron (NM_029394, intron 3 of 6)	intron (NM_029394, intron 3 of 6)	68481	NM_008908	19038	Mm.4587	NM_008908	ENSMUSG00000024538	Ppic	CyP-20c	peptidylprolyl isomerase C	protein-coding
mm_54494.1	chr6	35510070	35510101	-	1	NA	3' UTR (NM_008098, exon 4 of 4)	3' UTR (NM_008098, exon 4 of 4)	29803	NM_008098	14489	Mm.182746	NM_008098	ENSMUSG00000029840	Mtpn	5033418D15Rik|Gcdp|V1	myotrophin	protein-coding
mm_144913.1	chr18	37473539	37473562	+	1	NA	promoter-TSS (NM_053140)	promoter-TSS (NM_053140)	4	NM_053140	93886	Mm.283857	NM_053140	ENSMUSG00000047033	Pcdhb15	Pcdhb7|PcdhbO	protocadherin beta 15	protein-coding
mm_107754.1	chr12	59070231	59070279	+	1	NA	exon (NM_008891, exon 7 of 9)	exon (NM_008891, exon 7 of 9)	3336	NM_008891	18949	Mm.22347	NM_008891	ENSMUSG00000020994	Pnn	AU045199|D12Ertd512e	pinin	protein-coding
mm_102417.1	chr11	59208665	59208680	-	1	NA	exon (NM_024210, exon 1 of 7)	exon (NM_024210, exon 1 of 7)	311	NM_024210	67862	Mm.358708	NM_024210	ENSMUSG00000020441	2310033P09Rik	Mmtag2	RIKEN cDNA 2310033P09 gene	protein-coding
mm_74207.1	chr8	123893262	123893275	+	1	NA	exon (NM_009606, exon 3 of 7)	exon (NM_009606, exon 3 of 7)	1507	NM_001272041	11459	Mm.214950	NM_009606	ENSMUSG00000031972	Acta1	AA959943|Acta-2|Acts|Actsk-1	actin, alpha 1, skeletal muscle	protein-coding
mm_138364.1	chr17	35000903	35000930	+	1	NA	promoter-TSS (NM_011690)	promoter-TSS (NM_011690)	9	NM_011690	22321	Mm.28420	NM_011690	ENSMUSG00000007029	Vars	Bat6|D17H6S56E|G7a|Vars2	valyl-tRNA synthetase	protein-coding
mm_167022.1	chr7	65635956	65635958	-	1	NA	Intergenic	Intergenic	-8941	NM_172310	272396	Mm.35127	NM_172310	ENSMUSG00000030515	Tarsl2	A530046H20Rik	threonyl-tRNA synthetase-like 2	protein-coding
mm_124683.1	chr15	6431062	6431078	+	1	NA	exon (NM_001102400, exon 9 of 13)	exon (NM_001102400, exon 9 of 13)	-14263	NM_013485	12279	Mm.29095	NM_013485	ENSMUSG00000022149	C9	-	complement component 9	protein-coding
mm_86006.1	chr9	112233256	112233269	-	1	NA	promoter-TSS (NM_001177616)	promoter-TSS (NM_001177616)	-761	NM_001177616	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_156269.1	chrX	136833297	136833353	+	1	NA	exon (NM_011123, exon 4 of 7)	exon (NM_011123, exon 4 of 7)	10579	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_137863.1	chr17	31296192	31296253	+	1	NA	promoter-TSS (NM_001242427)	promoter-TSS (NM_001242427)	-2	NM_001242427	224674	Mm.311395	NM_153062	ENSMUSG00000024036	Slc37a1	G3PP	solute carrier family 37 (glycerol-3-phosphate transporter), member 1	protein-coding
mm_59238.1	chr7	24778334	24778341	+	1	NA	exon (NM_007675, exon 2 of 4)	exon (NM_007675, exon 2 of 4)	1133	NM_007675	26366	Mm.30300	NM_007675	ENSMUSG00000054169	Ceacam10	Bgp3|Cea10	carcinoembryonic antigen-related cell adhesion molecule 10	protein-coding
mm_99481.1	chr11	102604824	102604836	+	1	NA	exon (NM_020510, exon 1 of 1)	exon (NM_020510, exon 1 of 1)	399	NM_020510	57265	Mm.36416	NM_020510	ENSMUSG00000050288	Fzd2	AL033370|AW456835|Fz10|Fzd10|Mfz10|Mfz10a	frizzled class receptor 2	protein-coding
mm_48314.1	chr5	138810042	138810071	-	1	NA	TTS (NM_030565)	TTS (NM_030565)	-10024	NM_001195128	384244	Mm.485002	NM_001195128	ENSMUSG00000094504	Gm5294	EG384244	predicted gene 5294	protein-coding
mm_39289.1	chr5	4023344	4023357	+	1	NA	intron (NM_194462, intron 21 of 47)	intron (NM_194462, intron 21 of 47)	81347	NM_020010	13121	Mm.140158	NM_020010	ENSMUSG00000001467	Cyp51	AI426508|CYPLI|Cyp51a1|Ldm|P450-14DM|P450LI	cytochrome P450, family 51	protein-coding
mm_98611.1	chr11	95842707	95842721	+	1	NA	promoter-TSS (NM_001284397)	promoter-TSS (NM_001284397)	46	NM_001038664	14710	Mm.46299	NM_023121	ENSMUSG00000038811	Gngt2	AV096488	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 2	protein-coding
mm_171580.1	chr4	147492346	147492350	+	1	NA	intron (NM_001039209, intron 1 of 2)	intron (NM_001039209, intron 1 of 2)	-60929	NM_001014397	433804	Mm.332047	NM_001014397	ENSMUSG00000065999	Zfp985	Gm13154|OTTMUSG00000010673	zinc finger protein 985	protein-coding
mm_54940.1	chr6	48554658	48554666	-	1	NA	promoter-TSS (NM_177736)	promoter-TSS (NM_177736)	-137	NM_001110160	243371	Mm.290764	NM_177736	ENSMUSG00000073096	Lrrc61	BC027309	leucine rich repeat containing 61	protein-coding
mm_52556.1	chr6	116073830	116073832	+	1	NA	intron (NM_177412, intron 3 of 5)	ID_B1|SINE|B4	-78826	NM_026376	67784	Mm.3085	NM_026376	ENSMUSG00000030123	Plxnd1	6230425C21Rik|b2b1863Clo|b2b553Clo	plexin D1	protein-coding
mm_172000.1	chr6	107034559	107034563	+	1	NA	Intergenic	RLTR9E|LTR|ERVK	-234474	NM_175357	58799	Mm.290085	NM_021449	ENSMUSG00000005362	Crbn	2610203G15Rik|2900045O07Rik|AF229032|AW108261|piL	cereblon	protein-coding
mm_76008.1	chr8	72571034	72571067	-	1	NA	promoter-TSS (NM_172396)	promoter-TSS (NM_172396)	-2	NM_172396	66818	Mm.22565	NM_172396	ENSMUSG00000044600	Smim7	9130011J15Rik	small integral membrane protein 7	protein-coding
mm_123336.1	chr14	63128707	63128733	-	1	NA	intron (NM_007798, intron 1 of 9)	intron (NM_007798, intron 1 of 9)	6258	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_166736.1	chr6	123172889	123172896	+	1	NA	promoter-TSS (NM_001004159)	promoter-TSS (NM_001004159)	-131	NM_001004159	381809	Mm.333372	NM_001004159	ENSMUSG00000067767	Clec4b2	Aplra1|F830043G12Rik|mDCAR1	C-type lectin domain family 4, member b2	protein-coding
mm_83670.1	chr9	49756423	49756425	-	1	NA	intron (NM_001081445, intron 1 of 17)	intron (NM_001081445, intron 1 of 17)	42645	NM_001081445	17967	Mm.4974	NM_010875	ENSMUSG00000039542	Ncam1	CD56|E-NCAM|NCAM-1|Ncam	neural cell adhesion molecule 1	protein-coding
mm_161690.1	chr17	22165997	22165997	-	1	NA	promoter-TSS (NM_177596)	promoter-TSS (NM_177596)	-20	NM_177596	210853	Mm.441622	NM_177596	ENSMUSG00000063383	Zfp947	6720451E15|EG210853|Gm4769	zinc finger protein 947	protein-coding
mm_21373.1	chr2	157279557	157279578	-	1	NA	promoter-TSS (NM_001039557)	promoter-TSS (NM_001039557)	-18	NM_001039557	629499	Mm.384235	NM_001039557	ENSMUSG00000074627	Mroh8	4922505G16Rik	maestro heat-like repeat family member 8	protein-coding
mm_40255.1	chr5	38225887	38225899	+	1	NA	exon (NM_025281, exon 3 of 9)	exon (NM_025281, exon 3 of 9)	5411	NM_025281	17089	Mm.28560	NM_025281	ENSMUSG00000067367	Lyar	MLZ-264	Ly1 antibody reactive clone	protein-coding
mm_26663.1	chr3	154707631	154707654	+	1	NA	Intergenic	MLT1J|LTR|ERVL-MaLR	-3491	NM_175176	209601	Mm.331454	NM_175176	ENSMUSG00000078161	Erich3	1700013E18Rik|4922501L14Rik|5031409G23Rik|AI596448|Gm133	glutamate rich 3	protein-coding
mm_24923.1	chr3	96525164	96525186	+	1	NA	promoter-TSS (NM_027126)	promoter-TSS (NM_027126)	-10	NM_027126	69585	Mm.171314	NM_027126	ENSMUSG00000038403	Hfe2	2310035L15Rik|5230400G09Rik|AI414844|AI789733|DL-M|HJV|Rgmc|hemojuvelin	hemochromatosis type 2 (juvenile)	protein-coding
mm_64613.1	chr7	3502543	3502578	-	1	NA	promoter-TSS (NM_177363)	promoter-TSS (NM_177363)	-8	NM_177363	245126	Mm.245747	NM_177363	ENSMUSG00000053338	Tarm1	9930022N03Rik|ENSMUSG00000053338|Gm9904|OLT-2	T cell-interacting, activating receptor on myeloid cells 1	protein-coding
mm_55979.1	chr6	85869129	85869143	-	1	NA	promoter-TSS (NM_053096)	promoter-TSS (NM_053096)	1	NM_053096	93673	Mm.24251	NM_053096	ENSMUSG00000033634	Nat8f2	Cml2	N-acetyltransferase 8 (GCN5-related) family member 2	protein-coding
mm_95490.1	chr11	51607007	51607041	+	1	NA	promoter-TSS (NM_010448)	promoter-TSS (NM_010448)	-143	NM_010448	15384	Mm.256875	NM_010448	ENSMUSG00000020358	Hnrnpab	3010025C11Rik|CBF-A|Cgbfa|Hnrpab	heterogeneous nuclear ribonucleoprotein A/B	protein-coding
mm_7852.1	chr1	132391659	132391682	-	1	NA	promoter-TSS (NM_178874)	promoter-TSS (NM_178874)	-284	NM_178874	68875	Mm.273785	NM_178874	ENSMUSG00000042066	Tmcc2	1110063G11Rik	transmembrane and coiled-coil domains 2	protein-coding
mm_170118.1	chr17	39846684	39846687	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	3688	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_157988.1	chrX	94212906	94212922	-	1	NA	promoter-TSS (NM_012010)	promoter-TSS (NM_012010)	-263	NM_012010	26905	Mm.218851	NM_012010	ENSMUSG00000035150	Eif2s3x	AA409828|AA547477|AI314668|Eif-2gx	eukaryotic translation initiation factor 2, subunit 3, structural gene X-linked	protein-coding
mm_133576.1	chr16	91406465	91406486	+	1	NA	TTS (NM_010509)	TTS (NM_010509)	240	NM_008349	16155	Mm.4154	NM_008349	ENSMUSG00000022969	Il10rb	6620401D04Rik|AI528744|CRF2-4|Crfb4|D16H21S58|D21S58h|IL-10R2|Il10r2	interleukin 10 receptor, beta	protein-coding
mm_166354.1	chr5	121220307	121220309	+	1	NA	promoter-TSS (NM_181421)	promoter-TSS (NM_181421)	89	NM_181421	269700	Mm.184589	NM_181421	ENSMUSG00000042744	Gm15800	A130010L24|AU042671|BC019639|EG545802|OTTMUSG00000026283|mKIAA0614	predicted gene 15800	protein-coding
mm_109143.1	chr12	107129659	107129669	+	1	NA	Intergenic	MLT1A1|LTR|ERVL-MaLR	-413340	NR_015512	71033	Mm.159404	NR_015512	ENSMUSG00000085820	4933406K04Rik	4930426M03Rik|4930485I22Rik|4933427G14Rik	RIKEN cDNA 4933406K04 gene	ncRNA
mm_11002.1	chr2	26454965	26454965	+	1	NA	Intergenic	Intergenic	-9749	NM_153125	227648	Mm.206371	NM_153125	ENSMUSG00000026924	Sec16a	AU024582|C230052J16Rik	SEC16 homolog A, endoplasmic reticulum export factor	protein-coding
mm_62074.1	chr7	92777565	92777604	+	1	NA	intron (NM_029494, intron 1 of 4)	intron (NM_029494, intron 1 of 4)	35870	NM_029494	75985	Mm.323004	NM_029494	ENSMUSG00000030643	Rab30	5033421K01Rik|AI323892|Rsb30	RAB30, member RAS oncogene family	protein-coding
mm_7681.1	chr1	128589356	128589367	-	1	NA	exon (NM_009911, exon 2 of 2)	exon (NM_009911, exon 2 of 2)	2938	NM_009911	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding
mm_9071.1	chr1	168343005	168343015	-	1	NA	intron (NM_008783, intron 2 of 7)	intron (NM_008783, intron 2 of 7)	89159	NM_001291508	18514	Mm.43358	NM_008783	ENSMUSG00000052534	Pbx1	2310056B04Rik|D230003C07Rik|Pbx-1	pre B cell leukemia homeobox 1	protein-coding
mm_88646.1	chr10	79952407	79952413	+	1	NA	3' UTR (NM_001288626, exon 9 of 9)	3' UTR (NM_001288626, exon 9 of 9)	-7742	NM_175450	216156	Mm.35828	NM_175450	ENSMUSG00000035754	Wdr18	2310012I10Rik|AU044733|AW122032	WD repeat domain 18	protein-coding
mm_86158.1	chr9	118150080	118150106	-	1	NA	5' UTR (NM_026442, exon 1 of 4)	5' UTR (NM_026442, exon 1 of 4)	103	NM_026442	67899	Mm.9953	NM_026442	ENSMUSG00000039163	Cmc1	2010110K16Rik|2010312P05Rik|AI596001	COX assembly mitochondrial protein 1	protein-coding
mm_43518.1	chr5	137150533	137150558	+	1	NA	Intergenic	Intergenic	-34338	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_106509.1	chr11	120467331	120467371	-	1	NA	promoter-TSS (NM_008244)	promoter-TSS (NM_008244)	249	NM_197995	70317	Mm.485046	NM_197995	ENSMUSG00000057594	Arl16	2600005N12Rik	ADP-ribosylation factor-like 16	protein-coding
mm_138917.1	chr17	43607229	43607257	+	1	NA	exon (NM_013737, exon 10 of 12)	exon (NM_013737, exon 10 of 12)	-15734	NR_045444	73504	Mm.9277	NR_045444	ENSMUSG00000090307	1700071M16Rik	-	RIKEN cDNA 1700071M16 gene	ncRNA
mm_52051.1	chr6	97213944	97213956	+	1	NA	intron (NM_022992, intron 1 of 2)	intron (NM_022992, intron 1 of 2)	3158	NM_022992	65106	Mm.291014	NM_022992	ENSMUSG00000035199	Arl6ip5	5930404D22Rik|AV001879|Aip-5|Gtrap3-18|addiscin	ADP-ribosylation factor-like 6 interacting protein 5	protein-coding
mm_102560.1	chr11	61453922	61453982	-	1	NA	promoter-TSS (NM_009548)	promoter-TSS (NM_009548)	40	NM_009548	22671	Mm.89201	NM_009548	ENSMUSG00000010086	Rnf112	ZNF179|Zfp179|bfp|neurolastin	ring finger protein 112	protein-coding
mm_76636.1	chr8	92355837	92355852	-	1	NA	non-coding (NR_033641, exon 1 of 7)	non-coding (NR_033641, exon 1 of 7)	276	NR_110452	71296	Mm.86664	NR_033641	ENSMUSG00000031736	Crnde	4933436C20Rik	colorectal neoplasia differentially expressed (non-protein coding)	ncRNA
mm_64302.1	chr7	141861850	141861871	+	1	NA	exon (NM_028801, exon 31 of 49)	exon (NM_028801, exon 31 of 49)	22788	NM_028801	74180	Mm.200752	NM_028801	ENSMUSG00000066108	Muc5b	2300002I04Rik|A130042M24|AV085033|MUC5|MUC9|mucin 5b	mucin 5, subtype B, tracheobronchial	protein-coding
mm_120534.1	chr14	67233287	67233346	+	1	NA	promoter-TSS (NM_001276387)	promoter-TSS (NM_001276387)	24	NM_001276387	13592	Mm.319947	NM_010095	ENSMUSG00000022053	Ebf2	D14Ggc1e|EBF-2|Mmot1|O/E-3|OE-3	early B cell factor 2	protein-coding
mm_31321.1	chr4	46166069	46166076	+	1	NA	intron (NM_001033201, intron 16 of 22)	intron (NM_001033201, intron 16 of 22)	27561	NM_001033201	433702	Mm.389536	NM_001033201	ENSMUSG00000028330	Ncbp1	AU014645|AW538051|CBP80	nuclear cap binding protein subunit 1	protein-coding
mm_48694.1	chr5	146821042	146821052	-	1	NA	Intergenic	Intergenic	-11843	NM_019647	19933	Mm.316592	NM_019647	ENSMUSG00000041453	Rpl21	8430440E03Rik|L21	ribosomal protein L21	protein-coding
mm_97776.1	chr11	82115181	82115186	+	1	NA	promoter-TSS (NM_021443)	promoter-TSS (NM_021443)	-2	NM_021443	20307	Mm.42029	NM_021443	ENSMUSG00000009185	Ccl8	1810063B20Rik|AB023418|HC14|MCP-2|Mcp2|Scya8	chemokine (C-C motif) ligand 8	protein-coding
mm_152008.1	chr19	5929632	5929644	-	1	NA	Intergenic	Intergenic	-4822	NM_026772	104252	Mm.491103	NM_026772	ENSMUSG00000045664	Cdc42ep2	1110008C05Rik|Borg1|Cep2|D19Bwg1013e	CDC42 effector protein (Rho GTPase binding) 2	protein-coding
mm_152216.1	chr19	8252274	8252290	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-33382	NM_001347426	236293	Mm.440581	NM_172776	ENSMUSG00000075044	Slc22a29	D630002G06Rik	solute carrier family 22. member 29	protein-coding
mm_125714.1	chr15	68928424	68928452	+	1	NA	promoter-TSS (NM_010158)	promoter-TSS (NM_010158)	18	NM_010158	13992	Mm.17964	NM_010158	ENSMUSG00000022332	Khdrbs3	Etle|SLM-2|Salp|Slm2|T-STAR	KH domain containing, RNA binding, signal transduction associated 3	protein-coding
mm_145685.1	chr18	61639604	61639632	+	1	NA	promoter-TSS (NR_045420)	promoter-TSS (NR_045420)	-35	NR_045420	545261	Mm.426593	NR_045420	ENSMUSG00000098098	Bvht	Braveheart|Gm20748	braveheart long non-coding RNA	ncRNA
mm_43777.1	chr5	141867551	141867551	+	1	NA	intron (NM_177879, intron 5 of 44)	B4A|SINE|B4	-533946	NM_199068	17425	Mm.24214	NM_010812	ENSMUSG00000056493	Foxk1	A630048H08Rik|AI463295|ENSMUSG00000075577|Gm10868|Mnf	forkhead box K1	protein-coding
mm_167817.1	chr9	124282117	124282203	-	1	NA	Intergenic	Intergenic	30534	NM_001243118	630836	Mm.458553	NM_001243117	ENSMUSG00000074829	2010315B03Rik	BC029716	RIKEN cDNA 2010315B03 gene	protein-coding
mm_123483.1	chr14	65990442	65990485	-	1	NA	exon (NM_178747, exon 10 of 12)	exon (NM_178747, exon 10 of 12)	18747	NM_178747	268756	Mm.26207	NM_178747	ENSMUSG00000034450	Gulo	5730581M22|AU018375|BC028822|GLO|LGO|sfx|unh|unhip	gulonolactone (L-) oxidase	protein-coding
mm_12096.1	chr2	60901946	60901967	+	1	NA	intron (NM_020296, intron 1 of 13)	intron (NM_020296, intron 1 of 13)	-20518	NM_001141931	56878	Mm.259667	NM_020296	ENSMUSG00000026970	Rbms1	2600014B10Rik|AI255215|MSSP-1|MSSP-2|MSSP-3|YC1	RNA binding motif, single stranded interacting protein 1	protein-coding
mm_131472.1	chr16	17070221	17070239	+	1	NA	promoter-TSS (NM_023249)	promoter-TSS (NM_023249)	91	NM_001291047	106369	Mm.237941	NM_023249	ENSMUSG00000022773	Ypel1	0610009L05Rik|1700016N17Rik|1700019O22Rik|4921520K19Rik|4930511F14Rik|AV118478|DGL-1|Dgl1|Ppil2|mdgl-1	yippee-like 1 (Drosophila)	protein-coding
mm_127958.1	chr15	11905610	11905623	-	1	NA	promoter-TSS (NM_001039181)	promoter-TSS (NM_001039181)	58	NM_008728	18162	Mm.25259	NM_008728	ENSMUSG00000022206	Npr3	ANP-C|ANPR-C|EF-2|NPR-C|lgj|stri	natriuretic peptide receptor 3	protein-coding
mm_65326.1	chr7	24972631	24972644	-	1	NA	promoter-TSS (NM_010261)	promoter-TSS (NM_010261)	91	NM_010261	14470	Mm.22473	NM_010261	ENSMUSG00000003380	Rabac1	2310040I06Rik|Gbpap1|PRA1|prenylin	Rab acceptor 1 (prenylated)	protein-coding
mm_48509.1	chr5	142821442	142821456	-	1	NA	Intergenic	Intergenic	-4062	NM_001122730	231861	Mm.354649	NM_178242	ENSMUSG00000039477	Tnrc18	BC025631|EG381742|Zfp469	trinucleotide repeat containing 18	protein-coding
mm_80746.1	chr9	94971817	94971822	+	1	NA	intron (NM_177909, intron 9 of 15)	intron (NM_177909, intron 9 of 15)	219990	NR_106116	102465763		NR_106116	ENSMUSG00000098251	Mir7656	Gm27614|mmu-mir-7656	microRNA 7656	ncRNA
mm_149361.1	chr19	11121384	11121411	+	1	NA	intron (NM_027058, intron 1 of 6)	intron (NM_027058, intron 1 of 6)	9481	NM_027058	69369	Mm.391200	NM_027058	ENSMUSG00000024729	1700017D01Rik	-	RIKEN cDNA 1700017D01 gene	protein-coding
mm_170488.1	chr19	17926770	17926770	+	1	NA	Intergenic	Intergenic	-89138	NM_001190483	18552	Mm.3401	NM_001163144	ENSMUSG00000024713	Pcsk5	PC5|PC6|SPC6|b2b1549Clo|b2b585Clo	proprotein convertase subtilisin/kexin type 5	protein-coding
mm_114998.1	chr13	97847933	97847944	+	1	NA	Intergenic	Intergenic	287938	NR_046157	328314	Mm.138047	NR_046157	ENSMUSG00000110235	Gm5086	B230311A21|EG328314	predicted gene 5086	ncRNA
mm_163939.1	chr14	51145271	51145273	-	1	NA	3' UTR (NM_011271, exon 2 of 2)	3' UTR (NM_011271, exon 2 of 2)	1495	NM_011271	19752	Mm.235538	NM_011271	ENSMUSG00000035896	Rnase1	AI574248|Rib-1|Rib1	ribonuclease, RNase A family, 1 (pancreatic)	protein-coding
mm_130809.1	chr15	101734307	101734313	-	1	NA	3' UTR (NM_019956, exon 9 of 9)	3' UTR (NM_019956, exon 9 of 9)	8787	NM_019956	56735	Mm.358677	NM_019956	ENSMUSG00000051879	Krt71	AA589543|Ca|Cal4|Cu|Krt2-6g|mK6irs|mK6irs1	keratin 71	protein-coding
mm_87118.1	chr10	33256930	33256930	+	1	NA	promoter-TSS (NR_040657)	promoter-TSS (NR_040657)	-573	NR_040657	442820	Mm.490725	NR_040657		D830005E20Rik	-	RIKEN cDNA D830005E20 gene	ncRNA
mm_25555.1	chr3	116008376	116008402	+	1	NA	promoter-TSS (NM_001163514)	promoter-TSS (NM_001163514)	92	NM_001163514	58193	Mm.41739	NM_021388	ENSMUSG00000027963	Extl2	3000001D04Rik|AW146439	exostoses (multiple)-like 2	protein-coding
mm_55736.1	chr6	77472151	77472155	-	1	NA	intron (NM_001109764, intron 8 of 19)	intron (NM_001109764, intron 8 of 19)	-89678	NR_045141	70753	Mm.490700	NR_045141	ENSMUSG00000108077	6330415B21Rik	-	RIKEN cDNA 6330415B21 gene	ncRNA
mm_126908.1	chr15	90224278	90224291	+	1	NA	promoter-TSS (NM_001033441)	promoter-TSS (NM_001033441)	-27	NM_001033441	380959	Mm.17853	NM_001033441	ENSMUSG00000075470	Alg10b	AA469671|AU045404|AW123895|C85569|Deaf1|Gm917|nse5	asparagine-linked glycosylation 10B (alpha-1,2-glucosyltransferase)	protein-coding
mm_58002.1	chr6	136173639	136173655	-	1	NA	promoter-TSS (NM_008171)	promoter-TSS (NM_008171)	-136	NM_008171	14812	Mm.436649	NM_008171	ENSMUSG00000030209	Grin2b	AW490526|GluN2B|NR2B|Nmdar2b	glutamate receptor, ionotropic, NMDA2B (epsilon 2)	protein-coding
mm_172375.1	chr7	127286465	127286467	-	1	NA	Intergenic	Intergenic	-9794	NM_001253873	16408	Mm.1618	NM_008400	ENSMUSG00000030830	Itgal	(p180)|Cd11a|LFA-1|LFA-1A|Ly-15|Ly-21	integrin alpha L	protein-coding
mm_66999.1	chr7	64872994	64873037	-	1	NA	promoter-TSS (NM_023239)	promoter-TSS (NM_023239)	25	NM_023239	66647	Mm.19944	NM_023239	ENSMUSG00000070520	Ndnl2	5730494G16Rik|AI642138|BB044375|HCA4|Mageg1|Nsmce3|mage-g1	necdin-like 2	protein-coding
mm_160409.1	chr8	72099611	72099611	+	1	NA	promoter-TSS (NM_146539)	promoter-TSS (NM_146539)	-151	NM_146539	258532	Mm.377557	NM_146539	ENSMUSG00000061561	Olfr373	MOR282-2	olfactory receptor 373	protein-coding
mm_62126.1	chr7	96951516	96951526	+	1	NA	promoter-TSS (NM_153591)	promoter-TSS (NM_153591)	-6	NM_153591	244141	Mm.274864	NM_153591	ENSMUSG00000018995	Nars2	AI875199	asparaginyl-tRNA synthetase 2 (mitochondrial)(putative)	protein-coding
mm_91633.1	chr10	42192000	42192015	-	1	NA	intron (NM_019740, intron 3 of 3)	intron (NM_019740, intron 3 of 3)	84735	NM_019740	56484	Mm.338613	NM_019740	ENSMUSG00000048756	Foxo3	1110048B16Rik|2010203A17Rik|C76856|FKHRL1|Fkhr2|Foxo3a	forkhead box O3	protein-coding
mm_120911.1	chr14	76251492	76251494	+	1	NA	Intergenic	Intergenic	140602	NM_013745	27275	Mm.21138	NM_013745	ENSMUSG00000022009	Nufip1	Nufip	nuclear fragile X mental retardation protein interacting protein 1	protein-coding
mm_152270.1	chr19	8818947	8819008	-	1	NA	promoter-TSS (NM_001081196)	promoter-TSS (NM_001081196)	317	NM_027412	70387	Mm.261082	NM_027412	ENSMUSG00000071660	Ttc9c	2210019E14Rik|6330408J23Rik	tetratricopeptide repeat domain 9C	protein-coding
mm_1790.1	chr1	78674204	78674208	+	1	NA	intron (NM_028817, intron 2 of 15)	intron (NM_028817, intron 2 of 15)	15766	NM_001136226	195434	Mm.276016	NM_001001981	ENSMUSG00000079470	Utp14b	4932411L21Rik|jsd	UTP14B small subunit processome component	protein-coding
mm_137719.1	chr17	29100423	29100443	+	1	NA	3' UTR (NM_007669, exon 3 of 3)	3' UTR (NM_007669, exon 3 of 3)	6664	NM_007669	12575	Mm.195663	NM_007669	ENSMUSG00000023067	Cdkn1a	CAP20|CDKI|CIP1|Cdkn1|P21|SDI1|Waf1|mda6|p21Cip1|p21WAF	cyclin-dependent kinase inhibitor 1A (P21)	protein-coding
mm_12852.1	chr2	83706048	83706071	+	1	NA	Intergenic	RMER6B|LTR|ERVK	-18338	NM_008402	16410	Mm.227	NM_008402	ENSMUSG00000027087	Itgav	1110004F14Rik|2610028E01Rik|CD51|D430040G12Rik	integrin alpha V	protein-coding
mm_23218.1	chr3	47094222	47094239	+	1	NA	Intergenic	Lx2B|LINE|L1	-193448	NR_105800	102465199		NR_105800	ENSMUSG00000098417	Mir6379	Gm27730|mmu-mir-6379	microRNA 6379	ncRNA
mm_75147.1	chr8	35826422	35826430	-	1	NA	5' UTR (NM_027998, exon 1 of 1)	5' UTR (NM_027998, exon 1 of 1)	133	NM_027998	71908	Mm.37817	NM_027998	ENSMUSG00000055976	Cldn23	2310014B08Rik	claudin 23	protein-coding
mm_132873.1	chr16	48612161	48612206	+	1	NA	intron (NM_010816, intron 20 of 26)	intron (NM_010816, intron 20 of 26)	159773	NM_198297	77647	Mm.167298	NM_198297	ENSMUSG00000030775	Trat1	C030046M14Rik|Tcrim|Trim	T cell receptor associated transmembrane adaptor 1	protein-coding
mm_46258.1	chr5	99609873	99609873	-	1	NA	intron (NR_030692, intron 1 of 3)	intron (NR_030692, intron 1 of 3)	119187	NR_030692	319818	Mm.295233	NR_030692	ENSMUSG00000089809	A930011G23Rik	-	RIKEN cDNA A930011G23 gene	ncRNA
mm_136713.1	chr17	7928515	7928550	+	1	NA	intron (NM_145968, intron 4 of 9)	intron (NM_145968, intron 4 of 9)	2532	NM_145968	72536	Mm.119680	NM_145968	ENSMUSG00000033450	Tagap	2610315E15Rik	T cell activation Rho GTPase activating protein	protein-coding
mm_84304.1	chr9	63602450	63602460	-	1	NA	promoter-TSS (NM_025857)	promoter-TSS (NM_025857)	38	NM_030068	78250	Mm.444612	NM_030068	ENSMUSG00000037801	Iqch	4921504K03Rik	IQ motif containing H	protein-coding
mm_84299.1	chr9	63384773	63384798	-	1	NA	Intergenic	Intergenic	-6933	NM_011840	23938	Mm.325746	NM_011840	ENSMUSG00000058444	Map2k5	AI324775|AI428457|MEK5|Mapkk5|Prkmk5	mitogen-activated protein kinase kinase 5	protein-coding
mm_41659.1	chr5	98854782	98854809	+	1	NA	5' UTR (NM_001310677, exon 1 of 3)	5' UTR (NM_001310677, exon 1 of 3)	380	NM_001310677	110075	Mm.136461	NM_173404	ENSMUSG00000029335	Bmp3	9530029I04Rik	bone morphogenetic protein 3	protein-coding
mm_79461.1	chr9	56418698	56418709	+	1	NA	promoter-TSS (NM_025812)	promoter-TSS (NM_025812)	-143	NM_025812	66867	Mm.150856	NM_025812	ENSMUSG00000032329	Hmg20a	1200004E06Rik|5730490E10Rik|Hmgxb1|Ibraf	high mobility group 20A	protein-coding
mm_105968.1	chr11	115491294	115491339	-	1	NA	promoter-TSS (NR_136931)	promoter-TSS (NR_136931)	-213	NR_136931	102634812	Mm.390379	NR_136931		LOC102634812	-	ribosomal protein L39 pseudogene	pseudo
mm_90225.1	chr10	121034274	121034292	+	1	NA	5' UTR (NM_011915, exon 1 of 10)	5' UTR (NM_011915, exon 1 of 10)	279	NM_011915	24117	Mm.32831	NM_011915	ENSMUSG00000020218	Wif1	AW107799|WIF-1	Wnt inhibitory factor 1	protein-coding
mm_46124.1	chr5	92470893	92470905	-	1	NA	intron (NM_007644, intron 2 of 11)	B4A|SINE|B4	12342	NR_105843	102466159		NR_105843	ENSMUSG00000099160	Mir6415	Gm27714|mmu-mir-6415	microRNA 6415	ncRNA
mm_95115.1	chr11	34077463	34077480	+	1	NA	intron (NM_010696, intron 10 of 20)	intron (NM_010696, intron 10 of 20)	30270	NM_010696	16822	Mm.265350	NM_010696	ENSMUSG00000002699	Lcp2	AI323664|BB161688|SLP-76|SLP76|m1Khoe|twm	lymphocyte cytosolic protein 2	protein-coding
mm_55563.1	chr6	71360804	71360814	-	1	NA	Intergenic	Intergenic	-12618	NM_009857	12525	Mm.1858	NM_009857	ENSMUSG00000053977	Cd8a	BB154331|Ly-2|Ly-35|Ly-B|Lyt-2	CD8 antigen, alpha chain	protein-coding
mm_168901.1	chr12	55080570	55080570	+	1	NA	promoter-TSS (NM_011899)	promoter-TSS (NM_011899)	74	NM_011899	24067	Mm.471968	NM_011899	ENSMUSG00000073079	Srp54a	54kDa|Srp54	signal recognition particle 54A	protein-coding
mm_92422.1	chr10	77055751	77055763	-	1	NA	exon (NM_001109991, exon 38 of 41)	exon (NM_001109991, exon 38 of 41)	22545	NM_031196	20509	Mm.265060	NM_031196	ENSMUSG00000001436	Slc19a1	AI323572|RFC|RFC-1|RFC1	solute carrier family 19 (folate transporter), member 1	protein-coding
mm_105238.1	chr11	102318942	102319004	-	1	NA	5' UTR (NM_001302954, exon 1 of 20)	5' UTR (NM_001302954, exon 1 of 20)	123	NM_001302955	21429	Mm.2845	NM_011551	ENSMUSG00000020923	Ubtf	A930005G04Rik|NOR-90|Tcfubf|UBF|UBF-1|UBF1	upstream binding transcription factor, RNA polymerase I	protein-coding
mm_119621.1	chr14	51129008	51129018	+	1	NA	promoter-TSS (NM_030098)	promoter-TSS (NM_030098)	-55	NM_030098	78416	Mm.103835	NM_030098	ENSMUSG00000021880	Rnase6	9530043P15Rik|BB119466	ribonuclease, RNase A family, 6	protein-coding
mm_32103.1	chr4	98726774	98726783	+	1	NA	promoter-TSS (NM_001081202)	promoter-TSS (NM_001081202)	24	NM_001081202	381591	Mm.34340	NM_001081202	ENSMUSG00000087166	L1td1	AA546746|AB211064|D76865|ECAT11	LINE-1 type transposase domain containing 1	protein-coding
mm_127369.1	chr15	100761742	100761797	+	1	NA	promoter-TSS (NM_021530)	promoter-TSS (NM_021530)	22	NM_021530	59033	Mm.209856	NM_021530	ENSMUSG00000023032	Slc4a8	AW493845|C230026C11|NDCBE|kNBC-3	solute carrier family 4 (anion exchanger), member 8	protein-coding
mm_125784.1	chr15	74716603	74716608	+	1	NA	3' UTR (NM_028216, exon 3 of 3)	3' UTR (NM_028216, exon 3 of 3)	1766	NM_028216	72373	Mm.46395	NM_028216	ENSMUSG00000022598	Psca	2210408B04Rik	prostate stem cell antigen	protein-coding
mm_72340.1	chr8	79356121	79356151	+	1	NA	intron (NM_008539, intron 3 of 6)	intron (NM_008539, intron 3 of 6)	43332	NM_008539	17125	Mm.223717	NM_008539	ENSMUSG00000031681	Smad1	AI528653|Madh1|Madr1|Mlp1|MusMLP	SMAD family member 1	protein-coding
mm_63640.1	chr7	128541909	128541911	+	1	NA	exon (NM_013863, exon 3 of 4)	exon (NM_013863, exon 3 of 4)	18327	NM_013863	29810	Mm.84073	NM_013863	ENSMUSG00000030847	Bag3	AA407278|Bis|mg638	BCL2-associated athanogene 3	protein-coding
mm_116835.1	chr13	54687645	54687688	-	1	NA	5' UTR (NM_001146025, exon 1 of 11)	5' UTR (NM_001146025, exon 1 of 11)	142	NM_001146025	105239	Mm.25366	NM_134064	ENSMUSG00000034928	Rnf44	AI854545|mKIAA1100	ring finger protein 44	protein-coding
mm_123427.1	chr14	64440488	64440509	-	1	NA	intron (NM_001253712, intron 1 of 5)	intron (NM_001253712, intron 1 of 5)	528	NM_001253715	110265	Mm.26713	NM_026322	ENSMUSG00000054733	Msra	2310045J23Rik|6530413P12Rik|MSR-A	methionine sulfoxide reductase A	protein-coding
mm_68109.1	chr7	102019552	102019558	-	1	NA	TTS (NM_029211)	TTS (NM_029211)	-1400	NM_010531	16068	Mm.422756	NM_010531	ENSMUSG00000070427	Il18bp	IL-18BP|Igifbp|MC54L	interleukin 18 binding protein	protein-coding
mm_40484.1	chr5	55624581	55624607	+	1	NA	Intergenic	Intergenic	1274602	NR_038045	330086	Mm.254449	NM_177871	ENSMUSG00000105912	Gm10440	D130065D13|ENSMUSG00000072936	predicted gene 10440	ncRNA
mm_51129.1	chr6	68425568	68425584	+	1	NA	Intergenic	Intergenic	-859877	NR_003100	75070	Mm.463364	NR_003100		4930515G16Rik	-	myc induced nuclear antigen pseudogene	pseudo
mm_165563.1	chr3	14886627	14886648	+	1	NA	5' UTR (NM_009801, exon 1 of 7)	5' UTR (NM_009801, exon 1 of 7)	211	NM_009801	12349	Mm.1186	NM_009801	ENSMUSG00000027562	Car2	AI131712|CAII|Ca2|Car-2|Ltw-5|Lvtw-5	carbonic anhydrase 2	protein-coding
mm_80291.1	chr9	73093963	73093970	+	1	NA	intron (NM_001301230, intron 6 of 6)	intron (NM_001301230, intron 6 of 6)	-8432	NM_025890	66991	Mm.471745	NM_025890	ENSMUSG00000092622	Khdc3	2410004A20Rik|AI467128|FILIA|OEEP48	KH domain containing 3, subcortical maternal complex member	protein-coding
mm_82966.1	chr9	35687015	35687033	-	1	NA	exon (NM_001199953, exon 2 of 5)	exon (NM_001199953, exon 2 of 5)	347	NM_001199953	100312987	Mm.445254	NM_001167677	ENSMUSG00000091215	Pate1	Gm17252|Pate	prostate and testis expressed 1	protein-coding
mm_105777.1	chr11	109722082	109722095	-	1	NA	5' UTR (NM_153782, exon 1 of 11)	5' UTR (NM_153782, exon 1 of 11)	168	NM_153782	208659	Mm.208662	NM_153782	ENSMUSG00000020614	Fam20a	AI606893	family with sequence similarity 20, member A	protein-coding
mm_55397.1	chr6	60774236	60774237	-	1	NA	intron (NM_009221, intron 4 of 5)	L1_Mus3|LINE|L1	54768	NM_001042451	20617	Mm.17484	NM_009221	ENSMUSG00000025889	Snca	NACP|alphaSYN	synuclein, alpha	protein-coding
mm_169817.1	chr16	20651660	20651660	+	1	NA	promoter-TSS (NR_027485)	promoter-TSS (NR_027485)	8	NM_134101	21762	Mm.243234	NM_134101	ENSMUSG00000006998	Psmd2	9430095H01Rik|AA407121|TEG-190|Tex190	proteasome (prosome, macropain) 26S subunit, non-ATPase, 2	protein-coding
mm_128728.1	chr15	64095340	64095341	-	1	NA	intron (NM_010026, intron 28 of 30)	intron (NM_010026, intron 28 of 30)	-34892	NM_144846	223601	Mm.246108	NM_144846	ENSMUSG00000022378	Fam49b	0910001A06Rik|AW122079	family with sequence similarity 49, member B	protein-coding
mm_61590.1	chr7	80025274	80025284	+	1	NA	promoter-TSS (NM_175433)	promoter-TSS (NM_175433)	465	NM_001146000	209225	Mm.290925	NM_175433	ENSMUSG00000048897	Zfp710	5430400N05Rik|9830165K13|AI324798|Znf710	zinc finger protein 710	protein-coding
mm_105962.1	chr11	115463395	115463481	-	1	NA	intron (NM_001080934, intron 1 of 3)	intron (NM_001080934, intron 1 of 3)	965	NM_001080934	217316	Mm.25773	NM_001080934	ENSMUSG00000045775	Slc16a5	A130015N09Rik|MCT 5|MCT 6|MCT5	solute carrier family 16 (monocarboxylic acid transporters), member 5	protein-coding
mm_155614.1	chrX	83069407	83069409	+	1	NA	intron (NM_007868, intron 1 of 78)	B4A|SINE|B4	120538	NM_007868	13405	Mm.275608	NM_007868	ENSMUSG00000045103	Dmd	DXSmh7|DXSmh9|Dp427|Dp71|dys|mdx|pke	dystrophin, muscular dystrophy	protein-coding
mm_142289.1	chr17	40298219	40298227	-	1	NA	exon (NM_009638, exon 7 of 8)	exon (NM_009638, exon 7 of 8)	20984	NM_009638	11571	Mm.16781	NM_009638	ENSMUSG00000025431	Crisp1	AW324342|Aeg1|CRISP-1	cysteine-rich secretory protein 1	protein-coding
mm_118863.1	chr14	25842239	25842249	+	1	NA	promoter-TSS (NM_013469)	promoter-TSS (NM_013469)	89	NM_013469	11744	Mm.294083	NM_013469	ENSMUSG00000021866	Anxa11	A830099O17Rik|Anx11	annexin A11	protein-coding
mm_83522.1	chr9	46230037	46230046	-	1	NA	exon (NM_009692, exon 4 of 4)	exon (NM_009692, exon 4 of 4)	1411	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2|apo-AI|apoA-I	apolipoprotein A-I	protein-coding
mm_52543.1	chr6	115933983	115933990	+	1	NA	exon (NM_145383, exon 2 of 5)	exon (NM_145383, exon 2 of 5)	2059	NM_145383	212541	Mm.2965	NM_145383	ENSMUSG00000030324	Rho	Noerg1|Opn2|Ops|RP4	rhodopsin	protein-coding
mm_46008.1	chr5	90786433	90786467	-	1	NA	exon (NM_203320, exon 2 of 4)	exon (NM_203320, exon 2 of 4)	349	NM_203320	330122	Mm.244289	NM_203320	ENSMUSG00000029379	Cxcl3	Dcip1|Gm1960	chemokine (C-X-C motif) ligand 3	protein-coding
mm_80386.1	chr9	75468590	75468597	+	1	NA	Intergenic	Intergenic	27069	NM_001039522	235497	Mm.41508	NM_001006122	ENSMUSG00000042487	Leo1	Gm185	Leo1, Paf1/RNA polymerase II complex component	protein-coding
mm_44543.1	chr5	24555402	24555421	-	1	NA	promoter-TSS (NM_177676)	promoter-TSS (NM_177676)	58	NR_033188	231045	Mm.255800	NM_177676	ENSMUSG00000038199	4931409K22Rik	Iqca1l|Iqca1p1	RIKEN cDNA 4931409K22 gene	protein-coding
mm_107260.1	chr12	28802222	28802225	+	1	NA	intron (NM_201357, intron 3 of 8)	intron (NM_201357, intron 3 of 8)	50395	NM_201357	380752	Mm.273724	NM_201357	ENSMUSG00000036613	Tssc1	D12Ertd604e|Eipr1	tumor suppressing subtransferable candidate 1	protein-coding
mm_142786.1	chr17	50158814	50158825	-	1	NA	intron (NM_181397, intron 2 of 9)	intron (NM_181397, intron 2 of 9)	31678	NM_181397	76438	Mm.41854	NM_181397	ENSMUSG00000039316	Rftn1	2310015N21Rik|AI853526	raftlin lipid raft linker 1	protein-coding
mm_33979.1	chr4	137687391	137687428	+	1	NA	intron (NM_001256218, intron 2 of 24)	L2b|LINE|L2	5782	NM_001256218	110351	Mm.180763	NM_029563	ENSMUSG00000041351	Rap1gap	1300019I11Rik|2310004O14Rik|AI427470|ARPP-90|Gap|Rap1GAP1|Rap1ga1	Rap1 GTPase-activating protein	protein-coding
mm_128850.1	chr15	71728283	71728293	-	1	NA	promoter-TSS (NM_177819)	promoter-TSS (NM_177819)	-450	NM_177819	70363	Mm.126450	NM_177819	ENSMUSG00000036800	Fam135b	1700010C24Rik|A830008O07Rik	family with sequence similarity 135, member B	protein-coding
mm_18006.1	chr2	38230038	38230046	-	1	NA	intron (NM_146122, intron 2 of 21)	intron (NM_146122, intron 2 of 21)	57342	NM_146122	227801	Mm.314245	NM_146122	ENSMUSG00000035392	Dennd1a	6030446I19Rik|connecdenn	DENN/MADD domain containing 1A	protein-coding
mm_162436.1	chr1	105990722	105990750	+	1	NA	5' UTR (NM_001122675, exon 1 of 13)	5' UTR (NM_001122675, exon 1 of 13)	330	NM_001122675	227449	Mm.210188	NM_001122675	ENSMUSG00000038866	Zcchc2	9930114B20Rik|AW212015	zinc finger, CCHC domain containing 2	protein-coding
mm_59320.1	chr7	25301417	25301421	+	1	NA	promoter-TSS (NM_001081294)	promoter-TSS (NM_001081294)	60	NM_001081294	623131	Mm.172160	NM_001081294	ENSMUSG00000058741	Prr19	EG623131	proline rich 19	protein-coding
mm_69904.1	chr7	141639824	141639832	-	1	NA	intron (NM_001330001, intron 31 of 33)	intron (NM_001330001, intron 31 of 33)	15491	NM_001330001	353328	Mm.246621	NM_181729	ENSMUSG00000048191	Muc6	-	mucin 6, gastric	protein-coding
mm_19000.1	chr2	76870400	76870418	-	1	NA	exon (NM_011652, exon 103 of 313)	exon (NM_011652, exon 103 of 313)	112138	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_25540.1	chr3	115801085	115801099	+	1	NA	Intergenic	Intergenic	-86037	NM_007901	13609	Mm.982	NM_007901	ENSMUSG00000045092	S1pr1	AI849002|Edg1|Lpb1|S1p|S1p1	sphingosine-1-phosphate receptor 1	protein-coding
mm_57317.1	chr6	124729940	124729954	-	1	NA	intron (NM_001077705, intron 3 of 15)	intron (NM_001077705, intron 3 of 15)	3207	NM_013545	15170	Mm.271799	NM_013545	ENSMUSG00000004266	Ptpn6	70Z-SHP|Hcph|PTPTY-42|Ptp1C|SH-PTP1|SHP-1|hcp|me	protein tyrosine phosphatase, non-receptor type 6	protein-coding
mm_153856.1	chr19	46395723	46395756	-	1	NA	promoter-TSS (NM_016860)	promoter-TSS (NM_016860)	-4	NM_016860	54130	Mm.3118	NM_016860	ENSMUSG00000025228	Actr1a	Arp1|alpha-Arp1	ARP1 actin-related protein 1A, centractin alpha	protein-coding
mm_140335.1	chr17	86778502	86778505	+	1	NA	intron (NM_010137, intron 1 of 15)	intron (NM_010137, intron 1 of 15)	24639	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_40055.1	chr5	33996120	33996137	+	1	NA	5' UTR (NM_001001985, exon 1 of 3)	5' UTR (NM_001001985, exon 1 of 3)	144	NM_001001985	269642	Mm.274610	NM_001001985	ENSMUSG00000048142	Nat8l	1110038O08Rik|Shati	N-acetyltransferase 8-like	protein-coding
mm_51998.1	chr6	92816434	92816455	+	1	NA	intron (NM_175314, intron 20 of 29)	intron (NM_175314, intron 20 of 29)	84997	NM_175314	101401	Mm.158235	NM_175314	ENSMUSG00000030022	Adamts9	1810011L16Rik|8430403M15Rik|AW743315|E030027K14Rik	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 9	protein-coding
mm_113486.1	chr13	37376619	37376641	+	1	NA	intron (NM_010745, intron 2 of 4)	intron (NM_010745, intron 2 of 4)	31285	NM_010745	17084	Mm.2639	NM_010745	ENSMUSG00000021423	Ly86	MD-1|MD1|ly86_tv2	lymphocyte antigen 86	protein-coding
mm_50532.1	chr6	49045616	49045626	+	1	NA	intron (NM_053110, intron 4 of 10)	intron (NM_053110, intron 4 of 10)	9103	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_153254.1	chr19	36689320	36689368	-	1	NA	non-coding (NR_033510, exon 1 of 5)	non-coding (NR_033510, exon 1 of 5)	135	NR_033510	668215	Mm.394223	NR_033510	ENSMUSG00000087579	1500017E21Rik	-	RIKEN cDNA 1500017E21 gene	ncRNA
mm_145502.1	chr18	60391468	60391479	+	1	NA	3' UTR (NM_001146275, exon 3 of 3)	3' UTR (NM_001146275, exon 3 of 3)	15444	NM_001146275	60440	Mm.261140	NM_021792	ENSMUSG00000054072	Iigp1	2900074L10Rik|AI046432|AW111922|Ifgga1|Iigp|Irga6	interferon inducible GTPase 1	protein-coding
mm_156251.1	chrX	136590842	136590866	+	1	NA	Intergenic	Intergenic	72855	NM_001310690	245616	Mm.246625	NM_177749	ENSMUSG00000031424	Kir3dl1	Kirl1|Kirl2|Krl1	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1	protein-coding
mm_138610.1	chr17	35704905	35704910	+	1	NA	promoter-TSS (NM_172962)	promoter-TSS (NM_172962)	-768	NM_172962	12305	Mm.5021	NM_007584	ENSMUSG00000003534	Ddr1	6030432F18|AI323681|CD167a|Cak|Nep|PTK3A	discoidin domain receptor family, member 1	protein-coding
mm_25079.1	chr3	100162455	100162536	+	1	NA	promoter-TSS (NM_175552)	promoter-TSS (NM_175552)	32	NR_104341	14547	Mm.279228	NM_010269	ENSMUSG00000027865	Gdap2	C77050|D3Ertd801e	ganglioside-induced differentiation-associated-protein 2	protein-coding
mm_172503.1	chr7	67759506	67759514	-	1	NA	exon (NM_207663, exon 1 of 5)	exon (NM_207663, exon 1 of 5)	232	NM_183312	233335	Mm.60526	NM_183312	ENSMUSG00000030554	Synm	4930412K21Rik|AI852401|Dmn|E130104F11|Syn|Synemin	synemin, intermediate filament protein	protein-coding
mm_10871.1	chr2	25218753	25218799	+	1	NA	promoter-TSS (NM_026624)	promoter-TSS (NM_026624)	31	NM_026624	68222	Mm.227260	NM_026624	ENSMUSG00000026969	Fam166a	4931415M17	family with sequence similarity 166, member A	protein-coding
mm_97750.1	chr11	80477398	80477416	+	1	NA	5' UTR (NM_009871, exon 1 of 1)	5' UTR (NM_009871, exon 1 of 1)	361	NM_009871	12569	Mm.142275	NM_009871	ENSMUSG00000048895	Cdk5r1	Cdk5r|D11Bwg0379e|p25|p35	cyclin-dependent kinase 5, regulatory subunit 1 (p35)	protein-coding
mm_131574.1	chr16	18348342	18348352	+	1	NA	5' UTR (NM_001272029, exon 1 of 18)	5' UTR (NM_001272029, exon 1 of 18)	165	NM_001272029	11877	Mm.293599	NM_033474	ENSMUSG00000000325	Arvcf	-	armadillo repeat gene deleted in velo-cardio-facial syndrome	protein-coding
mm_167494.1	chr9	13179366	13179386	+	1	NA	Intergenic	Intergenic	66365	NM_001033181	77532	Mm.459434	NM_001033181	ENSMUSG00000079083	Jrkl	C030035D04Rik|HHMJG	Jrk-like	protein-coding
mm_52411.1	chr6	113389247	113389259	+	1	NA	promoter-TSS (NM_001142732)	promoter-TSS (NM_001142732)	-7	NM_001142732	101100	Mm.388573	NM_133923	ENSMUSG00000030276	Ttll3	4833441J24Rik|AI450050	tubulin tyrosine ligase-like family, member 3	protein-coding
mm_104024.1	chr11	85929840	85929850	-	1	NA	Intergenic	Intergenic	33080	NM_172798	21387	Mm.275336	NM_011536	ENSMUSG00000000094	Tbx4	3930401C23	T-box 4	protein-coding
mm_29262.1	chr3	107326575	107326578	-	1	NA	intron (NM_001045807, intron 1 of 1)	intron (NM_001045807, intron 1 of 1)	6713	NM_001045807	229700	Mm.27966	NM_001045807	ENSMUSG00000048109	Rbm15	C230088J01Rik|mKIAA1438	RNA binding motif protein 15	protein-coding
mm_8137.1	chr1	136255751	136255771	-	1	NA	Intergenic	MIRc|SINE|MIR	5112	NM_001101516	383563	Mm.40367	NM_001101516	ENSMUSG00000052759	Gpr25	Gm1300	G protein-coupled receptor 25	protein-coding
mm_16397.1	chr2	179560864	179560894	+	1	NA	intron (NM_001316723, intron 2 of 5)	intron (NM_001316723, intron 2 of 5)	118448	NM_009867	12561	Mm.184711	NM_009867	ENSMUSG00000000305	Cdh4	AW120700|R-CAD|R-Cadh|Rcad	cadherin 4	protein-coding
mm_153763.1	chr19	45591821	45591878	-	1	NA	intron (NM_013907, intron 5 of 8)	intron (NM_013907, intron 5 of 8)	31234	NM_172639	226162	Mm.21978	NM_172639	ENSMUSG00000041035	Dpcd	5330431N19Rik|Ndac	deleted in primary ciliary dyskinesia	protein-coding
mm_162784.1	chr10	70592772	70592776	-	1	NA	promoter-TSS (NM_001162846)	promoter-TSS (NM_001162846)	38	NM_001162846	70911	Mm.19825	NM_178621	ENSMUSG00000037747	Phyhipl	4921522K17Rik|AI267048	phytanoyl-CoA hydroxylase interacting protein-like	protein-coding
mm_87444.1	chr10	51481682	51481691	+	1	NA	exon (NM_008147, exon 4 of 9)	exon (NM_008147, exon 4 of 9)	1074	NM_001291892	14727	Mm.439661	NM_008147	ENSMUSG00000062593	Lilr4b	Gp49a|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4B	protein-coding
mm_66164.1	chr7	31256288	31256294	-	1	NA	Intergenic	Intergenic	-7445	NM_001310660	100043827		NM_001310660		Scgb2b1	Abpbg1|Gm4677	secretoglobin, family 2B, member 1	protein-coding
mm_161332.1	chr14	50642096	50642096	+	1	NA	promoter-TSS (NM_146299)	promoter-TSS (NM_146299)	-99	NM_146299	258296	Mm.377418	NM_146299	ENSMUSG00000050028	Olfr745	MOR106-11	olfactory receptor 745	protein-coding
mm_99259.1	chr11	101188275	101188303	+	1	NA	exon (NM_016782, exon 21 of 24)	exon (NM_016782, exon 21 of 24)	12172	NM_016782	53321	Mm.474527	NM_016782	ENSMUSG00000017167	Cntnap1	AI841080|Caspr|NCP1|Nrxn4|p190|shm	contactin associated protein-like 1	protein-coding
mm_165656.1	chr3	85887813	85887825	+	1	NA	promoter-TSS (NM_177130)	promoter-TSS (NM_177130)	-301	NM_177130	320302	Mm.482978	NM_177130	ENSMUSG00000031286	Glt28d2	4732486J07Rik|Glt28d1l	glycosyltransferase 28 domain containing 2	protein-coding
mm_158166.1	chrX	103493397	103493421	-	1	NA	promoter-TSS (NR_015508)	promoter-TSS (NR_015508)	-149	NR_015508	70252	Mm.380486	NR_015508	ENSMUSG00000097571	Jpx	2010000I03Rik|2510040I06Rik|Enox	Jpx transcript, Xist activator (non-protein coding)	ncRNA
mm_82632.1	chr9	21962342	21962367	-	1	NA	intron (NM_010149, intron 1 of 7)	intron (NM_010149, intron 1 of 7)	1222	NM_010149	13857	Mm.2653	NM_010149	ENSMUSG00000006235	Epor	-	erythropoietin receptor	protein-coding
mm_39504.1	chr5	21194584	21194587	+	1	NA	intron (NM_175437, intron 2 of 30)	B1_Mur1|SINE|Alu	8318	NM_175437	212167	Mm.121705	NM_175437	ENSMUSG00000039934	Gsap	A530088I07Rik|Pion	gamma-secretase activating protein	protein-coding
mm_119843.1	chr14	54436860	54436887	+	1	NA	exon (NM_008608, exon 4 of 10)	exon (NM_008608, exon 4 of 10)	5275	NM_008608	17387	Mm.280175	NM_008608	ENSMUSG00000000957	Mmp14	AI325305|MMP-X1|MT-MMP-1|MT1-MMP|sabe	matrix metallopeptidase 14 (membrane-inserted)	protein-coding
mm_116498.1	chr13	44979214	44979219	-	1	NA	intron (NM_025772, intron 5 of 9)	intron (NM_025772, intron 5 of 9)	22880	NM_025772	94245	Mm.352311	NM_025772	ENSMUSG00000057531	Dtnbp1	5430437B18Rik|AW048963|Bloc1s8|dysbindin|sdy	dystrobrevin binding protein 1	protein-coding
mm_134454.1	chr16	18411758	18411764	-	1	NA	exon (NM_001111062, exon 3 of 6)	exon (NM_001111062, exon 3 of 6)	1733	NM_001111063	12846	Mm.100940	NM_007744	ENSMUSG00000000326	Comt	Comt1|D16Wsu103e|D330014B15Rik	catechol-O-methyltransferase	protein-coding
mm_101650.1	chr11	36599275	36599301	-	1	NA	intron (NM_011856, intron 2 of 28)	intron (NM_011856, intron 2 of 28)	344953	NM_001290702	23964	Mm.439889	NM_011856	ENSMUSG00000049336	Tenm2	Odz2|Odz3|Ten-2|Ten-m2	teneurin transmembrane protein 2	protein-coding
mm_148911.1	chr19	6974952	6975003	+	1	NA	promoter-TSS (NM_008889)	promoter-TSS (NM_008889)	-71	NM_008889	18938	Mm.140	NM_008889	ENSMUSG00000056612	Ppp1r14b	AOM172|PHI-1|PLCB3N|Png	protein phosphatase 1, regulatory (inhibitor) subunit 14B	protein-coding
mm_29319.1	chr3	108017443	108017458	-	1	NA	intron (NM_010358, intron 1 of 7)	intron (NM_010358, intron 1 of 7)	523	NM_010358	14862	Mm.37199	NM_010358	ENSMUSG00000058135	Gstm1	Gstb-1|Gstb1	glutathione S-transferase, mu 1	protein-coding
mm_134223.1	chr16	11254310	11254336	-	1	NA	promoter-TSS (NM_001130008)	promoter-TSS (NM_001130008)	2	NM_001130008	14852	Mm.325827	NM_146066	ENSMUSG00000062203	Gspt1	AI314175|AI326449|AV307676|C79774|G1st|Gst-1	G1 to S phase transition 1	protein-coding
mm_67135.1	chr7	72306601	72306647	-	1	NA	promoter-TSS (NM_001024703)	promoter-TSS (NM_001024703)	-29	NM_001024703	244049	Mm.217412	NM_001024703	ENSMUSG00000032776	Mctp2	Gm489	multiple C2 domains, transmembrane 2	protein-coding
mm_101665.1	chr11	36770188	36770196	-	1	NA	intron (NM_011856, intron 2 of 28)	intron (NM_011856, intron 2 of 28)	174049	NM_001290702	23964	Mm.439889	NM_011856	ENSMUSG00000049336	Tenm2	Odz2|Odz3|Ten-2|Ten-m2	teneurin transmembrane protein 2	protein-coding
mm_16974.1	chr2	17731761	17731765	-	1	NA	promoter-TSS (NM_028757)	promoter-TSS (NM_028757)	-695	NM_028757	74103	Mm.120298	NM_028757	ENSMUSG00000053702	Nebl	1200007O21Rik|A630080F05Rik|BB140644|D830029A09Rik|Lnebl	nebulette	protein-coding
mm_88047.1	chr10	67539799	67539809	+	1	NA	exon (NM_010118, exon 2 of 2)	exon (NM_010118, exon 2 of 2)	1874	NM_001347458	13654	Mm.290421	NM_010118	ENSMUSG00000037868	Egr2	Egr-2|Krox-20|Krox20|NGF1-B|Zfp-25|Zfp-6	early growth response 2	protein-coding
mm_115432.1	chr13	117250587	117250606	+	1	NA	intron (NM_010330, intron 4 of 8)	B1_Mus1|SINE|Alu	30023	NM_010330	13723	Mm.274926	NM_010330	ENSMUSG00000021728	Emb	AL022799|Gp70	embigin	protein-coding
mm_108615.1	chr12	85524670	85524683	+	1	NA	Intergenic	Intergenic	50775	NM_010234	14281	Mm.246513	NM_010234	ENSMUSG00000021250	Fos	D12Rfj1|c-fos|cFos	FBJ osteosarcoma oncogene	protein-coding
mm_110525.1	chr12	54923103	54923143	-	1	NA	exon (NM_013815, exon 14 of 27)	exon (NM_013815, exon 14 of 27)	-60246	NM_007688	12632	Mm.276826	NM_007688	ENSMUSG00000062929	Cfl2	-	cofilin 2, muscle	protein-coding
mm_76998.1	chr8	107269704	107269728	-	1	NA	intron (NR_039557, intron 2 of 3).3	intron (NR_039557, intron 2 of 3).3	13552	NR_039557	100628577		NR_039557	ENSMUSG00000093061	Mir5098	mmu-mir-5098|mu-mir-5098	microRNA 5098	ncRNA
mm_99946.1	chr11	111073933	111073936	+	1	NA	3' UTR (NM_008425, exon 2 of 2)	3' UTR (NM_008425, exon 2 of 2)	7770	NM_008425	16518	Mm.4951	NM_008425	ENSMUSG00000041695	Kcnj2	IRK1|Kcnf1|Kir2.1	potassium inwardly-rectifying channel, subfamily J, member 2	protein-coding
mm_131507.1	chr16	17489601	17489627	+	1	NA	promoter-TSS (NM_175178)	promoter-TSS (NM_175178)	-63	NM_175178	72168	Mm.40038	NM_175178	ENSMUSG00000022763	Aifm3	2810401C16Rik|AI840249|Aifl	apoptosis-inducing factor, mitochondrion-associated 3	protein-coding
mm_126272.1	chr15	79141325	79141358	+	1	NA	promoter-TSS (NM_001310576)	promoter-TSS (NM_001310576)	16	NM_027231	69833	Mm.279861	NM_027231	ENSMUSG00000033020	Polr2f	1810060D16Rik|RPB6	polymerase (RNA) II (DNA directed) polypeptide F	protein-coding
mm_111946.1	chr12	109068174	109068247	-	1	NA	promoter-TSS (NM_001163175)	promoter-TSS (NM_001163175)	7	NM_001163175	380785	Mm.342085	NM_001163175	ENSMUSG00000040867	Begain	BM948371|Gm897	brain-enriched guanylate kinase-associated	protein-coding
mm_34583.1	chr4	150147510	150147520	+	1	NA	Intergenic	RLTR20A2B_MM|LTR|ERVK	-1457	NM_001085529	435818	Mm.359648	NM_001085529	ENSMUSG00000062064	Slc2a7	OTTMUSG00000010396	solute carrier family 2 (facilitated glucose transporter), member 7	protein-coding
mm_116847.1	chr13	54749909	54749920	-	1	NA	promoter-TSS (NM_001316710)	promoter-TSS (NM_001316710)	-40	NM_012014	26913	Mm.41812	NM_012014	ENSMUSG00000069227	Gprin1	GRIN1|Z16	G protein-regulated inducer of neurite outgrowth 1	protein-coding
mm_96335.1	chr11	65807211	65807227	+	1	NA	promoter-TSS (NM_026107)	promoter-TSS (NM_026107)	44	NM_001302375	52712	Mm.340052	NM_026107	ENSMUSG00000018347	Zkscan6	1700128E15Rik|D11Ertd714e|KOX11|Zfp535|Znf18	zinc finger with KRAB and SCAN domains 6	protein-coding
mm_113353.1	chr13	31820064	31820068	+	1	NA	intron (NM_146041, intron 10 of 10)	intron (NM_146041, intron 10 of 10)	13420	NM_008592	17300	Mm.12949	NM_008592	ENSMUSG00000050295	Foxc1	FREAC3|Fkh1|Mf1|Mf4|ch|fkh-1|frkhda	forkhead box C1	protein-coding
mm_18095.1	chr2	44986587	44986607	-	1	NA	3' UTR (NM_015753, exon 10 of 10)	3' UTR (NM_015753, exon 10 of 10)	36580	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_37257.1	chr4	118436980	118437021	-	1	NA	exon (NM_023223, exon 1 of 10)	exon (NM_023223, exon 1 of 10)	343	NM_023223	107995	Mm.261764	NM_023223	ENSMUSG00000006398	Cdc20	2310042N09Rik|C87100|p55CDC	cell division cycle 20	protein-coding
mm_24433.1	chr3	90541218	90541241	+	1	NA	promoter-TSS (NM_026416)	promoter-TSS (NM_026416)	6	NM_026416	67860	Mm.331185	NM_026416	ENSMUSG00000074457	S100a16	2300002L21Rik|AI325039|AI663996|DT1P1A7|S100F	S100 calcium binding protein A16	protein-coding
mm_152960.1	chr19	29360840	29360867	-	1	NA	5' UTR (NM_026362, exon 2 of 6)	5' UTR (NM_026362, exon 2 of 6)	1018	NM_026362	67759	Mm.275511	NM_026362	ENSMUSG00000016495	Plgrkt	1110007H22Rik|5033414D02Rik|AI852040|Plg-R(KT)|Plg-RKT	plasminogen receptor, C-terminal lysine transmembrane protein	protein-coding
mm_1160.1	chr1	60908994	60909033	+	1	NA	promoter-TSS (NM_009843)	promoter-TSS (NM_009843)	-12	NM_009843	12477	Mm.390	NM_009843	ENSMUSG00000026011	Ctla4	Cd152|Ctla-4|Ly-56	cytotoxic T-lymphocyte-associated protein 4	protein-coding
mm_147037.1	chr18	34860422	34860426	-	1	NA	promoter-TSS (NM_007913)	promoter-TSS (NM_007913)	-783	NM_007913	13653	Mm.181959	NM_007913	ENSMUSG00000038418	Egr1	A530045N19Rik|ETR103|Egr-1|Krox-1|Krox-24|Krox24|NGF1-A|NGFI-A|NGFIA|TIS8|Zenk|Zfp-6|Zif268|egr	early growth response 1	protein-coding
mm_107211.1	chr12	26444572	26444578	+	1	NA	3' UTR (NM_021384, exon 6 of 6)	3' UTR (NM_021384, exon 6 of 6)	11877	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_43471.1	chr5	136694122	136694134	+	1	NA	promoter-TSS (NM_001085387)	promoter-TSS (NM_001085387)	-49	NM_001085387	59310	Mm.5178	NM_021611	ENSMUSG00000005474	Myl10	1700027I08Rik|Mylc2pl|PLRLC	myosin, light chain 10, regulatory	protein-coding
mm_135705.1	chr16	52815759	52815767	-	1	NA	promoter-TSS (NR_040495)	promoter-TSS (NR_040495)	-19	NR_040495	73820	Mm.60493	NR_040495		4930404A05Rik	-	RIKEN cDNA 4930404A05 gene	ncRNA
mm_6741.1	chr1	83277107	83277145	-	1	NA	exon (NM_172430, exon 7 of 11)	exon (NM_172430, exon 7 of 11)	117364	NM_027725	71227	Mm.256482	NM_027725	ENSMUSG00000053161	Daw1	4930563E19Rik|4933429D11Rik|Wdr69|b2b1116Clo|b2b1584Clo	dynein assembly factor with WDR repeat domains 1	protein-coding
mm_69860.1	chr7	141435328	141435375	-	1	NA	promoter-TSS (NM_001177576)	promoter-TSS (NM_001177576)	-757	NM_001177576	68267	Mm.33729	NM_026646	ENSMUSG00000019082	Slc25a22	1300006L01Rik|AI060884|Gc1	solute carrier family 25 (mitochondrial carrier, glutamate), member 22	protein-coding
mm_23664.1	chr3	68494233	68494268	+	1	NA	promoter-TSS (NM_001282044)	promoter-TSS (NM_001282044)	69	NM_001282044	30953	Mm.331064	NM_013928	ENSMUSG00000027777	Schip1	Nf2ip|Schip-1	schwannomin interacting protein 1	protein-coding
mm_108177.1	chr12	76406500	76406509	+	1	NA	3' UTR (NM_001002012, exon 2 of 2)	3' UTR (NM_001002012, exon 2 of 2)	2134	NM_008301	15512	Mm.296181	NM_008301	ENSMUSG00000059970	Hspa2	70kDa|HSP70.2|HSP70A2|Hsp70-2	heat shock protein 2	protein-coding
mm_159310.1	chr2	181203011	181203011	-	1	NA	promoter-TSS (NM_009184)	promoter-TSS (NM_009184)	-222	NM_009184	20459	Mm.4497	NM_009184	ENSMUSG00000038751	Ptk6	BRK|Sik|Tksk|tks	PTK6 protein tyrosine kinase 6	protein-coding
mm_42761.1	chr5	121204517	121204556	+	1	NA	promoter-TSS (NM_011290)	promoter-TSS (NM_011290)	35	NM_011290	19988	Mm.262021	NM_011290	ENSMUSG00000029614	Rpl6	Taxreb107	ribosomal protein L6	protein-coding
mm_145081.1	chr18	42394368	42394370	+	1	NA	promoter-TSS (NM_138945)	promoter-TSS (NM_138945)	-228	NM_138945	18998	Mm.488204	NM_138945	ENSMUSG00000024497	Pou4f3	Brn3.1|Brn3c|ddl|dreidel	POU domain, class 4, transcription factor 3	protein-coding
mm_130048.1	chr15	89147029	89147064	-	1	NA	intron (NM_011161, intron 1 of 11)	intron (NM_011161, intron 1 of 11)	2560	NM_011161	19094	Mm.91969	NM_011161	ENSMUSG00000053137	Mapk11	P38b|Prkm11|Sapk2|Sapk2b|p38-2|p38beta|p38beta2	mitogen-activated protein kinase 11	protein-coding
mm_107677.1	chr12	54343718	54343731	+	1	NA	Intergenic	L1MA5|LINE|L1	47594	NR_033689	665239	Mm.26856	NR_033689		Gm7550	EG665239|Gm666	predicted gene 7550	ncRNA
mm_134326.1	chr16	16358529	16358573	-	1	NA	promoter-TSS (NM_001276341)	promoter-TSS (NM_001276341)	24	NM_001276341	74006	Mm.218820	NM_152816	ENSMUSG00000022789	Dnm1l	6330417M19Rik|AI450666|Dlp1|Dnmlp1|Drp1|python	dynamin 1-like	protein-coding
mm_157326.1	chrX	23296068	23296109	-	1	NA	intron (NM_026167, intron 3 of 8)	intron (NM_026167, intron 3 of 8)	-10529	NM_001290476	67455	Mm.224306	NM_026167	ENSMUSG00000036782	Klhl13	1200009K10Rik|AI451128|Bklhd2|D130072F20Rik	kelch-like 13	protein-coding
mm_3304.1	chr1	137807250	137807270	+	1	NA	Intergenic	Intergenic	-159195	NR_029795	735252		NR_029795	ENSMUSG00000065565	Mir181a-1	Mirn181a-1|Mirn213|miR-213|mir-181a-1|mmu-mir-213	microRNA 181a-1	ncRNA
mm_119053.1	chr14	30654368	30654424	+	1	NA	promoter-TSS (NM_177815)	promoter-TSS (NM_177815)	21	NM_177815	328370	Mm.259657	NM_177815	ENSMUSG00000052395	Rft1	D930025H04	RFT1 homolog	protein-coding
mm_43491.1	chr5	136953247	136953325	+	1	NA	promoter-TSS (NM_001163243)	promoter-TSS (NM_001163243)	11	NM_001347504	66437	Mm.25849	NM_025562	ENSMUSG00000019054	Fis1	2010003O14Rik|Ttc11	fission, mitochondrial 1	protein-coding
mm_65664.1	chr7	28146812	28146833	-	1	NA	exon (NM_001164655, exon 8 of 20)	exon (NM_001164655, exon 8 of 20)	17356	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_51684.1	chr6	86487504	86487516	+	1	NA	intron (NR_040292, intron 1 of 1)	intron (NR_040292, intron 1 of 1)	717	NR_040293	381792	Mm.333223	NR_040292	ENSMUSG00000101655	2310040G24Rik	-	RIKEN cDNA 2310040G24 gene	ncRNA
mm_2740.1	chr1	128399360	128399383	+	1	NA	intron (NM_177445, intron 4 of 15)	intron (NM_177445, intron 4 of 15)	18045	NM_177445	226414	Mm.28693	NM_145507	ENSMUSG00000026356	Dars	5730439G15Rik	aspartyl-tRNA synthetase	protein-coding
mm_95683.1	chr11	54214762	54214766	+	1	NA	Intergenic	Intergenic	-1476	NR_045506	71056	Mm.56332	NR_045506	ENSMUSG00000086209	4933405E24Rik	-	RIKEN cDNA 4933405E24 gene	ncRNA
mm_74712.1	chr8	17270602	17270603	-	1	NA	intron (NM_053171, intron 1 of 69)	intron (NM_053171, intron 1 of 69)	264783	NM_053171	94109	Mm.436988	NM_053171	ENSMUSG00000060924	Csmd1	B930082H09|mKIAA1890	CUB and Sushi multiple domains 1	protein-coding
mm_92749.1	chr10	81014879	81014901	-	1	NA	promoter-TSS (NM_010319)	promoter-TSS (NM_010319)	35	NM_010319	14708	Mm.222496	NM_010319	ENSMUSG00000048240	Gng7	AI840417	guanine nucleotide binding protein (G protein), gamma 7	protein-coding
mm_11823.1	chr2	44341763	44341767	+	1	NA	intron (NM_001301831, intron 13 of 14)	intron (NM_001301831, intron 13 of 14)	-276441	NR_040622	320872	Mm.445023	NR_040622	ENSMUSG00000085089	Arhgap15os	A430092G05Rik	Rho GTPase activating protein 15, opposite strand	ncRNA
mm_156645.1	chrX	157699154	157699166	+	1	NA	non-coding (NR_103722, exon 1 of 6)	non-coding (NR_103722, exon 1 of 6)	187	NR_103722	66106	Mm.140340	NM_025357	ENSMUSG00000041476	Smpx	1010001C09Rik|Csl	small muscle protein, X-linked	protein-coding
mm_156487.1	chrX	144336017	144336023	+	1	NA	intron (NR_037145, intron 3 of 26)	intron (NR_037145, intron 3 of 26)	18054	NM_026247	67574	Mm.249084	NM_026247	ENSMUSG00000041718	Alg13	2810046O15Rik|4833435D08Rik|Glt28d1|MDS031|OTTMUSG00000018917	asparagine-linked glycosylation 13	protein-coding
mm_87644.1	chr10	58391468	58391502	+	1	NA	intron (NM_201242, intron 1 of 9)	intron (NM_201242, intron 1 of 9)	-2888	NM_001193303	110829	Mm.57734	NM_026148	ENSMUSG00000019920	Lims1	2310016J22Rik|4921524A02Rik|AI507642|AU021743|AW551584|C430041B13Rik|Lims1l|PINCH|PINCH1	LIM and senescent cell antigen-like domains 1	protein-coding
mm_59232.1	chr7	24771674	24771675	+	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	-5530	NM_007675	26366	Mm.30300	NM_007675	ENSMUSG00000054169	Ceacam10	Bgp3|Cea10	carcinoembryonic antigen-related cell adhesion molecule 10	protein-coding
mm_114369.1	chr13	62964868	62964931	+	1	NA	promoter-TSS (NM_001289924)	promoter-TSS (NM_001289924)	6	NM_001289924	72061	Mm.188105	NM_028079	ENSMUSG00000021458	2010111I01Rik	2300006M17Rik|AP-O|AW742919|Aopep|ApO|mir-23b|mir-24-1|mir-27b	RIKEN cDNA 2010111I01 gene	protein-coding
mm_85256.1	chr9	99322668	99322679	-	1	NA	intron (NM_177775, intron 10 of 22)	intron (NM_177775, intron 10 of 22)	35857	NM_177775	272636	Mm.490440	NM_177775	ENSMUSG00000037681	Esyt3	D930024E11|D9Ertd280e|Fam62c|mKIAA4186	extended synaptotagmin-like protein 3	protein-coding
mm_78714.1	chr9	41474821	41474882	+	1	NA	promoter-TSS (NR_131931)	promoter-TSS (NR_131931)	-42	NR_131931	73144	Mm.38166	NM_001033153	ENSMUSG00000074415	3110039I08Rik	2610203C20Rik|AI848448|D230004N17Rik|D3Mgi9|Mir100hg	RIKEN cDNA 3110039I08 gene	ncRNA
mm_89100.1	chr10	84554843	84554850	+	1	NA	Intergenic	Intergenic	-1508	NR_040658	442847	Mm.128292	NR_040658	ENSMUSG00000097076	Platr7	C330046G13Rik	pluripotency associated transcript 7	ncRNA
mm_32139.1	chr4	99253844	99253858	+	1	NA	intron (NM_175029, intron 10 of 10)	B3A|SINE|B2	59704	NM_001145967	242557	Mm.241663	NM_175029	ENSMUSG00000028550	Atg4c	Apg4-C|Apg4c|Atg4cl|Autl1	autophagy related 4C, cysteine peptidase	protein-coding
mm_95705.1	chr11	54438475	54438503	+	1	NA	intron (NM_173753, intron 1 of 17)	CpG	310	NM_173753	216742	Mm.34087	NM_173753	ENSMUSG00000035992	Fnip1	A730024A03Rik|AI838773|AW557298	folliculin interacting protein 1	protein-coding
mm_61564.1	chr7	79660212	79660261	+	1	NA	promoter-TSS (NM_029835)	promoter-TSS (NM_029835)	40	NM_029835	77011	Mm.28132	NM_029835	ENSMUSG00000046591	Ticrr	5730590G19Rik|BC028450|Lrrk1	TOPBP1-interacting checkpoint and replication regulator	protein-coding
mm_164499.1	chr16	91534647	91534673	+	1	NA	Intergenic	Intergenic	-12434	NM_008338	15980	Mm.249364	NM_008338	ENSMUSG00000022965	Ifngr2	Ifgr2|Ifgt	interferon gamma receptor 2	protein-coding
mm_125934.1	chr15	76247685	76247695	+	1	NA	promoter-TSS (NR_105918)	promoter-TSS (NR_105918)	-501	NR_105918	102465575		NR_105918	ENSMUSG00000098625	Mir6953	Gm27738|mmu-mir-6953	microRNA 6953	ncRNA
mm_35044.1	chr4	4464127	4464129	-	1	NA	Intergenic	RLTR50A|LTR|ERVK	65330	NM_001277919	622019	Mm.246123	NM_001277919		Gm11780	OTTMUSG00000004194	predicted gene 11780	protein-coding
mm_99387.1	chr11	102097264	102097291	+	1	NA	Intergenic	Intergenic	4023	NM_008918	19064	Mm.1269	NM_008918	ENSMUSG00000017316	Ppy	AV061413|IGSPP|PP	pancreatic polypeptide	protein-coding
mm_71620.1	chr8	57332112	57332131	+	1	NA	promoter-TSS (NR_131041)	promoter-TSS (NR_131041)	-314	NR_131041	75996	Mm.399754	NR_131041	ENSMUSG00000097910	5033428I22Rik	-	RIKEN cDNA 5033428I22 gene	ncRNA
mm_161384.1	chr14	75190434	75190434	+	1	NA	intron (NM_008879, intron 2 of 16)	intron (NM_008879, intron 2 of 16)	-51853	NM_019775	56373	Mm.24242	NM_019775	ENSMUSG00000021999	Cpb2	1110032P04Rik|4930405E17Rik|AI255929|CPR|Cpu|TAFI	carboxypeptidase B2 (plasma)	protein-coding
mm_78919.1	chr9	45039778	45039792	+	1	NA	Intergenic	Intergenic	-2559	NM_007962	14012	Mm.33240	NM_007962	ENSMUSG00000032092	Mpzl2	Eva|Eva1	myelin protein zero-like 2	protein-coding
mm_5225.1	chr1	14304702	14304716	-	1	NA	intron (NM_001310459, intron 1 of 17)	intron (NM_001310459, intron 1 of 17)	5490	NM_001310459	14048	Mm.250185	NM_010164	ENSMUSG00000025932	Eya1	bor	EYA transcriptional coactivator and phosphatase 1	protein-coding
mm_38080.1	chr4	134128083	134128091	-	1	NA	intron (NM_080559, intron 1 of 2)	intron (NM_080559, intron 1 of 2)	666	NM_080559	73723	Mm.22240	NM_080559	ENSMUSG00000028843	Sh3bgrl3	1110004L05Rik|AU022188	SH3 domain binding glutamic acid-rich protein-like 3	protein-coding
mm_34472.1	chr4	148160657	148160680	+	1	NA	promoter-TSS (NM_001161852)	promoter-TSS (NM_001161852)	0	NM_176848	230904	Mm.262287	NM_176848	ENSMUSG00000041556	Fbxo2	FBG1|FBX2|Fbs1|Fbs2|NFB42|Prpl4	F-box protein 2	protein-coding
mm_76769.1	chr8	95808062	95808076	-	1	NA	promoter-TSS (NM_178078)	promoter-TSS (NM_178078)	-607	NM_001205226	234594	Mm.259220	NM_153164	ENSMUSG00000036550	Cnot1	6030411K04Rik|AA815922|D830048B13	CCR4-NOT transcription complex, subunit 1	protein-coding
mm_158262.1	chrX	109013390	109013398	-	1	NA	promoter-TSS (NM_016710)	promoter-TSS (NM_016710)	-14	NM_016710	50887	Mm.298443	NM_016710	ENSMUSG00000031245	Hmgn5	GARP45|NBP-45|Nsbp1	high-mobility group nucleosome binding domain 5	protein-coding
mm_92044.1	chr10	62494970	62494981	-	1	NA	exon (NM_011157, exon 3 of 3)	exon (NM_011157, exon 3 of 3)	-8170	NM_133672	30930	Mm.260703	NM_133672	ENSMUSG00000020078	Vps26a	AA407240|HB58|Vps26	VPS26 retromer complex component A	protein-coding
mm_97887.1	chr11	83293455	83293458	+	1	NA	promoter-TSS (NR_028364)	promoter-TSS (NR_028364)	26	NR_028364	103729	Mm.102205	NR_028364		AI450353	-	expressed sequence AI450353	ncRNA
mm_122593.1	chr14	50924806	50924896	-	1	NA	promoter-TSS (NM_009687)	promoter-TSS (NM_009687)	42	NM_133676	66246	Mm.274791	NM_133676	ENSMUSG00000006289	Osgep	1500019L24Rik|GCPL-1|PRSMG1	O-sialoglycoprotein endopeptidase	protein-coding
mm_96375.1	chr11	67238018	67238047	+	1	NA	5' UTR (NM_010855, exon 2 of 40)	5' UTR (NM_010855, exon 2 of 40)	220	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_33353.1	chr4	129382722	129382767	+	1	NA	Intergenic	RMER15|LTR|ERVL	-4716	NM_028603	73680	Mm.32997	NM_028603	ENSMUSG00000028807	Zbtb8a	2410081M15Rik|AI480941	zinc finger and BTB domain containing 8a	protein-coding
mm_172202.1	chr6	53402856	53402858	+	1	NA	intron (NM_001327821, intron 4 of 10)	L1Md_T|LINE|L1	115554	NM_001327821	231991	Mm.227444	NM_172728	ENSMUSG00000053007	Creb5	9430076C15Rik|CRE-BPa|Crebpa|D430026C09Rik	cAMP responsive element binding protein 5	protein-coding
mm_166788.1	chr6	145229436	145229442	-	1	NA	intron (NM_021284, intron 4 of 4)	B4|SINE|B4	18292	NM_133688	67636	Mm.486359	NM_133688	ENSMUSG00000040370	Lyrm5	4930469P12Rik|AL022899|Etfrf1|Ghiso	LYR motif containing 5	protein-coding
mm_102696.1	chr11	65788323	65788341	-	1	NA	promoter-TSS (NM_001316367)	promoter-TSS (NM_001316367)	27	NM_009157	26398	Mm.412922	NM_009157	ENSMUSG00000033352	Map2k4	JNKK1|MEK4|MKK4|PRKMK4|Sek1|Serk1	mitogen-activated protein kinase kinase 4	protein-coding
mm_20891.1	chr2	148872872	148872906	-	1	NA	exon (NM_009976, exon 2 of 3)	exon (NM_009976, exon 2 of 3)	2623	NM_009976	13010	Mm.4263	NM_009976	ENSMUSG00000027447	Cst3	CysC	cystatin C	protein-coding
mm_415.1	chr1	34236615	34236652	+	1	NA	intron (NM_001276764, intron 60 of 102)	intron (NM_001276764, intron 60 of 102)	76303	NM_010081	13518	Mm.336625	NM_010081	ENSMUSG00000026131	Dst	2310001O04Rik|A830042E19Rik|AW554249|BP230|BPAG1-n|Bpag|Bpag1|Macf2|ah|athetoid|dt|mKIAA0728|nmf203|nmf339	dystonin	protein-coding
mm_87349.1	chr10	43582690	43582731	+	1	NA	exon (NM_009846, exon 2 of 2)	exon (NM_009846, exon 2 of 2)	3541	NM_009846	12484	Mm.29742	NM_009846	ENSMUSG00000047139	Cd24a	Cd24|HSA|Ly-52|nectadrin	CD24a antigen	protein-coding
mm_8601.1	chr1	156034825	156034825	-	1	NA	promoter-TSS (NM_001160180)	promoter-TSS (NM_001160180)	-8	NM_001160019	208263	Mm.211654	NM_144791	ENSMUSG00000026466	Tor1aip1	LAP1|Lap1B	torsin A interacting protein 1	protein-coding
mm_60137.1	chr7	38029430	38029442	+	1	NA	Intergenic	ORR1D2|LTR|ERVL-MaLR	-9884	NM_011274	19777	Mm.387220	NM_011274	ENSMUSG00000030421	Uri1	C80913|NNX3|Rmp	URI1, prefoldin-like chaperone	protein-coding
mm_130464.1	chr15	98609403	98609424	-	1	NA	Intergenic	CpG	-1780	NM_007405	11512	Mm.157091	NM_007405	ENSMUSG00000022994	Adcy6	AC6|mKIAA0422	adenylate cyclase 6	protein-coding
mm_163213.1	chr11	100400913	100400913	-	1	NA	intron (NR_132425, intron 1 of 3)	intron (NR_132425, intron 1 of 3)	2797	NR_132425	102635937	Mm.421398	NR_132425		Gm12348	OTTMUSG00000006271	predicted gene 12348	ncRNA
mm_33615.1	chr4	132611619	132611636	+	1	NA	Intergenic	Intergenic	-27419	NM_210071	14050	Mm.227733	NM_010166	ENSMUSG00000028886	Eya3	AI844637	EYA transcriptional coactivator and phosphatase 3	protein-coding
mm_139081.1	chr17	46681977	46682034	+	1	NA	TTS (NM_009358)	TTS (NM_009358)	825	NM_001277312	17256	Mm.329083	NM_010787	ENSMUSG00000002768	Mea1	Mea-1	male enhanced antigen 1	protein-coding
mm_86969.1	chr10	25375251	25375265	+	1	NA	intron (NM_001199265, intron 1 of 19)	intron (NM_001199265, intron 1 of 19)	15460	NM_001199265	13822	Mm.306026	NM_013511	ENSMUSG00000019978	Epb41l2	4.1G|AW555191|D10Ertd398e|Epb4.1l2|NBL2	erythrocyte membrane protein band 4.1 like 2	protein-coding
mm_58998.1	chr7	19176484	19176512	+	1	NA	promoter-TSS (NM_001347582)	promoter-TSS (NM_001347582)	77	NM_001347582	72205	Mm.154121	NM_028153	ENSMUSG00000040811	Eml2	1600029N02Rik|EMAP-2	echinoderm microtubule associated protein like 2	protein-coding
mm_32556.1	chr4	109415680	109415689	+	1	NA	promoter-TSS (NM_001145948)	promoter-TSS (NM_001145948)	37	NM_001145948	230603	Mm.33091	NM_153392	ENSMUSG00000028555	Ttc39a	4922503N01Rik	tetratricopeptide repeat domain 39A	protein-coding
mm_86031.1	chr9	113671796	113671816	-	1	NA	exon (NM_001164677, exon 12 of 18)	exon (NM_001164677, exon 12 of 18)	36453	NM_001164678	18571	Mm.29816	NM_011052	ENSMUSG00000032504	Pdcd6ip	AI480591|AW544830|Aip1|Alix|C76364|Eig2|mKIAA1375	programmed cell death 6 interacting protein	protein-coding
mm_156571.1	chrX	151913840	151913846	+	1	NA	TTS (NR_029753)	TTS (NR_029753)	629	NR_029753	723947		NR_029753	ENSMUSG00000065536	Mir98	Mirn98|mir-98|mmu-mir-98	microRNA 98	ncRNA
mm_75191.1	chr8	38645803	38645804	-	1	NA	intron (NM_145841, intron 1 of 7)	intron (NM_145841, intron 1 of 7)	15705	NM_145841	244431	Mm.210388	NM_145841	ENSMUSG00000039539	Sgcz	C230085N17Rik	sarcoglycan zeta	protein-coding
mm_57682.1	chr6	128506815	128506828	-	1	NA	exon (NM_007376, exon 14 of 36)	exon (NM_007376, exon 14 of 36)	19899	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_34729.1	chr4	152178211	152178230	+	1	NA	exon (NM_133348, exon 1 of 9)	exon (NM_133348, exon 1 of 9)	120	NM_133348	70025	Mm.296191	NM_133348	ENSMUSG00000028937	Acot7	2410041A17Rik|Ach1|Act|Bach|CTE-IIa|Cte-II|Lach1	acyl-CoA thioesterase 7	protein-coding
mm_8083.1	chr1	135603244	135603261	-	1	NA	Intergenic	Intergenic	-17897	NM_173437	215690	Mm.34977	NM_173437	ENSMUSG00000009418	Nav1	9530089B19|9930003A20Rik|C230080M11Rik|Pomfil3|Unc53h1|mKIAA1151|steerin-1	neuron navigator 1	protein-coding
mm_139619.1	chr17	57362612	57362641	+	1	NA	intron (NM_010130, intron 2 of 21)	RLTR22_Mur|LTR|ERVK	3940	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_39831.1	chr5	30815050	30815060	+	1	NA	intron (NM_133350, intron 1 of 6)	intron (NM_133350, intron 1 of 6)	414	NM_133350	100732	Mm.332295	NM_133350	ENSMUSG00000029166	Mapre3	AI790651|EB2|EB3|EBF3|RP3	microtubule-associated protein, RP/EB family, member 3	protein-coding
mm_52119.1	chr6	97929809	97929822	+	1	NA	promoter-TSS (NM_001178049)	promoter-TSS (NM_001178049)	-2	NM_001178049	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_166999.1	chr7	46954339	46954341	+	1	NA	intron (NM_001040695, intron 3 of 11)	PB1D10|SINE|Alu	4178	NM_001040695	54122	Mm.1999	NM_016855	ENSMUSG00000043262	Uevld	8430408E05Rik|Attp	UEV and lactate/malate dehyrogenase domains	protein-coding
mm_7039.1	chr1	87101562	87101566	-	1	NA	promoter-TSS (NM_001081082)	promoter-TSS (NM_001081082)	42	NM_001081082	76768	Mm.58068	NM_001081082	ENSMUSG00000079440	Alpi	2010001C14Rik|Akp6|gIAP	alkaline phosphatase, intestinal	protein-coding
mm_72397.1	chr8	81768143	81768149	+	1	NA	exon (NM_001297596, exon 5 of 25)	exon (NM_001297596, exon 5 of 25)	425584	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_166869.1	chr7	24709288	24709290	+	1	NA	promoter-TSS (NM_199150)	promoter-TSS (NM_199150)	30	NM_199150	232972	Mm.293074	NM_199150	ENSMUSG00000045587	BC049730	Lypd10	cDNA sequence BC049730	protein-coding
mm_126936.1	chr15	91838256	91838265	+	1	NA	promoter-TSS (NM_207243)	promoter-TSS (NM_207243)	-66	NM_207243	239611	Mm.486225	NM_207243		Muc19	MUC-19|sld	mucin 19	protein-coding
mm_65663.1	chr7	28142248	28142258	-	1	NA	exon (NM_001164655, exon 6 of 20)	exon (NM_001164655, exon 6 of 20)	12787	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_165318.1	chr2	103797570	103797574	-	1	NA	promoter-TSS (NM_016739)	promoter-TSS (NM_016739)	68	NM_001111291	53872	Mm.427589	NM_016739	ENSMUSG00000027184	Caprin1	AL022980|Caprin-1|Gpiap|Gpiap1|Mmgpip137|P137|rng105	cell cycle associated protein 1	protein-coding
mm_11665.1	chr2	35266765	35266845	+	1	NA	promoter-TSS (NM_001206369)	promoter-TSS (NM_001206369)	61	NM_001206369	227753	Mm.443	NM_146120	ENSMUSG00000026879	Gsn	ADF	gelsolin	protein-coding
mm_11801.1	chr2	43739525	43739547	+	1	NA	Intergenic	Intergenic	-9288	NM_001301832	76117	Mm.217350	NM_153820	ENSMUSG00000049744	Arhgap15	5830480G12Rik	Rho GTPase activating protein 15	protein-coding
mm_163369.1	chr12	38781074	38781088	+	1	NA	intron (NM_001347379, intron 2 of 11)	intron (NM_001347379, intron 2 of 11)	999	NM_007960	14009	Mm.4866	NM_007960	ENSMUSG00000004151	Etv1	ER81|Etsrp81	ets variant 1	protein-coding
mm_113369.1	chr13	33002041	33002068	+	1	NA	Intergenic	L1MB7|LINE|L1	-2487	NM_009256	20723	Mm.245041	NM_009256	ENSMUSG00000045827	Serpinb9	BB283241|CAP-3|CAP3|PI-9|PI9|Spi6|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 9	protein-coding
mm_90315.1	chr10	127063528	127063538	+	1	NA	promoter-TSS (NM_009870)	promoter-TSS (NM_009870)	-70	NM_009870	12567	Mm.6839	NM_009870	ENSMUSG00000006728	Cdk4	Crk3	cyclin-dependent kinase 4	protein-coding
mm_23508.1	chr3	60529567	60529581	+	1	NA	5' UTR (NM_001253708, exon 2 of 9)	5' UTR (NM_001253708, exon 2 of 9)	28395	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_101502.1	chr11	32199338	32199352	-	1	NA	intron (NM_001134458, intron 1 of 8)	intron (NM_001134458, intron 1 of 8)	934	NM_001134458	16199	Mm.384	NM_008374	ENSMUSG00000020279	Il9r	-	interleukin 9 receptor	protein-coding
mm_82222.1	chr9	3024671	3024681	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	14067	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_31109.1	chr4	42921800	42921803	+	1	NA	intron (NM_001346526, intron 1 of 8)	L2c|LINE|L2	4550	NM_172690	230085	Mm.240965	NM_172690	ENSMUSG00000036062	Phf24	GINIP|N28178	PHD finger protein 24	protein-coding
mm_72111.1	chr8	71624029	71624058	+	1	NA	3' UTR (NM_146211, exon 12 of 12)	3' UTR (NM_146211, exon 12 of 12)	7063	NR_106035	102466799		NR_106035	ENSMUSG00000098976	Mir6769b	Gm27546|mmu-mir-6769b	microRNA 6769b	ncRNA
mm_65458.1	chr7	25466346	25466356	-	1	NA	exon (NM_001039186, exon 6 of 8)	exon (NM_001039186, exon 6 of 8)	11274	NM_001039185	26365	Mm.322502	NM_011926	ENSMUSG00000074272	Ceacam1	Bgp|Bgp1|C-CAM|CD66a|Cc1|Cea-1|Cea-7|Cea1|Cea7|Hv-2|Hv2|MHVR|MHVR1|Mhv-1|bb-1|mCEA1|mmCGM1|mmCGM1a|mmCGM2	carcinoembryonic antigen-related cell adhesion molecule 1	protein-coding
mm_72324.1	chr8	78509423	78509436	+	1	NA	promoter-TSS (NM_009033)	promoter-TSS (NM_009033)	101	NM_001282108	76775	Mm.334631	NM_029736	ENSMUSG00000031684	Slc10a7	2410193C02Rik|P7	solute carrier family 10 (sodium/bile acid cotransporter family), member 7	protein-coding
mm_118815.1	chr14	25466800	25466819	+	1	NA	intron (NM_001310666, intron 1 of 23)	intron (NM_001310666, intron 1 of 23)	7624	NM_183208	328365	Mm.227484	NM_183208	ENSMUSG00000007817	Zmiz1	BC065120|E330020C23|ENSMUSG00000072684|Gm10397|I920194n01|Rai17|Zimp10	zinc finger, MIZ-type containing 1	protein-coding
mm_143975.1	chr17	87433940	87433950	-	1	NA	3' UTR (NM_007589, exon 6 of 6)	3' UTR (NM_007589, exon 6 of 6)	-6204	NM_029298	75467	Mm.50108	NM_029298	ENSMUSG00000036557	Stpg4	1700011E24Rik|GSE	sperm tail PG rich repeat containing 4	protein-coding
mm_34554.1	chr4	149614117	149614133	+	1	NA	exon (NM_023051, exon 2 of 19)	exon (NM_023051, exon 2 of 19)	27657	NM_023051	65945	Mm.38993	NM_023051	ENSMUSG00000039953	Clstn1	1810034E21Rik|Cst-1|Cstn1	calsyntenin 1	protein-coding
mm_10793.1	chr2	24349486	24349496	+	1	NA	exon (NM_031167, exon 5 of 5)	exon (NM_031167, exon 5 of 5)	4120	NM_001039701	16181	Mm.882	NM_031167	ENSMUSG00000026981	Il1rn	F630041P17Rik|IL-1ra	interleukin 1 receptor antagonist	protein-coding
mm_73327.1	chr8	105279326	105279345	+	1	NA	intron (NM_030152, intron 2 of 3)	intron (NM_030152, intron 2 of 3)	2888	NM_030152	78688	Mm.475715	NM_030152	ENSMUSG00000014776	Nol3	ARC|B430311C09Rik|MYC|NOP|Nop30	nucleolar protein 3 (apoptosis repressor with CARD domain)	protein-coding
mm_96103.1	chr11	60537662	60537738	+	1	NA	promoter-TSS (NM_172943)	promoter-TSS (NM_172943)	17	NM_172943	268420	Mm.262056	NM_172943	ENSMUSG00000042650	Alkbh5	AW050020|AW215868|Abh5|E130207K11|Ofoxd	alkB homolog 5, RNA demethylase	protein-coding
mm_121544.1	chr14	122474563	122474573	+	1	NA	promoter-TSS (NM_009574)	promoter-TSS (NM_009574)	631	NR_045046	69248	Mm.235369	NR_045046	ENSMUSG00000085555	2610035F20Rik	-	RIKEN cDNA 2610035F20 gene	ncRNA
mm_39532.1	chr5	21375439	21375449	+	1	NA	exon (NM_008013, exon 2 of 2)	exon (NM_008013, exon 2 of 2)	2771	NM_008013	14190	Mm.292100	NM_008013	ENSMUSG00000039899	Fgl2	AI385601|musfiblp	fibrinogen-like protein 2	protein-coding
mm_136044.1	chr16	78376759	78376818	-	1	NA	promoter-TSS (NM_009770)	promoter-TSS (NM_009770)	22	NM_009770	12228	Mm.392910	NM_009770	ENSMUSG00000022863	Btg3	ANA|tob5	B cell translocation gene 3	protein-coding
mm_33569.1	chr4	132260522	132260538	+	1	NA	intron (NM_001122992, intron 1 of 10)	intron (NM_001122992, intron 1 of 10)	1019	NM_020273	56809	Mm.103489	NM_020273	ENSMUSG00000028901	Gmeb1	1110050A04Rik|AI256615|AI481278	glucocorticoid modulatory element binding protein 1	protein-coding
mm_79749.1	chr9	62368046	62368054	+	1	NA	intron (NM_009672, intron 1 of 6)	intron (NM_009672, intron 1 of 6)	26707	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	protein-coding
mm_64427.1	chr7	142577587	142577596	+	1	NA	promoter-TSS (NR_030416)	promoter-TSS (NR_030416)	-444	NR_030416	735280		NR_030416	ENSMUSG00000076275	Mir675	Mirn675|mir-675|mmu-mir-675	microRNA 675	ncRNA
mm_95305.1	chr11	46222584	46222594	+	1	NA	intron (NM_133769, intron 25 of 30)	intron (NM_133769, intron 25 of 30)	-9546	NR_105955	102465598		NR_105955	ENSMUSG00000099230	Mir6989	Gm27885|mmu-mir-6989	microRNA 6989	ncRNA
mm_155613.1	chrX	83043456	83043458	+	1	NA	intron (NM_007868, intron 1 of 78)	intron (NM_007868, intron 1 of 78)	94587	NM_007868	13405	Mm.275608	NM_007868	ENSMUSG00000045103	Dmd	DXSmh7|DXSmh9|Dp427|Dp71|dys|mdx|pke	dystrophin, muscular dystrophy	protein-coding
mm_104561.1	chr11	96829484	96829499	-	1	NA	promoter-TSS (NM_001130450)	promoter-TSS (NM_001130450)	11	NM_001130450	18023	Mm.6743	NM_008686	ENSMUSG00000038615	Nfe2l1	AA408798|AW212678|LCR-F1|Lcrf1|NRF1|TCF-11|TCF11	nuclear factor, erythroid derived 2,-like 1	protein-coding
mm_125626.1	chr15	61989393	61989405	+	1	NA	exon (NM_001177354, exon 3 of 3)	exon (NM_001177354, exon 3 of 3)	4058	NM_001177352	17869	Mm.2444	NM_010849	ENSMUSG00000022346	Myc	AU016757|Myc2|Niard|Nird|bHLHe39	myelocytomatosis oncogene	protein-coding
mm_1148.1	chr1	60755476	60755479	+	1	NA	intron (NM_007642, intron 1 of 3)	intron (NM_007642, intron 1 of 3)	9089	NM_007642	12487	Mm.255003	NM_007642	ENSMUSG00000026012	Cd28	-	CD28 antigen	protein-coding
mm_52800.1	chr6	121336801	121336850	+	1	NA	exon (NM_144512, exon 14 of 15)	exon (NM_144512, exon 14 of 15)	-6251	NM_001347433	14411	Mm.274506	NM_133661	ENSMUSG00000030109	Slc6a12	BGT1|GAT-2|GAT2|Gabt2	solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12	protein-coding
mm_13413.1	chr2	104112221	104112239	+	1	NA	intron (NM_007652, intron 3 of 3)	intron (NM_007652, intron 3 of 3)	-10539	NM_026634	68243	Mm.158191	NM_026634	ENSMUSG00000032671	A930018P22Rik	-	RIKEN cDNA A930018P22 gene	protein-coding
mm_121730.1	chr14	18238953	18239036	-	1	NA	5' UTR (NM_011584, exon 1 of 8)	5' UTR (NM_011584, exon 1 of 8)	112	NM_011584	353187	Mm.26587	NM_011584	ENSMUSG00000021775	Nr1d2	RVR|Rev-erb	nuclear receptor subfamily 1, group D, member 2	protein-coding
mm_76480.1	chr8	85550856	85550861	-	1	NA	intron (NM_019794, intron 3 of 8)	B1_Mur2|SINE|Alu	4413	NM_019794	56445	Mm.475573	NM_019794	ENSMUSG00000031701	Dnaja2	1500017M13Rik|2010206B19Rik|DNAJ|DNJ3|Dnaj3|HIRIP4|PRO3015|mDj3	DnaJ heat shock protein family (Hsp40) member A2	protein-coding
mm_29873.1	chr3	130842135	130842138	-	1	NA	Intergenic	Intergenic	-111738	NM_001005859	68436	Mm.140568	NM_026724	ENSMUSG00000062006	Rpl34	1100001I22Rik	ribosomal protein L34	protein-coding
mm_75778.1	chr8	69996264	69996298	-	1	NA	5' UTR (NM_001286450, exon 1 of 13)	5' UTR (NM_001286450, exon 1 of 13)	103	NM_001286450	234366	Mm.270044	NM_145596	ENSMUSG00000036180	Gatad2a	1110066C11Rik|BC031407|C80248	GATA zinc finger domain containing 2A	protein-coding
mm_137680.1	chr17	28817736	28817749	+	1	NA	exon (NM_001081315, exon 6 of 13)	exon (NM_001081315, exon 6 of 13)	16616	NM_001081315	268936	Mm.291877	NM_199061	ENSMUSG00000063952	Brpf3	AI413466|AW493400|mKIAA1286	bromodomain and PHD finger containing, 3	protein-coding
mm_17072.1	chr2	22745042	22745087	-	1	NA	Intergenic	Intergenic	-29263	NM_019456	54519	Mm.14255	NM_019456	ENSMUSG00000026786	Apbb1ip	9930118P07Rik|Prp48	amyloid beta (A4) precursor protein-binding, family B, member 1 interacting protein	protein-coding
mm_21348.1	chr2	157113403	157113405	-	1	NA	intron (NM_018851, intron 8 of 15)	B1_Mur2|SINE|Alu	21818	NM_001139520	56045	Mm.248478	NM_018851	ENSMUSG00000027639	Samhd1	E330031J07Rik|Mg11	SAM domain and HD domain, 1	protein-coding
mm_19408.1	chr2	91676057	91676078	-	1	NA	3' UTR (NM_145528, exon 16 of 16)	3' UTR (NM_145528, exon 16 of 16)	22859	NM_146124	228359	Mm.22413	NM_146124	ENSMUSG00000027247	Arhgap1	B230365D05Rik|C76222|Cdc42GAP|p50rhoGAP	Rho GTPase activating protein 1	protein-coding
mm_132043.1	chr16	27450388	27450393	+	1	NA	3' UTR (NM_001289436, exon 12 of 12)	3' UTR (NM_001289436, exon 12 of 12)	61434	NM_001289436	67501	Mm.258985	NM_026202	ENSMUSG00000038127	Ccdc50	C3orf6	coiled-coil domain containing 50	protein-coding
mm_3048.1	chr1	134040815	134040838	+	1	NA	exon (NM_021355, exon 2 of 3)	exon (NM_021355, exon 2 of 3)	3311	NM_021355	14264	Mm.287146	NM_021355	ENSMUSG00000041559	Fmod	AI131919|AU041740|SLRR2E	fibromodulin	protein-coding
mm_92480.1	chr10	78295384	78295388	-	1	NA	intron (NM_053014, intron 2 of 9)	intron (NM_053014, intron 2 of 9)	44821	NR_106119	102465765		NR_106119	ENSMUSG00000098885	Mir7659	Gm27433|mmu-mir-7659	microRNA 7659	ncRNA
mm_120589.1	chr14	69840467	69840477	+	1	NA	promoter-TSS (NM_028526)	promoter-TSS (NM_028526)	65	NM_028526	73523	Mm.23509	NM_028526	ENSMUSG00000022085	Pebp4	PEBP-4	phosphatidylethanolamine binding protein 4	protein-coding
mm_28303.1	chr3	89214330	89214372	-	1	NA	promoter-TSS (NM_013604)	promoter-TSS (NM_013604)	-16	NM_013604	17827	Mm.280943	NM_013604	ENSMUSG00000064068	Mtx1	Gcap6|Mtx	metaxin 1	protein-coding
mm_73361.1	chr8	105595094	105595102	+	1	NA	Intergenic	Intergenic	-10131	NM_001081241	75687	Mm.41261	NM_001081241	ENSMUSG00000038604	Fam65a	2310066E14Rik|AI837433	family with sequence similarity 65, member A	protein-coding
mm_56969.1	chr6	120187681	120187691	-	1	NA	intron (NM_016718, intron 1 of 3)	intron (NM_016718, intron 1 of 3)	-6137	NM_001347432	29862	Mm.103668	NM_016718	ENSMUSG00000041377	Ninj2	-	ninjurin 2	protein-coding
mm_156658.1	chrX	157711367	157711378	+	1	NA	intron (NR_045569, intron 3 of 6)	tRNA-Gly-GGA|tRNA|tRNA	12399	NR_103722	66106	Mm.140340	NM_025357	ENSMUSG00000041476	Smpx	1010001C09Rik|Csl	small muscle protein, X-linked	protein-coding
mm_7751.1	chr1	131097772	131097783	-	1	NA	promoter-TSS (NM_008551)	promoter-TSS (NM_008551)	66	NM_008551	17164	Mm.221235	NM_008551	ENSMUSG00000016528	Mapkapk2	AA960234|MAPKAP-K2|MK-2|MK2|Rps6kc1	MAP kinase-activated protein kinase 2	protein-coding
mm_155284.1	chrX	61183262	61183283	+	1	NA	TTS (NM_001166658)	TTS (NM_001166658)	2286	NM_001166658	631990	Mm.401324	NM_001166658	ENSMUSG00000090546	Cdr1	100039759|Cdr|Cdr34|EG631990|Gm2409|Gm7077	cerebellar degeneration related antigen 1	protein-coding
mm_50124.1	chr6	41536484	41536517	+	1	NA	Intergenic	Intergenic	14724	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_171408.1	chr4	129255614	129255621	+	1	NA	intron (NM_001285867, intron 1 of 6)	B2_Mm2|SINE|B2	5787	NM_001285867	97130	Mm.331907	NM_001033189	ENSMUSG00000050390	C77080	Kiaa1522|mKIAA1522	expressed sequence C77080	protein-coding
mm_125628.1	chr15	61989442	61989454	+	1	NA	exon (NM_001177354, exon 3 of 3)	exon (NM_001177354, exon 3 of 3)	4107	NM_001177352	17869	Mm.2444	NM_010849	ENSMUSG00000022346	Myc	AU016757|Myc2|Niard|Nird|bHLHe39	myelocytomatosis oncogene	protein-coding
mm_87589.1	chr10	57486512	57486520	+	1	NA	promoter-TSS (NR_045353)	promoter-TSS (NR_045353)	131	NM_008297	15500	Mm.261395	NM_008297	ENSMUSG00000019878	Hsf2	AI661205	heat shock factor 2	protein-coding
mm_121859.1	chr14	20674115	20674126	-	1	NA	promoter-TSS (NM_172596)	promoter-TSS (NM_172596)	-201	NM_172596	218811	Mm.173119	NM_172596	ENSMUSG00000039367	Sec24c	2610204K03Rik|mKIAA0079	Sec24 related gene family, member C (S. cerevisiae)	protein-coding
mm_43976.1	chr5	146260985	146261028	+	1	NA	intron (NM_153599, intron 2 of 12)	LSU-rRNA_Hsa|rRNA|rRNA	29331	NM_153599	264064	Mm.260576	NM_153599	ENSMUSG00000029635	Cdk8	-	cyclin-dependent kinase 8	protein-coding
mm_47645.1	chr5	125389216	125389222	-	1	NA	intron (NM_019639, intron 1 of 1)	intron (NM_019639, intron 1 of 1)	798	NM_019639	22190	Mm.331	NM_019639	ENSMUSG00000008348	Ubc	2700054O04Rik|AI194771|Rps27a|TI-225|Uba52|Ubb	ubiquitin C	protein-coding
mm_117371.1	chr13	71961703	71961705	-	1	NA	intron (NM_010573, intron 1 of 3)	intron (NM_010573, intron 1 of 3)	2019	NM_010573	16371	Mm.316056	NM_010573	ENSMUSG00000060969	Irx1	-	Iroquois related homeobox 1 (Drosophila)	protein-coding
mm_150584.1	chr19	40660172	40660182	+	1	NA	intron (NM_009848, intron 1 of 9)	intron (NM_009848, intron 1 of 9)	407	NM_009848	12495	Mm.2824	NM_009848	ENSMUSG00000048120	Entpd1	2610206B08Rik|AA408691|Cd39|NTPDase-1	ectonucleoside triphosphate diphosphohydrolase 1	protein-coding
mm_3002.1	chr1	133255680	133255728	+	1	NA	intron (NR_037984, intron 3 of 3)	intron (NR_037984, intron 3 of 3)	9607	NM_182930	240753	Mm.253559	NM_182930	ENSMUSG00000041757	Plekha6	9530028L01Rik|AU042621|Pepp3	pleckstrin homology domain containing, family A member 6	protein-coding
mm_135099.1	chr16	35363722	35363731	-	1	NA	intron (NM_133704, intron 1 of 6)	CpG	192	NM_133704	317717	Mm.259164	NM_133704	ENSMUSG00000034473	Sec22a	1810005C06Rik|Sec22l2	SEC22 homolog A, vesicle trafficking protein	protein-coding
mm_108221.1	chr12	77130835	77130847	+	1	NA	Intergenic	Intergenic	-107263	NM_001252614	53618	Mm.35628	NM_016893	ENSMUSG00000021065	Fut8	-	fucosyltransferase 8	protein-coding
mm_19455.1	chr2	92370969	92370992	-	1	NA	promoter-TSS (NM_001290775)	promoter-TSS (NM_001290775)	77	NM_001290774	228366	Mm.31158	NM_172670	ENSMUSG00000040434	Large2	5730485C17Rik|AI891893|Gyltl1b|Largel|mKIAA4105	LARGE xylosyl- and glucuronyltransferase 2	protein-coding
mm_69932.1	chr7	142061003	142061011	-	1	NA	promoter-TSS (NM_028308)	promoter-TSS (NM_028308)	27	NM_028308	101513	Mm.53259	NM_028308	ENSMUSG00000025147	Mob2	1110017M21Rik|2700078K21Rik|AI256456|Mmh	MOB kinase activator 2	protein-coding
mm_119623.1	chr14	51129056	51129072	+	1	NA	promoter-TSS (NM_030098)	promoter-TSS (NM_030098)	-4	NM_030098	78416	Mm.103835	NM_030098	ENSMUSG00000021880	Rnase6	9530043P15Rik|BB119466	ribonuclease, RNase A family, 6	protein-coding
mm_37861.1	chr4	132303168	132303180	-	1	NA	exon (NM_001081651, exon 1 of 2)	exon (NM_001081651, exon 1 of 2)	182	NM_001081651	242681	Mm.331927	NM_001081651	ENSMUSG00000089687	Rab42	9530096D07Rik|Rab42-ps	RAB42, member RAS oncogene family	protein-coding
mm_141978.1	chr17	35162314	35162337	-	1	NA	exon (NM_020027, exon 3 of 31)	exon (NM_020027, exon 3 of 31)	2552	NM_001199044	53761	Mm.272462	NM_020027	ENSMUSG00000024393	Prrc2a	3110039B05Rik|Bat-2|Bat2|D17H6S51E|G2|Wbp12|mKIAA4178	proline-rich coiled-coil 2A	protein-coding
mm_83804.1	chr9	53248107	53248117	-	1	NA	promoter-TSS (NM_029936)	promoter-TSS (NM_029936)	0	NM_029936	77591	Mm.133560	NM_029936	ENSMUSG00000053289	Ddx10	4632415A01Rik|AI646054	DEAD (Asp-Glu-Ala-Asp) box polypeptide 10	protein-coding
mm_165762.1	chr3	118663511	118663512	+	1	NA	intron (NM_170778, intron 2 of 22)	PB1D10|SINE|Alu	101333	NM_170778	99586	Mm.27907	NM_170778	ENSMUSG00000033308	Dpyd	AI315208|DPD|E330028L06Rik	dihydropyrimidine dehydrogenase	protein-coding
mm_66200.1	chr7	34230314	34230324	-	1	NA	promoter-TSS (NM_008155)	promoter-TSS (NM_008155)	17	NM_008155	14751	Mm.589	NM_008155	ENSMUSG00000036427	Gpi1	Amf|Gpi|Gpi-1|Gpi-1r|Gpi-1s|Gpi-1t|Gpi1-r|Gpi1-s|Gpi1-t|Gpi1s|MF|NK|NK/GPI|Nlk|Org|Pgi|Phi	glucose phosphate isomerase 1	protein-coding
mm_47484.1	chr5	123865484	123865488	-	1	NA	promoter-TSS (NM_030701)	promoter-TSS (NM_030701)	30	NM_030701	80885	Mm.440567	NM_030701	ENSMUSG00000045502	Hcar2	Gpr109a|Gpr109b|HM74|Niacr1|PUMA-G|Pumag|mHM74b	hydroxycarboxylic acid receptor 2	protein-coding
mm_62271.1	chr7	99536457	99536458	+	1	NA	intron (NM_177231, intron 1 of 15)	intron (NM_177231, intron 1 of 15)	971	NM_177231	109689	Mm.260193	NM_177231	ENSMUSG00000018909	Arrb1	1200006I17Rik|AW208571|G430100A01Rik	arrestin, beta 1	protein-coding
mm_91718.1	chr10	44458688	44458714	-	1	NA	promoter-TSS (NM_007548)	promoter-TSS (NM_007548)	47	NM_007548	12142	Mm.4800	NM_007548	ENSMUSG00000038151	Prdm1	Blimp-1|Blimp1|PRDI-BF1|ZNFPR1A1|b2b1765Clo	PR domain containing 1, with ZNF domain	protein-coding
mm_5008.1	chr1	192190772	192190821	+	1	NA	promoter-TSS (NM_001038607)	promoter-TSS (NM_001038607)	19	NM_010600	16510	Mm.4489	NM_010600	ENSMUSG00000058248	Kcnh1	EAG1|Kv10.1|M-eag	potassium voltage-gated channel, subfamily H (eag-related), member 1	protein-coding
mm_76197.1	chr8	82420089	82420101	-	1	NA	Intergenic	RMER19B|LTR|ERVK	-17509	NM_008357	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_37661.1	chr4	129058623	129058654	-	1	NA	exon (NM_029219, exon 1 of 9)	exon (NM_029219, exon 1 of 9)	367	NM_029219	75234	Mm.259672	NM_029219	ENSMUSG00000028793	Rnf19b	4930534K13Rik|4930555L03Rik|Ibrdc3	ring finger protein 19B	protein-coding
mm_107449.1	chr12	36677324	36677344	+	1	NA	intron (NM_178629, intron 9 of 9)	RMER1A|Other|Other	-138871	NR_039558	100628578		NR_039558	ENSMUSG00000092998	Mir5099	mmu-mir-5099|mu-mir-5099	microRNA 5099	ncRNA
mm_105761.1	chr11	109573647	109573660	-	1	NA	TTS (NM_001166177)	TTS (NM_001166177)	29942	NM_001166177	74008	Mm.482224	NM_028710	ENSMUSG00000020604	Arsg	6330406P08Rik|AI846872	arylsulfatase G	protein-coding
mm_136026.1	chr16	76373015	76373103	-	1	NA	promoter-TSS (NM_173440)	promoter-TSS (NM_173440)	-10	NM_173440	268903	Mm.74711	NM_173440	ENSMUSG00000048490	Nrip1	6030458L20Rik|8430438I05Rik|9630050P12|AA959574|AW456757|RIP140	nuclear receptor interacting protein 1	protein-coding
mm_166602.1	chr6	67533438	67533469	+	1	NA	TTS (NM_020047)	TTS (NM_020047)	2369	NM_020047	56753	Mm.439913	NM_020047	ENSMUSG00000051397	Tacstd2	C80403|EGP-1|GA733-1|Ly97|TROP2	tumor-associated calcium signal transducer 2	protein-coding
mm_1979.1	chr1	86582894	86582930	+	1	NA	promoter-TSS (NM_008801)	promoter-TSS (NM_008801)	-411	NM_008801	18582	Mm.12925	NM_008801	ENSMUSG00000026239	Pde6d	AI841218|PrBP/delta	phosphodiesterase 6D, cGMP-specific, rod, delta	protein-coding
mm_15204.1	chr2	154212974	154212978	+	1	NA	exon (NM_153418, exon 9 of 16)	exon (NM_153418, exon 9 of 16)	-10766	NM_144890	228802	Mm.167411	NM_144890	ENSMUSG00000038572	Bpifb5	Lplunc5	BPI fold containing family B, member 5	protein-coding
mm_18011.1	chr2	38287293	38287298	-	1	NA	promoter-TSS (NM_146122)	promoter-TSS (NM_146122)	89	NM_146122	227801	Mm.314245	NM_146122	ENSMUSG00000035392	Dennd1a	6030446I19Rik|connecdenn	DENN/MADD domain containing 1A	protein-coding
mm_179.1	chr1	13846591	13846618	+	1	NA	Intergenic	Intergenic	-59675	NR_004447	433273	Mm.304088	NR_004447	ENSMUSG00000097711	Gm5523	EG433273	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_28820.1	chr3	96283831	96283849	-	1	NA	3' UTR (NM_010186, exon 6 of 6)	3' UTR (NM_010186, exon 6 of 6)	10129	NM_010186	14129	Mm.150	NM_010186	ENSMUSG00000015947	Fcgr1	AI323638|AV092959|CD64|FcgammaRI|IGGHAFC	Fc receptor, IgG, high affinity I	protein-coding
mm_115888.1	chr13	21983575	21983581	-	1	NA	exon (NM_001162928, exon 1 of 1)	exon (NM_001162928, exon 1 of 1)	2384	NM_001162929	195236	Mm.204664	NM_001162928	ENSMUSG00000016982	Pom121l2	Gm24	POM121 membrane glycoprotein-like 2 (rat)	protein-coding
mm_172404.1	chr7	145034201	145034211	-	1	NA	Intergenic	RLTR9D|LTR|ERVK	-94281	NM_007631	12443	Mm.273049	NM_007631	ENSMUSG00000070348	Ccnd1	AI327039|CycD1|Cyl-1|PRAD1|bcl-1|cD1	cyclin D1	protein-coding
mm_87316.1	chr10	42827852	42827864	+	1	NA	intron (NM_153055, intron 19 of 20)	intron (NM_153055, intron 19 of 20)	-32654	NM_172938	268297	Mm.98731	NM_172938	ENSMUSG00000044770	Scml4	9330161D17|mFLJ00197	sex comb on midleg-like 4 (Drosophila)	protein-coding
mm_172451.1	chr7	32868126	32868132	-	1	NA	Intergenic	L1Md_T|LINE|L1	-38476	NM_001281524	668526	Mm.326965	NM_001281524	ENSMUSG00000098094	Scgb2b17	Abpbg17|EG668526|Gm9223	secretoglobin, family 2B, member 17	protein-coding
mm_142400.1	chr17	45433651	45433662	-	1	NA	promoter-TSS (NM_152810)	promoter-TSS (NM_152810)	51	NM_152810	71702	Mm.28270	NM_152810	ENSMUSG00000023932	Cdc5l	1200002I02Rik|AA408004|PCDC5RP	cell division cycle 5-like (S. pombe)	protein-coding
mm_74457.1	chr8	4214556	4214583	-	1	NA	exon (NM_207203, exon 6 of 7)	exon (NM_207203, exon 6 of 7)	2743	NM_207203	73072	Mm.477379	NM_207203	ENSMUSG00000064125	Prr36	-	proline rich 36	protein-coding
mm_160829.1	chr11	46311979	46311979	-	1	NA	5' UTR (NM_001252460, exon 1 of 31)	5' UTR (NM_001252460, exon 1 of 31)	379	NM_001252460	76884	Mm.154358	NM_133769	ENSMUSG00000020340	Cyfip2	1500004I01Rik|6430511D02Rik|AA930218|AU022376|Pir121|mKIAA1168	cytoplasmic FMR1 interacting protein 2	protein-coding
mm_153464.1	chr19	41264020	41264054	-	1	NA	promoter-TSS (NM_133352)	promoter-TSS (NM_133352)	-33	NM_133352	107358	Mm.246440	NM_133352	ENSMUSG00000025016	Tm9sf3	1810073M23Rik|2810031D16Rik|AI115521|AI413748|AW146116|AW549777|Smbp|mKIAA4036	transmembrane 9 superfamily member 3	protein-coding
mm_124934.1	chr15	12215189	12215219	+	1	NA	intron (NM_172958, intron 1 of 15)	intron (NM_172958, intron 1 of 15)	10110	NM_172958	268783	Mm.54460	NM_172958	ENSMUSG00000039458	Mtmr12	3Pap|4932703C11|C730015A02Rik|Pip3ap|mKIAA1682	myotubularin related protein 12	protein-coding
mm_167425.1	chr8	113971987	113971989	+	1	NA	Intergenic	Intergenic	-123149	NM_172466	208936	Mm.167471	NM_172466	ENSMUSG00000053399	Adamts18	9630038L21|ADAMTS21|E130314N14Rik	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 18	protein-coding
mm_37672.1	chr4	129121602	129121624	-	1	NA	promoter-TSS (NM_010471)	promoter-TSS (NM_010471)	134	NM_001130419	15444	Mm.384452	NM_010471	ENSMUSG00000028785	Hpca	-	hippocalcin	protein-coding
mm_19189.1	chr2	84421390	84421402	-	1	NA	intron (NM_018782, intron 1 of 15)	B1_Mur4|SINE|Alu	3870	NM_018782	54598	Mm.75467	NM_018782	ENSMUSG00000059588	Calcrl	AV071593|CRLR	calcitonin receptor-like	protein-coding
mm_13855.1	chr2	119695018	119695031	+	1	NA	intron (NM_030112, intron 2 of 17)	RSINE1|SINE|B4	19956	NM_030112	76246	Mm.33437	NM_030112	ENSMUSG00000027304	Rtf1	2900005O08Rik|6530416A09Rik|AI853581|AU043144|AW553985|Gtl7|cbp82	RTF1, Paf1/RNA polymerase II complex component	protein-coding
mm_66443.1	chr7	44849853	44849867	-	1	NA	promoter-TSS (NM_001253920)	promoter-TSS (NM_001253920)	-147	NM_001253920	67605	Mm.148007	NM_026270	ENSMUSG00000011096	Akt1s1	1110012J22Rik|AI227026|Lobe|Lobel|PRAS40	AKT1 substrate 1 (proline-rich)	protein-coding
mm_172280.1	chr6	88839573	88839588	-	1	NA	intron (NM_030251, intron 4 of 11)	intron (NM_030251, intron 4 of 11)	2355	NM_030251	80283	Mm.166858	NM_030251	ENSMUSG00000030083	Abtb1	AI847549|BC003234|BPOZ|EF1ABP	ankyrin repeat and BTB (POZ) domain containing 1	protein-coding
mm_126806.1	chr15	87625246	87625261	+	1	NA	promoter-TSS (NM_134096)	promoter-TSS (NM_134096)	23	NM_134096	106014	Mm.244319	NM_134096	ENSMUSG00000054863	Fam19a5	TAFA5|Tafa-5|Tara-5	family with sequence similarity 19, member A5	protein-coding
mm_2479.1	chr1	105846935	105846946	+	1	NA	3' UTR (NM_009399, exon 10 of 10)	3' UTR (NM_009399, exon 10 of 10)	66217	NM_009399	21934	Mm.6251	NM_009399	ENSMUSG00000026321	Tnfrsf11a	Ly109|ODFR|OFE|Rank|TRANCE-R|mRANK	tumor necrosis factor receptor superfamily, member 11a, NFKB activator	protein-coding
mm_131663.1	chr16	20629800	20629837	+	1	NA	promoter-TSS (NM_139293)	promoter-TSS (NM_139293)	-33	NM_177942	107522	Mm.263319	NM_025462	ENSMUSG00000022842	Ece2	1810009K13Rik|6330509A19Rik|9630025D12Rik|BB127715|Ece-2	endothelin converting enzyme 2	protein-coding
mm_109520.1	chr12	111454470	111454481	+	1	NA	3' UTR (NM_009396, exon 12 of 12)	3' UTR (NM_009396, exon 12 of 12)	11814	NM_009396	21928	Mm.255332	NM_009396	ENSMUSG00000021281	Tnfaip2	B94|Exoc3l3|M-sec|Tnfip2|tnfb94	tumor necrosis factor, alpha-induced protein 2	protein-coding
mm_100420.1	chr11	119436869	119436888	+	1	NA	Intergenic	Intergenic	46406	NR_035453	100316690		NR_035453	ENSMUSG00000088015	Mir1932	mir-1932|mmu-mir-1932	microRNA 1932	ncRNA
mm_170434.1	chr18	78696411	78696411	-	1	NA	Intergenic	L1_Mus2|LINE|L1	-99461	NM_030683	27411	Mm.44158	NM_030683	ENSMUSG00000024552	Slc14a2	UT-A1|UT-A3	solute carrier family 14 (urea transporter), member 2	protein-coding
mm_166466.1	chr5	142734038	142734047	+	1	NA	intron (NM_001122730, intron 22 of 27)	ID|SINE|ID	31941	NM_146257	243328	Mm.125942	NM_146257	ENSMUSG00000050822	Slc29a4	ENT4|mPMAT	solute carrier family 29 (nucleoside transporters), member 4	protein-coding
mm_109888.1	chr12	5375712	5375735	-	1	NA	promoter-TSS (NM_001164493)	promoter-TSS (NM_001164493)	-41	NM_001164493	208439	Mm.388281	NM_001164493	ENSMUSG00000020627	Klhl29	A230106N14Rik|Gm68|Kbtbd9|mKIAA1921	kelch-like 29	protein-coding
mm_87786.1	chr10	60297016	60297031	+	1	NA	intron (NM_011179, intron 8 of 14)	intron (NM_011179, intron 8 of 14)	12562	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_123090.1	chr14	55758464	55758489	-	1	NA	promoter-TSS (NM_009894)	promoter-TSS (NM_009894)	-52	NM_009894	12684	Mm.466766	NM_009894	ENSMUSG00000022219	Cideb	1110030C18Rik|AI790179|CIDE-B	cell death-inducing DNA fragmentation factor, alpha subunit-like effector B	protein-coding
mm_170830.1	chr2	176927801	176927808	-	1	NA	promoter-TSS (NM_001305137)	promoter-TSS (NM_001305137)	9	NM_001305136	100504263	Mm.379980	NM_001305136	ENSMUSG00000078894	2210418O10Rik	Gm6182	predicted gene 2210418O10Rik	protein-coding
mm_48513.1	chr5	142822811	142822821	-	1	NA	Intergenic	Intergenic	-5429	NM_001122730	231861	Mm.354649	NM_178242	ENSMUSG00000039477	Tnrc18	BC025631|EG381742|Zfp469	trinucleotide repeat containing 18	protein-coding
mm_153728.1	chr19	44407810	44407822	-	1	NA	promoter-TSS (NM_009127)	promoter-TSS (NM_009127)	-107	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_105513.1	chr11	106256046	106256103	-	1	NA	promoter-TSS (NM_025310)	promoter-TSS (NM_025310)	-111	NM_008950	19184	Mm.272361	NM_008950	ENSMUSG00000020708	Psmc5	mSUG1	protease (prosome, macropain) 26S subunit, ATPase 5	protein-coding
mm_39673.1	chr5	25516040	25516048	+	1	NA	promoter-TSS (NM_198621)	promoter-TSS (NM_198621)	-23	NM_198621	242891	Mm.291521	NM_198621	ENSMUSG00000038044	Cct8l1	Gm443	chaperonin containing TCP1, subunit 8 (theta)-like 1	protein-coding
mm_92540.1	chr10	79645733	79645744	-	1	NA	promoter-TSS (NM_001033473)	promoter-TSS (NM_001033473)	0	NM_001033473	382384	Mm.244510	NM_001033473	ENSMUSG00000035963	Odf3l2	Gm1157	outer dense fiber of sperm tails 3-like 2	protein-coding
mm_156738.1	chrX	159942949	159942976	+	1	NA	5' UTR (NM_001290664, exon 1 of 6)	5' UTR (NM_001290664, exon 1 of 6)	269	NM_001290664	58194	Mm.286495	NM_021389	ENSMUSG00000040990	Sh3kbp1	1200007H22Rik|1700125L08Rik|5830464D22Rik|AI447724|Cin85|IN85|Ruk|Seta	SH3-domain kinase binding protein 1	protein-coding
mm_77833.1	chr9	4309879	4309933	+	1	NA	promoter-TSS (NM_026962)	promoter-TSS (NM_026962)	90	NM_026962	69149	Mm.25946	NM_026962	ENSMUSG00000025893	Kbtbd3	2200003A07Rik|Bklhd3	kelch repeat and BTB (POZ) domain containing 3	protein-coding
mm_36728.1	chr4	99120857	99120894	-	1	NA	promoter-TSS (NM_026082)	promoter-TSS (NM_026082)	40	NM_001290636	67299	Mm.260623	NM_026082	ENSMUSG00000028556	Dock7	3110056M06Rik|Gm430	dedicator of cytokinesis 7	protein-coding
mm_18884.1	chr2	76673040	76673128	-	1	NA	promoter-TSS (NM_010222)	promoter-TSS (NM_010222)	14	NM_010222	14231	Mm.24720	NM_010222	ENSMUSG00000002732	Fkbp7	23kDa|FKBP-7|FKBP23	FK506 binding protein 7	protein-coding
mm_24431.1	chr3	90541178	90541186	+	1	NA	promoter-TSS (NM_026416)	promoter-TSS (NM_026416)	-41	NM_026416	67860	Mm.331185	NM_026416	ENSMUSG00000074457	S100a16	2300002L21Rik|AI325039|AI663996|DT1P1A7|S100F	S100 calcium binding protein A16	protein-coding
mm_64424.1	chr7	142577374	142577407	+	1	NA	promoter-TSS (NR_030416)	promoter-TSS (NR_030416)	-243	NR_030416	735280		NR_030416	ENSMUSG00000076275	Mir675	Mirn675|mir-675|mmu-mir-675	microRNA 675	ncRNA
mm_148195.1	chr18	79066736	79066748	-	1	NA	intron (NM_053099, intron 2 of 5)	intron (NM_053099, intron 2 of 5)	42649	NM_053099	240427	Mm.312871	NM_053099	ENSMUSG00000024548	Setbp1	C130092E12|Seb|mKIAA0437	SET binding protein 1	protein-coding
mm_10855.1	chr2	25054375	25054391	+	1	NA	promoter-TSS (NM_020276)	promoter-TSS (NM_020276)	4	NM_001177655	56876	Mm.42956	NM_020276	ENSMUSG00000006476	Nsmf	Jacob|Nelf	NMDA receptor synaptonuclear signaling and neuronal migration factor	protein-coding
mm_170868.1	chr2	18461129	18461135	+	1	NA	Intergenic	RLTR9E|LTR|ERVK	-68302	NM_007869	13418	Mm.246674	NM_007869	ENSMUSG00000026740	Dnajc1	4733401K02Rik|AA960110|D230036H06Rik|Dnajl1|ERdj1|ERj1p|MTJ1	DnaJ heat shock protein family (Hsp40) member C1	protein-coding
mm_41417.1	chr5	90868329	90868331	+	1	NA	Intergenic	BC1_Mm|scRNA|scRNA	-22915	NM_008176	14825	Mm.21013	NM_008176	ENSMUSG00000029380	Cxcl1	Fsp|Gro1|KC|Mgsa|N51|Scyb1|gro	chemokine (C-X-C motif) ligand 1	protein-coding
mm_151918.1	chr19	5799819	5799829	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	2848	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_141740.1	chr17	34122312	34122375	-	1	NA	promoter-TSS (NM_010238)	promoter-TSS (NM_010238)	264	NM_001204973	14312	Mm.3444	NM_010238	ENSMUSG00000024335	Brd2	AW228947|D17H6S113E|Frg-1|Fsrg-1|Fsrg1|Nat|Ring3|Rnf3|mKIAA4005	bromodomain containing 2	protein-coding
mm_129618.1	chr15	80014302	80014367	-	1	NA	5' UTR (NM_011057, exon 1 of 7)	5' UTR (NM_011057, exon 1 of 7)	474	NM_011057	18591	Mm.144089	NM_011057	ENSMUSG00000000489	Pdgfb	PDGF-B|Sis	platelet derived growth factor, B polypeptide	protein-coding
mm_91769.1	chr10	51527317	51527323	-	1	NA	Intergenic	RMER16-int|LTR|ERVK	36422	NM_013532	14728	Mm.34408	NM_013532	ENSMUSG00000062593	Lilrb4a	CD85K|Gp49b|HM18|ILT3|LIR-5|Lilrb4|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4A	protein-coding
mm_45439.1	chr5	67269499	67269505	-	1	NA	intron (NM_001285452, intron 5 of 6)	MTC|LTR|ERVL-MaLR	8937	NM_030108	67878	Mm.23217	NM_028975	ENSMUSG00000037720	Tmem33	1110006G02Rik|1600019D15Rik|2410089A21Rik|2700052H22Rik|5430406L04Rik|AA388285|AI314185|AI426615|db83	transmembrane protein 33	protein-coding
mm_122683.1	chr14	52014862	52014897	-	1	NA	promoter-TSS (NM_001253695)	promoter-TSS (NM_001253695)	-321	NM_001253695	69890	Mm.475652	NM_027248	ENSMUSG00000049295	Zfp219	2010302A17Rik	zinc finger protein 219	protein-coding
mm_109981.1	chr12	12941828	12941845	-	1	NA	promoter-TSS (NM_008709)	promoter-TSS (NM_008709)	0	NM_008709	18109	Mm.16469	NM_008709	ENSMUSG00000037169	Mycn	N-myc|Nmyc|Nmyc-1|Nmyc1|bHLHe37|c-nmyc	v-myc avian myelocytomatosis viral related oncogene, neuroblastoma derived	protein-coding
mm_165848.1	chr4	8822136	8822139	+	1	NA	intron (NM_001277149, intron 7 of 37)	AT_rich|Low_complexity|Low_complexity	131731	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_116497.1	chr13	44947165	44947188	-	1	NA	intron (NM_025772, intron 7 of 9)	intron (NM_025772, intron 7 of 9)	54920	NM_025772	94245	Mm.352311	NM_025772	ENSMUSG00000057531	Dtnbp1	5430437B18Rik|AW048963|Bloc1s8|dysbindin|sdy	dystrobrevin binding protein 1	protein-coding
mm_170578.1	chr1	95498613	95498614	+	1	NA	Intergenic	Intergenic	168981	NM_009183	20452	Mm.306228	NM_009183	ENSMUSG00000040710	St8sia4	PST|PST-1|SIAT8-D|ST8SiaIV|Siat8d	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4	protein-coding
mm_4832.1	chr1	186587316	186587350	+	1	NA	Intergenic	MIR|SINE|MIR	-28652	NR_131158	320449	Mm.404477	NR_131124	ENSMUSG00000103690	A730004F24Rik	-	RIKEN cDNA A730004F24 gene	ncRNA
mm_95057.1	chr11	32400879	32400898	+	1	NA	intron (NM_177364, intron 6 of 12)	intron (NM_177364, intron 6 of 12)	53077	NM_177364	268396	Mm.227616	NM_177364	ENSMUSG00000040711	Sh3pxd2b	G431001E03Rik|TSK4|fad49	SH3 and PX domains 2B	protein-coding
mm_19268.1	chr2	85033914	85033916	-	1	NA	intron (NM_145526, intron 1 of 11)	intron (NM_145526, intron 1 of 11)	1919	NM_145526	228139	Mm.440375	NM_145526	ENSMUSG00000027071	P2rx3	4930513E20Rik|P2X3	purinergic receptor P2X, ligand-gated ion channel, 3	protein-coding
mm_75862.1	chr8	70723588	70723605	-	1	NA	promoter-TSS (NM_201607)	promoter-TSS (NM_201607)	-468	NM_001310465	110385	Mm.255180	NM_201607	ENSMUSG00000031842	Pde4c	Dpde1|E130301F19Rik|dunce	phosphodiesterase 4C, cAMP specific	protein-coding
mm_20150.1	chr2	121551278	121551286	-	1	NA	intron (NM_172673, intron 13 of 14)	intron (NM_172673, intron 13 of 14)	44559	NM_001290986	241627	Mm.293284	NM_030234	ENSMUSG00000027242	Wdr76	5830411K18Rik|6030457D09|AA517836	WD repeat domain 76	protein-coding
mm_92470.1	chr10	78038268	78038299	-	1	NA	intron (NM_001271558, intron 7 of 11)	RMER20A|LTR|ERVK	-4004	NM_001081695	54427	Mm.13433	NM_019448	ENSMUSG00000000730	Dnmt3l	D6Ertd14e|ecat7	DNA (cytosine-5-)-methyltransferase 3-like	protein-coding
mm_39314.1	chr5	8056556	8056585	+	1	NA	promoter-TSS (NM_001080974)	promoter-TSS (NM_001080974)	28	NM_001080974	109552	Mm.96211	NM_025618	ENSMUSG00000003161	Sri	2210417O06Rik|2900070H08Rik|Sor	sorcin	protein-coding
mm_78914.1	chr9	44983660	44983663	+	1	NA	intron (NM_013487, intron 1 of 4)	B1F|SINE|Alu	1875	NM_013487	12500	Mm.4527	NM_013487	ENSMUSG00000032094	Cd3d	T3d	CD3 antigen, delta polypeptide	protein-coding
mm_97031.1	chr11	72266427	72266454	+	1	NA	promoter-TSS (NR_045922)	promoter-TSS (NR_045922)	164	NM_001004148	237831	Mm.340778	NM_001004148	ENSMUSG00000020805	Slc13a5	Indy|NaC2/NaCT|Nact|mINDY	solute carrier family 13 (sodium-dependent citrate transporter), member 5	protein-coding
mm_167555.1	chr9	35608320	35608326	-	1	NA	exon (NM_020264, exon 2 of 3)	exon (NM_020264, exon 2 of 3)	3562	NM_020264	56872	Mm.390143	NM_020264	ENSMUSG00000032099	Pate4	9530004K16Rik|Pate-B|Svs7	prostate and testis expressed 4	protein-coding
mm_86436.1	chr10	3872807	3872818	+	1	NA	intron (NM_001033253, intron 1 of 15)	intron (NM_001033253, intron 1 of 15)	145	NM_001033253	213783	Mm.150831	NM_001033253	ENSMUSG00000040624	Plekhg1	D10Ertd733e|Gm521|mKIAA1209	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	protein-coding
mm_91294.1	chr10	24915631	24915641	-	1	NA	exon (NM_007482, exon 8 of 8)	exon (NM_007482, exon 8 of 8)	4972	NR_105870	102465545		NR_105870	ENSMUSG00000099181	Mir6905	Gm27879|mmu-mir-6905	microRNA 6905	ncRNA
mm_138493.1	chr17	35200433	35200479	+	1	NA	exon (NM_013693, exon 4 of 4)	exon (NM_013693, exon 4 of 4)	1551	NM_013693	21926	Mm.1293	NM_013693	ENSMUSG00000024401	Tnf	DIF|TNF-a|TNF-alpha|TNFSF2|TNFalpha|Tnfa|Tnfsf1a|Tnlg1f	tumor necrosis factor	protein-coding
mm_49301.1	chr6	17749004	17749022	+	1	NA	promoter-TSS (NM_001083315)	promoter-TSS (NM_001083315)	-157	NM_001083315	64213	Mm.12051	NM_022332	ENSMUSG00000029534	St7	9430001H04Rik|Fam4a2|HELG|RAY1|SEN4|TSG7	suppression of tumorigenicity 7	protein-coding
mm_116044.1	chr13	27247912	27247955	-	1	NA	exon (NM_008865, exon 4 of 5)	exon (NM_008865, exon 4 of 5)	5503	NM_008865	18776	Mm.37203	NM_008865	ENSMUSG00000038891	Prl3b1	Csh2|Ghd8|PL|Pl-2|Pl2|mPL-II|mplII	prolactin family 3, subfamily b, member 1	protein-coding
mm_170423.1	chr18	7181091	7181110	+	1	NA	intron (NM_001081393, intron 18 of 20)	RLTR9F|LTR|ERVK	116801	NM_001081393	74934	Mm.107918	NM_001081393	ENSMUSG00000061802	Armc4	4930463I21Rik|b2b227.1Clo|b2b643Clo	armadillo repeat containing 4	protein-coding
mm_24734.1	chr3	95283165	95283188	+	1	NA	5' UTR (NM_133858, exon 1 of 10)	5' UTR (NM_133858, exon 1 of 10)	241	NM_199475	75007	Mm.279287	NM_133858	ENSMUSG00000038712	Fam63a	1810005H09Rik|4930504E06Rik|AA562754|AA960384|AW561904|cI-40|mKIAA1390|ni	family with sequence similarity 63, member A	protein-coding
mm_10119.1	chr2	3731063	3731067	+	1	NA	intron (NM_025626, intron 1 of 3)	intron (NM_025626, intron 1 of 3)	17607	NM_025626	66540	Mm.277864	NM_025626	ENSMUSG00000026655	Fam107b	3110001A13Rik|AA589595|AA959793|AI132312	family with sequence similarity 107, member B	protein-coding
mm_9885.1	chr1	186624298	186624303	-	1	NA	3' UTR (NM_009367, exon 7 of 7)	3' UTR (NM_009367, exon 7 of 7)	-65619	NR_131158	320449	Mm.404477	NR_131124	ENSMUSG00000103690	A730004F24Rik	-	RIKEN cDNA A730004F24 gene	ncRNA
mm_152858.1	chr19	24191478	24191481	-	1	NA	intron (NM_011597, intron 1 of 22)	B1_Mur1|SINE|Alu	-17339	NM_001198985	21873	Mm.104744	NM_011597	ENSMUSG00000024812	Tjp2	ZO-2	tight junction protein 2	protein-coding
mm_37521.1	chr4	124693548	124693565	-	1	NA	promoter-TSS (NM_026031)	promoter-TSS (NM_026031)	-2	NM_026031	67205	Mm.259121	NM_026031	ENSMUSG00000028907	Utp11l	2700082D03Rik|CGI-94|Cgi94|Utp11	UTP11-like, U3 small nucleolar ribonucleoprotein, (yeast)	protein-coding
mm_172010.1	chr6	109505319	109505319	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	676678	NM_138677	192193	Mm.21596	NM_138677	ENSMUSG00000030104	Edem1	A130059K23Rik|EDEM|mKIAA0212	ER degradation enhancer, mannosidase alpha-like 1	protein-coding
mm_70734.1	chr8	18882227	18882245	+	1	NA	3' UTR (NM_026792, exon 8 of 8)	3' UTR (NM_026792, exon 8 of 8)	35957	NM_026792	52123	Mm.24117	NM_026792	ENSMUSG00000031467	Agpat5	1110013A05Rik|D8Ertd319e	1-acylglycerol-3-phosphate O-acyltransferase 5 (lysophosphatidic acid acyltransferase, epsilon)	protein-coding
mm_7869.1	chr1	132707250	132707283	-	1	NA	promoter-TSS (NM_001160318)	promoter-TSS (NM_001160318)	60	NM_001160318	269116	Mm.326702	NM_182716	ENSMUSG00000026442	Nfasc	AA387016|D430023G06Rik|NF|mKIAA0756	neurofascin	protein-coding
mm_172863.1	chr9	40803523	40803526	+	1	NA	exon (NM_031165, exon 5 of 9)	exon (NM_031165, exon 5 of 9)	2251	NM_031165	15481	Mm.290774	NM_031165	ENSMUSG00000015656	Hspa8	2410008N15Rik|Hsc70|Hsc71|Hsc73|Hsp73|Hspa10	heat shock protein 8	protein-coding
mm_59190.1	chr7	24475505	24475543	+	1	NA	3' UTR (NM_011113, exon 7 of 7)	3' UTR (NM_011113, exon 7 of 7)	-6499	NM_153112	260299	Mm.178322	NM_153112	ENSMUSG00000054793	Cadm4	Igdf4c|Igsf4c|Tsll2	cell adhesion molecule 4	protein-coding
mm_742.1	chr1	43503238	43503243	+	1	NA	intron (NM_010879, intron 1 of 4)	intron (NM_010879, intron 1 of 4)	57489	NM_010879	17974	Mm.389903	NM_010879	ENSMUSG00000066877	Nck2	4833426I10Rik|Grb4|NCKbeta|Nck-2	non-catalytic region of tyrosine kinase adaptor protein 2	protein-coding
mm_32930.1	chr4	119232897	119232956	+	1	NA	promoter-TSS (NM_019782)	promoter-TSS (NM_019782)	11	NM_019782	56401	Mm.27961	NM_019782	ENSMUSG00000028641	P3h1	2410024C15Rik|Gros1|Lepre1	prolyl 3-hydroxylase 1	protein-coding
mm_168043.1	chrY	90804544	90804554	+	1	NA	intron (NM_133362, intron 2 of 3)	intron (NM_133362, intron 2 of 3)	19107	NM_133362	170942	Mm.76062	NM_133362	ENSMUSG00000096768	Erdr1	edr	erythroid differentiation regulator 1	protein-coding
mm_107173.1	chr12	24713730	24713735	+	1	NA	3' UTR (NM_009104, exon 10 of 10)	3' UTR (NM_009104, exon 10 of 10)	5478	NM_009104	20135	Mm.99	NM_009104	ENSMUSG00000020649	Rrm2	AA407299|R2	ribonucleotide reductase M2	protein-coding
mm_147503.1	chr18	50010695	50010703	-	1	NA	intron (NM_001177759, intron 1 of 1)	RSINE1|SINE|B4	31272	NM_001177759	106869	Mm.27740	NM_134131	ENSMUSG00000062210	Tnfaip8	AA987150|E130304C20Rik|ENSMUSG00000073567|Gg2-1|Gm10539|Nded|Ssc-2|Tipe	tumor necrosis factor, alpha-induced protein 8	protein-coding
mm_172664.1	chr8	43180223	43180227	-	1	NA	Intergenic	B1F|SINE|Alu	-2897	NM_001160412	622117	Mm.390031	NM_001160412	ENSMUSG00000091490	Triml2	EG622117|Tu4	tripartite motif family-like 2	protein-coding
mm_117621.1	chr13	91861323	91861334	-	1	NA	exon (NM_198415, exon 5 of 10)	exon (NM_198415, exon 5 of 10)	15557	NM_198415	76722	Mm.316438	NM_198415	ENSMUSG00000021622	Ckmt2	2300008A19Rik|ScCKmit	creatine kinase, mitochondrial 2	protein-coding
mm_28723.1	chr3	95684526	95684556	-	1	NA	exon (NM_144899, exon 4 of 18)	exon (NM_144899, exon 4 of 18)	3376	NM_144899	229595	Mm.490574	NM_144899	ENSMUSG00000015850	Adamtsl4	ADAMTSL-4|Tsrc1	ADAMTS-like 4	protein-coding
mm_22627.1	chr3	14766535	14766542	+	1	NA	exon (NM_001083957, exon 7 of 7)	exon (NM_001083957, exon 7 of 7)	11922	NM_001083957	12346	Mm.273195	NM_009799	ENSMUSG00000027556	Car1	AW555628|Ca1|Car-1	carbonic anhydrase 1	protein-coding
mm_89776.1	chr10	100590523	100590533	+	1	NA	Intergenic	Intergenic	-1269	NM_175128	68281	Mm.268474	NM_175128	ENSMUSG00000046567	4930430F08Rik	4930571E09Rik|A730088G13Rik|AW551239|C430008C19Rik	RIKEN cDNA 4930430F08 gene	protein-coding
mm_95726.1	chr11	54596130	54596155	+	1	NA	promoter-TSS (NM_001252498)	promoter-TSS (NM_001252498)	-4	NM_001252498	192786	Mm.254404	NM_175258	ENSMUSG00000037533	Rapgef6	A530068K01|AI844632|BB085664|C030018K18Rik|PDZ-GEF2|Pdzgef2|RA-GEF-2|Ragef2|mKIAA4052	Rap guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_84171.1	chr9	59948464	59948487	-	1	NA	exon (NM_013708, exon 5 of 8)	exon (NM_013708, exon 5 of 8)	1604	NM_013708	23958	Mm.103641	NM_013708	ENSMUSG00000032292	Nr2e3	A930035N01Rik|PNR|RNR|rd7	nuclear receptor subfamily 2, group E, member 3	protein-coding
mm_118758.1	chr14	22378168	22378172	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	164628	NR_046307	74896	Mm.444661	NR_046307		4930405A10Rik	4930456G20Rik	RIKEN cDNA 4930405A10 gene	ncRNA
mm_107192.1	chr12	25254764	25254804	+	1	NA	Intergenic	Intergenic	125610	NR_045844	432641	Mm.112955	NR_045844		Gm17746	-	predicted gene, 17746	ncRNA
mm_46389.1	chr5	104021800	104021865	-	1	NA	promoter-TSS (NM_053262)	promoter-TSS (NM_053262)	-36	NM_053262	114664	Mm.46019	NM_053262	ENSMUSG00000029311	Hsd17b11	Dhrs8|Pan1b|SDR2|retSDR2	hydroxysteroid (17-beta) dehydrogenase 11	protein-coding
mm_162974.1	chr11	16752198	16752202	+	1	NA	promoter-TSS (NM_007912)	promoter-TSS (NM_007912)	-3	NM_207655	13649	Mm.8534	NM_007912	ENSMUSG00000020122	Egfr	9030024J15Rik|AI552599|Erbb|Errb1|Errp|Wa5|wa-2|wa2	epidermal growth factor receptor	protein-coding
mm_139525.1	chr17	56638264	56638267	+	1	NA	intron (NM_175350, intron 6 of 21)	PB1D7|SINE|Alu	10122	NM_175350	106757	Mm.23401	NM_175350	ENSMUSG00000040828	Catsperd	4921529N20Rik|4933402B14Rik|619718|AW045609|Gm6095|Tmem146	catsper channel auxiliary subunit delta	protein-coding
mm_21795.1	chr2	164857804	164857823	-	1	NA	promoter-TSS (NM_011125)	promoter-TSS (NM_011125)	-105	NM_011125	18830	Mm.6105	NM_011125	ENSMUSG00000017754	Pltp	Bpife|OD107	phospholipid transfer protein	protein-coding
mm_104503.1	chr11	95960291	95960292	-	1	NA	3' UTR (NM_009951, exon 15 of 15)	3' UTR (NM_009951, exon 15 of 15)	3092	NR_037223	100526468		NR_037223	ENSMUSG00000093358	Mir3063	mmu-mir-3063	microRNA 3063	ncRNA
mm_89362.1	chr10	88433999	88434009	+	1	NA	exon (NM_001004164, exon 13 of 21)	exon (NM_001004164, exon 13 of 21)	-25583	NM_011517	20962	Mm.297977	NM_011517	ENSMUSG00000020059	Sycp3	Cor1|Scp3	synaptonemal complex protein 3	protein-coding
mm_146147.1	chr18	74787105	74787123	+	1	NA	intron (NM_177470, intron 1 of 9)	intron (NM_177470, intron 1 of 9)	7902	NM_177470	52538	Mm.245724	NM_177470	ENSMUSG00000036880	Acaa2	0610011L04Rik|AI255831|AI265397|D18Ertd240e	acetyl-Coenzyme A acyltransferase 2 (mitochondrial 3-oxoacyl-Coenzyme A thiolase)	protein-coding
mm_120217.1	chr14	62760486	62760493	+	1	NA	promoter-TSS (NR_045503)	promoter-TSS (NR_045503)	-12	NR_045503	71000	Mm.399410	NR_045503	ENSMUSG00000097775	4931440J10Rik	-	RIKEN cDNA 4931440J10 gene	ncRNA
mm_107196.1	chr12	25316187	25316198	+	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	187018	NR_045844	432641	Mm.112955	NR_045844		Gm17746	-	predicted gene, 17746	ncRNA
mm_159455.1	chr3	146943870	146943870	+	1	NA	intron (NM_001302957, intron 16 of 21)	intron (NM_001302957, intron 16 of 21)	91503	NM_001302958	70892	Mm.187793	NM_027594	ENSMUSG00000036745	Ttll7	1110049N09Rik|4921517B04Rik|C630030B20|mTTLL7	tubulin tyrosine ligase-like family, member 7	protein-coding
mm_110349.1	chr12	37081866	37081868	-	1	NA	Intergenic	Intergenic	-26679	NM_008584	17286	Mm.341398	NM_008584	ENSMUSG00000036144	Meox2	AI528662|Gax|Mox-2|Mox2	mesenchyme homeobox 2	protein-coding
mm_77239.1	chr8	115705183	115705193	-	1	NA	3' UTR (NM_001025577, exon 1 of 1)	3' UTR (NM_001025577, exon 1 of 1)	1706	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_83593.1	chr9	48480541	48480640	-	1	NA	promoter-TSS (NM_024233)	promoter-TSS (NM_024233)	21	NM_024233	104444	Mm.21911	NM_024233	ENSMUSG00000032026	Rexo2	1810038D15Rik|AW107347|Rex2|Sfn|Smfn	RNA exonuclease 2	protein-coding
mm_171483.1	chr4	146067547	146067552	+	1	NA	promoter-TSS (NR_030771)	promoter-TSS (NR_030771)	25	NR_030771	627585	Mm.424988	NM_001039233		Gm13034	OTTMUSG00000010105	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5 pseudogene	pseudo
mm_49810.1	chr6	36389155	36389173	+	1	NA	promoter-TSS (NR_015589)	promoter-TSS (NR_015589)	-930	NR_015589	319472	Mm.226434	NR_015589	ENSMUSG00000073154	9330158H04Rik	-	RIKEN cDNA 9330158H04 gene	ncRNA
mm_28541.1	chr3	92825036	92825046	-	1	NA	exon (NM_028629, exon 2 of 2)	exon (NM_028629, exon 2 of 2)	2206	NM_028629	433619	Mm.28359	NM_028629	ENSMUSG00000059832	Kprp	1110001M24Rik|AA589586	keratinocyte expressed, proline-rich	protein-coding
mm_111850.1	chr12	107939060	107939074	-	1	NA	intron (NM_001286343, intron 1 of 1)	intron (NM_001286343, intron 1 of 1)	64347	NM_001079883	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_152832.1	chr19	23246641	23246655	-	1	NA	intron (NM_153808, intron 8 of 23)	L2|LINE|L2	25951	NM_001252685	226026	Mm.23267	NM_153808	ENSMUSG00000024943	Smc5	MLZ-453|SMC-5|Smc5l1|mKIAA0594|mSMC5	structural maintenance of chromosomes 5	protein-coding
mm_134164.1	chr16	10795943	10795951	-	1	NA	TTS (NM_013637)	TTS (NM_013637)	876	NM_013637	19118	Mm.42733	NM_013637	ENSMUSG00000022501	Prm1	Prm-1	protamine 1	protein-coding
mm_106949.1	chr12	8771449	8771464	+	1	NA	promoter-TSS (NM_011519)	promoter-TSS (NM_011519)	60	NM_011519	20969	Mm.2580	NM_011519	ENSMUSG00000020592	Sdc1	AA408134|AA409076|CD138|Sstn|Synd|Synd1|syn-1	syndecan 1	protein-coding
mm_79476.1	chr9	56950900	56950932	+	1	NA	promoter-TSS (NM_178374)	promoter-TSS (NM_178374)	-8	NM_178374	66069	Mm.220984	NM_178374	ENSMUSG00000055334	Snupn	0610031A09Rik|Rnut1|Snupn1	snurportin 1	protein-coding
mm_9352.1	chr1	172082679	172082720	-	1	NA	promoter-TSS (NM_021607)	promoter-TSS (NM_021607)	50	NM_021607	59287	Mm.218203	NM_021607	ENSMUSG00000003458	Ncstn	9430068N19Rik|AA727311|Aph2|D1Dau13e|Kiaa0253|Nct|mKIAA0253	nicastrin	protein-coding
mm_148112.1	chr18	74303983	74303987	-	1	NA	intron (NR_029424, intron 4 of 8)	intron (NR_029424, intron 4 of 8)	20885	NM_028948	74453	Mm.182293	NM_028948	ENSMUSG00000035394	Cfap53	4933415I03Rik|Ccdc11	cilia and flagella associated protein 53	protein-coding
mm_100871.1	chr11	5915107	5915113	-	1	NA	promoter-TSS (NM_001287386)	promoter-TSS (NM_001287386)	25	NM_001287386	103988	Mm.220358	NM_010292	ENSMUSG00000041798	Gck	GLK|Gk|Gls006|HK4|HKIV|HXKP|Hlb62|MODY2	glucokinase	protein-coding
mm_83187.1	chr9	41004563	41004573	-	1	NA	promoter-TSS (NM_019465)	promoter-TSS (NM_019465)	60	NM_001281954	54698	Mm.42791	NM_019465	ENSMUSG00000032021	Crtam	-	cytotoxic and regulatory T cell molecule	protein-coding
mm_21248.1	chr2	156177764	156177780	-	1	NA	intron (NM_133242, intron 2 of 16)	intron (NM_133242, intron 2 of 16)	1808	NM_001291115	170791	Mm.392436	NM_133242	ENSMUSG00000027620	Rbm39	1500012C14Rik|2310040E03Rik|B330012G18Rik|C79248|R75070|Rnpc2|caper	RNA binding motif protein 39	protein-coding
mm_143858.1	chr17	84185988	84186021	-	1	NA	exon (NM_001001806, exon 2 of 2)	exon (NM_001001806, exon 2 of 2)	1943	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_114976.1	chr13	97243941	97243976	+	1	NA	intron (NM_007930, intron 1 of 2)	intron (NM_007930, intron 1 of 2)	2853	NM_007930	13803	Mm.241073	NM_007930	ENSMUSG00000041773	Enc1	Nrpb|PIG10	ectodermal-neural cortex 1	protein-coding
mm_7119.1	chr1	90775676	90775686	-	1	NA	exon (NM_001243009, exon 37 of 41)	exon (NM_001243009, exon 37 of 41)	68290	NM_001243009	12835	Mm.7562	NM_009935	ENSMUSG00000048126	Col6a3	AI507288|Col6a-3	collagen, type VI, alpha 3	protein-coding
mm_106365.1	chr11	118393984	118394021	-	1	NA	exon (NM_011150, exon 6 of 6)	exon (NM_011150, exon 6 of 6)	7929	NM_011150	19039	Mm.3152	NM_011150	ENSMUSG00000033880	Lgals3bp	90K|CyCAP|MAC-2BP|Ppicap|Tango10b	lectin, galactoside-binding, soluble, 3 binding protein	protein-coding
mm_106690.1	chr12	3365219	3365229	+	1	NA	promoter-TSS (NM_008445)	promoter-TSS (NM_008445)	92	NM_008445	16570	Mm.7688	NM_008445	ENSMUSG00000020668	Kif3c	mKIAA4058	kinesin family member 3C	protein-coding
mm_103954.1	chr11	84069180	84069205	-	1	NA	promoter-TSS (NM_019819)	promoter-TSS (NM_019819)	-835	NM_019819	56405	Mm.240885	NM_019819	ENSMUSG00000018648	Dusp14	1110014C10Rik|2310042C07Rik|D11Ertd395e|MKP-L|Mkp6	dual specificity phosphatase 14	protein-coding
mm_97350.1	chr11	77493195	77493213	+	1	NA	promoter-TSS (NM_001004144)	promoter-TSS (NM_001004144)	-208	NM_001004144	216963	Mm.290182	NM_001004144	ENSMUSG00000011877	Git1	Cat-1|p95Cat	G protein-coupled receptor kinase-interactor 1	protein-coding
mm_54789.1	chr6	41558392	41558414	-	1	NA	Intergenic	Intergenic	36627	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_68933.1	chr7	126496461	126496493	-	1	NA	exon (NM_183020, exon 11 of 23)	exon (NM_183020, exon 11 of 23)	5948	NM_001347658	233871	Mm.231450	NM_183020	ENSMUSG00000032637	Atxn2l	A2D|A2LG|A2RP|A2lp|Atxnl2	ataxin 2-like	protein-coding
mm_115911.1	chr13	23465769	23465773	-	1	NA	intron (NM_013483, intron 1 of 7)	intron (NM_013483, intron 1 of 7)	130	NM_013483	12231	Mm.1420	NM_013483	ENSMUSG00000000706	Btn1a1	Btn	butyrophilin, subfamily 1, member A1	protein-coding
mm_5678.1	chr1	43160081	43160089	-	1	NA	intron (NM_001289533, intron 1 of 5)	intron (NM_001289533, intron 1 of 5)	3876	NM_010212	14200	Mm.6799	NM_010212	ENSMUSG00000008136	Fhl2	FHL-2|SLIM-3|SLIM3	four and a half LIM domains 2	protein-coding
mm_164445.1	chr16	49855768	49855806	+	1	NA	exon (NM_010581, exon 1 of 10)	exon (NM_010581, exon 1 of 10)	133	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_131429.1	chr16	15604481	15604488	+	1	NA	Intergenic	RMER17B|LTR|ERVK	-9966	NM_023585	70620	Mm.235407	NM_023585	ENSMUSG00000022674	Ube2v2	1110021H13Rik|4632410D19Rik|5730524P06Rik|6820402M05|AI848315|C81524|MMS2	ubiquitin-conjugating enzyme E2 variant 2	protein-coding
mm_72603.1	chr8	84415827	84415836	+	1	NA	exon (NM_001252060, exon 1 of 48)	exon (NM_001252060, exon 1 of 48)	467	NM_001252061	12286	Mm.334658	NM_007578	ENSMUSG00000034656	Cacna1a	APCA|BI|Caca1a|Cacnl1a4|Cav2.1|Ccha1a|EA2|FHM|HPCA|MHP|MHP1|SCA6|alpha1A|la|nmf352|rkr|smrl|tg	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	protein-coding
mm_135897.1	chr16	65562668	65562678	-	1	NA	promoter-TSS (NM_026879)	promoter-TSS (NM_026879)	24	NM_026879	68942	Mm.432944	NM_026879	ENSMUSG00000004843	Chmp2b	1190006E07Rik	charged multivesicular body protein 2B	protein-coding
mm_68155.1	chr7	102250528	102250548	-	1	NA	promoter-TSS (NM_019566)	promoter-TSS (NM_019566)	-420	NM_019566	56212	Mm.259795	NM_019566	ENSMUSG00000073982	Rhog	2810426G09Rik|Arhg|Sid10750	ras homolog family member G	protein-coding
mm_144214.1	chr18	9745233	9745244	+	1	NA	intron (NM_130449, intron 2 of 9)	L1_Mur2|LINE|L1	37590	NM_130449	140792	Mm.218571	NM_130449	ENSMUSG00000036103	Colec12	CL-P1|SRCL|Scara4	collectin sub-family member 12	protein-coding
mm_114338.1	chr13	60739933	60739946	+	1	NA	intron (NM_029653, intron 18 of 25)	intron (NM_029653, intron 18 of 25)	46425	NM_199148	218275	Mm.222427	NM_199148	ENSMUSG00000042243	BC051665	-	cDNA sequence BC051665	protein-coding
mm_16755.1	chr2	9868861	9868871	-	1	NA	exon (NM_008091, exon 4 of 6)	exon (NM_008091, exon 4 of 6)	9734	NM_008091	14462	Mm.313866	NM_008091	ENSMUSG00000015619	Gata3	Gata-3|jal	GATA binding protein 3	protein-coding
mm_148454.1	chr19	4000583	4000659	+	1	NA	promoter-TSS (NM_025529)	promoter-TSS (NM_025529)	41	NM_025529	66387	Mm.259222	NM_025529	ENSMUSG00000024869	Nudt8	2310039H17Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 8	protein-coding
mm_91605.1	chr10	41303172	41303250	-	1	NA	promoter-TSS (NM_133999)	promoter-TSS (NM_133999)	30	NM_133999	103199	Mm.277242	NM_133999	ENSMUSG00000038417	Fig4	A530089I17Rik|AI326867|Sac3	FIG4 phosphoinositide 5-phosphatase	protein-coding
mm_108162.1	chr12	76367344	76367354	+	1	NA	intron (NM_028356, intron 1 of 2)	intron (NM_028356, intron 1 of 2)	2115	NM_001172104	109929	Mm.41880	NM_028356	ENSMUSG00000056459	Zbtb25	2810462M08Rik|2900064P18Rik|AI842128|Kup|Zfp-50|Zfp50	zinc finger and BTB domain containing 25	protein-coding
mm_110563.1	chr12	55821074	55821084	-	1	NA	5' UTR (NM_019994, exon 1 of 41)	5' UTR (NM_019994, exon 1 of 41)	437	NM_019994	56784	Mm.292180	NM_019994	ENSMUSG00000021027	Ralgapa1	2310003F20Rik|4930400K19Rik|AI563624|GRIPE|Garnl1|Tulip1|mKIAA0884	Ral GTPase activating protein, alpha subunit 1	protein-coding
mm_27860.1	chr3	79158223	79158248	-	1	NA	Intergenic	L1_Mur3|LINE|L1	-12360	NM_001099624	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_110951.1	chr12	76709956	76709995	-	1	NA	5' UTR (NM_013675, exon 1 of 36)	5' UTR (NM_013675, exon 1 of 36)	572	NM_013675	20741	Mm.32881	NM_013675	ENSMUSG00000021061	Sptb	AI842465|D330027P03Rik|Gm1301|Spnb-1|Spnb1|ja|jaundiced|mKIAA4219	spectrin beta, erythrocytic	protein-coding
mm_21331.1	chr2	157101481	157101496	-	1	NA	intron (NM_001139520, intron 15 of 16)	intron (NM_001139520, intron 15 of 16)	14433	NM_001177439	383766	Mm.480305	NM_001177439	ENSMUSG00000074628	Tldc2	Gm1332	TBC/LysM associated domain containing 2	protein-coding
mm_69604.1	chr7	137125724	137125749	-	1	NA	intron (NM_008598, intron 4 of 4)	intron (NM_008598, intron 4 of 4)	-108947	NR_045885	100038555	Mm.444788	NR_045885	ENSMUSG00000109722	Gm10578	ENSMUSG00000073800	predicted gene 10578	ncRNA
mm_167149.1	chr7	131000080	131000085	+	1	NA	Intergenic	PB1D7|SINE|Alu	-31994	NM_001347632	12945	Mm.4138	NM_007769	ENSMUSG00000047517	Dmbt1	CRP|CRP-[a]|CRP-[b]|Crpd|DBMT1|gp300|p80	deleted in malignant brain tumors 1	protein-coding
mm_123150.1	chr14	57099877	57099901	-	1	NA	3' UTR (NM_008125, exon 2 of 2)	3' UTR (NM_008125, exon 2 of 2)	4813	NM_008125	14619	Mm.390683	NM_008125	ENSMUSG00000046352	Gjb2	AI325222|Cnx26|Cx26|Gjb-2	gap junction protein, beta 2	protein-coding
mm_145118.1	chr18	44337174	44337206	+	1	NA	exon (NM_001033621, exon 2 of 10)	exon (NM_001033621, exon 2 of 10)	3116	NM_001033621	58916	Mm.143804	NM_001033621	ENSMUSG00000024471	Myot	5530402I04Rik|Ttid	myotilin	protein-coding
mm_87737.1	chr10	60161663	60161669	+	1	NA	Intergenic	RMER17A2|LTR|ERVK	34890	NR_105871	102465546		NR_105871	ENSMUSG00000105468	Mir6906	mmu-mir-6906	microRNA 6906	ncRNA
mm_75540.1	chr8	57432785	57432791	-	1	NA	Intergenic	Intergenic	-23135	NM_009136	20284	Mm.12886	NM_009136	ENSMUSG00000031610	Scrg1	AW124307	scrapie responsive gene 1	protein-coding
mm_80582.1	chr9	84234152	84234154	+	1	NA	Intergenic	Intergenic	285372	NM_199195	12040	Mm.12819	NM_199195	ENSMUSG00000032263	Bckdhb	BCKDE1B|BCKDH E1-beta	branched chain ketoacid dehydrogenase E1, beta polypeptide	protein-coding
mm_151914.1	chr19	5799732	5799738	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	2937	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_104902.1	chr11	99628232	99628242	-	1	NA	promoter-TSS (NM_001048196)	promoter-TSS (NM_001048196)	2	NM_001048196	665891	Mm.394141	NM_001048196	ENSMUSG00000063251	Krtap4-1	A030010K20Rik	keratin associated protein 4-1	protein-coding
mm_107079.1	chr12	16966169	16966179	+	1	NA	intron (NM_009072, intron 20 of 32)	intron (NM_009072, intron 20 of 32)	33944	NM_172574	217430	Mm.379451	NM_172574	ENSMUSG00000045679	Pqlc3	C78076|E030024M05Rik	PQ loop repeat containing	protein-coding
mm_29543.1	chr3	116712461	116712510	-	1	NA	promoter-TSS (NM_144902)	promoter-TSS (NM_144902)	-205	NM_144902	229782	Mm.190758	NM_144902	ENSMUSG00000027957	Slc35a3	2310050P13Rik	solute carrier family 35 (UDP-N-acetylglucosamine (UDP-GlcNAc) transporter), member 3	protein-coding
mm_78327.1	chr9	25186729	25186739	+	1	NA	Intergenic	Intergenic	-34953	NM_020586	80517	Mm.142843	NM_020586	ENSMUSG00000008429	Herpud2	5031400M07Rik|AB041580	HERPUD family member 2	protein-coding
mm_146970.1	chr18	33463643	33463658	-	1	NA	promoter-TSS (NM_001267717)	promoter-TSS (NM_001267717)	-16	NM_053078	27528	Mm.407415	NM_053078	ENSMUSG00000042834	Nrep	AI325076|D0H4S114|Harp|P311|PTZ17|SEZ17	neuronal regeneration related protein	protein-coding
mm_109996.1	chr12	15815971	15816006	-	1	NA	5' UTR (NM_144551, exon 1 of 3)	5' UTR (NM_144551, exon 1 of 3)	797	NM_144551	217410	Mm.491136	NM_144551	ENSMUSG00000020601	Trib2	AW319517|TRB-2|TRB2	tribbles pseudokinase 2	protein-coding
mm_93128.1	chr10	92072099	92072104	-	1	NA	promoter-TSS (NR_029812)	promoter-TSS (NR_029812)	84	NR_029812	723955		NR_029812	ENSMUSG00000065524	Mir135a-2	Mirn135a-2|mir-135a-2	microRNA 135a-2	ncRNA
mm_115061.1	chr13	100731014	100731077	+	1	NA	promoter-TSS (NM_009874)	promoter-TSS (NM_009874)	-103	NM_009874	12572	Mm.259718	NM_009874	ENSMUSG00000069089	Cdk7	AI323415|AI528512|C230069N13|Cdkn7|Crk4	cyclin-dependent kinase 7	protein-coding
mm_109559.1	chr12	111794754	111794764	+	1	NA	3' UTR (NM_001025363, exon 14 of 14)	3' UTR (NM_001025363, exon 14 of 14)	19120	NM_028875	74335	Mm.19082	NM_028875	ENSMUSG00000021287	Xrcc3	-	X-ray repair complementing defective repair in Chinese hamster cells 3	protein-coding
mm_5173.1	chr1	10233048	10233093	-	1	NA	promoter-TSS (NM_001102430)	promoter-TSS (NM_001102430)	-400	NM_001102430	211673	Mm.229141	NM_001102430	ENSMUSG00000067851	Arfgef1	ARFGEP1|BIG1|D130059B05Rik|D730028O18Rik|P200	ADP-ribosylation factor guanine nucleotide-exchange factor 1(brefeldin A-inhibited)	protein-coding
mm_158313.1	chrX	126915317	126915324	-	1	NA	Intergenic	Intergenic	-81316	NM_177705	237029	Mm.60998	NM_177705	ENSMUSG00000058670	4932411N23Rik	-	RIKEN cDNA 4932411N23 gene	protein-coding
mm_86507.1	chr10	7590075	7590124	+	1	NA	exon (NM_172784, exon 1 of 7)	exon (NM_172784, exon 1 of 7)	299	NM_172784	237253	Mm.206759	NM_172784	ENSMUSG00000019796	Lrp11	1700034J19Rik|6330533B21|9830160H19Rik	low density lipoprotein receptor-related protein 11	protein-coding
mm_45300.1	chr5	65335598	65335679	-	1	NA	promoter-TSS (NM_011258)	promoter-TSS (NM_011258)	1	NM_011258	19687	Mm.148877	NM_011258	ENSMUSG00000029191	Rfc1	140kDa|Alp145|RFC140|Recc1	replication factor C (activator 1) 1	protein-coding
mm_172862.1	chr9	40803417	40803423	+	1	NA	exon (NM_031165, exon 5 of 9)	exon (NM_031165, exon 5 of 9)	2147	NM_031165	15481	Mm.290774	NM_031165	ENSMUSG00000015656	Hspa8	2410008N15Rik|Hsc70|Hsc71|Hsc73|Hsp73|Hspa10	heat shock protein 8	protein-coding
mm_16131.1	chr2	170316550	170316560	+	1	NA	Intergenic	Intergenic	-39806	NR_040610	73303	Mm.443297	NR_040610	ENSMUSG00000086999	Bcas1os2	1700040N02Rik	breast carcinoma amplified sequence 1, opposite strand 2	ncRNA
mm_48409.1	chr5	140261693	140261716	-	1	NA	intron (NM_010752, intron 9 of 17)	intron (NM_010752, intron 9 of 17)	59848	NM_010752	17120	Mm.27250	NM_010752	ENSMUSG00000029554	Mad1l1	AI173502|AW550425|Mad1	MAD1 mitotic arrest deficient 1-like 1	protein-coding
mm_103315.1	chr11	73138246	73138310	-	1	NA	promoter-TSS (NM_010353)	promoter-TSS (NM_010353)	16	NM_010353	14841	Mm.42045	NM_010353	ENSMUSG00000050107	Gsg2	Haspin	germ cell associated 2, haspin	protein-coding
mm_4999.1	chr1	191906808	191906823	+	1	NA	promoter-TSS (NM_009579)	promoter-TSS (NM_009579)	34	NM_009579	22782	Mm.9024	NM_009579	ENSMUSG00000037434	Slc30a1	AI839647|C130040I11Rik|Znt1	solute carrier family 30 (zinc transporter), member 1	protein-coding
mm_56507.1	chr6	99339421	99339455	-	1	NA	intron (NM_001347345, intron 2 of 19)	intron (NM_001347345, intron 2 of 19)	-72923	NM_001197321	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_110167.1	chr12	27335137	27335144	-	1	NA	3' UTR (NM_009234, exon 1 of 1)	3' UTR (NM_009234, exon 1 of 1)	7578	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding
mm_128639.1	chr15	59273297	59273300	-	1	NA	Intergenic	Intergenic	-33650	NR_045613	100416830	Mm.490788	NR_045613	ENSMUSG00000098528	Zfp572	4930472F24Rik	zinc finger protein 572	pseudo
mm_128482.1	chr15	50890015	50890026	-	1	NA	promoter-TSS (NR_035444)	promoter-TSS (NR_035444)	21	NM_032000	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_13941.1	chr2	121171205	121171279	+	1	NA	promoter-TSS (NR_110985)	promoter-TSS (NR_110985)	74	NM_001290824	51885	Mm.383499	NM_153387	ENSMUSG00000027263	Tubgcp4	4932441P04Rik|76p|D2Ertd435e|GCP-4	tubulin, gamma complex associated protein 4	protein-coding
mm_119164.1	chr14	32029014	32029044	+	1	NA	promoter-TSS (NM_030166)	promoter-TSS (NM_030166)	-74	NM_030166	78754	Mm.40681	NM_030166	ENSMUSG00000021903	Galnt15	4631401E18Rik|Galntl2|mpp-GalNAc-T15	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 15	protein-coding
mm_54044.1	chr6	13677891	13677895	-	1	NA	promoter-TSS (NM_175312)	promoter-TSS (NM_175312)	73	NM_175312	101148	Mm.354863	NM_175312	ENSMUSG00000042742	Bmt2	AI666701|B630005N14Rik	base methyltransferase of 25S rRNA 2	protein-coding
mm_146130.1	chr18	74625500	74625512	+	1	NA	intron (NM_201600, intron 5 of 38)	intron (NM_201600, intron 5 of 38)	-94382	NR_045368	73606	Mm.444734	NR_045368		1700120E14Rik	-	RIKEN cDNA 1700120E14 gene	ncRNA
mm_148238.1	chr18	80597553	80597560	-	1	NA	Intergenic	Intergenic	-53010	NR_028424	100039348	Mm.254722	NR_028424		Gm2176	A430076E10Rik	glucosamine-6-phosphate deaminase 1 pseudogene	pseudo
mm_17519.1	chr2	29252361	29252371	-	1	NA	intron (NR_029460, intron 1 of 1)	CpG	627	NR_029460	76220	Mm.330108	NR_029460	ENSMUSG00000079499	6530402F18Rik	mKIAA1857	RIKEN cDNA 6530402F18 gene	ncRNA
mm_103762.1	chr11	81153646	81153662	-	1	NA	promoter-TSS (NM_007384)	promoter-TSS (NM_007384)	-751	NM_007384	11418	Mm.234998	NM_007384	ENSMUSG00000020704	Asic2	ACIC2|Accn1|BNC1|BNaC1|BNaC1a|Mdeg	acid-sensing (proton-gated) ion channel 2	protein-coding
mm_12438.1	chr2	70690368	70690390	+	1	NA	intron (NR_027343, intron 10 of 10)	intron (NR_027343, intron 10 of 10)	28870	NM_027352	70231	Mm.271950	NM_027352	ENSMUSG00000014959	Gorasp2	0610011A07Rik|2410043M02Rik|5730520M13Rik|9430094F20Rik|AW552058|ENSMUSG00000075299|GOLPH2|GRASP55|GRS2|p59	golgi reassembly stacking protein 2	protein-coding
mm_39430.1	chr5	16553596	16553615	+	1	NA	promoter-TSS (NM_001289461)	promoter-TSS (NM_001289461)	110	NM_010427	15234	Mm.267078	NM_010427	ENSMUSG00000028864	Hgf	C230052L06Rik|HGF/SF|NK1|NK2|SF|SF/HGF	hepatocyte growth factor	protein-coding
mm_40210.1	chr5	37047403	37047418	+	1	NA	Intergenic	Intergenic	-3447	NM_178394	76071	Mm.85280	NM_178394	ENSMUSG00000063646	Jakmip1	5830437M04Rik|C330021K24Rik|Gababrbp|Marlin-1	janus kinase and microtubule interacting protein 1	protein-coding
mm_79000.1	chr9	45408269	45408310	+	1	NA	intron (NM_052823, intron 2 of 5)	intron (NM_052823, intron 2 of 5)	2212	NM_007503	11936	Mm.22742	NM_007503	ENSMUSG00000059412	Fxyd2	Atp1g1	FXYD domain-containing ion transport regulator 2	protein-coding
mm_135055.1	chr16	33796037	33796060	-	1	NA	intron (NM_010739, intron 2 of 12)	intron (NM_010739, intron 2 of 12)	2011	NM_010739	17063	Mm.3177	NM_010739	ENSMUSG00000022824	Muc13	114/A10|14/A10|AI159736|Lrrp|Ly64|NJ-1	mucin 13, epithelial transmembrane	protein-coding
mm_154126.1	chr19	57239311	57239323	-	1	NA	Intergenic	Intergenic	-23285	NM_178688	226251	Mm.217161	NM_178688	ENSMUSG00000025085	Ablim1	2210411C18Rik|2610209L21Rik|4833406P10Rik|9330196J19Rik|AV079770|AW060987|AW215784|Limab1|mKIAA0059	actin-binding LIM protein 1	protein-coding
mm_73103.1	chr8	94602013	94602029	+	1	NA	promoter-TSS (NM_028221)	promoter-TSS (NM_028221)	80	NM_026274	67610	Mm.109074	NM_026274	ENSMUSG00000050079	Rspry1	4930470D19Rik|AI608258	ring finger and SPRY domain containing 1	protein-coding
mm_107828.1	chr12	69184178	69184218	+	1	NA	promoter-TSS (NM_025589)	promoter-TSS (NM_025589)	40	NM_146035	217664	Mm.206642	NM_146035	ENSMUSG00000043998	Mgat2	AA407964|CDGS2|GLCNACTII|GNT-II|GNT2	mannoside acetylglucosaminyltransferase 2	protein-coding
mm_153957.1	chr19	47692029	47692033	-	1	NA	promoter-TSS (NM_007732)	promoter-TSS (NM_007732)	11	NM_007732	12821	Mm.1225	NM_007732	ENSMUSG00000025064	Col17a1	BP180|Bpag|Bpag2	collagen, type XVII, alpha 1	protein-coding
mm_6988.1	chr1	86357314	86357344	-	1	NA	exon (NM_010880, exon 3 of 14)	exon (NM_010880, exon 3 of 14)	-1002	NR_002851	80828		NR_002851	ENSMUSG00000064823	Snord82	Rnu82|U82|Z25	small nucleolar RNA, C/D box 82	snoRNA
mm_90342.1	chr10	127129582	127129603	+	1	NA	Intergenic	B3|SINE|B2	-8432	NM_001171026	216440	Mm.295246	NM_177614	ENSMUSG00000040462	Os9	4632413K17Rik|AU022351	amplified in osteosarcoma	protein-coding
mm_137281.1	chr17	24728245	24728247	+	1	NA	intron (NM_001163945, intron 1 of 9)	intron (NM_001163945, intron 1 of 9)	417	NM_001163945	66211	Mm.46198	NM_025425	ENSMUSG00000002500	Rpl3l	1110057H16Rik	ribosomal protein L3-like	protein-coding
mm_81968.1	chr9	120959833	120959858	+	1	NA	3' UTR (NM_007614, exon 15 of 15)	3' UTR (NM_007614, exon 15 of 15)	4759	NR_106058	102465661		NR_106058	ENSMUSG00000106193	Mir7090	mmu-mir-7090	microRNA 7090	ncRNA
mm_55049.1	chr6	49042879	49042891	-	1	NA	exon (NM_053110, exon 2 of 11)	exon (NM_053110, exon 2 of 11)	6367	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_170544.1	chr19	40119822	40119839	+	1	NA	Intergenic	Lx2|LINE|L1	30151	NM_001167875	107141	Mm.474575	NM_134144	ENSMUSG00000054827	Cyp2c50	AI266900	cytochrome P450, family 2, subfamily c, polypeptide 50	protein-coding
mm_128424.1	chr15	46496163	46496187	-	1	NA	promoter-TSS (NR_040451)	promoter-TSS (NR_040451)	4	NR_040451	74726	Mm.78172	NR_040451		4930523O13Rik	4921524H24Rik	RIKEN cDNA 4930523O13 gene	ncRNA
mm_64536.1	chr7	144175629	144175646	+	1	NA	5' UTR (NM_001113373, exon 1 of 16)	5' UTR (NM_001113373, exon 1 of 16)	117	NM_001113373	210274	Mm.483624	NM_001081370	ENSMUSG00000037541	Shank2	ProSAP1|mKIAA1022	SH3/ankyrin domain gene 2	protein-coding
mm_65963.1	chr7	30435282	30435310	-	1	NA	exon (NM_007467, exon 17 of 17)	exon (NM_007467, exon 17 of 17)	10286	NM_007467	11803	Mm.2381	NM_007467	ENSMUSG00000006651	Aplp1	-	amyloid beta (A4) precursor-like protein 1	protein-coding
mm_31488.1	chr4	52814595	52814629	+	1	NA	promoter-TSS (NR_040661)	promoter-TSS (NR_040661)	8	NR_040661	75367	Mm.159510	NR_040661	ENSMUSG00000070984	4930552N02Rik	-	RIKEN cDNA 4930552N02 gene	ncRNA
mm_160462.1	chr8	109705910	109705910	+	1	NA	promoter-TSS (NM_029468)	promoter-TSS (NM_029468)	-109	NM_029468	75871	Mm.180410	NM_029468	ENSMUSG00000031728	Zfp821	4930566A11Rik|Znf821	zinc finger protein 821	protein-coding
mm_161239.1	chr13	96088871	96088871	-	1	NA	5' UTR (NM_029210, exon 2 of 13)	5' UTR (NM_029210, exon 2 of 13)	43706	NM_029210	75209	Mm.40436	NM_029210	ENSMUSG00000051111	Sv2c	4930527L09Rik|AI841971	synaptic vesicle glycoprotein 2c	protein-coding
mm_123808.1	chr14	70522210	70522254	-	1	NA	exon (NM_011359, exon 3 of 6)	exon (NM_011359, exon 3 of 6)	1849	NM_011359	20389	Mm.24040	NM_011359	ENSMUSG00000022097	Sftpc	Bricd6|SP-C|SP5|SPC|Sftp-2|Sftp2|pro-SpC	surfactant associated protein C	protein-coding
mm_7761.1	chr1	131138233	131138261	-	1	NA	promoter-TSS (NM_145508)	promoter-TSS (NM_145508)	-13	NM_145508	226419	Mm.39299	NM_145508	ENSMUSG00000016526	Dyrk3	BC006704	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 3	protein-coding
mm_121778.1	chr14	19890494	19890504	-	1	NA	intron (NM_001038637, intron 4 of 4)	RSINE1|SINE|B4	51574	NR_105025	52512	Mm.483998	NR_105025		D14Ertd670e	-	DNA segment, Chr 14, ERATO Doi 670, expressed	ncRNA
mm_7019.1	chr1	86582777	86582790	-	1	NA	promoter-TSS (NM_008801)	promoter-TSS (NM_008801)	-282	NM_008801	18582	Mm.12925	NM_008801	ENSMUSG00000026239	Pde6d	AI841218|PrBP/delta	phosphodiesterase 6D, cGMP-specific, rod, delta	protein-coding
mm_30786.1	chr4	19575495	19575505	+	1	NA	intron (NM_025476, intron 1 of 9)	intron (NM_025476, intron 1 of 9)	434	NM_025476	66302	Mm.440686	NM_025476	ENSMUSG00000028229	Rmdn1	Fam82b|RMD-1	regulator of microtubule dynamics 1	protein-coding
mm_107897.1	chr12	70672430	70672444	+	1	NA	Intergenic	Intergenic	-153077	NM_028127	319710	Mm.2962	NM_028127	ENSMUSG00000048285	Frmd6	2610019M19Rik|4930488L10Rik|AW212977|Willin	FERM domain containing 6	protein-coding
mm_93213.1	chr10	94944866	94944891	-	1	NA	promoter-TSS (NM_018797)	promoter-TSS (NM_018797)	-300	NM_018797	54712	Mm.256712	NM_018797	ENSMUSG00000074785	Plxnc1	2510048K12Rik|AW742158|CD232|Vespr	plexin C1	protein-coding
mm_82657.1	chr9	22076403	22076428	-	1	NA	exon (NM_012029, exon 4 of 9)	exon (NM_012029, exon 4 of 9)	-5039	NM_001310759	319601	Mm.347707	NM_177318	ENSMUSG00000038895	Zfp653	E430039K05Rik|Znf653	zinc finger protein 653	protein-coding
mm_87307.1	chr10	42678952	42678975	+	1	NA	promoter-TSS (NM_172416)	promoter-TSS (NM_172416)	47	NM_172416	14628	Mm.46636	NM_172416	ENSMUSG00000038280	Ostm1	1200002H13Rik|HSPC019|gl	osteopetrosis associated transmembrane protein 1	protein-coding
mm_114458.1	chr13	67194497	67194517	+	1	NA	promoter-TSS (NM_001048204)	promoter-TSS (NM_001048204)	1	NM_001048204	218311	Mm.82396	NM_183156	ENSMUSG00000051037	Zfp455	3732412P20Rik|Rslcan-10	zinc finger protein 455	protein-coding
mm_81280.1	chr9	108296854	108296871	+	1	NA	promoter-TSS (NM_001013814)	promoter-TSS (NM_001013814)	-60	NM_001013814	434437	Mm.390225	NM_001013814	ENSMUSG00000032607	Amt	EG434437	aminomethyltransferase	protein-coding
mm_22332.1	chr2	180702048	180702115	-	1	NA	promoter-TSS (NM_011805)	promoter-TSS (NM_011805)	21	NM_011805	23856	Mm.253836	NM_011805	ENSMUSG00000038914	Dido1	6720461J16Rik|D130048F08Rik|DATF-1|DIO-1|Datf1|dido	death inducer-obliterator 1	protein-coding
mm_77361.1	chr8	119693780	119693795	-	1	NA	Intergenic	L1MC4|LINE|L1	-6222	NM_026922	69047	Mm.46251	NM_026922	ENSMUSG00000034112	Atp2c2	1810010G06Rik|Spca2|mKIAA0703	ATPase, Ca++ transporting, type 2C, member 2	protein-coding
mm_48252.1	chr5	137787643	137787661	-	1	NA	promoter-TSS (NM_001005426)	promoter-TSS (NM_001005426)	-150	NM_001005426	381678	Mm.332765	NM_001005426	ENSMUSG00000037108	Zcwpw1	Gm1053	zinc finger, CW type with PWWP domain 1	protein-coding
mm_173164.1	chrX	4136328	4136328	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-60248	NM_001085543	627264	Mm.457960	NM_001085543	ENSMUSG00000094307	Btbd35f28	Gm14347|OTTMUSG00000016407	BTB domain containing 35, family member 28	protein-coding
mm_44970.1	chr5	36796723	36796744	-	1	NA	promoter-TSS (NM_026242)	promoter-TSS (NM_026242)	21	NM_026242	67568	Mm.332336	NM_026242	ENSMUSG00000055302	Mrfap1	9130413I22Rik|AL022827|Pam14	Morf4 family associated protein 1	protein-coding
mm_166302.1	chr5	104571391	104571391	+	1	NA	promoter-TSS (NM_001346671)	promoter-TSS (NM_001346671)	-281	NM_001346672	69623	Mm.69919	NM_027142		Zfp33b	2310012P17Rik	zinc finger protein 33B	protein-coding
mm_40895.1	chr5	75153582	75153609	+	1	NA	5' UTR (NM_001347719, exon 1 of 16)	5' UTR (NM_001347719, exon 1 of 16)	659	NM_001347719	18595	Mm.221403	NM_011058	ENSMUSG00000029231	Pdgfra	AI115593|CD140a|Pdgfr-2	platelet derived growth factor receptor, alpha polypeptide	protein-coding
mm_169024.1	chr13	113718560	113718582	+	1	NA	Intergenic	ERVB7_1-LTR_MM|LTR|ERVK	-54895	NM_019960	56534	Mm.41410	NM_019960	ENSMUSG00000051456	Hspb3	2310035K17Rik|AI844863|Hsbp3|spb3	heat shock protein 3	protein-coding
mm_43282.1	chr5	133073309	133073311	+	1	NA	Intergenic	Intergenic	-530967	NM_177047	319974	Mm.409595	NM_177047	ENSMUSG00000029673	Auts2	2700063G02Rik|A730011F23Rik|D830032G16Rik	autism susceptibility candidate 2	protein-coding
mm_148166.1	chr18	77778535	77778572	-	1	NA	exon (NM_007505, exon 4 of 12)	exon (NM_007505, exon 4 of 12)	4785	NM_007505	11946	Mm.276137	NM_007505	ENSMUSG00000025428	Atp5a1	AI035633|AL022851|AL023067|Atpm|D18Ertd206e|Mom2	ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1	protein-coding
mm_136881.1	chr17	13008201	13008211	+	1	NA	exon (NM_013671, exon 2 of 5)	exon (NM_013671, exon 2 of 5)	367	NM_013671	20656	Mm.290876	NM_013671	ENSMUSG00000006818	Sod2	MnSOD|Sod-2	superoxide dismutase 2, mitochondrial	protein-coding
mm_3334.1	chr1	137948686	137948690	+	1	NA	Intergenic	Intergenic	-17767	NR_029795	735252		NR_029795	ENSMUSG00000065565	Mir181a-1	Mirn181a-1|Mirn213|miR-213|mir-181a-1|mmu-mir-213	microRNA 181a-1	ncRNA
mm_144912.1	chr18	37473515	37473532	+	1	NA	promoter-TSS (NM_053140)	promoter-TSS (NM_053140)	-23	NM_053140	93886	Mm.283857	NM_053140	ENSMUSG00000047033	Pcdhb15	Pcdhb7|PcdhbO	protocadherin beta 15	protein-coding
mm_16324.1	chr2	174304756	174304758	+	1	NA	intron (NM_001310085, intron 2 of 12)	(CA)n|Simple_repeat|Simple_repeat	6898	NM_001310085	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_46805.1	chr5	113077123	113077131	-	1	NA	intron (NM_001159650, intron 5 of 5)	GA-rich|Low_complexity|Low_complexity	4457	NM_001159650	12962	Mm.378899	NM_021352	ENSMUSG00000029352	Crybb3	AI852419	crystallin, beta B3	protein-coding
mm_142540.1	chr17	46555461	46555484	-	1	NA	exon (NM_020493, exon 1 of 7)	exon (NM_020493, exon 1 of 7)	690	NM_020493	20807	Mm.45044	NM_020493	ENSMUSG00000015605	Srf	AW049942|AW240594	serum response factor	protein-coding
mm_10770.1	chr2	24215469	24215474	+	1	NA	promoter-TSS (NM_019450)	promoter-TSS (NM_019450)	54	NM_019450	54448	Mm.133095	NM_019450	ENSMUSG00000026984	Il1f6	Fil1|IL-1H1|IL1RP2|Il1f9|Il36a	interleukin 1 family, member 6	protein-coding
mm_109635.1	chr12	112768484	112768503	+	1	NA	exon (NM_178911, exon 11 of 11)	exon (NM_178911, exon 11 of 11)	7838	NM_178911	104759	Mm.203915	NM_178911	ENSMUSG00000052160	Pld4	AI132321|thss	phospholipase D family, member 4	protein-coding
mm_16723.1	chr2	7395880	7395912	-	1	NA	5' UTR (NM_001110232, exon 1 of 16)	5' UTR (NM_001110232, exon 1 of 16)	104	NM_001110232	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_101681.1	chr11	40684964	40684967	-	1	NA	intron (NM_134017, intron 3 of 6)	intron (NM_134017, intron 3 of 6)	7717	NM_134017	108645	Mm.293771	NM_134017	ENSMUSG00000042032	Mat2b	1110064C04Rik|2410018D16Rik|AI182287|AU022853|MAT-II|MATIIbeta|TGR	methionine adenosyltransferase II, beta	protein-coding
mm_144436.1	chr18	21093293	21093326	+	1	NA	exon (NM_008586, exon 11 of 15)	exon (NM_008586, exon 11 of 15)	20965	NM_008586	17288	Mm.2682	NM_008586	ENSMUSG00000024313	Mep1b	Mep-1b	meprin 1 beta	protein-coding
mm_158225.1	chrX	106143064	106143069	-	1	NA	promoter-TSS (NM_205820)	promoter-TSS (NM_205820)	-209	NM_205820	279572	Mm.336203	NM_205820	ENSMUSG00000033777	Tlr13	AI666735|Gm713	toll-like receptor 13	protein-coding
mm_89587.1	chr10	95782653	95782682	+	1	NA	Intergenic	ORR1A1|LTR|ERVL-MaLR	-157996	NM_001001932	216238	Mm.210035	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding
mm_11866.1	chr2	48949546	48949556	+	1	NA	promoter-TSS (NM_001177313)	promoter-TSS (NM_001177313)	43	NM_029924	109241	Mm.440436	NM_029924	ENSMUSG00000036792	Mbd5	9430004D19Rik|AA536666|AI426407|C030040A15Rik|Gm1630|OTTMUSG00000012483	methyl-CpG binding domain protein 5	protein-coding
mm_69671.1	chr7	139983949	139983972	-	1	NA	exon (NM_001291066, exon 20 of 24)	exon (NM_001291066, exon 20 of 24)	2914	NR_106029	102465643		NR_106029	ENSMUSG00000099092	Mir7062	Gm27339|mmu-mir-7062	microRNA 7062	ncRNA
mm_134533.1	chr16	19260876	19260889	-	1	NA	Intergenic	Intergenic	25859	NM_146451	258443	Mm.377506	NM_146451	ENSMUSG00000050742	Olfr164	MOR279-2	olfactory receptor 164	protein-coding
mm_61976.1	chr7	90615079	90615092	+	1	NA	Intergenic	Intergenic	-139090	NM_026734	68472	Mm.289791	NM_026734	ENSMUSG00000030614	Tmem126b	1110001A23Rik	transmembrane protein 126B	protein-coding
mm_118260.1	chr13	112447324	112447332	-	1	NA	Intergenic	Intergenic	-16742	NM_010560	16195	Mm.4364	NM_010560	ENSMUSG00000021756	Il6st	5133400A03Rik|AA389424|BB405851|CD130|D13Ertd699e|gp130	interleukin 6 signal transducer	protein-coding
mm_136426.1	chr16	94246068	94246082	-	1	NA	intron (NM_139145, intron 4 of 9)	ORR1D2|LTR|ERVL-MaLR	41781	NM_139145	110948	Mm.30921	NM_139145	ENSMUSG00000040820	Hlcs	410I21.SP6|D16Jhu34	holocarboxylase synthetase (biotin- [propriony-Coenzyme A-carboxylase (ATP-hydrolysing)] ligase)	protein-coding
mm_88085.1	chr10	68210223	68210225	+	1	NA	intron (NM_023598, intron 3 of 9)	intron (NM_023598, intron 3 of 9)	68502	NM_023598	71371	Mm.440357	NM_023598	ENSMUSG00000019947	Arid5b	4930580B11|5430435G07Rik|AI467247|Desrt|Mrf2|Mrf2alpha|Mrf2beta	AT rich interactive domain 5B (MRF1-like)	protein-coding
mm_132738.1	chr16	43889897	43889930	+	1	NA	promoter-TSS (NM_029128)	promoter-TSS (NM_029128)	11	NM_027801	212153	Mm.209835	NM_027801	ENSMUSG00000022701	Ccdc191	2610015P09Rik|8430422M09Rik|AU040712	coiled-coil domain containing 191	protein-coding
mm_5615.1	chr1	39720961	39720975	-	1	NA	promoter-TSS (NM_001145660)	promoter-TSS (NM_001145660)	21	NM_001145660	619289	Mm.334107	NM_001145660	ENSMUSG00000057173	Rfx8	4933400N17Rik	regulatory factor X 8	protein-coding
mm_19260.1	chr2	84799278	84799291	-	1	NA	intron (NM_019949, intron 1 of 3)	intron (NM_019949, intron 1 of 3)	456	NM_019949	56791	Mm.38261	NM_019949	ENSMUSG00000027078	Ube2l6	2810489I21Rik|RIG-B|UBCH8|Ubce8|Ubcm8	ubiquitin-conjugating enzyme E2L 6	protein-coding
mm_166561.1	chr6	46213953	46213955	+	1	NA	intron (NM_001004357, intron 9 of 23)	intron (NM_001004357, intron 9 of 23)	-1030442	NM_025771	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding
mm_96265.1	chr11	62648812	62648828	+	1	NA	promoter-TSS (NM_198861)	promoter-TSS (NM_198861)	156	NM_175002	216829	Mm.295306	NM_175002	ENSMUSG00000048497	Mmgt2	AI852046	membrane magnesium transporter 2	protein-coding
mm_107335.1	chr12	32378765	32378814	+	1	NA	promoter-TSS (NM_001162903)	promoter-TSS (NM_001162903)	0	NM_001162903	72123	Mm.341352	NM_028111	ENSMUSG00000090946	Ccdc71l	2010109K11Rik|AV375874	coiled-coil domain containing 71 like	protein-coding
mm_77569.1	chr8	123432280	123432289	-	1	NA	Intergenic	MuLV-int|LTR|ERV1	-10672	NM_001253784	23854	Mm.275127	NM_054046	ENSMUSG00000001482	Def8	AI449518|D8Ertd713e|DEF-8	differentially expressed in FDCP 8	protein-coding
mm_159143.1	chr2	86356302	86356302	-	1	NA	exon (NM_147018, exon 1 of 1)	exon (NM_147018, exon 1 of 1)	135	NM_147018	259020	Mm.377792	NM_147018	ENSMUSG00000075188	Olfr1056	MOR186-2	olfactory receptor 1056	protein-coding
mm_138542.1	chr17	35263064	35263074	+	1	NA	promoter-TSS (NM_001267808)	promoter-TSS (NM_001267808)	-25	NM_010380	14964	Mm.439675	NM_010380	ENSMUSG00000073411	H2-D1	H-2D|H2-D	histocompatibility 2, D region locus 1	protein-coding
mm_2704.1	chr1	127978432	127978447	+	1	NA	intron (NM_027678, intron 12 of 20)	intron (NM_027678, intron 12 of 20)	109666	NM_178690	226407	Mm.489713	NM_178690	ENSMUSG00000036104	Rab3gap1	1700003B17Rik|4732493F09Rik|AL117896|Rab3gap|p130	RAB3 GTPase activating protein subunit 1	protein-coding
mm_107248.1	chr12	27336214	27336223	+	1	NA	3' UTR (NM_009234, exon 1 of 1)	3' UTR (NM_009234, exon 1 of 1)	6500	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding
mm_82788.1	chr9	28996393	28996397	-	1	NA	3' UTR (NM_172290, exon 8 of 8)	3' UTR (NM_172290, exon 8 of 8)	966734	NM_172290	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding
mm_50716.1	chr6	52201199	52201244	+	1	NA	promoter-TSS (NR_015611)	promoter-TSS (NR_015611)	97	NR_015611	72628	Mm.348030	NR_015611	ENSMUSG00000085696	Hoxaas3	2700086A05Rik	Hoxa cluster antisense RNA 3	ncRNA
mm_11178.1	chr2	28702668	28702698	+	1	NA	intron (NM_001033874, intron 1 of 12)	intron (NM_001033874, intron 1 of 12)	2522	NM_001033874	68870	Mm.273318	NM_001033874	ENSMUSG00000026807	Ak8	1190002A17Rik|AK 8	adenylate kinase 8	protein-coding
mm_141756.1	chr17	34263092	34263111	-	1	NA	promoter-TSS (NM_207105)	promoter-TSS (NM_207105)	-126	NM_207105	14961	Mm.254067	NM_207105	ENSMUSG00000073421	H2-Ab1	AI845868|Abeta|H-2Ab|H2-Ab|I-Abeta|IAb|Ia-2|Ia2|Rmcs1	histocompatibility 2, class II antigen A, beta 1	protein-coding
mm_74079.1	chr8	122476153	122476194	+	1	NA	promoter-TSS (NM_153775)	promoter-TSS (NM_153775)	30	NM_153775	66965	Mm.482288	NM_153775	ENSMUSG00000049482	Ctu2	2310061F22Rik|C16orf84|Ncs2	cytosolic thiouridylase subunit 2	protein-coding
mm_136744.1	chr17	8356219	8356231	+	1	NA	Intergenic	Intergenic	15486	NM_178774	320111	Mm.442510	NM_178774	ENSMUSG00000055945	Prr18	9630019K15Rik	proline rich 18	protein-coding
mm_31592.1	chr4	57854739	57854754	+	1	NA	exon (NM_001035533, exon 1 of 4)	exon (NM_001035533, exon 1 of 4)	184	NM_001035533	11641	Mm.467752	NM_009649	ENSMUSG00000038729	Akap2	AA959716|AI649048|Akap-2|Akap-kl|B230340M18Rik|Prka2	A kinase (PRKA) anchor protein 2	protein-coding
mm_55697.1	chr6	72899287	72899303	-	1	NA	promoter-TSS (NM_001347231)	promoter-TSS (NM_001347231)	-3	NM_001347231	74287	Mm.29194	NM_019715	ENSMUSG00000055239	Kcmf1	1700094M07Rik|Debt91|Pmcf	potassium channel modulatory factor 1	protein-coding
mm_120006.1	chr14	55650202	55650226	+	1	NA	promoter-TSS (NM_001253889)	promoter-TSS (NM_001253889)	30	NM_001253889	71099	Mm.171300	NM_027673	ENSMUSG00000007591	Tssk4	1700020B19Rik|4933424F08Rik|TSK-4|TSSK-4	testis-specific serine kinase 4	protein-coding
mm_38792.1	chr4	148130652	148130672	-	1	NA	promoter-TSS (NM_027426)	promoter-TSS (NM_027426)	36	NM_027426	70433	Mm.275288	NM_027426	ENSMUSG00000029005	Draxin	2610109H07Rik|neucrin	dorsal inhibitory axon guidance protein	protein-coding
mm_94660.1	chr11	17159437	17159456	+	1	NA	5' UTR (NM_024459, exon 1 of 6)	5' UTR (NM_024459, exon 1 of 6)	148	NM_024459	19058	Mm.41840	NM_024459	ENSMUSG00000033953	Ppp3r1	CaNB1|Cnb1|MCIP1	protein phosphatase 3, regulatory subunit B, alpha isoform (calcineurin B, type I)	protein-coding
mm_61446.1	chr7	75575605	75575631	+	1	NA	intron (NM_029332, intron 3 of 36)	intron (NM_029332, intron 3 of 36)	120084	NM_029332	75547	Mm.216107	NM_029332	ENSMUSG00000066406	Akap13	1700026G02Rik|5730522G15Rik|5830460E08Rik|AKAP-13|AKAP-Lbc|BRX|Ht31|LBC|PROTO-LB|PROTO-LBC	A kinase (PRKA) anchor protein 13	protein-coding
mm_120697.1	chr14	70890437	70890467	+	1	NA	5' UTR (NM_008115, exon 1 of 9)	5' UTR (NM_008115, exon 1 of 9)	345	NM_001302094	14586	Mm.32619	NM_008115	ENSMUSG00000022103	Gfra2	-	glial cell line derived neurotrophic factor family receptor alpha 2	protein-coding
mm_115103.1	chr13	103332543	103332550	+	1	NA	intron (NM_175171, intron 1 of 28)	intron (NM_175171, intron 1 of 28)	1946	NM_175171	328329	Mm.202606	NM_175171	ENSMUSG00000034751	Mast4	4930420O11Rik|AI642422|mKIAA0303	microtubule associated serine/threonine kinase family member 4	protein-coding
mm_53273.1	chr6	128487423	128487437	+	1	NA	exon (NM_007376, exon 31 of 36)	exon (NM_007376, exon 31 of 36)	39290	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_164350.1	chr16	19968177	19968181	-	1	NA	intron (NM_183390, intron 1 of 6)	B1F2|SINE|Alu	14870	NM_183390	239743	Mm.86699	NM_183390	ENSMUSG00000043008	Klhl6	-	kelch-like 6	protein-coding
mm_68237.1	chr7	105395782	105395801	-	1	NA	intron (NM_001242363, intron 1 of 12)	intron (NM_001242363, intron 1 of 12)	4263	NM_001242364	74349	Mm.30254	NM_199009	ENSMUSG00000044465	Fam160a2	4632419K20Rik|6530415H11Rik|FHIP	family with sequence similarity 160, member A2	protein-coding
mm_132717.1	chr16	43508662	43508665	+	1	NA	intron (NM_181058, intron 3 of 6)	intron (NM_181058, intron 3 of 6)	-88467	NR_046026	626693	Mm.447083	NR_046026	ENSMUSG00000085499	Gm15713	OTTMUSG00000025617	predicted gene 15713	ncRNA
mm_75342.1	chr8	43306992	43307009	-	1	NA	promoter-TSS (NM_009556)	promoter-TSS (NM_009556)	9	NM_009556	22702	Mm.285848	NM_009556	ENSMUSG00000051176	Zfp42	Rex-1|Rex1|Zfp-42	zinc finger protein 42	protein-coding
mm_156586.1	chrX	152144241	152144251	+	1	NA	promoter-TSS (NM_001114664)	promoter-TSS (NM_001114664)	-22	NM_001114664	245666	Mm.33027	NM_001005475	ENSMUSG00000041115	Iqsec2	Brag1	IQ motif and Sec7 domain 2	protein-coding
mm_150996.1	chr19	46623388	46623451	+	1	NA	promoter-TSS (NM_001177813)	promoter-TSS (NM_001177813)	18	NM_001177813	226178	Mm.329895	NM_146099	ENSMUSG00000047731	Wbp1l	D19Wsu162e|Opal1	WW domain binding protein 1 like	protein-coding
mm_76810.1	chr8	104441609	104441609	-	1	NA	intron (NM_001013380, intron 2 of 12)	intron (NM_001013380, intron 2 of 12)	1438	NM_001013380	234663	Mm.289583	NM_001013380	ENSMUSG00000035770	Dync1li2	AA409702|C920003I06|Dncli2|Dnclic2|LIC2	dynein, cytoplasmic 1 light intermediate chain 2	protein-coding
mm_12002.1	chr2	57238464	57238482	+	1	NA	promoter-TSS (NM_010274)	promoter-TSS (NM_010274)	91	NM_010274	14571	Mm.3711	NM_010274	ENSMUSG00000026827	Gpd2	AA408484|AI448216|AU021455|AW494132|GPDH|Gdm1|Gpd-m|Gpdh-m|TISP38	glycerol phosphate dehydrogenase 2, mitochondrial	protein-coding
mm_102076.1	chr11	52271454	52271471	-	1	NA	intron (NM_001313981, intron 3 of 10)	B2_Mm2|SINE|B2	11133	NM_009331	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_89844.1	chr10	106879872	106879901	+	1	NA	intron (NM_001205341, intron 21 of 31)	intron (NM_001205341, intron 21 of 31)	243778	NM_001142804	380660	Mm.336072	NM_198636	ENSMUSG00000035948	Acss3	8430416H19Rik|Gm874	acyl-CoA synthetase short-chain family member 3	protein-coding
mm_164806.1	chr18	29733687	29733691	+	1	NA	Intergenic	Intergenic	-237273	NR_045391	78058	Mm.416952	NR_045391		4930578E11Rik	-	RIKEN cDNA 4930578E11 gene	ncRNA
mm_161924.1	chr18	75521765	75521765	-	1	NA	exon (NM_201354, exon 8 of 12)	exon (NM_201354, exon 8 of 12)	7120	NR_045879	100038353	Mm.440724	NR_045879	ENSMUSG00000097712	Gm10532	ENSMUSG00000073534	predicted gene 10532	ncRNA
mm_98862.1	chr11	97726806	97726825	+	1	NA	exon (NM_054051, exon 4 of 10)	exon (NM_054051, exon 4 of 10)	17889	NM_054051	108083	Mm.39700	NM_054051	ENSMUSG00000018547	Pip4k2b	AI848124|PI5P4Kbeta|Pip5k2b|c11	phosphatidylinositol-5-phosphate 4-kinase, type II, beta	protein-coding
mm_47430.1	chr5	123174433	123174460	-	1	NA	exon (NM_008277, exon 12 of 14)	exon (NM_008277, exon 12 of 14)	8240	NM_008277	15445	Mm.439709	NM_008277	ENSMUSG00000029445	Hpd	Fla|Flp|Hppd|Laf	4-hydroxyphenylpyruvic acid dioxygenase	protein-coding
mm_105173.1	chr11	101784609	101784637	-	1	NA	5' UTR (NM_001316366, exon 2 of 13)	5' UTR (NM_001316366, exon 2 of 13)	687	NM_008815	18612	Mm.5025	NM_008815	ENSMUSG00000017724	Etv4	AW414408|Pea-3|Pea3	ets variant 4	protein-coding
mm_142465.1	chr17	45601836	45601844	-	1	NA	promoter-TSS (NM_001177470)	promoter-TSS (NM_001177470)	75	NM_001177470	653016	Mm.45676	NM_001177468	ENSMUSG00000079471	Gm7325	EG653016|Esgp	predicted gene 7325	protein-coding
mm_28370.1	chr3	89904508	89904518	-	1	NA	intron (NM_001310676, intron 1 of 9)	B3A|SINE|B2	8683	NM_001310676	16194	Mm.2856	NM_010559	ENSMUSG00000027947	Il6ra	CD126|IL-6R|IL-6R-alpha|IL-6RA|Il6r	interleukin 6 receptor, alpha	protein-coding
mm_133793.1	chr16	95258373	95258397	+	1	NA	non-coding (NR_073406, exon 2 of 6)	non-coding (NR_073406, exon 2 of 6)	827	NM_001271690	16516	Mm.272239	NM_019664	ENSMUSG00000062609	Kcnj15	4930414N08Rik|AI182284|AI267127|IRKK|Kir4.2	potassium inwardly-rectifying channel, subfamily J, member 15	protein-coding
mm_40132.1	chr5	35042422	35042435	+	1	NA	exon (NM_019447, exon 2 of 14)	exon (NM_019447, exon 2 of 14)	919	NM_019447	54426	Mm.27369	NM_019447	ENSMUSG00000029102	Hgfac	HGFA	hepatocyte growth factor activator	protein-coding
mm_122535.1	chr14	47385794	47385798	-	1	NA	3' UTR (NM_010705, exon 6 of 6)	3' UTR (NM_010705, exon 6 of 6)	11936	NM_001145953	16854	Mm.248615	NM_010705	ENSMUSG00000050335	Lgals3	GBP|L-34|Mac-2|gal3	lectin, galactose binding, soluble 3	protein-coding
mm_34896.1	chr4	155625198	155625216	+	1	NA	promoter-TSS (NR_040441)	promoter-TSS (NR_040441)	338	NM_007661	12537	Mm.267410	NM_007661	ENSMUSG00000029062	Cdk11b	AA989746|CDK11-p110|CDK11-p46|CDK11-p58|Cdc11b|Cdc2l1|Cdc2l2|Cdk11|p58	cyclin-dependent kinase 11B	protein-coding
mm_154464.1	chrM	3382	3391	-	1	NA	NA	Intergenic	NA	NA								
mm_60593.1	chr7	44496589	44496600	+	1	NA	promoter-TSS (NM_197991)	promoter-TSS (NM_197991)	6	NM_028169	75538	Mm.258841	NM_028169	ENSMUSG00000051113	Fam71e1	0610007G24Rik|1700021N13Rik|1700021P22Rik|GARI-L5	family with sequence similarity 71, member E1	protein-coding
mm_159949.1	chr6	85765753	85765753	-	1	NA	promoter-TSS (NM_001037842)	promoter-TSS (NM_001037842)	-9	NM_001037842	93674	Mm.440772	NM_053097	ENSMUSG00000051262	Nat8f3	4833414A14Rik|4930583K21Rik|Cml3	N-acetyltransferase 8 (GCN5-related) family member 3	protein-coding
mm_150821.1	chr19	44493468	44493500	+	1	NA	promoter-TSS (NM_011720)	promoter-TSS (NM_011720)	12	NM_011720	22423	Mm.88365	NM_011720	ENSMUSG00000036961	Wnt8b	-	wingless-type MMTV integration site family, member 8B	protein-coding
mm_145122.1	chr18	44380768	44380810	+	1	NA	intron (NM_027490, intron 1 of 10)	CpG	289	NM_027490	70640	Mm.87629	NM_027490	ENSMUSG00000024472	Dcp2	2410015D23Rik|5730537H01Rik|AL118268	decapping mRNA 2	protein-coding
mm_164560.1	chr17	17827094	17827121	+	1	NA	Intergenic	CpG	-3081	NR_029536	387230		NR_029536	ENSMUSG00000065396	Mir99b	Mirn99b|mmu-mir-99b	microRNA 99b	ncRNA
mm_71421.1	chr8	46490966	46490966	+	1	NA	promoter-TSS (NM_001302163)	promoter-TSS (NM_001302163)	0	NM_001302163	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_57714.1	chr6	128707801	128707813	-	1	NA	intron (NM_001099918, intron 5 of 5)	intron (NM_001099918, intron 5 of 5)	15239	NM_001099918	100043861	Mm.66911	NM_001099918	ENSMUSG00000079299	Klrb1	4930431A04Rik|Gm4696|Klrb1g|Klrb6|Ly-55|Ly55|NKR-P1G|Nkrp-1e|Nkrp1g	killer cell lectin-like receptor subfamily B member 1	protein-coding
mm_133912.1	chr16	97555041	97555047	+	1	NA	intron (NR_003508, intron 10 of 13)	B3|SINE|B2	18961	NM_013606	17858	Mm.14157	NM_013606	ENSMUSG00000023341	Mx2	AI528743|Mx-2	MX dynamin-like GTPase 2	protein-coding
mm_5707.1	chr1	43522028	43522068	-	1	NA	intron (NM_010879, intron 2 of 4)	intron (NM_010879, intron 2 of 4)	76297	NM_010879	17974	Mm.389903	NM_010879	ENSMUSG00000066877	Nck2	4833426I10Rik|Grb4|NCKbeta|Nck-2	non-catalytic region of tyrosine kinase adaptor protein 2	protein-coding
mm_23855.1	chr3	83010116	83010165	+	1	NA	exon (NM_133862, exon 5 of 10)	exon (NM_133862, exon 5 of 10)	2416	NM_001317105	99571	Mm.16422	NM_133862	ENSMUSG00000033860	Fgg	3010002H13Rik|AI256424	fibrinogen gamma chain	protein-coding
mm_162243.1	chrX	155623313	155623313	-	1	NA	promoter-TSS (NM_001093750)	promoter-TSS (NM_001093750)	14	NM_001093750	211612	Mm.218811	NM_001093750	ENSMUSG00000041552	Ptchd1	9630036J22Rik|AI848149|Gm387	patched domain containing 1	protein-coding
mm_115447.1	chr13	118556146	118556161	+	1	NA	promoter-TSS (NR_045982)	promoter-TSS (NR_045982)	-15	NR_045982	75890	Mm.141235	NR_045982	ENSMUSG00000100727	1700003P14Rik	1700030O10Rik|4930584L06Rik	RIKEN cDNA 1700003P14 gene	ncRNA
mm_61195.1	chr7	63917242	63917248	+	1	NA	intron (NM_001256311, intron 1 of 2)	ORR1C1|LTR|ERVL-MaLR	388	NM_001256311	381994	Mm.425466	NM_001256311	ENSMUSG00000095061	E030018B13Rik	Gm1697	RIKEN cDNA E030018B13 gene	protein-coding
mm_108287.1	chr12	79138325	79138360	+	1	NA	intron (NM_009705, intron 2 of 7)	intron (NM_009705, intron 2 of 7)	7554	NM_009705	11847	Mm.3506	NM_009705	ENSMUSG00000021125	Arg2	AII|AU022422	arginase type II	protein-coding
mm_134065.1	chr16	8623928	8623933	-	1	NA	Intergenic	Intergenic	13771	NM_025708	66690	Mm.10068	NM_025708	ENSMUSG00000043140	Tmem186	2810440M13Rik|4432406C05Rik|AI648175|AW210586	transmembrane protein 186	protein-coding
mm_153013.1	chr19	30574171	30574179	-	1	NA	intron (NM_011160, intron 16 of 17)	intron (NM_011160, intron 16 of 17)	-24679	NM_010051	13380	Mm.214717	NM_010051	ENSMUSG00000024868	Dkk1	mdkk-1	dickkopf WNT signaling pathway inhibitor 1	protein-coding
mm_62916.1	chr7	118114072	118114113	+	1	NA	intron (NM_170669, intron 3 of 4)	URR1B|DNA|hAT-Charlie	2055	NM_170669	267019	Mm.288212	NM_170669	ENSMUSG00000008683	Rps15a	A630031B11Rik	ribosomal protein S15A	protein-coding
mm_169542.1	chr15	101151628	101151637	+	1	NA	Intergenic	Intergenic	-22493	NM_007395	11479	Mm.308467	NM_007395	ENSMUSG00000000532	Acvr1b	6820432J04|ActR-IB|ActRIB|Acvrlk4|Alk4|SKR2	activin A receptor, type 1B	protein-coding
mm_65629.1	chr7	27542775	27542809	-	1	NA	5' UTR (NM_011116, exon 3 of 14)	5' UTR (NM_011116, exon 3 of 14)	10426	NM_011116	18807	Mm.6483	NM_011116	ENSMUSG00000003363	Pld3	Sam-9	phospholipase D family, member 3	protein-coding
mm_59572.1	chr7	28115583	28115589	+	1	NA	intron (NM_001122603, intron 17 of 19)	intron (NM_001122603, intron 17 of 19)	-13880	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_109538.1	chr12	111548063	111548066	+	1	NA	Intergenic	B2_Mm1a|SINE|B2	7118	NR_033168	100316932	Mm.484709	NR_033168	ENSMUSG00000064493	Snora28	MBI-13	small nucleolar RNA, H/ACA box 28	snoRNA
mm_72012.1	chr8	70703518	70703523	+	1	NA	Intergenic	Intergenic	5781	NM_001286944	16478	Mm.419851	NM_010592	ENSMUSG00000071076	Jund	Jund1	jun D proto-oncogene	protein-coding
mm_60344.1	chr7	44356631	44356643	+	1	NA	exon (NM_001034115, exon 25 of 25)	exon (NM_001034115, exon 25 of 25)	18393	NM_027049	69349	Mm.358922	NM_027049	ENSMUSG00000008028	1700008O03Rik	-	RIKEN cDNA 1700008O03 gene	protein-coding
mm_133285.1	chr16	77448479	77448505	+	1	NA	intron (NR_015543, intron 2 of 4)	intron (NR_015543, intron 2 of 4)	119164	NR_015543	77994	Mm.394688	NR_015543	ENSMUSG00000090386	Mir99ahg	2810055G20Rik|D730043B02Rik	Mir99a and Mirlet7c-1 host gene (non-protein coding)	ncRNA
mm_172441.1	chr7	29965617	29965617	-	1	NA	Intergenic	Intergenic	-13724	NM_178384	72723	Mm.371648	NM_178384	ENSMUSG00000059975	Zfp74	2810054M15Rik|KRAB8|Zfp66|Znf569|mszf21|mszf77	zinc finger protein 74	protein-coding
mm_97700.1	chr11	80177378	80177381	+	1	NA	intron (NM_172133, intron 10 of 10)	intron (NM_172133, intron 10 of 10)	-6493	NM_028019	71956	Mm.22985	NM_028019	ENSMUSG00000020707	Rnf135	0610037N03Rik|2410006N06Rik	ring finger protein 135	protein-coding
mm_105276.1	chr11	102407858	102407895	-	1	NA	promoter-TSS (NM_026542)	promoter-TSS (NM_026542)	-359	NM_026542	68066	Mm.44226	NM_026542	ENSMUSG00000018677	Slc25a39	3010027G13Rik|D11Ertd333e	solute carrier family 25, member 39	protein-coding
mm_93311.1	chr10	98880114	98880142	-	1	NA	Intergenic	Intergenic	-35024	NM_026482	67972	Mm.166944	NM_026482	ENSMUSG00000019943	Atp2b1	2810442I22Rik|E130111D10Rik|Pmca1	ATPase, Ca++ transporting, plasma membrane 1	protein-coding
mm_31728.1	chr4	62965649	62965671	+	1	NA	promoter-TSS (NM_028326)	promoter-TSS (NM_028326)	86	NM_028326	72701	Mm.26479	NM_028326	ENSMUSG00000028358	Zfp618	2810031P15Rik|2810040O04Rik|AI415580|AI505139|D430033D05Rik|Nedd10|Znf618|bM257P7.1	zinc finger protein 618	protein-coding
mm_166176.1	chr5	30461840	30461861	-	1	NA	promoter-TSS (NM_001100395)	promoter-TSS (NM_001100395)	82	NM_001286421	83762	Mm.244502	NM_031875	ENSMUSG00000062372	Otof	-	otoferlin	protein-coding
mm_124061.1	chr14	78220491	78220537	-	1	NA	Intergenic	RMER17C|LTR|ERVK	-29036	NR_035499	100316715		NR_035499	ENSMUSG00000087932	Mir1971	mmu-mir-1971	microRNA 1971	ncRNA
mm_5100.1	chr1	5019343	5019397	-	1	NA	promoter-TSS (NM_001290372)	promoter-TSS (NM_001290372)	169	NM_021374	58175	Mm.103771	NM_021374	ENSMUSG00000002459	Rgs20	2900073E09Rik|Rgsz1	regulator of G-protein signaling 20	protein-coding
mm_140717.1	chr17	15374864	15374879	-	1	NA	exon (NM_007865, exon 2 of 11)	exon (NM_007865, exon 2 of 11)	952	NM_007865	13388	Mm.4875	NM_007865	ENSMUSG00000014773	Dll1	Delta1	delta-like 1 (Drosophila)	protein-coding
mm_118854.1	chr14	25751344	25751382	+	1	NA	intron (NM_001101433, intron 2 of 3)	intron (NM_001101433, intron 2 of 3)	17493	NM_001101433	71918	Mm.41904	NM_001101433	ENSMUSG00000055538	Zcchc24	2310047A01Rik	zinc finger, CCHC domain containing 24	protein-coding
mm_50817.1	chr6	54429654	54429664	+	1	NA	non-coding (NR_033635, exon 1 of 14)	non-coding (NR_033635, exon 1 of 14)	562	NR_033635	100042056	Mm.448157	NM_198118	ENSMUSG00000073067	9130019P16Rik	6430501H15Rik|OTTMUSG00000023151	RIKEN cDNA 9130019P16 gene	ncRNA
mm_58439.1	chr7	3298094	3298119	+	1	NA	3' UTR (NM_016969, exon 3 of 3)	3' UTR (NM_016969, exon 3 of 3)	5078	NM_001093766	50918	Mm.29874	NM_016969	ENSMUSG00000068566	Myadm	D7Wsu62e	myeloid-associated differentiation marker	protein-coding
mm_62550.1	chr7	102441777	102441825	+	1	NA	5' UTR (NM_009103, exon 1 of 19)	5' UTR (NM_009103, exon 1 of 19)	106	NM_009103	20133	Mm.197486	NM_009103	ENSMUSG00000030978	Rrm1	RnrM1	ribonucleotide reductase M1	protein-coding
mm_129040.1	chr15	75055287	75055290	-	1	NA	Intergenic	MURVY-LTR|LTR|ERV1	-6451	NM_001252056	17067	Mm.1583	NM_010741	ENSMUSG00000079018	Ly6c1	AA682074|AA959465|Ly-6C|Ly-6C1|Ly6c	lymphocyte antigen 6 complex, locus C1	protein-coding
mm_83710.1	chr9	50739366	50739379	-	1	NA	TTS (NM_025865)	TTS (NM_025865)	-1637	NM_001311069	330938	Mm.82598	NM_178118	ENSMUSG00000032064	Dixdc1	4930563F16Rik|BC048182|Ccd1|Ccd1Aalpha1L|Ccd1Abeta1L|Ccd1BalphaL|Ccd1BbetaL|Ccd1CL|mKIAA1735	DIX domain containing 1	protein-coding
mm_23397.1	chr3	57807018	57807031	+	1	NA	exon (NM_011883, exon 7 of 9)	exon (NM_011883, exon 7 of 9)	40733	NM_019410	18645	Mm.271744	NM_019410	ENSMUSG00000027805	Pfn2	Pfn	profilin 2	protein-coding
mm_158309.1	chrX	124109843	124109863	-	1	NA	Intergenic	Intergenic	26057	NM_001100616	100038941	Mm.388852	NM_001100616	ENSMUSG00000072049	Vmn2r121	EG625699	vomeronasal 2, receptor 121	protein-coding
mm_87351.1	chr10	43593393	43593403	+	1	NA	promoter-TSS (NR_033558)	promoter-TSS (NR_033558)	-29	NR_033558	414125	Mm.244305	NR_033558	ENSMUSG00000075184	F830002L21Rik	F930017D23Rik	RIKEN cDNA F830002L21 gene	ncRNA
mm_55450.1	chr6	67284016	67284060	-	1	NA	3' UTR (NM_025814, exon 8 of 8)	3' UTR (NM_025814, exon 8 of 8)	17059	NM_025814	66870	Mm.240490	NM_025814	ENSMUSG00000036371	Serbp1	1200009K13Rik|9330147J08Rik|AL022786|Pairbp1	serpine1 mRNA binding protein 1	protein-coding
mm_57902.1	chr6	131388383	131388397	-	1	NA	promoter-TSS (NM_011733)	promoter-TSS (NM_011733)	60	NM_139117	56449	Mm.458000	NM_011733	ENSMUSG00000030189	Ybx3	Csda|Dpba|MSY3|MSY4|Yb2|dbpA|oxyR	Y box protein 3	protein-coding
mm_115467.1	chr13	119429716	119429730	+	1	NA	intron (NM_145457, intron 1 of 10)	intron (NM_145457, intron 1 of 10)	821	NM_145457	218693	Mm.490243	NM_145457	ENSMUSG00000025451	Paip1	PAIP-1	polyadenylate binding protein-interacting protein 1	protein-coding
mm_144201.1	chr18	9450278	9450298	+	1	NA	promoter-TSS (NM_026484)	promoter-TSS (NM_026484)	-138	NM_026484	67974	Mm.86523	NM_026484	ENSMUSG00000024286	Ccny	1700025H17Rik|3110050L10Rik|4631402G10Rik|5730405I09Rik	cyclin Y	protein-coding
mm_30537.1	chr4	3574959	3574970	+	1	NA	promoter-TSS (NM_028097)	promoter-TSS (NM_028097)	85	NM_054089	116940	Mm.171323	NM_054089	ENSMUSG00000028233	Tgs1	D4Ertd800e|Ncoa6ip|Pimt	trimethylguanosine synthase 1	protein-coding
mm_168657.1	chr11	8884965	8884978	+	1	NA	Intergenic	(TGG)n|Simple_repeat|Simple_repeat	126220	NM_001303610	15574	Mm.42201	NM_008316	ENSMUSG00000020413	Hus1	-	HUS1 checkpoint clamp component	protein-coding
mm_8651.1	chr1	156444583	156444619	-	1	NA	exon (NM_009230, exon 5 of 16)	exon (NM_009230, exon 5 of 16)	-23686	NM_001346967	77352	Mm.428709	NM_001033180	ENSMUSG00000026601	Axdnd1	9430070O13Rik|Gm979	axonemal dynein light chain domain containing 1	protein-coding
mm_150150.1	chr19	31949954	31949965	+	1	NA	TTS (NM_001081074)	TTS (NM_001081074)	81198	NM_001081074	69865	Mm.87538	NM_001081074	ENSMUSG00000052595	A1cf	1810073H04Rik|ACF64|ACF65|ASP|Acf|MCM|MerCreMer|Tg(Myh6-cre/Esr1*)1Jmk|mer	APOBEC1 complementation factor	protein-coding
mm_128399.1	chr15	43869994	43870058	-	1	NA	promoter-TSS (NM_175502)	promoter-TSS (NM_175502)	3	NM_175502	239408	Mm.41219	NM_175502	ENSMUSG00000054409	Tmem74	AA549547|B230382K22Rik	transmembrane protein 74	protein-coding
mm_170228.1	chr17	81838566	81838578	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-100185	NM_011406	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_37697.1	chr4	129309873	129309886	-	1	NA	3' UTR (NM_009030, exon 12 of 12)	3' UTR (NM_009030, exon 12 of 12)	22258	NM_023485	68828	Mm.132243	NM_023485	ENSMUSG00000001333	Sync	1110057H03Rik|SNIP4	syncoilin	protein-coding
mm_51029.1	chr6	65433148	65433157	+	1	NA	intron (NM_175524, intron 1 of 5)	intron (NM_175524, intron 1 of 5)	51858	NM_175524	243407	Mm.389758	NM_175524	ENSMUSG00000029917	C130060K24Rik	-	RIKEN cDNA C130060K24 gene	protein-coding
mm_162367.1	chr1	65122080	65122083	+	1	NA	intron (NM_175293, intron 1 of 7)	B1_Mur2|SINE|Alu	1133	NM_175293	98303	Mm.348057	NM_175293	ENSMUSG00000044816	D630023F18Rik	AI314969	RIKEN cDNA D630023F18 gene	protein-coding
mm_152718.1	chr19	17560025	17560027	-	1	NA	3' UTR (NM_001163144, exon 21 of 21)	3' UTR (NM_001163144, exon 21 of 21)	165983	NM_019437	54391	Mm.7013	NM_019437	ENSMUSG00000024712	Rfk	0610038L10Rik|AF031381|KOI-4	riboflavin kinase	protein-coding
mm_157433.1	chrX	38587219	38587253	-	1	NA	Intergenic	Lx9|LINE|L1	-11040	NM_001110142	72584	Mm.327675	NM_028288	ENSMUSG00000031095	Cul4b	2700050M05Rik|AA409770|CUL-4B|mKIAA0695	cullin 4B	protein-coding
mm_155651.1	chrX	85870222	85870251	+	1	NA	promoter-TSS (NM_001163539)	promoter-TSS (NM_001163539)	-37	NM_001163539	71398	Mm.185296	NM_001163539	ENSMUSG00000025058	5430427O19Rik	-	RIKEN cDNA 5430427O19 gene	protein-coding
mm_136799.1	chr17	12151706	12151723	+	1	NA	5' UTR (NM_026644, exon 2 of 9)	5' UTR (NM_026644, exon 2 of 9)	32430	NM_026644	68262	Mm.258300	NM_026644	ENSMUSG00000023827	Agpat4	1500003P24Rik	1-acylglycerol-3-phosphate O-acyltransferase 4 (lysophosphatidic acid acyltransferase, delta)	protein-coding
mm_42287.1	chr5	114378944	114378957	+	1	NA	intron (NM_026145, intron 1 of 6)	intron (NM_026145, intron 1 of 6)	1555	NM_001159941	330171	Mm.238285	NM_026145	ENSMUSG00000001098	Kctd10	AW536343|C87062|mBACURD3	potassium channel tetramerisation domain containing 10	protein-coding
mm_104299.1	chr11	90390910	90390926	-	1	NA	promoter-TSS (NM_172563)	promoter-TSS (NM_172563)	-1	NM_172563	217082	Mm.158903	NM_172563	ENSMUSG00000003949	Hlf	E230015K02Rik	hepatic leukemia factor	protein-coding
mm_25830.1	chr3	129194646	129194656	+	1	NA	Intergenic	Intergenic	-5227	NM_001286942	18741	Mm.246804	NM_011098	ENSMUSG00000028023	Pitx2	9430085M16Rik|Brx1|Brx1b|Munc30|Otlx2|Ptx2|Rieg	paired-like homeodomain transcription factor 2	protein-coding
mm_7853.1	chr1	132391698	132391762	-	1	NA	promoter-TSS (NM_178874)	promoter-TSS (NM_178874)	-344	NM_178874	68875	Mm.273785	NM_178874	ENSMUSG00000042066	Tmcc2	1110063G11Rik	transmembrane and coiled-coil domains 2	protein-coding
mm_25143.1	chr3	102725118	102725140	+	1	NA	intron (NR_040588, intron 3 of 3)	intron (NR_040588, intron 3 of 3)	-9641	NM_027533	70747	Mm.27469	NM_027533	ENSMUSG00000027858	Tspan2	6330415F13Rik|B230119D02Rik|tspan-2	tetraspanin 2	protein-coding
mm_54540.1	chr6	36743046	36743050	-	1	NA	intron (NM_008973, intron 3 of 4)	intron (NM_008973, intron 3 of 4)	68313	NM_008973	19242	Mm.279690	NM_008973	ENSMUSG00000029838	Ptn	HARP|HB-GAM|HBBN|HBGF-8|HBNF|OSF|Osf-1|Osf1	pleiotrophin	protein-coding
mm_48062.1	chr5	136567243	136567287	-	1	NA	5' UTR (NM_009986, exon 1 of 24)	5' UTR (NM_009986, exon 1 of 24)	225	NM_001291234	13047	Mm.320317	NM_009986	ENSMUSG00000029705	Cux1	CDP|Cutl1|Cux|Cux-1	cut-like homeobox 1	protein-coding
mm_49262.1	chr6	17463928	17464071	+	1	NA	promoter-TSS (NM_008591)	promoter-TSS (NM_008591)	42	NM_008591	17295	Mm.86844	NM_008591	ENSMUSG00000009376	Met	AI838057|HGF|HGFR|Par4|c-Met	met proto-oncogene	protein-coding
mm_37108.1	chr4	116639151	116639163	-	1	NA	exon (NM_021473, exon 6 of 9)	exon (NM_021473, exon 6 of 9)	-11206	NM_016777	50927	Mm.257181	NM_016777	ENSMUSG00000028693	Nasp	5033430J04Rik|AI131596|AI317140|D4Ertd767e|Epcs32|Nasp-T	nuclear autoantigenic sperm protein (histone-binding)	protein-coding
mm_152390.1	chr19	10482670	10482708	-	1	NA	intron (NM_133689, intron 1 of 13)	intron (NM_133689, intron 1 of 13)	208	NM_133689	67752	Mm.25939	NM_133689	ENSMUSG00000035179	Ppp1r32	4930579J09Rik|AU015816|IIIG9|IIIG9L|IIIG9S	protein phosphatase 1, regulatory subunit 32	protein-coding
mm_157056.1	chrX	8131704	8131722	-	1	NA	5' UTR (NM_028542, exon 2 of 9)	5' UTR (NM_028542, exon 2 of 9)	1145	NM_001290783	73447	Mm.284162	NM_026137	ENSMUSG00000031166	Wdr13	1700060B08Rik|5730411P10Rik|DXHXS7467e|W51679|mMg21	WD repeat domain 13	protein-coding
mm_162232.1	chrX	151835221	151835221	+	1	NA	intron (NM_021523, intron 2 of 82)	intron (NM_021523, intron 2 of 82)	-24341	NR_130340	100526542		NR_130340	ENSMUSG00000093219	Mir3113	mmu-mir-3113	microRNA 3113	ncRNA
mm_130989.1	chr15	103376808	103376840	-	1	NA	Intergenic	Intergenic	-10033	NM_001314041	16402	Mm.16234	NM_010577	ENSMUSG00000000555	Itga5	Cd49e|Fnra|VLA5	integrin alpha 5 (fibronectin receptor alpha)	protein-coding
mm_113992.1	chr13	52583083	52583123	+	1	NA	promoter-TSS (NM_001198977)	promoter-TSS (NM_001198977)	-334	NM_001198977	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_115929.1	chr13	23571187	23571189	-	1	NA	promoter-TSS (NM_178196)	promoter-TSS (NM_178196)	32	NM_178187	319166	Mm.261665	NM_178187	ENSMUSG00000069272	Hist1h2ae	1190022L06	histone cluster 1, H2ae	protein-coding
mm_76723.1	chr8	94876251	94876263	-	1	NA	promoter-TSS (NM_053246)	promoter-TSS (NM_053246)	55	NM_053246	114255	Mm.203949	NM_053246	ENSMUSG00000040631	Dok4	-	docking protein 4	protein-coding
mm_116206.1	chr13	32776397	32776425	-	1	NA	intron (NM_001166030, intron 1 of 11)	intron (NM_001166030, intron 1 of 11)	5368	NM_001166030	238564	Mm.60041	NM_001166030	ENSMUSG00000044951	Mylk4	EG238564	myosin light chain kinase family, member 4	protein-coding
mm_150098.1	chr19	29470760	29470770	+	1	NA	3' UTR (NM_021396, exon 6 of 6)	3' UTR (NM_021396, exon 6 of 6)	51222	NR_015567	77779	Mm.458738	NR_015567	ENSMUSG00000097855	A930007I19Rik	-	RIKEN cDNA A930007I19 gene	ncRNA
mm_148766.1	chr19	6080018	6080028	+	1	NA	promoter-TSS (NM_001111317)	promoter-TSS (NM_001111317)	-15	NM_001111317	433215	Mm.437186	NM_001111317	ENSMUSG00000047733	Tmem262	-	transmembrane protein 262	protein-coding
mm_168101.1	chr10	13013336	13013338	+	1	NA	Intergenic	ORR1A0|LTR|ERVL-MaLR	4887	NM_175102	66125	Mm.29743	NM_175102	ENSMUSG00000078348	Sf3b5	10kDa|1110005L13Rik|AU043053|Sf3b10	splicing factor 3b, subunit 5	protein-coding
mm_122704.1	chr14	52180215	52180237	-	1	NA	exon (NM_033618, exon 7 of 26)	exon (NM_033618, exon 7 of 26)	17013	NM_033618	114741	Mm.21662	NM_033618	ENSMUSG00000035726	Supt16	Cdc68|Fact140|Spt16|Supt16h	suppressor of Ty 16	protein-coding
mm_151840.1	chr19	5726241	5726287	-	1	NA	promoter-TSS (NM_001114597)	promoter-TSS (NM_001114597)	53	NM_001114595	114601	Mm.210447	NM_053252	ENSMUSG00000024937	Ehbp1l1	G430002G23Rik	EH domain binding protein 1-like 1	protein-coding
mm_32156.1	chr4	99955716	99955736	+	1	NA	intron (NM_028132, intron 1 of 10)	intron (NM_028132, intron 1 of 10)	26275	NM_028132	72157	Mm.217764	NM_028132	ENSMUSG00000025791	Pgm2	2610020G18Rik|AA407108|AI098105|Pgm-2|Pgm1	phosphoglucomutase 2	protein-coding
mm_51643.1	chr6	86017277	86017286	+	1	NA	promoter-TSS (NM_012013)	promoter-TSS (NM_012013)	90	NM_012013	26910	Mm.8024	NM_012013	ENSMUSG00000030001	Figla	FIGalpha|bHLHc8	folliculogenesis specific basic helix-loop-helix	protein-coding
mm_63576.1	chr7	128117854	128117864	+	1	NA	3' UTR (NM_008401, exon 30 of 30)	3' UTR (NM_008401, exon 30 of 30)	-11709	NM_021334	16411	Mm.22378	NM_021334	ENSMUSG00000030789	Itgax	AI449405|Cd11c|Cr4|N418	integrin alpha X	protein-coding
mm_57542.1	chr6	126644834	126644844	-	1	NA	5' UTR (NM_010595, exon 1 of 2)	5' UTR (NM_010595, exon 1 of 2)	962	NM_010595	16485	Mm.40424	NM_010595	ENSMUSG00000047976	Kcna1	AI840627|Kca1-1|Kv1.1|MBK1|Mk-1|Shak|mceph	potassium voltage-gated channel, shaker-related subfamily, member 1	protein-coding
mm_23324.1	chr3	53475331	53475380	+	1	NA	exon (NM_173382, exon 9 of 13)	exon (NM_173382, exon 9 of 13)	11538	NM_173382	212127	Mm.491292	NM_173382	ENSMUSG00000049504	Proser1	2810046L04Rik|9330161F11	proline and serine rich 1	protein-coding
mm_104537.1	chr11	96350074	96350127	-	1	NA	Intergenic	Intergenic	-1532	NM_134032	103889	Mm.281153	NM_134032	ENSMUSG00000075588	Hoxb2	AI894218|Hox-2.8|Hoxbes2	homeobox B2	protein-coding
mm_134687.1	chr16	22439609	22439625	-	1	NA	promoter-TSS (NM_023794)	promoter-TSS (NM_023794)	-47	NM_023794	104156	Mm.155708	NM_023794	ENSMUSG00000013089	Etv5	1110005E01Rik|8430401F14Rik|ERM	ets variant 5	protein-coding
mm_31465.1	chr4	49536506	49536557	+	1	NA	3' UTR (NM_144903, exon 9 of 9)	3' UTR (NM_144903, exon 9 of 9)	13015	NM_144903	230163	Mm.482116	NM_144903	ENSMUSG00000028307	Aldob	Aldo-2|Aldo2|BC016435	aldolase B, fructose-bisphosphate	protein-coding
mm_9624.1	chr1	176756716	176756726	-	1	NA	exon (NM_001099637, exon 13 of 20)	exon (NM_001099637, exon 13 of 20)	15702	NR_029775	723921		NR_029775	ENSMUSG00000065573	Mir350	Mirn350|mir-350|mmu-mir-350	microRNA 350	ncRNA
mm_204.1	chr1	16111350	16111370	+	1	NA	intron (NM_133832, intron 2 of 5)	intron (NM_133832, intron 2 of 5)	5478	NM_133832	98711	Mm.274376	NM_133832	ENSMUSG00000025921	Rdh10	3110069K09Rik|4921506A21Rik|AI875664|AW549993|D1Ertd762e|m366Asp	retinol dehydrogenase 10 (all-trans)	protein-coding
mm_44822.1	chr5	33657838	33657887	-	1	NA	promoter-TSS (NM_026698)	promoter-TSS (NM_026698)	-30	NM_026698	68366	Mm.491151	NM_026698	ENSMUSG00000019295	Tmem129	0610039G24Rik|2410015J15Rik|AA409575	transmembrane protein 129	protein-coding
mm_137796.1	chr17	29680528	29680538	+	1	NA	intron (NR_132314, intron 10 of 27)	intron (NR_132314, intron 10 of 27)	19938	NM_028791	74157	Mm.390979	NM_028791	ENSMUSG00000024019	Cmtr1	1300018I05Rik|AI451264|Ftsjd2|MTr1	cap methyltransferase 1	protein-coding
mm_47452.1	chr5	123572977	123573031	-	1	NA	promoter-TSS (NM_029929)	promoter-TSS (NM_029929)	11	NM_029929	77573	Mm.41372	NM_029929	ENSMUSG00000029434	Vps33a	3830421M04Rik|AI503300|AW048546|AW554476|bf	VPS33A CORVET/HOPS core subunit	protein-coding
mm_156044.1	chrX	108484422	108484432	+	1	NA	Intergenic	Intergenic	349928	NM_001081477	382236	Mm.100112	NM_001081477	ENSMUSG00000063663	Brwd3	Brodl|D030064D06Rik|Gm596	bromodomain and WD repeat domain containing 3	protein-coding
mm_62109.1	chr7	96522343	96522357	+	1	NA	intron (NM_001310762, intron 4 of 32)	intron (NM_001310762, intron 4 of 32)	-180386	NR_046043	670727	Mm.421352	NR_046043	ENSMUSG00000085751	Gm15412	OTTMUSG00000021245	predicted gene 15412	ncRNA
mm_51766.1	chr6	87981705	87981717	+	1	NA	promoter-TSS (NR_026990)	promoter-TSS (NR_026990)	28	NR_026990	434064	Mm.371796	NR_026990	ENSMUSG00000084950	Gm5577	EG434064	predicted gene 5577	ncRNA
mm_16390.1	chr2	178659348	178659366	+	1	NA	Intergenic	Intergenic	228842	NM_198656	381409	Mm.330860	NM_198656	ENSMUSG00000039155	Cdh26	Gm1010	cadherin-like 26	protein-coding
mm_5207.1	chr1	13565940	13565957	-	1	NA	3' UTR (NM_028173, exon 11 of 11)	3' UTR (NM_028173, exon 11 of 11)	23962	NM_028173	72265	Mm.28765	NM_028173	ENSMUSG00000025935	Tram1	1810049E02Rik|TRAMP	translocating chain-associating membrane protein 1	protein-coding
mm_49048.1	chr6	4903251	4903272	+	1	NA	promoter-TSS (NM_181595)	promoter-TSS (NM_181595)	-59	NM_181595	243725	Mm.332901	NM_181595	ENSMUSG00000032827	Ppp1r9a	2810430P21Rik|4930518N04Rik|5330407E15|A230094E16Rik|BB181831|NRB|mKIAA1222|neurabin-I	protein phosphatase 1, regulatory (inhibitor) subunit 9A	protein-coding
mm_129772.1	chr15	82791046	82791058	-	1	NA	exon (NM_029562, exon 7 of 9)	exon (NM_029562, exon 7 of 9)	3193	NM_029562	76279	Mm.439931	NM_029562	ENSMUSG00000022445	Cyp2d26	1300006E06Rik	cytochrome P450, family 2, subfamily d, polypeptide 26	protein-coding
mm_94585.1	chr11	11692838	11692846	+	1	NA	intron (NM_001301866, intron 1 of 5)	intron (NM_001301866, intron 1 of 5)	2665	NM_001301863	22778	Mm.103545	NM_009578	ENSMUSG00000018654	Ikzf1	5832432G11Rik|Ikaros|LyF-1|Zfpn1a1|Znfn1a1|hlk-1|mKIAA4227	IKAROS family zinc finger 1	protein-coding
mm_152620.1	chr19	12463787	12463809	-	1	NA	3' UTR (NM_010821, exon 2 of 2)	3' UTR (NM_010821, exon 2 of 2)	3019	NM_010821	17476	Mm.3999	NM_010821	ENSMUSG00000046805	Mpeg1	MPS1|Mpg-1	macrophage expressed gene 1	protein-coding
mm_78525.1	chr9	34546319	34546321	+	1	NA	intron (NM_001190912, intron 1 of 15)	intron (NM_001190912, intron 1 of 15)	57589	NM_001190911	67703	Mm.220710	NM_026324	ENSMUSG00000032036	Kirrel3	1500010O20Rik|2900036G11Rik|NEPH2|SST4|mKIAA1867	kin of IRRE like 3 (Drosophila)	protein-coding
mm_71071.1	chr8	34154571	34154654	+	1	NA	promoter-TSS (NM_026432)	promoter-TSS (NM_026432)	49	NM_026432	67887	Mm.290353	NM_026432	ENSMUSG00000031532	Saraf	1810045K07Rik|Tmem66	store-operated calcium entry-associated regulatory factor	protein-coding
mm_143331.1	chr17	66449716	66449759	-	1	NA	promoter-TSS (NM_172963)	promoter-TSS (NM_172963)	13	NM_172963	68617	Mm.33421	NM_172963	ENSMUSG00000052105	Mtcl1	1110012J17Rik|Ccdc165|D130071O13|Kiaa0802|Soga2|mKIAA0802|t8219b25	microtubule crosslinking factor 1	protein-coding
mm_165182.1	chr2	29772550	29772556	+	1	NA	Intergenic	Intergenic	11025	NM_001177392	433416	Mm.330112	NM_001034887	ENSMUSG00000075425	Gm13547	OTTMUSG00000012686	predicted gene 13547	protein-coding
mm_85368.1	chr9	103221006	103221016	-	1	NA	exon (NM_133977, exon 9 of 17)	exon (NM_133977, exon 9 of 17)	9275	NM_133977	22041	Mm.37214	NM_133977	ENSMUSG00000032554	Trf	AI266983|Cd176|HP|Tf|Tfn|hpx	transferrin	protein-coding
mm_126065.1	chr15	77045104	77045139	+	1	NA	promoter-TSS (NM_001163621)	promoter-TSS (NM_001163621)	46	NM_001163621	71939	Mm.34173	NM_028010	ENSMUSG00000033576	Apol6	2310076O14Rik	apolipoprotein L 6	protein-coding
mm_91343.1	chr10	26374071	26374088	-	1	NA	promoter-TSS (NM_001347467)	promoter-TSS (NM_001347467)	-45	NM_001347467	237339	Mm.338439	NM_172787	ENSMUSG00000039089	L3mbtl3	AI481284|MBT-1	l(3)mbt-like 3 (Drosophila)	protein-coding
mm_92150.1	chr10	67096932	67096959	-	1	NA	promoter-TSS (NM_001204915)	promoter-TSS (NM_001204915)	43	NM_001204915	28193	Mm.41272	NM_178606	ENSMUSG00000019873	Reep3	D10Ucla1	receptor accessory protein 3	protein-coding
mm_130875.1	chr15	102244763	102244767	-	1	NA	intron (NM_011244, intron 3 of 9)	intron (NM_011244, intron 3 of 9)	1735	NM_001042727	19411	Mm.1273	NM_011244	ENSMUSG00000001288	Rarg	Nr1b3|RAR-gamma|RARD|RARgamma2	retinoic acid receptor, gamma	protein-coding
mm_122368.1	chr14	39429927	39429942	-	1	NA	intron (NM_001190187, intron 1 of 9)	intron (NM_001190187, intron 1 of 9)	-42495	NR_131973	432842	Mm.352566	NR_131973		LOC432842	-	uncharacterized LOC432842	ncRNA
mm_93300.1	chr10	96664189	96664199	-	1	NA	Intergenic	Intergenic	47193	NM_007569	12226	Mm.23811	NM_007569	ENSMUSG00000036478	Btg1	AI426953|AW546738	B cell translocation gene 1, anti-proliferative	protein-coding
mm_85615.1	chr9	107614467	107614532	-	1	NA	3' UTR (NM_008138, exon 9 of 9)	3' UTR (NM_008138, exon 9 of 9)	-5258	NM_001291539	20347	Mm.4083	NM_009153	ENSMUSG00000057969	Sema3b	SemA|Semaa|sema5|semaV	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B	protein-coding
mm_26703.1	chr3	157751812	157751845	+	1	NA	Intergenic	Intergenic	173235	NM_145953	107869	Mm.28301	NM_145953	ENSMUSG00000028179	Cth	0610010I13Rik|AI314617|BC019483|CSE|Cys3	cystathionase (cystathionine gamma-lyase)	protein-coding
mm_105611.1	chr11	106783950	106783969	-	1	NA	exon (NM_007840, exon 11 of 13)	exon (NM_007840, exon 11 of 13)	-1200	NR_037224	100526469		NR_037224	ENSMUSG00000093273	Mir3064	mir-3064|mmu-mir-3064	microRNA 3064	ncRNA
mm_105214.1	chr11	102164016	102164061	-	1	NA	3' UTR (NM_172947, exon 5 of 5)	3' UTR (NM_172947, exon 5 of 5)	-7631	NM_029649	76547	Mm.46529	NM_029649	ENSMUSG00000020921	Tmem101	2610511E22Rik	transmembrane protein 101	protein-coding
mm_5356.1	chr1	25697305	25697314	-	1	NA	intron (NM_175642, intron 2 of 30)	intron (NM_175642, intron 2 of 30)	132398	NM_175642	210933	Mm.336569	NM_175642	ENSMUSG00000033569	Adgrb3	A830096D10Rik|Bai3	adhesion G protein-coupled receptor B3	protein-coding
mm_130459.1	chr15	98593639	98593641	-	1	NA	exon (NM_007405, exon 20 of 22)	exon (NM_007405, exon 20 of 22)	13993	NM_007405	11512	Mm.157091	NM_007405	ENSMUSG00000022994	Adcy6	AC6|mKIAA0422	adenylate cyclase 6	protein-coding
mm_7984.1	chr1	134183655	134183667	-	1	NA	exon (NM_007695, exon 3 of 10)	exon (NM_007695, exon 3 of 10)	1257	NM_007695	12654	Mm.38274	NM_007695	ENSMUSG00000064246	Chil1	AW208766|Brp39|Chi3l1|Gp39	chitinase-like 1	protein-coding
mm_162988.1	chr11	23306691	23306718	+	1	NA	promoter-TSS (NM_001190401)	promoter-TSS (NM_001190401)	-191	NM_001190401	17847	Mm.119155	NM_001190401	ENSMUSG00000056342	Usp34	A530081C03Rik|Murr2	ubiquitin specific peptidase 34	protein-coding
mm_167440.1	chr8	120113864	120113893	-	1	NA	promoter-TSS (NM_001163762)	promoter-TSS (NM_001163762)	-274	NM_001163762	234797	Mm.101958	NM_172286	ENSMUSG00000031824	6430548M08Rik	AW049007|Kiaa0513|mKIAA0513	RIKEN cDNA 6430548M08 gene	protein-coding
mm_92506.1	chr10	78403076	78403082	-	1	NA	intron (NM_010925, intron 9 of 12)	intron (NM_010925, intron 9 of 12)	5466	NR_105872	102465547		NR_105872	ENSMUSG00000098376	Mir6907	Gm27351|mmu-mir-6907	microRNA 6907	ncRNA
mm_33960.1	chr4	137511067	137511103	+	1	NA	exon (NM_008305, exon 8 of 97)	exon (NM_008305, exon 8 of 97)	-27201	NR_105985	102465616		NR_105985	ENSMUSG00000099134	Mir7018	Gm27606|mmu-mir-7018	microRNA 7018	ncRNA
mm_156229.1	chrX	135839041	135839075	+	1	NA	promoter-TSS (NM_001163017)	promoter-TSS (NM_001163017)	24	NM_001163017	245607	Mm.489763	NM_001163015	ENSMUSG00000072966	Gprasp2	5330440H13Rik|GASP-2|GASP2|Prpl5	G protein-coupled receptor associated sorting protein 2	protein-coding
mm_66369.1	chr7	43651543	43651554	-	1	NA	exon (NM_031181, exon 7 of 7)	exon (NM_031181, exon 7 of 7)	8613	NM_031181	83382	Mm.157702	NM_031181	ENSMUSG00000030474	Siglece	Cd170|Siglec12|Siglec5|Siglec9|Siglecl1|mSiglec-E	sialic acid binding Ig-like lectin E	protein-coding
mm_15683.1	chr2	163629148	163629187	+	1	NA	exon (NM_012032, exon 7 of 10)	exon (NM_012032, exon 7 of 10)	-15683	NR_028113	68386	Mm.410649	NR_028113	ENSMUSG00000058812	0610039K10Rik	-	RIKEN cDNA 0610039K10 gene	ncRNA
mm_66037.1	chr7	30650108	30650122	-	1	NA	5' UTR (NM_133693, exon 1 of 10)	5' UTR (NM_133693, exon 1 of 10)	113	NM_133693	68035	Mm.401747	NM_133693	ENSMUSG00000036733	Rbm42	1700003D06Rik|3100004P22Rik	RNA binding motif protein 42	protein-coding
mm_36462.1	chr4	82505804	82505806	-	1	NA	promoter-TSS (NM_001113209)	promoter-TSS (NM_001113209)	-26	NM_008687	18028	Mm.317947	NM_008687	ENSMUSG00000008575	Nfib	6720429L07Rik|CTF|E030026I10Rik|NF-I/B|NF1-B|NFI-B	nuclear factor I/B	protein-coding
mm_156226.1	chrX	135796218	135796251	+	1	NA	5' UTR (NM_026081, exon 5 of 11)	5' UTR (NM_026081, exon 5 of 11)	-42800	NM_001163016	245607	Mm.489763	NM_001163015	ENSMUSG00000072966	Gprasp2	5330440H13Rik|GASP-2|GASP2|Prpl5	G protein-coupled receptor associated sorting protein 2	protein-coding
mm_164034.1	chr14	79660738	79660745	+	1	NA	intron (NM_010701, intron 2 of 6)	intron (NM_010701, intron 2 of 6)	1442	NM_001310655	16840	Mm.46561	NM_010701	ENSMUSG00000022025	Cnmd	Bricd3|ChM-I|Chmd|Lect1	chondromodulin	protein-coding
mm_15344.1	chr2	156065181	156065282	+	1	NA	promoter-TSS (NM_139151)	promoter-TSS (NM_139151)	18	NM_139151	245865	Mm.330713	NM_139151	ENSMUSG00000038180	Spag4	1700041K21Rik|MNCb-0953|Sun4|mKIAA4118	sperm associated antigen 4	protein-coding
mm_25114.1	chr3	101600612	101600633	+	1	NA	intron (NM_144900, intron 1 of 22)	intron (NM_144900, intron 1 of 22)	4085	NM_144900	11928	Mm.193670	NM_144900	ENSMUSG00000033161	Atp1a1	Atpa-1|BC010319	ATPase, Na+/K+ transporting, alpha 1 polypeptide	protein-coding
mm_44071.1	chr5	148777951	148777988	+	1	NA	promoter-TSS (NR_131106)	promoter-TSS (NR_131106)	6	NR_131106	78015	Mm.243839	NR_131106	ENSMUSG00000085740	4930505K14Rik	-	RIKEN cDNA 4930505K14 gene	ncRNA
mm_117702.1	chr13	95034290	95034316	-	1	NA	exon (NM_001170669, exon 15 of 19)	exon (NM_001170669, exon 15 of 19)	57959	NM_172590	218460	Mm.33856	NM_172590	ENSMUSG00000042015	Wdr41	B830029I03Rik|MSTP048	WD repeat domain 41	protein-coding
mm_83741.1	chr9	51102048	51102056	-	1	NA	promoter-TSS (NM_177702)	promoter-TSS (NM_177702)	26	NM_177702	235345	Mm.72828	NM_177702	ENSMUSG00000032057	4833427G06Rik	-	RIKEN cDNA 4833427G06 gene	protein-coding
mm_124656.1	chr15	5242100	5242123	+	1	NA	intron (NM_008965, intron 2 of 2)	intron (NM_008965, intron 2 of 2)	2076	NM_001136079	19219	Mm.18509	NM_008965	ENSMUSG00000039942	Ptger4	EP4|Ptgerep4	prostaglandin E receptor 4 (subtype EP4)	protein-coding
mm_22243.1	chr2	174614028	174614034	-	1	NA	Intergenic	Intergenic	-29503	NM_001099328	100043757	Mm.48711	NM_001099328	ENSMUSG00000050600	Zfp831	ENSMUSG00000050600|OTTMUSG00000017459	zinc finger protein 831	protein-coding
mm_82287.1	chr9	7604146	7604167	-	1	NA	Intergenic	Intergenic	-24075	NM_013903	30800	Mm.390121	NM_013903	ENSMUSG00000018620	Mmp20	-	matrix metallopeptidase 20 (enamelysin)	protein-coding
mm_121040.1	chr14	80021210	80021217	+	1	NA	exon (NM_001030294, exon 7 of 7)	exon (NM_001030294, exon 7 of 7)	20911	NM_001030294	380924	Mm.26456	NM_001030294	ENSMUSG00000022026	Olfm4	GC1|GW112|Gm296|Gm913|OlfD|pPD4	olfactomedin 4	protein-coding
mm_117070.1	chr13	59182785	59182787	-	1	NA	Intergenic	L1M4a2|LINE|L1	361665	NM_001284221	67269	Mm.153008	NM_023328	ENSMUSG00000021557	Agtpbp1	1700020N17Rik|2310001G17Rik|2900054O13Rik|4930445M19Rik|5730402G09Rik|CCP1|Nna1|nmf243|pcd	ATP/GTP binding protein 1	protein-coding
mm_162225.1	chrX	147403784	147403784	-	1	NA	5' UTR (NM_008356, exon 4 of 14)	5' UTR (NM_008356, exon 4 of 14)	25408	NM_001306059	16165	Mm.368330	NM_008356	ENSMUSG00000031289	Il13ra2	CD213a2|IL-13R-alpha-2	interleukin 13 receptor, alpha 2	protein-coding
mm_60940.1	chr7	46912301	46912303	+	1	NA	intron (NM_021884, intron 2 of 9)	intron (NM_021884, intron 2 of 9)	7628	NM_021884	22088	Mm.241334	NM_021884	ENSMUSG00000014402	Tsg101	AI255943|CC2	tumor susceptibility gene 101	protein-coding
mm_141082.1	chr17	25919677	25919740	-	1	NA	promoter-TSS (NM_139154)	promoter-TSS (NM_139154)	6	NM_139154	224624	Mm.328872	NM_139154	ENSMUSG00000025730	Rab40c	RAR3	Rab40C, member RAS oncogene family	protein-coding
mm_132030.1	chr16	27389005	27389031	+	1	NA	promoter-TSS (NM_001289436)	promoter-TSS (NM_001289436)	62	NM_001289436	67501	Mm.258985	NM_026202	ENSMUSG00000038127	Ccdc50	C3orf6	coiled-coil domain containing 50	protein-coding
mm_170353.1	chr1	85109782	85109789	-	1	NA	promoter-TSS (NM_213615)	promoter-TSS (NM_213615)	68	NM_213615	381287	Mm.487565	NM_213615	ENSMUSG00000089844	A530032D15Rik	Gm1888	RIKEN cDNA A530032D15Rik gene	protein-coding
mm_31079.1	chr4	41517424	41517436	+	1	NA	promoter-TSS (NM_001048005)	promoter-TSS (NM_001048005)	-7	NR_045726	76992	Mm.440546	NR_045726	ENSMUSG00000036162	Fam219aos	1700066J24Rik	family with sequence similarity 219, member A, opposite strand	ncRNA
mm_23117.1	chr3	37639946	37639964	+	1	NA	promoter-TSS (NM_011896)	promoter-TSS (NM_011896)	8	NM_001305442	24063	Mm.330986	NM_011896	ENSMUSG00000037211	Spry1	sprouty1|spry-1	sprouty homolog 1 (Drosophila)	protein-coding
mm_75583.1	chr8	61533562	61533613	-	1	NA	intron (NM_001081390, intron 12 of 19)	intron (NM_001081390, intron 12 of 19)	45853	NM_145595	234309	Mm.29059	NM_145595	ENSMUSG00000031641	Cbr4	A730083J17Rik|BC009118	carbonyl reductase 4	protein-coding
mm_73060.1	chr8	94386179	94386206	+	1	NA	promoter-TSS (NM_022331)	promoter-TSS (NM_022331)	-308	NM_022331	64209	Mm.29151	NM_022331	ENSMUSG00000031770	Herpud1	Herp|Mifl|SUP	homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1	protein-coding
mm_49913.1	chr6	39033500	39033511	+	1	NA	intron (NM_011539, intron 9 of 12)	intron (NM_011539, intron 9 of 12)	34081	NR_040523	69986	Mm.490941	NR_040523	ENSMUSG00000100121	1700025N23Rik	-	RIKEN cDNA 1700025N23 gene	ncRNA
mm_105841.1	chr11	113683930	113683957	-	1	NA	promoter-TSS (NM_177777)	promoter-TSS (NM_177777)	208	NM_138598	28081	Mm.351688	NM_138598	ENSMUSG00000041629	Fam104a	D11Wsu99e	family with sequence similarity 104, member A	protein-coding
mm_19866.1	chr2	114047312	114047318	-	1	NA	TTS (NM_009608)	TTS (NM_009608)	5560	NM_009608	11464	Mm.686	NM_009608	ENSMUSG00000068614	Actc1	Actc-1	actin, alpha, cardiac muscle 1	protein-coding
mm_127578.1	chr15	102296415	102296427	+	1	NA	intron (NM_001014976, intron 1 of 30)	CpG	128	NM_001014976	105988	Mm.288324	NM_001014976	ENSMUSG00000058290	Espl1	AL024103|AU045071|Cerp|ESP1|PRCE|SSE	extra spindle pole bodies 1, separase	protein-coding
mm_19167.1	chr2	84333545	84333558	-	1	NA	exon (NM_018782, exon 16 of 16)	exon (NM_018782, exon 16 of 16)	91715	NM_018782	54598	Mm.75467	NM_018782	ENSMUSG00000059588	Calcrl	AV071593|CRLR	calcitonin receptor-like	protein-coding
mm_51367.1	chr6	72699144	72699150	+	1	NA	intron (NM_001079822, intron 3 of 12)	intron (NM_001079822, intron 3 of 12)	69316	NR_040421	100038714	Mm.321330	NR_040421		Gm15401	ENSMUSG00000072999|OTTMUSG00000021199	predicted gene 15401	ncRNA
mm_138198.1	chr17	34291855	34291855	+	1	NA	Intergenic	Intergenic	-4084	NM_010378	14960	Mm.235338	NM_010378	ENSMUSG00000036594	H2-Aa	Aalpha|H-2Aa|H2Aa|I-Aalpha|IAalpha|Ia-1|Ia1	histocompatibility 2, class II antigen A, alpha	protein-coding
mm_125595.1	chr15	59648579	59648589	+	1	NA	promoter-TSS (NM_144549)	promoter-TSS (NM_144549)	-70	NM_144549	211770	Mm.40298	NM_144549	ENSMUSG00000032501	Trib1	A530090O15Rik|TRB-1|Trb1	tribbles pseudokinase 1	protein-coding
mm_94464.1	chr11	6474907	6474946	+	1	NA	exon (NM_011221, exon 1 of 1)	exon (NM_011221, exon 1 of 1)	1150	NM_011221	19291	Mm.296150	NM_011221	ENSMUSG00000094483	Purb	2310015K15Rik|AA114818|Cager-2|D11Bwg0414e	purine rich element binding protein B	protein-coding
mm_92579.1	chr10	79995320	79995348	-	1	NA	TTS (NM_007725)	TTS (NM_007725)	-2274	NM_001347081	27403	Mm.103351	NM_013850	ENSMUSG00000035722	Abca7	ABCX|Abc51	ATP-binding cassette, sub-family A (ABC1), member 7	protein-coding
mm_54914.1	chr6	47798431	47798444	-	1	NA	exon (NM_009787, exon 9 of 10)	exon (NM_009787, exon 9 of 10)	5215	NR_030485	735289		NR_030485	ENSMUSG00000076060	Mir704	Mirn704|mir-704|mmu-mir-704	microRNA 704	ncRNA
mm_145005.1	chr18	38419067	38419093	+	1	NA	5' UTR (NM_022996, exon 1 of 8)	5' UTR (NM_022996, exon 1 of 8)	105	NM_022996	65113	Mm.102496	NM_022996	ENSMUSG00000024425	Ndfip1	0610010M22Rik|N4wbp5	Nedd4 family interacting protein 1	protein-coding
mm_168002.1	chrY	847749	847750	-	1	NA	Intergenic	RLTR10D2|LTR|ERVK	29036	NM_011667	22202	Mm.422949	NM_011667	ENSMUSG00000069053	Uba1y	A1s9Y-1|Sby|Ube-2|Ube1ay|Ube1y|Ube1y-1|Ube1y1	ubiquitin-activating enzyme, Chr Y	protein-coding
mm_57470.1	chr6	125231703	125231737	-	1	NA	TTS (NM_001042564)	TTS (NM_001042564)	140	NM_145391	213233	Mm.296902	NM_145391	ENSMUSG00000038213	Tapbpl	BC017613|TAPBPL-R|Tapbplr	TAP binding protein-like	protein-coding
mm_131393.1	chr16	14317282	14317290	+	1	NA	promoter-TSS (NM_025345)	promoter-TSS (NM_025345)	46	NM_025345	66086	Mm.42072	NM_025345	ENSMUSG00000022677	Fopnl	0610037P05Rik	Fgfr1op N-terminal like	protein-coding
mm_143592.1	chr17	74489345	74489415	-	1	NA	promoter-TSS (NM_026417)	promoter-TSS (NM_026417)	-113	NM_026417	67864	Mm.41891	NM_026417	ENSMUSG00000024072	Yipf4	2310034L04Rik	Yip1 domain family, member 4	protein-coding
mm_41108.1	chr5	87775812	87775818	+	1	NA	exon (NM_001304768, exon 2 of 13)	exon (NM_001304768, exon 2 of 13)	1365	NM_007785	12993	Mm.4908	NM_007785	ENSMUSG00000061937	Csn1s2a	Csng|PP22	casein alpha s2-like A	protein-coding
mm_155178.1	chrX	53724640	53724644	+	1	NA	promoter-TSS (NM_029142)	promoter-TSS (NM_029142)	-189	NM_029142	75013	Mm.336332	NM_029142	ENSMUSG00000055555	4930502E18Rik	Ct55	RIKEN cDNA 4930502E18 gene	protein-coding
mm_38988.1	chr4	151062295	151062320	-	1	NA	3' UTR (NM_001081557, exon 24 of 24)	3' UTR (NM_001081557, exon 24 of 24)	-4354	NM_009498	22319	Mm.273930	NM_009498	ENSMUSG00000028955	Vamp3	D130027G05Rik|VAMP-3|ceb	vesicle-associated membrane protein 3	protein-coding
mm_108260.1	chr12	78481318	78481323	+	1	NA	exon (NM_172952, exon 6 of 24)	exon (NM_172952, exon 6 of 24)	-210215	NM_027597	70897	Mm.56514	NM_027597	ENSMUSG00000056987	Fam71d	4921509E07Rik|4930516C23Rik|GARI-L2	family with sequence similarity 71, member D	protein-coding
mm_126330.1	chr15	79892398	79892435	+	1	NA	promoter-TSS (NM_001160415)	promoter-TSS (NM_001160415)	8	NM_030255	80287	Mm.284059	NM_030255	ENSMUSG00000009585	Apobec3	Apobec|Arp3|BC003314|Cem15|Rfv3	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 3	protein-coding
mm_65276.1	chr7	24333923	24333955	-	1	NA	promoter-TSS (NM_001163810)	promoter-TSS (NM_001163810)	26	NM_001163810	69301	Mm.144202	NM_027028	ENSMUSG00000055826	Tescl	1700008P20Rik	tescalcin-like	protein-coding
mm_107654.1	chr12	52746709	52746712	+	1	NA	intron (NM_198111, intron 1 of 13)	intron (NM_198111, intron 1 of 13)	47327	NM_198111	238161	Mm.310822	NM_198111	ENSMUSG00000061603	Akap6	AI482140|Akapalpha|Akapbeta|PRKA	A kinase (PRKA) anchor protein 6	protein-coding
mm_91553.1	chr10	39926929	39926944	-	1	NA	promoter-TSS (NM_001163503)	promoter-TSS (NM_001163503)	-13	NM_001163503	72045	Mm.235981	NM_001163503	ENSMUSG00000039339	Mfsd4b2	2010001E11Rik|Naglt1b	major facilitator superfamily domain containing 4B2	protein-coding
mm_30228.1	chr3	145649971	145649992	-	1	NA	promoter-TSS (NM_010516)	promoter-TSS (NM_010516)	4	NM_010516	16007	Mm.1231	NM_010516	ENSMUSG00000028195	Cyr61	AI325051|CCN1|Igfbp10	cysteine rich protein 61	protein-coding
mm_68667.1	chr7	118856018	118856020	-	1	NA	promoter-TSS (NM_001168218)	promoter-TSS (NM_001168218)	-21	NM_023197	66356	Mm.482278	NM_023197	ENSMUSG00000030980	Knop1	2310008H09Rik|Tsg118	lysine rich nucleolar protein 1	protein-coding
mm_169960.1	chr16	94243385	94243395	-	1	NA	intron (NM_139145, intron 4 of 9)	intron (NM_139145, intron 4 of 9)	44466	NM_139145	110948	Mm.30921	NM_139145	ENSMUSG00000040820	Hlcs	410I21.SP6|D16Jhu34	holocarboxylase synthetase (biotin- [propriony-Coenzyme A-carboxylase (ATP-hydrolysing)] ligase)	protein-coding
mm_159797.1	chr5	112344162	112344162	+	1	NA	intron (NM_138646, intron 1 of 13)	intron (NM_138646, intron 1 of 13)	1067	NM_138646	192232	Mm.238043	NM_138646	ENSMUSG00000042328	Hps4	2010205O06Rik|AU040608|BLOC-3|C130020P05Rik|le|mKIAA1667	Hermansky-Pudlak syndrome 4	protein-coding
mm_154345.1	chrM	5359	5386	+	1	NA	NA	Intergenic	NA	NA								
mm_134606.1	chr16	20716102	20716122	-	1	NA	5' UTR (NM_009900, exon 1 of 24)	5' UTR (NM_009900, exon 1 of 24)	524	NM_009900	12724	Mm.177761	NM_009900	ENSMUSG00000022843	Clcn2	AL118368|ClC-2|Clc2|nmf240	chloride channel, voltage-sensitive 2	protein-coding
mm_5879.1	chr1	53825068	53825072	-	1	NA	intron (NM_001001883, intron 28 of 28)	intron (NM_001001883, intron 28 of 28)	-24354	NR_106149	102465783		NR_106149	ENSMUSG00000098443	Mir7681	Gm27806|mmu-mir-7681	microRNA 7681	ncRNA
mm_90974.1	chr10	13474668	13474703	-	1	NA	promoter-TSS (NM_001195065)	promoter-TSS (NM_001195065)	-289	NM_001195065	215789	Mm.283359	NM_001033257	ENSMUSG00000062866	Phactr2	AV158170|BC012871	phosphatase and actin regulator 2	protein-coding
mm_97281.1	chr11	76133945	76133947	+	1	NA	intron (NM_026664, intron 7 of 21)	intron (NM_026664, intron 7 of 21)	45684	NM_026664	68299	Mm.46397	NM_026664	ENSMUSG00000017288	Vps53	2010002A08Rik|2310040I21Rik|3100002B05Rik|Hccs1	VPS53 GARP complex subunit	protein-coding
mm_119952.1	chr14	55054871	55054875	+	1	NA	Intergenic	Intergenic	16411	NR_073535	100151693	Mm.378403	NR_073535	ENSMUSG00000072492	Gm10364	EG545052|ENSMUSG00000072492	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_52792.1	chr6	121264088	121264110	+	1	NA	intron (NM_011909, intron 8 of 10)	intron (NM_011909, intron 8 of 10)	18193	NM_011909	24110	Mm.326911	NM_011909	ENSMUSG00000030107	Usp18	1110058H21Rik|AW047653|UBP43|Ubp15	ubiquitin specific peptidase 18	protein-coding
mm_126052.1	chr15	76948781	76948791	+	1	NA	exon (NM_001347540, exon 2 of 5)	exon (NM_001347540, exon 2 of 5)	242	NM_054099	117171	Mm.322968	NM_054099	ENSMUSG00000063236	1110038F14Rik	-	RIKEN cDNA 1110038F14 gene	protein-coding
mm_155395.1	chrX	72918628	72918648	+	1	NA	promoter-TSS (NM_019405)	promoter-TSS (NM_019405)	117	NM_010941	18194	Mm.38792	NM_010941	ENSMUSG00000031349	Nsdhl	AI747449|Bpa|H105E3|Str|XAP104	NAD(P) dependent steroid dehydrogenase-like	protein-coding
mm_18127.1	chr2	45004536	45004551	-	1	NA	intron (NM_001289521, intron 3 of 8)	intron (NM_001289521, intron 3 of 8)	18634	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_48961.1	chr6	4541438	4541448	+	1	NA	TTS (NM_007743)	TTS (NM_007743)	35825	NM_007743	12843	Mm.277792	NM_007743	ENSMUSG00000029661	Col1a2	AA960264|AI325291|Col1a-2|Cola-2|Cola2|oim	collagen, type I, alpha 2	protein-coding
mm_133599.1	chr16	91465135	91465145	+	1	NA	promoter-TSS (NR_077219)	promoter-TSS (NR_077219)	36	NR_077219	100503120	Mm.387130	NR_077219	ENSMUSG00000084866	A930006K02Rik	-	RIKEN cDNA A930006K02 gene	ncRNA
mm_89021.1	chr10	82354246	82354277	+	1	NA	Intergenic	Intergenic	-112986	NM_001105557	237411		NM_172789	ENSMUSG00000062931	Zfp938	B230315N10Rik	zinc finger protein 938	protein-coding
mm_34909.1	chr4	155704879	155704887	+	1	NA	promoter-TSS (NM_026899)	promoter-TSS (NM_026899)	68	NM_026899	68991	Mm.294770	NM_026899	ENSMUSG00000029038	Ssu72	1190002E22Rik|1500011L16Rik|2610101M12Rik	Ssu72 RNA polymerase II CTD phosphatase homolog (yeast)	protein-coding
mm_40372.1	chr5	52190651	52190704	+	1	NA	promoter-TSS (NM_001042620)	promoter-TSS (NM_001042620)	-4	NR_015537	414108	Mm.383512	NR_015537	ENSMUSG00000097145	9230114K14Rik	-	RIKEN cDNA 9230114K14 gene	ncRNA
mm_137902.1	chr17	31854895	31854911	+	1	NA	exon (NM_010831, exon 2 of 14)	exon (NM_010831, exon 2 of 14)	889	NM_010831	17691	Mm.290941	NM_010831	ENSMUSG00000024042	Sik1	Msk|Sik|Snf1lk	salt inducible kinase 1	protein-coding
mm_23621.1	chr3	65806607	65806611	+	1	NA	intron (NM_001166659, intron 10 of 12)	L1MEc|LINE|L1	140381	NM_001166659	624866	Mm.296317	NM_001037923	ENSMUSG00000074579	Lekr1	EG546798|EG624866|Gm6534	leucine, glutamate and lysine rich 1	protein-coding
mm_53709.1	chr6	143183318	143183320	+	1	NA	intron (NM_029250, intron 2 of 7)	intron (NM_029250, intron 2 of 7)	16089	NM_029250	75320	Mm.272548	NM_029250	ENSMUSG00000030275	Etnk1	1110061E11Rik|4930555L11Rik|AI195356|AI841245|C80956|D6Ertd3e|EKI1	ethanolamine kinase 1	protein-coding
mm_116202.1	chr13	32338555	32338564	-	1	NA	promoter-TSS (NM_146041)	promoter-TSS (NM_146041)	-15	NM_146041	218138	Mm.247143	NM_146041	ENSMUSG00000038372	Gmds	BC031788|C87208	GDP-mannose 4, 6-dehydratase	protein-coding
mm_100569.1	chr11	120762793	120762793	+	1	NA	Intergenic	Intergenic	21411	NM_009053	19719	Mm.871	NM_009053	ENSMUSG00000025158	Rfng	-	RFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	protein-coding
mm_30276.1	chr3	146839366	146839367	-	1	NA	Intergenic	Intergenic	-13001	NM_001302957	70892	Mm.187793	NM_027594	ENSMUSG00000036745	Ttll7	1110049N09Rik|4921517B04Rik|C630030B20|mTTLL7	tubulin tyrosine ligase-like family, member 7	protein-coding
mm_46624.1	chr5	108405557	108405567	-	1	NA	intron (NM_008806, intron 3 of 21)	ORR1C1|LTR|ERVL-MaLR	17189	NM_008806	18587	Mm.1372	NM_008806	ENSMUSG00000029491	Pde6b	Pdeb|r|rd|rd-1|rd1|rd10	phosphodiesterase 6B, cGMP, rod receptor, beta polypeptide	protein-coding
mm_56116.1	chr6	87517387	87517393	-	1	NA	intron (NM_001037727, intron 1 of 10)	intron (NM_001037727, intron 1 of 10)	15869	NM_001037727	232201	Mm.119564	NM_175476	ENSMUSG00000030047	Arhgap25	A130039I20Rik	Rho GTPase activating protein 25	protein-coding
mm_140823.1	chr17	23610640	23610655	-	1	NA	exon (NM_001033425, exon 6 of 6)	exon (NM_001033425, exon 6 of 6)	9821	NM_001289482	332221	Mm.270315	NM_001033425	ENSMUSG00000023902	Zscan10	BC068284|Zfp206|Zkscan10|Znf206	zinc finger and SCAN domain containing 10	protein-coding
mm_32874.1	chr4	118527230	118527247	+	1	NA	promoter-TSS (NM_025572)	promoter-TSS (NM_025572)	-37	NM_025572	66451	Mm.34431	NM_025572	ENSMUSG00000028536	2610528J11Rik	TEMP	RIKEN cDNA 2610528J11 gene	protein-coding
mm_94109.1	chr10	128589680	128589694	-	1	NA	promoter-TSS (NM_010153)	promoter-TSS (NM_010153)	-186	NM_010153	13867	Mm.373043	NM_010153	ENSMUSG00000018166	Erbb3	C76256|Erbb-3|Erbb3r|Her3	erb-b2 receptor tyrosine kinase 3	protein-coding
mm_80751.1	chr9	95192923	95192926	+	1	NA	intron (NM_177909, intron 14 of 15)	intron (NM_177909, intron 14 of 15)	214346	NM_018763	54371	Mm.212446	NM_018763	ENSMUSG00000033350	Chst2	AI428561|AW121776|C130041E03Rik|Chts2|GST-2|GlcNAc6ST|Gn6st	carbohydrate sulfotransferase 2	protein-coding
mm_34367.1	chr4	144893090	144893103	+	1	NA	promoter-TSS (NM_011303)	promoter-TSS (NM_011303)	-41	NM_011303	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding
mm_49499.1	chr6	29760902	29760933	+	1	NA	3' UTR (NM_176996, exon 12 of 12)	3' UTR (NM_176996, exon 12 of 12)	-7526	NM_021414	74340	Mm.210899	NM_021414	ENSMUSG00000029772	Ahcyl2	4631427C17Rik|AI227036|Adohcyase3|mKIAA0828	S-adenosylhomocysteine hydrolase-like 2	protein-coding
mm_79199.1	chr9	48495407	48495451	+	1	NA	promoter-TSS (NM_001004191)	promoter-TSS (NM_001004191)	86	NM_001004191	434402	Mm.386950	NM_001004191	ENSMUSG00000042293	Gm5617	EG434402	predicted gene 5617	protein-coding
mm_96340.1	chr11	66911984	66912003	+	1	NA	promoter-TSS (NM_178656)	promoter-TSS (NM_178656)	2	NM_178656	193003	Mm.440256	NM_178656	ENSMUSG00000048070	Pirt	A530088H08Rik	phosphoinositide-interacting regulator of transient receptor potential channels	protein-coding
mm_167792.1	chr9	123924333	123924342	-	1	NA	Intergenic	Intergenic	44355	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_136020.1	chr16	76324787	76324792	-	1	NA	intron (NM_173440, intron 3 of 3)	intron (NM_173440, intron 3 of 3)	48260	NM_173440	268903	Mm.74711	NM_173440	ENSMUSG00000048490	Nrip1	6030458L20Rik|8430438I05Rik|9630050P12|AA959574|AW456757|RIP140	nuclear receptor interacting protein 1	protein-coding
mm_167856.1	chrX	12060511	12060511	+	1	NA	intron (NM_001168321, intron 2 of 13)	intron (NM_001168321, intron 2 of 13)	20042	NM_175045	71458	Mm.196328	NM_029510	ENSMUSG00000040363	Bcor	2900008C10Rik|5830466J11Rik|8430401K06Rik|BcorR|D930024N20Rik|mKIAA1575	BCL6 interacting corepressor	protein-coding
mm_86323.1	chr9	123021523	123021606	-	1	NA	exon (NM_025339, exon 1 of 3)	exon (NM_025339, exon 1 of 3)	238	NM_001164823	66079	Mm.482265	NM_025339	ENSMUSG00000066233	Tmem42	0610027O18Rik|4933429E06Rik|AV003444|D9Ertd662e	transmembrane protein 42	protein-coding
mm_122248.1	chr14	33978752	33978791	-	1	NA	promoter-TSS (NM_001013777)	promoter-TSS (NM_001013777)	-7	NM_001013777	382867	Mm.343728	NM_001013777	ENSMUSG00000044519	Zfp488	Gm1206|Znf488	zinc finger protein 488	protein-coding
mm_121683.1	chr14	13232898	13232903	-	1	NA	intron (NR_121588, intron 2 of 3)	L1_Mur2|LINE|L1	51738	NR_121589	328354	Mm.252404	NM_177813	ENSMUSG00000051729	Gm5087	C630025C03|EG328354	predicted gene 5087	ncRNA
mm_32172.1	chr4	100479129	100479146	+	1	NA	5' UTR (NM_001033773, exon 1 of 10)	5' UTR (NM_001033773, exon 1 of 10)	270	NM_001033773	381534	Mm.318133	NM_001033773	ENSMUSG00000069733	Ube2u	-	ubiquitin-conjugating enzyme E2U (putative)	protein-coding
mm_121069.1	chr14	96107742	96107772	+	1	NA	intron (NM_053105, intron 10 of 10)	RLTR44E|LTR|ERVK	226491	NM_025733	66732	Mm.75060	NM_025733	ENSMUSG00000034689	4921530L21Rik	-	RIKEN cDNA 4921530L21 gene	protein-coding
mm_122908.1	chr14	54953899	54953911	-	1	NA	exon (NM_010856, exon 21 of 39)	exon (NM_010856, exon 21 of 39)	-4763	NR_029724	387204		NR_029724	ENSMUSG00000065432	Mir208a	Mirn208|Mirn208a|mir-208|mir-208a|mmu-mir-208	microRNA 208a	ncRNA
mm_15070.1	chr2	153107703	153107709	+	1	NA	promoter-TSS (NM_010407)	promoter-TSS (NM_010407)	-762	NM_001172117	15162	Mm.715	NM_010407	ENSMUSG00000003283	Hck	AI849071|Bmk	hemopoietic cell kinase	protein-coding
mm_123759.1	chr14	70205827	70205871	-	1	NA	5' UTR (NM_001271407, exon 1 of 21)	5' UTR (NM_001271407, exon 1 of 21)	173	NM_001271407	20410	Mm.5068	NM_011366	ENSMUSG00000022091	Sorbs3	SCAM-1|SH3P3|Sh3d4|vinexin-g	sorbin and SH3 domain containing 3	protein-coding
mm_137082.1	chr17	21450437	21450447	+	1	NA	promoter-TSS (NM_009558)	promoter-TSS (NM_009558)	68	NM_009558	22709	Mm.293030	NM_009558	ENSMUSG00000023892	Zfp51	Zfp-51|zfec12	zinc finger protein 51	protein-coding
mm_22267.1	chr2	178414461	178414507	-	1	NA	promoter-TSS (NM_001081289)	promoter-TSS (NM_001081289)	-21	NM_001085501	228966	Mm.472736	NM_001085501	ENSMUSG00000049999	Ppp1r3d	2610024M03Rik|Gm359	protein phosphatase 1, regulatory subunit 3D	protein-coding
mm_33059.1	chr4	123201417	123201431	+	1	NA	promoter-TSS (NM_001085502)	promoter-TSS (NM_001085502)	-129	NM_001085502	230718	Mm.354635	NM_001085502	ENSMUSG00000054958	Nt5c1a	Cn1a|Gm49	5'-nucleotidase, cytosolic IA	protein-coding
mm_528.1	chr1	37687338	37687350	+	1	NA	intron (NM_028096, intron 1 of 9)	L1MD1|LINE|L1	32467	NM_028096	72097	Mm.142607	NM_028096	ENSMUSG00000026090	2010300C02Rik	-	RIKEN cDNA 2010300C02 gene	protein-coding
mm_138058.1	chr17	33928271	33928301	+	1	NA	3' UTR (NM_009318, exon 8 of 8)	3' UTR (NM_009318, exon 8 of 8)	-1608	NM_009059	19732	Mm.43777	NM_009059	ENSMUSG00000041354	Rgl2	KE1.5|Rab2l|Rgt2|Rlf	ral guanine nucleotide dissociation stimulator-like 2	protein-coding
mm_80851.1	chr9	98369753	98369760	+	1	NA	intron (NM_144533, intron 2 of 4)	intron (NM_144533, intron 2 of 4)	-53205	NM_011254	19659	Mm.279741	NM_011254	ENSMUSG00000046402	Rbp1	CRBPI|Crbp|Rbp-1	retinol binding protein 1, cellular	protein-coding
mm_145410.1	chr18	57472464	57472480	+	1	NA	intron (NM_001134697, intron 1 of 1)	intron (NM_001134697, intron 1 of 1)	3986	NM_001134697	629147	Mm.57415	NM_001134697	ENSMUSG00000069372	Ctxn3	ENSMUSG00000069372	cortexin 3	protein-coding
mm_38480.1	chr4	140702399	140702448	-	1	NA	exon (NM_173867, exon 2 of 13)	exon (NM_173867, exon 2 of 13)	950	NM_173867	108911	Mm.253	NM_173867	ENSMUSG00000040945	Rcc2	2610510H01Rik|2610529N02Rik|AA536646|AA675016|Td60|mKIAA1470	regulator of chromosome condensation 2	protein-coding
mm_38601.1	chr4	141859542	141859583	-	1	NA	3' UTR (NM_025994, exon 4 of 4)	3' UTR (NM_025994, exon 4 of 4)	-13203	NM_001033875	76701	Mm.489680	NM_001033875	ENSMUSG00000062478	Ctrc	1810044E12Rik	chymotrypsin C (caldecrin)	protein-coding
mm_93403.1	chr10	107912254	107912262	-	1	NA	promoter-TSS (NM_001177567)	promoter-TSS (NM_001177567)	-124	NM_001177567	628870	Mm.336090	NM_001177567	ENSMUSG00000091455	Otogl	EG628870|Gm6924	otogelin-like	protein-coding
mm_29610.1	chr3	121263244	121263252	-	1	NA	promoter-TSS (NM_178936)	promoter-TSS (NM_178936)	68	NM_178936	99887	Mm.26088	NM_178936	ENSMUSG00000028132	Tmem56	4930577M16Rik|AU018104|AW109744|C730036B01Rik	transmembrane protein 56	protein-coding
mm_170683.1	chr2	127208453	127208455	+	1	NA	promoter-TSS (NM_177214)	promoter-TSS (NM_177214)	50	NM_177214	320632	Mm.215860	NM_177214	ENSMUSG00000003660	Snrnp200	A330064G03Rik|Ascc3l1|BC011390|HELIC2|U5-200-KD|U5-200KD	small nuclear ribonucleoprotein 200 (U5)	protein-coding
mm_38897.1	chr4	149854467	149854472	-	1	NA	Intergenic	(A)n|Simple_repeat|Simple_repeat	-80202	NM_027460	70556	Mm.41877	NM_027460	ENSMUSG00000028982	Slc25a33	5730438N18Rik|Pnc1	solute carrier family 25, member 33	protein-coding
mm_91050.1	chr10	18743912	18743972	-	1	NA	promoter-TSS (NM_001033258)	promoter-TSS (NM_001033258)	-184	NM_001033258	215821	Mm.40491	NM_001033258	ENSMUSG00000019852	Arfgef3	9630004D11|B930094H20Rik|BIG3|D10Bwg1379e|mKIAA1244	ARFGEF family member 3	protein-coding
mm_78645.1	chr9	40286092	40286095	+	1	NA	intron (NM_178227, intron 5 of 5)	MTE2a|LTR|ERVL-MaLR	16877	NM_178227	235281	Mm.290083	NM_153522	ENSMUSG00000049281	Scn3b	1110001K16Rik|4833414B02Rik|Scnb3	sodium channel, voltage-gated, type III, beta	protein-coding
mm_89126.1	chr10	84917620	84917655	+	1	NA	promoter-TSS (NM_183172)	promoter-TSS (NM_183172)	24	NM_183172	237422	Mm.18936	NM_183172	ENSMUSG00000035620	Ric8b	BC051080|Ric-8|Ric-8b	RIC8 guanine nucleotide exchange factor B	protein-coding
mm_134762.1	chr16	23375058	23375063	-	1	NA	Intergenic	RMER19C|LTR|ERVK	-54073	NM_001004151	239766	Mm.208751	NM_001004151	ENSMUSG00000033383	Rtp1	Gm1766|Gm604	receptor transporter protein 1	protein-coding
mm_28458.1	chr3	90692718	90692733	-	1	NA	TTS (NM_001281852)	TTS (NM_001281852)	2996	NM_001281852	20202	Mm.2128	NM_009114	ENSMUSG00000056071	S100a9	60B8Ag|AW546964|BEE22|Cagb|GAGB|L1Ag|MRP14|p14	S100 calcium binding protein A9 (calgranulin B)	protein-coding
mm_83351.1	chr9	44344121	44344132	-	1	NA	5' UTR (NM_013551, exon 1 of 14)	5' UTR (NM_013551, exon 1 of 14)	102	NM_013551	15288	Mm.247676	NM_013551	ENSMUSG00000032126	Hmbs	PBGD|T25658|Ups|Uros1	hydroxymethylbilane synthase	protein-coding
mm_119363.1	chr14	41116711	41116724	+	1	NA	intron (NM_133653, intron 6 of 9)	intron (NM_133653, intron 6 of 9)	11684	NM_133653	11720	Mm.14064	NM_133653	ENSMUSG00000037798	Mat1a	AI046368|AdoMet|Ams|MAT|MATA1|SAMS|SAMS1	methionine adenosyltransferase I, alpha	protein-coding
mm_18697.1	chr2	71546402	71546469	-	1	NA	5' UTR (NM_010054, exon 1 of 3)	5' UTR (NM_010054, exon 1 of 3)	319	NM_010054	13392	Mm.3896	NM_010054	ENSMUSG00000023391	Dlx2	AW121999|Dlx-2|Tes-1	distal-less homeobox 2	protein-coding
mm_163173.1	chr11	87794751	87794768	+	1	NA	intron (NM_010824, intron 2 of 13)	intron (NM_010824, intron 2 of 13)	975	NM_010824	17523	Mm.4668	NM_010824	ENSMUSG00000009350	Mpo	mKIAA4033	myeloperoxidase	protein-coding
mm_158812.1	chrX	167307942	167307954	-	1	NA	exon (NM_001290758, exon 4 of 4)	exon (NM_001290758, exon 4 of 4)	22623	NM_001290757	170743	Mm.23979	NM_133211	ENSMUSG00000044583	Tlr7	-	toll-like receptor 7	protein-coding
mm_31960.1	chr4	86886014	86886039	+	1	NA	intron (NM_139306, intron 1 of 5)	intron (NM_139306, intron 1 of 5)	11612	NM_139306	230379	Mm.45019	NM_139306	ENSMUSG00000038007	Acer2	2410116I05Rik|Asah3l|CRG-L1|maCER2	alkaline ceramidase 2	protein-coding
mm_63982.1	chr7	139992639	139992666	+	1	NA	promoter-TSS (NM_001291066)	promoter-TSS (NM_001291066)	-90	NM_001291066	11501	Mm.15969	NM_007403	ENSMUSG00000025473	Adam8	ADAM 8|CD156|CD156a|E430039A18Rik|MS2	a disintegrin and metallopeptidase domain 8	protein-coding
mm_171884.1	chr5	33275111	33275127	-	1	NA	promoter-TSS (NM_001198861)	promoter-TSS (NM_001198861)	-115	NM_001198860	13016	Mm.7286	NM_013502	ENSMUSG00000037373	Ctbp1	BARS|CtBP3/BARS|D4S115h|D5H4S115|D5H4S115E	C-terminal binding protein 1	protein-coding
mm_543.1	chr1	38018047	38018060	+	1	NA	exon (NM_198303, exon 3 of 24)	exon (NM_198303, exon 3 of 24)	20043	NM_198303	226982	Mm.260943	NM_198303	ENSMUSG00000026083	Eif5b	A030003E17Rik|BC018347|IF2	eukaryotic translation initiation factor 5B	protein-coding
mm_139142.1	chr17	47511880	47511890	+	1	NA	intron (NM_001081635, intron 1 of 6)	intron (NM_001081635, intron 1 of 6)	6834	NM_001081635	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_17095.1	chr2	23040178	23040201	-	1	NA	promoter-TSS (NM_001077190)	promoter-TSS (NM_001077190)	52	NM_001077192	11308	Mm.205647	NM_007380	ENSMUSG00000058835	Abi1	E3B1|NAP1|Ssh3bp1|abi-1	abl-interactor 1	protein-coding
mm_54124.1	chr6	18407878	18407881	-	1	NA	intron (NM_080285, intron 10 of 22)	intron (NM_080285, intron 10 of 22)	106946	NM_080285	30785	Mm.224189	NM_080285	ENSMUSG00000000416	Cttnbp2	3010022N24Rik|4732477G22Rik|6430526E05|9130022E09Rik|AU040881|Cortbp2|ORF4|mKIAA1758	cortactin binding protein 2	protein-coding
mm_80709.1	chr9	92250166	92250187	+	1	NA	promoter-TSS (NM_011636)	promoter-TSS (NM_011636)	-18	NM_011636	22038	Mm.421956	NM_011636	ENSMUSG00000032369	Plscr1	MmTRA1a|MmTRA1b|Nor1|Tra1|Tra1a|Tra1b|Tras1|Tras2	phospholipid scramblase 1	protein-coding
mm_97621.1	chr11	78957411	78957427	+	1	NA	exon (NM_010927, exon 26 of 27)	exon (NM_010927, exon 26 of 27)	27505	NM_001159301	16859	Mm.341434	NM_010708	ENSMUSG00000001123	Lgals9	AA407335|AI194909|AI265545|LGALS35|Lgals5|gal-9|galectin-9	lectin, galactose binding, soluble 9	protein-coding
mm_159385.1	chr3	90726915	90726915	+	1	NA	promoter-TSS (NM_207263)	promoter-TSS (NM_207263)	9	NM_207263	384997	Mm.316644	NM_207263	ENSMUSG00000042250	Pglyrp4	Gm1478|Gm413	peptidoglycan recognition protein 4	protein-coding
mm_30368.1	chr3	152176353	152176380	-	1	NA	Intergenic	Lx5|LINE|L1	-10466	NM_016867	54120	Mm.97	NM_016867	ENSMUSG00000039131	Gipc2	2200002N01Rik|AU021850|Semcap2	GIPC PDZ domain containing family, member 2	protein-coding
mm_121121.1	chr14	101840559	101840569	+	1	NA	promoter-TSS (NM_001347628)	promoter-TSS (NM_001347628)	-59	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_69069.1	chr7	126949860	126949889	-	1	NA	promoter-TSS (NM_001039645)	promoter-TSS (NM_001039645)	-293	NM_001039645	233879	Mm.444143	NM_001039645	ENSMUSG00000046378	Asphd1	A830007L07Rik|Gm168	aspartate beta-hydroxylase domain containing 1	protein-coding
mm_138711.1	chr17	36121667	36121698	+	1	NA	promoter-TSS (NM_010395)	promoter-TSS (NM_010395)	-238	NR_046286	15024	Mm.426031	NM_010395	ENSMUSG00000079491	H2-T10	H-2T10	histocompatibility 2, T region locus 10	protein-coding
mm_14570.1	chr2	135312393	135312394	+	1	NA	intron (NM_019677, intron 11 of 32)	intron (NM_019677, intron 11 of 32)	-93437	NR_039540	100628568		NR_039540	ENSMUSG00000092830	Mir3963	mmu-mir-3963|mu-mir-3963	microRNA 3963	ncRNA
mm_127902.1	chr15	9507777	9507804	-	1	NA	3' UTR (NM_008372, exon 8 of 8)	3' UTR (NM_008372, exon 8 of 8)	22086	NM_008372	16197	Mm.389	NM_008372	ENSMUSG00000003882	Il7r	CD127|IL-7Ralpha	interleukin 7 receptor	protein-coding
mm_118934.1	chr14	27115159	27115201	+	1	NA	Intergenic	CpG	-28813	NM_001289686	71704	Mm.248606	NM_027871	ENSMUSG00000021895	Arhgef3	1200004I24Rik|9830169H03Rik|C76747|Xpln	Rho guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_26581.1	chr3	149326994	149327026	+	1	NA	Intergenic	Intergenic	52273	NR_040591	381482	Mm.393866	NR_040591		Gm1653	-	predicted gene 1653	ncRNA
mm_44155.1	chr5	150496478	150496480	+	1	NA	3' UTR (NM_172887, exon 61 of 61)	3' UTR (NM_172887, exon 61 of 61)	5740	NR_024513	194292	Mm.300184	NR_024513		Gm5	Gm1812	predicted gene 5	ncRNA
mm_136112.1	chr16	85542583	85542590	-	1	NA	intron (NM_144853, intron 2 of 3)	intron (NM_144853, intron 2 of 3)	7787	NM_144853	224405	Mm.213203	NM_144853	ENSMUSG00000041134	Cyyr1	-	cysteine and tyrosine-rich protein 1	protein-coding
mm_104421.1	chr11	94782701	94782705	-	1	NA	promoter-TSS (NM_001034896)	promoter-TSS (NM_001034896)	0	NM_001034896	544806	Mm.379774	NM_001034896	ENSMUSG00000075610	Tmem92	AU016430|Tmem92-ps	transmembrane protein 92	protein-coding
mm_44165.1	chr5	150756296	150756320	+	1	NA	intron (NM_001346503, intron 14 of 34)	intron (NM_001346503, intron 14 of 34)	82481	NM_001346503	100710	Mm.32959	NM_175310	ENSMUSG00000034021	Pds5b	AI646570|AS3|AW212954|Aprin|Tg(Wap-ERBB2)229Wzw|WAP-Her-2|mKIAA0979	PDS5 cohesin associated factor B	protein-coding
mm_124674.1	chr15	6422302	6422327	+	1	NA	exon (NM_001102400, exon 5 of 13)	exon (NM_001102400, exon 5 of 13)	-23019	NM_013485	12279	Mm.29095	NM_013485	ENSMUSG00000022149	C9	-	complement component 9	protein-coding
mm_29323.1	chr3	108017844	108017862	-	1	NA	5' UTR (NM_010358, exon 1 of 8)	5' UTR (NM_010358, exon 1 of 8)	120	NM_010358	14862	Mm.37199	NM_010358	ENSMUSG00000058135	Gstm1	Gstb-1|Gstb1	glutathione S-transferase, mu 1	protein-coding
mm_1499.1	chr1	72221752	72221774	+	1	NA	Intergenic	Intergenic	-9456	NM_001005423	381269	Mm.422636	NM_001005423	ENSMUSG00000039395	Mreg	Gm974|Wdt2|dsu	melanoregulin	protein-coding
mm_27689.1	chr3	65974747	65974766	-	1	NA	Intergenic	CpG	-16531	NM_019937	56706	Mm.175612	NM_019937	ENSMUSG00000027829	Ccnl1	2610030E23Rik|AU018493|Ccnl|ania-6a	cyclin L1	protein-coding
mm_78614.1	chr9	37545252	37545273	+	1	NA	3' UTR (NM_022029, exon 4 of 4)	3' UTR (NM_022029, exon 4 of 4)	6007	NM_020518	57276	Mm.27478	NM_020518	ENSMUSG00000001943	Vsig2	1190004B15Rik|2210413P10Rik|AU040484|CTX|Ctm	V-set and immunoglobulin domain containing 2	protein-coding
mm_64199.1	chr7	141468777	141468807	+	1	NA	promoter-TSS (NM_001111050)	promoter-TSS (NM_001111050)	3	NM_001111050	12476	Mm.30246	NM_009842	ENSMUSG00000025510	Cd151	PETA-3|SFA-1|Tspan24	CD151 antigen	protein-coding
mm_76658.1	chr8	93229518	93229611	-	1	NA	promoter-TSS (NM_133660)	promoter-TSS (NM_133660)	55	NM_133660	13897	Mm.63490	NM_133660	ENSMUSG00000061959	Ces1e	Eg|Es-22|Es22|egasyn	carboxylesterase 1E	protein-coding
mm_122239.1	chr14	33370138	33370147	-	1	NA	TTS (NM_153800)	TTS (NM_153800)	40882	NM_001310452	26419	Mm.21495	NM_016700	ENSMUSG00000021936	Mapk8	AI849689|JNK|JNK1|Prkm8|SAPK1	mitogen-activated protein kinase 8	protein-coding
mm_116407.1	chr13	41425241	41425256	-	1	NA	intron (NM_001111324, intron 2 of 7)	ID4_|SINE|ID	62112	NM_001111324	18003	Mm.288980	NM_017464	ENSMUSG00000021365	Nedd9	Cas-L|CasL|HEF1|MEF1|Nedd-9|p105	neural precursor cell expressed, developmentally down-regulated gene 9	protein-coding
mm_155811.1	chrX	99820184	99820200	+	1	NA	promoter-TSS (NM_001081283)	promoter-TSS (NM_001081283)	-877	NM_001081283	620592	Mm.388976	NM_001081283	ENSMUSG00000071719	Tmem28	EG620592|Fam155b|Tnen28	transmembrane protein 28	protein-coding
mm_26322.1	chr3	142530288	142530298	+	1	NA	promoter-TSS (NM_001083312)	promoter-TSS (NM_001083312)	-43	NM_001083312	229900	Mm.45740	NM_145545	ENSMUSG00000040253	Gbp7	9830147J24Rik	guanylate binding protein 7	protein-coding
mm_29215.1	chr3	107038307	107038335	-	1	NA	TTS (NM_008418)	TTS (NM_008418)	-1183	NR_033498	229694	Mm.347584	NM_173787	ENSMUSG00000056145	AI504432	A230102G19	expressed sequence AI504432	ncRNA
mm_8024.1	chr1	135105334	135105349	-	1	NA	promoter-TSS (NM_001033409)	promoter-TSS (NM_001033409)	-65	NM_001033409	329252	Mm.279594	NM_001033409	ENSMUSG00000042793	Lgr6	A530037C04Rik|D830026M09	leucine-rich repeat-containing G protein-coupled receptor 6	protein-coding
mm_14663.1	chr2	138278397	138278407	+	1	NA	promoter-TSS (NM_145534)	promoter-TSS (NM_145534)	-91	NM_145534	228662	Mm.153405	NM_145534	ENSMUSG00000062098	Btbd3	mKIAA0952	BTB (POZ) domain containing 3	protein-coding
mm_127202.1	chr15	99126619	99126640	+	1	NA	promoter-TSS (NM_139140)	promoter-TSS (NM_139140)	-216	NM_139140	72572	Mm.276650	NM_139140	ENSMUSG00000051934	Spats2	2700012F11Rik|59kDa|Scr59|p59	spermatogenesis associated, serine-rich 2	protein-coding
mm_115631.1	chr13	12106976	12106984	-	1	NA	promoter-TSS (NM_023868)	promoter-TSS (NM_023868)	-35	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding
mm_148646.1	chr19	5490558	5490606	+	1	NA	5' UTR (NM_007687, exon 1 of 4)	5' UTR (NM_007687, exon 1 of 4)	127	NM_007687	12631	Mm.329655	NM_007687	ENSMUSG00000056201	Cfl1	AA959946|Cof	cofilin 1, non-muscle	protein-coding
mm_155480.1	chrX	73675501	73675516	+	1	NA	intron (NM_001142810, intron 1 of 12)	intron (NM_001142810, intron 1 of 12)	2375	NM_001142809	102857	Mm.274553	NM_133987	ENSMUSG00000019558	Slc6a8	AA589632|CRT|CRTR|CT1|CTR5|Creat	solute carrier family 6 (neurotransmitter transporter, creatine), member 8	protein-coding
mm_101529.1	chr11	33162316	33162353	-	1	NA	intron (NM_008722, intron 1 of 10)	intron (NM_008722, intron 1 of 10)	872	NM_001252261	18148	Mm.485384	NM_008722	ENSMUSG00000057113	Npm1	B23|NO38|Npm	nucleophosmin 1	protein-coding
mm_60203.1	chr7	43430068	43430082	+	1	NA	promoter-TSS (NM_177693)	promoter-TSS (NM_177693)	-26	NM_177693	233187	Mm.267027	NM_177693	ENSMUSG00000004613	Lim2	19kDa|4833403J20|MP19|To3	lens intrinsic membrane protein 2	protein-coding
mm_62774.1	chr7	112361634	112361645	+	1	NA	Intergenic	MIR|SINE|MIR	-6669	NM_027587	100504195	Mm.291129	NM_027587	ENSMUSG00000030771	Micalcl	4921517J23Rik	MICAL C-terminal like	protein-coding
mm_170148.1	chr17	45563505	45563524	+	1	NA	promoter-TSS (NM_028662)	promoter-TSS (NM_028662)	-638	NM_028662	73836	Mm.289716	NM_028662	ENSMUSG00000037089	Slc35b2	1110003M08Rik|AA407792|AI842275|PAPST1|Slc35b1	solute carrier family 35, member B2	protein-coding
mm_120023.1	chr14	55765957	55765999	+	1	NA	promoter-TSS (NM_008519)	promoter-TSS (NM_008519)	16	NM_008519	16995	Mm.20853	NM_008519	ENSMUSG00000046908	Ltb4r1	BLT1|BLTR|Ltb4r|mBLTR	leukotriene B4 receptor 1	protein-coding
mm_139353.1	chr17	50509557	50509597	+	1	NA	promoter-TSS (NM_013880)	promoter-TSS (NM_013880)	30	NM_013880	224860	Mm.217362	NM_013880	ENSMUSG00000038910	Plcl2	PLC-L2|PRIP-2|Plce2|mKIAA1092	phospholipase C-like 2	protein-coding
mm_162607.1	chr1	183289841	183289850	+	1	NA	intron (NM_027861, intron 5 of 13)	RLTR17|LTR|ERVK	7163	NM_027861	71678	Mm.392270	NM_027861	ENSMUSG00000046836	Brox	0610010K06Rik	BRO1 domain and CAAX motif containing	protein-coding
mm_111533.1	chr12	100725059	100725081	-	1	NA	promoter-TSS (NM_001330702)	promoter-TSS (NM_001330702)	50	NM_001330702	73086	Mm.220417	NM_153587	ENSMUSG00000021180	Rps6ka5	3110005L17Rik|6330404E13Rik|AI854034|MSK1|MSPK1|RLPK|RLSK|S6K-alpha-5	ribosomal protein S6 kinase, polypeptide 5	protein-coding
mm_17029.1	chr2	19553909	19553922	-	1	NA	promoter-TSS (NM_027600)	promoter-TSS (NM_027600)	-5	NM_027600	70909	Mm.158488	NM_027600	ENSMUSG00000026734	4921504E06Rik	4921522E24Rik	RIKEN cDNA 4921504E06 gene	protein-coding
mm_52831.1	chr6	121363683	121363722	+	1	NA	exon (NM_133661, exon 14 of 15)	exon (NM_133661, exon 14 of 15)	17005	NM_133661	14411	Mm.274506	NM_133661	ENSMUSG00000030109	Slc6a12	BGT1|GAT-2|GAT2|Gabt2	solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12	protein-coding
mm_18727.1	chr2	72963798	72963826	-	1	NA	intron (NM_001018042, intron 4 of 6)	B1_Mus1|SINE|Alu	15469	NM_001098425	20687	Mm.124328	NM_011450	ENSMUSG00000027109	Sp3	D130027J01Rik	trans-acting transcription factor 3	protein-coding
mm_53550.1	chr6	136861854	136861856	+	1	NA	Intergenic	Lx8|LINE|L1	-4255	NM_026639	109978	Mm.31840	NM_026639	ENSMUSG00000030217	Art4	4432404K01Rik|ARTC4|DO|DOK1	ADP-ribosyltransferase 4	protein-coding
mm_172227.1	chr6	67267058	67267060	+	1	NA	promoter-TSS (NM_025814)	promoter-TSS (NM_025814)	80	NM_025814	66870	Mm.240490	NM_025814	ENSMUSG00000036371	Serbp1	1200009K13Rik|9330147J08Rik|AL022786|Pairbp1	serpine1 mRNA binding protein 1	protein-coding
mm_164154.1	chr15	64921458	64921485	-	1	NA	5' UTR (NM_009623, exon 1 of 18)	5' UTR (NM_009623, exon 1 of 18)	825	NM_001331075	11514	Mm.1425	NM_009623	ENSMUSG00000022376	Adcy8	AC8|AW060868	adenylate cyclase 8	protein-coding
mm_95972.1	chr11	58954676	58954696	+	1	NA	promoter-TSS (NM_178218)	promoter-TSS (NM_178218)	1	NM_178218	319162	Mm.212549	NM_178218	ENSMUSG00000078851	Hist3h2a	-	histone cluster 3, H2a	protein-coding
mm_27373.1	chr3	50442713	50442714	-	1	NA	intron (NM_011990, intron 1 of 11)	intron (NM_011990, intron 1 of 11)	900	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_118706.1	chr14	22164935	22164953	+	1	NA	intron (NM_028275, intron 2 of 6)	Lx8b|LINE|L1	145232	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_33524.1	chr4	130932134	130932144	+	1	NA	intron (NM_010686, intron 7 of 7)	MIRb|SINE|MIR	-12246	NM_010769	17180	Mm.271796	NM_010769	ENSMUSG00000040533	Matn1	CMP|Crtm|Mat1|matrilin-1	matrilin 1, cartilage matrix protein	protein-coding
mm_113183.1	chr13	24905636	24905647	+	1	NA	promoter-TSS (NR_045182)	promoter-TSS (NR_045182)	41	NR_045182	73326	Mm.458692	NR_045182		4932702P03Rik	1700047I16Rik	RIKEN cDNA 4932702P03 gene	ncRNA
mm_125891.1	chr15	75866073	75866100	+	1	NA	intron (NM_026960, intron 6 of 10)	intron (NM_026960, intron 6 of 10)	3747	NM_026960	69146	Mm.27385	NM_026960	ENSMUSG00000022575	Gsdmd	1810036L03Rik|AW558049|DF5L|Dfna5l|Gsdmdc1|M2-4	gasdermin D	protein-coding
mm_107563.1	chr12	43460166	43460170	+	1	NA	Intergenic	Lx7|LINE|L1	749900	NM_013760	27362	Mm.27432	NM_013760	ENSMUSG00000014905	Dnajb9	AA408011|AA673251|AA673481|AW556981|ERdj4|Mdg1|mDj7	DnaJ heat shock protein family (Hsp40) member B9	protein-coding
mm_98991.1	chr11	98764973	98765022	+	1	NA	3' UTR (NM_178060, exon 9 of 9)	3' UTR (NM_178060, exon 9 of 9)	10380	NM_145434	217166	Mm.390397	NM_145434	ENSMUSG00000020889	Nr1d1	A530070C09Rik|R75201	nuclear receptor subfamily 1, group D, member 1	protein-coding
mm_11008.1	chr2	26581012	26581023	+	1	NA	promoter-TSS (NM_178444)	promoter-TSS (NM_178444)	-39	NM_178444	353156	Mm.268933	NM_178444	ENSMUSG00000026921	Egfl7	VE-statin|Zneu1	EGF-like domain 7	protein-coding
mm_66247.1	chr7	35556034	35556070	-	1	NA	promoter-TSS (NM_033080)	promoter-TSS (NM_033080)	-124	NM_033080	110959	Mm.410206	NM_033080	ENSMUSG00000034875	Nudt19	D7Rp2|D7Rp2-r|D7Rp2-s|D7Rp2e|RP2-r|RP2-s	nudix (nucleoside diphosphate linked moiety X)-type motif 19	protein-coding
mm_109457.1	chr12	111160264	111160272	+	1	NA	non-coding (NR_130987, exon 4 of 4)	non-coding (NR_130987, exon 4 of 4)	-6102	NM_001286122	22031	Mm.27431	NM_011632	ENSMUSG00000021277	Traf3	AI528849|CAP-1|CD40bp|CRAF1|LAP1|T-BAM|amn	TNF receptor-associated factor 3	protein-coding
mm_108962.1	chr12	102398219	102398264	+	1	NA	exon (NM_011175, exon 11 of 14)	exon (NM_011175, exon 11 of 14)	41572	NM_011175	19141	Mm.17185	NM_011175	ENSMUSG00000021190	Lgmn	AEP|AI746452|AU022324|Prsc1	legumain	protein-coding
mm_157569.1	chrX	52548759	52548763	-	1	NA	intron (NM_016697, intron 2 of 7)	intron (NM_016697, intron 2 of 7)	-27082	NR_045367	100504594	Mm.447008	NR_045367	ENSMUSG00000055110	A630012P03Rik	-	RIKEN cDNA A630012P03 gene	ncRNA
mm_3901.1	chr1	161706070	161706073	+	1	NA	Intergenic	Intergenic	82424	NM_001205243	14103	Mm.3355	NM_010177	ENSMUSG00000000817	Fasl	APT1LG1|CD178|CD95-L|CD95L|Fas-L|Faslg|Tnfsf6|Tnlg1a|gld	Fas ligand (TNF superfamily, member 6)	protein-coding
mm_143233.1	chr17	63499453	63499526	-	1	NA	exon (NM_015794, exon 1 of 9)	exon (NM_015794, exon 1 of 9)	1091	NM_015794	50758	Mm.136366	NM_015794	ENSMUSG00000023965	Fbxl17	6330576B01Rik|AI452053|BB073797|C130023C01Rik|Fbx13|Fbxo13	F-box and leucine-rich repeat protein 17	protein-coding
mm_97043.1	chr11	72314439	72314455	+	1	NA	promoter-TSS (NM_001099688)	promoter-TSS (NM_001099688)	3	NM_001099688	628100	Mm.390365	NM_001099688	ENSMUSG00000070388	Fbxo39	1700010H23Rik	F-box protein 39	protein-coding
mm_11824.1	chr2	44927359	44927419	+	1	NA	Intergenic	CpG	-65767	NM_172662	227835	Mm.314312	NM_172662	ENSMUSG00000036890	Gtdc1	E330008O22Rik	glycosyltransferase-like domain containing 1	protein-coding
mm_34502.1	chr4	148664322	148664341	+	1	NA	intron (NM_001085505, intron 5 of 10)	intron (NM_001085505, intron 5 of 10)	21014	NM_001085505	230909	Mm.332067	NM_001085505	ENSMUSG00000070577	Gm572	b2b1167Clo	predicted gene 572	protein-coding
mm_60339.1	chr7	44335824	44335830	+	1	NA	intron (NM_001034115, intron 15 of 24)	intron (NM_001034115, intron 15 of 24)	25563	NM_001034115	243961	Mm.360368	NM_001034115	ENSMUSG00000038738	Shank1	-	SH3/ankyrin domain gene 1	protein-coding
mm_8308.1	chr1	144077404	144077435	-	1	NA	Intergenic	Intergenic	-73270	NM_009061	19735	Mm.28262	NM_009061	ENSMUSG00000026360	Rgs2	GOS8	regulator of G-protein signaling 2	protein-coding
mm_19567.1	chr2	101628959	101629014	-	1	NA	promoter-TSS (NM_026592)	promoter-TSS (NM_026592)	0	NM_026592	68170	Mm.31263	NM_026592	ENSMUSG00000027165	B230118H07Rik	NWC	RIKEN cDNA B230118H07 gene	protein-coding
mm_91801.1	chr10	53631690	53631690	-	1	NA	Intergenic	Intergenic	-1251	NM_027830	71567	Mm.278221	NM_027830	ENSMUSG00000058298	Mcm9	9030408O17Rik|Gm235|Mcmdc1	minichromosome maintenance 9 homologous recombination repair factor	protein-coding
mm_76368.1	chr8	84795318	84795321	-	1	NA	intron (NM_001081982, intron 1 of 9)	intron (NM_001081982, intron 1 of 9)	5019	NM_010906	18032	Mm.9394	NM_010906	ENSMUSG00000001911	Nfix	CTF|NF-I/X|NF1-X|NFI-X	nuclear factor I/X	protein-coding
mm_143546.1	chr17	74017144	74017150	-	1	NA	TTS (NM_053188)	TTS (NM_053188)	30769	NM_053188	94224	Mm.38933	NM_053188	ENSMUSG00000038541	Srd5a2	5ART2|S5AR 2	steroid 5 alpha-reductase 2	protein-coding
mm_19256.1	chr2	84774810	84774860	-	1	NA	intron (NM_009776, intron 1 of 7)	intron (NM_009776, intron 1 of 7)	594	NM_009776	12258	Mm.38888	NM_009776	ENSMUSG00000023224	Serping1	C1INH|C1nh	serine (or cysteine) peptidase inhibitor, clade G, member 1	protein-coding
mm_68532.1	chr7	113347377	113347413	-	1	NA	intron (NM_133700, intron 4 of 10)	intron (NM_133700, intron 4 of 10)	21944	NM_133700	68815	Mm.238034	NM_133700	ENSMUSG00000038187	Btbd10	1110056N09Rik|Gmrp1	BTB (POZ) domain containing 10	protein-coding
mm_63911.1	chr7	139214724	139214733	+	1	NA	exon (NM_027164, exon 2 of 11)	exon (NM_027164, exon 2 of 11)	-1421	NM_001162540	57740	Mm.65336	NM_021302	ENSMUSG00000015981	Stk32c	PKE|Pkek|YANK3	serine/threonine kinase 32C	protein-coding
mm_151016.1	chr19	46761640	46761656	+	1	NA	promoter-TSS (NM_001102471)	promoter-TSS (NM_001102471)	39	NM_001102471	94219	Mm.306903	NM_033569	ENSMUSG00000064105	Cnnm2	AU015877|AW048635|Acdp2|Clp2	cyclin M2	protein-coding
mm_10063.1	chr1	193508464	193508474	-	1	NA	promoter-TSS (NR_029592)	promoter-TSS (NR_029592)	-939	NR_029592	387201		NR_029592	ENSMUSG00000065533	Mir205	Mirn205|mir-205|mmu-mir-205	microRNA 205	ncRNA
mm_78010.1	chr9	13433150	13433154	+	1	NA	TTS (NR_028271)	TTS (NR_028271)	1791	NR_028271	18689	Mm.41972	NM_008835	ENSMUSG00000031802	Phxr4	Sp5	per-hexamer repeat gene 4	ncRNA
mm_84102.1	chr9	58279920	58279927	-	1	NA	Intergenic	Intergenic	26759	NM_026942	69106	Mm.216502	NM_026942	ENSMUSG00000032333	Stoml1	1810015E19Rik|AI847431|SLP1|STORP|UNC24|WPB72	stomatin-like 1	protein-coding
mm_24857.1	chr3	95882728	95882740	+	1	NA	promoter-TSS (NM_001033302)	promoter-TSS (NM_001033302)	-506	NM_001033302	229599	Mm.331218	NM_001033302	ENSMUSG00000038550	Ciart	Chrono|Gm129	circadian associated repressor of transcription	protein-coding
mm_66890.1	chr7	59281187	59281189	-	1	NA	intron (NM_173010, intron 4 of 8)	B1_Mus2|SINE|Alu	42961	NR_015479	330544	Mm.9002	NR_015479	ENSMUSG00000100826	C230091D08Rik	-	RIKEN cDNA C230091D08 gene	ncRNA
mm_21525.1	chr2	163639198	163639342	-	1	NA	exon (NM_012032, exon 2 of 10)	exon (NM_012032, exon 2 of 10)	-5580	NR_028113	68386	Mm.410649	NR_028113	ENSMUSG00000058812	0610039K10Rik	-	RIKEN cDNA 0610039K10 gene	ncRNA
mm_137277.1	chr17	24720182	24720189	+	1	NA	promoter-TSS (NR_028515)	promoter-TSS (NR_028515)	122	NM_008503	16898	Mm.157452	NM_008503	ENSMUSG00000044533	Rps2	Llrep3|S4	ribosomal protein S2	protein-coding
mm_27918.1	chr3	79531832	79531842	-	1	NA	intron (NM_001162999, intron 1 of 16)	intron (NM_001162999, intron 1 of 16)	35842	NM_001162999	329679	Mm.244005	NM_001162999	ENSMUSG00000061175	Fnip2	D630023B12Rik|mKIAA1450	folliculin interacting protein 2	protein-coding
mm_84884.1	chr9	79759468	79759492	-	1	NA	intron (NM_009945, intron 1 of 3)	intron (NM_009945, intron 1 of 3)	373	NM_009945	12866	Mm.152627	NM_009945	ENSMUSG00000032330	Cox7a2	COX7AL|Cox7a3|CoxVIIa-L	cytochrome c oxidase subunit VIIa 2	protein-coding
mm_169489.1	chr14	73955612	73955625	-	1	NA	Intergenic	Intergenic	-399909	NR_046059	74425	Mm.399498	NR_046059		4933402J15Rik	-	RIKEN cDNA 4933402J15 gene	ncRNA
mm_100842.1	chr11	5741118	5741139	-	1	NA	promoter-TSS (NM_178623)	promoter-TSS (NM_178623)	48	NM_178623	72046	Mm.271657	NM_178623	ENSMUSG00000049680	Urgcp	2010005J08Rik|9130001I21Rik|AW060359|Urg4|mKIAA1507	upregulator of cell proliferation	protein-coding
mm_2346.1	chr1	92906960	92907036	+	1	NA	promoter-TSS (NM_175118)	promoter-TSS (NM_175118)	9	NM_175118	67446	Mm.46179	NM_175118	ENSMUSG00000047067	Dusp28	0710001B24Rik|AV005521	dual specificity phosphatase 28	protein-coding
mm_144183.1	chr18	7613981	7613990	+	1	NA	intron (NM_001081287, intron 1 of 16)	intron (NM_001081287, intron 1 of 16)	12878	NM_001081287	75739	Mm.133293	NM_001081287	ENSMUSG00000057440	Mpp7	1110068J02Rik|2810038M04Rik|5430426E14Rik|AI415104|Gm955	membrane protein, palmitoylated 7 (MAGUK p55 subfamily member 7)	protein-coding
mm_132415.1	chr16	35068558	35068581	+	1	NA	intron (NM_023587, intron 3 of 6)	intron (NM_023587, intron 3 of 6)	46148	NM_023587	70757	Mm.27286	NM_023587	ENSMUSG00000035376	Hacd2	6330408J20Rik|AI255777|AI481689|Hcad2|Ptplb	3-hydroxyacyl-CoA dehydratase 2	protein-coding
mm_41578.1	chr5	93173028	93173047	+	1	NA	3' UTR (NM_001009818, exon 10 of 10)	3' UTR (NM_001009818, exon 10 of 10)	33458	NM_017367	12453	Mm.250419	NM_017367	ENSMUSG00000063015	Ccni	-	cyclin I	protein-coding
mm_60080.1	chr7	34095496	34095503	+	1	NA	promoter-TSS (NM_001099330)	promoter-TSS (NM_001099330)	68	NM_001099330	100043868	Mm.465197	NM_001099330	ENSMUSG00000078752	Scgb1b30	Abpa30|Gm12776|OTTMUSG00000008394	secretoglobin, family 1B, member 30	protein-coding
mm_1741.1	chr1	75450501	75450516	+	1	NA	promoter-TSS (NM_183022)	promoter-TSS (NM_183022)	-2	NM_183022	241118	Mm.110790	NM_183022	ENSMUSG00000033007	Asic4	Accn4|BNAC4	acid-sensing (proton-gated) ion channel family member 4	protein-coding
mm_83125.1	chr9	40423433	40423492	-	1	NA	intron (NM_172768, intron 1 of 19)	intron (NM_172768, intron 1 of 19)	32302	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_78095.1	chr9	18478360	18478361	+	1	NA	promoter-TSS (NM_028557)	promoter-TSS (NM_028557)	-35	NM_028557	73503	Mm.160088	NM_028557	ENSMUSG00000038691	Mbd3l1	1700070G05Rik|1700095H13Rik|Mbd3l	methyl-CpG binding domain protein 3-like 1	protein-coding
mm_29821.1	chr3	129332714	129332726	-	1	NA	promoter-TSS (NM_007934)	promoter-TSS (NM_007934)	29	NM_007934	13809	Mm.1193	NM_007934	ENSMUSG00000028024	Enpep	6030431M22Rik|APA|Bp-1/6C3|Ly-51|Ly51	glutamyl aminopeptidase	protein-coding
mm_160193.1	chr7	60450168	60450168	-	1	NA	Intergenic	Intergenic	-309949	NM_001082962	20646	Mm.274995	NM_013670	ENSMUSG00000102252	Snrpn	2410045I01Rik|HCERN3|Peg4|Pwcr1|SMN	small nuclear ribonucleoprotein N	protein-coding
mm_159637.1	chr4	139967779	139967779	-	1	NA	promoter-TSS (NR_035519)	promoter-TSS (NR_035519)	-159	NR_035519	100316727		NR_035519	ENSMUSG00000089294	Mir2139	mmu-mir-2139	microRNA 2139	ncRNA
mm_107366.1	chr12	32850510	32850576	+	1	NA	3' UTR (NM_021524, exon 11 of 11)	3' UTR (NM_021524, exon 11 of 11)	26427	NR_045032	100504486	Mm.440246	NR_045032		Gdap10	Gdap-ps	ganglioside-induced differentiation-associated-protein 10	ncRNA
mm_143854.1	chr17	84180734	84180750	-	1	NA	Intergenic	Intergenic	7205	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_20667.1	chr2	132145058	132145118	-	1	NA	promoter-TSS (NM_018824)	promoter-TSS (NM_018824)	20	NM_018824	54338	Mm.103581	NM_018824	ENSMUSG00000027340	Slc23a2	AI844736|NBTL1|SVCT2|Slc23a1|YSPL2|YSPL3|mKIAA0238	solute carrier family 23 (nucleobase transporters), member 2	protein-coding
mm_157468.1	chrX	47892445	47892455	-	1	NA	5' UTR (NM_001290708, exon 1 of 24)	5' UTR (NM_001290708, exon 1 of 24)	102	NM_053123	93761	Mm.229151	NM_053123	ENSMUSG00000031099	Smarca1	5730494M04Rik|Snf2l	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1	protein-coding
mm_13909.1	chr2	120500458	120500468	+	1	NA	intron (NM_007601, intron 15 of 23)	intron (NM_007601, intron 15 of 23)	23554	NM_001109761	12335	Mm.458021	NM_007601	ENSMUSG00000079110	Capn3	AI323605|Capa-3|Capa3|Lp82|p94	calpain 3	protein-coding
mm_41277.1	chr5	90246800	90246823	+	1	NA	intron (NM_198010, intron 27 of 32)	ORR1A2|LTR|ERVL-MaLR	-22815	NM_001163456	231430	Mm.319697	NM_001033310	ENSMUSG00000035505	Cox18	BC038311	cytochrome c oxidase assembly protein 18	protein-coding
mm_138707.1	chr17	36042993	36043012	+	1	NA	promoter-TSS (NM_001034909)	promoter-TSS (NM_001034909)	41	NM_001034909	547347	Mm.484641	NM_001034909	ENSMUSG00000073407	Gm6034	EG547347|H2-gs14-2	predicted gene 6034	protein-coding
mm_120135.1	chr14	60269394	60269406	+	1	NA	intron (NM_144843, intron 1 of 13)	intron (NM_144843, intron 1 of 13)	4195	NM_144843	219135	Mm.247007	NM_144843	ENSMUSG00000021987	Mtmr6	4022440C11Rik|AI428804|AU041072	myotubularin related protein 6	protein-coding
mm_7164.1	chr1	92006845	92006883	-	1	NA	intron (NM_207225, intron 5 of 26)	intron (NM_207225, intron 5 of 26)	173477	NM_207225	208727	Mm.318567	NM_207225	ENSMUSG00000026313	Hdac4	4932408F19Rik|HD4	histone deacetylase 4	protein-coding
mm_158482.1	chrX	142196962	142196982	-	1	NA	promoter-TSS (NM_001007576)	promoter-TSS (NM_001007576)	-36	NM_001007576	245650	Mm.208511	NM_001007576	ENSMUSG00000042282	Gucy2f	A930002I06|GC-F|GC2	guanylate cyclase 2f	protein-coding
mm_55632.1	chr6	72314781	72314789	-	1	NA	TTS (NM_001282071)	TTS (NM_001282071)	10175	NM_147779	20388	Mm.46033	NM_147779	ENSMUSG00000056370	Sftpb	AI562151|SF-B|SP-B|Sftp-3|Sftp3	surfactant associated protein B	protein-coding
mm_38479.1	chr4	140701070	140701089	-	1	NA	promoter-TSS (NM_173867)	promoter-TSS (NM_173867)	-394	NM_173867	108911	Mm.253	NM_173867	ENSMUSG00000040945	Rcc2	2610510H01Rik|2610529N02Rik|AA536646|AA675016|Td60|mKIAA1470	regulator of chromosome condensation 2	protein-coding
mm_37597.1	chr4	126744123	126744137	-	1	NA	3' UTR (NM_011986, exon 7 of 7)	3' UTR (NM_011986, exon 7 of 7)	-7861	NM_198960	332937	Mm.331881	NM_198960	ENSMUSG00000042477	Tfap2e	AI505200|AP-2e|Tcfap2e	transcription factor AP-2, epsilon	protein-coding
mm_122147.1	chr14	31206667	31206709	-	1	NA	5' UTR (NM_022656, exon 1 of 21)	5' UTR (NM_022656, exon 1 of 21)	138	NM_022656	64652	Mm.298728	NM_022656	ENSMUSG00000021910	Nisch	1200007D05Rik|3202002H23Rik|AW494485|I-1	nischarin	protein-coding
mm_164219.1	chr15	84987848	84987850	-	1	NA	5' UTR (NM_001033273, exon 1 of 10)	5' UTR (NM_001033273, exon 1 of 10)	122	NM_001033273	223739	Mm.323925	NM_001033273	ENSMUSG00000036046	5031439G07Rik	AW554572|mKIAA0930	RIKEN cDNA 5031439G07 gene	protein-coding
mm_9157.1	chr1	170959818	170959840	-	1	NA	TTS (NM_001077189)	TTS (NM_001077189)	16242	NM_001077189	14130	Mm.425062	NM_010187	ENSMUSG00000026656	Fcgr2b	AI528646|CD32|F630109E10Rik|Fc[g]RII|FcgRII|Fcgr2|Fcgr2a|Fcr-2|Fcr-3|Ly-17|Ly-m20|LyM-1|Lym-1|fcRII	Fc receptor, IgG, low affinity IIb	protein-coding
mm_138377.1	chr17	35016577	35016604	+	1	NA	promoter-TSS (NM_138582)	promoter-TSS (NM_138582)	11	NM_001347347	27762	Mm.56895	NM_138582	ENSMUSG00000007030	Vwa7	C6orf27|D17H6S56E-3|G7c|NG37	von Willebrand factor A domain containing 7	protein-coding
mm_122562.1	chr14	49686516	49686520	-	1	NA	intron (NM_026142, intron 6 of 7)	MTD|LTR|ERVL-MaLR	96849	NM_026142	67419	Mm.318710	NM_026142	ENSMUSG00000036242	3632451O06Rik	AU067705	RIKEN cDNA 3632451O06 gene	protein-coding
mm_70586.1	chr8	13171221	13171267	+	1	NA	exon (NM_010684, exon 5 of 9)	exon (NM_010684, exon 5 of 9)	12083	NM_010684	16783	Mm.16716	NM_010684	ENSMUSG00000031447	Lamp1	CD107a|LGP-120|LGP-A|Lamp-1|P2B	lysosomal-associated membrane protein 1	protein-coding
mm_44699.1	chr5	30545811	30545822	-	1	NA	promoter-TSS (NM_028483)	promoter-TSS (NM_028483)	20	NM_028483	73259	Mm.443299	NM_028483	ENSMUSG00000053194	Cib4	1700041E20Rik	calcium and integrin binding family member 4	protein-coding
mm_107408.1	chr12	33434104	33434110	+	1	NA	intron (NM_172253, intron 2 of 3)	intron (NM_172253, intron 2 of 3)	4483	NM_172253	28071	Mm.196472	NM_172253	ENSMUSG00000020561	Twistnb	2410173G11|2810024J17Rik|D16Wsu83e	twist basic helix-loop-helix transcription factor 1 neighbor	protein-coding
mm_113292.1	chr13	30336434	30336450	+	1	NA	promoter-TSS (NM_177322)	promoter-TSS (NM_177322)	86	NM_177322	11607	Mm.35062	NM_177322	ENSMUSG00000049115	Agtr1a	1810074K20Rik|AG2S|AI551199|AT1|AT1a|AT2R1|AT2R1A|Agtr-1a|Agtr1|Angtr-1a	angiotensin II receptor, type 1a	protein-coding
mm_94831.1	chr11	23401596	23401605	+	1	NA	intron (NM_001190401, intron 30 of 79)	intron (NM_001190401, intron 30 of 79)	94705	NM_001190401	17847	Mm.119155	NM_001190401	ENSMUSG00000056342	Usp34	A530081C03Rik|Murr2	ubiquitin specific peptidase 34	protein-coding
mm_11926.1	chr2	52110188	52110201	+	1	NA	exon (NM_175238, exon 30 of 36)	exon (NM_175238, exon 30 of 36)	37357	NM_175238	51869	Mm.254530	NM_175238	ENSMUSG00000036202	Rif1	5730435J01Rik|6530403D07Rik|AU016181|AW549474|D2Ertd145e	replication timing regulatory factor 1	protein-coding
mm_103706.1	chr11	79516654	79516664	-	1	NA	exon (NM_001077496, exon 2 of 2)	exon (NM_001077496, exon 2 of 2)	7103	NM_001077496	216984	Mm.439665	NM_001077496	ENSMUSG00000093938	Evi2b	Evi-2|Evi2	ecotropic viral integration site 2b	protein-coding
mm_25387.1	chr3	107216056	107216070	+	1	NA	exon (NM_001111143, exon 5 of 9)	exon (NM_001111143, exon 5 of 9)	5669	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_130019.1	chr15	88734189	88734214	-	1	NA	promoter-TSS (NM_001033274)	promoter-TSS (NM_001033274)	18	NM_001033274	223770	Mm.254438	NM_001033274	ENSMUSG00000022387	Brd1	1110059H06Rik|AI316859|mKIAA4191	bromodomain containing 1	protein-coding
mm_148597.1	chr19	5088649	5088655	+	1	NA	5' UTR (NM_026553, exon 1 of 8)	5' UTR (NM_026553, exon 1 of 8)	114	NM_026553	68090	Mm.44202	NM_026553	ENSMUSG00000024875	Yif1a	5330422J23Rik|54TM|Yif1|Yif1p	Yip1 interacting factor homolog A (S. cerevisiae)	protein-coding
mm_58231.1	chr6	144984359	144984373	-	1	NA	Intergenic	ORR1D2|LTR|ERVL-MaLR	64446	NM_001024468	12035	Mm.4606	NM_007532	ENSMUSG00000030268	Bcat1	BCATc|Eca39	branched chain aminotransferase 1, cytosolic	protein-coding
mm_118608.1	chr14	20929201	20929205	+	1	NA	promoter-TSS (NM_009502)	promoter-TSS (NM_009502)	-230	NM_009502	22330	Mm.279361	NM_009502	ENSMUSG00000021823	Vcl	9430097D22|AA571387|AI462105|AW545629	vinculin	protein-coding
mm_72909.1	chr8	90954924	90955059	+	1	NA	intron (NM_001310530, intron 1 of 37)	intron (NM_001310530, intron 1 of 37)	22742	NM_001310530	109151	Mm.100615	NM_177224	ENSMUSG00000056608	Chd9	1810014J18Rik|9030205D12Rik|A330063D19Rik|AD013|PRIC320|mKIAA0308	chromodomain helicase DNA binding protein 9	protein-coding
mm_164748.1	chr17	74523085	74523088	+	1	NA	Intergenic	B3|SINE|B2	-5209	NM_007566	12211	Mm.442564	NM_007566	ENSMUSG00000024073	Birc6	A430032G04Rik|A430040A19Rik|AA501170|Bruce|D630005A10Rik|mKIAA1289	baculoviral IAP repeat-containing 6	protein-coding
mm_93858.1	chr10	122569875	122569908	-	1	NA	promoter-TSS (NR_040616)	promoter-TSS (NR_040616)	0	NR_040616	319272	Mm.411763	NR_040616		A130077B15Rik	-	RIKEN cDNA A130077B15 gene	ncRNA
mm_155786.1	chrX	96713460	96713475	+	1	NA	promoter-TSS (NM_029536)	promoter-TSS (NM_029536)	-1	NM_029536	76206	Mm.256065	NM_029536	ENSMUSG00000031210	Gpr165	6530406P05Rik	G protein-coupled receptor 165	protein-coding
mm_124743.1	chr15	6599452	6599478	+	1	NA	intron (NM_011815, intron 1 of 17)	intron (NM_011815, intron 1 of 17)	19618	NM_011815	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_79614.1	chr9	58629125	58629134	+	1	NA	intron (NM_001293673, intron 3 of 7)	intron (NM_001293673, intron 3 of 7)	46889	NM_009145	20320	Mm.15125	NM_009145	ENSMUSG00000032336	Nptn	AW554172|SDR-1|Sdfr1	neuroplastin	protein-coding
mm_101788.1	chr11	46058110	46058132	-	1	NA	intron (NM_001291891, intron 1 of 22)	intron (NM_001291891, intron 1 of 22)	2137	NM_001291891	11492	Mm.89940	NM_009616	ENSMUSG00000011256	Adam19	AL024287|MADDAM|MTLNB|Mltnb	a disintegrin and metallopeptidase domain 19 (meltrin beta)	protein-coding
mm_105932.1	chr11	115133922	115133927	-	1	NA	promoter-TSS (NM_001169153)	promoter-TSS (NM_001169153)	68	NM_001347648	246746	Mm.277387	NM_145634	ENSMUSG00000047798	Cd300lf	CLIM1|CLM-1|CLM1|Digr2|F730004D16Rik|IREM1|IgSF13|LMIR3|Pigr3	CD300 molecule like family member F	protein-coding
mm_56216.1	chr6	89363580	89363593	-	1	NA	promoter-TSS (NM_008881)	promoter-TSS (NM_008881)	-973	NM_008881	18844	Mm.3789	NM_008881	ENSMUSG00000030084	Plxna1	2600013D04Rik|NOV|PlexA1|Plxn1|mKIAA4053	plexin A1	protein-coding
mm_135144.1	chr16	35856670	35856687	-	1	NA	exon (NM_001039530, exon 6 of 17)	exon (NM_001039530, exon 6 of 17)	14704	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_165095.1	chr19	53944260	53944264	-	1	NA	promoter-TSS (NM_019658)	promoter-TSS (NM_019658)	-44	NM_001168505	56392	Mm.228669	NM_019658	ENSMUSG00000024976	Shoc2	AU017287|Sur8|mKIAA0862	soc-2 (suppressor of clear) homolog (C. elegans)	protein-coding
mm_29882.1	chr3	131112040	131112060	-	1	NA	promoter-TSS (NM_001276403)	promoter-TSS (NM_001276403)	-741	NM_001276403	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_9240.1	chr1	171328924	171328951	-	1	NA	promoter-TSS (NM_001128609)	promoter-TSS (NM_001128609)	-208	NM_001128609	21945	Mm.270139	NM_011615	ENSMUSG00000013973	Dedd	CASP8IP1|DEFT|Dedpro1|FLDED1|KE05	death effector domain-containing	protein-coding
mm_103743.1	chr11	80142100	80142112	-	1	NA	promoter-TSS (NM_183275)	promoter-TSS (NM_183275)	47	NM_183275	68550	Mm.18466	NM_183275	ENSMUSG00000046909	Tefm	1110002N22Rik	transcription elongation factor, mitochondrial	protein-coding
mm_3040.1	chr1	134040275	134040279	+	1	NA	exon (NM_021355, exon 2 of 3)	exon (NM_021355, exon 2 of 3)	2762	NM_021355	14264	Mm.287146	NM_021355	ENSMUSG00000041559	Fmod	AI131919|AU041740|SLRR2E	fibromodulin	protein-coding
mm_3721.1	chr1	154201566	154201577	+	1	NA	intron (NM_001204908, intron 1 of 1)	intron (NM_001204908, intron 1 of 1)	384	NM_001204908	100503355	Mm.484410	NM_001204908	ENSMUSG00000066797	Zfp648	ENSMUSG00000066797|Gm10178|Gm203	zinc finger protein 648	protein-coding
mm_124290.1	chr14	103054586	103054594	-	1	NA	exon (NM_008392, exon 5 of 5)	exon (NM_008392, exon 5 of 5)	7578	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_55361.1	chr6	56923928	56923950	-	1	NA	promoter-TSS (NM_026004)	promoter-TSS (NM_026004)	-7	NM_026004	107569	Mm.158936	NM_026004	ENSMUSG00000029780	Nt5c3	1600024P05Rik|2610206B05Rik|3110004A18Rik|AI842776|Nt5c3a|Nt5y|PN-1|PN-I|PSN1|UMPH|Umph-1|Umph1|cN-III|lupin|p36	5'-nucleotidase, cytosolic III	protein-coding
mm_87556.1	chr10	54118134	54118151	+	1	NA	Intergenic	Intergenic	42220	NR_038016	100502920	Mm.403982	NR_038016	ENSMUSG00000097069	Gm16998	-	predicted gene, 16998	ncRNA
mm_102084.1	chr11	52281777	52281784	-	1	NA	intron (NM_001313981, intron 3 of 10)	intron (NM_001313981, intron 3 of 10)	815	NM_009331	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_1644.1	chr1	74588348	74588383	+	1	NA	promoter-TSS (NM_025784)	promoter-TSS (NM_025784)	76	NM_025784	66821	Mm.358700	NM_025784	ENSMUSG00000026172	Bcs1l	9130022O19Rik	BCS1-like (yeast)	protein-coding
mm_90835.1	chr10	8471817	8471822	-	1	NA	intron (NM_177387, intron 1 of 7)	RCHARR1|DNA|hAT-Charlie	47006	NM_177387	338362	Mm.41163	NM_177387	ENSMUSG00000047712	Ust	D930010O20Rik|UA2OST	uronyl-2-sulfotransferase	protein-coding
mm_68007.1	chr7	100938898	100939016	-	1	NA	exon (NM_183168, exon 3 of 3)	exon (NM_183168, exon 3 of 3)	-6796	NM_001081116	207212	Mm.29954	NM_001081116	ENSMUSG00000032875	Arhgef17	8030463K16|AI428794|AW558066|BC035332|mKIAA0337	Rho guanine nucleotide exchange factor (GEF) 17	protein-coding
mm_110153.1	chr12	26454049	26454160	-	1	NA	exon (NM_021384, exon 2 of 6)	exon (NM_021384, exon 2 of 6)	2348	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_50366.1	chr6	48674800	48674833	+	1	NA	Intergenic	Intergenic	-1319	NM_174960	317758	Mm.116971	NM_174960	ENSMUSG00000051124	Gimap9	A630002K24|BB145400	GTPase, IMAP family member 9	protein-coding
mm_8253.1	chr1	138842438	138842455	-	1	NA	promoter-TSS (NM_001042577)	promoter-TSS (NM_001042577)	-2	NM_001042577	16876	Mm.250732	NM_010714	ENSMUSG00000019230	Lhx9	3110009O07Rik|BB104635|LH2B	LIM homeobox protein 9	protein-coding
mm_104997.1	chr11	100356102	100356108	-	1	NA	promoter-TSS (NM_177981)	promoter-TSS (NM_177981)	36	NM_177981	15114	Mm.281700	NM_010404	ENSMUSG00000006930	Hap1	HAP-1	huntingtin-associated protein 1	protein-coding
mm_11064.1	chr2	27544849	27544875	+	1	NA	Intergenic	RMER19B|LTR|ERVK	29715	NM_080848	140858	Mm.28265	NM_080848	ENSMUSG00000026917	Wdr5	2410008O07Rik|AA408785|AA960360|Big|Big-3	WD repeat domain 5	protein-coding
mm_51761.1	chr6	87843743	87843780	+	1	NA	3' UTR (NM_013493, exon 5 of 5)	3' UTR (NM_013493, exon 5 of 5)	-5002	NM_133934	57905	Mm.241546	NM_133934	ENSMUSG00000030056	Isy1	5830446M03Rik|AI181014|AU020769	ISY1 splicing factor homolog	protein-coding
mm_161253.1	chr13	105082366	105082366	+	1	NA	intron (NM_025751, intron 1 of 7)	intron (NM_025751, intron 1 of 7)	244	NM_025751	66763	Mm.109093	NM_025751	ENSMUSG00000021718	4933425L06Rik	-	RIKEN cDNA 4933425L06 gene	protein-coding
mm_605.1	chr1	39903443	39903460	+	1	NA	intron (NM_001252200, intron 2 of 31)	intron (NM_001252200, intron 2 of 31)	2538	NM_008696	26921	Mm.491139	NM_008696	ENSMUSG00000026074	Map4k4	9430080K19Rik|AU043147|AU045934|AW046177|HGK|Nik	mitogen-activated protein kinase kinase kinase kinase 4	protein-coding
mm_87613.1	chr10	57786029	57786074	+	1	NA	intron (NM_021272, intron 2 of 3)	intron (NM_021272, intron 2 of 3)	1128	NM_021272	12140	Mm.3644	NM_021272	ENSMUSG00000019874	Fabp7	B-FABP|BFABP|Blbp|MRG	fatty acid binding protein 7, brain	protein-coding
mm_164131.1	chr15	41833456	41833459	+	1	NA	intron (NM_001130164, intron 1 of 5)	intron (NM_001130164, intron 1 of 5)	2499	NM_001130164	170719	Mm.254267	NM_130885	ENSMUSG00000022307	Oxr1	2210416C20Rik|C7|C7B	oxidation resistance 1	protein-coding
mm_136937.1	chr17	14249733	14249741	+	1	NA	Intergenic	Intergenic	-29769	NM_022315	64074	Mm.30162	NM_022315	ENSMUSG00000023886	Smoc2	1700056C05Rik|5430426J21Rik|Smoc2l	SPARC related modular calcium binding 2	protein-coding
mm_108703.1	chr12	86952737	86952744	+	1	NA	intron (NM_001289432, intron 1 of 4)	intron (NM_001289432, intron 1 of 4)	5397	NM_001289432	217732	Mm.22337	NM_173735	ENSMUSG00000034157	Cipc	2310044G17Rik|AI842544|AI853744|Kiaa1737|mKIAA1737	CLOCK interacting protein, circadian	protein-coding
mm_88363.1	chr10	75937177	75937195	+	1	NA	TTS (NM_001277132)	TTS (NM_001277132)	1613	NM_175329	103172	Mm.333849	NM_175329	ENSMUSG00000049422	Chchd10	1620401E04Rik|AI267078|Ndg2	coiled-coil-helix-coiled-coil-helix domain containing 10	protein-coding
mm_6646.1	chr1	79670167	79670167	-	1	NA	intron (NM_183027, intron 1 of 4)	intron (NM_183027, intron 1 of 4)	1805	NM_183027	252903	Mm.32409	NM_183027	ENSMUSG00000054702	Ap1s3	1190009B22|Jr2|[s]3A	adaptor-related protein complex AP-1, sigma 3	protein-coding
mm_126933.1	chr15	91706719	91706721	+	1	NA	intron (NM_025730, intron 12 of 50)	intron (NM_025730, intron 12 of 50)	33496	NM_025730	66725	Mm.37558	NM_025730	ENSMUSG00000036273	Lrrk2	4921513O20Rik|9330188B09Rik|AW561911|D630001M17Rik|Gm927|cI-46	leucine-rich repeat kinase 2	protein-coding
mm_40499.1	chr5	57719062	57719114	+	1	NA	5' UTR (NM_001310606, exon 1 of 3)	5' UTR (NM_001310606, exon 1 of 3)	1007	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_114948.1	chr13	96638964	96638967	+	1	NA	3' UTR (NM_001164222, exon 17 of 17)	3' UTR (NM_001164222, exon 17 of 17)	31971	NM_008255	15357	Mm.316652	NM_008255	ENSMUSG00000021670	Hmgcr	HMG-CoAR|Red	3-hydroxy-3-methylglutaryl-Coenzyme A reductase	protein-coding
mm_59915.1	chr7	30417390	30417426	+	1	NA	TTS (NM_011827)	TTS (NM_011827)	2446	NM_011827	23900	Mm.379050	NM_011827	ENSMUSG00000064109	Hcst	DAP10|KAP10	hematopoietic cell signal transducer	protein-coding
mm_141712.1	chr17	34024640	34024676	-	1	NA	promoter-TSS (NR_106154)	promoter-TSS (NR_106154)	22	NM_009066	19763	Mm.20343	NM_009066	ENSMUSG00000024325	Ring1	Ring1A	ring finger protein 1	protein-coding
mm_50969.1	chr6	60586769	60586792	+	1	NA	Intergenic	Intergenic	-183073	NR_015565	208079	Mm.131226	NM_177329	ENSMUSG00000046764	A530053G22Rik	-	RIKEN cDNA A530053G22 gene	ncRNA
mm_75108.1	chr8	34146975	34147013	-	1	NA	promoter-TSS (NM_026609)	promoter-TSS (NM_026609)	-255	NM_026609	68192	Mm.34212	NM_026609	ENSMUSG00000031513	Leprotl1	1110067H13Rik|1520402O14Rik|AI854296	leptin receptor overlapping transcript-like 1	protein-coding
mm_105464.1	chr11	105181323	105181365	-	1	NA	promoter-TSS (NR_027956)	promoter-TSS (NR_027956)	89	NR_027956	73431	Mm.351426	NM_028539		1700052K11Rik	AI840954	RIKEN cDNA 1700052K11 gene	ncRNA
mm_39213.1	chr4	156059808	156059830	-	1	NA	promoter-TSS (NR_132444)	promoter-TSS (NR_132444)	-17	NR_132444	100415901	Mm.437006	NR_132444	ENSMUSG00000086549	Gm13648	OTTMUSG00000013217	predicted gene 13648	ncRNA
mm_48013.1	chr5	136165836	136165851	-	1	NA	intron (NM_178751, intron 1 of 2)	RSINE1|SINE|B4	4813	NM_178751	269717	Mm.308396	NM_178751	ENSMUSG00000039747	Orai2	A730041O15Rik|Tmem142b	ORAI calcium release-activated calcium modulator 2	protein-coding
mm_156282.1	chrX	136837209	136837219	+	1	NA	3' UTR (NM_011123, exon 7 of 7)	3' UTR (NM_011123, exon 7 of 7)	14468	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_137747.1	chr17	29393846	29393851	+	1	NA	Intergenic	Intergenic	32934	NM_001159538	26382	Mm.279187	NM_013710	ENSMUSG00000024013	Fgd2	Tcd-2|Tcd2|ZFYVE4|tcs-2|tcs2	FYVE, RhoGEF and PH domain containing 2	protein-coding
mm_160147.1	chr7	40899074	40899074	+	1	NA	promoter-TSS (NM_021387)	promoter-TSS (NM_021387)	-204	NM_021387	58188	Mm.150675	NM_021387	ENSMUSG00000039257	Vstm2b	2900093B09Rik|AB030198	V-set and transmembrane domain containing 2B	protein-coding
mm_105037.1	chr11	100583113	100583129	-	1	NA	exon (NM_019795, exon 14 of 14)	exon (NM_019795, exon 14 of 14)	7230	NM_001146318	12799	Mm.15711	NM_009923	ENSMUSG00000006782	Cnp	CNPase|Cnp-1|Cnp1	2',3'-cyclic nucleotide 3' phosphodiesterase	protein-coding
mm_23922.1	chr3	83127504	83127540	+	1	NA	Intergenic	CpG	71984	NM_016784	53317	Mm.286349	NM_016784	ENSMUSG00000027998	Plrg1	AA958940|C80566|Tango4	pleiotropic regulator 1	protein-coding
mm_55323.1	chr6	55678549	55678569	-	1	NA	3' UTR (NM_009717, exon 2 of 2)	3' UTR (NM_009717, exon 2 of 2)	2704	NM_009717	11922	Mm.5106	NM_009717	ENSMUSG00000037984	Neurod6	Atoh2|Math-2|Math2|Nex|Nex1m|bHLHa2	neurogenic differentiation 6	protein-coding
mm_24847.1	chr3	95674466	95674482	+	1	NA	Intergenic	Intergenic	13443	NM_144899	229595	Mm.490574	NM_144899	ENSMUSG00000015850	Adamtsl4	ADAMTSL-4|Tsrc1	ADAMTS-like 4	protein-coding
mm_48126.1	chr5	137149655	137149683	-	1	NA	Intergenic	Intergenic	-33462	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_51178.1	chr6	70726756	70726791	+	1	NA	Intergenic	Intergenic	65402	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_98355.1	chr11	93885103	93885141	+	1	NA	intron (NM_001013375, intron 1 of 13)	CpG	644	NM_001013375	217109	Mm.379350	NM_001013375	ENSMUSG00000054079	Utp18	6230425C22Rik|6430513M13|Wdr50	UTP18 small subunit processome component	protein-coding
mm_30157.1	chr3	142881943	142882017	-	1	NA	promoter-TSS (NM_178654)	promoter-TSS (NM_178654)	24	NM_178654	109333	Mm.244236	NM_178654	ENSMUSG00000004591	Pkn2	6030436C20Rik|AI507382|PRK2|Prkcl2|Stk7	protein kinase N2	protein-coding
mm_13209.1	chr2	94406720	94406762	+	1	NA	promoter-TSS (NR_027831)	promoter-TSS (NR_027831)	34	NR_027831	66457	Mm.402557	NR_027831		2810002D19Rik	-	RIKEN cDNA 2810002D19 gene	ncRNA
mm_80346.1	chr9	75173994	75174004	+	1	NA	exon (NM_010864, exon 22 of 41)	exon (NM_010864, exon 22 of 41)	-58015	NM_001081322	208943	Mm.41339	NM_001081322	ENSMUSG00000033590	Myo5c	9130003O20Rik|BB085560|C330029I24	myosin VC	protein-coding
mm_129572.1	chr15	79687777	79687894	-	1	NA	promoter-TSS (NM_028792)	promoter-TSS (NM_028792)	37	NM_028792	74158	Mm.323393	NM_028792	ENSMUSG00000022426	Josd1	1300006C06Rik|mKIAA0063	Josephin domain containing 1	protein-coding
mm_138437.1	chr17	35110772	35110777	+	1	NA	exon (NM_148947, exon 2 of 3)	exon (NM_148947, exon 2 of 3)	2474	NM_148947	114652	Mm.222643	NM_148947	ENSMUSG00000034482	Ly6g5c	G5c|NG33	lymphocyte antigen 6 complex, locus G5C	protein-coding
mm_5871.1	chr1	53785149	53785159	-	1	NA	promoter-TSS (NM_133810)	promoter-TSS (NM_133810)	61	NM_133810	98267	Mm.25559	NM_133810	ENSMUSG00000026094	Stk17b	3110009A03Rik|AI120141|Drak2	serine/threonine kinase 17b (apoptosis-inducing)	protein-coding
mm_123156.1	chr14	57132052	57132065	-	1	NA	intron (NM_001010937, intron 1 of 2)	intron (NM_001010937, intron 1 of 2)	1553	NM_001271663	14623	Mm.25652	NM_008128	ENSMUSG00000040055	Gjb6	AA958971|Cx30|D14Bwg0506e	gap junction protein, beta 6	protein-coding
mm_28839.1	chr3	96580214	96580231	-	1	NA	intron (NM_001293701, intron 4 of 6)	RSINE1|SINE|B4	-13421	NR_040409	100038464	Mm.475126	NR_040409	ENSMUSG00000074398	Gm15441	ENSMUSG00000074398|OTTMUSG00000021867	predicted gene 15441	ncRNA
mm_106961.1	chr12	8922043	8922054	+	1	NA	exon (NM_008640, exon 1 of 7)	exon (NM_008640, exon 1 of 7)	741	NM_008640	17775	Mm.30071	NM_008640	ENSMUSG00000020585	Laptm4a	AA286466|LAPTM4|MTP|Mtrp|mKIAA0108	lysosomal-associated protein transmembrane 4A	protein-coding
mm_139553.1	chr17	56861550	56861561	+	1	NA	exon (NM_001039114, exon 6 of 15)	exon (NM_001039114, exon 6 of 15)	12892	NM_001039114	328845	Mm.179421	NM_001039114	ENSMUSG00000024207	Acsbg2	Bgr	acyl-CoA synthetase bubblegum family member 2	protein-coding
mm_68989.1	chr7	126595013	126595037	-	1	NA	promoter-TSS (NM_145636)	promoter-TSS (NM_145636)	-115	NM_145636	246779	Mm.222632	NM_145636	ENSMUSG00000044701	Il27	IL-27|IL-27p28|Il30|p28	interleukin 27	protein-coding
mm_20684.1	chr2	132578156	132578222	-	1	NA	promoter-TSS (NM_027096)	promoter-TSS (NM_027096)	59	NM_001291050	74182	Mm.211211	NM_027096	ENSMUSG00000027346	Gpcpd1	2310004G06Rik|2310032D16Rik|AU015213|Gde5|Prei4|mKIAA1434	glycerophosphocholine phosphodiesterase 1	protein-coding
mm_74817.1	chr8	22803884	22803892	-	1	NA	exon (NM_029505, exon 2 of 9)	exon (NM_029505, exon 2 of 9)	1766	NM_029505	64933	Mm.390023	NM_029505	ENSMUSG00000031539	Ap3m2	5830445E16Rik|AP-3B	adaptor-related protein complex 3, mu 2 subunit	protein-coding
mm_87701.1	chr10	59879570	59879613	+	1	NA	promoter-TSS (NM_019965)	promoter-TSS (NM_019965)	0	NM_019965	56709	Mm.103610	NM_019965	ENSMUSG00000020109	Dnajb12	Dj10|mDj10	DnaJ heat shock protein family (Hsp40) member B12	protein-coding
mm_16631.1	chr2	5714436	5714446	-	1	NA	5' UTR (NM_001290375, exon 1 of 11)	5' UTR (NM_001290375, exon 1 of 11)	321	NM_001290374	227541	Mm.191949	NM_177343	ENSMUSG00000039145	Camk1d	A630059D12Rik|CKLiK|CaMKIdelta|E030025C11Rik|mCKLiK	calcium/calmodulin-dependent protein kinase ID	protein-coding
mm_45900.1	chr5	88676136	88676186	-	1	NA	promoter-TSS (NM_178700)	promoter-TSS (NM_178700)	10	NM_178700	231413	Mm.332474	NM_178700	ENSMUSG00000044221	Grsf1	BB232551|C80280|D5Wsu31e	G-rich RNA sequence binding factor 1	protein-coding
mm_159862.1	chr5	140891134	140891134	-	1	NA	intron (NM_175362, intron 11 of 24)	G-rich|Low_complexity|Low_complexity	-60703	NM_010302	14673	Mm.370185	NM_010302	ENSMUSG00000000149	Gna12	AI414047|AI504261|Galpha12	guanine nucleotide binding protein, alpha 12	protein-coding
mm_46241.1	chr5	99223633	99223659	-	1	NA	intron (NM_145839, intron 10 of 13)	intron (NM_145839, intron 10 of 13)	29281	NM_181318	320292	Mm.259074	NM_145839	ENSMUSG00000089809	Rasgef1b	4732452O09Rik|GPIgamma4|Gpig4	RasGEF domain family, member 1B	protein-coding
mm_82440.1	chr9	15279889	15279919	-	1	NA	promoter-TSS (NM_144933)	promoter-TSS (NM_144933)	-37	NM_144933	234959	Mm.44151	NM_144933	ENSMUSG00000031935	Med17	77kDa|C330002H14Rik|Crsp6|Trap80	mediator complex subunit 17	protein-coding
mm_55336.1	chr6	56362267	56362285	-	1	NA	5' UTR (NM_001159953, exon 1 of 19)	5' UTR (NM_001159953, exon 1 of 19)	116	NM_001159952	18575	Mm.5145	NM_011054	ENSMUSG00000004347	Pde1c	-	phosphodiesterase 1C	protein-coding
mm_53757.1	chr6	145616010	145616026	+	1	NA	promoter-TSS (NM_009449)	promoter-TSS (NM_009449)	55	NM_009449	22147	Mm.270295	NM_009449	ENSMUSG00000067338	Tuba3b	M[a]7|Tuba7	tubulin, alpha 3B	protein-coding
mm_119712.1	chr14	53875940	53875946	+	1	NA	Intergenic	Intergenic	377986	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_37338.1	chr4	119657595	119657613	-	1	NA	exon (NM_008191, exon 2 of 3)	exon (NM_008191, exon 2 of 3)	1341	NM_008191	14916	Mm.278	NM_008191	ENSMUSG00000032978	Guca2b	AV066530|Gcap2|Ugn	guanylate cyclase activator 2b (retina)	protein-coding
mm_73603.1	chr8	109999004	109999025	+	1	NA	3' UTR (NM_146214, exon 12 of 12)	3' UTR (NM_146214, exon 12 of 12)	8578	NM_146214	234724	Mm.28110	NM_146214	ENSMUSG00000001670	Tat	-	tyrosine aminotransferase	protein-coding
mm_142461.1	chr17	45596684	45596699	-	1	NA	promoter-TSS (NM_001199114)	promoter-TSS (NM_001199114)	-789	NM_001199114	63959	Mm.29744	NM_022880	ENSMUSG00000023942	Slc29a1	1200014D21Rik|AA407560|ENT1	solute carrier family 29 (nucleoside transporters), member 1	protein-coding
mm_128567.1	chr15	56694580	56694603	-	1	NA	promoter-TSS (NM_008216)	promoter-TSS (NM_008216)	-45	NM_008216	15117	Mm.5148	NM_008216	ENSMUSG00000022367	Has2	-	hyaluronan synthase 2	protein-coding
mm_125631.1	chr15	61990035	61990058	+	1	NA	3' UTR (NM_001177354, exon 3 of 3)	3' UTR (NM_001177354, exon 3 of 3)	4705	NM_001177352	17869	Mm.2444	NM_010849	ENSMUSG00000022346	Myc	AU016757|Myc2|Niard|Nird|bHLHe39	myelocytomatosis oncogene	protein-coding
mm_144021.1	chr17	90035843	90035863	-	1	NA	3' UTR (NM_001347419, exon 3 of 3)	3' UTR (NM_001347419, exon 3 of 3)	52515	NM_001346962	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_38972.1	chr4	150907206	150907247	-	1	NA	intron (NM_020569, intron 2 of 6)	intron (NM_020569, intron 2 of 6)	2695	NM_020569	57320	Mm.277349	NM_020569	ENSMUSG00000028964	Park7	DJ-1|Dj1	Parkinson disease (autosomal recessive, early onset) 7	protein-coding
mm_114465.1	chr13	67744200	67744208	+	1	NA	intron (NR_027969, intron 1 of 2)	intron (NR_027969, intron 1 of 2)	10930	NM_001001130	22746	Mm.288396	NM_001001130	ENSMUSG00000058331	Zfp85	KRAB19|Rslcan2|Zfp71|Zfp85-rs1	zinc finger protein 85	protein-coding
mm_135996.1	chr16	75292347	75292359	-	1	NA	Intergenic	B4A|SINE|B4	293708	NM_001252513	320355	Mm.99517	NM_177142	ENSMUSG00000032948	Lipi	D930038D03Rik|lpd1	lipase, member I	protein-coding
mm_138001.1	chr17	33810516	33810529	+	1	NA	promoter-TSS (NM_030697)	promoter-TSS (NM_030697)	-1	NM_030697	80880	Mm.196330	NM_030697	ENSMUSG00000042099	Kank3	0610013D04Rik|Ankrd47|D17Ertd288e|NG28	KN motif and ankyrin repeat domains 3	protein-coding
mm_139877.1	chr17	70748090	70748103	+	1	NA	intron (NM_001347411, intron 9 of 14)	intron (NM_001347411, intron 9 of 14)	98681	NM_001164077	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_49563.1	chr6	30610977	30610983	+	1	NA	promoter-TSS (NM_144537)	promoter-TSS (NM_144537)	-30	NM_144537	74649	Mm.159276	NM_144537	ENSMUSG00000029788	Cpa5	4930430M09Rik	carboxypeptidase A5	protein-coding
mm_90054.1	chr10	116177394	116177417	+	1	NA	promoter-TSS (NM_001161838)	promoter-TSS (NM_001161838)	54	NM_001161840	19279	Mm.336316	NM_011217	ENSMUSG00000020151	Ptprr	Gmcp1|PTP-SL|PTPBR7|RPTPRR|mPTP213	protein tyrosine phosphatase, receptor type, R	protein-coding
mm_30191.1	chr3	144692417	144692420	-	1	NA	intron (NM_001282042, intron 7 of 9)	intron (NM_001282042, intron 7 of 9)	27917	NM_001282042	54673	Mm.271775	NM_019464	ENSMUSG00000037062	Sh3glb1	AA409932|AI314629|AU015566|Bif-1|mKIAA0491	SH3-domain GRB2-like B1 (endophilin)	protein-coding
mm_117415.1	chr13	74292284	74292343	-	1	NA	promoter-TSS (NM_009644)	promoter-TSS (NM_009644)	18	NM_009644	11624	Mm.290446	NM_009644	ENSMUSG00000021575	Ahrr	mKIAA1234	aryl-hydrocarbon receptor repressor	protein-coding
mm_143711.1	chr17	80726611	80726615	-	1	NA	intron (NM_001290345, intron 1 of 33)	intron (NM_001290345, intron 1 of 33)	1412	NM_001290345	225028	Mm.311948	NM_001081357	ENSMUSG00000024242	Map4k3	4833416M01Rik|4833416M07Rik|9530052P13Rik|Glk|MAPKKKK3|MEKKK 3|MEKKK3|RAB8IPL1	mitogen-activated protein kinase kinase kinase kinase 3	protein-coding
mm_12723.1	chr2	78357625	78357630	+	1	NA	Intergenic	Intergenic	120080	NM_177843	329436	Mm.235448	NM_177843		Gm14461	A830093M07|OTTMUSG00000016703	predicted gene 14461	protein-coding
mm_102969.1	chr11	69666163	69666169	-	1	NA	promoter-TSS (NR_110993)	promoter-TSS (NR_110993)	4	NM_001291058	12514	Mm.15819	NM_009853	ENSMUSG00000018774	Cd68	Lamp4|Scard1|gp110	CD68 antigen	protein-coding
mm_8146.1	chr1	136414958	136414980	-	1	NA	promoter-TSS (NM_026500)	promoter-TSS (NM_026500)	-302	NM_026500	67997	Mm.385462	NM_026500	ENSMUSG00000026404	Ddx59	1210002B07Rik|4833411G06Rik	DEAD (Asp-Glu-Ala-Asp) box polypeptide 59	protein-coding
mm_169756.1	chr15	90882528	90882528	+	1	NA	Intergenic	Intergenic	15948	NR_033583	20738	Mm.431547	NR_033583		Spn-ps	Cd43-ps	sialophorin, pseudogene	pseudo
mm_160139.1	chr7	30914344	30914344	-	1	NA	promoter-TSS (NM_001346089)	promoter-TSS (NM_001346089)	-23	NM_001346089	17136	Mm.241355	NM_010758	ENSMUSG00000036634	Mag	Gma|siglec-4a	myelin-associated glycoprotein	protein-coding
mm_167489.1	chr9	6168679	6168694	+	1	NA	promoter-TSS (NM_027924)	promoter-TSS (NM_027924)	74	NM_027924	71785	Mm.390122	NM_027924	ENSMUSG00000032006	Pdgfd	1110003I09Rik	platelet-derived growth factor, D polypeptide	protein-coding
mm_104087.1	chr11	86624287	86624297	-	1	NA	intron (NM_029478, intron 7 of 11)	intron (NM_029478, intron 7 of 11)	-31779	NR_106195	102465902		NR_106195	ENSMUSG00000099324	Mir8115	Gm28012|mmu-mir-8115	microRNA 8115	ncRNA
mm_78261.1	chr9	21927659	21927669	+	1	NA	promoter-TSS (NM_178577)	promoter-TSS (NM_178577)	-129	NM_001253870	235043	Mm.253329	NM_178577	ENSMUSG00000040883	Tmem205	-	transmembrane protein 205	protein-coding
mm_58360.1	chr6	148212379	148212391	-	1	NA	promoter-TSS (NM_026168)	promoter-TSS (NM_026168)	-11	NM_001286560	67456	Mm.59812	NM_026168	ENSMUSG00000030304	Ergic2	1200009B18Rik|4930572C01Rik|AA408438|Ptx1	ERGIC and golgi 2	protein-coding
mm_3912.1	chr1	161969180	161969259	+	1	NA	promoter-TSS (NM_026078)	promoter-TSS (NM_026078)	31	NM_026078	67292	Mm.45106	NM_026078	ENSMUSG00000026698	Pigc	3110030E07Rik|AW212108	phosphatidylinositol glycan anchor biosynthesis, class C	protein-coding
mm_61009.1	chr7	49364856	49364864	+	1	NA	intron (NM_175272, intron 2 of 37)	intron (NM_175272, intron 2 of 37)	118671	NM_175272	78286	Mm.333881	NM_175272	ENSMUSG00000052512	Nav2	5330421F07Rik|AU067780|BQ960892|HELAD1|POMFIL2|RAINB1|RAINB2|Unc53H2|mKIAA3015	neuron navigator 2	protein-coding
mm_91459.1	chr10	34096376	34096389	-	1	NA	exon (NM_178908, exon 1 of 2)	exon (NM_178908, exon 1 of 2)	137	NM_178908	103511	Mm.66334	NM_178908	ENSMUSG00000049872	Fam26e	BB146404	family with sequence similarity 26, member E	protein-coding
mm_53018.1	chr6	123653489	123653493	+	1	NA	Intergenic	L1VL4|LINE|L1	-2856	NM_001104637	546913	Mm.469875	NM_001104637	ENSMUSG00000095486	Vmn2r22	EG546913	vomeronasal 2, receptor 22	protein-coding
mm_89881.1	chr10	108332695	108332743	+	1	NA	5' UTR (NM_054056, exon 2 of 7)	5' UTR (NM_054056, exon 2 of 7)	530	NM_054056	114774	Mm.391419	NM_054056	ENSMUSG00000035873	Pawr	2310001G03Rik|PAR4|Par-4	PRKC, apoptosis, WT1, regulator	protein-coding
mm_72493.1	chr8	83715306	83715312	+	1	NA	5' UTR (NM_197982, exon 1 of 11)	5' UTR (NM_197982, exon 1 of 11)	132	NM_197982	68278	Mm.28222	NM_197982	ENSMUSG00000005481	Ddx39	2610307C23Rik|BAT1|DDXL|Ddx39a|URH49	DEAD (Asp-Glu-Ala-Asp) box polypeptide 39	protein-coding
mm_6697.1	chr1	80758482	80758499	-	1	NA	promoter-TSS (NM_175291)	promoter-TSS (NM_175291)	63	NM_175291	210293	Mm.133473	NM_175291	ENSMUSG00000038608	Dock10	9330153B10Rik|A630054M16Rik|Jr4|Jr5|R75174|ZIZ3|Zizimin3|mKIAA0694	dedicator of cytokinesis 10	protein-coding
mm_52719.1	chr6	119902689	119902734	+	1	NA	promoter-TSS (NM_011236)	promoter-TSS (NM_011236)	13	NM_001166381	19365	Mm.149	NM_011236	ENSMUSG00000030166	Rad52	Rad52yh	RAD52 homolog, DNA repair protein	protein-coding
mm_98224.1	chr11	88051157	88051169	+	1	NA	3' UTR (NM_001078167, exon 3 of 3)	3' UTR (NM_001078167, exon 3 of 3)	3790	NM_173374	110809	Mm.391719	NM_173374	ENSMUSG00000018379	Srsf1	1110054N12Rik|5730507C05Rik|6330415C05Rik|AI482334|AW491331|Asf|Sf2|Sfrs1	serine/arginine-rich splicing factor 1	protein-coding
mm_33957.1	chr4	137468768	137468831	+	1	NA	promoter-TSS (NM_008305)	promoter-TSS (NM_008305)	-4	NM_008305	15530	Mm.273662	NM_008305	ENSMUSG00000028763	Hspg2	AI852380|Pcn|Plc|per	perlecan (heparan sulfate proteoglycan 2)	protein-coding
mm_52625.1	chr6	117174166	117174172	+	1	NA	3' UTR (NM_021704, exon 3 of 3)	3' UTR (NM_021704, exon 3 of 3)	5634	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_76735.1	chr8	95113335	95113347	-	1	NA	promoter-TSS (NM_001145832)	promoter-TSS (NM_001145832)	1	NM_001145832	16582	Mm.378951	NM_010631	ENSMUSG00000031788	Kifc3	AI325457|BB123200	kinesin family member C3	protein-coding
mm_63690.1	chr7	130576859	130576871	+	1	NA	promoter-TSS (NM_206856)	promoter-TSS (NM_206856)	-619	NM_001004468	57752	Mm.86322	NM_021314	ENSMUSG00000030852	Tacc2	mKIAA4180	transforming, acidic coiled-coil containing protein 2	protein-coding
mm_115554.1	chr13	8979966	8979984	-	1	NA	exon (NM_027000, exon 11 of 17)	exon (NM_027000, exon 11 of 17)	16037	NM_027000	69237	Mm.41800	NM_027000	ENSMUSG00000021149	Gtpbp4	2610028C09Rik|Crfg|Gtpbp3|NGB|Nog1	GTP binding protein 4	protein-coding
mm_78367.1	chr9	27030160	27030197	+	1	NA	promoter-TSS (NM_178113)	promoter-TSS (NM_178113)	3	NM_178113	78658	Mm.251777	NM_178113	ENSMUSG00000035024	Ncapd3	2810487N22Rik|4632407J06Rik|AI195468|AU018739|B130055D15Rik|mKIAA0056	non-SMC condensin II complex, subunit D3	protein-coding
mm_163082.1	chr11	69091223	69091231	+	1	NA	3' UTR (NM_009497, exon 5 of 5)	3' UTR (NM_009497, exon 5 of 5)	2699	NM_009497	22318	Mm.28643	NM_009497	ENSMUSG00000020894	Vamp2	Syb-2|Syb2|sybII	vesicle-associated membrane protein 2	protein-coding
mm_167263.1	chr8	27175652	27175684	-	1	NA	Intergenic	Intergenic	-1022	NM_001080813	75767	Mm.205335	NM_029423	ENSMUSG00000031488	Rab11fip1	2010200K21Rik|4833414G05Rik|Rcp	RAB11 family interacting protein 1 (class I)	protein-coding
mm_134051.1	chr16	5371255	5371264	-	1	NA	Intergenic	Intergenic	-115303	NM_027446	70511	Mm.45780	NM_027446	ENSMUSG00000022544	Eef2kmt	5730409G15Rik|Fam86|Fam86a|eEF2-KMT	eukaryotic elongation factor 2 lysine methyltransferase	protein-coding
mm_162993.1	chr11	28853759	28853773	+	1	NA	intron (NM_146015, intron 1 of 10)	intron (NM_146015, intron 1 of 10)	561	NM_146015	216616	Mm.44176	NM_146015	ENSMUSG00000020467	Efemp1	-	epidermal growth factor-containing fibulin-like extracellular matrix protein 1	protein-coding
mm_39280.1	chr5	3927858	3927888	+	1	NA	promoter-TSS (NM_194462)	promoter-TSS (NM_194462)	-313	NM_194462	100986	Mm.46044	NM_194462	ENSMUSG00000040407	Akap9	5730481H23Rik|AKAP-9|AKAP450|AW545847|C79026|G1-448-15|PRKA9|mKIAA0803|mei2-5|repro12	A kinase (PRKA) anchor protein (yotiao) 9	protein-coding
mm_56437.1	chr6	97431403	97431453	-	1	NA	intron (NM_145148, intron 2 of 23)	intron (NM_145148, intron 2 of 23)	27858	NM_001346639	232288	Mm.27789	NM_145148	ENSMUSG00000030064	Frmd4b	6030440G05Rik|C87375|GOBLIN|GRSP1|R74720	FERM domain containing 4B	protein-coding
mm_34085.1	chr4	138831858	138831868	+	1	NA	promoter-TSS (NR_002926)	promoter-TSS (NR_002926)	6	NR_002926	18780	Mm.4675	NM_011108	ENSMUSG00000058908	Pla2g2a	EF|Mom1|Pla2|sPLA2|sPla2-IIA	phospholipase A2, group IIA (platelets, synovial fluid)	protein-coding
mm_147019.1	chr18	34605426	34605432	-	1	NA	intron (NM_030147, intron 16 of 21)	ID_B1|SINE|B4	-7961	NM_177773	271508	Mm.417609	NM_177773	ENSMUSG00000049357	4933408B17Rik	-	RIKEN cDNA 4933408B17 gene	protein-coding
mm_91938.1	chr10	60744708	60744723	-	1	NA	intron (NM_023596, intron 2 of 5)	intron (NM_023596, intron 2 of 5)	8067	NM_023596	71279	Mm.284462	NM_023596	ENSMUSG00000020100	Slc29a3	4933435C21Rik|AW987637|Ent3	solute carrier family 29 (nucleoside transporters), member 3	protein-coding
mm_28447.1	chr3	90512021	90512066	-	1	NA	exon (NM_011309, exon 2 of 3)	exon (NM_011309, exon 2 of 3)	2287	NM_011309	20193	Mm.24662	NM_011309	ENSMUSG00000044080	S100a1	AI266795|S100|S100a	S100 calcium binding protein A1	protein-coding
mm_35413.1	chr4	34834863	34834865	-	1	NA	intron (NM_013889, intron 4 of 7)	intron (NM_013889, intron 4 of 7)	48084	NM_013889	30046	Mm.38193	NM_013889	ENSMUSG00000039967	Zfp292	5730450D02Rik|5830493J20Rik|9430062L07Rik|AI449016|Krox-10|Zfp-15|Zfp15|Zn-15|Zn-16|mKIAA0530	zinc finger protein 292	protein-coding
mm_155625.1	chrX	83855368	83855370	+	1	NA	intron (NM_007868, intron 29 of 78)	intron (NM_007868, intron 29 of 78)	-367445	NM_021898	100502723	Mm.383210	NM_021898	ENSMUSG00000035522	Tsga8	Halap-X|Halapx	testis specific gene A8	protein-coding
mm_76808.1	chr8	104395874	104395886	-	1	NA	promoter-TSS (NM_153582)	promoter-TSS (NM_153582)	-73	NM_153582	97487	Mm.29658	NM_153582	ENSMUSG00000096188	Cmtm4	Cklfsf4|D19397|ENSMUSG00000051554|Gm9853	CKLF-like MARVEL transmembrane domain containing 4	protein-coding
mm_128888.1	chr15	73162030	73162047	-	1	NA	intron (NM_153178, intron 1 of 18)	intron (NM_153178, intron 1 of 18)	22909	NM_153178	239528	Mm.23095	NM_153178	ENSMUSG00000036698	Ago2	1110029L17Rik|2310051F07Rik|AI225898|AL022874|AW546247|ENSMUSG00000072493|Eif2c2|Gerp95|Gm10365|mKIAA4215	argonaute RISC catalytic subunit 2	protein-coding
mm_100919.1	chr11	6292155	6292167	-	1	NA	promoter-TSS (NM_001252288)	promoter-TSS (NM_001252288)	-397	NM_001252288	18293	Mm.276348	NM_010956	ENSMUSG00000020456	Ogdh	2210403E04Rik|2210412K19Rik|AA409584|d1401|mKIAA4192	oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)	protein-coding
mm_45488.1	chr5	71502657	71502659	-	1	NA	intron (NM_030052, intron 2 of 2)	AT_rich|Low_complexity|Low_complexity	45547	NM_030052	78174	Mm.60690	NM_030052	ENSMUSG00000049387	Cox7b2	4930503B16Rik	cytochrome c oxidase subunit VIIb2	protein-coding
mm_7531.1	chr1	124307184	124307187	-	1	NA	Intergenic	Intergenic	-261626	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_34905.1	chr4	155670480	155670502	+	1	NA	Intergenic	RLTR9D|LTR|ERVK	-1237	NM_001256107	76580	Mm.235738	NM_145124	ENSMUSG00000029060	Mib2	2210008I11Rik|Zzank1|skd	mindbomb E3 ubiquitin protein ligase 2	protein-coding
mm_7872.1	chr1	132741751	132741806	-	1	NA	promoter-TSS (NM_001160317)	promoter-TSS (NM_001160317)	19	NM_182716	269116	Mm.326702	NM_182716	ENSMUSG00000026442	Nfasc	AA387016|D430023G06Rik|NF|mKIAA0756	neurofascin	protein-coding
mm_51899.1	chr6	90619366	90619382	+	1	NA	5' UTR (NM_001037493, exon 1 of 10)	5' UTR (NM_001037493, exon 1 of 10)	128	NM_001037493	71699	Mm.272633	NM_027868	ENSMUSG00000030089	Slc41a3	1010001P06Rik|AI480742|SLC41A1-L2	solute carrier family 41, member 3	protein-coding
mm_118566.1	chr14	18271202	18271290	+	1	NA	promoter-TSS (NM_025586)	promoter-TSS (NM_025586)	110	NM_023526	69721	Mm.25648	NM_023526	ENSMUSG00000021772	Nkiras1	2400004O09Rik|KBRAS1|kappaB-Ras1	NFKB inhibitor interacting Ras-like protein 1	protein-coding
mm_94862.1	chr11	24077941	24077951	+	1	NA	promoter-TSS (NM_001242934)	promoter-TSS (NM_001242934)	-110	NM_016707	14025	Mm.53687	NM_016707	ENSMUSG00000000861	Bcl11a	2810047E18Rik|BCL-11A|Ctip1|D930021L15Rik|Evi9|Evi9a|Evi9b|Evi9c|mKIAA1809	B cell CLL/lymphoma 11A (zinc finger protein)	protein-coding
mm_123157.1	chr14	57132072	57132089	-	1	NA	intron (NM_001010937, intron 1 of 2)	intron (NM_001010937, intron 1 of 2)	1531	NM_001271663	14623	Mm.25652	NM_008128	ENSMUSG00000040055	Gjb6	AA958971|Cx30|D14Bwg0506e	gap junction protein, beta 6	protein-coding
mm_61602.1	chr7	80027151	80027196	+	1	NA	intron (NM_175433, intron 1 of 4)	CpG	945	NM_175433	209225	Mm.290925	NM_175433	ENSMUSG00000048897	Zfp710	5430400N05Rik|9830165K13|AI324798|Znf710	zinc finger protein 710	protein-coding
mm_1082.1	chr1	59544140	59544153	+	1	NA	intron (NM_001013771, intron 3 of 19)	intron (NM_001013771, intron 3 of 19)	27882	NM_001013771	381260	Mm.486706	NM_001013771	ENSMUSG00000047361	Gm973	AW554518	predicted gene 973	protein-coding
mm_154321.1	chrM	2281	2291	+	1	NA	NA	Intergenic	NA	NA								
mm_60619.1	chr7	44598376	44598389	+	1	NA	intron (NM_008422, intron 2 of 3)	intron (NM_008422, intron 2 of 3)	7496	NM_001290682	16504	Mm.40312	NM_008422	ENSMUSG00000062785	Kcnc3	KShIIID|Kcr2-3|Kv3.3	potassium voltage gated channel, Shaw-related subfamily, member 3	protein-coding
mm_8001.1	chr1	134540718	134540725	-	1	NA	TTS (NM_001145300)	TTS (NM_001145300)	8961	NM_001145300	71001	Mm.158529	NM_183292	ENSMUSG00000046367	Mgat4e	4931440L10Rik	MGAT4 family, member E	protein-coding
mm_156601.1	chrX	152781995	152782029	+	1	NA	promoter-TSS (NM_010951)	promoter-TSS (NM_010951)	91	NM_010951	18241	Mm.5157	NM_010951	ENSMUSG00000025333	Gpr143	Oa1	G protein-coupled receptor 143	protein-coding
mm_103243.1	chr11	70700106	70700170	-	1	NA	promoter-TSS (NM_213729)	promoter-TSS (NM_213729)	17	NM_001252482	103844	Mm.101581	NM_213729	ENSMUSG00000057054	Inca1	AI842396	inhibitor of CDK, cyclin A1 interacting protein 1	protein-coding
mm_121073.1	chr14	98167887	98167899	+	1	NA	intron (NM_007826, intron 1 of 11)	intron (NM_007826, intron 1 of 11)	1872	NM_001038610	13134	Mm.320593	NM_007826	ENSMUSG00000055639	Dach1	Dac|Dach	dachshund 1 (Drosophila)	protein-coding
mm_88328.1	chr10	75568649	75568673	+	1	NA	promoter-TSS (NM_001305992)	promoter-TSS (NM_001305992)	-1	NM_001305992	14598	Mm.4559	NM_008116	ENSMUSG00000006345	Ggt1	CD224|GGT|GGT 1|GGT-1|Ggtp|dwg	gamma-glutamyltransferase 1	protein-coding
mm_53768.1	chr6	145863845	145863886	+	1	NA	exon (NM_001271768, exon 5 of 5)	exon (NM_001271768, exon 5 of 5)	1555	NM_001271768	79362	Mm.154529	NM_024469	ENSMUSG00000030256	Bhlhe41	6430520M22Rik|Bhlhb2l|Bhlhb3|DEC2|Sharp1	basic helix-loop-helix family, member e41	protein-coding
mm_156306.1	chrX	136838021	136838025	+	1	NA	3' UTR (NM_011123, exon 7 of 7)	3' UTR (NM_011123, exon 7 of 7)	15277	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_109119.1	chr12	105685351	105685363	+	1	NA	promoter-TSS (NM_178613)	promoter-TSS (NM_178613)	5	NM_178613	66787	Mm.248019	NM_178613	ENSMUSG00000044715	Gskip	4933433P14Rik	GSK3B interacting protein	protein-coding
mm_81880.1	chr9	119341349	119341363	+	1	NA	promoter-TSS (NM_130864)	promoter-TSS (NM_130864)	62	NM_130864	113868	Mm.205266	NM_130864	ENSMUSG00000036138	Acaa1a	Acaa|Acaa1|D9Ertd25e|PTL	acetyl-Coenzyme A acyltransferase 1A	protein-coding
mm_55365.1	chr6	57535478	57535497	-	1	NA	promoter-TSS (NM_175523)	promoter-TSS (NM_175523)	-61	NM_175523	243382	Mm.396893	NM_175523	ENSMUSG00000037826	Ppm1k	2900063A19Rik|A930026L03Rik|PP2Cm	protein phosphatase 1K (PP2C domain containing)	protein-coding
mm_135828.1	chr16	58515834	58515836	-	1	NA	intron (NM_018784, intron 1 of 10)	intron (NM_018784, intron 1 of 10)	7477	NM_018784	54613	Mm.212742	NM_018784	ENSMUSG00000022747	St3gal6	1700023B24Rik|AI930218|AW552396|Siat10|St3galVI	ST3 beta-galactoside alpha-2,3-sialyltransferase 6	protein-coding
mm_620.1	chr1	40085199	40085228	+	1	NA	non-coding (NR_037980, exon 2 of 4)	non-coding (NR_037980, exon 2 of 4)	445	NM_010555	16178	Mm.1349	NM_010555	ENSMUSG00000026073	Il1r2	CD121b|Il1r-2	interleukin 1 receptor, type II	protein-coding
mm_83193.1	chr9	41014259	41014274	-	1	NA	3' UTR (NM_176860, exon 14 of 14)	3' UTR (NM_176860, exon 14 of 14)	-9638	NM_019465	54698	Mm.42791	NM_019465	ENSMUSG00000032021	Crtam	-	cytotoxic and regulatory T cell molecule	protein-coding
mm_129765.1	chr15	82642036	82642052	-	1	NA	promoter-TSS (NR_003552)	promoter-TSS (NR_003552)	1	NR_003552	68444	Mm.443212	NR_003552		Cyp2d13	1300007K12Rik	cytochrome P450, family 2, subfamily d, polypeptide 13	pseudo
mm_116637.1	chr13	49014584	49014623	-	1	NA	Intergenic	Intergenic	46491	NR_015601	68128	Mm.426304	NR_015601		Fam120aos	C030044B11Rik	family with sequence similarity 120A, opposite strand	ncRNA
mm_94531.1	chr11	9118537	9118556	+	1	NA	promoter-TSS (NM_001159402)	promoter-TSS (NM_001159402)	39	NM_001159402	22271	Mm.4610	NM_009477	ENSMUSG00000020407	Upp1	AI325217|UPase|UdRPase|Up|Upp	uridine phosphorylase 1	protein-coding
mm_59898.1	chr7	30308267	30308277	+	1	NA	promoter-TSS (NM_198027)	promoter-TSS (NM_198027)	-481	NM_198027	233065	Mm.276277	NM_198027	ENSMUSG00000042831	Alkbh6	AI839550|Abh6|C130099A02	alkB homolog 6	protein-coding
mm_165104.1	chr19	55893401	55893405	+	1	NA	intron (NR_138565, intron 4 of 15)	intron (NR_138565, intron 4 of 15)	-1918	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_22621.1	chr3	14644913	14644941	+	1	NA	intron (NM_024495, intron 1 of 6)	B4A|SINE|B4	3200	NM_024495	71934	Mm.158776	NM_024495	ENSMUSG00000027555	Car13	2310075C21Rik|Ca13	carbonic anhydrase 13	protein-coding
mm_160377.1	chr8	41015435	41015435	-	1	NA	exon (NM_001286413, exon 7 of 14)	exon (NM_001286413, exon 7 of 14)	-2033	NR_015457	78849	Mm.440930	NR_015457	ENSMUSG00000084960	B430010I23Rik	-	RIKEN cDNA B430010I23 gene	ncRNA
mm_71648.1	chr8	59419384	59419388	+	1	NA	Intergenic	RMER13B|LTR|ERVK	-406263	NR_126087	75017	Mm.60775	NR_126087	ENSMUSG00000110406	4930470O06Rik	-	RIKEN cDNA 4930470O06 gene	ncRNA
mm_13023.1	chr2	91035688	91035711	+	1	NA	promoter-TSS (NM_009023)	promoter-TSS (NM_009023)	72	NM_009023	19400	Mm.1272	NM_009023	ENSMUSG00000002104	Rapsn	43kDa|Nraps|Raps|rapsyn	receptor-associated protein of the synapse	protein-coding
mm_146921.1	chr18	31610517	31610546	-	1	NA	promoter-TSS (NM_026165)	promoter-TSS (NM_026165)	-629	NM_026165	67453	Mm.23896	NM_026165	ENSMUSG00000024259	Slc25a46	1200007B05Rik|AI325987	solute carrier family 25, member 46	protein-coding
mm_113024.1	chr13	22043190	22043208	+	1	NA	promoter-TSS (NM_178186)	promoter-TSS (NM_178186)	-31	NM_178198	319183	Mm.371766	NM_178198	ENSMUSG00000069300	Hist1h2bj	-	histone cluster 1, H2bj	protein-coding
mm_73265.1	chr8	104346954	104346995	+	1	NA	3' UTR (NM_024217, exon 5 of 5)	3' UTR (NM_024217, exon 5 of 5)	6380	NM_024217	68119	Mm.390108	NM_024217	ENSMUSG00000031875	Cmtm3	9430096L06Rik|AI413895|BNAS2|Cklfsf3	CKLF-like MARVEL transmembrane domain containing 3	protein-coding
mm_16319.1	chr2	174304555	174304561	+	1	NA	intron (NM_001310085, intron 2 of 12)	(CA)n|Simple_repeat|Simple_repeat	6699	NM_001310085	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_115393.1	chr13	113660823	113660856	+	1	NA	Intergenic	RLTR31B2|LTR|ERVK	2837	NM_019960	56534	Mm.41410	NM_019960	ENSMUSG00000051456	Hspb3	2310035K17Rik|AI844863|Hsbp3|spb3	heat shock protein 3	protein-coding
mm_59045.1	chr7	19345663	19345692	+	1	NA	exon (NM_007948, exon 2 of 10)	exon (NM_007948, exon 2 of 10)	606	NM_007948	13870	Mm.280913	NM_007948	ENSMUSG00000003549	Ercc1	Ercc-1	excision repair cross-complementing rodent repair deficiency, complementation group 1	protein-coding
mm_143327.1	chr17	66419699	66419699	-	1	NA	intron (NM_001114098, intron 3 of 14)	intron (NM_001114098, intron 3 of 14)	30051	NM_172963	68617	Mm.33421	NM_172963	ENSMUSG00000052105	Mtcl1	1110012J17Rik|Ccdc165|D130071O13|Kiaa0802|Soga2|mKIAA0802|t8219b25	microtubule crosslinking factor 1	protein-coding
mm_61048.1	chr7	49895603	49895612	+	1	NA	Intergenic	Intergenic	-14692	NM_001146013	104245	Mm.207053	NM_148931	ENSMUSG00000039728	Slc6a5	Glyt2|prestin	solute carrier family 6 (neurotransmitter transporter, glycine), member 5	protein-coding
mm_165341.1	chr2	118008313	118008334	+	1	NA	intron (NR_126479, intron 8 of 9)	intron (NR_126479, intron 8 of 9)	102879	NR_126479	329496	Mm.235844	NR_126479	ENSMUSG00000087203	Gm13986	C230060E24|OTTMUSG00000015236	predicted gene 13986	ncRNA
mm_97925.1	chr11	83639732	83639738	+	1	NA	Intergenic	Intergenic	9643	NM_011337	20302	Mm.1282	NM_011337	ENSMUSG00000000982	Ccl3	AI323804|G0S19-1|LD78alpha|MIP-1alpha|MIP1-(a)|MIP1-alpha|Mip1a|Scya3	chemokine (C-C motif) ligand 3	protein-coding
mm_146859.1	chr18	24439102	24439106	-	1	NA	Intergenic	Intergenic	-9934	NR_029573	387182		NR_029573	ENSMUSG00000065532	Mir187	Mirn187|mir-187|mmu-mir-187	microRNA 187	ncRNA
mm_58545.1	chr7	4526593	4526606	+	1	NA	intron (NM_001033548, intron 8 of 11)	intron (NM_001033548, intron 8 of 11)	-4156	NM_009406	21954	Mm.27674	NM_009406	ENSMUSG00000035458	Tnni3	Tn1|cTnI	troponin I, cardiac 3	protein-coding
mm_41696.1	chr5	100845710	100845728	+	1	NA	promoter-TSS (NM_172715)	promoter-TSS (NM_172715)	-510	NM_172715	231510	Mm.271911	NM_172715	ENSMUSG00000029314	Agpat9	1-AGPAT|1-AGPAT 9|4933407I02Rik|4933408F15|A230097K15Rik|GPAT-3|Gpat3|mGPAT3	1-acylglycerol-3-phosphate O-acyltransferase 9	protein-coding
mm_136294.1	chr16	91464838	91464891	-	1	NA	promoter-TSS (NR_077219)	promoter-TSS (NR_077219)	-240	NR_077219	100503120	Mm.387130	NR_077219	ENSMUSG00000084866	A930006K02Rik	-	RIKEN cDNA A930006K02 gene	ncRNA
mm_159074.1	chr2	25579953	25579953	-	1	NA	5' UTR (NM_001005424, exon 1 of 1)	5' UTR (NM_001005424, exon 1 of 1)	146	NM_001005424	381353	Mm.379511	NM_001005424	ENSMUSG00000029419	Gm996	-	predicted gene 996	protein-coding
mm_59612.1	chr7	28142563	28142573	+	1	NA	exon (NM_001164655, exon 6 of 20)	exon (NM_001164655, exon 6 of 20)	13102	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_98642.1	chr11	96194368	96194379	+	1	NA	promoter-TSS (NM_008267)	promoter-TSS (NM_008267)	12	NM_008267	15408	Mm.57221	NM_008267	ENSMUSG00000049604	Hoxb13	-	homeobox B13	protein-coding
mm_33002.1	chr4	120532220	120532256	+	1	NA	promoter-TSS (NM_177570)	promoter-TSS (NM_177570)	7	NM_177570	194219	Mm.29788	NM_177570	ENSMUSG00000047518	Slfnl1	4933406A14Rik	schlafen like 1	protein-coding
mm_159503.1	chr4	43854416	43854416	+	1	NA	exon (NM_019473, exon 1 of 1)	exon (NM_019473, exon 1 of 1)	124	NM_019473	29845	Mm.88841	NM_019473	ENSMUSG00000071000	Olfr155	GA_x5J8B7W5BNN-979337-980296|MOR262-14|OR37A|Olfr37a|mOR37a	olfactory receptor 155	protein-coding
mm_67155.1	chr7	73540889	73540919	-	1	NA	non-coding (NR_037569, exon 5 of 5)	non-coding (NR_037569, exon 5 of 5)	842	NM_001081345	244059	Mm.34539	NM_001081345	ENSMUSG00000078671	Chd2	2810013C04Rik|2810040A01Rik|5630401D06Rik|AI851092|BC029703|CHD-2	chromodomain helicase DNA binding protein 2	protein-coding
mm_20515.1	chr2	130662173	130662186	-	1	NA	exon (NM_029832, exon 3 of 9)	exon (NM_029832, exon 3 of 9)	2466	NM_029832	77006	Mm.440063	NM_029832	ENSMUSG00000068290	Ddrgk1	1110001I20Rik|2600009E05Rik|AI326138|Ufbp1	DDRGK domain containing 1	protein-coding
mm_106289.1	chr11	118210107	118210110	-	1	NA	intron (NM_001112699, intron 1 of 12)	AT_rich|Low_complexity|Low_complexity	2634	NM_001112700	19157	Mm.86413	NM_011180	ENSMUSG00000017132	Cyth1	CLM1|CTH-1|CYTIP|Pscd1	cytohesin 1	protein-coding
mm_98472.1	chr11	94950358	94950367	+	1	NA	exon (NM_007742, exon 48 of 51)	exon (NM_007742, exon 48 of 51)	14138	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_110718.1	chr12	69582986	69583050	-	1	NA	promoter-TSS (NM_001033236)	promoter-TSS (NM_001033236)	10	NM_001033236	207965	Mm.102487	NM_001033236	ENSMUSG00000049882	Vcpkmt	Gm71|Mettl21d|Mettl221d|VCP-KMT	valosin containing protein lysine (K) methyltransferase	protein-coding
mm_11287.1	chr2	30066783	30066798	+	1	NA	5' UTR (NM_001204875, exon 1 of 8)	5' UTR (NM_001204875, exon 1 of 8)	316	NM_001204875	56086	Mm.326055	NM_023871	ENSMUSG00000054766	Set	2610030F17Rik|5730420M11Rik|AA407739|I-2PP2A|StF-IT-1|TAF-I	SET nuclear oncogene	protein-coding
mm_58404.1	chr7	3219237	3219264	+	1	NA	promoter-TSS (NR_029642)	promoter-TSS (NR_029642)	9	NR_106140	102467000		NR_106140	ENSMUSG00000104747	Mir292b	mmu-mir-292b	microRNA 292b	ncRNA
mm_14408.1	chr2	130275508	130275509	+	1	NA	promoter-TSS (NR_028547)	promoter-TSS (NR_028547)	-7	NR_028547	100217452		NR_028547	ENSMUSG00000080610	Snord110	MBII-55	small nucleolar RNA, C/D box 110	snoRNA
mm_109988.1	chr12	14152042	14152069	-	1	NA	promoter-TSS (NM_029007)	promoter-TSS (NM_029007)	-17	NM_029007	105005	Mm.227253	NM_029007	ENSMUSG00000020607	Fam84a	2310003N02Rik|4731402F03Rik|AW125753|Nse1	family with sequence similarity 84, member A	protein-coding
mm_25498.1	chr3	109380672	109380677	+	1	NA	intron (NM_020505, intron 1 of 26)	RLTR12D|LTR|ERVK	39991	NM_020505	57257	Mm.282257	NM_020505	ENSMUSG00000033721	Vav3	A530094I06Rik|AA986410|Idd18.1	vav 3 oncogene	protein-coding
mm_96725.1	chr11	69684324	69684335	+	1	NA	exon (NM_001159503, exon 11 of 13)	exon (NM_001159503, exon 11 of 13)	1225	NM_001159505	69583	Mm.8983	NM_023517	ENSMUSG00000089669	Tnfsf13	2310026N09Rik|April|Tall2|Tnlg7b|Trdl1	tumor necrosis factor (ligand) superfamily, member 13	protein-coding
mm_54852.1	chr6	42591929	42591933	-	1	NA	exon (NM_203396, exon 4 of 7)	exon (NM_203396, exon 4 of 7)	5441	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_94408.1	chr11	5797988	5798005	+	1	NA	intron (NM_013810, intron 9 of 12)	intron (NM_013810, intron 9 of 12)	5800	NM_018870	56012	Mm.219627	NM_018870	ENSMUSG00000020475	Pgam2	-	phosphoglycerate mutase 2	protein-coding
mm_79417.1	chr9	55213901	55213911	+	1	NA	intron (NM_028049, intron 2 of 6)	intron (NM_028049, intron 2 of 6)	4971	NM_028049	71999	Mm.276429	NM_028049	ENSMUSG00000032309	Fbxo22	0610033L19Rik|1600016C16Rik	F-box protein 22	protein-coding
mm_168410.1	chr11	3146498	3146498	-	1	NA	intron (NM_030207, intron 14 of 32)	B2_Mm2|SINE|B2	22477	NR_003517	236604	Mm.247625	NM_001004146		Pisd-ps1	-	phosphatidylserine decarboxylase, pseudogene 1	pseudo
mm_42532.1	chr5	115859037	115859074	+	1	NA	intron (NM_007708, intron 2 of 46)	intron (NM_007708, intron 2 of 46)	13399	NM_007708	12704	Mm.8321	NM_007708	ENSMUSG00000029516	Cit	C030025P15Rik|CRIK|CRIK-SK|Cit-k	citron	protein-coding
mm_120670.1	chr14	70554229	70554239	+	1	NA	intron (NM_021877, intron 1 of 19)	CpG	178	NM_021877	15460	Mm.7598	NM_021877	ENSMUSG00000022096	Hr	ALUNC|AU|N|ba|bldy|hr|rh|rh-bmh|rhino	hairless	protein-coding
mm_16400.1	chr2	179976895	179976906	+	1	NA	promoter-TSS (NM_001081092)	promoter-TSS (NM_001081092)	47	NR_033782	66730	Mm.31773	NR_033782	ENSMUSG00000085704	4921531C22Rik	-	RIKEN cDNA 4921531C22 gene	ncRNA
mm_151997.1	chr19	5894101	5894155	-	1	NA	promoter-TSS (NM_198634)	promoter-TSS (NM_198634)	-21	NM_198634	332359	Mm.329642	NM_198634	ENSMUSG00000044390	Tigd3	-	tigger transposable element derived 3	protein-coding
mm_43567.1	chr5	137636741	137636755	+	1	NA	exon (NM_146164, exon 5 of 18)	exon (NM_146164, exon 5 of 18)	-4725	NM_001081962	751865	Mm.200763	NM_001081962	ENSMUSG00000079165	Sap25	-	sin3 associated polypeptide	protein-coding
mm_2181.1	chr1	88559902	88559923	+	1	NA	non-coding (NR_037971, exon 5 of 6)	non-coding (NR_037971, exon 5 of 6)	8395	NR_037971	100503197	Mm.99352	NR_037971	ENSMUSG00000100798	Gm19589	-	predicted gene, 19589	ncRNA
mm_124189.1	chr14	97515458	97515460	-	1	NA	Intergenic	RMER1A|Other|Other	654306	NM_001038610	13134	Mm.320593	NM_007826	ENSMUSG00000055639	Dach1	Dac|Dach	dachshund 1 (Drosophila)	protein-coding
mm_41377.1	chr5	90719219	90719225	+	1	NA	Intergenic	Lx8|LINE|L1	-40076	NM_009141	20311	Mm.4660	NM_009141	ENSMUSG00000029371	Cxcl5	AMCF-II|Cxcl6|ENA-78|GCP-2|LIX|Scyb5|Scyb6	chemokine (C-X-C motif) ligand 5	protein-coding
mm_79676.1	chr9	59750852	59750857	+	1	NA	promoter-TSS (NM_001172071)	promoter-TSS (NM_001172071)	-205	NM_001172070	71599	Mm.279070	NM_027838	ENSMUSG00000051705	Senp8	9130010J17Rik|AU020827|Den1|Nedp1|Prsc2	SUMO/sentrin specific peptidase 8	protein-coding
mm_160702.1	chr10	50895749	50895749	+	1	NA	promoter-TSS (NM_011376)	promoter-TSS (NM_011376)	98	NM_011376	20464	Mm.4774	NM_011376	ENSMUSG00000019913	Sim1	bHLHe14|mSIM1	single-minded homolog 1 (Drosophila)	protein-coding
mm_159133.1	chr2	75661468	75661468	+	1	NA	exon (NM_198090, exon 2 of 11)	exon (NM_198090, exon 2 of 11)	2178	NR_033513	627828	Mm.459502	NR_033513	ENSMUSG00000092086	Gm6793	EG627828	heterogeneous nuclear ribonucleoprotein A3 pseudogene	pseudo
mm_9537.1	chr1	173874423	173874435	-	1	NA	exon (NM_001170853, exon 4 of 10)	exon (NM_001170853, exon 4 of 10)	5758	NM_001170853	100040462	Mm.463437	NM_001170853	ENSMUSG00000090272	Mndal	Gm2785|Ifi212	myeloid nuclear differentiation antigen like	protein-coding
mm_139190.1	chr17	47598665	47598708	+	1	NA	TTS (NM_016859)	TTS (NM_016859)	5219	NM_007632	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_115902.1	chr13	23369157	23369217	-	1	NA	promoter-TSS (NM_001286156)	promoter-TSS (NM_001286156)	21	NM_001286156	218100	Mm.286454	NM_172586	ENSMUSG00000046351	Zfp322a	Znf322|Znf322a	zinc finger protein 322A	protein-coding
mm_120476.1	chr14	65975583	65975593	+	1	NA	exon (NM_013492, exon 5 of 9)	exon (NM_013492, exon 5 of 9)	7105	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_162136.1	chrX	73411610	73411610	+	1	NA	promoter-TSS (NM_001310531)	promoter-TSS (NM_001310531)	50	NM_001310531	22754	Mm.5060	NM_009566	ENSMUSG00000031374	Zfp92	-	zinc finger protein 92	protein-coding
mm_29936.1	chr3	131613775	131613785	-	1	NA	intron (NM_001289477, intron 10 of 12)	intron (NM_001289477, intron 10 of 12)	47748	NM_001289477	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_136990.1	chr17	17374547	17374594	+	1	NA	5' UTR (NM_025934, exon 1 of 10)	5' UTR (NM_025934, exon 1 of 10)	238	NM_025934	67045	Mm.35117	NM_025934	ENSMUSG00000023852	Riok2	2010110K24Rik|2410085M17Rik	RIO kinase 2 (yeast)	protein-coding
mm_56349.1	chr6	92988203	92988212	-	1	NA	intron (NR_015530, intron 1 of 2)	intron (NR_015530, intron 1 of 2)	47625	NR_015530	330385	Mm.483472	NR_015530	ENSMUSG00000097462	9530026P05Rik	B430306B02	RIKEN cDNA 9530026P05 gene	ncRNA
mm_22143.1	chr2	172043130	172043148	-	1	NA	5' UTR (NM_175631, exon 1 of 3)	5' UTR (NM_175631, exon 1 of 3)	327	NM_175631	228942	Mm.40555	NM_175631	ENSMUSG00000067578	Cbln4	AI848962	cerebellin 4 precursor protein	protein-coding
mm_43840.1	chr5	142973028	142973051	+	1	NA	3' UTR (NM_007984, exon 5 of 5)	3' UTR (NM_007984, exon 5 of 5)	12684	NM_007984	14086	Mm.289707	NM_007984	ENSMUSG00000029581	Fscn1	AI663989|Fan1|fascin-1	fascin actin-bundling protein 1	protein-coding
mm_12201.1	chr2	65930093	65930116	+	1	NA	intron (NM_178634, intron 2 of 5)	intron (NM_178634, intron 2 of 5)	-1761	NM_001290665	77771	Mm.102025	NM_153409	ENSMUSG00000044647	Csrnp3	A330102K23Rik|CSRNP-3|Csnrp3|Mbu1|taip-2	cysteine-serine-rich nuclear protein 3	protein-coding
mm_49507.1	chr6	29853984	29853998	+	1	NA	intron (NM_001347084, intron 1 of 17)	intron (NM_001347084, intron 1 of 17)	250	NM_001347084	74340	Mm.210899	NM_021414	ENSMUSG00000029772	Ahcyl2	4631427C17Rik|AI227036|Adohcyase3|mKIAA0828	S-adenosylhomocysteine hydrolase-like 2	protein-coding
mm_16921.1	chr2	13580077	13580103	-	1	NA	exon (NM_011701, exon 6 of 9)	exon (NM_011701, exon 6 of 9)	5779	NM_011701	22352	Mm.268000	NM_011701	ENSMUSG00000026728	Vim	-	vimentin	protein-coding
mm_135921.1	chr16	69800378	69800399	-	1	NA	promoter-TSS (NR_130991)	promoter-TSS (NR_130991)	-7	NR_130991	78110	Mm.211406	NR_130991	ENSMUSG00000107073	4930428D20Rik	-	RIKEN cDNA 4930428D20 gene	ncRNA
mm_29848.1	chr3	129946310	129946314	-	1	NA	intron (NM_001293644, intron 1 of 6)	Lx7|LINE|L1	23894	NM_025779	66815	Mm.31056	NM_025779	ENSMUSG00000027994	Ccdc109b	9030408N13Rik|MCUb	coiled-coil domain containing 109B	protein-coding
mm_38197.1	chr4	135433745	135433869	-	1	NA	promoter-TSS (NM_022980)	promoter-TSS (NM_022980)	-2	NM_022980	53902	Mm.331970	NM_022980	ENSMUSG00000059713	Rcan3	AU041093|Csp3|Dscr1l2	regulator of calcineurin 3	protein-coding
mm_6240.1	chr1	67038691	67038700	-	1	NA	5' UTR (NM_001190985, exon 1 of 9)	5' UTR (NM_001190985, exon 1 of 9)	139	NM_001190984	14768	Mm.20522	NM_021295	ENSMUSG00000026000	Lancl1	AW124738|Gpr69|Gpr69a|p40	LanC (bacterial lantibiotic synthetase component C)-like 1	protein-coding
mm_155443.1	chrX	73494978	73494988	+	1	NA	3' UTR (NM_007542, exon 8 of 8)	3' UTR (NM_007542, exon 8 of 8)	-8103	NM_001310537	320707	Mm.210095	NM_177236	ENSMUSG00000031376	Atp2b3	6430519O13Rik|Pmca3	ATPase, Ca++ transporting, plasma membrane 3	protein-coding
mm_5901.1	chr1	54809965	54810001	-	1	NA	intron (NM_001081433, intron 2 of 27)	intron (NM_001081433, intron 2 of 27)	116404	NM_001081433	329154	Mm.397910	NM_001081433	ENSMUSG00000052331	Ankrd44	4930444A19Rik|A130096K20|E130014H08Rik|PP6-ARS-B	ankyrin repeat domain 44	protein-coding
mm_51230.1	chr6	71374320	71374333	+	1	NA	intron (NM_001081110, intron 1 of 4)	intron (NM_001081110, intron 1 of 4)	899	NM_001081110	12525	Mm.1858	NM_009857	ENSMUSG00000053977	Cd8a	BB154331|Ly-2|Ly-35|Ly-B|Lyt-2	CD8 antigen, alpha chain	protein-coding
mm_113846.1	chr13	47201519	47201528	+	1	NA	intron (NM_001170643, intron 1 of 7)	intron (NM_001170643, intron 1 of 7)	7520	NM_001170643	218215	Mm.287609	NM_146042	ENSMUSG00000038068	Rnf144b	BC025007|E130105P19Rik|Ibrdc2|Pir2	ring finger protein 144B	protein-coding
mm_143013.1	chr17	56462144	56462243	-	1	NA	promoter-TSS (NM_001252456)	promoter-TSS (NM_001252456)	28	NM_001252456	19280	Mm.258771	NM_011218	ENSMUSG00000013236	Ptprs	AL022616|PTP|PTP-NU3|PTPNU-3|PTPsigma|Ptpt9|R-PTP-S|RPTPsigma	protein tyrosine phosphatase, receptor type, S	protein-coding
mm_71140.1	chr8	39046038	39046063	+	1	NA	intron (NM_030254, intron 1 of 7)	intron (NM_030254, intron 1 of 7)	40183	NM_030254	80286	Mm.272722	NM_030254	ENSMUSG00000039530	Tusc3	AU022242|BC003311|N33	tumor suppressor candidate 3	protein-coding
mm_128671.1	chr15	60187323	60187331	-	1	NA	Intergenic	Intergenic	-170709	NM_027668	71088	Mm.425950	NM_027668	ENSMUSG00000071749	4933412E24Rik	-	RIKEN cDNA 4933412E24 gene	protein-coding
mm_26151.1	chr3	138143484	138143496	+	1	NA	promoter-TSS (NM_175389)	promoter-TSS (NM_175389)	-48	NM_175389	108943	Mm.471692	NM_175389	ENSMUSG00000004127	Trmt10a	3110023L08Rik|AA794508|Rg9mtd2|Rnmtd2	tRNA methyltransferase 10A	protein-coding
mm_117593.1	chr13	89742382	89742392	-	1	NA	5' UTR (NM_001134474, exon 1 of 14)	5' UTR (NM_001134474, exon 1 of 14)	125	NM_001081249	13003	Mm.158700	NM_019389	ENSMUSG00000021614	Vcan	5430420N07Rik|9430051N09|Cspg2|DPEAAE|NG2|PG-M|PG-M(V0)|PG-M(V1)|hdf	versican	protein-coding
mm_19700.1	chr2	103766496	103766509	-	1	NA	TTS (NM_001111292)	TTS (NM_001111292)	-5252	NM_153126	98956	Mm.288005	NM_153126	ENSMUSG00000027185	Nat10	AI429152	N-acetyltransferase 10	protein-coding
mm_85563.1	chr9	106891909	106891920	-	1	NA	promoter-TSS (NM_029103)	promoter-TSS (NM_029103)	24	NM_029103	74840	Mm.29778	NM_029103	ENSMUSG00000032575	Manf	3230402M22Rik|AA407711|AA408789|AA673178|Armet|D17914|D18Mgi17	mesencephalic astrocyte-derived neurotrophic factor	protein-coding
mm_54770.1	chr6	41523940	41523954	-	1	NA	exon (NM_009430, exon 3 of 5)	exon (NM_009430, exon 3 of 5)	2171	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_726.1	chr1	42953107	42953164	+	1	NA	5' UTR (NM_053107, exon 1 of 2)	5' UTR (NM_053107, exon 1 of 2)	263	NM_053107	93690	Mm.444976	NM_053107	ENSMUSG00000041907	Gpr45	9230112G11Rik|AW046772	G protein-coupled receptor 45	protein-coding
mm_152812.1	chr19	23087525	23087532	-	1	NA	Intergenic	B2_Mm2|SINE|B2	-53698	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_114212.1	chr13	56163115	56163135	+	1	NA	Intergenic	Intergenic	15760	NM_145976	212937	Mm.116697	NM_145976	ENSMUSG00000049625	Tifab	-	TRAF-interacting protein with forkhead-associated domain, family member B	protein-coding
mm_80304.1	chr9	73217303	73217305	+	1	NA	Intergenic	Intergenic	103835	NM_198609	225215	Mm.379366	NM_198609	ENSMUSG00000032215	Rsl24d1	2410159K22Rik	ribosomal L24 domain containing 1	protein-coding
mm_75841.1	chr8	70601330	70601370	-	1	NA	intron (NM_133772, intron 4 of 16)	CpG	6869	NM_023627	71780	Mm.29357	NM_023627	ENSMUSG00000019139	Isyna1	1300017C10Rik|AU018670	myo-inositol 1-phosphate synthase A1	protein-coding
mm_107737.1	chr12	57951207	57951213	+	1	NA	Intergenic	Intergenic	-260594	NM_009216	20605	Mm.278336	NM_009216	ENSMUSG00000035431	Sstr1	SRIF-2|SS-1-R|SS1-R|SS1R|Smstr-1|Smstr1|sst1	somatostatin receptor 1	protein-coding
mm_60490.1	chr7	44478627	44478632	+	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	-5888	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_154375.1	chrM	11109	11119	+	1	NA	NA	Intergenic	NA	NA								
mm_52234.1	chr6	104492955	104492965	+	1	NA	promoter-TSS (NM_017383)	promoter-TSS (NM_017383)	-84	NM_017383	53870	Mm.321671	NM_017383	ENSMUSG00000030092	Cntn6	NB-3	contactin 6	protein-coding
mm_95221.1	chr11	44399981	44399989	+	1	NA	promoter-TSS (NM_001303244)	promoter-TSS (NM_001303244)	-78	NM_001303244	16160	Mm.239707	NM_008352	ENSMUSG00000004296	Il12b	Il-12b|Il-12p40|Il12p40|p40	interleukin 12b	protein-coding
mm_42243.1	chr5	113828907	113828911	+	1	NA	intron (NM_009151, intron 1 of 1)	B3|SINE|B2	1592	NM_009151	20345	Mm.332590	NM_009151	ENSMUSG00000048163	Selplg	CD162|Psgl-1|Psgl1|Selp1|Selpl	selectin, platelet (p-selectin) ligand	protein-coding
mm_79538.1	chr9	57910474	57910490	+	1	NA	promoter-TSS (NM_027086)	promoter-TSS (NM_027086)	-504	NM_027086	69459	Mm.41735	NM_027086	ENSMUSG00000055720	Ubl7	2300004C15Rik	ubiquitin-like 7 (bone marrow stromal cell-derived)	protein-coding
mm_164906.1	chr18	69923478	69923484	-	1	NA	Intergenic	Intergenic	-2078	NM_201362	381175	Mm.266831	NM_201362	ENSMUSG00000038903	Ccdc68	BC046343	coiled-coil domain containing 68	protein-coding
mm_64879.1	chr7	14446652	14446672	-	1	NA	promoter-TSS (NM_175250)	promoter-TSS (NM_175250)	-75	NM_175250	76971	Mm.290727	NM_175250	ENSMUSG00000030378	Sult2a8	2810007J24Rik	sulfotransferase family 2A, dehydroepiandrosterone (DHEA)-preferring, member 8	protein-coding
mm_58047.1	chr6	136828125	136828179	-	1	NA	promoter-TSS (NM_021714)	promoter-TSS (NM_021714)	64	NM_021714	60321	Mm.141197	NM_021714	ENSMUSG00000030216	Wbp11	2510026P17Rik|D6Wsu113e|Npwbp|SIPP1	WW domain binding protein 11	protein-coding
mm_122930.1	chr14	54961722	54961731	-	1	NA	intron (NM_001164171, intron 10 of 38)	intron (NM_001164171, intron 10 of 38)	4881	NM_001164171	17888	Mm.290003	NM_010856	ENSMUSG00000040752	Myh6	A830009F23Rik|AA517445|Myhc-a|Myhca|alpha-MHC	myosin, heavy polypeptide 6, cardiac muscle, alpha	protein-coding
mm_30495.1	chr3	157534063	157534075	-	1	NA	promoter-TSS (NM_017381)	promoter-TSS (NM_017381)	-328	NM_017381	53861	Mm.259036	NM_017381	ENSMUSG00000028180	Zranb2	AI227013|Zfp265|Zis|Znf265	zinc finger, RAN-binding domain containing 2	protein-coding
mm_30686.1	chr4	11342402	11342403	+	1	NA	intron (NM_194055, intron 14 of 15)	intron (NM_194055, intron 14 of 15)	-20271	NM_001081201	381510	Mm.331486	NM_001081201	ENSMUSG00000045205	Dpy19l4	Gm1023|Narg3	dpy-19-like 4 (C. elegans)	protein-coding
mm_25288.1	chr3	105803623	105803633	+	1	NA	Intergenic	Intergenic	-2247	NM_145541	109905	Mm.101922	NM_145541	ENSMUSG00000068798	Rap1a	AI848598|G-22K|Krev-1|Rap1	RAS-related protein-1a	protein-coding
mm_55015.1	chr6	48840743	48840757	-	1	NA	promoter-TSS (NM_025326)	promoter-TSS (NM_025326)	238	NM_023056	65963	Mm.28385	NM_023056	ENSMUSG00000029810	Tmem176b	1810009M01Rik|Clast1|Lr8	transmembrane protein 176B	protein-coding
mm_15951.1	chr2	165969662	165969688	+	1	NA	Intergenic	PB1|SINE|Alu	-22962	NM_008679	17979	Mm.469663	NM_008679	ENSMUSG00000027678	Ncoa3	2010305B15Rik|AW321064|Actr|Aib1|KAT13B|Rac3|Src3|Tram-1|Tram1|bHLHe42|p/Cip|pCip	nuclear receptor coactivator 3	protein-coding
mm_172521.1	chr7	81789497	81789509	+	1	NA	promoter-TSS (NM_026077)	promoter-TSS (NM_026077)	-50	NM_026077	67290	Mm.248391	NM_026077	ENSMUSG00000025102	3110040N11Rik	AI851475	RIKEN cDNA 3110040N11 gene	protein-coding
mm_107197.1	chr12	25318138	25318148	+	1	NA	Intergenic	Intergenic	188969	NR_045844	432641	Mm.112955	NR_045844		Gm17746	-	predicted gene, 17746	ncRNA
mm_109372.1	chr12	109649532	109649537	+	1	NA	promoter-TSS (NR_046304)	promoter-TSS (NR_046304)	-83	NR_046304	100861570		NR_046304	ENSMUSG00000084549	DQ267100	-	snoRNA DQ267100	snoRNA
mm_89165.1	chr10	86300547	86300562	+	1	NA	5' UTR (NM_011595, exon 1 of 5)	5' UTR (NM_011595, exon 1 of 5)	142	NM_011595	21859	Mm.4871	NM_011595	ENSMUSG00000020044	Timp3	Timp-3	tissue inhibitor of metalloproteinase 3	protein-coding
mm_48567.1	chr5	143269959	143270018	-	1	NA	promoter-TSS (NM_017467)	promoter-TSS (NM_017467)	34	NM_017467	54201	Mm.6666	NM_017467	ENSMUSG00000046658	Zfp316	Emzf1|Mzf3|Znf316	zinc finger protein 316	protein-coding
mm_58929.1	chr7	17973436	17973442	+	1	NA	exon (NM_023289, exon 2 of 4)	exon (NM_023289, exon 2 of 4)	1272	NM_023289	66996	Mm.36666	NM_023289	ENSMUSG00000030368	Ceacam11	1600015D01Rik	carcinoembryonic antigen-related cell adhesion molecule 11	protein-coding
mm_163481.1	chr12	107903929	107903932	+	1	NA	Intergenic	Intergenic	99484	NM_001079883	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_173009.1	chrM	290	295	+	1	NA	NA	Intergenic	NA	NA								
mm_139996.1	chr17	72938386	72938392	+	1	NA	intron (NM_029999, intron 2 of 2)	intron (NM_029999, intron 2 of 2)	20084	NM_029999	77889	Mm.154109	NM_029999	ENSMUSG00000024063	Lbh	1810009F10Rik|6720416L16Rik	limb-bud and heart	protein-coding
mm_166188.1	chr5	33061917	33061919	+	1	NA	Intergenic	L1_Mur2|LINE|L1	-42301	NM_019810	20537	Mm.25237	NM_019810	ENSMUSG00000011034	Slc5a1	Sglt1	solute carrier family 5 (sodium/glucose cotransporter), member 1	protein-coding
mm_36917.1	chr4	108105147	108105159	-	1	NA	exon (NM_011327, exon 4 of 16)	exon (NM_011327, exon 4 of 16)	13394	NM_011327	20280	Mm.379011	NM_011327	ENSMUSG00000028603	Scp2	AA409774|AA409893|C76618|C79031|NSL-TP|SCP-2|SCP-X|SCPX|ns-LTP	sterol carrier protein 2, liver	protein-coding
mm_42262.1	chr5	114130365	114130376	+	1	NA	promoter-TSS (NM_011677)	promoter-TSS (NM_011677)	-65	NM_001040691	22256	Mm.1393	NM_011677	ENSMUSG00000029591	Ung	UNG1|UNG2	uracil DNA glycosylase	protein-coding
mm_129760.1	chr15	82403332	82403337	-	1	NA	exon (NM_010005, exon 8 of 9)	exon (NM_010005, exon 8 of 9)	3860	NM_010005	13101	Mm.174372	NM_010005	ENSMUSG00000094806	Cyp2d10	AI303445|Cyp2d|P450-2D	cytochrome P450, family 2, subfamily d, polypeptide 10	protein-coding
mm_79853.1	chr9	64960196	64960205	+	1	NA	promoter-TSS (NM_001077631)	promoter-TSS (NM_001077631)	-632	NM_001077631	69882	Mm.272616	NM_175153	ENSMUSG00000034263	Vwa9	2010321M09Rik	von Willebrand factor A domain containing 9	protein-coding
mm_79747.1	chr9	62367977	62368017	+	1	NA	intron (NM_009672, intron 1 of 6)	intron (NM_009672, intron 1 of 6)	26654	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	protein-coding
mm_27414.1	chr3	51396717	51396757	-	1	NA	promoter-TSS (NM_026358)	promoter-TSS (NM_026358)	-190	NR_028121	67749	Mm.273339	NM_026358	ENSMUSG00000037161	Mgarp	4930583H14Rik|AI195347|CESP-1|HUMMR|Osap|Qsap	mitochondria localized glutamic acid rich protein	protein-coding
mm_7242.1	chr1	93635138	93635188	-	1	NA	intron (NM_021537, intron 2 of 11)	CpG	564	NM_021537	59041	Mm.28761	NM_021537	ENSMUSG00000026277	Stk25	1500019J11Rik|AU018434|C86992|Ste20-like|Ysk1	serine/threonine kinase 25 (yeast)	protein-coding
mm_109334.1	chr12	109581514	109581532	+	1	NA	Intergenic	Intergenic	1290	NR_030573	100124466		NR_030573	ENSMUSG00000077025	Mir493	Mirn493|mmu-mir-493	microRNA 493	ncRNA
mm_107415.1	chr12	34853689	34853689	+	1	NA	intron (NM_001271386, intron 2 of 27)	intron (NM_001271386, intron 2 of 27)	63406	NM_001271386	79221	Mm.310551	NM_024124	ENSMUSG00000004698	Hdac9	AV022454|D030072B18Rik|HD7B|HD9|HDRP|Hdac7b|Mitr|mKIAA0744	histone deacetylase 9	protein-coding
mm_123078.1	chr14	55727775	55727783	-	1	NA	Intergenic	Intergenic	-5603	NM_019519	56187	Mm.87216	NM_019519	ENSMUSG00000040472	Rabggta	gm	Rab geranylgeranyl transferase, a subunit	protein-coding
mm_8915.1	chr1	163313508	163313518	-	1	NA	5' UTR (NM_175686, exon 1 of 5)	5' UTR (NM_175686, exon 1 of 5)	137	NM_011127	18933	Mm.288642	NM_011127	ENSMUSG00000026586	Prrx1	A230024N07Rik|AA755424|AI385634|AI843499|K-2|Pmx|Pmx1|Prx1|mHox	paired related homeobox 1	protein-coding
mm_36243.1	chr4	63367522	63367527	-	1	NA	3' UTR (NM_001045514, exon 22 of 22)	3' UTR (NM_001045514, exon 22 of 22)	5075	NM_011016	18406	Mm.14173	NM_011016	ENSMUSG00000061540	Orm2	Agp1|Orm-2	orosomucoid 2	protein-coding
mm_130324.1	chr15	97665897	97665917	-	1	NA	Intergenic	Intergenic	39915	NM_028003	71919	Mm.12255	NM_028003	ENSMUSG00000022466	Rpap3	2310042P20Rik|D15Ertd682e	RNA polymerase II associated protein 3	protein-coding
mm_12901.1	chr2	84809345	84809356	+	1	NA	3' UTR (NM_019949, exon 4 of 4)	3' UTR (NM_019949, exon 4 of 4)	10522	NM_019949	56791	Mm.38261	NM_019949	ENSMUSG00000027078	Ube2l6	2810489I21Rik|RIG-B|UBCH8|Ubce8|Ubcm8	ubiquitin-conjugating enzyme E2L 6	protein-coding
mm_40821.1	chr5	72635005	72635038	+	1	NA	intron (NM_007723, intron 1 of 8)	PB1D7|SINE|Alu	7731	NM_007723	12788	Mm.436652	NM_007723	ENSMUSG00000067220	Cnga1	Cncg	cyclic nucleotide gated channel alpha 1	protein-coding
mm_57160.1	chr6	122764748	122764760	-	1	NA	Intergenic	CpG	-22009	NM_011401	20527	Mm.395108	NM_011401	ENSMUSG00000003153	Slc2a3	AA408729|AL023014|AL024341|AU040424|C78366|Glut-3|Glut3	solute carrier family 2 (facilitated glucose transporter), member 3	protein-coding
mm_144208.1	chr18	9707613	9707638	+	1	NA	promoter-TSS (NM_130449)	promoter-TSS (NM_130449)	-23	NM_130449	140792	Mm.218571	NM_130449	ENSMUSG00000036103	Colec12	CL-P1|SRCL|Scara4	collectin sub-family member 12	protein-coding
mm_49756.1	chr6	34755654	34755683	+	1	NA	exon (NM_145575, exon 5 of 12)	exon (NM_145575, exon 5 of 12)	-24764	NM_001289657	76223	Mm.150047	NM_178630	ENSMUSG00000038836	Agbl3	2900053G10Rik|4930431N21Rik|6530406M24Rik|CCP3	ATP/GTP binding protein-like 3	protein-coding
mm_41088.1	chr5	87682542	87682550	+	1	NA	TTS (NM_007784)	TTS (NM_007784)	16338	NM_001286016	12990	Mm.427467	NM_007784	ENSMUSG00000070702	Csn1s1	AA959832|AW212882|Csna	casein alpha s1	protein-coding
mm_98733.1	chr11	96352887	96352900	+	1	NA	intron (NM_134032, intron 1 of 1)	intron (NM_134032, intron 1 of 1)	1261	NM_134032	103889	Mm.281153	NM_134032	ENSMUSG00000075588	Hoxb2	AI894218|Hox-2.8|Hoxbes2	homeobox B2	protein-coding
mm_122341.1	chr14	37135246	37135271	-	1	NA	promoter-TSS (NM_001199122)	promoter-TSS (NM_001199122)	64	NM_078478	66092	Mm.182912	NM_078478	ENSMUSG00000041028	Ghitm	1010001P14Rik|C77840|MICS1|PTD010|Tmbim5	growth hormone inducible transmembrane protein	protein-coding
mm_19376.1	chr2	91194826	91194845	-	1	NA	5' UTR (NM_013839, exon 1 of 10)	5' UTR (NM_013839, exon 1 of 10)	200	NM_013839	22259	Mm.22690	NM_013839	ENSMUSG00000002108	Nr1h3	AU018371|LXR|RLD1|Unr1	nuclear receptor subfamily 1, group H, member 3	protein-coding
mm_125412.1	chr15	41788935	41788977	+	1	NA	promoter-TSS (NM_001130163)	promoter-TSS (NM_001130163)	-78	NM_001130165	170719	Mm.254267	NM_130885	ENSMUSG00000022307	Oxr1	2210416C20Rik|C7|C7B	oxidation resistance 1	protein-coding
mm_58840.1	chr7	16838153	16838163	+	1	NA	intron (NM_133789, intron 14 of 17)	intron (NM_133789, intron 14 of 17)	-4744	NM_001252458	101540	Mm.1881	NM_178900	ENSMUSG00000041187	Prkd2	AI325941|PKD2	protein kinase D2	protein-coding
mm_46661.1	chr5	108675641	108675652	-	1	NA	promoter-TSS (NM_001310692)	promoter-TSS (NM_001310692)	-281	NM_174870	231583	Mm.440571	NM_174870	ENSMUSG00000046959	Slc26a1	Sat1	solute carrier family 26 (sulfate transporter), member 1	protein-coding
mm_49722.1	chr6	34598616	34598626	+	1	NA	5' UTR (NM_001347100, exon 1 of 14)	5' UTR (NM_001347100, exon 1 of 14)	117	NM_001347100	109624	Mm.308134	NM_145575	ENSMUSG00000029761	Cald1	4833423D12Rik|AI195384|AV071549|AW536160|C920027I18Rik	caldesmon 1	protein-coding
mm_34413.1	chr4	145254731	145254779	+	1	NA	Intergenic	L1M5|LINE|L1	-7885	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_140153.1	chr17	80127700	80127710	+	1	NA	5' UTR (NM_176963, exon 1 of 7)	5' UTR (NM_176963, exon 1 of 7)	234	NM_176963	319625	Mm.29098	NM_176963	ENSMUSG00000035473	Galm	A530057M15Rik|AU015645|AU020959	galactose mutarotase	protein-coding
mm_33251.1	chr4	127168311	127168348	+	1	NA	promoter-TSS (NM_198618)	promoter-TSS (NM_198618)	-875	NM_198618	242667	Mm.331885	NM_198618	ENSMUSG00000042388	Dlgap3	BC058433|DAP-3|DAP3|Prpl8|Sapap3	discs, large (Drosophila) homolog-associated protein 3	protein-coding
mm_39400.1	chr5	14027916	14027920	+	1	NA	intron (NM_011348, intron 1 of 16)	intron (NM_011348, intron 1 of 16)	2642	NM_011348	20349	Mm.134093	NM_011348	ENSMUSG00000063531	Sema3e	6430702L12|AA408817|Semah|mKIAA0331	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	protein-coding
mm_136383.1	chr16	92826094	92826102	-	1	NA	promoter-TSS (NM_001111021)	promoter-TSS (NM_001111021)	-24	NM_001111022	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_90291.1	chr10	123634093	123634095	+	1	NA	intron (NR_045514, intron 2 of 5)	L2|LINE|L2	370018	NM_001252387	268354	Mm.51939	NM_182807	ENSMUSG00000044071	Fam19a2	6330575M02|FAM19A2 TAFA-2|TAFA2|Tafa-2	family with sequence similarity 19, member A2	protein-coding
mm_96516.1	chr11	68476308	68476344	+	1	NA	exon (NM_177320, exon 4 of 19)	exon (NM_177320, exon 4 of 19)	-26693	NM_001004435	104709	Mm.234573	NM_001004435	ENSMUSG00000046207	Pik3r6	BB220380|p84|p84 PIKAP|p87(PIKAP)|p87PIKAP	phosphoinositide-3-kinase, regulatory subunit 6	protein-coding
mm_145452.1	chr18	60222545	60222548	+	1	NA	intron (NM_001033767, intron 2 of 2)	MTE2a|LTR|ERVL-MaLR	10469	NM_001033767	240327	Mm.357104	NM_001033767	ENSMUSG00000073555	Gm4951	EG240327|Ifgga2	predicted gene 4951	protein-coding
mm_164144.1	chr15	59425130	59425132	+	1	NA	intron (NM_001164604, intron 3 of 4)	intron (NM_001164604, intron 3 of 4)	50933	NM_001164604	68501	Mm.27762	NM_026746	ENSMUSG00000059586	Nsmce2	1110014D18Rik|AI661537	NSE2/MMS21 homolog, SMC5-SMC6 complex SUMO ligase	protein-coding
mm_125236.1	chr15	34238062	34238062	+	1	NA	promoter-TSS (NM_033521)	promoter-TSS (NM_033521)	36	NM_033521	114128	Mm.197518	NM_033521	ENSMUSG00000022257	Laptm4b	C330023P13Rik|LAPTM4beta	lysosomal-associated protein transmembrane 4B	protein-coding
mm_73472.1	chr8	106683134	106683154	+	1	NA	promoter-TSS (NM_173037)	promoter-TSS (NM_173037)	76	NM_173037	272538	Mm.87151	NM_173037	ENSMUSG00000041949	Tango6	AW413431|E330010G16|Tmco7	transport and golgi organization 6	protein-coding
mm_37414.1	chr4	122861313	122861326	-	1	NA	intron (NM_001301067, intron 12 of 12)	intron (NM_001301067, intron 12 of 12)	24738	NM_007598	12331	Mm.8687	NM_007598	ENSMUSG00000028656	Cap1	-	CAP, adenylate cyclase-associated protein 1 (yeast)	protein-coding
mm_76491.1	chr8	85840783	85840794	-	1	NA	promoter-TSS (NM_199446)	promoter-TSS (NM_199446)	161	NM_028007	71927	Mm.61018	NM_028007	ENSMUSG00000031703	Itfg1	2310047C21Rik|AI314457|Cda08|D8Wsu49e	integrin alpha FG-GAP repeat containing 1	protein-coding
mm_145972.1	chr18	67933975	67933992	+	1	NA	intron (NM_172631, intron 1 of 5)	CpG	726	NM_172631	52662	Mm.440183	NM_172631	ENSMUSG00000024544	Ldlrad4	8230401C20Rik|A430083H02|A430108L08Rik|C18orf1|D18Ertd653e|D330030L18Rik	low density lipoprotein receptor class A domain containing 4	protein-coding
mm_71049.1	chr8	33697140	33697154	+	1	NA	exon (NM_010344, exon 13 of 13)	exon (NM_010344, exon 13 of 13)	-34767	NM_001167921	68153	Mm.286104	NM_026584	ENSMUSG00000031585	Gtf2e2	34kDa|AI462509|C330006J08Rik	general transcription factor II E, polypeptide 2 (beta subunit)	protein-coding
mm_97673.1	chr11	79711329	79711358	+	1	NA	promoter-TSS (NR_029579)	promoter-TSS (NR_029579)	-626	NR_029579	387188		NR_029579	ENSMUSG00000065395	Mir193a	Mir193|Mirn193|mir-193a|mmu-mir-193|mmu-mir-193a	microRNA 193a	ncRNA
mm_157426.1	chrX	38564926	38564934	-	1	NA	intron (NM_001110142, intron 3 of 22)	CpG	11266	NM_028288	72584	Mm.327675	NM_028288	ENSMUSG00000031095	Cul4b	2700050M05Rik|AA409770|CUL-4B|mKIAA0695	cullin 4B	protein-coding
mm_142100.1	chr17	35835443	35835480	-	1	NA	exon (NM_011655, exon 4 of 4)	exon (NM_011655, exon 4 of 4)	2840	NM_011655	22154	Mm.273538	NM_011655	ENSMUSG00000001525	Tubb5	AA408537|AI596182|B130022C14Rik|M(beta)5	tubulin, beta 5 class I	protein-coding
mm_122633.1	chr14	51145877	51145887	-	1	NA	exon (NM_011271, exon 2 of 2)	exon (NM_011271, exon 2 of 2)	885	NM_011271	19752	Mm.235538	NM_011271	ENSMUSG00000035896	Rnase1	AI574248|Rib-1|Rib1	ribonuclease, RNase A family, 1 (pancreatic)	protein-coding
mm_101813.1	chr11	46389426	46389448	-	1	NA	promoter-TSS (NM_001281968)	promoter-TSS (NM_001281968)	78	NM_001281968	16428	Mm.339927	NM_010583	ENSMUSG00000020395	Itk	Emt|Tcsk|Tsk	IL2 inducible T cell kinase	protein-coding
mm_24115.1	chr3	88158080	88158094	+	1	NA	exon (NM_001310587, exon 4 of 12)	exon (NM_001310587, exon 4 of 12)	15715	NM_001310593	17261	Mm.28184	NM_133665	ENSMUSG00000001419	Mef2d	C80750	myocyte enhancer factor 2D	protein-coding
mm_45796.1	chr5	87566110	87566119	-	1	NA	exon (NM_016771, exon 2 of 8)	exon (NM_016771, exon 2 of 8)	2892	NM_016771	53315	Mm.6824	NM_016771	ENSMUSG00000029273	Sult1d1	5033411P13Rik|AI987815|ST1d1|SULT-N|Sultn	sulfotransferase family 1D, member 1	protein-coding
mm_66548.1	chr7	45211522	45211541	-	1	NA	exon (NM_015789, exon 2 of 5)	exon (NM_015789, exon 2 of 5)	352	NM_015789	50722	Mm.27287	NM_015789	ENSMUSG00000030792	Dkkl1	AI414495|SGY|SGY-1|SGY1|Soggy|mSgy	dickkopf-like 1	protein-coding
mm_10012.1	chr1	191899178	191899208	-	1	NA	intron (NR_030669, intron 3 of 4)	intron (NR_030669, intron 3 of 4)	-7588	NM_009579	22782	Mm.9024	NM_009579	ENSMUSG00000037434	Slc30a1	AI839647|C130040I11Rik|Znt1	solute carrier family 30 (zinc transporter), member 1	protein-coding
mm_136200.1	chr16	89818192	89818202	-	1	NA	5' UTR (NM_001145887, exon 1 of 13)	5' UTR (NM_001145887, exon 1 of 13)	155	NM_001145887	21844	Mm.310902	NM_009384	ENSMUSG00000002489	Tiam1	AI847750|D16Ium10|D16Ium10e	T cell lymphoma invasion and metastasis 1	protein-coding
mm_84388.1	chr9	65423029	65423042	-	1	NA	promoter-TSS (NM_178933)	promoter-TSS (NM_178933)	-262	NM_178933	330962	Mm.335247	NM_178933	ENSMUSG00000053862	Slc51b	Ostb	solute carrier family 51, beta subunit	protein-coding
mm_41748.1	chr5	102845117	102845127	+	1	NA	5' UTR (NM_001346585, exon 1 of 7)	5' UTR (NM_001346585, exon 1 of 7)	115	NM_001346585	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding
mm_103809.1	chr11	82991788	82991838	-	1	NA	promoter-TSS (NM_172796)	promoter-TSS (NM_172796)	17	NM_172796	237886	Mm.270253	NM_172796	ENSMUSG00000069793	Slfn9	9830137M10Rik	schlafen 9	protein-coding
mm_3105.1	chr1	134494629	134494679	+	1	NA	promoter-TSS (NM_145510)	promoter-TSS (NM_145510)	-6	NM_145510	98710	Mm.198119	NM_145510	ENSMUSG00000042229	Rabif	AI842864|AW549708|E130318E12Rik|MSS4|RASGFR3	RAB interacting factor	protein-coding
mm_153966.1	chr19	47854911	47854921	-	1	NA	promoter-TSS (NM_010362)	promoter-TSS (NM_010362)	-57	NM_010362	14873	Mm.378931	NM_010362	ENSMUSG00000025068	Gsto1	AA407097|AI194287|AU018802|Gsto-1|Gstx|Spg-r|p28	glutathione S-transferase omega 1	protein-coding
mm_131667.1	chr16	20651665	20651712	+	1	NA	promoter-TSS (NR_027485)	promoter-TSS (NR_027485)	36	NM_134101	21762	Mm.243234	NM_134101	ENSMUSG00000006998	Psmd2	9430095H01Rik|AA407121|TEG-190|Tex190	proteasome (prosome, macropain) 26S subunit, non-ATPase, 2	protein-coding
mm_73328.1	chr8	105279364	105279374	+	1	NA	intron (NM_030152, intron 2 of 3)	intron (NM_030152, intron 2 of 3)	2922	NM_030152	78688	Mm.475715	NM_030152	ENSMUSG00000014776	Nol3	ARC|B430311C09Rik|MYC|NOP|Nop30	nucleolar protein 3 (apoptosis repressor with CARD domain)	protein-coding
mm_104728.1	chr11	98326203	98326211	-	1	NA	3' UTR (NM_010895, exon 2 of 2)	3' UTR (NM_010895, exon 2 of 2)	3438	NM_010895	18013	Mm.4814	NM_010895	ENSMUSG00000038255	Neurod2	Ndrf|bHLHa1	neurogenic differentiation 2	protein-coding
mm_14996.1	chr2	152353540	152353544	+	1	NA	intron (NR_033505, intron 1 of 4)	intron (NR_033505, intron 1 of 4)	7873	NR_033505	791417	Mm.451219	NR_033505	ENSMUSG00000068062	Gm14164	OTTMUSG00000015846	predicted gene 14164	ncRNA
mm_34764.1	chr4	152478177	152478183	+	1	NA	promoter-TSS (NM_010598)	promoter-TSS (NM_010598)	38	NM_153424	260305	Mm.302496	NM_153424	ENSMUSG00000039577	Nphp4	4930564O18Rik|nmf192	nephronophthisis 4 (juvenile) homolog (human)	protein-coding
mm_161860.1	chr18	31774210	31774210	+	1	NA	intron (NM_153515, intron 3 of 7)	(TTTTG)n|Simple_repeat|Simple_repeat	13594	NM_001242430	225339	Mm.290804	NM_153515	ENSMUSG00000041915	Ammecr1l	5430429D03Rik|AU022236|AU040755|AW111353|E230022H04Rik	AMME chromosomal region gene 1-like	protein-coding
mm_139181.1	chr17	47593614	47593620	+	1	NA	5' UTR (NM_007632, exon 1 of 5)	5' UTR (NM_007632, exon 1 of 5)	150	NM_007632	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_36840.1	chr4	106678633	106678642	-	1	NA	promoter-TSS (NM_001172073)	promoter-TSS (NM_001172073)	49	NM_001172073	72354	Mm.25806	NM_028209	ENSMUSG00000025413	Ttc4	2810002P21Rik|AF007005|L62	tetratricopeptide repeat domain 4	protein-coding
mm_11764.1	chr2	38533803	38533803	+	1	NA	intron (NM_001159631, intron 1 of 9)	intron (NM_001159631, intron 1 of 9)	21927	NM_001159631	59126	Mm.143818	NM_021606	ENSMUSG00000026749	Nek6	1300007C09Rik	NIMA (never in mitosis gene a)-related expressed kinase 6	protein-coding
mm_81081.1	chr9	106224283	106224301	+	1	NA	exon (NM_031178, exon 2 of 2)	exon (NM_031178, exon 2 of 2)	1694	NM_031178	81897	Mm.44889	NM_031178	ENSMUSG00000045322	Tlr9	-	toll-like receptor 9	protein-coding
mm_97668.1	chr11	79660705	79660727	+	1	NA	intron (NM_175543, intron 3 of 14)	CpG	14370	NR_045898	72218	Mm.443271	NR_045898	ENSMUSG00000086569	Rab11fip4os2	1700020F10Rik|4930542H20Rik|Rab11fib4os2	RAB11 family interacting protein 4 (class II), opposite strand 2	ncRNA
mm_85186.1	chr9	96696378	96696428	-	1	NA	intron (NM_175537, intron 2 of 2)	intron (NM_175537, intron 2 of 2)	35272	NM_175537	245007	Mm.485954	NM_175537	ENSMUSG00000040433	Zbtb38	A930014K01Rik|CIBZ	zinc finger and BTB domain containing 38	protein-coding
mm_33169.1	chr4	126024825	126024837	+	1	NA	intron (NR_045561, intron 1 of 15)	intron (NR_045561, intron 1 of 15)	172	NM_001252651	12986	Mm.271701	NM_007782	ENSMUSG00000028859	Csf3r	Cd114|Csfgr|G-CSF-R|G-CSFR	colony stimulating factor 3 receptor (granulocyte)	protein-coding
mm_90196.1	chr10	120213008	120213026	+	1	NA	intron (NM_026617, intron 1 of 6)	intron (NM_026617, intron 1 of 6)	4191	NM_026617	68212	Mm.157426	NM_026617	ENSMUSG00000020225	Tmbim4	0610007H07Rik|AU022431	transmembrane BAX inhibitor motif containing 4	protein-coding
mm_93397.1	chr10	107643544	107643557	-	1	NA	exon (NM_001081432, exon 22 of 45)	exon (NM_001081432, exon 22 of 45)	76477	NM_001081432	237523	Mm.391418	NM_001081432	ENSMUSG00000035916	Ptprq	-	protein tyrosine phosphatase, receptor type, Q	protein-coding
mm_142467.1	chr17	45602046	45602056	-	1	NA	promoter-TSS (NM_001177468)	promoter-TSS (NM_001177468)	16	NM_001177468	653016	Mm.45676	NM_001177468	ENSMUSG00000079471	Gm7325	EG653016|Esgp	predicted gene 7325	protein-coding
mm_10963.1	chr2	25701633	25701655	+	1	NA	exon (NM_153558, exon 4 of 7)	exon (NM_153558, exon 4 of 7)	1570	NM_153558	227627	Mm.44630	NM_153558	ENSMUSG00000062061	Obp2a	BC027556|Lcn13	odorant binding protein 2A	protein-coding
mm_19995.1	chr2	118728373	118728428	-	1	NA	promoter-TSS (NM_177568)	promoter-TSS (NM_177568)	38	NM_177568	18796	Mm.215156	NM_177568	ENSMUSG00000040061	Plcb2	AI550384|B230205M18Rik|B230399N12	phospholipase C, beta 2	protein-coding
mm_150317.1	chr19	34573626	34573683	+	1	NA	exon (NM_008332, exon 3 of 3)	exon (NM_008332, exon 3 of 3)	-9875	NM_010501	15959	Mm.426079	NM_010501	ENSMUSG00000074896	Ifit3	Ifi49|P49	interferon-induced protein with tetratricopeptide repeats 3	protein-coding
mm_31642.1	chr4	59581590	59581600	+	1	NA	promoter-TSS (NM_024255)	promoter-TSS (NM_024255)	32	NM_024255	72479	Mm.272905	NM_024255	ENSMUSG00000028383	Hsdl2	2610207I16Rik	hydroxysteroid dehydrogenase like 2	protein-coding
mm_80037.1	chr9	68966717	68966743	+	1	NA	intron (NM_013646, intron 1 of 10)	intron (NM_013646, intron 1 of 10)	201384	NR_033299	320440	Mm.483129	NM_177159		9530091C08Rik	-	RIKEN cDNA 9530091C08 gene	ncRNA
mm_156008.1	chrX	106920619	106920632	+	1	NA	promoter-TSS (NM_175271)	promoter-TSS (NM_175271)	0	NM_175271	78134	Mm.90147	NM_175271	ENSMUSG00000049929	Lpar4	5730485F04Rik|Gpr23|LPA4|p2y9	lysophosphatidic acid receptor 4	protein-coding
mm_166800.1	chr7	3502756	3502766	-	1	NA	promoter-TSS (NM_177363)	promoter-TSS (NM_177363)	-209	NM_177363	245126	Mm.245747	NM_177363	ENSMUSG00000053338	Tarm1	9930022N03Rik|ENSMUSG00000053338|Gm9904|OLT-2	T cell-interacting, activating receptor on myeloid cells 1	protein-coding
mm_30023.1	chr3	135665486	135665499	-	1	NA	intron (NM_008689, intron 3 of 24)	intron (NM_008689, intron 3 of 24)	26055	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_88426.1	chr10	77259281	77259348	+	1	NA	promoter-TSS (NM_030262)	promoter-TSS (NM_030262)	14	NM_030262	80294	Mm.203556	NM_030262	ENSMUSG00000020260	Pofut2	2310011G23Rik|AI256847|BC003494|C21orf80|FUT13	protein O-fucosyltransferase 2	protein-coding
mm_155673.1	chrX	90744858	90744872	+	1	NA	Intergenic	Intergenic	-147277	NM_001101450	212952	Mm.477436	NM_001101450	ENSMUSG00000091497	Gm44	-	predicted gene 44	protein-coding
mm_172007.1	chr6	109505294	109505305	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	676658	NM_138677	192193	Mm.21596	NM_138677	ENSMUSG00000030104	Edem1	A130059K23Rik|EDEM|mKIAA0212	ER degradation enhancer, mannosidase alpha-like 1	protein-coding
mm_150951.1	chr19	46328449	46328474	+	1	NA	5' UTR (NM_133694, exon 1 of 4)	5' UTR (NM_133694, exon 1 of 4)	277	NM_133694	68431	Mm.19973	NM_133694	ENSMUSG00000025226	Fbxl15	0710008C12Rik|Fbxo37	F-box and leucine-rich repeat protein 15	protein-coding
mm_94824.1	chr11	23284304	23284320	+	1	NA	exon (NM_134014, exon 14 of 26)	exon (NM_134014, exon 14 of 26)	-22583	NM_001190401	17847	Mm.119155	NM_001190401	ENSMUSG00000056342	Usp34	A530081C03Rik|Murr2	ubiquitin specific peptidase 34	protein-coding
mm_168966.1	chr12	80946388	80946388	+	1	NA	promoter-TSS (NR_045057)	promoter-TSS (NR_045057)	889	NM_001347415	20384	Mm.43331	NM_009159	ENSMUSG00000021134	Srsf5	Sfrs5	serine/arginine-rich splicing factor 5	protein-coding
mm_150440.1	chr19	37697793	37697805	+	1	NA	promoter-TSS (NM_007811)	promoter-TSS (NM_007811)	-9	NM_007811	13082	Mm.42230	NM_007811	ENSMUSG00000024987	Cyp26a1	Cyp26|P450RA|P450RAI|RAH	cytochrome P450, family 26, subfamily a, polypeptide 1	protein-coding
mm_24414.1	chr3	90509641	90509686	+	1	NA	promoter-TSS (NM_001293782)	promoter-TSS (NM_001293782)	-165	NM_001293782	66511	Mm.154136	NM_023215	ENSMUSG00000001017	Chtop	2500003M10Rik|Fop|Srag	chromatin target of PRMT1	protein-coding
mm_145177.1	chr18	47056054	47056071	+	1	NA	intron (NM_178377, intron 5 of 6)	ID_B1|SINE|B4	97186	NM_178377	69456	Mm.210734	NM_178377	ENSMUSG00000042705	Commd10	2310003A05Rik|AU019438|DRWMS2	COMM domain containing 10	protein-coding
mm_69332.1	chr7	128740472	128740525	-	1	NA	promoter-TSS (NM_145955)	promoter-TSS (NM_145955)	-69	NM_145955	210711	Mm.58882	NM_145955	ENSMUSG00000048170	Mcmbp	1110007A13Rik|AU017382|BC025641|MCM-BP	minichromosome maintenance complex binding protein	protein-coding
mm_22848.1	chr3	28245450	28245459	+	1	NA	Intergenic	Intergenic	-17760	NM_001163007	665113	Mm.126193	NM_026910	ENSMUSG00000027692	Tnik	1500031A17Rik|4831440I19Rik|AI451411|C530008O15Rik|C630040K21Rik	TRAF2 and NCK interacting kinase	protein-coding
mm_147187.1	chr18	37178701	37178716	-	1	NA	intron (NM_001003671, intron 3 of 3)	intron (NM_001003671, intron 3 of 3)	34739	NM_001003672	353237	Mm.308500	NM_001003672	ENSMUSG00000102697	Pcdhac2	CNRc2	protocadherin alpha subfamily C, 2	protein-coding
mm_68633.1	chr7	118188089	118188118	-	1	NA	intron (NM_001031814, intron 18 of 62)	ID_B1|SINE|B4	55534	NM_001031814	233789	Mm.309053	NM_177180	ENSMUSG00000030655	Smg1	2610207I05Rik|5430435M13Rik|C130002K18Rik|mKIAA0421	SMG1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)	protein-coding
mm_10603.1	chr2	18699031	18699037	+	1	NA	promoter-TSS (NM_001001334)	promoter-TSS (NM_001001334)	12	NM_001001334	381350	Mm.330024	NM_001001334	ENSMUSG00000037708	Spag6	Spag6l	sperm associated antigen 6	protein-coding
mm_113330.1	chr13	31191918	31191929	+	1	NA	Intergenic	Intergenic	49163	NR_045957	73924	Mm.417825	NR_045957	ENSMUSG00000087460	4930401O12Rik	-	RIKEN cDNA 4930401O12 gene	ncRNA
mm_12802.1	chr2	79786598	79786609	+	1	NA	intron (NR_110979, intron 4 of 4)	Lx5b|LINE|L1	78823	NM_001290743	75276	Mm.257373	NM_172420	ENSMUSG00000034683	Ppp1r1c	4930565M23Rik|4930579P15Rik	protein phosphatase 1, regulatory (inhibitor) subunit 1C	protein-coding
mm_48885.1	chr5	151233769	151233791	-	1	NA	Intergenic	CpG	-43587	NM_146258	243362	Mm.209272	NM_146258	ENSMUSG00000016128	Stard13	DLC2|GT650	StAR-related lipid transfer (START) domain containing 13	protein-coding
mm_77519.1	chr8	122895759	122895772	-	1	NA	non-coding (NR_037865, exon 10 of 14)	non-coding (NR_037865, exon 10 of 14)	47391	NM_007662	12555	Mm.1976	NM_007662	ENSMUSG00000031962	Cdh15	AI323380|Cdh14|Mcad	cadherin 15	protein-coding
mm_67210.1	chr7	74367138	74367151	-	1	NA	intron (NM_001038643, intron 2 of 10)	intron (NM_001038643, intron 2 of 10)	187636	NM_023908	108116	Mm.425467	NM_023908	ENSMUSG00000025790	Slco3a1	5830414C08Rik|Anr1|MJAM|OATP-D|R75096|Slc21a11	solute carrier organic anion transporter family, member 3a1	protein-coding
mm_14219.1	chr2	127357163	127357165	+	1	NA	3' UTR (NM_172539, exon 9 of 9)	3' UTR (NM_172539, exon 9 of 9)	-6122	NM_009633	11552	Mm.347390	NM_009633	ENSMUSG00000058620	Adra2b	Adra-2b|[a]2B|a2b-AR|alpha2-C2|alpha2B	adrenergic receptor, alpha 2b	protein-coding
mm_21739.1	chr2	164778036	164778053	-	1	NA	exon (NM_009394, exon 3 of 6)	exon (NM_009394, exon 3 of 6)	1690	NM_009394	21925	Mm.1716	NM_009394	ENSMUSG00000017300	Tnnc2	Tncs	troponin C2, fast	protein-coding
mm_133382.1	chr16	84715610	84715620	+	1	NA	TTS (NR_132106)	TTS (NR_132106)	1475	NR_029565	387173		NR_029565	ENSMUSG00000065397	Mir155	Mirn155|mir-155|mmu-mir-155	microRNA 155	ncRNA
mm_101197.1	chr11	19015120	19015123	-	1	NA	intron (NM_001193271, intron 2 of 12)	intron (NM_001193271, intron 2 of 12)	3848	NM_001193271	17268	Mm.356578	NM_010789	ENSMUSG00000020160	Meis1	C530044H18Rik|Evi8	Meis homeobox 1	protein-coding
mm_160206.1	chr7	84853466	84853466	+	1	NA	promoter-TSS (NM_146415)	promoter-TSS (NM_146415)	-105	NM_146415	258410	Mm.484702	NM_146415	ENSMUSG00000070460	Olfr291	MOR254-2	olfactory receptor 291	protein-coding
mm_101002.1	chr11	8468649	8468706	-	1	NA	intron (NM_001083587, intron 20 of 30)	intron (NM_001083587, intron 20 of 30)	195858	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_135352.1	chr16	43698954	43698962	-	1	NA	Intergenic	Intergenic	-34774	NM_001146325	100043314	Mm.390896	NM_001146325	ENSMUSG00000071552	Tigit	ENSMUSG00000071552|Vstm3	T cell immunoreceptor with Ig and ITIM domains	protein-coding
mm_97556.1	chr11	78931611	78931627	+	1	NA	exon (NM_010927, exon 5 of 27)	exon (NM_010927, exon 5 of 27)	6328	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_112669.1	chr13	16027418	16027443	+	1	NA	3' UTR (NM_008380, exon 5 of 5)	3' UTR (NM_008380, exon 5 of 5)	15579	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_75378.1	chr8	45382087	45382095	-	1	NA	5' UTR (NM_153535, exon 1 of 14)	5' UTR (NM_153535, exon 1 of 14)	200	NM_153535	212326	Mm.51259	NM_153535	ENSMUSG00000070044	Fam149a	AW213256|mKIAA4166	family with sequence similarity 149, member A	protein-coding
mm_36844.1	chr4	106678714	106678718	-	1	NA	promoter-TSS (NM_001172073)	promoter-TSS (NM_001172073)	-30	NM_001172073	72354	Mm.25806	NM_028209	ENSMUSG00000025413	Ttc4	2810002P21Rik|AF007005|L62	tetratricopeptide repeat domain 4	protein-coding
mm_50462.1	chr6	48908848	48908869	+	1	NA	3' UTR (NM_001161622, exon 5 of 5)	3' UTR (NM_001161622, exon 5 of 5)	3872	NM_001161621	76507	Mm.213898	NM_029638	ENSMUSG00000029811	Aoc1	1600012D06Rik|Abp1|DAO	amine oxidase, copper-containing 1	protein-coding
mm_50459.1	chr6	48907798	48907806	+	1	NA	exon (NM_001161622, exon 3 of 5)	exon (NM_001161622, exon 3 of 5)	2816	NM_001161621	76507	Mm.213898	NM_029638	ENSMUSG00000029811	Aoc1	1600012D06Rik|Abp1|DAO	amine oxidase, copper-containing 1	protein-coding
mm_169434.1	chr14	54318491	54318491	-	1	NA	Intergenic	IAPEY_LTR|LTR|ERVK	-35566	NM_010991	18348	Mm.436623	NM_010991	ENSMUSG00000048153	Olfr49	IC6|MOR1181	olfactory receptor 49	protein-coding
mm_109978.1	chr12	12940394	12940407	-	1	NA	5' UTR (NM_008709, exon 2 of 3)	5' UTR (NM_008709, exon 2 of 3)	1436	NM_008709	18109	Mm.16469	NM_008709	ENSMUSG00000037169	Mycn	N-myc|Nmyc|Nmyc-1|Nmyc1|bHLHe37|c-nmyc	v-myc avian myelocytomatosis viral related oncogene, neuroblastoma derived	protein-coding
mm_103278.1	chr11	72170791	72170819	-	1	NA	intron (NM_028963, intron 12 of 18)	L1MD1|LINE|L1	32566	NM_028963	74477	Mm.289697	NM_028963	ENSMUSG00000020807	4933427D14Rik	C85113|Kiaa0753|MNR	RIKEN cDNA 4933427D14 gene	protein-coding
mm_98422.1	chr11	94644371	94644386	+	1	NA	TTS (NM_177752)	TTS (NM_177752)	9376	NM_177752	268465	Mm.358937	NM_177752	ENSMUSG00000039055	Eme1	6820428D13	essential meiotic structure-specific endonuclease 1	protein-coding
mm_30389.1	chr3	152247254	152247266	-	1	NA	exon (NM_199465, exon 8 of 13)	exon (NM_199465, exon 8 of 13)	19060	NM_199465	68810	Mm.200188	NM_199465	ENSMUSG00000039103	Nexn	1110046H09Rik|AA553326|NELIN	nexilin	protein-coding
mm_83426.1	chr9	44980343	44980369	-	1	NA	promoter-TSS (NM_009850)	promoter-TSS (NM_009850)	75	NM_009850	12502	Mm.335106	NM_009850	ENSMUSG00000002033	Cd3g	Ctg-3|Ctg3|T3g	CD3 antigen, gamma polypeptide	protein-coding
mm_34961.1	chr4	156006905	156006931	+	1	NA	intron (NM_001302468, intron 4 of 6)	ORR1D2-int|LTR|ERVL-MaLR	-6777	NM_011659	22163	Mm.13885	NM_011659	ENSMUSG00000029075	Tnfrsf4	ACT35|CD134|Ly-70|Ox40|TXGP1L|Txgp1	tumor necrosis factor receptor superfamily, member 4	protein-coding
mm_138654.1	chr17	35868004	35868014	+	1	NA	exon (NM_001146711, exon 2 of 4)	exon (NM_001146711, exon 2 of 4)	1394	NM_175242	76448	Mm.359982	NM_175242	ENSMUSG00000034595	Ppp1r18	2310014H01Rik|AA407849|AI450394	protein phosphatase 1, regulatory subunit 18	protein-coding
mm_39636.1	chr5	24474156	24474184	+	1	NA	intron (NM_139153, intron 1 of 17)	intron (NM_139153, intron 1 of 17)	21993	NM_139153	213990	Mm.250703	NM_139153	ENSMUSG00000023353	Agap3	AGAP-3|AV028425|Centg3|Crag|Crag.|MRIP-1|cnt-g3	ArfGAP with GTPase domain, ankyrin repeat and PH domain 3	protein-coding
mm_70338.1	chr8	4524793	4524807	+	1	NA	3' UTR (NM_026058, exon 11 of 11)	3' UTR (NM_026058, exon 11 of 11)	31395	NM_026058	67260	Mm.35511	NM_026058	ENSMUSG00000008206	Cers4	2900019C14Rik|Lass4|Trh1	ceramide synthase 4	protein-coding
mm_134692.1	chr16	22561062	22561083	-	1	NA	intron (NM_001346673, intron 16 of 23)	intron (NM_001346673, intron 16 of 23)	-28888	NR_106170	102465887		NR_106170	ENSMUSG00000099071	Mir8095	Gm27566|mmu-mir-8095	microRNA 8095	ncRNA
mm_24423.1	chr3	90537231	90537241	+	1	NA	Intergenic	Intergenic	-3987	NM_026416	67860	Mm.331185	NM_026416	ENSMUSG00000074457	S100a16	2300002L21Rik|AI325039|AI663996|DT1P1A7|S100F	S100 calcium binding protein A16	protein-coding
mm_48097.1	chr5	137062986	137063005	-	1	NA	3' UTR (NM_008871, exon 9 of 9)	3' UTR (NM_008871, exon 9 of 9)	9277	NM_008871	18787	Mm.250422	NM_008871	ENSMUSG00000037411	Serpine1	PAI-1|PAI1|Planh1	serine (or cysteine) peptidase inhibitor, clade E, member 1	protein-coding
mm_103300.1	chr11	72550196	72550206	-	1	NA	promoter-TSS (NM_029932)	promoter-TSS (NM_029932)	45	NM_029932	77577	Mm.46185	NM_029932	ENSMUSG00000020798	Spns3	9830002I17Rik	spinster homolog 3	protein-coding
mm_3480.1	chr1	150105549	150105554	+	1	NA	exon (NM_011198, exon 10 of 10)	exon (NM_011198, exon 10 of 10)	5520	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_15295.1	chr2	155383034	155383044	+	1	NA	intron (NM_178111, intron 1 of 3)	intron (NM_178111, intron 1 of 3)	1183	NM_178111	68728	Mm.293605	NM_178111	ENSMUSG00000038375	Trp53inp2	1110029F20Rik|Tp53inp2	transformation related protein 53 inducible nuclear protein 2	protein-coding
mm_41550.1	chr5	92933318	92933337	+	1	NA	intron (NM_001077595, intron 2 of 9)	intron (NM_001077595, intron 2 of 9)	35334	NM_001077596	27428	Mm.46014	NM_015756	ENSMUSG00000029381	Shroom3	AL022960|D5Ertd287e|Shrm|Shrm3	shroom family member 3	protein-coding
mm_73854.1	chr8	117920080	117920089	+	1	NA	Intergenic	Intergenic	-118155	NM_026758	68533	Mm.181836	NM_026758	ENSMUSG00000031843	Mphosph6	1110001M01Rik|AA536809|C86426	M phase phosphoprotein 6	protein-coding
mm_121565.1	chr14	122534372	122534382	+	1	NA	promoter-TSS (NM_144844)	promoter-TSS (NM_144844)	49	NM_144844	110821	Mm.23876	NM_144844	ENSMUSG00000041650	Pcca	C79630	propionyl-Coenzyme A carboxylase, alpha polypeptide	protein-coding
mm_112704.1	chr13	18101822	18101828	+	1	NA	Intergenic	Intergenic	-1623	NR_046032	73992	Mm.159110	NR_046032		4930448F12Rik	-	RIKEN cDNA 4930448F12 gene	ncRNA
mm_105305.1	chr11	102688109	102688112	-	1	NA	intron (NM_025918, intron 4 of 4)	intron (NM_025918, intron 4 of 4)	9615	NM_025918	52715	Mm.277638	NM_025918	ENSMUSG00000020925	Ccdc43	2610001E01Rik|D11Ertd707e	coiled-coil domain containing 43	protein-coding
mm_22358.1	chr2	181020578	181020586	-	1	NA	Intergenic	B4A|SINE|B4	18595	NM_015730	11438	Mm.252369	NM_015730	ENSMUSG00000027577	Chrna4	Acra-4|Acra4|EBN1|ENFL1	cholinergic receptor, nicotinic, alpha polypeptide 4	protein-coding
mm_34524.1	chr4	149104237	149104247	+	1	NA	promoter-TSS (NM_001025296)	promoter-TSS (NM_001025296)	100	NM_001025296	13347	Mm.41433	NM_010044	ENSMUSG00000028974	Dffa	A330085O09Rik|DFF35|Dff45|ICAD|ICAD-L|ICAD-S	DNA fragmentation factor, alpha subunit	protein-coding
mm_76835.1	chr8	105264587	105264618	-	1	NA	promoter-TSS (NM_015821)	promoter-TSS (NM_015821)	-8	NM_001033161	71609	Mm.264255	NM_001033161	ENSMUSG00000031887	Tradd	9130005N23Rik|AA930854	TNFRSF1A-associated via death domain	protein-coding
mm_108553.1	chr12	84417257	84417300	+	1	NA	promoter-TSS (NM_025525)	promoter-TSS (NM_025525)	78	NM_025525	66381	Mm.24846	NM_025525	ENSMUSG00000098134	Rnf113a2	2310020H19Rik|AI426758|Rnf113a	ring finger protein 113A2	protein-coding
mm_29025.1	chr3	102165562	102165577	-	1	NA	intron (NM_177545, intron 5 of 7)	intron (NM_177545, intron 5 of 7)	39124	NM_177545	229658	Mm.118004	NM_177545	ENSMUSG00000027860	Vangl1	Kitenin|Lpp2|Stb2|Stbm	vang-like 1 (van gogh, Drosophila)	protein-coding
mm_98222.1	chr11	88049408	88049421	+	1	NA	exon (NM_173374, exon 4 of 4)	exon (NM_173374, exon 4 of 4)	2041	NM_173374	110809	Mm.391719	NM_173374	ENSMUSG00000018379	Srsf1	1110054N12Rik|5730507C05Rik|6330415C05Rik|AI482334|AW491331|Asf|Sf2|Sfrs1	serine/arginine-rich splicing factor 1	protein-coding
mm_140276.1	chr17	84957127	84957138	+	1	NA	promoter-TSS (NM_011151)	promoter-TSS (NM_011151)	291	NR_027929	68531	Mm.249695	NR_027929	ENSMUSG00000097047	1110020A21Rik	2600015P10Rik	RIKEN cDNA 1110020A21 gene	ncRNA
mm_54403.1	chr6	31562067	31562069	-	1	NA	intron (NM_013723, intron 1 of 7)	B1_Mm|SINE|Alu	1869	NM_013723	27205	Mm.89918	NM_013723	ENSMUSG00000025608	Podxl	AW121214|Ly102|PC|PCLP-1|Pclp1	podocalyxin-like	protein-coding
mm_151533.1	chr19	58818865	58818904	+	1	NA	intron (NM_001327998, intron 7 of 12)	intron (NM_001327998, intron 7 of 12)	-24470	NM_026208	67507	Mm.27027	NM_026208	ENSMUSG00000026931	1700019N19Rik	-	RIKEN cDNA 1700019N19 gene	protein-coding
mm_140031.1	chr17	74338701	74338749	+	1	NA	promoter-TSS (NM_001162870)	promoter-TSS (NM_001162870)	-262	NM_001162870	50850	Mm.19804	NM_016962	ENSMUSG00000024068	Spast	Spg4|mKIAA1083	spastin	protein-coding
mm_28685.1	chr3	95402782	95402786	-	1	NA	promoter-TSS (NR_015490)	promoter-TSS (NR_015490)	57	NR_015490	67654	Mm.75066	NR_015490	ENSMUSG00000105734	4930558C23Rik	-	RIKEN cDNA 4930558C23 gene	ncRNA
mm_66702.1	chr7	45920701	45920780	-	1	NA	5' UTR (NM_001146346, exon 1 of 5)	5' UTR (NM_001146346, exon 1 of 5)	109	NM_001146346	13732	Mm.20829	NM_010129	ENSMUSG00000040212	Emp3	H-4|H4|HNMP-1|MI-35|Ymp	epithelial membrane protein 3	protein-coding
mm_117721.1	chr13	95444828	95444841	-	1	NA	promoter-TSS (NM_198408)	promoter-TSS (NM_198408)	-3	NM_198408	12919	Mm.316614	NM_198408	ENSMUSG00000021680	Crhbp	CRH-BP	corticotropin releasing hormone binding protein	protein-coding
mm_43564.1	chr5	137630775	137630778	+	1	NA	intron (NR_033148, intron 1 of 21)	intron (NR_033148, intron 1 of 21)	1653	NR_033148	100316903	Mm.200763	NR_033148		Gm20605	Lrch4-sap25	predicted gene 20605	ncRNA
mm_145451.1	chr18	60214813	60214841	+	1	NA	intron (NM_001033767, intron 2 of 2)	intron (NM_001033767, intron 2 of 2)	2750	NM_001033767	240327	Mm.357104	NM_001033767	ENSMUSG00000073555	Gm4951	EG240327|Ifgga2	predicted gene 4951	protein-coding
mm_173005.1	chrM	2063	2082	+	1	NA	NA	LSU-rRNA_Hsa|rRNA|rRNA	NA	NA								
mm_63344.1	chr7	126967556	126967561	+	1	NA	intron (NM_001252566, intron 14 of 16)	intron (NM_001252566, intron 14 of 16)	-8356	NM_026638	52858	Mm.28219	NM_026638	ENSMUSG00000030682	Cdipt	9530042F15Rik|D7Bwg0575e|Pis|Pis1	CDP-diacylglycerol--inositol 3-phosphatidyltransferase (phosphatidylinositol synthase)	protein-coding
mm_35081.1	chr4	7442555	7442557	-	1	NA	Intergenic	ORR1B2|LTR|ERVL-MaLR	-118132	NR_040645	71510	Mm.410775	NR_040645	ENSMUSG00000086070	8430436N08Rik	-	RIKEN cDNA 8430436N08 gene	ncRNA
mm_141445.1	chr17	29852750	29852762	-	1	NA	intron (NM_001081160, intron 2 of 15)	intron (NM_001081160, intron 2 of 15)	35126	NM_001081160	74762	Mm.40901	NM_001081160	ENSMUSG00000043557	Mdga1	1200011I03Rik|GPIM|Mamdc3	MAM domain containing glycosylphosphatidylinositol anchor 1	protein-coding
mm_30822.1	chr4	21871033	21871036	+	1	NA	intron (NM_025669, intron 9 of 11)	intron (NM_025669, intron 9 of 11)	-8641	NM_172687	230027	Mm.5662	NM_172687	ENSMUSG00000028247	Coq3	4732433J24|C77934	coenzyme Q3 methyltransferase	protein-coding
mm_32899.1	chr4	119026798	119026811	+	1	NA	Intergenic	Intergenic	42307	NR_131914	433751	Mm.224312	NR_131914	ENSMUSG00000066060	Gm12866	OTTMUSG00000008833	predicted gene 12866	ncRNA
mm_113023.1	chr13	22035871	22035874	+	1	NA	promoter-TSS (NM_175659)	promoter-TSS (NM_175659)	51	NM_175665	319184	Mm.358955	NM_175665	ENSMUSG00000062727	Hist1h2bk	-	histone cluster 1, H2bk	protein-coding
mm_148874.1	chr19	6497878	6497921	+	1	NA	intron (NM_001205234, intron 17 of 22)	CpG	45171	NM_009203	20521	Mm.391146	NM_009203	ENSMUSG00000061742	Slc22a12	AI987855|OAT4L|Rst|Slc22al2|URAT1	solute carrier family 22 (organic anion/cation transporter), member 12	protein-coding
mm_50021.1	chr6	41118450	41118460	+	1	NA	Intergenic	Intergenic	-82946	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_129385.1	chr15	78191630	78191665	-	1	NA	3' UTR (NM_001330686, exon 4 of 4)	3' UTR (NM_001330686, exon 4 of 4)	12590	NM_001330686	19293	Mm.2766	NM_013645	ENSMUSG00000005716	Pvalb	PV|Parv|Pva	parvalbumin	protein-coding
mm_32777.1	chr4	116701824	116701836	+	1	NA	TTS (NM_025962)	TTS (NM_025962)	6555	NM_025962	67096	Mm.252785	NM_025962	ENSMUSG00000028690	Mmachc	1810037K07Rik|CblC	methylmalonic aciduria cblC type, with homocystinuria	protein-coding
mm_50573.1	chr6	49051850	49051856	+	1	NA	exon (NM_053110, exon 9 of 11)	exon (NM_053110, exon 9 of 11)	15335	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_86605.1	chr10	13553188	13553239	+	1	NA	promoter-TSS (NM_019961)	promoter-TSS (NM_019961)	-71	NM_001347361	56535	Mm.282711	NM_019961	ENSMUSG00000019809	Pex3	1700014F15Rik|2810027F19Rik|2900010N04Rik	peroxisomal biogenesis factor 3	protein-coding
mm_94401.1	chr11	5740741	5740755	+	1	NA	intron (NM_001077661, intron 1 of 5)	CpG	428	NM_178623	72046	Mm.271657	NM_178623	ENSMUSG00000049680	Urgcp	2010005J08Rik|9130001I21Rik|AW060359|Urg4|mKIAA1507	upregulator of cell proliferation	protein-coding
mm_39633.1	chr5	24451974	24451990	+	1	NA	promoter-TSS (NM_001256431)	promoter-TSS (NM_001256431)	-195	NM_001256431	213990	Mm.250703	NM_139153	ENSMUSG00000023353	Agap3	AGAP-3|AV028425|Centg3|Crag|Crag.|MRIP-1|cnt-g3	ArfGAP with GTPase domain, ankyrin repeat and PH domain 3	protein-coding
mm_140609.1	chr17	10721556	10721558	-	1	NA	intron (NM_027032, intron 2 of 4)	intron (NM_027032, intron 2 of 4)	118634	NM_027032	69310	Mm.18889	NM_027032	ENSMUSG00000037196	Pacrg	1700008H23Rik	PARK2 co-regulated	protein-coding
mm_54389.1	chr6	31218695	31218714	-	1	NA	promoter-TSS (NR_110471)	promoter-TSS (NR_110471)	-230	NR_110469	232685	Mm.443019	NM_144555	ENSMUSG00000044471	Lncpint	Lincpint|MNCb-1768|Pint|linc-Pint	long non-protein coding RNA, Trp53 induced transcript	ncRNA
mm_155227.1	chrX	57066496	57066510	+	1	NA	exon (NM_029371, exon 9 of 9)	exon (NM_029371, exon 9 of 9)	12669	NM_029371	72459	Mm.2152	NM_028242	ENSMUSG00000067873	Htatsf1	1600023H17Rik|2600017A12Rik|2700077B20Rik|TAT-SF1	HIV TAT specific factor 1	protein-coding
mm_33094.1	chr4	124696018	124696027	+	1	NA	Intergenic	Intergenic	-2468	NM_026031	67205	Mm.259121	NM_026031	ENSMUSG00000028907	Utp11l	2700082D03Rik|CGI-94|Cgi94|Utp11	UTP11-like, U3 small nucleolar ribonucleoprotein, (yeast)	protein-coding
mm_38230.1	chr4	136021686	136021694	-	1	NA	promoter-TSS (NM_013736)	promoter-TSS (NM_013736)	-41	NM_013736	27224	Mm.27663	NM_013736	ENSMUSG00000028668	Eloa	110kDa|AA408125|Tceb3|Tceb3a	elongin A	protein-coding
mm_158169.1	chrX	103623649	103623672	-	1	NA	promoter-TSS (NR_028381)	promoter-TSS (NR_028381)	94	NR_028381	78878	Mm.259724	NR_028380	ENSMUSG00000086370	Ftx	B230206F22Rik|BB219131|NCRNA00182|Thcytx	Ftx transcript, Xist regulator (non-protein coding)	ncRNA
mm_126303.1	chr15	79516397	79516487	+	1	NA	promoter-TSS (NM_134090)	promoter-TSS (NM_134090)	34	NM_134090	105785	Mm.298199	NM_134090	ENSMUSG00000010830	Kdelr3	AI173274	KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 3	protein-coding
mm_136950.1	chr17	14676985	14676992	+	1	NA	exon (NM_011581, exon 14 of 22)	exon (NM_011581, exon 14 of 22)	17274	NM_011581	21826	Mm.26688	NM_011581	ENSMUSG00000023885	Thbs2	TSP2|Thbs-2	thrombospondin 2	protein-coding
mm_100437.1	chr11	119486225	119486239	+	1	NA	Intergenic	Intergenic	-5115	NM_001164636	338371	Mm.271946	NM_177394	ENSMUSG00000039850	Endov	A730011L01Rik	endonuclease V	protein-coding
mm_67318.1	chr7	79596881	79596892	-	1	NA	intron (NM_019799, intron 9 of 10)	RSINE1|SINE|B4	20771	NM_019799	56315	Mm.10909	NM_019799	ENSMUSG00000030549	Rhcg	BB065800	Rhesus blood group-associated C glycoprotein	protein-coding
mm_55581.1	chr6	71397363	71397369	-	1	NA	intron (NM_024288, intron 6 of 8)	intron (NM_024288, intron 6 of 8)	23939	NM_001081110	12525	Mm.1858	NM_009857	ENSMUSG00000053977	Cd8a	BB154331|Ly-2|Ly-35|Ly-B|Lyt-2	CD8 antigen, alpha chain	protein-coding
mm_148793.1	chr19	6165767	6165777	+	1	NA	intron (NM_028967, intron 1 of 2)	B3A|SINE|B2	1314	NM_028967	74481	Mm.159219	NM_028967	ENSMUSG00000039699	Batf2	4933430F08Rik	basic leucine zipper transcription factor, ATF-like 2	protein-coding
mm_62012.1	chr7	91269311	91269314	+	1	NA	intron (NM_011807, intron 1 of 22)	intron (NM_011807, intron 1 of 22)	178526	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_122245.1	chr14	33447185	33447200	-	1	NA	promoter-TSS (NM_001310453)	promoter-TSS (NM_001310453)	-34	NM_016700	26419	Mm.21495	NM_016700	ENSMUSG00000021936	Mapk8	AI849689|JNK|JNK1|Prkm8|SAPK1	mitogen-activated protein kinase 8	protein-coding
mm_20269.1	chr2	126676064	126676096	-	1	NA	promoter-TSS (NM_010249)	promoter-TSS (NM_010249)	257	NM_001271470	14391	Mm.293266	NM_010249	ENSMUSG00000027361	Gabpb1	BABPB2|E4TF1|E4TF1-47|E4TF1-53|E4Tf1B|GABPB|GABPB-1|GABPB-2|GABPB1-1|GABPB1-2|NRF2B1|NRF2B2	GA repeat binding protein, beta 1	protein-coding
mm_69728.1	chr7	140787827	140787872	-	1	NA	promoter-TSS (NM_001143765)	promoter-TSS (NM_001143765)	5	NM_001143765	74075	Mm.46102	NM_001143765	ENSMUSG00000025480	Syce1	4933406J07Rik	synaptonemal complex central element protein 1	protein-coding
mm_71434.1	chr8	46506081	46506106	+	1	NA	intron (NM_001302163, intron 3 of 20)	intron (NM_001302163, intron 3 of 20)	15127	NM_001302163	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_17373.1	chr2	26933333	26933349	-	1	NA	promoter-TSS (NM_198628)	promoter-TSS (NM_198628)	170	NM_011512	20932	Mm.300594	NM_011512	ENSMUSG00000014867	Surf4	AL033340|AL033373|Surf-4	surfeit gene 4	protein-coding
mm_9218.1	chr1	171234277	171234287	-	1	NA	promoter-TSS (NM_010185)	promoter-TSS (NM_010185)	67	NM_010185	14127	Mm.22673	NM_010185	ENSMUSG00000058715	Fcer1g	AI573376|CD23|FcR-gamma|FcR[g]|FcRgamma|Fce1g|FcepsilonRI|Ly-50	Fc receptor, IgE, high affinity I, gamma polypeptide	protein-coding
mm_22921.1	chr3	31096375	31096378	+	1	NA	intron (NM_001271772, intron 1 of 8)	intron (NM_001271772, intron 1 of 8)	1318	NM_001039090	20482	Mm.15406	NM_011386	ENSMUSG00000027660	Skil	Skir|SnoN|sno	SKI-like	protein-coding
mm_70078.1	chr7	142653667	142653687	-	1	NA	3' UTR (NM_010514, exon 4 of 4)	3' UTR (NM_010514, exon 4 of 4)	1319	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_131164.1	chr16	6996694	6996722	+	1	NA	intron (NM_021477, intron 5 of 16)	intron (NM_021477, intron 5 of 16)	-73127	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_134355.1	chr16	16718112	16718120	-	1	NA	promoter-TSS (NR_045920)	promoter-TSS (NR_045920)	5	NR_045920	74066	Mm.61161	NM_028739		4933404G15Rik	4933401J20Rik	RIKEN cDNA 4933404G15 gene	ncRNA
mm_16274.1	chr2	173737479	173737490	+	1	NA	promoter-TSS (NM_019806)	promoter-TSS (NM_019806)	-87	NM_019806	56491	Mm.260456	NM_019806	ENSMUSG00000054455	Vapb	AI225786|AI840687|AI848259|D2Abb2e|R75548|VAP33b|Vamp33b	vesicle-associated membrane protein, associated protein B and C	protein-coding
mm_111456.1	chr12	98385985	98385991	-	1	NA	Intergenic	Intergenic	117353	NM_008152	14744	Mm.378924	NM_008152	ENSMUSG00000021886	Gpr65	Dig1|Gpcr25|TDAG8	G-protein coupled receptor 65	protein-coding
mm_94923.1	chr11	29508480	29508521	+	1	NA	3' UTR (NM_176841, exon 32 of 32)	3' UTR (NM_176841, exon 32 of 32)	6533	NM_026465	67939	Mm.251087	NM_026465	ENSMUSG00000032673	Prorsd1	2010316F05Rik|Ncrna00117|Prdxdd1	prolyl-tRNA synthetase domain containing 1	protein-coding
mm_72336.1	chr8	79225870	79225918	+	1	NA	intron (NM_026315, intron 2 of 5)	MTEa|LTR|ERVL-MaLR	22689	NM_026315	67687	Mm.178707	NM_026315	ENSMUSG00000031682	1700011L22Rik	-	RIKEN cDNA 1700011L22 gene	protein-coding
mm_159185.1	chr2	112242879	112242879	+	1	NA	intron (NM_207206, intron 5 of 13)	intron (NM_207206, intron 5 of 13)	3038	NM_207206	99010	Mm.33438	NM_207206	ENSMUSG00000027134	Lpcat4	AI505034|Agpat7|Aytl3|LPEAT2	lysophosphatidylcholine acyltransferase 4	protein-coding
mm_134363.1	chr16	16865940	16865947	-	1	NA	Intergenic	RMER17C|LTR|ERVK	-1958	NM_001190325	16136	Mm.184441	NM_001190325	ENSMUSG00000075370	Igll1	BB139905|Igl-5|Igll|Lambda5	immunoglobulin lambda-like polypeptide 1	protein-coding
mm_126338.1	chr15	79900241	79900249	+	1	NA	intron (NM_001160415, intron 5 of 8)	MIRb|SINE|MIR	5222	NM_001347041	80287	Mm.284059	NM_030255	ENSMUSG00000009585	Apobec3	Apobec|Arp3|BC003314|Cem15|Rfv3	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 3	protein-coding
mm_125068.1	chr15	25941079	25941089	+	1	NA	5' UTR (NM_001277315, exon 1 of 7)	5' UTR (NM_001277315, exon 1 of 7)	258	NM_025459	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_11579.1	chr2	32961666	32961692	+	1	NA	promoter-TSS (NM_009076)	promoter-TSS (NM_009076)	-33	NM_009076	269261	Mm.250030	NM_009076	ENSMUSG00000038900	Rpl12	E430018F03	ribosomal protein L12	protein-coding
mm_119783.1	chr14	54181561	54181567	+	1	NA	Intergenic	Intergenic	72365	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_102079.1	chr11	52277149	52277164	-	1	NA	intron (NM_001313981, intron 3 of 10)	intron (NM_001313981, intron 3 of 10)	5439	NM_009331	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_162619.1	chr1	183388954	183389013	+	1	NA	promoter-TSS (NM_021466)	promoter-TSS (NM_021466)	-2	NM_001277959	21339	Mm.383556	NM_021466	ENSMUSG00000072258	Taf1a	TAFI48|mTAFI48	TATA-box binding protein associated factor, RNA polymerase I, A	protein-coding
mm_144451.1	chr18	23310141	23310173	+	1	NA	5' UTR (NM_001285813, exon 1 of 22)	5' UTR (NM_001285813, exon 1 of 22)	137	NM_001285813	13527	Mm.94371	NM_010087	ENSMUSG00000024302	Dtna	2210407P21Rik|DTN-A|Dtn|Gm19389|a-DB-1|adbn	dystrobrevin alpha	protein-coding
mm_55301.1	chr6	54817646	54817650	-	1	NA	intron (NM_199143, intron 1 of 4)	intron (NM_199143, intron 1 of 4)	732	NM_199143	387524	Mm.286149	NM_199143	ENSMUSG00000058446	Znrf2	1190002C14Rik|AU044205|D6Ertd365e	zinc and ring finger 2	protein-coding
mm_115912.1	chr13	23465840	23465859	-	1	NA	promoter-TSS (NM_013483)	promoter-TSS (NM_013483)	52	NM_013483	12231	Mm.1420	NM_013483	ENSMUSG00000000706	Btn1a1	Btn	butyrophilin, subfamily 1, member A1	protein-coding
mm_20963.1	chr2	151961914	151961937	-	1	NA	Intergenic	Intergenic	5692	NR_035478	100316704		NR_035478	ENSMUSG00000088491	Mir1953	mir-1953|mmu-mir-1953	microRNA 1953	ncRNA
mm_11643.1	chr2	34958319	34958335	+	1	NA	intron (NM_009421, intron 4 of 10)	intron (NM_009421, intron 4 of 10)	3445	NM_009421	22029	Mm.239514	NM_009421	ENSMUSG00000026875	Traf1	4732496E14Rik	TNF receptor-associated factor 1	protein-coding
mm_5436.1	chr1	34842897	34842901	-	1	NA	5' UTR (NM_001160236, exon 1 of 7)	5' UTR (NM_001160236, exon 1 of 7)	151	NM_001160235	214469	Mm.120151	NM_174997	ENSMUSG00000037503	Fam168b	mKIAA4042	family with sequence similarity 168, member B	protein-coding
mm_114008.1	chr13	52596955	52596965	+	1	NA	promoter-TSS (NM_011518)	promoter-TSS (NM_011518)	78	NM_011518	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_33054.1	chr4	123116273	123116277	+	1	NA	promoter-TSS (NM_181859)	promoter-TSS (NM_181859)	27	NM_181859	353371	Mm.189660	NM_181859	ENSMUSG00000076438	Oxct2b	Scot-t2	3-oxoacid CoA transferase 2B	protein-coding
mm_76481.1	chr8	85553243	85553273	-	1	NA	exon (NM_019794, exon 3 of 9)	exon (NM_019794, exon 3 of 9)	2013	NM_019794	56445	Mm.475573	NM_019794	ENSMUSG00000031701	Dnaja2	1500017M13Rik|2010206B19Rik|DNAJ|DNJ3|Dnaj3|HIRIP4|PRO3015|mDj3	DnaJ heat shock protein family (Hsp40) member A2	protein-coding
mm_29455.1	chr3	113531420	113531445	-	1	NA	Intergenic	Lx|LINE|L1	43330	NM_007446	11722	Mm.439727	NM_007446	ENSMUSG00000074264	Amy1	Amy-1|Amy1a|C030014B17Rik	amylase 1, salivary	protein-coding
mm_136502.1	chr16	96443596	96443641	-	1	NA	promoter-TSS (NM_008405)	promoter-TSS (NM_008405)	-4	NM_008405	16415	Mm.12872	NM_008405	ENSMUSG00000000157	Itgb2l	5033406G21Rik|pactolus	integrin beta 2-like	protein-coding
mm_25292.1	chr3	105870899	105870912	+	1	NA	promoter-TSS (NM_001174169)	promoter-TSS (NM_001174169)	47	NM_001174169	69296	Mm.235024	NM_027025	ENSMUSG00000000562	Tmigd3	1700001d09rik|4930578J19Rik	transmembrane and immunoglobulin domain containing 3	protein-coding
mm_157203.1	chrX	12616738	12616747	-	1	NA	3' UTR (NM_027439, exon 9 of 9)	3' UTR (NM_027439, exon 9 of 9)	28983	NM_027439	70495	Mm.25148	NM_027439	ENSMUSG00000031007	Atp6ap2	(P)RR|5730403E06Rik|APT6M8-9|ATP6M8-9|Atp6ip2|M8-9|PRR	ATPase, H+ transporting, lysosomal accessory protein 2	protein-coding
mm_163332.1	chr12	8771431	8771444	+	1	NA	promoter-TSS (NM_011519)	promoter-TSS (NM_011519)	41	NM_011519	20969	Mm.2580	NM_011519	ENSMUSG00000020592	Sdc1	AA408134|AA409076|CD138|Sstn|Synd|Synd1|syn-1	syndecan 1	protein-coding
mm_9876.1	chr1	185329332	185329401	-	1	NA	promoter-TSS (NM_198653)	promoter-TSS (NM_198653)	35	NM_198653	381314	Mm.275841	NM_198653	ENSMUSG00000026618	Iars2	2010002H18Rik|C79125	isoleucine-tRNA synthetase 2, mitochondrial	protein-coding
mm_165820.1	chr3	146651362	146651373	-	1	NA	promoter-TSS (NM_029144)	promoter-TSS (NM_029144)	-50	NM_029144	75015	Mm.250432	NM_029144	ENSMUSG00000048652	4930503B20Rik	1700013A07Rik|1700095G21Rik|4930483N21Rik|Gm1652|Samd13	RIKEN cDNA 4930503B20 gene	protein-coding
mm_147736.1	chr18	61065430	61065437	-	1	NA	intron (NM_008809, intron 6 of 22)	intron (NM_008809, intron 6 of 22)	20283	NM_008809	18596	Mm.4146	NM_008809	ENSMUSG00000024620	Pdgfrb	AI528809|CD140b|PDGFR-1|Pdgfr	platelet derived growth factor receptor, beta polypeptide	protein-coding
mm_151909.1	chr19	5799581	5799594	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	3085	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_100454.1	chr11	119724990	119725021	+	1	NA	intron (NM_028898, intron 3 of 33)	intron (NM_028898, intron 3 of 33)	109360	NR_045313	319454	Mm.442144	NR_045312	ENSMUSG00000085081	Rptoros	A430071A18Rik	regulatory associated protein of MTOR, complex 1, opposite strand	ncRNA
mm_165915.1	chr4	57956312	57956358	-	1	NA	promoter-TSS (NM_011660)	promoter-TSS (NM_011660)	76	NM_011660	22166	Mm.260618	NM_011660	ENSMUSG00000028367	Txn1	ADF|AW550880|Trx1|Txn	thioredoxin 1	protein-coding
mm_33301.1	chr4	129008576	129008586	+	1	NA	non-coding (NR_138540, exon 6 of 7)	non-coding (NR_138540, exon 6 of 7)	15357	NM_001033966	11637	Mm.29460	NM_016895	ENSMUSG00000028792	Ak2	Ak-2|D4Ertd220e	adenylate kinase 2	protein-coding
mm_138681.1	chr17	35916919	35916929	+	1	NA	promoter-TSS (NM_025878)	promoter-TSS (NM_025878)	-272	NM_001163818	52040	Mm.29385	NM_175934	ENSMUSG00000039220	Ppp1r10	2610025H06Rik|Cat53|D17Ertd808e|Fb19|Pnuts	protein phosphatase 1, regulatory subunit 10	protein-coding
mm_30092.1	chr3	138239584	138239605	-	1	NA	promoter-TSS (NR_045760)	promoter-TSS (NR_045760)	69	NR_045760	68369	Mm.441136	NR_045760	ENSMUSG00000099146	0610031O16Rik	-	RIKEN cDNA 0610031O16 gene	ncRNA
mm_46538.1	chr5	105702039	105702045	-	1	NA	intron (NM_178701, intron 1 of 2)	intron (NM_178701, intron 1 of 2)	1232	NM_178701	231549	Mm.23837	NM_178701	ENSMUSG00000046079	Lrrc8d	2810473G09Rik|4930525N13Rik|A930019F03|Lrrc5	leucine rich repeat containing 8D	protein-coding
mm_47050.1	chr5	116083260	116083276	-	1	NA	promoter-TSS (NM_001101546)	promoter-TSS (NM_001101546)	-22	NM_001101546	545798	Mm.483995	NM_001101546	ENSMUSG00000079278	Tmem233	DSPB2|Gm13843|OTTMUSG00000014722	transmembrane protein 233	protein-coding
mm_146808.1	chr18	20746228	20746239	-	1	NA	5' UTR (NM_019737, exon 1 of 9)	5' UTR (NM_019737, exon 1 of 9)	171	NM_019737	56386	Mm.393827	NM_019737	ENSMUSG00000056124	B4galt6	AA536803|AU022389	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 6	protein-coding
mm_98174.1	chr11	87755890	87755901	+	1	NA	promoter-TSS (NR_029555)	promoter-TSS (NR_029555)	-969	NR_029555	387160		NR_029555	ENSMUSG00000105196	Mir142	Mirn142|miR-142|mir-142a|mmu-mir-142|mmu-mir-142a	microRNA 142	ncRNA
mm_39640.1	chr5	24586708	24586718	+	1	NA	promoter-TSS (NM_133913)	promoter-TSS (NM_133913)	-37	NM_133913	100910	Mm.140672	NM_133913	ENSMUSG00000038181	Chpf2	2010209O12Rik|AW060945|mKIAA1402|mir-671	chondroitin polymerizing factor 2	protein-coding
mm_108022.1	chr12	73616236	73616240	+	1	NA	intron (NM_001313977, intron 2 of 14)	intron (NM_001313977, intron 2 of 14)	31442	NM_008856	18755	Mm.341677	NM_008856	ENSMUSG00000021108	Prkch	Pkch	protein kinase C, eta	protein-coding
mm_155902.1	chrX	101673040	101673072	+	1	NA	exon (NM_001290535, exon 16 of 22)	exon (NM_001290535, exon 16 of 22)	32838	NM_001290535	108155	Mm.487332	NM_139144	ENSMUSG00000034160	Ogt	1110038P24Rik|4831420N21Rik|AI115525|Ogtl	O-linked N-acetylglucosamine (GlcNAc) transferase (UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase)	protein-coding
mm_99581.1	chr11	104231518	104231528	+	1	NA	promoter-TSS (NM_010838)	promoter-TSS (NM_010838)	87	NM_001285454	17762	Mm.1287	NM_010838	ENSMUSG00000018411	Mapt	AI413597|AW045860|Mtapt|Tau	microtubule-associated protein tau	protein-coding
mm_86733.1	chr10	19067272	19067282	+	1	NA	Intergenic	Intergenic	-51867	NM_009397	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_44695.1	chr5	30408031	30408033	-	1	NA	intron (NM_001313767, intron 5 of 45)	intron (NM_001313767, intron 5 of 45)	53900	NM_001286421	83762	Mm.244502	NM_031875	ENSMUSG00000062372	Otof	-	otoferlin	protein-coding
mm_2083.1	chr1	87676231	87676280	+	1	NA	intron (NM_010566, intron 5 of 26)	intron (NM_010566, intron 5 of 26)	55943	NM_001110193	16331	Mm.15105	NM_010566	ENSMUSG00000026288	Inpp5d	SHIP|SHIP-1|SHIP1|SIP-145|p150Ship|s-SHIP	inositol polyphosphate-5-phosphatase D	protein-coding
mm_6747.1	chr1	83408031	83408040	-	1	NA	5' UTR (NM_172430, exon 1 of 11)	5' UTR (NM_172430, exon 1 of 11)	165	NM_172430	77629	Mm.154303	NM_172430	ENSMUSG00000026163	Sphkap	4930544G21Rik|A930009L15Rik|AI852220|SKIP|mKIAA1678	SPHK1 interactor, AKAP domain containing	protein-coding
mm_71882.1	chr8	69812399	69812415	+	1	NA	intron (NM_198101, intron 7 of 20)	B2_Mm1t|SINE|B2	3720	NM_198101	78816	Mm.324305	NM_198101	ENSMUSG00000036246	Gmip	5031419I10Rik	Gem-interacting protein	protein-coding
mm_129553.1	chr15	79442073	79442106	-	1	NA	promoter-TSS (NM_013767)	promoter-TSS (NM_013767)	-32	NM_013767	27373	Mm.30199	NM_013767	ENSMUSG00000022433	Csnk1e	AI426939|AI551861|AW457082|CK1epsilon|CKIe|KC1epsilon|tau	casein kinase 1, epsilon	protein-coding
mm_154036.1	chr19	53528962	53528989	-	1	NA	promoter-TSS (NM_001085390)	promoter-TSS (NM_001085390)	-343	NM_001085390	240672	Mm.482424	NM_001085390	ENSMUSG00000034765	Dusp5	Gm337	dual specificity phosphatase 5	protein-coding
mm_14803.1	chr2	145886901	145886921	+	1	NA	3' UTR (NM_028724, exon 13 of 13)	3' UTR (NM_028724, exon 13 of 13)	-16330	NM_026425	67877	Mm.151168	NM_026425	ENSMUSG00000002728	Naa20	1500004D14Rik|2900026I01Rik|AU041458|D2Ertd186e|Nat5	N(alpha)-acetyltransferase 20, NatB catalytic subunit	protein-coding
mm_69875.1	chr7	141562953	141562976	-	1	NA	intron (NM_007459, intron 1 of 21)	intron (NM_007459, intron 1 of 21)	784	NM_007459	11772	Mm.253090	NM_007459	ENSMUSG00000002957	Ap2a2	2410074K14Rik|AF006990|AW146353|Adtab|C78001|L25	adaptor-related protein complex 2, alpha 2 subunit	protein-coding
mm_76113.1	chr8	80788657	80788688	-	1	NA	exon (NM_001301298, exon 4 of 11)	exon (NM_001301298, exon 4 of 11)	-49213	NM_053124	93762	Mm.246803	NM_053124	ENSMUSG00000031715	Smarca5	4933427E24Rik|D030040M08Rik|D330027N15Rik|MommeD4|Snf2h	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5	protein-coding
mm_62164.1	chr7	97211426	97211446	+	1	NA	intron (NM_001162477, intron 1 of 9)	intron (NM_001162477, intron 1 of 9)	114528	NM_001177412	244144	Mm.297541	NM_001177412	ENSMUSG00000035713	Usp35	Gm1088|Gm493	ubiquitin specific peptidase 35	protein-coding
mm_65442.1	chr7	25390099	25390124	-	1	NA	promoter-TSS (NM_001039507)	promoter-TSS (NM_001039507)	1	NM_001039507	16890	Mm.158548	NM_010719	ENSMUSG00000003123	Lipe	4933403G17Rik|HSL	lipase, hormone sensitive	protein-coding
mm_134234.1	chr16	11804986	11804998	-	1	NA	3' UTR (NM_146067, exon 4 of 4)	3' UTR (NM_146067, exon 4 of 4)	25290	NR_126430	73761	Mm.39183	NR_126430		4833415N18Rik	-	RIKEN cDNA 4833415N18 gene	ncRNA
mm_109684.1	chr12	113140501	113140565	+	1	NA	promoter-TSS (NM_001347443)	promoter-TSS (NM_001347443)	-72	NM_001347443	68337	Mm.133825	NM_024223	ENSMUSG00000006356	Crip2	0610010I23Rik|AW743261|C77570|CRP2|CRP4|Crp|ESP1|Hlp	cysteine rich protein 2	protein-coding
mm_70534.1	chr8	13037373	13037390	+	1	NA	promoter-TSS (NM_007972)	promoter-TSS (NM_007972)	73	NM_001242368	14058	Mm.262589	NM_007972	ENSMUSG00000031444	F10	Cf10|fX	coagulation factor X	protein-coding
mm_92762.1	chr10	81092555	81092561	-	1	NA	5' UTR (NM_145365, exon 3 of 12)	5' UTR (NM_145365, exon 3 of 12)	6314	NM_145365	208677	Mm.294693	NM_145365	ENSMUSG00000035041	Creb3l3	BC010786|CREB-H|D10Bur1e	cAMP responsive element binding protein 3-like 3	protein-coding
mm_127194.1	chr15	99055165	99055183	+	1	NA	promoter-TSS (NM_001163589)	promoter-TSS (NM_001163589)	0	NM_001163588	19132	Mm.2477	NM_013639	ENSMUSG00000023484	Prph	Prph1	peripherin	protein-coding
mm_123000.1	chr14	54992797	54992807	-	1	NA	exon (NM_080728, exon 4 of 41)	exon (NM_080728, exon 4 of 41)	1747	NM_080728	140781	Mm.457983	NM_080728	ENSMUSG00000053093	Myh7	B-MHC|MyHC-I|Myhc-b|Myhcb|beta-MHC	myosin, heavy polypeptide 7, cardiac muscle, beta	protein-coding
mm_45951.1	chr5	90366213	90366224	-	1	NA	promoter-TSS (NM_030886)	promoter-TSS (NM_030886)	-33	NM_198010	81702	Mm.245522	NM_030886	ENSMUSG00000055204	Ankrd17	4933425K22Rik|A130069E23Rik|A930008M01|AA407558|AA516750|AU040470|Foe|Gtar|Mask|mKIAA0697	ankyrin repeat domain 17	protein-coding
mm_87291.1	chr10	42502103	42502113	+	1	NA	promoter-TSS (NM_017472)	promoter-TSS (NM_017472)	54	NM_017472	54198	Mm.277870	NM_017472	ENSMUSG00000019804	Snx3	SDP3	sorting nexin 3	protein-coding
mm_117310.1	chr13	67495646	67495649	-	1	NA	intron (NM_001007575, intron 1 of 3)	intron (NM_001007575, intron 1 of 3)	4875	NM_001007575	238693	Mm.478914	NM_001007575	ENSMUSG00000071291	Zfp58	A530094I17Rik|Mfg-1|Mfg1|Rslcan5|Zfp817	zinc finger protein 58	protein-coding
mm_1292.1	chr1	64303186	64303217	+	1	NA	Intergenic	Intergenic	-181812	NM_033563	93691	Mm.29466	NM_033563	ENSMUSG00000025959	Klf7	9830124P08Rik	Kruppel-like factor 7 (ubiquitous)	protein-coding
mm_162166.1	chrX	97072596	97072596	+	1	NA	promoter-TSS (NM_001033361)	promoter-TSS (NM_001033361)	0	NM_001033361	245526	Mm.336164	NM_001033361	ENSMUSG00000031212	Pgr15l	-	G protein-coupled receptor 15-like	protein-coding
mm_155545.1	chrX	74311007	74311019	+	1	NA	3' UTR (NM_010273, exon 11 of 11)	3' UTR (NM_010273, exon 11 of 11)	-2020	NM_138607	108160	Mm.4370	NM_138607	ENSMUSG00000001962	Fam50a	D0HXS9928E|XAP-5	family with sequence similarity 50, member A	protein-coding
mm_108910.1	chr12	100206426	100206459	+	1	NA	3' UTR (NM_009790, exon 6 of 6)	3' UTR (NM_009790, exon 6 of 6)	6298	NM_001313934	12313	Mm.285993	NM_009790	ENSMUSG00000001175	Calm1	AI256814|AI327027|AI461935|AL024000|CaM|Calm	calmodulin 1	protein-coding
mm_93279.1	chr10	96077809	96077826	-	1	NA	Intergenic	Intergenic	137154	NM_001001932	216238	Mm.210035	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding
mm_81335.1	chr9	108517567	108517620	+	1	NA	intron (NM_175143, intron 1 of 9)	CpG	506	NM_175143	69232	Mm.335449	NM_175143	ENSMUSG00000006673	Qrich1	2610028H07Rik	glutamine-rich 1	protein-coding
mm_54906.1	chr6	47595054	47595065	-	1	NA	promoter-TSS (NM_001146689)	promoter-TSS (NM_001146689)	-29	NM_001146689	14056	Mm.246688	NM_007971	ENSMUSG00000029687	Ezh2	Enx-1|Enx1h|KMT6|mKIAA4065	enhancer of zeste 2 polycomb repressive complex 2 subunit	protein-coding
mm_79847.1	chr9	64812761	64812771	+	1	NA	intron (NM_001162917, intron 2 of 34)	intron (NM_001162917, intron 2 of 34)	1755	NM_001162917	102442	Mm.222473	NM_176935	ENSMUSG00000053641	Dennd4a	AI115600|AI851943|F730015K02Rik	DENN/MADD domain containing 4A	protein-coding
mm_87962.1	chr10	63386551	63386576	+	1	NA	promoter-TSS (NM_013888)	promoter-TSS (NM_013888)	0	NM_013888	30045	Mm.32550	NM_013888	ENSMUSG00000036764	Dnajc12	Jdp1|mJDP1	DnaJ heat shock protein family (Hsp40) member C12	protein-coding
mm_26420.1	chr3	142614487	142614494	+	1	NA	intron (NM_010259, intron 10 of 10)	L1_Mur2|LINE|L1	-6173	NM_010260	14469	Mm.24038	NM_010260	ENSMUSG00000028270	Gbp2	-	guanylate binding protein 2	protein-coding
mm_19255.1	chr2	84774797	84774807	-	1	NA	5' UTR (NM_009776, exon 2 of 8)	5' UTR (NM_009776, exon 2 of 8)	627	NM_009776	12258	Mm.38888	NM_009776	ENSMUSG00000023224	Serping1	C1INH|C1nh	serine (or cysteine) peptidase inhibitor, clade G, member 1	protein-coding
mm_94086.1	chr10	128497390	128497404	-	1	NA	5' UTR (NM_172259, exon 2 of 7)	5' UTR (NM_172259, exon 2 of 7)	1288	NM_172259	216459	Mm.291688	NM_172259	ENSMUSG00000039824	Myl6b	5730437E04Rik|BC037527|MLC1SA	myosin, light polypeptide 6B	protein-coding
mm_132149.1	chr16	32102927	32102938	+	1	NA	intron (NM_025892, intron 1 of 3)	intron (NM_025892, intron 1 of 3)	3130	NM_025892	66994	Mm.22990	NM_025892	ENSMUSG00000035790	Cep19	1500031L02Rik|AI428934|AL022620	centrosomal protein 19	protein-coding
mm_144746.1	chr18	35598688	35598698	+	1	NA	promoter-TSS (NM_026420)	promoter-TSS (NM_026420)	26	NM_026420	67869	Mm.126534	NM_026420	ENSMUSG00000037058	Paip2	2310050K10Rik|AU045972	polyadenylate-binding protein-interacting protein 2	protein-coding
mm_34388.1	chr4	144927173	144927189	+	1	NA	exon (NM_001172424, exon 7 of 7)	exon (NM_001172424, exon 7 of 7)	34044	NM_011303	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding
mm_41083.1	chr5	87678017	87678060	+	1	NA	intron (NM_001286015, intron 27 of 32)	intron (NM_001286015, intron 27 of 32)	11830	NM_001286016	12990	Mm.427467	NM_007784	ENSMUSG00000070702	Csn1s1	AA959832|AW212882|Csna	casein alpha s1	protein-coding
mm_160524.1	chr9	36128755	36128755	-	1	NA	promoter-TSS (NM_001167587)	promoter-TSS (NM_001167587)	24	NM_001167587	546123	Mm.445255	NM_001167587	ENSMUSG00000091411	Gm5916	EG546123	predicted gene 5916	protein-coding
mm_30156.1	chr3	142881918	142881939	-	1	NA	promoter-TSS (NM_178654)	promoter-TSS (NM_178654)	76	NM_178654	109333	Mm.244236	NM_178654	ENSMUSG00000004591	Pkn2	6030436C20Rik|AI507382|PRK2|Prkcl2|Stk7	protein kinase N2	protein-coding
mm_61098.1	chr7	51879068	51879090	+	1	NA	5' UTR (NM_001330607, exon 1 of 8)	5' UTR (NM_001330607, exon 1 of 8)	112	NM_001330607	14453	Mm.207360	NM_008087	ENSMUSG00000030498	Gas2	Gas-2	growth arrest specific 2	protein-coding
mm_114682.1	chr13	80893798	80893807	+	1	NA	3' UTR (NM_001042591, exon 8 of 8)	3' UTR (NM_001042591, exon 8 of 8)	10380	NM_001042591	105171	Mm.423137	NM_001042591	ENSMUSG00000074794	Arrdc3	AI450344|mKIAA1376	arrestin domain containing 3	protein-coding
mm_88906.1	chr10	81179335	81179349	+	1	NA	TTS (NR_028549)	TTS (NR_028549)	381	NR_028549	100217454		NR_028549	ENSMUSG00000064441	Snord37	MBII-376	small nucleolar RNA, C/D box 37	snoRNA
mm_30412.1	chr3	152264996	152265026	-	1	NA	intron (NM_199465, intron 1 of 12)	intron (NM_199465, intron 1 of 12)	1309	NM_199465	68810	Mm.200188	NM_199465	ENSMUSG00000039103	Nexn	1110046H09Rik|AA553326|NELIN	nexilin	protein-coding
mm_173108.1	chrX	157465833	157465834	-	1	NA	exon (NM_009214, exon 4 of 11)	exon (NM_009214, exon 4 of 11)	26213	NM_009214	20603	Mm.18652	NM_009214	ENSMUSG00000071708	Sms	AI427066|Gy|SPMSY|SpmST|gyro	spermine synthase	protein-coding
mm_162866.1	chr10	93437123	93437138	+	1	NA	Intergenic	MLT1A|LTR|ERVL-MaLR	4023	NR_106161	102465791		NR_106161	ENSMUSG00000098679	Mir7688	Gm27874|mmu-mir-7688	microRNA 7688	ncRNA
mm_158939.1	chr1	78197219	78197219	-	1	NA	promoter-TSS (NM_008781)	promoter-TSS (NM_008781)	-83	NM_001159520	18505	Mm.1371	NM_008781	ENSMUSG00000004872	Pax3	Pax-3|Sp|Splchl2|splotch	paired box 3	protein-coding
mm_38101.1	chr4	134371615	134371634	-	1	NA	exon (NM_019578, exon 1 of 11)	exon (NM_019578, exon 1 of 11)	923	NM_019578	56219	Mm.30978	NM_019578	ENSMUSG00000028838	Extl1	D430033M16Rik	exostoses (multiple)-like 1	protein-coding
mm_38828.1	chr4	149126689	149126698	-	1	NA	promoter-TSS (NM_007745)	promoter-TSS (NM_007745)	70	NM_007745	12854	Mm.6204	NM_007745	ENSMUSG00000028971	Cort	CST|PCST	cortistatin	protein-coding
mm_53658.1	chr6	141275328	141275340	+	1	NA	intron (NM_018779, intron 1 of 15)	(CA)n|Simple_repeat|Simple_repeat	26065	NM_018779	54611	Mm.103728	NM_018779	ENSMUSG00000041741	Pde3a	A930022O17Rik|C87899	phosphodiesterase 3A, cGMP inhibited	protein-coding
mm_100964.1	chr11	6638641	6638655	-	1	NA	promoter-TSS (NM_011709)	promoter-TSS (NM_011709)	1	NM_011709	22373	Mm.268094	NM_011709	ENSMUSG00000000381	Wap	-	whey acidic protein	protein-coding
mm_39953.1	chr5	32133691	32133708	+	1	NA	Intergenic	Intergenic	-2773	NM_008037	14284	Mm.24684	NM_008037	ENSMUSG00000029135	Fosl2	Fra-2	fos-like antigen 2	protein-coding
mm_102609.1	chr11	62457290	62457332	-	1	NA	promoter-TSS (NM_177229)	promoter-TSS (NM_177229)	21	NM_177229	20185	Mm.271814	NM_011308	ENSMUSG00000018501	Ncor1	5730405M06Rik|A230020K14Rik|N-CoR|RIP13|Rxrip13|mKIAA1047	nuclear receptor co-repressor 1	protein-coding
mm_45492.1	chr5	71657959	71657989	-	1	NA	5' UTR (NM_010251, exon 1 of 9)	5' UTR (NM_010251, exon 1 of 9)	334	NM_010251	14397	Mm.248731	NM_010251	ENSMUSG00000029211	Gabra4	Gabra-4	gamma-aminobutyric acid (GABA) A receptor, subunit alpha 4	protein-coding
mm_85302.1	chr9	100539515	100539522	-	1	NA	intron (NM_010878, intron 1 of 3)	L1M2a|LINE|L1	6616	NM_010878	17973	Mm.181485	NM_010878	ENSMUSG00000032475	Nck1	6330586M15Rik|D230010O13Rik|Nck|Nck-1	non-catalytic region of tyrosine kinase adaptor protein 1	protein-coding
mm_49693.1	chr6	33650082	33650093	+	1	NA	intron (NM_009148, intron 10 of 17)	intron (NM_009148, intron 10 of 17)	-379361	NM_028886	74354	Mm.127952	NM_028886	ENSMUSG00000056215	Lrguk	4921528H16Rik	leucine-rich repeats and guanylate kinase domain containing	protein-coding
mm_130987.1	chr15	103366589	103366600	-	1	NA	5' UTR (NM_010577, exon 1 of 30)	5' UTR (NM_010577, exon 1 of 30)	197	NM_010577	16402	Mm.16234	NM_010577	ENSMUSG00000000555	Itga5	Cd49e|Fnra|VLA5	integrin alpha 5 (fibronectin receptor alpha)	protein-coding
mm_169635.1	chr15	47540004	47540007	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	916700	NR_045811	75281	Mm.159487	NR_045811	ENSMUSG00000051198	4930548G14Rik	-	RIKEN cDNA 4930548G14 gene	ncRNA
mm_48139.1	chr5	137150323	137150332	-	1	NA	Intergenic	Intergenic	-34120	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_151818.1	chr19	5510447	5510465	-	1	NA	promoter-TSS (NM_001024560)	promoter-TSS (NM_001024560)	33	NM_001024560	225861	Mm.20071	NM_001024560	ENSMUSG00000056185	Snx32	B930037P14Rik|Snx6b	sorting nexin 32	protein-coding
mm_34121.1	chr4	139238894	139238906	+	1	NA	intron (NM_001271405, intron 1 of 8)	intron (NM_001271405, intron 1 of 8)	44789	NM_001271405	12345	Mm.2945	NM_009798	ENSMUSG00000028745	Capzb	1700120C01Rik|AI325129|CPB1|CPB2|CPbeat2|CPbeta1|CPbeta2|Cappb1	capping protein (actin filament) muscle Z-line, beta	protein-coding
mm_47378.1	chr5	122989087	122989111	-	1	NA	promoter-TSS (NM_001003953)	promoter-TSS (NM_001003953)	0	NM_001003953	30841	Mm.86406	NM_013910	ENSMUSG00000029475	Kdm2b	Cxxc2|Fbl10|Fbxl10|Jhdm1b|PCCX2	lysine (K)-specific demethylase 2B	protein-coding
mm_65602.1	chr7	27361329	27361340	-	1	NA	intron (NM_001199235, intron 15 of 17)	intron (NM_001199235, intron 15 of 17)	-5326	NM_138676	192192	Mm.21297	NM_138676	ENSMUSG00000089832	Shkbp1	B930062H15Rik|Sb1	Sh3kbp1 binding protein 1	protein-coding
mm_72896.1	chr8	90858081	90858086	+	1	NA	intron (NM_177224, intron 2 of 39)	B1F|SINE|Alu	29248	NM_177224	109151	Mm.100615	NM_177224	ENSMUSG00000056608	Chd9	1810014J18Rik|9030205D12Rik|A330063D19Rik|AD013|PRIC320|mKIAA0308	chromodomain helicase DNA binding protein 9	protein-coding
mm_124147.1	chr14	88470944	88471022	-	1	NA	exon (NM_178685, exon 2 of 3)	exon (NM_178685, exon 2 of 3)	413	NM_178685	219257	Mm.128861	NM_178685	ENSMUSG00000050505	Pcdh20	C630015B17Rik|Pcdh13	protocadherin 20	protein-coding
mm_96895.1	chr11	70437669	70437679	+	1	NA	promoter-TSS (NR_106064)	promoter-TSS (NR_106064)	-581	NR_106064	102465670		NR_106064	ENSMUSG00000099109	Mir7115	Gm27902|mmu-mir-7115	microRNA 7115	ncRNA
mm_111471.1	chr12	98575036	98575048	-	1	NA	promoter-TSS (NM_001316665)	promoter-TSS (NM_001316665)	85	NM_001316664	72258	Mm.196158	NM_029911	ENSMUSG00000033854	Kcnk10	1700024D23Rik|3010005K24Rik|Trek2	potassium channel, subfamily K, member 10	protein-coding
mm_168970.1	chr12	83360703	83360722	+	1	NA	intron (NM_058212, intron 2 of 8)	BGLII|LTR|ERVK	127024	NM_001267626	70127	Mm.151308	NM_058212	ENSMUSG00000021221	Dpf3	2810403B03Rik|6530402L11Rik|BAF45C|C78788|CERD4|cer-d4	D4, zinc and double PHD fingers, family 3	protein-coding
mm_155132.1	chrX	49493106	49493114	+	1	NA	intron (NM_001081123, intron 1 of 12)	intron (NM_001081123, intron 1 of 12)	22660	NM_001081123	75404	Mm.44305	NM_001081123	ENSMUSG00000036198	Arhgap36	1100001E04Rik|rho-gap	Rho GTPase activating protein 36	protein-coding
mm_135785.1	chr16	57071228	57071237	-	1	NA	intron (NM_183281, intron 1 of 6)	intron (NM_183281, intron 1 of 6)	114	NM_183281	69457	Mm.58105	NM_183281	ENSMUSG00000046748	Tmem45a2	2310005G13Rik	transmembrane protein 45A2	protein-coding
mm_1185.1	chr1	62483395	62483410	+	1	NA	intron (NM_001081050, intron 20 of 22)	intron (NM_001081050, intron 20 of 22)	-219915	NM_001077406	18187	Mm.266341	NM_010939	ENSMUSG00000025969	Nrp2	1110048P06Rik|Np-2|Np2|Npn-2|Npn2	neuropilin 2	protein-coding
mm_99042.1	chr11	98964812	98964827	+	1	NA	intron (NM_001176528, intron 1 of 7)	intron (NM_001176528, intron 1 of 7)	4348	NM_001176528	19401	Mm.439744	NM_009024	ENSMUSG00000037992	Rara	Nr1b1|RAR|RARalpha1	retinoic acid receptor, alpha	protein-coding
mm_24234.1	chr3	88950702	88950749	+	1	NA	promoter-TSS (NM_022994)	promoter-TSS (NM_022994)	-443	NM_001164533	65111	Mm.29028	NM_022994	ENSMUSG00000068921	Dap3	4921514D13Rik|DAP-3|MRP-S29|S29mt	death associated protein 3	protein-coding
mm_46317.1	chr5	100604196	100604229	-	1	NA	Intergenic	Intergenic	-32007	NM_139198	231507	Mm.34609	NM_139198	ENSMUSG00000029322	Plac8	C15|D5Wsu111e	placenta-specific 8	protein-coding
mm_25972.1	chr3	132904815	132904866	+	1	NA	exon (NM_001287103, exon 8 of 12)	exon (NM_001287103, exon 8 of 12)	-26244	NR_102298	101243624	Mm.306256	NR_102297	ENSMUSG00000106230	Gm29811	-	predicted gene, 29811	ncRNA
mm_146207.1	chr18	76856156	76856166	+	1	NA	promoter-TSS (NM_001109743)	promoter-TSS (NM_001109743)	-244	NM_001109743	664805	Mm.329543	NM_001109743	ENSMUSG00000091519	Skor2	Corl2|EG664805|Fussel18|Gm7348	SKI family transcriptional corepressor 2	protein-coding
mm_57009.1	chr6	121131014	121131049	-	1	NA	promoter-TSS (NM_001270475)	promoter-TSS (NM_001270475)	-9	NM_001270475	194401	Mm.122399	NM_153396	ENSMUSG00000051586	Mical3	C130040D16Rik|Mical-3|mKIAA1364	microtubule associated monooxygenase, calponin and LIM domain containing 3	protein-coding
mm_35421.1	chr4	35157405	35157500	-	1	NA	promoter-TSS (NM_178061)	promoter-TSS (NM_178061)	32	NM_178061	214944	Mm.32968	NM_178061	ENSMUSG00000073910	Mob3b	8430436F23Rik|A430018A01Rik|Mobkl2b	MOB kinase activator 3B	protein-coding
mm_60157.1	chr7	39518109	39518117	+	1	NA	intron (NM_001004139, intron 1 of 3)	intron (NM_001004139, intron 1 of 3)	347	NM_001004139	70227	Mm.333800	NM_001004139	ENSMUSG00000068959	Zfp619	3000002G13Rik	zinc finger protein 619	protein-coding
mm_56864.1	chr6	118419337	118419351	-	1	NA	promoter-TSS (NM_194339)	promoter-TSS (NM_194339)	73	NM_194339	213895	Mm.25269	NM_194339	ENSMUSG00000030138	Bms1	AA408648|AU020092|AU043373|BB007109|BC030906|Bms1l|mKIAA0187	BMS1, ribosome biogenesis factor	protein-coding
mm_131166.1	chr16	7039570	7039582	+	1	NA	intron (NM_021477, intron 5 of 16)	intron (NM_021477, intron 5 of 16)	-30259	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_97950.1	chr11	83664600	83664612	+	1	NA	TTS (NM_013652)	TTS (NM_013652)	2022	NM_013652	20303	Mm.244263	NM_013652	ENSMUSG00000018930	Ccl4	AT744.1|Act-2|MIP-1B|Mip1b|Scya4	chemokine (C-C motif) ligand 4	protein-coding
mm_122659.1	chr14	51912147	51912169	-	1	NA	intron (NM_013864, intron 1 of 15)	intron (NM_013864, intron 1 of 15)	1330	NM_001145959	29811	Mm.26722	NM_013864	ENSMUSG00000004558	Ndrg2	AI182517|AU040374|Ndr2|SYLD	N-myc downstream regulated gene 2	protein-coding
mm_114977.1	chr13	97244059	97244065	+	1	NA	intron (NM_007930, intron 1 of 2)	intron (NM_007930, intron 1 of 2)	2957	NM_007930	13803	Mm.241073	NM_007930	ENSMUSG00000041773	Enc1	Nrpb|PIG10	ectodermal-neural cortex 1	protein-coding
mm_95611.1	chr11	53457274	53457300	+	1	NA	promoter-TSS (NM_027917)	promoter-TSS (NM_027917)	82	NM_027917	71774	Mm.274370	NM_027917	ENSMUSG00000018387	Shroom1	Apx|Shrm1	shroom family member 1	protein-coding
mm_1874.1	chr1	85601016	85601018	+	1	NA	5' UTR (NM_001013817, exon 1 of 17)	5' UTR (NM_001013817, exon 1 of 17)	314	NM_001013817	434484	Mm.445821	NM_001013817	ENSMUSG00000070031	Sp140	-	Sp140 nuclear body protein	protein-coding
mm_44547.1	chr5	24577478	24577493	-	1	NA	promoter-TSS (NM_001190443)	promoter-TSS (NM_001190443)	-18	NM_001190443	27407	Mm.21629	NM_013853	ENSMUSG00000028953	Abcf2	0710005O05Rik|Drr3|E430001O06	ATP-binding cassette, sub-family F (GCN20), member 2	protein-coding
mm_64119.1	chr7	141079785	141079806	+	1	NA	promoter-TSS (NM_019762)	promoter-TSS (NM_019762)	26	NM_019762	56460	Mm.350037	NM_019762	ENSMUSG00000054065	Pkp3	2310056L12Rik	plakophilin 3	protein-coding
mm_156456.1	chrX	142825622	142825657	+	1	NA	intron (NM_001199360, intron 5 of 6)	L2a|LINE|L2	86639	NR_030523	723976		NR_030523	ENSMUSG00000076011	Mir652	Mirn652|miRX|mmu-mir-652	microRNA 652	ncRNA
mm_29.1	chr1	6214807	6214817	+	1	NA	5' UTR (NM_009826, exon 1 of 24)	5' UTR (NM_009826, exon 1 of 24)	150	NM_009826	12421	Mm.293811	NM_009826	ENSMUSG00000025907	Rb1cc1	2900055E04Rik|5930404L04Rik|Cc1|FIP200|LaXp180	RB1-inducible coiled-coil 1	protein-coding
mm_92256.1	chr10	70644696	70644707	-	1	NA	intron (NR_045291, intron 1 of 5)	Lx9|LINE|L1	7224	NR_045291	319646	Mm.483039	NR_045291	ENSMUSG00000037747	D630013N20Rik	-	RIKEN cDNA D630013N20 gene	ncRNA
mm_109849.1	chr12	4595154	4595156	-	1	NA	intron (NM_011365, intron 1 of 38)	intron (NM_011365, intron 1 of 38)	2147	NM_001198968	20403	Mm.341204	NM_011365	ENSMUSG00000020640	Itsn2	AI327390|Ese2|Sh3d1B|Sh3p18|mKIAA1256	intersectin 2	protein-coding
mm_144879.1	chr18	36793833	36793849	+	1	NA	promoter-TSS (NM_025594)	promoter-TSS (NM_025594)	-82	NM_025594	66492	Mm.251155	NM_025594	ENSMUSG00000001383	Zmat2	2610510D14Rik|2900082I05Rik	zinc finger, matrin type 2	protein-coding
mm_123687.1	chr14	69635121	69635144	-	1	NA	intron (NM_033325, intron 2 of 13)	B1_Mus2|SINE|Alu	25656	NM_033325	94352	Mm.116714	NM_033325	ENSMUSG00000034205	Loxl2	1110004B06Rik|4930526G11Rik|9430067E15Rik	lysyl oxidase-like 2	protein-coding
mm_107345.1	chr12	32819638	32819649	+	1	NA	promoter-TSS (NM_021524)	promoter-TSS (NM_021524)	-692	NM_021524	59027	Mm.202727	NM_021524	ENSMUSG00000020572	Nampt	1110035O14Rik|AI314458|AI480535|NAmPRTase|Pbef|Pbef1|Visfatin	nicotinamide phosphoribosyltransferase	protein-coding
mm_169632.1	chr15	47029500	47029505	+	1	NA	Intergenic	MT2_Mm|LTR|ERVL	406197	NR_045811	75281	Mm.159487	NR_045811	ENSMUSG00000051198	4930548G14Rik	-	RIKEN cDNA 4930548G14 gene	ncRNA
mm_117114.1	chr13	60508786	60508820	-	1	NA	Intergenic	Intergenic	-93144	NM_001285917	69635	Mm.24103	NM_029653	ENSMUSG00000021559	Dapk1	D13Ucla1|DAP-Kinase	death associated protein kinase 1	protein-coding
mm_112783.1	chr13	20096012	20096037	+	1	NA	intron (NM_080288, intron 1 of 21)	intron (NM_080288, intron 1 of 21)	5517	NM_080288	140580	Mm.342392	NM_080288	ENSMUSG00000041112	Elmo1	6330578D22Rik|C230095H21Rik|CED-12	engulfment and cell motility 1	protein-coding
mm_110144.1	chr12	26448612	26448644	-	1	NA	exon (NM_021384, exon 4 of 6)	exon (NM_021384, exon 4 of 6)	7824	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_81576.1	chr9	110422325	110422346	+	1	NA	exon (NM_008694, exon 4 of 4)	exon (NM_008694, exon 4 of 4)	2527	NM_008694	18054	Mm.236225	NM_008694	ENSMUSG00000032484	Ngp	bectenecin	neutrophilic granule protein	protein-coding
mm_162756.1	chr10	61175621	61175637	+	1	NA	intron (NM_001017409, intron 1 of 3)	intron (NM_001017409, intron 1 of 3)	367	NM_023064	65971	Mm.30227	NM_023064	ENSMUSG00000020096	Tbata	1700021K02Rik|AI428928|Spatial|Titest	thymus, brain and testes associated	protein-coding
mm_92402.1	chr10	76709299	76709356	-	1	NA	3' UTR (NM_009933, exon 35 of 35)	3' UTR (NM_009933, exon 35 of 35)	16717	NM_009933	12833	Mm.2509	NM_009933	ENSMUSG00000001119	Col6a1	AI747156|Col6a-1	collagen, type VI, alpha 1	protein-coding
mm_19270.1	chr2	85086457	85086464	-	1	NA	promoter-TSS (NR_040504)	promoter-TSS (NR_040504)	1	NR_040504	74687	Mm.66996	NR_040504	ENSMUSG00000086969	4930443O20Rik	-	RIKEN cDNA 4930443O20 gene	ncRNA
mm_15554.1	chr2	158439838	158439841	+	1	NA	intron (NM_001291137, intron 10 of 30)	intron (NM_001291137, intron 10 of 30)	29986	NM_001291138	228850	Mm.398185	NM_177227	ENSMUSG00000027652	Ralgapb	AI507211|B230339M05Rik|p170	Ral GTPase activating protein, beta subunit (non-catalytic)	protein-coding
mm_102796.1	chr11	68852984	68853003	-	1	NA	5' UTR (NM_023668, exon 1 of 9)	5' UTR (NM_023668, exon 1 of 9)	138	NM_023668	83431	Mm.31979	NM_023668	ENSMUSG00000018736	Ndel1	2600006O07Rik|MITAP1|NUDEL|mNudel	nudE neurodevelopment protein 1 like 1	protein-coding
mm_148442.1	chr19	3949014	3949042	+	1	NA	3' UTR (NM_019449, exon 11 of 11)	3' UTR (NM_019449, exon 11 of 11)	-9780	NM_028545	73458	Mm.482922	NM_028545	ENSMUSG00000037263	Aldh3b3	1700055N04Rik	aldehyde dehydrogenase 3 family, member B3	protein-coding
mm_22233.1	chr2	174438308	174438339	-	1	NA	exon (NM_022325, exon 2 of 6)	exon (NM_022325, exon 2 of 6)	716	NM_022325	64138	Mm.156919	NM_022325	ENSMUSG00000016256	Ctsz	AI787083|AU019819|CTSX|D2Wsu143e	cathepsin Z	protein-coding
mm_116090.1	chr13	28718801	28718805	-	1	NA	intron (NR_045053, intron 3 of 8)	intron (NR_045053, intron 3 of 8)	-7930	NR_105787	102466635		NR_105787	ENSMUSG00000099158	Mir6368	Gm27800|mmu-mir-6368	microRNA 6368	ncRNA
mm_4998.1	chr1	191906777	191906795	+	1	NA	promoter-TSS (NM_009579)	promoter-TSS (NM_009579)	5	NM_009579	22782	Mm.9024	NM_009579	ENSMUSG00000037434	Slc30a1	AI839647|C130040I11Rik|Znt1	solute carrier family 30 (zinc transporter), member 1	protein-coding
mm_12524.1	chr2	72174238	72174251	+	1	NA	intron (NM_019688, intron 6 of 29)	intron (NM_019688, intron 6 of 29)	-111393	NM_023057	65964	Mm.304143	NM_023057	ENSMUSG00000004085	Map3k20	AV006891|B230120H23Rik|MLTK|MLTKalpha|MLTKbeta|Zak	mitogen-activated protein kinase kinase kinase 20	protein-coding
mm_62413.1	chr7	101301422	101301433	+	1	NA	intron (NM_001111111, intron 1 of 17)	intron (NM_001111111, intron 1 of 17)	661	NM_001111111	73683	Mm.275744	NM_001111111	ENSMUSG00000047767	Atg16l2	2410118P20Rik	autophagy related 16-like 2 (S. cerevisiae)	protein-coding
mm_133722.1	chr16	93711925	93711937	+	1	NA	promoter-TSS (NM_026700)	promoter-TSS (NM_026700)	24	NM_027293	70028	Mm.23230	NM_026700	ENSMUSG00000022946	Dopey2	0610038M01Rik|2610510B01Rik|AI503246|C21orf5|mKIAA0933	dopey family member 2	protein-coding
mm_36914.1	chr4	108071644	108071652	-	1	NA	intron (NM_011327, intron 11 of 15)	intron (NM_011327, intron 11 of 15)	-15709	NR_105823	102465213		NR_105823	ENSMUSG00000098980	Mir6397	Gm28004|mmu-mir-6397	microRNA 6397	ncRNA
mm_58721.1	chr7	13024369	13024383	+	1	NA	5' UTR (NM_011588, exon 1 of 17)	5' UTR (NM_011588, exon 1 of 17)	224	NM_011588	21849	Mm.15701	NM_011588	ENSMUSG00000005566	Trim28	AA408787|KAP-1|KRIP-1|MommeD9|Tif1b|Tif1beta	tripartite motif-containing 28	protein-coding
mm_122390.1	chr14	40965603	40965605	-	1	NA	intron (NM_145928, intron 1 of 8)	PB1D10|SINE|Alu	1292	NM_145928	52588	Mm.28876	NM_145928	ENSMUSG00000037824	Tspan14	AA958793|D14Ertd226e|Tm4sf14|tspan-14	tetraspanin 14	protein-coding
mm_107933.1	chr12	71309877	71309910	+	1	NA	promoter-TSS (NM_021532)	promoter-TSS (NM_021532)	9	NM_001190466	59036	Mm.46662	NM_021532	ENSMUSG00000044548	Dact1	4921528D17Rik|AI115603|DAPPER|DAPPER1|FRODO|Frd1|Frodo1|MDpr1|MTNG3|THYEX3	dishevelled-binding antagonist of beta-catenin 1	protein-coding
mm_14389.1	chr2	129800583	129800641	+	1	NA	promoter-TSS (NM_183262)	promoter-TSS (NM_183262)	95	NM_001038635	67333	Mm.389329	NM_183262	ENSMUSG00000037885	Stk35	1700054C12Rik|CLIK1|Stk35l1	serine/threonine kinase 35	protein-coding
mm_22867.1	chr3	28805499	28805521	+	1	NA	promoter-TSS (NM_026517)	promoter-TSS (NM_026517)	-1	NM_001347226	68028	Mm.371630	NM_026517	ENSMUSG00000039221	Rpl22l1	3110001N18Rik|AU041196	ribosomal protein L22 like 1	protein-coding
mm_21833.1	chr2	165473188	165473202	-	1	NA	promoter-TSS (NM_054055)	promoter-TSS (NM_054055)	2	NM_054055	114644	Mm.250738	NM_054055	ENSMUSG00000018459	Slc13a3	NaDC-3|NaDC3|SDCT2	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 3	protein-coding
mm_130362.1	chr15	97770211	97770232	-	1	NA	Intergenic	Intergenic	-2555	NM_001177811	223864	Mm.24028	NM_144850	ENSMUSG00000022469	Rapgef3	2310016P22Rik|9330170P05Rik|Epac|Epac1	Rap guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_20438.1	chr2	129306793	129306805	-	1	NA	non-coding (NR_040371, exon 5 of 5)	non-coding (NR_040371, exon 5 of 5)	3173	NM_010554	16175	Mm.15534	NM_010554	ENSMUSG00000027399	Il1a	Il-1a	interleukin 1 alpha	protein-coding
mm_126599.1	chr15	82377188	82377191	+	1	NA	intron (NM_019823, intron 1 of 9)	intron (NM_019823, intron 1 of 9)	3071	NM_019823	56448	Mm.474216	NM_019823	ENSMUSG00000061740	Cyp2d22	2D22	cytochrome P450, family 2, subfamily d, polypeptide 22	protein-coding
mm_40265.1	chr5	38500163	38500168	+	1	NA	intron (NM_145559, intron 1 of 10)	RMER19C|LTR|ERVK	1987	NM_145559	117591	Mm.260137	NM_145559	ENSMUSG00000005107	Slc2a9	Glut9|SLC2A9B|SLC2a9A	solute carrier family 2 (facilitated glucose transporter), member 9	protein-coding
mm_20098.1	chr2	121036675	121036689	-	1	NA	5' UTR (NM_013513, exon 1 of 13)	5' UTR (NM_013513, exon 1 of 13)	195	NM_013513	13828	Mm.240051	NM_013513	ENSMUSG00000023216	Epb42	Epb4.2	erythrocyte membrane protein band 4.2	protein-coding
mm_125443.1	chr15	46324581	46324587	+	1	NA	promoter-TSS (NR_045509)	promoter-TSS (NR_045509)	-1	NR_045509	71120	Mm.158571	NR_045509	ENSMUSG00000099751	1700022A22Rik	4933413D07Rik	RIKEN cDNA 1700022A22 gene	ncRNA
mm_121221.1	chr14	103055155	103055165	+	1	NA	exon (NM_008392, exon 5 of 5)	exon (NM_008392, exon 5 of 5)	8148	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_157465.1	chrX	46293462	46293475	-	1	NA	intron (NR_045440, intron 2 of 2)	ORR1B1|LTR|ERVL-MaLR	35443	NR_045440	75133	Mm.417818	NR_045440	ENSMUSG00000085157	4930515L19Rik	-	RIKEN cDNA 4930515L19 gene	ncRNA
mm_29037.1	chr3	102778327	102778342	-	1	NA	intron (NM_001165940, intron 1 of 2)	intron (NM_001165940, intron 1 of 2)	4380	NM_009432	22094	Mm.110730	NM_009432	ENSMUSG00000027857	Tshb	-	thyroid stimulating hormone, beta subunit	protein-coding
mm_121381.1	chr14	118937926	118937992	+	1	NA	promoter-TSS (NM_008929)	promoter-TSS (NM_008929)	27	NM_008929	100037258	Mm.12616	NM_008929	ENSMUSG00000022136	Dnajc3	AA408985|AU067833|Dnajc3a|Dnajc3b|Prkri|mp58|p58|p58IPK	DnaJ heat shock protein family (Hsp40) member C3	protein-coding
mm_25974.1	chr3	133091828	133091842	+	1	NA	promoter-TSS (NM_026231)	promoter-TSS (NM_026231)	-20	NM_027927	71793	Mm.246726	NM_027927	ENSMUSG00000028016	Ints12	1110020M19Rik|2810027J24Rik|4930529N21Rik|A230056J18Rik|AI666778|Phf22|int12	integrator complex subunit 12	protein-coding
mm_68220.1	chr7	104411100	104411110	-	1	NA	exon (NM_009099, exon 8 of 8)	exon (NM_009099, exon 8 of 8)	-52459	NM_175648	244183	Mm.347647	NM_175648	ENSMUSG00000052749	Trim30b	A530023O14Rik|Trim30-1	tripartite motif-containing 30B	protein-coding
mm_91439.1	chr10	33927028	33927041	-	1	NA	TTS (NM_028287)	TTS (NM_028287)	21923	NM_001162957	212892	Mm.131949	NM_001162957	ENSMUSG00000039552	Rsph4a	A230081C05|Rshl3	radial spoke head 4 homolog A (Chlamydomonas)	protein-coding
mm_46015.1	chr5	90900709	90900753	-	1	NA	Intergenic	Intergenic	-3168	NM_009140	20310	Mm.4979	NM_009140	ENSMUSG00000058427	Cxcl2	CINC-2a|GROb|Gro2|MIP-2|MIP-2a|Mgsa-b|Mip2|Scyb|Scyb2	chemokine (C-X-C motif) ligand 2	protein-coding
mm_90390.1	chr10	127321916	127321930	+	1	NA	promoter-TSS (NM_001285785)	promoter-TSS (NM_001285785)	-41	NM_001285785	216445	Mm.227198	NM_146011	ENSMUSG00000040345	Arhgap9	AU043488	Rho GTPase activating protein 9	protein-coding
mm_94148.1	chr10	128743870	128743910	-	1	NA	5' UTR (NM_016811, exon 1 of 24)	5' UTR (NM_016811, exon 1 of 24)	166	NM_016811	13139	Mm.291235	NM_016811	ENSMUSG00000025357	Dgka	80kDa|AW146112|Dagk1	diacylglycerol kinase, alpha	protein-coding
mm_171462.1	chr4	145670778	145670785	+	1	NA	promoter-TSS (NM_001103158)	promoter-TSS (NM_001103158)	84	NM_001103158	100041379	Mm.276881	NM_001103158	ENSMUSG00000058186	Zfp980	Gm13242|OTTMUSG00000011070	zinc finger protein 980	protein-coding
mm_134894.1	chr16	29845724	29845769	-	1	NA	Intergenic	Intergenic	133378	NR_037689	328657	Mm.425982	NM_001033403		Gm1968	-	predicted gene 1968	ncRNA
mm_159999.1	chr6	119390162	119390162	-	1	NA	intron (NM_197985, intron 1 of 7)	intron (NM_197985, intron 1 of 7)	27321	NM_197985	68465	Mm.291826	NM_197985	ENSMUSG00000030168	Adipor2	1110001I14Rik|ADCR2|AI115388|AW554121|D6Ucla1e|Paqr2	adiponectin receptor 2	protein-coding
mm_167833.1	chr9	124424259	124424310	-	1	NA	non-coding (NR_015516, exon 1 of 1)	non-coding (NR_015516, exon 1 of 1)	497	NR_015516	75135	Mm.476814	NR_015516		4930526I15Rik	1600027J15Rik	RIKEN cDNA 4930526I15 gene	ncRNA
mm_72785.1	chr8	86806383	86806385	+	1	NA	Intergenic	RSINE1|SINE|B4	-60378	NM_009172	20437	Mm.324553	NM_009172	ENSMUSG00000036840	Siah1a	AA982064|AI853500|Sinh1a	seven in absentia 1A	protein-coding
mm_129730.1	chr15	82029587	82029604	-	1	NA	exon (NM_010247, exon 9 of 13)	exon (NM_010247, exon 9 of 13)	13226	NM_010247	14375	Mm.288809	NM_010247	ENSMUSG00000022471	Xrcc6	70kDa|G22p1|Ku70	X-ray repair complementing defective repair in Chinese hamster cells 6	protein-coding
mm_68623.1	chr7	118116172	118116198	-	1	NA	promoter-TSS (NM_170669)	promoter-TSS (NM_170669)	-38	NM_170669	267019	Mm.288212	NM_170669	ENSMUSG00000008683	Rps15a	A630031B11Rik	ribosomal protein S15A	protein-coding
mm_3420.1	chr1	146495600	146495606	+	1	NA	promoter-TSS (NM_153539)	promoter-TSS (NM_153539)	-63	NM_153539	215378	Mm.441817	NM_153539	ENSMUSG00000035131	Brinp3	B830045N13Rik|Fam5c	bone morphogenetic protein/retinoic acid inducible neural specific 3	protein-coding
mm_156224.1	chrX	135742687	135742744	+	1	NA	promoter-TSS (NM_001009575)	promoter-TSS (NM_001009575)	23	NM_001005385	67298	Mm.271980	NM_026081	ENSMUSG00000043384	Gprasp1	2210415K24Rik|3110031O14Rik|C87852|GASP|GASP1	G protein-coupled receptor associated sorting protein 1	protein-coding
mm_117140.1	chr13	60941917	60941923	-	1	NA	promoter-TSS (NM_009411)	promoter-TSS (NM_009411)	15	NM_009411	21984	Mm.2372	NM_009411	ENSMUSG00000033834	Tpbpa	AV033951|Tb-1|Tb1|Tpbp|b2b1247Clo	trophoblast specific protein alpha	protein-coding
mm_17159.1	chr2	25234204	25234223	-	1	NA	promoter-TSS (NM_080854)	promoter-TSS (NM_080854)	21	NM_080854	142681	Mm.346652	NM_080854	ENSMUSG00000006469	Slc34a3	AI649385|Npt2c|Npt2c-v1|NptIIc|naPi-2c	solute carrier family 34 (sodium phosphate), member 3	protein-coding
mm_28799.1	chr3	96197581	96197634	-	1	NA	promoter-TSS (NM_026975)	promoter-TSS (NM_026975)	-21	NM_026975	69168	Mm.104531	NM_026975	ENSMUSG00000015943	Bola1	1810037G04Rik	bolA-like 1 (E. coli)	protein-coding
mm_55537.1	chr6	70773859	70773895	-	1	NA	intron (NM_009075, intron 6 of 8)	intron (NM_009075, intron 6 of 8)	18298	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_882.1	chr1	52568477	52568487	+	1	NA	Intergenic	RLTR51A_Mm|LTR|ERVK?	-62223	NR_024590	227094	Mm.83541	NM_172654	ENSMUSG00000043015	Nemp2	5330401P04Rik|9830163O08|Tmem194b	nuclear envelope integral membrane protein 2	protein-coding
mm_80336.1	chr9	75052143	75052153	+	1	NA	intron (NM_021548, intron 1 of 2)	intron (NM_021548, intron 1 of 2)	14416	NM_021548	59046	Mm.247837	NM_021548	ENSMUSG00000007656	Arpp19	19kDa|2700024H10Rik|ARPP-19|AW559096|Arpp12	cAMP-regulated phosphoprotein 19	protein-coding
mm_11091.1	chr2	27886480	27886493	+	1	NA	promoter-TSS (NM_015734)	promoter-TSS (NM_015734)	61	NM_015734	12831	Mm.7281	NM_015734	ENSMUSG00000026837	Col5a1	AI413331	collagen, type V, alpha 1	protein-coding
mm_40654.1	chr5	65131000	65131010	+	1	NA	promoter-TSS (NM_175174)	promoter-TSS (NM_175174)	-226	NM_175174	71778	Mm.10281	NM_175174	ENSMUSG00000054920	Klhl5	1300013C10Rik	kelch-like 5	protein-coding
mm_60347.1	chr7	44358534	44358547	+	1	NA	TTS (NM_001034115)	TTS (NM_001034115)	16490	NM_027049	69349	Mm.358922	NM_027049	ENSMUSG00000008028	1700008O03Rik	-	RIKEN cDNA 1700008O03 gene	protein-coding
mm_52202.1	chr6	100760260	100760274	+	1	NA	intron (NM_198612, intron 3 of 6)	intron (NM_198612, intron 3 of 6)	55533	NM_198612	232313	Mm.272037	NM_198612	ENSMUSG00000030074	Gxylt2	Glt8d4|Gm152	glucoside xylosyltransferase 2	protein-coding
mm_29719.1	chr3	124426027	124426031	-	1	NA	promoter-TSS (NM_027939)	promoter-TSS (NM_027939)	-1	NM_027939	71824	Mm.331353	NM_027939	ENSMUSG00000027973	1700006A11Rik	-	RIKEN cDNA 1700006A11 gene	protein-coding
mm_50522.1	chr6	49043992	49044007	+	1	NA	exon (NM_053110, exon 3 of 11)	exon (NM_053110, exon 3 of 11)	7481	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_95227.1	chr11	44518954	44518958	+	1	NA	promoter-TSS (NM_001166553)	promoter-TSS (NM_001166553)	-8	NM_028862	74315	Mm.156771	NM_028862	ENSMUSG00000019189	Rnf145	3732413I11Rik|TMRF1	ring finger protein 145	protein-coding
mm_21286.1	chr2	156970485	156970494	-	1	NA	intron (NM_013865, intron 1 of 15)	MLT1F2|LTR|ERVL-MaLR	21622	NM_013865	29812	Mm.279256	NM_013865	ENSMUSG00000027634	Ndrg3	4833415O14Rik|AI747193|Ndr3	N-myc downstream regulated gene 3	protein-coding
mm_85641.1	chr9	107655301	107655343	-	1	NA	exon (NM_001199218, exon 13 of 16)	exon (NM_001199218, exon 13 of 16)	12077	NM_023805	76257	Mm.296560	NM_023805	ENSMUSG00000010064	Slc38a3	0610012J02Rik|D9Ucla2|Nat1|Slc38-3|Sn1|Snat3|mNAT	solute carrier family 38, member 3	protein-coding
mm_108430.1	chr12	82245731	82245745	+	1	NA	intron (NM_001167983, intron 2 of 23)	L1M4c|LINE|L1	-65611	NM_172579	217692	Mm.261333	NM_172579	ENSMUSG00000042700	Sipa1l1	4931426N11Rik|AW213287|Spar|mKIAA0440	signal-induced proliferation-associated 1 like 1	protein-coding
mm_115874.1	chr13	21721816	21721867	-	1	NA	promoter-TSS (NM_178200)	promoter-TSS (NM_178200)	-203	NM_178200	319186	Mm.277425	NM_178200	ENSMUSG00000096807	Hist1h2bm	H2b-291b	histone cluster 1, H2bm	protein-coding
mm_146807.1	chr18	20746127	20746135	-	1	NA	5' UTR (NM_019737, exon 1 of 9)	5' UTR (NM_019737, exon 1 of 9)	273	NM_019737	56386	Mm.393827	NM_019737	ENSMUSG00000056124	B4galt6	AA536803|AU022389	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 6	protein-coding
mm_33760.1	chr4	134343684	134343704	+	1	NA	intron (NM_001346578, intron 1 of 7)	intron (NM_001346578, intron 1 of 7)	228	NM_001346578	230810	Mm.358876	NM_001039677	ENSMUSG00000028836	Slc30a2	ZnT-2|Znt2	solute carrier family 30 (zinc transporter), member 2	protein-coding
mm_159962.1	chr6	89940666	89940666	-	1	NA	promoter-TSS (NM_011684)	promoter-TSS (NM_011684)	-159	NM_011684	22297	Mm.431981	NM_011684	ENSMUSG00000044248	Vmn1r45	V1RA9|V1r2|V1ra11|V1ra2|mV1R2	vomeronasal 1 receptor 45	protein-coding
mm_128525.1	chr15	54481879	54481879	-	1	NA	Intergenic	B4|SINE|B4	71105	NM_173422	239447	Mm.82400	NM_173422	ENSMUSG00000038591	Colec10	CL-L1	collectin sub-family member 10	protein-coding
mm_126622.1	chr15	83166068	83166086	+	1	NA	exon (NM_029787, exon 2 of 9)	exon (NM_029787, exon 2 of 9)	6131	NM_029787	109754	Mm.22560	NM_029787	ENSMUSG00000018042	Cyb5r3	0610016L08Rik|2500002N19Rik|C85115|Dia-1|Dia1|WU:AL591952.1-001|WU:AL591952.1-002|WU:AL591952.1-003|WU:Cyb5r3	cytochrome b5 reductase 3	protein-coding
mm_4564.1	chr1	177447448	177447458	+	1	NA	exon (NM_013915, exon 1 of 1)	exon (NM_013915, exon 1 of 1)	1632	NM_013915	30928	Mm.330700	NM_013915	ENSMUSG00000063659	Zbtb18	RP58|Zfp238|Znf238	zinc finger and BTB domain containing 18	protein-coding
mm_94720.1	chr11	20631957	20632006	+	1	NA	promoter-TSS (NM_001038625)	promoter-TSS (NM_001038625)	4	NM_001038625	58172	Mm.339676	NM_021372	ENSMUSG00000049800	Sertad2	AB041541|AU021878|Kiaa0127|MNCb-1504|SEI-2|Sei2|TRIP-Br2|mKIAA0127	SERTA domain containing 2	protein-coding
mm_125836.1	chr15	74958485	74958517	+	1	NA	exon (NM_001164036, exon 4 of 4)	exon (NM_001164036, exon 4 of 4)	3395	NM_001164040	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_154836.1	chrX	19160625	19160637	+	1	NA	Intergenic	Intergenic	-13660	NR_029807	723828		NR_029807	ENSMUSG00000065471	Mir222	Mirn222|mir-222|mmu-mir-222	microRNA 222	ncRNA
mm_69736.1	chr7	140882275	140882330	-	1	NA	promoter-TSS (NM_001127351)	promoter-TSS (NM_001127351)	7	NM_022433	64384	Mm.29760	NM_022433	ENSMUSG00000025486	Sirt3	2310003L23Rik|AI848213|Sir2l3	sirtuin 3	protein-coding
mm_2810.1	chr1	130874166	130874171	+	1	NA	exon (NM_026976, exon 2 of 8)	exon (NM_026976, exon 2 of 8)	8391	NM_026976	69169	Mm.46042	NM_026976	ENSMUSG00000042474	Fcmr	1810037B05Rik|Faim3|FcmuR|Toso	Fc fragment of IgM receptor	protein-coding
mm_15215.1	chr2	154223738	154223776	+	1	NA	promoter-TSS (NM_144890)	promoter-TSS (NM_144890)	15	NM_144890	228802	Mm.167411	NM_144890	ENSMUSG00000038572	Bpifb5	Lplunc5	BPI fold containing family B, member 5	protein-coding
mm_155526.1	chrX	74271397	74271509	+	1	NA	intron (NM_052835, intron 2 of 6)	intron (NM_052835, intron 2 of 6)	637	NM_052835	110954	Mm.100113	NM_052835	ENSMUSG00000008682	Rpl10	D0HXS648|DXHXS648|DXHXS648E|QM|QM16	ribosomal protein L10	protein-coding
mm_84803.1	chr9	77252067	77252076	-	1	NA	intron (NM_027150, intron 1 of 7)	intron (NM_027150, intron 1 of 7)	95799	NM_027150	69642	Mm.35008	NM_027150	ENSMUSG00000032355	Mlip	2310046A06Rik|AI931782|CIP	muscular LMNA-interacting protein	protein-coding
mm_66429.1	chr7	44668113	44668145	-	1	NA	intron (NM_001271540, intron 1 of 41)	intron (NM_001271540, intron 1 of 41)	-2626	NM_028021	71960	Mm.158289	NM_028021	ENSMUSG00000030739	Myh14	2400004E04Rik|II-C|NHMCII|NMHC II-C	myosin, heavy polypeptide 14	protein-coding
mm_65556.1	chr7	27133657	27133665	-	1	NA	TTS (NM_007817)	TTS (NM_007817)	13706	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_37803.1	chr4	130574151	130574237	-	1	NA	promoter-TSS (NM_025998)	promoter-TSS (NM_025998)	-158	NM_025998	67149	Mm.423029	NM_025998	ENSMUSG00000078532	Nkain1	2610200G18Rik|2810426C15Rik	Na+/K+ transporting ATPase interacting 1	protein-coding
mm_135724.1	chr16	55821930	55821947	-	1	NA	exon (NM_030612, exon 3 of 14)	exon (NM_030612, exon 3 of 14)	200	NM_001159394	80859	Mm.247272	NM_030612	ENSMUSG00000035356	Nfkbiz	AA408868|INAP|Mail	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, zeta	protein-coding
mm_10564.1	chr2	18055204	18055221	+	1	NA	promoter-TSS (NM_010804)	promoter-TSS (NM_010804)	-25	NM_010804	17354	Mm.209175	NM_010804	ENSMUSG00000026743	Mllt10	Af10|B130021D15Rik|D630001B22Rik|mKIAA4140	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 10	protein-coding
mm_98541.1	chr11	95010101	95010115	+	1	NA	5' UTR (NM_146025, exon 1 of 10)	5' UTR (NM_146025, exon 1 of 10)	229	NM_146025	217125	Mm.297199	NM_146025	ENSMUSG00000047181	Samd14	AI839049|AI854782|BC034054	sterile alpha motif domain containing 14	protein-coding
mm_84087.1	chr9	58204311	58204327	-	1	NA	promoter-TSS (NM_001161541)	promoter-TSS (NM_001161541)	0	NM_001161541	320563	Mm.186499	NM_177193	ENSMUSG00000051243	Islr2	B930052A04Rik|Linx|Mbu-3|mKIAA1465	immunoglobulin superfamily containing leucine-rich repeat 2	protein-coding
mm_50230.1	chr6	42351006	42351018	+	1	NA	exon (NM_001289618, exon 3 of 10)	exon (NM_001289618, exon 3 of 10)	1184	NM_001289619	22793	Mm.282303	NM_011777	ENSMUSG00000029860	Zyx	9530098H06Rik|R75157	zyxin	protein-coding
mm_33847.1	chr4	135856243	135856251	+	1	NA	exon (NM_001284196, exon 1 of 6)	exon (NM_001284196, exon 1 of 6)	176	NM_010178	14105	Mm.10229	NM_010178	ENSMUSG00000028676	Srsf10	FUSIP2|Fusip1|NSSR1|NSSR2|Nssr|SRrp40|Sfrs13a|Srsf13a|TASR|TASR1|TASR2	serine/arginine-rich splicing factor 10	protein-coding
mm_25614.1	chr3	118431420	118431465	+	1	NA	Intergenic	Intergenic	-2415	NR_029551	387155		NR_029551	ENSMUSG00000065569	Mir137	Mirn137|mir-137|mmu-mir-137	microRNA 137	ncRNA
mm_59897.1	chr7	30307664	30307676	+	1	NA	3' UTR (NM_001081114, exon 14 of 14)	3' UTR (NM_001081114, exon 14 of 14)	-1083	NM_198027	233065	Mm.276277	NM_198027	ENSMUSG00000042831	Alkbh6	AI839550|Abh6|C130099A02	alkB homolog 6	protein-coding
mm_68308.1	chr7	105749682	105749714	-	1	NA	exon (NM_009906, exon 6 of 13)	exon (NM_009906, exon 6 of 13)	2537	NM_009906	12751	Mm.20837	NM_009906	ENSMUSG00000030894	Tpp1	Cln2|LPIC|TPP-1|TPP-I	tripeptidyl peptidase I	protein-coding
mm_96706.1	chr11	69655585	69655608	+	1	NA	exon (NM_009235, exon 1 of 2)	exon (NM_009235, exon 1 of 2)	559	NM_009235	20670	Mm.347499	NM_009235	ENSMUSG00000041287	Sox15	-	SRY (sex determining region Y)-box 15	protein-coding
mm_126800.1	chr15	87544189	87544262	+	1	NA	promoter-TSS (NM_001252310)	promoter-TSS (NM_001252310)	-74	NM_001252310	106014	Mm.244319	NM_134096	ENSMUSG00000054863	Fam19a5	TAFA5|Tafa-5|Tara-5	family with sequence similarity 19, member A5	protein-coding
mm_11141.1	chr2	28496884	28496893	+	1	NA	promoter-TSS (NM_139197)	promoter-TSS (NM_139197)	-3	NM_139197	227671	Mm.484270	NM_139197	ENSMUSG00000026829	Gbgt1	Fgs|Fs	globoside alpha-1,3-N-acetylgalactosaminyltransferase 1	protein-coding
mm_98201.1	chr11	87796032	87796043	+	1	NA	exon (NM_010824, exon 6 of 14)	exon (NM_010824, exon 6 of 14)	2253	NM_010824	17523	Mm.4668	NM_010824	ENSMUSG00000009350	Mpo	mKIAA4033	myeloperoxidase	protein-coding
mm_158153.1	chrX	103475654	103475675	-	1	NA	non-coding (NR_001570, exon 1 of 8)	non-coding (NR_001570, exon 1 of 8)	7569	NR_001570	213742	Mm.274770	NR_001463	ENSMUSG00000086503	Xist	A430022B11|AI314753	inactive X specific transcripts	ncRNA
mm_50007.1	chr6	41059143	41059164	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-23644	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_127080.1	chr15	97467218	97467221	+	1	NA	Intergenic	RLTR41|LTR|ERV1	-219932	NM_001164602	105827	Mm.24005	NM_178114	ENSMUSG00000048218	Amigo2	AI415330|AMIGO-2|AW208913|Ali1	adhesion molecule with Ig like domain 2	protein-coding
mm_163521.1	chr12	115623641	115623653	-	1	NA	Intergenic	Intergenic	72147	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
mm_158832.1	chrX	168124345	168124375	-	1	NA	intron (NM_001033330, intron 3 of 19)	intron (NM_001033330, intron 3 of 19)	-1363	NM_001290427	333605	Mm.426168	NM_001033330	ENSMUSG00000049176	Frmpd4	Gm196|PKAP1|Pdzd10|Pdzk10|Preso1|preso	FERM and PDZ domain containing 4	protein-coding
mm_58255.1	chr6	145076067	145076088	-	1	NA	promoter-TSS (NM_007532)	promoter-TSS (NM_007532)	80	NM_007532	12035	Mm.4606	NM_007532	ENSMUSG00000030268	Bcat1	BCATc|Eca39	branched chain aminotransferase 1, cytosolic	protein-coding
mm_111167.1	chr12	83597141	83597177	-	1	NA	promoter-TSS (NM_183154)	promoter-TSS (NM_183154)	-12	NM_183154	217695	Mm.59257	NM_183154	ENSMUSG00000042628	Zfyve1	DFCP1|G630053K23|TAFF1|ZNFN2A1|mKIAA1589	zinc finger, FYVE domain containing 1	protein-coding
mm_95392.1	chr11	49250584	49250597	+	1	NA	promoter-TSS (NM_001110150)	promoter-TSS (NM_001110150)	38	NM_001110150	17308	Mm.196933	NM_010794	ENSMUSG00000020346	Mgat1	Mgat-1	mannoside acetylglucosaminyltransferase 1	protein-coding
mm_68393.1	chr7	109525707	109525715	-	1	NA	non-coding (NR_037617, exon 18 of 20)	non-coding (NR_037617, exon 18 of 20)	5579	NR_028079	100302499	Mm.482651	NR_028079	ENSMUSG00000065016	Snora3	MBI-28	small nucleolar RNA, H/ACA box 3	snoRNA
mm_124335.1	chr14	103844188	103844198	-	1	NA	promoter-TSS (NM_001276296)	promoter-TSS (NM_001276296)	283	NM_001136061	13618	Mm.229532	NM_007904	ENSMUSG00000022122	Ednrb	ET-B|ET-BR|ETR-b|ETb|Sox10m1	endothelin receptor type B	protein-coding
mm_61403.1	chr7	73409384	73409394	+	1	NA	exon (NM_177740, exon 3 of 4)	exon (NM_177740, exon 3 of 4)	-33615	NR_040324	319783	Mm.349813	NR_040324	ENSMUSG00000097756	A730056A06Rik	C76391	RIKEN cDNA A730056A06 gene	ncRNA
mm_139388.1	chr17	52213157	52213170	+	1	NA	Intergenic	Intergenic	330436	NR_045095	100504169	Mm.417731	NR_045095		Gm20098	-	predicted gene, 20098	ncRNA
mm_50787.1	chr6	54039559	54039575	+	1	NA	promoter-TSS (NM_001163640)	promoter-TSS (NM_001163640)	-365	NM_001163640	69993	Mm.321147	NM_023543	ENSMUSG00000004633	Chn2	1700026N20Rik|4930557O16Rik|ARHGAP3|Bch	chimerin 2	protein-coding
mm_11213.1	chr2	29629756	29629764	+	1	NA	intron (NM_001039087, intron 1 of 25)	intron (NM_001039087, intron 1 of 25)	10040	NM_001039086	107746	Mm.298274	NM_054050	ENSMUSG00000039844	Rapgef1	4932418O06Rik|C3G|Grf2	Rap guanine nucleotide exchange factor (GEF) 1	protein-coding
mm_172961.1	chr9	88482525	88482526	-	1	NA	promoter-TSS (NM_001284328)	promoter-TSS (NM_001284328)	-128	NM_001284328	56403	Mm.260545	NM_019666	ENSMUSG00000032423	Syncrip	2610109K23Rik|4632417O19Rik|GRY-RBP|Nsap1|Nsap1l|hnRNP Q|pp68	synaptotagmin binding, cytoplasmic RNA interacting protein	protein-coding
mm_36146.1	chr4	59474859	59474875	-	1	NA	3' UTR (NM_144904, exon 15 of 15)	3' UTR (NM_144904, exon 15 of 15)	-36234	NM_001163288	634731	Mm.483589	NM_001163288	ENSMUSG00000038578	Susd1	A530080P10|Gm12528|OTTMUSG00000007332	sushi domain containing 1	protein-coding
mm_68215.1	chr7	104409822	104409851	-	1	NA	3' UTR (NM_009099, exon 8 of 8)	3' UTR (NM_009099, exon 8 of 8)	-51190	NM_175648	244183	Mm.347647	NM_175648	ENSMUSG00000052749	Trim30b	A530023O14Rik|Trim30-1	tripartite motif-containing 30B	protein-coding
mm_14291.1	chr2	128833718	128833721	+	1	NA	intron (NM_028248, intron 8 of 18)	intron (NM_028248, intron 8 of 18)	15416	NM_028248	72477	Mm.259688	NM_028248	ENSMUSG00000014353	Tmem87b	2610301K12Rik|2810431I02Rik|AU014804	transmembrane protein 87B	protein-coding
mm_144592.1	chr18	32163016	32163020	+	1	NA	promoter-TSS (NM_011946)	promoter-TSS (NM_011946)	-71	NM_011946	26405	Mm.211762	NM_011946	ENSMUSG00000024383	Map3k2	9630061B06Rik|AI585793|Mekk2|Mekk2b	mitogen-activated protein kinase kinase kinase 2	protein-coding
mm_21255.1	chr2	156312396	156312434	-	1	NA	promoter-TSS (NM_027585)	promoter-TSS (NM_027585)	-58	NM_027585	70873	Mm.475234	NM_027585	ENSMUSG00000038085	Cnbd2	4921517L17Rik|5430421B09Rik|Cris	cyclic nucleotide binding domain containing 2	protein-coding
mm_24859.1	chr3	95893921	95893933	+	1	NA	promoter-TSS (NM_146104)	promoter-TSS (NM_146104)	6	NM_146134	226548	Mm.306954	NM_146104	ENSMUSG00000015750	Aph1a	6530402N02Rik|APH-1a	aph1 homolog A, gamma secretase subunit	protein-coding
mm_100898.1	chr11	6066372	6066384	-	1	NA	promoter-TSS (NM_001174054)	promoter-TSS (NM_001174054)	-630	NM_007595	12323	Mm.439733	NM_007595	ENSMUSG00000057897	Camk2b	CaMKII	calcium/calmodulin-dependent protein kinase II, beta	protein-coding
mm_50413.1	chr6	48746170	48746180	+	1	NA	promoter-TSS (NM_175035)	promoter-TSS (NM_175035)	-22	NM_175035	317757	Mm.455917	NM_175035	ENSMUSG00000043505	Gimap5	D630024P16|E230026N22Rik	GTPase, IMAP family member 5	protein-coding
mm_169205.1	chr13	66441160	66441160	-	1	NA	promoter-TSS (NM_001290196)	promoter-TSS (NM_001290196)	-42	NM_001290196	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
mm_16431.1	chr2	180394301	180394309	+	1	NA	intron (NR_045331, intron 3 of 3)	intron (NR_045331, intron 3 of 3)	-4074	NR_029901	723954		NR_029901	ENSMUSG00000065460	Mir133a-2	Mirn133a-2|mir-133a-2	microRNA 133a-2	ncRNA
mm_161966.1	chr19	8850543	8850543	+	1	NA	promoter-TSS (NM_001013019)	promoter-TSS (NM_001013019)	-242	NM_001013019	68852	Mm.265792	NM_001013019	ENSMUSG00000071656	Lrrn4cl	1110067I12Rik	LRRN4 C-terminal like	protein-coding
mm_107041.1	chr12	14018651	14018652	+	1	NA	Intergenic	Intergenic	133387	NM_029007	105005	Mm.227253	NM_029007	ENSMUSG00000020607	Fam84a	2310003N02Rik|4731402F03Rik|AW125753|Nse1	family with sequence similarity 84, member A	protein-coding
mm_82148.1	chr9	123774801	123774810	+	1	NA	intron (NM_009913, intron 2 of 2)	intron (NM_009913, intron 2 of 2)	7594	NM_001166625	12769	Mm.440604	NM_009913	ENSMUSG00000029530	Ccr9	A130091K22Rik|Cmkbr10|GPR-9-6	chemokine (C-C motif) receptor 9	protein-coding
mm_127889.1	chr15	9140375	9140388	-	1	NA	promoter-TSS (NM_013787)	promoter-TSS (NM_013787)	73	NM_013787	27401	Mm.35584	NM_013787	ENSMUSG00000054115	Skp2	4930500A04Rik|FBXL1|FWD1|p45	S-phase kinase-associated protein 2 (p45)	protein-coding
mm_72047.1	chr8	71330710	71330745	+	1	NA	exon (NM_001142322, exon 11 of 40)	exon (NM_001142322, exon 11 of 40)	-36121	NM_001145780	67023	Mm.41890	NM_025917	ENSMUSG00000002395	Use1	2010315L10Rik|5730403H22Rik|AV002165|D12|Ed2|Q-snare|p31	unconventional SNARE in the ER 1 homolog (S. cerevisiae)	protein-coding
mm_162742.1	chr10	56389140	56389158	+	1	NA	3' UTR (NM_010288, exon 2 of 2)	3' UTR (NM_010288, exon 2 of 2)	11849	NM_010288	14609	Mm.378921	NM_010288	ENSMUSG00000050953	Gja1	AU042049|AW546267|Cnx43|Cx43|Cx43alpha1|Gja-1|Npm1|connexin43	gap junction protein, alpha 1	protein-coding
mm_25421.1	chr3	107873843	107873877	+	1	NA	Intergenic	Intergenic	-3370	NM_133867	99662	Mm.108491	NM_133867	ENSMUSG00000040600	Eps8l3	AI504489|Eps8r3	EPS8-like 3	protein-coding
mm_142809.1	chr17	51084261	51084264	-	1	NA	intron (NM_028162, intron 2 of 21)	Lx3A|LINE|L1	75116	NM_001285993	72238	Mm.120650	NM_028162	ENSMUSG00000023923	Tbc1d5	1600014N05Rik	TBC1 domain family, member 5	protein-coding
mm_42253.1	chr5	114003814	114003831	+	1	NA	promoter-TSS (NM_001286397)	promoter-TSS (NM_001286397)	-62	NM_001286397	13142	Mm.20115	NM_010018	ENSMUSG00000042096	Dao	AI987963|DAAO|DAMOX|Dao-1|Dao1	D-amino acid oxidase	protein-coding
mm_82946.1	chr9	35546821	35546842	-	1	NA	exon (NM_013932, exon 9 of 12)	exon (NM_013932, exon 9 of 12)	11639	NM_013932	30959	Mm.291723	NM_013932	ENSMUSG00000032101	Ddx25	AW047046|GRTH	DEAD (Asp-Glu-Ala-Asp) box polypeptide 25	protein-coding
mm_160079.1	chr7	12775670	12775670	-	1	NA	promoter-TSS (NM_001017955)	promoter-TSS (NM_001017955)	-12	NM_001017955	232875	Mm.333573	NM_001017955	ENSMUSG00000070822	Zscan18	EG232875	zinc finger and SCAN domain containing 18	protein-coding
mm_40598.1	chr5	64264210	64264220	+	1	NA	intron (NM_001310611, intron 5 of 21)	intron (NM_001310611, intron 5 of 21)	33858	NM_001289514	57915	Mm.286353	NM_019636	ENSMUSG00000029174	Tbc1d1	1110062G02Rik|AI385682|AW555803|Nob1|Nobq1|Tbc1|mKIAA1108	TBC1 domain family, member 1	protein-coding
mm_152175.1	chr19	7382435	7382449	-	1	NA	promoter-TSS (NR_045703)	promoter-TSS (NR_045703)	-561	NR_045703	654802	Mm.414924	NR_045703		1700105P06Rik	-	RIKEN cDNA 1700105P06 gene	ncRNA
mm_95629.1	chr11	53631878	53631906	+	1	NA	3' UTR (NM_008355, exon 4 of 4)	3' UTR (NM_008355, exon 4 of 4)	2810	NM_008355	16163	Mm.1284	NM_008355	ENSMUSG00000020383	Il13	Il-13	interleukin 13	protein-coding
mm_125829.1	chr15	74957490	74957507	+	1	NA	intron (NM_001164039, intron 2 of 4)	intron (NM_001164039, intron 2 of 4)	2392	NM_001164040	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_6162.1	chr1	65051232	65051241	-	1	NA	promoter-TSS (NM_007777)	promoter-TSS (NM_007777)	-73	NM_007777	12968	Mm.258170	NM_007777	ENSMUSG00000070870	Cryge	Cryg-2|Cryg-6|DGcry-2|Elo	crystallin, gamma E	protein-coding
mm_54315.1	chr6	30174118	30174136	-	1	NA	promoter-TSS (NR_126541)	promoter-TSS (NR_126541)	-2	NR_126541	101447999		NR_126540		Mirc35hg	-	microRNA cluster 35, host gene	ncRNA
mm_36652.1	chr4	94603204	94603228	-	1	NA	promoter-TSS (NM_172695)	promoter-TSS (NM_172695)	31	NM_172695	18786	Mm.490101	NM_172695	ENSMUSG00000028577	Plaa	2410007N06|AI536418|AU018445|AW208417|D4Ertd618e|PLA2P|PLAP|Ufd3	phospholipase A2, activating protein	protein-coding
mm_76302.1	chr8	84249702	84249733	-	1	NA	promoter-TSS (NM_001007571)	promoter-TSS (NM_001007571)	44	NM_001007571	101966	Mm.200723	NM_001007571	ENSMUSG00000019362	D8Ertd738e	AA589584	DNA segment, Chr 8, ERATO Doi 738, expressed	protein-coding
mm_130723.1	chr15	101078808	101078830	-	1	NA	Intergenic	CpG	-24420	NM_001214911	668225	Mm.385011	NM_001214911	ENSMUSG00000095440	Fignl2	EG668225	fidgetin-like 2	protein-coding
mm_171927.1	chr5	61288691	61288709	-	1	NA	Intergenic	L1VL1|LINE|L1	-520143	NM_019468	14380	Mm.347430	NM_019468	ENSMUSG00000089992	G6pd2	G6pdx-ps1|Gpd-2|Gpd2	glucose-6-phosphate dehydrogenase 2	protein-coding
mm_48755.1	chr5	148329921	148329933	-	1	NA	3' UTR (NM_007513, exon 13 of 13)	3' UTR (NM_007513, exon 13 of 13)	62888	NM_001301424	11987	Mm.275489	NM_007513	ENSMUSG00000041313	Slc7a1	4831426K01Rik|AI447493|Atrc-1|Atrc1|Cat1|Rec-1|Rev-1|mCAT-1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 1	protein-coding
mm_8502.1	chr1	154080710	154080752	-	1	NA	Intergenic	Intergenic	-120456	NM_001204908	100503355	Mm.484410	NM_001204908	ENSMUSG00000066797	Zfp648	ENSMUSG00000066797|Gm10178|Gm203	zinc finger protein 648	protein-coding
mm_19377.1	chr2	91194864	91194881	-	1	NA	5' UTR (NM_013839, exon 1 of 10)	5' UTR (NM_013839, exon 1 of 10)	163	NM_013839	22259	Mm.22690	NM_013839	ENSMUSG00000002108	Nr1h3	AU018371|LXR|RLD1|Unr1	nuclear receptor subfamily 1, group H, member 3	protein-coding
mm_98450.1	chr11	94944906	94944936	+	1	NA	exon (NM_007742, exon 29 of 51)	exon (NM_007742, exon 29 of 51)	8697	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_129941.1	chr15	84856113	84856139	-	1	NA	promoter-TSS (NM_001081166)	promoter-TSS (NM_001081166)	3	NM_001081166	271305	Mm.101022	NM_001081166	ENSMUSG00000016624	Phf21b	A730032D07Rik	PHD finger protein 21B	protein-coding
mm_163089.1	chr11	69734680	69734695	-	1	NA	exon (NM_001291068, exon 29 of 29)	exon (NM_001291068, exon 29 of 29)	23946	NM_001291068	20020	Mm.16533	NM_009089	ENSMUSG00000005198	Polr2a	220kDa|Rpb1|Rpo2-1	polymerase (RNA) II (DNA directed) polypeptide A	protein-coding
mm_34622.1	chr4	150566559	150566584	+	1	NA	intron (NM_001085492, intron 11 of 22)	intron (NM_001085492, intron 11 of 22)	85603	NM_173774	242773	Mm.29280	NM_173774	ENSMUSG00000039838	Slc45a1	C230078B22|Dnb5	solute carrier family 45, member 1	protein-coding
mm_81232.1	chr9	107872961	107872999	+	1	NA	promoter-TSS (NM_029169)	promoter-TSS (NM_029169)	-161	NM_029169	19654	Mm.139926	NM_011251	ENSMUSG00000032582	Rbm6	4930506F14Rik|Def-3|NY-LU-12|g16|mKIAA4015	RNA binding motif protein 6	protein-coding
mm_74427.1	chr8	3685318	3685322	-	1	NA	intron (NM_001253739, intron 8 of 10)	(TG)n|Simple_repeat|Simple_repeat	5070	NM_001253739	14128	Mm.1233	NM_013517	ENSMUSG00000005540	Fcer2a	CD23|Fce2|Fcer2|Ly-42	Fc receptor, IgE, low affinity II, alpha polypeptide	protein-coding
mm_74042.1	chr8	121950744	121950766	+	1	NA	intron (NM_016812, intron 1 of 13)	CpG	263	NM_001285983	53325	Mm.287163	NM_016812	ENSMUSG00000025316	Banp	AA408158|SMAR1	BTG3 associated nuclear protein	protein-coding
mm_137125.1	chr17	22734827	22734858	+	1	NA	Intergenic	Intergenic	82905	NR_030709	100042679	Mm.484007	NR_030709		Gm16386	EG545191|ENSMUSG00000073442|Gm21017	zinc finger protein 946 pseudogene	pseudo
mm_144340.1	chr18	14783239	14783259	+	1	NA	promoter-TSS (NM_001100449)	promoter-TSS (NM_001100449)	4	NM_001100449	72504	Mm.312233	NM_001100449	ENSMUSG00000054321	Taf4b	105kDa|2610524B04Rik|4932409F03Rik|AW987595|TAFII-105|TAFII105|Taf2c2	TATA-box binding protein associated factor 4b	protein-coding
mm_48220.1	chr5	137625036	137625056	-	1	NA	promoter-TSS (NM_027708)	promoter-TSS (NM_027708)	32	NM_027708	71176	Mm.474695	NM_027708	ENSMUSG00000089984	Fbxo24	4933422D21Rik|Fbx24	F-box protein 24	protein-coding
mm_90910.1	chr10	11492175	11492178	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-117048	NM_013898	30058	Mm.214504	NM_013898	ENSMUSG00000048007	Timm8a1	DXHXS1274E|Ddp1|Fci-12|Tim8a|Timm8a	translocase of inner mitochondrial membrane 8A1	protein-coding
mm_88737.1	chr10	80264943	80265033	+	1	NA	promoter-TSS (NM_133188)	promoter-TSS (NM_133188)	-3	NM_001122604	70248	Mm.148693	NM_133188	ENSMUSG00000069565	Dazap1	2410042M16Rik|mPrrp	DAZ associated protein 1	protein-coding
mm_87488.1	chr10	51494646	51494658	+	1	NA	intron (NM_001291894, intron 6 of 8)	intron (NM_001291894, intron 6 of 8)	3754	NM_013532	14728	Mm.34408	NM_013532	ENSMUSG00000062593	Lilrb4a	CD85K|Gp49b|HM18|ILT3|LIR-5|Lilrb4|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4A	protein-coding
mm_20365.1	chr2	128382608	128382621	-	1	NA	intron (NR_028591, intron 1 of 1)	intron (NR_028591, intron 1 of 1)	46737	NR_028591	100043424	Mm.297222	NR_028589		Gm14005	OTTMUSG00000015351	predicted gene 14005	ncRNA
mm_59379.1	chr7	25899576	25899582	+	1	NA	intron (NM_009999, intron 1 of 8)	Lx4B|LINE|L1	1921	NM_009999	13088	Mm.218749	NM_009999	ENSMUSG00000030483	Cyp2b10	Cyp2b|Cyp2b20|p16	cytochrome P450, family 2, subfamily b, polypeptide 10	protein-coding
mm_168479.1	chr11	48992887	48992892	-	1	NA	promoter-TSS (NM_011579)	promoter-TSS (NM_011579)	-643	NM_011579	21822	Mm.15793	NM_011579	ENSMUSG00000078922	Tgtp1	Gtp2|Irgb6|Mg21|Tgtp	T cell specific GTPase 1	protein-coding
mm_159744.1	chr5	72736404	72736404	-	1	NA	exon (NM_013698, exon 1 of 14)	exon (NM_013698, exon 1 of 14)	198	NM_013698	22165	Mm.3264	NM_013698	ENSMUSG00000054892	Txk	A130089B16Rik|Btkl|PTK-RL-18|PTK4|Rlk	TXK tyrosine kinase	protein-coding
mm_106888.1	chr12	8012155	8012166	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	34483	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_94064.1	chr10	128369123	128369198	-	1	NA	5' UTR (NM_001081040, exon 1 of 5)	5' UTR (NM_001081040, exon 1 of 5)	877	NM_001081040	210582	Mm.296876	NM_001081040	ENSMUSG00000039914	Coq10a	Gm1	coenzyme Q10A	protein-coding
mm_82984.1	chr9	36493362	36493368	-	1	NA	Intergenic	L1_Mur2|LINE|L1	17727	NM_001128510	671003	Mm.475847	NM_001128510	ENSMUSG00000090710	Gm9513	Pate-P|Pate11	predicted gene 9513	protein-coding
mm_86372.1	chr9	123798123	123798130	-	1	NA	intron (NM_148925, intron 16 of 18)	intron (NM_148925, intron 16 of 18)	-8351	NM_030712	80901	Mm.124289	NM_030712	ENSMUSG00000048521	Cxcr6	BB217514|BONZO|STRL33	chemokine (C-X-C motif) receptor 6	protein-coding
mm_6112.1	chr1	64120977	64121044	-	1	NA	5' UTR (NM_033563, exon 1 of 4)	5' UTR (NM_033563, exon 1 of 4)	379	NM_033563	93691	Mm.29466	NM_033563	ENSMUSG00000025959	Klf7	9830124P08Rik	Kruppel-like factor 7 (ubiquitous)	protein-coding
mm_43732.1	chr5	139791509	139791517	+	1	NA	promoter-TSS (NM_010757)	promoter-TSS (NM_010757)	-23	NM_010757	17135	Mm.157313	NM_010757	ENSMUSG00000018143	Mafk	AW061068|NF-E2|Nfe2u	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein K (avian)	protein-coding
mm_67892.1	chr7	99479703	99479707	-	1	NA	promoter-TSS (NR_002173)	promoter-TSS (NR_002173)	2	NR_002173	449631	Mm.236868	NR_002173	ENSMUSG00000064966	Snord15b	Gm5775|Rnu15-b|Rnu15b|U15B	small nucleolar RNA, C/D box 14B	snoRNA
mm_87244.1	chr10	40936400	40936416	+	1	NA	exon (NM_031877, exon 8 of 9)	exon (NM_031877, exon 8 of 9)	52874	NM_031877	83767	Mm.41353	NM_031877	ENSMUSG00000019831	Wasf1	AI195380|AI838537|Scar|WAVE|WAVE-1	WAS protein family, member 1	protein-coding
mm_10868.1	chr2	25214692	25214700	+	1	NA	promoter-TSS (NM_028961)	promoter-TSS (NM_028961)	-66	NM_028961	74472	Mm.176944	NM_028961	ENSMUSG00000036770	Stpg3	4933433C11Rik	sperm tail PG rich repeat containing 3	protein-coding
mm_131306.1	chr16	11447306	11447314	+	1	NA	intron (NM_001290148, intron 5 of 13)	intron (NM_001290148, intron 5 of 13)	41662	NM_001290148	74478	Mm.325831	NM_028964	ENSMUSG00000071669	Snx29	4933437K13Rik|ENSMUSG00000079738|Gm11170|Gm1737|Gm930|Rundc2a	sorting nexin 29	protein-coding
mm_97804.1	chr11	82956946	82956959	+	1	NA	exon (NM_183201, exon 3 of 6)	exon (NM_183201, exon 3 of 6)	3729	NR_045932	76392	Mm.295205	NR_045932	ENSMUSG00000086327	Slfn5os	1700003F17Rik	schlafen 5, opposite strand	ncRNA
mm_8099.1	chr1	135848092	135848104	-	1	NA	intron (NM_001130174, intron 8 of 13)	intron (NM_001130174, intron 8 of 13)	7237	NM_001130176	21956	Mm.247470	NM_011619	ENSMUSG00000026414	Tnnt2	Tnt|cTnT	troponin T2, cardiac	protein-coding
mm_7888.1	chr1	133133599	133133606	-	1	NA	exon (NM_133819, exon 1 of 2)	exon (NM_133819, exon 1 of 2)	2436	NM_133819	108954	Mm.293628	NM_133819	ENSMUSG00000046062	Ppp1r15b	1810033K10Rik|AI606441|C530022L24Rik|CReP	protein phosphatase 1, regulatory (inhibitor) subunit 15b	protein-coding
mm_52931.1	chr6	122932223	122932239	+	1	NA	exon (NM_199311, exon 5 of 6)	exon (NM_199311, exon 5 of 6)	10383	NM_199311	269799	Mm.297275	NM_199311	ENSMUSG00000049037	Clec4a1	BC049354|Dcir4	C-type lectin domain family 4, member a1	protein-coding
mm_38120.1	chr4	134548184	134548195	-	1	NA	intron (NM_029100, intron 2 of 11)	intron (NM_029100, intron 2 of 11)	3977	NM_029100	74777	Mm.29773	NM_029100	ENSMUSG00000050989	Selenon	1110019I12Rik|AI414492|SelN|Sepn1	selenoprotein N	protein-coding
mm_154695.1	chrX	8131850	8131854	+	1	NA	5' UTR (NM_028542, exon 2 of 9)	5' UTR (NM_028542, exon 2 of 9)	1006	NM_001290783	73447	Mm.284162	NM_026137	ENSMUSG00000031166	Wdr13	1700060B08Rik|5730411P10Rik|DXHXS7467e|W51679|mMg21	WD repeat domain 13	protein-coding
mm_16078.1	chr2	168231230	168231239	+	1	NA	promoter-TSS (NM_010072)	promoter-TSS (NM_010072)	612	NM_001160330	69372	Mm.482182	NM_001160330	ENSMUSG00000074576	Mocs3	1700020H17Rik|Uba4	molybdenum cofactor synthesis 3	protein-coding
mm_23495.1	chr3	60516868	60516881	+	1	NA	intron (NM_001253710, intron 1 of 7)	intron (NM_001253710, intron 1 of 7)	15695	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_20190.1	chr2	122611223	122611233	-	1	NA	promoter-TSS (NM_025961)	promoter-TSS (NM_025961)	49	NM_025961	67092	Mm.29975	NM_025961	ENSMUSG00000027199	Gatm	1810003P21Rik|AI314789|AT	glycine amidinotransferase (L-arginine:glycine amidinotransferase)	protein-coding
mm_159735.1	chr5	64160027	64160027	+	1	NA	promoter-TSS (NM_019636)	promoter-TSS (NM_019636)	-233	NM_019636	57915	Mm.286353	NM_019636	ENSMUSG00000029174	Tbc1d1	1110062G02Rik|AI385682|AW555803|Nob1|Nobq1|Tbc1|mKIAA1108	TBC1 domain family, member 1	protein-coding
mm_104072.1	chr11	86586492	86586496	-	1	NA	intron (NM_029478, intron 11 of 11)	intron (NM_029478, intron 11 of 11)	-2336	NR_029738	387140		NR_029738	ENSMUSG00000065455	Mir21a	Mir21|Mirn21|mmu-mir-21|mmu-mir-21a	microRNA 21a	ncRNA
mm_90897.1	chr10	10475068	10475083	-	1	NA	Intergenic	RMER17B|LTR|ERVK	-2761	NM_001127353	215772	Mm.246573	NM_172547	ENSMUSG00000050994	Adgb	9130014G24Rik	androglobin	protein-coding
mm_27671.1	chr3	65392580	65392595	-	1	NA	promoter-TSS (NM_026155)	promoter-TSS (NM_026155)	-34	NM_026155	67437	Mm.232728	NM_026155	ENSMUSG00000027828	Ssr3	0610038P07Rik|AL022999|AU022074|AW553833|TRAPG	signal sequence receptor, gamma	protein-coding
mm_92317.1	chr10	75517325	75517362	-	1	NA	promoter-TSS (NM_026095)	promoter-TSS (NM_026095)	38	NM_175133	68778	Mm.29382	NM_175133	ENSMUSG00000033416	Gucd1	1110038D17Rik	guanylyl cyclase domain containing 1	protein-coding
mm_119469.1	chr14	47292307	47292310	+	1	NA	TTS (NM_080843)	TTS (NM_080843)	-6006	NM_178684	218975	Mm.212297	NM_178684	ENSMUSG00000021840	Mapk1ip1l	9130202B12|C130032J12Rik	mitogen-activated protein kinase 1 interacting protein 1-like	protein-coding
mm_140413.1	chr17	87650433	87650448	+	1	NA	exon (NM_008532, exon 10 of 10)	exon (NM_008532, exon 10 of 10)	14461	NM_008532	17075	Mm.4259	NM_008532	ENSMUSG00000045394	Epcam	CD326|EGP|EGP-2|Egp314|Ep-CAM|EpCAM1|GA733-2|Ly74|TROP1|Tacsd1|Tacstd1|gp40	epithelial cell adhesion molecule	protein-coding
mm_25513.1	chr3	110250184	110250204	+	1	NA	exon (NM_178891, exon 1 of 1)	exon (NM_178891, exon 1 of 1)	805	NM_178891	99890	Mm.36115	NM_178891	ENSMUSG00000049300	Prmt6	AW124876|BB233495|Hrmt1l6	protein arginine N-methyltransferase 6	protein-coding
mm_65437.1	chr7	25384962	25384972	-	1	NA	intron (NM_001039507, intron 4 of 9)	intron (NM_001039507, intron 4 of 9)	5145	NM_001039507	16890	Mm.158548	NM_010719	ENSMUSG00000003123	Lipe	4933403G17Rik|HSL	lipase, hormone sensitive	protein-coding
mm_164394.1	chr16	33753331	33753336	+	1	NA	intron (NM_175256, intron 12 of 14)	intron (NM_175256, intron 12 of 14)	-40704	NM_010739	17063	Mm.3177	NM_010739	ENSMUSG00000022824	Muc13	114/A10|14/A10|AI159736|Lrrp|Ly64|NJ-1	mucin 13, epithelial transmembrane	protein-coding
mm_148129.1	chr18	75697428	75697453	-	1	NA	5' UTR (NM_201354, exon 1 of 12)	5' UTR (NM_201354, exon 1 of 12)	256	NM_201354	269037	Mm.36745	NM_201354	ENSMUSG00000052928	Ctif	Gm672	CBP80/20-dependent translation initiation factor	protein-coding
mm_140444.1	chr17	88580374	88580389	+	1	NA	intron (NM_028658, intron 18 of 21)	intron (NM_028658, intron 18 of 21)	-46174	NM_029858	77057	Mm.482203	NM_029858	ENSMUSG00000033855	Ston1	4921524J06Rik|C86231|Salf|Sblf	stonin 1	protein-coding
mm_55602.1	chr6	71823757	71823793	-	1	NA	promoter-TSS (NM_025430)	promoter-TSS (NM_025430)	9	NM_025430	66223	Mm.28579	NM_025430	ENSMUSG00000052962	Mrpl35	1110066C01Rik	mitochondrial ribosomal protein L35	protein-coding
mm_78963.1	chr9	45246372	45246399	+	1	NA	intron (NM_001198971, intron 4 of 4)	intron (NM_001198971, intron 4 of 4)	20322	NR_106054	102466803		NR_106054	ENSMUSG00000098361	Mir7086	Gm27643|mmu-mir-7086	microRNA 7086	ncRNA
mm_8164.1	chr1	136953527	136953571	-	1	NA	promoter-TSS (NM_001159769)	promoter-TSS (NM_001159769)	81	NM_001159769	26424	Mm.16794	NM_030676	ENSMUSG00000026398	Nr5a2	AU020803|D1Ertd308e|Ftf|LRH-1|UF2-H3B	nuclear receptor subfamily 5, group A, member 2	protein-coding
mm_12543.1	chr2	72365013	72365016	+	1	NA	intron (NM_023057, intron 4 of 19)	intron (NM_023057, intron 4 of 19)	79313	NM_178084	65964	Mm.304143	NM_023057	ENSMUSG00000004085	Map3k20	AV006891|B230120H23Rik|MLTK|MLTKalpha|MLTKbeta|Zak	mitogen-activated protein kinase kinase kinase 20	protein-coding
mm_164785.1	chr18	8562036	8562039	-	1	NA	Intergenic	Intergenic	-650819	NM_008058	14370	Mm.184289	NM_008058	ENSMUSG00000036904	Fzd8	Fz8	frizzled class receptor 8	protein-coding
mm_42602.1	chr5	117510244	117510250	+	1	NA	intron (NM_001312914, intron 3 of 19)	intron (NM_001312914, intron 3 of 19)	96245	NM_001312914	333050	Mm.437947	NM_001034873	ENSMUSG00000061578	Ksr2	-	kinase suppressor of ras 2	protein-coding
mm_29236.1	chr3	107214761	107214766	-	1	NA	intron (NM_001111143, intron 5 of 8)	intron (NM_001111143, intron 5 of 8)	6969	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_47815.1	chr5	134221671	134221689	-	1	NA	3' UTR (NM_001286037, exon 11 of 11)	3' UTR (NM_001286037, exon 11 of 11)	7945	NM_001286037	17969	Mm.425296	NM_010876	ENSMUSG00000015950	Ncf1	NCF-47K|NOXO2|Ncf-1|p47-phox|p47<phox>|p47phox	neutrophil cytosolic factor 1	protein-coding
mm_57310.1	chr6	124723002	124723003	-	1	NA	intron (NM_001077705, intron 11 of 15)	intron (NM_001077705, intron 11 of 15)	-4612	NR_029792	723944		NR_029792	ENSMUSG00000065462	Mir200c	Mirn200c|mir-200c	microRNA 200c	ncRNA
mm_162712.1	chr10	28697613	28697615	+	1	NA	intron (NR_131208, intron 1 of 3)	Lx7|LINE|L1	29254	NM_178666	210757	Mm.123021	NM_178666	ENSMUSG00000049109	Themis	E430004N04Rik|Gasp|Spot|Tsepa|thylex	thymocyte selection associated	protein-coding
mm_63089.1	chr7	122301268	122301278	+	1	NA	intron (NM_001316672, intron 2 of 16)	intron (NM_001316672, intron 2 of 16)	12148	NM_008855	18751	Mm.207496	NM_008855	ENSMUSG00000052889	Prkcb	PKC-B|PKC-Beta|Pkcb|Prkcb1|Prkcb2	protein kinase C, beta	protein-coding
mm_114494.1	chr13	69957987	69958001	+	1	NA	Intergenic	Lx8b|LINE|L1	-1839	NR_138559	67550	Mm.158159	NR_138559		4933416O17Rik	-	RIKEN cDNA 4933416O17 gene	ncRNA
mm_12972.1	chr2	90745540	90745603	+	1	NA	exon (NM_018828, exon 1 of 17)	exon (NM_018828, exon 1 of 17)	201	NM_018828	55935	Mm.489638	NM_018828	ENSMUSG00000008200	Fnbp4	FBP30|Fnbp30|mKIAA1014	formin binding protein 4	protein-coding
mm_35688.1	chr4	44072533	44072557	-	1	NA	5' UTR (NM_001190414, exon 1 of 12)	5' UTR (NM_001190414, exon 1 of 12)	128	NM_001190414	50798	Mm.256718	NM_015828	ENSMUSG00000028479	Gne	2310066H07Rik|DMRV|GLCNE|IBM2|NM|Uae1	glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase	protein-coding
mm_83640.1	chr9	49504139	49504160	-	1	NA	3' UTR (NM_001311065, exon 18 of 18)	3' UTR (NM_001311065, exon 18 of 18)	-14139	NR_029465	100036537	Mm.437541	NR_029465	ENSMUSG00000079564	Gm11149	ENSMUSG00000060603|ENSMUSG00000079564	predicted gene 11149	ncRNA
mm_18446.1	chr2	60916486	60916492	-	1	NA	intron (NM_020296, intron 1 of 13)	MLT1A|LTR|ERVL-MaLR	-35051	NM_001141931	56878	Mm.259667	NM_020296	ENSMUSG00000026970	Rbms1	2600014B10Rik|AI255215|MSSP-1|MSSP-2|MSSP-3|YC1	RNA binding motif, single stranded interacting protein 1	protein-coding
mm_26681.1	chr3	155514486	155514502	+	1	NA	Intergenic	Intergenic	421060	NM_028938	74435	Mm.195711	NM_028938	ENSMUSG00000028182	Lrriq3	4930438B07Rik|4930511J15Rik|4933403H06Rik|BB020367|Lrrc44	leucine-rich repeats and IQ motif containing 3	protein-coding
mm_54535.1	chr6	36715669	36715685	-	1	NA	TTS (NM_008973)	TTS (NM_008973)	95684	NM_008973	19242	Mm.279690	NM_008973	ENSMUSG00000029838	Ptn	HARP|HB-GAM|HBBN|HBGF-8|HBNF|OSF|Osf-1|Osf1	pleiotrophin	protein-coding
mm_122884.1	chr14	54946484	54946502	-	1	NA	exon (NM_010856, exon 34 of 39)	exon (NM_010856, exon 34 of 39)	2649	NR_029724	387204		NR_029724	ENSMUSG00000065432	Mir208a	Mirn208|Mirn208a|mir-208|mir-208a|mmu-mir-208	microRNA 208a	ncRNA
mm_106368.1	chr11	118396824	118396838	-	1	NA	exon (NM_011150, exon 5 of 6)	exon (NM_011150, exon 5 of 6)	5100	NM_011150	19039	Mm.3152	NM_011150	ENSMUSG00000033880	Lgals3bp	90K|CyCAP|MAC-2BP|Ppicap|Tango10b	lectin, galactoside-binding, soluble, 3 binding protein	protein-coding
mm_130509.1	chr15	98845780	98845794	-	1	NA	exon (NM_001033276, exon 40 of 55)	exon (NM_001033276, exon 40 of 55)	-14279	NM_016781	19082	Mm.6670	NM_016781	ENSMUSG00000067713	Prkag1	AA571379|BB036179|Prkaac	protein kinase, AMP-activated, gamma 1 non-catalytic subunit	protein-coding
mm_137645.1	chr17	28532172	28532201	+	1	NA	intron (NM_026290, intron 2 of 5)	intron (NM_026290, intron 2 of 5)	1325	NM_026290	67645	Mm.46170	NM_026290	ENSMUSG00000024223	Armc12	4930511I11Rik|AV041658	armadillo repeat containing 12	protein-coding
mm_37340.1	chr4	119657648	119657665	-	1	NA	exon (NM_008191, exon 2 of 3)	exon (NM_008191, exon 2 of 3)	1289	NM_008191	14916	Mm.278	NM_008191	ENSMUSG00000032978	Guca2b	AV066530|Gcap2|Ugn	guanylate cyclase activator 2b (retina)	protein-coding
mm_2956.1	chr1	132729327	132729369	+	1	NA	promoter-TSS (NR_045892)	promoter-TSS (NR_045892)	-5	NR_045892	100038653	Mm.421275	NR_045892	ENSMUSG00000101126	Gm10538	ENSMUSG00000073566	predicted gene 10538	ncRNA
mm_87873.1	chr10	61482133	61482140	+	1	NA	intron (NM_153542, intron 1 of 4)	intron (NM_153542, intron 1 of 4)	6303	NM_153542	216011	Mm.136116	NM_153542	ENSMUSG00000037151	Lrrc20	BC036304	leucine rich repeat containing 20	protein-coding
mm_94107.1	chr10	128589623	128589642	-	1	NA	promoter-TSS (NM_010153)	promoter-TSS (NM_010153)	-131	NM_010153	13867	Mm.373043	NM_010153	ENSMUSG00000018166	Erbb3	C76256|Erbb-3|Erbb3r|Her3	erb-b2 receptor tyrosine kinase 3	protein-coding
mm_122312.1	chr14	36911421	36911453	-	1	NA	intron (NM_001347503, intron 2 of 7)	Lx8|LINE|L1	8098	NM_001347503	72972	Mm.27621	NM_027045	ENSMUSG00000058690	Ccser2	1700012P13Rik|2900054P12Rik|AI035535|AW108503|Fam190b|Gcap14	coiled-coil serine rich 2	protein-coding
mm_9528.1	chr1	173787231	173787233	-	1	NA	Intergenic	MMERVK10C-int|LTR|ERVK	-20313	NM_008329	15951	Mm.261270	NM_008329	ENSMUSG00000073489	Ifi204	Ifi16|p204	interferon activated gene 204	protein-coding
mm_75410.1	chr8	46471607	46471616	-	1	NA	intron (NM_007981, intron 1 of 20)	CpG	574	NM_007981	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_107830.1	chr12	69228633	69228641	+	1	NA	promoter-TSS (NM_011133)	promoter-TSS (NM_011133)	-447	NM_011133	18974	Mm.9199	NM_011133	ENSMUSG00000020974	Pole2	-	polymerase (DNA directed), epsilon 2 (p59 subunit)	protein-coding
mm_155877.1	chrX	101449062	101449068	+	1	NA	promoter-TSS (NM_013712)	promoter-TSS (NM_013712)	-44	NM_013712	26549	Mm.46232	NM_013712	ENSMUSG00000031312	Itgb1bp2	Chordc3	integrin beta 1 binding protein 2	protein-coding
mm_74102.1	chr8	122775498	122775514	+	1	NA	promoter-TSS (NM_144932)	promoter-TSS (NM_144932)	20	NM_144932	257633	Mm.334875	NM_144932	ENSMUSG00000015016	Acsf3	BB101783	acyl-CoA synthetase family member 3	protein-coding
mm_50965.1	chr6	59408760	59408762	+	1	NA	intron (NM_183183, intron 1 of 1)	intron (NM_183183, intron 1 of 1)	17529	NM_183183	243385	Mm.138080	NM_183183	ENSMUSG00000045441	Gprin3	C030038J10Rik|C730021L23	GPRIN family member 3	protein-coding
mm_172245.1	chr6	69284371	69284375	-	1	NA	Intergenic	Intergenic	42801	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_150870.1	chr19	45047846	45047873	+	1	NA	5' UTR (NM_053197, exon 1 of 11)	5' UTR (NM_053197, exon 1 of 11)	283	NM_001178013	94280	Mm.36169	NM_053197	ENSMUSG00000025212	Sfxn3	-	sideroflexin 3	protein-coding
mm_92959.1	chr10	85917070	85917099	-	1	NA	promoter-TSS (NM_181650)	promoter-TSS (NM_181650)	-98	NM_001302886	72843	Mm.25307	NM_181650	ENSMUSG00000035529	Prdm4	1700031E19Rik|2810470D21Rik|AW552272|SC-1|SC1	PR domain containing 4	protein-coding
mm_87210.1	chr10	39736850	39736857	+	1	NA	intron (NM_011264, intron 1 of 31)	AT_rich|Low_complexity|Low_complexity	4693	NM_011264	19714	Mm.439723	NM_011264	ENSMUSG00000019841	Rev3l	Rev|Rev3|Sez4	REV3 like, DNA directed polymerase zeta catalytic subunit	protein-coding
mm_21824.1	chr2	165326436	165326486	-	1	NA	promoter-TSS (NM_207706)	promoter-TSS (NM_207706)	18	NM_080287	140579	Mm.35064	NM_080287	ENSMUSG00000017670	Elmo2	1190002F24Rik|CED-12	engulfment and cell motility 2	protein-coding
mm_104769.1	chr11	98545774	98545788	-	1	NA	5' UTR (NM_011771, exon 1 of 8)	5' UTR (NM_011771, exon 1 of 8)	250	NM_011771	22780	Mm.133367	NM_011771	ENSMUSG00000018168	Ikzf3	5830411O07Rik|Aiolos|Zfpn1a3|Znfn1a3	IKAROS family zinc finger 3	protein-coding
mm_87260.1	chr10	41519875	41519927	+	1	NA	intron (NM_016898, intron 1 of 5)	CpG	401	NM_016898	53599	Mm.269815	NM_016898	ENSMUSG00000019818	Cd164	A115|A24|AA589639|AW540279|MGC-24|MSSP	CD164 antigen	protein-coding
mm_104957.1	chr11	100141679	100141690	-	1	NA	exon (NM_008471, exon 4 of 6)	exon (NM_008471, exon 4 of 6)	2015	NM_001313963	16669	Mm.439699	NM_008471	ENSMUSG00000020911	Krt19	AI663979|CK-19|EndoC|K19|Krt-1.19|Krt1-19	keratin 19	protein-coding
mm_103476.1	chr11	76494623	76494640	-	1	NA	promoter-TSS (NM_001346670)	promoter-TSS (NM_001346670)	-136	NM_001346670	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_95545.1	chr11	52306783	52306793	+	1	NA	Intergenic	Intergenic	-23774	NM_001313981	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_78161.1	chr9	21028068	21028085	+	1	NA	3' UTR (NM_010493, exon 7 of 7)	3' UTR (NM_010493, exon 7 of 7)	-1297	NM_023892	78369	Mm.30220	NM_023892	ENSMUSG00000001014	Icam4	1810015M19Rik|Cd242|ICAM-4	intercellular adhesion molecule 4, Landsteiner-Wiener blood group	protein-coding
mm_60399.1	chr7	44475600	44475611	+	1	NA	Intergenic	Intergenic	5258	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_98326.1	chr11	90276930	90276969	+	1	NA	3' UTR (NM_026178, exon 7 of 7)	3' UTR (NM_026178, exon 7 of 7)	27473	NM_026178	67468	Mm.277518	NM_026178	ENSMUSG00000003948	Mmd	1200017E07Rik|1810073C06Rik|AA690185	monocyte to macrophage differentiation-associated	protein-coding
mm_25133.1	chr3	102332227	102332228	+	1	NA	Intergenic	Intergenic	69822	NR_040391	319951	Mm.225196	NR_040391	ENSMUSG00000105891	A230001M10Rik	-	RIKEN cDNA A230001M10 gene	ncRNA
mm_81550.1	chr9	110329158	110329189	+	1	NA	Intergenic	Intergenic	-4115	NM_001103162	235623	Mm.288741	NM_001001144	ENSMUSG00000032485	Scap	9530044G19|mKIAA0199	SREBF chaperone	protein-coding
mm_97035.1	chr11	72267269	72267273	+	1	NA	promoter-TSS (NM_001004148)	promoter-TSS (NM_001004148)	427	NR_045922	73366	Mm.396157	NR_045922	ENSMUSG00000086951	1700051A21Rik	-	RIKEN cDNA 1700051A21 gene	ncRNA
mm_105329.1	chr11	102925052	102925064	-	1	NA	promoter-TSS (NM_197959)	promoter-TSS (NM_197959)	66	NM_197959	70218	Mm.32084	NM_197959	ENSMUSG00000051378	Kif18b	3000004C01Rik	kinesin family member 18B	protein-coding
mm_98929.1	chr11	98355323	98355330	+	1	NA	intron (NR_045477, intron 2 of 2)	intron (NR_045477, intron 2 of 2)	2957	NR_045477	69338	Mm.398308	NR_045477	ENSMUSG00000085944	1700003D09Rik	-	RIKEN cDNA 1700003D09 gene	ncRNA
mm_83199.1	chr9	41157672	41157720	-	1	NA	promoter-TSS (NM_176860)	promoter-TSS (NM_176860)	-202	NM_176860	72828	Mm.133615	NM_176860	ENSMUSG00000032020	Ubash3b	2810457I06Rik|BB125008|TULA-2|p70	ubiquitin associated and SH3 domain containing, B	protein-coding
mm_72033.1	chr8	70776763	70776773	+	1	NA	promoter-TSS (NR_029440)	promoter-TSS (NR_029440)	-56	NM_008841	18709	Mm.12945	NM_008841	ENSMUSG00000031834	Pik3r2	p85beta	phosphatidylinositol 3-kinase, regulatory subunit, polypeptide 2 (p85 beta)	protein-coding
mm_39492.1	chr5	20951035	20951045	+	1	NA	promoter-TSS (NR_030699)	promoter-TSS (NR_030699)	51	NR_030699	320770	Mm.491217	NR_030699	ENSMUSG00000101013	A630072M18Rik	Aptr	RIKEN cDNA A630072M18 gene	ncRNA
mm_153896.1	chr19	47015114	47015206	-	1	NA	promoter-TSS (NM_001164363)	promoter-TSS (NM_001164363)	29	NM_001164363	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_130057.1	chr15	89180704	89180765	-	1	NA	promoter-TSS (NM_001284506)	promoter-TSS (NM_001284506)	54	NM_001284506	140570	Mm.267514	NM_138749	ENSMUSG00000036606	Plxnb2	Debt|plexin-B2	plexin B2	protein-coding
mm_52826.1	chr6	121357516	121357549	+	1	NA	intron (NM_001347433, intron 7 of 14)	intron (NM_001347433, intron 7 of 14)	10835	NM_133661	14411	Mm.274506	NM_133661	ENSMUSG00000030109	Slc6a12	BGT1|GAT-2|GAT2|Gabt2	solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12	protein-coding
mm_4038.1	chr1	165774409	165774430	+	1	NA	3' UTR (NM_011804, exon 4 of 4)	3' UTR (NM_011804, exon 4 of 4)	10639	NM_011804	433375	Mm.294885	NM_011804	ENSMUSG00000040713	Creg1	AA755314|Creg	cellular repressor of E1A-stimulated genes 1	protein-coding
mm_18940.1	chr2	76760029	76760040	-	1	NA	exon (NM_011652, exon 262 of 313)	exon (NM_011652, exon 262 of 313)	84719	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_49778.1	chr6	34920942	34920954	+	1	NA	promoter-TSS (NM_009292)	promoter-TSS (NM_009292)	-12	NM_009292	20899	Mm.5171	NM_009292	ENSMUSG00000029848	Stra8	-	stimulated by retinoic acid gene 8	protein-coding
mm_114104.1	chr13	54732030	54732053	+	1	NA	intron (NM_001033364, intron 23 of 31)	IMPB_01|Satellite|Satellite	17833	NM_001316710	26913	Mm.41812	NM_012014	ENSMUSG00000069227	Gprin1	GRIN1|Z16	G protein-regulated inducer of neurite outgrowth 1	protein-coding
mm_20033.1	chr2	119743161	119743205	-	1	NA	intron (NM_146125, intron 1 of 6)	CpG	846	NM_146125	228550	Mm.65337	NM_146125	ENSMUSG00000027296	Itpka	-	inositol 1,4,5-trisphosphate 3-kinase A	protein-coding
mm_109702.1	chr12	113260161	113260171	+	1	NA	Intergenic	Intergenic	74263	NM_153776	69195	Mm.313244	NM_153776	ENSMUSG00000049036	Tmem121	2410008J05Rik|Hole	transmembrane protein 121	protein-coding
mm_44866.1	chr5	34336873	34336892	-	1	NA	promoter-TSS (NM_001304270)	promoter-TSS (NM_001304270)	-50	NM_001304270	19822	Mm.21281	NM_011278	ENSMUSG00000029110	Rnf4	AU018689|Gtrgeo8|SNURF	ring finger protein 4	protein-coding
mm_127052.1	chr15	96709890	96709933	+	1	NA	Intergenic	CpG	-10213	NM_175121	67760	Mm.46754	NM_175121	ENSMUSG00000022462	Slc38a2	5033402L14Rik|AI316867|ATA2|SAT2|mKIAA1382	solute carrier family 38, member 2	protein-coding
mm_114356.1	chr13	60940230	60940230	+	1	NA	exon (NM_009411, exon 3 of 5)	exon (NM_009411, exon 3 of 5)	1705	NM_009411	21984	Mm.2372	NM_009411	ENSMUSG00000033834	Tpbpa	AV033951|Tb-1|Tb1|Tpbp|b2b1247Clo	trophoblast specific protein alpha	protein-coding
mm_5398.1	chr1	33669746	33669792	-	1	NA	promoter-TSS (NR_033199)	promoter-TSS (NR_033199)	25	NM_008922	19076	Mm.27705	NM_008922	ENSMUSG00000026134	Prim2	AI323589	DNA primase, p58 subunit	protein-coding
mm_14468.1	chr2	131287322	131287324	+	1	NA	promoter-TSS (NR_029755)	promoter-TSS (NR_029755)	-729	NR_029755	723825		NR_029755	ENSMUSG00000065563	Mir103-2	Mirn103-2|mir-103-2	microRNA 103-2	ncRNA
mm_90571.1	chr10	128232073	128232094	+	1	NA	promoter-TSS (NM_001136082)	promoter-TSS (NM_001136082)	20	NM_001136082	21853	Mm.6458	NM_011589	ENSMUSG00000039994	Timeless	C77407|Debt69|tim	timeless circadian clock 1	protein-coding
mm_162485.1	chr1	135167593	135167593	-	1	NA	promoter-TSS (NM_134438)	promoter-TSS (NM_134438)	88	NM_134438	171469	Mm.272290	NM_134438	ENSMUSG00000026424	Gpr37l1	AW047233|CAG-18|D0Kist8	G protein-coupled receptor 37-like 1	protein-coding
mm_107796.1	chr12	62718742	62718746	+	1	NA	Intergenic	Intergenic	30957	NR_131949	73309	Mm.276558	NR_131949		Spanxn4	1700047L15Rik	SPANX family, member N4	ncRNA
mm_91702.1	chr10	44004463	44004479	-	1	NA	5' UTR (NM_172393, exon 1 of 20)	5' UTR (NM_172393, exon 1 of 20)	375	NM_172393	11630	Mm.292082	NM_172393	ENSMUSG00000019866	Aim1	AI462491|AI463325	absent in melanoma 1	protein-coding
mm_114220.1	chr13	56438303	56438324	+	1	NA	promoter-TSS (NM_177809)	promoter-TSS (NM_177809)	-42	NM_177809	328258	Mm.482177	NM_177809	ENSMUSG00000021509	Slc25a48	AU042651|E230025K15	solute carrier family 25, member 48	protein-coding
mm_31535.1	chr4	55366811	55366822	+	1	NA	exon (NM_009011, exon 2 of 10)	exon (NM_009011, exon 2 of 10)	16774	NM_009011	19359	Mm.196846	NM_009011	ENSMUSG00000028426	Rad23b	0610007D13Rik|AV001138|HR23B|mHR23B|p58	RAD23 homolog B, nucleotide excision repair protein	protein-coding
mm_82349.1	chr9	13826982	13827000	-	1	NA	promoter-TSS (NR_037622)	promoter-TSS (NR_037622)	62	NR_037622	74360	Mm.157212	NM_026665	ENSMUSG00000031922	Cep57	3110002L15Rik|4921510P06Rik|4931428M20Rik|AI467480|Tsp57|mKIAA0092	centrosomal protein 57	protein-coding
mm_110481.1	chr12	51866403	51866417	-	1	NA	Intergenic	Intergenic	-36874	NM_144788	207304	Mm.249391	NM_144788	ENSMUSG00000035247	Hectd1	A630086P08Rik|AI844876|b2b327Clo|opm	HECT domain containing 1	protein-coding
mm_115302.1	chr13	112182504	112182517	+	1	NA	Intergenic	ORR1D2|LTR|ERVL-MaLR	-105941	NM_001168403	77318	Mm.159895	NM_029898	ENSMUSG00000049985	Ankrd55	C030011J08Rik	ankyrin repeat domain 55	protein-coding
mm_61097.1	chr7	51879042	51879064	+	1	NA	promoter-TSS (NM_001330607)	promoter-TSS (NM_001330607)	86	NM_001330607	14453	Mm.207360	NM_008087	ENSMUSG00000030498	Gas2	Gas-2	growth arrest specific 2	protein-coding
mm_21571.1	chr2	164237031	164237041	-	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	1305	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_39672.1	chr5	25510867	25510867	+	1	NA	Intergenic	U1|snRNA|snRNA	-5200	NM_198621	242891	Mm.291521	NM_198621	ENSMUSG00000038044	Cct8l1	Gm443	chaperonin containing TCP1, subunit 8 (theta)-like 1	protein-coding
mm_140697.1	chr17	14203696	14203779	-	1	NA	promoter-TSS (NM_172826)	promoter-TSS (NM_172826)	94	NM_172826	240025	Mm.79993	NM_172826	ENSMUSG00000048826	Dact2	2900084M21Rik|A630024E20|Dpr2|Frd2|dapper2	dishevelled-binding antagonist of beta-catenin 2	protein-coding
mm_48448.1	chr5	140702024	140702035	-	1	NA	intron (NM_001347517, intron 1 of 22)	CpG	349	NM_028833	74239	Mm.179704	NM_028833	ENSMUSG00000036555	Iqce	1700028P05Rik|mKIAA1023	IQ motif containing E	protein-coding
mm_148302.1	chr18	82798763	82798788	-	1	NA	Intergenic	Intergenic	-39736	NR_045389	76961	Mm.396392	NR_045389	ENSMUSG00000101773	2210420H20Rik	-	RIKEN cDNA 2210420H20 gene	ncRNA
mm_95257.1	chr11	44650045	44650090	+	1	NA	intron (NM_007897, intron 6 of 15)	intron (NM_007897, intron 6 of 15)	31967	NM_001290710	13591	Mm.439662	NM_007897	ENSMUSG00000057098	Ebf1	Ebf|O/E-1|OE-1|Olf-1|Olf1	early B cell factor 1	protein-coding
mm_9735.1	chr1	180235710	180235715	-	1	NA	intron (NM_001128605, intron 5 of 10)	intron (NM_001128605, intron 5 of 10)	10238	NM_011183	19165	Mm.330850	NM_011183	ENSMUSG00000010609	Psen2	ALG-3|Ad4h|Alg3|PS-2|PS2|Psnl2|STM2	presenilin 2	protein-coding
mm_153498.1	chr19	41332435	41332458	-	1	NA	intron (NM_031376, intron 2 of 16)	intron (NM_031376, intron 2 of 16)	52624	NM_031376	83490	Mm.222266	NM_031376	ENSMUSG00000025017	Pik3ap1	1810044J04Rik|BCAP	phosphoinositide-3-kinase adaptor protein 1	protein-coding
mm_119442.1	chr14	46832100	46832112	+	1	NA	promoter-TSS (NM_026832)	promoter-TSS (NM_026832)	-138	NM_026832	68755	Mm.343809	NM_026832	ENSMUSG00000055128	Cgrrf1	1110038G02Rik|1810009H17Rik|CGR19	cell growth regulator with ring finger domain 1	protein-coding
mm_117796.1	chr13	97198352	97198362	-	1	NA	promoter-TSS (NM_010422)	promoter-TSS (NM_010422)	0	NM_010422	15212	Mm.27816	NM_010422	ENSMUSG00000021665	Hexb	-	hexosaminidase B	protein-coding
mm_88951.1	chr10	81364321	81364372	+	1	NA	TTS (NM_028657)	TTS (NM_028657)	1474	NM_001014836	432479	Mm.440450	NM_001014836	ENSMUSG00000020234	4930404N11Rik	2210409H10Rik|5730551K18Rik|AI854616	RIKEN cDNA 4930404N11 gene	protein-coding
mm_73099.1	chr8	94568361	94568375	+	1	NA	intron (NM_153507, intron 14 of 15)	MIRc|SINE|MIR	33358	NM_028221	102122	Mm.250425	NM_028221	ENSMUSG00000031774	Fam192a	1700001O11Rik|2310065K24Rik|AI596259|Nip30	family with sequence similarity 192, member A	protein-coding
mm_6075.1	chr1	61851469	61851475	-	1	NA	intron (NM_001081050, intron 2 of 22)	MLT1A|LTR|ERVL-MaLR	212648	NM_001081050	72823	Mm.35153	NM_001081050	ENSMUSG00000052062	Pard3b	1810008K04Rik|2010002N16Rik|2810455B10Rik|Als2cr19|PAR3B|PAR3L|PAR3beta	par-3 family cell polarity regulator beta	protein-coding
mm_110024.1	chr12	16790209	16790210	-	1	NA	intron (NM_015764, intron 1 of 34)	intron (NM_015764, intron 1 of 34)	10677	NM_015764	268527	Mm.428062	NM_015764	ENSMUSG00000036523	Greb1	5730583K22Rik|9130004E13|AF180470|AU023194|mKIAA0575	gene regulated by estrogen in breast cancer protein	protein-coding
mm_68050.1	chr7	101550776	101550807	-	1	NA	Intergenic	Intergenic	5011	NM_007490	11871	Mm.439746	NM_007490	ENSMUSG00000092517	Art2a-ps	ARTC2|Art2a|Ly92a|Rt-6|Rt6|Rt6-1	ADP-ribosyltransferase 2a, pseudogene	protein-coding
mm_103352.1	chr11	74831795	74831804	-	1	NA	intron (NM_010813, intron 1 of 5)	CpG-2219	875	NM_010813	17428	Mm.3759	NM_010813	ENSMUSG00000000282	Mnt	Rox|bHLHd3	max binding protein	protein-coding
mm_5984.1	chr1	58422845	58422849	-	1	NA	intron (NR_027854, intron 1 of 10)	intron (NR_027854, intron 1 of 10)	1241	NR_027853	12747	Mm.1761	NM_009905	ENSMUSG00000026034	Clk1	STY	CDC-like kinase 1	protein-coding
mm_133948.1	chr16	3976489	3976512	-	1	NA	5' UTR (NM_001081280, exon 1 of 18)	5' UTR (NM_001081280, exon 1 of 18)	132	NM_175547	268857	Mm.215994	NM_175547	ENSMUSG00000049871	Nlrc3	CLR16.2|D230007K08Rik|mFLJ00348	NLR family, CARD domain containing 3	protein-coding
mm_169770.1	chr15	99875455	99875455	-	1	NA	promoter-TSS (NM_001113545)	promoter-TSS (NM_001113545)	1	NM_001113545	65970	Mm.33207	NM_023063	ENSMUSG00000023022	Lima1	Eplin	LIM domain and actin binding 1	protein-coding
mm_38432.1	chr4	139352300	139352313	-	1	NA	promoter-TSS (NM_146157)	promoter-TSS (NM_146157)	270	NM_001290810	69902	Mm.27871	NM_023536	ENSMUSG00000028741	Mrto4	2610012O22Rik|Mg684|Mrt4	mRNA turnover 4, ribosome maturation factor	protein-coding
mm_67999.1	chr7	100931483	100931533	-	1	NA	exon (NM_001081116, exon 1 of 21)	exon (NM_001081116, exon 1 of 21)	653	NM_001081116	207212	Mm.29954	NM_001081116	ENSMUSG00000032875	Arhgef17	8030463K16|AI428794|AW558066|BC035332|mKIAA0337	Rho guanine nucleotide exchange factor (GEF) 17	protein-coding
mm_109686.1	chr12	113141505	113141509	+	1	NA	intron (NM_001347443, intron 1 of 6)	intron (NM_001347443, intron 1 of 6)	902	NM_001347443	68337	Mm.133825	NM_024223	ENSMUSG00000006356	Crip2	0610010I23Rik|AW743261|C77570|CRP2|CRP4|Crp|ESP1|Hlp	cysteine rich protein 2	protein-coding
mm_104799.1	chr11	98774033	98774043	-	1	NA	intron (NM_145434, intron 1 of 7)	CpG	1339	NM_145434	217166	Mm.390397	NM_145434	ENSMUSG00000020889	Nr1d1	A530070C09Rik|R75201	nuclear receptor subfamily 1, group D, member 1	protein-coding
mm_107364.1	chr12	32848612	32848626	+	1	NA	exon (NM_021524, exon 10 of 11)	exon (NM_021524, exon 10 of 11)	24503	NR_045032	100504486	Mm.440246	NR_045032		Gdap10	Gdap-ps	ganglioside-induced differentiation-associated-protein 10	ncRNA
mm_22585.1	chr3	13471748	13471758	+	1	NA	promoter-TSS (NM_001163328)	promoter-TSS (NM_001163328)	98	NM_001163328	76897	Mm.422625	NM_178631	ENSMUSG00000039717	Ralyl	0710005M24Rik	RALY RNA binding protein-like	protein-coding
mm_105895.1	chr11	114982526	114982559	-	1	NA	TTS (NM_145437)	TTS (NM_145437)	7344	NM_145437	217305	Mm.275986	NM_145437	ENSMUSG00000034641	Cd300ld	4732429D16Rik|CLM5|Cd300ld1|LMIR4|MAIR-IV|clm-5	CD300 molecule like family member d	protein-coding
mm_21825.1	chr2	165368703	165368714	-	1	NA	Intergenic	CpG	-6589	NM_001005425	381405	Mm.296323	NM_001005425	ENSMUSG00000056824	Zfp663	Gm1008	zinc finger protein 663	protein-coding
mm_25886.1	chr3	130874170	130874180	+	1	NA	Intergenic	Intergenic	-143777	NM_001005859	68436	Mm.140568	NM_026724	ENSMUSG00000062006	Rpl34	1100001I22Rik	ribosomal protein L34	protein-coding
mm_135816.1	chr16	57754708	57754724	-	1	NA	promoter-TSS (NM_007739)	promoter-TSS (NM_007739)	21	NM_007739	12837	Mm.130388	NM_007739	ENSMUSG00000068196	Col8a1	Col8a-1	collagen, type VIII, alpha 1	protein-coding
mm_39854.1	chr5	30921525	30921550	+	1	NA	promoter-TSS (NM_001310524)	promoter-TSS (NM_001310524)	-22	NM_001310525	16548	Mm.22451	NM_008439	ENSMUSG00000029162	Khk	-	ketohexokinase	protein-coding
mm_17400.1	chr2	27205495	27205497	-	1	NA	intron (NM_138665, intron 17 of 20)	intron (NM_138665, intron 17 of 20)	39989	NM_138942	13166	Mm.167781	NM_138942	ENSMUSG00000000889	Dbh	-	dopamine beta hydroxylase	protein-coding
mm_100882.1	chr11	6003180	6003191	-	1	NA	intron (NM_007595, intron 3 of 20)	intron (NM_007595, intron 3 of 20)	47427	NM_019661	56418	Mm.294821	NM_019661	ENSMUSG00000002741	Ykt6	0610042I15Rik|1810013M05Rik|AW105923	YKT6 v-SNARE homolog (S. cerevisiae)	protein-coding
mm_108049.1	chr12	73908376	73908381	+	1	NA	intron (NM_010431, intron 1 of 14)	CpG	511	NM_001313919	15251	Mm.3879	NM_010431	ENSMUSG00000021109	Hif1a	AA959795|HIF-1-alpha|HIF1-alpha|HIF1alpha|MOP1|bHLHe78	hypoxia inducible factor 1, alpha subunit	protein-coding
mm_45261.1	chr5	63968852	63968864	-	1	NA	promoter-TSS (NM_145923)	promoter-TSS (NM_145923)	39	NM_145923	100532	Mm.243632	NM_145923	ENSMUSG00000047881	Rell1	AA536743	RELT-like 1	protein-coding
mm_115856.1	chr13	21291344	21291356	-	1	NA	exon (NM_010343, exon 2 of 5)	exon (NM_010343, exon 2 of 5)	1336	NM_010343	14780	Mm.1332	NM_010343	ENSMUSG00000004344	Gpx5	AV379049|Arep	glutathione peroxidase 5	protein-coding
mm_48726.1	chr5	147400353	147400377	-	1	NA	5' UTR (NM_010229, exon 1 of 24)	5' UTR (NM_010229, exon 1 of 24)	124	NM_010229	14255	Mm.194	NM_010229	ENSMUSG00000042817	Flt3	B230315G04|CD135|Flk-2|Flk2|Flt-3|Ly72|wmfl	FMS-like tyrosine kinase 3	protein-coding
mm_69848.1	chr7	141414116	141414130	-	1	NA	promoter-TSS (NM_172116)	promoter-TSS (NM_172116)	2	NM_172116	213350	Mm.290953	NM_172116	ENSMUSG00000051007	Pddc1	BC023835|D230016J19Rik	Parkinson disease 7 domain containing 1	protein-coding
mm_15278.1	chr2	155249972	155250001	+	1	NA	non-coding (NR_111891, exon 4 of 4)	non-coding (NR_111891, exon 4 of 4)	13378	NM_001291108	67068	Mm.23693	NM_025947	ENSMUSG00000047459	Dynlrb1	2010012N15Rik|2010320M17Rik|9430076K19Rik|AV124457|DNLC2A|Dncl2a|km23-1	dynein light chain roadblock-type 1	protein-coding
mm_142355.1	chr17	43630687	43630697	-	1	NA	promoter-TSS (NM_198418)	promoter-TSS (NM_198418)	-393	NM_001161367	210510	Mm.329058	NM_198418	ENSMUSG00000040140	Tdrd6	AB097085|Tdr2	tudor domain containing 6	protein-coding
mm_132784.1	chr16	44943702	44943710	+	1	NA	promoter-TSS (NM_029018)	promoter-TSS (NM_029018)	28	NM_001128132	74603	Mm.297337	NM_027578	ENSMUSG00000036172	Cd200r3	4733401I18Rik|4833409J19Rik|AI505817|BB106877|mCD200RLb	CD200 receptor 3	protein-coding
mm_136833.1	chr17	12744693	12744700	+	1	NA	intron (NR_027773, intron 1 of 2)	intron (NR_027773, intron 1 of 2)	3385	NR_027784	104103	Mm.26553	NR_002853	ENSMUSG00000078247	Airn	2810051F02Rik|2810434M15Rik|AI256653|AI597500|AW049873|Air|B930018I07Rik|D17Ertd663e|IGF2RAS	antisense Igf2r RNA	ncRNA
mm_142056.1	chr17	35667326	35667348	-	1	NA	TTS (NM_010364)	TTS (NM_010364)	255	NM_175137	68915	Mm.32002	NM_175137	ENSMUSG00000038838	Vars2	1190004I24Rik|Vars2l|mKIAA1885	valyl-tRNA synthetase 2, mitochondrial	protein-coding
mm_99211.1	chr11	101023280	101023286	+	1	NA	intron (NM_001243050, intron 5 of 20)	intron (NM_001243050, intron 5 of 20)	-7057	NR_105893	102466767		NR_105893	ENSMUSG00000098415	Mir6928	Gm27728|mmu-mir-6928	microRNA 6928	ncRNA
mm_41034.1	chr5	86071617	86071628	+	1	NA	promoter-TSS (NM_019992)	promoter-TSS (NM_019992)	-124	NM_019992	56792	Mm.131237	NM_019992	ENSMUSG00000029254	Stap1	AI586015|Brdg1|STAP-1	signal transducing adaptor family member 1	protein-coding
mm_135813.1	chr16	57606797	57606811	-	1	NA	promoter-TSS (NM_025599)	promoter-TSS (NM_025599)	63	NM_025599	66497	Mm.425976	NM_025599	ENSMUSG00000022748	Cmss1	1110001A06Rik|2610528E23Rik|4930572F24Rik|AV099812|AV122629	cms small ribosomal subunit 1	protein-coding
mm_146834.1	chr18	22828518	22828521	-	1	NA	intron (NM_001347510, intron 5 of 9)	intron (NM_001347510, intron 5 of 9)	210144	NM_001161483	319211	Mm.209896	NM_199024	ENSMUSG00000041923	Nol4	1700013J13Rik|4930568N03Rik|Gm1262	nucleolar protein 4	protein-coding
mm_150795.1	chr19	44303445	44303455	+	1	NA	TTS (NR_039574)	TTS (NR_039574)	279	NR_039574	100628619		NR_039574	ENSMUSG00000093315	Mir5114	mmu-mir-5114|mu-mir-5114	microRNA 5114	ncRNA
mm_121628.1	chr14	8317859	8317881	-	1	NA	Intergenic	Intergenic	-8094	NM_183187	268709	Mm.256058	NM_183187	ENSMUSG00000021750	Fam107a	DRR1	family with sequence similarity 107, member A	protein-coding
mm_142205.1	chr17	36981222	36981234	-	1	NA	promoter-TSS (NM_029747)	promoter-TSS (NM_029747)	9	NM_029747	76797	Mm.159787	NM_029747	ENSMUSG00000064308	2410137M14Rik	-	RIKEN cDNA 2410137M14 gene	protein-coding
mm_31186.1	chr4	43555674	43555712	+	1	NA	exon (NM_011602, exon 5 of 57)	exon (NM_011602, exon 5 of 57)	6890	NM_011602	21894	Mm.208601	NM_011602	ENSMUSG00000028465	Tln1	Tln	talin 1	protein-coding
mm_87366.1	chr10	43947875	43947900	+	1	NA	TTS (NM_130892)	TTS (NM_130892)	46080	NM_130892	170728	Mm.390253	NM_130892	ENSMUSG00000019864	Rtn4ip1	D10Ertd690e|NIMP	reticulon 4 interacting protein 1	protein-coding
mm_156935.1	chrX	169879756	169879774	+	1	NA	5' UTR (NM_001290505, exon 1 of 10)	5' UTR (NM_001290505, exon 1 of 10)	146	NM_001290505	17318	Mm.34441	NM_010797	ENSMUSG00000035299	Mid1	61B3-R|DXHXS1141|Fxy|Trim18	midline 1	protein-coding
mm_136180.1	chr16	88878032	88878040	-	1	NA	promoter-TSS (NM_130857)	promoter-TSS (NM_130857)	2	NM_130857	77918	Mm.28425	NM_130857	ENSMUSG00000060469	Krtap19-3	A030006N06Rik|Krtap16-5	keratin associated protein 19-3	protein-coding
mm_17383.1	chr2	27024300	27024321	-	1	NA	exon (NM_172659, exon 6 of 10)	exon (NM_172659, exon 6 of 10)	3688	NM_172659	227659	Mm.41203	NM_172659	ENSMUSG00000036067	Slc2a6	A330096C23|F630103L12Rik|Glut6|Glut9	solute carrier family 2 (facilitated glucose transporter), member 6	protein-coding
mm_25284.1	chr3	105687754	105687767	+	1	NA	promoter-TSS (NM_017397)	promoter-TSS (NM_017397)	-189	NM_017397	53975	Mm.272826	NM_017397	ENSMUSG00000027905	Ddx20	GEMIN3|dp103	DEAD (Asp-Glu-Ala-Asp) box polypeptide 20	protein-coding
mm_19645.1	chr2	102861693	102861712	-	1	NA	intron (NM_001039150, intron 2 of 13)	intron (NM_001039150, intron 2 of 13)	39963	NM_001177785	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_156092.1	chrX	111894952	111894962	+	1	NA	Intergenic	CpG	-197878	NM_001290459	245596	Mm.246623	NM_001080549	ENSMUSG00000034551	Hdx	D030011N01Rik|Gm380	highly divergent homeobox	protein-coding
mm_28937.1	chr3	98882234	98882239	-	1	NA	intron (NM_019545, intron 4 of 8)	intron (NM_019545, intron 4 of 8)	10994	NM_019545	56185	Mm.281874	NM_019545	ENSMUSG00000027870	Hao2	AI325478|Hao-2|Hao3|Haox3	hydroxyacid oxidase 2	protein-coding
mm_1132.1	chr1	60409661	60409754	+	1	NA	promoter-TSS (NM_001198570)	promoter-TSS (NM_001198570)	88	NM_001198570	329165	Mm.212066	NM_198127	ENSMUSG00000026782	Abi2	8430425M24Rik|AI839867|C130078H13	abl-interactor 2	protein-coding
mm_49933.1	chr6	39442272	39442277	+	1	NA	Intergenic	RMER17C|LTR|ERVK	-21905	NM_018810	54484	Mm.270484	NM_018810	ENSMUSG00000029922	Mkrn1	RFP	makorin, ring finger protein, 1	protein-coding
mm_83733.1	chr9	51057075	51057085	-	1	NA	3' UTR (NM_001033534, exon 8 of 8)	3' UTR (NM_001033534, exon 8 of 8)	20014	NM_001033534	244864	Mm.335152	NM_001033534	ENSMUSG00000060594	Layn	E030012M19Rik|Gm511	layilin	protein-coding
mm_142937.1	chr17	56005890	56005911	-	1	NA	promoter-TSS (NR_102313)	promoter-TSS (NR_102313)	-294	NR_102313	106766	Mm.204991	NM_145934	ENSMUSG00000038781	Stap2	AW049765|STAP-2	signal transducing adaptor family member 2	protein-coding
mm_155623.1	chrX	83592132	83592137	+	1	NA	intron (NM_007868, intron 7 of 78)	(CAGA)n|Simple_repeat|Simple_repeat	-104210	NM_021898	100502723	Mm.383210	NM_021898	ENSMUSG00000035522	Tsga8	Halap-X|Halapx	testis specific gene A8	protein-coding
mm_100098.1	chr11	115628405	115628423	+	1	NA	promoter-TSS (NM_001252384)	promoter-TSS (NM_001252384)	-119	NM_001252395	67283	Mm.383426	NM_026071	ENSMUSG00000020744	Slc25a19	2900089E13Rik|DNC|MUP1|TPC	solute carrier family 25 (mitochondrial thiamine pyrophosphate carrier), member 19	protein-coding
mm_152427.1	chr19	10676681	10676727	-	1	NA	exon (NM_021453, exon 2 of 9)	exon (NM_021453, exon 2 of 9)	1367	NM_021453	58803	Mm.34037	NM_021453	ENSMUSG00000024738	Pga5	1110035E17Rik|Pepf	pepsinogen 5, group I	protein-coding
mm_14607.1	chr2	136502244	136502260	+	1	NA	Intergenic	Intergenic	-30069	NM_175667	319196	Mm.477841	NM_175667	ENSMUSG00000074771	Ankef1	AV276460|Ankrd5	ankyrin repeat and EF-hand domain containing 1	protein-coding
mm_116652.1	chr13	49187939	49187952	-	1	NA	intron (NM_013610, intron 1 of 3)	CpG	398	NM_013610	18081	Mm.18503	NM_013610	ENSMUSG00000037966	Ninj1	AU024536	ninjurin 1	protein-coding
mm_49335.1	chr6	21307871	21307877	+	1	NA	intron (NM_019697, intron 1 of 5)	Lx4A|LINE|L1	91765	NM_019697	16508	Mm.425316	NM_019697	ENSMUSG00000060882	Kcnd2	AI839615|AW555701|Kv4.2|R75121|mKIAA1044	potassium voltage-gated channel, Shal-related family, member 2	protein-coding
mm_68608.1	chr7	116308335	116308362	-	1	NA	promoter-TSS (NM_001305185)	promoter-TSS (NM_001305185)	28	NM_001305185	233765	Mm.3741	NM_172743	ENSMUSG00000045659	Plekha7	A430081P20Rik|AI414265	pleckstrin homology domain containing, family A member 7	protein-coding
mm_117196.1	chr13	63701931	63701966	-	1	NA	intron (NR_126476, intron 4 of 4)	intron (NR_126476, intron 4 of 4)	32350	NR_126476	75522	Mm.54259	NR_126476		1700024I08Rik	-	RIKEN cDNA 1700024I08 gene	ncRNA
mm_85881.1	chr9	111001892	111001897	-	1	NA	Intergenic	Intergenic	-12181	NM_153100	235636	Mm.441138	NM_153100	ENSMUSG00000066319	Rtp3	Tmem7	receptor transporter protein 3	protein-coding
mm_59972.1	chr7	30457485	30457493	+	1	NA	promoter-TSS (NM_172898)	promoter-TSS (NM_172898)	26	NM_172898	243911	Mm.113908	NM_172898	ENSMUSG00000036915	Kirrel2	C330019F22Rik|NEPH3|NLG1	kin of IRRE like 2 (Drosophila)	protein-coding
mm_84481.1	chr9	66844371	66844381	-	1	NA	3' UTR (NM_173413, exon 8 of 8)	3' UTR (NM_173413, exon 8 of 8)	-9670	NM_026674	68318	Mm.284229	NM_026674	ENSMUSG00000053040	Aph1c	0610008A10Rik|APH-1b|Aph1b	aph1 homolog C, gamma secretase subunit	protein-coding
mm_141833.1	chr17	34628381	34628398	-	1	NA	promoter-TSS (NM_001302396)	promoter-TSS (NM_001302396)	-110	NM_001302393	54397	Mm.373627	NM_019441	ENSMUSG00000015474	Ppt2	0610007M19Rik|AA672937	palmitoyl-protein thioesterase 2	protein-coding
mm_41841.1	chr5	104434299	104434337	+	1	NA	promoter-TSS (NM_001204203)	promoter-TSS (NM_001204203)	-793	NM_001204201	20750	Mm.288474	NM_009263	ENSMUSG00000029304	Spp1	2AR|Apl-1|BNSP|BSPI|Bsp|ETA-1|Eta|OP|Opn|Opnl|Ric|Spp-1	secreted phosphoprotein 1	protein-coding
mm_72819.1	chr8	88137845	88137902	+	1	NA	promoter-TSS (NR_106039)	promoter-TSS (NR_106039)	-12	NM_172757	234549	Mm.36291	NM_172757	ENSMUSG00000031657	Heatr3	C030036P15Rik	HEAT repeat containing 3	protein-coding
mm_28780.1	chr3	95990847	95990857	-	1	NA	exon (NM_023320, exon 5 of 6)	exon (NM_023320, exon 5 of 6)	4987	NM_023320	67220	Mm.458147	NM_023320	ENSMUSG00000015745	Plekho1	2810052M02Rik|CKIP-1|Ckip1|JZA-20|Jza2	pleckstrin homology domain containing, family O member 1	protein-coding
mm_113656.1	chr13	42680788	42680803	+	1	NA	promoter-TSS (NM_001302635)	promoter-TSS (NM_001302635)	-4	NM_001302635	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding
mm_32130.1	chr4	99037894	99037897	+	1	NA	exon (NM_013913, exon 7 of 7)	exon (NM_013913, exon 7 of 7)	6941	NM_013913	30924	Mm.28341	NM_013913	ENSMUSG00000028553	Angptl3	hypl	angiopoietin-like 3	protein-coding
mm_25012.1	chr3	97930276	97930284	+	1	NA	5' UTR (NM_001033779, exon 1 of 2)	5' UTR (NM_001033779, exon 1 of 2)	107	NM_001033779	433632	Mm.212421	NM_001033779		Gm5544	EG433632	predicted gene 5544	protein-coding
mm_55122.1	chr6	50456354	50456362	-	1	NA	promoter-TSS (NM_001163645)	promoter-TSS (NM_001163645)	-4	NM_001347213	71720	Mm.44153	NM_027881	ENSMUSG00000029822	Osbpl3	1200014M06Rik|6720421I08Rik|A530055M08|ORP-3|ORP3|OSBP3	oxysterol binding protein-like 3	protein-coding
mm_43699.1	chr5	139217755	139217758	+	1	NA	intron (NM_001256115, intron 2 of 21)	intron (NM_001256115, intron 2 of 21)	2598	NM_001256116	77053	Mm.210845	NM_024451	ENSMUSG00000036817	Sun1	4632417G13Rik|5730434D03Rik|Unc84a|mKIAA0810	Sad1 and UNC84 domain containing 1	protein-coding
mm_94254.1	chr11	3330947	3330961	+	1	NA	exon (NM_178149, exon 1 of 6)	exon (NM_178149, exon 1 of 6)	223	NM_178149	216505	Mm.390323	NM_178149	ENSMUSG00000034614	Pik3ip1	1500004A08Rik|5830455E04Rik|Crkd|Hgfl	phosphoinositide-3-kinase interacting protein 1	protein-coding
mm_3008.1	chr1	133352511	133352529	+	1	NA	intron (NM_031192, intron 1 of 8)	intron (NM_031192, intron 1 of 8)	1846	NM_031192	19701	Mm.220955	NM_031192	ENSMUSG00000070645	Ren1	D19352|Ren|Ren-1|Ren-A|Ren1c|Ren1d|Rn-1|Rnr	renin 1 structural	protein-coding
mm_43184.1	chr5	128596905	128596924	+	1	NA	intron (NR_015517, intron 1 of 5)	intron (NR_015517, intron 1 of 5)	3773	NR_015517	319616	Mm.387738	NR_015517	ENSMUSG00000072591	5930412G12Rik	-	RIKEN cDNA 5930412G12 gene	ncRNA
mm_90340.1	chr10	127092668	127092688	+	1	NA	3' UTR (NM_001301014, exon 18 of 18)	3' UTR (NM_001301014, exon 18 of 18)	13771	NM_001033263	216439	Mm.336761	NM_001033263	ENSMUSG00000025422	Agap2	AGAP-2|Centg1|PIKE|cnt-g1|mKIAA0167	ArfGAP with GTPase domain, ankyrin repeat and PH domain 2	protein-coding
mm_109650.1	chr12	112861073	112861086	+	1	NA	promoter-TSS (NM_019925)	promoter-TSS (NM_019925)	-163	NM_019925	56696	Mm.20455	NM_019925	ENSMUSG00000021298	Gpr132	G2a	G protein-coupled receptor 132	protein-coding
mm_29600.1	chr3	120886729	120886746	-	1	NA	promoter-TSS (NR_130170)	promoter-TSS (NR_130170)	-5	NR_130170	320739	Mm.388474	NR_130170		6530403H02Rik	-	RIKEN cDNA 6530403H02 gene	ncRNA
mm_77388.1	chr8	120177421	120177435	-	1	NA	promoter-TSS (NM_001033980)	promoter-TSS (NM_001033980)	41	NM_001033980	436062	Mm.334852	NM_001033980	ENSMUSG00000042269	Fam92b	1700120B06Rik	family with sequence similarity 92, member B	protein-coding
mm_127356.1	chr15	100620030	100620059	+	1	NA	3' UTR (NM_011873, exon 4 of 4)	3' UTR (NM_011873, exon 4 of 4)	4382	NM_011873	23994	Mm.486175	NM_011873	ENSMUSG00000000346	Dazap2	AI314727|Brbp|Gcap28|Prtb|gt6-12|mKIAA0058	DAZ associated protein 2	protein-coding
mm_99266.1	chr11	101246384	101246391	+	1	NA	promoter-TSS (NM_019444)	promoter-TSS (NM_019444)	53	NM_019444	54409	Mm.260698	NM_019444	ENSMUSG00000001240	Ramp2	-	receptor (calcitonin) activity modifying protein 2	protein-coding
mm_62143.1	chr7	97101354	97101366	+	1	NA	intron (NM_001162477, intron 1 of 9)	intron (NM_001162477, intron 1 of 9)	19609	NM_010248	14389	Mm.42033	NM_010248	ENSMUSG00000004508	Gab2	AI463667|D130058I17Rik|p97	growth factor receptor bound protein 2-associated protein 2	protein-coding
mm_11737.1	chr2	37776230	37776258	+	1	NA	promoter-TSS (NM_001163566)	promoter-TSS (NM_001163566)	-5	NM_001163566	241324	Mm.392369	NM_001163566	ENSMUSG00000035403	Crb2	5930402A21|BC043114	crumbs family member 2	protein-coding
mm_132034.1	chr16	27411074	27411084	+	1	NA	intron (NM_001025615, intron 4 of 9)	intron (NM_001025615, intron 4 of 9)	22123	NM_001289436	67501	Mm.258985	NM_026202	ENSMUSG00000038127	Ccdc50	C3orf6	coiled-coil domain containing 50	protein-coding
mm_93806.1	chr10	120899096	120899106	-	1	NA	promoter-TSS (NM_177092)	promoter-TSS (NM_177092)	-130	NM_177092	320183	Mm.169755	NM_177092	ENSMUSG00000051236	Msrb3	D430026P16Rik|I-8-23|MsrB2	methionine sulfoxide reductase B3	protein-coding
mm_71928.1	chr8	70270245	70270262	+	1	NA	Intergenic	Intergenic	-12746	NM_011984	26558	Mm.388127	NM_011984	ENSMUSG00000003573	Homer3	AW146114	homer scaffolding protein 3	protein-coding
mm_58918.1	chr7	17715053	17715066	+	1	NA	exon (NM_028480, exon 2 of 9)	exon (NM_028480, exon 2 of 9)	1807	NM_028480	73250	Mm.244138	NM_028480	ENSMUSG00000008789	Ceacam5	1600029H12Rik|Psg30	carcinoembryonic antigen-related cell adhesion molecule 5	protein-coding
mm_147799.1	chr18	61658015	61658029	-	1	NA	intron (NR_045402, intron 1 of 4)	(TG)n|Simple_repeat|Simple_repeat	7516	NR_045402	328968	Mm.392305	NR_045402		Carmn	Carmen|E330013P06|Gm16908|Mir143hg	cardiac mesoderm enhancer-associated non-coding RNA	ncRNA
mm_83114.1	chr9	40376427	40376444	-	1	NA	intron (NM_172768, intron 2 of 19)	intron (NM_172768, intron 2 of 19)	42963	NR_040728	73558	Mm.398307	NR_040728		1700110K17Rik	-	RIKEN cDNA 1700110K17 gene	ncRNA
mm_164832.1	chr18	37873255	37873255	+	1	NA	intron (NM_007858, intron 16 of 26)	L1MC5|LINE|L1	-18595	NR_105945	102465592		NR_105945	ENSMUSG00000098706	Mir6979	Gm27524|mmu-mir-6979	microRNA 6979	ncRNA
mm_41330.1	chr5	90491689	90491719	+	1	NA	exon (NM_007423, exon 2 of 15)	exon (NM_007423, exon 2 of 15)	990	NM_007423	11576	Mm.358570	NM_007423	ENSMUSG00000054932	Afp	-	alpha fetoprotein	protein-coding
mm_39571.1	chr5	23433153	23433163	+	1	NA	non-coding (NR_040469, exon 1 of 1)	non-coding (NR_040469, exon 1 of 1)	1195	NR_040469	269630	Mm.425231	NR_040469	ENSMUSG00000073147	5031425E22Rik	-	RIKEN cDNA 5031425E22 gene	ncRNA
mm_374.1	chr1	34005919	34005943	+	1	NA	intron (NM_001276764, intron 3 of 102)	intron (NM_001276764, intron 3 of 102)	-5894	NM_133833	13518	Mm.336625	NM_010081	ENSMUSG00000026131	Dst	2310001O04Rik|A830042E19Rik|AW554249|BP230|BPAG1-n|Bpag|Bpag1|Macf2|ah|athetoid|dt|mKIAA0728|nmf203|nmf339	dystonin	protein-coding
mm_140803.1	chr17	22081179	22081210	-	1	NA	Intergenic	CpG	84783	NM_177596	210853	Mm.441622	NM_177596	ENSMUSG00000063383	Zfp947	6720451E15|EG210853|Gm4769	zinc finger protein 947	protein-coding
mm_12696.1	chr2	76406582	76406592	+	1	NA	promoter-TSS (NM_145525)	promoter-TSS (NM_145525)	79	NM_001290733	99031	Mm.240435	NM_145525	ENSMUSG00000042359	Osbpl6	1110062M20Rik|AI596402|ORP-6|mKIAA4128	oxysterol binding protein-like 6	protein-coding
mm_122282.1	chr14	34502664	34502715	-	1	NA	promoter-TSS (NM_009758)	promoter-TSS (NM_009758)	-143	NM_009758	12166	Mm.237825	NM_009758	ENSMUSG00000021796	Bmpr1a	1110037I22Rik|ALK3|AU045487|BMPR-IA|Bmpr	bone morphogenetic protein receptor, type 1A	protein-coding
mm_114815.1	chr13	91606445	91606450	+	1	NA	intron (NM_024186, intron 4 of 15)	intron (NM_024186, intron 4 of 15)	-135074	NM_028790	74156	Mm.275963	NM_028790	ENSMUSG00000021620	Acot12	1300004O04Rik|4930449F15Rik|AV027244|Cach|mCACH-1	acyl-CoA thioesterase 12	protein-coding
mm_17866.1	chr2	34862045	34862055	-	1	NA	intron (NM_080554, intron 5 of 9)	PB1D9|SINE|Alu	8912	NM_080554	66998	Mm.270632	NM_080554	ENSMUSG00000026869	Psmd5	1500032A03Rik|AW475925|S5b|W91691|mKIAA0072	proteasome (prosome, macropain) 26S subunit, non-ATPase, 5	protein-coding
mm_77953.1	chr9	7561646	7561656	+	1	NA	exon (NM_008611, exon 4 of 10)	exon (NM_008611, exon 4 of 10)	3222	NM_008611	17394	Mm.16415	NM_008611	ENSMUSG00000005800	Mmp8	BB138268	matrix metallopeptidase 8	protein-coding
mm_95676.1	chr11	54101229	54101275	+	1	NA	intron (NM_011031, intron 1 of 15)	CpG	328	NM_011031	18452	Mm.3705	NM_011031	ENSMUSG00000018906	P4ha2	AA407196|C76437|P4hl	procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha II polypeptide	protein-coding
mm_144192.1	chr18	7869708	7869727	+	1	NA	intron (NM_153085, intron 1 of 13)	CpG	520	NM_153085	225131	Mm.204524	NM_153085	ENSMUSG00000024283	Wac	1110067P07Rik|A230035H12Rik|AI256735|AI256776|Wwp4	WW domain containing adaptor with coiled-coil	protein-coding
mm_82649.1	chr9	22018675	22018685	-	1	NA	exon (NM_010487, exon 7 of 7)	exon (NM_010487, exon 7 of 7)	15692	NM_008925	19089	Mm.214593	NM_008925	ENSMUSG00000003402	Prkcsh	80K-H|PKCSH	protein kinase C substrate 80K-H	protein-coding
mm_7525.1	chr1	124202683	124202684	-	1	NA	Intergenic	Intergenic	-157124	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_102737.1	chr11	67250963	67250988	-	1	NA	exon (NM_010855, exon 22 of 40)	exon (NM_010855, exon 22 of 40)	13163	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_73139.1	chr8	94977331	94977337	+	1	NA	5' UTR (NM_001198894, exon 1 of 14)	5' UTR (NM_001198894, exon 1 of 14)	225	NM_001198894	14766	Mm.290834	NM_018882	ENSMUSG00000031785	Adgrg1	Cyt28|Gpr56|TM7LN4|TM7XN1	adhesion G protein-coupled receptor G1	protein-coding
mm_41660.1	chr5	98854832	98854842	+	1	NA	5' UTR (NM_001310677, exon 1 of 3)	5' UTR (NM_001310677, exon 1 of 3)	422	NM_001310677	110075	Mm.136461	NM_173404	ENSMUSG00000029335	Bmp3	9530029I04Rik	bone morphogenetic protein 3	protein-coding
mm_166683.1	chr6	99618890	99618915	-	1	NA	Intergenic	Intergenic	47869	NM_025829	66892	Mm.32889	NM_025829	ENSMUSG00000093661	Eif4e3	1300018P11Rik|AI451927|eIF4E-3	eukaryotic translation initiation factor 4E member 3	protein-coding
mm_167670.1	chr9	74714290	74714292	+	1	NA	Intergenic	Intergenic	-134146	NR_045284	100503019	Mm.482658	NR_045284	ENSMUSG00000066477	Gm16551	-	predicted gene 16551	ncRNA
mm_75334.1	chr8	43305837	43305849	-	1	NA	intron (NM_009556, intron 1 of 3)	B1_Mur3|SINE|Alu	1166	NM_009556	22702	Mm.285848	NM_009556	ENSMUSG00000051176	Zfp42	Rex-1|Rex1|Zfp-42	zinc finger protein 42	protein-coding
mm_136574.1	chr17	3463011	3463040	+	1	NA	intron (NM_001122998, intron 14 of 26)	B4A|SINE|B4	-19290	NM_001286758	24001	Mm.137134	NM_011878	ENSMUSG00000023800	Tiam2	3000002F19Rik|STEF|mKIAA2016	T cell lymphoma invasion and metastasis 2	protein-coding
mm_89665.1	chr10	97483482	97483515	+	1	NA	exon (NM_007833, exon 2 of 8)	exon (NM_007833, exon 2 of 8)	1167	NM_007833	13179	Mm.56769	NM_007833	ENSMUSG00000019929	Dcn	DC|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding
mm_149815.1	chr19	23904578	23904583	+	1	NA	intron (NM_177034, intron 2 of 12)	intron (NM_177034, intron 2 of 12)	126439	NM_001114174	381217	Mm.426078	NM_001114174	ENSMUSG00000071604	Fam189a2	AI414343|AI666772|Gm967	family with sequence similarity 189, member A2	protein-coding
mm_98746.1	chr11	96487543	96487545	+	1	NA	intron (NM_001033186, intron 1 of 12)	B4|SINE|B4	22953	NM_001177898	78473	Mm.395840	NM_001033186	ENSMUSG00000057058	Skap1	1700091G21Rik|Scap1|Skap-55	src family associated phosphoprotein 1	protein-coding
mm_158399.1	chrX	136743142	136743145	-	1	NA	promoter-TSS (NM_001168227)	promoter-TSS (NM_001168227)	186	NR_033324	436230	Mm.443049	NM_001033001	ENSMUSG00000087368	BC065397	R75336|parl7	cDNA sequence BC065397	ncRNA
mm_156585.1	chrX	152144198	152144226	+	1	NA	promoter-TSS (NM_001114664)	promoter-TSS (NM_001114664)	-56	NM_001114664	245666	Mm.33027	NM_001005475	ENSMUSG00000041115	Iqsec2	Brag1	IQ motif and Sec7 domain 2	protein-coding
mm_86933.1	chr10	24189084	24189100	+	1	NA	TTS (NM_016797)	TTS (NM_016797)	-34425	NM_021509	59012	Mm.285934	NM_021509	ENSMUSG00000020000	Moxd1	3230402N08Rik|MNCb-5203	monooxygenase, DBH-like 1	protein-coding
mm_12235.1	chr2	68582429	68582457	+	1	NA	promoter-TSS (NM_177651)	promoter-TSS (NM_177651)	30	NM_177651	227998	Mm.67562	NM_177651	ENSMUSG00000053896	4933409G03Rik	-	RIKEN cDNA 4933409G03 gene	protein-coding
mm_137834.1	chr17	30871285	30871310	+	1	NA	intron (NM_013811, intron 91 of 92)	(TC)n|Simple_repeat|Simple_repeat	-30570	NM_021332	14652	Mm.390969	NM_021332	ENSMUSG00000024027	Glp1r	GLP-1R|GLP1Rc	glucagon-like peptide 1 receptor	protein-coding
mm_16938.1	chr2	14073852	14073867	-	1	NA	promoter-TSS (NM_011484)	promoter-TSS (NM_011484)	75	NR_038162	70957	Mm.399049	NR_038162	ENSMUSG00000086657	Stamos	4921530L18Rik	signal transducing adaptor molecule (SH3 domain and ITAM motif) 1, opposite strand	ncRNA
mm_170485.1	chr19	15699801	15699811	+	1	NA	Intergenic	BGLII|LTR|ERVK	224816	NM_001205339	107272	Mm.289936	NM_177420	ENSMUSG00000024640	Psat1	D8Ertd814e|EPIP|PSA|Psat	phosphoserine aminotransferase 1	protein-coding
mm_101025.1	chr11	8579246	8579267	-	1	NA	intron (NM_001083587, intron 3 of 30)	intron (NM_001083587, intron 3 of 30)	85279	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_42552.1	chr5	116635294	116635299	+	1	NA	Intergenic	Intergenic	-43479	NM_026886	68955	Mm.146779	NM_026886	ENSMUSG00000063919	Srrm4	1500001A10Rik|B230202K19Rik|bv|mKIAA1853|nSR100	serine/arginine repetitive matrix 4	protein-coding
mm_81487.1	chr9	110003177	110003192	+	1	NA	3' UTR (NM_001205331, exon 4 of 4)	3' UTR (NM_001205331, exon 4 of 4)	-48837	NM_001311163	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_127819.1	chr15	5108470	5108490	-	1	NA	promoter-TSS (NM_001163138)	promoter-TSS (NM_001163138)	53	NM_001163138	239319	Mm.31252	NM_001163138	ENSMUSG00000041849	Card6	D730008L15	caspase recruitment domain family, member 6	protein-coding
mm_12215.1	chr2	67508144	67508149	+	1	NA	exon (NM_001083919, exon 7 of 9)	exon (NM_001083919, exon 7 of 9)	62144	NM_001024618	241431	Mm.261043	NM_001024618	ENSMUSG00000027022	Xirp2	2310003D02Rik|2310008C07Rik|A530024P18Rik|AI452089|Cmya3|Gm352|Xin2	xin actin-binding repeat containing 2	protein-coding
mm_49669.1	chr6	31288989	31289000	+	1	NA	intron (NR_040261, intron 3 of 4)	intron (NR_040261, intron 3 of 4)	68643	NR_040261	73652	Mm.441297	NR_040257	ENSMUSG00000087380	2210408F21Rik	-	RIKEN cDNA 2210408F21 gene	ncRNA
mm_136471.1	chr16	95728917	95728962	-	1	NA	Intergenic	Intergenic	26532	NM_011809	23872	Mm.290207	NM_011809	ENSMUSG00000022895	Ets2	AU022856|Ets-2	E26 avian leukemia oncogene 2, 3' domain	protein-coding
mm_161457.1	chr15	76208698	76208698	-	1	NA	promoter-TSS (NM_201388)	promoter-TSS (NM_201388)	-45	NM_201387	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
mm_87334.1	chr10	43221467	43221501	+	1	NA	promoter-TSS (NM_001168289)	promoter-TSS (NM_001168289)	-2	NM_027772	71365	Mm.490430	NM_027772	ENSMUSG00000038240	Pdss2	5430420P03Rik|Gm60|Plmp|kd|mDLP1	prenyl (solanesyl) diphosphate synthase, subunit 2	protein-coding
mm_160862.1	chr11	59737180	59737180	+	1	NA	exon (NM_201245, exon 7 of 23)	exon (NM_201245, exon 7 of 23)	2974	NR_045476	69320	Mm.443242	NR_045476	ENSMUSG00000086330	1700007J10Rik	4930573L17Rik	RIKEN cDNA 1700007J10 gene	ncRNA
mm_5896.1	chr1	54557596	54557698	-	1	NA	promoter-TSS (NM_001163314)	promoter-TSS (NM_001163314)	37	NM_001163314	241062	Mm.103539	NM_175508	ENSMUSG00000073678	Pgap1	5033403E17Rik|9030223K07Rik|A530084K22|D230012E17Rik|oto	post-GPI attachment to proteins 1	protein-coding
mm_110140.1	chr12	26448155	26448175	-	1	NA	intron (NM_021384, intron 4 of 5)	intron (NM_021384, intron 4 of 5)	8287	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_165394.1	chr2	132006783	132006811	+	1	NA	intron (NM_175445, intron 4 of 10)	intron (NM_175445, intron 4 of 10)	23191	NM_175445	215653	Mm.204737	NM_175445	ENSMUSG00000027339	Rassf2	3830431H01Rik|9030412M04Rik|AI852669|AW495050	Ras association (RalGDS/AF-6) domain family member 2	protein-coding
mm_25593.1	chr3	116899672	116899687	+	1	NA	intron (NM_009146, intron 12 of 16)	B3A|SINE|B2	37999	NM_009146	20321	Mm.66293	NM_009146	ENSMUSG00000033386	Frrs1	AI131732|Sdfr2	ferric-chelate reductase 1	protein-coding
mm_74544.1	chr8	10483938	10483948	-	1	NA	intron (NM_001319151, intron 23 of 34)	MTEa|LTR|ERVL-MaLR	330032	NM_001319151	244281	Mm.422761	NM_001081397	ENSMUSG00000039057	Myo16	BM140241|C230040D10Rik|Gm1105|NYAP3|mKIAA0865	myosin XVI	protein-coding
mm_66363.1	chr7	43532458	43532464	-	1	NA	intron (NM_021293, intron 2 of 5)	intron (NM_021293, intron 2 of 5)	710	NM_001111058	12489	Mm.140157	NM_021293	ENSMUSG00000004609	Cd33	Siglec-3|gp67	CD33 antigen	protein-coding
mm_101725.1	chr11	42182531	42182539	-	1	NA	5' UTR (NM_010250, exon 1 of 10)	5' UTR (NM_010250, exon 1 of 10)	395	NM_010250	14394	Mm.439668	NM_010250	ENSMUSG00000010803	Gabra1	Gabra-1	gamma-aminobutyric acid (GABA) A receptor, subunit alpha 1	protein-coding
mm_148738.1	chr19	5929940	5929953	+	1	NA	Intergenic	Intergenic	-5130	NM_026772	104252	Mm.491103	NM_026772	ENSMUSG00000045664	Cdc42ep2	1110008C05Rik|Borg1|Cep2|D19Bwg1013e	CDC42 effector protein (Rho GTPase binding) 2	protein-coding
mm_79594.1	chr9	58435836	58435838	+	1	NA	Intergenic	Intergenic	-19336	NR_040736	74879	Mm.416924	NR_040736	ENSMUSG00000097651	4930461G14Rik	-	RIKEN cDNA 4930461G14 gene	ncRNA
mm_82.1	chr1	6842005	6842028	+	1	NA	intron (NM_001244692, intron 15 of 23)	intron (NM_001244692, intron 15 of 23)	111965	NR_045188	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding
mm_125955.1	chr15	76249268	76249342	+	1	NA	exon (NM_023168, exon 7 of 7)	exon (NM_023168, exon 7 of 7)	1114	NR_105918	102465575		NR_105918	ENSMUSG00000098625	Mir6953	Gm27738|mmu-mir-6953	microRNA 6953	ncRNA
mm_112088.1	chr12	112674754	112674764	-	1	NA	promoter-TSS (NM_001165894)	promoter-TSS (NM_001165894)	125	NM_001331107	11651	Mm.6645	NM_009652	ENSMUSG00000001729	Akt1	Akt|LTR-akt|PKB|PKB/Akt|PKBalpha|Rac	thymoma viral proto-oncogene 1	protein-coding
mm_165036.1	chr19	37434751	37434824	+	1	NA	promoter-TSS (NM_008245)	promoter-TSS (NM_008245)	-54	NM_008245	15242	Mm.33896	NM_008245	ENSMUSG00000024986	Hhex	Hex|Hex1|Hhex-rs2|Prh|Prhx	hematopoietically expressed homeobox	protein-coding
mm_55675.1	chr6	72557790	72557815	-	1	NA	exon (NM_001042534, exon 6 of 10)	exon (NM_001042534, exon 6 of 10)	8155	NM_001271395	12332	Mm.18626	NM_007599	ENSMUSG00000056737	Capg	gCap39|mbh1	capping protein (actin filament), gelsolin-like	protein-coding
mm_43952.1	chr5	145204524	145204574	+	1	NA	promoter-TSS (NM_001167944)	promoter-TSS (NM_001167944)	-10	NM_016683	22757	Mm.332842	NM_016683	ENSMUSG00000055991	Zkscan5	AI132486|AI326970|Zfp95|hKraba1	zinc finger with KRAB and SCAN domains 5	protein-coding
mm_138505.1	chr17	35235088	35235111	+	1	NA	promoter-TSS (NM_001347351)	promoter-TSS (NM_001347351)	89	NM_001347351	66237	Mm.396107	NM_023179	ENSMUSG00000024403	Atp6v1g2	1500002D01Rik|Atp6g2|NG38|VAG2	ATPase, H+ transporting, lysosomal V1 subunit G2	protein-coding
mm_167663.1	chr9	71485858	71485873	+	1	NA	promoter-TSS (NM_001164793)	promoter-TSS (NM_001164793)	118	NM_178602	28015	Mm.21094	NM_178602	ENSMUSG00000032199	Polr2m	AA407243|AA408799|AI303746|AW553238|D9Wsu138e|Grinl1a|mKIAA4185	polymerase (RNA) II (DNA directed) polypeptide M	protein-coding
mm_74030.1	chr8	121792450	121792472	+	1	NA	Intergenic	Intergenic	37108	NM_145605	234825	Mm.209329	NM_145605	ENSMUSG00000040263	Klhdc4	AA408426|AV352552|BC012312|G430025P05Rik	kelch domain containing 4	protein-coding
mm_163566.1	chr13	28532500	28532502	+	1	NA	intron (NR_045053, intron 7 of 8)	intron (NR_045053, intron 7 of 8)	178372	NR_105787	102466635		NR_105787	ENSMUSG00000099158	Mir6368	Gm27800|mmu-mir-6368	microRNA 6368	ncRNA
mm_129855.1	chr15	83174251	83174276	-	1	NA	Intergenic	Intergenic	-2055	NM_029787	109754	Mm.22560	NM_029787	ENSMUSG00000018042	Cyb5r3	0610016L08Rik|2500002N19Rik|C85115|Dia-1|Dia1|WU:AL591952.1-001|WU:AL591952.1-002|WU:AL591952.1-003|WU:Cyb5r3	cytochrome b5 reductase 3	protein-coding
mm_27160.1	chr3	33143009	33143024	-	1	NA	5' UTR (NM_001163516, exon 1 of 13)	5' UTR (NM_001163516, exon 1 of 13)	175	NM_001163516	58869	Mm.151332	NM_021483	ENSMUSG00000027674	Pex5l	1700016J08Rik|PXR2|Pex2|TRIP8b|pex5Rp	peroxisomal biogenesis factor 5-like	protein-coding
mm_167987.1	chrX	170009290	170009291	+	1	NA	Intergenic	Intergenic	-30373	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_72586.1	chr8	84338595	84338608	+	1	NA	Intergenic	Intergenic	-68199	NM_026350	67736	Mm.30095	NM_026350	ENSMUSG00000004994	Ccdc130	4930527D15Rik|C77430	coiled-coil domain containing 130	protein-coding
mm_154896.1	chrX	20870277	20870298	+	1	NA	5' UTR (NM_011593, exon 1 of 6)	5' UTR (NM_011593, exon 1 of 6)	121	NM_001294280	21857	Mm.8245	NM_011593	ENSMUSG00000001131	Timp1	Clgi|EPA|TIMP-1|TPA-S1|Timp	tissue inhibitor of metalloproteinase 1	protein-coding
mm_52132.1	chr6	97944565	97944580	+	1	NA	intron (NM_001113198, intron 2 of 9)	intron (NM_001113198, intron 2 of 9)	14755	NM_001178049	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_85453.1	chr9	105131776	105131833	-	1	NA	promoter-TSS (NM_029385)	promoter-TSS (NM_029385)	1	NM_029385	75686	Mm.305810	NM_029385	ENSMUSG00000032565	Nudt16	2310041H06Rik|2810047L04Rik|2900006H04Rik|AI851783	nudix (nucleoside diphosphate linked moiety X)-type motif 16	protein-coding
mm_50180.1	chr6	41605025	41605033	+	1	NA	promoter-TSS (NM_001146351)	promoter-TSS (NM_001146351)	-453	NM_001146351	13848	Mm.271976	NM_007680	ENSMUSG00000029869	Ephb6	Cekl|Mep	Eph receptor B6	protein-coding
mm_62487.1	chr7	101896818	101896850	+	1	NA	intron (NM_001291349, intron 1 of 4)	intron (NM_001291349, intron 1 of 4)	503	NM_001291349	75430	Mm.284491	NM_027532	ENSMUSG00000030649	Anapc15	3200002M19Rik|6330414C15Rik|APC15	anaphase prompoting complex C subunit 15	protein-coding
mm_8763.1	chr1	160792800	160792832	-	1	NA	5' UTR (NM_013862, exon 1 of 21)	5' UTR (NM_013862, exon 1 of 21)	122	NM_013862	29809	Mm.25833	NM_013862	ENSMUSG00000026721	Rabgap1l	5830411O09Rik|8430421H08Rik|9630005B12Rik|AW049894|HHL|Hh1|mKIAA0471	RAB GTPase activating protein 1-like	protein-coding
mm_77548.1	chr8	123236199	123236237	-	1	NA	promoter-TSS (NM_030176)	promoter-TSS (NM_030176)	-9	NM_030176	78779	Mm.41459	NM_030176	ENSMUSG00000033594	Spata2l	2610039E05Rik|AI648233|mKIAA4138	spermatogenesis associated 2-like	protein-coding
mm_141490.1	chr17	31277390	31277404	-	1	NA	promoter-TSS (NM_025290)	promoter-TSS (NM_025290)	-41	NM_025290	22092	Mm.12743	NM_025290	ENSMUSG00000024033	Rsph1	MCA|Tsga2	radial spoke head 1 homolog (Chlamydomonas)	protein-coding
mm_36344.1	chr4	73771092	73771099	-	1	NA	intron (NM_001017427, intron 3 of 17)	intron (NM_001017427, intron 3 of 17)	19507	NM_001017427	242505	Mm.389582	NM_001017427	ENSMUSG00000043003	Rasef	BC030882|RAB45	RAS and EF hand domain containing	protein-coding
mm_171449.1	chr4	145432386	145432387	+	1	NA	Intergenic	Intergenic	-31824	NR_002888	545700	Mm.389595	NR_002888	ENSMUSG00000052912	Smarca5-ps	9230115A19Rik|OTTMUSG00000011029	SWI/SNF related, matrix associated, actin depenent ragulator of chromatin, subfamily a, member 5, pseudogene	pseudo
mm_40649.1	chr5	65107596	65107613	+	1	NA	promoter-TSS (NM_001347355)	promoter-TSS (NM_001347355)	36	NM_001347355	71778	Mm.10281	NM_175174	ENSMUSG00000054920	Klhl5	1300013C10Rik	kelch-like 5	protein-coding
mm_43809.1	chr5	142904354	142904383	+	1	NA	exon (NM_007393, exon 4 of 6)	exon (NM_007393, exon 4 of 6)	2386	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_65422.1	chr7	25297479	25297532	-	1	NA	intron (NM_008776, intron 1 of 5)	CpG-12842	450	NM_008776	18476	Mm.597	NM_008776	ENSMUSG00000005447	Pafah1b3	Pafahg|mus[g]	platelet-activating factor acetylhydrolase, isoform 1b, subunit 3	protein-coding
mm_165709.1	chr3	98352169	98352173	-	1	NA	Intergenic	Intergenic	-12202	NM_016966	236539	Mm.16898	NM_016966	ENSMUSG00000053398	Phgdh	3-PGDH|3PGDH|4930479N23|A10|PGAD|PGD|PGDH|SERA	3-phosphoglycerate dehydrogenase	protein-coding
mm_125717.1	chr15	68929360	68929376	+	1	NA	intron (NM_010158, intron 1 of 8)	intron (NM_010158, intron 1 of 8)	948	NM_010158	13992	Mm.17964	NM_010158	ENSMUSG00000022332	Khdrbs3	Etle|SLM-2|Salp|Slm2|T-STAR	KH domain containing, RNA binding, signal transduction associated 3	protein-coding
mm_133384.1	chr16	84773653	84773655	+	1	NA	promoter-TSS (NM_023844)	promoter-TSS (NM_023844)	-469	NM_023844	67374	Mm.41758	NM_023844	ENSMUSG00000053062	Jam2	1110002N23Rik|2410030G21Rik|2410167M24Rik|JAM-2|JAM-B|Jcam2|VE-JAM	junction adhesion molecule 2	protein-coding
mm_28292.1	chr3	89093286	89093356	-	1	NA	promoter-TSS (NM_001083807)	promoter-TSS (NM_001083807)	42	NM_001083807	72296	Mm.27687	NM_028188	ENSMUSG00000041263	Rusc1	2210403N08Rik|AA408288|NESCA	RUN and SH3 domain containing 1	protein-coding
mm_92772.1	chr10	81167771	81167781	-	1	NA	promoter-TSS (NM_021501)	promoter-TSS (NM_021501)	-56	NM_021501	59004	Mm.34428	NM_021501	ENSMUSG00000004934	Pias4	PIASY|Pias-gamma|Piasg	protein inhibitor of activated STAT 4	protein-coding
mm_162412.1	chr1	87128603	87128605	+	1	NA	TTS (NM_007432)	TTS (NM_007432)	3596	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_24291.1	chr3	89246398	89246493	+	1	NA	promoter-TSS (NM_025327)	promoter-TSS (NM_025327)	7	NM_025327	66059	Mm.177991	NM_025327	ENSMUSG00000042747	Krtcap2	0610010I12Rik|Kcp2	keratinocyte associated protein 2	protein-coding
mm_101287.1	chr11	21997043	21997090	-	1	NA	intron (NM_011023, intron 4 of 4)	intron (NM_011023, intron 4 of 4)	4585	NM_011023	18423	Mm.129663	NM_011023	ENSMUSG00000005917	Otx1	A730044F23Rik|jv	orthodenticle homeobox 1	protein-coding
mm_53182.1	chr6	125432680	125432690	+	1	NA	Intergenic	Intergenic	-52181	NM_198604	213522	Mm.333396	NM_198604	ENSMUSG00000038167	Plekhg6	BC026778|Gm155	pleckstrin homology domain containing, family G (with RhoGef domain) member 6	protein-coding
mm_26523.1	chr3	145938005	145938063	+	1	NA	promoter-TSS (NM_025555)	promoter-TSS (NM_025555)	2	NM_025555	66421	Mm.25137	NM_025555	ENSMUSG00000036873	2410004B18Rik	4930572C24Rik	RIKEN cDNA 2410004B18 gene	protein-coding
mm_32240.1	chr4	102421550	102421573	+	1	NA	intron (NM_019840, intron 1 of 14)	intron (NM_019840, intron 1 of 14)	-148499	NM_001177980	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_34923.1	chr4	155803601	155803640	+	1	NA	promoter-TSS (NM_025570)	promoter-TSS (NM_025570)	2	NM_025570	66448	Mm.23825	NM_025570	ENSMUSG00000029066	Mrpl20	2610008D01Rik|4930425I20Rik	mitochondrial ribosomal protein L20	protein-coding
mm_86838.1	chr10	21396099	21396134	+	1	NA	3' UTR (NM_178713, exon 7 of 7)	3' UTR (NM_178713, exon 7 of 7)	18816	NM_178713	237320	Mm.90181	NM_178713	ENSMUSG00000037542	Aldh8a1	Raldh4	aldehyde dehydrogenase 8 family, member A1	protein-coding
mm_116427.1	chr13	41847522	41847532	-	1	NA	promoter-TSS (NM_001145875)	promoter-TSS (NM_001145875)	-39	NM_175417	109254	Mm.25195	NM_175417	ENSMUSG00000058022	Adtrp	9530008L14Rik	androgen dependent TFPI regulating protein	protein-coding
mm_154043.1	chr19	53944234	53944255	-	1	NA	promoter-TSS (NM_019658)	promoter-TSS (NM_019658)	-62	NM_001168505	56392	Mm.228669	NM_019658	ENSMUSG00000024976	Shoc2	AU017287|Sur8|mKIAA0862	soc-2 (suppressor of clear) homolog (C. elegans)	protein-coding
mm_15516.1	chr2	158313239	158313260	+	1	NA	intron (NM_008489, intron 3 of 14)	intron (NM_008489, intron 3 of 14)	6756	NM_008489	16803	Mm.218846	NM_008489	ENSMUSG00000016024	Lbp	Bpifd2|Ly88	lipopolysaccharide binding protein	protein-coding
mm_167750.1	chr9	109931888	109931892	+	1	NA	5' UTR (NM_008633, exon 1 of 19)	5' UTR (NM_008633, exon 1 of 19)	116	NM_008633	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_113833.1	chr13	47106402	47106411	+	1	NA	promoter-TSS (NM_025900)	promoter-TSS (NM_025900)	-185	NM_025900	110052	Mm.131150	NM_025900	ENSMUSG00000021377	Dek	1810019E15Rik|D13H6S231E	DEK oncogene (DNA binding)	protein-coding
mm_88985.1	chr10	81564446	81564456	+	1	NA	intron (NR_074087, intron 3 of 6)	intron (NR_074087, intron 3 of 6)	5007	NM_001276288	14797	Mm.180013	NM_010347	ENSMUSG00000054452	Aes	AL024115|Esp1|Grg|Grg-5|Grg5|Tle5	amino-terminal enhancer of split	protein-coding
mm_67267.1	chr7	75780507	75780528	-	1	NA	Intergenic	Intergenic	-67821	NM_001122780	207952	Mm.206223	NM_029652	ENSMUSG00000055652	Klhl25	2810402K13Rik|BC027373|Enc-1	kelch-like 25	protein-coding
mm_144471.1	chr18	23858068	23858091	+	1	NA	exon (NM_001162942, exon 5 of 8)	exon (NM_001162942, exon 5 of 8)	54109	NM_153058	212307	Mm.132237	NM_153058	ENSMUSG00000024277	Mapre2	AI314113|C820009F03Rik|D18Abb1e|EB1|EB2|RP1	microtubule-associated protein, RP/EB family, member 2	protein-coding
mm_20627.1	chr2	131991650	131991695	-	1	NA	Intergenic	Intergenic	38316	NM_175445	215653	Mm.204737	NM_175445	ENSMUSG00000027339	Rassf2	3830431H01Rik|9030412M04Rik|AI852669|AW495050	Ras association (RalGDS/AF-6) domain family member 2	protein-coding
mm_116778.1	chr13	52982701	52982707	-	1	NA	Intergenic	Intergenic	-1665	NM_017373	18030	Mm.136604	NM_017373	ENSMUSG00000056749	Nfil3	AV225605|E4BP4	nuclear factor, interleukin 3, regulated	protein-coding
mm_166991.1	chr7	46089099	46089099	+	1	NA	Intergenic	L1M2|LINE|L1	11138	NM_010602	16514	Mm.333863	NM_010602	ENSMUSG00000096146	Kcnj11	Kir6.2|mBIR	potassium inwardly rectifying channel, subfamily J, member 11	protein-coding
mm_58197.1	chr6	143100029	143100109	-	1	NA	promoter-TSS (NM_029897)	promoter-TSS (NM_029897)	83	NM_001286578	74741	Mm.130260	NM_029081	ENSMUSG00000030279	C2cd5	5730419I09Rik|C030008B15Rik|CDP138	C2 calcium-dependent domain containing 5	protein-coding
mm_78462.1	chr9	32501296	32501305	+	1	NA	intron (NM_008026, intron 1 of 8)	intron (NM_008026, intron 1 of 8)	40152	NM_008026	14247	Mm.258908	NM_008026	ENSMUSG00000016087	Fli1	EWSR2|Fli-1|SIC-1|Sic1	Friend leukemia integration 1	protein-coding
mm_93980.1	chr10	127349103	127349105	-	1	NA	TTS (NM_008382)	TTS (NM_008382)	2744	NM_008382	16326	Mm.3510	NM_008382	ENSMUSG00000047492	Inhbe	-	inhibin beta-E	protein-coding
mm_54012.1	chr6	8180260	8180270	-	1	NA	intron (NM_001037865, intron 1 of 34)	intron (NM_001037865, intron 1 of 34)	12352	NM_001037865	213945	Mm.297404	NM_001037865	ENSMUSG00000068794	Col28a1	Col28|Gm466	collagen, type XXVIII, alpha 1	protein-coding
mm_40021.1	chr5	33336228	33336254	+	1	NA	intron (NM_021500, intron 1 of 8)	CpG	669	NM_021500	59003	Mm.138617	NM_021500	ENSMUSG00000079562	Maea	1110030D19Rik|EMP|Gid9	macrophage erythroblast attacher	protein-coding
mm_30672.1	chr4	11156766	11156778	+	1	NA	intron (NM_021897, intron 1 of 3)	intron (NM_021897, intron 1 of 3)	331	NM_021897	60599	Mm.393018	NM_021897	ENSMUSG00000028211	Trp53inp1	2700057G22Rik|SIP|SIP18|SIP27|Stinp|Teap	transformation related protein 53 inducible nuclear protein 1	protein-coding
mm_156705.1	chrX	159627083	159627103	+	1	NA	promoter-TSS (NM_001135727)	promoter-TSS (NM_001135727)	-179	NM_001135727	58194	Mm.286495	NM_021389	ENSMUSG00000040990	Sh3kbp1	1200007H22Rik|1700125L08Rik|5830464D22Rik|AI447724|Cin85|IN85|Ruk|Seta	SH3-domain kinase binding protein 1	protein-coding
mm_53373.1	chr6	129462658	129462677	+	1	NA	non-coding (NR_132130, exon 6 of 6)	non-coding (NR_132130, exon 6 of 6)	10112	NM_001309637	56644	Mm.239516	NM_020008	ENSMUSG00000079293	Clec7a	BGR|Clecsf12|beta-GR	C-type lectin domain family 7, member a	protein-coding
mm_9592.1	chr1	174921748	174921756	-	1	NA	promoter-TSS (NM_011825)	promoter-TSS (NM_011825)	67	NM_011825	23893	Mm.25760	NM_011825	ENSMUSG00000050069	Grem2	Gremlin2|Prdc	gremlin 2, DAN family BMP antagonist	protein-coding
mm_123291.1	chr14	61556724	61556741	-	1	NA	5' UTR (NM_001310603, exon 1 of 4)	5' UTR (NM_001310603, exon 1 of 4)	154	NM_025697	66674	Mm.282706	NM_025697	ENSMUSG00000021930	Spryd7	6330409N04Rik|Clld6	SPRY domain containing 7	protein-coding
mm_29698.1	chr3	123117014	123117051	-	1	NA	exon (NM_080451, exon 3 of 5)	exon (NM_080451, exon 3 of 5)	-82045	NM_021503	59006	Mm.141157	NM_021503	ENSMUSG00000028116	Myoz2	1110012I24Rik|Fatz-2|Myozl2	myozenin 2	protein-coding
mm_9118.1	chr1	170211744	170211746	-	1	NA	intron (NM_010633, intron 2 of 7)	intron (NM_010633, intron 2 of 7)	3648	NM_010633	16589	Mm.209150	NM_010633	ENSMUSG00000026667	Uhmk1	4732477C12Rik|4930500M09Rik|AA673513|AI449218|AU021979|C820018A03Rik|KIS|Kist|OTTMUSG00000021542|P-CIP2	U2AF homology motif (UHM) kinase 1	protein-coding
mm_144873.1	chr18	36751101	36751113	+	1	NA	exon (NM_011879, exon 9 of 20)	exon (NM_011879, exon 9 of 20)	6451	NM_011879	24010	Mm.30234	NM_011879	ENSMUSG00000024474	Ik	MuRED	IK cytokine	protein-coding
mm_43370.1	chr5	135632639	135632647	+	1	NA	promoter-TSS (NM_146002)	promoter-TSS (NM_146002)	-11	NM_146002	215160	Mm.295438	NM_031398	ENSMUSG00000039917	Rhbdd2	0610011L13Rik|AI480532|Rhbdl7|Usmg1	rhomboid domain containing 2	protein-coding
mm_80471.1	chr9	78168831	78168833	+	1	NA	3' UTR (NM_001163780, exon 14 of 14)	3' UTR (NM_001163780, exon 14 of 14)	-7082	NR_040401	320295	Mm.131285	NR_040401	ENSMUSG00000097574	C920006O11Rik	-	RIKEN cDNA C920006O11 gene	ncRNA
mm_98851.1	chr11	97662445	97662462	+	1	NA	promoter-TSS (NM_139311)	promoter-TSS (NM_139311)	-959	NM_139311	246198	Mm.23685	NM_139311	ENSMUSG00000038437	Mllt6	AI315037|Af17	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 6	protein-coding
mm_81396.1	chr9	108991953	108991969	+	1	NA	promoter-TSS (NM_173019)	promoter-TSS (NM_173019)	59	NM_173019	270198	Mm.132391	NM_173019	ENSMUSG00000025648	Pfkfb4	C230090D14	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4	protein-coding
mm_90804.1	chr10	7664076	7664085	-	1	NA	promoter-TSS (NM_008786)	promoter-TSS (NM_008786)	-472	NM_001347228	18537	Mm.258431	NM_008786	ENSMUSG00000019795	Pcmt1	C79501|PIMT	protein-L-isoaspartate (D-aspartate) O-methyltransferase 1	protein-coding
mm_149843.1	chr19	25039228	25039231	+	1	NA	intron (NM_028785, intron 1 of 47)	intron (NM_028785, intron 1 of 47)	39700	NM_028785	76088	Mm.102485	NM_028785	ENSMUSG00000052085	Dock8	1200017A24Rik|5830472H07Rik|A130095G14Rik|AI461977	dedicator of cytokinesis 8	protein-coding
mm_158295.1	chrX	113171975	113171983	-	1	NA	intron (NM_018818, intron 1 of 14)	Lx8|LINE|L1	13536	NM_018818	12662	Mm.257316	NM_018818	ENSMUSG00000025531	Chm	Rep-1	choroidermia (RAB escort protein 1)	protein-coding
mm_55340.1	chr6	56568922	56568932	-	1	NA	Intergenic	CpG	135772	NM_025520	66373	Mm.25642	NM_025520	ENSMUSG00000091625	Lsm5	2010208O10Rik|2310034K10Rik	LSM5 homolog, U6 small nuclear RNA and mRNA degradation associated	protein-coding
mm_79540.1	chr9	57910543	57910552	+	1	NA	promoter-TSS (NM_027086)	promoter-TSS (NM_027086)	-439	NM_027086	69459	Mm.41735	NM_027086	ENSMUSG00000055720	Ubl7	2300004C15Rik	ubiquitin-like 7 (bone marrow stromal cell-derived)	protein-coding
mm_141289.1	chr17	28067009	28067014	-	1	NA	exon (NM_013687, exon 10 of 10)	exon (NM_013687, exon 10 of 10)	13573	NM_013687	21463	Mm.29758	NM_013687	ENSMUSG00000062859	Tcp11	D17Ken1|Tcp-11	t-complex protein 11	protein-coding
mm_158041.1	chrX	98890431	98890488	-	1	NA	5' UTR (NM_052976, exon 1 of 25)	5' UTR (NM_052976, exon 1 of 25)	566	NM_052976	94190	Mm.33536	NM_052976	ENSMUSG00000031214	Ophn1	C130037N19Rik|Wtgr	oligophrenin 1	protein-coding
mm_173144.1	chrX	21875446	21875447	+	1	NA	Intergenic	L1_Mm|LINE|L1	160546	NM_020049	56774	Mm.253984	NM_020049	ENSMUSG00000031089	Slc6a14	1110007A17Rik|9030613J17Rik|ATB0plus|CATB0plus	solute carrier family 6 (neurotransmitter transporter), member 14	protein-coding
mm_64185.1	chr7	141459687	141459695	+	1	NA	non-coding (NR_028142, exon 10 of 10)	non-coding (NR_028142, exon 10 of 10)	-1403	NM_001025103	213573	Mm.386851	NM_001025103	ENSMUSG00000048200	Cracr2b	6330520A15Rik|BC026645|Cracr2a|Efcab4|Efcab4a	calcium release activated channel regulator 2B	protein-coding
mm_112181.1	chr12	113422143	113422171	-	1	NA	Intergenic	Intergenic	-67408	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_91900.1	chr10	60162385	60162398	-	1	NA	Intergenic	LTRIS2|LTR|ERV1	35615	NR_105871	102465546		NR_105871	ENSMUSG00000105468	Mir6906	mmu-mir-6906	microRNA 6906	ncRNA
mm_71650.1	chr8	60195839	60195851	+	1	NA	Intergenic	Intergenic	-310279	NM_011834	23923	Mm.35020	NM_011834	ENSMUSG00000057228	Aadat	AI875679|Aadt|KATII|Kat2|Kyat2|mKat-2	aminoadipate aminotransferase	protein-coding
mm_112558.1	chr13	13030977	13030979	+	1	NA	Intergenic	Intergenic	-25648	NM_031191	18811	Mm.88796	NM_031191	ENSMUSG00000079092	Prl2c2	Ghd2|MRP-1|PLF-1|Plf|Plf1	prolactin family 2, subfamily c, member 2	protein-coding
mm_99369.1	chr11	101787765	101787776	+	1	NA	Intergenic	Intergenic	-2460	NM_001316365	18612	Mm.5025	NM_008815	ENSMUSG00000017724	Etv4	AW414408|Pea-3|Pea3	ets variant 4	protein-coding
mm_121218.1	chr14	103054865	103054875	+	1	NA	exon (NM_008392, exon 5 of 5)	exon (NM_008392, exon 5 of 5)	7858	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_105788.1	chr11	109828037	109828065	-	1	NA	promoter-TSS (NM_001162428)	promoter-TSS (NM_001162428)	-5	NM_001162428	69324	Mm.31700	NM_027038	ENSMUSG00000020617	1700012B07Rik	1700069D21Rik	RIKEN cDNA 1700012B07 gene	protein-coding
mm_147178.1	chr18	36766193	36766205	-	1	NA	promoter-TSS (NM_173383)	promoter-TSS (NM_173383)	15	NM_173383	213236	Mm.234464	NM_173383	ENSMUSG00000044595	Dnd1	BC034897|RBMS4|Ter	DND microRNA-mediated repression inhibitor 1	protein-coding
mm_76664.1	chr8	93379747	93379756	-	1	NA	Intergenic	Intergenic	-42542	NM_021456	12623	Mm.22720	NM_021456	ENSMUSG00000057074	Ces1g	Ces-1|Ces1|Ses-1	carboxylesterase 1G	protein-coding
mm_6433.1	chr1	73962998	73963053	-	1	NA	intron (NM_027884, intron 18 of 34)	intron (NM_027884, intron 18 of 34)	-98559	NR_045311	109198	Mm.359721	NR_045311	ENSMUSG00000100301	6030407O03Rik	-	RIKEN cDNA 6030407O03 gene	ncRNA
mm_17058.1	chr2	21205631	21205639	-	1	NA	promoter-TSS (NM_027728)	promoter-TSS (NM_027728)	-89	NM_001001297	208967	Mm.268841	NM_177588	ENSMUSG00000048550	Thnsl1	AW413632	threonine synthase-like 1 (bacterial)	protein-coding
mm_151956.1	chr19	5801354	5801365	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	1313	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_66930.1	chr7	61530121	61530134	-	1	NA	non-coding (NR_045727, exon 5 of 5)	non-coding (NR_045727, exon 5 of 5)	85200	NR_045727	319752	Mm.294476	NR_045727		B230209E15Rik	-	RIKEN cDNA B230209E15 gene	ncRNA
mm_138883.1	chr17	43389502	43389513	+	1	NA	promoter-TSS (NM_001081178)	promoter-TSS (NM_001081178)	41	NM_001081178	224792	Mm.23478	NM_001081178	ENSMUSG00000056492	Adgrf5	8430401C09Rik|9330185D23|AI528491|Gpr116|mKIAA0758	adhesion G protein-coupled receptor F5	protein-coding
mm_39795.1	chr5	30590057	30590069	+	1	NA	intron (NM_010608, intron 1 of 1)	intron (NM_010608, intron 1 of 1)	-1444	NR_040427	100502829	Mm.39944	NR_040427	ENSMUSG00000053214	Gm9899	ENSMUSG00000053214	predicted gene 9899	ncRNA
mm_86369.1	chr9	123797587	123797603	-	1	NA	exon (NM_001110253, exon 16 of 18)	exon (NM_001110253, exon 16 of 18)	-8882	NM_030712	80901	Mm.124289	NM_030712	ENSMUSG00000048521	Cxcr6	BB217514|BONZO|STRL33	chemokine (C-X-C motif) receptor 6	protein-coding
mm_43729.1	chr5	139722932	139722941	+	1	NA	intron (NM_174850, intron 1 of 16)	intron (NM_174850, intron 1 of 16)	13397	NM_174850	231830	Mm.240510	NM_174850	ENSMUSG00000036718	Micall2	A930021H16Rik|JRAB|MICAL-L2|mFLJ00139	MICAL-like 2	protein-coding
mm_70351.1	chr8	5117300	5117322	+	1	NA	Intergenic	Intergenic	-12024	NM_011388	20494	Mm.3500	NM_011388	ENSMUSG00000023073	Slc10a2	9130221J18Rik|AI605518|ASBT|IBAT|ISBT	solute carrier family 10, member 2	protein-coding
mm_56888.1	chr6	119035940	119035943	-	1	NA	intron (NM_001256002, intron 3 of 47)	intron (NM_001256002, intron 3 of 47)	72554	NM_001159534	12288	Mm.41628	NM_009781	ENSMUSG00000051331	Cacna1c	Cav1.2|Cchl1a1|D930026N18Rik|MBC|MELC-CC	calcium channel, voltage-dependent, L type, alpha 1C subunit	protein-coding
mm_32362.1	chr4	105172192	105172195	+	1	NA	intron (NM_080555, intron 1 of 5)	intron (NM_080555, intron 1 of 5)	14846	NM_080555	67916	Mm.348326	NM_080555	ENSMUSG00000028517	Plpp3	1110003O22Rik|2610002D05Rik|AV025606|D4Bwg0538e|D4Bwg1535e|Lpp3|Ppab2b|Ppap2b	phospholipid phosphatase 3	protein-coding
mm_89692.1	chr10	97565779	97565820	+	1	NA	5' UTR (NM_008524, exon 1 of 3)	5' UTR (NM_008524, exon 1 of 3)	298	NM_008524	17022	Mm.18888	NM_008524	ENSMUSG00000036446	Lum	Ldc|SLRR2D	lumican	protein-coding
mm_69319.1	chr7	128461390	128461400	-	1	NA	5' UTR (NM_009383, exon 1 of 12)	5' UTR (NM_009383, exon 1 of 12)	118	NM_009383	21843	Mm.242072	NM_009383	ENSMUSG00000030846	Tial1	5330433G13Rik|AL033329|TIAR|mTIAR	Tia1 cytotoxic granule-associated RNA binding protein-like 1	protein-coding
mm_170560.1	chr19	45451244	45451246	-	1	NA	intron (NM_001286465, intron 2 of 14)	intron (NM_001286465, intron 2 of 14)	87511	NM_001037758	12234	Mm.119717	NM_009771	ENSMUSG00000025217	Btrc	Beta-Trcp1|E3RS-IkappaB|E3RSIkappaB|FWD1|Fbw1a|HOS|Slimb|b-TrCP|beta-TrCP	beta-transducin repeat containing protein	protein-coding
mm_76679.1	chr8	94012121	94012141	-	1	NA	intron (NM_011787, intron 1 of 13)	CpG	509	NM_011787	23802	Mm.34641	NM_011787	ENSMUSG00000031751	Amfr	gp78	autocrine motility factor receptor	protein-coding
mm_58364.1	chr6	148444337	148444358	-	1	NA	promoter-TSS (NM_198967)	promoter-TSS (NM_198967)	5	NM_001347518	387314	Mm.137858	NM_198967	ENSMUSG00000030306	Tmtc1	Arg99|BC023818	transmembrane and tetratricopeptide repeat containing 1	protein-coding
mm_73527.1	chr8	107580900	107580997	+	1	NA	exon (NM_010817, exon 7 of 7)	exon (NM_010817, exon 7 of 7)	7534	NM_010817	17463	Mm.18347	NM_010817	ENSMUSG00000039067	Psmd7	AW107203|Mov-34|Mov34	proteasome (prosome, macropain) 26S subunit, non-ATPase, 7	protein-coding
mm_71606.1	chr8	56294579	56294592	+	1	NA	promoter-TSS (NM_008278)	promoter-TSS (NM_008278)	33	NM_008278	15446	Mm.18832	NM_008278	ENSMUSG00000031613	Hpgd	15-PGDH|AV026552	hydroxyprostaglandin dehydrogenase 15 (NAD)	protein-coding
mm_135533.1	chr16	49768792	49768802	-	1	NA	Intergenic	ORR1D1|LTR|ERVL-MaLR	69503	NM_028680	73916	Mm.241276	NM_028680	ENSMUSG00000032965	Ift57	4833420A15Rik|Esrrbl1|Hippi|MHS4R2	intraflagellar transport 57	protein-coding
mm_166135.1	chr4	155892244	155892250	+	1	NA	promoter-TSS (NM_001033490)	promoter-TSS (NM_001033490)	372	NM_207223	140500	Mm.219591	NM_207223	ENSMUSG00000029033	Acap3	Centb5|Kiaa1716-hp|mKIAA1716	ArfGAP with coiled-coil, ankyrin repeat and PH domains 3	protein-coding
mm_40955.1	chr5	76858741	76858752	+	1	NA	exon (NM_001163793, exon 6 of 9)	exon (NM_001163793, exon 6 of 9)	18147	NM_001163793	320827	Mm.101504	NM_001163793	ENSMUSG00000036377	C530008M17Rik	2810489J07Rik|4930529A19Rik|4931405B09Rik|Kiaa1211|mKIAA1211	RIKEN cDNA C530008M17 gene	protein-coding
mm_120481.1	chr14	65975706	65975716	+	1	NA	exon (NM_013492, exon 5 of 9)	exon (NM_013492, exon 5 of 9)	7228	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_141140.1	chr17	26287059	26287065	-	1	NA	Intergenic	Intergenic	34152	NR_037905	66978	Mm.440216	NM_025881	ENSMUSG00000024188	Luc7l	1810045C04Rik|2410018D03Rik	Luc7-like	protein-coding
mm_84682.1	chr9	72110874	72110916	-	1	NA	intron (NM_001253865, intron 1 of 14)	CpG	306	NM_001253862	21406	Mm.171615	NM_011544	ENSMUSG00000032228	Tcf12	A130037E08Rik|ALF1|HEB|HEBAlt|HTF-4|HTF4|ME1|REB|bHLHb20	transcription factor 12	protein-coding
mm_10186.1	chr2	4881850	4881860	+	1	NA	5' UTR (NM_175400, exon 1 of 9)	5' UTR (NM_175400, exon 1 of 9)	291	NM_175400	109079	Mm.34329	NM_175400	ENSMUSG00000026662	Sephs1	1110046B24Rik|AA589574|AI505014|AW111620|SELD|SPS|SPS1	selenophosphate synthetase 1	protein-coding
mm_7161.1	chr1	91931173	91931176	-	1	NA	3' UTR (NM_207225, exon 27 of 27)	3' UTR (NM_207225, exon 27 of 27)	129713	NM_007855	13345	Mm.9474	NM_007855	ENSMUSG00000007805	Twist2	Dermo1|bHLHa39	twist basic helix-loop-helix transcription factor 2	protein-coding
mm_45823.1	chr5	87692834	87692841	-	1	NA	3' UTR (NM_001286023, exon 7 of 7)	3' UTR (NM_001286023, exon 7 of 7)	6588	NM_001286020	12991	Mm.268737	NM_009972	ENSMUSG00000063157	Csn2	Csnb	casein beta	protein-coding
mm_81814.1	chr9	118040577	118040583	+	1	NA	promoter-TSS (NM_013727)	promoter-TSS (NM_013727)	58	NM_013727	27215	Mm.92705	NM_013727	ENSMUSG00000039285	Azi2	AA410145|AZ2	5-azacytidine induced gene 2	protein-coding
mm_112232.1	chr12	113482317	113482325	-	1	NA	Intergenic	Intergenic	-7244	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_220.1	chr1	16814298	16814304	+	1	NA	Intergenic	Intergenic	125845	NM_016923	17087	Mm.116844	NM_016923	ENSMUSG00000025779	Ly96	ESOP-1|MD-2|MD2	lymphocyte antigen 96	protein-coding
mm_13526.1	chr2	110021948	110021961	+	1	NA	exon (NM_026613, exon 2 of 6)	exon (NM_026613, exon 2 of 6)	4137	NM_026613	68201	Mm.181767	NM_026613	ENSMUSG00000027160	Ccdc34	2810027O19Rik|4930522P10Rik|AI596202	coiled-coil domain containing 34	protein-coding
mm_48355.1	chr5	139372178	139372201	-	1	NA	intron (NM_028469, intron 2 of 4)	CpG	-2444	NR_029768	723898		NR_029768	ENSMUSG00000065593	Mir339	Mirn339|mir-339|mmu-mir-339	microRNA 339	ncRNA
mm_84704.1	chr9	72691045	72691047	-	1	NA	intron (NM_010890, intron 6 of 28)	ID_B1|SINE|B4	28699	NM_010890	17999	Mm.279923	NM_010890	ENSMUSG00000032216	Nedd4	AA959633|AL023035|AU019897|E430025J12Rik|Nedd4-1|Nedd4a|mKIAA0093	neural precursor cell expressed, developmentally down-regulated 4	protein-coding
mm_65423.1	chr7	25297549	25297571	-	1	NA	intron (NM_008776, intron 1 of 5)	CpG-12842	395	NM_008776	18476	Mm.597	NM_008776	ENSMUSG00000005447	Pafah1b3	Pafahg|mus[g]	platelet-activating factor acetylhydrolase, isoform 1b, subunit 3	protein-coding
mm_118232.1	chr13	111489898	111489919	-	1	NA	5' UTR (NM_028487, exon 1 of 13)	5' UTR (NM_028487, exon 1 of 13)	133	NM_028487	73274	Mm.57286	NM_028487	ENSMUSG00000032745	Gpbp1	1700034P14Rik|AU019836|D230035M11Rik|Gpbp|mGPBP	GC-rich promoter binding protein 1	protein-coding
mm_114216.1	chr13	56288646	56288651	+	1	NA	TTS (NM_019568)	TTS (NM_019568)	7903	NM_019568	57266	Mm.30211	NM_019568	ENSMUSG00000021508	Cxcl14	1110031L23Rik|1200006I23Rik|AI414372|BMAC|BRAK|KS1|Kec|MIP-2g|MIP2gamma|NJAC|Scyb14|bolekine	chemokine (C-X-C motif) ligand 14	protein-coding
mm_78953.1	chr9	45138801	45138840	+	1	NA	promoter-TSS (NM_001013390)	promoter-TSS (NM_001013390)	-222	NM_001013390	399548	Mm.335112	NM_001013390	ENSMUSG00000046480	Scn4b	Gm1471	sodium channel, type IV, beta	protein-coding
mm_165155.1	chr2	22589151	22589159	+	1	NA	Intergenic	Intergenic	-33172	NM_008078	14417	Mm.4784	NM_008078	ENSMUSG00000026787	Gad2	6330404F12Rik|GAD(65)|GAD65|Gad-2	glutamic acid decarboxylase 2	protein-coding
mm_29313.1	chr3	107986409	107986466	-	1	NA	promoter-TSS (NM_008183)	promoter-TSS (NM_008183)	-1	NM_008183	14863	Mm.440086	NM_008183	ENSMUSG00000040562	Gstm2	Gstb-2|Gstb2	glutathione S-transferase, mu 2	protein-coding
mm_14314.1	chr2	129228025	129228045	+	1	NA	intron (NR_045838, intron 3 of 4)	intron (NR_045838, intron 3 of 4)	9066	NR_045838	329513	Mm.473529	NM_177847	ENSMUSG00000056738	A730036I17Rik	-	RIKEN cDNA A730036I17 gene	ncRNA
mm_38366.1	chr4	138343616	138343641	-	1	NA	intron (NM_028176, intron 2 of 3)	intron (NM_028176, intron 2 of 3)	-17332	NM_026880	68943	Mm.18539	NM_026880	ENSMUSG00000028756	Pink1	1190006F07Rik|AU042772|AW557854|BRPK|mFLJ00387	PTEN induced putative kinase 1	protein-coding
mm_89091.1	chr10	84206660	84206660	+	1	NA	Intergenic	Intergenic	233811	NM_001004363	77976	Mm.25874	NM_001004363	ENSMUSG00000020032	Nuak1	AU014801|AW494241|B230104P22Rik|Omphk1	NUAK family, SNF1-like kinase, 1	protein-coding
mm_106797.1	chr12	4917301	4917307	+	1	NA	promoter-TSS (NM_001099628)	promoter-TSS (NM_001099628)	-49	NM_001099628	320817	Mm.210966	NM_001099628	ENSMUSG00000052812	Atad2b	1110014E10Rik|BC032887|C79189|D530031C13Rik	ATPase family, AAA domain containing 2B	protein-coding
mm_86741.1	chr10	19186577	19186598	+	1	NA	intron (NR_038022, intron 1 of 1)	intron (NR_038022, intron 1 of 1)	19349	NR_038022	100504265	Mm.383417	NR_038021		Gm20139	-	predicted gene, 20139	ncRNA
mm_26510.1	chr3	145878986	145878996	+	1	NA	intron (NM_026993, intron 4 of 5)	intron (NM_026993, intron 4 of 5)	-45271	NM_009740	12042	Mm.239141	NM_009740	ENSMUSG00000028191	Bcl10	AI132454|BCL-10|C81403|CARMEN|CIPER|CLAP|ME10|cE10	B cell leukemia/lymphoma 10	protein-coding
mm_59215.1	chr7	24547496	24547504	+	1	NA	intron (NM_009532, intron 1 of 16)	intron (NM_009532, intron 1 of 16)	350	NM_009532	22594	Mm.4347	NM_009532	ENSMUSG00000051768	Xrcc1	Xrcc-1	X-ray repair complementing defective repair in Chinese hamster cells 1	protein-coding
mm_59177.1	chr7	24458045	24458077	+	1	NA	Intergenic	B3A|SINE|B2	-4422	NM_011113	18793	Mm.1359	NM_011113	ENSMUSG00000046223	Plaur	Cd87|u-PAR|uPAR	plasminogen activator, urokinase receptor	protein-coding
mm_154535.1	chrM	13850	13892	-	1	NA	NA	Intergenic	NA	NA								
mm_8937.1	chr1	164437417	164437425	-	1	NA	TTS (NM_001293313)	TTS (NM_001293313)	20934	NM_009721	11931	Mm.4550	NM_009721	ENSMUSG00000026576	Atp1b1	Atp4b|Atpb|Atpb-1|NKbeta1	ATPase, Na+/K+ transporting, beta 1 polypeptide	protein-coding
mm_154423.1	chrM	357	367	-	1	NA	NA	Intergenic	NA	NA								
mm_7757.1	chr1	131136330	131136341	-	1	NA	exon (NM_145508, exon 2 of 3)	exon (NM_145508, exon 2 of 3)	1899	NM_145508	226419	Mm.39299	NM_145508	ENSMUSG00000016526	Dyrk3	BC006704	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 3	protein-coding
mm_103617.1	chr11	78608170	78608173	-	1	NA	intron (NM_008702, intron 3 of 10)	intron (NM_008702, intron 3 of 10)	-57436	NM_133706	69071	Mm.29431	NM_133706	ENSMUSG00000037278	Tmem97	1810014L12Rik|AI115531|AL022956|D11Bhm182e	transmembrane protein 97	protein-coding
mm_124191.1	chr14	98104571	98104578	-	1	NA	intron (NM_007826, intron 1 of 11)	intron (NM_007826, intron 1 of 11)	65191	NM_001038610	13134	Mm.320593	NM_007826	ENSMUSG00000055639	Dach1	Dac|Dach	dachshund 1 (Drosophila)	protein-coding
mm_74508.1	chr8	8621292	8621320	-	1	NA	intron (NM_010111, intron 4 of 4)	intron (NM_010111, intron 4 of 4)	39467	NM_010111	13642	Mm.209813	NM_010111	ENSMUSG00000001300	Efnb2	ELF-2|Epl5|Eplg5|Htk-L|LERK-5|Lerk5|NLERK-1	ephrin B2	protein-coding
mm_2942.1	chr1	132316201	132316211	+	1	NA	promoter-TSS (NM_028778)	promoter-TSS (NM_028778)	81	NM_001195025	74137	Mm.100666	NM_028778	ENSMUSG00000009772	Nuak2	1200013B22Rik|Omphk2|Snark|mKIAA0537	NUAK family, SNF1-like kinase, 2	protein-coding
mm_170630.1	chr19	8019555	8019570	+	1	NA	Intergenic	IAPLTR4|LTR|ERVK	-53535	NM_134256	171405	Mm.326517	NM_134256	ENSMUSG00000067656	Slc22a27	Oat9|mOAT6-L|mOAT6-S	solute carrier family 22, member 27	protein-coding
mm_66044.1	chr7	30671557	30671566	-	1	NA	promoter-TSS (NR_027849)	promoter-TSS (NR_027849)	44	NR_027849	74927	Mm.87326	NM_183108	ENSMUSG00000049761	Pmis2	1700071L20Rik|4930479M11Rik	Pmis2, sperm specific protein	ncRNA
mm_172726.1	chr8	73750800	73750819	-	1	NA	Intergenic	Intergenic	-397269	NM_010687	16795	Mm.324371	NM_010687	ENSMUSG00000004383	Large1	BPFD#36|Gyltl1a|Large|Mbp-1|Mbp1|enr|fg|froggy|myd	LARGE xylosyl- and glucuronyltransferase 1	protein-coding
mm_120420.1	chr14	65368844	65368849	+	1	NA	intron (NM_199029, intron 1 of 9)	intron (NM_199029, intron 1 of 9)	10170	NM_199029	380912	Mm.270087	NM_199029	ENSMUSG00000034522	Zfp395	BC053701|Gm910	zinc finger protein 395	protein-coding
mm_107327.1	chr12	31671001	31671005	+	1	NA	intron (NM_001163126, intron 5 of 22)	Lx5c|LINE|L1	16134	NM_001163126	238123	Mm.173068	NM_001163126	ENSMUSG00000035933	Cog5	5430405C01Rik|C87247|D18362|GOLTC1|GTC90	component of oligomeric golgi complex 5	protein-coding
mm_20973.1	chr2	151973388	151973399	-	1	NA	promoter-TSS (NM_001289151)	promoter-TSS (NM_001289151)	1	NM_001289151	73847	Mm.272444	NM_028666	ENSMUSG00000027459	Fam110a	1700008J10Rik|5430432M24Rik|AI747080	family with sequence similarity 110, member A	protein-coding
mm_48866.1	chr5	150022733	150022766	-	1	NA	intron (NM_001289566, intron 1 of 16)	intron (NM_001289566, intron 1 of 16)	4074	NM_001289566	140498	Mm.444643	NM_080468	ENSMUSG00000053368	Rxfp2	Gpr106|Great|Lgr8	relaxin/insulin-like family peptide receptor 2	protein-coding
mm_45157.1	chr5	49510241	49510243	-	1	NA	Intergenic	Intergenic	-224583	NM_001199244	80334	Mm.160172	NM_030265	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding
mm_132994.1	chr16	55816774	55816793	+	1	NA	intron (NM_001159395, intron 7 of 12)	intron (NM_001159395, intron 7 of 12)	5355	NM_001159394	80859	Mm.247272	NM_030612	ENSMUSG00000035356	Nfkbiz	AA408868|INAP|Mail	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, zeta	protein-coding
mm_33691.1	chr4	133480127	133480149	+	1	NA	promoter-TSS (NM_175307)	promoter-TSS (NM_175307)	5	NM_175307	100342	Mm.204656	NM_175307	ENSMUSG00000046694	Fam46b	4732473B16Rik|AU045678|AU046069	family with sequence similarity 46, member B	protein-coding
mm_136682.1	chr17	6742353	6742376	+	1	NA	exon (NM_009510, exon 9 of 13)	exon (NM_009510, exon 9 of 13)	36534	NM_183368	83672	Mm.442201	NM_031395	ENSMUSG00000041831	Sytl3	A430092N21|Slp3|Slp3-a|Slp3-b|mFLJ00307	synaptotagmin-like 3	protein-coding
mm_55580.1	chr6	71397346	71397350	-	1	NA	intron (NM_024288, intron 6 of 8)	intron (NM_024288, intron 6 of 8)	23921	NM_001081110	12525	Mm.1858	NM_009857	ENSMUSG00000053977	Cd8a	BB154331|Ly-2|Ly-35|Ly-B|Lyt-2	CD8 antigen, alpha chain	protein-coding
mm_161723.1	chr17	27908258	27908258	-	1	NA	promoter-TSS (NM_026836)	promoter-TSS (NM_026836)	-534	NM_026836	68776	Mm.267998	NM_026836	ENSMUSG00000024218	Taf11	1110038O14Rik|28kDa|AI115401|AL024207|AW552398|PRO214|TAF2I|TAFII28	TATA-box binding protein associated factor 11	protein-coding
mm_11619.1	chr2	34772090	34772094	+	1	NA	promoter-TSS (NM_001163434)	promoter-TSS (NM_001163434)	2	NM_022310	14828	Mm.330160	NM_022310	ENSMUSG00000026864	Hspa5	AL022860|AU019543|Bip|D2Wsu141e|D2Wsu17e|Grp78|Hsce70|SEZ-7|Sez7|baffled|mBiP	heat shock protein 5	protein-coding
mm_92160.1	chr10	67540138	67540173	-	1	NA	exon (NM_010118, exon 2 of 2)	exon (NM_010118, exon 2 of 2)	2225	NM_001347458	13654	Mm.290421	NM_010118	ENSMUSG00000037868	Egr2	Egr-2|Krox-20|Krox20|NGF1-B|Zfp-25|Zfp-6	early growth response 2	protein-coding
mm_205.1	chr1	16253583	16253597	+	1	NA	intron (NM_001111272, intron 11 of 12)	intron (NM_001111272, intron 11 of 12)	147708	NM_133832	98711	Mm.274376	NM_133832	ENSMUSG00000025921	Rdh10	3110069K09Rik|4921506A21Rik|AI875664|AW549993|D1Ertd762e|m366Asp	retinol dehydrogenase 10 (all-trans)	protein-coding
mm_87794.1	chr10	60299791	60299827	+	1	NA	exon (NM_011179, exon 11 of 15)	exon (NM_011179, exon 11 of 15)	15348	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_123510.1	chr14	66236289	66236308	-	1	NA	intron (NM_001162365, intron 1 of 30)	RMER5|LTR|ERV1	-22746	NM_001162366	19229	Mm.21613	NM_172498	ENSMUSG00000059456	Ptk2b	CADTK|CAKB|CAKbeta|E430023O05Rik|FADK2|FAK2|PYK2|Raftk	PTK2 protein tyrosine kinase 2 beta	protein-coding
mm_55985.1	chr6	85957033	85957037	-	1	NA	intron (NM_028099, intron 3 of 8)	intron (NM_028099, intron 3 of 8)	4632	NM_028099	72102	Mm.24007	NM_028099	ENSMUSG00000030002	Dusp11	2010300F21Rik|AI481497	dual specificity phosphatase 11 (RNA/RNP complex 1-interacting)	protein-coding
mm_94556.1	chr11	11557402	11557431	+	1	NA	Intergenic	Intergenic	68150	NM_028669	73862	Mm.159077	NM_028669	ENSMUSG00000020191	4930415F15Rik	-	RIKEN cDNA 4930415F15 gene	protein-coding
mm_32494.1	chr4	108301316	108301327	+	1	NA	promoter-TSS (NM_001033634)	promoter-TSS (NM_001033634)	-231	NM_001033634	414872	Mm.426241	NM_001033634	ENSMUSG00000034636	Zyg11b	1110046I03Rik|2810482G21Rik|D4Mgi23|Gm431|mKIAA1730	zyg-ll family member B, cell cycle regulator	protein-coding
mm_141991.1	chr17	35173413	35173430	-	1	NA	intron (NM_019467, intron 1 of 7)	intron (NM_019467, intron 1 of 7)	2580	NM_019467	11629	Mm.10747	NM_019467	ENSMUSG00000024397	Aif1	AI607846|AIF-1|D17H6S50E|G1|Iba1	allograft inflammatory factor 1	protein-coding
mm_15741.1	chr2	164237311	164237314	+	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	1029	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_164019.1	chr14	75130628	75130634	-	1	NA	promoter-TSS (NM_001247984)	promoter-TSS (NM_001247984)	252	NM_027581	70859	Mm.320289	NM_027581	ENSMUSG00000021997	Lrrc63	4921509B22Rik	leucine rich repeat containing 63	protein-coding
mm_74765.1	chr8	20902495	20902501	-	1	NA	promoter-TSS (NM_001177471)	promoter-TSS (NM_001177471)	-525	NM_001177471	100504014	Mm.490239	NM_001177471	ENSMUSG00000082976	Gm15056	Defb52|OTTMUSG00000018888	predicted gene 15056	protein-coding
mm_62648.1	chr7	107684994	107684998	+	1	NA	intron (NM_001163557, intron 4 of 25)	intron (NM_001163557, intron 4 of 25)	73036	NM_001205227	320635	Mm.132828	NM_177216	ENSMUSG00000048065	Cyb5r2	D630003K02Rik|b5R.2	cytochrome b5 reductase 2	protein-coding
mm_157884.1	chrX	75843190	75843198	-	1	NA	promoter-TSS (NM_001346520)	promoter-TSS (NM_001346520)	-131	NM_001346520	102866	Mm.28777	NM_145629	ENSMUSG00000016382	Pls3	AI115446|AL024105	plastin 3 (T-isoform)	protein-coding
mm_144868.1	chr18	36735013	36735026	+	1	NA	promoter-TSS (NM_028036)	promoter-TSS (NM_028036)	-51	NM_028036	71983	Mm.135188	NM_028036	ENSMUSG00000006850	Tmco6	2410015B03Rik	transmembrane and coiled-coil domains 6	protein-coding
mm_100068.1	chr11	115412821	115412834	+	1	NA	TTS (NM_001347645)	TTS (NM_001347645)	7092	NM_027862	71679	Mm.371641	NM_027862	ENSMUSG00000034566	Atp5h	0610009D10Rik	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit D	protein-coding
mm_57523.1	chr6	125595021	125595023	-	1	NA	intron (NM_011708, intron 10 of 51)	MTD|LTR|ERVL-MaLR	42074	NM_011708	22371	Mm.22339	NM_011708	ENSMUSG00000001930	Vwf	6820430P06Rik|AI551257|B130011O06Rik|C630030D09|F8VWF|VWD	Von Willebrand factor	protein-coding
mm_78989.1	chr9	45402566	45402574	+	1	NA	promoter-TSS (NM_052823)	promoter-TSS (NM_052823)	-568	NM_052823	11936	Mm.22742	NM_007503	ENSMUSG00000059412	Fxyd2	Atp1g1	FXYD domain-containing ion transport regulator 2	protein-coding
mm_18193.1	chr2	45113930	45113952	-	1	NA	promoter-TSS (NM_015753)	promoter-TSS (NM_015753)	-662	NM_015753	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_109972.1	chr12	12938253	12938255	-	1	NA	intron (NM_008709, intron 2 of 2)	intron (NM_008709, intron 2 of 2)	3582	NM_008709	18109	Mm.16469	NM_008709	ENSMUSG00000037169	Mycn	N-myc|Nmyc|Nmyc-1|Nmyc1|bHLHe37|c-nmyc	v-myc avian myelocytomatosis viral related oncogene, neuroblastoma derived	protein-coding
mm_21458.1	chr2	160872553	160872622	-	1	NA	intron (NM_177263, intron 1 of 3)	CpG	403	NM_177263	320799	Mm.436734	NM_177263	ENSMUSG00000035877	Zhx3	1810059C13Rik|4932418O04Rik|9530010N21Rik|Tix1|mKIAA0395	zinc fingers and homeoboxes 3	protein-coding
mm_65620.1	chr7	27535914	27535934	-	1	NA	exon (NM_011116, exon 11 of 14)	exon (NM_011116, exon 11 of 14)	12663	NM_001033315	233020	Mm.429716	NM_001033315	ENSMUSG00000040424	Hipk4	Gm162	homeodomain interacting protein kinase 4	protein-coding
mm_140659.1	chr17	12851896	12851916	-	1	NA	intron (NM_008552, intron 6 of 8)	intron (NM_008552, intron 6 of 8)	16237	NM_008552	17171	Mm.425994	NM_008552	ENSMUSG00000068037	Mas1	Mas-1|Mgra	MAS1 oncogene	protein-coding
mm_39930.1	chr5	31613991	31614001	+	1	NA	promoter-TSS (NM_025796)	promoter-TSS (NM_025796)	45	NM_025796	66845	Mm.120763	NM_025796	ENSMUSG00000106918	Mrpl33	0610009M10Rik|L33mt|MRP-L33	mitochondrial ribosomal protein L33	protein-coding
mm_73474.1	chr8	106769432	106769464	+	1	NA	intron (NM_173037, intron 14 of 17)	intron (NM_173037, intron 14 of 17)	86380	NM_173037	272538	Mm.87151	NM_173037	ENSMUSG00000041949	Tango6	AW413431|E330010G16|Tmco7	transport and golgi organization 6	protein-coding
mm_41362.1	chr5	90507845	90507857	+	1	NA	exon (NM_007423, exon 13 of 15)	exon (NM_007423, exon 13 of 15)	-11098	NM_145146	280662	Mm.348786	NM_145146	ENSMUSG00000029369	Afm	Alf|alpha-Alb	afamin	protein-coding
mm_1789.1	chr1	78669512	78669530	+	1	NA	intron (NM_028817, intron 2 of 15)	B1F|SINE|Alu	11081	NM_001136226	195434	Mm.276016	NM_001001981	ENSMUSG00000079470	Utp14b	4932411L21Rik|jsd	UTP14B small subunit processome component	protein-coding
mm_97965.1	chr11	83748277	83748318	+	1	NA	intron (NM_183249, intron 1 of 2)	intron (NM_183249, intron 1 of 2)	1357	NM_183249	66107	Mm.902	NM_183249	ENSMUSG00000051748	Wfdc21	1100001G20Rik|Wdnm1-like	WAP four-disulfide core domain 21	protein-coding
mm_32370.1	chr4	105267509	105267526	+	1	NA	Intergenic	Intergenic	110170	NM_080555	67916	Mm.348326	NM_080555	ENSMUSG00000028517	Plpp3	1110003O22Rik|2610002D05Rik|AV025606|D4Bwg0538e|D4Bwg1535e|Lpp3|Ppab2b|Ppap2b	phospholipid phosphatase 3	protein-coding
mm_27436.1	chr3	51566301	51566303	-	1	NA	intron (NR_033624, intron 4 of 4)	intron (NR_033624, intron 4 of 4)	-5479	NM_080793	73251	Mm.192111	NM_080793	ENSMUSG00000037111	Setd7	1600028F23Rik|H3K4MT|KMT7|Set7|Set7/9|mKIAA1717	SET domain containing (lysine methyltransferase) 7	protein-coding
mm_26139.1	chr3	137918551	137918573	+	1	NA	promoter-TSS (NM_019920)	promoter-TSS (NM_019920)	7	NM_019920	56692	Mm.331392	NM_019920	ENSMUSG00000091512	Lamtor3	AW556229|Map2k1ip1|Mapbp|Mapksp1|Mp1	late endosomal/lysosomal adaptor, MAPK and MTOR activator 3	protein-coding
mm_168477.1	chr11	48979325	48979333	-	1	NA	promoter-TSS (NM_173434).2	promoter-TSS (NM_173434).2	52	NM_001114679	667214	Mm.441306	NM_001114679	ENSMUSG00000069893	9930111J21Rik1	9930111J21Rik|Iigp	RIKEN cDNA 9930111J21 gene 1	protein-coding
mm_55171.1	chr6	51920278	51920291	-	1	NA	intron (NM_018773, intron 6 of 12)	MIR|SINE|MIR	92265	NM_018773	54353	Mm.221479	NM_018773	ENSMUSG00000059182	Skap2	2610021A10Rik|AA960083|BB137539|RA70|SKAP-HOM|Saps|Scap2|mSKAP55R	src family associated phosphoprotein 2	protein-coding
mm_67125.1	chr7	70366147	70366163	-	1	NA	5' UTR (NM_183261, exon 1 of 3)	5' UTR (NM_183261, exon 1 of 3)	591	NM_183261	11819	Mm.158143	NM_009697	ENSMUSG00000030551	Nr2f2	2700033K02Rik|9430015G03Rik|ARP-1|Aporp1|COUP-TF2|COUP-TFII|COUPTFB|EAR3|SVP40|Tcfcoup2	nuclear receptor subfamily 2, group F, member 2	protein-coding
mm_7538.1	chr1	124465333	124465348	-	1	NA	Intergenic	Intergenic	-419781	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_129381.1	chr15	78174027	78174089	-	1	NA	promoter-TSS (NM_025931)	promoter-TSS (NM_025931)	50	NM_025931	67042	Mm.30191	NM_025931	ENSMUSG00000016637	Ift27	2600013G09Rik|Rabl4	intraflagellar transport 27	protein-coding
mm_110347.1	chr12	36253397	36253425	-	1	NA	promoter-TSS (NM_001177877)	promoter-TSS (NM_001177877)	-13	NM_001177877	71156	Mm.250837	NM_027699	ENSMUSG00000020545	Lrrc72	1700108M19Rik|4933421E18Rik	leucine rich repeat containing 72	protein-coding
mm_105459.1	chr11	104550587	104550590	-	1	NA	promoter-TSS (NM_010858)	promoter-TSS (NM_010858)	32	NM_001285990	217232	Mm.89845	NM_145436	ENSMUSG00000020687	Cdc27	AI452358|APC3|BC023187	cell division cycle 27	protein-coding
mm_130739.1	chr15	101253967	101253998	-	1	NA	Intergenic	CpG	-12864	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_4043.1	chr1	165774724	165774727	+	1	NA	3' UTR (NM_011804, exon 4 of 4)	3' UTR (NM_011804, exon 4 of 4)	10945	NM_011804	433375	Mm.294885	NM_011804	ENSMUSG00000040713	Creg1	AA755314|Creg	cellular repressor of E1A-stimulated genes 1	protein-coding
mm_87888.1	chr10	61782951	61782973	+	1	NA	intron (NM_207000, intron 1 of 8)	intron (NM_207000, intron 1 of 8)	902	NM_207000	404634	Mm.272870	NM_207000	ENSMUSG00000020086	H2afy2	macroH2A2	H2A histone family, member Y2	protein-coding
mm_60591.1	chr7	44484890	44484897	+	1	NA	non-coding (NR_131001, exon 1 of 2)	non-coding (NR_131001, exon 1 of 2)	376	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_169318.1	chr14	113288380	113288380	+	1	NA	Intergenic	IAPLTR1_Mm|LTR|ERVK	1266950	NR_030150	723922		NR_030150	ENSMUSG00000070099	Mir466	Mirn466|mmu-mir-466	microRNA 466	ncRNA
mm_168947.1	chr12	73772312	73772312	+	1	NA	intron (NM_001313977, intron 13 of 14)	(TTAGGG)n|Simple_repeat|Simple_repeat	-129012	NM_001313920	15251	Mm.3879	NM_010431	ENSMUSG00000021109	Hif1a	AA959795|HIF-1-alpha|HIF1-alpha|HIF1alpha|MOP1|bHLHe78	hypoxia inducible factor 1, alpha subunit	protein-coding
mm_18.1	chr1	5083170	5083186	+	1	NA	promoter-TSS (NM_133826)	promoter-TSS (NM_133826)	92	NM_001310442	108664	Mm.27082	NM_133826	ENSMUSG00000033793	Atp6v1h	0710001F19Rik|AU022349|CGI-11|SFD|SFDalpha|SFDbeta|VMA13	ATPase, H+ transporting, lysosomal V1 subunit H	protein-coding
mm_137587.1	chr17	28008280	28008307	+	1	NA	exon (NM_001286041, exon 11 of 24)	exon (NM_001286041, exon 11 of 24)	72291	NM_013687	21463	Mm.29758	NM_013687	ENSMUSG00000062859	Tcp11	D17Ken1|Tcp-11	t-complex protein 11	protein-coding
mm_132452.1	chr16	36041185	36041197	+	1	NA	promoter-TSS (NM_027113)	promoter-TSS (NM_027113)	1	NM_027113	69544	Mm.37802	NM_027113	ENSMUSG00000034379	Wdr5b	2310009C03Rik|AI606931	WD repeat domain 5B	protein-coding
mm_90092.1	chr10	116950634	116950647	+	1	NA	promoter-TSS (NR_038026)	promoter-TSS (NR_038026)	78	NR_038026	71086	Mm.214134	NR_038025		4933412E12Rik	-	RIKEN cDNA 4933412E12 gene	ncRNA
mm_113397.1	chr13	33084114	33084146	+	1	NA	promoter-TSS (NM_173052)	promoter-TSS (NM_173052)	27	NM_173052	282663	Mm.314490	NM_173052	ENSMUSG00000051029	Serpinb1b	6330533H24Rik|EIB|Serpin1b1|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 1b	protein-coding
mm_16681.1	chr2	6872620	6872703	-	1	NA	promoter-TSS (NM_001347094)	promoter-TSS (NM_001347094)	-626	NM_001347094	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_141102.1	chr17	26021737	26021741	-	1	NA	5' UTR (NM_153140, exon 1 of 12)	5' UTR (NM_153140, exon 1 of 12)	121	NM_153140	215445	Mm.41191	NM_153140	ENSMUSG00000037098	Rab11fip3	Cart1|D030060O14Rik|Rab11-FIP3|mKIAA0665	RAB11 family interacting protein 3 (class II)	protein-coding
mm_66517.1	chr7	45103805	45103811	-	1	NA	promoter-TSS (NM_010189)	promoter-TSS (NM_010189)	14	NM_010189	14132	Mm.3303	NM_010189	ENSMUSG00000003420	Fcgrt	FcRn	Fc receptor, IgG, alpha chain transporter	protein-coding
mm_166586.1	chr6	55154437	55154463	+	1	NA	Intergenic	Intergenic	20540	NM_009349	21743	Mm.299	NM_009349	ENSMUSG00000003477	Inmt	Temt	indolethylamine N-methyltransferase	protein-coding
mm_99094.1	chr11	99907919	99907922	+	1	NA	promoter-TSS (NM_027568)	promoter-TSS (NM_027568)	0	NM_027568	70831	Mm.347981	NM_027568	ENSMUSG00000070334	Krtap31-1	4733401H21Rik|AI506529	keratin associated protein 31-1	protein-coding
mm_66344.1	chr7	43480378	43480387	-	1	NA	intron (NM_001164518, intron 2 of 7)	intron (NM_001164518, intron 2 of 7)	9641	NM_001164518	210094	Mm.228087	NM_001164518	ENSMUSG00000013367	Iglon5	A230106M20Rik|Gm1431	IgLON family member 5	protein-coding
mm_93645.1	chr10	117357116	117357118	-	1	NA	intron (NM_001310609, intron 8 of 9)	AT_rich|Low_complexity|Low_complexity	19856	NM_001013391	432508	Mm.478881	NM_001013391	ENSMUSG00000055531	Cpsf6	4733401N12Rik|AI256641|CFIM|CFIM68|HPBRII-4|HPBRII-7	cleavage and polyadenylation specific factor 6	protein-coding
mm_146408.1	chr18	84087648	84087687	+	1	NA	promoter-TSS (NM_146090)	promoter-TSS (NM_146090)	-491	NM_146090	225791	Mm.147052	NM_146090	ENSMUSG00000049090	Zadh2	C530046K17Rik|PTGR-3|Pthr3	zinc binding alcohol dehydrogenase, domain containing 2	protein-coding
mm_89399.1	chr10	90365199	90365238	+	1	NA	intron (NM_001128086, intron 12 of 24)	B4A|SINE|B4	-210509	NM_001177397	77531	Mm.440605	NM_181398	ENSMUSG00000058589	Anks1b	AIDA-1b|C030032C09Rik|E530015N03Rik|ENSMUSG00000078431|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding
mm_116722.1	chr13	51702117	51702141	-	1	NA	3' UTR (NM_001281880, exon 17 of 17)	3' UTR (NM_001281880, exon 17 of 17)	50421	NM_029279	75420	Mm.275981	NM_029279	ENSMUSG00000035139	Secisbp2	2210413N07Rik|2810012K13Rik|SBP2	SECIS binding protein 2	protein-coding
mm_31315.1	chr4	46138485	46138521	+	1	NA	promoter-TSS (NM_173033)	promoter-TSS (NM_173033)	-8	NM_001033201	433702	Mm.389536	NM_001033201	ENSMUSG00000028330	Ncbp1	AU014645|AW538051|CBP80	nuclear cap binding protein subunit 1	protein-coding
mm_8521.1	chr1	154884007	154884019	-	1	NA	Intergenic	Intergenic	-158093	NM_009782	12290	Mm.267517	NM_009782	ENSMUSG00000004110	Cacna1e	A430040I15|BII|Cach6|Cacnl1a6|Cav2.3|Cchra1|alpha1E	calcium channel, voltage-dependent, R type, alpha 1E subunit	protein-coding
mm_6650.1	chr1	79761753	79761774	-	1	NA	promoter-TSS (NM_001111279)	promoter-TSS (NM_001111279)	6	NM_001111279	69368	Mm.293273	NM_027057	ENSMUSG00000073643	Wdfy1	1700013B03Rik|1700120F24Rik|FENS-1|Jr1|WDF1|ZFYVE17|mKIAA1435	WD repeat and FYVE domain containing 1	protein-coding
mm_163452.1	chr12	89635782	89635782	-	1	NA	intron (NM_172544, intron 14 of 19)	intron (NM_172544, intron 14 of 19)	-176701	NM_001252074	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding
mm_24495.1	chr3	92373848	92373858	+	1	NA	promoter-TSS (NR_003548)	promoter-TSS (NR_003548)	-62	NR_003548	20761	Mm.57083	NR_003548	ENSMUSG00000046203	Sprr2g	-	small proline-rich protein 2G	pseudo
mm_4875.1	chr1	187890670	187890672	+	1	NA	intron (NM_001243792, intron 2 of 7)	intron (NM_001243792, intron 2 of 7)	-107156	NM_011935	26381	Mm.89989	NM_011935	ENSMUSG00000026610	Esrrg	ERR3|Errg|NR3B3|mKIAA0832	estrogen-related receptor gamma	protein-coding
mm_25520.1	chr3	114030780	114030833	+	1	NA	5' UTR (NM_007729, exon 1 of 67)	5' UTR (NM_007729, exon 1 of 67)	266	NM_007729	12814	Mm.209715	NM_007729	ENSMUSG00000027966	Col11a1	C530001D20Rik|cho	collagen, type XI, alpha 1	protein-coding
mm_91608.1	chr10	41477578	41477580	-	1	NA	intron (NM_138315, intron 1 of 23)	intron (NM_138315, intron 1 of 23)	1265	NM_138315	171580	Mm.290431	NM_138315	ENSMUSG00000019823	Mical1	MICAL|MICAL-1|Nical	microtubule associated monooxygenase, calponin and LIM domain containing 1	protein-coding
mm_85491.1	chr9	106133629	106133635	-	1	NA	Intergenic	RMER15|LTR|ERVL	-20492	NR_029549	387153		NR_029549	ENSMUSG00000065407	Mir135a-1	Mir135a01|Mirn135|Mirn135a-1|mir-135a-1	microRNA 135a-1	ncRNA
mm_147839.1	chr18	62615677	62615693	-	1	NA	intron (NM_001168423, intron 1 of 4)	intron (NM_001168423, intron 1 of 4)	-19421	NM_001001803	408198	Mm.478742	NM_001001803	ENSMUSG00000060201	Spink7	EG408198|Ecg2	serine peptidase inhibitor, Kazal type 7 (putative)	protein-coding
mm_13843.1	chr2	119547676	119547689	+	1	NA	promoter-TSS (NM_172857)	promoter-TSS (NM_172857)	-25	NM_019769	56398	Mm.214765	NM_019769	ENSMUSG00000014077	Chp1	1500003O03Rik|AA960066|AI046351|Cahp|Chp|Sid470p|p24|vac	calcineurin-like EF hand protein 1	protein-coding
mm_95172.1	chr11	40734094	40734157	+	1	NA	promoter-TSS (NM_013552)	promoter-TSS (NM_013552)	464	NM_001290697	52653	Mm.276504	NM_026023	ENSMUSG00000020328	Nudcd2	-	NudC domain containing 2	protein-coding
mm_51191.1	chr6	71201601	71201610	+	1	NA	intron (NM_017399, intron 1 of 3)	intron (NM_017399, intron 1 of 3)	1717	NM_017399	14080	Mm.22126	NM_017399	ENSMUSG00000054422	Fabp1	Fabpl|L-FABP	fatty acid binding protein 1, liver	protein-coding
mm_63649.1	chr7	128689167	128689176	+	1	NA	5' UTR (NM_001346517, exon 1 of 6)	5' UTR (NM_001346517, exon 1 of 6)	301	NM_001346517	101490	Mm.490344	NM_178641	ENSMUSG00000042105	Inpp5f	5830435P03Rik|AI115354|AW561896|SAC2|cI-27|hSAC2|mKIAA0966	inositol polyphosphate-5-phosphatase F	protein-coding
mm_80416.1	chr9	77838831	77838837	+	1	NA	Intergenic	Intergenic	-78531	NM_134255	68801	Mm.430736	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	ELOVL family member 5, elongation of long chain fatty acids (yeast)	protein-coding
mm_74400.1	chr8	3279465	3279482	-	1	NA	5' UTR (NM_001330056, exon 1 of 22)	5' UTR (NM_001330056, exon 1 of 22)	144	NM_010568	16337	Mm.268003	NM_010568	ENSMUSG00000005534	Insr	4932439J01Rik|CD220|D630014A15Rik|IR|IR-A|IR-B	insulin receptor	protein-coding
mm_28870.1	chr3	97702653	97702664	-	1	NA	intron (NM_001039376, intron 36 of 46)	intron (NM_001039376, intron 36 of 46)	-12096	NR_106084	102466229		NR_106084	ENSMUSG00000098381	Mir7225	Gm27499|mmu-mir-7225	microRNA 7225	ncRNA
mm_5442.1	chr1	35439375	35439376	-	1	NA	Intergenic	Intergenic	589416	NM_145516	226971	Mm.292751	NM_145516	ENSMUSG00000026123	Plekhb2	2310009M15Rik|AU018239|Evt2|Phdc|evt-2	pleckstrin homology domain containing, family B (evectins) member 2	protein-coding
mm_27119.1	chr3	31225212	31225213	-	1	NA	intron (NM_172861, intron 6 of 7)	intron (NM_172861, intron 6 of 7)	75292	NM_008770	18417	Mm.4425	NM_008770	ENSMUSG00000037625	Cldn11	Claudin-11|Claudin11|Osp|Otm	claudin 11	protein-coding
mm_158423.1	chrX	139357704	139357740	-	1	NA	promoter-TSS (NR_045456)	promoter-TSS (NR_045456)	16	NR_045456	78526	Mm.439073	NR_045455	ENSMUSG00000086807	Platr21	C330013F16Rik	pluripotency associated transcript 21	ncRNA
mm_126375.1	chr15	80165768	80165771	+	1	NA	Intergenic	Intergenic	-7952	NM_010795	17309	Mm.299693	NM_010795	ENSMUSG00000042428	Mgat3	1110038J12Rik|AI848272|GnT-III	mannoside acetylglucosaminyltransferase 3	protein-coding
mm_16226.1	chr2	173154762	173154787	+	1	NA	exon (NM_011044, exon 4 of 10)	exon (NM_011044, exon 4 of 10)	1701	NM_011044	18534	Mm.266867	NM_011044	ENSMUSG00000027513	Pck1	AI265463|PEPCK|Pck-1	phosphoenolpyruvate carboxykinase 1, cytosolic	protein-coding
mm_133331.1	chr16	78440170	78440177	+	1	NA	Intergenic	Intergenic	-62992	NM_001297747	12228	Mm.392910	NM_009770	ENSMUSG00000022863	Btg3	ANA|tob5	B cell translocation gene 3	protein-coding
mm_10095.1	chr2	3336160	3336174	+	1	NA	promoter-TSS (NM_030063)	promoter-TSS (NM_030063)	-1	NM_030063	78245	Mm.99733	NM_030063	ENSMUSG00000026644	Acbd7	9230116B18Rik	acyl-Coenzyme A binding domain containing 7	protein-coding
mm_162319.1	chr1	38725235	38725238	+	1	NA	Intergenic	Intergenic	95979	NM_001029878	381338	Mm.487137	NM_028403	ENSMUSG00000048814	Lonrf2	2900060P06Rik|AI851349	LON peptidase N-terminal domain and ring finger 2	protein-coding
mm_93490.1	chr10	111997205	111997279	-	1	NA	promoter-TSS (NM_028608)	promoter-TSS (NM_028608)	22	NM_028608	73690	Mm.173790	NM_028608	ENSMUSG00000056888	Glipr1	2410114O14Rik|RTVP-1|RTVP1|mRTVP-1	GLI pathogenesis-related 1 (glioma)	protein-coding
mm_92230.1	chr10	69098556	69098559	-	1	NA	Intergenic	Intergenic	-109995	NM_001252636	69288	Mm.26659	NM_001081347	ENSMUSG00000019944	Rhobtb1	1700008H16Rik|3110048G13Rik|AI173445|AI573858|AV350930	Rho-related BTB domain containing 1	protein-coding
mm_14923.1	chr2	151458856	151458857	+	1	NA	Intergenic	L1_Mus3|LINE|L1	17295	NM_198655	381393	Mm.280614	NM_198655	ENSMUSG00000061525	4921509C19Rik	Gm1005	RIKEN cDNA 4921509C19 gene	protein-coding
mm_106410.1	chr11	119053391	119053401	-	1	NA	Intergenic	CpG	-12483	NM_013926	30951	Mm.99953	NM_013926	ENSMUSG00000025578	Cbx8	Pc3	chromobox 8	protein-coding
mm_5408.1	chr1	33813318	33813321	-	1	NA	intron (NM_001290699, intron 2 of 12)	intron (NM_001290699, intron 2 of 12)	1276	NM_133817	98403	Mm.289103	NM_133817	ENSMUSG00000042197	Zfp451	4930515K21Rik|4933435G09Rik|AI596398|COASTER|Kiaa0576-hp|Znf451|mKIAA1702	zinc finger protein 451	protein-coding
mm_60751.1	chr7	45486280	45486316	+	1	NA	promoter-TSS (NM_001290999)	promoter-TSS (NM_001290999)	35	NM_001290999	56734	Mm.439742	NM_008807	ENSMUSG00000023467	Tulp2	Pdet	tubby-like protein 2	protein-coding
mm_8677.1	chr1	156719059	156719076	-	1	NA	promoter-TSS (NM_145413)	promoter-TSS (NM_145413)	-157	NM_145413	215015	Mm.229107	NM_145413	ENSMUSG00000033557	Fam20b	C530043G21Rik|mKIAA0475	family with sequence similarity 20, member B	protein-coding
mm_17994.1	chr2	38154485	38154488	-	1	NA	intron (NM_146122, intron 3 of 21)	AT_rich|Low_complexity|Low_complexity	132898	NM_146122	227801	Mm.314245	NM_146122	ENSMUSG00000035392	Dennd1a	6030446I19Rik|connecdenn	DENN/MADD domain containing 1A	protein-coding
mm_158532.1	chrX	143861442	143861453	-	1	NA	3' UTR (NM_010025, exon 7 of 7)	3' UTR (NM_010025, exon 7 of 7)	-34035	NM_007603	12338	Mm.30290	NM_007603	ENSMUSG00000067276	Capn6	-	calpain 6	protein-coding
mm_132130.1	chr16	31852335	31852337	+	1	NA	intron (NR_045516, intron 18 of 24)	B2_Mm2|SINE|B2	-26474	NM_013900	30060	Mm.30988	NM_013900	ENSMUSG00000022780	Mfi2	CD228|MTf|Meltf	antigen p97 (melanoma associated) identified by monoclonal antibodies 133.2 and 96.5	protein-coding
mm_123454.1	chr14	65299349	65299386	-	1	NA	exon (NM_015795, exon 6 of 8)	exon (NM_015795, exon 6 of 8)	32666	NM_015795	50759	Mm.65308	NM_015795	ENSMUSG00000034532	Fbxo16	4932435C24Rik|Fbx16	F-box protein 16	protein-coding
mm_117819.1	chr13	98016103	98016159	-	1	NA	intron (NM_012026, intron 9 of 35)	intron (NM_012026, intron 9 of 35)	190034	NM_012026	110596	Mm.252718	NM_012026	ENSMUSG00000021662	Arhgef28	9230110L08Rik|AI323540|D13Bwg1089e|RIP2|Rgnef|RhoGEF|Rhoip2|p190RhoGEF	Rho guanine nucleotide exchange factor (GEF) 28	protein-coding
mm_103878.1	chr11	83529184	83529203	-	1	NA	exon (NM_013653, exon 2 of 3)	exon (NM_013653, exon 2 of 3)	1325	NM_013653	20304	Mm.284248	NM_013653	ENSMUSG00000035042	Ccl5	MuRantes|RANTES|SISd|Scya5|TCP228	chemokine (C-C motif) ligand 5	protein-coding
mm_91202.1	chr10	21160926	21160969	-	1	NA	promoter-TSS (NM_001198914)	promoter-TSS (NM_001198914)	37	NM_001198914	17863	Mm.52109	NM_010848	ENSMUSG00000019982	Myb	AI550390|M16449|c-myb	myeloblastosis oncogene	protein-coding
mm_156960.1	chrX	169989537	169989549	+	1	NA	3' UTR (NM_001290504, exon 10 of 10)	3' UTR (NM_001290504, exon 10 of 10)	-10626	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_69733.1	chr7	140881812	140881849	-	1	NA	promoter-TSS (NM_001127351)	promoter-TSS (NM_001127351)	39	NM_001127351	64384	Mm.29760	NM_022433	ENSMUSG00000025486	Sirt3	2310003L23Rik|AI848213|Sir2l3	sirtuin 3	protein-coding
mm_12650.1	chr2	74745720	74745758	+	1	NA	intron (NM_010468, intron 2 of 2)	intron (NM_010468, intron 2 of 2)	-6945	NR_110447	102634401	Mm.235021	NR_110447	ENSMUSG00000085015	LOC102634401	-	uncharacterized LOC102634401	ncRNA
mm_1372.1	chr1	66468290	66468302	+	1	NA	promoter-TSS (NM_175510)	promoter-TSS (NM_175510)	-151	NM_175510	329178	Mm.44798	NM_175510	ENSMUSG00000055567	Unc80	C030018G13Rik|C230061B10Rik|UNC-80	unc-80, NALCN activator	protein-coding
mm_119434.1	chr14	46379434	46379436	+	1	NA	promoter-TSS (NR_037981)	promoter-TSS (NR_037981)	-89	NR_037981	100041724	Mm.383311	NM_001099324	ENSMUSG00000079261	Gm15217	OTTMUSG00000019524	predicted gene 15217	ncRNA
mm_76767.1	chr8	95807417	95807453	-	1	NA	promoter-TSS (NM_178078)	promoter-TSS (NM_178078)	27	NM_178078	234594	Mm.259220	NM_153164	ENSMUSG00000036550	Cnot1	6030411K04Rik|AA815922|D830048B13	CCR4-NOT transcription complex, subunit 1	protein-coding
mm_33781.1	chr4	134864557	134864601	+	1	NA	promoter-TSS (NM_011270)	promoter-TSS (NM_011270)	43	NM_011270	19746	Mm.195461	NM_011270	ENSMUSG00000028825	Rhd	Rh|Rhced|Rhl1	Rh blood group, D antigen	protein-coding
mm_34056.1	chr4	138304836	138304892	+	1	NA	5' UTR (NM_007838, exon 1 of 11)	5' UTR (NM_007838, exon 1 of 11)	126	NM_007838	13200	Mm.7236	NM_007838	ENSMUSG00000028757	Ddost	-	dolichyl-di-phosphooligosaccharide-protein glycotransferase	protein-coding
mm_73719.1	chr8	112011393	112011447	+	1	NA	promoter-TSS (NM_001286384)	promoter-TSS (NM_001286384)	61	NM_020584	57321	Mm.213064	NM_020584	ENSMUSG00000033430	Terf2ip	Rap1	telomeric repeat binding factor 2, interacting protein	protein-coding
mm_45209.1	chr5	52992301	52992317	-	1	NA	promoter-TSS (NR_040413)	promoter-TSS (NR_040413)	-17	NR_040413	75954	Mm.258937	NR_040413	ENSMUSG00000106352	5033403H07Rik	-	RIKEN cDNA 5033403H07 gene	ncRNA
mm_146670.1	chr18	12236302	12236405	-	1	NA	promoter-TSS (NM_008720)	promoter-TSS (NM_008720)	33	NM_008720	18145	Mm.3484	NM_008720	ENSMUSG00000024413	Npc1	A430089E03Rik|C85354|D18Ertd139e|D18Ertd723e|lcsd|nmf164|spm	Niemann-Pick type C1	protein-coding
mm_7184.1	chr1	92730714	92730722	-	1	NA	Intergenic	Intergenic	-81877	NM_153114	260301	Mm.219545	NM_153114	ENSMUSG00000044055	Otos	OTOSP	otospiralin	protein-coding
mm_119739.1	chr14	54122038	54122040	+	1	NA	Intergenic	Intergenic	131890	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_167548.1	chr9	30563234	30563236	+	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	135906	NM_028874	102607	Mm.35084	NM_028874	ENSMUSG00000031993	Snx19	3526401K03Rik|AI195321|AI848208|mKIAA0254	sorting nexin 19	protein-coding
mm_123154.1	chr14	57130909	57130919	-	1	NA	5' UTR (NM_001271663, exon 2 of 3)	5' UTR (NM_001271663, exon 2 of 3)	2697	NM_001271663	14623	Mm.25652	NM_008128	ENSMUSG00000040055	Gjb6	AA958971|Cx30|D14Bwg0506e	gap junction protein, beta 6	protein-coding
mm_28164.1	chr3	87846590	87846601	-	1	NA	promoter-TSS (NM_021309)	promoter-TSS (NM_021309)	-160	NM_001025571	27371	Mm.86361	NM_021309	ENSMUSG00000028071	Sh2d2a	Lad|Ribp|Tsad	SH2 domain containing 2A	protein-coding
mm_107304.1	chr12	31073885	31073889	+	1	NA	promoter-TSS (NM_027828)	promoter-TSS (NM_027828)	-81	NM_027828	104943	Mm.248938	NM_027828	ENSMUSG00000036136	Fam110c	9030611O19Rik|AU019489	family with sequence similarity 110, member C	protein-coding
mm_91527.1	chr10	37140938	37140981	-	1	NA	Intergenic	Intergenic	-2033	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_11252.1	chr2	29891986	29892007	+	1	NA	intron (NM_013615, intron 2 of 16)	intron (NM_013615, intron 2 of 16)	1933	NM_013615	18286	Mm.330116	NM_013615	ENSMUSG00000026790	Odf2	AI848335|MMTEST29	outer dense fiber of sperm tails 2	protein-coding
mm_82871.1	chr9	32423840	32423851	-	1	NA	exon (NM_008026, exon 9 of 9)	exon (NM_008026, exon 9 of 9)	29860	NM_001168354	56379	Mm.390168	NM_019659	ENSMUSG00000041248	Kcnj1	Kir1.1|ROMK|Romk2	potassium inwardly-rectifying channel, subfamily J, member 1	protein-coding
mm_99267.1	chr11	101246406	101246422	+	1	NA	promoter-TSS (NM_019444)	promoter-TSS (NM_019444)	80	NM_019444	54409	Mm.260698	NM_019444	ENSMUSG00000001240	Ramp2	-	receptor (calcitonin) activity modifying protein 2	protein-coding
mm_119729.1	chr14	54074988	54074999	+	1	NA	Intergenic	Intergenic	178936	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_77689.1	chr8	126585688	126585714	-	1	NA	Intergenic	Intergenic	7735	NM_001164598	270110	Mm.334918	NM_001164598	ENSMUSG00000051495	Irf2bp2	E130305N23Rik|IRF-2BP2	interferon regulatory factor 2 binding protein 2	protein-coding
mm_117933.1	chr13	99434442	99434456	-	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-21623	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_56941.1	chr6	119933698	119933699	-	1	NA	intron (NM_001185021, intron 24 of 25)	intron (NM_001185021, intron 24 of 25)	31000	NM_001166381	19365	Mm.149	NM_011236	ENSMUSG00000030166	Rad52	Rad52yh	RAD52 homolog, DNA repair protein	protein-coding
mm_14395.1	chr2	129801567	129801605	+	1	NA	promoter-TSS (NR_029452)	promoter-TSS (NR_029452)	-127	NR_029452	654409	Mm.305555	NR_029452		4932416H05Rik	-	RIKEN cDNA 4932416H05 gene	ncRNA
mm_64644.1	chr7	4009514	4009524	-	1	NA	3' UTR (NM_178611, exon 7 of 7)	3' UTR (NM_178611, exon 7 of 7)	53685	NM_001302677	52855	Mm.290880	NM_178611	ENSMUSG00000055541	Lair1	5133400O11Rik|BB115266|D7Bwg0421e|Lair-1	leukocyte-associated Ig-like receptor 1	protein-coding
mm_136110.1	chr16	85494349	85494350	-	1	NA	intron (NM_144853, intron 2 of 3)	intron (NM_144853, intron 2 of 3)	56024	NM_144853	224405	Mm.213203	NM_144853	ENSMUSG00000041134	Cyyr1	-	cysteine and tyrosine-rich protein 1	protein-coding
mm_95337.1	chr11	46815718	46815738	+	1	NA	exon (NM_178759, exon 2 of 9)	exon (NM_178759, exon 2 of 9)	4929	NM_178759	276891	Mm.69002	NM_178759	ENSMUSG00000055546	Timd4	B430010N18Rik|TIM-4|Tim4	T cell immunoglobulin and mucin domain containing 4	protein-coding
mm_26099.1	chr3	136935572	136935591	+	1	NA	3' UTR (NM_001293622, exon 13 of 13)	3' UTR (NM_001293622, exon 13 of 13)	265515	NM_001293622	19055	Mm.331389	NM_008913	ENSMUSG00000028161	Ppp3ca	2900074D19Rik|CN|Caln|Calna|CnA	protein phosphatase 3, catalytic subunit, alpha isoform	protein-coding
mm_79560.1	chr9	58079338	58079356	+	1	NA	intron (NM_001166282, intron 6 of 19)	intron (NM_001166282, intron 6 of 19)	22878	NM_029212	382077	Mm.335193	NM_029212	ENSMUSG00000037716	Ccdc33	4930535E21Rik|Gm1117|Tzip1	coiled-coil domain containing 33	protein-coding
mm_165847.1	chr4	8736089	8736099	+	1	NA	intron (NM_001277149, intron 1 of 37)	(CA)n|Simple_repeat|Simple_repeat	45688	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_47105.1	chr5	118434817	118434848	-	1	NA	Intergenic	PB1D10|SINE|Alu	-125887	NM_001347445	76199	Mm.206238	NM_172424	ENSMUSG00000018076	Med13l	2210413I17Rik|6330591G05Rik|9030618F05Rik|Thrap2|Trap240L|mKIAA1025	mediator complex subunit 13-like	protein-coding
mm_120117.1	chr14	59526732	59526752	+	1	NA	intron (NM_026908, intron 7 of 10)	intron (NM_026908, intron 7 of 10)	71217	NM_001168537	71891	Mm.439850	NM_027986	ENSMUSG00000021982	Cdadc1	2310010M10Rik|AI449174|AI463398|BB130816|NYD-SP15	cytidine and dCMP deaminase domain containing 1	protein-coding
mm_96351.1	chr11	66957895	66957918	+	1	NA	promoter-TSS (NR_130646)	promoter-TSS (NR_130646)	12	NR_130646	71576	Mm.340077	NR_130315	ENSMUSG00000085683	9130409J20Rik	-	RIKEN cDNA 9130409J20 gene	ncRNA
mm_43765.1	chr5	140705100	140705110	+	1	NA	promoter-TSS (NM_181066)	promoter-TSS (NM_181066)	39	NM_001276287	231841	Mm.271932	NM_172724	ENSMUSG00000000148	Brat1	AA881470|Baat1	BRCA1-associated ATM activator 1	protein-coding
mm_113429.1	chr13	34652911	34652941	+	1	NA	promoter-TSS (NR_105041)	promoter-TSS (NR_105041)	3	NR_105041	101056149	Mm.421309	NR_105041	ENSMUSG00000086786	Gm15908	OTTMUSG00000027716	predicted gene 15908	ncRNA
mm_79958.1	chr9	66158207	66158271	+	1	NA	promoter-TSS (NM_010019)	promoter-TSS (NM_010019)	13	NM_010019	13143	Mm.304472	NM_010019	ENSMUSG00000032380	Dapk2	-	death-associated protein kinase 2	protein-coding
mm_18824.1	chr2	74659836	74659846	-	1	NA	promoter-TSS (NM_007967)	promoter-TSS (NM_007967)	-284	NM_007967	14029	Mm.25365	NM_007967	ENSMUSG00000001815	Evx2	Evx-2	even-skipped homeobox 2	protein-coding
mm_137573.1	chr17	27856444	27856511	+	1	NA	promoter-TSS (NM_001080769)	promoter-TSS (NM_001080769)	-30	NM_001080769	224648	Mm.291291	NM_001080769	ENSMUSG00000039512	Uhrf1bp1	1110020K19Rik|AA408674|F830021D11Rik|mKIAA4127	UHRF1 (ICBP90) binding protein 1	protein-coding
mm_150105.1	chr19	29499440	29499442	+	1	NA	Intergenic	Intergenic	22546	NR_015567	77779	Mm.458738	NR_015567	ENSMUSG00000097855	A930007I19Rik	-	RIKEN cDNA A930007I19 gene	ncRNA
mm_19590.1	chr2	102050496	102050499	-	1	NA	intron (NM_001290784, intron 4 of 5)	intron (NM_001290784, intron 4 of 5)	135963	NM_178886	241576	Mm.489740	NM_178886	ENSMUSG00000048058	Ldlrad3	6430500P08|AI194318|Lrad3	low density lipoprotein receptor class A domain containing 3	protein-coding
mm_117747.1	chr13	95892200	95892213	-	1	NA	promoter-TSS (NM_027711)	promoter-TSS (NM_027711)	-284	NM_027711	544963	Mm.38878	NM_027711	ENSMUSG00000021676	Iqgap2	4933417J23Rik|A630053O10|AI788777	IQ motif containing GTPase activating protein 2	protein-coding
mm_23527.1	chr3	60622152	60622169	+	1	NA	exon (NM_001253709, exon 7 of 9)	exon (NM_001253709, exon 7 of 9)	120981	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_36760.1	chr4	101356112	101356178	-	1	NA	non-coding (NR_040708, exon 1 of 2)	non-coding (NR_040708, exon 1 of 2)	103	NR_040708	77866	Mm.137053	NR_040708	ENSMUSG00000086782	E130102H24Rik	-	RIKEN cDNA E130102H24 gene	ncRNA
mm_163057.1	chr11	60931803	60931816	-	1	NA	promoter-TSS (NR_027800)	promoter-TSS (NR_027800)	58	NR_027800	24082	Mm.46270	NM_025293	ENSMUSG00000042549	Map2k3os	F3-1|Gm16516|Gtlf3a	mitogen-activated protein kinase kinase 3, opposite strand	ncRNA
mm_164755.1	chr17	84117058	84117075	+	1	NA	Intergenic	Intergenic	38406	NR_045458	74473	Mm.399575	NR_045458		4933433H22Rik	-	RIKEN cDNA 4933433H22 gene	ncRNA
mm_68984.1	chr7	126589821	126589845	-	1	NA	TTS (NM_138310)	TTS (NM_138310)	-4016	NM_001146311	12752	Mm.268930	NM_009907	ENSMUSG00000030720	Cln3	AI323623	ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease)	protein-coding
mm_4812.1	chr1	185363026	185363026	+	1	NA	promoter-TSS (NM_029735)	promoter-TSS (NM_029735)	-69	NM_029735	107508	Mm.154511	NM_029735	ENSMUSG00000026615	Eprs	2410081F06Rik|3010002K18Rik|C79379|Qprs	glutamyl-prolyl-tRNA synthetase	protein-coding
mm_38282.1	chr4	136890158	136890162	-	1	NA	exon (NM_007574, exon 3 of 3)	exon (NM_007574, exon 3 of 3)	2754	NM_007574	12262	Mm.439732	NM_007574	ENSMUSG00000036896	C1qc	AI385742|C1qg|Ciqc	complement component 1, q subcomponent, C chain	protein-coding
mm_147496.1	chr18	47369131	47369149	-	1	NA	promoter-TSS (NM_018744)	promoter-TSS (NM_018744)	-270	NM_001311097	20358	Mm.40909	NM_018744	ENSMUSG00000019647	Sema6a	A730020P05Rik|AI851735|Sema6A-1|Semaq|VIa	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A	protein-coding
mm_28789.1	chr3	95995836	95995857	-	1	NA	promoter-TSS (NM_023320)	promoter-TSS (NM_023320)	-7	NM_023320	67220	Mm.458147	NM_023320	ENSMUSG00000015745	Plekho1	2810052M02Rik|CKIP-1|Ckip1|JZA-20|Jza2	pleckstrin homology domain containing, family O member 1	protein-coding
mm_20698.1	chr2	132923476	132923480	-	1	NA	intron (NM_198029, intron 8 of 14)	RMER17C|LTR|ERVK	22558	NM_198029	241639	Mm.209784	NM_198029	ENSMUSG00000027356	Fermt1	5830467P10Rik|Kindlin-1	fermitin family member 1	protein-coding
mm_51162.1	chr6	70725809	70725833	+	1	NA	Intergenic	Intergenic	66354	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_68958.1	chr7	126566350	126566354	-	1	NA	promoter-TSS (NM_146200)	promoter-TSS (NM_146200)	14	NM_146200	56347	Mm.22776	NM_146200	ENSMUSG00000030738	Eif3c	110kDa|3230401O13Rik|Eif3s8|NIPIL(A3)|NipilA3|Xs|Xsl	eukaryotic translation initiation factor 3, subunit C	protein-coding
mm_133974.1	chr16	4475126	4475159	-	1	NA	Intergenic	CpG	47911	NM_175347	106393	Mm.35811	NM_175347	ENSMUSG00000022519	Srl	9830004M20Rik|AW108387|sar	sarcalumenin	protein-coding
mm_96244.1	chr11	62574478	62574522	+	1	NA	promoter-TSS (NM_011706)	promoter-TSS (NM_011706)	14	NM_011706	22368	Mm.288064	NM_011706	ENSMUSG00000018507	Trpv2	GRC|OTRPC2|VRL-1|Vrl1	transient receptor potential cation channel, subfamily V, member 2	protein-coding
mm_74691.1	chr8	15011770	15011771	-	1	NA	intron (NM_029116, intron 1 of 1)	CpG	745	NM_029116	74901	Mm.46675	NM_029116	ENSMUSG00000055675	Kbtbd11	2900016B01Rik|4930465M17Rik|mKIAA0711	kelch repeat and BTB (POZ) domain containing 11	protein-coding
mm_46701.1	chr5	110176450	110176463	-	1	NA	promoter-TSS (NM_008146)	promoter-TSS (NM_008146)	48	NR_040431	100504007	Mm.441495	NR_040430	ENSMUSG00000086247	Gm15787	OTTMUSG00000026209	predicted gene 15787	ncRNA
mm_109373.1	chr12	109650157	109650161	+	1	NA	promoter-TSS (NR_028434)	promoter-TSS (NR_028434)	542	NR_046304	100861570		NR_046304	ENSMUSG00000084549	DQ267100	-	snoRNA DQ267100	snoRNA
mm_146955.1	chr18	32835310	32835313	-	1	NA	intron (NR_045381, intron 1 of 4)	intron (NR_045381, intron 1 of 4)	-1914	NM_001110015	225348	Mm.38816	NM_144863	ENSMUSG00000038299	Wdr36	5730444A13Rik|Ta-wdrp	WD repeat domain 36	protein-coding
mm_161201.1	chr13	58183195	58183195	-	1	NA	exon (NM_152234, exon 7 of 10)	exon (NM_152234, exon 7 of 10)	25546	NM_198004	75731	Mm.293919	NM_198004	ENSMUSG00000050002	Idnk	5133401N09Rik	idnK gluconokinase homolog (E. coli)	protein-coding
mm_165765.1	chr3	121456665	121456670	+	1	NA	intron (NM_028044, intron 6 of 6)	B3|SINE|B2	30126	NM_028044	71994	Mm.275555	NM_028044	ENSMUSG00000053931	Cnn3	1600014M03Rik|C85854|Calpo3	calponin 3, acidic	protein-coding
mm_82371.1	chr9	14614950	14615034	-	1	NA	promoter-TSS (NM_001081395)	promoter-TSS (NM_001081395)	8	NM_001081395	75723	Mm.159552	NM_001081395	ENSMUSG00000013076	Amotl1	2310010G08Rik|2310067L22Rik|4932416D09Rik|JEAP|mFLJ00155	angiomotin-like 1	protein-coding
mm_52262.1	chr6	108213929	108213944	+	1	NA	intron (NM_010585, intron 1 of 61)	intron (NM_010585, intron 1 of 61)	840	NM_010585	16438	Mm.227912	NM_010585	ENSMUSG00000030102	Itpr1	D6Pas2|ENSMUSG00000072853|Gm10429|IP3R 1|IP3R1|InsP3R|Ip3r|Itpr-1|P400|Pcp-1|Pcp1|insP3R1|opt|wblo	inositol 1,4,5-trisphosphate receptor 1	protein-coding
mm_110025.1	chr12	16800529	16800540	-	1	NA	intron (NM_015764, intron 1 of 34)	CpG	352	NM_015764	268527	Mm.428062	NM_015764	ENSMUSG00000036523	Greb1	5730583K22Rik|9130004E13|AF180470|AU023194|mKIAA0575	gene regulated by estrogen in breast cancer protein	protein-coding
mm_87180.1	chr10	39133982	39134031	+	1	NA	promoter-TSS (NM_028006)	promoter-TSS (NM_028006)	-17	NM_028006	71924	Mm.297956	NM_028006	ENSMUSG00000019845	Tube1	2310061K05Rik|AI551343|Tube	epsilon-tubulin 1	protein-coding
mm_3363.1	chr1	138273723	138273769	+	1	NA	promoter-TSS (NM_177397)	promoter-TSS (NM_177397)	8	NM_177397	338375	Mm.114424	NM_177397	ENSMUSG00000026394	Atp6v1g3	-	ATPase, H+ transporting, lysosomal V1 subunit G3	protein-coding
mm_35543.1	chr4	41464817	41464892	-	1	NA	promoter-TSS (NM_025539)	promoter-TSS (NM_025539)	-6	NM_024241	109242	Mm.370288	NM_024241	ENSMUSG00000028438	Kif24	4933425J19Rik|9430029L23Rik	kinesin family member 24	protein-coding
mm_119509.1	chr14	47384621	47384642	+	1	NA	exon (NM_010705, exon 5 of 6)	exon (NM_010705, exon 5 of 6)	10771	NM_001145953	16854	Mm.248615	NM_010705	ENSMUSG00000050335	Lgals3	GBP|L-34|Mac-2|gal3	lectin, galactose binding, soluble 3	protein-coding
mm_34919.1	chr4	155761149	155761166	+	1	NA	promoter-TSS (NM_179203)	promoter-TSS (NM_179203)	-35	NR_027971	70448	Mm.70636	NM_175157	ENSMUSG00000054514	Atad3aos	2610204G22Rik	ATPase family, AAA domain containing 3A, opposite strand	ncRNA
mm_80928.1	chr9	102505962	102505972	+	1	NA	promoter-TSS (NM_024291)	promoter-TSS (NM_024291)	-171	NM_024291	16716	Mm.101692	NM_024291	ENSMUSG00000035606	Ky	CD1|D9Mgc44e|ky	kyphoscoliosis peptidase	protein-coding
mm_106896.1	chr12	8012580	8012588	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	34907	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_14450.1	chr2	131127393	131127461	+	1	NA	promoter-TSS (NM_028306)	promoter-TSS (NM_028306)	15	NM_028306	72630	Mm.277465	NM_028306	ENSMUSG00000074793	Hspa12b	2700081N06Rik	heat shock protein 12B	protein-coding
mm_73627.1	chr8	110703722	110703734	+	1	NA	intron (NM_146216, intron 14 of 18)	intron (NM_146216, intron 14 of 18)	-17748	NM_198625	244654	Mm.490385	NM_198625	ENSMUSG00000033763	Mtss1l	ABBA	metastasis suppressor 1-like	protein-coding
mm_38558.1	chr4	141644965	141644969	-	1	NA	intron (NM_001347237, intron 1 of 18)	intron (NM_001347237, intron 1 of 18)	19148	NM_001347237	69582	Mm.33220	NM_001033150	ENSMUSG00000028917	Plekhm2	2310034J19Rik|AI854247|mKIAA0842	pleckstrin homology domain containing, family M (with RUN domain) member 2	protein-coding
mm_152220.1	chr19	8344579	8344582	-	1	NA	exon (NM_177002, exon 7 of 10)	exon (NM_177002, exon 7 of 10)	60525	NM_177002	319800	Mm.426083	NM_177002	ENSMUSG00000052562	Slc22a30	AA986766|C730048C13Rik|UST1R	solute carrier family 22, member 30	protein-coding
mm_124288.1	chr14	103051506	103051541	-	1	NA	exon (NM_008392, exon 4 of 5)	exon (NM_008392, exon 4 of 5)	4511	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_102499.1	chr11	60418583	60418608	-	1	NA	intron (NM_025757, intron 1 of 5)	intron (NM_025757, intron 1 of 5)	1450	NM_025757	66771	Mm.29950	NM_025757	ENSMUSG00000018415	Gid4	4933439F18Rik	GID complex subunit 4, VID24 homolog	protein-coding
mm_101055.1	chr11	8664668	8664681	-	1	NA	promoter-TSS (NM_001083587)	promoter-TSS (NM_001083587)	-139	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_4429.1	chr1	172506227	172506267	+	1	NA	exon (NM_178598, exon 4 of 5)	exon (NM_178598, exon 4 of 5)	6001	NM_178598	21346	Mm.271711	NM_178598	ENSMUSG00000026547	Tagln2	2700094C18Rik|SM22beta|Sm22B|Sm22a	transgelin 2	protein-coding
mm_81249.1	chr9	107975644	107975648	+	1	NA	promoter-TSS (NM_023738)	promoter-TSS (NM_023738)	79	NM_023738	74153	Mm.277125	NM_023738	ENSMUSG00000032596	Uba7	1300004C08Rik|Ube1l	ubiquitin-like modifier activating enzyme 7	protein-coding
mm_90072.1	chr10	116372862	116372865	+	1	NA	exon (NM_029928, exon 30 of 32)	exon (NM_029928, exon 30 of 32)	-45258	NR_028107	67342	Mm.245800	NM_026098	ENSMUSG00000020164	Kcnmb4os1	1700058G18Rik	potassium large conductance calcium-activated channel, subfamily M, beta member 4, opposite strand 1	ncRNA
mm_151614.1	chr19	3900556	3900597	-	1	NA	intron (NM_001167784, intron 10 of 19)	B1_Mm|SINE|Alu	4654	NM_016921	27060	Mm.271689	NM_016921	ENSMUSG00000001750	Tcirg1	ATP6N1C|ATP6a3|Atp6i|OC-116|OPTB1|Stv1|TIRC7|Vph1|oc	T cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 protein A3	protein-coding
mm_10286.1	chr2	10153634	10153654	+	1	NA	5' UTR (NM_172471, exon 1 of 14)	5' UTR (NM_172471, exon 1 of 14)	101	NM_172471	209378	Mm.313876	NM_172471	ENSMUSG00000025780	Itih5	4631408O11Rik|5430408M01Rik|E130106B02	inter-alpha (globulin) inhibitor H5	protein-coding
mm_157368.1	chrX	37211046	37211054	-	1	NA	promoter-TSS (NM_001033234)	promoter-TSS (NM_001033234)	-9	NM_001033234	194854	Mm.296429	NM_001033234	ENSMUSG00000073243	Gm9	-	predicted gene 9	protein-coding
mm_125136.1	chr15	30457852	30457868	+	1	NA	intron (NM_008729, intron 2 of 22)	intron (NM_008729, intron 2 of 22)	285267	NM_008729	18163	Mm.321648	NM_008729	ENSMUSG00000022240	Ctnnd2	Catnd2|Nprap|neurojugin	catenin (cadherin associated protein), delta 2	protein-coding
mm_98424.1	chr11	94644646	94644669	+	1	NA	TTS (NM_177752)	TTS (NM_177752)	9097	NM_177752	268465	Mm.358937	NM_177752	ENSMUSG00000039055	Eme1	6820428D13	essential meiotic structure-specific endonuclease 1	protein-coding
mm_148755.1	chr19	6058236	6058246	+	1	NA	promoter-TSS (NM_026246)	promoter-TSS (NM_026246)	274	NM_001190436	14109	Mm.329631	NM_007990	ENSMUSG00000038274	Fau	MNSFbeta	Finkel-Biskis-Reilly murine sarcoma virus (FBR-MuSV) ubiquitously expressed (fox derived)	protein-coding
mm_18854.1	chr2	75676634	75676650	-	1	NA	exon (NM_010902, exon 5 of 5)	exon (NM_010902, exon 5 of 5)	17352	NR_033513	627828	Mm.459502	NR_033513	ENSMUSG00000092086	Gm6793	EG627828	heterogeneous nuclear ribonucleoprotein A3 pseudogene	pseudo
mm_130189.1	chr15	93712732	93712750	-	1	NA	Intergenic	MIR3|SINE|MIR	-116850	NM_001033217	106042	Mm.150314	NM_001033217	ENSMUSG00000036158	Prickle1	1110058P22Rik|AW215793|Prickle|b2b019Clo|mpk1	prickle planar cell polarity protein 1	protein-coding
mm_171708.1	chr4	7629328	7629330	+	1	NA	Intergenic	L1Md_T|LINE|L1	68641	NR_040645	71510	Mm.410775	NR_040645	ENSMUSG00000086070	8430436N08Rik	-	RIKEN cDNA 8430436N08 gene	ncRNA
mm_35638.1	chr4	43518439	43518455	-	1	NA	exon (NM_009416, exon 7 of 9)	exon (NM_009416, exon 7 of 9)	5107	NM_009416	22004	Mm.646	NM_009416	ENSMUSG00000028464	Tpm2	Tpm-2|Trop-2	tropomyosin 2, beta	protein-coding
mm_107769.1	chr12	59130995	59131029	+	1	NA	promoter-TSS (NM_001165253)	promoter-TSS (NM_001165253)	-441	NM_001165253	338320	Mm.213215	NM_146034	ENSMUSG00000021000	Mia2	Ctage5|D12Bwg0579e|Mea6|Mgea|Mgea6	melanoma inhibitory activity 2	protein-coding
mm_100391.1	chr11	119389975	119389985	+	1	NA	promoter-TSS (NR_035453)	promoter-TSS (NR_035453)	-492	NR_035453	100316690		NR_035453	ENSMUSG00000088015	Mir1932	mir-1932|mmu-mir-1932	microRNA 1932	ncRNA
mm_34174.1	chr4	140426380	140426425	+	1	NA	Intergenic	Intergenic	-179591	NM_198610	230868	Mm.298731	NM_198610	ENSMUSG00000040972	Igsf21	BC055811|Gm141	immunoglobulin superfamily, member 21	protein-coding
mm_27478.1	chr3	53657101	53657112	-	1	NA	5' UTR (NM_172862, exon 1 of 24)	5' UTR (NM_172862, exon 1 of 24)	249	NM_172862	242022	Mm.38378	NM_172862	ENSMUSG00000037016	Frem2	6030440P17Rik|8430406N05Rik|Gm409|b2b1562Clo|my|ne|nv1	Fras1 related extracellular matrix protein 2	protein-coding
mm_42029.1	chr5	108279631	108279643	+	1	NA	3' UTR (NM_026106, exon 3 of 3)	3' UTR (NM_026106, exon 3 of 3)	10740	NM_026106	13486	Mm.303534	NM_026106	ENSMUSG00000029265	Dr1	1700121L09Rik|Dr1l|NC2|NC2beta	down-regulator of transcription 1	protein-coding
mm_80626.1	chr9	88957025	88957036	+	1	NA	5' UTR (NM_009742, exon 1 of 2)	5' UTR (NM_009742, exon 1 of 2)	110	NM_009742	12044	Mm.425593	NM_009742	ENSMUSG00000102037	Bcl2a1a	A1|BB218357|Bcl2a1|Bfl-1|Hbpa1	B cell leukemia/lymphoma 2 related protein A1a	protein-coding
mm_44538.1	chr5	24540414	24540422	-	1	NA	promoter-TSS (NM_080444)	promoter-TSS (NM_080444)	39	NM_080444	117590	Mm.207071	NM_080444	ENSMUSG00000038204	Asb10	Asb-10|BB137407	ankyrin repeat and SOCS box-containing 10	protein-coding
mm_43109.1	chr5	124540744	124540786	+	1	NA	promoter-TSS (NM_019770)	promoter-TSS (NM_019770)	-26	NM_019770	56334	Mm.325307	NM_019770	ENSMUSG00000029390	Tmed2	1110032D12Rik|1810020N21Rik|Rnp24|Sid394|p24beta1	transmembrane p24 trafficking protein 2	protein-coding
mm_114607.1	chr13	75839875	75839881	+	1	NA	promoter-TSS (NM_053108)	promoter-TSS (NM_053108)	-8	NM_053108	93692	Mm.25844	NM_053108	ENSMUSG00000021591	Glrx	C86710|D13Wsu156e|Glrx1|Grx1|TTase	glutaredoxin	protein-coding
mm_169738.1	chr15	83930553	83930569	-	1	NA	intron (NM_001161628, intron 2 of 14)	L1Md_F2|LINE|L1	5534	NM_001161628	77627	Mm.196288	NM_029946	ENSMUSG00000022441	Efcab6	4931407K02Rik|4932408N08Rik|bM150J22.2|mKIAA1672	EF-hand calcium binding domain 6	protein-coding
mm_89695.1	chr10	97606866	97606900	+	1	NA	promoter-TSS (NM_008438)	promoter-TSS (NM_008438)	-322	NM_008438	16545	Mm.6228	NM_008438	ENSMUSG00000019932	Kera	CNA2|SLRR2B	keratocan	protein-coding
mm_32635.1	chr4	115000222	115000229	+	1	NA	5' UTR (NM_009185, exon 1 of 17)	5' UTR (NM_009185, exon 1 of 17)	107	NM_001304555	20460	Mm.3988	NM_009185	ENSMUSG00000028718	Stil	Sil	Scl/Tal1 interrupting locus	protein-coding
mm_72467.1	chr8	83348452	83348481	+	1	NA	promoter-TSS (NM_026233)	promoter-TSS (NM_026233)	-6	NM_026233	67555	Mm.84115	NM_026233	ENSMUSG00000035057	Mgat4d	4933434I20Rik|GnT1IP|GnT1IP-L	MGAT4 family, member C	protein-coding
mm_52451.1	chr6	113681912	113681925	+	1	NA	intron (NM_001113553, intron 8 of 11)	intron (NM_001113553, intron 8 of 11)	-15132	NM_001347356	381801	Mm.333322	NM_001033463	ENSMUSG00000056952	Tatdn2	AI646012|mKIAA0218	TatD DNase domain containing 2	protein-coding
mm_126361.1	chr15	80059571	80059571	+	1	NA	Intergenic	Intergenic	19008	NR_028282	100302601		NR_028282	ENSMUSG00000077734	Snord83b	MBII-10	small nucleolar RNA, C/D box 83B	snoRNA
mm_121654.1	chr14	10453444	10453467	-	1	NA	promoter-TSS (NM_001308286)	promoter-TSS (NM_001308286)	3	NM_001308286	14198	Mm.397619	NM_010210	ENSMUSG00000060579	Fhit	AW045638|Fra14A2	fragile histidine triad gene	protein-coding
mm_36846.1	chr4	106678934	106678942	-	1	NA	promoter-TSS (NM_001172073)	promoter-TSS (NM_001172073)	6	NM_028209	72354	Mm.25806	NM_028209	ENSMUSG00000025413	Ttc4	2810002P21Rik|AF007005|L62	tetratricopeptide repeat domain 4	protein-coding
mm_122180.1	chr14	31557883	31557894	-	1	NA	intron (NM_009937, intron 1 of 16)	intron (NM_009937, intron 1 of 16)	19495	NM_009937	382864	Mm.239821	NM_009937	ENSMUSG00000057606	Colq	A130034K24Rik	collagen-like tail subunit (single strand of homotrimer) of asymmetric acetylcholinesterase	protein-coding
mm_64766.1	chr7	4971772	4971778	-	1	NA	promoter-TSS (NM_001200041)	promoter-TSS (NM_001200041)	-814	NM_001200041	381835	Mm.297828	NM_001200041	ENSMUSG00000085272	Sbk3	Gm1078|Sgk110	SH3 domain binding kinase family, member 3	protein-coding
mm_97421.1	chr11	78032347	78032366	+	1	NA	promoter-TSS (NM_183286)	promoter-TSS (NM_183286)	43	NM_183286	70451	Mm.390342	NM_183286	ENSMUSG00000020834	Dhrs13	2610209N15Rik	dehydrogenase/reductase (SDR family) member 13	protein-coding
mm_84932.1	chr9	82908038	82908042	-	1	NA	intron (NM_001081216, intron 19 of 39)	L1MD|LINE|L1	67449	NM_001081216	83946	Mm.221688	NM_031879	ENSMUSG00000032253	Phip	2810004D21Rik|4632404O06Rik|Ndrp|Wdr11	pleckstrin homology domain interacting protein	protein-coding
mm_112907.1	chr13	20903010	20903029	+	1	NA	intron (NM_012054, intron 5 of 20)	intron (NM_012054, intron 5 of 20)	108906	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_38474.1	chr4	140665875	140665886	-	1	NA	promoter-TSS (NM_001112722)	promoter-TSS (NM_001112722)	7	NM_001290803	72754	Mm.29329	NM_172415	ENSMUSG00000040964	Arhgef10l	2810441C07Rik	Rho guanine nucleotide exchange factor (GEF) 10-like	protein-coding
mm_146625.1	chr18	10181327	10181356	-	1	NA	5' UTR (NM_009071, exon 1 of 33)	5' UTR (NM_009071, exon 1 of 33)	451	NM_009071	19877	Mm.6710	NM_009071	ENSMUSG00000024290	Rock1	1110055K06Rik|Rock-I	Rho-associated coiled-coil containing protein kinase 1	protein-coding
mm_26578.1	chr3	147389713	147389720	+	1	NA	Intergenic	Intergenic	537349	NM_001302958	70892	Mm.187793	NM_027594	ENSMUSG00000036745	Ttll7	1110049N09Rik|4921517B04Rik|C630030B20|mTTLL7	tubulin tyrosine ligase-like family, member 7	protein-coding
mm_35312.1	chr4	25281843	25281853	-	1	NA	promoter-TSS (NM_026194)	promoter-TSS (NM_026194)	-27	NM_026194	67490	Mm.226295	NM_026194	ENSMUSG00000040359	Ufl1	1810074P20Rik|AI429228|Kiaa0776|Maxer|Rcad|mKIAA0776	UFM1 specific ligase 1	protein-coding
mm_113767.1	chr13	44819955	44819971	+	1	NA	intron (NM_001205044, intron 2 of 18)	intron (NM_001205044, intron 2 of 18)	88692	NM_001205043	16468	Mm.25059	NM_021878	ENSMUSG00000038518	Jarid2	Jmj|jumonji	jumonji, AT rich interactive domain 2	protein-coding
mm_110135.1	chr12	26447203	26447210	-	1	NA	intron (NM_021384, intron 4 of 5)	intron (NM_021384, intron 4 of 5)	9246	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_25953.1	chr3	132085282	132085299	+	1	NA	promoter-TSS (NM_020265)	promoter-TSS (NM_020265)	-2	NM_020265	56811	Mm.103593	NM_020265	ENSMUSG00000028031	Dkk2	-	dickkopf WNT signaling pathway inhibitor 2	protein-coding
mm_164770.1	chr17	87107288	87107322	+	1	NA	promoter-TSS (NM_019654)	promoter-TSS (NM_019654)	-374	NM_019654	56468	Mm.126885	NM_019654	ENSMUSG00000037104	Socs5	1810018L08Rik|Cish5|mKIAA0671	suppressor of cytokine signaling 5	protein-coding
mm_7896.1	chr1	133424413	133424466	-	1	NA	promoter-TSS (NM_011439)	promoter-TSS (NM_011439)	-227	NM_011439	20668	Mm.8575	NM_011439	ENSMUSG00000070643	Sox13	AA407916|AW259412|AW540933|Sox-13	SRY (sex determining region Y)-box 13	protein-coding
mm_131333.1	chr16	13322502	13322506	+	1	NA	intron (NM_181860, intron 1 of 3)	intron (NM_181860, intron 1 of 3)	-35917	NM_153588	239719	Mm.270643	NM_153588	ENSMUSG00000009569	Mkl2	ENSMUSG00000075401|Gt4-1|MRTF-B|Mrtfb|mKIAA1243	MKL/myocardin-like 2	protein-coding
mm_7543.1	chr1	124504140	124504161	-	1	NA	Intergenic	RSINE1|SINE|B4	-458591	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_51622.1	chr6	85432012	85432045	+	1	NA	promoter-TSS (NM_144918)	promoter-TSS (NM_144918)	52	NM_144918	232187	Mm.219946	NM_144918	ENSMUSG00000033706	Smyd5	AW536703|NN8-4AG|Rai15|Rrg1	SET and MYND domain containing 5	protein-coding
mm_87824.1	chr10	60349353	60349362	+	1	NA	intron (NM_028732, intron 1 of 6)	intron (NM_028732, intron 1 of 6)	2506	NM_028732	74048	Mm.273584	NM_028732	ENSMUSG00000020101	Vsir	4632428N05Rik|Dies1|PD-1H|VISTA	V-set immunoregulatory receptor	protein-coding
mm_77680.1	chr8	125569791	125569834	-	1	NA	Intergenic	CpG	-14826	NR_015535	75930	Mm.195663	NR_015535	ENSMUSG00000110629	4930567H12Rik	4930579P07Rik	RIKEN cDNA 4930567H12 gene	ncRNA
mm_62483.1	chr7	101881298	101881320	+	1	NA	promoter-TSS (NM_001291353)	promoter-TSS (NM_001291353)	-16	NM_001291353	75430	Mm.284491	NM_027532	ENSMUSG00000030649	Anapc15	3200002M19Rik|6330414C15Rik|APC15	anaphase prompoting complex C subunit 15	protein-coding
mm_107916.1	chr12	71016659	71016690	+	1	NA	promoter-TSS (NR_045056)	promoter-TSS (NR_045056)	707	NM_001081195	238247	Mm.241601	NM_001081195	ENSMUSG00000048118	Arid4a	A630009N03|A630067N03Rik|MmRBBP1|Rbbp1	AT rich interactive domain 4A (RBP1-like)	protein-coding
mm_91339.1	chr10	26078952	26078968	-	1	NA	promoter-TSS (NM_029881)	promoter-TSS (NM_029881)	92	NM_029881	77220	Mm.266260	NM_029881	ENSMUSG00000049420	Tmem200a	C030003D03Rik	transmembrane protein 200A	protein-coding
mm_85275.1	chr9	99436750	99436760	-	1	NA	promoter-TSS (NM_008624)	promoter-TSS (NM_008624)	-43	NM_008624	17532	Mm.2045	NM_008624	ENSMUSG00000032470	Mras	2900078C09Rik|AI326250	muscle and microspikes RAS	protein-coding
mm_61451.1	chr7	75586262	75586272	+	1	NA	exon (NM_029332, exon 5 of 37)	exon (NM_029332, exon 5 of 37)	130733	NM_029332	75547	Mm.216107	NM_029332	ENSMUSG00000066406	Akap13	1700026G02Rik|5730522G15Rik|5830460E08Rik|AKAP-13|AKAP-Lbc|BRX|Ht31|LBC|PROTO-LB|PROTO-LBC	A kinase (PRKA) anchor protein 13	protein-coding
mm_78329.1	chr9	25252506	25252516	+	1	NA	promoter-TSS (NM_001205367)	promoter-TSS (NM_001205367)	72	NM_001205367	235072	Mm.270259	NM_009859	ENSMUSG00000001833	Sept7	Cdc10|E430034N22	septin 7	protein-coding
mm_111965.1	chr12	109615563	109615573	-	1	NA	intron (NR_028261, intron 2 of 20)	intron (NR_028261, intron 2 of 20)	-2690	NR_029918	723854		NR_029918	ENSMUSG00000065433	Mir370	Mirn370|mir-370|mmu-mir-370	microRNA 370	ncRNA
mm_35410.1	chr4	34805885	34805887	-	1	NA	exon (NM_013889, exon 8 of 8)	exon (NM_013889, exon 8 of 8)	-27520	NM_025471	66291	Mm.28071	NM_025471	ENSMUSG00000028295	Smim8	1810030N24Rik|2810406B13Rik	small integral membrane protein 8	protein-coding
mm_111957.1	chr12	109560554	109560585	-	1	NA	non-coding (NR_003633, exon 5 of 5)	non-coding (NR_003633, exon 5 of 5)	-3123	NR_030427	791079		NR_030427	ENSMUSG00000076451	Mir770	Mirn770|mir-770|mmu-mir-770	microRNA 770	ncRNA
mm_154611.1	chrX	7652468	7652486	+	1	NA	3' UTR (NM_009305, exon 7 of 7)	3' UTR (NM_009305, exon 7 of 7)	-4902	NM_001290624	54630	Mm.232232	NM_175097	ENSMUSG00000031145	Prickle3	Lmo6|Sfc16	prickle planar cell polarity protein 3	protein-coding
mm_168505.1	chr1	153486865	153486869	-	1	NA	intron (NM_007842, intron 1 of 27)	intron (NM_007842, intron 1 of 27)	793	NM_007842	13211	Mm.20000	NM_007842	ENSMUSG00000042699	Dhx9	AI326842|Ddx9|HEL-5|NDHII|RHA|mHEL-5	DEAH (Asp-Glu-Ala-His) box polypeptide 9	protein-coding
mm_61193.1	chr7	63905471	63905483	+	1	NA	intron (NM_021366, intron 1 of 1)	L1MC3|LINE|L1	-11380	NM_001256311	381994	Mm.425466	NM_001256311	ENSMUSG00000095061	E030018B13Rik	Gm1697	RIKEN cDNA E030018B13 gene	protein-coding
mm_72537.1	chr8	83997108	83997123	+	1	NA	promoter-TSS (NM_001081415)	promoter-TSS (NM_001081415)	-557	NM_001081415	666704	Mm.298091	NM_001081415	ENSMUSG00000079003	Samd1	AA589507	sterile alpha motif domain containing 1	protein-coding
mm_2885.1	chr1	131846729	131846755	+	1	NA	3' UTR (NM_173865, exon 11 of 11)	3' UTR (NM_173865, exon 11 of 11)	18730	NM_173865	98396	Mm.389181	NM_173865	ENSMUSG00000013275	Slc41a1	AI573938|B230315F01Rik	solute carrier family 41, member 1	protein-coding
mm_146681.1	chr18	12847825	12847836	-	1	NA	intron (NM_207530, intron 15 of 27)	(A)n|Simple_repeat|Simple_repeat	14883	NM_001252493	64291	Mm.259470	NM_020573	ENSMUSG00000044252	Osbpl1a	G430090F17Rik|Gm753|ORP-1|Osbpl1b	oxysterol binding protein-like 1A	protein-coding
mm_116987.1	chr13	56426502	56426508	-	1	NA	Intergenic	Intergenic	-11850	NM_177809	328258	Mm.482177	NM_177809	ENSMUSG00000021509	Slc25a48	AU042651|E230025K15	solute carrier family 25, member 48	protein-coding
mm_14760.1	chr2	145167506	145167520	+	1	NA	Intergenic	CpG	-75098	NM_053195	94249	Mm.217171	NM_053195	ENSMUSG00000063873	Slc24a3	NCKX3	solute carrier family 24 (sodium/potassium/calcium exchanger), member 3	protein-coding
mm_79700.1	chr9	60838061	60838073	+	1	NA	intron (NM_028283, intron 1 of 18)	intron (NM_028283, intron 1 of 18)	43519	NM_028283	72565	Mm.68819	NM_028283	ENSMUSG00000034485	Uaca	2700059D02Rik|nucling	uveal autoantigen with coiled-coil domains and ankyrin repeats	protein-coding
mm_57922.1	chr6	134243523	134243527	-	1	NA	intron (NM_001303102, intron 5 of 8)	intron (NM_001303102, intron 5 of 8)	-152804	NM_025778	66813	Mm.474472	NM_025778	ENSMUSG00000030200	Bcl2l14	4930452K23Rik|4933405K19Rik|9030625M01Rik|AI429211|Bclg	BCL2-like 14 (apoptosis facilitator)	protein-coding
mm_137949.1	chr17	32879105	32879118	+	1	NA	TTS (NM_207245)	TTS (NM_207245)	12492	NM_207245	240066	Mm.26636	NM_207245	ENSMUSG00000095325	Zfp870	AI173952	zinc finger protein 870	protein-coding
mm_143138.1	chr17	57218657	57218668	-	1	NA	exon (NM_009778, exon 21 of 41)	exon (NM_009778, exon 21 of 41)	-1434	NR_105944	102465591		NR_105944	ENSMUSG00000099066	Mir6978	Gm27858|mmu-mir-6978	microRNA 6978	ncRNA
mm_13776.1	chr2	118745778	118745799	+	1	NA	promoter-TSS (NM_001301269)	promoter-TSS (NM_001301269)	30	NM_001301269	100043272	Mm.398072	NM_001301269	ENSMUSG00000074918	Inafm2	5430417L22Rik|ENSMUSG00000074918	InaF motif containing 2	protein-coding
mm_150320.1	chr19	34573949	34573959	+	1	NA	exon (NM_008332, exon 3 of 3)	exon (NM_008332, exon 3 of 3)	-9575	NM_010501	15959	Mm.426079	NM_010501	ENSMUSG00000074896	Ifit3	Ifi49|P49	interferon-induced protein with tetratricopeptide repeats 3	protein-coding
mm_74521.1	chr8	9207369	9207382	-	1	NA	3' UTR (NM_173446, exon 3 of 3)	3' UTR (NM_173446, exon 3 of 3)	62706	NR_073360	74688	Mm.159298	NR_073360	ENSMUSG00000109215	4930453L07Rik	-	RIKEN cDNA 4930453L07 gene	ncRNA
mm_37750.1	chr4	129622946	129622952	-	1	NA	intron (NM_025455, intron 1 of 5)	intron (NM_025455, intron 1 of 5)	959	NM_025455	66264	Mm.383215	NM_025455	ENSMUSG00000028795	Ccdc28b	1110002E08Rik|1810010N17Rik	coiled coil domain containing 28B	protein-coding
mm_69821.1	chr7	141265720	141265739	-	1	NA	5' UTR (NM_001252601, exon 2 of 10)	5' UTR (NM_001252601, exon 2 of 10)	695	NM_001252601	54123	Mm.3233	NM_016850	ENSMUSG00000025498	Irf7	-	interferon regulatory factor 7	protein-coding
mm_91940.1	chr10	60816972	60816989	-	1	NA	intron (NM_029770, intron 1 of 16)	intron (NM_029770, intron 1 of 16)	14601	NM_029770	107449	Mm.290433	NM_029770	ENSMUSG00000020099	Unc5b	6330415E02Rik|A630020F16|D10Bwg0792e|Unc5h2	unc-5 netrin receptor B	protein-coding
mm_61434.1	chr7	73852428	73852450	+	1	NA	Intergenic	Intergenic	26515	NR_102375	100861851		NR_102375		Gm21269	-	predicted gene, 21269	ncRNA
mm_12154.1	chr2	62046492	62046505	+	1	NA	promoter-TSS (NM_001242379)	promoter-TSS (NM_001242379)	-17	NM_001242382	94229	Mm.314497	NM_033552	ENSMUSG00000026904	Slc4a10	NCBE|mKIAA4136	solute carrier family 4, sodium bicarbonate cotransporter-like, member 10	protein-coding
mm_6418.1	chr1	73905201	73905236	-	1	NA	Intergenic	Intergenic	-40752	NR_045311	109198	Mm.359721	NR_045311	ENSMUSG00000100301	6030407O03Rik	-	RIKEN cDNA 6030407O03 gene	ncRNA
mm_166275.1	chr5	90690121	90690122	+	1	NA	Intergenic	Intergenic	-49594	NM_001310656	73246	Mm.30172	NM_028478	ENSMUSG00000029370	Rassf6	1600016B17Rik	Ras association (RalGDS/AF-6) domain family member 6	protein-coding
mm_111109.1	chr12	80958130	80958138	-	1	NA	exon (NM_001177561, exon 3 of 5)	exon (NM_001177561, exon 3 of 5)	9945	NM_011387	20493	Mm.486361	NM_011387	ENSMUSG00000021135	Slc10a1	Ntcp	solute carrier family 10 (sodium/bile acid cotransporter family), member 1	protein-coding
mm_78637.1	chr9	40192309	40192337	+	1	NA	promoter-TSS (NM_030713)	promoter-TSS (NM_030713)	7	NM_030713	80902	Mm.132196	NM_030713	ENSMUSG00000025602	Zfp202	C130037E22Rik|Znf202	zinc finger protein 202	protein-coding
mm_129829.1	chr15	83133280	83133311	-	1	NA	exon (NM_178627, exon 5 of 9)	exon (NM_178627, exon 5 of 9)	-10494	NM_029101	74778	Mm.30056	NM_029101	ENSMUSG00000018040	Rrp7a	1110014J01Rik|AA408146|Kheg1	ribosomal RNA processing 7 homolog A (S. cerevisiae)	protein-coding
mm_87941.1	chr10	62895757	62895776	+	1	NA	Intergenic	Intergenic	-15752	NM_001253857	52463	Mm.17774	NM_027384	ENSMUSG00000047146	Tet1	2510010B09Rik|AA517754|BB001228|Cxxc6|D10Ertd17e|LCX|mKIAA1676	tet methylcytosine dioxygenase 1	protein-coding
mm_56724.1	chr6	115639185	115639206	-	1	NA	intron (NM_029780, intron 2 of 16)	intron (NM_029780, intron 2 of 16)	37257	NM_023290	67027	Mm.101316	NM_023290	ENSMUSG00000000439	Mkrn2	2610002L04Rik|C81377	makorin, ring finger protein, 2	protein-coding
mm_112818.1	chr13	20797671	20797684	+	1	NA	intron (NM_012054, intron 1 of 20)	intron (NM_012054, intron 1 of 20)	3564	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_26691.1	chr3	156703906	156703917	+	1	NA	intron (NM_177274, intron 1 of 6)	(T)n|Simple_repeat|Simple_repeat	142117	NM_001039094	320840	Mm.317293	NM_177274	ENSMUSG00000040037	Negr1	5330422G01Rik|KILON|Ntra	neuronal growth regulator 1	protein-coding
mm_137851.1	chr17	31069891	31069908	+	1	NA	intron (NM_009593, intron 2 of 14)	intron (NM_009593, intron 2 of 14)	12205	NM_009593	11307	Mm.15691	NM_009593	ENSMUSG00000024030	Abcg1	AW413978|Abc8|White	ATP-binding cassette, sub-family G (WHITE), member 1	protein-coding
mm_158978.1	chr1	121528587	121528587	-	1	NA	promoter-TSS (NM_010483)	promoter-TSS (NM_010483)	-122	NM_010483	15564	Mm.4833	NM_010483	ENSMUSG00000050534	Htr5b	5-Ht5b	5-hydroxytryptamine (serotonin) receptor 5B	protein-coding
mm_32516.1	chr4	108633097	108633103	+	1	NA	intron (NM_177045, intron 23 of 24)	intron (NM_177045, intron 23 of 24)	13144	NM_177045	319965	Mm.151129	NM_177045	ENSMUSG00000028582	Cc2d1b	A830039B04Rik|Freud2	coiled-coil and C2 domain containing 1B	protein-coding
mm_149729.1	chr19	21839960	21839964	+	1	NA	intron (NM_001033759, intron 18 of 23)	intron (NM_001033759, intron 18 of 23)	61622	NM_031997	83921	Mm.329776	NM_031997	ENSMUSG00000024754	Tmem2	-	transmembrane protein 2	protein-coding
mm_42307.1	chr5	114785782	114785791	+	1	NA	intron (NM_026718, intron 1 of 14)	intron (NM_026718, intron 1 of 14)	10646	NM_026718	68420	Mm.275554	NM_026718	ENSMUSG00000041870	Ankrd13a	1100001D10Rik|ANKRD13|AU046136	ankyrin repeat domain 13a	protein-coding
mm_82393.1	chr9	14676225	14676251	-	1	NA	Intergenic	Intergenic	-61238	NM_001081395	75723	Mm.159552	NM_001081395	ENSMUSG00000013076	Amotl1	2310010G08Rik|2310067L22Rik|4932416D09Rik|JEAP|mFLJ00155	angiomotin-like 1	protein-coding
mm_69281.1	chr7	128005153	128005168	-	1	NA	intron (NM_001079932, intron 1 of 5)	intron (NM_001079932, intron 1 of 5)	782	NM_001079932	434246	Mm.389924	NM_001079932	ENSMUSG00000042828	Trim72	BC067209|MG53	tripartite motif-containing 72	protein-coding
mm_156267.1	chrX	136832126	136832149	+	1	NA	exon (NM_011123, exon 3 of 7)	exon (NM_011123, exon 3 of 7)	9391	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_83450.1	chr9	45055319	45055349	-	1	NA	intron (NM_001093749, intron 1 of 5)	CpG	153	NM_001093749	319742	Mm.49611	NM_176993	ENSMUSG00000070305	Mpzl3	5430427F17Rik|A530065I17Rik|rc	myelin protein zero-like 3	protein-coding
mm_83952.1	chr9	56927973	56927995	-	1	NA	5' UTR (NM_175483, exon 1 of 2)	5' UTR (NM_175483, exon 1 of 2)	387	NM_175483	235406	Mm.191459	NM_175483	ENSMUSG00000032733	Snx33	E130307J07Rik|Sh3px3	sorting nexin 33	protein-coding
mm_159833.1	chr5	128601081	128601081	+	1	NA	promoter-TSS (NM_175284)	promoter-TSS (NM_175284)	-25	NM_175284	93897	Mm.197628	NM_175284	ENSMUSG00000081683	Fzd10	Fz-10	frizzled class receptor 10	protein-coding
mm_151870.1	chr19	5798026	5798028	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	-2046	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_104624.1	chr11	97310028	97310060	-	1	NA	Intergenic	Intergenic	-5672	NM_025927	67036	Mm.5381	NM_025927	ENSMUSG00000018882	Mrpl45	2600005P05Rik|AU043542|R75241	mitochondrial ribosomal protein L45	protein-coding
mm_111653.1	chr12	102818346	102818348	-	1	NA	intron (NM_172806, intron 4 of 11)	intron (NM_172806, intron 4 of 11)	60059	NM_172806	238386	Mm.63456	NM_172806	ENSMUSG00000041702	Btbd7	5730507E09Rik|8030448M07|E130118E17Rik|FUP1|mKIAA1525	BTB (POZ) domain containing 7	protein-coding
mm_108546.1	chr12	84362030	84362056	+	1	NA	promoter-TSS (NM_172581)	promoter-TSS (NM_172581)	75	NM_172582	217707	Mm.280062	NM_172582	ENSMUSG00000021235	Coq6	5930427M12Rik|AW742344	coenzyme Q6 monooxygenase	protein-coding
mm_170636.1	chr19	8725825	8725828	+	1	NA	promoter-TSS (NR_004445)	promoter-TSS (NR_004445)	-40	NR_004445	100127111	Mm.292489	NR_004445	ENSMUSG00000065087	Snord22	Rnu22|U22	small nucleolar RNA, C/D box 22	snoRNA
mm_16857.1	chr2	11646542	11646546	-	1	NA	intron (NM_008367, intron 1 of 7)	B3|SINE|B2	3752	NM_008367	16184	Mm.915	NM_008367	ENSMUSG00000026770	Il2ra	CD25|Il2r|Ly-43	interleukin 2 receptor, alpha chain	protein-coding
mm_121101.1	chr14	99759609	99759614	+	1	NA	Intergenic	Intergenic	390185	NM_010636	16597	Mm.396499	NM_010636	ENSMUSG00000072294	Klf12	2700063E05Rik|AI225908|AI315654|AP-2rep|B130052C06Rik|D530033K05Rik	Kruppel-like factor 12	protein-coding
mm_55649.1	chr6	72366953	72366963	-	1	NA	promoter-TSS (NM_001331167)	promoter-TSS (NM_001331167)	14	NM_001331167	66510	Mm.170023	NM_025607	ENSMUSG00000055850	Rnf181	1700047F16Rik|2500002L14Rik|6230415N01Rik|C77350	ring finger protein 181	protein-coding
mm_144595.1	chr18	32163074	32163115	+	1	NA	promoter-TSS (NM_011946)	promoter-TSS (NM_011946)	5	NM_011946	26405	Mm.211762	NM_011946	ENSMUSG00000024383	Map3k2	9630061B06Rik|AI585793|Mekk2|Mekk2b	mitogen-activated protein kinase kinase kinase 2	protein-coding
mm_117809.1	chr13	97711200	97711213	-	1	NA	Intergenic	MER5A|DNA|hAT-Charlie	151206	NR_046157	328314	Mm.138047	NR_046157	ENSMUSG00000110235	Gm5086	B230311A21|EG328314	predicted gene 5086	ncRNA
mm_157514.1	chrX	49779184	49779194	-	1	NA	Intergenic	L2a|LINE|L2	9054	NM_183336	209268	Mm.110505	NM_177591	ENSMUSG00000031111	Igsf1	5330413N23|5530402E03|AI747649|InhBP/p120|mKIAA0364	immunoglobulin superfamily, member 1	protein-coding
mm_62095.1	chr7	96209940	96209975	+	1	NA	promoter-TSS (NM_011858)	promoter-TSS (NM_011858)	-680	NM_011858	23966	Mm.254610	NM_011858	ENSMUSG00000048078	Tenm4	Doc4|ELM2|Odz4|R75022|Ten-m4|l(7)-3Rn|l7Rn3|mKIAA1302	teneurin transmembrane protein 4	protein-coding
mm_172514.1	chr7	76833254	76833255	+	1	NA	intron (NM_001199224, intron 21 of 22)	L1Md_A|LINE|L1	603367	NM_001199224	244071	Mm.322829	NM_172902	ENSMUSG00000025754	Agbl1	Ccp4|D430020F16|EG244071|Nna1-l1	ATP/GTP binding protein-like 1	protein-coding
mm_82723.1	chr9	25101517	25101520	-	1	NA	Intergenic	Intergenic	50263	NM_020586	80517	Mm.142843	NM_020586	ENSMUSG00000008429	Herpud2	5031400M07Rik|AB041580	HERPUD family member 2	protein-coding
mm_32563.1	chr4	109676623	109676643	+	1	NA	promoter-TSS (NM_007983)	promoter-TSS (NM_007983)	6	NM_007983	14084	Mm.318259	NM_007983	ENSMUSG00000010517	Faf1	AA408698|Dffrx|Fam	Fas-associated factor 1	protein-coding
mm_23645.1	chr3	67430102	67430184	+	1	NA	promoter-TSS (NM_138591)	promoter-TSS (NM_138591)	28	NM_138591	28030	Mm.122466	NM_138591	ENSMUSG00000027774	Gfm1	AW545374|D3Wsu133e|Gfm	G elongation factor, mitochondrial 1	protein-coding
mm_160417.1	chr8	83608764	83608764	+	1	NA	intron (NM_001308227, intron 1 of 2)	CpG	216	NM_001308227	81489	Mm.282092	NM_018808	ENSMUSG00000005483	Dnajb1	0610007I11Rik|DjB1|HSPF1|Hdj1|Hsp40	DnaJ heat shock protein family (Hsp40) member B1	protein-coding
mm_119108.1	chr14	31001415	31001464	+	1	NA	promoter-TSS (NM_001165930)	promoter-TSS (NM_001165930)	6	NM_029626	76485	Mm.8766	NM_029626	ENSMUSG00000021916	Glt8d1	2410004H05Rik|5430414N14Rik|AI450005	glycosyltransferase 8 domain containing 1	protein-coding
mm_5064.1	chr1	195013621	195013628	+	1	NA	Intergenic	Intergenic	-3775	NR_015566	320977	Mm.99905	NR_015566	ENSMUSG00000096929	A330023F24Rik	C030002C11Rik	RIKEN cDNA A330023F24 gene	ncRNA
mm_141064.1	chr17	25792348	25792380	-	1	NA	promoter-TSS (NM_001285984)	promoter-TSS (NM_001285984)	23	NM_001285982	214917	Mm.26783	NM_145410	ENSMUSG00000057411	Fam173a	-	family with sequence similarity 173, member A	protein-coding
mm_74961.1	chr8	26119293	26119303	-	1	NA	promoter-TSS (NM_029965)	promoter-TSS (NM_029965)	-74	NM_207659	320191	Mm.334464	NM_207659	ENSMUSG00000037234	Hook3	5830454D03Rik|AI317159|E330005F07Rik	hook microtubule tethering protein 3	protein-coding
mm_94986.1	chr11	31851372	31851379	+	1	NA	Intergenic	Intergenic	-19565	NM_001290676	67579	Mm.339792	NM_026252	ENSMUSG00000020300	Cpeb4	Cpe-bp4|Cpeb-4|mCPEB-4	cytoplasmic polyadenylation element binding protein 4	protein-coding
mm_80217.1	chr9	72532215	72532271	+	1	NA	promoter-TSS (NM_001033536)	promoter-TSS (NM_001033536)	3	NM_001033536	319758	Mm.32081	NM_001033536	ENSMUSG00000037674	Rfx7	2510005N23Rik|9930116O05Rik|D130086K05Rik|Rfxdc2	regulatory factor X, 7	protein-coding
mm_144946.1	chr18	37806492	37806496	+	1	NA	promoter-TSS (NM_033581)	promoter-TSS (NM_033581)	84	NM_033581	93706	Mm.247203	NM_033581	ENSMUSG00000102918	Pcdhgc3	PC43|Pcdh2	protocadherin gamma subfamily C, 3	protein-coding
mm_119889.1	chr14	54936457	54936478	+	1	NA	promoter-TSS (NM_026066)	promoter-TSS (NM_026066)	-3	NM_026066	67272	Mm.41614	NM_026066	ENSMUSG00000040759	Cmtm5	1500005P16Rik|2900052H21Rik|Cklfsf5	CKLF-like MARVEL transmembrane domain containing 5	protein-coding
mm_140359.1	chr17	86831521	86831567	+	1	NA	3' UTR (NM_010137, exon 16 of 16)	3' UTR (NM_010137, exon 16 of 16)	77680	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_46926.1	chr5	114690865	114690902	-	1	NA	promoter-TSS (NM_019821)	promoter-TSS (NM_019821)	52	NM_019821	56356	Mm.275766	NM_019821	ENSMUSG00000011884	Gltp	1110001F24Rik|C76925|C77564	glycolipid transfer protein	protein-coding
mm_2438.1	chr1	97770226	97770236	+	1	NA	promoter-TSS (NM_001310773)	promoter-TSS (NM_001310773)	59	NM_026250	252876	Mm.86090	NM_026250	ENSMUSG00000026333	Gin1	4930429M06Rik|8430411H10Rik|Gin-1|Zh2c2	gypsy retrotransposon integrase 1	protein-coding
mm_20158.1	chr2	122125814	122125828	-	1	NA	exon (NM_026251, exon 9 of 18)	exon (NM_026251, exon 9 of 18)	-7435	NM_145531	214585	Mm.222303	NM_145531	ENSMUSG00000033396	Spg11	6030465E24Rik|A330015I11|C530005A01Rik	spastic paraplegia 11	protein-coding
mm_78983.1	chr9	45389919	45389926	+	1	NA	intron (NM_022004, intron 1 of 7)	intron (NM_022004, intron 1 of 7)	-9787	NR_028499	11936	Mm.22742	NM_007503	ENSMUSG00000059412	Fxyd2	Atp1g1	FXYD domain-containing ion transport regulator 2	protein-coding
mm_41044.1	chr5	86092211	86092216	+	1	NA	intron (NM_001310639, intron 5 of 7)	intron (NM_001310639, intron 5 of 7)	20467	NM_001310639	56792	Mm.131237	NM_019992	ENSMUSG00000029254	Stap1	AI586015|Brdg1|STAP-1	signal transducing adaptor family member 1	protein-coding
mm_75563.1	chr8	58912306	58912337	-	1	NA	promoter-TSS (NM_175032)	promoter-TSS (NM_175032)	566	NM_173411	234290	Mm.39244	NM_173411	ENSMUSG00000049946	BC030500	-	cDNA sequence BC030500	protein-coding
mm_61584.1	chr7	79869627	79869643	+	1	NA	Intergenic	Intergenic	-27283	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_58342.1	chr6	147087024	147087037	-	1	NA	promoter-TSS (NM_001034903)	promoter-TSS (NM_001034903)	2	NM_001034903	545893	Mm.224739	NM_001034903	ENSMUSG00000072662	Mansc4	A430079E08|EG545893|Gm5887	MANSC domain containing 4	protein-coding
mm_125145.1	chr15	30646236	30646237	+	1	NA	intron (NM_008729, intron 6 of 22)	intron (NM_008729, intron 6 of 22)	-392890	NR_045186	73784	Mm.66947	NR_045186		4930430F21Rik	-	RIKEN cDNA 4930430F21 gene	ncRNA
mm_55256.1	chr6	53068563	53068656	-	1	NA	promoter-TSS (NM_173406)	promoter-TSS (NM_173406)	15	NM_173406	231986	Mm.386865	NM_173406	ENSMUSG00000063568	Jazf1	AI591476|C820002C15|Jaz1|Tip27	JAZF zinc finger 1	protein-coding
mm_117779.1	chr13	96671603	96671633	-	1	NA	promoter-TSS (NM_008255)	promoter-TSS (NM_008255)	-682	NM_008255	15357	Mm.316652	NM_008255	ENSMUSG00000021670	Hmgcr	HMG-CoAR|Red	3-hydroxy-3-methylglutaryl-Coenzyme A reductase	protein-coding
mm_9742.1	chr1	180365265	180365303	-	1	NA	intron (NM_001081175, intron 2 of 7)	intron (NM_001081175, intron 2 of 7)	-34735	NR_003623	277333	Mm.389223	NM_199472		Gm5069	EG277333	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_64319.1	chr7	141949648	141949656	+	1	NA	promoter-TSS (NM_029426)	promoter-TSS (NM_029426)	-99	NM_001009930	75770	Mm.274868	NM_029426	ENSMUSG00000053046	Brsk2	4833424K13Rik|SAD-A|SADA	BR serine/threonine kinase 2	protein-coding
mm_117421.1	chr13	74350207	74350247	-	1	NA	promoter-TSS (NM_024201)	promoter-TSS (NM_024201)	13	NM_023281	66945	Mm.158231	NM_023281	ENSMUSG00000021577	Sdha	1500032O14Rik|2310034D06Rik|4921513A11|C81073|FP|SDH2|SDHF	succinate dehydrogenase complex, subunit A, flavoprotein (Fp)	protein-coding
mm_60048.1	chr7	31059907	31059920	+	1	NA	promoter-TSS (NM_144556)	promoter-TSS (NM_144556)	-22	NM_144556	243914	Mm.389870	NM_144556	ENSMUSG00000036560	Lgi4	Lgil3|clp	leucine-rich repeat LGI family, member 4	protein-coding
mm_727.1	chr1	42954136	42954141	+	1	NA	intron (NM_053107, intron 1 of 1)	intron (NM_053107, intron 1 of 1)	1266	NM_053107	93690	Mm.444976	NM_053107	ENSMUSG00000041907	Gpr45	9230112G11Rik|AW046772	G protein-coupled receptor 45	protein-coding
mm_32978.1	chr4	120134433	120134450	+	1	NA	3' UTR (NM_010657, exon 9 of 9)	3' UTR (NM_010657, exon 9 of 9)	-26765	NM_007902	13615	Mm.284855	NM_007902	ENSMUSG00000028635	Edn2	ET-2|PPET2|VIC	endothelin 2	protein-coding
mm_14642.1	chr2	136891602	136891615	+	1	NA	promoter-TSS (NM_001286983)	promoter-TSS (NM_001286983)	-202	NM_001286983	59030	Mm.272570	NM_021527	ENSMUSG00000027274	Mkks	1300013E18Rik|AI463362|AI957237|Bbs6	McKusick-Kaufman syndrome	protein-coding
mm_98735.1	chr11	96353128	96353140	+	1	NA	exon (NM_134032, exon 2 of 2)	exon (NM_134032, exon 2 of 2)	1502	NM_134032	103889	Mm.281153	NM_134032	ENSMUSG00000075588	Hoxb2	AI894218|Hox-2.8|Hoxbes2	homeobox B2	protein-coding
mm_26225.1	chr3	138903150	138903164	+	1	NA	non-coding (NR_121195, exon 8 of 8)	non-coding (NR_121195, exon 8 of 8)	160949	NM_019571	56224	Mm.31927	NM_019571	ENSMUSG00000028152	Tspan5	2810455A09Rik|4930505M03Rik|NET-4|Tm4sf9	tetraspanin 5	protein-coding
mm_19734.1	chr2	104495099	104495105	-	1	NA	promoter-TSS (NM_001145824)	promoter-TSS (NM_001145824)	-613	NM_001145824	15259	Mm.257925	NM_010434	ENSMUSG00000027177	Hipk3	DYRK6|FIST3|PKY|mir-1902	homeodomain interacting protein kinase 3	protein-coding
mm_93500.1	chr10	112928851	112928876	-	1	NA	5' UTR (NM_001033474, exon 1 of 1)	5' UTR (NM_001033474, exon 1 of 1)	163	NM_001033474	382423	Mm.431239	NM_001033474	ENSMUSG00000074748	Atxn7l3b	4921506J03Rik|6230409E21Rik|AI315132|ENSMUSG00000074747	ataxin 7-like 3B	protein-coding
mm_21654.1	chr2	164335003	164335005	-	1	NA	TTS (NM_009301)	TTS (NM_009301)	2239	NM_009301	20944	Mm.140154	NM_009301	ENSMUSG00000017004	Svs5	BB115186|Semg1|Svp-1|Svp1|Svp5	seminal vesicle secretory protein 5	protein-coding
mm_109614.1	chr12	112760653	112760659	+	1	NA	promoter-TSS (NM_178911)	promoter-TSS (NM_178911)	1	NM_178911	104759	Mm.203915	NM_178911	ENSMUSG00000052160	Pld4	AI132321|thss	phospholipase D family, member 4	protein-coding
mm_67795.1	chr7	97737978	97737984	-	1	NA	exon (NM_175105, exon 1 of 3)	exon (NM_175105, exon 1 of 3)	266	NM_175105	66333	Mm.29756	NM_175105	ENSMUSG00000042797	Aqp11	1700015P13Rik|AI648923|sjds	aquaporin 11	protein-coding
mm_10711.1	chr2	22774475	22774481	+	1	NA	5' UTR (NM_019456, exon 1 of 14)	5' UTR (NM_019456, exon 1 of 14)	151	NM_019456	54519	Mm.14255	NM_019456	ENSMUSG00000026786	Apbb1ip	9930118P07Rik|Prp48	amyloid beta (A4) precursor protein-binding, family B, member 1 interacting protein	protein-coding
mm_56650.1	chr6	113377867	113377877	-	1	NA	promoter-TSS (NM_026552)	promoter-TSS (NM_026552)	-241	NM_026552	68089	Mm.289306	NM_026552	ENSMUSG00000079426	Arpc4	20kDa|5330419I20Rik|AI327076|p20-Arc	actin related protein 2/3 complex, subunit 4	protein-coding
mm_159102.1	chr2	37201249	37201249	+	1	NA	promoter-TSS (NM_146662)	promoter-TSS (NM_146662)	6	NM_146662	258656	Mm.377619	NM_146662	ENSMUSG00000059429	Olfr365	MOR138-1	olfactory receptor 365	protein-coding
mm_35619.1	chr4	43452552	43452563	-	1	NA	exon (NM_001110320, exon 5 of 9)	exon (NM_001110320, exon 5 of 9)	2069	NM_001110320	12517	Mm.188157	NM_007654	ENSMUSG00000028459	Cd72	CD72c|Ly-19|Ly-32|Ly-m19|Lyb-2	CD72 antigen	protein-coding
mm_145360.1	chr18	56676663	56676694	+	1	NA	Intergenic	RMER17C2|LTR|ERVK	-31135	NM_010721	16906	Mm.4105	NM_010721	ENSMUSG00000024590	Lmnb1	-	lamin B1	protein-coding
mm_119253.1	chr14	33923690	33923700	+	1	NA	5' UTR (NM_145741, exon 1 of 3)	5' UTR (NM_145741, exon 1 of 3)	108	NM_145741	14560	Mm.432071	NM_145741	ENSMUSG00000021943	Gdf10	Bmp3b	growth differentiation factor 10	protein-coding
mm_122760.1	chr14	54231429	54231443	-	1	NA	Intergenic	Lx9|LINE|L1	22493	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_94123.1	chr10	128669228	128669240	-	1	NA	TTS (NM_173733)	TTS (NM_173733)	4684	NM_173733	211389	Mm.23352	NM_173733	ENSMUSG00000049858	Suox	SO	sulfite oxidase	protein-coding
mm_43964.1	chr5	145280465	145280510	+	1	NA	Intergenic	Intergenic	-2856	NM_001081431	666311	Mm.260773	NM_001081431	ENSMUSG00000070420	Zscan25	EG666311|Zfp498	zinc finger and SCAN domain containing 25	protein-coding
mm_24409.1	chr3	90464714	90464726	+	1	NA	intron (NM_008727, intron 1 of 21)	intron (NM_008727, intron 1 of 21)	1146	NM_008727	18160	Mm.4627	NM_008727	ENSMUSG00000027931	Npr1	AI893888|GC-A|NPR-A|NPRA|Pndr	natriuretic peptide receptor 1	protein-coding
mm_78613.1	chr9	37545224	37545243	+	1	NA	3' UTR (NM_022029, exon 4 of 4)	3' UTR (NM_022029, exon 4 of 4)	5978	NM_020518	57276	Mm.27478	NM_020518	ENSMUSG00000001943	Vsig2	1190004B15Rik|2210413P10Rik|AU040484|CTX|Ctm	V-set and immunoglobulin domain containing 2	protein-coding
mm_154465.1	chrM	3399	3425	-	1	NA	NA	Intergenic	NA	NA								
mm_55492.1	chr6	69576516	69576522	-	1	NA	Intergenic	Intergenic	-249345	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_108173.1	chr12	76404525	76404529	+	1	NA	5' UTR (NM_008301, exon 1 of 1)	5' UTR (NM_008301, exon 1 of 1)	157	NM_008301	15512	Mm.296181	NM_008301	ENSMUSG00000059970	Hspa2	70kDa|HSP70.2|HSP70A2|Hsp70-2	heat shock protein 2	protein-coding
mm_111207.1	chr12	84382558	84382568	-	1	NA	intron (NM_001026214, intron 12 of 15)	intron (NM_001026214, intron 12 of 15)	18371	NM_001286058	12499	Mm.10211	NM_007647	ENSMUSG00000021236	Entpd5	AI196558|AI987697|Cd39l4|ER-UDPase|NTPDase-5|NTPDase5|Pcph|mNTPase	ectonucleoside triphosphate diphosphohydrolase 5	protein-coding
mm_91508.1	chr10	37136949	37136972	-	1	NA	intron (NM_008538, intron 1 of 1)	CpG	1966	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_16580.1	chr2	3512930	3512970	-	1	NA	promoter-TSS (NR_103465)	promoter-TSS (NR_103465)	-115	NM_177647	227526	Mm.211455	NM_177647	ENSMUSG00000039496	Cdnf	9330140G23|Armetl1	cerebral dopamine neurotrophic factor	protein-coding
mm_33841.1	chr4	135759724	135759737	+	1	NA	promoter-TSS (NM_001085509)	promoter-TSS (NM_001085509)	15	NM_001085509	242702	Mm.318639	NM_001085509	ENSMUSG00000037139	Myom3	8430427K15Rik|Gm434	myomesin family, member 3	protein-coding
mm_81031.1	chr9	104569736	104569746	+	1	NA	promoter-TSS (NM_028719)	promoter-TSS (NM_028719)	-47	NM_028719	74020	Mm.326240	NM_028719	ENSMUSG00000032564	Cpne4	3632411M23Rik|4933406O10Rik	copine IV	protein-coding
mm_93409.1	chr10	107912440	107912444	-	1	NA	promoter-TSS (NM_001177567)	promoter-TSS (NM_001177567)	-308	NM_001177567	628870	Mm.336090	NM_001177567	ENSMUSG00000091455	Otogl	EG628870|Gm6924	otogelin-like	protein-coding
mm_11333.1	chr2	30466380	30466384	+	1	NA	Intergenic	PB1D9|SINE|Alu	7817	NM_030244	72500	Mm.295464	NM_030244	ENSMUSG00000089762	Ier5l	2610524G09Rik	immediate early response 5-like	protein-coding
mm_30450.1	chr3	153852431	153852447	-	1	NA	promoter-TSS (NR_040373)	promoter-TSS (NR_040373)	-15	NR_040373	72317	Mm.440147	NR_040373	ENSMUSG00000086438	Asb17os	2510003D18Rik	ankyrin repeat and SOCS box-containing 17, opposite strand	ncRNA
mm_106652.1	chr11	121081159	121081165	-	1	NA	promoter-TSS (NM_145373)	promoter-TSS (NM_145373)	-23	NM_145373	209588	Mm.69553	NM_145373	ENSMUSG00000025165	Sectm1a	BC010462	secreted and transmembrane 1A	protein-coding
mm_33364.1	chr4	129512495	129512520	+	1	NA	Intergenic	Intergenic	-1074	NM_010807	17357	Mm.424974	NM_010807	ENSMUSG00000047945	Marcksl1	AL022768|AW215397|AW536807|D4Bc1|F52|MacMARCKS|Macs2|Macs3|Mlp|Mrp	MARCKS-like 1	protein-coding
mm_72169.1	chr8	72255762	72255767	+	1	NA	exon (NM_007456, exon 10 of 12)	exon (NM_007456, exon 10 of 12)	15746	NM_007456	11767	Mm.290086	NM_007456	ENSMUSG00000003033	Ap1m1	AA408894|AP47|Adtm1A|Cltnm|mu1A	adaptor-related protein complex AP-1, mu subunit 1	protein-coding
mm_10127.1	chr2	3770674	3770682	+	1	NA	intron (NM_025626, intron 1 of 3)	intron (NM_025626, intron 1 of 3)	57220	NM_025626	66540	Mm.277864	NM_025626	ENSMUSG00000026655	Fam107b	3110001A13Rik|AA589595|AA959793|AI132312	family with sequence similarity 107, member B	protein-coding
mm_68702.1	chr7	119642437	119642449	-	1	NA	intron (NM_054094, intron 6 of 13)	RLTR19-int|LTR|ERVK	24615	NM_054094	117147	Mm.427560	NM_054094	ENSMUSG00000033533	Acsm1	Acas3|Bucs1|Macs	acyl-CoA synthetase medium-chain family member 1	protein-coding
mm_109488.1	chr12	111442536	111442547	+	1	NA	promoter-TSS (NM_009396)	promoter-TSS (NM_009396)	-120	NM_009396	21928	Mm.255332	NM_009396	ENSMUSG00000021281	Tnfaip2	B94|Exoc3l3|M-sec|Tnfip2|tnfb94	tumor necrosis factor, alpha-induced protein 2	protein-coding
mm_10681.1	chr2	22227541	22227582	+	1	NA	promoter-TSS (NM_148413)	promoter-TSS (NM_148413)	58	NM_148413	667663	Mm.330033	NM_148413	ENSMUSG00000025716	Myo3a	9030416P08Rik	myosin IIIA	protein-coding
mm_11886.1	chr2	49700951	49700960	+	1	NA	intron (NM_008449, intron 9 of 25)	intron (NM_008449, intron 9 of 25)	81641	NM_008449	16574	Mm.256342	NM_008449	ENSMUSG00000026764	Kif5c	KINN|Khc|NKHC|NKHC2	kinesin family member 5C	protein-coding
mm_4772.1	chr1	182679932	182679943	+	1	NA	Intergenic	Intergenic	69243	NM_001033547	433386	Mm.338103	NM_001033547	ENSMUSG00000043429	Ccdc185	4922505E12Rik	coiled-coil domain containing 185	protein-coding
mm_33626.1	chr4	132794975	132794988	+	1	NA	intron (NM_001033308, intron 1 of 5)	intron (NM_001033308, intron 1 of 5)	1383	NM_001033308	230787	Mm.290912	NM_001033308	ENSMUSG00000037731	Themis2	ICB-1	thymocyte selection associated family member 2	protein-coding
mm_121030.1	chr14	79769887	79769897	+	1	NA	exon (NM_021543, exon 1 of 3)	exon (NM_021543, exon 1 of 3)	1420	NM_001042726	18530	Mm.390715	NM_021543	ENSMUSG00000036422	Pcdh8	1700080P15Rik|Papc	protocadherin 8	protein-coding
mm_161390.1	chr14	79350707	79350707	-	1	NA	intron (NM_025832, intron 13 of 19)	intron (NM_025832, intron 13 of 19)	39961	NM_025832	66897	Mm.24425	NM_025832	ENSMUSG00000022020	Naa16	1300019C06Rik|Narg1l	N(alpha)-acetyltransferase 16, NatA auxiliary subunit	protein-coding
mm_87610.1	chr10	57785011	57785023	+	1	NA	promoter-TSS (NM_021272)	promoter-TSS (NM_021272)	94	NM_021272	12140	Mm.3644	NM_021272	ENSMUSG00000019874	Fabp7	B-FABP|BFABP|Blbp|MRG	fatty acid binding protein 7, brain	protein-coding
mm_103296.1	chr11	72475043	72475070	-	1	NA	promoter-TSS (NM_001276383)	promoter-TSS (NM_001276383)	-29	NM_001276383	216892	Mm.212812	NM_153060	ENSMUSG00000040447	Spns2	-	spinster homolog 2	protein-coding
mm_153175.1	chr19	34493861	34493867	-	1	NA	3' UTR (NM_021460, exon 10 of 10)	3' UTR (NM_021460, exon 10 of 10)	-18729	NM_009890	12642	Mm.30824	NM_009890	ENSMUSG00000050370	Ch25h	AI462618|m25OH	cholesterol 25-hydroxylase	protein-coding
mm_32854.1	chr4	118229777	118229784	+	1	NA	intron (NM_011213, intron 13 of 32)	intron (NM_011213, intron 13 of 32)	-19216	NR_106085	102466820		NR_106085	ENSMUSG00000098596	Mir7226	Gm27630|mmu-mir-7226	microRNA 7226	ncRNA
mm_120627.1	chr14	70461754	70461779	+	1	NA	exon (NM_145981, exon 2 of 5)	exon (NM_145981, exon 2 of 5)	4249	NM_145981	105653	Mm.192598	NM_145981	ENSMUSG00000003469	Phyhip	AW049870|C630010D02Rik|Lnap1ip|PAHX-AP#1|PAHX-AP1	phytanoyl-CoA hydroxylase interacting protein	protein-coding
mm_80477.1	chr9	78198120	78198141	+	1	NA	intron (NM_010357, intron 1 of 6)	intron (NM_010357, intron 1 of 6)	6164	NM_010357	14860	Mm.2662	NM_010357	ENSMUSG00000032348	Gsta4	GST5.7|mGsta4	glutathione S-transferase, alpha 4	protein-coding
mm_71342.1	chr8	45627802	45627844	+	1	NA	promoter-TSS (NM_001310707)	promoter-TSS (NM_001310707)	72	NM_001310707	234214	Mm.211096	NM_172752	ENSMUSG00000031626	Sorbs2	2010203O03Rik|9430041O17Rik|A530071H08|Argbp2|mKIAA0777|nArgBP2	sorbin and SH3 domain containing 2	protein-coding
mm_170154.1	chr17	45571873	45571885	-	1	NA	exon (NM_008302, exon 2 of 11)	exon (NM_008302, exon 2 of 11)	1382	NM_008302	15516	Mm.2180	NM_008302	ENSMUSG00000023944	Hsp90ab1	90kDa|AL022974|C81438|Hsp84|Hsp84-1|Hsp90|Hspcb	heat shock protein 90 alpha (cytosolic), class B member 1	protein-coding
mm_17007.1	chr2	18844225	18844237	-	1	NA	3' UTR (NM_008845, exon 10 of 10)	3' UTR (NM_008845, exon 10 of 10)	-42413	NR_131254	66774	Mm.87075	NR_131254	ENSMUSG00000097638	Carlr	4933439G12Rik|Carl	cardiac and apoptosis-related long non-coding RNA	ncRNA
mm_162397.1	chr1	82587201	82587205	+	1	NA	promoter-TSS (NM_007735)	promoter-TSS (NM_007735)	282	NM_007734	12828	Mm.389135	NM_007734	ENSMUSG00000079465	Col4a3	[a]3(IV)|alpha3(IV)	collagen, type IV, alpha 3	protein-coding
mm_37004.1	chr4	111477497	111477501	-	1	NA	intron (NM_001048189, intron 6 of 12)	intron (NM_001048189, intron 6 of 12)	62493	NM_026279	67621	Mm.45533	NM_026279	ENSMUSG00000028545	Bend5	2310026E23Rik	BEN domain containing 5	protein-coding
mm_160864.1	chr11	61022732	61022732	+	1	NA	5' UTR (NM_001267593, exon 1 of 2)	5' UTR (NM_001267593, exon 1 of 2)	168	NM_001267593	16515	Mm.4970	NM_010603	ENSMUSG00000042529	Kcnj12	IRK-2|IRK2|Kir2.2|MB-IRK2	potassium inwardly-rectifying channel, subfamily J, member 12	protein-coding
mm_116555.1	chr13	46727633	46727649	-	1	NA	5' UTR (NM_175749, exon 1 of 22)	5' UTR (NM_175749, exon 1 of 22)	208	NM_175749	218210	Mm.255398	NM_175749	ENSMUSG00000021374	Nup153	B130015D15Rik|C88147	nucleoporin 153	protein-coding
mm_151676.1	chr19	4201572	4201589	-	1	NA	promoter-TSS (NM_011237)	promoter-TSS (NM_011237)	23	NM_011237	19367	Mm.277629	NM_011237	ENSMUSG00000024824	Rad9a	Rad9	RAD9 checkpoint clamp component A	protein-coding
mm_12856.1	chr2	83724413	83724419	+	1	NA	promoter-TSS (NM_008402)	promoter-TSS (NM_008402)	19	NM_008402	16410	Mm.227	NM_008402	ENSMUSG00000027087	Itgav	1110004F14Rik|2610028E01Rik|CD51|D430040G12Rik	integrin alpha V	protein-coding
mm_147666.1	chr18	60613531	60613558	-	1	NA	intron (NM_177340, intron 1 of 2)	intron (NM_177340, intron 1 of 2)	-3440	NM_001109975	104027	Mm.252321	NM_177340	ENSMUSG00000043079	Synpo	9030217H17Rik|9130229N11|9330140I15Rik|AW046661	synaptopodin	protein-coding
mm_38469.1	chr4	140648824	140648836	-	1	NA	promoter-TSS (NM_172415)	promoter-TSS (NM_172415)	-74	NM_172415	72754	Mm.29329	NM_172415	ENSMUSG00000040964	Arhgef10l	2810441C07Rik	Rho guanine nucleotide exchange factor (GEF) 10-like	protein-coding
mm_92557.1	chr10	79788925	79788984	-	1	NA	promoter-TSS (NM_001042710)	promoter-TSS (NM_001042710)	31	NM_001042710	73106	Mm.491308	NM_001042710	ENSMUSG00000020323	Prss57	2900092M14Rik|GLGL782|NSP4|Prssl1|UNQ782	protease, serine 57	protein-coding
mm_31521.1	chr4	54947224	54947234	+	1	NA	promoter-TSS (NM_172867)	promoter-TSS (NM_172867)	-716	NM_172867	242466	Mm.102904	NM_172867	ENSMUSG00000060206	Zfp462	6030417H05|9430078C22Rik|Gt4-2|Zfpip	zinc finger protein 462	protein-coding
mm_163696.1	chr13	101555978	101555978	+	1	NA	Intergenic	Intergenic	136652	NM_001024955	18708	Mm.259333	NM_001024955	ENSMUSG00000041417	Pik3r1	PI3K|p50alpha|p55alpha|p85alpha	phosphatidylinositol 3-kinase, regulatory subunit, polypeptide 1 (p85 alpha)	protein-coding
mm_158548.1	chrX	145505137	145505159	-	1	NA	Intergenic	Intergenic	-17509	NM_153319	27494	Mm.100068	NM_153319	ENSMUSG00000041688	Amot	CAG-2|D0Kist1|Sii6	angiomotin	protein-coding
mm_172332.1	chr7	10905040	10905052	-	1	NA	promoter-TSS (NM_001185173)	promoter-TSS (NM_001185173)	4	NM_001185173	665780	Mm.482067	NM_001185173	ENSMUSG00000095339	Zscan4b	EG665780	zinc finger and SCAN domain containing 4B	protein-coding
mm_22336.1	chr2	180709810	180709822	-	1	NA	promoter-TSS (NM_001289652)	promoter-TSS (NM_001289652)	183	NM_177852	23856	Mm.253836	NM_011805	ENSMUSG00000038914	Dido1	6720461J16Rik|D130048F08Rik|DATF-1|DIO-1|Datf1|dido	death inducer-obliterator 1	protein-coding
mm_54991.1	chr6	48770774	48770791	-	1	NA	promoter-TSS (NM_031247)	promoter-TSS (NM_031247)	69	NM_031247	83408	Mm.333050	NM_031247	ENSMUSG00000039264	Gimap3	2010110D23Rik|Gimap5|Ian4	GTPase, IMAP family member 3	protein-coding
mm_98141.1	chr11	87581046	87581067	+	1	NA	promoter-TSS (NM_011129)	promoter-TSS (NM_011129)	-5	NM_001284394	18952	Mm.2214	NM_011129	ENSMUSG00000020486	Sept4	ARTS|Bh5|OTTMUSG00000001265|Pnutl2	septin 4	protein-coding
mm_46745.1	chr5	111234693	111234699	-	1	NA	intron (NM_001267622, intron 11 of 22)	intron (NM_001267622, intron 11 of 22)	-96001	NM_001301644	56305	Mm.200516	NM_019640	ENSMUSG00000050017	Pitpnb	PI-TP-beta	phosphatidylinositol transfer protein, beta	protein-coding
mm_112048.1	chr12	111712910	111712932	-	1	NA	promoter-TSS (NM_026511)	promoter-TSS (NM_026511)	32	NM_001324481	70369	Mm.44239	NM_027404	ENSMUSG00000049792	Bag5	1600025G07Rik|4930405J06Rik|Bag-5	BCL2-associated athanogene 5	protein-coding
mm_107671.1	chr12	53783606	53783609	+	1	NA	intron (NM_013780, intron 4 of 11)	intron (NM_013780, intron 4 of 11)	420267	NM_028133	112407	Mm.133037	NM_028133	ENSMUSG00000035105	Egln3	2610021G09Rik|AI505553|AI648162|Hif-p4h-3|Phd3|SM-20	egl-9 family hypoxia-inducible factor 3	protein-coding
mm_66583.1	chr7	45370560	45370617	-	1	NA	promoter-TSS (NM_011698)	promoter-TSS (NM_011698)	-24	NM_011698	22342	Mm.20472	NM_011698	ENSMUSG00000003872	Lin7b	LIN-7B|MALS-2|Veli2	lin-7 homolog B (C. elegans)	protein-coding
mm_145162.1	chr18	46609279	46609282	+	1	NA	3' UTR (NM_010120, exon 3 of 3)	3' UTR (NM_010120, exon 3 of 3)	11576	NM_010120	13664	Mm.262037	NM_010120	ENSMUSG00000057561	Eif1a	C76390|Ef1a|Eftu|Eif4c|eIF-1A|eIF-4C	eukaryotic translation initiation factor 1A	protein-coding
mm_64834.1	chr7	12961809	12961827	-	1	NA	Intergenic	Intergenic	-4046	NM_178732	243834	Mm.133086	NM_178732	ENSMUSG00000004500	Zfp324	A930002M05|D430030K24Rik|ZF5128	zinc finger protein 324	protein-coding
mm_122227.1	chr14	33112251	33112262	-	1	NA	intron (NM_001146022, intron 13 of 58)	intron (NM_001146022, intron 13 of 58)	72810	NM_001146022	545030	Mm.318345	NM_001146022	ENSMUSG00000051506	Wdfy4	Gm18810	WD repeat and FYVE domain containing 4	protein-coding
mm_80279.1	chr9	73012136	73012164	+	1	NA	exon (NM_001286546, exon 8 of 8)	exon (NM_001286546, exon 8 of 8)	26646	NM_028181	72278	Mm.268475	NM_028181	ENSMUSG00000034563	Ccpg1	1700030B06Rik|1810073J13Rik|9430028F23Rik|AI426686|AI875170|CPR8|D9Ertd392e	cell cycle progression 1	protein-coding
mm_146405.1	chr18	83359019	83359033	+	1	NA	Intergenic	Intergenic	-33142	NR_045361	70960	Mm.410834	NR_045361		4921531P14Rik	1700108N05Rik	RIKEN cDNA 4921531P14 gene	ncRNA
mm_32247.1	chr4	102570135	102570150	+	1	NA	promoter-TSS (NM_001177980)	promoter-TSS (NM_001177980)	82	NM_001177980	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_55600.1	chr6	71642137	71642138	-	1	NA	Intergenic	Intergenic	-9220	NM_001038695	104263	Mm.260479	NM_173001	ENSMUSG00000053470	Kdm3a	1700105C21Rik|C230043E16Rik|JHDM2a|Jmjd1|Jmjd1a|KDM2A|TGSA|Tsga	lysine (K)-specific demethylase 3A	protein-coding
mm_129589.1	chr15	79789042	79789057	-	1	NA	3' UTR (NM_001013360, exon 8 of 8)	3' UTR (NM_001013360, exon 8 of 8)	-14582	NM_017470	54152	Mm.288159	NM_017470	ENSMUSG00000022420	Dnal4	D15Ertd424e|Dnalc4	dynein, axonemal, light chain 4	protein-coding
mm_41287.1	chr5	90462778	90462807	+	1	NA	exon (NM_009654, exon 3 of 15)	exon (NM_009654, exon 3 of 15)	1922	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_121680.1	chr14	12823032	12823133	-	1	NA	promoter-TSS (NM_001042617)	promoter-TSS (NM_001042617)	-3	NM_012061	27062	Mm.260881	NM_012061	ENSMUSG00000054423	Cadps	AU067781|CAPS|CAPS1|mKIAA1121	Ca2+-dependent secretion activator	protein-coding
mm_17110.1	chr2	24349624	24349654	-	1	NA	3' UTR (NM_031167, exon 5 of 5)	3' UTR (NM_031167, exon 5 of 5)	4268	NM_001039701	16181	Mm.882	NM_031167	ENSMUSG00000026981	Il1rn	F630041P17Rik|IL-1ra	interleukin 1 receptor antagonist	protein-coding
mm_23903.1	chr3	83031861	83031882	+	1	NA	exon (NM_010196, exon 5 of 5)	exon (NM_010196, exon 5 of 5)	5718	NM_001111048	14161	Mm.88793	NM_010196	ENSMUSG00000028001	Fga	ENSMUSG00000059807|Fib	fibrinogen alpha chain	protein-coding
mm_151966.1	chr19	5801799	5801998	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	774	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_58890.1	chr7	17090567	17090575	+	1	NA	exon (NM_007676, exon 2 of 5)	exon (NM_007676, exon 2 of 5)	16531	NM_007676	26436	Mm.143686	NM_007676	ENSMUSG00000066760	Psg16	Cea11|PSG|bCEA	pregnancy specific glycoprotein 16	protein-coding
mm_97816.1	chr11	82963071	82963085	+	1	NA	3' UTR (NM_183201, exon 6 of 6)	3' UTR (NM_183201, exon 6 of 6)	-2397	NR_045932	76392	Mm.295205	NR_045932	ENSMUSG00000086327	Slfn5os	1700003F17Rik	schlafen 5, opposite strand	ncRNA
mm_124256.1	chr14	101892645	101892666	-	1	NA	intron (NM_001347628, intron 8 of 26)	intron (NM_001347628, intron 8 of 26)	52032	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_165022.1	chr19	32258247	32258249	+	1	NA	intron (NM_144792, intron 3 of 9)	MLTR18B_MM|LTR|ERVK	-47235	NM_001168526	208449	Mm.329810	NM_144792	ENSMUSG00000040451	Sgms1	9530058O11Rik|AI841905|C80702|Mob|Sms1|Sor1|Tmem23	sphingomyelin synthase 1	protein-coding
mm_72628.1	chr8	84660214	84660224	+	1	NA	Intergenic	Intergenic	2633	NM_010499	15936	Mm.399	NM_010499	ENSMUSG00000053560	Ier2	AI317238|Ch1|Pip92	immediate early response 2	protein-coding
mm_28141.1	chr3	87263594	87263594	-	1	NA	promoter-TSS (NM_030707)	promoter-TSS (NM_030707)	-70	NM_030707	80891	Mm.45173	NM_030707	ENSMUSG00000015852	Fcrls	2810439C17Rik|9330158F12|FcRH2sc|Fcrh2|IFGP2|IgSR|MMAN-g|Msr2|moFcRH2sc	Fc receptor-like S, scavenger receptor	protein-coding
mm_94682.1	chr11	19019093	19019109	+	1	NA	promoter-TSS (NM_010789)	promoter-TSS (NM_010789)	-132	NM_010789	17268	Mm.356578	NM_010789	ENSMUSG00000020160	Meis1	C530044H18Rik|Evi8	Meis homeobox 1	protein-coding
mm_152560.1	chr19	11494576	11494603	-	1	NA	intron (NM_001164202, intron 1 of 4)	intron (NM_001164202, intron 1 of 4)	2551	NM_001164202	666926	Mm.486382	NM_001164202	ENSMUSG00000058470	Gm8369	EG666926	predicted gene 8369	protein-coding
mm_121689.1	chr14	13955027	13955029	-	1	NA	intron (NM_025435, intron 1 of 7)	intron (NM_025435, intron 1 of 7)	6285	NM_001285780	66231	Mm.295875	NM_025435	ENSMUSG00000053453	Thoc7	Nif3l1bp1	THO complex 7	protein-coding
mm_106170.1	chr11	116679194	116679203	-	1	NA	intron (NM_009180, intron 7 of 8)	intron (NM_009180, intron 7 of 8)	4601	NR_028570	100216538		NR_028570	ENSMUSG00000065094	Snord1a	snR38	small nucleolar RNA, C/D box 1A	snoRNA
mm_171492.1	chr4	146156836	146156840	+	1	NA	promoter-TSS (NM_001177545)	promoter-TSS (NM_001177545)	11	NM_001177546	667666	Mm.459230	NM_001177545	ENSMUSG00000066007	Zfp600	Gm13164|OTTMUSG00000010694	zinc finger protein 600	protein-coding
mm_79533.1	chr9	57765206	57765235	+	1	NA	exon (NM_007713, exon 1 of 13)	exon (NM_007713, exon 1 of 13)	640	NM_007713	102414	Mm.25720	NM_007713	ENSMUSG00000032316	Clk3	AI256811	CDC-like kinase 3	protein-coding
mm_40302.1	chr5	43672330	43672355	+	1	NA	intron (NM_172274, intron 4 of 39)	intron (NM_172274, intron 4 of 39)	9963	NM_172274	231214	Mm.44434	NM_172274	ENSMUSG00000039765	Cc2d2a	5730509K17Rik|b2b1035Clo	coiled-coil and C2 domain containing 2A	protein-coding
mm_157855.1	chrX	75035295	75035316	-	1	NA	intron (NM_181584, intron 1 of 9)	intron (NM_181584, intron 1 of 9)	49600	NM_181584	210710	Mm.267056	NM_181584	ENSMUSG00000032750	Gab3	5930433H21Rik	growth factor receptor bound protein 2-associated protein 3	protein-coding
mm_160326.1	chr8	3690195	3690195	-	1	NA	intron (NM_013517, intron 2 of 11)	intron (NM_013517, intron 2 of 11)	195	NM_001253739	14128	Mm.1233	NM_013517	ENSMUSG00000005540	Fcer2a	CD23|Fce2|Fcer2|Ly-42	Fc receptor, IgE, low affinity II, alpha polypeptide	protein-coding
mm_31208.1	chr4	43937320	43937331	+	1	NA	exon (NM_016678, exon 17 of 21)	exon (NM_016678, exon 17 of 21)	-20377	NM_027450	384009	Mm.22213	NM_027450	ENSMUSG00000028480	Glipr2	5730414A08Rik|C77180|GAPR-1	GLI pathogenesis-related 2	protein-coding
mm_134567.1	chr16	20356294	20356322	-	1	NA	intron (NM_013790, intron 25 of 29)	MERVL_2A-int|LTR|ERVL	-30904	NM_183158	224044	Mm.276400	NM_183158	ENSMUSG00000022818	Cyp2ab1	EG224044|F730023N20	cytochrome P450, family 2, subfamily ab, polypeptide 1	protein-coding
mm_141757.1	chr17	34264129	34264147	-	1	NA	intron (NM_207105, intron 1 of 5)	intron (NM_207105, intron 1 of 5)	911	NM_207105	14961	Mm.254067	NM_207105	ENSMUSG00000073421	H2-Ab1	AI845868|Abeta|H-2Ab|H2-Ab|I-Abeta|IAb|Ia-2|Ia2|Rmcs1	histocompatibility 2, class II antigen A, beta 1	protein-coding
mm_75725.1	chr8	69113698	69113715	-	1	NA	TTS (NM_007509)	TTS (NM_007509)	-24484	NM_153054	110877	Mm.19301	NM_153054	ENSMUSG00000036330	Slc18a1	4832416I10Rik|Vat1|Vmat1	solute carrier family 18 (vesicular monoamine), member 1	protein-coding
mm_64609.1	chr7	3290136	3290151	-	1	NA	promoter-TSS (NM_016969)	promoter-TSS (NM_016969)	-412	NM_016969	50918	Mm.29874	NM_016969	ENSMUSG00000068566	Myadm	D7Wsu62e	myeloid-associated differentiation marker	protein-coding
mm_49344.1	chr6	21950379	21950401	+	1	NA	intron (NM_001311061, intron 2 of 11)	intron (NM_001311061, intron 2 of 11)	775	NM_023626	71777	Mm.39999	NM_023626	ENSMUSG00000029670	Ing3	1300013A07Rik|P47ING3	inhibitor of growth family, member 3	protein-coding
mm_165519.1	chr2	173768244	173768264	+	1	NA	intron (NM_019806, intron 2 of 5)	intron (NM_019806, intron 2 of 5)	30683	NM_019806	56491	Mm.260456	NM_019806	ENSMUSG00000054455	Vapb	AI225786|AI840687|AI848259|D2Abb2e|R75548|VAP33b|Vamp33b	vesicle-associated membrane protein, associated protein B and C	protein-coding
mm_137297.1	chr17	24804313	24804325	+	1	NA	promoter-TSS (NM_029197)	promoter-TSS (NM_029197)	-63	NM_029197	75178	Mm.52592	NM_029197	ENSMUSG00000024155	Meiob	4930528F23Rik|MLZ-675	meiosis specific with OB domains	protein-coding
mm_158516.1	chrX	143393894	143393922	-	1	NA	5' UTR (NM_031258, exon 1 of 9)	5' UTR (NM_031258, exon 1 of 9)	354	NM_031258	83453	Mm.157697	NM_031258	ENSMUSG00000031283	Chrdl1	CHL|CHL1|Nrln1|VOPT	chordin-like 1	protein-coding
mm_135395.1	chr16	44531123	44531133	-	1	NA	intron (NM_172506, intron 1 of 18)	intron (NM_172506, intron 1 of 18)	27001	NR_037242	100526478		NR_037242	ENSMUSG00000093046	Mir3081	mir-3081|mmu-mir-3081	microRNA 3081	ncRNA
mm_102978.1	chr11	69672408	69672418	-	1	NA	promoter-TSS (NM_144958)	promoter-TSS (NM_144958)	10	NM_144958	13681	Mm.26680	NM_144958	ENSMUSG00000059796	Eif4a1	BM-010|Ddx2a|Eif4	eukaryotic translation initiation factor 4A1	protein-coding
mm_165838.1	chr3	158016369	158016383	-	1	NA	exon (NM_001093753, exon 8 of 12)	exon (NM_001093753, exon 8 of 12)	15378	NM_001093753	69207	Mm.223946	NM_026989	ENSMUSG00000055436	Srsf11	0610009J05Rik|2610019N13Rik|BF642805|Sfrs11	serine/arginine-rich splicing factor 11	protein-coding
mm_38074.1	chr4	134127724	134127791	-	1	NA	TTS (NM_026257)	TTS (NM_026257)	996	NM_080559	73723	Mm.22240	NM_080559	ENSMUSG00000028843	Sh3bgrl3	1110004L05Rik|AU022188	SH3 domain binding glutamic acid-rich protein-like 3	protein-coding
mm_34878.1	chr4	155577132	155577164	+	1	NA	exon (NM_001159637, exon 2 of 12)	exon (NM_001159637, exon 2 of 12)	13333	NM_001159637	192185	Mm.28347	NM_138671	ENSMUSG00000029063	Nadk	4432404C02Rik|BC004012	NAD kinase	protein-coding
mm_404.1	chr1	34186870	34186881	+	1	NA	exon (NM_134448, exon 35 of 98)	exon (NM_134448, exon 35 of 98)	26545	NM_010081	13518	Mm.336625	NM_010081	ENSMUSG00000026131	Dst	2310001O04Rik|A830042E19Rik|AW554249|BP230|BPAG1-n|Bpag|Bpag1|Macf2|ah|athetoid|dt|mKIAA0728|nmf203|nmf339	dystonin	protein-coding
mm_78806.1	chr9	44066994	44067024	+	1	NA	promoter-TSS (NM_198092)	promoter-TSS (NM_198092)	-12	NM_198092	53376	Mm.272770	NM_016808	ENSMUSG00000032010	Usp2	B930035K21Rik|Ubp41	ubiquitin specific peptidase 2	protein-coding
mm_49392.1	chr6	25663715	25663715	+	1	NA	Intergenic	Intergenic	26265	NM_010338	14763	Mm.409670	NM_010338	ENSMUSG00000039904	Gpr37	AI848630|Pael-R	G protein-coupled receptor 37	protein-coding
mm_40482.1	chr5	54377543	54377550	+	1	NA	Intergenic	Lx9|LINE|L1	27554	NR_038045	330086	Mm.254449	NM_177871	ENSMUSG00000105912	Gm10440	D130065D13|ENSMUSG00000072936	predicted gene 10440	ncRNA
mm_140608.1	chr17	10721538	10721550	-	1	NA	intron (NM_027032, intron 2 of 4)	intron (NM_027032, intron 2 of 4)	118647	NM_027032	69310	Mm.18889	NM_027032	ENSMUSG00000037196	Pacrg	1700008H23Rik	PARK2 co-regulated	protein-coding
mm_144019.1	chr17	89200704	89200719	-	1	NA	promoter-TSS (NM_013523)	promoter-TSS (NM_013523)	-36	NM_013523	14309	Mm.57155	NM_013523	ENSMUSG00000032937	Fshr	-	follicle stimulating hormone receptor	protein-coding
mm_48014.1	chr5	136166096	136166101	-	1	NA	intron (NM_178751, intron 1 of 2)	intron (NM_178751, intron 1 of 2)	4558	NM_178751	269717	Mm.308396	NM_178751	ENSMUSG00000039747	Orai2	A730041O15Rik|Tmem142b	ORAI calcium release-activated calcium modulator 2	protein-coding
mm_84551.1	chr9	67573294	67573311	-	1	NA	Intergenic	Intergenic	-13599	NM_001081242	70549	Mm.33645	NM_027458	ENSMUSG00000052698	Tln2	5730421P04Rik|AI507121|AI787438|AL118320|mKIAA0320	talin 2	protein-coding
mm_41911.1	chr5	105591303	105591334	+	1	NA	intron (NM_133897, intron 3 of 3)	B4|SINE|B4	71847	NM_133897	100604	Mm.319847	NM_133897	ENSMUSG00000054720	Lrrc8c	AD158|AI326115|E430036I04Rik|fad158	leucine rich repeat containing 8 family, member C	protein-coding
mm_172322.1	chr7	106529213	106529213	-	1	NA	Intergenic	Intergenic	-88140	NR_003967	209380	Mm.461779	NM_001001318		Gm4759	EG209380	GTPase, very large interferon inducible 1 pseudogene	pseudo
mm_72904.1	chr8	90896292	90896297	+	1	NA	intron (NM_177224, intron 2 of 39)	intron (NM_177224, intron 2 of 39)	-35955	NM_001310530	109151	Mm.100615	NM_177224	ENSMUSG00000056608	Chd9	1810014J18Rik|9030205D12Rik|A330063D19Rik|AD013|PRIC320|mKIAA0308	chromodomain helicase DNA binding protein 9	protein-coding
mm_38452.1	chr4	140246795	140246824	-	1	NA	promoter-TSS (NM_198610)	promoter-TSS (NM_198610)	2	NM_198610	230868	Mm.298731	NM_198610	ENSMUSG00000040972	Igsf21	BC055811|Gm141	immunoglobulin superfamily, member 21	protein-coding
mm_55772.1	chr6	78467879	78467925	-	1	NA	exon (NM_011260, exon 3 of 6)	exon (NM_011260, exon 3 of 6)	972	NM_011260	19695	Mm.252385	NM_011260	ENSMUSG00000030017	Reg3g	AI449515|REG-3-gamma|reg III-gamma	regenerating islet-derived 3 gamma	protein-coding
mm_91721.1	chr10	44460961	44460967	-	1	NA	Intergenic	(A)n|Simple_repeat|Simple_repeat	-2216	NM_007548	12142	Mm.4800	NM_007548	ENSMUSG00000038151	Prdm1	Blimp-1|Blimp1|PRDI-BF1|ZNFPR1A1|b2b1765Clo	PR domain containing 1, with ZNF domain	protein-coding
mm_65870.1	chr7	29505755	29505765	-	1	NA	promoter-TSS (NM_001081028)	promoter-TSS (NM_001081028)	-300	NM_001081028	74206	Mm.447042	NM_001081028	ENSMUSG00000030583	Sipa1l3	2610511M17Rik	signal-induced proliferation-associated 1 like 3	protein-coding
mm_92329.1	chr10	75781393	75781410	-	1	NA	promoter-TSS (NM_133994)	promoter-TSS (NM_133994)	13	NM_133994	103140	Mm.5731	NM_133994	ENSMUSG00000001665	Gstt3	AI118089	glutathione S-transferase, theta 3	protein-coding
mm_99426.1	chr11	102393583	102393589	+	1	NA	5' UTR (NM_001252347, exon 1 of 11)	5' UTR (NM_001252347, exon 1 of 11)	183	NM_001252347	51799	Mm.2560	NM_016759	ENSMUSG00000006575	Rundc3a	RPIP-8|Rap2ip|Rpip8	RUN domain containing 3A	protein-coding
mm_12234.1	chr2	68582410	68582416	+	1	NA	promoter-TSS (NM_177651)	promoter-TSS (NM_177651)	0	NM_177651	227998	Mm.67562	NM_177651	ENSMUSG00000053896	4933409G03Rik	-	RIKEN cDNA 4933409G03 gene	protein-coding
mm_167584.1	chr9	46049816	46049829	+	1	NA	intron (NM_027498, intron 1 of 24)	MIR|SINE|MIR	37002	NM_027498	70661	Mm.219459	NM_027498	ENSMUSG00000034135	Sik3	5730525O22Rik|9030204A07Rik|AI447252|AI846254|AI849445|Qsk|SIK-3|mKIAA0999	SIK family kinase 3	protein-coding
mm_73442.1	chr8	106210145	106210151	+	1	NA	promoter-TSS (NM_145404)	promoter-TSS (NM_145404)	785	NM_001007567	66432	Mm.269029	NM_001007567	ENSMUSG00000033106	Slc7a6os	2010007L18Rik|2400002F02Rik	solute carrier family 7, member 6 opposite strand	protein-coding
mm_64695.1	chr7	4526449	4526516	-	1	NA	exon (NM_001033548, exon 9 of 12)	exon (NM_001033548, exon 9 of 12)	-4039	NM_009406	21954	Mm.27674	NM_009406	ENSMUSG00000035458	Tnni3	Tn1|cTnI	troponin I, cardiac 3	protein-coding
mm_69346.1	chr7	130201183	130201191	-	1	NA	intron (NM_001347638, intron 4 of 15)	intron (NM_001347638, intron 4 of 15)	65621	NM_010207	14183	Mm.16340	NM_010207	ENSMUSG00000030849	Fgfr2	AU043015|AW556123|Bek|Fgfr-2|Fgfr-7|Fgfr7|KGFR|KGFRTr|svs	fibroblast growth factor receptor 2	protein-coding
mm_57395.1	chr6	124857708	124857755	-	1	NA	promoter-TSS (NM_013534)	promoter-TSS (NM_013534)	-44	NM_013534	14789	Mm.9002	NM_013534	ENSMUSG00000023191	P3h3	BC016431|Grcb|Leprel2	prolyl 3-hydroxylase 3	protein-coding
mm_26975.1	chr3	25144183	25144248	-	1	NA	Intergenic	CpG	-360209	NM_001326288	635702	Mm.448351	NM_001326288	ENSMUSG00000102758	Naaladl2	2810043G22Rik|EG635702|Gm1021	N-acetylated alpha-linked acidic dipeptidase-like 2	protein-coding
mm_131381.1	chr16	14159633	14159643	+	1	NA	promoter-TSS (NR_030252)	promoter-TSS (NR_030252)	12	NR_030252	723916		NR_030252	ENSMUSG00000070074	Mir484	Mirn484|mir-484|mmu-mir-484	microRNA 484	ncRNA
mm_68238.1	chr7	105396180	105396185	-	1	NA	intron (NM_001242363, intron 1 of 12)	intron (NM_001242363, intron 1 of 12)	3872	NM_001242364	74349	Mm.30254	NM_199009	ENSMUSG00000044465	Fam160a2	4632419K20Rik|6530415H11Rik|FHIP	family with sequence similarity 160, member A2	protein-coding
mm_96233.1	chr11	62551263	62551285	+	1	NA	promoter-TSS (NR_002875).2	promoter-TSS (NR_002875).2	103	NM_011664	22187	Mm.371592	NM_011664	ENSMUSG00000019505	Ubb	AL033289|Rps27a|Uba52|Ubb2|Ubc	ubiquitin B	protein-coding
mm_43818.1	chr5	142929774	142929778	+	1	NA	Intergenic	B1_Mus2|SINE|Alu	-23022	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_53911.1	chr6	3988835	3988881	-	1	NA	promoter-TSS (NR_138566)	promoter-TSS (NR_138566)	0	NR_138566	21789	Mm.25612	NM_009364	ENSMUSG00000029664	Tfpi2	AV000670|PP5/TFPI-2	tissue factor pathway inhibitor 2	protein-coding
mm_77935.1	chr9	7354825	7354832	+	1	NA	exon (NM_008605, exon 7 of 10)	exon (NM_008605, exon 7 of 10)	7454	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_173151.1	chrX	32209423	32209423	+	1	NA	Intergenic	RLTR1B|LTR|ERV1	-68971	NM_001168334	100040482	Mm.479861	NM_001168334	ENSMUSG00000096194	Btbd35f2	Gm2799	BTB domain containing 35, family member 2	protein-coding
mm_40102.1	chr5	34650688	34650723	+	1	NA	intron (NM_029278, intron 7 of 17)	intron (NM_029278, intron 7 of 17)	9443	NM_029278	75416	Mm.40292	NM_029278	ENSMUSG00000036693	Nop14	2610033H07Rik|Nol14	NOP14 nucleolar protein	protein-coding
mm_45712.1	chr5	84321735	84321742	-	1	NA	intron (NM_007937, intron 3 of 15)	B3|SINE|B2	95644	NM_007937	13839	Mm.137991	NM_007937	ENSMUSG00000029245	Epha5	AI854630|AW125296|Cek7|Ehk1|Els1|Hek7|Rek7|bsk	Eph receptor A5	protein-coding
mm_155728.1	chrX	96160142	96160182	+	1	NA	exon (NM_010833, exon 8 of 13)	exon (NM_010833, exon 8 of 13)	64117	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_99379.1	chr11	102041502	102041506	+	1	NA	promoter-TSS (NM_001160713)	promoter-TSS (NM_001160713)	-7	NM_001160711	52685	Mm.266885	NM_027987	ENSMUSG00000017309	Cd300lg	2310016B05Rik|Clm9|D11Ertd736e	CD300 molecule like family member G	protein-coding
mm_43896.1	chr5	144190268	144190270	+	1	NA	promoter-TSS (NM_010800)	promoter-TSS (NM_010800)	-17	NM_010800	17341	Mm.386767	NM_010800	ENSMUSG00000052271	Bhlha15	1810009C13Rik|Bhlhb8|MIST-1|Mist1	basic helix-loop-helix family, member a15	protein-coding
mm_105557.1	chr11	106487798	106487821	-	1	NA	promoter-TSS (NM_023913)	promoter-TSS (NM_023913)	-13	NM_023913	78943	Mm.340943	NM_023913	ENSMUSG00000020715	Ern1	9030414B18Rik|AI225830|C85377|Ire1a|Ire1alpha|Ire1p	endoplasmic reticulum (ER) to nucleus signalling 1	protein-coding
mm_140845.1	chr17	23676563	23676583	-	1	NA	exon (NM_013749, exon 2 of 4)	exon (NM_013749, exon 2 of 4)	876	NM_001161746	27279	Mm.28518	NM_013749	ENSMUSG00000023905	Tnfrsf12a	AI255180|C87282|Fn14|HPIP|TWEAK-R|TweakR	tumor necrosis factor receptor superfamily, member 12a	protein-coding
mm_72993.1	chr8	93017067	93017104	+	1	NA	Intergenic	Lx9|LINE|L1	31107	NM_001013764	244595	Mm.390089	NM_001013764	ENSMUSG00000071047	Ces1a	Ces1l|EG244595|Gm4976	carboxylesterase 1A	protein-coding
mm_162227.1	chrX	148180838	148180838	+	1	NA	intron (NM_001081648, intron 1 of 6)	intron (NM_001081648, intron 1 of 6)	114	NM_001081648	434864	Mm.484933	NM_001081648	ENSMUSG00000072930	Gm15107	OTTMUSG00000019001|Ott-like	predicted gene 15107	protein-coding
mm_64349.1	chr7	142382625	142382670	+	1	NA	exon (NM_009983, exon 4 of 9)	exon (NM_009983, exon 4 of 9)	5223	NM_009983	13033	Mm.231395	NM_009983	ENSMUSG00000007891	Ctsd	CD|CatD	cathepsin D	protein-coding
mm_128596.1	chr15	58135048	58135095	-	1	NA	promoter-TSS (NM_027435)	promoter-TSS (NM_027435)	11	NM_027435	70472	Mm.221758	NM_027435	ENSMUSG00000022360	Atad2	2610509G12Rik	ATPase family, AAA domain containing 2	protein-coding
mm_42912.1	chr5	122650377	122650393	+	1	NA	promoter-TSS (NM_001284402)	promoter-TSS (NM_001284402)	-39	NM_001284402	18439	Mm.42026	NM_011027	ENSMUSG00000029468	P2rx7	AI467586|P2X(7)|P2X7R	purinergic receptor P2X, ligand-gated ion channel, 7	protein-coding
mm_60639.1	chr7	44836287	44836294	+	1	NA	promoter-TSS (NM_010215)	promoter-TSS (NM_010215)	2	NM_010215	14204	Mm.2565	NM_010215	ENSMUSG00000074141	Il4i1	Fig1|Fig1-ps|LAAO|LAO	interleukin 4 induced 1	protein-coding
mm_172080.1	chr6	145932917	145932924	-	1	NA	intron (NM_001310837, intron 1 of 2)	LSU-rRNA_Hsa|rRNA|rRNA	1047	NM_001310837	16651	Mm.49689	NM_010656	ENSMUSG00000030255	Sspn	Krag	sarcospan	protein-coding
mm_2873.1	chr1	131797384	131797418	+	1	NA	promoter-TSS (NM_178079)	promoter-TSS (NM_178079)	6	NM_178079	212933	Mm.23844	NM_178079	ENSMUSG00000042251	Pm20d1	4732466D17Rik|AI098026	peptidase M20 domain containing 1	protein-coding
mm_32135.1	chr4	99194272	99194282	+	1	NA	5' UTR (NM_001145967, exon 1 of 11)	5' UTR (NM_001145967, exon 1 of 11)	130	NM_001145967	242557	Mm.241663	NM_175029	ENSMUSG00000028550	Atg4c	Apg4-C|Apg4c|Atg4cl|Autl1	autophagy related 4C, cysteine peptidase	protein-coding
mm_58459.1	chr7	3338815	3338842	+	1	NA	intron (NM_133189, intron 2 of 4)	intron (NM_133189, intron 2 of 4)	2243	NM_133189	81904	Mm.214994	NM_133189	ENSMUSG00000069806	Cacng7	-	calcium channel, voltage-dependent, gamma subunit 7	protein-coding
mm_109844.1	chr12	4593687	4593695	-	1	NA	intron (NM_011365, intron 1 of 38)	intron (NM_011365, intron 1 of 38)	683	NM_001198968	20403	Mm.341204	NM_011365	ENSMUSG00000020640	Itsn2	AI327390|Ese2|Sh3d1B|Sh3p18|mKIAA1256	intersectin 2	protein-coding
mm_6807.1	chr1	84157189	84157222	-	1	NA	intron (NM_001003948, intron 2 of 2)	intron (NM_001003948, intron 2 of 2)	61756	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_170646.1	chr19	9753776	9753781	+	1	NA	Intergenic	L1Md_T|LINE|L1	145755	NM_016692	16319	Mm.29755	NM_016692	ENSMUSG00000024660	Incenp	2700067E22Rik|AU019509|C130081E20|C77457	inner centromere protein	protein-coding
mm_66797.1	chr7	47132699	47132712	-	1	NA	promoter-TSS (NM_001163565)	promoter-TSS (NM_001163565)	-107	NM_001163565	19259	Mm.4654	NM_013643	ENSMUSG00000030854	Ptpn5	Step	protein tyrosine phosphatase, non-receptor type 5	protein-coding
mm_131028.1	chr16	3730017	3730030	+	1	NA	Intergenic	Intergenic	-11899	NM_001161791	54483	Mm.143718	NM_019453	ENSMUSG00000022534	Mefv	FMF|TRIM20|pyrin	Mediterranean fever	protein-coding
mm_22822.1	chr3	27227291	27227302	+	1	NA	intron (NM_178772, intron 3 of 4)	L2a|LINE|L2	44292	NM_178772	320024	Mm.24576	NM_178772	ENSMUSG00000027698	Nceh1	Aadacl1|B230106I24Rik|CPO-BP|Nceh	neutral cholesterol ester hydrolase 1	protein-coding
mm_146054.1	chr18	69638068	69638078	+	1	NA	intron (NM_013685, intron 10 of 19)	B4A|SINE|B4	-287486	NM_201362	381175	Mm.266831	NM_201362	ENSMUSG00000038903	Ccdc68	BC046343	coiled-coil domain containing 68	protein-coding
mm_9428.1	chr1	172496127	172496135	-	1	NA	intron (NM_033608, intron 16 of 20)	intron (NM_033608, intron 16 of 20)	-4115	NM_178598	21346	Mm.271711	NM_178598	ENSMUSG00000026547	Tagln2	2700094C18Rik|SM22beta|Sm22B|Sm22a	transgelin 2	protein-coding
mm_134831.1	chr16	26105635	26105654	-	1	NA	exon (NM_173379, exon 1 of 15)	exon (NM_173379, exon 1 of 15)	140	NM_173379	210530	Mm.326869	NM_173379	ENSMUSG00000038168	P3h2	4832416N06|AW553532|Leprel1|Mlat4	prolyl 3-hydroxylase 2	protein-coding
mm_102264.1	chr11	55336598	55336631	-	1	NA	Intergenic	Intergenic	-24357	NM_001029988	245827	Mm.339363	NM_001029988	ENSMUSG00000055333	Fat2	EMI2|Fath2|Gm523|mKIAA0811	FAT atypical cadherin 2	protein-coding
mm_109733.1	chr12	117127210	117127210	+	1	NA	intron (NM_011215, intron 12 of 22)	intron (NM_011215, intron 12 of 22)	24059	NR_033538	100038689	Mm.445351	NR_033538	ENSMUSG00000099907	Gm10421	ENSMUSG00000072792	predicted gene 10421	ncRNA
mm_137000.1	chr17	17448895	17448924	+	1	NA	intron (NM_025681, intron 4 of 5)	intron (NM_025681, intron 4 of 5)	46223	NM_025681	66643	Mm.268018	NM_025681	ENSMUSG00000047786	Lix1	5730466L18Rik	limb and CNS expressed 1	protein-coding
mm_152101.1	chr19	6921754	6921803	-	1	NA	promoter-TSS (NM_007953)	promoter-TSS (NM_007953)	30	NM_007953	26379	Mm.386776	NM_007953	ENSMUSG00000024955	Esrra	ERRalpha|Err1|Estrra|Nr3b1	estrogen related receptor, alpha	protein-coding
mm_133126.1	chr16	65815993	65816005	+	1	NA	intron (NM_028572, intron 1 of 3)	intron (NM_028572, intron 1 of 3)	366	NM_028572	73569	Mm.25670	NM_028572	ENSMUSG00000091243	Vgll3	1700110N18Rik|4832416J22|C80713|Vgl-3|Vito-2	vestigial like family member 3	protein-coding
mm_156483.1	chrX	144318066	144318080	+	1	NA	exon (NM_026247, exon 1 of 4)	exon (NM_026247, exon 1 of 4)	107	NM_026247	67574	Mm.249084	NM_026247	ENSMUSG00000041718	Alg13	2810046O15Rik|4833435D08Rik|Glt28d1|MDS031|OTTMUSG00000018917	asparagine-linked glycosylation 13	protein-coding
mm_83682.1	chr9	50479530	50479538	-	1	NA	Intergenic	Intergenic	-14991	NM_029639	76509	Mm.29959	NM_029639	ENSMUSG00000032068	Plet1	0610037B23Rik|1600029D21Rik|AA407923|AU043048	placenta expressed transcript 1	protein-coding
mm_123713.1	chr14	69824849	69824859	-	1	NA	Intergenic	B1F|SINE|Alu	-15553	NM_028560	73523	Mm.23509	NM_028526	ENSMUSG00000022085	Pebp4	PEBP-4	phosphatidylethanolamine binding protein 4	protein-coding
mm_32683.1	chr4	115828062	115828103	+	1	NA	promoter-TSS (NM_175308)	promoter-TSS (NM_175308)	-10	NM_175308	100465	Mm.35571	NM_175308	ENSMUSG00000028709	Mob3c	AW822253|D130076I06Rik|Mobkl2c	MOB kinase activator 3C	protein-coding
mm_110571.1	chr12	56345793	56345842	-	1	NA	promoter-TSS (NM_145442)	promoter-TSS (NM_145442)	77	NM_145442	217588	Mm.25656	NM_145442	ENSMUSG00000021028	Mbip	4933408E06Rik	MAP3K12 binding inhibitory protein 1	protein-coding
mm_150569.1	chr19	40111277	40111312	+	1	NA	exon (NM_001167875, exon 7 of 8)	exon (NM_001167875, exon 7 of 8)	21615	NM_001167875	107141	Mm.474575	NM_134144	ENSMUSG00000054827	Cyp2c50	AI266900	cytochrome P450, family 2, subfamily c, polypeptide 50	protein-coding
mm_144960.1	chr18	37819504	37819518	+	1	NA	promoter-TSS (NM_033583)	promoter-TSS (NM_033583)	-35	NM_033583	93708	Mm.247203	NM_033583	ENSMUSG00000102543	Pcdhgc5	-	protocadherin gamma subfamily C, 5	protein-coding
mm_55964.1	chr6	85513292	85513292	-	1	NA	exon (NM_020596, exon 1 of 2)	exon (NM_020596, exon 1 of 2)	250	NM_020596	13656	Mm.44137	NM_020596	ENSMUSG00000071341	Egr4	NGF1-C|NGFI-C|NGFIC|pAT133	early growth response 4	protein-coding
mm_164323.1	chr16	5049368	5049375	+	1	NA	promoter-TSS (NM_026666)	promoter-TSS (NM_026666)	539	NM_001079814	74022	Mm.21652	NM_028720	ENSMUSG00000022536	Glyr1	2810419J22Rik|3930401K13Rik|AW545332|Npac	glyoxylate reductase 1 homolog (Arabidopsis)	protein-coding
mm_4674.1	chr1	180419485	180419497	+	1	NA	intron (NM_001081175, intron 5 of 7)	intron (NM_001081175, intron 5 of 7)	64013	NM_001081227	381310	Mm.44791	NM_001081227	ENSMUSG00000053963	Stum	6330403A02Rik|ENSMUSG00000056615|Gm10001|R75555	mechanosensory transduction mediator	protein-coding
mm_129594.1	chr15	79804712	79804716	-	1	NA	promoter-TSS (NM_030689)	promoter-TSS (NM_030689)	-5	NM_030689	73340	Mm.38438	NM_030689	ENSMUSG00000022421	Nptxr	1200009K17Rik|1700036C17Rik|5730406O18Rik|AI452369|AI785356|D15Bwg0580e|NPR|Npcd	neuronal pentraxin receptor	protein-coding
mm_113887.1	chr13	49188246	49188261	+	1	NA	intron (NM_013610, intron 1 of 3)	intron (NM_013610, intron 1 of 3)	706	NM_013610	18081	Mm.18503	NM_013610	ENSMUSG00000037966	Ninj1	AU024536	ninjurin 1	protein-coding
mm_133122.1	chr16	65815405	65815409	+	1	NA	promoter-TSS (NM_028572)	promoter-TSS (NM_028572)	-226	NM_028572	73569	Mm.25670	NM_028572	ENSMUSG00000091243	Vgll3	1700110N18Rik|4832416J22|C80713|Vgl-3|Vito-2	vestigial like family member 3	protein-coding
mm_109923.1	chr12	8637027	8637039	-	1	NA	Intergenic	Intergenic	-37101	NM_001160221	80913	Mm.341243	NM_030723	ENSMUSG00000020594	Pum2	5730503J23Rik|Pumm2	pumilio RNA-binding family member 2	protein-coding
mm_171392.1	chr4	12232780	12232790	+	1	NA	Intergenic	Intergenic	-60770	NM_026558	68099	Mm.25340	NM_026558	ENSMUSG00000028218	Fam92a	6720467C03Rik|Fam92a1	family with sequence similarity 92, member A	protein-coding
mm_66603.1	chr7	45459689	45459731	-	1	NA	5' UTR (NM_010240, exon 1 of 4)	5' UTR (NM_010240, exon 1 of 4)	176	NM_010240	14325	Mm.30357	NM_010240	ENSMUSG00000050708	Ftl1	Ftl|Ftl-1|L-ferritin	ferritin light polypeptide 1	protein-coding
mm_105256.1	chr11	102356167	102356192	-	1	NA	exon (NM_011403, exon 13 of 20)	exon (NM_011403, exon 13 of 20)	9102	NM_011403	20533	Mm.7248	NM_011403	ENSMUSG00000006574	Slc4a1	Ae1|CD233|Empb3|l11Jus51	solute carrier family 4 (anion exchanger), member 1	protein-coding
mm_22024.1	chr2	168010703	168010713	-	1	NA	promoter-TSS (NM_001080708)	promoter-TSS (NM_001080708)	-115	NM_001080708	69553	Mm.68454	NM_001080708	ENSMUSG00000074577	Fam65c	2310033K02Rik|Gm124	family with sequence similarity 65, member C	protein-coding
mm_105880.1	chr11	114929096	114929126	-	1	NA	intron (NM_199221, intron 1 of 3)	MER63A|DNA|hAT-Blackjack	5275	NM_001347651	217304	Mm.185355	NM_199221	ENSMUSG00000063193	Cd300lb	CLM-7|Clm7|Gm253|LMIR5	CD300 molecule like family member B	protein-coding
mm_71612.1	chr8	56551167	56551177	+	1	NA	promoter-TSS (NM_015791)	promoter-TSS (NM_015791)	38	NM_015791	50753	Mm.251174	NM_015791	ENSMUSG00000038206	Fbxo8	Fbx8	F-box protein 8	protein-coding
mm_55864.1	chr6	83456790	83456806	-	1	NA	promoter-TSS (NM_001347313)	promoter-TSS (NM_001347313)	-406	NM_001347313	194388	Mm.211030	NM_183138	ENSMUSG00000034832	Tet3	B430006D22Rik|BC037432|D230004J03Rik	tet methylcytosine dioxygenase 3	protein-coding
mm_165144.1	chr2	18698982	18698985	+	1	NA	promoter-TSS (NM_001001334)	promoter-TSS (NM_001001334)	-39	NM_001001334	381350	Mm.330024	NM_001001334	ENSMUSG00000037708	Spag6	Spag6l	sperm associated antigen 6	protein-coding
mm_72741.1	chr8	85086809	85086844	+	1	NA	exon (NM_010764, exon 5 of 24)	exon (NM_010764, exon 5 of 24)	3557	NM_010764	17159	Mm.4219	NM_010764	ENSMUSG00000005142	Man2b1	AW107687|LAMAN	mannosidase 2, alpha B1	protein-coding
mm_102537.1	chr11	61206194	61206203	-	1	NA	Intergenic	Intergenic	-2544	NM_007436	11670	Mm.4257	NM_007436	ENSMUSG00000019102	Aldh3a1	Ahd-4|Ahd4|Aldh|Aldh3	aldehyde dehydrogenase family 3, subfamily A1	protein-coding
mm_9147.1	chr1	170913666	170913668	-	1	NA	promoter-TSS (NM_001029984)	promoter-TSS (NM_001029984)	-726	NM_001029984	435653	Mm.337931	NM_001029984	ENSMUSG00000070524	Fcrlb	FREB-2|FREB2|FcRL2|Fcrlm2|Fcry|mFCRL2	Fc receptor-like B	protein-coding
mm_10782.1	chr2	24336905	24336925	+	1	NA	promoter-TSS (NM_031167)	promoter-TSS (NM_031167)	55	NM_031167	16181	Mm.882	NM_031167	ENSMUSG00000026981	Il1rn	F630041P17Rik|IL-1ra	interleukin 1 receptor antagonist	protein-coding
mm_107017.1	chr12	12547913	12547944	+	1	NA	Intergenic	Intergenic	121989	NR_136889	102637952	Mm.421393	NR_136889		Gm34637	-	predicted gene, 34637	ncRNA
mm_23329.1	chr3	54156040	54156074	+	1	NA	promoter-TSS (NM_016984)	promoter-TSS (NM_016984)	0	NM_001253683	22066	Mm.10100	NM_016984	ENSMUSG00000027748	Trpc4	CCE1|STRPC4|Trp4|Trrp4	transient receptor potential cation channel, subfamily C, member 4	protein-coding
mm_45158.1	chr5	49524791	49524805	-	1	NA	Intergenic	CpG	-239139	NM_001199244	80334	Mm.160172	NM_030265	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding
mm_121378.1	chr14	118787947	118787951	+	1	NA	promoter-TSS (NM_001160098)	promoter-TSS (NM_001160098)	78	NM_001160097	58187	Mm.390755	NM_021386	ENSMUSG00000022132	Cldn10	6720456I16Rik|Cldn10a|Cldn10b|D14Ertd728e	claudin 10	protein-coding
mm_77802.1	chr9	3032436	3032456	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	6297	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_123496.1	chr14	66179522	66179525	-	1	NA	intron (NM_001162366, intron 4 of 29)	intron (NM_001162366, intron 4 of 29)	34029	NM_001162366	19229	Mm.21613	NM_172498	ENSMUSG00000059456	Ptk2b	CADTK|CAKB|CAKbeta|E430023O05Rik|FADK2|FAK2|PYK2|Raftk	PTK2 protein tyrosine kinase 2 beta	protein-coding
mm_149696.1	chr19	21275051	21275079	+	1	NA	intron (NM_009551, intron 1 of 5)	intron (NM_009551, intron 1 of 5)	2787	NM_009551	22682	Mm.292405	NM_009551	ENSMUSG00000024750	Zfand5	2310057A04Rik|5830475F03Rik|AA415485|Za20d2|Zfp216	zinc finger, AN1-type domain 5	protein-coding
mm_107100.1	chr12	17728199	17728212	+	1	NA	intron (NM_016677, intron 1 of 3)	intron (NM_016677, intron 1 of 3)	37391	NM_016677	53602	Mm.313619	NM_016677	ENSMUSG00000071379	Hpcal1	NVP-3|Nvp3|VILIP3|Vnsl3|Vsnl3	hippocalcin-like 1	protein-coding
mm_156314.1	chrX	136993223	136993244	+	1	NA	promoter-TSS (NM_025893)	promoter-TSS (NM_025893)	78	NM_001035509	66995	Mm.440155	NM_025893	ENSMUSG00000031428	Zcchc18	1500031H04Rik|Sizn2	zinc finger, CCHC domain containing 18	protein-coding
mm_125396.1	chr15	41447360	41447369	+	1	NA	promoter-TSS (NM_001130166)	promoter-TSS (NM_001130166)	-118	NM_001130166	170719	Mm.254267	NM_130885	ENSMUSG00000022307	Oxr1	2210416C20Rik|C7|C7B	oxidation resistance 1	protein-coding
mm_140315.1	chr17	86232743	86232753	+	1	NA	intron (NM_011104, intron 1 of 14)	intron (NM_011104, intron 1 of 14)	54430	NR_045435	72104	Mm.443401	NR_045435	ENSMUSG00000100738	2010106C02Rik	-	RIKEN cDNA 2010106C02 gene	ncRNA
mm_81600.1	chr9	110532643	110532692	+	1	NA	promoter-TSS (NM_001081340)	promoter-TSS (NM_001081340)	70	NM_001081340	235626	Mm.288949	NM_001081340	ENSMUSG00000044791	Setd2	4921524K10Rik|BC031601|KMT3A	SET domain containing 2	protein-coding
mm_79878.1	chr9	65208548	65208557	+	1	NA	Intergenic	RMER17A2|LTR|ERVK	-6138	NM_177460	214424	Mm.31129	NM_177460	ENSMUSG00000032392	Parp16	ARTD15|BC055447|C79952|PARP-16	poly (ADP-ribose) polymerase family, member 16	protein-coding
mm_153021.1	chr19	31126098	31126106	-	1	NA	intron (NM_011160, intron 3 of 17)	intron (NM_011160, intron 3 of 17)	43261	NM_031249	83410	Mm.22031	NM_031249	ENSMUSG00000053536	Cstf2t	64kDa|C77975|tCstF-64|tauCstF-64	cleavage stimulation factor, 3' pre-RNA subunit 2, tau	protein-coding
mm_98781.1	chr11	96829598	96829643	+	1	NA	promoter-TSS (NM_001130450)	promoter-TSS (NM_001130450)	-118	NM_001130450	18023	Mm.6743	NM_008686	ENSMUSG00000038615	Nfe2l1	AA408798|AW212678|LCR-F1|Lcrf1|NRF1|TCF-11|TCF11	nuclear factor, erythroid derived 2,-like 1	protein-coding
mm_139093.1	chr17	46890626	46890652	+	1	NA	promoter-TSS (NM_178385)	promoter-TSS (NM_178385)	18	NM_178385	72726	Mm.33780	NM_178385	ENSMUSG00000036430	Tbcc	2810055C19Rik	tubulin-specific chaperone C	protein-coding
mm_79777.1	chr9	62851048	62851054	+	1	NA	3' UTR (NM_001033175, exon 7 of 7)	3' UTR (NM_001033175, exon 7 of 7)	-7053	NM_001102468	75600	Mm.440576	NM_138304	ENSMUSG00000032246	Calml4	2010002G05Rik	calmodulin-like 4	protein-coding
mm_73646.1	chr8	110919827	110919856	+	1	NA	promoter-TSS (NM_009179)	promoter-TSS (NM_009179)	-24	NM_009179	20444	Mm.200388	NM_009179	ENSMUSG00000031749	St3gal2	AI429591|AW822065|ST3GalII|Siat5	ST3 beta-galactoside alpha-2,3-sialyltransferase 2	protein-coding
mm_172328.1	chr7	10799070	10799082	-	1	NA	promoter-TSS (NR_033707)	promoter-TSS (NR_033707)	-11	NR_033707	434555	Mm.379679	NR_033707	ENSMUSG00000110097	Zscan4a	BQ559217	zinc finger and SCAN domain containing 4A	pseudo
mm_93263.1	chr10	95564174	95564181	-	1	NA	promoter-TSS (NM_027722)	promoter-TSS (NM_027722)	-10	NM_027722	71207	Mm.24397	NM_027722	ENSMUSG00000020029	Nudt4	4933436C10Rik|DIPP2|DIPP2alpha|DIPP2beta|HDCMB47P	nudix (nucleoside diphosphate linked moiety X)-type motif 4	protein-coding
mm_135806.1	chr16	57350549	57350578	-	1	NA	intron (NM_025599, intron 1 of 9)	intron (NM_025599, intron 1 of 9)	-2714	NM_001040397	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding
mm_35808.1	chr4	46650103	46650125	-	1	NA	promoter-TSS (NM_198664)	promoter-TSS (NM_198664)	85	NM_198664	381605	Mm.331595	NM_198664	ENSMUSG00000039813	Tbc1d2	A630005A06Rik|BC022630|Gm1037|PARIS-1|PARIS1	TBC1 domain family, member 2	protein-coding
mm_141030.1	chr17	25256275	25256293	-	1	NA	promoter-TSS (NM_001163270)	promoter-TSS (NM_001163270)	80	NM_001163270	545192	Mm.328859	NM_001163270	ENSMUSG00000047507	Baiap3	Bap3|Gm937	BAI1-associated protein 3	protein-coding
mm_5906.1	chr1	54926409	54926415	-	1	NA	promoter-TSS (NM_001081433)	promoter-TSS (NM_001081433)	-25	NM_001081433	329154	Mm.397910	NM_001081433	ENSMUSG00000052331	Ankrd44	4930444A19Rik|A130096K20|E130014H08Rik|PP6-ARS-B	ankyrin repeat domain 44	protein-coding
mm_173183.1	chrX	58073533	58073535	+	1	NA	Intergenic	L1_Mur3|LINE|L1	42906	NM_009575	22773	Mm.255890	NM_009575	ENSMUSG00000067860	Zic3	Bn|Ka	zinc finger protein of the cerebellum 3	protein-coding
mm_73845.1	chr8	117548908	117548919	+	1	NA	intron (NM_172285, intron 2 of 32)	(TGGG)n|Simple_repeat|Simple_repeat	50638	NM_172285	234779	Mm.192699	NM_172285	ENSMUSG00000034330	Plcg2	PLC-gamma-2|PLCgamma2|Plcg-2	phospholipase C, gamma 2	protein-coding
mm_104903.1	chr11	99635077	99635086	-	1	NA	promoter-TSS (NM_026807)	promoter-TSS (NM_026807)	3	NM_026807	68673	Mm.351893	NM_026807	ENSMUSG00000044649	Krtap4-2	1110033F04Rik|AI604442	keratin associated protein 4-2	protein-coding
mm_62553.1	chr7	102442684	102442693	+	1	NA	intron (NM_009103, intron 1 of 18)	intron (NM_009103, intron 1 of 18)	993	NM_009103	20133	Mm.197486	NM_009103	ENSMUSG00000030978	Rrm1	RnrM1	ribonucleotide reductase M1	protein-coding
mm_113652.1	chr13	42307235	42307243	+	1	NA	3' UTR (NM_010104, exon 5 of 5)	3' UTR (NM_010104, exon 5 of 5)	5763	NM_010104	13614	Mm.14543	NM_010104	ENSMUSG00000021367	Edn1	ET-1|PPET1|preproET	endothelin 1	protein-coding
mm_69995.1	chr7	142385617	142385631	-	1	NA	intron (NM_009983, intron 1 of 8)	intron (NM_009983, intron 1 of 8)	2246	NM_009983	13033	Mm.231395	NM_009983	ENSMUSG00000007891	Ctsd	CD|CatD	cathepsin D	protein-coding
mm_164978.1	chr19	8839129	8839143	-	1	NA	promoter-TSS (NM_008144)	promoter-TSS (NM_008144)	110	NM_010316	14704	Mm.329700	NM_010316	ENSMUSG00000071658	Gng3	-	guanine nucleotide binding protein (G protein), gamma 3	protein-coding
mm_33183.1	chr4	126096751	126096767	+	1	NA	5' UTR (NM_138721, exon 1 of 2)	5' UTR (NM_138721, exon 1 of 2)	106	NM_138721	116748	Mm.41865	NM_138721	ENSMUSG00000050188	Lsm10	-	U7 snRNP-specific Sm-like protein LSM10	protein-coding
mm_39111.1	chr4	154928188	154928205	-	1	NA	promoter-TSS (NM_178931)	promoter-TSS (NM_178931)	-119	NM_178931	230979	Mm.215147	NM_178931	ENSMUSG00000042333	Tnfrsf14	Atar|HveA|Hvem|Tnfrs14	tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)	protein-coding
mm_62279.1	chr7	99594639	99594645	+	1	NA	exon (NM_178220, exon 11 of 15)	exon (NM_178220, exon 11 of 15)	32461	NM_001195529	100503386	Mm.180719	NM_001195529	ENSMUSG00000096606	Tpbgl	EG245190|Gm4980	trophoblast glycoprotein-like	protein-coding
mm_158750.1	chrX	165327098	165327125	-	1	NA	promoter-TSS (NM_183427)	promoter-TSS (NM_183427)	-130	NM_183427	237213	Mm.113877	NM_183427	ENSMUSG00000018589	Glra2	-	glycine receptor, alpha 2 subunit	protein-coding
mm_92051.1	chr10	62503938	62503952	-	1	NA	intron (NM_011157, intron 1 of 2)	intron (NM_011157, intron 1 of 2)	3810	NM_011157	19073	Mm.338790	NM_011157	ENSMUSG00000020077	Srgn	Prg|Prg1|Sgc	serglycin	protein-coding
mm_81947.1	chr9	120492704	120492731	+	1	NA	5' UTR (NM_026892, exon 1 of 4)	5' UTR (NM_026892, exon 1 of 4)	111	NM_026892	68969	Mm.28753	NM_026892	ENSMUSG00000006941	Eif1b	1500010M16Rik|3110001N14Rik|Gc20	eukaryotic translation initiation factor 1B	protein-coding
mm_125572.1	chr15	59315196	59315210	+	1	NA	5' UTR (NM_009270, exon 1 of 11)	5' UTR (NM_009270, exon 1 of 11)	111	NM_009270	20775	Mm.296169	NM_009270	ENSMUSG00000022351	Sqle	AI323792	squalene epoxidase	protein-coding
mm_100769.1	chr11	4704335	4704351	-	1	NA	promoter-TSS (NM_026015)	promoter-TSS (NM_026015)	1	NM_197979	66152	Mm.269736	NM_197979	ENSMUSG00000059534	Uqcr10	1110020P15Rik|AA960494|Ucrc	ubiquinol-cytochrome c reductase, complex III subunit X	protein-coding
mm_112049.1	chr12	111712937	111712939	-	1	NA	promoter-TSS (NM_026511)	promoter-TSS (NM_026511)	15	NM_001324481	70369	Mm.44239	NM_027404	ENSMUSG00000049792	Bag5	1600025G07Rik|4930405J06Rik|Bag-5	BCL2-associated athanogene 5	protein-coding
mm_145293.1	chr18	53252169	53252179	+	1	NA	intron (NM_029394, intron 1 of 6)	URR1B|DNA|hAT-Charlie	6512	NM_029394	69226	Mm.32414	NM_029394	ENSMUSG00000024535	Snx24	2810011K15Rik|5730433I16Rik|AI451341	sorting nexing 24	protein-coding
mm_30097.1	chr3	138289867	138289883	-	1	NA	exon (NM_007409, exon 8 of 9)	exon (NM_007409, exon 8 of 9)	12230	NM_007409	11522	Mm.2409	NM_007409	ENSMUSG00000074207	Adh1	ADH-AA|AI194826|Adh-1|Adh-1-t|Adh-1e|Adh-1t|Adh-3e|Adh1-e|Adh1-t|Adh1tl|Adh3-e	alcohol dehydrogenase 1 (class I)	protein-coding
mm_168567.1	chr11	69670235	69670242	-	1	NA	exon (NM_144958, exon 4 of 11)	exon (NM_144958, exon 4 of 11)	2185	NM_144958	13681	Mm.26680	NM_144958	ENSMUSG00000059796	Eif4a1	BM-010|Ddx2a|Eif4	eukaryotic translation initiation factor 4A1	protein-coding
mm_89720.1	chr10	98914562	98914576	+	1	NA	promoter-TSS (NM_026482)	promoter-TSS (NM_026482)	-583	NM_026482	67972	Mm.166944	NM_026482	ENSMUSG00000019943	Atp2b1	2810442I22Rik|E130111D10Rik|Pmca1	ATPase, Ca++ transporting, plasma membrane 1	protein-coding
mm_101890.1	chr11	48997781	48997786	-	1	NA	Intergenic	Intergenic	-5537	NM_011579	21822	Mm.15793	NM_011579	ENSMUSG00000078922	Tgtp1	Gtp2|Irgb6|Mg21|Tgtp	T cell specific GTPase 1	protein-coding
mm_150061.1	chr19	29384254	29384263	+	1	NA	intron (NM_021893, intron 6 of 6)	PB1D10|SINE|Alu	16820	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_79095.1	chr9	46242914	46242918	+	1	NA	exon (NM_007468, exon 3 of 3)	exon (NM_007468, exon 3 of 3)	2072	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_100091.1	chr11	115581766	115581776	+	1	NA	exon (NM_001002929, exon 15 of 19)	exon (NM_001002929, exon 15 of 19)	17327	NM_001002929	445007	Mm.4379	NM_001002929	ENSMUSG00000020739	Nup85	Pcnt1|frount	nucleoporin 85	protein-coding
mm_3707.1	chr1	153900560	153900568	+	1	NA	TTS (NR_106194)	TTS (NR_106194)	635	NM_008131	14645	Mm.210745	NM_008131	ENSMUSG00000026473	Glul	GS|Glns	glutamate-ammonia ligase (glutamine synthetase)	protein-coding
mm_141955.1	chr17	35115530	35115540	-	1	NA	promoter-TSS (NM_148939)	promoter-TSS (NM_148939)	-135	NM_148939	266614	Mm.104680	NM_148939	ENSMUSG00000043807	Ly6g5b	-	lymphocyte antigen 6 complex, locus G5B	protein-coding
mm_34213.1	chr4	140963195	140963214	+	1	NA	intron (NM_023374, intron 1 of 7)	intron (NM_023374, intron 1 of 7)	1933	NM_023374	67680	Mm.246965	NM_023374	ENSMUSG00000009863	Sdhb	0710008N11Rik	succinate dehydrogenase complex, subunit B, iron sulfur (Ip)	protein-coding
mm_62637.1	chr7	107664768	107664781	+	1	NA	intron (NM_001163557, intron 3 of 25)	intron (NM_001163557, intron 3 of 25)	57930	NM_001163557	19024	Mm.2817	NM_008905	ENSMUSG00000036528	Ppfibp2	Cclp1	PTPRF interacting protein, binding protein 2 (liprin beta 2)	protein-coding
mm_9132.1	chr1	170824818	170824820	-	1	NA	intron (NM_001081304, intron 7 of 15)	intron (NM_001081304, intron 7 of 15)	42952	NM_001081304	226641	Mm.377046	NM_001081304	ENSMUSG00000026663	Atf6	9130025P16Rik|9630036G24|AA789574|Atf6alpha|ESTM49	activating transcription factor 6	protein-coding
mm_77196.1	chr8	112030815	112030845	-	1	NA	Intergenic	Lx3B|LINE|L1	19471	NM_020584	57321	Mm.213064	NM_020584	ENSMUSG00000033430	Terf2ip	Rap1	telomeric repeat binding factor 2, interacting protein	protein-coding
mm_58615.1	chr7	5062257	5062267	+	1	NA	5' UTR (NM_001205231, exon 1 of 12)	5' UTR (NM_001205231, exon 1 of 12)	119	NM_001205231	22185	Mm.360389	NM_133671	ENSMUSG00000030435	U2af2	65kDa	U2 small nuclear ribonucleoprotein auxiliary factor (U2AF) 2	protein-coding
mm_132295.1	chr16	33381097	33381135	+	1	NA	promoter-TSS (NR_045709)	promoter-TSS (NR_045709)	341	NM_011749	22661	Mm.392667	NM_011749	ENSMUSG00000022811	Zfp148	2210405J08Rik|AI480666|AW045217|BERF-1|BFCOL1|ZBP-89|Znf148	zinc finger protein 148	protein-coding
mm_73716.1	chr8	111940711	111940739	+	1	NA	promoter-TSS (NM_026693)	promoter-TSS (NM_026693)	22	NM_026693	93739	Mm.371666	NM_026693	ENSMUSG00000031950	Gabarapl2	0610012F20Rik|2900019O08Rik|AI173605|GATE-16|Gef2	gamma-aminobutyric acid (GABA) A receptor-associated protein-like 2	protein-coding
mm_31132.1	chr4	43209287	43209309	+	1	NA	intron (NM_001310758, intron 10 of 38)	intron (NM_001310758, intron 10 of 38)	-57861	NM_177195	320571	Mm.74465	NM_177195	ENSMUSG00000028457	Atp8b5	4930417M19Rik|Feta	ATPase, class I, type 8B, member 5	protein-coding
mm_68084.1	chr7	101870767	101870777	-	1	NA	promoter-TSS (NM_008034)	promoter-TSS (NM_008034)	16	NM_001252554	14275	Mm.2135	NM_008034	ENSMUSG00000001827	Folr1	FBP1|Folbp-1|Folbp1	folate receptor 1 (adult)	protein-coding
mm_33221.1	chr4	126677679	126677689	+	1	NA	promoter-TSS (NM_011970)	promoter-TSS (NM_011970)	41	NM_011970	26445	Mm.22233	NM_011970	ENSMUSG00000028837	Psmb2	AU045357|AW108089|C7-I|D4Wsu33e|HC7-I	proteasome (prosome, macropain) subunit, beta type 2	protein-coding
mm_43495.1	chr5	136967828	136967840	+	1	NA	promoter-TSS (NM_021719)	promoter-TSS (NM_021719)	-35	NM_021719	60363	Mm.87202	NM_021719	ENSMUSG00000001739	Cldn15	2210009B08Rik|BB107105	claudin 15	protein-coding
mm_128106.1	chr15	27995321	27995338	-	1	NA	intron (NM_001081302, intron 1 of 56)	intron (NM_001081302, intron 1 of 56)	30519	NM_001081302	223435	Mm.485422	NM_001081302	ENSMUSG00000022263	Trio	6720464I07Rik|AA408740|Solo	triple functional domain (PTPRF interacting)	protein-coding
mm_80163.1	chr9	71215780	71215792	+	1	NA	promoter-TSS (NM_009022)	promoter-TSS (NM_009022)	-3	NM_009022	19378	Mm.42016	NM_009022	ENSMUSG00000013584	Aldh1a2	AV116159|Aldh1a7|Raldh1|Raldh2	aldehyde dehydrogenase family 1, subfamily A2	protein-coding
mm_100519.1	chr11	120530768	120530784	+	1	NA	promoter-TSS (NM_008101)	promoter-TSS (NM_008101)	49	NM_008101	14527	Mm.22329	NM_008101	ENSMUSG00000025127	Gcgr	GR	glucagon receptor	protein-coding
mm_16795.1	chr2	10097118	10097131	-	1	NA	exon (NM_010582, exon 19 of 21)	exon (NM_010582, exon 19 of 21)	16512	NM_025280	16588	Mm.35498	NM_025280	ENSMUSG00000037262	Kin	Kin17	Kin17 DNA and RNA binding protein	protein-coding
mm_130431.1	chr15	98165582	98165598	-	1	NA	promoter-TSS (NM_001170711)	promoter-TSS (NM_001170711)	-12	NM_001170711	78541	Mm.200766	NM_030121	ENSMUSG00000048175	Asb8	4930539L19Rik|AI788835|C430011H06Rik	ankyrin repeat and SOCS box-containing 8	protein-coding
mm_67075.1	chr7	68250514	68250520	-	1	NA	intron (NM_030101, intron 1 of 3)	ORR1B1-int|LTR|ERVL-MaLR	13716	NM_030101	78444	Mm.425468	NM_030101	ENSMUSG00000030553	Pgpep1l	C330024D12Rik	pyroglutamyl-peptidase I-like	protein-coding
mm_105702.1	chr11	108262685	108262703	-	1	NA	intron (NM_011101, intron 2 of 16)	Lx9|LINE|L1	81194	NM_011101	18750	Mm.222178	NM_011101	ENSMUSG00000050965	Prkca	AI875142|Pkca	protein kinase C, alpha	protein-coding
mm_146815.1	chr18	20896411	20896421	-	1	NA	promoter-TSS (NM_029491)	promoter-TSS (NM_029491)	-338	NM_029491	75964	Mm.273769	NM_029491	ENSMUSG00000033382	Trappc8	5033403J15Rik|AI845423|D030074E01Rik|Trs85|mKIAA1012	trafficking protein particle complex 8	protein-coding
mm_107111.1	chr12	17992840	17992850	+	1	NA	Intergenic	CpG	302031	NM_016677	53602	Mm.313619	NM_016677	ENSMUSG00000071379	Hpcal1	NVP-3|Nvp3|VILIP3|Vnsl3|Vsnl3	hippocalcin-like 1	protein-coding
mm_141100.1	chr17	26008879	26008922	-	1	NA	intron (NM_153140, intron 3 of 11)	intron (NM_153140, intron 3 of 11)	12960	NM_153140	215445	Mm.41191	NM_153140	ENSMUSG00000037098	Rab11fip3	Cart1|D030060O14Rik|Rab11-FIP3|mKIAA0665	RAB11 family interacting protein 3 (class II)	protein-coding
mm_157043.1	chrX	7977969	7977975	-	1	NA	Intergenic	Intergenic	-10062	NM_008089	14460	Mm.335973	NM_008089	ENSMUSG00000031162	Gata1	Gata-1|Gf-1|eryf1	GATA binding protein 1	protein-coding
mm_151455.1	chr19	57999110	57999115	+	1	NA	intron (NM_181415, intron 27 of 28)	intron (NM_181415, intron 27 of 28)	-52055	NR_049196	100885835		NR_049196	ENSMUSG00000093757	Mir5623	Gm26068|mir-5623|mmu-mir-5623	microRNA 5623	ncRNA
mm_140938.1	chr17	24443078	24443090	-	1	NA	promoter-TSS (NM_025718)	promoter-TSS (NM_025718)	17	NM_025718	66705	Mm.29017	NM_025718	ENSMUSG00000024136	Dnase1l2	4733401H14Rik	deoxyribonuclease 1-like 2	protein-coding
mm_83120.1	chr9	40407985	40407995	-	1	NA	intron (NM_172768, intron 2 of 19)	intron (NM_172768, intron 2 of 19)	47774	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_151143.1	chr19	53085102	53085110	+	1	NA	TTS (NR_045320)	TTS (NR_045320)	8854	NR_045320	78457	Mm.76932	NR_045320	ENSMUSG00000099988	1700054A03Rik	-	RIKEN cDNA 1700054A03 gene	ncRNA
mm_95909.1	chr11	58206118	58206128	+	1	NA	exon (NM_018738, exon 3 of 3)	exon (NM_018738, exon 3 of 3)	6567	NM_018738	16145	Mm.33902	NM_018738	ENSMUSG00000078853	Igtp	AW558444|Irgm3	interferon gamma induced GTPase	protein-coding
mm_45470.1	chr5	69341672	69341685	-	1	NA	promoter-TSS (NM_175519)	promoter-TSS (NM_175519)	31	NM_175519	243043	Mm.234821	NM_175519	ENSMUSG00000037653	Kctd8	A730087N02Rik	potassium channel tetramerisation domain containing 8	protein-coding
mm_21332.1	chr2	157101631	157101649	-	1	NA	intron (NM_001139520, intron 15 of 16)	ID_B1|SINE|B4	14585	NM_001177439	383766	Mm.480305	NM_001177439	ENSMUSG00000074628	Tldc2	Gm1332	TBC/LysM associated domain containing 2	protein-coding
mm_29842.1	chr3	129831124	129831186	-	1	NA	5' UTR (NM_026578, exon 1 of 7)	5' UTR (NM_026578, exon 1 of 7)	241	NM_026578	68147	Mm.24873	NM_026578	ENSMUSG00000028010	Gar1	AA409823|AI326794|C430047J18Rik|Nola1	GAR1 ribonucleoprotein	protein-coding
mm_147067.1	chr18	35214913	35214934	-	1	NA	5' UTR (NM_178005, exon 1 of 2)	5' UTR (NM_178005, exon 1 of 2)	101	NM_178005	107065	Mm.39900	NM_178005	ENSMUSG00000071862	Lrrtm2	AI851755|BB129880|C630011A14Rik|mKIAA0416	leucine rich repeat transmembrane neuronal 2	protein-coding
mm_147659.1	chr18	60591884	60591900	-	1	NA	promoter-TSS (NM_133363)	promoter-TSS (NM_133363)	-176	NM_133363	170947	Mm.159257	NM_133363	ENSMUSG00000049173	Myoz3	4833419K08Rik|Fatz-3	myozenin 3	protein-coding
mm_122982.1	chr14	54983602	54983646	-	1	NA	exon (NM_080728, exon 24 of 41)	exon (NM_080728, exon 24 of 41)	-7848	NR_030607	100124433		NR_030607	ENSMUSG00000077928	Mir208b	Mirn208b|mir-208b	microRNA 208b	ncRNA
mm_35779.1	chr4	46404225	46404240	-	1	NA	promoter-TSS (NM_053149)	promoter-TSS (NM_053149)	-49	NM_053149	93966	Mm.25793	NM_053149	ENSMUSG00000028332	Hemgn	4921524M03Rik|AI317176|EDAG|Hgn|mNDR	hemogen	protein-coding
mm_155537.1	chrX	74304161	74304171	+	1	NA	promoter-TSS (NM_010273)	promoter-TSS (NM_010273)	-846	NM_010273	14567	Mm.205830	NM_010273	ENSMUSG00000015291	Gdi1	GDIA|GDIalpha	guanosine diphosphate (GDP) dissociation inhibitor 1	protein-coding
mm_112139.1	chr12	113014225	113014263	-	1	NA	promoter-TSS (NM_001291445)	promoter-TSS (NM_001291445)	-264	NM_001291445	217893	Mm.35754	NM_198165	ENSMUSG00000021143	Pacs2	6720425G15Rik|AW208651|AW489976|E230011J22|Pacs1l|mKIAA0602	phosphofurin acidic cluster sorting protein 2	protein-coding
mm_165753.1	chr3	108904228	108904244	-	1	NA	exon (NM_025845, exon 6 of 6)	exon (NM_025845, exon 6 of 6)	7468	NM_025845	66921	Mm.51049	NM_025845	ENSMUSG00000027881	Prpf38b	1110021E09Rik|AU018955	PRP38 pre-mRNA processing factor 38 (yeast) domain containing B	protein-coding
mm_63412.1	chr7	127344398	127344430	+	1	NA	exon (NM_146202, exon 2 of 2)	exon (NM_146202, exon 2 of 2)	900	NM_146202	233890	Mm.23031	NM_146202	ENSMUSG00000047371	Zfp768	BC026432|Znf768	zinc finger protein 768	protein-coding
mm_120617.1	chr14	70359989	70360024	+	1	NA	Intergenic	Intergenic	-8582	NM_001135151	213053	Mm.270647	NM_144808	ENSMUSG00000022094	Slc39a14	FAD-123|ZIP-14|Zip14|fad123	solute carrier family 39 (zinc transporter), member 14	protein-coding
mm_73597.1	chr8	109998793	109998823	+	1	NA	exon (NM_146214, exon 12 of 12)	exon (NM_146214, exon 12 of 12)	8372	NM_146214	234724	Mm.28110	NM_146214	ENSMUSG00000001670	Tat	-	tyrosine aminotransferase	protein-coding
mm_88534.1	chr10	78404929	78404940	+	1	NA	exon (NM_010925, exon 8 of 13)	exon (NM_010925, exon 8 of 13)	3611	NR_105872	102465547		NR_105872	ENSMUSG00000098376	Mir6907	Gm27351|mmu-mir-6907	microRNA 6907	ncRNA
mm_12149.1	chr2	61805025	61805038	+	1	NA	exon (NM_009322, exon 1 of 6)	exon (NM_009322, exon 1 of 6)	578	NM_009322	21375	Mm.308525	NM_009322	ENSMUSG00000035033	Tbr1	-	T-box brain gene 1	protein-coding
mm_61869.1	chr7	89406957	89406961	+	1	NA	intron (NM_008055, intron 1 of 1)	intron (NM_008055, intron 1 of 1)	2593	NM_008055	14366	Mm.86755	NM_008055	ENSMUSG00000049791	Fzd4	Fz4	frizzled class receptor 4	protein-coding
mm_129481.1	chr15	78770843	78770856	-	1	NA	intron (NM_008595, intron 1 of 7)	intron (NM_008595, intron 1 of 7)	2596	NM_008595	17305	Mm.149235	NM_008595	ENSMUSG00000018169	Mfng	AW546563	MFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	protein-coding
mm_13815.1	chr2	119237206	119237217	+	1	NA	promoter-TSS (NM_016907)	promoter-TSS (NM_016907)	-149	NM_016907	20732	Mm.104955	NM_016907	ENSMUSG00000027315	Spint1	HAI-1	serine protease inhibitor, Kunitz type 1	protein-coding
mm_2723.1	chr1	128178919	128178932	+	1	NA	exon (NM_181750, exon 10 of 27)	exon (NM_181750, exon 10 of 27)	-23436	NR_029543	387147		NR_029543	ENSMUSG00000065520	Mir128-1	Mirn128|Mirn128-1|Mirn128a|mir-128-1	microRNA 128-1	ncRNA
mm_95007.1	chr11	31913306	31913309	+	1	NA	intron (NM_001290676, intron 3 of 8)	intron (NM_001290676, intron 3 of 8)	42367	NM_026252	67579	Mm.339792	NM_026252	ENSMUSG00000020300	Cpeb4	Cpe-bp4|Cpeb-4|mCPEB-4	cytoplasmic polyadenylation element binding protein 4	protein-coding
mm_61900.1	chr7	90130062	90130084	+	1	NA	promoter-TSS (NM_001252521)	promoter-TSS (NM_001252521)	-137	NR_046007	78329	Mm.389940	NR_046006	ENSMUSG00000097162	2310010J17Rik	-	RIKEN cDNA 2310010J17 gene	ncRNA
mm_163602.1	chr13	46728008	46728045	-	1	NA	promoter-TSS (NM_175749)	promoter-TSS (NM_175749)	-177	NM_175749	218210	Mm.255398	NM_175749	ENSMUSG00000021374	Nup153	B130015D15Rik|C88147	nucleoporin 153	protein-coding
mm_56363.1	chr6	93912521	93912563	-	1	NA	intron (NM_001029850, intron 2 of 23)	intron (NM_001029850, intron 2 of 23)	421	NR_104594	14924	Mm.217216	NM_010367	ENSMUSG00000045095	Magi1	AIP3|BAP1|Baiap1|Gukmi1|MAGI1c|Magi-1|TNRC19|WWP3|mKIAA4129	membrane associated guanylate kinase, WW and PDZ domain containing 1	protein-coding
mm_172251.1	chr6	70129133	70129139	+	1	NA	Intergenic	L1VL2|LINE|L1	663039	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_116442.1	chr13	43154740	43154744	-	1	NA	exon (NM_025935, exon 6 of 8)	exon (NM_025935, exon 6 of 8)	16759	NM_001252639	67046	Mm.269213	NM_025935	ENSMUSG00000021368	Tbc1d7	2610009C09Rik	TBC1 domain family, member 7	protein-coding
mm_162929.1	chr10	122805895	122805940	+	1	NA	intron (NM_176919, intron 3 of 8)	intron (NM_176919, intron 3 of 8)	126602	NR_106182	102466884		NR_106182	ENSMUSG00000099225	Mir8104	Gm27380|mmu-mir-8104	microRNA 8104	ncRNA
mm_17543.1	chr2	29845642	29845645	-	1	NA	promoter-TSS (NR_029838)	promoter-TSS (NR_029838)	-4	NR_106110	102466839		NR_106110	ENSMUSG00000105010	Mir219b	mmu-mir-219b	microRNA 219b	ncRNA
mm_6154.1	chr1	64956824	64956835	-	1	NA	promoter-TSS (NM_001039493)	promoter-TSS (NM_001039493)	-5	NM_001039493	241075	Mm.239534	NM_175509	ENSMUSG00000051344	Plekhm3	9430067K14Rik|A230102O09Rik|AI449570|DAPR|Plekhm1l	pleckstrin homology domain containing, family M, member 3	protein-coding
mm_19349.1	chr2	90917765	90917827	-	1	NA	exon (NM_025576, exon 1 of 5)	exon (NM_025576, exon 1 of 5)	254	NM_025576	66461	Mm.23926	NM_025576		Ptpmt1	1110001D10Rik|2810004N20Rik|PLIP	protein tyrosine phosphatase, mitochondrial 1	protein-coding
mm_34897.1	chr4	155625523	155625555	+	1	NA	promoter-TSS (NR_040441)	promoter-TSS (NR_040441)	670	NM_007661	12537	Mm.267410	NM_007661	ENSMUSG00000029062	Cdk11b	AA989746|CDK11-p110|CDK11-p46|CDK11-p58|Cdc11b|Cdc2l1|Cdc2l2|Cdk11|p58	cyclin-dependent kinase 11B	protein-coding
mm_109396.1	chr12	109891966	109891968	+	1	NA	Intergenic	RLTR51A_Mm|LTR|ERVK?	144089	NR_037233	100499517		NR_037233	ENSMUSG00000093351	Mir3072	mir-3072|mmu-mir-3072	microRNA 3072	ncRNA
mm_155742.1	chrX	96166634	96166644	+	1	NA	3' UTR (NM_010833, exon 13 of 13)	3' UTR (NM_010833, exon 13 of 13)	70594	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_116263.1	chr13	34345175	34345273	-	1	NA	promoter-TSS (NM_001033167)	promoter-TSS (NM_001033167)	-42	NM_001033167	73102	Mm.23932	NM_001033167	ENSMUSG00000038267	Slc22a23	3110004L20Rik	solute carrier family 22, member 23	protein-coding
mm_127947.1	chr15	10715299	10715315	-	1	NA	promoter-TSS (NM_001166408)	promoter-TSS (NM_001166408)	407	NR_045065	75259	Mm.33928	NR_045063	ENSMUSG00000097058	4930556M19Rik	1700009D01Rik|C130022M03Rik	RIKEN cDNA 4930556M19 gene	ncRNA
mm_133123.1	chr16	65815509	65815522	+	1	NA	promoter-TSS (NM_028572)	promoter-TSS (NM_028572)	-118	NM_028572	73569	Mm.25670	NM_028572	ENSMUSG00000091243	Vgll3	1700110N18Rik|4832416J22|C80713|Vgl-3|Vito-2	vestigial like family member 3	protein-coding
mm_99384.1	chr11	102096337	102096343	+	1	NA	Intergenic	Intergenic	4960	NM_008918	19064	Mm.1269	NM_008918	ENSMUSG00000017316	Ppy	AV061413|IGSPP|PP	pancreatic polypeptide	protein-coding
mm_43336.1	chr5	135023522	135023580	+	1	NA	promoter-TSS (NM_016801)	promoter-TSS (NM_016801)	69	NR_133683	20907	Mm.6225	NM_016801	ENSMUSG00000007207	Stx1a	HPC-1	syntaxin 1A (brain)	protein-coding
mm_71838.1	chr8	68904500	68904514	+	1	NA	3' UTR (NM_008509, exon 10 of 10)	3' UTR (NM_008509, exon 10 of 10)	23952	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_87753.1	chr10	60277703	60277719	+	1	NA	promoter-TSS (NM_011179)	promoter-TSS (NM_011179)	83	NM_001146121	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_113496.1	chr13	37418663	37418685	+	1	NA	3' UTR (NM_010745, exon 5 of 5)	3' UTR (NM_010745, exon 5 of 5)	73329	NM_010745	17084	Mm.2639	NM_010745	ENSMUSG00000021423	Ly86	MD-1|MD1|ly86_tv2	lymphocyte antigen 86	protein-coding
mm_56639.1	chr6	113238527	113238551	-	1	NA	intron (NM_026849, intron 1 of 18)	intron (NM_026849, intron 1 of 18)	696	NM_026849	97287	Mm.197816	NM_026849	ENSMUSG00000030269	Mtmr14	1110061O04Rik|AW553738|C76151	myotubularin related protein 14	protein-coding
mm_122479.1	chr14	45658059	45658085	-	1	NA	promoter-TSS (NM_001042719)	promoter-TSS (NM_001042719)	-19	NR_039593	100628600		NR_039593	ENSMUSG00000093167	Mir5131	mmu-mir-5131|mu-mir-5131	microRNA 5131	ncRNA
mm_26102.1	chr3	137287893	137287897	+	1	NA	Intergenic	RLTR44E|LTR|ERVK	-53183	NM_001163522	59308	Mm.27343	NM_016885	ENSMUSG00000054690	Emcn	0610012K22Rik|AI315669|Muc14	endomucin	protein-coding
mm_155525.1	chrX	74270850	74270870	+	1	NA	promoter-TSS (NM_052835)	promoter-TSS (NM_052835)	44	NM_052835	110954	Mm.100113	NM_052835	ENSMUSG00000008682	Rpl10	D0HXS648|DXHXS648|DXHXS648E|QM|QM16	ribosomal protein L10	protein-coding
mm_122793.1	chr14	54417840	54417865	-	1	NA	promoter-TSS (NM_011405)	promoter-TSS (NM_011405)	-150	NM_011405	20540	Mm.142455	NM_011405	ENSMUSG00000000958	Slc7a7	AI790233|my+lat1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 7	protein-coding
mm_38958.1	chr4	150686511	150686515	-	1	NA	Intergenic	Intergenic	-34339	NM_173774	242773	Mm.29280	NM_173774	ENSMUSG00000039838	Slc45a1	C230078B22|Dnb5	solute carrier family 45, member 1	protein-coding
mm_117443.1	chr13	74754341	74754367	-	1	NA	exon (NM_009817, exon 4 of 31)	exon (NM_009817, exon 4 of 31)	16382	NM_001301156	12380	Mm.29163	NM_009817	ENSMUSG00000021585	Cast	-	calpastatin	protein-coding
mm_31516.1	chr4	53835123	53835123	+	1	NA	intron (NM_028053, intron 1 of 5)	PB1D10|SINE|Alu	9078	NM_028053	52076	Mm.27184	NM_028053	ENSMUSG00000028420	Tmem38b	1600017F22Rik|AA437809|AV051057|D4Ertd89e|TRIC-B|mg33b	transmembrane protein 38B	protein-coding
mm_157771.1	chrX	73717831	73717842	-	1	NA	promoter-TSS (NM_001313698)	promoter-TSS (NM_001313698)	-21	NM_001313698	27061	Mm.17	NM_012060	ENSMUSG00000002015	Bcap31	Bap31	B cell receptor associated protein 31	protein-coding
mm_153320.1	chr19	38118308	38118319	-	1	NA	exon (NM_011255, exon 5 of 6)	exon (NM_011255, exon 5 of 6)	6498	NM_011255	19662	Mm.2605	NM_011255	ENSMUSG00000024990	Rbp4	Rbp-4	retinol binding protein 4, plasma	protein-coding
mm_57593.1	chr6	127769307	127769364	-	1	NA	promoter-TSS (NM_201371)	promoter-TSS (NM_201371)	-176	NM_201371	381813	Mm.39750	NM_201371	ENSMUSG00000030350	Prmt8	Hrmt1l3|Hrmt1l4	protein arginine N-methyltransferase 8	protein-coding
mm_51443.1	chr6	80173796	80173807	+	1	NA	intron (NM_001347261, intron 2 of 2)	ORR1A2|LTR|ERVL-MaLR	154158	NM_178731	243499	Mm.483425	NM_178731	ENSMUSG00000052581	Lrrtm4	7530419J18Rik|A230052N11	leucine rich repeat transmembrane neuronal 4	protein-coding
mm_89609.1	chr10	96023970	96023980	+	1	NA	exon (NM_001001932, exon 17 of 29)	exon (NM_001001932, exon 17 of 29)	83312	NM_001001932	216238	Mm.210035	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding
mm_157414.1	chrX	38442123	38442143	-	1	NA	exon (NM_001017959, exon 2 of 9)	exon (NM_001017959, exon 2 of 9)	14327	NM_010685	16784	Mm.486	NM_010685	ENSMUSG00000016534	Lamp2	CD107b|LGP-B|Lamp II|Lamp-2|Lamp-2a|Lamp-2b|Lamp-2c|Mac3	lysosomal-associated membrane protein 2	protein-coding
mm_134093.1	chr16	9571970	9571970	-	1	NA	Intergenic	Intergenic	420563	NM_008170	14811	Mm.2953	NM_008170	ENSMUSG00000059003	Grin2a	GluN2A|NMDAR2A|NR2A	glutamate receptor, ionotropic, NMDA2A (epsilon 1)	protein-coding
mm_124018.1	chr14	76515521	76515535	-	1	NA	intron (NR_045660, intron 3 of 3)	G-rich|Low_complexity|Low_complexity	5327	NR_045660	75789	Mm.159571	NR_045660	ENSMUSG00000097172	4930444M15Rik	-	RIKEN cDNA 4930444M15 gene	ncRNA
mm_53044.1	chr6	124701624	124701637	+	1	NA	intron (NM_145130, intron 7 of 12)	intron (NM_145130, intron 7 of 12)	10548	NM_013536	14791	Mm.6390	NM_013536	ENSMUSG00000004268	Emg1	C2f|Grcc2f	EMG1 N1-specific pseudouridine methyltransferase	protein-coding
mm_39549.1	chr5	21737143	21737179	+	1	NA	promoter-TSS (NM_028431)	promoter-TSS (NM_028431)	1	NM_028431	73078	Mm.301655	NM_028431	ENSMUSG00000029017	Pmpcb	3110004O18Rik|MPP11|MPPB|MPPP52	peptidase (mitochondrial processing) beta	protein-coding
mm_38421.1	chr4	139192615	139192637	-	1	NA	promoter-TSS (NM_009798)	promoter-TSS (NM_009798)	-273	NM_009798	12345	Mm.2945	NM_009798	ENSMUSG00000028745	Capzb	1700120C01Rik|AI325129|CPB1|CPB2|CPbeat2|CPbeta1|CPbeta2|Cappb1	capping protein (actin filament) muscle Z-line, beta	protein-coding
mm_98483.1	chr11	94951106	94951150	+	1	NA	exon (NM_007742, exon 50 of 51)	exon (NM_007742, exon 50 of 51)	14904	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_101664.1	chr11	36686246	36686250	-	1	NA	intron (NM_011856, intron 2 of 28)	intron (NM_011856, intron 2 of 28)	257993	NM_001290702	23964	Mm.439889	NM_011856	ENSMUSG00000049336	Tenm2	Odz2|Odz3|Ten-2|Ten-m2	teneurin transmembrane protein 2	protein-coding
mm_14340.1	chr2	129593050	129593058	+	1	NA	promoter-TSS (NM_001291022)	promoter-TSS (NM_001291022)	-115	NM_001291019	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_122385.1	chr14	40899368	40899378	-	1	NA	Intergenic	MLT1J2|LTR|ERVL-MaLR	-6408	NM_177816	328381	Mm.235694	NM_177816	ENSMUSG00000037833	Sh2d4b	A430109M18Rik|D030001E08	SH2 domain containing 4B	protein-coding
mm_163530.1	chr13	8996157	8996209	+	1	NA	promoter-TSS (NM_027000)	promoter-TSS (NM_027000)	-171	NM_027000	69237	Mm.41800	NM_027000	ENSMUSG00000021149	Gtpbp4	2610028C09Rik|Crfg|Gtpbp3|NGB|Nog1	GTP binding protein 4	protein-coding
mm_14309.1	chr2	129130153	129130171	+	1	NA	intron (NM_025395, intron 1 of 3)	intron (NM_025395, intron 1 of 3)	462	NM_025395	66170	Mm.40621	NM_025395	ENSMUSG00000037938	Chchd5	1110027L01Rik|AW045710	coiled-coil-helix-coiled-coil-helix domain containing 5	protein-coding
mm_95190.1	chr11	42466997	42466999	+	1	NA	intron (NM_001347314, intron 3 of 9)	intron (NM_001347314, intron 3 of 9)	45648	NM_001347314	14401	Mm.338723	NM_008070	ENSMUSG00000007653	Gabrb2	AI834970|C030002O17Rik|C030021G16Rik|Gabrab2|Gabrb-2	gamma-aminobutyric acid (GABA) A receptor, subunit beta 2	protein-coding
mm_18326.1	chr2	57124057	57124071	-	1	NA	promoter-TSS (NM_001139509)	promoter-TSS (NM_001139509)	-61	NM_001139509	18227	Mm.3507	NM_013613	ENSMUSG00000026826	Nr4a2	HZF-3|NOT|Nurr1|RNR-1|TINOR|TINUR	nuclear receptor subfamily 4, group A, member 2	protein-coding
mm_164723.1	chr17	57045570	57045602	-	1	NA	exon (NM_025877, exon 10 of 10)	exon (NM_025877, exon 10 of 10)	-3932	NM_175333	103775	Mm.33647	NM_175333	ENSMUSG00000011486	Slc25a41	4933406J04Rik|AI507137	solute carrier family 25, member 41	protein-coding
mm_18195.1	chr2	45117302	45117345	-	1	NA	Intergenic	Intergenic	-4044	NM_015753	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_44184.1	chr5	151371375	151371378	+	1	NA	intron (NR_045699, intron 1 of 3)	(T)n|Simple_repeat|Simple_repeat	2701	NR_045699	625175	Mm.443286	NR_045699	ENSMUSG00000097321	1700028E10Rik	A630054D14|Gm6561	RIKEN cDNA 1700028E10 gene	ncRNA
mm_90455.1	chr10	127725373	127725387	+	1	NA	promoter-TSS (NM_009312)	promoter-TSS (NM_009312)	-12	NM_009312	21334	Mm.2374	NM_009312	ENSMUSG00000025400	Tac2	PPT-B|Tac3	tachykinin 2	protein-coding
mm_35196.1	chr4	16163493	16163505	-	1	NA	promoter-TSS (NR_045765)	promoter-TSS (NR_045765)	144	NM_138952	192656	Mm.112765	NM_138952	ENSMUSG00000041135	Ripk2	2210420D18Rik|CARD3|CARDIAK|CCK|D4Bwg0615e|RICK|RIP2	receptor (TNFRSF)-interacting serine-threonine kinase 2	protein-coding
mm_31547.1	chr4	55540182	55540186	+	1	NA	Intergenic	Intergenic	-7709	NM_010637	16600	Mm.4325	NM_010637	ENSMUSG00000003032	Klf4	EZF|Gklf|Zie	Kruppel-like factor 4 (gut)	protein-coding
mm_117794.1	chr13	97198274	97198282	-	1	NA	promoter-TSS (NM_010422)	promoter-TSS (NM_010422)	79	NM_010422	15212	Mm.27816	NM_010422	ENSMUSG00000021665	Hexb	-	hexosaminidase B	protein-coding
mm_29018.1	chr3	101924281	101924299	-	1	NA	5' UTR (NM_001039371, exon 1 of 12)	5' UTR (NM_001039371, exon 1 of 12)	163	NM_001039371	242126	Mm.90204	NM_001039371	ENSMUSG00000033147	Slc22a15	2610034P21Rik|4930477M19|A530052I06Rik|BB219042	solute carrier family 22 (organic anion/cation transporter), member 15	protein-coding
mm_73281.1	chr8	104831592	104831598	+	1	NA	promoter-TSS (NM_198171)	promoter-TSS (NM_198171)	-49	NM_198171	234669	Mm.443387	NM_198171	ENSMUSG00000050097	Ces2b	-	carboxyesterase 2B	protein-coding
mm_70147.1	chr7	143458937	143458959	-	1	NA	3' UTR (NM_001161624, exon 4 of 4)	3' UTR (NM_001161624, exon 4 of 4)	2102	NM_009876	12577	Mm.168789	NM_009876	ENSMUSG00000037664	Cdkn1c	AL024410|CDKI|Kip2|p57(kip2)|p57Kip2	cyclin-dependent kinase inhibitor 1C (P57)	protein-coding
mm_170903.1	chr2	30070223	30070225	+	1	NA	exon (NM_001204875, exon 6 of 8)	exon (NM_001204875, exon 6 of 8)	3750	NM_001204875	56086	Mm.326055	NM_023871	ENSMUSG00000054766	Set	2610030F17Rik|5730420M11Rik|AA407739|I-2PP2A|StF-IT-1|TAF-I	SET nuclear oncogene	protein-coding
mm_51706.1	chr6	86668823	86668827	+	1	NA	intron (NM_010751, intron 1 of 5)	CpG	334	NM_010751	17119	Mm.279580	NM_010751	ENSMUSG00000001156	Mxd1	AW122478|Mad|Mad1	MAX dimerization protein 1	protein-coding
mm_37619.1	chr4	127061127	127061143	-	1	NA	promoter-TSS (NM_026670)	promoter-TSS (NM_026670)	-3	NM_026670	68310	Mm.273806	NM_026670	ENSMUSG00000043872	Zmym1	5830412B09Rik|AW209050	zinc finger, MYM domain containing 1	protein-coding
mm_82294.1	chr9	7836837	7836850	-	1	NA	promoter-TSS (NM_001291503)	promoter-TSS (NM_001291503)	-37	NM_001291503	11797	Mm.335659	NM_007465	ENSMUSG00000057367	Birc2	AW146227|Api1|Api2|Birc3|C-IAP1|C330006D17Rik|HIAP1|HIAP2|IAP1|IAP2|MIAP1|MIAP2|MIHB|MIHC|RNF48|cIAP1|cIAP2|mcIAP1	baculoviral IAP repeat-containing 2	protein-coding
mm_73316.1	chr8	105225171	105225193	+	1	NA	promoter-TSS (NM_145604)	promoter-TSS (NM_145604)	-6	NM_145604	234678	Mm.27186	NM_145604	ENSMUSG00000031889	D230025D16Rik	BC006874|Lin10	RIKEN cDNA D230025D16 gene	protein-coding
mm_169884.1	chr16	43143257	43143257	-	1	NA	intron (NM_001285805, intron 2 of 10)	intron (NM_001285805, intron 2 of 10)	-104027	NM_181058	56490	Mm.136238	NM_019778	ENSMUSG00000022708	Zbtb20	1300017A20Rik|7330412A13Rik|A930017C21Rik|D16Wsu73e|DPZF|HOF|ODA-8S|Oda8|Zfp288	zinc finger and BTB domain containing 20	protein-coding
mm_89297.1	chr10	87913665	87913684	+	1	NA	exon (NM_010512, exon 3 of 5)	exon (NM_010512, exon 3 of 5)	52563	NM_001111276	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_91821.1	chr10	56115533	56115538	-	1	NA	exon (NM_001163833, exon 2 of 2)	exon (NM_001163833, exon 2 of 2)	8618	NM_001163833	73390	Mm.181475	NM_133751	ENSMUSG00000047669	Msl3l2	1700060H10Rik	male-specific lethal 3-like 2 (Drosophila)	protein-coding
mm_18186.1	chr2	45112084	45112094	-	1	NA	promoter-TSS (NR_110571)	promoter-TSS (NR_110571)	-171	NR_110571	433424	Mm.441408	NR_110571	ENSMUSG00000052248	Zeb2os	Gm13476|OTTMUSG00000012358|Zeb2nat	zinc finger E-box binding homeobox 2, opposite strand	ncRNA
mm_24090.1	chr3	87976109	87976119	+	1	NA	exon (NM_016701, exon 4 of 4)	exon (NM_016701, exon 4 of 4)	5021	NM_016701	18008	Mm.331129	NM_016701	ENSMUSG00000004891	Nes	AA166324|C78523|ESTM46	nestin	protein-coding
mm_59000.1	chr7	19176649	19176693	+	1	NA	exon (NM_001347582, exon 1 of 22)	exon (NM_001347582, exon 1 of 22)	250	NM_001347582	72205	Mm.154121	NM_028153	ENSMUSG00000040811	Eml2	1600029N02Rik|EMAP-2	echinoderm microtubule associated protein like 2	protein-coding
mm_62942.1	chr7	119526181	119526200	+	1	NA	promoter-TSS (NM_178758)	promoter-TSS (NM_178758)	-75	NM_178758	272428	Mm.185183	NM_178758	ENSMUSG00000030972	Acsm5	C730019D22|C730027J19Rik	acyl-CoA synthetase medium-chain family member 5	protein-coding
mm_58809.1	chr7	16399593	16399629	+	1	NA	Intergenic	CpG	-1585	NM_198631	330474	Mm.333594	NM_198631	ENSMUSG00000059273	Zc3h4	Bwq1|Gm768|Kiaa1064-hp|mKIAA1064	zinc finger CCCH-type containing 4	protein-coding
mm_2721.1	chr1	128171653	128171657	+	1	NA	intron (NM_181750, intron 7 of 26)	intron (NM_181750, intron 7 of 26)	-30706	NR_029543	387147		NR_029543	ENSMUSG00000065520	Mir128-1	Mirn128|Mirn128-1|Mirn128a|mir-128-1	microRNA 128-1	ncRNA
mm_172144.1	chr6	37686811	37686813	-	1	NA	Intergenic	Intergenic	156639	NM_145364	208665	Mm.262635	NM_145364	ENSMUSG00000038641	Akr1d1	-	aldo-keto reductase family 1, member D1	protein-coding
mm_72498.1	chr8	83740364	83740378	+	1	NA	intron (NM_001163031, intron 1 of 17)	intron (NM_001163031, intron 1 of 17)	940	NM_001163029	26364	Mm.334648	NM_011925	ENSMUSG00000002885	Adgre5	AA409984|Cd97|TM7LN1	adhesion G protein-coupled receptor E5	protein-coding
mm_57852.1	chr6	129471473	129471504	-	1	NA	intron (NR_132130, intron 1 of 5)	intron (NR_132130, intron 1 of 5)	1291	NM_001309637	56644	Mm.239516	NM_020008	ENSMUSG00000079293	Clec7a	BGR|Clecsf12|beta-GR	C-type lectin domain family 7, member a	protein-coding
mm_75364.1	chr8	45294804	45294823	-	1	NA	promoter-TSS (NM_008455)	promoter-TSS (NM_008455)	22	NM_008455	16621	Mm.482691	NM_008455	ENSMUSG00000109764	Klkb1	APS|Kal-3|Kal3|Klk3|PSA	kallikrein B, plasma 1	protein-coding
mm_62562.1	chr7	103870942	103870957	+	1	NA	Intergenic	Intergenic	11292	NM_013618	18367	Mm.445781	NM_013618	ENSMUSG00000058200	Olfr66	5'[b]1|5'beta1|MOR1-3|ORL532	olfactory receptor 66	protein-coding
mm_83806.1	chr9	53536620	53536693	-	1	NA	promoter-TSS (NM_001081152)	promoter-TSS (NM_001081152)	15	NM_007499	11920	Mm.5088	NM_007499	ENSMUSG00000034218	Atm	AI256621|C030026E19Rik	ataxia telangiectasia mutated	protein-coding
mm_52224.1	chr6	103511357	103511373	+	1	NA	intron (NM_007697, intron 1 of 26)	intron (NM_007697, intron 1 of 26)	489	NM_007697	12661	Mm.251288	NM_007697	ENSMUSG00000030077	Chl1	A530023M13Rik|AI465420|CALL|LICAM2	cell adhesion molecule L1-like	protein-coding
mm_142073.1	chr17	35700487	35700516	-	1	NA	promoter-TSS (NM_001198833)	promoter-TSS (NM_001198833)	89	NM_001198833	12305	Mm.5021	NM_007584	ENSMUSG00000003534	Ddr1	6030432F18|AI323681|CD167a|Cak|Nep|PTK3A	discoidin domain receptor family, member 1	protein-coding
mm_77443.1	chr8	121792185	121792189	-	1	NA	Intergenic	Intergenic	37382	NM_145605	234825	Mm.209329	NM_145605	ENSMUSG00000040263	Klhdc4	AA408426|AV352552|BC012312|G430025P05Rik	kelch domain containing 4	protein-coding
mm_90515.1	chr10	128043210	128043220	+	1	NA	exon (NM_001113199, exon 3 of 9)	exon (NM_001113199, exon 3 of 9)	7869	NM_001113199	17938	Mm.3746	NM_013608	ENSMUSG00000061315	Naca	AL022831|AL024382|Gm1878|mKIAA0363|skNAC	nascent polypeptide-associated complex alpha polypeptide	protein-coding
mm_67993.1	chr7	100894609	100894630	-	1	NA	intron (NM_001081116, intron 1 of 20)	CpG	-12210	NR_037289	100526508		NR_037289	ENSMUSG00000093296	Mir3102	mmu-mir-3102	microRNA 3102	ncRNA
mm_162814.1	chr10	79694594	79694600	+	1	NA	exon (NM_008504, exon 4 of 5)	exon (NM_008504, exon 4 of 5)	771	NM_001302499	16904	Mm.378960	NM_008504	ENSMUSG00000054206	Gzmm	Lmet1|MMET-1	granzyme M (lymphocyte met-ase 1)	protein-coding
mm_86993.1	chr10	26107747	26107754	+	1	NA	Intergenic	L1_Mus1|LINE|L1	-28698	NM_029881	77220	Mm.266260	NM_029881	ENSMUSG00000049420	Tmem200a	C030003D03Rik	transmembrane protein 200A	protein-coding
mm_11543.1	chr2	32646618	32646633	+	1	NA	promoter-TSS (NM_001146350)	promoter-TSS (NM_001146350)	30	NM_001146348	13805	Mm.225297	NM_007932	ENSMUSG00000026814	Eng	AI528660|AI662476|CD105|Endo|S-endoglin	endoglin	protein-coding
mm_169281.1	chr1	39519530	39519548	+	1	NA	Intergenic	U3|snRNA|snRNA	-16263	NM_028043	52846	Mm.259421	NM_028043	ENSMUSG00000003135	Cnot11	2410015L18Rik|C40|D1Bwg0212e	CCR4-NOT transcription complex, subunit 11	protein-coding
mm_86298.1	chr9	122305414	122305426	-	1	NA	Intergenic	LTR33|LTR|ERVL	-10997	NM_133979	102566	Mm.87676	NM_133979	ENSMUSG00000037949	Ano10	AI604832|Tmem16k	anoctamin 10	protein-coding
mm_43658.1	chr5	138622839	138622893	+	1	NA	promoter-TSS (NM_183025)	promoter-TSS (NM_183025)	7	NM_183025	243308	Mm.36612	NM_183025	ENSMUSG00000056014	A430033K04Rik	C86988	RIKEN cDNA A430033K04 gene	protein-coding
mm_156454.1	chrX	142739081	142739082	+	1	NA	promoter-TSS (NR_030523)	promoter-TSS (NR_030523)	81	NR_030523	723976		NR_030523	ENSMUSG00000076011	Mir652	Mirn652|miRX|mmu-mir-652	microRNA 652	ncRNA
mm_130870.1	chr15	102224461	102224465	-	1	NA	exon (NM_013566, exon 4 of 15)	exon (NM_013566, exon 4 of 15)	7472	NM_013566	16421	Mm.58	NM_013566	ENSMUSG00000001281	Itgb7	Ly69	integrin beta 7	protein-coding
mm_26903.1	chr3	19311270	19311314	-	1	NA	promoter-TSS (NM_001122759)	promoter-TSS (NM_001122759)	30	NM_001122759	18583	Mm.355614	NM_008802	ENSMUSG00000069094	Pde7a	AU015378|AW047537	phosphodiesterase 7A	protein-coding
mm_30607.1	chr4	6394915	6394966	+	1	NA	3' UTR (NM_016807, exon 9 of 9)	3' UTR (NM_016807, exon 9 of 9)	29260	NM_001098227	53378	Mm.247473	NM_016807	ENSMUSG00000028249	Sdcbp	MDA-9|Sycl|syntenin-1	syndecan binding protein	protein-coding
mm_69993.1	chr7	142385507	142385589	-	1	NA	exon (NM_009983, exon 2 of 9)	exon (NM_009983, exon 2 of 9)	2322	NM_009983	13033	Mm.231395	NM_009983	ENSMUSG00000007891	Ctsd	CD|CatD	cathepsin D	protein-coding
mm_37852.1	chr4	132212061	132212130	-	1	NA	5' UTR (NM_145393, exon 1 of 5)	5' UTR (NM_145393, exon 1 of 5)	161	NM_145393	213541	Mm.23998	NM_145393	ENSMUSG00000040025	Ythdf2	9430020E02Rik|HGRG8|NY-REN-2	YTH domain family 2	protein-coding
mm_55485.1	chr6	69185409	69185416	-	1	NA	Intergenic	Intergenic	141762	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_103856.1	chr11	83286681	83286699	-	1	NA	promoter-TSS (NM_001166028)	promoter-TSS (NM_001166028)	36	NM_001166028	237890	Mm.297670	NM_001166028	ENSMUSG00000082101	Slfn14	Gm20|Slfn14-ps	schlafen 14	protein-coding
mm_47176.1	chr5	120748756	120748772	-	1	NA	exon (NM_145227, exon 2 of 11)	exon (NM_145227, exon 2 of 11)	1084	NM_145227	246728	Mm.260926	NM_145227	ENSMUSG00000032690	Oas2	Oasl11	2'-5' oligoadenylate synthetase 2	protein-coding
mm_7870.1	chr1	132707305	132707317	-	1	NA	promoter-TSS (NM_001160318)	promoter-TSS (NM_001160318)	15	NM_001160318	269116	Mm.326702	NM_182716	ENSMUSG00000026442	Nfasc	AA387016|D430023G06Rik|NF|mKIAA0756	neurofascin	protein-coding
mm_78286.1	chr9	22156904	22156914	+	1	NA	promoter-TSS (NM_001082532)	promoter-TSS (NM_001082532)	63	NM_001082532	66268	Mm.28924	NM_025457	ENSMUSG00000010607	Pigyl	1810008A14Rik|PIG-Y|Pigy	phosphatidylinositol glycan anchor biosynthesis, class Y-like	protein-coding
mm_6089.1	chr1	63176806	63176817	-	1	NA	promoter-TSS (NM_001160039)	promoter-TSS (NM_001160039)	11	NM_145518	227197	Mm.290791	NM_145518	ENSMUSG00000025968	Ndufs1	5830412M15Rik|9930026A05Rik	NADH dehydrogenase (ubiquinone) Fe-S protein 1	protein-coding
mm_170788.1	chr2	175062412	175062429	+	1	NA	intron (NM_001085546, intron 3 of 3)	intron (NM_001085546, intron 3 of 3)	5349	NM_001085546	664987		NM_001085546	ENSMUSG00000078905	Gm14393	OTTMUSG00000016546	predicted gene 14393	protein-coding
mm_111918.1	chr12	108875542	108875550	-	1	NA	intron (NM_011710, intron 5 of 10)	intron (NM_011710, intron 5 of 10)	17652	NM_001164488	22375	Mm.38433	NM_011710	ENSMUSG00000021266	Wars	TrpRS|WRS	tryptophanyl-tRNA synthetase	protein-coding
mm_87549.1	chr10	53959282	53959319	+	1	NA	intron (NM_008548, intron 6 of 12)	MLT2B2|LTR|ERVL	116496	NM_008548	17155	Mm.117294	NM_008548	ENSMUSG00000003746	Man1a	Man1a1|PCR1	mannosidase 1, alpha	protein-coding
mm_16351.1	chr2	174346597	174346601	+	1	NA	non-coding (NR_003258, exon 13 of 13)	non-coding (NR_003258, exon 13 of 13)	16510	NM_001077510	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_17449.1	chr2	28555883	28555885	-	1	NA	TTS (NM_009885)	TTS (NM_009885)	7519	NM_009885	12613	Mm.236017	NM_009885	ENSMUSG00000026818	Cel	1810036E18Rik|BAL	carboxyl ester lipase	protein-coding
mm_28516.1	chr3	92584441	92584449	-	1	NA	exon (NM_008574, exon 2 of 2)	exon (NM_008574, exon 2 of 2)	4579	NM_008574	17235	Mm.331192	NM_008574		Smcp	Mcs|Mcsp	sperm mitochondria-associated cysteine-rich protein	protein-coding
mm_41467.1	chr5	91138044	91138045	+	1	NA	Intergenic	Intergenic	-1555	NM_009704	11839	Mm.8039	NM_009704	ENSMUSG00000029378	Areg	AR|Mcub|Sdgf	amphiregulin	protein-coding
mm_93425.1	chr10	108879747	108879751	-	1	NA	intron (NM_001252341, intron 3 of 11)	intron (NM_001252341, intron 3 of 11)	131226	NM_009306	20979	Mm.289702	NM_009306	ENSMUSG00000035864	Syt1	AW124717|G630098F17Rik|SytI	synaptotagmin I	protein-coding
mm_70791.1	chr8	22506573	22506591	+	1	NA	intron (NM_011394, intron 1 of 10)	intron (NM_011394, intron 1 of 10)	-29703	NM_001146117	102032	Mm.378231	NM_001012667	ENSMUSG00000031534	Smim19	AI316807|BG694986|EST-c39	small integral membrane protein 19	protein-coding
mm_26335.1	chr3	142546956	142546967	+	1	NA	3' UTR (NM_001083312, exon 11 of 11)	3' UTR (NM_001083312, exon 11 of 11)	-13091	NM_018734	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_133135.1	chr16	66288544	66288546	+	1	NA	Intergenic	Intergenic	-368573	NR_040512	75501	Mm.394300	NR_040512	ENSMUSG00000092599	1700010K23Rik	-	RIKEN cDNA 1700010K23 gene	ncRNA
mm_126471.1	chr15	81400133	81400215	+	1	NA	promoter-TSS (NM_133726)	promoter-TSS (NM_133726)	-14	NM_177310	321003	Mm.390833	NM_177310	ENSMUSG00000022401	Xpnpep3	APP3|E430012M05Rik	X-prolyl aminopeptidase 3, mitochondrial	protein-coding
mm_69305.1	chr7	128393628	128393644	-	1	NA	intron (NM_026418, intron 3 of 4)	intron (NM_026418, intron 3 of 4)	24536	NM_026418	67865	Mm.18635	NM_026418	ENSMUSG00000030844	Rgs10	2310010N19Rik	regulator of G-protein signalling 10	protein-coding
mm_24489.1	chr3	92339133	92339146	+	1	NA	promoter-TSS (NM_011470)	promoter-TSS (NM_011470)	-1	NM_011470	20758	Mm.87820	NM_011470	ENSMUSG00000042212	Sprr2d	-	small proline-rich protein 2D	protein-coding
mm_61196.1	chr7	63936627	63936636	+	1	NA	intron (NM_021366, intron 1 of 1)	intron (NM_021366, intron 1 of 1)	2284	NM_021366	50794	Mm.240473	NM_021366	ENSMUSG00000052040	Klf13	0610043C13Rik|9430029L20Rik|Bteb3|FKLF-2|FKLF2|NSLP1|RFLAT-1|RFLAT1	Kruppel-like factor 13	protein-coding
mm_97912.1	chr11	83500109	83500117	+	1	NA	intron (NM_027427, intron 10 of 15)	intron (NM_027427, intron 10 of 15)	21986	NM_001045543	629303	Mm.390417	NM_001045543	ENSMUSG00000018925	Heatr9	Gm11435|OTTMUSG00000000990	HEAT repeat containing 9	protein-coding
mm_80347.1	chr9	75174062	75174072	+	1	NA	exon (NM_010864, exon 22 of 41)	exon (NM_010864, exon 22 of 41)	-57947	NM_001081322	208943	Mm.41339	NM_001081322	ENSMUSG00000033590	Myo5c	9130003O20Rik|BB085560|C330029I24	myosin VC	protein-coding
mm_94719.1	chr11	20594042	20594044	+	1	NA	intron (NM_021372, intron 1 of 1)	intron (NM_021372, intron 1 of 1)	-37934	NM_001038625	58172	Mm.339676	NM_021372	ENSMUSG00000049800	Sertad2	AB041541|AU021878|Kiaa0127|MNCb-1504|SEI-2|Sei2|TRIP-Br2|mKIAA0127	SERTA domain containing 2	protein-coding
mm_9873.1	chr1	185085952	185085968	-	1	NA	Intergenic	ORR1C2|LTR|ERVL-MaLR	-86411	NM_145515	226778	Mm.7445	NM_145515	ENSMUSG00000026620	Mark1	AW491150|B930025N23Rik|Emk3|Par-1c|mKIAA1477|mPar-1c	MAP/microtubule affinity regulating kinase 1	protein-coding
mm_102147.1	chr11	53632142	53632168	-	1	NA	exon (NM_008355, exon 4 of 4)	exon (NM_008355, exon 4 of 4)	2547	NM_008355	16163	Mm.1284	NM_008355	ENSMUSG00000020383	Il13	Il-13	interleukin 13	protein-coding
mm_166576.1	chr6	52118402	52118402	+	1	NA	Intergenic	Intergenic	15453	NR_110440	102635415	Mm.333063	NR_110440	ENSMUSG00000085412	Halr1	Gm15055|Haunt|Linchoxa1|OTTMUSG00000018881|linc-Evx1|linc-Hoxa1|linc1547	Hoxa adjacent long noncoding RNA 1	ncRNA
mm_105762.1	chr11	109580869	109580881	-	1	NA	intron (NM_145940, intron 8 of 12)	intron (NM_145940, intron 8 of 12)	30514	NM_145940	52639	Mm.35817	NM_145940	ENSMUSG00000041895	Wipi1	4930533H01Rik|AW411817|D11Ertd498e	WD repeat domain, phosphoinositide interacting 1	protein-coding
mm_81243.1	chr9	107961505	107961507	+	1	NA	intron (NM_011634, intron 6 of 14)	intron (NM_011634, intron 6 of 14)	10543	NM_011634	22036	Mm.297870	NM_011634	ENSMUSG00000032586	Traip	Trip	TRAF-interacting protein	protein-coding
mm_66482.1	chr7	45017241	45017255	-	1	NA	promoter-TSS (NM_009101)	promoter-TSS (NM_009101)	-759	NM_009101	20130	Mm.389894	NM_009101	ENSMUSG00000038387	Rras	AI573426	related RAS viral (r-ras) oncogene	protein-coding
mm_152898.1	chr19	24961546	24961630	-	1	NA	promoter-TSS (NM_146097)	promoter-TSS (NM_146097)	28	NR_033744	226043	Mm.272127	NM_146097	ENSMUSG00000024878	Cbwd1	AV349248|BC018472	COBW domain containing 1	protein-coding
mm_48159.1	chr5	137152510	137152516	-	1	NA	Intergenic	Intergenic	-36306	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_3969.1	chr1	164152024	164152044	+	1	NA	exon (NM_007976, exon 1 of 25)	exon (NM_007976, exon 1 of 25)	183	NR_037987	100503816	Mm.398579	NR_037987	ENSMUSG00000086593	Gm16548	-	predicted gene 16548	ncRNA
mm_69364.1	chr7	130547274	130547350	-	1	NA	promoter-TSS (NM_001162855)	promoter-TSS (NM_001162855)	69	NM_001162855	67872	Mm.21714	NM_001162855	ENSMUSG00000040331	Nsmce4a	2410003A14Rik	NSE4 homolog A, SMC5-SMC6 complex component	protein-coding
mm_173034.1	chrX	105929295	105929295	-	1	NA	promoter-TSS (NM_009530)	promoter-TSS (NM_009530)	77	NM_009530	22589	Mm.10141	NM_009530	ENSMUSG00000031229	Atrx	4833408C14Rik|AI447451|ATR2|DXHXS6677E|HP1-BP38|Hp1bp2|Hp1bp38|MRXS3|RAD54L|Rad54|XH2|Xnp|ZNF-HX	alpha thalassemia/mental retardation syndrome X-linked	protein-coding
mm_37766.1	chr4	129696850	129696860	-	1	NA	promoter-TSS (NM_199305)	promoter-TSS (NM_199305)	-17	NM_199305	230770	Mm.257157	NM_199305	ENSMUSG00000053730	Tmem39b	6330509E05Rik|BC037095	transmembrane protein 39b	protein-coding
mm_127005.1	chr15	95800659	95800666	+	1	NA	intron (NM_175344, intron 1 of 19)	Lx8|LINE|L1	9819	NM_001253813	105722	Mm.38087	NM_175344	ENSMUSG00000064210	Ano6	2900059G15Rik|AA407480|AW554778|F730003B03Rik|Tmem16f	anoctamin 6	protein-coding
mm_81671.1	chr9	111029595	111029604	+	1	NA	exon (NM_008522, exon 12 of 17)	exon (NM_008522, exon 12 of 17)	10307	NM_008522	17002	Mm.282359	NM_008522	ENSMUSG00000032496	Ltf	Csp82|Lf|MMS10R|Ms10r	lactotransferrin	protein-coding
mm_143878.1	chr17	84187940	84187954	-	1	NA	promoter-TSS (NM_001001806)	promoter-TSS (NM_001001806)	0	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_146349.1	chr18	82554522	82554539	+	1	NA	promoter-TSS (NM_001025251)	promoter-TSS (NM_001025251)	22	NM_001025254	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_143776.1	chr17	81707600	81707600	-	1	NA	intron (NR_104580, intron 1 of 8)	intron (NR_104580, intron 1 of 8)	30787	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_128738.1	chr15	64304997	64305018	-	1	NA	intron (NM_010026, intron 3 of 30)	RMER4B|LTR|ERVK	7666	NM_001276462	13196	Mm.277236	NM_010026	ENSMUSG00000022377	Asap1	AV239055|DEF-1|Ddef1|PAP|mKIAA1249|s19	ArfGAP with SH3 domain, ankyrin repeat and PH domain1	protein-coding
mm_88669.1	chr10	80017668	80017687	+	1	NA	intron (NM_001347074, intron 1 of 22)	intron (NM_001347074, intron 1 of 22)	762	NM_001347074	70719	Mm.243954	NM_027521	ENSMUSG00000035697	Hmha1	6330406L22Rik|AW539505|Ha-1	histocompatibility (minor) HA-1	protein-coding
mm_142691.1	chr17	47754234	47754245	-	1	NA	intron (NM_001161723, intron 1 of 8)	intron (NM_001161723, intron 1 of 8)	16308	NM_001161723	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_14486.1	chr2	131855369	131855378	+	1	NA	3' UTR (NM_001166206, exon 2 of 2)	3' UTR (NM_001166206, exon 2 of 2)	4374	NM_001166206	71995	Mm.22	NM_028045	ENSMUSG00000037482	Erv3	1600014E20Rik|AA389086|AI426069|AI448024|D19349	endogenous retroviral sequence 3	protein-coding
mm_159665.1	chr4	152158867	152158867	+	1	NA	promoter-TSS (NM_008236)	promoter-TSS (NM_008236)	0	NM_001301805	15206	Mm.57038	NM_008236	ENSMUSG00000028940	Hes2	HES-2	hairy and enhancer of split 2 (Drosophila)	protein-coding
mm_145949.1	chr18	67401833	67401852	+	1	NA	exon (NM_026473, exon 4 of 4)	exon (NM_026473, exon 4 of 4)	11111	NM_026473	67951	Mm.181860	NM_026473	ENSMUSG00000001473	Tubb6	2310057H16Rik|BB220206	tubulin, beta 6 class V	protein-coding
mm_129108.1	chr15	76051917	76051942	-	1	NA	intron (NM_001310543, intron 24 of 35)	intron (NM_001310543, intron 24 of 35)	12959	NR_105917	102466772		NR_105917	ENSMUSG00000098451	Mir6952	Gm27948|mmu-mir-6952	microRNA 6952	ncRNA
mm_56870.1	chr6	118562227	118562280	-	1	NA	promoter-TSS (NM_001081112)	promoter-TSS (NM_001081112)	3	NM_001081112	232339	Mm.276116	NM_001081112	ENSMUSG00000007827	Ankrd26	5730521P14Rik|BC008111|mKIAA1074	ankyrin repeat domain 26	protein-coding
mm_146237.1	chr18	77186060	77186078	+	1	NA	5' UTR (NM_013666, exon 1 of 8)	5' UTR (NM_013666, exon 1 of 8)	222	NM_013666	225742	Mm.365178	NM_013666	ENSMUSG00000025425	St8sia5	ST8SiaV|Siat8e	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 5	protein-coding
mm_24988.1	chr3	97032424	97032432	+	1	NA	promoter-TSS (NM_008121)	promoter-TSS (NM_008121)	26	NM_008121	14613	Mm.281816	NM_008121	ENSMUSG00000057123	Gja5	5730555N10Rik|Cnx40|Cx40|Gja-5	gap junction protein, alpha 5	protein-coding
mm_21275.1	chr2	156887173	156887225	-	1	NA	promoter-TSS (NM_029983)	promoter-TSS (NM_029983)	-121	NM_029983	77799	Mm.29264	NM_029983	ENSMUSG00000027636	Sla2	A930009E21Rik|AI430952|SLAP-2|SLAP2	Src-like-adaptor 2	protein-coding
mm_80260.1	chr9	72842742	72842774	+	1	NA	exon (NM_175485, exon 3 of 20)	exon (NM_175485, exon 3 of 20)	35484	NM_175485	235472	Mm.31696	NM_175485	ENSMUSG00000036030	Prtg	A230098A12Rik|Igdcc5	protogenin	protein-coding
mm_7199.1	chr1	93015973	93016048	-	1	NA	3' UTR (NM_008440, exon 48 of 48)	3' UTR (NM_008440, exon 48 of 48)	9676	NM_001159658	208760	Mm.235537	NM_177587	ENSMUSG00000045091	Aqp12	AB084104|mAQP12	aquaporin 12	protein-coding
mm_138674.1	chr17	35909730	35909755	+	1	NA	TTS (NM_025878)	TTS (NM_025878)	326	NM_001142745	73242	Mm.273155	NM_028476	ENSMUSG00000024426	Atat1	0610011P08Rik|2610008K08Rik|2610110G12Rik|3110080J08Rik|Mec17|TAT	alpha tubulin acetyltransferase 1	protein-coding
mm_156864.1	chrX	164436943	164436951	+	1	NA	promoter-TSS (NM_026853)	promoter-TSS (NM_026853)	-47	NM_026853	68854	Mm.33225	NM_026853	ENSMUSG00000031382	Asb11	1110067L12Rik|1600009D24Rik	ankyrin repeat and SOCS box-containing 11	protein-coding
mm_123707.1	chr14	69805466	69805504	-	1	NA	promoter-TSS (NM_153514)	promoter-TSS (NM_153514)	60	NM_153514	246710	Mm.102367	NM_153514	ENSMUSG00000022075	Rhobtb2	Dbc2|E130206H14Rik|mKIAA0717	Rho-related BTB domain containing 2	protein-coding
mm_140939.1	chr17	24443094	24443109	-	1	NA	promoter-TSS (NM_025718)	promoter-TSS (NM_025718)	0	NM_025718	66705	Mm.29017	NM_025718	ENSMUSG00000024136	Dnase1l2	4733401H14Rik	deoxyribonuclease 1-like 2	protein-coding
mm_22087.1	chr2	168767092	168767104	-	1	NA	5' UTR (NM_201396, exon 1 of 3)	5' UTR (NM_201396, exon 1 of 3)	103	NM_201395	99377	Mm.434054	NM_175303	ENSMUSG00000027547	Sall4	5730441M18Rik|AA407717|AL022809|AW536104|C330011P20Rik|C78083|C78563|Tex20	sal-like 4 (Drosophila)	protein-coding
mm_112240.1	chr12	113482446	113482470	-	1	NA	Intergenic	Intergenic	-7107	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_171267.1	chr3	88284869	88284875	-	1	NA	intron (NM_029801, intron 3 of 3)	RLTR10A|LTR|ERVK	11966	NM_029801	76927	Mm.273330	NM_029801	ENSMUSG00000010538	Tsacc	1700021C14Rik|SIP	TSSK6 activating co-chaperone	protein-coding
mm_65376.1	chr7	25087476	25087488	-	1	NA	Intergenic	Intergenic	9693	NR_105855	102465968		NR_105855	ENSMUSG00000098441	Mir6537	Gm27808|mmu-mir-6537	microRNA 6537	ncRNA
mm_47259.1	chr5	121711456	121711479	-	1	NA	promoter-TSS (NM_009125)	promoter-TSS (NM_009125)	-142	NM_009125	20239	Mm.260900	NM_009125	ENSMUSG00000042605	Atxn2	9630045M23Rik|ATX2|AW544490|Sca2	ataxin 2	protein-coding
mm_126502.1	chr15	81772334	81772346	+	1	NA	intron (NM_001081016, intron 5 of 22)	intron (NM_001081016, intron 5 of 22)	27492	NM_001081016	20286	Mm.432075	NM_001081016	ENSMUSG00000022390	Zc3h7b	Gm627|Scrg3|Zc2h7b|mKIAA1031	zinc finger CCCH type containing 7B	protein-coding
mm_31391.1	chr4	48043841	48043849	+	1	NA	Intergenic	Intergenic	-1460	NM_015743	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_131413.1	chr16	14501873	14501883	+	1	NA	Intergenic	Intergenic	-60439	NR_033556	545280	Mm.123679	NR_033556	ENSMUSG00000075395	A630010A05Rik	-	RIKEN cDNA A630010A05 gene	ncRNA
mm_136932.1	chr17	13874917	13874926	+	1	NA	intron (NM_010806, intron 22 of 32)	intron (NM_010806, intron 22 of 32)	-73452	NM_001122977	635895	Mm.388844	NM_001122977	ENSMUSG00000067941	Gm7168	EG635895	predicted gene 7168	protein-coding
mm_18531.1	chr2	63184555	63184566	-	1	NA	promoter-TSS (NM_133207)	promoter-TSS (NM_133207)	-273	NM_133207	170738	Mm.242532	NM_133207	ENSMUSG00000059742	Kcnh7	9330137I11Rik|Kv11.3|erg3	potassium voltage-gated channel, subfamily H (eag-related), member 7	protein-coding
mm_91960.1	chr10	61147626	61147644	-	1	NA	promoter-TSS (NM_001316673)	promoter-TSS (NM_001316673)	49	NM_009163	20397	Mm.412319	NM_009163	ENSMUSG00000020097	Sgpl1	AI428538|D10Xrf456|S1PL|Spl	sphingosine phosphate lyase 1	protein-coding
mm_25979.1	chr3	133310089	133310091	+	1	NA	promoter-TSS (NM_001293641)	promoter-TSS (NM_001293641)	-20	NM_001293641	74776	Mm.210305	NM_146141	ENSMUSG00000028013	Ppa2	1110013G13Rik|Sid6306	pyrophosphatase (inorganic) 2	protein-coding
mm_65489.1	chr7	25687265	25687279	-	1	NA	TTS (NM_172148)	TTS (NM_172148)	270	NM_011577	21803	Mm.248380	NM_011577	ENSMUSG00000002603	Tgfb1	TGF-beta1|TGFbeta1|Tgfb|Tgfb-1	transforming growth factor, beta 1	protein-coding
mm_69174.1	chr7	127218010	127218022	-	1	NA	exon (NM_017461, exon 3 of 11)	exon (NM_017461, exon 3 of 11)	429	NM_017461	54204	Mm.18	NM_017461	ENSMUSG00000000486	Sept1	Diff6|Pnutl3	septin 1	protein-coding
mm_151094.1	chr19	47834937	47834945	+	1	NA	intron (NM_027559, intron 2 of 37)	PB1|SINE|Alu	2420	NM_027559	100048534	Mm.29457	NM_027559	ENSMUSG00000044948	Cfap43	4632415N18Rik|4930428C11Rik|4930463G05Rik|AI429486|D19Ertd652e|Wdr96	cilia and flagella associated protein 43	protein-coding
mm_27125.1	chr3	31690585	31690592	-	1	NA	Intergenic	Intergenic	-212115	NM_028231	72413	Mm.64790	NM_028231	ENSMUSG00000037610	Kcnmb2	2700049B16Rik|3110031N04Rik	potassium large conductance calcium-activated channel, subfamily M, beta member 2	protein-coding
mm_88038.1	chr10	67535664	67535673	+	1	NA	Intergenic	CpG	-2201	NM_010118	13654	Mm.290421	NM_010118	ENSMUSG00000037868	Egr2	Egr-2|Krox-20|Krox20|NGF1-B|Zfp-25|Zfp-6	early growth response 2	protein-coding
mm_22200.1	chr2	173436722	173436730	-	1	NA	Intergenic	L1M4|LINE|L1	-85866	NM_028158	72221	Mm.46132	NM_028158	ENSMUSG00000027518	1700021F07Rik	-	RIKEN cDNA 1700021F07 gene	protein-coding
mm_134916.1	chr16	30310825	30310833	-	1	NA	promoter-TSS (NM_008148)	promoter-TSS (NM_008148)	-48	NM_008148	14729	Mm.3519	NM_008148	ENSMUSG00000047953	Gp5	GPV	glycoprotein 5 (platelet)	protein-coding
mm_9205.1	chr1	171229736	171229746	-	1	NA	3' UTR (NM_010185, exon 5 of 5)	3' UTR (NM_010185, exon 5 of 5)	4608	NM_010185	14127	Mm.22673	NM_010185	ENSMUSG00000058715	Fcer1g	AI573376|CD23|FcR-gamma|FcR[g]|FcRgamma|Fce1g|FcepsilonRI|Ly-50	Fc receptor, IgE, high affinity I, gamma polypeptide	protein-coding
mm_56570.1	chr6	102564435	102564456	-	1	NA	Intergenic	CpG	-99778	NM_008779	18488	Mm.435479	NM_008779	ENSMUSG00000030075	Cntn3	Pang	contactin 3	protein-coding
mm_66020.1	chr7	30603579	30603585	-	1	NA	3' UTR (NM_026815, exon 8 of 8)	3' UTR (NM_026815, exon 8 of 8)	9152	NM_026815	109637	Mm.25471	NM_026815	ENSMUSG00000006313	Upk1a	1110031P12Rik|AU019298|C87192|Tspan21|Upk1	uroplakin 1A	protein-coding
mm_24477.1	chr3	90696035	90696041	+	1	NA	promoter-TSS (NM_001281852)	promoter-TSS (NM_001281852)	-317	NM_009114	20202	Mm.2128	NM_009114	ENSMUSG00000056071	S100a9	60B8Ag|AW546964|BEE22|Cagb|GAGB|L1Ag|MRP14|p14	S100 calcium binding protein A9 (calgranulin B)	protein-coding
mm_84696.1	chr9	72407115	72407125	-	1	NA	Intergenic	Intergenic	-31409	NM_008613	17427	Mm.387671	NM_008613	ENSMUSG00000032221	Mns1	AW546487	meiosis-specific nuclear structural protein 1	protein-coding
mm_56408.1	chr6	97205521	97205531	-	1	NA	intron (NM_001301858, intron 1 of 16)	CpG	121	NM_001301858	22200	Mm.277626	NM_011666	ENSMUSG00000030061	Uba3	A830034N06Rik|AI256736|AI848246|AW546539|Ube1c	ubiquitin-like modifier activating enzyme 3	protein-coding
mm_68178.1	chr7	103851818	103851824	-	1	NA	TTS (NM_008221)	TTS (NM_008221)	1386	NM_008221	15135	Mm.440164	NM_008221	ENSMUSG00000052187	Hbb-y	Ey|Hby	hemoglobin Y, beta-like embryonic chain	protein-coding
mm_90494.1	chr10	128033633	128033675	+	1	NA	Intergenic	Intergenic	-1692	NM_013608	17938	Mm.3746	NM_013608	ENSMUSG00000061315	Naca	AL022831|AL024382|Gm1878|mKIAA0363|skNAC	nascent polypeptide-associated complex alpha polypeptide	protein-coding
mm_87418.1	chr10	50620801	50620807	+	1	NA	intron (NM_198007, intron 4 of 41)	intron (NM_198007, intron 4 of 41)	28135	NM_198007	77987	Mm.222497	NM_198007	ENSMUSG00000038774	Ascc3	ASC1p200|B630009I04Rik|BC023451|D430001L07Rik|D630041L21|Helic1|RNAH	activating signal cointegrator 1 complex subunit 3	protein-coding
mm_48937.1	chr6	4538672	4538690	+	1	NA	exon (NM_007743, exon 50 of 52)	exon (NM_007743, exon 50 of 52)	33063	NM_007743	12843	Mm.277792	NM_007743	ENSMUSG00000029661	Col1a2	AA960264|AI325291|Col1a-2|Cola-2|Cola2|oim	collagen, type I, alpha 2	protein-coding
mm_99478.1	chr11	102604520	102604532	+	1	NA	promoter-TSS (NM_020510)	promoter-TSS (NM_020510)	95	NM_020510	57265	Mm.36416	NM_020510	ENSMUSG00000050288	Fzd2	AL033370|AW456835|Fz10|Fzd10|Mfz10|Mfz10a	frizzled class receptor 2	protein-coding
mm_137762.1	chr17	29489801	29489817	+	1	NA	Intergenic	Intergenic	-1236	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_70134.1	chr7	143242569	143242583	-	1	NA	non-coding (NR_001461, exon 1 of 1)	non-coding (NR_001461, exon 1 of 1)	53971	NR_001461	63830	Mm.356096	NR_001461	ENSMUSG00000101609	Kcnq1ot1	Kvlqt1-as|Lit1|Tssc8	KCNQ1 overlapping transcript 1	ncRNA
mm_21557.1	chr2	164087590	164087593	-	1	NA	intron (NM_021420, intron 4 of 10)	intron (NM_021420, intron 4 of 10)	13413	NM_021420	58231	Mm.234472	NM_021420	ENSMUSG00000018209	Stk4	AI447339|AU020804|Kas-2|Mst1|Ysk3	serine/threonine kinase 4	protein-coding
mm_36811.1	chr4	103215137	103215141	-	1	NA	promoter-TSS (NM_177732)	promoter-TSS (NM_177732)	-255	NM_177732	242585	Mm.281800	NM_177732	ENSMUSG00000028521	Slc35d1	AI834976|C330011J09|UGTREL7|mKIAA0260	solute carrier family 35 (UDP-glucuronic acid/UDP-N-acetylgalactosamine dual transporter), member D1	protein-coding
mm_96112.1	chr11	60699685	60699710	+	1	NA	promoter-TSS (NM_001159405)	promoter-TSS (NM_001159405)	7	NM_008502	16897	Mm.285453	NM_008502	ENSMUSG00000020536	Llgl1	AI325176|Lgl1|Llglh|Mgl1	lethal giant larvae homolog 1 (Drosophila)	protein-coding
mm_1845.1	chr1	82924916	82924917	+	1	NA	Intergenic	Intergenic	85456	NM_001347077	15463	Mm.392569	NM_010472	ENSMUSG00000026159	Agfg1	AU045498|C130049H11Rik|C85612|D730048C23Rik|Hrb|RAB|Rip	ArfGAP with FG repeats 1	protein-coding
mm_83373.1	chr9	44525969	44525972	-	1	NA	intron (NM_007551, intron 1 of 1)	B1_Mur4|SINE|Alu	451	NM_007551	12145	Mm.6246	NM_007551	ENSMUSG00000047880	Cxcr5	Blr1|CXC-R5|CXCR-5|Gpcr6|MDR15	chemokine (C-X-C motif) receptor 5	protein-coding
mm_54423.1	chr6	33055934	33055950	-	1	NA	intron (NM_025336, intron 1 of 7)	intron (NM_025336, intron 1 of 7)	4210	NM_025336	66075	Mm.21501	NM_025336	ENSMUSG00000053768	Chchd3	0610041L09Rik|1700039J09Rik|AW558177	coiled-coil-helix-coiled-coil-helix domain containing 3	protein-coding
mm_108990.1	chr12	102877291	102877313	+	1	NA	intron (NM_172806, intron 1 of 11)	intron (NM_172806, intron 1 of 11)	1104	NM_172806	238386	Mm.63456	NM_172806	ENSMUSG00000041702	Btbd7	5730507E09Rik|8030448M07|E130118E17Rik|FUP1|mKIAA1525	BTB (POZ) domain containing 7	protein-coding
mm_24565.1	chr3	93443923	93443929	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	1596	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_64514.1	chr7	143823136	143823151	+	1	NA	promoter-TSS (NM_007856)	promoter-TSS (NM_007856)	-24	NM_007856	13360	Mm.249342	NM_007856	ENSMUSG00000058454	Dhcr7	AA409147	7-dehydrocholesterol reductase	protein-coding
mm_148096.1	chr18	73836844	73836847	-	1	NA	Intergenic	RMER6A|LTR|ERVK	-21453	NM_145494	107029	Mm.36817	NM_145494	ENSMUSG00000024556	Me2	AW120568|D030040L20Rik|NAD-ME	malic enzyme 2, NAD(+)-dependent, mitochondrial	protein-coding
mm_24966.1	chr3	96727581	96727608	+	1	NA	promoter-TSS (NM_026406)	promoter-TSS (NM_026406)	-17	NM_026406	67845	Mm.386792	NM_026406	ENSMUSG00000028098	Rnf115	2610028E05Rik|AU042696|Zfp364	ring finger protein 115	protein-coding
mm_56628.1	chr6	112900385	112900396	-	1	NA	intron (NM_080448, intron 1 of 21)	intron (NM_080448, intron 1 of 21)	46876	NM_080448	259302	Mm.236401	NM_080448	ENSMUSG00000030257	Srgap3	AI452337|Arhgap14|D130026O08Rik|Gbi|MEGAP|WRP|mKIAA0411	SLIT-ROBO Rho GTPase activating protein 3	protein-coding
mm_17565.1	chr2	30205729	30205741	-	1	NA	promoter-TSS (NM_172404)	promoter-TSS (NM_172404)	-36	NM_172404	70266	Mm.216089	NM_172404	ENSMUSG00000039648	Kyat1	2010009K05Rik|AI182306|Ccbl1|Gtk|Kat1|KatI	kynurenine aminotransferase 1	protein-coding
mm_22518.1	chr3	7626905	7626942	+	1	NA	Intergenic	Intergenic	-13163	NM_001313888	16196	Mm.3825	NM_008371	ENSMUSG00000040329	Il7	A630026I06Rik|Il-7|hlb368	interleukin 7	protein-coding
mm_52767.1	chr6	121027501	121027536	+	1	NA	intron (NR_138097, intron 11 of 18)	intron (NR_138097, intron 11 of 18)	-36946	NR_138098	100043793	Mm.448053	NR_138098		Gm4651	-	predicted gene 4651	ncRNA
mm_31694.1	chr4	62388724	62388744	+	1	NA	exon (NM_175090, exon 5 of 5)	exon (NM_175090, exon 5 of 5)	19889	NM_139291	66440	Mm.109930	NM_139291	ENSMUSG00000066149	Cdc26	2010012C09Rik	cell division cycle 26	protein-coding
mm_134151.1	chr16	10785526	10785543	-	1	NA	promoter-TSS (NM_001271603)	promoter-TSS (NM_001271603)	2	NM_009896	12703	Mm.130	NM_009896	ENSMUSG00000038037	Socs1	Cish1|Cish7|JAB|SOCS-1|SSI-1	suppressor of cytokine signaling 1	protein-coding
mm_63472.1	chr7	127603191	127603209	+	1	NA	TTS (NR_027915)	TTS (NR_027915)	1245	NR_027915	68232	Mm.347960	NM_026628	ENSMUSG00000099579	1700120K04Rik	-	RIKEN cDNA 1700120K04 gene	ncRNA
mm_114293.1	chr13	58807885	58807902	+	1	NA	5' UTR (NM_001025074, exon 1 of 18)	5' UTR (NM_001025074, exon 1 of 18)	196	NM_001025074	18212	Mm.130054	NM_008745	ENSMUSG00000055254	Ntrk2	GP145-TrkB/GP95-TrkB|Tkrb|trk-B|trkB	neurotrophic tyrosine kinase, receptor, type 2	protein-coding
mm_1453.1	chr1	67230691	67230697	+	1	NA	3' UTR (NM_001080809, exon 38 of 38)	3' UTR (NM_001080809, exon 38 of 38)	107667	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_33582.1	chr4	132535543	132535585	+	1	NA	promoter-TSS (NM_172400)	promoter-TSS (NM_172400)	5	NM_172400	68598	Mm.29685	NM_172400	ENSMUSG00000054405	Dnajc8	1110021D09Rik|2010009J04Rik|AL024084|AU019262|AU044514	DnaJ heat shock protein family (Hsp40) member C8	protein-coding
mm_159860.1	chr5	140611869	140611869	+	1	NA	exon (NM_008494, exon 2 of 8)	exon (NM_008494, exon 2 of 8)	4528	NM_008494	16848	Mm.12834	NM_008494	ENSMUSG00000029570	Lfng	AW061165	LFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	protein-coding
mm_170980.1	chr2	71420320	71420324	+	1	NA	exon (NM_026115, exon 5 of 11)	exon (NM_026115, exon 5 of 11)	5846	NR_039557	100628577		NR_039557	ENSMUSG00000093061	Mir5098	mmu-mir-5098|mu-mir-5098	microRNA 5098	ncRNA
mm_80449.1	chr9	77979831	77979841	+	1	NA	exon (NM_134255, exon 6 of 8)	exon (NM_134255, exon 6 of 8)	62471	NM_134255	68801	Mm.430736	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	ELOVL family member 5, elongation of long chain fatty acids (yeast)	protein-coding
mm_163074.1	chr11	67695402	67695406	+	1	NA	promoter-TSS (NM_009038)	promoter-TSS (NM_009038)	78	NM_009038	19674	Mm.439726	NM_009038	ENSMUSG00000020907	Rcvrn	CAR|S-modulin	recoverin	protein-coding
mm_6431.1	chr1	73962943	73962953	-	1	NA	intron (NM_027884, intron 18 of 34)	intron (NM_027884, intron 18 of 34)	-98482	NR_045311	109198	Mm.359721	NR_045311	ENSMUSG00000100301	6030407O03Rik	-	RIKEN cDNA 6030407O03 gene	ncRNA
mm_27964.1	chr3	80688320	80688334	-	1	NA	3' UTR (NM_013540, exon 16 of 16)	3' UTR (NM_013540, exon 16 of 16)	114464	NM_013540	14800	Mm.220224	NM_013540	ENSMUSG00000033981	Gria2	GluA2|GluR-B|Glur-2|Glur2	glutamate receptor, ionotropic, AMPA2 (alpha 2)	protein-coding
mm_70562.1	chr8	13105619	13105627	+	1	NA	promoter-TSS (NM_178708)	promoter-TSS (NM_178708)	-98	NM_146207	99375	Mm.212861	NM_146207	ENSMUSG00000031446	Cul4a	2810470J21Rik|AW495282	cullin 4A	protein-coding
mm_10694.1	chr2	22622475	22622487	+	1	NA	5' UTR (NM_008078, exon 1 of 16)	5' UTR (NM_008078, exon 1 of 16)	154	NM_008078	14417	Mm.4784	NM_008078	ENSMUSG00000026787	Gad2	6330404F12Rik|GAD(65)|GAD65|Gad-2	glutamic acid decarboxylase 2	protein-coding
mm_154484.1	chrM	4634	4650	-	1	NA	NA	Intergenic	NA	NA								
mm_63355.1	chr7	126979034	126979070	+	1	NA	intron (NM_026638, intron 4 of 5)	intron (NM_026638, intron 4 of 5)	3138	NM_001347656	52858	Mm.28219	NM_026638	ENSMUSG00000030682	Cdipt	9530042F15Rik|D7Bwg0575e|Pis|Pis1	CDP-diacylglycerol--inositol 3-phosphatidyltransferase (phosphatidylinositol synthase)	protein-coding
mm_34913.1	chr4	155705323	155705349	+	1	NA	5' UTR (NM_026899, exon 1 of 5)	5' UTR (NM_026899, exon 1 of 5)	521	NM_026899	68991	Mm.294770	NM_026899	ENSMUSG00000029038	Ssu72	1190002E22Rik|1500011L16Rik|2610101M12Rik	Ssu72 RNA polymerase II CTD phosphatase homolog (yeast)	protein-coding
mm_68738.1	chr7	121064169	121064184	-	1	NA	3' UTR (NM_030691, exon 6 of 6)	3' UTR (NM_030691, exon 6 of 6)	10354	NM_030691	80719	Mm.160384	NM_030691	ENSMUSG00000035004	Igsf6	-	immunoglobulin superfamily, member 6	protein-coding
mm_12940.1	chr2	85136449	85136459	+	1	NA	promoter-TSS (NM_011784)	promoter-TSS (NM_011784)	94	NM_011784	23796	Mm.29368	NM_011784	ENSMUSG00000044338	Aplnr	APJ|Agtrl1|msr/apj	apelin receptor	protein-coding
mm_32393.1	chr4	106622529	106622542	+	1	NA	promoter-TSS (NM_177667)	promoter-TSS (NM_177667)	86	NM_177667	230576	Mm.41945	NM_177667	ENSMUSG00000034919	Ttc22	4732467L16Rik	tetratricopeptide repeat domain 22	protein-coding
mm_63331.1	chr7	126950506	126950516	+	1	NA	promoter-TSS (NM_001039645)	promoter-TSS (NM_001039645)	-24	NM_144926	233878	Mm.283926	NM_144926	ENSMUSG00000030683	Sez6l2	AI835913|AW121566|BSRP-A|Psk1	seizure related 6 homolog like 2	protein-coding
mm_45207.1	chr5	52992256	52992260	-	1	NA	promoter-TSS (NR_040413)	promoter-TSS (NR_040413)	34	NR_040413	75954	Mm.258937	NR_040413	ENSMUSG00000106352	5033403H07Rik	-	RIKEN cDNA 5033403H07 gene	ncRNA
mm_145963.1	chr18	67775744	67775747	+	1	NA	TTS (NR_045376)	TTS (NR_045376)	869	NM_001039088	72124	Mm.307315	NM_028112	ENSMUSG00000079614	Seh1l	2610007A16Rik|AW540070|SEC13L|SEH1A|SEH1B|Seh1	SEH1-like (S. cerevisiae	protein-coding
mm_60899.1	chr7	46427630	46427644	+	1	NA	exon (NM_001112739, exon 2 of 4)	exon (NM_001112739, exon 2 of 4)	31169	NM_001112739	16502	Mm.249386	NM_008421	ENSMUSG00000058975	Kcnc1	C230009H10Rik|KShIIIB|KV4|Kcr2-1|Kv3.1|NGK2|Shaw	potassium voltage gated channel, Shaw-related subfamily, member 1	protein-coding
mm_51035.1	chr6	65590455	65590459	+	1	NA	promoter-TSS (NM_001001495)	promoter-TSS (NM_001001495)	59	NM_001001495	414084	Mm.117558	NM_001001495	ENSMUSG00000044162	Tnip3	9030611K07Rik|ABIN-3|LIND	TNFAIP3 interacting protein 3	protein-coding
mm_53817.1	chr6	147073499	147073525	+	1	NA	Intergenic	Intergenic	13520	NM_001034903	545893	Mm.224739	NM_001034903	ENSMUSG00000072662	Mansc4	A430079E08|EG545893|Gm5887	MANSC domain containing 4	protein-coding
mm_70263.1	chr8	3536819	3536825	+	1	NA	intron (NM_001122818, intron 26 of 34)	intron (NM_001122818, intron 26 of 34)	21438	NM_015801	50767	Mm.23085	NM_015801	ENSMUSG00000004565	Pnpla6	AI661849|MSws|Nte	patatin-like phospholipase domain containing 6	protein-coding
mm_140507.1	chr17	5440230	5440263	-	1	NA	promoter-TSS (NM_027457)	promoter-TSS (NM_027457)	14	NM_027457	70544	Mm.46654	NM_027457	ENSMUSG00000004945	Tmem242	1110008A10Rik|2310046K16Rik|5730437N04Rik	transmembrane protein 242	protein-coding
mm_150988.1	chr19	46516254	46516309	+	1	NA	3' UTR (NM_053100, exon 6 of 6)	3' UTR (NM_053100, exon 6 of 6)	14633	NM_053100	93679	Mm.392177	NM_053100	ENSMUSG00000025034	Trim8	AA408830|BB006755|GERP|Rnf27	tripartite motif-containing 8	protein-coding
mm_22733.1	chr3	19691933	19691944	+	1	NA	TTS (NM_001081281)	TTS (NM_001081281)	3458	NM_205769	12918	Mm.290689	NM_205769	ENSMUSG00000049796	Crh	CRF|Gm1347	corticotropin releasing hormone	protein-coding
mm_47000.1	chr5	115348653	115348663	-	1	NA	exon (NM_007748, exon 2 of 3)	exon (NM_007748, exon 2 of 3)	297	NM_007748	12861	Mm.43415	NM_007748	ENSMUSG00000041697	Cox6a1	VIaL	cytochrome c oxidase subunit VIa polypeptide 1	protein-coding
mm_54396.1	chr6	31399401	31399420	-	1	NA	promoter-TSS (NR_040300)	promoter-TSS (NR_040300)	582	NM_013791	27418	Mm.238038	NM_013791	ENSMUSG00000025609	Mkln1	A130067F06Rik|AU015903|BB154892	muskelin 1, intracellular mediator containing kelch motifs	protein-coding
mm_169886.1	chr16	45056379	45056379	-	1	NA	Intergenic	Intergenic	-37674	NM_026439	67896	Mm.181074	NM_026439	ENSMUSG00000022665	Ccdc80	2610001E17Rik|DRO1|Ssg1|Urb	coiled-coil domain containing 80	protein-coding
mm_139937.1	chr17	71107530	71107541	+	1	NA	intron (NM_010867, intron 27 of 37)	intron (NM_010867, intron 27 of 37)	-76443	NM_022882	64898	Mm.227924	NM_022882	ENSMUSG00000024052	Lpin2	2610511G02Rik|AI481352|AW742896	lipin 2	protein-coding
mm_41032.1	chr5	86071546	86071562	+	1	NA	promoter-TSS (NM_019992)	promoter-TSS (NM_019992)	-192	NM_019992	56792	Mm.131237	NM_019992	ENSMUSG00000029254	Stap1	AI586015|Brdg1|STAP-1	signal transducing adaptor family member 1	protein-coding
mm_70930.1	chr8	25813614	25813633	+	1	NA	3' UTR (NM_011485, exon 7 of 7)	3' UTR (NM_011485, exon 7 of 7)	5149	NM_011485	20845	Mm.293314	NM_011485	ENSMUSG00000031574	Star	AV363654|D8Ertd419e|stARD1	steroidogenic acute regulatory protein	protein-coding
mm_145440.1	chr18	59063690	59063700	+	1	NA	intron (NM_173759, intron 1 of 2)	intron (NM_173759, intron 1 of 2)	1314	NR_033765	225583	Mm.209711	NM_173759	ENSMUSG00000050875	A730017C20Rik	-	RIKEN cDNA A730017C20 gene	protein-coding
mm_80084.1	chr9	70207343	70207356	+	1	NA	promoter-TSS (NM_181072)	promoter-TSS (NM_181072)	-1	NM_181072	71602	Mm.249311	NM_181072	ENSMUSG00000032220	Myo1e	2310020N23Rik|9130023P14Rik|AA407778|myosin-1e|myr 3	myosin IE	protein-coding
mm_91366.1	chr10	29313376	29313409	-	1	NA	promoter-TSS (NM_025855)	promoter-TSS (NM_025855)	-108	NM_025855	52665	Mm.28930	NM_025855	ENSMUSG00000019883	Echdc1	1700028A24Rik|AI314462|AI930038|D10Ertd667e|MMCD	enoyl Coenzyme A hydratase domain containing 1	protein-coding
mm_71339.1	chr8	45579943	45579947	+	1	NA	intron (NM_172752, intron 1 of 22)	RMER1B|Other|Other	-47806	NM_001310707	234214	Mm.211096	NM_172752	ENSMUSG00000031626	Sorbs2	2010203O03Rik|9430041O17Rik|A530071H08|Argbp2|mKIAA0777|nArgBP2	sorbin and SH3 domain containing 2	protein-coding
mm_9673.1	chr1	178329179	178329193	-	1	NA	3' UTR (NM_016805, exon 14 of 14)	3' UTR (NM_016805, exon 14 of 14)	8598	NM_016805	51810	Mm.86589	NM_016805	ENSMUSG00000039630	Hnrnpu	AA408410|AI256620|AL024194|AL024437|AW557595|C86794|Hnrpu|SAFA|Sp120|hnRNP U	heterogeneous nuclear ribonucleoprotein U	protein-coding
mm_83195.1	chr9	41075719	41075722	-	1	NA	intron (NM_176860, intron 1 of 13)	intron (NM_176860, intron 1 of 13)	-71092	NM_019465	54698	Mm.42791	NM_019465	ENSMUSG00000032021	Crtam	-	cytotoxic and regulatory T cell molecule	protein-coding
mm_37650.1	chr4	128787212	128787214	-	1	NA	exon (NM_001081098, exon 5 of 9)	exon (NM_001081098, exon 5 of 9)	18899	NM_001081098	230761	Mm.22616	NM_001081098	ENSMUSG00000028799	Zfp362	-	zinc finger protein 362	protein-coding
mm_165353.1	chr2	121171577	121171587	+	1	NA	promoter-TSS (NM_001290820)	promoter-TSS (NM_001290820)	414	NM_001290824	51885	Mm.383499	NM_153387	ENSMUSG00000027263	Tubgcp4	4932441P04Rik|76p|D2Ertd435e|GCP-4	tubulin, gamma complex associated protein 4	protein-coding
mm_23852.1	chr3	83008636	83008671	+	1	NA	exon (NM_133862, exon 4 of 10)	exon (NM_133862, exon 4 of 10)	929	NM_001317105	99571	Mm.16422	NM_133862	ENSMUSG00000033860	Fgg	3010002H13Rik|AI256424	fibrinogen gamma chain	protein-coding
mm_156249.1	chrX	136271669	136271687	+	1	NA	3' UTR (NM_009750, exon 3 of 3)	3' UTR (NM_009750, exon 3 of 3)	1425	NM_001110234	12070	Mm.90787	NM_009750	ENSMUSG00000046432	Bex3	AL033356|DXWsu67e|Gcap27|Nade|Ngfrap1	brain expressed X-linked 3	protein-coding
mm_91776.1	chr10	52194976	52194990	-	1	NA	5' UTR (NM_011282, exon 1 of 44)	5' UTR (NM_011282, exon 1 of 44)	261	NM_011282	19886	Mm.236163	NM_011282	ENSMUSG00000019893	Ros1	Ros-1|c-ros	Ros1 proto-oncogene	protein-coding
mm_75332.1	chr8	43180303	43180322	-	1	NA	Intergenic	Intergenic	-2810	NM_001160412	622117	Mm.390031	NM_001160412	ENSMUSG00000091490	Triml2	EG622117|Tu4	tripartite motif family-like 2	protein-coding
mm_52478.1	chr6	114306864	114306867	+	1	NA	intron (NM_178703, intron 7 of 15)	(T)n|Simple_repeat|Simple_repeat	24230	NM_178703	232333	Mm.5260	NM_178703	ENSMUSG00000030310	Slc6a1	A730043E01|GABATHG|GABATR|GAT-1|Gabt|Gabt1|Gat1|XT-1|Xtrp1	solute carrier family 6 (neurotransmitter transporter, GABA), member 1	protein-coding
mm_122301.1	chr14	34673732	34673779	-	1	NA	promoter-TSS (NM_001301330)	promoter-TSS (NM_001301330)	-173	NM_001004436	218914	Mm.27957	NM_001004436	ENSMUSG00000041408	Wapl	A530089A20Rik|BC037674|DIF-2|FOE|Wapal	WAPL cohesin release factor	protein-coding
mm_9418.1	chr1	172326249	172326255	-	1	NA	exon (NM_008429, exon 3 of 4)	exon (NM_008429, exon 3 of 4)	3011	NM_008429	16524	Mm.261168	NM_008429	ENSMUSG00000038026	Kcnj9	1700085N21Rik|Girk3|Kir3.3|mbGIRK3	potassium inwardly-rectifying channel, subfamily J, member 9	protein-coding
mm_133562.1	chr16	91393848	91393867	+	1	NA	exon (NM_010509, exon 7 of 9)	exon (NM_010509, exon 7 of 9)	-12378	NM_008349	16155	Mm.4154	NM_008349	ENSMUSG00000022969	Il10rb	6620401D04Rik|AI528744|CRF2-4|Crfb4|D16H21S58|D21S58h|IL-10R2|Il10r2	interleukin 10 receptor, beta	protein-coding
mm_109873.1	chr12	4916538	4916552	-	1	NA	promoter-TSS (NM_001099628)	promoter-TSS (NM_001099628)	-808	NM_001099628	320817	Mm.210966	NM_001099628	ENSMUSG00000052812	Atad2b	1110014E10Rik|BC032887|C79189|D530031C13Rik	ATPase family, AAA domain containing 2B	protein-coding
mm_106126.1	chr11	116426029	116426062	-	1	NA	Intergenic	Intergenic	-8049	NM_176902	319370	Mm.258466	NM_176902	ENSMUSG00000050628	Ubald2	1110014K08Rik|D030012E24Rik|Fam100b	UBA-like domain containing 2	protein-coding
mm_10144.1	chr2	4300463	4300522	+	1	NA	intron (NM_172475, intron 1 of 22)	intron (NM_172475, intron 1 of 22)	-100484	NM_001177843	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding
mm_133739.1	chr16	93957800	93957802	+	1	NA	intron (NM_019500, intron 1 of 2)	intron (NM_019500, intron 1 of 2)	-27984	NM_001165926	56173	Mm.328716	NM_019500	ENSMUSG00000047109	Cldn14	AI851731	claudin 14	protein-coding
mm_54309.1	chr6	30047924	30047954	-	1	NA	promoter-TSS (NM_001164227)	promoter-TSS (NM_001164227)	-49	NM_010938	18181	Mm.259258	NM_010938	ENSMUSG00000058440	Nrf1	C87038|D6Ertd415e	nuclear respiratory factor 1	protein-coding
mm_27617.1	chr3	59262964	59263008	-	1	NA	promoter-TSS (NM_027571)	promoter-TSS (NM_027571)	-155	NM_027571	70839	Mm.422675	NM_027571	ENSMUSG00000036353	P2ry12	2900079B22Rik|4921504D23Rik|P2Y12	purinergic receptor P2Y, G-protein coupled 12	protein-coding
mm_119669.1	chr14	52437108	52437116	+	1	NA	Intergenic	ORR1B2-int|LTR|ERVL-MaLR	-13281	NM_020514	57271	Mm.88824	NM_020514	ENSMUSG00000035626	Olfr1509	MOR244-3|Mor83|Or83	olfactory receptor 1509	protein-coding
mm_134596.1	chr16	20610742	20610757	-	1	NA	promoter-TSS (NM_025462)	promoter-TSS (NM_025462)	0	NM_145939	208624	Mm.24950	NM_145939	ENSMUSG00000033809	Alg3	D16Ertd36e|not	asparagine-linked glycosylation 3 (alpha-1,3-mannosyltransferase)	protein-coding
mm_5561.1	chr1	38831378	38831389	-	1	NA	Intergenic	Intergenic	-10168	NM_001029878	381338	Mm.487137	NM_028403	ENSMUSG00000048814	Lonrf2	2900060P06Rik|AI851349	LON peptidase N-terminal domain and ring finger 2	protein-coding
mm_66420.1	chr7	44532065	44532078	-	1	NA	promoter-TSS (NM_019866)	promoter-TSS (NM_019866)	0	NM_019866	272382	Mm.8012	NM_019866	ENSMUSG00000008193	Spib	Spi-B	Spi-B transcription factor (Spi-1/PU.1 related)	protein-coding
mm_28763.1	chr3	95891930	95891936	-	1	NA	promoter-TSS (NM_153513)	promoter-TSS (NM_153513)	72	NM_001346514	229600	Mm.89556	NM_153513	ENSMUSG00000038543	BC028528	L259	cDNA sequence BC028528	protein-coding
mm_819.1	chr1	46425465	46425515	+	1	NA	promoter-TSS (NM_001310335)	promoter-TSS (NM_001310335)	-28	NM_001310335	100101919	Mm.383402	NM_001310335	ENSMUSG00000101337	Dnah7c	Dnahc7c	dynein, axonemal, heavy chain 7C	protein-coding
mm_120526.1	chr14	66911230	66911247	+	1	NA	promoter-TSS (NM_175498)	promoter-TSS (NM_175498)	30	NM_175498	239157	Mm.44358	NM_175498	ENSMUSG00000046204	Pnma2	A830049P17Rik|mKIAA0883	paraneoplastic antigen MA2	protein-coding
mm_93487.1	chr10	111997130	111997140	-	1	NA	5' UTR (NM_028608, exon 1 of 6)	5' UTR (NM_028608, exon 1 of 6)	129	NM_028608	73690	Mm.173790	NM_028608	ENSMUSG00000056888	Glipr1	2410114O14Rik|RTVP-1|RTVP1|mRTVP-1	GLI pathogenesis-related 1 (glioma)	protein-coding
mm_44343.1	chr5	17780680	17780696	-	1	NA	Intergenic	Intergenic	55208	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_25975.1	chr3	133091845	133091873	+	1	NA	promoter-TSS (NM_026231)	promoter-TSS (NM_026231)	4	NM_027927	71793	Mm.246726	NM_027927	ENSMUSG00000028016	Ints12	1110020M19Rik|2810027J24Rik|4930529N21Rik|A230056J18Rik|AI666778|Phf22|int12	integrator complex subunit 12	protein-coding
mm_2779.1	chr1	130826677	130826755	+	1	NA	promoter-TSS (NM_011082)	promoter-TSS (NM_011082)	32	NM_011082	18703	Mm.276414	NM_011082	ENSMUSG00000026417	Pigr	-	polymeric immunoglobulin receptor	protein-coding
mm_161689.1	chr17	21962474	21962474	-	1	NA	promoter-TSS (NM_001025373)	promoter-TSS (NM_001025373)	-10	NM_001199048	73233	Mm.311219	NM_001199048	ENSMUSG00000071267	Zfp942	3110048L19Rik	zinc finger protein 942	protein-coding
mm_16438.1	chr2	180396902	180396912	+	1	NA	intron (NR_045331, intron 3 of 3)	intron (NR_045331, intron 3 of 3)	-1472	NR_029901	723954		NR_029901	ENSMUSG00000065460	Mir133a-2	Mirn133a-2|mir-133a-2	microRNA 133a-2	ncRNA
mm_225.1	chr1	17601915	17601934	+	1	NA	promoter-TSS (NM_053191)	promoter-TSS (NM_053191)	23	NM_053191	94227	Mm.442452	NM_053191	ENSMUSG00000067780	Pi15	P24TI|P25TI|PI-15|SugarCrisp	peptidase inhibitor 15	protein-coding
mm_135056.1	chr16	33818933	33818947	-	1	NA	3' UTR (NM_010739, exon 13 of 13)	3' UTR (NM_010739, exon 13 of 13)	-10725	NM_010580	16419	Mm.6424	NM_010580	ENSMUSG00000022817	Itgb5	AA475909|AI874634|ESTM23|[b]-5|[b]5|[b]5A|[b]5B|beta-5|beta5	integrin beta 5	protein-coding
mm_160949.1	chr11	97013569	97013569	+	1	NA	promoter-TSS (NM_031183)	promoter-TSS (NM_031183)	0	NM_031183	83395	Mm.156282	NM_031183	ENSMUSG00000038560	Sp6	1110025J03Rik|AA591031|AI592962|Epfn|Klf14	trans-acting transcription factor 6	protein-coding
mm_58456.1	chr7	3332173	3332210	+	1	NA	Intergenic	Intergenic	-4394	NM_133189	81904	Mm.214994	NM_133189	ENSMUSG00000069806	Cacng7	-	calcium channel, voltage-dependent, gamma subunit 7	protein-coding
mm_38257.1	chr4	136819668	136819684	-	1	NA	intron (NM_001290753, intron 1 of 15)	intron (NM_001290753, intron 1 of 15)	16336	NM_001290753	13844	Mm.250981	NM_010142	ENSMUSG00000028664	Ephb2	Cek5|Drt|ETECK|Erk|Hek5|Nuk|Prkm5|Qek5|Sek3|Tyro5	Eph receptor B2	protein-coding
mm_156829.1	chrX	164269524	164269571	+	1	NA	5' UTR (NM_027153, exon 1 of 10)	5' UTR (NM_027153, exon 1 of 10)	116	NM_027153	69656	Mm.293463	NM_027153	ENSMUSG00000031379	Pir	2310042L19Rik|Pirnl	pirin	protein-coding
mm_118460.1	chr14	9156971	9156972	+	1	NA	Intergenic	Intergenic	490581	NR_045968	74859	Mm.84041	NR_045968	ENSMUSG00000097898	4930455B14Rik	1700027C12Rik	RIKEN cDNA 4930455B14 gene	ncRNA
mm_140713.1	chr17	15239302	15239317	-	1	NA	intron (NR_046164, intron 2 of 4)	intron (NR_046164, intron 2 of 4)	1474	NR_046164	328747	Mm.256835	NR_046164	ENSMUSG00000097624	Gm5091	C330048F19	predicted gene 5091	ncRNA
mm_104416.1	chr11	94677405	94677496	-	1	NA	promoter-TSS (NM_145828)	promoter-TSS (NM_145828)	43	NM_145828	217119	Mm.100638	NM_145828	ENSMUSG00000020868	Xylt2	E030002B02Rik|XT-II|XT2|xylT-II	xylosyltransferase II	protein-coding
mm_39057.1	chr4	153975039	153975067	-	1	NA	promoter-TSS (NM_177673)	promoter-TSS (NM_177673)	28	NM_007859	13368	Mm.388918	NM_007859	ENSMUSG00000029027	Dffb	40kDa|5730477D02Rik|CAD|CPAN|DFF40|Didff	DNA fragmentation factor, beta subunit	protein-coding
mm_12586.1	chr2	73452825	73452834	+	1	NA	intron (NM_153138, intron 1 of 7)	intron (NM_153138, intron 1 of 7)	1060	NM_001289722	215280	Mm.223504	NM_153138	ENSMUSG00000075284	Wipf1	AI115543|D2Ertd120e|WIP|Waspip	WAS/WASL interacting protein family, member 1	protein-coding
mm_119146.1	chr14	31336659	31336719	+	1	NA	promoter-TSS (NM_009796)	promoter-TSS (NM_009796)	-35	NM_009796	12339	Mm.201535	NM_009796	ENSMUSG00000021893	Capn7	AU022319|PalBH	calpain 7	protein-coding
mm_79047.1	chr9	46228834	46228844	+	1	NA	intron (NM_009692, intron 1 of 3)	intron (NM_009692, intron 1 of 3)	209	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2|apo-AI|apoA-I	apolipoprotein A-I	protein-coding
mm_132558.1	chr16	38089042	38089064	+	1	NA	promoter-TSS (NM_019827)	promoter-TSS (NM_019827)	52	NM_019827	56637	Mm.394930	NM_019827	ENSMUSG00000022812	Gsk3b	7330414F15Rik|8430431H08Rik|C86142|GSK-3|GSK-3beta|GSK3	glycogen synthase kinase 3 beta	protein-coding
mm_163751.1	chr13	119767719	119767739	+	1	NA	intron (NM_001302550, intron 6 of 6)	RSINE1|SINE|B4	-11847	NM_175538	245269	Mm.403943	NM_175538	ENSMUSG00000095930	Nim1k	E130304F04Rik|Nim1	NIM1 serine/threonine protein kinase	protein-coding
mm_135707.1	chr16	55283282	55283287	-	1	NA	promoter-TSS (NM_178720)	promoter-TSS (NM_178720)	-47	NM_178720	239852	Mm.245045	NM_178720	ENSMUSG00000064310	Zpld1	9430016A21Rik	zona pellucida like domain containing 1	protein-coding
mm_288.1	chr1	21349670	21349700	+	1	NA	promoter-TSS (NM_183322)	promoter-TSS (NM_183322)	8	NM_183322	368204	Mm.26006	NM_183322	ENSMUSG00000067750	Khdc1a	AU014713|C88118|Ndg1	KH domain containing 1A	protein-coding
mm_139042.1	chr17	46227828	46227830	+	1	NA	exon (NM_028198, exon 18 of 32)	exon (NM_028198, exon 18 of 32)	-3702	NR_030466	751553		NR_030466	ENSMUSG00000076141	Mir693	Mirn693|mir-693|mmu-mir-693	microRNA 693	ncRNA
mm_16299.1	chr2	174289502	174289516	+	1	NA	intron (NR_002846, intron 1 of 4)	intron (NR_002846, intron 1 of 4)	5189	NM_022000	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_156012.1	chrX	107089312	107089337	+	1	NA	promoter-TSS (NM_172435)	promoter-TSS (NM_172435)	-11	NM_172435	78826	Mm.74639	NM_172435	ENSMUSG00000050921	P2ry10	5830408N17Rik|Lypsr2|P2Y10	purinergic receptor P2Y, G-protein coupled 10	protein-coding
mm_61240.1	chr7	65644885	65644911	+	1	NA	promoter-TSS (NM_172310)	promoter-TSS (NM_172310)	0	NM_172310	272396	Mm.35127	NM_172310	ENSMUSG00000030515	Tarsl2	A530046H20Rik	threonyl-tRNA synthetase-like 2	protein-coding
mm_110599.1	chr12	56535925	56535937	-	1	NA	intron (NM_009385, intron 1 of 2)	CpG	977	NM_009385	21869	Mm.89972	NM_009385	ENSMUSG00000001496	Nkx2-1	AV026640|Nkx2.1|T/EBP|Titf1|Ttf-1	NK2 homeobox 1	protein-coding
mm_141273.1	chr17	27820446	27820464	-	1	NA	promoter-TSS (NM_001271511)	promoter-TSS (NM_001271511)	87	NM_001033279	224647	Mm.196577	NM_001033279	ENSMUSG00000056692	D17Wsu92e	AU020189|C030010A15|C80239	DNA segment, Chr 17, Wayne State University 92, expressed	protein-coding
mm_7972.1	chr1	134063283	134063298	-	1	NA	Intergenic	Intergenic	15865	NM_007570	12227	Mm.392646	NM_007570	ENSMUSG00000020423	Btg2	AA959598|APRO1|Pc3|TIS21	B cell translocation gene 2, anti-proliferative	protein-coding
mm_12432.1	chr2	70661479	70661482	+	1	NA	promoter-TSS (NM_027352)	promoter-TSS (NM_027352)	-29	NR_027343	70231	Mm.271950	NM_027352	ENSMUSG00000014959	Gorasp2	0610011A07Rik|2410043M02Rik|5730520M13Rik|9430094F20Rik|AW552058|ENSMUSG00000075299|GOLPH2|GRASP55|GRS2|p59	golgi reassembly stacking protein 2	protein-coding
mm_110121.1	chr12	26444053	26444071	-	1	NA	3' UTR (NM_021384, exon 6 of 6)	3' UTR (NM_021384, exon 6 of 6)	12390	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_34886.1	chr4	155589736	155589751	+	1	NA	3' UTR (NM_001159637, exon 12 of 12)	3' UTR (NM_001159637, exon 12 of 12)	-11673	NM_177186	320541	Mm.306018	NM_177186	ENSMUSG00000042202	Slc35e2	A530082C11Rik|AI957035	solute carrier family 35, member E2	protein-coding
mm_32922.1	chr4	119136891	119136917	+	1	NA	3' UTR (NM_011400, exon 10 of 10)	3' UTR (NM_011400, exon 10 of 10)	28159	NM_011400	20525	Mm.21002	NM_011400	ENSMUSG00000028645	Slc2a1	Glut-1|Glut1	solute carrier family 2 (facilitated glucose transporter), member 1	protein-coding
mm_46923.1	chr5	114669884	114669914	-	1	NA	3' UTR (NM_019821, exon 5 of 5)	3' UTR (NM_019821, exon 5 of 5)	-11478	NM_022017	63873	Mm.266450	NM_022017	ENSMUSG00000014158	Trpv4	0610033B08Rik|OTRPC4|Trp12|VR-OAC|VRL-2|VROAC	transient receptor potential cation channel, subfamily V, member 4	protein-coding
mm_20686.1	chr2	132601169	132601171	-	1	NA	intron (NR_033469, intron 1 of 3)	intron (NR_033469, intron 1 of 3)	2974	NR_033469	767814	Mm.371752	NR_033468	ENSMUSG00000074783	AU019990	-	expressed sequence AU019990	ncRNA
mm_113521.1	chr13	37809474	37809522	+	1	NA	Intergenic	Intergenic	-16540	NM_026830	68750	Mm.491109	NM_026830	ENSMUSG00000039087	Rreb1	1110037N09Rik|AA414966|B930013M22Rik	ras responsive element binding protein 1	protein-coding
mm_110859.1	chr12	73409692	73409719	-	1	NA	promoter-TSS (NR_046013)	promoter-TSS (NR_046013)	-142	NR_046013	380765	Mm.490476	NR_046013		D830013O20Rik	Gm891	RIKEN cDNA D830013O20 gene	ncRNA
mm_26302.1	chr3	142510192	142510224	+	1	NA	intron (NM_153564, intron 10 of 10)	intron (NM_153564, intron 10 of 10)	13274	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_135690.1	chr16	52429490	52429498	-	1	NA	intron (NM_009655, intron 1 of 15)	intron (NM_009655, intron 1 of 15)	23587	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_84031.1	chr9	57765067	57765084	-	1	NA	exon (NM_007713, exon 1 of 13)	exon (NM_007713, exon 1 of 13)	785	NM_007713	102414	Mm.25720	NM_007713	ENSMUSG00000032316	Clk3	AI256811	CDC-like kinase 3	protein-coding
mm_125730.1	chr15	73162396	73162404	+	1	NA	intron (NM_153178, intron 1 of 18)	Lx9|LINE|L1	22547	NM_153178	239528	Mm.23095	NM_153178	ENSMUSG00000036698	Ago2	1110029L17Rik|2310051F07Rik|AI225898|AL022874|AW546247|ENSMUSG00000072493|Eif2c2|Gerp95|Gm10365|mKIAA4215	argonaute RISC catalytic subunit 2	protein-coding
mm_86424.1	chr10	3788896	3788899	+	1	NA	intron (NM_001159942, intron 1 of 16)	intron (NM_001159942, intron 1 of 16)	48520	NM_001159942	213783	Mm.150831	NM_001033253	ENSMUSG00000040624	Plekhg1	D10Ertd733e|Gm521|mKIAA1209	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	protein-coding
mm_118226.1	chr13	110941211	110941257	-	1	NA	Intergenic	Intergenic	-37388	NR_131194	102636142	Mm.417611	NR_131194		4930526H09Rik	-	RIKEN cDNA 4930526H09 gene	ncRNA
mm_44347.1	chr5	17785750	17785839	-	1	NA	exon (NM_001159558, exon 15 of 16)	exon (NM_001159558, exon 15 of 16)	50102	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_145042.1	chr18	39539340	39539360	+	1	NA	Intergenic	Intergenic	-52105	NM_008173	14815	Mm.129481	NM_008173	ENSMUSG00000024431	Nr3c1	GR|Grl-1|Grl1	nuclear receptor subfamily 3, group C, member 1	protein-coding
mm_77761.1	chr9	3000135	3000163	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	38594	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_102706.1	chr11	66526636	66526703	-	1	NA	promoter-TSS (NM_001034874)	promoter-TSS (NM_001034874)	-543	NM_001034874	380702	Mm.351764	NM_001034874	ENSMUSG00000053930	Shisa6	Gm879|ckamp52	shisa family member 6	protein-coding
mm_53448.1	chr6	134431861	134431867	+	1	NA	intron (NM_025778, intron 5 of 6)	intron (NM_025778, intron 5 of 6)	35535	NM_025778	66813	Mm.474472	NM_025778	ENSMUSG00000030200	Bcl2l14	4930452K23Rik|4933405K19Rik|9030625M01Rik|AI429211|Bclg	BCL2-like 14 (apoptosis facilitator)	protein-coding
mm_81359.1	chr9	108682413	108682420	+	1	NA	exon (NM_020520, exon 7 of 9)	exon (NM_020520, exon 7 of 9)	-9727	NM_008924	19087	Mm.253102	NM_008924	ENSMUSG00000032601	Prkar2a	1110061A24Rik|AI317181|AI836829|RII(alpha)	protein kinase, cAMP dependent regulatory, type II alpha	protein-coding
mm_10189.1	chr2	4895875	4895880	+	1	NA	intron (NM_175400, intron 5 of 8)	intron (NM_175400, intron 5 of 8)	14313	NM_175400	109079	Mm.34329	NM_175400	ENSMUSG00000026662	Sephs1	1110046B24Rik|AA589574|AI505014|AW111620|SELD|SPS|SPS1	selenophosphate synthetase 1	protein-coding
mm_45934.1	chr5	89883322	89883343	-	1	NA	promoter-TSS (NM_177872)	promoter-TSS (NM_177872)	2	NM_177872	330119	Mm.133062	NM_177872	ENSMUSG00000043635	Adamts3	1100001H14Rik|6330442E02Rik	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 3	protein-coding
mm_82379.1	chr9	14634273	14634277	-	1	NA	Intergenic	Intergenic	-19275	NM_001081395	75723	Mm.159552	NM_001081395	ENSMUSG00000013076	Amotl1	2310010G08Rik|2310067L22Rik|4932416D09Rik|JEAP|mFLJ00155	angiomotin-like 1	protein-coding
mm_56213.1	chr6	89357710	89357721	-	1	NA	5' UTR (NM_008881, exon 2 of 32)	5' UTR (NM_008881, exon 2 of 32)	4898	NM_008881	18844	Mm.3789	NM_008881	ENSMUSG00000030084	Plxna1	2600013D04Rik|NOV|PlexA1|Plxn1|mKIAA4053	plexin A1	protein-coding
mm_21138.1	chr2	154214068	154214080	-	1	NA	exon (NM_153418, exon 11 of 16)	exon (NM_153418, exon 11 of 16)	-9668	NM_144890	228802	Mm.167411	NM_144890	ENSMUSG00000038572	Bpifb5	Lplunc5	BPI fold containing family B, member 5	protein-coding
mm_70855.1	chr8	24044475	24044488	+	1	NA	intron (NM_001277239, intron 7 of 7)	intron (NM_001277239, intron 7 of 7)	374820	NM_177086	320158	Mm.121274	NM_177086	ENSMUSG00000037492	Zmat4	9630048M01Rik	zinc finger, matrin type 4	protein-coding
mm_121083.1	chr14	99100017	99100028	+	1	NA	promoter-TSS (NM_028315)	promoter-TSS (NM_028315)	-252	NM_028315	72662	Mm.163339	NM_028315	ENSMUSG00000033166	Dis3	2810028N01Rik	DIS3 homolog, exosome endoribonuclease and 3'-5' exoribonuclease	protein-coding
mm_83444.1	chr9	45009264	45009271	-	1	NA	intron (NM_007648, intron 2 of 7)	intron (NM_007648, intron 2 of 7)	323	NM_007648	12501	Mm.210361	NM_007648	ENSMUSG00000032093	Cd3e	AI504783|CD3|CD3epsilon|T3e	CD3 antigen, epsilon polypeptide	protein-coding
mm_72001.1	chr8	70673199	70673267	+	1	NA	promoter-TSS (NM_015816)	promoter-TSS (NM_015816)	2	NM_015816	50783	Mm.248188	NM_015816	ENSMUSG00000031848	Lsm4	-	LSM4 homolog, U6 small nuclear RNA and mRNA degradation associated	protein-coding
mm_113246.1	chr13	27354115	27354120	+	1	NA	TTS (NM_010088)	TTS (NM_010088)	8444	NM_001289919	13529	Mm.291450	NM_010088	ENSMUSG00000018259	Prl8a2	D/tPRP|DPRP|Dtprp|Ghd11|mdPRP	prolactin family 8, subfamily a, member 2	protein-coding
mm_39975.1	chr5	32297629	32297630	+	1	NA	intron (NM_001081407, intron 18 of 58)	intron (NM_001081407, intron 18 of 58)	-55951	NM_172147	665270	Mm.160067	NM_030072	ENSMUSG00000029134	Plb1	4632413E21Rik|4930433E17Rik|4930539A06Rik|BC033606	phospholipase B1	protein-coding
mm_51276.1	chr6	72140950	72140977	+	1	NA	intron (NM_001035228, intron 3 of 6)	RSINE1|SINE|B4	-17766	NR_045165	71265	Mm.442035	NR_045163	ENSMUSG00000108709	4933431G14Rik	4930565C19Rik	RIKEN cDNA 4933431G14 gene	ncRNA
mm_90239.1	chr10	121395322	121395369	+	1	NA	3' UTR (NM_029364, exon 14 of 14)	3' UTR (NM_029364, exon 14 of 14)	30255	NM_029364	75612	Mm.207683	NM_029364	ENSMUSG00000034707	Gns	2610016K11Rik|AU042285|C87209|G6S|N28088	glucosamine (N-acetyl)-6-sulfatase	protein-coding
mm_15320.1	chr2	155747178	155747189	+	1	NA	Intergenic	MT2B1|LTR|ERVL	-4034	NM_011171	19124	Mm.3243	NM_011171	ENSMUSG00000027611	Procr	AI325044|Ccca|Ccd41|Epcr	protein C receptor, endothelial	protein-coding
mm_33754.1	chr4	134343144	134343154	+	1	NA	promoter-TSS (NM_001346578)	promoter-TSS (NM_001346578)	103	NM_001039677	230810	Mm.358876	NM_001039677	ENSMUSG00000028836	Slc30a2	ZnT-2|Znt2	solute carrier family 30 (zinc transporter), member 2	protein-coding
mm_126715.1	chr15	85336288	85336303	+	1	NA	promoter-TSS (NM_016843)	promoter-TSS (NM_016843)	-86	NM_016843	54138	Mm.248906	NM_016843	ENSMUSG00000016541	Atxn10	AI325283|C77170|E46|Sca10|TEG-169|Tex169	ataxin 10	protein-coding
mm_166151.1	chr5	6818537	6818540	+	1	NA	intron (NM_001163223, intron 2 of 3)	intron (NM_001163223, intron 2 of 3)	-485626	NM_027603	70920	Mm.158494	NM_027603	ENSMUSG00000040514	4921511H03Rik	-	RIKEN cDNA 4921511H03 gene	protein-coding
mm_148277.1	chr18	81927688	81927696	-	1	NA	Intergenic	Intergenic	64388	NR_039589	100628596		NR_039589	ENSMUSG00000093036	Mir5127	mmu-mir-5127|mu-mir-5127	microRNA 5127	ncRNA
mm_48403.1	chr5	140215429	140215437	-	1	NA	intron (NM_010752, intron 10 of 17)	L1ME4a|LINE|L1	106119	NM_010752	17120	Mm.27250	NM_010752	ENSMUSG00000029554	Mad1l1	AI173502|AW550425|Mad1	MAD1 mitotic arrest deficient 1-like 1	protein-coding
mm_155804.1	chrX	99044004	99044016	+	1	NA	intron (NM_199018, intron 1 of 13)	intron (NM_199018, intron 1 of 13)	1429	NM_199018	236920	Mm.236928	NM_199018	ENSMUSG00000031216	Stard8	Dlc3|mKIAA0189	START domain containing 8	protein-coding
mm_19375.1	chr2	91194794	91194821	-	1	NA	5' UTR (NM_013839, exon 1 of 10)	5' UTR (NM_013839, exon 1 of 10)	228	NM_013839	22259	Mm.22690	NM_013839	ENSMUSG00000002108	Nr1h3	AU018371|LXR|RLD1|Unr1	nuclear receptor subfamily 1, group H, member 3	protein-coding
mm_114685.1	chr13	81064605	81064607	+	1	NA	intron (NR_015587, intron 1 of 1)	intron (NR_015587, intron 1 of 1)	100532	NR_015587	319983	Mm.343027	NR_015587	ENSMUSG00000097098	9330111N05Rik	-	RIKEN cDNA 9330111N05 gene	ncRNA
mm_127538.1	chr15	102104390	102104418	+	1	NA	intron (NM_153533, intron 1 of 28)	intron (NM_153533, intron 1 of 28)	1416	NM_153533	209039	Mm.29389	NM_153533	ENSMUSG00000037003	Tns2	C1-ten|Tenc1|nep|nph	tensin 2	protein-coding
mm_144565.1	chr18	31771954	31771988	+	1	NA	exon (NM_001242430, exon 3 of 8)	exon (NM_001242430, exon 3 of 8)	11355	NM_001242430	225339	Mm.290804	NM_153515	ENSMUSG00000041915	Ammecr1l	5430429D03Rik|AU022236|AU040755|AW111353|E230022H04Rik	AMME chromosomal region gene 1-like	protein-coding
mm_79656.1	chr9	59656173	59656175	+	1	NA	promoter-TSS (NM_011099)	promoter-TSS (NM_011099)	-194	NM_011099	18746	Mm.326167	NM_011099	ENSMUSG00000032294	Pkm	AA414905|AL024370|AL024424|Pk-2|Pk-3|Pk3|Pkm2	pyruvate kinase, muscle	protein-coding
mm_16688.1	chr2	6884875	6884899	-	1	NA	exon (NM_001110228, exon 1 of 14)	exon (NM_001110228, exon 1 of 14)	109	NM_010160	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_124591.1	chr15	3274702	3274795	+	1	NA	exon (NM_009155, exon 2 of 5)	exon (NM_009155, exon 2 of 5)	3771	NM_009155	20363	Mm.392203	NM_009155	ENSMUSG00000064373	Selenop	AU018766|D15Ucla1|Se-P|Sepp1|selp	selenoprotein P	protein-coding
mm_144966.1	chr18	37824582	37824634	+	1	NA	intron (NM_033583, intron 1 of 3)	intron (NM_033583, intron 1 of 3)	5062	NM_033583	93708	Mm.247203	NM_033583	ENSMUSG00000102543	Pcdhgc5	-	protocadherin gamma subfamily C, 5	protein-coding
mm_63949.1	chr7	139894784	139894854	+	1	NA	5' UTR (NM_177261, exon 1 of 31)	5' UTR (NM_177261, exon 1 of 31)	123	NM_177261	76484	Mm.44442	NM_177261	ENSMUSG00000066129	Kndc1	2410012C07Rik|B830014K08Rik|VKIND|very-kind	kinase non-catalytic C-lobe domain (KIND) containing 1	protein-coding
mm_84833.1	chr9	78347128	78347135	-	1	NA	promoter-TSS (NM_008182)	promoter-TSS (NM_008182)	14	NM_008182	14858	Mm.422778	NM_008182	ENSMUSG00000057933	Gsta2	Gst2-2|Gstc-2|Gstc2	glutathione S-transferase, alpha 2 (Yc2)	protein-coding
mm_169216.1	chr13	66698298	66698302	-	1	NA	Intergenic	Intergenic	207050	NM_026219	67530	Mm.379136	NM_026219	ENSMUSG00000021520	Uqcrb	2210415M14Rik|QP-C|QPC|UQBC|UQBP|UQPC	ubiquinol-cytochrome c reductase binding protein	protein-coding
mm_172429.1	chr7	28392666	28392673	-	1	NA	promoter-TSS (NM_019458)	promoter-TSS (NM_019458)	21	NM_026042	67224	Mm.41647	NM_026042	ENSMUSG00000003444	Med29	2810405O22Rik|AU020902|Ixl	mediator complex subunit 29	protein-coding
mm_159101.1	chr2	36936892	36936892	+	1	NA	promoter-TSS (NM_146624)	promoter-TSS (NM_146624)	-229	NM_146624	258617	Mm.377595	NM_146624	ENSMUSG00000070943	Olfr356	MOR134-1	olfactory receptor 356	protein-coding
mm_95592.1	chr11	53332187	53332207	+	1	NA	intron (NM_026479, intron 3 of 3)	intron (NM_026479, intron 3 of 3)	7508	NM_026479	67966	Mm.288072	NM_026479	ENSMUSG00000018239	Zcchc10	2410141K03Rik|AA675321|D11Ertd416e	zinc finger, CCHC domain containing 10	protein-coding
mm_73836.1	chr8	117460950	117460989	+	1	NA	3' UTR (NM_001163262, exon 21 of 21)	3' UTR (NM_001163262, exon 21 of 21)	1704	NR_106046	102465653		NR_106046	ENSMUSG00000098483	Mir7078	Gm27386|mmu-mir-7078	microRNA 7078	ncRNA
mm_6640.1	chr1	79436330	79436348	-	1	NA	exon (NM_009129, exon 2 of 2)	exon (NM_009129, exon 2 of 2)	3751	NM_009129	20254	Mm.5038	NM_009129	ENSMUSG00000050711	Scg2	Chgc|SgII	secretogranin II	protein-coding
mm_155463.1	chrX	73528678	73528711	+	1	NA	exon (NM_177236, exon 3 of 21)	exon (NM_177236, exon 3 of 21)	25608	NM_177236	320707	Mm.210095	NM_177236	ENSMUSG00000031376	Atp2b3	6430519O13Rik|Pmca3	ATPase, Ca++ transporting, plasma membrane 3	protein-coding
mm_126904.1	chr15	89568328	89568383	+	1	NA	promoter-TSS (NM_013455)	promoter-TSS (NM_013455)	29	NM_001277246	11434	Mm.57	NM_013455	ENSMUSG00000022622	Acr	-	acrosin prepropeptide	protein-coding
mm_96110.1	chr11	60554946	60554960	+	1	NA	3' UTR (NM_172943, exon 4 of 4)	3' UTR (NM_172943, exon 4 of 4)	17270	NM_172943	268420	Mm.262056	NM_172943	ENSMUSG00000042650	Alkbh5	AW050020|AW215868|Abh5|E130207K11|Ofoxd	alkB homolog 5, RNA demethylase	protein-coding
mm_83107.1	chr9	40346190	40346200	-	1	NA	intron (NM_172768, intron 2 of 19)	RLTR51A_Mm|LTR|ERVK?	12723	NR_040728	73558	Mm.398307	NR_040728		1700110K17Rik	-	RIKEN cDNA 1700110K17 gene	ncRNA
mm_164543.1	chr17	8372075	8372097	+	1	NA	promoter-TSS (NM_001161832)	promoter-TSS (NM_001161832)	-310	NM_001161832	21331	Mm.482744	NM_013682		T2	brachyury2	brachyury 2	protein-coding
mm_101397.1	chr11	26584753	26584799	-	1	NA	intron (NM_001252447, intron 2 of 11)	intron (NM_001252447, intron 2 of 11)	9144	NM_027260	69922	Mm.285351	NM_027260	ENSMUSG00000064090	Vrk2	2810003O05Rik|AI447698	vaccinia related kinase 2	protein-coding
mm_138266.1	chr17	34598444	34598450	+	1	NA	exon (NM_007425, exon 3 of 11)	exon (NM_007425, exon 3 of 11)	597	NR_073173	11596	Mm.3383	NM_007425	ENSMUSG00000015452	Ager	RAGE	advanced glycosylation end product-specific receptor	protein-coding
mm_76589.1	chr8	89042636	89042655	-	1	NA	intron (NM_021390, intron 1 of 3)	CpG-14342	1517	NM_021390	58198	Mm.214361	NM_021390	ENSMUSG00000031665	Sall1	Msal-3	sal-like 1 (Drosophila)	protein-coding
mm_124210.1	chr14	99339637	99339658	-	1	NA	Intergenic	Intergenic	40956	NM_009769	12224	Mm.30262	NM_009769	ENSMUSG00000005148	Klf5	4930520J07Rik|Bteb2|CKLF|IKLF	Kruppel-like factor 5	protein-coding
mm_98516.1	chr11	94952522	94952584	+	1	NA	3' UTR (NM_007742, exon 51 of 51)	3' UTR (NM_007742, exon 51 of 51)	-15040	NM_018792	54388	Mm.30482	NM_018792	ENSMUSG00000038994	Hils1	H1.9|TISP64	histone H1-like protein in spermatids 1	protein-coding
mm_153358.1	chr19	40173673	40173682	-	1	NA	intron (NM_145499, intron 3 of 8)	intron (NM_145499, intron 3 of 8)	13609	NM_145499	226105	Mm.29119	NM_145499	ENSMUSG00000060613	Cyp2c70	-	cytochrome P450, family 2, subfamily c, polypeptide 70	protein-coding
mm_61398.1	chr7	73375567	73375578	+	1	NA	promoter-TSS (NM_177740)	promoter-TSS (NM_177740)	52	NM_177740	244058	Mm.333943	NM_177740	ENSMUSG00000070509	Rgma	BC059072|C230063O06	repulsive guidance molecule family member A	protein-coding
mm_115657.1	chr13	12459126	12459126	-	1	NA	intron (NM_001291060, intron 1 of 8)	intron (NM_001291060, intron 1 of 8)	190	NM_001291055	56048	Mm.474138	NM_018886	ENSMUSG00000057554	Lgals8	1200015E08Rik|AI326142|D13Ertd524e|Lgals-8	lectin, galactose binding, soluble 8	protein-coding
mm_2167.1	chr1	88259195	88259197	+	1	NA	exon (NM_001281466, exon 40 of 42)	exon (NM_001281466, exon 40 of 42)	10212	NR_040291	78605	Mm.384762	NR_040291		6430706D22Rik	-	RIKEN cDNA 6430706D22 gene	ncRNA
mm_116935.1	chr13	55836072	55836099	-	1	NA	Intergenic	CpG	-4660	NM_011097	18740	Mm.135195	NM_011097	ENSMUSG00000021506	Pitx1	Bft|P-OTX|Potx|Ptx1	paired-like homeodomain transcription factor 1	protein-coding
mm_42692.1	chr5	119835171	119835176	+	1	NA	5' UTR (NM_011537, exon 1 of 9)	5' UTR (NM_011537, exon 1 of 9)	510	NM_011537	21388	Mm.103636	NM_011537	ENSMUSG00000018263	Tbx5	-	T-box 5	protein-coding
mm_37077.1	chr4	116167592	116167607	-	1	NA	promoter-TSS (NM_133681)	promoter-TSS (NM_133681)	-1	NM_133681	66805	Mm.45994	NM_133681	ENSMUSG00000028699	Tspan1	9030418M05Rik	tetraspanin 1	protein-coding
mm_37531.1	chr4	124851153	124851203	-	1	NA	promoter-TSS (NM_001142727)	promoter-TSS (NM_001142727)	419	NM_153566	230734	Mm.258568	NM_153566	ENSMUSG00000028889	Yrdc	AV303379|BC023823|IRIP|ITIP	yrdC domain containing (E.coli)	protein-coding
mm_146354.1	chr18	82572814	82572887	+	1	NA	exon (NM_010777, exon 5 of 7)	exon (NM_010777, exon 5 of 7)	18342	NM_001025254	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_32061.1	chr4	97777649	97777659	+	1	NA	promoter-TSS (NM_001122953)	promoter-TSS (NM_001122953)	28	NM_010905	18027	Mm.31274	NM_010905	ENSMUSG00000028565	Nfia	1110047K16Rik|9430022M17Rik|CTF|NF1-A|NF1A	nuclear factor I/A	protein-coding
mm_8730.1	chr1	160105726	160105731	-	1	NA	intron (NM_177839, intron 16 of 21)	intron (NM_177839, intron 16 of 21)	-27743	NR_038031	75255	Mm.414845	NR_038030	ENSMUSG00000026729	4930562F07Rik	-	RIKEN cDNA 4930562F07 gene	ncRNA
mm_92283.1	chr10	71285269	71285279	-	1	NA	promoter-TSS (NM_145420)	promoter-TSS (NM_145420)	-12	NM_145420	216080	Mm.270530	NM_145420	ENSMUSG00000019927	Ube2d1	UBCH5	ubiquitin-conjugating enzyme E2D 1	protein-coding
mm_54438.1	chr6	34395950	34395957	-	1	NA	intron (NM_172398, intron 9 of 9)	intron (NM_172398, intron 9 of 9)	11706	NM_172398	67861	Mm.70371	NM_172398	ENSMUSG00000061758	Akr1b10	2310005E10Rik|Akr1b16	aldo-keto reductase family 1, member B10 (aldose reductase)	protein-coding
mm_95203.1	chr11	43474282	43474340	+	1	NA	promoter-TSS (NM_026979)	promoter-TSS (NM_026979)	5	NM_026979	69183	Mm.390374	NM_026979	ENSMUSG00000046491	C1qtnf2	1810033K05Rik|CTRP2	C1q and tumor necrosis factor related protein 2	protein-coding
mm_120165.1	chr14	60762565	60762576	+	1	NA	3' UTR (NM_001033272, exon 13 of 13)	3' UTR (NM_001033272, exon 13 of 13)	-5564	NM_183175	239126	Mm.319636	NM_183175	ENSMUSG00000071347	C1qtnf9	9130217G22Rik|CTRP9|Ciqtnf9	C1q and tumor necrosis factor related protein 9	protein-coding
mm_3817.1	chr1	159232263	159232281	+	1	NA	promoter-TSS (NM_011931)	promoter-TSS (NM_011931)	-54	NM_011931	26374	Mm.328135	NM_011931	ENSMUSG00000040782	Rfwd2	AI316802|C80879|Cop1	ring finger and WD repeat domain 2	protein-coding
mm_7575.1	chr1	124846032	124846042	-	1	NA	Intergenic	Intergenic	589690	NM_023735	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding
mm_78752.1	chr9	42296849	42296857	+	1	NA	Intergenic	Intergenic	-32553	NM_172769	235293	Mm.32700	NM_172769	ENSMUSG00000032018	Sc5d	A830037K02|A830073K23Rik|Sc5dl	sterol-C5-desaturase	protein-coding
mm_72578.1	chr8	84200836	84200846	+	1	NA	Intergenic	Intergenic	-7677	NR_029740	387216		NR_029740	ENSMUSG00000065611	Mir23a	Mirn23a|mir-23a|mmu-mir-23a	microRNA 23a	ncRNA
mm_69837.1	chr7	141327511	141327556	-	1	NA	promoter-TSS (NM_001141950)	promoter-TSS (NM_001141950)	192	NM_016874	54006	Mm.28392	NM_016874	ENSMUSG00000058886	Deaf1	AU042387|C230009B13Rik|NUDR	deformed epidermal autoregulatory factor 1 (Drosophila)	protein-coding
mm_158857.1	chrY	818584	818633	+	1	NA	promoter-TSS (NM_011667)	promoter-TSS (NM_011667)	-105	NM_011667	22202	Mm.422949	NM_011667	ENSMUSG00000069053	Uba1y	A1s9Y-1|Sby|Ube-2|Ube1ay|Ube1y|Ube1y-1|Ube1y1	ubiquitin-activating enzyme, Chr Y	protein-coding
mm_42676.1	chr5	119680369	119680423	+	1	NA	exon (NM_011535, exon 7 of 8)	exon (NM_011535, exon 7 of 8)	9163	NM_011535	21386	Mm.219139	NM_011535	ENSMUSG00000018604	Tbx3	D5Ertd189e	T-box 3	protein-coding
mm_150594.1	chr19	40679600	40679617	+	1	NA	intron (NM_009848, intron 1 of 9)	intron (NM_009848, intron 1 of 9)	19838	NM_009848	12495	Mm.2824	NM_009848	ENSMUSG00000048120	Entpd1	2610206B08Rik|AA408691|Cd39|NTPDase-1	ectonucleoside triphosphate diphosphohydrolase 1	protein-coding
mm_98299.1	chr11	90030665	90030684	+	1	NA	5' UTR (NM_026433, exon 1 of 3)	5' UTR (NM_026433, exon 1 of 3)	326	NM_026433	67888	Mm.212428	NM_026433	ENSMUSG00000069763	Tmem100	1810057C19Rik|AV011897	transmembrane protein 100	protein-coding
mm_66835.1	chr7	48878123	48878152	-	1	NA	intron (NM_001013368, intron 3 of 12)	intron (NM_001013368, intron 3 of 12)	2904	NM_001013368	108961	Mm.240566	NM_001013368	ENSMUSG00000046179	E2f8	4432406C08Rik|AA410048	E2F transcription factor 8	protein-coding
mm_112274.1	chr12	114263139	114263145	-	1	NA	Intergenic	Intergenic	206324	NR_106062	102465663		NR_106062	ENSMUSG00000105438	Mir7094-1	mmu-mir-7094-1	microRNA 7094-1	ncRNA
mm_155523.1	chrX	74257418	74257446	+	1	NA	3' UTR (NM_007927, exon 6 of 6)	3' UTR (NM_007927, exon 6 of 6)	2745	NM_007927	13726	Mm.18892	NM_007927	ENSMUSG00000001964	Emd	AW550900|Sta	emerin	protein-coding
mm_124786.1	chr15	7975035	7975048	+	1	NA	intron (NM_001081402, intron 10 of 17)	ORR1B2|LTR|ERVL-MaLR	124168	NM_001081402	545085	Mm.321312	NM_198413	ENSMUSG00000039828	Wdr70	4833422F06Rik	WD repeat domain 70	protein-coding
mm_128467.1	chr15	50821673	50821689	-	1	NA	intron (NM_001310485, intron 5 of 7)	intron (NM_001310485, intron 5 of 7)	67368	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_94004.1	chr10	127595576	127595586	-	1	NA	intron (NM_008512, intron 6 of 88)	intron (NM_008512, intron 6 of 88)	25567	NM_008512	16971	Mm.271854	NM_008512	ENSMUSG00000040249	Lrp1	A2mr|AI316852|CD91|Lrp|b2b1554Clo	low density lipoprotein receptor-related protein 1	protein-coding
mm_98728.1	chr11	96351951	96351968	+	1	NA	exon (NM_134032, exon 1 of 2)	exon (NM_134032, exon 1 of 2)	327	NM_134032	103889	Mm.281153	NM_134032	ENSMUSG00000075588	Hoxb2	AI894218|Hox-2.8|Hoxbes2	homeobox B2	protein-coding
mm_13104.1	chr2	91498321	91498330	+	1	NA	intron (NM_172668, intron 30 of 37)	intron (NM_172668, intron 30 of 37)	40794	NM_001145857	228357	Mm.275149	NM_172668	ENSMUSG00000027253	Lrp4	6430526J12Rik|D230026E03|Megf7|mdig	low density lipoprotein receptor-related protein 4	protein-coding
mm_8306.1	chr1	144004143	144004155	-	1	NA	promoter-TSS (NM_009061)	promoter-TSS (NM_009061)	0	NM_009061	19735	Mm.28262	NM_009061	ENSMUSG00000026360	Rgs2	GOS8	regulator of G-protein signaling 2	protein-coding
mm_160443.1	chr8	95575202	95575202	-	1	NA	promoter-TSS (NM_027640)	promoter-TSS (NM_027640)	-5	NM_027640	70993	Mm.486561	NM_027640	ENSMUSG00000048400	Prss54	4931432M23Rik|Klkbl4	protease, serine 54	protein-coding
mm_85317.1	chr9	101243727	101243741	-	1	NA	intron (NM_001161362, intron 1 of 13)	L2|LINE|L2	8098	NM_001161362	235542	Mm.335386	NM_172144	ENSMUSG00000043154	Ppp2r3a	3222402P14Rik|A730042E07	protein phosphatase 2, regulatory subunit B'', alpha	protein-coding
mm_136847.1	chr17	12775242	12775252	+	1	NA	intron (NR_027773, intron 1 of 2)	intron (NR_027773, intron 1 of 2)	-5541	NM_010515	16004	Mm.26553	NM_010515	ENSMUSG00000023830	Igf2r	AI661837|CD222|CI-MPR|M6P/IGF2R|Mpr300	insulin-like growth factor 2 receptor	protein-coding
mm_69530.1	chr7	135652326	135652337	-	1	NA	promoter-TSS (NR_015548)	promoter-TSS (NR_015548)	-17	NR_015548	67765	Mm.445272	NR_015548	ENSMUSG00000097471	5830432E09Rik	-	RIKEN cDNA 5830432E09 gene	ncRNA
mm_111439.1	chr12	94652177	94652180	-	1	NA	Intergenic	Intergenic	724840	NR_106201	102466888		NR_106201	ENSMUSG00000098931	Mir8099-2	Gm27692|mmu-mir-8099-2	microRNA 8099-2	ncRNA
mm_2915.1	chr1	132008861	132008885	+	1	NA	intron (NM_007923, intron 1 of 4)	intron (NM_007923, intron 1 of 4)	1268	NM_007923	13714	Mm.254233	NM_007923	ENSMUSG00000026436	Elk4	2310011G17Rik|A130026I01Rik|BB162516|SAP-1|Sap1	ELK4, member of ETS oncogene family	protein-coding
mm_71117.1	chr8	36094854	36094868	+	1	NA	promoter-TSS (NM_172911)	promoter-TSS (NM_172911)	33	NM_172911	244418	Mm.244971	NM_172911	ENSMUSG00000050271	Prag1	9830148H23|D8Ertd82e|NACK|Sgk223|mFLJ00269	PEAK1 related kinase activating pseudokinase 1	protein-coding
mm_103775.1	chr11	82715448	82715449	-	1	NA	Intergenic	L1ME3C|LINE|L1	48873	NM_009839	12467	Mm.4126	NM_009839	ENSMUSG00000020698	Cct6b	CCT-zeta-2|CCTzeta-2|Cctz-2|TCP-1-zeta-2	chaperonin containing Tcp1, subunit 6b (zeta)	protein-coding
mm_156831.1	chrX	164373280	164373294	+	1	NA	promoter-TSS (NM_010216)	promoter-TSS (NM_010216)	-235	NM_001308489	14205	Mm.297978	NM_010216	ENSMUSG00000031380	Vegfd	AI325264|Figf|VEGF-D	vascular endothelial growth factor D	protein-coding
mm_125171.1	chr15	31339270	31339297	+	1	NA	intron (NM_027496, intron 1 of 3)	B3A|SINE|B2	28476	NM_001164441	67434	Mm.102470	NM_026153	ENSMUSG00000022237	Ankrd33b	0610012A05Rik|3021401C12Rik|5730557B15Rik	ankyrin repeat domain 33B	protein-coding
mm_110259.1	chr12	31713819	31713825	-	1	NA	5' UTR (NM_175191, exon 1 of 3)	5' UTR (NM_175191, exon 1 of 3)	104	NM_175191	73010	Mm.441517	NM_175191	ENSMUSG00000044067	Gpr22	2900068K05Rik|AW061316	G protein-coupled receptor 22	protein-coding
mm_26237.1	chr3	141465117	141465129	+	1	NA	promoter-TSS (NM_009472)	promoter-TSS (NM_009472)	-441	NM_009472	22253	Mm.24430	NM_009472	ENSMUSG00000059921	Unc5c	B130051O18Rik|Unc5h3|rcm	unc-5 netrin receptor C	protein-coding
mm_112533.1	chr13	9536814	9536824	+	1	NA	exon (NM_001081426, exon 5 of 37)	exon (NM_001081426, exon 5 of 37)	226991	NM_001347471	66505	Mm.397307	NM_144516	ENSMUSG00000021156	Zmynd11	2210402G22Rik|BS69	zinc finger, MYND domain containing 11	protein-coding
mm_30066.1	chr3	137919081	137919086	-	1	NA	intron (NM_019920, intron 2 of 6)	intron (NM_019920, intron 2 of 6)	528	NM_019920	56692	Mm.331392	NM_019920	ENSMUSG00000091512	Lamtor3	AW556229|Map2k1ip1|Mapbp|Mapksp1|Mp1	late endosomal/lysosomal adaptor, MAPK and MTOR activator 3	protein-coding
mm_54269.1	chr6	28833050	28833067	-	1	NA	intron (NM_019776, intron 16 of 23)	CpG	-1311	NM_138682	192198	Mm.443660	NM_138682	ENSMUSG00000049939	Lrrc4	MBAG1|NGL-2|NGL2|NLG-2|Nag14	leucine rich repeat containing 4	protein-coding
mm_147306.1	chr18	39661209	39661214	-	1	NA	Intergenic	Lx8b|LINE|L1	-112286	NM_011033	18459	Mm.9493	NM_011033	ENSMUSG00000051732	Pabpc2	Pabp|Pabp+|Pabp2	poly(A) binding protein, cytoplasmic 2	protein-coding
mm_164360.1	chr16	22892822	22892824	+	1	NA	intron (NR_075099, intron 1 of 5)	T-rich|Low_complexity|Low_complexity	808	NM_001276449	11625	Mm.197554	NM_013465	ENSMUSG00000022868	Ahsg	-	alpha-2-HS-glycoprotein	protein-coding
mm_22265.1	chr2	178407584	178407598	-	1	NA	promoter-TSS (NM_177191)	promoter-TSS (NM_177191)	67	NM_177191	320558	Mm.70781	NM_177191	ENSMUSG00000060445	Sycp2	3830402K23Rik|4930518F03Rik	synaptonemal complex protein 2	protein-coding
mm_57246.1	chr6	123283317	123283327	-	1	NA	3' UTR (NM_019948, exon 6 of 6)	3' UTR (NM_019948, exon 6 of 6)	6549	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_138566.1	chr17	35358970	35358989	+	1	NA	Intergenic	Intergenic	16646	NM_010392	15013	Mm.427969	NM_010392	ENSMUSG00000091705	H2-Q2	BE136769|ENSMUSG00000079507|Gm11132|H-2Q2|gs14-2	histocompatibility 2, Q region locus 2	protein-coding
mm_28290.1	chr3	89089956	89090008	-	1	NA	promoter-TSS (NM_001083808)	promoter-TSS (NM_001083808)	49	NM_001083808	72296	Mm.27687	NM_028188	ENSMUSG00000041263	Rusc1	2210403N08Rik|AA408288|NESCA	RUN and SH3 domain containing 1	protein-coding
mm_70023.1	chr7	142575924	142576017	-	1	NA	non-coding (NR_130974, exon 5 of 5)	non-coding (NR_130974, exon 5 of 5)	1177	NR_030416	735280		NR_030416	ENSMUSG00000076275	Mir675	Mirn675|mir-675|mmu-mir-675	microRNA 675	ncRNA
mm_43043.1	chr5	124070643	124070667	+	1	NA	intron (NM_019875, intron 11 of 11)	intron (NM_019875, intron 11 of 11)	25143	NM_019875	56325	Mm.254839	NM_019875	ENSMUSG00000029408	Abcb9	TAPL|mKIAA1520	ATP-binding cassette, sub-family B (MDR/TAP), member 9	protein-coding
mm_65762.1	chr7	28646772	28646780	-	1	NA	Intergenic	RMER6B|LTR|ERVK	-15761	NM_175319	101744	Mm.26022	NM_175319	ENSMUSG00000037469	Acp7	AU017076|C330005M16Rik|Papl	acid phosphatase 7, tartrate resistant	protein-coding
mm_116478.1	chr13	43560115	43560171	-	1	NA	promoter-TSS (NM_001081059)	promoter-TSS (NM_001081059)	48	NM_001081059	76137	Mm.426290	NM_001081059	ENSMUSG00000021371	Mcur1	6230416A05Rik|AU015498|AV136929|AW554392|C88263|Ccdc90a	mitochondrial calcium uniporter regulator 1	protein-coding
mm_29167.1	chr3	106485904	106485926	-	1	NA	promoter-TSS (NM_028110)	promoter-TSS (NM_028110)	-2	NR_033207	69206	Mm.14816	NM_001033146	ENSMUSG00000091575	2010016I18Rik	-	RIKEN cDNA 2010016I18 gene	ncRNA
mm_50831.1	chr6	54718994	54719012	+	1	NA	Intergenic	Intergenic	37379	NM_001289740	68235	Mm.233860	NM_026629	ENSMUSG00000038065	Mturn	2410066E13Rik|AI448550|B230212L03Rik	maturin, neural progenitor differentiation regulator homolog (Xenopus)	protein-coding
mm_632.1	chr1	40325587	40325609	+	1	NA	intron (NM_133193, intron 1 of 10)	intron (NM_133193, intron 1 of 10)	971	NM_133193	107527	Mm.155583	NM_133193	ENSMUSG00000070942	Il1rl2	AI481289|AW551444|IL-1Rrp2	interleukin 1 receptor-like 2	protein-coding
mm_108903.1	chr12	100199595	100199598	+	1	NA	promoter-TSS (NM_001313934)	promoter-TSS (NM_001313934)	161	NM_009790	12313	Mm.285993	NM_009790	ENSMUSG00000001175	Calm1	AI256814|AI327027|AI461935|AL024000|CaM|Calm	calmodulin 1	protein-coding
mm_145900.1	chr18	65634821	65634824	+	1	NA	intron (NM_207255, intron 3 of 5)	intron (NM_207255, intron 3 of 5)	-15207	NR_105742	100526497		NR_105742	ENSMUSG00000077113	Mir466p	mmu-mir-466p	microRNA 466p	ncRNA
mm_101599.1	chr11	34744658	34744686	-	1	NA	intron (NM_033374, intron 2 of 51)	Lx2B|LINE|L1	39233	NM_033374	94176	Mm.380679	NM_033374	ENSMUSG00000020143	Dock2	AI662014|AW122239|CED-5|Hch|MBC	dedicator of cyto-kinesis 2	protein-coding
mm_17785.1	chr2	32982148	32982166	-	1	NA	promoter-TSS (NM_019488)	promoter-TSS (NM_019488)	-101	NM_019488	56017	Mm.305754	NM_019488	ENSMUSG00000026791	Slc2a8	D2Ertd44e|GLUT8|GlutX1	solute carrier family 2, (facilitated glucose transporter), member 8	protein-coding
mm_108440.1	chr12	82339782	82339790	+	1	NA	intron (NM_172579, intron 1 of 20)	intron (NM_172579, intron 1 of 20)	28437	NM_172579	217692	Mm.261333	NM_172579	ENSMUSG00000042700	Sipa1l1	4931426N11Rik|AW213287|Spar|mKIAA0440	signal-induced proliferation-associated 1 like 1	protein-coding
mm_6948.1	chr1	85752454	85752464	-	1	NA	TTS (NR_106172)	TTS (NR_106172)	511	NR_106172	102466882		NR_106172	ENSMUSG00000098634	Mir8096	Gm27479|mmu-mir-8096	microRNA 8096	ncRNA
mm_156422.1	chrX	140923179	140923181	+	1	NA	promoter-TSS (NM_026103)	promoter-TSS (NM_026103)	-9	NM_026103	78789	Mm.244932	NM_026103	ENSMUSG00000031430	Vsig1	1700062D20Rik|4930405J24Rik	V-set and immunoglobulin domain containing 1	protein-coding
mm_126535.1	chr15	82022694	82022726	+	1	NA	intron (NM_010247, intron 4 of 12)	intron (NM_010247, intron 4 of 12)	6341	NM_010247	14375	Mm.288809	NM_010247	ENSMUSG00000022471	Xrcc6	70kDa|G22p1|Ku70	X-ray repair complementing defective repair in Chinese hamster cells 6	protein-coding
mm_12838.1	chr2	81669694	81669696	+	1	NA	Intergenic	Intergenic	-383963	NM_175513	241514	Mm.119383	NM_175513	ENSMUSG00000070866	Zfp804a	C630007C17Rik|Znf804a	zinc finger protein 804A	protein-coding
mm_80012.1	chr9	67852488	67852505	+	1	NA	exon (NM_177184, exon 2 of 85)	exon (NM_177184, exon 2 of 85)	12100	NM_177184	320528	Mm.241454	NM_177184	ENSMUSG00000035284	Vps13c	AI552542|AV026040|C230055H22Rik|W51662|chorein	vacuolar protein sorting 13C	protein-coding
mm_66439.1	chr7	44816587	44816608	-	1	NA	promoter-TSS (NM_030693)	promoter-TSS (NM_030693)	61	NR_033136	107503	Mm.389890	NM_030693	ENSMUSG00000038539	Atf5	AFTA|Atf7|Atfx|ODA-10	activating transcription factor 5	protein-coding
mm_32962.1	chr4	119814505	119814526	+	1	NA	promoter-TSS (NM_010657)	promoter-TSS (NM_010657)	-163	NM_010657	16656	Mm.302758	NM_010657	ENSMUSG00000028634	Hivep3	2900056N03Rik|A130075N07|AI848000|E030045D18Rik|KBP-1|KBP1|Krc|Rc|Schnurri-3|Shn3|Zas3	human immunodeficiency virus type I enhancer binding protein 3	protein-coding
mm_72398.1	chr8	81768499	81768508	+	1	NA	intron (NM_001024617, intron 6 of 24)	intron (NM_001024617, intron 6 of 24)	425941	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_13014.1	chr2	90965069	90965080	+	1	NA	intron (NM_001244891, intron 2 of 14)	intron (NM_001244891, intron 2 of 14)	24677	NM_017368	13046	Mm.29495	NM_017368	ENSMUSG00000005506	Celf1	1600010O03Rik|AA407467|Brunol2|CUG-BP|CUG-BP1|CUGBP|Cugbp1|D2Wsu101e|HNAB50|NAB50	CUGBP, Elav-like family member 1	protein-coding
mm_157361.1	chrX	37104524	37104528	-	1	NA	exon (NM_026573, exon 4 of 10)	exon (NM_026573, exon 4 of 10)	5796	NM_026573	68134	Mm.271160	NM_026573	ENSMUSG00000036572	Upf3b	5730594O13Rik|AI317193|AW541158|RENT3B|UPF3X	UPF3 regulator of nonsense transcripts homolog B (yeast)	protein-coding
mm_74148.1	chr8	123310661	123310665	+	1	NA	intron (NM_016925, intron 6 of 42)	intron (NM_016925, intron 6 of 42)	7913	NM_016925	14087	Mm.6536	NM_016925	ENSMUSG00000032815	Fanca	AW208693|FACA	Fanconi anemia, complementation group A	protein-coding
mm_111729.1	chr12	103773565	103773579	-	1	NA	promoter-TSS (NM_009246)	promoter-TSS (NM_009246)	61	NM_009246	20703	Mm.439695	NM_009246	ENSMUSG00000071177	Serpina1d	AI118301|Dom4|PI4|Spi1-4	serine (or cysteine) peptidase inhibitor, clade A, member 1D	protein-coding
mm_155899.1	chrX	101653619	101653624	+	1	NA	intron (NM_139144, intron 4 of 21)	intron (NM_139144, intron 4 of 21)	13403	NM_001290535	108155	Mm.487332	NM_139144	ENSMUSG00000034160	Ogt	1110038P24Rik|4831420N21Rik|AI115525|Ogtl	O-linked N-acetylglucosamine (GlcNAc) transferase (UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase)	protein-coding
mm_157666.1	chrX	58039902	58039904	-	1	NA	Intergenic	Intergenic	9275	NM_009575	22773	Mm.255890	NM_009575	ENSMUSG00000067860	Zic3	Bn|Ka	zinc finger protein of the cerebellum 3	protein-coding
mm_100575.1	chr11	120766250	120766266	+	1	NA	Intergenic	Intergenic	17946	NM_009053	19719	Mm.871	NM_009053	ENSMUSG00000025158	Rfng	-	RFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	protein-coding
mm_35778.1	chr4	46404150	46404160	-	1	NA	promoter-TSS (NM_053149)	promoter-TSS (NM_053149)	28	NM_053149	93966	Mm.25793	NM_053149	ENSMUSG00000028332	Hemgn	4921524M03Rik|AI317176|EDAG|Hgn|mNDR	hemogen	protein-coding
mm_50853.1	chr6	54897050	54897053	+	1	NA	Intergenic	Intergenic	74610	NM_001171007	107607	Mm.28498	NM_172729	ENSMUSG00000038058	Nod1	C230079P11|Card4|F830007N14Rik|Nlrc1	nucleotide-binding oligomerization domain containing 1	protein-coding
mm_88475.1	chr10	77606662	77606680	+	1	NA	promoter-TSS (NM_001301671)	promoter-TSS (NM_001301671)	73	NM_001301671	20610	Mm.24433	NM_019929	ENSMUSG00000020265	Sumo3	2810014B19Rik|D10Ertd345e|SMT3A|SUMO-3|Smt3h1	small ubiquitin-like modifier 3	protein-coding
mm_73392.1	chr8	105708271	105708302	+	1	NA	promoter-TSS (NM_198299)	promoter-TSS (NM_198299)	-17	NM_027655	71046	Mm.280888	NM_027655	ENSMUSG00000013158	4933405L10Rik	-	RIKEN cDNA 4933405L10 gene	protein-coding
mm_155058.1	chrX	42424381	42424390	+	1	NA	Intergenic	Intergenic	-78180	NM_011364	20400	Mm.441197	NM_011364	ENSMUSG00000005696	Sh2d1a	Gm686|SAP	SH2 domain containing 1A	protein-coding
mm_160941.1	chr11	94996156	94996156	+	1	NA	intron (NM_172261, intron 1 of 9)	CT-rich|Low_complexity|Low_complexity	4944	NM_172261	217124	Mm.229087	NM_172261	ENSMUSG00000038976	Ppp1r9b	SPL|Spn	protein phosphatase 1, regulatory subunit 9B	protein-coding
mm_60649.1	chr7	44857138	44857190	+	1	NA	promoter-TSS (NM_021549)	promoter-TSS (NM_021549)	18	NM_001290766	59047	Mm.238254	NM_021549	ENSMUSG00000002963	Pnkp	1810009G08Rik|PNK	polynucleotide kinase 3'- phosphatase	protein-coding
mm_43366.1	chr5	135404910	135404920	+	1	NA	Intergenic	Intergenic	-10369	NM_148932	107939	Mm.28399	NM_148932	ENSMUSG00000053293	Pom121	2610027A18Rik|C80273|mKIAA0618	nuclear pore membrane protein 121	protein-coding
mm_42500.1	chr5	115489532	115489534	+	1	NA	Intergenic	U4|snRNA|snRNA	-5049	NM_133760	75387	Mm.332616	NM_133760	ENSMUSG00000029524	Sirt4	4930596O17Rik	sirtuin 4	protein-coding
mm_140260.1	chr17	84613164	84613175	+	1	NA	intron (NM_177606, intron 27 of 29)	intron (NM_177606, intron 27 of 29)	-13330	NM_172256	213575	Mm.246119	NM_172256	ENSMUSG00000024253	Dync2li1	4933404O11Rik|CGI-60|D2lic|LIC3|mD2LIC	dynein cytoplasmic 2 light intermediate chain 1	protein-coding
mm_142098.1	chr17	35835131	35835195	-	1	NA	exon (NM_011655, exon 4 of 4)	exon (NM_011655, exon 4 of 4)	3138	NM_011655	22154	Mm.273538	NM_011655	ENSMUSG00000001525	Tubb5	AA408537|AI596182|B130022C14Rik|M(beta)5	tubulin, beta 5 class I	protein-coding
mm_157595.1	chrX	53240087	53240098	-	1	NA	Intergenic	Intergenic	29713	NM_030167	78755	Mm.28559	NM_030167	ENSMUSG00000036022	Fam122b	4632404H22Rik|AI256344|SPACIA2	family with sequence similarity 122, member B	protein-coding
mm_75126.1	chr8	34890669	34890719	-	1	NA	intron (NM_175091, intron 3 of 26)	intron (NM_175091, intron 3 of 26)	74996	NM_175091	21951	Mm.88364	NM_175091	ENSMUSG00000031529	Tnks	4930554K12Rik|AI662855|ARTD5|C86528|D130072O21Rik|TANK1|mTNKS1	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase	protein-coding
mm_150035.1	chr19	29377075	29377087	+	1	NA	intron (NM_021893, intron 3 of 6)	L2a|LINE|L2	9643	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_53701.1	chr6	142814345	142814385	+	1	NA	non-coding (NR_045707, exon 1 of 7)	non-coding (NR_045707, exon 1 of 7)	134	NR_045707	665037	Mm.401493	NR_045707	ENSMUSG00000072683	Gm7457	EG665037|ENSMUSG00000072683	predicted gene 7457	ncRNA
mm_126111.1	chr15	78253273	78253303	+	1	NA	intron (NM_008677, intron 3 of 9)	intron (NM_008677, intron 3 of 9)	8477	NM_008677	17972	Mm.2068	NM_008677	ENSMUSG00000071715	Ncf4	AI451400|p40phox	neutrophil cytosolic factor 4	protein-coding
mm_79599.1	chr9	58488135	58488161	+	1	NA	promoter-TSS (NM_176921)	promoter-TSS (NM_176921)	-455	NM_176921	319477	Mm.153674	NM_176921	ENSMUSG00000066607	6030419C18Rik	-	RIKEN cDNA 6030419C18 gene	protein-coding
mm_15966.1	chr2	166059313	166059328	+	1	NA	exon (NM_008679, exon 15 of 23)	exon (NM_008679, exon 15 of 23)	66683	NM_008679	17979	Mm.469663	NM_008679	ENSMUSG00000027678	Ncoa3	2010305B15Rik|AW321064|Actr|Aib1|KAT13B|Rac3|Src3|Tram-1|Tram1|bHLHe42|p/Cip|pCip	nuclear receptor coactivator 3	protein-coding
mm_104962.1	chr11	100143706	100143742	-	1	NA	promoter-TSS (NM_001313963)	promoter-TSS (NM_001313963)	-25	NM_001313963	16669	Mm.439699	NM_008471	ENSMUSG00000020911	Krt19	AI663979|CK-19|EndoC|K19|Krt-1.19|Krt1-19	keratin 19	protein-coding
mm_140941.1	chr17	24455266	24455345	-	1	NA	promoter-TSS (NM_007893)	promoter-TSS (NM_007893)	87	NM_001301784	13560	Mm.163132	NM_007893	ENSMUSG00000024137	E4f1	p120E4F|phi-AP3	E4F transcription factor 1	protein-coding
mm_110430.1	chr12	46819189	46819204	-	1	NA	promoter-TSS (NM_021361)	promoter-TSS (NM_021361)	-421	NM_021361	664883	Mm.247195	NM_021361	ENSMUSG00000021047	Nova1	9430099M15Rik|G630039L02|Nova-1	neuro-oncological ventral antigen 1	protein-coding
mm_88681.1	chr10	80053967	80053984	+	1	NA	promoter-TSS (NM_001037741)	promoter-TSS (NM_001037741)	-44	NM_001037741	625249	Mm.332810	NM_008162	ENSMUSG00000075706	Gpx4	GPx-4|GSHPx-4|PHGPx|mtPHGPx|snGPx	glutathione peroxidase 4	protein-coding
mm_81686.1	chr9	111118292	111118312	+	1	NA	5' UTR (NM_001164838, exon 1 of 15)	5' UTR (NM_001164838, exon 1 of 15)	191	NM_001164838	71268	Mm.302287	NM_027742	ENSMUSG00000032497	Lrrfip2	5133400F20Rik|AI850587	leucine rich repeat (in FLII) interacting protein 2	protein-coding
mm_26637.1	chr3	153260800	153260841	+	1	NA	intron (NM_011372, intron 3 of 4)	intron (NM_011372, intron 3 of 4)	37829	NR_126464	75489	Mm.443252	NR_126464	ENSMUSG00000105023	1700012D16Rik	-	RIKEN cDNA 1700012D16 gene	ncRNA
mm_14949.1	chr2	151973413	151973425	+	1	NA	promoter-TSS (NM_001289151)	promoter-TSS (NM_001289151)	-25	NM_001289151	73847	Mm.272444	NM_028666	ENSMUSG00000027459	Fam110a	1700008J10Rik|5430432M24Rik|AI747080	family with sequence similarity 110, member A	protein-coding
mm_59924.1	chr7	30422462	30422470	+	1	NA	promoter-TSS (NM_172142)	promoter-TSS (NM_172142)	-838	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_142835.1	chr17	51787026	51787043	-	1	NA	intron (NM_009122, intron 5 of 10)	(A)n|Simple_repeat|Simple_repeat	25020	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_34648.1	chr4	150847082	150847104	+	1	NA	intron (NR_040649, intron 3 of 3)	intron (NR_040649, intron 3 of 3)	7856	NR_040649	73348	Mm.396218	NR_040649	ENSMUSG00000078492	1700045H11Rik	-	RIKEN cDNA 1700045H11 gene	ncRNA
mm_113456.1	chr13	35958851	35958862	+	1	NA	Intergenic	ORR1B2|LTR|ERVL-MaLR	-9050	NM_029628	76487	Mm.44745	NM_029628	ENSMUSG00000050423	Ppp1r3g	1600032L17Rik	protein phosphatase 1, regulatory (inhibitor) subunit 3G	protein-coding
mm_69441.1	chr7	132932149	132932161	-	1	NA	Intergenic	Intergenic	-17467	NM_207302	360216	Mm.389984	NM_207302	ENSMUSG00000030967	Zranb1	9330160G10Rik|D7Wsu87e|Gm1956|Trabid	zinc finger, RAN-binding domain containing 1	protein-coding
mm_114377.1	chr13	63151535	63151547	+	1	NA	intron (NM_001289926, intron 5 of 15)	intron (NM_001289926, intron 5 of 15)	-88488	NR_110520	72061	Mm.188105	NM_028079	ENSMUSG00000021458	2010111I01Rik	2300006M17Rik|AP-O|AW742919|Aopep|ApO|mir-23b|mir-24-1|mir-27b	RIKEN cDNA 2010111I01 gene	protein-coding
mm_28372.1	chr3	89913145	89913172	-	1	NA	promoter-TSS (NM_010559)	promoter-TSS (NM_010559)	38	NM_001310676	16194	Mm.2856	NM_010559	ENSMUSG00000027947	Il6ra	CD126|IL-6R|IL-6R-alpha|IL-6RA|Il6r	interleukin 6 receptor, alpha	protein-coding
mm_45576.1	chr5	73632422	73632434	-	1	NA	promoter-TSS (NM_153568)	promoter-TSS (NM_153568)	-7	NM_153568	231296	Mm.168948	NM_153568	ENSMUSG00000067206	Lrrc66	-	leucine rich repeat containing 66	protein-coding
mm_67858.1	chr7	98975975	98975997	-	1	NA	intron (NM_178635, intron 12 of 14)	LTR53|LTR|ERVL	137141	NM_001285795	22411	Mm.22182	NM_009519	ENSMUSG00000015957	Wnt11	-	wingless-type MMTV integration site family, member 11	protein-coding
mm_126231.1	chr15	78947938	78947946	+	1	NA	5' UTR (NM_001039155, exon 1 of 8)	5' UTR (NM_001039155, exon 1 of 8)	218	NM_001039155	110253	Mm.123714	NM_138579	ENSMUSG00000033088	Triobp	AI428493|EST478828|Tara|mKIAA1662	TRIO and F-actin binding protein	protein-coding
mm_133999.1	chr16	4769724	4769742	-	1	NA	exon (NM_025670, exon 4 of 6)	exon (NM_025670, exon 4 of 6)	20202	NM_025670	66626	Mm.157648	NM_025670	ENSMUSG00000004071	Cdip1	2700048O17Rik|5730403B10Rik|AU018521|AW742692|CDIP	cell death inducing Trp53 target 1	protein-coding
mm_89495.1	chr10	93833842	93833861	+	1	NA	intron (NM_001206851, intron 1 of 6)	CpG	2296	NM_001206851	327799	Mm.491598	NM_183199	ENSMUSG00000020020	Usp44	E430004F17Rik	ubiquitin specific peptidase 44	protein-coding
mm_80511.1	chr9	79755405	79755424	+	1	NA	3' UTR (NM_009945, exon 4 of 4)	3' UTR (NM_009945, exon 4 of 4)	4439	NM_009945	12866	Mm.152627	NM_009945	ENSMUSG00000032330	Cox7a2	COX7AL|Cox7a3|CoxVIIa-L	cytochrome c oxidase subunit VIIa 2	protein-coding
mm_12888.1	chr2	84773306	84773332	+	1	NA	exon (NM_009776, exon 3 of 8)	exon (NM_009776, exon 3 of 8)	2110	NM_009776	12258	Mm.38888	NM_009776	ENSMUSG00000023224	Serping1	C1INH|C1nh	serine (or cysteine) peptidase inhibitor, clade G, member 1	protein-coding
mm_32873.1	chr4	118527117	118527156	+	1	NA	promoter-TSS (NM_025572)	promoter-TSS (NM_025572)	-139	NM_025572	66451	Mm.34431	NM_025572	ENSMUSG00000028536	2610528J11Rik	TEMP	RIKEN cDNA 2610528J11 gene	protein-coding
mm_100415.1	chr11	119428068	119428088	+	1	NA	Intergenic	Intergenic	37606	NR_035453	100316690		NR_035453	ENSMUSG00000088015	Mir1932	mir-1932|mmu-mir-1932	microRNA 1932	ncRNA
mm_128973.1	chr15	74832394	74832396	-	1	NA	Intergenic	Intergenic	9248	NM_001033229	110115	Mm.322606	NM_001033229	ENSMUSG00000075604	Cyp11b1	AA389061|CPN1|Cyp11b|Cyp11b-1|FHI	cytochrome P450, family 11, subfamily b, polypeptide 1	protein-coding
mm_32056.1	chr4	97777396	97777402	+	1	NA	promoter-TSS (NM_001122953)	promoter-TSS (NM_001122953)	-227	NM_001122953	18027	Mm.31274	NM_010905	ENSMUSG00000028565	Nfia	1110047K16Rik|9430022M17Rik|CTF|NF1-A|NF1A	nuclear factor I/A	protein-coding
mm_147899.1	chr18	65328683	65328696	-	1	NA	intron (NM_001037294, intron 4 of 12)	MIRb|SINE|MIR	65199	NM_001037294	225638	Mm.296528	NM_001037294	ENSMUSG00000032845	Alpk2	Gm549|Hak	alpha-kinase 2	protein-coding
mm_109209.1	chr12	108677633	108677641	+	1	NA	intron (NM_001163394, intron 7 of 13)	intron (NM_001163394, intron 7 of 13)	19017	NR_029771	723909		NR_029771	ENSMUSG00000065436	Mir342	Mirn342|mmu-mir-342	microRNA 342	ncRNA
mm_121185.1	chr14	103049372	103049385	+	1	NA	exon (NM_008392, exon 2 of 5)	exon (NM_008392, exon 2 of 5)	2366	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_68922.1	chr7	126470193	126470216	-	1	NA	intron (NR_110346, intron 4 of 9)	intron (NR_110346, intron 4 of 9)	2890	NR_110346	20399	Mm.8538	NM_011363	ENSMUSG00000030733	Sh2b1	AI425885|C530001K22Rik|Irip|Psm|SH2-B|SH2-Bb|Sh2bpsm1|mKIAA1299	SH2B adaptor protein 1	protein-coding
mm_65028.1	chr7	18484486	18484488	-	1	NA	promoter-TSS (NM_001029893)	promoter-TSS (NM_001029893)	-338	NM_001029893	574429	Mm.296754	NM_001029893	ENSMUSG00000070799	Psg26	EG574429|cea14	pregnancy-specific glycoprotein 26	protein-coding
mm_151366.1	chr19	55925952	55925979	+	1	NA	intron (NM_009333, intron 12 of 12)	intron (NM_009333, intron 12 of 12)	30644	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_126219.1	chr15	78913932	78913966	+	1	NA	promoter-TSS (NM_020271)	promoter-TSS (NM_020271)	30	NM_020271	57028	Mm.263169	NM_020271	ENSMUSG00000022436	Pdxp	1600027H05Rik|AB041662|PLPP	pyridoxal (pyridoxine, vitamin B6) phosphatase	protein-coding
mm_61040.1	chr7	49759101	49759163	+	1	NA	promoter-TSS (NM_001146052)	promoter-TSS (NM_001146052)	26	NM_001146049	53415	Mm.20801	NM_016865	ENSMUSG00000039745	Htatip2	AW111545|Cc3|Tip30	HIV-1 Tat interactive protein 2	protein-coding
mm_12858.1	chr2	83761734	83761747	+	1	NA	intron (NM_008402, intron 4 of 29)	intron (NM_008402, intron 4 of 29)	37343	NM_008402	16410	Mm.227	NM_008402	ENSMUSG00000027087	Itgav	1110004F14Rik|2610028E01Rik|CD51|D430040G12Rik	integrin alpha V	protein-coding
mm_72294.1	chr8	75213483	75213492	+	1	NA	promoter-TSS (NM_029182)	promoter-TSS (NM_029182)	-457	NM_029182	75141	Mm.179267	NM_029182	ENSMUSG00000034472	Rasd2	4930526B11Rik|AU045414|Rhes|TEM-2|TEM2	RASD family, member 2	protein-coding
mm_164064.1	chr14	118052089	118052097	-	1	NA	5' UTR (NM_010024, exon 1 of 8)	5' UTR (NM_010024, exon 1 of 8)	153	NM_010024	13190	Mm.19987	NM_010024	ENSMUSG00000022129	Dct	DT|TRP-2|TRP2|Tyrp-2|Tyrp2|slaty|slt	dopachrome tautomerase	protein-coding
mm_108360.1	chr12	80790548	80790574	+	1	NA	promoter-TSS (NM_178682)	promoter-TSS (NM_178682)	29	NM_001242419	217684	Mm.341776	NM_178682	ENSMUSG00000021133	Susd6	4933426M11Rik|mKIAA0247	sushi domain containing 6	protein-coding
mm_162020.1	chr19	45742918	45742918	-	1	NA	promoter-TSS (NM_010205)	promoter-TSS (NM_010205)	-34	NM_001166362	14179	Mm.4012	NM_010205	ENSMUSG00000025219	Fgf8	Aigf|Fgf-8	fibroblast growth factor 8	protein-coding
mm_157206.1	chrX	12732968	12732972	-	1	NA	intron (NM_012005, intron 10 of 29)	B1F2|SINE|Alu	29003	NM_012005	26896	Mm.17616	NM_012005	ENSMUSG00000064127	Med14	9930001L01Rik|AU041628|Crsp2|ENSMUSG00000073278|Gm641|ORF1|Trap170	mediator complex subunit 14	protein-coding
mm_96355.1	chr11	67023548	67023555	+	1	NA	Intergenic	RMER17C|LTR|ERVK	-1603	NM_001291042	338369	Mm.128138	NM_177392	ENSMUSG00000050270	Tmem220	-	transmembrane protein 220	protein-coding
mm_151040.1	chr19	47023572	47023582	+	1	NA	exon (NM_146100, exon 3 of 3)	exon (NM_146100, exon 3 of 3)	-8388	NM_001164363	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_169554.1	chr15	103243744	103243750	+	1	NA	exon (NM_010447, exon 8 of 10)	exon (NM_010447, exon 8 of 10)	3293	NR_002883	434858	Mm.391346	NR_002883		Gm5643	EG434858	heterogeneous nuclear ribonucleoprotein A1 pseudogene	pseudo
mm_116648.1	chr13	49183849	49183857	-	1	NA	Intergenic	Intergenic	-3694	NM_013610	18081	Mm.18503	NM_013610	ENSMUSG00000037966	Ninj1	AU024536	ninjurin 1	protein-coding
mm_55451.1	chr6	67292255	67292265	-	1	NA	exon (NM_008354, exon 16 of 16)	exon (NM_008354, exon 16 of 16)	25281	NM_025814	66870	Mm.240490	NM_025814	ENSMUSG00000036371	Serbp1	1200009K13Rik|9330147J08Rik|AL022786|Pairbp1	serpine1 mRNA binding protein 1	protein-coding
mm_156175.1	chrX	130330315	130330325	+	1	NA	intron (NM_172493, intron 26 of 26)	intron (NM_172493, intron 26 of 26)	580578	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diaph2	Dia3|Diap2|Drf2|E430022I22Rik	diaphanous related formin 2	protein-coding
mm_25448.1	chr3	108312906	108312930	+	1	NA	intron (NM_001271599, intron 3 of 20)	RMER17C|LTR|ERVK	28854	NM_019972	20661	Mm.157119	NM_019972	ENSMUSG00000068747	Sort1	2900053A11Rik|AI852375|Ntr3|Ntsr3	sortilin 1	protein-coding
mm_30997.1	chr4	40143369	40143444	+	1	NA	5' UTR (NM_007386, exon 1 of 21)	5' UTR (NM_007386, exon 1 of 21)	141	NM_007386	11428	Mm.331547	NM_007386	ENSMUSG00000028405	Aco1	Aco-1|Irebp|Irp1	aconitase 1	protein-coding
mm_70888.1	chr8	25532126	25532136	+	1	NA	intron (NM_001079908, intron 1 of 17)	intron (NM_001079908, intron 1 of 17)	13372	NM_001079908	14182	Mm.265716	NM_010206	ENSMUSG00000031565	Fgfr1	AW208770|Eask|FGFR-I|FLG|Fgfr-1|Flt-2|Hspy|MFR|bFGF-R-1|c-fgr	fibroblast growth factor receptor 1	protein-coding
mm_89307.1	chr10	87916359	87916376	+	1	NA	intron (NM_001111274, intron 4 of 4)	MLT1B|LTR|ERVL-MaLR	-50304	NR_000040	22172	Mm.391420	NR_000040		Tyms-ps	-	thymidylate synthase, pseudogene	pseudo
mm_126573.1	chr15	82256192	82256204	+	1	NA	non-coding (NR_037698, exon 1 of 2)	non-coding (NR_037698, exon 1 of 2)	175	NR_037698	76505	Mm.23023	NR_037697	ENSMUSG00000068099	1500009C09Rik	-	RIKEN cDNA 1500009C09 gene	ncRNA
mm_168781.1	chr12	18070534	18070553	-	1	NA	Intergenic	RLTR10C|LTR|ERVK	379729	NM_016677	53602	Mm.313619	NM_016677	ENSMUSG00000071379	Hpcal1	NVP-3|Nvp3|VILIP3|Vnsl3|Vsnl3	hippocalcin-like 1	protein-coding
mm_81008.1	chr9	103721264	103721306	+	1	NA	intron (NM_178638, intron 2 of 5)	intron (NM_178638, intron 2 of 5)	40552	NM_178638	81907	Mm.384704	NM_178638	ENSMUSG00000042757	Tmem108	AI462967|B130017P16Rik|R74726	transmembrane protein 108	protein-coding
mm_137968.1	chr17	33524171	33524231	+	1	NA	non-coding (NR_137626, exon 1 of 23)	non-coding (NR_137626, exon 1 of 23)	116	NM_001329147	224697	Mm.29304	NM_172619	ENSMUSG00000024299	Adamts10	9430006O18|AW045948|Adam-ts10|Adamts-10|Znmp	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 10	protein-coding
mm_28914.1	chr3	98853131	98853143	-	1	NA	exon (NM_001304800, exon 4 of 4)	exon (NM_001304800, exon 4 of 4)	6657	NM_001304800	15492	Mm.140811	NM_008293	ENSMUSG00000027871	Hsd3b1	3-beta-HSD I|D3Ertd383e	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1	protein-coding
mm_132586.1	chr16	38362235	38362251	+	1	NA	promoter-TSS (NM_022318)	promoter-TSS (NM_022318)	53	NM_022318	64082	Mm.390856	NM_022318	ENSMUSG00000022803	Popdc2	AV006127|Pop2	popeye domain containing 2	protein-coding
mm_82918.1	chr9	35070354	35070358	-	1	NA	intron (NM_009178, intron 1 of 10)	intron (NM_009178, intron 1 of 10)	-46372	NR_029475	78934	Mm.391688	NR_029475	ENSMUSG00000070315	4930581F22Rik	-	RIKEN cDNA 4930581F22 gene	ncRNA
mm_96597.1	chr11	69090942	69090950	+	1	NA	3' UTR (NM_009497, exon 5 of 5)	3' UTR (NM_009497, exon 5 of 5)	2418	NM_009497	22318	Mm.28643	NM_009497	ENSMUSG00000020894	Vamp2	Syb-2|Syb2|sybII	vesicle-associated membrane protein 2	protein-coding
mm_46845.1	chr5	113507166	113507168	-	1	NA	Intergenic	Intergenic	-43253	NM_177292	320916	Mm.102783	NM_177292	ENSMUSG00000063430	Wscd2	4933413A10Rik|C530024P05Rik|Gm450	WSC domain containing 2	protein-coding
mm_64154.1	chr7	141329308	141329312	+	1	NA	intron (NR_024509, intron 1 of 2)	intron (NR_024509, intron 1 of 2)	1180	NM_027797	71448	Mm.248960	NM_027797	ENSMUSG00000025505	Tmem80	5530601I19Rik	transmembrane protein 80	protein-coding
mm_164513.1	chr16	95585554	95585560	-	1	NA	intron (NM_001302152, intron 1 of 10)	CpG	1036	NM_001302152	13876	Mm.164531	NM_133659	ENSMUSG00000040732	Erg	D030036I24Rik	avian erythroblastosis virus E-26 (v-ets) oncogene related	protein-coding
mm_43172.1	chr5	127564296	127564299	+	1	NA	3' UTR (NM_175432, exon 9 of 9)	3' UTR (NM_175432, exon 9 of 9)	53095	NM_133895	100561	Mm.28506	NM_133895	ENSMUSG00000029416	Slc15a4	AA987064|AW742963|C130069N12Rik|PHT1|PTR4	solute carrier family 15, member 4	protein-coding
mm_7905.1	chr1	133661346	133661386	-	1	NA	promoter-TSS (NM_001166552)	promoter-TSS (NM_001166552)	33	NM_001276767	70579	Mm.245357	NM_144530	ENSMUSG00000102976	Zc3h11a	1110003F06Rik|5730454B08Rik|G630041M05Rik|Zc3hdc11a|Zc3hh11a|mKIAA0663	zinc finger CCCH type containing 11A	protein-coding
mm_130551.1	chr15	98985823	98985843	-	1	NA	promoter-TSS (NR_045991)	promoter-TSS (NR_045991)	-132	NR_045991	75951	Mm.441657	NR_045991	ENSMUSG00000097587	4930578M01Rik	3010001K12Rik	RIKEN cDNA 4930578M01 gene	ncRNA
mm_13203.1	chr2	93461362	93461378	+	1	NA	intron (NR_040532, intron 2 of 4)	intron (NR_040532, intron 2 of 4)	481	NM_001271461	12521	Mm.4261	NM_007656	ENSMUSG00000027215	Cd82	AA682076|AL023070|C33|IA4|Kai1|Tspan27	CD82 antigen	protein-coding
mm_99366.1	chr11	101732978	101733008	+	1	NA	promoter-TSS (NM_144831)	promoter-TSS (NM_144831)	37	NM_144831	217207	Mm.28186	NM_144831	ENSMUSG00000034931	Dhx8	Ddx8|mDEAH6|mKIAA4096	DEAH (Asp-Glu-Ala-His) box polypeptide 8	protein-coding
mm_35572.1	chr4	41681084	41681086	-	1	NA	intron (NM_016673, intron 2 of 9)	B1_Mur3|SINE|Alu	14368	NM_001136056	12804	Mm.425178	NM_016673	ENSMUSG00000028444	Cntfr	Cntfralpha	ciliary neurotrophic factor receptor	protein-coding
mm_62009.1	chr7	91262693	91262722	+	1	NA	intron (NM_011807, intron 1 of 22)	intron (NM_011807, intron 1 of 22)	171921	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_2118.1	chr1	87878206	87878214	+	1	NA	intron (NM_177646, intron 1 of 29)	intron (NM_177646, intron 1 of 29)	-23911	NR_136921	100503175	Mm.426422	NR_136921	ENSMUSG00000101942	Gm19582	-	predicted gene, 19582	ncRNA
mm_169933.1	chr1	66033254	66033259	+	1	NA	Intergenic	Intergenic	106734	NM_027010	12969	Mm.275362	NM_027010	ENSMUSG00000025945	Crygf	3110001K11Rik|Cryg-2|DGcry-2|Len-2	crystallin, gamma F	protein-coding
mm_110518.1	chr12	54862498	54862517	-	1	NA	intron (NM_007688, intron 1 of 3)	CpG	370	NM_007688	12632	Mm.276826	NM_007688	ENSMUSG00000062929	Cfl2	-	cofilin 2, muscle	protein-coding
mm_37438.1	chr4	122961450	122961453	-	1	NA	promoter-TSS (NM_029662)	promoter-TSS (NM_029662)	-263	NM_029662	76574	Mm.331842	NM_029662	ENSMUSG00000028655	Mfsd2a	1700018O18Rik|Mfsd2|NLS1	major facilitator superfamily domain containing 2A	protein-coding
mm_130262.1	chr15	96642884	96642984	-	1	NA	promoter-TSS (NM_001166456)	promoter-TSS (NM_001166456)	-21	NM_001166458	105727	Mm.103568	NM_134086	ENSMUSG00000023169	Slc38a1	AA408026|AA409865|AL022800|AU015942|NAT2	solute carrier family 38, member 1	protein-coding
mm_98384.1	chr11	94209829	94209852	+	1	NA	Intergenic	Intergenic	-1614	NM_009427	22057	Mm.259673	NM_009427	ENSMUSG00000037573	Tob1	Tob|Trob	transducer of ErbB-2.1	protein-coding
mm_83943.1	chr9	56851946	56852018	-	1	NA	promoter-TSS (NM_198673)	promoter-TSS (NM_198673)	-19	NM_198673	382075	Mm.335177	NM_198673	ENSMUSG00000045620	Odf3l1	BC049697|Gm1116	outer dense fiber of sperm tails 3-like 1	protein-coding
mm_151666.1	chr19	4163348	4163358	-	1	NA	promoter-TSS (NM_021485)	promoter-TSS (NM_021485)	-108	NM_021485	58988	Mm.271937	NM_021485	ENSMUSG00000024830	Rps6kb2	70kDa|S6K2	ribosomal protein S6 kinase, polypeptide 2	protein-coding
mm_100035.1	chr11	114983013	114983025	+	1	NA	3' UTR (NM_145437, exon 4 of 4)	3' UTR (NM_145437, exon 4 of 4)	6867	NM_145437	217305	Mm.275986	NM_145437	ENSMUSG00000034641	Cd300ld	4732429D16Rik|CLM5|Cd300ld1|LMIR4|MAIR-IV|clm-5	CD300 molecule like family member d	protein-coding
mm_2763.1	chr1	130478494	130478497	+	1	NA	Intergenic	Lx9|LINE|L1	-15751	NM_010016	13136	Mm.101591	NM_010016	ENSMUSG00000026399	Cd55	Daf|Daf-GPI|Daf1|GPI-DAF	CD55 molecule, decay accelerating factor for complement	protein-coding
mm_90596.1	chr10	128303323	128303352	+	1	NA	promoter-TSS (NM_001252327)	promoter-TSS (NM_001252327)	2	NM_001252326	103135	Mm.244183	NM_133992	ENSMUSG00000005682	Pan2	1200014O24Rik|AI047843|AW742773|Usp52|mKIAA0710	PAN2 poly(A) specific ribonuclease subunit	protein-coding
mm_3877.1	chr1	161034582	161034614	+	1	NA	promoter-TSS (NM_173424)	promoter-TSS (NM_173424)	-339	NM_173424	240869	Mm.296127	NM_173424	ENSMUSG00000043467	Zbtb37	D430004I08Rik	zinc finger and BTB domain containing 37	protein-coding
mm_172496.1	chr7	63606088	63606091	+	1	NA	intron (NM_130880, intron 1 of 13)	intron (NM_130880, intron 1 of 13)	161317	NM_130880	170711	Mm.156872	NM_130880	ENSMUSG00000033510	Otud7a	AJ430384|Otud7	OTU domain containing 7A	protein-coding
mm_111986.1	chr12	110485618	110485668	-	1	NA	promoter-TSS (NM_001081458)	promoter-TSS (NM_001081458)	-96	NM_001081457	26931	Mm.240396	NM_012023	ENSMUSG00000017843	Ppp2r5c	2610043M05Rik|2700063L20Rik|AI060890|AW545884|C85228|D12Bwg0916e|mKIAA0044	protein phosphatase 2, regulatory subunit B', gamma	protein-coding
mm_106206.1	chr11	116850912	116850931	-	1	NA	3' UTR (NM_011358, exon 3 of 3)	3' UTR (NM_011358, exon 3 of 3)	2173	NM_011358	20382	Mm.21841	NM_011358	ENSMUSG00000034120	Srsf2	D11Wsu175e|MRF-1|Pr264|SC35|Sfrs10|Sfrs2	serine/arginine-rich splicing factor 2	protein-coding
mm_114357.1	chr13	60955167	60955168	+	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	-13232	NM_009411	21984	Mm.2372	NM_009411	ENSMUSG00000033834	Tpbpa	AV033951|Tb-1|Tb1|Tpbp|b2b1247Clo	trophoblast specific protein alpha	protein-coding
mm_63487.1	chr7	127748168	127748177	+	1	NA	intron (NM_172748, intron 1 of 10)	intron (NM_172748, intron 1 of 10)	1397	NM_172748	233902	Mm.259353	NM_172748	ENSMUSG00000030811	Fbxl19	6030430O11|BC059812|Fbl19	F-box and leucine-rich repeat protein 19	protein-coding
mm_144424.1	chr18	21001277	21001287	+	1	NA	promoter-TSS (NM_207623)	promoter-TSS (NM_207623)	-18	NM_019706	56515	Mm.253542	NM_019706	ENSMUSG00000024317	Rnf138	2410015A17Rik|2810480D20Rik|STRIN|Trif|Trif-d	ring finger protein 138	protein-coding
mm_126815.1	chr15	88600281	88600332	+	1	NA	promoter-TSS (NM_027306)	promoter-TSS (NM_027306)	4	NM_027306	70073	Mm.45306	NM_027306	ENSMUSG00000054117	Zdhhc25	1700030J15Rik	zinc finger, DHHC domain containing 25	protein-coding
mm_121692.1	chr14	13961293	13961303	-	1	NA	promoter-TSS (NM_025435)	promoter-TSS (NM_025435)	15	NM_001285780	66231	Mm.295875	NM_025435	ENSMUSG00000053453	Thoc7	Nif3l1bp1	THO complex 7	protein-coding
mm_129067.1	chr15	75664083	75664091	-	1	NA	exon (NM_028404, exon 11 of 14)	exon (NM_028404, exon 11 of 14)	14703	NM_028404	72960	Mm.182401	NM_028404	ENSMUSG00000000934	Top1mt	2900052H09Rik	DNA topoisomerase 1, mitochondrial	protein-coding
mm_162466.1	chr1	131135407	131135424	+	1	NA	intron (NM_145508, intron 2 of 2)	intron (NM_145508, intron 2 of 2)	2819	NM_145508	226419	Mm.39299	NM_145508	ENSMUSG00000016526	Dyrk3	BC006704	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 3	protein-coding
mm_154513.1	chrM	12388	12432	-	1	NA	NA	Intergenic	NA	NA								
mm_101483.1	chr11	31359335	31359338	-	1	NA	TTS (NM_011491)	TTS (NM_011491)	10725	NM_011491	20856	Mm.32506	NM_011491	ENSMUSG00000020303	Stc2	AW125853|Stc2l|mustc2	stanniocalcin 2	protein-coding
mm_137644.1	chr17	28530835	28530879	+	1	NA	promoter-TSS (NM_026290)	promoter-TSS (NM_026290)	-4	NM_026290	67645	Mm.46170	NM_026290	ENSMUSG00000024223	Armc12	4930511I11Rik|AV041658	armadillo repeat containing 12	protein-coding
mm_85668.1	chr9	107676074	107676078	-	1	NA	exon (NM_008140, exon 8 of 9)	exon (NM_008140, exon 8 of 9)	3516	NM_008140	14685	Mm.284853	NM_008140	ENSMUSG00000034837	Gnat1	Gnat-1|Ird1|Ird2|Tralpha|irdc|irdr|transducin	guanine nucleotide binding protein, alpha transducing 1	protein-coding
mm_168976.1	chr12	88274496	88274504	-	1	NA	promoter-TSS (NM_001013824)	promoter-TSS (NM_001013824)	-3	NM_001013824	435337	Mm.441366	NM_001013824	ENSMUSG00000079029	Gm5662	EG435337	predicted gene 5662	protein-coding
mm_146668.1	chr18	12220099	12220139	-	1	NA	intron (NM_008720, intron 3 of 24)	intron (NM_008720, intron 3 of 24)	16267	NM_008720	18145	Mm.3484	NM_008720	ENSMUSG00000024413	Npc1	A430089E03Rik|C85354|D18Ertd139e|D18Ertd723e|lcsd|nmf164|spm	Niemann-Pick type C1	protein-coding
mm_60350.1	chr7	44359106	44359114	+	1	NA	TTS (NM_001034115)	TTS (NM_001034115)	15920	NM_027049	69349	Mm.358922	NM_027049	ENSMUSG00000008028	1700008O03Rik	-	RIKEN cDNA 1700008O03 gene	protein-coding
mm_16663.1	chr2	6721607	6721629	-	1	NA	promoter-TSS (NM_001310447)	promoter-TSS (NM_001310447)	44	NM_001310447	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_66695.1	chr7	45919347	45919359	-	1	NA	exon (NM_010129, exon 4 of 5)	exon (NM_010129, exon 4 of 5)	1496	NM_001146346	13732	Mm.20829	NM_010129	ENSMUSG00000040212	Emp3	H-4|H4|HNMP-1|MI-35|Ymp	epithelial membrane protein 3	protein-coding
mm_144415.1	chr18	20962450	20962465	+	1	NA	intron (NM_026301, intron 1 of 5)	intron (NM_026301, intron 1 of 5)	17832	NM_026301	67664	Mm.45980	NM_026301	ENSMUSG00000033107	Rnf125	4930553F04Rik	ring finger protein 125	protein-coding
mm_166053.1	chr4	132345664	132345673	-	1	NA	promoter-TSS (NM_133878)	promoter-TSS (NM_133878)	82	NM_001197082	100088	Mm.255045	NM_133878	ENSMUSG00000028896	Rcc1	4931417M11Rik|AI326872|Chc1	regulator of chromosome condensation 1	protein-coding
mm_112805.1	chr13	20605395	20605414	+	1	NA	3' UTR (NM_080288, exon 22 of 22)	3' UTR (NM_080288, exon 22 of 22)	132414	NM_198093	140580	Mm.342392	NM_080288	ENSMUSG00000041112	Elmo1	6330578D22Rik|C230095H21Rik|CED-12	engulfment and cell motility 1	protein-coding
mm_89605.1	chr10	95993421	95993433	+	1	NA	exon (NM_001001932, exon 6 of 29)	exon (NM_001001932, exon 6 of 29)	52764	NM_001001932	216238	Mm.210035	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding
mm_125868.1	chr15	75498738	75498759	+	1	NA	Intergenic	Intergenic	49296	NM_001347049	102637705		NM_001347049	ENSMUSG00000093626	Ly6l	Gm20654	lymphocyte antigen 6 complex, locus L	protein-coding
mm_91842.1	chr10	57532417	57532487	-	1	NA	promoter-TSS (NM_019760)	promoter-TSS (NM_019760)	77	NM_019760	56442	Mm.29344	NM_019760	ENSMUSG00000019877	Serinc1	1500011D18Rik|AI315070|AIGP-2|TMS-2|Tde1l|Tde2|Tms2|mKIAA1253	serine incorporator 1	protein-coding
mm_139051.1	chr17	46297853	46297863	+	1	NA	promoter-TSS (NM_001286013)	promoter-TSS (NM_001286013)	-70	NM_001286013	106565	Mm.23633	NM_134120	ENSMUSG00000047428	Dlk2	AI413481|DLK-2|Egfl9	delta-like 2 homolog (Drosophila)	protein-coding
mm_47049.1	chr5	116083235	116083251	-	1	NA	promoter-TSS (NM_001101546)	promoter-TSS (NM_001101546)	3	NM_001101546	545798	Mm.483995	NM_001101546	ENSMUSG00000079278	Tmem233	DSPB2|Gm13843|OTTMUSG00000014722	transmembrane protein 233	protein-coding
mm_50763.1	chr6	53576317	53576320	+	1	NA	intron (NM_172728, intron 1 of 6)	intron (NM_172728, intron 1 of 6)	2944	NM_172728	231991	Mm.227444	NM_172728	ENSMUSG00000053007	Creb5	9430076C15Rik|CRE-BPa|Crebpa|D430026C09Rik	cAMP responsive element binding protein 5	protein-coding
mm_9860.1	chr1	184811287	184811303	-	1	NA	promoter-TSS (NM_001290273)	promoter-TSS (NM_001290273)	5	NM_001290273	66112	Mm.272457	NM_001081361	ENSMUSG00000026621	Marc1	1300013F15Rik|Mosc1	mitochondrial amidoxime reducing component 1	protein-coding
mm_2473.1	chr1	105701405	105701408	+	1	NA	intron (NM_173187, intron 10 of 28)	intron (NM_173187, intron 10 of 28)	37545	NM_173187	227446	Mm.337339	NM_029349	ENSMUSG00000026319	2310035C23Rik	6430401N10|Kiaa1468|mKIAA1468	RIKEN cDNA 2310035C23 gene	protein-coding
mm_110711.1	chr12	69371943	69372007	-	1	NA	promoter-TSS (NM_007481)	promoter-TSS (NM_007481)	-175	NM_007481	11845	Mm.27308	NM_007481	ENSMUSG00000044147	Arf6	AI788669|AW496366	ADP-ribosylation factor 6	protein-coding
mm_45087.1	chr5	44099196	44099217	-	1	NA	intron (NM_001163577, intron 1 of 27)	intron (NM_001163577, intron 1 of 27)	2530	NM_008935	19126	Mm.6250	NM_008935	ENSMUSG00000029086	Prom1	4932416E19Rik|AC133|CD133|Prom|Prom-1|Proml1	prominin 1	protein-coding
mm_3967.1	chr1	164151872	164151882	+	1	NA	promoter-TSS (NM_007976)	promoter-TSS (NM_007976)	42	NM_007976	14067	Mm.12900	NM_007976	ENSMUSG00000026579	F5	AI173222|Cf-5|Cf5	coagulation factor V	protein-coding
mm_83315.1	chr9	44134482	44134510	-	1	NA	promoter-TSS (NM_023061)	promoter-TSS (NM_023061)	-162	NM_023061	84004	Mm.275003	NM_023061	ENSMUSG00000032135	Mcam	1-gicerin|AV025631|CD146|CD149|Muc18|s-endo|s-gicerin	melanoma cell adhesion molecule	protein-coding
mm_78708.1	chr9	41376899	41376908	+	1	NA	intron (NR_131928, intron 1 of 4)	intron (NR_131928, intron 1 of 4)	377	NR_131928	73144	Mm.38166	NM_001033153	ENSMUSG00000074415	3110039I08Rik	2610203C20Rik|AI848448|D230004N17Rik|D3Mgi9|Mir100hg	RIKEN cDNA 3110039I08 gene	ncRNA
mm_109959.1	chr12	12492254	12492260	-	1	NA	Intergenic	MLT1F-int|LTR|ERVL-MaLR	-99782	NR_045829	70858	Mm.410838	NR_045829		4921511I17Rik	-	RIKEN cDNA 4921511I17 gene	ncRNA
mm_71604.1	chr8	55940454	55940472	+	1	NA	promoter-TSS (NM_080438)	promoter-TSS (NM_080438)	-362	NM_080438	110304	Mm.307061	NM_080438	ENSMUSG00000038257	Glra3	-	glycine receptor, alpha 3 subunit	protein-coding
mm_70929.1	chr8	25813367	25813379	+	1	NA	3' UTR (NM_011485, exon 7 of 7)	3' UTR (NM_011485, exon 7 of 7)	4899	NM_011485	20845	Mm.293314	NM_011485	ENSMUSG00000031574	Star	AV363654|D8Ertd419e|stARD1	steroidogenic acute regulatory protein	protein-coding
mm_115775.1	chr13	19311286	19311292	-	1	NA	Intergenic	Intergenic	84524	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_47029.1	chr5	115652954	115652966	-	1	NA	intron (NM_001080808, intron 7 of 8)	intron (NM_001080808, intron 7 of 8)	7387	NR_105997	102465623		NR_105997	ENSMUSG00000099254	Mir7030	Gm27267|mmu-mir-7030	microRNA 7030	ncRNA
mm_162856.1	chr10	90113329	90113332	+	1	NA	intron (NM_001128086, intron 8 of 24)	Lx3B|LINE|L1	239821	NM_001128086	77531	Mm.440605	NM_181398	ENSMUSG00000058589	Anks1b	AIDA-1b|C030032C09Rik|E530015N03Rik|ENSMUSG00000078431|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding
mm_30825.1	chr4	21874036	21874048	+	1	NA	exon (NM_025669, exon 11 of 12)	exon (NM_025669, exon 11 of 12)	-5633	NM_172687	230027	Mm.5662	NM_172687	ENSMUSG00000028247	Coq3	4732433J24|C77934	coenzyme Q3 methyltransferase	protein-coding
mm_72.1	chr1	6671898	6671935	+	1	NA	intron (NM_001244693, intron 2 of 22)	(TTTTC)n|Simple_repeat|Simple_repeat	-58135	NR_045189	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding
mm_144826.1	chr18	36348740	36348779	+	1	NA	5' UTR (NM_001081365, exon 1 of 3)	5' UTR (NM_001081365, exon 1 of 3)	135	NM_001081365	66060	Mm.272527	NM_001081365	ENSMUSG00000046727	Cystm1	0610010O12Rik	cysteine-rich transmembrane module containing 1	protein-coding
mm_35774.1	chr4	46404028	46404036	-	1	NA	5' UTR (NM_053149, exon 1 of 4)	5' UTR (NM_053149, exon 1 of 4)	151	NM_053149	93966	Mm.25793	NM_053149	ENSMUSG00000028332	Hemgn	4921524M03Rik|AI317176|EDAG|Hgn|mNDR	hemogen	protein-coding
mm_9483.1	chr1	173490934	173490940	-	1	NA	Intergenic	Intergenic	45020	NM_001024721	545384	Mm.371698	NM_001024721	ENSMUSG00000070501	Ifi214	Pyhin-B|p214	interferon activated gene 214	protein-coding
mm_56338.1	chr6	92773334	92773338	-	1	NA	3' UTR (NM_175314, exon 30 of 30)	3' UTR (NM_175314, exon 30 of 30)	-67152	NM_001081146	243548	Mm.248820	NM_001081146	ENSMUSG00000030020	Prickle2	6230400G14Rik|6720451F06Rik|mpk2	prickle planar cell polarity protein 2	protein-coding
mm_69540.1	chr7	135695591	135695620	-	1	NA	exon (NM_001081117, exon 12 of 14)	exon (NM_001081117, exon 12 of 14)	20774	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_123658.1	chr14	69243971	69244013	-	1	NA	3' UTR (NM_026331, exon 4 of 4)	3' UTR (NM_026331, exon 4 of 4)	41111	NM_026331	67712	Mm.293635	NM_026331	ENSMUSG00000034248	Slc25a37	1700020E22Rik|4930513O14Rik|4930526G11Rik|AI848481|C330015G08Rik|Mfrn|Mfrn1|Mscp|frascati|mitoferrin	solute carrier family 25, member 37	protein-coding
mm_127116.1	chr15	97975604	97975630	+	1	NA	TTS (NM_001113515)	TTS (NM_001113515)	11388	NM_001252153	380967	Mm.196630	NM_201359	ENSMUSG00000052369	Tmem106c	AI046681|BC046621|D15Ertd405e	transmembrane protein 106C	protein-coding
mm_31189.1	chr4	43562673	43562693	+	1	NA	promoter-TSS (NM_013497)	promoter-TSS (NM_013497)	49	NM_013497	12913	Mm.12407	NM_013497	ENSMUSG00000028466	Creb3	AU044960|AW538053|C80076|LZIP|LZIP-1|LZIP-2|Luman	cAMP responsive element binding protein 3	protein-coding
mm_85772.1	chr9	109051676	109051687	-	1	NA	intron (NM_025858, intron 3 of 5)	intron (NM_025858, intron 3 of 5)	-3185	NM_026381	66940	Mm.196533	NM_025858	ENSMUSG00000025647	Shisa5	2310008D10Rik|6430628I05Rik|Scotin|mShisa5	shisa family member 5	protein-coding
mm_162170.1	chrX	101274870	101274870	+	1	NA	intron (NM_021521, intron 1 of 44)	intron (NM_021521, intron 1 of 44)	779	NM_021521	59024	Mm.20873	NM_021521	ENSMUSG00000079487	Med12	230kDa|Mopa|OPA-1|Tnrc11|Trap230	mediator complex subunit 12	protein-coding
mm_148880.1	chr19	6531147	6531229	+	1	NA	intron (NM_001205235, intron 21 of 21)	CpG	11882	NM_009203	20521	Mm.391146	NM_009203	ENSMUSG00000061742	Slc22a12	AI987855|OAT4L|Rst|Slc22al2|URAT1	solute carrier family 22 (organic anion/cation transporter), member 12	protein-coding
mm_580.1	chr1	39362993	39362997	+	1	NA	3' UTR (NM_008719, exon 21 of 21)	3' UTR (NM_008719, exon 21 of 21)	-4856	NM_053257	114641	Mm.379302	NM_053257	ENSMUSG00000073702	Rpl31	Dts	ribosomal protein L31	protein-coding
mm_60727.1	chr7	45406416	45406463	+	1	NA	exon (NM_010596, exon 1 of 2)	exon (NM_010596, exon 1 of 2)	479	NM_010596	16495	Mm.12955	NM_010596	ENSMUSG00000038201	Kcna7	Kv1.7	potassium voltage-gated channel, shaker-related subfamily, member 7	protein-coding
mm_4406.1	chr1	172475428	172475434	+	1	NA	promoter-TSS (NM_029612)	promoter-TSS (NM_029612)	71	NM_029612	98365	Mm.150050	NM_029612	ENSMUSG00000026548	Slamf9	2310026I04Rik|AI462096|CD2F-10|CD84-H1|Cd2f10|SF2001	SLAM family member 9	protein-coding
mm_108952.1	chr12	102357130	102357152	+	1	NA	intron (NM_177620, intron 4 of 9)	intron (NM_177620, intron 4 of 9)	73500	NM_001161365	217835	Mm.24145	NM_177620	ENSMUSG00000044456	Rin3	6430500K07|C86933	Ras and Rab interactor 3	protein-coding
mm_51423.1	chr6	78426950	78426979	+	1	NA	exon (NM_009042, exon 3 of 6)	exon (NM_009042, exon 3 of 6)	981	NM_009042	19692	Mm.142731	NM_009042	ENSMUSG00000059654	Reg1	-	regenerating islet-derived 1	protein-coding
mm_37345.1	chr4	119733576	119733586	-	1	NA	Intergenic	CpG	-74636	NM_008191	14916	Mm.278	NM_008191	ENSMUSG00000032978	Guca2b	AV066530|Gcap2|Ugn	guanylate cyclase activator 2b (retina)	protein-coding
mm_74789.1	chr8	22185759	22185817	-	1	NA	promoter-TSS (NM_001004140)	promoter-TSS (NM_001004140)	31	NM_001004140	80986	Mm.22448	NM_001004140	ENSMUSG00000037725	Ckap2	AI461656|AW228814|LB1	cytoskeleton associated protein 2	protein-coding
mm_149300.1	chr19	10699380	10699394	+	1	NA	intron (NM_181403, intron 1 of 4)	intron (NM_181403, intron 1 of 4)	10572	NM_181403	107305	Mm.19091	NM_181403	ENSMUSG00000048832	Vps37c	5730409F24Rik|AU042646	vacuolar protein sorting 37C	protein-coding
mm_28058.1	chr3	84220854	84220896	-	1	NA	promoter-TSS (NM_030706)	promoter-TSS (NM_030706)	2	NM_030706	80890	Mm.44876	NM_030706	ENSMUSG00000027993	Trim2	mKIAA0517|narf	tripartite motif-containing 2	protein-coding
mm_40911.1	chr5	75601575	75601578	+	1	NA	intron (NM_021099, intron 1 of 20)	intron (NM_021099, intron 1 of 20)	26585	NM_021099	16590	Mm.247073	NM_021099	ENSMUSG00000005672	Kit	Bs|CD117|Fdc|Gsfsco1|Gsfsco5|Gsfsow3|SCO1|SCO5|SOW3|Ssm|Tr-kit|W|c-KIT	KIT proto-oncogene receptor tyrosine kinase	protein-coding
mm_100320.1	chr11	118004644	118004648	+	1	NA	intron (NM_133757, intron 6 of 9)	intron (NM_133757, intron 6 of 9)	2376	NR_105898	102466768		NR_105898	ENSMUSG00000098958	Mir6933	Gm27856|mmu-mir-6933	microRNA 6933	ncRNA
mm_15280.1	chr2	155276419	155276474	+	1	NA	promoter-TSS (NR_046364)	promoter-TSS (NR_046364)	82	NR_046364	66734	Mm.196239	NM_025735	ENSMUSG00000027602	Map1lc3a	1010001H21Rik|4922501H04Rik|LC3|LC3a	microtubule-associated protein 1 light chain 3 alpha	protein-coding
mm_112761.1	chr13	19349036	19349050	+	1	NA	Intergenic	Intergenic	46770	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_994.1	chr1	58712397	58712434	+	1	NA	promoter-TSS (NM_207653)	promoter-TSS (NM_207653)	-871	NM_009805	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_90957.1	chr10	13292039	13292071	-	1	NA	intron (NM_001195065, intron 1 of 12)	intron (NM_001195065, intron 1 of 12)	32105	NM_001195096	215789	Mm.283359	NM_001033257	ENSMUSG00000062866	Phactr2	AV158170|BC012871	phosphatase and actin regulator 2	protein-coding
mm_51470.1	chr6	82960242	82960252	+	1	NA	intron (NM_033079, intron 2 of 9)	intron (NM_033079, intron 2 of 9)	13325	NM_033079	110958	Mm.100652	NM_033079	ENSMUSG00000030041	M1ap	D6Mm5e	meiosis 1 associated protein	protein-coding
mm_8034.1	chr1	135167539	135167554	-	1	NA	5' UTR (NM_134438, exon 1 of 2)	5' UTR (NM_134438, exon 1 of 2)	135	NM_134438	171469	Mm.272290	NM_134438	ENSMUSG00000026424	Gpr37l1	AW047233|CAG-18|D0Kist8	G protein-coupled receptor 37-like 1	protein-coding
mm_47817.1	chr5	134228251	134228264	-	1	NA	intron (NR_104383, intron 1 of 11)	intron (NR_104383, intron 1 of 11)	1368	NM_001286037	17969	Mm.425296	NM_010876	ENSMUSG00000015950	Ncf1	NCF-47K|NOXO2|Ncf-1|p47-phox|p47<phox>|p47phox	neutrophil cytosolic factor 1	protein-coding
mm_17515.1	chr2	29194652	29194671	-	1	NA	TTS (NM_133500)	TTS (NM_133500)	53438	NM_001305805	171171	Mm.442448	NM_133500	ENSMUSG00000035513	Ntng2	2610016D08Rik|Lmnt2	netrin G2	protein-coding
mm_30183.1	chr3	144555324	144555365	-	1	NA	intron (NM_011828, intron 1 of 6)	intron (NM_011828, intron 1 of 6)	14872	NM_011828	23908	Mm.12863	NM_011828	ENSMUSG00000040151	Hs2st1	AW214369|Hs2st|mKIAA0448	heparan sulfate 2-O-sulfotransferase 1	protein-coding
mm_155274.1	chrX	61116360	61116397	+	1	NA	promoter-TSS (NR_030706)	promoter-TSS (NR_030706)	0	NR_030706	331424	Mm.127263	NM_177916	ENSMUSG00000071753	C230004F18Rik	-	RIKEN cDNA C230004F18 gene	ncRNA
mm_142719.1	chr17	48038287	48038306	-	1	NA	promoter-TSS (NM_029689)	promoter-TSS (NM_029689)	-3	NM_029689	76651	Mm.76918	NM_029689	ENSMUSG00000094928	1700122O11Rik	-	RIKEN cDNA 1700122O11 gene	protein-coding
mm_151386.1	chr19	56396835	56396853	+	1	NA	promoter-TSS (NM_007611)	promoter-TSS (NM_007611)	-285	NM_007611	12369	Mm.35687	NM_007611	ENSMUSG00000025076	Casp7	AI314680|CMH-1|ICE-IAP3|Mch3|caspase-7|mCASP-7	caspase 7	protein-coding
mm_172140.1	chr6	36809912	36809912	-	1	NA	5' UTR (NM_008973, exon 1 of 5)	5' UTR (NM_008973, exon 1 of 5)	1449	NM_008973	19242	Mm.279690	NM_008973	ENSMUSG00000029838	Ptn	HARP|HB-GAM|HBBN|HBGF-8|HBNF|OSF|Osf-1|Osf1	pleiotrophin	protein-coding
mm_47328.1	chr5	122491708	122491739	-	1	NA	exon (NM_009722, exon 4 of 21)	exon (NM_009722, exon 4 of 21)	10502	NM_001110140	11938	Mm.227583	NM_009722	ENSMUSG00000029467	Atp2a2	9530097L16Rik|D5Wsu150e|SERCA2|SERCA2B|Serca2a|mKIAA4195	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	protein-coding
mm_48458.1	chr5	140773700	140773704	-	1	NA	intron (NM_010302, intron 2 of 3)	intron (NM_010302, intron 2 of 3)	49575	NM_173405	231842	Mm.491298	NM_173405	ENSMUSG00000050022	Amz1	5330426I05|6530401C20Rik	archaelysin family metallopeptidase 1	protein-coding
mm_48979.1	chr6	4755357	4755357	+	1	NA	exon (NM_130877, exon 2 of 2)	exon (NM_130877, exon 2 of 2)	8051	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_53576.1	chr6	137410776	137410788	+	1	NA	promoter-TSS (NM_001164403)	promoter-TSS (NM_001164403)	61	NM_001164403	19277	Mm.186361	NM_011216	ENSMUSG00000030223	Ptpro	D28|GLEPP1|PTPBK|PTPROt|PTPU2|PTPoc|PTPphi|Ptpn15|R-PTP-O	protein tyrosine phosphatase, receptor type, O	protein-coding
mm_135562.1	chr16	50070736	50070755	-	1	NA	intron (NR_045935, intron 1 of 3)	intron (NR_045935, intron 1 of 3)	2107	NR_045935	224180	Mm.146439	NM_175010		Gm4827	B130050K08|EG224180	predicted gene 4827	ncRNA
mm_162819.1	chr10	80228323	80228352	+	1	NA	5' UTR (NM_023431, exon 2 of 14)	5' UTR (NM_023431, exon 2 of 14)	1739	NM_023431	68114	Mm.273418	NM_023431	ENSMUSG00000020156	Mum1	2610019J09|9430059D04Rik|UBE-1C2	melanoma associated antigen (mutated) 1	protein-coding
mm_399.1	chr1	34124620	34124630	+	1	NA	intron (NM_001276764, intron 8 of 102)	intron (NM_001276764, intron 8 of 102)	7266	NR_105861	102466987		NR_105861	ENSMUSG00000105982	Mir6896	mmu-mir-6896	microRNA 6896	ncRNA
mm_49211.1	chr6	15725879	15725899	+	1	NA	intron (NM_175088, intron 2 of 4)	intron (NM_175088, intron 2 of 4)	5228	NM_175088	16543	Mm.1314	NM_175088	ENSMUSG00000041390	Mdfic	Kdt1|Mdfid	MyoD family inhibitor domain containing	protein-coding
mm_86163.1	chr9	118478723	118478736	-	1	NA	exon (NM_010136, exon 1 of 6)	exon (NM_010136, exon 1 of 6)	540	NM_010136	13813	Mm.200692	NM_010136	ENSMUSG00000032446	Eomes	C77258|TBR-2|Tbr2	eomesodermin	protein-coding
mm_55553.1	chr6	71262541	71262584	-	1	NA	promoter-TSS (NM_001160127)	promoter-TSS (NM_001160127)	-281	NM_009762	12180	Mm.234274	NM_009762	ENSMUSG00000055027	Smyd1	4632404M21Rik|Bop|C78565|Zmynd18	SET and MYND domain containing 1	protein-coding
mm_43523.1	chr5	137152254	137152293	+	1	NA	Intergenic	Intergenic	-36066	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_69291.1	chr7	128206441	128206451	-	1	NA	promoter-TSS (NM_009943)	promoter-TSS (NM_009943)	-80	NM_009943	12862	Mm.43824	NM_009943	ENSMUSG00000030785	Cox6a2	CoxVIaH|VIaH	cytochrome c oxidase subunit VIa polypeptide 2	protein-coding
mm_46419.1	chr5	104113569	104113579	-	1	NA	5' UTR (NM_010097, exon 1 of 11)	5' UTR (NM_010097, exon 1 of 11)	514	NM_010097	13602	Mm.29027	NM_010097	ENSMUSG00000029309	Sparcl1	Ecm2|Sc1|hevin|mast9	SPARC-like 1	protein-coding
mm_135815.1	chr16	57645077	57645080	-	1	NA	intron (NM_007739, intron 2 of 3)	Lx3A|LINE|L1	-38211	NM_025599	66497	Mm.425976	NM_025599	ENSMUSG00000022748	Cmss1	1110001A06Rik|2610528E23Rik|4930572F24Rik|AV099812|AV122629	cms small ribosomal subunit 1	protein-coding
mm_60210.1	chr7	43440846	43440855	+	1	NA	promoter-TSS (NM_028849)	promoter-TSS (NM_028849)	34	NM_028849	74276	Mm.159153	NM_028849	ENSMUSG00000038973	Cldnd2	1700071E18Rik	claudin domain containing 2	protein-coding
mm_66337.1	chr7	43313234	43313285	-	1	NA	promoter-TSS (NM_027264)	promoter-TSS (NM_027264)	2	NM_027264	69930	Mm.45367	NM_027264	ENSMUSG00000012640	Zfp715	2610041B18Rik|mszf15	zinc finger protein 715	protein-coding
mm_7954.1	chr1	133921347	133921357	-	1	NA	promoter-TSS (NM_054077)	promoter-TSS (NM_054077)	49	NM_054077	116847	Mm.214514	NM_054077	ENSMUSG00000041577	Prelp	7330409J17Rik|SLRR2A	proline arginine-rich end leucine-rich repeat	protein-coding
mm_156880.1	chrX	166238924	166239024	+	1	NA	promoter-TSS (NM_001177961)	promoter-TSS (NM_001177961)	31	NM_001177962	14758	Mm.222320	NM_023122	ENSMUSG00000031342	Gpm6b	AI593561|Gpm6|M6B	glycoprotein m6b	protein-coding
mm_15273.1	chr2	155219654	155219658	+	1	NA	intron (NM_008395, intron 23 of 24)	intron (NM_008395, intron 23 of 24)	-16877	NR_111891	67068	Mm.23693	NM_025947	ENSMUSG00000047459	Dynlrb1	2010012N15Rik|2010320M17Rik|9430076K19Rik|AV124457|DNLC2A|Dncl2a|km23-1	dynein light chain roadblock-type 1	protein-coding
mm_3953.1	chr1	164062130	164062170	+	1	NA	promoter-TSS (NM_001164059)	promoter-TSS (NM_001164059)	74	NM_001164059	20343	Mm.1461	NM_011346	ENSMUSG00000026581	Sell	AI528707|CD62L|L-selectin|LECAM-1|Lnhr|Ly-22|Ly-m22|Lyam-1|Lyam1	selectin, lymphocyte	protein-coding
mm_12133.1	chr2	61653590	61653614	+	1	NA	3' UTR (NM_001164072, exon 8 of 8)	3' UTR (NM_001164072, exon 8 of 8)	-58092	NM_021526	59029	Mm.218198	NM_021526	ENSMUSG00000026914	Psmd14	2610312C03Rik|3200001M20Rik|AA986732|Pad1|Poh1|rpm11	proteasome (prosome, macropain) 26S subunit, non-ATPase, 14	protein-coding
mm_82865.1	chr9	32344242	32344255	-	1	NA	promoter-TSS (NM_010605)	promoter-TSS (NM_010605)	-11	NM_010605	16521	Mm.69472	NM_010605	ENSMUSG00000032034	Kcnj5	GIRK4|Kir3.4	potassium inwardly-rectifying channel, subfamily J, member 5	protein-coding
mm_105787.1	chr11	109828022	109828028	-	1	NA	promoter-TSS (NM_001162428)	promoter-TSS (NM_001162428)	21	NM_027038	69324	Mm.31700	NM_027038	ENSMUSG00000020617	1700012B07Rik	1700069D21Rik	RIKEN cDNA 1700012B07 gene	protein-coding
mm_64876.1	chr7	14439639	14439677	-	1	NA	intron (NM_175250, intron 1 of 6)	MTD|LTR|ERVL-MaLR	-1107	NM_001199306	76971	Mm.290727	NM_175250	ENSMUSG00000030378	Sult2a8	2810007J24Rik	sulfotransferase family 2A, dehydroepiandrosterone (DHEA)-preferring, member 8	protein-coding
mm_101840.1	chr11	48799402	48799405	-	1	NA	promoter-TSS (NM_008143)	promoter-TSS (NM_008143)	-957	NM_008143	14694	Mm.5305	NM_008143	ENSMUSG00000020372	Rack1	AL033335|GB-like|Gnb2-rs1|Gnb2l1|p205	receptor for activated C kinase 1	protein-coding
mm_22509.1	chr3	7612703	7612705	+	1	NA	5' UTR (NM_001313890, exon 1 of 6)	5' UTR (NM_001313890, exon 1 of 6)	189	NM_001313890	16196	Mm.3825	NM_008371	ENSMUSG00000040329	Il7	A630026I06Rik|Il-7|hlb368	interleukin 7	protein-coding
mm_2595.1	chr1	119526126	119526180	+	1	NA	promoter-TSS (NM_146103)	promoter-TSS (NM_146103)	-1	NM_146103	226351	Mm.439806	NM_146103	ENSMUSG00000098923	Tmem185b	2500001K11Rik	transmembrane protein 185B	protein-coding
mm_161094.1	chr12	91590422	91590422	-	1	NA	promoter-TSS (NM_031391)	promoter-TSS (NM_031391)	65	NM_175335	83602	Mm.275728	NM_031391	ENSMUSG00000020962	Gtf2a1	6330549H03Rik|AA536742|AA959775|AW060250|TfIIAa/b|Tfiia1	general transcription factor II A, 1	protein-coding
mm_106842.1	chr12	8007430	8007432	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	29754	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_137998.1	chr17	33759974	33760023	+	1	NA	intron (NM_008997, intron 1 of 4)	CpG	488	NM_008997	19326	Mm.387587	NM_008997	ENSMUSG00000077450	Rab11b	A730055L17Rik	RAB11B, member RAS oncogene family	protein-coding
mm_18390.1	chr2	60125813	60125823	-	1	NA	promoter-TSS (NM_001001182)	promoter-TSS (NM_001001182)	-78	NM_001001182	407823	Mm.228071	NM_001001182	ENSMUSG00000026987	Baz2b	5830435C13Rik|BC053917|D2Ertd794e	bromodomain adjacent to zinc finger domain, 2B	protein-coding
mm_126871.1	chr15	89373935	89373961	+	1	NA	promoter-TSS (NM_001111288)	promoter-TSS (NM_001111288)	-130	NM_001111288	100126824	Mm.287977	NM_001111288	ENSMUSG00000091780	Sco2	-	SCO2 cytochrome c oxidase assembly protein	protein-coding
mm_141367.1	chr17	28943836	28943840	-	1	NA	Intergenic	Intergenic	-1576	NM_153390	69307	Mm.107605	NM_153390	ENSMUSG00000045378	Pxt1	1700001G18Rik|Stepp	peroxisomal, testis specific 1	protein-coding
mm_148462.1	chr19	4081435	4081467	+	1	NA	Intergenic	Intergenic	-1037	NM_001160253	29866	Mm.46268	NM_013878	ENSMUSG00000024857	Cabp2	-	calcium binding protein 2	protein-coding
mm_51631.1	chr6	85587525	85587544	+	1	NA	promoter-TSS (NM_145223)	promoter-TSS (NM_145223)	3	NM_145223	236266	Mm.246967	NM_145223	ENSMUSG00000063810	Alms1	bbb	Alstrom syndrome 1	protein-coding
mm_142387.1	chr17	44814591	44814595	-	1	NA	promoter-TSS (NM_009820)	promoter-TSS (NM_009820)	34	NM_009820	12393	Mm.391013	NM_009820	ENSMUSG00000039153	Runx2	AML3|Cbf|Cbfa-1|Cbfa1|LS3|Osf2|PEBP2aA|Pebp2a1|Pebpa2a	runt related transcription factor 2	protein-coding
mm_161900.1	chr18	53464298	53464298	+	1	NA	promoter-TSS (NM_001033281)	promoter-TSS (NM_001033281)	-248	NM_001033281	225518	Mm.297645	NM_001033281	ENSMUSG00000069378	Prdm6	Gm92|PRISM	PR domain containing 6	protein-coding
mm_99461.1	chr11	102435259	102435267	+	1	NA	exon (NM_008175, exon 10 of 13)	exon (NM_008175, exon 10 of 13)	4941	NM_008175	14824	Mm.1568	NM_008175	ENSMUSG00000034708	Grn	Pgrn|epithelin	granulin	protein-coding
mm_79916.1	chr9	65545939	65545964	+	1	NA	Intergenic	Intergenic	34136	NM_153119	102595	Mm.247303	NM_153119	ENSMUSG00000050721	Plekho2	AI840980|Plekhq1	pleckstrin homology domain containing, family O member 2	protein-coding
mm_148239.1	chr18	80597562	80597574	-	1	NA	Intergenic	Intergenic	-53022	NR_028424	100039348	Mm.254722	NR_028424		Gm2176	A430076E10Rik	glucosamine-6-phosphate deaminase 1 pseudogene	pseudo
mm_57484.1	chr6	125254185	125254258	-	1	NA	Intergenic	MLTR14|LTR|ERV1	-11304	NR_015527	73870	Mm.440681	NR_015527	ENSMUSG00000108129	4930417O13Rik	-	RIKEN cDNA 4930417O13 gene	ncRNA
mm_65667.1	chr7	28290696	28290721	-	1	NA	exon (NM_175033, exon 1 of 6)	exon (NM_175033, exon 1 of 6)	426	NM_175033	280621	Mm.212777	NM_175033	ENSMUSG00000046750	Selenov	Selv	selenoprotein V	protein-coding
mm_73657.1	chr8	110961169	110961171	+	1	NA	intron (NM_009179, intron 2 of 6)	intron (NM_009179, intron 2 of 6)	36653	NM_007916	13680	Mm.287901	NM_007916	ENSMUSG00000015023	Ddx19a	DBP5|Ddx19|Eif4a-rs1	DEAD (Asp-Glu-Ala-Asp) box polypeptide 19a	protein-coding
mm_119951.1	chr14	55053865	55053925	+	1	NA	Intergenic	Intergenic	15433	NR_073535	100151693	Mm.378403	NR_073535	ENSMUSG00000072492	Gm10364	EG545052|ENSMUSG00000072492	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_45460.1	chr5	67815802	67815840	-	1	NA	intron (NM_001284345, intron 1 of 36)	L2c|LINE|L2	31610	NM_009727	11980	Mm.153230	NM_009727	ENSMUSG00000037685	Atp8a1	AI481521|AI853962|APLT|AW743152|AW822227|Atp3a2|B230107D19Rik|ClassI	ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1	protein-coding
mm_21095.1	chr2	153225397	153225442	-	1	NA	promoter-TSS (NM_198617)	promoter-TSS (NM_198617)	22	NM_198617	241732	Mm.277243	NM_198617	ENSMUSG00000074671	Tspyl3	AW212607|Gm36	TSPY-like 3	protein-coding
mm_152471.1	chr19	10974650	10974662	-	1	NA	promoter-TSS (NM_023529)	promoter-TSS (NM_023529)	14	NM_023529	69826	Mm.273404	NM_023529	ENSMUSG00000024731	Ms4a10	2010001N17Rik	membrane-spanning 4-domains, subfamily A, member 10	protein-coding
mm_114603.1	chr13	75771125	75771150	+	1	NA	3' UTR (NM_138953, exon 12 of 12)	3' UTR (NM_138953, exon 12 of 12)	63653	NM_138953	192657	Mm.21288	NM_138953	ENSMUSG00000001542	Ell2	-	elongation factor RNA polymerase II 2	protein-coding
mm_121695.1	chr14	13961846	13961858	-	1	NA	promoter-TSS (NM_025435)	promoter-TSS (NM_025435)	-539	NM_025435	66231	Mm.295875	NM_025435	ENSMUSG00000053453	Thoc7	Nif3l1bp1	THO complex 7	protein-coding
mm_160833.1	chr11	46750699	46750699	+	1	NA	promoter-TSS (NM_134248)	promoter-TSS (NM_134248)	188	NM_001166631	171283	Mm.17771	NM_134248	ENSMUSG00000040405	Havcr1	AI503787|KIM-1|TIM-1|Tim1|Timd1	hepatitis A virus cellular receptor 1	protein-coding
mm_102290.1	chr11	55406579	55406608	-	1	NA	exon (NM_009242, exon 4 of 10)	exon (NM_009242, exon 4 of 10)	13487	NM_009242	20692	Mm.291442	NM_009242	ENSMUSG00000018593	Sparc	BM-40|ON	secreted acidic cysteine rich glycoprotein	protein-coding
mm_160704.1	chr10	51631562	51631562	-	1	NA	promoter-TSS (NM_153071)	promoter-TSS (NM_153071)	-104	NM_153071	210198	Mm.221031	NM_153071	ENSMUSG00000019905	Gprc6a	-	G protein-coupled receptor, family C, group 6, member A	protein-coding
mm_134999.1	chr16	32174468	32174480	-	1	NA	Intergenic	Intergenic	-5326	NM_001033539	328660	Mm.441006	NM_001033539	ENSMUSG00000075269	Bex6	B020003O03Rik	brain expressed family member 6	protein-coding
mm_53392.1	chr6	129582168	129582182	+	1	NA	intron (NM_153590, intron 3 of 6)	intron (NM_153590, intron 3 of 6)	3889	NM_153590	243655	Mm.30968	NM_153590	ENSMUSG00000050241	Klre1	Klre-1|NKG2I	killer cell lectin-like receptor family E member 1	protein-coding
mm_111811.1	chr12	105489324	105489334	-	1	NA	3' UTR (NM_001252508, exon 2 of 2)	3' UTR (NM_001252508, exon 2 of 2)	-24104	NR_102381	104932	Mm.274150	NR_102381		AU015791	-	expressed sequence AU015791	ncRNA
mm_103037.1	chr11	69761683	69761710	-	1	NA	5' UTR (NM_019871, exon 1 of 2)	5' UTR (NM_019871, exon 1 of 2)	148	NM_019871	56293	Mm.6211	NM_019871	ENSMUSG00000018776	Slc35g3	Amac1	solute carrier family 35, member G3	protein-coding
mm_153586.1	chr19	43510207	43510218	-	1	NA	intron (NM_010324, intron 2 of 8)	B3A|SINE|B2	14393	NM_010324	14718	Mm.19039	NM_010324	ENSMUSG00000025190	Got1	AI789014|Got-1|cAspAT|cCAT	glutamic-oxaloacetic transaminase 1, soluble	protein-coding
mm_71747.1	chr8	65209136	65209161	+	1	NA	Intergenic	RLTR9A3A|LTR|ERVK	-79611	NR_033217	407795	Mm.387876	NR_033217	ENSMUSG00000074300	BC030870	-	cDNA sequence BC030870	ncRNA
mm_134271.1	chr16	13986836	13986854	-	1	NA	promoter-TSS (NM_001270718)	promoter-TSS (NM_001270718)	22	NM_001270718	74482	Mm.484026	NM_028968	ENSMUSG00000065968	Ifitm7	4933438K12Rik|Mil4	interferon induced transmembrane protein 7	protein-coding
mm_140964.1	chr17	24650271	24650311	-	1	NA	promoter-TSS (NM_023055)	promoter-TSS (NM_023055)	14	NM_023055	65962	Mm.21587	NM_023055	ENSMUSG00000002504	Slc9a3r2	0610011L07Rik|1200011K07Rik|2010007A20Rik|E3karp|NHERF-2|Nherf2|Octs2|Sip-1|Sip1|Sryip1|Tka-1	solute carrier family 9 (sodium/hydrogen exchanger), member 3 regulator 2	protein-coding
mm_157366.1	chrX	37194800	37194800	-	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	-3562	NM_019443	54405	Mm.34869	NM_019443	ENSMUSG00000016427	Ndufa1	1810049F12Rik|MWFE	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 1	protein-coding
mm_60517.1	chr7	44479887	44479900	+	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	-4624	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_106925.1	chr12	8351541	8351545	+	1	NA	Intergenic	Intergenic	38110	NM_021429	58240	Mm.309954	NM_021429	ENSMUSG00000020605	Hs1bp3	-	HCLS1 binding protein 3	protein-coding
mm_24840.1	chr3	95661678	95661751	+	1	NA	3' UTR (NM_008562, exon 3 of 3)	3' UTR (NM_008562, exon 3 of 3)	2993	NM_008562	17210	Mm.1639	NM_008562	ENSMUSG00000038612	Mcl1	AW556805|Mcl-1	myeloid cell leukemia sequence 1	protein-coding
mm_87106.1	chr10	33195970	33195976	+	1	NA	exon (NM_029726, exon 8 of 38)	exon (NM_029726, exon 8 of 38)	60384	NR_040657	442820	Mm.490725	NR_040657		D830005E20Rik	-	RIKEN cDNA D830005E20 gene	ncRNA
mm_57931.1	chr6	134566885	134566908	-	1	NA	promoter-TSS (NM_008514)	promoter-TSS (NM_008514)	17	NM_008514	16974	Mm.321990	NM_008514	ENSMUSG00000030201	Lrp6	C030016K15Rik|Cd|Gw|ska26|ska<m26Jus>|skax26	low density lipoprotein receptor-related protein 6	protein-coding
mm_84633.1	chr9	70934809	70934847	-	1	NA	promoter-TSS (NM_008280)	promoter-TSS (NM_008280)	-20	NM_008280	15450	Mm.390187	NM_008280	ENSMUSG00000032207	Lipc	AI256194|HL|Hpl	lipase, hepatic	protein-coding
mm_79744.1	chr9	62366938	62366948	+	1	NA	intron (NM_009672, intron 1 of 6)	intron (NM_009672, intron 1 of 6)	25600	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	protein-coding
mm_74689.1	chr8	14995995	14996011	-	1	NA	intron (NM_172751, intron 27 of 28)	intron (NM_172751, intron 27 of 28)	-15022	NM_029116	74901	Mm.46675	NM_029116	ENSMUSG00000055675	Kbtbd11	2900016B01Rik|4930465M17Rik|mKIAA0711	kelch repeat and BTB (POZ) domain containing 11	protein-coding
mm_97779.1	chr11	82215150	82215162	+	1	NA	Intergenic	Intergenic	-35344	NM_011329	20290	Mm.1283	NM_011329	ENSMUSG00000020702	Ccl1	BF534335|I-309|Scya1|Tca-3	chemokine (C-C motif) ligand 1	protein-coding
mm_138422.1	chr17	35069582	35069590	+	1	NA	3' UTR (NM_023463, exon 3 of 3)	3' UTR (NM_023463, exon 3 of 3)	2261	NM_023463	68468	Mm.215096	NM_023463	ENSMUSG00000092586	Ly6g6c	1110003M04Rik|AU016360|G6c|NG24	lymphocyte antigen 6 complex, locus G6C	protein-coding
mm_68701.1	chr7	119642415	119642431	-	1	NA	intron (NM_054094, intron 6 of 13)	RLTR19-int|LTR|ERVK	24595	NM_054094	117147	Mm.427560	NM_054094	ENSMUSG00000033533	Acsm1	Acas3|Bucs1|Macs	acyl-CoA synthetase medium-chain family member 1	protein-coding
mm_72447.1	chr8	83165579	83165607	+	1	NA	5' UTR (NM_001111304, exon 1 of 21)	5' UTR (NM_001111304, exon 1 of 21)	241	NM_027758	71310	Mm.24031	NM_027758	ENSMUSG00000031709	Tbc1d9	4933431N12Rik|AI847101|AW490653|C76116	TBC1 domain family, member 9	protein-coding
mm_7662.1	chr1	128417273	128417283	-	1	NA	5' UTR (NM_145507, exon 1 of 4)	5' UTR (NM_145507, exon 1 of 4)	138	NM_177445	226414	Mm.28693	NM_145507	ENSMUSG00000026356	Dars	5730439G15Rik	aspartyl-tRNA synthetase	protein-coding
mm_96396.1	chr11	67250534	67250542	+	1	NA	exon (NM_010855, exon 21 of 40)	exon (NM_010855, exon 21 of 40)	12726	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_35698.1	chr4	44153988	44153991	-	1	NA	intron (NM_175201, intron 1 of 10)	ID_B1|SINE|B4	13549	NM_175201	73469	Mm.262859	NM_175201	ENSMUSG00000035696	Rnf38	1700065B19Rik|2610202O07Rik|AA673263|Oip1	ring finger protein 38	protein-coding
mm_139961.1	chr17	71642798	71642804	+	1	NA	exon (NM_175639, exon 11 of 18)	exon (NM_175639, exon 11 of 18)	1162	NR_028551	100217456		NR_028551	ENSMUSG00000092887	Snord53	MBII-35	small nucleolar RNA, C/D box 53	snoRNA
mm_90071.1	chr10	116365360	116365372	+	1	NA	intron (NM_029928, intron 26 of 31)	(GA)n|Simple_repeat|Simple_repeat	-52755	NR_028107	67342	Mm.245800	NM_026098	ENSMUSG00000020164	Kcnmb4os1	1700058G18Rik	potassium large conductance calcium-activated channel, subfamily M, beta member 4, opposite strand 1	ncRNA
mm_82392.1	chr9	14676049	14676054	-	1	NA	Intergenic	Intergenic	-61051	NM_001081395	75723	Mm.159552	NM_001081395	ENSMUSG00000013076	Amotl1	2310010G08Rik|2310067L22Rik|4932416D09Rik|JEAP|mFLJ00155	angiomotin-like 1	protein-coding
mm_117985.1	chr13	100174567	100174580	-	1	NA	intron (NM_010872, intron 8 of 15)	intron (NM_010872, intron 8 of 15)	27549	NM_001126182	17948	Mm.89961	NM_010872	ENSMUSG00000078945	Naip2	Birc1b|Naip-rs6	NLR family, apoptosis inhibitory protein 2	protein-coding
mm_151576.1	chr19	61151604	61151618	+	1	NA	Intergenic	Intergenic	-10771	NR_131954	414758	Mm.100056	NM_001001737	ENSMUSG00000074733	Zfp950	5830428H23Rik|AU016073|BC055757|Gm34518|Zfp826|mszf84	zinc finger protein 950	protein-coding
mm_21236.1	chr2	156111955	156111965	-	1	NA	promoter-TSS (NM_029397)	promoter-TSS (NM_029397)	5	NM_170598	75710	Mm.27660	NM_029397	ENSMUSG00000089824	Rbm12	5730420G12Rik|9430070C08Rik|AI852903|SWAN|mKIAA0765	RNA binding motif protein 12	protein-coding
mm_171261.1	chr3	83943758	83943775	-	1	NA	intron (NM_172681, intron 7 of 34)	RLTR17|LTR|ERVK	96395	NM_172681	229473	Mm.28838	NM_172681	ENSMUSG00000033767	D930015E06Rik	Kiaa0922|mKIAA0922	RIKEN cDNA D930015E06 gene	protein-coding
mm_33176.1	chr4	126054951	126054971	+	1	NA	exon (NM_025544, exon 7 of 8)	exon (NM_025544, exon 7 of 8)	-3604	NM_172701	230751	Mm.38907	NM_172701	ENSMUSG00000042616	Oscp1	1810007P19Rik|5730415O04|6030436A01Rik	organic solute carrier partner 1	protein-coding
mm_132656.1	chr16	41564729	41564733	+	1	NA	intron (NM_001347236, intron 1 of 6)	intron (NM_001347236, intron 1 of 6)	31389	NM_175548	268890	Mm.310524	NM_175548	ENSMUSG00000061080	Lsamp	5430428I19|AW046674|B130007O04Rik|D930023J12Rik|Lam|Lamp	limbic system-associated membrane protein	protein-coding
mm_111306.1	chr12	85747701	85747709	-	1	NA	intron (NM_145447, intron 1 of 9)	intron (NM_145447, intron 1 of 9)	1166	NM_145447	217721	Mm.301076	NM_145447	ENSMUSG00000034258	Mfsd7c	CCT|Flvcr2	major facilitator superfamily domain containing 7C	protein-coding
mm_155187.1	chrX	56346391	56346415	+	1	NA	promoter-TSS (NM_030139)	promoter-TSS (NM_030139)	3	NM_030139	78619	Mm.207345	NM_030139	ENSMUSG00000073176	Zfp449	9530049C15Rik	zinc finger protein 449	protein-coding
mm_129586.1	chr15	79774384	79774394	-	1	NA	promoter-TSS (NM_017470)	promoter-TSS (NM_017470)	78	NM_017470	54152	Mm.288159	NM_017470	ENSMUSG00000022420	Dnal4	D15Ertd424e|Dnalc4	dynein, axonemal, light chain 4	protein-coding
mm_149786.1	chr19	23140941	23140951	+	1	NA	promoter-TSS (NM_010638)	promoter-TSS (NM_010638)	-280	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_72522.1	chr8	83976864	83976864	+	1	NA	promoter-TSS (NM_001277898)	promoter-TSS (NM_001277898)	-19	NM_001277898	18747	Mm.19111	NM_008854	ENSMUSG00000005469	Prkaca	PKCD|Pkaca	protein kinase, cAMP dependent, catalytic, alpha	protein-coding
mm_44591.1	chr5	24995694	24995707	-	1	NA	promoter-TSS (NM_001310480)	promoter-TSS (NM_001310480)	53	NM_001310480	108099	Mm.33649	NM_145401	ENSMUSG00000028944	Prkag2	2410051C13Rik|AAKG|AAKG2|AI854673|H91620p|WPWS	protein kinase, AMP-activated, gamma 2 non-catalytic subunit	protein-coding
mm_6666.1	chr1	80289881	80289884	-	1	NA	intron (NM_001313728, intron 5 of 16)	intron (NM_001313728, intron 5 of 16)	50808	NM_001313728	26554	Mm.12665	NM_016716	ENSMUSG00000004364	Cul3	KIAA0617	cullin 3	protein-coding
mm_145952.1	chr18	67641563	67641586	+	1	NA	promoter-TSS (NM_001081073)	promoter-TSS (NM_001081073)	-25	NM_134138	107047	Mm.150701	NM_134138	ENSMUSG00000024537	Psmg2	1700017I17Rik|AW545363|Clast3|Tnfsf5ip1	proteasome (prosome, macropain) assembly chaperone 2	protein-coding
mm_77074.1	chr8	110142992	110143002	-	1	NA	3' UTR (NM_007586, exon 11 of 11)	3' UTR (NM_007586, exon 11 of 11)	25209	NM_007586	12308	Mm.2755	NM_007586	ENSMUSG00000003657	Calb2	CR	calbindin 2	protein-coding
mm_25562.1	chr3	116562966	116563004	+	1	NA	promoter-TSS (NM_175413)	promoter-TSS (NM_175413)	12	NM_175413	109245	Mm.216027	NM_027321	ENSMUSG00000027961	Lrrc39	2010005E21Rik|9430028I06Rik|Myomasp	leucine rich repeat containing 39	protein-coding
mm_102333.1	chr11	57829309	57829313	-	1	NA	3' UTR (NM_008213, exon 2 of 2)	3' UTR (NM_008213, exon 2 of 2)	2836	NM_008213	15110	Mm.4746	NM_008213	ENSMUSG00000037335	Hand1	Ehand1|Hxt|Th1|Thing1|bHLHa27|eHAND	heart and neural crest derivatives expressed transcript 1	protein-coding
mm_101880.1	chr11	48913951	48913960	-	1	NA	intron (NM_001045540, intron 2 of 2)	intron (NM_001045540, intron 2 of 2)	-11803	NM_001024230	432555	Mm.338931	NM_001024230	ENSMUSG00000058163	Gm5431	EG432555|Irgb9b8	predicted gene 5431	protein-coding
mm_86957.1	chr10	24954228	24954239	+	1	NA	Intergenic	Intergenic	-26763	NM_007482	11846	Mm.154144	NM_007482	ENSMUSG00000019987	Arg1	AI|AI256583|Arg-1|PGIF	arginase, liver	protein-coding
mm_72045.1	chr8	71272750	71272784	+	1	NA	promoter-TSS (NM_001142322)	promoter-TSS (NM_001142322)	53	NM_001142323	17925	Mm.33779	NM_015742	ENSMUSG00000004677	Myo9b	-	myosin IXb	protein-coding
mm_57687.1	chr6	128513783	128513814	-	1	NA	exon (NM_007376, exon 11 of 36)	exon (NM_007376, exon 11 of 36)	12922	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_129343.1	chr15	77842134	77842154	-	1	NA	promoter-TSS (NM_022410)	promoter-TSS (NM_022410)	31	NM_022410	17886	Mm.29677	NM_022410	ENSMUSG00000022443	Myh9	Fltn|Myhn-1|Myhn1|NMHCIIA|NMMHC-A|NMMHC-IIA|TU72.6	myosin, heavy polypeptide 9, non-muscle	protein-coding
mm_50257.1	chr6	42980666	42980666	+	1	NA	Intergenic	Intergenic	25166	NM_146656	258650	Mm.377613	NM_146656	ENSMUSG00000073110	Olfr444	MOR261-2	olfactory receptor 444	protein-coding
mm_73063.1	chr8	94386511	94386519	+	1	NA	promoter-TSS (NM_022331)	promoter-TSS (NM_022331)	15	NM_022331	64209	Mm.29151	NM_022331	ENSMUSG00000031770	Herpud1	Herp|Mifl|SUP	homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1	protein-coding
mm_6860.1	chr1	84275089	84275114	-	1	NA	intron (NM_001003948, intron 1 of 2)	ORR1D2|LTR|ERVL-MaLR	9544	NM_001003948	98496	Mm.187470	NM_001003948	ENSMUSG00000045658	Pid1	5033414K04Rik|NYGGF4	phosphotyrosine interaction domain containing 1	protein-coding
mm_141141.1	chr17	26465099	26465135	-	1	NA	Intergenic	Intergenic	43355	NM_013642	19252	Mm.239041	NM_013642	ENSMUSG00000024190	Dusp1	3CH134|MKP1|Ptpn16|U19515|erp|mkp-1	dual specificity phosphatase 1	protein-coding
mm_48361.1	chr5	139408441	139408455	-	1	NA	intron (NM_177000, intron 1 of 1)	intron (NM_177000, intron 1 of 1)	2061	NM_177000	319772	Mm.440271	NM_177000	ENSMUSG00000044092	C130050O18Rik	-	RIKEN cDNA C130050O18 gene	protein-coding
mm_29495.1	chr3	115888087	115888137	-	1	NA	promoter-TSS (NR_027895)	promoter-TSS (NR_027895)	8	NR_027895	68161	Mm.392043	NR_015487	ENSMUSG00000054426	A930005H10Rik	-	RIKEN cDNA A930005H10 gene	ncRNA
mm_32456.1	chr4	107368076	107368084	+	1	NA	5' UTR (NM_028355, exon 1 of 18)	5' UTR (NM_028355, exon 1 of 18)	296	NM_028355	72787	Mm.28478	NM_028355	ENSMUSG00000028614	Ndc1	2810475A17Rik|AI450313|Tmem48|sks	NDC1 transmembrane nucleoporin	protein-coding
mm_128760.1	chr15	65912348	65912357	-	1	NA	promoter-TSS (NM_010953)	promoter-TSS (NM_010953)	-65	NM_010953	18256	Mm.41776	NM_010953	ENSMUSG00000015001	Oc90	Ocn-95|PLA2L|Pla2ll|oc95	otoconin 90	protein-coding
mm_128900.1	chr15	73296712	73296724	-	1	NA	intron (NM_001130409, intron 12 of 29)	intron (NM_001130409, intron 12 of 29)	-41836	NR_029561	387169		NR_029561	ENSMUSG00000065612	Mir151	Mirn151|mir-151|mmu-mir-151	microRNA 151	ncRNA
mm_167322.1	chr8	68157564	68157566	+	1	NA	Intergenic	Intergenic	-118963	NM_028182	72281	Mm.40974	NM_028182	ENSMUSG00000053886	Sh2d4a	2210402M20Rik|SH2A	SH2 domain containing 4A	protein-coding
mm_62683.1	chr7	110018255	110018267	+	1	NA	promoter-TSS (NM_181517)	promoter-TSS (NM_181517)	-164	NM_181517	233726	Mm.222328	NM_181517	ENSMUSG00000066232	Ipo7	A330055O14Rik|C330016G14|Imp7|Ranbp7	importin 7	protein-coding
mm_29408.1	chr3	108911453	108911492	-	1	NA	5' UTR (NM_025845, exon 1 of 6)	5' UTR (NM_025845, exon 1 of 6)	232	NM_025845	66921	Mm.51049	NM_025845	ENSMUSG00000027881	Prpf38b	1110021E09Rik|AU018955	PRP38 pre-mRNA processing factor 38 (yeast) domain containing B	protein-coding
mm_26213.1	chr3	138756593	138756595	+	1	NA	intron (NM_019571, intron 1 of 7)	intron (NM_019571, intron 1 of 7)	14386	NM_019571	56224	Mm.31927	NM_019571	ENSMUSG00000028152	Tspan5	2810455A09Rik|4930505M03Rik|NET-4|Tm4sf9	tetraspanin 5	protein-coding
mm_110360.1	chr12	40037920	40038013	-	1	NA	promoter-TSS (NM_007487)	promoter-TSS (NM_007487)	21	NM_001039515	11861	Mm.12723	NM_007487	ENSMUSG00000047446	Arl4a	AI467555|Arl4	ADP-ribosylation factor-like 4A	protein-coding
mm_23405.1	chr3	58414742	58414771	+	1	NA	promoter-TSS (NM_001347233)	promoter-TSS (NM_001347233)	36	NM_001081229	72033	Mm.218409	NM_001081229	ENSMUSG00000027806	Tsc22d2	1810043J12Rik|5530402M19Rik	TSC22 domain family, member 2	protein-coding
mm_52107.1	chr6	97884047	97884050	+	1	NA	intron (NM_001113198, intron 1 of 9)	intron (NM_001113198, intron 1 of 9)	-45769	NM_001178049	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_130835.1	chr15	101849050	101849060	-	1	NA	exon (NM_008473, exon 2 of 9)	exon (NM_008473, exon 2 of 9)	1731	NM_008473	16678	Mm.183137	NM_008473	ENSMUSG00000046834	Krt1	Krt-2.1|Krt2-1|Krt86	keratin 1	protein-coding
mm_165716.1	chr3	100489414	100489418	-	1	NA	promoter-TSS (NM_001142952)	promoter-TSS (NM_001142952)	-224	NM_001142952	74645	Mm.226900	NM_001142952	ENSMUSG00000044468	Fam46c	4930431B09Rik|AI449797	family with sequence similarity 46, member C	protein-coding
mm_4385.1	chr1	172210324	172210345	+	1	NA	3' UTR (NM_009813, exon 11 of 11)	3' UTR (NM_009813, exon 11 of 11)	-3530	NM_011063	18611	Mm.544	NM_011063	ENSMUSG00000013698	Pea15a	Mat1|PEA-15|Pea15|Pkcs15	phosphoprotein enriched in astrocytes 15A	protein-coding
mm_139576.1	chr17	57062526	57062542	+	1	NA	intron (NM_001347408, intron 1 of 4)	CpG	257	NM_177638	224912	Mm.284447	NM_177638	ENSMUSG00000044279	Crb3	5730439B18|AU015179|AU041752	crumbs family member 3	protein-coding
mm_135325.1	chr16	38800194	38800209	-	1	NA	promoter-TSS (NM_178924)	promoter-TSS (NM_178924)	2	NM_178924	22268	Mm.130793	NM_178924	ENSMUSG00000049436	Upk1b	AI413235|Tspan20|UPIb|Upk1	uroplakin 1B	protein-coding
mm_46965.1	chr5	115152371	115152381	-	1	NA	intron (NM_175403, intron 1 of 4)	intron (NM_175403, intron 1 of 4)	5800	NM_175403	109154	Mm.153963	NM_175403	ENSMUSG00000048578	Mlec	2410014A08Rik|AI850530|ESTM19|X83352|mKIAA0152	malectin	protein-coding
mm_7511.1	chr1	123853955	123853957	-	1	NA	intron (NM_199021, intron 3 of 25)	intron (NM_199021, intron 3 of 25)	191603	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_148093.1	chr18	73815704	73815714	-	1	NA	promoter-TSS (NM_145494)	promoter-TSS (NM_145494)	-317	NM_145494	107029	Mm.36817	NM_145494	ENSMUSG00000024556	Me2	AW120568|D030040L20Rik|NAD-ME	malic enzyme 2, NAD(+)-dependent, mitochondrial	protein-coding
mm_134720.1	chr16	22896602	22896614	-	1	NA	exon (NM_001276450, exon 5 of 7)	exon (NM_001276450, exon 5 of 7)	-2222	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_102921.1	chr11	69600248	69600271	-	1	NA	3' UTR (NM_013415, exon 7 of 7)	3' UTR (NM_013415, exon 7 of 7)	5701	NM_013415	11932	Mm.235204	NM_013415	ENSMUSG00000041329	Atp1b2	Amog|Atpb-2	ATPase, Na+/K+ transporting, beta 2 polypeptide	protein-coding
mm_16112.1	chr2	169684287	169684290	+	1	NA	intron (NM_080455, intron 1 of 1)	intron (NM_080455, intron 1 of 1)	50642	NM_080455	228911	Mm.315789	NM_080455	ENSMUSG00000047907	Tshz2	2900073F20Rik|B830045G17|Mtsh2|Sdccag33l|Tsh2|Zfp218|mKIAA4248|teashirt2	teashirt zinc finger family member 2	protein-coding
mm_30595.1	chr4	6365727	6365737	+	1	NA	promoter-TSS (NM_016807)	promoter-TSS (NM_016807)	52	NM_001098227	53378	Mm.247473	NM_016807	ENSMUSG00000028249	Sdcbp	MDA-9|Sycl|syntenin-1	syndecan binding protein	protein-coding
mm_110602.1	chr12	56535999	56536023	-	1	NA	intron (NM_009385, intron 1 of 2)	CpG	897	NM_009385	21869	Mm.89972	NM_009385	ENSMUSG00000001496	Nkx2-1	AV026640|Nkx2.1|T/EBP|Titf1|Ttf-1	NK2 homeobox 1	protein-coding
mm_109408.1	chr12	110447213	110447230	+	1	NA	promoter-TSS (NM_001135001)	promoter-TSS (NM_001135001)	42	NM_001135001	26931	Mm.240396	NM_012023	ENSMUSG00000017843	Ppp2r5c	2610043M05Rik|2700063L20Rik|AI060890|AW545884|C85228|D12Bwg0916e|mKIAA0044	protein phosphatase 2, regulatory subunit B', gamma	protein-coding
mm_161354.1	chr14	55721974	55721974	-	1	NA	5' UTR (NM_019519, exon 1 of 16)	5' UTR (NM_019519, exon 1 of 16)	202	NM_019519	56187	Mm.87216	NM_019519	ENSMUSG00000040472	Rabggta	gm	Rab geranylgeranyl transferase, a subunit	protein-coding
mm_9326.1	chr1	171844827	171844846	-	1	NA	intron (NM_001289470, intron 2 of 8)	(CAAAA)n|Simple_repeat|Simple_repeat	5139	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_165678.1	chr3	90659951	90659990	+	1	NA	Intergenic	MLTR14|LTR|ERV1	5668	NM_199422	381493	Mm.291525	NM_199422	ENSMUSG00000063767	S100a7a	AY465109|Gm1020|S100A7L1|S100A7f|S100a15|S100a15a|S100a17l1	S100 calcium binding protein A7A	protein-coding
mm_82578.1	chr9	21142051	21142068	-	1	NA	exon (NM_016742, exon 5 of 8)	exon (NM_016742, exon 5 of 8)	7847	NM_016742	12539	Mm.32331	NM_016742	ENSMUSG00000019471	Cdc37	p50|p50Cdc37	cell division cycle 37	protein-coding
mm_157296.1	chrX	20927686	20927706	-	1	NA	exon (NM_008823, exon 7 of 9)	exon (NM_008823, exon 7 of 9)	3859	NM_008823	18636	Mm.3064	NM_008823	ENSMUSG00000001128	Cfp	BCFG|Pfc	complement factor properdin	protein-coding
mm_111216.1	chr12	84408992	84409034	-	1	NA	promoter-TSS (NM_028377)	promoter-TSS (NM_028377)	16	NM_007647	12499	Mm.10211	NM_007647	ENSMUSG00000021236	Entpd5	AI196558|AI987697|Cd39l4|ER-UDPase|NTPDase-5|NTPDase5|Pcph|mNTPase	ectonucleoside triphosphate diphosphohydrolase 5	protein-coding
mm_98634.1	chr11	96124486	96124506	+	1	NA	Intergenic	CpG	-9290	NM_172799	237930	Mm.249912	NM_172799	ENSMUSG00000038756	Ttll6	4932418K24Rik|D11Moh43e|D11Moh44e|t8130b59	tubulin tyrosine ligase-like family, member 6	protein-coding
mm_36192.1	chr4	62326089	62326116	-	1	NA	exon (NM_001045528, exon 15 of 28)	exon (NM_001045528, exon 15 of 28)	34446	NM_001045528	338355	Mm.357792	NM_001045528	ENSMUSG00000066151	Fkbp15	BB131447|C430014M02Rik|FKBO133|FKBP-133|FKBP-15|FKBP133|mKIAA0674	FK506 binding protein 15	protein-coding
mm_136437.1	chr16	94498648	94498677	-	1	NA	3' UTR (NM_007834, exon 8 of 8)	3' UTR (NM_007834, exon 8 of 8)	27967	NM_007834	13185	Mm.7472	NM_007834	ENSMUSG00000022898	Dscr3	AW538125|Dcra	Down syndrome critical region gene 3	protein-coding
mm_3580.1	chr1	151132981	151132994	+	1	NA	Intergenic	Intergenic	-5047	NR_038011	402734	Mm.337666	NR_038011		C730036E19Rik	lncLSTR	RIKEN cDNA C730036E19 gene	ncRNA
mm_32016.1	chr4	94820770	94820785	+	1	NA	intron (NM_001290549, intron 8 of 22)	Lx7|LINE|L1	81488	NM_001290551	21687	Mm.14313	NM_013690	ENSMUSG00000006386	Tek	AA517024|Cd202b|Hyk|STK1|Tie-2|Tie2	endothelial-specific receptor tyrosine kinase	protein-coding
mm_113279.1	chr13	30003406	30003414	+	1	NA	Intergenic	Intergenic	-17347	NM_010093	13557	Mm.268356	NM_010093	ENSMUSG00000016477	E2f3	E2F3b|E2f3a	E2F transcription factor 3	protein-coding
mm_147377.1	chr18	43687631	43687655	-	1	NA	5' UTR (NM_001163637, exon 1 of 22)	5' UTR (NM_001163637, exon 1 of 22)	130	NM_001163637	76217	Mm.134602	NM_001163637	ENSMUSG00000024502	Jakmip2	6430702L21Rik|AI850334|D930046L20Rik	janus kinase and microtubule interacting protein 2	protein-coding
mm_74718.1	chr8	17380928	17380938	-	1	NA	intron (NM_053171, intron 1 of 69)	intron (NM_053171, intron 1 of 69)	154452	NM_053171	94109	Mm.436988	NM_053171	ENSMUSG00000060924	Csmd1	B930082H09|mKIAA1890	CUB and Sushi multiple domains 1	protein-coding
mm_134210.1	chr16	11176057	11176070	-	1	NA	intron (NM_145931, intron 1 of 22)	CpG	330	NR_027502	106205	Mm.226860	NM_145931	ENSMUSG00000037965	Zc3h7a	A430104C18Rik|AI447294|AW556219|HSPC055|Zc3h7|Zc3hdc7	zinc finger CCCH type containing 7 A	protein-coding
mm_38242.1	chr4	136574057	136574106	-	1	NA	exon (NM_133872, exon 4 of 19)	exon (NM_133872, exon 4 of 19)	28642	NM_133872	99982	Mm.28540	NM_133872	ENSMUSG00000036940	Kdm1a	1810043O07Rik|AA408884|Aof2|D4Ertd478e|Kdm1|Lsd1|mKIAA0601	lysine (K)-specific demethylase 1A	protein-coding
mm_65703.1	chr7	28377866	28377879	-	1	NA	exon (NM_011756, exon 2 of 2)	exon (NM_011756, exon 2 of 2)	1356	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_41120.1	chr5	87781817	87781823	+	1	NA	exon (NM_001304768, exon 8 of 13)	exon (NM_001304768, exon 8 of 13)	7370	NM_007785	12993	Mm.4908	NM_007785	ENSMUSG00000061937	Csn1s2a	Csng|PP22	casein alpha s2-like A	protein-coding
mm_57843.1	chr6	129467566	129467586	-	1	NA	exon (NM_020008, exon 4 of 6)	exon (NM_020008, exon 4 of 6)	5203	NM_001309637	56644	Mm.239516	NM_020008	ENSMUSG00000079293	Clec7a	BGR|Clecsf12|beta-GR	C-type lectin domain family 7, member a	protein-coding
mm_78210.1	chr9	21491364	21491376	+	1	NA	intron (NM_001253894, intron 14 of 20)	intron (NM_001253894, intron 14 of 20)	5194	NR_029585	387194		NR_029585	ENSMUSG00000065547	Mir199a-1	Mirn199|Mirn199a-1|mir-199a-1	microRNA 199a-1	ncRNA
mm_26478.1	chr3	144677648	144677663	+	1	NA	Intergenic	Intergenic	42680	NM_001282042	54673	Mm.271775	NM_019464	ENSMUSG00000037062	Sh3glb1	AA409932|AI314629|AU015566|Bif-1|mKIAA0491	SH3-domain GRB2-like B1 (endophilin)	protein-coding
mm_133179.1	chr16	72563413	72563421	+	1	NA	Intergenic	Intergenic	-99732	NM_019413	19876	Mm.310772	NM_019413	ENSMUSG00000022883	Robo1	AW494633|AW742721|DUTT1|Gm310	roundabout guidance receptor 1	protein-coding
mm_6244.1	chr1	67038825	67038872	-	1	NA	promoter-TSS (NM_001190985)	promoter-TSS (NM_001190985)	-14	NM_001190984	14768	Mm.20522	NM_021295	ENSMUSG00000026000	Lancl1	AW124738|Gpr69|Gpr69a|p40	LanC (bacterial lantibiotic synthetase component C)-like 1	protein-coding
mm_159410.1	chr3	103279270	103279270	+	1	NA	promoter-TSS (NM_053170)	promoter-TSS (NM_053170)	-23	NM_053170	94093	Mm.195036	NM_053170	ENSMUSG00000033014	Trim33	8030451N04Rik|AI413936|Ecto|Tif1g	tripartite motif-containing 33	protein-coding
mm_66746.1	chr7	46712097	46712123	-	1	NA	3' UTR (NM_011315, exon 4 of 4)	3' UTR (NM_011315, exon 4 of 4)	-1459	NM_030233	78935	Mm.289866	NM_030233	ENSMUSG00000006763	Saal1	5031425D22Rik|SPACIA1	serum amyloid A-like 1	protein-coding
mm_130154.1	chr15	91191406	91191432	-	1	NA	exon (NM_011994, exon 1 of 10)	exon (NM_011994, exon 1 of 10)	388	NM_011994	26874	Mm.295456	NM_011994	ENSMUSG00000055782	Abcd2	ABC39|ALDL1|ALDR|ALDRP	ATP-binding cassette, sub-family D (ALD), member 2	protein-coding
mm_19050.1	chr2	77259819	77259832	-	1	NA	intron (NM_175465, intron 1 of 17)	ID4|SINE|ID	20767	NM_175465	228071	Mm.27120	NM_175465	ENSMUSG00000042272	Sestd1	1500031J16Rik|A930010O20|Solo/Trio8	SEC14 and spectrin domains 1	protein-coding
mm_69051.1	chr7	126861829	126861895	-	1	NA	promoter-TSS (NM_153580)	promoter-TSS (NM_153580)	-110	NM_172746	233876	Mm.363427	NM_172746	ENSMUSG00000042606	Hirip3	B130036O03|C86302	HIRA interacting protein 3	protein-coding
mm_26631.1	chr3	152912721	152912734	+	1	NA	intron (NM_012028, intron 2 of 4)	intron (NM_012028, intron 2 of 4)	69480	NM_012028	26938	Mm.40915	NM_012028	ENSMUSG00000039037	St6galnac5	AI851940|Siat7e	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 5	protein-coding
mm_155211.1	chrX	56786536	56786564	+	1	NA	promoter-TSS (NM_001287800)	promoter-TSS (NM_001287800)	23	NM_001287800	14199	Mm.3126	NM_010211	ENSMUSG00000023092	Fhl1	FHL-1|KyoT|RAM14-1|SLIM|SLIM-1	four and a half LIM domains 1	protein-coding
mm_161210.1	chr13	62558605	62558605	-	1	NA	promoter-TSS (NM_001162911)	promoter-TSS (NM_001162911)	-6	NM_001162911	77117	Mm.470091	NM_175252	ENSMUSG00000074865	Zfp934	6720457D02Rik	zinc finger protein 934	protein-coding
mm_165774.1	chr3	128610939	128610951	+	1	NA	Intergenic	Intergenic	-379340	NR_045704	402774	Mm.209170	NR_045704	ENSMUSG00000105816	D030025E07Rik	-	RIKEN cDNA D030025E07 gene	ncRNA
mm_134365.1	chr16	17111192	17111196	-	1	NA	promoter-TSS (NM_144954)	promoter-TSS (NM_144954)	58	NM_001252445	66053	Mm.253614	NM_144954	ENSMUSG00000022771	Ppil2	0610009L05Rik|1700016N17Rik|4921520K19Rik|4930511F14Rik|AA589416|C130078A06Rik|CYC4	peptidylprolyl isomerase (cyclophilin)-like 2	protein-coding
mm_163139.1	chr11	79339640	79339640	+	1	NA	promoter-TSS (NM_010897)	promoter-TSS (NM_010897)	-252	NM_010897	18015	Mm.255596	NM_010897	ENSMUSG00000020716	Nf1	AW494271|Dsk9|E030030H24Rik|Mhdadsk9|Nf-1	neurofibromin 1	protein-coding
mm_11631.1	chr2	34775720	34775748	+	1	NA	exon (NM_001163434, exon 9 of 9)	exon (NM_001163434, exon 9 of 9)	3644	NM_022310	14828	Mm.330160	NM_022310	ENSMUSG00000026864	Hspa5	AL022860|AU019543|Bip|D2Wsu141e|D2Wsu17e|Grp78|Hsce70|SEZ-7|Sez7|baffled|mBiP	heat shock protein 5	protein-coding
mm_8184.1	chr1	138082167	138082191	-	1	NA	intron (NM_001111316, intron 22 of 31)	intron (NM_001111316, intron 22 of 31)	92947	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_140362.1	chr17	86917400	86917438	+	1	NA	promoter-TSS (NM_030104)	promoter-TSS (NM_030104)	71	NM_030104	78469	Mm.67234	NM_030104	ENSMUSG00000037689	Tmem247	1700090G07Rik	transmembrane protein 247	protein-coding
mm_48965.1	chr6	4600899	4600956	+	1	NA	promoter-TSS (NM_145398)	promoter-TSS (NM_145398)	-139	NM_145398	213819	Mm.270703	NM_145398	ENSMUSG00000015189	Casd1	Cas1|Cast1	CAS1 domain containing 1	protein-coding
mm_155774.1	chrX	96334328	96334349	+	1	NA	intron (NM_001310755, intron 3 of 10)	L1MEd|LINE|L1	33581	NM_001310754	245525	Mm.166749	NM_172931	ENSMUSG00000045802	Hsf3	B230358A15Rik|HSF 3|HSTF 3	heat shock transcription factor 3	protein-coding
mm_68290.1	chr7	105736391	105736404	-	1	NA	promoter-TSS (NM_001161724)	promoter-TSS (NM_001161724)	187	NM_025897	101867	Mm.231400	NM_025897	ENSMUSG00000030888	Rrp8	1500003O22Rik|2900001K19Rik|AW538116	ribosomal RNA processing 8, methyltransferase, homolog (yeast)	protein-coding
mm_51689.1	chr6	86526276	86526299	+	1	NA	promoter-TSS (NM_011865)	promoter-TSS (NM_011865)	-122	NM_011865	23983	Mm.274146	NM_011865	ENSMUSG00000051695	Pcbp1	WBP17|[a]CP-1|alphaCP-1|hnRNP E1	poly(rC) binding protein 1	protein-coding
mm_25597.1	chr3	116903578	116903606	+	1	NA	3' UTR (NM_001113478, exon 17 of 17)	3' UTR (NM_001113478, exon 17 of 17)	41912	NM_009146	20321	Mm.66293	NM_009146	ENSMUSG00000033386	Frrs1	AI131732|Sdfr2	ferric-chelate reductase 1	protein-coding
mm_162220.1	chrX	140813497	140813497	-	1	NA	promoter-TSS (NM_031381)	promoter-TSS (NM_031381)	-64	NM_031381	83555	Mm.193025	NM_031381	ENSMUSG00000042386	Tex13b	4933403J23Rik|Tex13	testis expressed 13B	protein-coding
mm_60069.1	chr7	31302751	31302764	+	1	NA	promoter-TSS (NM_207262)	promoter-TSS (NM_207262)	-12	NM_207262	381970	Mm.333771	NM_207262	ENSMUSG00000036521	Scgb2b2	Abpbg2|Abpe|lacrimal	secretoglobin, family 2B, member 2	protein-coding
mm_106975.1	chr12	9030016	9030045	+	1	NA	promoter-TSS (NM_029321)	promoter-TSS (NM_029321)	33	NM_029321	75516	Mm.37581	NM_029321	ENSMUSG00000066637	Ttc32	1700013G20Rik	tetratricopeptide repeat domain 32	protein-coding
mm_77871.1	chr9	6168471	6168488	+	1	NA	promoter-TSS (NM_027924)	promoter-TSS (NM_027924)	-133	NM_027924	71785	Mm.390122	NM_027924	ENSMUSG00000032006	Pdgfd	1110003I09Rik	platelet-derived growth factor, D polypeptide	protein-coding
mm_130566.1	chr15	99424535	99424549	-	1	NA	intron (NM_001001884, intron 8 of 12)	intron (NM_001001884, intron 8 of 12)	31323	NM_001171035	110213	Mm.16769	NM_026669	ENSMUSG00000023010	Tmbim6	5031406P05Rik|Bi1|Tegt	transmembrane BAX inhibitor motif containing 6	protein-coding
mm_111223.1	chr12	84617327	84617419	-	1	NA	promoter-TSS (NM_008992)	promoter-TSS (NM_008992)	93	NM_008992	19300	Mm.229109	NM_008992	ENSMUSG00000021240	Abcd4	P69r|P70R|Pxmp1l	ATP-binding cassette, sub-family D (ALD), member 4	protein-coding
mm_57653.1	chr6	128438674	128438698	-	1	NA	promoter-TSS (NM_010219)	promoter-TSS (NM_010219)	-55	NM_010219	14228	Mm.12758	NM_010219	ENSMUSG00000030357	Fkbp4	59kDa|AL022792|AW208983|FKBP-4|FKBP-52|FKBP52|FKPB52|p59	FK506 binding protein 4	protein-coding
mm_96406.1	chr11	67251851	67251886	+	1	NA	exon (NM_010855, exon 23 of 40)	exon (NM_010855, exon 23 of 40)	14056	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_122994.1	chr14	54990954	54990967	-	1	NA	exon (NM_080728, exon 9 of 41)	exon (NM_080728, exon 9 of 41)	3589	NM_080728	140781	Mm.457983	NM_080728	ENSMUSG00000053093	Myh7	B-MHC|MyHC-I|Myhc-b|Myhcb|beta-MHC	myosin, heavy polypeptide 7, cardiac muscle, beta	protein-coding
mm_157513.1	chrX	49288230	49288265	-	1	NA	promoter-TSS (NM_145951)	promoter-TSS (NM_145951)	-5	NM_001271450	209224	Mm.327730	NM_145951	ENSMUSG00000031109	Enox2	APK1|Cova1|tNOX	ecto-NOX disulfide-thiol exchanger 2	protein-coding
mm_57158.1	chr6	122742510	122742527	-	1	NA	5' UTR (NM_011401, exon 1 of 10)	5' UTR (NM_011401, exon 1 of 10)	227	NM_011401	20527	Mm.395108	NM_011401	ENSMUSG00000003153	Slc2a3	AA408729|AL023014|AL024341|AU040424|C78366|Glut-3|Glut3	solute carrier family 2 (facilitated glucose transporter), member 3	protein-coding
mm_44555.1	chr5	24601962	24602007	-	1	NA	promoter-TSS (NM_025891)	promoter-TSS (NM_025891)	18	NM_025891	66993	Mm.436539	NM_025891	ENSMUSG00000028949	Smarcd3	1500001J14Rik|2210409C08Rik|BAF60C	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3	protein-coding
mm_83364.1	chr9	44418031	44418056	-	1	NA	promoter-TSS (NM_201372)	promoter-TSS (NM_201372)	-36	NM_201372	382073	Mm.259573	NM_201372	ENSMUSG00000043923	Ccdc84	D630044F24Rik|Gm1114	coiled-coil domain containing 84	protein-coding
mm_31469.1	chr4	49632000	49632010	+	1	NA	promoter-TSS (NM_001163263)	promoter-TSS (NM_001163263)	-55	NM_001163263	109331	Mm.24765	NM_182999	ENSMUSG00000028309	Rnf20	4833430L21Rik|AW540162|C79397|mKIAA4116	ring finger protein 20	protein-coding
mm_43256.1	chr5	130222329	130222390	+	1	NA	promoter-TSS (NM_027854)	promoter-TSS (NM_027854)	24	NM_027854	71667	Mm.258508	NM_027854	ENSMUSG00000053094	Tmem248	0610007L01Rik|A930023A16Rik|AW557951|G430067H08Rik	transmembrane protein 248	protein-coding
mm_163570.1	chr13	30136464	30136491	+	1	NA	promoter-TSS (NM_153546)	promoter-TSS (NM_153546)	-13	NM_153546	218121	Mm.89682	NM_153546	ENSMUSG00000038732	Mboat1	9130215M02Rik|BC023845|LPEAT1|Moact1|Oact1	membrane bound O-acyltransferase domain containing 1	protein-coding
mm_162813.1	chr10	79686440	79686446	+	1	NA	intron (NM_177613, intron 4 of 4)	intron (NM_177613, intron 4 of 4)	-2577	NM_001302485	16904	Mm.378960	NM_008504	ENSMUSG00000054206	Gzmm	Lmet1|MMET-1	granzyme M (lymphocyte met-ase 1)	protein-coding
mm_41176.1	chr5	88008070	88008097	+	1	NA	exon (NM_011422, exon 3 of 3)	exon (NM_011422, exon 3 of 3)	5558	NM_011422	20599	Mm.261199	NM_011422	ENSMUSG00000029280	Smr3a	AA589601|MSG1|MSG3|Smr1|Smr3	submaxillary gland androgen regulated protein 3A	protein-coding
mm_125341.1	chr15	39076965	39076973	+	1	NA	promoter-TSS (NM_026778)	promoter-TSS (NM_026778)	37	NM_026778	68588	Mm.41556	NM_026778	ENSMUSG00000054196	Cthrc1	1110014B07Rik	collagen triple helix repeat containing 1	protein-coding
mm_10791.1	chr2	24349409	24349422	+	1	NA	exon (NM_031167, exon 5 of 5)	exon (NM_031167, exon 5 of 5)	4044	NM_001039701	16181	Mm.882	NM_031167	ENSMUSG00000026981	Il1rn	F630041P17Rik|IL-1ra	interleukin 1 receptor antagonist	protein-coding
mm_133635.1	chr16	91659659	91659713	+	1	NA	exon (NM_019973, exon 3 of 5)	exon (NM_019973, exon 3 of 5)	11862	NM_178880	20658	Mm.46401	NM_019973	ENSMUSG00000022961	Son	2900011L12Rik|AA409051|AU067731|C81487|mKIAA1019|nrebp	Son DNA binding protein	protein-coding
mm_163878.1	chr14	19419602	19419640	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	182966	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_118064.1	chr13	102901898	102901899	-	1	NA	intron (NM_175171, intron 4 of 28)	intron (NM_175171, intron 4 of 28)	141643	NR_130171	76624	Mm.426384	NR_130171	ENSMUSG00000091906	1700099I09Rik	-	RIKEN cDNA 1700099I09 gene	ncRNA
mm_140881.1	chr17	23829096	23829143	-	1	NA	promoter-TSS (NM_026305)	promoter-TSS (NM_026305)	-10	NM_026305	67673	Mm.153758	NM_026305	ENSMUSG00000055839	Elob	0610040H15Rik|Tceb2	elongin B	protein-coding
mm_104094.1	chr11	86683762	86683847	-	1	NA	promoter-TSS (NM_001098810)	promoter-TSS (NM_001098810)	18	NM_029478	75909	Mm.390398	NM_029478	ENSMUSG00000018171	Vmp1	3110098I04Rik|4930579A11Rik|AI787464|Tango5|Tmem49|mir-21a|ni-2	vacuole membrane protein 1	protein-coding
mm_51138.1	chr6	68980361	68980370	+	1	NA	Intergenic	RLTR44C|LTR|ERVK	346809	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_62079.1	chr7	92928709	92928724	+	1	NA	exon (NM_028243, exon 8 of 9)	exon (NM_028243, exon 8 of 9)	53463	NM_028243	72461	Mm.389969	NM_028243	ENSMUSG00000061119	Prcp	2510048K03Rik|2610104A14Rik|AI451719|HUMPCP|PCP	prolylcarboxypeptidase (angiotensinase C)	protein-coding
mm_162247.1	chrX	159988437	159988437	+	1	NA	promoter-TSS (NM_001163085)	promoter-TSS (NM_001163085)	4	NM_001163085	270672	Mm.386889	NM_001163085	ENSMUSG00000031303	Map3k15	BC031147|MEKK15	mitogen-activated protein kinase kinase kinase 15	protein-coding
mm_129688.1	chr15	81466044	81466057	-	1	NA	promoter-TSS (NM_019712)	promoter-TSS (NM_019712)	-266	NM_019712	56438	Mm.29405	NM_019712	ENSMUSG00000022400	Rbx1	1500002P15Rik|AA517855|ROC1	ring-box 1	protein-coding
mm_114262.1	chr13	56963842	56963845	+	1	NA	Intergenic	Intergenic	-68054	NM_001302373	26946	Mm.62409	NM_012035	ENSMUSG00000021541	Trpc7	TRP7|Trrp8	transient receptor potential cation channel, subfamily C, member 7	protein-coding
mm_137224.1	chr17	24251965	24252010	+	1	NA	promoter-TSS (NM_007634)	promoter-TSS (NM_007634)	-578	NM_007634	12449	Mm.77695	NM_007634	ENSMUSG00000072082	Ccnf	CycF|Fbxo1	cyclin F	protein-coding
mm_18559.1	chr2	65238504	65238530	-	1	NA	5' UTR (NM_177025, exon 1 of 14)	5' UTR (NM_177025, exon 1 of 14)	109	NM_177025	319876	Mm.34159	NM_027225	ENSMUSG00000034903	Cobll1	1810047P18Rik|Coblr1|D430044D16Rik	Cobl-like 1	protein-coding
mm_21272.1	chr2	156862966	156863006	-	1	NA	promoter-TSS (NM_026124)	promoter-TSS (NM_026124)	-41	NR_027914	74487	Mm.490465	NR_015591	ENSMUSG00000085741	5430405H02Rik	2610307N17Rik	RIKEN cDNA 5430405H02 gene	ncRNA
mm_64333.1	chr7	142303529	142303536	+	1	NA	promoter-TSS (NM_015809)	promoter-TSS (NM_015809)	30	NM_015809	50775	Mm.389990	NM_015809	ENSMUSG00000045236	Krtap5-4	-	keratin associated protein 5-4	protein-coding
mm_30194.1	chr3	144710476	144710493	-	1	NA	intron (NM_001282042, intron 2 of 9)	intron (NM_001282042, intron 2 of 9)	9851	NM_001282042	54673	Mm.271775	NM_019464	ENSMUSG00000037062	Sh3glb1	AA409932|AI314629|AU015566|Bif-1|mKIAA0491	SH3-domain GRB2-like B1 (endophilin)	protein-coding
mm_44089.1	chr5	149235271	149235287	+	1	NA	Intergenic	MLT1F|LTR|ERVL-MaLR	-29725	NM_001308462	11690	Mm.19844	NM_009663	ENSMUSG00000060063	Alox5ap	Flap	arachidonate 5-lipoxygenase activating protein	protein-coding
mm_142975.1	chr17	56140334	56140384	-	1	NA	promoter-TSS (NM_001130456)	promoter-TSS (NM_001130456)	-16	NM_001130456	20359	Mm.8029	NM_013662	ENSMUSG00000001227	Sema6b	Sema|Seman|VIb|semaZ	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B	protein-coding
mm_150832.1	chr19	44756698	44756714	+	1	NA	promoter-TSS (NM_011037)	promoter-TSS (NM_011037)	-688	NM_011037	18504	Mm.192158	NM_011037	ENSMUSG00000004231	Pax2	Opdc|Pax-2	paired box 2	protein-coding
mm_74960.1	chr8	26119126	26119233	-	1	NA	promoter-TSS (NM_029965)	promoter-TSS (NM_029965)	45	NM_207659	320191	Mm.334464	NM_207659	ENSMUSG00000037234	Hook3	5830454D03Rik|AI317159|E330005F07Rik	hook microtubule tethering protein 3	protein-coding
mm_114112.1	chr13	54913250	54913250	+	1	NA	Intergenic	Intergenic	-36161	NM_001311128	107448	Mm.23573	NM_153131	ENSMUSG00000025876	Unc5a	Unc5h1|mKIAA1976	unc-5 netrin receptor A	protein-coding
mm_70976.1	chr8	27172284	27172291	+	1	NA	intron (NM_029423, intron 1 of 4)	intron (NM_029423, intron 1 of 4)	2359	NM_029423	75767	Mm.205335	NM_029423	ENSMUSG00000031488	Rab11fip1	2010200K21Rik|4833414G05Rik|Rcp	RAB11 family interacting protein 1 (class I)	protein-coding
mm_164239.1	chr15	92396952	92396968	+	1	NA	exon (NM_001164593, exon 1 of 10)	exon (NM_001164593, exon 1 of 10)	150	NM_001164593	239618	Mm.309826	NM_001164593	ENSMUSG00000036218	Pdzrn4	1110017D07Rik|LNX4|SAMCAP3L|mKIAA3027	PDZ domain containing RING finger 4	protein-coding
mm_54952.1	chr6	48681806	48681817	-	1	NA	Intergenic	Intergenic	-2767	NM_001243200	107526	Mm.333048	NM_174990	ENSMUSG00000054435	Gimap4	AU019574|E430007K16Rik|Ian-1|Ian1|Imap4	GTPase, IMAP family member 4	protein-coding
mm_95950.1	chr11	58390240	58390250	+	1	NA	exon (NM_001083884, exon 7 of 7)	exon (NM_001083884, exon 7 of 7)	9599	NM_001330197	70163	Mm.24119	NM_027339	ENSMUSG00000013643	Lypd8	2210415F13Rik	LY6/PLAUR domain containing 8	protein-coding
mm_6475.1	chr1	74069212	74069230	-	1	NA	intron (NM_027884, intron 2 of 34)	intron (NM_027884, intron 2 of 34)	55226	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_135131.1	chr16	35844050	35844064	-	1	NA	intron (NM_001039530, intron 12 of 16)	intron (NM_001039530, intron 12 of 16)	27325	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_43664.1	chr5	138754639	138754652	+	1	NA	promoter-TSS (NM_030565)	promoter-TSS (NM_030565)	-436	NM_030565	80752	Mm.320355	NM_030565	ENSMUSG00000025854	Fam20c	C76981|DMP-4|DMP4|GEF-CK|mKIAA4081	family with sequence similarity 20, member C	protein-coding
mm_163579.1	chr13	33569531	33569540	-	1	NA	promoter-TSS (NR_131141)	promoter-TSS (NR_131141)	-218	NR_131141	619715	Mm.390575	NR_131140		Gm6093	EG619715	predicted gene 6093	ncRNA
mm_42010.1	chr5	108065747	108065767	+	1	NA	promoter-TSS (NM_013827)	promoter-TSS (NM_013827)	83	NM_013827	17765	Mm.257149	NM_013827	ENSMUSG00000029267	Mtf2	9230112N11Rik|AA537621|C76717|M96|Pcl2	metal response element binding transcription factor 2	protein-coding
mm_64254.1	chr7	141744650	141744664	+	1	NA	exon (NM_023566, exon 28 of 46)	exon (NM_023566, exon 28 of 46)	-44354	NM_010844	17833	Mm.334332	NM_010844	ENSMUSG00000037974	Muc5ac	2210005L13Rik|MGM	mucin 5, subtypes A and C, tracheobronchial/gastric	protein-coding
mm_166695.1	chr6	113740729	113740734	-	1	NA	promoter-TSS (NM_024206)	promoter-TSS (NM_024206)	-50	NM_024206	110379	Mm.29296	NM_024206	ENSMUSG00000030298	Sec13	1110003H02Rik|Sec13l1|Sec13r	SEC13 homolog, nuclear pore and COPII coat complex component	protein-coding
mm_49256.1	chr6	17463433	17463442	+	1	NA	promoter-TSS (NM_008591)	promoter-TSS (NM_008591)	-520	NM_008591	17295	Mm.86844	NM_008591	ENSMUSG00000009376	Met	AI838057|HGF|HGFR|Par4|c-Met	met proto-oncogene	protein-coding
mm_159253.1	chr2	152572743	152572743	+	1	NA	promoter-TSS (NM_207276)	promoter-TSS (NM_207276)	-1	NM_207276	403172	Mm.84518	NM_207276	ENSMUSG00000056544	Defb21	4930525K10Rik|Gm121	defensin beta 21	protein-coding
mm_109125.1	chr12	105761392	105761427	+	1	NA	intron (NM_030187, intron 12 of 17)	intron (NM_030187, intron 12 of 17)	-23288	NM_011112	18789	Mm.255877	NM_011112	ENSMUSG00000021111	Papola	Pap|PapIII|Plap	poly (A) polymerase alpha	protein-coding
mm_110497.1	chr12	54203795	54203811	-	1	NA	promoter-TSS (NM_028133)	promoter-TSS (NM_028133)	71	NM_028133	112407	Mm.133037	NM_028133	ENSMUSG00000035105	Egln3	2610021G09Rik|AI505553|AI648162|Hif-p4h-3|Phd3|SM-20	egl-9 family hypoxia-inducible factor 3	protein-coding
mm_2316.1	chr1	91984782	91984790	+	1	NA	intron (NM_207225, intron 9 of 26)	intron (NM_207225, intron 9 of 26)	183325	NM_007855	13345	Mm.9474	NM_007855	ENSMUSG00000007805	Twist2	Dermo1|bHLHa39	twist basic helix-loop-helix transcription factor 2	protein-coding
mm_43762.1	chr5	140702465	140702473	+	1	NA	promoter-TSS (NM_028833)	promoter-TSS (NM_028833)	-91	NM_001347517	74239	Mm.179704	NM_028833	ENSMUSG00000036555	Iqce	1700028P05Rik|mKIAA1023	IQ motif containing E	protein-coding
mm_109572.1	chr12	112107293	112107302	+	1	NA	intron (NM_001081169, intron 1 of 14)	intron (NM_001081169, intron 1 of 14)	614	NM_001081169	104816	Mm.77133	NM_001081169	ENSMUSG00000037686	Aspg	A530050D06Rik|AI429460|Gm690	asparaginase	protein-coding
mm_72518.1	chr8	83955678	83955688	+	1	NA	promoter-TSS (NM_024184)	promoter-TSS (NM_024184)	-11	NM_024184	66929	Mm.29680	NM_024184	ENSMUSG00000005470	Asf1b	1700003K02Rik|AA409591	anti-silencing function 1B histone chaperone	protein-coding
mm_15938.1	chr2	165730085	165730096	+	1	NA	intron (NM_001271962, intron 8 of 15)	intron (NM_001271962, intron 8 of 15)	74792	NM_010165	14049	Mm.282719	NM_010165	ENSMUSG00000017897	Eya2	Eab1	EYA transcriptional coactivator and phosphatase 2	protein-coding
mm_114021.1	chr13	52620936	52620947	+	1	NA	intron (NM_001198977, intron 4 of 13)	IMPB_01|Satellite|Satellite	24059	NM_011518	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_92952.1	chr10	85198427	85198440	-	1	NA	Intergenic	ORR1B2|LTR|ERVL-MaLR	-13379	NM_007771	12952	Mm.26237	NM_007771	ENSMUSG00000020038	Cry1	AU020726|AU021000|Phll1	cryptochrome 1 (photolyase-like)	protein-coding
mm_7512.1	chr1	123887335	123887357	-	1	NA	intron (NM_199021, intron 2 of 25)	intron (NM_199021, intron 2 of 25)	158213	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_64624.1	chr7	3677479	3677502	-	1	NA	promoter-TSS (NM_181820)	promoter-TSS (NM_181820)	63	NM_181820	353499	Mm.360398	NM_181820	ENSMUSG00000019734	Tmc4	-	transmembrane channel-like gene family 4	protein-coding
mm_17603.1	chr2	30890076	30890106	-	1	NA	3' UTR (NM_022415, exon 3 of 3)	3' UTR (NM_022415, exon 3 of 3)	13206	NM_022415	64292	Mm.28768	NM_022415	ENSMUSG00000050737	Ptges	2410099E23Rik|D2Ertd369e|Pges|mPGES|mPGES-1	prostaglandin E synthase	protein-coding
mm_37993.1	chr4	133658839	133658844	-	1	NA	Intergenic	RMER17C|LTR|ERVK	13806	NM_001145955	230801	Mm.217004	NM_178698	ENSMUSG00000043257	Pigv	B330013B03|D430024F16Rik	phosphatidylinositol glycan anchor biosynthesis, class V	protein-coding
mm_124996.1	chr15	23036421	23036441	+	1	NA	promoter-TSS (NM_001081299)	promoter-TSS (NM_001081299)	-32	NM_001081299	320865	Mm.241965	NM_001081299	ENSMUSG00000040420	Cdh18	B230220E17Rik|Cdh14l	cadherin 18	protein-coding
mm_146907.1	chr18	31317002	31317041	-	1	NA	5' UTR (NM_009065, exon 1 of 5)	5' UTR (NM_009065, exon 1 of 5)	107	NM_009065	19762	Mm.5163	NM_009065	ENSMUSG00000057455	Rit2	RIBA|Rin|Roc2	Ras-like without CAAX 2	protein-coding
mm_35108.1	chr4	9643639	9643714	-	1	NA	promoter-TSS (NM_001177853)	promoter-TSS (NM_001177853)	41	NM_001177853	65973	Mm.222206	NM_023066	ENSMUSG00000028207	Asph	2310005F16Rik|3110001L23Rik|AI848629|AW261690|AW561901|BAH|C79816|cI-37	aspartate-beta-hydroxylase	protein-coding
mm_34684.1	chr4	151862178	151862219	+	1	NA	promoter-TSS (NM_001195565)	promoter-TSS (NM_001195565)	-430	NM_001195565	100072	Mm.318846	NM_001081557	ENSMUSG00000014592	Camta1	1810059M14Rik|2310058O09Rik|AI316882|AW987475|mKIAA0833	calmodulin binding transcription activator 1	protein-coding
mm_168561.1	chr11	6895057	6895057	-	1	NA	Intergenic	Intergenic	-168432	NM_009622	432530	Mm.259733	NM_009622	ENSMUSG00000020431	Adcy1	AC1|D11Bwg1392e|I-AC|brl|mKIAA4070	adenylate cyclase 1	protein-coding
mm_104419.1	chr11	94760936	94760959	-	1	NA	5' UTR (NM_001105561, exon 1 of 5)	5' UTR (NM_001105561, exon 1 of 5)	235	NM_001105561	217122	Mm.24063	NM_183153		Gm11545	A430060F13Rik|C86086|OTTMUSG00000002043	predicted gene 11545	protein-coding
mm_111944.1	chr12	109053311	109053321	-	1	NA	intron (NM_001163175, intron 1 of 6)	CpG-3504	14901	NM_001163175	380785	Mm.342085	NM_001163175	ENSMUSG00000040867	Begain	BM948371|Gm897	brain-enriched guanylate kinase-associated	protein-coding
mm_18200.1	chr2	45197387	45197402	-	1	NA	Intergenic	Intergenic	-84115	NM_015753	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_11138.1	chr2	28477084	28477093	+	1	NA	Intergenic	Intergenic	9022	NM_001166031	118451	Mm.294951	NM_080452	ENSMUSG00000035772	Mrps2	1500019M10Rik	mitochondrial ribosomal protein S2	protein-coding
mm_105957.1	chr11	115419892	115419901	-	1	NA	promoter-TSS (NM_027862)	promoter-TSS (NM_027862)	23	NM_027862	71679	Mm.371641	NM_027862	ENSMUSG00000034566	Atp5h	0610009D10Rik	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit D	protein-coding
mm_105638.1	chr11	106999462	106999473	-	1	NA	promoter-TSS (NM_010655)	promoter-TSS (NM_010655)	58	NM_010655	16647	Mm.12508	NM_010655	ENSMUSG00000018362	Kpna2	2410044B12Rik|IPOA1|PTAC58|Rch1	karyopherin (importin) alpha 2	protein-coding
mm_142565.1	chr17	46674264	46674274	-	1	NA	promoter-TSS (NM_144857)	promoter-TSS (NM_144857)	-14	NM_144857	224823	Mm.45101	NM_144857	ENSMUSG00000023971	Rrp36	-	ribosomal RNA processing 36 homolog (S. cerevisiae)	protein-coding
mm_55770.1	chr6	78467579	78467606	-	1	NA	exon (NM_011260, exon 4 of 6)	exon (NM_011260, exon 4 of 6)	1282	NM_011260	19695	Mm.252385	NM_011260	ENSMUSG00000030017	Reg3g	AI449515|REG-3-gamma|reg III-gamma	regenerating islet-derived 3 gamma	protein-coding
mm_92954.1	chr10	85266335	85266354	-	1	NA	Intergenic	Intergenic	-81290	NM_007771	12952	Mm.26237	NM_007771	ENSMUSG00000020038	Cry1	AU020726|AU021000|Phll1	cryptochrome 1 (photolyase-like)	protein-coding
mm_131852.1	chr16	23062116	23062122	+	1	NA	intron (NM_023125, intron 3 of 10)	RLTR11A|LTR|ERVK	3819	NM_001102412	16644	Mm.2160	NM_023125	ENSMUSG00000022875	Kng1	Kng	kininogen 1	protein-coding
mm_135795.1	chr16	57198997	57199019	-	1	NA	intron (NM_026254, intron 5 of 17)	intron (NM_026254, intron 5 of 17)	-31676	NM_023175	52633	Mm.383203	NM_023175	ENSMUSG00000022751	Nit2	1190017B19Rik|D16Ertd502e	nitrilase family, member 2	protein-coding
mm_142120.1	chr17	35868297	35868333	-	1	NA	exon (NM_001146711, exon 2 of 4)	exon (NM_001146711, exon 2 of 4)	1700	NM_175242	76448	Mm.359982	NM_175242	ENSMUSG00000034595	Ppp1r18	2310014H01Rik|AA407849|AI450394	protein phosphatase 1, regulatory subunit 18	protein-coding
mm_7278.1	chr1	97645514	97645522	-	1	NA	3' UTR (NM_133825, exon 3 of 3)	3' UTR (NM_133825, exon 3 of 3)	16500	NM_133825	52392	Mm.12309	NM_133825	ENSMUSG00000044768	D1Ertd622e	AI987691|AW047450	DNA segment, Chr 1, ERATO Doi 622, expressed	protein-coding
mm_35267.1	chr4	19900924	19900934	-	1	NA	intron (NM_175406, intron 2 of 7)	intron (NM_175406, intron 2 of 7)	21637	NM_175406	242341	Mm.19298	NM_175406	ENSMUSG00000028238	Atp6v0d2	1620401A02Rik|AI324824|V-ATPase	ATPase, H+ transporting, lysosomal V0 subunit D2	protein-coding
mm_94026.1	chr10	127668873	127668883	-	1	NA	TTS (NR_045171)	TTS (NR_045171)	1755	NR_045171	72243	Mm.482902	NR_045171	ENSMUSG00000040195	1700012D01Rik	-	RIKEN cDNA 1700012D01 gene	ncRNA
mm_152054.1	chr19	6278196	6278220	-	1	NA	intron (NM_010119, intron 1 of 4)	intron (NM_010119, intron 1 of 4)	1312	NM_010119	13660	Mm.30169	NM_010119	ENSMUSG00000024772	Ehd1	AA409636|Past1|RME-1	EH-domain containing 1	protein-coding
mm_161529.1	chr15	101892726	101892726	-	1	NA	exon (NM_001033177, exon 1 of 9)	exon (NM_001033177, exon 1 of 9)	194	NM_001033177	77055	Mm.195788	NM_001033177	ENSMUSG00000075402	Krt76	2310001L23Rik	keratin 76	protein-coding
mm_76035.1	chr8	77387306	77387324	-	1	NA	intron (NM_030113, intron 11 of 22)	B3A|SINE|B2	-129741	NR_028125	70345	Mm.411813	NR_028125	ENSMUSG00000097882	0610038B21Rik	-	RIKEN cDNA 0610038B21 gene	ncRNA
mm_71431.1	chr8	46492954	46492988	+	1	NA	exon (NM_007981, exon 2 of 21)	exon (NM_007981, exon 2 of 21)	2005	NM_001302163	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_71871.1	chr8	69209084	69209094	+	1	NA	promoter-TSS (NM_001013379)	promoter-TSS (NM_001013379)	43	NM_001013379	234358	Mm.334577	NM_001013379	ENSMUSG00000059897	Zfp930	-	zinc finger protein 930	protein-coding
mm_166595.1	chr6	64734581	64734590	+	1	NA	Intergenic	CpG	5439	NM_007500	11921	Mm.57229	NM_007500	ENSMUSG00000073043	Atoh1	Hath1|MATH-1|Math1|bHLHa14	atonal bHLH transcription factor 1	protein-coding
mm_49434.1	chr6	29281139	29281148	+	1	NA	promoter-TSS (NM_001101486)	promoter-TSS (NM_001101486)	2	NM_001101486	245884	Mm.33683	NM_001101486	ENSMUSG00000079652	Fam71f2	AI507611|GARI	family with sequence similarity 71, member F2	protein-coding
mm_105941.1	chr11	115187860	115187868	-	1	NA	promoter-TSS (NM_025400)	promoter-TSS (NM_025400)	377	NM_001033393	320534	Mm.260587	NM_001033393	ENSMUSG00000045980	Tmem104	C630005D06Rik|mFLJ00021	transmembrane protein 104	protein-coding
mm_91136.1	chr10	19632172	19632174	-	1	NA	intron (NM_178258, intron 4 of 4)	intron (NM_178258, intron 4 of 4)	10145	NM_178258	237310	Mm.331979	NM_178258	ENSMUSG00000039760	Il22ra2	CRF2-10|CRF2-s1|CRF2X|Il-22bp	interleukin 22 receptor, alpha 2	protein-coding
mm_144322.1	chr18	12743143	12743145	+	1	NA	intron (NM_027687, intron 1 of 5)	intron (NM_027687, intron 1 of 5)	1789	NM_027687	71132	Mm.179740	NM_027687	ENSMUSG00000024430	Cabyr	1700016C01Rik|4933421A18Rik|CBP86|FSP-2	calcium-binding tyrosine-(Y)-phosphorylation regulated (fibrousheathin 2)	protein-coding
mm_173128.1	chrX	170008976	170008989	-	1	NA	Intergenic	Intergenic	-30065	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_124430.1	chr14	118236993	118237013	-	1	NA	promoter-TSS (NM_177753)	promoter-TSS (NM_177753)	27	NM_177753	223227	Mm.70950	NM_177753	ENSMUSG00000061517	Sox21	Sox25	SRY (sex determining region Y)-box 21	protein-coding
mm_86412.1	chr10	3366352	3366380	+	1	NA	5' UTR (NM_133485, exon 1 of 4)	5' UTR (NM_133485, exon 1 of 4)	216	NM_133485	76142	Mm.308126	NM_133485	ENSMUSG00000040653	Ppp1r14c	6330514J04Rik|KEPI	protein phosphatase 1, regulatory (inhibitor) subunit 14c	protein-coding
mm_155380.1	chrX	71812775	71812795	+	1	NA	Intergenic	Intergenic	-3295	NM_001290781	67048	Mm.41102	NM_001081356	ENSMUSG00000073131	Vma21	2610030H06Rik|AI840175	VMA21 vacuolar H+-ATPase homolog (S. cerevisiae)	protein-coding
mm_58147.1	chr6	142322942	142322957	-	1	NA	promoter-TSS (NM_130861)	promoter-TSS (NM_130861)	32	NM_130861	108096	Mm.206599	NM_130861	ENSMUSG00000063975	Slco1a5	Oatp-3|Oatp3|Slc21a7	solute carrier organic anion transporter family, member 1a5	protein-coding
mm_86785.1	chr10	20171957	20171975	+	1	NA	intron (NM_001198635, intron 1 of 17)	intron (NM_001198635, intron 1 of 17)	23046	NM_001198635	17761	Mm.20928	NM_008635	ENSMUSG00000019996	Map7	E-MAP-115|MAP-7|Mtap7|R75000|mshi|mste|ste	microtubule-associated protein 7	protein-coding
mm_130872.1	chr15	102231896	102231917	-	1	NA	promoter-TSS (NM_013566)	promoter-TSS (NM_013566)	29	NM_013566	16421	Mm.58	NM_013566	ENSMUSG00000001281	Itgb7	Ly69	integrin beta 7	protein-coding
mm_85498.1	chr9	106158110	106158132	-	1	NA	promoter-TSS (NM_174846)	promoter-TSS (NM_174846)	17	NM_001039586	235582	Mm.335420	NM_174846	ENSMUSG00000020258	Glyctk	6230410P16Rik|C430006L12	glycerate kinase	protein-coding
mm_136537.1	chr16	97763422	97763426	-	1	NA	intron (NM_023663, intron 1 of 7)	CpG	331	NM_023663	72388	Mm.35290	NM_023663	ENSMUSG00000005251	Ripk4	2310069J12Rik|AI552420|ANKK2|Ankrd3|DIk|PKK|RIP4	receptor-interacting serine-threonine kinase 4	protein-coding
mm_162806.1	chr10	77874575	77874577	+	1	NA	intron (NM_001287074, intron 8 of 11)	intron (NM_001287074, intron 8 of 11)	12601	NM_001101631	100041351	Mm.441672	NM_001101631		Gm3285	-	predicted gene 3285	protein-coding
mm_108508.1	chr12	83987731	83987753	+	1	NA	promoter-TSS (NM_134188)	promoter-TSS (NM_134188)	-119	NM_134188	171210	Mm.371675	NM_134188	ENSMUSG00000021226	Acot2	AA571646|MTE-I|Mte1	acyl-CoA thioesterase 2	protein-coding
mm_39698.1	chr5	27160627	27160639	+	1	NA	intron (NM_207282, intron 1 of 25)	intron (NM_207282, intron 1 of 25)	-101302	NM_001136060	13483	Mm.42078	NM_010075	ENSMUSG00000061576	Dpp6	B930011P16Rik|D5Buc3|D5Buc4|D5Buc5|DPP VI|Dpp-6|Gm1377|In(5)6H-p|Peplb|Rw	dipeptidylpeptidase 6	protein-coding
mm_147952.1	chr18	66860498	66860508	-	1	NA	promoter-TSS (NM_016977)	promoter-TSS (NM_016977)	-16	NM_016977	17202	Mm.229447	NM_016977	ENSMUSG00000047259	Mc4r	Mc4-r	melanocortin 4 receptor	protein-coding
mm_105847.1	chr11	113709522	113709528	-	1	NA	promoter-TSS (NM_001164532)	promoter-TSS (NM_001164532)	1	NM_026682	52670	Mm.229207	NM_026682	ENSMUSG00000018727	Cpsf4l	0610010C04Rik|1500000C01Rik|D11Ertd636e	cleavage and polyadenylation specific factor 4-like	protein-coding
mm_98220.1	chr11	88047694	88047727	+	1	NA	5' UTR (NM_001078167, exon 1 of 3)	5' UTR (NM_001078167, exon 1 of 3)	337	NM_173374	110809	Mm.391719	NM_173374	ENSMUSG00000018379	Srsf1	1110054N12Rik|5730507C05Rik|6330415C05Rik|AI482334|AW491331|Asf|Sf2|Sfrs1	serine/arginine-rich splicing factor 1	protein-coding
mm_10480.1	chr2	14604253	14604271	+	1	NA	promoter-TSS (NM_023116)	promoter-TSS (NM_023116)	-44	NM_023116	12296	Mm.313930	NM_023116	ENSMUSG00000057914	Cacnb2	AW060387|CAB2|Cavbeta2|Cchb2	calcium channel, voltage-dependent, beta 2 subunit	protein-coding
mm_36366.1	chr4	76435793	76435796	-	1	NA	intron (NM_011211, intron 10 of 39)	intron (NM_011211, intron 10 of 39)	-1157508	NM_025849	66928	Mm.24332	NM_025849	ENSMUSG00000028398	Tmem261	1700027K24Rik|3110001D03Rik	transmembrane protein 261	protein-coding
mm_164561.1	chr17	17831643	17831654	+	1	NA	TTS (NR_029539)	TTS (NR_029539)	673	NM_001162909	75202	Mm.227456	NM_029205	ENSMUSG00000080316	Spaca6	4930546H06Rik|9530079D04Rik|B230206P06Rik|Ncrna00085|SPACA6A|let-7e|mir-125a|mir-99b	sperm acrosome associated 6	protein-coding
mm_112369.1	chr12	119182136	119182144	-	1	NA	intron (NM_177290, intron 6 of 13)	ID4_|SINE|ID	56136	NM_177290	320910	Mm.217000	NM_177290	ENSMUSG00000025321	Itgb8	4832412O06Rik	integrin beta 8	protein-coding
mm_116049.1	chr13	27390840	27390848	-	1	NA	promoter-TSS (NM_025532)	promoter-TSS (NM_025532)	2	NM_025532	66392	Mm.5099	NM_025532	ENSMUSG00000069258	Prl2b1	2310047B08Rik|Ghd12|PLP-K|Plpk|Prlpk|mPLP-K	prolactin family 2, subfamily b, member 1	protein-coding
mm_52122.1	chr6	97941173	97941192	+	1	NA	exon (NM_001178049, exon 2 of 10)	exon (NM_001178049, exon 2 of 10)	11365	NM_001178049	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_117829.1	chr13	98263027	98263047	-	1	NA	promoter-TSS (NM_178918)	promoter-TSS (NM_178918)	-39	NM_001271392	68558	Mm.209642	NM_023472	ENSMUSG00000021661	Ankra2	1110004M18Rik|Ankra	ankyrin repeat, family A (RFXANK-like), 2	protein-coding
mm_124900.1	chr15	10713678	10713686	+	1	NA	promoter-TSS (NM_030690)	promoter-TSS (NM_030690)	-142	NM_030690	75646	Mm.212395	NM_030690	ENSMUSG00000022246	Rai14	1700008J19Rik|1700020L11Rik|Ankycorbin|Norpeg|mKIAA1334	retinoic acid induced 14	protein-coding
mm_30848.1	chr4	24966429	24966502	+	1	NA	Intergenic	CpG	-6954	NM_030733	81006	Mm.160412	NM_030733	ENSMUSG00000040372	Gpr63	PSP24beta|Psp24-2	G protein-coupled receptor 63	protein-coding
mm_57978.1	chr6	135725569	135725580	-	1	NA	Intergenic	Intergenic	66661	NR_126088	75024	Mm.399147	NR_126088	ENSMUSG00000107396	4930425L21Rik	4930473P14Rik	RIKEN cDNA 4930425L21 gene	ncRNA
mm_40797.1	chr5	67608581	67608614	+	1	NA	exon (NM_001033415, exon 1 of 2)	exon (NM_001033415, exon 1 of 2)	714	NM_001033415	330096	Mm.442747	NM_001033415	ENSMUSG00000050010	Shisa3	D830007B15Rik	shisa family member 3	protein-coding
mm_105712.1	chr11	108343856	108343866	-	1	NA	promoter-TSS (NM_011101)	promoter-TSS (NM_011101)	27	NM_011101	18750	Mm.222178	NM_011101	ENSMUSG00000050965	Prkca	AI875142|Pkca	protein kinase C, alpha	protein-coding
mm_35823.1	chr4	47057016	47057018	-	1	NA	exon (NM_001024136, exon 1 of 15)	exon (NM_001024136, exon 1 of 15)	289	NM_001024136	75691	Mm.86866	NM_001024136	ENSMUSG00000066191	Anks6	2210417J20Rik|Ankrd14|Gm635|SamCystin|Samd6|b2b1801.1Clo	ankyrin repeat and sterile alpha motif domain containing 6	protein-coding
mm_1416.1	chr1	67159422	67159432	+	1	NA	intron (NM_001080809, intron 11 of 37)	intron (NM_001080809, intron 11 of 37)	36400	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_64416.1	chr7	142538994	142539001	+	1	NA	intron (NM_011288, intron 4 of 4)	intron (NM_011288, intron 4 of 4)	5880	NM_011288	19935	Mm.12144	NM_011288	ENSMUSG00000037772	Mrpl23	L23mrp|Rpl23|Rpl23l	mitochondrial ribosomal protein L23	protein-coding
mm_29562.1	chr3	116808179	116808198	-	1	NA	promoter-TSS (NM_001081326)	promoter-TSS (NM_001081326)	-22	NM_001081326	77559	Mm.237099	NM_001081326	ENSMUSG00000033400	Agl	1110061O17Rik|9430004C13Rik|9630046L06Rik|AI850929|C77197	amylo-1,6-glucosidase, 4-alpha-glucanotransferase	protein-coding
mm_42427.1	chr5	115332859	115332872	+	1	NA	TTS (NM_029645)	TTS (NM_029645)	5688	NR_036616	108014	Mm.287826	NM_025573	ENSMUSG00000029538	Srsf9	25kDa|2610029M16Rik|SRp30c|Sfrs9	serine/arginine-rich splicing factor 9	protein-coding
mm_31528.1	chr4	55042791	55042838	+	1	NA	intron (NM_172867, intron 7 of 12)	intron (NM_172867, intron 7 of 12)	94869	NM_172867	242466	Mm.102904	NM_172867	ENSMUSG00000060206	Zfp462	6030417H05|9430078C22Rik|Gt4-2|Zfpip	zinc finger protein 462	protein-coding
mm_138516.1	chr17	35237896	35237918	+	1	NA	3' UTR (NM_023179, exon 3 of 3)	3' UTR (NM_023179, exon 3 of 3)	1311	NM_023179	66237	Mm.396107	NM_023179	ENSMUSG00000024403	Atp6v1g2	1500002D01Rik|Atp6g2|NG38|VAG2	ATPase, H+ transporting, lysosomal V1 subunit G2	protein-coding
mm_51563.1	chr6	83544985	83544986	+	1	NA	intron (NM_024239, intron 9 of 9)	Lx9|LINE|L1	-8734	NM_009610	11468	Mm.292865	NM_009610	ENSMUSG00000059430	Actg2	ACTA3|Act-4|Act4|SMGA	actin, gamma 2, smooth muscle, enteric	protein-coding
mm_140562.1	chr17	8272527	8272529	-	1	NA	Intergenic	Intergenic	-11285	NM_018819	55951	Mm.288510	NM_018819	ENSMUSG00000023861	Mpc1	0610006G08Rik|3830411I18Rik|Brp44l	mitochondrial pyruvate carrier 1	protein-coding
mm_128265.1	chr15	36789593	36789596	-	1	NA	intron (NM_001253806, intron 2 of 5)	intron (NM_001253806, intron 2 of 5)	1338	NM_001253807	22631	Mm.3360	NM_011740	ENSMUSG00000022285	Ywhaz	1110013I11Rik|14-3-3zeta|AI596267|AL022924|AU020854	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide	protein-coding
mm_127940.1	chr15	10589287	10589298	-	1	NA	exon (NM_030690, exon 11 of 18)	exon (NM_030690, exon 11 of 18)	-11001	NR_033541	100038608	Mm.450744	NR_033541		Gm10389	ENSMUSG00000072658	predicted gene 10389	ncRNA
mm_9365.1	chr1	172199195	172199207	-	1	NA	exon (NM_001329871, exon 3 of 4)	exon (NM_001329871, exon 3 of 4)	7603	NM_001329871	18611	Mm.544	NM_011063	ENSMUSG00000013698	Pea15a	Mat1|PEA-15|Pea15|Pkcs15	phosphoprotein enriched in astrocytes 15A	protein-coding
mm_25357.1	chr3	107090875	107090905	+	1	NA	Intergenic	Intergenic	-10677	NM_008417	16490	Mm.39285	NM_008417	ENSMUSG00000040724	Kcna2	Akr6a4|ENSMUSG00000074335|Gm10672|Kca1-2|Kv1.2|Mk-2	potassium voltage-gated channel, shaker-related subfamily, member 2	protein-coding
mm_61650.1	chr7	80405532	80405541	+	1	NA	promoter-TSS (NM_001081454)	promoter-TSS (NM_001081454)	-100	NM_001081454	18550	Mm.5241	NM_011046	ENSMUSG00000030530	Furin	9130404I01Rik|Fur|PACE|Pcsk3|SPC1	furin (paired basic amino acid cleaving enzyme)	protein-coding
mm_133571.1	chr16	91406213	91406223	+	1	NA	promoter-TSS (NM_008349)	promoter-TSS (NM_008349)	-17	NM_008349	16155	Mm.4154	NM_008349	ENSMUSG00000022969	Il10rb	6620401D04Rik|AI528744|CRF2-4|Crfb4|D16H21S58|D21S58h|IL-10R2|Il10r2	interleukin 10 receptor, beta	protein-coding
mm_117639.1	chr13	92483997	92484037	-	1	NA	promoter-TSS (NM_001163627)	promoter-TSS (NM_001163627)	14	NM_001163627	73942	Mm.85935	NM_001163627	ENSMUSG00000034334	Fam151b	4930405M20Rik	family with sequence similarity 151, member B	protein-coding
mm_162335.1	chr1	44174674	44174688	+	1	NA	intron (NM_011729, intron 11 of 14)	intron (NM_011729, intron 11 of 14)	26937	NM_011729	22592	Mm.2213	NM_011729	ENSMUSG00000026048	Ercc5	Xpg	excision repair cross-complementing rodent repair deficiency, complementation group 5	protein-coding
mm_31487.1	chr4	52607205	52607215	+	1	NA	intron (NM_026652, intron 1 of 1)	intron (NM_026652, intron 1 of 1)	10936	NM_026652	68274	Mm.85045	NM_026652	ENSMUSG00000028314	Toporsl	4930547C10Rik	topoisomerase I binding, arginine/serine-rich like	protein-coding
mm_129707.1	chr15	81729865	81729913	-	1	NA	promoter-TSS (NM_011241)	promoter-TSS (NM_011241)	30	NM_011241	19387	Mm.270975	NM_011241	ENSMUSG00000022391	Rangap1	C79654|Fug1|mKIAA1835	RAN GTPase activating protein 1	protein-coding
mm_83613.1	chr9	48655807	48655813	-	1	NA	3' UTR (NM_001033324, exon 7 of 7)	3' UTR (NM_001033324, exon 7 of 7)	-50687	NM_010924	18113	Mm.8362	NM_010924	ENSMUSG00000032271	Nnmt	-	nicotinamide N-methyltransferase	protein-coding
mm_67826.1	chr7	98291123	98291154	-	1	NA	intron (NM_025408, intron 1 of 10)	intron (NM_025408, intron 1 of 10)	18389	NM_025408	66190	Mm.334041	NM_025408	ENSMUSG00000030760	Acer3	1110057L18Rik|5430429L08Rik|AV015045|Phca	alkaline ceramidase 3	protein-coding
mm_67465.1	chr7	80406311	80406321	-	1	NA	promoter-TSS (NM_001081454)	promoter-TSS (NM_001081454)	-880	NM_001081454	18550	Mm.5241	NM_011046	ENSMUSG00000030530	Furin	9130404I01Rik|Fur|PACE|Pcsk3|SPC1	furin (paired basic amino acid cleaving enzyme)	protein-coding
mm_125186.1	chr15	32254816	32254819	+	1	NA	intron (NM_009154, intron 1 of 22)	intron (NM_009154, intron 1 of 22)	10004	NM_009154	20356	Mm.260374	NM_009154	ENSMUSG00000022231	Sema5a	5930434A13|9130201M22Rik|AI464145|Semaf|semF	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A	protein-coding
mm_20825.1	chr2	146198045	146198057	-	1	NA	Intergenic	Lx8|LINE|L1	-23946	NM_016889	53626	Mm.379070	NM_016889	ENSMUSG00000068154	Insm1	IA-1	insulinoma-associated 1	protein-coding
mm_51102.1	chr6	67272160	67272196	+	1	NA	exon (NM_025814, exon 4 of 8)	exon (NM_025814, exon 4 of 8)	5199	NM_025814	66870	Mm.240490	NM_025814	ENSMUSG00000036371	Serbp1	1200009K13Rik|9330147J08Rik|AL022786|Pairbp1	serpine1 mRNA binding protein 1	protein-coding
mm_117792.1	chr13	97190567	97190610	-	1	NA	intron (NM_010422, intron 3 of 13)	LSU-rRNA_Hsa|rRNA|rRNA	7769	NM_010422	15212	Mm.27816	NM_010422	ENSMUSG00000021665	Hexb	-	hexosaminidase B	protein-coding
mm_40674.1	chr5	65536882	65536900	+	1	NA	promoter-TSS (NM_016786)	promoter-TSS (NM_016786)	-354	NM_016786	53323	Mm.319512	NM_016786	ENSMUSG00000029203	Ube2k	AW492011|D5Ertd601e|E2-25k|HIP-2|Hip2|Hypg|Lig	ubiquitin-conjugating enzyme E2K	protein-coding
mm_14353.1	chr2	129608961	129608972	+	1	NA	exon (NM_001177647, exon 2 of 6)	exon (NM_001177647, exon 2 of 6)	15797	NM_001291022	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_107590.1	chr12	47833980	47833994	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	467475	NR_039586	100628593		NR_039586	ENSMUSG00000092981	Mir5125	mmu-mir-5125|mu-mir-5125	microRNA 5125	ncRNA
mm_107584.1	chr12	44546767	44546775	+	1	NA	intron (NM_001146031, intron 9 of 27)	intron (NM_001146031, intron 9 of 27)	217886	NM_001146031	319504	Mm.208439	NM_176930	ENSMUSG00000020598	Nrcam	Bravo|C030017F07Rik|C130076O07Rik|mKIAA0343	neuronal cell adhesion molecule	protein-coding
mm_958.1	chr1	57845594	57845617	+	1	NA	promoter-TSS (NM_001164566)	promoter-TSS (NM_001164566)	34	NM_001164566	67198	Mm.159989	NM_144882	ENSMUSG00000038305	Spats2l	2810022L02Rik|A230104H11Rik|AA987173|AI480531|AI842453|AW413586	spermatogenesis associated, serine-rich 2-like	protein-coding
mm_46451.1	chr5	105116807	105116822	-	1	NA	3' UTR (NM_001256005, exon 11 of 11)	3' UTR (NM_001256005, exon 11 of 11)	-6522	NM_172777	236573	Mm.425261	NM_172777	ENSMUSG00000029298	Gbp9	-	guanylate-binding protein 9	protein-coding
mm_30280.1	chr3	148917658	148917660	-	1	NA	intron (NM_001081298, intron 1 of 23)	intron (NM_001081298, intron 1 of 23)	36976	NM_001081298	99633	Mm.9776	NM_001081298	ENSMUSG00000028184	Adgrl2	AI450192|CIRL-2|Gm619|Lec1|Lphh1|Lphn2|mKIAA0786	adhesion G protein-coupled receptor L2	protein-coding
mm_130996.1	chr15	103430389	103430431	-	1	NA	promoter-TSS (NM_028797)	promoter-TSS (NM_028797)	17	NM_028797	74174	Mm.325325	NM_028797	ENSMUSG00000022487	Gtsf1	1700006H03Rik|Cue110	gametocyte specific factor 1	protein-coding
mm_56229.1	chr6	90659867	90659872	-	1	NA	3' UTR (NM_001134384, exon 14 of 14)	3' UTR (NM_001134384, exon 14 of 14)	40623	NM_001037493	71699	Mm.272633	NM_027868	ENSMUSG00000030089	Slc41a3	1010001P06Rik|AI480742|SLC41A1-L2	solute carrier family 41, member 3	protein-coding
mm_164681.1	chr17	47010477	47010493	-	1	NA	promoter-TSS (NM_001177374)	promoter-TSS (NM_001177374)	47	NM_146078	224826	Mm.28234	NM_146078	ENSMUSG00000023977	Ubr2	9930021A08Rik|AI462103|AW540746|E130209G04Rik|ENSMUSG00000043296|mKIAA0349	ubiquitin protein ligase E3 component n-recognin 2	protein-coding
mm_90714.1	chr10	4388038	4388063	-	1	NA	promoter-TSS (NM_001033466)	promoter-TSS (NM_001033466)	58	NM_001033466	381990	Mm.262466	NM_001033466	ENSMUSG00000075327	Zbtb2	Gm1103	zinc finger and BTB domain containing 2	protein-coding
mm_151292.1	chr19	55346122	55346148	+	1	NA	intron (NM_001293685, intron 3 of 8)	B4A|SINE|B4	30078	NM_001293686	53611	Mm.258637	NM_016862	ENSMUSG00000024983	Vti1a	1110014F16Rik|1110018K19Rik|4921537J05Rik|MVti1|MVti1a|Vti1|Vti1-rp2	vesicle transport through interaction with t-SNAREs 1A	protein-coding
mm_49955.1	chr6	40628602	40628610	+	1	NA	promoter-TSS (NM_001171003)	promoter-TSS (NM_001171003)	-225	NM_001171003	232714	Mm.33401	NM_001171003	ENSMUSG00000068587	Mgam	6030407P20Rik|MGA	maltase-glucoamylase	protein-coding
mm_168015.1	chrY	87116804	87116806	+	1	NA	Intergenic	Intergenic	-1587286	NM_001160131	100040911	Mm.457993	NM_001160131	ENSMUSG00000095650	Gm20854	-	predicted gene, 20854	protein-coding
mm_158018.1	chrX	95965047	95965059	-	1	NA	Intergenic	Intergenic	-8079	NM_152822	76130	Mm.274318	NM_152822	ENSMUSG00000057421	Las1l	1810030A06Rik|5830482G23Rik	LAS1-like (S. cerevisiae)	protein-coding
mm_109797.1	chr12	3297293	3297309	-	1	NA	intron (NM_016676, intron 1 of 5)	intron (NM_016676, intron 1 of 5)	12668	NM_016676	19325	Mm.378993	NM_016676	ENSMUSG00000020671	Rab10	AW107754	RAB10, member RAS oncogene family	protein-coding
mm_96748.1	chr11	69877237	69877244	+	1	NA	intron (NM_001195710, intron 3 of 6)	intron (NM_001195710, intron 3 of 6)	778	NM_001195710	100503361	Mm.340490	NM_001195710	ENSMUSG00000094845	Tmem95	432576	transmembrane protein 95	protein-coding
mm_30199.1	chr3	144720069	144720208	-	1	NA	5' UTR (NM_019464, exon 1 of 9)	5' UTR (NM_019464, exon 1 of 9)	197	NM_001282042	54673	Mm.271775	NM_019464	ENSMUSG00000037062	Sh3glb1	AA409932|AI314629|AU015566|Bif-1|mKIAA0491	SH3-domain GRB2-like B1 (endophilin)	protein-coding
mm_142854.1	chr17	51812059	51812084	-	1	NA	promoter-TSS (NM_001163630)	promoter-TSS (NM_001163630)	-17	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_156445.1	chrX	142681399	142681439	+	1	NA	promoter-TSS (NM_001199357)	promoter-TSS (NM_001199357)	19	NM_001199357	209497	Mm.249648	NM_177592	ENSMUSG00000047045	Tmem164	AI316850|AI852450|AW547186|F730011B02	transmembrane protein 164	protein-coding
mm_106627.1	chr11	120866602	120866604	-	1	NA	exon (NM_027745, exon 16 of 19)	exon (NM_027745, exon 16 of 19)	-42056	NM_007988	14104	Mm.236443	NM_007988	ENSMUSG00000025153	Fasn	A630082H08Rik|FAS	fatty acid synthase	protein-coding
mm_131492.1	chr16	17276338	17276358	+	1	NA	promoter-TSS (NM_177473)	promoter-TSS (NM_177473)	48	NM_177473	224019	Mm.246388	NM_177473	ENSMUSG00000055692	Tmem191c	4933405M22Rik|D16Bwg1494e|MNCb-4137	transmembrane protein 191C	protein-coding
mm_157033.1	chrX	7947744	7947751	-	1	NA	5' UTR (NM_010413, exon 1 of 29)	5' UTR (NM_010413, exon 1 of 29)	142	NM_001130416	15185	Mm.29854	NM_010413	ENSMUSG00000031161	Hdac6	Hd6|Hdac5|Sfc6|mHDA2	histone deacetylase 6	protein-coding
mm_157887.1	chrX	75874523	75874533	-	1	NA	promoter-TSS (NM_145629)	promoter-TSS (NM_145629)	46	NM_145629	102866	Mm.28777	NM_145629	ENSMUSG00000016382	Pls3	AI115446|AL024105	plastin 3 (T-isoform)	protein-coding
mm_130932.1	chr15	103193381	103193384	-	1	NA	3' UTR (NM_001110216, exon 6 of 6)	3' UTR (NM_001110216, exon 6 of 6)	21970	NM_007626	12419	Mm.262059	NM_007626	ENSMUSG00000009575	Cbx5	2610029O15Rik|C75991|HP1|Hp1a|Hp1alpha	chromobox 5	protein-coding
mm_72044.1	chr8	71272691	71272746	+	1	NA	promoter-TSS (NM_001142322)	promoter-TSS (NM_001142322)	4	NM_001142323	17925	Mm.33779	NM_015742	ENSMUSG00000004677	Myo9b	-	myosin IXb	protein-coding
mm_138221.1	chr17	34325636	34325642	+	1	NA	promoter-TSS (NM_001033978)	promoter-TSS (NM_001033978)	-36	NM_001033978	381091	Mm.139204	NM_001033978	ENSMUSG00000067341	H2-Eb2	A130038H09Rik|H-2Eb2|Ia-5|Ia5|Iebeta2	histocompatibility 2, class II antigen E beta2	protein-coding
mm_153394.1	chr19	40406814	40406827	-	1	NA	intron (NM_001034963, intron 1 of 22)	intron (NM_001034963, intron 1 of 22)	-4510	NM_001034964	20411	Mm.210815	NM_009166	ENSMUSG00000025006	Sorbs1	2310065E01Rik|9530001P15Rik|CAP|SH3P12|Sh3d5|mKIAA1296	sorbin and SH3 domain containing 1	protein-coding
mm_32487.1	chr4	107953908	107953940	+	1	NA	promoter-TSS (NR_131071)	promoter-TSS (NR_131071)	-8	NR_131071	77223	Mm.401926	NR_131071	ENSMUSG00000086713	4930407G08Rik	-	RIKEN cDNA 4930407G08 gene	ncRNA
mm_42705.1	chr5	120116527	120116551	+	1	NA	promoter-TSS (NM_028762)	promoter-TSS (NM_028762)	26	NM_028762	74111	Mm.41022	NM_028762	ENSMUSG00000029594	Rbm19	1200009A02Rik|AV302714|NPO	RNA binding motif protein 19	protein-coding
mm_91411.1	chr10	31599797	31599800	-	1	NA	intron (NM_001146349, intron 1 of 5)	intron (NM_001146349, intron 1 of 5)	9927	NM_001146349	268291	Mm.295212	NM_001146349	ENSMUSG00000063760	Rnf217	AU016819|Ibrdc1	ring finger protein 217	protein-coding
mm_107151.1	chr12	24498571	24498587	+	1	NA	promoter-TSS (NM_020614)	promoter-TSS (NM_020614)	-2	NM_020614	21340	Mm.39082	NM_020614	ENSMUSG00000059669	Taf1b	4930408G01Rik|A230108M10Rik|TAFI68|Tafi86|p63	TATA-box binding protein associated factor, RNA polymerase I, B	protein-coding
mm_25111.1	chr3	101462070	101462092	+	1	NA	3' UTR (NM_207205, exon 11 of 11)	3' UTR (NM_207205, exon 11 of 11)	84956	NM_207205	78908	Mm.257997	NM_207205	ENSMUSG00000042035	Igsf3	1700016K10Rik|2810035F16Rik|4833439O17Rik|mKIAA0466	immunoglobulin superfamily, member 3	protein-coding
mm_35037.1	chr4	4138172	4138215	-	1	NA	5' UTR (NM_001002927, exon 1 of 2)	5' UTR (NM_001002927, exon 1 of 2)	252	NM_001002927	18619	Mm.475097	NM_001002927	ENSMUSG00000045573	Penk	AI326464|ENK|PPA|Penk1	preproenkephalin	protein-coding
mm_118061.1	chr13	102825173	102825176	-	1	NA	intron (NM_175171, intron 5 of 28)	intron (NM_175171, intron 5 of 28)	64919	NR_130171	76624	Mm.426384	NR_130171	ENSMUSG00000091906	1700099I09Rik	-	RIKEN cDNA 1700099I09 gene	ncRNA
mm_131241.1	chr16	10489760	10489804	+	1	NA	promoter-TSS (NM_001243761)	promoter-TSS (NM_001243761)	1	NM_001243761	12265	Mm.249560	NM_007575	ENSMUSG00000022504	Ciita	C2ta|EG669998|Gm9475|Mhc2ta	class II transactivator	protein-coding
mm_15015.1	chr2	152604419	152604439	+	1	NA	5' UTR (NM_001037247, exon 1 of 2)	5' UTR (NM_001037247, exon 1 of 2)	102	NM_001037247	266620	Mm.330669	NM_001037247	ENSMUSG00000044863	Defb36	BD-36|Defb123|mBD-36	defensin beta 36	protein-coding
mm_163940.1	chr14	51145475	51145477	-	1	NA	exon (NM_011271, exon 2 of 2)	exon (NM_011271, exon 2 of 2)	1291	NM_011271	19752	Mm.235538	NM_011271	ENSMUSG00000035896	Rnase1	AI574248|Rib-1|Rib1	ribonuclease, RNase A family, 1 (pancreatic)	protein-coding
mm_52348.1	chr6	111402396	111402398	+	1	NA	intron (NM_001346640, intron 8 of 10)	intron (NM_001346640, intron 8 of 10)	756799	NM_177328	108073	Mm.240881	NM_177328	ENSMUSG00000056755	Grm7	6330570A01Rik|BB176677|C030018L03|E130018M02Rik|Gpr1g|Gprc1g|SMN2|Tg(SMN2)89Ahmb|mGluR7	glutamate receptor, metabotropic 7	protein-coding
mm_12083.1	chr2	60072012	60072047	+	1	NA	intron (NM_001001182, intron 2 of 35)	B1_Mur1|SINE|Alu	53711	NM_001001182	407823	Mm.228071	NM_001001182	ENSMUSG00000026987	Baz2b	5830435C13Rik|BC053917|D2Ertd794e	bromodomain adjacent to zinc finger domain, 2B	protein-coding
mm_82829.1	chr9	31149795	31149833	-	1	NA	3' UTR (NM_009691, exon 16 of 16)	3' UTR (NM_009691, exon 16 of 16)	-18015	NM_011176	19143	Mm.243926	NM_011176	ENSMUSG00000031995	St14	Epithin|MT-SP1|Prss14|Tmprss14|mCAP3|matriptase	suppression of tumorigenicity 14 (colon carcinoma)	protein-coding
mm_162950.1	chr11	3393367	3393369	-	1	NA	intron (NM_010718, intron 1 of 15)	RSINE1|SINE|B4	15870	NM_010718	16886	Mm.124176	NM_010718	ENSMUSG00000020451	Limk2	Limk-2|whe	LIM motif-containing protein kinase 2	protein-coding
mm_65636.1	chr7	27761333	27761353	-	1	NA	Intergenic	RLTR11A|LTR|ERVK	-4330	NR_033484	100043229	Mm.458666	NR_033484	ENSMUSG00000109143	Gm10046	ENSMUSG00000058661	predicted gene 10046	ncRNA
mm_26562.1	chr3	146500162	146500185	+	1	NA	promoter-TSS (NM_001316756)	promoter-TSS (NM_001316756)	337	NM_010318	14707	Mm.140804	NM_010318	ENSMUSG00000068523	Gng5	G(y)5	guanine nucleotide binding protein (G protein), gamma 5	protein-coding
mm_24825.1	chr3	95651761	95651799	+	1	NA	Intergenic	PB1D11|SINE|Alu	-6941	NM_008562	17210	Mm.1639	NM_008562	ENSMUSG00000038612	Mcl1	AW556805|Mcl-1	myeloid cell leukemia sequence 1	protein-coding
mm_131259.1	chr16	10791434	10791448	+	1	NA	promoter-TSS (NM_013638)	promoter-TSS (NM_013638)	-527	NM_013638	19120	Mm.291887	NM_013638	ENSMUSG00000050058	Prm3	BC061127|PX|Pxg	protamine 3	protein-coding
mm_434.1	chr1	34579513	34579523	+	1	NA	promoter-TSS (NM_213727)	promoter-TSS (NM_213727)	-175	NM_213727	211383	Mm.330696	NM_213727	ENSMUSG00000045174	Amer3	9430069J07Rik|Fam123c	APC membrane recruitment 3	protein-coding
mm_52308.1	chr6	108828563	108828565	+	1	NA	promoter-TSS (NM_138677)	promoter-TSS (NM_138677)	-77	NM_138677	192193	Mm.21596	NM_138677	ENSMUSG00000030104	Edem1	A130059K23Rik|EDEM|mKIAA0212	ER degradation enhancer, mannosidase alpha-like 1	protein-coding
mm_107770.1	chr12	59131426	59131469	+	1	NA	promoter-TSS (NM_001165253)	promoter-TSS (NM_001165253)	-6	NM_001165253	338320	Mm.213215	NM_146034	ENSMUSG00000021000	Mia2	Ctage5|D12Bwg0579e|Mea6|Mgea|Mgea6	melanoma inhibitory activity 2	protein-coding
mm_49190.1	chr6	15185640	15185655	+	1	NA	5' UTR (NM_001286607, exon 1 of 17)	5' UTR (NM_001286607, exon 1 of 17)	141	NM_001286607	114142	Mm.332919	NM_053242	ENSMUSG00000029563	Foxp2	2810043D05Rik|AI449000|CAG-16|D0Kist7	forkhead box P2	protein-coding
mm_14000.1	chr2	121956652	121956664	+	1	NA	promoter-TSS (NM_008545)	promoter-TSS (NM_008545)	-566	NM_008545	17147	Mm.389349	NM_008545	ENSMUSG00000074881	Mageb3	Mage-b3|Mage-ps1|Mage-rs3|Smage3	melanoma antigen, family B, 3	protein-coding
mm_89743.1	chr10	99107149	99107189	+	1	NA	promoter-TSS (NM_027740)	promoter-TSS (NM_027740)	-2	NM_027740	382406	Mm.440656	NM_027740	ENSMUSG00000019952	Poc1b	4933430F16Rik|Wdr51b	POC1 centriolar protein B	protein-coding
mm_8141.1	chr1	136280546	136280562	-	1	NA	exon (NM_001081360, exon 13 of 19)	exon (NM_001081360, exon 13 of 19)	-19681	NM_001101516	383563	Mm.40367	NM_001101516	ENSMUSG00000052759	Gpr25	Gm1300	G protein-coupled receptor 25	protein-coding
mm_108704.1	chr12	86960364	86960391	+	1	NA	exon (NM_001289430, exon 3 of 4)	exon (NM_001289430, exon 3 of 4)	13034	NM_001289432	217732	Mm.22337	NM_173735	ENSMUSG00000034157	Cipc	2310044G17Rik|AI842544|AI853744|Kiaa1737|mKIAA1737	CLOCK interacting protein, circadian	protein-coding
mm_157461.1	chrX	44789984	44790067	-	1	NA	5' UTR (NM_178739, exon 1 of 2)	5' UTR (NM_178739, exon 1 of 2)	136	NM_001190718	245404	Mm.55685	NM_178739	ENSMUSG00000045284	Dcaf12l1	9330180J20|A230038L21Rik|Decaf12l1|Wdr40b	DDB1 and CUL4 associated factor 12-like 1	protein-coding
mm_112227.1	chr12	113430590	113430603	-	1	NA	Intergenic	Intergenic	-58969	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_30151.1	chr3	142604204	142604222	-	1	NA	exon (NM_010259, exon 6 of 11)	exon (NM_010259, exon 6 of 11)	9366	NM_010259	14468	Mm.457978	NM_010259	ENSMUSG00000040264	Gbp2b	Gbp-1|Gbp1|Mag-1|Mpa-1|Mpa1	guanylate binding protein 2b	protein-coding
mm_70989.1	chr8	27296325	27296356	+	1	NA	non-coding (NR_003107, exon 1 of 1)	non-coding (NR_003107, exon 1 of 1)	295	NR_003107	732482	Mm.463248	NR_003107		Gm9731	-	Fam58a pseudogene	pseudo
mm_112436.1	chr13	5155188	5155192	+	1	NA	Intergenic	ORR1A3|LTR|ERVL-MaLR	-546026	NM_018859	56043	Mm.251908	NM_018859	ENSMUSG00000045410	Akr1e1	1810061I10Rik|Akr1e2	aldo-keto reductase family 1, member E1	protein-coding
mm_17539.1	chr2	29773508	29773517	-	1	NA	Intergenic	L1MC3|LINE|L1	11984	NM_001177392	433416	Mm.330112	NM_001034887	ENSMUSG00000075425	Gm13547	OTTMUSG00000012686	predicted gene 13547	protein-coding
mm_49536.1	chr6	30175326	30175341	+	1	NA	Intergenic	Intergenic	-1208	NR_126541	101447999		NR_126540		Mirc35hg	-	microRNA cluster 35, host gene	ncRNA
mm_73113.1	chr8	94749275	94749318	+	1	NA	intron (NM_009137, intron 2 of 2)	B4A|SINE|B4	3612	NM_009137	20299	Mm.12895	NM_009137	ENSMUSG00000031779	Ccl22	ABCD-1|DCBCK|MDC|Scya22	chemokine (C-C motif) ligand 22	protein-coding
mm_131922.1	chr16	23320798	23320805	+	1	NA	intron (NM_001252505, intron 3 of 7)	intron (NM_001252505, intron 3 of 7)	30331	NM_001252506	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_106190.1	chr11	116807770	116807781	-	1	NA	3' UTR (NM_001347633, exon 5 of 5)	3' UTR (NM_001347633, exon 5 of 5)	20271	NM_026280	67622	Mm.64962	NM_026280	ENSMUSG00000020814	Mxra7	1810057P16Rik|E130302J09Rik	matrix-remodelling associated 7	protein-coding
mm_87007.1	chr10	26822561	26822579	+	1	NA	intron (NM_176837, intron 1 of 14)	intron (NM_176837, intron 1 of 14)	50058	NM_176837	73910	Mm.356496	NM_176837	ENSMUSG00000039031	Arhgap18	4833419J07Rik|AI314906|AI843501	Rho GTPase activating protein 18	protein-coding
mm_108275.1	chr12	78862100	78862113	+	1	NA	promoter-TSS (NM_026114)	promoter-TSS (NM_026114)	34	NM_026114	13665	Mm.196220	NM_026114	ENSMUSG00000021116	Eif2s1	0910001O23Rik|2410026C18Rik|35kDa|Eif2a|eIF2alpha	eukaryotic translation initiation factor 2, subunit 1 alpha	protein-coding
mm_43919.1	chr5	144768142	144768154	+	1	NA	promoter-TSS (NM_001081362)	promoter-TSS (NM_001081362)	-644	NM_001081362	100683	Mm.273570	NM_001081362	ENSMUSG00000045482	Trrap	AI481500	transformation/transcription domain-associated protein	protein-coding
mm_23595.1	chr3	64977587	64977597	+	1	NA	Intergenic	Intergenic	-131776	NM_010597	16497	Mm.316402	NM_010597	ENSMUSG00000027827	Kcnab1	Akr8a8|Kvbeta1.1|mKv(beta)1	potassium voltage-gated channel, shaker-related subfamily, beta member 1	protein-coding
mm_40224.1	chr5	37245939	37245949	+	1	NA	5' UTR (NM_007765, exon 1 of 14)	5' UTR (NM_007765, exon 1 of 14)	180	NM_007765	12933	Mm.290995	NM_007765	ENSMUSG00000029121	Crmp1	CRMP-1|DRP-1|Dpysl1|ULIP-3|Ulip3	collapsin response mediator protein 1	protein-coding
mm_50217.1	chr6	42349595	42349629	+	1	NA	promoter-TSS (NM_001289618)	promoter-TSS (NM_001289618)	-216	NM_011777	22793	Mm.282303	NM_011777	ENSMUSG00000029860	Zyx	9530098H06Rik|R75157	zyxin	protein-coding
mm_92917.1	chr10	83648714	83648731	-	1	NA	promoter-TSS (NM_145220)	promoter-TSS (NM_145220)	-58	NM_145220	216190	Mm.282985	NM_145220	ENSMUSG00000020263	Appl2	Dip3b	adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 2	protein-coding
mm_149042.1	chr19	8820254	8820314	+	1	NA	promoter-TSS (NM_027412)	promoter-TSS (NM_027412)	883	NM_001081196	68693	Mm.476519	NM_001081196	ENSMUSG00000071659	Hnrnpul2	1110031M08Rik|AI465155|Hnrpul2	heterogeneous nuclear ribonucleoprotein U-like 2	protein-coding
mm_55578.1	chr6	71396292	71396306	-	1	NA	intron (NM_024288, intron 7 of 8)	intron (NM_024288, intron 7 of 8)	22872	NM_001081110	12525	Mm.1858	NM_009857	ENSMUSG00000053977	Cd8a	BB154331|Ly-2|Ly-35|Ly-B|Lyt-2	CD8 antigen, alpha chain	protein-coding
mm_157594.1	chrX	53209821	53209834	-	1	NA	Intergenic	Intergenic	59978	NM_030167	78755	Mm.28559	NM_030167	ENSMUSG00000036022	Fam122b	4632404H22Rik|AI256344|SPACIA2	family with sequence similarity 122, member B	protein-coding
mm_129015.1	chr15	74923578	74923603	-	1	NA	Intergenic	Intergenic	-31461	NM_001164039	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_172074.1	chr6	140738707	140738724	-	1	NA	Intergenic	ERVB7_1-LTR_MM|LTR|ERVK	111830	NM_001309436	11569	Mm.86453	NM_009637	ENSMUSG00000030232	Aebp2	AU023766|B230313N05Rik	AE binding protein 2	protein-coding
mm_124867.1	chr15	10177602	10177608	+	1	NA	5' UTR (NM_011169, exon 1 of 10)	5' UTR (NM_011169, exon 1 of 10)	367	NM_011169	19116	Mm.10516	NM_011169	ENSMUSG00000005268	Prlr	AI987712|Pr-1|Pr-3|Prlr-rs1	prolactin receptor	protein-coding
mm_138097.1	chr17	34048418	34048425	+	1	NA	intron (NM_001317722, intron 7 of 64)	intron (NM_001317722, intron 7 of 64)	9283	NM_001317722	12815	Mm.20230	NM_009926	ENSMUSG00000024330	Col11a2	-	collagen, type XI, alpha 2	protein-coding
mm_165253.1	chr2	71981043	71981059	+	1	NA	promoter-TSS (NM_001204167)	promoter-TSS (NM_001204167)	-164	NM_001204167	56508	Mm.196153	NM_019688	ENSMUSG00000049044	Rapgef4	1300003D15Rik|5730402K07Rik|6330581N18Rik|EPAC 2|Epac-2|Epac2|mKIAA4040	Rap guanine nucleotide exchange factor (GEF) 4	protein-coding
mm_54613.1	chr6	38354244	38354292	-	1	NA	5' UTR (NM_028421, exon 1 of 12)	5' UTR (NM_028421, exon 1 of 12)	335	NM_028864	78781	Mm.25243	NM_028421	ENSMUSG00000029826	Zc3hav1	1200014N16Rik|2900058M19Rik|9130009D18Rik|9830115L13Rik|ARTD13|D6Bwg1452e|ZAP	zinc finger CCCH type, antiviral 1	protein-coding
mm_168131.1	chr10	25454986	25454996	+	1	NA	intron (NM_001199265, intron 3 of 19)	U2|snRNA|snRNA	46623	NM_013511	13822	Mm.306026	NM_013511	ENSMUSG00000019978	Epb41l2	4.1G|AW555191|D10Ertd398e|Epb4.1l2|NBL2	erythrocyte membrane protein band 4.1 like 2	protein-coding
mm_155479.1	chrX	73675447	73675449	+	1	NA	intron (NM_001142810, intron 1 of 12)	intron (NM_001142810, intron 1 of 12)	2315	NM_001142809	102857	Mm.274553	NM_133987	ENSMUSG00000019558	Slc6a8	AA589632|CRT|CRTR|CT1|CTR5|Creat	solute carrier family 6 (neurotransmitter transporter, creatine), member 8	protein-coding
mm_128051.1	chr15	25766585	25766595	-	1	NA	intron (NM_019472, intron 19 of 40)	RMER10B|LTR|ERVL	-76708	NM_001034851	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_6034.1	chr1	59551136	59551146	-	1	NA	exon (NM_001013771, exon 6 of 20)	exon (NM_001013771, exon 6 of 20)	34877	NM_001013771	381260	Mm.486706	NM_001013771	ENSMUSG00000047361	Gm973	AW554518	predicted gene 973	protein-coding
mm_91975.1	chr10	61452773	61452813	-	1	NA	promoter-TSS (NM_010124)	promoter-TSS (NM_010124)	-124	NM_010124	13688	Mm.259516	NM_010124	ENSMUSG00000020091	Eif4ebp2	2810011I19Rik|4E-BP2|AA792569|BC010348|PHAS-II	eukaryotic translation initiation factor 4E binding protein 2	protein-coding
mm_68072.1	chr7	101869035	101869073	-	1	NA	intron (NM_001252552, intron 2 of 6)	intron (NM_001252552, intron 2 of 6)	1734	NM_001252554	14275	Mm.2135	NM_008034	ENSMUSG00000001827	Folr1	FBP1|Folbp-1|Folbp1	folate receptor 1 (adult)	protein-coding
mm_167993.1	chrX	170010122	170010176	+	1	NA	Intergenic	CpG	-31232	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_32215.1	chr4	101647677	101647711	+	1	NA	promoter-TSS (NM_175036)	promoter-TSS (NM_175036)	-89	NM_175036	230514	Mm.4756	NM_175036	ENSMUSG00000035212	Leprot	LEPR|OB-RGRP|Obrgrp|VPS55	leptin receptor overlapping transcript	protein-coding
mm_57104.1	chr6	122591161	122591183	-	1	NA	5' UTR (NM_031159, exon 4 of 8)	5' UTR (NM_031159, exon 4 of 8)	11272	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_160709.1	chr10	58813240	58813240	+	1	NA	promoter-TSS (NM_172788)	promoter-TSS (NM_172788)	-119	NM_172788	237353	Mm.333078	NM_172788	ENSMUSG00000037990	Sh3rf3	4831416G18Rik|Igfbp5-ip|Sh3md4|Sh3rf31	SH3 domain containing ring finger 3	protein-coding
mm_55157.1	chr6	51581671	51581712	-	1	NA	intron (NM_028035, intron 5 of 6)	intron (NM_028035, intron 5 of 6)	37168	NM_001127348	71982	Mm.294166	NM_028035	ENSMUSG00000038301	Snx10	2410004M09Rik	sorting nexin 10	protein-coding
mm_78939.1	chr9	45122437	45122467	+	1	NA	intron (NM_001014761, intron 1 of 3)	intron (NM_001014761, intron 1 of 3)	4576	NM_001014761	72821	Mm.229373	NM_001014761	ENSMUSG00000070304	Scn2b	2810451E09Rik|AI840361|Gm183	sodium channel, voltage-gated, type II, beta	protein-coding
mm_616.1	chr1	40059349	40059351	+	1	NA	Intergenic	MIRc|SINE|MIR	-25418	NM_010555	16178	Mm.1349	NM_010555	ENSMUSG00000026073	Il1r2	CD121b|Il1r-2	interleukin 1 receptor, type II	protein-coding
mm_148781.1	chr19	6112907	6112914	+	1	NA	exon (NM_001009546, exon 13 of 18)	exon (NM_001009546, exon 13 of 18)	5676	NM_133678	66406	Mm.303924	NM_133678	ENSMUSG00000024790	Sac3d1	2410004C24Rik|AU015683|shd1	SAC3 domain containing 1	protein-coding
mm_96424.1	chr11	67257108	67257116	+	1	NA	exon (NM_010855, exon 35 of 40)	exon (NM_010855, exon 35 of 40)	19300	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_57691.1	chr6	128521121	128521137	-	1	NA	exon (NM_007376, exon 7 of 36)	exon (NM_007376, exon 7 of 36)	5591	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_66672.1	chr7	45742282	45742317	-	1	NA	intron (NM_017465, intron 1 of 6)	intron (NM_017465, intron 1 of 6)	-16483	NM_027055	69363	Mm.45607	NM_027055	ENSMUSG00000070563	Spaca4	1700008E09Rik|AV043694|Samp14	sperm acrosome associated 4	protein-coding
mm_26028.1	chr3	135439385	135439440	+	1	NA	promoter-TSS (NR_030689)	promoter-TSS (NR_030689)	653	NM_025356	66105	Mm.49884	NM_025356	ENSMUSG00000078578	Ube2d3	1100001F19Rik|9430029A22Rik|AA414951	ubiquitin-conjugating enzyme E2D 3	protein-coding
mm_157138.1	chrX	9459322	9459332	-	1	NA	intron (NM_007807, intron 3 of 12)	intron (NM_007807, intron 3 of 12)	9997	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_89071.1	chr10	82985385	82985436	+	1	NA	promoter-TSS (NM_021439)	promoter-TSS (NM_021439)	-87	NM_021439	58250	Mm.360747	NM_021439	ENSMUSG00000034612	Chst11	1110020P09Rik|C4ST|C4ST-1|C4ST1|C4s	carbohydrate sulfotransferase 11	protein-coding
mm_161791.1	chr17	47385472	47385472	+	1	NA	promoter-TSS (NM_146079)	promoter-TSS (NM_146079)	79	NM_146079	107477	Mm.59151	NM_146079	ENSMUSG00000023979	Guca1b	BC018258|GCAP2	guanylate cyclase activator 1B	protein-coding
mm_113648.1	chr13	42301783	42301813	+	1	NA	5' UTR (NM_010104, exon 1 of 5)	5' UTR (NM_010104, exon 1 of 5)	322	NM_010104	13614	Mm.14543	NM_010104	ENSMUSG00000021367	Edn1	ET-1|PPET1|preproET	endothelin 1	protein-coding
mm_143258.1	chr17	65580833	65580844	-	1	NA	exon (NM_013933, exon 6 of 6)	exon (NM_013933, exon 6 of 6)	32717	NM_013933	30960	Mm.266767	NM_013933	ENSMUSG00000024091	Vapa	33kDa|VAP33	vesicle-associated membrane protein, associated protein A	protein-coding
mm_41013.1	chr5	81021636	81021646	+	1	NA	promoter-TSS (NM_198702)	promoter-TSS (NM_198702)	48	NM_198702	319387	Mm.273631	NM_198702	ENSMUSG00000037605	Adgrl3	5430402I23Rik|CIRL-3|D130075K09Rik|Gm1379|LEC3|Lphn3|mKIAA0768	adhesion G protein-coupled receptor L3	protein-coding
mm_75615.1	chr8	62892683	62892684	-	1	NA	Intergenic	L1Md_F2|LINE|L1	-58549	NM_001252620	72902	Mm.334552	NM_023689	ENSMUSG00000054162	Spock3	2900045C01Rik|AI428471|mKIAA4039	sparc/osteonectin, cwcv and kazal-like domains proteoglycan 3	protein-coding
mm_57781.1	chr6	129239827	129239833	-	1	NA	Intergenic	Intergenic	-1348	NR_040266	76432	Mm.261738	NR_040265	ENSMUSG00000097354	2310001H17Rik	AI646108	RIKEN cDNA 2310001H17 gene	ncRNA
mm_63693.1	chr7	130624556	130624573	+	1	NA	exon (NM_001004468, exon 3 of 22)	exon (NM_001004468, exon 3 of 22)	47080	NM_206856	57752	Mm.86322	NM_021314	ENSMUSG00000030852	Tacc2	mKIAA4180	transforming, acidic coiled-coil containing protein 2	protein-coding
mm_27953.1	chr3	79825589	79825601	-	1	NA	intron (NM_027495, intron 7 of 11)	intron (NM_027495, intron 7 of 11)	17067	NM_027495	70652	Mm.46635	NM_027495	ENSMUSG00000027956	Tmem144	1110057I03Rik|5730537D05Rik	transmembrane protein 144	protein-coding
mm_124267.1	chr14	102981459	102981461	-	1	NA	exon (NM_177715, exon 1 of 1)	exon (NM_177715, exon 1 of 1)	1172	NR_039592	100628599		NR_039592	ENSMUSG00000092901	Mir5130	mir-5130|mmu-mir-5130|mu-mir-5130	microRNA 5130	ncRNA
mm_97467.1	chr11	78266936	78266952	+	1	NA	exon (NM_001002004, exon 10 of 39)	exon (NM_001002004, exon 10 of 39)	5190	NM_001002004	72503	Mm.237103	NM_001002004	ENSMUSG00000010277	2610507B11Rik	AU022687|D11Bhm178e|D11Bhm179e|E1|Kiaa0100|mKIAA0100	RIKEN cDNA 2610507B11 gene	protein-coding
mm_115175.1	chr13	108214390	108214454	+	1	NA	promoter-TSS (NM_029001)	promoter-TSS (NM_029001)	18	NM_029001	74559	Mm.286127	NM_029001	ENSMUSG00000021696	Elovl7	9130013K24Rik|AI840082	ELOVL family member 7, elongation of long chain fatty acids (yeast)	protein-coding
mm_47829.1	chr5	134270715	134270718	-	1	NA	intron (NM_001080747, intron 11 of 33)	B1_Mur2|SINE|Alu	-41091	NR_104383	17969	Mm.425296	NM_010876	ENSMUSG00000015950	Ncf1	NCF-47K|NOXO2|Ncf-1|p47-phox|p47<phox>|p47phox	neutrophil cytosolic factor 1	protein-coding
mm_125777.1	chr15	74636867	74636882	+	1	NA	promoter-TSS (NM_001177437)	promoter-TSS (NM_001177437)	-556	NM_001177437	69439	Mm.263708	NM_001177437	ENSMUSG00000022603	Mroh4	1700016M24Rik	maestro heat-like repeat family member 4	protein-coding
mm_119003.1	chr14	29018206	29018226	+	1	NA	promoter-TSS (NM_176920)	promoter-TSS (NM_176920)	8	NM_176920	319476	Mm.95780	NM_176920	ENSMUSG00000045776	Lrtm1	A930016D02Rik	leucine-rich repeats and transmembrane domains 1	protein-coding
mm_154511.1	chrM	12219	12271	-	1	NA	NA	Intergenic	NA	NA								
mm_26966.1	chr3	23939453	23939465	-	1	NA	intron (NM_001326288, intron 11 of 13)	RMER17D|LTR|ERVK	844547	NM_001326288	635702	Mm.448351	NM_001326288	ENSMUSG00000102758	Naaladl2	2810043G22Rik|EG635702|Gm1021	N-acetylated alpha-linked acidic dipeptidase-like 2	protein-coding
mm_92678.1	chr10	80577256	80577274	-	1	NA	promoter-TSS (NM_078477)	promoter-TSS (NM_078477)	31	NM_078477	118445	Mm.41513	NM_078477	ENSMUSG00000035397	Klf16	AI843742|BTEB4|DRRF	Kruppel-like factor 16	protein-coding
mm_117719.1	chr13	95444701	95444711	-	1	NA	5' UTR (NM_198408, exon 1 of 7)	5' UTR (NM_198408, exon 1 of 7)	125	NM_198408	12919	Mm.316614	NM_198408	ENSMUSG00000021680	Crhbp	CRH-BP	corticotropin releasing hormone binding protein	protein-coding
mm_130867.1	chr15	102204228	102204268	-	1	NA	promoter-TSS (NM_001289690)	promoter-TSS (NM_001289690)	-323	NM_001289690	68744	Mm.352945	NM_153194	ENSMUSG00000046897	Zfp740	1110034O07Rik|AW548228|Znf740	zinc finger protein 740	protein-coding
mm_139970.1	chr17	71769674	71769678	+	1	NA	promoter-TSS (NM_001271484)	promoter-TSS (NM_001271484)	-15	NR_073185	78785	Mm.196382	NM_030179	ENSMUSG00000024059	Clip4	1700024K14Rik|1700074B05Rik|4833417L20Rik|5830409B12Rik|Rsnl2	CAP-GLY domain containing linker protein family, member 4	protein-coding
mm_71892.1	chr8	69832763	69832781	+	1	NA	promoter-TSS (NM_001024954)	promoter-TSS (NM_001024954)	68	NM_001024954	80720	Mm.210823	NM_030555	ENSMUSG00000031860	Pbx4	2410015M21Rik|AI429113|AW045266	pre B cell leukemia homeobox 4	protein-coding
mm_34167.1	chr4	139908022	139908061	+	1	NA	Intergenic	Intergenic	25033	NR_045160	71235	Mm.61253	NR_045159	ENSMUSG00000085928	4933427I22Rik	-	RIKEN cDNA 4933427I22 gene	ncRNA
mm_154357.1	chrM	6201	6223	+	1	NA	NA	Intergenic	NA	NA								
mm_72810.1	chr8	87473380	87473398	+	1	NA	promoter-TSS (NM_019626)	promoter-TSS (NM_019626)	273	NR_125722	100040294	Mm.213632	NR_033430	ENSMUSG00000097248	Gm2694	C230036H16Rik|linc1582	predicted gene 2694	ncRNA
mm_153390.1	chr19	40382859	40382873	-	1	NA	intron (NM_001034963, intron 4 of 22)	intron (NM_001034963, intron 4 of 22)	19444	NM_001034964	20411	Mm.210815	NM_009166	ENSMUSG00000025006	Sorbs1	2310065E01Rik|9530001P15Rik|CAP|SH3P12|Sh3d5|mKIAA1296	sorbin and SH3 domain containing 1	protein-coding
mm_85115.1	chr9	95407282	95407299	-	1	NA	promoter-TSS (NM_018763)	promoter-TSS (NM_018763)	-20	NM_018763	54371	Mm.212446	NM_018763	ENSMUSG00000033350	Chst2	AI428561|AW121776|C130041E03Rik|Chts2|GST-2|GlcNAc6ST|Gn6st	carbohydrate sulfotransferase 2	protein-coding
mm_95015.1	chr11	31965605	31965611	+	1	NA	promoter-TSS (NM_026262)	promoter-TSS (NM_026262)	-25	NM_026262	67592	Mm.78654	NM_026262	ENSMUSG00000020299	4930524B15Rik	-	RIKEN cDNA 4930524B15 gene	protein-coding
mm_149313.1	chr19	10783524	10783533	+	1	NA	intron (NR_027805, intron 2 of 3)	intron (NR_027805, intron 2 of 3)	42581	NR_027805	403202	Mm.34482	NM_207529	ENSMUSG00000067577	A430093F15Rik	Gm674	RIKEN cDNA A430093F15 gene	ncRNA
mm_21448.1	chr2	160619942	160619976	-	1	NA	Intergenic	Intergenic	-25938	NM_009408	21969	Mm.217233	NM_009408	ENSMUSG00000070544	Top1	AI467334|D130064I21Rik|Top-1	topoisomerase (DNA) I	protein-coding
mm_154980.1	chrX	37827362	37827425	+	1	NA	exon (NM_008955, exon 2 of 4)	exon (NM_008955, exon 2 of 4)	338	NM_008955	19202	Mm.10105	NM_008955	ENSMUSG00000006200	Rhox6	AV213605|AW548842|Psx1	reproductive homeobox 6	protein-coding
mm_66255.1	chr7	35647109	35647112	-	1	NA	intron (NM_019746, intron 1 of 5)	CpG	372	NM_019746	56330	Mm.371609	NM_019746	ENSMUSG00000030417	Pdcd5	2200003D22Rik|AA408513|Tfar19	programmed cell death 5	protein-coding
mm_49339.1	chr6	21384656	21384660	+	1	NA	intron (NM_019697, intron 1 of 5)	Charlie1a|DNA|hAT-Charlie	168549	NM_019697	16508	Mm.425316	NM_019697	ENSMUSG00000060882	Kcnd2	AI839615|AW555701|Kv4.2|R75121|mKIAA1044	potassium voltage-gated channel, Shal-related family, member 2	protein-coding
mm_15662.1	chr2	163323269	163323280	+	1	NA	TTS (NM_001098799)	TTS (NM_001098799)	74699	NM_021566	59091	Mm.34459	NM_021566	ENSMUSG00000017817	Jph2	1110002E14Rik|JP-2|Jp2	junctophilin 2	protein-coding
mm_147239.1	chr18	38297041	38297055	-	1	NA	5' UTR (NM_001164621, exon 1 of 10)	5' UTR (NM_001164621, exon 1 of 10)	243	NM_001164621	56736	Mm.228903	NM_020012	ENSMUSG00000060450	Rnf14	2310075C09Rik|2610005D23Rik|AA986456|AU041447|D18Ertd188e|D7Bwg0165e|Triad2	ring finger protein 14	protein-coding
mm_89667.1	chr10	97503808	97503810	+	1	NA	intron (NM_001190451, intron 3 of 7)	Lx7|LINE|L1	21478	NM_007833	13179	Mm.56769	NM_007833	ENSMUSG00000019929	Dcn	DC|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding
mm_90420.1	chr10	127476575	127476593	+	1	NA	exon (NM_001168293, exon 13 of 24)	exon (NM_001168293, exon 13 of 24)	-25133	NM_177707	237611	Mm.32087	NM_177707	ENSMUSG00000040287	Stac3	9830125E18	SH3 and cysteine rich domain 3	protein-coding
mm_1268.1	chr1	63200594	63200641	+	1	NA	5' UTR (NM_001285937, exon 1 of 6)	5' UTR (NM_001285937, exon 1 of 6)	259	NM_001285936	73884	Mm.86986	NM_028673	ENSMUSG00000027520	Zdbf2	4930431J08Rik|9330107J05Rik	zinc finger, DBF-type containing 2	protein-coding
mm_152806.1	chr19	21942420	21942428	-	1	NA	Intergenic	Intergenic	164084	NM_031997	83921	Mm.329776	NM_031997	ENSMUSG00000024754	Tmem2	-	transmembrane protein 2	protein-coding
mm_171005.1	chr2	80196254	80196255	+	1	NA	Intergenic	RLTR10D2|LTR|ERVK	-66842	NM_001159582	18573	Mm.40678	NM_016744	ENSMUSG00000059173	Pde1a	AI987702|AW125737	phosphodiesterase 1A, calmodulin-dependent	protein-coding
mm_24558.1	chr3	93443619	93443623	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	1291	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_85591.1	chr9	107334316	107334322	-	1	NA	intron (NM_133984, intron 4 of 10)	intron (NM_133984, intron 4 of 10)	4031	NM_133984	69536	Mm.259467	NM_133984	ENSMUSG00000032579	Hemk1	2310008M14Rik|AW049265	HemK methyltransferase family member 1	protein-coding
mm_94992.1	chr11	31871523	31871533	+	1	NA	5' UTR (NM_026252, exon 1 of 10)	5' UTR (NM_026252, exon 1 of 10)	588	NM_026252	67579	Mm.339792	NM_026252	ENSMUSG00000020300	Cpeb4	Cpe-bp4|Cpeb-4|mCPEB-4	cytoplasmic polyadenylation element binding protein 4	protein-coding
mm_13398.1	chr2	103970250	103970269	+	1	NA	promoter-TSS (NM_008505)	promoter-TSS (NM_008505)	-28	NM_008505	16909	Mm.29266	NM_008505	ENSMUSG00000032698	Lmo2	Rbtn-2|Rbtn2|Rhom-2|Ttg2	LIM domain only 2	protein-coding
mm_36886.1	chr4	107253442	107253491	-	1	NA	promoter-TSS (NM_029985)	promoter-TSS (NM_029985)	67	NM_029985	77809	Mm.29681	NM_029985	ENSMUSG00000028617	Lrrc42	A930011F22Rik|AA536996	leucine rich repeat containing 42	protein-coding
mm_37970.1	chr4	133498515	133498531	-	1	NA	promoter-TSS (NM_001081156)	promoter-TSS (NM_001081156)	27	NM_001081156	69539	Mm.151594	NM_001081156	ENSMUSG00000056596	Trnp1	2300002D11Rik|Trnp	TMF1-regulated nuclear protein 1	protein-coding
mm_121919.1	chr14	23298789	23298793	-	1	NA	TTS (NM_001253365)	TTS (NM_001253365)	-204220	NR_033550	791307	Mm.364384	NR_033550	ENSMUSG00000068680	Gm10248	ENSMUSG00000068680	predicted gene 10248	ncRNA
mm_150587.1	chr19	40660676	40660694	+	1	NA	intron (NM_009848, intron 1 of 9)	intron (NM_009848, intron 1 of 9)	915	NM_009848	12495	Mm.2824	NM_009848	ENSMUSG00000048120	Entpd1	2610206B08Rik|AA408691|Cd39|NTPDase-1	ectonucleoside triphosphate diphosphohydrolase 1	protein-coding
mm_160516.1	chr9	22113954	22113954	-	1	NA	promoter-TSS (NR_106052)	promoter-TSS (NR_106052)	59	NR_106052	102466221		NR_106052	ENSMUSG00000098646	Mir7084	Gm27978|mmu-mir-7084	microRNA 7084	ncRNA
mm_15943.1	chr2	165874996	165875012	+	1	NA	intron (NM_027230, intron 2 of 23)	intron (NM_027230, intron 2 of 23)	3433	NM_001291158	228880	Mm.227598	NM_027230	ENSMUSG00000039671	Zmynd8	1110013E22Rik|2010005I16Rik|3632413B07Rik|AI316811|AL024039|Prkcbp1|RACK7	zinc finger, MYND-type containing 8	protein-coding
mm_155336.1	chrX	66653038	66653045	+	1	NA	promoter-TSS (NM_198863)	promoter-TSS (NM_198863)	-118	NM_198863	245450	Mm.336081	NM_198863	ENSMUSG00000036790	Slitrk2	A930040J07	SLIT and NTRK-like family, member 2	protein-coding
mm_130267.1	chr15	96689926	96689940	-	1	NA	3' UTR (NM_175121, exon 16 of 16)	3' UTR (NM_175121, exon 16 of 16)	9765	NM_175121	67760	Mm.46754	NM_175121	ENSMUSG00000022462	Slc38a2	5033402L14Rik|AI316867|ATA2|SAT2|mKIAA1382	solute carrier family 38, member 2	protein-coding
mm_146578.1	chr18	7373737	7373740	-	1	NA	intron (NM_001081287, intron 13 of 16)	L1_Mur1|LINE|L1	-75837	NM_001081393	74934	Mm.107918	NM_001081393	ENSMUSG00000061802	Armc4	4930463I21Rik|b2b227.1Clo|b2b643Clo	armadillo repeat containing 4	protein-coding
mm_116558.1	chr13	46727796	46727862	-	1	NA	promoter-TSS (NM_175749)	promoter-TSS (NM_175749)	20	NM_175749	218210	Mm.255398	NM_175749	ENSMUSG00000021374	Nup153	B130015D15Rik|C88147	nucleoporin 153	protein-coding
mm_131329.1	chr16	13119243	13119264	+	1	NA	intron (NM_015769, intron 2 of 10)	RLTR11A|LTR|ERVK	9517	NM_015769	50505	Mm.287837	NM_015769	ENSMUSG00000022545	Ercc4	AI606920|Xpf	excision repair cross-complementing rodent repair deficiency, complementation group 4	protein-coding
mm_26727.1	chr3	4656981	4657025	-	1	NA	Intergenic	Lx8|LINE|L1	-141705	NR_045272	100503859	Mm.75172	NR_045272	ENSMUSG00000098659	1110015O18Rik	-	RIKEN cDNA 1110015O18 gene	ncRNA
mm_34124.1	chr4	139257085	139257100	+	1	NA	intron (NM_001037761, intron 2 of 9)	intron (NM_001037761, intron 2 of 9)	53608	NM_145384	212555	Mm.45131	NM_145384	ENSMUSG00000028744	Pqlc2	BC019216	PQ loop repeat containing 2	protein-coding
mm_78864.1	chr9	44398410	44398423	+	1	NA	5' UTR (NM_008063, exon 1 of 8)	5' UTR (NM_008063, exon 1 of 8)	240	NM_008063	14385	Mm.30087	NM_008063	ENSMUSG00000032114	Slc37a4	100043178|G6PT|G6pt1|GSD-1b|mG6PT	solute carrier family 37 (glucose-6-phosphate transporter), member 4	protein-coding
mm_159072.1	chr2	25423260	25423260	+	1	NA	promoter-TSS (NM_001177367)	promoter-TSS (NM_001177367)	18	NM_001289456	14347	Mm.1203	NM_013524	ENSMUSG00000036587	Fut7	AI853193|FTVII|Fuc-TVII|FucT-VII	fucosyltransferase 7	protein-coding
mm_95605.1	chr11	53370940	53370945	+	1	NA	intron (NM_033565, intron 2 of 20)	B1_Mur4|SINE|Alu	20175	NM_033565	93736	Mm.395281	NM_033565	ENSMUSG00000049470	Aff4	AF5Q31|Alf4|Laf4l|MCEF	AF4/FMR2 family, member 4	protein-coding
mm_67222.1	chr7	74542933	74542974	-	1	NA	intron (NM_001038643, intron 1 of 10)	intron (NM_001038643, intron 1 of 10)	11827	NM_023908	108116	Mm.425467	NM_023908	ENSMUSG00000025790	Slco3a1	5830414C08Rik|Anr1|MJAM|OATP-D|R75096|Slc21a11	solute carrier organic anion transporter family, member 3a1	protein-coding
mm_32175.1	chr4	100776642	100776656	+	1	NA	promoter-TSS (NM_198037)	promoter-TSS (NM_198037)	-30	NM_198037	320508	Mm.151962	NM_198037	ENSMUSG00000028532	Cachd1	1190007F10Rik|AI852726|B430218L07Rik|Vwcd1|mKIAA1573	cache domain containing 1	protein-coding
mm_100409.1	chr11	119423085	119423102	+	1	NA	Intergenic	Intergenic	32621	NR_035453	100316690		NR_035453	ENSMUSG00000088015	Mir1932	mir-1932|mmu-mir-1932	microRNA 1932	ncRNA
mm_19044.1	chr2	77147151	77147152	-	1	NA	intron (NM_001025576, intron 2 of 23)	BGLII|LTR|ERVK	23484	NM_001025576	545428	Mm.26579	NM_001025576	ENSMUSG00000044033	Ccdc141	2610301F02Rik|CAMDI|ENSMUSG00000075261	coiled-coil domain containing 141	protein-coding
mm_18723.1	chr2	72938057	72938081	-	1	NA	exon (NM_001098425, exon 5 of 5)	exon (NM_001098425, exon 5 of 5)	41212	NM_001098425	20687	Mm.124328	NM_011450	ENSMUSG00000027109	Sp3	D130027J01Rik	trans-acting transcription factor 3	protein-coding
mm_79313.1	chr9	52067394	52067408	+	1	NA	exon (NM_009041, exon 6 of 14)	exon (NM_009041, exon 6 of 14)	-18696	NR_023357	629557	Mm.422775	NR_023357		Gm6981	EG629557	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_78489.1	chr9	32700271	32700298	+	1	NA	intron (NM_011808, intron 1 of 7)	intron (NM_011808, intron 1 of 7)	4242	NM_001038642	23871	Mm.292415	NM_011808	ENSMUSG00000032035	Ets1	AI196000|AI448617|D230050P06|Ets-1|Tpl1|vs	E26 avian leukemia oncogene 1, 5' domain	protein-coding
mm_164368.1	chr16	24025733	24025747	+	1	NA	Intergenic	Intergenic	-37128	NM_009744	12053	Mm.347398	NM_009744	ENSMUSG00000022508	Bcl6	Bcl5	B cell leukemia/lymphoma 6	protein-coding
mm_70958.1	chr8	26978770	26978795	+	1	NA	exon (NM_001101502, exon 2 of 2)	exon (NM_001101502, exon 2 of 2)	1446	NM_001110508	353310	Mm.212469	NM_001101502	ENSMUSG00000085795	Zfp703	1110032O19Rik|AI430822|AL022941|Csmn1|End2|Zeppo1|Znf703|Zpo1	zinc finger protein 703	protein-coding
mm_96700.1	chr11	69633746	69633750	+	1	NA	intron (NM_011814, intron 1 of 16)	intron (NM_011814, intron 1 of 16)	777	NM_011814	23879	Mm.41930	NM_011814	ENSMUSG00000018765	Fxr2	Fxr2h	fragile X mental retardation, autosomal homolog 2	protein-coding
mm_104612.1	chr11	97239713	97239717	-	1	NA	intron (NM_008942, intron 9 of 22)	B1_Mur3|SINE|Alu	40861	NM_008942	19155	Mm.29824	NM_008942	ENSMUSG00000001441	Npepps	AAP-S|MP100|Psa|R74825|goku	aminopeptidase puromycin sensitive	protein-coding
mm_6863.1	chr1	84278418	84278436	-	1	NA	intron (NM_001003948, intron 1 of 2)	intron (NM_001003948, intron 1 of 2)	6218	NM_001003948	98496	Mm.187470	NM_001003948	ENSMUSG00000045658	Pid1	5033414K04Rik|NYGGF4	phosphotyrosine interaction domain containing 1	protein-coding
mm_72707.1	chr8	84980352	84980365	+	1	NA	Intergenic	CpG	-1610	NM_008416	16477	Mm.1167	NM_008416	ENSMUSG00000052837	Junb	-	jun B proto-oncogene	protein-coding
mm_118133.1	chr13	104816890	104816905	-	1	NA	promoter-TSS (NM_026072)	promoter-TSS (NM_026072)	56	NM_026072	67285	Mm.235398	NM_026072	ENSMUSG00000021715	Cwc27	3110009E13Rik|NY-CO-10|Sdccag10	CWC27 spliceosome-associated protein	protein-coding
mm_112278.1	chr12	114358257	114358270	-	1	NA	Intergenic	Intergenic	111203	NR_106062	102465663		NR_106062	ENSMUSG00000105438	Mir7094-1	mmu-mir-7094-1	microRNA 7094-1	ncRNA
mm_163488.1	chr12	109453627	109453631	+	1	NA	non-coding (NR_033813, exon 2 of 6)	non-coding (NR_033813, exon 2 of 6)	174	NM_010052	13386	Mm.157069	NM_010052	ENSMUSG00000040856	Dlk1	AW742678|DLK-1|DlkI|FA1|Ly107|Peg9|SCP1|ZOG|pG2|pref-1	delta-like 1 homolog (Drosophila)	protein-coding
mm_38454.1	chr4	140519829	140519839	-	1	NA	intron (NM_001290803, intron 27 of 28)	intron (NM_001290803, intron 27 of 28)	128922	NM_001112723	72754	Mm.29329	NM_172415	ENSMUSG00000040964	Arhgef10l	2810441C07Rik	Rho guanine nucleotide exchange factor (GEF) 10-like	protein-coding
mm_111557.1	chr12	101073541	101073544	-	1	NA	intron (NM_211355, intron 1 of 14)	B4|SINE|B4	-8909	NR_038048	319760	Mm.440198	NM_176997	ENSMUSG00000097121	D130020L05Rik	9430007L23Rik	RIKEN cDNA D130020L05 gene	ncRNA
mm_127151.1	chr15	98567997	98568018	+	1	NA	promoter-TSS (NM_009833)	promoter-TSS (NM_009833)	-371	NM_009833	12455	Mm.29941	NM_009833	ENSMUSG00000011960	Ccnt1	2810478G24Rik|AI115585|CycT1	cyclin T1	protein-coding
mm_89577.1	chr10	95634495	95634532	+	1	NA	Intergenic	Intergenic	-70346	NM_027722	71207	Mm.24397	NM_027722	ENSMUSG00000020029	Nudt4	4933436C10Rik|DIPP2|DIPP2alpha|DIPP2beta|HDCMB47P	nudix (nucleoside diphosphate linked moiety X)-type motif 4	protein-coding
mm_91987.1	chr10	61874866	61874879	-	1	NA	intron (NM_001304757, intron 17 of 37)	intron (NM_001304757, intron 17 of 37)	-91008	NM_207000	404634	Mm.272870	NM_207000	ENSMUSG00000020086	H2afy2	macroH2A2	H2A histone family, member Y2	protein-coding
mm_39276.1	chr5	3845196	3845202	+	1	NA	promoter-TSS (NM_172879)	promoter-TSS (NM_172879)	26	NM_172879	242838	Mm.482273	NM_172879	ENSMUSG00000040367	Lrrd1	4932412H11Rik	leucine rich repeats and death domain containing 1	protein-coding
mm_163145.1	chr11	81675966	81675968	+	1	NA	intron (NM_001034013, intron 1 of 9)	intron (NM_001034013, intron 1 of 9)	-102428	NM_001033765	237880	Mm.435528	NM_001033765		1700071K01Rik	-	RIKEN cDNA 1700071K01 gene	protein-coding
mm_86567.1	chr10	11323420	11323424	+	1	NA	Intergenic	Intergenic	-20023	NM_010146	13853	Mm.89946	NM_010146	ENSMUSG00000055493	Epm2a	TG-B|Tg(TcraK,TcrbK)TG-BFlv	epilepsy, progressive myoclonic epilepsy, type 2 gene alpha	protein-coding
mm_3520.1	chr1	150107522	150107532	+	1	NA	3' UTR (NM_011198, exon 10 of 10)	3' UTR (NM_011198, exon 10 of 10)	7496	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_83443.1	chr9	45002615	45002627	-	1	NA	intron (NM_007648, intron 4 of 7)	intron (NM_007648, intron 4 of 7)	6969	NM_007648	12501	Mm.210361	NM_007648	ENSMUSG00000032093	Cd3e	AI504783|CD3|CD3epsilon|T3e	CD3 antigen, epsilon polypeptide	protein-coding
mm_126309.1	chr15	79659189	79659194	+	1	NA	promoter-TSS (NM_028634)	promoter-TSS (NM_028634)	-36	NM_028634	73739	Mm.294441	NM_028634	ENSMUSG00000022428	Cby1	1110014P06Rik|CBY|PGEA14|Pgea1|arb1	chibby family member 1, beta catenin antagonist	protein-coding
mm_36053.1	chr4	57338946	57338951	-	1	NA	Intergenic	Intergenic	25344	NR_038179	73349	Mm.393774	NR_038178		1700042G15Rik	-	RIKEN cDNA 1700042G15 gene	ncRNA
mm_70455.1	chr8	11798721	11798730	+	1	NA	intron (NM_001113517, intron 6 of 18)	intron (NM_001113517, intron 6 of 18)	40395	NM_001113518	54126	Mm.244068	NM_017402	ENSMUSG00000031511	Arhgef7	Cool|PIX|Pak3bp|betaPix|betaPix-b|betaPix-c|cool-1|mKIAA0142|p85Cool1|p85SPR	Rho guanine nucleotide exchange factor (GEF7)	protein-coding
mm_105717.1	chr11	108344120	108344180	-	1	NA	promoter-TSS (NM_011101)	promoter-TSS (NM_011101)	-262	NM_011101	18750	Mm.222178	NM_011101	ENSMUSG00000050965	Prkca	AI875142|Pkca	protein kinase C, alpha	protein-coding
mm_25631.1	chr3	119242277	119242278	+	1	NA	intron (NM_170778, intron 18 of 22)	intron (NM_170778, intron 18 of 22)	541111	NM_001310711	56195	Mm.29966	NM_019550	ENSMUSG00000028134	Ptbp2	Ptb2|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding
mm_54747.1	chr6	41033020	41033024	-	1	NA	exon (NM_023333, exon 3 of 5)	exon (NM_023333, exon 3 of 5)	2487	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_143338.1	chr17	66495456	66495457	-	1	NA	3' UTR (NM_024448, exon 6 of 6)	3' UTR (NM_024448, exon 6 of 6)	24214	NM_024448	19328	Mm.248313	NM_024448	ENSMUSG00000023460	Rab12	2900054P15Rik|AW555448|C77700	RAB12, member RAS oncogene family	protein-coding
mm_70050.1	chr7	142578094	142578121	-	1	NA	promoter-TSS (NR_130974)	promoter-TSS (NR_130974)	39	NR_130974	14955	Mm.14802	NR_001592	ENSMUSG00000000031	H19	AI747191	H19, imprinted maternally expressed transcript	ncRNA
mm_45523.1	chr5	72627938	72627942	-	1	NA	intron (NM_007723, intron 1 of 8)	(C)n|Simple_repeat|Simple_repeat	14812	NM_007723	12788	Mm.436652	NM_007723	ENSMUSG00000067220	Cnga1	Cncg	cyclic nucleotide gated channel alpha 1	protein-coding
mm_99914.1	chr11	110145615	110145625	+	1	NA	exon (NM_147220, exon 13 of 39)	exon (NM_147220, exon 13 of 39)	22533	NM_147220	217262	Mm.291459	NM_147220	ENSMUSG00000041797	Abca9	D630040K07Rik	ATP-binding cassette, sub-family A (ABC1), member 9	protein-coding
mm_97215.1	chr11	75630816	75630830	+	1	NA	promoter-TSS (NM_008916)	promoter-TSS (NM_008916)	-197	NM_008916	19062	Mm.1458	NM_008916	ENSMUSG00000006127	Inpp5k	C62|Pps|SKIP	inositol polyphosphate 5-phosphatase K	protein-coding
mm_22958.1	chr3	32414846	32414893	+	1	NA	Intergenic	L1ME4b|LINE|L1	-21282	NM_008839	18706	Mm.260521	NM_008839	ENSMUSG00000027665	Pik3ca	6330412C24Rik|caPI3K|p110|p110alpha	phosphatidylinositol 3-kinase, catalytic, alpha polypeptide	protein-coding
mm_81121.1	chr9	106463154	106463204	+	1	NA	TTS (NM_001159652)	TTS (NM_001159652)	2761	NM_001159652	436090	Mm.482905	NM_001159652	ENSMUSG00000091735	Gpr62	4933402E03Rik	G protein-coupled receptor 62	protein-coding
mm_105068.1	chr11	100724281	100724291	-	1	NA	intron (NM_024456, intron 1 of 5)	intron (NM_024456, intron 1 of 5)	10436	NM_029307	75482	Mm.46175	NM_029307	ENSMUSG00000017832	Hspb9	1700007H20Rik	heat shock protein, alpha-crystallin-related, B9	protein-coding
mm_144499.1	chr18	24470799	24470814	+	1	NA	promoter-TSS (NM_026529)	promoter-TSS (NM_026529)	-65	NM_026529	68046	Mm.276574	NM_026529	ENSMUSG00000024273	2700062C07Rik	AI195775|C87515	RIKEN cDNA 2700062C07 gene	protein-coding
mm_95379.1	chr11	49096707	49096735	+	1	NA	3' UTR (NM_001271677, exon 3 of 3)	3' UTR (NM_001271677, exon 3 of 3)	9704	NM_008330	15953	Mm.24769	NM_008330	ENSMUSG00000078920	Ifi47	47kDa|IRG-47|Ifggc1|Igrd|Iigp4|Iipg4|Irgd	interferon gamma inducible protein 47	protein-coding
mm_150707.1	chr19	42524865	42524866	+	1	NA	intron (NM_177464, intron 1 of 6)	intron (NM_177464, intron 1 of 6)	6060	NM_177464	52013	Mm.254169	NM_177464	ENSMUSG00000025184	R3hcc1l	1700036B12Rik|AI450607|C10orf28|D19Ertd386e|GIDRP86|Gidrp88	R3H domain and coiled-coil containing 1 like	protein-coding
mm_84010.1	chr9	57645189	57645207	-	1	NA	5' UTR (NM_007783, exon 1 of 13)	5' UTR (NM_007783, exon 1 of 13)	455	NM_007783	12988	Mm.21974	NM_007783	ENSMUSG00000032312	Csk	AW212630|p50CSK	c-src tyrosine kinase	protein-coding
mm_161603.1	chr16	38455376	38455376	+	1	NA	Intergenic	Intergenic	-2687	NM_007414	11544	Mm.20047	NM_007414	ENSMUSG00000002844	Adprh	Arh1	ADP-ribosylarginine hydrolase	protein-coding
mm_128957.1	chr15	74799541	74799554	-	1	NA	intron (NM_029627, intron 1 of 3)	intron (NM_029627, intron 1 of 3)	421	NM_029627	76486	Mm.273319	NM_029627	ENSMUSG00000044678	Ly6k	2410015A16Rik|3110035B01Rik|mLy-6K	lymphocyte antigen 6 complex, locus K	protein-coding
mm_23049.1	chr3	35113504	35113517	+	1	NA	Intergenic	Intergenic	-190859	NR_105799	102466155		NR_105799	ENSMUSG00000098862	Mir6378	Gm27706|mmu-mir-6378	microRNA 6378	ncRNA
mm_125469.1	chr15	53639109	53639113	+	1	NA	intron (NM_177225, intron 4 of 4)	MLT2B4|LTR|ERVL	263325	NM_177225	320679	Mm.442455	NM_177225	ENSMUSG00000058656	Samd12	A830094I09Rik	sterile alpha motif domain containing 12	protein-coding
mm_59108.1	chr7	19809579	19809587	+	1	NA	exon (NM_033601, exon 7 of 9)	exon (NM_033601, exon 7 of 9)	-12774	NM_023224	80794	Mm.81698	NM_023224	ENSMUSG00000040525	Cblc	2310076I21Rik|2310079L19Rik|Cbl3	Casitas B-lineage lymphoma c	protein-coding
mm_74643.1	chr8	13287815	13287856	-	1	NA	promoter-TSS (NM_172282)	promoter-TSS (NM_172282)	-178	NM_172282	234076	Mm.219813	NM_172282	ENSMUSG00000038497	Tmco3	B230339H12Rik|C87304	transmembrane and coiled-coil domains 3	protein-coding
mm_169049.1	chr13	17803287	17803296	-	1	NA	intron (NM_027118, intron 1 of 13)	intron (NM_027118, intron 1 of 13)	1806	NM_001081058	69562	Mm.193924	NM_027118	ENSMUSG00000041297	Cdk13	2310015O17Rik|Cdc2l5	cyclin-dependent kinase 13	protein-coding
mm_143202.1	chr17	62784059	62784063	-	1	NA	intron (NM_010109, intron 1 of 3)	intron (NM_010109, intron 1 of 3)	97256	NM_207654	13640	Mm.7978	NM_010109	ENSMUSG00000048915	Efna5	AL-1|AV158822|EFL-5|Ephrin-A5|Epl7|LERK-7|RAGS	ephrin A5	protein-coding
mm_112692.1	chr13	17694622	17694630	+	1	NA	promoter-TSS (NM_025479)	promoter-TSS (NM_025479)	139	NM_138654	192136	Mm.364180	NM_138654	ENSMUSG00000055137	Sugct	5033411D12Rik|D17907	succinyl-CoA glutarate-CoA transferase	protein-coding
mm_147917.1	chr18	65587050	65587082	-	1	NA	intron (NM_207255, intron 2 of 5)	ID_B1|SINE|B4	6836	NM_207255	328977	Mm.286232	NM_207255	ENSMUSG00000042439	Zfp532	C530030I18Rik|Znf532|mKIAA1629	zinc finger protein 532	protein-coding
mm_160495.1	chr9	3379279	3379279	+	1	NA	intron (NM_026303, intron 10 of 11)	L1_Mus2|LINE|L1	-24806	NM_027545	244672	Mm.245482	NM_027545	ENSMUSG00000025898	Cwf19l2	3230401L03Rik|9030209E10	CWF19-like 2, cell cycle control (S. pombe)	protein-coding
mm_109845.1	chr12	4593703	4593736	-	1	NA	intron (NM_011365, intron 1 of 38)	intron (NM_011365, intron 1 of 38)	711	NM_001198968	20403	Mm.341204	NM_011365	ENSMUSG00000020640	Itsn2	AI327390|Ese2|Sh3d1B|Sh3p18|mKIAA1256	intersectin 2	protein-coding
mm_7323.1	chr1	100180378	100180388	-	1	NA	intron (NM_172851, intron 10 of 23)	L1Md_F2|LINE|L1	407618	NM_172851	241175	Mm.251301	NM_172851	ENSMUSG00000067028	Cntnap5b	C230078M14Rik|Caspr5-2	contactin associated protein-like 5B	protein-coding
mm_92035.1	chr10	62486773	62486784	-	1	NA	promoter-TSS (NM_001113355)	promoter-TSS (NM_001113355)	27	NM_133672	30930	Mm.260703	NM_133672	ENSMUSG00000020078	Vps26a	AA407240|HB58|Vps26	VPS26 retromer complex component A	protein-coding
mm_147268.1	chr18	38929134	38929145	-	1	NA	intron (NM_001033789, intron 3 of 4)	intron (NM_001033789, intron 3 of 4)	-10440	NM_010197	14164	Mm.241282	NM_010197	ENSMUSG00000036585	Fgf1	Dffrx|Fam|Fgf-1|Fgfa	fibroblast growth factor 1	protein-coding
mm_140067.1	chr17	74841234	74841244	+	1	NA	intron (NM_152817, intron 16 of 19)	intron (NM_152817, intron 16 of 19)	123489	NM_152817	74196	Mm.209503	NM_152817	ENSMUSG00000024078	Ttc27	2610511O17Rik	tetratricopeptide repeat domain 27	protein-coding
mm_9577.1	chr1	174024401	174024438	-	1	NA	intron (NM_172648, intron 4 of 6)	intron (NM_172648, intron 4 of 6)	7336	NM_172648	226695	Mm.425061	NM_172648	ENSMUSG00000054203	Ifi205	D3|D3cDNA|Ifi205a	interferon activated gene 205	protein-coding
mm_147054.1	chr18	34940237	34940247	-	1	NA	exon (NM_010481, exon 13 of 17)	exon (NM_010481, exon 13 of 17)	-8239	NM_144866	225363	Mm.329353	NM_144866	ENSMUSG00000024360	Etf1	AI463371|D6Ertd109e|ERF|ERF1|SUP45L1|TB3-1	eukaryotic translation termination factor 1	protein-coding
mm_3180.1	chr1	135766086	135766175	+	1	NA	promoter-TSS (NM_013750)	promoter-TSS (NM_013750)	45	NM_013750	27280	Mm.34346	NM_013750	ENSMUSG00000041801	Phlda3	Tih1	pleckstrin homology like domain, family A, member 3	protein-coding
mm_74896.1	chr8	25158148	25158157	-	1	NA	TTS (NR_106187)	TTS (NR_106187)	1081	NR_106187	102467006		NR_106187	ENSMUSG00000099142	Mir8108	Gm27484|mmu-mir-8108	microRNA 8108	ncRNA
mm_155707.1	chrX	95968901	95968907	+	1	NA	Intergenic	RMER17C|LTR|ERVK	-11930	NM_152822	76130	Mm.274318	NM_152822	ENSMUSG00000057421	Las1l	1810030A06Rik|5830482G23Rik	LAS1-like (S. cerevisiae)	protein-coding
mm_85069.1	chr9	91130389	91130399	-	1	NA	Intergenic	Intergenic	235405	NM_009573	22771	Mm.335350	NM_009573	ENSMUSG00000032368	Zic1	ZIC|ZNF201	zinc finger protein of the cerebellum 1	protein-coding
mm_118518.1	chr14	14686799	14686837	+	1	NA	Intergenic	Intergenic	-16207	NM_001033270	218756	Mm.258893	NM_001033270	ENSMUSG00000021733	Slc4a7	E430014N10Rik|NBC3|NBCn1|NBCn1-G	solute carrier family 4, sodium bicarbonate cotransporter, member 7	protein-coding
mm_110245.1	chr12	31337257	31337261	-	1	NA	intron (NM_007861, intron 8 of 13)	B1F2|SINE|Alu	14212	NM_007861	13382	Mm.3131	NM_007861	ENSMUSG00000020664	Dld	-	dihydrolipoamide dehydrogenase	protein-coding
mm_87348.1	chr10	43579924	43579945	+	1	NA	intron (NM_009846, intron 1 of 1)	intron (NM_009846, intron 1 of 1)	765	NM_009846	12484	Mm.29742	NM_009846	ENSMUSG00000047139	Cd24a	Cd24|HSA|Ly-52|nectadrin	CD24a antigen	protein-coding
mm_161944.1	chr19	4185475	4185475	-	1	NA	exon (NM_178650, exon 9 of 10)	exon (NM_178650, exon 9 of 10)	5572	NM_178650	108995	Mm.288312	NM_178650	ENSMUSG00000040247	Tbc1d10c	1810062O14Rik|AI428527	TBC1 domain family, member 10c	protein-coding
mm_118487.1	chr14	12284178	12284194	+	1	NA	promoter-TSS (NM_146051)	promoter-TSS (NM_146051)	-17	NM_001284384	218734	Mm.44068	NM_146051	ENSMUSG00000033111	3830406C13Rik	-	RIKEN cDNA 3830406C13 gene	protein-coding
mm_163492.1	chr12	109568182	109568196	+	1	NA	non-coding (NR_003633, exon 5 of 5)	non-coding (NR_003633, exon 5 of 5)	-3801	NR_030438	751547		NR_030438	ENSMUSG00000076316	Mir673	Mirn673|mir-673|mmu-mir-673	microRNA 673	ncRNA
mm_16448.1	chr2	180456300	180456302	+	1	NA	Intergenic	CpG	-4677	NM_148933	108115	Mm.133687	NM_148933	ENSMUSG00000038963	Slco4a1	OATP-E|Slc21a12	solute carrier organic anion transporter family, member 4a1	protein-coding
mm_51651.1	chr6	86028854	86028862	+	1	NA	5' UTR (NM_001271860, exon 1 of 13)	5' UTR (NM_001271860, exon 1 of 13)	177	NM_001271860	11519	Mm.104155	NM_013458	ENSMUSG00000030000	Add2	2900072M03Rik|add97	adducin 2 (beta)	protein-coding
mm_133058.1	chr16	58436583	58436598	+	1	NA	intron (NM_028523, intron 3 of 15)	B2_Mm2|SINE|B2	28055	NM_028523	73379	Mm.373589	NM_028523	ENSMUSG00000035107	Dcbld2	1700055P21Rik|AW146002|CLCP1|Esdn	discoidin, CUB and LCCL domain containing 2	protein-coding
mm_102481.1	chr11	60115227	60115237	-	1	NA	intron (NM_009021, intron 1 of 5)	CpG	10219	NM_009021	19377	Mm.296366	NM_009021	ENSMUSG00000062115	Rai1	Gt1	retinoic acid induced 1	protein-coding
mm_18671.1	chr2	70825895	70825934	-	1	NA	promoter-TSS (NM_172664)	promoter-TSS (NM_172664)	-434	NM_172664	228012	Mm.136511	NM_172664	ENSMUSG00000041997	Tlk1	4930545J15Rik	tousled-like kinase 1	protein-coding
mm_77676.1	chr8	124949166	124949372	-	1	NA	promoter-TSS (NM_053207)	promoter-TSS (NM_053207)	-15	NM_053207	112405	Mm.140619	NM_053207	ENSMUSG00000031987	Egln1	AI503754|C1orf12|HIF-PH2|HPH-2|Hif-p4h-2|ORF13|Phd2|SM-20	egl-9 family hypoxia-inducible factor 1	protein-coding
mm_54508.1	chr6	35511355	35511381	-	1	NA	3' UTR (NM_008098, exon 4 of 4)	3' UTR (NM_008098, exon 4 of 4)	28520	NM_008098	14489	Mm.182746	NM_008098	ENSMUSG00000029840	Mtpn	5033418D15Rik|Gcdp|V1	myotrophin	protein-coding
mm_98655.1	chr11	96271143	96271153	+	1	NA	promoter-TSS (NM_008270)	promoter-TSS (NM_008270)	-182	NM_008270	15417	Mm.258271	NM_008270	ENSMUSG00000020875	Hoxb9	Hox-2.5	homeobox B9	protein-coding
mm_90465.1	chr10	127776346	127776356	+	1	NA	promoter-TSS (NM_153133)	promoter-TSS (NM_153133)	-54	NM_153133	103142	Mm.235814	NM_153133	ENSMUSG00000056148	Rdh9	AI121090|Crad3	retinol dehydrogenase 9	protein-coding
mm_96860.1	chr11	70092654	70092698	+	1	NA	promoter-TSS (NM_007493)	promoter-TSS (NM_007493)	32	NM_001313927	11890	Mm.1357	NM_007493	ENSMUSG00000040963	Asgr2	ASGPR2|Asgr|Asgr-2|HL-2	asialoglycoprotein receptor 2	protein-coding
mm_93154.1	chr10	93083367	93083371	-	1	NA	Intergenic	Intergenic	-1773	NM_001347060	380654	Mm.34980	NM_001347060	ENSMUSG00000020014	Cfap54	4930485B16Rik|Gm872	cilia and flagella associated protein 54	protein-coding
mm_32596.1	chr4	111750654	111750664	+	1	NA	intron (NM_026470, intron 3 of 12)	intron (NM_026470, intron 3 of 12)	30649	NM_026470	67946	Mm.275526	NM_026470	ENSMUSG00000034401	Spata6	1700062C23Rik|AI790763|Hash|KRP|Mash	spermatogenesis associated 6	protein-coding
mm_172957.1	chr9	88482152	88482155	-	1	NA	5' UTR (NM_001284328, exon 1 of 12)	5' UTR (NM_001284328, exon 1 of 12)	244	NM_019666	56403	Mm.260545	NM_019666	ENSMUSG00000032423	Syncrip	2610109K23Rik|4632417O19Rik|GRY-RBP|Nsap1|Nsap1l|hnRNP Q|pp68	synaptotagmin binding, cytoplasmic RNA interacting protein	protein-coding
mm_130800.1	chr15	101707428	101707445	-	1	NA	exon (NM_027011, exon 9 of 9)	exon (NM_027011, exon 9 of 9)	5455	NM_027011	110308	Mm.451847	NM_027011	ENSMUSG00000061527	Krt5	3300001P10Rik|AW146334|CK5|K5|Krt2-5|Tfip8	keratin 5	protein-coding
mm_126326.1	chr15	79883508	79883527	+	1	NA	Intergenic	CpG	-8891	NM_001160415	80287	Mm.284059	NM_030255	ENSMUSG00000009585	Apobec3	Apobec|Arp3|BC003314|Cem15|Rfv3	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 3	protein-coding
mm_104591.1	chr11	97041396	97041402	-	1	NA	promoter-TSS (NM_027026)	promoter-TSS (NM_027026)	-30	NM_027026	69297	Mm.250465	NM_027026	ENSMUSG00000020878	Lrrc46	1700006D24Rik	leucine rich repeat containing 46	protein-coding
mm_80473.1	chr9	78175899	78175922	+	1	NA	promoter-TSS (NR_040401)	promoter-TSS (NR_040401)	-4	NR_040401	320295	Mm.131285	NR_040401	ENSMUSG00000097574	C920006O11Rik	-	RIKEN cDNA C920006O11 gene	ncRNA
mm_126745.1	chr15	85735622	85735650	+	1	NA	promoter-TSS (NM_011144)	promoter-TSS (NM_011144)	72	NM_001113418	19013	Mm.212789	NM_011144	ENSMUSG00000022383	Ppara	4933429D07Rik|AW742785|Nr1c1|PPAR-alpha|PPARalpha|Ppar	peroxisome proliferator activated receptor alpha	protein-coding
mm_153682.1	chr19	44396689	44396703	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	11013	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_104319.1	chr11	93955719	93955729	-	1	NA	promoter-TSS (NM_001077529)	promoter-TSS (NM_001077529)	59	NM_001077529	18103	Mm.1260	NM_008705	ENSMUSG00000020857	Nme2	NM23-H2|NM23B|nm23-M2	NME/NM23 nucleoside diphosphate kinase 2	protein-coding
mm_40536.1	chr5	57959118	57959121	+	1	NA	intron (NM_001310608, intron 3 of 3)	intron (NM_001310608, intron 3 of 3)	241038	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_137663.1	chr17	28692271	28692300	+	1	NA	promoter-TSS (NM_001168513)	promoter-TSS (NM_001168513)	-283	NM_001168513	26416	Mm.311337	NM_011951	ENSMUSG00000053436	Mapk14	CSBP2|Crk1|Csbp1|Mxi2|PRKM14|PRKM15|p38|p38-alpha|p38MAPK|p38a|p38alpha	mitogen-activated protein kinase 14	protein-coding
mm_131441.1	chr16	16072794	16072797	+	1	NA	intron (NM_146068, intron 5 of 19)	intron (NM_146068, intron 5 of 19)	74056	NM_146068	224008	Mm.244703	NM_146068	ENSMUSG00000041974	Spidr	2310008H04Rik|Kiaa0146	scaffolding protein involved in DNA repair	protein-coding
mm_157596.1	chrX	53240102	53240107	-	1	NA	Intergenic	Intergenic	29701	NM_030167	78755	Mm.28559	NM_030167	ENSMUSG00000036022	Fam122b	4632404H22Rik|AI256344|SPACIA2	family with sequence similarity 122, member B	protein-coding
mm_73195.1	chr8	95534132	95534132	+	1	NA	promoter-TSS (NM_172914)	promoter-TSS (NM_172914)	32	NM_172914	244608	Mm.248902	NM_172914	ENSMUSG00000036598	Ccdc113	4933409I22|BC060957	coiled-coil domain containing 113	protein-coding
mm_76133.1	chr8	80880508	80880534	-	1	NA	promoter-TSS (NM_001301298)	promoter-TSS (NM_001301298)	-2	NM_001301298	14388	Mm.277409	NM_021356	ENSMUSG00000031714	Gab1	AA408973|AW107238	growth factor receptor bound protein 2-associated protein 1	protein-coding
mm_153870.1	chr19	46701345	46701383	-	1	NA	intron (NM_025563, intron 4 of 4)	PB1|SINE|Alu	-6079	NM_020577	57344	Mm.28566	NM_020577	ENSMUSG00000003559	As3mt	2310045H08Rik|Cyt19	arsenic (+3 oxidation state) methyltransferase	protein-coding
mm_128853.1	chr15	71954387	71954393	-	1	NA	intron (NM_027174, intron 12 of 63)	intron (NM_027174, intron 12 of 63)	79837	NM_027174	69700	Mm.322500	NM_027174	ENSMUSG00000079022	Col22a1	2310067L16Rik|C80743	collagen, type XXII, alpha 1	protein-coding
mm_100498.1	chr11	120480042	120480058	+	1	NA	exon (NM_008244, exon 18 of 22)	exon (NM_008244, exon 18 of 22)	-4619	NM_027204	56282	Mm.133851	NM_027204	ENSMUSG00000039640	Mrpl12	0610034O11Rik|1500031N16Rik|MRP-L12|Rpml12	mitochondrial ribosomal protein L12	protein-coding
mm_142648.1	chr17	47507987	47508006	-	1	NA	intron (NM_001081635, intron 1 of 6)	intron (NM_001081635, intron 1 of 6)	2945	NM_001081635	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_170229.1	chr17	82153553	82153562	-	1	NA	Intergenic	RLTR9C|LTR|ERVK	-415170	NM_011406	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_36870.1	chr4	107135048	107135050	-	1	NA	3' UTR (NM_025617, exon 5 of 5)	3' UTR (NM_025617, exon 5 of 5)	38158	NM_172873	242603	Mm.257231	NM_172873	ENSMUSG00000047636	Cdcp2	D030010E02Rik	CUB domain containing protein 2	protein-coding
mm_109542.1	chr12	111583663	111583665	+	1	NA	intron (NM_022801, intron 1 of 15)	intron (NM_022801, intron 1 of 15)	9154	NM_022801	17169	Mm.260504	NM_021516	ENSMUSG00000007411	Mark3	1600015G02Rik|A430080F22Rik|C-TAK1|ETK-1|ETK1|Emk2|MPK10	MAP/microtubule affinity regulating kinase 3	protein-coding
mm_29155.1	chr3	106014610	106014624	-	1	NA	promoter-TSS (NM_001200028)	promoter-TSS (NM_001200028)	29	NM_001200028	100503311	Mm.386825	NM_029604	ENSMUSG00000010136	Pifo	1700027A23Rik	primary cilia formation	protein-coding
mm_23446.1	chr3	59898496	59898504	+	1	NA	Intergenic	Intergenic	-26714	NM_177661	229333	Mm.75765	NM_177661	ENSMUSG00000036951	C130079G13Rik	-	RIKEN cDNA C130079G13 gene	protein-coding
mm_36645.1	chr4	94477168	94477207	-	1	NA	Intergenic	MTEa|LTR|ERVL-MaLR	79609	NM_026368	67770	Mm.35170	NM_026368	ENSMUSG00000028578	Caap1	5830433M19Rik|AI536248|CAAP	caspase activity and apoptosis inhibitor 1	protein-coding
mm_86354.1	chr9	123678814	123678850	-	1	NA	promoter-TSS (NM_139142)	promoter-TSS (NM_139142)	0	NM_139142	102680	Mm.440867	NM_139142	ENSMUSG00000036814	Slc6a20a	A730081N20Rik|AU022428|Xt3s1|Xtrp3s1	solute carrier family 6 (neurotransmitter transporter), member 20A	protein-coding
mm_24314.1	chr3	89421620	89421636	+	1	NA	promoter-TSS (NM_001113331)	promoter-TSS (NM_001113331)	7	NM_001113331	20416	Mm.86595	NM_011368	ENSMUSG00000042626	Shc1	Shc|ShcA|p66|p66shc	src homology 2 domain-containing transforming protein C1	protein-coding
mm_43714.1	chr5	139405312	139405320	+	1	NA	intron (NM_028469, intron 2 of 4)	intron (NM_028469, intron 2 of 4)	-1071	NM_177000	319772	Mm.440271	NM_177000	ENSMUSG00000044092	C130050O18Rik	-	RIKEN cDNA C130050O18 gene	protein-coding
mm_162630.1	chr1	187078560	187078571	+	1	NA	intron (NM_028848, intron 9 of 9)	intron (NM_028848, intron 9 of 9)	-46573	NR_040554	69308	Mm.490882	NR_040554	ENSMUSG00000089730	1700007P06Rik	-	RIKEN cDNA 1700007P06 gene	ncRNA
mm_59913.1	chr7	30415711	30415741	+	1	NA	intron (NM_011662, intron 4 of 4)	intron (NM_011662, intron 4 of 4)	1938	NM_011662	22177	Mm.46301	NM_011662	ENSMUSG00000030579	Tyrobp	DAP12|KARAP|Ly83	TYRO protein tyrosine kinase binding protein	protein-coding
mm_40609.1	chr5	64515943	64515943	+	1	NA	Intergenic	Intergenic	38935	NR_045413	77382	Mm.366742	NR_045411	ENSMUSG00000105352	C030018K13Rik	-	RIKEN cDNA C030018K13 gene	ncRNA
mm_70876.1	chr8	25101915	25101953	+	1	NA	promoter-TSS (NM_031257)	promoter-TSS (NM_031257)	-123	NM_031257	83436	Mm.261122	NM_031257	ENSMUSG00000031557	Plekha2	6430512N22Rik|AI851530|AU041791|TAPP2|W91773	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 2	protein-coding
mm_100494.1	chr11	120467760	120467765	+	1	NA	promoter-TSS (NM_197995)	promoter-TSS (NM_197995)	127	NM_001159328	15239	Mm.7919	NM_008244	ENSMUSG00000025793	Hgs	Hgr|Hrs|ZFYVE8|tn	HGF-regulated tyrosine kinase substrate	protein-coding
mm_42531.1	chr5	115845230	115845301	+	1	NA	promoter-TSS (NM_007708)	promoter-TSS (NM_007708)	-391	NM_007708	12704	Mm.8321	NM_007708	ENSMUSG00000029516	Cit	C030025P15Rik|CRIK|CRIK-SK|Cit-k	citron	protein-coding
mm_42003.1	chr5	107905176	107905178	+	1	NA	intron (NM_016980, intron 6 of 7)	intron (NM_016980, intron 6 of 7)	4649	NM_016980	100503670	Mm.277897	NM_016980	ENSMUSG00000058558	Rpl5	U21RNA	ribosomal protein L5	protein-coding
mm_105166.1	chr11	101771440	101771461	-	1	NA	exon (NM_001316366, exon 11 of 13)	exon (NM_001316366, exon 11 of 13)	13860	NM_008815	18612	Mm.5025	NM_008815	ENSMUSG00000017724	Etv4	AW414408|Pea-3|Pea3	ets variant 4	protein-coding
mm_31789.1	chr4	63668597	63668607	+	1	NA	Intergenic	Intergenic	-46173	NM_029324	75524	Mm.38543	NM_029324	ENSMUSG00000058935	1700018C11Rik	bM230C2.3	RIKEN cDNA 1700018C11 gene	protein-coding
mm_63318.1	chr7	126928901	126928905	+	1	NA	promoter-TSS (NM_172747)	promoter-TSS (NM_172747)	24	NM_172747	233877	Mm.245897	NM_172747	ENSMUSG00000030685	Kctd13	1500003N18Rik|AV259508|PDIP1alpha|Pdip1|Poldip1	potassium channel tetramerisation domain containing 13	protein-coding
mm_37514.1	chr4	123907441	123907444	-	1	NA	intron (NM_019660, intron 2 of 4)	intron (NM_019660, intron 2 of 4)	2429	NM_019660	56309	Mm.446553	NM_019660	ENSMUSG00000028647	Mycbp	5730488M09Rik|AW552132|AW742590|Amy-1	MYC binding protein	protein-coding
mm_141910.1	chr17	34969805	34969807	-	1	NA	3' UTR (NM_010479, exon 1 of 1)	3' UTR (NM_010479, exon 1 of 1)	2350	NM_010479	193740	Mm.6388	NM_010479	ENSMUSG00000091971	Hspa1a	Hsp70-3|Hsp70.3|Hsp72|hsp68|hsp70A1	heat shock protein 1A	protein-coding
mm_71249.1	chr8	40915649	40915665	+	1	NA	intron (NM_007514, intron 11 of 11)	intron (NM_007514, intron 11 of 11)	-10576	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_142088.1	chr17	35779919	35779931	-	1	NA	intron (NR_045459, intron 2 of 2)	B1F|SINE|Alu	7475	NR_045459	74601	Mm.410840	NR_045459	ENSMUSG00000092171	4833427F10Rik	-	RIKEN cDNA 4833427F10 gene	ncRNA
mm_128169.1	chr15	34099517	34099533	-	1	NA	exon (NM_026002, exon 2 of 12)	exon (NM_026002, exon 2 of 12)	16806	NM_026002	67154	Mm.130883	NM_026002	ENSMUSG00000022255	Mtdh	2610103J23Rik|3D3|3D3/Lyric|AEG-1|AV353288|D8Bwg1112e|Lyric	metadherin	protein-coding
mm_172207.1	chr6	57863495	57863501	-	1	NA	Intergenic	Lx3A|LINE|L1	-19041	NM_134183	171201	Mm.377179	NM_134183	ENSMUSG00000058588	Vmn1r21	V1rc28	vomeronasal 1 receptor 21	protein-coding
mm_43258.1	chr5	130222411	130222425	+	1	NA	promoter-TSS (NM_027854)	promoter-TSS (NM_027854)	83	NM_027854	71667	Mm.258508	NM_027854	ENSMUSG00000053094	Tmem248	0610007L01Rik|A930023A16Rik|AW557951|G430067H08Rik	transmembrane protein 248	protein-coding
mm_121090.1	chr14	99301664	99301686	+	1	NA	exon (NM_009769, exon 2 of 4)	exon (NM_009769, exon 2 of 4)	2984	NM_009769	12224	Mm.30262	NM_009769	ENSMUSG00000005148	Klf5	4930520J07Rik|Bteb2|CKLF|IKLF	Kruppel-like factor 5	protein-coding
mm_8886.1	chr1	162881562	162881565	-	1	NA	intron (NM_018881, intron 6 of 8)	intron (NM_018881, intron 6 of 8)	-14953	NM_010231	14261	Mm.976	NM_010231	ENSMUSG00000040181	Fmo1	-	flavin containing monooxygenase 1	protein-coding
mm_91784.1	chr10	52382075	52382142	-	1	NA	promoter-TSS (NM_053187)	promoter-TSS (NM_053187)	16	NM_053187	94221	Mm.390258	NM_053187	ENSMUSG00000019861	Gopc	2210402P09Rik|AI844555|CAL|FIG|GOPC1|PIST	golgi associated PDZ and coiled-coil motif containing	protein-coding
mm_63582.1	chr7	128118163	128118175	+	1	NA	3' UTR (NM_008401, exon 30 of 30)	3' UTR (NM_008401, exon 30 of 30)	-11399	NM_021334	16411	Mm.22378	NM_021334	ENSMUSG00000030789	Itgax	AI449405|Cd11c|Cr4|N418	integrin alpha X	protein-coding
mm_138125.1	chr17	34157634	34157675	+	1	NA	intron (NM_010387, intron 3 of 5)	intron (NM_010387, intron 3 of 5)	4463	NM_010387	14999	Mm.460938	NM_010387	ENSMUSG00000079547	H2-DMb1	AI385589|H-2Mb1|H2-Mb1	histocompatibility 2, class II, locus Mb1	protein-coding
mm_132161.1	chr16	32183933	32183934	+	1	NA	intron (NM_001033539, intron 1 of 2)	MT2B2|LTR|ERVL	4133	NM_001033539	328660	Mm.441006	NM_001033539	ENSMUSG00000075269	Bex6	B020003O03Rik	brain expressed family member 6	protein-coding
mm_54798.1	chr6	41687518	41687523	-	1	NA	intron (NM_032540, intron 18 of 18)	intron (NM_032540, intron 18 of 18)	3089	NM_029671	76606	Mm.272520	NM_029671	ENSMUSG00000029867	1700034O15Rik	-	RIKEN cDNA 1700034O15 gene	protein-coding
mm_168328.1	chr11	116389624	116389630	+	1	NA	intron (NM_027258, intron 2 of 18)	IAPLTR1_Mm|LTR|ERVK	23405	NM_027258	217340	Mm.426344	NM_027258	ENSMUSG00000052949	Rnf157	2610036E23Rik|A130073L17Rik|mKIAA1917	ring finger protein 157	protein-coding
mm_137240.1	chr17	24470394	24470481	+	1	NA	promoter-TSS (NM_025954)	promoter-TSS (NM_025954)	-36	NM_025954	67078	Mm.28541	NM_025954	ENSMUSG00000043445	Pgp	1700012G19Rik|AI481330|AUM|G3PP	phosphoglycolate phosphatase	protein-coding
mm_72469.1	chr8	83389835	83389845	+	1	NA	promoter-TSS (NM_001329627)	promoter-TSS (NM_001329627)	-2	NM_001329627	12745	Mm.358581	NM_009904	ENSMUSG00000002190	Clgn	4930459O04Rik|A2/6|AI528775|Cln	calmegin	protein-coding
mm_47835.1	chr5	134313216	134313219	-	1	NA	intron (NM_001080746, intron 1 of 34)	B1_Mur2|SINE|Alu	1543	NM_001080746	14886	Mm.261570	NM_010365	ENSMUSG00000060261	Gtf2i	6030441I21Rik|BAP-135|Diws1t|GtfII-I|Spin|TFII-I|WBSCR6	general transcription factor II I	protein-coding
mm_161132.1	chr12	113489511	113489511	+	1	NA	promoter-TSS (NM_001009545)	promoter-TSS (NM_001009545)	-54	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_6342.1	chr1	71637336	71637346	-	1	NA	exon (NM_001276413, exon 12 of 44)	exon (NM_001276413, exon 12 of 44)	15893	NM_010233	14268	Mm.193099	NM_010233	ENSMUSG00000026193	Fn1	E330027I09|Fn|Fn-1	fibronectin 1	protein-coding
mm_96962.1	chr11	70647296	70647306	+	1	NA	promoter-TSS (NM_024211)	promoter-TSS (NM_024211)	14	NM_027445	70510	Mm.261818	NM_027445	ENSMUSG00000040746	Rnf167	0610010G05Rik|5730408C10Rik|AU019305|AV328608	ring finger protein 167	protein-coding
mm_133986.1	chr16	4560088	4560101	-	1	NA	promoter-TSS (NM_031182)	promoter-TSS (NM_031182)	-374	NM_031182	83383	Mm.273210	NM_031182	ENSMUSG00000005718	Tfap4	AI642933|AP-4|D930048N17Rik|Tcfap4|bHLHc41	transcription factor AP4	protein-coding
mm_60601.1	chr7	44533687	44533691	+	1	NA	exon (NM_011131, exon 24 of 27)	exon (NM_011131, exon 24 of 27)	-1618	NM_019866	272382	Mm.8012	NM_019866	ENSMUSG00000008193	Spib	Spi-B	Spi-B transcription factor (Spi-1/PU.1 related)	protein-coding
mm_109968.1	chr12	12850715	12850723	-	1	NA	Intergenic	Intergenic	91117	NM_008709	18109	Mm.16469	NM_008709	ENSMUSG00000037169	Mycn	N-myc|Nmyc|Nmyc-1|Nmyc1|bHLHe37|c-nmyc	v-myc avian myelocytomatosis viral related oncogene, neuroblastoma derived	protein-coding
mm_150167.1	chr19	32485788	32485802	+	1	NA	promoter-TSS (NM_010799)	promoter-TSS (NM_010799)	26	NM_010799	17330	Mm.255116	NM_010799	ENSMUSG00000024896	Minpp1	AA408516	multiple inositol polyphosphate histidine phosphatase 1	protein-coding
mm_76991.1	chr8	107065616	107065628	-	1	NA	promoter-TSS (NM_025458)	promoter-TSS (NM_025458)	22	NM_025458	66269	Mm.23032	NM_025458	ENSMUSG00000031919	Tmed6	1810015P03Rik|1810018I24Rik	transmembrane p24 trafficking protein 6	protein-coding
mm_95307.1	chr11	46222632	46222668	+	1	NA	exon (NM_001252459, exon 25 of 31)	exon (NM_001252459, exon 25 of 31)	-9485	NR_105955	102465598		NR_105955	ENSMUSG00000099230	Mir6989	Gm27885|mmu-mir-6989	microRNA 6989	ncRNA
mm_6512.1	chr1	74393855	74393881	-	1	NA	promoter-TSS (NR_029743)	promoter-TSS (NR_029743)	-442	NR_029743	387219		NR_029743	ENSMUSG00000065468	Mir26b	Mirn26b|mir-26b|mmu-mir-26b	microRNA 26b	ncRNA
mm_38627.1	chr4	142084528	142084563	-	1	NA	promoter-TSS (NM_145402)	promoter-TSS (NM_145402)	-241	NM_145402	214359	Mm.27587	NM_145402	ENSMUSG00000040616	Tmem51	BC003277	transmembrane protein 51	protein-coding
mm_46590.1	chr5	107725411	107725422	-	1	NA	intron (NM_001267621, intron 1 of 6)	CpG	389	NM_001267621	14581	Mm.2078	NM_010278	ENSMUSG00000029275	Gfi1	AW495828|Gfi-1|Pal-1|Pal1	growth factor independent 1	protein-coding
mm_163498.1	chr12	111920343	111920381	+	1	NA	Intergenic	Intergenic	-12307	NM_011625	21981	Mm.313076	NM_011625	ENSMUSG00000021285	Ppp1r13b	AI449786|ASPP1|AW545810|Tp53bp2|Trp53bp2|p85	protein phosphatase 1, regulatory (inhibitor) subunit 13B	protein-coding
mm_68553.1	chr7	114415129	114415166	-	1	NA	promoter-TSS (NM_011055)	promoter-TSS (NM_011055)	14	NR_029437	71045	Mm.235682	NR_029437	ENSMUSG00000087475	4933406I18Rik	4933403D24Rik	RIKEN cDNA 4933406I18 gene	ncRNA
mm_5003.1	chr1	191977369	191977389	+	1	NA	promoter-TSS (NM_001303132)	promoter-TSS (NM_001303132)	9	NM_023727	74023	Mm.274393	NM_023727	ENSMUSG00000049353	Rd3	3322402L07Rik|rd-3|rd3	retinal degeneration 3	protein-coding
mm_32140.1	chr4	99569519	99569534	+	1	NA	Intergenic	RLTR27|LTR|ERVK	-86773	NM_010425	15221	Mm.4758	NM_010425	ENSMUSG00000067261	Foxd3	CWH3|Genesis|Hfh2	forkhead box D3	protein-coding
mm_3175.1	chr1	135739475	135739482	+	1	NA	exon (NM_007791, exon 2 of 6)	exon (NM_007791, exon 2 of 6)	10281	NM_007791	13007	Mm.196484	NM_007791	ENSMUSG00000026421	Csrp1	AA408841|AA959891|AW545626|CRP1|Csrp	cysteine and glycine-rich protein 1	protein-coding
mm_116800.1	chr13	53915741	53915749	-	1	NA	Intergenic	RMER19C|LTR|ERVK	139035	NM_001291801	13488	Mm.54161	NM_010076	ENSMUSG00000021478	Drd1	C030036C15Rik|Drd-1|Drd1a|Gpcr15	dopamine receptor D1	protein-coding
mm_149244.1	chr19	10204202	10204237	+	1	NA	promoter-TSS (NM_001271614)	promoter-TSS (NM_001271614)	17	NM_026919	69038	Mm.375100	NM_026919	ENSMUSG00000036372	Tmem258	1810006K21Rik	transmembrane protein 258	protein-coding
mm_20691.1	chr2	132792660	132792702	-	1	NA	exon (NM_007694, exon 4 of 5)	exon (NM_007694, exon 4 of 5)	11403	NM_007694	12653	Mm.255241	NM_007694	ENSMUSG00000027350	Chgb	Scg-1	chromogranin B	protein-coding
mm_88713.1	chr10	80154011	80154086	+	1	NA	exon (NM_001305798, exon 5 of 8)	exon (NM_001305798, exon 5 of 8)	4366	NM_001305799	59090	Mm.143813	NM_021565	ENSMUSG00000035621	Midn	3000003C15Rik	midnolin	protein-coding
mm_36662.1	chr4	95050430	95050445	-	1	NA	exon (NM_010591, exon 1 of 1)	exon (NM_010591, exon 1 of 1)	1785	NM_010591	16476	Mm.275071	NM_010591	ENSMUSG00000052684	Jun	AP-1|Junc|c-jun	jun proto-oncogene	protein-coding
mm_17720.1	chr2	32388092	32388096	-	1	NA	promoter-TSS (NM_008491)	promoter-TSS (NM_008491)	-355	NM_008491	16819	Mm.9537	NM_008491	ENSMUSG00000026822	Lcn2	24p3|AW212229|NRL|Sip24	lipocalin 2	protein-coding
mm_12826.1	chr2	80324385	80324388	+	1	NA	intron (NM_024181, intron 4 of 22)	intron (NM_024181, intron 4 of 22)	8920	NM_024181	66861	Mm.21762	NM_024181	ENSMUSG00000027006	Dnajc10	1200006L06Rik|D2Ertd706e|ERdj5|JPDI	DnaJ heat shock protein family (Hsp40) member C10	protein-coding
mm_93505.1	chr10	114419524	114419525	-	1	NA	intron (NM_146241, intron 15 of 18)	intron (NM_146241, intron 15 of 18)	381846	NM_146241	237553	Mm.445550	NM_146241	ENSMUSG00000050663	Trhde	9330155P21Rik	TRH-degrading enzyme	protein-coding
mm_91994.1	chr10	62110977	62111060	-	1	NA	promoter-TSS (NM_027251)	promoter-TSS (NM_027251)	-5	NM_027251	69894	Mm.294126	NM_027251	ENSMUSG00000020083	2010107G23Rik	AA545165	RIKEN cDNA 2010107G23 gene	protein-coding
mm_9448.1	chr1	172590651	172590666	-	1	NA	promoter-TSS (NM_029084)	promoter-TSS (NM_029084)	-90	NM_029084	74748	Mm.179812	NM_029084	ENSMUSG00000053318	Slamf8	5830408F06Rik|Blame|SBBI42	SLAM family member 8	protein-coding
mm_170039.1	chr17	24169391	24169398	-	1	NA	promoter-TSS (NM_009729)	promoter-TSS (NM_009729)	1	NR_037854	100039636	Mm.30155	NR_037854		Atp6v0c-ps2	Atp6l-ps2|Gm15487	ATPase, H+ transporting, lysosomal V0 subunit C, pseudogene 2	pseudo
mm_81462.1	chr9	109861601	109861610	+	1	NA	Intergenic	Intergenic	-12149	NM_009921	12796	Mm.3834	NM_009921	ENSMUSG00000038357	Camp	CAP18|Cnlp|Cramp|FALL39|MCLP	cathelicidin antimicrobial peptide	protein-coding
mm_56572.1	chr6	106729902	106729910	-	1	NA	intron (NM_008370, intron 10 of 12)	intron (NM_008370, intron 10 of 12)	19131	NM_008370	16192	Mm.3448	NM_008370	ENSMUSG00000005364	Il5ra	CD125|CDw125|Il5r	interleukin 5 receptor, alpha	protein-coding
mm_126845.1	chr15	89076129	89076147	+	1	NA	promoter-TSS (NM_026485)	promoter-TSS (NM_026485)	74	NM_026485	67976	Mm.284710	NM_026485	ENSMUSG00000015363	Trabd	5730502D15Rik|AL023039	TraB domain containing	protein-coding
mm_95974.1	chr11	58961766	58961780	+	1	NA	promoter-TSS (NM_001318003)	promoter-TSS (NM_001318003)	62	NM_001318003	382523		NM_001318003		Gm12260	H3t|OTTMUSG00000005773	predicted gene 12260	protein-coding
mm_73941.1	chr8	120101434	120101455	+	1	NA	promoter-TSS (NM_133967)	promoter-TSS (NM_133967)	28	NM_133967	102193	Mm.240076	NM_133967	ENSMUSG00000031823	Zdhhc7	AL024087|Gramp2	zinc finger, DHHC domain containing 7	protein-coding
mm_52821.1	chr6	121356819	121356847	+	1	NA	intron (NM_001347433, intron 6 of 14)	intron (NM_001347433, intron 6 of 14)	10136	NM_133661	14411	Mm.274506	NM_133661	ENSMUSG00000030109	Slc6a12	BGT1|GAT-2|GAT2|Gabt2	solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12	protein-coding
mm_103603.1	chr11	78404623	78404636	-	1	NA	non-coding (NR_003282, exon 5 of 5)	non-coding (NR_003282, exon 5 of 5)	10144	NR_003282	790911	Mm.457257	NR_003282	ENSMUSG00000085747	Slc13a2os	Gm11194|OTTMUSG00000000132	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 2, opposite strand	ncRNA
mm_101250.1	chr11	20742005	20742015	-	1	NA	promoter-TSS (NM_001252503)	promoter-TSS (NM_001252503)	-454	NM_181411	216549	Mm.356580	NM_181411	ENSMUSG00000049659	Aftph	-	aftiphilin	protein-coding
mm_61973.1	chr7	90476684	90476712	+	1	NA	promoter-TSS (NM_026734)	promoter-TSS (NM_026734)	-703	NM_026734	68472	Mm.289791	NM_026734	ENSMUSG00000030614	Tmem126b	1110001A23Rik	transmembrane protein 126B	protein-coding
mm_165935.1	chr4	69925823	69925841	+	1	NA	Intergenic	Intergenic	484603	NM_001313762	214444	Mm.370777	NM_145990	ENSMUSG00000039298	Cdk5rap2	2900018K03Rik|an|mKIAA1633	CDK5 regulatory subunit associated protein 2	protein-coding
mm_120421.1	chr14	65375340	65375386	+	1	NA	intron (NM_199029, intron 1 of 9)	intron (NM_199029, intron 1 of 9)	16687	NM_199029	380912	Mm.270087	NM_199029	ENSMUSG00000034522	Zfp395	BC053701|Gm910	zinc finger protein 395	protein-coding
mm_72970.1	chr8	92880781	92880795	+	1	NA	intron (NM_173014, intron 8 of 13)	intron (NM_173014, intron 8 of 13)	-20607	NM_027112	69543	Mm.440514	NM_027112	ENSMUSG00000078144	Capns2	2310005G05Rik|30K-2	calpain, small subunit 2	protein-coding
mm_74433.1	chr8	3748923	3748935	-	1	NA	promoter-TSS (NM_133238)	promoter-TSS (NM_133238)	55	NM_133238	170786	Mm.32510	NM_133238	ENSMUSG00000031494	Cd209a	CD209|CDSIGN|CIRE|DC-SIGN|DC-SIGN1|Dcsign|SIGN-R1|SIGNR5	CD209a antigen	protein-coding
mm_27726.1	chr3	69004554	69004564	-	1	NA	promoter-TSS (NM_133786)	promoter-TSS (NM_133786)	11	NM_026641	68259	Mm.389451	NM_026641	ENSMUSG00000027778	Ift80	4921524P20Rik|Wdr56|mKIAA1374	intraflagellar transport 80	protein-coding
mm_103957.1	chr11	84129559	84129580	-	1	NA	promoter-TSS (NM_172562)	promoter-TSS (NM_172562)	-1	NM_172562	217031	Mm.45159	NM_172562	ENSMUSG00000018651	Tada2a	AV319371|D030022J10Rik|Tada2l	transcriptional adaptor 2A	protein-coding
mm_77413.1	chr8	120628613	120628621	-	1	NA	intron (NM_001308449, intron 1 of 3)	intron (NM_001308449, intron 1 of 3)	5765	NM_197988	68918	Mm.473736	NM_197988	ENSMUSG00000043687	1190005I06Rik	-	RIKEN cDNA 1190005I06 gene	protein-coding
mm_5268.1	chr1	17267034	17267039	-	1	NA	Intergenic	U2|snRNA|snRNA	121663	NM_010267	14545	Mm.18218	NM_010267	ENSMUSG00000025777	Gdap1	-	ganglioside-induced differentiation-associated-protein 1	protein-coding
mm_37789.1	chr4	130334899	130334902	-	1	NA	intron (NM_153160, intron 5 of 7)	B1_Mus1|SINE|Alu	25043	NM_153160	619605	Mm.297196	NM_153160	ENSMUSG00000028772	Zcchc17	2810055E05Rik|HSPC251|LDC4|pNO40|pS1D	zinc finger, CCHC domain containing 17	protein-coding
mm_80069.1	chr9	69467955	69467960	+	1	NA	intron (NM_007585, intron 3 of 12)	MIR|SINE|MIR	11013	NR_037296	100526560		NR_037296	ENSMUSG00000093042	Mir3109	mir-3109|mmu-mir-3109	microRNA 3109	ncRNA
mm_167241.1	chr8	19980051	19980062	+	1	NA	intron (NM_001270553, intron 6 of 9)	CpG	250480	NM_001039553	626415	Mm.425517	NM_001039553	ENSMUSG00000096265	4930467E23Rik	ENSMUSG00000074453|OTTMUSG00000018948|TSAP	RIKEN cDNA 4930467E23 gene	protein-coding
mm_129241.1	chr15	76656736	76656747	-	1	NA	5' UTR (NM_001276321, exon 1 of 4)	5' UTR (NM_001276321, exon 1 of 4)	160	NM_001276321	54151	Mm.247752	NM_019396	ENSMUSG00000053929	Cyhr1	1110031M01Rik|AU042374|Chrp	cysteine and histidine rich 1	protein-coding
mm_118519.1	chr14	14703043	14703073	+	1	NA	promoter-TSS (NM_001033270)	promoter-TSS (NM_001033270)	33	NM_001033270	218756	Mm.258893	NM_001033270	ENSMUSG00000021733	Slc4a7	E430014N10Rik|NBC3|NBCn1|NBCn1-G	solute carrier family 4, sodium bicarbonate cotransporter, member 7	protein-coding
mm_83087.1	chr9	40306995	40307018	-	1	NA	intron (NM_172768, intron 12 of 19)	intron (NM_172768, intron 12 of 19)	-26466	NR_040728	73558	Mm.398307	NR_040728		1700110K17Rik	-	RIKEN cDNA 1700110K17 gene	ncRNA
mm_74535.1	chr8	9728022	9728047	-	1	NA	intron (NM_001347127, intron 1 of 3)	intron (NM_001347127, intron 1 of 3)	42989	NM_173446	270028	Mm.268163	NM_173446	ENSMUSG00000079157	Fam155a	6430500D16|AW121567|Tmem28	family with sequence similarity 155, member A	protein-coding
mm_44282.1	chr5	8067645	8067688	-	1	NA	3' UTR (NM_025618, exon 8 of 8)	3' UTR (NM_025618, exon 8 of 8)	11124	NM_001080974	109552	Mm.96211	NM_025618	ENSMUSG00000003161	Sri	2210417O06Rik|2900070H08Rik|Sor	sorcin	protein-coding
mm_119510.1	chr14	47384673	47384690	+	1	NA	exon (NM_010705, exon 5 of 6)	exon (NM_010705, exon 5 of 6)	10821	NM_001145953	16854	Mm.248615	NM_010705	ENSMUSG00000050335	Lgals3	GBP|L-34|Mac-2|gal3	lectin, galactose binding, soluble 3	protein-coding
mm_132534.1	chr16	37868384	37868481	+	1	NA	promoter-TSS (NM_177093)	promoter-TSS (NM_177093)	32	NM_177093	320184	Mm.390882	NM_177093	ENSMUSG00000034158	Lrrc58	1810012N18Rik|C330018J07Rik	leucine rich repeat containing 58	protein-coding
mm_58573.1	chr7	4812937	4813030	+	1	NA	promoter-TSS (NM_133777)	promoter-TSS (NM_133777)	-643	NM_133777	77891	Mm.389787	NM_133777	ENSMUSG00000060860	Ube2s	0910001J09Rik|6720465F12Rik|AA409170|E2-EPF	ubiquitin-conjugating enzyme E2S	protein-coding
mm_117777.1	chr13	96670839	96670903	-	1	NA	promoter-TSS (NM_008255)	promoter-TSS (NM_008255)	65	NM_008255	15357	Mm.316652	NM_008255	ENSMUSG00000021670	Hmgcr	HMG-CoAR|Red	3-hydroxy-3-methylglutaryl-Coenzyme A reductase	protein-coding
mm_15343.1	chr2	156017656	156017674	+	1	NA	exon (NM_025516, exon 11 of 13)	exon (NM_025516, exon 11 of 13)	9540	NM_025516	66366	Mm.141276	NM_025516	ENSMUSG00000005881	Ergic3	2310015B14Rik|AV318804|CGI-54|D2Ucla1|NY-BR-84|Sdbcag84	ERGIC and golgi 3	protein-coding
mm_74080.1	chr8	122476197	122476223	+	1	NA	promoter-TSS (NM_153775)	promoter-TSS (NM_153775)	67	NM_153775	66965	Mm.482288	NM_153775	ENSMUSG00000049482	Ctu2	2310061F22Rik|C16orf84|Ncs2	cytosolic thiouridylase subunit 2	protein-coding
mm_83122.1	chr9	40408062	40408072	-	1	NA	intron (NM_172768, intron 2 of 19)	intron (NM_172768, intron 2 of 19)	47697	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_58594.1	chr7	5020442	5020452	+	1	NA	promoter-TSS (NM_001290426)	promoter-TSS (NM_001290426)	71	NM_001033383	319748	Mm.86607	NM_001033383	ENSMUSG00000074405	Zfp865	6430526N21Rik|Znf865	zinc finger protein 865	protein-coding
mm_5013.1	chr1	192841668	192841676	+	1	NA	promoter-TSS (NR_040468)	promoter-TSS (NR_040468)	-33	NR_040468	73455	Mm.414869	NR_040468		1700065J18Rik	-	RIKEN cDNA 1700065J18 gene	ncRNA
mm_42724.1	chr5	120589021	120589061	+	1	NA	promoter-TSS (NM_145853)	promoter-TSS (NM_145853)	18	NM_029408	75732	Mm.425285	NM_029408	ENSMUSG00000029601	Iqcd	4933433C09Rik|AI662646	IQ motif containing D	protein-coding
mm_168207.1	chr10	71318759	71318765	+	1	NA	Intergenic	Intergenic	26087	NM_134007	52637	Mm.254114	NM_134007	ENSMUSG00000037710	Cisd1	AU043990|AW743335|D10Ertd214e|Zcd1|mitoNEET	CDGSH iron sulfur domain 1	protein-coding
mm_36427.1	chr4	82293257	82293270	-	1	NA	3' UTR (NM_001113209, exon 12 of 12)	3' UTR (NM_001113209, exon 12 of 12)	212516	NM_001286127	18028	Mm.317947	NM_008687	ENSMUSG00000008575	Nfib	6720429L07Rik|CTF|E030026I10Rik|NF-I/B|NF1-B|NFI-B	nuclear factor I/B	protein-coding
mm_102872.1	chr11	69409147	69409160	-	1	NA	intron (NM_001017426, intron 1 of 22)	intron (NM_001017426, intron 1 of 22)	4522	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_119325.1	chr14	37581099	37581101	+	1	NA	Intergenic	Intergenic	-445778	NM_078478	66092	Mm.182912	NM_078478	ENSMUSG00000041028	Ghitm	1010001P14Rik|C77840|MICS1|PTD010|Tmbim5	growth hormone inducible transmembrane protein	protein-coding
mm_156420.1	chrX	140907603	140907635	+	1	NA	promoter-TSS (NM_030181)	promoter-TSS (NM_030181)	11	NM_030181	78789	Mm.244932	NM_026103	ENSMUSG00000031430	Vsig1	1700062D20Rik|4930405J24Rik	V-set and immunoglobulin domain containing 1	protein-coding
mm_137519.1	chr17	27203300	27203316	+	1	NA	intron (NM_146075, intron 1 of 8)	intron (NM_146075, intron 1 of 8)	1130	NM_146075	224640	Mm.29689	NM_146075	ENSMUSG00000044857	Lemd2	BC026588|Lem2|NET25	LEM domain containing 2	protein-coding
mm_18397.1	chr2	60252494	60252494	-	1	NA	intron (NM_025422, intron 4 of 4)	intron (NM_025422, intron 4 of 4)	31990	NM_025422	66205	Mm.227281	NM_025422	ENSMUSG00000060703	Cd302	1110055L24Rik|AI159627	CD302 antigen	protein-coding
mm_153497.1	chr19	41332359	41332376	-	1	NA	intron (NM_031376, intron 2 of 16)	intron (NM_031376, intron 2 of 16)	52703	NM_031376	83490	Mm.222266	NM_031376	ENSMUSG00000025017	Pik3ap1	1810044J04Rik|BCAP	phosphoinositide-3-kinase adaptor protein 1	protein-coding
mm_84047.1	chr9	58102259	58102269	-	1	NA	promoter-TSS (NM_029212)	promoter-TSS (NM_029212)	33	NM_001311085	382077	Mm.335193	NM_029212	ENSMUSG00000037716	Ccdc33	4930535E21Rik|Gm1117|Tzip1	coiled-coil domain containing 33	protein-coding
mm_96114.1	chr11	60699759	60699845	+	1	NA	5' UTR (NM_001159405, exon 1 of 22)	5' UTR (NM_001159405, exon 1 of 22)	112	NM_008502	16897	Mm.285453	NM_008502	ENSMUSG00000020536	Llgl1	AI325176|Lgl1|Llglh|Mgl1	lethal giant larvae homolog 1 (Drosophila)	protein-coding
mm_51019.1	chr6	65042685	65042695	+	1	NA	promoter-TSS (NM_007958)	promoter-TSS (NM_007958)	23	NM_007958	13990	Mm.99113	NM_007958	ENSMUSG00000029920	Smarcad1	AV081750|AW226546|D6Pas1|Etl1|mKIAA1122	SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1	protein-coding
mm_149916.1	chr19	26606612	26606639	+	1	NA	intron (NM_011416, intron 1 of 32)	CpG	1465	NM_011416	67155	Mm.342988	NM_011416	ENSMUSG00000024921	Smarca2	2610209L14Rik|SNF2alpha|Snf2l2|brahma|brm	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	protein-coding
mm_146176.1	chr18	75368157	75368189	+	1	NA	5' UTR (NM_001042660, exon 1 of 4)	5' UTR (NM_001042660, exon 1 of 4)	808	NM_001042660	17131	Mm.34407	NM_008543	ENSMUSG00000025880	Smad7	Madh7	SMAD family member 7	protein-coding
mm_25112.1	chr3	101527047	101527056	+	1	NA	Intergenic	Intergenic	77656	NM_144900	11928	Mm.193670	NM_144900	ENSMUSG00000033161	Atp1a1	Atpa-1|BC010319	ATPase, Na+/K+ transporting, alpha 1 polypeptide	protein-coding
mm_50234.1	chr6	42351151	42351164	+	1	NA	intron (NM_001289619, intron 3 of 8)	intron (NM_001289619, intron 3 of 8)	1329	NM_001289619	22793	Mm.282303	NM_011777	ENSMUSG00000029860	Zyx	9530098H06Rik|R75157	zyxin	protein-coding
mm_95381.1	chr11	49174616	49174616	+	1	NA	intron (NM_172793, intron 6 of 9)	intron (NM_172793, intron 6 of 9)	12473	NM_172793	237754	Mm.130787	NM_172793	ENSMUSG00000040283	Btnl9	B430208I01|Btn3|D330012D11Rik	butyrophilin-like 9	protein-coding
mm_144065.1	chr17	90868023	90868025	-	1	NA	TTS (NR_045463)	TTS (NR_045463)	6855	NR_045463	78800	Mm.410772	NR_045463	ENSMUSG00000090160	4930480K15Rik	-	RIKEN cDNA 4930480K15 gene	ncRNA
mm_165458.1	chr2	158175423	158175456	-	1	NA	Intergenic	Intergenic	-16569	NR_036606	73399	Mm.416861	NR_036606	ENSMUSG00000078957	1700060C20Rik	-	RIKEN cDNA 1700060C20 gene	ncRNA
mm_112389.1	chr12	119238466	119238476	-	1	NA	promoter-TSS (NM_177290)	promoter-TSS (NM_177290)	-195	NM_177290	320910	Mm.217000	NM_177290	ENSMUSG00000025321	Itgb8	4832412O06Rik	integrin beta 8	protein-coding
mm_158707.1	chrX	162375468	162375472	-	1	NA	Intergenic	B4A|SINE|B4	-216029	NM_001290526	195727	Mm.336313	NM_001081052	ENSMUSG00000059493	Nhs	Gm389|Gm48|Nhs1|Xcat	Nance-Horan syndrome (human)	protein-coding
mm_78178.1	chr9	21184173	21184186	+	1	NA	promoter-TSS (NM_001310750)	promoter-TSS (NM_001310750)	78	NM_001310750	18577	Mm.191749	NM_019798	ENSMUSG00000032177	Pde4a	D9Ertd60e|Dpde2	phosphodiesterase 4A, cAMP specific	protein-coding
mm_56519.1	chr6	99504791	99504798	-	1	NA	intron (NM_001347345, intron 1 of 19)	intron (NM_001347345, intron 1 of 19)	16199	NM_001347345	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_122551.1	chr14	48667512	48667550	-	1	NA	5' UTR (NM_001286482, exon 1 of 5)	5' UTR (NM_001286482, exon 1 of 5)	113	NM_001286482	18424	Mm.134516	NM_144841	ENSMUSG00000021848	Otx2	E130306E05Rik	orthodenticle homeobox 2	protein-coding
mm_137938.1	chr17	32659081	32659091	+	1	NA	promoter-TSS (NM_001101588)	promoter-TSS (NM_001101588)	-397	NM_001101588	631304	Mm.328950	NM_001101588	ENSMUSG00000090700	Cyp4f40	EG631304	cytochrome P450, family 4, subfamily f, polypeptide 40	protein-coding
mm_119734.1	chr14	54120371	54120393	+	1	NA	Intergenic	Intergenic	133547	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_8176.1	chr1	138073664	138073705	-	1	NA	exon (NM_001268286, exon 23 of 29)	exon (NM_001268286, exon 23 of 29)	101442	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_28764.1	chr3	95891939	95891985	-	1	NA	promoter-TSS (NM_153513)	promoter-TSS (NM_153513)	43	NM_001346514	229600	Mm.89556	NM_153513	ENSMUSG00000038543	BC028528	L259	cDNA sequence BC028528	protein-coding
mm_4346.1	chr1	171857097	171857111	+	1	NA	intron (NM_001289470, intron 3 of 8)	L1_Mur3|LINE|L1	17407	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_152777.1	chr19	21172489	21172514	-	1	NA	Intergenic	Intergenic	67791	NR_126458	75354	Mm.243873	NR_126458		4930554I06Rik	-	RIKEN cDNA 4930554I06 gene	ncRNA
mm_31202.1	chr4	43727207	43727243	+	1	NA	promoter-TSS (NM_027511)	promoter-TSS (NM_027511)	27	NM_027511	100039781	Mm.18796	NM_027511	ENSMUSG00000071001	Hrct1	3830408D24Rik	histidine rich carboxyl terminus 1	protein-coding
mm_11236.1	chr2	29827369	29827403	+	1	NA	promoter-TSS (NM_026615)	promoter-TSS (NM_026615)	-3	NM_026615	68205	Mm.20273	NM_026615	ENSMUSG00000069020	Urm1	2900073H19Rik	ubiquitin related modifier 1	protein-coding
mm_100824.1	chr11	5261723	5261754	-	1	NA	promoter-TSS (NM_032396)	promoter-TSS (NM_032396)	-128	NM_032396	84035	Mm.209989	NM_032396	ENSMUSG00000020393	Kremen1	AV002070|Kremen|Krm1	kringle containing transmembrane protein 1	protein-coding
mm_153755.1	chr19	45236828	45236872	-	1	NA	Intergenic	Intergenic	-1614	NM_010691	16814	Mm.116815	NM_010691	ENSMUSG00000025216	Lbx1	Lbx1h	ladybird homeobox homolog 1 (Drosophila)	protein-coding
mm_83664.1	chr9	49630290	49630292	-	1	NA	intron (NM_001081445, intron 1 of 17)	intron (NM_001081445, intron 1 of 17)	112003	NR_029465	100036537	Mm.437541	NR_029465	ENSMUSG00000079564	Gm11149	ENSMUSG00000060603|ENSMUSG00000079564	predicted gene 11149	ncRNA
mm_130138.1	chr15	90898440	90898446	-	1	NA	promoter-TSS (NR_033583)	promoter-TSS (NR_033583)	33	NR_033583	20738	Mm.431547	NR_033583		Spn-ps	Cd43-ps	sialophorin, pseudogene	pseudo
mm_50293.1	chr6	47454986	47454994	+	1	NA	intron (NM_012042, intron 1 of 21)	CpG	666	NM_012042	26965	Mm.87611	NM_012042	ENSMUSG00000029686	Cul1	-	cullin 1	protein-coding
mm_91541.1	chr10	39613636	39613686	-	1	NA	intron (NM_134000, intron 1 of 8)	PB1D10|SINE|Alu	727	NM_134000	103213	Mm.436686	NM_134000	ENSMUSG00000019842	Traf3ip2	AI429613|Act1|CIKS	TRAF3 interacting protein 2	protein-coding
mm_30669.1	chr4	11155185	11155202	+	1	NA	Intergenic	Intergenic	-1248	NM_001199105	60599	Mm.393018	NM_021897	ENSMUSG00000028211	Trp53inp1	2700057G22Rik|SIP|SIP18|SIP27|Stinp|Teap	transformation related protein 53 inducible nuclear protein 1	protein-coding
mm_162654.1	chr10	4156356	4156358	+	1	NA	TTS (NM_001170786)	TTS (NM_001170786)	-109972	NM_031185	83397	Mm.27481	NM_031185	ENSMUSG00000038587	Akap12	AI317366|SSeCKS|Srcs5|Tsga12	A kinase (PRKA) anchor protein (gravin) 12	protein-coding
mm_143509.1	chr17	72593615	72593625	-	1	NA	intron (NM_007439, intron 1 of 28)	intron (NM_007439, intron 1 of 28)	10687	NM_007439	11682	Mm.311854	NM_007439	ENSMUSG00000055471	Alk	CD246|Tcrz	anaplastic lymphoma kinase	protein-coding
mm_67475.1	chr7	80522455	80522462	-	1	NA	intron (NM_001042527, intron 1 of 21)	MT2B1|LTR|ERVL	12540	NM_007550	12144	Mm.12932	NM_007550	ENSMUSG00000030528	Blm	-	Bloom syndrome, RecQ helicase-like	protein-coding
mm_60113.1	chr7	35451395	35451397	+	1	NA	intron (NM_021291, intron 2 of 12)	intron (NM_021291, intron 2 of 12)	2217	NM_021291	30962	Mm.45874	NM_021291	ENSMUSG00000030492	Slc7a9	CSNU3	solute carrier family 7 (cationic amino acid transporter, y+ system), member 9	protein-coding
mm_111840.1	chr12	107928874	107928879	-	1	NA	intron (NM_001286343, intron 1 of 1)	intron (NM_001286343, intron 1 of 1)	74538	NM_001079883	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_20835.1	chr2	147186390	147186413	-	1	NA	promoter-TSS (NM_001077632)	promoter-TSS (NM_001077632)	1	NM_001077632	18088	Mm.330639	NM_010919	ENSMUSG00000027434	Nkx2-2	Nkx-2.2|Nkx2.2|tinman	NK2 homeobox 2	protein-coding
mm_62614.1	chr7	107209183	107209199	+	1	NA	promoter-TSS (NM_029660)	promoter-TSS (NM_029660)	-254	NM_029660	76572	Mm.128134	NM_029660	ENSMUSG00000073894	Rbmxl2	1700012H05Rik|Hnrnpg-t	RNA binding motif protein, X-linked-like 2	protein-coding
mm_54627.1	chr6	38689046	38689073	-	1	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	25990	NM_001101507	665180	Mm.349066	NM_001101507	ENSMUSG00000079598	Clec2l	AI414054|AW122724|Gm1064	C-type lectin domain family 2, member L	protein-coding
mm_91251.1	chr10	22731875	22731916	-	1	NA	promoter-TSS (NM_011603)	promoter-TSS (NM_011603)	-448	NM_011603	237336	Mm.86670	NM_011603	ENSMUSG00000071359	Tbpl1	4732475G08|AW011832|AW491032|D18347|STD|TLF|TRF2|TRP|Tlp	TATA box binding protein-like 1	protein-coding
mm_94346.1	chr11	4883187	4883222	+	1	NA	intron (NM_008698, intron 1 of 9)	intron (NM_008698, intron 1 of 9)	-8141	NR_105883	102466764		NR_105883	ENSMUSG00000098296	Mir6918	Gm27968|mmu-mir-6918	microRNA 6918	ncRNA
mm_170125.1	chr17	39846974	39846974	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	3977	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_53276.1	chr6	128648961	128648965	+	1	NA	Intergenic	Intergenic	-13422	NM_053165	94071	Mm.197689	NM_053165	ENSMUSG00000030364	Clec2h	Clrf|clr-f	C-type lectin domain family 2, member h	protein-coding
mm_38245.1	chr4	136602610	136602616	-	1	NA	5' UTR (NM_133872, exon 1 of 19)	5' UTR (NM_133872, exon 1 of 19)	110	NM_133872	99982	Mm.28540	NM_133872	ENSMUSG00000036940	Kdm1a	1810043O07Rik|AA408884|Aof2|D4Ertd478e|Kdm1|Lsd1|mKIAA0601	lysine (K)-specific demethylase 1A	protein-coding
mm_82705.1	chr9	22486352	22486365	-	1	NA	intron (NM_178415, intron 2 of 22)	RLTR17|LTR|ERVK	10643	NM_178415	319845	Mm.176725	NM_178415	ENSMUSG00000035919	Bbs9	E130103I17Rik	Bardet-Biedl syndrome 9 (human)	protein-coding
mm_71005.1	chr8	31111817	31111891	+	1	NA	promoter-TSS (NM_175136)	promoter-TSS (NM_175136)	8	NM_175136	68867	Mm.29532	NM_175136	ENSMUSG00000039328	Rnf122	1110063C11Rik	ring finger protein 122	protein-coding
mm_59086.1	chr7	19696269	19696274	+	1	NA	TTS (NM_009696)	TTS (NM_009696)	2127	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_108064.1	chr12	73937717	73937732	+	1	NA	exon (NM_010431, exon 8 of 15)	exon (NM_010431, exon 8 of 15)	-26806	NM_178392	75627	Mm.25937	NM_178392	ENSMUSG00000021113	Snapc1	2700033G17Rik|AU015787	small nuclear RNA activating complex, polypeptide 1	protein-coding
mm_136284.1	chr16	91362762	91362772	-	1	NA	Intergenic	Intergenic	-10016	NM_010509	15976	Mm.6834	NM_010509	ENSMUSG00000022971	Ifnar2	AI747302|Ifnar-2	interferon (alpha and beta) receptor 2	protein-coding
mm_37566.1	chr4	126236585	126236632	-	1	NA	intron (NM_001347198, intron 9 of 17)	intron (NM_001347198, intron 9 of 17)	19711	NM_144941	245877	Mm.266716	NM_144941	ENSMUSG00000028849	Map7d1	AV028413|BC019977|Mtap7d1|Parcc1|Rprc1|mKIAA1187	MAP7 domain containing 1	protein-coding
mm_101949.1	chr11	50238481	50238522	-	1	NA	promoter-TSS (NM_001313968)	promoter-TSS (NM_001313968)	31	NM_001313968	17001	Mm.245151	NM_008521	ENSMUSG00000020377	Ltc4s	-	leukotriene C4 synthase	protein-coding
mm_1577.1	chr1	74281157	74281176	+	1	NA	exon (NM_146110, exon 9 of 11)	exon (NM_146110, exon 9 of 11)	2566	NM_174985	227289	Mm.246587	NM_174985	ENSMUSG00000064272	Gpbar1	BG37|GPCR|GPR131|M-BAR|TGR5	G protein-coupled bile acid receptor 1	protein-coding
mm_128527.1	chr15	54847325	54847331	-	1	NA	intron (NM_001136077, intron 22 of 25)	intron (NM_001136077, intron 22 of 25)	72818	NM_015744	18606	Mm.250256	NM_015744	ENSMUSG00000022425	Enpp2	ATX|E-NPP 2|Npps2|PD-Ialpha|Pdnp2|lysoPLD	ectonucleotide pyrophosphatase/phosphodiesterase 2	protein-coding
mm_41884.1	chr5	105415739	105415849	+	1	NA	promoter-TSS (NM_001033550)	promoter-TSS (NM_001033550)	19	NM_001033550	433926	Mm.439781	NM_001033550	ENSMUSG00000070639	Lrrc8b	R75581|Ta-lrrp|mKIAA0231	leucine rich repeat containing 8 family, member B	protein-coding
mm_61226.1	chr7	64502040	64502048	+	1	NA	promoter-TSS (NM_001291167)	promoter-TSS (NM_001291167)	-94	NM_001291166	11784	Mm.4657	NM_007461	ENSMUSG00000030519	Apba2	X11-like|X11L|XllL|mXllL	amyloid beta (A4) precursor protein-binding, family A, member 2	protein-coding
mm_6292.1	chr1	71028604	71028614	-	1	NA	3' UTR (NM_007525, exon 11 of 11)	3' UTR (NM_007525, exon 11 of 11)	74363	NM_007525	12021	Mm.10764	NM_007525	ENSMUSG00000026196	Bard1	ENSMUSG00000060893|ENSMUSG00000073653	BRCA1 associated RING domain 1	protein-coding
mm_40968.1	chr5	76998202	76998235	+	1	NA	exon (NM_025691, exon 19 of 19)	exon (NM_025691, exon 19 of 19)	-5837	NM_206935	384185	Mm.451858	NM_206935	ENSMUSG00000063820	Arl9	1700110A09Rik	ADP-ribosylation factor-like 9	protein-coding
mm_102270.1	chr11	55394746	55394756	-	1	NA	3' UTR (NM_009242, exon 10 of 10)	3' UTR (NM_009242, exon 10 of 10)	25329	NM_009242	20692	Mm.291442	NM_009242	ENSMUSG00000018593	Sparc	BM-40|ON	secreted acidic cysteine rich glycoprotein	protein-coding
mm_59237.1	chr7	24778218	24778218	+	1	NA	exon (NM_007675, exon 2 of 4)	exon (NM_007675, exon 2 of 4)	1014	NM_007675	26366	Mm.30300	NM_007675	ENSMUSG00000054169	Ceacam10	Bgp3|Cea10	carcinoembryonic antigen-related cell adhesion molecule 10	protein-coding
mm_53775.1	chr6	146171000	146171039	+	1	NA	intron (NM_010586, intron 50 of 55)	ORR1E|LTR|ERVL-MaLR	236872	NM_010656	16651	Mm.49689	NM_010656	ENSMUSG00000030255	Sspn	Krag	sarcospan	protein-coding
mm_129795.1	chr15	82870837	82870842	-	1	NA	intron (NM_001114140, intron 1 of 5)	Lx9|LINE|L1	27622	NR_027799	21378	Mm.417272	NR_027799		Tbrg3	TB-11	transforming growth factor beta regulated gene 3	ncRNA
mm_69091.1	chr7	127017365	127017392	-	1	NA	promoter-TSS (NM_030240)	promoter-TSS (NM_030240)	-26	NM_030240	67278	Mm.345385	NM_030240	ENSMUSG00000030680	Pagr1a	2900092E17Rik|C77040|PA1|PAGR1	PAXIP1 associated glutamate rich protein 1A	protein-coding
mm_135848.1	chr16	59492448	59492449	-	1	NA	TTS (NM_025910)	TTS (NM_025910)	20673	NM_025910	67014	Mm.289150	NM_025910	ENSMUSG00000022724	Mina	1810047J07Rik|2410057H13Rik|3830408E23Rik|AI449204	myc induced nuclear antigen	protein-coding
mm_12312.1	chr2	69135800	69135861	+	1	NA	promoter-TSS (NM_181547)	promoter-TSS (NM_181547)	30	NM_181547	329416	Mm.90047	NM_181547	ENSMUSG00000034738	Nostrin	Daip2|mDaIP2	nitric oxide synthase trafficker	protein-coding
mm_147948.1	chr18	66476556	66476561	-	1	NA	Intergenic	Intergenic	17954	NM_021451	58801	Mm.271878	NM_021451	ENSMUSG00000024521	Pmaip1	Noxa	phorbol-12-myristate-13-acetate-induced protein 1	protein-coding
mm_24945.1	chr3	96596702	96596712	+	1	NA	promoter-TSS (NM_001024851)	promoter-TSS (NM_001024851)	71	NM_001024851	545554	Mm.267664	NM_001024851	ENSMUSG00000049097	Ankrd34a	AW060394|Ankrd34	ankyrin repeat domain 34A	protein-coding
mm_135164.1	chr16	35871373	35871388	-	1	NA	promoter-TSS (NM_001039530)	promoter-TSS (NM_001039530)	2	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_95645.1	chr11	53723733	53723747	+	1	NA	exon (NM_010558, exon 3 of 4)	exon (NM_010558, exon 3 of 4)	2946	NM_010558	16191	Mm.4461	NM_010558	ENSMUSG00000036117	Il5	Il-5	interleukin 5	protein-coding
mm_44219.1	chr5	4758000	4758022	-	1	NA	5' UTR (NM_021457, exon 1 of 1)	5' UTR (NM_021457, exon 1 of 1)	205	NM_021457	14362	Mm.246003	NM_021457	ENSMUSG00000044674	Fzd1	AW227548|FZ-1|Fz1	frizzled class receptor 1	protein-coding
mm_149533.1	chr19	12464903	12464906	+	1	NA	3' UTR (NM_010821, exon 2 of 2)	3' UTR (NM_010821, exon 2 of 2)	4125	NM_010821	17476	Mm.3999	NM_010821	ENSMUSG00000046805	Mpeg1	MPS1|Mpg-1	macrophage expressed gene 1	protein-coding
mm_126386.1	chr15	80173643	80173683	+	1	NA	promoter-TSS (NM_010795)	promoter-TSS (NM_010795)	-58	NM_010795	17309	Mm.299693	NM_010795	ENSMUSG00000042428	Mgat3	1110038J12Rik|AI848272|GnT-III	mannoside acetylglucosaminyltransferase 3	protein-coding
mm_102580.1	chr11	61761584	61761590	-	1	NA	intron (NM_001164243, intron 1 of 10)	(A)n|Simple_repeat|Simple_repeat	501	NM_144806	212627	Mm.27703	NM_144806	ENSMUSG00000020528	Prpsap2	A230054F23Rik	phosphoribosyl pyrophosphate synthetase-associated protein 2	protein-coding
mm_163641.1	chr13	61804273	61804308	+	1	NA	Intergenic	Intergenic	32710	NR_028430	432812	Mm.317358	NR_028430		BC052688	-	cDNA sequence BC052688	pseudo
mm_16268.1	chr2	173659808	173659816	+	1	NA	promoter-TSS (NM_024436)	promoter-TSS (NM_024436)	-33	NM_024436	19334	Mm.275304	NM_024436	ENSMUSG00000027519	Rab22a	3732413A17Rik|AI662177|AW319644|AW550514|E130120E14Rik|Rab22	RAB22A, member RAS oncogene family	protein-coding
mm_21053.1	chr2	152627267	152627281	-	1	NA	intron (NM_009047, intron 1 of 4)	CpG	266	NM_009047	19700	Mm.8752	NM_009047	ENSMUSG00000000359	Rem1	E030011C07Rik|Ras|Rem	rad and gem related GTP binding protein 1	protein-coding
mm_74290.1	chr8	125910427	125910469	+	1	NA	promoter-TSS (NM_145608)	promoter-TSS (NM_145608)	-2	NM_145608	234878	Mm.216458	NM_145608	ENSMUSG00000031853	Map3k21	Mlk4|mKIAA1804	mitogen-activated protein kinase kinase kinase 21	protein-coding
mm_64169.1	chr7	141447860	141447903	+	1	NA	promoter-TSS (NR_034049)	promoter-TSS (NR_034049)	231	NM_026020	67186	Mm.380435	NM_026020	ENSMUSG00000025508	Rplp2	2700049I22Rik	ribosomal protein, large P2	protein-coding
mm_68480.1	chr7	110926680	110926705	-	1	NA	intron (NM_194464, intron 4 of 20)	MLT1K|LTR|ERVL-MaLR	19495	NM_010826	17540	Mm.250023	NM_010826	ENSMUSG00000005611	Mrvi1	BB115629|Irag|Ris1	MRV integration site 1	protein-coding
mm_133730.1	chr16	93798856	93798904	+	1	NA	intron (NM_027293, intron 27 of 36)	intron (NM_027293, intron 27 of 36)	-33241	NM_001045529	338467	Mm.287329	NM_001045529	ENSMUSG00000039456	Morc3	1110051N18Rik|AI452146|BF318192|D16Jhu32e|NXP2|Zcwcc3	microrchidia 3	protein-coding
mm_152172.1	chr19	7341572	7341647	-	1	NA	5' UTR (NM_001080388, exon 1 of 17)	5' UTR (NM_001080388, exon 1 of 17)	251	NM_001080389	13728	Mm.258986	NM_007928	ENSMUSG00000024969	Mark2	EMK-1|Emk|Par-1|Par-1b	MAP/microtubule affinity regulating kinase 2	protein-coding
mm_43165.1	chr5	127241786	127241798	+	1	NA	promoter-TSS (NM_175432)	promoter-TSS (NM_175432)	-34	NM_175432	208213	Mm.444235	NM_175432	ENSMUSG00000034324	Tmem132c	2810482M11Rik|3230401P16|4632425D07Rik	transmembrane protein 132C	protein-coding
mm_49238.1	chr6	17287035	17287047	+	1	NA	exon (NM_016900, exon 3 of 3)	exon (NM_016900, exon 3 of 3)	5856	NM_016900	12390	Mm.396075	NM_016900	ENSMUSG00000000058	Cav2	AI447843	caveolin 2	protein-coding
mm_109555.1	chr12	111758849	111758915	+	1	NA	promoter-TSS (NM_001025363)	promoter-TSS (NM_001025363)	14	NM_001025361	16593	Mm.278357	NM_008450	ENSMUSG00000021288	Klc1	AI874768|Kns2	kinesin light chain 1	protein-coding
mm_71317.1	chr8	43703476	43703493	+	1	NA	Intergenic	Intergenic	-3993	NM_001079931	384814	Mm.491652	NM_001079931		Gm5347	EG384814	predicted gene 5347	protein-coding
mm_75125.1	chr8	34890618	34890667	-	1	NA	intron (NM_175091, intron 3 of 26)	intron (NM_175091, intron 3 of 26)	75048	NM_175091	21951	Mm.88364	NM_175091	ENSMUSG00000031529	Tnks	4930554K12Rik|AI662855|ARTD5|C86528|D130072O21Rik|TANK1|mTNKS1	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase	protein-coding
mm_94173.1	chr10	128821577	128821632	-	1	NA	promoter-TSS (NM_024180)	promoter-TSS (NM_024180)	27	NM_024180	66844	Mm.235562	NM_024180	ENSMUSG00000025353	Ormdl2	0610012C09Rik	ORM1-like 2 (S. cerevisiae)	protein-coding
mm_38181.1	chr4	135272755	135272773	-	1	NA	promoter-TSS (NM_013885)	promoter-TSS (NM_013885)	-4	NM_013885	29876	Mm.257765	NM_013885	ENSMUSG00000037242	Clic4	D0Jmb3|TU-74|mc3s5|mtCLIC	chloride intracellular channel 4 (mitochondrial)	protein-coding
mm_107934.1	chr12	71355436	71355454	+	1	NA	Intergenic	Intergenic	28763	NR_136902	67348	Mm.54261	NR_136902	ENSMUSG00000100668	1700083H02Rik	100041190|Gm3190	RIKEN cDNA 1700083H02 gene	ncRNA
mm_4329.1	chr1	171854195	171854220	+	1	NA	3' UTR (NM_001252472, exon 3 of 3)	3' UTR (NM_001252472, exon 3 of 3)	14510	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_169341.1	chr14	13694588	13694591	+	1	NA	Intergenic	L1Md_T|LINE|L1	23713	NM_177624	218739	Mm.39919	NM_177624	ENSMUSG00000044772	Sntn	A430083B19Rik	sentan, cilia apical structure protein	protein-coding
mm_88122.1	chr10	69219420	69219436	+	1	NA	intron (NM_001252637, intron 2 of 10)	intron (NM_001252637, intron 2 of 10)	6234	NM_001252638	69288	Mm.26659	NM_001081347	ENSMUSG00000019944	Rhobtb1	1700008H16Rik|3110048G13Rik|AI173445|AI573858|AV350930	Rho-related BTB domain containing 1	protein-coding
mm_68153.1	chr7	102250467	102250479	-	1	NA	promoter-TSS (NM_019566)	promoter-TSS (NM_019566)	-355	NM_019566	56212	Mm.259795	NM_019566	ENSMUSG00000073982	Rhog	2810426G09Rik|Arhg|Sid10750	ras homolog family member G	protein-coding
mm_40702.1	chr5	65861162	65861172	+	1	NA	Intergenic	Intergenic	-2402	NM_001081105	74734	Mm.20323	NM_001081105	ENSMUSG00000029204	Rhoh	5830400A04Rik|AU019774|Arhh	ras homolog family member H	protein-coding
mm_51008.1	chr6	64734644	64734660	+	1	NA	Intergenic	CpG	5506	NM_007500	11921	Mm.57229	NM_007500	ENSMUSG00000073043	Atoh1	Hath1|MATH-1|Math1|bHLHa14	atonal bHLH transcription factor 1	protein-coding
mm_150582.1	chr19	40659786	40659802	+	1	NA	promoter-TSS (NM_009848)	promoter-TSS (NM_009848)	24	NM_009848	12495	Mm.2824	NM_009848	ENSMUSG00000048120	Entpd1	2610206B08Rik|AA408691|Cd39|NTPDase-1	ectonucleoside triphosphate diphosphohydrolase 1	protein-coding
mm_133319.1	chr16	77670246	77670248	+	1	NA	Intergenic	Intergenic	23974	NR_029540	723952		NR_029540	ENSMUSG00000065472	Mir125b-2	Mirn125b-2|mir-125b-2	microRNA 125b-2	ncRNA
mm_109148.1	chr12	107183549	107183566	+	1	NA	Intergenic	Lx8|LINE|L1	-467233	NR_015512	71033	Mm.159404	NR_015512	ENSMUSG00000085820	4933406K04Rik	4930426M03Rik|4930485I22Rik|4933427G14Rik	RIKEN cDNA 4933406K04 gene	ncRNA
mm_66032.1	chr7	30626128	30626139	-	1	NA	promoter-TSS (NM_025628)	promoter-TSS (NM_025628)	18	NM_025628	110323	Mm.400	NM_025628	ENSMUSG00000036751	Cox6b1	2010000G05Rik|Cox6b	cytochrome c oxidase, subunit VIb polypeptide 1	protein-coding
mm_144167.1	chr18	6490135	6490165	+	1	NA	TTS (NR_035446)	TTS (NR_035446)	496	NR_035446	100316773		NR_035446	ENSMUSG00000084514	Mir1893	Mirn1893|mmu-mir-1893	microRNA 1893	ncRNA
mm_134536.1	chr16	19701325	19701335	-	1	NA	exon (NM_177356, exon 2 of 6)	exon (NM_177356, exon 2 of 6)	5035	NM_177356	239739	Mm.258059	NM_177356	ENSMUSG00000041247	Lamp3	1200002D17Rik|Cd208|DC-LAMP|DCLAMP|LAMP|TSC403	lysosomal-associated membrane protein 3	protein-coding
mm_100130.1	chr11	115974551	115974555	+	1	NA	promoter-TSS (NM_133663)	promoter-TSS (NM_133663)	-172	NM_001005608	192897	Mm.213873	NM_133663	ENSMUSG00000020758	Itgb4	AA407042|C230078O20|CD104	integrin beta 4	protein-coding
mm_154602.1	chrX	7632755	7632790	+	1	NA	exon (NM_019582, exon 44 of 48)	exon (NM_019582, exon 44 of 48)	-5808	NM_009305	20977	Mm.223674	NM_009305	ENSMUSG00000031144	Syp	A230093K24Rik|AI848995|Syn|p38	synaptophysin	protein-coding
mm_31318.1	chr4	46138713	46138794	+	1	NA	promoter-TSS (NM_173033)	promoter-TSS (NM_173033)	242	NM_001033201	433702	Mm.389536	NM_001033201	ENSMUSG00000028330	Ncbp1	AU014645|AW538051|CBP80	nuclear cap binding protein subunit 1	protein-coding
mm_73302.1	chr8	105131852	105131856	+	1	NA	promoter-TSS (NM_146213)	promoter-TSS (NM_146213)	54	NM_146213	234677	Mm.120297	NM_146213	ENSMUSG00000060560	Ces4a	Ces8	carboxylesterase 4A	protein-coding
mm_111681.1	chr12	103382592	103382592	-	1	NA	intron (NR_033587, intron 1 of 5)	ORR1A2|LTR|ERVL-MaLR	5698	NR_033587	68149	Mm.127378	NM_026580	ENSMUSG00000021203	Otub2	2010015L18Rik|4930586I02Rik|AI413508|AW557219|OTB2|OTU2	OTU domain, ubiquitin aldehyde binding 2	protein-coding
mm_2816.1	chr1	130878347	130878359	+	1	NA	intron (NM_026976, intron 6 of 7)	CpG	9058	NM_053095	93672	Mm.196691	NM_053095	ENSMUSG00000026420	Il24	FISP|Mda-7|Mda7|St16	interleukin 24	protein-coding
mm_98002.1	chr11	84173497	84173525	+	1	NA	Intergenic	Intergenic	-6035	NM_001037932	628813	Mm.390389	NM_001037932	ENSMUSG00000051452	Gm11437	AI463690|OTTMUSG00000000997	predicted gene 11437	protein-coding
mm_127855.1	chr15	8347472	8347476	-	1	NA	intron (NM_201232, intron 10 of 45)	MTE2b|LTR|ERVL-MaLR	96989	NM_027707	71175	Mm.240329	NM_027707	ENSMUSG00000022141	Nipbl	Idn3	Nipped-B homolog (Drosophila)	protein-coding
mm_127274.1	chr15	99725699	99725712	+	1	NA	promoter-TSS (NM_183256)	promoter-TSS (NM_183256)	87	NM_183256	66379	Mm.5265	NM_183256	ENSMUSG00000023020	Cox14	2310016M24Rik|AA959804	cytochrome c oxidase assembly protein 14	protein-coding
mm_160000.1	chr6	119449190	119449190	-	1	NA	intron (NM_009525, intron 1 of 4)	intron (NM_009525, intron 1 of 4)	196	NM_001271757	22419	Mm.321818	NM_009525	ENSMUSG00000030170	Wnt5b	AW545702|Wnt-5b	wingless-type MMTV integration site family, member 5B	protein-coding
mm_49013.1	chr6	4758500	4758510	+	1	NA	3' UTR (NM_130877, exon 2 of 2)	3' UTR (NM_130877, exon 2 of 2)	11199	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_41968.1	chr5	107333119	107333134	+	1	NA	intron (NM_001079873, intron 1 of 6)	intron (NM_001079873, intron 1 of 6)	1932	NM_054054	114642	Mm.182836	NM_054054	ENSMUSG00000029279	Brdt	7420412D09Rik|Brd6|Fsrg3	bromodomain, testis-specific	protein-coding
mm_155875.1	chrX	101447917	101447938	+	1	NA	3' UTR (NM_001252518, exon 12 of 12)	3' UTR (NM_001252518, exon 12 of 12)	-1182	NM_013712	26549	Mm.46232	NM_013712	ENSMUSG00000031312	Itgb1bp2	Chordc3	integrin beta 1 binding protein 2	protein-coding
mm_37716.1	chr4	129542675	129542707	-	1	NA	promoter-TSS (NM_008228)	promoter-TSS (NM_008228)	-45	NM_008228	433759	Mm.202504	NM_008228	ENSMUSG00000028800	Hdac1	HD1|Hdac1-ps|MommeD5|RPD3	histone deacetylase 1	protein-coding
mm_73298.1	chr8	105083620	105083622	+	1	NA	promoter-TSS (NM_001159415)	promoter-TSS (NM_001159415)	-134	NM_144511	13909	Mm.482444	NM_144511	ENSMUSG00000062181	Ces3b	Ces31L|Ces3L|EG13909|ES31L|Es31|Gm4738	carboxylesterase 3B	protein-coding
mm_130060.1	chr15	89181119	89181146	-	1	NA	promoter-TSS (NM_001284506)	promoter-TSS (NM_001284506)	-344	NM_138749	140570	Mm.267514	NM_138749	ENSMUSG00000036606	Plxnb2	Debt|plexin-B2	plexin B2	protein-coding
mm_46479.1	chr5	105131868	105131882	-	1	NA	intron (NM_008620, intron 3 of 10)	intron (NM_008620, intron 3 of 10)	7677	NM_008620	17472	Mm.440525	NM_008620	ENSMUSG00000079363	Gbp4	AW228052|Mag-2|Mpa-2|Mpa2	guanylate binding protein 4	protein-coding
mm_21762.1	chr2	164840361	164840371	-	1	NA	exon (NM_011125, exon 14 of 16)	exon (NM_011125, exon 14 of 16)	6593	NM_008906	19025	Mm.359633	NM_008906	ENSMUSG00000017760	Ctsa	AU019505|PPCA|Ppgb	cathepsin A	protein-coding
mm_98064.1	chr11	85832840	85832850	+	1	NA	promoter-TSS (NR_077059)	promoter-TSS (NR_077059)	230	NM_009324	21385	Mm.287052	NM_009324	ENSMUSG00000000093	Tbx2	-	T-box 2	protein-coding
mm_89774.1	chr10	100544392	100544433	+	1	NA	intron (NM_146009, intron 36 of 52)	intron (NM_146009, intron 36 of 52)	44847	NM_175128	68281	Mm.268474	NM_175128	ENSMUSG00000046567	4930430F08Rik	4930571E09Rik|A730088G13Rik|AW551239|C430008C19Rik	RIKEN cDNA 4930430F08 gene	protein-coding
mm_118614.1	chr14	21032455	21032465	+	1	NA	3' UTR (NM_009502, exon 21 of 21)	3' UTR (NM_009502, exon 21 of 21)	19982	NM_018829	55946	Mm.376269	NM_018829	ENSMUSG00000021824	Ap3m1	1200013D09Rik|C78982|R75378	adaptor-related protein complex 3, mu 1 subunit	protein-coding
mm_21409.1	chr2	158117789	158117809	-	1	NA	3' UTR (NM_009373, exon 13 of 13)	3' UTR (NM_009373, exon 13 of 13)	-26002	NR_040609	72340	Mm.443395	NR_040609	ENSMUSG00000100860	2010009K17Rik	-	RIKEN cDNA 2010009K17 gene	ncRNA
mm_31689.1	chr4	62360186	62360227	+	1	NA	promoter-TSS (NM_175090)	promoter-TSS (NM_175090)	342	NM_001045528	338355	Mm.357792	NM_001045528	ENSMUSG00000066151	Fkbp15	BB131447|C430014M02Rik|FKBO133|FKBP-133|FKBP-15|FKBP133|mKIAA0674	FK506 binding protein 15	protein-coding
mm_125684.1	chr15	66798733	66798742	+	1	NA	intron (NM_009192, intron 3 of 8)	intron (NM_009192, intron 3 of 8)	33092	NM_001029841	20491	Mm.7601	NM_009192	ENSMUSG00000022372	Sla	Slap|Slap-1	src-like adaptor	protein-coding
mm_55663.1	chr6	72437073	72437086	-	1	NA	exon (NM_145569, exon 3 of 9)	exon (NM_145569, exon 3 of 9)	-1604	NR_046011	78108	Mm.440743	NR_046011	ENSMUSG00000108591	Particl	4930414L22Rik|AI449819	promoter of Mat2a antisense radiation induced circulating long non-coding RNA	ncRNA
mm_96634.1	chr11	69324146	69324156	+	1	NA	promoter-TSS (NM_172560)	promoter-TSS (NM_172560)	165	NM_001024206	245828	Mm.28073	NM_001024206	ENSMUSG00000049299	Trappc1	BET5|D11Ertd172e|MUM2	trafficking protein particle complex 1	protein-coding
mm_151117.1	chr19	47864617	47864638	+	1	NA	promoter-TSS (NM_030051)	promoter-TSS (NM_030051)	-918	NM_030051	68214	Mm.63791	NM_026619	ENSMUSG00000025069	Gsto2	1700020F09Rik|4930425C18Rik|GSTO 2-2	glutathione S-transferase omega 2	protein-coding
mm_167333.1	chr8	70758257	70758267	+	1	NA	TTS (NM_183170)	TTS (NM_183170)	2659	NM_183170	234384	Mm.213010	NM_183170	ENSMUSG00000035559	Mpv17l2	Fksg24	MPV17 mitochondrial membrane protein-like 2	protein-coding
mm_154716.1	chrX	9199866	9199907	+	1	NA	promoter-TSS (NM_173414)	promoter-TSS (NM_173414)	-87	NM_173414	236285	Mm.245119	NM_173414	ENSMUSG00000047344	Lancl3	6030463G20Rik	LanC lantibiotic synthetase component C-like 3 (bacterial)	protein-coding
mm_106159.1	chr11	116626869	116626875	-	1	NA	5' UTR (NM_172572, exon 1 of 19)	5' UTR (NM_172572, exon 1 of 19)	147	NM_172572	217344	Mm.89695	NM_172572	ENSMUSG00000020806	Rhbdf2	4732465I17Rik|Rhbdl6|cub	rhomboid 5 homolog 2	protein-coding
mm_86868.1	chr10	21994027	21994045	+	1	NA	promoter-TSS (NM_011361)	promoter-TSS (NM_011361)	146	NM_001161850	20393	Mm.28405	NM_011361	ENSMUSG00000019970	Sgk1	Sgk	serum/glucocorticoid regulated kinase 1	protein-coding
mm_135424.1	chr16	45275735	45275743	-	1	NA	Intergenic	Intergenic	51402	NM_177584	208154	Mm.38199	NM_177584	ENSMUSG00000052013	Btla	A630002H24	B and T lymphocyte associated	protein-coding
mm_127582.1	chr15	102326173	102326181	+	1	NA	promoter-TSS (NM_027044)	promoter-TSS (NM_027044)	61	NM_027044	56612	Mm.158264	NM_020031	ENSMUSG00000001289	Pfdn5	1190001O17Rik|1700010A06Rik|D15Ertd697e|Eig1|MM-1	prefoldin 5	protein-coding
mm_122752.1	chr14	54197879	54197885	-	1	NA	Intergenic	Intergenic	56047	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_116360.1	chr13	40730097	40730100	-	1	NA	5' UTR (NM_001122948, exon 1 of 7)	5' UTR (NM_001122948, exon 1 of 7)	359	NM_001122948	21418	Mm.85544	NM_011547	ENSMUSG00000021359	Tfap2a	AP-2|AP2alpha|Ap-2 (a)|Ap2|Ap2tf|Tcfap2a	transcription factor AP-2, alpha	protein-coding
mm_66572.1	chr7	45325324	45325343	-	1	NA	non-coding (NR_110499, exon 1 of 1)	non-coding (NR_110499, exon 1 of 1)	375	NR_110499	100040970	Mm.289810	NR_110499	ENSMUSG00000046721	Rpl14-ps1	ENSMUSG00000046721|Gm9811	ribosomal protein L14, pseudogene 1	pseudo
mm_63078.1	chr7	122219651	122219673	+	1	NA	5' UTR (NM_027363, exon 1 of 7)	5' UTR (NM_027363, exon 1 of 7)	166	NM_027363	70261	Mm.96997	NM_027363	ENSMUSG00000030865	Chp2	2010110P09Rik|Cbhp2	calcineurin-like EF hand protein 2	protein-coding
mm_86891.1	chr10	22301780	22301803	+	1	NA	intron (NM_009018, intron 5 of 5)	ORR1C1|LTR|ERVL-MaLR	-4929	NR_015465	606736	Mm.387042	NR_015465	ENSMUSG00000097352	C920009B18Rik	-	RIKEN cDNA C920009B18 gene	ncRNA
mm_47411.1	chr5	123135508	123135530	-	1	NA	Intergenic	CpG	-2890	NM_175092	23912	Mm.253876	NM_175092	ENSMUSG00000029449	Rhof	AI845056|AV026554|Arhf|Ifld1|Rif	ras homolog family member F (in filopodia)	protein-coding
mm_10179.1	chr2	4700222	4700232	+	1	NA	Intergenic	Intergenic	-17604	NM_001190400	209645	Mm.149539	NM_178663	ENSMUSG00000048186	Bend7	1110017O21Rik|E130319B15Rik	BEN domain containing 7	protein-coding
mm_149986.1	chr19	29251582	29251665	+	1	NA	promoter-TSS (NM_008413)	promoter-TSS (NM_008413)	-180	NM_001048177	16452	Mm.275839	NM_008413	ENSMUSG00000024789	Jak2	Fd17	Janus kinase 2	protein-coding
mm_136266.1	chr16	91043903	91043914	-	1	NA	intron (NM_026110, intron 1 of 17)	CpG	471	NM_026110	67367	Mm.347	NM_026110	ENSMUSG00000022974	Paxbp1	1810007M14Rik|C21orf66|Gcfc|Gcfc1|Pax3/7bp	PAX3 and PAX7 binding protein 1	protein-coding
mm_163898.1	chr14	27745649	27745650	+	1	NA	intron (NM_177814, intron 2 of 15)	L1MCa|LINE|L1	123242	NM_177814	238988	Mm.318004	NM_177814	ENSMUSG00000040640	Erc2	6430531D06|CAST|CAST1/ERC2|D14Ertd171e|ELKS2alpha	ELKS/RAB6-interacting/CAST family member 2	protein-coding
mm_120539.1	chr14	67234732	67234736	+	1	NA	intron (NM_010095, intron 1 of 16)	intron (NM_010095, intron 1 of 16)	1442	NM_001276387	13592	Mm.319947	NM_010095	ENSMUSG00000022053	Ebf2	D14Ggc1e|EBF-2|Mmot1|O/E-3|OE-3	early B cell factor 2	protein-coding
mm_105654.1	chr11	107213961	107213965	-	1	NA	intron (NM_145823, intron 9 of 9)	intron (NM_145823, intron 9 of 9)	-24582	NM_001161329	68979	Mm.294617	NM_133702	ENSMUSG00000018433	Nol11	1500002M01Rik|AU015220|AU019874	nucleolar protein 11	protein-coding
mm_37001.1	chr4	110351891	110351905	-	1	NA	promoter-TSS (NM_001163397)	promoter-TSS (NM_001163397)	13	NM_001163397	15572	Mm.3970	NM_010488	ENSMUSG00000028546	Elavl4	Elav|Hud|PNEM	ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4 (Hu antigen D)	protein-coding
mm_51412.1	chr6	78380793	78380818	+	1	NA	promoter-TSS (NM_011259)	promoter-TSS (NM_011259)	96	NM_011259	19694	Mm.2552	NM_011259	ENSMUSG00000079516	Reg3a	AV063448	regenerating islet-derived 3 alpha	protein-coding
mm_24692.1	chr3	95015722	95015751	+	1	NA	promoter-TSS (NM_030074)	promoter-TSS (NM_030074)	-498	NM_030074	78266	Mm.389478	NM_030074	ENSMUSG00000019338	Zfp687	4931408L03Rik|Znf687|mKIAA1441	zinc finger protein 687	protein-coding
mm_40830.1	chr5	72914308	72914349	+	1	NA	promoter-TSS (NM_001113423)	promoter-TSS (NM_001113423)	-34	NM_001113423	75991	Mm.121285	NM_153567	ENSMUSG00000036087	Slain2	5033405K12Rik|8030444K12Rik|AI596370	SLAIN motif family, member 2	protein-coding
mm_86950.1	chr10	24902118	24902167	+	1	NA	exon (NM_001166416, exon 20 of 30)	exon (NM_001166416, exon 20 of 30)	-8522	NR_105870	102465545		NR_105870	ENSMUSG00000099181	Mir6905	Gm27879|mmu-mir-6905	microRNA 6905	ncRNA
mm_166881.1	chr7	25517678	25517687	-	1	NA	3' UTR (NM_001113369, exon 7 of 7)	3' UTR (NM_001113369, exon 7 of 7)	22322	NM_001113368	26367	Mm.439731	NM_007543	ENSMUSG00000054385	Ceacam2	AI267129|Bgp2|Ceacam2-L	carcinoembryonic antigen-related cell adhesion molecule 2	protein-coding
mm_118883.1	chr14	26331069	26331072	+	1	NA	Intergenic	Intergenic	-26477	NR_038005	71106	Mm.158564	NR_038005	ENSMUSG00000021874	4933413J09Rik	GCSE	RIKEN cDNA 4933413J09 gene	ncRNA
mm_25967.1	chr3	132766572	132766574	+	1	NA	intron (NM_001163455, intron 22 of 25)	intron (NM_001163455, intron 22 of 25)	82429	NM_001163455	271981	Mm.257864	NM_173032	ENSMUSG00000028030	Tbck	1700120J03Rik|9430001M19|A630047E20Rik|C030007I09Rik|Tbckl	TBC1 domain containing kinase	protein-coding
mm_52794.1	chr6	121270471	121270487	+	1	NA	exon (NM_011909, exon 11 of 11)	exon (NM_011909, exon 11 of 11)	24573	NM_011909	24110	Mm.326911	NM_011909	ENSMUSG00000030107	Usp18	1110058H21Rik|AW047653|UBP43|Ubp15	ubiquitin specific peptidase 18	protein-coding
mm_71116.1	chr8	36094709	36094720	+	1	NA	promoter-TSS (NM_172911)	promoter-TSS (NM_172911)	-114	NM_172911	244418	Mm.244971	NM_172911	ENSMUSG00000050271	Prag1	9830148H23|D8Ertd82e|NACK|Sgk223|mFLJ00269	PEAK1 related kinase activating pseudokinase 1	protein-coding
mm_10328.1	chr2	11339542	11339546	+	1	NA	promoter-TSS (NR_040369)	promoter-TSS (NR_040369)	55	NR_040369	100503147	Mm.91961	NR_040369	ENSMUSG00000086006	Gm13293	OTTMUSG00000011311	predicted gene 13293	ncRNA
mm_143771.1	chr17	81670162	81670261	-	1	NA	intron (NR_104580, intron 1 of 8)	CpG	68176	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_100070.1	chr11	115420060	115420119	+	1	NA	promoter-TSS (NM_027862)	promoter-TSS (NM_027862)	-37	NM_183285	70382	Mm.276299	NM_183285	ENSMUSG00000016940	Kctd2	2310012I15Rik	potassium channel tetramerisation domain containing 2	protein-coding
mm_161823.1	chr17	72604197	72604197	-	1	NA	5' UTR (NM_007439, exon 1 of 29)	5' UTR (NM_007439, exon 1 of 29)	110	NM_007439	11682	Mm.311854	NM_007439	ENSMUSG00000055471	Alk	CD246|Tcrz	anaplastic lymphoma kinase	protein-coding
mm_142612.1	chr17	46857667	46857678	-	1	NA	Intergenic	RLTR20A4|LTR|ERVK	-26259	NM_001100452	210982	Mm.37642	NM_001100452	ENSMUSG00000036568	Gltscr1l	mKIAA0240	GLTSCR1-like	protein-coding
mm_107581.1	chr12	44525712	44525730	+	1	NA	intron (NM_001146031, intron 3 of 27)	intron (NM_001146031, intron 3 of 27)	196836	NM_001146031	319504	Mm.208439	NM_176930	ENSMUSG00000020598	Nrcam	Bravo|C030017F07Rik|C130076O07Rik|mKIAA0343	neuronal cell adhesion molecule	protein-coding
mm_152631.1	chr19	12501479	12501505	-	1	NA	5' UTR (NM_172442, exon 1 of 9)	5' UTR (NM_172442, exon 1 of 9)	504	NM_172442	207521	Mm.247695	NM_172442	ENSMUSG00000039982	Dtx4	AI449438|BC044798|D930042H13|RNF155	deltex 4, E3 ubiquitin ligase	protein-coding
mm_152944.1	chr19	28963864	28963893	-	1	NA	promoter-TSS (NM_028922)	promoter-TSS (NM_028922)	-42	NM_028922	74411	Mm.441887	NM_028922	ENSMUSG00000040105	Plpp6	4932443D16Rik|Ppapdc2	phospholipid phosphatase 6	protein-coding
mm_55461.1	chr6	67534731	67534745	-	1	NA	3' UTR (NM_020047, exon 1 of 1)	3' UTR (NM_020047, exon 1 of 1)	1084	NM_020047	56753	Mm.439913	NM_020047	ENSMUSG00000051397	Tacstd2	C80403|EGP-1|GA733-1|Ly97|TROP2	tumor-associated calcium signal transducer 2	protein-coding
mm_94192.1	chr10	128999346	128999351	-	1	NA	Intergenic	RLTR48B|LTR|ERV1	9434	NM_146861	18373	Mm.377111	NM_146861	ENSMUSG00000069430	Olfr9	MOR269-3	olfactory receptor 9	protein-coding
mm_127983.1	chr15	12514676	12514684	-	1	NA	intron (NM_001081064, intron 1 of 23)	L2c|LINE|L2	77876	NM_001081064	68070	Mm.423205	NM_001081064	ENSMUSG00000022197	Pdzd2	4930537L06Rik|A930022H17Rik|Gm21706|Gm82|Pdzk3|mKIAA0300	PDZ domain containing 2	protein-coding
mm_122317.1	chr14	36919552	36919562	-	1	NA	promoter-TSS (NM_001347503)	promoter-TSS (NM_001347503)	-22	NM_001347503	72972	Mm.27621	NM_027045	ENSMUSG00000058690	Ccser2	1700012P13Rik|2900054P12Rik|AI035535|AW108503|Fam190b|Gcap14	coiled-coil serine rich 2	protein-coding
mm_88084.1	chr10	68137783	68137796	+	1	NA	intron (NM_023598, intron 4 of 9)	intron (NM_023598, intron 4 of 9)	140937	NM_023598	71371	Mm.440357	NM_023598	ENSMUSG00000019947	Arid5b	4930580B11|5430435G07Rik|AI467247|Desrt|Mrf2|Mrf2alpha|Mrf2beta	AT rich interactive domain 5B (MRF1-like)	protein-coding
mm_152107.1	chr19	6934192	6934218	-	1	NA	intron (NM_008431, intron 1 of 6)	CpG	310	NM_008431	16528	Mm.12894	NM_008431	ENSMUSG00000024957	Kcnk4	MLZ-622|TRAAK|TRAAKt|Tex40	potassium channel, subfamily K, member 4	protein-coding
mm_114961.1	chr13	97071564	97071626	+	1	NA	promoter-TSS (NM_001100458)	promoter-TSS (NM_001100458)	-48	NM_001100458	320557	Mm.458280	NM_001100458	ENSMUSG00000041817	Fam169a	B230112C05Rik|SLAP75	family with sequence similarity 169, member A	protein-coding
mm_65245.1	chr7	19831872	19831900	-	1	NA	Intergenic	Intergenic	-9131	NM_033601	12051	Mm.439658	NM_033601	ENSMUSG00000053175	Bcl3	AI528691|Bcl-3	B cell leukemia/lymphoma 3	protein-coding
mm_161012.1	chr11	118911384	118911384	-	1	NA	intron (NM_001285437, intron 1 of 13)	intron (NM_001285437, intron 1 of 13)	213	NM_001285437	52897	Mm.341103	NM_001024931	ENSMUSG00000025576	Rbfox3	Fox-3|Hrnbp3|NeuN|Neuna60	RNA binding protein, fox-1 homolog (C. elegans) 3	protein-coding
mm_156581.1	chrX	152026552	152026567	+	1	NA	exon (NM_019710, exon 5 of 25)	exon (NM_019710, exon 5 of 25)	10131	NM_019710	24061	Mm.482095	NM_019710	ENSMUSG00000041133	Smc1a	5830426I24Rik|SMC-1A|Sb1.8|Smc1|Smc1alpha|Smc1l1|Smcb|mKIAA0178	structural maintenance of chromosomes 1A	protein-coding
mm_79332.1	chr9	53341083	53341101	+	1	NA	intron (NM_176846, intron 3 of 5)	intron (NM_176846, intron 3 of 5)	39422	NM_176846	320051	Mm.277540	NM_176846	ENSMUSG00000034584	Exph5	AC079869.22gm5|B130009M24Rik|E030050P12|Kiaa0624|Slac2b|slac2-b	exophilin 5	protein-coding
mm_107383.1	chr12	33147701	33147716	+	1	NA	promoter-TSS (NM_028139)	promoter-TSS (NM_028139)	22	NM_028139	380753	Mm.41540	NM_028139	ENSMUSG00000020564	Atxn7l1	2810423G08Rik|Atxn7l4	ataxin 7-like 1	protein-coding
mm_15242.1	chr2	154657138	154657161	+	1	NA	5' UTR (NM_029362, exon 1 of 5)	5' UTR (NM_029362, exon 1 of 5)	123	NM_029362	75608	Mm.262480	NM_029362	ENSMUSG00000038467	Chmp4b	2010012F05Rik|C76846|Snf7-2	charged multivesicular body protein 4B	protein-coding
mm_114054.1	chr13	54366437	54366437	+	1	NA	Intergenic	Intergenic	-4912	NM_009946	12890	Mm.268902	NM_009946	ENSMUSG00000025867	Cplx2	921-L|AI413745|AW492120	complexin 2	protein-coding
mm_95440.1	chr11	50225476	50225492	+	1	NA	5' UTR (NM_145926, exon 1 of 15)	5' UTR (NM_145926, exon 1 of 15)	149	NM_145926	103534	Mm.86759	NM_145926	ENSMUSG00000036620	Mgat4b	AA407995|GnTIVb	mannoside acetylglucosaminyltransferase 4, isoenzyme B	protein-coding
mm_25759.1	chr3	123691015	123691031	+	1	NA	promoter-TSS (NR_121616)	promoter-TSS (NR_121616)	-171	NR_121616	83398	Mm.443908	NM_031186	ENSMUSG00000027977	Ndst3	4921531K01Rik|4930511P15Rik|N-HSST 3|NDST-3	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 3	protein-coding
mm_165010.1	chr19	25407047	25407073	+	1	NA	intron (NM_181404, intron 4 of 13)	intron (NM_181404, intron 4 of 13)	-98646	NM_015826	50796	Mm.391208	NM_015826	ENSMUSG00000024837	Dmrt1	-	doublesex and mab-3 related transcription factor 1	protein-coding
mm_166456.1	chr5	138170975	138170986	-	1	NA	intron (NM_008568, intron 1 of 14)	CpG	882	NM_008568	17220	Mm.378965	NM_008568	ENSMUSG00000029730	Mcm7	AI747533|Mcmd7|mCDC47	minichromosome maintenance complex component 7	protein-coding
mm_163677.1	chr13	87048308	87048310	+	1	NA	Intergenic	RLTR53_Mm|LTR|ERVK	-1001514	NM_007749	12867	Mm.378898	NM_007749	ENSMUSG00000017778	Cox7c	COXVIIc|Cox7c1	cytochrome c oxidase subunit VIIc	protein-coding
mm_30366.1	chr3	152108737	152108772	-	1	NA	intron (NM_016867, intron 3 of 5)	B1F|SINE|Alu	57146	NM_016867	54120	Mm.97	NM_016867	ENSMUSG00000039131	Gipc2	2200002N01Rik|AU021850|Semcap2	GIPC PDZ domain containing family, member 2	protein-coding
mm_81628.1	chr9	110849495	110849504	+	1	NA	intron (NM_183103, intron 1 of 4)	intron (NM_183103, intron 1 of 4)	4993	NM_183103	74306	Mm.87419	NM_183103	ENSMUSG00000049719	Prss46	1700112C13Rik|79H19B|Tessp6	protease, serine 46	protein-coding
mm_104412.1	chr11	94601966	94601983	-	1	NA	promoter-TSS (NM_153807)	promoter-TSS (NM_153807)	-188	NM_153807	264895	Mm.386885	NM_153807	ENSMUSG00000076435	Acsf2	-	acyl-CoA synthetase family member 2	protein-coding
mm_91085.1	chr10	19015205	19015209	-	1	NA	5' UTR (NM_009397, exon 1 of 9)	5' UTR (NM_009397, exon 1 of 9)	203	NM_009397	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_70751.1	chr8	19535827	19535843	+	1	NA	Intergenic	Intergenic	40738	NM_139220	246080	Mm.207067	NM_139220	ENSMUSG00000037790	Defb7	BD-7|Defb15	defensin beta 7	protein-coding
mm_7804.1	chr1	131526476	131526548	-	1	NA	intron (NM_001081011, intron 1 of 22)	CpG	849	NM_001081011	14270	Mm.276259	NM_019520	ENSMUSG00000026425	Srgap2	9930124L22Rik|AI448945|FBP2|Fnbp2|srGAP3	SLIT-ROBO Rho GTPase activating protein 2	protein-coding
mm_29957.1	chr3	133234887	133234897	-	1	NA	promoter-TSS (NM_029953)	promoter-TSS (NM_029953)	-3	NM_029953	77669	Mm.98630	NM_029953	ENSMUSG00000040969	Arhgef38	9130221D24Rik|D630013G24Rik	Rho guanine nucleotide exchange factor (GEF) 38	protein-coding
mm_39228.1	chr4	156228505	156228538	-	1	NA	promoter-TSS (NM_001008233)	promoter-TSS (NM_001008233)	21	NM_001008233	231002	Mm.423124	NM_001008233	ENSMUSG00000078485	Plekhn1	BC025458	pleckstrin homology domain containing, family N member 1	protein-coding
mm_6935.1	chr1	85598797	85598822	-	1	NA	promoter-TSS (NM_030194)	promoter-TSS (NM_030194)	1	NM_030194	109032	Mm.335802	NM_030194	ENSMUSG00000070034	Sp110	5031415C07Rik|52kDa|5830484A20Rik|ENSMUSG00000075603|Ifi75|Ipr1	Sp110 nuclear body protein	protein-coding
mm_65888.1	chr7	29943748	29943757	-	1	NA	intron (NM_178384, intron 1 of 4)	intron (NM_178384, intron 1 of 4)	8141	NM_178384	72723	Mm.371648	NM_178384	ENSMUSG00000059975	Zfp74	2810054M15Rik|KRAB8|Zfp66|Znf569|mszf21|mszf77	zinc finger protein 74	protein-coding
mm_23009.1	chr3	34196778	34196790	+	1	NA	Intergenic	Intergenic	-115430	NM_026332	67713	Mm.274266	NM_026332	ENSMUSG00000027679	Dnajc19	1810055D05Rik|AA959924|Tim14	DnaJ heat shock protein family (Hsp40) member C19	protein-coding
mm_3351.1	chr1	138159227	138159238	+	1	NA	intron (NM_001111316, intron 1 of 31)	intron (NM_001111316, intron 1 of 31)	15894	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_47148.1	chr5	120560903	120560932	-	1	NA	intron (NM_145853, intron 2 of 27)	intron (NM_145853, intron 2 of 27)	27696	NM_145853	252972	Mm.114054	NM_145853	ENSMUSG00000032741	Tpcn1	5730403B01Rik|Tpc1|mKIAA1169	two pore channel 1	protein-coding
mm_67825.1	chr7	98284096	98284096	-	1	NA	intron (NM_025408, intron 1 of 10)	intron (NM_025408, intron 1 of 10)	25431	NM_025408	66190	Mm.334041	NM_025408	ENSMUSG00000030760	Acer3	1110057L18Rik|5430429L08Rik|AV015045|Phca	alkaline ceramidase 3	protein-coding
mm_24729.1	chr3	95282963	95282973	+	1	NA	promoter-TSS (NM_133858)	promoter-TSS (NM_133858)	33	NM_199475	75007	Mm.279287	NM_133858	ENSMUSG00000038712	Fam63a	1810005H09Rik|4930504E06Rik|AA562754|AA960384|AW561904|cI-40|mKIAA1390|ni	family with sequence similarity 63, member A	protein-coding
mm_103479.1	chr11	76494896	76494915	-	1	NA	promoter-TSS (NM_001346670)	promoter-TSS (NM_001346670)	-410	NM_001346670	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_70810.1	chr8	23039566	23039567	+	1	NA	intron (NM_001277284, intron 1 of 42)	intron (NM_001277284, intron 1 of 42)	4467	NM_001277284	11733	Mm.334444	NM_031158	ENSMUSG00000031543	Ank1	Ank-1|nb|pale	ankyrin 1, erythroid	protein-coding
mm_136693.1	chr17	6978964	6978986	+	1	NA	5' UTR (NM_026611, exon 1 of 9)	5' UTR (NM_026611, exon 1 of 9)	115	NM_026611	68195	Mm.181237	NM_026611	ENSMUSG00000094724	Rnaset2b	0610007O07Rik|4833423A10Rik|4930532K22Rik|C79750|RNASE6PL|Rnaset2	ribonuclease T2B	protein-coding
mm_54976.1	chr6	48739208	48739221	-	1	NA	intron (NM_175860, intron 1 of 2)	intron (NM_175860, intron 1 of 2)	167	NM_008376	16205	Mm.252599	NM_008376	ENSMUSG00000090019	Gimap1	IAP38|Imap38|imap	GTPase, IMAP family member 1	protein-coding
mm_146759.1	chr18	16808617	16808677	-	1	NA	5' UTR (NM_007664, exon 1 of 16)	5' UTR (NM_007664, exon 1 of 16)	599	NM_007664	12558	Mm.257437	NM_007664	ENSMUSG00000024304	Cdh2	CDHN|N-CAD|Ncad	cadherin 2	protein-coding
mm_154897.1	chrX	20871110	20871128	+	1	NA	exon (NM_011593, exon 2 of 6)	exon (NM_011593, exon 2 of 6)	953	NM_001294280	21857	Mm.8245	NM_011593	ENSMUSG00000001131	Timp1	Clgi|EPA|TIMP-1|TPA-S1|Timp	tissue inhibitor of metalloproteinase 1	protein-coding
mm_1437.1	chr1	67211249	67211311	+	1	NA	intron (NM_001080809, intron 29 of 37)	intron (NM_001080809, intron 29 of 37)	88253	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_53607.1	chr6	138422236	138422246	+	1	NA	promoter-TSS (NR_126073)	promoter-TSS (NR_126073)	-864	NR_126073	319702	Mm.403785	NR_126072	ENSMUSG00000089957	A830011K09Rik	-	RIKEN cDNA A830011K09 gene	ncRNA
mm_56018.1	chr6	86526197	86526207	-	1	NA	promoter-TSS (NM_011865)	promoter-TSS (NM_011865)	-37	NM_011865	23983	Mm.274146	NM_011865	ENSMUSG00000051695	Pcbp1	WBP17|[a]CP-1|alphaCP-1|hnRNP E1	poly(rC) binding protein 1	protein-coding
mm_66678.1	chr7	45785027	45785031	-	1	NA	promoter-TSS (NM_001290990)	promoter-TSS (NM_001290990)	-351	NM_001290990	381983	Mm.44928	NM_001005511	ENSMUSG00000062044	Lmtk3	BC059845|aatyk3	lemur tyrosine kinase 3	protein-coding
mm_150955.1	chr19	46367979	46367988	+	1	NA	exon (NM_029186, exon 4 of 9)	exon (NM_029186, exon 4 of 9)	11103	NM_029186	75146	Mm.159290	NM_029186	ENSMUSG00000025227	Mfsd13a	4930449A08Rik|4930538D17Rik|Tmem180	major facilitator superfamily domain containing 13a	protein-coding
mm_39965.1	chr5	32138726	32138736	+	1	NA	intron (NM_008037, intron 1 of 3)	intron (NM_008037, intron 1 of 3)	2259	NM_008037	14284	Mm.24684	NM_008037	ENSMUSG00000029135	Fosl2	Fra-2	fos-like antigen 2	protein-coding
mm_158852.1	chrX	169994086	169994122	-	1	NA	Intergenic	CpG	-15187	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_19221.1	chr2	84650699	84650709	-	1	NA	promoter-TSS (NM_001085449)	promoter-TSS (NM_001085449)	36	NM_001085449	12388	Mm.35738	NM_007615	ENSMUSG00000034101	Ctnnd1	AA409437|AU019353|Catns|Ctnnd|P120|mKIAA0384	catenin (cadherin associated protein), delta 1	protein-coding
mm_117951.1	chr13	99441685	99441778	-	1	NA	exon (NM_008634, exon 4 of 7)	exon (NM_008634, exon 4 of 7)	-28905	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_110748.1	chr12	69979061	69979082	-	1	NA	intron (NM_022028, intron 2 of 4)	intron (NM_022028, intron 2 of 4)	7931	NM_022028	64010	Mm.390480	NM_022028	ENSMUSG00000021067	Sav1	1700040G09Rik|Salv|Sav|WW45|Wwp3|Wwp4	salvador family WW domain containing 1	protein-coding
mm_12892.1	chr2	84798402	84798417	+	1	NA	promoter-TSS (NM_019949)	promoter-TSS (NM_019949)	-419	NM_019949	56791	Mm.38261	NM_019949	ENSMUSG00000027078	Ube2l6	2810489I21Rik|RIG-B|UBCH8|Ubce8|Ubcm8	ubiquitin-conjugating enzyme E2L 6	protein-coding
mm_149896.1	chr19	25505621	25505673	+	1	NA	promoter-TSS (NM_015826)	promoter-TSS (NM_015826)	-59	NM_015826	50796	Mm.391208	NM_015826	ENSMUSG00000024837	Dmrt1	-	doublesex and mab-3 related transcription factor 1	protein-coding
mm_130384.1	chr15	97856967	97856977	-	1	NA	3' UTR (NM_009504, exon 10 of 10)	3' UTR (NM_009504, exon 10 of 10)	-12470	NM_001204278	56233	Mm.384027	NM_019572	ENSMUSG00000022475	Hdac7	5830434K02Rik|HD7|HD7a|Hdac7a|mFLJ00062	histone deacetylase 7	protein-coding
mm_48992.1	chr6	4756412	4756421	+	1	NA	exon (NM_130877, exon 2 of 2)	exon (NM_130877, exon 2 of 2)	9110	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_156400.1	chrX	139808634	139808649	+	1	NA	5' UTR (NM_016675, exon 2 of 2)	5' UTR (NM_016675, exon 2 of 2)	7833	NM_016675	12738	Mm.117068	NM_016675	ENSMUSG00000047230	Cldn2	AL022813	claudin 2	protein-coding
mm_97040.1	chr11	72305502	72305517	+	1	NA	intron (NM_001037713, intron 3 of 5)	ORR1E|LTR|ERVL-MaLR	3880	NM_001037713	327959	Mm.291131	NM_001037713	ENSMUSG00000040483	Xaf1	Fbox39	XIAP associated factor 1	protein-coding
mm_26948.1	chr3	20270294	20270327	-	1	NA	exon (NM_029706, exon 3 of 11)	exon (NM_029706, exon 3 of 11)	5423	NM_029706	76703	Mm.34692	NM_029706	ENSMUSG00000011463	Cpb1	0910001A18Rik|1810063F02Rik|2210008M23Rik|AI504870	carboxypeptidase B1 (tissue)	protein-coding
mm_107393.1	chr12	33314376	33314408	+	1	NA	intron (NM_001033436, intron 1 of 7)	intron (NM_001033436, intron 1 of 7)	11877	NM_001033436	380753	Mm.41540	NM_028139	ENSMUSG00000020564	Atxn7l1	2810423G08Rik|Atxn7l4	ataxin 7-like 1	protein-coding
mm_163112.1	chr11	70657756	70657760	+	1	NA	intron (NM_001276285, intron 1 of 11)	intron (NM_001276285, intron 1 of 11)	582	NM_007933	13808	Mm.251322	NM_007933	ENSMUSG00000060600	Eno3	Eno-3|MSE	enolase 3, beta muscle	protein-coding
mm_157117.1	chrX	9440003	9440031	-	1	NA	exon (NM_007807, exon 12 of 13)	exon (NM_007807, exon 12 of 13)	29307	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_31358.1	chr4	47208266	47208276	+	1	NA	5' UTR (NM_009928, exon 1 of 40)	5' UTR (NM_009928, exon 1 of 40)	259	NM_009928	12819	Mm.233547	NM_009928	ENSMUSG00000028339	Col15a1	-	collagen, type XV, alpha 1	protein-coding
mm_172440.1	chr7	29965597	29965597	-	1	NA	Intergenic	CpG	-13704	NM_178384	72723	Mm.371648	NM_178384	ENSMUSG00000059975	Zfp74	2810054M15Rik|KRAB8|Zfp66|Znf569|mszf21|mszf77	zinc finger protein 74	protein-coding
mm_108482.1	chr12	83663912	83663927	+	1	NA	intron (NM_027349, intron 9 of 18)	intron (NM_027349, intron 9 of 18)	-24644	NM_008943	19164	Mm.998	NM_008943	ENSMUSG00000019969	Psen1	Ad3h|PS-1|PS1|S182	presenilin 1	protein-coding
mm_92993.1	chr10	86703561	86703607	-	1	NA	exon (NM_011631, exon 3 of 18)	exon (NM_011631, exon 3 of 18)	1860	NM_011631	22027	Mm.87773	NM_011631	ENSMUSG00000020048	Hsp90b1	ERp99|GRP94|TA-3|Targ2|Tra-1|Tra1|endoplasmin|gp96	heat shock protein 90, beta (Grp94), member 1	protein-coding
mm_139908.1	chr17	70875810	70875812	+	1	NA	Intergenic	Intergenic	-22279	NM_001164074	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_76240.1	chr8	83578043	83578046	-	1	NA	intron (NM_134118, intron 1 of 12)	intron (NM_134118, intron 1 of 12)	11286	NM_025843	66916	Mm.29683	NM_025843	ENSMUSG00000033938	Ndufb7	1110002H15Rik	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 7	protein-coding
mm_65584.1	chr7	27310440	27310453	-	1	NA	intron (NM_001113549, intron 23 of 29)	intron (NM_001113549, intron 23 of 29)	23202	NM_001113549	108075	Mm.272251	NM_175641	ENSMUSG00000040488	Ltbp4	2310046A13Rik	latent transforming growth factor beta binding protein 4	protein-coding
mm_22019.1	chr2	167988268	167988291	-	1	NA	intron (NM_001080708, intron 13 of 21)	intron (NM_001080708, intron 13 of 21)	22314	NM_001080708	69553	Mm.68454	NM_001080708	ENSMUSG00000074577	Fam65c	2310033K02Rik|Gm124	family with sequence similarity 65, member C	protein-coding
mm_163676.1	chr13	85126849	85126882	+	1	NA	Intergenic	Intergenic	-62520	NM_001347587	66671	Mm.18474	NM_023243	ENSMUSG00000021548	Ccnh	6330408H09Rik|AI661354|AV102684|AW538719	cyclin H	protein-coding
mm_104647.1	chr11	97547203	97547224	-	1	NA	intron (NM_018873, intron 3 of 19)	CpG	27913	NM_018873	56013	Mm.342665	NM_018873	ENSMUSG00000038453	Srcin1	P140|SNIP|mKIAA1684|p140Cap	SRC kinase signaling inhibitor 1	protein-coding
mm_66961.1	chr7	62463273	62463276	-	1	NA	3' UTR (NM_013788, exon 1 of 1)	3' UTR (NM_013788, exon 1 of 1)	1236	NM_013788	27412	Mm.422745	NM_013788	ENSMUSG00000070526	Peg12	Frat3	paternally expressed 12	protein-coding
mm_6420.1	chr1	73905358	73905365	-	1	NA	Intergenic	Intergenic	-40895	NR_045311	109198	Mm.359721	NR_045311	ENSMUSG00000100301	6030407O03Rik	-	RIKEN cDNA 6030407O03 gene	ncRNA
mm_34467.1	chr4	148140979	148141008	+	1	NA	exon (NM_027985, exon 2 of 8)	exon (NM_027985, exon 2 of 8)	503	NM_027985	71890	Mm.9648	NM_027985	ENSMUSG00000029003	Mad2l2	2310033C13Rik|G1-453-4|MAD2B|REV7|repro22	MAD2 mitotic arrest deficient-like 2	protein-coding
mm_167763.1	chr9	110422897	110422920	-	1	NA	3' UTR (NM_008694, exon 4 of 4)	3' UTR (NM_008694, exon 4 of 4)	3100	NM_008694	18054	Mm.236225	NM_008694	ENSMUSG00000032484	Ngp	bectenecin	neutrophilic granule protein	protein-coding
mm_73313.1	chr8	105178470	105178486	+	1	NA	intron (NM_001161456, intron 2 of 4)	intron (NM_001161456, intron 2 of 4)	7804	NM_001161458	12400	Mm.2018	NM_022309	ENSMUSG00000031885	Cbfb	AI893578|PEA2|PEBP2b|Pebp2|Pebpb2	core binding factor beta	protein-coding
mm_123436.1	chr14	64576115	64576138	-	1	NA	Intergenic	Intergenic	-11989	NR_040709	268755	Mm.194050	NR_040709	ENSMUSG00000097545	Mir124a-1hg	A930011O12Rik|Rncr3|mir-124-1|mir-3078	Mir124-1 host gene (non-protein coding)	ncRNA
mm_107547.1	chr12	40794260	40794271	+	1	NA	intron (NM_172803, intron 32 of 52)	intron (NM_172803, intron 32 of 52)	-229825	NM_053122	93757	Mm.363813	NM_053122	ENSMUSG00000056899	Immp2l	AI853880|IMP2	IMP2 inner mitochondrial membrane peptidase-like (S. cerevisiae)	protein-coding
mm_8465.1	chr1	153332725	153332804	-	1	NA	promoter-TSS (NM_010683)	promoter-TSS (NM_010683)	22	NM_010683	226519	Mm.1249	NM_010683	ENSMUSG00000026478	Lamc1	Lamb2	laminin, gamma 1	protein-coding
mm_61598.1	chr7	80026348	80026369	+	1	NA	5' UTR (NM_175433, exon 1 of 5)	5' UTR (NM_175433, exon 1 of 5)	130	NM_175433	209225	Mm.290925	NM_175433	ENSMUSG00000048897	Zfp710	5430400N05Rik|9830165K13|AI324798|Znf710	zinc finger protein 710	protein-coding
mm_126877.1	chr15	89425290	89425294	+	1	NA	non-coding (NR_004843, exon 11 of 27)	non-coding (NR_004843, exon 11 of 27)	570	NM_009948	12895	Mm.227738	NM_009948	ENSMUSG00000078937	Cpt1b	Cpt1|Cpt1-m|Cpti|Cpti-m|M-cpti	carnitine palmitoyltransferase 1b, muscle	protein-coding
mm_2207.1	chr1	89580289	89580302	+	1	NA	intron (NM_001037136, intron 1 of 16)	CpG	103597	NR_015540	74403	Mm.444291	NR_015540		4933400F21Rik	1700091C04Rik|4930565K10Rik	RIKEN cDNA 4933400F21 gene	ncRNA
mm_9888.1	chr1	186689368	186689410	-	1	NA	intron (NM_009367, intron 1 of 6)	intron (NM_009367, intron 1 of 6)	16600	NM_009367	21808	Mm.18213	NM_009367	ENSMUSG00000039239	Tgfb2	BB105277|Tgf-beta2|Tgfb-2	transforming growth factor, beta 2	protein-coding
mm_63541.1	chr7	128062636	128062646	+	1	NA	promoter-TSS (NM_008401)	promoter-TSS (NM_008401)	1	NM_008401	16409	Mm.262106	NM_008401	ENSMUSG00000030786	Itgam	CD11b/CD18|CR3|CR3A|Cd11b|F730045J24Rik|Ly-40|MAC1|Mac-1|Mac-1a	integrin alpha M	protein-coding
mm_47836.1	chr5	134313788	134313820	-	1	NA	intron (NM_001080746, intron 1 of 34)	CpG	956	NM_001080746	14886	Mm.261570	NM_010365	ENSMUSG00000060261	Gtf2i	6030441I21Rik|BAP-135|Diws1t|GtfII-I|Spin|TFII-I|WBSCR6	general transcription factor II I	protein-coding
mm_75436.1	chr8	47323167	47323175	-	1	NA	intron (NM_175162, intron 1 of 4)	RMER17C|LTR|ERVK	29177	NM_175162	71069	Mm.23973	NM_175162	ENSMUSG00000038143	Stox2	4933409N07Rik|AI449080|AI835114|mKIAA1392	storkhead box 2	protein-coding
mm_94533.1	chr11	9118620	9118634	+	1	NA	5' UTR (NM_001159402, exon 1 of 9)	5' UTR (NM_001159402, exon 1 of 9)	120	NM_001159402	22271	Mm.4610	NM_009477	ENSMUSG00000020407	Upp1	AI325217|UPase|UdRPase|Up|Upp	uridine phosphorylase 1	protein-coding
mm_11309.1	chr2	30266804	30266886	+	1	NA	promoter-TSS (NM_001252571)	promoter-TSS (NM_001252571)	26	NM_001252570	227696	Mm.297949	NM_172267	ENSMUSG00000079484	Phyhd1	-	phytanoyl-CoA dioxygenase domain containing 1	protein-coding
mm_123366.1	chr14	63164948	63164962	-	1	NA	intron (NM_010191, intron 3 of 9)	intron (NM_010191, intron 3 of 9)	14623	NM_010191	14137	Mm.474432	NM_010191	ENSMUSG00000021273	Fdft1	SQS|SS	farnesyl diphosphate farnesyl transferase 1	protein-coding
mm_133747.1	chr16	94328393	94328411	+	1	NA	promoter-TSS (NM_133229)	promoter-TSS (NM_133229)	-20	NM_133229	170765	Mm.42604	NM_133229	ENSMUSG00000022941	Ripply3	Dscr6	ripply transcriptional repressor 3	protein-coding
mm_153773.1	chr19	45742857	45742863	-	1	NA	promoter-TSS (NM_010205)	promoter-TSS (NM_010205)	24	NM_001166361	14179	Mm.4012	NM_010205	ENSMUSG00000025219	Fgf8	Aigf|Fgf-8	fibroblast growth factor 8	protein-coding
mm_48234.1	chr5	137720696	137720710	-	1	NA	Intergenic	Intergenic	19295	NM_175521	243300	Mm.74750	NM_175521	ENSMUSG00000045348	Nyap1	6430598A04Rik	neuronal tyrosine-phosphorylated phosphoinositide 3-kinase adaptor 1	protein-coding
mm_61123.1	chr7	55768256	55768266	+	1	NA	promoter-TSS (NM_001310740)	promoter-TSS (NM_001310740)	77	NM_178706	233274	Mm.44425	NM_178706	ENSMUSG00000051504	Siglech	6430529G09Rik|Siglec-H	sialic acid binding Ig-like lectin H	protein-coding
mm_124308.1	chr14	103099500	103099550	-	1	NA	promoter-TSS (NM_015822)	promoter-TSS (NM_015822)	-16	NM_015822	50789	Mm.214746	NM_015822	ENSMUSG00000022124	Fbxl3	AU041772|AW212966|FBK|Fbl3a|Fbxl3a|Ovtm|Play68	F-box and leucine-rich repeat protein 3	protein-coding
mm_38978.1	chr4	150914402	150914480	-	1	NA	Intergenic	CpG	-4520	NM_020569	57320	Mm.277349	NM_020569	ENSMUSG00000028964	Park7	DJ-1|Dj1	Parkinson disease (autosomal recessive, early onset) 7	protein-coding
mm_66367.1	chr7	43533195	43533209	-	1	NA	promoter-TSS (NM_001111058)	promoter-TSS (NM_001111058)	-31	NM_021293	12489	Mm.140157	NM_021293	ENSMUSG00000004609	Cd33	Siglec-3|gp67	CD33 antigen	protein-coding
mm_165109.1	chr19	57698182	57698183	+	1	NA	intron (NM_181415, intron 15 of 28)	B1_Mm|SINE|Alu	87148	NM_181415	226255	Mm.245340	NM_181415	ENSMUSG00000054843	Atrnl1	AI504415|AW555641|Alp|Atrnl|Atrnlp	attractin like 1	protein-coding
mm_37786.1	chr4	130275543	130275590	-	1	NA	promoter-TSS (NM_001253386)	promoter-TSS (NM_001253386)	20	NM_172702	230779	Mm.45132	NM_172702	ENSMUSG00000023232	Serinc2	2310004K20Rik|AW121759|FKSG84|TDE2|Tde2l	serine incorporator 2	protein-coding
mm_84310.1	chr9	63667551	63667568	-	1	NA	exon (NM_016769, exon 3 of 9)	exon (NM_016769, exon 3 of 9)	64904	NM_025857	66939	Mm.34338	NM_025857	ENSMUSG00000037257	Aagab	2310007F21Rik|p34	alpha- and gamma-adaptin binding protein	protein-coding
mm_84281.1	chr9	62811867	62811955	-	1	NA	promoter-TSS (NM_010193)	promoter-TSS (NM_010193)	-263	NM_010193	14155	Mm.24069	NM_010193	ENSMUSG00000032244	Fem1b	mKIAA0396	feminization 1 homolog b (C. elegans)	protein-coding
mm_41641.1	chr5	98031096	98031110	+	1	NA	promoter-TSS (NM_133738)	promoter-TSS (NM_133738)	-141	NM_133738	71914	Mm.24842	NM_133738	ENSMUSG00000029338	Antxr2	2310046B19Rik|AW561899|CMG-2|CMG2|cI-35	anthrax toxin receptor 2	protein-coding
mm_52696.1	chr6	119175248	119175292	+	1	NA	promoter-TSS (NM_001033379)	promoter-TSS (NM_001033379)	17	NM_001033379	319618	Mm.250197	NM_001033379	ENSMUSG00000041477	Dcp1b	B930050E02Rik	decapping mRNA 1B	protein-coding
mm_127195.1	chr15	99055896	99055916	+	1	NA	intron (NM_013639, intron 1 of 7)	intron (NM_013639, intron 1 of 7)	732	NM_001163589	19132	Mm.2477	NM_013639	ENSMUSG00000023484	Prph	Prph1	peripherin	protein-coding
mm_105346.1	chr11	102997602	102997618	-	1	NA	intron (NM_026551, intron 3 of 4)	intron (NM_026551, intron 3 of 4)	2311	NR_105896	102466988		NR_105896	ENSMUSG00000098613	Mir6931	Gm27303|mmu-mir-6931	microRNA 6931	ncRNA
mm_19468.1	chr2	92458882	92458907	-	1	NA	exon (NM_145832, exon 2 of 3)	exon (NM_145832, exon 2 of 3)	900	NM_211358	228368	Mm.273990	NM_145832	ENSMUSG00000049922	Slc35c1	E430007K15Rik|fuct1	solute carrier family 35, member C1	protein-coding
mm_150174.1	chr19	32595414	32595448	+	1	NA	promoter-TSS (NM_001201470)	promoter-TSS (NM_001201470)	-284	NM_001201470	23972	Mm.203916	NM_011864	ENSMUSG00000024899	Papss2	1810018P12Rik|AI159688|AtpsU2|Atpsk2|Sk2|bm	3'-phosphoadenosine 5'-phosphosulfate synthase 2	protein-coding
mm_22495.1	chr3	6620569	6620575	+	1	NA	promoter-TSS (NM_027048)	promoter-TSS (NM_027048)	-129	NM_027048	69347	Mm.45822	NM_027048	ENSMUSG00000069118	1700008P02Rik	-	RIKEN cDNA 1700008P02 gene	protein-coding
mm_133573.1	chr16	91406343	91406349	+	1	NA	TTS (NM_010509)	TTS (NM_010509)	111	NM_008349	16155	Mm.4154	NM_008349	ENSMUSG00000022969	Il10rb	6620401D04Rik|AI528744|CRF2-4|Crfb4|D16H21S58|D21S58h|IL-10R2|Il10r2	interleukin 10 receptor, beta	protein-coding
mm_144539.1	chr18	25754504	25754507	+	1	NA	promoter-TSS (NM_001146295)	promoter-TSS (NM_001146295)	-522	NM_001174074	108013	Mm.266435	NM_133195	ENSMUSG00000024268	Celf4	A230070D14Rik|BRUNOL-4|Brul4|Brunol4|C130060B05Rik	CUGBP, Elav-like family member 4	protein-coding
mm_30236.1	chr3	146149666	146149689	-	1	NA	promoter-TSS (NM_026656)	promoter-TSS (NM_026656)	-156	NM_026656	68279	Mm.116862	NM_026656	ENSMUSG00000011008	Mcoln2	3300002C04Rik|AI549968|C86638|TRPML2	mucolipin 2	protein-coding
mm_151571.1	chr19	60811575	60811619	+	1	NA	promoter-TSS (NM_026437)	promoter-TSS (NM_026437)	27	NM_001167829	67894	Mm.26148	NM_026437	ENSMUSG00000024993	Fam45a	1810055E12Rik	family with sequence similarity 45, member A	protein-coding
mm_24043.1	chr3	87846989	87846999	+	1	NA	5' UTR (NM_021309, exon 1 of 7)	5' UTR (NM_021309, exon 1 of 7)	239	NM_021309	27371	Mm.86361	NM_021309	ENSMUSG00000028071	Sh2d2a	Lad|Ribp|Tsad	SH2 domain containing 2A	protein-coding
mm_155964.1	chrX	106027301	106027323	+	1	NA	promoter-TSS (NM_009726)	promoter-TSS (NM_009726)	88	NM_009726	11977	Mm.254297	NM_009726	ENSMUSG00000033792	Atp7a	MNK	ATPase, Cu++ transporting, alpha polypeptide	protein-coding
mm_97110.1	chr11	74650568	74650579	+	1	NA	intron (NM_001081158, intron 1 of 25)	intron (NM_001081158, intron 1 of 25)	1078	NM_001081158	74148	Mm.214574	NM_001081158	ENSMUSG00000020741	Cluh	1300001I01Rik|Kiaa0664|mKIAA0664	clustered mitochondria (cluA/CLU1) homolog	protein-coding
mm_52710.1	chr6	119479532	119479547	+	1	NA	promoter-TSS (NM_133940)	promoter-TSS (NM_133940)	-129	NM_133940	101358	Mm.125477	NM_133940	ENSMUSG00000030019	Fbxl14	AW322056|Fbx14l	F-box and leucine-rich repeat protein 14	protein-coding
mm_1272.1	chr1	63323945	63323962	+	1	NA	Intergenic	RLTR44C|LTR|ERVK	50684	NM_001267872	73884	Mm.86986	NM_028673	ENSMUSG00000027520	Zdbf2	4930431J08Rik|9330107J05Rik	zinc finger, DBF-type containing 2	protein-coding
mm_80874.1	chr9	98955429	98955447	+	1	NA	promoter-TSS (NR_003248)	promoter-TSS (NR_003248)	-128	NR_003248	768252	Mm.129645	NR_003248	ENSMUSG00000097072	Foxl2os	ENSMUSG00000074122	forkhead box L2, opposite strand	ncRNA
mm_134500.1	chr16	18876599	18876609	-	1	NA	promoter-TSS (NM_010922)	promoter-TSS (NM_010922)	33	NM_010922	18100	Mm.20918	NM_010922	ENSMUSG00000022706	Mrpl40	Nlvcf	mitochondrial ribosomal protein L40	protein-coding
mm_67193.1	chr7	73964132	73964154	-	1	NA	intron (NM_009181, intron 4 of 5)	intron (NM_009181, intron 4 of 5)	49539	NM_009181	20450	Mm.4954	NM_009181	ENSMUSG00000025789	St8sia2	AI323367|ST8SiaII|STX|Siat8b	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 2	protein-coding
mm_66004.1	chr7	30562938	30562953	-	1	NA	promoter-TSS (NM_170760)	promoter-TSS (NM_170760)	239	NM_025498	66340	Mm.86557	NM_025498	ENSMUSG00000036835	Psenen	1700023M09Rik|Pen-2	presenilin enhancer gamma secretase subunit	protein-coding
mm_20553.1	chr2	131071263	131071280	-	1	NA	exon (NM_011426, exon 18 of 21)	exon (NM_011426, exon 18 of 21)	-7457	NM_001163529	110751	Mm.108550	NM_033615	ENSMUSG00000027318	Adam33	Adaml	a disintegrin and metallopeptidase domain 33	protein-coding
mm_137737.1	chr17	29360910	29360920	+	1	NA	promoter-TSS (NM_013710)	promoter-TSS (NM_013710)	1	NM_001159538	26382	Mm.279187	NM_013710	ENSMUSG00000024013	Fgd2	Tcd-2|Tcd2|ZFYVE4|tcs-2|tcs2	FYVE, RhoGEF and PH domain containing 2	protein-coding
mm_172715.1	chr8	70527788	70527793	+	1	NA	promoter-TSS (NM_001199631)	promoter-TSS (NM_001199631)	47	NM_010223	14232	Mm.141864	NM_010223	ENSMUSG00000019428	Fkbp8	38kDa|FKBP-38|FKBP-8|Fkbp38	FK506 binding protein 8	protein-coding
mm_48807.1	chr5	148969840	148969859	-	1	NA	Intergenic	Intergenic	19599	NR_040686	71473	Mm.90306	NR_040686	ENSMUSG00000079069	8430423G03Rik	-	RIKEN cDNA 8430423G03 gene	ncRNA
mm_137457.1	chr17	26561516	26561592	+	1	NA	promoter-TSS (NM_026170)	promoter-TSS (NM_026170)	42	NM_026170	67458	Mm.30496	NM_026170	ENSMUSG00000001576	Ergic1	1200007D18Rik|maa-136	endoplasmic reticulum-golgi intermediate compartment (ERGIC) 1	protein-coding
mm_99466.1	chr11	102435742	102435756	+	1	NA	exon (NM_008175, exon 11 of 13)	exon (NM_008175, exon 11 of 13)	5427	NM_008175	14824	Mm.1568	NM_008175	ENSMUSG00000034708	Grn	Pgrn|epithelin	granulin	protein-coding
mm_61682.1	chr7	80994889	80994892	+	1	NA	intron (NM_178707, intron 1 of 9)	intron (NM_178707, intron 1 of 9)	1206	NM_178707	233410	Mm.29525	NM_178707	ENSMUSG00000005621	Zfp592	8430405N24|A730014M16Rik|Znf592|mKIAA0211	zinc finger protein 592	protein-coding
mm_128402.1	chr15	44427828	44427912	-	1	NA	promoter-TSS (NM_175009)	promoter-TSS (NM_175009)	-241	NM_175009	223527	Mm.291828	NM_175009	ENSMUSG00000022338	Eny2	1810057B09Rik|6720481I12|DC6|Ey2	enhancer of yellow 2 homolog (Drosophila)	protein-coding
mm_56190.1	chr6	88601304	88601308	-	1	NA	intron (NM_001278671, intron 4 of 5)	BC1_Mm|scRNA|scRNA	26142	NM_001278671	74589	Mm.196226	NM_029013	ENSMUSG00000033182	Kbtbd12	4833415F11Rik|4933428M03Rik|Klhdc6	kelch repeat and BTB (POZ) domain containing 12	protein-coding
mm_50543.1	chr6	49046223	49046241	+	1	NA	intron (NM_053110, intron 4 of 10)	intron (NM_053110, intron 4 of 10)	9714	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_134830.1	chr16	26099747	26099749	-	1	NA	intron (NM_173379, intron 1 of 14)	intron (NM_173379, intron 1 of 14)	6036	NM_173379	210530	Mm.326869	NM_173379	ENSMUSG00000038168	P3h2	4832416N06|AW553532|Leprel1|Mlat4	prolyl 3-hydroxylase 2	protein-coding
mm_108169.1	chr12	76404279	76404289	+	1	NA	promoter-TSS (NM_008301)	promoter-TSS (NM_008301)	-86	NM_008301	15512	Mm.296181	NM_008301	ENSMUSG00000059970	Hspa2	70kDa|HSP70.2|HSP70A2|Hsp70-2	heat shock protein 2	protein-coding
mm_30076.1	chr3	137997776	137997779	-	1	NA	Intergenic	Intergenic	-16228	NM_001310753	26377	Mm.254835	NM_011932	ENSMUSG00000028159	Dapp1	Bam32	dual adaptor for phosphotyrosine and 3-phosphoinositides 1	protein-coding
mm_21684.1	chr2	164431246	164431256	-	1	NA	exon (NM_011521, exon 2 of 5)	exon (NM_011521, exon 2 of 5)	11937	NM_011521	20971	Mm.3815	NM_011521	ENSMUSG00000017009	Sdc4	AA959608|AW108331|S4|Synd4|ryudocan|syndecan-4	syndecan 4	protein-coding
mm_118557.1	chr14	17962802	17962821	+	1	NA	intron (NM_001113417, intron 3 of 9)	intron (NM_001113417, intron 3 of 9)	-18833	NM_009380	21834	Mm.32563	NM_009380	ENSMUSG00000021779	Thrb	Nr1a2|T3R[b]|T3Rbeta|Thrb1|Thrb2|c-erbAbeta	thyroid hormone receptor beta	protein-coding
mm_148201.1	chr18	79109939	79109953	-	1	NA	promoter-TSS (NM_053099)	promoter-TSS (NM_053099)	-555	NM_053099	240427	Mm.312871	NM_053099	ENSMUSG00000024548	Setbp1	C130092E12|Seb|mKIAA0437	SET binding protein 1	protein-coding
mm_91919.1	chr10	60299828	60299872	-	1	NA	exon (NM_011179, exon 11 of 15)	exon (NM_011179, exon 11 of 15)	15389	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_154797.1	chrX	13281014	13281031	+	1	NA	promoter-TSS (NM_010028)	promoter-TSS (NM_010028)	0	NM_010028	13205	Mm.289662	NM_010028	ENSMUSG00000000787	Ddx3x	D1Pas1-rs2|Ddx3|Fin14	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 3, X-linked	protein-coding
mm_52390.1	chr6	113283851	113283880	+	1	NA	intron (NM_170673, intron 4 of 19)	intron (NM_170673, intron 4 of 19)	1558	NM_170673	211232	Mm.65597	NM_170673	ENSMUSG00000030270	Cpne9	A730016F12Rik|mKIAA4217	copine family member IX	protein-coding
mm_16740.1	chr2	9377954	9377964	-	1	NA	Intergenic	Intergenic	188444	NR_038180	73438	Mm.23558	NR_038180	ENSMUSG00000085580	1700061F12Rik	-	RIKEN cDNA 1700061F12 gene	ncRNA
mm_28365.1	chr3	89871746	89871752	-	1	NA	intron (NM_001310676, intron 9 of 9)	intron (NM_001310676, intron 9 of 9)	40379	NM_172530	214547	Mm.225	NM_172530	ENSMUSG00000046280	She	9430022A14	src homology 2 domain-containing transforming protein E	protein-coding
mm_28720.1	chr3	95673814	95673825	-	1	NA	Intergenic	Intergenic	14098	NM_144899	229595	Mm.490574	NM_144899	ENSMUSG00000015850	Adamtsl4	ADAMTSL-4|Tsrc1	ADAMTS-like 4	protein-coding
mm_23385.1	chr3	56575507	56575537	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	-391821	NM_030595	26422	Mm.384353	NM_030595	ENSMUSG00000027799	Nbea	Lyst2|mKIAA1544	neurobeachin	protein-coding
mm_107521.1	chr12	40461122	40461138	+	1	NA	intron (NM_172803, intron 1 of 52)	intron (NM_172803, intron 1 of 52)	15077	NM_172803	238130	Mm.341423	NM_172803	ENSMUSG00000035954	Dock4	5330406C03|6330411N01Rik|AF263288|C030023J22|mKIAA0716	dedicator of cytokinesis 4	protein-coding
mm_169226.1	chr13	66874054	66874073	+	1	NA	Intergenic	Intergenic	31287	NM_026219	67530	Mm.379136	NM_026219	ENSMUSG00000021520	Uqcrb	2210415M14Rik|QP-C|QPC|UQBC|UQBP|UQPC	ubiquinol-cytochrome c reductase binding protein	protein-coding
mm_13385.1	chr2	103957977	103958021	+	1	NA	promoter-TSS (NM_001142337)	promoter-TSS (NM_001142337)	4	NM_001142337	16909	Mm.29266	NM_008505	ENSMUSG00000032698	Lmo2	Rbtn-2|Rbtn2|Rhom-2|Ttg2	LIM domain only 2	protein-coding
mm_143671.1	chr17	79934588	79934600	-	1	NA	Intergenic	Intergenic	-38471	NM_001286647	56298	Mm.175403	NM_019717	ENSMUSG00000059811	Atl2	2010110I21Rik|AA407293|AV334690|Aip-2|Arl6ip2	atlastin GTPase 2	protein-coding
mm_85511.1	chr9	106247904	106247912	-	1	NA	promoter-TSS (NM_020559)	promoter-TSS (NM_020559)	46	NM_020559	11655	Mm.290578	NM_020559	ENSMUSG00000032786	Alas1	ALAS|ALAS-N|Alas-1|Alas-h	aminolevulinic acid synthase 1	protein-coding
mm_41295.1	chr5	90464122	90464122	+	1	NA	exon (NM_009654, exon 4 of 15)	exon (NM_009654, exon 4 of 15)	3252	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_143128.1	chr17	57213817	57213843	-	1	NA	exon (NM_009778, exon 27 of 41)	exon (NM_009778, exon 27 of 41)	3398	NR_105944	102465591		NR_105944	ENSMUSG00000099066	Mir6978	Gm27858|mmu-mir-6978	microRNA 6978	ncRNA
mm_136620.1	chr17	5493156	5493196	+	1	NA	5' UTR (NM_146073, exon 1 of 9)	5' UTR (NM_146073, exon 1 of 9)	576	NM_146073	224454	Mm.487663	NM_146073	ENSMUSG00000034265	Zdhhc14	B530001K09Rik|New1cp	zinc finger, DHHC domain containing 14	protein-coding
mm_60858.1	chr7	45872802	45872857	+	1	NA	promoter-TSS (NM_133950)	promoter-TSS (NM_133950)	-11	NM_133950	68137	Mm.298433	NM_133950	ENSMUSG00000002778	Kdelr1	8030486F04Rik|AW215843|Erd2.1	KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 1	protein-coding
mm_105480.1	chr11	105938969	105938983	-	1	NA	intron (NM_007805, intron 1 of 5)	intron (NM_007805, intron 1 of 5)	5171	NM_007805	13056	Mm.149403	NM_007805	ENSMUSG00000019590	Cyb561	-	cytochrome b-561	protein-coding
mm_2218.1	chr1	89871108	89871137	+	1	NA	intron (NM_001037136, intron 15 of 16)	intron (NM_001037136, intron 15 of 16)	60054	NM_010262	14472	Mm.204730	NM_010262	ENSMUSG00000034486	Gbx2	D130058E05Rik|Gbx-2|MMoxA|Stra7	gastrulation brain homeobox 2	protein-coding
mm_155175.1	chrX	53607960	53607978	+	1	NA	promoter-TSS (NM_028375)	promoter-TSS (NM_028375)	47	NM_028375	72865	Mm.158897	NM_028375	ENSMUSG00000051851	Cxx1c	2900027G03Rik|Mar8.1|Mart8a	CAAX box 1C	protein-coding
mm_15880.1	chr2	164838080	164838112	+	1	NA	exon (NM_008906, exon 12 of 15)	exon (NM_008906, exon 12 of 15)	4323	NM_008906	19025	Mm.359633	NM_008906	ENSMUSG00000017760	Ctsa	AU019505|PPCA|Ppgb	cathepsin A	protein-coding
mm_26495.1	chr3	145576197	145576266	+	1	NA	promoter-TSS (NM_001081094)	promoter-TSS (NM_001081094)	15	NM_001346521	229937	Mm.24586	NM_001081094	ENSMUSG00000074182	Znhit6	2410019A14Rik	zinc finger, HIT type 6	protein-coding
mm_32256.1	chr4	102570625	102570644	+	1	NA	5' UTR (NM_001177980, exon 1 of 10)	5' UTR (NM_001177980, exon 1 of 10)	574	NM_001177980	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_39653.1	chr5	24709063	24709079	+	1	NA	exon (NM_001305264, exon 15 of 15)	exon (NM_001305264, exon 15 of 15)	21609	NM_001081441	269633	Mm.392539	NM_026621	ENSMUSG00000055235	Wdr86	2810046M22Rik|BC059069	WD repeat domain 86	protein-coding
mm_170323.1	chr18	4199242	4199258	-	1	NA	Intergenic	Intergenic	33418	NM_026092	67328	Mm.158148	NM_026092	ENSMUSG00000024233	Lyzl1	1700038F02Rik|Lyc2|Lyzd1	lysozyme-like 1	protein-coding
mm_14791.1	chr2	145860735	145860747	+	1	NA	exon (NM_028724, exon 9 of 13)	exon (NM_028724, exon 9 of 13)	-42500	NM_026425	67877	Mm.151168	NM_026425	ENSMUSG00000002728	Naa20	1500004D14Rik|2900026I01Rik|AU041458|D2Ertd186e|Nat5	N(alpha)-acetyltransferase 20, NatB catalytic subunit	protein-coding
mm_18071.1	chr2	42643824	42643827	-	1	NA	intron (NM_053011, intron 1 of 90)	intron (NM_053011, intron 1 of 90)	9773	NM_053011	94217	Mm.441398	NM_053011	ENSMUSG00000049252	Lrp1b	9630004P12Rik|LRP-DIT	low density lipoprotein-related protein 1B (deleted in tumors)	protein-coding
mm_106881.1	chr12	8011674	8011689	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	34004	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_161720.1	chr17	27512695	27512695	-	1	NA	Intergenic	CpG	-9162	NM_001291045	268934	Mm.358940	NM_001013385	ENSMUSG00000063239	Grm4	Gprc1d|mGluR4	glutamate receptor, metabotropic 4	protein-coding
mm_18959.1	chr2	76794546	76794557	-	1	NA	exon (NM_011652, exon 205 of 313)	exon (NM_011652, exon 205 of 313)	119236	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_11768.1	chr2	38586079	38586089	+	1	NA	3' UTR (NM_021606, exon 10 of 10)	3' UTR (NM_021606, exon 10 of 10)	57822	NM_011187	19177	Mm.389251	NM_011187	ENSMUSG00000026750	Psmb7	AU020723|MC14	proteasome (prosome, macropain) subunit, beta type 7	protein-coding
mm_85320.1	chr9	101251777	101251802	-	1	NA	promoter-TSS (NM_001161362)	promoter-TSS (NM_001161362)	43	NM_001161362	235542	Mm.335386	NM_172144	ENSMUSG00000043154	Ppp2r3a	3222402P14Rik|A730042E07	protein phosphatase 2, regulatory subunit B'', alpha	protein-coding
mm_117763.1	chr13	96132670	96132687	-	1	NA	promoter-TSS (NM_029210)	promoter-TSS (NM_029210)	-101	NM_029210	75209	Mm.40436	NM_029210	ENSMUSG00000051111	Sv2c	4930527L09Rik|AI841971	synaptic vesicle glycoprotein 2c	protein-coding
mm_28622.1	chr3	95042543	95042579	-	1	NA	promoter-TSS (NM_008951)	promoter-TSS (NM_008951)	53	NM_001282017	19185	Mm.2261	NM_008951	ENSMUSG00000005625	Psmd4	Af1|Mcb1|angiocidin	proteasome (prosome, macropain) 26S subunit, non-ATPase, 4	protein-coding
mm_37995.1	chr4	133660865	133660910	-	1	NA	TTS (NM_178698)	TTS (NM_178698)	11760	NM_001145955	230801	Mm.217004	NM_178698	ENSMUSG00000043257	Pigv	B330013B03|D430024F16Rik	phosphatidylinositol glycan anchor biosynthesis, class V	protein-coding
mm_14532.1	chr2	132781450	132781460	+	1	NA	5' UTR (NM_007694, exon 1 of 5)	5' UTR (NM_007694, exon 1 of 5)	177	NM_007694	12653	Mm.255241	NM_007694	ENSMUSG00000027350	Chgb	Scg-1	chromogranin B	protein-coding
mm_100247.1	chr11	117308136	117308158	+	1	NA	intron (NM_001113487, intron 2 of 10)	intron (NM_001113487, intron 2 of 10)	-23568	NM_017380	53860	Mm.38450	NM_017380	ENSMUSG00000059248	Sept9	MSF1|Msf|PNUTL4|Sint1	septin 9	protein-coding
mm_56837.1	chr6	117179361	117179377	-	1	NA	3' UTR (NM_001012477, exon 4 of 4)	3' UTR (NM_001012477, exon 4 of 4)	10834	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_110180.1	chr12	27337536	27337555	-	1	NA	3' UTR (NM_009234, exon 1 of 1)	3' UTR (NM_009234, exon 1 of 1)	5173	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding
mm_141957.1	chr17	35117843	35117867	-	1	NA	exon (NM_009975, exon 6 of 7)	exon (NM_009975, exon 6 of 7)	-2455	NM_148939	266614	Mm.104680	NM_148939	ENSMUSG00000043807	Ly6g5b	-	lymphocyte antigen 6 complex, locus G5B	protein-coding
mm_109319.1	chr12	109561612	109561625	+	1	NA	non-coding (NR_003633, exon 5 of 5)	non-coding (NR_003633, exon 5 of 5)	-2074	NR_030427	791079		NR_030427	ENSMUSG00000076451	Mir770	Mirn770|mir-770|mmu-mir-770	microRNA 770	ncRNA
mm_21996.1	chr2	167689212	167689239	-	1	NA	exon (NM_009883, exon 1 of 1)	exon (NM_009883, exon 1 of 1)	310	NM_001287738	12608	Mm.439656	NM_009883	ENSMUSG00000056501	Cebpb	C/EBPbeta|CRP2|IL-6DBP|LAP|LIP|NF-IL6|NF-M|Nfil6	CCAAT/enhancer binding protein (C/EBP), beta	protein-coding
mm_163851.1	chr14	19418311	19418321	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	184271	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_52154.1	chr6	98005076	98005089	+	1	NA	intron (NM_008601, intron 5 of 8)	intron (NM_008601, intron 5 of 8)	13299	NM_008601	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_2545.1	chr1	107529004	107529014	+	1	NA	promoter-TSS (NM_001160307)	promoter-TSS (NM_001160307)	6	NM_198028	241197	Mm.123919	NM_198028	ENSMUSG00000092572	Serpinb10	9830131G07|BB233602|Serpinb10-ps	serine (or cysteine) peptidase inhibitor, clade B (ovalbumin), member 10	protein-coding
mm_118309.1	chr13	113101877	113101895	-	1	NA	promoter-TSS (NM_010370)	promoter-TSS (NM_010370)	-905	NM_010370	14938	Mm.15510	NM_010370	ENSMUSG00000023132	Gzma	AW494114|Ctla-3|Ctla3|Hf|Hf1|SE1|TSP-1|TSP1	granzyme A	protein-coding
mm_96501.1	chr11	68432113	68432170	+	1	NA	promoter-TSS (NM_177320)	promoter-TSS (NM_177320)	16	NM_177320	320207	Mm.244960	NM_177320	ENSMUSG00000020901	Pik3r5	AV230647|F730038I15Rik	phosphoinositide-3-kinase, regulatory subunit 5, p101	protein-coding
mm_54289.1	chr6	29260844	29260862	-	1	NA	Intergenic	Intergenic	-11635	NM_001190461	69573	Mm.45161	NM_023516	ENSMUSG00000043421	Hilpda	2310016C08Rik|AW049004|Hig2	hypoxia inducible lipid droplet associated	protein-coding
mm_77665.1	chr8	124716736	124716742	-	1	NA	intron (NM_145607, intron 1 of 17)	intron (NM_145607, intron 1 of 17)	5236	NM_145607	234875	Mm.38436	NM_145607	ENSMUSG00000037300	Ttc13	BC017545	tetratricopeptide repeat domain 13	protein-coding
mm_67780.1	chr7	97332104	97332114	-	1	NA	promoter-TSS (NM_001039039)	promoter-TSS (NM_001039039)	-214	NM_001039039	622320	Mm.334029	NM_001039039	ENSMUSG00000044952	Kctd21	EG622320	potassium channel tetramerisation domain containing 21	protein-coding
mm_56495.1	chr6	99204956	99204974	-	1	NA	intron (NM_001347345, intron 4 of 19)	intron (NM_001347345, intron 4 of 19)	61550	NM_001197321	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_150535.1	chr19	39296661	39296676	+	1	NA	intron (NM_007815, intron 3 of 8)	intron (NM_007815, intron 3 of 8)	9583	NM_007815	13095	Mm.20764	NM_007815	ENSMUSG00000003053	Cyp2c29	AHOH|AHOHase|AI159681|AI196010|Ah-2|Ahh-1|Cyp2c|P450-2C	cytochrome P450, family 2, subfamily c, polypeptide 29	protein-coding
mm_33154.1	chr4	125490689	125490704	+	1	NA	promoter-TSS (NM_001081097)	promoter-TSS (NM_001081097)	-135	NM_001081097	14807	Mm.40896	NM_001081097	ENSMUSG00000001985	Grik3	9630027E11|GluK3|GluR7-3|Glur-7|Glur7	glutamate receptor, ionotropic, kainate 3	protein-coding
mm_148376.1	chr19	3205596	3205622	+	1	NA	Intergenic	Intergenic	-7906	NR_045304	70011	Mm.393871	NR_045304	ENSMUSG00000100969	1700030N03Rik	1700087C08Rik	RIKEN cDNA 1700030N03 gene	ncRNA
mm_81106.1	chr9	106452080	106452097	+	1	NA	exon (NM_029631, exon 4 of 4)	exon (NM_029631, exon 4 of 4)	-1750	NM_021567	59092	Mm.286394	NM_021567	ENSMUSG00000023495	Pcbp4	1200003L19Rik|AlphaCP-4	poly(rC) binding protein 4	protein-coding
mm_45249.1	chr5	59986002	59986002	-	1	NA	promoter-TSS (NR_040683)	promoter-TSS (NR_040683)	0	NR_040683	71057	Mm.50817	NR_040682	ENSMUSG00000106013	4933402J10Rik	-	RIKEN cDNA 4933402J10 gene	ncRNA
mm_60174.1	chr7	41599251	41599266	+	1	NA	Intergenic	CpG	-34273	NM_023363	67607	Mm.384626	NM_023363	ENSMUSG00000074165	Zfp788	2810426N06Rik|AI256342|AI605193	zinc finger protein 788	protein-coding
mm_112424.1	chr13	4191209	4191226	+	1	NA	promoter-TSS (NM_013778)	promoter-TSS (NM_013778)	30	NM_013778	27384	Mm.27447	NM_013778	ENSMUSG00000021213	Akr1c13	mKIAA4014	aldo-keto reductase family 1, member C13	protein-coding
mm_100573.1	chr11	120763130	120763145	+	1	NA	Intergenic	Intergenic	21067	NM_009053	19719	Mm.871	NM_009053	ENSMUSG00000025158	Rfng	-	RFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	protein-coding
mm_71599.1	chr8	54978894	54978905	+	1	NA	intron (NM_001253756, intron 1 of 5)	intron (NM_001253756, intron 1 of 5)	24171	NM_001253756	234267	Mm.241700	NM_153581	ENSMUSG00000031517	Gpm6a	Gpm6|M6A	glycoprotein m6a	protein-coding
mm_10419.1	chr2	13580631	13580656	+	1	NA	exon (NM_011701, exon 7 of 9)	exon (NM_011701, exon 7 of 9)	6332	NM_011701	22352	Mm.268000	NM_011701	ENSMUSG00000026728	Vim	-	vimentin	protein-coding
mm_131173.1	chr16	7069798	7069812	+	1	NA	promoter-TSS (NM_183188)	promoter-TSS (NM_183188)	-30	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_73591.1	chr8	109993917	109993928	+	1	NA	exon (NM_146214, exon 5 of 12)	exon (NM_146214, exon 5 of 12)	3486	NM_146214	234724	Mm.28110	NM_146214	ENSMUSG00000001670	Tat	-	tyrosine aminotransferase	protein-coding
mm_35150.1	chr4	11966325	11966335	-	1	NA	promoter-TSS (NM_001290387)	promoter-TSS (NM_001290387)	120	NM_001098230	381511	Mm.331489	NM_001033453	ENSMUSG00000049225	Pdp1	Gm1024|Ppm2c	pyruvate dehyrogenase phosphatase catalytic subunit 1	protein-coding
mm_39138.1	chr4	155223069	155223086	-	1	NA	promoter-TSS (NM_011385)	promoter-TSS (NM_011385)	-542	NM_011385	20481	Mm.28520	NM_011385	ENSMUSG00000029050	Ski	2310012I02Rik|2610001A11Rik|AA062172|AA589460|BC004088	ski sarcoma viral oncogene homolog (avian)	protein-coding
mm_9813.1	chr1	182019928	182019989	-	1	NA	promoter-TSS (NM_010135)	promoter-TSS (NM_010135)	22	NM_008680	13800	Mm.87759	NM_008680	ENSMUSG00000022995	Enah	Mena|NDPP-1|Ndpp1|WBP8	enabled homolog (Drosophila)	protein-coding
mm_16818.1	chr2	11398526	11398538	-	1	NA	promoter-TSS (NR_040615)	promoter-TSS (NR_040615)	-32	NR_040615	77543	Mm.490670	NR_040615	ENSMUSG00000102674	8030442B05Rik	-	RIKEN cDNA 8030442B05 gene	ncRNA
mm_13059.1	chr2	91115161	91115171	+	1	NA	exon (NM_011355, exon 5 of 5)	exon (NM_011355, exon 5 of 5)	-2978	NM_008653	17868	Mm.10728	NM_008653	ENSMUSG00000002100	Mybpc3	-	myosin binding protein C, cardiac	protein-coding
mm_14506.1	chr2	132253350	132253388	+	1	NA	promoter-TSS (NM_011045)	promoter-TSS (NM_011045)	-189	NM_011045	18538	Mm.7141	NM_011045	ENSMUSG00000027342	Pcna	-	proliferating cell nuclear antigen	protein-coding
mm_79979.1	chr9	66918839	66918862	+	1	NA	intron (NM_173413, intron 1 of 7)	intron (NM_173413, intron 1 of 7)	855	NM_173413	235442	Mm.260376	NM_173413	ENSMUSG00000036943	Rab8b	5930437D16|D330025I23Rik	RAB8B, member RAS oncogene family	protein-coding
mm_12155.1	chr2	62046512	62046571	+	1	NA	promoter-TSS (NM_001242379)	promoter-TSS (NM_001242379)	26	NM_033552	94229	Mm.314497	NM_033552	ENSMUSG00000026904	Slc4a10	NCBE|mKIAA4136	solute carrier family 4, sodium bicarbonate cotransporter-like, member 10	protein-coding
mm_159727.1	chr5	41822001	41822001	-	1	NA	exon (NM_001081422, exon 10 of 27)	exon (NM_001081422, exon 10 of 27)	22314	NM_001310601	665775	Mm.158726	NM_001081422	ENSMUSG00000061755	Bod1l	A230054D04Rik|AI853319|FAM44A|mKIAA1327	biorientation of chromosomes in cell division 1-like	protein-coding
mm_34844.1	chr4	155409287	155409289	+	1	NA	promoter-TSS (NM_001166029)	promoter-TSS (NM_001166029)	98	NM_001166029	544678	Mm.472798	NM_177674	ENSMUSG00000078490	Cfap74	2010015L04Rik|A530045M11	cilia and flagella associated protein 74	protein-coding
mm_58940.1	chr7	18245203	18245216	+	1	NA	promoter-TSS (NM_153749)	promoter-TSS (NM_153749)	-138	NM_153749	266815	Mm.106769	NM_153749	ENSMUSG00000054005	Mill1	5530400I18Rik	MHC I like leukocyte 1	protein-coding
mm_17018.1	chr2	18998069	18998084	-	1	NA	promoter-TSS (NR_024323)	promoter-TSS (NR_024323)	45	NM_008845	18718	Mm.313977	NM_008845	ENSMUSG00000026737	Pip4k2a	AW742916|Pip5k2a	phosphatidylinositol-5-phosphate 4-kinase, type II, alpha	protein-coding
mm_65266.1	chr7	19935488	19935509	-	1	NA	Intergenic	RMER19A|LTR|ERVK	-14355	NM_027514	52118	Mm.227506	NM_027514	ENSMUSG00000040511	Pvr	3830421F03Rik|CD155|D7Ertd458e|HVED|PVS|Taa1|Tage4|mE4|necl-5	poliovirus receptor	protein-coding
mm_127259.1	chr15	99704172	99704187	+	1	NA	intron (NM_031842, intron 4 of 12)	intron (NM_031842, intron 4 of 12)	1892	NM_031842	83797	Mm.273756	NM_031842	ENSMUSG00000023018	Smarcd1	AA407987|Baf60a|D15Kz1	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1	protein-coding
mm_21630.1	chr2	164277298	164277305	-	1	NA	exon (NM_009300, exon 2 of 3)	exon (NM_009300, exon 2 of 3)	1006	NM_009300	20941	Mm.1286	NM_009300	ENSMUSG00000016998	Svs4	SVS-IV|Svp-2|Svp-4|Svp2|Svp4	seminal vesicle secretory protein 4	protein-coding
mm_120358.1	chr14	64093714	64093737	+	1	NA	promoter-TSS (NM_001193631)	promoter-TSS (NM_001193631)	29	NM_001193631	100504162	Mm.72752	NM_001193631	ENSMUSG00000052099	Prss51	1700007N14Rik	protease, serine 51	protein-coding
mm_12628.1	chr2	74704826	74704837	+	1	NA	promoter-TSS (NM_001290730)	promoter-TSS (NM_001290730)	216	NM_001290731	15437	Mm.280673	NM_008276	ENSMUSG00000027102	Hoxd8	4921540P06Rik|AI047735|Hox-4.3|Hox-5.4	homeobox D8	protein-coding
mm_76011.1	chr8	72988521	72988539	-	1	NA	intron (NM_001317391, intron 7 of 15)	RMER6A|LTR|ERVK	-27982	NR_039551	100628574		NR_039551	ENSMUSG00000093140	Mir28b	mmu-mir-28b	microRNA 28b	ncRNA
mm_166932.1	chr7	35119332	35119335	+	1	NA	promoter-TSS (NM_001287514)	promoter-TSS (NM_001287514)	40	NM_007678	12606	Mm.349667	NM_007678	ENSMUSG00000034957	Cebpa	C/ebpalpha|CBF-A|Cebp	CCAAT/enhancer binding protein (C/EBP), alpha	protein-coding
mm_104017.1	chr11	85524945	85524951	-	1	NA	intron (NM_138681, intron 16 of 25)	intron (NM_138681, intron 16 of 25)	171784	NM_001166643	192197	Mm.209989	NM_138681	ENSMUSG00000059439	Bcas3	1500019F07Rik|2610028P08Rik|AU021018|BC028339|K20D4|rudhira	breast carcinoma amplified sequence 3	protein-coding
mm_23409.1	chr3	58461117	58461120	+	1	NA	3' UTR (NM_001347233, exon 3 of 3)	3' UTR (NM_001347233, exon 3 of 3)	46398	NM_001081229	72033	Mm.218409	NM_001081229	ENSMUSG00000027806	Tsc22d2	1810043J12Rik|5530402M19Rik	TSC22 domain family, member 2	protein-coding
mm_159492.1	chr4	42756526	42756526	-	1	NA	promoter-TSS (NM_011888).2	promoter-TSS (NM_011888).2	-8	NM_011888	24047	Mm.6660	NM_011888	ENSMUSG00000071005	Ccl19	CKb11|ELC|MIP3B|Scya19|exodus-3	chemokine (C-C motif) ligand 19	protein-coding
mm_169035.1	chr13	13437579	13437579	+	1	NA	promoter-TSS (NM_010917)	promoter-TSS (NM_010917)	-23	NM_010917	18073	Mm.4691	NM_010917	ENSMUSG00000005397	Nid1	A630025O17|Nid|entactin|entactin-1|nidogen-1	nidogen 1	protein-coding
mm_511.1	chr1	37299860	37299870	+	1	NA	promoter-TSS (NM_030266)	promoter-TSS (NM_030266)	27	NM_001290797	269180	Mm.5294	NM_030266	ENSMUSG00000026113	Inpp4a	107kDa|9630012D15|D130048C09Rik|R74740	inositol polyphosphate-4-phosphatase, type I	protein-coding
mm_14622.1	chr2	136772980	136772982	+	1	NA	intron (NM_011428, intron 5 of 7)	intron (NM_011428, intron 5 of 7)	59531	NM_001291056	20614	Mm.45953	NM_011428	ENSMUSG00000027273	Snap25	Bdr|GENA70|SNAP-25|SUP|sp	synaptosomal-associated protein 25	protein-coding
mm_158671.1	chrX	157598399	157598437	-	1	NA	intron (NM_172307, intron 1 of 10)	CpG	297	NM_172307	270669	Mm.37577	NM_172307	ENSMUSG00000046873	Mbtps2	9630032G22Rik|AI662535	membrane-bound transcription factor peptidase, site 2	protein-coding
mm_4158.1	chr1	171029238	171029255	+	1	NA	exon (NM_144559, exon 5 of 5)	exon (NM_144559, exon 5 of 5)	10320	NM_144559	246256	Mm.251254	NM_144559	ENSMUSG00000059089	Fcgr4	4833442P21Rik|CD16-2|FcgRIV|FcgammaRIV|Fcgr3a|Fcrl3	Fc receptor, IgG, low affinity IV	protein-coding
mm_158020.1	chrX	95965193	95965230	-	1	NA	Intergenic	Intergenic	-8237	NM_152822	76130	Mm.274318	NM_152822	ENSMUSG00000057421	Las1l	1810030A06Rik|5830482G23Rik	LAS1-like (S. cerevisiae)	protein-coding
mm_131762.1	chr16	22891386	22891395	+	1	NA	promoter-TSS (NM_001276450)	promoter-TSS (NM_001276450)	-625	NR_075099	11625	Mm.197554	NM_013465	ENSMUSG00000022868	Ahsg	-	alpha-2-HS-glycoprotein	protein-coding
mm_157217.1	chrX	13014144	13014187	-	1	NA	Intergenic	Intergenic	-27850	NR_038158	70489	Mm.383563	NR_038158	ENSMUSG00000087424	5730405O15Rik	-	RIKEN cDNA 5730405O15 gene	ncRNA
mm_22957.1	chr3	32398461	32398469	+	1	NA	Intergenic	T-rich|Low_complexity|Low_complexity	-32800	NM_009517	22401	Mm.35705	NM_009517	ENSMUSG00000027663	Zmat3	Wig1	zinc finger matrin type 3	protein-coding
mm_107205.1	chr12	26443789	26443818	+	1	NA	3' UTR (NM_021384, exon 6 of 6)	3' UTR (NM_021384, exon 6 of 6)	12649	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_73175.1	chr8	95056656	95056666	+	1	NA	exon (NM_001042715, exon 3 of 18)	exon (NM_001042715, exon 3 of 18)	1558	NM_001042715	330830	Mm.277112	NM_001042715	ENSMUSG00000031786	Drc7	Ccdc135|Gm770|SRG-L|SRG-S	dynein regulatory complex subunit 7	protein-coding
mm_73675.1	chr8	111536267	111536301	+	1	NA	promoter-TSS (NM_133206)	promoter-TSS (NM_133206)	-356	NM_001168622	170737	Mm.271578	NM_133206	ENSMUSG00000033545	Znrf1	B830022L21Rik|Rnf42|Zrfp1|nin283	zinc and ring finger 1	protein-coding
mm_145707.1	chr18	62922291	62922308	+	1	NA	promoter-TSS (NM_133237)	promoter-TSS (NM_133237)	-28	NM_133237	494504	Mm.391102	NM_133237	ENSMUSG00000071847	Apcdd1	AB023957|AU041258|Drapc1|EIG180	adenomatosis polyposis coli down-regulated 1	protein-coding
mm_63343.1	chr7	126967536	126967544	+	1	NA	intron (NM_001252566, intron 14 of 16)	intron (NM_001252566, intron 14 of 16)	-8374	NM_026638	52858	Mm.28219	NM_026638	ENSMUSG00000030682	Cdipt	9530042F15Rik|D7Bwg0575e|Pis|Pis1	CDP-diacylglycerol--inositol 3-phosphatidyltransferase (phosphatidylinositol synthase)	protein-coding
mm_141572.1	chr17	32319013	32319013	-	1	NA	intron (NR_131218, intron 1 of 13)	intron (NR_131218, intron 1 of 13)	2225	NM_019774	56399	Mm.328945	NM_019774	ENSMUSG00000024045	Akap8	1200016A02Rik|AA673585|AKAP-8|AKAP95|AU015639	A kinase (PRKA) anchor protein 8	protein-coding
mm_107201.1	chr12	25335326	25335338	+	1	NA	Intergenic	Intergenic	206158	NR_045844	432641	Mm.112955	NR_045844		Gm17746	-	predicted gene, 17746	ncRNA
mm_109533.1	chr12	111540214	111540227	+	1	NA	promoter-TSS (NR_033168)	promoter-TSS (NR_033168)	-726	NR_033168	100316932	Mm.484709	NR_033168	ENSMUSG00000064493	Snora28	MBI-13	small nucleolar RNA, H/ACA box 28	snoRNA
mm_5487.1	chr1	36891681	36891694	-	1	NA	intron (NM_018872, intron 1 of 40)	intron (NM_018872, intron 1 of 40)	47840	NM_018872	56030	Mm.186943	NM_018872	ENSMUSG00000026116	Tmem131	2610524E03Rik|CC28|D1Bwg0491e|Neg|RW1|YR-23|mKIAA0257	transmembrane protein 131	protein-coding
mm_140262.1	chr17	84626459	84626512	+	1	NA	promoter-TSS (NM_172256)	promoter-TSS (NM_172256)	-14	NM_172256	213575	Mm.246119	NM_172256	ENSMUSG00000024253	Dync2li1	4933404O11Rik|CGI-60|D2lic|LIC3|mD2LIC	dynein cytoplasmic 2 light intermediate chain 1	protein-coding
mm_71725.1	chr8	61976821	61976833	+	1	NA	intron (NM_001293783, intron 17 of 37)	intron (NM_001293783, intron 17 of 37)	48740	NM_001293783	234311	Mm.275233	NM_144928	ENSMUSG00000037921	Ddx60	9830118M07	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	protein-coding
mm_138445.1	chr17	35135175	35135181	+	1	NA	promoter-TSS (NM_001252469)	promoter-TSS (NM_001252469)	0	NM_001252468	224727	Mm.203962	NM_057171	ENSMUSG00000024392	Bag6	2410045D21Rik|AA408914|BAG-6|Bat3|D17H6S52E|G3|Scythe	BCL2-associated athanogene 6	protein-coding
mm_13099.1	chr2	91259867	91259877	+	1	NA	5' UTR (NM_028733, exon 2 of 11)	5' UTR (NM_028733, exon 2 of 11)	2543	NM_028733	80708	Mm.236650	NM_028733	ENSMUSG00000027257	Pacsin3	4921507A02Rik|6330413E15Rik|AW413130	protein kinase C and casein kinase substrate in neurons 3	protein-coding
mm_70526.1	chr8	12984371	12984379	+	1	NA	intron (NM_001159486, intron 3 of 29)	intron (NM_001159486, intron 3 of 29)	34957	NM_001159485	17207	Mm.334413	NM_178076	ENSMUSG00000031442	Mcf2l	C130040G20Rik|Dbs|Ost|mKIAA0362	mcf.2 transforming sequence-like	protein-coding
mm_45022.1	chr5	38561659	38561680	-	1	NA	promoter-TSS (NM_011715)	promoter-TSS (NM_011715)	-74	NM_011715	22388	Mm.2654	NM_011715	ENSMUSG00000005103	Wdr1	Aip1|D5Wsu185e|rede	WD repeat domain 1	protein-coding
mm_126763.1	chr15	85859753	85859775	+	1	NA	promoter-TSS (NM_013882)	promoter-TSS (NM_013882)	57	NM_001168672	29870	Mm.20858	NM_013882	ENSMUSG00000022385	Gtse1	B99|Gtse-1	G two S phase expressed protein 1	protein-coding
mm_162869.1	chr10	94036365	94036375	+	1	NA	promoter-TSS (NM_001304720)	promoter-TSS (NM_001304720)	369	NM_053072	13998	Mm.269596	NM_053072	ENSMUSG00000020021	Fgd6	AA123052|Etohd4|ZFYVE24	FYVE, RhoGEF and PH domain containing 6	protein-coding
mm_156369.1	chrX	139617385	139617395	+	1	NA	intron (NM_023270, intron 1 of 6)	intron (NM_023270, intron 1 of 6)	6770	NM_023270	66889	Mm.27764	NM_023270	ENSMUSG00000031438	Rnf128	1300002C13Rik|AI987883|GRAIL|Greul1	ring finger protein 128	protein-coding
mm_134103.1	chr16	9995316	9995343	-	1	NA	Intergenic	CpG	-2796	NM_008170	14811	Mm.2953	NM_008170	ENSMUSG00000059003	Grin2a	GluN2A|NMDAR2A|NR2A	glutamate receptor, ionotropic, NMDA2A (epsilon 1)	protein-coding
mm_31327.1	chr4	46450913	46450994	+	1	NA	promoter-TSS (NM_130889)	promoter-TSS (NM_130889)	27	NM_130889	67628	Mm.263913	NM_130889	ENSMUSG00000028333	Anp32b	2410015B15Rik|PAL31|PHAPI2a|Ssp29	acidic (leucine-rich) nuclear phosphoprotein 32 family, member B	protein-coding
mm_62633.1	chr7	107639157	107639191	+	1	NA	intron (NM_001163557, intron 2 of 25)	B4|SINE|B4	32330	NM_001163557	19024	Mm.2817	NM_008905	ENSMUSG00000036528	Ppfibp2	Cclp1	PTPRF interacting protein, binding protein 2 (liprin beta 2)	protein-coding
mm_8853.1	chr1	162710503	162710515	-	1	NA	exon (NM_001081290, exon 12 of 35)	exon (NM_001081290, exon 12 of 35)	30047	NM_001081290	226562	Mm.245446	NM_001081290	ENSMUSG00000040225	Prrc2c	1810043M20Rik|9630039I18Rik|A630006J20|Bat2d|Bat2d1|Bat2l2|E130112L15Rik|Prrc3|mKIAA1096	proline-rich coiled-coil 2C	protein-coding
mm_60670.1	chr7	45017954	45018009	+	1	NA	promoter-TSS (NM_009101)	promoter-TSS (NM_009101)	-26	NM_009101	20130	Mm.389894	NM_009101	ENSMUSG00000038387	Rras	AI573426	related RAS viral (r-ras) oncogene	protein-coding
mm_85060.1	chr9	90243114	90243120	-	1	NA	intron (NM_194334, intron 2 of 12)	intron (NM_194334, intron 2 of 12)	27652	NM_194334	67016	Mm.335347	NM_194334	ENSMUSG00000037410	Tbc1d2b	1810061M12Rik|AI480956|AV021536|AV023399|AW491493|mKIAA1055	TBC1 domain family, member 2B	protein-coding
mm_61246.1	chr7	65803986	65803992	+	1	NA	promoter-TSS (NR_045301)	promoter-TSS (NR_045301)	-63	NR_045301	100503969	Mm.383527	NR_045301		1810008I18Rik	-	RIKEN cDNA 1810008I18 gene	ncRNA
mm_134302.1	chr16	15626274	15626277	-	1	NA	intron (NM_008565, intron 13 of 15)	intron (NM_008565, intron 13 of 15)	11125	NM_008565	17217	Mm.1500	NM_008565	ENSMUSG00000022673	Mcm4	19G|AI325074|AU045576|Cdc21|Mcmd4|mKIAA4003|mcdc21	minichromosome maintenance complex component 4	protein-coding
mm_80831.1	chr9	97015954	97015983	+	1	NA	intron (NM_145134, intron 1 of 2)	intron (NM_145134, intron 1 of 2)	2387	NM_145134	211949	Mm.491271	NM_145134	ENSMUSG00000046997	Spsb4	D030068E18Rik|SSB-4|Ssb4	splA/ryanodine receptor domain and SOCS box containing 4	protein-coding
mm_92783.1	chr10	81291181	81291198	-	1	NA	promoter-TSS (NM_013769)	promoter-TSS (NM_013769)	78	NM_013769	27375	Mm.27984	NM_013769	ENSMUSG00000034917	Tjp3	-	tight junction protein 3	protein-coding
mm_31531.1	chr4	55082484	55082491	+	1	NA	3' UTR (NM_172867, exon 13 of 13)	3' UTR (NM_172867, exon 13 of 13)	134542	NM_172867	242466	Mm.102904	NM_172867	ENSMUSG00000060206	Zfp462	6030417H05|9430078C22Rik|Gt4-2|Zfpip	zinc finger protein 462	protein-coding
mm_40461.1	chr5	53614979	53614991	+	1	NA	intron (NM_001277116, intron 3 of 12)	intron (NM_001277116, intron 3 of 12)	24499	NM_001080927	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_164052.1	chr14	103017033	103017065	-	1	NA	intron (NR_045657, intron 2 of 2)	intron (NR_045657, intron 2 of 2)	16754	NR_045657	71264	Mm.399572	NR_045657		4933432I03Rik	-	RIKEN cDNA 4933432I03 gene	ncRNA
mm_24832.1	chr3	95658739	95658749	+	1	NA	promoter-TSS (NM_008562)	promoter-TSS (NM_008562)	23	NM_008562	17210	Mm.1639	NM_008562	ENSMUSG00000038612	Mcl1	AW556805|Mcl-1	myeloid cell leukemia sequence 1	protein-coding
mm_10936.1	chr2	25468831	25468878	+	1	NA	exon (NM_008963, exon 3 of 7)	exon (NM_008963, exon 3 of 7)	895	NM_008963	19215	Mm.1008	NM_008963	ENSMUSG00000015090	Ptgds	21kDa|L-PGDS|PGD2|PGDS|PGDS2|Ptgs3	prostaglandin D2 synthase (brain)	protein-coding
mm_13697.1	chr2	117121461	117121473	+	1	NA	5' UTR (NM_001277256, exon 1 of 5)	5' UTR (NM_001277256, exon 1 of 5)	396	NM_033524	114715	Mm.245890	NM_033524	ENSMUSG00000027351	Spred1	5730461F13Rik|AL024345|AW047647	sprouty protein with EVH-1 domain 1, related sequence	protein-coding
mm_157481.1	chrX	48173343	48173358	-	1	NA	3' UTR (NM_172465, exon 10 of 10)	3' UTR (NM_172465, exon 10 of 10)	26914	NM_028773	74131	Mm.276131	NM_028773	ENSMUSG00000031101	Sash3	1200013B08Rik|AW413946|SLY1	SAM and SH3 domain containing 3	protein-coding
mm_154626.1	chrX	7728547	7728579	+	1	NA	promoter-TSS (NM_138602)	promoter-TSS (NM_138602)	-8	NM_138602	54637	Mm.28850	NM_138602	ENSMUSG00000031149	Praf2	AA986329|C78013|DXImx39e|JM4|Sfc20	PRA1 domain family 2	protein-coding
mm_30738.1	chr4	14169976	14169984	+	1	NA	Intergenic	Intergenic	121329	NR_131155	100040030	Mm.366499	NR_131155		Gm2560	-	predicted gene 2560	ncRNA
mm_55429.1	chr6	65779690	65779694	-	1	NA	intron (NM_029549, intron 1 of 10)	intron (NM_029549, intron 1 of 10)	730	NM_029549	70779	Mm.263355	NM_027547	ENSMUSG00000029913	Prdm5	4432417F03Rik|6530401I24Rik|AI197291|E130112L17Rik|PFM2	PR domain containing 5	protein-coding
mm_133615.1	chr16	91547830	91547840	+	1	NA	intron (NM_008338, intron 1 of 6)	intron (NM_008338, intron 1 of 6)	741	NM_008338	15980	Mm.249364	NM_008338	ENSMUSG00000022965	Ifngr2	Ifgr2|Ifgt	interferon gamma receptor 2	protein-coding
mm_151352.1	chr19	55898264	55898274	+	1	NA	intron (NM_001142924, intron 1 of 11)	intron (NM_001142924, intron 1 of 11)	2948	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_37783.1	chr4	130275200	130275210	-	1	NA	promoter-TSS (NM_001253386)	promoter-TSS (NM_001253386)	15	NM_001253386	230779	Mm.45132	NM_172702	ENSMUSG00000023232	Serinc2	2310004K20Rik|AW121759|FKSG84|TDE2|Tde2l	serine incorporator 2	protein-coding
mm_29164.1	chr3	106406091	106406110	-	1	NA	promoter-TSS (NM_178412)	promoter-TSS (NM_178412)	82	NM_178412	229688	Mm.261645	NM_178412	ENSMUSG00000027902	Chil6	BYm|Chil8	chitinase-like 6	protein-coding
mm_74146.1	chr8	123280972	123280982	+	1	NA	intron (NM_016925, intron 30 of 42)	PB1D7|SINE|Alu	-26755	NM_028200	72325	Mm.276193	NM_028200	ENSMUSG00000001062	Vps9d1	1300018I17Rik|2410004N05Rik|5DOS1|Vsp9d1	VPS9 domain containing 1	protein-coding
mm_156923.1	chrX	169220278	169220290	+	1	NA	exon (NM_001287530, exon 2 of 13)	exon (NM_001287530, exon 2 of 13)	-33075	NM_009666	11704	Mm.391342	NM_009666	ENSMUSG00000031354	Amelx	ALGN|AMGL|AMGX|Amel|Amg|LRAP|Rgsc888	amelogenin, X-linked	protein-coding
mm_69810.1	chr7	141263526	141263570	-	1	NA	TTS (NM_001081118)	TTS (NM_001081118)	2876	NM_001252601	54123	Mm.3233	NM_016850	ENSMUSG00000025498	Irf7	-	interferon regulatory factor 7	protein-coding
mm_135054.1	chr16	33787167	33787176	-	1	NA	Intergenic	Intergenic	-6866	NM_010739	17063	Mm.3177	NM_010739	ENSMUSG00000022824	Muc13	114/A10|14/A10|AI159736|Lrrp|Ly64|NJ-1	mucin 13, epithelial transmembrane	protein-coding
mm_106065.1	chr11	116132878	116132912	-	1	NA	exon (NM_024177, exon 7 of 9)	exon (NM_024177, exon 7 of 9)	-1767	NM_178802	338364	Mm.439976	NM_178802	ENSMUSG00000054517	Trim65	4732463G12Rik	tripartite motif-containing 65	protein-coding
mm_152440.1	chr19	10738972	10738982	-	1	NA	promoter-TSS (NM_007650)	promoter-TSS (NM_007650)	-3	NM_007650	12507	Mm.779	NM_007650	ENSMUSG00000024669	Cd5	Ly-1|Ly-12|Ly-A|Lyt-1	CD5 antigen	protein-coding
mm_68067.1	chr7	101868448	101868498	-	1	NA	5' UTR (NM_008034, exon 3 of 7)	5' UTR (NM_008034, exon 3 of 7)	2315	NM_001252554	14275	Mm.2135	NM_008034	ENSMUSG00000001827	Folr1	FBP1|Folbp-1|Folbp1	folate receptor 1 (adult)	protein-coding
mm_16685.1	chr2	6884558	6884568	-	1	NA	intron (NM_001110229, intron 2 of 14)	intron (NM_001110229, intron 2 of 14)	433	NM_010160	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_52764.1	chr6	120927166	120927183	+	1	NA	Intergenic	Intergenic	-10354	NM_007544	12122	Mm.235081	NM_007544	ENSMUSG00000004446	Bid	2700049M22Rik|AI875481|AU022477	BH3 interacting domain death agonist	protein-coding
mm_127191.1	chr15	99030378	99030397	+	1	NA	5' UTR (NM_009448, exon 1 of 4)	5' UTR (NM_009448, exon 1 of 4)	496	NM_009448	22146	Mm.88212	NM_009448	ENSMUSG00000043091	Tuba1c	M[a]6|Tuba6	tubulin, alpha 1C	protein-coding
mm_145584.1	chr18	60984438	60984451	+	1	NA	exon (NM_001286809, exon 5 of 6)	exon (NM_001286809, exon 5 of 6)	20890	NM_001286809	12322	Mm.131530	NM_009792	ENSMUSG00000024617	Camk2a	CaMKII|R74975|mKIAA0968	calcium/calmodulin-dependent protein kinase II alpha	protein-coding
mm_154094.1	chr19	56952004	56952020	-	1	NA	intron (NM_001177797, intron 1 of 18)	Lx7|LINE|L1	56563	NM_146102	226250	Mm.226284	NM_146102	ENSMUSG00000025083	Afap1l2	AU041783|C86904|mKIAA1914	actin filament associated protein 1-like 2	protein-coding
mm_23408.1	chr3	58415317	58415324	+	1	NA	5' UTR (NM_001347233, exon 1 of 3)	5' UTR (NM_001347233, exon 1 of 3)	600	NM_001081229	72033	Mm.218409	NM_001081229	ENSMUSG00000027806	Tsc22d2	1810043J12Rik|5530402M19Rik	TSC22 domain family, member 2	protein-coding
mm_116289.1	chr13	35167804	35167806	-	1	NA	Intergenic	Intergenic	-13818	NR_045616	100503727	Mm.32214	NR_045616	ENSMUSG00000102099	1700011B04Rik	-	RIKEN cDNA 1700011B04 gene	ncRNA
mm_41505.1	chr5	92346993	92347025	+	1	NA	3' UTR (NM_021274, exon 4 of 4)	3' UTR (NM_021274, exon 4 of 4)	1880	NM_021274	15945	Mm.877	NM_021274	ENSMUSG00000034855	Cxcl10	C7|CRG-2|INP10|IP-10|IP10|Ifi10|Scyb10|gIP-10|mob-1	chemokine (C-X-C motif) ligand 10	protein-coding
mm_34597.1	chr4	150236771	150236780	+	1	NA	promoter-TSS (NM_001025388).2	promoter-TSS (NM_001025388).2	-422	NM_023119	13806	Mm.70666	NM_023119	ENSMUSG00000063524	Eno1	0610008I15|AL022784|Eno-1|MBP-1	enolase 1, alpha non-neuron	protein-coding
mm_492.1	chr1	36779947	36779952	+	1	NA	intron (NM_009539, intron 9 of 12)	intron (NM_009539, intron 9 of 12)	965	NM_001289612	22637	Mm.8038	NM_009539	ENSMUSG00000026117	Zap70	Srk|ZAP-70|mrtle|mur	zeta-chain (TCR) associated protein kinase	protein-coding
mm_53384.1	chr6	129533155	129533181	+	1	NA	promoter-TSS (NM_020590)	promoter-TSS (NM_020590)	-24	NM_020590	57436	Mm.14638	NM_020590	ENSMUSG00000030161	Gabarapl1	3110025G09Rik|9130422N19Rik|AI196471|Apg8l|Atg8l|GECI|MNCb-0091	gamma-aminobutyric acid (GABA) A receptor-associated protein-like 1	protein-coding
mm_70821.1	chr8	23139003	23139019	+	1	NA	promoter-TSS (NM_001310437)	promoter-TSS (NM_001310437)	-19	NM_001310436	11733	Mm.334444	NM_031158	ENSMUSG00000031543	Ank1	Ank-1|nb|pale	ankyrin 1, erythroid	protein-coding
mm_99747.1	chr11	106580698	106580716	+	1	NA	intron (NM_198292, intron 1 of 11)	intron (NM_198292, intron 1 of 11)	32223	NM_198292	21763	Mm.102407	NM_198292	ENSMUSG00000040548	Tex2	4930568E07Rik|AI553404|Def-5|Taz4	testis expressed gene 2	protein-coding
mm_1958.1	chr1	86424154	86424160	+	1	NA	Intergenic	ORR1D2|LTR|ERVL-MaLR	-2172	NM_027966	71863	Mm.179627	NM_027966	ENSMUSG00000036574	1700019O17Rik	-	RIKEN cDNA 1700019O17 gene	protein-coding
mm_87876.1	chr10	61648561	61648578	+	1	NA	promoter-TSS (NM_026438)	promoter-TSS (NM_026438)	-52	NM_026438	67895	Mm.28897	NM_026438	ENSMUSG00000020089	Ppa1	2010317E03Rik|Pyp	pyrophosphatase (inorganic) 1	protein-coding
mm_170845.1	chr2	177498226	177498228	+	1	NA	promoter-TSS (NR_036450)	promoter-TSS (NR_036450)	1	NR_036450	433520	Mm.425117	NM_001024825		Gm14403	OTTMUSG00000016571	predicted gene 14403	ncRNA
mm_33323.1	chr4	129105505	129105528	+	1	NA	promoter-TSS (NM_001290706)	promoter-TSS (NM_001290706)	-14	NM_025452	66260	Mm.25295	NM_025452	ENSMUSG00000028786	Tmem54	1810017F10Rik|AI507302	transmembrane protein 54	protein-coding
mm_98275.1	chr11	89016878	89016893	+	1	NA	3' UTR (NM_009546, exon 9 of 9)	3' UTR (NM_009546, exon 9 of 9)	17482	NM_009546	217069	Mm.248445	NM_009546	ENSMUSG00000000275	Trim25	AA960166|AL022677|EFP|Zfp147	tripartite motif-containing 25	protein-coding
mm_5252.1	chr1	16619304	16619314	-	1	NA	promoter-TSS (NM_001271017)	promoter-TSS (NM_001271017)	29	NM_025773	66799	Mm.122430	NM_025773	ENSMUSG00000025939	Ube2w	6130401J04Rik	ubiquitin-conjugating enzyme E2W (putative)	protein-coding
mm_15925.1	chr2	165066984	165067002	+	1	NA	intron (NM_170702, intron 6 of 7)	intron (NM_170702, intron 6 of 7)	11357	NM_011611	21939	Mm.271833	NM_011611	ENSMUSG00000017652	Cd40	AI326936|Bp50|GP39|HIGM1|IGM|IMD3|T-BAM|TRAP|Tnfrsf5|p50	CD40 antigen	protein-coding
mm_1566.1	chr1	74233043	74233055	+	1	NA	Intergenic	RLTR33|LTR|ERVK	-3501	NM_029711	76709	Mm.337038	NM_029711	ENSMUSG00000006304	Arpc2	2210023N03Rik|34kDa|p34-Arc	actin related protein 2/3 complex, subunit 2	protein-coding
mm_11126.1	chr2	28229751	28229761	+	1	NA	3' UTR (NM_001038613, exon 6 of 6)	3' UTR (NM_001038613, exon 6 of 6)	24067	NM_019498	56177	Mm.43278	NM_019498	ENSMUSG00000026833	Olfm1	AMY|AW742568|Noe1|OlfA|Pancortin|Pancortin3	olfactomedin 1	protein-coding
mm_81553.1	chr9	110333403	110333435	+	1	NA	promoter-TSS (NM_001001144)	promoter-TSS (NM_001001144)	63	NM_001001144	235623	Mm.288741	NM_001001144	ENSMUSG00000032485	Scap	9530044G19|mKIAA0199	SREBF chaperone	protein-coding
mm_130102.1	chr15	89429334	89429351	-	1	NA	intron (NR_037153, intron 1 of 9)	CpG	585	NR_037154	12651	Mm.485045	NM_007692	ENSMUSG00000022617	Chkb	Chetk|Chkl|Ck|Ck/Ek|Ck/Ek-beta|Ckb|Ckekb|Ek	choline kinase beta	protein-coding
mm_169093.1	chr1	34074813	34074815	+	1	NA	intron (NM_133833, intron 1 of 92)	intron (NM_133833, intron 1 of 92)	-42545	NR_105861	102466987		NR_105861	ENSMUSG00000105982	Mir6896	mmu-mir-6896	microRNA 6896	ncRNA
mm_85113.1	chr9	95407228	95407239	-	1	NA	promoter-TSS (NM_018763)	promoter-TSS (NM_018763)	37	NM_018763	54371	Mm.212446	NM_018763	ENSMUSG00000033350	Chst2	AI428561|AW121776|C130041E03Rik|Chts2|GST-2|GlcNAc6ST|Gn6st	carbohydrate sulfotransferase 2	protein-coding
mm_63051.1	chr7	121865071	121865093	+	1	NA	promoter-TSS (NM_011325)	promoter-TSS (NM_011325)	44	NR_073548	20277	Mm.7709	NM_011325	ENSMUSG00000030873	Scnn1b	-	sodium channel, nonvoltage-gated 1 beta	protein-coding
mm_125457.1	chr15	52044889	52044892	+	1	NA	exon (NM_175503, exon 2 of 2)	exon (NM_175503, exon 2 of 2)	4783	NM_175503	239435	Mm.24204	NM_175503	ENSMUSG00000068522	Aard	A5D3|AV328152	alanine and arginine rich domain containing protein	protein-coding
mm_26242.1	chr3	141465568	141465570	+	1	NA	promoter-TSS (NM_009472)	promoter-TSS (NM_009472)	5	NM_001293561	22253	Mm.24430	NM_009472	ENSMUSG00000059921	Unc5c	B130051O18Rik|Unc5h3|rcm	unc-5 netrin receptor C	protein-coding
mm_904.1	chr1	53823726	53823746	+	1	NA	intron (NM_001001883, intron 28 of 28)	intron (NM_001001883, intron 28 of 28)	-25688	NR_106149	102465783		NR_106149	ENSMUSG00000098443	Mir7681	Gm27806|mmu-mir-7681	microRNA 7681	ncRNA
mm_167891.1	chrX	61184007	61184022	+	1	NA	exon (NM_001166658, exon 1 of 1)	exon (NM_001166658, exon 1 of 1)	1544	NM_001166658	631990	Mm.401324	NM_001166658	ENSMUSG00000090546	Cdr1	100039759|Cdr|Cdr34|EG631990|Gm2409|Gm7077	cerebellar degeneration related antigen 1	protein-coding
mm_109678.1	chr12	113132830	113132852	+	1	NA	intron (NM_001346696, intron 16 of 19)	intron (NM_001346696, intron 16 of 19)	-7395	NM_024223	68337	Mm.133825	NM_024223	ENSMUSG00000006356	Crip2	0610010I23Rik|AW743261|C77570|CRP2|CRP4|Crp|ESP1|Hlp	cysteine rich protein 2	protein-coding
mm_29681.1	chr3	122984405	122984512	-	1	NA	promoter-TSS (NM_133857)	promoter-TSS (NM_133857)	-11	NM_133857	99526	Mm.491248	NM_133857	ENSMUSG00000039701	Usp53	AA939927|Phxr3|Sp6|mKIAA1350|mbo	ubiquitin specific peptidase 53	protein-coding
mm_135075.1	chr16	34262946	34262972	-	1	NA	intron (NM_001164268, intron 10 of 33)	intron (NM_001164268, intron 10 of 33)	251068	NM_001164268	545156	Mm.82274	NM_177357	ENSMUSG00000061751	Kalrn	2210407G14Rik|AV235988|DUET|E530005C20Rik|Gm539|Hapip|TRAD	kalirin, RhoGEF kinase	protein-coding
mm_119849.1	chr14	54440806	54440818	+	1	NA	3' UTR (NM_008608, exon 10 of 10)	3' UTR (NM_008608, exon 10 of 10)	9214	NM_008608	17387	Mm.280175	NM_008608	ENSMUSG00000000957	Mmp14	AI325305|MMP-X1|MT-MMP-1|MT1-MMP|sabe	matrix metallopeptidase 14 (membrane-inserted)	protein-coding
mm_27795.1	chr3	75647938	75647941	-	1	NA	intron (NR_040539, intron 2 of 2)	intron (NR_040539, intron 2 of 2)	7792	NR_040539	69193	Mm.374088	NR_040539	ENSMUSG00000099370	Platr10	2410007B07Rik	pluripotency associated transcript 10	ncRNA
mm_15823.1	chr2	164564154	164564173	+	1	NA	exon (NM_026323, exon 3 of 5)	exon (NM_026323, exon 3 of 5)	1447	NM_026323	67701	Mm.27289	NM_026323	ENSMUSG00000017723	Wfdc2	1600023A02Rik|HE4|WAP5	WAP four-disulfide core domain 2	protein-coding
mm_148580.1	chr19	5024043	5024155	+	1	NA	promoter-TSS (NM_007854)	promoter-TSS (NM_007854)	93	NM_007854	13340	Mm.4930	NM_007854	ENSMUSG00000024891	Slc29a2	Der12|Ent2|Hnp36	solute carrier family 29 (nucleoside transporters), member 2	protein-coding
mm_153486.1	chr19	41305981	41306008	-	1	NA	intron (NM_031376, intron 9 of 16)	intron (NM_031376, intron 9 of 16)	-41990	NM_133352	107358	Mm.246440	NM_133352	ENSMUSG00000025016	Tm9sf3	1810073M23Rik|2810031D16Rik|AI115521|AI413748|AW146116|AW549777|Smbp|mKIAA4036	transmembrane 9 superfamily member 3	protein-coding
mm_59345.1	chr7	25627155	25627168	+	1	NA	promoter-TSS (NM_146184)	promoter-TSS (NM_146184)	-463	NM_001036740	232984	Mm.192369	NM_146184	ENSMUSG00000059479	B3gnt8	B3galt7|B7galt7|BC025206	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 8	protein-coding
mm_113926.1	chr13	49608031	49608063	+	1	NA	promoter-TSS (NM_008760)	promoter-TSS (NM_008760)	-24	NM_008760	18295	Mm.4258	NM_008760	ENSMUSG00000021390	Ogn	3110079A16Rik|OG|OIF|SLRR3A|mimecan|mimican	osteoglycin	protein-coding
mm_146380.1	chr18	82585167	82585188	+	1	NA	3' UTR (NM_010777, exon 7 of 7)	3' UTR (NM_010777, exon 7 of 7)	30669	NM_001025254	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_113615.1	chr13	41487142	41487170	+	1	NA	intron (NM_001111324, intron 1 of 7)	intron (NM_001111324, intron 1 of 7)	204	NM_001111324	18003	Mm.288980	NM_017464	ENSMUSG00000021365	Nedd9	Cas-L|CasL|HEF1|MEF1|Nedd-9|p105	neural precursor cell expressed, developmentally down-regulated gene 9	protein-coding
mm_11143.1	chr2	28506946	28506977	+	1	NA	Intergenic	B1_Mus1|SINE|Alu	-6206	NM_009058	19730	Mm.5236	NM_009058	ENSMUSG00000026821	Ralgds	Gnds|Rgds|mKIAA1308	ral guanine nucleotide dissociation stimulator	protein-coding
mm_111263.1	chr12	85151265	85151275	-	1	NA	promoter-TSS (NM_146244)	promoter-TSS (NM_146244)	-6	NM_146244	238323	Mm.44829	NM_146244	ENSMUSG00000019235	Rps6kl1	A830084F09Rik|AW046440	ribosomal protein S6 kinase-like 1	protein-coding
mm_91397.1	chr10	30793310	30793313	-	1	NA	intron (NM_172495, intron 1 of 15)	MusHAL1|LINE|L1	9796	NM_172495	211329	Mm.297903	NM_172495	ENSMUSG00000039697	Ncoa7	9030406N13Rik	nuclear receptor coactivator 7	protein-coding
mm_139824.1	chr17	68187909	68187920	+	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	-85883	NM_177278	320858	Mm.137356	NM_177278	ENSMUSG00000041565	L3mbtl4	A730037L19Rik|D930040M24Rik	l(3)mbt-like 4 (Drosophila)	protein-coding
mm_93683.1	chr10	117815064	117815076	-	1	NA	3' UTR (NM_024457, exon 8 of 8)	3' UTR (NM_024457, exon 8 of 8)	-22365	NM_134010	103468	Mm.12568	NM_134010	ENSMUSG00000052798	Nup107	AW541137|C76801	nucleoporin 107	protein-coding
mm_6360.1	chr1	72146916	72146931	-	1	NA	Intergenic	Intergenic	65384	NM_001005423	381269	Mm.422636	NM_001005423	ENSMUSG00000039395	Mreg	Gm974|Wdt2|dsu	melanoregulin	protein-coding
mm_29912.1	chr3	131474771	131474792	-	1	NA	Intergenic	Intergenic	-89987	NM_001289479	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_141840.1	chr17	34729388	34729397	-	1	NA	intron (NM_009780, intron 38 of 40)	intron (NM_009780, intron 38 of 40)	14505	NM_009780	12268	Mm.477109	NM_009780	ENSMUSG00000073418	C4b	C4|Ss	complement component 4B (Chido blood group)	protein-coding
mm_116056.1	chr13	27438641	27438655	-	1	NA	promoter-TSS (NM_011167)	promoter-TSS (NM_011167)	40	NM_001271379	19112	Mm.142728	NM_011167	ENSMUSG00000021345	Prl8a6	Ghd13|PLP-C1|PLP-Ca|PLP-calpha|Prlpc|Prlpc1	prolactin family 8, subfamily a, member 6	protein-coding
mm_106801.1	chr12	4944913	4944933	+	1	NA	exon (NM_001099628, exon 7 of 31)	exon (NM_001099628, exon 7 of 31)	27570	NM_001099628	320817	Mm.210966	NM_001099628	ENSMUSG00000052812	Atad2b	1110014E10Rik|BC032887|C79189|D530031C13Rik	ATPase family, AAA domain containing 2B	protein-coding
mm_26588.1	chr3	151294230	151294243	+	1	NA	Intergenic	Intergenic	-143646	NM_133222	170757	Mm.317261	NM_133222	ENSMUSG00000039167	Adgrl4	1110033N21Rik|ETL1|Eltd1|Etl	adhesion G protein-coupled receptor L4	protein-coding
mm_65405.1	chr7	25230950	25230956	-	1	NA	TTS (NR_046001)	TTS (NR_046001)	2230	NR_046001	77124	Mm.294664	NM_178400	ENSMUSG00000090330	9130221H12Rik	AU016887	RIKEN cDNA 9130221H12 gene	ncRNA
mm_101372.1	chr11	23770800	23770808	-	1	NA	5' UTR (NM_009044, exon 1 of 10)	5' UTR (NM_009044, exon 1 of 10)	166	NM_009044	19696	Mm.4869	NM_009044	ENSMUSG00000020275	Rel	c-Rel	reticuloendotheliosis oncogene	protein-coding
mm_56104.1	chr6	87483382	87483392	-	1	NA	intron (NM_001037727, intron 4 of 10)	intron (NM_001037727, intron 4 of 10)	12940	NR_104483	232201	Mm.119564	NM_175476	ENSMUSG00000030047	Arhgap25	A130039I20Rik	Rho GTPase activating protein 25	protein-coding
mm_24169.1	chr3	88564448	88564459	+	1	NA	exon (NM_033526, exon 7 of 11)	exon (NM_033526, exon 7 of 11)	10737	NM_033526	94232	Mm.303059	NM_033526	ENSMUSG00000008604	Ubqln4	A1Up|A1u|AI663987|CIP75|UBIN	ubiquilin 4	protein-coding
mm_19520.1	chr2	94066748	94066755	-	1	NA	intron (NM_019657, intron 4 of 10)	intron (NM_019657, intron 4 of 10)	-56021	NM_026944	69113	Mm.272498	NM_026944	ENSMUSG00000040174	Alkbh3	1700108H04Rik|1810020C19Rik|Abh3|mABH3	alkB homolog 3, alpha-ketoglutarate-dependent dioxygenase	protein-coding
mm_166863.1	chr7	24457911	24457921	+	1	NA	Intergenic	Intergenic	-4567	NM_011113	18793	Mm.1359	NM_011113	ENSMUSG00000046223	Plaur	Cd87|u-PAR|uPAR	plasminogen activator, urokinase receptor	protein-coding
mm_106044.1	chr11	116079555	116079602	-	1	NA	exon (NM_016852, exon 8 of 8)	exon (NM_016852, exon 8 of 8)	-1617	NM_001009573	70450	Mm.259460	NM_001009573	ENSMUSG00000057948	Unc13d	2610108D09Rik|Jinx|Munc13-4|mFLJ00067	unc-13 homolog D (C. elegans)	protein-coding
mm_102099.1	chr11	52360940	52360955	-	1	NA	promoter-TSS (NM_011694)	promoter-TSS (NM_011694)	85	NM_011694	22333	Mm.3555	NM_011694	ENSMUSG00000020402	Vdac1	AL033343|Vdac5|mVDAC1|mVDAC5	voltage-dependent anion channel 1	protein-coding
mm_155830.1	chrX	100730157	100730167	+	1	NA	promoter-TSS (NM_001305941)	promoter-TSS (NM_001305941)	-24	NM_001305941	71584	Mm.283495	NM_023608	ENSMUSG00000019359	Gdpd2	9130017L10Rik|Gde3|Obdpf	glycerophosphodiester phosphodiesterase domain containing 2	protein-coding
mm_84827.1	chr9	78108618	78108650	-	1	NA	promoter-TSS (NM_001163780)	promoter-TSS (NM_001163780)	22	NM_023605	71538	Mm.28584	NM_023605	ENSMUSG00000001366	Fbxo9	9030401P18Rik|AA986398	f-box protein 9	protein-coding
mm_149309.1	chr19	10741892	10741897	+	1	NA	intron (NR_027805, intron 1 of 3)	intron (NR_027805, intron 1 of 3)	947	NR_027805	403202	Mm.34482	NM_207529	ENSMUSG00000067577	A430093F15Rik	Gm674	RIKEN cDNA A430093F15 gene	ncRNA
mm_106152.1	chr11	116610474	116610485	-	1	NA	5' UTR (NM_172572, exon 2 of 19)	5' UTR (NM_172572, exon 2 of 19)	13773	NM_001167680	217344	Mm.89695	NM_172572	ENSMUSG00000020806	Rhbdf2	4732465I17Rik|Rhbdl6|cub	rhomboid 5 homolog 2	protein-coding
mm_85464.1	chr9	105495154	105495189	-	1	NA	promoter-TSS (NM_175025)	promoter-TSS (NM_175025)	-38	NM_001253836	235574	Mm.326247	NM_175025	ENSMUSG00000032570	Atp2c1	1700121J11Rik|ATP2C1A|AW061228|BCPM|D930003G21Rik|HHD|SPCA|pmr1	ATPase, Ca++-sequestering	protein-coding
mm_172254.1	chr6	70240997	70241011	-	1	NA	Intergenic	Intergenic	551171	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_44127.1	chr5	149641578	149641615	+	1	NA	Intergenic	Intergenic	-5260	NM_001347534	15505	Mm.270681	NM_013559	ENSMUSG00000029657	Hsph1	105kDa|AI790491|Hsp105|Hsp110|hsp-E7I|hsp110/105	heat shock 105kDa/110kDa protein 1	protein-coding
mm_126302.1	chr15	79428981	79428987	+	1	NA	intron (NM_001289898, intron 4 of 10)	intron (NM_001289898, intron 4 of 10)	12834	NM_001289899	27373	Mm.30199	NM_013767	ENSMUSG00000022433	Csnk1e	AI426939|AI551861|AW457082|CK1epsilon|CKIe|KC1epsilon|tau	casein kinase 1, epsilon	protein-coding
mm_113602.1	chr13	41236318	41236334	+	1	NA	Intergenic	Intergenic	-13518	NM_001135577	108934	Mm.38578	NM_001135577	ENSMUSG00000091264	Smim13	2900036K02Rik	small integral membrane protein 13	protein-coding
mm_130954.1	chr15	103255434	103255445	-	1	NA	promoter-TSS (NM_008685)	promoter-TSS (NM_008685)	0	NM_008685	18022	Mm.457989	NM_008685	ENSMUSG00000058794	Nfe2	NF-E2|NF-E2/P45|p45|p45NFE2|p45nf-e2	nuclear factor, erythroid derived 2	protein-coding
mm_170298.1	chr18	32560019	32560025	-	1	NA	promoter-TSS (NM_001048207)	promoter-TSS (NM_001048207)	12	NM_001347610	71683	Mm.292145	NM_027863	ENSMUSG00000090523	Gypc	0610037F22Rik|Cd236r	glycophorin C	protein-coding
mm_167642.1	chr9	64796378	64796386	-	1	NA	Intergenic	Intergenic	-14629	NM_001162917	102442	Mm.222473	NM_176935	ENSMUSG00000053641	Dennd4a	AI115600|AI851943|F730015K02Rik	DENN/MADD domain containing 4A	protein-coding
mm_55804.1	chr6	82857657	82857690	-	1	NA	Intergenic	Intergenic	24180	NR_040520	69652	Mm.96357	NR_040520	ENSMUSG00000100291	2310069B03Rik	-	RIKEN cDNA 2310069B03 gene	ncRNA
mm_162802.1	chr10	77515820	77515826	-	1	NA	promoter-TSS (NM_133998)	promoter-TSS (NM_133998)	-10	NM_133998	108707	Mm.259547	NM_133998	ENSMUSG00000032977	Fam207a	1810008A18Rik|AI303072	family with sequence similarity 207, member A	protein-coding
mm_118251.1	chr13	112172163	112172206	-	1	NA	Intergenic	Intergenic	-116267	NM_001168403	77318	Mm.159895	NM_029898	ENSMUSG00000049985	Ankrd55	C030011J08Rik	ankyrin repeat domain 55	protein-coding
mm_134920.1	chr16	30388691	30388701	-	1	NA	promoter-TSS (NM_001128094)	promoter-TSS (NM_001128094)	-166	NM_001128096	224088	Mm.8924	NM_001128094	ENSMUSG00000022533	Atp13a3	AU022875|Gm1745|Gm541|Gm542	ATPase type 13A3	protein-coding
mm_18601.1	chr2	67516470	67516476	-	1	NA	exon (NM_001083919, exon 7 of 9)	exon (NM_001083919, exon 7 of 9)	70471	NM_001024618	241431	Mm.261043	NM_001024618	ENSMUSG00000027022	Xirp2	2310003D02Rik|2310008C07Rik|A530024P18Rik|AI452089|Cmya3|Gm352|Xin2	xin actin-binding repeat containing 2	protein-coding
mm_149464.1	chr19	11531273	11531300	+	1	NA	TTS (NM_027209)	TTS (NM_027209)	-5563	NM_025658	66607	Mm.441056	NM_025658	ENSMUSG00000024678	Ms4a4d	2210417J23Rik	membrane-spanning 4-domains, subfamily A, member 4D	protein-coding
mm_40018.1	chr5	33162144	33162154	+	1	NA	3' UTR (NM_019810, exon 15 of 15)	3' UTR (NM_019810, exon 15 of 15)	56089	NM_133903	100689	Mm.34694	NM_133903	ENSMUSG00000037379	Spon2	2310045I24Rik|AI504350|M-spondin|Mindin|Mspondin	spondin 2, extracellular matrix protein	protein-coding
mm_55644.1	chr6	72347819	72347829	-	1	NA	intron (NM_026696, intron 2 of 3)	intron (NM_026696, intron 2 of 3)	507	NM_026696	68364	Mm.52711	NM_026696	ENSMUSG00000058706	0610030E20Rik	1500031N04Rik|2810411C16Rik|AI461894	RIKEN cDNA 0610030E20 gene	protein-coding
mm_135408.1	chr16	44746338	44746368	-	1	NA	promoter-TSS (NM_025332)	promoter-TSS (NM_025332)	10	NM_001159329	66067	Mm.34520	NM_025332	ENSMUSG00000022668	Gtpbp8	0610037H22Rik	GTP-binding protein 8 (putative)	protein-coding
mm_106604.1	chr11	120781827	120781841	-	1	NA	exon (NM_009053, exon 8 of 8)	exon (NM_009053, exon 8 of 8)	2370	NM_009053	19719	Mm.871	NM_009053	ENSMUSG00000025158	Rfng	-	RFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	protein-coding
mm_67519.1	chr7	80905061	80905081	-	1	NA	promoter-TSS (NM_001291280)	promoter-TSS (NM_001291280)	-9	NM_001291280	68039	Mm.22246	NM_026523	ENSMUSG00000025723	Nmb	3110023K12Rik	neuromedin B	protein-coding
mm_73901.1	chr8	119442479	119442512	+	1	NA	exon (NM_027950, exon 3 of 6)	exon (NM_027950, exon 3 of 6)	-4224	NM_054095	117148	Mm.356184	NM_054095	ENSMUSG00000031837	Necab2	Efcbp2	N-terminal EF-hand calcium binding protein 2	protein-coding
mm_104557.1	chr11	96824131	96824159	-	1	NA	promoter-TSS (NM_001130451)	promoter-TSS (NM_001130451)	-18	NM_001130451	18023	Mm.6743	NM_008686	ENSMUSG00000038615	Nfe2l1	AA408798|AW212678|LCR-F1|Lcrf1|NRF1|TCF-11|TCF11	nuclear factor, erythroid derived 2,-like 1	protein-coding
mm_41021.1	chr5	81512828	81512832	+	1	NA	intron (NM_001347371, intron 7 of 23)	intron (NM_001347371, intron 7 of 23)	491237	NM_198702	319387	Mm.273631	NM_198702	ENSMUSG00000037605	Adgrl3	5430402I23Rik|CIRL-3|D130075K09Rik|Gm1379|LEC3|Lphn3|mKIAA0768	adhesion G protein-coupled receptor L3	protein-coding
mm_53903.1	chr6	3494588	3494598	-	1	NA	promoter-TSS (NM_178899)	promoter-TSS (NM_178899)	-95	NM_178899	101202	Mm.206911	NM_178899	ENSMUSG00000044156	Hepacam2	AI987662	HEPACAM family member 2	protein-coding
mm_39904.1	chr5	31251744	31251758	+	1	NA	promoter-TSS (NM_027221)	promoter-TSS (NM_027221)	45	NM_027221	69815	Mm.389609	NM_027221	ENSMUSG00000029149	Krtcap3	2010001C09Rik|AW321088|Kcp3	keratinocyte associated protein 3	protein-coding
mm_130782.1	chr15	101550658	101550665	-	1	NA	promoter-TSS (NM_053249)	promoter-TSS (NM_053249)	-2	NM_053249	114566	Mm.458432	NM_053249	ENSMUSG00000049548	Krt82	Krt2-20	keratin 82	protein-coding
mm_24270.1	chr3	89202917	89202962	+	1	NA	promoter-TSS (NM_001077411)	promoter-TSS (NM_001077411)	14	NR_122037	14466	Mm.5031	NM_008094	ENSMUSG00000028048	Gba	GBA1|GC|GCase|GLUC|betaGC	glucosidase, beta, acid	protein-coding
mm_36858.1	chr4	106859588	106859596	-	1	NA	Intergenic	Intergenic	-51878	NM_198438	72475	Mm.195635	NM_023672	ENSMUSG00000061887	Ssbp3	2610021L12Rik|2610200M23Rik|5730488C10Rik|AI854733|AW551939|LAST|SSDP1	single-stranded DNA binding protein 3	protein-coding
mm_154827.1	chrX	17725444	17725462	+	1	NA	Intergenic	RMER17B2|LTR|ERVK	-153128	NM_028058	72018	Mm.41558	NM_028058	ENSMUSG00000025040	Fundc1	1500005J14Rik|1810033P05Rik	FUN14 domain containing 1	protein-coding
mm_162095.1	chrX	37571413	37571413	+	1	NA	promoter-TSS (NM_001085356)	promoter-TSS (NM_001085356)	-8	NM_001085356	434764	Mm.379498	NM_001085356	ENSMUSG00000095741	Rhox2f	EG434764|Rhox2.6|Rhox2e	reproductive homeobox 2F	protein-coding
mm_154451.1	chrM	2068	2109	-	1	NA	NA	LSU-rRNA_Hsa|rRNA|rRNA	NA	NA								
mm_144571.1	chr18	31804085	31804120	+	1	NA	promoter-TSS (NM_028866)	promoter-TSS (NM_028866)	45	NM_001170966	74320	Mm.277705	NM_028866	ENSMUSG00000024400	Wdr33	1110001N06Rik|2310011G05Rik|2810021O11Rik|8430413N20Rik|WDC146	WD repeat domain 33	protein-coding
mm_99544.1	chr11	103344732	103344759	+	1	NA	promoter-TSS (NM_133715)	promoter-TSS (NM_133715)	-8	NR_045346	653030	Mm.440684	NR_045346	ENSMUSG00000085887	Arhgap27os3	F830206d12rik|Gm11648|OTTMUSG00000003073	Rho GTPase activating protein 27, opposite strand 3	ncRNA
mm_551.1	chr1	38019169	38019192	+	1	NA	exon (NM_198303, exon 4 of 24)	exon (NM_198303, exon 4 of 24)	21170	NM_198303	226982	Mm.260943	NM_198303	ENSMUSG00000026083	Eif5b	A030003E17Rik|BC018347|IF2	eukaryotic translation initiation factor 5B	protein-coding
mm_120937.1	chr14	76515943	76515953	+	1	NA	non-coding (NR_045660, exon 3 of 4)	non-coding (NR_045660, exon 3 of 4)	4907	NR_045660	75789	Mm.159571	NR_045660	ENSMUSG00000097172	4930444M15Rik	-	RIKEN cDNA 4930444M15 gene	ncRNA
mm_10139.1	chr2	4152589	4152610	+	1	NA	promoter-TSS (NM_172475)	promoter-TSS (NM_172475)	-264	NM_172475	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding
mm_154459.1	chrM	3022	3048	-	1	NA	NA	Intergenic	NA	NA								
mm_100057.1	chr11	115245263	115245280	+	1	NA	3' UTR (NM_001033393, exon 10 of 10)	3' UTR (NM_001033393, exon 10 of 10)	21972	NM_010350	14813	Mm.39090	NM_010350	ENSMUSG00000020734	Grin2c	GluN2C|NMDAR2C|NR2C	glutamate receptor, ionotropic, NMDA2C (epsilon 3)	protein-coding
mm_61145.1	chr7	57590566	57590572	+	1	NA	promoter-TSS (NM_001038701)	promoter-TSS (NM_001038701)	51	NM_001038701	14402	Mm.8004	NM_008071	ENSMUSG00000033676	Gabrb3	A230092K12Rik|AW049585|Cp1|Gabrb-3|beta3	gamma-aminobutyric acid (GABA) A receptor, subunit beta 3	protein-coding
mm_134322.1	chr16	16146772	16146836	-	1	NA	promoter-TSS (NM_146068)	promoter-TSS (NM_146068)	47	NM_146068	224008	Mm.244703	NM_146068	ENSMUSG00000041974	Spidr	2310008H04Rik|Kiaa0146	scaffolding protein involved in DNA repair	protein-coding
mm_47180.1	chr5	120749849	120749868	-	1	NA	promoter-TSS (NM_145227)	promoter-TSS (NM_145227)	-10	NM_001347448	246728	Mm.260926	NM_145227	ENSMUSG00000032690	Oas2	Oasl11	2'-5' oligoadenylate synthetase 2	protein-coding
mm_154322.1	chrM	2323	2333	+	1	NA	NA	Intergenic	NA	NA								
mm_139967.1	chr17	71673278	71673288	+	1	NA	promoter-TSS (NM_177087)	promoter-TSS (NM_177087)	22	NM_177087	320159	Mm.187372	NM_177087	ENSMUSG00000045761	Fam179a	4632412N22Rik	family with sequence similarity 179, member A	protein-coding
mm_169163.1	chr13	65469863	65469879	+	1	NA	Intergenic	RLTR27|LTR|ERVK	191017	NM_178364	170936	Mm.151546	NM_178364	ENSMUSG00000021514	Zfp369	B930030B22Rik|D230020H11Rik|NRIF2	zinc finger protein 369	protein-coding
mm_89294.1	chr10	87913606	87913622	+	1	NA	intron (NM_001314010, intron 3 of 4)	intron (NM_001314010, intron 3 of 4)	52503	NM_001111276	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_127910.1	chr15	9529739	9529772	-	1	NA	5' UTR (NM_008372, exon 1 of 8)	5' UTR (NM_008372, exon 1 of 8)	121	NM_008372	16197	Mm.389	NM_008372	ENSMUSG00000003882	Il7r	CD127|IL-7Ralpha	interleukin 7 receptor	protein-coding
mm_38020.1	chr4	133754398	133754408	-	1	NA	promoter-TSS (NM_001080819)	promoter-TSS (NM_001080819)	-792	NM_001080819	93760	Mm.22478	NM_001080819	ENSMUSG00000007880	Arid1a	1110030E03Rik|BAF250a|Osa1|Smarcf1	AT rich interactive domain 1A (SWI-like)	protein-coding
mm_106874.1	chr12	8010671	8010686	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	33001	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_106990.1	chr12	10391074	10391089	+	1	NA	TTS (NM_001310582)	TTS (NM_001310582)	301	NM_023697	105014	Mm.119343	NM_023697	ENSMUSG00000020621	Rdh14	3110030G19Rik|AW215439|PAN2	retinol dehydrogenase 14 (all-trans and 9-cis)	protein-coding
mm_66049.1	chr7	30729436	30729453	-	1	NA	promoter-TSS (NM_027215)	promoter-TSS (NM_027215)	90	NM_027215	69804	Mm.27499	NM_027215	ENSMUSG00000006315	Tmem147	2010004E11Rik|5033425B17Rik|Nifie14	transmembrane protein 147	protein-coding
mm_58661.1	chr7	6730564	6730646	+	1	NA	promoter-TSS (NM_001290994)	promoter-TSS (NM_001290994)	22	NM_001290994	57775	Mm.40752	NM_021323	ENSMUSG00000051527	Usp29	Ocat	ubiquitin specific peptidase 29	protein-coding
mm_58620.1	chr7	5069047	5069065	+	1	NA	intron (NM_133671, intron 5 of 11)	intron (NM_133671, intron 5 of 11)	6913	NM_001205231	22185	Mm.360389	NM_133671	ENSMUSG00000030435	U2af2	65kDa	U2 small nuclear ribonucleoprotein auxiliary factor (U2AF) 2	protein-coding
mm_25426.1	chr3	107877228	107877252	+	1	NA	promoter-TSS (NM_133867)	promoter-TSS (NM_133867)	10	NM_133867	99662	Mm.108491	NM_133867	ENSMUSG00000040600	Eps8l3	AI504489|Eps8r3	EPS8-like 3	protein-coding
mm_136696.1	chr17	7138496	7138502	+	1	NA	Intergenic	Intergenic	-31616	NM_011299	20112	Mm.268383	NM_011299	ENSMUSG00000023809	Rps6ka2	90kDa|D17Wsu134e|Rps6ka-rs1|Rsk3|p90rsk|pp90rsk	ribosomal protein S6 kinase, polypeptide 2	protein-coding
mm_144170.1	chr18	6557153	6557158	+	1	NA	Intergenic	Intergenic	-41047	NM_007935	13831	Mm.312133	NM_007935	ENSMUSG00000024240	Epc1	2400007E14Rik|5730566F07Rik|A930032N02Rik|mir-1893	enhancer of polycomb homolog 1 (Drosophila)	protein-coding
mm_73711.1	chr8	111688651	111688671	+	1	NA	TTS (NR_106044)	TTS (NR_106044)	1013	NR_106044	102466993		NR_106044	ENSMUSG00000099129	Mir7076	Gm27318|mmu-mir-7076	microRNA 7076	ncRNA
mm_2162.1	chr1	88227006	88227064	+	1	NA	promoter-TSS (NM_001281466)	promoter-TSS (NM_001281466)	15	NM_001281466	100040766	Mm.386915	NM_001177364	ENSMUSG00000079429	Mroh2a	ENSMUSG00000044873|Heatr7b1|OTTMUSG00000020804	maestro heat-like repeat family member 2A	protein-coding
mm_157099.1	chrX	9437536	9437543	-	1	NA	3' UTR (NM_007807, exon 13 of 13)	3' UTR (NM_007807, exon 13 of 13)	31785	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_76653.1	chr8	93191899	93191917	-	1	NA	intron (NM_053200, intron 3 of 13)	intron (NM_053200, intron 3 of 13)	5896	NM_053200	104158	Mm.292803	NM_053200	ENSMUSG00000056973	Ces1d	Ces3|TGH	carboxylesterase 1D	protein-coding
mm_100765.1	chr11	4594751	4594820	-	1	NA	promoter-TSS (NM_028860)	promoter-TSS (NM_028860)	30	NM_028860	74302	Mm.425669	NM_028860	ENSMUSG00000034354	Mtmr3	1700092A20Rik|AI255150|AW557713|FYVE-DSP1|ZFYVE10|mKIAA0371	myotubularin related protein 3	protein-coding
mm_85440.1	chr9	104102551	104102568	-	1	NA	intron (NM_145700, intron 1 of 2)	intron (NM_145700, intron 1 of 2)	24084	NM_145700	252837	Mm.269254	NM_145700	ENSMUSG00000079355	Ackr4	A630091E18Rik|CCBP2|CCR11|CCX-CKR|CCX-CKR1|Ccrl1|Cmkbrl1|PPR1|VSHK1	atypical chemokine receptor 4	protein-coding
mm_8736.1	chr1	160212692	160212714	-	1	NA	5' UTR (NM_009786, exon 1 of 6)	5' UTR (NM_009786, exon 1 of 6)	189	NM_009786	12301	Mm.10702	NM_009786	ENSMUSG00000014226	Cacybp	SIP	calcyclin binding protein	protein-coding
mm_24958.1	chr3	96676243	96676255	+	1	NA	intron (NM_001081139, intron 1 of 12)	intron (NM_001081139, intron 1 of 12)	6118	NM_001081139	213121	Mm.39732	NM_001081139	ENSMUSG00000038354	Ankrd35	4732436F15Rik	ankyrin repeat domain 35	protein-coding
mm_139568.1	chr17	57011581	57011596	+	1	NA	promoter-TSS (NM_133801)	promoter-TSS (NM_133801)	-300	NM_133801	98053	Mm.24632	NM_133801	ENSMUSG00000002658	Gtf2f1	2810405L04Rik|C76800|RAP74	general transcription factor IIF, polypeptide 1	protein-coding
mm_132321.1	chr16	33794048	33794064	+	1	NA	promoter-TSS (NM_010739)	promoter-TSS (NM_010739)	19	NM_010739	17063	Mm.3177	NM_010739	ENSMUSG00000022824	Muc13	114/A10|14/A10|AI159736|Lrrp|Ly64|NJ-1	mucin 13, epithelial transmembrane	protein-coding
mm_83901.1	chr9	56160941	56160968	-	1	NA	5' UTR (NM_019793, exon 1 of 7)	5' UTR (NM_019793, exon 1 of 7)	116	NM_019793	56434	Mm.28484	NM_019793	ENSMUSG00000032324	Tspan3	1700055K04Rik|TM4-A|Tm4sf8	tetraspanin 3	protein-coding
mm_114830.1	chr13	92355187	92355210	+	1	NA	promoter-TSS (NM_010829)	promoter-TSS (NM_010829)	-195	NM_010829	17686	Mm.343101	NM_010829	ENSMUSG00000014850	Msh3	D13Em1|Rep-3|Rep3	mutS homolog 3	protein-coding
mm_75056.1	chr8	33641941	33641981	-	1	NA	promoter-TSS (NM_178648)	promoter-TSS (NM_178648)	15	NM_178648	108159	Mm.29301	NM_178648	ENSMUSG00000052906	Ubxn8	D0H8S2298E|Rep-8|Rep8h|Ubxd6	UBX domain protein 8	protein-coding
mm_74956.1	chr8	26026701	26026705	-	1	NA	3' UTR (NM_207659, exon 22 of 22)	3' UTR (NM_207659, exon 22 of 22)	-11102	NM_008033	14272	Mm.3496	NM_008033	ENSMUSG00000015994	Fnta	FTA	farnesyltransferase, CAAX box, alpha	protein-coding
mm_56467.1	chr6	98945577	98945591	-	1	NA	exon (NM_053202, exon 13 of 19)	exon (NM_053202, exon 13 of 19)	82714	NM_001197322	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_50254.1	chr6	42585961	42585971	+	1	NA	Intergenic	Intergenic	11406	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_96079.1	chr11	60104917	60104967	+	1	NA	promoter-TSS (NM_009021)	promoter-TSS (NM_009021)	-71	NM_009021	19377	Mm.296366	NM_009021	ENSMUSG00000062115	Rai1	Gt1	retinoic acid induced 1	protein-coding
mm_170014.1	chr17	17326065	17326073	-	1	NA	Intergenic	RLTR9D|LTR|ERVK	31626	NM_001324550	100862203	Mm.484235	NM_001324550		Gm6712	EG626854	predicted gene 6712	protein-coding
mm_101153.1	chr11	16912727	16912732	-	1	NA	3' UTR (NM_207655, exon 28 of 28)	3' UTR (NM_207655, exon 28 of 28)	38553	NR_110421	72735	Mm.268598	NR_015469		Eldr	2810442I21Rik|4930500E12Rik|Fabl	Egfr long non-coding downstream RNA	ncRNA
mm_63948.1	chr7	139834431	139834440	+	1	NA	5' UTR (NM_177469, exon 1 of 8)	5' UTR (NM_177469, exon 1 of 8)	261	NM_177469	52389	Mm.39863	NM_177469	ENSMUSG00000025475	Adgra1	2900059M17Rik|D7Ertd680e|Gpr123	adhesion G protein-coupled receptor A1	protein-coding
mm_90341.1	chr10	127093038	127093041	+	1	NA	3' UTR (NM_001301014, exon 18 of 18)	3' UTR (NM_001301014, exon 18 of 18)	14132	NM_001033263	216439	Mm.336761	NM_001033263	ENSMUSG00000025422	Agap2	AGAP-2|Centg1|PIKE|cnt-g1|mKIAA0167	ArfGAP with GTPase domain, ankyrin repeat and PH domain 2	protein-coding
mm_88607.1	chr10	79814667	79814684	+	1	NA	intron (NM_023128, intron 6 of 8)	intron (NM_023128, intron 6 of 8)	-6346	NM_030218	78906	Mm.33087	NM_030218	ENSMUSG00000035852	Misp	9130017N09Rik	mitotic spindle positioning	protein-coding
mm_159899.1	chr6	38570157	38570157	+	1	NA	intron (NM_001331223, intron 4 of 12)	MIR3|SINE|MIR	14434	NM_001331223	192196	Mm.276133	NM_138680	ENSMUSG00000029823	Luc7l2	4930471C18Rik|AA522013|AU015269|CGI59|Cgi74	LUC7-like 2 (S. cerevisiae)	protein-coding
mm_94608.1	chr11	16257660	16257672	+	1	NA	promoter-TSS (NM_001290539)	promoter-TSS (NM_001290539)	-58	NM_001290539	211739	Mm.284015	NM_145967	ENSMUSG00000048834	Vstm2a	Vstm2	V-set and transmembrane domain containing 2A	protein-coding
mm_138261.1	chr17	34592523	34592566	+	1	NA	promoter-TSS (NM_017463)	promoter-TSS (NM_017463)	73	NM_017463	18515	Mm.390957	NM_017463	ENSMUSG00000034673	Pbx2	AU043397|G17	pre B cell leukemia homeobox 2	protein-coding
mm_15990.1	chr2	167056850	167056864	+	1	NA	exon (NM_001033196, exon 3 of 14)	exon (NM_001033196, exon 3 of 14)	-6077	NR_138563	68949	Mm.391959	NM_001081005		Zfas1	1500012F01Rik|Zfos1	zinc finger, NFX1-type containing 1, antisense RNA 1	ncRNA
mm_70574.1	chr8	13165861	13165872	+	1	NA	exon (NM_010684, exon 2 of 9)	exon (NM_010684, exon 2 of 9)	6705	NM_010684	16783	Mm.16716	NM_010684	ENSMUSG00000031447	Lamp1	CD107a|LGP-120|LGP-A|Lamp-1|P2B	lysosomal-associated membrane protein 1	protein-coding
mm_92088.1	chr10	62834966	62834976	-	1	NA	intron (NM_027384, intron 3 of 10)	intron (NM_027384, intron 3 of 10)	-42603	NM_026201	67500	Mm.196371	NM_026201	ENSMUSG00000020074	Ccar1	2610511G16Rik|9430036H15Rik|Carp1	cell division cycle and apoptosis regulator 1	protein-coding
mm_56770.1	chr6	116423987	116423987	-	1	NA	intron (NM_009662, intron 5 of 13)	intron (NM_009662, intron 5 of 13)	37191	NM_009662	11689	Mm.41072	NM_009662	ENSMUSG00000025701	Alox5	5-LO|5-LOX|5LO|5LX|AI850497|F730011J02	arachidonate 5-lipoxygenase	protein-coding
mm_156317.1	chrX	136993324	136993330	+	1	NA	promoter-TSS (NM_001114179)	promoter-TSS (NM_001114179)	172	NM_001035509	66995	Mm.440155	NM_025893	ENSMUSG00000031428	Zcchc18	1500031H04Rik|Sizn2	zinc finger, CCHC domain containing 18	protein-coding
mm_147657.1	chr18	60591764	60591778	-	1	NA	promoter-TSS (NM_133363)	promoter-TSS (NM_133363)	-55	NM_133363	170947	Mm.159257	NM_133363	ENSMUSG00000049173	Myoz3	4833419K08Rik|Fatz-3	myozenin 3	protein-coding
mm_21079.1	chr2	152831666	152831735	-	1	NA	promoter-TSS (NM_009743)	promoter-TSS (NM_009743)	28	NM_009743	12048	Mm.238213	NM_009743	ENSMUSG00000007659	Bcl2l1	Bcl(X)L|Bcl-XL|Bcl2l|BclX|bcl-x|bcl2-L-1	BCL2-like 1	protein-coding
mm_123335.1	chr14	63104187	63104221	-	1	NA	Intergenic	Intergenic	-18258	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_97267.1	chr11	75765191	75765201	+	1	NA	3' UTR (NM_009536, exon 6 of 6)	3' UTR (NM_009536, exon 6 of 6)	-30613	NR_136933	102641247	Mm.411386	NR_136932		Gm12339	OTTMUSG00000006218	predicted gene 12339	ncRNA
mm_4422.1	chr1	172501241	172501257	+	1	NA	intron (NM_178598, intron 1 of 4)	intron (NM_178598, intron 1 of 4)	1003	NM_178598	21346	Mm.271711	NM_178598	ENSMUSG00000026547	Tagln2	2700094C18Rik|SM22beta|Sm22B|Sm22a	transgelin 2	protein-coding
mm_170226.1	chr17	80938764	80938783	-	1	NA	Intergenic	Intergenic	-5859	NM_026516	68027	Mm.357108	NM_026516	ENSMUSG00000024245	Tmem178	2810417M05Rik|Tmem178a	transmembrane protein 178	protein-coding
mm_137275.1	chr17	24720068	24720083	+	1	NA	promoter-TSS (NR_028515)	promoter-TSS (NR_028515)	12	NM_008503	16898	Mm.157452	NM_008503	ENSMUSG00000044533	Rps2	Llrep3|S4	ribosomal protein S2	protein-coding
mm_153381.1	chr19	40376771	40376781	-	1	NA	exon (NM_178362, exon 7 of 29)	exon (NM_178362, exon 7 of 29)	25534	NM_001034964	20411	Mm.210815	NM_009166	ENSMUSG00000025006	Sorbs1	2310065E01Rik|9530001P15Rik|CAP|SH3P12|Sh3d5|mKIAA1296	sorbin and SH3 domain containing 1	protein-coding
mm_143315.1	chr17	66111517	66111524	-	1	NA	promoter-TSS (NM_026833)	promoter-TSS (NM_026833)	-26	NM_026833	68767	Mm.296545	NM_026833	ENSMUSG00000024101	Washc1	1110049F14Rik|ORF19|Wash|Wash1	WASH complex subunit 1	protein-coding
mm_167712.1	chr9	96911151	96911155	+	1	NA	Intergenic	Lx8|LINE|L1	-21679	NM_001289645	235534	Mm.233031	NM_153420	ENSMUSG00000043587	Pxylp1	9430094M07Rik|Acpl2|BB177120|C130099A20Rik	2-phosphoxylose phosphatase 1	protein-coding
mm_143977.1	chr17	87438674	87438690	-	1	NA	intron (NM_007589, intron 2 of 5)	B1_Mus2|SINE|Alu	8253	NM_007589	12314	Mm.329243	NM_007589	ENSMUSG00000036438	Calm2	1500001E21Rik|AL024017	calmodulin 2	protein-coding
mm_72408.1	chr8	81775743	81775760	+	1	NA	intron (NM_001024617, intron 7 of 24)	intron (NM_001024617, intron 7 of 24)	433189	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_79798.1	chr9	64117226	64117242	+	1	NA	promoter-TSS (NM_145835)	promoter-TSS (NM_145835)	87	NM_145835	235435	Mm.436581	NM_145835	ENSMUSG00000032401	Lctl	E130104I05Rik|KLPH	lactase-like	protein-coding
mm_160939.1	chr11	94653767	94653767	+	1	NA	promoter-TSS (NM_177752)	promoter-TSS (NM_177752)	-13	NM_177752	268465	Mm.358937	NM_177752	ENSMUSG00000039055	Eme1	6820428D13	essential meiotic structure-specific endonuclease 1	protein-coding
mm_92286.1	chr10	71344786	71344790	-	1	NA	promoter-TSS (NM_134007)	promoter-TSS (NM_134007)	61	NM_134007	52637	Mm.254114	NM_134007	ENSMUSG00000037710	Cisd1	AU043990|AW743335|D10Ertd214e|Zcd1|mitoNEET	CDGSH iron sulfur domain 1	protein-coding
mm_147510.1	chr18	50568744	50568746	-	1	NA	promoter-TSS (NM_026108)	promoter-TSS (NM_026108)	-46	NM_026108	67365	Mm.158150	NM_026108	ENSMUSG00000048875	Hdhd1a	1700121L12Rik|GS1|Hdhd1|Pudp	haloacid dehalogenase-like hydrolase domain containing 1A	protein-coding
mm_86100.1	chr9	115310073	115310094	-	1	NA	5' UTR (NM_024222, exon 1 of 16)	5' UTR (NM_024222, exon 1 of 16)	338	NM_024222	68292	Mm.296158	NM_024222	ENSMUSG00000032437	Stt3b	1300006C19Rik|Simp	STT3, subunit of the oligosaccharyltransferase complex, homolog B (S. cerevisiae)	protein-coding
mm_162468.1	chr1	132007467	132007478	-	1	NA	promoter-TSS (NM_007923)	promoter-TSS (NM_007923)	-133	NM_007923	13714	Mm.254233	NM_007923	ENSMUSG00000026436	Elk4	2310011G17Rik|A130026I01Rik|BB162516|SAP-1|Sap1	ELK4, member of ETS oncogene family	protein-coding
mm_16029.1	chr2	167589593	167589616	+	1	NA	Intergenic	L2a|LINE|L2	42401	NM_001311146	66589	Mm.278783	NM_023230	ENSMUSG00000078923	Ube2v1	0610011J09Rik|AI256840|CROC-1|CROC1|D7Bwg1382e|UEV-1	ubiquitin-conjugating enzyme E2 variant 1	protein-coding
mm_58450.1	chr7	3308952	3308958	+	1	NA	intron (NM_001291434, intron 3 of 16)	intron (NM_001291434, intron 3 of 16)	5423	NM_011102	18752	Mm.7980	NM_011102	ENSMUSG00000078816	Prkcg	PKCgamma|Pkcc|Prkcc	protein kinase C, gamma	protein-coding
mm_120649.1	chr14	70530820	70530847	+	1	NA	promoter-TSS (NM_145219)	promoter-TSS (NM_145219)	12	NM_145219	213469	Mm.41708	NM_145219	ENSMUSG00000033595	Lgi3	AI841179|AW049851	leucine-rich repeat LGI family, member 3	protein-coding
mm_4059.1	chr1	165851589	165851591	+	1	NA	intron (NM_001113391, intron 1 of 7)	intron (NM_001113391, intron 1 of 7)	62909	NM_001113392	12503	Mm.217308	NM_031162	ENSMUSG00000005763	Cd247	4930549J05Rik|A430104F18Rik|AW552088|Cd3|Cd3-eta|Cd3-zeta|Cd3h|Cd3z|Cd3zeta|T3z|Tcrk|Tcrz	CD247 antigen	protein-coding
mm_90568.1	chr10	128231631	128231641	+	1	NA	promoter-TSS (NM_001136082)	promoter-TSS (NM_001136082)	-427	NM_001164080	21853	Mm.6458	NM_011589	ENSMUSG00000039994	Timeless	C77407|Debt69|tim	timeless circadian clock 1	protein-coding
mm_173028.1	chrX	105279376	105279381	+	1	NA	Intergenic	BGLII|LTR|ERVK	64991	NR_029910	723861		NR_029910	ENSMUSG00000065499	Mir384	Mirn384|mir-384|mmu-mir-384	microRNA 384	ncRNA
mm_39892.1	chr5	31193223	31193235	+	1	NA	promoter-TSS (NM_001127356)	promoter-TSS (NM_001127356)	-75	NM_153680	266781	Mm.6118	NM_153680	ENSMUSG00000029146	Snx17	5830447M19Rik|AI790646|D5Ertd260e|b2b1625.1Clo|mKIAA0064	sorting nexin 17	protein-coding
mm_78425.1	chr9	31252607	31252619	+	1	NA	Intergenic	Intergenic	-18788	NM_001101597	638580	Mm.373655	NM_001101597		Gm7244	EG638580	predicted gene 7244	protein-coding
mm_139879.1	chr17	70751336	70751365	+	1	NA	intron (NM_001347411, intron 9 of 14)	intron (NM_001347411, intron 9 of 14)	95427	NM_001164077	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_41091.1	chr5	87694543	87694547	+	1	NA	exon (NM_001286023, exon 5 of 7)	exon (NM_001286023, exon 5 of 7)	4880	NM_001286020	12991	Mm.268737	NM_009972	ENSMUSG00000063157	Csn2	Csnb	casein beta	protein-coding
mm_114142.1	chr13	55315530	55315541	+	1	NA	3' UTR (NM_008739, exon 23 of 23)	3' UTR (NM_008739, exon 23 of 23)	6445	NM_009000	19336	Mm.220923	NM_009000	ENSMUSG00000034789	Rab24	6530406O07Rik	RAB24, member RAS oncogene family	protein-coding
mm_166603.1	chr6	67533802	67533818	+	1	NA	TTS (NM_020047)	TTS (NM_020047)	2012	NM_020047	56753	Mm.439913	NM_020047	ENSMUSG00000051397	Tacstd2	C80403|EGP-1|GA733-1|Ly97|TROP2	tumor-associated calcium signal transducer 2	protein-coding
mm_134660.1	chr16	22121303	22121332	-	1	NA	intron (NM_183029, intron 2 of 15)	L1MA5|LINE|L1	41982	NM_183029	319765	Mm.489442	NM_183029	ENSMUSG00000033581	Igf2bp2	C330012H03Rik|IMP-2|Imp2|Neilsen	insulin-like growth factor 2 mRNA binding protein 2	protein-coding
mm_160759.1	chr10	86763916	86763916	+	1	NA	exon (NM_001003910, exon 14 of 16)	exon (NM_001003910, exon 14 of 16)	-15089	NM_175331	103466	Mm.200446	NM_175331	ENSMUSG00000054027	Nt5dc3	AU040402|AW540062|C630002B14Rik|TU12B1-TY	5'-nucleotidase domain containing 3	protein-coding
mm_31383.1	chr4	47996449	47996461	+	1	NA	Intergenic	B1_Mur1|SINE|Alu	-48850	NM_015743	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_138875.1	chr17	43138597	43138601	+	1	NA	Intergenic	Intergenic	19692	NR_045155	545207	Mm.329050	NR_045153		E130008D07Rik	-	RIKEN cDNA E130008D07 gene	ncRNA
mm_38585.1	chr4	141821353	141821362	-	1	NA	exon (NM_007919, exon 5 of 8)	exon (NM_007919, exon 5 of 8)	4648	NM_007919	13706	Mm.45316	NM_007919	ENSMUSG00000058579	Cela2a	Ela-2|Ela2|Ela2a	chymotrypsin-like elastase family, member 2A	protein-coding
mm_149163.1	chr19	9018495	9018553	+	1	NA	TTS (NR_105786)	TTS (NR_105786)	620	NR_105786	102465190		NR_105786	ENSMUSG00000099308	Mir6367	Gm27467|mmu-mir-6367	microRNA 6367	ncRNA
mm_130317.1	chr15	97338487	97338492	-	1	NA	intron (NM_172293, intron 3 of 5)	intron (NM_172293, intron 3 of 5)	-91202	NM_001164602	105827	Mm.24005	NM_178114	ENSMUSG00000048218	Amigo2	AI415330|AMIGO-2|AW208913|Ali1	adhesion molecule with Ig like domain 2	protein-coding
mm_104861.1	chr11	99386043	99386086	-	1	NA	exon (NM_010660, exon 7 of 8)	exon (NM_010660, exon 7 of 8)	3300	NM_010660	16661	Mm.22662	NM_010660	ENSMUSG00000019761	Krt10	D130054E02Rik|K10|K1C1|Krt-1.10|Krt1-10	keratin 10	protein-coding
mm_139025.1	chr17	46159269	46159277	+	1	NA	Intergenic	Intergenic	-1759	NM_019581	56055	Mm.22147	NM_019581	ENSMUSG00000023952	Gtpbp2	nmf205	GTP binding protein 2	protein-coding
mm_153931.1	chr19	47416189	47416202	-	1	NA	intron (NM_001164717, intron 2 of 13)	intron (NM_001164717, intron 2 of 13)	48216	NM_001164717	14218	Mm.127560	NM_008018	ENSMUSG00000053617	Sh3pxd2a	2310014D11Rik|AA589508|AI256723|AI413738|C230050L11|EG329070|Fish|Gm5098|Sh3md1|TSK5|Tks5	SH3 and PX domains 2A	protein-coding
mm_11110.1	chr2	28193108	28193114	+	1	NA	promoter-TSS (NM_001038613)	promoter-TSS (NM_001038613)	18	NM_001038614	56177	Mm.43278	NM_019498	ENSMUSG00000026833	Olfm1	AMY|AW742568|Noe1|OlfA|Pancortin|Pancortin3	olfactomedin 1	protein-coding
mm_124100.1	chr14	79300992	79300999	-	1	NA	intron (NM_025427, intron 1 of 4)	CpG	640	NM_025427	66214	Mm.29811	NM_025427	ENSMUSG00000022018	Rgcc	1190002H23Rik|Rgc-32|Rgc32	regulator of cell cycle	protein-coding
mm_132102.1	chr16	31428746	31428755	+	1	NA	promoter-TSS (NM_001122683)	promoter-TSS (NM_001122683)	-3	NM_001122683	71911	Mm.293470	NM_175177	ENSMUSG00000046598	Bdh1	2310032J20Rik|AI327223|Bdh	3-hydroxybutyrate dehydrogenase, type 1	protein-coding
mm_108262.1	chr12	78691496	78691512	+	1	NA	promoter-TSS (NM_029069)	promoter-TSS (NM_029069)	-31	NM_027597	70897	Mm.56514	NM_027597	ENSMUSG00000056987	Fam71d	4921509E07Rik|4930516C23Rik|GARI-L2	family with sequence similarity 71, member D	protein-coding
mm_106483.1	chr11	120231466	120231477	-	1	NA	Intergenic	CpG	-1476	NM_001347621	268515	Mm.309498	NM_198423	ENSMUSG00000039741	Bahcc1	B930044J06|BC060615	BAH domain and coiled-coil containing 1	protein-coding
mm_112221.1	chr12	113429309	113429348	-	1	NA	Intergenic	Intergenic	-60237	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_2228.1	chr1	90915065	90915114	+	1	NA	promoter-TSS (NM_053015)	promoter-TSS (NM_053015)	-11	NM_053015	171531	Mm.105208	NM_053015	ENSMUSG00000026303	Mlph	2210418F23Rik|5031433I09Rik|AW228792|D1Wsu84e|Slac-2a|l(1)-3Rk|l1Rk3|ln	melanophilin	protein-coding
mm_53845.1	chr6	148992682	148992692	+	1	NA	3' UTR (NM_177192, exon 21 of 21)	3' UTR (NM_177192, exon 21 of 21)	-46255	NM_019643	56306	Mm.18637	NM_019643	ENSMUSG00000039985	Fam60a	Ppcs1|Pptcs1|Tera	family with sequence similarity 60, member A	protein-coding
mm_8188.1	chr1	138099596	138099607	-	1	NA	exon (NM_001268286, exon 10 of 29)	exon (NM_001268286, exon 10 of 29)	75525	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_69350.1	chr7	130262817	130262828	-	1	NA	intron (NM_001347638, intron 1 of 15)	intron (NM_001347638, intron 1 of 15)	3986	NM_010207	14183	Mm.16340	NM_010207	ENSMUSG00000030849	Fgfr2	AU043015|AW556123|Bek|Fgfr-2|Fgfr-7|Fgfr7|KGFR|KGFRTr|svs	fibroblast growth factor receptor 2	protein-coding
mm_13779.1	chr2	118772767	118772780	+	1	NA	promoter-TSS (NM_001145644)	promoter-TSS (NM_001145644)	4	NM_001145644	53906	Mm.36777	NM_025308	ENSMUSG00000046804	Phgr1	1810007E14Rik|AA238765	proline/histidine/glycine-rich 1	protein-coding
mm_101096.1	chr11	11890395	11890407	-	1	NA	promoter-TSS (NM_016672)	promoter-TSS (NM_016672)	7	NM_016672	13195	Mm.12906	NM_016672	ENSMUSG00000020182	Ddc	Aadc	dopa decarboxylase	protein-coding
mm_45136.1	chr5	48914506	48914508	-	1	NA	intron (NM_001199244, intron 1 of 7)	intron (NM_001199244, intron 1 of 7)	-24950	NM_030265	80334	Mm.160172	NM_030265	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding
mm_44066.1	chr5	148400147	148400149	+	1	NA	promoter-TSS (NM_007513)	promoter-TSS (NM_007513)	-244	NM_007513	11987	Mm.275489	NM_007513	ENSMUSG00000041313	Slc7a1	4831426K01Rik|AI447493|Atrc-1|Atrc1|Cat1|Rec-1|Rev-1|mCAT-1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 1	protein-coding
mm_108338.1	chr12	80168939	80168977	+	1	NA	exon (NM_134156, exon 20 of 21)	exon (NM_134156, exon 20 of 21)	-36114	NR_033514	69548	Mm.269712	NR_033514	ENSMUSG00000097729	2310015A10Rik	5330419I17Rik	RIKEN cDNA 2310015A10 gene	ncRNA
mm_141248.1	chr17	27547331	27547337	-	1	NA	Intergenic	Intergenic	-9240	NM_001166536	15361	Mm.4438	NM_016660	ENSMUSG00000046711	Hmga1	AL023995|Hmga1a|Hmga1b|Hmgi|Hmgiy|Hmgy	high mobility group AT-hook 1	protein-coding
mm_29985.1	chr3	135424048	135424084	-	1	NA	promoter-TSS (NM_025902)	promoter-TSS (NM_025902)	-633	NM_025902	67006	Mm.269993	NM_025902	ENSMUSG00000028165	Cisd2	1500009M05Rik|1500026J14Rik|1500031D15Rik|AI848398|B630006A20Rik|Miner1|Naf-1|Noxp70|Zcd2	CDGSH iron sulfur domain 2	protein-coding
mm_131678.1	chr16	20673866	20673887	+	1	NA	5' UTR (NM_145941, exon 2 of 33)	5' UTR (NM_145941, exon 2 of 33)	1149	NM_001304432	208643	Mm.260256	NM_145941	ENSMUSG00000045983	Eif4g1	E030015G23Rik|eIF-4-gamma 1|eIF-4G 1|eIF-4G1|eIF4GI	eukaryotic translation initiation factor 4, gamma 1	protein-coding
mm_2672.1	chr1	127213332	127213362	+	1	NA	intron (NM_145128, intron 1 of 17)	ID_B1|SINE|B4	8361	NM_145128	107895	Mm.214682	NM_145128	ENSMUSG00000036155	Mgat5	4930471A21Rik|5330407H02Rik|AI480971|GlcNAc-TV	mannoside acetylglucosaminyltransferase 5	protein-coding
mm_35106.1	chr4	9613891	9613924	-	1	NA	intron (NM_023066, intron 3 of 23)	intron (NM_023066, intron 3 of 23)	29810	NM_001177853	65973	Mm.222206	NM_023066	ENSMUSG00000028207	Asph	2310005F16Rik|3110001L23Rik|AI848629|AW261690|AW561901|BAH|C79816|cI-37	aspartate-beta-hydroxylase	protein-coding
mm_39049.1	chr4	153241482	153241492	-	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	241343	NM_001099299	230959	Mm.318874	NM_001099299	ENSMUSG00000039546	Ajap1	Gm573	adherens junction associated protein 1	protein-coding
mm_75726.1	chr8	69121410	69121422	-	1	NA	Intergenic	Intergenic	19537	NM_199364	211134	Mm.409446	NM_199364	ENSMUSG00000036306	Lzts1	F37|FEZ1|PSD-Zip70	leucine zipper, putative tumor suppressor 1	protein-coding
mm_8372.1	chr1	150971332	150971336	-	1	NA	intron (NM_001024720, intron 1 of 106)	intron (NM_001024720, intron 1 of 106)	22101	NM_001024720	545370	Mm.379425	NM_001024720	ENSMUSG00000066842	Hmcn1	EG545370|FIBL-6|Gm201	hemicentin 1	protein-coding
mm_49879.1	chr6	38605116	38605120	+	1	NA	3' UTR (NM_001170849, exon 8 of 8)	3' UTR (NM_001170849, exon 8 of 8)	32121	NM_001033171	74253	Mm.121859	NM_001033171	ENSMUSG00000071537	Klrg2	2310020F24Rik	killer cell lectin-like receptor subfamily G, member 2	protein-coding
mm_170508.1	chr19	27751372	27751377	+	1	NA	Intergenic	Intergenic	231574	NM_001166414	19726	Mm.313321	NM_011265	ENSMUSG00000040929	Rfx3	C230093O12Rik|MRFX3	regulatory factor X, 3 (influences HLA class II expression)	protein-coding
mm_142351.1	chr17	43628606	43628613	-	1	NA	exon (NM_198418, exon 1 of 5)	exon (NM_198418, exon 1 of 5)	1690	NM_001161366	210510	Mm.329058	NM_198418	ENSMUSG00000040140	Tdrd6	AB097085|Tdr2	tudor domain containing 6	protein-coding
mm_62578.1	chr7	104465674	104465686	+	1	NA	promoter-TSS (NM_009099)	promoter-TSS (NM_009099)	-487	NM_009099	20128	Mm.295578	NM_009099	ENSMUSG00000030921	Trim30a	Rpt-1|Rpt1|Trim30	tripartite motif-containing 30A	protein-coding
mm_97334.1	chr11	77293439	77293439	+	1	NA	intron (NM_177710, intron 1 of 14)	intron (NM_177710, intron 1 of 14)	-54841	NM_001291190	237860	Mm.440381	NM_177710	ENSMUSG00000037926	Ssh2	SSH-2|SSH-2L|mSSH-2L	slingshot homolog 2 (Drosophila)	protein-coding
mm_37532.1	chr4	124862208	124862261	-	1	NA	promoter-TSS (NM_001007573)	promoter-TSS (NM_001007573)	-63	NM_001007573	215090	Mm.472762	NM_001007573	ENSMUSG00000042763	Maneal	Gm50	mannosidase, endo-alpha-like	protein-coding
mm_118071.1	chr13	102958119	102958173	-	1	NA	intron (NM_175171, intron 4 of 28)	intron (NM_175171, intron 4 of 28)	197891	NR_130171	76624	Mm.426384	NR_130171	ENSMUSG00000091906	1700099I09Rik	-	RIKEN cDNA 1700099I09 gene	ncRNA
mm_113341.1	chr13	31785224	31785232	+	1	NA	Intergenic	Intergenic	-21418	NM_008592	17300	Mm.12949	NM_008592	ENSMUSG00000050295	Foxc1	FREAC3|Fkh1|Mf1|Mf4|ch|fkh-1|frkhda	forkhead box C1	protein-coding
mm_707.1	chr1	40720680	40720685	+	1	NA	intron (NM_001033289, intron 2 of 11)	intron (NM_001033289, intron 2 of 11)	38970	NM_001033289	226999	Mm.256414	NM_001033289	ENSMUSG00000026062	Slc9a2	2210416H12Rik|4932415O19Rik|AV333884|NHE2	solute carrier family 9 (sodium/hydrogen exchanger), member 2	protein-coding
mm_61711.1	chr7	81243146	81243149	+	1	NA	intron (NM_008803, intron 1 of 21)	intron (NM_008803, intron 1 of 21)	29343	NM_008803	18584	Mm.371577	NM_008803	ENSMUSG00000025584	Pde8a	AI551852|Pde8	phosphodiesterase 8A	protein-coding
mm_10669.1	chr2	20968732	20968744	+	1	NA	promoter-TSS (NR_033225)	promoter-TSS (NR_033225)	-136	NR_033225	433408	Mm.386941	NR_033225		Gm13375	OTTMUSG00000011664	predicted gene 13375	ncRNA
mm_77482.1	chr8	122476037	122476088	-	1	NA	promoter-TSS (NM_153775)	promoter-TSS (NM_153775)	2	NM_001033142	68718	Mm.34356	NM_001033142	ENSMUSG00000014470	Rnf166	1110031E24Rik|AW555115|Zfp313l	ring finger protein 166	protein-coding
mm_102905.1	chr11	69555567	69555613	-	1	NA	3' UTR (NM_007911, exon 5 of 5)	3' UTR (NM_007911, exon 5 of 5)	4647	NM_007911	13643	Mm.249637	NM_007911	ENSMUSG00000003934	Efnb3	EFL-6|ELF-3|Elk-L3|Epl8|LERK-8|NLERK-2	ephrin B3	protein-coding
mm_41413.1	chr5	90787744	90787768	+	1	NA	3' UTR (NM_203320, exon 4 of 4)	3' UTR (NM_203320, exon 4 of 4)	1655	NM_203320	330122	Mm.244289	NM_203320	ENSMUSG00000029379	Cxcl3	Dcip1|Gm1960	chemokine (C-X-C motif) ligand 3	protein-coding
mm_121407.1	chr14	119321560	119321570	+	1	NA	intron (NM_015820, intron 1 of 1)	L1MA6|LINE|L1	183300	NM_015820	50787	Mm.445777	NM_015820	ENSMUSG00000053465	Hs6st3	6OST3|HS6ST-3	heparan sulfate 6-O-sulfotransferase 3	protein-coding
mm_25870.1	chr3	129935106	129935121	+	1	NA	intron (NM_001293644, intron 1 of 6)	ORR1C2|LTR|ERVL-MaLR	33698	NM_009811	12368	Mm.281379	NM_009811	ENSMUSG00000027997	Casp6	CASP-6|Mch2	caspase 6	protein-coding
mm_158231.1	chrX	106312936	106312955	-	1	NA	Intergenic	Intergenic	3119	NR_105803	102465963		NR_105803	ENSMUSG00000099128	Mir6382	Gm27319|mmu-mir-6382	microRNA 6382	ncRNA
mm_93509.1	chr10	114802299	114802322	-	1	NA	promoter-TSS (NM_146241)	promoter-TSS (NM_146241)	-940	NM_146241	237553	Mm.445550	NM_146241	ENSMUSG00000050663	Trhde	9330155P21Rik	TRH-degrading enzyme	protein-coding
mm_15610.1	chr2	160747330	160747341	+	1	NA	intron (NM_021280, intron 2 of 33)	intron (NM_021280, intron 2 of 33)	16025	NM_021280	18803	Mm.44463	NM_021280	ENSMUSG00000016933	Plcg1	AI894140|Cded|Plc-1|Plc-gamma1|Plcg-1	phospholipase C, gamma 1	protein-coding
mm_163585.1	chr13	36885432	36885432	+	1	NA	intron (NM_001166391, intron 13 of 14)	intron (NM_001166391, intron 13 of 14)	-150955	NM_153529	68404	Mm.232930	NM_153529	ENSMUSG00000039114	Nrn1	0710008J23Rik|Cpg15|Nrn	neuritin 1	protein-coding
mm_101861.1	chr11	48871318	48871337	-	1	NA	promoter-TSS (NM_008326)	promoter-TSS (NM_008326)	19	NM_008326	15944	Mm.29938	NM_008326	ENSMUSG00000046879	Irgm1	Ifggd3|Ifi1|Iigp3|Iipg3|Irgm|LRG-47	immunity-related GTPase family M member 1	protein-coding
mm_152346.1	chr19	9984807	9984840	-	1	NA	TTS (NM_011913)	TTS (NM_011913)	2177	NM_010239	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
mm_135866.1	chr16	60605612	60605643	-	1	NA	promoter-TSS (NM_007938)	promoter-TSS (NM_007938)	-96	NM_007938	13840	Mm.455790	NM_007938	ENSMUSG00000055540	Epha6	Ehk2|Hek12|m-ehk2	Eph receptor A6	protein-coding
mm_12665.1	chr2	75659254	75659266	+	1	NA	promoter-TSS (NM_198090)	promoter-TSS (NM_198090)	1	NM_053263	229279	Mm.316306	NM_053263	ENSMUSG00000059005	Hnrnpa3	2410013L13Rik|2610209F03Rik|2610510D13Rik|Hnrpa3	heterogeneous nuclear ribonucleoprotein A3	protein-coding
mm_54026.1	chr6	8778540	8778550	-	1	NA	promoter-TSS (NM_010492)	promoter-TSS (NM_010492)	-61	NM_010492	15893	Mm.275683	NM_010492	ENSMUSG00000062995	Ica1	69kDa|ICA69	islet cell autoantigen 1	protein-coding
mm_10045.1	chr1	193130259	193130271	-	1	NA	promoter-TSS (NM_145415)	promoter-TSS (NM_145415)	-14	NM_145415	215193	Mm.173758	NM_145415	ENSMUSG00000016181	Diexf	AA408296|AW045375|Def	digestive organ expansion factor homolog (zebrafish)	protein-coding
mm_98241.1	chr11	88162380	88162386	+	1	NA	intron (NM_198013, intron 1 of 10)	intron (NM_198013, intron 1 of 10)	-7182	NM_001172099	103841	Mm.374846	NM_198013	ENSMUSG00000018378	Cuedc1	AI841487|C330016O16Rik	CUE domain containing 1	protein-coding
mm_103029.1	chr11	69735327	69735337	-	1	NA	exon (NM_001291068, exon 29 of 29)	exon (NM_001291068, exon 29 of 29)	23301	NM_001291068	20020	Mm.16533	NM_009089	ENSMUSG00000005198	Polr2a	220kDa|Rpb1|Rpo2-1	polymerase (RNA) II (DNA directed) polypeptide A	protein-coding
mm_110371.1	chr12	40199318	40199331	-	1	NA	promoter-TSS (NM_001033437)	promoter-TSS (NM_001033437)	-9	NM_001033437	380755	Mm.390463	NM_001033437	ENSMUSG00000071342	Lsmem1	Gm889	leucine-rich single-pass membrane protein 1	protein-coding
mm_99150.1	chr11	100574966	100574982	+	1	NA	promoter-TSS (NM_009923)	promoter-TSS (NM_009923)	35	NM_009923	12799	Mm.15711	NM_009923	ENSMUSG00000006782	Cnp	CNPase|Cnp-1|Cnp1	2',3'-cyclic nucleotide 3' phosphodiesterase	protein-coding
mm_126459.1	chr15	80948485	80948549	+	1	NA	promoter-TSS (NM_009634)	promoter-TSS (NM_009634)	27	NM_009634	11564	Mm.38151	NM_009634	ENSMUSG00000022407	Adsl	Adl|Asl	adenylosuccinate lyase	protein-coding
mm_173036.1	chrX	107057553	107057572	-	1	NA	Intergenic	Lx8|LINE|L1	-31773	NM_172435	78826	Mm.74639	NM_172435	ENSMUSG00000050921	P2ry10	5830408N17Rik|Lypsr2|P2Y10	purinergic receptor P2Y, G-protein coupled 10	protein-coding
mm_62677.1	chr7	109521088	109521090	+	1	NA	TTS (NR_028079)	TTS (NR_028079)	957	NR_028079	100302499	Mm.482651	NR_028079	ENSMUSG00000065016	Snora3	MBI-28	small nucleolar RNA, H/ACA box 3	snoRNA
mm_122507.1	chr14	46884988	46885029	-	1	NA	exon (NM_028966, exon 2 of 12)	exon (NM_028966, exon 2 of 12)	2043	NM_001037221	74480	Mm.214454	NM_028966	ENSMUSG00000021838	Samd4	1700024G08Rik|1700111L17Rik|4933436G17Rik|Samd4a|Smaug|Smaug1|sunk	sterile alpha motif domain containing 4	protein-coding
mm_164249.1	chr15	97976889	97976895	-	1	NA	intron (NM_031163, intron 52 of 53)	intron (NM_031163, intron 52 of 53)	12663	NM_001252153	380967	Mm.196630	NM_201359	ENSMUSG00000052369	Tmem106c	AI046681|BC046621|D15Ertd405e	transmembrane protein 106C	protein-coding
mm_170734.1	chr2	152344089	152344102	-	1	NA	promoter-TSS (NM_175093)	promoter-TSS (NM_175093)	-35	NM_175093	228775	Mm.276018	NM_144554	ENSMUSG00000032715	Trib3	Ifld2|Nipk|SINK|SKIP3|TRB-3|Trb3	tribbles pseudokinase 3	protein-coding
mm_133502.1	chr16	90727491	90727531	+	1	NA	promoter-TSS (NM_025642)	promoter-TSS (NM_025642)	-140	NM_025642	66578	Mm.180363	NM_025642	ENSMUSG00000022978	Mis18a	2610039C10Rik|2810018N07Rik	MIS18 kinetochore protein A	protein-coding
mm_38930.1	chr4	150192512	150192516	-	1	NA	exon (NM_009802, exon 6 of 8)	exon (NM_009802, exon 6 of 8)	8621	NM_009802	12353	Mm.232523	NM_009802	ENSMUSG00000028972	Car6	Ca6|DOC1	carbonic anhydrase 6	protein-coding
mm_61733.1	chr7	81873042	81873053	+	1	NA	intron (NR_111910, intron 5 of 7)	intron (NR_111910, intron 5 of 7)	10360	NM_001291282	107769	Mm.221412	NM_145375	ENSMUSG00000038623	Tm6sf1	AI428514|BC023123|C630016D09Rik	transmembrane 6 superfamily member 1	protein-coding
mm_69690.1	chr7	139992476	139992500	-	1	NA	promoter-TSS (NM_001291066)	promoter-TSS (NM_001291066)	74	NM_007403	11501	Mm.15969	NM_007403	ENSMUSG00000025473	Adam8	ADAM 8|CD156|CD156a|E430039A18Rik|MS2	a disintegrin and metallopeptidase domain 8	protein-coding
mm_11634.1	chr2	34775886	34775972	+	1	NA	exon (NM_001163434, exon 9 of 9)	exon (NM_001163434, exon 9 of 9)	3839	NM_022310	14828	Mm.330160	NM_022310	ENSMUSG00000026864	Hspa5	AL022860|AU019543|Bip|D2Wsu141e|D2Wsu17e|Grp78|Hsce70|SEZ-7|Sez7|baffled|mBiP	heat shock protein 5	protein-coding
mm_53699.1	chr6	142756878	142756888	+	1	NA	exon (NM_009908, exon 1 of 8)	exon (NM_009908, exon 1 of 8)	197	NM_009908	12764	Mm.3820	NM_009908	ENSMUSG00000030282	Cmas	AW208911|CMPNeu5Ac|D6Bwg0250e	cytidine monophospho-N-acetylneuraminic acid synthetase	protein-coding
mm_135041.1	chr16	32877724	32877742	-	1	NA	promoter-TSS (NM_001159349)	promoter-TSS (NM_001159349)	-51	NM_027226	69823	Mm.12831	NM_027226	ENSMUSG00000022800	Fyttd1	2010005M05Rik|3830411L18Rik|3830421F13Rik|4933423A17Rik|AI098218|AW539567|C85190	forty-two-three domain containing 1	protein-coding
mm_161091.1	chr12	87954659	87954659	+	1	NA	intron (NM_001270792, intron 1 of 3).2	intron (NM_001270792, intron 1 of 3).2	179	NM_001270792	100039087	Mm.458830	NM_001270792	ENSMUSG00000096276	Gm2042	-	predicted gene 2042	protein-coding
mm_53211.1	chr6	126163278	126163286	+	1	NA	intron (NM_008742, intron 1 of 1)	intron (NM_008742, intron 1 of 1)	1678	NM_001164035	18205	Mm.267570	NM_008742	ENSMUSG00000049107	Ntf3	AI316846|AI835689|HDNF|NGF-2|Nt3|Ntf-3	neurotrophin 3	protein-coding
mm_27353.1	chr3	50417246	50417256	-	1	NA	intron (NM_011990, intron 6 of 11)	intron (NM_011990, intron 6 of 11)	26362	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_158603.1	chrX	152016345	152016351	-	1	NA	promoter-TSS (NM_025660)	promoter-TSS (NM_025660)	-53	NM_025660	66611	Mm.158120	NM_025660	ENSMUSG00000025257	Ribc1	2610028I09Rik|W08639	RIB43A domain with coiled-coils 1	protein-coding
mm_88967.1	chr10	81395268	81395274	+	1	NA	TTS (NM_001099917)	TTS (NM_001099917)	2207	NM_001099917	72273	Mm.253147	NM_001099917	ENSMUSG00000078439	Smim24	2210404O07Rik	small integral membrane protein 24	protein-coding
mm_56243.1	chr6	90731401	90731426	-	1	NA	intron (NM_001134384, intron 1 of 13)	intron (NM_001134384, intron 1 of 13)	-14884	NM_001134383	232227	Mm.196943	NM_182784	ENSMUSG00000034312	Iqsec1	AW561907|BC026481|BRAG2|D6Ertd349e|cI-43	IQ motif and Sec7 domain 1	protein-coding
mm_33750.1	chr4	134268335	134268345	+	1	NA	Intergenic	Intergenic	-14234	NM_001099296	72690	Mm.100168	NM_001099296	ENSMUSG00000050105	Grrp1	2810043G13Rik|Fam110d	glycine/arginine rich protein 1	protein-coding
mm_131732.1	chr16	21867973	21867981	+	1	NA	Intergenic	Intergenic	-23992	NM_172821	71751	Mm.420837	NM_172821	ENSMUSG00000033618	Map3k13	C130026N12Rik|LZK	mitogen-activated protein kinase kinase kinase 13	protein-coding
mm_168847.1	chr12	23800938	23800948	-	1	NA	Intergenic	CpG	296326	NM_001256489	66808	Mm.379124	NM_001256489	ENSMUSG00000073158	9030624G23Rik	-	RIKEN cDNA 9030624G23 gene	protein-coding
mm_141808.1	chr17	34603400	34603410	-	1	NA	exon (NM_019403, exon 1 of 6)	exon (NM_019403, exon 1 of 6)	156	NM_019403	54197	Mm.274542	NM_019403	ENSMUSG00000015478	Rnf5	2410131O05Rik|AA407576|NG2	ring finger protein 5	protein-coding
mm_42179.1	chr5	112261944	112261974	+	1	NA	intron (NM_023695, intron 3 of 5)	(TTCA)n|Simple_repeat|Simple_repeat	6139	NM_001312893	12960	Mm.29488	NM_023695	ENSMUSG00000029343	Crybb1	3110006K12Rik|BB1CRY	crystallin, beta B1	protein-coding
mm_158232.1	chrX	106387425	106387426	-	1	NA	Intergenic	Intergenic	77599	NR_105803	102465963		NR_105803	ENSMUSG00000099128	Mir6382	Gm27319|mmu-mir-6382	microRNA 6382	ncRNA
mm_34453.1	chr4	148041173	148041198	+	1	NA	promoter-TSS (NM_001161798)	promoter-TSS (NM_001161798)	-4	NR_027809	17769	Mm.89959	NM_010840	ENSMUSG00000029009	Mthfr	AI323986	5,10-methylenetetrahydrofolate reductase	protein-coding
mm_165021.1	chr19	32172545	32172546	-	1	NA	intron (NM_001168525, intron 5 of 9)	ORR1C2|LTR|ERVL-MaLR	38468	NM_001168526	208449	Mm.329810	NM_144792	ENSMUSG00000040451	Sgms1	9530058O11Rik|AI841905|C80702|Mob|Sms1|Sor1|Tmem23	sphingomyelin synthase 1	protein-coding
mm_98984.1	chr11	98741872	98741894	+	1	NA	promoter-TSS (NM_001313983)	promoter-TSS (NM_001313983)	98	NM_001313983	21833	Mm.265917	NM_178060	ENSMUSG00000058756	Thra	6430529J03Rik|AW259572|Erba|Nr1a1|Rvr|T3R[a]|T3Ralpha|Thra1|Thra2|c-erbA-1|c-erbA-alpha|c-erbAalpha	thyroid hormone receptor alpha	protein-coding
mm_13798.1	chr2	118926497	118926554	+	1	NA	promoter-TSS (NM_028117)	promoter-TSS (NM_028117)	28	NM_028117	72136	Mm.486238	NM_028117	ENSMUSG00000074916	Chst14	2600016L03Rik|D4ST-1|D4st1	carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 14	protein-coding
mm_138591.1	chr17	35506427	35506444	+	1	NA	exon (NM_013633, exon 1 of 5)	exon (NM_013633, exon 1 of 5)	403	NM_013633	18999	Mm.17031	NM_013633	ENSMUSG00000024406	Pou5f1	NF-A3|Oct-3|Oct-3/4|Oct-4|Oct3|Oct3/4|Oct4|Otf-3|Otf-4|Otf3|Otf3-rs7|Otf3g|Otf4	POU domain, class 5, transcription factor 1	protein-coding
mm_161483.1	chr15	83023056	83023056	-	1	NA	promoter-TSS (NM_028728)	promoter-TSS (NM_028728)	82	NM_028728	74039	Mm.32584	NM_028728	ENSMUSG00000058099	Nfam1	4921501M20Rik|Cnaip	Nfat activating molecule with ITAM motif 1	protein-coding
mm_164434.1	chr16	48873090	48873103	+	1	NA	intron (NM_181596, intron 2 of 3)	intron (NM_181596, intron 2 of 3)	488	NM_181596	245195	Mm.231288	NM_181596	ENSMUSG00000022651	Retnlg	Fizz3|Relmg|Xcp1	resistin like gamma	protein-coding
mm_103999.1	chr11	84870713	84870807	-	1	NA	promoter-TSS (NM_153144)	promoter-TSS (NM_153144)	-22	NM_153144	217039	Mm.356653	NM_153144	ENSMUSG00000020530	Ggnbp2	AI451896|C75939|D330017P12Rik|DIF-3|Zfp403	gametogenetin binding protein 2	protein-coding
mm_86563.1	chr10	11281584	11281620	+	1	NA	promoter-TSS (NM_001168297)	promoter-TSS (NM_001168297)	15	NM_001168297	71865	Mm.276229	NM_027968	ENSMUSG00000047648	Fbxo30	1700026A16Rik|MUSA1	F-box protein 30	protein-coding
mm_33876.1	chr4	136172267	136172288	+	1	NA	promoter-TSS (NM_177733)	promoter-TSS (NM_177733)	3	NM_177733	242705	Mm.307932	NM_177733	ENSMUSG00000018983	E2f2	E2F-2	E2F transcription factor 2	protein-coding
mm_98522.1	chr11	94967590	94967612	+	1	NA	promoter-TSS (NM_018792)	promoter-TSS (NM_018792)	8	NM_018792	54388	Mm.30482	NM_018792	ENSMUSG00000038994	Hils1	H1.9|TISP64	histone H1-like protein in spermatids 1	protein-coding
mm_121727.1	chr14	17172857	17172880	-	1	NA	Intergenic	CpG	67310	NR_144493	100417973		NR_144493		Pou5f1-rs6	Gm18927|Oct4P3|Otf3-rs6|Otf3f	POU domain, class 5, transcription factor 1, related sequence 6	pseudo
mm_162585.1	chr1	180848678	180848688	-	1	NA	Intergenic	Intergenic	-2468	NM_145943	208768	Mm.272625	NM_145943	ENSMUSG00000038806	Sde2	-	SDE2 telomere maintenance homolog (S. pombe)	protein-coding
mm_116002.1	chr13	24603795	24603805	-	1	NA	intron (NR_024599, intron 1 of 1)	intron (NR_024599, intron 1 of 1)	967	NR_024599	76024	Mm.440710	NR_024599		Gm11346	5830431A10Rik|AI447617|Gm11347|OTTMUSG00000000601|OTTMUSG00000000602	X-linked lymphocyte-regulated 5 pseudogene	pseudo
mm_151140.1	chr19	53051410	53051423	+	1	NA	Intergenic	Intergenic	-12762	NM_133216	170750	Mm.99776	NM_133216	ENSMUSG00000025027	Xpnpep1	D230045I08Rik|sAMP	X-prolyl aminopeptidase (aminopeptidase P) 1, soluble	protein-coding
mm_31934.1	chr4	86575669	86575689	+	1	NA	promoter-TSS (NM_178376)	promoter-TSS (NM_178376)	6	NM_178376	68441	Mm.31178	NM_178376	ENSMUSG00000070934	Rraga	1300010C19Rik|AI255374|FIP-1|RAGA	Ras-related GTP binding A	protein-coding
mm_4066.1	chr1	166130248	166130266	+	1	NA	promoter-TSS (NM_021610)	promoter-TSS (NM_021610)	-203	NM_021610	59290	Mm.46357	NM_021610	ENSMUSG00000000544	Gpa33	2010310L10Rik|2210401D16Rik|BB116197	glycoprotein A33 (transmembrane)	protein-coding
mm_100969.1	chr11	6706916	6706916	-	1	NA	Intergenic	Intergenic	13121	NR_046025	626419	Mm.390334	NR_046025	ENSMUSG00000086808	Gm11981	OTTMUSG00000005129	predicted gene 11981	ncRNA
mm_162472.1	chr1	133046086	133046098	+	1	NA	promoter-TSS (NM_001099276)	promoter-TSS (NM_001099276)	80	NM_001099276	240752	Mm.387308	NM_001099276	ENSMUSG00000026447	Pik3c2b	C330011J12Rik|Gm199|PI3K-C2beta|PI3KC2beta	phosphoinositide-3-kinase, class 2, beta polypeptide	protein-coding
mm_106202.1	chr11	116843286	116843299	-	1	NA	promoter-TSS (NM_028865)	promoter-TSS (NM_028865)	157	NM_033398	107817	Mm.481684	NM_033398	ENSMUSG00000056962	Jmjd6	5730436I23Rik|D11Ertd195e|PSR|PtdSerR|Ptdsr|mKIAA0585	jumonji domain containing 6	protein-coding
mm_54821.1	chr6	42351594	42351653	-	1	NA	exon (NM_001289618, exon 4 of 10)	exon (NM_001289618, exon 4 of 10)	1795	NM_001289619	22793	Mm.282303	NM_011777	ENSMUSG00000029860	Zyx	9530098H06Rik|R75157	zyxin	protein-coding
mm_103716.1	chr11	79525847	79525853	-	1	NA	TTS (NM_010161)	TTS (NM_010161)	-2088	NM_001077496	216984	Mm.439665	NM_001077496	ENSMUSG00000093938	Evi2b	Evi-2|Evi2	ecotropic viral integration site 2b	protein-coding
mm_156395.1	chrX	139807759	139807768	+	1	NA	intron (NM_016675, intron 1 of 1)	intron (NM_016675, intron 1 of 1)	6955	NM_016675	12738	Mm.117068	NM_016675	ENSMUSG00000047230	Cldn2	AL022813	claudin 2	protein-coding
mm_47944.1	chr5	135394247	135394269	-	1	NA	exon (NM_148932, exon 1 of 13)	exon (NM_148932, exon 1 of 13)	288	NM_148932	107939	Mm.28399	NM_148932	ENSMUSG00000053293	Pom121	2610027A18Rik|C80273|mKIAA0618	nuclear pore membrane protein 121	protein-coding
mm_35176.1	chr4	15148978	15149009	-	1	NA	5' UTR (NM_178617, exon 1 of 13)	5' UTR (NM_178617, exon 1 of 13)	138	NM_178617	69352	Mm.389031	NM_178617	ENSMUSG00000040536	Necab1	1700003H21Rik|Efcbp1|STIP-1	N-terminal EF-hand calcium binding protein 1	protein-coding
mm_27938.1	chr3	79591298	79591322	-	1	NA	promoter-TSS (NM_026352)	promoter-TSS (NM_026352)	-79	NM_026352	67738	Mm.295252	NM_026352	ENSMUSG00000027804	Ppid	4930564J03Rik|CYP-40|Ppidl|Ppif	peptidylprolyl isomerase D (cyclophilin D)	protein-coding
mm_154607.1	chrX	7644821	7644836	+	1	NA	intron (NM_009305, intron 4 of 6)	intron (NM_009305, intron 4 of 6)	6248	NM_009305	20977	Mm.223674	NM_009305	ENSMUSG00000031144	Syp	A230093K24Rik|AI848995|Syn|p38	synaptophysin	protein-coding
mm_132173.1	chr16	32332239	32332266	+	1	NA	promoter-TSS (NM_177633)	promoter-TSS (NM_177633)	0	NM_177633	224111	Mm.31275	NM_177633	ENSMUSG00000053774	Ubxn7	A630090P18|AI196514|Ubxd7|mKIAA0794	UBX domain protein 7	protein-coding
mm_60635.1	chr7	44816365	44816375	+	1	NA	promoter-TSS (NM_030693)	promoter-TSS (NM_030693)	0	NM_001171024	100328588	Mm.2565	NM_001171024	ENSMUSG00000074141	Gm21948	Nup62-il4i1	predicted gene, 21948	protein-coding
mm_93523.1	chr10	115290282	115290324	-	1	NA	3' UTR (NM_024454, exon 7 of 7)	3' UTR (NM_024454, exon 7 of 7)	25288	NM_024454	216344	Mm.21936	NM_024454	ENSMUSG00000020132	Rab21	9630024B22	RAB21, member RAS oncogene family	protein-coding
mm_122731.1	chr14	52328359	52328370	-	1	NA	5' UTR (NM_015772, exon 1 of 2)	5' UTR (NM_015772, exon 1 of 2)	306	NM_015772	50524	Mm.39487	NM_015772	ENSMUSG00000049532	Sall2	AI225809|AW559097|Msal-2|Sal-2|mKIAA0360|p150(Sal2)	sal-like 2 (Drosophila)	protein-coding
mm_96201.1	chr11	62057235	62057238	+	1	NA	intron (NM_001310526, intron 3 of 7)	L1MD1|LINE|L1	-19788	NM_001029936	432572	Mm.438022	NM_001029936	ENSMUSG00000042331	Specc1	2810012G08Rik|B230396K10Rik|Cytsb	sperm antigen with calponin homology and coiled-coil domains 1	protein-coding
mm_162365.1	chr1	65080377	65080415	+	1	NA	exon (NM_144761, exon 3 of 3)	exon (NM_144761, exon 3 of 3)	1894	NM_144761	12965	Mm.440053	NM_144761	ENSMUSG00000073658	Crygb	Cryg-3|DGcry-3|Nop	crystallin, gamma B	protein-coding
mm_118458.1	chr14	8666350	8666360	+	1	NA	promoter-TSS (NM_028934)	promoter-TSS (NM_028934)	-35	NR_045968	74859	Mm.84041	NR_045968	ENSMUSG00000097898	4930455B14Rik	1700027C12Rik	RIKEN cDNA 4930455B14 gene	ncRNA
mm_111545.1	chr12	100899545	100899581	-	1	NA	promoter-TSS (NM_001177674)	promoter-TSS (NM_001177674)	-39	NM_001177674	238377	Mm.32160	NM_175493	ENSMUSG00000047415	Gpr68	BB131428|Ogr1	G protein-coupled receptor 68	protein-coding
mm_152130.1	chr19	7019341	7019415	-	1	NA	promoter-TSS (NM_153795)	promoter-TSS (NM_153795)	91	NM_153795	108101	Mm.157591	NM_153795	ENSMUSG00000024965	Fermt3	C79673|Kindlin3	fermitin family member 3	protein-coding
mm_8351.1	chr1	150266074	150266074	-	1	NA	Intergenic	L1_Mus1|LINE|L1	-53343	NM_024458	20028	Mm.440883	NM_024458	ENSMUSG00000006007	Pdc	Rpr-1|Rpr1	phosducin	protein-coding
mm_50199.1	chr6	42038455	42038470	+	1	NA	promoter-TSS (NM_009299)	promoter-TSS (NM_009299)	68	NM_009299	20939	Mm.4119	NM_009299	ENSMUSG00000023289	Sva	-	seminal vesicle antigen	protein-coding
mm_163383.1	chr12	53284082	53284086	+	1	NA	intron (NM_013780, intron 1 of 11)	intron (NM_013780, intron 1 of 11)	35407	NM_013780	27386	Mm.247044	NM_013780	ENSMUSG00000021010	Npas3	4930423H22Rik|bHLHe12	neuronal PAS domain protein 3	protein-coding
mm_89245.1	chr10	87858682	87858695	+	1	NA	promoter-TSS (NM_010512)	promoter-TSS (NM_010512)	-364	NM_001111275	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_22144.1	chr2	172225739	172225739	-	1	NA	Intergenic	MLT1E2|LTR|ERVL-MaLR	-22753	NM_008561	17201	Mm.57183	NM_008561	ENSMUSG00000038537	Mc3r	MC3-R	melanocortin 3 receptor	protein-coding
mm_110910.1	chr12	76177252	76177265	-	1	NA	promoter-TSS (NR_104386)	promoter-TSS (NR_104386)	1	NM_010157	13983	Mm.2561	NM_010157	ENSMUSG00000021055	Esr2	ER[b]|ERbeta|Estrb	estrogen receptor 2 (beta)	protein-coding
mm_16934.1	chr2	14055930	14055956	-	1	NA	promoter-TSS (NM_013935)	promoter-TSS (NM_013935)	92	NM_001012396	30963	Mm.241205	NM_013935	ENSMUSG00000063275	Hacd1	Ptpla	3-hydroxyacyl-CoA dehydratase 1	protein-coding
mm_25427.1	chr3	107884787	107884811	+	1	NA	exon (NM_133867, exon 12 of 19)	exon (NM_133867, exon 12 of 19)	7569	NM_133867	99662	Mm.108491	NM_133867	ENSMUSG00000040600	Eps8l3	AI504489|Eps8r3	EPS8-like 3	protein-coding
mm_154645.1	chrX	7790014	7790029	+	1	NA	promoter-TSS (NM_001290455)	promoter-TSS (NM_001290455)	28	NM_207670	54645	Mm.194811	NM_207670	ENSMUSG00000031153	Gripap1	AI854681|DXImx47e|GRASP-1|Sfc10|mKIAA1167	GRIP1 associated protein 1	protein-coding
mm_154411.1	chrM	15352	15364	+	1	NA	NA	Intergenic	NA	NA								
mm_55582.1	chr6	71397380	71397396	-	1	NA	intron (NM_024288, intron 6 of 8)	intron (NM_024288, intron 6 of 8)	23961	NM_001081110	12525	Mm.1858	NM_009857	ENSMUSG00000053977	Cd8a	BB154331|Ly-2|Ly-35|Ly-B|Lyt-2	CD8 antigen, alpha chain	protein-coding
mm_147126.1	chr18	35910409	35910416	-	1	NA	Intergenic	Intergenic	-54418	NM_028707	74002	Mm.196944	NM_028707	ENSMUSG00000024347	Psd2	6330404E20Rik|AW125584|EFA6C	pleckstrin and Sec7 domain containing 2	protein-coding
mm_93559.1	chr10	116473629	116473644	-	1	NA	promoter-TSS (NM_021452)	promoter-TSS (NM_021452)	-113	NM_021452	58802	Mm.440652	NM_021452	ENSMUSG00000054934	Kcnmb4	1700058G18Rik|2900045G12Rik	potassium large conductance calcium-activated channel, subfamily M, beta member 4	protein-coding
mm_27853.1	chr3	79157161	79157173	-	1	NA	Intergenic	L1_Mur3|LINE|L1	-11292	NM_001099624	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_99723.1	chr11	106300388	106300390	+	1	NA	exon (NM_008117, exon 5 of 5)	exon (NM_008117, exon 5 of 5)	1507	NM_008117	14599	Mm.343934	NM_008117	ENSMUSG00000020713	Gh	Gh1|Ghb1	growth hormone	protein-coding
mm_67266.1	chr7	75780420	75780431	-	1	NA	Intergenic	Intergenic	-67913	NM_001122780	207952	Mm.206223	NM_029652	ENSMUSG00000055652	Klhl25	2810402K13Rik|BC027373|Enc-1	kelch-like 25	protein-coding
mm_20626.1	chr2	131954994	131955008	-	1	NA	3' UTR (NM_001278257, exon 3 of 3)	3' UTR (NM_001278257, exon 3 of 3)	3964	NM_001278520	26434	Mm.180750	NM_023043	ENSMUSG00000027338	Prnd	AI450264|Dpl|PrPLP|doppel	prion protein dublet	protein-coding
mm_2568.1	chr1	118391225	118391230	+	1	NA	intron (NM_001293300, intron 1 of 40)	intron (NM_001293300, intron 1 of 40)	2169	NM_001293301	76707	Mm.138740	NM_029709	ENSMUSG00000064302	Clasp1	1700030C23Rik|5730583A19Rik|B130045P17Rik|CLASP1alpha	CLIP associating protein 1	protein-coding
mm_46199.1	chr5	98030971	98030992	-	1	NA	promoter-TSS (NM_133738)	promoter-TSS (NM_133738)	-19	NM_133738	71914	Mm.24842	NM_133738	ENSMUSG00000029338	Antxr2	2310046B19Rik|AW561899|CMG-2|CMG2|cI-35	anthrax toxin receptor 2	protein-coding
mm_169633.1	chr15	47180970	47180971	+	1	NA	Intergenic	L1Md_T|LINE|L1	557665	NR_045811	75281	Mm.159487	NR_045811	ENSMUSG00000051198	4930548G14Rik	-	RIKEN cDNA 4930548G14 gene	ncRNA
mm_135494.1	chr16	46120239	46120254	-	1	NA	promoter-TSS (NM_032465)	promoter-TSS (NM_032465)	2	NM_032465	84544	Mm.29204	NM_032465	ENSMUSG00000022657	Cd96	1700109I12Rik|Tactile	CD96 antigen	protein-coding
mm_164836.1	chr18	39701519	39701537	+	1	NA	Intergenic	Intergenic	-71969	NM_011033	18459	Mm.9493	NM_011033	ENSMUSG00000051732	Pabpc2	Pabp|Pabp+|Pabp2	poly(A) binding protein, cytoplasmic 2	protein-coding
mm_40038.1	chr5	33799580	33799585	+	1	NA	Intergenic	Intergenic	-16878	NM_019694	56384	Mm.260538	NM_019694	ENSMUSG00000005299	Letm1	-	leucine zipper-EF-hand containing transmembrane protein 1	protein-coding
mm_138028.1	chr17	33919057	33919063	+	1	NA	promoter-TSS (NM_009318)	promoter-TSS (NM_009318)	-418	NM_001025313	21356	Mm.154457	NM_009318	ENSMUSG00000024308	Tapbp	D17Wsu91e|TPN	TAP binding protein	protein-coding
mm_67781.1	chr7	97332117	97332142	-	1	NA	promoter-TSS (NM_001039039)	promoter-TSS (NM_001039039)	-194	NM_001039039	622320	Mm.334029	NM_001039039	ENSMUSG00000044952	Kctd21	EG622320	potassium channel tetramerisation domain containing 21	protein-coding
mm_94730.1	chr11	20741755	20741787	+	1	NA	promoter-TSS (NM_001252503)	promoter-TSS (NM_001252503)	-215	NM_181411	216549	Mm.356580	NM_181411	ENSMUSG00000049659	Aftph	-	aftiphilin	protein-coding
mm_141296.1	chr17	28080116	28080139	-	1	NA	exon (NM_013687, exon 2 of 10)	exon (NM_013687, exon 2 of 10)	457	NM_013687	21463	Mm.29758	NM_013687	ENSMUSG00000062859	Tcp11	D17Ken1|Tcp-11	t-complex protein 11	protein-coding
mm_115649.1	chr13	12309706	12309717	-	1	NA	exon (NM_033268, exon 3 of 21)	exon (NM_033268, exon 3 of 21)	31021	NM_033268	11472	Mm.37638	NM_033268	ENSMUSG00000052374	Actn2	1110008F24Rik	actinin alpha 2	protein-coding
mm_24154.1	chr3	88424795	88424800	+	1	NA	5' UTR (NM_178696, exon 1 of 4)	5' UTR (NM_178696, exon 1 of 4)	337	NM_001281795	229517	Mm.301740	NM_178696	ENSMUSG00000050144	Slc25a44	6720482A19|B430110G05Rik	solute carrier family 25, member 44	protein-coding
mm_151706.1	chr19	4498575	4498596	-	1	NA	promoter-TSS (NM_027237)	promoter-TSS (NM_027237)	-2	NM_027237	69861	Mm.282978	NM_027237	ENSMUSG00000042041	2010003K11Rik	-	RIKEN cDNA 2010003K11 gene	protein-coding
mm_87379.1	chr10	44599878	44599906	+	1	NA	Intergenic	Intergenic	-141144	NM_007548	12142	Mm.4800	NM_007548	ENSMUSG00000038151	Prdm1	Blimp-1|Blimp1|PRDI-BF1|ZNFPR1A1|b2b1765Clo	PR domain containing 1, with ZNF domain	protein-coding
mm_158617.1	chrX	152644489	152644544	-	1	NA	promoter-TSS (NM_001290687)	promoter-TSS (NM_001290687)	32	NM_001290686	110380	Mm.40796	NM_172441	ENSMUSG00000045180	Shroom2	4832440C16|Apxl|C630003H05Rik|Shrm2	shroom family member 2	protein-coding
mm_29897.1	chr3	131344893	131344926	-	1	NA	promoter-TSS (NM_028943)	promoter-TSS (NM_028943)	14	NM_028943	74442	Mm.273360	NM_028943	ENSMUSG00000050931	Sgms2	4933405A16Rik|5133401H06Rik|AI854299	sphingomyelin synthase 2	protein-coding
mm_149879.1	chr19	25237243	25237269	+	1	NA	promoter-TSS (NM_181404)	promoter-TSS (NM_181404)	54	NM_181404	107351	Mm.260722	NM_181404	ENSMUSG00000032702	Kank1	A930031B09Rik|AU015049|AW121052|Ankrd15|D330024H06Rik|mKIAA0172	KN motif and ankyrin repeat domains 1	protein-coding
mm_132160.1	chr16	32179855	32179857	+	1	NA	promoter-TSS (NM_001033539)	promoter-TSS (NM_001033539)	56	NM_001033539	328660	Mm.441006	NM_001033539	ENSMUSG00000075269	Bex6	B020003O03Rik	brain expressed family member 6	protein-coding
mm_165552.1	chr3	12155269	12155287	+	1	NA	Intergenic	Intergenic	-310919	NR_040751	100038545	Mm.388494	NR_040751	ENSMUSG00000104015	Gm10745	ENSMUSG00000074696	predicted gene 10745	ncRNA
mm_65119.1	chr7	19403791	19403818	-	1	NA	intron (NM_001286039, intron 1 of 12)	CpG	300	NM_001286039	232943	Mm.213403	NM_146182	ENSMUSG00000040714	Klc3	BC017147|Klct	kinesin light chain 3	protein-coding
mm_16531.1	chr2	181578363	181578374	+	1	NA	promoter-TSS (NR_027289)	promoter-TSS (NR_027289)	-112	NR_027289	100271841	Mm.438007	NR_027289	ENSMUSG00000010492	Uckl1os	Gm16119|OTTMUSG00000030649	uridine-cytidine kinase 1-like 1, opposite strand	ncRNA
mm_38508.1	chr4	141139748	141139772	-	1	NA	promoter-TSS (NR_102344)	promoter-TSS (NR_102344)	36	NR_102344	213491	Mm.332006	NM_174996	ENSMUSG00000040842	Szrd1	1110022I03|D4Ertd22e	SUZ RNA binding domain containing 1	protein-coding
mm_91035.1	chr10	18234891	18234913	-	1	NA	promoter-TSS (NM_144820)	promoter-TSS (NM_144820)	79	NM_001346751	215814	Mm.296565	NM_144820	ENSMUSG00000059554	Ccdc28a	1700009P13Rik|AI480677	coiled-coil domain containing 28A	protein-coding
mm_102089.1	chr11	52282759	52282772	-	1	NA	promoter-TSS (NM_009331)	promoter-TSS (NM_009331)	-170	NM_009331	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_115568.1	chr13	9765362	9765370	-	1	NA	promoter-TSS (NM_001347480)	promoter-TSS (NM_001347480)	-45	NM_144516	66505	Mm.397307	NM_144516	ENSMUSG00000021156	Zmynd11	2210402G22Rik|BS69	zinc finger, MYND domain containing 11	protein-coding
mm_11469.1	chr2	32363169	32363177	+	1	NA	promoter-TSS (NM_001252534)	promoter-TSS (NM_001252534)	-25	NM_001252537	68379	Mm.170508	NM_028412	ENSMUSG00000039205	Ciz1	0610038H21Rik|2900056O04Rik|LSFR1|ZNF356	CDKN1A interacting zinc finger protein 1	protein-coding
mm_84254.1	chr9	62510553	62510570	-	1	NA	intron (NM_175484, intron 1 of 11)	intron (NM_175484, intron 1 of 11)	26483	NM_175484	235431	Mm.335229	NM_175484	ENSMUSG00000041729	Coro2b	CLIPINC|E130012P22Rik	coronin, actin binding protein, 2B	protein-coding
mm_41614.1	chr5	96793454	96793528	+	1	NA	5' UTR (NM_013470, exon 1 of 13)	5' UTR (NM_013470, exon 1 of 13)	106	NM_013470	11745	Mm.7214	NM_013470	ENSMUSG00000029484	Anxa3	Anx3	annexin A3	protein-coding
mm_113939.1	chr13	49682211	49682221	+	1	NA	promoter-TSS (NM_172015)	promoter-TSS (NM_172015)	86	NM_172015	105148	Mm.21118	NM_172015	ENSMUSG00000037851	Iars	2510016L12Rik|AI327140|AU044614|E430001P04Rik|ILRS	isoleucine-tRNA synthetase	protein-coding
mm_24515.1	chr3	92689308	92689337	+	1	NA	Intergenic	Intergenic	-2112	NM_027137	69611	Mm.176243	NM_027137	ENSMUSG00000103243	Lce1d	2310037L11Rik|AI415320|Sprrl7	late cornified envelope 1D	protein-coding
mm_54192.1	chr6	24515037	24515083	-	1	NA	promoter-TSS (NM_172535)	promoter-TSS (NM_172535)	7	NM_172535	214704	Mm.61131	NM_172535	ENSMUSG00000046192	Iqub	4932408B21Rik|Trs4	IQ motif and ubiquitin domain containing	protein-coding
mm_85179.1	chr9	96630626	96630645	-	1	NA	intron (NM_053268, intron 1 of 23)	intron (NM_053268, intron 1 of 23)	868	NM_053268	114713	Mm.124502	NM_053268	ENSMUSG00000032413	Rasa2	5430433H21Rik|AA517451|AU023900|GAP1m	RAS p21 protein activator 2	protein-coding
mm_28029.1	chr3	83046798	83046808	-	1	NA	exon (NM_181849, exon 2 of 8)	exon (NM_181849, exon 2 of 8)	3060	NM_181849	110135	Mm.30063	NM_181849	ENSMUSG00000033831	Fgb	2510049G14Rik	fibrinogen beta chain	protein-coding
mm_3490.1	chr1	150105870	150105876	+	1	NA	3' UTR (NM_011198, exon 10 of 10)	3' UTR (NM_011198, exon 10 of 10)	5842	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_56825.1	chr6	117173615	117173635	-	1	NA	3' UTR (NM_021704, exon 3 of 3)	3' UTR (NM_021704, exon 3 of 3)	5090	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_100472.1	chr11	120007323	120007324	+	1	NA	TTS (NM_001037755)	TTS (NM_001037755)	-7444	NR_037225	100526518		NR_037225	ENSMUSG00000105524	Mir3065	mir-3065|mmu-mir-3065	microRNA 3065	ncRNA
mm_4260.1	chr1	171437553	171437566	+	1	NA	promoter-TSS (NM_172647)	promoter-TSS (NM_172647)	-2	NM_172647	16456	Mm.294882	NM_172647	ENSMUSG00000038235	F11r	9130004G24|AA638916|ESTM33|JAM|JAM-1|JAM-A|Jcam|Jcam1|Ly106	F11 receptor	protein-coding
mm_4582.1	chr1	178236505	178236508	+	1	NA	intron (NM_024282, intron 1 of 4)	MTC|LTR|ERVL-MaLR	49089	NM_024282	78825	Mm.440132	NM_024282	ENSMUSG00000026502	Desi2	5830417C01Rik|DeSI-2|Fam152a|Pppde1	desumoylating isopeptidase 2	protein-coding
mm_17111.1	chr2	24349913	24349948	-	1	NA	3' UTR (NM_031167, exon 5 of 5)	3' UTR (NM_031167, exon 5 of 5)	4559	NM_001039701	16181	Mm.882	NM_031167	ENSMUSG00000026981	Il1rn	F630041P17Rik|IL-1ra	interleukin 1 receptor antagonist	protein-coding
mm_112337.1	chr12	116010138	116010141	-	1	NA	Intergenic	Intergenic	-37585	NM_001004066	56220	Mm.254997	NM_019565	ENSMUSG00000042063	Zfp386	Kzf1|mKIAA4205	zinc finger protein 386 (Kruppel-like)	protein-coding
mm_3251.1	chr1	136133037	136133039	+	1	NA	intron (NM_001039472, intron 1 of 34)	intron (NM_001039472, intron 1 of 34)	1637	NM_001039472	16565	Mm.276135	NM_019962	ENSMUSG00000041642	Kif21b	2610511N21Rik|mKIAA0449	kinesin family member 21B	protein-coding
mm_86961.1	chr10	25109977	25109987	+	1	NA	Intergenic	Intergenic	90188	NM_001347460	432442	Mm.485937	NM_018747	ENSMUSG00000039166	Akap7	6430401D08|AI662165|AKAP15|Akap18|BB170514	A kinase (PRKA) anchor protein 7	protein-coding
mm_53810.1	chr6	146933388	146933419	+	1	NA	intron (NM_026221, intron 1 of 26)	intron (NM_026221, intron 1 of 26)	21018	NM_001164236	73344	Mm.391543	NM_028509	ENSMUSG00000040163	1700034J05Rik	-	RIKEN cDNA 1700034J05 gene	protein-coding
mm_66908.1	chr7	60002984	60002995	-	1	NA	intron (NM_001082962, intron 2 of 10)	intron (NM_001082962, intron 2 of 10)	2167	NM_013670	20646	Mm.274995	NM_013670	ENSMUSG00000102252	Snrpn	2410045I01Rik|HCERN3|Peg4|Pwcr1|SMN	small nuclear ribonucleoprotein N	protein-coding
mm_68279.1	chr7	105599333	105599346	-	1	NA	exon (NM_017371, exon 4 of 10)	exon (NM_017371, exon 4 of 10)	777	NM_017371	15458	Mm.3485	NM_017371	ENSMUSG00000030895	Hpx	Hpxn|hx	hemopexin	protein-coding
mm_84970.1	chr9	85319516	85319528	-	1	NA	TTS (NM_001160378)	TTS (NM_001160378)	7602	NM_001160378	212943	Mm.74610	NM_001160378	ENSMUSG00000032265	Fam46a	BAP014|D930050G01Rik	family with sequence similarity 46, member A	protein-coding
mm_145126.1	chr18	44423530	44423561	+	1	NA	3' UTR (NM_027490, exon 11 of 11)	3' UTR (NM_027490, exon 11 of 11)	43045	NM_027490	70640	Mm.87629	NM_027490	ENSMUSG00000024472	Dcp2	2410015D23Rik|5730537H01Rik|AL118268	decapping mRNA 2	protein-coding
mm_67928.1	chr7	99906225	99906231	-	1	NA	intron (NM_001164258, intron 11 of 18)	intron (NM_001164258, intron 11 of 18)	47010	NM_001164258	446101	Mm.440757	NM_001164258	ENSMUSG00000035211	Xrra1	AI449753	X-ray radiation resistance associated 1	protein-coding
mm_162553.1	chr1	171419095	171419099	+	1	NA	promoter-TSS (NM_001164525)	promoter-TSS (NM_001164525)	64	NM_001164525	226654	Mm.46366	NM_001164525	ENSMUSG00000103711	Tstd1	AV065366|EG226654|Gm4848|KAT	thiosulfate sulfurtransferase (rhodanese)-like domain containing 1	protein-coding
mm_84244.1	chr9	62344019	62344058	-	1	NA	intron (NM_009672, intron 1 of 6)	CpG	2695	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	protein-coding
mm_41604.1	chr5	96374147	96374165	+	1	NA	5' UTR (NM_175473, exon 1 of 74)	5' UTR (NM_175473, exon 1 of 74)	201	NM_175473	231470	Mm.291120	NM_175473	ENSMUSG00000034687	Fras1	E130113P14Rik|bl|mKIAA1500	Fraser extracellular matrix complex subunit 1	protein-coding
mm_36960.1	chr4	109156836	109156851	-	1	NA	intron (NM_001346502, intron 2 of 23)	intron (NM_001346502, intron 2 of 23)	-38807	NM_001134791	100273	Mm.366315	NM_133885	ENSMUSG00000028559	Osbpl9	2600011I06Rik|AU015843|Orp-9	oxysterol binding protein-like 9	protein-coding
mm_128513.1	chr15	53331935	53331938	-	1	NA	intron (NM_010162, intron 1 of 10)	intron (NM_010162, intron 1 of 10)	14247	NM_010162	14042	Mm.309395	NM_010162	ENSMUSG00000061731	Ext1	AA409028	exostoses (multiple) 1	protein-coding
mm_108894.1	chr12	100110149	100110193	+	1	NA	Intergenic	CpG	-2160	NM_008947	19179	Mm.157105	NM_008947	ENSMUSG00000021178	Psmc1	AI325227|P26s4|Rpt2/S4|S4|rpt2	protease (prosome, macropain) 26S subunit, ATPase 1	protein-coding
mm_25942.1	chr3	131490352	131490405	+	1	NA	Intergenic	CpG	-74390	NM_001289479	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_85905.1	chr9	111056413	111056470	-	1	NA	intron (NM_001302377, intron 2 of 2)	intron (NM_001302377, intron 2 of 2)	803	NM_001302377	54199	Mm.7336	NM_017466	ENSMUSG00000043953	Ccrl2	1810047I05Rik|Ackr5|CCR11|Cmkbr1l2|E01|L-CCR	chemokine (C-C motif) receptor-like 2	protein-coding
mm_148932.1	chr19	7018693	7018731	+	1	NA	exon (NM_153795, exon 2 of 15)	exon (NM_153795, exon 2 of 15)	757	NM_153795	108101	Mm.157591	NM_153795	ENSMUSG00000024965	Fermt3	C79673|Kindlin3	fermitin family member 3	protein-coding
mm_64518.1	chr7	143830205	143830249	+	1	NA	5' UTR (NM_007856, exon 2 of 9)	5' UTR (NM_007856, exon 2 of 9)	7060	NM_007856	13360	Mm.249342	NM_007856	ENSMUSG00000058454	Dhcr7	AA409147	7-dehydrocholesterol reductase	protein-coding
mm_226.1	chr1	17601952	17601954	+	1	NA	promoter-TSS (NM_053191)	promoter-TSS (NM_053191)	52	NM_053191	94227	Mm.442452	NM_053191	ENSMUSG00000067780	Pi15	P24TI|P25TI|PI-15|SugarCrisp	peptidase inhibitor 15	protein-coding
mm_35890.1	chr4	49544913	49544925	-	1	NA	intron (NM_144903, intron 1 of 8)	intron (NM_144903, intron 1 of 8)	4627	NM_144903	230163	Mm.482116	NM_144903	ENSMUSG00000028307	Aldob	Aldo-2|Aldo2|BC016435	aldolase B, fructose-bisphosphate	protein-coding
mm_146113.1	chr18	74268232	74268246	+	1	NA	promoter-TSS (NM_013594)	promoter-TSS (NM_013594)	-49	NM_013594	17190	Mm.22522	NM_013594	ENSMUSG00000024561	Mbd1	Cxxc3|PCM1	methyl-CpG binding domain protein 1	protein-coding
mm_77586.1	chr8	123859424	123859521	-	1	NA	intron (NM_028536, intron 1 of 3)	CpG-14647	737	NM_028536	73420	Mm.157746	NM_028536	ENSMUSG00000031971	Ccsap	1700054N08Rik|AI853424	centriole, cilia and spindle associated protein	protein-coding
mm_97439.1	chr11	78178677	78178695	+	1	NA	promoter-TSS (NM_001291236)	promoter-TSS (NM_001291236)	28	NM_026708	68385	Mm.390375	NM_026708	ENSMUSG00000019437	Tlcd1	-	TLC domain containing 1	protein-coding
mm_45008.1	chr5	38491949	38491961	-	1	NA	intron (NM_145559, intron 1 of 10)	intron (NM_145559, intron 1 of 10)	-8570	NM_001012363	117591	Mm.260137	NM_145559	ENSMUSG00000005107	Slc2a9	Glut9|SLC2A9B|SLC2a9A	solute carrier family 2 (facilitated glucose transporter), member 9	protein-coding
mm_157990.1	chrX	94459775	94459776	-	1	NA	Intergenic	Intergenic	17043	NR_045323	100503393	Mm.402891	NR_045323	ENSMUSG00000084904	Gm14827	OTTMUSG00000018126	predicted gene 14827	ncRNA
mm_93166.1	chr10	93276559	93276573	-	1	NA	intron (NM_013508, intron 2 of 4)	intron (NM_013508, intron 2 of 4)	34593	NM_001322268	13713	Mm.4454	NM_013508	ENSMUSG00000008398	Elk3	D430049E23Rik|Erp|Etrp|Net|Sap-2	ELK3, member of ETS oncogene family	protein-coding
mm_163831.1	chr14	19417656	19417666	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	184926	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_147191.1	chr18	37644063	37644073	-	1	NA	5' UTR (NM_175770, exon 1 of 2)	5' UTR (NM_175770, exon 1 of 2)	136	NM_175770	24074	Mm.236009	NM_175770	ENSMUSG00000051316	Taf7	55kDa|AI607308|BB007175|TAFII55|Taf2f	TATA-box binding protein associated factor 7	protein-coding
mm_115348.1	chr13	112673366	112673374	+	1	NA	intron (NM_178746, intron 2 of 14)	intron (NM_178746, intron 2 of 14)	12604	NM_178746	268706	Mm.40834	NM_175376	ENSMUSG00000047789	Slc38a9	4833412L08Rik|6720411P22Rik|9130023D20Rik|9430067K09Rik|A730092C09	solute carrier family 38, member 9	protein-coding
mm_10469.1	chr2	14331136	14331196	+	1	NA	exon (NM_008625, exon 30 of 30)	exon (NM_008625, exon 30 of 30)	-57232	NM_001012305	277468	Mm.44662	NM_001012305	ENSMUSG00000036949	Slc39a12	AW046938|Gm731	solute carrier family 39 (zinc transporter), member 12	protein-coding
mm_39019.1	chr4	152131459	152131486	-	1	NA	intron (NM_207688, intron 3 of 10)	CpG-10714	-2547	NM_019585	56226	Mm.264215	NM_019585	ENSMUSG00000028943	Espn	je	espin	protein-coding
mm_22374.1	chr2	181155452	181155487	-	1	NA	5' UTR (NM_007906, exon 2 of 8)	5' UTR (NM_007906, exon 2 of 8)	1546	NM_007906	13628	Mm.2645	NM_007906	ENSMUSG00000016349	Eef1a2	Eef1a|S1|wasted|wst	eukaryotic translation elongation factor 1 alpha 2	protein-coding
mm_63416.1	chr7	127470992	127471006	+	1	NA	promoter-TSS (NM_145589)	promoter-TSS (NM_145589)	-615	NM_145589	233895	Mm.44183	NM_145589	ENSMUSG00000030822	Prr14	BC006909	proline rich 14	protein-coding
mm_124780.1	chr15	7442397	7442406	+	1	NA	Intergenic	Intergenic	-44006	NM_001289498	268780	Mm.203208	NM_178748	ENSMUSG00000042961	Egflam	5930412K08|AU040377	EGF-like, fibronectin type III and laminin G domains	protein-coding
mm_75099.1	chr8	34108793	34108809	-	1	NA	promoter-TSS (NM_011722)	promoter-TSS (NM_011722)	-89	NM_011722	22428	Mm.150373	NM_011722	ENSMUSG00000031516	Dctn6	AU044699|WS-3|p27	dynactin 6	protein-coding
mm_42384.1	chr5	114934187	114934215	+	1	NA	intron (NM_145209, intron 5 of 6)	B2_Mm2|SINE|B2	-8001	NM_028211	72357	Mm.292672	NM_028211	ENSMUSG00000029559	2210016L21Rik	-	RIKEN cDNA 2210016L21 gene	protein-coding
mm_105851.1	chr11	113710099	113710105	-	1	NA	promoter-TSS (NM_001164532)	promoter-TSS (NM_001164532)	-85	NM_029794	52670	Mm.229207	NM_026682	ENSMUSG00000018727	Cpsf4l	0610010C04Rik|1500000C01Rik|D11Ertd636e	cleavage and polyadenylation specific factor 4-like	protein-coding
mm_22382.1	chr2	181156847	181156859	-	1	NA	5' UTR (NM_007906, exon 1 of 8)	5' UTR (NM_007906, exon 1 of 8)	162	NM_007906	13628	Mm.2645	NM_007906	ENSMUSG00000016349	Eef1a2	Eef1a|S1|wasted|wst	eukaryotic translation elongation factor 1 alpha 2	protein-coding
mm_129109.1	chr15	76069395	76069455	-	1	NA	TTS (NM_028364)	TTS (NM_028364)	359	NM_134089	105782	Mm.25568	NM_134089	ENSMUSG00000022568	Scrib	AI118201|CRIB|Crc|SCRIB1|Scrb1|mKIAA0147|vartul	scribbled planar cell polarity	protein-coding
mm_83907.1	chr9	56244051	56244099	-	1	NA	intron (NM_172924, intron 4 of 6)	intron (NM_172924, intron 4 of 6)	-83005	NM_019793	56434	Mm.28484	NM_019793	ENSMUSG00000032324	Tspan3	1700055K04Rik|TM4-A|Tm4sf8	tetraspanin 3	protein-coding
mm_116651.1	chr13	49187914	49187924	-	1	NA	intron (NM_013610, intron 1 of 3)	CpG	372	NM_013610	18081	Mm.18503	NM_013610	ENSMUSG00000037966	Ninj1	AU024536	ninjurin 1	protein-coding
mm_36854.1	chr4	106840022	106840050	-	1	NA	Intergenic	CpG	-35029	NM_001347159	329910	Mm.222956	NM_025590	ENSMUSG00000034853	Acot11	1110020M10Rik|2010309H15Rik|AW060409|BFIT|BFIT1|Thea|Them1|mKIAA0707	acyl-CoA thioesterase 11	protein-coding
mm_37944.1	chr4	133159248	133159254	-	1	NA	intron (NM_153423, intron 1 of 8)	intron (NM_153423, intron 1 of 8)	28618	NM_153423	242687	Mm.23566	NM_153423	ENSMUSG00000028868	Wasf2	AW742646|D4Ertd13e|WAVE2	WAS protein family, member 2	protein-coding
mm_12036.1	chr2	58762258	58762274	+	1	NA	intron (NM_001289659, intron 2 of 7)	intron (NM_001289659, intron 2 of 7)	7082	NM_029692	76654	Mm.200370	NM_029692	ENSMUSG00000026839	Upp2	1700124F02Rik|AI266885|UDRPASE2|UP2|UPASE2	uridine phosphorylase 2	protein-coding
mm_26807.1	chr3	10194713	10194719	-	1	NA	exon (NM_011598, exon 2 of 4)	exon (NM_011598, exon 2 of 4)	2567	NM_011598	21884	Mm.26654	NM_011598	ENSMUSG00000027528	Fabp9	1700007P10Rik|Perf|Perf15|Tlbp	fatty acid binding protein 9, testis	protein-coding
mm_60071.1	chr7	33635146	33635147	+	1	NA	intron (NR_045685, intron 1 of 2)	intron (NR_045685, intron 1 of 2)	18135	NR_045685	353109	Mm.63867	NR_045685	ENSMUSG00000083896	Scgb2b23-ps	1700028O08Rik|Abpbg23-ps|C2y|Scgb2b1|Scgb2b1-ps	secretoglobin, family 2B, member 23, pseudogene	pseudo
mm_112407.1	chr13	3556972	3557018	+	1	NA	exon (NM_008112, exon 6 of 11)	exon (NM_008112, exon 6 of 11)	18920	NM_008112	14569	Mm.153226	NM_008112	ENSMUSG00000021218	Gdi2	GDI-B|GDIB|Gdi3	guanosine diphosphate (GDP) dissociation inhibitor 2	protein-coding
mm_57724.1	chr6	128891050	128891101	-	1	NA	promoter-TSS (NM_001254946)	promoter-TSS (NM_001254946)	49	NM_001254946	232406	Mm.30745	NM_001254946	ENSMUSG00000090164	BC035044	-	cDNA sequence BC035044	protein-coding
mm_55950.1	chr6	85333413	85333441	-	1	NA	promoter-TSS (NM_178639)	promoter-TSS (NM_178639)	-5	NM_178639	94282	Mm.121485	NM_178639	ENSMUSG00000033720	Sfxn5	C230001H08Rik	sideroflexin 5	protein-coding
mm_129208.1	chr15	76519864	76519891	-	1	NA	intron (NM_130893, intron 1 of 1)	GA-rich|Low_complexity|Low_complexity	2252	NM_130893	170729	Mm.218747	NM_130893	ENSMUSG00000048385	Scrt1	-	scratch family zinc finger 1	protein-coding
mm_120253.1	chr14	63011695	63011699	+	1	NA	promoter-TSS (NM_001039121)	promoter-TSS (NM_001039121)	-74	NM_001039121	654458	Mm.390737	NM_001039121	ENSMUSG00000075572	Defb43	BD-43|EG654458|mBD-43	defensin beta 43	protein-coding
mm_101159.1	chr11	16972880	16972919	-	1	NA	3' UTR (NM_019549, exon 10 of 10)	3' UTR (NM_019549, exon 10 of 10)	21489	NM_176982	319701	Mm.120672	NM_176982	ENSMUSG00000044966	Fbxo48	A630050E13Rik	F-box protein 48	protein-coding
mm_16804.1	chr2	10123458	10123467	-	1	NA	exon (NM_010582, exon 5 of 21)	exon (NM_010582, exon 5 of 21)	7221	NM_010582	16425	Mm.182043	NM_010582	ENSMUSG00000037254	Itih2	AI747202|Intin2|Itih-2	inter-alpha trypsin inhibitor, heavy chain 2	protein-coding
mm_67403.1	chr7	79935259	79935371	-	1	NA	promoter-TSS (NM_027420)	promoter-TSS (NM_027420)	-51	NM_027420	70420	Mm.34266	NM_027420	ENSMUSG00000039043	Arpin	2610034B18Rik	actin-related protein 2/3 complex inhibitor	protein-coding
mm_131630.1	chr16	20186511	20186519	+	1	NA	intron (NM_001033237, intron 10 of 29)	intron (NM_001033237, intron 10 of 29)	-10281	NR_030454	735274		NR_030454	ENSMUSG00000106252	Mir684-1	Mirn684-1	microRNA 684-1	ncRNA
mm_126747.1	chr15	85735812	85735823	+	1	NA	promoter-TSS (NM_011144)	promoter-TSS (NM_011144)	41	NM_011144	19013	Mm.212789	NM_011144	ENSMUSG00000022383	Ppara	4933429D07Rik|AW742785|Nr1c1|PPAR-alpha|PPARalpha|Ppar	peroxisome proliferator activated receptor alpha	protein-coding
mm_169758.1	chr15	9354850	9354850	-	1	NA	intron (NM_144845, intron 3 of 6)	RLTRETN_Mm|LTR|ERVK	19252	NM_144845	223337	Mm.422853	NM_144845	ENSMUSG00000049152	Ugt3a2	AI313915	UDP glycosyltransferases 3 family, polypeptide A2	protein-coding
mm_96981.1	chr11	70656601	70656614	+	1	NA	promoter-TSS (NM_007933)	promoter-TSS (NM_007933)	-569	NM_001136062	13808	Mm.251322	NM_007933	ENSMUSG00000060600	Eno3	Eno-3|MSE	enolase 3, beta muscle	protein-coding
mm_101259.1	chr11	20898686	20898693	-	1	NA	Intergenic	Intergenic	-67581	NM_173752	216551	Mm.76694	NM_173752	ENSMUSG00000042363	Lgalsl	1110067D22Rik|A530071M23|Grpa|Hspc159|Lgalsla	lectin, galactoside binding-like	protein-coding
mm_95043.1	chr11	32277587	32277613	+	1	NA	exon (NM_010405, exon 2 of 3)	exon (NM_010405, exon 2 of 3)	1000	NM_010405	15126	Mm.141758	NM_010405	ENSMUSG00000055609	Hba-x	AI450015|Hbz	hemoglobin X, alpha-like embryonic chain in Hba complex	protein-coding
mm_172187.1	chr6	50566472	50566478	-	1	NA	promoter-TSS (NM_007808)	promoter-TSS (NM_007808)	-1	NM_007808	13063	Mm.35389	NM_007808	ENSMUSG00000063694	Cycs	-	cytochrome c, somatic	protein-coding
mm_53380.1	chr6	129512651	129512675	+	1	NA	5' UTR (NM_001081186, exon 1 of 5)	5' UTR (NM_001081186, exon 1 of 5)	106	NM_001081186	330428	Mm.44237	NM_001081186	ENSMUSG00000030160	Tmem52b	D630042F21Rik	transmembrane protein 52B	protein-coding
mm_1534.1	chr1	72849578	72849609	+	1	NA	exon (NM_008342, exon 3 of 4)	exon (NM_008342, exon 3 of 4)	24206	NM_001310659	16008	Mm.141936	NM_008342	ENSMUSG00000039323	Igfbp2	AI255832|IBP-2|Igfbp-2|mIGFBP-2	insulin-like growth factor binding protein 2	protein-coding
mm_86564.1	chr10	11283215	11283218	+	1	NA	intron (NM_001168297, intron 1 of 2)	intron (NM_001168297, intron 1 of 2)	1629	NM_001168297	71865	Mm.276229	NM_027968	ENSMUSG00000047648	Fbxo30	1700026A16Rik|MUSA1	F-box protein 30	protein-coding
mm_80890.1	chr9	99575777	99575829	+	1	NA	promoter-TSS (NM_031403)	promoter-TSS (NM_031403)	4	NM_031403	83703	Mm.31324	NM_031403	ENSMUSG00000032469	Dbr1	AW018415	debranching RNA lariats 1	protein-coding
mm_176.1	chr1	13668774	13668794	+	1	NA	promoter-TSS (NM_001011873)	promoter-TSS (NM_001011873)	13	NM_001011873	381246	Mm.311142	NM_001011873	ENSMUSG00000067813	Xkr9	Gm1620|XRG9	X-linked Kx blood group related 9	protein-coding
mm_117255.1	chr13	64366940	64367095	-	1	NA	exon (NM_009984, exon 5 of 8)	exon (NM_009984, exon 5 of 8)	3503	NM_009984	13039	Mm.930	NM_009984	ENSMUSG00000021477	Ctsl	1190035F06Rik|CatL|Ctsl1|MEP|fs|nkt	cathepsin L	protein-coding
mm_78265.1	chr9	21955748	21955769	+	1	NA	promoter-TSS (NM_025870)	promoter-TSS (NM_025870)	5	NM_025870	66962	Mm.46647	NM_025870	ENSMUSG00000051238	Swsap1	2310047B19Rik	SWIM type zinc finger 7 associated protein 1	protein-coding
mm_28935.1	chr3	98882160	98882170	-	1	NA	intron (NM_019545, intron 4 of 8)	intron (NM_019545, intron 4 of 8)	11065	NM_019545	56185	Mm.281874	NM_019545	ENSMUSG00000027870	Hao2	AI325478|Hao-2|Hao3|Haox3	hydroxyacid oxidase 2	protein-coding
mm_117997.1	chr13	100492552	100492601	-	1	NA	promoter-TSS (NM_022011)	promoter-TSS (NM_022011)	33	NM_022011	23894	Mm.272533	NM_022011	ENSMUSG00000021639	Gtf2h2	44kDa|BTF2 p44|BTF2-p44|Btf2p44|p44	general transcription factor II H, polypeptide 2	protein-coding
mm_3994.1	chr1	164458518	164458530	+	1	NA	promoter-TSS (NM_009721)	promoter-TSS (NM_009721)	-169	NM_009721	11931	Mm.4550	NM_009721	ENSMUSG00000026576	Atp1b1	Atp4b|Atpb|Atpb-1|NKbeta1	ATPase, Na+/K+ transporting, beta 1 polypeptide	protein-coding
mm_145730.1	chr18	64264852	64264862	+	1	NA	intron (NM_009182, intron 2 of 5)	intron (NM_009182, intron 2 of 5)	10498	NM_009182	20451	Mm.252110	NM_009182	ENSMUSG00000056812	St8sia3	AI847333|ST8SiaIII|Siat8c	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3	protein-coding
mm_115140.1	chr13	104816546	104816569	+	1	NA	promoter-TSS (NM_026075)	promoter-TSS (NM_026075)	396	NM_026072	67285	Mm.235398	NM_026072	ENSMUSG00000021715	Cwc27	3110009E13Rik|NY-CO-10|Sdccag10	CWC27 spliceosome-associated protein	protein-coding
mm_17232.1	chr2	25574902	25574921	-	1	NA	promoter-TSS (NM_029293)	promoter-TSS (NM_029293)	-40	NM_029293	75454	Mm.458079	NM_029293	ENSMUSG00000036504	Phpt1	1700008C22Rik|PHP|Php14	phosphohistidine phosphatase 1	protein-coding
mm_14233.1	chr2	127590322	127590369	+	1	NA	intron (NM_029963, intron 1 of 11)	RMER15|LTR|ERVL	2919	NM_029963	77721	Mm.274601	NM_029963	ENSMUSG00000027374	Mrps5	1620401I16Rik|AI850294	mitochondrial ribosomal protein S5	protein-coding
mm_26721.1	chr3	159528827	159528830	+	1	NA	intron (NM_029523, intron 11 of 11)	B1_Mur3|SINE|Alu	33395	NM_001172093	76131	Mm.371655	NM_029523	ENSMUSG00000028175	Depdc1a	5830484J08Rik|Depdc1	DEP domain containing 1a	protein-coding
mm_129642.1	chr15	80562498	80562507	-	1	NA	Intergenic	Intergenic	-2032	NM_001163189	383075	Mm.297626	NM_001163189	ENSMUSG00000050439	Enthd1	Gm1242|Gm86	ENTH domain containing 1	protein-coding
mm_96300.1	chr11	63151114	63151145	+	1	NA	exon (NM_008885, exon 4 of 5)	exon (NM_008885, exon 4 of 5)	18326	NM_001302260	18858	Mm.1237	NM_008885	ENSMUSG00000018217	Pmp22	22kDa|Gas-3|HNPP|Tr|trembler	peripheral myelin protein 22	protein-coding
mm_18432.1	chr2	60824930	60824948	-	1	NA	intron (NM_020296, intron 2 of 13)	MTC|LTR|ERVL-MaLR	56499	NM_001141932	56878	Mm.259667	NM_020296	ENSMUSG00000026970	Rbms1	2600014B10Rik|AI255215|MSSP-1|MSSP-2|MSSP-3|YC1	RNA binding motif, single stranded interacting protein 1	protein-coding
mm_28822.1	chr3	96287202	96287229	-	1	NA	exon (NM_010186, exon 4 of 6)	exon (NM_010186, exon 4 of 6)	6754	NM_010186	14129	Mm.150	NM_010186	ENSMUSG00000015947	Fcgr1	AI323638|AV092959|CD64|FcgammaRI|IGGHAFC	Fc receptor, IgG, high affinity I	protein-coding
mm_36276.1	chr4	63743751	63743768	-	1	NA	intron (NM_177371, intron 1 of 3)	intron (NM_177371, intron 1 of 3)	1354	NM_177371	326623	Mm.208152	NM_177371	ENSMUSG00000050395	Tnfsf15	Tl1|Tl1a|Tnlg1b|Vegi	tumor necrosis factor (ligand) superfamily, member 15	protein-coding
mm_63214.1	chr7	126272527	126272587	+	1	NA	promoter-TSS (NM_145587)	promoter-TSS (NM_145587)	-62	NM_145587	104175	Mm.29660	NM_145587	ENSMUSG00000042978	Sbk1	Sbk	SH3-binding kinase 1	protein-coding
mm_46674.1	chr5	109461283	109461294	-	1	NA	Intergenic	Intergenic	41275	NM_001104628	384221	Mm.469879	NM_001104628	ENSMUSG00000091879	Vmn2r17	EG384221	vomeronasal 2, receptor 17	protein-coding
mm_129950.1	chr15	85036879	85036892	-	1	NA	promoter-TSS (NM_133750)	promoter-TSS (NM_133750)	-177	NM_133750	73225	Mm.247535	NM_133750	ENSMUSG00000022434	Fam118a	-	family with sequence similarity 118, member A	protein-coding
mm_68638.1	chr7	118275382	118275437	-	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	31502	NR_027879	67745	Mm.483404	NM_183267	ENSMUSG00000055159	4930583K01Rik	-	RIKEN cDNA 4930583K01 gene	ncRNA
mm_6921.1	chr1	84840287	84840325	-	1	NA	intron (NM_025386, intron 1 of 3)	intron (NM_025386, intron 1 of 3)	465	NM_025386	66153	Mm.381192	NM_025386	ENSMUSG00000073633	Fbxo36	0610008D19Rik|1110020F21Rik|2410002G19Rik|D1Ertd757e	F-box protein 36	protein-coding
mm_152997.1	chr19	29926384	29926401	-	1	NA	intron (NM_133775, intron 1 of 7)	intron (NM_133775, intron 1 of 7)	1278	NM_133775	77125	Mm.182359	NM_133775	ENSMUSG00000024810	Il33	9230117N10Rik|Il-33|Il1f11|NF-HEV	interleukin 33	protein-coding
mm_25084.1	chr3	100489464	100489496	+	1	NA	promoter-TSS (NM_001142952)	promoter-TSS (NM_001142952)	-288	NM_001142952	74645	Mm.226900	NM_001142952	ENSMUSG00000044468	Fam46c	4930431B09Rik|AI449797	family with sequence similarity 46, member C	protein-coding
mm_72436.1	chr8	83087280	83087286	+	1	NA	3' UTR (NM_177378, exon 7 of 7)	3' UTR (NM_177378, exon 7 of 7)	-78069	NM_001111304	71310	Mm.24031	NM_027758	ENSMUSG00000031709	Tbc1d9	4933431N12Rik|AI847101|AW490653|C76116	TBC1 domain family, member 9	protein-coding
mm_166897.1	chr7	28379533	28379545	-	1	NA	promoter-TSS (NM_011756)	promoter-TSS (NM_011756)	-311	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_26445.1	chr3	142635784	142635814	+	1	NA	exon (NM_010260, exon 10 of 11)	exon (NM_010260, exon 10 of 11)	-11853	NR_105802	102465200		NR_105802	ENSMUSG00000098871	Mir6381	Gm27963|mmu-mir-6381	microRNA 6381	ncRNA
mm_157612.1	chrX	53776356	53776377	-	1	NA	promoter-TSS (NM_001009549)	promoter-TSS (NM_001009549)	28	NM_001009549	333473	Mm.327378	NM_001009549	ENSMUSG00000059334	Zfp36l3	AY661338	zinc finger protein 36, C3H type-like 3	protein-coding
mm_59928.1	chr7	30423382	30423408	+	1	NA	promoter-TSS (NM_172142)	promoter-TSS (NM_172142)	91	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_162580.1	chr1	178337070	178337087	-	1	NA	exon (NM_016805, exon 1 of 14)	exon (NM_016805, exon 1 of 14)	706	NM_016805	51810	Mm.86589	NM_016805	ENSMUSG00000039630	Hnrnpu	AA408410|AI256620|AL024194|AL024437|AW557595|C86794|Hnrpu|SAFA|Sp120|hnRNP U	heterogeneous nuclear ribonucleoprotein U	protein-coding
mm_170200.1	chr17	6941878	6941890	+	1	NA	intron (NM_001083945, intron 1 of 7)	LSU-rRNA_Hsa|rRNA|rRNA	6472	NM_001083945	100037282	Mm.29830	NM_001083945	ENSMUSG00000023806	Rsph3b	Rshl2b	radial spoke 3B homolog (Chlamydomonas)	protein-coding
mm_43795.1	chr5	142813998	142814003	+	1	NA	intron (NM_178242, intron 2 of 15)	intron (NM_178242, intron 2 of 15)	3387	NM_178242	231861	Mm.354649	NM_178242	ENSMUSG00000039477	Tnrc18	BC025631|EG381742|Zfp469	trinucleotide repeat containing 18	protein-coding
mm_81437.1	chr9	109095605	109095609	+	1	NA	5' UTR (NM_172775, exon 1 of 38)	5' UTR (NM_172775, exon 1 of 38)	171	NM_172775	235611	Mm.53862	NM_172775	ENSMUSG00000053646	Plxnb1	2900002G15Rik|AU042020|mKIAA0407	plexin B1	protein-coding
mm_102785.1	chr11	68401058	68401076	-	1	NA	Intergenic	Intergenic	-14241	NM_008744	18208	Mm.39095	NM_008744	ENSMUSG00000020902	Ntn1	AI561871|BC019633|Netrin-1	netrin 1	protein-coding
mm_87473.1	chr10	51491974	51492038	+	1	NA	exon (NM_013532, exon 4 of 9)	exon (NM_013532, exon 4 of 9)	1108	NM_013532	14728	Mm.34408	NM_013532	ENSMUSG00000062593	Lilrb4a	CD85K|Gp49b|HM18|ILT3|LIR-5|Lilrb4|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4A	protein-coding
mm_9464.1	chr1	173227194	173227247	-	1	NA	promoter-TSS (NM_010184)	promoter-TSS (NM_010184)	9	NM_010184	14125	Mm.5266	NM_010184	ENSMUSG00000005339	Fcer1a	FcERI|Fce1a|Fcr-5|fcepsilonri	Fc receptor, IgE, high affinity I, alpha polypeptide	protein-coding
mm_87688.1	chr10	59369082	59369087	+	1	NA	intron (NM_001316370, intron 11 of 13)	intron (NM_001316370, intron 11 of 13)	-34601	NM_023530	69836	Mm.30268	NM_023530	ENSMUSG00000009646	Pla2g12b	2010002E04Rik|Fksg71|Pla2g13|hlb218	phospholipase A2, group XIIB	protein-coding
mm_48913.1	chr6	4003927	4003942	+	1	NA	promoter-TSS (NM_025331)	promoter-TSS (NM_025331)	-53	NM_025331	66066	Mm.25547	NM_025331	ENSMUSG00000032766	Gng11	0610037B21Rik	guanine nucleotide binding protein (G protein), gamma 11	protein-coding
mm_116663.1	chr13	49200596	49200608	-	1	NA	Intergenic	Intergenic	13055	NM_013610	18081	Mm.18503	NM_013610	ENSMUSG00000037966	Ninj1	AU024536	ninjurin 1	protein-coding
mm_171250.1	chr3	7910348	7910357	+	1	NA	Intergenic	L1Md_T|LINE|L1	44535	NR_040587	75476	Mm.491752	NR_040587	ENSMUSG00000100010	1700010I02Rik	-	RIKEN cDNA 1700010I02 gene	ncRNA
mm_53737.1	chr6	145121888	145121906	+	1	NA	5' UTR (NM_008511, exon 1 of 19)	5' UTR (NM_008511, exon 1 of 19)	158	NM_008511	16970	Mm.843	NM_008511	ENSMUSG00000030263	Lrmp	D6Int3|D6Int4|D6Int5|D6Int7|D6Int8|Jaw1	lymphoid-restricted membrane protein	protein-coding
mm_21021.1	chr2	152398048	152398076	-	1	NA	promoter-TSS (NM_011438)	promoter-TSS (NM_011438)	-16	NM_011438	20667	Mm.28424	NM_011438	ENSMUSG00000051817	Sox12	2010205A02Rik	SRY (sex determining region Y)-box 12	protein-coding
mm_58211.1	chr6	144097433	144097436	-	1	NA	intron (NM_001113559, intron 3 of 13)	intron (NM_001113559, intron 3 of 13)	112134	NM_001113559	20678	Mm.1752	NM_011444	ENSMUSG00000041540	Sox5	A730017D01Rik|AI528773	SRY (sex determining region Y)-box 5	protein-coding
mm_31745.1	chr4	63344310	63344317	+	1	NA	promoter-TSS (NM_008768)	promoter-TSS (NM_008768)	-243	NM_008768	18405	Mm.4777	NM_008768	ENSMUSG00000039196	Orm1	Agp-1|Agp-2|Orm-1	orosomucoid 1	protein-coding
mm_138131.1	chr17	34187703	34187749	+	1	NA	promoter-TSS (NM_013585)	promoter-TSS (NM_013585)	170	NM_013683	21354	Mm.482076	NM_013683	ENSMUSG00000037321	Tap1	ABC17|APT1|Abcb2|Ham-1|Ham1|MTP1|PSF1|RING4|TAP|Tap-1|Y3	transporter 1, ATP-binding cassette, sub-family B (MDR/TAP)	protein-coding
mm_95780.1	chr11	54909845	54909856	+	1	NA	TTS (NM_021327)	TTS (NM_021327)	6996	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_164088.1	chr15	8444866	8444877	-	1	NA	promoter-TSS (NM_027707)	promoter-TSS (NM_027707)	-408	NM_201232	71175	Mm.240329	NM_027707	ENSMUSG00000022141	Nipbl	Idn3	Nipped-B homolog (Drosophila)	protein-coding
mm_15971.1	chr2	166080715	166080725	+	1	NA	intron (NM_001252579, intron 14 of 20)	intron (NM_001252579, intron 14 of 20)	74565	NM_001252578	72043	Mm.1011	NM_028072	ENSMUSG00000006800	Sulf2	2010004N24Rik|AU020235|MSulf-2|mKIAA1247	sulfatase 2	protein-coding
mm_55074.1	chr6	49111054	49111059	-	1	NA	intron (NM_023670, intron 6 of 14)	intron (NM_023670, intron 6 of 14)	37261	NM_029353	75593	Mm.439947	NM_029353	ENSMUSG00000029815	Malsu1	2410003K15Rik|Matsu1	mitochondrial assembly of ribosomal large subunit 1	protein-coding
mm_84812.1	chr9	77399309	77399353	-	1	NA	promoter-TSS (NR_040378)	promoter-TSS (NR_040378)	85	NR_040378	70487	Mm.58958	NR_040378	ENSMUSG00000099170	5730403I07Rik	-	RIKEN cDNA 5730403I07 gene	ncRNA
mm_47476.1	chr5	123721064	123721074	-	1	NA	promoter-TSS (NM_027494)	promoter-TSS (NM_027494)	-25	NM_027494	70650	Mm.279427	NM_027494	ENSMUSG00000029427	Zcchc8	5730565F05Rik	zinc finger, CCHC domain containing 8	protein-coding
mm_1323.1	chr1	65100624	65100643	+	1	NA	exon (NM_007774, exon 3 of 3)	exon (NM_007774, exon 3 of 3)	2730	NM_007774	12964	Mm.26904	NM_007774	ENSMUSG00000044429	Cryga	Cryg-4|DGcry-4	crystallin, gamma A	protein-coding
mm_152513.1	chr19	11279433	11279444	-	1	NA	intron (NM_183190, intron 1 of 4)	intron (NM_183190, intron 1 of 4)	4375	NM_183190	269063	Mm.268940	NM_183190	ENSMUSG00000054523	Ms4a5	-	membrane-spanning 4-domains, subfamily A, member 5	protein-coding
mm_95126.1	chr11	34091445	34091464	+	1	NA	3' UTR (NM_010696, exon 21 of 21)	3' UTR (NM_010696, exon 21 of 21)	44253	NM_010696	16822	Mm.265350	NM_010696	ENSMUSG00000002699	Lcp2	AI323664|BB161688|SLP-76|SLP76|m1Khoe|twm	lymphocyte cytosolic protein 2	protein-coding
mm_6310.1	chr1	71590813	71590839	-	1	NA	exon (NM_001276413, exon 41 of 44)	exon (NM_001276413, exon 41 of 44)	33670	NM_026195	108147	Mm.38010	NM_026195	ENSMUSG00000026192	Atic	2610509C24Rik|AA536954|AW212393	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	protein-coding
mm_143569.1	chr17	74295059	74295077	-	1	NA	promoter-TSS (NM_133771)	promoter-TSS (NM_133771)	-205	NM_133771	76890	Mm.311874	NM_133771	ENSMUSG00000058704	Memo1	0610016J10Rik|D930048L02Rik	mediator of cell motility 1	protein-coding
mm_115253.1	chr13	110397479	110397509	+	1	NA	exon (NM_152804, exon 6 of 14)	exon (NM_152804, exon 6 of 14)	2450	NM_152804	20620	Mm.380	NM_152804	ENSMUSG00000021701	Plk2	Snk	polo-like kinase 2	protein-coding
mm_150157.1	chr19	32224545	32224548	+	1	NA	intron (NM_001168525, intron 4 of 9)	intron (NM_001168525, intron 4 of 9)	-13533	NM_001168526	208449	Mm.329810	NM_144792	ENSMUSG00000040451	Sgms1	9530058O11Rik|AI841905|C80702|Mob|Sms1|Sor1|Tmem23	sphingomyelin synthase 1	protein-coding
mm_160470.1	chr8	115706658	115706658	-	1	NA	exon (NM_001025577, exon 1 of 1)	exon (NM_001025577, exon 1 of 1)	236	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_85628.1	chr9	107616239	107616268	-	1	NA	exon (NM_008138, exon 7 of 9)	exon (NM_008138, exon 7 of 9)	-7012	NM_001291539	20347	Mm.4083	NM_009153	ENSMUSG00000057969	Sema3b	SemA|Semaa|sema5|semaV	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B	protein-coding
mm_67008.1	chr7	65347555	65347557	-	1	NA	intron (NM_009386, intron 2 of 27)	intron (NM_009386, intron 2 of 27)	23688	NM_001163574	21872	Mm.4342	NM_009386	ENSMUSG00000030516	Tjp1	ZO1	tight junction protein 1	protein-coding
mm_17596.1	chr2	30796674	30796700	-	1	NA	intron (NR_028486, intron 4 of 6)	intron (NR_028486, intron 4 of 6)	5050	NM_198000	73598	Mm.34166	NM_198000	ENSMUSG00000044320	1700001O22Rik	1700113K14Rik|4930549G18Rik	RIKEN cDNA 1700001O22 gene	protein-coding
mm_80352.1	chr9	75184348	75184402	+	1	NA	exon (NM_010864, exon 26 of 41)	exon (NM_010864, exon 26 of 41)	-47639	NM_001081322	208943	Mm.41339	NM_001081322	ENSMUSG00000033590	Myo5c	9130003O20Rik|BB085560|C330029I24	myosin VC	protein-coding
mm_111003.1	chr12	78861611	78861617	-	1	NA	promoter-TSS (NM_026114)	promoter-TSS (NM_026114)	24	NM_023721	73834	Mm.311549	NM_023721	ENSMUSG00000021114	Atp6v1d	1110004P10Rik|Atp6m|VATD|Vma8	ATPase, H+ transporting, lysosomal V1 subunit D	protein-coding
mm_96722.1	chr11	69666473	69666493	+	1	NA	promoter-TSS (NR_110993)	promoter-TSS (NR_110993)	-313	NR_110993	12514	Mm.15819	NM_009853	ENSMUSG00000018774	Cd68	Lamp4|Scard1|gp110	CD68 antigen	protein-coding
mm_133343.1	chr16	81203374	81203376	+	1	NA	intron (NM_001113208, intron 1 of 17)	intron (NM_001113208, intron 1 of 17)	2678	NM_010954	17968	Mm.433941	NM_010954	ENSMUSG00000022762	Ncam2	Ncam-2|Ocam|RNCAM	neural cell adhesion molecule 2	protein-coding
mm_22967.1	chr3	32708223	32708234	+	1	NA	promoter-TSS (NM_019673)	promoter-TSS (NM_019673)	-318	NM_019673	56456	Mm.41077	NM_019673	ENSMUSG00000027671	Actl6a	2810432C06Rik|AI851094|ARP4|Actl6|Baf53a|C79802	actin-like 6A	protein-coding
mm_43910.1	chr5	144256114	144256134	+	1	NA	intron (NM_018772, intron 2 of 2)	intron (NM_018772, intron 2 of 2)	899	NM_018772	55950	Mm.38011	NM_018772	ENSMUSG00000047843	Bri3	I3	brain protein I3	protein-coding
mm_78151.1	chr9	21017096	21017102	+	1	NA	intron (NM_010493, intron 1 of 6)	intron (NM_010493, intron 1 of 6)	1159	NM_010493	15894	Mm.435508	NM_010493	ENSMUSG00000037405	Icam1	CD54|Icam-1|Ly-47|MALA-2	intercellular adhesion molecule 1	protein-coding
mm_163306.1	chr12	3309535	3309548	-	1	NA	5' UTR (NM_016676, exon 1 of 6)	5' UTR (NM_016676, exon 1 of 6)	428	NM_016676	19325	Mm.378993	NM_016676	ENSMUSG00000020671	Rab10	AW107754	RAB10, member RAS oncogene family	protein-coding
mm_172123.1	chr6	3201241	3201245	+	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	-87276	NR_036696	667335	Mm.380219	NR_036696	ENSMUSG00000106779	Gm8579	EG667335	spermatogenesis associated glutamate (E)-rich protein 4a pseudogene	pseudo
mm_163361.1	chr12	32767573	32767579	-	1	NA	Intergenic	Intergenic	-52759	NM_021524	59027	Mm.202727	NM_021524	ENSMUSG00000020572	Nampt	1110035O14Rik|AI314458|AI480535|NAmPRTase|Pbef|Pbef1|Visfatin	nicotinamide phosphoribosyltransferase	protein-coding
mm_3479.1	chr1	150105531	150105534	+	1	NA	exon (NM_011198, exon 10 of 10)	exon (NM_011198, exon 10 of 10)	5501	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_75493.1	chr8	50555981	50555983	-	1	NA	Intergenic	Intergenic	187870	NR_046067	100039954	Mm.400419	NR_046067	ENSMUSG00000110281	Gm2516	-	predicted gene 2516	ncRNA
mm_151598.1	chr19	3510894	3510897	-	1	NA	intron (NM_029456, intron 7 of 22)	intron (NM_029456, intron 7 of 22)	64854	NM_001164159	52036	Mm.284686	NM_028999	ENSMUSG00000024908	Ppp6r3	4930528G08Rik|9130026N02Rik|D19Bwg1430e|D19Ertd703e|Pp6r3|Ppcs3|Pptcs3|Sapl|Saps3|mKIAA1558	protein phosphatase 6, regulatory subunit 3	protein-coding
mm_64869.1	chr7	14123043	14123053	-	1	NA	promoter-TSS (NM_001101586)	promoter-TSS (NM_001101586)	-55	NM_001101586	629203	Mm.482066	NM_001101586	ENSMUSG00000074375	Sult2a3	EG629203|Gm6955	sulfotransferase family 2A, dehydroepiandrosterone (DHEA)-preferring, member 3	protein-coding
mm_76254.1	chr8	83733497	83733500	-	1	NA	exon (NM_001163029, exon 4 of 18)	exon (NM_001163029, exon 4 of 18)	7813	NM_001163029	26364	Mm.334648	NM_011925	ENSMUSG00000002885	Adgre5	AA409984|Cd97|TM7LN1	adhesion G protein-coupled receptor E5	protein-coding
mm_138230.1	chr17	34377125	34377154	+	1	NA	promoter-TSS (NM_001111094)	promoter-TSS (NM_001111094)	7	NM_001111094	100038862	Mm.440426	NM_201405	ENSMUSG00000062638	Btnl1	Btnl3|Gm316|Gm33	butyrophilin-like 1	protein-coding
mm_19994.1	chr2	118728346	118728367	-	1	NA	promoter-TSS (NM_177568)	promoter-TSS (NM_177568)	82	NM_177568	18796	Mm.215156	NM_177568	ENSMUSG00000040061	Plcb2	AI550384|B230205M18Rik|B230399N12	phospholipase C, beta 2	protein-coding
mm_95663.1	chr11	53771758	53771768	+	1	NA	intron (NM_001159393, intron 2 of 9)	intron (NM_001159393, intron 2 of 9)	1290	NM_001159396	16362	Mm.105218	NM_008390	ENSMUSG00000018899	Irf1	AU020929|Irf-1	interferon regulatory factor 1	protein-coding
mm_135101.1	chr16	35413181	35413192	-	1	NA	intron (NM_028295, intron 11 of 16)	L2|LINE|L2	-49268	NM_133704	317717	Mm.259164	NM_133704	ENSMUSG00000034473	Sec22a	1810005C06Rik|Sec22l2	SEC22 homolog A, vesicle trafficking protein	protein-coding
mm_38807.1	chr4	148166367	148166373	-	1	NA	TTS (NM_176848)	TTS (NM_176848)	5702	NM_176848	230904	Mm.262287	NM_176848	ENSMUSG00000041556	Fbxo2	FBG1|FBX2|Fbs1|Fbs2|NFB42|Prpl4	F-box protein 2	protein-coding
mm_124454.1	chr14	119007446	119007498	-	1	NA	intron (NM_001081252, intron 33 of 38)	ORR1D2|LTR|ERVL-MaLR	69540	NM_008929	100037258	Mm.12616	NM_008929	ENSMUSG00000022136	Dnajc3	AA408985|AU067833|Dnajc3a|Dnajc3b|Prkri|mp58|p58|p58IPK	DnaJ heat shock protein family (Hsp40) member C3	protein-coding
mm_58092.1	chr6	137516996	137517019	-	1	NA	intron (NM_001271589, intron 3 of 13)	intron (NM_001271589, intron 3 of 13)	2888	NM_001271589	13860	Mm.235346	NM_007945	ENSMUSG00000015766	Eps8	AW261790	epidermal growth factor receptor pathway substrate 8	protein-coding
mm_127832.1	chr15	6592689	6592699	-	1	NA	intron (NM_011815, intron 1 of 17)	intron (NM_011815, intron 1 of 17)	12847	NM_011815	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_146235.1	chr18	77185816	77185879	+	1	NA	promoter-TSS (NM_013666)	promoter-TSS (NM_013666)	0	NM_153124	225742	Mm.365178	NM_013666	ENSMUSG00000025425	St8sia5	ST8SiaV|Siat8e	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 5	protein-coding
mm_102928.1	chr11	69600754	69600758	-	1	NA	3' UTR (NM_013415, exon 7 of 7)	3' UTR (NM_013415, exon 7 of 7)	5204	NM_013415	11932	Mm.235204	NM_013415	ENSMUSG00000041329	Atp1b2	Amog|Atpb-2	ATPase, Na+/K+ transporting, beta 2 polypeptide	protein-coding
mm_1615.1	chr1	74391563	74391573	+	1	NA	promoter-TSS (NM_153088)	promoter-TSS (NM_153088)	-41	NM_153088	227292	Mm.165042	NM_153088	ENSMUSG00000026176	Ctdsp1	GIP|NLIIF|Nif3|SCP1	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 1	protein-coding
mm_106491.1	chr11	120237357	120237367	-	1	NA	intron (NM_001347621, intron 2 of 27)	CpG-2934	4415	NM_198423	268515	Mm.309498	NM_198423	ENSMUSG00000039741	Bahcc1	B930044J06|BC060615	BAH domain and coiled-coil containing 1	protein-coding
mm_82939.1	chr9	35305298	35305325	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	24206	NR_040715	71133	Mm.158577	NR_040715	ENSMUSG00000111746	4933422A05Rik	-	RIKEN cDNA 4933422A05 gene	ncRNA
mm_9075.1	chr1	168431268	168431269	-	1	NA	intron (NM_008783, intron 1 of 7)	intron (NM_008783, intron 1 of 7)	901	NM_001291508	18514	Mm.43358	NM_008783	ENSMUSG00000052534	Pbx1	2310056B04Rik|D230003C07Rik|Pbx-1	pre B cell leukemia homeobox 1	protein-coding
mm_53753.1	chr6	145341482	145341494	+	1	NA	Intergenic	CpG	-46137	NR_003625	381827	Mm.179075	NM_001001987		1700073E17Rik	-	ribosomal protein L7 pseudogene	pseudo
mm_116318.1	chr13	37729824	37729830	-	1	NA	Intergenic	B1F2|SINE|Alu	-96211	NM_026830	68750	Mm.491109	NM_026830	ENSMUSG00000039087	Rreb1	1110037N09Rik|AA414966|B930013M22Rik	ras responsive element binding protein 1	protein-coding
mm_92004.1	chr10	62327667	62327679	-	1	NA	intron (NM_010438, intron 4 of 21)	intron (NM_010438, intron 4 of 21)	12748	NM_001146100	15275	Mm.196605	NM_010438	ENSMUSG00000037012	Hk1	BB404130|Hk-1|Hk1-s|dea|mHk1-s	hexokinase 1	protein-coding
mm_78542.1	chr9	35305267	35305290	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	24173	NR_040715	71133	Mm.158577	NR_040715	ENSMUSG00000111746	4933422A05Rik	-	RIKEN cDNA 4933422A05 gene	ncRNA
mm_169615.1	chr15	38037917	38037919	-	1	NA	exon (NM_001081359, exon 9 of 59)	exon (NM_001081359, exon 9 of 59)	40936	NM_001112721	70790	Mm.476840	NM_027553	ENSMUSG00000037487	Ubr5	Edd|Edd1	ubiquitin protein ligase E3 component n-recognin 5	protein-coding
mm_127085.1	chr15	97729413	97729455	+	1	NA	intron (NM_001168693, intron 1 of 9)	intron (NM_001168693, intron 1 of 9)	1971	NM_001168693	19011	Mm.1001	NM_008902	ENSMUSG00000022468	Endou	Pp11r|Tcl-30	endonuclease, polyU-specific	protein-coding
mm_32351.1	chr4	104936293	104936306	+	1	NA	intron (NM_001285953, intron 1 of 19)	intron (NM_001285953, intron 1 of 19)	22843	NM_001285952	242594	Mm.65181	NM_001162980	ENSMUSG00000078612	1700024P16Rik	C1orf168|Gm620	RIKEN cDNA 1700024P16 gene	protein-coding
mm_133903.1	chr16	97548690	97548705	+	1	NA	intron (NM_013606, intron 7 of 13)	L1_Mur3|LINE|L1	12614	NM_013606	17858	Mm.14157	NM_013606	ENSMUSG00000023341	Mx2	AI528743|Mx-2	MX dynamin-like GTPase 2	protein-coding
mm_154533.1	chrM	13815	13833	-	1	NA	NA	Intergenic	NA	NA								
mm_107516.1	chr12	40445994	40446015	+	1	NA	promoter-TSS (NM_178845)	promoter-TSS (NM_178845)	-49	NM_172803	238130	Mm.341423	NM_172803	ENSMUSG00000035954	Dock4	5330406C03|6330411N01Rik|AF263288|C030023J22|mKIAA0716	dedicator of cytokinesis 4	protein-coding
mm_101517.1	chr11	32527552	32527579	-	1	NA	promoter-TSS (NM_027031)	promoter-TSS (NM_027031)	9	NM_027031	69306	Mm.288704	NM_027031	ENSMUSG00000044056	Efcab9	1700007I06Rik|4930403C08Rik	EF-hand calcium binding domain 9	protein-coding
mm_91980.1	chr10	61680260	61680276	-	1	NA	promoter-TSS (NM_009120)	promoter-TSS (NM_009120)	22	NR_126477	75539		NR_126477		1700022H01Rik	-	RIKEN cDNA 1700022H01 gene	ncRNA
mm_96642.1	chr11	69327861	69327868	+	1	NA	intron (NM_010599, intron 1 of 13)	intron (NM_010599, intron 1 of 13)	1606	NM_010599	16499	Mm.232472	NM_010599	ENSMUSG00000018470	Kcnab3	C330022D06Rik|Kcnab4|mKv(beta)4	potassium voltage-gated channel, shaker-related subfamily, beta member 3	protein-coding
mm_78117.1	chr9	20643353	20643368	+	1	NA	promoter-TSS (NM_013911)	promoter-TSS (NM_013911)	42	NM_025401	66177	Mm.390165	NM_025401	ENSMUSG00000084786	Ubl5	1110030M22Rik|beacon	ubiquitin-like 5	protein-coding
mm_129882.1	chr15	83464596	83464614	-	1	NA	promoter-TSS (NM_001159509)	promoter-TSS (NM_001159509)	1	NM_001159509	23970	Mm.23978	NM_011862	ENSMUSG00000016664	Pacsin2	AI197433	protein kinase C and casein kinase substrate in neurons 2	protein-coding
mm_99086.1	chr11	99421014	99421017	+	1	NA	intron (NM_010661, intron 1 of 7)	intron (NM_010661, intron 1 of 7)	1244	NM_010661	268482	Mm.436651	NM_010661	ENSMUSG00000020912	Krt12	AI835216|K12|Krt-12|Krt1-12	keratin 12	protein-coding
mm_13165.1	chr2	92609491	92609498	+	1	NA	intron (NM_023850, intron 1 of 2)	intron (NM_023850, intron 1 of 2)	9787	NM_023850	76969	Mm.38021	NM_023850	ENSMUSG00000027221	Chst1	2610008E20Rik|AW125896|C6ST|GST-1|Gst1|KSGAL6ST	carbohydrate (keratan sulfate Gal-6) sulfotransferase 1	protein-coding
mm_119242.1	chr14	33589224	33589230	+	1	NA	promoter-TSS (NM_008978)	promoter-TSS (NM_008978)	-43	NM_008978	19256	Mm.8019	NM_008978	ENSMUSG00000021940	Ptpn20	typ	protein tyrosine phosphatase, non-receptor type 20	protein-coding
mm_138768.1	chr17	37071723	37071726	+	1	NA	intron (NM_019439, intron 20 of 22)	intron (NM_019439, intron 20 of 22)	14512	NM_146477	258469	Mm.271392	NM_146477	ENSMUSG00000056600	Olfr90	MOR256-21|bM573K1.2	olfactory receptor 90	protein-coding
mm_153583.1	chr19	43502954	43502969	-	1	NA	exon (NM_010324, exon 8 of 9)	exon (NM_010324, exon 8 of 9)	21644	NM_010324	14718	Mm.19039	NM_010324	ENSMUSG00000025190	Got1	AI789014|Got-1|cAspAT|cCAT	glutamic-oxaloacetic transaminase 1, soluble	protein-coding
mm_71294.1	chr8	41218090	41218099	+	1	NA	Intergenic	RLTR20B3A_MM|LTR|ERVK	-2938	NM_145594	234199	Mm.277955	NM_145594	ENSMUSG00000031594	Fgl1	Mfire1	fibrinogen-like protein 1	protein-coding
mm_130937.1	chr15	103215286	103215361	-	1	NA	promoter-TSS (NM_001110216)	promoter-TSS (NM_001110216)	29	NM_007626	12419	Mm.262059	NM_007626	ENSMUSG00000009575	Cbx5	2610029O15Rik|C75991|HP1|Hp1a|Hp1alpha	chromobox 5	protein-coding
mm_73388.1	chr8	105693927	105694013	+	1	NA	intron (NM_001033320, intron 8 of 16)	CpG	3064	NM_001033320	234695	Mm.471640	NM_001033320	ENSMUSG00000050357	Carmil2	CG1399-PB|D130029J02Rik|Gm585|Rltpr	capping protein regulator and myosin 1 linker 2	protein-coding
mm_111411.1	chr12	91384347	91384360	-	1	NA	promoter-TSS (NM_181815)	promoter-TSS (NM_181815)	56	NM_181815	75216	Mm.312204	NM_181815	ENSMUSG00000061533	Cep128	4930534B04Rik|5430424K18Rik|AI449708|AI480494|E230024F20	centrosomal protein 128	protein-coding
mm_54019.1	chr6	8647799	8647806	-	1	NA	intron (NM_001252266, intron 10 of 11)	intron (NM_001252266, intron 10 of 11)	110656	NM_001252266	15893	Mm.275683	NM_010492	ENSMUSG00000062995	Ica1	69kDa|ICA69	islet cell autoantigen 1	protein-coding
mm_102438.1	chr11	59523725	59523727	-	1	NA	Intergenic	Intergenic	-17086	NM_172941	268417	Mm.239793	NM_172941	ENSMUSG00000020472	Zkscan17	Nizp1|Zfp496|Znf496	zinc finger with KRAB and SCAN domains 17	protein-coding
mm_107630.1	chr12	51829345	51829393	+	1	NA	5' UTR (NM_144788, exon 1 of 43)	5' UTR (NM_144788, exon 1 of 43)	167	NM_144788	207304	Mm.249391	NM_144788	ENSMUSG00000035247	Hectd1	A630086P08Rik|AI844876|b2b327Clo|opm	HECT domain containing 1	protein-coding
mm_29253.1	chr3	107219652	107219686	-	1	NA	exon (NM_001111143, exon 2 of 9)	exon (NM_001111143, exon 2 of 9)	2063	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_1535.1	chr1	72849613	72849621	+	1	NA	exon (NM_008342, exon 3 of 4)	exon (NM_008342, exon 3 of 4)	24230	NM_001310659	16008	Mm.141936	NM_008342	ENSMUSG00000039323	Igfbp2	AI255832|IBP-2|Igfbp-2|mIGFBP-2	insulin-like growth factor binding protein 2	protein-coding
mm_127458.1	chr15	101272147	101272156	+	1	NA	intron (NM_010444, intron 3 of 6)	intron (NM_010444, intron 3 of 6)	5305	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_75107.1	chr8	34146775	34146810	-	1	NA	promoter-TSS (NM_026609)	promoter-TSS (NM_026609)	-53	NM_026609	68192	Mm.34212	NM_026609	ENSMUSG00000031513	Leprotl1	1110067H13Rik|1520402O14Rik|AI854296	leptin receptor overlapping transcript-like 1	protein-coding
mm_135298.1	chr16	38622367	38622384	-	1	NA	intron (NM_020260, intron 6 of 11)	B3A|SINE|B2	59561	NM_026407	67846	Mm.310476	NM_026407	ENSMUSG00000002845	Tmem39a	2610033C09Rik	transmembrane protein 39a	protein-coding
mm_166294.1	chr5	104094632	104094666	+	1	NA	exon (NM_010097, exon 3 of 11)	exon (NM_010097, exon 3 of 11)	-17041	NM_001163772	100271704	Mm.366664	NM_001163772	ENSMUSG00000091034	Gm17660	Scpppq1	predicted gene, 17660	protein-coding
mm_8194.1	chr1	138117590	138117594	-	1	NA	intron (NM_011210, intron 3 of 29)	intron (NM_011210, intron 3 of 29)	57534	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_10073.1	chr1	194999445	194999472	-	1	NA	Intergenic	Intergenic	-17941	NR_015566	320977	Mm.99905	NR_015566	ENSMUSG00000096929	A330023F24Rik	C030002C11Rik	RIKEN cDNA A330023F24 gene	ncRNA
mm_161296.1	chr14	27652875	27652875	+	1	NA	exon (NM_001347497, exon 2 of 20)	exon (NM_001347497, exon 2 of 20)	30468	NM_177814	238988	Mm.318004	NM_177814	ENSMUSG00000040640	Erc2	6430531D06|CAST|CAST1/ERC2|D14Ertd171e|ELKS2alpha	ELKS/RAB6-interacting/CAST family member 2	protein-coding
mm_2969.1	chr1	133046192	133046206	+	1	NA	5' UTR (NM_001099276, exon 1 of 33)	5' UTR (NM_001099276, exon 1 of 33)	187	NM_001099276	240752	Mm.387308	NM_001099276	ENSMUSG00000026447	Pik3c2b	C330011J12Rik|Gm199|PI3K-C2beta|PI3KC2beta	phosphoinositide-3-kinase, class 2, beta polypeptide	protein-coding
mm_24083.1	chr3	87953063	87953071	+	1	NA	3' UTR (NM_007759, exon 4 of 4)	3' UTR (NM_007759, exon 4 of 4)	4374	NM_007759	12904	Mm.4757	NM_007759	ENSMUSG00000004885	Crabp2	AI893628|Crabp-2|CrabpII	cellular retinoic acid binding protein II	protein-coding
mm_97172.1	chr11	75531691	75531732	+	1	NA	promoter-TSS (NM_001199283)	promoter-TSS (NM_001199283)	17	NM_173388	215113	Mm.11186	NM_173388	ENSMUSG00000038178	Slc43a2	7630402D21Rik|BC042513|Lat4	solute carrier family 43, member 2	protein-coding
mm_66163.1	chr7	31156362	31156400	-	1	NA	Intergenic	ORR1D2|LTR|ERVL-MaLR	-5331	NM_027898	52857	Mm.27366	NM_027898	ENSMUSG00000001248	Gramd1a	1300003M23Rik|AI415002|AW547240|D7Bwg0611e	GRAM domain containing 1A	protein-coding
mm_27202.1	chr3	35722935	35722945	-	1	NA	Intergenic	Intergenic	-31198	NM_029570	76295	Mm.239416	NM_029570	ENSMUSG00000037400	Atp11b	1110019I14Rik|ATPIF|ATPIR|mKIAA0956	ATPase, class VI, type 11B	protein-coding
mm_132915.1	chr16	49078887	49078894	+	1	NA	intron (NM_001166210, intron 7 of 40)	intron (NM_001166210, intron 7 of 40)	21404	NM_001166210	667772	Mm.301387	NM_001166210	ENSMUSG00000092009	Myh15	EG667772	myosin, heavy chain 15	protein-coding
mm_143906.1	chr17	84958507	84958527	-	1	NA	promoter-TSS (NR_027930)	promoter-TSS (NR_027930)	516	NM_001159496	19043	Mm.249695	NM_011151	ENSMUSG00000061130	Ppm1b	PP2CB	protein phosphatase 1B, magnesium dependent, beta isoform	protein-coding
mm_99250.1	chr11	101087284	101087323	+	1	NA	promoter-TSS (NM_001159385)	promoter-TSS (NM_001159385)	13	NM_001159384	21428	Mm.628	NM_011550	ENSMUSG00000017801	Mlx	Tcfl4|Tf4|bHLHd13	MAX-like protein X	protein-coding
mm_170419.1	chr18	68692271	68692272	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-47129	NR_105774	102465183		NR_105774	ENSMUSG00000099300	Mir6356	Gm27461|mmu-mir-6356	microRNA 6356	ncRNA
mm_137459.1	chr17	26571167	26571173	+	1	NA	intron (NM_026170, intron 1 of 9)	intron (NM_026170, intron 1 of 9)	9658	NM_026170	67458	Mm.30496	NM_026170	ENSMUSG00000001576	Ergic1	1200007D18Rik|maa-136	endoplasmic reticulum-golgi intermediate compartment (ERGIC) 1	protein-coding
mm_28308.1	chr3	89238702	89238736	-	1	NA	intron (NR_121683, intron 7 of 10)	intron (NR_121683, intron 7 of 10)	6294	NR_121683	360213	Mm.331156	NM_183037	ENSMUSG00000042766	Trim46	TRIFIC	tripartite motif-containing 46	protein-coding
mm_128036.1	chr15	25364160	25364249	-	1	NA	3' UTR (NM_027395, exon 2 of 2)	3' UTR (NM_027395, exon 2 of 2)	49560	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	brain abundant, membrane attached signal protein 1	protein-coding
mm_102188.1	chr11	54249002	54249012	-	1	NA	intron (NM_009969, intron 2 of 3)	intron (NM_009969, intron 2 of 3)	892	NM_009969	12981	Mm.4922	NM_009969	ENSMUSG00000018916	Csf2	Csfgm|GMCSF|Gm-CSf|MGI-IGM	colony stimulating factor 2 (granulocyte-macrophage)	protein-coding
mm_12575.1	chr2	73271927	73271939	+	1	NA	promoter-TSS (NM_001005343)	promoter-TSS (NM_001005343)	7	NM_001005343	381373	Mm.330293	NM_001005343	ENSMUSG00000068859	Sp9	-	trans-acting transcription factor 9	protein-coding
mm_62388.1	chr7	100938881	100938916	+	1	NA	exon (NM_183168, exon 3 of 3)	exon (NM_183168, exon 3 of 3)	-6737	NM_001081116	207212	Mm.29954	NM_001081116	ENSMUSG00000032875	Arhgef17	8030463K16|AI428794|AW558066|BC035332|mKIAA0337	Rho guanine nucleotide exchange factor (GEF) 17	protein-coding
mm_86497.1	chr10	6788579	6788617	+	1	NA	promoter-TSS (NM_001304950)	promoter-TSS (NM_001304950)	22	NM_001039652	18390	Mm.438000	NM_011013	ENSMUSG00000000766	Oprm1	M-OR-1|MOP-R|MOR-1|MOR-1O|Oprm|mor|muOR	opioid receptor, mu 1	protein-coding
mm_30277.1	chr3	147204639	147204641	-	1	NA	Intergenic	Intergenic	352273	NM_001302958	70892	Mm.187793	NM_027594	ENSMUSG00000036745	Ttll7	1110049N09Rik|4921517B04Rik|C630030B20|mTTLL7	tubulin tyrosine ligase-like family, member 7	protein-coding
mm_145363.1	chr18	56678643	56678668	+	1	NA	Intergenic	Intergenic	-29158	NM_010721	16906	Mm.4105	NM_010721	ENSMUSG00000024590	Lmnb1	-	lamin B1	protein-coding
mm_89023.1	chr10	82569140	82569144	+	1	NA	Intergenic	Intergenic	54086	NM_001135569	544717	Mm.334867	NM_001135567	ENSMUSG00000063320	1190007I07Rik	-	RIKEN cDNA 1190007I07 gene	protein-coding
mm_81287.1	chr9	108306472	108306484	+	1	NA	promoter-TSS (NM_133986)	promoter-TSS (NM_133986)	318	NM_016802	11848	Mm.757	NM_016802	ENSMUSG00000007815	Rhoa	Arha|Arha1|Arha2	ras homolog family member A	protein-coding
mm_42277.1	chr5	114155427	114155433	+	1	NA	Intergenic	Intergenic	-10088	NM_133904	100705	Mm.81793	NM_133904	ENSMUSG00000042010	Acacb	AI597064|AW743042|Acc2|Accb	acetyl-Coenzyme A carboxylase beta	protein-coding
mm_129724.1	chr15	81960852	81960872	-	1	NA	promoter-TSS (NM_001282040)	promoter-TSS (NM_001282040)	68	NM_001282040	29858	Mm.18939	NM_013872	ENSMUSG00000022474	Pmm1	C77612	phosphomannomutase 1	protein-coding
mm_43143.1	chr5	125441674	125441674	+	1	NA	exon (NM_029752, exon 1 of 3)	exon (NM_029752, exon 1 of 3)	106	NM_029752	76809	Mm.290720	NM_029752	ENSMUSG00000037905	Bri3bp	2410150I18Rik|AI841257|AW742481	Bri3 binding protein	protein-coding
mm_22893.1	chr3	30791901	30791903	+	1	NA	promoter-TSS (NM_027016)	promoter-TSS (NM_027016)	-974	NM_027016	69276	Mm.26017	NM_027016	ENSMUSG00000027706	Sec62	3100002M17Rik|AI844545|AW545092|Dtrp1|HTP1|Tloc1	SEC62 homolog (S. cerevisiae)	protein-coding
mm_69221.1	chr7	127588238	127588250	-	1	NA	promoter-TSS (NM_172281)	promoter-TSS (NM_172281)	351	NM_001033040	233899	Mm.25220	NM_001033040	ENSMUSG00000057176	Ccdc189	Gm166	coiled-coil domain containing 189	protein-coding
mm_114268.1	chr13	58128981	58129056	+	1	NA	promoter-TSS (NM_029872)	promoter-TSS (NM_029872)	-462	NM_029872	77134	Mm.490274	NM_029872	ENSMUSG00000007836	Hnrnpa0	1110055B05Rik|3010025E17Rik|Hnrpa0|hnRNP A0	heterogeneous nuclear ribonucleoprotein A0	protein-coding
mm_24028.1	chr3	87535876	87535892	+	1	NA	exon (NM_012051, exon 5 of 5)	exon (NM_012051, exon 5 of 5)	10306	NM_012051	27049	Mm.219460	NM_012051	ENSMUSG00000003382	Etv3	AI414410|METS|Pe1	ets variant 3	protein-coding
mm_126593.1	chr15	82354395	82354445	+	1	NA	promoter-TSS (NM_025987)	promoter-TSS (NM_025987)	-129	NM_025987	67130	Mm.27570	NM_025987	ENSMUSG00000022450	Ndufa6	14kDa|2700038D15Rik|B230217P19Rik	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 6 (B14)	protein-coding
mm_4721.1	chr1	181144428	181144457	+	1	NA	promoter-TSS (NM_026171)	promoter-TSS (NM_026171)	-238	NM_026171	67459	Mm.263464	NM_026171	ENSMUSG00000026516	Nvl	1200009I24Rik	nuclear VCP-like	protein-coding
mm_155476.1	chrX	73641451	73641462	+	1	NA	exon (NM_029352, exon 3 of 4)	exon (NM_029352, exon 3 of 4)	2015	NM_029352	75590	Mm.16479	NM_029352	ENSMUSG00000031383	Dusp9	Dusp4|Mpk4|Pyst3	dual specificity phosphatase 9	protein-coding
mm_133363.1	chr16	84703617	84703663	+	1	NA	Intergenic	Intergenic	-9383	NR_132106	100653389	Mm.261808	NR_132106	ENSMUSG00000097418	Mir155hg	Bic|Gm26667	Mir155 host gene (non-protein coding)	ncRNA
mm_52456.1	chr6	113690957	113690976	+	1	NA	exon (NM_172161, exon 12 of 13)	exon (NM_172161, exon 12 of 13)	-6084	NM_001347356	381801	Mm.333322	NM_001033463	ENSMUSG00000056952	Tatdn2	AI646012|mKIAA0218	TatD DNase domain containing 2	protein-coding
mm_138242.1	chr17	34564334	34564343	+	1	NA	promoter-TSS (NM_010929)	promoter-TSS (NM_010929)	43	NM_010929	18132	Mm.173813	NM_010929	ENSMUSG00000015468	Notch4	Int-3|Int3|N4	notch 4	protein-coding
mm_99376.1	chr11	101984886	101984901	+	1	NA	promoter-TSS (NM_028207)	promoter-TSS (NM_028207)	-102	NM_028207	72349	Mm.196295	NM_028207	ENSMUSG00000003518	Dusp3	2210015O03Rik|5031436O03Rik|T-DSP11|VHR	dual specificity phosphatase 3 (vaccinia virus phosphatase VH1-related)	protein-coding
mm_90534.1	chr10	128086373	128086389	+	1	NA	exon (NM_016774, exon 7 of 10)	exon (NM_016774, exon 7 of 10)	1095	NR_030442	751518		NR_030442	ENSMUSG00000093245	Mir677	Mirn677|mir-677|mmu-mir-677	microRNA 677	ncRNA
mm_3528.1	chr1	150167413	150167423	+	1	NA	Intergenic	ORR1B2|LTR|ERVL-MaLR	-2470	NR_110420	102639566	Mm.417208	NR_110420	ENSMUSG00000097754	Ptgs2os2	Gm26687|Linc-cox2|Lincrna-cox2	prostaglandin-endoperoxide synthase 2, opposite strand 2	ncRNA
mm_18595.1	chr2	66750635	66750635	-	1	NA	intron (NM_009135, intron 4 of 24)	intron (NM_009135, intron 4 of 24)	34275	NM_009135	20272	Mm.38127	NM_009135	ENSMUSG00000034810	Scn7a	1110034K09Rik|AI642000|NaG|Nav2|Nav2.3|Nax|Scn6a	sodium channel, voltage-gated, type VII, alpha	protein-coding
mm_14075.1	chr2	122798173	122798192	+	1	NA	exon (NM_001162503, exon 5 of 10)	exon (NM_001162503, exon 5 of 10)	16183	NM_021507	59010	Mm.28986	NM_021507	ENSMUSG00000005803	Sqrdl	0610039J17Rik|4930557M22Rik|SQOR	sulfide quinone reductase-like (yeast)	protein-coding
mm_18628.1	chr2	69206147	69206191	-	1	NA	promoter-TSS (NM_001199123)	promoter-TSS (NM_001199123)	44	NM_025565	66442	Mm.272969	NM_025565	ENSMUSG00000005233	Spc25	2600017H08Rik|2610205L13Rik|Spbc25	SPC25, NDC80 kinetochore complex component, homolog (S. cerevisiae)	protein-coding
mm_3833.1	chr1	159931066	159931076	+	1	NA	Intergenic	Intergenic	-113309	NR_028111	67647	Mm.171518	NM_001024470	ENSMUSG00000090394	4930523C07Rik	-	RIKEN cDNA 4930523C07 gene	protein-coding
mm_18763.1	chr2	73454821	73454827	-	1	NA	promoter-TSS (NM_001289722)	promoter-TSS (NM_001289722)	-935	NM_001289722	215280	Mm.223504	NM_153138	ENSMUSG00000075284	Wipf1	AI115543|D2Ertd120e|WIP|Waspip	WAS/WASL interacting protein family, member 1	protein-coding
mm_81835.1	chr9	118478625	118478635	+	1	NA	5' UTR (NM_010136, exon 1 of 6)	5' UTR (NM_010136, exon 1 of 6)	441	NM_010136	13813	Mm.200692	NM_010136	ENSMUSG00000032446	Eomes	C77258|TBR-2|Tbr2	eomesodermin	protein-coding
mm_132674.1	chr16	42907564	42907684	+	1	NA	promoter-TSS (NM_001285805)	promoter-TSS (NM_001285805)	-21	NM_001285805	56490	Mm.136238	NM_019778	ENSMUSG00000022708	Zbtb20	1300017A20Rik|7330412A13Rik|A930017C21Rik|D16Wsu73e|DPZF|HOF|ODA-8S|Oda8|Zfp288	zinc finger and BTB domain containing 20	protein-coding
mm_48119.1	chr5	137139103	137139105	-	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	-22897	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_61144.1	chr7	57590527	57590553	+	1	NA	promoter-TSS (NM_001038701)	promoter-TSS (NM_001038701)	22	NM_001038701	14402	Mm.8004	NM_008071	ENSMUSG00000033676	Gabrb3	A230092K12Rik|AW049585|Cp1|Gabrb-3|beta3	gamma-aminobutyric acid (GABA) A receptor, subunit beta 3	protein-coding
mm_129953.1	chr15	85042272	85042278	-	1	NA	intron (NM_133750, intron 1 of 8)	intron (NM_133750, intron 1 of 8)	5213	NM_133750	73225	Mm.247535	NM_133750	ENSMUSG00000022434	Fam118a	-	family with sequence similarity 118, member A	protein-coding
mm_171386.1	chr4	12124296	12124308	+	1	NA	Intergenic	Intergenic	-15815	NM_028226	72397	Mm.430709	NM_028226	ENSMUSG00000046667	Rbm12b1	3000004N20Rik|Rbm12b|Rbm12ba	RNA binding motif protein 12 B1	protein-coding
mm_160845.1	chr11	50850585	50850585	+	1	NA	promoter-TSS (NM_173372)	promoter-TSS (NM_173372)	-100	NM_173372	108072	Mm.134265	NM_173372	ENSMUSG00000000617	Grm6	BC021919|Gm3|Gprc1f|mGluR6|nerg1|nob2|nob3|nob4	glutamate receptor, metabotropic 6	protein-coding
mm_2001.1	chr1	87127018	87127027	+	1	NA	exon (NM_007432, exon 9 of 11)	exon (NM_007432, exon 9 of 11)	2014	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_66836.1	chr7	48880980	48880990	-	1	NA	promoter-TSS (NM_001013368)	promoter-TSS (NM_001013368)	56	NM_001013368	108961	Mm.240566	NM_001013368	ENSMUSG00000046179	E2f8	4432406C08Rik|AA410048	E2F transcription factor 8	protein-coding
mm_3545.1	chr1	150407344	150407363	+	1	NA	exon (NM_133780, exon 9 of 52)	exon (NM_133780, exon 9 of 52)	-14298	NM_145511	226499	Mm.222093	NM_145511	ENSMUSG00000006010	BC003331	1810053E15Rik|Odr4|odr-4	cDNA sequence BC003331	protein-coding
mm_38716.1	chr4	145229060	145229088	-	1	NA	exon (NM_011610, exon 2 of 10)	exon (NM_011610, exon 2 of 10)	17796	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_42708.1	chr5	120431892	120431905	+	1	NA	promoter-TSS (NM_008499)	promoter-TSS (NM_008499)	12	NM_008499	16873	Mm.5151	NM_008499	ENSMUSG00000029595	Lhx5	Lim2	LIM homeobox protein 5	protein-coding
mm_161339.1	chr14	51552938	51552938	+	1	NA	5' UTR (NM_001013816, exon 1 of 5)	5' UTR (NM_001013816, exon 1 of 5)	148	NM_001013816	434459	Mm.359230	NM_001013816	ENSMUSG00000079244	Gm5622	EG434459	predicted gene 5622	protein-coding
mm_98116.1	chr11	87121581	87121583	+	1	NA	intron (NM_025377, intron 3 of 3)	intron (NM_025377, intron 3 of 3)	-5493	NM_197987	68729	Mm.17436	NM_197987	ENSMUSG00000018548	Trim37	1110032A10Rik|2810004E07Rik|AI848587|AU043018|MUL|TEF3|mKIAA0898	tripartite motif-containing 37	protein-coding
mm_97179.1	chr11	75532269	75532280	+	1	NA	5' UTR (NM_001199283, exon 1 of 14)	5' UTR (NM_001199283, exon 1 of 14)	162	NM_001199283	215113	Mm.11186	NM_173388	ENSMUSG00000038178	Slc43a2	7630402D21Rik|BC042513|Lat4	solute carrier family 43, member 2	protein-coding
mm_74951.1	chr8	25976748	25976758	-	1	NA	promoter-TSS (NM_029884)	promoter-TSS (NM_029884)	-9	NM_029884	52120	Mm.28326	NM_029884	ENSMUSG00000037260	Hgsnat	9430010M12Rik|AW208455|D8Ertd354e|Tmem76	heparan-alpha-glucosaminide N-acetyltransferase	protein-coding
mm_34598.1	chr4	150236790	150236796	+	1	NA	promoter-TSS (NM_001025388).2	promoter-TSS (NM_001025388).2	-404	NM_023119	13806	Mm.70666	NM_023119	ENSMUSG00000063524	Eno1	0610008I15|AL022784|Eno-1|MBP-1	enolase 1, alpha non-neuron	protein-coding
mm_92304.1	chr10	75131685	75131705	-	1	NA	intron (NM_001081412, intron 4 of 22)	intron (NM_001081412, intron 4 of 22)	70799	NM_001081412	110279	Mm.333722	NM_001081412	ENSMUSG00000009681	Bcr	5133400C09Rik|AI561783|AI853148|mKIAA3017	breakpoint cluster region	protein-coding
mm_84199.1	chr9	60649744	60649745	-	1	NA	intron (NM_001311095, intron 7 of 15)	intron (NM_001311095, intron 7 of 15)	37790	NM_001311095	102747	Mm.269413	NM_145616	ENSMUSG00000047766	Lrrc49	AI430817|AW050057|D430025H09Rik|PGs4|p79	leucine rich repeat containing 49	protein-coding
mm_126640.1	chr15	83772053	83772057	+	1	NA	Intergenic	Intergenic	-7968	NM_172610	223726	Mm.36395	NM_172610	ENSMUSG00000041708	Mpped1	6230403M19|AW456965|D15Bwg0669e	metallophosphoesterase domain containing 1	protein-coding
mm_8120.1	chr1	136131176	136131185	-	1	NA	promoter-TSS (NM_001039472)	promoter-TSS (NM_001039472)	3	NR_046168	329253	Mm.487858	NR_046167	ENSMUSG00000086264	Gm15850	6530439I21|OTTMUSG00000026868	predicted gene 15850	ncRNA
mm_166071.1	chr4	135756777	135756780	-	1	NA	Intergenic	YREP_Mm|Unknown|Unknown	-2937	NM_001085509	242702	Mm.318639	NM_001085509	ENSMUSG00000037139	Myom3	8430427K15Rik|Gm434	myomesin family, member 3	protein-coding
mm_79438.1	chr9	56089967	56089987	+	1	NA	promoter-TSS (NM_011193)	promoter-TSS (NM_011193)	1	NM_011193	19200	Mm.2534	NM_011193	ENSMUSG00000032322	Pstpip1	CD2BP1|def-2	proline-serine-threonine phosphatase-interacting protein 1	protein-coding
mm_119617.1	chr14	51114456	51114466	+	1	NA	Intergenic	Intergenic	-2092	NM_203508	219026	Mm.297297	NM_203508	ENSMUSG00000072575	Eddm3b	Fam12|Gm75	epididymal protein 3B	protein-coding
mm_129650.1	chr15	80711995	80712005	-	1	NA	intron (NM_144812, intron 1 of 24)	CpG	687	NM_144812	213988	Mm.131328	NM_144812	ENSMUSG00000047888	Tnrc6b	2700090M07Rik|A730065C02Rik|AI848765|D230019K20Rik	trinucleotide repeat containing 6b	protein-coding
mm_163750.1	chr13	119756113	119756148	+	1	NA	promoter-TSS (NM_175538)	promoter-TSS (NM_175538)	-248	NM_175538	245269	Mm.403943	NM_175538	ENSMUSG00000095930	Nim1k	E130304F04Rik|Nim1	NIM1 serine/threonine protein kinase	protein-coding
mm_8426.1	chr1	152524829	152524844	-	1	NA	exon (NM_016846, exon 16 of 18)	exon (NM_016846, exon 16 of 18)	100381	NM_016846	19731	Mm.245270	NM_016846	ENSMUSG00000026482	Rgl1	Rgl|mKIAA0959	ral guanine nucleotide dissociation stimulator,-like 1	protein-coding
mm_4162.1	chr1	171029389	171029403	+	1	NA	3' UTR (NM_144559, exon 5 of 5)	3' UTR (NM_144559, exon 5 of 5)	10470	NM_144559	246256	Mm.251254	NM_144559	ENSMUSG00000059089	Fcgr4	4833442P21Rik|CD16-2|FcgRIV|FcgammaRIV|Fcgr3a|Fcrl3	Fc receptor, IgG, low affinity IV	protein-coding
mm_27527.1	chr3	57387712	57387734	-	1	NA	Intergenic	Intergenic	-37687	NM_145539	229302	Mm.26618	NM_145539	ENSMUSG00000027801	Tm4sf4	Iltmp	transmembrane 4 superfamily member 4	protein-coding
mm_86110.1	chr9	115310565	115310570	-	1	NA	promoter-TSS (NM_024222)	promoter-TSS (NM_024222)	-146	NM_024222	68292	Mm.296158	NM_024222	ENSMUSG00000032437	Stt3b	1300006C19Rik|Simp	STT3, subunit of the oligosaccharyltransferase complex, homolog B (S. cerevisiae)	protein-coding
mm_101493.1	chr11	31779629	31779632	-	1	NA	Intergenic	Intergenic	44917	NR_102310	414116	Mm.150222	NR_102310	ENSMUSG00000085772	D630024D03Rik	-	RIKEN cDNA D630024D03 gene	ncRNA
mm_91248.1	chr10	22731337	22731385	-	1	NA	promoter-TSS (NM_011603)	promoter-TSS (NM_011603)	86	NM_011603	237336	Mm.86670	NM_011603	ENSMUSG00000071359	Tbpl1	4732475G08|AW011832|AW491032|D18347|STD|TLF|TRF2|TRP|Tlp	TATA box binding protein-like 1	protein-coding
mm_103579.1	chr11	78165522	78165551	-	1	NA	promoter-TSS (NM_009423)	promoter-TSS (NM_009423)	14	NM_009423	22032	Mm.390418	NM_009423	ENSMUSG00000017386	Traf4	A530032M13Rik|CART1|msp2	TNF receptor associated factor 4	protein-coding
mm_35439.1	chr4	39259791	39259796	-	1	NA	Intergenic	U1|snRNA|snRNA	-190500	NM_001081095	75471	Mm.23522	NM_001081095	ENSMUSG00000028287	1700009N14Rik	AI429145	RIKEN cDNA 1700009N14 gene	protein-coding
mm_9038.1	chr1	167243129	167243163	-	1	NA	intron (NM_030724, intron 1 of 6)	intron (NM_030724, intron 1 of 6)	41981	NM_030724	80914	Mm.280895	NM_030724	ENSMUSG00000026558	Uck2	AA407809|AI481316|AU018180|AU020720|TSA903|UK|UMK|Umpk	uridine-cytidine kinase 2	protein-coding
mm_55172.1	chr6	51920324	51920332	-	1	NA	intron (NM_018773, intron 6 of 12)	MIR|SINE|MIR	92221	NM_018773	54353	Mm.221479	NM_018773	ENSMUSG00000059182	Skap2	2610021A10Rik|AA960083|BB137539|RA70|SKAP-HOM|Saps|Scap2|mSKAP55R	src family associated phosphoprotein 2	protein-coding
mm_76941.1	chr8	105942363	105942403	-	1	NA	exon (NM_008490, exon 2 of 6)	exon (NM_008490, exon 2 of 6)	1019	NM_008490	16816	Mm.1593	NM_008490	ENSMUSG00000035237	Lcat	AI046659|D8Wsu61e	lecithin cholesterol acyltransferase	protein-coding
mm_50779.1	chr6	53681113	53681143	+	1	NA	exon (NM_172728, exon 4 of 7)	exon (NM_172728, exon 4 of 7)	107754	NM_172728	231991	Mm.227444	NM_172728	ENSMUSG00000053007	Creb5	9430076C15Rik|CRE-BPa|Crebpa|D430026C09Rik	cAMP responsive element binding protein 5	protein-coding
mm_113121.1	chr13	24518198	24518229	+	1	NA	Intergenic	Intergenic	-63976	NM_001286100	193385	Mm.217319	NM_029679	ENSMUSG00000036006	Fam65b	-	family with sequence similarity 65, member B	protein-coding
mm_12871.1	chr2	83879109	83879114	+	1	NA	exon (NM_175514, exon 8 of 8)	exon (NM_175514, exon 8 of 8)	62115	NM_027964	71861	Mm.116957	NM_027964	ENSMUSG00000034552	Zswim2	1700025P14Rik|4933437F18Rik|MEX	zinc finger SWIM-type containing 2	protein-coding
mm_84531.1	chr9	67049647	67049662	-	1	NA	promoter-TSS (NM_001164251)	promoter-TSS (NM_001164251)	-441	NM_001164251	22003	Mm.121878	NM_024427	ENSMUSG00000032366	Tpm1	AA986836|AI854628|TM2|Tm3|Tmpa|Tpm-1|alpha-TM	tropomyosin 1, alpha	protein-coding
mm_134110.1	chr16	9995629	9995669	-	1	NA	Intergenic	CpG	-3116	NM_008170	14811	Mm.2953	NM_008170	ENSMUSG00000059003	Grin2a	GluN2A|NMDAR2A|NR2A	glutamate receptor, ionotropic, NMDA2A (epsilon 1)	protein-coding
mm_74675.1	chr8	13974716	13974737	-	1	NA	promoter-TSS (NM_173744)	promoter-TSS (NM_173744)	51	NM_173744	72148	Mm.5727	NM_173744	ENSMUSG00000050052	Tdrp	2610019F03Rik	testis development related protein	protein-coding
mm_115747.1	chr13	17993307	17993362	-	1	NA	promoter-TSS (NM_025904)	promoter-TSS (NM_025904)	17	NM_025904	67008	Mm.252918	NM_025904	ENSMUSG00000075054	Yae1d1	1600012F09Rik	Yae1 domain containing 1	protein-coding
mm_126548.1	chr15	82036450	82036472	+	1	NA	intron (NM_010247, intron 11 of 12)	(T)n|Simple_repeat|Simple_repeat	11137	NM_011482	20826	Mm.299312	NM_011482	ENSMUSG00000063480	Nhp2l1	FA-1|Fta1|Snu13|Ssfa1	NHP2 non-histone chromosome protein 2-like 1 (S. cerevisiae)	protein-coding
mm_22558.1	chr3	9853249	9853282	+	1	NA	Intergenic	Intergenic	-19586	NM_001195031	94212	Mm.23897	NM_053182	ENSMUSG00000027508	Pag1	Cbp|F730007C19Rik|Pag	phosphoprotein associated with glycosphingolipid microdomains 1	protein-coding
mm_106590.1	chr11	120730305	120730312	-	1	NA	exon (NM_007621, exon 6 of 8)	exon (NM_007621, exon 6 of 8)	1713	NM_007621	12409	Mm.21454	NM_007621	ENSMUSG00000025150	Cbr2	MLCR	carbonyl reductase 2	protein-coding
mm_159848.1	chr5	136986990	136986990	+	1	NA	promoter-TSS (NM_011962)	promoter-TSS (NM_011962)	-29	NM_011962	26433	Mm.251003	NM_011962	ENSMUSG00000004846	Plod3	AI414586|LH3	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3	protein-coding
mm_57591.1	chr6	127769143	127769164	-	1	NA	promoter-TSS (NM_201371)	promoter-TSS (NM_201371)	6	NM_201371	381813	Mm.39750	NM_201371	ENSMUSG00000030350	Prmt8	Hrmt1l3|Hrmt1l4	protein arginine N-methyltransferase 8	protein-coding
mm_55648.1	chr6	72362384	72362417	-	1	NA	promoter-TSS (NM_001331169)	promoter-TSS (NM_001331169)	32	NR_138581	66510	Mm.170023	NM_025607	ENSMUSG00000055850	Rnf181	1700047F16Rik|2500002L14Rik|6230415N01Rik|C77350	ring finger protein 181	protein-coding
mm_76088.1	chr8	79399500	79399510	-	1	NA	promoter-TSS (NM_008539)	promoter-TSS (NM_008539)	-37	NM_008539	17125	Mm.223717	NM_008539	ENSMUSG00000031681	Smad1	AI528653|Madh1|Madr1|Mlp1|MusMLP	SMAD family member 1	protein-coding
mm_138736.1	chr17	36970803	36970835	+	1	NA	Intergenic	Intergenic	10418	NM_029747	76797	Mm.159787	NM_029747	ENSMUSG00000064308	2410137M14Rik	-	RIKEN cDNA 2410137M14 gene	protein-coding
mm_140716.1	chr17	15368581	15368591	-	1	NA	exon (NM_007865, exon 9 of 11)	exon (NM_007865, exon 9 of 11)	7237	NM_007865	13388	Mm.4875	NM_007865	ENSMUSG00000014773	Dll1	Delta1	delta-like 1 (Drosophila)	protein-coding
mm_147962.1	chr18	67134072	67134082	-	1	NA	intron (NM_010307, intron 1 of 11)	CpG	517	NM_010307	14680	Mm.440746	NM_010307	ENSMUSG00000024524	Gnal	2610011C15Rik|9630020G10Rik|Galphaolf|Gna10|Golf	guanine nucleotide binding protein, alpha stimulating, olfactory type	protein-coding
mm_16885.1	chr2	13011567	13011577	-	1	NA	promoter-TSS (NM_153155)	promoter-TSS (NM_153155)	-708	NM_153155	227580	Mm.229322	NM_153155	ENSMUSG00000049630	C1ql3	1110065A22Rik|AI661623|C1ql|C1qtnf13|CTRP13|K100	C1q-like 3	protein-coding
mm_83752.1	chr9	51274897	51274911	-	1	NA	intron (NM_001195681, intron 2 of 4)	intron (NM_001195681, intron 2 of 4)	3650	NM_001195681	100502940	Mm.235705	NM_001195681	ENSMUSG00000079559	Gm684	-	predicted gene 684	protein-coding
mm_104784.1	chr11	98587194	98587253	-	1	NA	promoter-TSS (NM_025661)	promoter-TSS (NM_025661)	22	NM_025661	66612	Mm.180546	NM_025661	ENSMUSG00000038150	Ormdl3	2810011N17Rik|AI315223	ORM1-like 3 (S. cerevisiae)	protein-coding
mm_72784.1	chr8	86745680	86745684	+	1	NA	promoter-TSS (NR_027829)	promoter-TSS (NR_027829)	-17	NR_027829	666945	Mm.391806	NR_027829		Gm10638	ENSMUSG00000074178	predicted gene 10638	ncRNA
mm_127964.1	chr15	11991017	11991050	-	1	NA	exon (NM_011294, exon 3 of 5)	exon (NM_011294, exon 3 of 5)	4974	NM_011294	20024	Mm.41746	NM_011294	ENSMUSG00000022205	Sub1	AI842364|P15|P9|Pc4|Rpo2tc1	SUB1 homolog (S. cerevisiae)	protein-coding
mm_5680.1	chr1	43163822	43163832	-	1	NA	5' UTR (NM_010212, exon 1 of 6)	5' UTR (NM_010212, exon 1 of 6)	134	NM_010212	14200	Mm.6799	NM_010212	ENSMUSG00000008136	Fhl2	FHL-2|SLIM-3|SLIM3	four and a half LIM domains 2	protein-coding
mm_60105.1	chr7	35397047	35397125	+	1	NA	promoter-TSS (NM_178643)	promoter-TSS (NM_178643)	-7	NM_028120	72140	Mm.133263	NM_028120	ENSMUSG00000023072	Cep89	2610507L03Rik|Ccdc123	centrosomal protein 89	protein-coding
mm_68578.1	chr7	115846163	115846173	-	1	NA	promoter-TSS (NM_001277326)	promoter-TSS (NM_001277326)	-28	NM_001277326	20679	Mm.323365	NM_011445	ENSMUSG00000051910	Sox6	AI987981|SOX-LZ	SRY (sex determining region Y)-box 6	protein-coding
mm_75470.1	chr8	47990536	47990577	-	1	NA	promoter-TSS (NM_133791)	promoter-TSS (NM_133791)	-5	NM_133791	52357	Mm.235074	NM_133791	ENSMUSG00000031563	Wwc2	5330431C14Rik|AU022508|C85457|D8Ertd594e	WW, C2 and coiled-coil domain containing 2	protein-coding
mm_169510.1	chr14	8408836	8408853	+	1	NA	Intergenic	Intergenic	-30081	NM_146050	18300	Mm.25351	NM_146050	ENSMUSG00000021749	Oit1	2310076N21Rik|AV067083|EF-7|Fam3d	oncoprotein induced transcript 1	protein-coding
mm_146466.1	chr18	87004356	87004359	+	1	NA	Intergenic	Intergenic	292292	NM_172633	12405	Mm.70775	NM_172633	ENSMUSG00000024647	Cbln2	6330593N19Rik|A730004O05	cerebellin 2 precursor protein	protein-coding
mm_145988.1	chr18	68300346	68300348	+	1	NA	promoter-TSS (NM_026440)	promoter-TSS (NM_026440)	-8	NM_026440	67897	Mm.27544	NM_026440	ENSMUSG00000009535	Rnmt	2610002P10Rik|AI848273|Rg7mt1|mKIAA0398	RNA (guanine-7-) methyltransferase	protein-coding
mm_35239.1	chr4	19877251	19877287	-	1	NA	3' UTR (NM_175406, exon 8 of 8)	3' UTR (NM_175406, exon 8 of 8)	45297	NM_175406	242341	Mm.19298	NM_175406	ENSMUSG00000028238	Atp6v0d2	1620401A02Rik|AI324824|V-ATPase	ATPase, H+ transporting, lysosomal V0 subunit D2	protein-coding
mm_62060.1	chr7	92447636	92447646	+	1	NA	3' UTR (NM_001243047, exon 11 of 11)	3' UTR (NM_001243047, exon 11 of 11)	-113508	NM_025515	66365	Mm.21173	NM_025515	ENSMUSG00000030613	Ccdc90b	2310015N07Rik|C86558	coiled-coil domain containing 90B	protein-coding
mm_92582.1	chr10	80024296	80024318	-	1	NA	intron (NM_001347074, intron 10 of 22)	intron (NM_001347074, intron 10 of 22)	4632	NM_027521	70719	Mm.243954	NM_027521	ENSMUSG00000035697	Hmha1	6330406L22Rik|AW539505|Ha-1	histocompatibility (minor) HA-1	protein-coding
mm_17675.1	chr2	32260045	32260053	-	1	NA	promoter-TSS (NM_011675)	promoter-TSS (NM_011675)	56	NM_011675	22245	Mm.425076	NM_011675	ENSMUSG00000002550	Uck1	URK1|Umpk	uridine-cytidine kinase 1	protein-coding
mm_60838.1	chr7	45721237	45721244	+	1	NA	promoter-TSS (NM_001033170)	promoter-TSS (NM_001033170)	20	NM_001033170	73813	Mm.322591	NM_001033170	ENSMUSG00000054161	Fam83e	4930403C10Rik	family with sequence similarity 83, member E	protein-coding
mm_136248.1	chr16	90937237	90937255	-	1	NA	3' UTR (NM_001045515, exon 33 of 33)	3' UTR (NM_001045515, exon 33 of 33)	-2397	NM_026502	68001	Mm.45374	NM_026502	ENSMUSG00000022972	1110004E09Rik	-	RIKEN cDNA 1110004E09 gene	protein-coding
mm_2042.1	chr1	87264604	87264633	+	1	NA	exon (NM_028889, exon 1 of 4)	exon (NM_028889, exon 1 of 4)	254	NM_028889	98363	Mm.247951	NM_028889	ENSMUSG00000026255	Efhd1	4931430I01Rik|AI452351|PP3051|mitocalcin	EF hand domain containing 1	protein-coding
mm_137139.1	chr17	23604710	23604725	+	1	NA	intron (NM_001289482, intron 1 of 3)	ID_B1|SINE|B4	3891	NM_001289482	332221	Mm.270315	NM_001033425	ENSMUSG00000023902	Zscan10	BC068284|Zfp206|Zkscan10|Znf206	zinc finger and SCAN domain containing 10	protein-coding
mm_91545.1	chr10	39729840	39729844	-	1	NA	intron (NR_038037, intron 1 of 2)	intron (NR_038037, intron 1 of 2)	2165	NR_038037	327744	Mm.295265	NM_183198	ENSMUSG00000087177	E130307A14Rik	-	RIKEN cDNA E130307A14 gene	ncRNA
mm_141144.1	chr17	26504328	26504340	-	1	NA	Intergenic	Intergenic	4138	NM_013642	19252	Mm.239041	NM_013642	ENSMUSG00000024190	Dusp1	3CH134|MKP1|Ptpn16|U19515|erp|mkp-1	dual specificity phosphatase 1	protein-coding
mm_165965.1	chr4	95193293	95193326	+	1	NA	Intergenic	Intergenic	-141087	NM_010591	16476	Mm.275071	NM_010591	ENSMUSG00000052684	Jun	AP-1|Junc|c-jun	jun proto-oncogene	protein-coding
mm_58900.1	chr7	17150366	17150374	+	1	NA	promoter-TSS (NM_054059)	promoter-TSS (NM_054059)	-30	NM_054059	384557	Mm.486145	NM_054059	ENSMUSG00000053228	Ceacam3	EG384557|Psg24|cea12	carcinoembryonic antigen-related cell adhesion molecule 3	protein-coding
mm_15285.1	chr2	155276620	155276620	+	1	NA	non-coding (NR_046364, exon 1 of 3)	non-coding (NR_046364, exon 1 of 3)	256	NR_046364	66734	Mm.196239	NM_025735	ENSMUSG00000027602	Map1lc3a	1010001H21Rik|4922501H04Rik|LC3|LC3a	microtubule-associated protein 1 light chain 3 alpha	protein-coding
mm_81493.1	chr9	110027701	110027719	+	1	NA	exon (NM_008633, exon 5 of 19)	exon (NM_008633, exon 5 of 19)	-24311	NM_001311163	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_87994.1	chr10	66698239	66698247	+	1	NA	Intergenic	Intergenic	222141	NR_138560	68488	Mm.338835	NR_138560		1110002J07Rik	-	RIKEN cDNA 1110002J07 gene	ncRNA
mm_123608.1	chr14	68087408	68087430	-	1	NA	exon (NM_010910, exon 4 of 4)	exon (NM_010910, exon 4 of 4)	3535	NM_010910	18039	Mm.1956	NM_010910	ENSMUSG00000022055	Nefl	AI847934|CMT2E|NF-L|NF68|Nfl	neurofilament, light polypeptide	protein-coding
mm_2606.1	chr1	120121281	120121297	+	1	NA	promoter-TSS (NM_007830)	promoter-TSS (NM_007830)	102	NM_001172074	73103	Mm.271602	NM_028439	ENSMUSG00000026388	3110009E18Rik	-	RIKEN cDNA 3110009E18 gene	protein-coding
mm_96124.1	chr11	60776908	60776948	+	1	NA	promoter-TSS (NM_001085440)	promoter-TSS (NM_001085440)	437	NM_009410	21975	Mm.10708	NM_009410	ENSMUSG00000002814	Top3a	-	topoisomerase (DNA) III alpha	protein-coding
mm_103435.1	chr11	75906674	75906684	-	1	NA	intron (NM_029548, intron 2 of 7)	intron (NM_029548, intron 2 of 7)	4380	NM_029548	380714	Mm.425697	NM_029548	ENSMUSG00000020847	Rph3al	Gm1753|Noc2	rabphilin 3A-like (without C2 domains)	protein-coding
mm_131745.1	chr16	22119810	22119822	+	1	NA	intron (NM_183029, intron 2 of 15)	intron (NM_183029, intron 2 of 15)	43483	NM_183029	319765	Mm.489442	NM_183029	ENSMUSG00000033581	Igf2bp2	C330012H03Rik|IMP-2|Imp2|Neilsen	insulin-like growth factor 2 mRNA binding protein 2	protein-coding
mm_31677.1	chr4	62286425	62286438	+	1	NA	promoter-TSS (NM_025286)	promoter-TSS (NM_025286)	2	NM_025286	20530	Mm.292539	NM_025286	ENSMUSG00000066152	Slc31a2	AI604396|CTR2	solute carrier family 31, member 2	protein-coding
mm_87450.1	chr10	51482845	51482884	+	1	NA	intron (NM_001291892, intron 4 of 8)	intron (NM_001291892, intron 4 of 8)	2252	NM_001291892	14727	Mm.439661	NM_008147	ENSMUSG00000062593	Lilr4b	Gp49a|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4B	protein-coding
mm_86241.1	chr9	121044884	121044900	-	1	NA	intron (NM_177589, intron 34 of 36)	intron (NM_177589, intron 34 of 36)	89806	NR_106058	102465661		NR_106058	ENSMUSG00000106193	Mir7090	mmu-mir-7090	microRNA 7090	ncRNA
mm_43601.1	chr5	137857190	137857200	+	1	NA	exon (NM_133209, exon 2 of 5)	exon (NM_133209, exon 2 of 5)	854	NM_133209	170741	Mm.347593	NM_133209	ENSMUSG00000066684	Pilrb1	FDFACT|Fdact|Pilrb	paired immunoglobin-like type 2 receptor beta 1	protein-coding
mm_101448.1	chr11	30197994	30198009	-	1	NA	5' UTR (NM_009260, exon 1 of 31)	5' UTR (NM_009260, exon 1 of 31)	256	NM_009260	20742	Mm.123110	NM_009260	ENSMUSG00000020315	Sptbn1	9930031C03Rik|AL033301|SPTB2|Spnb-2|Spnb2|elf1|elf3|mKIAA4049	spectrin beta, non-erythrocytic 1	protein-coding
mm_168345.1	chr11	12129190	12129192	+	1	NA	Intergenic	Intergenic	-91771	NM_010345	14783	Mm.273117	NM_010345	ENSMUSG00000020176	Grb10	5730571D09Rik|AI325020|Meg1|mKIAA0207	growth factor receptor bound protein 10	protein-coding
mm_29878.1	chr3	131019640	131019652	-	1	NA	Intergenic	Intergenic	-90651	NM_010703	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_1217.1	chr1	62727166	62727177	+	1	NA	intron (NM_001077405, intron 2 of 15)	(CA)n|Simple_repeat|Simple_repeat	23854	NM_001077405	18187	Mm.266341	NM_010939	ENSMUSG00000025969	Nrp2	1110048P06Rik|Np-2|Np2|Npn-2|Npn2	neuropilin 2	protein-coding
mm_34988.1	chr4	156027469	156027478	+	1	NA	intron (NM_021985, intron 2 of 3)	intron (NM_021985, intron 2 of 3)	1131	NM_021985	21936	Mm.3180	NM_009400	ENSMUSG00000041954	Tnfrsf18	AITR|Gitr	tumor necrosis factor receptor superfamily, member 18	protein-coding
mm_40155.1	chr5	35575117	35575150	+	1	NA	promoter-TSS (NM_030208)	promoter-TSS (NM_030208)	-63	NM_030208	78890	Mm.98522	NM_030208	ENSMUSG00000029097	Trmt44	2310079F23Rik|Mettl19	tRNA methyltransferase 44	protein-coding
mm_54499.1	chr6	35510354	35510364	-	1	NA	3' UTR (NM_008098, exon 4 of 4)	3' UTR (NM_008098, exon 4 of 4)	29529	NM_008098	14489	Mm.182746	NM_008098	ENSMUSG00000029840	Mtpn	5033418D15Rik|Gcdp|V1	myotrophin	protein-coding
mm_100840.1	chr11	5707730	5707732	-	1	NA	promoter-TSS (NM_026080)	promoter-TSS (NM_026080)	-32	NM_026080	64660	Mm.7328	NM_026080	ENSMUSG00000020477	Mrps24	3110030K20Rik|AI414579|Rpms24	mitochondrial ribosomal protein S24	protein-coding
mm_151264.1	chr19	54045246	54045248	+	1	NA	promoter-TSS (NM_007417)	promoter-TSS (NM_007417)	65	NM_007417	11551	Mm.235195	NM_007417	ENSMUSG00000033717	Adra2a	AW122659|Adra-2|Adra-2a|alpha(2A)AR|alpha2-C10|alpha2A|alpha2A-AR	adrenergic receptor, alpha 2a	protein-coding
mm_33864.1	chr4	135929798	135929810	+	1	NA	intron (NM_024243, intron 3 of 7)	ID4|SINE|ID	9078	NM_024243	71665	Mm.439940	NM_024243	ENSMUSG00000028673	Fuca1	0610006A03Rik|9530055J05Rik|Afuc|Fuca	fucosidase, alpha-L- 1, tissue	protein-coding
mm_126803.1	chr15	87624297	87624309	+	1	NA	promoter-TSS (NM_134096)	promoter-TSS (NM_134096)	-927	NM_134096	106014	Mm.244319	NM_134096	ENSMUSG00000054863	Fam19a5	TAFA5|Tafa-5|Tara-5	family with sequence similarity 19, member A5	protein-coding
mm_41668.1	chr5	99365545	99365558	+	1	NA	intron (NR_030692, intron 3 of 3)	intron (NR_030692, intron 3 of 3)	-112624	NM_145839	320292	Mm.259074	NM_145839	ENSMUSG00000089809	Rasgef1b	4732452O09Rik|GPIgamma4|Gpig4	RasGEF domain family, member 1B	protein-coding
mm_99553.1	chr11	103638951	103638955	+	1	NA	promoter-TSS (NM_027083)	promoter-TSS (NM_027083)	17	NR_131143	78629	Mm.398236	NR_131109		1700072I22Rik	-	RIKEN cDNA 1700072I22 gene	ncRNA
mm_156387.1	chrX	139800700	139800724	+	1	NA	promoter-TSS (NM_016675)	promoter-TSS (NM_016675)	-96	NM_016675	12738	Mm.117068	NM_016675	ENSMUSG00000047230	Cldn2	AL022813	claudin 2	protein-coding
mm_120758.1	chr14	73366356	73366373	+	1	NA	exon (NM_008410, exon 3 of 6)	exon (NM_008410, exon 3 of 6)	18907	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_96353.1	chr11	66957939	66957976	+	1	NA	promoter-TSS (NR_130646)	promoter-TSS (NR_130646)	63	NR_130646	71576	Mm.340077	NR_130315	ENSMUSG00000085683	9130409J20Rik	-	RIKEN cDNA 9130409J20 gene	ncRNA
mm_66262.1	chr7	35729745	35729793	-	1	NA	exon (NM_178704, exon 4 of 19)	exon (NM_178704, exon 4 of 19)	24685	NM_178704	233115	Mm.257808	NM_178704	ENSMUSG00000043671	Dpy19l3	6030410G08|9330164H19Rik	dpy-19-like 3 (C. elegans)	protein-coding
mm_19028.1	chr2	76968504	76968532	-	1	NA	exon (NM_011652, exon 9 of 313)	exon (NM_011652, exon 9 of 313)	14029	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_94006.1	chr10	127609840	127609846	-	1	NA	intron (NM_008512, intron 3 of 88)	intron (NM_008512, intron 3 of 88)	11305	NM_008512	16971	Mm.271854	NM_008512	ENSMUSG00000040249	Lrp1	A2mr|AI316852|CD91|Lrp|b2b1554Clo	low density lipoprotein receptor-related protein 1	protein-coding
mm_141302.1	chr17	28080596	28080639	-	1	NA	promoter-TSS (NM_013687)	promoter-TSS (NM_013687)	22	NM_001085555	21463	Mm.29758	NM_013687	ENSMUSG00000062859	Tcp11	D17Ken1|Tcp-11	t-complex protein 11	protein-coding
mm_25861.1	chr3	129836730	129836747	+	1	NA	promoter-TSS (NM_007686)	promoter-TSS (NM_007686)	-1	NM_001329552	12630	Mm.117180	NM_007686	ENSMUSG00000058952	Cfi	-	complement component factor i	protein-coding
mm_141067.1	chr17	25796965	25796981	-	1	NA	promoter-TSS (NM_133719)	promoter-TSS (NM_133719)	72	NM_133719	70083	Mm.41925	NM_133719	ENSMUSG00000002274	Metrn	1810034B16Rik|Hyrac	meteorin, glial cell differentiation regulator	protein-coding
mm_84573.1	chr9	69034288	69034299	-	1	NA	intron (NM_013646, intron 1 of 10)	intron (NM_013646, intron 1 of 10)	-255548	NM_001289916	19883	Mm.378450	NM_013646	ENSMUSG00000032238	Rora	9530021D13Rik|Nr1f1|ROR1|ROR2|ROR3|nmf267|sg|staggerer|tmgc26	RAR-related orphan receptor alpha	protein-coding
mm_41933.1	chr5	105700839	105700871	+	1	NA	promoter-TSS (NM_178701)	promoter-TSS (NM_178701)	45	NM_178701	231549	Mm.23837	NM_178701	ENSMUSG00000046079	Lrrc8d	2810473G09Rik|4930525N13Rik|A930019F03|Lrrc5	leucine rich repeat containing 8D	protein-coding
mm_5939.1	chr1	56637409	56637415	-	1	NA	promoter-TSS (NM_027661)	promoter-TSS (NM_027661)	39	NM_027661	71066	Mm.152656	NM_027661	ENSMUSG00000045336	Hsfy2	4933413G11Rik|Hspy2l	heat shock transcription factor, Y-linked 2	protein-coding
mm_19884.1	chr2	114050337	114050344	-	1	NA	exon (NM_009608, exon 3 of 7)	exon (NM_009608, exon 3 of 7)	2535	NM_009608	11464	Mm.686	NM_009608	ENSMUSG00000068614	Actc1	Actc-1	actin, alpha, cardiac muscle 1	protein-coding
mm_168881.1	chr12	43037641	43037644	+	1	NA	Intergenic	L1Md_T|LINE|L1	1172426	NM_013760	27362	Mm.27432	NM_013760	ENSMUSG00000014905	Dnajb9	AA408011|AA673251|AA673481|AW556981|ERdj4|Mdg1|mDj7	DnaJ heat shock protein family (Hsp40) member B9	protein-coding
mm_107764.1	chr12	59095654	59095658	+	1	NA	promoter-TSS (NM_177321)	promoter-TSS (NM_177321)	-144	NM_001329047	338320	Mm.213215	NM_146034	ENSMUSG00000021000	Mia2	Ctage5|D12Bwg0579e|Mea6|Mgea|Mgea6	melanoma inhibitory activity 2	protein-coding
mm_82938.1	chr9	35305238	35305266	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	24147	NR_040715	71133	Mm.158577	NR_040715	ENSMUSG00000111746	4933422A05Rik	-	RIKEN cDNA 4933422A05 gene	ncRNA
mm_4592.1	chr1	178336210	178336214	+	1	NA	intron (NM_016805, intron 1 of 13)	intron (NM_016805, intron 1 of 13)	1572	NM_016805	51810	Mm.86589	NM_016805	ENSMUSG00000039630	Hnrnpu	AA408410|AI256620|AL024194|AL024437|AW557595|C86794|Hnrpu|SAFA|Sp120|hnRNP U	heterogeneous nuclear ribonucleoprotein U	protein-coding
mm_173111.1	chrX	158870032	158870037	+	1	NA	Intergenic	L1Md_T|LINE|L1	-385748	NM_148945	110651	Mm.328476	NM_148945	ENSMUSG00000031309	Rps6ka3	MAPKAPK-1b|MPK-9|Rsk2|S6K-alpha3|p90RSK3|pp90RSK2	ribosomal protein S6 kinase polypeptide 3	protein-coding
mm_102784.1	chr11	68400813	68400836	-	1	NA	Intergenic	Intergenic	-13998	NM_008744	18208	Mm.39095	NM_008744	ENSMUSG00000020902	Ntn1	AI561871|BC019633|Netrin-1	netrin 1	protein-coding
mm_29280.1	chr3	107665075	107665119	-	1	NA	3' UTR (NM_145542, exon 17 of 17)	3' UTR (NM_145542, exon 17 of 17)	31451	NM_145542	229709	Mm.220328	NM_145542	ENSMUSG00000027893	Ahcyl1	1110034F20Rik|AA409031|AA414901|Ahcy-rs3|DCAL|Irbit	S-adenosylhomocysteine hydrolase-like 1	protein-coding
mm_130401.1	chr15	97976125	97976142	-	1	NA	exon (NM_001113515, exon 53 of 53)	exon (NM_001113515, exon 53 of 53)	11904	NM_001252153	380967	Mm.196630	NM_201359	ENSMUSG00000052369	Tmem106c	AI046681|BC046621|D15Ertd405e	transmembrane protein 106C	protein-coding
mm_88481.1	chr10	77622292	77622361	+	1	NA	promoter-TSS (NM_019803)	promoter-TSS (NM_019803)	5	NM_019803	22213	Mm.458125	NM_019803	ENSMUSG00000009293	Ube2g2	1110003O05Rik|D10Xrf369|UBC7|Ubc7p	ubiquitin-conjugating enzyme E2G 2	protein-coding
mm_11609.1	chr2	34406925	34406938	+	1	NA	promoter-TSS (NM_177345)	promoter-TSS (NM_177345)	80	NM_001290626	227743	Mm.270866	NM_177345	ENSMUSG00000038696	Mapkap1	AI591529|D230039K05Rik|Sin1	mitogen-activated protein kinase associated protein 1	protein-coding
mm_26493.1	chr3	145292717	145292776	+	1	NA	5' UTR (NM_027770, exon 1 of 60)	5' UTR (NM_027770, exon 1 of 60)	274	NM_001317733	71355	Mm.235570	NM_027770	ENSMUSG00000028197	Col24a1	5430404K19Rik	collagen, type XXIV, alpha 1	protein-coding
mm_40845.1	chr5	73304614	73304637	+	1	NA	exon (NM_001159889, exon 6 of 7)	exon (NM_001159889, exon 6 of 7)	11831	NM_001159888	68095	Mm.247039	NM_023429	ENSMUSG00000029152	Ociad1	6030432N09Rik|AI481327|AW557942|Asrij|B230209J16Rik|BB021357|Emi2|Imi2|OCIA|TPA018	OCIA domain containing 1	protein-coding
mm_117801.1	chr13	97207085	97207089	-	1	NA	Intergenic	RMER5|LTR|ERV1	-8730	NM_010422	15212	Mm.27816	NM_010422	ENSMUSG00000021665	Hexb	-	hexosaminidase B	protein-coding
mm_148563.1	chr19	4756489	4756497	+	1	NA	promoter-TSS (NM_025717)	promoter-TSS (NM_025717)	-32	NM_025717	66704	Mm.396734	NM_025717	ENSMUSG00000033760	Rbm4b	4921506I22Rik|AI504630|AI506404|Lark2|Neosin	RNA binding motif protein 4B	protein-coding
mm_82320.1	chr9	8004415	8004436	-	1	NA	5' UTR (NM_001171147, exon 1 of 9)	5' UTR (NM_001171147, exon 1 of 9)	171	NM_001171147	22601	Mm.221992	NM_009534	ENSMUSG00000053110	Yap1	AI325207|Yap|Yap65|Yki|Yorkie	yes-associated protein 1	protein-coding
mm_132308.1	chr16	33684505	33684532	+	1	NA	promoter-TSS (NM_175256)	promoter-TSS (NM_175256)	52	NM_175256	77446	Mm.245741	NM_172934	ENSMUSG00000075254	Heg1	4632417D23Rik|5530401I02Rik|9530025L16Rik|BC038614|Gm629|OTTMUSG00000027315	heart development protein with EGF-like domains 1	protein-coding
mm_108192.1	chr12	76765844	76765857	+	1	NA	intron (NM_206534, intron 1 of 3)	intron (NM_206534, intron 1 of 3)	277	NM_206534	211151	Mm.80970	NM_206534	ENSMUSG00000090258	Churc1	1700030P15Rik|My015|chch	churchill domain containing 1	protein-coding
mm_10470.1	chr2	14331372	14331382	+	1	NA	3' UTR (NM_008625, exon 30 of 30)	3' UTR (NM_008625, exon 30 of 30)	-57021	NM_001012305	277468	Mm.44662	NM_001012305	ENSMUSG00000036949	Slc39a12	AW046938|Gm731	solute carrier family 39 (zinc transporter), member 12	protein-coding
mm_172272.1	chr6	83907163	83907168	-	1	NA	Intergenic	ORR1A1|LTR|ERVL-MaLR	-7188	NM_001166371	18139	Mm.132392	NM_008717	ENSMUSG00000030016	Zfp638	AI323587|Np220|Zfml|Znf638|mNP220	zinc finger protein 638	protein-coding
mm_134582.1	chr16	20405829	20405849	-	1	NA	exon (NM_013790, exon 3 of 30)	exon (NM_013790, exon 3 of 30)	20555	NM_013790	27416	Mm.20845	NM_013790	ENSMUSG00000022822	Abcc5	2900011L11Rik|AI132311|Abcc5a|Abcc5b|Mrp5	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	protein-coding
mm_21593.1	chr2	164237698	164237711	-	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	637	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_37616.1	chr4	126968201	126968236	-	1	NA	promoter-TSS (NM_001114399)	promoter-TSS (NM_001114399)	-295	NM_001114399	67785	Mm.165401	NM_001114399	ENSMUSG00000042446	Zmym4	6330503C17Rik|AI480785|AW493829|CDIR|D630001M21|MYM|Zfp262|Znf262|mKIAA0425	zinc finger, MYM-type 4	protein-coding
mm_100872.1	chr11	5915127	5915141	-	1	NA	promoter-TSS (NM_001287386)	promoter-TSS (NM_001287386)	1	NM_001287386	103988	Mm.220358	NM_010292	ENSMUSG00000041798	Gck	GLK|Gk|Gls006|HK4|HKIV|HXKP|Hlb62|MODY2	glucokinase	protein-coding
mm_18646.1	chr2	69550907	69550924	-	1	NA	exon (NM_001081088, exon 3 of 79)	exon (NM_001081088, exon 3 of 79)	35152	NM_001081088	14725	Mm.23847	NM_001081088	ENSMUSG00000027070	Lrp2	AI315343|AW536255|D230004K18Rik|Gp330|Megalin|b2b1625.2Clo	low density lipoprotein receptor-related protein 2	protein-coding
mm_77458.1	chr8	121944850	121944880	-	1	NA	promoter-TSS (NM_007608)	promoter-TSS (NM_007608)	47	NM_007608	12352	Mm.116761	NM_007608	ENSMUSG00000025317	Car5a	CAV|Ca5a|Car5	carbonic anhydrase 5a, mitochondrial	protein-coding
mm_55189.1	chr6	52191263	52191285	-	1	NA	exon (NM_008265, exon 1 of 2)	exon (NM_008265, exon 1 of 2)	429	NM_008265	15401	Mm.439647	NM_008265	ENSMUSG00000000942	Hoxa4	AV206827|Hox-1.4	homeobox A4	protein-coding
mm_167838.1	chr9	124440658	124440710	+	1	NA	Intergenic	Intergenic	16897	NR_015516	75135	Mm.476814	NR_015516		4930526I15Rik	1600027J15Rik	RIKEN cDNA 4930526I15 gene	ncRNA
mm_118587.1	chr14	20546158	20546161	+	1	NA	promoter-TSS (NR_033571)	promoter-TSS (NR_033571)	-134	NR_033571	75602	Mm.437061	NR_033571	ENSMUSG00000084925	1810062O18Rik	-	RIKEN cDNA 1810062O18 gene	ncRNA
mm_92786.1	chr10	81291501	81291526	-	1	NA	promoter-TSS (NM_013769)	promoter-TSS (NM_013769)	68	NM_001282095	27375	Mm.27984	NM_013769	ENSMUSG00000034917	Tjp3	-	tight junction protein 3	protein-coding
mm_58771.1	chr7	15901657	15901665	+	1	NA	promoter-TSS (NM_001145190)	promoter-TSS (NM_001145190)	15	NM_001145190	546024	Mm.259041	NM_001033638	ENSMUSG00000074365	Crxos	AA606869|AY590891|Crxos1|Egam1	cone-rod homeobox, opposite strand	protein-coding
mm_151568.1	chr19	60764184	60764208	+	1	NA	exon (NM_010123, exon 20 of 22)	exon (NM_010123, exon 20 of 22)	8209	NM_178421	332397	Mm.186390	NM_178421	ENSMUSG00000072437	Nanos1	NOS-1	nanos homolog 1 (Drosophila)	protein-coding
mm_160224.1	chr7	101920752	101920752	-	1	NA	promoter-TSS (NM_001162974)	promoter-TSS (NM_001162974)	22	NM_001162974	69358	Mm.214841	NM_027053	ENSMUSG00000064307	Lrrc51	1700008D07Rik|Lrtomt	leucine rich repeat containing 51	protein-coding
mm_25389.1	chr3	107218146	107218150	+	1	NA	exon (NM_001111143, exon 4 of 9)	exon (NM_001111143, exon 4 of 9)	3584	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_128498.1	chr15	51991680	51991752	-	1	NA	promoter-TSS (NM_009009)	promoter-TSS (NM_009009)	44	NM_009009	19357	Mm.182628	NM_009009	ENSMUSG00000022314	Rad21	SCC1|mKIAA0078	RAD21 cohesin complex component	protein-coding
mm_49591.1	chr6	30645096	30645167	+	1	NA	exon (NM_025350, exon 10 of 10)	exon (NM_025350, exon 10 of 10)	5913	NM_025350	109697	Mm.25377	NM_025350	ENSMUSG00000054446	Cpa1	0910001L12Rik|Cpa	carboxypeptidase A1, pancreatic	protein-coding
mm_116974.1	chr13	56178932	56178936	-	1	NA	promoter-TSS (NM_001168615)	promoter-TSS (NM_001168615)	-49	NM_001168615	212937	Mm.116697	NM_145976	ENSMUSG00000049625	Tifab	-	TRAF-interacting protein with forkhead-associated domain, family member B	protein-coding
mm_38331.1	chr4	137430518	137430525	-	1	NA	promoter-TSS (NM_026419)	promoter-TSS (NM_026419)	-1	NM_026419	67868	Mm.297477	NM_026419	ENSMUSG00000023433	Cela3b	0910001F22Rik|2310074F01Rik|AI504000|Ela3|Ela3b	chymotrypsin-like elastase family, member 3B	protein-coding
mm_155819.1	chrX	100585439	100585463	+	1	NA	Intergenic	Intergenic	9418	NM_020621	57385	Mm.117118	NM_020621	ENSMUSG00000044359	P2ry4	P2Y4|P2Y4R	pyrimidinergic receptor P2Y, G-protein coupled, 4	protein-coding
mm_93956.1	chr10	127263347	127263368	-	1	NA	promoter-TSS (NM_001039000)	promoter-TSS (NM_001039000)	6	NM_008447	16572	Mm.30355	NM_008447	ENSMUSG00000074657	Kif5a	D10Bwg0738e|Khc|Kif5|Kns|mKIAA4086	kinesin family member 5A	protein-coding
mm_41286.1	chr5	90462750	90462776	+	1	NA	exon (NM_009654, exon 3 of 15)	exon (NM_009654, exon 3 of 15)	1893	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_131773.1	chr16	22894778	22894785	+	1	NA	promoter-TSS (NR_110508)	promoter-TSS (NR_110508)	-395	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_17622.1	chr2	30982183	30982224	-	1	NA	promoter-TSS (NM_028846)	promoter-TSS (NM_028846)	-76	NM_028846	74270	Mm.346654	NM_028846	ENSMUSG00000026854	Usp20	1700055M05Rik|AI467231|Vdu2	ubiquitin specific peptidase 20	protein-coding
mm_150213.1	chr19	32952632	32952658	+	1	NA	Intergenic	ORR1B2|LTR|ERVL-MaLR	195068	NM_008960	19211	Mm.245395	NM_008960	ENSMUSG00000013663	Pten	2310035O07Rik|A130070J02Rik|AI463227|B430203M17Rik|MMAC1|TEP1	phosphatase and tensin homolog	protein-coding
mm_44088.1	chr5	149229214	149229242	+	1	NA	Intergenic	CpG	-35776	NM_001308462	11690	Mm.19844	NM_009663	ENSMUSG00000060063	Alox5ap	Flap	arachidonate 5-lipoxygenase activating protein	protein-coding
mm_1212.1	chr1	62726854	62726943	+	1	NA	intron (NM_001077405, intron 2 of 15)	(CA)n|Simple_repeat|Simple_repeat	23581	NM_001077405	18187	Mm.266341	NM_010939	ENSMUSG00000025969	Nrp2	1110048P06Rik|Np-2|Np2|Npn-2|Npn2	neuropilin 2	protein-coding
mm_51658.1	chr6	86195082	86195092	+	1	NA	promoter-TSS (NM_031199)	promoter-TSS (NM_031199)	-140	NM_031199	21802	Mm.137222	NM_031199	ENSMUSG00000029999	Tgfa	wa-1|wa1	transforming growth factor alpha	protein-coding
mm_160103.1	chr7	20008224	20008224	+	1	NA	intron (NM_194058, intron 1 of 9)	intron (NM_194058, intron 1 of 9)	201	NM_194058	243874	Mm.277114	NM_194058	ENSMUSG00000060508	Nlrp9b	Nalp-delta|Nalp9b|Nlrp9	NLR family, pyrin domain containing 9B	protein-coding
mm_136570.1	chr17	3453216	3453226	+	1	NA	intron (NM_001122998, intron 12 of 26)	intron (NM_001122998, intron 12 of 26)	-29094	NM_001286758	24001	Mm.137134	NM_011878	ENSMUSG00000023800	Tiam2	3000002F19Rik|STEF|mKIAA2016	T cell lymphoma invasion and metastasis 2	protein-coding
mm_79067.1	chr9	46233318	46233326	+	1	NA	exon (NM_001289755, exon 4 of 4)	exon (NM_001289755, exon 4 of 4)	1977	NM_001289833	11814	Mm.390161	NM_023114	ENSMUSG00000032081	Apoc3	apo-CIII|apoC-III	apolipoprotein C-III	protein-coding
mm_63737.1	chr7	130898212	130898215	+	1	NA	intron (NM_001346515, intron 6 of 12)	intron (NM_001346515, intron 6 of 12)	-10055	NR_106028	102466219		NR_106028	ENSMUSG00000104914	Mir7061	mmu-mir-7061	microRNA 7061	ncRNA
mm_75618.1	chr8	64592872	64592899	-	1	NA	3' UTR (NM_013494, exon 9 of 9)	3' UTR (NM_013494, exon 9 of 9)	-78444	NR_030491	735270		NR_030491	ENSMUSG00000076042	Mir710	Mirn710|mmu-mir-710	microRNA 710	ncRNA
mm_165181.1	chr2	29772201	29772204	-	1	NA	Intergenic	Intergenic	10674	NM_001177392	433416	Mm.330112	NM_001034887	ENSMUSG00000075425	Gm13547	OTTMUSG00000012686	predicted gene 13547	protein-coding
mm_88501.1	chr10	77838355	77838366	+	1	NA	intron (NM_001287074, intron 2 of 11)	(CA)n|Simple_repeat|Simple_repeat	2413	NM_001024709	544710	Mm.441890	NM_001024709		Krtap10-10	EG544710	keratin associated protein 10-10	protein-coding
mm_74621.1	chr8	13104816	13104839	-	1	NA	promoter-TSS (NM_146207)	promoter-TSS (NM_146207)	516	NM_178708	234069	Mm.103427	NM_178708	ENSMUSG00000038542	Pcid2	A730042J05Rik	PCI domain containing 2	protein-coding
mm_107309.1	chr12	31074015	31074030	+	1	NA	promoter-TSS (NM_027828)	promoter-TSS (NM_027828)	54	NM_027828	104943	Mm.248938	NM_027828	ENSMUSG00000036136	Fam110c	9030611O19Rik|AU019489	family with sequence similarity 110, member C	protein-coding
mm_113871.1	chr13	48662908	48662922	+	1	NA	promoter-TSS (NM_007526)	promoter-TSS (NM_007526)	-121	NM_007526	12022	Mm.42241	NM_007526	ENSMUSG00000021381	Barx1	-	BarH-like homeobox 1	protein-coding
mm_101942.1	chr11	50207898	50207909	-	1	NA	exon (NM_011018, exon 2 of 8)	exon (NM_011018, exon 2 of 8)	2917	NM_001290769	18412	Mm.40828	NM_011018	ENSMUSG00000015837	Sqstm1	A170|OSF-6|Osi|STAP|STONE14|p62	sequestosome 1	protein-coding
mm_40.1	chr1	6482757	6482786	+	1	NA	Intergenic	(T)n|Simple_repeat|Simple_repeat	-4460	NM_001244693	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding
mm_31702.1	chr4	62559815	62559821	+	1	NA	promoter-TSS (NM_019492)	promoter-TSS (NM_019492)	-29	NM_019492	50780	Mm.286753	NM_019492	ENSMUSG00000059810	Rgs3	4930506N09Rik|C2PA-RGS3|C2pa|PDZ-RGS3|RGS3S	regulator of G-protein signaling 3	protein-coding
mm_121743.1	chr14	18709648	18709675	-	1	NA	intron (NM_144839, intron 3 of 5)	intron (NM_144839, intron 3 of 5)	183966	NM_144839	218793	Mm.23551	NM_144839	ENSMUSG00000058317	Ube2e2	BC016265	ubiquitin-conjugating enzyme E2E 2	protein-coding
mm_61038.1	chr7	49639029	49639038	+	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	-2198	NM_001005232	13172	Mm.307176	NM_001005232	ENSMUSG00000030507	Dbx1	AI426026|Dbx	developing brain homeobox 1	protein-coding
mm_50598.1	chr6	49111228	49111258	+	1	NA	intron (NM_023670, intron 6 of 14)	MER20|DNA|hAT-Charlie	37448	NM_029353	75593	Mm.439947	NM_029353	ENSMUSG00000029815	Malsu1	2410003K15Rik|Matsu1	mitochondrial assembly of ribosomal large subunit 1	protein-coding
mm_138724.1	chr17	36898216	36898226	+	1	NA	promoter-TSS (NM_146077)	promoter-TSS (NM_146077)	91	NM_146077	224762	Mm.213417	NM_146077	ENSMUSG00000058063	Trim31	BC026666|HCG1|HCGI|RNF	tripartite motif-containing 31	protein-coding
mm_74337.1	chr8	127093572	127093574	+	1	NA	intron (NM_001309391, intron 1 of 24)	intron (NM_001309391, intron 1 of 24)	29517	NM_001309391	93742	Mm.299254	NM_033620	ENSMUSG00000025812	Pard3	AA960621|AI256638|Asip|D8Ertd580e|Par-3|Par3|Pard-3|Pard3a|Phip	par-3 family cell polarity regulator	protein-coding
mm_19193.1	chr2	84433099	84433109	-	1	NA	exon (NM_011576, exon 9 of 9)	exon (NM_011576, exon 9 of 9)	-7838	NM_018782	54598	Mm.75467	NM_018782	ENSMUSG00000059588	Calcrl	AV071593|CRLR	calcitonin receptor-like	protein-coding
mm_70745.1	chr8	19163912	19163919	+	1	NA	Intergenic	Intergenic	6028	NM_153115	78128	Mm.229357	NM_153115	ENSMUSG00000079842	Spag11a	9230111C08Rik|Bin1b|EP2Q|EP2e|Spag11	sperm associated antigen 11A	protein-coding
mm_124582.1	chr14	124677090	124677110	-	1	NA	promoter-TSS (NM_207667)	promoter-TSS (NM_207667)	27	NM_207667	14169	Mm.206362	NM_010201	ENSMUSG00000025551	Fgf14	FHF-4|Fhf4|mFHF-4(1B)	fibroblast growth factor 14	protein-coding
mm_109018.1	chr12	103451093	103451132	+	1	NA	exon (NM_145449, exon 7 of 7)	exon (NM_145449, exon 7 of 7)	6111	NM_145449	217845	Mm.298416	NM_145449	ENSMUSG00000021208	Ifi27l2b	1810023F06Rik|ISG12(b2)	interferon, alpha-inducible protein 27 like 2B	protein-coding
mm_136350.1	chr16	92695067	92695089	-	1	NA	intron (NM_001111023, intron 1 of 5)	intron (NM_001111023, intron 1 of 5)	2251	NM_001111023	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_137122.1	chr17	22674345	22674379	+	1	NA	Intergenic	Intergenic	73214	NM_001104575	628185	Mm.390947	NM_001104575	ENSMUSG00000094921	Vmn2r112	EG628185|V2rp1	vomeronasal 2, receptor 112	protein-coding
mm_89733.1	chr10	98994897	98994901	+	1	NA	intron (NM_026482, intron 8 of 20)	L1_Mus3|LINE|L1	79747	NM_026482	67972	Mm.166944	NM_026482	ENSMUSG00000019943	Atp2b1	2810442I22Rik|E130111D10Rik|Pmca1	ATPase, Ca++ transporting, plasma membrane 1	protein-coding
mm_122143.1	chr14	31184975	31185010	-	1	NA	exon (NM_022656, exon 13 of 21)	exon (NM_022656, exon 13 of 21)	-16351	NM_138672	192187	Mm.220821	NM_138672	ENSMUSG00000042286	Stab1	FEEL-1|FELE-1|MFEEL-1|MS-1|STAB-1|mKIAA0246	stabilin 1	protein-coding
mm_101271.1	chr11	21370573	21370583	-	1	NA	promoter-TSS (NM_139297)	promoter-TSS (NM_139297)	51	NM_139297	216558	Mm.28877	NM_139297	ENSMUSG00000001891	Ugp2	UDPGP|UGPase	UDP-glucose pyrophosphorylase 2	protein-coding
mm_159405.1	chr3	98563962	98563962	-	1	NA	promoter-TSS (NM_001111336).3	promoter-TSS (NM_001111336).3	-19	NM_001111336	15495	Mm.14309	NM_008294	ENSMUSG00000095143	Hsd3b4	-	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 4	protein-coding
mm_141371.1	chr17	29007862	29007872	-	1	NA	promoter-TSS (NM_134115)	promoter-TSS (NM_134115)	70	NM_134115	106504	Mm.439986	NM_134115	ENSMUSG00000024006	Stk38	5830476G13Rik|9530097A09Rik|AA617404|Ndr1	serine/threonine kinase 38	protein-coding
mm_26356.1	chr3	142549310	142549334	+	1	NA	3' UTR (NM_001083312, exon 11 of 11)	3' UTR (NM_001083312, exon 11 of 11)	-10730	NM_018734	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_41565.1	chr5	93150135	93150145	+	1	NA	intron (NM_001347377, intron 3 of 10)	intron (NM_001347377, intron 3 of 10)	56355	NM_017367	12453	Mm.250419	NM_017367	ENSMUSG00000063015	Ccni	-	cyclin I	protein-coding
mm_51699.1	chr6	86607838	86607846	+	1	NA	Intergenic	Intergenic	-20332	NM_026414	67855	Mm.183043	NM_026414	ENSMUSG00000033508	Asprv1	2300003P22Rik|AA986851|SASP|SASPase|Taps	aspartic peptidase, retroviral-like 1	protein-coding
mm_110196.1	chr12	27340441	27340457	-	1	NA	3' UTR (NM_009234, exon 1 of 1)	3' UTR (NM_009234, exon 1 of 1)	2269	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding
mm_22890.1	chr3	30732350	30732351	+	1	NA	Intergenic	BC1_Mm|scRNA|scRNA	-13943	NM_029489	75953	Mm.308084	NM_029489	ENSMUSG00000051860	Samd7	4930597A01Rik	sterile alpha motif domain containing 7	protein-coding
mm_13322.1	chr2	102777467	102777487	+	1	NA	exon (NM_011393, exon 10 of 10)	exon (NM_011393, exon 10 of 10)	71039	NM_001077515	20511	Mm.267547	NM_011393	ENSMUSG00000005089	Slc1a2	1700091C19Rik|2900019G14Rik|AI159670|Eaat2|GLT-1|GLT1|MGLT1	solute carrier family 1 (glial high affinity glutamate transporter), member 2	protein-coding
mm_58722.1	chr7	13024393	13024421	+	1	NA	5' UTR (NM_011588, exon 1 of 17)	5' UTR (NM_011588, exon 1 of 17)	255	NM_011588	21849	Mm.15701	NM_011588	ENSMUSG00000005566	Trim28	AA408787|KAP-1|KRIP-1|MommeD9|Tif1b|Tif1beta	tripartite motif-containing 28	protein-coding
mm_162923.1	chr10	121034229	121034231	+	1	NA	5' UTR (NM_011915, exon 1 of 10)	5' UTR (NM_011915, exon 1 of 10)	226	NM_011915	24117	Mm.32831	NM_011915	ENSMUSG00000020218	Wif1	AW107799|WIF-1	Wnt inhibitory factor 1	protein-coding
mm_100633.1	chr11	121717177	121717184	+	1	NA	3' UTR (NM_144797, exon 4 of 4)	3' UTR (NM_144797, exon 4 of 4)	14753	NM_144797	210029	Mm.153566	NM_144797	ENSMUSG00000039208	Metrnl	9430048M07Rik|BC019776	meteorin, glial cell differentiation regulator-like	protein-coding
mm_161923.1	chr18	75114630	75114630	+	1	NA	intron (NM_027727, intron 8 of 16)	intron (NM_027727, intron 8 of 16)	95858	NM_027727	69190	Mm.173826	NM_027727	ENSMUSG00000035765	Dym	1810041M12Rik|4933427L07Rik|C030019K18Rik	dymeclin	protein-coding
mm_150521.1	chr19	39036539	39036543	+	1	NA	intron (NM_028089, intron 7 of 8)	intron (NM_028089, intron 7 of 8)	-24465	NM_028191	72303	Mm.482578	NM_028191	ENSMUSG00000067231	Cyp2c65	2210009K14Rik	cytochrome P450, family 2, subfamily c, polypeptide 65	protein-coding
mm_141999.1	chr17	35196174	35196200	-	1	NA	3' UTR (NM_008518, exon 3 of 3)	3' UTR (NM_008518, exon 3 of 3)	1215	NR_105939	102465588		NR_105939	ENSMUSG00000098291	Mir6973a	Gm27967|mmu-mir-6973a	microRNA 6973a	ncRNA
mm_141916.1	chr17	34999310	34999341	-	1	NA	exon (NM_033075, exon 2 of 2)	exon (NM_033075, exon 2 of 2)	1421	NM_033075	110956	Mm.22506	NM_033075		D17H6S56E-5	G7e	DNA segment, Chr 17, human D6S56E 5	protein-coding
mm_69737.1	chr7	140900386	140900396	-	1	NA	promoter-TSS (NM_007751)	promoter-TSS (NM_007751)	55	NM_007751	12869	Mm.3841	NM_007751	ENSMUSG00000025488	Cox8b	Cox8h|CoxVIII-H	cytochrome c oxidase subunit VIIIb	protein-coding
mm_84161.1	chr9	59544594	59544607	-	1	NA	intron (NM_010421, intron 1 of 13)	intron (NM_010421, intron 1 of 13)	5060	NM_010421	15211	Mm.2284	NM_010421	ENSMUSG00000025232	Hexa	Hex-1	hexosaminidase A	protein-coding
mm_84539.1	chr9	67266920	67266930	-	1	NA	intron (NM_001081242, intron 44 of 57)	intron (NM_001081242, intron 44 of 57)	-30199	NR_029576	387185		NR_029576	ENSMUSG00000076379	Mir190a	Mir190|Mirn190|mir-190|mir-190a|mmu-mir-190|mmu-mir-190a	microRNA 190a	ncRNA
mm_129518.1	chr15	79109002	79109002	-	1	NA	promoter-TSS (NM_177461)	promoter-TSS (NM_177461)	19	NM_177461	27008	Mm.196480	NM_177461	ENSMUSG00000033039	Micall1	AI448246|D15Mit260|D15N2e|EST573322|EST820961|MIRab13|mKIAA1668	microtubule associated monooxygenase, calponin and LIM domain containing -like 1	protein-coding
mm_154244.1	chr19	60766430	60766442	-	1	NA	exon (NM_010123, exon 19 of 22)	exon (NM_010123, exon 19 of 22)	7949	NR_034047	100217439		NR_034047		Snora19	MBI-51	small nucleolar RNA, H/ACA box 19	snoRNA
mm_53904.1	chr6	3498302	3498312	-	1	NA	promoter-TSS (NM_024260)	promoter-TSS (NM_024260)	-86	NM_001167751	73288	Mm.45539	NM_024260	ENSMUSG00000001376	Vps50	1700034M03Rik|8430415E05Rik|BLM|C87205|Ccdc132|mKIAA1861	VPS50 EARP/GARPII complex subunit	protein-coding
mm_22472.1	chr3	5218547	5218561	+	1	NA	promoter-TSS (NM_030708)	promoter-TSS (NM_030708)	0	NM_030708	80892	Mm.41522	NM_030708	ENSMUSG00000025255	Zfhx4	A930021B15|C130041O22Rik|Zfh-4|Zfh4	zinc finger homeodomain 4	protein-coding
mm_58973.1	chr7	19024246	19024270	+	1	NA	promoter-TSS (NM_026605)	promoter-TSS (NM_026605)	-119	NM_026605	68188	Mm.130902	NM_026605	ENSMUSG00000023118	Sympk	1500016F02Rik|4632415H16Rik|AA125406|AI449890|SPK|SYM	symplekin	protein-coding
mm_41023.1	chr5	81571579	81571582	+	1	NA	intron (NM_001347371, intron 8 of 23)	intron (NM_001347371, intron 8 of 23)	549987	NM_198702	319387	Mm.273631	NM_198702	ENSMUSG00000037605	Adgrl3	5430402I23Rik|CIRL-3|D130075K09Rik|Gm1379|LEC3|Lphn3|mKIAA0768	adhesion G protein-coupled receptor L3	protein-coding
mm_61652.1	chr7	80422991	80422993	+	1	NA	Intergenic	Intergenic	-17556	NM_001081454	18550	Mm.5241	NM_011046	ENSMUSG00000030530	Furin	9130404I01Rik|Fur|PACE|Pcsk3|SPC1	furin (paired basic amino acid cleaving enzyme)	protein-coding
mm_66219.1	chr7	34546784	34546798	-	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	106050	NM_146188	233107	Mm.486198	NM_146188	ENSMUSG00000030499	Kctd15	BC031749	potassium channel tetramerisation domain containing 15	protein-coding
mm_167629.1	chr9	61808203	61808209	+	1	NA	Intergenic	Intergenic	106304	NM_018853	56040	Mm.3158	NM_018853	ENSMUSG00000007892	Rplp1	2410042H16Rik|Arpp1|C430017H15Rik	ribosomal protein, large, P1	protein-coding
mm_172110.1	chr6	3200905	3200905	+	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	-87614	NR_036696	667335	Mm.380219	NR_036696	ENSMUSG00000106779	Gm8579	EG667335	spermatogenesis associated glutamate (E)-rich protein 4a pseudogene	pseudo
mm_152649.1	chr19	12540816	12540831	-	1	NA	Intergenic	Intergenic	-32687	NM_001346545	107373	Mm.1643	NM_026640	ENSMUSG00000024691	Fam111a	4632417K18Rik|AW413625	family with sequence similarity 111, member A	protein-coding
mm_112760.1	chr13	19347539	19347554	+	1	NA	Intergenic	Intergenic	48267	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_15351.1	chr2	156196708	156196775	+	1	NA	promoter-TSS (NM_172674)	promoter-TSS (NM_172674)	94	NM_172674	228829	Mm.427078	NM_172674	ENSMUSG00000038116	Phf20	6820402O20Rik	PHD finger protein 20	protein-coding
mm_122471.1	chr14	45582033	45582040	-	1	NA	Intergenic	Intergenic	38326	NR_045809	67651	Mm.55930	NR_045809		4930527F14Rik	-	RIKEN cDNA 4930527F14 gene	ncRNA
mm_144561.1	chr18	31759889	31759973	+	1	NA	promoter-TSS (NM_001242430)	promoter-TSS (NM_001242430)	107	NM_153515	225339	Mm.290804	NM_153515	ENSMUSG00000041915	Ammecr1l	5430429D03Rik|AU022236|AU040755|AW111353|E230022H04Rik	AMME chromosomal region gene 1-like	protein-coding
mm_131074.1	chr16	4707126	4707130	+	1	NA	3' UTR (NM_023646, exon 12 of 12)	3' UTR (NM_023646, exon 12 of 12)	12228	NM_001290763	67824	Mm.28451	NM_026393	ENSMUSG00000063445	Nmral1	1110025F24Rik|AI256624	NmrA-like family domain containing 1	protein-coding
mm_171710.1	chr4	78772974	78772979	-	1	NA	Intergenic	RLTR9F|LTR|ERVK	178929	NR_131142	623726		NR_131142		A430085M09Rik	EG623726	RIKEN cDNA A430085M09 gene	ncRNA
mm_27928.1	chr3	79564913	79564917	-	1	NA	intron (NM_001162999, intron 1 of 16)	intron (NM_001162999, intron 1 of 16)	2764	NM_001162999	329679	Mm.244005	NM_001162999	ENSMUSG00000061175	Fnip2	D630023B12Rik|mKIAA1450	folliculin interacting protein 2	protein-coding
mm_113236.1	chr13	27259483	27259494	+	1	NA	promoter-TSS (NM_025896)	promoter-TSS (NM_025896)	-1	NM_025896	67000	Mm.69279	NM_025896	ENSMUSG00000038883	Prl3a1	1600016E11Rik|Ghd9|PLP-H|PLP-I|Plpi|Prlpi	prolactin family 3, subfamily a, member 1	protein-coding
mm_146515.1	chr18	3507811	3507817	-	1	NA	promoter-TSS (NM_026505)	promoter-TSS (NM_026505)	-143	NM_026505	68010	Mm.284863	NM_026505	ENSMUSG00000024232	Bambi	2610003H06Rik	BMP and activin membrane-bound inhibitor	protein-coding
mm_16522.1	chr2	181511225	181511231	+	1	NA	intron (NM_001291204, intron 3 of 4)	B1_Mur1|SINE|Alu	-9257	NM_016775	13002	Mm.140761	NM_016775	ENSMUSG00000000826	Dnajc5	2610314I24Rik|AU018536|Csp	DnaJ heat shock protein family (Hsp40) member C5	protein-coding
mm_138004.1	chr17	33817836	33817866	+	1	NA	exon (NM_030697, exon 3 of 11)	exon (NM_030697, exon 3 of 11)	6647	NM_016844	54127	Mm.352374	NM_016844	ENSMUSG00000067288	Rps28	-	ribosomal protein S28	protein-coding
mm_69574.1	chr7	135700957	135700963	-	1	NA	exon (NM_001081117, exon 12 of 14)	exon (NM_001081117, exon 12 of 14)	15419	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_120745.1	chr14	73234924	73234932	+	1	NA	intron (NM_009029, intron 17 of 26)	intron (NM_009029, intron 17 of 26)	-2963	NM_175116	67168	Mm.390681	NM_175116	ENSMUSG00000033446	Lpar6	2610302I02Rik|P2ry5|P2y5	lysophosphatidic acid receptor 6	protein-coding
mm_125588.1	chr15	59620089	59620104	+	1	NA	Intergenic	Intergenic	-28558	NM_144549	211770	Mm.40298	NM_144549	ENSMUSG00000032501	Trib1	A530090O15Rik|TRB-1|Trb1	tribbles pseudokinase 1	protein-coding
mm_85950.1	chr9	112113953	112113964	-	1	NA	intron (NM_001177618, intron 17 of 18)	intron (NM_001177618, intron 17 of 18)	4753	NR_029823	723815		NR_029823	ENSMUSG00000065441	Mir128-2	Mirn128-2|Mirn128b|mir-128-2|mir-128b	microRNA 128-2	ncRNA
mm_117976.1	chr13	100078688	100078722	-	1	NA	exon (NM_001081061, exon 9 of 39)	exon (NM_001081061, exon 9 of 39)	25365	NM_001081061	544971	Mm.288546	NM_001081061	ENSMUSG00000049658	Bdp1	AI662220|AW049390|AW456745|B130055N23Rik|G630013P12Rik|TAF3B1|TFC5|TFIIIB150|TFIIIB90|Tfnr|mKIAA1241	B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB	protein-coding
mm_108227.1	chr12	77238741	77238799	+	1	NA	promoter-TSS (NR_045554)	promoter-TSS (NR_045554)	31	NR_045554	53618	Mm.35628	NM_016893	ENSMUSG00000021065	Fut8	-	fucosyltransferase 8	protein-coding
mm_79804.1	chr9	64175423	64175426	+	1	NA	promoter-TSS (NR_028548)	promoter-TSS (NR_028548)	-8	NR_028548	100217453		NR_028548	ENSMUSG00000094411	Snord16a	MBII-98	small nucleolar RNA, C/D box 16A	snoRNA
mm_116917.1	chr13	55513428	55513443	-	1	NA	promoter-TSS (NM_001114088)	promoter-TSS (NM_001114088)	11	NM_026131	67399	Mm.275648	NM_026131	ENSMUSG00000021493	Pdlim7	LMP	PDZ and LIM domain 7	protein-coding
mm_111445.1	chr12	98249383	98249403	-	1	NA	intron (NM_008079, intron 5 of 16)	intron (NM_008079, intron 5 of 16)	10066	NM_008079	14420	Mm.5120	NM_008079	ENSMUSG00000021003	Galc	2310068B06Rik|A930008M05Rik|AW212969|AW413532|Gacy|twi|twitcher	galactosylceramidase	protein-coding
mm_100619.1	chr11	121592565	121592572	+	1	NA	intron (NM_029878, intron 25 of 38)	intron (NM_029878, intron 25 of 38)	-73226	NM_178763	319530	Mm.11395	NM_178763	ENSMUSG00000039238	Zfp750	A030007D23Rik|Znf750	zinc finger protein 750	protein-coding
mm_91020.1	chr10	17724354	17724366	-	1	NA	exon (NM_010828, exon 2 of 2)	exon (NM_010828, exon 2 of 2)	1132	NM_010828	17684	Mm.272321	NM_010828	ENSMUSG00000039910	Cited2	AI835299|ER154-like|Mrg1|Msg2|p35srj	Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 2	protein-coding
mm_141827.1	chr17	34627167	34627191	-	1	NA	promoter-TSS (NM_019441)	promoter-TSS (NM_019441)	-31	NM_019441	54397	Mm.373627	NM_019441	ENSMUSG00000015474	Ppt2	0610007M19Rik|AA672937	palmitoyl-protein thioesterase 2	protein-coding
mm_117402.1	chr13	73700722	73700728	-	1	NA	promoter-TSS (NM_028878)	promoter-TSS (NM_028878)	-30	NM_028878	74338	Mm.271635	NM_028878	ENSMUSG00000021565	Slc6a19	4632401C08Rik|B<0>AT1	solute carrier family 6 (neurotransmitter transporter), member 19	protein-coding
mm_67663.1	chr7	86775810	86775839	-	1	NA	promoter-TSS (NM_001159706)	promoter-TSS (NM_001159706)	40	NM_016770	53320	Mm.269137	NM_016770	ENSMUSG00000001773	Folh1	GCP2|mopsm	folate hydrolase 1	protein-coding
mm_32768.1	chr4	116693818	116693855	+	1	NA	exon (NM_011034, exon 5 of 6)	exon (NM_011034, exon 5 of 6)	-7814	NR_040442	100502959	Mm.395400	NR_040442		AV051173	-	expressed sequence AV051173	ncRNA
mm_41022.1	chr5	81556348	81556362	+	1	NA	intron (NM_001347371, intron 7 of 23)	intron (NM_001347371, intron 7 of 23)	534762	NM_198702	319387	Mm.273631	NM_198702	ENSMUSG00000037605	Adgrl3	5430402I23Rik|CIRL-3|D130075K09Rik|Gm1379|LEC3|Lphn3|mKIAA0768	adhesion G protein-coupled receptor L3	protein-coding
mm_53704.1	chr6	142967777	142967793	+	1	NA	Intergenic	Intergenic	-3333	NM_011374	20449	Mm.260838	NM_011374	ENSMUSG00000030283	St8sia1	9330109E03Rik|GD3S|Sia-T|Siat8|Siat8a	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 1	protein-coding
mm_169040.1	chr13	14034255	14034259	+	1	NA	intron (NR_130788, intron 1 of 16)	PB1D11|SINE|Alu	5381	NR_130788	70430	Mm.260209	NM_178337	ENSMUSG00000039233	Tbce	2610206D02Rik|C530005D02Rik|pmn	tubulin-specific chaperone E	protein-coding
mm_153237.1	chr19	36112318	36112323	-	1	NA	3' UTR (NM_013468, exon 9 of 9)	3' UTR (NM_013468, exon 9 of 9)	7524	NM_013468	107765	Mm.10279	NM_013468	ENSMUSG00000024803	Ankrd1	Alrp|CARP|Crap|MARP1	ankyrin repeat domain 1 (cardiac muscle)	protein-coding
mm_78982.1	chr9	45389892	45389906	+	1	NA	intron (NM_022004, intron 1 of 7)	intron (NM_022004, intron 1 of 7)	-9810	NR_028499	11936	Mm.22742	NM_007503	ENSMUSG00000059412	Fxyd2	Atp1g1	FXYD domain-containing ion transport regulator 2	protein-coding
mm_70858.1	chr8	24413095	24413101	+	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	25848	NM_026931	69068	Mm.25775	NM_026931	ENSMUSG00000056313	1810011O10Rik	1110065B09Rik|AW121743|AW321058	RIKEN cDNA 1810011O10 gene	protein-coding
mm_120184.1	chr14	61380313	61380313	+	1	NA	intron (NM_008466, intron 10 of 16)	intron (NM_008466, intron 10 of 16)	-19868	NM_026598	68177	Mm.22758	NM_026598	ENSMUSG00000021928	Ebpl	5730442K12Rik|EBRP	emopamil binding protein-like	protein-coding
mm_29412.1	chr3	108972249	108972252	-	1	NA	3' UTR (NM_001163567, exon 11 of 11)	3' UTR (NM_001163567, exon 11 of 11)	31693	NM_001078646	66715	Mm.158124	NM_025723	ENSMUSG00000045662	Henmt1	4921515J06Rik|Hen1|mHEN1	HEN1 methyltransferase homolog 1 (Arabidopsis)	protein-coding
mm_126868.1	chr15	89355756	89355782	+	1	NA	promoter-TSS (NM_001271601)	promoter-TSS (NM_001271601)	50	NM_001271601	52683	Mm.143167	NM_001115132	ENSMUSG00000008690	Ncaph2	-	non-SMC condensin II complex, subunit H2	protein-coding
mm_153482.1	chr19	41276948	41276968	-	1	NA	intron (NM_031376, intron 16 of 16)	intron (NM_031376, intron 16 of 16)	-12954	NM_133352	107358	Mm.246440	NM_133352	ENSMUSG00000025016	Tm9sf3	1810073M23Rik|2810031D16Rik|AI115521|AI413748|AW146116|AW549777|Smbp|mKIAA4036	transmembrane 9 superfamily member 3	protein-coding
mm_7091.1	chr1	88654710	88654714	-	1	NA	Intergenic	Intergenic	47479	NM_177305	320982	Mm.27968	NM_177305	ENSMUSG00000049866	Arl4c	A630084M22Rik|Arl7|LAK	ADP-ribosylation factor-like 4C	protein-coding
mm_60293.1	chr7	44012673	44012690	+	1	NA	promoter-TSS (NM_010644)	promoter-TSS (NM_010644)	3	NM_010644	16618	Mm.439663	NM_010644	ENSMUSG00000053719	Klk1b26	Egfbp2|Klk26|PRECE-2|mGK-26|mGK26	kallikrein 1-related petidase b26	protein-coding
mm_54467.1	chr6	34907896	34907917	-	1	NA	intron (NM_001013366, intron 3 of 14)	intron (NM_001013366, intron 3 of 14)	2925	NM_001013366	101240	Mm.152120	NM_001013366	ENSMUSG00000058486	Wdr91	9530020G05Rik|AI987683|AU018665	WD repeat domain 91	protein-coding
mm_127118.1	chr15	98004750	98004751	+	1	NA	promoter-TSS (NM_001113515)	promoter-TSS (NM_001113515)	-26	NM_001113515	12824	Mm.2423	NM_031163	ENSMUSG00000022483	Col2a1	Col2|Col2a|Col2a-1|Del1|Dmm|Lpk|Rgsc856	collagen, type II, alpha 1	protein-coding
mm_150272.1	chr19	34243403	34243436	+	1	NA	exon (NM_007392, exon 8 of 9)	exon (NM_007392, exon 8 of 9)	11954	NM_007392	11475	Mm.213025	NM_007392	ENSMUSG00000035783	Acta2	0610041G09Rik|Actvs|SMalphaA|a-SMA|alphaSMA	actin, alpha 2, smooth muscle, aorta	protein-coding
mm_3552.1	chr1	150417474	150417488	+	1	NA	exon (NM_133780, exon 20 of 52)	exon (NM_133780, exon 20 of 52)	-24426	NM_145511	226499	Mm.222093	NM_145511	ENSMUSG00000006010	BC003331	1810053E15Rik|Odr4|odr-4	cDNA sequence BC003331	protein-coding
mm_21596.1	chr2	164237748	164237780	-	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	577	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_153863.1	chr19	46619961	46619970	-	1	NA	intron (NM_001177812, intron 2 of 4)	intron (NM_001177812, intron 2 of 4)	-3436	NM_001177813	226178	Mm.329895	NM_146099	ENSMUSG00000047731	Wbp1l	D19Wsu162e|Opal1	WW domain binding protein 1 like	protein-coding
mm_52606.1	chr6	117173623	117173639	+	1	NA	3' UTR (NM_021704, exon 3 of 3)	3' UTR (NM_021704, exon 3 of 3)	5096	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_24202.1	chr3	88616285	88616293	+	1	NA	promoter-TSS (NM_001198911)	promoter-TSS (NM_001198911)	82	NM_001198911	16800	Mm.239329	NM_008487	ENSMUSG00000028059	Arhgef2	AA408978|GEF|GEF-H1|GEFH1|LFP40|Lbcl1|Lfc|P40|mKIAA0651	rho/rac guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_15884.1	chr2	164839577	164839600	+	1	NA	TTS (NM_011125)	TTS (NM_011125)	5815	NM_008906	19025	Mm.359633	NM_008906	ENSMUSG00000017760	Ctsa	AU019505|PPCA|Ppgb	cathepsin A	protein-coding
mm_143225.1	chr17	63311292	63311295	-	1	NA	intron (NR_130176, intron 1 of 3)	intron (NR_130176, intron 1 of 3)	1680	NR_130176	414079	Mm.444282	NR_130176	ENSMUSG00000090565	4930405O22Rik	-	RIKEN cDNA 4930405O22 gene	ncRNA
mm_123756.1	chr14	70203409	70203453	-	1	NA	intron (NM_011366, intron 1 of 20)	intron (NM_011366, intron 1 of 20)	1192	NM_001271408	20410	Mm.5068	NM_011366	ENSMUSG00000022091	Sorbs3	SCAM-1|SH3P3|Sh3d4|vinexin-g	sorbin and SH3 domain containing 3	protein-coding
mm_58765.1	chr7	15881682	15881686	+	1	NA	promoter-TSS (NR_038092)	promoter-TSS (NR_038092)	-933	NR_038092	546024	Mm.259041	NM_001033638	ENSMUSG00000074365	Crxos	AA606869|AY590891|Crxos1|Egam1	cone-rod homeobox, opposite strand	protein-coding
mm_58689.1	chr7	12881166	12881204	+	1	NA	promoter-TSS (NM_153802)	promoter-TSS (NM_153802)	7	NM_153802	243833	Mm.293823	NM_153802	ENSMUSG00000060397	Zfp128	9630016P15Rik|Znf8|mZnf8	zinc finger protein 128	protein-coding
mm_130398.1	chr15	97976019	97976051	-	1	NA	3' UTR (NM_001113515, exon 53 of 53)	3' UTR (NM_001113515, exon 53 of 53)	11806	NM_001252153	380967	Mm.196630	NM_201359	ENSMUSG00000052369	Tmem106c	AI046681|BC046621|D15Ertd405e	transmembrane protein 106C	protein-coding
mm_112083.1	chr12	112674017	112674027	-	1	NA	5' UTR (NM_001165894, exon 1 of 14)	5' UTR (NM_001165894, exon 1 of 14)	254	NM_001165894	11651	Mm.6645	NM_009652	ENSMUSG00000001729	Akt1	Akt|LTR-akt|PKB|PKB/Akt|PKBalpha|Rac	thymoma viral proto-oncogene 1	protein-coding
mm_9633.1	chr1	176814167	176814189	-	1	NA	promoter-TSS (NM_029756)	promoter-TSS (NM_029756)	-482	NM_029756	76816	Mm.171399	NM_029756	ENSMUSG00000026504	Sdccag8	2700048G21Rik|5730470G24Rik|Cccap	serologically defined colon cancer antigen 8	protein-coding
mm_88311.1	chr10	75430048	75430057	+	1	NA	exon (NM_133995, exon 6 of 10)	exon (NM_133995, exon 6 of 10)	-19458	NR_045841	71125	Mm.399516	NR_045841		4933407G14Rik	-	RIKEN cDNA 4933407G14 gene	ncRNA
mm_86376.1	chr9	123839837	123839841	-	1	NA	intron (NM_148925, intron 4 of 18)	intron (NM_148925, intron 4 of 18)	11822	NM_148925	17281	Mm.252941	NM_148925	ENSMUSG00000025241	Fyco1	2810409M01Rik|Mem2|RUFY3|ZFYVE7	FYVE and coiled-coil domain containing 1	protein-coding
mm_43736.1	chr5	139801013	139801017	+	1	NA	3' UTR (NM_010757, exon 3 of 3)	3' UTR (NM_010757, exon 3 of 3)	9479	NM_010757	17135	Mm.157313	NM_010757	ENSMUSG00000018143	Mafk	AW061068|NF-E2|Nfe2u	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein K (avian)	protein-coding
mm_46623.1	chr5	108405516	108405540	-	1	NA	intron (NM_008806, intron 3 of 21)	ORR1C1|LTR|ERVL-MaLR	17155	NM_008806	18587	Mm.1372	NM_008806	ENSMUSG00000029491	Pde6b	Pdeb|r|rd|rd-1|rd1|rd10	phosphodiesterase 6B, cGMP, rod receptor, beta polypeptide	protein-coding
mm_51900.1	chr6	90662809	90662829	+	1	NA	exon (NM_001134384, exon 14 of 14)	exon (NM_001134384, exon 14 of 14)	43573	NM_001037493	71699	Mm.272633	NM_027868	ENSMUSG00000030089	Slc41a3	1010001P06Rik|AI480742|SLC41A1-L2	solute carrier family 41, member 3	protein-coding
mm_76571.1	chr8	88664280	88664290	-	1	NA	exon (NM_145857, exon 4 of 13)	exon (NM_145857, exon 4 of 13)	16938	NM_145857	257632	Mm.222633	NM_145857	ENSMUSG00000055994	Nod2	ACUG|BLAU|CD|Card15|F830032C23Rik|IBD1|Nlrc2	nucleotide-binding oligomerization domain containing 2	protein-coding
mm_151567.1	chr19	60756369	60756391	+	1	NA	exon (NM_178421, exon 1 of 1)	exon (NM_178421, exon 1 of 1)	393	NM_178421	332397	Mm.186390	NM_178421	ENSMUSG00000072437	Nanos1	NOS-1	nanos homolog 1 (Drosophila)	protein-coding
mm_57601.1	chr6	127796300	127796330	-	1	NA	Intergenic	Intergenic	-8172	NR_106092	102466996		NR_106092	ENSMUSG00000104804	Mir7233	mmu-mir-7233	microRNA 7233	ncRNA
mm_84296.1	chr9	63377815	63377829	-	1	NA	promoter-TSS (NM_011840)	promoter-TSS (NM_011840)	30	NM_011840	23938	Mm.325746	NM_011840	ENSMUSG00000058444	Map2k5	AI324775|AI428457|MEK5|Mapkk5|Prkmk5	mitogen-activated protein kinase kinase 5	protein-coding
mm_28697.1	chr3	95539206	95539225	-	1	NA	intron (NM_001267695, intron 3 of 7)	RLTR26B_MM|LTR|ERVK	12429	NM_001267695	13040	Mm.3619	NM_021281	ENSMUSG00000038642	Ctss	Cats	cathepsin S	protein-coding
mm_41656.1	chr5	98854435	98854466	+	1	NA	promoter-TSS (NM_001310677)	promoter-TSS (NM_001310677)	35	NM_001310677	110075	Mm.136461	NM_173404	ENSMUSG00000029335	Bmp3	9530029I04Rik	bone morphogenetic protein 3	protein-coding
mm_29470.1	chr3	115641511	115641531	-	1	NA	Intergenic	Lx8|LINE|L1	73534	NM_007901	13609	Mm.982	NM_007901	ENSMUSG00000045092	S1pr1	AI849002|Edg1|Lpb1|S1p|S1p1	sphingosine-1-phosphate receptor 1	protein-coding
mm_109985.1	chr12	13456006	13456010	-	1	NA	intron (NM_027706, intron 40 of 51)	intron (NM_027706, intron 40 of 51)	171638	NR_136761	102639399	Mm.122052	NR_136761		Gm35725	-	predicted gene, 35725	ncRNA
mm_40625.1	chr5	64812361	64812378	+	1	NA	intron (NM_008453, intron 1 of 5)	intron (NM_008453, intron 1 of 5)	8846	NM_008453	16599	Mm.392759	NM_008453	ENSMUSG00000029178	Klf3	9930027G08Rik|AL024007|Bklf|Tef-2	Kruppel-like factor 3 (basic)	protein-coding
mm_133177.1	chr16	72358470	72358473	+	1	NA	Intergenic	Lx3_Mus|LINE|L1	-124144	NR_131115	319533	Mm.373754	NR_131115		8030451O07Rik	-	RIKEN cDNA 8030451O07 gene	ncRNA
mm_173190.1	chrX	61345430	61345433	-	1	NA	Intergenic	L1Md_T|LINE|L1	154138	NR_033502	320247	Mm.447372	NR_033502		C030023E24Rik	-	RIKEN cDNA C030023E24 gene	ncRNA
mm_112576.1	chr13	13634940	13634964	+	1	NA	exon (NM_010748, exon 5 of 53)	exon (NM_010748, exon 5 of 53)	44543	NM_010748	17101	Mm.342337	NM_010748	ENSMUSG00000019726	Lyst	D13Sfk13|beige|bg	lysosomal trafficking regulator	protein-coding
mm_90210.1	chr10	120729689	120729695	+	1	NA	Intergenic	MLT1G3|LTR|ERVL-MaLR	-36040	NR_038000	70874	Mm.427286	NR_038000	ENSMUSG00000044544	4921513I03Rik	-	RIKEN cDNA 4921513I03 gene	ncRNA
mm_127250.1	chr15	99670575	99670634	+	1	NA	promoter-TSS (NM_009597)	promoter-TSS (NM_009597)	-114	NM_009597	11419	Mm.440107	NM_009597	ENSMUSG00000023017	Asic1	AI843610|ASIC|ASIC1a|Accn2|B530003N02Rik|BNaC2	acid-sensing (proton-gated) ion channel 1	protein-coding
mm_68491.1	chr7	111074819	111074838	-	1	NA	exon (NM_013507, exon 18 of 22)	exon (NM_013507, exon 18 of 22)	8202	NM_001040131	13690	Mm.185453	NM_013507	ENSMUSG00000005610	Eif4g2	DAP-5|E130105L11Rik|Nat1|Natm1|p97	eukaryotic translation initiation factor 4, gamma 2	protein-coding
mm_56944.1	chr6	119961257	119961261	-	1	NA	intron (NM_001185021, intron 8 of 25)	intron (NM_001185021, intron 8 of 25)	58561	NM_001166381	19365	Mm.149	NM_011236	ENSMUSG00000030166	Rad52	Rad52yh	RAD52 homolog, DNA repair protein	protein-coding
mm_44345.1	chr5	17782764	17782774	-	1	NA	3' UTR (NM_001159558, exon 16 of 16)	3' UTR (NM_001159558, exon 16 of 16)	53127	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_37082.1	chr4	116371770	116371783	-	1	NA	intron (NM_008641, intron 4 of 28)	intron (NM_008641, intron 4 of 28)	92405	NM_001042743	17776	Mm.9287	NM_008641	ENSMUSG00000003810	Mast2	MAST205|Mtssk	microtubule associated serine/threonine kinase 2	protein-coding
mm_138761.1	chr17	37050938	37050950	+	1	NA	intron (NM_019439, intron 5 of 22)	CpG	4978	NM_019439	54393	Mm.32191	NM_019439	ENSMUSG00000024462	Gabbr1	GABAB1|GABAbR1|bM573K1.1	gamma-aminobutyric acid (GABA) B receptor, 1	protein-coding
mm_23626.1	chr3	65974880	65974900	+	1	NA	Intergenic	CpG	-16665	NM_019937	56706	Mm.175612	NM_019937	ENSMUSG00000027829	Ccnl1	2610030E23Rik|AU018493|Ccnl|ania-6a	cyclin L1	protein-coding
mm_107885.1	chr12	70453075	70453080	+	1	NA	promoter-TSS (NM_028339)	promoter-TSS (NM_028339)	-77	NM_028339	72736	Mm.204670	NM_028339	ENSMUSG00000021072	Tmx1	2810425A04Rik|AI465319|Txndc1	thioredoxin-related transmembrane protein 1	protein-coding
mm_148821.1	chr19	6299727	6299748	+	1	NA	3' UTR (NM_010119, exon 5 of 5)	3' UTR (NM_010119, exon 5 of 5)	-6720	NM_001033342	240505	Mm.329622	NM_001033342	ENSMUSG00000024769	Cdc42bpg	BC046418|MRCKgamma	CDC42 binding protein kinase gamma (DMPK-like)	protein-coding
mm_55446.1	chr6	67237903	67237913	-	1	NA	Intergenic	Intergenic	-29071	NM_001113564	66870	Mm.240490	NM_025814	ENSMUSG00000036371	Serbp1	1200009K13Rik|9330147J08Rik|AL022786|Pairbp1	serpine1 mRNA binding protein 1	protein-coding
mm_35084.1	chr4	7455279	7455298	-	1	NA	Intergenic	Intergenic	-105400	NR_040645	71510	Mm.410775	NR_040645	ENSMUSG00000086070	8430436N08Rik	-	RIKEN cDNA 8430436N08 gene	ncRNA
mm_81924.1	chr9	120174890	120174900	+	1	NA	3' UTR (NM_001039364, exon 3 of 3)	3' UTR (NM_001039364, exon 3 of 3)	25153	NM_001039364	17433	Mm.486167	NM_008614	ENSMUSG00000032517	Mobp	AI835053|AI839848|MOBP155|MOBP170|MOBP69|MOBP73|MOBP81|R74645	myelin-associated oligodendrocytic basic protein	protein-coding
mm_63295.1	chr7	126807753	126807783	+	1	NA	Intergenic	Intergenic	-7321	NM_001177308	11674	Mm.275831	NM_007438	ENSMUSG00000030695	Aldoa	Aldo-1|Aldo1	aldolase A, fructose-bisphosphate	protein-coding
mm_129971.1	chr15	85809234	85809245	-	1	NA	exon (NM_001164626, exon 2 of 4)	exon (NM_001164626, exon 2 of 4)	2458	NM_001164626	72355	Mm.33706	NM_197998	ENSMUSG00000064284	Cdpf1	2210021J22Rik	cysteine rich, DPF motif domain containing 1	protein-coding
mm_47209.1	chr5	121009002	121009017	-	1	NA	promoter-TSS (NM_001302345)	promoter-TSS (NM_001302345)	-525	NM_001302345	19894	Mm.181166	NM_011286	ENSMUSG00000029608	Rph3a	2900002P20Rik|AU022689|AW108370	rabphilin 3A	protein-coding
mm_37244.1	chr4	118144480	118144492	-	1	NA	intron (NM_172382, intron 16 of 18)	intron (NM_172382, intron 16 of 18)	-9540	NM_001161774	20441	Mm.251002	NM_009176	ENSMUSG00000028538	St3gal3	ST3GalIII|ST3N|Siat3|Siat6	ST3 beta-galactoside alpha-2,3-sialyltransferase 3	protein-coding
mm_94262.1	chr11	3514862	3514894	+	1	NA	5' UTR (NM_053267, exon 1 of 5)	5' UTR (NM_053267, exon 1 of 5)	194	NM_053267	114679	Mm.34046	NM_053267	ENSMUSG00000075702	Selenom	1500040L08Rik|A230103K18|Selm|Sepm	selenoprotein M	protein-coding
mm_166538.1	chr6	30903575	30903583	+	1	NA	intron (NM_054073, intron 5 of 7)	intron (NM_054073, intron 5 of 7)	-6785	NM_017478	54160	Mm.39896	NM_017478	ENSMUSG00000025607	Copg2	AW227625|gamma-2-COP	coatomer protein complex, subunit gamma 2	protein-coding
mm_49306.1	chr6	17822964	17822988	+	1	NA	intron (NM_001289624, intron 2 of 15)	intron (NM_001289624, intron 2 of 15)	73806	NM_022332	64213	Mm.12051	NM_022332	ENSMUSG00000029534	St7	9430001H04Rik|Fam4a2|HELG|RAY1|SEN4|TSG7	suppression of tumorigenicity 7	protein-coding
mm_128496.1	chr15	51967842	51967862	-	1	NA	exon (NM_009009, exon 11 of 14)	exon (NM_009009, exon 11 of 14)	23908	NM_009009	19357	Mm.182628	NM_009009	ENSMUSG00000022314	Rad21	SCC1|mKIAA0078	RAD21 cohesin complex component	protein-coding
mm_166035.1	chr4	129008095	129008107	+	1	NA	exon (NM_016895, exon 6 of 7)	exon (NM_016895, exon 6 of 7)	14877	NM_001033966	11637	Mm.29460	NM_016895	ENSMUSG00000028792	Ak2	Ak-2|D4Ertd220e	adenylate kinase 2	protein-coding
mm_129461.1	chr15	78573166	78573204	-	1	NA	promoter-TSS (NM_009008)	promoter-TSS (NM_009008)	-402	NM_009008	19354	Mm.1972	NM_009008	ENSMUSG00000033220	Rac2	AI323801|AI452260	RAS-related C3 botulinum substrate 2	protein-coding
mm_163302.1	chr11	120660669	120660684	-	1	NA	intron (NM_175263, intron 1 of 11)	CpG-2953	161	NM_175263	77583	Mm.32839	NM_175263	ENSMUSG00000042988	Notum	5730593N15Rik	notum pectinacetylesterase homolog (Drosophila)	protein-coding
mm_165845.1	chr4	6806994	6807006	-	1	NA	intron (NM_145711, intron 3 of 8)	intron (NM_145711, intron 3 of 8)	183723	NM_145711	252838	Mm.435828	NM_145711	ENSMUSG00000041272	Tox	1700007F02Rik	thymocyte selection-associated high mobility group box	protein-coding
mm_45609.1	chr5	75569912	75569918	-	1	NA	Intergenic	Intergenic	-5072	NM_001122733	16590	Mm.247073	NM_021099	ENSMUSG00000005672	Kit	Bs|CD117|Fdc|Gsfsco1|Gsfsco5|Gsfsow3|SCO1|SCO5|SOW3|Ssm|Tr-kit|W|c-KIT	KIT proto-oncogene receptor tyrosine kinase	protein-coding
mm_154584.1	chrX	7572700	7572723	+	1	NA	promoter-TSS (NR_029473)	promoter-TSS (NR_029473)	-889	NR_029473	78185	Mm.160055	NR_029473	ENSMUSG00000039545	Ppp1r3fos	4930524L23Rik	protein phosphatase 1, regulatory subunit 3F, opposite strand	ncRNA
mm_68245.1	chr7	105481954	105481964	-	1	NA	exon (NM_028444, exon 1 of 2)	exon (NM_028444, exon 1 of 2)	238	NM_028444	109042	Mm.3124	NM_028444	ENSMUSG00000037060	Prkcdbp	3110015B12Rik|6330514M23Rik|SRBC	protein kinase C, delta binding protein	protein-coding
mm_166973.1	chr7	44669278	44669283	-	1	NA	intron (NM_001271540, intron 1 of 41)	CpG	1563	NM_001271540	71960	Mm.158289	NM_028021	ENSMUSG00000030739	Myh14	2400004E04Rik|II-C|NHMCII|NMHC II-C	myosin, heavy polypeptide 14	protein-coding
mm_22580.1	chr3	10367010	10367026	+	1	NA	promoter-TSS (NM_025519)	promoter-TSS (NM_025519)	45	NM_025519	66371	Mm.366147	NM_025519	ENSMUSG00000027536	Chmp4c	2010012P02Rik|2210015K02Rik|2310010I16Rik|Shax3|Snf7-3	charged multivesicular body protein 4C	protein-coding
mm_118331.1	chr13	113769895	113769900	-	1	NA	Intergenic	Intergenic	-24611	NM_172595	218639	Mm.79837	NM_172595	ENSMUSG00000042348	Arl15	A430036I03|Arfrp2|C230032K13Rik	ADP-ribosylation factor-like 15	protein-coding
mm_69571.1	chr7	135700887	135700891	-	1	NA	exon (NM_001081117, exon 12 of 14)	exon (NM_001081117, exon 12 of 14)	15490	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_54545.1	chr6	36810004	36810024	-	1	NA	5' UTR (NM_008973, exon 1 of 5)	5' UTR (NM_008973, exon 1 of 5)	1347	NM_008973	19242	Mm.279690	NM_008973	ENSMUSG00000029838	Ptn	HARP|HB-GAM|HBBN|HBGF-8|HBNF|OSF|Osf-1|Osf1	pleiotrophin	protein-coding
mm_74706.1	chr8	17091099	17091099	-	1	NA	intron (NM_053171, intron 2 of 69)	intron (NM_053171, intron 2 of 69)	444286	NM_053171	94109	Mm.436988	NM_053171	ENSMUSG00000060924	Csmd1	B930082H09|mKIAA1890	CUB and Sushi multiple domains 1	protein-coding
mm_67851.1	chr7	98694192	98694215	-	1	NA	non-coding (NR_144495, exon 1 of 1)	non-coding (NR_144495, exon 1 of 1)	8725	NR_144495	100040769	Mm.126401	NR_144495		Gm15506	OTTMUSG00000023003	predicted gene 15506	ncRNA
mm_22786.1	chr3	22077551	22077554	+	1	NA	intron (NM_030732, intron 1 of 15)	intron (NM_030732, intron 1 of 15)	900	NM_030732	81004	Mm.202966	NM_030732	ENSMUSG00000027630	Tbl1xr1	8030499H02Rik|A630076E03Rik|AW539987|C21|C230089I12Rik|DC42|Ira1|TBLR1	transducin (beta)-like 1X-linked receptor 1	protein-coding
mm_132182.1	chr16	32400822	32400834	+	1	NA	5' UTR (NM_001160402, exon 1 of 5)	5' UTR (NM_001160402, exon 1 of 5)	322	NM_001160402	277203	Mm.484240	NM_001160402	ENSMUSG00000079625	Tm4sf19	EG277203	transmembrane 4 L six family member 19	protein-coding
mm_155748.1	chrX	96167153	96167163	+	1	NA	3' UTR (NM_010833, exon 13 of 13)	3' UTR (NM_010833, exon 13 of 13)	71113	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_107732.1	chr12	57513029	57513041	+	1	NA	Intergenic	Intergenic	33086	NM_008259	15375	Mm.4578	NM_008259	ENSMUSG00000035451	Foxa1	Hnf-3a|Hnf3a|Tcf-3a|Tcf3a	forkhead box A1	protein-coding
mm_146549.1	chr18	6216900	6216931	-	1	NA	exon (NM_008448, exon 14 of 26)	exon (NM_008448, exon 14 of 26)	24609	NM_008448	16573	Mm.223744	NM_008448	ENSMUSG00000006740	Kif5b	AL022807|Khc|Khcs|Kns1|Ukhc	kinesin family member 5B	protein-coding
mm_138576.1	chr17	35428104	35428115	+	1	NA	exon (NM_207648, exon 4 of 5)	exon (NM_207648, exon 4 of 5)	3232	NM_207648	110557	Mm.439827	NM_207648	ENSMUSG00000073409	H2-Q6	0610037M15Rik|H-2Q6|Qa-6|Qa6	histocompatibility 2, Q region locus 6	protein-coding
mm_132199.1	chr16	32550236	32550269	+	1	NA	Intergenic	Intergenic	53971	NM_199309	245308	Mm.76859	NM_199309	ENSMUSG00000052363	Zdhhc19	Gm1744|Gm616	zinc finger, DHHC domain containing 19	protein-coding
mm_108685.1	chr12	86834138	86834173	+	1	NA	Intergenic	Intergenic	50659	NM_145836	238330	Mm.248358	NM_145836	ENSMUSG00000034168	Irf2bpl	6430527G18Rik|Eap1	interferon regulatory factor 2 binding protein-like	protein-coding
mm_159812.1	chr5	120648799	120648799	+	1	NA	promoter-TSS (NM_001281999)	promoter-TSS (NM_001281999)	-13	NM_013832	19415	Mm.41209	NM_013832	ENSMUSG00000029602	Rasal1	MRASAL	RAS protein activator like 1 (GAP1 like)	protein-coding
mm_99468.1	chr11	102435881	102435895	+	1	NA	exon (NM_008175, exon 11 of 13)	exon (NM_008175, exon 11 of 13)	5566	NM_008175	14824	Mm.1568	NM_008175	ENSMUSG00000034708	Grn	Pgrn|epithelin	granulin	protein-coding
mm_153197.1	chr19	34526277	34526293	-	1	NA	intron (NM_021460, intron 1 of 9)	intron (NM_021460, intron 1 of 9)	1189	NM_001111100	16889	Mm.157545	NM_021460	ENSMUSG00000024781	Lipa	AA960673|Lal|Lip-1|Lip1	lysosomal acid lipase A	protein-coding
mm_137578.1	chr17	27909338	27909409	+	1	NA	promoter-TSS (NM_001286041)	promoter-TSS (NM_001286041)	67	NM_181413	224650	Mm.32556	NM_181413	ENSMUSG00000024219	Anks1	Anks1a|mKIAA0229	ankyrin repeat and SAM domain containing 1	protein-coding
mm_143672.1	chr17	79973274	79973287	-	1	NA	Intergenic	B4|SINE|B4	-77157	NM_001286647	56298	Mm.175403	NM_019717	ENSMUSG00000059811	Atl2	2010110I21Rik|AA407293|AV334690|Aip-2|Arl6ip2	atlastin GTPase 2	protein-coding
mm_5477.1	chr1	36683116	36683154	-	1	NA	promoter-TSS (NM_201365)	promoter-TSS (NM_201365)	48	NM_001126046	381337	Mm.17413	NM_027957	ENSMUSG00000046337	Fam178b	1700024G10Rik|Gm990	family with sequence similarity 178, member B	protein-coding
mm_39648.1	chr5	24645502	24645506	+	1	NA	promoter-TSS (NR_003953)	promoter-TSS (NR_003953)	51	NR_003953	72252	Mm.87446	NR_003953	ENSMUSG00000038165	1700022A21Rik	-	glycerol-3-phosphate dehydrogenase 1-like pseudogene	pseudo
mm_114329.1	chr13	60641000	60641008	+	1	NA	intron (NM_029653, intron 2 of 25)	(T)n|Simple_repeat|Simple_repeat	38793	NM_134062	69635	Mm.24103	NM_029653	ENSMUSG00000021559	Dapk1	D13Ucla1|DAP-Kinase	death associated protein kinase 1	protein-coding
mm_51962.1	chr6	91758043	91758061	+	1	NA	3' UTR (NM_009320, exon 15 of 15)	3' UTR (NM_009320, exon 15 of 15)	49341	NM_001159507	243547	Mm.333264	NM_001033353	ENSMUSG00000030098	Grip2	-	glutamate receptor interacting protein 2	protein-coding
mm_914.1	chr1	55027598	55027600	+	1	NA	promoter-TSS (NM_031179)	promoter-TSS (NM_031179)	-121	NM_031179	81898	Mm.279736	NM_031179	ENSMUSG00000025982	Sf3b1	155kDa|2810001M05Rik|AA409119|Prp10|SAP155|SF3b155|TA-8|Targ4	splicing factor 3b, subunit 1	protein-coding
mm_30155.1	chr3	142853696	142853719	-	1	NA	exon (NM_178654, exon 2 of 22)	exon (NM_178654, exon 2 of 22)	28297	NM_178654	109333	Mm.244236	NM_178654	ENSMUSG00000004591	Pkn2	6030436C20Rik|AI507382|PRK2|Prkcl2|Stk7	protein kinase N2	protein-coding
mm_41055.1	chr5	86804305	86804319	+	1	NA	promoter-TSS (NM_177680)	promoter-TSS (NM_177680)	46	NM_001347376	231386	Mm.196325	NM_177680	ENSMUSG00000035851	Ythdc1	A730098D12Rik|C80342|mKIAA1966	YTH domain containing 1	protein-coding
mm_24939.1	chr3	96561332	96561347	+	1	NA	3' UTR (NM_023719, exon 8 of 8)	3' UTR (NM_023719, exon 8 of 8)	3382	NM_023719	56338	Mm.410189	NM_023719	ENSMUSG00000038393	Txnip	1200008J08Rik|AA682105|Hyplip1|THIF|Tbp-2|VDUP1	thioredoxin interacting protein	protein-coding
mm_22042.1	chr2	168207264	168207302	-	1	NA	promoter-TSS (NM_009628)	promoter-TSS (NM_009628)	-171	NM_001310088	11538	Mm.201322	NM_009628	ENSMUSG00000051149	Adnp	AA589558|mKIAA0784	activity-dependent neuroprotective protein	protein-coding
mm_62098.1	chr7	96210278	96210288	+	1	NA	promoter-TSS (NM_011858)	promoter-TSS (NM_011858)	-354	NM_011858	23966	Mm.254610	NM_011858	ENSMUSG00000048078	Tenm4	Doc4|ELM2|Odz4|R75022|Ten-m4|l(7)-3Rn|l7Rn3|mKIAA1302	teneurin transmembrane protein 4	protein-coding
mm_26853.1	chr3	14802604	14802637	-	1	NA	intron (NM_009799, intron 1 of 7)	intron (NM_009799, intron 1 of 7)	5745	NM_009799	12346	Mm.273195	NM_009799	ENSMUSG00000027556	Car1	AW555628|Ca1|Car-1	carbonic anhydrase 1	protein-coding
mm_7163.1	chr1	91984656	91984663	-	1	NA	intron (NM_207225, intron 10 of 26)	intron (NM_207225, intron 10 of 26)	183198	NM_007855	13345	Mm.9474	NM_007855	ENSMUSG00000007805	Twist2	Dermo1|bHLHa39	twist basic helix-loop-helix transcription factor 2	protein-coding
mm_60124.1	chr7	36698213	36698244	+	1	NA	5' UTR (NM_172298, exon 1 of 2)	5' UTR (NM_172298, exon 1 of 2)	110	NM_172298	243931	Mm.44141	NM_172298	ENSMUSG00000021217	Tshz3	A630038G13Rik|Tsh3|Zfp537|mKIAA1474|teashirt3	teashirt zinc finger family member 3	protein-coding
mm_72600.1	chr8	84415349	84415392	+	1	NA	promoter-TSS (NM_001252060)	promoter-TSS (NM_001252060)	6	NM_001252061	12286	Mm.334658	NM_007578	ENSMUSG00000034656	Cacna1a	APCA|BI|Caca1a|Cacnl1a4|Cav2.1|Ccha1a|EA2|FHM|HPCA|MHP|MHP1|SCA6|alpha1A|la|nmf352|rkr|smrl|tg	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	protein-coding
mm_106116.1	chr11	116359061	116359103	-	1	NA	intron (NM_027258, intron 6 of 18)	intron (NM_027258, intron 6 of 18)	-23728	NM_008240	15223	Mm.378938	NM_008240	ENSMUSG00000034227	Foxj1	FKHL-13|HFH-4|Hfh4	forkhead box J1	protein-coding
mm_5503.1	chr1	37418897	37418911	-	1	NA	3' UTR (NM_198006, exon 3 of 3)	3' UTR (NM_198006, exon 3 of 3)	11199	NM_198006	76178	Mm.28085	NM_198006	ENSMUSG00000026112	Coa5	1700001A24Rik|6330578E17Rik|Pet191	cytochrome C oxidase assembly factor 5	protein-coding
mm_85907.1	chr9	111056585	111056607	-	1	NA	intron (NM_001302377, intron 2 of 2)	intron (NM_001302377, intron 2 of 2)	648	NM_001302377	54199	Mm.7336	NM_017466	ENSMUSG00000043953	Ccrl2	1810047I05Rik|Ackr5|CCR11|Cmkbr1l2|E01|L-CCR	chemokine (C-C motif) receptor-like 2	protein-coding
mm_59440.1	chr7	27132524	27132554	+	1	NA	exon (NM_007817, exon 9 of 10)	exon (NM_007817, exon 9 of 10)	12584	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_79901.1	chr9	65371696	65371708	+	1	NA	exon (NM_001111145, exon 3 of 7)	exon (NM_001111145, exon 3 of 7)	10642	NM_001111145	208080	Mm.291862	NM_001111145	ENSMUSG00000086228	Ubap1l	Gm514	ubiquitin-associated protein 1-like	protein-coding
mm_172467.1	chr7	43177554	43177570	+	1	NA	promoter-TSS (NM_001034893)	promoter-TSS (NM_001034893)	-26	NM_001034893	668620	Mm.388871	NM_001034893	ENSMUSG00000064194	Zfp936	EG435970|EG668620|Gm9272|I1C0022H11Rik	zinc finger protein 936	protein-coding
mm_36047.1	chr4	57300305	57300317	-	1	NA	intron (NM_011207, intron 1 of 25)	CpG	1526	NM_011207	545622	Mm.246552	NM_011207	ENSMUSG00000038764	Ptpn3	9530011I20Rik|PTP-H1|PTPCL	protein tyrosine phosphatase, non-receptor type 3	protein-coding
mm_24316.1	chr3	89429590	89429612	+	1	NA	promoter-TSS (NM_001293768)	promoter-TSS (NM_001293768)	-613	NM_001293768	68911	Mm.22521	NM_026869	ENSMUSG00000047824	Pygo2	1190004M21Rik	pygopus 2	protein-coding
mm_113163.1	chr13	24804910	24804929	+	1	NA	exon (NM_024473, exon 2 of 5)	exon (NM_024473, exon 2 of 5)	3262	NM_024473	79555	Mm.266668	NM_024473	ENSMUSG00000019132	BC005537	8030460C05Rik|C78201	cDNA sequence BC005537	protein-coding
mm_168473.1	chr11	48753646	48753646	-	1	NA	Intergenic	Intergenic	-46714	NM_008143	14694	Mm.5305	NM_008143	ENSMUSG00000020372	Rack1	AL033335|GB-like|Gnb2-rs1|Gnb2l1|p205	receptor for activated C kinase 1	protein-coding
mm_6736.1	chr1	82994742	82994744	-	1	NA	Intergenic	Intergenic	43705	NM_030556	80721	Mm.261542	NM_030556	ENSMUSG00000038496	Slc19a3	A230084E24Rik|AI788884|ThTr2	solute carrier family 19, member 3	protein-coding
mm_2072.1	chr1	87637126	87637130	+	1	NA	intron (NM_010566, intron 2 of 26)	intron (NM_010566, intron 2 of 26)	16816	NM_001110193	16331	Mm.15105	NM_010566	ENSMUSG00000026288	Inpp5d	SHIP|SHIP-1|SHIP1|SIP-145|p150Ship|s-SHIP	inositol polyphosphate-5-phosphatase D	protein-coding
mm_73482.1	chr8	107031115	107031126	+	1	NA	promoter-TSS (NM_126165)	promoter-TSS (NM_126165)	-206	NM_126165	116733	Mm.236004	NM_126165	ENSMUSG00000031913	Vps4a	4930589C15Rik|AI325971|AW553189	vacuolar protein sorting 4A	protein-coding
mm_125905.1	chr15	75993726	75993734	+	1	NA	promoter-TSS (NM_177922)	promoter-TSS (NM_177922)	-39	NM_177922	332110	Mm.40843	NM_177922	ENSMUSG00000063704	Mapk15	BC048082	mitogen-activated protein kinase 15	protein-coding
mm_33250.1	chr4	127168292	127168304	+	1	NA	promoter-TSS (NM_198618)	promoter-TSS (NM_198618)	-906	NM_198618	242667	Mm.331885	NM_198618	ENSMUSG00000042388	Dlgap3	BC058433|DAP-3|DAP3|Prpl8|Sapap3	discs, large (Drosophila) homolog-associated protein 3	protein-coding
mm_3128.1	chr1	134962554	134962568	+	1	NA	promoter-TSS (NM_026024)	promoter-TSS (NM_026024)	-4	NM_026024	67196	Mm.284587	NM_026024	ENSMUSG00000026429	Ube2t	2700084L22Rik|C80607	ubiquitin-conjugating enzyme E2T	protein-coding
mm_130993.1	chr15	103429548	103429565	-	1	NA	intron (NM_028797, intron 1 of 8)	intron (NM_028797, intron 1 of 8)	871	NM_028797	74174	Mm.325325	NM_028797	ENSMUSG00000022487	Gtsf1	1700006H03Rik|Cue110	gametocyte specific factor 1	protein-coding
mm_120346.1	chr14	63814646	63814646	+	1	NA	intron (NM_173393, intron 2 of 2)	intron (NM_173393, intron 2 of 2)	-45666	NM_028228	72400	Mm.379214	NM_028228	ENSMUSG00000021958	Pinx1	2210403I16Rik|2610028A01Rik|67-11-3|AU024023|LPTS|LPTS1	PIN2/TERF1 interacting, telomerase inhibitor 1	protein-coding
mm_64108.1	chr7	141060963	141061046	+	1	NA	promoter-TSS (NM_177897)	promoter-TSS (NM_177897)	-270	NM_177897	330671	Mm.133741	NM_177897	ENSMUSG00000055629	B4galnt4	BC038881|Gm1095|beta4GalNAcT4	beta-1,4-N-acetyl-galactosaminyl transferase 4	protein-coding
mm_123613.1	chr14	68120542	68120555	-	1	NA	exon (NM_008691, exon 3 of 3)	exon (NM_008691, exon 3 of 3)	-3204	NR_045897	100043072	Mm.242832	NR_045897		A230070E04Rik	Gm4210	RIKEN cDNA A230070E04 gene	ncRNA
mm_1078.1	chr1	59482665	59482702	+	1	NA	5' UTR (NM_008057, exon 1 of 1)	5' UTR (NM_008057, exon 1 of 1)	536	NM_008057	14369	Mm.297906	NM_008057	ENSMUSG00000041075	Fzd7	Fz7	frizzled class receptor 7	protein-coding
mm_82138.1	chr9	123766962	123766971	+	1	NA	promoter-TSS (NM_001166625)	promoter-TSS (NM_001166625)	-245	NM_009913	12769	Mm.440604	NM_009913	ENSMUSG00000029530	Ccr9	A130091K22Rik|Cmkbr10|GPR-9-6	chemokine (C-C motif) receptor 9	protein-coding
mm_84831.1	chr9	78209255	78209334	-	1	NA	TTS (NM_010357)	TTS (NM_010357)	17328	NM_010357	14860	Mm.2662	NM_010357	ENSMUSG00000032348	Gsta4	GST5.7|mGsta4	glutathione S-transferase, alpha 4	protein-coding
mm_59096.1	chr7	19696921	19696931	+	1	NA	exon (NM_009696, exon 4 of 4)	exon (NM_009696, exon 4 of 4)	1472	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_25767.1	chr3	125680980	125681033	+	1	NA	intron (NM_022565, intron 6 of 13)	RMER2|LTR|ERV1	257544	NM_011674	22239	Mm.306021	NM_011674	ENSMUSG00000032854	Ugt8a	AI850488|AW455908|Cgt|Ugt8|mCerGT	UDP galactosyltransferase 8A	protein-coding
mm_145895.1	chr18	65588112	65588128	+	1	NA	intron (NM_207255, intron 2 of 5)	intron (NM_207255, intron 2 of 5)	7890	NM_207255	328977	Mm.286232	NM_207255	ENSMUSG00000042439	Zfp532	C530030I18Rik|Znf532|mKIAA1629	zinc finger protein 532	protein-coding
mm_74132.1	chr8	123206540	123206540	+	1	NA	intron (NM_145606, intron 5 of 6)	CpG	6248	NM_145606	234852	Mm.41596	NM_145606	ENSMUSG00000000743	Chmp1a	2900018H07Rik|Pcoln3	charged multivesicular body protein 1A	protein-coding
mm_103924.1	chr11	83640193	83640203	-	1	NA	Intergenic	Intergenic	9180	NM_011337	20302	Mm.1282	NM_011337	ENSMUSG00000000982	Ccl3	AI323804|G0S19-1|LD78alpha|MIP-1alpha|MIP1-(a)|MIP1-alpha|Mip1a|Scya3	chemokine (C-C motif) ligand 3	protein-coding
mm_102387.1	chr11	58933257	58933295	-	1	NA	3' UTR (NM_022423, exon 4 of 4)	3' UTR (NM_022423, exon 4 of 4)	5630	NM_022423	108660	Mm.249986	NM_022423	ENSMUSG00000020496	Rnf187	2410016F01Rik|AB030190|RACO-1	ring finger protein 187	protein-coding
mm_37626.1	chr4	127330776	127330786	-	1	NA	promoter-TSS (NM_001160012)	promoter-TSS (NM_001160012)	55	NM_001160012	14620	Mm.90003	NM_008126	ENSMUSG00000042367	Gjb3	Cnx31|Cx31|D4Wsu144e|Gjb-3	gap junction protein, beta 3	protein-coding
mm_72105.1	chr8	71611103	71611157	+	1	NA	5' UTR (NM_146211, exon 1 of 12)	5' UTR (NM_146211, exon 1 of 12)	106	NM_146211	234407	Mm.240885	NM_146211	ENSMUSG00000034807	Colgalt1	2810024B22Rik|Glt25d1	collagen beta(1-O)galactosyltransferase 1	protein-coding
mm_18808.1	chr2	73911324	73911328	-	1	NA	promoter-TSS (NM_175015)	promoter-TSS (NM_175015)	0	NM_175015	228033	Mm.2966	NM_175015	ENSMUSG00000018770	Atp5g3	6030447M23	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit C3 (subunit 9)	protein-coding
mm_158366.1	chrX	134964743	134964767	-	1	NA	promoter-TSS (NM_031259)	promoter-TSS (NM_031259)	-1	NM_031259	83454	Mm.103155	NM_031259	ENSMUSG00000009941	Nxf2	4930455N06Rik|Nxf-b	nuclear RNA export factor 2	protein-coding
mm_42616.1	chr5	118027820	118027836	+	1	NA	promoter-TSS (NM_021344)	promoter-TSS (NM_021344)	4	NM_021344	57816	Mm.273285	NM_021344	ENSMUSG00000029359	Tesc	1010001A17Rik|2410011K10Rik|TE-1	tescalcin	protein-coding
mm_125726.1	chr15	73153499	73153526	+	1	NA	intron (NM_153178, intron 1 of 18)	B4A|SINE|B4	31435	NM_153178	239528	Mm.23095	NM_153178	ENSMUSG00000036698	Ago2	1110029L17Rik|2310051F07Rik|AI225898|AL022874|AW546247|ENSMUSG00000072493|Eif2c2|Gerp95|Gm10365|mKIAA4215	argonaute RISC catalytic subunit 2	protein-coding
mm_114599.1	chr13	75769571	75769626	+	1	NA	exon (NM_138953, exon 10 of 12)	exon (NM_138953, exon 10 of 12)	62114	NM_138953	192657	Mm.21288	NM_138953	ENSMUSG00000001542	Ell2	-	elongation factor RNA polymerase II 2	protein-coding
mm_13593.1	chr2	112507102	112507112	+	1	NA	intron (NM_028844, intron 1 of 5)	intron (NM_028844, intron 1 of 5)	14143	NM_028844	74268	Mm.315125	NM_028844	ENSMUSG00000003604	Aven	1700013A01Rik|1700056A21Rik|mAven-L|mAven-S	apoptosis, caspase activation inhibitor	protein-coding
mm_134881.1	chr16	28930574	28930596	-	1	NA	promoter-TSS (NM_177718)	promoter-TSS (NM_177718)	-887	NM_177718	239796	Mm.155887	NM_177718	ENSMUSG00000051065	Mb21d2	1600021P15Rik|A430031N04|C87006	Mab-21 domain containing 2	protein-coding
mm_113864.1	chr13	48261195	48261199	+	1	NA	promoter-TSS (NM_031166)	promoter-TSS (NM_031166)	-230	NM_031166	15904	Mm.458006	NM_031166	ENSMUSG00000021379	Id4	Idb4|bHLHb27	inhibitor of DNA binding 4	protein-coding
mm_87832.1	chr10	60369681	60369696	+	1	NA	3' UTR (NM_001159572, exon 7 of 7)	3' UTR (NM_001159572, exon 7 of 7)	22837	NM_028732	74048	Mm.273584	NM_028732	ENSMUSG00000020101	Vsir	4632428N05Rik|Dies1|PD-1H|VISTA	V-set immunoregulatory receptor	protein-coding
mm_99822.1	chr11	108747705	108747706	+	1	NA	intron (NM_029586, intron 1 of 4)	MLT1B|LTR|ERVL-MaLR	65087	NM_029586	76380	Mm.344071	NM_029586	ENSMUSG00000020728	Cep112	1700001M19Rik|1700029K01Rik|8430407H02Rik|AV043680|AV207351|Ccdc46|Macoco	centrosomal protein 112	protein-coding
mm_74588.1	chr8	11470352	11470354	-	1	NA	intron (NM_011227, intron 1 of 1)	RLTR40|LTR|ERVK	-7576	NR_126558	102132	Mm.37632	NR_126558	ENSMUSG00000096957	E230013L22Rik	AI645545	RIKEN cDNA E230013L22 gene	ncRNA
mm_55932.1	chr6	84588632	84588645	-	1	NA	intron (NM_175475, intron 1 of 6)	G-rich|Low_complexity|Low_complexity	5172	NM_175475	232174	Mm.255246	NM_175475	ENSMUSG00000063415	Cyp26b1	CP26|P450RAI-2	cytochrome P450, family 26, subfamily b, polypeptide 1	protein-coding
mm_44590.1	chr5	24995677	24995681	-	1	NA	promoter-TSS (NM_001310480)	promoter-TSS (NM_001310480)	74	NM_001310480	108099	Mm.33649	NM_145401	ENSMUSG00000028944	Prkag2	2410051C13Rik|AAKG|AAKG2|AI854673|H91620p|WPWS	protein kinase, AMP-activated, gamma 2 non-catalytic subunit	protein-coding
mm_114252.1	chr13	56702984	56703112	+	1	NA	promoter-TSS (NM_008541)	promoter-TSS (NM_008541)	-4	NM_001164041	17129	Mm.272920	NM_008541	ENSMUSG00000021540	Smad5	1110051M15Rik|AI451355|Dwf-C|Madh5|MusMLP	SMAD family member 5	protein-coding
mm_96953.1	chr11	70606657	70606670	+	1	NA	intron (NM_016713, intron 13 of 30)	intron (NM_016713, intron 13 of 30)	-9231	NM_001145537	668433	Mm.425687	NM_001145537	ENSMUSG00000087279	4930544D05Rik	-	RIKEN cDNA 4930544D05 gene	protein-coding
mm_137811.1	chr17	30005780	30005793	+	1	NA	intron (NM_148926, intron 1 of 4)	intron (NM_148926, intron 1 of 4)	699	NM_148926	21769	Mm.220972	NM_148926	ENSMUSG00000044477	Zfand3	AW539211|TEG-27|Tex27	zinc finger, AN1-type domain 3	protein-coding
mm_12453.1	chr2	71211999	71212012	+	1	NA	promoter-TSS (NM_001198877)	promoter-TSS (NM_001198877)	59	NM_010064	13427	Mm.249479	NM_010064	ENSMUSG00000027012	Dync1i2	3110079H08Rik|AW554389|Dncic2	dynein cytoplasmic 1 intermediate chain 2	protein-coding
mm_30923.1	chr4	32733114	32733118	+	1	NA	intron (NM_001081392, intron 60 of 101)	intron (NM_001081392, intron 60 of 101)	-67143	NM_175364	108755	Mm.1182	NM_175364	ENSMUSG00000045854	Lyrm2	2610208E05Rik	LYR motif containing 2	protein-coding
mm_90310.1	chr10	126998938	126998952	+	1	NA	TTS (NR_030259)	TTS (NR_030259)	505	NR_030259	723882		NR_030259	ENSMUSG00000072837	Mir546	Mirn546|mmu-mir-546	microRNA 546	ncRNA
mm_112911.1	chr13	20917660	20917676	+	1	NA	intron (NM_012054, intron 11 of 20)	(T)n|Simple_repeat|Simple_repeat	123555	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_143192.1	chr17	62604957	62604958	-	1	NA	3' UTR (NM_207654, exon 5 of 5)	3' UTR (NM_207654, exon 5 of 5)	276360	NM_207654	13640	Mm.7978	NM_010109	ENSMUSG00000048915	Efna5	AL-1|AV158822|EFL-5|Ephrin-A5|Epl7|LERK-7|RAGS	ephrin A5	protein-coding
mm_21598.1	chr2	164237848	164237852	-	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	491	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_16687.1	chr2	6884608	6884634	-	1	NA	intron (NM_001110229, intron 2 of 14)	intron (NM_001110229, intron 2 of 14)	375	NM_010160	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_160186.1	chr7	48643871	48643871	-	1	NA	promoter-TSS (NM_207537)	promoter-TSS (NM_207537)	-70	NM_207537	404238	Mm.377926	NM_207537	ENSMUSG00000070546	Mrgprb3	MrgB3	MAS-related GPR, member B3	protein-coding
mm_35884.1	chr4	49540880	49540901	-	1	NA	intron (NM_144903, intron 5 of 8)	intron (NM_144903, intron 5 of 8)	8656	NM_144903	230163	Mm.482116	NM_144903	ENSMUSG00000028307	Aldob	Aldo-2|Aldo2|BC016435	aldolase B, fructose-bisphosphate	protein-coding
mm_90222.1	chr10	121034169	121034197	+	1	NA	5' UTR (NM_011915, exon 1 of 10)	5' UTR (NM_011915, exon 1 of 10)	179	NM_011915	24117	Mm.32831	NM_011915	ENSMUSG00000020218	Wif1	AW107799|WIF-1	Wnt inhibitory factor 1	protein-coding
mm_153114.1	chr19	33012821	33012854	-	1	NA	Intergenic	Intergenic	255260	NM_008960	19211	Mm.245395	NM_008960	ENSMUSG00000013663	Pten	2310035O07Rik|A130070J02Rik|AI463227|B430203M17Rik|MMAC1|TEP1	phosphatase and tensin homolog	protein-coding
mm_28128.1	chr3	86999348	86999372	-	1	NA	promoter-TSS (NM_007639)	promoter-TSS (NM_007639)	-20	NM_007639	12479	Mm.1894	NM_007639	ENSMUSG00000028076	Cd1d1	AI747460|CD1.1|Cd1a|Cd1d|Ly-38	CD1d1 antigen	protein-coding
mm_129267.1	chr15	76906305	76906315	-	1	NA	TTS (NM_012053)	TTS (NM_012053)	2239	NM_012053	26961	Mm.30066	NM_012053	ENSMUSG00000003970	Rpl8	-	ribosomal protein L8	protein-coding
mm_13163.1	chr2	92608324	92608333	+	1	NA	intron (NM_023850, intron 1 of 2)	intron (NM_023850, intron 1 of 2)	8621	NM_023850	76969	Mm.38021	NM_023850	ENSMUSG00000027221	Chst1	2610008E20Rik|AW125896|C6ST|GST-1|Gst1|KSGAL6ST	carbohydrate (keratan sulfate Gal-6) sulfotransferase 1	protein-coding
mm_17331.1	chr2	26516380	26516383	-	1	NA	Intergenic	Intergenic	12454	NR_132655	102639736		NR_132655		Gm35978	-	predicted gene, 35978	ncRNA
mm_128445.1	chr15	50763358	50763368	-	1	NA	intron (NM_001310481, intron 4 of 5)	intron (NM_001310481, intron 4 of 5)	125686	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_106315.1	chr11	118302926	118302939	-	1	NA	3' UTR (NM_011594, exon 5 of 5)	3' UTR (NM_011594, exon 5 of 5)	-12688	NM_001033528	72344	Mm.232293	NM_001033528	ENSMUSG00000033909	Usp36	2700002L06Rik|mKIAA1453	ubiquitin specific peptidase 36	protein-coding
mm_130851.1	chr15	101954250	101954265	-	1	NA	promoter-TSS (NM_212487)	promoter-TSS (NM_212487)	30	NM_212487	332131	Mm.325105	NM_212487	ENSMUSG00000050463	Krt78	2310030B04Rik|Kb40	keratin 78	protein-coding
mm_173071.1	chrX	136068143	136068161	-	1	NA	promoter-TSS (NM_009749)	promoter-TSS (NM_009749)	84	NM_009749	12069	Mm.94160	NM_009749	ENSMUSG00000042750	Bex2	AL024066|Bex1	brain expressed X-linked 2	protein-coding
mm_89283.1	chr10	87865021	87865037	+	1	NA	intron (NM_001314010, intron 3 of 4)	intron (NM_001314010, intron 3 of 4)	3918	NM_001111276	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_60282.1	chr7	43970055	43970080	+	1	NA	intron (NM_010645, intron 2 of 4)	intron (NM_010645, intron 2 of 4)	3316	NM_010645	16623	Mm.447819	NM_010645	ENSMUSG00000063133	Klk1b1	Klk1|mGK-1|mK1	kallikrein 1-related peptidase b1	protein-coding
mm_22980.1	chr3	32817643	32817661	+	1	NA	promoter-TSS (NM_001013024)	promoter-TSS (NM_001013024)	26	NM_001013024	72607	Mm.316153	NM_001013024	ENSMUSG00000056900	Usp13	2700071E21Rik|AI848077|ISOT3|IsoT-3	ubiquitin specific peptidase 13 (isopeptidase T-3)	protein-coding
mm_27082.1	chr3	30013137	30013149	-	1	NA	promoter-TSS (NM_007963)	promoter-TSS (NM_007963)	61	NM_007963	14013	Mm.56965	NM_007963	ENSMUSG00000027684	Mecom	D630039M04Rik|Evi-1|Evi1|Jbo|Mds|Mds1|Mds1-Evi1|Prdm3|Znfpr1b1	MDS1 and EVI1 complex locus	protein-coding
mm_73602.1	chr8	109998950	109998958	+	1	NA	3' UTR (NM_146214, exon 12 of 12)	3' UTR (NM_146214, exon 12 of 12)	8518	NM_146214	234724	Mm.28110	NM_146214	ENSMUSG00000001670	Tat	-	tyrosine aminotransferase	protein-coding
mm_161857.1	chr18	20896011	20896011	-	1	NA	promoter-TSS (NM_029491)	promoter-TSS (NM_029491)	67	NM_177038	75964	Mm.273769	NM_029491	ENSMUSG00000033382	Trappc8	5033403J15Rik|AI845423|D030074E01Rik|Trs85|mKIAA1012	trafficking protein particle complex 8	protein-coding
mm_14678.1	chr2	139601219	139601221	+	1	NA	intron (NM_175467, intron 10 of 12)	L1MA5|LINE|L1	-76958	NM_001276489	319909	Mm.41113	NM_001126490	ENSMUSG00000074766	Ism1	5430433G21Rik|Ism	isthmin 1, angiogenesis inhibitor	protein-coding
mm_126170.1	chr15	78561199	78561227	+	1	NA	3' UTR (NM_009008, exon 7 of 7)	3' UTR (NM_009008, exon 7 of 7)	11570	NM_009008	19354	Mm.1972	NM_009008	ENSMUSG00000033220	Rac2	AI323801|AI452260	RAS-related C3 botulinum substrate 2	protein-coding
mm_103825.1	chr11	83012416	83012426	-	1	NA	intron (NM_181545, intron 4 of 5)	intron (NM_181545, intron 4 of 5)	8301	NM_001167743	276950	Mm.491599	NM_181545	ENSMUSG00000035208	Slfn8	-	schlafen 8	protein-coding
mm_12456.1	chr2	71260844	71260856	+	1	NA	exon (NM_001198877, exon 18 of 19)	exon (NM_001198877, exon 18 of 19)	48904	NM_010064	13427	Mm.249479	NM_010064	ENSMUSG00000027012	Dync1i2	3110079H08Rik|AW554389|Dncic2	dynein cytoplasmic 1 intermediate chain 2	protein-coding
mm_85886.1	chr9	111053654	111053674	-	1	NA	Intergenic	RSINE1|SINE|B4	3580	NM_001302377	54199	Mm.7336	NM_017466	ENSMUSG00000043953	Ccrl2	1810047I05Rik|Ackr5|CCR11|Cmkbr1l2|E01|L-CCR	chemokine (C-C motif) receptor-like 2	protein-coding
mm_67466.1	chr7	80406340	80406353	-	1	NA	promoter-TSS (NM_001081454)	promoter-TSS (NM_001081454)	-910	NM_001081454	18550	Mm.5241	NM_011046	ENSMUSG00000030530	Furin	9130404I01Rik|Fur|PACE|Pcsk3|SPC1	furin (paired basic amino acid cleaving enzyme)	protein-coding
mm_20826.1	chr2	146261369	146261387	-	1	NA	intron (NR_040619, intron 2 of 3)	intron (NR_040619, intron 2 of 3)	2092	NR_040619	77806	Mm.392819	NR_040619	ENSMUSG00000085958	A930019D19Rik	-	RIKEN cDNA A930019D19 gene	ncRNA
mm_123710.1	chr14	69805631	69805668	-	1	NA	promoter-TSS (NM_153514)	promoter-TSS (NM_153514)	-104	NM_153514	246710	Mm.102367	NM_153514	ENSMUSG00000022075	Rhobtb2	Dbc2|E130206H14Rik|mKIAA0717	Rho-related BTB domain containing 2	protein-coding
mm_78087.1	chr9	17987791	17987813	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-304465	NM_025844	66917	Mm.103534	NM_025844	ENSMUSG00000001774	Chordc1	1110001O09Rik|AA409036|Chp-1|morgana	cysteine and histidine-rich domain (CHORD)-containing, zinc-binding protein 1	protein-coding
mm_132597.1	chr16	38458928	38458980	+	1	NA	promoter-TSS (NM_009855)	promoter-TSS (NM_009855)	21	NM_009855	12519	Mm.89474	NM_009855	ENSMUSG00000075122	Cd80	B71|Cd28l|Ly-53|Ly53|MIC17|TSA1	CD80 antigen	protein-coding
mm_106379.1	chr11	118491234	118491246	-	1	NA	exon (NM_001285438, exon 14 of 14)	exon (NM_001285438, exon 14 of 14)	14280	NM_172573	217364	Mm.473963	NM_172573	ENSMUSG00000033857	Engase	C130099A03|D230014K01Rik	endo-beta-N-acetylglucosaminidase	protein-coding
mm_128114.1	chr15	28025983	28026001	-	1	NA	promoter-TSS (NM_001081302)	promoter-TSS (NM_001081302)	-144	NM_001081302	223435	Mm.485422	NM_001081302	ENSMUSG00000022263	Trio	6720464I07Rik|AA408740|Solo	triple functional domain (PTPRF interacting)	protein-coding
mm_115828.1	chr13	21286503	21286512	-	1	NA	TTS (NM_010343)	TTS (NM_010343)	6179	NM_010343	14780	Mm.1332	NM_010343	ENSMUSG00000004344	Gpx5	AV379049|Arep	glutathione peroxidase 5	protein-coding
mm_42395.1	chr5	114937430	114937459	+	1	NA	3' UTR (NM_145209, exon 7 of 7)	3' UTR (NM_145209, exon 7 of 7)	-4758	NM_028211	72357	Mm.292672	NM_028211	ENSMUSG00000029559	2210016L21Rik	-	RIKEN cDNA 2210016L21 gene	protein-coding
mm_11207.1	chr2	29346804	29346842	+	1	NA	promoter-TSS (NM_026896)	promoter-TSS (NM_026896)	13	NM_029615	68975	Mm.330109	NM_026896	ENSMUSG00000026799	Med27	1500015J03Rik|2310042P07Rik|AA682045|Crsp8|D2Ertd434e	mediator complex subunit 27	protein-coding
mm_799.1	chr1	45347703	45347764	+	1	NA	exon (NM_009930, exon 50 of 51)	exon (NM_009930, exon 50 of 51)	36195	NM_009930	12825	Mm.249555	NM_009930	ENSMUSG00000026043	Col3a1	AW550625|Col3a-1|Tsk-2|Tsk2	collagen, type III, alpha 1	protein-coding
mm_31092.1	chr4	41755307	41755318	+	1	NA	promoter-TSS (NM_016658)	promoter-TSS (NM_016658)	84	NM_016658	14430	Mm.439669	NM_016658	ENSMUSG00000036073	Galt	AW553376	galactose-1-phosphate uridyl transferase	protein-coding
mm_59054.1	chr7	19414165	19414171	+	1	NA	exon (NM_007710, exon 2 of 8)	exon (NM_007710, exon 2 of 8)	3074	NM_007710	12715	Mm.2375	NM_007710	ENSMUSG00000030399	Ckm	Ckmm|M-CK|MCK	creatine kinase, muscle	protein-coding
mm_27922.1	chr3	79532842	79532845	-	1	NA	intron (NM_001162999, intron 1 of 16)	intron (NM_001162999, intron 1 of 16)	34836	NM_001162999	329679	Mm.244005	NM_001162999	ENSMUSG00000061175	Fnip2	D630023B12Rik|mKIAA1450	folliculin interacting protein 2	protein-coding
mm_68210.1	chr7	104400821	104400861	-	1	NA	Intergenic	Intergenic	-42195	NM_175648	244183	Mm.347647	NM_175648	ENSMUSG00000052749	Trim30b	A530023O14Rik|Trim30-1	tripartite motif-containing 30B	protein-coding
mm_116234.1	chr13	33569311	33569324	-	1	NA	promoter-TSS (NR_131141)	promoter-TSS (NR_131141)	0	NR_131141	619715	Mm.390575	NR_131140		Gm6093	EG619715	predicted gene 6093	ncRNA
mm_12692.1	chr2	76370032	76370042	+	1	NA	promoter-TSS (NM_153405)	promoter-TSS (NM_153405)	53	NM_153405	241490	Mm.33310	NM_153405	ENSMUSG00000042369	Rbm45	Drb1|Drbp1|G430095G15Rik	RNA binding motif protein 45	protein-coding
mm_107911.1	chr12	70990311	70990318	+	1	NA	intron (NM_001310596, intron 7 of 10)	B1_Mur2|SINE|Alu	15691	NM_011184	19167	Mm.296338	NM_011184	ENSMUSG00000060073	Psma3	Lmpc8	proteasome (prosome, macropain) subunit, alpha type 3	protein-coding
mm_92626.1	chr10	80320507	80320553	-	1	NA	promoter-TSS (NM_025521)	promoter-TSS (NM_025521)	18	NM_025521	66374	Mm.383824	NM_025521	ENSMUSG00000020133	2310011J03Rik	AI452186|AW545358	RIKEN cDNA 2310011J03 gene	protein-coding
mm_168321.1	chr11	114668642	114668642	+	1	NA	promoter-TSS (NM_001048058)	promoter-TSS (NM_001048058)	99	NM_001048057	67671	Mm.238817	NM_023372	ENSMUSG00000057322	Rpl38	0610025G13Rik|Rbt|Ts|Tss	ribosomal protein L38	protein-coding
mm_162926.1	chr10	121750447	121750457	+	1	NA	exon (NM_173022, exon 3 of 3)	exon (NM_173022, exon 3 of 3)	10515	NM_173022	270802	Mm.209172	NM_173022	ENSMUSG00000053684	BC048403	E030027L10	cDNA sequence BC048403	protein-coding
mm_34848.1	chr4	155466595	155466604	+	1	NA	Intergenic	Intergenic	-2515	NM_001253856	69671	Mm.45401	NM_027161	ENSMUSG00000023153	Tmem52	2310043I08Rik	transmembrane protein 52	protein-coding
mm_51271.1	chr6	72115223	72115238	+	1	NA	intron (NM_011375, intron 1 of 6)	intron (NM_011375, intron 1 of 6)	7710	NR_045163	71265	Mm.442035	NR_045163	ENSMUSG00000108709	4933431G14Rik	4930565C19Rik	RIKEN cDNA 4933431G14 gene	ncRNA
mm_88625.1	chr10	79880981	79881020	+	1	NA	intron (NM_011178, intron 2 of 4)	intron (NM_011178, intron 2 of 4)	1333	NM_011178	19152	Mm.2364	NM_011178	ENSMUSG00000057729	Prtn3	PR3|mPR3	proteinase 3	protein-coding
mm_61291.1	chr7	67647485	67647557	+	1	NA	5' UTR (NM_025905, exon 1 of 12)	5' UTR (NM_025905, exon 1 of 12)	111	NM_025905	67009	Mm.249356	NM_025905	ENSMUSG00000030555	Ttc23	1600012K10Rik	tetratricopeptide repeat domain 23	protein-coding
mm_48044.1	chr5	136438825	136438828	-	1	NA	intron (NM_001291239, intron 2 of 22)	YREP_Mm|Unknown|Unknown	-63023	NR_030500	723975		NR_030500	ENSMUSG00000106479	Mir721	Mirn721|miRY|mir-721|mmu-mir-721	microRNA 721	ncRNA
mm_6923.1	chr1	84840503	84840540	-	1	NA	intron (NM_025386, intron 1 of 3)	intron (NM_025386, intron 1 of 3)	680	NM_025386	66153	Mm.381192	NM_025386	ENSMUSG00000073633	Fbxo36	0610008D19Rik|1110020F21Rik|2410002G19Rik|D1Ertd757e	F-box protein 36	protein-coding
mm_156807.1	chrX	163921247	163921250	+	1	NA	intron (NM_001290378, intron 4 of 4)	intron (NM_001290378, intron 4 of 4)	12231	NM_001290379	108012	Mm.426783	NM_026887	ENSMUSG00000031367	Ap1s2	1500012A13Rik|AI853648|EST1	adaptor-related protein complex 1, sigma 2 subunit	protein-coding
mm_96490.1	chr11	67798251	67798259	+	1	NA	promoter-TSS (NM_001013013)	promoter-TSS (NM_001013013)	-16	NM_001013013	68460	Mm.22167	NM_001013013	ENSMUSG00000033044	Dhrs7c	1110001P11Rik|AI120487|SRP-35	dehydrogenase/reductase (SDR family) member 7C	protein-coding
mm_18640.1	chr2	69414634	69414637	-	1	NA	Intergenic	Intergenic	34173	NM_175512	241452	Mm.211655	NM_175512	ENSMUSG00000027068	Dhrs9	C730025I08Rik|Rdh15	dehydrogenase/reductase (SDR family) member 9	protein-coding
mm_116858.1	chr13	54765630	54765648	-	1	NA	exon (NM_033610, exon 2 of 6)	exon (NM_033610, exon 2 of 6)	801	NM_033610	104069	Mm.200843	NM_033610	ENSMUSG00000034891	Sncb	AI838531|betaSYN	synuclein, beta	protein-coding
mm_121443.1	chr14	120430239	120430271	+	1	NA	3' UTR (NM_207515, exon 8 of 8)	3' UTR (NM_207515, exon 8 of 8)	-48206	NM_029519	76108	Mm.261448	NM_029519	ENSMUSG00000051615	Rap2a	5830461H18Rik	RAS related protein 2a	protein-coding
mm_76097.1	chr8	80057990	80058017	-	1	NA	promoter-TSS (NM_020259)	promoter-TSS (NM_020259)	5	NM_020259	15245	Mm.254493	NM_020259	ENSMUSG00000064325	Hhip	Hhip1	Hedgehog-interacting protein	protein-coding
mm_52388.1	chr6	113282327	113282344	+	1	NA	promoter-TSS (NM_170673)	promoter-TSS (NM_170673)	28	NM_170673	211232	Mm.65597	NM_170673	ENSMUSG00000030270	Cpne9	A730016F12Rik|mKIAA4217	copine family member IX	protein-coding
mm_163992.1	chr14	63835093	63835102	+	1	NA	Intergenic	Intergenic	-25215	NM_028228	72400	Mm.379214	NM_028228	ENSMUSG00000021958	Pinx1	2210403I16Rik|2610028A01Rik|67-11-3|AU024023|LPTS|LPTS1	PIN2/TERF1 interacting, telomerase inhibitor 1	protein-coding
mm_127550.1	chr15	102147876	102147901	+	1	NA	exon (NM_008344, exon 2 of 4)	exon (NM_008344, exon 2 of 4)	-2687	NM_146064	223920	Mm.358862	NM_146064	ENSMUSG00000023045	Soat2	ACAT2|D15Wsu97e	sterol O-acyltransferase 2	protein-coding
mm_114690.1	chr13	81783221	81783307	+	1	NA	promoter-TSS (NM_007684)	promoter-TSS (NM_007684)	-28	NM_007684	12626	Mm.12481	NM_007684	ENSMUSG00000021537	Cetn3	MmCEN3	centrin 3	protein-coding
mm_140792.1	chr17	19574386	19574390	-	1	NA	Intergenic	MYSERV6-int|LTR|ERVK	-2843	NM_001104563	627576	Mm.469857	NM_001104563	ENSMUSG00000094892	Vmn2r101	EG627576	vomeronasal 2, receptor 101	protein-coding
mm_122111.1	chr14	30943276	30943294	-	1	NA	promoter-TSS (NM_008406)	promoter-TSS (NM_008406)	4	NM_008406	16424	Mm.3227	NM_008406	ENSMUSG00000006529	Itih1	ITI-HC1|Intin1|Itih-1	inter-alpha trypsin inhibitor, heavy chain 1	protein-coding
mm_94672.1	chr11	17324950	17324965	+	1	NA	Intergenic	Intergenic	67269	NM_001330649	57316	Mm.287982	NM_020558	ENSMUSG00000000581	C1d	1110036E10Rik|AI875855|SUN-CoR	C1D nuclear receptor co-repressor	protein-coding
mm_41559.1	chr5	93093499	93093549	+	1	NA	5' UTR (NM_001310669, exon 1 of 11)	5' UTR (NM_001310669, exon 1 of 11)	108	NM_001347377	52398	Mm.394184	NM_001009818	ENSMUSG00000058013	Sept11	6230410I01Rik|AW548875|D5Ertd606e	septin 11	protein-coding
mm_38045.1	chr4	133967925	133967951	-	1	NA	promoter-TSS (NM_016957)	promoter-TSS (NM_016957)	53	NM_016957	15331	Mm.319660	NM_016957	ENSMUSG00000003038	Hmgn2	HMG-17|Hmg17	high mobility group nucleosomal binding domain 2	protein-coding
mm_34415.1	chr4	145268038	145268059	+	1	NA	TTS (NM_009401)	TTS (NM_009401)	-21178	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_136741.1	chr17	8340711	8340747	+	1	NA	promoter-TSS (NM_178774)	promoter-TSS (NM_178774)	-10	NM_178774	320111	Mm.442510	NM_178774	ENSMUSG00000055945	Prr18	9630019K15Rik	proline rich 18	protein-coding
mm_70461.1	chr8	11840569	11840579	+	1	NA	promoter-TSS (NM_029326)	promoter-TSS (NM_029326)	53	NM_029326	75528	Mm.440342	NM_029326	ENSMUSG00000031512	Tex29	1700018L24Rik	testis expressed 29	protein-coding
mm_18371.1	chr2	59943028	59943039	-	1	NA	intron (NM_001001182, intron 13 of 35)	intron (NM_001001182, intron 13 of 35)	-60427	NM_028118	72137	Mm.288734	NM_028118	ENSMUSG00000026988	Wdsub1	1700048E19Rik|2610014F08Rik	WD repeat, SAM and U-box domain containing 1	protein-coding
mm_172067.1	chr6	136533016	136533018	+	1	NA	intron (NM_019426, intron 1 of 14)	intron (NM_019426, intron 1 of 14)	14166	NM_019426	54343	Mm.173271	NM_019426	ENSMUSG00000030213	Atf7ip	2610204M12Rik|AM|Mcaf1	activating transcription factor 7 interacting protein	protein-coding
mm_120632.1	chr14	70466724	70466733	+	1	NA	intron (NM_145981, intron 4 of 4)	intron (NM_145981, intron 4 of 4)	9211	NM_145981	105653	Mm.192598	NM_145981	ENSMUSG00000003469	Phyhip	AW049870|C630010D02Rik|Lnap1ip|PAHX-AP#1|PAHX-AP1	phytanoyl-CoA hydroxylase interacting protein	protein-coding
mm_168341.1	chr11	120594764	120594769	-	1	NA	3' UTR (NM_011568, exon 6 of 6)	3' UTR (NM_011568, exon 6 of 6)	3599	NM_011568	21681	Mm.1886	NM_011568	ENSMUSG00000025134	Alyref	ALY|REF1|Refbp1|Thoc4	Aly/REF export factor	protein-coding
mm_94399.1	chr11	5628741	5628754	+	1	NA	exon (NM_023816, exon 16 of 27)	exon (NM_023816, exon 16 of 27)	59063	NM_023816	76389	Mm.67300	NM_023816	ENSMUSG00000020481	Ankrd36	1700008J08Rik|1700012M14Rik|Ankrd48	ankyrin repeat domain 36	protein-coding
mm_112449.1	chr13	5861863	5861875	+	1	NA	intron (NM_011803, intron 1 of 3)	CpG	380	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_97098.1	chr11	73267500	73267539	+	1	NA	promoter-TSS (NM_145099)	promoter-TSS (NM_145099)	-101	NM_145099	246788	Mm.75196	NM_145099	ENSMUSG00000043029	Trpv3	1110036I10Rik|AI644701|Nh|VRL3	transient receptor potential cation channel, subfamily V, member 3	protein-coding
mm_158300.1	chrX	116287380	116287382	-	1	NA	Intergenic	Intergenic	-161563	NM_001033471	382239	Mm.336224	NM_001033471	ENSMUSG00000072995	Cpxcr1	Gm1143	CPX chromosome region, candidate 1	protein-coding
mm_114463.1	chr13	67728737	67728766	+	1	NA	promoter-TSS (NR_027969)	promoter-TSS (NR_027969)	422	NM_145622	235907	Mm.440123	NM_145622	ENSMUSG00000071281	Zfp65	KRAB5|Zfp71-rs1|pz114	zinc finger protein 65	protein-coding
mm_32062.1	chr4	97777756	97777779	+	1	NA	5' UTR (NM_001122953, exon 1 of 10)	5' UTR (NM_001122953, exon 1 of 10)	141	NM_010905	18027	Mm.31274	NM_010905	ENSMUSG00000028565	Nfia	1110047K16Rik|9430022M17Rik|CTF|NF1-A|NF1A	nuclear factor I/A	protein-coding
mm_125377.1	chr15	40654913	40654921	+	1	NA	promoter-TSS (NM_011766)	promoter-TSS (NM_011766)	-125	NM_011766	22762	Mm.39496	NM_011766	ENSMUSG00000022306	Zfpm2	B330005D23Rik|FOG-2|FOG2	zinc finger protein, multitype 2	protein-coding
mm_10665.1	chr2	20796845	20796848	+	1	NA	intron (NM_029895, intron 14 of 18)	RLTR16|LTR|ERVK	170875	NM_001081364	71435	Mm.28507	NM_001081364	ENSMUSG00000036591	Arhgap21	5530401C11Rik|AA416458|ARHGAP10	Rho GTPase activating protein 21	protein-coding
mm_48576.1	chr5	143405241	143405258	-	1	NA	intron (NM_025841, intron 1 of 4)	intron (NM_025841, intron 1 of 4)	1429	NM_025841	66913	Mm.181880	NM_025841	ENSMUSG00000079111	Kdelr2	1110007A14Rik	KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 2	protein-coding
mm_68973.1	chr7	126585529	126585591	-	1	NA	exon (NM_138310, exon 2 of 4)	exon (NM_138310, exon 2 of 4)	257	NM_001146311	12752	Mm.268930	NM_009907	ENSMUSG00000030720	Cln3	AI323623	ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease)	protein-coding
mm_62670.1	chr7	109010843	109010845	+	1	NA	promoter-TSS (NM_021885)	promoter-TSS (NM_021885)	-36	NM_021885	22141	Mm.439722	NM_021885	ENSMUSG00000031028	Tub	rd5|tub	tubby candidate gene	protein-coding
mm_75608.1	chr8	61927968	61928044	-	1	NA	promoter-TSS (NM_001293783)	promoter-TSS (NM_001293783)	-81	NM_001293783	234311	Mm.275233	NM_144928	ENSMUSG00000037921	Ddx60	9830118M07	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	protein-coding
mm_25390.1	chr3	107218165	107218213	+	1	NA	exon (NM_001111143, exon 4 of 9)	exon (NM_001111143, exon 4 of 9)	3543	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_33653.1	chr4	133077519	133077533	+	1	NA	3' UTR (NM_146155, exon 7 of 7)	3' UTR (NM_146155, exon 7 of 7)	-53107	NM_153423	242687	Mm.23566	NM_153423	ENSMUSG00000028868	Wasf2	AW742646|D4Ertd13e|WAVE2	WAS protein family, member 2	protein-coding
mm_141049.1	chr17	25433776	25433790	-	1	NA	promoter-TSS (NM_021415)	promoter-TSS (NM_021415)	0	NM_021415	58226	Mm.268378	NM_021415	ENSMUSG00000024112	Cacna1h	Cav3.2|MNCb-1209|alpha13.2	calcium channel, voltage-dependent, T type, alpha 1H subunit	protein-coding
mm_172536.1	chr7	95041878	95041885	-	1	NA	Intergenic	(TC)n|Simple_repeat|Simple_repeat	-1129363	NM_001310762	23966	Mm.254610	NM_011858	ENSMUSG00000048078	Tenm4	Doc4|ELM2|Odz4|R75022|Ten-m4|l(7)-3Rn|l7Rn3|mKIAA1302	teneurin transmembrane protein 4	protein-coding
mm_34946.1	chr4	155892282	155892304	+	1	NA	promoter-TSS (NM_001033490)	promoter-TSS (NM_001033490)	418	NM_207223	140500	Mm.219591	NM_207223	ENSMUSG00000029033	Acap3	Centb5|Kiaa1716-hp|mKIAA1716	ArfGAP with coiled-coil, ankyrin repeat and PH domains 3	protein-coding
mm_6252.1	chr1	68938641	68938645	-	1	NA	intron (NM_010154, intron 1 of 26)	intron (NM_010154, intron 1 of 26)	169416	NM_010154	13869	Mm.442420	NM_010154	ENSMUSG00000062209	Erbb4	Her4|c-erbB-4	erb-b2 receptor tyrosine kinase 4	protein-coding
mm_89770.1	chr10	100099166	100099182	+	1	NA	3' UTR (NM_013598, exon 10 of 10)	3' UTR (NM_013598, exon 10 of 10)	83353	NM_013598	17311	Mm.45124	NM_013598	ENSMUSG00000019966	Kitl	Clo|Con|Gb|Kitlg|Mgf|SCF|SF|SLF|Sl|blz|contrasted	kit ligand	protein-coding
mm_81925.1	chr9	120174963	120174976	+	1	NA	3' UTR (NM_001039364, exon 3 of 3)	3' UTR (NM_001039364, exon 3 of 3)	25227	NM_001039364	17433	Mm.486167	NM_008614	ENSMUSG00000032517	Mobp	AI835053|AI839848|MOBP155|MOBP170|MOBP69|MOBP73|MOBP81|R74645	myelin-associated oligodendrocytic basic protein	protein-coding
mm_124782.1	chr15	7442497	7442524	+	1	NA	Intergenic	Intergenic	-44115	NM_001289498	268780	Mm.203208	NM_178748	ENSMUSG00000042961	Egflam	5930412K08|AU040377	EGF-like, fibronectin type III and laminin G domains	protein-coding
mm_43088.1	chr5	124450406	124450424	+	1	NA	intron (NM_001310725, intron 2 of 6)	intron (NM_001310725, intron 2 of 6)	3711	NM_001310727	67956	Mm.137966	NM_030241	ENSMUSG00000049327	Kmt5a	2410195B05Rik|AA617402|AW536475|PR-SET7|PR/SET07|Setd8	lysine methyltransferase 5A	protein-coding
mm_68403.1	chr7	109616333	109616345	-	1	NA	non-coding (NR_037617, exon 1 of 20)	non-coding (NR_037617, exon 1 of 20)	229	NR_037617	76954	Mm.252009	NM_029811	ENSMUSG00000031024	St5	2010004M01Rik|2610305K15Rik	suppression of tumorigenicity 5	protein-coding
mm_113744.1	chr13	44729795	44729807	+	1	NA	promoter-TSS (NM_021878)	promoter-TSS (NM_021878)	-973	NM_021878	16468	Mm.25059	NM_021878	ENSMUSG00000038518	Jarid2	Jmj|jumonji	jumonji, AT rich interactive domain 2	protein-coding
mm_26772.1	chr3	8964038	8964101	-	1	NA	promoter-TSS (NM_001025262)	promoter-TSS (NM_001025262)	-15	NM_001025261	21985	Mm.371590	NM_009412	ENSMUSG00000027506	Tpd52	AI043038|mD52	tumor protein D52	protein-coding
mm_39981.1	chr5	32459177	32459189	+	1	NA	5' UTR (NM_172707, exon 1 of 8)	5' UTR (NM_172707, exon 1 of 8)	213	NM_172707	19046	Mm.241931	NM_172707	ENSMUSG00000014956	Ppp1cb	1200010B19	protein phosphatase 1, catalytic subunit, beta isoform	protein-coding
mm_93262.1	chr10	95564136	95564154	-	1	NA	promoter-TSS (NM_027722)	promoter-TSS (NM_027722)	22	NM_027722	71207	Mm.24397	NM_027722	ENSMUSG00000020029	Nudt4	4933436C10Rik|DIPP2|DIPP2alpha|DIPP2beta|HDCMB47P	nudix (nucleoside diphosphate linked moiety X)-type motif 4	protein-coding
mm_139816.1	chr17	67021055	67021061	+	1	NA	intron (NM_008984, intron 7 of 30)	intron (NM_008984, intron 7 of 30)	5177	NR_049205	100885844		NR_049205	ENSMUSG00000093508	Mir5709	Gm22041|mir-5709|mmu-mir-5709	microRNA 5709	ncRNA
mm_80986.1	chr9	103225060	103225079	+	1	NA	exon (NM_133977, exon 5 of 17)	exon (NM_133977, exon 5 of 17)	5217	NM_133977	22041	Mm.37214	NM_133977	ENSMUSG00000032554	Trf	AI266983|Cd176|HP|Tf|Tfn|hpx	transferrin	protein-coding
mm_135181.1	chr16	35981739	35981769	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-1609	NM_008465	16646	Mm.3991	NM_008465	ENSMUSG00000022905	Kpna1	AW494490|IPOA5|NPI1|Rch2|mSRP1	karyopherin (importin) alpha 1	protein-coding
mm_9561.1	chr1	173974965	173975039	-	1	NA	exon (NM_011940, exon 3 of 7)	exon (NM_011940, exon 3 of 7)	7842	NM_008327	26388	Mm.218770	NM_008327	ENSMUSG00000026535	Ifi202b	Ifbip-1|Ifi202|Ifi202a|p202	interferon activated gene 202B	protein-coding
mm_96912.1	chr11	70459900	70459956	+	1	NA	promoter-TSS (NM_023158)	promoter-TSS (NM_023158)	56	NM_023158	66102	Mm.425692	NM_023158	ENSMUSG00000018920	Cxcl16	0910001K24Rik|AV290116|BB024863|CXCL16v1|CXCL16v2|SR-PSOX|Zmynd15|b2b498Clo	chemokine (C-X-C motif) ligand 16	protein-coding
mm_131940.1	chr16	23988958	23988986	+	1	NA	promoter-TSS (NM_009744)	promoter-TSS (NM_009744)	-360	NM_009744	12053	Mm.347398	NM_009744	ENSMUSG00000022508	Bcl6	Bcl5	B cell leukemia/lymphoma 6	protein-coding
mm_101284.1	chr11	21572038	21572049	-	1	NA	promoter-TSS (NM_001316675)	promoter-TSS (NM_001316675)	-109	NM_001316675	17449	Mm.212703	NM_008618	ENSMUSG00000020321	Mdh1	B230377B03Rik|D17921|MDH-s|MDHA|Mor-2|Mor2	malate dehydrogenase 1, NAD (soluble)	protein-coding
mm_169973.1	chr17	14094415	14094429	-	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	109409	NM_172826	240025	Mm.79993	NM_172826	ENSMUSG00000048826	Dact2	2900084M21Rik|A630024E20|Dpr2|Frd2|dapper2	dishevelled-binding antagonist of beta-catenin 2	protein-coding
mm_130620.1	chr15	100403259	100403270	-	1	NA	exon (NM_001146161, exon 10 of 16)	exon (NM_001146161, exon 10 of 16)	19791	NM_001146161	18174	Mm.234608	NM_008732	ENSMUSG00000023030	Slc11a2	DCT1|DMT1|Nramp2|mk|van	solute carrier family 11 (proton-coupled divalent metal ion transporters), member 2	protein-coding
mm_95136.1	chr11	34833720	34833772	+	1	NA	promoter-TSS (NM_027411)	promoter-TSS (NM_027411)	-105	NM_027411	70385	Mm.194368	NM_027411	ENSMUSG00000069910	Spdl1	1700018I02Rik|2600001J17Rik|2810049B11Rik|AA409762|Ccdc99	spindle apparatus coiled-coil protein 1	protein-coding
mm_142982.1	chr17	56276704	56276714	-	1	NA	promoter-TSS (NM_174989)	promoter-TSS (NM_174989)	58	NM_174989	106759	Mm.203952	NM_174989	ENSMUSG00000047123	Ticam1	AW046014|AW547018|TICAM-1|TRIF	toll-like receptor adaptor molecule 1	protein-coding
mm_166265.1	chr5	88328206	88328208	-	1	NA	exon (NM_008644, exon 3 of 3)	exon (NM_008644, exon 3 of 3)	10895	NM_008644	17830	Mm.200411	NM_008644	ENSMUSG00000064156	Prol1	Muc10	proline rich, lacrimal 1	protein-coding
mm_29919.1	chr3	131490179	131490235	-	1	NA	Intergenic	CpG	-74561	NM_001289479	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_97530.1	chr11	78512244	78512296	+	1	NA	promoter-TSS (NM_026389)	promoter-TSS (NM_026389)	-26	NM_026389	67811	Mm.197493	NM_026389	ENSMUSG00000001100	Poldip2	1300003F06Rik|Pdip38	polymerase (DNA-directed), delta interacting protein 2	protein-coding
mm_152254.1	chr19	8740572	8740579	-	1	NA	promoter-TSS (NM_001177347)	promoter-TSS (NM_001177347)	-143	NM_001177347	74307	Mm.48791	NM_001177347	ENSMUSG00000090840	1700092M07Rik	-	RIKEN cDNA 1700092M07 gene	protein-coding
mm_84197.1	chr9	60649675	60649677	-	1	NA	intron (NM_001311095, intron 7 of 15)	intron (NM_001311095, intron 7 of 15)	37858	NM_001311095	102747	Mm.269413	NM_145616	ENSMUSG00000047766	Lrrc49	AI430817|AW050057|D430025H09Rik|PGs4|p79	leucine rich repeat containing 49	protein-coding
mm_64911.1	chr7	16204155	16204213	-	1	NA	intron (NM_001285931, intron 9 of 16)	intron (NM_001285931, intron 9 of 16)	17809	NM_001285931	71723	Mm.75259	NM_027883	ENSMUSG00000006019	Dhx34	1200013B07Rik|1810012L18Rik|Ddx34|mKIAA0134	DEAH (Asp-Glu-Ala-His) box polypeptide 34	protein-coding
mm_19970.1	chr2	118011868	118011875	-	1	NA	intron (NR_126479, intron 8 of 9)	intron (NR_126479, intron 8 of 9)	99331	NR_126479	329496	Mm.235844	NR_126479	ENSMUSG00000087203	Gm13986	C230060E24|OTTMUSG00000015236	predicted gene 13986	ncRNA
mm_49956.1	chr6	40628614	40628627	+	1	NA	promoter-TSS (NM_001171003)	promoter-TSS (NM_001171003)	-211	NM_001171003	232714	Mm.33401	NM_001171003	ENSMUSG00000068587	Mgam	6030407P20Rik|MGA	maltase-glucoamylase	protein-coding
mm_121433.1	chr14	120412303	120412315	+	1	NA	intron (NM_175341, intron 8 of 8)	B4A|SINE|B4	-66152	NM_029519	76108	Mm.261448	NM_029519	ENSMUSG00000051615	Rap2a	5830461H18Rik	RAS related protein 2a	protein-coding
mm_81916.1	chr9	120114898	120114956	+	1	NA	intron (NM_144793, intron 1 of 6)	intron (NM_144793, intron 1 of 6)	4528	NM_144793	208638	Mm.236656	NM_144793	ENSMUSG00000032519	Slc25a38	AV019094|BC010801|appoptosin	solute carrier family 25, member 38	protein-coding
mm_60233.1	chr7	43690149	43690166	+	1	NA	promoter-TSS (NM_174866)	promoter-TSS (NM_174866)	-261	NM_174866	317653	Mm.247377	NM_174866	ENSMUSG00000044737	Klk14	GK14	kallikrein related-peptidase 14	protein-coding
mm_37307.1	chr4	119294401	119294445	-	1	NA	promoter-TSS (NM_011732)	promoter-TSS (NM_011732)	90	NM_011732	22608	Mm.258204	NM_011732	ENSMUSG00000028639	Ybx1	1700102N10Rik|C79409|EF1A|MSY1|Nsep1|YB-1|dbpB|mYB-1a	Y box protein 1	protein-coding
mm_118320.1	chr13	113600727	113600731	-	1	NA	intron (NM_130796, intron 1 of 1)	B4A|SINE|B4	17835	NM_130796	170625	Mm.33721	NM_130796	ENSMUSG00000042364	Snx18	Snag1	sorting nexin 18	protein-coding
mm_63464.1	chr7	127573637	127573660	+	1	NA	intron (NM_026888, intron 1 of 9)	C-rich|Low_complexity|Low_complexity	300	NM_026888	68961	Mm.274473	NM_026888	ENSMUSG00000030815	Phkg2	1500017I02Rik	phosphorylase kinase, gamma 2 (testis)	protein-coding
mm_103760.1	chr11	81075753	81075753	-	1	NA	intron (NM_001034013, intron 1 of 9)	intron (NM_001034013, intron 1 of 9)	77150	NM_007384	11418	Mm.234998	NM_007384	ENSMUSG00000020704	Asic2	ACIC2|Accn1|BNC1|BNaC1|BNaC1a|Mdeg	acid-sensing (proton-gated) ion channel 2	protein-coding
mm_52029.1	chr6	96032996	96033022	+	1	NA	Intergenic	Intergenic	-80145	NM_182808	320265	Mm.489890	NM_182808	ENSMUSG00000059187	Fam19a1	C630007B19Rik|FAM19A1 TAFA-1|TAFA1|Tafa-1	family with sequence similarity 19, member A1	protein-coding
mm_74836.1	chr8	23209022	23209030	-	1	NA	promoter-TSS (NM_018743)	promoter-TSS (NM_018743)	-573	NM_018743	102247	Mm.200898	NM_018743	ENSMUSG00000031545	Gpat4	AU041707|AW545732|Agpat6|Tsarg7	glycerol-3-phosphate acyltransferase 4	protein-coding
mm_20472.1	chr2	129410456	129410465	-	1	NA	Intergenic	Intergenic	-39321	NM_008361	16176	Mm.222830	NM_008361	ENSMUSG00000027398	Il1b	IL-1beta|Il-1b	interleukin 1 beta	protein-coding
mm_7890.1	chr1	133258507	133258514	-	1	NA	non-coding (NR_037984, exon 2 of 4)	non-coding (NR_037984, exon 2 of 4)	11298	NR_037984	100502933	Mm.487491	NR_037984	ENSMUSG00000101693	Gm19461	-	predicted gene, 19461	ncRNA
mm_134849.1	chr16	27370215	27370217	-	1	NA	promoter-TSS (NM_198166)	promoter-TSS (NM_198166)	23	NM_198166	224065	Mm.326918	NM_198166	ENSMUSG00000056423	Uts2b	Gm538|U2B|Urp|Uts2d	urotensin 2B	protein-coding
mm_84580.1	chr9	69443326	69443329	-	1	NA	Intergenic	Intergenic	-10356	NM_007585	12306	Mm.238343	NM_007585	ENSMUSG00000032231	Anxa2	AW215814|Cal1h	annexin A2	protein-coding
mm_41940.1	chr5	105731690	105731700	+	1	NA	intron (NM_178701, intron 1 of 2)	intron (NM_178701, intron 1 of 2)	30885	NM_178701	231549	Mm.23837	NM_178701	ENSMUSG00000046079	Lrrc8d	2810473G09Rik|4930525N13Rik|A930019F03|Lrrc5	leucine rich repeat containing 8D	protein-coding
mm_19980.1	chr2	118479020	118479045	-	1	NA	exon (NM_009273, exon 3 of 5)	exon (NM_009273, exon 3 of 5)	664	NM_009273	20813	Mm.363404	NM_009273	ENSMUSG00000009549	Srp14	14kDa|AW536328	signal recognition particle 14	protein-coding
mm_135474.1	chr16	45926409	45926411	-	1	NA	Intergenic	Intergenic	-82032	NM_001252442	208177	Mm.211477	NM_153412	ENSMUSG00000033149	Phldb2	AV253284|C820004H04Rik|LL5b|LL5beta	pleckstrin homology like domain, family B, member 2	protein-coding
mm_139685.1	chr17	57419403	57419420	+	1	NA	intron (NM_010130, intron 11 of 21)	intron (NM_010130, intron 11 of 21)	60725	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_143563.1	chr17	74243509	74243512	-	1	NA	intron (NM_133771, intron 4 of 8)	AT_rich|Low_complexity|Low_complexity	51353	NM_133771	76890	Mm.311874	NM_133771	ENSMUSG00000058704	Memo1	0610016J10Rik|D930048L02Rik	mediator of cell motility 1	protein-coding
mm_76369.1	chr8	84800273	84800283	-	1	NA	promoter-TSS (NM_010906)	promoter-TSS (NM_010906)	60	NM_010906	18032	Mm.9394	NM_010906	ENSMUSG00000001911	Nfix	CTF|NF-I/X|NF1-X|NFI-X	nuclear factor I/X	protein-coding
mm_113031.1	chr13	23493846	23493857	+	1	NA	Intergenic	Intergenic	-4994	NM_001289614	238555	Mm.129668	NM_175938	ENSMUSG00000053216	Btn2a2	Btn2|D030063K05	butyrophilin, subfamily 2, member A2	protein-coding
mm_23578.1	chr3	63380414	63380460	+	1	NA	3' UTR (NM_008604, exon 23 of 23)	3' UTR (NM_008604, exon 23 of 23)	84342	NM_001289463	17380	Mm.296022	NM_008604	ENSMUSG00000027820	Mme	6030454K05Rik|C85356|CALLA|CD10|NEP|SFE	membrane metallo endopeptidase	protein-coding
mm_46308.1	chr5	100563011	100563013	-	1	NA	intron (NM_139198, intron 1 of 4)	intron (NM_139198, intron 1 of 4)	9193	NM_139198	231507	Mm.34609	NM_139198	ENSMUSG00000029322	Plac8	C15|D5Wsu111e	placenta-specific 8	protein-coding
mm_121761.1	chr14	19653404	19653416	-	1	NA	Intergenic	(TC)n|Simple_repeat|Simple_repeat	-50823	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_157639.1	chrX	57223911	57223920	-	1	NA	3' UTR (NM_011616, exon 5 of 5)	3' UTR (NM_011616, exon 5 of 5)	11772	NM_011616	21947	Mm.4861	NM_011616	ENSMUSG00000031132	Cd40lg	CD154|CD40-L|Cd40l|HIGM1|IGM|IMD3|Ly-62|Ly62|T-BAM|TRAP|Tnfsf5|Tnlg8b|gp39	CD40 ligand	protein-coding
mm_107068.1	chr12	16894895	16894904	+	1	NA	promoter-TSS (NM_009072)	promoter-TSS (NM_009072)	-79	NM_009072	19878	Mm.276024	NM_009072	ENSMUSG00000020580	Rock2	B230113H15Rik|ROKalpha|Rho-kinase|Rock-II|Rock2m|mKIAA0619	Rho-associated coiled-coil containing protein kinase 2	protein-coding
mm_2153.1	chr1	88186588	88186590	+	1	NA	intron (NM_201643, intron 1 of 4)	intron (NM_201643, intron 1 of 4)	-14022	NM_013701	22236	Mm.300095	NM_013701	ENSMUSG00000090171	Ugt1a2	UDPGT 1-2|Ugt1	UDP glucuronosyltransferase 1 family, polypeptide A2	protein-coding
mm_9803.1	chr1	181901493	181901497	-	1	NA	3' UTR (NM_010135, exon 15 of 15)	3' UTR (NM_010135, exon 15 of 15)	-59094	NM_133815	98386	Mm.4538	NM_133815	ENSMUSG00000004880	Lbr	AI505894|ic	lamin B receptor	protein-coding
mm_105337.1	chr11	102994675	102994695	-	1	NA	3' UTR (NM_026551, exon 5 of 5)	3' UTR (NM_026551, exon 5 of 5)	5236	NR_105896	102466988		NR_105896	ENSMUSG00000098613	Mir6931	Gm27303|mmu-mir-6931	microRNA 6931	ncRNA
mm_14119.1	chr2	125893378	125893388	+	1	NA	exon (NM_001291002, exon 4 of 10)	exon (NM_001291002, exon 4 of 10)	27160	NM_001291002	69976	Mm.20216	NM_175154	ENSMUSG00000027207	Galk2	2810017M24Rik|AI327030|Gk2	galactokinase 2	protein-coding
mm_155422.1	chrX	73492012	73492022	+	1	NA	exon (NM_007542, exon 4 of 8)	exon (NM_007542, exon 4 of 8)	8416	NM_007542	12111	Mm.2608	NM_007542	ENSMUSG00000031375	Bgn	BG|DSPG1|PG-S1|PGI|SLRR1A	biglycan	protein-coding
mm_96943.1	chr11	70540510	70540546	+	1	NA	5' UTR (NM_001302476, exon 1 of 10)	5' UTR (NM_001302476, exon 1 of 10)	256	NM_001302476	18806	Mm.260177	NM_008876	ENSMUSG00000020828	Pld2	PLD1C	phospholipase D2	protein-coding
mm_62467.1	chr7	101663742	101663790	+	1	NA	promoter-TSS (NM_009191)	promoter-TSS (NM_009191)	-2	NM_009191	20480	Mm.3990	NM_009191	ENSMUSG00000001829	Clpb	AL118244|Skd3	ClpB caseinolytic peptidase B	protein-coding
mm_124520.1	chr14	122024089	122024094	-	1	NA	Intergenic	Intergenic	-10583	NM_001037744	223262	Mm.297637	NM_001037744	ENSMUSG00000071229	Timm8a2	-	translocase of inner mitochondrial membrane 8A2	protein-coding
mm_153110.1	chr19	32957037	32957062	-	1	NA	Intergenic	Intergenic	199472	NM_008960	19211	Mm.245395	NM_008960	ENSMUSG00000013663	Pten	2310035O07Rik|A130070J02Rik|AI463227|B430203M17Rik|MMAC1|TEP1	phosphatase and tensin homolog	protein-coding
mm_6971.1	chr1	86301389	86301404	-	1	NA	Intergenic	Intergenic	-1825	NM_145222	227327	Mm.86467	NM_145222	ENSMUSG00000079445	B3gnt7	C330001H22Rik|beta-3GnT7	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 7	protein-coding
mm_92170.1	chr10	67571947	67571969	-	1	NA	Intergenic	Intergenic	-23003	NM_001005419	211488	Mm.297250	NM_001005419	ENSMUSG00000057134	Ado	Gm237	2-aminoethanethiol (cysteamine) dioxygenase	protein-coding
mm_121561.1	chr14	122484406	122484417	+	1	NA	Intergenic	Intergenic	9027	NM_009574	22772	Mm.308936	NM_009574	ENSMUSG00000061524	Zic2	HPE5|Ku	zinc finger protein of the cerebellum 2	protein-coding
mm_64512.1	chr7	143757103	143757117	+	1	NA	Intergenic	Intergenic	9883	NM_203492	381974	Mm.297839	NM_203492	ENSMUSG00000050276	Mrgprg	Gm1098|Mrgg	MAS-related GPR, member G	protein-coding
mm_12537.1	chr2	72285814	72285824	+	1	NA	5' UTR (NM_178084, exon 1 of 10)	5' UTR (NM_178084, exon 1 of 10)	118	NM_178084	65964	Mm.304143	NM_023057	ENSMUSG00000004085	Map3k20	AV006891|B230120H23Rik|MLTK|MLTKalpha|MLTKbeta|Zak	mitogen-activated protein kinase kinase kinase 20	protein-coding
mm_70899.1	chr8	25601618	25601670	+	1	NA	promoter-TSS (NM_001308482)	promoter-TSS (NM_001308482)	43	NM_001308481	234135	Mm.217337	NM_001001735	ENSMUSG00000054823	Whsc1l1	6720429E03|A530023P05|AI528490|NSD3|WHISTLE	Wolf-Hirschhorn syndrome candidate 1-like 1 (human)	protein-coding
mm_39420.1	chr5	15934763	15934787	+	1	NA	promoter-TSS (NM_001110843)	promoter-TSS (NM_001110843)	84	NM_001110844	12293	Mm.159842	NM_009784	ENSMUSG00000040118	Cacna2d1	Ca(v)alpha2delta1|Cacna2|Cchl2a	calcium channel, voltage-dependent, alpha2/delta subunit 1	protein-coding
mm_126996.1	chr15	95095401	95095405	+	1	NA	3' UTR (NM_178789, exon 8 of 8)	3' UTR (NM_178789, exon 8 of 8)	53915	NR_015482	100043315	Mm.159041	NR_015482	ENSMUSG00000100603	LOC100043315	-	uncharacterized LOC100043315	ncRNA
mm_114812.1	chr13	91504478	91504489	+	1	NA	intron (NM_024272, intron 1 of 16)	intron (NM_024272, intron 1 of 16)	43386	NM_024186	66970	Mm.343095	NM_024186	ENSMUSG00000003992	Ssbp2	1500004K09Rik|2310079I02Rik|9330163K02Rik|A830008M03Rik|AU067692|AW558684|Hspc116|SSDP2	single-stranded DNA binding protein 2	protein-coding
mm_50461.1	chr6	48908836	48908845	+	1	NA	3' UTR (NM_001161622, exon 5 of 5)	3' UTR (NM_001161622, exon 5 of 5)	3854	NM_001161621	76507	Mm.213898	NM_029638	ENSMUSG00000029811	Aoc1	1600012D06Rik|Abp1|DAO	amine oxidase, copper-containing 1	protein-coding
mm_59635.1	chr7	28157585	28157594	+	1	NA	exon (NM_001164655, exon 16 of 20)	exon (NM_001164655, exon 16 of 20)	-12159	NM_007991	14113	Mm.4595	NM_007991	ENSMUSG00000046865	Fbl	AL022665|FIB|FLRN|RNU3IP1	fibrillarin	protein-coding
mm_74352.1	chr8	128148780	128148795	+	1	NA	Intergenic	ORR1D1|LTR|ERVL-MaLR	129438	NR_105822	102465212		NR_105822	ENSMUSG00000099326	Mir21c	Gm28013|mmu-mir-21c	microRNA 21c	ncRNA
mm_119197.1	chr14	32599923	32599932	+	1	NA	promoter-TSS (NM_001001796)	promoter-TSS (NM_001001796)	0	NM_001001796	107751	Mm.119274	NM_001001796	ENSMUSG00000041730	Prrxl1	Drg11|Drgx	paired related homeobox protein-like 1	protein-coding
mm_136484.1	chr16	96082364	96082374	-	1	NA	promoter-TSS (NM_145125)	promoter-TSS (NM_145125)	59	NM_001103179	93871	Mm.240871	NM_145125	ENSMUSG00000022914	Brwd1	5330419I02Rik|D530019K20Rik|G1-403-16|Wdr9|repro5	bromodomain and WD repeat domain containing 1	protein-coding
mm_105715.1	chr11	108343945	108343954	-	1	NA	promoter-TSS (NM_011101)	promoter-TSS (NM_011101)	-61	NM_011101	18750	Mm.222178	NM_011101	ENSMUSG00000050965	Prkca	AI875142|Pkca	protein kinase C, alpha	protein-coding
mm_112130.1	chr12	112942103	112942150	-	1	NA	promoter-TSS (NM_001316724)	promoter-TSS (NM_001316724)	16	NM_025399	66174	Mm.7070	NM_025399	ENSMUSG00000002804	Nudt14	1110030M18Rik|UGPPase	nudix (nucleoside diphosphate linked moiety X)-type motif 14	protein-coding
mm_34661.1	chr4	150866967	150866988	+	1	NA	exon (NM_133753, exon 4 of 4)	exon (NM_133753, exon 4 of 4)	11886	NM_133753	74155	Mm.318841	NM_133753	ENSMUSG00000028967	Errfi1	1300002F13Rik|AI788755|Mig-6|Mig6|RALT	ERBB receptor feedback inhibitor 1	protein-coding
mm_83417.1	chr9	44882181	44882216	-	1	NA	promoter-TSS (NM_001081049)	promoter-TSS (NM_001081049)	-924	NM_001081049	214162	Mm.2389	NM_001081049	ENSMUSG00000002028	Kmt2a	6430520K01|ALL-1|All1|Cxxc7|HRX|HTRX1|Mll|Mll1|mKIAA4050	lysine (K)-specific methyltransferase 2A	protein-coding
mm_102629.1	chr11	62539042	62539072	-	1	NA	exon (NM_028448, exon 1 of 5)	exon (NM_028448, exon 1 of 5)	204	NM_028448	73139	Mm.390409	NM_028448	ENSMUSG00000018509	Cenpv	3110013H01Rik|AA671303|Prr6	centromere protein V	protein-coding
mm_25490.1	chr3	109340628	109340646	+	1	NA	promoter-TSS (NM_020505)	promoter-TSS (NM_020505)	-46	NM_020505	57257	Mm.282257	NM_020505	ENSMUSG00000033721	Vav3	A530094I06Rik|AA986410|Idd18.1	vav 3 oncogene	protein-coding
mm_158766.1	chrX	166585594	166585605	-	1	NA	5' UTR (NM_019397, exon 1 of 12)	5' UTR (NM_019397, exon 1 of 12)	117	NM_019397	54156	Mm.37707	NM_019397	ENSMUSG00000000402	Egfl6	Maeg	EGF-like-domain, multiple 6	protein-coding
mm_13294.1	chr2	101992163	101992172	+	1	NA	intron (NM_001290784, intron 4 of 5)	intron (NM_001290784, intron 4 of 5)	105905	NM_029635	76501	Mm.330424	NM_029635	ENSMUSG00000027163	Commd9	1810029F08Rik|AA409293	COMM domain containing 9	protein-coding
mm_39800.1	chr5	30622694	30622704	+	1	NA	exon (NM_010608, exon 2 of 2)	exon (NM_010608, exon 2 of 2)	-25237	NR_049199	100885838		NR_049199	ENSMUSG00000093710	Mir5625	Gm23930|mmu-mir-5625	microRNA 5625	ncRNA
mm_135412.1	chr16	45025402	45025410	-	1	NA	Intergenic	Intergenic	-68647	NM_026439	67896	Mm.181074	NM_026439	ENSMUSG00000022665	Ccdc80	2610001E17Rik|DRO1|Ssg1|Urb	coiled-coil domain containing 80	protein-coding
mm_135614.1	chr16	52270765	52270778	-	1	NA	exon (NM_001331110, exon 12 of 15)	exon (NM_001331110, exon 12 of 15)	182310	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_106833.1	chr12	8004978	8004988	+	1	NA	exon (NM_009693, exon 25 of 29)	exon (NM_009693, exon 25 of 29)	27306	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_61099.1	chr7	51879213	51879223	+	1	NA	5' UTR (NM_001330607, exon 1 of 8)	5' UTR (NM_001330607, exon 1 of 8)	251	NM_001330607	14453	Mm.207360	NM_008087	ENSMUSG00000030498	Gas2	Gas-2	growth arrest specific 2	protein-coding
mm_160599.1	chr9	75409259	75409259	-	1	NA	promoter-TSS (NR_040719)	promoter-TSS (NR_040719)	100	NM_027418	50772	Mm.480076	NM_015806	ENSMUSG00000042688	Mapk6	2610021I23Rik|D130053K17Rik|Erk3|Mapk4|Mapk63|Prkm4|Prkm6	mitogen-activated protein kinase 6	protein-coding
mm_111197.1	chr12	84194008	84194067	-	1	NA	promoter-TSS (NM_001163502)	promoter-TSS (NM_001163502)	-22	NM_001163502	238317	Mm.31256	NM_001163501	ENSMUSG00000042507	Elmsan1	9430029N19Rik|C130039O16Rik|Gm260	ELM2 and Myb/SANT-like domain containing 1	protein-coding
mm_132860.1	chr16	48431282	48431323	+	1	NA	promoter-TSS (NM_010816)	promoter-TSS (NM_010816)	65	NM_010816	17450	Mm.250060	NM_010816	ENSMUSG00000022652	Morc1	Morc	microrchidia 1	protein-coding
mm_126023.1	chr15	76695686	76695702	+	1	NA	TTS (NM_033371)	TTS (NM_033371)	-1032	NM_182805	76282	Mm.30130	NM_182805	ENSMUSG00000022546	Gpt	1300007J06Rik|2310022B03Rik|ALT|ALT1|Gpt-1|Gpt1	glutamic pyruvic transaminase, soluble	protein-coding
mm_96567.1	chr11	69027295	69027336	+	1	NA	exon (NM_001281465, exon 8 of 23)	exon (NM_001281465, exon 8 of 23)	11404	NM_001013256	68964	Mm.285785	NM_001013256	ENSMUSG00000020898	Ctc1	1500010J02Rik|AAF-132|AAF132	CTS telomere maintenance complex component 1	protein-coding
mm_81141.1	chr9	106821895	106821994	+	1	NA	promoter-TSS (NM_001015507)	promoter-TSS (NM_001015507)	-32	NM_001015507	321006	Mm.440089	NM_001015507	ENSMUSG00000040325	Vprbp	AI447437|B930007L02Rik|mKIAA0800	Vpr (HIV-1) binding protein	protein-coding
mm_80173.1	chr9	72111182	72111196	+	1	NA	promoter-TSS (NM_001253862)	promoter-TSS (NM_001253862)	12	NM_001253862	21406	Mm.171615	NM_011544	ENSMUSG00000032228	Tcf12	A130037E08Rik|ALF1|HEB|HEBAlt|HTF-4|HTF4|ME1|REB|bHLHb20	transcription factor 12	protein-coding
mm_143948.1	chr17	86798899	86798900	-	1	NA	intron (NM_010137, intron 2 of 15)	intron (NM_010137, intron 2 of 15)	45035	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_47361.1	chr5	122849873	122849890	-	1	NA	promoter-TSS (NM_030564)	promoter-TSS (NM_030564)	-307	NM_030564	80751	Mm.388529	NM_030564	ENSMUSG00000029474	Rnf34	AW061037|AW536122|BC004042|C88279|RIFF	ring finger protein 34	protein-coding
mm_109187.1	chr12	108488232	108488241	+	1	NA	intron (NM_001043335, intron 3 of 21)	intron (NM_001043335, intron 3 of 21)	65420	NM_001043335	68519	Mm.236645	NM_001043335	ENSMUSG00000058070	Eml1	1110008N23Rik|A930030P13Rik|AA171013|AI847476|AI853955|ELP79|EMAP|EMAPL|heco	echinoderm microtubule associated protein like 1	protein-coding
mm_92093.1	chr10	62865332	62865345	-	1	NA	intron (NM_027384, intron 1 of 10)	intron (NM_027384, intron 1 of 10)	14676	NM_027384	52463	Mm.17774	NM_027384	ENSMUSG00000047146	Tet1	2510010B09Rik|AA517754|BB001228|Cxxc6|D10Ertd17e|LCX|mKIAA1676	tet methylcytosine dioxygenase 1	protein-coding
mm_9548.1	chr1	173921648	173921671	-	1	NA	3' UTR (NM_001302650, exon 9 of 9)	3' UTR (NM_001302650, exon 9 of 9)	-8613	NM_001033450	381308	Mm.490248	NM_001033450	ENSMUSG00000026536	Ifi211	A730048F03|Ifi205b|Mnda|ifi-205-B	interferon activated gene 211	protein-coding
mm_145048.1	chr18	40256290	40256309	+	1	NA	promoter-TSS (NR_045177)	promoter-TSS (NR_045177)	-663	NR_045177	73001	Mm.428647	NR_045177	ENSMUSG00000071860	2900055J20Rik	-	RIKEN cDNA 2900055J20 gene	ncRNA
mm_153964.1	chr19	47837292	47837305	-	1	NA	promoter-TSS (NM_027559)	promoter-TSS (NM_027559)	63	NM_027559	100048534	Mm.29457	NM_027559	ENSMUSG00000044948	Cfap43	4632415N18Rik|4930428C11Rik|4930463G05Rik|AI429486|D19Ertd652e|Wdr96	cilia and flagella associated protein 43	protein-coding
mm_76603.1	chr8	90348279	90348302	-	1	NA	promoter-TSS (NM_172913)	promoter-TSS (NM_172913)	-38	NM_172913	244579	Mm.302755	NM_172913	ENSMUSG00000043668	Tox3	500-9|BC052044|C230068E13|CAGF9|Tnrc9	TOX high mobility group box family member 3	protein-coding
mm_89150.1	chr10	86022104	86022128	+	1	NA	promoter-TSS (NM_001310745)	promoter-TSS (NM_001310745)	-38	NM_001310745	69754	Mm.44236	NM_153195	ENSMUSG00000001786	Fbxo7	2410015K21Rik|A230052G17Rik|AI117679|AW260462|C85118	F-box protein 7	protein-coding
mm_40852.1	chr5	73491046	73491110	+	1	NA	promoter-TSS (NM_178896)	promoter-TSS (NM_178896)	52	NM_178896	100737	Mm.220312	NM_178896	ENSMUSG00000051674	Dcun1d4	AI836376	DCN1, defective in cullin neddylation 1, domain containing 4 (S. cerevisiae)	protein-coding
mm_75205.1	chr8	39605025	39605080	-	1	NA	3' UTR (NM_031195, exon 9 of 9)	3' UTR (NM_031195, exon 9 of 9)	37626	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_67827.1	chr7	98309472	98309514	-	1	NA	promoter-TSS (NM_025408)	promoter-TSS (NM_025408)	34	NM_025408	66190	Mm.334041	NM_025408	ENSMUSG00000030760	Acer3	1110057L18Rik|5430429L08Rik|AV015045|Phca	alkaline ceramidase 3	protein-coding
mm_52275.1	chr6	108658760	108658770	+	1	NA	intron (NR_104577, intron 1 of 6)	intron (NR_104577, intron 1 of 6)	-1864	NM_011498	20893	Mm.2436	NM_011498	ENSMUSG00000030103	Bhlhe40	Bhlhb2|C130042M06Rik|CR8|Clast5|Dec1|Sharp2|Stra13|Stra14	basic helix-loop-helix family, member e40	protein-coding
mm_125892.1	chr15	75867132	75867140	+	1	NA	exon (NM_026960, exon 11 of 11)	exon (NM_026960, exon 11 of 11)	4797	NM_026960	69146	Mm.27385	NM_026960	ENSMUSG00000022575	Gsdmd	1810036L03Rik|AW558049|DF5L|Dfna5l|Gsdmdc1|M2-4	gasdermin D	protein-coding
mm_89259.1	chr10	87859357	87859367	+	1	NA	exon (NM_010512, exon 1 of 5)	exon (NM_010512, exon 1 of 5)	310	NM_010512	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_158472.1	chrX	141207622	141207629	-	1	NA	intron (NM_053185, intron 14 of 44)	intron (NM_053185, intron 14 of 44)	-250914	NM_001164177	53380	Mm.17640	NM_016883	ENSMUSG00000031429	Psmd10	AW554874	proteasome (prosome, macropain) 26S subunit, non-ATPase, 10	protein-coding
mm_69865.1	chr7	141443990	141444016	-	1	NA	promoter-TSS (NM_022654)	promoter-TSS (NM_022654)	-648	NM_022654	57913	Mm.334321	NM_022654	ENSMUSG00000025507	Pidd1	1200011D09Rik|AU042446|Lrdd|Pidd	p53 induced death domain protein 1	protein-coding
mm_47794.1	chr5	132437416	132437425	-	1	NA	intron (NM_177047, intron 1 of 18)	(A)n|Simple_repeat|Simple_repeat	104923	NM_177047	319974	Mm.409595	NM_177047	ENSMUSG00000029673	Auts2	2700063G02Rik|A730011F23Rik|D830032G16Rik	autism susceptibility candidate 2	protein-coding
mm_22717.1	chr3	19310849	19310859	+	1	NA	intron (NM_001122759, intron 1 of 12)	CpG	468	NM_001122759	18583	Mm.355614	NM_008802	ENSMUSG00000069094	Pde7a	AU015378|AW047537	phosphodiesterase 7A	protein-coding
mm_98843.1	chr11	97598504	97598524	+	1	NA	promoter-TSS (NR_045496)	promoter-TSS (NR_045496)	3	NR_045496	69729	Mm.233452	NR_045496	ENSMUSG00000085860	2410003L11Rik	-	RIKEN cDNA 2410003L11 gene	ncRNA
mm_153296.1	chr19	37697674	37697694	-	1	NA	promoter-TSS (NM_007811)	promoter-TSS (NM_007811)	-124	NM_007811	13082	Mm.42230	NM_007811	ENSMUSG00000024987	Cyp26a1	Cyp26|P450RA|P450RAI|RAH	cytochrome P450, family 26, subfamily a, polypeptide 1	protein-coding
mm_57305.1	chr6	124712039	124712071	-	1	NA	promoter-TSS (NM_007531)	promoter-TSS (NM_007531)	123	NM_013536	14791	Mm.6390	NM_013536	ENSMUSG00000004268	Emg1	C2f|Grcc2f	EMG1 N1-specific pseudouridine methyltransferase	protein-coding
mm_112347.1	chr12	117151264	117151276	-	1	NA	promoter-TSS (NR_033538)	promoter-TSS (NR_033538)	-1	NR_033538	100038689	Mm.445351	NR_033538	ENSMUSG00000099907	Gm10421	ENSMUSG00000072792	predicted gene 10421	ncRNA
mm_28242.1	chr3	88461304	88461314	-	1	NA	promoter-TSS (NM_001163489)	promoter-TSS (NM_001163489)	-127	NM_001163489	20351	Mm.439752	NM_013658	ENSMUSG00000028064	Sema4a	AI132332|SemB|Semab	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A	protein-coding
mm_161391.1	chr14	93888314	93888314	-	1	NA	exon (NM_001271798, exon 2 of 4)	exon (NM_001271798, exon 2 of 4)	574	NM_001271800	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding
mm_19651.1	chr2	102896053	102896076	-	1	NA	intron (NM_001039150, intron 1 of 13)	ID4_|SINE|ID	5601	NM_001177785	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_11498.1	chr2	32534587	32534602	+	1	NA	promoter-TSS (NM_153560)	promoter-TSS (NM_153560)	-765	NM_153560	98952	Mm.4065	NM_153560	ENSMUSG00000039157	Fam102a	AI426465|C230093N12Rik|Eeig1	family with sequence similarity 102, member A	protein-coding
mm_95928.1	chr11	58330745	58330777	+	1	NA	promoter-TSS (NM_024480)	promoter-TSS (NM_024480)	-29	NM_001308168	79566	Mm.290534	NM_024480	ENSMUSG00000013646	Sh3bp5l	2310074E09Rik|BC003251|mKIAA1720	SH3 binding domain protein 5 like	protein-coding
mm_141569.1	chr17	32284660	32284706	-	1	NA	promoter-TSS (NM_001286630)	promoter-TSS (NM_001286630)	-550	NM_020508	57261	Mm.253518	NM_020508	ENSMUSG00000024002	Brd4	Brd5|HUNK1|MCAP|WI-11513	bromodomain containing 4	protein-coding
mm_35067.1	chr4	6454263	6454330	-	1	NA	promoter-TSS (NM_010945)	promoter-TSS (NM_010945)	-25	NM_010945	18201	Mm.3059	NM_010945	ENSMUSG00000028245	Nsmaf	AA959567|C630007J05|Fan	neutral sphingomyelinase (N-SMase) activation associated factor	protein-coding
mm_135505.1	chr16	46498531	46498542	-	1	NA	Intergenic	Intergenic	-1569	NM_021497	58998	Mm.40477	NM_021495	ENSMUSG00000022656	Nectin3	2610301B19Rik|3000002N23Rik|4921513D19Rik|AA407785|AU016832|AW538082|CD113|Pvrl3	nectin cell adhesion molecule 3	protein-coding
mm_64130.1	chr7	141167996	141168015	+	1	NA	intron (NM_001172100, intron 1 of 9)	intron (NM_001172100, intron 1 of 9)	681	NM_001172101	107702	Mm.197493	NM_145135	ENSMUSG00000038650	Rnh1	AW546468|C80305|RNH	ribonuclease/angiogenin inhibitor 1	protein-coding
mm_160780.1	chr10	127452036	127452036	+	1	NA	intron (NM_027900, intron 3 of 23)	intron (NM_027900, intron 3 of 23)	31169	NM_001168293	71750	Mm.29342	NM_027900	ENSMUSG00000025404	R3hdm2	1300003K24Rik|AU041262|mKIAA1002	R3H domain containing 2	protein-coding
mm_22245.1	chr2	174614088	174614113	-	1	NA	Intergenic	Intergenic	-29434	NM_001099328	100043757	Mm.48711	NM_001099328	ENSMUSG00000050600	Zfp831	ENSMUSG00000050600|OTTMUSG00000017459	zinc finger protein 831	protein-coding
mm_58465.1	chr7	3367381	3367402	+	1	NA	TTS (NM_133189)	TTS (NM_133189)	-26651	NM_133190	81905	Mm.357990	NM_133190	ENSMUSG00000053395	Cacng8	-	calcium channel, voltage-dependent, gamma subunit 8	protein-coding
mm_167020.1	chr7	65472207	65472209	+	1	NA	Intergenic	Intergenic	-100964	NM_009386	21872	Mm.4342	NM_009386	ENSMUSG00000030516	Tjp1	ZO1	tight junction protein 1	protein-coding
mm_99179.1	chr11	100860179	100860185	+	1	NA	promoter-TSS (NM_001164062)	promoter-TSS (NM_001164062)	-302	NM_001164062	20850	Mm.277403	NM_011488	ENSMUSG00000004043	Stat5a	AA959963|STAT5	signal transducer and activator of transcription 5A	protein-coding
mm_78502.1	chr9	32743941	32743949	+	1	NA	intron (NM_011808, intron 6 of 7)	intron (NM_011808, intron 6 of 7)	47903	NM_001038642	23871	Mm.292415	NM_011808	ENSMUSG00000032035	Ets1	AI196000|AI448617|D230050P06|Ets-1|Tpl1|vs	E26 avian leukemia oncogene 1, 5' domain	protein-coding
mm_167843.1	chrM	14049	14053	-	1	NA	NA	Intergenic	NA	NA								
mm_34275.1	chr4	141424433	141424437	+	1	NA	3' UTR (NM_013868, exon 3 of 3)	3' UTR (NM_013868, exon 3 of 3)	3656	NM_013868	29818	Mm.46181	NM_013868	ENSMUSG00000006221	Hspb7	27kDa|Hsp25-2|cvHsp	heat shock protein family, member 7 (cardiovascular)	protein-coding
mm_52386.1	chr6	113267868	113267892	+	1	NA	intron (NM_026849, intron 13 of 18)	(T)n|Simple_repeat|Simple_repeat	-14427	NM_170673	211232	Mm.65597	NM_170673	ENSMUSG00000030270	Cpne9	A730016F12Rik|mKIAA4217	copine family member IX	protein-coding
mm_13731.1	chr2	117989498	117989513	+	1	NA	intron (NR_126479, intron 8 of 9)	intron (NR_126479, intron 8 of 9)	121697	NR_126479	329496	Mm.235844	NR_126479	ENSMUSG00000087203	Gm13986	C230060E24|OTTMUSG00000015236	predicted gene 13986	ncRNA
mm_46299.1	chr5	100429532	100429547	-	1	NA	promoter-TSS (NR_034038)	promoter-TSS (NR_034038)	-4	NR_034038	100503199	Mm.392282	NR_034038	ENSMUSG00000097772	5430416N02Rik	100041797|Adapt33|Gm3514	RIKEN cDNA 5430416N02 gene	ncRNA
mm_56718.1	chr6	115536970	115536998	-	1	NA	Intergenic	Intergenic	-7720	NM_199033	381802	Mm.291208	NM_199033	ENSMUSG00000042389	Tsen2	AU067695	tRNA splicing endonuclease subunit 2	protein-coding
mm_150840.1	chr19	44935432	44935465	+	1	NA	exon (NM_001081225, exon 3 of 20)	exon (NM_001081225, exon 3 of 20)	4329	NM_001081225	226151	Mm.212609	NM_172638	ENSMUSG00000036097	Fam178a	3632432H19|6030443O07Rik|AU014917|Slf2	family with sequence similarity 178, member A	protein-coding
mm_85338.1	chr9	102626538	102626564	-	1	NA	promoter-TSS (NM_001081122)	promoter-TSS (NM_001081122)	255	NM_181394	69010	Mm.2000	NM_181394	ENSMUSG00000035048	Anapc13	1810004D07Rik|APC13|SWM1	anaphase promoting complex subunit 13	protein-coding
mm_37224.1	chr4	117929467	117929475	-	1	NA	5' UTR (NM_001284191, exon 1 of 6)	5' UTR (NM_001284191, exon 1 of 6)	292	NM_001284191	11876	Mm.56897	NM_009711	ENSMUSG00000028539	Artn	neublastin	artemin	protein-coding
mm_95493.1	chr11	51636056	51636076	+	1	NA	promoter-TSS (NM_025346)	promoter-TSS (NM_025346)	-170	NM_025346	66089	Mm.288183	NM_025346	ENSMUSG00000001054	Rmnd5b	0610039K22Rik|Gid2	required for meiotic nuclear division 5 homolog B	protein-coding
mm_157345.1	chrX	36903496	36903506	-	1	NA	promoter-TSS (NM_029891)	promoter-TSS (NM_029891)	-602	NM_029891	77286	Mm.21649	NM_029891	ENSMUSG00000044149	Nkrf	9430034D17Rik|AW124770|C80287	NF-kappaB repressing factor	protein-coding
mm_13075.1	chr2	91202793	91202798	+	1	NA	promoter-TSS (NM_007387)	promoter-TSS (NM_007387)	-117	NM_007387	11432	Mm.45570	NM_007387	ENSMUSG00000002103	Acp2	Acp-2|LAP	acid phosphatase 2, lysosomal	protein-coding
mm_102454.1	chr11	59826957	59826965	-	1	NA	intron (NM_011991, intron 6 of 11)	U1|snRNA|snRNA	12806	NM_011991	26572	Mm.40	NM_011991	ENSMUSG00000019373	Cops3	Csn3|Sgn3	COP9 signalosome subunit 3	protein-coding
mm_79334.1	chr9	53341228	53341242	+	1	NA	intron (NM_176846, intron 3 of 5)	intron (NM_176846, intron 3 of 5)	39565	NM_176846	320051	Mm.277540	NM_176846	ENSMUSG00000034584	Exph5	AC079869.22gm5|B130009M24Rik|E030050P12|Kiaa0624|Slac2b|slac2-b	exophilin 5	protein-coding
mm_78124.1	chr9	20644852	20644864	+	1	NA	promoter-TSS (NM_001310746)	promoter-TSS (NM_001310746)	34	NM_001310746	66177	Mm.390165	NM_025401	ENSMUSG00000084786	Ubl5	1110030M22Rik|beacon	ubiquitin-like 5	protein-coding
mm_1033.1	chr1	58755958	58755968	+	1	NA	3' UTR (NM_207653, exon 10 of 10)	3' UTR (NM_207653, exon 10 of 10)	25411	NM_001293805	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_78794.1	chr9	44046628	44046653	+	1	NA	exon (NM_009382, exon 3 of 4)	exon (NM_009382, exon 3 of 4)	3256	NM_009382	21838	Mm.3951	NM_009382	ENSMUSG00000032011	Thy1	CD90|T25|Thy-1|Thy-1.2|Thy1.1|Thy1.2	thymus cell antigen 1, theta	protein-coding
mm_2513.1	chr1	106230851	106230858	+	1	NA	intron (NM_133821, intron 1 of 16)	intron (NM_133821, intron 1 of 16)	58985	NM_133821	98432	Mm.24115	NM_133821	ENSMUSG00000044340	Phlpp1	AI836256|Phlpp|Plekhe1|SCOP|mKIAA0606	PH domain and leucine rich repeat protein phosphatase 1	protein-coding
mm_10092.1	chr2	3284233	3284290	+	1	NA	promoter-TSS (NM_008708)	promoter-TSS (NM_008708)	49	NM_001290370	18108	Mm.65021	NM_008708	ENSMUSG00000026643	Nmt2	A930001K02Rik|AI605445|AU044698|hNMT-2	N-myristoyltransferase 2	protein-coding
mm_24224.1	chr3	88716839	88716883	+	1	NA	promoter-TSS (NM_001163310)	promoter-TSS (NM_001163310)	7	NM_001163310	19769	Mm.4009	NM_009069	ENSMUSG00000028057	Rit1	RIBB|ROC1|Rit	Ras-like without CAAX 1	protein-coding
mm_116654.1	chr13	49187998	49188011	-	1	NA	intron (NM_013610, intron 1 of 3)	CpG	457	NM_013610	18081	Mm.18503	NM_013610	ENSMUSG00000037966	Ninj1	AU024536	ninjurin 1	protein-coding
mm_171512.1	chr4	146497695	146497700	-	1	NA	Intergenic	MMERGLN_LTR|LTR|ERV1	-4303	NM_001243138	100041433	Mm.441741	NM_001243138	ENSMUSG00000056300	Zfp981	Gm13247|OTTMUSG00000011075	zinc finger protein 981	protein-coding
mm_99564.1	chr11	103809729	103809730	+	1	NA	intron (NM_009521, intron 2 of 4)	intron (NM_009521, intron 2 of 4)	35554	NM_009521	22415	Mm.159091	NM_009521	ENSMUSG00000000125	Wnt3	Int-4|Wnt-3	wingless-type MMTV integration site family, member 3	protein-coding
mm_124891.1	chr15	10314091	10314091	+	1	NA	intron (NM_001253781, intron 2 of 9)	intron (NM_001253781, intron 2 of 9)	20440	NM_001253782	19116	Mm.10516	NM_011169	ENSMUSG00000005268	Prlr	AI987712|Pr-1|Pr-3|Prlr-rs1	prolactin receptor	protein-coding
mm_169013.1	chr13	107890143	107890149	-	1	NA	promoter-TSS (NM_145456)	promoter-TSS (NM_145456)	-82	NM_145456	67263	Mm.490418	NM_145456	ENSMUSG00000032846	Zswim6	2900036G02Rik|mKIAA1577	zinc finger SWIM-type containing 6	protein-coding
mm_69599.1	chr7	135716412	135716472	-	1	NA	promoter-TSS (NM_001081117)	promoter-TSS (NM_001081117)	-63	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_143441.1	chr17	70853473	70853473	-	1	NA	promoter-TSS (NM_001164074)	promoter-TSS (NM_001164074)	59	NM_001164074	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_116014.1	chr13	24761444	24761458	-	1	NA	intron (NM_020567, intron 1 of 6)	intron (NM_020567, intron 1 of 6)	486	NM_020567	57441	Mm.12239	NM_020567	ENSMUSG00000006715	Gmnn	AW546347|Gem	geminin	protein-coding
mm_50208.1	chr6	42249840	42249848	+	1	NA	exon (NM_029555, exon 7 of 8)	exon (NM_029555, exon 7 of 8)	3909	NM_029555	76263	Mm.267014	NM_029555	ENSMUSG00000029864	Gstk1	0610025I19Rik|AW260476|DsbA-L	glutathione S-transferase kappa 1	protein-coding
mm_112676.1	chr13	16027834	16027852	+	1	NA	3' UTR (NM_008380, exon 5 of 5)	3' UTR (NM_008380, exon 5 of 5)	15992	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_110693.1	chr12	69197055	69197070	-	1	NA	promoter-TSS (NR_033222)	promoter-TSS (NR_033222)	-149	NR_033222	414085	Mm.256223	NR_033222	ENSMUSG00000097061	9330151L19Rik	-	RIKEN cDNA 9330151L19 gene	ncRNA
mm_120278.1	chr14	63129386	63129402	+	1	NA	intron (NM_007798, intron 1 of 9)	intron (NM_007798, intron 1 of 9)	6932	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_86684.1	chr10	18407659	18407715	+	1	NA	promoter-TSS (NM_173390)	promoter-TSS (NM_173390)	12	NM_173390	215819	Mm.297971	NM_173390	ENSMUSG00000039835	Nhsl1	5730409E15Rik|A630035H13Rik|A730096F01|BC013565|D10Bwg0940e|mKIAA1357	NHS-like 1	protein-coding
mm_21915.1	chr2	166713733	166713743	-	1	NA	promoter-TSS (NM_177782)	promoter-TSS (NM_177782)	94	NM_177782	277360	Mm.34420	NM_177782	ENSMUSG00000039621	Prex1	G630042G04|P-REX1|Setd6	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	protein-coding
mm_42245.1	chr5	113843167	113843175	+	1	NA	3' UTR (NM_011779, exon 11 of 11)	3' UTR (NM_011779, exon 11 of 11)	-12670	NM_009151	20345	Mm.332590	NM_009151	ENSMUSG00000048163	Selplg	CD162|Psgl-1|Psgl1|Selp1|Selpl	selectin, platelet (p-selectin) ligand	protein-coding
mm_131535.1	chr16	17759165	17759171	+	1	NA	promoter-TSS (NM_145479)	promoter-TSS (NM_145479)	-453	NM_145479	224023	Mm.282807	NM_145479	ENSMUSG00000022750	Klhl22	2610318I18Rik|Kelchl	kelch-like 22	protein-coding
mm_47479.1	chr5	123745072	123745120	-	1	NA	exon (NM_001005525, exon 2 of 10)	exon (NM_001005525, exon 2 of 10)	4318	NM_001005525	208606	Mm.276341	NM_025438	ENSMUSG00000029422	Rsrc2	1500011J06Rik	arginine/serine-rich coiled-coil 2	protein-coding
mm_42226.1	chr5	113490581	113490598	+	1	NA	Intergenic	CpG	-59831	NM_177292	320916	Mm.102783	NM_177292	ENSMUSG00000063430	Wscd2	4933413A10Rik|C530024P05Rik|Gm450	WSC domain containing 2	protein-coding
mm_143412.1	chr17	70834529	70834553	-	1	NA	Intergenic	CpG	12236	NM_001164077	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_39003.1	chr4	151988951	151989011	-	1	NA	promoter-TSS (NM_001145929)	promoter-TSS (NM_001145929)	5	NM_175152	69876	Mm.226820	NM_175152	ENSMUSG00000039759	Thap3	2010013E08Rik|2210418H06Rik	THAP domain containing, apoptosis associated protein 3	protein-coding
mm_50457.1	chr6	48907708	48907716	+	1	NA	exon (NM_001161622, exon 3 of 5)	exon (NM_001161622, exon 3 of 5)	2726	NM_001161621	76507	Mm.213898	NM_029638	ENSMUSG00000029811	Aoc1	1600012D06Rik|Abp1|DAO	amine oxidase, copper-containing 1	protein-coding
mm_79251.1	chr9	50617309	50617361	+	1	NA	promoter-TSS (NM_028300)	promoter-TSS (NM_028300)	14	NM_028300	72614	Mm.147232	NM_028300	ENSMUSG00000000167	Pih1d2	2700059L22Rik	PIH1 domain containing 2	protein-coding
mm_6187.1	chr1	65110190	65110274	-	1	NA	intron (NM_175293, intron 5 of 7)	intron (NM_175293, intron 5 of 7)	-6869	NM_007774	12964	Mm.26904	NM_007774	ENSMUSG00000044429	Cryga	Cryg-4|DGcry-4	crystallin, gamma A	protein-coding
mm_150747.1	chr19	43787139	43787177	+	1	NA	intron (NM_013806, intron 2 of 31)	intron (NM_013806, intron 2 of 31)	4850	NM_013806	12780	Mm.39054	NM_013806	ENSMUSG00000025194	Abcc2	AI173996|Abc30|Cmoat|Mrp2|cMRP	ATP-binding cassette, sub-family C (CFTR/MRP), member 2	protein-coding
mm_158909.1	chr1	39194250	39194250	+	1	NA	promoter-TSS (NM_008719)	promoter-TSS (NM_008719)	-22	NM_008719	18143	Mm.2380	NM_008719	ENSMUSG00000026077	Npas2	MOP4|bHLHe9	neuronal PAS domain protein 2	protein-coding
mm_51140.1	chr6	70215402	70215404	+	1	NA	Intergenic	Intergenic	576772	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_111972.1	chr12	110019882	110019898	-	1	NA	Intergenic	Lx9|LINE|L1	138183	NR_045466	67280	Mm.390495	NR_045466		3110009F21Rik	-	RIKEN cDNA 3110009F21 gene	ncRNA
mm_170473.1	chr19	11121490	11121493	+	1	NA	intron (NM_027058, intron 1 of 6)	intron (NM_027058, intron 1 of 6)	9387	NM_027058	69369	Mm.391200	NM_027058	ENSMUSG00000024729	1700017D01Rik	-	RIKEN cDNA 1700017D01 gene	protein-coding
mm_95988.1	chr11	59002921	59002950	+	1	NA	intron (NM_001171512, intron 89 of 103)	intron (NM_001171512, intron 89 of 103)	24842	NM_053168	94091	Mm.248049	NM_053168	ENSMUSG00000020455	Trim11	-	tripartite motif-containing 11	protein-coding
mm_147967.1	chr18	67243070	67243073	-	1	NA	intron (NM_172630, intron 2 of 10)	intron (NM_172630, intron 2 of 10)	2759	NM_172630	225651	Mm.235792	NM_172630	ENSMUSG00000062526	Mppe1	A530095G11	metallophosphoesterase 1	protein-coding
mm_77129.1	chr8	111338153	111338231	-	1	NA	promoter-TSS (NM_001310613)	promoter-TSS (NM_001310613)	13	NM_001310613	74568	Mm.207971	NM_029005	ENSMUSG00000012519	Mlkl	9130019I15Rik	mixed lineage kinase domain-like	protein-coding
mm_110966.1	chr12	76822737	76822757	-	1	NA	promoter-TSS (NM_134050)	promoter-TSS (NM_134050)	-223	NM_134050	104886	Mm.172847	NM_134050	ENSMUSG00000021062	Rab15	2310012G06Rik|AI840042	RAB15, member RAS oncogene family	protein-coding
mm_32098.1	chr4	98546798	98546805	+	1	NA	5' UTR (NM_007704, exon 1 of 18)	5' UTR (NM_007704, exon 1 of 18)	167	NM_001005787	12695	Mm.90218	NM_007704	ENSMUSG00000061859	Patj	Cipp|Inadl	PATJ, crumbs cell polarity complex component	protein-coding
mm_93982.1	chr10	127351800	127351825	-	1	NA	promoter-TSS (NM_008382)	promoter-TSS (NM_008382)	36	NM_008382	16326	Mm.3510	NM_008382	ENSMUSG00000047492	Inhbe	-	inhibin beta-E	protein-coding
mm_27815.1	chr3	78627437	78627459	-	1	NA	Intergenic	ORR1D2|LTR|ERVL-MaLR	517439	NM_001310536	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_139318.1	chr17	48410149	48410162	+	1	NA	promoter-TSS (NM_010913)	promoter-TSS (NM_010913)	155	NM_207219	106821	Mm.203943	NM_207219	ENSMUSG00000040771	Oard1	AI314976|AW558560	O-acyl-ADP-ribose deacylase 1	protein-coding
mm_162509.1	chr1	152400705	152400739	-	1	NA	intron (NM_177756, intron 1 of 11)	intron (NM_177756, intron 1 of 11)	855	NM_177756	269132	Mm.23782	NM_177756	ENSMUSG00000032649	Colgalt2	AI427652|D730024P12|Glt25d2	collagen beta(1-O)galactosyltransferase 2	protein-coding
mm_51165.1	chr6	70726496	70726506	+	1	NA	Intergenic	Intergenic	65674	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_95923.1	chr11	58286441	58286454	+	1	NA	Intergenic	Intergenic	-20622	NM_182996	103836	Mm.41440	NM_182996	ENSMUSG00000037243	Zfp692	AI746306|AI839920|Zfp692-ps|Znf692	zinc finger protein 692	protein-coding
mm_102508.1	chr11	60727271	60727271	-	1	NA	promoter-TSS (NM_022009)	promoter-TSS (NM_022009)	-8	NM_001302207	14248	Mm.339755	NM_022009	ENSMUSG00000002812	Flii	3632430F08Rik|Fliih	flightless I actin binding protein	protein-coding
mm_36461.1	chr4	82505750	82505802	-	1	NA	promoter-TSS (NM_001113209)	promoter-TSS (NM_001113209)	3	NM_001286127	18028	Mm.317947	NM_008687	ENSMUSG00000008575	Nfib	6720429L07Rik|CTF|E030026I10Rik|NF-I/B|NF1-B|NFI-B	nuclear factor I/B	protein-coding
mm_128652.1	chr15	59650604	59650614	-	1	NA	intron (NM_144549, intron 1 of 2)	intron (NM_144549, intron 1 of 2)	1955	NM_144549	211770	Mm.40298	NM_144549	ENSMUSG00000032501	Trib1	A530090O15Rik|TRB-1|Trb1	tribbles pseudokinase 1	protein-coding
mm_100366.1	chr11	119053584	119053603	+	1	NA	Intergenic	CpG	-12680	NM_013926	30951	Mm.99953	NM_013926	ENSMUSG00000025578	Cbx8	Pc3	chromobox 8	protein-coding
mm_2282.1	chr1	91322106	91322114	+	1	NA	promoter-TSS (NM_001033292)	promoter-TSS (NM_001033292)	35	NM_001033292	227357	Mm.318167	NM_001033292	ENSMUSG00000049515	Espnl	Gm556	espin-like	protein-coding
mm_142076.1	chr17	35702004	35702016	-	1	NA	promoter-TSS (NM_001198831)	promoter-TSS (NM_001198831)	34	NM_001198831	12305	Mm.5021	NM_007584	ENSMUSG00000003534	Ddr1	6030432F18|AI323681|CD167a|Cak|Nep|PTK3A	discoidin domain receptor family, member 1	protein-coding
mm_164245.1	chr15	95705097	95705098	+	1	NA	Intergenic	L1MC1|LINE|L1	46494	NR_131148	629300	Mm.247258	NR_131148		Gm6961	EG629300	predicted gene 6961	ncRNA
mm_131350.1	chr16	13672034	13672045	+	1	NA	5' UTR (NM_001177552, exon 1 of 6)	5' UTR (NM_001177552, exon 1 of 6)	181	NM_025653	67118	Mm.223689	NM_025653	ENSMUSG00000022684	Bfar	3010001A07Rik|3110001I22Rik|AI666707|AW107665|Bar|Rnf47	bifunctional apoptosis regulator	protein-coding
mm_8410.1	chr1	152042681	152042686	-	1	NA	intron (NM_197990, intron 1 of 5)	intron (NM_197990, intron 1 of 5)	47637	NM_197990	69399	Mm.278031	NM_197990	ENSMUSG00000032666	1700025G04Rik	2610510E02Rik|2900042O04Rik|ENSMUSG00000073540	RIKEN cDNA 1700025G04 gene	protein-coding
mm_73592.1	chr8	109996085	109996117	+	1	NA	exon (NM_146214, exon 8 of 12)	exon (NM_146214, exon 8 of 12)	5665	NM_146214	234724	Mm.28110	NM_146214	ENSMUSG00000001670	Tat	-	tyrosine aminotransferase	protein-coding
mm_85428.1	chr9	103500356	103500401	-	1	NA	intron (NM_178638, intron 3 of 5)	intron (NM_178638, intron 3 of 5)	-20050	NM_001002896	107993	Mm.335403	NM_001002896	ENSMUSG00000032556	Bfsp2	AI448593|CP49	beaded filament structural protein 2, phakinin	protein-coding
mm_99005.1	chr11	98809788	98809810	+	1	NA	promoter-TSS (NM_138660)	promoter-TSS (NM_138660)	-9	NM_138660	192160	Mm.40120	NM_138660	ENSMUSG00000078676	Casc3	Btz|Mln51	cancer susceptibility candidate 3	protein-coding
mm_17367.1	chr2	26902830	26902906	-	1	NA	promoter-TSS (NM_009298)	promoter-TSS (NM_009298)	19	NM_009298	20935	Mm.245577	NM_009298	ENSMUSG00000036160	Surf6	D2Wsu129e|Surf-6	surfeit gene 6	protein-coding
mm_117278.1	chr13	65112964	65112987	-	1	NA	promoter-TSS (NM_001083901)	promoter-TSS (NM_001083901)	7	NM_001083901	66631	Mm.239196	NM_133680	ENSMUSG00000038212	Mfsd14b	5730414C17Rik|AU045608|AW539692|Hiatl1	major facilitator superfamily domain containing 14B	protein-coding
mm_122974.1	chr14	54975980	54976006	-	1	NA	promoter-TSS (NR_030607)	promoter-TSS (NR_030607)	-217	NR_030607	100124433		NR_030607	ENSMUSG00000077928	Mir208b	Mirn208b|mir-208b	microRNA 208b	ncRNA
mm_109620.1	chr12	112764495	112764514	+	1	NA	exon (NM_178911, exon 5 of 11)	exon (NM_178911, exon 5 of 11)	3849	NM_178911	104759	Mm.203915	NM_178911	ENSMUSG00000052160	Pld4	AI132321|thss	phospholipase D family, member 4	protein-coding
mm_66988.1	chr7	64001775	64001788	-	1	NA	Intergenic	Intergenic	-62866	NM_021366	50794	Mm.240473	NM_021366	ENSMUSG00000052040	Klf13	0610043C13Rik|9430029L20Rik|Bteb3|FKLF-2|FKLF2|NSLP1|RFLAT-1|RFLAT1	Kruppel-like factor 13	protein-coding
mm_146688.1	chr18	12862625	12862714	-	1	NA	promoter-TSS (NM_001252492)	promoter-TSS (NM_001252492)	44	NM_001252493	64291	Mm.259470	NM_020573	ENSMUSG00000044252	Osbpl1a	G430090F17Rik|Gm753|ORP-1|Osbpl1b	oxysterol binding protein-like 1A	protein-coding
mm_153550.1	chr19	42089282	42089293	-	1	NA	Intergenic	Intergenic	-1148	NM_145501	84095	Mm.117037	NM_145501	ENSMUSG00000025178	Pi4k2a	Pi4k2	phosphatidylinositol 4-kinase type 2 alpha	protein-coding
mm_113804.1	chr13	46501899	46501916	+	1	NA	promoter-TSS (NM_026056)	promoter-TSS (NM_026056)	4	NM_026056	67252	Mm.44529	NM_026056	ENSMUSG00000021373	Cap2	2810452G09Rik|AV045235	CAP, adenylate cyclase-associated protein, 2 (yeast)	protein-coding
mm_23319.1	chr3	53463575	53463590	+	1	NA	promoter-TSS (NM_172501)	promoter-TSS (NM_172501)	-235	NM_173382	212127	Mm.491292	NM_173382	ENSMUSG00000049504	Proser1	2810046L04Rik|9330161F11	proline and serine rich 1	protein-coding
mm_126927.1	chr15	91673186	91673268	+	1	NA	promoter-TSS (NM_025730)	promoter-TSS (NM_025730)	3	NM_025730	66725	Mm.37558	NM_025730	ENSMUSG00000036273	Lrrk2	4921513O20Rik|9330188B09Rik|AW561911|D630001M17Rik|Gm927|cI-46	leucine-rich repeat kinase 2	protein-coding
mm_74098.1	chr8	122611619	122611663	+	1	NA	promoter-TSS (NM_016722)	promoter-TSS (NM_016722)	15	NM_021502	59005	Mm.38746	NM_021502	ENSMUSG00000015013	Trappc2l	1810017G16Rik|AB030200|Hspc176|Tca17	trafficking protein particle complex 2-like	protein-coding
mm_113677.1	chr13	42785072	42785087	+	1	NA	intron (NM_001005740, intron 1 of 12)	intron (NM_001005740, intron 1 of 12)	75498	NM_001005740	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding
mm_122244.1	chr14	33447143	33447179	-	1	NA	promoter-TSS (NM_001310453)	promoter-TSS (NM_001310453)	-3	NM_016700	26419	Mm.21495	NM_016700	ENSMUSG00000021936	Mapk8	AI849689|JNK|JNK1|Prkm8|SAPK1	mitogen-activated protein kinase 8	protein-coding
mm_158000.1	chrX	94542064	94542072	-	1	NA	promoter-TSS (NM_019791)	promoter-TSS (NM_019791)	6	NM_019791	94275	Mm.27578	NM_019791	ENSMUSG00000025151	Maged1	2810433C11Rik|5430405L04Rik|DXBwg1492e|Dlixin|Dlxin-1|Dlxin1|MAGE-D1|NRAGE|mFLJ00163	melanoma antigen, family D, 1	protein-coding
mm_64938.1	chr7	16310072	16310098	-	1	NA	intron (NM_133234, intron 1 of 3)	CpG	502	NM_133234	170770	Mm.7660	NM_133234	ENSMUSG00000002083	Bbc3	PUMA|PUMA/JFY1	BCL2 binding component 3	protein-coding
mm_111318.1	chr12	86042788	86042809	-	1	NA	intron (NM_001081423, intron 33 of 33)	intron (NM_001081423, intron 33 of 33)	36243	NM_009368	21809	Mm.3992	NM_009368	ENSMUSG00000021253	Tgfb3	TGF-beta-3|Tgfb-3	transforming growth factor, beta 3	protein-coding
mm_3132.1	chr1	135108929	135108947	+	1	NA	exon (NM_007955, exon 37 of 38)	exon (NM_007955, exon 37 of 38)	-3662	NM_001033409	329252	Mm.279594	NM_001033409	ENSMUSG00000042793	Lgr6	A530037C04Rik|D830026M09	leucine-rich repeat-containing G protein-coupled receptor 6	protein-coding
mm_44086.1	chr5	149184649	149184673	+	1	NA	5' UTR (NM_001115151, exon 1 of 9)	5' UTR (NM_001115151, exon 1 of 9)	101	NM_001115149	231915	Mm.29402	NM_001013378	ENSMUSG00000041264	Uspl1	E430026A01Rik	ubiquitin specific peptidase like 1	protein-coding
mm_94605.1	chr11	14599241	14599243	+	1	NA	promoter-TSS (NM_001164166)	promoter-TSS (NM_001164166)	2	NM_001164166	432536	Mm.33646	NM_001164166	ENSMUSG00000084135	Pom121l12	1700054H16Rik	POM121 membrane glycoprotein-like 12	protein-coding
mm_134249.1	chr16	13611749	13611753	-	1	NA	intron (NM_028761, intron 18 of 23)	Lx8|LINE|L1	56419	NM_028761	74108	Mm.182350	NM_028761	ENSMUSG00000022685	Parn	1200003I18Rik|DAN	poly(A)-specific ribonuclease (deadenylation nuclease)	protein-coding
mm_110048.1	chr12	17715840	17715845	-	1	NA	intron (NM_016677, intron 1 of 3)	intron (NM_016677, intron 1 of 3)	25028	NM_016677	53602	Mm.313619	NM_016677	ENSMUSG00000071379	Hpcal1	NVP-3|Nvp3|VILIP3|Vnsl3|Vsnl3	hippocalcin-like 1	protein-coding
mm_20072.1	chr2	120539484	120539496	-	1	NA	exon (NM_011743, exon 4 of 22)	exon (NM_011743, exon 4 of 22)	24341	NM_011743	20402	Mm.485295	NM_011743	ENSMUSG00000027288	Zfp106	Cd-1|D2Dcr28|H3a|Sh3bp3|Znf106|sirm	zinc finger protein 106	protein-coding
mm_136797.1	chr17	12119351	12119361	+	1	NA	promoter-TSS (NM_026644)	promoter-TSS (NM_026644)	72	NM_026644	68262	Mm.258300	NM_026644	ENSMUSG00000023827	Agpat4	1500003P24Rik	1-acylglycerol-3-phosphate O-acyltransferase 4 (lysophosphatidic acid acyltransferase, delta)	protein-coding
mm_109832.1	chr12	4038869	4038879	-	1	NA	promoter-TSS (NM_001082483)	promoter-TSS (NM_001082483)	41	NM_001082483	668212	Mm.210266	NM_001082483	ENSMUSG00000020658	Efr3b	AI852640|C030014M07Rik|mKIAA0953	EFR3 homolog B	protein-coding
mm_10899.1	chr2	25272488	25272517	+	1	NA	promoter-TSS (NM_175300)	promoter-TSS (NM_175300)	36	NM_175300	99152	Mm.291624	NM_175300	ENSMUSG00000026965	Anapc2	9230107K09Rik|AL024279|Apc2|Emi4|Imi4|mKIAA1406	anaphase promoting complex subunit 2	protein-coding
mm_166867.1	chr7	24636614	24636614	+	1	NA	promoter-TSS (NM_133743)	promoter-TSS (NM_133743)	44	NM_133743	72434	Mm.281093	NM_133743	ENSMUSG00000057454	Lypd3	2310061G07Rik|C4.4a	Ly6/Plaur domain containing 3	protein-coding
mm_163406.1	chr12	75529263	75529265	+	1	NA	intron (NM_012024, intron 2 of 13)	intron (NM_012024, intron 2 of 13)	66936	NM_012024	26932	Mm.259626	NM_012024	ENSMUSG00000021051	Ppp2r5e	4633401M22Rik|AI449017|B56beta	protein phosphatase 2, regulatory subunit B', epsilon	protein-coding
mm_57795.1	chr6	129275434	129275439	-	1	NA	promoter-TSS (NM_001033122)	promoter-TSS (NM_001033122)	-67	NM_001033122	12515	Mm.74745	NM_001033122	ENSMUSG00000030156	Cd69	5830438K24Rik|AI452015|AIM|VEA	CD69 antigen	protein-coding
mm_119900.1	chr14	54944287	54944326	+	1	NA	exon (NM_010856, exon 36 of 39)	exon (NM_010856, exon 36 of 39)	4836	NR_029724	387204		NR_029724	ENSMUSG00000065432	Mir208a	Mirn208|Mirn208a|mir-208|mir-208a|mmu-mir-208	microRNA 208a	ncRNA
mm_20106.1	chr2	121101161	121101165	-	1	NA	intron (NM_001160424, intron 5 of 11)	intron (NM_001160424, intron 5 of 11)	8628	NM_001160424	640543	Mm.478785	NM_001160424	ENSMUSG00000079103	Tgm7	TGMZ|TGz	transglutaminase 7	protein-coding
mm_67641.1	chr7	84439187	84439195	-	1	NA	Intergenic	Intergenic	-29153	NM_007488	11864	Mm.38594	NM_007488	ENSMUSG00000015709	Arnt2	Hif-2b|bHLHe1|mKIAA0307	aryl hydrocarbon receptor nuclear translocator 2	protein-coding
mm_3294.1	chr1	136683376	136683410	+	1	NA	promoter-TSS (NR_045325)	promoter-TSS (NR_045325)	-3	NR_045324	100503460	Mm.30630	NR_045324	ENSMUSG00000097113	Gm19705	-	predicted gene, 19705	ncRNA
mm_88349.1	chr10	75842539	75842542	+	1	NA	Intergenic	Intergenic	-7659	NM_010361	14872	Mm.24118	NM_010361	ENSMUSG00000033318	Gstt2	AI266894|Yrs|mGSTT2	glutathione S-transferase, theta 2	protein-coding
mm_29346.1	chr3	108284551	108284579	-	1	NA	intron (NM_001271599, intron 1 of 20)	GC_rich|Low_complexity|Low_complexity	501	NM_019972	20661	Mm.157119	NM_019972	ENSMUSG00000068747	Sort1	2900053A11Rik|AI852375|Ntr3|Ntsr3	sortilin 1	protein-coding
mm_168628.1	chr1	180936990	180937008	+	1	NA	intron (NM_010094, intron 2 of 3)	CpG	1977	NM_010094	13590	Mm.378911	NM_010094	ENSMUSG00000038793	Lefty1	AI450052|Ebaf|Leftb|Stra3|Tgfb4|lefty|lefty-1	left right determination factor 1	protein-coding
mm_35916.1	chr4	53029120	53029126	-	1	NA	Intergenic	Intergenic	17243	NM_025623	66536	Mm.38244	NM_025623	ENSMUSG00000015247	Nipsnap3b	2700063N13Rik|Nipsnap3a	nipsnap homolog 3B (C. elegans)	protein-coding
mm_96762.1	chr11	69914287	69914297	+	1	NA	promoter-TSS (NM_019726)	promoter-TSS (NM_019726)	100	NM_019726	56310	Mm.477738	NM_019726	ENSMUSG00000023170	Gps2	AI505953	G protein pathway suppressor 2	protein-coding
mm_32111.1	chr4	98923816	98923842	+	1	NA	promoter-TSS (NM_146144)	promoter-TSS (NM_146144)	19	NM_146144	230484	Mm.371692	NM_146144	ENSMUSG00000028560	Usp1	-	ubiquitin specific peptidase 1	protein-coding
mm_40384.1	chr5	52369093	52369115	+	1	NA	3' UTR (NM_011435, exon 2 of 2)	3' UTR (NM_011435, exon 2 of 2)	5300	NM_011435	20657	Mm.2407	NM_011435	ENSMUSG00000072941	Sod3	AI314465|EC-SOD	superoxide dismutase 3, extracellular	protein-coding
mm_5405.1	chr1	33757923	33757946	-	1	NA	promoter-TSS (NM_145392)	promoter-TSS (NM_145392)	-184	NM_145392	213539	Mm.247037	NM_145392	ENSMUSG00000042215	Bag2	2610042A13Rik|BC016230	BCL2-associated athanogene 2	protein-coding
mm_81112.1	chr9	106453881	106453911	+	1	NA	promoter-TSS (NM_021567)	promoter-TSS (NM_021567)	58	NM_021567	59092	Mm.286394	NM_021567	ENSMUSG00000023495	Pcbp4	1200003L19Rik|AlphaCP-4	poly(rC) binding protein 4	protein-coding
mm_132921.1	chr16	49781809	49781827	+	1	NA	Intergenic	Intergenic	-73836	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_112064.1	chr12	111980125	111980166	-	1	NA	exon (NM_001127685, exon 2 of 3)	exon (NM_001127685, exon 2 of 3)	606	NM_001127685	217874	Mm.134213	NM_001127685	ENSMUSG00000091402	Rd3l	A930011N13	retinal degeneration 3-like	protein-coding
mm_31269.1	chr4	45331931	45331932	+	1	NA	Intergenic	Intergenic	-10170	NM_153167	242418	Mm.317668	NM_153167	ENSMUSG00000035572	Dcaf10	AA959934|Wdr32	DDB1 and CUL4 associated factor 10	protein-coding
mm_53062.1	chr6	124857141	124857165	+	1	NA	intron (NM_013534, intron 1 of 14)	CpG	534	NM_013534	14789	Mm.9002	NM_013534	ENSMUSG00000023191	P3h3	BC016431|Grcb|Leprel2	prolyl 3-hydroxylase 3	protein-coding
mm_108597.1	chr12	85389452	85389459	+	1	NA	Intergenic	L2b|LINE|L2	-14738	NM_026775	68581	Mm.379159	NM_026775	ENSMUSG00000021248	Tmed10	1110014C03Rik|Tmp21|p23|p24delta1	transmembrane p24 trafficking protein 10	protein-coding
mm_119361.1	chr14	41116193	41116203	+	1	NA	intron (NM_133653, intron 6 of 9)	intron (NM_133653, intron 6 of 9)	11165	NM_133653	11720	Mm.14064	NM_133653	ENSMUSG00000037798	Mat1a	AI046368|AdoMet|Ams|MAT|MATA1|SAMS|SAMS1	methionine adenosyltransferase I, alpha	protein-coding
mm_117837.1	chr13	98688453	98688480	-	1	NA	exon (NM_001025606, exon 3 of 4)	exon (NM_001025606, exon 3 of 4)	6365	NM_001025606	380863	Mm.28264	NM_001025606	ENSMUSG00000052485	Tmem171	Gm905	transmembrane protein 171	protein-coding
mm_144477.1	chr18	23943851	23943853	+	1	NA	Intergenic	Intergenic	-10836	NM_027007	69256	Mm.218343	NM_027007	ENSMUSG00000024276	Zfp397	2810411K16Rik|6720480F11Rik|AI461664	zinc finger protein 397	protein-coding
mm_63612.1	chr7	128205894	128205922	+	1	NA	TTS (NM_001029872)	TTS (NM_001029872)	458	NM_009943	12862	Mm.43824	NM_009943	ENSMUSG00000030785	Cox6a2	CoxVIaH|VIaH	cytochrome c oxidase subunit VIa polypeptide 2	protein-coding
mm_7703.1	chr1	130423067	130423082	-	1	NA	promoter-TSS (NM_007827)	promoter-TSS (NM_007827)	-31	NM_001317361	13137	Mm.436759	NM_007827	ENSMUSG00000026401	Cd55b	AI323748|Daf|Daf-TM|Daf2|TM-DAF	CD55 molecule, decay accelerating factor for complement B	protein-coding
mm_11708.1	chr2	36222464	36222480	+	1	NA	Intergenic	Intergenic	-7954	NM_008969	19224	Mm.275434	NM_008969	ENSMUSG00000047250	Ptgs1	COX1|Cox-1|Cox-3|PGHS-1|PHS 1|Pghs1	prostaglandin-endoperoxide synthase 1	protein-coding
mm_75952.1	chr8	71671724	71671772	-	1	NA	promoter-TSS (NM_001029873)	promoter-TSS (NM_001029873)	9	NM_001029873	382018	Mm.334606	NM_001029873	ENSMUSG00000034799	Unc13a	2410078G03Rik|Munc13-1	unc-13 homolog A (C. elegans)	protein-coding
mm_37293.1	chr4	119187315	119187337	-	1	NA	exon (NM_013848, exon 4 of 13)	exon (NM_013848, exon 4 of 13)	2685	NM_013848	27028	Mm.290753	NM_013848	ENSMUSG00000028644	Ermap	AA409279|AI666418	erythroblast membrane-associated protein	protein-coding
mm_77739.1	chr8	126944977	126944978	-	1	NA	intron (NM_024214, intron 1 of 4)	intron (NM_024214, intron 1 of 4)	944	NM_024214	67952	Mm.6932	NM_024214	ENSMUSG00000093904	Tomm20	1810060K07Rik|BB284719|Gm19268|MAS20|MOM19|TOM20|mKIAA0016	translocase of outer mitochondrial membrane 20 homolog (yeast)	protein-coding
mm_116755.1	chr13	52530672	52530684	-	1	NA	5' UTR (NM_001024474, exon 1 of 2)	5' UTR (NM_001024474, exon 1 of 2)	158	NM_001024474	68203	Mm.29362	NM_001024474	ENSMUSG00000047842	Diras2	2900052J15Rik|AI414999	DIRAS family, GTP-binding RAS-like 2	protein-coding
mm_157665.1	chrX	58039769	58039779	-	1	NA	Intergenic	Intergenic	9146	NM_009575	22773	Mm.255890	NM_009575	ENSMUSG00000067860	Zic3	Bn|Ka	zinc finger protein of the cerebellum 3	protein-coding
mm_160948.1	chr11	96365904	96365904	+	1	NA	exon (NM_008266, exon 1 of 2)	exon (NM_008266, exon 1 of 2)	146	NM_008266	15407	Mm.890	NM_008266	ENSMUSG00000018973	Hoxb1	Hox-2.9	homeobox B1	protein-coding
mm_75026.1	chr8	31918818	31918829	-	1	NA	promoter-TSS (NM_178591)	promoter-TSS (NM_178591)	-620	NM_178591	211323	Mm.153432	NM_178591	ENSMUSG00000062991	Nrg1	6030402G23Rik|ARIA|D230005F13Rik|GGF|GGFII|HRG|HRGalpha|Hgl|NDF|SMDF	neuregulin 1	protein-coding
mm_158678.1	chrX	159257210	159257246	-	1	NA	intron (NM_148945, intron 1 of 21)	intron (NM_148945, intron 1 of 21)	1446	NM_001346675	110651	Mm.328476	NM_148945	ENSMUSG00000031309	Rps6ka3	MAPKAPK-1b|MPK-9|Rsk2|S6K-alpha3|p90RSK3|pp90RSK2	ribosomal protein S6 kinase polypeptide 3	protein-coding
mm_79434.1	chr9	56042012	56042033	+	1	NA	5' UTR (NM_001278274, exon 1 of 2)	5' UTR (NM_001278274, exon 1 of 2)	177	NM_011992	26611	Mm.1782	NM_011992	ENSMUSG00000032320	Rcn2	AA408742|Tcbp49	reticulocalbin 2	protein-coding
mm_67912.1	chr7	99706828	99706873	-	1	NA	promoter-TSS (NM_001252530)	promoter-TSS (NM_001252530)	-8	NM_001252530	101488	Mm.11249	NM_175316	ENSMUSG00000030737	Slco2b1	AI060904|AI852653|OATP-B|Slc21a9	solute carrier organic anion transporter family, member 2b1	protein-coding
mm_51822.1	chr6	89096174	89096178	+	1	NA	promoter-TSS (NR_134977)	promoter-TSS (NR_134977)	66	NR_134977	232217	Mm.281744	NM_175017	ENSMUSG00000055403	4933427D06Rik	-	RIKEN cDNA 4933427D06 gene	ncRNA
mm_89604.1	chr10	95991605	95991626	+	1	NA	intron (NM_001001932, intron 5 of 28)	intron (NM_001001932, intron 5 of 28)	50952	NM_001001932	216238	Mm.210035	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding
mm_168280.1	chr1	107794159	107794170	+	1	NA	Intergenic	MT2_Mm|LTR|ERVL	-123095	NR_102306	319596	Mm.136054	NR_102306	ENSMUSG00000100457	D830032E09Rik	-	RIKEN cDNA D830032E09 gene	ncRNA
mm_171358.1	chr4	116075070	116075070	-	1	NA	promoter-TSS (NM_153521)	promoter-TSS (NM_153521)	0	NM_025641	66576	Mm.181721	NM_025641	ENSMUSG00000063882	Uqcrh	2210416J04Rik|2310021J10Rik|2610041P16Rik	ubiquinol-cytochrome c reductase hinge protein	protein-coding
mm_2100.1	chr1	87803639	87803662	+	1	NA	promoter-TSS (NM_009118)	promoter-TSS (NM_009118)	-30	NM_009118	20215	Mm.1276	NM_009118	ENSMUSG00000056055	Sag	A930001K18Rik|Arr1|Irbp|arrestin	S-antigen, retina and pineal gland (arrestin)	protein-coding
mm_46808.1	chr5	113077204	113077223	-	1	NA	intron (NM_001159650, intron 5 of 5)	B1_Mur3|SINE|Alu	4371	NM_001159650	12962	Mm.378899	NM_021352	ENSMUSG00000029352	Crybb3	AI852419	crystallin, beta B3	protein-coding
mm_56567.1	chr6	102265697	102265699	-	1	NA	promoter-TSS (NR_131018)	promoter-TSS (NR_131018)	-402	NR_131018	75893	Mm.2968	NR_131017	ENSMUSG00000107563	4930587E11Rik	4930523E13Rik	RIKEN cDNA 4930587E11 gene	ncRNA
mm_117630.1	chr13	92131799	92131809	-	1	NA	Intergenic	CpG	-143762	NM_009027	19418	Mm.248630	NM_009027	ENSMUSG00000021708	Rasgrf2	6330417G04Rik|AW048350|Grf2|Ras-GRF2	RAS protein-specific guanine nucleotide-releasing factor 2	protein-coding
mm_100348.1	chr11	118428209	118428231	+	1	NA	promoter-TSS (NM_001204129)	promoter-TSS (NM_001204129)	-237	NM_001204129	56745	Mm.23845	NM_019959	ENSMUSG00000017446	C1qtnf1	1600017K21Rik|CTRP1|Zsig37	C1q and tumor necrosis factor related protein 1	protein-coding
mm_30760.1	chr4	15284375	15284419	+	1	NA	3' UTR (NM_181401, exon 3 of 3)	3' UTR (NM_181401, exon 3 of 3)	18577	NM_181401	100201	Mm.394111	NM_181401	ENSMUSG00000043252	Tmem64	9630015D15Rik|AI790744|AV300874	transmembrane protein 64	protein-coding
mm_67894.1	chr7	99482324	99482334	-	1	NA	TTS (NR_002172)	TTS (NR_002172)	603	NR_002172	449630	Mm.454449	NR_002172	ENSMUSG00000065822	Snord15a	EG449630|Gm5774|RNU15A|Rnu15-a|U15A	small nucleolar RNA, C/D box 15A	snoRNA
mm_99547.1	chr11	103355695	103355707	+	1	NA	intron (NM_001205236, intron 3 of 17)	intron (NM_001205236, intron 3 of 17)	7991	NM_183288	544817	Mm.259113	NM_133715	ENSMUSG00000034255	Arhgap27	2310069I04Rik|5730442P18Rik|Gm21552|Sh3d20	Rho GTPase activating protein 27	protein-coding
mm_136178.1	chr16	88869446	88869449	-	1	NA	promoter-TSS (NM_130876)	promoter-TSS (NM_130876)	-37	NM_130876	170657	Mm.196822	NM_130876	ENSMUSG00000060691	Krtap19-1	Krtap16-2|Krtap16-9	keratin associated protein 19-1	protein-coding
mm_6721.1	chr1	82506529	82506554	-	1	NA	intron (NM_007735, intron 22 of 47)	intron (NM_007735, intron 22 of 47)	80308	NM_007735	12829	Mm.40253	NM_007735	ENSMUSG00000067158	Col4a4	E130010M05Rik|[a]4(IV)	collagen, type IV, alpha 4	protein-coding
mm_98315.1	chr11	90187702	90187707	+	1	NA	Intergenic	Intergenic	-61772	NM_026178	67468	Mm.277518	NM_026178	ENSMUSG00000003948	Mmd	1200017E07Rik|1810073C06Rik|AA690185	monocyte to macrophage differentiation-associated	protein-coding
mm_101702.1	chr11	40755446	40755464	-	1	NA	promoter-TSS (NM_009831)	promoter-TSS (NM_009831)	-169	NM_009831	12450	Mm.2103	NM_009831	ENSMUSG00000020326	Ccng1	AI314029	cyclin G1	protein-coding
mm_117525.1	chr13	81657139	81657144	-	1	NA	promoter-TSS (NM_030257)	promoter-TSS (NM_030257)	-665	NM_030257	80289	Mm.259969	NM_030257	ENSMUSG00000035840	Lysmd3	1110030H10Rik|BC003322	LysM, putative peptidoglycan-binding, domain containing 3	protein-coding
mm_43975.1	chr5	146231212	146231274	+	1	NA	promoter-TSS (NM_153599)	promoter-TSS (NM_153599)	-432	NM_153599	264064	Mm.260576	NM_153599	ENSMUSG00000029635	Cdk8	-	cyclin-dependent kinase 8	protein-coding
mm_44479.1	chr5	23434225	23434236	-	1	NA	promoter-TSS (NM_026984)	promoter-TSS (NM_026984)	123	NR_040469	269630	Mm.425231	NR_040469	ENSMUSG00000073147	5031425E22Rik	-	RIKEN cDNA 5031425E22 gene	ncRNA
mm_54450.1	chr6	34746139	34746159	-	1	NA	intron (NM_001347100, intron 5 of 13)	intron (NM_001347100, intron 5 of 13)	-34283	NM_001289657	76223	Mm.150047	NM_178630	ENSMUSG00000038836	Agbl3	2900053G10Rik|4930431N21Rik|6530406M24Rik|CCP3	ATP/GTP binding protein-like 3	protein-coding
mm_76092.1	chr8	79711621	79711630	-	1	NA	promoter-TSS (NM_026904)	promoter-TSS (NM_026904)	115	NM_015751	24015	Mm.5831	NM_015751	ENSMUSG00000058355	Abce1	C79080|Oabp|RLI|RNS41|Rnaseli	ATP-binding cassette, sub-family E (OABP), member 1	protein-coding
mm_144365.1	chr18	20436170	20436183	+	1	NA	promoter-TSS (NM_181564)	promoter-TSS (NM_181564)	1	NM_181564	16769	Mm.358619	NM_181564	ENSMUSG00000001804	Dsg4	CDHF13|lah	desmoglein 4	protein-coding
mm_35944.1	chr4	53109320	53109323	-	1	NA	intron (NM_013454, intron 5 of 49)	intron (NM_013454, intron 5 of 49)	50574	NM_013454	11303	Mm.277376	NM_013454	ENSMUSG00000015243	Abca1	ABC-1|Abc1	ATP-binding cassette, sub-family A (ABC1), member 1	protein-coding
mm_113427.1	chr13	34162954	34163033	+	1	NA	promoter-TSS (NM_001110515)	promoter-TSS (NM_001110515)	29	NM_001110515	69666	Mm.24788	NM_001101430	ENSMUSG00000071451	Psmg4	PAC-4|mPAC4	proteasome (prosome, macropain) assembly chaperone 4	protein-coding
mm_35740.1	chr4	45320581	45320634	-	1	NA	promoter-TSS (NM_025513)	promoter-TSS (NM_025513)	-4	NM_025513	66362	Mm.275788	NM_025513	ENSMUSG00000028322	Exosc3	2310005D06Rik|AI593501|Rrp40	exosome component 3	protein-coding
mm_36147.1	chr4	59474881	59474898	-	1	NA	3' UTR (NM_144904, exon 15 of 15)	3' UTR (NM_144904, exon 15 of 15)	-36256	NM_001163288	634731	Mm.483589	NM_001163288	ENSMUSG00000038578	Susd1	A530080P10|Gm12528|OTTMUSG00000007332	sushi domain containing 1	protein-coding
mm_132687.1	chr16	43176798	43176803	+	1	NA	intron (NM_001285805, intron 2 of 10)	ID_B1|SINE|B4	-70484	NM_181058	56490	Mm.136238	NM_019778	ENSMUSG00000022708	Zbtb20	1300017A20Rik|7330412A13Rik|A930017C21Rik|D16Wsu73e|DPZF|HOF|ODA-8S|Oda8|Zfp288	zinc finger and BTB domain containing 20	protein-coding
mm_139860.1	chr17	69969388	69969440	+	1	NA	5' UTR (NM_001347412, exon 1 of 14)	5' UTR (NM_001347412, exon 1 of 14)	341	NM_001347411	224997	Mm.311840	NM_027712	ENSMUSG00000003279	Dlgap1	4933422O14Rik|9630002F18|AI845682|AI848168|BB075781|D17Bwg0511e|GKAP/SAPAP|GKPA/SAPAP|Gkap|Sapap1|mKIAA4162	discs, large (Drosophila) homolog-associated protein 1	protein-coding
mm_143254.1	chr17	65540748	65540773	-	1	NA	promoter-TSS (NM_001289485)	promoter-TSS (NM_001289485)	22	NM_001008973	381107	Mm.141275	NM_001008973	ENSMUSG00000045036	Tmem232	E130009J12Rik|Gm940|Tes13-L|Tes13-S	transmembrane protein 232	protein-coding
mm_33861.1	chr4	135911852	135911883	+	1	NA	5' UTR (NM_001305278, exon 1 of 2)	5' UTR (NM_001305278, exon 1 of 2)	187	NM_001305278	12802	Mm.297251	NM_009924	ENSMUSG00000062585	Cnr2	CB-2|CB2|CB2-R	cannabinoid receptor 2 (macrophage)	protein-coding
mm_161662.1	chr17	8242505	8242505	+	1	NA	promoter-TSS (NM_009835)	promoter-TSS (NM_009835)	-21	NM_009835	12458	Mm.8007	NM_009835	ENSMUSG00000040899	Ccr6	CC-CKR-6|CCR-6|Cmkbr6|KY411	chemokine (C-C motif) receptor 6	protein-coding
mm_95903.1	chr11	58202617	58202628	+	1	NA	intron (NM_018738, intron 2 of 2)	ID_B1|SINE|B4	3066	NM_018738	16145	Mm.33902	NM_018738	ENSMUSG00000078853	Igtp	AW558444|Irgm3	interferon gamma induced GTPase	protein-coding
mm_55021.1	chr6	48841099	48841139	-	1	NA	promoter-TSS (NM_001164209)	promoter-TSS (NM_001164209)	18	NM_001286652	65963	Mm.28385	NM_023056	ENSMUSG00000029810	Tmem176b	1810009M01Rik|Clast1|Lr8	transmembrane protein 176B	protein-coding
mm_109997.1	chr12	15816012	15816020	-	1	NA	5' UTR (NM_144551, exon 1 of 3)	5' UTR (NM_144551, exon 1 of 3)	769	NM_144551	217410	Mm.491136	NM_144551	ENSMUSG00000020601	Trib2	AW319517|TRB-2|TRB2	tribbles pseudokinase 2	protein-coding
mm_80815.1	chr9	96537270	96537296	+	1	NA	Intergenic	Intergenic	-58608	NM_001311135	19823	Mm.28235	NM_011279	ENSMUSG00000051234	Rnf7	Rbx2|SAG	ring finger protein 7	protein-coding
mm_30913.1	chr4	32615429	32615468	+	1	NA	promoter-TSS (NM_011997)	promoter-TSS (NM_011997)	-22	NM_001122978	26885	Mm.22279	NM_011997	ENSMUSG00000028282	Casp8ap2	D4Ertd659e|FLASH	caspase 8 associated protein 2	protein-coding
mm_72927.1	chr8	91106564	91106595	+	1	NA	intron (NM_011250, intron 15 of 21)	intron (NM_011250, intron 15 of 21)	27448	NM_001302337	14339	Mm.324588	NM_010241	ENSMUSG00000031667	Aktip	AL023020|Fif|Ft|Ft1|Fts	thymoma viral proto-oncogene 1 interacting protein	protein-coding
mm_12495.1	chr2	71787116	71787133	+	1	NA	5' UTR (NM_008397, exon 1 of 26)	5' UTR (NM_008397, exon 1 of 26)	185	NM_001277970	16403	Mm.225096	NM_008397	ENSMUSG00000027111	Itga6	5033401O05Rik|AI115430|Cd49f|VLA-6	integrin alpha 6	protein-coding
mm_154257.1	chr19	60767613	60767651	-	1	NA	exon (NM_010123, exon 18 of 22)	exon (NM_010123, exon 18 of 22)	6753	NR_034047	100217439		NR_034047		Snora19	MBI-51	small nucleolar RNA, H/ACA box 19	snoRNA
mm_144263.1	chr18	11052645	11052661	+	1	NA	promoter-TSS (NR_105023)	promoter-TSS (NR_105023)	-86	NR_105023	68434	Mm.57626	NR_105022	ENSMUSG00000097222	1010001N08Rik	Gata6as	RIKEN cDNA 1010001N08 gene	ncRNA
mm_128995.1	chr15	74839075	74839084	-	1	NA	exon (NM_001033229, exon 4 of 9)	exon (NM_001033229, exon 4 of 9)	2564	NM_001033229	110115	Mm.322606	NM_001033229	ENSMUSG00000075604	Cyp11b1	AA389061|CPN1|Cyp11b|Cyp11b-1|FHI	cytochrome P450, family 11, subfamily b, polypeptide 1	protein-coding
mm_109362.1	chr12	109636225	109636241	+	1	NA	TTS (NR_046302)	TTS (NR_046302)	221	NR_046302	449562		NR_046302	ENSMUSG00000088294	AF357425	MBII-48	snoRNA AF357425	snoRNA
mm_83871.1	chr9	55026542	55026599	-	1	NA	promoter-TSS (NM_145129)	promoter-TSS (NM_145129)	-11	NM_145129	110834	Mm.63569	NM_145129	ENSMUSG00000032303	Chrna3	(a)3|A730007P14Rik|Acra-3|Acra3	cholinergic receptor, nicotinic, alpha polypeptide 3	protein-coding
mm_97361.1	chr11	77505549	77505559	+	1	NA	exon (NM_001004144, exon 16 of 20)	exon (NM_001004144, exon 16 of 20)	7719	NM_001024920	216964	Mm.341211	NM_001024920	ENSMUSG00000044328	Trp53i13	2410019G02Rik|Tp53i13	transformation related protein 53 inducible protein 13	protein-coding
mm_166187.1	chr5	33018639	33018668	-	1	NA	promoter-TSS (NM_011738)	promoter-TSS (NM_011738)	-163	NM_011738	22629	Mm.332314	NM_011738	ENSMUSG00000018965	Ywhah	-	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta polypeptide	protein-coding
mm_59341.1	chr7	25474748	25474773	+	1	NA	exon (NM_001039186, exon 3 of 8)	exon (NM_001039186, exon 3 of 8)	2865	NM_001039185	26365	Mm.322502	NM_011926	ENSMUSG00000074272	Ceacam1	Bgp|Bgp1|C-CAM|CD66a|Cc1|Cea-1|Cea-7|Cea1|Cea7|Hv-2|Hv2|MHVR|MHVR1|Mhv-1|bb-1|mCEA1|mmCGM1|mmCGM1a|mmCGM2	carcinoembryonic antigen-related cell adhesion molecule 1	protein-coding
mm_28432.1	chr3	90465815	90465819	-	1	NA	promoter-TSS (NM_008727)	promoter-TSS (NM_008727)	49	NM_008727	18160	Mm.4627	NM_008727	ENSMUSG00000027931	Npr1	AI893888|GC-A|NPR-A|NPRA|Pndr	natriuretic peptide receptor 1	protein-coding
mm_64451.1	chr7	142659022	142659032	+	1	NA	promoter-TSS (NM_010514)	promoter-TSS (NM_010514)	-223	NM_010514	16002	Mm.3862	NM_010514	ENSMUSG00000048583	Igf2	AL033362|Igf-2|Igf-II|M6pr|Mpr|Peg2	insulin-like growth factor 2	protein-coding
mm_78641.1	chr9	40269380	40269423	+	1	NA	5' UTR (NM_001083917, exon 1 of 7)	5' UTR (NM_001083917, exon 1 of 7)	185	NM_178227	235281	Mm.290083	NM_153522	ENSMUSG00000049281	Scn3b	1110001K16Rik|4833414B02Rik|Scnb3	sodium channel, voltage-gated, type III, beta	protein-coding
mm_151308.1	chr19	55743140	55743162	+	1	NA	exon (NM_001142918, exon 3 of 15)	exon (NM_001142918, exon 3 of 15)	1341	NM_001142923	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_161420.1	chr15	36179332	36179332	+	1	NA	promoter-TSS (NM_012031)	promoter-TSS (NM_012031)	-198	NM_012031	26942	Mm.295539	NM_012031	ENSMUSG00000037617	Spag1	tpis	sperm associated antigen 1	protein-coding
mm_139649.1	chr17	57386710	57386722	+	1	NA	intron (NM_010130, intron 2 of 21)	intron (NM_010130, intron 2 of 21)	28030	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_16053.1	chr2	167773152	167773159	+	1	NA	Intergenic	Intergenic	81978	NR_015500	329562	Mm.123101	NM_177851	ENSMUSG00000006462	A530013C23Rik	-	RIKEN cDNA A530013C23 gene	ncRNA
mm_44326.1	chr5	9725795	9725862	-	1	NA	promoter-TSS (NM_181850)	promoter-TSS (NM_181850)	-476	NM_181850	108069	Mm.318966	NM_181850	ENSMUSG00000003974	Grm3	0710001G23Rik|Gprc1c|mGlu3|mGluR3	glutamate receptor, metabotropic 3	protein-coding
mm_155872.1	chrX	101396510	101396512	+	1	NA	Intergenic	Intergenic	12779	NM_001302497	14618	Mm.21198	NM_008124	ENSMUSG00000047797	Gjb1	Cnx32|Cx32|connexin-32	gap junction protein, beta 1	protein-coding
mm_85680.1	chr9	107872404	107872422	-	1	NA	intron (NM_011251, intron 1 of 20)	CpG	406	NM_011251	19654	Mm.139926	NM_011251	ENSMUSG00000032582	Rbm6	4930506F14Rik|Def-3|NY-LU-12|g16|mKIAA4015	RNA binding motif protein 6	protein-coding
mm_43207.1	chr5	129174276	129174322	+	1	NA	intron (NM_001347486, intron 15 of 24)	intron (NM_001347486, intron 15 of 24)	77549	NM_001347486	243277	Mm.440501	NM_177734	ENSMUSG00000044017	Adgrd1	E230012M21Rik|Gpr133	adhesion G protein-coupled receptor D1	protein-coding
mm_52734.1	chr6	120405221	120405224	+	1	NA	intron (NM_145997, intron 15 of 27)	B1_Mur4|SINE|Alu	-40853	NR_045558	67200	Mm.45767	NM_026028	ENSMUSG00000030177	Ccdc77	2400002C23Rik|2700091N06Rik|AV168274	coiled-coil domain containing 77	protein-coding
mm_55929.1	chr6	84587992	84588010	-	1	NA	exon (NM_175475, exon 2 of 7)	exon (NM_175475, exon 2 of 7)	5809	NM_175475	232174	Mm.255246	NM_175475	ENSMUSG00000063415	Cyp26b1	CP26|P450RAI-2	cytochrome P450, family 26, subfamily b, polypeptide 1	protein-coding
mm_172782.1	chr8	98892253	98892255	+	1	NA	Intergenic	RLTR10D2|LTR|ERVK	-119633	NR_110579	100873092	Mm.414599	NR_110579	ENSMUSG00000089819	Gm15679	OTTMUSG00000025218	predicted gene 15679	ncRNA
mm_115385.1	chr13	113209487	113209499	+	1	NA	promoter-TSS (NM_023612)	promoter-TSS (NM_023612)	-166	NM_023612	71690	Mm.38929	NM_023612	ENSMUSG00000042379	Esm1	0610042H23Rik|AV004503|ESM-1	endothelial cell-specific molecule 1	protein-coding
mm_143298.1	chr17	65951157	65951199	-	1	NA	promoter-TSS (NM_023053)	promoter-TSS (NM_023053)	9	NM_023053	65960	Mm.10153	NM_023053	ENSMUSG00000024098	Twsg1	1810013J15Rik|9030422N06Rik|AW552143|D17Ertd403e|Tsg|Twg	twisted gastrulation BMP signaling modulator 1	protein-coding
mm_72580.1	chr8	84200932	84200947	+	1	NA	Intergenic	CpG	-7579	NR_029740	387216		NR_029740	ENSMUSG00000065611	Mir23a	Mirn23a|mir-23a|mmu-mir-23a	microRNA 23a	ncRNA
mm_98350.1	chr11	93401605	93401643	+	1	NA	intron (NM_028296, intron 3 of 8)	B1F|SINE|Alu	302334	NM_028296	72605	Mm.342160	NM_028296	ENSMUSG00000056158	Car10	2700029L05Rik|BB085816|Ca10	carbonic anhydrase 10	protein-coding
mm_108472.1	chr12	83646154	83646193	+	1	NA	exon (NM_027349, exon 4 of 19)	exon (NM_027349, exon 4 of 19)	13939	NM_027349	67039	Mm.46005	NM_027349	ENSMUSG00000010608	Rbm25	2600011C06Rik|2610015J01Rik|A130095G20Rik|AI159652|AL023075|AU043498|RNPC7	RNA binding motif protein 25	protein-coding
mm_65758.1	chr7	28629793	28629802	-	1	NA	intron (NM_175319, intron 1 of 12)	intron (NM_175319, intron 1 of 12)	1218	NM_175319	101744	Mm.26022	NM_175319	ENSMUSG00000037469	Acp7	AU017076|C330005M16Rik|Papl	acid phosphatase 7, tartrate resistant	protein-coding
mm_159557.1	chr4	107580985	107580985	+	1	NA	intron (NM_147221, intron 4 of 10)	intron (NM_147221, intron 4 of 10)	103177	NM_019872	56296	Mm.141324	NM_019872	ENSMUSG00000028610	Dmrtb1	Dmrt6|Prp13	DMRT-like family B with proline-rich C-terminal, 1	protein-coding
mm_30420.1	chr3	152266155	152266167	-	1	NA	intron (NM_199465, intron 1 of 12)	intron (NM_199465, intron 1 of 12)	159	NM_199465	68810	Mm.200188	NM_199465	ENSMUSG00000039103	Nexn	1110046H09Rik|AA553326|NELIN	nexilin	protein-coding
mm_1050.1	chr1	58802578	58802580	+	1	NA	promoter-TSS (NM_001277926)	promoter-TSS (NM_001277926)	77	NM_001080126	12370	Mm.336851	NM_009812	ENSMUSG00000026029	Casp8	CASP-8|FLICE|MACH|Mch5	caspase 8	protein-coding
mm_154566.1	chrX	6415737	6415747	+	1	NA	promoter-TSS (NM_001313764)	promoter-TSS (NM_001313764)	0	NM_001313764	208431	Mm.23208	NM_001040459	ENSMUSG00000068270	Shroom4	D430043L16Rik|Gm724|Shrm4	shroom family member 4	protein-coding
mm_54554.1	chr6	37145978	37145979	-	1	NA	intron (NM_001347104, intron 2 of 32)	intron (NM_001347104, intron 2 of 32)	153998	NM_001081206	320127	Mm.119469	NM_001081206	ENSMUSG00000038665	Dgki	C130010K08Rik	diacylglycerol kinase, iota	protein-coding
mm_148753.1	chr19	6058135	6058206	+	1	NA	promoter-TSS (NM_026246)	promoter-TSS (NM_026246)	203	NM_001190436	14109	Mm.329631	NM_007990	ENSMUSG00000038274	Fau	MNSFbeta	Finkel-Biskis-Reilly murine sarcoma virus (FBR-MuSV) ubiquitously expressed (fox derived)	protein-coding
mm_84626.1	chr9	70657122	70657188	-	1	NA	promoter-TSS (NM_172772)	promoter-TSS (NM_172772)	19	NM_172772	235461	Mm.170855	NM_172772	ENSMUSG00000042444	Fam63b	AI465301|B230380D07Rik|mKIAA1164	family with sequence similarity 63, member B	protein-coding
mm_162386.1	chr1	74541460	74541466	+	1	NA	intron (NM_176972, intron 1 of 25)	intron (NM_176972, intron 1 of 25)	-1426	NM_001081456	18802	Mm.290731	NM_148937	ENSMUSG00000026173	Plcd4	4921507K24Rik	phospholipase C, delta 4	protein-coding
mm_72611.1	chr8	84597908	84597920	+	1	NA	intron (NM_001252059, intron 30 of 45)	PB1D9|SINE|Alu	64938	NM_010499	15936	Mm.399	NM_010499	ENSMUSG00000053560	Ier2	AI317238|Ch1|Pip92	immediate early response 2	protein-coding
mm_137853.1	chr17	31104108	31104116	+	1	NA	exon (NM_009593, exon 6 of 15)	exon (NM_009593, exon 6 of 15)	25499	NM_011575	21786	Mm.4641	NM_011575	ENSMUSG00000024029	Tff3	ITF|mITF	trefoil factor 3, intestinal	protein-coding
mm_169743.1	chr15	86195126	86195126	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-8985	NM_145475	223753	Mm.222685	NM_145475	ENSMUSG00000035891	Cerk	AI848610|D330016D08Rik|mKIAA1646	ceramide kinase	protein-coding
mm_70618.1	chr8	13483707	13483711	+	1	NA	exon (NM_019521, exon 4 of 15)	exon (NM_019521, exon 4 of 15)	10826	NM_019521	14456	Mm.3982	NM_019521	ENSMUSG00000031451	Gas6	Gas-6	growth arrest specific 6	protein-coding
mm_160414.1	chr8	79118231	79118231	+	1	NA	exon (NM_178267, exon 6 of 15)	exon (NM_178267, exon 6 of 15)	89794	NM_178267	622675	Mm.48724	NM_178267	ENSMUSG00000071064	Zfp827	2810449M09Rik|D630040G17Rik|Znf827	zinc finger protein 827	protein-coding
mm_89530.1	chr10	94498917	94498924	+	1	NA	Intergenic	B3|SINE|B2	-15937	NM_172051	319880	Mm.23047	NM_172051	ENSMUSG00000020023	Tmcc3	AW488095|C630016B22Rik|C88213|Tmcc1	transmembrane and coiled coil domains 3	protein-coding
mm_13717.1	chr2	117181260	117181272	+	1	NA	3' UTR (NM_033524, exon 7 of 7)	3' UTR (NM_033524, exon 7 of 7)	-3861	NR_030440	732489		NR_030440	ENSMUSG00000076376	Mir674	Mirn674|mir-674|mmu-mir-674	microRNA 674	ncRNA
mm_116401.1	chr13	41359878	41359881	-	1	NA	promoter-TSS (NM_017464)	promoter-TSS (NM_017464)	-878	NM_017464	18003	Mm.288980	NM_017464	ENSMUSG00000021365	Nedd9	Cas-L|CasL|HEF1|MEF1|Nedd-9|p105	neural precursor cell expressed, developmentally down-regulated gene 9	protein-coding
mm_89484.1	chr10	93641042	93641056	+	1	NA	promoter-TSS (NM_021320)	promoter-TSS (NM_021320)	0	NM_021320	57764	Mm.483868	NM_021320	ENSMUSG00000020019	Ntn4	-	netrin 4	protein-coding
mm_42156.1	chr5	112156234	112156240	+	1	NA	Intergenic	Intergenic	-50526	NR_045377	75569	Mm.243721	NR_045377	ENSMUSG00000101683	1700028D13Rik	-	RIKEN cDNA 1700028D13 gene	ncRNA
mm_152483.1	chr19	11049412	11049423	-	1	NA	intron (NR_102366, intron 1 of 2)	MLTR14|LTR|ERV1	1149	NR_102366	107350	Mm.6381	NM_001177351	ENSMUSG00000075010	AW112010	-	expressed sequence AW112010	ncRNA
mm_38748.1	chr4	145276673	145276688	-	1	NA	intron (NM_009401, intron 11 of 12)	intron (NM_009401, intron 11 of 12)	-29810	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_36621.1	chr4	91363879	91363882	-	1	NA	intron (NM_001347149, intron 1 of 7)	B1_Mur3|SINE|Alu	8175	NM_010486	15569	Mm.318042	NM_010486	ENSMUSG00000008489	Elavl2	Hub|mel-N1	ELAV (embryonic lethal, abnormal vision, Drosophila)-like 2 (Hu antigen B)	protein-coding
mm_96155.1	chr11	61485704	61485741	+	1	NA	exon (NM_029568, exon 2 of 6)	exon (NM_029568, exon 2 of 6)	278	NM_029568	76293	Mm.272278	NM_029568	ENSMUSG00000042436	Mfap4	1110007F23Rik	microfibrillar-associated protein 4	protein-coding
mm_85747.1	chr9	108578658	108578675	-	1	NA	promoter-TSS (NM_031392)	promoter-TSS (NM_031392)	4	NM_031392	83669	Mm.335454	NM_031392	ENSMUSG00000066357	Wdr6	mWDR6	WD repeat domain 6	protein-coding
mm_112720.1	chr13	19190861	19190877	+	1	NA	Intergenic	Intergenic	204944	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_13867.1	chr2	119799575	119799592	+	1	NA	promoter-TSS (NM_019392)	promoter-TSS (NM_019392)	69	NM_019392	22174	Mm.2901	NM_019392	ENSMUSG00000027298	Tyro3	AI323366|Brt|Dtk|Etk-2|Rse|Sky|TK19-2|Tif|etk2/tyro3|tk19-1	TYRO3 protein tyrosine kinase 3	protein-coding
mm_79716.1	chr9	61373609	61373650	+	1	NA	intron (NM_001083927, intron 1 of 19)	CpG	1263	NM_001083927	21887	Mm.24255	NM_009389	ENSMUSG00000032280	Tle3	2610103N05Rik|ESG|Grg3a|Grg3b|mKIAA1547	transducin-like enhancer of split 3	protein-coding
mm_158510.1	chrX	142966710	142966734	-	1	NA	promoter-TSS (NM_019496)	promoter-TSS (NM_019496)	6	NM_019496	56068	Mm.143724	NM_019496	ENSMUSG00000042225	Ammecr1	6230420G18Rik	Alport syndrome, mental retardation, midface hypoplasia and elliptocytosis chromosomal region gene 1	protein-coding
mm_118245.1	chr13	111808939	111809018	-	1	NA	promoter-TSS (NM_011945)	promoter-TSS (NM_011945)	5	NM_011945	26401	Mm.15918	NM_011945	ENSMUSG00000021754	Map3k1	MAPKKK1|MEKK1|Mekk	mitogen-activated protein kinase kinase kinase 1	protein-coding
mm_166241.1	chr5	74009029	74009042	-	1	NA	intron (NM_177561, intron 5 of 8)	RLTR17B_Mm|LTR|ERVK	59376	NM_177561	69727	Mm.48795	NM_177561	ENSMUSG00000054814	Usp46	1190009E20Rik|2410018I08Rik|AI451644	ubiquitin specific peptidase 46	protein-coding
mm_29634.1	chr3	121787811	121787816	-	1	NA	intron (NM_008991, intron 4 of 22)	intron (NM_008991, intron 4 of 22)	27402	NM_008991	19299	Mm.399042	NM_008991	ENSMUSG00000028127	Abcd3	AI313901|AU018866|AW146054|PMP68|PMP70|Pxmp1	ATP-binding cassette, sub-family D (ALD), member 3	protein-coding
mm_20206.1	chr2	125397812	125397842	-	1	NA	exon (NM_007993, exon 9 of 66)	exon (NM_007993, exon 9 of 66)	108611	NM_007993	14118	Mm.271644	NM_007993	ENSMUSG00000027204	Fbn1	AI536462|B430209H23|Fib-1|Tsk	fibrillin 1	protein-coding
mm_37241.1	chr4	118134870	118134962	-	1	NA	promoter-TSS (NM_001285521)	promoter-TSS (NM_001285521)	30	NM_001285520	20441	Mm.251002	NM_009176	ENSMUSG00000028538	St3gal3	ST3GalIII|ST3N|Siat3|Siat6	ST3 beta-galactoside alpha-2,3-sialyltransferase 3	protein-coding
mm_47315.1	chr5	122459539	122459559	-	1	NA	exon (NM_009722, exon 16 of 21)	exon (NM_009722, exon 16 of 21)	37105	NM_019805	56317	Mm.37341	NM_019805	ENSMUSG00000029466	Anapc7	APC7|AW545589	anaphase promoting complex subunit 7	protein-coding
mm_34540.1	chr4	149518128	149518157	+	1	NA	promoter-TSS (NM_023465)	promoter-TSS (NM_023465)	-99	NM_023465	67087	Mm.299735	NM_023465	ENSMUSG00000028988	Ctnnbip1	1110008O09Rik|2310001I19Rik|AW457332|Catnbip1|Icat	catenin beta interacting protein 1	protein-coding
mm_49835.1	chr6	37870996	37871015	+	1	NA	5' UTR (NM_145076, exon 1 of 19)	5' UTR (NM_145076, exon 1 of 19)	194	NM_145076	21848	Mm.41063	NM_145076	ENSMUSG00000029833	Trim24	A130082H20Rik|AI447469|D430004I05Rik|TIF1|TIF1-alpha|TIF1alpha|Tif1a	tripartite motif-containing 24	protein-coding
mm_134285.1	chr16	14212550	14212559	-	1	NA	exon (NM_013607, exon 26 of 42)	exon (NM_013607, exon 26 of 42)	49279	NM_001114085	67203	Mm.24105	NM_023317	ENSMUSG00000022678	Nde1	2810027M15Rik|AU042936|AW822251|Nude|mNudE	nudE neurodevelopment protein 1	protein-coding
mm_49093.1	chr6	7562354	7562354	+	1	NA	intron (NM_009311, intron 6 of 6)	intron (NM_009311, intron 6 of 6)	7283	NM_009311	21333	Mm.1440	NM_009311	ENSMUSG00000061762	Tac1	4930528L02Rik|NK-1|NK1|Nkna|PPT-A|PPTA|SP	tachykinin 1	protein-coding
mm_22156.1	chr2	172806826	172806832	-	1	NA	Intergenic	Intergenic	133492	NM_007557	12162	Mm.595	NM_007557	ENSMUSG00000008999	Bmp7	OP1	bone morphogenetic protein 7	protein-coding
mm_30756.1	chr4	15265799	15265809	+	1	NA	promoter-TSS (NM_181401)	promoter-TSS (NM_181401)	-16	NM_181401	100201	Mm.394111	NM_181401	ENSMUSG00000043252	Tmem64	9630015D15Rik|AI790744|AV300874	transmembrane protein 64	protein-coding
mm_161330.1	chr14	50453077	50453077	+	1	NA	promoter-TSS (NM_146667)	promoter-TSS (NM_146667)	23	NM_146667	258661	Mm.377624	NM_146667	ENSMUSG00000095917	Olfr740	MOR106-4	olfactory receptor 740	protein-coding
mm_165654.1	chr3	84155522	84155532	+	1	NA	intron (NM_029797, intron 1 of 7)	CpG	259	NM_029797	76915	Mm.274829	NM_029797	ENSMUSG00000033752	Mnd1	2610034E18Rik|AI591601|Gaj	meiotic nuclear divisions 1	protein-coding
mm_40406.1	chr5	53049347	53049363	+	1	NA	promoter-TSS (NM_011402)	promoter-TSS (NM_011402)	2	NM_011402	20531	Mm.284891	NM_011402	ENSMUSG00000029188	Slc34a2	AA536683|D5Ertd227e|NaPi-2b|Npt2b	solute carrier family 34 (sodium phosphate), member 2	protein-coding
mm_37442.1	chr4	123323597	123323601	-	1	NA	promoter-TSS (NM_022033)	promoter-TSS (NM_022033)	80	NM_022033	64059	Mm.270287	NM_022033	ENSMUSG00000076436	Oxct2a	Oxct|Oxct2|Scot|Scot-t1	3-oxoacid CoA transferase 2A	protein-coding
mm_50425.1	chr6	48841558	48841568	+	1	NA	promoter-TSS (NM_001164209)	promoter-TSS (NM_001164209)	80	NM_025326	66058	Mm.27061	NM_025326	ENSMUSG00000023367	Tmem176a	0610011I04Rik|AU040201|AU041743|Keg2	transmembrane protein 176A	protein-coding
mm_148783.1	chr19	6112941	6112946	+	1	NA	exon (NM_001009546, exon 13 of 18)	exon (NM_001009546, exon 13 of 18)	5643	NM_133678	66406	Mm.303924	NM_133678	ENSMUSG00000024790	Sac3d1	2410004C24Rik|AU015683|shd1	SAC3 domain containing 1	protein-coding
mm_51654.1	chr6	86078038	86078063	+	1	NA	promoter-TSS (NM_001271861)	promoter-TSS (NM_001271861)	2	NM_001271859	11519	Mm.104155	NM_013458	ENSMUSG00000030000	Add2	2900072M03Rik|add97	adducin 2 (beta)	protein-coding
mm_168001.1	chrY	206180	206199	+	1	NA	promoter-TSS (NR_126545)	promoter-TSS (NR_126545)	39	NR_126545	69438		NR_126545	ENSMUSG00000101796	1700020D14Rik	-	RIKEN cDNA 1700020D14 gene	ncRNA
mm_77666.1	chr8	124721957	124721999	-	1	NA	promoter-TSS (NM_026855)	promoter-TSS (NM_026855)	-3	NM_145607	234875	Mm.38436	NM_145607	ENSMUSG00000037300	Ttc13	BC017545	tetratricopeptide repeat domain 13	protein-coding
mm_31175.1	chr4	43492824	43492841	+	1	NA	promoter-TSS (NM_001037913)	promoter-TSS (NM_001037913)	227	NR_001460	19782		NR_001460	ENSMUSG00000088088	Rmrp	1110032O22Rik|Rmrpr	RNA component of mitochondrial RNAase P	ncRNA
mm_42180.1	chr5	112261983	112262023	+	1	NA	intron (NM_023695, intron 3 of 5)	intron (NM_023695, intron 3 of 5)	6183	NM_001312893	12960	Mm.29488	NM_023695	ENSMUSG00000029343	Crybb1	3110006K12Rik|BB1CRY	crystallin, beta B1	protein-coding
mm_55261.1	chr6	53681079	53681094	-	1	NA	exon (NM_172728, exon 4 of 7)	exon (NM_172728, exon 4 of 7)	107712	NM_172728	231991	Mm.227444	NM_172728	ENSMUSG00000053007	Creb5	9430076C15Rik|CRE-BPa|Crebpa|D430026C09Rik	cAMP responsive element binding protein 5	protein-coding
mm_57022.1	chr6	122279932	122279956	-	1	NA	intron (NM_016970, intron 1 of 4)	intron (NM_016970, intron 1 of 4)	2889	NM_016970	50928	Mm.20434	NM_016970	ENSMUSG00000030114	Klrg1	2F1-Ag|MAFA|MAFA-L	killer cell lectin-like receptor subfamily G, member 1	protein-coding
mm_127595.1	chr15	102393788	102393801	+	1	NA	Intergenic	Intergenic	-12522	NM_013672	20683	Mm.4618	NM_013672	ENSMUSG00000001280	Sp1	1110003E12Rik|AA450830|AI845540|Sp1-1	trans-acting transcription factor 1	protein-coding
mm_146398.1	chr18	82910864	82910885	+	1	NA	promoter-TSS (NM_183033)	promoter-TSS (NM_183033)	-5	NM_183033	329003	Mm.326526	NM_183033	ENSMUSG00000058881	Zfp516	C330029B10Rik|D230016L03|Zfp26l|Znf516|mKIAA0222	zinc finger protein 516	protein-coding
mm_94988.1	chr11	31870902	31870923	+	1	NA	promoter-TSS (NM_026252)	promoter-TSS (NM_026252)	-28	NM_001290676	67579	Mm.339792	NM_026252	ENSMUSG00000020300	Cpeb4	Cpe-bp4|Cpeb-4|mCPEB-4	cytoplasmic polyadenylation element binding protein 4	protein-coding
mm_132989.1	chr16	52468680	52468688	+	1	NA	Intergenic	Intergenic	-15603	NM_001331110	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_92080.1	chr10	62756541	62756576	-	1	NA	exon (NM_026201, exon 17 of 25)	exon (NM_026201, exon 17 of 25)	9048	NR_028557	100217463		NR_028557		Snord98	MBII-419	small nucleolar RNA, C/D box 98	snoRNA
mm_141713.1	chr17	34025487	34025513	-	1	NA	promoter-TSS (NR_029800)	promoter-TSS (NR_029800)	-408	NR_029800	723823		NR_029800	ENSMUSG00000065555	Mir219a-1	Mir219-1|Mirn219-1|mir-219a-1|mmu-mir-219a-1	microRNA 219a-1	ncRNA
mm_61993.1	chr7	91108818	91108829	+	1	NA	intron (NM_011807, intron 1 of 22)	intron (NM_011807, intron 1 of 22)	18037	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_17970.1	chr2	37591576	37591578	-	1	NA	intron (NM_009261, intron 14 of 16)	intron (NM_009261, intron 14 of 16)	55708	NM_009261	20744	Mm.237095	NM_009261	ENSMUSG00000026915	Strbp	6430510M02Rik|AI852513|C230082I21Rik|C86322|Spnr	spermatid perinuclear RNA binding protein	protein-coding
mm_7875.1	chr1	133010688	133010727	-	1	NA	intron (NM_001302801, intron 4 of 10)	intron (NM_001302801, intron 4 of 10)	14709	NR_126506	17248	Mm.426531	NM_008575	ENSMUSG00000054387	Mdm4	4933417N07Rik|AA414968|AL023055|AU018793|AU021806|C85810|Mdmx	transformed mouse 3T3 cell double minute 4	protein-coding
mm_21799.1	chr2	164911176	164911210	-	1	NA	intron (NM_199027, intron 1 of 27)	CpG	557	NM_199027	329559	Mm.330776	NM_199027	ENSMUSG00000039834	Zfp335	1810045J01Rik|NIF-1|Nif1|Znf335	zinc finger protein 335	protein-coding
mm_22308.1	chr2	180386754	180386763	-	1	NA	promoter-TSS (NR_040745)	promoter-TSS (NR_040745)	-873	NR_040745	320485	Mm.405172	NR_040745		B230312C02Rik	-	RIKEN cDNA B230312C02 gene	ncRNA
mm_156241.1	chrX	136225544	136225555	+	1	NA	exon (NM_001127169, exon 3 of 3)	exon (NM_001127169, exon 3 of 3)	1508	NM_001127169	100040972	Mm.18125	NM_001127169	ENSMUSG00000079428	Tceal7	1110018P05Rik	transcription elongation factor A (SII)-like 7	protein-coding
mm_45859.1	chr5	87788625	87788637	-	1	NA	3' UTR (NM_001304768, exon 13 of 13)	3' UTR (NM_001304768, exon 13 of 13)	14181	NM_007785	12993	Mm.4908	NM_007785	ENSMUSG00000061937	Csn1s2a	Csng|PP22	casein alpha s2-like A	protein-coding
mm_54455.1	chr6	34746461	34746574	-	1	NA	intron (NM_001347100, intron 5 of 13)	intron (NM_001347100, intron 5 of 13)	-33915	NM_001289657	76223	Mm.150047	NM_178630	ENSMUSG00000038836	Agbl3	2900053G10Rik|4930431N21Rik|6530406M24Rik|CCP3	ATP/GTP binding protein-like 3	protein-coding
mm_167113.1	chr7	117449738	117449767	-	1	NA	intron (NM_175645, intron 1 of 11)	intron (NM_175645, intron 1 of 11)	68773	NM_175645	233781	Mm.461427	NM_175645	ENSMUSG00000030657	Xylt1	8030490L12	xylosyltransferase 1	protein-coding
mm_42995.1	chr5	123344667	123344675	+	1	NA	exon (NM_029850, exon 1 of 6)	exon (NM_029850, exon 1 of 6)	223	NM_029850	77045	Mm.151960	NM_029850	ENSMUSG00000029438	Bcl7a	4432415N06Rik|AI448316	B cell CLL/lymphoma 7A	protein-coding
mm_22839.1	chr3	27689676	27689680	+	1	NA	intron (NM_173182, intron 1 of 25)	ID_B1|SINE|B4	20761	NM_173182	72007	Mm.38832	NM_173182	ENSMUSG00000039286	Fndc3b	1600019O04Rik|AW550168|Fad104|mKIAA4164	fibronectin type III domain containing 3B	protein-coding
mm_148215.1	chr18	80236674	80236679	-	1	NA	intron (NM_001136181, intron 2 of 4)	CpG	10426	NM_001136181	66255	Mm.272341	NM_001136181	ENSMUSG00000078963	Hsbp1l1	1810005K13Rik	heat shock factor binding protein 1-like 1	protein-coding
mm_68609.1	chr7	116334133	116334188	-	1	NA	promoter-TSS (NM_026533)	promoter-TSS (NM_026533)	30	NM_026533	68052	Mm.14798	NM_026533	ENSMUSG00000090862	Rps13	2700063M04Rik	ribosomal protein S13	protein-coding
mm_71068.1	chr8	34146326	34146337	+	1	NA	intron (NM_026609, intron 1 of 3)	intron (NM_026609, intron 1 of 3)	408	NM_026609	68192	Mm.34212	NM_026609	ENSMUSG00000031513	Leprotl1	1110067H13Rik|1520402O14Rik|AI854296	leptin receptor overlapping transcript-like 1	protein-coding
mm_28769.1	chr3	95904684	95904692	-	1	NA	promoter-TSS (NM_011797)	promoter-TSS (NM_011797)	-49	NM_011797	23831	Mm.489647	NM_011797	ENSMUSG00000038526	Car14	AW536446|Ca14	carbonic anhydrase 14	protein-coding
mm_42732.1	chr5	120621602	120621616	+	1	NA	intron (NM_028041, intron 10 of 19)	intron (NM_028041, intron 10 of 19)	8479	NM_028041	71990	Mm.24495	NM_028041	ENSMUSG00000029599	Ddx54	2410015A15Rik|AI414901|DP97	DEAD (Asp-Glu-Ala-Asp) box polypeptide 54	protein-coding
mm_132448.1	chr16	35983425	35983435	+	1	NA	promoter-TSS (NM_008465)	promoter-TSS (NM_008465)	67	NM_008465	16646	Mm.3991	NM_008465	ENSMUSG00000022905	Kpna1	AW494490|IPOA5|NPI1|Rch2|mSRP1	karyopherin (importin) alpha 1	protein-coding
mm_138793.1	chr17	37492285	37492320	+	1	NA	promoter-TSS (NM_146328)	promoter-TSS (NM_146328)	-166	NM_146328	258325	Mm.484339	NM_146328	ENSMUSG00000090894	Olfr110	MOR249-2	olfactory receptor 110	protein-coding
mm_82873.1	chr9	32424153	32424174	-	1	NA	exon (NM_008026, exon 9 of 9)	exon (NM_008026, exon 9 of 9)	30178	NM_001168354	56379	Mm.390168	NM_019659	ENSMUSG00000041248	Kcnj1	Kir1.1|ROMK|Romk2	potassium inwardly-rectifying channel, subfamily J, member 1	protein-coding
mm_137544.1	chr17	27556874	27556885	+	1	NA	5' UTR (NM_016660, exon 1 of 5)	intron (NM_001025427, intron 1 of 4)	226	NM_001166477	111241	Mm.426212	NM_001166476	ENSMUSG00000078249	Hmga1-rs1	ENSMUSG00000041059|Hmgi-rs1	high mobility group AT-hook I, related sequence 1	protein-coding
mm_57350.1	chr6	124756827	124756847	-	1	NA	promoter-TSS (NM_007881)	promoter-TSS (NM_007881)	-350	NM_007881	13498	Mm.333380	NM_007881	ENSMUSG00000004263	Atn1	Atr1|Drpla|atrophin-1	atrophin 1	protein-coding
mm_142798.1	chr17	50190654	50190662	-	1	NA	promoter-TSS (NM_181397)	promoter-TSS (NM_181397)	-161	NM_181397	76438	Mm.41854	NM_181397	ENSMUSG00000039316	Rftn1	2310015N21Rik|AI853526	raftlin lipid raft linker 1	protein-coding
mm_118514.1	chr14	14346619	14346627	+	1	NA	intron (NM_008369, intron 1 of 11)	intron (NM_008369, intron 1 of 11)	128	NM_008369	16188	Mm.425857	NM_008369	ENSMUSG00000068758	Il3ra	CD123|CDw123|SUT-1	interleukin 3 receptor, alpha chain	protein-coding
mm_171626.1	chr4	17171910	17171912	+	1	NA	Intergenic	L1Md_F3|LINE|L1	-680982	NR_135158	17389	Mm.187315	NM_019724	ENSMUSG00000028226	Mmp16	MT-MMP 3|MT3-MMP|Mt3mmp	matrix metallopeptidase 16	protein-coding
mm_57524.1	chr6	125812293	125812324	-	1	NA	intron (NM_153589, intron 9 of 25)	intron (NM_153589, intron 9 of 25)	121889	NM_153589	243634	Mm.333398	NM_153589	ENSMUSG00000038115	Ano2	BC033409|Tmem16b	anoctamin 2	protein-coding
mm_102304.1	chr11	55608190	55608204	-	1	NA	promoter-TSS (NM_020492)	promoter-TSS (NM_020492)	1	NM_001290821	14654	Mm.89320	NM_020492	ENSMUSG00000000263	Glra1	nmf11|oscillator|ot|spasmodic|spd	glycine receptor, alpha 1 subunit	protein-coding
mm_134883.1	chr16	29233037	29233040	-	1	NA	intron (NM_001284375, intron 28 of 28)	intron (NM_001284375, intron 28 of 28)	23343	NM_013751	27281	Mm.103650	NM_013751	ENSMUSG00000022525	Hrasls	2810012B06Rik|A-C1|HRSL1|Hrasrs	HRAS-like suppressor	protein-coding
mm_37350.1	chr4	120032367	120032386	-	1	NA	intron (NM_010657, intron 2 of 8)	intron (NM_010657, intron 2 of 8)	-128830	NM_007902	13615	Mm.284855	NM_007902	ENSMUSG00000028635	Edn2	ET-2|PPET2|VIC	endothelin 2	protein-coding
mm_44679.1	chr5	30072365	30072368	-	1	NA	intron (NR_033402, intron 1 of 6)	intron (NR_033402, intron 1 of 6)	1259	NR_033402	22171	Mm.268395	NM_021288	ENSMUSG00000025747	Tyms	Ts	thymidylate synthase	protein-coding
mm_167563.1	chr9	40469764	40469769	+	1	NA	Intergenic	Intergenic	-14002	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_131092.1	chr16	4886272	4886284	+	1	NA	5' UTR (NM_029657, exon 1 of 17)	5' UTR (NM_029657, exon 1 of 17)	178	NM_001252437	17237	Mm.291326	NM_029657	ENSMUSG00000022517	Mgrn1	2610042J20Rik|mKIAA0544|md|nc	mahogunin, ring finger 1	protein-coding
mm_161859.1	chr18	25754104	25754104	-	1	NA	promoter-TSS (NM_001146295)	promoter-TSS (NM_001146295)	-121	NM_001174074	108013	Mm.266435	NM_133195	ENSMUSG00000024268	Celf4	A230070D14Rik|BRUNOL-4|Brul4|Brunol4|C130060B05Rik	CUGBP, Elav-like family member 4	protein-coding
mm_158173.1	chrX	103821860	103821921	-	1	NA	promoter-TSS (NM_009197)	promoter-TSS (NM_009197)	98	NM_009197	20502	Mm.388973	NM_009197	ENSMUSG00000033965	Slc16a2	AW105741|Mct8|Xpct	solute carrier family 16 (monocarboxylic acid transporters), member 2	protein-coding
mm_51273.1	chr6	72115305	72115317	+	1	NA	intron (NM_011375, intron 1 of 6)	intron (NM_011375, intron 1 of 6)	7629	NR_045163	71265	Mm.442035	NR_045163	ENSMUSG00000108709	4933431G14Rik	4930565C19Rik	RIKEN cDNA 4933431G14 gene	ncRNA
mm_93173.1	chr10	93311164	93311194	-	1	NA	promoter-TSS (NM_001322268)	promoter-TSS (NM_001322268)	-20	NM_001322265	13713	Mm.4454	NM_013508	ENSMUSG00000008398	Elk3	D430049E23Rik|Erp|Etrp|Net|Sap-2	ELK3, member of ETS oncogene family	protein-coding
mm_94765.1	chr11	21238565	21238579	+	1	NA	promoter-TSS (NM_001290628)	promoter-TSS (NM_001290628)	-460	NM_139061	245944	Mm.170103	NM_139061	ENSMUSG00000020128	Vps54	Hcc8|Vps54l|mSLP8|wr	VPS54 GARP complex subunit	protein-coding
mm_150181.1	chr19	32637615	32637660	+	1	NA	intron (NM_001201470, intron 3 of 11)	intron (NM_001201470, intron 3 of 11)	17632	NM_011864	23972	Mm.203916	NM_011864	ENSMUSG00000024899	Papss2	1810018P12Rik|AI159688|AtpsU2|Atpsk2|Sk2|bm	3'-phosphoadenosine 5'-phosphosulfate synthase 2	protein-coding
mm_60830.1	chr7	45708152	45708192	+	1	NA	intron (NM_016974, intron 2 of 3)	intron (NM_016974, intron 2 of 3)	2925	NM_016974	13170	Mm.24222	NM_016974	ENSMUSG00000059824	Dbp	-	D site albumin promoter binding protein	protein-coding
mm_46014.1	chr5	90897585	90897627	-	1	NA	Intergenic	Intergenic	-6293	NM_009140	20310	Mm.4979	NM_009140	ENSMUSG00000058427	Cxcl2	CINC-2a|GROb|Gro2|MIP-2|MIP-2a|Mgsa-b|Mip2|Scyb|Scyb2	chemokine (C-X-C motif) ligand 2	protein-coding
mm_42259.1	chr5	114065458	114065476	+	1	NA	intron (NM_026805, intron 2 of 15)	intron (NM_026805, intron 2 of 15)	25913	NM_026805	68666	Mm.63584	NM_026805	ENSMUSG00000042078	Svop	1110030H18Rik|AI415691|msvop	SV2 related protein	protein-coding
mm_164487.1	chr16	81850607	81850609	+	1	NA	Intergenic	Lx5|LINE|L1	649911	NM_010954	17968	Mm.433941	NM_010954	ENSMUSG00000022762	Ncam2	Ncam-2|Ocam|RNCAM	neural cell adhesion molecule 2	protein-coding
mm_33223.1	chr4	126706052	126706083	+	1	NA	exon (NM_011970, exon 4 of 6)	exon (NM_011970, exon 4 of 6)	28424	NM_011970	26445	Mm.22233	NM_011970	ENSMUSG00000028837	Psmb2	AU045357|AW108089|C7-I|D4Wsu33e|HC7-I	proteasome (prosome, macropain) subunit, beta type 2	protein-coding
mm_137682.1	chr17	28823610	28823659	+	1	NA	intron (NM_001081315, intron 8 of 12)	intron (NM_001081315, intron 8 of 12)	22508	NM_001081315	268936	Mm.291877	NM_199061	ENSMUSG00000063952	Brpf3	AI413466|AW493400|mKIAA1286	bromodomain and PHD finger containing, 3	protein-coding
mm_133360.1	chr16	84703001	84703017	+	1	NA	Intergenic	Intergenic	-10014	NR_132106	100653389	Mm.261808	NR_132106	ENSMUSG00000097418	Mir155hg	Bic|Gm26667	Mir155 host gene (non-protein coding)	ncRNA
mm_96428.1	chr11	67277207	67277223	+	1	NA	promoter-TSS (NM_177369)	promoter-TSS (NM_177369)	91	NM_177369	17885	Mm.340163	NM_177369	ENSMUSG00000055775	Myh8	4832426G23Rik|AI327267|MHCp|MyHC-pn|Myhs-p|Myhsp	myosin, heavy polypeptide 8, skeletal muscle, perinatal	protein-coding
mm_100367.1	chr11	119081374	119081415	+	1	NA	exon (NM_007625, exon 5 of 5)	exon (NM_007625, exon 5 of 5)	4843	NM_007625	12418	Mm.268070	NM_007625	ENSMUSG00000039989	Cbx4	MPc2|PC2	chromobox 4	protein-coding
mm_153127.1	chr19	34165962	34165992	-	1	NA	promoter-TSS (NM_024204)	promoter-TSS (NM_024204)	64	NM_024204	52024	Mm.183030	NM_024204	ENSMUSG00000024774	Ankrd22	5430429D21Rik|D19Ertd675e	ankyrin repeat domain 22	protein-coding
mm_115975.1	chr13	24178250	24178253	-	1	NA	exon (NM_026825, exon 3 of 38)	exon (NM_026825, exon 3 of 38)	102539	NM_001311122	68732	Mm.211047	NM_026825	ENSMUSG00000021338	Carmil1	1110037D04Rik|AI425970|CARMIL|CARML1|D130057M20|Lrrc16|Lrrc16a	capping protein regulator and myosin 1 linker 1	protein-coding
mm_9516.1	chr1	173748207	173748209	-	1	NA	intron (NM_008329, intron 8 of 8)	BGLII_B|LTR|ERVK	-6399	NM_001204910	226691	Mm.440876	NM_001204910	ENSMUSG00000073490	Ifi207	AI607873|Pyhin-A	interferon activated gene 207	protein-coding
mm_13600.1	chr2	112618995	112619001	+	1	NA	intron (NM_001165935, intron 1 of 4)	intron (NM_001165935, intron 1 of 4)	59316	NM_001165935	74268	Mm.315125	NM_028844	ENSMUSG00000003604	Aven	1700013A01Rik|1700056A21Rik|mAven-L|mAven-S	apoptosis, caspase activation inhibitor	protein-coding
mm_51402.1	chr6	78372824	78372864	+	1	NA	exon (NM_011036, exon 5 of 6)	exon (NM_011036, exon 5 of 6)	1959	NM_011036	18489	Mm.2553	NM_011036	ENSMUSG00000071356	Reg3b	HIP|PAP1|Pap|REG-III	regenerating islet-derived 3 beta	protein-coding
mm_54062.1	chr6	13871478	13871487	-	1	NA	promoter-TSS (NR_024619)	promoter-TSS (NR_024619)	1	NR_024619	66520	Mm.29615	NM_183258		2610001J05Rik	C79299	RIKEN cDNA 2610001J05 gene	ncRNA
mm_901.1	chr1	53784468	53784476	+	1	NA	intron (NM_133810, intron 1 of 7)	intron (NM_133810, intron 1 of 7)	743	NM_133810	98267	Mm.25559	NM_133810	ENSMUSG00000026094	Stk17b	3110009A03Rik|AI120141|Drak2	serine/threonine kinase 17b (apoptosis-inducing)	protein-coding
mm_21804.1	chr2	165004348	165004359	-	1	NA	intron (NM_144892, intron 5 of 7)	intron (NM_144892, intron 5 of 7)	30426	NM_144892	228869	Mm.233080	NM_144892	ENSMUSG00000039804	Ncoa5	CIA	nuclear receptor coactivator 5	protein-coding
mm_140297.1	chr17	85620997	85621012	+	1	NA	5' UTR (NM_011381, exon 1 of 2)	5' UTR (NM_011381, exon 1 of 2)	170	NM_011381	20473	Mm.370208	NM_011381	ENSMUSG00000038805	Six3	E130112M24Rik|Six3a|Six3alpha|Six3b|Six3beta	sine oculis-related homeobox 3	protein-coding
mm_27204.1	chr3	35754431	35754457	-	1	NA	intron (NM_029570, intron 1 of 29)	CpG	306	NM_029570	76295	Mm.239416	NM_029570	ENSMUSG00000037400	Atp11b	1110019I14Rik|ATPIF|ATPIR|mKIAA0956	ATPase, class VI, type 11B	protein-coding
mm_153659.1	chr19	44395292	44395314	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	12406	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_47213.1	chr5	121009442	121009480	-	1	NA	promoter-TSS (NM_011286)	promoter-TSS (NM_011286)	77	NM_011286	19894	Mm.181166	NM_011286	ENSMUSG00000029608	Rph3a	2900002P20Rik|AU022689|AW108370	rabphilin 3A	protein-coding
mm_132566.1	chr16	38104533	38104537	+	1	NA	intron (NM_001347232, intron 1 of 11)	intron (NM_001347232, intron 1 of 11)	-15275	NR_033221	414072	Mm.483602	NR_033221		BC031361	-	cDNA sequence BC031361	ncRNA
mm_131626.1	chr16	20112505	20112517	+	1	NA	intron (NM_029436, intron 3 of 7)	intron (NM_029436, intron 3 of 7)	14957	NM_029436	75785	Mm.392450	NM_029436	ENSMUSG00000062901	Klhl24	1110046J11Rik|4930429H24Rik|6530402O20Rik|C85082	kelch-like 24	protein-coding
mm_156512.1	chrX	150550965	150550982	+	1	NA	intron (NM_001102446, intron 1 of 10)	intron (NM_001102446, intron 1 of 10)	-3528	NR_106147	102465782		NR_106147	ENSMUSG00000099172	Mir3620	Gm27984|mmu-mir-3620	microRNA 3620	ncRNA
mm_61877.1	chr7	89560012	89560017	+	1	NA	Intergenic	Intergenic	-42428	NM_029614	76453	Mm.250438	NM_029614	ENSMUSG00000039405	Prss23	2310046G15Rik|4930479H08Rik|AI790574|Spuve	protease, serine 23	protein-coding
mm_36615.1	chr4	89294532	89294545	-	1	NA	promoter-TSS (NR_132431)	promoter-TSS (NR_132431)	81	NM_009877	12578	Mm.4733	NM_009877	ENSMUSG00000044303	Cdkn2a	ARF-INK4a|Arf|INK4a-ARF|Ink4a/Arf|MTS1|Pctr1|p16|p16(INK4a)|p16INK4a|p19<ARF>|p19ARF	cyclin-dependent kinase inhibitor 2A	protein-coding
mm_19616.1	chr2	102812174	102812189	-	1	NA	3' UTR (NM_009851, exon 19 of 19)	3' UTR (NM_009851, exon 19 of 19)	89484	NM_001177785	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_58959.1	chr7	18925408	18925459	+	1	NA	promoter-TSS (NM_001029877)	promoter-TSS (NM_001029877)	-455	NM_001029877	384569	Mm.262724	NM_001029877	ENSMUSG00000030411	Nova2	Gm1424	neuro-oncological ventral antigen 2	protein-coding
mm_130527.1	chr15	98898459	98898467	-	1	NA	promoter-TSS (NM_007857)	promoter-TSS (NM_007857)	77	NM_007857	13363	Mm.324688	NM_007857	ENSMUSG00000023000	Dhh	C78960	desert hedgehog	protein-coding
mm_44564.1	chr5	24624398	24624445	-	1	NA	Intergenic	Intergenic	-21032	NR_003953	72252	Mm.87446	NR_003953	ENSMUSG00000038165	1700022A21Rik	-	glycerol-3-phosphate dehydrogenase 1-like pseudogene	pseudo
mm_67631.1	chr7	84232875	84232893	-	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	-80991	NM_133722	70178	Mm.23914	NM_133722	ENSMUSG00000038459	Abhd17c	2210412D01Rik|AL023007|Fam108c|Fam108c1	abhydrolase domain containing 17C	protein-coding
mm_34120.1	chr4	139233513	139233527	+	1	NA	intron (NM_001271405, intron 1 of 8)	intron (NM_001271405, intron 1 of 8)	39409	NM_001271405	12345	Mm.2945	NM_009798	ENSMUSG00000028745	Capzb	1700120C01Rik|AI325129|CPB1|CPB2|CPbeat2|CPbeta1|CPbeta2|Cappb1	capping protein (actin filament) muscle Z-line, beta	protein-coding
mm_53066.1	chr6	124914179	124914211	+	1	NA	exon (NM_026988, exon 5 of 5)	exon (NM_026988, exon 5 of 5)	-2490	NM_008479	16768	Mm.4528	NM_008479	ENSMUSG00000030124	Lag3	CD223|LAG-3|Ly66	lymphocyte-activation gene 3	protein-coding
mm_170184.1	chr17	6122223	6122233	-	1	NA	intron (NM_001103181, intron 1 of 13)	ORR1A2|LTR|ERVL-MaLR	15398	NM_001103181	68842	Mm.449307	NM_054040	ENSMUSG00000034377	Tulp4	1110057P05Rik|2210038L17Rik|Tusp	tubby like protein 4	protein-coding
mm_82048.1	chr9	122351895	122351939	+	1	NA	intron (NM_026179, intron 1 of 6)	CpG	301	NM_026179	67469	Mm.280254	NM_026179	ENSMUSG00000032540	Abhd5	1300003D03Rik|2010002J10Rik|CDS|CGI-58|IECN5|NCIE2	abhydrolase domain containing 5	protein-coding
mm_31742.1	chr4	63215541	63215549	+	1	NA	5' UTR (NM_025685, exon 1 of 61)	5' UTR (NM_025685, exon 1 of 61)	133	NM_025685	373864	Mm.194116	NM_025685	ENSMUSG00000045672	Col27a1	5730512J02Rik|AI449266	collagen, type XXVII, alpha 1	protein-coding
mm_127112.1	chr15	97964221	97964271	+	1	NA	promoter-TSS (NM_201359)	promoter-TSS (NM_201359)	17	NM_001252153	380967	Mm.196630	NM_201359	ENSMUSG00000052369	Tmem106c	AI046681|BC046621|D15Ertd405e	transmembrane protein 106C	protein-coding
mm_125167.1	chr15	31331984	31331991	+	1	NA	intron (NM_027496, intron 1 of 3)	MLT1A0|LTR|ERVL-MaLR	35772	NM_001164441	67434	Mm.102470	NM_026153	ENSMUSG00000022237	Ankrd33b	0610012A05Rik|3021401C12Rik|5730557B15Rik	ankyrin repeat domain 33B	protein-coding
mm_4041.1	chr1	165774596	165774606	+	1	NA	3' UTR (NM_011804, exon 4 of 4)	3' UTR (NM_011804, exon 4 of 4)	10821	NM_011804	433375	Mm.294885	NM_011804	ENSMUSG00000040713	Creg1	AA755314|Creg	cellular repressor of E1A-stimulated genes 1	protein-coding
mm_34515.1	chr4	148901129	148901202	+	1	NA	intron (NM_027195, intron 3 of 15)	CpG	96773	NM_027195	69743	Mm.233879	NM_027195	ENSMUSG00000028977	Casz1	2410019P08Rik|AV096627|BC040081|Cst|D4Ertd432e	castor zinc finger 1	protein-coding
mm_3900.1	chr1	161705498	161705516	+	1	NA	Intergenic	Intergenic	82988	NM_001205243	14103	Mm.3355	NM_010177	ENSMUSG00000000817	Fasl	APT1LG1|CD178|CD95-L|CD95L|Fas-L|Faslg|Tnfsf6|Tnlg1a|gld	Fas ligand (TNF superfamily, member 6)	protein-coding
mm_146520.1	chr18	4352917	4352923	-	1	NA	promoter-TSS (NM_007746)	promoter-TSS (NM_007746)	33	NM_007746	26410	Mm.3275	NM_007746	ENSMUSG00000024235	Map3k8	Cot|Cot/Tpl2|Est|Estf|Tpl-2|Tpl2|c-COT	mitogen-activated protein kinase kinase kinase 8	protein-coding
mm_44197.1	chr5	3641433	3641471	-	1	NA	exon (NM_026033, exon 5 of 5)	exon (NM_026033, exon 5 of 5)	6484	NM_026033	67210	Mm.178424	NM_026033	ENSMUSG00000007415	Gatad1	2310031E19Rik|2810047M21Rik|8430439A17Rik|9130430G15Rik|B330017N08Rik|ENSMUSG00000073241|Odag	GATA zinc finger domain containing 1	protein-coding
mm_149458.1	chr19	11518494	11518534	+	1	NA	promoter-TSS (NM_027209)	promoter-TSS (NM_027209)	-45	NM_027209	69774	Mm.436639	NM_027209	ENSMUSG00000024677	Ms4a6b	1810027D10Rik	membrane-spanning 4-domains, subfamily A, member 6B	protein-coding
mm_121324.1	chr14	113315089	113315129	+	1	NA	Intergenic	Intergenic	1293679	NR_030150	723922		NR_030150	ENSMUSG00000070099	Mir466	Mirn466|mmu-mir-466	microRNA 466	ncRNA
mm_172039.1	chr6	12692362	12692365	+	1	NA	intron (NM_001164805, intron 1 of 26)	(GGAA)n|Simple_repeat|Simple_repeat	56890	NM_001164805	330267	Mm.11989	NM_001164805	ENSMUSG00000032625	Thsd7a	Gm837	thrombospondin, type I, domain containing 7A	protein-coding
mm_30749.1	chr4	14899410	14899411	+	1	NA	intron (NM_028264, intron 4 of 6)	intron (NM_028264, intron 4 of 6)	-31231	NM_001243100	100038514	Mm.331495	NM_001243100		Gm11837	OTTMUSG00000004551	predicted gene 11837	protein-coding
mm_158458.1	chrX	140599448	140599449	-	1	NA	intron (NM_001077364, intron 1 of 3)	CpG	1074	NM_001077364	14605	Mm.22216	NM_010286	ENSMUSG00000031431	Tsc22d3	DIP|Dsip1|Gilz|TSC-22R|Tilz3	TSC22 domain family, member 3	protein-coding
mm_132711.1	chr16	43503381	43503457	+	1	NA	intron (NM_181058, intron 3 of 6)	intron (NM_181058, intron 3 of 6)	-83223	NR_046026	626693	Mm.447083	NR_046026	ENSMUSG00000085499	Gm15713	OTTMUSG00000025617	predicted gene 15713	ncRNA
mm_146264.1	chr18	77835180	77835190	+	1	NA	exon (NM_013831, exon 2 of 15)	exon (NM_013831, exon 2 of 15)	40635	NM_013831	19201	Mm.57174	NM_013831	ENSMUSG00000025429	Pstpip2	MAYP|cmo	proline-serine-threonine phosphatase-interacting protein 2	protein-coding
mm_18125.1	chr2	44997650	44997659	-	1	NA	exon (NM_015753, exon 8 of 10)	exon (NM_015753, exon 8 of 10)	25523	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_59615.1	chr7	28144199	28144209	+	1	NA	exon (NM_001164655, exon 7 of 20)	exon (NM_001164655, exon 7 of 20)	14738	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_96838.1	chr11	70018422	70018484	+	1	NA	promoter-TSS (NM_007864)	promoter-TSS (NM_007864)	-152	NM_001109752	13385	Mm.27256	NM_007864	ENSMUSG00000020886	Dlg4	Dlgh4|PSD-95|PSD95|SAP90|SAP90A	discs, large homolog 4 (Drosophila)	protein-coding
mm_153395.1	chr19	40415294	40415314	-	1	NA	intron (NM_001034963, intron 1 of 22)	intron (NM_001034963, intron 1 of 22)	-12994	NM_001034964	20411	Mm.210815	NM_009166	ENSMUSG00000025006	Sorbs1	2310065E01Rik|9530001P15Rik|CAP|SH3P12|Sh3d5|mKIAA1296	sorbin and SH3 domain containing 1	protein-coding
mm_157602.1	chrX	53370514	53370528	-	1	NA	promoter-TSS (NM_027409)	promoter-TSS (NM_027409)	38	NM_027409	70380	Mm.491083	NM_027409	ENSMUSG00000023074	Mospd1	1810018L05Rik	motile sperm domain containing 1	protein-coding
mm_80878.1	chr9	98986421	98986431	+	1	NA	promoter-TSS (NM_001122851)	promoter-TSS (NM_001122851)	53	NM_011810	23873	Mm.74605	NM_011810	ENSMUSG00000032463	Faim	-	Fas apoptotic inhibitory molecule	protein-coding
mm_93799.1	chr10	120898883	120898896	-	1	NA	promoter-TSS (NM_177092)	promoter-TSS (NM_177092)	82	NM_177092	320183	Mm.169755	NM_177092	ENSMUSG00000051236	Msrb3	D430026P16Rik|I-8-23|MsrB2	methionine sulfoxide reductase B3	protein-coding
mm_159049.1	chr1	185322888	185322888	-	1	NA	exon (NM_198653, exon 7 of 23)	exon (NM_198653, exon 7 of 23)	6513	NM_198653	381314	Mm.275841	NM_198653	ENSMUSG00000026618	Iars2	2010002H18Rik|C79125	isoleucine-tRNA synthetase 2, mitochondrial	protein-coding
mm_101698.1	chr11	40752323	40752355	-	1	NA	exon (NM_009831, exon 3 of 6)	exon (NM_009831, exon 3 of 6)	2947	NM_009831	12450	Mm.2103	NM_009831	ENSMUSG00000020326	Ccng1	AI314029	cyclin G1	protein-coding
mm_11550.1	chr2	32719562	32719609	+	1	NA	Intergenic	Intergenic	-1470	NR_045535	27387	Mm.9593	NM_013781	ENSMUSG00000059013	Sh2d3c	Chat|Nsp3|Shep1	SH2 domain containing 3C	protein-coding
mm_36119.1	chr4	58912082	58912120	-	1	NA	intron (NM_172381, intron 1 of 48)	CpG	624	NM_172381	230249	Mm.234801	NM_172381	ENSMUSG00000050812	AI314180	AW558785|BB181316|mKIAA0368	expressed sequence AI314180	protein-coding
mm_26085.1	chr3	136692260	136692272	+	1	NA	intron (NM_008913, intron 1 of 13)	(T)n|Simple_repeat|Simple_repeat	22200	NM_001293622	19055	Mm.331389	NM_008913	ENSMUSG00000028161	Ppp3ca	2900074D19Rik|CN|Caln|Calna|CnA	protein phosphatase 3, catalytic subunit, alpha isoform	protein-coding
mm_8702.1	chr1	158712891	158712895	-	1	NA	3' UTR (NM_001085376, exon 22 of 22)	3' UTR (NM_001085376, exon 22 of 22)	207268	NR_030441	735253		NR_030441	ENSMUSG00000070103	Mir488	Mirn488|mir-488|mmu-mir-488	microRNA 488	ncRNA
mm_14374.1	chr2	129630312	129630333	+	1	NA	3' UTR (NM_001291022, exon 5 of 5)	3' UTR (NM_001291022, exon 5 of 5)	37153	NM_001291022	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_31606.1	chr4	58327269	58327279	+	1	NA	intron (NM_001037130, intron 5 of 12)	intron (NM_001037130, intron 5 of 12)	41312	NM_010944	18198	Mm.16148	NM_010944	ENSMUSG00000057280	Musk	Mdk4|Mlk|Nsk1|Nsk2|Nsk3	muscle, skeletal, receptor tyrosine kinase	protein-coding
mm_32602.1	chr4	111973033	111973072	+	1	NA	5' UTR (NM_177818, exon 1 of 4)	5' UTR (NM_177818, exon 1 of 4)	125	NM_001142775	328505	Mm.226771	NM_177818	ENSMUSG00000049214	Skint7	C130057D23Rik	selection and upkeep of intraepithelial T cells 7	protein-coding
mm_165730.1	chr3	106130921	106130923	+	1	NA	exon (NM_023186, exon 10 of 11)	exon (NM_023186, exon 10 of 11)	17540	NM_023186	81600	Mm.46418	NM_023186	ENSMUSG00000062778	Chia1	2200003E03Rik|AMCase|Chia|YNL	chitinase, acidic 1	protein-coding
mm_140896.1	chr17	24073429	24073474	-	1	NA	promoter-TSS (NM_027008)	promoter-TSS (NM_027008)	34	NM_027008	69259	Mm.28171	NM_027008	ENSMUSG00000016946	Kctd5	2610030N08Rik|mKIAA0176	potassium channel tetramerisation domain containing 5	protein-coding
mm_170817.1	chr2	176423635	176423644	+	1	NA	promoter-TSS (NM_001033123).3	promoter-TSS (NM_001033123).3	-16	NM_001033123	13999		NM_001033123	ENSMUSG00000078889	Gm14288	OTTMUSG00000016199	predicted gene 14288	protein-coding
mm_89982.1	chr10	111725129	111725133	+	1	NA	Intergenic	Intergenic	-130858	NR_045344	71321	Mm.410785	NR_045344	ENSMUSG00000097082	4933440J02Rik	-	RIKEN cDNA 4933440J02 gene	ncRNA
mm_101642.1	chr11	36433104	36433114	-	1	NA	intron (NM_011856, intron 2 of 28)	intron (NM_011856, intron 2 of 28)	-453020	NM_170779	211652	Mm.31267	NM_170779	ENSMUSG00000018849	Wwc1	AA408228|AU017197|BC037006|Kibra|mKIAA0869	WW, C2 and coiled-coil domain containing 1	protein-coding
mm_77055.1	chr8	109579041	109579055	-	1	NA	5' UTR (NM_017370, exon 1 of 5)	5' UTR (NM_017370, exon 1 of 5)	124	NM_017370	15439	Mm.26730	NM_017370	ENSMUSG00000031722	Hp	HP-1|preHP2	haptoglobin	protein-coding
mm_111747.1	chr12	103947113	103947141	-	1	NA	exon (NM_009247, exon 5 of 5)	exon (NM_009247, exon 5 of 5)	9770	NM_009247	20704	Mm.312593	NM_009247	ENSMUSG00000072849	Serpina1e	Dom5|PI5|Spi1-5	serine (or cysteine) peptidase inhibitor, clade A, member 1E	protein-coding
mm_19565.1	chr2	101624092	101624094	-	1	NA	promoter-TSS (NM_009020)	promoter-TSS (NM_009020)	-655	NM_009020	19374	Mm.4988	NM_009020	ENSMUSG00000032864	Rag2	Rag-2	recombination activating gene 2	protein-coding
mm_57647.1	chr6	128438516	128438551	-	1	NA	promoter-TSS (NM_010219)	promoter-TSS (NM_010219)	98	NM_010219	14228	Mm.12758	NM_010219	ENSMUSG00000030357	Fkbp4	59kDa|AL022792|AW208983|FKBP-4|FKBP-52|FKBP52|FKPB52|p59	FK506 binding protein 4	protein-coding
mm_172656.1	chr8	37467737	37467751	-	1	NA	Intergenic	RLTR9E|LTR|ERVK	-443506	NR_126063	414128	Mm.450976	NR_126063	ENSMUSG00000110242	G630064G18Rik	-	RIKEN cDNA G630064G18 gene	ncRNA
mm_11228.1	chr2	29802627	29802647	+	1	NA	promoter-TSS (NM_011989)	promoter-TSS (NM_011989)	-43	NM_011989	26569	Mm.330113	NM_011989	ENSMUSG00000059316	Slc27a4	BB144259|FATP4	solute carrier family 27 (fatty acid transporter), member 4	protein-coding
mm_100650.1	chr11	3148909	3148916	-	1	NA	intron (NM_030207, intron 14 of 32)	RLTR6B_Mm|LTR|ERV1	24891	NR_003517	236604	Mm.247625	NM_001004146		Pisd-ps1	-	phosphatidylserine decarboxylase, pseudogene 1	pseudo
mm_58759.1	chr7	13623974	13623982	+	1	NA	promoter-TSS (NM_001184980)	promoter-TSS (NM_001184980)	11	NM_001184980	434264	Mm.359414	NM_001184980	ENSMUSG00000078799	Sult2a5	EG434264|Gm15438|OTTMUSG00000021844	sulfotransferase family 2A, dehydroepiandrosterone (DHEA)-preferring, member 5	protein-coding
mm_98126.1	chr11	87331613	87331631	+	1	NA	intron (NR_106195, intron 6 of 8)	L1M4|LINE|L1	27372	NM_177167	320472	Mm.341988	NM_177167	ENSMUSG00000046442	Ppm1e	AW049266|B930008A12Rik|POPX1|PP2CH|mKIAA1072	protein phosphatase 1E (PP2C domain containing)	protein-coding
mm_141080.1	chr17	25868695	25868719	-	1	NA	promoter-TSS (NM_026633)	promoter-TSS (NM_026633)	31	NM_026633	68241	Mm.328870	NM_026633	ENSMUSG00000025732	Fam195a	9530058B02Rik|Mcrip2	family with sequence similarity 195, member A	protein-coding
mm_14879.1	chr2	148820117	148820124	+	1	NA	promoter-TSS (NM_027024)	promoter-TSS (NM_027024)	21	NM_027024	69294	Mm.46167	NM_027024	ENSMUSG00000036924	Cst13	1700006C19Rik|Cymg1|Mtcg1	cystatin 13	protein-coding
mm_96311.1	chr11	63158797	63158811	+	1	NA	3' UTR (NM_008885, exon 5 of 5)	3' UTR (NM_008885, exon 5 of 5)	26001	NM_001302260	18858	Mm.1237	NM_008885	ENSMUSG00000018217	Pmp22	22kDa|Gas-3|HNPP|Tr|trembler	peripheral myelin protein 22	protein-coding
mm_84568.1	chr9	68969472	68969489	-	1	NA	intron (NM_013646, intron 1 of 10)	intron (NM_013646, intron 1 of 10)	204134	NR_033299	320440	Mm.483129	NM_177159		9530091C08Rik	-	RIKEN cDNA 9530091C08 gene	ncRNA
mm_41928.1	chr5	105698900	105698920	+	1	NA	Intergenic	Intergenic	-1059	NM_001122768	231549	Mm.23837	NM_178701	ENSMUSG00000046079	Lrrc8d	2810473G09Rik|4930525N13Rik|A930019F03|Lrrc5	leucine rich repeat containing 8D	protein-coding
mm_39219.1	chr4	156197480	156197496	-	1	NA	promoter-TSS (NM_021604)	promoter-TSS (NM_021604)	0	NM_021604	11603	Mm.273098	NM_021604	ENSMUSG00000041936	Agrn	Agrin|nmf380	agrin	protein-coding
mm_124957.1	chr15	12924046	12924063	+	1	NA	intron (NM_001130149, intron 29 of 34)	intron (NM_001130149, intron 29 of 34)	99239	NM_001130149	14000	Mm.293142	NM_026799	ENSMUSG00000022191	Drosha	1110013A17Rik|AI874853|Etohi2|Rn3|Rnasen	drosha, ribonuclease type III	protein-coding
mm_69295.1	chr7	128237985	128237995	-	1	NA	promoter-TSS (NM_177001)	promoter-TSS (NM_177001)	41	NM_177001	100043133	Mm.183647	NM_177001	ENSMUSG00000062944	9130023H24Rik	GLI4	RIKEN cDNA 9130023H24 gene	protein-coding
mm_78977.1	chr9	45370398	45370463	+	1	NA	5' UTR (NM_022004, exon 1 of 8)	5' UTR (NM_022004, exon 1 of 8)	245	NM_022004	59095	Mm.208287	NM_022004	ENSMUSG00000066705	Fxyd6	0610030I18Rik|Php	FXYD domain-containing ion transport regulator 6	protein-coding
mm_94065.1	chr10	128400295	128400308	-	1	NA	5' UTR (NM_028051, exon 1 of 11)	5' UTR (NM_028051, exon 1 of 11)	165	NM_028051	72002	Mm.22983	NM_028051	ENSMUSG00000039878	Slc39a5	1810013D05Rik|2010205A06Rik|Zip5	solute carrier family 39 (metal ion transporter), member 5	protein-coding
mm_149677.1	chr19	20492218	20492241	+	1	NA	promoter-TSS (NR_015502)	promoter-TSS (NR_015502)	-486	NR_015502	320092	Mm.482524	NR_015502		E030003E18Rik	1700127G21Rik	RIKEN cDNA E030003E18 gene	ncRNA
mm_39376.1	chr5	12383378	12383395	+	1	NA	5' UTR (NM_028882, exon 1 of 18)	5' UTR (NM_028882, exon 1 of 18)	220	NM_028882	108151	Mm.89313	NM_028882	ENSMUSG00000040254	Sema3d	4631426B19Rik	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D	protein-coding
mm_82475.1	chr9	16502196	16502209	-	1	NA	Intergenic	CpG	-123971	NM_001080814	270120	Mm.195010	NM_001080814	ENSMUSG00000074505	Fat3	9430076A06Rik|D430038H04Rik|Gm1132|Gm510|MFAT3F	FAT atypical cadherin 3	protein-coding
mm_97013.1	chr11	71019594	71019617	+	1	NA	promoter-TSS (NM_001291148)	promoter-TSS (NM_001291148)	-6	NM_025993	67139	Mm.28227	NM_025993	ENSMUSG00000040599	Mis12	2510025F08Rik|AU044651|Misc12	MIS12 kinetochore complex component	protein-coding
mm_6135.1	chr1	64691037	64691068	-	1	NA	promoter-TSS (NM_001097644)	promoter-TSS (NM_001097644)	-293	NM_001097644	227210	Mm.39706	NM_001097644	ENSMUSG00000070871	Ccnyl1	9630037P07Rik|AW554339	cyclin Y-like 1	protein-coding
mm_19989.1	chr2	118637527	118637564	-	1	NA	intron (NM_009773, intron 20 of 22)	intron (NM_009773, intron 20 of 22)	-26032	NM_001033254	214230	Mm.241857	NM_001033254	ENSMUSG00000074923	Pak6	4732456M09	p21 protein (Cdc42/Rac)-activated kinase 6	protein-coding
mm_159985.1	chr6	114398002	114398002	+	1	NA	promoter-TSS (NM_008285)	promoter-TSS (NM_008285)	66	NM_001317125	15465	Mm.333327	NM_008285	ENSMUSG00000053004	Hrh1	Bphs|H1R|HH1R|Hir	histamine receptor H1	protein-coding
mm_161204.1	chr13	58404871	58404871	+	1	NA	intron (NM_001168248, intron 2 of 3)	intron (NM_001168248, intron 2 of 3)	-1528	NM_001301341	15387	Mm.142872	NM_025279	ENSMUSG00000021546	Hnrnpk	Hnrpk|KBBP|NOVA	heterogeneous nuclear ribonucleoprotein K	protein-coding
mm_3248.1	chr1	136131383	136131404	+	1	NA	promoter-TSS (NM_001039472)	promoter-TSS (NM_001039472)	-8	NM_001039472	16565	Mm.276135	NM_019962	ENSMUSG00000041642	Kif21b	2610511N21Rik|mKIAA0449	kinesin family member 21B	protein-coding
mm_165768.1	chr3	121577494	121577507	+	1	NA	Intergenic	Intergenic	-45156	NM_145394	213603	Mm.33062	NM_145394	ENSMUSG00000039865	Slc44a3	BC010552	solute carrier family 44, member 3	protein-coding
mm_45508.1	chr5	72504178	72504188	-	1	NA	promoter-TSS (NM_016869)	promoter-TSS (NM_016869)	25	NM_016869	53419	Mm.332425	NM_016869	ENSMUSG00000005220	Corin	AV273130|Lrp4	corin	protein-coding
mm_11721.1	chr2	36251712	36251727	+	1	NA	3' UTR (NM_008969, exon 11 of 11)	3' UTR (NM_008969, exon 11 of 11)	21293	NM_008969	19224	Mm.275434	NM_008969	ENSMUSG00000047250	Ptgs1	COX1|Cox-1|Cox-3|PGHS-1|PHS 1|Pghs1	prostaglandin-endoperoxide synthase 1	protein-coding
mm_109014.1	chr12	103388728	103388765	+	1	NA	promoter-TSS (NM_001177841)	promoter-TSS (NM_001177841)	64	NM_001177841	68149	Mm.127378	NM_026580	ENSMUSG00000021203	Otub2	2010015L18Rik|4930586I02Rik|AI413508|AW557219|OTB2|OTU2	OTU domain, ubiquitin aldehyde binding 2	protein-coding
mm_24748.1	chr3	95318825	95318870	+	1	NA	promoter-TSS (NM_001320492)	promoter-TSS (NM_001320492)	17	NM_001320492	76893	Mm.181009	NM_029789	ENSMUSG00000015714	Cers2	0610013I17Rik|AI225939|Lass2|TRH3	ceramide synthase 2	protein-coding
mm_126345.1	chr15	79905463	79905520	+	1	NA	exon (NM_001160415, exon 6 of 9)	exon (NM_001160415, exon 6 of 9)	10468	NM_001347041	80287	Mm.284059	NM_030255	ENSMUSG00000009585	Apobec3	Apobec|Arp3|BC003314|Cem15|Rfv3	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 3	protein-coding
mm_86750.1	chr10	19531768	19531778	+	1	NA	Intergenic	L2c|LINE|L2	-60176	NM_010511	15979	Mm.549	NM_010511	ENSMUSG00000020009	Ifngr1	CD119|IFN-gammaR|Ifgr|Ifngr|Nktar	interferon gamma receptor 1	protein-coding
mm_106139.1	chr11	116490300	116490365	-	1	NA	promoter-TSS (NM_026364)	promoter-TSS (NM_026364)	14	NM_026364	67763	Mm.25125	NM_026364	ENSMUSG00000015869	Prpsap1	5730409F23Rik|PAP39	phosphoribosyl pyrophosphate synthetase-associated protein 1	protein-coding
mm_72563.1	chr8	84125893	84125932	+	1	NA	promoter-TSS (NM_001013384)	promoter-TSS (NM_001013384)	-77	NM_001013384	244550	Mm.334654	NM_001013384	ENSMUSG00000012889	Podnl1	5832418A03Rik|Gm506	podocan-like 1	protein-coding
mm_156619.1	chrX	153723582	153723646	+	1	NA	promoter-TSS (NM_027327)	promoter-TSS (NM_027327)	60	NM_027327	70123	Mm.146408	NM_027327	ENSMUSG00000086316	2210013O21Rik	AI181827|Thp5	RIKEN cDNA 2210013O21 gene	protein-coding
mm_154840.1	chrX	20059536	20059574	+	1	NA	promoter-TSS (NM_021715)	promoter-TSS (NM_021715)	-15	NM_021715	60322	Mm.44827	NM_021715	ENSMUSG00000037347	Chst7	2600013M07Rik|C6ST-2|GST5|Gn6st-4|glcNAc6ST-4	carbohydrate (N-acetylglucosamino) sulfotransferase 7	protein-coding
mm_67882.1	chr7	99347137	99347166	-	1	NA	exon (NM_009825, exon 4 of 5)	exon (NM_009825, exon 4 of 5)	6088	NM_009825	12406	Mm.22708	NM_009825	ENSMUSG00000070436	Serpinh1	BERF-1|Cbp1|Cbp2|Hsp47|J6|Serpinh2|gp46	serine (or cysteine) peptidase inhibitor, clade H, member 1	protein-coding
mm_131372.1	chr16	13830609	13830619	+	1	NA	intron (NR_144374, intron 4 of 7)	intron (NR_144374, intron 4 of 7)	11363	NM_001346111	18203	Mm.380410	NM_010946	ENSMUSG00000022681	Ntan1	PNAA|PNAD	N-terminal Asn amidase	protein-coding
mm_135959.1	chr16	74736249	74736253	-	1	NA	Intergenic	Intergenic	-325339	NM_175549	268902	Mm.171736	NM_175549	ENSMUSG00000052516	Robo2	2600013A04Rik|9430089E08Rik|BB097918|D230004I22Rik|mKIAA1568	roundabout guidance receptor 2	protein-coding
mm_4099.1	chr1	167350185	167350234	+	1	NA	5' UTR (NM_019993, exon 1 of 11)	5' UTR (NM_019993, exon 1 of 11)	218	NM_019993	56752	Mm.292539	NM_019993	ENSMUSG00000026687	Aldh9a1	AA139417|Abaldh|ESTM40|TMABA-DH|Tmabadh	aldehyde dehydrogenase 9, subfamily A1	protein-coding
mm_80536.1	chr9	80305766	80305776	+	1	NA	intron (NM_001039546, intron 31 of 32)	intron (NM_001039546, intron 31 of 32)	140737	NM_001039546	17920	Mm.4040	NM_008662	ENSMUSG00000033577	Myo6	BC029719|Tlc|sv	myosin VI	protein-coding
mm_28183.1	chr3	88027452	88027462	-	1	NA	promoter-TSS (NM_022031)	promoter-TSS (NM_022031)	54	NM_022031	73940	Mm.294467	NM_022031	ENSMUSG00000004894	Hapln2	4930401E20Rik|Bral1	hyaluronan and proteoglycan link protein 2	protein-coding
mm_135858.1	chr16	59632570	59632583	-	1	NA	intron (NM_001347244, intron 1 of 8)	intron (NM_001347244, intron 1 of 8)	-4369	NR_040564	75145	Mm.399348	NR_040564		4930547E14Rik	-	RIKEN cDNA 4930547E14 gene	ncRNA
mm_61706.1	chr7	81213752	81213763	+	1	NA	promoter-TSS (NM_008803)	promoter-TSS (NM_008803)	-47	NM_008803	18584	Mm.371577	NM_008803	ENSMUSG00000025584	Pde8a	AI551852|Pde8	phosphodiesterase 8A	protein-coding
mm_72347.1	chr8	79639643	79639730	+	1	NA	promoter-TSS (NM_001256033)	promoter-TSS (NM_001256033)	10	NM_001081164	73945	Mm.34348	NM_001081164	ENSMUSG00000036990	Otud4	4930431L18Rik|AI449692|D8Ertd69e|mKIAA1046	OTU domain containing 4	protein-coding
mm_65292.1	chr7	24457759	24457769	-	1	NA	Intergenic	B1F|SINE|Alu	-4719	NM_011113	18793	Mm.1359	NM_011113	ENSMUSG00000046223	Plaur	Cd87|u-PAR|uPAR	plasminogen activator, urokinase receptor	protein-coding
mm_158437.1	chrX	140062551	140062583	-	1	NA	promoter-TSS (NM_001081668)	promoter-TSS (NM_001081668)	1	NM_001081668	279706	Mm.102590	NM_001081668	ENSMUSG00000072944	Nup62cl	Gm719	nucleoporin 62 C-terminal like	protein-coding
mm_153361.1	chr19	40183561	40183577	-	1	NA	intron (NM_145499, intron 2 of 8)	intron (NM_145499, intron 2 of 8)	3717	NM_145499	226105	Mm.29119	NM_145499	ENSMUSG00000060613	Cyp2c70	-	cytochrome P450, family 2, subfamily c, polypeptide 70	protein-coding
mm_83953.1	chr9	56928057	56928122	-	1	NA	5' UTR (NM_175483, exon 1 of 2)	5' UTR (NM_175483, exon 1 of 2)	282	NM_175483	235406	Mm.191459	NM_175483	ENSMUSG00000032733	Snx33	E130307J07Rik|Sh3px3	sorting nexin 33	protein-coding
mm_126631.1	chr15	83523404	83523407	+	1	NA	Intergenic	Intergenic	-3457	NM_007546	12124	Mm.267006	NM_007546	ENSMUSG00000016758	Bik	Biklk|Blk|Nbk	BCL2-interacting killer	protein-coding
mm_136039.1	chr16	77421969	77422015	-	1	NA	intron (NR_015543, intron 2 of 4)	intron (NR_015543, intron 2 of 4)	92664	NR_015543	77994	Mm.394688	NR_015543	ENSMUSG00000090386	Mir99ahg	2810055G20Rik|D730043B02Rik	Mir99a and Mirlet7c-1 host gene (non-protein coding)	ncRNA
mm_96733.1	chr11	69758289	69758296	+	1	NA	5' UTR (NM_001291068, exon 1 of 29)	5' UTR (NM_001291068, exon 1 of 29)	341	NM_001291068	20020	Mm.16533	NM_009089	ENSMUSG00000005198	Polr2a	220kDa|Rpb1|Rpo2-1	polymerase (RNA) II (DNA directed) polypeptide A	protein-coding
mm_22426.1	chr2	181598961	181598980	-	1	NA	exon (NM_172676, exon 1 of 5)	exon (NM_172676, exon 1 of 5)	177	NM_172676	229011	Mm.205422	NM_172676	ENSMUSG00000038605	Samd10	D930033N23Rik|E130318E08	sterile alpha motif domain containing 10	protein-coding
mm_112536.1	chr13	9684256	9684278	+	1	NA	TTS (NM_001347480)	TTS (NM_001347480)	79543	NM_001347471	66505	Mm.397307	NM_144516	ENSMUSG00000021156	Zmynd11	2210402G22Rik|BS69	zinc finger, MYND domain containing 11	protein-coding
mm_49601.1	chr6	30738045	30738059	+	1	NA	promoter-TSS (NM_001252292)	promoter-TSS (NM_001252292)	-1	NM_001252292	17294	Mm.335639	NM_008590	ENSMUSG00000051855	Mest	AA408879|AI256745|Peg1	mesoderm specific transcript	protein-coding
mm_104827.1	chr11	99089263	99089275	-	1	NA	promoter-TSS (NM_172564)	promoter-TSS (NM_172564)	37	NM_172564	217169	Mm.262067	NM_172564	ENSMUSG00000017607	Tns4	9930017A07Rik|AA589547|AU016405|Cten	tensin 4	protein-coding
mm_160026.1	chr6	130233340	130233340	-	1	NA	promoter-TSS (NM_001110323)	promoter-TSS (NM_001110323)	-18	NM_001110323	16638	Mm.441781	NM_014194	ENSMUSG00000067599	Klra7	LGL-1|Ly-49G.1|Ly-49G.2|Ly-49G.3|Ly49G.4|Ly49g|Ly49g1|Ly49g2	killer cell lectin-like receptor, subfamily A, member 7	protein-coding
mm_106853.1	chr12	8008583	8008593	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	30911	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_167569.1	chr9	42399551	42399558	-	1	NA	intron (NM_009347, intron 1 of 23)	intron (NM_009347, intron 1 of 23)	375	NM_009347	21683	Mm.42209	NM_009347	ENSMUSG00000037705	Tecta	Tctna	tectorin alpha	protein-coding
mm_27522.1	chr3	57295125	57295196	-	1	NA	intron (NM_008536, intron 2 of 6)	intron (NM_008536, intron 2 of 6)	6759	NM_008536	17112	Mm.856	NM_008536	ENSMUSG00000027800	Tm4sf1	L6|M3s1	transmembrane 4 superfamily member 1	protein-coding
mm_126534.1	chr15	82017806	82017808	+	1	NA	intron (NM_010247, intron 2 of 12)	intron (NM_010247, intron 2 of 12)	1438	NM_010247	14375	Mm.288809	NM_010247	ENSMUSG00000022471	Xrcc6	70kDa|G22p1|Ku70	X-ray repair complementing defective repair in Chinese hamster cells 6	protein-coding
mm_87894.1	chr10	62071015	62071020	+	1	NA	Intergenic	Intergenic	39996	NM_027251	69894	Mm.294126	NM_027251	ENSMUSG00000020083	2010107G23Rik	AA545165	RIKEN cDNA 2010107G23 gene	protein-coding
mm_144977.1	chr18	37955545	37955623	+	1	NA	promoter-TSS (NM_010411)	promoter-TSS (NM_010411)	25	NM_153793	225392	Mm.233516	NM_153793	ENSMUSG00000044024	Rell2	4631403P03Rik|ependolin	RELT-like 2	protein-coding
mm_65014.1	chr7	17093872	17093903	-	1	NA	exon (NM_007676, exon 3 of 5)	exon (NM_007676, exon 3 of 5)	19847	NM_007676	26436	Mm.143686	NM_007676	ENSMUSG00000066760	Psg16	Cea11|PSG|bCEA	pregnancy specific glycoprotein 16	protein-coding
mm_52168.1	chr6	99053470	99053475	+	1	NA	intron (NM_001347345, intron 6 of 19)	intron (NM_001347345, intron 6 of 19)	-25174	NM_001197322	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_72478.1	chr8	83608510	83608520	+	1	NA	promoter-TSS (NM_001308227)	promoter-TSS (NM_001308227)	-33	NM_001308227	81489	Mm.282092	NM_018808	ENSMUSG00000005483	Dnajb1	0610007I11Rik|DjB1|HSPF1|Hdj1|Hsp40	DnaJ heat shock protein family (Hsp40) member B1	protein-coding
mm_77695.1	chr8	126589588	126589607	-	1	NA	3' UTR (NM_001164598, exon 2 of 2)	3' UTR (NM_001164598, exon 2 of 2)	3839	NM_001164598	270110	Mm.334918	NM_001164598	ENSMUSG00000051495	Irf2bp2	E130305N23Rik|IRF-2BP2	interferon regulatory factor 2 binding protein 2	protein-coding
mm_74632.1	chr8	13192363	13192366	-	1	NA	intron (NM_025768, intron 2 of 7)	intron (NM_025768, intron 2 of 7)	-3266	NR_035494	100316713		NR_035494	ENSMUSG00000088054	Mir1968	mir-1968|mmu-mir-1968	microRNA 1968	ncRNA
mm_84333.1	chr9	64022084	64022101	-	1	NA	promoter-TSS (NM_008542)	promoter-TSS (NM_008542)	-33	NM_008542	17130	Mm.325757	NM_008542	ENSMUSG00000036867	Smad6	Madh6|b2b390Clo	SMAD family member 6	protein-coding
mm_159676.1	chr4	155667131	155667131	-	1	NA	5' UTR (NM_001256107, exon 2 of 20)	5' UTR (NM_001256107, exon 2 of 20)	2123	NM_001256108	76580	Mm.235738	NM_145124	ENSMUSG00000029060	Mib2	2210008I11Rik|Zzank1|skd	mindbomb E3 ubiquitin protein ligase 2	protein-coding
mm_170598.1	chr19	5802398	5802399	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	274	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_16077.1	chr2	168231221	168231225	+	1	NA	promoter-TSS (NM_010072)	promoter-TSS (NM_010072)	601	NM_001160330	69372	Mm.482182	NM_001160330	ENSMUSG00000074576	Mocs3	1700020H17Rik|Uba4	molybdenum cofactor synthesis 3	protein-coding
mm_30538.1	chr4	3574985	3574993	+	1	NA	promoter-TSS (NM_028097)	promoter-TSS (NM_028097)	110	NM_054089	116940	Mm.171323	NM_054089	ENSMUSG00000028233	Tgs1	D4Ertd800e|Ncoa6ip|Pimt	trimethylguanosine synthase 1	protein-coding
mm_57649.1	chr6	128438577	128438588	-	1	NA	promoter-TSS (NM_010219)	promoter-TSS (NM_010219)	49	NM_010219	14228	Mm.12758	NM_010219	ENSMUSG00000030357	Fkbp4	59kDa|AL022792|AW208983|FKBP-4|FKBP-52|FKBP52|FKPB52|p59	FK506 binding protein 4	protein-coding
mm_55962.1	chr6	85502929	85502965	-	1	NA	promoter-TSS (NM_001289674)	promoter-TSS (NM_001289674)	47	NM_001001160	330369	Mm.38777	NM_001001160	ENSMUSG00000047013	Fbxo41	9630017H13|D6Ertd538e	F-box protein 41	protein-coding
mm_151707.1	chr19	4498604	4498614	-	1	NA	promoter-TSS (NM_027237)	promoter-TSS (NM_027237)	-26	NM_027237	69861	Mm.282978	NM_027237	ENSMUSG00000042041	2010003K11Rik	-	RIKEN cDNA 2010003K11 gene	protein-coding
mm_56036.1	chr6	86650161	86650173	-	1	NA	3' UTR (NM_010751, exon 6 of 6)	3' UTR (NM_010751, exon 6 of 6)	18992	NM_010751	17119	Mm.279580	NM_010751	ENSMUSG00000001156	Mxd1	AW122478|Mad|Mad1	MAX dimerization protein 1	protein-coding
mm_143764.1	chr17	81627898	81627925	-	1	NA	intron (NR_104580, intron 2 of 8)	MIR|SINE|MIR	110476	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_76176.1	chr8	82394652	82394663	-	1	NA	intron (NM_001254747, intron 1 of 7)	intron (NM_001254747, intron 1 of 7)	7929	NM_001254747	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_61101.1	chr7	51880301	51880307	+	1	NA	intron (NM_008087, intron 1 of 7)	intron (NM_008087, intron 1 of 7)	1337	NM_001330607	14453	Mm.207360	NM_008087	ENSMUSG00000030498	Gas2	Gas-2	growth arrest specific 2	protein-coding
mm_32505.1	chr4	108467039	108467042	+	1	NA	intron (NM_175472, intron 2 of 30)	U6|snRNA|snRNA	7614	NM_175472	230594	Mm.25181	NM_175472	ENSMUSG00000034610	Zcchc11	6030404K05Rik|9230115F04Rik|PPAPD3|mKIAA0191	zinc finger, CCHC domain containing 11	protein-coding
mm_56008.1	chr6	86497789	86497800	-	1	NA	Intergenic	Intergenic	-9567	NR_040292	381792	Mm.333223	NR_040292	ENSMUSG00000101655	2310040G24Rik	-	RIKEN cDNA 2310040G24 gene	ncRNA
mm_122759.1	chr14	54227357	54227383	-	1	NA	Intergenic	Intergenic	26559	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_37829.1	chr4	131990821	131990830	-	1	NA	intron (NM_001128606, intron 6 of 17)	intron (NM_001128606, intron 6 of 17)	58253	NM_001128606	269587	Mm.30038	NM_183428	ENSMUSG00000028906	Epb41	4.1R|AI415518|D4Ertd442e|Elp-1|Elp1|Epb4.1|mKIAA4056	erythrocyte membrane protein band 4.1	protein-coding
mm_141631.1	chr17	32947351	32947368	-	1	NA	promoter-TSS (NM_130882)	promoter-TSS (NM_130882)	2	NM_130882	170716	Mm.254838	NM_130882	ENSMUSG00000024055	Cyp4f13	0610030I10Rik|Cypf13	cytochrome P450, family 4, subfamily f, polypeptide 13	protein-coding
mm_78791.1	chr9	44045775	44045787	+	1	NA	intron (NM_009382, intron 1 of 3)	intron (NM_009382, intron 1 of 3)	2397	NM_009382	21838	Mm.3951	NM_009382	ENSMUSG00000032011	Thy1	CD90|T25|Thy-1|Thy-1.2|Thy1.1|Thy1.2	thymus cell antigen 1, theta	protein-coding
mm_142550.1	chr17	46599756	46599761	-	1	NA	intron (NM_175168, intron 1 of 19)	intron (NM_175168, intron 1 of 19)	29746	NM_175168	71461	Mm.181833	NM_175168	ENSMUSG00000023972	Ptk7	8430404F20Rik|chz|mPTK7/CCK4	PTK7 protein tyrosine kinase 7	protein-coding
mm_122324.1	chr14	36968748	36968766	-	1	NA	promoter-TSS (NM_027045)	promoter-TSS (NM_027045)	7	NM_027045	72972	Mm.27621	NM_027045	ENSMUSG00000058690	Ccser2	1700012P13Rik|2900054P12Rik|AI035535|AW108503|Fam190b|Gcap14	coiled-coil serine rich 2	protein-coding
mm_164784.1	chr18	7926034	7926038	+	1	NA	intron (NM_153085, intron 13 of 13)	intron (NM_153085, intron 13 of 13)	56839	NM_153085	225131	Mm.204524	NM_153085	ENSMUSG00000024283	Wac	1110067P07Rik|A230035H12Rik|AI256735|AI256776|Wwp4	WW domain containing adaptor with coiled-coil	protein-coding
mm_128753.1	chr15	64921386	64921403	-	1	NA	5' UTR (NM_009623, exon 1 of 18)	5' UTR (NM_009623, exon 1 of 18)	902	NM_001331075	11514	Mm.1425	NM_009623	ENSMUSG00000022376	Adcy8	AC8|AW060868	adenylate cyclase 8	protein-coding
mm_108731.1	chr12	87443905	87443934	+	1	NA	promoter-TSS (NM_001013372)	promoter-TSS (NM_001013372)	23	NM_026958	380773	Mm.355701	NM_026958	ENSMUSG00000021040	Slirp	1810035L17Rik	SRA stem-loop interacting RNA binding protein	protein-coding
mm_19757.1	chr2	105126503	105126515	-	1	NA	promoter-TSS (NM_144783)	promoter-TSS (NM_144783)	1	NR_015462	329480	Mm.246679	NR_015462	ENSMUSG00000074987	Wt1os	6030498F17|AI314831|Wt1-as	Wilms tumor 1 homolog, opposite strand	ncRNA
mm_88628.1	chr10	79886303	79886319	+	1	NA	promoter-TSS (NM_015779)	promoter-TSS (NM_015779)	-1	NM_015779	50701	Mm.262194	NM_015779	ENSMUSG00000020125	Elane	Ela2|F430011M15Rik|NE	elastase, neutrophil expressed	protein-coding
mm_159342.1	chr3	59006721	59006721	+	1	NA	promoter-TSS (NM_177855)	promoter-TSS (NM_177855)	-257	NM_177855	329650	Mm.240059	NM_177855	ENSMUSG00000056476	Med12l	A130035F20|A630079M02|AU044581|TRALPUSH	mediator complex subunit 12-like	protein-coding
mm_35102.1	chr4	9287318	9287350	-	1	NA	intron (NM_028940, intron 2 of 5)	intron (NM_028940, intron 2 of 5)	18017	NM_028940	74438	Mm.473368	NM_028940	ENSMUSG00000041216	Clvs1	4933402J24Rik|Clvl1|Rlbp1l1	clavesin 1	protein-coding
mm_40054.1	chr5	33996095	33996111	+	1	NA	5' UTR (NM_001001985, exon 1 of 3)	5' UTR (NM_001001985, exon 1 of 3)	119	NM_001001985	269642	Mm.274610	NM_001001985	ENSMUSG00000048142	Nat8l	1110038O08Rik|Shati	N-acetyltransferase 8-like	protein-coding
mm_104940.1	chr11	100117403	100117428	-	1	NA	TTS (NM_010662)	TTS (NM_010662)	3162	NM_001313949	16663	Mm.4646	NM_010662	ENSMUSG00000044041	Krt13	CK13|K13|Krt-1.13|Krt1-13	keratin 13	protein-coding
mm_74860.1	chr8	24818548	24818556	-	1	NA	intron (NM_001272059, intron 2 of 18)	intron (NM_001272059, intron 2 of 18)	5817	NM_001272058	11499	Mm.143889	NM_007401	ENSMUSG00000031554	Adam5	tMDC II|tMDCII	a disintegrin and metallopeptidase domain 5	protein-coding
mm_96319.1	chr11	63989768	63989772	+	1	NA	intron (NM_178379, intron 5 of 6)	intron (NM_178379, intron 5 of 6)	25544	NR_131111	78883	Mm.410764	NR_131111	ENSMUSG00000086359	9630013K17Rik	-	RIKEN cDNA 9630013K17 gene	ncRNA
mm_108870.1	chr12	99609201	99609210	+	1	NA	intron (NR_136760, intron 2 of 3)	intron (NR_136760, intron 2 of 3)	18769	NR_045288	73457	Mm.383439	NR_045288	ENSMUSG00000100211	1700064M15Rik	-	RIKEN cDNA 1700064M15 gene	ncRNA
mm_45534.1	chr5	72752789	72752797	-	1	NA	promoter-TSS (NM_001289495)	promoter-TSS (NM_001289495)	-16	NM_001122754	22165	Mm.3264	NM_013698	ENSMUSG00000054892	Txk	A130089B16Rik|Btkl|PTK-RL-18|PTK4|Rlk	TXK tyrosine kinase	protein-coding
mm_61261.1	chr7	66079759	66079775	+	1	NA	exon (NM_024439, exon 1 of 6)	exon (NM_024439, exon 1 of 6)	118	NM_024439	109815	Mm.482127	NM_024439	ENSMUSG00000075701	Selenos	1500011E07Rik|C78786|H-4|H-47|H4|H47|Sels|Vimp	selenoprotein S	protein-coding
mm_170557.1	chr19	4192120	4192120	+	1	NA	promoter-TSS (NM_031868)	promoter-TSS (NM_031868)	-54	NM_031868	19045	Mm.1970	NM_031868	ENSMUSG00000040385	Ppp1ca	Ppp1c|dism2	protein phosphatase 1, catalytic subunit, alpha isoform	protein-coding
mm_17122.1	chr2	24733202	24733209	-	1	NA	intron (NM_007579, intron 4 of 45)	intron (NM_007579, intron 4 of 45)	29947	NM_001042528	12287	Mm.4424	NM_007579	ENSMUSG00000004113	Cacna1b	AW050276|AW060892|AW822256|BIII|Cav2.2|Cchn1a|alpha(1B)	calcium channel, voltage-dependent, N type, alpha 1B subunit	protein-coding
mm_34306.1	chr4	141793790	141793809	+	1	NA	5' UTR (NM_015733, exon 1 of 9)	5' UTR (NM_015733, exon 1 of 9)	187	NM_001277932	12371	Mm.88829	NM_015733	ENSMUSG00000028914	Casp9	AI115399|APAF-3|AW493809|CASP-9|Caspase-9|ICE-LAP6|Mch6	caspase 9	protein-coding
mm_170299.1	chr18	32769219	32769229	+	1	NA	intron (NR_045381, intron 2 of 4)	BGLII|LTR|ERVK	-46159	NM_021367	53603	Mm.143716	NM_021367	ENSMUSG00000024379	Tslp	-	thymic stromal lymphopoietin	protein-coding
mm_23086.1	chr3	36863167	36863177	+	1	NA	promoter-TSS (NM_172679)	promoter-TSS (NM_172679)	66	NM_172679	229227	Mm.207907	NM_172679	ENSMUSG00000037270	4932438A13Rik	4732443H21|B830039D19Rik|D630029K19Rik|FSA|Kiaa1109|Tweek	RIKEN cDNA 4932438A13 gene	protein-coding
mm_28625.1	chr3	95133899	95133913	-	1	NA	promoter-TSS (NM_153121)	promoter-TSS (NM_153121)	106	NM_027013	69269	Mm.182944	NM_027013	ENSMUSG00000092607	Scnm1	3110001I17Rik|Scnm1-ps	sodium channel modifier 1	protein-coding
mm_136837.1	chr17	12746672	12746684	+	1	NA	intron (NR_027773, intron 1 of 2)	RMER5|LTR|ERV1	5367	NR_027784	104103	Mm.26553	NR_002853	ENSMUSG00000078247	Airn	2810051F02Rik|2810434M15Rik|AI256653|AI597500|AW049873|Air|B930018I07Rik|D17Ertd663e|IGF2RAS	antisense Igf2r RNA	ncRNA
mm_40004.1	chr5	32898320	32898353	+	1	NA	intron (NM_177786, intron 11 of 32)	B1_Mur2|SINE|Alu	34615	NM_001170567	277854	Mm.101524	NM_177786	ENSMUSG00000037426	Depdc5	AV016528	DEP domain containing 5	protein-coding
mm_21532.1	chr2	163645148	163645152	-	1	NA	promoter-TSS (NM_012032)	promoter-TSS (NM_012032)	-7	NM_012032	26943	Mm.218473	NM_012032	ENSMUSG00000017707	Serinc3	AA959945|AA960047|AIGP1|DIFF33|TMS-1|Tde1	serine incorporator 3	protein-coding
mm_100881.1	chr11	5989659	5989670	-	1	NA	exon (NM_001174054, exon 10 of 21)	exon (NM_001174054, exon 10 of 21)	33906	NM_019661	56418	Mm.294821	NM_019661	ENSMUSG00000002741	Ykt6	0610042I15Rik|1810013M05Rik|AW105923	YKT6 v-SNARE homolog (S. cerevisiae)	protein-coding
mm_74325.1	chr8	126868063	126868069	+	1	NA	Intergenic	Intergenic	77855	NM_024214	67952	Mm.6932	NM_024214	ENSMUSG00000093904	Tomm20	1810060K07Rik|BB284719|Gm19268|MAS20|MOM19|TOM20|mKIAA0016	translocase of outer mitochondrial membrane 20 homolog (yeast)	protein-coding
mm_72356.1	chr8	79711895	79711910	+	1	NA	promoter-TSS (NM_026904)	promoter-TSS (NM_026904)	82	NM_026904	68999	Mm.257445	NM_026904	ENSMUSG00000036977	Anapc10	1500026N15Rik|A830003M23Rik|APC10	anaphase promoting complex subunit 10	protein-coding
mm_85671.1	chr9	107676597	107676615	-	1	NA	exon (NM_008140, exon 6 of 9)	exon (NM_008140, exon 6 of 9)	2986	NM_008140	14685	Mm.284853	NM_008140	ENSMUSG00000034837	Gnat1	Gnat-1|Ird1|Ird2|Tralpha|irdc|irdr|transducin	guanine nucleotide binding protein, alpha transducing 1	protein-coding
mm_75439.1	chr8	47413647	47413686	-	1	NA	Intergenic	CpG	-61318	NM_175162	71069	Mm.23973	NM_175162	ENSMUSG00000038143	Stox2	4933409N07Rik|AI449080|AI835114|mKIAA1392	storkhead box 2	protein-coding
mm_62613.1	chr7	107209168	107209177	+	1	NA	promoter-TSS (NM_029660)	promoter-TSS (NM_029660)	-273	NM_029660	76572	Mm.128134	NM_029660	ENSMUSG00000073894	Rbmxl2	1700012H05Rik|Hnrnpg-t	RNA binding motif protein, X-linked-like 2	protein-coding
mm_144465.1	chr18	23753673	23753688	+	1	NA	promoter-TSS (NM_001162941)	promoter-TSS (NM_001162941)	-45	NM_001162941	212307	Mm.132237	NM_153058	ENSMUSG00000024277	Mapre2	AI314113|C820009F03Rik|D18Abb1e|EB1|EB2|RP1	microtubule-associated protein, RP/EB family, member 2	protein-coding
mm_79218.1	chr9	49340384	49340386	+	1	NA	promoter-TSS (NM_010077)	promoter-TSS (NM_010077)	-277	NM_010077	13489	Mm.41970	NM_010077	ENSMUSG00000032259	Drd2	D2R|Drd-2	dopamine receptor D2	protein-coding
mm_21548.1	chr2	164070444	164070459	-	1	NA	intron (NM_001291155, intron 1 of 6)	CpG	651	NM_025996	67145	Mm.23173	NM_025996	ENSMUSG00000018322	Tomm34	2610100K07Rik|TOM34	translocase of outer mitochondrial membrane 34	protein-coding
mm_6471.1	chr1	74068642	74068677	-	1	NA	intron (NM_027884, intron 2 of 34)	CpG-274	55788	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_53081.1	chr6	124965579	124965590	+	1	NA	promoter-TSS (NM_001164089)	promoter-TSS (NM_001164089)	-55	NM_001164089	26894	Mm.244536	NM_012003	ENSMUSG00000030127	Cops7a	D6Ertd35e	COP9 signalosome subunit 7A	protein-coding
mm_98774.1	chr11	96777842	96777864	+	1	NA	promoter-TSS (NM_028965)	promoter-TSS (NM_028965)	-298	NM_001163389	74479	Mm.270781	NM_028965	ENSMUSG00000020876	Snx11	4933439F10Rik|A930041K09Rik|AI117694	sorting nexin 11	protein-coding
mm_10547.1	chr2	16650179	16650190	+	1	NA	exon (NM_026162, exon 6 of 14)	exon (NM_026162, exon 6 of 14)	293880	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding
mm_155292.1	chrX	61183869	61183876	+	1	NA	3' UTR (NM_001166658, exon 1 of 1)	3' UTR (NM_001166658, exon 1 of 1)	1686	NM_001166658	631990	Mm.401324	NM_001166658	ENSMUSG00000090546	Cdr1	100039759|Cdr|Cdr34|EG631990|Gm2409|Gm7077	cerebellar degeneration related antigen 1	protein-coding
mm_127378.1	chr15	100870628	100870667	+	1	NA	promoter-TSS (NM_001077499)	promoter-TSS (NM_001077499)	2	NM_001077499	20273	Mm.385012	NM_011323	ENSMUSG00000023033	Scn8a	AI853486|C630029C19Rik|NaCh6|Nav1.6|dmu|med|mnd-2|mnd2|nmf2|nmf335|nmf58|nur14|seal	sodium channel, voltage-gated, type VIII, alpha	protein-coding
mm_18035.1	chr2	38727194	38727241	-	1	NA	3' UTR (NM_010264, exon 11 of 11)	3' UTR (NM_010264, exon 11 of 11)	-12675	NM_139051	26423	Mm.31387	NM_139051	ENSMUSG00000026751	Nr5a1	Ad4BP|ELP|ELP-3|Ftz-F1|Ftzf1|SF-1|SF1|STF-1	nuclear receptor subfamily 5, group A, member 1	protein-coding
mm_8085.1	chr1	135631220	135631224	-	1	NA	Intergenic	Intergenic	-45867	NM_173437	215690	Mm.34977	NM_173437	ENSMUSG00000009418	Nav1	9530089B19|9930003A20Rik|C230080M11Rik|Pomfil3|Unc53h1|mKIAA1151|steerin-1	neuron navigator 1	protein-coding
mm_170571.1	chr19	51142767	51142779	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-464127	NM_001290356	58178	Mm.313672	NM_021377	ENSMUSG00000043531	Sorcs1	Sorcs|mSorCS	sortilin-related VPS10 domain containing receptor 1	protein-coding
mm_139644.1	chr17	57377689	57377699	+	1	NA	intron (NM_010130, intron 2 of 21)	Lx5b|LINE|L1	19008	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_18964.1	chr2	76807388	76807399	-	1	NA	intron (NM_028004, intron 67 of 191)	intron (NM_028004, intron 67 of 191)	132078	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_164812.1	chr18	32980234	32980240	+	1	NA	intron (NM_009793, intron 1 of 10)	B1_Mur3|SINE|Alu	41196	NM_009793	12326	Mm.222329	NM_009793	ENSMUSG00000038128	Camk4	A430110E23Rik|AI666733|CaMKIV|CaMKIV/Gr|D18Bwg0362e	calcium/calmodulin-dependent protein kinase IV	protein-coding
mm_25976.1	chr3	133091887	133091907	+	1	NA	promoter-TSS (NM_026231)	promoter-TSS (NM_026231)	42	NM_027927	71793	Mm.246726	NM_027927	ENSMUSG00000028016	Ints12	1110020M19Rik|2810027J24Rik|4930529N21Rik|A230056J18Rik|AI666778|Phf22|int12	integrator complex subunit 12	protein-coding
mm_38682.1	chr4	145054248	145054259	-	1	NA	exon (NM_001276465, exon 63 of 70)	exon (NM_001276465, exon 63 of 70)	136413	NM_001276502	230895	Mm.240310	NM_001033190	ENSMUSG00000020220	Vps13d	-	vacuolar protein sorting 13D	protein-coding
mm_170607.1	chr19	5845207	5845212	-	1	NA	non-coding (NR_003513, exon 1 of 1)	non-coding (NR_003513, exon 1 of 1)	269	NR_131212	66961	Mm.281895	NR_003513	ENSMUSG00000092274	Neat1	2310043N10Rik|VINC	nuclear paraspeckle assembly transcript 1 (non-protein coding)	ncRNA
mm_158469.1	chrX	141207548	141207550	-	1	NA	intron (NM_053185, intron 14 of 44)	intron (NM_053185, intron 14 of 44)	-250838	NM_001164177	53380	Mm.17640	NM_016883	ENSMUSG00000031429	Psmd10	AW554874	proteasome (prosome, macropain) 26S subunit, non-ATPase, 10	protein-coding
mm_145860.1	chr18	65456223	65456245	+	1	NA	intron (NM_172833, intron 8 of 15)	intron (NM_172833, intron 8 of 15)	25237	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_76201.1	chr8	82848115	82848121	-	1	NA	Intergenic	Intergenic	-15238	NM_177378	330812	Mm.491438	NM_177378	ENSMUSG00000047747	Rnf150	A630007N06Rik|C030044C12Rik|Greul5|mKIAA1214	ring finger protein 150	protein-coding
mm_135647.1	chr16	52386805	52386815	-	1	NA	intron (NM_009655, intron 1 of 15)	intron (NM_009655, intron 1 of 15)	66271	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_61433.1	chr7	73816585	73816600	+	1	NA	promoter-TSS (NR_077222)	promoter-TSS (NR_077222)	-89	NR_077222	100579147	Mm.109205	NR_077222	ENSMUSG00000074067	Gm10619	4932443D20|ENSMUSG00000074067	predicted gene 10619	ncRNA
mm_29046.1	chr3	103364240	103364266	-	1	NA	Intergenic	Intergenic	84960	NM_001079830	94093	Mm.195036	NM_053170	ENSMUSG00000033014	Trim33	8030451N04Rik|AI413936|Ecto|Tif1g	tripartite motif-containing 33	protein-coding
mm_90698.1	chr10	130330973	130330979	+	1	NA	intron (NM_183264, intron 1 of 8)	intron (NM_183264, intron 1 of 8)	8124	NM_183264	67596	Mm.131264	NM_183264	ENSMUSG00000034833	Tespa1	5830405N20Rik|A430001F24Rik|AI450549	thymocyte expressed, positive selection associated 1	protein-coding
mm_15081.1	chr2	153161525	153161553	+	1	NA	5' UTR (NM_133847, exon 1 of 18)	5' UTR (NM_133847, exon 1 of 18)	238	NM_133847	99237	Mm.330674	NM_133847	ENSMUSG00000068040	Tm9sf4	AA986553|AU045326|B930079E06|mKIAA0255	transmembrane 9 superfamily protein member 4	protein-coding
mm_60512.1	chr7	44479641	44479692	+	1	NA	Intergenic	Intergenic	-4851	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_38436.1	chr4	139380375	139380404	-	1	NA	promoter-TSS (NM_001160319)	promoter-TSS (NM_001160319)	-270	NM_001160319	69116	Mm.271956	NM_001160319	ENSMUSG00000066036	Ubr4	1810009A16Rik|A930005E13Rik|D930005K06Rik|Gm1032|Gm1666|N28143|RBAF600|Zubr1|mKIAA0462|p600	ubiquitin protein ligase E3 component n-recognin 4	protein-coding
mm_109314.1	chr12	109561023	109561054	+	1	NA	non-coding (NR_003633, exon 5 of 5)	non-coding (NR_003633, exon 5 of 5)	-2654	NR_030427	791079		NR_030427	ENSMUSG00000076451	Mir770	Mirn770|mir-770|mmu-mir-770	microRNA 770	ncRNA
mm_4454.1	chr1	172699056	172699066	+	1	NA	3' UTR (NM_007768, exon 2 of 2)	3' UTR (NM_007768, exon 2 of 2)	1005	NM_007768	12944	Mm.28767	NM_007768	ENSMUSG00000037942	Crp	AI255847	C-reactive protein, pentraxin-related	protein-coding
mm_48828.1	chr5	149068297	149068307	-	1	NA	Intergenic	Intergenic	-15245	NM_010439	15289	Mm.207047	NM_010439	ENSMUSG00000066551	Hmgb1	HMG-1|Hmg1|SBP-1|p30	high mobility group box 1	protein-coding
mm_57226.1	chr6	123282494	123282504	-	1	NA	3' UTR (NM_019948, exon 6 of 6)	3' UTR (NM_019948, exon 6 of 6)	7372	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_135961.1	chr16	74760650	74760660	-	1	NA	Intergenic	Intergenic	-349743	NM_175549	268902	Mm.171736	NM_175549	ENSMUSG00000052516	Robo2	2600013A04Rik|9430089E08Rik|BB097918|D230004I22Rik|mKIAA1568	roundabout guidance receptor 2	protein-coding
mm_65994.1	chr7	30552347	30552375	-	1	NA	promoter-TSS (NM_183321)	promoter-TSS (NM_183321)	-89	NM_183321	333193	Mm.34885	NM_183321	ENSMUSG00000036864	Proser3	-	proline and serine rich 3	protein-coding
mm_55333.1	chr6	56361874	56361891	-	1	NA	5' UTR (NM_001159953, exon 1 of 19)	5' UTR (NM_001159953, exon 1 of 19)	510	NM_001159952	18575	Mm.5145	NM_011054	ENSMUSG00000004347	Pde1c	-	phosphodiesterase 1C	protein-coding
mm_4481.1	chr1	173440719	173440729	+	1	NA	intron (NM_001013779, intron 2 of 8)	intron (NM_001013779, intron 2 of 8)	20120	NM_001013779	383619	Mm.131453	NM_001013779	ENSMUSG00000037860	Aim2	Gm1313|Ifi210	absent in melanoma 2	protein-coding
mm_121127.1	chr14	101840812	101840839	+	1	NA	5' UTR (NM_001347628, exon 1 of 27)	5' UTR (NM_001347628, exon 1 of 27)	202	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_38195.1	chr4	135380812	135380839	-	1	NA	5' UTR (NM_001243306, exon 2 of 6)	5' UTR (NM_001243306, exon 2 of 6)	4847	NM_001168498	230822	Mm.35548	NM_145555	ENSMUSG00000043924	Ncmap	A330049M08Rik|AA545175|Mp11	noncompact myelin associated protein	protein-coding
mm_45018.1	chr5	38561125	38561141	-	1	NA	exon (NM_011715, exon 2 of 15)	exon (NM_011715, exon 2 of 15)	462	NM_011715	22388	Mm.2654	NM_011715	ENSMUSG00000005103	Wdr1	Aip1|D5Wsu185e|rede	WD repeat domain 1	protein-coding
mm_132150.1	chr16	32105087	32105122	+	1	NA	intron (NM_025892, intron 3 of 3)	MTD|LTR|ERVL-MaLR	5302	NM_025892	66994	Mm.22990	NM_025892	ENSMUSG00000035790	Cep19	1500031L02Rik|AI428934|AL022620	centrosomal protein 19	protein-coding
mm_73734.1	chr8	113643179	113643197	+	1	NA	promoter-TSS (NM_001048145)	promoter-TSS (NM_001048145)	-25	NM_029139	668110	Mm.390078	NM_029139	ENSMUSG00000033409	Syce1l	4930481F22Rik|MMRP|PSESS|mmrp2	synaptonemal complex central element protein 1 like	protein-coding
mm_40993.1	chr5	77285669	77285681	+	1	NA	Intergenic	Intergenic	12918	NR_039557	100628577		NR_039557	ENSMUSG00000093061	Mir5098	mmu-mir-5098|mu-mir-5098	microRNA 5098	ncRNA
mm_21277.1	chr2	156928048	156928084	-	1	NA	3' UTR (NM_180956, exon 17 of 17)	3' UTR (NM_180956, exon 17 of 17)	-40988	NM_029983	77799	Mm.29264	NM_029983	ENSMUSG00000027636	Sla2	A930009E21Rik|AI430952|SLAP-2|SLAP2	Src-like-adaptor 2	protein-coding
mm_22549.1	chr3	9402995	9403027	+	1	NA	promoter-TSS (NR_015499)	promoter-TSS (NR_015499)	-67	NR_015499	320088	Mm.212908	NR_015499	ENSMUSG00000097365	C030034L19Rik	A130044O20Rik	RIKEN cDNA C030034L19 gene	ncRNA
mm_54201.1	chr6	24664961	24665038	-	1	NA	promoter-TSS (NM_028459)	promoter-TSS (NM_028459)	-4	NM_028459	73178	Mm.1574	NM_028459	ENSMUSG00000029684	Wasl	2900021I12Rik|3110031I02Rik|N-WASP	Wiskott-Aldrich syndrome-like (human)	protein-coding
mm_105475.1	chr11	105936511	105936524	-	1	NA	intron (NM_007805, intron 3 of 5)	intron (NM_007805, intron 3 of 5)	7630	NM_007805	13056	Mm.149403	NM_007805	ENSMUSG00000019590	Cyb561	-	cytochrome b-561	protein-coding
mm_28474.1	chr3	92081354	92081366	-	1	NA	exon (NM_008508, exon 2 of 2)	exon (NM_008508, exon 2 of 2)	1782	NM_008508	16939	Mm.1121	NM_008508	ENSMUSG00000043165	Lor	AI036317|S77319	loricrin	protein-coding
mm_38896.1	chr4	149854076	149854083	-	1	NA	Intergenic	URR1A|DNA|hAT-Charlie	-79812	NM_027460	70556	Mm.41877	NM_027460	ENSMUSG00000028982	Slc25a33	5730438N18Rik|Pnc1	solute carrier family 25, member 33	protein-coding
mm_155123.1	chrX	48872047	48872051	+	1	NA	intron (NM_001085499, intron 8 of 20)	intron (NM_001085499, intron 8 of 20)	5664	NM_001085499	209005	Mm.336054	NM_001085499	ENSMUSG00000079606	Gm595	-	predicted gene 595	protein-coding
mm_85716.1	chr9	108209510	108209532	-	1	NA	exon (NM_001276486, exon 4 of 4)	exon (NM_001276486, exon 4 of 4)	-19138	NM_007567	12217	Mm.20425	NM_007567	ENSMUSG00000032589	Bsn	-	bassoon	protein-coding
mm_29670.1	chr3	122629744	122629766	-	1	NA	Intergenic	Intergenic	-10041	NM_153118	214459	Mm.209491	NM_153118	ENSMUSG00000039735	Fnbp1l	2610318I01Rik|AW548221|TOCA1|toca-1	formin binding protein 1-like	protein-coding
mm_116719.1	chr13	51701397	51701418	-	1	NA	3' UTR (NM_001281880, exon 17 of 17)	3' UTR (NM_001281880, exon 17 of 17)	49699	NM_029279	75420	Mm.275981	NM_029279	ENSMUSG00000035139	Secisbp2	2210413N07Rik|2810012K13Rik|SBP2	SECIS binding protein 2	protein-coding
mm_111650.1	chr12	102757691	102757695	-	1	NA	promoter-TSS (NM_025666)	promoter-TSS (NM_025666)	117	NM_001142939	100859931	Mm.291222	NM_001142939	ENSMUSG00000041716	Gm20604	AK010878-Moap1	predicted gene 20604	protein-coding
mm_160855.1	chr11	58307506	58307506	+	1	NA	intron (NM_001040686, intron 1 of 11)	CpG	437	NM_001040686	103836	Mm.41440	NM_182996	ENSMUSG00000037243	Zfp692	AI746306|AI839920|Zfp692-ps|Znf692	zinc finger protein 692	protein-coding
mm_112780.1	chr13	20090636	20090642	+	1	NA	5' UTR (NM_080288, exon 1 of 22)	5' UTR (NM_080288, exon 1 of 22)	132	NM_080288	140580	Mm.342392	NM_080288	ENSMUSG00000041112	Elmo1	6330578D22Rik|C230095H21Rik|CED-12	engulfment and cell motility 1	protein-coding
mm_111715.1	chr12	103729278	103729297	-	1	NA	exon (NM_009244, exon 4 of 5)	exon (NM_009244, exon 4 of 5)	8902	NM_009244	20701	Mm.439692	NM_009244	ENSMUSG00000071178	Serpina1b	D12Ucla2|Dom2|PI2|Spi1-2	serine (or cysteine) preptidase inhibitor, clade A, member 1B	protein-coding
mm_76037.1	chr8	77387490	77387502	-	1	NA	intron (NM_030113, intron 11 of 22)	intron (NM_030113, intron 11 of 22)	-129560	NR_028125	70345	Mm.411813	NR_028125	ENSMUSG00000097882	0610038B21Rik	-	RIKEN cDNA 0610038B21 gene	ncRNA
mm_118097.1	chr13	103907747	103907750	-	1	NA	intron (NM_001005868, intron 1 of 26)	intron (NM_001005868, intron 1 of 26)	12838	NM_001289473	59079	Mm.277354	NM_021563	ENSMUSG00000021709	Erbin	1700028E05Rik|Erbb2ip|mKIAA1225	Erbb2 interacting protein	protein-coding
mm_132536.1	chr16	37868566	37868733	+	1	NA	exon (NM_177093, exon 1 of 4)	exon (NM_177093, exon 1 of 4)	249	NM_177093	320184	Mm.390882	NM_177093	ENSMUSG00000034158	Lrrc58	1810012N18Rik|C330018J07Rik	leucine rich repeat containing 58	protein-coding
mm_32818.1	chr4	117445799	117445814	+	1	NA	intron (NM_025739, intron 2 of 14)	intron (NM_025739, intron 2 of 14)	51246	NM_025739	66743	Mm.318331	NM_025739	ENSMUSG00000028677	Rnf220	4732477A13|4931406I20Rik|5730503K05Rik|AV302541	ring finger protein 220	protein-coding
mm_124769.1	chr15	6741955	6741959	+	1	NA	intron (NM_030168, intron 3 of 37)	PB1D7|SINE|Alu	33576	NM_030168	78757	Mm.275811	NM_030168	ENSMUSG00000050310	Rictor	4921505C17Rik|6030405M08Rik|AVO3|AW492497|D530039E11Rik	RPTOR independent companion of MTOR, complex 2	protein-coding
mm_76144.1	chr8	81882012	81882014	-	1	NA	intron (NM_001024617, intron 8 of 24)	intron (NM_001024617, intron 8 of 24)	520573	NM_001254747	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_87634.1	chr10	58332820	58332834	+	1	NA	intron (NM_026148, intron 1 of 9)	Lx9|LINE|L1	9361	NM_026148	110829	Mm.57734	NM_026148	ENSMUSG00000019920	Lims1	2310016J22Rik|4921524A02Rik|AI507642|AU021743|AW551584|C430041B13Rik|Lims1l|PINCH|PINCH1	LIM and senescent cell antigen-like domains 1	protein-coding
mm_150581.1	chr19	40659661	40659689	+	1	NA	promoter-TSS (NM_009848)	promoter-TSS (NM_009848)	-95	NM_009848	12495	Mm.2824	NM_009848	ENSMUSG00000048120	Entpd1	2610206B08Rik|AA408691|Cd39|NTPDase-1	ectonucleoside triphosphate diphosphohydrolase 1	protein-coding
mm_27466.1	chr3	52634447	52634455	-	1	NA	Intergenic	Intergenic	-105273	NR_038079	329639	Mm.131245	NR_038079	ENSMUSG00000102785	Gm2447	100039832|A530017F20	predicted gene 2447	ncRNA
mm_169983.1	chr17	15010424	15010436	+	1	NA	promoter-TSS (NM_001123367)	promoter-TSS (NM_001123367)	-246	NM_001123367	100041639	Mm.440445	NM_001123367	ENSMUSG00000079710	Gm3448	-	predicted gene 3448	protein-coding
mm_111693.1	chr12	103653492	103653501	-	1	NA	intron (NM_007618, intron 2 of 4)	MER20|DNA|hAT-Charlie	3722	NM_007618	12401	Mm.290079	NM_007618	ENSMUSG00000060807	Serpina6	Cbg	serine (or cysteine) peptidase inhibitor, clade A, member 6	protein-coding
mm_168037.1	chrY	90742715	90742730	-	1	NA	Intergenic	CpG	12328	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_99893.1	chr11	109613443	109613460	+	1	NA	Intergenic	Intergenic	-2062	NM_145940	52639	Mm.35817	NM_145940	ENSMUSG00000041895	Wipi1	4930533H01Rik|AW411817|D11Ertd498e	WD repeat domain, phosphoinositide interacting 1	protein-coding
mm_161842.1	chr17	88668613	88668613	+	1	NA	promoter-TSS (NM_023630)	promoter-TSS (NM_023630)	-47	NM_023630	71828	Mm.61330	NM_023630	ENSMUSG00000024154	Gtf2a1l	1700011N16Rik|Alf|Gtf2a1lf	general transcription factor IIA, 1-like	protein-coding
mm_64895.1	chr7	15950028	15950043	-	1	NA	3' UTR (NM_153068, exon 6 of 6)	3' UTR (NM_153068, exon 6 of 6)	-3927	NM_133831	68077	Mm.277634	NM_133831	ENSMUSG00000041560	Gltscr2	5330430H08Rik|9430097C02Rik|AU041936|AW536441|PICT-1|R74911	glioma tumor suppressor candidate region gene 2	protein-coding
mm_7607.1	chr1	126492684	126492724	-	1	NA	5' UTR (NM_172484, exon 1 of 15)	5' UTR (NM_172484, exon 1 of 15)	223	NM_172484	210356	Mm.377234	NM_172484	ENSMUSG00000049690	Nckap5	8430408F21|D130011D22Rik|E030049G20Rik|Erih1|Erih2|Gm1548|Nap5	NCK-associated protein 5	protein-coding
mm_73760.1	chr8	115186666	115186668	+	1	NA	intron (NM_019573, intron 8 of 8)	MIR|SINE|MIR	520227	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_51091.1	chr6	67205506	67205523	+	1	NA	Intergenic	(T)n|Simple_repeat|Simple_repeat	-61465	NM_001113564	66870	Mm.240490	NM_025814	ENSMUSG00000036371	Serbp1	1200009K13Rik|9330147J08Rik|AL022786|Pairbp1	serpine1 mRNA binding protein 1	protein-coding
mm_24555.1	chr3	93443497	93443505	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	1171	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_97478.1	chr11	78324226	78324236	+	1	NA	promoter-TSS (NM_009657)	promoter-TSS (NM_009657)	33	NM_009657	11676	Mm.7729	NM_009657	ENSMUSG00000017390	Aldoc	AI847350|AU040929|Aldo3|Scrg2	aldolase C, fructose-bisphosphate	protein-coding
mm_101710.1	chr11	42000835	42000867	-	1	NA	promoter-TSS (NM_008073)	promoter-TSS (NM_008073)	-137	NM_008073	14406	Mm.5309	NM_008073	ENSMUSG00000020436	Gabrg2	GABAA-R|Gabrg-2|gamma2	gamma-aminobutyric acid (GABA) A receptor, subunit gamma 2	protein-coding
mm_164619.1	chr17	31162760	31162782	-	1	NA	exon (NM_009362, exon 2 of 3)	exon (NM_009362, exon 2 of 3)	2282	NM_009362	21784	Mm.2854	NM_009362	ENSMUSG00000024032	Tff1	Bcei|PS2	trefoil factor 1	protein-coding
mm_171355.1	chr4	110718235	110718236	-	1	NA	intron (NM_001048189, intron 3 of 12)	intron (NM_001048189, intron 3 of 12)	320537	NM_030231	78933	Mm.435620	NM_030231	ENSMUSG00000061298	Agbl4	4930578N11Rik|4931433A01Rik	ATP/GTP binding protein-like 4	protein-coding
mm_118892.1	chr14	26630941	26630962	+	1	NA	3' UTR (NM_001285466, exon 18 of 18)	3' UTR (NM_001285466, exon 18 of 18)	-7246	NM_007479	11843	Mm.297768	NM_007479	ENSMUSG00000021877	Arf4	AA407803	ADP-ribosylation factor 4	protein-coding
mm_49054.1	chr6	5048278	5048284	+	1	NA	intron (NM_181595, intron 3 of 15)	intron (NM_181595, intron 3 of 15)	144961	NM_181595	243725	Mm.332901	NM_181595	ENSMUSG00000032827	Ppp1r9a	2810430P21Rik|4930518N04Rik|5330407E15|A230094E16Rik|BB181831|NRB|mKIAA1222|neurabin-I	protein phosphatase 1, regulatory (inhibitor) subunit 9A	protein-coding
mm_50322.1	chr6	48073633	48073645	+	1	NA	intron (NM_001347142, intron 4 of 6)	RLTR34B_MM|LTR|ERVK	12954	NM_001347142	69228	Mm.207555	NM_001163475	ENSMUSG00000057691	Zfp746	2810407L07Rik|AI317225|Znf746	zinc finger protein 746	protein-coding
mm_115663.1	chr13	12461563	12461573	-	1	NA	5' UTR (NM_001291060, exon 1 of 9)	5' UTR (NM_001291060, exon 1 of 9)	170	NM_001291060	56048	Mm.474138	NM_018886	ENSMUSG00000057554	Lgals8	1200015E08Rik|AI326142|D13Ertd524e|Lgals-8	lectin, galactose binding, soluble 8	protein-coding
mm_140026.1	chr17	73949767	73949771	+	1	NA	intron (NM_011723, intron 1 of 35)	intron (NM_011723, intron 1 of 35)	427	NM_011723	22436	Mm.11223	NM_011723	ENSMUSG00000024066	Xdh	XO|Xor|Xox-1|Xox1	xanthine dehydrogenase	protein-coding
mm_31753.1	chr4	63346041	63346057	+	1	NA	exon (NM_008768, exon 4 of 6)	exon (NM_008768, exon 4 of 6)	1493	NM_008768	18405	Mm.4777	NM_008768	ENSMUSG00000039196	Orm1	Agp-1|Agp-2|Orm-1	orosomucoid 1	protein-coding
mm_130332.1	chr15	97721104	97721110	-	1	NA	promoter-TSS (NM_008902)	promoter-TSS (NM_008902)	43	NM_008902	19011	Mm.1001	NM_008902	ENSMUSG00000022468	Endou	Pp11r|Tcl-30	endonuclease, polyU-specific	protein-coding
mm_164815.1	chr18	34032455	34032483	+	1	NA	Intergenic	Intergenic	-25263	NM_013512	13824	Mm.3465	NM_013512	ENSMUSG00000024376	Epb41l4a	Epb4.1l4|Epb4.1l4a|NBL4	erythrocyte membrane protein band 4.1 like 4a	protein-coding
mm_90325.1	chr10	127075266	127075325	+	1	NA	Intergenic	Intergenic	-3612	NM_001301014	216439	Mm.336761	NM_001033263	ENSMUSG00000025422	Agap2	AGAP-2|Centg1|PIKE|cnt-g1|mKIAA0167	ArfGAP with GTPase domain, ankyrin repeat and PH domain 2	protein-coding
mm_144269.1	chr18	11059015	11059029	+	1	NA	intron (NM_010258, intron 2 of 6)	intron (NM_010258, intron 2 of 6)	-6455	NR_105023	68434	Mm.57626	NR_105022	ENSMUSG00000097222	1010001N08Rik	Gata6as	RIKEN cDNA 1010001N08 gene	ncRNA
mm_69791.1	chr7	141100527	141100551	-	1	NA	promoter-TSS (NM_023059)	promoter-TSS (NM_023059)	7	NM_023059	24058	Mm.38017	NM_023059	ENSMUSG00000025494	Sigirr	AI256711|TIR8	single immunoglobulin and toll-interleukin 1 receptor (TIR) domain	protein-coding
mm_92773.1	chr10	81167839	81167849	-	1	NA	promoter-TSS (NM_021501)	promoter-TSS (NM_021501)	-124	NM_021501	59004	Mm.34428	NM_021501	ENSMUSG00000004934	Pias4	PIASY|Pias-gamma|Piasg	protein inhibitor of activated STAT 4	protein-coding
mm_145239.1	chr18	50395132	50395148	+	1	NA	Intergenic	MLT1K|LTR|ERVL-MaLR	116771	NM_001004061	225497	Mm.329435	NM_001004061	ENSMUSG00000035420	Fam170a	Gm93|Znfd	family with sequence similarity 170, member A	protein-coding
mm_11142.1	chr2	28496916	28496963	+	1	NA	promoter-TSS (NM_139197)	promoter-TSS (NM_139197)	48	NM_139197	227671	Mm.484270	NM_139197	ENSMUSG00000026829	Gbgt1	Fgs|Fs	globoside alpha-1,3-N-acetylgalactosaminyltransferase 1	protein-coding
mm_102222.1	chr11	54909928	54909946	-	1	NA	TTS (NM_021327)	TTS (NM_021327)	7083	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_126595.1	chr15	82358291	82358294	+	1	NA	Intergenic	Intergenic	-4001	NM_025987	67130	Mm.27570	NM_025987	ENSMUSG00000022450	Ndufa6	14kDa|2700038D15Rik|B230217P19Rik	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 6 (B14)	protein-coding
mm_19283.1	chr2	89946972	89946989	-	1	NA	Intergenic	Intergenic	-2867	NM_146341	258338	Mm.354180	NM_146341	ENSMUSG00000068806	Olfr1259	MOR232-9	olfactory receptor 1259	protein-coding
mm_82301.1	chr9	7864738	7864751	-	1	NA	intron (NM_007464, intron 1 of 8)	intron (NM_007464, intron 1 of 8)	8426	NM_007464	11796	Mm.2026	NM_007464	ENSMUSG00000032000	Birc3	AW107670|Api1|Api2|Birc2|C-IAP2|HIAP2|IAP1|IAP2|MIAP1|MIAP2|MIHB|MIHC|RNF49|cIAP-1|cIAP-2|cIAP1|cIAP2	baculoviral IAP repeat-containing 3	protein-coding
mm_151035.1	chr19	47016827	47016829	+	1	NA	intron (NM_146100, intron 1 of 2)	intron (NM_146100, intron 1 of 2)	-1639	NM_001164363	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_26364.1	chr3	142560109	142560134	+	1	NA	promoter-TSS (NM_018734)	promoter-TSS (NM_018734)	69	NM_001289492	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_11844.1	chr2	45196753	45196785	+	1	NA	Intergenic	Intergenic	-83490	NM_015753	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_49263.1	chr6	17464093	17464113	+	1	NA	5' UTR (NM_008591, exon 1 of 22)	5' UTR (NM_008591, exon 1 of 22)	146	NM_008591	17295	Mm.86844	NM_008591	ENSMUSG00000009376	Met	AI838057|HGF|HGFR|Par4|c-Met	met proto-oncogene	protein-coding
mm_46873.1	chr5	113832531	113832545	-	1	NA	Intergenic	Intergenic	-2037	NM_009151	20345	Mm.332590	NM_009151	ENSMUSG00000048163	Selplg	CD162|Psgl-1|Psgl1|Selp1|Selpl	selectin, platelet (p-selectin) ligand	protein-coding
mm_9236.1	chr1	171287932	171287976	-	1	NA	promoter-TSS (NM_013919)	promoter-TSS (NM_013919)	7	NM_013919	30941	Mm.27510	NM_013919	ENSMUSG00000053483	Usp21	ESTM28|Usp16|Usp23|W53272	ubiquitin specific peptidase 21	protein-coding
mm_115469.1	chr13	119462753	119462810	+	1	NA	promoter-TSS (NM_026127)	promoter-TSS (NM_026127)	22	NM_026127	67392	Mm.390641	NM_026127	ENSMUSG00000062822	4833420G17Rik	2210017J06Rik|5730533D17Rik|AW107518|C85193	RIKEN cDNA 4833420G17 gene	protein-coding
mm_161964.1	chr19	8713861	8713861	-	1	NA	promoter-TSS (NM_008577)	promoter-TSS (NM_008577)	36	NM_008577	17254	Mm.4114	NM_008577	ENSMUSG00000010095	Slc3a2	4F2|4F2HC|AI314110|Cd98|Ly-10|Ly-m10|Ly10|Mdu1|Mgp-2hc|NACAE	solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2	protein-coding
mm_1867.1	chr1	85276900	85276947	+	1	NA	Intergenic	Intergenic	-6357	NM_001037909	620078	Mm.386456	NM_175219	ENSMUSG00000052477	C130026I21Rik	4930565N07Rik|OTTMUSG00000029174	RIKEN cDNA C130026I21 gene	protein-coding
mm_30530.1	chr4	3090777	3090802	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	-81294	NM_001167534	100312470	Mm.480297	NM_001167534	ENSMUSG00000094798	Vmn1r2	Gm11776|OTTMUSG00000004179	vomeronasal 1 receptor 2	protein-coding
mm_6761.1	chr1	84102307	84102308	-	1	NA	intron (NM_001003948, intron 2 of 2)	intron (NM_001003948, intron 2 of 2)	116654	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_153700.1	chr19	44397564	44397592	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	10131	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_75270.1	chr8	40855096	40855102	-	1	NA	Intergenic	Intergenic	-7268	NM_007514	11988	Mm.4676	NM_007514	ENSMUSG00000031596	Slc7a2	20.5|AI158848|Atrc2|CAT-2|Cat2|Tea	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	protein-coding
mm_83041.1	chr9	37348396	37348422	-	1	NA	promoter-TSS (NM_001081429)	promoter-TSS (NM_001081429)	-17	NM_001081429	245902	Mm.390150	NM_001081429	ENSMUSG00000034303	Ccdc15	A630039F14Rik|D030074L19	coiled-coil domain containing 15	protein-coding
mm_4887.1	chr1	188262018	188262028	+	1	NA	promoter-TSS (NM_021408)	promoter-TSS (NM_021408)	-815	NM_021408	22283	Mm.331238	NM_021408	ENSMUSG00000026609	Ush2a	A930011D15Rik|A930037M10Rik|Gm676|Gm983|Mush2a|Usherin|Ushrn	Usher syndrome 2A	protein-coding
mm_65641.1	chr7	27970777	27970780	-	1	NA	intron (NM_001081021, intron 5 of 5)	L1_Mur3|LINE|L1	8379	NM_001081021	338354	Mm.389873	NM_001081021	ENSMUSG00000063047	Zfp780b	B230208L21Rik	zinc finger protein 780B	protein-coding
mm_20798.1	chr2	144260678	144260680	-	1	NA	intron (NM_001199188, intron 4 of 13)	intron (NM_001199188, intron 4 of 13)	5523	NR_030762	100313519	Mm.453538	NR_030762	ENSMUSG00000077714	Snord17	MBI-43	small nucleolar RNA, C/D box 17	snoRNA
mm_10422.1	chr2	13581600	13581630	+	1	NA	exon (NM_011701, exon 8 of 9)	exon (NM_011701, exon 8 of 9)	7304	NM_011701	22352	Mm.268000	NM_011701	ENSMUSG00000026728	Vim	-	vimentin	protein-coding
mm_54826.1	chr6	42585741	42585753	-	1	NA	Intergenic	Intergenic	11625	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_51155.1	chr6	70721711	70721716	+	1	NA	Intergenic	Intergenic	70462	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_146565.1	chr18	6490809	6490869	-	1	NA	promoter-TSS (NM_001276350)	promoter-TSS (NM_001276350)	18	NM_001276350	13831	Mm.312133	NM_007935	ENSMUSG00000024240	Epc1	2400007E14Rik|5730566F07Rik|A930032N02Rik|mir-1893	enhancer of polycomb homolog 1 (Drosophila)	protein-coding
mm_55372.1	chr6	57825145	57825166	-	1	NA	promoter-TSS (NM_146168)	promoter-TSS (NM_146168)	-30	NM_146168	232023	Mm.24642	NM_146168	ENSMUSG00000037788	Vopp1	AW146242|Ecop	vesicular, overexpressed in cancer, prosurvival protein 1	protein-coding
mm_41167.1	chr5	87964401	87964407	+	1	NA	intron (NR_045924, intron 1 of 4)	intron (NR_045924, intron 1 of 4)	14947	NR_045924	73471	Mm.396240	NR_045924	ENSMUSG00000099605	1700066N21Rik	-	RIKEN cDNA 1700066N21 gene	ncRNA
mm_72388.1	chr8	81766333	81766339	+	1	NA	intron (NM_001297593, intron 4 of 23)	intron (NM_001297593, intron 4 of 23)	423774	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_110987.1	chr12	77124423	77124461	-	1	NA	Intergenic	Intergenic	-113662	NM_001252614	53618	Mm.35628	NM_016893	ENSMUSG00000021065	Fut8	-	fucosyltransferase 8	protein-coding
mm_169627.1	chr15	41922037	41922039	+	1	NA	Intergenic	Intergenic	-52318	NM_175456	223513	Mm.148913	NM_175456	ENSMUSG00000042895	Abra	C130068O12Rik|STARS	actin-binding Rho activating protein	protein-coding
mm_155636.1	chrX	85048310	85048333	+	1	NA	promoter-TSS (NM_001314037)	promoter-TSS (NM_001314037)	26	NM_001314034	13405	Mm.275608	NM_007868	ENSMUSG00000045103	Dmd	DXSmh7|DXSmh9|Dp427|Dp71|dys|mdx|pke	dystrophin, muscular dystrophy	protein-coding
mm_125541.1	chr15	58141436	58141442	+	1	NA	promoter-TSS (NM_001326602)	promoter-TSS (NM_001326602)	73	NM_001326599	76773	Mm.26771	NM_029734	ENSMUSG00000022359	Wdyhv1	2410187C16Rik|AU014961|AW550036|Ntaq1	WDYHV motif containing 1	protein-coding
mm_92667.1	chr10	80433616	80433655	-	1	NA	promoter-TSS (NM_011548)	promoter-TSS (NM_011548)	18	NM_001164150	21423	Mm.3406	NM_011548	ENSMUSG00000020167	Tcf3	A1|AA408400|ALF2|AW209082|E12|E12/E47|E2A|E47|KA1|ME2|Pan1|Pan2|TCF-3|Tcfe2a|VDIR|bHLHb21	transcription factor 3	protein-coding
mm_75459.1	chr8	47714490	47714511	-	1	NA	promoter-TSS (NM_172407)	promoter-TSS (NM_172407)	-569	NM_172407	70925	Mm.393807	NM_172407	ENSMUSG00000038069	Cdkn2aip	4921511I16Rik|AW208986|CARF	CDKN2A interacting protein	protein-coding
mm_119922.1	chr14	54963015	54963032	+	1	NA	exon (NM_010856, exon 7 of 39)	exon (NM_010856, exon 7 of 39)	3584	NM_001164171	17888	Mm.290003	NM_010856	ENSMUSG00000040752	Myh6	A830009F23Rik|AA517445|Myhc-a|Myhca|alpha-MHC	myosin, heavy polypeptide 6, cardiac muscle, alpha	protein-coding
mm_137294.1	chr17	24779725	24779751	+	1	NA	Intergenic	Intergenic	-24644	NM_029197	75178	Mm.52592	NM_029197	ENSMUSG00000024155	Meiob	4930528F23Rik|MLZ-675	meiosis specific with OB domains	protein-coding
mm_59630.1	chr7	28156731	28156734	+	1	NA	exon (NM_001164655, exon 15 of 20)	exon (NM_001164655, exon 15 of 20)	-13016	NM_007991	14113	Mm.4595	NM_007991	ENSMUSG00000046865	Fbl	AL022665|FIB|FLRN|RNU3IP1	fibrillarin	protein-coding
mm_56127.1	chr6	87534918	87534932	-	1	NA	Intergenic	Intergenic	-1666	NM_001286610	232201	Mm.119564	NM_175476	ENSMUSG00000030047	Arhgap25	A130039I20Rik	Rho GTPase activating protein 25	protein-coding
mm_37319.1	chr4	119383733	119383780	-	1	NA	promoter-TSS (NM_028506)	promoter-TSS (NM_028506)	78	NM_028506	73332	Mm.425204	NM_028506	ENSMUSG00000028637	Ccdc30	1700001O02Rik|1700041C02Rik|1700111D19Rik|4930445I03Rik	coiled-coil domain containing 30	protein-coding
mm_116914.1	chr13	55508300	55508326	-	1	NA	promoter-TSS (NR_105910)	promoter-TSS (NR_105910)	-621	NR_105910	102465570		NR_105910	ENSMUSG00000099096	Mir6945	Gm27779|mmu-mir-6945	microRNA 6945	ncRNA
mm_73186.1	chr8	95335311	95335323	+	1	NA	intron (NM_133954, intron 2 of 6)	intron (NM_133954, intron 2 of 6)	3033	NM_133954	101985	Mm.29069	NM_133954	ENSMUSG00000031792	Usb1	AA960436	U6 snRNA biogenesis 1	protein-coding
mm_143723.1	chr17	81375985	81375999	-	1	NA	non-coding (NR_104580, exon 9 of 9)	non-coding (NR_104580, exon 9 of 9)	-310907	NM_028138	72167	Mm.273257	NM_028138	ENSMUSG00000024246	Thumpd2	2810025A12Rik	THUMP domain containing 2	protein-coding
mm_851.1	chr1	52119472	52119499	+	1	NA	promoter-TSS (NM_001205314)	promoter-TSS (NM_001205314)	47	NM_001205314	20846	Mm.277406	NM_009283	ENSMUSG00000026104	Stat1	2010005J02Rik|AA408197	signal transducer and activator of transcription 1	protein-coding
mm_132745.1	chr16	44142620	44142630	+	1	NA	intron (NM_028108, intron 1 of 4)	intron (NM_028108, intron 1 of 4)	2816	NM_028108	72117	Mm.278726	NM_028108	ENSMUSG00000022698	Naa50	2600005K24Rik|2810441M03Rik|AW112078|Mak3|Mak3p|Nat13|Nat5|San	N(alpha)-acetyltransferase 50, NatE catalytic subunit	protein-coding
mm_32975.1	chr4	120097724	120097741	+	1	NA	exon (NM_010657, exon 4 of 9)	exon (NM_010657, exon 4 of 9)	-63474	NM_007902	13615	Mm.284855	NM_007902	ENSMUSG00000028635	Edn2	ET-2|PPET2|VIC	endothelin 2	protein-coding
mm_79924.1	chr9	65630605	65630617	+	1	NA	promoter-TSS (NM_028030)	promoter-TSS (NM_028030)	29	NM_028030	71973	Mm.29148	NM_028030	ENSMUSG00000032387	Rbpms2	2400008B06Rik|AI316523	RNA binding protein with multiple splicing 2	protein-coding
mm_55102.1	chr6	49882071	49882074	-	1	NA	Intergenic	Intergenic	59362	NM_023456	109648	Mm.154796	NM_023456	ENSMUSG00000029819	Npy	0710005A05Rik	neuropeptide Y	protein-coding
mm_79227.1	chr9	50239731	50239731	+	1	NA	Intergenic	Intergenic	-6549	NR_131161	71873		NR_131161	ENSMUSG00000110916	2310003N18Rik	-	RIKEN cDNA 2310003N18 gene	ncRNA
mm_150232.1	chr19	33976719	33976732	+	1	NA	TTS (NM_026334)	TTS (NM_026334)	15477	NM_026334	67717	Mm.329816	NM_026334	ENSMUSG00000024768	Lipf	2310051B21Rik|AV082900	lipase, gastric	protein-coding
mm_135598.1	chr16	50732708	50732775	-	1	NA	promoter-TSS (NR_028300)	promoter-TSS (NR_028300)	32	NR_028300	68190	Mm.139089	NR_028300		Dubr	5330426P16Rik|Dum	Dppa2 upstream binding RNA	ncRNA
mm_28587.1	chr3	94377285	94377290	-	1	NA	promoter-TSS (NM_001293734)	promoter-TSS (NM_001293734)	-145	NM_001293734	19885	Mm.4372	NM_011281	ENSMUSG00000028150	Rorc	Nr1f3|RORgamma|TOR|Thor	RAR-related orphan receptor gamma	protein-coding
mm_30949.1	chr4	33132553	33132561	+	1	NA	promoter-TSS (NM_008075)	promoter-TSS (NM_008075)	1	NM_008075	14408	Mm.14116	NM_008075	ENSMUSG00000028280	Gabrr1	GABA-C	gamma-aminobutyric acid (GABA) C receptor, subunit rho 1	protein-coding
mm_105610.1	chr11	106783344	106783362	-	1	NA	promoter-TSS (NR_037224)	promoter-TSS (NR_037224)	-594	NR_037224	100526469		NR_037224	ENSMUSG00000093273	Mir3064	mir-3064|mmu-mir-3064	microRNA 3064	ncRNA
mm_138727.1	chr17	36943026	36943038	+	1	NA	promoter-TSS (NM_001099632)	promoter-TSS (NM_001099632)	-19	NM_001099632	386454	Mm.105324	NM_001099632	ENSMUSG00000036492	Rnf39	BC038661|Gm1786|Gm1787|Gm320|LIRF	ring finger protein 39	protein-coding
mm_563.1	chr1	38034066	38034076	+	1	NA	exon (NM_198303, exon 9 of 24)	exon (NM_198303, exon 9 of 24)	36061	NM_198303	226982	Mm.260943	NM_198303	ENSMUSG00000026083	Eif5b	A030003E17Rik|BC018347|IF2	eukaryotic translation initiation factor 5B	protein-coding
mm_50268.1	chr6	45060114	45060124	+	1	NA	promoter-TSS (NM_001004357)	promoter-TSS (NM_001004357)	58	NM_001004357	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding
mm_118989.1	chr14	28505464	28505491	+	1	NA	promoter-TSS (NM_009524)	promoter-TSS (NM_009524)	4	NM_009524	22418	Mm.287544	NM_009524	ENSMUSG00000021994	Wnt5a	8030457G12Rik|Wnt-5a	wingless-type MMTV integration site family, member 5A	protein-coding
mm_19566.1	chr2	101628931	101628954	-	1	NA	promoter-TSS (NM_026592)	promoter-TSS (NM_026592)	44	NM_026592	68170	Mm.31263	NM_026592	ENSMUSG00000027165	B230118H07Rik	NWC	RIKEN cDNA B230118H07 gene	protein-coding
mm_58035.1	chr6	136781719	136781806	-	1	NA	promoter-TSS (NM_001127318)	promoter-TSS (NM_001127318)	-20	NM_001127318	14917	Mm.222729	NM_145067	ENSMUSG00000042638	Gucy2c	AI893437|GC-C|Gcc	guanylate cyclase 2c	protein-coding
mm_48036.1	chr5	136276259	136276260	-	1	NA	intron (NM_001291233, intron 23 of 23)	intron (NM_001291233, intron 23 of 23)	-31319	NM_018825	23921	Mm.425294	NM_018825	ENSMUSG00000005057	Sh2b2	Aps	SH2B adaptor protein 2	protein-coding
mm_55159.1	chr6	51681942	51681944	-	1	NA	Intergenic	Intergenic	137420	NM_001127348	71982	Mm.294166	NM_028035	ENSMUSG00000038301	Snx10	2410004M09Rik	sorting nexin 10	protein-coding
mm_104485.1	chr11	95712759	95712768	-	1	NA	promoter-TSS (NR_045780)	promoter-TSS (NR_045780)	-9	NR_045780	432396	Mm.426849	NR_045780	ENSMUSG00000086191	Zfp652os	1110035M17Rik	zinc finger protein 652, opposite strand	ncRNA
mm_19551.1	chr2	98666321	98666331	-	1	NA	Intergenic	SYNREP_MM|Satellite|Satellite	1198669	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_171171.1	chr3	30969396	30969396	-	1	NA	promoter-TSS (NM_153421)	promoter-TSS (NM_153421)	19	NM_001165954	241915	Mm.233173	NM_153421	ENSMUSG00000037652	Phc3	E030046K01Rik|Edr3|Hph3	polyhomeotic-like 3 (Drosophila)	protein-coding
mm_90726.1	chr10	5194701	5194763	-	1	NA	promoter-TSS (NM_001079686)	promoter-TSS (NM_001079686)	-25	NM_001079686	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_167545.1	chr9	26923193	26923196	-	1	NA	promoter-TSS (NM_001281475)	promoter-TSS (NM_001281475)	-113	NM_001281475	382064	Mm.335028	NM_001177509	ENSMUSG00000079644	Gm1110	-	predicted gene 1110	protein-coding
mm_31615.1	chr4	59035176	59035247	+	1	NA	promoter-TSS (NM_025277)	promoter-TSS (NM_025277)	55	NM_025277	14700	Mm.41780	NM_025277	ENSMUSG00000038607	Gng10	AV006524	guanine nucleotide binding protein (G protein), gamma 10	protein-coding
mm_79329.1	chr9	53333203	53333210	+	1	NA	intron (NM_176846, intron 1 of 5)	intron (NM_176846, intron 1 of 5)	31536	NM_176846	320051	Mm.277540	NM_176846	ENSMUSG00000034584	Exph5	AC079869.22gm5|B130009M24Rik|E030050P12|Kiaa0624|Slac2b|slac2-b	exophilin 5	protein-coding
mm_8205.1	chr1	138123670	138123681	-	1	NA	intron (NM_001111316, intron 2 of 31)	intron (NM_001111316, intron 2 of 31)	51451	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_141519.1	chr17	31684308	31684355	-	1	NA	Intergenic	RMER10A|LTR|ERVL	6400	NM_001278570	12954	Mm.1228	NM_013501	ENSMUSG00000024041	Cryaa	Acry-1|Crya-1|Crya1|DAcry-1|lop18	crystallin, alpha A	protein-coding
mm_89386.1	chr10	89750982	89750985	+	1	NA	intron (NM_029166, intron 1 of 20)	L2a|LINE|L2	5992	NM_029166	75089	Mm.268922	NM_029166	ENSMUSG00000019951	Uhrf1bp1l	2010319N22Rik|4930506D01Rik|AA589495|C80672|E030041M21Rik|mKIAA0701	UHRF1 (ICBP90) binding protein 1-like	protein-coding
mm_117455.1	chr13	74808762	74808772	-	1	NA	promoter-TSS (NM_009817)	promoter-TSS (NM_009817)	-7	NM_001301153	12380	Mm.29163	NM_009817	ENSMUSG00000021585	Cast	-	calpastatin	protein-coding
mm_157277.1	chrX	20617263	20617289	-	1	NA	promoter-TSS (NM_145627)	promoter-TSS (NM_145627)	-227	NM_001167775	236732	Mm.279194	NM_145627	ENSMUSG00000031060	Rbm10	E430039K10Rik	RNA binding motif protein 10	protein-coding
mm_48557.1	chr5	143113009	143113019	-	1	NA	promoter-TSS (NM_207110)	promoter-TSS (NM_207110)	6	NM_207110	108086	Mm.381440	NM_080561	ENSMUSG00000045078	Rnf216	2810055G22Rik|AI647468|AU019462|C86502|F830018F18Rik|TRIAD3|UIP83|Ubce7ip1	ring finger protein 216	protein-coding
mm_3264.1	chr1	136364974	136364985	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-18875	NM_001347110	67886	Mm.144143	NM_001081360	ENSMUSG00000041570	Camsap2	1600013L13Rik|4930541M15Rik|Camsap1l1|mKIAA1078	calmodulin regulated spectrin-associated protein family, member 2	protein-coding
mm_151475.1	chr19	58673742	58673751	+	1	NA	intron (NM_026925, intron 4 of 12)	intron (NM_026925, intron 4 of 12)	3381	NM_026925	69060	Mm.20407	NM_026925	ENSMUSG00000046008	Pnlip	1810007A24Rik|PL|PTL	pancreatic lipase	protein-coding
mm_79431.1	chr9	56027485	56027508	+	1	NA	promoter-TSS (NR_033529)	promoter-TSS (NR_033529)	-140	NR_033529	665005	Mm.384788	NR_033529		Gm7444	EG665005	ring finger protein 19A pseudogene	pseudo
mm_79359.1	chr9	54286390	54286398	+	1	NA	promoter-TSS (NM_177350)	promoter-TSS (NM_177350)	-92	NM_177350	235379	Mm.123549	NM_177350	ENSMUSG00000046167	Gldn	CRG-L2|Clom|Colm|Crgl2|Crlg2	gliomedin	protein-coding
mm_32980.1	chr4	120134932	120134942	+	1	NA	3' UTR (NM_010657, exon 9 of 9)	3' UTR (NM_010657, exon 9 of 9)	-26269	NM_007902	13615	Mm.284855	NM_007902	ENSMUSG00000028635	Edn2	ET-2|PPET2|VIC	endothelin 2	protein-coding
mm_38397.1	chr4	138863454	138863491	-	1	NA	promoter-TSS (NM_001122954)	promoter-TSS (NM_001122954)	-3	NM_001122954	18784	Mm.486532	NM_011110	ENSMUSG00000041193	Pla2g5	PLA2|sPLA2	phospholipase A2, group V	protein-coding
mm_30656.1	chr4	8913813	8913846	+	1	NA	Intergenic	Intergenic	223423	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_67236.1	chr7	75308357	75308370	-	1	NA	promoter-TSS (NM_001109753)	promoter-TSS (NM_001109753)	23	NM_001109753	64176	Mm.273082	NM_153579	ENSMUSG00000053025	Sv2b	A830038F04Rik|AI850768|mKIAA0735	synaptic vesicle glycoprotein 2 b	protein-coding
mm_108974.1	chr12	102612679	102612688	+	1	NA	intron (NM_172584, intron 3 of 9)	intron (NM_172584, intron 3 of 9)	57742	NM_007693	12652	Mm.4137	NM_007693	ENSMUSG00000021194	Chga	ChrA|cgA	chromogranin A	protein-coding
mm_144239.1	chr18	10725512	10725522	+	1	NA	promoter-TSS (NM_144860)	promoter-TSS (NM_144860)	-108	NM_144860	225164	Mm.21500	NM_144860	ENSMUSG00000024294	Mib1	DIP-1|E430019M12Rik|Mib|mKIAA1323	mindbomb E3 ubiquitin protein ligase 1	protein-coding
mm_24775.1	chr3	95531918	95531925	+	1	NA	intron (NM_001267695, intron 2 of 7)	B1_Mur3|SINE|Alu	5135	NM_001267695	13040	Mm.3619	NM_021281	ENSMUSG00000038642	Ctss	Cats	cathepsin S	protein-coding
mm_99274.1	chr11	101259220	101259248	+	1	NA	3' UTR (NM_026776, exon 6 of 6)	3' UTR (NM_026776, exon 6 of 6)	-1333	NM_175638	69847	Mm.23656	NM_175638	ENSMUSG00000035112	Wnk4	2010002J11Rik|Pha2b|Prkwnk4	WNK lysine deficient protein kinase 4	protein-coding
mm_91755.1	chr10	50592361	50592389	-	1	NA	promoter-TSS (NM_198007)	promoter-TSS (NM_198007)	-294	NM_198007	77987	Mm.222497	NM_198007	ENSMUSG00000038774	Ascc3	ASC1p200|B630009I04Rik|BC023451|D430001L07Rik|D630041L21|Helic1|RNAH	activating signal cointegrator 1 complex subunit 3	protein-coding
mm_25764.1	chr3	125404073	125404131	+	1	NA	promoter-TSS (NM_022565)	promoter-TSS (NM_022565)	11	NM_022565	64580	Mm.444289	NM_022565	ENSMUSG00000027971	Ndst4	4930439H17Rik	N-deacetylase/N-sulfotransferase (heparin glucosaminyl) 4	protein-coding
mm_112245.1	chr12	113482628	113482637	-	1	NA	Intergenic	Intergenic	-6933	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_147267.1	chr18	38918643	38918710	-	1	NA	promoter-TSS (NM_010197)	promoter-TSS (NM_010197)	23	NM_010197	14164	Mm.241282	NM_010197	ENSMUSG00000036585	Fgf1	Dffrx|Fam|Fgf-1|Fgfa	fibroblast growth factor 1	protein-coding
mm_81876.1	chr9	119162621	119162643	+	1	NA	Intergenic	CpG	-5539	NM_146230	235674	Mm.379402	NM_146230	ENSMUSG00000010651	Acaa1b	-	acetyl-Coenzyme A acyltransferase 1B	protein-coding
mm_62885.1	chr7	114846305	114846323	+	1	NA	intron (NM_173767, intron 11 of 12)	intron (NM_173767, intron 11 of 12)	100548	NM_173767	233752	Mm.83037	NM_173767	ENSMUSG00000048782	Insc	3830422K02Rik|C730020D23	inscuteable homolog (Drosophila)	protein-coding
mm_99637.1	chr11	105190805	105190808	+	1	NA	intron (NM_001294329, intron 2 of 19)	intron (NM_001294329, intron 2 of 19)	9279	NM_001294329	24086	Mm.126976	NM_011903	ENSMUSG00000020694	Tlk2	4933403M19Rik|PKU-alpha|PKUalpha|Tlk	tousled-like kinase 2 (Arabidopsis)	protein-coding
mm_40873.1	chr5	74093076	74093100	+	1	NA	promoter-TSS (NR_145131)	promoter-TSS (NR_145131)	28	NR_145131	70036	Mm.46547	NR_015531	ENSMUSG00000053656	Dancr	2700023E23Rik	differentiation antagonizing non-protein coding RNA	ncRNA
mm_11152.1	chr2	28533424	28533482	+	1	NA	promoter-TSS (NM_001145835)	promoter-TSS (NM_001145835)	-11	NM_001145835	19730	Mm.5236	NM_009058	ENSMUSG00000026821	Ralgds	Gnds|Rgds|mKIAA1308	ral guanine nucleotide dissociation stimulator	protein-coding
mm_116317.1	chr13	37477843	37477871	-	1	NA	Intergenic	Intergenic	132512	NM_010745	17084	Mm.2639	NM_010745	ENSMUSG00000021423	Ly86	MD-1|MD1|ly86_tv2	lymphocyte antigen 86	protein-coding
mm_14530.1	chr2	132781420	132781426	+	1	NA	5' UTR (NM_007694, exon 1 of 5)	5' UTR (NM_007694, exon 1 of 5)	145	NM_007694	12653	Mm.255241	NM_007694	ENSMUSG00000027350	Chgb	Scg-1	chromogranin B	protein-coding
mm_25380.1	chr3	107212764	107212791	+	1	NA	exon (NM_001111143, exon 8 of 9)	exon (NM_001111143, exon 8 of 9)	8955	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_122174.1	chr14	31529627	31529636	-	1	NA	exon (NM_009937, exon 13 of 17)	exon (NM_009937, exon 13 of 17)	34552	NM_028932	74427	Mm.491208	NM_028932	ENSMUSG00000021890	Eaf1	4933403C17Rik|AI666536	ELL associated factor 1	protein-coding
mm_173091.1	chrX	150738898	150738915	-	1	NA	Intergenic	L1Md_A|LINE|L1	74797	NM_001199246	80884	Mm.22575	NM_030700	ENSMUSG00000025268	Maged2	4833439A22Rik|Mage-d2|ORF1	melanoma antigen, family D, 2	protein-coding
mm_136041.1	chr16	78267832	78267838	-	1	NA	Intergenic	MTE2a|LTR|ERVL-MaLR	-12381	NR_045698	100503619	Mm.387531	NR_045698	ENSMUSG00000109841	E330011O21Rik	-	RIKEN cDNA E330011O21 gene	ncRNA
mm_160659.1	chr9	119378197	119378197	+	1	NA	intron (NM_001033209, intron 9 of 18)	intron (NM_001033209, intron 9 of 18)	20816	NM_001199568	102448	Mm.219497	NM_001033209	ENSMUSG00000035769	Xylb	AI132223|AI327421	xylulokinase homolog (H. influenzae)	protein-coding
mm_145098.1	chr18	43265789	43265796	+	1	NA	intron (NM_178749, intron 5 of 12)	B4A|SINE|B4	58095	NM_178749	269019	Mm.150401	NM_178749	ENSMUSG00000039954	Stk32a	A930015B13Rik|YANK1	serine/threonine kinase 32A	protein-coding
mm_165271.1	chr2	75704597	75704614	-	1	NA	promoter-TSS (NM_010902)	promoter-TSS (NM_010902)	58	NR_132727	18024	Mm.1025	NM_010902	ENSMUSG00000015839	Nfe2l2	Nrf2	nuclear factor, erythroid derived 2, like 2	protein-coding
mm_39337.1	chr5	8799778	8799780	+	1	NA	intron (NM_011075, intron 2 of 27)	RSINE1|SINE|B4	1632	NM_011075	18669	Mm.146649	NM_011075	ENSMUSG00000028970	Abcb1b	Abcb1|Mdr1|Mdr1b|Pgy-1|Pgy1|mdr	ATP-binding cassette, sub-family B (MDR/TAP), member 1B	protein-coding
mm_119067.1	chr14	30825658	30825665	+	1	NA	promoter-TSS (NM_028839)	promoter-TSS (NM_028839)	67	NM_028839	69179	Mm.143025	NM_028839	ENSMUSG00000006526	Tmem110	1810038N08Rik|2310014H19Rik|AW554125|STIMATE	transmembrane protein 110	protein-coding
mm_132953.1	chr16	49955792	49955795	+	1	NA	Intergenic	LTR33B|LTR|ERVL	-24667	NR_045001	628951	Mm.428032	NR_045001		Gm6936	-	predicted gene 6936	ncRNA
mm_123134.1	chr14	56552040	56552071	-	1	NA	exon (NM_001014996, exon 7 of 17)	exon (NM_001014996, exon 7 of 17)	19791	NM_001014996	219103	Mm.212525	NM_001014996	ENSMUSG00000064128	Cenpj	4932437H03Rik|CPAP|Gm81|LAP|LIP1|Sas4	centromere protein J	protein-coding
mm_102250.1	chr11	55123964	55123981	-	1	NA	TTS (NM_172258)	TTS (NM_172258)	25987	NM_010299	14667	Mm.287807	NM_010299	ENSMUSG00000000594	Gm2a	AA408702|AW215435|GM2-AP|SAP-3	GM2 ganglioside activator protein	protein-coding
mm_154852.1	chrX	20549707	20549717	+	1	NA	promoter-TSS (NM_009060)	promoter-TSS (NM_009060)	-106	NM_009060	19733	Mm.2118	NM_009060	ENSMUSG00000023070	Rgn	AI265316|GNL|SMP30	regucalcin	protein-coding
mm_145613.1	chr18	61105597	61105603	+	1	NA	promoter-TSS (NM_001037859)	promoter-TSS (NM_001037859)	28	NM_001037859	12978	Mm.22574	NM_007779	ENSMUSG00000024621	Csf1r	AI323359|CD115|CSF-1R|Csfmr|Fim-2|Fim2|Fms|M-CSF-R|M-CSFR	colony stimulating factor 1 receptor	protein-coding
mm_76130.1	chr8	80880310	80880327	-	1	NA	5' UTR (NM_001301298, exon 1 of 11)	5' UTR (NM_001301298, exon 1 of 11)	161	NM_021356	14388	Mm.277409	NM_021356	ENSMUSG00000031714	Gab1	AA408973|AW107238	growth factor receptor bound protein 2-associated protein 1	protein-coding
mm_47379.1	chr5	122989261	122989280	-	1	NA	promoter-TSS (NM_001003953)	promoter-TSS (NM_001003953)	-84	NR_045820	109202	Mm.30769	NM_175405	ENSMUSG00000056735	A930024E05Rik	-	RIKEN cDNA A930024E05 gene	ncRNA
mm_81264.1	chr9	108045390	108045402	+	1	NA	intron (NM_013785, intron 5 of 5)	intron (NM_013785, intron 5 of 5)	-3894	NM_177910	331026	Mm.22554	NM_177910	ENSMUSG00000070284	Gmppb	AI317178|E430010H19	GDP-mannose pyrophosphorylase B	protein-coding
mm_171222.1	chr3	60490023	60490031	-	1	NA	intron (NM_001253713, intron 2 of 9)	IAPLTR1_Mm|LTR|ERVK	-11152	NM_001253711	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_164743.1	chr17	73871199	73871214	-	1	NA	Intergenic	Intergenic	66365	NM_020578	57440	Mm.18526	NM_020578	ENSMUSG00000024065	Ehd3	Ehd2	EH-domain containing 3	protein-coding
mm_122923.1	chr14	54961008	54961028	-	1	NA	exon (NM_010856, exon 12 of 39)	exon (NM_010856, exon 12 of 39)	5589	NM_001164171	17888	Mm.290003	NM_010856	ENSMUSG00000040752	Myh6	A830009F23Rik|AA517445|Myhc-a|Myhca|alpha-MHC	myosin, heavy polypeptide 6, cardiac muscle, alpha	protein-coding
mm_162602.1	chr1	183194599	183194603	-	1	NA	intron (NM_001278218, intron 1 of 8)	intron (NM_001278218, intron 1 of 8)	26928	NM_001278218	68897	Mm.327216	NM_026866	ENSMUSG00000030768	Disp1	1190008H24Rik|DispA	dispatched RND transporter family member 1	protein-coding
mm_137269.1	chr17	24698295	24698345	+	1	NA	5' UTR (NM_027988, exon 2 of 9)	5' UTR (NM_027988, exon 2 of 9)	2086	NM_027988	71893	Mm.390971	NM_027988	ENSMUSG00000019320	Noxo1	2310034C04Rik|P41NOX|P41NOXA|P41NOXB|P41NOXC|Snx28|hslt	NADPH oxidase organizer 1	protein-coding
mm_33637.1	chr4	132974124	132974155	+	1	NA	promoter-TSS (NM_010208)	promoter-TSS (NM_010208)	44	NM_010208	14191	Mm.271665	NM_010208	ENSMUSG00000028874	Fgr	-	FGR proto-oncogene, Src family tyrosine kinase	protein-coding
mm_45521.1	chr5	72616776	72616784	-	1	NA	exon (NM_007723, exon 4 of 9)	exon (NM_007723, exon 4 of 9)	25972	NM_007723	12788	Mm.436652	NM_007723	ENSMUSG00000067220	Cnga1	Cncg	cyclic nucleotide gated channel alpha 1	protein-coding
mm_57068.1	chr6	122577963	122577985	-	1	NA	3' UTR (NM_031159, exon 8 of 8)	3' UTR (NM_031159, exon 8 of 8)	24165	NM_009645	11628	Mm.391503	NM_009645	ENSMUSG00000040627	Aicda	Aid|Arp2	activation-induced cytidine deaminase	protein-coding
mm_78863.1	chr9	44398368	44398394	+	1	NA	5' UTR (NM_008063, exon 1 of 8)	5' UTR (NM_008063, exon 1 of 8)	205	NM_008063	14385	Mm.30087	NM_008063	ENSMUSG00000032114	Slc37a4	100043178|G6PT|G6pt1|GSD-1b|mG6PT	solute carrier family 37 (glucose-6-phosphate transporter), member 4	protein-coding
mm_89864.1	chr10	108162271	108162279	+	1	NA	promoter-TSS (NM_027892)	promoter-TSS (NM_027892)	-125	NM_027892	17931	Mm.422959	NM_027892	ENSMUSG00000019907	Ppp1r12a	1200015F06Rik|5730577I22Rik|AA792106|AV099298|D10Ertd625e|Mypt1	protein phosphatase 1, regulatory (inhibitor) subunit 12A	protein-coding
mm_60031.1	chr7	30977086	30977091	+	1	NA	promoter-TSS (NM_175240)	promoter-TSS (NM_175240)	45	NM_175240	76415	Mm.259739	NM_175240	ENSMUSG00000046826	Fam187b	1700020B09Rik|Tmem162	family with sequence similarity 187, member B	protein-coding
mm_170134.1	chr17	39847524	39847537	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	4533	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_33106.1	chr4	124708351	124708354	+	1	NA	3' UTR (NM_010213, exon 6 of 6)	3' UTR (NM_010213, exon 6 of 6)	-6509	NM_029157	75062	Mm.25779	NM_029157	ENSMUSG00000028902	Sf3a3	4930512K19Rik|60kDa	splicing factor 3a, subunit 3	protein-coding
mm_153952.1	chr19	47691849	47691875	-	1	NA	5' UTR (NM_007732, exon 1 of 53)	5' UTR (NM_007732, exon 1 of 53)	180	NM_007732	12821	Mm.1225	NM_007732	ENSMUSG00000025064	Col17a1	BP180|Bpag|Bpag2	collagen, type XVII, alpha 1	protein-coding
mm_125172.1	chr15	31350200	31350207	+	1	NA	intron (NM_027496, intron 1 of 3)	intron (NM_027496, intron 1 of 3)	17556	NM_001164441	67434	Mm.102470	NM_026153	ENSMUSG00000022237	Ankrd33b	0610012A05Rik|3021401C12Rik|5730557B15Rik	ankyrin repeat domain 33B	protein-coding
mm_35679.1	chr4	43662011	43662021	-	1	NA	intron (NM_175517, intron 3 of 6)	intron (NM_175517, intron 3 of 6)	-5571	NM_026871	68917	Mm.25285	NM_026871	ENSMUSG00000028470	Hint2	1190005L05Rik	histidine triad nucleotide binding protein 2	protein-coding
mm_115319.1	chr13	112373370	112373407	+	1	NA	intron (NM_001168403, intron 10 of 11)	B4A|SINE|B4	84870	NM_001168404	77318	Mm.159895	NM_029898	ENSMUSG00000049985	Ankrd55	C030011J08Rik	ankyrin repeat domain 55	protein-coding
mm_122098.1	chr14	30912711	30912725	-	1	NA	exon (NM_008407, exon 17 of 21)	exon (NM_008407, exon 17 of 21)	10869	NM_008407	16426	Mm.4517	NM_008407	ENSMUSG00000006522	Itih3	AW108094|ITI-HC3|Intin3|Itih-3	inter-alpha trypsin inhibitor, heavy chain 3	protein-coding
mm_73102.1	chr8	94601929	94602003	+	1	NA	promoter-TSS (NM_028221)	promoter-TSS (NM_028221)	25	NM_026274	67610	Mm.109074	NM_026274	ENSMUSG00000050079	Rspry1	4930470D19Rik|AI608258	ring finger and SPRY domain containing 1	protein-coding
mm_28756.1	chr3	95855778	95855822	-	1	NA	promoter-TSS (NM_001316751)	promoter-TSS (NM_001316751)	-47	NM_027541	70767	Mm.279872	NM_027541	ENSMUSG00000015748	Prpf3	3632413F13Rik	pre-mRNA processing factor 3	protein-coding
mm_152191.1	chr19	7469606	7469607	-	1	NA	intron (NM_001003934, intron 1 of 8)	B1_Mur4|SINE|Alu	-8912	NR_028566	100216530	Mm.453052	NR_028566	ENSMUSG00000064899	Snord118	MBI-34	small nucleolar RNA, C/D box 118	snoRNA
mm_127635.1	chr15	102471188	102471196	+	1	NA	intron (NM_001174073, intron 1 of 12)	CpG	560	NM_001174073	18521	Mm.236513	NM_011042	ENSMUSG00000056851	Pcbp2	AW412548|Hnrpx|alphaCP-2	poly(rC) binding protein 2	protein-coding
mm_87607.1	chr10	57784915	57784939	+	1	NA	promoter-TSS (NM_021272)	promoter-TSS (NM_021272)	4	NM_021272	12140	Mm.3644	NM_021272	ENSMUSG00000019874	Fabp7	B-FABP|BFABP|Blbp|MRG	fatty acid binding protein 7, brain	protein-coding
mm_166003.1	chr4	116053857	116053868	-	1	NA	promoter-TSS (NM_028142)	promoter-TSS (NM_028142)	14	NM_028142	72181	Mm.282560	NM_028142	ENSMUSG00000028706	Nsun4	2310010O12Rik|2810405F18Rik|AI507900|Shtap	NOL1/NOP2/Sun domain family, member 4	protein-coding
mm_86682.1	chr10	18361003	18361004	+	1	NA	Intergenic	PB1D9|SINE|Alu	-46672	NM_173390	215819	Mm.297971	NM_173390	ENSMUSG00000039835	Nhsl1	5730409E15Rik|A630035H13Rik|A730096F01|BC013565|D10Bwg0940e|mKIAA1357	NHS-like 1	protein-coding
mm_42566.1	chr5	117146751	117146760	+	1	NA	intron (NM_001081308, intron 1 of 19)	L1M5|LINE|L1	13167	NM_183306	330177	Mm.24343	NM_183306	ENSMUSG00000061288	Taok3	2900006A08Rik|A130052D22|A430105I05Rik	TAO kinase 3	protein-coding
mm_93949.1	chr10	127243711	127243756	-	1	NA	exon (NM_001039000, exon 9 of 29)	exon (NM_001039000, exon 9 of 29)	19630	NM_008447	16572	Mm.30355	NM_008447	ENSMUSG00000074657	Kif5a	D10Bwg0738e|Khc|Kif5|Kns|mKIAA4086	kinesin family member 5A	protein-coding
mm_69257.1	chr7	127876101	127876152	-	1	NA	5' UTR (NM_146259, exon 1 of 3)	5' UTR (NM_146259, exon 1 of 3)	697	NM_146259	244219	Mm.207872	NM_146259	ENSMUSG00000049728	Zfp668	BC030314|E130018B19Rik|Znf668	zinc finger protein 668	protein-coding
mm_119287.1	chr14	34378839	34378852	+	1	NA	intron (NM_153127, intron 1 of 6)	intron (NM_153127, intron 1 of 6)	3341	NM_153127	105450	Mm.272673	NM_153127	ENSMUSG00000041445	Mmrn2	AA986839|ENDOGLYX1|Emilin3|EndoGlyx-1	multimerin 2	protein-coding
mm_124202.1	chr14	98169753	98169806	-	1	NA	promoter-TSS (NM_001038610)	promoter-TSS (NM_001038610)	-14	NM_007826	13134	Mm.320593	NM_007826	ENSMUSG00000055639	Dach1	Dac|Dach	dachshund 1 (Drosophila)	protein-coding
mm_31002.1	chr4	40160297	40160301	+	1	NA	intron (NM_007386, intron 1 of 20)	intron (NM_007386, intron 1 of 20)	17034	NM_007386	11428	Mm.331547	NM_007386	ENSMUSG00000028405	Aco1	Aco-1|Irebp|Irp1	aconitase 1	protein-coding
mm_124801.1	chr15	8445566	8445570	+	1	NA	Intergenic	CpG-4777	-1105	NM_201232	71175	Mm.240329	NM_027707	ENSMUSG00000022141	Nipbl	Idn3	Nipped-B homolog (Drosophila)	protein-coding
mm_143932.1	chr17	86145140	86145184	-	1	NA	promoter-TSS (NM_030133)	promoter-TSS (NM_030133)	13	NM_030133	78586	Mm.146236	NM_030133	ENSMUSG00000024135	Srbd1	AI461933|C85414|D530025C17Rik	S1 RNA binding domain 1	protein-coding
mm_65709.1	chr7	28378144	28378151	-	1	NA	exon (NM_011756, exon 2 of 2)	exon (NM_011756, exon 2 of 2)	1081	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_81380.1	chr9	108914651	108914657	+	1	NA	promoter-TSS (NM_027066)	promoter-TSS (NM_027066)	35	NM_027066	69384	Mm.158271	NM_027066	ENSMUSG00000025652	Tmem89	1700024B07Rik	transmembrane protein 89	protein-coding
mm_99641.1	chr11	105292623	105292629	+	1	NA	promoter-TSS (NM_008626)	promoter-TSS (NM_008626)	-20	NM_008626	17534	Mm.235616	NM_008626	ENSMUSG00000020695	Mrc2	Endo180|mKIAA0709|uPARAP	mannose receptor, C type 2	protein-coding
mm_80456.1	chr9	77982857	77982863	+	1	NA	3' UTR (NM_134255, exon 8 of 8)	3' UTR (NM_134255, exon 8 of 8)	65495	NM_134255	68801	Mm.430736	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	ELOVL family member 5, elongation of long chain fatty acids (yeast)	protein-coding
mm_84943.1	chr9	82975476	82975493	-	1	NA	promoter-TSS (NM_001081216)	promoter-TSS (NM_001081216)	5	NM_001081216	83946	Mm.221688	NM_031879	ENSMUSG00000032253	Phip	2810004D21Rik|4632404O06Rik|Ndrp|Wdr11	pleckstrin homology domain interacting protein	protein-coding
mm_53671.1	chr6	141683229	141683239	+	1	NA	exon (NM_020495, exon 15 of 16)	exon (NM_020495, exon 15 of 16)	53716	NM_020495	28253	Mm.272223	NM_020495	ENSMUSG00000030236	Slco1b2	7330442B20Rik|OATP-C|OATP2|Oatp1b2|Oatp4|Slc21a10|Slc21a6|lst-1|mlst-1	solute carrier organic anion transporter family, member 1b2	protein-coding
mm_134190.1	chr16	10971287	10971291	-	1	NA	intron (NM_019980, intron 1 of 3)	intron (NM_019980, intron 1 of 3)	21832	NM_019980	56722	Mm.294753	NM_019980	ENSMUSG00000022500	Litaf	3222402J11Rik|C85531|N4WBP3|TBX1	LPS-induced TN factor	protein-coding
mm_154985.1	chrX	38189733	38189750	+	1	NA	promoter-TSS (NM_020256)	promoter-TSS (NM_020256)	-52	NM_020256	56805	Mm.391248	NM_020256	ENSMUSG00000048047	Zbtb33	AW260253|E130014G12Rik|Kaiso|Znf-kaiso	zinc finger and BTB domain containing 33	protein-coding
mm_121738.1	chr14	18331856	18331862	-	1	NA	promoter-TSS (NM_009455)	promoter-TSS (NM_009455)	-15	NM_009455	22194	Mm.4429	NM_009455	ENSMUSG00000021774	Ube2e1	UbcM3|Ubce5|ubcM2	ubiquitin-conjugating enzyme E2E 1	protein-coding
mm_131016.1	chr15	103563334	103563344	-	1	NA	exon (NM_008134, exon 3 of 4)	exon (NM_008134, exon 3 of 4)	1742	NM_001289587	14663	Mm.219621	NM_008134	ENSMUSG00000022491	Glycam1	MC26|Sgp50|glyCAM-1	glycosylation dependent cell adhesion molecule 1	protein-coding
mm_37088.1	chr4	116464152	116464274	-	1	NA	promoter-TSS (NM_001042743)	promoter-TSS (NM_001042743)	-32	NM_008641	17776	Mm.9287	NM_008641	ENSMUSG00000003810	Mast2	MAST205|Mtssk	microtubule associated serine/threonine kinase 2	protein-coding
mm_155783.1	chrX	96456363	96456388	+	1	NA	promoter-TSS (NM_001159627)	promoter-TSS (NM_001159627)	29	NM_001159627	15203	Mm.277092	NM_010417	ENSMUSG00000031209	Heph	C130006F04Rik|Cpl|mKIAA0698|sla	hephaestin	protein-coding
mm_84383.1	chr9	65422859	65422873	-	1	NA	promoter-TSS (NM_178933)	promoter-TSS (NM_178933)	-93	NM_178933	330962	Mm.335247	NM_178933	ENSMUSG00000053862	Slc51b	Ostb	solute carrier family 51, beta subunit	protein-coding
mm_41743.1	chr5	102768870	102768889	+	1	NA	promoter-TSS (NM_001286468)	promoter-TSS (NM_001286468)	69	NM_001286468	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding
mm_46500.1	chr5	105133675	105133692	-	1	NA	intron (NM_008620, intron 3 of 10)	Lx|LINE|L1	5869	NM_008620	17472	Mm.440525	NM_008620	ENSMUSG00000079363	Gbp4	AW228052|Mag-2|Mpa-2|Mpa2	guanylate binding protein 4	protein-coding
mm_80594.1	chr9	85845319	85845321	+	1	NA	3' UTR (NM_001164792, exon 2 of 2)	3' UTR (NM_001164792, exon 2 of 2)	2468	NM_001164792	21983	Mm.20864	NM_011627	ENSMUSG00000035274	Tpbg	5T4|AW495680|WAIF1	trophoblast glycoprotein	protein-coding
mm_61020.1	chr7	49484268	49484284	+	1	NA	intron (NM_175272, intron 10 of 37)	intron (NM_175272, intron 10 of 37)	152559	NM_001005232	13172	Mm.307176	NM_001005232	ENSMUSG00000030507	Dbx1	AI426026|Dbx	developing brain homeobox 1	protein-coding
mm_132939.1	chr16	49856307	49856331	+	1	NA	intron (NM_010581, intron 1 of 9)	intron (NM_010581, intron 1 of 9)	665	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_4876.1	chr1	187898647	187898652	+	1	NA	intron (NM_001243792, intron 2 of 7)	intron (NM_001243792, intron 2 of 7)	-99178	NM_011935	26381	Mm.89989	NM_011935	ENSMUSG00000026610	Esrrg	ERR3|Errg|NR3B3|mKIAA0832	estrogen-related receptor gamma	protein-coding
mm_72075.1	chr8	71559178	71559191	+	1	NA	promoter-TSS (NM_001100462)	promoter-TSS (NM_001100462)	-313	NM_001100462	434325	Mm.33613	NM_001100462	ENSMUSG00000043664	Tmem221	-	transmembrane protein 221	protein-coding
mm_19853.1	chr2	113817975	113817978	-	1	NA	intron (NM_009162, intron 2 of 5)	intron (NM_009162, intron 2 of 5)	11115	NM_009162	20394	Mm.4836	NM_009162	ENSMUSG00000023236	Scg5	7B2|AI325031|Sgne-1|Sgne1	secretogranin V	protein-coding
mm_93076.1	chr10	89434666	89434705	-	1	NA	intron (NM_001079876, intron 2 of 10)	intron (NM_001079876, intron 2 of 10)	9282	NM_001284344	237436	Mm.11982	NM_001033331	ENSMUSG00000074802	Gas2l3	8430435B07Rik|Gm240	growth arrest-specific 2 like 3	protein-coding
mm_1058.1	chr1	58973595	58973613	+	1	NA	promoter-TSS (NM_172406)	promoter-TSS (NM_172406)	33	NM_172656	227154	Mm.286006	NM_172656	ENSMUSG00000026027	Stradb	AA792893|Als2cr2|B830008M19|D1Ucla2|ILPIP|ILPIPA|PRO1038|Papk|Syradb	STE20-related kinase adaptor beta	protein-coding
mm_14402.1	chr2	130048545	130048569	+	1	NA	3' UTR (NM_009374, exon 13 of 13)	3' UTR (NM_009374, exon 13 of 13)	-32149	NR_105757	102466628		NR_105757	ENSMUSG00000098347	Mir6339	Gm27848|mmu-mir-6339	microRNA 6339	ncRNA
mm_21499.1	chr2	163472511	163472522	-	1	NA	promoter-TSS (NR_028122)	promoter-TSS (NR_028122)	-29	NR_028122	69517	Mm.395343	NR_028122	ENSMUSG00000053353	2310001K24Rik	-	RIKEN cDNA 2310001K24 gene	ncRNA
mm_71011.1	chr8	31150432	31150434	+	1	NA	non-coding (NR_103719, exon 1 of 8)	non-coding (NR_103719, exon 1 of 8)	117	NR_103719	234138	Mm.349800	NM_144927	ENSMUSG00000031577	Tti2	-	TELO2 interacting protein 2	protein-coding
mm_49961.1	chr6	40642982	40643003	+	1	NA	exon (NM_001171003, exon 2 of 48)	exon (NM_001171003, exon 2 of 48)	14161	NM_001171003	232714	Mm.33401	NM_001171003	ENSMUSG00000068587	Mgam	6030407P20Rik|MGA	maltase-glucoamylase	protein-coding
mm_65090.1	chr7	19264811	19264828	-	1	NA	exon (NM_001282022, exon 2 of 13)	exon (NM_001282022, exon 2 of 13)	7035	NM_001282021	22323	Mm.9684	NM_009499	ENSMUSG00000030403	Vasp	-	vasodilator-stimulated phosphoprotein	protein-coding
mm_49182.1	chr6	15184732	15184745	+	1	NA	promoter-TSS (NM_001286607)	promoter-TSS (NM_001286607)	-768	NM_212435	114142	Mm.332919	NM_053242	ENSMUSG00000029563	Foxp2	2810043D05Rik|AI449000|CAG-16|D0Kist7	forkhead box P2	protein-coding
mm_51241.1	chr6	71544343	71544367	+	1	NA	intron (NM_025783, intron 1 of 5)	CpG	501	NM_025783	66700	Mm.181278	NM_025783	ENSMUSG00000053119	Chmp3	25.1|4921505F14Rik|9130011K15Rik|CGI-49|D6Ertd286e|NEDF|Vps24	charged multivesicular body protein 3	protein-coding
mm_122091.1	chr14	30625451	30625482	-	1	NA	intron (NM_011103, intron 1 of 17)	CpG	742	NM_011103	18753	Mm.2314	NM_011103	ENSMUSG00000021948	Prkcd	AI385711|D14Ertd420e|PKC[d]|PKCdelta|Pkcd	protein kinase C, delta	protein-coding
mm_69331.1	chr7	128740435	128740470	-	1	NA	promoter-TSS (NM_145955)	promoter-TSS (NM_145955)	-23	NM_145955	210711	Mm.58882	NM_145955	ENSMUSG00000048170	Mcmbp	1110007A13Rik|AU017382|BC025641|MCM-BP	minichromosome maintenance complex binding protein	protein-coding
mm_160068.1	chr7	5805475	5805475	-	1	NA	promoter-TSS (NM_030742)	promoter-TSS (NM_030742)	-30	NM_030742	81017	Mm.160382	NM_030742	ENSMUSG00000058631	Vmn1r63	V1R1|V1rd1|V3R1	vomeronasal 1 receptor 63	protein-coding
mm_6455.1	chr1	74016631	74016641	-	1	NA	intron (NM_027884, intron 3 of 34)	intron (NM_027884, intron 3 of 34)	107811	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_101878.1	chr11	48902105	48902128	-	1	NA	promoter-TSS (NM_001024230)	promoter-TSS (NM_001024230)	36	NM_001024230	432555	Mm.338931	NM_001024230	ENSMUSG00000058163	Gm5431	EG432555|Irgb9b8	predicted gene 5431	protein-coding
mm_72570.1	chr8	84127796	84127806	+	1	NA	exon (NM_001013384, exon 5 of 10)	exon (NM_001013384, exon 5 of 10)	1812	NM_001013384	244550	Mm.334654	NM_001013384	ENSMUSG00000012889	Podnl1	5832418A03Rik|Gm506	podocan-like 1	protein-coding
mm_135737.1	chr16	55838645	55838661	-	1	NA	promoter-TSS (NM_030612)	promoter-TSS (NM_030612)	-12	NM_001159395	80859	Mm.247272	NM_030612	ENSMUSG00000035356	Nfkbiz	AA408868|INAP|Mail	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, zeta	protein-coding
mm_138159.1	chr17	34256711	34256722	+	1	NA	Intergenic	MTEb|LTR|ERVL-MaLR	-6511	NM_207105	14961	Mm.254067	NM_207105	ENSMUSG00000073421	H2-Ab1	AI845868|Abeta|H-2Ab|H2-Ab|I-Abeta|IAb|Ia-2|Ia2|Rmcs1	histocompatibility 2, class II antigen A, beta 1	protein-coding
mm_33297.1	chr4	128981428	128981458	+	1	NA	Intergenic	Intergenic	-11781	NM_016895	11637	Mm.29460	NM_016895	ENSMUSG00000028792	Ak2	Ak-2|D4Ertd220e	adenylate kinase 2	protein-coding
mm_106550.1	chr11	120581554	120581632	-	1	NA	promoter-TSS (NM_133796)	promoter-TSS (NM_133796)	27	NM_133796	192662	Mm.30016	NM_133796	ENSMUSG00000025132	Arhgdia	5330430M07Rik|Gdi-1|Rho-GDI|RhoDGI|RhoGDI-1	Rho GDP dissociation inhibitor (GDI) alpha	protein-coding
mm_13518.1	chr2	109929203	109929245	+	1	NA	intron (NM_172671, intron 1 of 17)	intron (NM_172671, intron 1 of 17)	11577	NM_172671	107515	Mm.277351	NM_172671	ENSMUSG00000050199	Lgr4	9130225G07|A330106J01Rik|A930009A08Rik|Gpr48	leucine-rich repeat-containing G protein-coupled receptor 4	protein-coding
mm_87168.1	chr10	37137527	37137530	+	1	NA	intron (NM_008538, intron 1 of 1)	intron (NM_008538, intron 1 of 1)	1398	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_82988.1	chr9	36533801	36533811	-	1	NA	3' UTR (NM_001033783, exon 3 of 3)	3' UTR (NM_001033783, exon 3 of 3)	8157	NM_001033783	434396	Mm.118836	NM_001033783	ENSMUSG00000074448	Gm5615	EG434396|Pate-H|Pate9	predicted gene 5615	protein-coding
mm_154135.1	chr19	57315068	57315083	-	1	NA	Intergenic	Intergenic	41115	NR_045319	78120	Mm.445892	NR_045319		4930449E18Rik	-	RIKEN cDNA 4930449E18 gene	ncRNA
mm_22526.1	chr3	7647102	7647111	+	1	NA	Intergenic	Intergenic	-33346	NM_001313888	16196	Mm.3825	NM_008371	ENSMUSG00000040329	Il7	A630026I06Rik|Il-7|hlb368	interleukin 7	protein-coding
mm_103949.1	chr11	84068360	84068367	-	1	NA	promoter-TSS (NM_019819)	promoter-TSS (NM_019819)	-6	NM_019819	56405	Mm.240885	NM_019819	ENSMUSG00000018648	Dusp14	1110014C10Rik|2310042C07Rik|D11Ertd395e|MKP-L|Mkp6	dual specificity phosphatase 14	protein-coding
mm_117584.1	chr13	89658105	89658126	-	1	NA	intron (NM_001081249, intron 13 of 14)	(A)n|Simple_repeat|Simple_repeat	84397	NM_001081249	13003	Mm.158700	NM_019389	ENSMUSG00000021614	Vcan	5430420N07Rik|9430051N09|Cspg2|DPEAAE|NG2|PG-M|PG-M(V0)|PG-M(V1)|hdf	versican	protein-coding
mm_136560.1	chr17	3167023	3167027	+	1	NA	intron (NM_134123, intron 6 of 19)	MTD-int|LTR|ERVL-MaLR	52053	NM_134123	106583	Mm.124373	NM_134123	ENSMUSG00000046201	Scaf8	A630086M08Rik|A930036P18Rik|AA408306|AI447644|AI448652|AU015035|Rbm16|mKIAA1116	SR-related CTD-associated factor 8	protein-coding
mm_15239.1	chr2	154656914	154656924	+	1	NA	promoter-TSS (NM_029362)	promoter-TSS (NM_029362)	-107	NM_029362	75608	Mm.262480	NM_029362	ENSMUSG00000038467	Chmp4b	2010012F05Rik|C76846|Snf7-2	charged multivesicular body protein 4B	protein-coding
mm_68977.1	chr7	126589166	126589176	-	1	NA	TTS (NM_138310)	TTS (NM_138310)	-3354	NM_001146311	12752	Mm.268930	NM_009907	ENSMUSG00000030720	Cln3	AI323623	ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease)	protein-coding
mm_79881.1	chr9	65215342	65215387	+	1	NA	5' UTR (NM_177460, exon 2 of 7)	5' UTR (NM_177460, exon 2 of 7)	674	NM_177460	214424	Mm.31129	NM_177460	ENSMUSG00000032392	Parp16	ARTD15|BC055447|C79952|PARP-16	poly (ADP-ribose) polymerase family, member 16	protein-coding
mm_90763.1	chr10	5550810	5550835	-	1	NA	promoter-TSS (NM_153399)	promoter-TSS (NM_153399)	-130	NM_001347732	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_153266.1	chr19	37077457	37077468	-	1	NA	intron (NM_001290826, intron 7 of 10)	intron (NM_001290826, intron 7 of 10)	-96381	NR_045329	319931	Mm.446730	NR_045329	ENSMUSG00000097591	A330032B11Rik	-	RIKEN cDNA A330032B11 gene	ncRNA
mm_48983.1	chr6	4755567	4755573	+	1	NA	exon (NM_130877, exon 2 of 2)	exon (NM_130877, exon 2 of 2)	8264	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_89682.1	chr10	97517661	97517673	+	1	NA	3' UTR (NM_007833, exon 8 of 8)	3' UTR (NM_007833, exon 8 of 8)	35336	NM_007833	13179	Mm.56769	NM_007833	ENSMUSG00000019929	Dcn	DC|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding
mm_105576.1	chr11	106613033	106613052	-	1	NA	promoter-TSS (NM_198292)	promoter-TSS (NM_198292)	-112	NM_198292	21763	Mm.102407	NM_198292	ENSMUSG00000040548	Tex2	4930568E07Rik|AI553404|Def-5|Taz4	testis expressed gene 2	protein-coding
mm_77332.1	chr8	119545081	119545083	-	1	NA	intron (NM_019709, intron 4 of 23)	intron (NM_019709, intron 4 of 23)	13679	NM_001167910	56453	Mm.206934	NM_019709	ENSMUSG00000031835	Mbtps1	0610038M03Rik|AV003995|S1P|SKI-1|Ski1|mKIAA0091	membrane-bound transcription factor peptidase, site 1	protein-coding
mm_110823.1	chr12	72408935	72408945	-	1	NA	5' UTR (NM_001286448, exon 1 of 7)	5' UTR (NM_001286448, exon 1 of 7)	114	NM_001286448	104001	Mm.221275	NM_153457	ENSMUSG00000021087	Rtn1	Nsp	reticulon 1	protein-coding
mm_97181.1	chr11	75533456	75533530	+	1	NA	intron (NM_173388, intron 2 of 13)	intron (NM_173388, intron 2 of 13)	1381	NM_001199283	215113	Mm.11186	NM_173388	ENSMUSG00000038178	Slc43a2	7630402D21Rik|BC042513|Lat4	solute carrier family 43, member 2	protein-coding
mm_94003.1	chr10	127595506	127595531	-	1	NA	intron (NM_008512, intron 6 of 88)	intron (NM_008512, intron 6 of 88)	25630	NM_008512	16971	Mm.271854	NM_008512	ENSMUSG00000040249	Lrp1	A2mr|AI316852|CD91|Lrp|b2b1554Clo	low density lipoprotein receptor-related protein 1	protein-coding
mm_132904.1	chr16	48872638	48872650	+	1	NA	promoter-TSS (NM_181596)	promoter-TSS (NM_181596)	36	NM_181596	245195	Mm.231288	NM_181596	ENSMUSG00000022651	Retnlg	Fizz3|Relmg|Xcp1	resistin like gamma	protein-coding
mm_53730.1	chr6	145121158	145121168	+	1	NA	promoter-TSS (NM_008511)	promoter-TSS (NM_008511)	-576	NM_008511	16970	Mm.843	NM_008511	ENSMUSG00000030263	Lrmp	D6Int3|D6Int4|D6Int5|D6Int7|D6Int8|Jaw1	lymphoid-restricted membrane protein	protein-coding
mm_67239.1	chr7	75308918	75308939	-	1	NA	promoter-TSS (NM_001109753)	promoter-TSS (NM_001109753)	226	NR_045814	68954	Mm.46960	NR_045812	ENSMUSG00000097247	1500012K07Rik	-	RIKEN cDNA 1500012K07 gene	ncRNA
mm_130278.1	chr15	96699732	96699734	-	1	NA	promoter-TSS (NM_175121)	promoter-TSS (NM_175121)	-35	NM_175121	67760	Mm.46754	NM_175121	ENSMUSG00000022462	Slc38a2	5033402L14Rik|AI316867|ATA2|SAT2|mKIAA1382	solute carrier family 38, member 2	protein-coding
mm_30685.1	chr4	11322231	11322248	+	1	NA	promoter-TSS (NM_001081201)	promoter-TSS (NM_001081201)	-108	NM_001081201	381510	Mm.331486	NM_001081201	ENSMUSG00000045205	Dpy19l4	Gm1023|Narg3	dpy-19-like 4 (C. elegans)	protein-coding
mm_74948.1	chr8	25976667	25976716	-	1	NA	promoter-TSS (NM_029884)	promoter-TSS (NM_029884)	53	NM_029884	52120	Mm.28326	NM_029884	ENSMUSG00000037260	Hgsnat	9430010M12Rik|AW208455|D8Ertd354e|Tmem76	heparan-alpha-glucosaminide N-acetyltransferase	protein-coding
mm_103380.1	chr11	75415061	75415077	-	1	NA	exon (NM_011340, exon 5 of 8)	exon (NM_011340, exon 5 of 8)	7554	NM_011340	20317	Mm.2044	NM_011340	ENSMUSG00000000753	Serpinf1	AI195227|EPC-1|Pedf|Pedfl|Sdf3	serine (or cysteine) peptidase inhibitor, clade F, member 1	protein-coding
mm_140499.1	chr17	4030940	4030944	-	1	NA	Intergenic	Intergenic	52053	NR_045764	75815	Mm.183387	NR_045764		4930470H14Rik	-	RIKEN cDNA 4930470H14 gene	ncRNA
mm_27277.1	chr3	41082938	41082948	-	1	NA	exon (NM_027558, exon 1 of 3)	exon (NM_027558, exon 1 of 3)	103	NM_027558	70804	Mm.40321	NM_027558	ENSMUSG00000049940	Pgrmc2	4631434O19Rik|5730409G06Rik|DG6|PMBP	progesterone receptor membrane component 2	protein-coding
mm_108998.1	chr12	102993510	102993522	+	1	NA	intron (NM_001081017, intron 2 of 48)	intron (NM_001081017, intron 2 of 48)	44657	NM_001081017	217843	Mm.387073	NM_177621	ENSMUSG00000021198	Unc79	9030205A07Rik|Mlca3	unc-79 homolog (C. elegans)	protein-coding
mm_149864.1	chr19	25127113	25127125	+	1	NA	exon (NM_028785, exon 19 of 48)	exon (NM_028785, exon 19 of 48)	-110083	NM_181404	107351	Mm.260722	NM_181404	ENSMUSG00000032702	Kank1	A930031B09Rik|AU015049|AW121052|Ankrd15|D330024H06Rik|mKIAA0172	KN motif and ankyrin repeat domains 1	protein-coding
mm_51080.1	chr6	66963307	66963309	+	1	NA	intron (NM_001177560, intron 3 of 4)	intron (NM_001177560, intron 3 of 4)	66417	NM_001177558	14701	Mm.234342	NM_025278	ENSMUSG00000036402	Gng12	2010305F15Rik|AA536815|AI115529|AI314170|AI842738	guanine nucleotide binding protein (G protein), gamma 12	protein-coding
mm_14214.1	chr2	127336153	127336166	+	1	NA	promoter-TSS (NM_010090)	promoter-TSS (NM_010090)	0	NM_010090	13537	Mm.4729	NM_010090	ENSMUSG00000027368	Dusp2	PAC1	dual specificity phosphatase 2	protein-coding
mm_53791.1	chr6	146642606	146642616	+	1	NA	promoter-TSS (NM_025315)	promoter-TSS (NM_025315)	32	NM_025315	108098	Mm.26212	NM_025315	ENSMUSG00000030291	Med21	0610007L03Rik|AI449604|D19234|D6Ertd782e|Srb7|Surb7	mediator complex subunit 21	protein-coding
mm_172181.1	chr6	49236591	49236592	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-21637	NM_023670	140488	Mm.281018	NM_023670	ENSMUSG00000029814	Igf2bp3	2610101N11Rik|AA522010|AL022933|AU045931|IMP-3|IMP3|Koc13|Neilsen|mimp3	insulin-like growth factor 2 mRNA binding protein 3	protein-coding
mm_49776.1	chr6	34908075	34908105	+	1	NA	intron (NM_001013366, intron 3 of 14)	intron (NM_001013366, intron 3 of 14)	2741	NM_001013366	101240	Mm.152120	NM_001013366	ENSMUSG00000058486	Wdr91	9530020G05Rik|AI987683|AU018665	WD repeat domain 91	protein-coding
mm_102614.1	chr11	62457918	62457930	-	1	NA	promoter-TSS (NM_177229)	promoter-TSS (NM_177229)	-536	NM_001039536	327942	Mm.390358	NM_199026	ENSMUSG00000014245	Pigl	Gm737	phosphatidylinositol glycan anchor biosynthesis, class L	protein-coding
mm_64953.1	chr7	16401133	16401155	-	1	NA	promoter-TSS (NM_198631)	promoter-TSS (NM_198631)	-52	NM_198631	330474	Mm.333594	NM_198631	ENSMUSG00000059273	Zc3h4	Bwq1|Gm768|Kiaa1064-hp|mKIAA1064	zinc finger CCCH-type containing 4	protein-coding
mm_73918.1	chr8	119700018	119700062	+	1	NA	promoter-TSS (NM_026922)	promoter-TSS (NM_026922)	31	NM_026922	69047	Mm.46251	NM_026922	ENSMUSG00000034112	Atp2c2	1810010G06Rik|Spca2|mKIAA0703	ATPase, Ca++ transporting, type 2C, member 2	protein-coding
mm_173358.1	chrY	90819337	90819344	+	1	NA	Intergenic	(CAGAGA)n|Simple_repeat|Simple_repeat	20066	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_73460.1	chr8	106636290	106636295	+	1	NA	intron (NM_009864, intron 2 of 15)	PB1|SINE|Alu	32942	NM_009864	12550	Mm.35605	NM_009864	ENSMUSG00000000303	Cdh1	AA960649|ARC-1|E-cad|Ecad|L-CAM|UVO|Um	cadherin 1	protein-coding
mm_160158.1	chr7	44207412	44207412	+	1	NA	promoter-TSS (NM_010915)	promoter-TSS (NM_010915)	-21	NM_010915	18048	Mm.440886	NM_010915	ENSMUSG00000066513	Klk1b4	Ngfa|alpha-NGF|mGk-4	kallikrein 1-related pepidase b4	protein-coding
mm_6165.1	chr1	65062099	65062118	-	1	NA	exon (NM_007776, exon 3 of 3)	exon (NM_007776, exon 3 of 3)	1332	NM_007776	12967	Mm.425031	NM_007776	ENSMUSG00000067299	Crygd	Aey4|Cryg-1|DGcry-1|Lop12	crystallin, gamma D	protein-coding
mm_57191.1	chr6	122849600	122849632	-	1	NA	3' UTR (NM_009779, exon 2 of 2)	3' UTR (NM_009779, exon 2 of 2)	6541	NM_009779	12267	Mm.2408	NM_009779	ENSMUSG00000040552	C3ar1	AZ3B|C3AR|HNFAG09	complement component 3a receptor 1	protein-coding
mm_25487.1	chr3	109267177	109267214	+	1	NA	Intergenic	Intergenic	-73488	NM_020505	57257	Mm.282257	NM_020505	ENSMUSG00000033721	Vav3	A530094I06Rik|AA986410|Idd18.1	vav 3 oncogene	protein-coding
mm_40075.1	chr5	34336953	34336959	+	1	NA	promoter-TSS (NM_001304270)	promoter-TSS (NM_001304270)	24	NM_001304270	19822	Mm.21281	NM_011278	ENSMUSG00000029110	Rnf4	AU018689|Gtrgeo8|SNURF	ring finger protein 4	protein-coding
mm_172533.1	chr7	88278176	88278178	+	1	NA	promoter-TSS (NM_009982)	promoter-TSS (NM_009982)	92	NM_001311790	13032	Mm.89295	NM_009982	ENSMUSG00000030560	Ctsc	AI047818|CatC|DPP1|DPPI	cathepsin C	protein-coding
mm_28066.1	chr3	84259919	84259937	-	1	NA	promoter-TSS (NM_001271727)	promoter-TSS (NM_001271727)	-149	NM_001271727	80890	Mm.44876	NM_030706	ENSMUSG00000027993	Trim2	mKIAA0517|narf	tripartite motif-containing 2	protein-coding
mm_45221.1	chr5	53213448	53213473	-	1	NA	promoter-TSS (NM_172710)	promoter-TSS (NM_172710)	-8	NM_172710	231238	Mm.235020	NM_172710	ENSMUSG00000029189	Sel1l3	2310045A20Rik|AI429585|mKIAA0746	sel-1 suppressor of lin-12-like 3 (C. elegans)	protein-coding
mm_89690.1	chr10	97565683	97565695	+	1	NA	5' UTR (NM_008524, exon 1 of 3)	5' UTR (NM_008524, exon 1 of 3)	188	NM_008524	17022	Mm.18888	NM_008524	ENSMUSG00000036446	Lum	Ldc|SLRR2D	lumican	protein-coding
mm_140508.1	chr17	5492457	5492479	-	1	NA	promoter-TSS (NM_146073)	promoter-TSS (NM_146073)	-132	NM_146073	224454	Mm.487663	NM_146073	ENSMUSG00000034265	Zdhhc14	B530001K09Rik|New1cp	zinc finger, DHHC domain containing 14	protein-coding
mm_129038.1	chr15	75012923	75012931	-	1	NA	Intergenic	MT2C_Mm|LTR|ERVL	-14896	NM_010738	110454	Mm.425949	NM_010738	ENSMUSG00000075602	Ly6a	Ly-6A.2|Ly-6A/E|Ly-6E.1|Sca-1|Sca1|TAP	lymphocyte antigen 6 complex, locus A	protein-coding
mm_56392.1	chr6	95333993	95333994	-	1	NA	promoter-TSS (NR_033559)	promoter-TSS (NR_033559)	0	NR_033559	414067	Mm.355990	NR_033559	ENSMUSG00000068180	AY512915	-	cDNA sequence AY512915	ncRNA
mm_105603.1	chr11	106779458	106779472	-	1	NA	promoter-TSS (NR_027785)	promoter-TSS (NR_027785)	50	NR_027785	50776	Mm.859	NM_015810	ENSMUSG00000020718	Polg2	-	polymerase (DNA directed), gamma 2, accessory subunit	protein-coding
mm_154142.1	chr19	58123709	58123715	-	1	NA	intron (NM_181415, intron 28 of 28)	Lx9|LINE|L1	72545	NR_049196	100885835		NR_049196	ENSMUSG00000093757	Mir5623	Gm26068|mir-5623|mmu-mir-5623	microRNA 5623	ncRNA
mm_28192.1	chr3	88141627	88141639	-	1	NA	promoter-TSS (NM_001310593)	promoter-TSS (NM_001310593)	-739	NM_001310587	17261	Mm.28184	NM_133665	ENSMUSG00000001419	Mef2d	C80750	myocyte enhancer factor 2D	protein-coding
mm_6897.1	chr1	84742015	84742018	-	1	NA	intron (NM_133975, intron 30 of 40)	intron (NM_133975, intron 30 of 40)	-45795	NM_152915	227325	Mm.292560	NM_152915	ENSMUSG00000036766	Dner	A930026D19Rik|BET|Bret	delta/notch-like EGF repeat containing	protein-coding
mm_168242.1	chr10	81863893	81863900	+	1	NA	promoter-TSS (NM_001243067).2	promoter-TSS (NM_001243067).2	-38	NM_001243067	73610	Mm.490466	NM_001243067	ENSMUSG00000096795	Zfp433	1700123A16Rik	zinc finger protein 433	protein-coding
mm_85854.1	chr9	110728340	110728343	-	1	NA	intron (NM_001083935, intron 4 of 14)	intron (NM_001083935, intron 4 of 14)	14269	NM_001083936	19228	Mm.3542	NM_011199	ENSMUSG00000032492	Pth1r	PPR|Pthr|Pthr1	parathyroid hormone 1 receptor	protein-coding
mm_103204.1	chr11	70652215	70652225	-	1	NA	TTS (NM_001316728)	TTS (NM_001316728)	2430	NM_011072	18643	Mm.2647	NM_011072	ENSMUSG00000018293	Pfn1	Pfn	profilin 1	protein-coding
mm_145117.1	chr18	44334115	44334123	+	1	NA	promoter-TSS (NM_001033621)	promoter-TSS (NM_001033621)	45	NM_001033621	58916	Mm.143804	NM_001033621	ENSMUSG00000024471	Myot	5530402I04Rik|Ttid	myotilin	protein-coding
mm_54869.1	chr6	42597832	42597838	-	1	NA	promoter-TSS (NM_203396)	promoter-TSS (NM_203396)	-463	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_107944.1	chr12	71959658	71959659	+	1	NA	intron (NM_172464, intron 16 of 25)	intron (NM_172464, intron 16 of 25)	70115	NM_001286452	208846	Mm.87417	NM_026102	ENSMUSG00000034574	Daam1	-	dishevelled associated activator of morphogenesis 1	protein-coding
mm_102835.1	chr11	69237030	69237044	-	1	NA	promoter-TSS (NM_008192)	promoter-TSS (NM_008192)	-15	NM_008192	14919	Mm.291816	NM_008192	ENSMUSG00000020890	Gucy2e	GC-E|GC1|ROS-GC1	guanylate cyclase 2e	protein-coding
mm_40822.1	chr5	72644410	72644418	+	1	NA	Intergenic	Intergenic	-1662	NM_007723	12788	Mm.436652	NM_007723	ENSMUSG00000067220	Cnga1	Cncg	cyclic nucleotide gated channel alpha 1	protein-coding
mm_5649.1	chr1	40516523	40516529	-	1	NA	5' UTR (NM_010553, exon 3 of 13)	5' UTR (NM_010553, exon 3 of 13)	1164	NM_010553	16174	Mm.20466	NM_010553	ENSMUSG00000026068	Il18rap	AcPL|IL-18R-beta|IL-18RAcP|IL-18Rbeta|IL-1RAcPL	interleukin 18 receptor accessory protein	protein-coding
mm_117780.1	chr13	97015305	97015316	-	1	NA	Intergenic	Intergenic	19052	NM_025585	66479	Mm.390629	NM_025585	ENSMUSG00000052075	1700029F12Rik	-	RIKEN cDNA 1700029F12 gene	protein-coding
mm_83166.1	chr9	40489750	40489760	-	1	NA	Intergenic	Intergenic	-33991	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_57339.1	chr6	124746859	124746878	-	1	NA	exon (NM_007881, exon 5 of 10)	exon (NM_007881, exon 5 of 10)	-5789	NM_013535	14790	Mm.439877	NM_013535	ENSMUSG00000072772	Grcc10	2310033H05Rik|C10	gene rich cluster, C10 gene	protein-coding
mm_3484.1	chr1	150105662	150105677	+	1	NA	exon (NM_011198, exon 10 of 10)	exon (NM_011198, exon 10 of 10)	5638	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_71453.1	chr8	46521696	46521709	+	1	NA	intron (NM_001302163, intron 11 of 20)	intron (NM_001302163, intron 11 of 20)	-30367	NM_027973	71876	Mm.22108	NM_027973	ENSMUSG00000031629	Cenpu	1700029A22Rik|Mlf1ip	centromere protein U	protein-coding
mm_70270.1	chr8	3596521	3596524	+	1	NA	intron (NM_001347112, intron 1 of 17)	intron (NM_001347112, intron 1 of 17)	9072	NM_001347111	69697	Mm.390010	NM_027171	ENSMUSG00000044433	Camsap3	2310057J16Rik|Kiaa1543|Nezha	calmodulin regulated spectrin-associated protein family, member 3	protein-coding
mm_11147.1	chr2	28513244	28513323	+	1	NA	5' UTR (NM_009058, exon 1 of 18)	5' UTR (NM_009058, exon 1 of 18)	116	NM_001145834	19730	Mm.5236	NM_009058	ENSMUSG00000026821	Ralgds	Gnds|Rgds|mKIAA1308	ral guanine nucleotide dissociation stimulator	protein-coding
mm_14767.1	chr2	145675471	145675493	+	1	NA	Intergenic	Intergenic	-25713	NR_033220	408057	Mm.486711	NR_033220	ENSMUSG00000087594	BC039771	-	cDNA sequence BC039771	ncRNA
mm_71624.1	chr8	57436395	57436414	+	1	NA	Intergenic	Intergenic	-19519	NM_009136	20284	Mm.12886	NM_009136	ENSMUSG00000031610	Scrg1	AW124307	scrapie responsive gene 1	protein-coding
mm_148108.1	chr18	74207772	74207790	-	1	NA	promoter-TSS (NM_001164355)	promoter-TSS (NM_001164355)	37	NM_001164355	66468	Mm.283406	NM_025581	ENSMUSG00000036223	Ska1	2810433K01Rik|AV117428	spindle and kinetochore associated complex subunit 1	protein-coding
mm_43994.1	chr5	146832900	146832947	+	1	NA	promoter-TSS (NM_019647)	promoter-TSS (NM_019647)	33	NM_019647	19933	Mm.316592	NM_019647	ENSMUSG00000041453	Rpl21	8430440E03Rik|L21	ribosomal protein L21	protein-coding
mm_102199.1	chr11	54619010	54619057	-	1	NA	intron (NM_175258, intron 7 of 27)	intron (NM_175258, intron 7 of 27)	22887	NM_001252497	192786	Mm.254404	NM_175258	ENSMUSG00000037533	Rapgef6	A530068K01|AI844632|BB085664|C030018K18Rik|PDZ-GEF2|Pdzgef2|RA-GEF-2|Ragef2|mKIAA4052	Rap guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_45084.1	chr5	44073762	44073784	-	1	NA	intron (NM_001163582, intron 1 of 21)	intron (NM_001163582, intron 1 of 21)	20995	NM_001163581	19126	Mm.6250	NM_008935	ENSMUSG00000029086	Prom1	4932416E19Rik|AC133|CD133|Prom|Prom-1|Proml1	prominin 1	protein-coding
mm_120205.1	chr14	61682576	61682610	+	1	NA	promoter-TSS (NR_028264)	promoter-TSS (NR_028264)	-220	NR_028264	668253	Mm.32886	NR_028264	ENSMUSG00000097589	Dleu2	1810047A16Rik|4932411A06Rik|7730401J12Rik|AI197277|AI788824|Alt1|Gm9069|Leu2	deleted in lymphocytic leukemia, 2	ncRNA
mm_71477.1	chr8	46552025	46552079	+	1	NA	promoter-TSS (NM_027973)	promoter-TSS (NM_027973)	-17	NM_027973	71876	Mm.22108	NM_027973	ENSMUSG00000031629	Cenpu	1700029A22Rik|Mlf1ip	centromere protein U	protein-coding
mm_159435.1	chr3	117360713	117360713	-	1	NA	5' UTR (NM_177664, exon 1 of 7)	5' UTR (NM_177664, exon 1 of 7)	163	NM_177664	229791	Mm.140138	NM_177664	ENSMUSG00000044667	Plppr4	A330086D10|D3Bwg0562e|Lppr4|PRG-1|mKIAA0455	phospholipid phosphatase related 4	protein-coding
mm_118358.1	chr13	115101619	115101656	-	1	NA	5' UTR (NM_001033228, exon 1 of 29)	5' UTR (NM_001033228, exon 1 of 29)	327	NM_001033228	109700	Mm.317280	NM_001033228	ENSMUSG00000042284	Itga1	CD49A|E130012M19Rik|Vla1	integrin alpha 1	protein-coding
mm_91786.1	chr10	53337318	53337330	-	1	NA	promoter-TSS (NM_001141927)	promoter-TSS (NM_001141927)	-362	NM_023129	18821	Mm.34145	NM_023129	ENSMUSG00000038583	Pln	Plb	phospholamban	protein-coding
mm_79018.1	chr9	45852705	45852718	+	1	NA	intron (NM_011792, intron 1 of 8)	intron (NM_011792, intron 1 of 8)	14166	NM_011792	23821	Mm.24044	NM_011792	ENSMUSG00000032086	Bace1	ASP2|Bace|C76936	beta-site APP cleaving enzyme 1	protein-coding
mm_43080.1	chr5	124447027	124447037	+	1	NA	intron (NM_001310727, intron 1 of 6)	intron (NM_001310727, intron 1 of 6)	328	NM_001310727	67956	Mm.137966	NM_030241	ENSMUSG00000049327	Kmt5a	2410195B05Rik|AA617402|AW536475|PR-SET7|PR/SET07|Setd8	lysine methyltransferase 5A	protein-coding
mm_66284.1	chr7	37772869	37772891	-	1	NA	Intergenic	CpG	-3128	NM_172385	243937	Mm.322505	NM_172385	ENSMUSG00000043456	Zfp536	9630010P11Rik|Znf536|mKIAA0390	zinc finger protein 536	protein-coding
mm_58859.1	chr7	16905972	16906013	+	1	NA	promoter-TSS (NM_008967)	promoter-TSS (NM_008967)	-498	NM_008967	19222	Mm.287572	NM_008967	ENSMUSG00000043017	Ptgir	IP|PGI2	prostaglandin I receptor (IP)	protein-coding
mm_146563.1	chr18	6490703	6490738	-	1	NA	promoter-TSS (NR_035446)	promoter-TSS (NR_035446)	-74	NR_035446	100316773		NR_035446	ENSMUSG00000084514	Mir1893	Mirn1893|mmu-mir-1893	microRNA 1893	ncRNA
mm_57817.1	chr6	129462680	129462686	-	1	NA	non-coding (NR_132130, exon 6 of 6)	non-coding (NR_132130, exon 6 of 6)	10096	NM_001309637	56644	Mm.239516	NM_020008	ENSMUSG00000079293	Clec7a	BGR|Clecsf12|beta-GR	C-type lectin domain family 7, member a	protein-coding
mm_113999.1	chr13	52583453	52583474	+	1	NA	promoter-TSS (NM_001198977)	promoter-TSS (NM_001198977)	26	NM_001198977	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_95870.1	chr11	58049596	58049643	+	1	NA	intron (NM_028451, intron 10 of 18)	intron (NM_028451, intron 10 of 18)	40555	NM_028451	73158	Mm.248843	NM_028451	ENSMUSG00000037331	Larp1	1810024J12Rik|3110040D16Rik|Larp|mKIAA0731	La ribonucleoprotein domain family, member 1	protein-coding
mm_148120.1	chr18	75297284	75297294	-	1	NA	promoter-TSS (NR_045394)	promoter-TSS (NR_045394)	28	NR_045394	100503117	Mm.250517	NR_045393	ENSMUSG00000102047	2010010A06Rik	5033420E22Rik	RIKEN cDNA 2010010A06 gene	ncRNA
mm_7730.1	chr1	130733851	130733853	-	1	NA	intron (NM_177604, intron 1 of 3)	intron (NM_177604, intron 1 of 3)	1876	NM_177604	212439	Mm.268547	NM_177604	ENSMUSG00000042510	AA986860	E030025M07|Sarg	expressed sequence AA986860	protein-coding
mm_120405.1	chr14	65076466	65076468	+	1	NA	exon (NM_018788, exon 3 of 7)	exon (NM_018788, exon 3 of 7)	21639	NM_018788	54616	Mm.103748	NM_018788	ENSMUSG00000021978	Extl3	2900009G18Rik|AU040105|Ext1l|mKIAA0519	exostoses (multiple)-like 3	protein-coding
mm_57839.1	chr6	129465534	129465540	-	1	NA	exon (NM_020008, exon 5 of 6)	exon (NM_020008, exon 5 of 6)	7242	NM_001309637	56644	Mm.239516	NM_020008	ENSMUSG00000079293	Clec7a	BGR|Clecsf12|beta-GR	C-type lectin domain family 7, member a	protein-coding
mm_43990.1	chr5	146706662	146706673	+	1	NA	Intergenic	Intergenic	88289	NM_011669	22217	Mm.167971	NM_011669	ENSMUSG00000029640	Usp12	Ubh1	ubiquitin specific peptidase 12	protein-coding
mm_69645.1	chr7	138909493	138909513	-	1	NA	promoter-TSS (NM_009760)	promoter-TSS (NM_009760)	3	NM_009760	12176	Mm.378890	NM_009760	ENSMUSG00000078566	Bnip3	Nip3	BCL2/adenovirus E1B interacting protein 3	protein-coding
mm_165560.1	chr3	14886435	14886483	+	1	NA	promoter-TSS (NM_009801)	promoter-TSS (NM_009801)	33	NM_009801	12349	Mm.1186	NM_009801	ENSMUSG00000027562	Car2	AI131712|CAII|Ca2|Car-2|Ltw-5|Lvtw-5	carbonic anhydrase 2	protein-coding
mm_163955.1	chr14	54686171	54686184	+	1	NA	promoter-TSS (NM_021437)	promoter-TSS (NM_021437)	6	NM_021437	58248	Mm.197509	NM_021437	ENSMUSG00000040822	1700123O20Rik	MNCb-2990	RIKEN cDNA 1700123O20 gene	protein-coding
mm_15350.1	chr2	156179586	156179609	+	1	NA	promoter-TSS (NM_001291115)	promoter-TSS (NM_001291115)	-17	NM_001291115	170791	Mm.392436	NM_133242	ENSMUSG00000027620	Rbm39	1500012C14Rik|2310040E03Rik|B330012G18Rik|C79248|R75070|Rnpc2|caper	RNA binding motif protein 39	protein-coding
mm_171748.1	chr5	100415982	100415982	-	1	NA	intron (NM_026969, intron 1 of 27)	CpG	252	NM_026969	69162	Mm.18634	NM_026969	ENSMUSG00000035325	Sec31a	1810024J13Rik|ABP125|ABP130|AU042160|HSPC275|Sec31l1	Sec31 homolog A (S. cerevisiae)	protein-coding
mm_122851.1	chr14	54779803	54779815	-	1	NA	intron (NM_016972, intron 1 of 10)	intron (NM_016972, intron 1 of 10)	2077	NM_016972	50934	Mm.276831	NM_016972	ENSMUSG00000022180	Slc7a8	AA408822|LAT2	solute carrier family 7 (cationic amino acid transporter, y+ system), member 8	protein-coding
mm_144071.1	chr17	91024675	91024677	-	1	NA	intron (NM_001346957, intron 1 of 18)	intron (NM_001346957, intron 1 of 18)	64929	NM_001346957	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_110154.1	chr12	26455207	26455224	-	1	NA	intron (NM_021384, intron 1 of 5)	intron (NM_021384, intron 1 of 5)	1237	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_136234.1	chr16	90726780	90726793	-	1	NA	intron (NM_025642, intron 1 of 4)	intron (NM_025642, intron 1 of 4)	585	NM_025642	66578	Mm.180363	NM_025642	ENSMUSG00000022978	Mis18a	2610039C10Rik|2810018N07Rik	MIS18 kinetochore protein A	protein-coding
mm_113714.1	chr13	43603860	43603870	+	1	NA	Intergenic	Intergenic	-11932	NM_183204	328234	Mm.40588	NM_183204	ENSMUSG00000044164	Rnf182	C630023L15Rik	ring finger protein 182	protein-coding
mm_104507.1	chr11	95982563	95982573	-	1	NA	intron (NM_009951, intron 2 of 14)	intron (NM_009951, intron 2 of 14)	-19185	NR_037223	100526468		NR_037223	ENSMUSG00000093358	Mir3063	mmu-mir-3063	microRNA 3063	ncRNA
mm_139088.1	chr17	46832365	46832372	+	1	NA	promoter-TSS (NM_001100452)	promoter-TSS (NM_001100452)	-955	NM_001100452	210982	Mm.37642	NM_001100452	ENSMUSG00000036568	Gltscr1l	mKIAA0240	GLTSCR1-like	protein-coding
mm_87945.1	chr10	62947012	62947073	+	1	NA	promoter-TSS (NM_177372)	promoter-TSS (NM_177372)	13	NM_177372	327762	Mm.21492	NM_177372	ENSMUSG00000036875	Dna2	Dna2l|E130315B21Rik	DNA replication helicase/nuclease 2	protein-coding
mm_113766.1	chr13	44808627	44808633	+	1	NA	intron (NM_001205044, intron 2 of 18)	intron (NM_001205044, intron 2 of 18)	77359	NM_001205043	16468	Mm.25059	NM_021878	ENSMUSG00000038518	Jarid2	Jmj|jumonji	jumonji, AT rich interactive domain 2	protein-coding
mm_2714.1	chr1	128141974	128141990	+	1	NA	intron (NM_181750, intron 1 of 26)	intron (NM_181750, intron 1 of 26)	38676	NM_181750	226412	Mm.221041	NM_181750	ENSMUSG00000056211	R3hdm1	R3hdm	R3H domain containing 1	protein-coding
mm_50482.1	chr6	48988294	48988308	+	1	NA	exon (NM_172888, exon 1 of 5)	exon (NM_172888, exon 1 of 5)	1440	NM_172888	243377	Mm.446302	NM_172888	ENSMUSG00000039215	Svs1	9530003A11	seminal vesicle secretory protein 1	protein-coding
mm_74188.1	chr8	123653808	123653818	+	1	NA	promoter-TSS (NM_133955)	promoter-TSS (NM_133955)	-116	NM_133955	69581	Mm.168257	NM_133955	ENSMUSG00000039960	Rhou	2310026M05Rik|AI182090|Arhu|CDC42L1|G28K|WRCH-1|WRCH1|mG28K	ras homolog family member U	protein-coding
mm_111617.1	chr12	102404320	102404352	-	1	NA	exon (NM_011175, exon 5 of 14)	exon (NM_011175, exon 5 of 14)	35477	NM_011175	19141	Mm.17185	NM_011175	ENSMUSG00000021190	Lgmn	AEP|AI746452|AU022324|Prsc1	legumain	protein-coding
mm_10203.1	chr2	4976114	4976164	+	1	NA	promoter-TSS (NM_001165932)	promoter-TSS (NM_001165932)	17	NM_026754	68527	Mm.27791	NM_026754	ENSMUSG00000026668	Ucma	1110017I16Rik|AW121955|Grp	upper zone of growth plate and cartilage matrix associated	protein-coding
mm_157497.1	chrX	48454313	48454325	-	1	NA	intron (NM_019680, intron 1 of 8)	CpG	8813	NM_019680	56501	Mm.36808	NM_019680	ENSMUSG00000031103	Elf4	AV314029|BC042423|ENSMUSG00000053512|Gm9907|Mef	E74-like factor 4 (ets domain transcription factor)	protein-coding
mm_124510.1	chr14	121915873	121915892	-	1	NA	promoter-TSS (NM_182806)	promoter-TSS (NM_182806)	-108	NM_182806	110168	Mm.37405	NM_182806	ENSMUSG00000050350	Gpr18	-	G protein-coupled receptor 18	protein-coding
mm_69917.1	chr7	141704554	141704573	-	1	NA	intron (NM_023566, intron 27 of 45)	intron (NM_023566, intron 27 of 45)	14223	NM_023566	17831	Mm.2041	NM_023566		Muc2	2010015E03Rik|MCM|wnn	mucin 2	protein-coding
mm_118970.1	chr14	27876143	27876153	+	1	NA	intron (NM_177814, intron 3 of 15)	intron (NM_177814, intron 3 of 15)	253741	NM_177814	238988	Mm.318004	NM_177814	ENSMUSG00000040640	Erc2	6430531D06|CAST|CAST1/ERC2|D14Ertd171e|ELKS2alpha	ELKS/RAB6-interacting/CAST family member 2	protein-coding
mm_87104.1	chr10	33175787	33175801	+	1	NA	exon (NM_029726, exon 5 of 38)	exon (NM_029726, exon 5 of 38)	80563	NR_040657	442820	Mm.490725	NR_040657		D830005E20Rik	-	RIKEN cDNA D830005E20 gene	ncRNA
mm_133644.1	chr16	91740113	91740137	+	1	NA	intron (NM_001110275, intron 1 of 28)	intron (NM_001110275, intron 1 of 28)	10754	NM_010587	16443	Mm.40546	NM_010587	ENSMUSG00000022957	Itsn1	AA517634|AA545208|AI316805|AI839402|AI848451|Ehsh1|Ese1|Itsn|Sh3p17	intersectin 1 (SH3 domain protein 1A)	protein-coding
mm_108811.1	chr12	95692196	95692207	+	1	NA	promoter-TSS (NM_201518)	promoter-TSS (NM_201518)	-25	NM_201518	399558	Mm.341948	NM_201518	ENSMUSG00000047414	Flrt2	-	fibronectin leucine rich transmembrane protein 2	protein-coding
mm_63544.1	chr7	128062699	128062730	+	1	NA	promoter-TSS (NM_008401)	promoter-TSS (NM_008401)	74	NM_008401	16409	Mm.262106	NM_008401	ENSMUSG00000030786	Itgam	CD11b/CD18|CR3|CR3A|Cd11b|F730045J24Rik|Ly-40|MAC1|Mac-1|Mac-1a	integrin alpha M	protein-coding
mm_58373.1	chr6	148946461	148946498	-	1	NA	promoter-TSS (NM_019643)	promoter-TSS (NM_019643)	-47	NM_019643	56306	Mm.18637	NM_019643	ENSMUSG00000039985	Fam60a	Ppcs1|Pptcs1|Tera	family with sequence similarity 60, member A	protein-coding
mm_52654.1	chr6	117841259	117841286	+	1	NA	promoter-TSS (NM_001346650)	promoter-TSS (NM_001346650)	-3	NM_001346652	232337	Mm.290847	NM_177684	ENSMUSG00000059689	Zfp637	AI646709|BC021601|Znf32	zinc finger protein 637	protein-coding
mm_131869.1	chr16	23175224	23175237	+	1	NA	Intergenic	Intergenic	28694	NM_009605	11450	Mm.3969	NM_009605	ENSMUSG00000022878	Adipoq	30kDa|APN|Acdc|Acrp30|Ad|GBP28|adipo|apM1	adiponectin, C1Q and collagen domain containing	protein-coding
mm_5589.1	chr1	39553325	39553367	-	1	NA	intron (NM_001033135, intron 6 of 6)	B4|SINE|B4	-4506	NR_028555	100217461		NR_028555	ENSMUSG00000077704	Snord89	MBII-289	small nucleolar RNA, C/D box 89	snoRNA
mm_101743.1	chr11	43379242	43379294	-	1	NA	Intergenic	Intergenic	-4807	NR_029558	387164		NR_029558	ENSMUSG00000065601	Mir146	Mirn146|miR-146a|mmu-mir-146	microRNA 146	ncRNA
mm_90498.1	chr10	128035364	128035380	+	1	NA	promoter-TSS (NM_013608)	promoter-TSS (NM_013608)	26	NM_001113199	17938	Mm.3746	NM_013608	ENSMUSG00000061315	Naca	AL022831|AL024382|Gm1878|mKIAA0363|skNAC	nascent polypeptide-associated complex alpha polypeptide	protein-coding
mm_111002.1	chr12	78861467	78861609	-	1	NA	promoter-TSS (NM_026114)	promoter-TSS (NM_026114)	100	NM_023721	73834	Mm.311549	NM_023721	ENSMUSG00000021114	Atp6v1d	1110004P10Rik|Atp6m|VATD|Vma8	ATPase, H+ transporting, lysosomal V1 subunit D	protein-coding
mm_152708.1	chr19	17356632	17356636	-	1	NA	promoter-TSS (NM_173442)	promoter-TSS (NM_173442)	33	NM_173442	14537	Mm.244825	NM_010265	ENSMUSG00000038843	Gcnt1	5630400D21Rik|B130048E03|C2 GlcNAcT|C2GNT|IGnT	glucosaminyl (N-acetyl) transferase 1, core 2	protein-coding
mm_2144.1	chr1	88095130	88095134	+	1	NA	exon (NM_201642, exon 1 of 5)	exon (NM_201642, exon 1 of 5)	131	NM_201642	394432	Mm.300095	NM_201642	ENSMUSG00000090124	Ugt1a7c	A10'|A13|Ugt1a10	UDP glucuronosyltransferase 1 family, polypeptide A7C	protein-coding
mm_109325.1	chr12	109563765	109563768	+	1	NA	promoter-TSS (NR_030427)	promoter-TSS (NR_030427)	74	NR_030427	791079		NR_030427	ENSMUSG00000076451	Mir770	Mirn770|mir-770|mmu-mir-770	microRNA 770	ncRNA
mm_80604.1	chr9	86701427	86701476	+	1	NA	TTS (NR_045835)	TTS (NR_045835)	-5537	NM_008615	17436	Mm.148155	NM_008615	ENSMUSG00000032418	Me1	D9Ertd267e|Mdh-1|Mod-1|Mod1	malic enzyme 1, NADP(+)-dependent, cytosolic	protein-coding
mm_40356.1	chr5	47984321	47984346	+	1	NA	non-coding (NR_111900, exon 1 of 36)	non-coding (NR_111900, exon 1 of 36)	1178	NM_001291228	20563	Mm.289739	NM_178804	ENSMUSG00000031558	Slit2	Drad-1|E030015M03Rik|E130320P19Rik|Slil3|mKIAA4141|slit-2	slit homolog 2 (Drosophila)	protein-coding
mm_90010.1	chr10	115251641	115251669	+	1	NA	promoter-TSS (NM_025706)	promoter-TSS (NM_025706)	-162	NM_025706	66687	Mm.22252	NM_025706	ENSMUSG00000020130	Tbc1d15	4432405K22Rik|AU022358|AU023730|AW557774|Ly6dl|Rab7-GAP	TBC1 domain family, member 15	protein-coding
mm_15176.1	chr2	154162607	154162613	+	1	NA	promoter-TSS (NM_025990)	promoter-TSS (NM_025990)	3	NM_025990	67135	Mm.140317	NM_025990	ENSMUSG00000027484	Bpifa5	2310021H06Rik|2310074B19Rik|Pluncl|Splunc5|Tpl	BPI fold containing family A, member 5	protein-coding
mm_79710.1	chr9	61372310	61372320	+	1	NA	promoter-TSS (NM_009389)	promoter-TSS (NM_009389)	-51	NM_001083928	21887	Mm.24255	NM_009389	ENSMUSG00000032280	Tle3	2610103N05Rik|ESG|Grg3a|Grg3b|mKIAA1547	transducin-like enhancer of split 3	protein-coding
mm_29209.1	chr3	106790048	106790072	-	1	NA	promoter-TSS (NM_007651)	promoter-TSS (NM_007651)	89	NM_007651	12508	Mm.316861	NM_007651	ENSMUSG00000040747	Cd53	AI323659|Ox-44|Tspan25	CD53 antigen	protein-coding
mm_72906.1	chr8	90908566	90908597	+	1	NA	intron (NM_177224, intron 2 of 39)	CpG	-23668	NM_001310530	109151	Mm.100615	NM_177224	ENSMUSG00000056608	Chd9	1810014J18Rik|9030205D12Rik|A330063D19Rik|AD013|PRIC320|mKIAA0308	chromodomain helicase DNA binding protein 9	protein-coding
mm_156612.1	chrX	153498178	153498191	+	1	NA	promoter-TSS (NM_018798)	promoter-TSS (NM_018798)	-48	NM_018798	54609	Mm.430772	NM_018798	ENSMUSG00000050148	Ubqln2	Chap1|Dsk2|HRIHFB2157|Plic-2|Plic2	ubiquilin 2	protein-coding
mm_8185.1	chr1	138083645	138083663	-	1	NA	exon (NM_001268286, exon 18 of 29)	exon (NM_001268286, exon 18 of 29)	91472	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_65239.1	chr7	19770510	19770526	-	1	NA	promoter-TSS (NM_020486)	promoter-TSS (NM_020486)	14	NM_020486	57278	Mm.29236	NM_020486	ENSMUSG00000002980	Bcam	1200005K12Rik|B-CAM|Gplu|Lu	basal cell adhesion molecule	protein-coding
mm_130331.1	chr15	97720444	97720448	-	1	NA	intron (NM_001168693, intron 3 of 9)	intron (NM_001168693, intron 3 of 9)	704	NM_008902	19011	Mm.1001	NM_008902	ENSMUSG00000022468	Endou	Pp11r|Tcl-30	endonuclease, polyU-specific	protein-coding
mm_32471.1	chr4	107707095	107707099	+	1	NA	Intergenic	Intergenic	-22935	NM_019872	56296	Mm.141324	NM_019872	ENSMUSG00000028610	Dmrtb1	Dmrt6|Prp13	DMRT-like family B with proline-rich C-terminal, 1	protein-coding
mm_50244.1	chr6	42353475	42353482	+	1	NA	intron (NM_001289619, intron 4 of 8)	intron (NM_001289619, intron 4 of 8)	3650	NM_001289619	22793	Mm.282303	NM_011777	ENSMUSG00000029860	Zyx	9530098H06Rik|R75157	zyxin	protein-coding
mm_40422.1	chr5	53466077	53466110	+	1	NA	Intergenic	Intergenic	-89686	NM_001080928	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_139697.1	chr17	57445082	57445094	+	1	NA	exon (NM_010130, exon 15 of 22)	exon (NM_010130, exon 15 of 22)	86402	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_15946.1	chr2	165900783	165900793	+	1	NA	Intergenic	Intergenic	-15950	NM_001252587	228880	Mm.227598	NM_027230	ENSMUSG00000039671	Zmynd8	1110013E22Rik|2010005I16Rik|3632413B07Rik|AI316811|AL024039|Prkcbp1|RACK7	zinc finger, MYND-type containing 8	protein-coding
mm_78480.1	chr9	32695807	32695816	+	1	NA	promoter-TSS (NM_001038642)	promoter-TSS (NM_001038642)	-231	NM_011808	23871	Mm.292415	NM_011808	ENSMUSG00000032035	Ets1	AI196000|AI448617|D230050P06|Ets-1|Tpl1|vs	E26 avian leukemia oncogene 1, 5' domain	protein-coding
mm_23191.1	chr3	40959543	40959546	+	1	NA	intron (NM_001040399, intron 1 of 9)	B1_Mus2|SINE|Alu	8913	NM_001040399	214048	Mm.46782	NM_027663	ENSMUSG00000025762	Larp1b	1700108L22Rik|4933421B21Rik|AA690246|Larp2	La ribonucleoprotein domain family, member 1B	protein-coding
mm_113812.1	chr13	46638227	46638230	+	1	NA	intron (NM_026056, intron 9 of 12)	intron (NM_026056, intron 9 of 12)	-31294	NM_001033192	97863	Mm.275934	NM_001033192	ENSMUSG00000069237	Fam8a1	C78339	family with sequence similarity 8, member A1	protein-coding
mm_143556.1	chr17	74173881	74173902	-	1	NA	Intergenic	Intergenic	120972	NM_133771	76890	Mm.311874	NM_133771	ENSMUSG00000058704	Memo1	0610016J10Rik|D930048L02Rik	mediator of cell motility 1	protein-coding
mm_111332.1	chr12	86734215	86734226	-	1	NA	promoter-TSS (NM_001195767)	promoter-TSS (NM_001195767)	-149	NM_001195767	627607	Mm.341880	NM_001195767	ENSMUSG00000059114	Lrrc74a	EG627607|Gm6772|Lrrc74	leucine rich repeat containing 74A	protein-coding
mm_94199.1	chr11	3101487	3101499	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	-22528	NR_003517	236604	Mm.247625	NM_001004146		Pisd-ps1	-	phosphatidylserine decarboxylase, pseudogene 1	pseudo
mm_173280.1	chrY	1480666	1480666	+	1	NA	Intergenic	L1Md_T|LINE|L1	-20884	NM_148943	107868	Mm.347376	NM_148943	ENSMUSG00000069044	Usp9y	Dffry|Fafl2	ubiquitin specific peptidase 9, Y chromosome	protein-coding
mm_29000.1	chr3	101582134	101582152	-	1	NA	exon (NM_144900, exon 16 of 23)	exon (NM_144900, exon 16 of 23)	22564	NM_144900	11928	Mm.193670	NM_144900	ENSMUSG00000033161	Atp1a1	Atpa-1|BC010319	ATPase, Na+/K+ transporting, alpha 1 polypeptide	protein-coding
mm_72113.1	chr8	71668404	71668411	+	1	NA	intron (NM_001029873, intron 1 of 41)	intron (NM_001029873, intron 1 of 41)	3350	NM_001029873	382018	Mm.334606	NM_001029873	ENSMUSG00000034799	Unc13a	2410078G03Rik|Munc13-1	unc-13 homolog A (C. elegans)	protein-coding
mm_53159.1	chr6	125321224	125321237	+	1	NA	promoter-TSS (NM_011324)	promoter-TSS (NM_011324)	-110	NM_011324	20276	Mm.144114	NM_011324	ENSMUSG00000030340	Scnn1a	ENaC|SCNEA|Scnn1|mENaC	sodium channel, nonvoltage-gated 1 alpha	protein-coding
mm_118175.1	chr13	106936887	106936898	-	1	NA	promoter-TSS (NM_029665)	promoter-TSS (NM_029665)	23	NM_029665	76582	Mm.132208	NM_029665	ENSMUSG00000042590	Ipo11	1700081H05Rik|2510001A17Rik|AI314624|AW555235|E330021B14Rik|Ranbp11	importin 11	protein-coding
mm_22864.1	chr3	28729088	28729098	+	1	NA	TTS (NM_031197)	TTS (NM_031197)	31190	NM_031197	20526	Mm.18443	NM_031197	ENSMUSG00000027690	Slc2a2	AI266973|Glut-2|Glut2	solute carrier family 2 (facilitated glucose transporter), member 2	protein-coding
mm_98225.1	chr11	88055862	88055864	+	1	NA	Intergenic	Intergenic	8490	NM_173374	110809	Mm.391719	NM_173374	ENSMUSG00000018379	Srsf1	1110054N12Rik|5730507C05Rik|6330415C05Rik|AI482334|AW491331|Asf|Sf2|Sfrs1	serine/arginine-rich splicing factor 1	protein-coding
mm_76416.1	chr8	84966162	84966169	-	1	NA	promoter-TSS (NM_027187)	promoter-TSS (NM_027187)	-154	NM_027187	69724	Mm.182470	NM_027187	ENSMUSG00000052926	Rnaseh2a	2400006P09Rik|RNASEHI|RNHIA|RNHL	ribonuclease H2, large subunit	protein-coding
mm_162127.1	chrX	73064652	73064652	+	1	NA	promoter-TSS (NM_153169)	promoter-TSS (NM_153169)	-135	NM_153169	245468	Mm.256249	NM_153169	ENSMUSG00000046287	Pnma3	-	paraneoplastic antigen MA3	protein-coding
mm_28244.1	chr3	88498562	88498646	-	1	NA	intron (NM_001002011, intron 1 of 11)	intron (NM_001002011, intron 1 of 11)	4748	NM_001111102	16905	Mm.243014	NM_019390	ENSMUSG00000028063	Lmna	Dhe	lamin A	protein-coding
mm_162276.1	chr1	13063066	13063067	+	1	NA	Intergenic	Intergenic	64097	NM_001081209	383491	Mm.309380	NM_001081209	ENSMUSG00000042414	Prdm14	-	PR domain containing 14	protein-coding
mm_38691.1	chr4	145212828	145212851	-	1	NA	3' UTR (NM_011610, exon 10 of 10)	3' UTR (NM_011610, exon 10 of 10)	-17834	NM_001276465	230895	Mm.240310	NM_001033190	ENSMUSG00000020220	Vps13d	-	vacuolar protein sorting 13D	protein-coding
mm_109573.1	chr12	112110613	112110619	+	1	NA	intron (NM_001081169, intron 1 of 14)	intron (NM_001081169, intron 1 of 14)	-1307	NR_049197	100885836		NR_049197	ENSMUSG00000106228	Mir3073b	mir-3073b|mmu-mir-3073b	microRNA 3073b	ncRNA
mm_103109.1	chr11	69980469	69980575	-	1	NA	promoter-TSS (NM_026017)	promoter-TSS (NM_026017)	-192	NM_001253700	54351	Mm.13430	NM_018740	ENSMUSG00000018565	Elp5	Derp6|Rai12	elongator acetyltransferase complex subunit 5	protein-coding
mm_89956.1	chr10	111295055	111295062	+	1	NA	3' UTR (NM_001003717, exon 23 of 23)	3' UTR (NM_001003717, exon 23 of 23)	-3621	NM_027914	71769	Mm.45256	NM_027914	ENSMUSG00000035759	Bbs10	1300007O09Rik|AI452285	Bardet-Biedl syndrome 10 (human)	protein-coding
mm_27156.1	chr3	33083074	33083076	-	1	NA	promoter-TSS (NM_021483)	promoter-TSS (NM_021483)	-15	NM_001289505	58869	Mm.151332	NM_021483	ENSMUSG00000027674	Pex5l	1700016J08Rik|PXR2|Pex2|TRIP8b|pex5Rp	peroxisomal biogenesis factor 5-like	protein-coding
mm_128514.1	chr15	53345768	53345784	-	1	NA	5' UTR (NM_010162, exon 1 of 11)	5' UTR (NM_010162, exon 1 of 11)	407	NM_010162	14042	Mm.309395	NM_010162	ENSMUSG00000061731	Ext1	AA409028	exostoses (multiple) 1	protein-coding
mm_7069.1	chr1	87668158	87668159	-	1	NA	intron (NM_010566, intron 4 of 26)	intron (NM_010566, intron 4 of 26)	47846	NM_001110193	16331	Mm.15105	NM_010566	ENSMUSG00000026288	Inpp5d	SHIP|SHIP-1|SHIP1|SIP-145|p150Ship|s-SHIP	inositol polyphosphate-5-phosphatase D	protein-coding
mm_19436.1	chr2	91963705	91963713	-	1	NA	promoter-TSS (NM_138306)	promoter-TSS (NM_138306)	-146	NM_138306	104418	Mm.314923	NM_138306	ENSMUSG00000040479	Dgkz	E130307B02Rik|ENSMUSG00000075035|F730209L11Rik|mDGK[z]	diacylglycerol kinase zeta	protein-coding
mm_49095.1	chr6	7844634	7844677	+	1	NA	promoter-TSS (NM_052993)	promoter-TSS (NM_052993)	-569	NM_052993	94192	Mm.102752	NM_052993	ENSMUSG00000042460	C1galt1	2210410E06Rik|AV284120|T-synthase	core 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase, 1	protein-coding
mm_75676.1	chr8	67950340	67950388	-	1	NA	intron (NM_177698, intron 3 of 14)	intron (NM_177698, intron 3 of 14)	24210	NM_177698	234353	Mm.32525	NM_027626	ENSMUSG00000030465	Psd3	4931420C21Rik|AI661273|BC003498|D430018P08|EFA6D	pleckstrin and Sec7 domain containing 3	protein-coding
mm_62224.1	chr7	98491950	98491961	+	1	NA	Intergenic	Intergenic	-2267	NM_001113379	434215	Mm.323057	NM_001113379	ENSMUSG00000090958	Lrrc32	AI426318|D11S833Eh|D7H11S833E|EG434215|Garp	leucine rich repeat containing 32	protein-coding
mm_82188.1	chr9	123938251	123938258	+	1	NA	Intergenic	Intergenic	30438	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_58917.1	chr7	17713234	17713262	+	1	NA	promoter-TSS (NM_028480)	promoter-TSS (NM_028480)	-4	NM_028480	73250	Mm.244138	NM_028480	ENSMUSG00000008789	Ceacam5	1600029H12Rik|Psg30	carcinoembryonic antigen-related cell adhesion molecule 5	protein-coding
mm_78250.1	chr9	21723605	21723615	+	1	NA	promoter-TSS (NM_001252659)	promoter-TSS (NM_001252659)	34	NM_010700	16835	Mm.3213	NM_010700	ENSMUSG00000032193	Ldlr	Hlb301	low density lipoprotein receptor	protein-coding
mm_161379.1	chr14	70545589	70545589	+	1	NA	5' UTR (NM_180588, exon 1 of 8)	5' UTR (NM_180588, exon 1 of 8)	338	NM_180588	72549	Mm.46742	NM_180588	ENSMUSG00000033589	Reep4	2700029E10Rik	receptor accessory protein 4	protein-coding
mm_64720.1	chr7	4658556	4658605	-	1	NA	5' UTR (NM_172894, exon 1 of 24)	5' UTR (NM_172894, exon 1 of 24)	370	NM_172894	243819	Mm.258670	NM_172894	ENSMUSG00000052296	Ppp6r1	2010309P17Rik|AI836219|B430201G11Rik|D030074N20Rik|Pp6r1|Saps1|mKIAA1115	protein phosphatase 6, regulatory subunit 1	protein-coding
mm_106850.1	chr12	8008281	8008290	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	30608	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_164627.1	chr17	31681262	31681286	+	1	NA	3' UTR (NM_001278570, exon 3 of 3)	3' UTR (NM_001278570, exon 3 of 3)	3343	NM_001278570	12954	Mm.1228	NM_013501	ENSMUSG00000024041	Cryaa	Acry-1|Crya-1|Crya1|DAcry-1|lop18	crystallin, alpha A	protein-coding
mm_38793.1	chr4	148130679	148130706	-	1	NA	promoter-TSS (NM_027426)	promoter-TSS (NM_027426)	6	NM_027426	70433	Mm.275288	NM_027426	ENSMUSG00000029005	Draxin	2610109H07Rik|neucrin	dorsal inhibitory axon guidance protein	protein-coding
mm_167046.1	chr7	81313895	81313897	+	1	NA	intron (NM_008803, intron 11 of 21)	Lx4A|LINE|L1	31338	NM_009092	20068	Mm.42767	NM_009092	ENSMUSG00000061787	Rps17	-	ribosomal protein S17	protein-coding
mm_14847.1	chr2	148395854	148395882	+	1	NA	exon (NM_009219, exon 1 of 1)	exon (NM_009219, exon 1 of 1)	491	NM_009219	20608	Mm.35324	NM_009219	ENSMUSG00000037014	Sstr4	Smstr4|sst4	somatostatin receptor 4	protein-coding
mm_23357.1	chr3	55140034	55140049	+	1	NA	promoter-TSS (NM_001290141)	promoter-TSS (NM_001290141)	3	NM_177203	320604	Mm.213909	NM_177203	ENSMUSG00000048655	Ccdc169	A730037C10Rik	coiled-coil domain containing 169	protein-coding
mm_54805.1	chr6	41704264	41704323	-	1	NA	promoter-TSS (NM_032540)	promoter-TSS (NM_032540)	32	NM_032540	23925	Mm.19958	NM_032540	ENSMUSG00000029866	Kel	CD238|Ece3	Kell blood group	protein-coding
mm_43997.1	chr5	146833014	146833024	+	1	NA	5' UTR (NM_019647, exon 1 of 6)	5' UTR (NM_019647, exon 1 of 6)	129	NM_019647	19933	Mm.316592	NM_019647	ENSMUSG00000041453	Rpl21	8430440E03Rik|L21	ribosomal protein L21	protein-coding
mm_49903.1	chr6	38950575	38950586	+	1	NA	intron (NM_011539, intron 2 of 12)	intron (NM_011539, intron 2 of 12)	31594	NM_011539	21391	Mm.4054	NM_011539	ENSMUSG00000029925	Tbxas1	CYP5|CYP5A1|THAS|TS|TXAS|TXS	thromboxane A synthase 1, platelet	protein-coding
mm_132250.1	chr16	32751432	32751443	+	1	NA	exon (NM_080457, exon 2 of 27)	exon (NM_080457, exon 2 of 27)	15551	NM_080457	140474	Mm.214599	NM_080457	ENSMUSG00000079620	Muc4	4933405I11Rik|Asgp	mucin 4	protein-coding
mm_85051.1	chr9	90107033	90107035	-	1	NA	intron (NM_001039147, intron 3 of 12)	intron (NM_001039147, intron 3 of 12)	7786	NM_001039147	21761	Mm.426209	NM_024431	ENSMUSG00000062270	Morf4l1	MORFRG15|MRG15|TEG-189|Tex189|mKIAA4002	mortality factor 4 like 1	protein-coding
mm_26655.1	chr3	154597160	154597172	+	1	NA	promoter-TSS (NM_172474)	promoter-TSS (NM_172474)	-68	NM_172474	209584	Mm.347513	NM_172474	ENSMUSG00000047583	Tyw3	5230400J09Rik	tRNA-yW synthesizing protein 3 homolog (S. cerevisiae)	protein-coding
mm_95516.1	chr11	52098816	52098842	+	1	NA	promoter-TSS (NM_019411)	promoter-TSS (NM_019411)	5	NM_019411	19052	Mm.260288	NM_019411	ENSMUSG00000020349	Ppp2ca	PP2A|R75353	protein phosphatase 2 (formerly 2A), catalytic subunit, alpha isoform	protein-coding
mm_9786.1	chr1	181234420	181234459	-	1	NA	Intergenic	Intergenic	-22461	NM_145514	226757	Mm.289082	NM_145514	ENSMUSG00000038733	Wdr26	1600024A01Rik|AA693241|AI447817|AU044014|C77982|Gid7	WD repeat domain 26	protein-coding
mm_123539.1	chr14	66815464	66815515	-	1	NA	exon (NM_009955, exon 9 of 14)	exon (NM_009955, exon 9 of 14)	53111	NM_009955	12934	Mm.352648	NM_009955	ENSMUSG00000022048	Dpysl2	AI851130|Crmp2|DRP2|Musunc33|TOAD-64|Ulip2	dihydropyrimidinase-like 2	protein-coding
mm_162790.1	chr10	75517959	75517977	-	1	NA	promoter-TSS (NM_026095)	promoter-TSS (NM_026095)	4	NM_001347201	68778	Mm.29382	NM_175133	ENSMUSG00000033416	Gucd1	1110038D17Rik	guanylyl cyclase domain containing 1	protein-coding
mm_139360.1	chr17	50528980	50528999	+	1	NA	intron (NM_013880, intron 1 of 5)	ID4|SINE|ID	19442	NM_013880	224860	Mm.217362	NM_013880	ENSMUSG00000038910	Plcl2	PLC-L2|PRIP-2|Plce2|mKIAA1092	phospholipase C-like 2	protein-coding
mm_170923.1	chr2	37358618	37358621	-	1	NA	intron (NM_026176, intron 1 of 3)	intron (NM_026176, intron 1 of 3)	713	NM_026176	67466	Mm.30709	NM_026176	ENSMUSG00000009030	Pdcl	1200011E13Rik|AW108059|PhLP1	phosducin-like	protein-coding
mm_92908.1	chr10	83534067	83534127	-	1	NA	promoter-TSS (NM_153543)	promoter-TSS (NM_153543)	43	NM_153543	216188	Mm.263138	NM_153543	ENSMUSG00000020256	Aldh1l2	D330038I09Rik|mtFDH	aldehyde dehydrogenase 1 family, member L2	protein-coding
mm_78350.1	chr9	25308032	25308037	+	1	NA	3' UTR (NM_001205367, exon 13 of 13)	3' UTR (NM_001205367, exon 13 of 13)	55595	NM_001205367	235072	Mm.270259	NM_009859	ENSMUSG00000001833	Sept7	Cdc10|E430034N22	septin 7	protein-coding
mm_47416.1	chr5	123139970	123139980	-	1	NA	Intergenic	Intergenic	-2218	NM_001040398	208043	Mm.250391	NM_177581	ENSMUSG00000038384	Setd1b	AA516740|BC035291|KMT2G|mKIAA1076	SET domain containing 1B	protein-coding
mm_52311.1	chr6	108828634	108828721	+	1	NA	promoter-TSS (NM_138677)	promoter-TSS (NM_138677)	36	NM_138677	192193	Mm.21596	NM_138677	ENSMUSG00000030104	Edem1	A130059K23Rik|EDEM|mKIAA0212	ER degradation enhancer, mannosidase alpha-like 1	protein-coding
mm_95608.1	chr11	53433348	53433357	+	1	NA	promoter-TSS (NM_008110)	promoter-TSS (NM_008110)	66	NM_008110	14566	Mm.9714	NM_008110	ENSMUSG00000018238	Gdf9	Gdf-9	growth differentiation factor 9	protein-coding
mm_70938.1	chr8	25910216	25910219	+	1	NA	intron (NM_008432, intron 19 of 26)	intron (NM_008432, intron 19 of 26)	60594	NM_008432	16532	Mm.289679	NM_008432	ENSMUSG00000031576	Kcnu1	Kcnma3|Slo3|mSlo3	potassium channel, subfamily U, member 1	protein-coding
mm_119137.1	chr14	31208310	31208325	+	1	NA	promoter-TSS (NM_009393)	promoter-TSS (NM_009393)	5	NM_009393	21924	Mm.439921	NM_009393	ENSMUSG00000091898	Tnnc1	AI874626|TnC|cTnC|cTnI|tncc	troponin C, cardiac/slow skeletal	protein-coding
mm_169016.1	chr13	109163838	109163840	+	1	NA	intron (NM_011056, intron 3 of 16)	intron (NM_011056, intron 3 of 16)	-160905	NR_030644	100124489		NR_030644	ENSMUSG00000076946	Mir582	Mirn582|mir-582|mmu-mir-582	microRNA 582	ncRNA
mm_23529.1	chr3	60626734	60626746	+	1	NA	3' UTR (NM_001253711, exon 8 of 8)	3' UTR (NM_001253711, exon 8 of 8)	125561	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_93079.1	chr10	89481012	89481016	-	1	NA	intron (NM_009108, intron 3 of 8)	intron (NM_009108, intron 3 of 8)	25644	NM_001163700	20186	Mm.3095	NM_009108	ENSMUSG00000047638	Nr1h4	AI957360|Fxr|HRR1|RIP14|Rxrip14	nuclear receptor subfamily 1, group H, member 4	protein-coding
mm_102180.1	chr11	54028712	54028721	-	1	NA	promoter-TSS (NM_001330304)	promoter-TSS (NM_001330304)	-612	NM_001330304	30805	Mm.274590	NM_019687	ENSMUSG00000020334	Slc22a4	Octn1	solute carrier family 22 (organic cation transporter), member 4	protein-coding
mm_73669.1	chr8	111337839	111337900	+	1	NA	5' UTR (NM_001310613, exon 1 of 11)	5' UTR (NM_001310613, exon 1 of 11)	336	NM_001310613	74568	Mm.207971	NM_029005	ENSMUSG00000012519	Mlkl	9130019I15Rik	mixed lineage kinase domain-like	protein-coding
mm_10442.1	chr2	14261177	14261226	+	1	NA	TTS (NR_030609)	TTS (NR_030609)	198	NR_030609	100124488		NR_030609	ENSMUSG00000077897	Mir511	Mirn511|mir-511|mmu-mir-511	microRNA 511	ncRNA
mm_148038.1	chr18	70244561	70244565	-	1	NA	promoter-TSS (NM_029346)	promoter-TSS (NM_029346)	21	NM_029346	75577	Mm.58214	NM_029346	ENSMUSG00000024512	Dynap	2310002L13Rik	dynactin associated protein	protein-coding
mm_37321.1	chr4	119383829	119383839	-	1	NA	promoter-TSS (NM_028506)	promoter-TSS (NM_028506)	0	NM_028506	73332	Mm.425204	NM_028506	ENSMUSG00000028637	Ccdc30	1700001O02Rik|1700041C02Rik|1700111D19Rik|4930445I03Rik	coiled-coil domain containing 30	protein-coding
mm_52494.1	chr6	114688771	114688780	+	1	NA	intron (NM_001253718, intron 8 of 19)	intron (NM_001253718, intron 8 of 19)	45678	NM_001253717	74244	Mm.275332	NM_028835	ENSMUSG00000030314	Atg7	1810013K23Rik|Agp7|Apg7l|Atg7l|Gm21553	autophagy related 7	protein-coding
mm_87646.1	chr10	58394382	58394395	+	1	NA	promoter-TSS (NM_001193303)	promoter-TSS (NM_001193303)	15	NM_001346676	110829	Mm.57734	NM_026148	ENSMUSG00000019920	Lims1	2310016J22Rik|4921524A02Rik|AI507642|AU021743|AW551584|C430041B13Rik|Lims1l|PINCH|PINCH1	LIM and senescent cell antigen-like domains 1	protein-coding
mm_60929.1	chr7	46850202	46850215	+	1	NA	exon (NM_001136069, exon 4 of 8)	exon (NM_001136069, exon 4 of 8)	3126	NM_001136069	16828	Mm.29324	NM_010699	ENSMUSG00000063229	Ldha	Ldh1|Ldhm|l7R2	lactate dehydrogenase A	protein-coding
mm_131691.1	chr16	20684241	20684242	+	1	NA	promoter-TSS (NR_028530)	promoter-TSS (NR_028530)	-15	NR_028530	100217430		NR_028530		Snord66	MBII-142|snoRNA142	small nucleolar RNA, C/D box 66	snoRNA
mm_145259.1	chr18	52559226	52559245	+	1	NA	Intergenic	Intergenic	-29368	NM_001286182	16948	Mm.172	NM_010728	ENSMUSG00000024529	Lox	AI893619|TSC-160|rrg	lysyl oxidase	protein-coding
mm_89450.1	chr10	93145343	93145353	+	1	NA	Intergenic	Charlie24|DNA|hAT-Charlie	-15528	NM_146239	237459	Mm.217404	NM_146239	ENSMUSG00000020015	Cdk17	6430598J10Rik|Pctk2	cyclin-dependent kinase 17	protein-coding
mm_109305.1	chr12	109560684	109560708	+	1	NA	non-coding (NR_003633, exon 5 of 5)	non-coding (NR_003633, exon 5 of 5)	-2996	NR_030427	791079		NR_030427	ENSMUSG00000076451	Mir770	Mirn770|mir-770|mmu-mir-770	microRNA 770	ncRNA
mm_103145.1	chr11	70239795	70239860	-	1	NA	promoter-TSS (NM_173742)	promoter-TSS (NM_173742)	25	NM_173742	52898	Mm.29852	NM_173742	ENSMUSG00000040904	Rnasek	2310033H11Rik|AA571397|D11Bwg0434e	ribonuclease, RNase K	protein-coding
mm_55109.1	chr6	50382832	50382847	-	1	NA	promoter-TSS (NM_027881)	promoter-TSS (NM_027881)	-2	NM_027881	71720	Mm.44153	NM_027881	ENSMUSG00000029822	Osbpl3	1200014M06Rik|6720421I08Rik|A530055M08|ORP-3|ORP3|OSBP3	oxysterol binding protein-like 3	protein-coding
mm_96465.1	chr11	67613786	67613797	+	1	NA	intron (NM_001109657, intron 2 of 13)	ORR1F|LTR|ERVL-MaLR	17236	NM_001277079	14457	Mm.40338	NM_008088	ENSMUSG00000033066	Gas7	AW124766|B230343A10Rik|Gas7-cb	growth arrest specific 7	protein-coding
mm_153633.1	chr19	44029089	44029098	-	1	NA	exon (NM_001167905, exon 1 of 8)	exon (NM_001167905, exon 1 of 8)	154	NM_001001446	226143	Mm.329866	NM_001001446	ENSMUSG00000025197	Cyp2c44	AW107714|BC034834|b2b386Clo	cytochrome P450, family 2, subfamily c, polypeptide 44	protein-coding
mm_121132.1	chr14	101869419	101869432	+	1	NA	intron (NM_001347628, intron 1 of 26)	intron (NM_001347628, intron 1 of 26)	28802	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_67439.1	chr7	80387384	80387394	-	1	NA	intron (NM_010194, intron 1 of 18)	intron (NM_010194, intron 1 of 18)	557	NM_010194	14159	Mm.48757	NM_010194	ENSMUSG00000053158	Fes	AI586313|BB137047|FPS|c-fes	feline sarcoma oncogene	protein-coding
mm_150509.1	chr19	39023958	39023969	+	1	NA	intron (NM_028089, intron 4 of 8)	Lx9|LINE|L1	16944	NM_028089	72082	Mm.142581	NM_028089	ENSMUSG00000025002	Cyp2c55	2010318C06Rik	cytochrome P450, family 2, subfamily c, polypeptide 55	protein-coding
mm_169188.1	chr13	66027567	66027570	+	1	NA	Intergenic	Intergenic	-85885	NM_001177832	628709	Mm.390595	NM_001177832	ENSMUSG00000095909	Gm10324	ENSMUSG00000071302	predicted gene 10324	protein-coding
mm_13871.1	chr2	119872481	119872491	+	1	NA	Intergenic	Intergenic	-24742	NM_001164274	29808	Mm.87532	NM_013720	ENSMUSG00000033943	Mga	AV312082|C130042M01Rik|C80739|D030062C11Rik|Mad5	MAX gene associated	protein-coding
mm_37764.1	chr4	129696759	129696804	-	1	NA	promoter-TSS (NM_199305)	promoter-TSS (NM_199305)	57	NM_199305	230770	Mm.257157	NM_199305	ENSMUSG00000053730	Tmem39b	6330509E05Rik|BC037095	transmembrane protein 39b	protein-coding
mm_39913.1	chr5	31452459	31452503	+	1	NA	promoter-TSS (NM_172993)	promoter-TSS (NM_172993)	45	NM_172993	269639	Mm.259127	NM_172993	ENSMUSG00000062761	Zfp512	2500002M11Rik|AI450173|D230008H22|Znf512	zinc finger protein 512	protein-coding
mm_30676.1	chr4	11169800	11169808	+	1	NA	exon (NM_021897, exon 4 of 4)	exon (NM_021897, exon 4 of 4)	13363	NM_021897	60599	Mm.393018	NM_021897	ENSMUSG00000028211	Trp53inp1	2700057G22Rik|SIP|SIP18|SIP27|Stinp|Teap	transformation related protein 53 inducible nuclear protein 1	protein-coding
mm_159745.1	chr5	72948574	72948574	+	1	NA	exon (NM_001113423, exon 3 of 8)	exon (NM_001113423, exon 3 of 8)	34212	NM_153567	75991	Mm.121285	NM_153567	ENSMUSG00000036087	Slain2	5033405K12Rik|8030444K12Rik|AI596370	SLAIN motif family, member 2	protein-coding
mm_138671.1	chr17	35879954	35879962	+	1	NA	exon (NM_026987, exon 1 of 20)	exon (NM_026987, exon 1 of 20)	180	NM_026987	69192	Mm.390986	NM_026987	ENSMUSG00000024422	Dhx16	2410006N22Rik|DBP2|Ddx16|mKIAA0577	DEAH (Asp-Glu-Ala-His) box polypeptide 16	protein-coding
mm_152871.1	chr19	24350757	24350758	-	1	NA	intron (NM_008846, intron 11 of 14)	intron (NM_008846, intron 11 of 14)	-70171	NM_008044	14297	Mm.7319	NM_008044	ENSMUSG00000059363	Fxn	FA|FARR|Frda|X25	frataxin	protein-coding
mm_130967.1	chr15	103319607	103319612	-	1	NA	intron (NM_013866, intron 3 of 7)	B1F|SINE|Alu	-9171	NM_030720	80910	Mm.160369	NM_030720	ENSMUSG00000063234	Gpr84	EX33	G protein-coupled receptor 84	protein-coding
mm_18593.1	chr2	66686181	66686189	-	1	NA	intron (NM_009135, intron 19 of 24)	Lx8|LINE|L1	-51223	NM_001290675	20274	Mm.440889	NM_018852	ENSMUSG00000075316	Scn9a	Nav1.7|PN1|mKIAA4197	sodium channel, voltage-gated, type IX, alpha	protein-coding
mm_102557.1	chr11	61453517	61453553	-	1	NA	intron (NM_009548, intron 2 of 14)	intron (NM_009548, intron 2 of 14)	457	NM_009548	22671	Mm.89201	NM_009548	ENSMUSG00000010086	Rnf112	ZNF179|Zfp179|bfp|neurolastin	ring finger protein 112	protein-coding
mm_155447.1	chrX	73495113	73495132	+	1	NA	3' UTR (NM_007542, exon 8 of 8)	3' UTR (NM_007542, exon 8 of 8)	-7964	NM_001310537	320707	Mm.210095	NM_177236	ENSMUSG00000031376	Atp2b3	6430519O13Rik|Pmca3	ATPase, Ca++ transporting, plasma membrane 3	protein-coding
mm_2939.1	chr1	132302894	132302899	+	1	NA	intron (NM_144810, intron 2 of 4)	AT_rich|Low_complexity|Low_complexity	4270	NM_144810	213417	Mm.39723	NM_144810	ENSMUSG00000042115	Klhdc8a	A630065K24Rik	kelch domain containing 8A	protein-coding
mm_88910.1	chr10	81179654	81179674	+	1	NA	TTS (NR_028549)	TTS (NR_028549)	703	NR_028549	100217454		NR_028549	ENSMUSG00000064441	Snord37	MBII-376	small nucleolar RNA, C/D box 37	snoRNA
mm_52011.1	chr6	93452323	93452325	+	1	NA	Intergenic	Intergenic	460639	NR_104594	14924	Mm.217216	NM_010367	ENSMUSG00000045095	Magi1	AIP3|BAP1|Baiap1|Gukmi1|MAGI1c|Magi-1|TNRC19|WWP3|mKIAA4129	membrane associated guanylate kinase, WW and PDZ domain containing 1	protein-coding
mm_83800.1	chr9	53157329	53157340	-	1	NA	intron (NM_029936, intron 14 of 17)	intron (NM_029936, intron 14 of 17)	90778	NM_029936	77591	Mm.133560	NM_029936	ENSMUSG00000053289	Ddx10	4632415A01Rik|AI646054	DEAD (Asp-Glu-Ala-Asp) box polypeptide 10	protein-coding
mm_168845.1	chr12	23800859	23800863	-	1	NA	Intergenic	CpG	296408	NM_001256489	66808	Mm.379124	NM_001256489	ENSMUSG00000073158	9030624G23Rik	-	RIKEN cDNA 9030624G23 gene	protein-coding
mm_17974.1	chr2	37656527	37656529	-	1	NA	Intergenic	L2|LINE|L2	-9243	NM_009261	20744	Mm.237095	NM_009261	ENSMUSG00000026915	Strbp	6430510M02Rik|AI852513|C230082I21Rik|C86322|Spnr	spermatid perinuclear RNA binding protein	protein-coding
mm_107763.1	chr12	59095572	59095633	+	1	NA	promoter-TSS (NM_177321)	promoter-TSS (NM_177321)	-198	NM_001329047	338320	Mm.213215	NM_146034	ENSMUSG00000021000	Mia2	Ctage5|D12Bwg0579e|Mea6|Mgea|Mgea6	melanoma inhibitory activity 2	protein-coding
mm_46118.1	chr5	92435076	92435103	-	1	NA	5' UTR (NM_183392, exon 1 of 12)	5' UTR (NM_183392, exon 1 of 12)	110	NM_183392	269113	Mm.275289	NM_183392	ENSMUSG00000034826	Nup54	3110079L04Rik|54kDa	nucleoporin 54	protein-coding
mm_149727.1	chr19	21792817	21792841	+	1	NA	exon (NM_031997, exon 3 of 25)	exon (NM_031997, exon 3 of 25)	14489	NM_031997	83921	Mm.329776	NM_031997	ENSMUSG00000024754	Tmem2	-	transmembrane protein 2	protein-coding
mm_58982.1	chr7	19076243	19076273	+	1	NA	promoter-TSS (NM_010058)	promoter-TSS (NM_010058)	58	NM_010058	13401	Mm.2852	NM_010058	ENSMUSG00000030410	Dmwd	DMR-N9|Dm9	dystrophia myotonica-containing WD repeat motif	protein-coding
mm_115112.1	chr13	103919626	103919652	+	1	NA	intron (NM_001005868, intron 1 of 26)	intron (NM_001005868, intron 1 of 26)	947	NM_001289473	59079	Mm.277354	NM_021563	ENSMUSG00000021709	Erbin	1700028E05Rik|Erbb2ip|mKIAA1225	Erbb2 interacting protein	protein-coding
mm_143020.1	chr17	56512450	56512465	-	1	NA	promoter-TSS (NM_011483)	promoter-TSS (NM_011483)	26	NM_011483	20834	Mm.76862	NM_011483	ENSMUSG00000044526	Znrf4	1700094M01Rik|Ssrzf1|spzn	zinc and ring finger 4	protein-coding
mm_23782.1	chr3	79336623	79336646	+	1	NA	Intergenic	Intergenic	-8742	NM_001142953	100233207	Mm.373801	NM_001142953	ENSMUSG00000091685	Gm17359	-	predicted gene, 17359	protein-coding
mm_119412.1	chr14	45038178	45038179	+	1	NA	Intergenic	L1MB5|LINE|L1	50067	NM_008964	19217	Mm.4630	NM_008964	ENSMUSG00000037759	Ptger2	EP2|Ptgerep2	prostaglandin E receptor 2 (subtype EP2)	protein-coding
mm_116197.1	chr13	31681456	31681482	-	1	NA	Intergenic	Intergenic	55653	NM_010225	14238	Mm.125548	NM_010225	ENSMUSG00000038402	Foxf2	FREAC2|Fkh20|LUN	forkhead box F2	protein-coding
mm_79921.1	chr9	65587188	65587221	+	1	NA	promoter-TSS (NM_172453)	promoter-TSS (NM_172453)	-1	NM_172453	208084	Mm.211032	NM_172453	ENSMUSG00000041064	Pif1	4631410M14|AI449441	PIF1 5'-to-3' DNA helicase	protein-coding
mm_18400.1	chr2	60275602	60275603	-	1	NA	intron (NM_001290660, intron 1 of 5)	intron (NM_001290660, intron 1 of 5)	8882	NM_025422	66205	Mm.227281	NM_025422	ENSMUSG00000060703	Cd302	1110055L24Rik|AI159627	CD302 antigen	protein-coding
mm_102395.1	chr11	59002183	59002193	-	1	NA	intron (NM_001171512, intron 89 of 103)	intron (NM_001171512, intron 89 of 103)	24095	NM_053168	94091	Mm.248049	NM_053168	ENSMUSG00000020455	Trim11	-	tripartite motif-containing 11	protein-coding
mm_151214.1	chr19	53633988	53634005	+	1	NA	exon (NM_007790, exon 19 of 29)	exon (NM_007790, exon 19 of 29)	33600	NM_007790	13006	Mm.14910	NM_007790	ENSMUSG00000024974	Smc3	Bamacan|Cspg6|HCAP|Mmip1|SMC-3|SmcD	structural maintenance of chromosomes 3	protein-coding
mm_124588.1	chr15	3273160	3273193	+	1	NA	intron (NM_009155, intron 1 of 4)	B1_Mur2|SINE|Alu	2199	NM_009155	20363	Mm.392203	NM_009155	ENSMUSG00000064373	Selenop	AU018766|D15Ucla1|Se-P|Sepp1|selp	selenoprotein P	protein-coding
mm_60505.1	chr7	44479503	44479505	+	1	NA	Intergenic	L1MC4|LINE|L1	-5013	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_64323.1	chr7	141949876	141949898	+	1	NA	5' UTR (NM_029426, exon 1 of 19)	5' UTR (NM_029426, exon 1 of 19)	136	NM_001009929	75770	Mm.274868	NM_029426	ENSMUSG00000053046	Brsk2	4833424K13Rik|SAD-A|SADA	BR serine/threonine kinase 2	protein-coding
mm_115636.1	chr13	12244086	12244112	-	1	NA	intron (NM_001081128, intron 7 of 32)	intron (NM_001081128, intron 7 of 32)	14014	NM_001081128	238505	Mm.40335	NM_001081128	ENSMUSG00000021311	Mtr	AI894170|D830038K18Rik|MS	5-methyltetrahydrofolate-homocysteine methyltransferase	protein-coding
mm_12469.1	chr2	71421663	71421682	+	1	NA	exon (NM_026115, exon 8 of 11)	exon (NM_026115, exon 8 of 11)	7196	NR_039557	100628577		NR_039557	ENSMUSG00000093061	Mir5098	mmu-mir-5098|mu-mir-5098	microRNA 5098	ncRNA
mm_152185.1	chr19	7431019	7431037	-	1	NA	exon (NM_053076, exon 5 of 7)	exon (NM_053076, exon 5 of 7)	8455	NR_105957	102466781		NR_105957	ENSMUSG00000098293	Mir6991	Gm27966|mmu-mir-6991	microRNA 6991	ncRNA
mm_34291.1	chr4	141573266	141573288	+	1	NA	Intergenic	Intergenic	26647	NM_001163256	74202	Mm.490327	NM_133754	ENSMUSG00000006219	Fblim1	2410043F08Rik|Cal|Fblp1|Gt10|migfilin|migfilin(s)	filamin binding LIM protein 1	protein-coding
mm_162963.1	chr11	7199821	7199828	+	1	NA	exon (NM_008341, exon 2 of 4)	exon (NM_008341, exon 2 of 4)	2037	NM_008341	16006	Mm.21300	NM_008341	ENSMUSG00000020429	Igfbp1	-	insulin-like growth factor binding protein 1	protein-coding
mm_93005.1	chr10	87008016	87008031	-	1	NA	promoter-TSS (NM_138673)	promoter-TSS (NM_138673)	-81	NM_138673	192188	Mm.279611	NM_138673	ENSMUSG00000035459	Stab2	FEEL-2|FELL|MFEEL-2|STAB-2	stabilin 2	protein-coding
mm_24943.1	chr3	96596614	96596626	+	1	NA	promoter-TSS (NM_001024851)	promoter-TSS (NM_001024851)	-16	NM_001024851	545554	Mm.267664	NM_001024851	ENSMUSG00000049097	Ankrd34a	AW060394|Ankrd34	ankyrin repeat domain 34A	protein-coding
mm_156353.1	chrX	139334154	139334162	+	1	NA	exon (NM_011635, exon 1 of 3)	exon (NM_011635, exon 1 of 3)	475	NM_011635	22037	Mm.1297	NM_011635	ENSMUSG00000051257	Trap1a	Tra-P1A	tumor rejection antigen P1A	protein-coding
mm_74063.1	chr8	122376901	122376929	+	1	NA	intron (NM_001029994, intron 1 of 17)	CpG	299	NM_001029993	76014	Mm.241489	NM_001029993	ENSMUSG00000017478	Zc3h18	1190001B23Rik|5830416A07Rik|Nhn1	zinc finger CCCH-type containing 18	protein-coding
mm_104399.1	chr11	94507338	94507345	-	1	NA	intron (NM_170671, intron 12 of 18)	intron (NM_170671, intron 12 of 18)	-7367	NM_027984	71889	Mm.248620	NM_027984	ENSMUSG00000010080	Epn3	2310022G12Rik	epsin 3	protein-coding
mm_64780.1	chr7	5038414	5038426	-	1	NA	promoter-TSS (NM_001039532)	promoter-TSS (NM_001039532)	26	NM_001039532	654801	Mm.333548	NM_001039532	ENSMUSG00000043290	Zfp784	C730049F21Rik|Znf784	zinc finger protein 784	protein-coding
mm_161548.1	chr16	9992486	9992486	-	1	NA	promoter-TSS (NM_008170)	promoter-TSS (NM_008170)	47	NM_008170	14811	Mm.2953	NM_008170	ENSMUSG00000059003	Grin2a	GluN2A|NMDAR2A|NR2A	glutamate receptor, ionotropic, NMDA2A (epsilon 1)	protein-coding
mm_18489.1	chr2	62602899	62602909	-	1	NA	intron (NM_001164477, intron 11 of 14)	intron (NM_001164477, intron 11 of 14)	-28883	NM_007986	14089	Mm.41816	NM_007986	ENSMUSG00000000392	Fap	SIMP	fibroblast activation protein	protein-coding
mm_31693.1	chr4	62388595	62388624	+	1	NA	exon (NM_175090, exon 5 of 5)	exon (NM_175090, exon 5 of 5)	20014	NM_139291	66440	Mm.109930	NM_139291	ENSMUSG00000066149	Cdc26	2010012C09Rik	cell division cycle 26	protein-coding
mm_58784.1	chr7	16116720	16116740	+	1	NA	3' UTR (NM_025898, exon 11 of 11)	3' UTR (NM_025898, exon 11 of 11)	-3146	NM_133727	70394	Mm.41101	NM_133727	ENSMUSG00000006021	Kptn	2310042D10Rik|2E4|C030013F01Rik	kaptin	protein-coding
mm_166089.1	chr4	139460262	139460279	+	1	NA	exon (NM_001160319, exon 78 of 106)	exon (NM_001160319, exon 78 of 106)	-70278	NM_183148	212632	Mm.30464	NM_183148	ENSMUSG00000041025	Iffo2	C79267	intermediate filament family orphan 2	protein-coding
mm_116903.1	chr13	55426799	55426811	-	1	NA	promoter-TSS (NM_021489)	promoter-TSS (NM_021489)	-1	NM_021489	58992	Mm.42224	NM_021489	ENSMUSG00000021492	F12	FXII|HAF	coagulation factor XII (Hageman factor)	protein-coding
mm_156530.1	chrX	151046947	151046975	+	1	NA	promoter-TSS (NM_008001)	promoter-TSS (NM_008001)	-209	NM_008001	14163	Mm.8142	NM_008001	ENSMUSG00000025265	Fgd1	ZFYVE3	FYVE, RhoGEF and PH domain containing 1	protein-coding
mm_63185.1	chr7	125552261	125552306	+	1	NA	promoter-TSS (NM_001008700)	promoter-TSS (NM_001008700)	1	NM_001008700	16190	Mm.233802	NM_010557	ENSMUSG00000030748	Il4ra	CD124|Il4r	interleukin 4 receptor, alpha	protein-coding
mm_159925.1	chr6	56924111	56924111	+	1	NA	promoter-TSS (NM_026004)	promoter-TSS (NM_026004)	-179	NM_026004	107569	Mm.158936	NM_026004	ENSMUSG00000029780	Nt5c3	1600024P05Rik|2610206B05Rik|3110004A18Rik|AI842776|Nt5c3a|Nt5y|PN-1|PN-I|PSN1|UMPH|Umph-1|Umph1|cN-III|lupin|p36	5'-nucleotidase, cytosolic III	protein-coding
mm_127615.1	chr15	102460404	102460418	+	1	NA	exon (NM_025385, exon 4 of 5)	exon (NM_025385, exon 4 of 5)	1241	NM_025385	66151	Mm.393955	NM_025385	ENSMUSG00000023048	Prr13	1110020C13Rik|2010324E22Rik	proline rich 13	protein-coding
mm_24174.1	chr3	88575796	88575810	+	1	NA	Intergenic	RLTR11A2|LTR|ERVK	-3868	NM_025448	66256	Mm.7091	NM_025448	ENSMUSG00000041355	Ssr2	1500032E05Rik|AI315033|AU020133|TLAP|TRAPB|TRAPbeta	signal sequence receptor, beta	protein-coding
mm_39576.1	chr5	23434436	23434471	+	1	NA	promoter-TSS (NM_026984)	promoter-TSS (NM_026984)	24	NM_026984	69188	Mm.205190	NM_026984	ENSMUSG00000029004	Kmt2e	1810033J14Rik|9530077A04Rik|D230038D11Rik|Mll5|NKp44L	lysine (K)-specific methyltransferase 2E	protein-coding
mm_134317.1	chr16	15895798	15895804	-	1	NA	intron (NM_146068, intron 17 of 19)	intron (NM_146068, intron 17 of 19)	8515	NM_007679	12609	Mm.347407	NM_007679	ENSMUSG00000071637	Cebpd	c/EBPdelta	CCAAT/enhancer binding protein (C/EBP), delta	protein-coding
mm_43055.1	chr5	124185504	124185513	+	1	NA	intron (NM_011256, intron 2 of 24)	intron (NM_011256, intron 2 of 24)	1674	NM_001289472	19679	Mm.44261	NM_011256	ENSMUSG00000029406	Pitpnm2	NIR3|RDGBA2|Rdgb2|mKIAA1457	phosphatidylinositol transfer protein, membrane-associated 2	protein-coding
mm_101771.1	chr11	44260506	44260524	-	1	NA	Intergenic	MTE2a|LTR|ERVL-MaLR	-139548	NM_001303244	16160	Mm.239707	NM_008352	ENSMUSG00000004296	Il12b	Il-12b|Il-12p40|Il12p40|p40	interleukin 12b	protein-coding
mm_76751.1	chr8	95434763	95434780	-	1	NA	promoter-TSS (NM_008187)	promoter-TSS (NM_008187)	98	NM_008187	14894	Mm.2080	NM_008187	ENSMUSG00000031796	Cfap20	2600014O15Rik|AL024127|Gtl3|T10-2A2	cilia and flagella associated protein 20	protein-coding
mm_161581.1	chr16	31663414	31663414	+	1	NA	promoter-TSS (NM_001252435)	promoter-TSS (NM_001252435)	-29	NM_001252435	13383	Mm.382	NM_007862	ENSMUSG00000022770	Dlg1	B130052P05Rik|Dlgh1|E-dlg/SAP97|SAP-97|SAP97|mKIAA4187	discs, large homolog 1 (Drosophila)	protein-coding
mm_89933.1	chr10	111247833	111247850	+	1	NA	intron (NM_175489, intron 4 of 23)	intron (NM_175489, intron 4 of 23)	-50838	NM_027914	71769	Mm.45256	NM_027914	ENSMUSG00000035759	Bbs10	1300007O09Rik|AI452285	Bardet-Biedl syndrome 10 (human)	protein-coding
mm_140947.1	chr17	24527831	24527884	-	1	NA	promoter-TSS (NR_045289)	promoter-TSS (NR_045289)	81	NM_153792	224619	Mm.275150	NM_153792	ENSMUSG00000052752	Traf7	RFWD1	TNF receptor-associated factor 7	protein-coding
mm_153167.1	chr19	34493406	34493427	-	1	NA	3' UTR (NM_021460, exon 10 of 10)	3' UTR (NM_021460, exon 10 of 10)	-18281	NM_009890	12642	Mm.30824	NM_009890	ENSMUSG00000050370	Ch25h	AI462618|m25OH	cholesterol 25-hydroxylase	protein-coding
mm_64697.1	chr7	4528150	4528161	-	1	NA	intron (NM_001033548, intron 4 of 11)	intron (NM_001033548, intron 4 of 11)	4287	NM_001033548	436022	Mm.425359	NM_001033548	ENSMUSG00000055809	Dnaaf3	6030429G01Rik|b2b1739Clo	dynein, axonemal assembly factor 3	protein-coding
mm_25773.1	chr3	126596353	126596372	+	1	NA	promoter-TSS (NM_001293663)	promoter-TSS (NM_001293663)	-589	NM_001293663	108058	Mm.255822	NM_023813	ENSMUSG00000053819	Camk2d	2810011D23Rik|8030469K03Rik|CaMK II|[d]-CaMKII	calcium/calmodulin-dependent protein kinase II, delta	protein-coding
mm_115616.1	chr13	12053979	12053989	-	1	NA	intron (NM_023868, intron 1 of 104)	intron (NM_023868, intron 1 of 104)	52961	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding
mm_99066.1	chr11	99168126	99168159	+	1	NA	Intergenic	Intergenic	-13065	NM_007719	12775	Mm.2932	NM_007719	ENSMUSG00000037944	Ccr7	CC-CKR-7|CCR-7|CD197|Cdw197|Cmkbr7|EBI1|Ebi1h	chemokine (C-C motif) receptor 7	protein-coding
mm_26410.1	chr3	142608243	142608255	+	1	NA	exon (NM_010259, exon 8 of 11)	exon (NM_010259, exon 8 of 11)	-12414	NM_010260	14469	Mm.24038	NM_010260	ENSMUSG00000028270	Gbp2	-	guanylate binding protein 2	protein-coding
mm_157317.1	chrX	21179027	21179040	-	1	NA	Intergenic	Intergenic	42632	NM_001252013	100503481	Mm.272069	NM_001252013		4930453H23Rik	-	RIKEN cDNA 4930453H23 gene	protein-coding
mm_163560.1	chr13	24614086	24614093	-	1	NA	promoter-TSS (NM_001286101)	promoter-TSS (NM_001286101)	-517	NM_001286101	193385	Mm.217319	NM_029679	ENSMUSG00000036006	Fam65b	-	family with sequence similarity 65, member B	protein-coding
mm_105595.1	chr11	106750186	106750202	-	1	NA	Intergenic	Intergenic	-1032	NM_001271375	380732	Mm.343952	NM_001033435	ENSMUSG00000040528	Milr1	Allergin-1|Gm885|Mca32	mast cell immunoglobulin like receptor 1	protein-coding
mm_136603.1	chr17	5189900	5189917	+	1	NA	intron (NM_001085355, intron 4 of 19)	CpG	194834	NM_001085355	239985	Mm.133401	NM_001085355	ENSMUSG00000069729	Arid1b	8030481M12|9330189K18Rik|AI836955|Ardi1b|B230217J03Rik|mKIAA1235	AT rich interactive domain 1B (SWI-like)	protein-coding
mm_128986.1	chr15	74834599	74834643	-	1	NA	TTS (NM_001033229)	TTS (NM_001033229)	7022	NM_001033229	110115	Mm.322606	NM_001033229	ENSMUSG00000075604	Cyp11b1	AA389061|CPN1|Cyp11b|Cyp11b-1|FHI	cytochrome P450, family 11, subfamily b, polypeptide 1	protein-coding
mm_150565.1	chr19	39568054	39568056	+	1	NA	exon (NM_010003, exon 9 of 9)	exon (NM_010003, exon 9 of 9)	57233	NM_010003	13098	Mm.42101	NM_010003	ENSMUSG00000025003	Cyp2c39	CYPIIC39	cytochrome P450, family 2, subfamily c, polypeptide 39	protein-coding
mm_169805.1	chr16	18533237	18533246	-	1	NA	intron (NR_104347, intron 2 of 8)	SSU-rRNA_Hsa|rRNA|rRNA	34370	NR_104347	13972	Mm.236139	NM_023120	ENSMUSG00000000884	Gnb1l	ESTM55|Gm16314|Me49f07|OTTMUSG00000033458|Wdr14|Wdvcf	guanine nucleotide binding protein (G protein), beta polypeptide 1-like	protein-coding
mm_87501.1	chr10	52022521	52022534	+	1	NA	promoter-TSS (NM_001300957)	promoter-TSS (NM_001300957)	25	NM_153786	215031	Mm.87237	NM_153786	ENSMUSG00000049641	Vgll2	C130057C21Rik|VITO-1|Vito1|vgl-2	vestigial like family member 2	protein-coding
mm_1859.1	chr1	84869147	84869163	+	1	NA	intron (NM_025386, intron 1 of 3)	intron (NM_025386, intron 1 of 3)	29314	NM_025386	66153	Mm.381192	NM_025386	ENSMUSG00000073633	Fbxo36	0610008D19Rik|1110020F21Rik|2410002G19Rik|D1Ertd757e	F-box protein 36	protein-coding
mm_52488.1	chr6	114644830	114644832	+	1	NA	intron (NM_028835, intron 1 of 18)	intron (NM_028835, intron 1 of 18)	1734	NM_001253717	74244	Mm.275332	NM_028835	ENSMUSG00000030314	Atg7	1810013K23Rik|Agp7|Apg7l|Atg7l|Gm21553	autophagy related 7	protein-coding
mm_81745.1	chr9	113930965	113930987	+	1	NA	promoter-TSS (NM_001083319)	promoter-TSS (NM_001083319)	42	NM_013699	22221	Mm.28052	NM_013699	ENSMUSG00000009741	Ubp1	Cp2b|LBP-1a|LBP-1b|NF2d9	upstream binding protein 1	protein-coding
mm_5236.1	chr1	14931247	14931252	-	1	NA	Intergenic	Intergenic	-12387	NM_177781	277328	Mm.186329	NM_177781	ENSMUSG00000032769	Trpa1	Anktm1|TRPA1b	transient receptor potential cation channel, subfamily A, member 1	protein-coding
mm_94486.1	chr11	6636706	6636721	+	1	NA	exon (NM_011709, exon 3 of 4)	exon (NM_011709, exon 3 of 4)	1936	NM_011709	22373	Mm.268094	NM_011709	ENSMUSG00000000381	Wap	-	whey acidic protein	protein-coding
mm_30631.1	chr4	8800213	8800237	+	1	NA	intron (NM_001277149, intron 3 of 37)	intron (NM_001277149, intron 3 of 37)	109819	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_97143.1	chr11	75348494	75348560	+	1	NA	promoter-TSS (NM_026653)	promoter-TSS (NM_026653)	94	NM_001102611	319822	Mm.340377	NM_177009	ENSMUSG00000018809	Smyd4	G430029E23Rik	SET and MYND domain containing 4	protein-coding
mm_114468.1	chr13	67779786	67779796	+	1	NA	promoter-TSS (NM_028402)	promoter-TSS (NM_028402)	98	NM_028402	72958	Mm.53849	NM_028402	ENSMUSG00000090659	Zfp493	2900054J07Rik|Rslcan12	zinc finger protein 493	protein-coding
mm_40631.1	chr5	64822985	64823010	+	1	NA	exon (NM_008453, exon 4 of 6)	exon (NM_008453, exon 4 of 6)	19474	NM_008453	16599	Mm.392759	NM_008453	ENSMUSG00000029178	Klf3	9930027G08Rik|AL024007|Bklf|Tef-2	Kruppel-like factor 3 (basic)	protein-coding
mm_151147.1	chr19	53140472	53140505	+	1	NA	promoter-TSS (NM_001164099)	promoter-TSS (NM_001164099)	45	NM_001164101	27360	Mm.426080	NM_013758	ENSMUSG00000025026	Add3	AI463285|R75380	adducin 3 (gamma)	protein-coding
mm_152516.1	chr19	11279692	11279696	-	1	NA	intron (NM_183190, intron 1 of 4)	intron (NM_183190, intron 1 of 4)	4119	NM_183190	269063	Mm.268940	NM_183190	ENSMUSG00000054523	Ms4a5	-	membrane-spanning 4-domains, subfamily A, member 5	protein-coding
mm_1420.1	chr1	67168311	67168319	+	1	NA	exon (NM_001080809, exon 16 of 38)	exon (NM_001080809, exon 16 of 38)	45288	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_48101.1	chr5	137067012	137067028	-	1	NA	exon (NM_008871, exon 5 of 9)	exon (NM_008871, exon 5 of 9)	5252	NM_008871	18787	Mm.250422	NM_008871	ENSMUSG00000037411	Serpine1	PAI-1|PAI1|Planh1	serine (or cysteine) peptidase inhibitor, clade E, member 1	protein-coding
mm_12880.1	chr2	84678475	84678477	+	1	NA	promoter-TSS (NM_001290751)	promoter-TSS (NM_001290751)	74	NM_025885	381379	Mm.219643	NM_025885	ENSMUSG00000027080	Med19	2410018M14Rik|3110040A13Rik|LCMR1	mediator complex subunit 19	protein-coding
mm_1582.1	chr1	74285040	74285072	+	1	NA	promoter-TSS (NM_025580)	promoter-TSS (NM_025580)	22	NM_001039509	56695	Mm.384726	NM_019999	ENSMUSG00000026179	Pnkd	2210013N15Rik|2810403H05Rik|AI854243|Brp17|MNCb-5687|MR-1|Tahccp2	paroxysmal nonkinesiogenic dyskinesia	protein-coding
mm_49720.1	chr6	34598531	34598587	+	1	NA	promoter-TSS (NM_001347100)	promoter-TSS (NM_001347100)	55	NM_001347100	109624	Mm.308134	NM_145575	ENSMUSG00000029761	Cald1	4833423D12Rik|AI195384|AV071549|AW536160|C920027I18Rik	caldesmon 1	protein-coding
mm_79627.1	chr9	59291618	59291628	+	1	NA	promoter-TSS (NM_028121)	promoter-TSS (NM_028121)	51	NM_028121	72141	Mm.22456	NM_028121	ENSMUSG00000025236	Adpgk	2610017G09Rik|Adp-gk|C77577	ADP-dependent glucokinase	protein-coding
mm_138673.1	chr17	35888126	35888139	+	1	NA	exon (NM_026987, exon 15 of 20)	exon (NM_026987, exon 15 of 20)	8354	NM_026987	69192	Mm.390986	NM_026987	ENSMUSG00000024422	Dhx16	2410006N22Rik|DBP2|Ddx16|mKIAA0577	DEAH (Asp-Glu-Ala-His) box polypeptide 16	protein-coding
mm_26738.1	chr3	6169802	6169806	-	1	NA	Intergenic	MTE2b|LTR|ERVL-MaLR	450639	NM_027048	69347	Mm.45822	NM_027048	ENSMUSG00000069118	1700008P02Rik	-	RIKEN cDNA 1700008P02 gene	protein-coding
mm_84958.1	chr9	83447958	83447975	-	1	NA	intron (NR_102437, intron 2 of 2)	CpG	-6839	NM_029434	75782	Mm.199698	NM_027448	ENSMUSG00000032258	Lca5	4930431B11Rik|5730406O13Rik|AV274874|ORF64	Leber congenital amaurosis 5 (human)	protein-coding
mm_123450.1	chr14	65194976	65194993	-	1	NA	3' UTR (NM_021458, exon 7 of 7)	3' UTR (NM_021458, exon 7 of 7)	67479	NM_021458	14365	Mm.214687	NM_021458	ENSMUSG00000007989	Fzd3	AU020229|D930050A07Rik|Fz3	frizzled class receptor 3	protein-coding
mm_146392.1	chr18	82855895	82855898	+	1	NA	promoter-TSS (NR_125720)	promoter-TSS (NR_125720)	-1	NR_125720	73985	Mm.399211	NR_125720	ENSMUSG00000097738	4930445N18Rik	3010027C24Rik	RIKEN cDNA 4930445N18 gene	ncRNA
mm_12043.1	chr2	58790176	58790191	+	1	NA	3' UTR (NM_001289659, exon 8 of 8)	3' UTR (NM_001289659, exon 8 of 8)	34999	NM_029692	76654	Mm.200370	NM_029692	ENSMUSG00000026839	Upp2	1700124F02Rik|AI266885|UDRPASE2|UP2|UPASE2	uridine phosphorylase 2	protein-coding
mm_148304.1	chr18	83107858	83107869	-	1	NA	Intergenic	Intergenic	-187303	NR_033307	75853	Mm.420737	NR_033307		4930592I03Rik	-	RIKEN cDNA 4930592I03 gene	ncRNA
mm_145115.1	chr18	44315710	44315717	+	1	NA	Intergenic	Intergenic	-18361	NM_001033621	58916	Mm.143804	NM_001033621	ENSMUSG00000024471	Myot	5530402I04Rik|Ttid	myotilin	protein-coding
mm_67353.1	chr7	79836319	79836335	-	1	NA	exon (NM_008486, exon 10 of 20)	exon (NM_008486, exon 10 of 20)	6025	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_163358.1	chr12	29345940	29345940	-	1	NA	Intergenic	Intergenic	-182444	NM_001093775	17933	Mm.253067	NM_008666	ENSMUSG00000061911	Myt1l	2900046C06Rik|2900093J19Rik|C630034G21Rik|Nztf1|Pmng1|Png-1|mKIAA1106	myelin transcription factor 1-like	protein-coding
mm_20713.1	chr2	134644020	134644042	-	1	NA	promoter-TSS (NM_029148)	promoter-TSS (NM_029148)	90	NM_029148	52837	Mm.264096	NM_029148	ENSMUSG00000034723	Tmx4	2810417D04Rik|4930500L08Rik|AI843224|AW046784|D2Bwg1356e|Txndc13|mKIAA1162	thioredoxin-related transmembrane protein 4	protein-coding
mm_158686.1	chrX	160735802	160735812	-	1	NA	Intergenic	Intergenic	-15835	NM_011147	237178	Mm.296779	NM_011147	ENSMUSG00000062168	Ppef1	PPEF-1	protein phosphatase with EF hand calcium-binding domain 1	protein-coding
mm_163526.1	chr12	117843441	117843474	+	1	NA	promoter-TSS (NM_146040)	promoter-TSS (NM_146040)	-404	NM_146040	217946	Mm.281149	NM_146040	ENSMUSG00000021175	Cdca7l	BC006933|JPO2	cell division cycle associated 7 like	protein-coding
mm_171164.1	chr3	25731224	25731224	+	1	NA	intron (NM_001163387, intron 3 of 5)	intron (NM_001163387, intron 3 of 5)	422083	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_127873.1	chr15	8444450	8444506	-	1	NA	promoter-TSS (NM_027707)	promoter-TSS (NM_027707)	-15	NM_201232	71175	Mm.240329	NM_027707	ENSMUSG00000022141	Nipbl	Idn3	Nipped-B homolog (Drosophila)	protein-coding
mm_67152.1	chr7	73532273	73532276	-	1	NA	intron (NM_001081345, intron 2 of 38)	B1_Mur2|SINE|Alu	9472	NM_001081345	244059	Mm.34539	NM_001081345	ENSMUSG00000078671	Chd2	2810013C04Rik|2810040A01Rik|5630401D06Rik|AI851092|BC029703|CHD-2	chromodomain helicase DNA binding protein 2	protein-coding
mm_87536.1	chr10	53525976	53525980	+	1	NA	Intergenic	RMER19C|LTR|ERVK	-6989	NR_037973	100502868	Mm.297722	NR_037973		Gm20597	B230314j19	predicted gene, 20597	ncRNA
mm_20512.1	chr2	130638353	130638390	-	1	NA	intron (NM_197945, intron 1 of 4)	intron (NM_197945, intron 1 of 4)	4473	NM_197945	241638	Mm.440130	NM_197945	ENSMUSG00000037703	Lzts3	Prosapip1	leucine zipper, putative tumor suppressor family member 3	protein-coding
mm_23795.1	chr3	79629118	79629134	+	1	NA	promoter-TSS (NM_025794)	promoter-TSS (NM_025794)	47	NM_029482	75939	Mm.221520	NM_029482	ENSMUSG00000027811	4930579G24Rik	-	RIKEN cDNA 4930579G24 gene	protein-coding
mm_419.1	chr1	34307930	34307942	+	1	NA	3' UTR (NM_134448, exon 98 of 98)	3' UTR (NM_134448, exon 98 of 98)	125263	NR_039562	100628580		NR_039562	ENSMUSG00000092852	Mir5103	mir-5103|mmu-mir-5103|mu-mir-5103	microRNA 5103	ncRNA
mm_133294.1	chr16	77500007	77500035	+	1	NA	intron (NR_015543, intron 3 of 4)	intron (NR_015543, intron 3 of 4)	-98915	NR_029535	387229		NR_029535	ENSMUSG00000065530	Mir99a	Mirn99a|mir-99a|mmu-mir-99a	microRNA 99a	ncRNA
mm_108847.1	chr12	98270136	98270155	+	1	NA	intron (NM_008152, intron 1 of 1)	intron (NM_008152, intron 1 of 1)	1510	NM_008152	14744	Mm.378924	NM_008152	ENSMUSG00000021886	Gpr65	Dig1|Gpcr25|TDAG8	G-protein coupled receptor 65	protein-coding
mm_148575.1	chr19	4871077	4871091	+	1	NA	exon (NM_013456, exon 6 of 21)	exon (NM_013456, exon 6 of 21)	6825	NM_013456	11474	Mm.5316	NM_013456	ENSMUSG00000006457	Actn3	-	actinin alpha 3	protein-coding
mm_46548.1	chr5	106574681	106574698	-	1	NA	Intergenic	CpG	-116523	NM_001005477	104382	Mm.271593	NM_001005477	ENSMUSG00000034384	Barhl2	E130309B19Rik|MBH1	BarH-like 2 (Drosophila)	protein-coding
mm_172853.1	chr9	37453718	37453718	+	1	NA	Intergenic	Intergenic	-20543	NM_001164767	19649	Mm.212826	NM_011248	ENSMUSG00000032128	Robo3	Rbig1|Rig-1|Rig1|Robo3a|Robo3b	roundabout guidance receptor 3	protein-coding
mm_76174.1	chr8	82392533	82392548	-	1	NA	intron (NM_001254747, intron 1 of 7)	intron (NM_001254747, intron 1 of 7)	10046	NM_001254747	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_138418.1	chr17	35069438	35069442	+	1	NA	exon (NM_023463, exon 3 of 3)	exon (NM_023463, exon 3 of 3)	2115	NM_023463	68468	Mm.215096	NM_023463	ENSMUSG00000092586	Ly6g6c	1110003M04Rik|AU016360|G6c|NG24	lymphocyte antigen 6 complex, locus G6C	protein-coding
mm_64470.1	chr7	143005719	143005735	+	1	NA	promoter-TSS (NM_001128082)	promoter-TSS (NM_001128082)	68	NM_001128081	27027	Mm.28172	NM_020286	ENSMUSG00000000244	Tspan32	AW208513|Art-1|BB235973|D7Wsu37e|Phemx|Tssc6	tetraspanin 32	protein-coding
mm_156289.1	chrX	136837462	136837468	+	1	NA	3' UTR (NM_011123, exon 7 of 7)	3' UTR (NM_011123, exon 7 of 7)	14719	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_173014.1	chrM	673	673	+	1	NA	NA	Intergenic	NA	NA								
mm_70766.1	chr8	21935311	21935319	+	1	NA	Intergenic	Intergenic	-2605	NM_139222	246082	Mm.390015	NM_139222	ENSMUSG00000048500	Defb15	BD-15	defensin beta 15	protein-coding
mm_58103.1	chr6	137571008	137571032	-	1	NA	promoter-TSS (NM_001271587)	promoter-TSS (NM_001271587)	-11	NM_001271587	13860	Mm.235346	NM_007945	ENSMUSG00000015766	Eps8	AW261790	epidermal growth factor receptor pathway substrate 8	protein-coding
mm_171017.1	chr2	83966511	83966528	+	1	NA	Intergenic	CpG	-25293	NM_027964	71861	Mm.116957	NM_027964	ENSMUSG00000034552	Zswim2	1700025P14Rik|4933437F18Rik|MEX	zinc finger SWIM-type containing 2	protein-coding
mm_132332.1	chr16	33819490	33819517	+	1	NA	3' UTR (NM_010739, exon 13 of 13)	3' UTR (NM_010739, exon 13 of 13)	-10162	NM_010580	16419	Mm.6424	NM_010580	ENSMUSG00000022817	Itgb5	AA475909|AI874634|ESTM23|[b]-5|[b]5|[b]5A|[b]5B|beta-5|beta5	integrin beta 5	protein-coding
mm_172299.1	chr7	101302227	101302245	-	1	NA	promoter-TSS (NM_001111111)	promoter-TSS (NM_001111111)	-148	NM_001111111	73683	Mm.275744	NM_001111111	ENSMUSG00000047767	Atg16l2	2410118P20Rik	autophagy related 16-like 2 (S. cerevisiae)	protein-coding
mm_10890.1	chr2	25263293	25263347	+	1	NA	exon (NM_175286, exon 1 of 4)	exon (NM_175286, exon 1 of 4)	722	NM_175286	97031	Mm.308539	NM_175286	ENSMUSG00000048707	Tprn	C430004E15Rik|C87750	taperin	protein-coding
mm_10137.1	chr2	4131660	4131664	+	1	NA	TTS (NR_040500)	TTS (NR_040500)	9479	NR_040500	73489	Mm.488103	NR_040500	ENSMUSG00000084859	1700080N15Rik	4933408D14Rik	RIKEN cDNA 1700080N15 gene	ncRNA
mm_27643.1	chr3	63865378	63865380	-	1	NA	Intergenic	Intergenic	-14388	NM_001177732	269437	Mm.316391	NM_183191	ENSMUSG00000036834	Plch1	BC042549|PLC-eta-1|PLCeta1|Plcl3	phospholipase C, eta 1	protein-coding
mm_107512.1	chr12	40222251	40222260	+	1	NA	TTS (NR_035459)	TTS (NR_035459)	556	NR_035459	100316693		NR_035459	ENSMUSG00000089371	Mir1938	mir-1938|mmu-mir-1938	microRNA 1938	ncRNA
mm_153248.1	chr19	36264191	36264200	-	1	NA	Intergenic	Intergenic	-114872	NM_029508	76073	Mm.259180	NM_029508	ENSMUSG00000024805	Pcgf5	0610009F02Rik|1110054A01Rik|5830406C17Rik|5830443C21Rik|9530023M17Rik|AI324127	polycomb group ring finger 5	protein-coding
mm_31510.1	chr4	53712668	53712676	+	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	-1510	NM_139309	246179	Mm.247210	NM_139309	ENSMUSG00000028414	Fktn	D830030O17Rik|Fcmd	fukutin	protein-coding
mm_11276.1	chr2	30062018	30062043	+	1	NA	promoter-TSS (NM_023871)	promoter-TSS (NM_023871)	34	NM_023871	56086	Mm.326055	NM_023871	ENSMUSG00000054766	Set	2610030F17Rik|5730420M11Rik|AA407739|I-2PP2A|StF-IT-1|TAF-I	SET nuclear oncogene	protein-coding
mm_66317.1	chr7	40898605	40898619	-	1	NA	promoter-TSS (NM_021387)	promoter-TSS (NM_021387)	-288	NR_040329	320210	Mm.126237	NR_040329	ENSMUSG00000100600	A230077H06Rik	-	RIKEN cDNA A230077H06 gene	ncRNA
mm_150002.1	chr19	29286329	29286341	+	1	NA	exon (NM_008413, exon 10 of 25)	exon (NM_008413, exon 10 of 25)	34532	NM_008413	16452	Mm.275839	NM_008413	ENSMUSG00000024789	Jak2	Fd17	Janus kinase 2	protein-coding
mm_5701.1	chr1	43198336	43198342	-	1	NA	Intergenic	Intergenic	-1578	NM_001289533	14200	Mm.6799	NM_010212	ENSMUSG00000008136	Fhl2	FHL-2|SLIM-3|SLIM3	four and a half LIM domains 2	protein-coding
mm_106519.1	chr11	120551148	120551158	-	1	NA	promoter-TSS (NM_026814)	promoter-TSS (NM_026814)	-21	NM_026814	68701	Mm.46477	NM_026814	ENSMUSG00000025129	Ppp1r27	1110033I14Rik|Dysfip1|toonin	protein phosphatase 1, regulatory subunit 27	protein-coding
mm_25480.1	chr3	109025982	109025997	+	1	NA	intron (NM_001163567, intron 1 of 10)	intron (NM_001163567, intron 1 of 10)	1618	NM_001163567	329739	Mm.69013	NM_001163567	ENSMUSG00000040339	Fam102b	1600010D10Rik|B430201A12Rik	family with sequence similarity 102, member B	protein-coding
mm_90616.1	chr10	128391265	128391266	+	1	NA	3' UTR (NM_172790, exon 28 of 28)	3' UTR (NM_172790, exon 28 of 28)	2433	NR_105880	102465979		NR_105880	ENSMUSG00000106600	Mir6915	mmu-mir-6915	microRNA 6915	ncRNA
mm_13662.1	chr2	114056285	114056328	+	1	NA	intron (NR_028422, intron 1 of 2)	L1MA8|LINE|L1	1910	NR_028422	100303644	Mm.330469	NR_028422	ENSMUSG00000092397	C130080G10Rik	-	RIKEN cDNA C130080G10 gene	ncRNA
mm_132221.1	chr16	32631634	32631650	+	1	NA	3' UTR (NM_011638, exon 19 of 19)	3' UTR (NM_011638, exon 19 of 19)	-13001	NM_001110147	51789	Mm.251115	NM_016788	ENSMUSG00000022791	Tnk2	Ack|Ack-1|Ack1|Cdgip|Pyk1	tyrosine kinase, non-receptor, 2	protein-coding
mm_26957.1	chr3	21936037	21936044	-	1	NA	Intergenic	Intergenic	-140612	NM_030732	81004	Mm.202966	NM_030732	ENSMUSG00000027630	Tbl1xr1	8030499H02Rik|A630076E03Rik|AW539987|C21|C230089I12Rik|DC42|Ira1|TBLR1	transducin (beta)-like 1X-linked receptor 1	protein-coding
mm_60343.1	chr7	44356340	44356353	+	1	NA	intron (NM_001034115, intron 24 of 24)	MIR|SINE|MIR	18684	NM_027049	69349	Mm.358922	NM_027049	ENSMUSG00000008028	1700008O03Rik	-	RIKEN cDNA 1700008O03 gene	protein-coding
mm_66743.1	chr7	46712027	46712055	-	1	NA	TTS (NM_011315)	TTS (NM_011315)	-1390	NM_030233	78935	Mm.289866	NM_030233	ENSMUSG00000006763	Saal1	5031425D22Rik|SPACIA1	serum amyloid A-like 1	protein-coding
mm_134848.1	chr16	27348440	27348470	-	1	NA	intron (NM_198112, intron 4 of 4)	intron (NM_198112, intron 4 of 4)	21784	NM_198166	224065	Mm.326918	NM_198166	ENSMUSG00000056423	Uts2b	Gm538|U2B|Urp|Uts2d	urotensin 2B	protein-coding
mm_69226.1	chr7	127615227	127615269	-	1	NA	promoter-TSS (NM_177226)	promoter-TSS (NM_177226)	-815	NM_177226	320683	Mm.156718	NM_177226	ENSMUSG00000045639	Zfp629	9330199A09Rik|Znf629	zinc finger protein 629	protein-coding
mm_112586.1	chr13	13769363	13769376	+	1	NA	intron (NM_010748, intron 50 of 52)	intron (NM_010748, intron 50 of 52)	-14690	NM_001302997	14706	Mm.215394	NM_010317	ENSMUSG00000021303	Gng4	-	guanine nucleotide binding protein (G protein), gamma 4	protein-coding
mm_153211.1	chr19	34747101	34747115	-	1	NA	promoter-TSS (NM_172838)	promoter-TSS (NM_172838)	3	NM_172838	240638	Mm.74636	NM_172838	ENSMUSG00000009378	Slc16a12	3230401A21|AW210596	solute carrier family 16 (monocarboxylic acid transporters), member 12	protein-coding
mm_126706.1	chr15	85228860	85228873	+	1	NA	intron (NM_001347088, intron 4 of 14)	intron (NM_001347088, intron 4 of 14)	22858	NM_010180	14114	Mm.297992	NM_010180	ENSMUSG00000006369	Fbln1	-	fibulin 1	protein-coding
mm_168891.1	chr12	4720161	4720162	+	1	NA	intron (NM_029107, intron 6 of 7)	BGLII_B|LTR|ERVK	18222	NM_029107	74855	Mm.269534	NM_029107	ENSMUSG00000079177	Fam228a	4930417G10Rik	family with sequence similarity 228, member A	protein-coding
mm_8589.1	chr1	156005791	156005810	-	1	NA	3' UTR (NM_144791, exon 7 of 7)	3' UTR (NM_144791, exon 7 of 7)	29017	NM_001160019	208263	Mm.211654	NM_144791	ENSMUSG00000026466	Tor1aip1	LAP1|Lap1B	torsin A interacting protein 1	protein-coding
mm_73304.1	chr8	105131892	105131903	+	1	NA	promoter-TSS (NM_146213)	promoter-TSS (NM_146213)	97	NM_146213	234677	Mm.120297	NM_146213	ENSMUSG00000060560	Ces4a	Ces8	carboxylesterase 4A	protein-coding
mm_145465.1	chr18	60247324	60247338	+	1	NA	3' UTR (NM_001033767, exon 3 of 3)	3' UTR (NM_001033767, exon 3 of 3)	25936	NM_001034859	225594	Mm.329460	NM_001034859	ENSMUSG00000068606	Gm4841	EG225594|Ifgga3	predicted gene 4841	protein-coding
mm_152024.1	chr19	6047411	6047424	-	1	NA	intron (NM_001164709, intron 1 of 15)	CpG	272	NM_001164709	74126	Mm.149870	NM_028769	ENSMUSG00000024807	Syvn1	1200010C09Rik|AW211966|C85322|D530017H19Rik|Hrd1	synovial apoptosis inhibitor 1, synoviolin	protein-coding
mm_30265.1	chr3	146770448	146770456	-	1	NA	promoter-TSS (NM_001164198)	promoter-TSS (NM_001164198)	-214	NM_001164198	18749	Mm.16766	NM_011100	ENSMUSG00000005034	Prkacb	CbPKA|Pkacb	protein kinase, cAMP dependent, catalytic, beta	protein-coding
mm_2857.1	chr1	131688671	131688734	+	1	NA	promoter-TSS (NM_145509)	promoter-TSS (NM_145509)	7	NM_001311096	226421	Mm.44508	NM_145509	ENSMUSG00000052688	Rab7b	5430435G22Rik	RAB7B, member RAS oncogene family	protein-coding
mm_95026.1	chr11	32024773	32024800	+	1	NA	intron (NM_001290680, intron 3 of 4)	intron (NM_001290680, intron 3 of 4)	23509	NM_001290681	18197	Mm.3304	NM_008741	ENSMUSG00000020297	Nsg2	-	neuron specific gene family member 2	protein-coding
mm_121810.1	chr14	20388823	20388912	-	1	NA	promoter-TSS (NM_134081)	promoter-TSS (NM_134081)	43	NM_134081	108671	Mm.2871	NM_134081	ENSMUSG00000021811	Dnajc9	5330419I01Rik|AU020082	DnaJ heat shock protein family (Hsp40) member C9	protein-coding
mm_110829.1	chr12	72628930	72628938	-	1	NA	Intergenic	Intergenic	35894	NM_025522	66375	Mm.289653	NM_025522	ENSMUSG00000021094	Dhrs7	2310016E22Rik|5730564L20Rik|AW061210|Retdsr4|Retsdr4	dehydrogenase/reductase (SDR family) member 7	protein-coding
mm_144413.1	chr18	20961595	20961637	+	1	NA	intron (NM_026301, intron 1 of 5)	CpG	16991	NM_026301	67664	Mm.45980	NM_026301	ENSMUSG00000033107	Rnf125	4930553F04Rik	ring finger protein 125	protein-coding
mm_139164.1	chr17	47557701	47557709	+	1	NA	intron (NM_001081635, intron 1 of 6)	intron (NM_001081635, intron 1 of 6)	-35762	NM_007632	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_83980.1	chr9	57265808	57265818	-	1	NA	Intergenic	Intergenic	-3214	NM_028820	74211	Mm.428905	NM_028820	ENSMUSG00000032300	1700017B05Rik	AA682102|D9Ertd278e	RIKEN cDNA 1700017B05 gene	protein-coding
mm_145198.1	chr18	49945218	49945227	+	1	NA	intron (NM_001081371, intron 37 of 42)	intron (NM_001081371, intron 37 of 42)	-34205	NM_001177760	106869	Mm.27740	NM_134131	ENSMUSG00000062210	Tnfaip8	AA987150|E130304C20Rik|ENSMUSG00000073567|Gg2-1|Gm10539|Nded|Ssc-2|Tipe	tumor necrosis factor, alpha-induced protein 8	protein-coding
mm_36578.1	chr4	88032736	88032749	-	1	NA	intron (NM_027326, intron 1 of 10)	CpG	665	NM_027326	70122	Mm.288898	NM_027326	ENSMUSG00000028496	Mllt3	2210011H10Rik|2610012I03Rik|3830408D16Rik|Af9|D4Ertd321e	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 3	protein-coding
mm_118468.1	chr14	11553569	11553597	+	1	NA	promoter-TSS (NM_008981)	promoter-TSS (NM_008981)	30	NM_008981	19270	Mm.431266	NM_008981	ENSMUSG00000021745	Ptprg	5430405N12Rik|AW046354|AW549872|RPTPgamma	protein tyrosine phosphatase, receptor type, G	protein-coding
mm_171189.1	chr3	43306285	43306288	-	1	NA	Intergenic	L1Md_A|LINE|L1	1563668	NM_027271	73852	Mm.29006	NM_027271	ENSMUSG00000025766	D3Ertd751e	2810009O15Rik|4930415G15Rik	DNA segment, Chr 3, ERATO Doi 751, expressed	protein-coding
mm_71641.1	chr8	57512522	57512567	+	1	NA	intron (NM_008252, intron 1 of 4)	CpG	701	NM_008252	97165	Mm.276881	NM_008252	ENSMUSG00000054717	Hmgb2	C80539|HMG-2|Hmg2	high mobility group box 2	protein-coding
mm_163083.1	chr11	69091460	69091466	+	1	NA	3' UTR (NM_009497, exon 5 of 5)	3' UTR (NM_009497, exon 5 of 5)	2935	NM_009497	22318	Mm.28643	NM_009497	ENSMUSG00000020894	Vamp2	Syb-2|Syb2|sybII	vesicle-associated membrane protein 2	protein-coding
mm_156356.1	chrX	139335844	139335856	+	1	NA	intron (NM_011635, intron 1 of 2)	intron (NM_011635, intron 1 of 2)	2167	NM_011635	22037	Mm.1297	NM_011635	ENSMUSG00000051257	Trap1a	Tra-P1A	tumor rejection antigen P1A	protein-coding
mm_103069.1	chr11	69878031	69878058	-	1	NA	promoter-TSS (NM_001195710)	promoter-TSS (NM_001195710)	-26	NM_001195710	100503361	Mm.340490	NM_001195710	ENSMUSG00000094845	Tmem95	432576	transmembrane protein 95	protein-coding
mm_42474.1	chr5	115465090	115465113	+	1	NA	Intergenic	RLTR11A|LTR|ERVK	-1165	NM_011107	18778	Mm.20190	NM_011107	ENSMUSG00000029522	Pla2g1b	Pla2a|sPLA2IB	phospholipase A2, group IB, pancreas	protein-coding
mm_143632.1	chr17	78937032	78937074	-	1	NA	promoter-TSS (NM_028611)	promoter-TSS (NM_028611)	17	NM_001024806	12607	Mm.24169	NM_009882	ENSMUSG00000024081	Cebpz	AI848081|CBF2|Cbf|Cebpa-rs1	CCAAT/enhancer binding protein zeta	protein-coding
mm_123085.1	chr14	55745681	55745701	-	1	NA	promoter-TSS (NM_026403)	promoter-TSS (NM_026403)	-2	NM_026403	67842	Mm.180338	NM_026403	ENSMUSG00000019297	Nop9	2610027L16Rik	NOP9 nucleolar protein	protein-coding
mm_115131.1	chr13	104287933	104287962	+	1	NA	non-coding (NR_136938, exon 1 of 27)	non-coding (NR_136938, exon 1 of 27)	112	NM_001081020	108154	Mm.208125	NM_175496	ENSMUSG00000046169	Adamts6	A930019D11Rik|ADAM-TS6|b2b1879.1Clo|b2b2029Clo|b2b2182Clo|b2b2187.1Clo|b2b2228Clo	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 6	protein-coding
mm_66297.1	chr7	38023514	38023526	-	1	NA	Intergenic	Intergenic	-3968	NM_011274	19777	Mm.387220	NM_011274	ENSMUSG00000030421	Uri1	C80913|NNX3|Rmp	URI1, prefoldin-like chaperone	protein-coding
mm_75124.1	chr8	34869763	34869769	-	1	NA	intron (NM_175091, intron 8 of 26)	B1F1|SINE|Alu	62156	NM_176933	319520	Mm.170276	NM_176933	ENSMUSG00000031530	Dusp4	2700078F24Rik|AI844617|BB104621|E130306H24Rik|MKP2	dual specificity phosphatase 4	protein-coding
mm_22844.1	chr3	27984273	27984290	+	1	NA	5' UTR (NM_008875, exon 1 of 26)	5' UTR (NM_008875, exon 1 of 26)	110	NM_008875	18805	Mm.212039	NM_008875	ENSMUSG00000027695	Pld1	AA536939|C85393|Pld1a|Pld1b|mPLD1	phospholipase D1	protein-coding
mm_77420.1	chr8	121070301	121070323	-	1	NA	intron (NR_130109, intron 2 of 6)	intron (NR_130109, intron 2 of 6)	12798	NR_045471	68790	Mm.246916	NR_045471	ENSMUSG00000097336	Fendrr	1110050K14Rik|LL66|linc-Foxf1a|lincFoxf1	Foxf1 adjacent non-coding developmental regulatory RNA	ncRNA
mm_37801.1	chr4	130548384	130548388	-	1	NA	intron (NM_025998, intron 1 of 6)	B4|SINE|B4	25650	NM_025998	67149	Mm.423029	NM_025998	ENSMUSG00000078532	Nkain1	2610200G18Rik|2810426C15Rik	Na+/K+ transporting ATPase interacting 1	protein-coding
mm_119797.1	chr14	54207100	54207108	+	1	NA	Intergenic	Intergenic	46825	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_164564.1	chr17	17871166	17871173	+	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	12770	NM_013521	14293	Mm.56951	NM_013521	ENSMUSG00000045551	Fpr1	FPR|LXA4R|fMLF-R	formyl peptide receptor 1	protein-coding
mm_63183.1	chr7	125548372	125548398	+	1	NA	Intergenic	Intergenic	-3897	NM_001008700	16190	Mm.233802	NM_010557	ENSMUSG00000030748	Il4ra	CD124|Il4r	interleukin 4 receptor, alpha	protein-coding
mm_94051.1	chr10	128180207	128180218	-	1	NA	promoter-TSS (NM_001039080)	promoter-TSS (NM_001039080)	85	NM_001039080	56516	Mm.42247	NM_019711	ENSMUSG00000040043	Rbms2	2610315E04Rik|Scr3	RNA binding motif, single stranded interacting protein 2	protein-coding
mm_139713.1	chr17	57462761	57462778	+	1	NA	intron (NM_010130, intron 18 of 21)	(GGGAGA)n|Simple_repeat|Simple_repeat	82545	NM_001104591	224916	Mm.469889	NM_001104591	ENSMUSG00000090655	Vmn2r120	EG224916	vomeronasal 2, receptor 120	protein-coding
mm_48483.1	chr5	141380929	141380947	-	1	NA	intron (NM_177879, intron 1 of 44)	intron (NM_177879, intron 1 of 44)	139404	NM_177879	330222	Mm.151931	NM_177879	ENSMUSG00000039683	Sdk1	5330440E10|6720466O15Rik	sidekick cell adhesion molecule 1	protein-coding
mm_83014.1	chr9	36782796	36782812	-	1	NA	exon (NM_001199494, exon 9 of 11)	exon (NM_001199494, exon 9 of 11)	14264	NM_007915	13663	Mm.4337	NM_007915	ENSMUSG00000062762	Ei24	AA536736|AI115355|PIG8	etoposide induced 2.4 mRNA	protein-coding
mm_70481.1	chr8	12395844	12395852	+	1	NA	5' UTR (NM_009233, exon 1 of 1)	5' UTR (NM_009233, exon 1 of 1)	329	NM_009233	20664	Mm.39088	NM_009233	ENSMUSG00000096014	Sox1	BB176347|Sox-1	SRY (sex determining region Y)-box 1	protein-coding
mm_87400.1	chr10	45577812	45577914	+	1	NA	promoter-TSS (NM_172473)	promoter-TSS (NM_172473)	34	NM_172473	209462	Mm.458633	NM_172473	ENSMUSG00000038822	Hace1	1700042J16Rik|A730034A22Rik|BC025474	HECT domain and ankyrin repeat containing, E3 ubiquitin protein ligase 1	protein-coding
mm_135365.1	chr16	44027939	44027969	-	1	NA	promoter-TSS (NM_001172107)	promoter-TSS (NM_001172107)	-9	NM_001172107	207798	Mm.19316	NM_153528	ENSMUSG00000036292	Gramd1c	4921521N14Rik	GRAM domain containing 1C	protein-coding
mm_61169.1	chr7	59248729	59248732	+	1	NA	intron (NM_173010, intron 2 of 8)	L1MB2|LINE|L1	19978	NM_011668	22215	Mm.9002	NM_011668	ENSMUSG00000025326	Ube3a	4732496B02|5830462N02Rik|A130086L21Rik|Hpve6a|mKIAA4216	ubiquitin protein ligase E3A	protein-coding
mm_133213.1	chr16	75659364	75659380	+	1	NA	Intergenic	Intergenic	66481	NM_198302	224344	Mm.273214	NM_198302	ENSMUSG00000032940	Rbm11	A330018F01	RNA binding motif protein 11	protein-coding
mm_65842.1	chr7	29247727	29247745	-	1	NA	TTS (NM_001110201)	TTS (NM_001110201)	731	NM_028179	72275	Mm.441142	NM_028179	ENSMUSG00000030587	2200002D01Rik	2010005J02Rik|H2RSP|IMUP|IMUP-1|IMUP-2	RIKEN cDNA 2200002D01 gene	protein-coding
mm_32189.1	chr4	101187628	101187632	+	1	NA	intron (NM_146145, intron 4 of 24)	intron (NM_146145, intron 4 of 24)	77652	NM_146145	16451	Mm.289657	NM_146145	ENSMUSG00000028530	Jak1	AA960307|BAP004|C130039L05Rik	Janus kinase 1	protein-coding
mm_21624.1	chr2	164277158	164277164	-	1	NA	exon (NM_009300, exon 2 of 3)	exon (NM_009300, exon 2 of 3)	1146	NM_009300	20941	Mm.1286	NM_009300	ENSMUSG00000016998	Svs4	SVS-IV|Svp-2|Svp-4|Svp2|Svp4	seminal vesicle secretory protein 4	protein-coding
mm_54550.1	chr6	36810162	36810187	-	1	NA	5' UTR (NM_008973, exon 1 of 5)	5' UTR (NM_008973, exon 1 of 5)	1187	NM_008973	19242	Mm.279690	NM_008973	ENSMUSG00000029838	Ptn	HARP|HB-GAM|HBBN|HBGF-8|HBNF|OSF|Osf-1|Osf1	pleiotrophin	protein-coding
mm_64881.1	chr7	14616699	14616702	-	1	NA	intron (NR_045120, intron 1 of 12)	intron (NR_045120, intron 1 of 12)	5778	NR_045120	100417675	Mm.372763	NR_045119	ENSMUSG00000041596	Nlrp5-ps	Gm18756	NLR family, pyrin domain containing 5, pseudogene	pseudo
mm_101559.1	chr11	33992982	33993009	-	1	NA	5' UTR (NM_001190886, exon 1 of 8)	5' UTR (NM_001190886, exon 1 of 8)	198	NM_001190886	70357	Mm.252514	NM_027398	ENSMUSG00000053519	Kcnip1	KCHIP1|Kchip1.2	Kv channel-interacting protein 1	protein-coding
mm_41434.1	chr5	90904113	90904137	+	1	NA	exon (NM_009140, exon 2 of 4)	exon (NM_009140, exon 2 of 4)	226	NM_009140	20310	Mm.4979	NM_009140	ENSMUSG00000058427	Cxcl2	CINC-2a|GROb|Gro2|MIP-2|MIP-2a|Mgsa-b|Mip2|Scyb|Scyb2	chemokine (C-X-C motif) ligand 2	protein-coding
mm_107012.1	chr12	12022998	12023001	+	1	NA	Intergenic	Intergenic	-140100	NR_003964	627110	Mm.194735	NR_003964		Tubb2a-ps2	C79445	tubulin, beta 2a, pseudogene 2	pseudo
mm_139354.1	chr17	50509751	50509793	+	1	NA	exon (NM_013880, exon 1 of 6)	exon (NM_013880, exon 1 of 6)	225	NM_013880	224860	Mm.217362	NM_013880	ENSMUSG00000038910	Plcl2	PLC-L2|PRIP-2|Plce2|mKIAA1092	phospholipase C-like 2	protein-coding
mm_70028.1	chr7	142576433	142576488	-	1	NA	TTS (NR_030416)	TTS (NR_030416)	687	NR_030416	735280		NR_030416	ENSMUSG00000076275	Mir675	Mirn675|mir-675|mmu-mir-675	microRNA 675	ncRNA
mm_61636.1	chr7	80290000	80290007	+	1	NA	exon (NM_178070, exon 20 of 23)	exon (NM_178070, exon 20 of 23)	-4448	NM_145150	233406	Mm.227274	NM_145150	ENSMUSG00000038943	Prc1	D7Ertd348e	protein regulator of cytokinesis 1	protein-coding
mm_38632.1	chr4	142239441	142239451	-	1	NA	promoter-TSS (NM_001109685)	promoter-TSS (NM_001109685)	-45	NM_001109685	71529	Mm.255986	NM_144531	ENSMUSG00000040606	Kazn	2310007B04Rik|9030409G11Rik|AI256607|AI666764|AW061099|Kaz|Kazrin	kazrin, periplakin interacting protein	protein-coding
mm_43300.1	chr5	134600239	134600288	+	1	NA	3' UTR (NM_022964, exon 12 of 12)	3' UTR (NM_022964, exon 12 of 12)	14762	NM_022964	56743	Mm.391375	NM_020044	ENSMUSG00000040751	Lat2	AW125574|LAB|NTAL|WSCR5|Wbscr15|Wbscr5	linker for activation of T cells family, member 2	protein-coding
mm_3191.1	chr1	135801571	135801580	+	1	NA	intron (NM_001112702, intron 2 of 8)	intron (NM_001112702, intron 2 of 8)	2064	NM_001112702	21952	Mm.44379	NM_021467	ENSMUSG00000026418	Tnni1	2700018B22Rik|AI747285|ssTnI	troponin I, skeletal, slow 1	protein-coding
mm_23833.1	chr3	81932667	81932680	+	1	NA	promoter-TSS (NM_177662)	promoter-TSS (NM_177662)	72	NM_177662	229445	Mm.254642	NM_177662	ENSMUSG00000028015	Ctso	A330105D01Rik|AI118514	cathepsin O	protein-coding
mm_73777.1	chr8	116921716	116921733	+	1	NA	promoter-TSS (NM_028131)	promoter-TSS (NM_028131)	-16	NM_028131	72155	Mm.23185	NM_028131	ENSMUSG00000031756	Cenpn	2610510J17Rik|AI426416|AW545024	centromere protein N	protein-coding
mm_20664.1	chr2	132120138	132120154	-	1	NA	intron (NM_018824, intron 1 of 15)	ORR1B1|LTR|ERVL-MaLR	24962	NM_018824	54338	Mm.103581	NM_018824	ENSMUSG00000027340	Slc23a2	AI844736|NBTL1|SVCT2|Slc23a1|YSPL2|YSPL3|mKIAA0238	solute carrier family 23 (nucleobase transporters), member 2	protein-coding
mm_18211.1	chr2	48949207	48949256	-	1	NA	promoter-TSS (NM_001177313)	promoter-TSS (NM_001177313)	36	NM_001177313	26428	Mm.291059	NM_011958	ENSMUSG00000026761	Orc4	Orc4P|Orc4l|mMmORC4	origin recognition complex, subunit 4	protein-coding
mm_29299.1	chr3	107911279	107911300	-	1	NA	Intergenic	Intergenic	-15076	NR_015459	329735	Mm.270500	NM_177858	ENSMUSG00000086968	4933431E20Rik	-	RIKEN cDNA 4933431E20 gene	ncRNA
mm_134739.1	chr16	23029063	23029076	-	1	NA	promoter-TSS (NM_201375)	promoter-TSS (NM_201375)	32	NM_201375	385643	Mm.440414	NM_201375	ENSMUSG00000060459	Kng2	-	kininogen 2	protein-coding
mm_17024.1	chr2	19388936	19388944	-	1	NA	intron (NM_029619, intron 3 of 4)	intron (NM_029619, intron 3 of 4)	17304	NM_029619	76467	Mm.27166	NM_029619	ENSMUSG00000023094	Msrb2	2310050L06Rik|Mrsb|Msrb|Pilb	methionine sulfoxide reductase B2	protein-coding
mm_147408.1	chr18	44662269	44662306	-	1	NA	promoter-TSS (NM_001085374)	promoter-TSS (NM_001085374)	-21	NM_001085374	328949	Mm.312511	NM_001033406	ENSMUSG00000071856	Mcc	D18Ertd451e|E330037C19	mutated in colorectal cancers	protein-coding
mm_99337.1	chr11	101468201	101468235	+	1	NA	promoter-TSS (NM_009708)	promoter-TSS (NM_009708)	-120	NM_009708	11858	Mm.378883	NM_009708	ENSMUSG00000001313	Rnd2	Arhn|Rohn	Rho family GTPase 2	protein-coding
mm_38931.1	chr4	150192539	150192558	-	1	NA	exon (NM_009802, exon 6 of 8)	exon (NM_009802, exon 6 of 8)	8587	NM_009802	12353	Mm.232523	NM_009802	ENSMUSG00000028972	Car6	Ca6|DOC1	carbonic anhydrase 6	protein-coding
mm_4667.1	chr1	180382306	180382334	+	1	NA	intron (NM_001081175, intron 2 of 7)	intron (NM_001081175, intron 2 of 7)	-51771	NR_003623	277333	Mm.389223	NM_199472		Gm5069	EG277333	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_44160.1	chr5	150665298	150665308	+	1	NA	intron (NM_201369, intron 1 of 5)	CpG	309	NM_201369	381695	Mm.246934	NM_201369	ENSMUSG00000029655	N4bp2l2	2700092H06Rik|zag1	NEDD4 binding protein 2-like 2	protein-coding
mm_122232.1	chr14	33185140	33185166	-	1	NA	promoter-TSS (NM_001146022)	promoter-TSS (NM_001146022)	-87	NM_001146022	545030	Mm.318345	NM_001146022	ENSMUSG00000051506	Wdfy4	Gm18810	WD repeat and FYVE domain containing 4	protein-coding
mm_159900.1	chr6	38570508	38570508	+	1	NA	intron (NM_001331223, intron 4 of 12)	intron (NM_001331223, intron 4 of 12)	14785	NM_001331223	192196	Mm.276133	NM_138680	ENSMUSG00000029823	Luc7l2	4930471C18Rik|AA522013|AU015269|CGI59|Cgi74	LUC7-like 2 (S. cerevisiae)	protein-coding
mm_139212.1	chr17	47728770	47728792	+	1	NA	exon (NM_025973, exon 2 of 9)	exon (NM_025973, exon 2 of 9)	1939	NM_025973	109820	Mm.22957	NM_025973	ENSMUSG00000023987	Pgc	2210410L06Rik|Upg-1|Upg1	progastricsin (pepsinogen C)	protein-coding
mm_111136.1	chr12	81568210	81568240	-	1	NA	5' UTR (NM_020330, exon 1 of 2)	5' UTR (NM_020330, exon 1 of 2)	249	NM_020330	56622	Mm.117130	NM_020330	ENSMUSG00000008438	Adam21	Adam31	a disintegrin and metallopeptidase domain 21	protein-coding
mm_115986.1	chr13	24329024	24329035	-	1	NA	intron (NM_001111110, intron 1 of 16)	MuLV-int|LTR|ERV1	1625	NM_001111110	12763	Mm.8396	NM_007717	ENSMUSG00000016756	Cmah	-	cytidine monophospho-N-acetylneuraminic acid hydroxylase	protein-coding
mm_93746.1	chr10	120159605	120159619	-	1	NA	intron (NM_028679, intron 8 of 11)	MLTR18_MM|LTR|ERVK	41925	NM_028679	73914	Mm.146194	NM_028679	ENSMUSG00000020227	Irak3	4833428C18Rik|AI563835|IRAK-M	interleukin-1 receptor-associated kinase 3	protein-coding
mm_147818.1	chr18	61754924	61754929	-	1	NA	intron (NM_178928, intron 5 of 18)	intron (NM_178928, intron 5 of 18)	28536	NR_029432	68982	Mm.441992	NR_029432	ENSMUSG00000098702	1500015A07Rik	-	RIKEN cDNA 1500015A07 gene	ncRNA
mm_143317.1	chr17	66188222	66188224	-	1	NA	Intergenic	Intergenic	64703	NM_001003919	320209	Mm.259605	NM_001003919	ENSMUSG00000035842	Ddx11	4732462I11Rik|CHL1|CHLR1|KRG2|essa15a	DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11	protein-coding
mm_49040.1	chr6	4760056	4760099	+	1	NA	3' UTR (NM_130877, exon 2 of 2)	3' UTR (NM_130877, exon 2 of 2)	12771	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_68221.1	chr7	104412298	104412320	-	1	NA	exon (NM_009099, exon 6 of 8)	exon (NM_009099, exon 6 of 8)	52884	NM_009099	20128	Mm.295578	NM_009099	ENSMUSG00000030921	Trim30a	Rpt-1|Rpt1|Trim30	tripartite motif-containing 30A	protein-coding
mm_83971.1	chr9	57203074	57203086	-	1	NA	Intergenic	Intergenic	27805	NR_033784	67319	Mm.234187	NR_033784	ENSMUSG00000100282	1700041C23Rik	-	RIKEN cDNA 1700041C23 gene	ncRNA
mm_98408.1	chr11	94352170	94352192	+	1	NA	exon (NM_029600, exon 27 of 31)	exon (NM_029600, exon 27 of 31)	24180	NM_146024	71452	Mm.141054	NM_027799	ENSMUSG00000020864	Ankrd40	1110011C06Rik|5530600A18Rik|Gcap15	ankyrin repeat domain 40	protein-coding
mm_71684.1	chr8	61224188	61224211	+	1	NA	promoter-TSS (NM_021506)	promoter-TSS (NM_021506)	28	NM_021506	59009	Mm.27949	NM_021506	ENSMUSG00000031642	Sh3rf1	2200003J05Rik|Posh|R75531|Sh3md2	SH3 domain containing ring finger 1	protein-coding
mm_56198.1	chr6	88874050	88874070	-	1	NA	promoter-TSS (NM_176973)	promoter-TSS (NM_176973)	-16	NM_176973	319655	Mm.302613	NM_176973	ENSMUSG00000033152	Podxl2	D130074J02Rik|PODLX2	podocalyxin-like 2	protein-coding
mm_135175.1	chr16	35938942	35938979	-	1	NA	promoter-TSS (NM_001013371)	promoter-TSS (NM_001013371)	67	NM_001013371	209200	Mm.390852	NM_001013371	ENSMUSG00000049502	Dtx3l	AU042200|BC023741	deltex 3-like, E3 ubiquitin ligase	protein-coding
mm_124540.1	chr14	122464214	122464224	-	1	NA	exon (NM_022987, exon 1 of 2)	exon (NM_022987, exon 1 of 2)	1439	NM_022987	65100	Mm.390761	NM_022987	ENSMUSG00000041703	Zic5	1700049L20Rik|Opr	zinc finger protein of the cerebellum 5	protein-coding
mm_91165.1	chr10	20689091	20689103	-	1	NA	intron (NM_013875, intron 1 of 12)	ID4_|SINE|ID	35981	NM_013875	29863	Mm.425617	NM_013875	ENSMUSG00000019990	Pde7b	-	phosphodiesterase 7B	protein-coding
mm_96301.1	chr11	63151214	63151234	+	1	NA	exon (NM_008885, exon 4 of 5)	exon (NM_008885, exon 4 of 5)	18421	NM_001302260	18858	Mm.1237	NM_008885	ENSMUSG00000018217	Pmp22	22kDa|Gas-3|HNPP|Tr|trembler	peripheral myelin protein 22	protein-coding
mm_139674.1	chr17	57412402	57412424	+	1	NA	intron (NM_010130, intron 9 of 21)	intron (NM_010130, intron 9 of 21)	53727	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_21713.1	chr2	164608658	164608662	-	1	NA	exon (NM_001080550, exon 3 of 8)	exon (NM_001080550, exon 3 of 8)	4726	NM_001276432	277343	Mm.383292	NM_001080550	ENSMUSG00000070533	Wfdc8	Gm706	WAP four-disulfide core domain 8	protein-coding
mm_93393.1	chr10	107494720	107494742	-	1	NA	promoter-TSS (NM_008657)	promoter-TSS (NM_008657)	-2	NM_008657	17878	Mm.11	NM_008657	ENSMUSG00000035923	Myf6	MRF4|bHLHc4|herculin	myogenic factor 6	protein-coding
mm_139267.1	chr17	47785730	47785739	+	1	NA	promoter-TSS (NM_011549)	promoter-TSS (NM_011549)	-10	NM_011549	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_159790.1	chr5	108585402	108585402	-	1	NA	exon (NM_153569, exon 19 of 28)	exon (NM_153569, exon 19 of 28)	-35375	NM_007756	12889	Mm.5195	NM_007756	ENSMUSG00000033615	Cplx1	921-S	complexin 1	protein-coding
mm_21410.1	chr2	158118880	158118886	-	1	NA	exon (NM_009373, exon 12 of 13)	exon (NM_009373, exon 12 of 13)	-27086	NR_040609	72340	Mm.443395	NR_040609	ENSMUSG00000100860	2010009K17Rik	-	RIKEN cDNA 2010009K17 gene	ncRNA
mm_160329.1	chr8	4134535	4134535	+	1	NA	promoter-TSS (NM_027343)	promoter-TSS (NM_027343)	-201	NM_027343	70192	Mm.390006	NM_027343	ENSMUSG00000079168	Cd209g	2310066I10Rik|AI481039|SIGNR7	CD209g antigen	protein-coding
mm_38180.1	chr4	135272735	135272747	-	1	NA	promoter-TSS (NM_013885)	promoter-TSS (NM_013885)	19	NM_013885	29876	Mm.257765	NM_013885	ENSMUSG00000037242	Clic4	D0Jmb3|TU-74|mc3s5|mtCLIC	chloride intracellular channel 4 (mitochondrial)	protein-coding
mm_40223.1	chr5	37245824	37245883	+	1	NA	promoter-TSS (NM_007765)	promoter-TSS (NM_007765)	89	NM_007765	12933	Mm.290995	NM_007765	ENSMUSG00000029121	Crmp1	CRMP-1|DRP-1|Dpysl1|ULIP-3|Ulip3	collapsin response mediator protein 1	protein-coding
mm_156066.1	chrX	109160923	109160967	+	1	NA	3' UTR (NM_019989, exon 4 of 4)	3' UTR (NM_019989, exon 4 of 4)	-35811	NM_001037917	622976	Mm.482747	NM_001037917	ENSMUSG00000048621	Gm6377	EG622976	predicted gene 6377	protein-coding
mm_151621.1	chr19	3905270	3905292	-	1	NA	promoter-TSS (NM_016921)	promoter-TSS (NM_016921)	-51	NM_016921	27060	Mm.271689	NM_016921	ENSMUSG00000001750	Tcirg1	ATP6N1C|ATP6a3|Atp6i|OC-116|OPTB1|Stv1|TIRC7|Vph1|oc	T cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 protein A3	protein-coding
mm_15166.1	chr2	154011441	154011451	+	1	NA	exon (NM_008953, exon 5 of 9)	exon (NM_008953, exon 5 of 9)	3170	NM_008953	19194	Mm.29197	NM_008953	ENSMUSG00000042459	Bpifa2	Bpifa2e|Psp	BPI fold containing family A, member 2	protein-coding
mm_104740.1	chr11	98400394	98400446	-	1	NA	promoter-TSS (NM_001033537)	promoter-TSS (NM_001033537)	70	NM_001033537	320655	Mm.86519	NM_001033537	ENSMUSG00000038208	Pgap3	CAB2|D430035D22Rik|Perld1	post-GPI attachment to proteins 3	protein-coding
mm_4113.1	chr1	167689109	167689126	+	1	NA	promoter-TSS (NM_033652)	promoter-TSS (NM_033652)	-441	NM_033652	110648	Mm.330081	NM_033652	ENSMUSG00000026686	Lmx1a	Lmx1.1|dr|dreher|sst	LIM homeobox transcription factor 1 alpha	protein-coding
mm_98344.1	chr11	93099285	93099331	+	1	NA	promoter-TSS (NM_028296)	promoter-TSS (NM_028296)	18	NM_028296	72605	Mm.342160	NM_028296	ENSMUSG00000056158	Car10	2700029L05Rik|BB085816|Ca10	carbonic anhydrase 10	protein-coding
mm_143024.1	chr17	56571501	56571513	-	1	NA	exon (NM_001029979, exon 10 of 21)	exon (NM_001029979, exon 10 of 21)	13076	NM_001029979	224902	Mm.214973	NM_001029979	ENSMUSG00000042625	Safb2	AA389433|AI255170|mKIAA0138	scaffold attachment factor B2	protein-coding
mm_63783.1	chr7	131877083	131877089	+	1	NA	Intergenic	Intergenic	-89374	NM_173410	233919	Mm.208740	NM_173410	ENSMUSG00000040125	Gpr26	9630036A11Rik|A730021D22	G protein-coupled receptor 26	protein-coding
mm_136220.1	chr16	90052365	90052367	-	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-77667	NM_001145886	21844	Mm.310902	NM_009384	ENSMUSG00000002489	Tiam1	AI847750|D16Ium10|D16Ium10e	T cell lymphoma invasion and metastasis 1	protein-coding
mm_159186.1	chr2	112559443	112559443	+	1	NA	promoter-TSS (NM_001165935)	promoter-TSS (NM_001165935)	-239	NM_001165935	74268	Mm.315125	NM_028844	ENSMUSG00000003604	Aven	1700013A01Rik|1700056A21Rik|mAven-L|mAven-S	apoptosis, caspase activation inhibitor	protein-coding
mm_55145.1	chr6	51466220	51466225	-	1	NA	exon (NM_182650, exon 6 of 10)	exon (NM_182650, exon 6 of 10)	3672	NM_182650	53379	Mm.155896	NM_016806	ENSMUSG00000004980	Hnrnpa2b1	9130414A06Rik|Hnrpa2|Hnrpa2b1|hnrnp-A	heterogeneous nuclear ribonucleoprotein A2/B1	protein-coding
mm_146199.1	chr18	76241893	76241959	+	1	NA	5' UTR (NM_010754, exon 1 of 11)	5' UTR (NM_010754, exon 1 of 11)	225	NM_010754	17126	Mm.152699	NM_010754	ENSMUSG00000024563	Smad2	7120426M23Rik|Madh2|Madr2|Smad-2|mMad2	SMAD family member 2	protein-coding
mm_63740.1	chr7	130900562	130900596	+	1	NA	exon (NM_133942, exon 5 of 10)	exon (NM_133942, exon 5 of 10)	-7689	NR_106028	102466219		NR_106028	ENSMUSG00000104914	Mir7061	mmu-mir-7061	microRNA 7061	ncRNA
mm_100394.1	chr11	119390507	119390522	+	1	NA	promoter-TSS (NR_035453)	promoter-TSS (NR_035453)	42	NR_035453	100316690		NR_035453	ENSMUSG00000088015	Mir1932	mir-1932|mmu-mir-1932	microRNA 1932	ncRNA
mm_161410.1	chr15	7810883	7810883	+	1	NA	5' UTR (NM_010275, exon 1 of 3)	5' UTR (NM_010275, exon 1 of 3)	835	NM_001301332	14573	Mm.4679	NM_010275	ENSMUSG00000022144	Gdnf	AI385739|ATF	glial cell line derived neurotrophic factor	protein-coding
mm_115731.1	chr13	17752979	17752986	-	1	NA	intron (NM_027118, intron 5 of 13)	intron (NM_027118, intron 5 of 13)	5509	NR_035412	100316665		NR_035412	ENSMUSG00000080574	Mir466i	Mirn466i|mmu-mir-466i	microRNA 466i	ncRNA
mm_12008.1	chr2	57317407	57317445	+	1	NA	intron (NM_001145820, intron 6 of 16)	B3|SINE|B2	79044	NM_010274	14571	Mm.3711	NM_010274	ENSMUSG00000026827	Gpd2	AA408484|AI448216|AU021455|AW494132|GPDH|Gdm1|Gpd-m|Gpdh-m|TISP38	glycerol phosphate dehydrogenase 2, mitochondrial	protein-coding
mm_69814.1	chr7	141263955	141263971	-	1	NA	exon (NM_001252601, exon 8 of 10)	exon (NM_001252601, exon 8 of 10)	2461	NM_001252601	54123	Mm.3233	NM_016850	ENSMUSG00000025498	Irf7	-	interferon regulatory factor 7	protein-coding
mm_61421.1	chr7	73618696	73618709	+	1	NA	Intergenic	CpG	-60307	NR_037569	69170	Mm.34539	NR_037569	ENSMUSG00000101970	1810026B05Rik	-	RIKEN cDNA 1810026B05 gene	ncRNA
mm_106223.1	chr11	117083708	117083731	-	1	NA	Intergenic	Intergenic	6371	NR_105853	102465258		NR_105853	ENSMUSG00000104740	Mir6516	mmu-mir-6516	microRNA 6516	ncRNA
mm_112585.1	chr13	13765535	13765548	+	1	NA	intron (NM_010748, intron 50 of 52)	Lx7|LINE|L1	-18518	NM_001302997	14706	Mm.215394	NM_010317	ENSMUSG00000021303	Gng4	-	guanine nucleotide binding protein (G protein), gamma 4	protein-coding
mm_113556.1	chr13	38151344	38151354	+	1	NA	promoter-TSS (NM_023842)	promoter-TSS (NM_023842)	55	NM_023842	109620	Mm.355327	NM_023842	ENSMUSG00000054889	Dsp	2300002E22Rik|5730453H04Rik|AA407887|AA407888|AW109828|DP|rul	desmoplakin	protein-coding
mm_86257.1	chr9	121586936	121586946	-	1	NA	promoter-TSS (NR_040740)	promoter-TSS (NR_040740)	-79	NR_040740	75384	Mm.445955	NR_040740	ENSMUSG00000084995	Lyzl4os	4930589B17Rik|4930596M17Rik	lysozyme-like 4, opposite strand	ncRNA
mm_43617.1	chr5	138097650	138097650	+	1	NA	intron (NM_133906, intron 5 of 5)	intron (NM_133906, intron 5 of 5)	12566	NM_029869	74570	Mm.213114	NM_029869	ENSMUSG00000029729	Zkscan1	5930429A01Rik|9130423L19Rik|9230118B16Rik|AI646829|AI788588|C87323|KOX18|PHZ-37|ZNF139	zinc finger with KRAB and SCAN domains 1	protein-coding
mm_48786.1	chr5	148589870	148589877	-	1	NA	Intergenic	RMER17C|LTR|ERVK	-37085	NM_011908	24109	Mm.21846	NM_011908	ENSMUSG00000001687	Ubl3	AW108023|HCG	ubiquitin-like 3	protein-coding
mm_80195.1	chr9	72396328	72396345	+	1	NA	Intergenic	Intergenic	-42193	NM_008613	17427	Mm.387671	NM_008613	ENSMUSG00000032221	Mns1	AW546487	meiosis-specific nuclear structural protein 1	protein-coding
mm_112204.1	chr12	113426891	113426906	-	1	NA	Intergenic	Intergenic	-62667	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_170371.1	chr18	54699229	54699234	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	87487	NR_045400	328957	Mm.402781	NR_045400		9330117O12Rik	9330117O12	RIKEN cDNA 9330117O12 gene	ncRNA
mm_151294.1	chr19	55425242	55425254	+	1	NA	intron (NM_001293685, intron 6 of 8)	intron (NM_001293685, intron 6 of 8)	109191	NM_001293686	53611	Mm.258637	NM_016862	ENSMUSG00000024983	Vti1a	1110014F16Rik|1110018K19Rik|4921537J05Rik|MVti1|MVti1a|Vti1|Vti1-rp2	vesicle transport through interaction with t-SNAREs 1A	protein-coding
mm_44693.1	chr5	30232367	30232409	-	1	NA	promoter-TSS (NM_027652)	promoter-TSS (NM_027652)	-193	NM_027652	28042	Mm.168854	NM_027652	ENSMUSG00000075703	Selenoi	4933402G07Rik|AI448296|AI452230|C79563|D5Wsu178e|Ept1|SELI|mKIAA1724	selenoprotein I	protein-coding
mm_80251.1	chr9	72749376	72749393	+	1	NA	3' UTR (NM_010890, exon 29 of 29)	3' UTR (NM_010890, exon 29 of 29)	-57890	NM_175485	235472	Mm.31696	NM_175485	ENSMUSG00000036030	Prtg	A230098A12Rik|Igdcc5	protogenin	protein-coding
mm_169132.1	chr1	35885973	35885974	-	1	NA	Intergenic	Intergenic	-182427	NM_015818	50785	Mm.213566	NM_015818	ENSMUSG00000045216	Hs6st1	6Ost1	heparan sulfate 6-O-sulfotransferase 1	protein-coding
mm_91680.1	chr10	43656330	43656332	-	1	NA	Intergenic	RSINE1|SINE|B4	62904	NR_033558	414125	Mm.244305	NR_033558	ENSMUSG00000075184	F830002L21Rik	F930017D23Rik	RIKEN cDNA F830002L21 gene	ncRNA
mm_36090.1	chr4	58482099	58482110	-	1	NA	intron (NM_001290486, intron 2 of 2)	Lx7|LINE|L1	17299	NM_001290486	14745	Mm.4772	NM_010336	ENSMUSG00000038668	Lpar1	AI326300|Edg2|Gpcr26|Kdt2|lpA1|vzg-1	lysophosphatidic acid receptor 1	protein-coding
mm_54393.1	chr6	31220300	31220368	-	1	NA	promoter-TSS (NR_040262)	promoter-TSS (NR_040262)	-17	NR_040258	73652	Mm.441297	NR_040257	ENSMUSG00000087380	2210408F21Rik	-	RIKEN cDNA 2210408F21 gene	ncRNA
mm_162882.1	chr10	101963743	101963743	-	1	NA	intron (NM_001205098, intron 2 of 7)	Lx7|LINE|L1	191051	NR_037211	100526516		NR_037211	ENSMUSG00000092952	Mir3059	mir-3059|mmu-mir-3059	microRNA 3059	ncRNA
mm_71979.1	chr8	70594467	70594512	+	1	NA	promoter-TSS (NM_023627)	promoter-TSS (NM_023627)	8	NM_023627	71780	Mm.29357	NM_023627	ENSMUSG00000019139	Isyna1	1300017C10Rik|AU018670	myo-inositol 1-phosphate synthase A1	protein-coding
mm_98158.1	chr11	87657622	87657626	+	1	NA	3' UTR (NM_001045527, exon 6 of 6)	3' UTR (NM_001045527, exon 6 of 6)	-5463	NM_172448	207742	Mm.440230	NM_172448	ENSMUSG00000034177	Rnf43	4732452J19Rik	ring finger protein 43	protein-coding
mm_122666.1	chr14	51914066	51914076	-	1	NA	promoter-TSS (NM_001145959)	promoter-TSS (NM_001145959)	-583	NM_013864	29811	Mm.26722	NM_013864	ENSMUSG00000004558	Ndrg2	AI182517|AU040374|Ndr2|SYLD	N-myc downstream regulated gene 2	protein-coding
mm_33707.1	chr4	133672674	133672733	+	1	NA	promoter-TSS (NM_178698)	promoter-TSS (NM_178698)	-56	NM_001145956	230801	Mm.217004	NM_178698	ENSMUSG00000043257	Pigv	B330013B03|D430024F16Rik	phosphatidylinositol glycan anchor biosynthesis, class V	protein-coding
mm_91897.1	chr10	60003035	60003048	-	1	NA	promoter-TSS (NM_001199187)	promoter-TSS (NM_001199187)	94	NM_001347451	52717	Mm.21793	NM_025514	ENSMUSG00000020107	Anapc16	2310005G07Rik|APC16|D10Ertd641e	anaphase promoting complex subunit 16	protein-coding
mm_45639.1	chr5	76905380	76905393	-	1	NA	intron (NM_173765, intron 1 of 15)	CpG	128	NM_173765	231326	Mm.39271	NM_173765	ENSMUSG00000055923	Aasdh	A230062G08Rik|A830035E16|Acsf4|U26	aminoadipate-semialdehyde dehydrogenase	protein-coding
mm_161327.1	chr14	50126701	50126701	+	1	NA	exon (NM_146319, exon 1 of 1)	exon (NM_146319, exon 1 of 1)	148	NM_146319	258316	Mm.223012	NM_146319	ENSMUSG00000059488	Olfr727	MOR246-2	olfactory receptor 727	protein-coding
mm_170190.1	chr17	6493172	6493186	-	1	NA	Intergenic	Intergenic	-42185	NR_033520	547127	Mm.297552	NM_001045538		Tmem181b-ps	Tmem181b	transmembrane protein 181B, pseudogene	pseudo
mm_157278.1	chrX	20617449	20617471	-	1	NA	promoter-TSS (NM_145627)	promoter-TSS (NM_145627)	-43	NM_001167775	236732	Mm.279194	NM_145627	ENSMUSG00000031060	Rbm10	E430039K10Rik	RNA binding motif protein 10	protein-coding
mm_8648.1	chr1	156439310	156439319	-	1	NA	exon (NM_009230, exon 10 of 16)	exon (NM_009230, exon 10 of 16)	-18399	NM_001346967	77352	Mm.428709	NM_001033180	ENSMUSG00000026601	Axdnd1	9430070O13Rik|Gm979	axonemal dynein light chain domain containing 1	protein-coding
mm_149477.1	chr19	11749994	11749996	+	1	NA	intron (NM_008118, intron 3 of 8)	intron (NM_008118, intron 3 of 8)	2436	NM_008118	14603	Mm.456	NM_008118	ENSMUSG00000024682	Gif	AV073125	gastric intrinsic factor	protein-coding
mm_115927.1	chr13	23571132	23571141	-	1	NA	promoter-TSS (NM_178196)	promoter-TSS (NM_178196)	84	NM_178187	319166	Mm.261665	NM_178187	ENSMUSG00000069272	Hist1h2ae	1190022L06	histone cluster 1, H2ae	protein-coding
mm_10638.1	chr2	20519594	20519651	+	1	NA	5' UTR (NM_178059, exon 2 of 19)	5' UTR (NM_178059, exon 2 of 19)	109	NM_001177631	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding
mm_30568.1	chr4	3790392	3790395	+	1	NA	3' UTR (NM_001111096, exon 13 of 13)	3' UTR (NM_001111096, exon 13 of 13)	45262	NM_026147	67427	Mm.21938	NM_026147	ENSMUSG00000028234	Rps20	4632426K06Rik|Dsk4	ribosomal protein S20	protein-coding
mm_10376.1	chr2	11777767	11777797	+	1	NA	promoter-TSS (NM_177268)	promoter-TSS (NM_177268)	29	NM_177268	320816	Mm.260201	NM_177268	ENSMUSG00000047909	Ankrd16	2810455F06Rik|AI646698|D430029B21Rik	ankyrin repeat domain 16	protein-coding
mm_159434.1	chr3	116614451	116614451	-	1	NA	5' UTR (NM_030016, exon 1 of 12)	5' UTR (NM_030016, exon 1 of 12)	136	NM_030016	229780	Mm.259648	NM_030016	ENSMUSG00000033439	Trmt13	4631408H19Rik|A330067P21|A930028L21Rik|Ccdc76	tRNA methyltransferase 13	protein-coding
mm_13831.1	chr2	119325814	119325817	+	1	NA	promoter-TSS (NM_019454)	promoter-TSS (NM_019454)	31	NM_019454	54485	Mm.143719	NM_019454	ENSMUSG00000027314	Dll4	Delta4	delta-like 4 (Drosophila)	protein-coding
mm_5321.1	chr1	22805995	22806007	-	1	NA	promoter-TSS (NM_001012625)	promoter-TSS (NM_001012625)	-277	NM_001012624	116837	Mm.60061	NM_053270	ENSMUSG00000041670	Rims1	C030033M19Rik|RIM1|RIM1a|RIM1alpha|Rab3ip1|Rim|Serg1|mKIAA0340	regulating synaptic membrane exocytosis 1	protein-coding
mm_76867.1	chr8	105497024	105497068	-	1	NA	promoter-TSS (NM_175160)	promoter-TSS (NM_175160)	-176	NM_175160	70796	Mm.100917	NM_175160	ENSMUSG00000039199	Zdhhc1	4432412D04Rik	zinc finger, DHHC domain containing 1	protein-coding
mm_29414.1	chr3	108972412	108972447	-	1	NA	3' UTR (NM_001163567, exon 11 of 11)	3' UTR (NM_001163567, exon 11 of 11)	31872	NM_001078646	66715	Mm.158124	NM_025723	ENSMUSG00000045662	Henmt1	4921515J06Rik|Hen1|mHEN1	HEN1 methyltransferase homolog 1 (Arabidopsis)	protein-coding
mm_48960.1	chr6	4541039	4541055	+	1	NA	3' UTR (NM_007743, exon 52 of 52)	3' UTR (NM_007743, exon 52 of 52)	35429	NM_007743	12843	Mm.277792	NM_007743	ENSMUSG00000029661	Col1a2	AA960264|AI325291|Col1a-2|Cola-2|Cola2|oim	collagen, type I, alpha 2	protein-coding
mm_104302.1	chr11	90554019	90554027	-	1	NA	intron (NM_011505, intron 12 of 17)	intron (NM_011505, intron 12 of 17)	84085	NM_011505	20913	Mm.207203	NM_011505	ENSMUSG00000020546	Stxbp4	6030470M02Rik|Synip	syntaxin binding protein 4	protein-coding
mm_110030.1	chr12	16800974	16801014	-	1	NA	promoter-TSS (NM_015764)	promoter-TSS (NM_015764)	-108	NM_015764	268527	Mm.428062	NM_015764	ENSMUSG00000036523	Greb1	5730583K22Rik|9130004E13|AF180470|AU023194|mKIAA0575	gene regulated by estrogen in breast cancer protein	protein-coding
mm_139173.1	chr17	47588547	47588550	+	1	NA	intron (NM_001081635, intron 2 of 6)	PB1D7|SINE|Alu	-4919	NM_007632	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_139701.1	chr17	57451400	57451423	+	1	NA	intron (NM_010130, intron 17 of 21)	intron (NM_010130, intron 17 of 21)	92725	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_110122.1	chr12	26444110	26444112	-	1	NA	3' UTR (NM_021384, exon 6 of 6)	3' UTR (NM_021384, exon 6 of 6)	12341	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_137245.1	chr17	24488584	24488666	+	1	NA	promoter-TSS (NM_027937)	promoter-TSS (NM_027937)	-158	NM_027937	268932	Mm.70989	NM_027937	ENSMUSG00000033597	Caskin1	3300002N10Rik|C130061I24|C630036E02Rik|mKIAA1306	CASK interacting protein 1	protein-coding
mm_100010.1	chr11	114852220	114852242	+	1	NA	5' UTR (NM_147217, exon 1 of 4)	5' UTR (NM_147217, exon 1 of 4)	201	NM_147217	70355	Mm.242413	NM_147217	ENSMUSG00000051043	Gprc5c	1110028I06Rik|3200002M13Rik|Raig3	G protein-coupled receptor, family C, group 5, member C	protein-coding
mm_106096.1	chr11	116199007	116199037	-	1	NA	promoter-TSS (NM_015729)	promoter-TSS (NM_015729)	23	NM_001271898	11430	Mm.356689	NM_015729	ENSMUSG00000020777	Acox1	AOX|Acox|D130055E20Rik|Paox	acyl-Coenzyme A oxidase 1, palmitoyl	protein-coding
mm_150067.1	chr19	29386380	29386384	+	1	NA	3' UTR (NM_021893, exon 7 of 7)	3' UTR (NM_021893, exon 7 of 7)	18944	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_165956.1	chr4	87230034	87230060	-	1	NA	intron (NM_172426, intron 1 of 10)	intron (NM_172426, intron 1 of 10)	493	NM_172426	76376	Mm.490487	NM_172426	ENSMUSG00000037996	Slc24a2	2810021B17Rik|6330417K15Rik|AI847460|Nckx2	solute carrier family 24 (sodium/potassium/calcium exchanger), member 2	protein-coding
mm_138969.1	chr17	44777295	44777333	+	1	NA	5' UTR (NM_178652, exon 1 of 12)	5' UTR (NM_178652, exon 1 of 12)	143	NM_178652	109115	Mm.431327	NM_178652	ENSMUSG00000038954	Supt3	2310066G22Rik|AI315192|SPT3|SPT3L|Supt3h	suppressor of Ty 3	protein-coding
mm_27931.1	chr3	79567748	79567764	-	1	NA	promoter-TSS (NM_001162999)	promoter-TSS (NM_001162999)	-77	NM_001162999	329679	Mm.244005	NM_001162999	ENSMUSG00000061175	Fnip2	D630023B12Rik|mKIAA1450	folliculin interacting protein 2	protein-coding
mm_136289.1	chr16	91406831	91406860	-	1	NA	intron (NM_008349, intron 1 of 6)	intron (NM_008349, intron 1 of 6)	610	NM_008349	16155	Mm.4154	NM_008349	ENSMUSG00000022969	Il10rb	6620401D04Rik|AI528744|CRF2-4|Crfb4|D16H21S58|D21S58h|IL-10R2|Il10r2	interleukin 10 receptor, beta	protein-coding
mm_106947.1	chr12	8771379	8771394	+	1	NA	promoter-TSS (NM_011519)	promoter-TSS (NM_011519)	-10	NM_011519	20969	Mm.2580	NM_011519	ENSMUSG00000020592	Sdc1	AA408134|AA409076|CD138|Sstn|Synd|Synd1|syn-1	syndecan 1	protein-coding
mm_24407.1	chr3	90433792	90433820	+	1	NA	promoter-TSS (NM_178876)	promoter-TSS (NM_178876)	-170	NM_178876	229543	Mm.268564	NM_145540	ENSMUSG00000027933	Ints3	C77668	integrator complex subunit 3	protein-coding
mm_79111.1	chr9	46270169	46270179	+	1	NA	exon (NM_080434, exon 4 of 4)	exon (NM_080434, exon 4 of 4)	1566	NM_080434	66113	Mm.29738	NM_080434	ENSMUSG00000032079	Apoa5	1300007O05Rik|Apoav|RAP3	apolipoprotein A-V	protein-coding
mm_60753.1	chr7	45486361	45486399	+	1	NA	5' UTR (NM_001290999, exon 1 of 10)	5' UTR (NM_001290999, exon 1 of 10)	117	NM_001290999	56734	Mm.439742	NM_008807	ENSMUSG00000023467	Tulp2	Pdet	tubby-like protein 2	protein-coding
mm_71028.1	chr8	33599609	33599655	+	1	NA	promoter-TSS (NM_017374)	promoter-TSS (NM_017374)	11	NM_017374	19053	Mm.29301	NM_017374	ENSMUSG00000009630	Ppp2cb	AI115466|D8Ertd766e|PP2Ac	protein phosphatase 2 (formerly 2A), catalytic subunit, beta isoform	protein-coding
mm_127311.1	chr15	100246184	100246204	+	1	NA	intron (NM_007497, intron 3 of 6)	intron (NM_007497, intron 3 of 6)	18335	NM_007497	11908	Mm.676	NM_007497	ENSMUSG00000023027	Atf1	-	activating transcription factor 1	protein-coding
mm_57176.1	chr6	122848204	122848219	-	1	NA	3' UTR (NM_009779, exon 2 of 2)	3' UTR (NM_009779, exon 2 of 2)	7946	NM_009779	12267	Mm.2408	NM_009779	ENSMUSG00000040552	C3ar1	AZ3B|C3AR|HNFAG09	complement component 3a receptor 1	protein-coding
mm_23296.1	chr3	52268394	52268405	+	1	NA	promoter-TSS (NM_019739)	promoter-TSS (NM_019739)	62	NM_019739	56458	Mm.29891	NM_019739	ENSMUSG00000044167	Foxo1	AI876417|Afxh|FKHR|Fkhr1|Foxo1a	forkhead box O1	protein-coding
mm_44385.1	chr5	17828884	17828890	-	1	NA	exon (NM_001159558, exon 4 of 16)	exon (NM_001159558, exon 4 of 16)	7009	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_64638.1	chr7	3984207	3984218	-	1	NA	Intergenic	Intergenic	-68711	NR_028115	18726	Mm.440989	NM_011090	ENSMUSG00000030427	Lilra6	7M1|Pira3	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	protein-coding
mm_77823.1	chr9	3404059	3404098	+	1	NA	promoter-TSS (NM_027545)	promoter-TSS (NM_027545)	-7	NM_027545	244672	Mm.245482	NM_027545	ENSMUSG00000025898	Cwf19l2	3230401L03Rik|9030209E10	CWF19-like 2, cell cycle control (S. pombe)	protein-coding
mm_127157.1	chr15	98626681	98626687	+	1	NA	Intergenic	Intergenic	-5644	NM_001044741	12297	Mm.3544	NM_007581	ENSMUSG00000003352	Cacnb3	Beta3|CAB3|Ca(v)beta3|Cchb3	calcium channel, voltage-dependent, beta 3 subunit	protein-coding
mm_94371.1	chr11	5099267	5099279	+	1	NA	promoter-TSS (NM_177370)	promoter-TSS (NM_177370)	0	NM_001290492	279766	Mm.260866	NM_177370	ENSMUSG00000034175	Rhbdd3	Ptag	rhomboid domain containing 3	protein-coding
mm_135234.1	chr16	36957319	36957336	-	1	NA	exon (NM_008225, exon 10 of 14)	exon (NM_008225, exon 10 of 14)	21809	NM_001037321	207215	Mm.211899	NM_001037321	ENSMUSG00000047746	Fbxo40	9830003A13Rik|mKIAA1195	F-box protein 40	protein-coding
mm_7209.1	chr1	93076244	93076255	-	1	NA	exon (NM_008440, exon 6 of 48)	exon (NM_008440, exon 6 of 48)	6231	NM_001294150	16560	Mm.276408	NM_008440	ENSMUSG00000014602	Kif1a	ATSV|C630002N23Rik|Gm1626|Kns1	kinesin family member 1A	protein-coding
mm_45190.1	chr5	52115934	52115979	-	1	NA	Intergenic	CpG	20061	NR_105845	102466648		NR_105845	ENSMUSG00000098726	Mir6417	Gm27334|mmu-mir-6417	microRNA 6417	ncRNA
mm_5153.1	chr1	9943591	9943608	-	1	NA	intron (NR_024067, intron 1 of 3)	(A)n|Simple_repeat|Simple_repeat	519	NR_024067	73824	Mm.28311	NR_024067	ENSMUSG00000098234	Snhg6	1110008H02Rik	small nucleolar RNA host gene 6	ncRNA
mm_27411.1	chr3	51394898	51394901	-	1	NA	intron (NM_026358, intron 1 of 3)	ID4|SINE|ID	1648	NM_026358	67749	Mm.273339	NM_026358	ENSMUSG00000037161	Mgarp	4930583H14Rik|AI195347|CESP-1|HUMMR|Osap|Qsap	mitochondria localized glutamic acid rich protein	protein-coding
mm_36223.1	chr4	62520055	62520079	-	1	NA	promoter-TSS (NM_001276446)	promoter-TSS (NM_001276446)	-4	NM_008525	17025	Mm.6988	NM_008525	ENSMUSG00000028393	Alad	ALADH|Lv	aminolevulinate, delta-, dehydratase	protein-coding
mm_63395.1	chr7	127296237	127296247	+	1	NA	promoter-TSS (NM_001253873)	promoter-TSS (NM_001253873)	-18	NM_001253873	16408	Mm.1618	NM_008400	ENSMUSG00000030830	Itgal	(p180)|Cd11a|LFA-1|LFA-1A|Ly-15|Ly-21	integrin alpha L	protein-coding
mm_53376.1	chr6	129471687	129471694	+	1	NA	intron (NR_132130, intron 1 of 5)	intron (NR_132130, intron 1 of 5)	1089	NM_001309637	56644	Mm.239516	NM_020008	ENSMUSG00000079293	Clec7a	BGR|Clecsf12|beta-GR	C-type lectin domain family 7, member a	protein-coding
mm_154508.1	chrM	12125	12146	-	1	NA	NA	Intergenic	NA	NA								
mm_103885.1	chr11	83574328	83574349	-	1	NA	3' UTR (NM_011338, exon 4 of 4)	3' UTR (NM_011338, exon 4 of 4)	4298	NM_011338	20308	Mm.416125	NM_011338	ENSMUSG00000019122	Ccl9	CCF18|MRP-2|Scya10|Scya9	chemokine (C-C motif) ligand 9	protein-coding
mm_32434.1	chr4	107200632	107200735	+	1	NA	3' UTR (NM_029565, exon 8 of 8)	3' UTR (NM_029565, exon 8 of 8)	-8497	NM_001081272	546840	Mm.331755	NM_001081272	ENSMUSG00000070877	Ldlrad1	OTTMUSG00000008594	low density lipoprotein receptor class A domain containing 1	protein-coding
mm_88928.1	chr10	81257278	81257309	+	1	NA	promoter-TSS (NM_001285854)	promoter-TSS (NM_001285854)	-6	NM_001285854	17179	Mm.2918	NM_010768	ENSMUSG00000004933	Matk	CHK|HYL|Ntk|p56ntk	megakaryocyte-associated tyrosine kinase	protein-coding
mm_163300.1	chr11	120479649	120479680	+	1	NA	exon (NM_008244, exon 16 of 22)	exon (NM_008244, exon 16 of 22)	-5005	NM_027204	56282	Mm.133851	NM_027204	ENSMUSG00000039640	Mrpl12	0610034O11Rik|1500031N16Rik|MRP-L12|Rpml12	mitochondrial ribosomal protein L12	protein-coding
mm_50735.1	chr6	52714051	52714078	+	1	NA	intron (NM_025816, intron 1 of 17)	CpG	335	NM_025816	52440	Mm.389757	NM_025816	ENSMUSG00000004535	Tax1bp1	1200003J11Rik|1700069J21Rik|AA930106|D6Ertd404e|D6Ertd772e|T6bp|TXBP151	Tax1 (human T cell leukemia virus type I) binding protein 1	protein-coding
mm_127344.1	chr15	100615621	100615677	+	1	NA	promoter-TSS (NM_011873)	promoter-TSS (NM_011873)	-13	NM_011873	23994	Mm.486175	NM_011873	ENSMUSG00000000346	Dazap2	AI314727|Brbp|Gcap28|Prtb|gt6-12|mKIAA0058	DAZ associated protein 2	protein-coding
mm_98725.1	chr11	96351597	96351635	+	1	NA	promoter-TSS (NM_134032)	promoter-TSS (NM_134032)	-16	NM_134032	103889	Mm.281153	NM_134032	ENSMUSG00000075588	Hoxb2	AI894218|Hox-2.8|Hoxbes2	homeobox B2	protein-coding
mm_171113.1	chr3	13821386	13821401	-	1	NA	intron (NM_178631, intron 3 of 9)	IAPLTR1_Mm|LTR|ERVK	-124979	NM_001163329	76897	Mm.422625	NM_178631	ENSMUSG00000039717	Ralyl	0710005M24Rik	RALY RNA binding protein-like	protein-coding
mm_81448.1	chr9	109816580	109816587	+	1	NA	promoter-TSS (NM_183136)	promoter-TSS (NM_183136)	-44	NM_183136	78709	Mm.99613	NM_183136	ENSMUSG00000050074	Spink8	C630041L24Rik	serine peptidase inhibitor, Kazal type 8	protein-coding
mm_136225.1	chr16	90143830	90143857	-	1	NA	non-coding (NR_033476, exon 1 of 1)	non-coding (NR_033476, exon 1 of 1)	1606	NR_033476	100038709	Mm.484070	NR_033476		Gm10789	ENSMUSG00000074924	predicted gene 10789	ncRNA
mm_4827.1	chr1	185487329	185487344	+	1	NA	Intergenic	Intergenic	-9970	NR_033600	114668	Mm.379303	NR_033600	ENSMUSG00000102185	5033404E19Rik	-	NSA2 ribosome biogenesis homolog pseudogene	pseudo
mm_157761.1	chrX	73495200	73495294	-	1	NA	3' UTR (NM_007542, exon 8 of 8)	3' UTR (NM_007542, exon 8 of 8)	-7839	NM_001310537	320707	Mm.210095	NM_177236	ENSMUSG00000031376	Atp2b3	6430519O13Rik|Pmca3	ATPase, Ca++ transporting, plasma membrane 3	protein-coding
mm_80409.1	chr9	77656666	77656685	+	1	NA	3' UTR (NM_172925, exon 3 of 3)	3' UTR (NM_172925, exon 3 of 3)	19943	NM_172925	244923	Mm.138238	NM_172925	ENSMUSG00000044938	Klhl31	9830147P19Rik|D930047P17Rik|Kbtbd1	kelch-like 31	protein-coding
mm_68867.1	chr7	126428986	126428998	-	1	NA	5' UTR (NM_030566, exon 1 of 13)	5' UTR (NM_030566, exon 1 of 13)	225	NM_030566	70314	Mm.35467	NM_030566	ENSMUSG00000030727	Rabep2	2610011A08Rik|AI462746|Fra	rabaptin, RAB GTPase binding effector protein 2	protein-coding
mm_93087.1	chr10	89621220	89621237	-	1	NA	promoter-TSS (NM_182959)	promoter-TSS (NM_182959)	21	NM_182959	216227	Mm.233921	NM_182959	ENSMUSG00000019935	Slc17a8	BC042593|Vglut3	solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 8	protein-coding
mm_85221.1	chr9	97018824	97018835	-	1	NA	promoter-TSS (NM_145134)	promoter-TSS (NM_145134)	-474	NM_145134	211949	Mm.491271	NM_145134	ENSMUSG00000046997	Spsb4	D030068E18Rik|SSB-4|Ssb4	splA/ryanodine receptor domain and SOCS box containing 4	protein-coding
mm_117808.1	chr13	97711180	97711188	-	1	NA	Intergenic	MER5A|DNA|hAT-Charlie	151184	NR_046157	328314	Mm.138047	NR_046157	ENSMUSG00000110235	Gm5086	B230311A21|EG328314	predicted gene 5086	ncRNA
mm_115816.1	chr13	19732930	19732954	-	1	NA	promoter-TSS (NM_175688)	promoter-TSS (NM_175688)	9	NM_175688	319293	Mm.246657	NM_175688	ENSMUSG00000047462	A530099J19Rik	-	RIKEN cDNA A530099J19 gene	protein-coding
mm_115284.1	chr13	111867932	111867942	+	1	NA	promoter-TSS (NR_130345)	promoter-TSS (NR_130345)	1	NR_130345	102636620	Mm.402328	NR_130345	ENSMUSG00000086111	Gm15326	OTTMUSG00000020187	predicted gene 15326	ncRNA
mm_78490.1	chr9	32701293	32701312	+	1	NA	intron (NM_011808, intron 1 of 7)	intron (NM_011808, intron 1 of 7)	5260	NM_001038642	23871	Mm.292415	NM_011808	ENSMUSG00000032035	Ets1	AI196000|AI448617|D230050P06|Ets-1|Tpl1|vs	E26 avian leukemia oncogene 1, 5' domain	protein-coding
mm_123544.1	chr14	66824845	66824854	-	1	NA	intron (NM_009955, intron 7 of 13)	MLTR14|LTR|ERV1	43751	NM_009955	12934	Mm.352648	NM_009955	ENSMUSG00000022048	Dpysl2	AI851130|Crmp2|DRP2|Musunc33|TOAD-64|Ulip2	dihydropyrimidinase-like 2	protein-coding
mm_90958.1	chr10	13301108	13301116	-	1	NA	intron (NM_001195065, intron 1 of 12)	intron (NM_001195065, intron 1 of 12)	23048	NM_001195096	215789	Mm.283359	NM_001033257	ENSMUSG00000062866	Phactr2	AV158170|BC012871	phosphatase and actin regulator 2	protein-coding
mm_89757.1	chr10	99443700	99443733	+	1	NA	Intergenic	Intergenic	-165455	NR_038019	100504202	Mm.403801	NR_038019		Gm20110	-	predicted gene, 20110	ncRNA
mm_96045.1	chr11	59557488	59557503	+	1	NA	intron (NM_145827, intron 6 of 9)	intron (NM_145827, intron 6 of 9)	14243	NM_001011789	257962	Mm.377316	NM_001011789	ENSMUSG00000059610	Olfr222	MOR256-45P	olfactory receptor 222	protein-coding
mm_7165.1	chr1	92048522	92048528	-	1	NA	intron (NM_207225, intron 3 of 26)	intron (NM_207225, intron 3 of 26)	131816	NM_207225	208727	Mm.318567	NM_207225	ENSMUSG00000026313	Hdac4	4932408F19Rik|HD4	histone deacetylase 4	protein-coding
mm_134029.1	chr16	5010644	5010672	-	1	NA	intron (NM_133185, intron 6 of 10)	intron (NM_133185, intron 6 of 10)	2895	NM_133185	66049	Mm.27792	NM_133185	ENSMUSG00000022540	Rogdi	0610011C19Rik|AU020118|C76152|Lzf	rogdi homolog	protein-coding
mm_18207.1	chr2	48911925	48911940	-	1	NA	intron (NM_011958, intron 10 of 13)	L1M4|LINE|L1	37335	NM_001177313	26428	Mm.291059	NM_011958	ENSMUSG00000026761	Orc4	Orc4P|Orc4l|mMmORC4	origin recognition complex, subunit 4	protein-coding
mm_62183.1	chr7	97480907	97480917	+	1	NA	promoter-TSS (NM_027256)	promoter-TSS (NM_027256)	-44	NM_027256	101861	Mm.27383	NM_027256	ENSMUSG00000025133	Ints4	2610034N24Rik|AA692684|AW493223	integrator complex subunit 4	protein-coding
mm_80478.1	chr9	78204274	78204287	+	1	NA	exon (NM_010357, exon 4 of 7)	exon (NM_010357, exon 4 of 7)	12314	NM_010357	14860	Mm.2662	NM_010357	ENSMUSG00000032348	Gsta4	GST5.7|mGsta4	glutathione S-transferase, alpha 4	protein-coding
mm_152711.1	chr19	17372865	17372875	-	1	NA	promoter-TSS (NM_010265)	promoter-TSS (NM_010265)	-26	NM_010265	14537	Mm.244825	NM_010265	ENSMUSG00000038843	Gcnt1	5630400D21Rik|B130048E03|C2 GlcNAcT|C2GNT|IGnT	glucosaminyl (N-acetyl) transferase 1, core 2	protein-coding
mm_165122.1	chr2	4017686	4017696	+	1	NA	promoter-TSS (NM_001347086)	promoter-TSS (NM_001347086)	8	NM_001347086	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding
mm_6766.1	chr1	84105755	84105765	-	1	NA	intron (NM_001003948, intron 2 of 2)	ORR1F|LTR|ERVL-MaLR	113201	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_91307.1	chr10	24920694	24920711	-	1	NA	exon (NM_007482, exon 3 of 8)	exon (NM_007482, exon 3 of 8)	6768	NM_007482	11846	Mm.154144	NM_007482	ENSMUSG00000019987	Arg1	AI|AI256583|Arg-1|PGIF	arginase, liver	protein-coding
mm_76456.1	chr8	85286396	85286416	-	1	NA	exon (NM_022997, exon 5 of 17)	exon (NM_022997, exon 5 of 17)	13091	NM_022997	65114	Mm.296520	NM_022997	ENSMUSG00000031696	Vps35	AI647796|Mem3	VPS35 retromer complex component	protein-coding
mm_82206.1	chr9	124103418	124103422	+	1	NA	intron (NM_009915, intron 1 of 2)	intron (NM_009915, intron 1 of 2)	1237	NM_009915	12772	Mm.6272	NM_009915	ENSMUSG00000049103	Ccr2	Cc-ckr-2|Ccr2a|Ccr2b|Ckr2|Ckr2a|Ckr2b|Cmkbr2|mJe-r	chemokine (C-C motif) receptor 2	protein-coding
mm_139064.1	chr17	46520787	46520807	+	1	NA	exon (NM_001081335, exon 23 of 41)	exon (NM_001081335, exon 23 of 41)	24008	NM_207161	381101	Mm.35801	NM_207161	ENSMUSG00000040658	Dnph1	C76683|Rcl	2'-deoxynucleoside 5'-phosphate N-hydrolase 1	protein-coding
mm_5194.1	chr1	13360700	13360708	-	1	NA	intron (NM_008678, intron 1 of 22)	RLTR12BD_Mm|LTR|ERVK	11725	NM_001302702	17978	Mm.2537	NM_008678	ENSMUSG00000005886	Ncoa2	D1Ertd433e|GRIP-1|Grip1|KAT13C|NCoA-2|SRC-2|TIF2|bHLHe75	nuclear receptor coactivator 2	protein-coding
mm_123928.1	chr14	73365779	73365870	-	1	NA	exon (NM_008410, exon 4 of 6)	exon (NM_008410, exon 4 of 6)	19447	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_98811.1	chr11	97188469	97188481	+	1	NA	promoter-TSS (NM_008379)	promoter-TSS (NM_008379)	-583	NM_008379	16211	Mm.251013	NM_008379	ENSMUSG00000001440	Kpnb1	AA409963|IPOB|Impnb	karyopherin (importin) beta 1	protein-coding
mm_111805.1	chr12	105032057	105032060	-	1	NA	promoter-TSS (NR_037229)	promoter-TSS (NR_037229)	221	NR_003145	69434	Mm.380736	NR_003145		Snhg10	1700026B20Rik|AI642517	small nucleolar RNA host gene 10	ncRNA
mm_129653.1	chr15	80896889	80896902	-	1	NA	intron (NM_144812, intron 14 of 24)	intron (NM_144812, intron 14 of 24)	-43144	NR_039573	100628612		NR_039573	ENSMUSG00000092868	Mir5113	mir-5113|mmu-mir-5113|mu-mir-5113	microRNA 5113	ncRNA
mm_118463.1	chr14	11227512	11227514	+	1	NA	Intergenic	Intergenic	-54964	NR_105811	102466641		NR_105811	ENSMUSG00000099218	Mir5124b	Gm27681|mmu-mir-5124b	microRNA 5124b	ncRNA
mm_15806.1	chr2	164486857	164486898	+	1	NA	promoter-TSS (NM_001048228)	promoter-TSS (NM_001048228)	0	NM_001048228	52840	Mm.256927	NM_026797	ENSMUSG00000017734	Dbndd2	1110017A21Rik|2900022J10Rik|AU041050|AW048677|D2Bwg0891e|Nkip|R74724	dysbindin (dystrobrevin binding protein 1) domain containing 2	protein-coding
mm_70408.1	chr8	11398669	11398681	+	1	NA	exon (NM_009932, exon 5 of 48)	exon (NM_009932, exon 5 of 48)	-79254	NR_126558	102132	Mm.37632	NR_126558	ENSMUSG00000096957	E230013L22Rik	AI645545	RIKEN cDNA E230013L22 gene	ncRNA
mm_66616.1	chr7	45466895	45466901	-	1	NA	promoter-TSS (NM_007527)	promoter-TSS (NM_007527)	0	NM_007527	12028	Mm.19904	NM_007527	ENSMUSG00000003873	Bax	-	BCL2-associated X protein	protein-coding
mm_145264.1	chr18	52646207	52646225	+	1	NA	promoter-TSS (NM_030097)	promoter-TSS (NM_030097)	-4	NM_030097	78414	Mm.273327	NM_030097	ENSMUSG00000024532	1700034E13Rik	-	RIKEN cDNA 1700034E13 gene	protein-coding
mm_55764.1	chr6	78466815	78466828	-	1	NA	exon (NM_011260, exon 5 of 6)	exon (NM_011260, exon 5 of 6)	2053	NM_011260	19695	Mm.252385	NM_011260	ENSMUSG00000030017	Reg3g	AI449515|REG-3-gamma|reg III-gamma	regenerating islet-derived 3 gamma	protein-coding
mm_165343.1	chr2	118011913	118011921	-	1	NA	intron (NR_126479, intron 8 of 9)	intron (NR_126479, intron 8 of 9)	99285	NR_126479	329496	Mm.235844	NR_126479	ENSMUSG00000087203	Gm13986	C230060E24|OTTMUSG00000015236	predicted gene 13986	ncRNA
mm_48823.1	chr5	149051605	149051624	-	1	NA	promoter-TSS (NM_001313894)	promoter-TSS (NM_001313894)	2	NM_001313894	15289	Mm.207047	NM_010439	ENSMUSG00000066551	Hmgb1	HMG-1|Hmg1|SBP-1|p30	high mobility group box 1	protein-coding
mm_82450.1	chr9	15357693	15357759	-	1	NA	promoter-TSS (NM_176976)	promoter-TSS (NM_176976)	62	NM_176976	319675	Mm.218317	NM_176976	ENSMUSG00000046111	Cep295	5830418K08Rik|5832426L23Rik|Gm1131|Kiaa1731	centrosomal protein 295	protein-coding
mm_84188.1	chr9	60193704	60193718	-	1	NA	intron (NM_001040426, intron 7 of 17)	ID4_|SINE|ID	-52491	NM_172444	207596	Mm.28791	NM_172444	ENSMUSG00000032289	Thsd4	ADAMTSL-6|ADAMTSL6|AI585901|Adamtsl4|B230114P05Rik	thrombospondin, type I, domain containing 4	protein-coding
mm_36418.1	chr4	78211950	78211999	-	1	NA	promoter-TSS (NM_011211)	promoter-TSS (NM_011211)	-79	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding
mm_149271.1	chr19	10582282	10582313	+	1	NA	intron (NM_001282067, intron 4 of 8)	intron (NM_001282067, intron 4 of 8)	-4911	NR_126092	72982	Mm.391194	NM_028411	ENSMUSG00000024666	Tmem138	1700113I01Rik|2900055D14Rik	transmembrane protein 138	protein-coding
mm_22776.1	chr3	20306935	20306939	+	1	NA	Intergenic	Lx2B2|LINE|L1	-31204	NM_029706	76703	Mm.34692	NM_029706	ENSMUSG00000011463	Cpb1	0910001A18Rik|1810063F02Rik|2210008M23Rik|AI504870	carboxypeptidase B1 (tissue)	protein-coding
mm_93892.1	chr10	125328958	125328968	-	1	NA	promoter-TSS (NM_011391)	promoter-TSS (NM_011391)	-428	NM_011391	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|Mct2	solute carrier family 16 (monocarboxylic acid transporters), member 7	protein-coding
mm_119690.1	chr14	53544976	53544990	+	1	NA	Intergenic	Intergenic	708946	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_49073.1	chr6	5789541	5789543	+	1	NA	intron (NM_001191026, intron 5 of 16)	intron (NM_001191026, intron 5 of 16)	63903	NM_001191026	13426	Mm.20893	NM_010063	ENSMUSG00000029757	Dync1i1	DH IC-1|DHIC-1|DIC|Dncic1|IC74	dynein cytoplasmic 1 intermediate chain 1	protein-coding
mm_47061.1	chr5	116392767	116392773	-	1	NA	Intergenic	Intergenic	30094	NM_030704	80888	Mm.21549	NM_030704	ENSMUSG00000041548	Hspb8	AU018630|AW413033|Cryac|D5Ucla4|E2IG1|H11|H11K|HSP20-like|HSP22	heat shock protein 8	protein-coding
mm_170490.1	chr19	18671157	18671157	+	1	NA	exon (NM_026120, exon 1 of 8)	exon (NM_026120, exon 1 of 8)	377	NM_026120	67383	Mm.306602	NM_026120	ENSMUSG00000024726	Carnmt1	2410127L17Rik	carnosine N-methyltransferase 1	protein-coding
mm_54529.1	chr6	36715422	36715431	-	1	NA	TTS (NM_008973)	TTS (NM_008973)	95935	NM_008973	19242	Mm.279690	NM_008973	ENSMUSG00000029838	Ptn	HARP|HB-GAM|HBBN|HBGF-8|HBNF|OSF|Osf-1|Osf1	pleiotrophin	protein-coding
mm_70138.1	chr7	143296515	143296525	-	1	NA	promoter-TSS (NR_001461)	promoter-TSS (NR_001461)	27	NR_001461	63830	Mm.356096	NR_001461	ENSMUSG00000101609	Kcnq1ot1	Kvlqt1-as|Lit1|Tssc8	KCNQ1 overlapping transcript 1	ncRNA
mm_102449.1	chr11	59787285	59787295	-	1	NA	promoter-TSS (NR_110894)	promoter-TSS (NR_110894)	-68	NR_110894	194908	Mm.344651	NM_183139	ENSMUSG00000043648	Pld6	4933433K01Rik|Gm10|Zuc|mZuc|mitoPLD	phospholipase D family, member 6	protein-coding
mm_161918.1	chr18	67638905	67638905	-	1	NA	intron (NM_001081073, intron 2 of 11)	B1_Mur2|SINE|Alu	2431	NM_001081073	225659	Mm.111928	NM_001081073	ENSMUSG00000073542	Cep76	6230425F05Rik|9630013E05	centrosomal protein 76	protein-coding
mm_1672.1	chr1	74792024	74792076	+	1	NA	promoter-TSS (NM_009518)	promoter-TSS (NM_009518)	31	NM_009518	22409	Mm.5130	NM_009518	ENSMUSG00000026167	Wnt10a	-	wingless-type MMTV integration site family, member 10A	protein-coding
mm_9556.1	chr1	173942446	173942472	-	1	NA	promoter-TSS (NM_001302651)	promoter-TSS (NM_001302651)	33	NM_001302649	15950	Mm.463437	NM_008328	ENSMUSG00000039997	Ifi203	Mndal	interferon activated gene 203	protein-coding
mm_41414.1	chr5	90794531	90794546	+	1	NA	promoter-TSS (NM_011339)	promoter-TSS (NM_011339)	4	NM_011339	20309	Mm.64326	NM_011339	ENSMUSG00000029375	Cxcl15	Il8|Scyb15|lungkine|weche	chemokine (C-X-C motif) ligand 15	protein-coding
mm_3706.1	chr1	153899938	153899953	+	1	NA	promoter-TSS (NM_008131)	promoter-TSS (NM_008131)	16	NM_008131	14645	Mm.210745	NM_008131	ENSMUSG00000026473	Glul	GS|Glns	glutamate-ammonia ligase (glutamine synthetase)	protein-coding
mm_81883.1	chr9	119341488	119341499	+	1	NA	5' UTR (NM_130864, exon 1 of 12)	5' UTR (NM_130864, exon 1 of 12)	199	NM_130864	113868	Mm.205266	NM_130864	ENSMUSG00000036138	Acaa1a	Acaa|Acaa1|D9Ertd25e|PTL	acetyl-Coenzyme A acyltransferase 1A	protein-coding
mm_134691.1	chr16	22535392	22535397	-	1	NA	intron (NM_001346673, intron 19 of 23)	intron (NM_001346673, intron 19 of 23)	-3210	NR_106170	102465887		NR_106170	ENSMUSG00000099071	Mir8095	Gm27566|mmu-mir-8095	microRNA 8095	ncRNA
mm_5039.1	chr1	193611217	193611219	+	1	NA	Intergenic	Intergenic	-103688	NR_029592	387201		NR_029592	ENSMUSG00000065533	Mir205	Mirn205|mir-205|mmu-mir-205	microRNA 205	ncRNA
mm_128022.1	chr15	24857531	24857548	-	1	NA	Intergenic	Intergenic	556225	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	brain abundant, membrane attached signal protein 1	protein-coding
mm_81238.1	chr9	107928441	107928483	+	1	NA	promoter-TSS (NM_026338)	promoter-TSS (NM_026338)	-7	NM_026338	67722	Mm.390222	NM_026338	ENSMUSG00000066368	Actl11	4921517D21Rik	actin-like 11	protein-coding
mm_22081.1	chr2	168765336	168765361	-	1	NA	intron (NM_201395, intron 1 of 3)	intron (NM_201395, intron 1 of 3)	1853	NM_201395	99377	Mm.434054	NM_175303	ENSMUSG00000027547	Sall4	5730441M18Rik|AA407717|AL022809|AW536104|C330011P20Rik|C78083|C78563|Tex20	sal-like 4 (Drosophila)	protein-coding
mm_25977.1	chr3	133091924	133091953	+	1	NA	promoter-TSS (NM_026231)	promoter-TSS (NM_026231)	83	NM_027927	71793	Mm.246726	NM_027927	ENSMUSG00000028016	Ints12	1110020M19Rik|2810027J24Rik|4930529N21Rik|A230056J18Rik|AI666778|Phf22|int12	integrator complex subunit 12	protein-coding
mm_109463.1	chr12	111202766	111202783	+	1	NA	intron (NM_001286122, intron 1 of 9)	intron (NM_001286122, intron 1 of 9)	-18283	NR_130987	78062	Mm.427248	NR_130987	ENSMUSG00000083193	4930595D18Rik	-	RIKEN cDNA 4930595D18 gene	ncRNA
mm_110068.1	chr12	21389571	21389574	-	1	NA	TTS (NM_011739)	TTS (NM_011739)	-15940	NM_009615	11491	Mm.27681	NM_009615	ENSMUSG00000052593	Adam17	CD156b|Tace	a disintegrin and metallopeptidase domain 17	protein-coding
mm_9446.1	chr1	172590589	172590606	-	1	NA	promoter-TSS (NM_029084)	promoter-TSS (NM_029084)	-29	NM_029084	74748	Mm.179812	NM_029084	ENSMUSG00000053318	Slamf8	5830408F06Rik|Blame|SBBI42	SLAM family member 8	protein-coding
mm_32641.1	chr4	115057042	115057060	+	1	NA	promoter-TSS (NM_001287388)	promoter-TSS (NM_001287388)	625	NM_011527	21349	Mm.239869	NM_011527	ENSMUSG00000028717	Tal1	Hpt|SCL/tal-1|Scl|bHLHa17|tal-1	T cell acute lymphocytic leukemia 1	protein-coding
mm_156367.1	chrX	139610597	139610600	+	1	NA	promoter-TSS (NM_023270)	promoter-TSS (NM_023270)	-22	NM_023270	66889	Mm.27764	NM_023270	ENSMUSG00000031438	Rnf128	1300002C13Rik|AI987883|GRAIL|Greul1	ring finger protein 128	protein-coding
mm_141085.1	chr17	25941927	25941981	-	1	NA	promoter-TSS (NM_011822)	promoter-TSS (NM_011822)	35	NM_001291025	14755	Mm.362054	NM_011822	ENSMUSG00000025728	Pigq	Gpi1|Gpi1h|Gpi1p|Gpih	phosphatidylinositol glycan anchor biosynthesis, class Q	protein-coding
mm_76856.1	chr8	105403812	105403813	-	1	NA	intron (NM_001301173, intron 2 of 15)	intron (NM_001301173, intron 2 of 15)	9690	NM_177791	279499	Mm.67628	NM_177791	ENSMUSG00000051648	Kctd19	4922504H04Rik	potassium channel tetramerisation domain containing 19	protein-coding
mm_41317.1	chr5	90471817	90471820	+	1	NA	intron (NM_009654, intron 10 of 14)	intron (NM_009654, intron 10 of 14)	10948	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_73402.1	chr8	105880876	105880939	+	1	NA	promoter-TSS (NM_181594)	promoter-TSS (NM_181594)	26	NM_181594	234699	Mm.28979	NM_181594	ENSMUSG00000036270	Edc4	BC022641	enhancer of mRNA decapping 4	protein-coding
mm_95638.1	chr11	53719445	53719460	+	1	NA	Intergenic	Lx8|LINE|L1	-1342	NM_010558	16191	Mm.4461	NM_010558	ENSMUSG00000036117	Il5	Il-5	interleukin 5	protein-coding
mm_52086.1	chr6	97829374	97829393	+	1	NA	intron (NM_001113198, intron 1 of 9)	intron (NM_001113198, intron 1 of 9)	22325	NM_001113198	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_102940.1	chr11	69602744	69602783	-	1	NA	exon (NM_013415, exon 4 of 7)	exon (NM_013415, exon 4 of 7)	3197	NM_013415	11932	Mm.235204	NM_013415	ENSMUSG00000041329	Atp1b2	Amog|Atpb-2	ATPase, Na+/K+ transporting, beta 2 polypeptide	protein-coding
mm_142376.1	chr17	44735576	44735588	-	1	NA	exon (NM_001271631, exon 1 of 5)	exon (NM_001271631, exon 1 of 5)	594	NR_073425	12393	Mm.391013	NM_009820	ENSMUSG00000039153	Runx2	AML3|Cbf|Cbfa-1|Cbfa1|LS3|Osf2|PEBP2aA|Pebp2a1|Pebpa2a	runt related transcription factor 2	protein-coding
mm_136022.1	chr16	76339286	76339312	-	1	NA	intron (NM_173440, intron 2 of 3)	intron (NM_173440, intron 2 of 3)	33750	NM_173440	268903	Mm.74711	NM_173440	ENSMUSG00000048490	Nrip1	6030458L20Rik|8430438I05Rik|9630050P12|AA959574|AW456757|RIP140	nuclear receptor interacting protein 1	protein-coding
mm_14089.1	chr2	125154022	125154032	+	1	NA	exon (NM_001079690, exon 2 of 28)	exon (NM_001079690, exon 2 of 28)	1427	NM_001079690	20495	Mm.3914	NM_011389	ENSMUSG00000027202	Slc12a1	AI788571|D630042G03Rik|Nkcc2|mBSC1|urehr3	solute carrier family 12, member 1	protein-coding
mm_131146.1	chr16	6517967	6517977	+	1	NA	intron (NM_021477, intron 3 of 16)	intron (NM_021477, intron 3 of 16)	542385	NR_045799	68238	Mm.434605	NR_045799	ENSMUSG00000101481	1700123O21Rik	-	RIKEN cDNA 1700123O21 gene	ncRNA
mm_72130.1	chr8	71881726	71881780	+	1	NA	promoter-TSS (NM_145624)	promoter-TSS (NM_145624)	-315	NM_145624	236193	Mm.290790	NM_145624	ENSMUSG00000056019	Zfp709	BC021921|GIOT-4|HIT-40	zinc finger protein 709	protein-coding
mm_15068.1	chr2	153069214	153069225	+	1	NA	intron (NM_145536, intron 2 of 8)	intron (NM_145536, intron 2 of 8)	3264	NM_145536	228788	Mm.299979	NM_145536	ENSMUSG00000027474	Ccm2l	-	cerebral cavernous malformation 2-like	protein-coding
mm_141076.1	chr17	25844515	25844565	-	1	NA	TTS (NM_001163766)	TTS (NM_001163766)	311	NM_145999	214952	Mm.40907	NM_145999	ENSMUSG00000025733	Rhot2	Arht2|Miro2	ras homolog family member T2	protein-coding
mm_39815.1	chr5	30711591	30711597	+	1	NA	promoter-TSS (NM_023047)	promoter-TSS (NM_023047)	-301	NM_023047	65254	Mm.27732	NM_023047	ENSMUSG00000029168	Dpysl5	CRAM|CRMP-5|Crmp5	dihydropyrimidinase-like 5	protein-coding
mm_72782.1	chr8	86745603	86745632	+	1	NA	promoter-TSS (NR_027829)	promoter-TSS (NR_027829)	-82	NR_027829	666945	Mm.391806	NR_027829		Gm10638	ENSMUSG00000074178	predicted gene 10638	ncRNA
mm_1366.1	chr1	66413495	66413505	+	1	NA	exon (NM_001310634, exon 7 of 15)	exon (NM_001310634, exon 7 of 15)	-54947	NM_175510	329178	Mm.44798	NM_175510	ENSMUSG00000055567	Unc80	C030018G13Rik|C230061B10Rik|UNC-80	unc-80, NALCN activator	protein-coding
mm_47562.1	chr5	124425908	124425946	-	1	NA	promoter-TSS (NM_001081203)	promoter-TSS (NM_001081203)	-13	NM_001081203	243272	Mm.23879	NM_001081203	ENSMUSG00000038095	Sbno1	9330180L10Rik|AI849128|AW557836|BC021875|Sbno|mSno1|sno	strawberry notch homolog 1 (Drosophila)	protein-coding
mm_8274.1	chr1	139699162	139699163	-	1	NA	intron (NM_001029977, intron 14 of 14)	intron (NM_001029977, intron 14 of 14)	82077	NM_001029977	214403	Mm.337613	NM_001029977	ENSMUSG00000070594	Gm4788	Cfhrc|EG214403	predicted gene 4788	protein-coding
mm_17487.1	chr2	28583012	28583020	-	1	NA	5' UTR (NM_001290484, exon 1 of 12)	5' UTR (NM_001290484, exon 1 of 12)	263	NM_148928	70239	Mm.274120	NM_148928	ENSMUSG00000026816	Gtf3c5	2700084A09Rik|TFIIIC63|TFiiiC2-63	general transcription factor IIIC, polypeptide 5	protein-coding
mm_46333.1	chr5	101665196	101665211	-	1	NA	promoter-TSS (NM_144955)	promoter-TSS (NM_144955)	-492	NM_144955	18096	Mm.193072	NM_144955	ENSMUSG00000035187	Nkx6-1	NKX6A|Nkx6.1	NK6 homeobox 1	protein-coding
mm_110944.1	chr12	76612679	76612701	-	1	NA	exon (NM_013675, exon 16 of 36)	exon (NM_013675, exon 16 of 36)	-64765	NR_046044	100504549	Mm.440349	NR_046044		AI463170	-	expressed sequence AI463170	ncRNA
mm_110261.1	chr12	31713861	31713871	-	1	NA	promoter-TSS (NM_175191)	promoter-TSS (NM_175191)	60	NM_175191	73010	Mm.441517	NM_175191	ENSMUSG00000044067	Gpr22	2900068K05Rik|AW061316	G protein-coupled receptor 22	protein-coding
mm_122909.1	chr14	54953939	54953963	-	1	NA	exon (NM_010856, exon 21 of 39)	exon (NM_010856, exon 21 of 39)	-4809	NR_029724	387204		NR_029724	ENSMUSG00000065432	Mir208a	Mirn208|Mirn208a|mir-208|mir-208a|mmu-mir-208	microRNA 208a	ncRNA
mm_7067.1	chr1	87650650	87650675	-	1	NA	intron (NM_010566, intron 2 of 26)	intron (NM_010566, intron 2 of 26)	30350	NM_001110193	16331	Mm.15105	NM_010566	ENSMUSG00000026288	Inpp5d	SHIP|SHIP-1|SHIP1|SIP-145|p150Ship|s-SHIP	inositol polyphosphate-5-phosphatase D	protein-coding
mm_165209.1	chr2	34963163	34963167	+	1	NA	Intergenic	Intergenic	-1393	NM_001326601	22029	Mm.239514	NM_009421	ENSMUSG00000026875	Traf1	4732496E14Rik	TNF receptor-associated factor 1	protein-coding
mm_137156.1	chr17	23726477	23726493	+	1	NA	5' UTR (NM_023058, exon 1 of 8)	5' UTR (NM_023058, exon 1 of 8)	149	NM_023058	268930	Mm.182193	NM_023058	ENSMUSG00000023908	Pkmyt1	6230424P17|AW209059|Myt1	protein kinase, membrane associated tyrosine/threonine 1	protein-coding
mm_131849.1	chr16	23060425	23060435	+	1	NA	exon (NM_001102411, exon 2 of 10)	exon (NM_001102411, exon 2 of 10)	2130	NM_001102412	16644	Mm.2160	NM_023125	ENSMUSG00000022875	Kng1	Kng	kininogen 1	protein-coding
mm_61579.1	chr7	79842478	79842509	+	1	NA	promoter-TSS (NM_008486)	promoter-TSS (NM_008486)	-141	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_165377.1	chr2	128428917	128428933	-	1	NA	intron (NR_028591, intron 1 of 1)	intron (NR_028591, intron 1 of 1)	426	NR_028591	100043424	Mm.297222	NR_028589		Gm14005	OTTMUSG00000015351	predicted gene 14005	ncRNA
mm_99254.1	chr11	101123440	101123465	+	1	NA	exon (NM_134024, exon 5 of 11)	exon (NM_134024, exon 5 of 11)	3321	NM_134024	103733	Mm.479145	NM_134024	ENSMUSG00000035198	Tubg1	1500010O08Rik|AI451582|AI503389|Tubg	tubulin, gamma 1	protein-coding
mm_39572.1	chr5	23433442	23433531	+	1	NA	promoter-TSS (NM_026984)	promoter-TSS (NM_026984)	867	NR_040469	269630	Mm.425231	NR_040469	ENSMUSG00000073147	5031425E22Rik	-	RIKEN cDNA 5031425E22 gene	ncRNA
mm_36055.1	chr4	57339018	57339047	-	1	NA	Intergenic	Intergenic	25260	NR_038179	73349	Mm.393774	NR_038178		1700042G15Rik	-	RIKEN cDNA 1700042G15 gene	ncRNA
mm_142418.1	chr17	45568273	45568282	-	1	NA	TTS (NM_028662)	TTS (NM_028662)	4125	NM_028662	73836	Mm.289716	NM_028662	ENSMUSG00000037089	Slc35b2	1110003M08Rik|AA407792|AI842275|PAPST1|Slc35b1	solute carrier family 35, member B2	protein-coding
mm_28225.1	chr3	88453406	88453412	-	1	NA	intron (NM_001163491, intron 2 of 14)	intron (NM_001163491, intron 2 of 14)	2352	NM_013658	20351	Mm.439752	NM_013658	ENSMUSG00000028064	Sema4a	AI132332|SemB|Semab	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A	protein-coding
mm_88572.1	chr10	79669872	79669905	+	1	NA	intron (NM_148934, intron 1 of 1)	CpG	478	NM_148934	110012	Mm.22623	NM_148934	ENSMUSG00000020308	Tpgs1	AV005629|Gm16517|Gtrgeo22|PGs1	tubulin polyglutamylase complex subunit 1	protein-coding
mm_42250.1	chr5	113989885	113989909	+	1	NA	intron (NM_198109, intron 1 of 14)	intron (NM_198109, intron 1 of 14)	3860	NM_198109	231637	Mm.389682	NM_198109	ENSMUSG00000042121	Ssh1	AW551225|Gm1394|Gm1395|SSH-1|SSH-1L	slingshot homolog 1 (Drosophila)	protein-coding
mm_130615.1	chr15	99967068	99967077	-	1	NA	Intergenic	Intergenic	-2993	NM_001080948	207214	Mm.28811	NM_001024526	ENSMUSG00000023025	Larp4	DXErtd793|DXErtd793e	La ribonucleoprotein domain family, member 4	protein-coding
mm_27831.1	chr3	79100008	79100024	-	1	NA	intron (NM_001310536, intron 3 of 23)	intron (NM_001310536, intron 3 of 23)	44871	NM_001310536	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_114012.1	chr13	52609359	52609373	+	1	NA	intron (NM_011518, intron 1 of 13)	(TG)n|Simple_repeat|Simple_repeat	12484	NM_011518	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_165386.1	chr2	130768285	130768288	-	1	NA	intron (NM_029432, intron 17 of 36)	ORR1D2-int|LTR|ERVL-MaLR	35815	NR_024097	100043766	Mm.447040	NR_024097		Gm14057	OTTMUSG00000015563	Ppp1r14c pseudogene	pseudo
mm_74557.1	chr8	10928450	10928464	-	1	NA	promoter-TSS (NR_030715)	promoter-TSS (NR_030715)	0	NR_030715	665306	Mm.358758	NR_030715	ENSMUSG00000038917	3930402G23Rik	-	RIKEN cDNA 3930402G23 gene	ncRNA
mm_104305.1	chr11	90663928	90663934	-	1	NA	intron (NM_028011, intron 7 of 15)	(A)n|Simple_repeat|Simple_repeat	23670	NM_028011	71943	Mm.167868	NM_028011	ENSMUSG00000020541	Tom1l1	2310045L10Rik|C80573|Srcasm	target of myb1-like 1 (chicken)	protein-coding
mm_173154.1	chrX	33554471	33554475	-	1	NA	Intergenic	L1Md_T|LINE|L1	22841	NM_001145038	100040732	Mm.465135	NM_001145038	ENSMUSG00000078324	Btbd35f14	Gm2933	BTB domain containing 35, family member 14	protein-coding
mm_111274.1	chr12	85339499	85339532	-	1	NA	promoter-TSS (NM_145138)	promoter-TSS (NM_145138)	-153	NM_145138	217718	Mm.29071	NM_145138	ENSMUSG00000034290	Nek9	C130021H08Rik	NIMA (never in mitosis gene a)-related expressed kinase 9	protein-coding
mm_20887.1	chr2	148851184	148851194	-	1	NA	promoter-TSS (NM_029960)	promoter-TSS (NM_029960)	-255	NM_029960	77705	Mm.159975	NM_029960	ENSMUSG00000027446	9230104L09Rik	mCST E2	RIKEN cDNA 9230104L09 gene	protein-coding
mm_92462.1	chr10	77924286	77924305	-	1	NA	intron (NM_138301, intron 22 of 33)	intron (NM_138301, intron 22 of 33)	-21759	NM_145152	237387	Mm.133301	NM_145152	ENSMUSG00000051652	Lrrc3	1300011L04Rik|C21orf102	leucine rich repeat containing 3	protein-coding
mm_59760.1	chr7	28830088	28830092	+	1	NA	intron (NM_016772, intron 5 of 9)	intron (NM_016772, intron 5 of 9)	-3704	NM_010706	16855	Mm.210336	NM_010706	ENSMUSG00000053964	Lgals4	gal-4	lectin, galactose binding, soluble 4	protein-coding
mm_29267.1	chr3	107458896	107458920	-	1	NA	promoter-TSS (NM_145922)	promoter-TSS (NM_145922)	-10	NM_145922	99738	Mm.101976	NM_145922	ENSMUSG00000027895	Kcnc4	AI850292|KSHIIIC|Kcr2-4|Kv3.4	potassium voltage gated channel, Shaw-related subfamily, member 4	protein-coding
mm_157084.1	chrX	9436140	9436154	-	1	NA	3' UTR (NM_007807, exon 13 of 13)	3' UTR (NM_007807, exon 13 of 13)	33177	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_128392.1	chr15	43170837	43170854	-	1	NA	promoter-TSS (NM_172815)	promoter-TSS (NM_172815)	-27	NM_172815	239405	Mm.193274	NM_172815	ENSMUSG00000051920	Rspo2	2610028F08Rik|AA673245|D430027K22|ftls	R-spondin 2	protein-coding
mm_147142.1	chr18	36515768	36515787	-	1	NA	promoter-TSS (NM_010415)	promoter-TSS (NM_010415)	28	NM_010415	15200	Mm.289681	NM_010415	ENSMUSG00000024486	Hbegf	AW047313|Dtr|Dts|Hegfl	heparin-binding EGF-like growth factor	protein-coding
mm_135677.1	chr16	52419998	52420015	-	1	NA	intron (NM_009655, intron 1 of 15)	intron (NM_009655, intron 1 of 15)	33075	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_117194.1	chr13	63573143	63573146	-	1	NA	5' UTR (NM_001328514, exon 1 of 24)	5' UTR (NM_001328514, exon 1 of 24)	316	NM_001328514	19206	Mm.228798	NM_008957	ENSMUSG00000021466	Ptch1	A230106A15Rik|Ptc|Ptc1|Ptch|mes	patched 1	protein-coding
mm_12351.1	chr2	69749379	69749404	+	1	NA	exon (NM_001081086, exon 14 of 14)	exon (NM_001081086, exon 14 of 14)	26303	NM_001081086	228005	Mm.11815	NM_001081086	ENSMUSG00000042133	Ppig	AU019516|AU022200|B230312B02Rik|CYP|SRCyp	peptidyl-prolyl isomerase G (cyclophilin G)	protein-coding
mm_21442.1	chr2	160327170	160327192	-	1	NA	exon (NM_001033411, exon 1 of 3)	exon (NM_001033411, exon 1 of 3)	313	NM_001033411	329554	Mm.291144	NM_001033411	ENSMUSG00000074623	Gm826	-	predicted gene 826	protein-coding
mm_156531.1	chrX	151046980	151046993	+	1	NA	promoter-TSS (NM_008001)	promoter-TSS (NM_008001)	-184	NM_008001	14163	Mm.8142	NM_008001	ENSMUSG00000025265	Fgd1	ZFYVE3	FYVE, RhoGEF and PH domain containing 1	protein-coding
mm_28533.1	chr3	92687210	92687211	-	1	NA	promoter-TSS (NM_027137)	promoter-TSS (NM_027137)	0	NM_027137	69611	Mm.176243	NM_027137	ENSMUSG00000103243	Lce1d	2310037L11Rik|AI415320|Sprrl7	late cornified envelope 1D	protein-coding
mm_74389.1	chr8	128732860	128732878	+	1	NA	3' UTR (NM_010578, exon 16 of 16)	3' UTR (NM_010578, exon 16 of 16)	47215	NM_010578	16412	Mm.263396	NM_010578	ENSMUSG00000025809	Itgb1	4633401G24Rik|AA409975|AA960159|CD29|ENSMUSG00000051907|Fnrb|Gm9863|gpIIa	integrin beta 1 (fibronectin receptor beta)	protein-coding
mm_99185.1	chr11	100860448	100860537	+	1	NA	promoter-TSS (NM_001164062)	promoter-TSS (NM_001164062)	8	NM_001164062	20850	Mm.277403	NM_011488	ENSMUSG00000004043	Stat5a	AA959963|STAT5	signal transducer and activator of transcription 5A	protein-coding
mm_69193.1	chr7	127286497	127286497	-	1	NA	Intergenic	Intergenic	-9763	NM_001253873	16408	Mm.1618	NM_008400	ENSMUSG00000030830	Itgal	(p180)|Cd11a|LFA-1|LFA-1A|Ly-15|Ly-21	integrin alpha L	protein-coding
mm_152598.1	chr19	11640829	11640840	-	1	NA	promoter-TSS (NM_133246)	promoter-TSS (NM_133246)	17	NM_133246	170813	Mm.240438	NM_133246	ENSMUSG00000024681	Ms4a3	HTm4	membrane-spanning 4-domains, subfamily A, member 3	protein-coding
mm_80619.1	chr9	88548014	88548123	+	1	NA	promoter-TSS (NM_001142943)	promoter-TSS (NM_001142943)	48	NM_001163061	71640	Mm.259988	NM_001142943	ENSMUSG00000032425	Zfp949	4930422I07Rik	zinc finger protein 949	protein-coding
mm_167740.1	chr9	107338299	107338302	-	1	NA	promoter-TSS (NM_133984)	promoter-TSS (NM_133984)	50	NM_133984	69536	Mm.259467	NM_133984	ENSMUSG00000032579	Hemk1	2310008M14Rik|AW049265	HemK methyltransferase family member 1	protein-coding
mm_144408.1	chr18	20961303	20961350	+	1	NA	intron (NM_026301, intron 1 of 5)	intron (NM_026301, intron 1 of 5)	16701	NM_026301	67664	Mm.45980	NM_026301	ENSMUSG00000033107	Rnf125	4930553F04Rik	ring finger protein 125	protein-coding
mm_86851.1	chr10	21593187	21593187	+	1	NA	promoter-TSS (NR_027968)	promoter-TSS (NR_027968)	42	NR_027968	67692	Mm.54306	NM_183266	ENSMUSG00000050844	1700020N01Rik	-	RIKEN cDNA 1700020N01 gene	ncRNA
mm_16827.1	chr2	11480350	11480362	-	1	NA	exon (NM_001177754, exon 14 of 16)	exon (NM_001177754, exon 14 of 16)	21734	NM_001177754	170768	Mm.19669	NM_133232	ENSMUSG00000026773	Pfkfb3	E330010H22Rik|iPFK-2|uPFK-2	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	protein-coding
mm_103246.1	chr11	70812495	70812501	-	1	NA	promoter-TSS (NM_001045526)	promoter-TSS (NM_001045526)	63	NM_001045526	327957	Mm.164325	NM_001045526	ENSMUSG00000057135	Scimp	A430084P05Rik	SLP adaptor and CSK interacting membrane protein	protein-coding
mm_33730.1	chr4	134098801	134098804	+	1	NA	Intergenic	Intergenic	-3729	NM_013706	23833	Mm.24130	NM_013706	ENSMUSG00000000682	Cd52	AI463198|B7|B7-Ag|CAMPATH-1|CLS1|MB7	CD52 antigen	protein-coding
mm_4206.1	chr1	171247353	171247377	+	1	NA	promoter-TSS (NM_153064)	promoter-TSS (NM_153064)	-243	NM_153064	226646	Mm.21669	NM_153064	ENSMUSG00000013593	Ndufs2	CI-49kD	NADH dehydrogenase (ubiquinone) Fe-S protein 2	protein-coding
mm_111750.1	chr12	103949281	103949317	-	1	NA	exon (NM_009247, exon 3 of 5)	exon (NM_009247, exon 3 of 5)	7598	NM_009247	20704	Mm.312593	NM_009247	ENSMUSG00000072849	Serpina1e	Dom5|PI5|Spi1-5	serine (or cysteine) peptidase inhibitor, clade A, member 1E	protein-coding
mm_74338.1	chr8	127095677	127095680	+	1	NA	intron (NM_001309391, intron 1 of 24)	intron (NM_001309391, intron 1 of 24)	31622	NM_001309391	93742	Mm.299254	NM_033620	ENSMUSG00000025812	Pard3	AA960621|AI256638|Asip|D8Ertd580e|Par-3|Par3|Pard-3|Pard3a|Phip	par-3 family cell polarity regulator	protein-coding
mm_153873.1	chr19	46863538	46863550	-	1	NA	intron (NM_033569, intron 4 of 7)	intron (NM_033569, intron 4 of 7)	98807	NM_029810	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_77669.1	chr8	124863009	124863019	-	1	NA	promoter-TSS (NM_025615)	promoter-TSS (NM_025615)	15	NM_025615	66523	Mm.436864	NM_025615	ENSMUSG00000031984	2810004N23Rik	3110004G14Rik|Ayu21-55|Gt(pU21)55Imeg|GtAyu21-55	RIKEN cDNA 2810004N23 gene	protein-coding
mm_143107.1	chr17	57105917	57105948	-	1	NA	promoter-TSS (NR_033508)	promoter-TSS (NR_033508)	10	NR_033508	100169874	Mm.76700	NR_033508	ENSMUSG00000079414	Gm11110	ENSMUSG00000079414	predicted gene 11110	ncRNA
mm_149652.1	chr19	18670781	18670810	+	1	NA	promoter-TSS (NM_026120)	promoter-TSS (NM_026120)	15	NM_026120	67383	Mm.306602	NM_026120	ENSMUSG00000024726	Carnmt1	2410127L17Rik	carnosine N-methyltransferase 1	protein-coding
mm_129155.1	chr15	76232555	76232634	-	1	NA	TTS (NM_001163575)	TTS (NM_001163575)	-1216	NM_011117	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
mm_103964.1	chr11	84443062	84443071	-	1	NA	intron (NM_019816, intron 11 of 12)	intron (NM_019816, intron 11 of 12)	70435	NM_019816	56321	Mm.257482	NM_019816	ENSMUSG00000018697	Aatf	4933415H02Rik|5830465M17Rik|Che-1|Trb	apoptosis antagonizing transcription factor	protein-coding
mm_56377.1	chr6	94251475	94251478	-	1	NA	intron (NM_001029850, intron 1 of 23)	BC1_Mm|scRNA|scRNA	-14034	NR_130996	78178	Mm.452749	NR_130996	ENSMUSG00000045095	4930511A08Rik	-	RIKEN cDNA 4930511A08 gene	ncRNA
mm_29911.1	chr3	131474619	131474630	-	1	NA	Intergenic	Intergenic	-90144	NM_001289479	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_68769.1	chr7	121981568	121981577	-	1	NA	exon (NM_001033318, exon 1 of 17)	exon (NM_001033318, exon 1 of 17)	121	NM_001033318	233824	Mm.442015	NM_001033318	ENSMUSG00000034951	Cog7	5630400E24Rik|Gm167	component of oligomeric golgi complex 7	protein-coding
mm_114658.1	chr13	78118194	78118204	+	1	NA	intron (NM_001163420, intron 8 of 8)	intron (NM_001163420, intron 8 of 8)	78250	NM_001347538	13865	Mm.439653	NM_010151	ENSMUSG00000069171	Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR-3|EAR3|Erbal3|SVP44|Tcfcoup1	nuclear receptor subfamily 2, group F, member 1	protein-coding
mm_94151.1	chr10	128744015	128744085	-	1	NA	promoter-TSS (NM_016811)	promoter-TSS (NM_016811)	6	NM_016811	13139	Mm.291235	NM_016811	ENSMUSG00000025357	Dgka	80kDa|AW146112|Dagk1	diacylglycerol kinase, alpha	protein-coding
mm_19136.1	chr2	80438642	80438644	-	1	NA	intron (NM_011356, intron 1 of 5)	intron (NM_011356, intron 1 of 5)	8753	NM_011356	20378	Mm.427436	NM_011356	ENSMUSG00000027004	Frzb	Frp|Sfrp3|frezzled|fritz|frzb-1	frizzled-related protein	protein-coding
mm_144509.1	chr18	24708618	24708633	+	1	NA	promoter-TSS (NM_001289655)	promoter-TSS (NM_001289655)	2	NM_001289655	225288	Mm.329322	NM_175276	ENSMUSG00000034295	Fhod3	A930009H06Rik|FHOS2|mKIAA1695	formin homology 2 domain containing 3	protein-coding
mm_124455.1	chr14	119034624	119034643	-	1	NA	intron (NM_001081252, intron 24 of 38)	ID4_|SINE|ID	64801	NM_001081252	66435	Mm.213406	NM_025561	ENSMUSG00000042104	Uggt2	1810064L21Rik|3110001A05Rik|3110027P15Rik|A230065J02Rik|AW047562|Ugcgl2	UDP-glucose glycoprotein glucosyltransferase 2	protein-coding
mm_160459.1	chr8	109608666	109608666	-	1	NA	promoter-TSS (NM_020046)	promoter-TSS (NM_020046)	7	NM_020046	56749	Mm.23894	NM_020046	ENSMUSG00000031730	Dhodh	2810417D19Rik|AI834883	dihydroorotate dehydrogenase	protein-coding
mm_90037.1	chr10	115817131	115817141	+	1	NA	promoter-TSS (NM_001168680)	promoter-TSS (NM_001168680)	-148	NM_001168680	216350	Mm.22270	NM_146010	ENSMUSG00000034127	Tspan8	C76990|E330007O21Rik|Tm4sf3	tetraspanin 8	protein-coding
mm_9140.1	chr1	170867790	170867800	-	1	NA	promoter-TSS (NM_001081304)	promoter-TSS (NM_001081304)	-24	NM_001081304	226641	Mm.377046	NM_001081304	ENSMUSG00000026663	Atf6	9130025P16Rik|9630036G24|AA789574|Atf6alpha|ESTM49	activating transcription factor 6	protein-coding
mm_59281.1	chr7	24907619	24907632	+	1	NA	intron (NM_001130152, intron 1 of 28)	intron (NM_001130152, intron 1 of 28)	3279	NM_001130152	16801	Mm.3181	NM_008488	ENSMUSG00000040940	Arhgef1	Lbcl2|Lsc	Rho guanine nucleotide exchange factor (GEF) 1	protein-coding
mm_35011.1	chr4	3574763	3574774	-	1	NA	promoter-TSS (NM_028097)	promoter-TSS (NM_028097)	0	NM_028097	72098	Mm.441135	NM_028097	ENSMUSG00000028232	Tmem68	2010300G19Rik|AA408325|AW123402	transmembrane protein 68	protein-coding
mm_165807.1	chr3	144720359	144720365	-	1	NA	promoter-TSS (NM_019464)	promoter-TSS (NM_019464)	-27	NM_001282037	54673	Mm.271775	NM_019464	ENSMUSG00000037062	Sh3glb1	AA409932|AI314629|AU015566|Bif-1|mKIAA0491	SH3-domain GRB2-like B1 (endophilin)	protein-coding
mm_49708.1	chr6	34412354	34412373	+	1	NA	promoter-TSS (NM_009731)	promoter-TSS (NM_009731)	1	NM_009731	11997	Mm.482073	NM_009731	ENSMUSG00000052131	Akr1b7	AR|Avdp|MVDP	aldo-keto reductase family 1, member B7	protein-coding
mm_28202.1	chr3	88296399	88296410	-	1	NA	promoter-TSS (NM_009836)	promoter-TSS (NM_009836)	434	NM_029801	76927	Mm.273330	NM_029801	ENSMUSG00000010538	Tsacc	1700021C14Rik|SIP	TSSK6 activating co-chaperone	protein-coding
mm_43140.1	chr5	125394434	125394449	+	1	NA	Intergenic	RMER17C|LTR|ERVK	-4424	NM_019639	22190	Mm.331	NM_019639	ENSMUSG00000008348	Ubc	2700054O04Rik|AI194771|Rps27a|TI-225|Uba52|Ubb	ubiquitin C	protein-coding
mm_116646.1	chr13	49183720	49183732	-	1	NA	Intergenic	Intergenic	-3821	NM_013610	18081	Mm.18503	NM_013610	ENSMUSG00000037966	Ninj1	AU024536	ninjurin 1	protein-coding
mm_113544.1	chr13	37896561	37896566	+	1	NA	intron (NR_033615, intron 4 of 9)	intron (NR_033615, intron 4 of 9)	7692	NM_001177869	68750	Mm.491109	NM_026830	ENSMUSG00000039087	Rreb1	1110037N09Rik|AA414966|B930013M22Rik	ras responsive element binding protein 1	protein-coding
mm_160205.1	chr7	84370943	84370943	-	1	NA	intron (NM_007488, intron 1 of 18)	intron (NM_007488, intron 1 of 18)	39095	NM_007488	11864	Mm.38594	NM_007488	ENSMUSG00000015709	Arnt2	Hif-2b|bHLHe1|mKIAA0307	aryl hydrocarbon receptor nuclear translocator 2	protein-coding
mm_163316.1	chr12	6748478	6748499	+	1	NA	Intergenic	Intergenic	631842	NR_045045	73575	Mm.179463	NR_045045	ENSMUSG00000102096	1700101O22Rik	-	RIKEN cDNA 1700101O22 gene	ncRNA
mm_80922.1	chr9	101097894	101097904	+	1	NA	intron (NM_001100451, intron 1 of 1)	intron (NM_001100451, intron 1 of 1)	23137	NM_001100451	77853	Mm.326206	NM_001100451	ENSMUSG00000066415	Msl2	E130103E02Rik|Msl2l1|Rnf184	male-specific lethal 2 homolog (Drosophila)	protein-coding
mm_79389.1	chr9	54801777	54801801	+	1	NA	Intergenic	Intergenic	37041	NM_013496	12903	Mm.34797	NM_013496	ENSMUSG00000032291	Crabp1	AI326249|CRABP-I|Crabp-1|CrabpI|Rbp-5	cellular retinoic acid binding protein I	protein-coding
mm_26893.1	chr3	19163012	19163085	-	1	NA	promoter-TSS (NM_028840)	promoter-TSS (NM_028840)	17	NM_028840	74252	Mm.200383	NM_028840	ENSMUSG00000027599	Armc1	2310016N05Rik|2900046P06Rik|3110009G21Rik|AA409258|AW048872|Arcp|C330014L16Rik	armadillo repeat containing 1	protein-coding
mm_10999.1	chr2	26389371	26389381	+	1	NA	promoter-TSS (NM_001085407)	promoter-TSS (NM_001085407)	28	NM_173180	66865	Mm.250359	NM_173180	ENSMUSG00000026926	Pmpca	1200002L24Rik|4933435E07Rik|Alpha-MPP|P-55	peptidase (mitochondrial processing) alpha	protein-coding
mm_110061.1	chr12	21286308	21286327	-	1	NA	promoter-TSS (NM_008403)	promoter-TSS (NM_008403)	20	NM_018813	54451	Mm.356778	NM_018813	ENSMUSG00000054309	Cpsf3	-	cleavage and polyadenylation specificity factor 3	protein-coding
mm_88021.1	chr10	67186074	67186100	+	1	NA	5' UTR (NM_001242396, exon 1 of 25)	5' UTR (NM_001242396, exon 1 of 25)	337	NM_001242396	108829	Mm.23846	NM_207221	ENSMUSG00000037876	Jmjd1c	5430433L24Rik|D630035I23Rik|Jmjdic|TRIP8	jumonji domain containing 1C	protein-coding
mm_126915.1	chr15	91199454	91199462	+	1	NA	Intergenic	CpG	-7651	NM_011994	26874	Mm.295456	NM_011994	ENSMUSG00000055782	Abcd2	ABC39|ALDL1|ALDR|ALDRP	ATP-binding cassette, sub-family D (ALD), member 2	protein-coding
mm_9607.1	chr1	175692625	175692663	-	1	NA	promoter-TSS (NM_010098)	promoter-TSS (NM_010098)	-12	NM_010098	13603	Mm.32744	NM_010098	ENSMUSG00000026525	Opn3	ERO|Ecpn	opsin 3	protein-coding
mm_18715.1	chr2	72442901	72442910	-	1	NA	TTS (NM_023057)	TTS (NM_023057)	-33314	NM_025866	66953	Mm.270676	NM_025866	ENSMUSG00000055612	Cdca7	2310021G01Rik|AU044109|JPO1	cell division cycle associated 7	protein-coding
mm_37670.1	chr4	129121235	129121315	-	1	NA	promoter-TSS (NM_010471)	promoter-TSS (NM_010471)	28	NM_010471	15444	Mm.384452	NM_010471	ENSMUSG00000028785	Hpca	-	hippocalcin	protein-coding
mm_8622.1	chr1	156270666	156270676	-	1	NA	exon (NM_001277730, exon 13 of 18)	exon (NM_001277730, exon 13 of 18)	32677	NM_001134741	214575	Mm.252800	NM_001134741	ENSMUSG00000060985	Tdrd5	Gm103	tudor domain containing 5	protein-coding
mm_102828.1	chr11	69094716	69094726	-	1	NA	Intergenic	Intergenic	-4235	NM_011065	18626	Mm.7373	NM_011065	ENSMUSG00000020893	Per1	Hftm|Per|m-rigui|mPer1	period circadian clock 1	protein-coding
mm_114376.1	chr13	63151509	63151530	+	1	NA	intron (NM_001289926, intron 5 of 15)	intron (NM_001289926, intron 5 of 15)	-88510	NR_110520	72061	Mm.188105	NM_028079	ENSMUSG00000021458	2010111I01Rik	2300006M17Rik|AP-O|AW742919|Aopep|ApO|mir-23b|mir-24-1|mir-27b	RIKEN cDNA 2010111I01 gene	protein-coding
mm_34209.1	chr4	140961283	140961293	+	1	NA	promoter-TSS (NM_023374)	promoter-TSS (NM_023374)	17	NM_023374	67680	Mm.246965	NM_023374	ENSMUSG00000009863	Sdhb	0710008N11Rik	succinate dehydrogenase complex, subunit B, iron sulfur (Ip)	protein-coding
mm_129796.1	chr15	82884386	82884388	-	1	NA	intron (NM_001114140, intron 1 of 5)	intron (NM_001114140, intron 1 of 5)	14074	NR_027799	21378	Mm.417272	NR_027799		Tbrg3	TB-11	transforming growth factor beta regulated gene 3	ncRNA
mm_43677.1	chr5	138799613	138799636	+	1	NA	intron (NM_030565, intron 5 of 9)	B4|SINE|B4	-20456	NM_001195128	384244	Mm.485002	NM_001195128	ENSMUSG00000094504	Gm5294	EG384244	predicted gene 5294	protein-coding
mm_101256.1	chr11	20831224	20831265	-	1	NA	promoter-TSS (NM_173752)	promoter-TSS (NM_173752)	-136	NM_173752	216551	Mm.76694	NM_173752	ENSMUSG00000042363	Lgalsl	1110067D22Rik|A530071M23|Grpa|Hspc159|Lgalsla	lectin, galactoside binding-like	protein-coding
mm_11127.1	chr2	28229951	28229970	+	1	NA	3' UTR (NM_001038613, exon 6 of 6)	3' UTR (NM_001038613, exon 6 of 6)	24271	NM_019498	56177	Mm.43278	NM_019498	ENSMUSG00000026833	Olfm1	AMY|AW742568|Noe1|OlfA|Pancortin|Pancortin3	olfactomedin 1	protein-coding
mm_46277.1	chr5	100039610	100039621	-	1	NA	promoter-TSS (NM_016690)	promoter-TSS (NM_016690)	-379	NM_026421	67870	Mm.11311	NM_026421	ENSMUSG00000029326	Enoph1	2310057D15Rik|BB183658|C81437	enolase-phosphatase 1	protein-coding
mm_172887.1	chr9	53690145	53690154	-	1	NA	intron (NM_175562, intron 1 of 1)	intron (NM_175562, intron 1 of 1)	16083	NM_175562	270160	Mm.290285	NM_175562	ENSMUSG00000055069	Rab39	C230094F14Rik|Rab39a	RAB39, member RAS oncogene family	protein-coding
mm_104415.1	chr11	94653923	94653942	-	1	NA	promoter-TSS (NM_177752)	promoter-TSS (NM_177752)	141	NM_053161	94064	Mm.34951	NM_053161	ENSMUSG00000024414	Mrpl27	A630055F16Rik|D11Moh47|D18Ertd643e	mitochondrial ribosomal protein L27	protein-coding
mm_4458.1	chr1	172699257	172699261	+	1	NA	3' UTR (NM_007768, exon 2 of 2)	3' UTR (NM_007768, exon 2 of 2)	1203	NM_007768	12944	Mm.28767	NM_007768	ENSMUSG00000037942	Crp	AI255847	C-reactive protein, pentraxin-related	protein-coding
mm_116669.1	chr13	49208040	49208053	-	1	NA	exon (NM_026738, exon 2 of 6)	exon (NM_026738, exon 2 of 6)	7980	NM_026738	68480	Mm.3336	NM_026738	ENSMUSG00000037960	Card19	1110007C09Rik|AI851695|Bincard	caspase recruitment domain family, member 19	protein-coding
mm_31757.1	chr4	63363022	63363037	+	1	NA	exon (NM_011016, exon 2 of 6)	exon (NM_011016, exon 2 of 6)	580	NM_011016	18406	Mm.14173	NM_011016	ENSMUSG00000061540	Orm2	Agp1|Orm-2	orosomucoid 2	protein-coding
mm_83674.1	chr9	49798906	49798931	-	1	NA	5' UTR (NM_001311065, exon 1 of 18)	5' UTR (NM_001311065, exon 1 of 18)	151	NM_001081445	17967	Mm.4974	NM_010875	ENSMUSG00000039542	Ncam1	CD56|E-NCAM|NCAM-1|Ncam	neural cell adhesion molecule 1	protein-coding
mm_119175.1	chr14	32165574	32165599	+	1	NA	promoter-TSS (NM_001284319)	promoter-TSS (NM_001284319)	0	NM_001284319	27057	Mm.371598	NM_019744	ENSMUSG00000056234	Ncoa4	ARA70|Rfg	nuclear receptor coactivator 4	protein-coding
mm_139435.1	chr17	53584125	53584141	+	1	NA	promoter-TSS (NM_001190846)	promoter-TSS (NM_001190846)	7	NM_001190846	18519	Mm.255025	NM_020005	ENSMUSG00000000708	Kat2b	A930006P13Rik|AI461839|AW536563|Pcaf|p/CAF	K(lysine) acetyltransferase 2B	protein-coding
mm_115472.1	chr13	119488081	119488093	+	1	NA	promoter-TSS (NM_001177666)	promoter-TSS (NM_001177666)	48	NM_001039244	633640	Mm.46679	NM_001039244	ENSMUSG00000074634	Tmem267	EG633640|Gm7120	transmembrane protein 267	protein-coding
mm_13872.1	chr2	119872506	119872555	+	1	NA	Intergenic	CpG	-24698	NM_001164274	29808	Mm.87532	NM_013720	ENSMUSG00000033943	Mga	AV312082|C130042M01Rik|C80739|D030062C11Rik|Mad5	MAX gene associated	protein-coding
mm_136748.1	chr17	8525198	8525239	+	1	NA	Intergenic	Intergenic	-1583	NM_001290707	23984	Mm.87161	NM_011866	ENSMUSG00000023868	Pde10a	-	phosphodiesterase 10A	protein-coding
mm_46796.1	chr5	112896351	112896405	-	1	NA	promoter-TSS (NM_028901)	promoter-TSS (NM_028901)	-16	NM_028901	74376	Mm.441903	NM_028901	ENSMUSG00000072720	Myo18b	4932408L24Rik|4933411E19Rik|Gm448	myosin XVIIIb	protein-coding
mm_155042.1	chrX	42150147	42150168	+	1	NA	promoter-TSS (NM_021465)	promoter-TSS (NM_021465)	-544	NM_021465	20843	Mm.290422	NM_021465	ENSMUSG00000025862	Stag2	9230105L23Rik|B230112I07Rik|SA-2|SAP2	stromal antigen 2	protein-coding
mm_75118.1	chr8	34689881	34689906	-	1	NA	Intergenic	MER88|LTR|ERVL	-49577	NR_040706	330734	Mm.149998	NR_040706	ENSMUSG00000109819	B930018H19Rik	B930018H19	RIKEN cDNA B930018H19 gene	ncRNA
mm_124902.1	chr15	10717580	10717583	+	1	NA	intron (NR_045063, intron 2 of 6)	intron (NR_045063, intron 2 of 6)	2681	NR_045065	75259	Mm.33928	NR_045063	ENSMUSG00000097058	4930556M19Rik	1700009D01Rik|C130022M03Rik	RIKEN cDNA 4930556M19 gene	ncRNA
mm_77143.1	chr8	111537418	111537427	-	1	NA	promoter-TSS (NM_001168623)	promoter-TSS (NM_001168623)	782	NM_001168621	170737	Mm.271578	NM_133206	ENSMUSG00000033545	Znrf1	B830022L21Rik|Rnf42|Zrfp1|nin283	zinc and ring finger 1	protein-coding
mm_135233.1	chr16	36935952	36935962	-	1	NA	intron (NM_008225, intron 1 of 13)	intron (NM_008225, intron 1 of 13)	974	NM_008225	15163	Mm.4091	NM_008225	ENSMUSG00000022831	Hcls1	AW213261|HS1	hematopoietic cell specific Lyn substrate 1	protein-coding
mm_33917.1	chr4	136479873	136479877	+	1	NA	intron (NM_024452, intron 1 of 4)	B2_Mm2|SINE|B2	10114	NM_024452	269593	Mm.485824	NM_024452	ENSMUSG00000001089	Luzp1	2700072H04Rik|AI266952|Luzp|mFLJ00226	leucine zipper protein 1	protein-coding
mm_143180.1	chr17	57275471	57275487	-	1	NA	Intergenic	CpG	-3621	NM_001163816	22324	Mm.248172	NM_011691	ENSMUSG00000034116	Vav1	Vav|vav-T	vav 1 oncogene	protein-coding
mm_84547.1	chr9	67428819	67428867	-	1	NA	intron (NM_001081242, intron 2 of 57)	intron (NM_001081242, intron 2 of 57)	130860	NM_001081242	70549	Mm.33645	NM_027458	ENSMUSG00000052698	Tln2	5730421P04Rik|AI507121|AI787438|AL118320|mKIAA0320	talin 2	protein-coding
mm_41907.1	chr5	105579568	105579577	+	1	NA	exon (NM_133897, exon 3 of 4)	exon (NM_133897, exon 3 of 4)	60101	NM_133897	100604	Mm.319847	NM_133897	ENSMUSG00000054720	Lrrc8c	AD158|AI326115|E430036I04Rik|fad158	leucine rich repeat containing 8 family, member C	protein-coding
mm_136382.1	chr16	92826005	92826080	-	1	NA	promoter-TSS (NM_001111021)	promoter-TSS (NM_001111021)	32	NM_001111021	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_41031.1	chr5	86065787	86065812	+	1	NA	promoter-TSS (NM_001345902)	promoter-TSS (NM_001345902)	-216	NM_007683	12617	Mm.4649	NM_007683	ENSMUSG00000029253	Cenpc1	CENP-C|Cenpc	centromere protein C1	protein-coding
mm_57181.1	chr6	122848608	122848611	-	1	NA	3' UTR (NM_009779, exon 2 of 2)	3' UTR (NM_009779, exon 2 of 2)	7548	NM_009779	12267	Mm.2408	NM_009779	ENSMUSG00000040552	C3ar1	AZ3B|C3AR|HNFAG09	complement component 3a receptor 1	protein-coding
mm_152460.1	chr19	10880390	10880411	-	1	NA	intron (NM_134142, intron 1 of 3)	MER5B|DNA|hAT-Charlie	1343	NM_134142	68539	Mm.251890	NM_134142	ENSMUSG00000034659	Tmem109	1110006I15Rik|AA958958|C77652	transmembrane protein 109	protein-coding
mm_93534.1	chr10	115362476	115362497	-	1	NA	promoter-TSS (NM_133683)	promoter-TSS (NM_133683)	-224	NM_133683	67226	Mm.29647	NM_133683	ENSMUSG00000069520	Tmem19	2810428F02Rik|AW125171	transmembrane protein 19	protein-coding
mm_168339.1	chr11	119395452	119395460	-	1	NA	Intergenic	Intergenic	4984	NR_035453	100316690		NR_035453	ENSMUSG00000088015	Mir1932	mir-1932|mmu-mir-1932	microRNA 1932	ncRNA
mm_140802.1	chr17	21967790	21967808	-	1	NA	intron (NM_001025373, intron 1 of 3)	intron (NM_001025373, intron 1 of 3)	5240	NM_001025373	74670	Mm.26540	NM_001025373	ENSMUSG00000053347	Zfp943	4930432O21Rik	zinc finger prtoein 943	protein-coding
mm_101727.1	chr11	42182925	42182935	-	1	NA	promoter-TSS (NM_010250)	promoter-TSS (NM_010250)	0	NM_010250	14394	Mm.439668	NM_010250	ENSMUSG00000010803	Gabra1	Gabra-1	gamma-aminobutyric acid (GABA) A receptor, subunit alpha 1	protein-coding
mm_12811.1	chr2	80302360	80302364	+	1	NA	Intergenic	Intergenic	9892	NM_177256	320769	Mm.60992	NM_177256	ENSMUSG00000050114	Prdx6b	1-cysPrx-P1|4930414C22Rik|Aop2-rs1|Prdx5-rs1|Prdx6-ps1|Prdx6-rs1|Prdx6-rs1-ps	peroxiredoxin 6B	protein-coding
mm_92550.1	chr10	79761496	79761496	-	1	NA	exon (NM_144528, exon 6 of 9)	exon (NM_144528, exon 6 of 9)	5456	NM_144528	70294	Mm.466670	NM_144528	ENSMUSG00000035890	Rnf126	2610010O19Rik	ring finger protein 126	protein-coding
mm_30355.1	chr3	151764123	151764162	-	1	NA	Intergenic	Intergenic	-1251	NM_031367	15061	Mm.219544	NM_031367	ENSMUSG00000039146	Ifi44l	H-28|H28|H28-1|NS1178	interferon-induced protein 44 like	protein-coding
mm_95495.1	chr11	51755942	51755944	+	1	NA	intron (NM_001290785, intron 1 of 22)	intron (NM_001290785, intron 1 of 22)	891	NM_001290785	77371	Mm.33878	NM_175255	ENSMUSG00000036391	Sec24a	-	Sec24 related gene family, member A (S. cerevisiae)	protein-coding
mm_62008.1	chr7	91262366	91262374	+	1	NA	intron (NM_011807, intron 1 of 22)	intron (NM_011807, intron 1 of 22)	171584	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_3573.1	chr1	150518738	150518742	+	1	NA	Intergenic	L1MA4|LINE|L1	-52575	NM_001110146	96875	Mm.174256	NM_021400	ENSMUSG00000006014	Prg4	CACP|DOL54|JCAP|MSF|SZP|lubricin	proteoglycan 4 (megakaryocyte stimulating factor, articular superficial zone protein)	protein-coding
mm_4642.1	chr1	179975936	179975939	+	1	NA	intron (NM_001346805, intron 1 of 34)	MTD|LTR|ERVL-MaLR	14848	NM_001033285	226751	Mm.259655	NM_001033285	ENSMUSG00000026490	Cdc42bpa	A930014J19Rik|DMPK-like	CDC42 binding protein kinase alpha	protein-coding
mm_163164.1	chr11	86579102	86579107	+	1	NA	Intergenic	Intergenic	5054	NR_029738	387140		NR_029738	ENSMUSG00000065455	Mir21a	Mir21|Mirn21|mmu-mir-21|mmu-mir-21a	microRNA 21a	ncRNA
mm_141893.1	chr17	34862123	34862238	-	1	NA	TTS (NM_013484)	TTS (NM_013484)	334	NM_001142706	14962	Mm.653	NM_008198	ENSMUSG00000090231	Cfb	AI195813|AI255840|B|Bf|C2|Fb|H2-Bf	complement factor B	protein-coding
mm_8820.1	chr1	162188852	162188859	-	1	NA	intron (NM_001038619, intron 14 of 20)	intron (NM_001038619, intron 14 of 20)	-28768	NR_002870	474332	Mm.479755	NR_002870	ENSMUSG00000078190	Dnm3os	6030416H16Rik|Hag2|Npn1|P/L01	dynamin 3, opposite strand	ncRNA
mm_151471.1	chr19	58671786	58671831	+	1	NA	exon (NM_026925, exon 3 of 13)	exon (NM_026925, exon 3 of 13)	1443	NM_026925	69060	Mm.20407	NM_026925	ENSMUSG00000046008	Pnlip	1810007A24Rik|PL|PTL	pancreatic lipase	protein-coding
mm_152497.1	chr19	11096905	11096906	-	1	NA	TTS (NM_027058)	TTS (NM_027058)	-15802	NM_022430	64381	Mm.34460	NM_022430	ENSMUSG00000024730	Ms4a8a	2010004L09Rik|AI481240|CD20L5|Ms4a8	membrane-spanning 4-domains, subfamily A, member 8A	protein-coding
mm_141217.1	chr17	27167790	27167801	-	1	NA	promoter-TSS (NM_173027)	promoter-TSS (NM_173027)	-31	NM_173027	271424	Mm.209679	NM_173027	ENSMUSG00000024210	Ip6k3	D830007E07Rik|Ihpk3	inositol hexaphosphate kinase 3	protein-coding
mm_63729.1	chr7	130865960	130865970	+	1	NA	promoter-TSS (NM_133942)	promoter-TSS (NM_133942)	55	NM_133942	101476	Mm.323554	NM_133942	ENSMUSG00000040268	Plekha1	AA960558|C920009D07Rik|TAPP1	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 1	protein-coding
mm_107049.1	chr12	16170469	16170475	+	1	NA	Intergenic	Intergenic	-353687	NM_144551	217410	Mm.491136	NM_144551	ENSMUSG00000020601	Trib2	AW319517|TRB-2|TRB2	tribbles pseudokinase 2	protein-coding
mm_87993.1	chr10	66698211	66698217	+	1	NA	Intergenic	Intergenic	222170	NR_138560	68488	Mm.338835	NR_138560		1110002J07Rik	-	RIKEN cDNA 1110002J07 gene	ncRNA
mm_99770.1	chr11	107025588	107025598	+	1	NA	Intergenic	Intergenic	-2630	NM_001163473	69066	Mm.40679	NM_001163473	ENSMUSG00000078607	1810010H24Rik	OTTMUSG00000003581	RIKEN cDNA 1810010H24 gene	protein-coding
mm_138882.1	chr17	43389437	43389497	+	1	NA	promoter-TSS (NM_001081178)	promoter-TSS (NM_001081178)	1	NM_001081178	224792	Mm.23478	NM_001081178	ENSMUSG00000056492	Adgrf5	8430401C09Rik|9330185D23|AI528491|Gpr116|mKIAA0758	adhesion G protein-coupled receptor F5	protein-coding
mm_157068.1	chrX	8192893	8192908	-	1	NA	TTS (NM_145907)	TTS (NM_145907)	612	NM_007898	13595	Mm.27183	NM_007898	ENSMUSG00000031168	Ebp	AI255399|Pabp|SI|Td|mSI	phenylalkylamine Ca2+ antagonist (emopamil) binding protein	protein-coding
mm_161060.1	chr12	70290540	70290540	-	1	NA	intron (NM_053167, intron 2 of 13)	intron (NM_053167, intron 2 of 13)	-17965	NR_037248	100526482		NR_037248	ENSMUSG00000078026	Mir466o	Mir4660|mmu-mir-466o	microRNA 466o	ncRNA
mm_129989.1	chr15	86150566	86150570	-	1	NA	intron (NM_145475, intron 7 of 12)	B1_Mur1|SINE|Alu	35573	NM_145475	223753	Mm.222685	NM_145475	ENSMUSG00000035891	Cerk	AI848610|D330016D08Rik|mKIAA1646	ceramide kinase	protein-coding
mm_453.1	chr1	36105703	36105732	+	1	NA	3' UTR (NM_015818, exon 2 of 2)	3' UTR (NM_015818, exon 2 of 2)	37317	NM_015818	50785	Mm.213566	NM_015818	ENSMUSG00000045216	Hs6st1	6Ost1	heparan sulfate 6-O-sulfotransferase 1	protein-coding
mm_70645.1	chr8	14136153	14136155	+	1	NA	intron (NM_001145965, intron 1 of 14)	intron (NM_001145965, intron 1 of 14)	40279	NM_172910	244310	Mm.404697	NM_172910	ENSMUSG00000047495	Dlgap2	6430596N04Rik|Dap-2|Dap2|Sapap2	discs, large (Drosophila) homolog-associated protein 2	protein-coding
mm_136199.1	chr16	89733180	89733184	-	1	NA	Intergenic	Intergenic	85170	NM_001145887	21844	Mm.310902	NM_009384	ENSMUSG00000002489	Tiam1	AI847750|D16Ium10|D16Ium10e	T cell lymphoma invasion and metastasis 1	protein-coding
mm_140357.1	chr17	86831449	86831468	+	1	NA	3' UTR (NM_010137, exon 16 of 16)	3' UTR (NM_010137, exon 16 of 16)	77594	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_171999.1	chr6	106151456	106151456	-	1	NA	intron (NM_001109751, intron 3 of 18)	PB1D7|SINE|Alu	32691	NM_001109751	269784	Mm.321683	NM_173004	ENSMUSG00000064293	Cntn4	9630050B05|Axcam|BIG-2	contactin 4	protein-coding
mm_93620.1	chr10	117277754	117277803	-	1	NA	3' UTR (NM_017372, exon 4 of 4)	3' UTR (NM_017372, exon 4 of 4)	4494	NM_017372	17105	Mm.45436	NM_017372	ENSMUSG00000069516	Lyz2	AI326280|Lys|Lysm|Lyzf2|Lyzs|Lzm|Lzm-s1|Lzp	lysozyme 2	protein-coding
mm_125763.1	chr15	74516206	74516219	+	1	NA	promoter-TSS (NM_174991)	promoter-TSS (NM_174991)	16	NM_174991	107831	Mm.43133	NM_174991	ENSMUSG00000034730	Adgrb1	B830018M07Rik|Bai1|R75078|mKIAA4089	adhesion G protein-coupled receptor B1	protein-coding
mm_112196.1	chr12	113425766	113425776	-	1	NA	Intergenic	(CAGCT)n|Simple_repeat|Simple_repeat	-63794	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_23814.1	chr3	79886903	79886955	+	1	NA	exon (NM_133187, exon 1 of 4)	exon (NM_133187, exon 1 of 4)	999	NM_133187	68659	Mm.427274	NM_133187	ENSMUSG00000027955	Fam198b	1110032E23Rik|2210419I08Rik|AV011458|Ened	family with sequence similarity 198, member B	protein-coding
mm_99756.1	chr11	106751256	106751280	+	1	NA	promoter-TSS (NM_001271373)	promoter-TSS (NM_001271373)	42	NM_001033435	380732	Mm.343952	NM_001033435	ENSMUSG00000040528	Milr1	Allergin-1|Gm885|Mca32	mast cell immunoglobulin like receptor 1	protein-coding
mm_67699.1	chr7	89518535	89518555	-	1	NA	promoter-TSS (NM_029614)	promoter-TSS (NM_029614)	-959	NM_029614	76453	Mm.250438	NM_029614	ENSMUSG00000039405	Prss23	2310046G15Rik|4930479H08Rik|AI790574|Spuve	protease, serine 23	protein-coding
mm_140565.1	chr17	8299730	8299738	-	1	NA	intron (NR_073374, intron 1 of 4)	intron (NR_073374, intron 1 of 4)	-11369	NM_134114	106489	Mm.311080	NM_134114	ENSMUSG00000073468	Sft2d1	5630401J11Rik|AA409698	SFT2 domain containing 1	protein-coding
mm_6289.1	chr1	69759652	69759663	-	1	NA	Intergenic	Intergenic	-67313	NM_029160	66722	Mm.440554	NM_025728	ENSMUSG00000053153	Spag16	4921511D23Rik|4930524F24Rik|4930585K05Rik|AV261009|Pf20|Wdr29	sperm associated antigen 16	protein-coding
mm_168617.1	chr1	177756208	177756210	-	1	NA	Intergenic	RLTR16|LTR|ERVK	26395	NM_027077	69428	Mm.84467	NM_027077	ENSMUSG00000015962	1700016C15Rik	-	RIKEN cDNA 1700016C15 gene	protein-coding
mm_41408.1	chr5	90787425	90787440	+	1	NA	intron (NM_203320, intron 3 of 3)	intron (NM_203320, intron 3 of 3)	1331	NM_203320	330122	Mm.244289	NM_203320	ENSMUSG00000029379	Cxcl3	Dcip1|Gm1960	chemokine (C-X-C motif) ligand 3	protein-coding
mm_28312.1	chr3	89245812	89245825	-	1	NA	promoter-TSS (NM_025327)	promoter-TSS (NM_025327)	79	NM_183037	360213	Mm.331156	NM_183037	ENSMUSG00000042766	Trim46	TRIFIC	tripartite motif-containing 46	protein-coding
mm_87401.1	chr10	45577917	45577928	+	1	NA	promoter-TSS (NM_172473)	promoter-TSS (NM_172473)	93	NM_172473	209462	Mm.458633	NM_172473	ENSMUSG00000038822	Hace1	1700042J16Rik|A730034A22Rik|BC025474	HECT domain and ankyrin repeat containing, E3 ubiquitin protein ligase 1	protein-coding
mm_138346.1	chr17	34931332	34931343	+	1	NA	promoter-TSS (NM_010893)	promoter-TSS (NM_010893)	84	NM_010893	18010	Mm.8856	NM_010893	ENSMUSG00000007038	Neu1	AA407268|AA407316|Aglp|Apl|Bat-7|Bat7|G9|Map-2|Neu|Neu-1	neuraminidase 1	protein-coding
mm_171595.1	chr4	147702572	147702590	-	1	NA	promoter-TSS (NM_001127188)	promoter-TSS (NM_001127188)	50	NM_001127188	100503584	Mm.276881	NM_001127188	ENSMUSG00000062518	Zfp534	Gm13159|OTTMUSG00000010681	zinc finger protein 534	protein-coding
mm_120352.1	chr14	63992426	63992443	+	1	NA	promoter-TSS (NM_146246)	promoter-TSS (NM_146246)	3	NM_146246	271209	Mm.300655	NM_146246	ENSMUSG00000046049	Rp1l1	BC031365|BE983540|Dcdc4|Rp1hl1	retinitis pigmentosa 1 homolog like 1	protein-coding
mm_114979.1	chr13	97250721	97250722	+	1	NA	3' UTR (NM_007930, exon 3 of 3)	3' UTR (NM_007930, exon 3 of 3)	9616	NM_007930	13803	Mm.241073	NM_007930	ENSMUSG00000041773	Enc1	Nrpb|PIG10	ectodermal-neural cortex 1	protein-coding
mm_145466.1	chr18	60271491	60271497	+	1	NA	intron (NM_001034859, intron 1 of 1)	MTD|LTR|ERVL-MaLR	1773	NM_001034859	225594	Mm.329460	NM_001034859	ENSMUSG00000068606	Gm4841	EG225594|Ifgga3	predicted gene 4841	protein-coding
mm_8614.1	chr1	156036150	156036157	-	1	NA	exon (NM_144791, exon 1 of 7)	intron (NM_172843, intron 1 of 6)	117	NM_001160182	240832	Mm.253335	NM_022329	ENSMUSG00000050565	Tor1aip2	1110020D10Rik|15kDa|A130072J07|AA103493|AW060462|AW610675|C77739|Ifrg15|Lull1	torsin A interacting protein 2	protein-coding
mm_4350.1	chr1	171896585	171896602	+	1	NA	Intergenic	Intergenic	-20869	NM_001347187	30925	Mm.486404	NM_030710	ENSMUSG00000015314	Slamf6	KAL1|KAL1b|Ly108|NTB-A|NTBA|SF2000	SLAM family member 6	protein-coding
mm_41882.1	chr5	105409342	105409373	+	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-6418	NM_001033550	433926	Mm.439781	NM_001033550	ENSMUSG00000070639	Lrrc8b	R75581|Ta-lrrp|mKIAA0231	leucine rich repeat containing 8 family, member B	protein-coding
mm_110206.1	chr12	27341685	27341697	-	1	NA	exon (NM_009234, exon 1 of 1)	exon (NM_009234, exon 1 of 1)	1027	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding
mm_171671.1	chr4	48686777	48686796	-	1	NA	Intergenic	LTRIS2|LTR|ERV1	23272	NM_026509	68016	Mm.133444	NM_026509	ENSMUSG00000028348	Murc	2310039E09Rik	muscle-related coiled-coil protein	protein-coding
mm_86204.1	chr9	119982982	119983003	-	1	NA	intron (NM_153287, intron 1 of 4)	CpG	1666	NM_153287	215418	Mm.491094	NM_153287	ENSMUSG00000032515	Csrnp1	4931429D10Rik|Axud1|CSRNP-1|URAX1|taip-3	cysteine-serine-rich nuclear protein 1	protein-coding
mm_121118.1	chr14	101840455	101840465	+	1	NA	promoter-TSS (NM_001347628)	promoter-TSS (NM_001347628)	-163	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_11707.1	chr2	36216750	36216786	+	1	NA	Intergenic	Intergenic	-13658	NM_008969	19224	Mm.275434	NM_008969	ENSMUSG00000047250	Ptgs1	COX1|Cox-1|Cox-3|PGHS-1|PHS 1|Pghs1	prostaglandin-endoperoxide synthase 1	protein-coding
mm_5591.1	chr1	39555641	39555673	-	1	NA	exon (NM_001033135, exon 6 of 7)	exon (NM_001033135, exon 6 of 7)	-6817	NR_028555	100217461		NR_028555	ENSMUSG00000077704	Snord89	MBII-289	small nucleolar RNA, C/D box 89	snoRNA
mm_52288.1	chr6	108663120	108663142	+	1	NA	intron (NM_011498, intron 4 of 4)	intron (NM_011498, intron 4 of 4)	-2197	NR_104577	75394	Mm.395061	NR_040757	ENSMUSG00000087341	0610040F04Rik	-	RIKEN cDNA 0610040F04 gene	ncRNA
mm_162560.1	chr1	172206757	172206759	-	1	NA	promoter-TSS (NM_001329871)	promoter-TSS (NM_001329871)	46	NM_001329871	18611	Mm.544	NM_011063	ENSMUSG00000013698	Pea15a	Mat1|PEA-15|Pea15|Pkcs15	phosphoprotein enriched in astrocytes 15A	protein-coding
mm_107077.1	chr12	16965123	16965155	+	1	NA	exon (NM_009072, exon 19 of 33)	exon (NM_009072, exon 19 of 33)	34979	NM_172574	217430	Mm.379451	NM_172574	ENSMUSG00000045679	Pqlc3	C78076|E030024M05Rik	PQ loop repeat containing	protein-coding
mm_154625.1	chrX	7728535	7728545	+	1	NA	promoter-TSS (NM_138602)	promoter-TSS (NM_138602)	-31	NM_138602	54637	Mm.28850	NM_138602	ENSMUSG00000031149	Praf2	AA986329|C78013|DXImx39e|JM4|Sfc20	PRA1 domain family 2	protein-coding
mm_88065.1	chr10	67647436	67647447	+	1	NA	Intergenic	Intergenic	-98486	NM_001005419	211488	Mm.297250	NM_001005419	ENSMUSG00000057134	Ado	Gm237	2-aminoethanethiol (cysteamine) dioxygenase	protein-coding
mm_72084.1	chr8	71579233	71579237	+	1	NA	intron (NM_011977, intron 3 of 13)	intron (NM_011977, intron 3 of 13)	10308	NM_011977	26457	Mm.38165	NM_011977	ENSMUSG00000031808	Slc27a1	FATP1|Fatp	solute carrier family 27 (fatty acid transporter), member 1	protein-coding
mm_96967.1	chr11	70647654	70647658	+	1	NA	promoter-TSS (NM_024211)	promoter-TSS (NM_024211)	369	NM_027445	70510	Mm.261818	NM_027445	ENSMUSG00000040746	Rnf167	0610010G05Rik|5730408C10Rik|AU019305|AV328608	ring finger protein 167	protein-coding
mm_59202.1	chr7	24507205	24507215	+	1	NA	non-coding (NR_110958, exon 1 of 3)	non-coding (NR_110958, exon 1 of 3)	123	NR_110958	232969	Mm.181332	NM_146183	ENSMUSG00000064264	Zfp428	2410005H09Rik|AV271806|AW047854|Znf428	zinc finger protein 428	protein-coding
mm_115269.1	chr13	111580261	111580291	+	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-90235	NM_001122963	73274	Mm.57286	NM_028487	ENSMUSG00000032745	Gpbp1	1700034P14Rik|AU019836|D230035M11Rik|Gpbp|mGPBP	GC-rich promoter binding protein 1	protein-coding
mm_22412.1	chr2	181365307	181365371	-	1	NA	promoter-TSS (NM_001165995)	promoter-TSS (NM_001165995)	65	NM_001165991	76688	Mm.87720	NM_029702	ENSMUSG00000038671	Arfrp1	1500006I01Rik|AI480700	ADP-ribosylation factor related protein 1	protein-coding
mm_34160.1	chr4	139484912	139484932	+	1	NA	intron (NM_001160319, intron 103 of 105)	intron (NM_001160319, intron 103 of 105)	-45626	NM_183148	212632	Mm.30464	NM_183148	ENSMUSG00000041025	Iffo2	C79267	intermediate filament family orphan 2	protein-coding
mm_26543.1	chr3	146150257	146150285	+	1	NA	promoter-TSS (NM_001005846)	promoter-TSS (NM_001005846)	97	NM_001005846	68279	Mm.116862	NM_026656	ENSMUSG00000011008	Mcoln2	3300002C04Rik|AI549968|C86638|TRPML2	mucolipin 2	protein-coding
mm_161530.1	chr15	102111177	102111177	+	1	NA	exon (NM_153533, exon 18 of 29)	exon (NM_153533, exon 18 of 29)	8189	NM_153533	209039	Mm.29389	NM_153533	ENSMUSG00000037003	Tns2	C1-ten|Tenc1|nep|nph	tensin 2	protein-coding
mm_112508.1	chr13	8885886	8885893	+	1	NA	exon (NM_145360, exon 1 of 5)	exon (NM_145360, exon 1 of 5)	283	NM_145360	319554	Mm.29847	NM_145360	ENSMUSG00000058258	Idi1	4832416K17Rik	isopentenyl-diphosphate delta isomerase	protein-coding
mm_149160.1	chr19	9018060	9018070	+	1	NA	TTS (NR_105786)	TTS (NR_105786)	161	NR_105786	102465190		NR_105786	ENSMUSG00000099308	Mir6367	Gm27467|mmu-mir-6367	microRNA 6367	ncRNA
mm_69531.1	chr7	135693311	135693322	-	1	NA	exon (NM_001081117, exon 13 of 14)	exon (NM_001081117, exon 13 of 14)	23063	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_40066.1	chr5	34196791	34196793	+	1	NA	intron (NM_001015039, intron 11 of 12)	intron (NM_001015039, intron 11 of 12)	-9082	NM_010753	17122	Mm.259260	NM_010753	ENSMUSG00000037235	Mxd4	2810410A03Rik|Mad4|bHLHc12	Max dimerization protein 4	protein-coding
mm_52089.1	chr6	97830948	97830958	+	1	NA	intron (NM_001113198, intron 1 of 9)	intron (NM_001113198, intron 1 of 9)	23895	NM_001113198	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_80290.1	chr9	73065896	73065910	+	1	NA	intron (NM_001301232, intron 1 of 5)	intron (NM_001301232, intron 1 of 5)	1755	NM_001301232	11891	Mm.34867	NM_023635	ENSMUSG00000032202	Rab27a	2210402C08Rik|2410003M20Rik|4933437C11Rik|ash	RAB27A, member RAS oncogene family	protein-coding
mm_7729.1	chr1	130732619	130732622	-	1	NA	intron (NM_177604, intron 1 of 3)	B1F2|SINE|Alu	644	NM_177604	212439	Mm.268547	NM_177604	ENSMUSG00000042510	AA986860	E030025M07|Sarg	expressed sequence AA986860	protein-coding
mm_161615.1	chr16	50431132	50431132	-	1	NA	intron (NM_001347240, intron 1 of 16)	intron (NM_001347240, intron 1 of 16)	1257	NM_027444	70508	Mm.28940	NM_027444	ENSMUSG00000022641	Bbx	5530401J07Rik|5730403O13Rik	bobby sox HMG box containing	protein-coding
mm_164191.1	chr15	78611428	78611507	+	1	NA	exon (NM_028195, exon 8 of 13)	exon (NM_028195, exon 8 of 13)	14420	NM_028195	72318	Mm.32911	NM_028195	ENSMUSG00000018008	Cyth4	2510004M07Rik|5830469K17Rik|AI467541|Pscd4|mFLJ00017	cytohesin 4	protein-coding
mm_9053.1	chr1	167308583	167308613	-	1	NA	promoter-TSS (NM_001039483)	promoter-TSS (NM_001039483)	-72	NM_001039483	68944	Mm.330045	NM_026881	ENSMUSG00000052428	Tmco1	1190006A08Rik|4930403O06Rik|AA109065|AU022572|ESTM39	transmembrane and coiled-coil domains 1	protein-coding
mm_119519.1	chr14	47473117	47473141	+	1	NA	intron (NM_030236, intron 1 of 1)	CpG	568	NM_001146085	78938	Mm.11935	NM_030236	ENSMUSG00000037536	Fbxo34	2900057B08Rik|5830426G16Rik	F-box protein 34	protein-coding
mm_35332.1	chr4	26501743	26501783	-	1	NA	Intergenic	Intergenic	-155111	NM_172865	242362	Mm.245602	NM_172865	ENSMUSG00000040520	Manea	4932703L02Rik	mannosidase, endo-alpha	protein-coding
mm_116574.1	chr13	47100269	47100273	-	1	NA	intron (NM_025900, intron 4 of 10)	intron (NM_025900, intron 4 of 10)	5950	NM_025900	110052	Mm.131150	NM_025900	ENSMUSG00000021377	Dek	1810019E15Rik|D13H6S231E	DEK oncogene (DNA binding)	protein-coding
mm_102268.1	chr11	55394662	55394725	-	1	NA	3' UTR (NM_009242, exon 10 of 10)	3' UTR (NM_009242, exon 10 of 10)	25387	NM_009242	20692	Mm.291442	NM_009242	ENSMUSG00000018593	Sparc	BM-40|ON	secreted acidic cysteine rich glycoprotein	protein-coding
mm_88117.1	chr10	69213163	69213228	+	1	NA	promoter-TSS (NM_001252638)	promoter-TSS (NM_001252638)	1	NM_001252638	69288	Mm.26659	NM_001081347	ENSMUSG00000019944	Rhobtb1	1700008H16Rik|3110048G13Rik|AI173445|AI573858|AV350930	Rho-related BTB domain containing 1	protein-coding
mm_65244.1	chr7	19824249	19824259	-	1	NA	Intergenic	Intergenic	-1499	NM_033601	12051	Mm.439658	NM_033601	ENSMUSG00000053175	Bcl3	AI528691|Bcl-3	B cell leukemia/lymphoma 3	protein-coding
mm_94566.1	chr11	11686216	11686282	+	1	NA	5' UTR (NM_009578, exon 1 of 7)	5' UTR (NM_009578, exon 1 of 7)	324	NM_001025597	22778	Mm.103545	NM_009578	ENSMUSG00000018654	Ikzf1	5832432G11Rik|Ikaros|LyF-1|Zfpn1a1|Znfn1a1|hlk-1|mKIAA4227	IKAROS family zinc finger 1	protein-coding
mm_64397.1	chr7	142498833	142498849	+	1	NA	promoter-TSS (NM_001163669)	promoter-TSS (NM_001163669)	5	NM_001347551	21957	Mm.389992	NM_011620	ENSMUSG00000061723	Tnnt3	fTnT	troponin T3, skeletal, fast	protein-coding
mm_168533.1	chr1	161035817	161035822	+	1	NA	non-coding (NR_002840, exon 1 of 4)	non-coding (NR_002840, exon 1 of 4)	653	NR_002840	14455	Mm.270065	NR_002840	ENSMUSG00000053332	Gas5	Gas-5|Mir5117|Snhg2	growth arrest specific 5	ncRNA
mm_21505.1	chr2	163587588	163587599	-	1	NA	Intergenic	Intergenic	-14721	NM_181734	76080	Mm.89828	NM_029512	ENSMUSG00000017679	Ttpal	3110080A02Rik|5830472M02Rik	tocopherol (alpha) transfer protein-like	protein-coding
mm_95352.1	chr11	48817177	48817184	+	1	NA	5' UTR (NM_145377, exon 1 of 6)	5' UTR (NM_145377, exon 1 of 6)	211	NM_145377	211007	Mm.794	NM_145377	ENSMUSG00000040365	Trim41	AW552703|BC020156|R75223|RINCK	tripartite motif-containing 41	protein-coding
mm_69674.1	chr7	139984608	139984620	-	1	NA	intron (NM_007403, intron 19 of 23)	intron (NM_007403, intron 19 of 23)	2260	NR_106029	102465643		NR_106029	ENSMUSG00000099092	Mir7062	Gm27339|mmu-mir-7062	microRNA 7062	ncRNA
mm_108785.1	chr12	90738093	90738096	+	1	NA	exon (NM_010050, exon 1 of 2)	exon (NM_010050, exon 1 of 2)	943	NM_010050	13371	Mm.21389	NM_010050	ENSMUSG00000007682	Dio2	5DII|AI324267|DIOII	deiodinase, iodothyronine, type II	protein-coding
mm_49973.1	chr6	40778815	40778817	+	1	NA	intron (NR_035473, intron 2 of 3)	intron (NR_035473, intron 2 of 3)	108678	NM_139296	194357	Mm.207087	NM_139296	ENSMUSG00000029885	Moxd2	Dbhl1	monooxygenase, DBH-like 2	protein-coding
mm_157252.1	chrX	19150671	19150692	-	1	NA	Intergenic	Intergenic	-3710	NR_029807	723828		NR_029807	ENSMUSG00000065471	Mir222	Mirn222|mir-222|mmu-mir-222	microRNA 222	ncRNA
mm_61309.1	chr7	67952878	67952922	+	1	NA	exon (NM_010513, exon 1 of 21)	exon (NM_010513, exon 1 of 21)	643	NM_010513	16001	Mm.275742	NM_010513	ENSMUSG00000005533	Igf1r	A330103N21Rik|CD221|D930020L01|IGF-1R|hyft	insulin-like growth factor I receptor	protein-coding
mm_45391.1	chr5	66150907	66150960	-	1	NA	promoter-TSS (NM_001291226)	promoter-TSS (NM_001291226)	45	NM_001291226	245945	Mm.36863	NM_139065	ENSMUSG00000070780	Rbm47	9530077J19Rik	RNA binding motif protein 47	protein-coding
mm_62311.1	chr7	100227741	100227781	+	1	NA	5' UTR (NM_027629, exon 1 of 14)	5' UTR (NM_027629, exon 1 of 14)	154	NM_027629	70974	Mm.440524	NM_027629	ENSMUSG00000030729	Pgm2l1	4931406N15Rik|AI553438|BM32A	phosphoglucomutase 2-like 1	protein-coding
mm_10120.1	chr2	3733068	3733075	+	1	NA	intron (NM_025626, intron 1 of 3)	intron (NM_025626, intron 1 of 3)	19613	NM_025626	66540	Mm.277864	NM_025626	ENSMUSG00000026655	Fam107b	3110001A13Rik|AA589595|AA959793|AI132312	family with sequence similarity 107, member B	protein-coding
mm_117328.1	chr13	68582074	68582084	-	1	NA	promoter-TSS (NR_131892)	promoter-TSS (NR_131892)	25	NM_001308475	210009	Mm.205514	NM_172480	ENSMUSG00000034617	Mtrr	4732420G08|MSR	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	protein-coding
mm_111708.1	chr12	103695018	103695023	-	1	NA	promoter-TSS (NM_001164742)	promoter-TSS (NM_001164742)	-331	NM_001164742	68348	Mm.20149	NM_026687	ENSMUSG00000021081	Serpina1f	0610012A11Rik|AI327419|Serpina2|epserin	serine (or cysteine) peptidase inhibitor, clade A, member 1F	protein-coding
mm_165707.1	chr3	97998417	97998425	-	1	NA	Intergenic	Intergenic	-15117	NM_010928	18129	Mm.485843	NM_010928	ENSMUSG00000027878	Notch2	AI853703|N2	notch 2	protein-coding
mm_116533.1	chr13	45872302	45872312	-	1	NA	intron (NM_001199304, intron 2 of 6)	intron (NM_001199304, intron 2 of 6)	92684	NM_001199304	20238	Mm.342683	NM_009124	ENSMUSG00000046876	Atxn1	2900016G23Rik|Atx1|C85907|ENSMUSG00000074917|Gm10786|Sca1	ataxin 1	protein-coding
mm_80690.1	chr9	91378615	91378623	+	1	NA	intron (NM_009576, intron 2 of 4)	CpG	9647	NM_009576	22774	Mm.8062	NM_009576	ENSMUSG00000036972	Zic4	-	zinc finger protein of the cerebellum 4	protein-coding
mm_79306.1	chr9	52047968	52047990	+	1	NA	promoter-TSS (NM_009041)	promoter-TSS (NM_009041)	38	NM_001104617	19684	Mm.245746	NM_009041	ENSMUSG00000032050	Rdx	AA516625	radixin	protein-coding
mm_82303.1	chr9	7867983	7867988	-	1	NA	intron (NM_007464, intron 1 of 8)	MMERGLN-int|LTR|ERV1	5185	NM_007464	11796	Mm.2026	NM_007464	ENSMUSG00000032000	Birc3	AW107670|Api1|Api2|Birc2|C-IAP2|HIAP2|IAP1|IAP2|MIAP1|MIAP2|MIHB|MIHC|RNF49|cIAP-1|cIAP-2|cIAP1|cIAP2	baculoviral IAP repeat-containing 3	protein-coding
mm_92509.1	chr10	78412950	78413021	-	1	NA	promoter-TSS (NM_010925)	promoter-TSS (NM_010925)	58	NM_010925	18114	Mm.38344	NM_010925	ENSMUSG00000061032	Rrp1	AL033305|AL033306|AU018604|NNP-1|Nnp1	ribosomal RNA processing 1 homolog (S. cerevisiae)	protein-coding
mm_140535.1	chr17	6756091	6756103	-	1	NA	intron (NM_009510, intron 2 of 12)	intron (NM_009510, intron 2 of 12)	26683	NM_009510	22350	Mm.277812	NM_009510	ENSMUSG00000052397	Ezr	AW146364|R75297|Vil2|p81	ezrin	protein-coding
mm_151030.1	chr19	47014673	47014691	+	1	NA	promoter-TSS (NM_146100)	promoter-TSS (NM_146100)	-16	NM_146100	226180	Mm.276251	NM_146100	ENSMUSG00000034336	Ina	AV028420|NF-66|NF66	internexin neuronal intermediate filament protein, alpha	protein-coding
mm_61709.1	chr7	81222062	81222064	+	1	NA	intron (NM_008803, intron 1 of 21)	intron (NM_008803, intron 1 of 21)	8259	NM_008803	18584	Mm.371577	NM_008803	ENSMUSG00000025584	Pde8a	AI551852|Pde8	phosphodiesterase 8A	protein-coding
mm_125505.1	chr15	55307859	55307861	+	1	NA	5' UTR (NM_181277, exon 1 of 48)	5' UTR (NM_181277, exon 1 of 48)	110	NM_181277	12818	Mm.297859	NM_181277	ENSMUSG00000022371	Col14a1	5730412L22Rik|AW108078	collagen, type XIV, alpha 1	protein-coding
mm_135170.1	chr16	35932529	35932548	-	1	NA	exon (NM_001013371, exon 3 of 5)	exon (NM_001013371, exon 3 of 5)	-5932	NM_030253	80285	Mm.49074	NM_030253	ENSMUSG00000022906	Parp9	ARTD9|AW214463|BC003281|Bagl|Bal|PARP-9	poly (ADP-ribose) polymerase family, member 9	protein-coding
mm_11612.1	chr2	34564971	34564977	+	1	NA	intron (NM_001290626, intron 7 of 10)	intron (NM_001290626, intron 7 of 10)	158123	NM_001290626	227743	Mm.270866	NM_177345	ENSMUSG00000038696	Mapkap1	AI591529|D230039K05Rik|Sin1	mitogen-activated protein kinase associated protein 1	protein-coding
mm_110065.1	chr12	21373551	21373592	-	1	NA	promoter-TSS (NM_009615)	promoter-TSS (NM_009615)	61	NR_102380	11491	Mm.27681	NM_009615	ENSMUSG00000052593	Adam17	CD156b|Tace	a disintegrin and metallopeptidase domain 17	protein-coding
mm_161583.1	chr16	32148013	32148013	-	1	NA	intron (NM_001347181, intron 1 of 2)	intron (NM_001347181, intron 1 of 2)	17463	NM_146069	224109	Mm.33498	NM_146069	ENSMUSG00000052384	Nrros	E430025L02Rik|Lrcc33|Lrrc33	negative regulator of reactive oxygen species	protein-coding
mm_106418.1	chr11	119186500	119186548	-	1	NA	intron (NM_001347625, intron 3 of 11)	intron (NM_001347625, intron 3 of 11)	-32387	NR_105899	102465563		NR_105899	ENSMUSG00000098704	Mir6934	Gm27523|mmu-mir-6934	microRNA 6934	ncRNA
mm_171782.1	chr5	110110332	110110344	+	1	NA	intron (NM_001163996, intron 1 of 4)	intron (NM_001163996, intron 1 of 4)	246	NM_001163996	675812	Mm.442122	NM_001163996	ENSMUSG00000023284	Zfp605	A830023I12Rik	zinc finger protein 605	protein-coding
mm_116183.1	chr13	30974049	30974098	-	1	NA	promoter-TSS (NM_025588)	promoter-TSS (NM_025588)	-26	NM_025588	66482	Mm.293510	NM_025588	ENSMUSG00000021357	Exoc2	2410030I24Rik|AI648199|Sec5|Sec5l1	exocyst complex component 2	protein-coding
mm_166130.1	chr4	155352715	155352715	+	1	NA	intron (NM_008860, intron 4 of 17)	intron (NM_008860, intron 4 of 17)	-6926	NM_001039079	18762	Mm.28561	NM_008860	ENSMUSG00000029053	Prkcz	AI098070|C80388|Pkcz|R74924|aPKCzeta|nPKC-zeta|zetaPKC	protein kinase C, zeta	protein-coding
mm_38529.1	chr4	141545865	141545897	-	1	NA	promoter-TSS (NR_030695)	promoter-TSS (NR_030695)	-281	NR_030695	320456	Mm.32859	NM_177163		B330016D10Rik	-	RIKEN cDNA B330016D10 gene	ncRNA
mm_48633.1	chr5	145140012	145140046	-	1	NA	promoter-TSS (NM_001033313)	promoter-TSS (NM_001033313)	60	NM_001033313	231887	Mm.188851	NM_001033313	ENSMUSG00000029623	Pdap1	HASPP28|PAP|PAP1	PDGFA associated protein 1	protein-coding
mm_105371.1	chr11	103208566	103208566	-	1	NA	promoter-TSS (NM_001254724)	promoter-TSS (NM_001254724)	-18	NM_001254724	69441	Mm.380648	NM_027082	ENSMUSG00000020940	1700023F06Rik	-	RIKEN cDNA 1700023F06 gene	protein-coding
mm_34552.1	chr4	149587244	149587274	+	1	NA	intron (NM_001290989, intron 1 of 17)	CpG	791	NM_023051	65945	Mm.38993	NM_023051	ENSMUSG00000039953	Clstn1	1810034E21Rik|Cst-1|Cstn1	calsyntenin 1	protein-coding
mm_114644.1	chr13	76817400	76817403	+	1	NA	intron (NM_030174, intron 10 of 20)	intron (NM_030174, intron 10 of 20)	318067	NM_134071	105377	Mm.209730	NM_134071	ENSMUSG00000021597	Slf1	2700017A04Rik|AW545819|Ankrd32|Brctd1|Brctx|C730024G01Rik	SMC5-SMC6 complex localization factor 1	protein-coding
mm_138200.1	chr17	34293842	34293848	+	1	NA	Intergenic	Intergenic	-6074	NM_010378	14960	Mm.235338	NM_010378	ENSMUSG00000036594	H2-Aa	Aalpha|H-2Aa|H2Aa|I-Aalpha|IAalpha|Ia-1|Ia1	histocompatibility 2, class II antigen A, alpha	protein-coding
mm_158378.1	chrX	135598779	135598786	-	1	NA	Intergenic	MT2C_Mm|LTR|ERVL	-4927	NM_130888	170722	Mm.103373	NM_130888	ENSMUSG00000031410	Nxf7	Nx7|Nxf6|nfx-a1|nxf-a|nxf-a2	nuclear RNA export factor 7	protein-coding
mm_155012.1	chrX	41401615	41401625	+	1	NA	promoter-TSS (NM_001290451)	promoter-TSS (NM_001290451)	91	NM_001290451	53623	Mm.327681	NM_016886	ENSMUSG00000001986	Gria3	2900064I19Rik|GluA3|GluR-C|GluR-K3|Glur-3|Glur3|Gluralpha3	glutamate receptor, ionotropic, AMPA3 (alpha 3)	protein-coding
mm_74891.1	chr8	25104662	25104689	-	1	NA	Intergenic	Intergenic	-2864	NM_031257	83436	Mm.261122	NM_031257	ENSMUSG00000031557	Plekha2	6430512N22Rik|AI851530|AU041791|TAPP2|W91773	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 2	protein-coding
mm_138618.1	chr17	35823510	35823547	+	1	NA	TTS (NM_133662)	TTS (NM_133662)	171	NM_008027	14251	Mm.2931	NM_008027	ENSMUSG00000059714	Flot1	reggie-2	flotillin 1	protein-coding
mm_122437.1	chr14	45219335	45219345	-	1	NA	promoter-TSS (NM_027518)	promoter-TSS (NM_027518)	85	NM_172597	70561	Mm.28129	NM_172597	ENSMUSG00000021830	Txndc16	5730420B22Rik|C77647	thioredoxin domain containing 16	protein-coding
mm_58743.1	chr7	13277156	13277214	+	1	NA	promoter-TSS (NM_001199310)	promoter-TSS (NM_001199310)	-128	NM_001199310	16881	Mm.288179	NM_010715	ENSMUSG00000056394	Lig1	AL033288|LigI	ligase I, DNA, ATP-dependent	protein-coding
mm_171095.1	chr3	128955109	128955127	-	1	NA	Intergenic	Intergenic	-244760	NM_001286942	18741	Mm.246804	NM_011098	ENSMUSG00000028023	Pitx2	9430085M16Rik|Brx1|Brx1b|Munc30|Otlx2|Ptx2|Rieg	paired-like homeodomain transcription factor 2	protein-coding
mm_27730.1	chr3	69044661	69044667	-	1	NA	promoter-TSS (NM_025863)	promoter-TSS (NM_025863)	78	NM_025863	66949	Mm.176695	NM_025863	ENSMUSG00000034317	Trim59	2310035M22Rik|2700022F13Rik|Mrf1|TSBF1	tripartite motif-containing 59	protein-coding
mm_132057.1	chr16	29646437	29646440	+	1	NA	intron (NM_001199177, intron 28 of 29)	B1_Mur3|SINE|Alu	67104	NM_001199177	74143	Mm.274285	NM_133752	ENSMUSG00000038084	Opa1	1200011N24Rik|AI225888|AI847218|lilr3|mKIAA0567	OPA1, mitochondrial dynamin like GTPase	protein-coding
mm_125841.1	chr15	74958720	74958747	+	1	NA	3' UTR (NM_001164036, exon 4 of 4)	3' UTR (NM_001164036, exon 4 of 4)	3627	NM_001164040	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_103892.1	chr11	83575166	83575178	-	1	NA	3' UTR (NM_011338, exon 4 of 4)	3' UTR (NM_011338, exon 4 of 4)	3464	NM_011338	20308	Mm.416125	NM_011338	ENSMUSG00000019122	Ccl9	CCF18|MRP-2|Scya10|Scya9	chemokine (C-C motif) ligand 9	protein-coding
mm_120653.1	chr14	70531621	70531630	+	1	NA	intron (NM_145219, intron 1 of 7)	intron (NM_145219, intron 1 of 7)	804	NM_145219	213469	Mm.41708	NM_145219	ENSMUSG00000033595	Lgi3	AI841179|AW049851	leucine-rich repeat LGI family, member 3	protein-coding
mm_96678.1	chr11	69419149	69419173	+	1	NA	Intergenic	Intergenic	-5486	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_163794.1	chr14	14893409	14893411	+	1	NA	intron (NM_001195229, intron 22 of 34)	MTD|LTR|ERVL-MaLR	72595	NM_001195229	674895	Mm.317563	NM_001034865	ENSMUSG00000042567	Nek10	Gm282	NIMA (never in mitosis gene a)- related kinase 10	protein-coding
mm_114073.1	chr13	54382734	54382752	+	1	NA	3' UTR (NM_009946, exon 4 of 4)	3' UTR (NM_009946, exon 4 of 4)	11394	NM_009946	12890	Mm.268902	NM_009946	ENSMUSG00000025867	Cplx2	921-L|AI413745|AW492120	complexin 2	protein-coding
mm_96288.1	chr11	63128996	63129006	+	1	NA	promoter-TSS (NM_001302258)	promoter-TSS (NM_001302258)	19	NM_001302261	18858	Mm.1237	NM_008885	ENSMUSG00000018217	Pmp22	22kDa|Gas-3|HNPP|Tr|trembler	peripheral myelin protein 22	protein-coding
mm_37460.1	chr4	123471802	123471806	-	1	NA	exon (NM_001199136, exon 36 of 98)	exon (NM_001199136, exon 36 of 98)	-59893	NM_001167918	442834	Mm.483803	NM_001167918		D830031N03Rik	Kiaa0754|mKIAA0754	RIKEN cDNA D830031N03 gene	protein-coding
mm_172765.1	chr8	92717003	92717003	-	1	NA	Intergenic	Intergenic	42714	NM_001301137	64379	Mm.137247	NM_022428	ENSMUSG00000031738	Irx6	-	Iroquois related homeobox 6 (Drosophila)	protein-coding
mm_151216.1	chr19	53660988	53661003	+	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-16311	NM_001170847	73713	Mm.313695	NM_001170847	ENSMUSG00000043639	Rbm20	1110018J23Rik|2010003H22Rik|AI646761	RNA binding motif protein 20	protein-coding
mm_138922.1	chr17	43667390	43667393	+	1	NA	promoter-TSS (NM_001285948)	promoter-TSS (NM_001285948)	19	NM_018887	56050	Mm.17991	NM_018887	ENSMUSG00000023963	Cyp39a1	mCYP39A1	cytochrome P450, family 39, subfamily a, polypeptide 1	protein-coding
mm_38399.1	chr4	138913916	138913983	-	1	NA	promoter-TSS (NM_028453)	promoter-TSS (NM_028453)	-2	NM_028453	73162	Mm.238081	NM_028453	ENSMUSG00000041161	Otud3	3110030K17Rik	OTU domain containing 3	protein-coding
mm_40330.1	chr5	43910721	43910733	+	1	NA	3' UTR (NM_007646, exon 8 of 8)	3' UTR (NM_007646, exon 8 of 8)	41918	NM_007646	12494	Mm.249873	NM_007646	ENSMUSG00000029084	Cd38	ADPRC 1|Cd38-rs1|I-19	CD38 antigen	protein-coding
mm_20696.1	chr2	132815979	132816052	-	1	NA	promoter-TSS (NM_025676)	promoter-TSS (NM_025676)	39	NM_175113	66926	Mm.34199	NM_175113	ENSMUSG00000037376	Trmt6	3300001M20Rik|AU016412|AW492787|CGI-09|mKIAA1153	tRNA methyltransferase 6	protein-coding
mm_141323.1	chr17	28441375	28441387	-	1	NA	intron (NM_010220, intron 1 of 10)	intron (NM_010220, intron 1 of 10)	44768	NM_010220	14229	Mm.276405	NM_010220	ENSMUSG00000024222	Fkbp5	D17Ertd592e|Dit1|FKBP-5|FKBP51	FK506 binding protein 5	protein-coding
mm_15055.1	chr2	152911377	152911377	+	1	NA	promoter-TSS (NM_001081044)	promoter-TSS (NM_001081044)	25	NM_001081044	228785	Mm.250604	NM_001081044	ENSMUSG00000027470	Mylk2	9830004H17Rik|BB138278	myosin, light polypeptide kinase 2, skeletal muscle	protein-coding
mm_57411.1	chr6	124865829	124865837	-	1	NA	3' UTR (NM_013488, exon 10 of 10)	3' UTR (NM_013488, exon 10 of 10)	-1916	NM_013533	14788	Mm.2514	NM_013533	ENSMUSG00000038390	Gpr162	A-2|BC031437|Grca	G protein-coupled receptor 162	protein-coding
mm_170165.1	chr17	53689326	53689332	-	1	NA	promoter-TSS (NM_028232)	promoter-TSS (NM_028232)	-14	NM_028232	72415	Mm.153202	NM_028232	ENSMUSG00000023940	Sgol1	3300001M08Rik|C81037|Sgo1	shugoshin-like 1 (S. pombe)	protein-coding
mm_103608.1	chr11	78497735	78497793	-	1	NA	promoter-TSS (NM_001168521)	promoter-TSS (NM_001168521)	-10	NM_172795	237868	Mm.210332	NM_172795	ENSMUSG00000050132	Sarm1	A830091I15Rik|C78606|MyD885|Sarm	sterile alpha and HEAT/Armadillo motif containing 1	protein-coding
mm_130627.1	chr15	100415791	100415801	-	1	NA	intron (NM_008732, intron 1 of 16)	intron (NM_008732, intron 1 of 16)	7259	NM_001146161	18174	Mm.234608	NM_008732	ENSMUSG00000023030	Slc11a2	DCT1|DMT1|Nramp2|mk|van	solute carrier family 11 (proton-coupled divalent metal ion transporters), member 2	protein-coding
mm_138482.1	chr17	35195108	35195148	+	1	NA	TTS (NR_105939)	TTS (NR_105939)	156	NR_105939	102465588		NR_105939	ENSMUSG00000098291	Mir6973a	Gm27967|mmu-mir-6973a	microRNA 6973a	ncRNA
mm_143459.1	chr17	70990718	70990727	-	1	NA	promoter-TSS (NM_023402)	promoter-TSS (NM_023402)	-206	NM_023402	67938	Mm.261329	NM_023402	ENSMUSG00000034868	Myl12b	1500001M02Rik|C77744|Mylc2b|RLC-B	myosin, light chain 12B, regulatory	protein-coding
mm_143979.1	chr17	87446855	87446869	-	1	NA	promoter-TSS (NM_007589)	promoter-TSS (NM_007589)	73	NM_007589	12314	Mm.329243	NM_007589	ENSMUSG00000036438	Calm2	1500001E21Rik|AL024017	calmodulin 2	protein-coding
mm_126415.1	chr15	80287270	80287293	+	1	NA	promoter-TSS (NM_001044308)	promoter-TSS (NM_001044308)	43	NM_001044308	239556	Mm.291058	NM_001044308	ENSMUSG00000022416	Cacna1i	Ca(V)3.3	calcium channel, voltage-dependent, alpha 1I subunit	protein-coding
mm_31428.1	chr4	48085459	48085468	+	1	NA	3' UTR (NM_015743, exon 8 of 8)	3' UTR (NM_015743, exon 8 of 8)	34217	NM_001307989	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_112287.1	chr12	114469561	114469588	-	1	NA	promoter-TSS (NR_106062)	promoter-TSS (NR_106062)	-108	NR_106062	102465663		NR_106062	ENSMUSG00000105438	Mir7094-1	mmu-mir-7094-1	microRNA 7094-1	ncRNA
mm_88940.1	chr10	81318025	81318028	+	1	NA	3' UTR (NM_001146687, exon 17 of 17)	3' UTR (NM_001146687, exon 17 of 17)	-3077	NM_027381	70312	Mm.87628	NM_027381	ENSMUSG00000034889	Cactin	2510012J08Rik	cactin, spliceosome C complex subunit	protein-coding
mm_10676.1	chr2	21367568	21367596	+	1	NA	promoter-TSS (NM_001004761)	promoter-TSS (NM_001004761)	15	NM_001004761	241263	Mm.166647	NM_175706	ENSMUSG00000045967	Gpr158	5330427M13Rik|mKIAA1136	G protein-coupled receptor 158	protein-coding
mm_139773.1	chr17	64753464	64753485	+	1	NA	3' UTR (NM_008549, exon 22 of 22)	3' UTR (NM_008549, exon 22 of 22)	-13637	NR_105051	101202683	Mm.393309	NR_105051		Dreh	-	down-regulated in hepatocellular carcinoma	ncRNA
mm_170911.1	chr2	34650346	34650361	-	1	NA	Intergenic	(CGG)n|Simple_repeat|Simple_repeat	104879	NM_025709	66691	Mm.156452	NM_025709	ENSMUSG00000026867	Gapvd1	2010005B09Rik|4432404J10Rik|AW108497|Gapex-5|RAP6|RME-6|mKIAA1521	GTPase activating protein and VPS9 domains 1	protein-coding
mm_119947.1	chr14	54991267	54991279	+	1	NA	intron (NM_080728, intron 7 of 40)	intron (NM_080728, intron 7 of 40)	3276	NM_080728	140781	Mm.457983	NM_080728	ENSMUSG00000053093	Myh7	B-MHC|MyHC-I|Myhc-b|Myhcb|beta-MHC	myosin, heavy polypeptide 7, cardiac muscle, beta	protein-coding
mm_100016.1	chr11	114890185	114890203	+	1	NA	5' UTR (NM_170758, exon 1 of 7)	5' UTR (NM_170758, exon 1 of 7)	153	NM_170758	217303	Mm.294439	NM_170758	ENSMUSG00000034652	Cd300a	B230315M08Rik|Clm8|LMIR1|MAIR-I|MAIR-Ia|MMAC8|Pigr4|mcpir1	CD300A molecule	protein-coding
mm_109586.1	chr12	112604253	112604263	+	1	NA	exon (NM_198411, exon 8 of 23)	exon (NM_198411, exon 8 of 23)	15474	NM_198411	70435	Mm.250193	NM_198411	ENSMUSG00000037679	Inf2	2610204M08Rik|AA589465|AW125550|EG629699	inverted formin, FH2 and WH2 domain containing	protein-coding
mm_13231.1	chr2	97630757	97630768	+	1	NA	exon (NM_178725, exon 3 of 3)	exon (NM_178725, exon 3 of 3)	163105	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_5715.1	chr1	44079663	44079668	-	1	NA	Intergenic	Intergenic	22723	NM_029368	75623	Mm.348017	NM_029368	ENSMUSG00000026049	Tex30	1700029F09Rik|3110030D08Rik	testis expressed 30	protein-coding
mm_16962.1	chr2	17460611	17460635	-	1	NA	intron (NM_028757, intron 4 of 6)	intron (NM_028757, intron 4 of 6)	-102891	NR_105847	102465964		NR_105847	ENSMUSG00000099161	Mir6419	Gm27713|mmu-mir-6419	microRNA 6419	ncRNA
mm_37699.1	chr4	129335298	129335317	-	1	NA	promoter-TSS (NM_009030)	promoter-TSS (NM_009030)	63	NM_009030	19646	Mm.12145	NM_009030	ENSMUSG00000057236	Rbbp4	RBAP48|mRbAp48	retinoblastoma binding protein 4	protein-coding
mm_116721.1	chr13	51701901	51701926	-	1	NA	3' UTR (NM_001281880, exon 17 of 17)	3' UTR (NM_001281880, exon 17 of 17)	50205	NM_029279	75420	Mm.275981	NM_029279	ENSMUSG00000035139	Secisbp2	2210413N07Rik|2810012K13Rik|SBP2	SECIS binding protein 2	protein-coding
mm_66351.1	chr7	43527328	43527338	-	1	NA	TTS (NM_001111058)	TTS (NM_001111058)	5838	NM_001111058	12489	Mm.140157	NM_021293	ENSMUSG00000004609	Cd33	Siglec-3|gp67	CD33 antigen	protein-coding
mm_24647.1	chr3	94386956	94386974	+	1	NA	intron (NR_121656, intron 1 of 9)	intron (NR_121656, intron 1 of 9)	9533	NR_121656	19885	Mm.4372	NM_011281	ENSMUSG00000028150	Rorc	Nr1f3|RORgamma|TOR|Thor	RAR-related orphan receptor gamma	protein-coding
mm_46282.1	chr5	100159262	100159314	-	1	NA	intron (NM_182841, intron 1 of 7)	CpG	520	NM_182841	231503	Mm.99790	NM_182841	ENSMUSG00000050640	Tmem150c	-	transmembrane protein 150C	protein-coding
mm_97927.1	chr11	83640502	83640508	+	1	NA	Intergenic	Intergenic	8873	NM_011337	20302	Mm.1282	NM_011337	ENSMUSG00000000982	Ccl3	AI323804|G0S19-1|LD78alpha|MIP-1alpha|MIP1-(a)|MIP1-alpha|Mip1a|Scya3	chemokine (C-C motif) ligand 3	protein-coding
mm_156752.1	chrX	160390685	160390730	+	1	NA	promoter-TSS (NM_178712)	promoter-TSS (NM_178712)	17	NM_001290445	237175	Mm.213016	NM_178712	ENSMUSG00000031298	Adgrg2	AW212196|B830041D06Rik|Gpr64|Me6	adhesion G protein-coupled receptor G2	protein-coding
mm_66476.1	chr7	44997536	44997605	-	1	NA	promoter-TSS (NM_016849)	promoter-TSS (NM_016849)	9	NM_029410	75736	Mm.261006	NM_029410	ENSMUSG00000003190	Bcl2l12	2810475P17Rik|5430429M05Rik|Bcl-L12|Bcl2-L12	BCL2-like 12 (proline rich)	protein-coding
mm_123441.1	chr14	64949633	64949674	-	1	NA	promoter-TSS (NM_001253731)	promoter-TSS (NM_001253731)	204	NM_177338	219150	Mm.344074	NM_177338	ENSMUSG00000021972	Hmbox1	AI451877|AI604847|F830020C16Rik	homeobox containing 1	protein-coding
mm_100838.1	chr11	5542245	5542267	-	1	NA	promoter-TSS (NM_134033)	promoter-TSS (NM_134033)	-39	NM_134033	104479	Mm.210403	NM_134033	ENSMUSG00000020482	Ccdc117	1110004K02Rik|1700026O03Rik|AU018638|AU042822|AV173073|BC018601	coiled-coil domain containing 117	protein-coding
mm_29802.1	chr3	127780386	127780396	-	1	NA	5' UTR (NM_027808, exon 1 of 14)	5' UTR (NM_027808, exon 1 of 14)	136	NM_027808	71481	Mm.158704	NM_027808	ENSMUSG00000028028	Alpk1	8430410J10Rik|LAK	alpha-kinase 1	protein-coding
mm_50389.1	chr6	48706293	48706314	+	1	NA	intron (NM_153175, intron 1 of 2)	intron (NM_153175, intron 1 of 2)	1941	NM_153175	231931	Mm.321047	NM_153175	ENSMUSG00000047867	Gimap6	4833419H03Rik|Ian6|mFLJ00102	GTPase, IMAP family member 6	protein-coding
mm_13302.1	chr2	102550118	102550128	+	1	NA	5' UTR (NM_173749, exon 1 of 11)	5' UTR (NM_173749, exon 1 of 11)	102	NM_173749	210622	Mm.28649	NM_173749	ENSMUSG00000027188	Pamr1	5930437L24|E430002G05Rik|Ramp	peptidase domain containing associated with muscle regeneration 1	protein-coding
mm_113541.1	chr13	37864910	37864920	+	1	NA	intron (NM_001039188, intron 1 of 9)	intron (NM_001039188, intron 1 of 9)	-23519	NR_033218	68750	Mm.491109	NM_026830	ENSMUSG00000039087	Rreb1	1110037N09Rik|AA414966|B930013M22Rik	ras responsive element binding protein 1	protein-coding
mm_152765.1	chr19	20390666	20390679	-	1	NA	promoter-TSS (NM_010730)	promoter-TSS (NM_010730)	-1	NM_010730	16952	Mm.248360	NM_010730	ENSMUSG00000024659	Anxa1	Anx-1|Anx-A1|C430014K04Rik|Lpc-1|Lpc1	annexin A1	protein-coding
mm_101761.1	chr11	43598671	43598675	-	1	NA	exon (NM_008375, exon 2 of 4)	exon (NM_008375, exon 2 of 4)	2889	NM_008375	16204	Mm.142716	NM_008375	ENSMUSG00000020405	Fabp6	GT|I-15P|I-BABP|ILBP|ILBP3|Illbp	fatty acid binding protein 6, ileal (gastrotropin)	protein-coding
mm_88153.1	chr10	69551157	69551181	+	1	NA	intron (NM_170730, intron 1 of 17)	B4|SINE|B4	17461	NM_146005	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_133694.1	chr16	92612857	92612879	+	1	NA	intron (NM_001111023, intron 5 of 5)	intron (NM_001111023, intron 5 of 5)	84461	NM_001111023	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_132599.1	chr16	38522780	38522801	+	1	NA	promoter-TSS (NM_024273)	promoter-TSS (NM_024273)	-127	NM_024273	76916	Mm.132231	NM_024273	ENSMUSG00000002846	Timmdc1	2810021C21Rik|4930455C21Rik|AV135763	translocase of inner mitochondrial membrane domain containing 1	protein-coding
mm_101747.1	chr11	43379397	43379407	-	1	NA	Intergenic	Intergenic	-4941	NR_029558	387164		NR_029558	ENSMUSG00000065601	Mir146	Mirn146|miR-146a|mmu-mir-146	microRNA 146	ncRNA
mm_103196.1	chr11	70647053	70647063	-	1	NA	promoter-TSS (NM_024211)	promoter-TSS (NM_024211)	-19	NM_024211	67863	Mm.296082	NM_024211	ENSMUSG00000014606	Slc25a11	2310022P18Rik|2oxoc	solute carrier family 25 (mitochondrial carrier oxoglutarate carrier), member 11	protein-coding
mm_20264.1	chr2	126675225	126675268	-	1	NA	intron (NM_001271470, intron 1 of 8)	CpG	346	NM_001271469	14391	Mm.293266	NM_010249	ENSMUSG00000027361	Gabpb1	BABPB2|E4TF1|E4TF1-47|E4TF1-53|E4Tf1B|GABPB|GABPB-1|GABPB-2|GABPB1-1|GABPB1-2|NRF2B1|NRF2B2	GA repeat binding protein, beta 1	protein-coding
mm_11639.1	chr2	34874413	34874481	+	1	NA	promoter-TSS (NM_030021)	promoter-TSS (NM_030021)	51	NM_030021	77996	Mm.215255	NM_030021	ENSMUSG00000026870	Cutal	D730039F16Rik	cutA divalent cation tolerance homolog-like	protein-coding
mm_5963.1	chr1	56972438	56972482	-	1	NA	non-coding (NR_024325, exon 1 of 1)	non-coding (NR_024325, exon 1 of 1)	991	NR_024325	329160	Mm.419039	NR_024325	ENSMUSG00000087022	9130024F11Rik	B530002L08|EG329160	RIKEN cDNA 9130024F11 gene	ncRNA
mm_30648.1	chr4	8840335	8840347	+	1	NA	intron (NM_001277149, intron 17 of 37)	intron (NM_001277149, intron 17 of 37)	149935	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_166880.1	chr7	25427410	25427420	+	1	NA	intron (NR_015569, intron 4 of 6)	intron (NR_015569, intron 4 of 6)	-14529	NM_153576	232983	Mm.10545	NM_153576	ENSMUSG00000060188	Cxcl17	VCC-1|Vcc1	chemokine (C-X-C motif) ligand 17	protein-coding
mm_114315.1	chr13	60029623	60029629	+	1	NA	promoter-TSS (NR_046142)	promoter-TSS (NR_046142)	-85	NR_046142	328263	Mm.123405	NR_046142		A530065N20Rik	A530065N20	RIKEN cDNA A530046M15 gene	ncRNA
mm_140944.1	chr17	24479035	24479083	-	1	NA	promoter-TSS (NM_019988)	promoter-TSS (NM_019988)	19	NM_001252464	56716	Mm.289516	NM_019988	ENSMUSG00000024142	Mlst8	0610033N12Rik|AA409454|AI505104|AI851821|Gbl	MTOR associated protein, LST8 homolog (S. cerevisiae)	protein-coding
mm_140076.1	chr17	75178679	75178688	+	1	NA	promoter-TSS (NM_001331237)	promoter-TSS (NM_001331237)	-98	NM_001331236	268977	Mm.269747	NM_019919	ENSMUSG00000001870	Ltbp1	9430031G15Rik|9830146M04|Ltbp-1|Ltbp1L|TGF-beta1-BP-1|Tgfb|b2b1000Clo	latent transforming growth factor beta binding protein 1	protein-coding
mm_26539.1	chr3	146149823	146149829	+	1	NA	promoter-TSS (NM_026656)	promoter-TSS (NM_026656)	-7	NM_026656	68279	Mm.116862	NM_026656	ENSMUSG00000011008	Mcoln2	3300002C04Rik|AI549968|C86638|TRPML2	mucolipin 2	protein-coding
mm_83202.1	chr9	41579547	41579563	-	1	NA	intron (NR_131930, intron 3 of 3)	intron (NR_131930, intron 3 of 3)	-1698	NR_015483	73144	Mm.38166	NM_001033153	ENSMUSG00000074415	3110039I08Rik	2610203C20Rik|AI848448|D230004N17Rik|D3Mgi9|Mir100hg	RIKEN cDNA 3110039I08 gene	ncRNA
mm_150689.1	chr19	42120230	42120267	+	1	NA	3' UTR (NM_145501, exon 9 of 9)	3' UTR (NM_145501, exon 9 of 9)	8745	NM_027106	69534	Mm.30060	NM_027106	ENSMUSG00000018821	Avpi1	2310008N12Rik|AA410041|VIT32|esu|mVIT32	arginine vasopressin-induced 1	protein-coding
mm_93535.1	chr10	115362504	115362528	-	1	NA	promoter-TSS (NM_133683)	promoter-TSS (NM_133683)	-254	NM_133683	67226	Mm.29647	NM_133683	ENSMUSG00000069520	Tmem19	2810428F02Rik|AW125171	transmembrane protein 19	protein-coding
mm_90528.1	chr10	128085511	128085528	+	1	NA	TTS (NR_030442)	TTS (NR_030442)	233	NR_030442	751518		NR_030442	ENSMUSG00000093245	Mir677	Mirn677|mir-677|mmu-mir-677	microRNA 677	ncRNA
mm_142714.1	chr17	47924461	47924482	-	1	NA	5' UTR (NM_028767, exon 1 of 17)	5' UTR (NM_028767, exon 1 of 17)	161	NM_028767	74123	Mm.240062	NM_028767	ENSMUSG00000023991	Foxp4	1200010K03Rik|2310007G05Rik|mFKHLA	forkhead box P4	protein-coding
mm_88438.1	chr10	77541940	77541966	+	1	NA	intron (NM_008404, intron 1 of 15)	intron (NM_008404, intron 1 of 15)	11605	NM_008404	16414	Mm.1137	NM_008404	ENSMUSG00000000290	Itgb2	2E6|AI528527|Cd18|LAD|LCAMB|Lfa1|MF17	integrin beta 2	protein-coding
mm_4107.1	chr1	167598421	167598438	+	1	NA	promoter-TSS (NM_009107)	promoter-TSS (NM_009107)	67	NM_009107	20183	Mm.3475	NM_009107	ENSMUSG00000015843	Rxrg	Nr2b3	retinoid X receptor gamma	protein-coding
mm_92717.1	chr10	80798192	80798216	-	1	NA	promoter-TSS (NM_013651)	promoter-TSS (NM_013651)	422	NM_023900	78670	Mm.41479	NM_023900	ENSMUSG00000035278	Plekhj1	9530063M10Rik	pleckstrin homology domain containing, family J member 1	protein-coding
mm_144176.1	chr18	6765036	6765050	+	1	NA	promoter-TSS (NM_181070)	promoter-TSS (NM_181070)	-124	NM_181070	19330	Mm.132802	NM_181070	ENSMUSG00000073639	Rab18	AA959686	RAB18, member RAS oncogene family	protein-coding
mm_149564.1	chr19	12795899	12795911	+	1	NA	non-coding (NR_024093, exon 1 of 13)	non-coding (NR_024093, exon 1 of 13)	218	NR_024093	664779	Mm.290924	NM_001039718	ENSMUSG00000024695	Gm44505	Zfp91-Cntf|Zfp91Cntf	predicted readthrough transcript (NMD candidate), 44505	ncRNA
mm_3798.1	chr1	157506758	157506776	+	1	NA	promoter-TSS (NM_033354)	promoter-TSS (NM_033354)	-29	NM_033354	89867	Mm.87114	NM_033354	ENSMUSG00000026589	Sec16b	Lztr2|Rgpr|Rgpr-p117	SEC16 homolog B (S. cerevisiae)	protein-coding
mm_92493.1	chr10	78307604	78307619	-	1	NA	intron (NM_053014, intron 2 of 9)	intron (NM_053014, intron 2 of 9)	32596	NR_106119	102465765		NR_106119	ENSMUSG00000098885	Mir7659	Gm27433|mmu-mir-7659	microRNA 7659	ncRNA
mm_37748.1	chr4	129619070	129619118	-	1	NA	promoter-TSS (NM_198026)	promoter-TSS (NM_198026)	-1	NM_198026	230767	Mm.441132	NM_198026	ENSMUSG00000040795	Iqcc	BC026978	IQ motif containing C	protein-coding
mm_158245.1	chrX	106840573	106840581	-	1	NA	promoter-TSS (NM_199468)	promoter-TSS (NM_199468)	66	NM_199468	213436	Mm.85581	NM_199468	ENSMUSG00000047686	Zcchc5	D430021I08Rik|Gm375|Mar3|Mart3|ZHC5	zinc finger, CCHC domain containing 5	protein-coding
mm_80512.1	chr9	79792954	79792995	+	1	NA	promoter-TSS (NR_040734)	promoter-TSS (NR_040734)	456	NM_133718	69981	Mm.486324	NM_133718	ENSMUSG00000032328	Tmem30a	2010200I23Rik|AW540225|Cdc50a|D9Wsu20e	transmembrane protein 30A	protein-coding
mm_136814.1	chr17	12395618	12395637	+	1	NA	exon (NM_008877, exon 8 of 19)	exon (NM_008877, exon 8 of 19)	17018	NM_008877	18815	Mm.971	NM_008877	ENSMUSG00000059481	Plg	AI649309|Pg	plasminogen	protein-coding
mm_133603.1	chr16	91485068	91485105	+	1	NA	promoter-TSS (NM_010508)	promoter-TSS (NM_010508)	-129	NM_010508	15975	Mm.502	NM_010508	ENSMUSG00000022967	Ifnar1	CD118|Ifar|Ifnar|Ifrc|Infar	interferon (alpha and beta) receptor 1	protein-coding
mm_100629.1	chr11	121702757	121702766	+	1	NA	exon (NM_144797, exon 1 of 4)	exon (NM_144797, exon 1 of 4)	334	NM_144797	210029	Mm.153566	NM_144797	ENSMUSG00000039208	Metrnl	9430048M07Rik|BC019776	meteorin, glial cell differentiation regulator-like	protein-coding
mm_91022.1	chr10	17912446	17912448	-	1	NA	intron (NM_001033432, intron 2 of 3)	intron (NM_001033432, intron 2 of 3)	35620	NM_001033432	380629	Mm.276430	NM_001033432	ENSMUSG00000039879	Heca	Gm869|HDC|HDCL	hdc homolog, cell cycle regulator	protein-coding
mm_117873.1	chr13	98925614	98925624	-	1	NA	intron (NM_178716, intron 1 of 23)	intron (NM_178716, intron 1 of 23)	765	NM_178716	238799	Mm.173286	NM_178716	ENSMUSG00000009470	Tnpo1	AU021749|D13Ertd688e|IPO2|Kpnb2|MIP|MIP1|TRN	transportin 1	protein-coding
mm_79509.1	chr9	57504013	57504068	+	1	NA	promoter-TSS (NM_133982)	promoter-TSS (NM_133982)	-62	NM_133982	102614	Mm.274421	NM_133982	ENSMUSG00000062309	Rpp25	AI851155	ribonuclease P/MRP 25 subunit	protein-coding
mm_120372.1	chr14	64587361	64587372	+	1	NA	promoter-TSS (NR_040709)	promoter-TSS (NR_040709)	-749	NR_040709	268755	Mm.194050	NR_040709	ENSMUSG00000097545	Mir124a-1hg	A930011O12Rik|Rncr3|mir-124-1|mir-3078	Mir124-1 host gene (non-protein coding)	ncRNA
mm_120247.1	chr14	62992436	62992438	+	1	NA	Intergenic	Intergenic	-5640	NM_001039125	654465	Mm.424929	NM_001039125	ENSMUSG00000075573	Defb47	Defb41|EG654465	defensin beta 47	protein-coding
mm_49347.1	chr6	21986132	21986150	+	1	NA	5' UTR (NM_001081351, exon 1 of 22)	5' UTR (NM_001081351, exon 1 of 22)	231	NM_001081351	214642	Mm.221404	NM_001081351	ENSMUSG00000062980	Cped1	6720481P07|A430107O13Rik|AI552584	cadherin-like and PC-esterase domain containing 1	protein-coding
mm_32623.1	chr4	114511489	114511494	+	1	NA	intron (NM_001085549, intron 2 of 6)	intron (NM_001085549, intron 2 of 6)	104767	NM_001085549	666048	Mm.331779	NM_001085549	ENSMUSG00000070867	Trabd2b	Gm12824|Hkat|OTTMUSG00000008561	TraB domain containing 2B	protein-coding
mm_148600.1	chr19	5286881	5286924	+	1	NA	exon (NM_030109, exon 10 of 21)	exon (NM_030109, exon 10 of 21)	8553	NM_030109	319322	Mm.196532	NM_030109	ENSMUSG00000024853	Sf3b2	145kDa|2610311M13Rik|2810441F20Rik|B230398H18Rik|SAP145|SF3b1|SF3b145|SF3b150	splicing factor 3b, subunit 2	protein-coding
mm_116226.1	chr13	33034633	33034648	-	1	NA	intron (NM_011452, intron 4 of 6)	intron (NM_011452, intron 4 of 6)	7226	NM_011452	20706	Mm.45371	NM_011452	ENSMUSG00000021403	Serpinb9b	1600019A21Rik|R86|SPI-CI|Spi10|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 9b	protein-coding
mm_74195.1	chr8	123805887	123805895	+	1	NA	promoter-TSS (NM_009003)	promoter-TSS (NM_009003)	-105	NM_009003	19341	Mm.9221	NM_009003	ENSMUSG00000019478	Rab4a	AI848268|Rab4	RAB4A, member RAS oncogene family	protein-coding
mm_48236.1	chr5	137720845	137720848	-	1	NA	Intergenic	Intergenic	19152	NM_175521	243300	Mm.74750	NM_175521	ENSMUSG00000045348	Nyap1	6430598A04Rik	neuronal tyrosine-phosphorylated phosphoinositide 3-kinase adaptor 1	protein-coding
mm_73040.1	chr8	94266826	94266838	+	1	NA	intron (NM_172410, intron 4 of 22)	intron (NM_172410, intron 4 of 22)	52231	NM_172410	71805	Mm.458170	NM_172410	ENSMUSG00000032939	Nup93	2410008G02Rik	nucleoporin 93	protein-coding
mm_79486.1	chr9	56995555	56995576	+	1	NA	5' UTR (NM_019651, exon 1 of 13)	5' UTR (NM_019651, exon 1 of 13)	597	NM_019651	56294	Mm.325643	NM_019651	ENSMUSG00000032290	Ptpn9	MEG2	protein tyrosine phosphatase, non-receptor type 9	protein-coding
mm_164113.1	chr15	31338712	31338730	-	1	NA	intron (NM_027496, intron 1 of 3)	ORR1D2|LTR|ERVL-MaLR	29038	NM_001164441	67434	Mm.102470	NM_026153	ENSMUSG00000022237	Ankrd33b	0610012A05Rik|3021401C12Rik|5730557B15Rik	ankyrin repeat domain 33B	protein-coding
mm_14054.1	chr2	122561458	122561476	+	1	NA	Intergenic	Lx8|LINE|L1	49810	NM_025961	67092	Mm.29975	NM_025961	ENSMUSG00000027199	Gatm	1810003P21Rik|AI314789|AT	glycine amidinotransferase (L-arginine:glycine amidinotransferase)	protein-coding
mm_26068.1	chr3	135887197	135887211	+	1	NA	3' UTR (NM_001135150, exon 9 of 9)	3' UTR (NM_001135150, exon 9 of 9)	-46935	NR_040540	71038	Mm.410798	NR_040540	ENSMUSG00000106306	4933401H06Rik	-	RIKEN cDNA 4933401H06 gene	ncRNA
mm_114957.1	chr13	97071289	97071317	+	1	NA	promoter-TSS (NM_001100458)	promoter-TSS (NM_001100458)	-340	NM_001100458	320557	Mm.458280	NM_001100458	ENSMUSG00000041817	Fam169a	B230112C05Rik|SLAP75	family with sequence similarity 169, member A	protein-coding
mm_140187.1	chr17	83214763	83214774	+	1	NA	promoter-TSS (NM_134117)	promoter-TSS (NM_134117)	-515	NM_134117	106522	Mm.311974	NM_134117	ENSMUSG00000024247	Pkdcc	AI115348|AW548124|Adtk1|ESTM17|MAd1|Sgk493|Vlk|X83346	protein kinase domain containing, cytoplasmic	protein-coding
mm_152521.1	chr19	11304364	11304374	-	1	NA	Intergenic	Intergenic	-20556	NM_183190	269063	Mm.268940	NM_183190	ENSMUSG00000054523	Ms4a5	-	membrane-spanning 4-domains, subfamily A, member 5	protein-coding
mm_7251.1	chr1	93731932	93731944	-	1	NA	promoter-TSS (NM_001310761)	promoter-TSS (NM_001310761)	-12	NM_001310761	67026	Mm.272356	NM_025920	ENSMUSG00000026279	Thap4	2010320B01Rik	THAP domain containing 4	protein-coding
mm_87662.1	chr10	58493061	58493100	+	1	NA	exon (NM_011240, exon 28 of 29)	exon (NM_011240, exon 28 of 29)	-4857	NM_001162956	76138	Mm.211744	NM_001162956	ENSMUSG00000038010	Ccdc138	6230424H07Rik|BC042726	coiled-coil domain containing 138	protein-coding
mm_49725.1	chr6	34682937	34682975	+	1	NA	intron (NM_001347100, intron 2 of 13)	intron (NM_001347100, intron 2 of 13)	-26488	NM_145575	109624	Mm.308134	NM_145575	ENSMUSG00000029761	Cald1	4833423D12Rik|AI195384|AV071549|AW536160|C920027I18Rik	caldesmon 1	protein-coding
mm_128934.1	chr15	74636778	74636807	-	1	NA	promoter-TSS (NM_001177437)	promoter-TSS (NM_001177437)	-474	NM_001177437	69439	Mm.263708	NM_001177437	ENSMUSG00000022603	Mroh4	1700016M24Rik	maestro heat-like repeat family member 4	protein-coding
mm_103033.1	chr11	69735469	69735510	-	1	NA	exon (NM_001291068, exon 29 of 29)	exon (NM_001291068, exon 29 of 29)	23144	NM_001291068	20020	Mm.16533	NM_009089	ENSMUSG00000005198	Polr2a	220kDa|Rpb1|Rpo2-1	polymerase (RNA) II (DNA directed) polypeptide A	protein-coding
mm_139174.1	chr17	47588869	47588875	+	1	NA	intron (NM_001081635, intron 2 of 6)	intron (NM_001081635, intron 2 of 6)	-4595	NM_007632	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_33727.1	chr4	134093608	134093629	+	1	NA	TTS (NM_013706)	TTS (NM_013706)	1455	NM_013706	23833	Mm.24130	NM_013706	ENSMUSG00000000682	Cd52	AI463198|B7|B7-Ag|CAMPATH-1|CLS1|MB7	CD52 antigen	protein-coding
mm_46195.1	chr5	98030618	98030627	-	1	NA	5' UTR (NM_133738, exon 1 of 17)	5' UTR (NM_133738, exon 1 of 17)	340	NM_133738	71914	Mm.24842	NM_133738	ENSMUSG00000029338	Antxr2	2310046B19Rik|AW561899|CMG-2|CMG2|cI-35	anthrax toxin receptor 2	protein-coding
mm_80936.1	chr9	102694350	102694354	+	1	NA	Intergenic	RMER19C|LTR|ERVK	-23452	NM_019764	56332	Mm.21145	NM_019764	ENSMUSG00000032531	Amotl2	AW549739|C79691|Lccp|MASCOT|mKIAA0989	angiomotin-like 2	protein-coding
mm_95151.1	chr11	35769463	35769475	+	1	NA	promoter-TSS (NM_145962)	promoter-TSS (NM_145962)	-26	NM_145962	211347	Mm.255044	NM_145962	ENSMUSG00000018846	Pank3	-	pantothenate kinase 3	protein-coding
mm_96159.1	chr11	61487072	61487113	+	1	NA	exon (NM_029568, exon 5 of 6)	exon (NM_029568, exon 5 of 6)	1648	NM_029568	76293	Mm.272278	NM_029568	ENSMUSG00000042436	Mfap4	1110007F23Rik	microfibrillar-associated protein 4	protein-coding
mm_99715.1	chr11	106256174	106256189	+	1	NA	promoter-TSS (NM_025310)	promoter-TSS (NM_025310)	-4	NM_008950	19184	Mm.272361	NM_008950	ENSMUSG00000020708	Psmc5	mSUG1	protease (prosome, macropain) 26S subunit, ATPase 5	protein-coding
mm_165407.1	chr2	143282776	143282776	+	1	NA	Intergenic	Intergenic	204284	NM_020595	57329	Mm.157751	NM_020595	ENSMUSG00000027416	Otor	CDRAP|Fdp|MIA|MIAL	otoraplin	protein-coding
mm_146950.1	chr18	32559824	32559836	-	1	NA	5' UTR (NM_001048207, exon 1 of 3)	5' UTR (NM_001048207, exon 1 of 3)	204	NM_001347610	71683	Mm.292145	NM_027863	ENSMUSG00000090523	Gypc	0610037F22Rik|Cd236r	glycophorin C	protein-coding
mm_119813.1	chr14	54223716	54223733	+	1	NA	Intergenic	Intergenic	30205	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_3793.1	chr1	157412682	157412683	+	1	NA	promoter-TSS (NM_177644)	promoter-TSS (NM_177644)	-87	NM_177644	226525	Mm.235028	NM_177644	ENSMUSG00000070565	Rasal2	6530401P13|A330066M24Rik	RAS protein activator like 2	protein-coding
mm_49242.1	chr6	17307255	17307270	+	1	NA	promoter-TSS (NM_001243064)	promoter-TSS (NM_001243064)	-378	NM_001243064	12389	Mm.28278	NM_007616	ENSMUSG00000007655	Cav1	Cav|Cav-1	caveolin 1, caveolae protein	protein-coding
mm_36028.1	chr4	57120017	57120034	-	1	NA	intron (NM_019427, intron 1 of 15)	intron (NM_019427, intron 1 of 15)	23131	NM_019427	54357	Mm.28217	NM_019427	ENSMUSG00000028434	Epb41l4b	6430543G08Rik|AA589614|AU021054|BB007528|D4Ertd346e|Ehm2|Epb4.1l4b|Lulu2	erythrocyte membrane protein band 4.1 like 4b	protein-coding
mm_171697.1	chr4	70249383	70249385	-	1	NA	intron (NM_145990, intron 28 of 36)	CpG	161051	NM_001313762	214444	Mm.370777	NM_145990	ENSMUSG00000039298	Cdk5rap2	2900018K03Rik|an|mKIAA1633	CDK5 regulatory subunit associated protein 2	protein-coding
mm_148421.1	chr19	3936680	3936696	+	1	NA	intron (NM_001161428, intron 3 of 9)	intron (NM_001161428, intron 3 of 9)	1502	NM_001161428	54445	Mm.262094	NM_019449	ENSMUSG00000036908	Unc93b1	Unc-93B1|Unc93b	unc-93 homolog B1 (C. elegans)	protein-coding
mm_83882.1	chr9	55292138	55292144	-	1	NA	Intergenic	ORR1B2|LTR|ERVL-MaLR	-8516	NM_032002	83961	Mm.443874	NM_032002	ENSMUSG00000032311	Nrg4	AI552600	neuregulin 4	protein-coding
mm_41396.1	chr5	90772494	90772509	+	1	NA	promoter-TSS (NM_019932)	promoter-TSS (NM_019932)	66	NM_019932	56744	Mm.332490	NM_019932	ENSMUSG00000029373	Pf4	Cxcl4|Scyb4	platelet factor 4	protein-coding
mm_142023.1	chr17	35205166	35205223	-	1	NA	promoter-TSS (NR_105940)	promoter-TSS (NR_105940)	157	NM_010735	16992	Mm.87787	NM_010735	ENSMUSG00000024402	Lta	LT|LT-[a]|LT-alpha|LT[a]|LTalpha|Ltx|TNF-beta|TNFSF1|Tnfb|Tnfsf1b|Tnlg1e|hlb382	lymphotoxin A	protein-coding
mm_132977.1	chr16	52060540	52060548	+	1	NA	intron (NM_001033238, intron 3 of 17)	intron (NM_001033238, intron 3 of 17)	28995	NM_001033238	208650	Mm.328206	NM_001033238	ENSMUSG00000022637	Cblb	AI429560|AI851073|Cbl-b	Casitas B-lineage lymphoma b	protein-coding
mm_87263.1	chr10	41519991	41520000	+	1	NA	intron (NM_016898, intron 1 of 5)	intron (NM_016898, intron 1 of 5)	495	NM_016898	53599	Mm.269815	NM_016898	ENSMUSG00000019818	Cd164	A115|A24|AA589639|AW540279|MGC-24|MSSP	CD164 antigen	protein-coding
mm_127364.1	chr15	100695768	100695796	+	1	NA	intron (NM_001161767, intron 10 of 11)	MTD|LTR|ERVL-MaLR	-7862	NM_033612	109901	Mm.2131	NM_033612	ENSMUSG00000023031	Cela1	1810009A17Rik|1810062B19Rik|Ela-1|Ela1|PC-TsF	chymotrypsin-like elastase family, member 1	protein-coding
mm_139939.1	chr17	71179182	71179194	+	1	NA	Intergenic	Intergenic	-4790	NM_022882	64898	Mm.227924	NM_022882	ENSMUSG00000024052	Lpin2	2610511G02Rik|AI481352|AW742896	lipin 2	protein-coding
mm_29722.1	chr3	125938485	125938496	-	1	NA	promoter-TSS (NM_011674)	promoter-TSS (NM_011674)	60	NM_011674	22239	Mm.306021	NM_011674	ENSMUSG00000032854	Ugt8a	AI850488|AW455908|Cgt|Ugt8|mCerGT	UDP galactosyltransferase 8A	protein-coding
mm_160993.1	chr11	109303999	109303999	-	1	NA	Intergenic	B1_Mur2|SINE|Alu	-5818	NM_011268	19739	Mm.38548	NM_011268	ENSMUSG00000020599	Rgs9	RGS9-1|Rgs9-2	regulator of G-protein signaling 9	protein-coding
mm_91902.1	chr10	60214500	60214512	-	1	NA	intron (NM_016803, intron 1 of 3)	intron (NM_016803, intron 1 of 3)	4754	NM_016803	53374	Mm.12866	NM_016803	ENSMUSG00000057337	Chst3	C6ST|C6ST-1|GST-0	carbohydrate (chondroitin 6/keratan) sulfotransferase 3	protein-coding
mm_155973.1	chrX	106125588	106125594	+	1	NA	3' UTR (NM_009726, exon 23 of 23)	3' UTR (NM_009726, exon 23 of 23)	-17684	NM_205820	279572	Mm.336203	NM_205820	ENSMUSG00000033777	Tlr13	AI666735|Gm713	toll-like receptor 13	protein-coding
mm_65909.1	chr7	30194001	30194033	-	1	NA	exon (NM_009795, exon 2 of 11)	exon (NM_009795, exon 2 of 11)	1031	NM_009795	12336	Mm.439782	NM_009795	ENSMUSG00000001794	Capns1	Capa-4|Capa4|Capn4|D7Ertd146e	calpain, small subunit 1	protein-coding
mm_52922.1	chr6	122875347	122875351	+	1	NA	intron (NM_026267, intron 1 of 7)	intron (NM_026267, intron 1 of 7)	792	NM_026267	67602	Mm.288114	NM_026267	ENSMUSG00000030327	Necap1	1200016B17Rik|AI747569|mFLJ00061	NECAP endocytosis associated 1	protein-coding
mm_130174.1	chr15	93336801	93336852	-	1	NA	non-coding (NR_028315, exon 1 of 5)	non-coding (NR_028315, exon 1 of 5)	109	NR_028315	67057	Mm.4714	NM_024189	ENSMUSG00000022634	Yaf2	2810021M11Rik	YY1 associated factor 2	protein-coding
mm_126348.1	chr15	79907390	79907422	+	1	NA	3' UTR (NM_001160415, exon 9 of 9)	3' UTR (NM_001160415, exon 9 of 9)	12383	NM_001347041	80287	Mm.284059	NM_030255	ENSMUSG00000009585	Apobec3	Apobec|Arp3|BC003314|Cem15|Rfv3	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 3	protein-coding
mm_102324.1	chr11	57649466	57649498	-	1	NA	intron (NM_134189, intron 1 of 11)	intron (NM_134189, intron 1 of 11)	4040	NM_134189	171212	Mm.271670	NM_134189	ENSMUSG00000020520	Galnt10	AU018154|C330012K04Rik|GalNAc-T10|GalNAc-T9|Galnt9|ppGaNTase	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 10	protein-coding
mm_139623.1	chr17	57362742	57362796	+	1	NA	intron (NM_010130, intron 2 of 21)	RLTR22_Mur|LTR|ERVK	4083	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_40826.1	chr5	72875880	72875884	+	1	NA	Intergenic	Intergenic	-7434	NM_001113460	21682	Mm.319581	NM_013689	ENSMUSG00000029217	Tec	-	tec protein tyrosine kinase	protein-coding
mm_64935.1	chr7	16295460	16295486	-	1	NA	Intergenic	Intergenic	-8678	NM_001136471	243846	Mm.482401	NM_172297	ENSMUSG00000041375	Ccdc9	2600011L02Rik	coiled-coil domain containing 9	protein-coding
mm_159113.1	chr2	55436689	55436689	+	1	NA	intron (NM_008426, intron 1 of 3)	intron (NM_008426, intron 1 of 3)	719	NM_008426	16519	Mm.5127	NM_008426	ENSMUSG00000026824	Kcnj3	GIRK-1|GIRK1|Kcnf3|Kir3.1	potassium inwardly-rectifying channel, subfamily J, member 3	protein-coding
mm_2924.1	chr1	132143375	132143386	+	1	NA	Intergenic	Intergenic	-3695	NM_008795	18557	Mm.28130	NM_008795	ENSMUSG00000026437	Cdk18	AA682070|Ctk18|Pctk3	cyclin-dependent kinase 18	protein-coding
mm_157708.1	chrX	64275946	64275956	-	1	NA	intron (NM_178740, intron 1 of 2)	CpG	1045	NM_178740	245446	Mm.101707	NM_178740	ENSMUSG00000046699	Slitrk4	6430513G13|D930039I09Rik	SLIT and NTRK-like family, member 4	protein-coding
mm_57107.1	chr6	122592864	122592874	-	1	NA	intron (NM_031159, intron 3 of 7)	intron (NM_031159, intron 3 of 7)	9575	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_45518.1	chr5	72556284	72556316	-	1	NA	exon (NM_133921, exon 3 of 23)	exon (NM_133921, exon 3 of 23)	3345	NM_133921	100978	Mm.187453	NM_133921	ENSMUSG00000072889	Nfxl1	1700012H24Rik|AW538212|D430033A06Rik|DNABF|GCF|Gm1058|TCF9	nuclear transcription factor, X-box binding-like 1	protein-coding
mm_17794.1	chr2	33130467	33130479	-	1	NA	Intergenic	CpG	-43269	NM_178888	99326	Mm.41290	NM_178888	ENSMUSG00000038860	Garnl3	AW120551	GTPase activating RANGAP domain-like 3	protein-coding
mm_138832.1	chr17	39848210	39848236	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	5226	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_59954.1	chr7	30427114	30427122	+	1	NA	exon (NM_172142, exon 9 of 11)	exon (NM_172142, exon 9 of 11)	3814	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_131222.1	chr16	8944890	8944910	+	1	NA	Intergenic	Intergenic	114800	NM_001081400	69053	Mm.390868	NM_001081400	ENSMUSG00000022507	1810013L24Rik	1110017P05Rik|3010002C02Rik|AA792997|AW124177|Gm19906|R74903	RIKEN cDNA 1810013L24 gene	protein-coding
mm_90669.1	chr10	128861426	128861475	+	1	NA	intron (NM_025364, intron 9 of 10)	intron (NM_025364, intron 9 of 10)	30268	NM_010272	14561	Mm.299218	NM_010272	ENSMUSG00000025352	Gdf11	BMP-11|Bmp11	growth differentiation factor 11	protein-coding
mm_46120.1	chr5	92435190	92435216	-	1	NA	promoter-TSS (NM_183392)	promoter-TSS (NM_183392)	-4	NM_183392	269113	Mm.275289	NM_183392	ENSMUSG00000034826	Nup54	3110079L04Rik|54kDa	nucleoporin 54	protein-coding
mm_168747.1	chr12	115567601	115567617	-	1	NA	Intergenic	Intergenic	128185	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
mm_88176.1	chr10	69924137	69924151	+	1	NA	intron (NM_146005, intron 24 of 42)	(TGGGGG)n|Simple_repeat|Simple_repeat	-1388	NM_170687	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_153113.1	chr19	32980285	32980305	-	1	NA	Intergenic	Intergenic	222718	NM_008960	19211	Mm.245395	NM_008960	ENSMUSG00000013663	Pten	2310035O07Rik|A130070J02Rik|AI463227|B430203M17Rik|MMAC1|TEP1	phosphatase and tensin homolog	protein-coding
mm_40029.1	chr5	33427806	33427812	+	1	NA	Intergenic	RMER15|LTR|ERVL	6281	NM_011320	672284		NM_011320	ENSMUSG00000029112	Nkx1-1	Nkx-1.1|Sax2	NK1 transcription factor related, locus 1 (Drosophila)	protein-coding
mm_42898.1	chr5	122422441	122422495	+	1	NA	promoter-TSS (NM_019805)	promoter-TSS (NM_019805)	24	NM_019805	56317	Mm.37341	NM_019805	ENSMUSG00000029466	Anapc7	APC7|AW545589	anaphase promoting complex subunit 7	protein-coding
mm_122512.1	chr14	47167891	47167909	-	1	NA	intron (NM_008102, intron 2 of 5)	L1M5|LINE|L1	21502	NM_008102	14528	Mm.10651	NM_008102	ENSMUSG00000037580	Gch1	GTP-CH|GTPCH|Gch	GTP cyclohydrolase 1	protein-coding
mm_147690.1	chr18	60733485	60733503	-	1	NA	Intergenic	Intergenic	-20105	NM_008306	15531	Mm.181862	NM_008306	ENSMUSG00000054008	Ndst1	1200015G06Rik|HSNST|HSNST 1|Hsst|N-HSST|N-HSST 1|NDST-1|b2b2230Clo	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 1	protein-coding
mm_93948.1	chr10	127243441	127243452	-	1	NA	exon (NM_001039000, exon 10 of 29)	exon (NM_001039000, exon 10 of 29)	19917	NM_008447	16572	Mm.30355	NM_008447	ENSMUSG00000074657	Kif5a	D10Bwg0738e|Khc|Kif5|Kns|mKIAA4086	kinesin family member 5A	protein-coding
mm_102074.1	chr11	52264786	52264804	-	1	NA	intron (NM_001313981, intron 3 of 10)	intron (NM_001313981, intron 3 of 10)	17800	NM_009331	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_103881.1	chr11	83530506	83530533	-	1	NA	promoter-TSS (NM_013653)	promoter-TSS (NM_013653)	-1	NM_013653	20304	Mm.284248	NM_013653	ENSMUSG00000035042	Ccl5	MuRantes|RANTES|SISd|Scya5|TCP228	chemokine (C-C motif) ligand 5	protein-coding
mm_79303.1	chr9	51962906	51962917	+	1	NA	intron (NM_001301728, intron 1 of 3)	intron (NM_001301728, intron 1 of 3)	691	NM_007996	14148	Mm.1061	NM_007996	ENSMUSG00000032051	Fdx1	-	ferredoxin 1	protein-coding
mm_153569.1	chr19	42612767	42612781	-	1	NA	promoter-TSS (NM_053083)	promoter-TSS (NM_053083)	32	NM_001164311	67573	Mm.178767	NM_053083	ENSMUSG00000025185	Loxl4	4833426I20Rik|Loxc	lysyl oxidase-like 4	protein-coding
mm_58549.1	chr7	4690730	4690754	+	1	NA	promoter-TSS (NM_001003920)	promoter-TSS (NM_001003920)	-186	NM_001003920	381979	Mm.297064	NM_001003920	ENSMUSG00000035390	Brsk1	Gm1100|SAD-B|SADB	BR serine/threonine kinase 1	protein-coding
mm_89778.1	chr10	100592387	100592406	+	1	NA	promoter-TSS (NM_001081246)	promoter-TSS (NM_001081246)	10	NM_001081246	66605	Mm.72646	NM_001081246	ENSMUSG00000056912	1700017N19Rik	-	RIKEN cDNA 1700017N19 gene	protein-coding
mm_82158.1	chr9	123781256	123781306	+	1	NA	3' UTR (NM_001166625, exon 4 of 4)	3' UTR (NM_001166625, exon 4 of 4)	14070	NM_001166625	12769	Mm.440604	NM_009913	ENSMUSG00000029530	Ccr9	A130091K22Rik|Cmkbr10|GPR-9-6	chemokine (C-C motif) receptor 9	protein-coding
mm_169219.1	chr13	6674433	6674441	-	1	NA	Intergenic	L1Md_T|LINE|L1	-25666	NM_001291071	56421	Mm.273874	NM_019703	ENSMUSG00000021196	Pfkp	1200015H23Rik|9330125N24Rik|ATP-PFK|PFK-C|PFK-P	phosphofructokinase, platelet	protein-coding
mm_119944.1	chr14	54988310	54988344	+	1	NA	exon (NM_080728, exon 16 of 41)	exon (NM_080728, exon 16 of 41)	6222	NM_080728	140781	Mm.457983	NM_080728	ENSMUSG00000053093	Myh7	B-MHC|MyHC-I|Myhc-b|Myhcb|beta-MHC	myosin, heavy polypeptide 7, cardiac muscle, beta	protein-coding
mm_114259.1	chr13	56747785	56747801	+	1	NA	Intergenic	Intergenic	44125	NM_001164042	17129	Mm.272920	NM_008541	ENSMUSG00000021540	Smad5	1110051M15Rik|AI451355|Dwf-C|Madh5|MusMLP	SMAD family member 5	protein-coding
mm_51136.1	chr6	68680348	68680354	+	1	NA	Intergenic	Intergenic	646823	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_61722.1	chr7	81858966	81858977	+	1	NA	promoter-TSS (NM_145375)	promoter-TSS (NM_145375)	-30	NR_111910	107769	Mm.221412	NM_145375	ENSMUSG00000038623	Tm6sf1	AI428514|BC023123|C630016D09Rik	transmembrane 6 superfamily member 1	protein-coding
mm_23301.1	chr3	52468556	52468568	+	1	NA	Intergenic	L3|LINE|CR1	200225	NM_019739	56458	Mm.29891	NM_019739	ENSMUSG00000044167	Foxo1	AI876417|Afxh|FKHR|Fkhr1|Foxo1a	forkhead box O1	protein-coding
mm_49996.1	chr6	41047569	41047578	+	1	NA	Intergenic	Intergenic	-12064	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_118152.1	chr13	105249687	105249708	-	1	NA	exon (NM_027934, exon 4 of 8)	exon (NM_027934, exon 4 of 8)	43317	NM_027934	71816	Mm.317015	NM_027934	ENSMUSG00000021720	Rnf180	3110001E11Rik|Rines	ring finger protein 180	protein-coding
mm_93624.1	chr10	117278013	117278024	-	1	NA	3' UTR (NM_017372, exon 4 of 4)	3' UTR (NM_017372, exon 4 of 4)	4254	NM_017372	17105	Mm.45436	NM_017372	ENSMUSG00000069516	Lyz2	AI326280|Lys|Lysm|Lyzf2|Lyzs|Lzm|Lzm-s1|Lzp	lysozyme 2	protein-coding
mm_89662.1	chr10	97483425	97483443	+	1	NA	exon (NM_007833, exon 2 of 8)	exon (NM_007833, exon 2 of 8)	1103	NM_007833	13179	Mm.56769	NM_007833	ENSMUSG00000019929	Dcn	DC|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding
mm_88493.1	chr10	77835939	77835956	+	1	NA	promoter-TSS (NM_001024709)	promoter-TSS (NM_001024709)	0	NM_001024709	544710	Mm.441890	NM_001024709		Krtap10-10	EG544710	keratin associated protein 10-10	protein-coding
mm_151227.1	chr19	53717920	53717937	+	1	NA	intron (NM_001170847, intron 1 of 13)	intron (NM_001170847, intron 1 of 13)	40622	NM_001170847	73713	Mm.313695	NM_001170847	ENSMUSG00000043639	Rbm20	1110018J23Rik|2010003H22Rik|AI646761	RNA binding motif protein 20	protein-coding
mm_156888.1	chrX	166386580	166386593	+	1	NA	3' UTR (NM_001177959, exon 7 of 7)	3' UTR (NM_001177959, exon 7 of 7)	42033	NM_001177960	14758	Mm.222320	NM_023122	ENSMUSG00000031342	Gpm6b	AI593561|Gpm6|M6B	glycoprotein m6b	protein-coding
mm_114536.1	chr13	73648177	73648198	+	1	NA	intron (NM_009354, intron 14 of 15)	intron (NM_009354, intron 14 of 15)	21186	NM_009354	21752	Mm.10109	NM_009354	ENSMUSG00000021611	Tert	EST2|TCS1|TP2|TR|TRT	telomerase reverse transcriptase	protein-coding
mm_127497.1	chr15	101412418	101412433	+	1	NA	promoter-TSS (NM_033073)	promoter-TSS (NM_033073)	22	NM_033073	110310	Mm.486285	NM_033073	ENSMUSG00000023039	Krt7	D15Wsu77e|K7|Krt2-7	keratin 7	protein-coding
mm_35137.1	chr4	11386634	11386652	-	1	NA	5' UTR (NM_001290383, exon 1 of 16)	5' UTR (NM_001290383, exon 1 of 16)	135	NM_001347052	207920	Mm.387719	NM_194055	ENSMUSG00000040728	Esrp1	2210008M09Rik|A630065D16|BC031468|Rbm35a	epithelial splicing regulatory protein 1	protein-coding
mm_157423.1	chrX	38564520	38564555	-	1	NA	intron (NM_001110142, intron 3 of 22)	intron (NM_001110142, intron 3 of 22)	11659	NM_028288	72584	Mm.327675	NM_028288	ENSMUSG00000031095	Cul4b	2700050M05Rik|AA409770|CUL-4B|mKIAA0695	cullin 4B	protein-coding
mm_110309.1	chr12	33147544	33147590	-	1	NA	promoter-TSS (NM_028139)	promoter-TSS (NM_028139)	19	NR_015602	320046	Mm.208337	NR_015602	ENSMUSG00000052125	F730043M19Rik	-	RIKEN cDNA F730043M19 gene	ncRNA
mm_65363.1	chr7	25030012	25030012	-	1	NA	intron (NM_008168, intron 12 of 19)	B1_Mus1|SINE|Alu	-24075	NM_001290469	232975	Mm.44101	NM_144921	ENSMUSG00000040907	Atp1a3	Atpa-2	ATPase, Na+/K+ transporting, alpha 3 polypeptide	protein-coding
mm_151283.1	chr19	55266608	55266638	+	1	NA	intron (NM_027976, intron 1 of 21)	intron (NM_027976, intron 1 of 21)	13254	NM_027976	433256	Mm.292056	NM_027976	ENSMUSG00000024981	Acsl5	1700030F05Rik|ACS2|ACS5|Facl5	acyl-CoA synthetase long-chain family member 5	protein-coding
mm_132979.1	chr16	52074425	52074441	+	1	NA	intron (NM_001033238, intron 3 of 17)	intron (NM_001033238, intron 3 of 17)	42884	NM_001033238	208650	Mm.328206	NM_001033238	ENSMUSG00000022637	Cblb	AI429560|AI851073|Cbl-b	Casitas B-lineage lymphoma b	protein-coding
mm_80376.1	chr9	75408116	75408124	+	1	NA	intron (NM_015806, intron 1 of 5)	intron (NM_015806, intron 1 of 5)	1239	NM_027418	50772	Mm.480076	NM_015806	ENSMUSG00000042688	Mapk6	2610021I23Rik|D130053K17Rik|Erk3|Mapk4|Mapk63|Prkm4|Prkm6	mitogen-activated protein kinase 6	protein-coding
mm_111579.1	chr12	101819049	101819061	-	1	NA	promoter-TSS (NM_011812)	promoter-TSS (NM_011812)	64	NM_011812	23876	Mm.288381	NM_011812	ENSMUSG00000021186	Fbln5	A55|DANCE|EVEC	fibulin 5	protein-coding
mm_5421.1	chr1	34073845	34073879	-	1	NA	intron (NM_133833, intron 1 of 92)	intron (NM_133833, intron 1 of 92)	-43497	NR_105861	102466987		NR_105861	ENSMUSG00000105982	Mir6896	mmu-mir-6896	microRNA 6896	ncRNA
mm_105165.1	chr11	101770379	101770406	-	1	NA	exon (NM_001316366, exon 13 of 13)	exon (NM_001316366, exon 13 of 13)	14918	NM_008815	18612	Mm.5025	NM_008815	ENSMUSG00000017724	Etv4	AW414408|Pea-3|Pea3	ets variant 4	protein-coding
mm_92184.1	chr10	68044153	68044169	-	1	NA	TTS (NM_001081346)	TTS (NM_001081346)	64563	NM_001081346	170799	Mm.209844	NM_133244	ENSMUSG00000037846	Rtkn2	B130039D23Rik|Mbf|Plekhk1	rhotekin 2	protein-coding
mm_141142.1	chr17	26490916	26490918	-	1	NA	Intergenic	Intergenic	17555	NM_013642	19252	Mm.239041	NM_013642	ENSMUSG00000024190	Dusp1	3CH134|MKP1|Ptpn16|U19515|erp|mkp-1	dual specificity phosphatase 1	protein-coding
mm_101618.1	chr11	35841940	35841991	-	1	NA	exon (NM_170779, exon 21 of 23)	exon (NM_170779, exon 21 of 23)	-7437	NM_025936	104458	Mm.284906	NM_025936	ENSMUSG00000018848	Rars	2610011N19Rik|2610037E21Rik|AL033339|AW985894	arginyl-tRNA synthetase	protein-coding
mm_116701.1	chr13	50443868	50443894	-	1	NA	Intergenic	Intergenic	-23426	NM_001033400	328250	Mm.315205	NM_001033400	ENSMUSG00000071909	Nutm2	Fam22|Gm806	NUT family member 2	protein-coding
mm_19768.1	chr2	105670292	105670298	-	1	NA	promoter-TSS (NR_002867)	promoter-TSS (NR_002867)	35	NR_002867	402728	Mm.444553	NR_002867	ENSMUSG00000086029	Pax6os1	4831410G09Rik|Pax6os	paired box 6 opposite strand 1	ncRNA
mm_91246.1	chr10	22731295	22731305	-	1	NA	5' UTR (NM_011603, exon 1 of 7)	5' UTR (NM_011603, exon 1 of 7)	147	NM_011603	237336	Mm.86670	NM_011603	ENSMUSG00000071359	Tbpl1	4732475G08|AW011832|AW491032|D18347|STD|TLF|TRF2|TRP|Tlp	TATA box binding protein-like 1	protein-coding
mm_65336.1	chr7	24978513	24978521	-	1	NA	3' UTR (NM_001290469, exon 23 of 23)	3' UTR (NM_001290469, exon 23 of 23)	-5789	NM_010261	14470	Mm.22473	NM_010261	ENSMUSG00000003380	Rabac1	2310040I06Rik|Gbpap1|PRA1|prenylin	Rab acceptor 1 (prenylated)	protein-coding
mm_73623.1	chr8	110522385	110522387	+	1	NA	intron (NM_172916, intron 42 of 86)	RLTR1B|LTR|ERV1	-20030	NR_105058	100861869	Mm.84499	NR_105058		Gm21283	-	predicted gene, 21283	ncRNA
mm_171365.1	chr4	117818136	117818140	-	1	NA	Intergenic	RMER19C|LTR|ERVK	-17120	NM_008135	14664	Mm.244549	NM_008135	ENSMUSG00000028542	Slc6a9	Glyt-1|Glyt1	solute carrier family 6 (neurotransmitter transporter, glycine), member 9	protein-coding
mm_47787.1	chr5	132195104	132195142	-	1	NA	intron (NM_177047, intron 2 of 18)	intron (NM_177047, intron 2 of 18)	314854	NR_040704	75369	Mm.389696	NR_040704	ENSMUSG00000105773	4930563F08Rik	-	RIKEN cDNA 4930563F08 gene	ncRNA
mm_36851.1	chr4	106799780	106799840	-	1	NA	promoter-TSS (NM_025590)	promoter-TSS (NM_025590)	21	NM_025590	329910	Mm.222956	NM_025590	ENSMUSG00000034853	Acot11	1110020M10Rik|2010309H15Rik|AW060409|BFIT|BFIT1|Thea|Them1|mKIAA0707	acyl-CoA thioesterase 11	protein-coding
mm_79100.1	chr9	46243143	46243153	+	1	NA	exon (NM_007468, exon 3 of 3)	exon (NM_007468, exon 3 of 3)	2304	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_102946.1	chr11	69617590	69617594	-	1	NA	intron (NM_011367, intron 1 of 7)	intron (NM_011367, intron 1 of 7)	313	NM_011367	20415	Mm.1431	NM_011367	ENSMUSG00000005202	Shbg	ABP	sex hormone binding globulin	protein-coding
mm_148135.1	chr18	76015639	76015643	-	1	NA	intron (NM_145356, intron 3 of 4)	intron (NM_145356, intron 3 of 4)	82830	NR_045365	73009	Mm.443541	NR_045365		2900057B20Rik	-	RIKEN cDNA 2900057B20 gene	ncRNA
mm_89003.1	chr10	81620591	81620597	+	1	NA	Intergenic	Intergenic	6728	NM_001163430	50721	Mm.25643	NM_181586	ENSMUSG00000034748	Sirt6	2810449N18Rik|AI043036|Sir2l6	sirtuin 6	protein-coding
mm_124027.1	chr14	76693789	76693798	-	1	NA	Intergenic	Intergenic	16225	NR_015485	73272	Mm.116804	NR_015485	ENSMUSG00000101009	1700108F19Rik	1700020I02Rik|BB065030	RIKEN cDNA 1700108F19 gene	ncRNA
mm_48047.1	chr5	136459981	136459989	-	1	NA	intron (NM_001291239, intron 2 of 22)	PB1D9|SINE|Alu	-84182	NR_030500	723975		NR_030500	ENSMUSG00000106479	Mir721	Mirn721|miRY|mir-721|mmu-mir-721	microRNA 721	ncRNA
mm_165781.1	chr3	130730291	130730296	-	1	NA	promoter-TSS (NM_001287581)	promoter-TSS (NM_001287581)	36	NM_001199350	619547	Mm.391636	NM_001199350		Rpl34-ps1	EG619547|ENSMUSG00000068396|Gm10239	ribosomal protein L34, pseudogene 1	protein-coding
mm_155034.1	chrX	42068677	42068766	+	1	NA	non-coding (NR_125870, exon 1 of 6)	non-coding (NR_125870, exon 1 of 6)	323	NR_125870	11798	Mm.259879	NM_009688	ENSMUSG00000025860	Xiap	1110015C02Rik|Aipa|Api3|Birc4|IAP3|ILP-1|MIHA	X-linked inhibitor of apoptosis	protein-coding
mm_68983.1	chr7	126589448	126589464	-	1	NA	TTS (NM_138310)	TTS (NM_138310)	-3639	NM_001146311	12752	Mm.268930	NM_009907	ENSMUSG00000030720	Cln3	AI323623	ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease)	protein-coding
mm_77596.1	chr8	123892297	123892314	-	1	NA	exon (NM_009606, exon 6 of 7)	exon (NM_009606, exon 6 of 7)	2470	NM_001272041	11459	Mm.214950	NM_009606	ENSMUSG00000031972	Acta1	AA959943|Acta-2|Acts|Actsk-1	actin, alpha 1, skeletal muscle	protein-coding
mm_23747.1	chr3	69373730	69373774	+	1	NA	intron (NM_178726, intron 1 of 3)	intron (NM_178726, intron 1 of 3)	56834	NM_178726	242083	Mm.40577	NM_178726	ENSMUSG00000027784	Ppm1l	3222401G13|5930404J21Rik|AI481720|AW045850|PP2C|PP2Cepsilon|Pp2ce|Ppp2ce|mKIAA4175	protein phosphatase 1 (formerly 2C)-like	protein-coding
mm_54972.1	chr6	48738906	48738913	-	1	NA	promoter-TSS (NM_008376)	promoter-TSS (NM_008376)	-138	NM_175860	16205	Mm.252599	NM_008376	ENSMUSG00000090019	Gimap1	IAP38|Imap38|imap	GTPase, IMAP family member 1	protein-coding
mm_11736.1	chr2	37551387	37551389	+	1	NA	intron (NM_146121, intron 19 of 25)	B1_Mus1|SINE|Alu	34762	NM_177383	338346	Mm.445325	NM_177383	ENSMUSG00000053164	Gpr21	C230004C13Rik	G protein-coupled receptor 21	protein-coding
mm_65208.1	chr7	19697595	19697607	-	1	NA	exon (NM_009696, exon 3 of 4)	exon (NM_009696, exon 3 of 4)	797	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_38559.1	chr4	141652373	141652413	-	1	NA	intron (NM_001347237, intron 1 of 18)	intron (NM_001347237, intron 1 of 18)	11722	NM_001347237	69582	Mm.33220	NM_001033150	ENSMUSG00000028917	Plekhm2	2310034J19Rik|AI854247|mKIAA0842	pleckstrin homology domain containing, family M (with RUN domain) member 2	protein-coding
mm_45294.1	chr5	65046878	65046881	-	1	NA	Intergenic	RMER17C|LTR|ERVK	-60689	NM_001347355	71778	Mm.10281	NM_175174	ENSMUSG00000054920	Klhl5	1300013C10Rik	kelch-like 5	protein-coding
mm_101686.1	chr11	40694929	40694948	-	1	NA	5' UTR (NM_001199274, exon 1 of 7)	5' UTR (NM_001199274, exon 1 of 7)	265	NM_001199274	108645	Mm.293771	NM_134017	ENSMUSG00000042032	Mat2b	1110064C04Rik|2410018D16Rik|AI182287|AU022853|MAT-II|MATIIbeta|TGR	methionine adenosyltransferase II, beta	protein-coding
mm_90218.1	chr10	121034015	121034038	+	1	NA	promoter-TSS (NM_011915)	promoter-TSS (NM_011915)	22	NM_011915	24117	Mm.32831	NM_011915	ENSMUSG00000020218	Wif1	AW107799|WIF-1	Wnt inhibitory factor 1	protein-coding
mm_158316.1	chrX	128548423	128548475	-	1	NA	Intergenic	Intergenic	-503075	NR_045441	75274	Mm.108718	NR_045441	ENSMUSG00000086244	4930558G05Rik	-	RIKEN cDNA 4930558G05 gene	ncRNA
mm_151907.1	chr19	5799494	5799500	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	3175	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_34900.1	chr4	155638512	155638523	+	1	NA	intron (NM_001347308, intron 7 of 20)	intron (NM_001347308, intron 7 of 20)	13648	NM_007661	12537	Mm.267410	NM_007661	ENSMUSG00000029062	Cdk11b	AA989746|CDK11-p110|CDK11-p46|CDK11-p58|Cdc11b|Cdc2l1|Cdc2l2|Cdk11|p58	cyclin-dependent kinase 11B	protein-coding
mm_131549.1	chr16	17894245	17894257	+	1	NA	promoter-TSS (NM_009435)	promoter-TSS (NM_009435)	48	NM_009435	22114	Mm.439725	NM_009435	ENSMUSG00000041566	Tssk1	Stk22a|TSK-1|Tsk1|Tssk|Tssk1b	testis-specific serine kinase 1	protein-coding
mm_92894.1	chr10	82958391	82958440	-	1	NA	Intergenic	Intergenic	-27082	NM_021439	58250	Mm.360747	NM_021439	ENSMUSG00000034612	Chst11	1110020P09Rik|C4ST|C4ST-1|C4ST1|C4s	carbohydrate sulfotransferase 11	protein-coding
mm_149390.1	chr19	11386783	11386799	+	1	NA	intron (NM_001310331, intron 4 of 6)	intron (NM_001310331, intron 4 of 6)	11303	NM_001310331	666907		NM_001310331	ENSMUSG00000101389	Ms4a4a	EG666907	membrane-spanning 4-domains, subfamily A, member 4A	protein-coding
mm_83330.1	chr9	44233984	44234003	-	1	NA	promoter-TSS (NM_007619)	promoter-TSS (NM_007619)	53	NM_007619	12402	Mm.266871	NM_007619	ENSMUSG00000034342	Cbl	4732447J05Rik|Cbl-2|c-Cbl|cbl	Casitas B-lineage lymphoma	protein-coding
mm_58344.1	chr6	147243795	147243806	-	1	NA	Intergenic	Lx8|LINE|L1	20213	NM_008970	19227	Mm.28440	NM_008970	ENSMUSG00000048776	Pthlh	PLP|PTH-like|Pthrp	parathyroid hormone-like peptide	protein-coding
mm_169787.1	chr16	13109791	13109792	+	1	NA	promoter-TSS (NM_015769)	promoter-TSS (NM_015769)	55	NM_015769	50505	Mm.287837	NM_015769	ENSMUSG00000022545	Ercc4	AI606920|Xpf	excision repair cross-complementing rodent repair deficiency, complementation group 4	protein-coding
mm_12907.1	chr2	84839409	84839424	+	1	NA	promoter-TSS (NM_024497)	promoter-TSS (NM_024497)	8	NM_001081349	72401	Mm.22716	NM_024497	ENSMUSG00000027075	Slc43a1	2610016F07Rik|AA986141|Lat3|PB39|Pov1|R00504	solute carrier family 43, member 1	protein-coding
mm_36289.1	chr4	63997056	63997071	-	1	NA	intron (NM_011607, intron 12 of 25)	B4A|SINE|B4	49952	NM_011607	21923	Mm.980	NM_011607	ENSMUSG00000028364	Tnc	AI528729|C130033P17Rik|Hxb|TN|TN-C|Ten|cytotactin|tenascin-C	tenascin C	protein-coding
mm_162687.1	chr10	17947463	17947482	+	1	NA	intron (NM_001033432, intron 1 of 3)	CpG	595	NM_001033432	380629	Mm.276430	NM_001033432	ENSMUSG00000039879	Heca	Gm869|HDC|HDCL	hdc homolog, cell cycle regulator	protein-coding
mm_152236.1	chr19	8709741	8709785	-	1	NA	exon (NM_008577, exon 4 of 9)	exon (NM_008577, exon 4 of 9)	4134	NM_008577	17254	Mm.4114	NM_008577	ENSMUSG00000010095	Slc3a2	4F2|4F2HC|AI314110|Cd98|Ly-10|Ly-m10|Ly10|Mdu1|Mgp-2hc|NACAE	solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2	protein-coding
mm_165382.1	chr2	129225465	129225466	+	1	NA	non-coding (NR_045838, exon 2 of 5)	non-coding (NR_045838, exon 2 of 5)	6496	NR_045838	329513	Mm.473529	NM_177847	ENSMUSG00000056738	A730036I17Rik	-	RIKEN cDNA A730036I17 gene	ncRNA
mm_121428.1	chr14	120326630	120326642	+	1	NA	intron (NM_175341, intron 2 of 8)	B4|SINE|B4	50967	NM_175341	105559	Mm.238266	NM_175341	ENSMUSG00000022139	Mbnl2	1110002M11Rik|AI047808|AI837313|AI849185|AL118326|MBLL|R75232|mKIAA4072	muscleblind-like 2	protein-coding
mm_149586.1	chr19	16132747	16132773	+	1	NA	promoter-TSS (NM_008139)	promoter-TSS (NM_008139)	-71	NM_008139	14682	Mm.439701	NM_008139	ENSMUSG00000024639	Gnaq	1110005L02Rik|6230401I02Rik|AA408290|AW060788|Dsk1|Dsk10|Galphaq|Gq|GqI	guanine nucleotide binding protein, alpha q polypeptide	protein-coding
mm_65937.1	chr7	30363091	30363137	-	1	NA	promoter-TSS (NM_175478)	promoter-TSS (NM_175478)	-342	NM_175478	233067	Mm.23157	NM_175478	ENSMUSG00000036957	Lrfn3	A530045B06Rik|SALM4	leucine rich repeat and fibronectin type III domain containing 3	protein-coding
mm_107997.1	chr12	73336758	73336770	+	1	NA	intron (NM_001037717, intron 6 of 15)	intron (NM_001037717, intron 6 of 15)	49916	NM_001037717	625098	Mm.32075	NM_001037717	ENSMUSG00000044712	Slc38a6	AW322671|EG625098	solute carrier family 38, member 6	protein-coding
mm_61865.1	chr7	88430864	88430865	+	1	NA	intron (NM_028238, intron 1 of 2)	intron (NM_028238, intron 1 of 2)	591	NM_028238	72433	Mm.276669	NM_028238	ENSMUSG00000030559	Rab38	2310011F14Rik|AU043391|cht	RAB38, member RAS oncogene family	protein-coding
mm_4906.1	chr1	190059324	190059325	+	1	NA	Intergenic	Intergenic	111356	NM_008937	19130	Mm.132579	NM_008937	ENSMUSG00000010175	Prox1	A230003G05Rik	prospero homeobox 1	protein-coding
mm_149772.1	chr19	23087886	23087894	+	1	NA	Intergenic	B1_Mus1|SINE|Alu	-53336	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_104214.1	chr11	88342906	88342915	-	1	NA	3' UTR (NM_054043, exon 14 of 14)	3' UTR (NM_054043, exon 14 of 14)	-9863	NR_039545	100628571		NR_039545	ENSMUSG00000092985	Mir378b	mir-378b|mmu-mir-378b	microRNA 378b	ncRNA
mm_131555.1	chr16	18028712	18028713	+	1	NA	Intergenic	Intergenic	-24148	NM_010047	13353	Mm.27155	NM_010047	ENSMUSG00000003531	Dgcr6	-	DiGeorge syndrome critical region gene 6	protein-coding
mm_44335.1	chr5	15883798	15883805	-	1	NA	promoter-TSS (NR_045974)	promoter-TSS (NR_045974)	-35	NR_045974	75058	Mm.183467	NR_045974	ENSMUSG00000105185	4930519H02Rik	-	RIKEN cDNA 4930519H02 gene	ncRNA
mm_53430.1	chr6	134045450	134045472	+	1	NA	intron (NM_007961, intron 1 of 7)	intron (NM_007961, intron 1 of 7)	9761	NM_007961	14011	Mm.269995	NM_007961	ENSMUSG00000030199	Etv6	AW123102|AW557856|Tel	ets variant 6	protein-coding
mm_21045.1	chr2	152540104	152540114	-	1	NA	promoter-TSS (NM_001001444)	promoter-TSS (NM_001001444)	-68	NM_001001444	75400	Mm.45560	NM_001001444	ENSMUSG00000044249	Defb29	0610030I09Rik|BD-29|mBD-29	defensin beta 29	protein-coding
mm_134967.1	chr16	31996676	31996697	-	1	NA	intron (NM_177103, intron 1 of 9)	(A)n|Simple_repeat|Simple_repeat	6601	NM_177103	320213	Mm.152890	NM_023801	ENSMUSG00000022772	Senp5	6230429P13Rik|A730063F07Rik|AI851888|BB189556|SMT3IP3	SUMO/sentrin specific peptidase 5	protein-coding
mm_114689.1	chr13	81754219	81754228	+	1	NA	TTS (NM_028372)	TTS (NM_028372)	-29069	NM_007684	12626	Mm.12481	NM_007684	ENSMUSG00000021537	Cetn3	MmCEN3	centrin 3	protein-coding
mm_9370.1	chr1	172206655	172206665	-	1	NA	5' UTR (NM_001329871, exon 1 of 4)	5' UTR (NM_001329871, exon 1 of 4)	144	NM_001329871	18611	Mm.544	NM_011063	ENSMUSG00000013698	Pea15a	Mat1|PEA-15|Pea15|Pkcs15	phosphoprotein enriched in astrocytes 15A	protein-coding
mm_107225.1	chr12	26473404	26473415	+	1	NA	intron (NM_020557, intron 2 of 4)	intron (NM_020557, intron 2 of 4)	4194	NM_020557	22169	Mm.271839	NM_020557	ENSMUSG00000020638	Cmpk2	1200004E04Rik|TDKI|Tyki	cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial	protein-coding
mm_88839.1	chr10	80857115	80857137	+	1	NA	intron (NM_175195, intron 1 of 14)	intron (NM_175195, intron 1 of 14)	1851	NM_175195	73218	Mm.3285	NM_175195	ENSMUSG00000035206	Sppl2b	3110056O03Rik|AW550292|PSL1	signal peptide peptidase like 2B	protein-coding
mm_40744.1	chr5	66686935	66686956	+	1	NA	3' UTR (NM_011670, exon 9 of 9)	3' UTR (NM_011670, exon 9 of 9)	-10448	NR_102714	101202684	Mm.381468	NR_102714	ENSMUSG00000087601	Uchl1os	Gm16832|Uchl1as	ubiquitin carboxy-terminal hydrolase L1, opposite strand	ncRNA
mm_99147.1	chr11	100545684	100545736	+	1	NA	promoter-TSS (NM_028918)	promoter-TSS (NM_028918)	78	NM_028918	74407	Mm.31590	NM_028918	ENSMUSG00000006784	Ttc25	4933404O19Rik	tetratricopeptide repeat domain 25	protein-coding
mm_19871.1	chr2	114047587	114047617	-	1	NA	exon (NM_009608, exon 7 of 7)	exon (NM_009608, exon 7 of 7)	5273	NM_009608	11464	Mm.686	NM_009608	ENSMUSG00000068614	Actc1	Actc-1	actin, alpha, cardiac muscle 1	protein-coding
mm_167042.1	chr7	80246360	80246364	+	1	NA	promoter-TSS (NM_177765)	promoter-TSS (NM_177765)	-14	NM_177765	269954	Mm.276780	NM_177765	ENSMUSG00000045467	Ttll13	1700111A04Rik|4921538O11|BC024578	tubulin tyrosine ligase-like family, member 13	protein-coding
mm_95671.1	chr11	53980045	53980049	+	1	NA	promoter-TSS (NM_019723)	promoter-TSS (NM_019723)	-20	NM_019723	56517	Mm.154284	NM_019723	ENSMUSG00000063652	Slc22a21	Octn3|Slc22a9	solute carrier family 22 (organic cation transporter), member 21	protein-coding
mm_150446.1	chr19	38055003	38055047	+	1	NA	promoter-TSS (NM_001164362)	promoter-TSS (NM_001164362)	0	NM_028293	74107	Mm.9916	NM_028293	ENSMUSG00000024989	Cep55	1200008O12Rik|2700032M20Rik	centrosomal protein 55	protein-coding
mm_84136.1	chr9	59036942	59036955	-	1	NA	promoter-TSS (NM_008684)	promoter-TSS (NM_008684)	-507	NM_001042752	18007	Mm.42249	NM_008684	ENSMUSG00000032340	Neo1	2610028H22Rik|AI327052|D930014N22Rik|Igdcc2	neogenin	protein-coding
mm_162527.1	chr1	163313710	163313712	-	1	NA	promoter-TSS (NM_175686)	promoter-TSS (NM_175686)	-61	NM_175686	18933	Mm.288642	NM_011127	ENSMUSG00000026586	Prrx1	A230024N07Rik|AA755424|AI385634|AI843499|K-2|Pmx|Pmx1|Prx1|mHox	paired related homeobox 1	protein-coding
mm_131759.1	chr16	22880260	22880266	+	1	NA	TTS (NM_026400)	TTS (NM_026400)	-11752	NR_075099	11625	Mm.197554	NM_013465	ENSMUSG00000022868	Ahsg	-	alpha-2-HS-glycoprotein	protein-coding
mm_148649.1	chr19	5493546	5493571	+	1	NA	3' UTR (NM_007687, exon 4 of 4)	3' UTR (NM_007687, exon 4 of 4)	3103	NM_007687	12631	Mm.329655	NM_007687	ENSMUSG00000056201	Cfl1	AA959946|Cof	cofilin 1, non-muscle	protein-coding
mm_122798.1	chr14	54517354	54517401	-	1	NA	promoter-TSS (NM_013768)	promoter-TSS (NM_013768)	93	NM_001313906	27374	Mm.196585	NM_013768	ENSMUSG00000023110	Prmt5	Jbp1|Skb1	protein arginine N-methyltransferase 5	protein-coding
mm_154052.1	chr19	55103071	55103089	-	1	NA	Intergenic	Intergenic	-3633	NM_008149	14732	Mm.210196	NM_008149	ENSMUSG00000024978	Gpam	GPAT|GPAT1	glycerol-3-phosphate acyltransferase, mitochondrial	protein-coding
mm_132380.1	chr16	34921615	34921636	+	1	NA	exon (NM_139300, exon 16 of 32)	exon (NM_139300, exon 16 of 32)	17704	NR_040536	76649	Mm.420532	NR_040536	ENSMUSG00000100593	1700119H24Rik	-	RIKEN cDNA 1700119H24 gene	ncRNA
mm_76175.1	chr8	82392652	82392662	-	1	NA	intron (NM_001254747, intron 1 of 7)	intron (NM_001254747, intron 1 of 7)	9929	NM_001254747	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_151775.1	chr19	5307072	5307114	-	1	NA	exon (NM_001024717, exon 3 of 3)	exon (NM_001024717, exon 3 of 3)	8762	NM_001024717	545276	Mm.447174	NM_001024717	ENSMUSG00000047658	Gal3st3	-	galactose-3-O-sulfotransferase 3	protein-coding
mm_85814.1	chr9	110388228	110388243	-	1	NA	exon (NM_001081043, exon 20 of 25)	exon (NM_001081043, exon 20 of 25)	19975	NM_001081043	104831	Mm.335477	NM_001081043	ENSMUSG00000036057	Ptpn23	AI462446|PTP-TD14	protein tyrosine phosphatase, non-receptor type 23	protein-coding
mm_122002.1	chr14	26916881	26916922	-	1	NA	Intergenic	ID_B1|SINE|B4	22297	NM_080856	142687	Mm.138259	NM_080856	ENSMUSG00000021898	Asb14	Asb-14	ankyrin repeat and SOCS box-containing 14	protein-coding
mm_90668.1	chr10	128831266	128831298	+	1	NA	intron (NM_025364, intron 1 of 10)	B2_Mm1a|SINE|B2	9511	NM_025364	66118	Mm.235562	NM_025364	ENSMUSG00000078427	Sarnp	1110005A23Rik|Cip29	SAP domain containing ribonucleoprotein	protein-coding
mm_17909.1	chr2	35315638	35315648	-	1	NA	3' UTR (NM_013515, exon 7 of 7)	3' UTR (NM_013515, exon 7 of 7)	21366	NM_013515	13830	Mm.295284	NM_013515	ENSMUSG00000026880	Stom	Epb7.2	stomatin	protein-coding
mm_41897.1	chr5	105519405	105519425	+	1	NA	promoter-TSS (NM_133897)	promoter-TSS (NM_133897)	-56	NM_133897	100604	Mm.319847	NM_133897	ENSMUSG00000054720	Lrrc8c	AD158|AI326115|E430036I04Rik|fad158	leucine rich repeat containing 8 family, member C	protein-coding
mm_85843.1	chr9	110624351	110624358	-	1	NA	promoter-TSS (NM_026012)	promoter-TSS (NM_026012)	39	NM_026012	67169	Mm.46680	NM_026012	ENSMUSG00000032491	Nradd	2610311B09Rik|BB104149|NRDD|NRH2|PLAIDD	neurotrophin receptor associated death domain	protein-coding
mm_46861.1	chr5	113819283	113819297	-	1	NA	exon (NM_009151, exon 2 of 2)	exon (NM_009151, exon 2 of 2)	11211	NM_009151	20345	Mm.332590	NM_009151	ENSMUSG00000048163	Selplg	CD162|Psgl-1|Psgl1|Selp1|Selpl	selectin, platelet (p-selectin) ligand	protein-coding
mm_46504.1	chr5	105134786	105134795	-	1	NA	intron (NM_008620, intron 3 of 10)	intron (NM_008620, intron 3 of 10)	4762	NM_008620	17472	Mm.440525	NM_008620	ENSMUSG00000079363	Gbp4	AW228052|Mag-2|Mpa-2|Mpa2	guanylate binding protein 4	protein-coding
mm_159801.1	chr5	113357288	113357288	+	1	NA	promoter-TSS (NM_001012726)	promoter-TSS (NM_001012726)	-6	NM_001012726	503692	Mm.348794	NM_001012726	ENSMUSG00000053873	Aym1	-	activator of yeast meiotic promoters 1	protein-coding
mm_132877.1	chr16	48786560	48786577	+	1	NA	Intergenic	Intergenic	-14612	NM_198297	77647	Mm.167298	NM_198297	ENSMUSG00000030775	Trat1	C030046M14Rik|Tcrim|Trim	T cell receptor associated transmembrane adaptor 1	protein-coding
mm_125676.1	chr15	66579183	66579185	+	1	NA	intron (NM_001081409, intron 1 of 20)	intron (NM_001081409, intron 1 of 20)	1612	NM_001081409	239510	Mm.267473	NM_178718	ENSMUSG00000072501	Phf20l1	CGI-72|E130113K22Rik	PHD finger protein 20-like 1	protein-coding
mm_98507.1	chr11	94952266	94952272	+	1	NA	3' UTR (NM_007742, exon 51 of 51)	3' UTR (NM_007742, exon 51 of 51)	-15324	NM_018792	54388	Mm.30482	NM_018792	ENSMUSG00000038994	Hils1	H1.9|TISP64	histone H1-like protein in spermatids 1	protein-coding
mm_172987.1	chrM	113	113	+	1	NA	NA	Intergenic	NA	NA								
mm_170691.1	chr2	132215313	132215323	-	1	NA	Intergenic	Intergenic	32470	NM_027478	70612	Mm.30116	NM_027478	ENSMUSG00000027341	Tmem230	5730494N06Rik|AA407821	transmembrane protein 230	protein-coding
mm_40866.1	chr5	73946380	73946389	+	1	NA	Intergenic	RLTR17|LTR|ERVK	122027	NM_177561	69727	Mm.48795	NM_177561	ENSMUSG00000054814	Usp46	1190009E20Rik|2410018I08Rik|AI451644	ubiquitin specific peptidase 46	protein-coding
mm_160225.1	chr7	101998454	101998454	+	1	NA	exon (NM_133947, exon 14 of 25)	exon (NM_133947, exon 14 of 25)	19701	NM_010531	16068	Mm.422756	NM_010531	ENSMUSG00000070427	Il18bp	IL-18BP|Igifbp|MC54L	interleukin 18 binding protein	protein-coding
mm_142971.1	chr17	56133818	56133854	-	1	NA	promoter-TSS (NM_013662)	promoter-TSS (NM_013662)	16	NM_013662	20359	Mm.8029	NM_013662	ENSMUSG00000001227	Sema6b	Sema|Seman|VIb|semaZ	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B	protein-coding
mm_122927.1	chr14	54961381	54961391	-	1	NA	intron (NM_001164171, intron 10 of 38)	intron (NM_001164171, intron 10 of 38)	5221	NM_001164171	17888	Mm.290003	NM_010856	ENSMUSG00000040752	Myh6	A830009F23Rik|AA517445|Myhc-a|Myhca|alpha-MHC	myosin, heavy polypeptide 6, cardiac muscle, alpha	protein-coding
mm_8466.1	chr1	153332810	153332820	-	1	NA	promoter-TSS (NM_010683)	promoter-TSS (NM_010683)	-29	NM_010683	226519	Mm.1249	NM_010683	ENSMUSG00000026478	Lamc1	Lamb2	laminin, gamma 1	protein-coding
mm_117971.1	chr13	100015533	100015543	-	1	NA	5' UTR (NM_030026, exon 1 of 17)	5' UTR (NM_030026, exon 1 of 17)	101	NM_030026	78038	Mm.137327	NM_030026	ENSMUSG00000021646	Mccc2	4930552N12Rik|MCCB	methylcrotonoyl-Coenzyme A carboxylase 2 (beta)	protein-coding
mm_130641.1	chr15	100551960	100552010	-	1	NA	promoter-TSS (NM_001289603)	promoter-TSS (NM_001289603)	23	NM_033476	21422	Mm.219040	NM_033476	ENSMUSG00000009733	Tfcp2	CP-2|CP2|D230015P20Rik|LBP-1c|LBP-1d|LBP1|LSF|Tcfcp2|UBP-1	transcription factor CP2	protein-coding
mm_71327.1	chr8	44957035	44957038	+	1	NA	intron (NM_001081286, intron 1 of 25)	MTD|LTR|ERVL-MaLR	6828	NM_001081286	14107	Mm.27365	NM_001081286	ENSMUSG00000070047	Fat1	2310038E12Rik|AU023433|Fath|mFat1	FAT atypical cadherin 1	protein-coding
mm_61105.1	chr7	51887981	51887995	+	1	NA	exon (NM_001330607, exon 2 of 8)	exon (NM_001330607, exon 2 of 8)	9021	NM_001330607	14453	Mm.207360	NM_008087	ENSMUSG00000030498	Gas2	Gas-2	growth arrest specific 2	protein-coding
mm_67011.1	chr7	65370890	65370900	-	1	NA	5' UTR (NM_001163574, exon 1 of 27)	5' UTR (NM_001163574, exon 1 of 27)	349	NM_001163574	21872	Mm.4342	NM_009386	ENSMUSG00000030516	Tjp1	ZO1	tight junction protein 1	protein-coding
mm_143117.1	chr17	57207568	57207616	-	1	NA	exon (NM_009778, exon 34 of 41)	exon (NM_009778, exon 34 of 41)	9636	NR_105944	102465591		NR_105944	ENSMUSG00000099066	Mir6978	Gm27858|mmu-mir-6978	microRNA 6978	ncRNA
mm_92505.1	chr10	78353638	78353645	-	1	NA	Intergenic	Intergenic	-1941	NM_053014	28169	Mm.141230	NM_053014	ENSMUSG00000001211	Agpat3	AW061257|AW493985|D10Jhu12e|lpaat3	1-acylglycerol-3-phosphate O-acyltransferase 3	protein-coding
mm_11341.1	chr2	30719259	30719294	+	1	NA	Intergenic	Intergenic	-1934	NR_037272	100526499		NR_037272	ENSMUSG00000093091	Mir3089	mir-3089|mmu-mir-3089	microRNA 3089	ncRNA
mm_133146.1	chr16	70313999	70314003	+	1	NA	promoter-TSS (NM_028803)	promoter-TSS (NM_028803)	52	NM_028803	74185	Mm.396102	NM_028803	ENSMUSG00000022707	Gbe1	2310045H19Rik|2810426P10Rik|D16Ertd536e	glucan (1,4-alpha-), branching enzyme 1	protein-coding
mm_88108.1	chr10	69151287	69151306	+	1	NA	Intergenic	Intergenic	-57256	NM_001252636	69288	Mm.26659	NM_001081347	ENSMUSG00000019944	Rhobtb1	1700008H16Rik|3110048G13Rik|AI173445|AI573858|AV350930	Rho-related BTB domain containing 1	protein-coding
mm_16339.1	chr2	174336742	174336764	+	1	NA	non-coding (NR_003258, exon 4 of 13)	non-coding (NR_003258, exon 4 of 13)	6664	NM_001077510	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_44914.1	chr5	35679417	35679537	-	1	NA	5' UTR (NM_001042615, exon 1 of 7)	5' UTR (NM_001042615, exon 1 of 7)	303	NM_001042615	78558	Mm.274255	NM_030127	ENSMUSG00000029096	Htra3	2210021K23Rik|9530081K03Rik|Prsp|Tasp	HtrA serine peptidase 3	protein-coding
mm_103028.1	chr11	69735314	69735322	-	1	NA	exon (NM_001291068, exon 29 of 29)	exon (NM_001291068, exon 29 of 29)	23315	NM_001291068	20020	Mm.16533	NM_009089	ENSMUSG00000005198	Polr2a	220kDa|Rpb1|Rpo2-1	polymerase (RNA) II (DNA directed) polypeptide A	protein-coding
mm_151203.1	chr19	53539621	53539638	+	1	NA	intron (NM_001085390, intron 3 of 3)	intron (NM_001085390, intron 3 of 3)	10311	NM_001085390	240672	Mm.482424	NM_001085390	ENSMUSG00000034765	Dusp5	Gm337	dual specificity phosphatase 5	protein-coding
mm_54981.1	chr6	48741329	48741344	-	1	NA	5' UTR (NM_008376, exon 2 of 3)	5' UTR (NM_008376, exon 2 of 3)	2289	NM_008376	16205	Mm.252599	NM_008376	ENSMUSG00000090019	Gimap1	IAP38|Imap38|imap	GTPase, IMAP family member 1	protein-coding
mm_95557.1	chr11	52311026	52311048	+	1	NA	Intergenic	Intergenic	-28023	NM_001313981	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_79049.1	chr9	46228952	46228980	+	1	NA	exon (NM_009692, exon 2 of 4)	exon (NM_009692, exon 2 of 4)	336	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2|apo-AI|apoA-I	apolipoprotein A-I	protein-coding
mm_44558.1	chr5	24602230	24602288	-	1	NA	promoter-TSS (NM_025891)	promoter-TSS (NM_025891)	-257	NM_025891	66993	Mm.436539	NM_025891	ENSMUSG00000028949	Smarcd3	1500001J14Rik|2210409C08Rik|BAF60C	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3	protein-coding
mm_154278.1	chr19	60790618	60790672	-	1	NA	promoter-TSS (NM_010123)	promoter-TSS (NM_010123)	48	NM_010123	13669	Mm.2238	NM_010123	ENSMUSG00000024991	Eif3a	A830012B05Rik|Csma|Eif3|Eif3s10|mKIAA0139	eukaryotic translation initiation factor 3, subunit A	protein-coding
mm_170686.1	chr2	130385338	130385358	-	1	NA	Intergenic	Intergenic	12281	NM_019696	56264	Mm.112701	NM_019696	ENSMUSG00000027408	Cpxm1	AA986902|Cpx-1|Cpx1|Cpxm	carboxypeptidase X 1 (M14 family)	protein-coding
mm_110660.1	chr12	59071621	59071672	-	1	NA	exon (NM_008891, exon 9 of 9)	exon (NM_008891, exon 9 of 9)	4727	NM_008891	18949	Mm.22347	NM_008891	ENSMUSG00000020994	Pnn	AU045199|D12Ertd512e	pinin	protein-coding
mm_42753.1	chr5	120812880	120812884	+	1	NA	promoter-TSS (NM_033541)	promoter-TSS (NM_033541)	244	NM_001083925	23961	Mm.233471	NM_001083925	ENSMUSG00000029605	Oas1b	Flv|L1|Mmu-L1|Oas1|Oias-2|Oias2|Wnv	2'-5' oligoadenylate synthetase 1B	protein-coding
mm_63121.1	chr7	122969848	122969858	+	1	NA	promoter-TSS (NM_175023)	promoter-TSS (NM_175023)	606	NR_045614	73951	Mm.389936	NR_045614		4930413G21Rik	-	RIKEN cDNA 4930413G21 gene	ncRNA
mm_20353.1	chr2	127831818	127831875	-	1	NA	promoter-TSS (NM_001113179)	promoter-TSS (NM_001113179)	13	NM_001113179	12235	Mm.2185	NM_009772	ENSMUSG00000027379	Bub1	AL022991|Bub1a|C80208|D2Xrf87	BUB1, mitotic checkpoint serine/threonine kinase	protein-coding
mm_91539.1	chr10	39526109	39526111	-	1	NA	intron (NM_001122892, intron 6 of 12)	intron (NM_001122892, intron 6 of 12)	-86824	NM_134000	103213	Mm.436686	NM_134000	ENSMUSG00000019842	Traf3ip2	AI429613|Act1|CIKS	TRAF3 interacting protein 2	protein-coding
mm_57439.1	chr6	124959465	124959578	-	1	NA	3' UTR (NM_012003, exon 8 of 8)	3' UTR (NM_012003, exon 8 of 8)	5876	NM_012003	26894	Mm.244536	NM_012003	ENSMUSG00000030127	Cops7a	D6Ertd35e	COP9 signalosome subunit 7A	protein-coding
mm_82238.1	chr9	3258864	3258902	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-59070	NR_027988	114673	Mm.422774	NM_053265	ENSMUSG00000042360	4930433N12Rik	-	RIKEN cDNA 4930433N12 gene	ncRNA
mm_105781.1	chr11	109771494	109771532	-	1	NA	Intergenic	Intergenic	-49257	NM_153782	208659	Mm.208662	NM_153782	ENSMUSG00000020614	Fam20a	AI606893	family with sequence similarity 20, member A	protein-coding
mm_87409.1	chr10	45807780	45807801	+	1	NA	promoter-TSS (NR_040624)	promoter-TSS (NR_040624)	86	NR_040624	320363	Mm.123343	NR_040624	ENSMUSG00000110874	D030045P18Rik	-	RIKEN cDNA D030045P18 gene	ncRNA
mm_12303.1	chr2	69109870	69109892	+	1	NA	3' UTR (NM_001347161, exon 11 of 11)	3' UTR (NM_001347161, exon 11 of 11)	-25919	NM_181547	329416	Mm.90047	NM_181547	ENSMUSG00000034738	Nostrin	Daip2|mDaIP2	nitric oxide synthase trafficker	protein-coding
mm_145800.1	chr18	65350051	65350071	+	1	NA	exon (NM_001037294, exon 4 of 13)	exon (NM_001037294, exon 4 of 13)	43827	NM_001037294	225638	Mm.296528	NM_001037294	ENSMUSG00000032845	Alpk2	Gm549|Hak	alpha-kinase 2	protein-coding
mm_72116.1	chr8	71676473	71676492	+	1	NA	promoter-TSS (NM_001190830)	promoter-TSS (NM_001190830)	99	NM_010589	16453	Mm.249645	NM_010589	ENSMUSG00000031805	Jak3	fae|wil	Janus kinase 3	protein-coding
mm_106093.1	chr11	116198660	116198663	-	1	NA	promoter-TSS (NM_027107)	promoter-TSS (NM_027107)	-194	NM_027107	69535	Mm.390347	NM_027107	ENSMUSG00000020778	Ten1	2310004N24Rik	TEN1 telomerase capping complex subunit	protein-coding
mm_156671.1	chrX	159211205	159211224	+	1	NA	Intergenic	Intergenic	-44568	NM_148945	110651	Mm.328476	NM_148945	ENSMUSG00000031309	Rps6ka3	MAPKAPK-1b|MPK-9|Rsk2|S6K-alpha3|p90RSK3|pp90RSK2	ribosomal protein S6 kinase polypeptide 3	protein-coding
mm_56454.1	chr6	97863399	97863402	-	1	NA	intron (NM_001113198, intron 1 of 9)	intron (NM_001113198, intron 1 of 9)	56342	NM_001113198	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_125574.1	chr15	59374232	59374279	+	1	NA	promoter-TSS (NM_026746)	promoter-TSS (NM_026746)	57	NM_001164604	68501	Mm.27762	NM_026746	ENSMUSG00000059586	Nsmce2	1110014D18Rik|AI661537	NSE2/MMS21 homolog, SMC5-SMC6 complex SUMO ligase	protein-coding
mm_11898.1	chr2	50066447	50066469	+	1	NA	promoter-TSS (NM_177139)	promoter-TSS (NM_177139)	29	NM_177139	320343	Mm.130607	NM_177139	ENSMUSG00000050447	Lypd6	E130115E03Rik	LY6/PLAUR domain containing 6	protein-coding
mm_18813.1	chr2	74544535	74544555	-	1	NA	intron (NM_001110209, intron 8 of 13)	intron (NM_001110209, intron 8 of 13)	34403	NM_001110209	69605	Mm.156113	NM_027133	ENSMUSG00000009207	Lnpk	2310011O18Rik|4921514L11Rik|9530051D01Rik|AI666268|Lnp|Lnpk1|Ul|ulnaless	lunapark, ER junction formation factor	protein-coding
mm_105734.1	chr11	109289541	109289585	-	1	NA	intron (NM_001165934, intron 1 of 16)	intron (NM_001165934, intron 1 of 16)	8618	NM_001165934	19739	Mm.38548	NM_011268	ENSMUSG00000020599	Rgs9	RGS9-1|Rgs9-2	regulator of G-protein signaling 9	protein-coding
mm_66411.1	chr7	44485690	44485690	-	1	NA	TTS (NR_131001)	TTS (NR_131001)	1173	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_114899.1	chr13	94462476	94462494	+	1	NA	exon (NM_009680, exon 15 of 27)	exon (NM_009680, exon 15 of 27)	103525	NM_009680	11774	Mm.21185	NM_009680	ENSMUSG00000021686	Ap3b1	AP-3|AU015684|C78395|Hps2|beta3A|pe|pearl|rim2	adaptor-related protein complex 3, beta 1 subunit	protein-coding
mm_58783.1	chr7	16098596	16098672	+	1	NA	promoter-TSS (NM_025898)	promoter-TSS (NM_025898)	-9	NM_025898	108124	Mm.104540	NM_025898	ENSMUSG00000006024	Napa	1500039N14Rik|AW209189|RA81|SNAPA|SNARE|a-SNAP|hyh	N-ethylmaleimide sensitive fusion protein attachment protein alpha	protein-coding
mm_4549.1	chr1	177442281	177442378	+	1	NA	Intergenic	CpG	-2332	NM_001012330	30928	Mm.330700	NM_013915	ENSMUSG00000063659	Zbtb18	RP58|Zfp238|Znf238	zinc finger and BTB domain containing 18	protein-coding
mm_37509.1	chr4	123859521	123859558	-	1	NA	Intergenic	Intergenic	-45474	NM_019660	56309	Mm.446553	NM_019660	ENSMUSG00000028647	Mycbp	5730488M09Rik|AW552132|AW742590|Amy-1	MYC binding protein	protein-coding
mm_166565.1	chr6	48834139	48834145	-	1	NA	intron (NM_023056, intron 6 of 6)	intron (NM_023056, intron 6 of 6)	6846	NM_023056	65963	Mm.28385	NM_023056	ENSMUSG00000029810	Tmem176b	1810009M01Rik|Clast1|Lr8	transmembrane protein 176B	protein-coding
mm_122990.1	chr14	54989128	54989140	-	1	NA	exon (NM_080728, exon 14 of 41)	exon (NM_080728, exon 14 of 41)	5415	NM_080728	140781	Mm.457983	NM_080728	ENSMUSG00000053093	Myh7	B-MHC|MyHC-I|Myhc-b|Myhcb|beta-MHC	myosin, heavy polypeptide 7, cardiac muscle, beta	protein-coding
mm_97834.1	chr11	83064783	83064802	+	1	NA	promoter-TSS (NM_011408)	promoter-TSS (NM_011408)	-320	NM_011408	20556	Mm.278689	NM_011408	ENSMUSG00000072620	Slfn2	Shlf2	schlafen 2	protein-coding
mm_146908.1	chr18	31317044	31317128	-	1	NA	promoter-TSS (NM_009065)	promoter-TSS (NM_009065)	42	NM_009065	19762	Mm.5163	NM_009065	ENSMUSG00000057455	Rit2	RIBA|Rin|Roc2	Ras-like without CAAX 2	protein-coding
mm_125385.1	chr15	40658187	40658193	+	1	NA	intron (NM_011766, intron 1 of 7)	(T)n|Simple_repeat|Simple_repeat	3148	NM_011766	22762	Mm.39496	NM_011766	ENSMUSG00000022306	Zfpm2	B330005D23Rik|FOG-2|FOG2	zinc finger protein, multitype 2	protein-coding
mm_67889.1	chr7	99382298	99382313	-	1	NA	intron (NM_201352, intron 1 of 17)	CpG	756	NM_201352	233552	Mm.286317	NM_201352	ENSMUSG00000035314	Gdpd5	BC024955|Gde2	glycerophosphodiester phosphodiesterase domain containing 5	protein-coding
mm_137643.1	chr17	28530829	28530833	+	1	NA	promoter-TSS (NM_026290)	promoter-TSS (NM_026290)	-30	NM_026290	67645	Mm.46170	NM_026290	ENSMUSG00000024223	Armc12	4930511I11Rik|AV041658	armadillo repeat containing 12	protein-coding
mm_145576.1	chr18	60963518	60963603	+	1	NA	promoter-TSS (NM_001286809)	promoter-TSS (NM_001286809)	6	NM_001286809	12322	Mm.131530	NM_009792	ENSMUSG00000024617	Camk2a	CaMKII|R74975|mKIAA0968	calcium/calmodulin-dependent protein kinase II alpha	protein-coding
mm_46493.1	chr5	105132385	105132396	-	1	NA	intron (NM_008620, intron 3 of 10)	L1M2|LINE|L1	7162	NM_008620	17472	Mm.440525	NM_008620	ENSMUSG00000079363	Gbp4	AW228052|Mag-2|Mpa-2|Mpa2	guanylate binding protein 4	protein-coding
mm_58257.1	chr6	145076107	145076107	-	1	NA	promoter-TSS (NM_007532)	promoter-TSS (NM_007532)	50	NM_007532	12035	Mm.4606	NM_007532	ENSMUSG00000030268	Bcat1	BCATc|Eca39	branched chain aminotransferase 1, cytosolic	protein-coding
mm_156668.1	chrX	159210387	159210395	+	1	NA	Intergenic	Intergenic	-45391	NM_148945	110651	Mm.328476	NM_148945	ENSMUSG00000031309	Rps6ka3	MAPKAPK-1b|MPK-9|Rsk2|S6K-alpha3|p90RSK3|pp90RSK2	ribosomal protein S6 kinase polypeptide 3	protein-coding
mm_65026.1	chr7	18432034	18432065	-	1	NA	promoter-TSS (NM_054063)	promoter-TSS (NM_054063)	6	NM_054063	114871	Mm.362025	NM_054063	ENSMUSG00000030373	Psg28	cea16	pregnancy-specific glycoprotein 28	protein-coding
mm_89735.1	chr10	99009481	99009492	+	1	NA	exon (NM_026482, exon 13 of 21)	exon (NM_026482, exon 13 of 21)	94334	NM_026482	67972	Mm.166944	NM_026482	ENSMUSG00000019943	Atp2b1	2810442I22Rik|E130111D10Rik|Pmca1	ATPase, Ca++ transporting, plasma membrane 1	protein-coding
mm_97307.1	chr11	76679832	76679840	+	1	NA	promoter-TSS (NM_177709)	promoter-TSS (NM_177709)	-37	NM_177709	237858	Mm.127006	NM_177709	ENSMUSG00000046275	Tusc5	C130069F04Rik|DSPB1|Lost1	tumor suppressor candidate 5	protein-coding
mm_70881.1	chr8	25201455	25201457	+	1	NA	promoter-TSS (NM_177089)	promoter-TSS (NM_177089)	86	NM_199323	320165	Mm.308452	NM_177089	ENSMUSG00000065954	Tacc1	4833447E04Rik|AA960202|B230378H13Rik	transforming, acidic coiled-coil containing protein 1	protein-coding
mm_39761.1	chr5	30013085	30013089	+	1	NA	promoter-TSS (NM_031168)	promoter-TSS (NM_031168)	-27	NM_001314054	16193	Mm.1019	NM_031168	ENSMUSG00000025746	Il6	Il-6	interleukin 6	protein-coding
mm_69764.1	chr7	141009797	141009815	-	1	NA	exon (NM_025378, exon 2 of 2)	exon (NM_025378, exon 2 of 2)	938	NM_025378	66141	Mm.141021	NM_025378	ENSMUSG00000025492	Ifitm3	1110004C05Rik|Cd225|Cdw217|DSPA2b|Fgls|IP15|mil-1	interferon induced transmembrane protein 3	protein-coding
mm_127292.1	chr15	100154170	100154214	+	1	NA	promoter-TSS (NM_172819)	promoter-TSS (NM_172819)	-204	NM_172819	239667	Mm.243658	NM_172819	ENSMUSG00000023026	Dip2b	4932422C22|AI317237|AI854602|mKIAA1463	disco interacting protein 2 homolog B	protein-coding
mm_146496.1	chr18	3281018	3281030	-	1	NA	5' UTR (NM_001311067, exon 1 of 4)	5' UTR (NM_001311067, exon 1 of 4)	108	NM_001311066	12916	Mm.5244	NM_013498	ENSMUSG00000063889	Crem	ICER|ICERI	cAMP responsive element modulator	protein-coding
mm_123423.1	chr14	64417802	64417833	-	1	NA	promoter-TSS (NM_001253716)	promoter-TSS (NM_001253716)	-538	NM_001347639	110265	Mm.26713	NM_026322	ENSMUSG00000054733	Msra	2310045J23Rik|6530413P12Rik|MSR-A	methionine sulfoxide reductase A	protein-coding
mm_168725.1	chr12	110695208	110695222	-	1	NA	exon (NM_010480, exon 3 of 11)	exon (NM_010480, exon 3 of 11)	1180	NM_010480	15519	Mm.1843	NM_010480	ENSMUSG00000021270	Hsp90aa1	86kDa|89kDa|AL024080|AL024147|Hsp86-1|Hsp89|Hsp90|Hspca|hsp4	heat shock protein 90, alpha (cytosolic), class A member 1	protein-coding
mm_97328.1	chr11	77009252	77009262	+	1	NA	intron (NM_010484, intron 1 of 13)	intron (NM_010484, intron 1 of 13)	10660	NM_010484	15567	Mm.300318	NM_010484	ENSMUSG00000020838	Slc6a4	5-HTT|AI323329|Htt|Sert	solute carrier family 6 (neurotransmitter transporter, serotonin), member 4	protein-coding
mm_71353.1	chr8	45658310	45658323	+	1	NA	intron (NM_001310707, intron 1 of 23)	intron (NM_001310707, intron 1 of 23)	-3677	NM_001310708	234214	Mm.211096	NM_172752	ENSMUSG00000031626	Sorbs2	2010203O03Rik|9430041O17Rik|A530071H08|Argbp2|mKIAA0777|nArgBP2	sorbin and SH3 domain containing 2	protein-coding
mm_135630.1	chr16	52301756	52301767	-	1	NA	intron (NM_009655, intron 3 of 15)	intron (NM_009655, intron 3 of 15)	151320	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_7910.1	chr1	133690003	133690016	-	1	NA	promoter-TSS (NM_001159649)	promoter-TSS (NM_001159649)	7	NM_172842	240754	Mm.36534	NM_172842	ENSMUSG00000051998	Lax1	A530029E09|E430019B13Rik	lymphocyte transmembrane adaptor 1	protein-coding
mm_148768.1	chr19	6085040	6085051	+	1	NA	promoter-TSS (NM_024231)	promoter-TSS (NM_024231)	-52	NM_026410	67849	Mm.23526	NM_026410	ENSMUSG00000024791	Cdca5	2610036L13Rik|AL024086|AW536684|C85404	cell division cycle associated 5	protein-coding
mm_38491.1	chr4	140845771	140845785	-	1	NA	promoter-TSS (NM_011059)	promoter-TSS (NM_011059)	0	NM_011059	18599	Mm.20854	NM_011059	ENSMUSG00000025329	Padi1	AV236283|Pdi1	peptidyl arginine deiminase, type I	protein-coding
mm_138578.1	chr17	35470084	35470095	+	1	NA	promoter-TSS (NM_010391)	promoter-TSS (NM_010391)	0	NM_010391	15007	Mm.88795	NM_010391	ENSMUSG00000067235	H2-Q10	H-2Q10|Q10|Qa10	histocompatibility 2, Q region locus 10	protein-coding
mm_31271.1	chr4	45342193	45342242	+	1	NA	exon (NM_153167, exon 1 of 7)	exon (NM_153167, exon 1 of 7)	116	NM_153167	242418	Mm.317668	NM_153167	ENSMUSG00000035572	Dcaf10	AA959934|Wdr32	DDB1 and CUL4 associated factor 10	protein-coding
mm_96475.1	chr11	67652718	67652766	+	1	NA	intron (NM_001109657, intron 4 of 13)	intron (NM_001109657, intron 4 of 13)	-42584	NM_009038	19674	Mm.439726	NM_009038	ENSMUSG00000020907	Rcvrn	CAR|S-modulin	recoverin	protein-coding
mm_66622.1	chr7	45475004	45475016	-	1	NA	3' UTR (NM_027903, exon 7 of 7)	3' UTR (NM_027903, exon 7 of 7)	-8112	NM_007527	12028	Mm.19904	NM_007527	ENSMUSG00000003873	Bax	-	BCL2-associated X protein	protein-coding
mm_151765.1	chr19	5272893	5272901	-	1	NA	5' UTR (NM_153129, exon 1 of 24)	5' UTR (NM_153129, exon 1 of 24)	222	NM_153129	107975	Mm.234923	NM_153129	ENSMUSG00000024855	Pacs1	AI325977	phosphofurin acidic cluster sorting protein 1	protein-coding
mm_34431.1	chr4	145670665	145670677	+	1	NA	promoter-TSS (NM_001103158)	promoter-TSS (NM_001103158)	-26	NM_001103158	100041379	Mm.276881	NM_001103158	ENSMUSG00000058186	Zfp980	Gm13242|OTTMUSG00000011070	zinc finger protein 980	protein-coding
mm_124431.1	chr14	118237017	118237035	-	1	NA	promoter-TSS (NM_177753)	promoter-TSS (NM_177753)	4	NM_177753	223227	Mm.70950	NM_177753	ENSMUSG00000061517	Sox21	Sox25	SRY (sex determining region Y)-box 21	protein-coding
mm_5070.1	chr1	195131631	195131644	+	1	NA	promoter-TSS (NM_013499)	promoter-TSS (NM_013499)	-67	NM_013499	12946	Mm.301652	NM_013499	ENSMUSG00000016481	Cr1l	Crry|Mcp|mCRY	complement component (3b/4b) receptor 1-like	protein-coding
mm_8078.1	chr1	135585489	135585516	-	1	NA	promoter-TSS (NM_173437)	promoter-TSS (NM_173437)	-147	NM_173437	215690	Mm.34977	NM_173437	ENSMUSG00000009418	Nav1	9530089B19|9930003A20Rik|C230080M11Rik|Pomfil3|Unc53h1|mKIAA1151|steerin-1	neuron navigator 1	protein-coding
mm_165616.1	chr3	57387326	57387343	+	1	NA	Intergenic	Intergenic	-38076	NM_145539	229302	Mm.26618	NM_145539	ENSMUSG00000027801	Tm4sf4	Iltmp	transmembrane 4 superfamily member 4	protein-coding
mm_46836.1	chr5	113310730	113310788	-	1	NA	promoter-TSS (NM_001254731)	promoter-TSS (NM_001254731)	27	NM_001162965	52850	Mm.200203	NM_172718	ENSMUSG00000042216	Sgsm1	2410098H20Rik|AA408781|D5Bwg1524e|E130107M15|NuIP|Rutbc2	small G protein signaling modulator 1	protein-coding
mm_135902.1	chr16	67072628	67072630	-	1	NA	intron (NM_178721, intron 1 of 9)	intron (NM_178721, intron 1 of 9)	415511	NR_040512	75501	Mm.394300	NR_040512	ENSMUSG00000092599	1700010K23Rik	-	RIKEN cDNA 1700010K23 gene	ncRNA
mm_85156.1	chr9	96333205	96333255	-	1	NA	3' UTR (NM_007502, exon 7 of 7)	3' UTR (NM_007502, exon 7 of 7)	31069	NM_007502	11933	Mm.424	NM_007502	ENSMUSG00000032412	Atp1b3	AA409958|AI664000|AW212096	ATPase, Na+/K+ transporting, beta 3 polypeptide	protein-coding
mm_104280.1	chr11	89733727	89733736	-	1	NA	Intergenic	Intergenic	-36795	NM_001327810	382543	Mm.60997	NM_172534	ENSMUSG00000047773	Ankfn1	4932411E22Rik|Gm1175|nmf9	ankyrin-repeat and fibronectin type III domain containing 1	protein-coding
mm_164273.1	chr15	101740241	101740249	+	1	NA	intron (NM_019956, intron 2 of 8)	intron (NM_019956, intron 2 of 8)	2852	NM_019956	56735	Mm.358677	NM_019956	ENSMUSG00000051879	Krt71	AA589543|Ca|Cal4|Cu|Krt2-6g|mK6irs|mK6irs1	keratin 71	protein-coding
mm_113336.1	chr13	31625794	31625800	+	1	NA	promoter-TSS (NM_010225)	promoter-TSS (NM_010225)	-19	NM_010225	14238	Mm.125548	NM_010225	ENSMUSG00000038402	Foxf2	FREAC2|Fkh20|LUN	forkhead box F2	protein-coding
mm_111789.1	chr12	104856493	104856505	-	1	NA	intron (NM_001040682, intron 1 of 12)	intron (NM_001040682, intron 1 of 12)	8577	NR_104436	94040	Mm.244078	NM_053155	ENSMUSG00000021097	Clmn	9330188N17Rik|AI428889|AI788815|mKIAA1188	calmin	protein-coding
mm_95941.1	chr11	58384608	58384620	+	1	NA	exon (NM_001083884, exon 5 of 7)	exon (NM_001083884, exon 5 of 7)	3968	NM_001330197	70163	Mm.24119	NM_027339	ENSMUSG00000013643	Lypd8	2210415F13Rik	LY6/PLAUR domain containing 8	protein-coding
mm_137553.1	chr17	27561364	27561377	+	1	NA	intron (NM_001166546, intron 3 of 4)	intron (NM_001166546, intron 3 of 4)	4357	NM_001002895	106672	Mm.61488	NM_001002895	ENSMUSG00000062753	AI413582	AI854251	expressed sequence AI413582	protein-coding
mm_171248.1	chr3	78967165	78967182	-	1	NA	Intergenic	Intergenic	177714	NM_001310536	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_50012.1	chr6	41062322	41062338	+	1	NA	Intergenic	Intergenic	-26821	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_70366.1	chr8	8693497	8693498	+	1	NA	Intergenic	MER92B|LTR|ERV1	-2960	NM_176849	234023	Mm.251655	NM_176849	ENSMUSG00000040459	Arglu1	9430010O03Rik|C130008N12	arginine and glutamate rich 1	protein-coding
mm_88241.1	chr10	71704283	71704294	+	1	NA	Intergenic	Intergenic	276402	NR_003644	108950	Mm.212793	NM_175390	ENSMUSG00000043859	1700049L16Rik	-	hematological and neurological expressed 1-like pseudogene	pseudo
mm_99440.1	chr11	102433031	102433051	+	1	NA	exon (NM_008175, exon 2 of 13)	exon (NM_008175, exon 2 of 13)	2719	NM_008175	14824	Mm.1568	NM_008175	ENSMUSG00000034708	Grn	Pgrn|epithelin	granulin	protein-coding
mm_133280.1	chr16	77421624	77421637	+	1	NA	intron (NR_015543, intron 2 of 4)	intron (NR_015543, intron 2 of 4)	92302	NR_015543	77994	Mm.394688	NR_015543	ENSMUSG00000090386	Mir99ahg	2810055G20Rik|D730043B02Rik	Mir99a and Mirlet7c-1 host gene (non-protein coding)	ncRNA
mm_51941.1	chr6	91705851	91705879	+	1	NA	intron (NM_009320, intron 2 of 14)	ID_B1|SINE|B4	21798	NM_009320	21366	Mm.395650	NM_009320	ENSMUSG00000030096	Slc6a6	AA589629|C80501|Taut	solute carrier family 6 (neurotransmitter transporter, taurine), member 6	protein-coding
mm_32222.1	chr4	101717634	101717644	+	1	NA	5' UTR (NM_001122899, exon 1 of 19)	5' UTR (NM_001122899, exon 1 of 19)	232	NM_010704	16847	Mm.259282	NM_010704	ENSMUSG00000057722	Lepr	LEPROT|Leprb|Modb1|OB-RGRP|Obr|db|diabetes|obese-like|obl	leptin receptor	protein-coding
mm_164215.1	chr15	83790438	83790441	+	1	NA	intron (NM_172610, intron 1 of 6)	intron (NM_172610, intron 1 of 6)	10416	NM_172610	223726	Mm.36395	NM_172610	ENSMUSG00000041708	Mpped1	6230403M19|AW456965|D15Bwg0669e	metallophosphoesterase domain containing 1	protein-coding
mm_25763.1	chr3	124385668	124385680	+	1	NA	Intergenic	Intergenic	40354	NM_027939	71824	Mm.331353	NM_027939	ENSMUSG00000027973	1700006A11Rik	-	RIKEN cDNA 1700006A11 gene	protein-coding
mm_155390.1	chrX	71962956	71962968	+	1	NA	promoter-TSS (NM_001081135)	promoter-TSS (NM_001081135)	-20	NM_001081135	208748	Mm.25626	NM_001081135	ENSMUSG00000033361	Prrg3	Gm368	proline rich Gla (G-carboxyglutamic acid) 3 (transmembrane)	protein-coding
mm_3036.1	chr1	134037491	134037530	+	1	NA	promoter-TSS (NM_021355)	promoter-TSS (NM_021355)	-5	NM_021355	14264	Mm.287146	NM_021355	ENSMUSG00000041559	Fmod	AI131919|AU041740|SLRR2E	fibromodulin	protein-coding
mm_130683.1	chr15	100681178	100681264	-	1	NA	exon (NM_033612, exon 6 of 8)	exon (NM_033612, exon 6 of 8)	6699	NM_033612	109901	Mm.2131	NM_033612	ENSMUSG00000023031	Cela1	1810009A17Rik|1810062B19Rik|Ela-1|Ela1|PC-TsF	chymotrypsin-like elastase family, member 1	protein-coding
mm_83060.1	chr9	37545314	37545325	-	1	NA	3' UTR (NM_022029, exon 4 of 4)	3' UTR (NM_022029, exon 4 of 4)	6064	NM_020518	57276	Mm.27478	NM_020518	ENSMUSG00000001943	Vsig2	1190004B15Rik|2210413P10Rik|AU040484|CTX|Ctm	V-set and immunoglobulin domain containing 2	protein-coding
mm_125518.1	chr15	57694791	57694837	+	1	NA	5' UTR (NM_199449, exon 1 of 4)	5' UTR (NM_199449, exon 1 of 4)	147	NM_199449	387609	Mm.36557	NM_199449	ENSMUSG00000071757	Zhx2	Afr-1|Afr1|Raf|mKIAA0854	zinc fingers and homeoboxes 2	protein-coding
mm_170471.1	chr19	11121018	11121035	+	1	NA	intron (NM_027058, intron 1 of 6)	intron (NM_027058, intron 1 of 6)	9852	NM_027058	69369	Mm.391200	NM_027058	ENSMUSG00000024729	1700017D01Rik	-	RIKEN cDNA 1700017D01 gene	protein-coding
mm_156444.1	chrX	142680811	142680841	+	1	NA	promoter-TSS (NM_001199357)	promoter-TSS (NM_001199357)	-574	NM_177592	209497	Mm.249648	NM_177592	ENSMUSG00000047045	Tmem164	AI316850|AI852450|AW547186|F730011B02	transmembrane protein 164	protein-coding
mm_85869.1	chr9	110880053	110880087	-	1	NA	promoter-TSS (NM_001146059)	promoter-TSS (NM_001146059)	13	NM_146260	20776	Mm.390229	NM_146260	ENSMUSG00000049555	Tmie	5131400L21Rik|Mm.87012|sr	transmembrane inner ear	protein-coding
mm_168532.1	chr1	161035549	161035550	+	1	NA	non-coding (NR_002840, exon 1 of 4)	non-coding (NR_002840, exon 1 of 4)	383	NR_002840	14455	Mm.270065	NR_002840	ENSMUSG00000053332	Gas5	Gas-5|Mir5117|Snhg2	growth arrest specific 5	ncRNA
mm_136384.1	chr16	93123093	93123096	-	1	NA	Intergenic	Intergenic	230095	NR_040486	69857	Mm.81192	NR_040486	ENSMUSG00000100277	1810053B23Rik	1810008L18Rik|1810056K14Rik	RIKEN cDNA 1810053B23 gene	ncRNA
mm_99873.1	chr11	109400822	109400840	+	1	NA	3' UTR (NM_010303, exon 4 of 4)	3' UTR (NM_010303, exon 4 of 4)	-25115	NM_025275	13929	Mm.211850	NM_025275	ENSMUSG00000020610	Amz2	AA408420|ESTM12|X83328	archaelysin family metallopeptidase 2	protein-coding
mm_64924.1	chr7	16259186	16259201	-	1	NA	5' UTR (NM_001173550, exon 1 of 2)	5' UTR (NM_001173550, exon 1 of 2)	145	NM_001173550	12273	Mm.247623	NM_007577	ENSMUSG00000049130	C5ar1	C5aR|C5r1|Cd88|D7Msu1	complement component 5a receptor 1	protein-coding
mm_17670.1	chr2	32137906	32137982	-	1	NA	Intergenic	CpG	-13204	NM_172661	227723	Mm.25504	NM_172661	ENSMUSG00000039262	Prrc2b	5830434P21Rik|AI173903|Bat2l|Bat2l1|D430039P21|mKIAA0515	proline-rich coiled-coil 2B	protein-coding
mm_65974.1	chr7	30442255	30442277	-	1	NA	exon (NM_007467, exon 6 of 17)	exon (NM_007467, exon 6 of 17)	3316	NM_007467	11803	Mm.2381	NM_007467	ENSMUSG00000006651	Aplp1	-	amyloid beta (A4) precursor-like protein 1	protein-coding
mm_104703.1	chr11	97996172	97996190	-	1	NA	promoter-TSS (NM_207231)	promoter-TSS (NM_207231)	-8	NM_207231	217151	Mm.277896	NM_207231	ENSMUSG00000038352	Arl5c	Arl12|BC065791	ADP-ribosylation factor-like 5C	protein-coding
mm_89633.1	chr10	96401057	96401068	+	1	NA	Intergenic	Intergenic	174855	NR_110448	74881	Mm.410819	NR_110448		4930459C07Rik	-	RIKEN cDNA 4930459C07 gene	ncRNA
mm_41599.1	chr5	96163216	96163222	+	1	NA	Intergenic	Intergenic	-1229	NM_144910	231464	Mm.28374	NM_144910	ENSMUSG00000034724	Cnot6l	4932442K20Rik	CCR4-NOT transcription complex, subunit 6-like	protein-coding
mm_47629.1	chr5	125294063	125294080	-	1	NA	exon (NM_001205082, exon 7 of 12)	exon (NM_001205082, exon 7 of 12)	47023	NM_016741	20778	Mm.282242	NM_016741	ENSMUSG00000037936	Scarb1	AI120173|CD36|Cd36l1|Chohd1|Cla-1|Cla1|D5Ertd460e|Hdlq1|Hlb398|SR-B1|SR-BI|SRBI|Srb1|mSR-BI	scavenger receptor class B, member 1	protein-coding
mm_26127.1	chr3	137867879	137867913	+	1	NA	TTS (NM_016750)	TTS (NM_016750)	221	NM_001033155	70604	Mm.256488	NM_001033155	ENSMUSG00000074212	Dnajb14	5730496F10Rik	DnaJ heat shock protein family (Hsp40) member B14	protein-coding
mm_18700.1	chr2	71663117	71663165	-	1	NA	intron (NR_039557, intron 2 of 3).2	intron (NR_039557, intron 2 of 3).2	-56276	NR_037979	381371	Mm.330284	NM_201366	ENSMUSG00000064263	Platr26	Gm1631	pluripotency associated transcript 26	ncRNA
mm_88489.1	chr10	77715769	77715773	+	1	NA	promoter-TSS (NM_001205035)	promoter-TSS (NM_001205035)	-36	NM_001205035	100502921	Mm.486156	NM_001205035	ENSMUSG00000094146	Gm10142	ENSMUSG00000064028	predicted gene 10142	protein-coding
mm_158989.1	chr1	133365308	133365308	+	1	NA	intron (NM_175443, intron 1 of 7)	intron (NM_175443, intron 1 of 7)	1736	NM_175443	214253	Mm.52111	NM_175443	ENSMUSG00000070644	Etnk2	4933417N20Rik|AI197444|EKI 2|Eki2|Tuc1	ethanolamine kinase 2	protein-coding
mm_78042.1	chr9	14500612	14500620	+	1	NA	promoter-TSS (NM_023153)	promoter-TSS (NM_023153)	-3	NM_023153	66070	Mm.245938	NM_023153	ENSMUSG00000004096	Cwc15	0610040D20Rik|2900052N06Rik|Ed1|c11orf5|mED1	CWC15 spliceosome-associated protein	protein-coding
mm_139398.1	chr17	52304541	52304549	+	1	NA	Intergenic	Intergenic	-298164	NM_001031811	211468	Mm.399068	NM_001031811	ENSMUSG00000035580	Kcnh8	C130090D05Rik|ELK|ELK1|ELK3|Kv12.1	potassium voltage-gated channel, subfamily H (eag-related), member 8	protein-coding
mm_51280.1	chr6	72153733	72153747	+	1	NA	3' UTR (NM_011375, exon 7 of 7)	3' UTR (NM_011375, exon 7 of 7)	-30543	NR_045165	71265	Mm.442035	NR_045163	ENSMUSG00000108709	4933431G14Rik	4930565C19Rik	RIKEN cDNA 4933431G14 gene	ncRNA
mm_9597.1	chr1	175479411	175479424	-	1	NA	intron (NM_001347195, intron 2 of 17)	intron (NM_001347195, intron 2 of 17)	13128	NM_011880	24012	Mm.7956	NM_011880	ENSMUSG00000026527	Rgs7	-	regulator of G protein signaling 7	protein-coding
mm_168578.1	chr11	71659047	71659064	-	1	NA	Intergenic	ERVB7_1-LTR_MM|LTR|ERVK	-91648	NM_177618	216881	Mm.48648	NM_177618	ENSMUSG00000020811	Wscd1	mKIAA0523	WSC domain containing 1	protein-coding
mm_140111.1	chr17	78835529	78835612	+	1	NA	promoter-TSS (NM_181649)	promoter-TSS (NM_181649)	54	NM_181649	53951	Mm.220253	NM_181649	ENSMUSG00000050668	Gpatch11	2310002B06Rik|C80922|Ccdc75|L26697	G patch domain containing 11	protein-coding
mm_113187.1	chr13	24937209	24937219	+	1	NA	promoter-TSS (NR_102323)	promoter-TSS (NR_102323)	-187	NR_102323	493800	Mm.458692	NR_102323		9330162012Rik	-	cDNA RIKEN 9330162012 gene	ncRNA
mm_49503.1	chr6	29773007	29773010	+	1	NA	intron (NM_001171000, intron 1 of 16)	B1F1|SINE|Alu	4565	NM_001171000	74340	Mm.210899	NM_021414	ENSMUSG00000029772	Ahcyl2	4631427C17Rik|AI227036|Adohcyase3|mKIAA0828	S-adenosylhomocysteine hydrolase-like 2	protein-coding
mm_85811.1	chr9	110387709	110387729	-	1	NA	exon (NM_001081043, exon 20 of 25)	exon (NM_001081043, exon 20 of 25)	20491	NM_001081043	104831	Mm.335477	NM_001081043	ENSMUSG00000036057	Ptpn23	AI462446|PTP-TD14	protein tyrosine phosphatase, non-receptor type 23	protein-coding
mm_44204.1	chr5	3803063	3803079	-	1	NA	promoter-TSS (NM_001003909)	promoter-TSS (NM_001003909)	53	NM_001289528	70797	Mm.130148	NM_001003909	ENSMUSG00000040351	Ankib1	2310061P20Rik|4631416I11Rik|AW494740|C80642|mKIAA1386	ankyrin repeat and IBR domain containing 1	protein-coding
mm_45256.1	chr5	63650310	63650316	-	1	NA	exon (NM_177006, exon 1 of 7)	exon (NM_177006, exon 1 of 7)	1210	NM_177006	319807	Mm.319487	NM_028470	ENSMUSG00000090061	Nwd2	3110047P20Rik|B830017A01Rik|Hn1-ps2|mKIAA1239	NACHT and WD repeat domain containing 2	protein-coding
mm_130385.1	chr15	97857536	97857562	-	1	NA	exon (NM_009504, exon 10 of 10)	exon (NM_009504, exon 10 of 10)	-13047	NM_001204278	56233	Mm.384027	NM_019572	ENSMUSG00000022475	Hdac7	5830434K02Rik|HD7|HD7a|Hdac7a|mFLJ00062	histone deacetylase 7	protein-coding
mm_63198.1	chr7	125630647	125630660	+	1	NA	intron (NM_021887, intron 7 of 8)	intron (NM_021887, intron 7 of 8)	27224	NM_021887	60504	Mm.155643	NM_021887	ENSMUSG00000030745	Il21r	NILR	interleukin 21 receptor	protein-coding
mm_164833.1	chr18	38464594	38464607	+	1	NA	TTS (NM_022996)	TTS (NM_022996)	45625	NM_022996	65113	Mm.102496	NM_022996	ENSMUSG00000024425	Ndfip1	0610010M22Rik|N4wbp5	Nedd4 family interacting protein 1	protein-coding
mm_60235.1	chr7	43695046	43695068	+	1	NA	3' UTR (NM_174866, exon 5 of 5)	3' UTR (NM_174866, exon 5 of 5)	4639	NM_174866	317653	Mm.247377	NM_174866	ENSMUSG00000044737	Klk14	GK14	kallikrein related-peptidase 14	protein-coding
mm_11558.1	chr2	32757238	32757299	+	1	NA	promoter-TSS (NM_152800)	promoter-TSS (NM_152800)	34	NM_152800	30933	Mm.200695	NM_152800	ENSMUSG00000009563	Tor2a	Prosalusin	torsin family 2, member A	protein-coding
mm_31163.1	chr4	43443080	43443090	+	1	NA	5' UTR (NM_011571, exon 1 of 10)	5' UTR (NM_011571, exon 1 of 10)	808	NM_011571	21754	Mm.485441	NM_011571	ENSMUSG00000028458	Tesk1	AI326901	testis specific protein kinase 1	protein-coding
mm_163958.1	chr14	54894047	54894049	+	1	NA	promoter-TSS (NM_019402)	promoter-TSS (NM_019402)	-95	NM_019402	54196	Mm.7723	NM_019402	ENSMUSG00000022194	Pabpn1	PAB2|Pabp3|mPABII	poly(A) binding protein, nuclear 1	protein-coding
mm_71626.1	chr8	57436458	57436462	+	1	NA	Intergenic	Intergenic	-19463	NM_009136	20284	Mm.12886	NM_009136	ENSMUSG00000031610	Scrg1	AW124307	scrapie responsive gene 1	protein-coding
mm_100814.1	chr11	5099324	5099356	-	1	NA	promoter-TSS (NM_177370)	promoter-TSS (NM_177370)	67	NM_177370	279766	Mm.260866	NM_177370	ENSMUSG00000034175	Rhbdd3	Ptag	rhomboid domain containing 3	protein-coding
mm_92707.1	chr10	80754915	80754938	-	1	NA	promoter-TSS (NM_199322)	promoter-TSS (NM_199322)	-280	NM_199322	208266	Mm.152371	NM_199322	ENSMUSG00000061589	Dot1l	A630076O07|AW907654|Dot1|KMT4|mDot1	DOT1-like, histone H3 methyltransferase (S. cerevisiae)	protein-coding
mm_145478.1	chr18	60376518	60376545	+	1	NA	intron (NM_021792, intron 1 of 1)	RMER17A|LTR|ERVK	502	NM_001146275	60440	Mm.261140	NM_021792	ENSMUSG00000054072	Iigp1	2900074L10Rik|AI046432|AW111922|Ifgga1|Iigp|Irga6	interferon inducible GTPase 1	protein-coding
mm_13924.1	chr2	120692994	120693009	+	1	NA	Intergenic	Intergenic	38516	NM_026891	68968	Mm.2289	NM_026891	ENSMUSG00000027284	Cdan1	1500015A01Rik|AI448026|AW492297|CDA-I|CDA1|CDAI	congenital dyserythropoietic anemia, type I (human)	protein-coding
mm_84365.1	chr9	64810896	64810906	-	1	NA	promoter-TSS (NM_001162917)	promoter-TSS (NM_001162917)	-110	NM_001162917	102442	Mm.222473	NM_176935	ENSMUSG00000053641	Dennd4a	AI115600|AI851943|F730015K02Rik	DENN/MADD domain containing 4A	protein-coding
mm_35770.1	chr4	46389104	46389123	-	1	NA	intron (NM_001347095, intron 1 of 4)	CpG	310	NM_029086	74753	Mm.45973	NM_029086	ENSMUSG00000028331	Trmo	5830415F09Rik|AV014846|Nap1	tRNA methyltransferase O	protein-coding
mm_41725.1	chr5	102481547	102481560	+	1	NA	5' UTR (NM_029270, exon 1 of 10)	5' UTR (NM_029270, exon 1 of 10)	162	NM_029270	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding
mm_22919.1	chr3	31095053	31095123	+	1	NA	promoter-TSS (NM_001039090)	promoter-TSS (NM_001039090)	30	NM_001039090	20482	Mm.15406	NM_011386	ENSMUSG00000027660	Skil	Skir|SnoN|sno	SKI-like	protein-coding
mm_29485.1	chr3	115714803	115714813	-	1	NA	5' UTR (NM_007901, exon 1 of 2)	5' UTR (NM_007901, exon 1 of 2)	247	NM_007901	13609	Mm.982	NM_007901	ENSMUSG00000045092	S1pr1	AI849002|Edg1|Lpb1|S1p|S1p1	sphingosine-1-phosphate receptor 1	protein-coding
mm_24661.1	chr3	94484339	94484351	+	1	NA	intron (NR_110353, intron 1 of 11)	intron (NR_110353, intron 1 of 11)	1623	NR_110353	78784	Mm.44292	NM_172434	ENSMUSG00000028137	Celf3	4930415M08Rik|BRUNOL1|CAGH4|ERDA4|Tnrc4	CUGBP, Elav-like family member 3	protein-coding
mm_62283.1	chr7	99859060	99859120	+	1	NA	promoter-TSS (NM_001164258)	promoter-TSS (NM_001164258)	-128	NM_001164258	446101	Mm.440757	NM_001164258	ENSMUSG00000035211	Xrra1	AI449753	X-ray radiation resistance associated 1	protein-coding
mm_7626.1	chr1	127537440	127537446	-	1	NA	intron (NM_028135, intron 4 of 7)	intron (NM_028135, intron 4 of 7)	140578	NM_028135	72160	Mm.281287	NM_028135	ENSMUSG00000026347	Tmem163	2610024A01Rik|SV31	transmembrane protein 163	protein-coding
mm_36942.1	chr4	108780783	108780803	-	1	NA	intron (NM_001347163, intron 1 of 18)	CpG	295	NM_001347163	230597	Mm.196776	NM_183300	ENSMUSG00000034557	Zfyve9	Madhip|NSP|SARA|SMADIP	zinc finger, FYVE domain containing 9	protein-coding
mm_42116.1	chr5	110839974	110840022	+	1	NA	promoter-TSS (NM_016681)	promoter-TSS (NM_016681)	-19	NM_016681	50883	Mm.279308	NM_016681	ENSMUSG00000029521	Chek2	CHK2|Cds1|HUCDS1|Rad53	checkpoint kinase 2	protein-coding
mm_76272.1	chr8	84105007	84105017	-	1	NA	promoter-TSS (NM_172502)	promoter-TSS (NM_172502)	-250	NM_172502	212123	Mm.260557	NM_172502	ENSMUSG00000037103	Dcaf15	6720484B16	DDB1 and CUL4 associated factor 15	protein-coding
mm_165731.1	chr3	106349647	106349648	-	1	NA	Intergenic	Intergenic	56535	NM_178412	229688	Mm.261645	NM_178412	ENSMUSG00000027902	Chil6	BYm|Chil8	chitinase-like 6	protein-coding
mm_155168.1	chrX	53273419	53273429	+	1	NA	promoter-TSS (NM_028671)	promoter-TSS (NM_028671)	-9	NM_028671	73866	Mm.84527	NM_028671	ENSMUSG00000036013	Fam122c	4930432H15Rik|4930527G05Rik	family with sequence similarity 122, member C	protein-coding
mm_65155.1	chr7	19629356	19629451	-	1	NA	promoter-TSS (NM_009046)	promoter-TSS (NM_009046)	35	NM_001290457	19698	Mm.1741	NM_009046	ENSMUSG00000002983	Relb	shep	avian reticuloendotheliosis viral (v-rel) oncogene related B	protein-coding
mm_78563.1	chr9	35740983	35740989	+	1	NA	promoter-TSS (NM_001167588)	promoter-TSS (NM_001167588)	-63	NM_001167588	100312949	Mm.475848	NM_001167588	ENSMUSG00000091174	Gm17677	Pate-n|Pate10	predicted gene, 17677	protein-coding
mm_33315.1	chr4	129072162	129072165	+	1	NA	intron (NM_029219, intron 2 of 8)	intron (NM_029219, intron 2 of 8)	13892	NM_029219	75234	Mm.259672	NM_029219	ENSMUSG00000028793	Rnf19b	4930534K13Rik|4930555L03Rik|Ibrdc3	ring finger protein 19B	protein-coding
mm_17273.1	chr2	26091934	26091959	-	1	NA	5' UTR (NM_001037098, exon 1 of 6)	5' UTR (NM_001037098, exon 1 of 6)	450	NM_001037098	67991	Mm.131074	NM_026495	ENSMUSG00000026932	Nacc2	0610020I02Rik|AI448087|Btbd14a|C030048H19Rik	nucleus accumbens associated 2, BEN and BTB (POZ) domain containing	protein-coding
mm_55905.1	chr6	83703509	83703514	-	1	NA	non-coding (NR_002873, exon 2 of 2)	non-coding (NR_002873, exon 2 of 2)	7295	NR_075094	574519	Mm.487605	NR_002871	ENSMUSG00000085794	Vax2os	Vas2os|Vax2os1|Vax2os2	ventral anterior homeobox 2, opposite strand	ncRNA
mm_34653.1	chr4	150854054	150854063	+	1	NA	intron (NR_040649, intron 1 of 3)	intron (NR_040649, intron 1 of 3)	891	NR_040649	73348	Mm.396218	NR_040649	ENSMUSG00000078492	1700045H11Rik	-	RIKEN cDNA 1700045H11 gene	ncRNA
mm_791.1	chr1	45337418	45337439	+	1	NA	exon (NM_009930, exon 31 of 51)	exon (NM_009930, exon 31 of 51)	25890	NM_009930	12825	Mm.249555	NM_009930	ENSMUSG00000026043	Col3a1	AW550625|Col3a-1|Tsk-2|Tsk2	collagen, type III, alpha 1	protein-coding
mm_149328.1	chr19	10842972	10842993	+	1	NA	5' UTR (NM_023044, exon 1 of 8)	5' UTR (NM_023044, exon 1 of 8)	438	NM_023044	65221	Mm.27387	NM_023044	ENSMUSG00000024737	Slc15a3	Ci1|cI-1	solute carrier family 15, member 3	protein-coding
mm_131531.1	chr16	17646704	17646709	+	1	NA	exon (NM_001166164, exon 1 of 8)	exon (NM_001166164, exon 1 of 8)	236	NM_001166164	72315	Mm.297777	NM_001166164	ENSMUSG00000041617	Ccdc74a	2310015A05Rik	coiled-coil domain containing 74A	protein-coding
mm_35741.1	chr4	45346623	45346657	-	1	NA	intron (NM_153167, intron 1 of 6)	LSU-rRNA_Hsa|rRNA|rRNA	4539	NM_153167	242418	Mm.317668	NM_153167	ENSMUSG00000035572	Dcaf10	AA959934|Wdr32	DDB1 and CUL4 associated factor 10	protein-coding
mm_63733.1	chr7	130875396	130875437	+	1	NA	intron (NM_001346515, intron 1 of 12)	intron (NM_001346515, intron 1 of 12)	9506	NM_133942	101476	Mm.323554	NM_133942	ENSMUSG00000040268	Plekha1	AA960558|C920009D07Rik|TAPP1	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 1	protein-coding
mm_18498.1	chr2	62610471	62610492	-	1	NA	exon (NM_027835, exon 7 of 16)	exon (NM_027835, exon 7 of 16)	35774	NM_027835	71586	Mm.136224	NM_027835	ENSMUSG00000026896	Ifih1	9130009C22Rik|Helicard|Hlcd|MDA5|RLR-2	interferon induced with helicase C domain 1	protein-coding
mm_104974.1	chr11	100207508	100207526	-	1	NA	promoter-TSS (NM_016958)	promoter-TSS (NM_016958)	-7	NM_001313956	16664	Mm.439898	NM_016958	ENSMUSG00000045545	Krt14	AI626930|CK-14|K14|Krt-1.14|Krt1-14	keratin 14	protein-coding
mm_50306.1	chr6	47813759	47813787	+	1	NA	promoter-TSS (NM_009787)	promoter-TSS (NM_009787)	-261	NM_009787	12304	Mm.2442	NM_009787	ENSMUSG00000025823	Pdia4	AI987846|Cai|ERp-72|Erp72	protein disulfide isomerase associated 4	protein-coding
mm_142919.1	chr17	53689267	53689309	-	1	NA	promoter-TSS (NM_028232)	promoter-TSS (NM_028232)	27	NM_028232	72415	Mm.153202	NM_028232	ENSMUSG00000023940	Sgol1	3300001M08Rik|C81037|Sgo1	shugoshin-like 1 (S. pombe)	protein-coding
mm_17993.1	chr2	38149748	38149756	-	1	NA	intron (NM_146122, intron 3 of 21)	AT_rich|Low_complexity|Low_complexity	137632	NM_146122	227801	Mm.314245	NM_146122	ENSMUSG00000035392	Dennd1a	6030446I19Rik|connecdenn	DENN/MADD domain containing 1A	protein-coding
mm_110857.1	chr12	73325456	73325493	-	1	NA	intron (NM_001037717, intron 5 of 15)	intron (NM_001037717, intron 5 of 15)	38626	NM_001037717	625098	Mm.32075	NM_001037717	ENSMUSG00000044712	Slc38a6	AW322671|EG625098	solute carrier family 38, member 6	protein-coding
mm_128235.1	chr15	36608368	36608377	-	1	NA	exon (NM_008774, exon 1 of 15)	exon (NM_008774, exon 1 of 15)	601	NM_008774	18458	Mm.371570	NM_008774	ENSMUSG00000022283	Pabpc1	PABP|Pabp1|PabpI|Pabpl1|ePAB	poly(A) binding protein, cytoplasmic 1	protein-coding
mm_139346.1	chr17	50239401	50239407	+	1	NA	non-coding (NR_131975, exon 1 of 2)	non-coding (NR_131975, exon 1 of 2)	196	NR_131975	446210	Mm.378184	NM_001004437	ENSMUSG00000067103	AY702103	STDP2	cDNA sequence AY702103	ncRNA
mm_171895.1	chr5	39798246	39798249	+	1	NA	Intergenic	Intergenic	-153616	NM_010474	15476	Mm.12559	NM_010474	ENSMUSG00000051022	Hs3st1	3-Ost|D5Wsu110e|Hsg3ost	heparan sulfate (glucosamine) 3-O-sulfotransferase 1	protein-coding
mm_132204.1	chr16	32551817	32551820	+	1	NA	Intergenic	Lx8|LINE|L1	55537	NM_199309	245308	Mm.76859	NM_199309	ENSMUSG00000052363	Zdhhc19	Gm1744|Gm616	zinc finger, DHHC domain containing 19	protein-coding
mm_172740.1	chr8	7856494	7856498	-	1	NA	Intergenic	ERVB7_1-LTR_MM|LTR|ERVK	804277	NM_010111	13642	Mm.209813	NM_010111	ENSMUSG00000001300	Efnb2	ELF-2|Epl5|Eplg5|Htk-L|LERK-5|Lerk5|NLERK-1	ephrin B2	protein-coding
mm_29775.1	chr3	127282399	127282401	-	1	NA	intron (NM_001327938, intron 1 of 47)	intron (NM_001327938, intron 1 of 47)	121095	NR_105029	100862268	Mm.444603	NR_105029	ENSMUSG00000097456	LOC100862268	-	uncharacterized LOC100862268	ncRNA
mm_167508.1	chr9	13317584	13317589	+	1	NA	Intergenic	B4A|SINE|B4	70630	NM_025534	66396	Mm.290620	NM_025534	ENSMUSG00000079084	Ccdc82	2310043N13Rik	coiled-coil domain containing 82	protein-coding
mm_67816.1	chr7	98164720	98164724	-	1	NA	intron (NM_007602, intron 1 of 12)	intron (NM_007602, intron 1 of 12)	-2380	NM_001301250	12337	Mm.326847	NM_007602	ENSMUSG00000035547	Capn5	nCL-3	calpain 5	protein-coding
mm_71768.1	chr8	66431371	66431372	+	1	NA	intron (NM_175188, intron 6 of 7)	intron (NM_175188, intron 6 of 7)	45070	NM_001166375	72925	Mm.380457	NM_175188	ENSMUSG00000036469	March1	2900024D24Rik|BB085186	membrane-associated ring finger (C3HC4) 1	protein-coding
mm_14732.1	chr2	144270879	144270949	+	1	NA	promoter-TSS (NM_024225)	promoter-TSS (NM_024225)	10	NM_001289630	74528	Mm.386817	NM_028984	ENSMUSG00000027424	Mgme1	8430406I07Rik|AI426476	mitochondrial genome maintainance exonuclease 1	protein-coding
mm_90934.1	chr10	12869490	12869517	-	1	NA	Intergenic	CpG	-7768	NM_011682	22288	Mm.331784	NM_011682	ENSMUSG00000019820	Utrn	AA589569|DRP|Dmdl	utrophin	protein-coding
mm_99090.1	chr11	99665254	99665256	+	1	NA	3' UTR (NM_026834, exon 1 of 1)	3' UTR (NM_026834, exon 1 of 1)	705	NM_026834	68768	Mm.416844	NM_026834	ENSMUSG00000075566	Krtap4-6	1110054P19Rik	keratin associated protein 4-6	protein-coding
mm_21845.1	chr2	165852203	165852219	-	1	NA	intron (NM_001252584, intron 2 of 22)	intron (NM_001252584, intron 2 of 22)	5962	NM_001252585	228880	Mm.227598	NM_027230	ENSMUSG00000039671	Zmynd8	1110013E22Rik|2010005I16Rik|3632413B07Rik|AI316811|AL024039|Prkcbp1|RACK7	zinc finger, MYND-type containing 8	protein-coding
mm_125274.1	chr15	36179668	36179701	+	1	NA	5' UTR (NM_012031, exon 1 of 19)	5' UTR (NM_012031, exon 1 of 19)	154	NM_012031	26942	Mm.295539	NM_012031	ENSMUSG00000037617	Spag1	tpis	sperm associated antigen 1	protein-coding
mm_120342.1	chr14	63606492	63606527	+	1	NA	promoter-TSS (NM_173393)	promoter-TSS (NM_173393)	-21	NM_173393	219149	Mm.32071	NM_173393	ENSMUSG00000035067	Xkr6	2700008G24Rik|BC024502|Xrg6	X-linked Kx blood group related 6	protein-coding
mm_109891.1	chr12	7380309	7380321	-	1	NA	promoter-TSS (NR_045045)	promoter-TSS (NR_045045)	15	NR_045045	73575	Mm.179463	NR_045045	ENSMUSG00000102096	1700101O22Rik	-	RIKEN cDNA 1700101O22 gene	ncRNA
mm_65827.1	chr7	29179188	29179224	-	1	NA	exon (NM_026545, exon 2 of 7)	exon (NM_026545, exon 2 of 7)	1467	NM_026545	57296	Mm.273152	NM_026545	ENSMUSG00000030591	Psmd8	6720456J22Rik|AA407360|AL033291|AL033322|AL033323|C76433	proteasome (prosome, macropain) 26S subunit, non-ATPase, 8	protein-coding
mm_135580.1	chr16	50432304	50432314	-	1	NA	promoter-TSS (NM_027444)	promoter-TSS (NM_027444)	80	NM_027444	70508	Mm.28940	NM_027444	ENSMUSG00000022641	Bbx	5530401J07Rik|5730403O13Rik	bobby sox HMG box containing	protein-coding
mm_47092.1	chr5	117402972	117402981	-	1	NA	Intergenic	Intergenic	-11026	NM_001312914	333050	Mm.437947	NM_001034873	ENSMUSG00000061578	Ksr2	-	kinase suppressor of ras 2	protein-coding
mm_157768.1	chrX	73716146	73716187	-	1	NA	promoter-TSS (NM_012060)	promoter-TSS (NM_012060)	38	NM_012060	27061	Mm.17	NM_012060	ENSMUSG00000002015	Bcap31	Bap31	B cell receptor associated protein 31	protein-coding
mm_133616.1	chr16	91550538	91550545	+	1	NA	intron (NM_008338, intron 1 of 6)	(T)n|Simple_repeat|Simple_repeat	3447	NM_008338	15980	Mm.249364	NM_008338	ENSMUSG00000022965	Ifngr2	Ifgr2|Ifgt	interferon gamma receptor 2	protein-coding
mm_70538.1	chr8	13039327	13039335	+	1	NA	intron (NM_001242368, intron 2 of 8)	MTEa|LTR|ERVL-MaLR	2023	NM_001242368	14058	Mm.262589	NM_007972	ENSMUSG00000031444	F10	Cf10|fX	coagulation factor X	protein-coding
mm_58891.1	chr7	17090639	17090646	+	1	NA	exon (NM_007676, exon 2 of 5)	exon (NM_007676, exon 2 of 5)	16602	NM_007676	26436	Mm.143686	NM_007676	ENSMUSG00000066760	Psg16	Cea11|PSG|bCEA	pregnancy specific glycoprotein 16	protein-coding
mm_92028.1	chr10	62456311	62456322	-	1	NA	3' UTR (NM_001113355, exon 9 of 9)	3' UTR (NM_001113355, exon 9 of 9)	-6623	NM_181423	338359	Mm.235898	NM_181423	ENSMUSG00000020079	Supv3l1	6330443E10Rik	suppressor of var1, 3-like 1 (S. cerevisiae)	protein-coding
mm_16519.1	chr2	181497170	181497216	+	1	NA	promoter-TSS (NM_001291200)	promoter-TSS (NM_001291200)	51	NM_001291204	66314	Mm.136648	NM_025482	ENSMUSG00000000827	Tpd52l2	2810411G23Rik|AU016537|C86069|D54	tumor protein D52-like 2	protein-coding
mm_159449.1	chr3	141212221	141212221	-	1	NA	5' UTR (NM_008811, exon 1 of 1)	5' UTR (NM_008811, exon 1 of 1)	134	NM_008811	18598	Mm.4223	NM_008811	ENSMUSG00000047674	Pdha2	Pdhal	pyruvate dehydrogenase E1 alpha 2	protein-coding
mm_1656.1	chr1	74713144	74713166	+	1	NA	promoter-TSS (NM_024264)	promoter-TSS (NM_024264)	-380	NM_024264	104086	Mm.85083	NM_024264	ENSMUSG00000026170	Cyp27a1	1300013A03Rik|Cyp27	cytochrome P450, family 27, subfamily a, polypeptide 1	protein-coding
mm_53976.1	chr6	6578595	6578672	-	1	NA	promoter-TSS (NM_009169)	promoter-TSS (NM_009169)	25	NM_009169	20422	Mm.2469	NM_009169	ENSMUSG00000042541	Shfm1	DSS1|Shfdg1|Shfg	split hand/foot malformation (ectrodactyly) type 1	protein-coding
mm_72164.1	chr8	72240035	72240045	+	1	NA	promoter-TSS (NM_007456)	promoter-TSS (NM_007456)	22	NM_007456	11767	Mm.290086	NM_007456	ENSMUSG00000003033	Ap1m1	AA408894|AP47|Adtm1A|Cltnm|mu1A	adaptor-related protein complex AP-1, mu subunit 1	protein-coding
mm_61799.1	chr7	84196549	84196552	+	1	NA	Intergenic	Intergenic	-44657	NM_133722	70178	Mm.23914	NM_133722	ENSMUSG00000038459	Abhd17c	2210412D01Rik|AL023007|Fam108c|Fam108c1	abhydrolase domain containing 17C	protein-coding
mm_151560.1	chr19	60144683	60144697	+	1	NA	promoter-TSS (NR_026942)	promoter-TSS (NR_026942)	15	NR_026942	107376	Mm.245813	NR_026942	ENSMUSG00000053117	E330013P04Rik	9930018I18Rik|AW492152	RIKEN cDNA E330013P04 gene	ncRNA
mm_34339.1	chr4	143412921	143412983	+	1	NA	5' UTR (NM_172877, exon 1 of 5)	5' UTR (NM_172877, exon 1 of 5)	526	NM_172877	242736	Mm.275953	NM_172877	ENSMUSG00000046862	Pramef8	4732496O08Rik|AU023234	PRAME family member 8	protein-coding
mm_82719.1	chr9	24745332	24745332	-	1	NA	intron (NM_020496, intron 6 of 6)	RLTR16|LTR|ERVK	28971	NM_020496	57246	Mm.31452	NM_020496	ENSMUSG00000031965	Tbx20	9430010M06Rik|AL022859|Tbx12	T-box 20	protein-coding
mm_106402.1	chr11	118909488	118909575	-	1	NA	promoter-TSS (NM_001039167)	promoter-TSS (NM_001039167)	41	NM_001024931	52897	Mm.341103	NM_001024931	ENSMUSG00000025576	Rbfox3	Fox-3|Hrnbp3|NeuN|Neuna60	RNA binding protein, fox-1 homolog (C. elegans) 3	protein-coding
mm_67459.1	chr7	80403305	80403309	-	1	NA	promoter-TSS (NM_011046)	promoter-TSS (NM_011046)	-495	NM_011046	18550	Mm.5241	NM_011046	ENSMUSG00000030530	Furin	9130404I01Rik|Fur|PACE|Pcsk3|SPC1	furin (paired basic amino acid cleaving enzyme)	protein-coding
mm_106852.1	chr12	8008409	8008421	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	30738	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_20819.1	chr2	144714559	144714562	-	1	NA	intron (NM_025314, intron 4 of 5)	Lx10|LINE|L1	-109106	NM_025490	66328	Mm.45377	NM_025490	ENSMUSG00000027431	Scp2d1	1700010M22Rik	SCP2 sterol-binding domain containing 1	protein-coding
mm_103870.1	chr11	83525847	83525875	-	1	NA	TTS (NM_013653)	TTS (NM_013653)	-3762	NM_001045543	629303	Mm.390417	NM_001045543	ENSMUSG00000018925	Heatr9	Gm11435|OTTMUSG00000000990	HEAT repeat containing 9	protein-coding
mm_62547.1	chr7	102433536	102433539	+	1	NA	intron (NM_009287, intron 11 of 11)	intron (NM_009287, intron 11 of 11)	-8158	NM_009103	20133	Mm.197486	NM_009103	ENSMUSG00000030978	Rrm1	RnrM1	ribonucleotide reductase M1	protein-coding
mm_112166.1	chr12	113407308	113407318	-	1	NA	Intergenic	Intergenic	-82252	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_158403.1	chrX	136837605	136837612	-	1	NA	3' UTR (NM_011123, exon 7 of 7)	3' UTR (NM_011123, exon 7 of 7)	14862	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_85638.1	chr9	107655096	107655116	-	1	NA	exon (NM_001199218, exon 14 of 16)	exon (NM_001199218, exon 14 of 16)	12293	NM_023805	76257	Mm.296560	NM_023805	ENSMUSG00000010064	Slc38a3	0610012J02Rik|D9Ucla2|Nat1|Slc38-3|Sn1|Snat3|mNAT	solute carrier family 38, member 3	protein-coding
mm_73172.1	chr8	95020904	95020943	+	1	NA	intron (NM_173036, intron 1 of 11)	intron (NM_173036, intron 1 of 11)	3231	NM_173036	54672	Mm.27995	NM_173036	ENSMUSG00000060470	Adgrg3	A030001G24Rik|AW214383|Gpr97|Pb1|Pb99	adhesion G protein-coupled receptor G3	protein-coding
mm_89745.1	chr10	99108139	99108206	+	1	NA	promoter-TSS (NM_015737)	promoter-TSS (NM_015737)	37	NM_015737	14426	Mm.314	NM_015737	ENSMUSG00000090035	Galnt4	AV011803	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 4	protein-coding
mm_68893.1	chr7	126448649	126448674	-	1	NA	exon (NM_007504, exon 15 of 23)	exon (NM_007504, exon 15 of 23)	14412	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_44150.1	chr5	150260157	150260261	+	1	NA	5' UTR (NM_172887, exon 1 of 61)	5' UTR (NM_172887, exon 1 of 61)	279	NM_172887	320365	Mm.216590	NM_172887	ENSMUSG00000056602	Fry	13CDNA73|9330186A19Rik|AF346502|AI462658|C87180|D930046M03|cg003|mKIAA4143	FRY microtubule binding protein	protein-coding
mm_129219.1	chr15	76538729	76538773	-	1	NA	promoter-TSS (NM_013909)	promoter-TSS (NM_013909)	-5	NM_013909	30840	Mm.275279	NM_013909	ENSMUSG00000022559	Fbxl6	AU021795|Fbl6	F-box and leucine-rich repeat protein 6	protein-coding
mm_67253.1	chr7	75575280	75575305	-	1	NA	intron (NM_029332, intron 3 of 36)	intron (NM_029332, intron 3 of 36)	119758	NM_029332	75547	Mm.216107	NM_029332	ENSMUSG00000066406	Akap13	1700026G02Rik|5730522G15Rik|5830460E08Rik|AKAP-13|AKAP-Lbc|BRX|Ht31|LBC|PROTO-LB|PROTO-LBC	A kinase (PRKA) anchor protein 13	protein-coding
mm_20613.1	chr2	131855029	131855067	-	1	NA	3' UTR (NM_001166206, exon 2 of 2)	3' UTR (NM_001166206, exon 2 of 2)	4699	NM_001166206	71995	Mm.22	NM_028045	ENSMUSG00000037482	Erv3	1600014E20Rik|AA389086|AI426069|AI448024|D19349	endogenous retroviral sequence 3	protein-coding
mm_88114.1	chr10	69208547	69208557	+	1	NA	promoter-TSS (NM_001252636)	promoter-TSS (NM_001252636)	0	NM_001252636	69288	Mm.26659	NM_001081347	ENSMUSG00000019944	Rhobtb1	1700008H16Rik|3110048G13Rik|AI173445|AI573858|AV350930	Rho-related BTB domain containing 1	protein-coding
mm_98582.1	chr11	95748395	95748401	+	1	NA	promoter-TSS (NM_201609)	promoter-TSS (NM_201609)	-669	NM_201609	268469	Mm.389038	NM_201609	ENSMUSG00000075595	Zfp652	9530033F24Rik|ZNF652	zinc finger protein 652	protein-coding
mm_6177.1	chr1	65100651	65100662	-	1	NA	exon (NM_007774, exon 3 of 3)	exon (NM_007774, exon 3 of 3)	2707	NM_007774	12964	Mm.26904	NM_007774	ENSMUSG00000044429	Cryga	Cryg-4|DGcry-4	crystallin, gamma A	protein-coding
mm_106258.1	chr11	117873465	117873481	-	1	NA	promoter-TSS (NM_027919)	promoter-TSS (NM_027919)	53	NM_027919	71776	Mm.3200	NM_027919	ENSMUSG00000017713	Tha1	1300017K07Rik|GLY1	threonine aldolase 1	protein-coding
mm_127295.1	chr15	100181438	100181448	+	1	NA	intron (NM_001159361, intron 21 of 37)	intron (NM_001159361, intron 21 of 37)	6593	NR_037311	100499528		NR_037311	ENSMUSG00000092752	Mir3473a	Mir3473|mir-3473a|mmu-mir-3473|mmu-mir-3473a	microRNA 3473a	ncRNA
mm_45634.1	chr5	76363788	76363791	-	1	NA	promoter-TSS (NM_019515)	promoter-TSS (NM_019515)	-12	NM_019515	56183	Mm.154879	NM_019515	ENSMUSG00000029236	Nmu	-	neuromedin U	protein-coding
mm_105779.1	chr11	109722215	109722289	-	1	NA	promoter-TSS (NM_153782)	promoter-TSS (NM_153782)	4	NM_153782	208659	Mm.208662	NM_153782	ENSMUSG00000020614	Fam20a	AI606893	family with sequence similarity 20, member A	protein-coding
mm_43306.1	chr5	134703066	134703080	+	1	NA	3' UTR (NM_007925, exon 37 of 37)	3' UTR (NM_007925, exon 37 of 37)	-14483	NM_010717	16885	Mm.15409	NM_010717	ENSMUSG00000029674	Limk1	KIZ-1|LIMK-1|Limk	LIM-domain containing, protein kinase	protein-coding
mm_129684.1	chr15	81408262	81408273	-	1	NA	promoter-TSS (NM_021317)	promoter-TSS (NM_021317)	6	NM_021317	57755	Mm.440590	NM_021317	ENSMUSG00000047108	Dnajb7	4933424H20Rik|Dj5|mDj5	DnaJ heat shock protein family (Hsp40) member B7	protein-coding
mm_145335.1	chr18	56431896	56431905	+	1	NA	promoter-TSS (NM_026240)	promoter-TSS (NM_026240)	-232	NM_026240	107022	Mm.24356	NM_026240	ENSMUSG00000001700	Gramd3	9030613F08Rik|9130427A09Rik|AW061306|NS3TP2	GRAM domain containing 3	protein-coding
mm_72141.1	chr8	72135248	72135264	+	1	NA	promoter-TSS (NM_001001491)	promoter-TSS (NM_001001491)	-36	NM_001001491	326618	Mm.295124	NM_001001491	ENSMUSG00000031799	Tpm4	2610528G24Rik|Tpm4.2|Tpm4.2cy	tropomyosin 4	protein-coding
mm_14861.1	chr2	148789350	148789406	+	1	NA	promoter-TSS (NM_027054)	promoter-TSS (NM_027054)	17	NM_027054	69362	Mm.280779	NM_027054	ENSMUSG00000027443	Cst12	1700006F03Rik|CRES3	cystatin 12	protein-coding
mm_11935.1	chr2	52732269	52732273	+	1	NA	intron (NM_019667, intron 1 of 13)	intron (NM_019667, intron 1 of 13)	9878	NM_019667	56324	Mm.263639	NM_019667	ENSMUSG00000055371	Stam2	1200004O12Rik|5730456G07Rik|BB145015|Hbp	signal transducing adaptor molecule (SH3 domain and ITAM motif) 2	protein-coding
mm_83391.1	chr9	44605345	44605371	-	1	NA	intron (NM_001110826, intron 1 of 13)	CpG	466	NM_181324	13209	Mm.267061	NM_007841	ENSMUSG00000032097	Ddx6	1110001P04Rik|E230023J21Rik|HLR2|mRCK/P54|p54|rck	DEAD (Asp-Glu-Ala-Asp) box polypeptide 6	protein-coding
mm_73013.1	chr8	93963484	93963499	+	1	NA	exon (NM_010308, exon 7 of 9)	exon (NM_010308, exon 7 of 9)	49149	NM_011787	23802	Mm.34641	NM_011787	ENSMUSG00000031751	Amfr	gp78	autocrine motility factor receptor	protein-coding
mm_163433.1	chr12	85374180	85374212	-	1	NA	intron (NM_026775, intron 1 of 4)	intron (NM_026775, intron 1 of 4)	521	NM_026775	68581	Mm.379159	NM_026775	ENSMUSG00000021248	Tmed10	1110014C03Rik|Tmp21|p23|p24delta1	transmembrane p24 trafficking protein 10	protein-coding
mm_56376.1	chr6	94241325	94241336	-	1	NA	intron (NM_001029850, intron 1 of 23)	intron (NM_001029850, intron 1 of 23)	-3888	NR_130996	78178	Mm.452749	NR_130996	ENSMUSG00000045095	4930511A08Rik	-	RIKEN cDNA 4930511A08 gene	ncRNA
mm_133931.1	chr16	3723357	3723384	-	1	NA	Intergenic	Intergenic	-5246	NM_001161791	54483	Mm.143718	NM_019453	ENSMUSG00000022534	Mefv	FMF|TRIM20|pyrin	Mediterranean fever	protein-coding
mm_141909.1	chr17	34969419	34969427	-	1	NA	TTS (NM_010479)	TTS (NM_010479)	2733	NM_010479	193740	Mm.6388	NM_010479	ENSMUSG00000091971	Hspa1a	Hsp70-3|Hsp70.3|Hsp72|hsp68|hsp70A1	heat shock protein 1A	protein-coding
mm_24222.1	chr3	88685803	88685852	+	1	NA	promoter-TSS (NM_028814)	promoter-TSS (NM_028814)	33	NM_028814	74200	Mm.251800	NM_028814	ENSMUSG00000028060	2810403A07Rik	A430106P18Rik|AI256352|AI451678|Blom7|Kiaa0907	RIKEN cDNA 2810403A07 gene	protein-coding
mm_40331.1	chr5	43910845	43910862	+	1	NA	3' UTR (NM_007646, exon 8 of 8)	3' UTR (NM_007646, exon 8 of 8)	42044	NM_007646	12494	Mm.249873	NM_007646	ENSMUSG00000029084	Cd38	ADPRC 1|Cd38-rs1|I-19	CD38 antigen	protein-coding
mm_166330.1	chr5	113550414	113550414	+	1	NA	promoter-TSS (NM_177292)	promoter-TSS (NM_177292)	-6	NM_177292	320916	Mm.102783	NM_177292	ENSMUSG00000063430	Wscd2	4933413A10Rik|C530024P05Rik|Gm450	WSC domain containing 2	protein-coding
mm_15982.1	chr2	166805507	166805605	+	1	NA	promoter-TSS (NM_001085495)	promoter-TSS (NM_001085495)	-25	NM_001085495	99371	Mm.297192	NM_001085495	ENSMUSG00000074582	Arfgef2	AI463430|AW493672|BIG2|E230011G24Rik	ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited)	protein-coding
mm_141852.1	chr17	34802475	34802476	-	1	NA	intron (NM_009995, intron 7 of 9)	intron (NM_009995, intron 7 of 9)	1951	NM_009995	13079	Mm.440407	NM_009995	ENSMUSG00000024365	Cyp21a1	21-OH|21OH|21OHA|21OHB|CYP21OH-A|Cyp21|Cyp21-ps1|Cyp21B|Cyp21a2-ps|Cyp21a2ps|Oh21-1|Oh21-2	cytochrome P450, family 21, subfamily a, polypeptide 1	protein-coding
mm_2820.1	chr1	131020073	131020084	+	1	NA	intron (NM_010548, intron 1 of 4)	intron (NM_010548, intron 1 of 4)	233	NM_010548	16153	Mm.874	NM_010548	ENSMUSG00000016529	Il10	CSIF|Il-10	interleukin 10	protein-coding
mm_145227.1	chr18	50095714	50095718	+	1	NA	Intergenic	B3A|SINE|B2	-32485	NM_008292	15488	Mm.277857	NM_008292	ENSMUSG00000024507	Hsd17b4	17-beta-HSD|17[b]-HSD|DBP|MFE-2|MFP2|MPF-2|Mfp-2|perMFE-2	hydroxysteroid (17-beta) dehydrogenase 4	protein-coding
mm_106099.1	chr11	116238084	116238097	-	1	NA	promoter-TSS (NM_025276)	promoter-TSS (NM_025276)	1	NM_025276	14027	Mm.293683	NM_025276	ENSMUSG00000034282	Evpl	-	envoplakin	protein-coding
mm_49358.1	chr6	22330832	22330835	+	1	NA	intron (NM_138587, intron 3 of 9)	intron (NM_138587, intron 3 of 9)	25248	NM_138587	27999	Mm.490307	NM_138587	ENSMUSG00000029672	Fam3c	D6Wsu176e|Ilei	family with sequence similarity 3, member C	protein-coding
mm_30592.1	chr4	6357795	6357806	+	1	NA	Intergenic	Intergenic	-7880	NM_016807	53378	Mm.247473	NM_016807	ENSMUSG00000028249	Sdcbp	MDA-9|Sycl|syntenin-1	syndecan binding protein	protein-coding
mm_54730.1	chr6	40585832	40585847	-	1	NA	promoter-TSS (NM_021364)	promoter-TSS (NM_021364)	-34	NM_001038604	23845	Mm.103765	NM_021364	ENSMUSG00000029915	Clec5a	Clecsf5|Ly100|MDL-1|Mdl1	C-type lectin domain family 5, member a	protein-coding
mm_104714.1	chr11	98053244	98053261	-	1	NA	5' UTR (NM_146028, exon 1 of 11)	5' UTR (NM_146028, exon 1 of 11)	210	NM_146028	217154	Mm.181008	NM_146028	ENSMUSG00000017400	Stac2	24b2|24b2/STAC2|AW240854	SH3 and cysteine rich domain 2	protein-coding
mm_48254.1	chr5	137827840	137827847	-	1	NA	intron (NM_153510, intron 3 of 6)	B3|SINE|B2	8435	NM_153510	231805	Mm.379385	NM_153510	ENSMUSG00000046245	Pilra	AV021745|FDF03	paired immunoglobin-like type 2 receptor alpha	protein-coding
mm_8215.1	chr1	138145038	138145040	-	1	NA	intron (NM_001111316, intron 1 of 31)	intron (NM_001111316, intron 1 of 31)	30087	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_9848.1	chr1	184732429	184732439	-	1	NA	promoter-TSS (NM_008250)	promoter-TSS (NM_008250)	59	NM_008250	15284	Mm.1347	NM_008250	ENSMUSG00000039377	Hlx	Hlx1	H2.0-like homeobox	protein-coding
mm_156540.1	chrX	151169500	151169518	+	1	NA	Intergenic	CpG	-28569	NM_001271679	279561	Mm.441474	NM_001271678	ENSMUSG00000041245	Wnk3	Prkwnk3|Wnk3-ps	WNK lysine deficient protein kinase 3	protein-coding
mm_12101.1	chr2	61533483	61533499	+	1	NA	Intergenic	RMER1B|Other|Other	-45095	NM_011529	21353	Mm.244393	NM_011529	ENSMUSG00000064289	Tank	C86182|E430026L09Rik|I-TRAF	TRAF family member-associated Nf-kappa B activator	protein-coding
mm_67875.1	chr7	99182736	99182746	-	1	NA	promoter-TSS (NM_026384)	promoter-TSS (NM_026384)	-28	NM_026384	67800	Mm.180189	NM_026384	ENSMUSG00000030747	Dgat2	0610010B06Rik|ARAT|DGAT-2	diacylglycerol O-acyltransferase 2	protein-coding
mm_42720.1	chr5	120519710	120519752	+	1	NA	exon (NM_133221, exon 3 of 16)	exon (NM_133221, exon 3 of 16)	8539	NM_001177594	170756	Mm.291070	NM_133221	ENSMUSG00000032754	Slc8b1	AF261233|NCKX6|NCLX|Slc24a6	solute carrier family 8 (sodium/lithium/calcium exchanger), member B1	protein-coding
mm_108621.1	chr12	85598403	85598438	+	1	NA	promoter-TSS (NM_030887)	promoter-TSS (NM_030887)	-685	NM_001205052	81703	Mm.103560	NM_030887	ENSMUSG00000034271	Jdp2	Jundm2|Jundp2|TIF	Jun dimerization protein 2	protein-coding
mm_100295.1	chr11	117829371	117829382	+	1	NA	intron (NM_027827, intron 2 of 10)	intron (NM_027827, intron 2 of 10)	-3362	NM_009387	21877	Mm.2661	NM_009387	ENSMUSG00000025574	Tk1	D530002A18Rik|Tk-1|Tk1a|Tk1b	thymidine kinase 1	protein-coding
mm_74345.1	chr8	127447670	127447678	+	1	NA	intron (NM_001309391, intron 20 of 24)	intron (NM_001309391, intron 20 of 24)	148022	NM_001013580	93742	Mm.299254	NM_033620	ENSMUSG00000025812	Pard3	AA960621|AI256638|Asip|D8Ertd580e|Par-3|Par3|Pard-3|Pard3a|Phip	par-3 family cell polarity regulator	protein-coding
mm_45497.1	chr5	72168119	72168138	-	1	NA	promoter-TSS (NM_178599)	promoter-TSS (NM_178599)	55	NM_178599	27784	Mm.44223	NM_178599	ENSMUSG00000029213	Commd8	C77770|D5Buc26e	COMM domain containing 8	protein-coding
mm_66205.1	chr7	34242334	34242358	-	1	NA	exon (NM_172741, exon 10 of 13)	exon (NM_172741, exon 10 of 13)	-12010	NM_008155	14751	Mm.589	NM_008155	ENSMUSG00000036427	Gpi1	Amf|Gpi|Gpi-1|Gpi-1r|Gpi-1s|Gpi-1t|Gpi1-r|Gpi1-s|Gpi1-t|Gpi1s|MF|NK|NK/GPI|Nlk|Org|Pgi|Phi	glucose phosphate isomerase 1	protein-coding
mm_57058.1	chr6	122486459	122486556	-	1	NA	promoter-TSS (NM_027664)	promoter-TSS (NM_027664)	-202	NM_027664	108653	Mm.277939	NM_027664	ENSMUSG00000040649	Rimklb	4931417E21Rik|4933426K21Rik|AA097693|AI325948|AU015629|Naags	ribosomal modification protein rimK-like family member B	protein-coding
mm_39373.1	chr5	12383301	12383322	+	1	NA	5' UTR (NM_028882, exon 1 of 18)	5' UTR (NM_028882, exon 1 of 18)	145	NM_028882	108151	Mm.89313	NM_028882	ENSMUSG00000040254	Sema3d	4631426B19Rik	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D	protein-coding
mm_109299.1	chr12	109559955	109559957	+	1	NA	non-coding (NR_003633, exon 5 of 5)	non-coding (NR_003633, exon 5 of 5)	-3736	NR_030427	791079		NR_030427	ENSMUSG00000076451	Mir770	Mirn770|mir-770|mmu-mir-770	microRNA 770	ncRNA
mm_151582.1	chr19	61224514	61224545	+	1	NA	3' UTR (NM_009970, exon 12 of 12)	3' UTR (NM_009970, exon 12 of 12)	3889	NM_009970	12982	Mm.287228	NM_009970	ENSMUSG00000059326	Csf2ra	CD116|Csfgmra|GM-CSF-Ra|GM-CSFR	colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)	protein-coding
mm_150340.1	chr19	34583137	34583140	+	1	NA	promoter-TSS (NM_010501)	promoter-TSS (NM_010501)	-391	NM_010501	15959	Mm.426079	NM_010501	ENSMUSG00000074896	Ifit3	Ifi49|P49	interferon-induced protein with tetratricopeptide repeats 3	protein-coding
mm_125663.1	chr15	64613792	64613806	+	1	NA	Intergenic	Intergenic	-230880	NM_010026	13196	Mm.277236	NM_010026	ENSMUSG00000022377	Asap1	AV239055|DEF-1|Ddef1|PAP|mKIAA1249|s19	ArfGAP with SH3 domain, ankyrin repeat and PH domain1	protein-coding
mm_100875.1	chr11	5971727	5971738	-	1	NA	3' UTR (NM_001174054, exon 21 of 21)	3' UTR (NM_001174054, exon 21 of 21)	15974	NM_019661	56418	Mm.294821	NM_019661	ENSMUSG00000002741	Ykt6	0610042I15Rik|1810013M05Rik|AW105923	YKT6 v-SNARE homolog (S. cerevisiae)	protein-coding
mm_97357.1	chr11	77500888	77500927	+	1	NA	intron (NM_001004144, intron 6 of 19)	intron (NM_001004144, intron 6 of 19)	7495	NM_001004144	216963	Mm.290182	NM_001004144	ENSMUSG00000011877	Git1	Cat-1|p95Cat	G protein-coupled receptor kinase-interactor 1	protein-coding
mm_148683.1	chr19	5689746	5689823	+	1	NA	promoter-TSS (NM_144868)	promoter-TSS (NM_144868)	653	NM_022012	26403	Mm.185026	NM_022012	ENSMUSG00000004054	Map3k11	2610017K16Rik|Mlk3|PTK1|SPRK	mitogen-activated protein kinase kinase kinase 11	protein-coding
mm_34577.1	chr4	150103605	150103607	+	1	NA	3' UTR (NM_177366, exon 4 of 4)	3' UTR (NM_177366, exon 4 of 4)	-15738	NM_019741	56485	Mm.260220	NM_019741	ENSMUSG00000028976	Slc2a5	AI526984|Glut5|Slc5a	solute carrier family 2 (facilitated glucose transporter), member 5	protein-coding
mm_65676.1	chr7	28316811	28316822	-	1	NA	exon (NM_013676, exon 25 of 30)	exon (NM_013676, exon 25 of 30)	-4770	NM_025616	66525	Mm.167913	NM_025616	ENSMUSG00000003438	Timm50	2810403L02Rik|AU015082|TIM50L	translocase of inner mitochondrial membrane 50	protein-coding
mm_53946.1	chr6	5193818	5193831	-	1	NA	5' UTR (NM_011134, exon 1 of 9)	5' UTR (NM_011134, exon 1 of 9)	122	NM_011134	18979	Mm.237657	NM_011134	ENSMUSG00000002588	Pon1	Pon	paraoxonase 1	protein-coding
mm_80558.1	chr9	83548280	83548298	+	1	NA	promoter-TSS (NM_172507)	promoter-TSS (NM_172507)	-49	NM_172507	212531	Mm.491246	NM_172507	ENSMUSG00000032261	Sh3bgrl2	A930014C21Rik|AA408038|B930089I21	SH3 domain binding glutamic acid-rich protein like 2	protein-coding
mm_168334.1	chr11	118304511	118304512	+	1	NA	intron (NM_011594, intron 4 of 4)	MMERVK9C_I-int|LTR|ERVK	-14267	NM_001033528	72344	Mm.232293	NM_001033528	ENSMUSG00000033909	Usp36	2700002L06Rik|mKIAA1453	ubiquitin specific peptidase 36	protein-coding
mm_160644.1	chr9	109876060	109876060	+	1	NA	exon (NM_007658, exon 1 of 15)	exon (NM_007658, exon 1 of 15)	481	NM_007658	12530	Mm.307103	NM_007658	ENSMUSG00000032477	Cdc25a	D9Ertd393e	cell division cycle 25A	protein-coding
mm_145059.1	chr18	40332479	40332483	+	1	NA	intron (NM_026135, intron 1 of 1)	intron (NM_026135, intron 1 of 1)	74120	NM_026135	383348	Mm.76366	NM_026135	ENSMUSG00000051401	Kctd16	4930434H12Rik|Gm1267	potassium channel tetramerisation domain containing 16	protein-coding
mm_123698.1	chr14	69707574	69707614	-	1	NA	promoter-TSS (NM_001146012)	promoter-TSS (NM_001146012)	-10	NM_001146012	71843	Mm.27738	NM_001146012	ENSMUSG00000034194	R3hcc1	1700020M16Rik|AA407796	R3H domain and coiled-coil containing 1	protein-coding
mm_157510.1	chrX	49273758	49273768	-	1	NA	intron (NM_001271450, intron 2 of 15)	intron (NM_001271450, intron 2 of 15)	14479	NM_001271449	209224	Mm.327730	NM_145951	ENSMUSG00000031109	Enox2	APK1|Cova1|tNOX	ecto-NOX disulfide-thiol exchanger 2	protein-coding
mm_10524.1	chr2	16384665	16384685	+	1	NA	intron (NM_026162, intron 1 of 13)	intron (NM_026162, intron 1 of 13)	28371	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding
mm_145320.1	chr18	54640479	54640508	+	1	NA	TTS (NR_045400)	TTS (NR_045400)	28749	NR_045400	328957	Mm.402781	NR_045400		9330117O12Rik	9330117O12	RIKEN cDNA 9330117O12 gene	ncRNA
mm_73459.1	chr8	106604252	106604262	+	1	NA	intron (NM_009864, intron 1 of 15)	intron (NM_009864, intron 1 of 15)	907	NM_009864	12550	Mm.35605	NM_009864	ENSMUSG00000000303	Cdh1	AA960649|ARC-1|E-cad|Ecad|L-CAM|UVO|Um	cadherin 1	protein-coding
mm_9195.1	chr1	171222436	171222471	-	1	NA	promoter-TSS (NM_001037170)	promoter-TSS (NM_001037170)	61	NM_001037170	641376	Mm.288374	NM_001037170	ENSMUSG00000005674	Tomm40l	-	translocase of outer mitochondrial membrane 40 homolog-like (yeast)	protein-coding
mm_29996.1	chr3	135588315	135588322	-	1	NA	intron (NM_008689, intron 24 of 24)	intron (NM_008689, intron 24 of 24)	102707	NM_027288	110173	Mm.280536	NM_027288	ENSMUSG00000028164	Manba	2410030O07Rik|B930014J03Rik|Bmn	mannosidase, beta A, lysosomal	protein-coding
mm_80916.1	chr9	100807303	100807305	+	1	NA	intron (NM_009282, intron 9 of 33)	B2_Mm2|SINE|B2	163681	NM_009282	20842	Mm.42135	NM_009282	ENSMUSG00000037286	Stag1	AU045003|SA-1|Scc3	stromal antigen 1	protein-coding
mm_105470.1	chr11	105456675	105456751	-	1	NA	promoter-TSS (NM_001039242)	promoter-TSS (NM_001039242)	22	NM_172568	632687	Mm.121570	NM_172568	ENSMUSG00000078627	March10	4933417C16Rik|AV039223|OTTMUSG00000002847|Rnf190	membrane-associated ring finger (C3HC4) 10	protein-coding
mm_83740.1	chr9	51102036	51102044	-	1	NA	promoter-TSS (NM_177702)	promoter-TSS (NM_177702)	38	NM_177702	235345	Mm.72828	NM_177702	ENSMUSG00000032057	4833427G06Rik	-	RIKEN cDNA 4833427G06 gene	protein-coding
mm_14454.1	chr2	131186984	131187001	+	1	NA	promoter-TSS (NM_001111075)	promoter-TSS (NM_001111075)	44	NM_001111075	12531	Mm.38444	NM_023117	ENSMUSG00000027330	Cdc25b	AI604853	cell division cycle 25B	protein-coding
mm_69826.1	chr7	141266416	141266430	-	1	NA	promoter-TSS (NM_001252601)	promoter-TSS (NM_001252601)	1	NM_001252601	54123	Mm.3233	NM_016850	ENSMUSG00000025498	Irf7	-	interferon regulatory factor 7	protein-coding
mm_19544.1	chr2	98662865	98662882	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	1195216	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_88786.1	chr10	80608850	80608854	+	1	NA	promoter-TSS (NR_105877)	promoter-TSS (NR_105877)	-408	NR_105877	102465550		NR_105877	ENSMUSG00000099283	Mir6912	Gm27990|mmu-mir-6912	microRNA 6912	ncRNA
mm_84213.1	chr9	61635009	61635052	-	1	NA	Intergenic	Intergenic	262664	NM_001083927	21887	Mm.24255	NM_009389	ENSMUSG00000032280	Tle3	2610103N05Rik|ESG|Grg3a|Grg3b|mKIAA1547	transducin-like enhancer of split 3	protein-coding
mm_100781.1	chr11	4808377	4808387	-	1	NA	intron (NM_001252251, intron 4 of 16)	intron (NM_001252251, intron 4 of 16)	24753	NM_001252253	18016	Mm.297109	NM_010898	ENSMUSG00000009073	Nf2	merlin	neurofibromin 2	protein-coding
mm_38783.1	chr4	148080242	148080254	-	1	NA	3' UTR (NM_001301281, exon 5 of 5)	3' UTR (NM_001301281, exon 5 of 5)	7816	NM_009642	11610	Mm.46247	NM_009642	ENSMUSG00000029007	Agtrap	3300002E14Rik|AT1R|Atrap|D4Wsu124e	angiotensin II, type I receptor-associated protein	protein-coding
mm_50431.1	chr6	48845127	48845157	+	1	NA	exon (NM_025326, exon 7 of 7)	exon (NM_025326, exon 7 of 7)	3486	NM_001098271	66058	Mm.27061	NM_025326	ENSMUSG00000023367	Tmem176a	0610011I04Rik|AU040201|AU041743|Keg2	transmembrane protein 176A	protein-coding
mm_37813.1	chr4	130935073	130935114	-	1	NA	3' UTR (NM_010686, exon 8 of 8)	3' UTR (NM_010686, exon 8 of 8)	-9292	NM_010769	17180	Mm.271796	NM_010769	ENSMUSG00000040533	Matn1	CMP|Crtm|Mat1|matrilin-1	matrilin 1, cartilage matrix protein	protein-coding
mm_26564.1	chr3	146521157	146521183	+	1	NA	exon (NM_027332, exon 1 of 5)	exon (NM_027332, exon 1 of 5)	253	NM_027332	70285	Mm.28128	NM_027332	ENSMUSG00000028187	Rpf1	2210420E24Rik|2310066N05Rik|Bxdc5	ribosome production factor 1 homolog	protein-coding
mm_54640.1	chr6	38837267	38837268	-	1	NA	promoter-TSS (NM_001136065)	promoter-TSS (NM_001136065)	44	NM_001136065	15258	Mm.23790	NM_010433	ENSMUSG00000061436	Hipk2	1110014O20Rik|B230339E18Rik|Stank	homeodomain interacting protein kinase 2	protein-coding
mm_134527.1	chr16	19236869	19236892	-	1	NA	Intergenic	RMER17B|LTR|ERVK	49861	NM_146451	258443	Mm.377506	NM_146451	ENSMUSG00000050742	Olfr164	MOR279-2	olfactory receptor 164	protein-coding
mm_167781.1	chr9	118926664	118926674	+	1	NA	5' UTR (NM_133710, exon 1 of 8)	5' UTR (NM_133710, exon 1 of 8)	133	NM_133710	69274	Mm.439928	NM_133710	ENSMUSG00000047409	Ctdspl	2810418J22Rik|AI426263|HYA22|SCP3	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase-like	protein-coding
mm_72307.1	chr8	77518325	77518327	+	1	NA	promoter-TSS (NM_030113)	promoter-TSS (NM_030113)	-419	NM_030113	78514	Mm.165974	NM_030113	ENSMUSG00000037148	Arhgap10	A930033B01Rik|PSGAP-m|PSGAP-s	Rho GTPase activating protein 10	protein-coding
mm_122658.1	chr14	51912000	51912003	-	1	NA	intron (NM_013864, intron 1 of 15)	intron (NM_013864, intron 1 of 15)	1487	NM_001145959	29811	Mm.26722	NM_013864	ENSMUSG00000004558	Ndrg2	AI182517|AU040374|Ndr2|SYLD	N-myc downstream regulated gene 2	protein-coding
mm_28116.1	chr3	86799181	86799194	-	1	NA	intron (NM_001195497, intron 11 of 15)	intron (NM_001195497, intron 11 of 15)	121697	NM_001195496	70762	Mm.44490	NM_027539	ENSMUSG00000028078	Dclk2	6330415M09Rik|AU044875|CL2|CLICK2|Click-II|Dcamkl2	doublecortin-like kinase 2	protein-coding
mm_7059.1	chr1	87394722	87394734	-	1	NA	promoter-TSS (NM_001110227)	promoter-TSS (NM_001110227)	1	NM_001110227	100040591	Mm.443539	NM_001110227	ENSMUSG00000079436	Kcnj13	-	potassium inwardly-rectifying channel, subfamily J, member 13	protein-coding
mm_143033.1	chr17	56609959	56609971	-	1	NA	promoter-TSS (NM_153152)	promoter-TSS (NM_153152)	-194	NM_153152	224904	Mm.34002	NM_153152	ENSMUSG00000049760	2410015M20Rik	Mic13|QIL1|sr104	RIKEN cDNA 2410015M20 gene	protein-coding
mm_110856.1	chr12	73324203	73324211	-	1	NA	intron (NM_001037717, intron 5 of 15)	intron (NM_001037717, intron 5 of 15)	37359	NM_001037717	625098	Mm.32075	NM_001037717	ENSMUSG00000044712	Slc38a6	AW322671|EG625098	solute carrier family 38, member 6	protein-coding
mm_64084.1	chr7	140954446	140954451	+	1	NA	TTS (NM_030694)	TTS (NM_030694)	1513	NM_030694	80876	Mm.379266	NM_030694	ENSMUSG00000060591	Ifitm2	DSPA2c|Ifitm3l|fragilis3|mil-3	interferon induced transmembrane protein 2	protein-coding
mm_63594.1	chr7	128139260	128139270	+	1	NA	intron (NM_021334, intron 14 of 29)	intron (NM_021334, intron 14 of 29)	9697	NM_021334	16411	Mm.22378	NM_021334	ENSMUSG00000030789	Itgax	AI449405|Cd11c|Cr4|N418	integrin alpha X	protein-coding
mm_133957.1	chr16	4045158	4045163	-	1	NA	intron (NM_026508, intron 14 of 17)	intron (NM_026508, intron 14 of 17)	8015	NM_010061	13419	Mm.291048	NM_010061	ENSMUSG00000005980	Dnase1	AI788650|DNaseI|Dnl1	deoxyribonuclease I	protein-coding
mm_19909.1	chr2	114201417	114201445	-	1	NA	promoter-TSS (NM_175466)	promoter-TSS (NM_175466)	1	NM_175466	228491	Mm.132523	NM_175466	ENSMUSG00000040321	Zfp770	6430601A21Rik|Znf770	zinc finger protein 770	protein-coding
mm_50416.1	chr6	48746238	48746302	+	1	NA	promoter-TSS (NM_175035)	promoter-TSS (NM_175035)	73	NM_175035	317757	Mm.455917	NM_175035	ENSMUSG00000043505	Gimap5	D630024P16|E230026N22Rik	GTPase, IMAP family member 5	protein-coding
mm_113425.1	chr13	34090703	34090719	+	1	NA	intron (NR_046184, intron 3 of 4)	RMER19A|LTR|ERVK	-12703	NM_009450	22151	Mm.422827	NM_009450	ENSMUSG00000058672	Tubb2a	M(beta)2|Tubb2	tubulin, beta 2A class IIA	protein-coding
mm_137431.1	chr17	26275796	26275799	+	1	NA	exon (NM_025881, exon 6 of 9)	exon (NM_025881, exon 6 of 9)	22887	NR_037905	66978	Mm.440216	NM_025881	ENSMUSG00000024188	Luc7l	1810045C04Rik|2410018D03Rik	Luc7-like	protein-coding
mm_37614.1	chr4	126968160	126968177	-	1	NA	promoter-TSS (NM_001114399)	promoter-TSS (NM_001114399)	-245	NM_001114399	67785	Mm.165401	NM_001114399	ENSMUSG00000042446	Zmym4	6330503C17Rik|AI480785|AW493829|CDIR|D630001M21|MYM|Zfp262|Znf262|mKIAA0425	zinc finger, MYM-type 4	protein-coding
mm_136147.1	chr16	87495824	87495877	-	1	NA	promoter-TSS (NM_009840)	promoter-TSS (NM_009840)	19	NM_009840	12469	Mm.328673	NM_009840	ENSMUSG00000025613	Cct8	AI132397|Cctq|Tcpq	chaperonin containing Tcp1, subunit 8 (theta)	protein-coding
mm_109357.1	chr12	109630094	109630106	+	1	NA	intron (NR_028261, intron 6 of 20)	MLT1F|LTR|ERVL-MaLR	-5912	NR_046302	449562		NR_046302	ENSMUSG00000088294	AF357425	MBII-48	snoRNA AF357425	snoRNA
mm_89052.1	chr10	82877316	82877338	+	1	NA	exon (NM_001042523, exon 5 of 15)	exon (NM_001042523, exon 5 of 15)	10701	NM_025499	66341	Mm.443284	NM_025499	ENSMUSG00000109864	Eid3	1700027M21Rik|NS4EB	EP300 interacting inhibitor of differentiation 3	protein-coding
mm_65275.1	chr7	24316591	24316659	-	1	NA	promoter-TSS (NM_009568)	promoter-TSS (NM_009568)	41	NM_009568	22756	Mm.295762	NM_009568	ENSMUSG00000074282	Zfp94	-	zinc finger protein 94	protein-coding
mm_56604.1	chr6	112271301	112271307	-	1	NA	Intergenic	Intergenic	-2454	NM_144799	30937	Mm.234441	NM_144799	ENSMUSG00000057604	Lmcd1	AW455500|AW553074|dyxin	LIM and cysteine-rich domains 1	protein-coding
mm_73839.1	chr8	117461140	117461158	+	1	NA	3' UTR (NM_001163262, exon 21 of 21)	3' UTR (NM_001163262, exon 21 of 21)	1884	NR_106046	102465653		NR_106046	ENSMUSG00000098483	Mir7078	Gm27386|mmu-mir-7078	microRNA 7078	ncRNA
mm_107721.1	chr12	56535292	56535302	+	1	NA	intron (NM_009385, intron 1 of 2)	intron (NM_009385, intron 1 of 2)	1611	NM_009385	21869	Mm.89972	NM_009385	ENSMUSG00000001496	Nkx2-1	AV026640|Nkx2.1|T/EBP|Titf1|Ttf-1	NK2 homeobox 1	protein-coding
mm_21171.1	chr2	154689547	154689599	-	1	NA	exon (NM_029362, exon 2 of 5)	exon (NM_029362, exon 2 of 5)	32547	NM_029362	75608	Mm.262480	NM_029362	ENSMUSG00000038467	Chmp4b	2010012F05Rik|C76846|Snf7-2	charged multivesicular body protein 4B	protein-coding
mm_17511.1	chr2	29124811	29124831	-	1	NA	promoter-TSS (NM_198033)	promoter-TSS (NM_198033)	-171	NM_198033	269254	Mm.41867	NM_198033	ENSMUSG00000043535	Setx	A130090N03|A930037J23Rik|AOA2|AW060766|Als4|SCAR1|Sen1|mKIAA0625	senataxin	protein-coding
mm_31292.1	chr4	45972289	45972325	+	1	NA	promoter-TSS (NM_146142)	promoter-TSS (NM_146142)	10	NM_146142	100121	Mm.275413	NM_146142	ENSMUSG00000035517	Tdrd7	5730495N10Rik|AI447470|PCTAIRE2BP	tudor domain containing 7	protein-coding
mm_55092.1	chr6	49254274	49254288	-	1	NA	intron (NM_001347209, intron 1 of 7)	ID_B1|SINE|B4	9771	NM_001347209	101214	Mm.196598	NM_198102	ENSMUSG00000029817	Tra2a	1500010G04Rik|AL022798|G430041M01Rik|mAWMS1	transformer 2 alpha homolog (Drosophila)	protein-coding
mm_166873.1	chr7	25305936	25305960	+	1	NA	promoter-TSS (NM_183311)	promoter-TSS (NM_183311)	-160	NM_183311	330485	Mm.260740	NM_183311	ENSMUSG00000043843	Tmem145	B930076A02Rik	transmembrane protein 145	protein-coding
mm_58595.1	chr7	5020454	5020463	+	1	NA	promoter-TSS (NM_001290426)	promoter-TSS (NM_001290426)	82	NM_001033383	319748	Mm.86607	NM_001033383	ENSMUSG00000074405	Zfp865	6430526N21Rik|Znf865	zinc finger protein 865	protein-coding
mm_147518.1	chr18	52527742	52527764	-	1	NA	intron (NM_001286181, intron 3 of 7)	intron (NM_001286181, intron 3 of 7)	1968	NM_001286181	16948	Mm.172	NM_010728	ENSMUSG00000024529	Lox	AI893619|TSC-160|rrg	lysyl oxidase	protein-coding
mm_29048.1	chr3	103414618	103414619	-	1	NA	Intergenic	RMER15|LTR|ERVL	135325	NM_001079830	94093	Mm.195036	NM_053170	ENSMUSG00000033014	Trim33	8030451N04Rik|AI413936|Ecto|Tif1g	tripartite motif-containing 33	protein-coding
mm_25313.1	chr3	106131965	106132059	+	1	NA	exon (NM_023186, exon 11 of 11)	exon (NM_023186, exon 11 of 11)	18630	NM_023186	81600	Mm.46418	NM_023186	ENSMUSG00000062778	Chia1	2200003E03Rik|AMCase|Chia|YNL	chitinase, acidic 1	protein-coding
mm_27808.1	chr3	78508759	78508761	-	1	NA	Intergenic	Intergenic	636127	NM_001310536	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_88366.1	chr10	75943047	75943063	+	1	NA	Intergenic	Intergenic	-2383	NM_001277132	333670	Mm.291320	NM_001037714	ENSMUSG00000050157	Gm867	Gm736	predicted gene 867	protein-coding
mm_96494.1	chr11	67966443	67966497	+	1	NA	promoter-TSS (NM_018768)	promoter-TSS (NM_018768)	-13	NM_018768	55943	Mm.3973	NM_018768	ENSMUSG00000020903	Stx8	0610007H08Rik|1110002H11Rik|4930571E13Rik|CARB	syntaxin 8	protein-coding
mm_13257.1	chr2	98665078	98665100	+	1	NA	Intergenic	SYNREP_MM|Satellite|Satellite	1197432	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_11022.1	chr2	26628442	26628462	+	1	NA	promoter-TSS (NM_019833)	promoter-TSS (NM_019833)	-5	NM_019833	56279	Mm.279863	NM_019833	ENSMUSG00000036186	Fam69b	AB030186|AW209000|B230317C12Rik|PIP49	family with sequence similarity 69, member B	protein-coding
mm_50359.1	chr6	48647310	48647318	+	1	NA	promoter-TSS (NM_001286629)	promoter-TSS (NM_001286629)	-47	NM_001286629	243374	Mm.86514	NM_212486	ENSMUSG00000064262	Gimap8	Gm457|IAN9|IMAP8	GTPase, IMAP family member 8	protein-coding
mm_13271.1	chr2	98667227	98667256	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	1199584	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_98802.1	chr11	97041555	97041563	+	1	NA	promoter-TSS (NM_027026)	promoter-TSS (NM_027026)	-27	NM_026154	107732	Mm.208946	NM_026154	ENSMUSG00000001445	Mrpl10	0610040E02Rik|C78440|MRP-L8|Rpml8	mitochondrial ribosomal protein L10	protein-coding
mm_48379.1	chr5	139736292	139736332	-	1	NA	promoter-TSS (NM_174850)	promoter-TSS (NM_174850)	21	NM_174850	231830	Mm.240510	NM_174850	ENSMUSG00000036718	Micall2	A930021H16Rik|JRAB|MICAL-L2|mFLJ00139	MICAL-like 2	protein-coding
mm_128524.1	chr15	54312386	54312396	-	1	NA	Intergenic	Intergenic	-33907	NM_008764	18383	Mm.15383	NM_008764	ENSMUSG00000063727	Tnfrsf11b	OCIF|Opg|TR1	tumor necrosis factor receptor superfamily, member 11b (osteoprotegerin)	protein-coding
mm_153089.1	chr19	32389867	32389890	-	1	NA	non-coding (NR_033198, exon 2 of 2)	non-coding (NR_033198, exon 2 of 2)	662	NR_033198	67188	Mm.391160	NR_033198	ENSMUSG00000097787	2700046G09Rik	-	RIKEN cDNA 2700046G09 gene	ncRNA
mm_18447.1	chr2	60924636	60924643	-	1	NA	intron (NM_020296, intron 1 of 13)	intron (NM_020296, intron 1 of 13)	38565	NM_020296	56878	Mm.259667	NM_020296	ENSMUSG00000026970	Rbms1	2600014B10Rik|AI255215|MSSP-1|MSSP-2|MSSP-3|YC1	RNA binding motif, single stranded interacting protein 1	protein-coding
mm_12223.1	chr2	67670189	67670191	+	1	NA	Intergenic	Lx9|LINE|L1	-5267	NR_106083	102465706		NR_106083	ENSMUSG00000098299	Mir7224	Gm27971|mmu-mir-7224	microRNA 7224	ncRNA
mm_172396.1	chr7	141174574	141174587	+	1	NA	Intergenic	RLTR17|LTR|ERVK	-1729	NM_001172100	107702	Mm.197493	NM_145135	ENSMUSG00000038650	Rnh1	AW546468|C80305|RNH	ribonuclease/angiogenin inhibitor 1	protein-coding
mm_82888.1	chr9	32541359	32541416	-	1	NA	promoter-TSS (NM_008026)	promoter-TSS (NM_008026)	65	NM_008026	14247	Mm.258908	NM_008026	ENSMUSG00000016087	Fli1	EWSR2|Fli-1|SIC-1|Sic1	Friend leukemia integration 1	protein-coding
mm_70595.1	chr8	13288174	13288220	+	1	NA	promoter-TSS (NM_001042649)	promoter-TSS (NM_001042649)	-71	NM_001042650	102323	Mm.368890	NM_001024504	ENSMUSG00000038506	Dcun1d2	AW495713|mFLJ10704	DCN1, defective in cullin neddylation 1, domain containing 2 (S. cerevisiae)	protein-coding
mm_109901.1	chr12	7950056	7950089	-	1	NA	Intergenic	Intergenic	-27605	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_55570.1	chr6	71391297	71391313	-	1	NA	3' UTR (NM_024288, exon 9 of 9)	3' UTR (NM_024288, exon 9 of 9)	17878	NM_001081110	12525	Mm.1858	NM_009857	ENSMUSG00000053977	Cd8a	BB154331|Ly-2|Ly-35|Ly-B|Lyt-2	CD8 antigen, alpha chain	protein-coding
mm_134893.1	chr16	29834723	29834736	-	1	NA	Intergenic	Intergenic	144395	NR_037689	328657	Mm.425982	NM_001033403		Gm1968	-	predicted gene 1968	ncRNA
mm_164606.1	chr17	30414718	30414729	-	1	NA	intron (NM_172618, intron 6 of 11)	intron (NM_172618, intron 6 of 11)	-18543	NR_030688	623169	Mm.440508	NR_030688		Gm6402	EG623169	ribosomal protein S17 pseudogene	pseudo
mm_44114.1	chr5	149439650	149439663	+	1	NA	promoter-TSS (NM_029464)	promoter-TSS (NM_029464)	-4	NM_029464	75860	Mm.159605	NM_029464	ENSMUSG00000029660	Tex26	4930588N13Rik	testis expressed 26	protein-coding
mm_119943.1	chr14	54986505	54986521	+	1	NA	exon (NM_080728, exon 19 of 41)	exon (NM_080728, exon 19 of 41)	8036	NM_080728	140781	Mm.457983	NM_080728	ENSMUSG00000053093	Myh7	B-MHC|MyHC-I|Myhc-b|Myhcb|beta-MHC	myosin, heavy polypeptide 7, cardiac muscle, beta	protein-coding
mm_51347.1	chr6	72550184	72550209	+	1	NA	intron (NM_001271395, intron 1 of 9)	intron (NM_001271395, intron 1 of 9)	549	NM_001271395	12332	Mm.18626	NM_007599	ENSMUSG00000056737	Capg	gCap39|mbh1	capping protein (actin filament), gelsolin-like	protein-coding
mm_102720.1	chr11	67116819	67116826	-	1	NA	intron (NR_038055, intron 2 of 4)	intron (NR_038055, intron 2 of 4)	3258	NR_038055	74184	Mm.162554	NR_038055	ENSMUSG00000087410	2310065F04Rik	linc-Myh	RIKEN cDNA 2310065F04 gene	ncRNA
mm_97698.1	chr11	80173404	80173423	+	1	NA	intron (NM_172133, intron 7 of 10)	intron (NM_172133, intron 7 of 10)	-10459	NM_028019	71956	Mm.22985	NM_028019	ENSMUSG00000020707	Rnf135	0610037N03Rik|2410006N06Rik	ring finger protein 135	protein-coding
mm_61741.1	chr7	82209488	82209499	+	1	NA	Intergenic	Intergenic	-50415	NM_001277955	20408	Mm.736	NM_017400	ENSMUSG00000030638	Sh3gl3	EEN-B2|SH3P13|Sh3d2c|Sh3d2c2	SH3-domain GRB2-like 3	protein-coding
mm_45148.1	chr5	49216152	49216158	-	1	NA	intron (NM_001199244, intron 1 of 7)	intron (NM_001199244, intron 1 of 7)	69504	NM_001199244	80334	Mm.160172	NM_030265	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding
mm_120450.1	chr14	65968614	65968625	+	1	NA	5' UTR (NM_013492, exon 1 of 9)	5' UTR (NM_013492, exon 1 of 9)	136	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_13633.1	chr2	113708679	113708702	+	1	NA	promoter-TSS (NR_040614)	promoter-TSS (NR_040614)	-140	NR_040614	75166	Mm.410811	NR_040614	ENSMUSG00000084798	4930533B01Rik	-	RIKEN cDNA 4930533B01 gene	ncRNA
mm_96821.1	chr11	69994602	69994613	+	1	NA	3' UTR (NM_019749, exon 4 of 4)	3' UTR (NM_019749, exon 4 of 4)	-1159	NM_001291125	78246	Mm.20805	NM_030064	ENSMUSG00000018572	Phf23	JUNE-1	PHD finger protein 23	protein-coding
mm_98872.1	chr11	97799628	97799647	+	1	NA	promoter-TSS (NM_010688)	promoter-TSS (NM_010688)	-35	NM_010688	16796	Mm.271967	NM_010688	ENSMUSG00000038366	Lasp1	AA408629|Def-4|SH3P6|Tg(Col1a1-lacZ)1Ngma	LIM and SH3 protein 1	protein-coding
mm_75301.1	chr8	41101881	41101923	-	1	NA	intron (NM_001005863, intron 1 of 13)	intron (NM_001005863, intron 1 of 13)	12765	NM_001286413	102103	Mm.149438	NM_001005863	ENSMUSG00000045636	Mtus1	AI481402|ATBP135|Atip1|B430010I23Rik|B430305I03Rik|C85752|Cctsg1-440|MD44|MTSG1|mKIAA1288	mitochondrial tumor suppressor 1	protein-coding
mm_142816.1	chr17	51744960	51744962	-	1	NA	intron (NM_009122, intron 9 of 10)	intron (NM_009122, intron 9 of 10)	67093	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_756.1	chr1	43933609	43933626	+	1	NA	promoter-TSS (NM_009418)	promoter-TSS (NM_009418)	-377	NM_001310540	22019	Mm.401675	NM_009418	ENSMUSG00000041763	Tpp2	TPP-2|TppII	tripeptidyl peptidase II	protein-coding
mm_143433.1	chr17	70851628	70851643	-	1	NA	promoter-TSS (NM_001164075)	promoter-TSS (NM_001164075)	99	NM_001164075	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_57455.1	chr6	125165708	125165766	-	1	NA	promoter-TSS (NM_008084)	promoter-TSS (NM_008084)	36	NM_008084	14433	Mm.304088	NM_008084	ENSMUSG00000057666	Gapdh	Gapd	glyceraldehyde-3-phosphate dehydrogenase	protein-coding
mm_109281.1	chr12	109547986	109547996	+	1	NA	intron (NR_027651, intron 5 of 8)	intron (NR_027651, intron 5 of 8)	2593	NR_003633	17263	Mm.289645	NM_144513	ENSMUSG00000021268	Meg3	2900016C05Rik|3110050O07Rik|6330408G06Rik|AI425946|AW108224|D12Bwg1266e|Gtl2|R74756|R75394	maternally expressed 3	ncRNA
mm_105697.1	chr11	108044679	108044683	-	1	NA	intron (NM_011101, intron 5 of 16)	intron (NM_011101, intron 5 of 16)	47833	NR_106082	102465705		NR_106082	ENSMUSG00000098989	Mir7223	Gm28009|mmu-mir-7223	microRNA 7223	ncRNA
mm_15974.1	chr2	166156476	166156514	+	1	NA	promoter-TSS (NM_028072)	promoter-TSS (NM_028072)	-812	NM_028072	72043	Mm.1011	NM_028072	ENSMUSG00000006800	Sulf2	2010004N24Rik|AU020235|MSulf-2|mKIAA1247	sulfatase 2	protein-coding
mm_68149.1	chr7	102250076	102250086	-	1	NA	promoter-TSS (NM_019566)	promoter-TSS (NM_019566)	37	NM_019566	56212	Mm.259795	NM_019566	ENSMUSG00000073982	Rhog	2810426G09Rik|Arhg|Sid10750	ras homolog family member G	protein-coding
mm_147096.1	chr18	35649493	35649499	-	1	NA	promoter-TSS (NM_027222)	promoter-TSS (NM_027222)	-129	NM_027222	69816	Mm.27252	NM_027222	ENSMUSG00000024353	Mzb1	2010001M09Rik|AV064572|PACAP|pERp1	marginal zone B and B1 cell-specific protein 1	protein-coding
mm_84339.1	chr9	64178344	64178379	-	1	NA	promoter-TSS (NM_183316)	promoter-TSS (NM_183316)	-936	NM_183316	330959	Mm.24082	NM_183316	ENSMUSG00000032398	Snapc5	2010103A03Rik	small nuclear RNA activating complex, polypeptide 5	protein-coding
mm_21761.1	chr2	164840162	164840192	-	1	NA	exon (NM_011125, exon 15 of 16)	exon (NM_011125, exon 15 of 16)	6404	NM_008906	19025	Mm.359633	NM_008906	ENSMUSG00000017760	Ctsa	AU019505|PPCA|Ppgb	cathepsin A	protein-coding
mm_158667.1	chrX	157557155	157557189	-	1	NA	intron (NM_172307, intron 7 of 10)	intron (NM_172307, intron 7 of 10)	11813	NM_001098723	100073351	Mm.491276	NM_001098723	ENSMUSG00000046873	Yy2	-	Yy2 transcription factor	protein-coding
mm_50606.1	chr6	49372347	49372383	+	1	NA	intron (NM_001172216, intron 1 of 5)	intron (NM_001172216, intron 1 of 5)	4626	NM_172727	231946	Mm.35199	NM_172727	ENSMUSG00000047115	Fam221a	D330028D13Rik	family with sequence similarity 221, member A	protein-coding
mm_108672.1	chr12	86520557	86520572	+	1	NA	3' UTR (NM_011934, exon 7 of 7)	3' UTR (NM_011934, exon 7 of 7)	98920	NM_011934	26380	Mm.235550	NM_011934	ENSMUSG00000021255	Esrrb	Err2|Errb|Estrrb|Nr3b2	estrogen related receptor, beta	protein-coding
mm_61059.1	chr7	49959796	49959799	+	1	NA	TTS (NM_001146013)	TTS (NM_001146013)	-15553	NM_001037906	338352	Mm.383528	NM_001037906	ENSMUSG00000055409	Nell1	B230343H07Rik|l7R6	NEL-like 1	protein-coding
mm_128501.1	chr15	52478352	52478381	-	1	NA	Intergenic	B4|SINE|B4	182813	NM_172816	239436	Mm.208831	NM_172816	ENSMUSG00000022315	Slc30a8	C820002P14Rik|ZnT-8|ZnT8	solute carrier family 30 (zinc transporter), member 8	protein-coding
mm_3385.1	chr1	139501735	139501746	+	1	NA	promoter-TSS (NM_031164)	promoter-TSS (NM_031164)	33	NM_031164	14060	Mm.30105	NM_031164	ENSMUSG00000026368	F13b	Cf-13b|Cf13b	coagulation factor XIII, beta subunit	protein-coding
mm_103876.1	chr11	83527663	83527674	-	1	NA	intron (NM_013653, intron 2 of 2)	intron (NM_013653, intron 2 of 2)	2850	NM_013653	20304	Mm.284248	NM_013653	ENSMUSG00000035042	Ccl5	MuRantes|RANTES|SISd|Scya5|TCP228	chemokine (C-C motif) ligand 5	protein-coding
mm_147775.1	chr18	61484811	61484829	-	1	NA	promoter-TSS (NR_045419)	promoter-TSS (NR_045419)	-213	NR_045419	442846	Mm.417648	NR_045419		A530050N04Rik	-	RIKEN cDNA A530050N04 gene	ncRNA
mm_67183.1	chr7	73816463	73816480	-	1	NA	promoter-TSS (NR_077222)	promoter-TSS (NR_077222)	32	NR_077222	100579147	Mm.109205	NR_077222	ENSMUSG00000074067	Gm10619	4932443D20|ENSMUSG00000074067	predicted gene 10619	ncRNA
mm_126576.1	chr15	82268794	82268820	+	1	NA	Intergenic	Intergenic	-6128	NM_011889	24050	Mm.309707	NM_011889	ENSMUSG00000022456	Sept3	3110018K01Rik|AV154067|B530002E20Rik|Sep3	septin 3	protein-coding
mm_20543.1	chr2	131068126	131068164	-	1	NA	Intergenic	Intergenic	-4331	NM_001163529	110751	Mm.108550	NM_033615	ENSMUSG00000027318	Adam33	Adaml	a disintegrin and metallopeptidase domain 33	protein-coding
mm_150028.1	chr19	29373748	29373762	+	1	NA	exon (NM_021893, exon 3 of 7)	exon (NM_021893, exon 3 of 7)	6317	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_19609.1	chr2	102746713	102746717	-	1	NA	intron (NM_001077515, intron 5 of 10)	intron (NM_001077515, intron 5 of 10)	40277	NM_001077515	20511	Mm.267547	NM_011393	ENSMUSG00000005089	Slc1a2	1700091C19Rik|2900019G14Rik|AI159670|Eaat2|GLT-1|GLT1|MGLT1	solute carrier family 1 (glial high affinity glutamate transporter), member 2	protein-coding
mm_37882.1	chr4	132422561	132422575	-	1	NA	promoter-TSS (NM_175306)	promoter-TSS (NM_175306)	-122	NM_175306	100169	Mm.158361	NM_175306	ENSMUSG00000066043	Phactr4	3110001B12Rik|AI527228|AW495572|C330013F19Rik|N28169|mKIAA4120	phosphatase and actin regulator 4	protein-coding
mm_18176.1	chr2	45110216	45110234	-	1	NA	promoter-TSS (NM_001289521)	promoter-TSS (NM_001289521)	52	NM_001289521	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_17632.1	chr2	31053597	31053608	-	1	NA	3' UTR (NM_019406, exon 9 of 9)	3' UTR (NM_019406, exon 9 of 9)	42898	NM_001177650	14269	Mm.52297	NM_019406	ENSMUSG00000075415	Fnbp1	1110057E06Rik|2210010H06Rik|FBP1|Fbp17	formin binding protein 1	protein-coding
mm_53832.1	chr6	148109426	148109433	+	1	NA	intron (NM_001347516, intron 1 of 11)	intron (NM_001347516, intron 1 of 11)	62013	NM_178797	330450	Mm.447274	NM_178797	ENSMUSG00000030303	Far2	A230046P18|AW048109|BC055759|Mlstd1	fatty acyl CoA reductase 2	protein-coding
mm_170739.1	chr2	154892695	154892696	-	1	NA	exon (NM_026030, exon 1 of 9)	exon (NM_026030, exon 1 of 9)	211	NM_026030	67204	Mm.377134	NM_026030	ENSMUSG00000074656	Eif2s2	2810026E11Rik|38kDa|AA408636|AA571381|AA986487|AW822225|D2Ertd303e|EIF2|EIF2B	eukaryotic translation initiation factor 2, subunit 2 (beta)	protein-coding
mm_52576.1	chr6	116354870	116354870	+	1	NA	intron (NM_001302385, intron 2 of 6)	Lx5c|LINE|L1	16848	NM_027920	71779	Mm.27064	NM_027920	ENSMUSG00000025702	March8	1300017E09Rik|MARCH-VIII|Mir	membrane-associated ring finger (C3HC4) 8	protein-coding
mm_120370.1	chr14	64587290	64587305	+	1	NA	promoter-TSS (NR_040709)	promoter-TSS (NR_040709)	-818	NR_040709	268755	Mm.194050	NR_040709	ENSMUSG00000097545	Mir124a-1hg	A930011O12Rik|Rncr3|mir-124-1|mir-3078	Mir124-1 host gene (non-protein coding)	ncRNA
mm_55551.1	chr6	71262238	71262255	-	1	NA	promoter-TSS (NM_001160127)	promoter-TSS (NM_001160127)	35	NM_001160127	12180	Mm.234274	NM_009762	ENSMUSG00000055027	Smyd1	4632404M21Rik|Bop|C78565|Zmynd18	SET and MYND domain containing 1	protein-coding
mm_68303.1	chr7	105746504	105746530	-	1	NA	3' UTR (NM_009906, exon 13 of 13)	3' UTR (NM_009906, exon 13 of 13)	-2179	NM_020024	24075	Mm.274846	NM_020024	ENSMUSG00000043866	Taf10	30kDa|AU041226|TAFII30|Taf2h	TATA-box binding protein associated factor 10	protein-coding
mm_107141.1	chr12	21417270	21417280	+	1	NA	5' UTR (NM_011739, exon 1 of 5)	5' UTR (NM_011739, exon 1 of 5)	161	NM_011739	22630	Mm.289630	NM_011739	ENSMUSG00000076432	Ywhaq	2700028P07Rik|AA409740|AU021156|R74690	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide	protein-coding
mm_23505.1	chr3	60528743	60528779	+	1	NA	5' UTR (NM_001253708, exon 2 of 9)	5' UTR (NM_001253708, exon 2 of 9)	27582	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_49897.1	chr6	38919090	38919100	+	1	NA	5' UTR (NM_011539, exon 1 of 13)	5' UTR (NM_011539, exon 1 of 13)	109	NM_011539	21391	Mm.4054	NM_011539	ENSMUSG00000029925	Tbxas1	CYP5|CYP5A1|THAS|TS|TXAS|TXS	thromboxane A synthase 1, platelet	protein-coding
mm_74875.1	chr8	25038957	25038974	-	1	NA	promoter-TSS (NM_001081187)	promoter-TSS (NM_001081187)	-3	NM_001081187	330723	Mm.334452	NM_001081187	ENSMUSG00000037406	Htra4	B430206E18Rik	HtrA serine peptidase 4	protein-coding
mm_166657.1	chr6	87533304	87533334	-	1	NA	promoter-TSS (NM_001286610)	promoter-TSS (NM_001286610)	-60	NM_001286610	232201	Mm.119564	NM_175476	ENSMUSG00000030047	Arhgap25	A130039I20Rik	Rho GTPase activating protein 25	protein-coding
mm_152609.1	chr19	11869115	11869128	-	1	NA	Intergenic	Intergenic	2093	NM_001011775	257938	Mm.377309	NM_001011775	ENSMUSG00000067545	Olfr1419	MOR266-10	olfactory receptor 1419	protein-coding
mm_48438.1	chr5	140623476	140623500	-	1	NA	exon (NM_175274, exon 14 of 14)	exon (NM_175274, exon 14 of 14)	16147	NM_008494	16848	Mm.12834	NM_008494	ENSMUSG00000029570	Lfng	AW061165	LFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	protein-coding
mm_122065.1	chr14	30469887	30469895	-	1	NA	intron (NM_028981, intron 1 of 46)	intron (NM_028981, intron 1 of 46)	-9674	NM_133761	75901	Mm.28733	NM_133761	ENSMUSG00000021962	Dcp1a	1110066A22Rik|4930568L04Rik|AU019772|D14Ertd817e|Mitc1|SMIF	decapping mRNA 1A	protein-coding
mm_123749.1	chr14	70192780	70192786	-	1	NA	promoter-TSS (NM_001271409)	promoter-TSS (NM_001271409)	-537	NM_001271409	20410	Mm.5068	NM_011366	ENSMUSG00000022091	Sorbs3	SCAM-1|SH3P3|Sh3d4|vinexin-g	sorbin and SH3 domain containing 3	protein-coding
mm_14810.1	chr2	145934801	145934813	+	1	NA	promoter-TSS (NM_025820)	promoter-TSS (NM_025820)	23	NM_175280	78774	Mm.136347	NM_175280	ENSMUSG00000037143	Cfap61	4930529M08Rik|BB178539|BC024760	cilia and flagella associated protein 61	protein-coding
mm_21716.1	chr2	164608902	164608921	-	1	NA	5' UTR (NM_001080550, exon 2 of 8)	5' UTR (NM_001080550, exon 2 of 8)	4475	NM_001276432	277343	Mm.383292	NM_001080550	ENSMUSG00000070533	Wfdc8	Gm706	WAP four-disulfide core domain 8	protein-coding
mm_22628.1	chr3	14766544	14766593	+	1	NA	exon (NM_001083957, exon 7 of 7)	exon (NM_001083957, exon 7 of 7)	11892	NM_001083957	12346	Mm.273195	NM_009799	ENSMUSG00000027556	Car1	AW555628|Ca1|Car-1	carbonic anhydrase 1	protein-coding
mm_63758.1	chr7	131110995	131111029	+	1	NA	exon (NM_007769, exon 43 of 47)	exon (NM_007769, exon 43 of 47)	35271	NM_173409	233918	Mm.78341	NM_173409	ENSMUSG00000013668	4933402N03Rik	4930412O05	RIKEN cDNA 4933402N03 gene	protein-coding
mm_16589.1	chr2	4141129	4141146	-	1	NA	promoter-TSS (NR_040500)	promoter-TSS (NR_040500)	4	NR_040500	73489	Mm.488103	NR_040500	ENSMUSG00000084859	1700080N15Rik	4933408D14Rik	RIKEN cDNA 1700080N15 gene	ncRNA
mm_62230.1	chr7	98539395	98539404	+	1	NA	Intergenic	L1MB8|LINE|L1	45177	NM_001113379	434215	Mm.323057	NM_001113379	ENSMUSG00000090958	Lrrc32	AI426318|D11S833Eh|D7H11S833E|EG434215|Garp	leucine rich repeat containing 32	protein-coding
mm_31532.1	chr4	55350044	55350078	+	1	NA	promoter-TSS (NM_009011)	promoter-TSS (NM_009011)	19	NM_009011	19359	Mm.196846	NM_009011	ENSMUSG00000028426	Rad23b	0610007D13Rik|AV001138|HR23B|mHR23B|p58	RAD23 homolog B, nucleotide excision repair protein	protein-coding
mm_51707.1	chr6	86668864	86668906	+	1	NA	intron (NM_010751, intron 1 of 5)	CpG	274	NM_010751	17119	Mm.279580	NM_010751	ENSMUSG00000001156	Mxd1	AW122478|Mad|Mad1	MAX dimerization protein 1	protein-coding
mm_169604.1	chr15	36657767	36657770	-	1	NA	Intergenic	Intergenic	-48795	NM_008774	18458	Mm.371570	NM_008774	ENSMUSG00000022283	Pabpc1	PABP|Pabp1|PabpI|Pabpl1|ePAB	poly(A) binding protein, cytoplasmic 1	protein-coding
mm_58058.1	chr6	136857650	136857678	-	1	NA	promoter-TSS (NM_026639)	promoter-TSS (NM_026639)	-64	NM_026639	109978	Mm.31840	NM_026639	ENSMUSG00000030217	Art4	4432404K01Rik|ARTC4|DO|DOK1	ADP-ribosyltransferase 4	protein-coding
mm_35359.1	chr4	32351432	32351440	-	1	NA	Intergenic	Intergenic	-65999	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_53803.1	chr6	146861799	146861805	+	1	NA	intron (NM_027059, intron 6 of 9)	intron (NM_027059, intron 6 of 9)	11692	NM_027059	69371	Mm.252733	NM_027059	ENSMUSG00000030292	Smco2	1700023A16Rik	single-pass membrane protein with coiled-coil domains 2	protein-coding
mm_105856.1	chr11	113751310	113751327	-	1	NA	promoter-TSS (NM_020006)	promoter-TSS (NM_020006)	-158	NM_020006	56699	Mm.293378	NM_020006	ENSMUSG00000041598	Cdc42ep4	1500041M20Rik|Borg4|CEP4	CDC42 effector protein (Rho GTPase binding) 4	protein-coding
mm_39525.1	chr5	21266185	21266198	+	1	NA	intron (NM_175437, intron 19 of 30)	MTD|LTR|ERVL-MaLR	79924	NM_175437	212167	Mm.121705	NM_175437	ENSMUSG00000039934	Gsap	A530088I07Rik|Pion	gamma-secretase activating protein	protein-coding
mm_78177.1	chr9	21184114	21184130	+	1	NA	promoter-TSS (NM_001310750)	promoter-TSS (NM_001310750)	21	NM_001310750	18577	Mm.191749	NM_019798	ENSMUSG00000032177	Pde4a	D9Ertd60e|Dpde2	phosphodiesterase 4A, cAMP specific	protein-coding
mm_38702.1	chr4	145215116	145215133	-	1	NA	3' UTR (NM_011610, exon 10 of 10)	3' UTR (NM_011610, exon 10 of 10)	-20119	NM_001276465	230895	Mm.240310	NM_001033190	ENSMUSG00000020220	Vps13d	-	vacuolar protein sorting 13D	protein-coding
mm_157545.1	chrX	51206018	51206033	-	1	NA	promoter-TSS (NM_134163)	promoter-TSS (NM_134163)	-35	NM_134163	171170	Mm.295324	NM_134163	ENSMUSG00000036109	Mbnl3	A530038J18Rik|AI661274|CHCR|E430034C16Rik|MBLX|MBLX39|MBXL	muscleblind-like 3 (Drosophila)	protein-coding
mm_35327.1	chr4	26332044	26332047	-	1	NA	intron (NM_172865, intron 3 of 4)	intron (NM_172865, intron 3 of 4)	14607	NM_172865	242362	Mm.245602	NM_172865	ENSMUSG00000040520	Manea	4932703L02Rik	mannosidase, endo-alpha	protein-coding
mm_20890.1	chr2	148872021	148872047	-	1	NA	exon (NM_009976, exon 3 of 3)	exon (NM_009976, exon 3 of 3)	3478	NM_009976	13010	Mm.4263	NM_009976	ENSMUSG00000027447	Cst3	CysC	cystatin C	protein-coding
mm_121748.1	chr14	18893665	18893717	-	1	NA	promoter-TSS (NM_144839)	promoter-TSS (NM_144839)	-64	NM_144839	218793	Mm.23551	NM_144839	ENSMUSG00000058317	Ube2e2	BC016265	ubiquitin-conjugating enzyme E2E 2	protein-coding
mm_70632.1	chr8	13780792	13780801	+	1	NA	intron (NM_027276, intron 17 of 17)	intron (NM_027276, intron 17 of 17)	-4819	NM_025924	67031	Mm.44858	NM_025924	ENSMUSG00000038398	Upf3a	2600001C03Rik|4930546M19Rik|RENT3A|UPF3	UPF3 regulator of nonsense transcripts homolog A (yeast)	protein-coding
mm_1264.1	chr1	63177747	63177760	+	1	NA	promoter-TSS (NM_001160039)	promoter-TSS (NM_001160039)	922	NM_018796	55949	Mm.2718	NM_018796	ENSMUSG00000025967	Eef1b2	2810017J07Rik|Eef1b	eukaryotic translation elongation factor 1 beta 2	protein-coding
mm_169824.1	chr16	22910998	22911004	-	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	-7381	NM_001083905	59083	Mm.28461	NM_021564	ENSMUSG00000022871	Fetub	2310011O17Rik|AI255764|D17980|Gugu	fetuin beta	protein-coding
mm_131890.1	chr16	23226343	23226353	+	1	NA	intron (NM_001252505, intron 1 of 7)	intron (NM_001252505, intron 1 of 7)	327	NM_001252505	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_22252.1	chr2	174853282	174853301	-	1	NA	Intergenic	Intergenic	92672	NM_007903	13616	Mm.9478	NM_007903	ENSMUSG00000027524	Edn3	ET-3|PPET3|ls|tmgc48	endothelin 3	protein-coding
mm_58036.1	chr6	136781813	136781829	-	1	NA	promoter-TSS (NM_001127318)	promoter-TSS (NM_001127318)	-79	NM_001127318	14917	Mm.222729	NM_145067	ENSMUSG00000042638	Gucy2c	AI893437|GC-C|Gcc	guanylate cyclase 2c	protein-coding
mm_163265.1	chr11	114675503	114675505	+	1	NA	promoter-TSS (NM_053273)	promoter-TSS (NM_053273)	36	NM_053273	117160	Mm.271934	NM_053273	ENSMUSG00000034714	Ttyh2	1110001A03Rik	tweety family member 2	protein-coding
mm_122310.1	chr14	36906306	36906315	-	1	NA	intron (NM_001347503, intron 3 of 7)	intron (NM_001347503, intron 3 of 7)	13225	NM_001347503	72972	Mm.27621	NM_027045	ENSMUSG00000058690	Ccser2	1700012P13Rik|2900054P12Rik|AI035535|AW108503|Fam190b|Gcap14	coiled-coil serine rich 2	protein-coding
mm_170431.1	chr18	77038707	77038725	+	1	NA	intron (NM_027721, intron 1 of 13)	MLTR25A|LTR|ERVK	8580	NM_027721	71206	Mm.35803	NM_027721	ENSMUSG00000025420	Katnal2	3110023G01Rik|4933439B08Rik	katanin p60 subunit A-like 2	protein-coding
mm_91825.1	chr10	56228637	56228695	-	1	NA	promoter-TSS (NM_001033385)	promoter-TSS (NM_001033385)	23	NM_001033385	544696	Mm.411188	NM_001033385	ENSMUSG00000038122	Tbc1d32	Bromi|D630037F22Rik|b2b2284Clo	TBC1 domain family, member 32	protein-coding
mm_80706.1	chr9	92250062	92250068	+	1	NA	promoter-TSS (NM_011636)	promoter-TSS (NM_011636)	-129	NM_011636	22038	Mm.421956	NM_011636	ENSMUSG00000032369	Plscr1	MmTRA1a|MmTRA1b|Nor1|Tra1|Tra1a|Tra1b|Tras1|Tras2	phospholipid scramblase 1	protein-coding
mm_21946.1	chr2	167062559	167062605	-	1	NA	promoter-TSS (NR_138563)	promoter-TSS (NR_138563)	-352	NR_138563	68949	Mm.391959	NM_001081005		Zfas1	1500012F01Rik|Zfos1	zinc finger, NFX1-type containing 1, antisense RNA 1	ncRNA
mm_97356.1	chr11	77498185	77498190	+	1	NA	intron (NM_001004144, intron 1 of 19)	intron (NM_001004144, intron 1 of 19)	4775	NM_001004144	216963	Mm.290182	NM_001004144	ENSMUSG00000011877	Git1	Cat-1|p95Cat	G protein-coupled receptor kinase-interactor 1	protein-coding
mm_113950.1	chr13	50950181	50950189	+	1	NA	Intergenic	Intergenic	150542	NR_029463	77428	Mm.405630	NR_029463		9430083A17Rik	-	RIKEN cDNA 9430083A17 gene	ncRNA
mm_42622.1	chr5	118154945	118154955	+	1	NA	intron (NM_172721, intron 1 of 10)	intron (NM_172721, intron 1 of 10)	508	NM_172721	231672	Mm.221769	NM_172721	ENSMUSG00000032867	Fbxw8	4930438M06Rik|FBW6|FBW8|FBXO29|Fbx29	F-box and WD-40 domain protein 8	protein-coding
mm_94729.1	chr11	20740694	20740725	+	1	NA	intron (NM_001290545, intron 1 of 9)	intron (NM_001290545, intron 1 of 9)	847	NM_001290545	216549	Mm.356580	NM_181411	ENSMUSG00000049659	Aftph	-	aftiphilin	protein-coding
mm_131002.1	chr15	103538022	103538032	-	1	NA	promoter-TSS (NM_021391)	promoter-TSS (NM_021391)	-35	NM_021391	58200	Mm.143788	NM_021391	ENSMUSG00000022490	Ppp1r1a	0610038N18Rik|I-1	protein phosphatase 1, regulatory (inhibitor) subunit 1A	protein-coding
mm_61275.1	chr7	66743616	66743624	+	1	NA	5' UTR (NM_001164201, exon 1 of 11)	5' UTR (NM_001164201, exon 1 of 11)	116	NM_001164201	545975	Mm.380104	NM_001164201	ENSMUSG00000030510	Cers3	4930550L11Rik|Gm488|Lass3|T3L	ceramide synthase 3	protein-coding
mm_100000.1	chr11	114851393	114851426	+	1	NA	promoter-TSS (NM_147217)	promoter-TSS (NM_147217)	-123	NM_001110337	70355	Mm.242413	NM_147217	ENSMUSG00000051043	Gprc5c	1110028I06Rik|3200002M13Rik|Raig3	G protein-coupled receptor, family C, group 5, member C	protein-coding
mm_52926.1	chr6	122922597	122922619	+	1	NA	intron (NM_199311, intron 1 of 5)	intron (NM_199311, intron 1 of 5)	760	NM_199311	269799	Mm.297275	NM_199311	ENSMUSG00000049037	Clec4a1	BC049354|Dcir4	C-type lectin domain family 4, member a1	protein-coding
mm_10221.1	chr2	5954582	5954621	+	1	NA	intron (NM_001081132, intron 1 of 21)	MIRb|SINE|MIR	3132	NM_001081132	326622	Mm.31102	NM_001081132	ENSMUSG00000043241	Upf2	-	UPF2 regulator of nonsense transcripts homolog (yeast)	protein-coding
mm_84646.1	chr9	71485877	71485887	-	1	NA	promoter-TSS (NM_001164793)	promoter-TSS (NM_001164793)	101	NM_178602	28015	Mm.21094	NM_178602	ENSMUSG00000032199	Polr2m	AA407243|AA408799|AI303746|AW553238|D9Wsu138e|Grinl1a|mKIAA4185	polymerase (RNA) II (DNA directed) polypeptide M	protein-coding
mm_17468.1	chr2	28559357	28559395	-	1	NA	exon (NM_009885, exon 7 of 11)	exon (NM_009885, exon 7 of 11)	4027	NM_009885	12613	Mm.236017	NM_009885	ENSMUSG00000026818	Cel	1810036E18Rik|BAL	carboxyl ester lipase	protein-coding
mm_60659.1	chr7	44943206	44943214	+	1	NA	promoter-TSS (NM_001077591)	promoter-TSS (NM_001077591)	-30	NM_001077591	22116	Mm.84502	NM_011651	ENSMUSG00000059891	Tsks	Stk22s1|Tssks1	testis-specific serine kinase substrate	protein-coding
mm_60888.1	chr7	46396674	46396686	+	1	NA	5' UTR (NM_001112739, exon 1 of 4)	5' UTR (NM_001112739, exon 1 of 4)	212	NM_001112739	16502	Mm.249386	NM_008421	ENSMUSG00000058975	Kcnc1	C230009H10Rik|KShIIIB|KV4|Kcr2-1|Kv3.1|NGK2|Shaw	potassium voltage gated channel, Shaw-related subfamily, member 1	protein-coding
mm_68871.1	chr7	126446907	126446914	-	1	NA	exon (NM_007504, exon 21 of 23)	exon (NM_007504, exon 21 of 23)	16163	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_98636.1	chr11	96124756	96124781	+	1	NA	Intergenic	Intergenic	-9018	NM_172799	237930	Mm.249912	NM_172799	ENSMUSG00000038756	Ttll6	4932418K24Rik|D11Moh43e|D11Moh44e|t8130b59	tubulin tyrosine ligase-like family, member 6	protein-coding
mm_36919.1	chr4	108118506	108118521	-	1	NA	promoter-TSS (NM_011327)	promoter-TSS (NM_011327)	34	NM_011327	20280	Mm.379011	NM_011327	ENSMUSG00000028603	Scp2	AA409774|AA409893|C76618|C79031|NSL-TP|SCP-2|SCP-X|SCPX|ns-LTP	sterol carrier protein 2, liver	protein-coding
mm_105839.1	chr11	113683282	113683312	-	1	NA	intron (NM_138598, intron 1 of 2)	intron (NM_138598, intron 1 of 2)	854	NM_138598	28081	Mm.351688	NM_138598	ENSMUSG00000041629	Fam104a	D11Wsu99e	family with sequence similarity 104, member A	protein-coding
mm_49348.1	chr6	21986156	21986175	+	1	NA	5' UTR (NM_001081351, exon 1 of 22)	5' UTR (NM_001081351, exon 1 of 22)	255	NM_001081351	214642	Mm.221404	NM_001081351	ENSMUSG00000062980	Cped1	6720481P07|A430107O13Rik|AI552584	cadherin-like and PC-esterase domain containing 1	protein-coding
mm_103353.1	chr11	74831993	74832010	-	1	NA	intron (NM_010813, intron 1 of 5)	CpG-2219	1077	NM_010813	17428	Mm.3759	NM_010813	ENSMUSG00000000282	Mnt	Rox|bHLHd3	max binding protein	protein-coding
mm_159518.1	chr4	60662313	60662313	-	1	NA	promoter-TSS (NM_001134644).3	promoter-TSS (NM_001134644).3	52	NM_001134644	100048885	Mm.422695	NM_001134644		Gm2083	-	major urinary protein LOC100048885	protein-coding
mm_44908.1	chr5	35663586	35663603	-	1	NA	intron (NM_001042615, intron 6 of 6)	(TGGA)n|Simple_repeat|Simple_repeat	16186	NM_001042615	78558	Mm.274255	NM_030127	ENSMUSG00000029096	Htra3	2210021K23Rik|9530081K03Rik|Prsp|Tasp	HtrA serine peptidase 3	protein-coding
mm_70123.1	chr7	143053380	143053459	-	1	NA	non-coding (NR_015529, exon 1 of 4)	non-coding (NR_015529, exon 1 of 4)	267	NR_110355	97423	Mm.5250	NM_133790	ENSMUSG00000059277	R74862	-	expressed sequence R74862	ncRNA
mm_93933.1	chr10	127177001	127177030	-	1	NA	intron (NM_177615, intron 6 of 16)	intron (NM_177615, intron 6 of 16)	3630	NM_177615	216441	Mm.248373	NM_177615	ENSMUSG00000040441	Slc26a10	C78409|D630010I07	solute carrier family 26, member 10	protein-coding
mm_25772.1	chr3	126596327	126596343	+	1	NA	promoter-TSS (NM_001293663)	promoter-TSS (NM_001293663)	-616	NM_001293663	108058	Mm.255822	NM_023813	ENSMUSG00000053819	Camk2d	2810011D23Rik|8030469K03Rik|CaMK II|[d]-CaMKII	calcium/calmodulin-dependent protein kinase II, delta	protein-coding
mm_104009.1	chr11	85139900	85139922	-	1	NA	promoter-TSS (NM_001029934)	promoter-TSS (NM_001029934)	44	NM_001029934	237898	Mm.178524	NM_001029934	ENSMUSG00000000804	Usp32	2900074J03Rik|6430526O11Rik|AW045245	ubiquitin specific peptidase 32	protein-coding
mm_130116.1	chr15	89477059	89477085	-	1	NA	intron (NM_009713, intron 1 of 8)	intron (NM_009713, intron 1 of 8)	352	NM_009713	11883	Mm.620	NM_009713	ENSMUSG00000022620	Arsa	AS-A|ASA|AW212749|As-2|As2|TISP73	arylsulfatase A	protein-coding
mm_121624.1	chr14	8309771	8309784	-	1	NA	promoter-TSS (NM_183187)	promoter-TSS (NM_183187)	-1	NM_183187	268709	Mm.256058	NM_183187	ENSMUSG00000021750	Fam107a	DRR1	family with sequence similarity 107, member A	protein-coding
mm_30148.1	chr3	142546020	142546048	-	1	NA	exon (NM_001083312, exon 10 of 11)	exon (NM_001083312, exon 10 of 11)	-14018	NM_018734	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_12585.1	chr2	73452797	73452809	+	1	NA	intron (NM_153138, intron 1 of 7)	intron (NM_153138, intron 1 of 7)	1086	NM_001289722	215280	Mm.223504	NM_153138	ENSMUSG00000075284	Wipf1	AI115543|D2Ertd120e|WIP|Waspip	WAS/WASL interacting protein family, member 1	protein-coding
mm_75700.1	chr8	68212255	68212266	-	1	NA	Intergenic	Intergenic	-64268	NM_028182	72281	Mm.40974	NM_028182	ENSMUSG00000053886	Sh2d4a	2210402M20Rik|SH2A	SH2 domain containing 4A	protein-coding
mm_123559.1	chr14	66868115	66868148	-	1	NA	promoter-TSS (NM_001034881)	promoter-TSS (NM_001034881)	469	NM_009955	12934	Mm.352648	NM_009955	ENSMUSG00000022048	Dpysl2	AI851130|Crmp2|DRP2|Musunc33|TOAD-64|Ulip2	dihydropyrimidinase-like 2	protein-coding
mm_119059.1	chr14	30716378	30716415	+	1	NA	intron (NM_001166532, intron 1 of 20)	CpG	781	NM_001166532	54650	Mm.294662	NM_019460	ENSMUSG00000006527	Sfmbt1	4930442N21Rik|9330180L21Rik|AA536974|Sfmbt|Smr	Scm-like with four mbt domains 1	protein-coding
mm_170979.1	chr2	70825315	70825329	-	1	NA	exon (NM_172664, exon 1 of 20)	exon (NM_172664, exon 1 of 20)	158	NM_172664	228012	Mm.136511	NM_172664	ENSMUSG00000041997	Tlk1	4930545J15Rik	tousled-like kinase 1	protein-coding
mm_103708.1	chr11	79516720	79516728	-	1	NA	exon (NM_001077496, exon 2 of 2)	exon (NM_001077496, exon 2 of 2)	7038	NM_001077496	216984	Mm.439665	NM_001077496	ENSMUSG00000093938	Evi2b	Evi-2|Evi2	ecotropic viral integration site 2b	protein-coding
mm_55055.1	chr6	49047330	49047362	-	1	NA	exon (NM_053110, exon 5 of 11)	exon (NM_053110, exon 5 of 11)	10828	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_133349.1	chr16	84301746	84301766	+	1	NA	Intergenic	Intergenic	-69387	NR_040567	75247	Mm.417813	NR_040567		4930553E22Rik	-	RIKEN cDNA 4930553E22 gene	ncRNA
mm_59535.1	chr7	27731613	27731621	+	1	NA	5' UTR (NM_009560, exon 1 of 5)	5' UTR (NM_009560, exon 1 of 5)	208	NM_009560	22718	Mm.66913	NM_009560	ENSMUSG00000037640	Zfp60	6330516O17Rik|AI426106|AI449354|Mfg-3|Mfg3	zinc finger protein 60	protein-coding
mm_73859.1	chr8	118283720	118283738	+	1	NA	5' UTR (NM_019707, exon 1 of 14)	5' UTR (NM_019707, exon 1 of 14)	118	NM_019707	12554	Mm.334841	NM_019707	ENSMUSG00000031841	Cdh13	4932416G01Rik|Cdht|Tcad	cadherin 13	protein-coding
mm_37107.1	chr4	116639072	116639107	-	1	NA	exon (NM_021473, exon 6 of 9)	exon (NM_021473, exon 6 of 9)	-11138	NM_016777	50927	Mm.257181	NM_016777	ENSMUSG00000028693	Nasp	5033430J04Rik|AI131596|AI317140|D4Ertd767e|Epcs32|Nasp-T	nuclear autoantigenic sperm protein (histone-binding)	protein-coding
mm_103190.1	chr11	70615673	70615690	-	1	NA	promoter-TSS (NM_001145537)	promoter-TSS (NM_001145537)	-213	NM_001145537	668433	Mm.425687	NM_001145537	ENSMUSG00000087279	4930544D05Rik	-	RIKEN cDNA 4930544D05 gene	protein-coding
mm_110831.1	chr12	72664736	72664756	-	1	NA	promoter-TSS (NM_025522)	promoter-TSS (NM_025522)	82	NM_025522	66375	Mm.289653	NM_025522	ENSMUSG00000021094	Dhrs7	2310016E22Rik|5730564L20Rik|AW061210|Retdsr4|Retsdr4	dehydrogenase/reductase (SDR family) member 7	protein-coding
mm_125205.1	chr15	33083214	33083295	+	1	NA	5' UTR (NM_018755, exon 1 of 9)	5' UTR (NM_018755, exon 1 of 9)	125	NM_176073	54381	Mm.158251	NM_018755	ENSMUSG00000039007	Cpq	1190003P12Rik|2610034C17Rik|Hls2|Lal-1|Pgcp	carboxypeptidase Q	protein-coding
mm_24706.1	chr3	95160970	95160973	+	1	NA	intron (NR_073550, intron 1 of 18)	CpG	551	NR_073551	20360	Mm.23662	NM_011351	ENSMUSG00000038777	Sema6c	Semay|mKIAA1869	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C	protein-coding
mm_127525.1	chr15	102073916	102073934	+	1	NA	5' UTR (NM_145625, exon 1 of 15)	5' UTR (NM_145625, exon 1 of 15)	152	NM_145625	75705	Mm.290022	NM_145625	ENSMUSG00000058655	Eif4b	2310046H11Rik|AL024095|C85189|Eif4a2	eukaryotic translation initiation factor 4B	protein-coding
mm_95822.1	chr11	55395431	55395444	+	1	NA	3' UTR (NM_009242, exon 10 of 10)	3' UTR (NM_009242, exon 10 of 10)	24643	NM_009242	20692	Mm.291442	NM_009242	ENSMUSG00000018593	Sparc	BM-40|ON	secreted acidic cysteine rich glycoprotein	protein-coding
mm_147436.1	chr18	46504011	46504046	-	1	NA	TTS (NM_173423)	TTS (NM_173423)	21943	NM_173423	240263	Mm.38249	NM_173423	ENSMUSG00000033319	Fem1c	2610312A07Rik|3632443A22Rik|AI646567	fem-1 homolog c (C.elegans)	protein-coding
mm_140238.1	chr17	84119912	84119920	+	1	NA	Intergenic	Intergenic	41256	NR_045458	74473	Mm.399575	NR_045458		4933433H22Rik	-	RIKEN cDNA 4933433H22 gene	ncRNA
mm_44431.1	chr5	21002835	21002847	-	1	NA	intron (NM_011203, intron 9 of 17)	intron (NM_011203, intron 9 of 17)	-51019	NM_001080977	242860	Mm.254286	NM_001080977	ENSMUSG00000039968	Rsbn1l	8430412F05Rik|AI447441|C330002G24Rik	round spermatid basic protein 1-like	protein-coding
mm_56919.1	chr6	119389023	119389031	-	1	NA	intron (NM_197985, intron 1 of 7)	CpG	28456	NM_197985	68465	Mm.291826	NM_197985	ENSMUSG00000030168	Adipor2	1110001I14Rik|ADCR2|AI115388|AW554121|D6Ucla1e|Paqr2	adiponectin receptor 2	protein-coding
mm_130480.1	chr15	98740241	98740351	-	1	NA	3' UTR (NM_007478, exon 5 of 5)	3' UTR (NM_007478, exon 5 of 5)	-12098	NM_024169	66120	Mm.30729	NM_024169	ENSMUSG00000003355	Fkbp11	1110002O23Rik|FKBP-11	FK506 binding protein 11	protein-coding
mm_157869.1	chrX	75416295	75416327	-	1	NA	promoter-TSS (NM_001166459)	promoter-TSS (NM_001166459)	273	NM_010839	105886298	Mm.16366	NM_010839	ENSMUSG00000090110	Cmc4	Mtcp1nb|p8MTCP1	C-x(9)-C motif containing 4	protein-coding
mm_84043.1	chr9	57836714	57836805	-	1	NA	Intergenic	CpG	-2525	NM_019689	56380	Mm.425588	NM_019689	ENSMUSG00000004661	Arid3b	Bdp|Dri2	AT rich interactive domain 3B (BRIGHT-like)	protein-coding
mm_31064.1	chr4	41316810	41316830	+	1	NA	Intergenic	Intergenic	-1919	NM_026893	68970	Mm.28891	NM_026893	ENSMUSG00000028436	Dcaf12	1500001L20Rik|5830424K06Rik|AA420338|AI851081|Wdr40a	DDB1 and CUL4 associated factor 12	protein-coding
mm_116256.1	chr13	34077993	34078015	-	1	NA	promoter-TSS (NM_009450)	promoter-TSS (NM_009450)	4	NM_009450	22151	Mm.422827	NM_009450	ENSMUSG00000058672	Tubb2a	M(beta)2|Tubb2	tubulin, beta 2A class IIA	protein-coding
mm_50957.1	chr6	58862880	58862910	+	1	NA	intron (NM_028705, intron 8 of 24)	intron (NM_028705, intron 8 of 24)	29195	NM_028705	73998	Mm.191892	NM_028705	ENSMUSG00000029804	Herc3	5730409F18Rik|AI646603|mKIAA0032	hect domain and RLD 3	protein-coding
mm_116353.1	chr13	38967116	38967150	-	1	NA	TTS (NR_131019)	TTS (NR_131019)	-6258	NM_001170431	108652	Mm.255506	NM_134060	ENSMUSG00000021432	Slc35b3	4921526O06Rik|AI428480|CGI-19|PABST2|PAPST2	solute carrier family 35, member B3	protein-coding
mm_78895.1	chr9	44630933	44630936	+	1	NA	intron (NM_007841, intron 10 of 13)	intron (NM_007841, intron 10 of 13)	26042	NM_181324	13209	Mm.267061	NM_007841	ENSMUSG00000032097	Ddx6	1110001P04Rik|E230023J21Rik|HLR2|mRCK/P54|p54|rck	DEAD (Asp-Glu-Ala-Asp) box polypeptide 6	protein-coding
mm_153684.1	chr19	44396719	44396733	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	10983	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_21939.1	chr2	167060139	167060174	-	1	NA	intron (NM_001033196, intron 1 of 13)	intron (NM_001033196, intron 1 of 13)	-2778	NR_138563	68949	Mm.391959	NM_001081005		Zfas1	1500012F01Rik|Zfos1	zinc finger, NFX1-type containing 1, antisense RNA 1	ncRNA
mm_42918.1	chr5	122718311	122718324	+	1	NA	exon (NM_011026, exon 3 of 12)	exon (NM_011026, exon 3 of 12)	10773	NM_001310718	18438	Mm.290884	NM_011026	ENSMUSG00000029470	P2rx4	AI504491|AW555605|D5Ertd444e|P2X4	purinergic receptor P2X, ligand-gated ion channel 4	protein-coding
mm_130402.1	chr15	97976144	97976154	-	1	NA	exon (NM_001113515, exon 53 of 53)	exon (NM_001113515, exon 53 of 53)	11920	NM_001252153	380967	Mm.196630	NM_201359	ENSMUSG00000052369	Tmem106c	AI046681|BC046621|D15Ertd405e	transmembrane protein 106C	protein-coding
mm_163808.1	chr14	19416127	19416159	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	186444	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_106922.1	chr12	8332202	8332214	+	1	NA	intron (NM_021429, intron 4 of 6)	intron (NM_021429, intron 4 of 6)	18775	NM_021429	58240	Mm.309954	NM_021429	ENSMUSG00000020605	Hs1bp3	-	HCLS1 binding protein 3	protein-coding
mm_23726.1	chr3	69016693	69016707	+	1	NA	exon (NM_133786, exon 7 of 24)	exon (NM_133786, exon 7 of 24)	6798	NR_029735	723949		NR_029735	ENSMUSG00000065606	Mir16-2	Mirn16-2|mir-16-2	microRNA 16-2	ncRNA
mm_68935.1	chr7	126501981	126502049	-	1	NA	intron (NM_183020, intron 1 of 22)	CpG	410	NM_001347658	233871	Mm.231450	NM_183020	ENSMUSG00000032637	Atxn2l	A2D|A2LG|A2RP|A2lp|Atxnl2	ataxin 2-like	protein-coding
mm_79513.1	chr9	57521197	57521203	+	1	NA	promoter-TSS (NM_007747)	promoter-TSS (NM_007747)	-32	NM_007747	12858	Mm.273403	NM_007747	ENSMUSG00000000088	Cox5a	AA959768|CcOX	cytochrome c oxidase subunit Va	protein-coding
mm_97831.1	chr11	83064467	83064471	+	1	NA	promoter-TSS (NM_011408)	promoter-TSS (NM_011408)	-643	NM_011408	20556	Mm.278689	NM_011408	ENSMUSG00000072620	Slfn2	Shlf2	schlafen 2	protein-coding
mm_68883.1	chr7	126447921	126447945	-	1	NA	exon (NM_007504, exon 17 of 23)	exon (NM_007504, exon 17 of 23)	15140	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_75786.1	chr8	70095148	70095158	-	1	NA	3' UTR (NM_007789, exon 15 of 15)	3' UTR (NM_007789, exon 15 of 15)	7433	NR_106033	102465646		NR_106033	ENSMUSG00000099042	Mir7066	Gm27290|mmu-mir-7066	microRNA 7066	ncRNA
mm_139243.1	chr17	47733804	47733811	+	1	NA	exon (NM_025973, exon 8 of 9)	exon (NM_025973, exon 8 of 9)	-3230	NM_001161722	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_89542.1	chr10	94575109	94575119	+	1	NA	promoter-TSS (NM_001168684)	promoter-TSS (NM_001168684)	-143	NM_001168684	319880	Mm.23047	NM_172051	ENSMUSG00000020023	Tmcc3	AW488095|C630016B22Rik|C88213|Tmcc1	transmembrane and coiled coil domains 3	protein-coding
mm_51877.1	chr6	90559392	90559414	+	1	NA	exon (NM_027406, exon 3 of 23)	exon (NM_027406, exon 3 of 23)	8555	NM_027406	107747	Mm.30035	NM_027406	ENSMUSG00000030088	Aldh1l1	1810048F20Rik|FDH|Fthfd|Neut2	aldehyde dehydrogenase 1 family, member L1	protein-coding
mm_4750.1	chr1	182255350	182255359	+	1	NA	Intergenic	Intergenic	27405	NM_007853	13244	Mm.29648	NM_007853	ENSMUSG00000038633	Degs1	AA536663|Degs|Des1|Mdes	delta(4)-desaturase, sphingolipid 1	protein-coding
mm_152264.1	chr19	8798422	8798432	-	1	NA	intron (NM_026329, intron 1 of 7)	intron (NM_026329, intron 1 of 7)	130	NM_026329	67710	Mm.22117	NM_026329	ENSMUSG00000071662	Polr2g	2410046K11Rik|A230108L04Rik|C76415|RBP7|Rpo2-7l	polymerase (RNA) II (DNA directed) polypeptide G	protein-coding
mm_121990.1	chr14	26442844	26442852	-	1	NA	intron (NM_001347494, intron 10 of 19)	intron (NM_001347494, intron 10 of 19)	85301	NR_038005	71106	Mm.158564	NR_038005	ENSMUSG00000021874	4933413J09Rik	GCSE	RIKEN cDNA 4933413J09 gene	ncRNA
mm_112275.1	chr12	114288627	114288643	-	1	NA	Intergenic	Intergenic	180831	NR_106062	102465663		NR_106062	ENSMUSG00000105438	Mir7094-1	mmu-mir-7094-1	microRNA 7094-1	ncRNA
mm_70295.1	chr8	3676504	3676547	+	1	NA	promoter-TSS (NM_025701)	promoter-TSS (NM_025701)	48	NM_025701	66682	Mm.29090	NM_025701	ENSMUSG00000040236	Trappc5	4021401A16Rik|TRS31	trafficking protein particle complex 5	protein-coding
mm_125804.1	chr15	74918754	74918768	+	1	NA	Intergenic	Intergenic	-36290	NM_001164039	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_130176.1	chr15	93336923	93336980	-	1	NA	promoter-TSS (NM_024189)	promoter-TSS (NM_024189)	-16	NM_024189	67057	Mm.4714	NM_024189	ENSMUSG00000022634	Yaf2	2810021M11Rik	YY1 associated factor 2	protein-coding
mm_157907.1	chrX	78091366	78091377	-	1	NA	promoter-TSS (NM_008754)	promoter-TSS (NM_008754)	3	NM_008754	18249	Mm.430771	NM_008754	ENSMUSG00000067684	Obp1a	OBP-1a|OBP5	odorant binding protein IA	protein-coding
mm_73475.1	chr8	106870828	106870840	+	1	NA	promoter-TSS (NM_001331048)	promoter-TSS (NM_001331048)	-2	NM_001331048	15118	Mm.56986	NM_008217	ENSMUSG00000031910	Has3	-	hyaluronan synthase 3	protein-coding
mm_26184.1	chr3	138342285	138342300	+	1	NA	Intergenic	Intergenic	29006	NM_026945	69117	Mm.46265	NM_026945	ENSMUSG00000053054	Adh6a	1810009C16Rik|Adh5a	alcohol dehydrogenase 6A (class V)	protein-coding
mm_130617.1	chr15	99972715	99972738	-	1	NA	promoter-TSS (NM_001284521)	promoter-TSS (NM_001284521)	-54	NM_001024526	207214	Mm.28811	NM_001024526	ENSMUSG00000023025	Larp4	DXErtd793|DXErtd793e	La ribonucleoprotein domain family, member 4	protein-coding
mm_141358.1	chr17	28770233	28770255	-	1	NA	intron (NM_011950, intron 2 of 11)	intron (NM_011950, intron 2 of 11)	927	NM_011950	26415	Mm.27970	NM_011950	ENSMUSG00000004864	Mapk13	SAPK4|Serk4	mitogen-activated protein kinase 13	protein-coding
mm_67998.1	chr7	100930962	100930974	-	1	NA	exon (NM_001081116, exon 1 of 21)	exon (NM_001081116, exon 1 of 21)	1193	NM_001081116	207212	Mm.29954	NM_001081116	ENSMUSG00000032875	Arhgef17	8030463K16|AI428794|AW558066|BC035332|mKIAA0337	Rho guanine nucleotide exchange factor (GEF) 17	protein-coding
mm_932.1	chr1	55450189	55450220	+	1	NA	intron (NM_001114663, intron 1 of 5)	(CA)n|Simple_repeat|Simple_repeat	44258	NM_001114663	227120	Mm.194183	NM_001114663	ENSMUSG00000038349	Plcl1	C230017K02Rik|PLC-L|PLC-L1|PLCE|PLCL|PLDL1|PRIP|PRIP-1	phospholipase C-like 1	protein-coding
mm_100385.1	chr11	119317059	119317066	+	1	NA	5' UTR (NM_130886, exon 3 of 22)	5' UTR (NM_130886, exon 3 of 22)	2275	NM_130886	170720	Mm.130832	NM_130886	ENSMUSG00000013483	Card14	Bimp2|CARMA2	caspase recruitment domain family, member 14	protein-coding
mm_110138.1	chr12	26447924	26447943	-	1	NA	intron (NM_021384, intron 4 of 5)	ID_B1|SINE|B4	8519	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_49235.1	chr6	17281217	17281227	+	1	NA	promoter-TSS (NM_001277756)	promoter-TSS (NM_001277756)	37	NM_016900	12390	Mm.396075	NM_016900	ENSMUSG00000000058	Cav2	AI447843	caveolin 2	protein-coding
mm_16441.1	chr2	180398457	180398462	+	1	NA	promoter-TSS (NR_029901)	promoter-TSS (NR_029901)	80	NR_029901	723954		NR_029901	ENSMUSG00000065460	Mir133a-2	Mirn133a-2|mir-133a-2	microRNA 133a-2	ncRNA
mm_6426.1	chr1	73930810	73930828	-	1	NA	intron (NM_001289895, intron 22 of 32)	intron (NM_001289895, intron 22 of 32)	-66353	NR_045311	109198	Mm.359721	NR_045311	ENSMUSG00000100301	6030407O03Rik	-	RIKEN cDNA 6030407O03 gene	ncRNA
mm_36869.1	chr4	107066838	107066866	-	1	NA	promoter-TSS (NM_025500)	promoter-TSS (NM_025500)	14	NM_025500	56280	Mm.29517	NM_025500	ENSMUSG00000028622	Mrpl37	2300004O14Rik|AI132596|MRP-L2|Rpml2	mitochondrial ribosomal protein L37	protein-coding
mm_76040.1	chr8	77466061	77466071	-	1	NA	intron (NM_030113, intron 1 of 22)	intron (NM_030113, intron 1 of 22)	-50990	NR_028125	70345	Mm.411813	NR_028125	ENSMUSG00000097882	0610038B21Rik	-	RIKEN cDNA 0610038B21 gene	ncRNA
mm_94984.1	chr11	31832116	31832136	+	1	NA	Intergenic	Intergenic	-7579	NR_102312	414116	Mm.150222	NR_102310	ENSMUSG00000085772	D630024D03Rik	-	RIKEN cDNA D630024D03 gene	ncRNA
mm_160924.1	chr11	85896819	85896819	+	1	NA	promoter-TSS (NM_172798)	promoter-TSS (NM_172798)	54	NM_172798	21387	Mm.275336	NM_011536	ENSMUSG00000000094	Tbx4	3930401C23	T-box 4	protein-coding
mm_85091.1	chr9	92227243	92227265	-	1	NA	Intergenic	Intergenic	-22940	NM_011636	22038	Mm.421956	NM_011636	ENSMUSG00000032369	Plscr1	MmTRA1a|MmTRA1b|Nor1|Tra1|Tra1a|Tra1b|Tras1|Tras2	phospholipid scramblase 1	protein-coding
mm_167829.1	chr9	124423698	124423719	-	1	NA	promoter-TSS (NR_015516)	promoter-TSS (NR_015516)	-79	NR_102721	75135	Mm.476814	NR_015516		4930526I15Rik	1600027J15Rik	RIKEN cDNA 4930526I15 gene	ncRNA
mm_159165.1	chr2	92221462	92221462	+	1	NA	promoter-TSS (NM_001109690)	promoter-TSS (NM_001109690)	-100	NM_001109690	192285	Mm.330408	NM_138755	ENSMUSG00000058318	Phf21a	80kDa|Bhc|Bhc80|D030065N23Rik|PFTF1	PHD finger protein 21A	protein-coding
mm_74928.1	chr8	25602051	25602060	-	1	NA	promoter-TSS (NM_001308482)	promoter-TSS (NM_001308482)	-229	NM_001001735	234135	Mm.217337	NM_001001735	ENSMUSG00000054823	Whsc1l1	6720429E03|A530023P05|AI528490|NSD3|WHISTLE	Wolf-Hirschhorn syndrome candidate 1-like 1 (human)	protein-coding
mm_36158.1	chr4	59914851	59914860	-	1	NA	exon (NM_021053, exon 1 of 4)	exon (NM_021053, exon 1 of 4)	201	NM_021053	30936	Mm.284433	NM_021053	ENSMUSG00000028386	Slc46a2	5430429N04Rik|Ly110|TSO-1C12|Tscot	solute carrier family 46, member 2	protein-coding
mm_126795.1	chr15	86415435	86415438	+	1	NA	intron (NM_145476, intron 11 of 12)	intron (NM_145476, intron 11 of 12)	200977	NM_145476	223754	Mm.28904	NM_145476	ENSMUSG00000051864	Tbc1d22a	BC023106|D15Ertd781e	TBC1 domain family, member 22a	protein-coding
mm_89296.1	chr10	87913649	87913662	+	1	NA	exon (NM_010512, exon 3 of 5)	exon (NM_010512, exon 3 of 5)	52544	NM_001111276	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_68082.1	chr7	101870688	101870707	-	1	NA	promoter-TSS (NM_008034)	promoter-TSS (NM_008034)	91	NM_001252554	14275	Mm.2135	NM_008034	ENSMUSG00000001827	Folr1	FBP1|Folbp-1|Folbp1	folate receptor 1 (adult)	protein-coding
mm_127523.1	chr15	102073645	102073654	+	1	NA	promoter-TSS (NM_145625)	promoter-TSS (NM_145625)	-124	NM_145625	75705	Mm.290022	NM_145625	ENSMUSG00000058655	Eif4b	2310046H11Rik|AL024095|C85189|Eif4a2	eukaryotic translation initiation factor 4B	protein-coding
mm_141114.1	chr17	26087393	26087421	-	1	NA	exon (NM_011933, exon 4 of 9)	exon (NM_011933, exon 4 of 9)	2757	NM_011933	26378	Mm.292869	NM_011933	ENSMUSG00000036775	Decr2	-	2-4-dienoyl-Coenzyme A reductase 2, peroxisomal	protein-coding
mm_74857.1	chr8	24814096	24814104	-	1	NA	intron (NM_001272059, intron 5 of 18)	MTD|LTR|ERVL-MaLR	10269	NM_001272058	11499	Mm.143889	NM_007401	ENSMUSG00000031554	Adam5	tMDC II|tMDCII	a disintegrin and metallopeptidase domain 5	protein-coding
mm_74542.1	chr8	9976341	9976355	-	1	NA	promoter-TSS (NM_176953)	promoter-TSS (NM_176953)	-25	NM_176953	319583	Mm.80584	NM_176953	ENSMUSG00000049717	Lig4	5830471N16Rik|tiny	ligase IV, DNA, ATP-dependent	protein-coding
mm_23744.1	chr3	69343879	69343889	+	1	NA	intron (NM_178726, intron 1 of 3)	intron (NM_178726, intron 1 of 3)	26966	NM_178726	242083	Mm.40577	NM_178726	ENSMUSG00000027784	Ppm1l	3222401G13|5930404J21Rik|AI481720|AW045850|PP2C|PP2Cepsilon|Pp2ce|Ppp2ce|mKIAA4175	protein phosphatase 1 (formerly 2C)-like	protein-coding
mm_22489.1	chr3	5860332	5860367	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-284101	NM_001163305	19302	Mm.132336	NM_008994	ENSMUSG00000040374	Pex2	D3Ertd138e|PAF-1|PMP35|Pxmp3	peroxisomal biogenesis factor 2	protein-coding
mm_67580.1	chr7	82771681	82771716	-	1	NA	intron (NM_175317, intron 18 of 19)	intron (NM_175317, intron 18 of 19)	-16054	NR_046004	77800	Mm.444811	NR_046004	ENSMUSG00000086690	4933406J10Rik	A930009F24Rik	RIKEN cDNA 4933406J10 gene	ncRNA
mm_20940.1	chr2	151039364	151039403	-	1	NA	promoter-TSS (NM_026086)	promoter-TSS (NM_026086)	-4	NM_026086	67311	Mm.480682	NM_026086	ENSMUSG00000053916	Nanp	1600031M04Rik|Hdhd4	N-acetylneuraminic acid phosphatase	protein-coding
mm_46443.1	chr5	105101616	105101626	-	1	NA	intron (NM_172777, intron 3 of 10)	L1M3|LINE|L1	8671	NM_172777	236573	Mm.425261	NM_172777	ENSMUSG00000029298	Gbp9	-	guanylate-binding protein 9	protein-coding
mm_95672.1	chr11	54080598	54080601	+	1	NA	Intergenic	MTEa|LTR|ERVL-MaLR	-11582	NM_019417	30794	Mm.21830	NM_019417	ENSMUSG00000020388	Pdlim4	Ril	PDZ and LIM domain 4	protein-coding
mm_45254.1	chr5	62766154	62766246	-	1	NA	promoter-TSS (NM_178407)	promoter-TSS (NM_178407)	-23	NM_178407	212285	Mm.244403	NM_178407	ENSMUSG00000037999	Arap2	Centd1|Gm148|mKIAA0580	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2	protein-coding
mm_83288.1	chr9	43107138	43107142	-	1	NA	Intergenic	Intergenic	-1422	NM_027144	69632	Mm.275266	NM_027144	ENSMUSG00000059495	Arhgef12	2310014B11Rik|AU019857|Larg|mKIAA0382	Rho guanine nucleotide exchange factor (GEF) 12	protein-coding
mm_58988.1	chr7	19092971	19092982	+	1	NA	exon (NM_001190490, exon 16 of 16)	exon (NM_001190490, exon 16 of 16)	-1568	NM_011383	20475	Mm.3410	NM_011383	ENSMUSG00000040841	Six5	Dmahp|MDMAHP|TrexBF	sine oculis-related homeobox 5	protein-coding
mm_39508.1	chr5	21220626	21220675	+	1	NA	intron (NM_175437, intron 6 of 30)	intron (NM_175437, intron 6 of 30)	34383	NM_175437	212167	Mm.121705	NM_175437	ENSMUSG00000039934	Gsap	A530088I07Rik|Pion	gamma-secretase activating protein	protein-coding
mm_18050.1	chr2	39190663	39190685	-	1	NA	promoter-TSS (NM_178778)	promoter-TSS (NM_178778)	56	NM_178778	320271	Mm.204836	NM_178778	ENSMUSG00000035236	Scai	9330112M16|A930041I02Rik|AI662729	suppressor of cancer cell invasion	protein-coding
mm_91111.1	chr10	19185885	19185900	-	1	NA	intron (NR_038022, intron 1 of 1)	intron (NR_038022, intron 1 of 1)	18654	NR_038022	100504265	Mm.383417	NR_038021		Gm20139	-	predicted gene, 20139	ncRNA
mm_82286.1	chr9	7604128	7604130	-	1	NA	Intergenic	Intergenic	-24102	NM_013903	30800	Mm.390121	NM_013903	ENSMUSG00000018620	Mmp20	-	matrix metallopeptidase 20 (enamelysin)	protein-coding
mm_71931.1	chr8	70282979	70283044	+	1	NA	promoter-TSS (NM_001146153)	promoter-TSS (NM_001146153)	12	NM_001146153	26558	Mm.388127	NM_011984	ENSMUSG00000003573	Homer3	AW146114	homer scaffolding protein 3	protein-coding
mm_135052.1	chr16	33786969	33787019	-	1	NA	Intergenic	Intergenic	-7043	NM_010739	17063	Mm.3177	NM_010739	ENSMUSG00000022824	Muc13	114/A10|14/A10|AI159736|Lrrp|Ly64|NJ-1	mucin 13, epithelial transmembrane	protein-coding
mm_133778.1	chr16	94969201	94969230	+	1	NA	intron (NM_001025584, intron 1 of 4)	intron (NM_001025584, intron 1 of 4)	28481	NM_001025584	16522	Mm.328720	NM_010606	ENSMUSG00000043301	Kcnj6	BIR1|GIRK2|KATP2|KCNJ7|Kir3.2|weaver|wv	potassium inwardly-rectifying channel, subfamily J, member 6	protein-coding
mm_117856.1	chr13	98815121	98815201	-	1	NA	5' UTR (NM_172591, exon 1 of 26)	5' UTR (NM_172591, exon 1 of 26)	288	NM_172591	218503	Mm.23928	NM_172591	ENSMUSG00000041685	Fcho2	5832424M12Rik|AA387320	FCH domain only 2	protein-coding
mm_110643.1	chr12	58269055	58269057	-	1	NA	5' UTR (NM_025809, exon 1 of 1)	5' UTR (NM_025809, exon 1 of 1)	202	NM_025809	66864	Mm.280563	NM_025809	ENSMUSG00000045930	Clec14a	1200003C23Rik|AI642649	C-type lectin domain family 14, member a	protein-coding
mm_142505.1	chr17	46096635	46096647	-	1	NA	Intergenic	Intergenic	-14363	NM_026768	68565	Mm.287443	NM_026768	ENSMUSG00000023967	Mrps18a	1110004O20Rik|C79712	mitochondrial ribosomal protein S18A	protein-coding
mm_146761.1	chr18	16809066	16809087	-	1	NA	5' UTR (NM_007664, exon 1 of 16)	5' UTR (NM_007664, exon 1 of 16)	170	NM_007664	12558	Mm.257437	NM_007664	ENSMUSG00000024304	Cdh2	CDHN|N-CAD|Ncad	cadherin 2	protein-coding
mm_33042.1	chr4	122936524	122936528	+	1	NA	Intergenic	Intergenic	24662	NM_029662	76574	Mm.331842	NM_029662	ENSMUSG00000028655	Mfsd2a	1700018O18Rik|Mfsd2|NLS1	major facilitator superfamily domain containing 2A	protein-coding
mm_93488.1	chr10	111997149	111997156	-	1	NA	5' UTR (NM_028608, exon 1 of 6)	5' UTR (NM_028608, exon 1 of 6)	112	NM_028608	73690	Mm.173790	NM_028608	ENSMUSG00000056888	Glipr1	2410114O14Rik|RTVP-1|RTVP1|mRTVP-1	GLI pathogenesis-related 1 (glioma)	protein-coding
mm_65950.1	chr7	30420365	30420373	-	1	NA	promoter-TSS (NM_011827)	promoter-TSS (NM_011827)	-515	NM_011827	23900	Mm.379050	NM_011827	ENSMUSG00000064109	Hcst	DAP10|KAP10	hematopoietic cell signal transducer	protein-coding
mm_8873.1	chr1	162859920	162859973	-	1	NA	promoter-TSS (NM_001330291)	promoter-TSS (NM_001330291)	54	NM_001330291	14261	Mm.976	NM_010231	ENSMUSG00000040181	Fmo1	-	flavin containing monooxygenase 1	protein-coding
mm_172232.1	chr6	67746682	67746688	-	1	NA	Intergenic	IAP1-MM_I-int|LTR|ERVK	-180986	NR_003100	75070	Mm.463364	NR_003100		4930515G16Rik	-	myc induced nuclear antigen pseudogene	pseudo
mm_117885.1	chr13	99412817	99412839	-	1	NA	promoter-TSS (NR_015515)	promoter-TSS (NR_015515)	-2	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_105110.1	chr11	100970571	100970583	-	1	NA	promoter-TSS (NM_008986)	promoter-TSS (NM_008986)	40	NM_008986	19285	Mm.21864	NM_008986	ENSMUSG00000004044	Ptrf	2310075E07Rik|AW546441|Cav-p60|Cavin	polymerase I and transcript release factor	protein-coding
mm_12670.1	chr2	75720948	75720950	+	1	NA	Intergenic	B2_Mm2|SINE|B2	-16286	NM_010902	18024	Mm.1025	NM_010902	ENSMUSG00000015839	Nfe2l2	Nrf2	nuclear factor, erythroid derived 2, like 2	protein-coding
mm_133181.1	chr16	72636900	72636900	+	1	NA	Intergenic	Intergenic	-26249	NM_019413	19876	Mm.310772	NM_019413	ENSMUSG00000022883	Robo1	AW494633|AW742721|DUTT1|Gm310	roundabout guidance receptor 1	protein-coding
mm_157959.1	chrX	88115633	88115675	-	1	NA	promoter-TSS (NM_001160403)	promoter-TSS (NM_001160403)	-31	NM_001160403	331461	Mm.121680	NM_001160403	ENSMUSG00000052372	Il1rapl1	6330532G10Rik|C030039N24|IL1R8|IL1RAPL|MRX34|OPHN4|TIGIRR-2	interleukin 1 receptor accessory protein-like 1	protein-coding
mm_102140.1	chr11	53586906	53586925	-	1	NA	exon (NM_008443, exon 9 of 18)	exon (NM_008443, exon 9 of 18)	19546	NM_001290806	16568	Mm.88694	NM_008443	ENSMUSG00000018395	Kif3a	Kif3|Kifl|Kns3	kinesin family member 3A	protein-coding
mm_154506.1	chrM	12013	12033	-	1	NA	NA	Intergenic	NA	NA								
mm_153415.1	chr19	40588471	40588471	-	1	NA	promoter-TSS (NM_153554)	promoter-TSS (NM_153554)	-8	NM_153554	56454	Mm.233117	NM_019698	ENSMUSG00000025007	Aldh18a1	2810433K04Rik|AI429789|Pycs	aldehyde dehydrogenase 18 family, member A1	protein-coding
mm_23610.1	chr3	65528002	65528021	+	1	NA	promoter-TSS (NM_178892)	promoter-TSS (NM_178892)	-436	NM_178892	99929	Mm.246398	NM_178892	ENSMUSG00000034640	Tiparp	ARTD14|AW558171|PARP7	TCDD-inducible poly(ADP-ribose) polymerase	protein-coding
mm_38664.1	chr4	144438767	144438807	-	1	NA	promoter-TSS (NM_027056)	promoter-TSS (NM_027056)	-15	NM_027056	69364	Mm.158267	NM_027056	ENSMUSG00000028589	1700012P22Rik	-	RIKEN cDNA 1700012P22 gene	protein-coding
mm_25559.1	chr3	116534759	116534772	+	1	NA	exon (NM_010022, exon 5 of 11)	exon (NM_010022, exon 5 of 11)	21686	NM_010022	13171	Mm.3636	NM_010022	ENSMUSG00000000340	Dbt	D3Wsu60e	dihydrolipoamide branched chain transacylase E2	protein-coding
mm_7881.1	chr1	133020251	133020273	-	1	NA	intron (NM_008575, intron 1 of 11)	RLTR23|LTR|ERV1	5154	NR_126506	17248	Mm.426531	NM_008575	ENSMUSG00000054387	Mdm4	4933417N07Rik|AA414968|AL023055|AU018793|AU021806|C85810|Mdmx	transformed mouse 3T3 cell double minute 4	protein-coding
mm_167306.1	chr8	60522453	60522470	+	1	NA	intron (NM_011834, intron 4 of 12)	L1VL4|LINE|L1	16337	NM_011834	23923	Mm.35020	NM_011834	ENSMUSG00000057228	Aadat	AI875679|Aadt|KATII|Kat2|Kyat2|mKat-2	aminoadipate aminotransferase	protein-coding
mm_135798.1	chr16	57211157	57211167	-	1	NA	intron (NM_026254, intron 4 of 17)	intron (NM_026254, intron 4 of 17)	20304	NM_026254	67581	Mm.257819	NM_026254	ENSMUSG00000022749	Tbc1d23	4930451A13Rik|AU015720|AU043671|AU043778|D030022P07Rik|W51689	TBC1 domain family, member 23	protein-coding
mm_158027.1	chrX	96293426	96293453	-	1	NA	promoter-TSS (NM_177789)	promoter-TSS (NM_177789)	-1	NM_177789	278180	Mm.26781	NM_177789	ENSMUSG00000044206	Vsig4	A530061A11|BC025105|CRIg|Z39IG	V-set and immunoglobulin domain containing 4	protein-coding
mm_3187.1	chr1	135799434	135799480	+	1	NA	promoter-TSS (NM_021467)	promoter-TSS (NM_021467)	36	NM_021467	21952	Mm.44379	NM_021467	ENSMUSG00000026418	Tnni1	2700018B22Rik|AI747285|ssTnI	troponin I, skeletal, slow 1	protein-coding
mm_83110.1	chr9	40376122	40376139	-	1	NA	intron (NM_172768, intron 2 of 19)	AmnSINE2|SINE|Deu	42658	NR_040728	73558	Mm.398307	NR_040728		1700110K17Rik	-	RIKEN cDNA 1700110K17 gene	ncRNA
mm_100678.1	chr11	3452356	3452378	-	1	NA	promoter-TSS (NR_045276)	promoter-TSS (NR_045276)	-70	NR_028317	71523	Mm.72795	NM_027820	ENSMUSG00000034587	8430429K09Rik	-	RIKEN cDNA 8430429K09 gene	ncRNA
mm_1814.1	chr1	82316568	82316630	+	1	NA	promoter-TSS (NM_029777)	promoter-TSS (NM_029777)	20	NM_029777	76867	Mm.226994	NM_029777	ENSMUSG00000026142	Rhbdd1	4930418P06Rik|RRP4|mRHBDD1	rhomboid domain containing 1	protein-coding
mm_57999.1	chr6	136173273	136173303	-	1	NA	intron (NM_008171, intron 1 of 14)	intron (NM_008171, intron 1 of 14)	223	NM_008171	14812	Mm.436649	NM_008171	ENSMUSG00000030209	Grin2b	AW490526|GluN2B|NR2B|Nmdar2b	glutamate receptor, ionotropic, NMDA2B (epsilon 2)	protein-coding
mm_133831.1	chr16	95900530	95900540	+	1	NA	intron (NR_040484, intron 1 of 3)	L1MC5|LINE|L1	-1822	NR_040485	69776	Mm.120470	NR_040484	ENSMUSG00000086899	1600002D24Rik	-	RIKEN cDNA 1600002D24 gene	ncRNA
mm_147764.1	chr18	61375190	61375236	-	1	NA	intron (NM_133249, intron 1 of 11)	(TG)n|Simple_repeat|Simple_repeat	25218	NM_133249	170826	Mm.415302	NM_133249	ENSMUSG00000033871	Ppargc1b	4631412G21Rik|Perc	peroxisome proliferative activated receptor, gamma, coactivator 1 beta	protein-coding
mm_45295.1	chr5	65091599	65091616	-	1	NA	Intergenic	Intergenic	-15961	NM_001347355	71778	Mm.10281	NM_175174	ENSMUSG00000054920	Klhl5	1300013C10Rik	kelch-like 5	protein-coding
mm_157062.1	chrX	8132892	8132898	-	1	NA	promoter-TSS (NM_026137)	promoter-TSS (NM_026137)	-37	NM_026137	73447	Mm.284162	NM_026137	ENSMUSG00000031166	Wdr13	1700060B08Rik|5730411P10Rik|DXHXS7467e|W51679|mMg21	WD repeat domain 13	protein-coding
mm_16034.1	chr2	167661754	167661767	+	1	NA	promoter-TSS (NM_145538)	promoter-TSS (NM_145538)	-216	NM_145538	407243	Mm.4863	NM_145538	ENSMUSG00000090213	Tmem189	AI840826|Kua	transmembrane protein 189	protein-coding
mm_171108.1	chr3	134880935	134880935	+	1	NA	intron (NM_021382, intron 3 of 4)	intron (NM_021382, intron 3 of 4)	51928	NM_021382	21338	Mm.103810	NM_021382	ENSMUSG00000028172	Tacr3	Nk3r|Nkr|Tac3r	tachykinin receptor 3	protein-coding
mm_171344.1	chr4	106098832	106098838	+	1	NA	Intergenic	RLTR18B|LTR|ERVK	-217378	NM_183225	329908	Mm.234544	NM_183225	ENSMUSG00000028514	Usp24	2700066K03Rik|2810030C21Rik|AI414051|B130021E18|C79851	ubiquitin specific peptidase 24	protein-coding
mm_80326.1	chr9	75011826	75011830	+	1	NA	intron (NM_001113283, intron 6 of 12)	intron (NM_001113283, intron 6 of 12)	-25786	NM_001142655	59046	Mm.247837	NM_021548	ENSMUSG00000007656	Arpp19	19kDa|2700024H10Rik|ARPP-19|AW559096|Arpp12	cAMP-regulated phosphoprotein 19	protein-coding
mm_145998.1	chr18	68344524	68344535	+	1	NA	Intergenic	MTC-int|LTR|ERVL-MaLR	6926	NM_013596	17203	Mm.8003	NM_013596	ENSMUSG00000007480	Mc5r	-	melanocortin 5 receptor	protein-coding
mm_74069.1	chr8	122431713	122431770	+	1	NA	intron (NM_001301284, intron 1 of 4)	intron (NM_001301284, intron 1 of 4)	1199	NM_001301284	13057	Mm.271671	NM_007806	ENSMUSG00000006519	Cyba	b558|nmf333|p22-phox|p22phox	cytochrome b-245, alpha polypeptide	protein-coding
mm_151129.1	chr19	48205514	48205525	+	1	NA	promoter-TSS (NM_025696)	promoter-TSS (NM_025696)	-506	NM_025696	66673	Mm.70980	NM_025696	ENSMUSG00000063434	Sorcs3	6330404A12Rik|AW045579	sortilin-related VPS10 domain containing receptor 3	protein-coding
mm_143805.1	chr17	83514600	83514619	-	1	NA	promoter-TSS (NM_001159529)	promoter-TSS (NM_001159529)	-276	NM_001159529	20463	Mm.30072	NM_009187	ENSMUSG00000024248	Cox7a2l	COX7AR|COX7RP|EB1|SIG-81|SIG81|Silg81	cytochrome c oxidase subunit VIIa polypeptide 2-like	protein-coding
mm_123178.1	chr14	57664927	57664934	-	1	NA	promoter-TSS (NM_020506)	promoter-TSS (NM_020506)	26	NM_020506	57258	Mm.202747	NM_020506	ENSMUSG00000021952	Xpo4	B430309A01Rik|mKIAA1721	exportin 4	protein-coding
mm_87955.1	chr10	63182802	63182808	+	1	NA	intron (NM_182992, intron 2 of 19)	RLTR41|LTR|ERV1	21147	NM_182992	68802	Mm.259767	NM_182992	ENSMUSG00000020067	Mypn	1110056A04Rik|9830112J03|AI853556|mKIAA4170	myopalladin	protein-coding
mm_120265.1	chr14	63122467	63122477	+	1	NA	promoter-TSS (NM_007798)	promoter-TSS (NM_007798)	10	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_50677.1	chr6	51544715	51544732	+	1	NA	5' UTR (NM_028035, exon 1 of 7)	5' UTR (NM_028035, exon 1 of 7)	200	NM_001127348	71982	Mm.294166	NM_028035	ENSMUSG00000038301	Snx10	2410004M09Rik	sorting nexin 10	protein-coding
mm_120303.1	chr14	63140486	63140508	+	1	NA	intron (NM_007798, intron 8 of 9)	intron (NM_007798, intron 8 of 9)	18035	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_152723.1	chr19	18596730	18596733	-	1	NA	intron (NM_017375, intron 2 of 9)	intron (NM_017375, intron 2 of 9)	35082	NM_017375	20409	Mm.172222	NM_017375	ENSMUSG00000024725	Ostf1	C78236|SH3P2|Sh3d3	osteoclast stimulating factor 1	protein-coding
mm_108689.1	chr12	86894566	86894571	+	1	NA	Intergenic	Intergenic	-9754	NM_145836	238330	Mm.248358	NM_145836	ENSMUSG00000034168	Irf2bpl	6430527G18Rik|Eap1	interferon regulatory factor 2 binding protein-like	protein-coding
mm_130790.1	chr15	101676448	101676466	-	1	NA	3' UTR (NM_010669, exon 9 of 9)	3' UTR (NM_010669, exon 9 of 9)	3832	NM_010669	16688	Mm.441891	NM_010669	ENSMUSG00000023041	Krt6b	BB144589|Krt2-6b|mK6[b]	keratin 6B	protein-coding
mm_46390.1	chr5	104021929	104021945	-	1	NA	promoter-TSS (NM_053262)	promoter-TSS (NM_053262)	-141	NM_053262	114664	Mm.46019	NM_053262	ENSMUSG00000029311	Hsd17b11	Dhrs8|Pan1b|SDR2|retSDR2	hydroxysteroid (17-beta) dehydrogenase 11	protein-coding
mm_2333.1	chr1	92831731	92831749	+	1	NA	promoter-TSS (NM_016696)	promoter-TSS (NM_016696)	54	NM_016696	14733	Mm.297976	NM_016696	ENSMUSG00000034220	Gpc1	AI462976	glypican 1	protein-coding
mm_51949.1	chr6	91734855	91734860	+	1	NA	intron (NM_009320, intron 5 of 14)	B1F|SINE|Alu	50790	NM_009320	21366	Mm.395650	NM_009320	ENSMUSG00000030096	Slc6a6	AA589629|C80501|Taut	solute carrier family 6 (neurotransmitter transporter, taurine), member 6	protein-coding
mm_79355.1	chr9	54249907	54249927	+	1	NA	Intergenic	Intergenic	-36569	NM_177350	235379	Mm.123549	NM_177350	ENSMUSG00000046167	Gldn	CRG-L2|Clom|Colm|Crgl2|Crlg2	gliomedin	protein-coding
mm_141641.1	chr17	33305847	33305863	-	1	NA	Intergenic	Intergenic	16311	NM_001142957	100043468	Mm.276296	NM_001142957	ENSMUSG00000096910	Zfp955b	A430003O12Rik|C430039G02Rik|C530035A18Rik|Gm4455|Zfp883b	zinc finger protein 955B	protein-coding
mm_139106.1	chr17	47313941	47313957	+	1	NA	5' UTR (NM_172622, exon 3 of 17)	5' UTR (NM_172622, exon 3 of 17)	-54938	NM_001146212	64657	Mm.216250	NM_183086	ENSMUSG00000034729	Mrps10	1110038B19Rik|AW743084|Rpms10	mitochondrial ribosomal protein S10	protein-coding
mm_14793.1	chr2	145860880	145860886	+	1	NA	exon (NM_028724, exon 9 of 13)	exon (NM_028724, exon 9 of 13)	-42358	NM_026425	67877	Mm.151168	NM_026425	ENSMUSG00000002728	Naa20	1500004D14Rik|2900026I01Rik|AU041458|D2Ertd186e|Nat5	N(alpha)-acetyltransferase 20, NatB catalytic subunit	protein-coding
mm_38909.1	chr4	149976758	149976774	-	1	NA	Intergenic	RMER17C2|LTR|ERVK	-21760	NM_029035	74646	Mm.30	NM_029035	ENSMUSG00000039911	Spsb1	1110014L01Rik|4930422J18Rik|AI596360|AI854583|SSB-1|SSB1	splA/ryanodine receptor domain and SOCS box containing 1	protein-coding
mm_164831.1	chr18	37808734	37808740	+	1	NA	exon (NM_033581, exon 1 of 4)	exon (NM_033581, exon 1 of 4)	2327	NM_033581	93706	Mm.247203	NM_033581	ENSMUSG00000102918	Pcdhgc3	PC43|Pcdh2	protocadherin gamma subfamily C, 3	protein-coding
mm_124752.1	chr15	6638982	6638995	+	1	NA	intron (NM_011815, intron 7 of 17)	intron (NM_011815, intron 7 of 17)	59141	NM_011815	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_171526.1	chr4	146611011	146611011	+	1	NA	Intergenic	Intergenic	-64138	NR_045468	67524	Mm.444300	NR_045468	ENSMUSG00000086046	1700095A21Rik	-	RIKEN cDNA 1700095A21 gene	ncRNA
mm_43760.1	chr5	140612542	140612577	+	1	NA	exon (NM_008494, exon 4 of 8)	exon (NM_008494, exon 4 of 8)	5218	NM_008494	16848	Mm.12834	NM_008494	ENSMUSG00000029570	Lfng	AW061165	LFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	protein-coding
mm_75384.1	chr8	45410331	45410359	-	1	NA	intron (NM_126166, intron 1 of 6)	intron (NM_126166, intron 1 of 6)	194	NM_126166	142980	Mm.33874	NM_126166	ENSMUSG00000031639	Tlr3	AI957183	toll-like receptor 3	protein-coding
mm_135939.1	chr16	74279638	74279643	-	1	NA	intron (NM_175549, intron 2 of 27)	intron (NM_175549, intron 2 of 27)	62427	NR_030464	751561		NR_030464	ENSMUSG00000104758	Mir691	Mirn691|mir-691|mmu-mir-691	microRNA 691	ncRNA
mm_130735.1	chr15	101250364	101250396	-	1	NA	Intergenic	RMER15-int|LTR|ERVL	-16466	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_164306.1	chr15	103897449	103897456	+	1	NA	exon (NM_009267, exon 3 of 4)	exon (NM_009267, exon 3 of 4)	1848	NM_009268	20771	Mm.30276	NM_009268		Mucl1	Spt-2|Spt2	mucin-like 1	protein-coding
mm_48741.1	chr5	147722638	147722640	-	1	NA	intron (NM_010228, intron 1 of 29)	intron (NM_010228, intron 1 of 29)	3349	NM_010228	14254	Mm.389712	NM_010228	ENSMUSG00000029648	Flt1	AI323757|Flt-1|VEGFR-1|VEGFR1|sFlt1	FMS-like tyrosine kinase 1	protein-coding
mm_99218.1	chr11	101031486	101031497	+	1	NA	intron (NM_001243050, intron 9 of 20)	intron (NM_001243050, intron 9 of 20)	1151	NR_105893	102466767		NR_105893	ENSMUSG00000098415	Mir6928	Gm27728|mmu-mir-6928	microRNA 6928	ncRNA
mm_16725.1	chr2	7395926	7395934	-	1	NA	promoter-TSS (NM_001110232)	promoter-TSS (NM_001110232)	70	NM_001110232	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_154873.1	chrX	20687965	20688039	+	1	NA	promoter-TSS (NM_011049)	promoter-TSS (NM_011049)	48	NM_001310456	18555	Mm.102574	NM_011049	ENSMUSG00000031065	Cdk16	Crk5|Pctaire1|Pctk1	cyclin-dependent kinase 16	protein-coding
mm_34704.1	chr4	152107720	152107761	+	1	NA	exon (NM_001285999, exon 12 of 21)	exon (NM_001285999, exon 12 of 21)	-8194	NM_001291010	85030	Mm.101198	NM_033042	ENSMUSG00000024793	Tnfrsf25	APO-3|DDR3|DR3|LARD|TR3|TRAMP|Tnfrsf12|WSL-1|WSL-LR|Wsl	tumor necrosis factor receptor superfamily, member 25	protein-coding
mm_141566.1	chr17	32276728	32276744	-	1	NA	intron (NM_198094, intron 1 of 12)	B2_Mm2|SINE|B2	7387	NM_198094	57261	Mm.253518	NM_020508	ENSMUSG00000024002	Brd4	Brd5|HUNK1|MCAP|WI-11513	bromodomain containing 4	protein-coding
mm_86914.1	chr10	23796646	23796660	+	1	NA	promoter-TSS (NM_183116)	promoter-TSS (NM_183116)	-333	NM_183116	76306	Mm.294271	NM_183116	ENSMUSG00000037455	Slc18b1	1110021L09Rik	solute carrier family 18, subfamily B, member 1	protein-coding
mm_50196.1	chr6	41860306	41860308	+	1	NA	promoter-TSS (NM_032542)	promoter-TSS (NM_032542)	-32	NM_032542	84543	Mm.138766	NM_032542	ENSMUSG00000014104	Sval2	SLP-M	seminal vesicle antigen-like 2	protein-coding
mm_111162.1	chr12	83562444	83562462	-	1	NA	intron (NM_183154, intron 4 of 11)	intron (NM_183154, intron 4 of 11)	34694	NM_183154	217695	Mm.59257	NM_183154	ENSMUSG00000042628	Zfyve1	DFCP1|G630053K23|TAFF1|ZNFN2A1|mKIAA1589	zinc finger, FYVE domain containing 1	protein-coding
mm_4504.1	chr1	173730479	173730510	+	1	NA	exon (NM_001204910, exon 5 of 8)	exon (NM_001204910, exon 5 of 8)	11315	NM_001204910	226691	Mm.440876	NM_001204910	ENSMUSG00000073490	Ifi207	AI607873|Pyhin-A	interferon activated gene 207	protein-coding
mm_64192.1	chr7	141462722	141462723	+	1	NA	intron (NM_001025103, intron 1 of 9)	intron (NM_001025103, intron 1 of 9)	1628	NM_001025103	213573	Mm.386851	NM_001025103	ENSMUSG00000048200	Cracr2b	6330520A15Rik|BC026645|Cracr2a|Efcab4|Efcab4a	calcium release activated channel regulator 2B	protein-coding
mm_98183.1	chr11	87774472	87774472	+	1	NA	intron (NM_172449, intron 16 of 31)	(T)n|Simple_repeat|Simple_repeat	13931	NM_172449	207777	Mm.342019	NM_172449	ENSMUSG00000034156	Bzrap1	D230016K05|PRAX-1|Tspoap1|mKIAA0612	benzodiazepine receptor associated protein 1	protein-coding
mm_152110.1	chr19	6942407	6942443	-	1	NA	promoter-TSS (NM_001285453)	promoter-TSS (NM_001285453)	25	NM_001177361	107173	Mm.276555	NM_207220	ENSMUSG00000024958	Gpr137	AI428855	G protein-coupled receptor 137	protein-coding
mm_161481.1	chr15	82394021	82394021	-	1	NA	promoter-TSS (NR_106153)	promoter-TSS (NR_106153)	1	NM_001104531	545123	Mm.482764	NM_001104531	ENSMUSG00000068085	Cyp2d11	Cyp2d|P450-2D	cytochrome P450, family 2, subfamily d, polypeptide 11	protein-coding
mm_140791.1	chr17	19574356	19574384	-	1	NA	Intergenic	MYSERV6-int|LTR|ERVK	-2861	NM_001104563	627576	Mm.469857	NM_001104563	ENSMUSG00000094892	Vmn2r101	EG627576	vomeronasal 2, receptor 101	protein-coding
mm_152627.1	chr19	12476967	12476979	-	1	NA	intron (NM_172442, intron 7 of 8)	intron (NM_172442, intron 7 of 8)	16194	NM_010821	17476	Mm.3999	NM_010821	ENSMUSG00000046805	Mpeg1	MPS1|Mpg-1	macrophage expressed gene 1	protein-coding
mm_145664.1	chr18	61130941	61130963	+	1	NA	TTS (NM_178277)	TTS (NM_178277)	13484	NR_105949	102466212		NR_105949	ENSMUSG00000098389	Mir6983	Gm27496|mmu-mir-6983	microRNA 6983	ncRNA
mm_72855.1	chr8	88361532	88361575	+	1	NA	exon (NM_012047, exon 2 of 17)	exon (NM_012047, exon 2 of 17)	638	NM_012047	26992	Mm.5400	NM_012047	ENSMUSG00000031660	Brd7	BP75|CELTIX1|Ptpn13ip	bromodomain containing 7	protein-coding
mm_37720.1	chr4	129556476	129556549	-	1	NA	intron (NM_001162432, intron 6 of 12)	intron (NM_001162432, intron 6 of 12)	1299	NR_106199	102465997		NR_106199	ENSMUSG00000099070	Mir8119	Gm27567|mmu-mir-8119	microRNA 8119	ncRNA
mm_167205.1	chr7	144240931	144240936	+	1	NA	intron (NM_001113373, intron 4 of 15)	intron (NM_001113373, intron 4 of 15)	-43452	NM_001081370	210274	Mm.483624	NM_001081370	ENSMUSG00000037541	Shank2	ProSAP1|mKIAA1022	SH3/ankyrin domain gene 2	protein-coding
mm_102260.1	chr11	55314569	55314596	-	1	NA	Intergenic	Intergenic	-2325	NM_001029988	245827	Mm.339363	NM_001029988	ENSMUSG00000055333	Fat2	EMI2|Fath2|Gm523|mKIAA0811	FAT atypical cadherin 2	protein-coding
mm_58995.1	chr7	19149811	19149844	+	1	NA	promoter-TSS (NM_026943)	promoter-TSS (NM_026943)	-11	NM_026943	107686	Mm.29135	NM_026943	ENSMUSG00000040824	Snrpd2	1810009A06Rik|SMD2	small nuclear ribonucleoprotein D2	protein-coding
mm_85534.1	chr9	106550239	106550251	-	1	NA	intron (NM_026645, intron 6 of 7)	intron (NM_026645, intron 6 of 7)	11380	NM_026645	68265	Mm.141451	NM_026645	ENSMUSG00000023577	Iqcf3	1700012F17Rik|AV040440	IQ motif containing F3	protein-coding
mm_31599.1	chr4	57893721	57893733	+	1	NA	3' UTR (NM_001035533, exon 4 of 4)	3' UTR (NM_001035533, exon 4 of 4)	22537	NM_178727	242484	Mm.23214	NM_178727	ENSMUSG00000052117	D630039A03Rik	-	RIKEN cDNA D630039A03 gene	protein-coding
mm_138714.1	chr17	36167607	36167634	+	1	NA	exon (NM_001081032, exon 3 of 8)	exon (NM_001081032, exon 3 of 8)	917	NM_001081032	667977	Mm.441651	NM_001081032	ENSMUSG00000073402	Gm8909	EG667977|H2-Tw5l|H2-gs17	predicted gene 8909	protein-coding
mm_25516.1	chr3	113630226	113630240	+	1	NA	promoter-TSS (NM_001038696)	promoter-TSS (NM_001038696)	-84	NM_001038696	67225	Mm.316928	NM_026043	ENSMUSG00000027981	Rnpc3	2810441O16Rik|AI447568|C030014B17Rik	RNA-binding region (RNP1, RRM) containing 3	protein-coding
mm_96044.1	chr11	59557375	59557392	+	1	NA	intron (NM_145827, intron 6 of 9)	L1MB3|LINE|L1	14355	NM_001011789	257962	Mm.377316	NM_001011789	ENSMUSG00000059610	Olfr222	MOR256-45P	olfactory receptor 222	protein-coding
mm_153629.1	chr19	44021620	44021636	-	1	NA	exon (NM_001167905, exon 2 of 8)	exon (NM_001167905, exon 2 of 8)	7619	NM_001001446	226143	Mm.329866	NM_001001446	ENSMUSG00000025197	Cyp2c44	AW107714|BC034834|b2b386Clo	cytochrome P450, family 2, subfamily c, polypeptide 44	protein-coding
mm_78476.1	chr9	32695679	32695686	+	1	NA	promoter-TSS (NM_001038642)	promoter-TSS (NM_001038642)	-360	NM_011808	23871	Mm.292415	NM_011808	ENSMUSG00000032035	Ets1	AI196000|AI448617|D230050P06|Ets-1|Tpl1|vs	E26 avian leukemia oncogene 1, 5' domain	protein-coding
mm_103768.1	chr11	81901935	81901938	-	1	NA	intron (NM_001034013, intron 1 of 9)	intron (NM_001034013, intron 1 of 9)	41259	NR_038010	71388	Mm.158687	NR_038010	ENSMUSG00000020703	5530401A14Rik	-	RIKEN cDNA 5530401A14 gene	ncRNA
mm_37094.1	chr4	116610737	116610751	-	1	NA	exon (NM_016777, exon 7 of 16)	exon (NM_016777, exon 7 of 16)	-13114	NR_029450	654318	Mm.255685	NR_029450	ENSMUSG00000085408	C530005A16Rik	D930044c15rik	RIKEN cDNA C530005A16 gene	ncRNA
mm_123390.1	chr14	63405229	63405241	-	1	NA	intron (NM_007549, intron 1 of 12)	L2|LINE|L2	11952	NM_007549	12143	Mm.3962	NM_007549	ENSMUSG00000014453	Blk	-	B lymphoid kinase	protein-coding
mm_80575.1	chr9	84037824	84037842	+	1	NA	intron (NM_001305935, intron 8 of 10)	intron (NM_001305935, intron 8 of 10)	89052	NM_199195	12040	Mm.12819	NM_199195	ENSMUSG00000032263	Bckdhb	BCKDE1B|BCKDH E1-beta	branched chain ketoacid dehydrogenase E1, beta polypeptide	protein-coding
mm_172151.1	chr6	41200069	41200085	-	1	NA	Intergenic	Intergenic	-102195	NM_011646	22074	Mm.383263	NM_011646	ENSMUSG00000054106	Try4	0910001B19Rik|Td	trypsin 4	protein-coding
mm_1711.1	chr1	75236578	75236588	+	1	NA	promoter-TSS (NM_001159885)	promoter-TSS (NM_001159885)	-119	NM_001159885	56812	Mm.489660	NM_020266	ENSMUSG00000026203	Dnajb2	2700059H22Rik|Dnajb10|Hsj1|mDj8	DnaJ heat shock protein family (Hsp40) member B2	protein-coding
mm_88577.1	chr10	79682307	79682322	+	1	NA	5' UTR (NM_177613, exon 1 of 5)	5' UTR (NM_177613, exon 1 of 5)	119	NM_177613	216150	Mm.21981	NM_177613	ENSMUSG00000020307	Cdc34	AI327276|UBE2R1	cell division cycle 34	protein-coding
mm_55651.1	chr6	72366986	72366991	-	1	NA	promoter-TSS (NM_001331167)	promoter-TSS (NM_001331167)	-16	NM_001331167	66510	Mm.170023	NM_025607	ENSMUSG00000055850	Rnf181	1700047F16Rik|2500002L14Rik|6230415N01Rik|C77350	ring finger protein 181	protein-coding
mm_129742.1	chr15	82224331	82224361	-	1	NA	promoter-TSS (NM_028075)	promoter-TSS (NM_028075)	-10	NM_028075	72049	Mm.240047	NM_028075	ENSMUSG00000068105	Tnfrsf13c	2010006P15Rik|BAFF-R|Baffr|Bcmd|Bcmd-1|Bcmd1|Lvis22	tumor necrosis factor receptor superfamily, member 13c	protein-coding
mm_104843.1	chr11	99230689	99230704	-	1	NA	5' UTR (NM_020618, exon 1 of 11)	5' UTR (NM_020618, exon 1 of 11)	321	NM_020618	57376	Mm.379086	NM_020618	ENSMUSG00000037935	Smarce1	2810417B20Rik|5830412H02Rik|9030408N19Rik|Baf27	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1	protein-coding
mm_36464.1	chr4	82505859	82505867	-	1	NA	promoter-TSS (NM_001113209)	promoter-TSS (NM_001113209)	-84	NM_008687	18028	Mm.317947	NM_008687	ENSMUSG00000008575	Nfib	6720429L07Rik|CTF|E030026I10Rik|NF-I/B|NF1-B|NFI-B	nuclear factor I/B	protein-coding
mm_129151.1	chr15	76229523	76229540	-	1	NA	promoter-TSS (NM_201385)	promoter-TSS (NM_201385)	-34	NM_201385	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
mm_10655.1	chr2	20671865	20671875	+	1	NA	intron (NM_029895, intron 4 of 18)	intron (NM_029895, intron 4 of 18)	152357	NM_001177631	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding
mm_108570.1	chr12	84807079	84807094	+	1	NA	intron (NM_013589, intron 14 of 34)	intron (NM_013589, intron 14 of 34)	33816	NM_028863	74316	Mm.25719	NM_028863	ENSMUSG00000021241	Isca2	0710001C05Rik|5730594E03Rik|Hbld1	iron-sulfur cluster assembly 2	protein-coding
mm_5359.1	chr1	25781897	25781900	-	1	NA	intron (NM_175642, intron 2 of 30)	intron (NM_175642, intron 2 of 30)	47809	NM_175642	210933	Mm.336569	NM_175642	ENSMUSG00000033569	Adgrb3	A830096D10Rik|Bai3	adhesion G protein-coupled receptor B3	protein-coding
mm_12229.1	chr2	68554496	68554502	+	1	NA	Intergenic	RLTR6-int|LTR|ERV1	-27914	NM_177651	227998	Mm.67562	NM_177651	ENSMUSG00000053896	4933409G03Rik	-	RIKEN cDNA 4933409G03 gene	protein-coding
mm_97693.1	chr11	80154556	80154569	+	1	NA	intron (NM_172133, intron 1 of 10)	CpG	400	NM_172133	216991	Mm.341520	NM_172133	ENSMUSG00000020709	Adap2	Centa2	ArfGAP with dual PH domains 2	protein-coding
mm_140365.1	chr17	86962669	86962687	+	1	NA	promoter-TSS (NM_145491)	promoter-TSS (NM_145491)	-433	NM_145491	104215	Mm.826	NM_145491	ENSMUSG00000024143	Rhoq	Arhq|TC10A|Tc10	ras homolog family member Q	protein-coding
mm_109475.1	chr12	111421529	111421539	+	1	NA	5' UTR (NM_001289489, exon 2 of 13)	5' UTR (NM_001289489, exon 2 of 13)	4089	NM_001289488	74190	Mm.248640	NM_028807	ENSMUSG00000021280	Exoc3l4	1200009I06Rik|1600013K19Rik	exocyst complex component 3-like 4	protein-coding
mm_90593.1	chr10	128285047	128285050	+	1	NA	exon (NM_019963, exon 20 of 24)	exon (NM_019963, exon 20 of 24)	13036	NM_031252	83430	Mm.125482	NM_031252	ENSMUSG00000025383	Il23a	IL-23|p19	interleukin 23, alpha subunit p19	protein-coding
mm_84417.1	chr9	65574690	65574705	-	1	NA	intron (NM_153119, intron 1 of 5)	intron (NM_153119, intron 1 of 5)	5390	NM_153119	102595	Mm.247303	NM_153119	ENSMUSG00000050721	Plekho2	AI840980|Plekhq1	pleckstrin homology domain containing, family O member 2	protein-coding
mm_67398.1	chr7	79880268	79880298	-	1	NA	3' UTR (NM_009682, exon 6 of 6)	3' UTR (NM_009682, exon 6 of 6)	-37931	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_20758.1	chr2	140671441	140671458	-	1	NA	promoter-TSS (NM_178382)	promoter-TSS (NM_178382)	27	NM_001172160	71436	Mm.426781	NM_178382	ENSMUSG00000051379	Flrt3	5530600M07Rik|C430047I10Rik|mKIAA1469	fibronectin leucine rich transmembrane protein 3	protein-coding
mm_158185.1	chrX	104201179	104201205	-	1	NA	promoter-TSS (NM_001077354)	promoter-TSS (NM_001077354)	-75	NM_001077354	245555	Mm.381907	NM_001077354	ENSMUSG00000046449	C77370	A230051P11|C77386|KIDLIA|Kiaa2022|Xpn|mKIAA2022	expressed sequence C77370	protein-coding
mm_21269.1	chr2	156862758	156862795	-	1	NA	promoter-TSS (NM_026124)	promoter-TSS (NM_026124)	169	NR_015591	74487	Mm.490465	NR_015591	ENSMUSG00000085741	5430405H02Rik	2610307N17Rik	RIKEN cDNA 5430405H02 gene	ncRNA
mm_98656.1	chr11	96271210	96271224	+	1	NA	promoter-TSS (NM_008270)	promoter-TSS (NM_008270)	-113	NM_008270	15417	Mm.258271	NM_008270	ENSMUSG00000020875	Hoxb9	Hox-2.5	homeobox B9	protein-coding
mm_41150.1	chr5	87929757	87929774	+	1	NA	exon (NM_007786, exon 4 of 5)	exon (NM_007786, exon 4 of 5)	4132	NM_007786	12994	Mm.296303	NM_007786	ENSMUSG00000001622	Csn3	AW208918|CSN10|Csnk	casein kappa	protein-coding
mm_43186.1	chr5	128600822	128600828	+	1	NA	promoter-TSS (NM_175284)	promoter-TSS (NM_175284)	-138	NR_015517	319616	Mm.387738	NR_015517	ENSMUSG00000072591	5930412G12Rik	-	RIKEN cDNA 5930412G12 gene	ncRNA
mm_1123.1	chr1	60098255	60098290	+	1	NA	promoter-TSS (NM_139150)	promoter-TSS (NM_139150)	25	NM_139150	241066	Mm.276441	NM_139150	ENSMUSG00000026017	Carf	Als2cr8|ECBRC-FC1|ECBRC-FC2	calcium response factor	protein-coding
mm_30088.1	chr3	138143718	138143732	-	1	NA	promoter-TSS (NM_001163457)	promoter-TSS (NM_001163457)	187	NM_175389	108943	Mm.471692	NM_175389	ENSMUSG00000004127	Trmt10a	3110023L08Rik|AA794508|Rg9mtd2|Rnmtd2	tRNA methyltransferase 10A	protein-coding
mm_149712.1	chr19	21653303	21653320	+	1	NA	promoter-TSS (NM_025423)	promoter-TSS (NM_025423)	2	NM_146096	226016	Mm.28796	NM_146096	ENSMUSG00000047368	Abhd17b	5730446C15Rik|Cgi67|Fam108b|Fam108b1	abhydrolase domain containing 17B	protein-coding
mm_81131.1	chr9	106499968	106499972	+	1	NA	promoter-TSS (NM_001146701)	promoter-TSS (NM_001146701)	3	NM_001146701	74267	Mm.116682	NM_028843	ENSMUSG00000066383	Iqcf1	1700055J15Rik	IQ motif containing F1	protein-coding
mm_85050.1	chr9	90096731	90096734	-	1	NA	intron (NM_001039147, intron 8 of 12)	intron (NM_001039147, intron 8 of 12)	18088	NM_001039147	21761	Mm.426209	NM_024431	ENSMUSG00000062270	Morf4l1	MORFRG15|MRG15|TEG-189|Tex189|mKIAA4002	mortality factor 4 like 1	protein-coding
mm_84415.1	chr9	65571792	65571823	-	1	NA	intron (NM_153119, intron 2 of 5)	intron (NM_153119, intron 2 of 5)	8280	NM_153119	102595	Mm.247303	NM_153119	ENSMUSG00000050721	Plekho2	AI840980|Plekhq1	pleckstrin homology domain containing, family O member 2	protein-coding
mm_129386.1	chr15	78191692	78191702	-	1	NA	intron (NM_013645, intron 4 of 4)	intron (NM_013645, intron 4 of 4)	12540	NM_001330686	19293	Mm.2766	NM_013645	ENSMUSG00000005716	Pvalb	PV|Parv|Pva	parvalbumin	protein-coding
mm_88790.1	chr10	80622212	80622216	+	1	NA	promoter-TSS (NM_134002)	promoter-TSS (NM_134002)	-566	NM_134002	103236	Mm.29873	NM_134002	ENSMUSG00000003345	Csnk1g2	2810429I12Rik|AI463719	casein kinase 1, gamma 2	protein-coding
mm_69833.1	chr7	141274022	141274033	-	1	NA	exon (NM_028069, exon 6 of 14)	exon (NM_028069, exon 6 of 14)	2759	NM_028069	72040	Mm.29080	NM_028069	ENSMUSG00000025497	Cdhr5	1810074H01Rik|AI481143|Mucdhl|Mupcdh	cadherin-related family member 5	protein-coding
mm_147084.1	chr18	35629800	35629818	-	1	NA	Intergenic	Intergenic	-2582	NM_011397	20522	Mm.22702	NM_011397	ENSMUSG00000024354	Slc23a1	D18Ucla2|SVCT1|Slc23a2|YSPL3	solute carrier family 23 (nucleobase transporters), member 1	protein-coding
mm_85529.1	chr9	106476160	106476196	-	1	NA	intron (NM_001311150, intron 1 of 10)	intron (NM_001311150, intron 1 of 10)	771	NM_001311150	235587	Mm.273659	NM_145619	ENSMUSG00000023249	Parp3	A930002C11Rik|AW990611|Adprt3|Adprtl3|PARP-3|pADPRT-3	poly (ADP-ribose) polymerase family, member 3	protein-coding
mm_143203.1	chr17	62803203	62803203	-	1	NA	intron (NM_010109, intron 1 of 3)	intron (NM_010109, intron 1 of 3)	78114	NM_207654	13640	Mm.7978	NM_010109	ENSMUSG00000048915	Efna5	AL-1|AV158822|EFL-5|Ephrin-A5|Epl7|LERK-7|RAGS	ephrin A5	protein-coding
mm_107864.1	chr12	69907748	69907754	+	1	NA	intron (NM_178628, intron 1 of 14)	intron (NM_178628, intron 1 of 14)	-14588	NM_201519	399510	Mm.291936	NM_201519	ENSMUSG00000034761	Map4k5	4432415E19Rik|GCKR|KHS|MAPKKKK5	mitogen-activated protein kinase kinase kinase kinase 5	protein-coding
mm_150743.1	chr19	43782618	43782625	+	1	NA	intron (NM_013806, intron 1 of 31)	intron (NM_013806, intron 1 of 31)	313	NM_013806	12780	Mm.39054	NM_013806	ENSMUSG00000025194	Abcc2	AI173996|Abc30|Cmoat|Mrp2|cMRP	ATP-binding cassette, sub-family C (CFTR/MRP), member 2	protein-coding
mm_158302.1	chrX	119897549	119897549	-	1	NA	Intergenic	LTRIS4B|LTR|ERV1	-29647	NM_053114	93728	Mm.125979	NM_053114	ENSMUSG00000034732	Pabpc5	C820015E17	poly(A) binding protein, cytoplasmic 5	protein-coding
mm_10594.1	chr2	18676953	18676968	+	1	NA	promoter-TSS (NM_007552)	promoter-TSS (NM_007552)	-58	NM_007552	12151	Mm.289584	NM_007552	ENSMUSG00000026739	Bmi1	AW546694|Bmi-1|Pcgf4	Bmi1 polycomb ring finger oncogene	protein-coding
mm_11837.1	chr2	45111179	45111192	+	1	NA	promoter-TSS (NM_001289521)	promoter-TSS (NM_001289521)	47	NR_110572	433424	Mm.441408	NR_110571	ENSMUSG00000052248	Zeb2os	Gm13476|OTTMUSG00000012358|Zeb2nat	zinc finger E-box binding homeobox 2, opposite strand	ncRNA
mm_5897.1	chr1	54585191	54585214	-	1	NA	Intergenic	Intergenic	-27518	NM_001163314	241062	Mm.103539	NM_175508	ENSMUSG00000073678	Pgap1	5033403E17Rik|9030223K07Rik|A530084K22|D230012E17Rik|oto	post-GPI attachment to proteins 1	protein-coding
mm_82954.1	chr9	35570089	35570121	-	1	NA	promoter-TSS (NM_029762)	promoter-TSS (NM_029762)	-36	NM_029762	76832	Mm.482285	NM_029762	ENSMUSG00000050555	Hyls1	3010015K02Rik	hydrolethalus syndrome 1	protein-coding
mm_152045.1	chr19	6141179	6141190	-	1	NA	promoter-TSS (NM_019722)	promoter-TSS (NM_019722)	-47	NM_019722	56327	Mm.21071	NM_019722	ENSMUSG00000024944	Arl2	2610009M23Rik|AI115441|AW553335	ADP-ribosylation factor-like 2	protein-coding
mm_35735.1	chr4	45084539	45084603	-	1	NA	promoter-TSS (NM_001024142)	promoter-TSS (NM_001024142)	33	NM_001024142	269529	Mm.389552	NM_001024142	ENSMUSG00000048232	Fbxo10	FBX10|Gm634	F-box protein 10	protein-coding
mm_128233.1	chr15	36607847	36607855	-	1	NA	intron (NM_008774, intron 1 of 14)	intron (NM_008774, intron 1 of 14)	1122	NM_008774	18458	Mm.371570	NM_008774	ENSMUSG00000022283	Pabpc1	PABP|Pabp1|PabpI|Pabpl1|ePAB	poly(A) binding protein, cytoplasmic 1	protein-coding
mm_110064.1	chr12	21373527	21373546	-	1	NA	promoter-TSS (NM_009615)	promoter-TSS (NM_009615)	96	NR_102380	11491	Mm.27681	NM_009615	ENSMUSG00000052593	Adam17	CD156b|Tace	a disintegrin and metallopeptidase domain 17	protein-coding
mm_127592.1	chr15	102391143	102391173	+	1	NA	Intergenic	Intergenic	-15158	NM_013672	20683	Mm.4618	NM_013672	ENSMUSG00000001280	Sp1	1110003E12Rik|AA450830|AI845540|Sp1-1	trans-acting transcription factor 1	protein-coding
mm_52848.1	chr6	121846816	121846846	+	1	NA	intron (NM_008645, intron 4 of 35)	intron (NM_008645, intron 4 of 35)	8290	NM_008645	17836	Mm.1311	NM_008645	ENSMUSG00000059908	Mug1	-	murinoglobulin 1	protein-coding
mm_163562.1	chr13	24966953	24966954	-	1	NA	intron (NM_008156, intron 12 of 25)	intron (NM_008156, intron 12 of 25)	23801	NM_008156	14756	Mm.291831	NM_008156	ENSMUSG00000021340	Gpld1	6330541J12Rik|AW546131	glycosylphosphatidylinositol specific phospholipase D1	protein-coding
mm_148139.1	chr18	76632866	76632875	-	1	NA	Intergenic	Intergenic	-223535	NM_001109743	664805	Mm.329543	NM_001109743	ENSMUSG00000091519	Skor2	Corl2|EG664805|Fussel18|Gm7348	SKI family transcriptional corepressor 2	protein-coding
mm_76187.1	chr8	82402527	82402567	-	1	NA	promoter-TSS (NM_001254747)	promoter-TSS (NM_001254747)	39	NM_001254747	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_165494.1	chr2	165793326	165793332	-	1	NA	intron (NM_027230, intron 20 of 23)	intron (NM_027230, intron 20 of 23)	64844	NM_001252585	228880	Mm.227598	NM_027230	ENSMUSG00000039671	Zmynd8	1110013E22Rik|2010005I16Rik|3632413B07Rik|AI316811|AL024039|Prkcbp1|RACK7	zinc finger, MYND-type containing 8	protein-coding
mm_138232.1	chr17	34392307	34392314	+	1	NA	Intergenic	RLTR21|LTR|ERVK	-6510	NM_001001177	407788	Mm.73205	NM_001001177	ENSMUSG00000057246	BC051142	NG8|TSBP|Tesb|Tesbp	cDNA sequence BC051142	protein-coding
mm_40662.1	chr5	65348329	65348346	+	1	NA	promoter-TSS (NM_031180)	promoter-TSS (NM_031180)	-74	NM_031180	83379	Mm.45274	NM_031180	ENSMUSG00000029195	Klb	AV071179|betaKlotho	klotho beta	protein-coding
mm_24524.1	chr3	93144783	93144798	+	1	NA	promoter-TSS (NM_001081200)	promoter-TSS (NM_001081200)	3	NM_001081200	381457	Mm.458570	NM_001081200	ENSMUSG00000078657	Crnn	Gm1015	cornulin	protein-coding
mm_161419.1	chr15	36164804	36164804	-	1	NA	promoter-TSS (NM_001081253)	promoter-TSS (NM_001081253)	80	NM_001081253	78803	Mm.26393	NM_175281	ENSMUSG00000048230	Fbxo43	4930533G20Rik|Emi2	F-box protein 43	protein-coding
mm_50768.1	chr6	53620454	53620472	+	1	NA	intron (NM_001327821, intron 7 of 10)	L1M5|LINE|L1	47089	NM_172728	231991	Mm.227444	NM_172728	ENSMUSG00000053007	Creb5	9430076C15Rik|CRE-BPa|Crebpa|D430026C09Rik	cAMP responsive element binding protein 5	protein-coding
mm_83482.1	chr9	45907586	45907589	-	1	NA	promoter-TSS (NM_178709)	promoter-TSS (NM_178709)	-676	NM_001310840	235315	Mm.3255	NM_178709	ENSMUSG00000042790	Rnf214	D130054N24Rik	ring finger protein 214	protein-coding
mm_136239.1	chr16	90934510	90934521	-	1	NA	intron (NM_026502, intron 1 of 6)	CpG	334	NM_026502	68001	Mm.45374	NM_026502	ENSMUSG00000022972	1110004E09Rik	-	RIKEN cDNA 1110004E09 gene	protein-coding
mm_171314.1	chr3	95357171	95357186	-	1	NA	promoter-TSS (NM_001163642)	promoter-TSS (NM_001163642)	24	NM_001163641	84505	Mm.490259	NM_018877	ENSMUSG00000015697	Setdb1	AU022152|ESET|KMT1E|mKIAA0067	SET domain, bifurcated 1	protein-coding
mm_103500.1	chr11	76577673	76577695	-	1	NA	promoter-TSS (NM_198894)	promoter-TSS (NM_198894)	55	NM_198894	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_82825.1	chr9	31131756	31131773	-	1	NA	promoter-TSS (NM_011176)	promoter-TSS (NM_011176)	35	NM_011176	19143	Mm.243926	NM_011176	ENSMUSG00000031995	St14	Epithin|MT-SP1|Prss14|Tmprss14|mCAP3|matriptase	suppression of tumorigenicity 14 (colon carcinoma)	protein-coding
mm_31082.1	chr4	41569829	41569876	+	1	NA	promoter-TSS (NM_027993)	promoter-TSS (NM_027993)	58	NM_175138	68922	Mm.79127	NM_175138	ENSMUSG00000061322	Dnaic1	1110066F04Rik|BB124644|Dnai1|b2b1526Clo	dynein, axonemal, intermediate chain 1	protein-coding
mm_42790.1	chr5	121525519	121525563	+	1	NA	intron (NM_010765, intron 13 of 13)	intron (NM_010765, intron 13 of 13)	-3846	NM_172126	280668	Mm.1453	NM_172126	ENSMUSG00000072647	Adam1a	Adam1|Ftna	a disintegrin and metallopeptidase domain 1a	protein-coding
mm_43900.1	chr5	144223713	144223771	+	1	NA	promoter-TSS (NM_027410)	promoter-TSS (NM_027410)	-164	NM_027410	70381	Mm.239412	NM_027410	ENSMUSG00000066621	Tecpr1	2210010N04Rik|mKIAA1358	tectonin beta-propeller repeat containing 1	protein-coding
mm_157314.1	chrX	21058219	21058225	-	1	NA	intron (NM_001013387, intron 2 of 4)	L1M3|LINE|L1	3816	NM_001013387	319535	Mm.170163	NM_001013387	ENSMUSG00000054737	Zfp182	6330583I20Rik|Znf182	zinc finger protein 182	protein-coding
mm_126693.1	chr15	85017208	85017212	+	1	NA	promoter-TSS (NM_023478)	promoter-TSS (NM_023478)	69	NM_023478	22270	Mm.46214	NM_023478	ENSMUSG00000022435	Upk3a	1110017C07Rik|UP3a|UPIII|Upk3	uroplakin 3A	protein-coding
mm_147463.1	chr18	46613006	46613019	-	1	NA	Intergenic	Intergenic	15308	NM_010120	13664	Mm.262037	NM_010120	ENSMUSG00000057561	Eif1a	C76390|Ef1a|Eftu|Eif4c|eIF-1A|eIF-4C	eukaryotic translation initiation factor 1A	protein-coding
mm_134673.1	chr16	22402626	22402637	-	1	NA	intron (NM_023794, intron 7 of 12)	intron (NM_023794, intron 7 of 12)	36939	NM_023794	104156	Mm.155708	NM_023794	ENSMUSG00000013089	Etv5	1110005E01Rik|8430401F14Rik|ERM	ets variant 5	protein-coding
mm_146122.1	chr18	74442464	74442479	+	1	NA	promoter-TSS (NM_201600)	promoter-TSS (NM_201600)	-148	NM_201600	17919	Mm.260098	NM_008661	ENSMUSG00000025885	Myo5b	AI661750|mKIAA1119	myosin VB	protein-coding
mm_15324.1	chr2	155751200	155751284	+	1	NA	promoter-TSS (NM_011171)	promoter-TSS (NM_011171)	25	NM_011171	19124	Mm.3243	NM_011171	ENSMUSG00000027611	Procr	AI325044|Ccca|Ccd41|Epcr	protein C receptor, endothelial	protein-coding
mm_150443.1	chr19	37985610	37985612	+	1	NA	intron (NM_001302140, intron 7 of 53)	intron (NM_001302140, intron 7 of 53)	57966	NM_001099634	226101	Mm.34674	NM_177035	ENSMUSG00000048612	Myof	2310004N10Rik|2310051D19Rik|E030042N20Rik|Fer1l3	myoferlin	protein-coding
mm_68878.1	chr7	126447498	126447512	-	1	NA	exon (NM_007504, exon 19 of 23)	exon (NM_007504, exon 19 of 23)	15568	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_36723.1	chr4	98817688	98817706	-	1	NA	promoter-TSS (NM_172872)	promoter-TSS (NM_172872)	-160	NM_172872	242553	Mm.440211	NM_172872	ENSMUSG00000035407	Kank4	AU021071|Ankrd38|BC060737|C130031J23	KN motif and ankyrin repeat domains 4	protein-coding
mm_163836.1	chr14	19417802	19417826	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	184773	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_173229.1	chrX	7907760	7907760	+	1	NA	TTS (NM_011591)	TTS (NM_011591)	8083	NM_001313693	21855	Mm.27393	NM_011591	ENSMUSG00000031158	Timm17b	17kDa|Sfc3|mTim17b	translocase of inner mitochondrial membrane 17b	protein-coding
mm_38457.1	chr4	140581748	140581773	-	1	NA	intron (NM_001290803, intron 9 of 28)	intron (NM_001290803, intron 9 of 28)	66996	NM_001112723	72754	Mm.29329	NM_172415	ENSMUSG00000040964	Arhgef10l	2810441C07Rik	Rho guanine nucleotide exchange factor (GEF) 10-like	protein-coding
mm_8075.1	chr1	135585309	135585313	-	1	NA	promoter-TSS (NM_173437)	promoter-TSS (NM_173437)	44	NM_173437	215690	Mm.34977	NM_173437	ENSMUSG00000009418	Nav1	9530089B19|9930003A20Rik|C230080M11Rik|Pomfil3|Unc53h1|mKIAA1151|steerin-1	neuron navigator 1	protein-coding
mm_82169.1	chr9	123845438	123845450	+	1	NA	intron (NM_148925, intron 1 of 18)	intron (NM_148925, intron 1 of 18)	6217	NM_148925	17281	Mm.252941	NM_148925	ENSMUSG00000025241	Fyco1	2810409M01Rik|Mem2|RUFY3|ZFYVE7	FYVE and coiled-coil domain containing 1	protein-coding
mm_86144.1	chr9	117251899	117251920	-	1	NA	5' UTR (NM_001172126, exon 1 of 13)	5' UTR (NM_001172126, exon 1 of 13)	574	NM_001172123	207181	Mm.326411	NM_178660	ENSMUSG00000039607	Rbms3	6720477E09Rik|8430436O14Rik	RNA binding motif, single stranded interacting protein	protein-coding
mm_43504.1	chr5	136987418	136987430	+	1	NA	promoter-TSS (NM_001310748)	promoter-TSS (NM_001310748)	405	NM_011962	26433	Mm.251003	NM_011962	ENSMUSG00000004846	Plod3	AI414586|LH3	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3	protein-coding
mm_23305.1	chr3	52709192	52709193	+	1	NA	Intergenic	(T)n|Simple_repeat|Simple_repeat	-30532	NR_038079	329639	Mm.131245	NR_038079	ENSMUSG00000102785	Gm2447	100039832|A530017F20	predicted gene 2447	ncRNA
mm_97727.1	chr11	80389075	80389092	+	1	NA	non-coding (NR_045038, exon 4 of 17)	non-coding (NR_045038, exon 4 of 17)	5804	NM_001130171	22680	Mm.401332	NM_011751	ENSMUSG00000017421	Zfp207	8430401D15Rik|BuGZ|Zep|Znf207	zinc finger protein 207	protein-coding
mm_66967.1	chr7	62823690	62823715	-	1	NA	Intergenic	Intergenic	-359192	NM_013788	27412	Mm.422745	NM_013788	ENSMUSG00000070526	Peg12	Frat3	paternally expressed 12	protein-coding
mm_13339.1	chr2	102787510	102787518	+	1	NA	3' UTR (NM_001077514, exon 11 of 11)	3' UTR (NM_001077514, exon 11 of 11)	81076	NM_001077515	20511	Mm.267547	NM_011393	ENSMUSG00000005089	Slc1a2	1700091C19Rik|2900019G14Rik|AI159670|Eaat2|GLT-1|GLT1|MGLT1	solute carrier family 1 (glial high affinity glutamate transporter), member 2	protein-coding
mm_122309.1	chr14	36906272	36906302	-	1	NA	intron (NM_001347503, intron 3 of 7)	intron (NM_001347503, intron 3 of 7)	13248	NM_001347503	72972	Mm.27621	NM_027045	ENSMUSG00000058690	Ccser2	1700012P13Rik|2900054P12Rik|AI035535|AW108503|Fam190b|Gcap14	coiled-coil serine rich 2	protein-coding
mm_144157.1	chr18	5594200	5594230	+	1	NA	intron (NM_011546, intron 1 of 7)	intron (NM_011546, intron 1 of 7)	-1778	NR_033552	791318	Mm.84339	NR_033552	ENSMUSG00000063087	Gm10125	ENSMUSG00000063087|Zeb1os	predicted gene 10125	ncRNA
mm_23048.1	chr3	35113476	35113483	+	1	NA	Intergenic	Intergenic	-190828	NR_105799	102466155		NR_105799	ENSMUSG00000098862	Mir6378	Gm27706|mmu-mir-6378	microRNA 6378	ncRNA
mm_56343.1	chr6	92870106	92870107	-	1	NA	intron (NM_175314, intron 11 of 29)	intron (NM_175314, intron 11 of 29)	31335	NM_175314	101401	Mm.158235	NM_175314	ENSMUSG00000030022	Adamts9	1810011L16Rik|8430403M15Rik|AW743315|E030027K14Rik	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 9	protein-coding
mm_12657.1	chr2	75482127	75482132	+	1	NA	Intergenic	Intergenic	-37950	NR_040635	77269	Mm.389278	NR_040635		9430019J16Rik	-	RIKEN cDNA 9430019J16 gene	ncRNA
mm_64285.1	chr7	141845361	141845370	+	1	NA	exon (NM_028801, exon 9 of 49)	exon (NM_028801, exon 9 of 49)	6293	NM_028801	74180	Mm.200752	NM_028801	ENSMUSG00000066108	Muc5b	2300002I04Rik|A130042M24|AV085033|MUC5|MUC9|mucin 5b	mucin 5, subtype B, tracheobronchial	protein-coding
mm_15138.1	chr2	153974752	153974762	+	1	NA	promoter-TSS (NM_001080811)	promoter-TSS (NM_001080811)	-188	NM_001080811	545477	Mm.379973	NM_001080811	ENSMUSG00000078998	Bpifa6	EG545477|Gm5840|Splunc6	BPI fold containing family A, member 6	protein-coding
mm_88170.1	chr10	69764934	69764942	+	1	NA	intron (NM_170730, intron 1 of 17)	intron (NM_170730, intron 1 of 17)	-160594	NM_170687	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_101807.1	chr11	46358031	46358031	-	1	NA	intron (NM_010583, intron 5 of 16)	intron (NM_010583, intron 5 of 16)	31484	NM_001281968	16428	Mm.339927	NM_010583	ENSMUSG00000020395	Itk	Emt|Tcsk|Tsk	IL2 inducible T cell kinase	protein-coding
mm_99766.1	chr11	106999679	106999683	+	1	NA	promoter-TSS (NM_010655)	promoter-TSS (NM_010655)	-156	NM_010655	16647	Mm.12508	NM_010655	ENSMUSG00000018362	Kpna2	2410044B12Rik|IPOA1|PTAC58|Rch1	karyopherin (importin) alpha 2	protein-coding
mm_69560.1	chr7	135700344	135700375	-	1	NA	exon (NM_001081117, exon 12 of 14)	exon (NM_001081117, exon 12 of 14)	16020	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_53237.1	chr6	127453668	127453685	+	1	NA	promoter-TSS (NM_181402)	promoter-TSS (NM_181402)	-47	NM_181402	101187	Mm.110818	NM_181402	ENSMUSG00000037997	Parp11	5330431N24Rik|AI851877|ARTD11|HIN1L|PARP-11	poly (ADP-ribose) polymerase family, member 11	protein-coding
mm_58384.1	chr6	149307783	149307797	-	1	NA	Intergenic	MERV1_LTR|LTR|ERV1	-1624	NM_001289661	67246	Mm.333515	NM_026054	ENSMUSG00000032712	2810474O19Rik	6720435I21Rik|AA536804|AU020969|GET|Kiaa1551	RIKEN cDNA 2810474O19 gene	protein-coding
mm_6045.1	chr1	59763337	59763356	-	1	NA	promoter-TSS (NM_007561)	promoter-TSS (NM_007561)	-933	NM_007561	12168	Mm.7106	NM_007561	ENSMUSG00000067336	Bmpr2	2610024H22Rik|AL117858|AW546137|BB189135|BMP-2|BMPR-2|BMPR-II|BMPRII|BRK-3|Gm20272	bone morphogenetic protein receptor, type II (serine/threonine kinase)	protein-coding
mm_19466.1	chr2	92434028	92434053	-	1	NA	promoter-TSS (NM_009963)	promoter-TSS (NM_009963)	29	NM_009963	12953	Mm.254181	NM_009963	ENSMUSG00000068742	Cry2	AV006279|D130054K12Rik	cryptochrome 2 (photolyase-like)	protein-coding
mm_156065.1	chrX	109160794	109160901	+	1	NA	3' UTR (NM_019989, exon 4 of 4)	3' UTR (NM_019989, exon 4 of 4)	-35909	NM_001037917	622976	Mm.482747	NM_001037917	ENSMUSG00000048621	Gm6377	EG622976	predicted gene 6377	protein-coding
mm_133133.1	chr16	65839808	65839811	+	1	NA	intron (NM_028572, intron 3 of 3)	intron (NM_028572, intron 3 of 3)	24176	NM_028572	73569	Mm.25670	NM_028572	ENSMUSG00000091243	Vgll3	1700110N18Rik|4832416J22|C80713|Vgl-3|Vito-2	vestigial like family member 3	protein-coding
mm_92687.1	chr10	80656486	80656519	-	1	NA	exon (NM_145361, exon 1 of 9)	exon (NM_145361, exon 1 of 9)	569	NM_145361	208198	Mm.60720	NM_145361	ENSMUSG00000003344	Btbd2	2610037C03Rik|4930512K17Rik	BTB (POZ) domain containing 2	protein-coding
mm_102598.1	chr11	62343246	62343293	-	1	NA	exon (NM_001252313, exon 30 of 45)	exon (NM_001252313, exon 30 of 45)	61796	NM_029704	72795	Mm.489722	NM_028360	ENSMUSG00000042298	Ttc19	2010204O13Rik|2810460C24Rik|AI505442	tetratricopeptide repeat domain 19	protein-coding
mm_67372.1	chr7	79841727	79841737	-	1	NA	exon (NM_008486, exon 1 of 20)	exon (NM_008486, exon 1 of 20)	620	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_20732.1	chr2	137082149	137082153	-	1	NA	3' UTR (NM_013822, exon 26 of 26)	3' UTR (NM_013822, exon 26 of 26)	34369	NM_013822	16449	Mm.22398	NM_013822	ENSMUSG00000027276	Jag1	ABE2|Gsfabe2|Htu|Ozz|Ser-1	jagged 1	protein-coding
mm_42866.1	chr5	122232261	122232282	+	1	NA	intron (NM_028752, intron 2 of 6)	RLTR40|LTR|ERVK	21984	NM_028752	74096	Mm.28804	NM_028752	ENSMUSG00000064267	Hvcn1	0610039P13Rik|AI450555|BTS|HV1|Vsop.|mVSOP	hydrogen voltage-gated channel 1	protein-coding
mm_41180.1	chr5	88268924	88268934	+	1	NA	promoter-TSS (NM_001110779)	promoter-TSS (NM_001110779)	10	NM_001110779	665615	Mm.366701	NM_001110779	ENSMUSG00000090302	Gm7714	EG665615	predicted gene 7714	protein-coding
mm_39124.1	chr4	155019400	155019437	-	1	NA	Intergenic	Intergenic	-8434	NM_001113360	269615	Mm.379458	NM_175556	ENSMUSG00000029055	Plch2	A930027K05Rik|PLCeta2|Plc-eta2|Plcl4	phospholipase C, eta 2	protein-coding
mm_58851.1	chr7	16875303	16875392	+	1	NA	promoter-TSS (NM_001081655)	promoter-TSS (NM_001081655)	30	NM_001081655	629378	Mm.491123	NM_001081655	ENSMUSG00000078794	Dact3	EG666671|naa-3	dishevelled-binding antagonist of beta-catenin 3	protein-coding
mm_124517.1	chr14	121965099	121965116	-	1	NA	promoter-TSS (NM_183031)	promoter-TSS (NM_183031)	86	NM_183031	321019	Mm.265618	NM_183031	ENSMUSG00000051212	Gpr183	Ebi2	G protein-coupled receptor 183	protein-coding
mm_25072.1	chr3	99885384	99885419	+	1	NA	promoter-TSS (NM_028892)	promoter-TSS (NM_028892)	-16	NM_028892	74362	Mm.55847	NM_028892	ENSMUSG00000027867	Spag17	4931427F14Rik|PF6|Spag17-ps	sperm associated antigen 17	protein-coding
mm_59443.1	chr7	27133211	27133223	+	1	NA	exon (NM_007817, exon 10 of 10)	exon (NM_007817, exon 10 of 10)	13262	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_142713.1	chr17	47924433	47924450	-	1	NA	5' UTR (NM_028767, exon 1 of 17)	5' UTR (NM_028767, exon 1 of 17)	191	NM_028767	74123	Mm.240062	NM_028767	ENSMUSG00000023991	Foxp4	1200010K03Rik|2310007G05Rik|mFKHLA	forkhead box P4	protein-coding
mm_31081.1	chr4	41569792	41569822	+	1	NA	promoter-TSS (NM_027993)	promoter-TSS (NM_027993)	13	NM_175138	68922	Mm.79127	NM_175138	ENSMUSG00000061322	Dnaic1	1110066F04Rik|BB124644|Dnai1|b2b1526Clo	dynein, axonemal, intermediate chain 1	protein-coding
mm_137332.1	chr17	25089376	25089384	+	1	NA	intron (NM_134126, intron 22 of 29)	intron (NM_134126, intron 22 of 29)	-8266	NM_001001183	407831	Mm.34379	NM_001001183	ENSMUSG00000024168	Tmem204	-	transmembrane protein 204	protein-coding
mm_24740.1	chr3	95283445	95283517	+	1	NA	5' UTR (NM_133858, exon 1 of 10)	5' UTR (NM_133858, exon 1 of 10)	546	NM_199475	75007	Mm.279287	NM_133858	ENSMUSG00000038712	Fam63a	1810005H09Rik|4930504E06Rik|AA562754|AA960384|AW561904|cI-40|mKIAA1390|ni	family with sequence similarity 63, member A	protein-coding
mm_58408.1	chr7	3289013	3289047	+	1	NA	promoter-TSS (NM_001093764)	promoter-TSS (NM_001093764)	-8	NM_001093764	50918	Mm.29874	NM_016969	ENSMUSG00000068566	Myadm	D7Wsu62e	myeloid-associated differentiation marker	protein-coding
mm_151979.1	chr19	5828297	5828311	-	1	NA	non-coding (NR_131212, exon 1 of 1)	non-coding (NR_131212, exon 1 of 1)	17174	NR_131212	66961	Mm.281895	NR_003513	ENSMUSG00000092274	Neat1	2310043N10Rik|VINC	nuclear paraspeckle assembly transcript 1 (non-protein coding)	ncRNA
mm_14706.1	chr2	142902966	142902976	+	1	NA	promoter-TSS (NR_131921)	promoter-TSS (NR_131921)	6	NR_131921	75053	Mm.72638	NR_131921	ENSMUSG00000086504	Kif16bos	4930511F01Rik	kinesin family member 16B, opposite strand	ncRNA
mm_37356.1	chr4	120532110	120532122	-	1	NA	promoter-TSS (NM_177570)	promoter-TSS (NM_177570)	-115	NM_177570	194219	Mm.29788	NM_177570	ENSMUSG00000047518	Slfnl1	4933406A14Rik	schlafen like 1	protein-coding
mm_91066.1	chr10	19005575	19005589	-	1	NA	exon (NM_009397, exon 6 of 9)	exon (NM_009397, exon 6 of 9)	6381	NM_001166402	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_141326.1	chr17	28452030	28452034	-	1	NA	intron (NM_010220, intron 1 of 10)	intron (NM_010220, intron 1 of 10)	34117	NM_010220	14229	Mm.276405	NM_010220	ENSMUSG00000024222	Fkbp5	D17Ertd592e|Dit1|FKBP-5|FKBP51	FK506 binding protein 5	protein-coding
mm_61868.1	chr7	89404371	89404401	+	1	NA	promoter-TSS (NM_008055)	promoter-TSS (NM_008055)	20	NM_008055	14366	Mm.86755	NM_008055	ENSMUSG00000049791	Fzd4	Fz4	frizzled class receptor 4	protein-coding
mm_54242.1	chr6	28247214	28247224	-	1	NA	exon (NM_001081678, exon 4 of 6)	exon (NM_001081678, exon 4 of 6)	14382	NM_001081678	627049	Mm.84441	NM_001081678	ENSMUSG00000039841	Zfp800	AA407452|Znf800	zinc finger protein 800	protein-coding
mm_32807.1	chr4	117124661	117124677	+	1	NA	non-coding (NR_024078, exon 2 of 7)	non-coding (NR_024078, exon 2 of 7)	1056	NR_024078	78611	Mm.446227	NM_001033187		Btbd19	9530048O09Rik|BB115071	BTB (POZ) domain containing 19	ncRNA
mm_159054.1	chr1	189786797	189786797	+	1	NA	exon (NM_008976, exon 2 of 19)	exon (NM_008976, exon 2 of 19)	58529	NM_008976	19250	Mm.4498	NM_008976	ENSMUSG00000026604	Ptpn14	C130080N23Rik|OTTMUSG00000022087|PTP36	protein tyrosine phosphatase, non-receptor type 14	protein-coding
mm_101994.1	chr11	50943771	50943775	-	1	NA	Intergenic	Intergenic	9859	NM_008936	19127	Mm.1386	NM_008936	ENSMUSG00000044542	Prop1	Prop-1|df	paired like homeodomain factor 1	protein-coding
mm_84990.1	chr9	86571776	86571847	-	1	NA	promoter-TSS (NM_001145969)	promoter-TSS (NM_001145969)	31	NM_001163746	109785	Mm.390201	NM_028352	ENSMUSG00000056131	Pgm3	2810473H05Rik|Agm1|BB187688|C77933|PAGM|Pgm-3	phosphoglucomutase 3	protein-coding
mm_75631.1	chr8	64693046	64693074	-	1	NA	promoter-TSS (NM_013494)	promoter-TSS (NM_013494)	49	NM_013494	12876	Mm.31395	NM_013494	ENSMUSG00000037852	Cpe	CPH|Cph-1|Cph1|R74677|fat	carboxypeptidase E	protein-coding
mm_136309.1	chr16	91647692	91647714	-	1	NA	promoter-TSS (NM_019973)	promoter-TSS (NM_019973)	-121	NM_019973	20658	Mm.46401	NM_019973	ENSMUSG00000022961	Son	2900011L12Rik|AA409051|AU067731|C81487|mKIAA1019|nrebp	Son DNA binding protein	protein-coding
mm_42992.1	chr5	123344337	123344347	+	1	NA	promoter-TSS (NM_029850)	promoter-TSS (NM_029850)	-106	NM_029850	77045	Mm.151960	NM_029850	ENSMUSG00000029438	Bcl7a	4432415N06Rik|AI448316	B cell CLL/lymphoma 7A	protein-coding
mm_7437.1	chr1	119997212	119997249	-	1	NA	Intergenic	Intergenic	-2020	NM_001115074	226356	Mm.297290	NM_001115074	ENSMUSG00000036962	Cfap221	Gm101|Pcdp1	cilia and flagella associated protein 221	protein-coding
mm_152426.1	chr19	10676664	10676670	-	1	NA	exon (NM_021453, exon 2 of 9)	exon (NM_021453, exon 2 of 9)	1404	NM_021453	58803	Mm.34037	NM_021453	ENSMUSG00000024738	Pga5	1110035E17Rik|Pepf	pepsinogen 5, group I	protein-coding
mm_29807.1	chr3	127789870	127789901	-	1	NA	promoter-TSS (NM_145133)	promoter-TSS (NM_145133)	-28	NM_145133	211550	Mm.31852	NM_145133	ENSMUSG00000046688	Tifa	T2bp	TRAF-interacting protein with forkhead-associated domain	protein-coding
mm_155677.1	chrX	91413630	91413630	+	1	NA	Intergenic	Intergenic	21130	NM_001114678	278167	Mm.473682	NM_001114678	ENSMUSG00000094861	Gm5072	EG278167	predicted gene 5072	protein-coding
mm_29039.1	chr3	102782709	102782715	-	1	NA	promoter-TSS (NM_009432)	promoter-TSS (NM_009432)	2	NM_009432	22094	Mm.110730	NM_009432	ENSMUSG00000027857	Tshb	-	thyroid stimulating hormone, beta subunit	protein-coding
mm_33608.1	chr4	132581185	132581204	+	1	NA	3' UTR (NM_001081211, exon 2 of 2)	3' UTR (NM_001081211, exon 2 of 2)	17127	NM_001081211	19204	Mm.89389	NM_001081211	ENSMUSG00000056529	Ptafr	PAFR	platelet-activating factor receptor	protein-coding
mm_77822.1	chr9	3404040	3404050	+	1	NA	promoter-TSS (NM_027545)	promoter-TSS (NM_027545)	-40	NM_027545	244672	Mm.245482	NM_027545	ENSMUSG00000025898	Cwf19l2	3230401L03Rik|9030209E10	CWF19-like 2, cell cycle control (S. pombe)	protein-coding
mm_124152.1	chr14	93202107	93202117	-	1	NA	intron (NM_001346722, intron 4 of 4)	intron (NM_001346722, intron 4 of 4)	686776	NM_001271800	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding
mm_151047.1	chr19	47024759	47024776	+	1	NA	TTS (NM_146100)	TTS (NM_146100)	-9578	NM_001164363	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_89330.1	chr10	87932802	87932819	+	1	NA	3' UTR (NM_010512, exon 5 of 5)	3' UTR (NM_010512, exon 5 of 5)	-33861	NR_000040	22172	Mm.391420	NR_000040		Tyms-ps	-	thymidylate synthase, pseudogene	pseudo
mm_37204.1	chr4	117872549	117872560	-	1	NA	promoter-TSS (NM_001034876)	promoter-TSS (NM_001034876)	-84	NM_001034876	381546	Mm.440118	NM_001034876	ENSMUSG00000078588	Ccdc24	Gm1028	coiled-coil domain containing 24	protein-coding
mm_170178.1	chr17	60783469	60783469	+	1	NA	Intergenic	L1Md_T|LINE|L1	-1770147	NM_026497	67993	Mm.36507	NM_026497	ENSMUSG00000024228	Nudt12	0610016O18Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 12	protein-coding
mm_171716.1	chr4	82193454	82193460	-	1	NA	Intergenic	L1Md_T|LINE|L1	128077	NR_040659	545641	Mm.216028	NR_040659	ENSMUSG00000085022	Gm5860	EG545641	predicted gene 5860	ncRNA
mm_39718.1	chr5	28078079	28078089	+	1	NA	3' UTR (NM_153526, exon 5 of 5)	3' UTR (NM_153526, exon 5 of 5)	6672	NM_153526	231070	Mm.30221	NM_153526	ENSMUSG00000045294	Insig1	1810013C12Rik|Insig-1	insulin induced gene 1	protein-coding
mm_17407.1	chr2	27246780	27246784	-	1	NA	5' UTR (NM_138665, exon 1 of 21)	5' UTR (NM_138665, exon 1 of 21)	521	NM_138665	192166	Mm.278467	NM_138665	ENSMUSG00000009614	Sardh	-	sarcosine dehydrogenase	protein-coding
mm_143436.1	chr17	70851887	70851893	-	1	NA	promoter-TSS (NM_001164075)	promoter-TSS (NM_001164075)	-156	NM_001164075	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_99536.1	chr11	103193101	103193113	+	1	NA	exon (NM_001077698, exon 14 of 26)	exon (NM_001077698, exon 14 of 26)	15441	NM_001254724	69441	Mm.380648	NM_027082	ENSMUSG00000020940	1700023F06Rik	-	RIKEN cDNA 1700023F06 gene	protein-coding
mm_36545.1	chr4	86669493	86669507	-	1	NA	intron (NM_007408, intron 1 of 7)	intron (NM_007408, intron 1 of 7)	559	NM_007408	11520	Mm.381	NM_007408	ENSMUSG00000028494	Plin2	AA407157|ADPH|Adfp|Adrp	perilipin 2	protein-coding
mm_45760.1	chr5	86890683	86890694	-	1	NA	3' UTR (NM_153598, exon 6 of 6)	3' UTR (NM_153598, exon 6 of 6)	16249	NM_153598	100727	Mm.281844	NM_153598	ENSMUSG00000029260	Ugt2b34	AI788959	UDP glucuronosyltransferase 2 family, polypeptide B34	protein-coding
mm_14743.1	chr2	144375356	144375358	+	1	NA	intron (NM_181417, intron 2 of 10)	intron (NM_181417, intron 2 of 10)	6322	NM_181417	228714	Mm.227925	NM_181417	ENSMUSG00000027425	Csrp2bp	2510008M08Rik|ATAC2|AU023459|D2Ertd473e|D2Wsu131e|E430020F17|Kat14	cysteine and glycine-rich protein 2 binding protein	protein-coding
mm_30274.1	chr3	146812952	146812983	-	1	NA	promoter-TSS (NM_011100)	promoter-TSS (NM_011100)	-21	NM_011100	18749	Mm.16766	NM_011100	ENSMUSG00000005034	Prkacb	CbPKA|Pkacb	protein kinase, cAMP dependent, catalytic, beta	protein-coding
mm_104868.1	chr11	99388068	99388101	-	1	NA	exon (NM_010660, exon 2 of 8)	exon (NM_010660, exon 2 of 8)	1280	NM_010660	16661	Mm.22662	NM_010660	ENSMUSG00000019761	Krt10	D130054E02Rik|K10|K1C1|Krt-1.10|Krt1-10	keratin 10	protein-coding
mm_121878.1	chr14	21052178	21052225	-	1	NA	promoter-TSS (NM_134079)	promoter-TSS (NM_134079)	241	NM_018829	55946	Mm.376269	NM_018829	ENSMUSG00000021824	Ap3m1	1200013D09Rik|C78982|R75378	adaptor-related protein complex 3, mu 1 subunit	protein-coding
mm_107355.1	chr12	32821626	32821629	+	1	NA	intron (NM_021524, intron 1 of 10)	intron (NM_021524, intron 1 of 10)	1292	NM_021524	59027	Mm.202727	NM_021524	ENSMUSG00000020572	Nampt	1110035O14Rik|AI314458|AI480535|NAmPRTase|Pbef|Pbef1|Visfatin	nicotinamide phosphoribosyltransferase	protein-coding
mm_48783.1	chr5	148552784	148552843	-	1	NA	promoter-TSS (NM_011908)	promoter-TSS (NM_011908)	-25	NM_011908	24109	Mm.21846	NM_011908	ENSMUSG00000001687	Ubl3	AW108023|HCG	ubiquitin-like 3	protein-coding
mm_130718.1	chr15	101052252	101052264	-	1	NA	3' UTR (NM_001214911, exon 1 of 1)	3' UTR (NM_001214911, exon 1 of 1)	2141	NM_001214911	668225	Mm.385011	NM_001214911	ENSMUSG00000095440	Fignl2	EG668225	fidgetin-like 2	protein-coding
mm_46927.1	chr5	114690907	114690970	-	1	NA	promoter-TSS (NM_019821)	promoter-TSS (NM_019821)	-3	NM_019821	56356	Mm.275766	NM_019821	ENSMUSG00000011884	Gltp	1110001F24Rik|C76925|C77564	glycolipid transfer protein	protein-coding
mm_57498.1	chr6	125344395	125344407	-	1	NA	3' UTR (NM_011324, exon 12 of 12)	3' UTR (NM_011324, exon 12 of 12)	-5322	NM_011609	21937	Mm.1258	NM_011609	ENSMUSG00000030341	Tnfrsf1a	CD120a|FPF|TNF-R|TNF-R-I|TNF-R1|TNF-R55|TNF-alphaR1|TNFAR|TNFR60|TNFRI|TNFRp55|TNFalpha-R1|Tnfr-2|Tnfr1|p55|p55-R	tumor necrosis factor receptor superfamily, member 1a	protein-coding
mm_27820.1	chr3	79075392	79075425	-	1	NA	intron (NM_001310536, intron 19 of 23)	Kanga2_a|DNA|TcMar-Tc2	69479	NM_001310536	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_25790.1	chr3	126830035	126830040	+	1	NA	intron (NM_001346636, intron 16 of 20)	intron (NM_001346636, intron 16 of 20)	113349	NM_001034168	109676	Mm.220242	NM_178655	ENSMUSG00000032826	Ank2	100043364|AI835472|AW491075|Ank-2|Gm4392	ankyrin 2, brain	protein-coding
mm_33055.1	chr4	123183457	123183601	+	1	NA	promoter-TSS (NM_174998)	promoter-TSS (NM_174998)	25	NM_174998	170638	Mm.270641	NM_174998	ENSMUSG00000046093	Hpcal4	AI846570|NVP-2	hippocalcin-like 4	protein-coding
mm_75964.1	chr8	71723309	71723357	-	1	NA	intron (NR_131256, intron 1 of 25)	intron (NR_131256, intron 1 of 25)	2348	NR_131256	74015	Mm.22025	NM_028715	ENSMUSG00000070000	Fcho1	3322402E17Rik|N28152	FCH domain only 1	protein-coding
mm_140854.1	chr17	23700143	23700172	-	1	NA	Intergenic	CpG	-16131	NM_020293	56863	Mm.491368	NM_020293	ENSMUSG00000066720	Cldn9	nmf329	claudin 9	protein-coding
mm_3732.1	chr1	155098234	155098259	+	1	NA	3' UTR (NM_010500, exon 1 of 1)	3' UTR (NM_010500, exon 1 of 1)	1390	NM_010500	15939	Mm.12246	NM_010500	ENSMUSG00000056708	Ier5	-	immediate early response 5	protein-coding
mm_164973.1	chr19	7483289	7483290	-	1	NA	promoter-TSS (NM_053076)	promoter-TSS (NM_053076)	2	NM_001271486	20168	Mm.246990	NM_053076	ENSMUSG00000024758	Rtn3	RTN3-A1	reticulon 3	protein-coding
mm_44967.1	chr5	36767396	36767437	-	1	NA	Intergenic	MLTR73|LTR|ERV1	-18737	NM_133724	117197	Mm.46744	NM_133724	ENSMUSG00000060708	Bloc1s4	2610101N07Rik|Blos4|Cno	biogenesis of lysosomal organelles complex-1, subunit 4, cappuccino	protein-coding
mm_7600.1	chr1	125989250	125989252	-	1	NA	intron (NM_001081756, intron 14 of 16)	intron (NM_001081756, intron 14 of 16)	-76323	NM_001311089	72585	Mm.490405	NM_145100	ENSMUSG00000026344	Lypd1	2700050C12Rik|AI853408|C530008O16Rik|Lynx2|Lypdc1	Ly6/Plaur domain containing 1	protein-coding
mm_146033.1	chr18	69521786	69521802	+	1	NA	intron (NM_013685, intron 6 of 19)	intron (NM_013685, intron 6 of 19)	176073	NM_001083967	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding
mm_25996.1	chr3	134239255	134239279	+	1	NA	intron (NM_001004367, intron 2 of 3)	intron (NM_001004367, intron 2 of 3)	1316	NR_035435	100316832		NR_035435	ENSMUSG00000084564	Mir1895	Mirn1895|mmu-mir-1895	microRNA 1895	ncRNA
mm_8219.1	chr1	138162545	138162557	-	1	NA	intron (NM_001111316, intron 1 of 31)	intron (NM_001111316, intron 1 of 31)	12575	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_101224.1	chr11	20200928	20200938	-	1	NA	promoter-TSS (NM_008996)	promoter-TSS (NM_008996)	-669	NM_008996	19324	Mm.271944	NM_008996	ENSMUSG00000020149	Rab1a	Gtbp|Rab-1|Rab1|Ypt1|mKIAA3012	RAB1A, member RAS oncogene family	protein-coding
mm_160413.1	chr8	75213909	75213909	+	1	NA	promoter-TSS (NM_029182)	promoter-TSS (NM_029182)	-35	NM_029182	75141	Mm.179267	NM_029182	ENSMUSG00000034472	Rasd2	4930526B11Rik|AU045414|Rhes|TEM-2|TEM2	RASD family, member 2	protein-coding
mm_84325.1	chr9	64017032	64017049	-	1	NA	intron (NM_008542, intron 1 of 3)	intron (NM_008542, intron 1 of 3)	5019	NM_008542	17130	Mm.325757	NM_008542	ENSMUSG00000036867	Smad6	Madh6|b2b390Clo	SMAD family member 6	protein-coding
mm_113208.1	chr13	25056207	25056219	+	1	NA	5' UTR (NM_177577, exon 1 of 10)	5' UTR (NM_177577, exon 1 of 10)	209	NM_177577	195208	Mm.284719	NM_177577	ENSMUSG00000035910	Dcdc2a	AW492955|Dcdc2|RU2	doublecortin domain containing 2a	protein-coding
mm_118087.1	chr13	103764503	103764505	-	1	NA	promoter-TSS (NM_172592)	promoter-TSS (NM_172592)	78	NM_172592	218543	Mm.458176	NM_172592	ENSMUSG00000032621	Srek1	8430401B01|AI450757|AI462342|SRrp508|SRrp86|Sfrs12|Srsf12	splicing regulatory glutamine/lysine-rich protein 1	protein-coding
mm_5172.1	chr1	10233008	10233020	-	1	NA	promoter-TSS (NM_001102430)	promoter-TSS (NM_001102430)	-344	NM_001102430	211673	Mm.229141	NM_001102430	ENSMUSG00000067851	Arfgef1	ARFGEP1|BIG1|D130059B05Rik|D730028O18Rik|P200	ADP-ribosylation factor guanine nucleotide-exchange factor 1(brefeldin A-inhibited)	protein-coding
mm_83818.1	chr9	53667061	53667103	-	1	NA	exon (NM_001161618, exon 1 of 18)	exon (NM_001161618, exon 1 of 18)	425	NM_001161618	75717	Mm.218910	NM_027807	ENSMUSG00000032030	Cul5	4921514I20Rik|8430423K24Rik|AI852817|C030032G03Rik|C330021I08Rik|VACM-1|VACM1	cullin 5	protein-coding
mm_163322.1	chr12	7988709	7988724	+	1	NA	exon (NM_009693, exon 10 of 29)	exon (NM_009693, exon 10 of 29)	11039	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_107688.1	chr12	55302825	55302864	+	1	NA	5' UTR (NM_025373, exon 1 of 7)	5' UTR (NM_025373, exon 1 of 7)	156	NM_021529	59032	Mm.427307	NM_021529	ENSMUSG00000021022	Ppp2r3c	4930511A21Rik|5730412A08Rik|G4-1|G5pr	protein phosphatase 2, regulatory subunit B'', gamma	protein-coding
mm_163650.1	chr13	64161466	64161470	+	1	NA	promoter-TSS (NM_019986)	promoter-TSS (NM_019986)	-398	NM_019986	56541	Mm.40989	NM_019986	ENSMUSG00000021476	Habp4	4933413D03Rik|4933428J01Rik	hyaluronic acid binding protein 4	protein-coding
mm_21674.1	chr2	164425861	164425874	-	1	NA	3' UTR (NM_011521, exon 5 of 5)	3' UTR (NM_011521, exon 5 of 5)	17321	NM_011521	20971	Mm.3815	NM_011521	ENSMUSG00000017009	Sdc4	AA959608|AW108331|S4|Synd4|ryudocan|syndecan-4	syndecan 4	protein-coding
mm_105178.1	chr11	101785203	101785220	-	1	NA	promoter-TSS (NM_001316366)	promoter-TSS (NM_001316366)	99	NM_008815	18612	Mm.5025	NM_008815	ENSMUSG00000017724	Etv4	AW414408|Pea-3|Pea3	ets variant 4	protein-coding
mm_100184.1	chr11	116657124	116657140	+	1	NA	promoter-TSS (NM_001163318)	promoter-TSS (NM_001163318)	24	NM_001163318	100038570	Mm.390349	NM_001163318	ENSMUSG00000075410	Prcd	Gm11744|OTTMUSG00000003947	progressive rod cone degeneration protein	protein-coding
mm_82712.1	chr9	24503320	24503328	-	1	NA	promoter-TSS (NM_172920)	promoter-TSS (NM_172920)	-184	NM_172920	244745	Mm.38526	NM_172920	ENSMUSG00000043067	Dpy19l1	1100001I19Rik|6030402K12|AI225861|AW558481	dpy-19-like 1 (C. elegans)	protein-coding
mm_45978.1	chr5	90472673	90472686	-	1	NA	exon (NM_009654, exon 12 of 15)	exon (NM_009654, exon 12 of 15)	11809	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_43494.1	chr5	136967816	136967826	+	1	NA	promoter-TSS (NM_021719)	promoter-TSS (NM_021719)	-48	NM_021719	60363	Mm.87202	NM_021719	ENSMUSG00000001739	Cldn15	2210009B08Rik|BB107105	claudin 15	protein-coding
mm_58842.1	chr7	16842897	16842954	+	1	NA	promoter-TSS (NM_178900)	promoter-TSS (NM_178900)	23	NM_001252458	101540	Mm.1881	NM_178900	ENSMUSG00000041187	Prkd2	AI325941|PKD2	protein kinase D2	protein-coding
mm_114234.1	chr13	56609489	56609489	+	1	NA	promoter-TSS (NM_009369)	promoter-TSS (NM_009369)	-114	NM_009369	21810	Mm.14455	NM_009369	ENSMUSG00000035493	Tgfbi	68kDa|AI181842|AI747162|Beta-ig|big-h3	transforming growth factor, beta induced	protein-coding
mm_20189.1	chr2	122610009	122610015	-	1	NA	intron (NM_025961, intron 1 of 8)	intron (NM_025961, intron 1 of 8)	1265	NM_025961	67092	Mm.29975	NM_025961	ENSMUSG00000027199	Gatm	1810003P21Rik|AI314789|AT	glycine amidinotransferase (L-arginine:glycine amidinotransferase)	protein-coding
mm_158360.1	chrX	134601142	134601155	-	1	NA	promoter-TSS (NM_001313716)	promoter-TSS (NM_001313716)	-31	NM_001313716	56258	Mm.315909	NM_019868	ENSMUSG00000045427	Hnrnph2	DXHXS1271E|Ftp-3|Ftp3|H'|HNRNP|Hnrph2	heterogeneous nuclear ribonucleoprotein H2	protein-coding
mm_56885.1	chr6	119031196	119031219	-	1	NA	intron (NM_001256002, intron 3 of 47)	L1ME3D|LINE|L1	77288	NM_001159534	12288	Mm.41628	NM_009781	ENSMUSG00000051331	Cacna1c	Cav1.2|Cchl1a1|D930026N18Rik|MBC|MELC-CC	calcium channel, voltage-dependent, L type, alpha 1C subunit	protein-coding
mm_4246.1	chr1	171389241	171389247	+	1	NA	TTS (NM_027893)	TTS (NM_027893)	284	NM_001005508	226652	Mm.251048	NM_001005508	ENSMUSG00000048865	Arhgap30	6030405P05Rik|Gm102|mFLJ00267	Rho GTPase activating protein 30	protein-coding
mm_14543.1	chr2	132816170	132816207	+	1	NA	promoter-TSS (NM_025676)	promoter-TSS (NM_025676)	47	NM_001291054	66634	Mm.157070	NM_025676	ENSMUSG00000027353	Mcm8	5730432L01Rik	minichromosome maintenance 8 homologous recombination repair factor	protein-coding
mm_95394.1	chr11	49609698	49609728	+	1	NA	promoter-TSS (NM_008029)	promoter-TSS (NM_008029)	34	NM_008029	14257	Mm.3291	NM_008029	ENSMUSG00000020357	Flt4	AI323512|Chy|Flt-4|VEGFR-3|VEGFR3	FMS-like tyrosine kinase 4	protein-coding
mm_78346.1	chr9	25301466	25301478	+	1	NA	exon (NM_001205367, exon 10 of 13)	exon (NM_001205367, exon 10 of 13)	49033	NM_001205367	235072	Mm.270259	NM_009859	ENSMUSG00000001833	Sept7	Cdc10|E430034N22	septin 7	protein-coding
mm_40981.1	chr5	77126685	77126701	+	1	NA	Intergenic	Intergenic	-11570	NM_175606	74318	Mm.181852	NM_175606	ENSMUSG00000059325	Hopx	1110018K11Rik|1200015P04Rik|2300002F06Rik|AI848177|AW490897|Cameo|Hdop|Hod|Hop|Ob1|Obl|Toto	HOP homeobox	protein-coding
mm_103303.1	chr11	72607076	72607089	-	1	NA	promoter-TSS (NM_025985)	promoter-TSS (NM_025985)	-179	NM_025985	67128	Mm.458052	NM_025985	ENSMUSG00000020794	Ube2g1	2700059C12Rik|AI256795|AU014992|AW552068|D130023C12Rik	ubiquitin-conjugating enzyme E2G 1	protein-coding
mm_97485.1	chr11	78324674	78324689	+	1	NA	exon (NM_009657, exon 2 of 8)	exon (NM_009657, exon 2 of 8)	483	NM_009657	11676	Mm.7729	NM_009657	ENSMUSG00000017390	Aldoc	AI847350|AU040929|Aldo3|Scrg2	aldolase C, fructose-bisphosphate	protein-coding
mm_151600.1	chr19	3533418	3533427	-	1	NA	intron (NM_001164159, intron 1 of 21)	RLTR1B|LTR|ERV1	42327	NM_001164159	52036	Mm.284686	NM_028999	ENSMUSG00000024908	Ppp6r3	4930528G08Rik|9130026N02Rik|D19Bwg1430e|D19Ertd703e|Pp6r3|Ppcs3|Pptcs3|Sapl|Saps3|mKIAA1558	protein phosphatase 6, regulatory subunit 3	protein-coding
mm_1230.1	chr1	62768969	62769003	+	1	NA	intron (NM_001077405, intron 10 of 15)	intron (NM_001077405, intron 10 of 15)	25746	NR_040601	74992	Mm.401979	NR_040601		4930487H11Rik	-	RIKEN cDNA 4930487H11 gene	ncRNA
mm_4981.1	chr1	191623314	191623317	+	1	NA	3' UTR (NM_178632, exon 20 of 20)	3' UTR (NM_178632, exon 20 of 20)	47679	NM_001306204	77065	Mm.338175	NM_178632	ENSMUSG00000037461	Ints7	5930412E23Rik|int7	integrator complex subunit 7	protein-coding
mm_141498.1	chr17	31559561	31559575	-	1	NA	Intergenic	RLTR17|LTR|ERVK	-5205	NR_027493	18771	Mm.259295	NM_016670	ENSMUSG00000006705	Pknox1	D17Wsu76e|PREP1	Pbx/knotted 1 homeobox	protein-coding
mm_15603.1	chr2	160698171	160698197	+	1	NA	exon (NM_009408, exon 9 of 21)	exon (NM_009408, exon 9 of 21)	-33126	NM_021280	18803	Mm.44463	NM_021280	ENSMUSG00000016933	Plcg1	AI894140|Cded|Plc-1|Plc-gamma1|Plcg-1	phospholipase C, gamma 1	protein-coding
mm_134143.1	chr16	10784709	10784719	-	1	NA	exon (NM_001271603, exon 2 of 2)	exon (NM_001271603, exon 2 of 2)	822	NM_009896	12703	Mm.130	NM_009896	ENSMUSG00000038037	Socs1	Cish1|Cish7|JAB|SOCS-1|SSI-1	suppressor of cytokine signaling 1	protein-coding
mm_168990.1	chr12	99645145	99645156	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-17176	NR_045288	73457	Mm.383439	NR_045288	ENSMUSG00000100211	1700064M15Rik	-	RIKEN cDNA 1700064M15 gene	ncRNA
mm_42889.1	chr5	122391943	122391958	+	1	NA	promoter-TSS (NM_019824)	promoter-TSS (NM_019824)	72	NM_019824	56378	Mm.275942	NM_019824	ENSMUSG00000029465	Arpc3	1110006A04Rik|p21-ARC|p21-Ar|p21Arc	actin related protein 2/3 complex, subunit 3	protein-coding
mm_5866.1	chr1	53776642	53776662	-	1	NA	5' UTR (NM_133810, exon 2 of 8)	5' UTR (NM_133810, exon 2 of 8)	8563	NM_133810	98267	Mm.25559	NM_133810	ENSMUSG00000026094	Stk17b	3110009A03Rik|AI120141|Drak2	serine/threonine kinase 17b (apoptosis-inducing)	protein-coding
mm_132183.1	chr16	32419697	32419753	+	1	NA	promoter-TSS (NM_001347183)	promoter-TSS (NM_001347183)	23	NM_001347183	66061	Mm.302693	NM_025329	ENSMUSG00000014075	Tctex1d2	0610012D17Rik|2410011K15Rik	Tctex1 domain containing 2	protein-coding
mm_78811.1	chr9	44068204	44068210	+	1	NA	intron (NM_198092, intron 1 of 12)	intron (NM_198092, intron 1 of 12)	1186	NM_198092	53376	Mm.272770	NM_016808	ENSMUSG00000032010	Usp2	B930035K21Rik|Ubp41	ubiquitin specific peptidase 2	protein-coding
mm_32888.1	chr4	118963791	118963796	+	1	NA	exon (NM_133892, exon 2 of 7)	exon (NM_133892, exon 2 of 7)	1826	NM_133892	100470	Mm.26698	NM_133892	ENSMUSG00000024903	Lao1	AW990848	L-amino acid oxidase 1	protein-coding
mm_112881.1	chr13	20857309	20857321	+	1	NA	intron (NM_012054, intron 4 of 20)	intron (NM_012054, intron 4 of 20)	63202	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_125262.1	chr15	35371294	35371369	+	1	NA	promoter-TSS (NM_177151)	promoter-TSS (NM_177151)	-215	NM_177151	666173	Mm.309250	NM_177151	ENSMUSG00000037646	Vps13b	1810042B05Rik|2310042E16Rik|4732488H20|C330002D13Rik|C87206|Coh1|D230005K13|mKIAA0532|mKIAA5032	vacuolar protein sorting 13B	protein-coding
mm_30065.1	chr3	137918401	137918432	-	1	NA	promoter-TSS (NM_019920)	promoter-TSS (NM_019920)	-139	NM_019920	56692	Mm.331392	NM_019920	ENSMUSG00000091512	Lamtor3	AW556229|Map2k1ip1|Mapbp|Mapksp1|Mp1	late endosomal/lysosomal adaptor, MAPK and MTOR activator 3	protein-coding
mm_152606.1	chr19	11818920	11818965	-	1	NA	5' UTR (NM_001286543, exon 1 of 12)	5' UTR (NM_001286543, exon 1 of 12)	461	NM_001286543	20908	Mm.272264	NM_011502	ENSMUSG00000041488	Stx3	Syn-3	syntaxin 3	protein-coding
mm_43568.1	chr5	137636757	137636806	+	1	NA	exon (NM_146164, exon 5 of 18)	exon (NM_146164, exon 5 of 18)	-4692	NM_001081962	751865	Mm.200763	NM_001081962	ENSMUSG00000079165	Sap25	-	sin3 associated polypeptide	protein-coding
mm_14325.1	chr2	129366033	129366058	+	1	NA	exon (NM_008361, exon 6 of 7)	exon (NM_008361, exon 6 of 7)	-3857	NR_015474	329514	Mm.207315	NM_177848	ENSMUSG00000074805	Il1bos	9430083I22|Gm14047|OTTMUSG00000015529	interleukin 1 beta, opposite strand	ncRNA
mm_128587.1	chr15	58076457	58076515	-	1	NA	promoter-TSS (NM_001042438)	promoter-TSS (NM_001042438)	22	NM_001042438	22770	Mm.244931	NM_009572	ENSMUSG00000022361	Zhx1	-	zinc fingers and homeoboxes 1	protein-coding
mm_105097.1	chr11	100939358	100939456	-	1	NA	5' UTR (NM_011486, exon 1 of 24)	5' UTR (NM_011486, exon 1 of 24)	133	NM_213660	20848	Mm.249934	NM_011486	ENSMUSG00000004040	Stat3	1110034C02Rik|AW109958|Aprf	signal transducer and activator of transcription 3	protein-coding
mm_164837.1	chr18	41573335	41573335	-	1	NA	Intergenic	Intergenic	377859	NM_029942	77619	Mm.30649	NM_029942	ENSMUSG00000056671	Prelid2	1700003A01Rik|C330008K14Rik	PRELI domain containing 2	protein-coding
mm_30281.1	chr3	148927956	148927957	-	1	NA	intron (NM_001081298, intron 1 of 23)	intron (NM_001081298, intron 1 of 23)	26679	NM_001081298	99633	Mm.9776	NM_001081298	ENSMUSG00000028184	Adgrl2	AI450192|CIRL-2|Gm619|Lec1|Lphh1|Lphn2|mKIAA0786	adhesion G protein-coupled receptor L2	protein-coding
mm_57021.1	chr6	122279821	122279843	-	1	NA	intron (NM_016970, intron 1 of 4)	intron (NM_016970, intron 1 of 4)	3001	NM_016970	50928	Mm.20434	NM_016970	ENSMUSG00000030114	Klrg1	2F1-Ag|MAFA|MAFA-L	killer cell lectin-like receptor subfamily G, member 1	protein-coding
mm_134098.1	chr16	9967455	9967465	-	1	NA	intron (NM_008170, intron 1 of 11)	ID4_|SINE|ID	25073	NM_008170	14811	Mm.2953	NM_008170	ENSMUSG00000059003	Grin2a	GluN2A|NMDAR2A|NR2A	glutamate receptor, ionotropic, NMDA2A (epsilon 1)	protein-coding
mm_154202.1	chr19	59031619	59031659	-	1	NA	intron (NM_175172, intron 7 of 14)	(TCTA)n|Simple_repeat|Simple_repeat	44430	NM_175172	71653	Mm.37338	NM_175172	ENSMUSG00000041362	Shtn1	4930506M07Rik|Kiaa1598|Shootin1|mKIAA1598	shootin 1	protein-coding
mm_79524.1	chr9	57589509	57589566	+	1	NA	promoter-TSS (NM_027895)	promoter-TSS (NM_027895)	85	NM_027895	71742	Mm.155877	NM_027895	ENSMUSG00000032308	Ulk3	1200015E14Rik	unc-51-like kinase 3	protein-coding
mm_71362.1	chr8	45690122	45690144	+	1	NA	intron (NM_001310708, intron 1 of 19)	intron (NM_001310708, intron 1 of 19)	28140	NM_001310708	234214	Mm.211096	NM_172752	ENSMUSG00000031626	Sorbs2	2010203O03Rik|9430041O17Rik|A530071H08|Argbp2|mKIAA0777|nArgBP2	sorbin and SH3 domain containing 2	protein-coding
mm_38071.1	chr4	134106893	134106893	-	1	NA	intron (NR_045571, intron 1 of 13)	intron (NR_045571, intron 1 of 13)	4310	NM_026257	67586	Mm.282029	NM_026257	ENSMUSG00000012126	Ubxn11	4930506L07Rik|D4Bwg1540e|Soc|Soci|Ubxd5	UBX domain protein 11	protein-coding
mm_61810.1	chr7	87246820	87246832	+	1	NA	5' UTR (NM_001285835, exon 1 of 18)	5' UTR (NM_001285835, exon 1 of 18)	177	NM_001285833	50490	Mm.31748	NM_015760	ENSMUSG00000030562	Nox4	AI648021	NADPH oxidase 4	protein-coding
mm_95059.1	chr11	32422694	32422715	+	1	NA	exon (NM_177364, exon 13 of 13)	exon (NM_177364, exon 13 of 13)	-32668	NM_173784	327900	Mm.260956	NM_173784	ENSMUSG00000044949	Ubtd2	4930571L24|9630054F20Rik|AI645720	ubiquitin domain containing 2	protein-coding
mm_159475.1	chr4	32864399	32864399	-	1	NA	intron (NM_001012451, intron 1 of 15)	intron (NM_001012451, intron 1 of 15)	59106	NM_080471	140577	Mm.214766	NM_080471	ENSMUSG00000040183	Ankrd6	-	ankyrin repeat domain 6	protein-coding
mm_45923.1	chr5	89441882	89441892	-	1	NA	intron (NM_008096, intron 4 of 12)	intron (NM_008096, intron 4 of 12)	16011	NM_008096	14473	Mm.196595	NM_008096	ENSMUSG00000035540	Gc	DBP|VDB	group specific component	protein-coding
mm_63055.1	chr7	121914211	121914230	+	1	NA	exon (NM_011325, exon 8 of 13)	exon (NM_011325, exon 8 of 13)	49182	NR_073548	20277	Mm.7709	NM_011325	ENSMUSG00000030873	Scnn1b	-	sodium channel, nonvoltage-gated 1 beta	protein-coding
mm_67322.1	chr7	79721221	79721233	-	1	NA	TTS (NM_175640)	TTS (NM_175640)	-7041	NM_001291222	16576	Mm.101633	NM_010626	ENSMUSG00000050382	Kif7	-	kinesin family member 7	protein-coding
mm_138853.1	chr17	40934677	40934751	+	1	NA	promoter-TSS (NM_031863)	promoter-TSS (NM_031863)	29	NM_008650	17850	Mm.259884	NM_008650	ENSMUSG00000023921	Mut	D230010K02Rik|Mcm	methylmalonyl-Coenzyme A mutase	protein-coding
mm_151370.1	chr19	55931704	55931716	+	1	NA	exon (NM_001142922, exon 14 of 14)	exon (NM_001142922, exon 14 of 14)	36389	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_34446.1	chr4	148000736	148000754	+	1	NA	promoter-TSS (NM_008725)	promoter-TSS (NM_008725)	23	NM_008725	230899	Mm.482123	NM_008725	ENSMUSG00000041616	Nppa	ANP|Anf|Pnd	natriuretic peptide type A	protein-coding
mm_127569.1	chr15	102279431	102279445	+	1	NA	promoter-TSS (NM_134100)	promoter-TSS (NM_134100)	-18	NM_134100	106073	Mm.287740	NM_134100	ENSMUSG00000045665	Mfsd5	AA409375|AW556797|D15Mgi27	major facilitator superfamily domain containing 5	protein-coding
mm_3374.1	chr1	138971235	138971245	+	1	NA	intron (NM_181347, intron 1 of 20)	intron (NM_181347, intron 1 of 20)	3519	NM_181347	329260	Mm.337604	NM_181347	ENSMUSG00000056268	Dennd1b	4632404N19Rik|4930467M19Rik|6820401H01Rik|F730008N07Rik	DENN/MADD domain containing 1B	protein-coding
mm_92776.1	chr10	81179379	81179413	-	1	NA	TTS (NR_028549)	TTS (NR_028549)	435	NR_028549	100217454		NR_028549	ENSMUSG00000064441	Snord37	MBII-376	small nucleolar RNA, C/D box 37	snoRNA
mm_47746.1	chr5	130255410	130255418	-	1	NA	promoter-TSS (NM_178897)	promoter-TSS (NM_178897)	116	NM_023248	66711	Mm.280484	NM_023248	ENSMUSG00000025337	Sbds	4733401P19Rik|AI836084|CGI-97|SDS	Shwachman-Bodian-Diamond syndrome homolog (human)	protein-coding
mm_28834.1	chr3	96557790	96557802	-	1	NA	promoter-TSS (NM_023719)	promoter-TSS (NM_023719)	-161	NM_001009935	56338	Mm.410189	NM_023719	ENSMUSG00000038393	Txnip	1200008J08Rik|AA682105|Hyplip1|THIF|Tbp-2|VDUP1	thioredoxin interacting protein	protein-coding
mm_54713.1	chr6	39725488	39725504	-	1	NA	promoter-TSS (NM_139294)	promoter-TSS (NM_139294)	-33	NM_139294	109880	Mm.245513	NM_139294	ENSMUSG00000002413	Braf	9930012E13Rik|AA120551|AA387315|AA473386|B-raf|Braf-2|Braf2|C230098H17|C87398|D6Ertd631e	Braf transforming gene	protein-coding
mm_130081.1	chr15	89377059	89377102	-	1	NA	promoter-TSS (NM_138302)	promoter-TSS (NM_138302)	-43	NM_138302	72962	Mm.287977	NM_138302	ENSMUSG00000022615	Tymp	2900072D10Rik|Ecgf1|PD-ECGF|PDECGF|Pdgfec	thymidine phosphorylase	protein-coding
mm_112465.1	chr13	5867887	5867898	+	1	NA	3' UTR (NM_011803, exon 4 of 4)	3' UTR (NM_011803, exon 4 of 4)	6403	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_86013.1	chr9	112234809	112234822	-	1	NA	promoter-TSS (NM_001177619)	promoter-TSS (NM_001177619)	26	NM_001177619	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_18972.1	chr2	76832134	76832136	-	1	NA	exon (NM_011652, exon 155 of 313)	exon (NM_011652, exon 155 of 313)	150412	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_42646.1	chr5	118637707	118637713	+	1	NA	intron (NM_001347445, intron 2 of 30)	(T)n|Simple_repeat|Simple_repeat	76991	NM_172424	76199	Mm.206238	NM_172424	ENSMUSG00000018076	Med13l	2210413I17Rik|6330591G05Rik|9030618F05Rik|Thrap2|Trap240L|mKIAA1025	mediator complex subunit 13-like	protein-coding
mm_2155.1	chr1	88186627	88186637	+	1	NA	intron (NM_201643, intron 1 of 4)	intron (NM_201643, intron 1 of 4)	-13979	NM_013701	22236	Mm.300095	NM_013701	ENSMUSG00000090171	Ugt1a2	UDPGT 1-2|Ugt1	UDP glucuronosyltransferase 1 family, polypeptide A2	protein-coding
mm_10618.1	chr2	19371414	19371449	+	1	NA	promoter-TSS (NM_029619)	promoter-TSS (NM_029619)	-205	NM_029619	76467	Mm.27166	NM_029619	ENSMUSG00000023094	Msrb2	2310050L06Rik|Mrsb|Msrb|Pilb	methionine sulfoxide reductase B2	protein-coding
mm_163819.1	chr14	19416683	19416707	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	185892	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_103393.1	chr11	75431314	75431324	-	1	NA	TTS (NM_008878)	TTS (NM_008878)	8182	NM_008878	18816	Mm.279733	NM_008878	ENSMUSG00000038224	Serpinf2	AI747498|Pli|Serpimf2	serine (or cysteine) peptidase inhibitor, clade F, member 2	protein-coding
mm_19684.1	chr2	103455114	103455131	-	1	NA	exon (NM_009804, exon 12 of 13)	exon (NM_009804, exon 12 of 13)	30031	NM_009804	12359	Mm.4215	NM_009804	ENSMUSG00000027187	Cat	2210418N07|Cas-1|Cas1|Cs-1	catalase	protein-coding
mm_86768.1	chr10	19934235	19934286	+	1	NA	promoter-TSS (NM_008580)	promoter-TSS (NM_008580)	-266	NM_008580	26408	Mm.6595	NM_008580	ENSMUSG00000071369	Map3k5	7420452D20Rik|ASK|ASK1|MAPKKK5|Mekk5	mitogen-activated protein kinase kinase kinase 5	protein-coding
mm_147724.1	chr18	60848983	60848993	-	1	NA	promoter-TSS (NM_011552)	promoter-TSS (NM_011552)	-24	NM_001198984	21453	Mm.486251	NM_011552	ENSMUSG00000024613	Tcof1	AA408847|AW209012|treacle	treacle ribosome biogenesis factor 1	protein-coding
mm_171846.1	chr5	16903830	16903832	+	1	NA	Intergenic	L1Md_T|LINE|L1	349930	NM_001289461	15234	Mm.267078	NM_010427	ENSMUSG00000028864	Hgf	C230052L06Rik|HGF/SF|NK1|NK2|SF|SF/HGF	hepatocyte growth factor	protein-coding
mm_89356.1	chr10	88201224	88201232	+	1	NA	5' UTR (NM_001122960, exon 1 of 7)	5' UTR (NM_001122960, exon 1 of 7)	131	NM_027487	67282	Mm.208465	NM_026070	ENSMUSG00000020056	Washc3	2900091E11Rik|5730495F03Rik|Ccdc53	WASH complex subunit 3	protein-coding
mm_106505.1	chr11	120437755	120437761	-	1	NA	promoter-TSS (NM_001195023)	promoter-TSS (NM_001195023)	-58	NM_199469	217365	Mm.309520	NM_199469	ENSMUSG00000039703	Nploc4	AK129375|Npl4|mKIAA1499	NPL4 homolog, ubiquitin recognition factor	protein-coding
mm_122850.1	chr14	54768354	54768395	-	1	NA	intron (NM_016972, intron 1 of 10)	intron (NM_016972, intron 1 of 10)	13512	NM_016972	50934	Mm.276831	NM_016972	ENSMUSG00000022180	Slc7a8	AA408822|LAT2	solute carrier family 7 (cationic amino acid transporter, y+ system), member 8	protein-coding
mm_13464.1	chr2	105675637	105675651	+	1	NA	promoter-TSS (NM_013627)	promoter-TSS (NM_013627)	-100	NM_001244200	18508	Mm.3608	NM_013627	ENSMUSG00000027168	Pax6	1500038E17Rik|AEY11|Dey|Gsfaey11|Pax-6|Sey	paired box 6	protein-coding
mm_118224.1	chr13	110545445	110545461	-	1	NA	Intergenic	Intergenic	150409	NM_152804	20620	Mm.380	NM_152804	ENSMUSG00000021701	Plk2	Snk	polo-like kinase 2	protein-coding
mm_36460.1	chr4	82505719	82505739	-	1	NA	promoter-TSS (NM_001113209)	promoter-TSS (NM_001113209)	50	NM_001286127	18028	Mm.317947	NM_008687	ENSMUSG00000008575	Nfib	6720429L07Rik|CTF|E030026I10Rik|NF-I/B|NF1-B|NFI-B	nuclear factor I/B	protein-coding
mm_144710.1	chr18	34932290	34932312	+	1	NA	promoter-TSS (NM_144866)	promoter-TSS (NM_144866)	-298	NM_144866	225363	Mm.329353	NM_144866	ENSMUSG00000024360	Etf1	AI463371|D6Ertd109e|ERF|ERF1|SUP45L1|TB3-1	eukaryotic translation termination factor 1	protein-coding
mm_27711.1	chr3	67515664	67515700	-	1	NA	promoter-TSS (NM_001164763)	promoter-TSS (NM_001164763)	-159	NM_001164763	109222	Mm.38002	NM_001164763	ENSMUSG00000049404	Rarres1	5430417P09Rik|AI662122	retinoic acid receptor responder (tazarotene induced) 1	protein-coding
mm_36900.1	chr4	107803366	107803369	-	1	NA	exon (NM_001080926, exon 2 of 19)	exon (NM_001080926, exon 2 of 19)	1108	NM_001080926	16975	Mm.442134	NM_053073	ENSMUSG00000028613	Lrp8	4932703M08Rik|AA921429|AI848122|ApoER2|Lr8b	low density lipoprotein receptor-related protein 8, apolipoprotein e receptor	protein-coding
mm_52659.1	chr6	117900296	117900307	+	1	NA	promoter-TSS (NM_001166432)	promoter-TSS (NM_001166432)	-39	NM_001166432	98758	Mm.422979	NM_133834	ENSMUSG00000042079	Hnrnpf	4833420I20Rik|AA407306|Hnrpf	heterogeneous nuclear ribonucleoprotein F	protein-coding
mm_11760.1	chr2	38513241	38513250	+	1	NA	intron (NM_001159631, intron 1 of 9)	intron (NM_001159631, intron 1 of 9)	1369	NM_001159631	59126	Mm.143818	NM_021606	ENSMUSG00000026749	Nek6	1300007C09Rik	NIMA (never in mitosis gene a)-related expressed kinase 6	protein-coding
mm_27957.1	chr3	79852761	79852784	-	1	NA	Intergenic	MLT1F|LTR|ERVL-MaLR	-10110	NM_027495	70652	Mm.46635	NM_027495	ENSMUSG00000027956	Tmem144	1110057I03Rik|5730537D05Rik	transmembrane protein 144	protein-coding
mm_5788.1	chr1	51879422	51879446	-	1	NA	intron (NM_001290982, intron 2 of 28)	intron (NM_001290982, intron 2 of 28)	36544	NM_001290982	17912	Mm.3390	NM_010863	ENSMUSG00000018417	Myo1b	AA406997|MIH-L|MMIa	myosin IB	protein-coding
mm_111266.1	chr12	85270586	85270608	-	1	NA	promoter-TSS (NM_001304475)	promoter-TSS (NM_001304475)	2	NM_175337	217716	Mm.311981	NM_145446	ENSMUSG00000021245	Mlh3	AV125803|BB126472	mutL homolog 3	protein-coding
mm_150456.1	chr19	38264559	38264574	+	1	NA	promoter-TSS (NM_020278)	promoter-TSS (NM_020278)	-216	NM_020278	56839	Mm.298251	NM_020278	ENSMUSG00000067242	Lgi1	BB130740	leucine-rich repeat LGI family, member 1	protein-coding
mm_62054.1	chr7	92447468	92447478	+	1	NA	3' UTR (NM_001243047, exon 11 of 11)	3' UTR (NM_001243047, exon 11 of 11)	-113676	NM_025515	66365	Mm.21173	NM_025515	ENSMUSG00000030613	Ccdc90b	2310015N07Rik|C86558	coiled-coil domain containing 90B	protein-coding
mm_118485.1	chr14	12190004	12190025	+	1	NA	promoter-TSS (NM_001347593)	promoter-TSS (NM_001347593)	71	NM_001347593	19270	Mm.431266	NM_008981	ENSMUSG00000021745	Ptprg	5430405N12Rik|AW046354|AW549872|RPTPgamma	protein tyrosine phosphatase, receptor type, G	protein-coding
mm_18434.1	chr2	60842437	60842463	-	1	NA	exon (NM_001141932, exon 2 of 15)	exon (NM_001141932, exon 2 of 15)	38988	NM_001141932	56878	Mm.259667	NM_020296	ENSMUSG00000026970	Rbms1	2600014B10Rik|AI255215|MSSP-1|MSSP-2|MSSP-3|YC1	RNA binding motif, single stranded interacting protein 1	protein-coding
mm_42004.1	chr5	107905345	107905353	+	1	NA	intron (NM_016980, intron 6 of 7)	(T)n|Simple_repeat|Simple_repeat	4821	NM_016980	100503670	Mm.277897	NM_016980	ENSMUSG00000058558	Rpl5	U21RNA	ribosomal protein L5	protein-coding
mm_138244.1	chr17	34564374	34564385	+	1	NA	promoter-TSS (NM_010929)	promoter-TSS (NM_010929)	84	NM_010929	18132	Mm.173813	NM_010929	ENSMUSG00000015468	Notch4	Int-3|Int3|N4	notch 4	protein-coding
mm_1490.1	chr1	71733540	71733559	+	1	NA	Intergenic	BC1_Mm|scRNA|scRNA	80214	NR_040308	100042814	Mm.405775	NR_040308	ENSMUSG00000073652	Apol7d	ENSMUSG00000073652|Gm15456|OTTMUSG00000022136	apolipoprotein L 7d	ncRNA
mm_159520.1	chr4	61439816	61439816	-	1	NA	promoter-TSS (NM_001286096)	promoter-TSS (NM_001286096)	-112	NM_001200004	100039150	Mm.237772	NM_001200004	ENSMUSG00000096674	Mup15	Gm2068|Mup13	major urinary protein 15	protein-coding
mm_77154.1	chr8	111686617	111686621	-	1	NA	exon (NM_025583, exon 7 of 7)	exon (NM_025583, exon 7 of 7)	3055	NR_106044	102466993		NR_106044	ENSMUSG00000099129	Mir7076	Gm27318|mmu-mir-7076	microRNA 7076	ncRNA
mm_9015.1	chr1	166126849	166126860	-	1	NA	intron (NM_001033344, intron 2 of 5)	intron (NM_001033344, intron 2 of 5)	1044	NM_001033344	240892	Mm.35315	NM_001033344	ENSMUSG00000026564	Dusp27	C130085G02Rik|Gm209	dual specificity phosphatase 27 (putative)	protein-coding
mm_165881.1	chr4	41631689	41631703	+	1	NA	intron (NM_175138, intron 16 of 19)	intron (NM_175138, intron 16 of 19)	8606	NM_027147	69638	Mm.372459	NM_027147	ENSMUSG00000028445	Enho	1110065P19Rik|2310040A07Rik	energy homeostasis associated	protein-coding
mm_41421.1	chr5	90891235	90891250	+	1	NA	promoter-TSS (NM_008176)	promoter-TSS (NM_008176)	-3	NM_008176	14825	Mm.21013	NM_008176	ENSMUSG00000029380	Cxcl1	Fsp|Gro1|KC|Mgsa|N51|Scyb1|gro	chemokine (C-X-C motif) ligand 1	protein-coding
mm_150841.1	chr19	44954743	44954746	+	1	NA	intron (NM_001081225, intron 9 of 19)	intron (NM_001081225, intron 9 of 19)	23625	NM_001081225	226151	Mm.212609	NM_172638	ENSMUSG00000036097	Fam178a	3632432H19|6030443O07Rik|AU014917|Slf2	family with sequence similarity 178, member A	protein-coding
mm_75353.1	chr8	44935154	44935172	-	1	NA	Intergenic	CpG	-15045	NM_001081286	14107	Mm.27365	NM_001081286	ENSMUSG00000070047	Fat1	2310038E12Rik|AU023433|Fath|mFat1	FAT atypical cadherin 1	protein-coding
mm_5466.1	chr1	36535720	36535764	-	1	NA	promoter-TSS (NM_153502)	promoter-TSS (NM_153502)	-3	NM_153502	78321	Mm.41421	NM_153502	ENSMUSG00000067653	Ankrd23	1110058D09Rik|2310041C05Rik|AI853437|Darp|MARP3	ankyrin repeat domain 23	protein-coding
mm_95526.1	chr11	52232176	52232180	+	1	NA	intron (NM_011543, intron 1 of 5)	CpG	183	NM_011543	21402	Mm.42944	NM_011543	ENSMUSG00000036309	Skp1a	15kDa|2610043E24Rik|2610206H23Rik|EMC19|OCP-II|OCP2|SKP1|Tceb1l|p19A|p19Skp1	S-phase kinase-associated protein 1A	protein-coding
mm_9023.1	chr1	166238726	166238762	-	1	NA	promoter-TSS (NM_175296)	promoter-TSS (NM_175296)	0	NM_175296	98558	Mm.26189	NM_175296	ENSMUSG00000040629	Mael	4933405K18Rik|AU019877	maelstrom spermatogenic transposon silencer	protein-coding
mm_164254.1	chr15	98610237	98610239	-	1	NA	Intergenic	Intergenic	-2605	NM_007405	11512	Mm.157091	NM_007405	ENSMUSG00000022994	Adcy6	AC6|mKIAA0422	adenylate cyclase 6	protein-coding
mm_25475.1	chr3	108911807	108911824	+	1	NA	promoter-TSS (NM_025845)	promoter-TSS (NM_025845)	-111	NM_025845	66921	Mm.51049	NM_025845	ENSMUSG00000027881	Prpf38b	1110021E09Rik|AU018955	PRP38 pre-mRNA processing factor 38 (yeast) domain containing B	protein-coding
mm_72491.1	chr8	83715228	83715238	+	1	NA	promoter-TSS (NM_197982)	promoter-TSS (NM_197982)	56	NM_197982	68278	Mm.28222	NM_197982	ENSMUSG00000005481	Ddx39	2610307C23Rik|BAT1|DDXL|Ddx39a|URH49	DEAD (Asp-Glu-Ala-Asp) box polypeptide 39	protein-coding
mm_70454.1	chr8	11797412	11797448	+	1	NA	intron (NM_001113517, intron 6 of 18)	intron (NM_001113517, intron 6 of 18)	39100	NM_001113518	54126	Mm.244068	NM_017402	ENSMUSG00000031511	Arhgef7	Cool|PIX|Pak3bp|betaPix|betaPix-b|betaPix-c|cool-1|mKIAA0142|p85Cool1|p85SPR	Rho guanine nucleotide exchange factor (GEF7)	protein-coding
mm_2017.1	chr1	87127958	87127974	+	1	NA	TTS (NM_007432)	TTS (NM_007432)	2958	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_46850.1	chr5	113644260	113644281	-	1	NA	intron (NM_008153, intron 1 of 2)	intron (NM_008153, intron 1 of 2)	6120	NM_008153	14747	Mm.5196	NM_008153	ENSMUSG00000042190	Cmklr1	ChemR23|DEZ|Gpcr27|mcmklr1	chemokine-like receptor 1	protein-coding
mm_156162.1	chrX	130006022	130006034	+	1	NA	intron (NM_172493, intron 17 of 26)	intron (NM_172493, intron 17 of 26)	256286	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diaph2	Dia3|Diap2|Drf2|E430022I22Rik	diaphanous related formin 2	protein-coding
mm_150058.1	chr19	29383649	29383678	+	1	NA	intron (NM_021893, intron 5 of 6)	intron (NM_021893, intron 5 of 6)	16225	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_54666.1	chr6	39206710	39206750	-	1	NA	promoter-TSS (NM_001033430)	promoter-TSS (NM_001033430)	43	NM_001033430	338523	Mm.293175	NM_001033430	ENSMUSG00000042599	Kdm7a	A630082K20Rik|BB041802|ENSMUSG00000073143|Jhdm1d|mKIAA1718	lysine (K)-specific demethylase 7A	protein-coding
mm_97866.1	chr11	83118330	83118358	+	1	NA	intron (NM_011407, intron 1 of 1)	intron (NM_011407, intron 1 of 1)	1499	NM_011407	20555	Mm.10948	NM_011407	ENSMUSG00000078763	Slfn1	AV316259	schlafen 1	protein-coding
mm_32761.1	chr4	116689894	116689908	+	1	NA	intron (NM_011034, intron 2 of 5)	intron (NM_011034, intron 2 of 5)	-3879	NR_040442	100502959	Mm.395400	NR_040442		AV051173	-	expressed sequence AV051173	ncRNA
mm_349.1	chr1	31222783	31222792	+	1	NA	promoter-TSS (NM_029062)	promoter-TSS (NM_029062)	-52	NM_029062	74708	Mm.246796	NM_029062	ENSMUSG00000026063	Pih1d3	4930521A18Rik	PIH1 domain containing 3	protein-coding
mm_20895.1	chr2	148875453	148875488	-	1	NA	promoter-TSS (NM_009976)	promoter-TSS (NM_009976)	42	NM_009976	13010	Mm.4263	NM_009976	ENSMUSG00000027447	Cst3	CysC	cystatin C	protein-coding
mm_173068.1	chrX	134541641	134541642	-	1	NA	promoter-TSS (NM_013898).2	promoter-TSS (NM_013898).2	29	NM_013898	30058	Mm.214504	NM_013898	ENSMUSG00000048007	Timm8a1	DXHXS1274E|Ddp1|Fci-12|Tim8a|Timm8a	translocase of inner mitochondrial membrane 8A1	protein-coding
mm_160587.1	chr9	65141322	65141322	+	1	NA	5' UTR (NM_008988, exon 1 of 14)	5' UTR (NM_008988, exon 1 of 14)	133	NM_008988	19289	Mm.41529	NM_008988	ENSMUSG00000032394	Igdcc3	2810401C09Rik|AI851425|Punc|WI-14920	immunoglobulin superfamily, DCC subclass, member 3	protein-coding
mm_7990.1	chr1	134235142	134235152	-	1	NA	promoter-TSS (NM_001291928)	promoter-TSS (NM_001291928)	-291	NM_001291928	11539	Mm.298908	NM_009629	ENSMUSG00000042429	Adora1	A1-AR|A1AR|A1R|AA1R|AI848715|BB176431|Ri	adenosine A1 receptor	protein-coding
mm_97967.1	chr11	83771976	83771979	+	1	NA	intron (NM_145432, intron 11 of 19)	intron (NM_145432, intron 11 of 19)	18340	NM_145432	217026	Mm.117874	NM_145432	ENSMUSG00000000976	Heatr6	2700008B19Rik|BB135312|BB249351	HEAT repeat containing 6	protein-coding
mm_100634.1	chr11	121717315	121717330	+	1	NA	TTS (NM_144797)	TTS (NM_144797)	14895	NM_144797	210029	Mm.153566	NM_144797	ENSMUSG00000039208	Metrnl	9430048M07Rik|BC019776	meteorin, glial cell differentiation regulator-like	protein-coding
mm_42983.1	chr5	123252088	123252136	+	1	NA	Intergenic	Intergenic	23922	NM_026000	67151	Mm.278997	NM_026000	ENSMUSG00000029440	Psmd9	1500011J20Rik|2610202L11Rik|Bridge-1|P27	proteasome (prosome, macropain) 26S subunit, non-ATPase, 9	protein-coding
mm_104035.1	chr11	86268132	86268149	-	1	NA	3' UTR (NM_001080931, exon 30 of 30)	3' UTR (NM_001080931, exon 30 of 30)	-10572	NM_027421	70422	Mm.171304	NM_027421	ENSMUSG00000018068	Ints2	2810417D08Rik|AA408260|AI987735|mKIAA1287	integrator complex subunit 2	protein-coding
mm_83142.1	chr9	40455444	40455456	-	1	NA	exon (NM_172768, exon 1 of 20)	exon (NM_172768, exon 1 of 20)	314	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_114171.1	chr13	55477579	55477589	+	1	NA	TTS (NR_105909)	TTS (NR_105909)	192	NR_105909	102465569		NR_105909	ENSMUSG00000098341	Mir6944	Gm27710|mmu-mir-6944	microRNA 6944	ncRNA
mm_58458.1	chr7	3332919	3332950	+	1	NA	Intergenic	G-rich|Low_complexity|Low_complexity	-3651	NM_133189	81904	Mm.214994	NM_133189	ENSMUSG00000069806	Cacng7	-	calcium channel, voltage-dependent, gamma subunit 7	protein-coding
mm_79379.1	chr9	54764795	54764813	+	1	NA	promoter-TSS (NM_001284507)	promoter-TSS (NM_001284507)	56	NM_013496	12903	Mm.34797	NM_013496	ENSMUSG00000032291	Crabp1	AI326249|CRABP-I|Crabp-1|CrabpI|Rbp-5	cellular retinoic acid binding protein I	protein-coding
mm_158056.1	chrX	101059615	101059642	-	1	NA	promoter-TSS (NM_001167997)	promoter-TSS (NM_001167997)	11	NM_031384	83558	Mm.134024	NM_031384	ENSMUSG00000009670	Tex11	4930565P14Rik|BB024231|ZIP4H	testis expressed gene 11	protein-coding
mm_83816.1	chr9	53632694	53632704	-	1	NA	intron (NM_027807, intron 10 of 18)	intron (NM_027807, intron 10 of 18)	-22349	NM_144784	110446	Mm.293233	NM_144784	ENSMUSG00000032047	Acat1	6330585C21Rik|Acat	acetyl-Coenzyme A acetyltransferase 1	protein-coding
mm_86201.1	chr9	119980472	119980475	-	1	NA	intron (NM_153287, intron 1 of 4)	intron (NM_153287, intron 1 of 4)	4185	NM_153287	215418	Mm.491094	NM_153287	ENSMUSG00000032515	Csrnp1	4931429D10Rik|Axud1|CSRNP-1|URAX1|taip-3	cysteine-serine-rich nuclear protein 1	protein-coding
mm_16860.1	chr2	11655113	11655124	-	1	NA	intron (NM_008367, intron 1 of 7)	B1F|SINE|Alu	12326	NM_008367	16184	Mm.915	NM_008367	ENSMUSG00000026770	Il2ra	CD25|Il2r|Ly-43	interleukin 2 receptor, alpha chain	protein-coding
mm_22175.1	chr2	173213801	173213815	-	1	NA	TTS (NM_001139519)	TTS (NM_001139519)	5114	NM_021394	58203	Mm.116687	NM_021394	ENSMUSG00000027514	Zbp1	2010010H03Rik|Dai|Dlm1|mZaDLM	Z-DNA binding protein 1	protein-coding
mm_130340.1	chr15	97731382	97731393	-	1	NA	promoter-TSS (NM_001168693)	promoter-TSS (NM_001168693)	18	NM_001168693	19011	Mm.1001	NM_008902	ENSMUSG00000022468	Endou	Pp11r|Tcl-30	endonuclease, polyU-specific	protein-coding
mm_154255.1	chr19	60766914	60766934	-	1	NA	exon (NM_010123, exon 19 of 22)	exon (NM_010123, exon 19 of 22)	7461	NR_034047	100217439		NR_034047		Snora19	MBI-51	small nucleolar RNA, H/ACA box 19	snoRNA
mm_116092.1	chr13	28757854	28757869	-	1	NA	intron (NR_045053, intron 3 of 8)	intron (NR_045053, intron 3 of 8)	-46988	NR_105787	102466635		NR_105787	ENSMUSG00000099158	Mir6368	Gm27800|mmu-mir-6368	microRNA 6368	ncRNA
mm_1392.1	chr1	67128923	67128933	+	1	NA	intron (NM_001080809, intron 1 of 37)	intron (NM_001080809, intron 1 of 37)	5901	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_23687.1	chr3	68691373	68691411	+	1	NA	promoter-TSS (NM_008351)	promoter-TSS (NM_008351)	-32	NM_008351	16159	Mm.103783	NM_008351	ENSMUSG00000027776	Il12a	IL-12p35|Il-12a|Ll12a|p35	interleukin 12a	protein-coding
mm_125769.1	chr15	74563671	74563696	+	1	NA	intron (NM_174991, intron 17 of 30)	GC_rich|Low_complexity|Low_complexity	47487	NM_174991	107831	Mm.43133	NM_174991	ENSMUSG00000034730	Adgrb1	B830018M07Rik|Bai1|R75078|mKIAA4089	adhesion G protein-coupled receptor B1	protein-coding
mm_77454.1	chr8	121882959	121882984	-	1	NA	3' UTR (NM_011404, exon 10 of 10)	3' UTR (NM_011404, exon 10 of 10)	24715	NM_011404	20539	Mm.22374	NM_011404	ENSMUSG00000040010	Slc7a5	4F2LC|D0H16S474E|LAT1|TA1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 5	protein-coding
mm_15268.1	chr2	155133487	155133497	+	1	NA	promoter-TSS (NM_001243712)	promoter-TSS (NM_001243712)	11	NM_008395	16396	Mm.208286	NM_008395	ENSMUSG00000027598	Itch	6720481N21Rik|8030492O04Rik|A130065M08|AIP4|C230047C07Rik	itchy, E3 ubiquitin protein ligase	protein-coding
mm_118967.1	chr14	27623641	27623698	+	1	NA	intron (NM_177814, intron 1 of 15)	intron (NM_177814, intron 1 of 15)	1262	NM_177814	238988	Mm.318004	NM_177814	ENSMUSG00000040640	Erc2	6430531D06|CAST|CAST1/ERC2|D14Ertd171e|ELKS2alpha	ELKS/RAB6-interacting/CAST family member 2	protein-coding
mm_29184.1	chr3	106542200	106542212	-	1	NA	intron (NM_133869, intron 1 of 8)	PB1D11|SINE|Alu	-5592	NM_001286986	67171	Mm.290488	NM_026013	ENSMUSG00000027900	Dram2	2010305N14Rik|2610318G18Rik|AI647667|Tmem77	DNA-damage regulated autophagy modulator 2	protein-coding
mm_166299.1	chr5	104114022	104114037	-	1	NA	promoter-TSS (NM_010097)	promoter-TSS (NM_010097)	59	NM_010097	13602	Mm.29027	NM_010097	ENSMUSG00000029309	Sparcl1	Ecm2|Sc1|hevin|mast9	SPARC-like 1	protein-coding
mm_124393.1	chr14	111674687	111674701	-	1	NA	promoter-TSS (NM_198865)	promoter-TSS (NM_198865)	-421	NM_198865	75409	Mm.235097	NM_029273	ENSMUSG00000033214	Slitrk5	2610019D03Rik	SLIT and NTRK-like family, member 5	protein-coding
mm_60770.1	chr7	45554993	45555007	+	1	NA	promoter-TSS (NM_025330)	promoter-TSS (NM_025330)	72	NM_025330	66065	Mm.285710	NM_025330	ENSMUSG00000030825	Hsd17b14	0610039E24Rik|Dhrs10|retSDR3	hydroxysteroid (17-beta) dehydrogenase 14	protein-coding
mm_102135.1	chr11	53479961	53479990	-	1	NA	5' UTR (NM_183173, exon 1 of 1)	5' UTR (NM_183173, exon 1 of 1)	220	NM_183173	237761	Mm.145208	NM_183173	ENSMUSG00000044352	Sowaha	A830006N08Rik|Ankrd43	sosondowah ankyrin repeat domain family member A	protein-coding
mm_144060.1	chr17	90747207	90747217	-	1	NA	intron (NM_001346957, intron 3 of 18)	MIR|SINE|MIR	46264	NR_136930	102634634		NR_136930		Gm20491	-	enolase 1, alpha non-neuron pseudogene	pseudo
mm_144305.1	chr18	12504144	12504156	+	1	NA	promoter-TSS (NM_001347461)	promoter-TSS (NM_001347461)	-49	NM_001347461	16774	Mm.42012	NM_010680	ENSMUSG00000024421	Lama3	Lama3B|[a]3B	laminin, alpha 3	protein-coding
mm_97086.1	chr11	73138288	73138290	+	1	NA	promoter-TSS (NM_010353)	promoter-TSS (NM_010353)	5	NM_010353	14841	Mm.42045	NM_010353	ENSMUSG00000050107	Gsg2	Haspin	germ cell associated 2, haspin	protein-coding
mm_113631.1	chr13	42049596	42049606	+	1	NA	Intergenic	CpG	-2420	NM_007772	110521	Mm.4808	NM_007772	ENSMUSG00000021366	Hivep1	Cryabp1	human immunodeficiency virus type I enhancer binding protein 1	protein-coding
mm_38223.1	chr4	135987014	135987018	-	1	NA	exon (NM_025411, exon 1 of 6)	exon (NM_025411, exon 1 of 6)	228	NM_025411	66193	Mm.29131	NM_025411	ENSMUSG00000028669	Pithd1	1110049F12Rik|AA408179|Trp26	PITH (C-terminal proteasome-interacting domain of thioredoxin-like) domain containing 1	protein-coding
mm_141288.1	chr17	28066835	28066863	-	1	NA	3' UTR (NM_013687, exon 10 of 10)	3' UTR (NM_013687, exon 10 of 10)	13735	NM_013687	21463	Mm.29758	NM_013687	ENSMUSG00000062859	Tcp11	D17Ken1|Tcp-11	t-complex protein 11	protein-coding
mm_154993.1	chrX	38396887	38396888	+	1	NA	Intergenic	Intergenic	59573	NM_010685	16784	Mm.486	NM_010685	ENSMUSG00000016534	Lamp2	CD107b|LGP-B|Lamp II|Lamp-2|Lamp-2a|Lamp-2b|Lamp-2c|Mac3	lysosomal-associated membrane protein 2	protein-coding
mm_20079.1	chr2	120609320	120609380	-	1	NA	promoter-TSS (NM_025475)	promoter-TSS (NM_025475)	8	NM_001159612	66606	Mm.428639	NM_025657	ENSMUSG00000027286	Lrrc57	2810002D13Rik|AA407405	leucine rich repeat containing 57	protein-coding
mm_91684.1	chr10	43901713	43901752	-	1	NA	promoter-TSS (NM_130892)	promoter-TSS (NM_130892)	4	NM_001081054	76563	Mm.5904	NM_001081054	ENSMUSG00000019863	Qrsl1	2700038P16Rik|C80053|GatA	glutaminyl-tRNA synthase (glutamine-hydrolyzing)-like 1	protein-coding
mm_90402.1	chr10	127326070	127326099	+	1	NA	exon (NM_001285785, exon 6 of 16)	exon (NM_001285785, exon 6 of 16)	2357	NM_146011	216445	Mm.227198	NM_146011	ENSMUSG00000040345	Arhgap9	AU043488	Rho GTPase activating protein 9	protein-coding
mm_150173.1	chr19	32543461	32543472	+	1	NA	Intergenic	RMER20B|LTR|ERVK	-52249	NM_001201470	23972	Mm.203916	NM_011864	ENSMUSG00000024899	Papss2	1810018P12Rik|AI159688|AtpsU2|Atpsk2|Sk2|bm	3'-phosphoadenosine 5'-phosphosulfate synthase 2	protein-coding
mm_10873.1	chr2	25225364	25225375	+	1	NA	promoter-TSS (NM_146116)	promoter-TSS (NM_146116)	-667	NM_146116	227613	Mm.227260	NM_146116	ENSMUSG00000036752	Tubb4b	4930542G03Rik|Tubb2c|Tubb2c1	tubulin, beta 4B class IVB	protein-coding
mm_95908.1	chr11	58206097	58206115	+	1	NA	exon (NM_018738, exon 3 of 3)	exon (NM_018738, exon 3 of 3)	6550	NM_018738	16145	Mm.33902	NM_018738	ENSMUSG00000078853	Igtp	AW558444|Irgm3	interferon gamma induced GTPase	protein-coding
mm_70112.1	chr7	142669931	142669937	-	1	NA	non-coding (NR_002855, exon 4 of 4)	non-coding (NR_002855, exon 4 of 4)	-3118	NM_001315488	16002	Mm.3862	NM_010514	ENSMUSG00000048583	Igf2	AL033362|Igf-2|Igf-II|M6pr|Mpr|Peg2	insulin-like growth factor 2	protein-coding
mm_43685.1	chr5	138809846	138809890	+	1	NA	3' UTR (NM_030565, exon 10 of 10)	3' UTR (NM_030565, exon 10 of 10)	-10212	NM_001195128	384244	Mm.485002	NM_001195128	ENSMUSG00000094504	Gm5294	EG384244	predicted gene 5294	protein-coding
mm_105582.1	chr11	106688973	106688976	-	1	NA	exon (NM_008816, exon 7 of 15)	exon (NM_008816, exon 7 of 15)	26307	NM_001305158	18613	Mm.343951	NM_008816	ENSMUSG00000020717	Pecam1	C85791|Cd31|PECAM-1|Pecam	platelet/endothelial cell adhesion molecule 1	protein-coding
mm_5885.1	chr1	53978608	53978617	-	1	NA	intron (NM_001001883, intron 2 of 28)	intron (NM_001001883, intron 2 of 28)	129188	NR_106149	102465783		NR_106149	ENSMUSG00000098443	Mir7681	Gm27806|mmu-mir-7681	microRNA 7681	ncRNA
mm_147276.1	chr18	39185154	39185158	-	1	NA	intron (NM_175164, intron 11 of 22)	intron (NM_175164, intron 11 of 22)	192011	NM_175164	71302	Mm.329396	NM_175164	ENSMUSG00000036452	Arhgap26	1810044B20Rik|2610010G17Rik|4933432P15Rik|AI853435|mKIAA0621	Rho GTPase activating protein 26	protein-coding
mm_59713.1	chr7	28766277	28766323	+	1	NA	promoter-TSS (NM_001122766)	promoter-TSS (NM_001122766)	344	NM_001306222	18036	Mm.220333	NM_010908	ENSMUSG00000030595	Nfkbib	I(Kappa)B(beta)|I-kappa-B-beta|IKB-beta|IKappaBbeta|IkB|IkBb|NF-kappa-BIB|ikB-B	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, beta	protein-coding
mm_91208.1	chr10	21161563	21161587	-	1	NA	promoter-TSS (NM_001198914)	promoter-TSS (NM_001198914)	-591	NM_010848	17863	Mm.52109	NM_010848	ENSMUSG00000019982	Myb	AI550390|M16449|c-myb	myeloblastosis oncogene	protein-coding
mm_96801.1	chr11	69981382	69981390	+	1	NA	promoter-TSS (NM_018740)	promoter-TSS (NM_018740)	-151	NM_018740	54351	Mm.13430	NM_018740	ENSMUSG00000018565	Elp5	Derp6|Rai12	elongator acetyltransferase complex subunit 5	protein-coding
mm_77886.1	chr9	7282380	7282399	+	1	NA	3' UTR (NM_008607, exon 10 of 10)	3' UTR (NM_008607, exon 10 of 10)	9875	NM_008607	17386	Mm.5022	NM_008607	ENSMUSG00000050578	Mmp13	Clg|MMP-13|Mmp1	matrix metallopeptidase 13	protein-coding
mm_80446.1	chr9	77976763	77976773	+	1	NA	exon (NM_134255, exon 5 of 8)	exon (NM_134255, exon 5 of 8)	59403	NM_134255	68801	Mm.430736	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	ELOVL family member 5, elongation of long chain fatty acids (yeast)	protein-coding
mm_27305.1	chr3	49757242	49757250	-	1	NA	promoter-TSS (NM_130448)	promoter-TSS (NM_130448)	70	NM_130448	73173	Mm.87246	NM_130448	ENSMUSG00000037892	Pcdh18	3110038E07Rik|BB095589|PCDH68L	protocadherin 18	protein-coding
mm_21986.1	chr2	167589404	167589457	-	1	NA	Intergenic	L2a|LINE|L2	42575	NM_001311146	66589	Mm.278783	NM_023230	ENSMUSG00000078923	Ube2v1	0610011J09Rik|AI256840|CROC-1|CROC1|D7Bwg1382e|UEV-1	ubiquitin-conjugating enzyme E2 variant 1	protein-coding
mm_140809.1	chr17	22314815	22314846	-	1	NA	Intergenic	Intergenic	46570	NM_176962	319615	Mm.442162	NM_176962	ENSMUSG00000033972	Zfp944	6330416L07Rik	zinc finger protein 944	protein-coding
mm_143120.1	chr17	57210192	57210197	-	1	NA	exon (NM_009778, exon 30 of 41)	exon (NM_009778, exon 30 of 41)	7034	NR_105944	102465591		NR_105944	ENSMUSG00000099066	Mir6978	Gm27858|mmu-mir-6978	microRNA 6978	ncRNA
mm_150171.1	chr19	32543325	32543335	+	1	NA	Intergenic	B1F|SINE|Alu	-52385	NM_001201470	23972	Mm.203916	NM_011864	ENSMUSG00000024899	Papss2	1810018P12Rik|AI159688|AtpsU2|Atpsk2|Sk2|bm	3'-phosphoadenosine 5'-phosphosulfate synthase 2	protein-coding
mm_28815.1	chr3	96259810	96259815	-	1	NA	Intergenic	Intergenic	3505	NM_033596	97122	Mm.227295	NM_033596	ENSMUSG00000091405	Hist2h4	H4|X04652	histone cluster 2, H4	protein-coding
mm_1389.1	chr1	67122856	67122862	+	1	NA	promoter-TSS (NM_001080809)	promoter-TSS (NM_001080809)	-168	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_87600.1	chr10	57650955	57650960	+	1	NA	promoter-TSS (NM_001190402)	promoter-TSS (NM_001190402)	-24	NM_001039050	18768	Mm.262135	NM_008863	ENSMUSG00000019876	Pkib	Pkibeta|Prkacn2	protein kinase inhibitor beta, cAMP dependent, testis specific	protein-coding
mm_3924.1	chr1	162571629	162571641	+	1	NA	intron (NM_001347125, intron 1 of 7)	intron (NM_001347125, intron 1 of 7)	807	NM_001347125	53330	Mm.10699	NM_016796	ENSMUSG00000026696	Vamp4	D1Ertd147e	vesicle-associated membrane protein 4	protein-coding
mm_169866.1	chr16	34007477	34007498	-	1	NA	intron (NM_177357, intron 51 of 59)	intron (NM_177357, intron 51 of 59)	-40484	NM_009471	22247	Mm.13145	NM_009471	ENSMUSG00000022814	Umps	1700095D23Rik|AA408257|AL033308|BB164745	uridine monophosphate synthetase	protein-coding
mm_113742.1	chr13	44729601	44729614	+	1	NA	Intergenic	Intergenic	-1167	NM_021878	16468	Mm.25059	NM_021878	ENSMUSG00000038518	Jarid2	Jmj|jumonji	jumonji, AT rich interactive domain 2	protein-coding
mm_98033.1	chr11	85311402	85311412	+	1	NA	5' UTR (NM_016910, exon 1 of 6)	5' UTR (NM_016910, exon 1 of 6)	153	NM_016910	53892	Mm.45609	NM_016910	ENSMUSG00000020525	Ppm1d	AV338790|Wip1	protein phosphatase 1D magnesium-dependent, delta isoform	protein-coding
mm_98686.1	chr11	96298755	96298770	+	1	NA	promoter-TSS (NM_008269)	promoter-TSS (NM_008269)	-409	NM_008269	15414	Mm.215	NM_008269	ENSMUSG00000000690	Hoxb6	Hox-2.2	homeobox B6	protein-coding
mm_73308.1	chr8	105170762	105170813	+	1	NA	5' UTR (NM_001161458, exon 1 of 6)	5' UTR (NM_001161458, exon 1 of 6)	113	NM_001161458	12400	Mm.2018	NM_022309	ENSMUSG00000031885	Cbfb	AI893578|PEA2|PEBP2b|Pebp2|Pebpb2	core binding factor beta	protein-coding
mm_127309.1	chr15	100228230	100228280	+	1	NA	intron (NM_007497, intron 1 of 6)	CpG	396	NM_007497	11908	Mm.676	NM_007497	ENSMUSG00000023027	Atf1	-	activating transcription factor 1	protein-coding
mm_163002.1	chr11	33915378	33915378	-	1	NA	intron (NM_001190886, intron 1 of 7)	intron (NM_001190886, intron 1 of 7)	-47635	NM_031169	16533	Mm.6206	NM_031169	ENSMUSG00000020155	Kcnmb1	BKbeta1	potassium large conductance calcium-activated channel, subfamily M, beta member 1	protein-coding
mm_23740.1	chr3	69222413	69222427	+	1	NA	promoter-TSS (NM_027843)	promoter-TSS (NM_027843)	1	NM_027843	71619	Mm.98122	NM_027843	ENSMUSG00000098207	Arl14	9130014L17Rik|Arf7	ADP-ribosylation factor-like 14	protein-coding
mm_29645.1	chr3	121847190	121847198	-	1	NA	Intergenic	Lx5b|LINE|L1	-31979	NM_008991	19299	Mm.399042	NM_008991	ENSMUSG00000028127	Abcd3	AI313901|AU018866|AW146054|PMP68|PMP70|Pxmp1	ATP-binding cassette, sub-family D (ALD), member 3	protein-coding
mm_99861.1	chr11	109365504	109365514	+	1	NA	intron (NM_010303, intron 1 of 3)	intron (NM_010303, intron 1 of 3)	-1855	NR_038097	100036768	Mm.467767	NR_038097	ENSMUSG00000056687	Gm11696	OTTMUSG00000003456	predicted gene 11696	ncRNA
mm_24313.1	chr3	89419179	89419193	+	1	NA	promoter-TSS (NM_016904)	promoter-TSS (NM_016904)	635	NM_011368	20416	Mm.86595	NM_011368	ENSMUSG00000042626	Shc1	Shc|ShcA|p66|p66shc	src homology 2 domain-containing transforming protein C1	protein-coding
mm_18466.1	chr2	62394934	62394940	-	1	NA	intron (NM_001159543, intron 2 of 24)	MLT-int|LTR|ERVL-MaLR	17294	NM_010074	13482	Mm.1151	NM_010074	ENSMUSG00000035000	Dpp4	Cd26|Dpp-4|THAM	dipeptidylpeptidase 4	protein-coding
mm_22715.1	chr3	19188289	19188293	+	1	NA	promoter-TSS (NM_026182)	promoter-TSS (NM_026182)	70	NR_045575	67472	Mm.45125	NM_026182	ENSMUSG00000027601	Mtfr1	1300002C08Rik|1700080D04Rik|2810026O10Rik|4930579E05Rik|Chppr|Fam54a2	mitochondrial fission regulator 1	protein-coding
mm_154151.1	chr19	58454581	58454641	-	1	NA	intron (NR_104342, intron 1 of 11)	CpG	787	NM_001285457	14585	Mm.88367	NM_010279	ENSMUSG00000025089	Gfra1	AU042498	glial cell line derived neurotrophic factor family receptor alpha 1	protein-coding
mm_81479.1	chr9	109945916	109945934	+	1	NA	intron (NM_001205330, intron 1 of 18)	ID_B1|SINE|B4	14151	NM_008633	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_77735.1	chr8	126908186	126908196	-	1	NA	Intergenic	Intergenic	37730	NM_024214	67952	Mm.6932	NM_024214	ENSMUSG00000093904	Tomm20	1810060K07Rik|BB284719|Gm19268|MAS20|MOM19|TOM20|mKIAA0016	translocase of outer mitochondrial membrane 20 homolog (yeast)	protein-coding
mm_98525.1	chr11	94990925	94990970	+	1	NA	promoter-TSS (NM_172261)	promoter-TSS (NM_172261)	-265	NM_172261	217124	Mm.229087	NM_172261	ENSMUSG00000038976	Ppp1r9b	SPL|Spn	protein phosphatase 1, regulatory subunit 9B	protein-coding
mm_83296.1	chr9	43239796	43239810	-	1	NA	promoter-TSS (NM_178644)	promoter-TSS (NM_178644)	13	NM_178644	102644	Mm.246479	NM_178644	ENSMUSG00000032014	Oaf	AL024221|D130038B21Rik|D9Ucla1	out at first homolog	protein-coding
mm_147193.1	chr18	37644138	37644178	-	1	NA	promoter-TSS (NM_175770)	promoter-TSS (NM_175770)	46	NM_175770	24074	Mm.236009	NM_175770	ENSMUSG00000051316	Taf7	55kDa|AI607308|BB007175|TAFII55|Taf2f	TATA-box binding protein associated factor 7	protein-coding
mm_149914.1	chr19	26605192	26605196	+	1	NA	promoter-TSS (NM_011416)	promoter-TSS (NM_011416)	34	NM_011416	67155	Mm.342988	NM_011416	ENSMUSG00000024921	Smarca2	2610209L14Rik|SNF2alpha|Snf2l2|brahma|brm	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	protein-coding
mm_27145.1	chr3	32764050	32764083	-	1	NA	Intergenic	Intergenic	27003	NM_025316	66046	Mm.28058	NM_025316	ENSMUSG00000027673	Ndufb5	0610007D05Rik|AU015782|CI-SGDH|SGDH	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 5	protein-coding
mm_29001.1	chr3	101583813	101583833	-	1	NA	exon (NM_144900, exon 14 of 23)	exon (NM_144900, exon 14 of 23)	20884	NM_144900	11928	Mm.193670	NM_144900	ENSMUSG00000033161	Atp1a1	Atpa-1|BC010319	ATPase, Na+/K+ transporting, alpha 1 polypeptide	protein-coding
mm_79845.1	chr9	64811505	64811507	+	1	NA	5' UTR (NM_001162917, exon 2 of 35)	5' UTR (NM_001162917, exon 2 of 35)	495	NM_001162917	102442	Mm.222473	NM_176935	ENSMUSG00000053641	Dennd4a	AI115600|AI851943|F730015K02Rik	DENN/MADD domain containing 4A	protein-coding
mm_138168.1	chr17	34264528	34264564	+	1	NA	intron (NM_207105, intron 1 of 5)	CpG	1319	NM_207105	14961	Mm.254067	NM_207105	ENSMUSG00000073421	H2-Ab1	AI845868|Abeta|H-2Ab|H2-Ab|I-Abeta|IAb|Ia-2|Ia2|Rmcs1	histocompatibility 2, class II antigen A, beta 1	protein-coding
mm_133293.1	chr16	77497652	77497680	+	1	NA	intron (NR_015543, intron 3 of 4)	intron (NR_015543, intron 3 of 4)	-101270	NR_029535	387229		NR_029535	ENSMUSG00000065530	Mir99a	Mirn99a|mir-99a|mmu-mir-99a	microRNA 99a	ncRNA
mm_41249.1	chr5	88782538	88782573	+	1	NA	3' UTR (NM_007832, exon 7 of 7)	3' UTR (NM_007832, exon 7 of 7)	17542	NM_007832	13178	Mm.298892	NM_007832	ENSMUSG00000029366	Dck	-	deoxycytidine kinase	protein-coding
mm_81158.1	chr9	107296211	107296221	+	1	NA	promoter-TSS (NM_009895)	promoter-TSS (NM_009895)	-443	NM_001317354	12700	Mm.4592	NM_009895	ENSMUSG00000032578	Cish	CIS-1|CIS1|Cis|F17|F23|SOCS	cytokine inducible SH2-containing protein	protein-coding
mm_109855.1	chr12	4769040	4769051	-	1	NA	promoter-TSS (NM_028376)	promoter-TSS (NM_028376)	222	NM_175431	207921	Mm.184898	NM_175431	ENSMUSG00000050545	Fam228b	A830093I24Rik	family with sequence similarity 228, member B	protein-coding
mm_166177.1	chr5	30461953	30461969	-	1	NA	promoter-TSS (NM_001100395)	promoter-TSS (NM_001100395)	-29	NM_001100395	83762	Mm.244502	NM_031875	ENSMUSG00000062372	Otof	-	otoferlin	protein-coding
mm_24831.1	chr3	95658715	95658723	+	1	NA	promoter-TSS (NM_008562)	promoter-TSS (NM_008562)	-2	NM_008562	17210	Mm.1639	NM_008562	ENSMUSG00000038612	Mcl1	AW556805|Mcl-1	myeloid cell leukemia sequence 1	protein-coding
mm_43912.1	chr5	144277219	144277258	+	1	NA	non-coding (NR_040432, exon 1 of 3)	non-coding (NR_040432, exon 1 of 3)	177	NR_040432	100504231	Mm.441035	NR_040432	ENSMUSG00000086894	Gm15708	OTTMUSG00000025583	predicted gene 15708	ncRNA
mm_128035.1	chr15	25363998	25364011	-	1	NA	3' UTR (NM_027395, exon 2 of 2)	3' UTR (NM_027395, exon 2 of 2)	49760	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	brain abundant, membrane attached signal protein 1	protein-coding
mm_33600.1	chr4	132568606	132568656	+	1	NA	intron (NM_001081211, intron 1 of 1)	B4|SINE|B4	4564	NM_001081211	19204	Mm.89389	NM_001081211	ENSMUSG00000056529	Ptafr	PAFR	platelet-activating factor receptor	protein-coding
mm_82030.1	chr9	121937778	121937805	+	1	NA	intron (NR_033553, intron 1 of 4)	RMER21A|LTR|ERV1	516	NR_033553	69430	Mm.482910	NR_033553	ENSMUSG00000043773	1700048O20Rik	1700022O21Rik	RIKEN cDNA 1700048O20 gene	ncRNA
mm_75890.1	chr8	70873478	70873501	-	1	NA	promoter-TSS (NM_026964)	promoter-TSS (NM_026964)	1	NM_026964	234388	Mm.295791	NM_026964	ENSMUSG00000007721	Ccdc124	1810023B24Rik	coiled-coil domain containing 124	protein-coding
mm_78516.1	chr9	32926512	32926525	+	1	NA	intron (NR_131058, intron 1 of 3)	intron (NR_131058, intron 1 of 3)	2448	NR_131058	330917	Mm.488283	NR_131058		Gm27162	A430016B06	predicted gene 27162	ncRNA
mm_41066.1	chr5	87010193	87010203	+	1	NA	intron (NM_172881, intron 5 of 5)	B3A|SINE|B2	9338	NM_172881	243085	Mm.312095	NM_172881	ENSMUSG00000035811	Ugt2b35	C730031G17	UDP glucuronosyltransferase 2 family, polypeptide B35	protein-coding
mm_1310.1	chr1	65028058	65028061	+	1	NA	intron (NM_001310617, intron 1 of 8)	intron (NM_001310617, intron 1 of 8)	4700	NM_027582	70861	Mm.18725	NM_027582	ENSMUSG00000025955	Akr1cl	4921521F21Rik|AI451536|AI503553	aldo-keto reductase family 1, member C-like	protein-coding
mm_159752.1	chr5	86822827	86822827	+	1	NA	exon (NM_177680, exon 9 of 17)	exon (NM_177680, exon 9 of 17)	18337	NM_177680	231386	Mm.196325	NM_177680	ENSMUSG00000035851	Ythdc1	A730098D12Rik|C80342|mKIAA1966	YTH domain containing 1	protein-coding
mm_103413.1	chr11	75461128	75461182	-	1	NA	promoter-TSS (NR_030711)	promoter-TSS (NR_030711)	-384	NR_030711	100042498	Mm.482242	NR_030711	ENSMUSG00000085148	Mir22hg	2210403K04Rik|mir-22	Mir22 host gene (non-protein coding)	ncRNA
mm_13632.1	chr2	113708671	113708673	+	1	NA	promoter-TSS (NR_040614)	promoter-TSS (NR_040614)	-122	NR_040614	75166	Mm.410811	NR_040614	ENSMUSG00000084798	4930533B01Rik	-	RIKEN cDNA 4930533B01 gene	ncRNA
mm_130185.1	chr15	93520202	93520217	-	1	NA	intron (NM_001033217, intron 1 of 7)	intron (NM_001033217, intron 1 of 7)	75682	NM_001033217	106042	Mm.150314	NM_001033217	ENSMUSG00000036158	Prickle1	1110058P22Rik|AW215793|Prickle|b2b019Clo|mpk1	prickle planar cell polarity protein 1	protein-coding
mm_121411.1	chr14	119458329	119458342	+	1	NA	intron (NM_015820, intron 1 of 1)	intron (NM_015820, intron 1 of 1)	-290892	NR_045621	75432	Mm.443277	NR_045621	ENSMUSG00000100274	1700006F04Rik	-	RIKEN cDNA 1700006F04 gene	ncRNA
mm_123208.1	chr14	59370541	59370555	-	1	NA	Intergenic	LTRIS2|LTR|ERV1	-5058	NM_199015	219132	Mm.479285	NM_199015	ENSMUSG00000068245	Phf11d	D14Ertd668e|Phf11|Phf11l	PHD finger protein 11D	protein-coding
mm_76288.1	chr8	84200618	84200655	-	1	NA	Intergenic	Intergenic	-7882	NR_029740	387216		NR_029740	ENSMUSG00000065611	Mir23a	Mirn23a|mir-23a|mmu-mir-23a	microRNA 23a	ncRNA
mm_162410.1	chr1	87127589	87127594	+	1	NA	exon (NM_007432, exon 11 of 11)	exon (NM_007432, exon 11 of 11)	2583	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_60666.1	chr7	45017864	45017872	+	1	NA	promoter-TSS (NM_009101)	promoter-TSS (NM_009101)	-139	NM_009101	20130	Mm.389894	NM_009101	ENSMUSG00000038387	Rras	AI573426	related RAS viral (r-ras) oncogene	protein-coding
mm_29417.1	chr3	108972808	108972828	-	1	NA	3' UTR (NM_001163567, exon 11 of 11)	3' UTR (NM_001163567, exon 11 of 11)	32261	NM_001078646	66715	Mm.158124	NM_025723	ENSMUSG00000045662	Henmt1	4921515J06Rik|Hen1|mHEN1	HEN1 methyltransferase homolog 1 (Arabidopsis)	protein-coding
mm_61412.1	chr7	73556824	73556838	+	1	NA	intron (NR_037569, intron 1 of 4)	intron (NR_037569, intron 1 of 4)	1564	NR_037569	69170	Mm.34539	NR_037569	ENSMUSG00000101970	1810026B05Rik	-	RIKEN cDNA 1810026B05 gene	ncRNA
mm_142314.1	chr17	42876552	42876560	-	1	NA	promoter-TSS (NM_009847)	promoter-TSS (NM_009847)	-132	NM_009847	12488	Mm.218637	NM_009847	ENSMUSG00000061665	Cd2ap	AL024079|C78928|METS-1|Mets1	CD2-associated protein	protein-coding
mm_109584.1	chr12	112604061	112604072	+	1	NA	exon (NM_198411, exon 8 of 23)	exon (NM_198411, exon 8 of 23)	15282	NM_198411	70435	Mm.250193	NM_198411	ENSMUSG00000037679	Inf2	2610204M08Rik|AA589465|AW125550|EG629699	inverted formin, FH2 and WH2 domain containing	protein-coding
mm_109342.1	chr12	109597487	109597496	+	1	NA	Intergenic	Intergenic	-2088	NM_184109	353326	Mm.23062	NM_184109	ENSMUSG00000085925	Rtl1	6430411K18Rik|Mar|Mart1|Mor1|Peg11	retrotransposon-like 1	protein-coding
mm_101987.1	chr11	50827657	50827663	-	1	NA	promoter-TSS (NM_013922)	promoter-TSS (NM_013922)	71	NM_013922	30944	Mm.103674	NM_013922	ENSMUSG00000044807	Zfp354c	5330421P20Rik|AJ18|AW743325|Kid3|Tcf17l2|Znf354c|mKIAA4218	zinc finger protein 354C	protein-coding
mm_75473.1	chr8	48552894	48552898	-	1	NA	intron (NM_011857, intron 2 of 28)	intron (NM_011857, intron 2 of 28)	121794	NM_001145937	23965	Mm.42191	NM_011857	ENSMUSG00000031561	Tenm3	2610100B16Rik|Odz1|Odz3|Ten-m3|mKIAA1455	teneurin transmembrane protein 3	protein-coding
mm_13889.1	chr2	120033454	120033466	+	1	NA	promoter-TSS (NM_145378)	promoter-TSS (NM_145378)	27	NM_145378	211429	Mm.41467	NM_145378	ENSMUSG00000098488	Pla2g4b	A030011C02Rik|Gm1013|cPLA2-beta	phospholipase A2, group IVB (cytosolic)	protein-coding
mm_38214.1	chr4	135969486	135969508	-	1	NA	exon (NM_011942, exon 8 of 10)	exon (NM_011942, exon 8 of 10)	3097	NM_011942	26394	Mm.34302	NM_011942	ENSMUSG00000028670	Lypla2	LysoII	lysophospholipase 2	protein-coding
mm_101214.1	chr11	20083960	20084008	-	1	NA	intron (NM_146243, intron 4 of 8)	intron (NM_146243, intron 4 of 8)	28967	NM_146243	66713	Mm.259045	NM_146243	ENSMUSG00000020152	Actr2	4921510D23Rik|AA409782|Arp2|D6Ertd746e	ARP2 actin-related protein 2	protein-coding
mm_82776.1	chr9	27030011	27030114	-	1	NA	promoter-TSS (NM_178113)	promoter-TSS (NM_178113)	32	NM_178027	69091	Mm.218717	NM_178027	ENSMUSG00000031988	Vps26b	1810012I05Rik|2310075A12Rik|AI848392	VPS26 retromer complex component B	protein-coding
mm_10013.1	chr1	191907583	191907607	-	1	NA	promoter-TSS (NR_030669)	promoter-TSS (NR_030669)	-68	NR_030669	98736	Mm.379232	NM_001024489	ENSMUSG00000055833	1700034H15Rik	4930557M11Rik|BB016121	RIKEN cDNA 1700034H15 gene	ncRNA
mm_129047.1	chr15	75239073	75239089	-	1	NA	Intergenic	Intergenic	-29340	NM_008530	17071	Mm.377095	NM_008530	ENSMUSG00000022583	Ly6f	-	lymphocyte antigen 6 complex, locus F	protein-coding
mm_21467.1	chr2	160961372	160961380	-	1	NA	exon (NM_173368, exon 33 of 37)	exon (NM_173368, exon 33 of 37)	-49037	NM_182840	280635	Mm.330747	NM_182840	ENSMUSG00000050700	Emilin3	1110013O17Rik|EMILIN-3|EMILIN-5|EMILIN-T|Emilin5	elastin microfibril interfacer 3	protein-coding
mm_166317.1	chr5	110446913	110446913	+	1	NA	intron (NM_001317042, intron 1 of 2)	intron (NM_001317042, intron 1 of 2)	1590	NM_001317042	381668	Mm.348782	NM_028596	ENSMUSG00000043323	Fbrsl1	2410025L10Rik|AI467568|Gm1049|Gm29766|mKIAA1545	fibrosin-like 1	protein-coding
mm_49723.1	chr6	34606446	34606449	+	1	NA	intron (NM_001347100, intron 1 of 13)	intron (NM_001347100, intron 1 of 13)	7943	NM_001347100	109624	Mm.308134	NM_145575	ENSMUSG00000029761	Cald1	4833423D12Rik|AI195384|AV071549|AW536160|C920027I18Rik	caldesmon 1	protein-coding
mm_160682.1	chr10	17723455	17723455	+	1	NA	5' UTR (NM_010828, exon 1 of 2)	5' UTR (NM_010828, exon 1 of 2)	227	NM_010828	17684	Mm.272321	NM_010828	ENSMUSG00000039910	Cited2	AI835299|ER154-like|Mrg1|Msg2|p35srj	Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 2	protein-coding
mm_29708.1	chr3	123508331	123508341	-	1	NA	promoter-TSS (NR_028574)	promoter-TSS (NR_028574)	0	NR_028574	69895	Mm.260791	NR_028574	ENSMUSG00000104960	Snhg8	1110065M07Rik|2010109N14Rik	small nucleolar RNA host gene 8	ncRNA
mm_103747.1	chr11	80377976	80378025	-	1	NA	promoter-TSS (NM_027472)	promoter-TSS (NM_027472)	15	NM_027472	70591	Mm.86860	NM_027472	ENSMUSG00000057181	5730455P16Rik	-	RIKEN cDNA 5730455P16 gene	protein-coding
mm_24194.1	chr3	88607638	88607667	+	1	NA	Intergenic	Intergenic	-8555	NM_001198911	16800	Mm.239329	NM_008487	ENSMUSG00000028059	Arhgef2	AA408978|GEF|GEF-H1|GEFH1|LFP40|Lbcl1|Lfc|P40|mKIAA0651	rho/rac guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_29534.1	chr3	116662572	116662584	-	1	NA	promoter-TSS (NM_008246)	promoter-TSS (NM_008246)	99	NM_008246	15247	Mm.280077	NM_008246	ENSMUSG00000089911	Mfsd14a	Hiat1	major facilitator superfamily domain containing 14A	protein-coding
mm_94784.1	chr11	21976570	21976572	+	1	NA	Intergenic	Intergenic	25080	NM_011023	18423	Mm.129663	NM_011023	ENSMUSG00000005917	Otx1	A730044F23Rik|jv	orthodenticle homeobox 1	protein-coding
mm_170138.1	chr17	39847964	39847969	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	4969	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_150950.1	chr19	46328222	46328232	+	1	NA	promoter-TSS (NM_133694)	promoter-TSS (NM_133694)	43	NM_133694	68431	Mm.19973	NM_133694	ENSMUSG00000025226	Fbxl15	0710008C12Rik|Fbxo37	F-box and leucine-rich repeat protein 15	protein-coding
mm_154899.1	chrX	20925526	20925540	+	1	NA	TTS (NM_008823)	TTS (NM_008823)	-4615	NM_013680	20964	Mm.439844	NM_013680	ENSMUSG00000037217	Syn1	Syn-1|Syn1-S	synapsin I	protein-coding
mm_166868.1	chr7	24709223	24709228	+	1	NA	promoter-TSS (NM_199150)	promoter-TSS (NM_199150)	-34	NM_199150	232972	Mm.293074	NM_199150	ENSMUSG00000045587	BC049730	Lypd10	cDNA sequence BC049730	protein-coding
mm_40191.1	chr5	36484624	36484634	+	1	NA	promoter-TSS (NM_001170454)	promoter-TSS (NM_001170454)	41	NM_025725	66717	Mm.42368	NM_025725	ENSMUSG00000050677	Ccdc96	4921513E08Rik	coiled-coil domain containing 96	protein-coding
mm_131018.1	chr15	103563409	103563429	-	1	NA	exon (NM_008134, exon 3 of 4)	exon (NM_008134, exon 3 of 4)	1662	NM_001289587	14663	Mm.219621	NM_008134	ENSMUSG00000022491	Glycam1	MC26|Sgp50|glyCAM-1	glycosylation dependent cell adhesion molecule 1	protein-coding
mm_69204.1	chr7	127406776	127406799	-	1	NA	promoter-TSS (NM_001167832)	promoter-TSS (NM_001167832)	35	NM_146203	233893	Mm.297097	NM_146203	ENSMUSG00000045757	Zfp764	8030466O12Rik	zinc finger protein 764	protein-coding
mm_102893.1	chr11	69418135	69418147	-	1	NA	Intergenic	CpG	-4466	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_127064.1	chr15	97373371	97373384	+	1	NA	intron (NM_172293, intron 4 of 5)	intron (NM_172293, intron 4 of 5)	-126090	NM_001164602	105827	Mm.24005	NM_178114	ENSMUSG00000048218	Amigo2	AI415330|AMIGO-2|AW208913|Ali1	adhesion molecule with Ig like domain 2	protein-coding
mm_77554.1	chr8	123284127	123284160	-	1	NA	exon (NM_016925, exon 28 of 43)	exon (NM_016925, exon 28 of 43)	-29921	NM_028200	72325	Mm.276193	NM_028200	ENSMUSG00000001062	Vps9d1	1300018I17Rik|2410004N05Rik|5DOS1|Vsp9d1	VPS9 domain containing 1	protein-coding
mm_56364.1	chr6	93912587	93912623	-	1	NA	intron (NM_001029850, intron 2 of 23)	intron (NM_001029850, intron 2 of 23)	358	NR_104594	14924	Mm.217216	NM_010367	ENSMUSG00000045095	Magi1	AIP3|BAP1|Baiap1|Gukmi1|MAGI1c|Magi-1|TNRC19|WWP3|mKIAA4129	membrane associated guanylate kinase, WW and PDZ domain containing 1	protein-coding
mm_131138.1	chr16	6348657	6348680	+	1	NA	intron (NM_021477, intron 2 of 16)	intron (NM_021477, intron 2 of 16)	373081	NR_045799	68238	Mm.434605	NR_045799	ENSMUSG00000101481	1700123O21Rik	-	RIKEN cDNA 1700123O21 gene	ncRNA
mm_4271.1	chr1	171559161	171559181	+	1	NA	promoter-TSS (NM_018729)	promoter-TSS (NM_018729)	-22	NM_018729	18106	Mm.2299	NM_018729	ENSMUSG00000004709	Cd244	2B4|C9.1|F730046O15Rik|Ly90|NAIL|NKR2B4|Nmrk|SLAMF4	CD244 natural killer cell receptor 2B4	protein-coding
mm_45972.1	chr5	90469557	90469604	-	1	NA	exon (NM_009654, exon 9 of 15)	exon (NM_009654, exon 9 of 15)	8710	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_67272.1	chr7	75782081	75782126	-	1	NA	Intergenic	CpG	-66235	NM_001122780	207952	Mm.206223	NM_029652	ENSMUSG00000055652	Klhl25	2810402K13Rik|BC027373|Enc-1	kelch-like 25	protein-coding
mm_684.1	chr1	40515443	40515458	+	1	NA	promoter-TSS (NM_010553)	promoter-TSS (NM_010553)	88	NM_010553	16174	Mm.20466	NM_010553	ENSMUSG00000026068	Il18rap	AcPL|IL-18R-beta|IL-18RAcP|IL-18Rbeta|IL-1RAcPL	interleukin 18 receptor accessory protein	protein-coding
mm_20632.1	chr2	131994615	131994640	-	1	NA	3' UTR (NM_175445, exon 11 of 11)	3' UTR (NM_175445, exon 11 of 11)	35361	NM_175445	215653	Mm.204737	NM_175445	ENSMUSG00000027339	Rassf2	3830431H01Rik|9030412M04Rik|AI852669|AW495050	Ras association (RalGDS/AF-6) domain family member 2	protein-coding
mm_42594.1	chr5	117397512	117397529	+	1	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	-8497	NM_028128	72151	Mm.27997	NM_028128	ENSMUSG00000029363	Rfc5	2610020K06Rik|2610209F07Rik|36.5kDa|36kDa|Recc5	replication factor C (activator 1) 5	protein-coding
mm_77960.1	chr9	7692340	7692366	+	1	NA	promoter-TSS (NM_001319986)	promoter-TSS (NM_001319986)	12	NM_001319986	17393	Mm.4825	NM_010810	ENSMUSG00000018623	Mmp7	MAT|MMP-7	matrix metallopeptidase 7	protein-coding
mm_77851.1	chr9	5306142	5306161	+	1	NA	exon (NM_009807, exon 8 of 10)	exon (NM_009807, exon 8 of 10)	-2698	NM_007609	12363	Mm.1569	NM_007609	ENSMUSG00000033538	Casp4	CASP-11|CASP-4|Casp11|Caspl|ich-3	caspase 4, apoptosis-related cysteine peptidase	protein-coding
mm_116103.1	chr13	28885335	28885382	-	1	NA	promoter-TSS (NR_045054)	promoter-TSS (NR_045054)	64	NR_045054	72518	Mm.37454	NR_045053		2610307P16Rik	AI666457	RIKEN cDNA 2610307P16 gene	ncRNA
mm_81786.1	chr9	114756834	114756842	+	1	NA	TTS (NM_133978)	TTS (NM_133978)	25155	NM_133978	102545	Mm.35600	NM_133978	ENSMUSG00000032436	Cmtm7	AI481279|Cklfsf7|LNV	CKLF-like MARVEL transmembrane domain containing 7	protein-coding
mm_79415.1	chr9	55209270	55209297	+	1	NA	intron (NM_028049, intron 1 of 6)	CpG	348	NM_028049	71999	Mm.276429	NM_028049	ENSMUSG00000032309	Fbxo22	0610033L19Rik|1600016C16Rik	F-box protein 22	protein-coding
mm_18691.1	chr2	71537679	71537681	-	1	NA	non-coding (NR_002854, exon 1 of 2)	non-coding (NR_002854, exon 1 of 2)	211	NR_002854	111970	Mm.4543	NR_002854		Dlx1as	Dix1as|Dlx1os	distal-less homeobox 1, antisense	ncRNA
mm_159929.1	chr6	63256903	63256903	+	1	NA	promoter-TSS (NM_008167)	promoter-TSS (NM_008167)	46	NM_008167	14804	Mm.439651	NM_008167	ENSMUSG00000071424	Grid2	B230104L07Rik|GluD2|GluRdelta2|Lc|Lc<J>|MMS10-AC|Ms10ac|cpr|ho|nmf408|tpr	glutamate receptor, ionotropic, delta 2	protein-coding
mm_29216.1	chr3	107066713	107066713	-	1	NA	Intergenic	Intergenic	27209	NR_033498	229694	Mm.347584	NM_173787	ENSMUSG00000056145	AI504432	A230102G19	expressed sequence AI504432	ncRNA
mm_81438.1	chr9	109096660	109096662	+	1	NA	intron (NM_172775, intron 1 of 37)	intron (NM_172775, intron 1 of 37)	1225	NM_172775	235611	Mm.53862	NM_172775	ENSMUSG00000053646	Plxnb1	2900002G15Rik|AU042020|mKIAA0407	plexin B1	protein-coding
mm_122430.1	chr14	45041199	45041222	-	1	NA	Intergenic	Intergenic	53099	NM_008964	19217	Mm.4630	NM_008964	ENSMUSG00000037759	Ptger2	EP2|Ptgerep2	prostaglandin E receptor 2 (subtype EP2)	protein-coding
mm_55837.1	chr6	83155804	83155812	-	1	NA	promoter-TSS (NM_027948)	promoter-TSS (NM_027948)	571	NM_023790	75659	Mm.130665	NM_023790	ENSMUSG00000030032	Wdr54	1700030E05Rik	WD repeat domain 54	protein-coding
mm_169761.1	chr15	97167254	97167254	-	1	NA	Intergenic	MLTR31F_MM|LTR|ERVK	-79853	NM_172293	239647	Mm.130036	NM_172293	ENSMUSG00000044250	Pced1b	Fam113b	PC-esterase domain containing 1B	protein-coding
mm_7009.1	chr1	86488849	86488859	-	1	NA	Intergenic	Intergenic	-37882	NM_008972	19231	Mm.19187	NM_008972	ENSMUSG00000026238	Ptma	Thym	prothymosin alpha	protein-coding
mm_26583.1	chr3	150049726	150049731	+	1	NA	Intergenic	Intergenic	774991	NR_040591	381482	Mm.393866	NR_040591		Gm1653	-	predicted gene 1653	ncRNA
mm_52561.1	chr6	116208117	116208130	+	1	NA	promoter-TSS (NM_026585)	promoter-TSS (NM_026585)	90	NM_026585	28006	Mm.28524	NM_026585	ENSMUSG00000024104	Washc2	A130095H06|C530005J20Rik|D6Wsu116e|Fam21	WASH complex subunit 2	protein-coding
mm_162164.1	chrX	95733263	95733263	-	1	NA	promoter-TSS (NM_029590)	promoter-TSS (NM_029590)	2	NM_029590	76386	Mm.443249	NM_029590		1700010D01Rik	-	RIKEN cDNA 1700010D01 gene	protein-coding
mm_75392.1	chr8	45999710	45999713	-	1	NA	5' UTR (NM_001039562, exon 1 of 5)	5' UTR (NM_001039562, exon 1 of 5)	139	NM_001039562	654824	Mm.334517	NM_001039562	ENSMUSG00000050914	Ankrd37	-	ankyrin repeat domain 37	protein-coding
mm_142600.1	chr17	46763749	46763766	-	1	NA	promoter-TSS (NM_011195)	promoter-TSS (NM_011195)	-45	NM_011195	19208	Mm.215173	NM_011195	ENSMUSG00000036858	Ptcra	gp33|pT-alpha|pT-alpha-TCR|pT[a]|pTa|pTalpha	pre T cell antigen receptor alpha	protein-coding
mm_106078.1	chr11	116174704	116174721	-	1	NA	exon (NM_015729, exon 12 of 14)	exon (NM_015729, exon 12 of 14)	-6534	NM_172571	217335	Mm.35241	NM_172571	ENSMUSG00000020776	Fbf1	1110033G01Rik|5930413D20|mKIAA1863	Fas (TNFRSF6) binding factor 1	protein-coding
mm_99152.1	chr11	100575883	100575900	+	1	NA	promoter-TSS (NM_001146318)	promoter-TSS (NM_001146318)	0	NM_001146318	12799	Mm.15711	NM_009923	ENSMUSG00000006782	Cnp	CNPase|Cnp-1|Cnp1	2',3'-cyclic nucleotide 3' phosphodiesterase	protein-coding
mm_147740.1	chr18	61108594	61108630	-	1	NA	intron (NM_001037859, intron 2 of 21)	intron (NM_001037859, intron 2 of 21)	3040	NM_001037859	12978	Mm.22574	NM_007779	ENSMUSG00000024621	Csf1r	AI323359|CD115|CSF-1R|Csfmr|Fim-2|Fim2|Fms|M-CSF-R|M-CSFR	colony stimulating factor 1 receptor	protein-coding
mm_170126.1	chr17	39847088	39847089	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	4091	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_91884.1	chr10	59875585	59875588	-	1	NA	Intergenic	ORR1C2|LTR|ERVL-MaLR	-4005	NM_019965	56709	Mm.103610	NM_019965	ENSMUSG00000020109	Dnajb12	Dj10|mDj10	DnaJ heat shock protein family (Hsp40) member B12	protein-coding
mm_88002.1	chr10	67096325	67096336	+	1	NA	intron (NM_178606, intron 1 of 7)	CpG	658	NM_001204915	28193	Mm.41272	NM_178606	ENSMUSG00000019873	Reep3	D10Ucla1	receptor accessory protein 3	protein-coding
mm_120148.1	chr14	60485196	60485204	+	1	NA	Intergenic	Intergenic	106914	NM_001164705	72125	Mm.275499	NM_028113	ENSMUSG00000021986	Amer2	2600011E07Rik|Fam123a	APC membrane recruitment 2	protein-coding
mm_53546.1	chr6	136827831	136827839	+	1	NA	intron (NM_021714, intron 1 of 11)	CpG	381	NM_021714	60321	Mm.141197	NM_021714	ENSMUSG00000030216	Wbp11	2510026P17Rik|D6Wsu113e|Npwbp|SIPP1	WW domain binding protein 11	protein-coding
mm_171919.1	chr5	5782688	5782689	-	1	NA	Intergenic	Intergenic	-33371	NM_027399	70358	Mm.85429	NM_027399	ENSMUSG00000015652	Steap1	2410007B19Rik|Prss24|Steap	six transmembrane epithelial antigen of the prostate 1	protein-coding
mm_54265.1	chr6	28421565	28421592	-	1	NA	5' UTR (NM_028900, exon 1 of 2)	5' UTR (NM_028900, exon 1 of 2)	146	NM_028900	74375	Mm.332950	NM_028900	ENSMUSG00000029708	Gcc1	4932417P04Rik	golgi coiled coil 1	protein-coding
mm_106810.1	chr12	6126343	6126345	+	1	NA	Intergenic	Intergenic	749842	NR_015579	72669	Mm.10434	NM_028318		2810032G03Rik	AI461720	RIKEN cDNA 2810032G03 gene	ncRNA
mm_24907.1	chr3	96219859	96219873	+	1	NA	promoter-TSS (NM_178213)	promoter-TSS (NM_178213)	-50	NM_178213	621893		NM_178213	ENSMUSG00000063689	Hist2h2ab	EG621893|H2a-613a	histone cluster 2, H2ab	protein-coding
mm_127789.1	chr15	3582137	3582151	-	1	NA	promoter-TSS (NM_001286370)	promoter-TSS (NM_001286370)	-302	NM_001286370	14600	Mm.3986	NM_010284	ENSMUSG00000055737	Ghr	GHBP|GHR/BP	growth hormone receptor	protein-coding
mm_39743.1	chr5	29569439	29569448	+	1	NA	5' UTR (NM_133907, exon 1 of 23)	5' UTR (NM_133907, exon 1 of 23)	201	NM_133907	100763	Mm.137746	NM_133907	ENSMUSG00000039000	Ube3c	AI853514|mKIAA0010	ubiquitin protein ligase E3C	protein-coding
mm_62017.1	chr7	91508645	91508648	+	1	NA	intron (NM_011807, intron 2 of 22)	intron (NM_011807, intron 2 of 22)	417860	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_24159.1	chr3	88514045	88514067	+	1	NA	Intergenic	B1_Mur1|SINE|Alu	-10704	NM_001002011	16905	Mm.243014	NM_019390	ENSMUSG00000028063	Lmna	Dhe	lamin A	protein-coding
mm_159559.1	chr4	107968179	107968179	+	1	NA	promoter-TSS (NM_146255)	promoter-TSS (NM_146255)	-155	NM_146255	242607	Mm.192040	NM_146255	ENSMUSG00000008932	Slc1a7	A930031E15Rik|Eaat5	solute carrier family 1 (glutamate transporter), member 7	protein-coding
mm_90937.1	chr10	12923040	12923073	-	1	NA	promoter-TSS (NR_038028)	promoter-TSS (NR_038028)	71	NR_038027	320273	Mm.417706	NR_038027	ENSMUSG00000097378	B230208H11Rik	-	RIKEN cDNA B230208H11 gene	ncRNA
mm_7144.1	chr1	91250041	91250075	-	1	NA	promoter-TSS (NM_026454)	promoter-TSS (NM_026454)	-261	NM_026454	67921	Mm.337238	NM_026454	ENSMUSG00000034343	Ube2f	2510010F15Rik|AI851109	ubiquitin-conjugating enzyme E2F (putative)	protein-coding
mm_38447.1	chr4	139994018	139994019	-	1	NA	Intergenic	PB1D11|SINE|Alu	-25992	NM_173427	242721	Mm.60400	NM_173427	ENSMUSG00000078234	Klhdc7a	B230308G19Rik	kelch domain containing 7A	protein-coding
mm_35864.1	chr4	49481198	49481208	-	1	NA	Intergenic	Intergenic	25355	NM_007519	12012	Mm.2859	NM_007519	ENSMUSG00000039653	Baat	AI118337|AI158864|BAT	bile acid-Coenzyme A: amino acid N-acyltransferase	protein-coding
mm_55284.1	chr6	54531098	54531106	-	1	NA	intron (NM_027268, intron 3 of 7)	intron (NM_027268, intron 3 of 7)	35280	NM_027268	69938	Mm.41557	NM_027268	ENSMUSG00000019124	Scrn1	2810019K23Rik|6330535A03Rik|AI852905|SES1|mKIAA0193	secernin 1	protein-coding
mm_7855.1	chr1	132391807	132391822	-	1	NA	promoter-TSS (NM_178874)	promoter-TSS (NM_178874)	-428	NM_178874	68875	Mm.273785	NM_178874	ENSMUSG00000042066	Tmcc2	1110063G11Rik	transmembrane and coiled-coil domains 2	protein-coding
mm_82821.1	chr9	31030282	31030313	-	1	NA	promoter-TSS (NM_001115130)	promoter-TSS (NM_001115130)	-347	NM_001115130	235132	Mm.239355	NM_172765	ENSMUSG00000047412	Zbtb44	6030404E16Rik|Btbd15|E230011F09	zinc finger and BTB domain containing 44	protein-coding
mm_134393.1	chr16	17467750	17467763	-	1	NA	intron (NM_001277231, intron 1 of 1)	B4A|SINE|B4	15771	NM_007764	12929	Mm.21048	NM_007764	ENSMUSG00000006134	Crkl	1110025F07Rik|AA589403|AI325100|Crkol	v-crk avian sarcoma virus CT10 oncogene homolog-like	protein-coding
mm_31295.1	chr4	45972395	45972405	+	1	NA	5' UTR (NM_146142, exon 1 of 17)	5' UTR (NM_146142, exon 1 of 17)	103	NM_146142	100121	Mm.275413	NM_146142	ENSMUSG00000035517	Tdrd7	5730495N10Rik|AI447470|PCTAIRE2BP	tudor domain containing 7	protein-coding
mm_13221.1	chr2	97125120	97125122	+	1	NA	intron (NM_001289743, intron 4 of 6)	Lx8|LINE|L1	-342536	NM_001289744	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_155171.1	chrX	53434953	53434972	+	1	NA	promoter-TSS (NR_034074)	promoter-TSS (NR_034074)	44	NR_034074	69501	Mm.63828	NM_175147	ENSMUSG00000060967	Etd	1700030K02Rik	embryonic testis differentiation	ncRNA
mm_61848.1	chr7	88297134	88297176	+	1	NA	exon (NM_009982, exon 3 of 7)	exon (NM_009982, exon 3 of 7)	19070	NM_001311790	13032	Mm.89295	NM_009982	ENSMUSG00000030560	Ctsc	AI047818|CatC|DPP1|DPPI	cathepsin C	protein-coding
mm_166961.1	chr7	44480355	44480358	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-4161	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_94046.1	chr10	128179979	128179990	-	1	NA	5' UTR (NM_001039080, exon 1 of 14)	5' UTR (NM_001039080, exon 1 of 14)	313	NM_001039080	56516	Mm.42247	NM_019711	ENSMUSG00000040043	Rbms2	2610315E04Rik|Scr3	RNA binding motif, single stranded interacting protein 2	protein-coding
mm_125028.1	chr15	25752861	25752897	+	1	NA	intron (NM_019472, intron 19 of 40)	intron (NM_019472, intron 19 of 40)	-90419	NM_001034851	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_71929.1	chr8	70274739	70274751	+	1	NA	Intergenic	L2|LINE|L2	-8254	NM_011984	26558	Mm.388127	NM_011984	ENSMUSG00000003573	Homer3	AW146114	homer scaffolding protein 3	protein-coding
mm_109631.1	chr12	112767596	112767612	+	1	NA	exon (NM_178911, exon 8 of 11)	exon (NM_178911, exon 8 of 11)	6949	NM_178911	104759	Mm.203915	NM_178911	ENSMUSG00000052160	Pld4	AI132321|thss	phospholipase D family, member 4	protein-coding
mm_44185.1	chr5	151400106	151400146	+	1	NA	intron (NR_045700, intron 2 of 3)	RLTR51B_Mm|LTR|ERVK?	-6378	NR_131166	100042166	Mm.443286	NR_131166	ENSMUSG00000097321	Gm3704	-	predicted gene 3704	ncRNA
mm_22515.1	chr3	7618880	7618892	+	1	NA	Intergenic	Intergenic	-5126	NM_001313888	16196	Mm.3825	NM_008371	ENSMUSG00000040329	Il7	A630026I06Rik|Il-7|hlb368	interleukin 7	protein-coding
mm_39726.1	chr5	28317887	28317890	+	1	NA	intron (NM_028234, intron 1 of 18)	intron (NM_028234, intron 1 of 18)	699	NM_028234	381626	Mm.304075	NM_028234	ENSMUSG00000048271	Rbm33	3200001K10Rik|6430512A10Rik|AA386890|Prr8	RNA binding motif protein 33	protein-coding
mm_45512.1	chr5	72504278	72504289	-	1	NA	promoter-TSS (NM_016869)	promoter-TSS (NM_016869)	-75	NM_016869	53419	Mm.332425	NM_016869	ENSMUSG00000005220	Corin	AV273130|Lrp4	corin	protein-coding
mm_166705.1	chr6	115932157	115932174	+	1	NA	exon (NM_145383, exon 1 of 5)	exon (NM_145383, exon 1 of 5)	238	NM_145383	212541	Mm.2965	NM_145383	ENSMUSG00000030324	Rho	Noerg1|Opn2|Ops|RP4	rhodopsin	protein-coding
mm_39409.1	chr5	14521704	14521719	+	1	NA	exon (NM_011995, exon 2 of 25)	exon (NM_011995, exon 2 of 25)	6793	NM_001110796	26875	Mm.146275	NM_011995	ENSMUSG00000061601	Pclo	Acz|Pico	piccolo (presynaptic cytomatrix protein)	protein-coding
mm_134966.1	chr16	31948433	31948542	-	1	NA	promoter-TSS (NR_027897)	promoter-TSS (NR_027897)	34	NR_027897	106264	Mm.347369	NM_025320	ENSMUSG00000107002	0610012G03Rik	AI839730	RIKEN cDNA 0610012G03 gene	ncRNA
mm_162081.1	chrX	26545534	26545534	-	1	NA	promoter-TSS (NM_001136476)	promoter-TSS (NM_001136476)	31	NM_001136476	664829	Mm.489202	NM_001136476	ENSMUSG00000095063	Slx	EG664958|Xmr	Sycp3 like X-linked	protein-coding
mm_116433.1	chr13	42052940	42052944	-	1	NA	intron (NM_007772, intron 1 of 8)	intron (NM_007772, intron 1 of 8)	921	NM_007772	110521	Mm.4808	NM_007772	ENSMUSG00000021366	Hivep1	Cryabp1	human immunodeficiency virus type I enhancer binding protein 1	protein-coding
mm_149151.1	chr19	9010812	9010838	+	1	NA	exon (NM_009643, exon 5 of 5)	exon (NM_009643, exon 5 of 5)	-7079	NR_105786	102465190		NR_105786	ENSMUSG00000099308	Mir6367	Gm27467|mmu-mir-6367	microRNA 6367	ncRNA
mm_83704.1	chr9	50693801	50693814	-	1	NA	intron (NM_178118, intron 6 of 19)	intron (NM_178118, intron 6 of 19)	-34027	NM_145614	235339	Mm.285076	NM_145614	ENSMUSG00000000168	Dlat	6332404G05Rik|DLTA|PDC-E2	dihydrolipoamide S-acetyltransferase (E2 component of pyruvate dehydrogenase complex)	protein-coding
mm_880.1	chr1	52500010	52500071	+	1	NA	intron (NM_008667, intron 1 of 7)	CpG	408	NM_008667	17936	Mm.25903	NM_008667	ENSMUSG00000002881	Nab1	-	Ngfi-A binding protein 1	protein-coding
mm_95752.1	chr11	54902848	54902858	+	1	NA	promoter-TSS (NM_008161)	promoter-TSS (NM_008161)	-1	NM_001329860	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_45952.1	chr5	90366505	90366609	-	1	NA	promoter-TSS (NM_030886)	promoter-TSS (NM_030886)	-372	NM_198010	81702	Mm.245522	NM_030886	ENSMUSG00000055204	Ankrd17	4933425K22Rik|A130069E23Rik|A930008M01|AA407558|AA516750|AU040470|Foe|Gtar|Mask|mKIAA0697	ankyrin repeat domain 17	protein-coding
mm_40108.1	chr5	34761816	34761826	+	1	NA	promoter-TSS (NM_010414)	promoter-TSS (NM_010414)	81	NM_010414	15194	Mm.209071	NM_010414	ENSMUSG00000029104	Htt	AI256365|C430023I11Rik|Hd|Hdh|IT15	huntingtin	protein-coding
mm_41540.1	chr5	92859444	92859472	+	1	NA	intron (NM_001077595, intron 1 of 9)	ID4|SINE|ID	-38535	NM_001077596	27428	Mm.46014	NM_015756	ENSMUSG00000029381	Shroom3	AL022960|D5Ertd287e|Shrm|Shrm3	shroom family member 3	protein-coding
mm_111239.1	chr12	84773054	84773064	-	1	NA	promoter-TSS (NM_028863)	promoter-TSS (NM_028863)	53	NM_023409	67963	Mm.282556	NM_023409	ENSMUSG00000021242	Npc2	2700012J19Rik|AA408070|AU045843|HE1	Niemann-Pick type C2	protein-coding
mm_65726.1	chr7	28381015	28381021	-	1	NA	Intergenic	Intergenic	-1790	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_115158.1	chr13	107063691	107063701	+	1	NA	Intergenic	MLT1L|LTR|ERVL-MaLR	41126	NR_015471	100040322	Mm.133867	NR_015471		3830408C21Rik	-	RIKEN cDNA 3830408C21 gene	ncRNA
mm_104098.1	chr11	86695065	86695090	-	1	NA	3' UTR (NM_001003908, exon 32 of 32)	3' UTR (NM_001003908, exon 32 of 32)	10996	NM_001098810	217057	Mm.24868	NM_175004	ENSMUSG00000072582	Ptrh2	A230072I16Rik|Bit1|CGI-147	peptidyl-tRNA hydrolase 2	protein-coding
mm_102489.1	chr11	60222855	60222872	-	1	NA	Intergenic	CpG	-2236	NM_001313979	20787	Mm.278701	NM_011480	ENSMUSG00000020538	Srebf1	ADD1|SREBP-1a|SREBP1|SREBP1c|bHLHd1	sterol regulatory element binding transcription factor 1	protein-coding
mm_30017.1	chr3	135665284	135665296	-	1	NA	intron (NM_008689, intron 3 of 24)	intron (NM_008689, intron 3 of 24)	26257	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_170468.1	chr18	9916868	9916871	+	1	NA	Intergenic	Intergenic	-41311	NM_153552	225160	Mm.219648	NM_153552	ENSMUSG00000024287	Thoc1	3110002N20Rik|AW107452|NMP-84	THO complex 1	protein-coding
mm_2792.1	chr1	130851408	130851420	+	1	NA	3' UTR (NM_011082, exon 11 of 11)	3' UTR (NM_011082, exon 11 of 11)	-14363	NM_026976	69169	Mm.46042	NM_026976	ENSMUSG00000042474	Fcmr	1810037B05Rik|Faim3|FcmuR|Toso	Fc fragment of IgM receptor	protein-coding
mm_170706.1	chr2	140152033	140152042	+	1	NA	intron (NM_001081090, intron 8 of 13)	B1_Mus1|SINE|Alu	18521	NM_001081090	66580	Mm.21228	NM_001081090	ENSMUSG00000045624	Esf1	2610101J03Rik|ABTAP|AW545818|C79684	ESF1 nucleolar pre-rRNA processing protein homolog	protein-coding
mm_28237.1	chr3	88456398	88456441	-	1	NA	promoter-TSS (NM_013658)	promoter-TSS (NM_013658)	-658	NM_013658	20351	Mm.439752	NM_013658	ENSMUSG00000028064	Sema4a	AI132332|SemB|Semab	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A	protein-coding
mm_137818.1	chr17	30135174	30135193	+	1	NA	intron (NM_148926, intron 2 of 4)	intron (NM_148926, intron 2 of 4)	121352	NR_105839	102465223		NR_105839	ENSMUSG00000098522	Mir6412	Gm27364|mmu-mir-6412	microRNA 6412	ncRNA
mm_120696.1	chr14	70890288	70890290	+	1	NA	5' UTR (NM_008115, exon 1 of 9)	5' UTR (NM_008115, exon 1 of 9)	182	NM_001302094	14586	Mm.32619	NM_008115	ENSMUSG00000022103	Gfra2	-	glial cell line derived neurotrophic factor family receptor alpha 2	protein-coding
mm_72965.1	chr8	92840224	92840235	+	1	NA	intron (NM_008610, intron 8 of 12)	intron (NM_008610, intron 8 of 12)	12932	NM_008610	17390	Mm.29564	NM_008610	ENSMUSG00000031740	Mmp2	Clg4a|GelA|MMP-2	matrix metallopeptidase 2	protein-coding
mm_86278.1	chr9	121839425	121839439	-	1	NA	promoter-TSS (NM_028384)	promoter-TSS (NM_028384)	29	NM_028384	100502861	Mm.335550	NM_028384	ENSMUSG00000079235	Ccdc13	2900041A11Rik|Gm188	coiled-coil domain containing 13	protein-coding
mm_43638.1	chr5	138229835	138229849	+	1	NA	5' UTR (NM_001013773, exon 2 of 6)	5' UTR (NM_001013773, exon 2 of 6)	3938	NM_001013773	381680	Mm.156846	NM_001013773	ENSMUSG00000047592	Nxpe5	-	neurexophilin and PC-esterase domain family, member 5	protein-coding
mm_53075.1	chr6	124935331	124935357	+	1	NA	exon (NM_001170341, exon 8 of 9)	exon (NM_001170341, exon 8 of 9)	3956	NM_001170341	30853	Mm.29737	NM_145385	ENSMUSG00000030120	Mlf2	AI256856|AU018944|C77284	myeloid leukemia factor 2	protein-coding
mm_133938.1	chr16	3895562	3895596	-	1	NA	intron (NM_029090, intron 2 of 6)	ORR1E|LTR|ERVL-MaLR	10960	NM_001290689	74763	Mm.28403	NM_029090	ENSMUSG00000005982	Naa60	1200013P24Rik|AI315146|Nat15	N(alpha)-acetyltransferase 60, NatF catalytic subunit	protein-coding
mm_110159.1	chr12	26469237	26469247	-	1	NA	promoter-TSS (NM_020557)	promoter-TSS (NM_020557)	27	NM_020557	22169	Mm.271839	NM_020557	ENSMUSG00000020638	Cmpk2	1200004E04Rik|TDKI|Tyki	cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial	protein-coding
mm_144438.1	chr18	21651432	21651443	+	1	NA	promoter-TSS (NM_001271580)	promoter-TSS (NM_001271580)	-128	NM_001271580	74644	Mm.329311	NM_001271580		4930426D05Rik	-	RIKEN cDNA 4930426D05 gene	protein-coding
mm_73117.1	chr8	94750022	94750033	+	1	NA	3' UTR (NM_009137, exon 3 of 3)	3' UTR (NM_009137, exon 3 of 3)	4343	NM_009137	20299	Mm.12895	NM_009137	ENSMUSG00000031779	Ccl22	ABCD-1|DCBCK|MDC|Scya22	chemokine (C-C motif) ligand 22	protein-coding
mm_25452.1	chr3	108383830	108383886	+	1	NA	promoter-TSS (NM_001190161)	promoter-TSS (NM_001190161)	20	NM_019976	56742	Mm.389499	NM_019976	ENSMUSG00000068744	Psrc1	5430413I02Rik|AL033312|Dda3	proline/serine-rich coiled-coil 1	protein-coding
mm_53841.1	chr6	148355108	148355128	+	1	NA	non-coding (NR_003634, exon 1 of 1)	non-coding (NR_003634, exon 1 of 1)	462	NR_003634	66184	Mm.391542	NM_025405	ENSMUSG00000063171	Rps4l	1110033J19Rik|AA407494|Rps4y2	ribosomal protein S4-like	pseudo
mm_44116.1	chr5	149439708	149439721	+	1	NA	promoter-TSS (NM_029464)	promoter-TSS (NM_029464)	54	NM_001310765	75860	Mm.159605	NM_029464	ENSMUSG00000029660	Tex26	4930588N13Rik	testis expressed 26	protein-coding
mm_14715.1	chr2	143915274	143915337	+	1	NA	promoter-TSS (NM_019771)	promoter-TSS (NM_019771)	-26	NM_019771	56431	Mm.28919	NM_019771	ENSMUSG00000015932	Dstn	2610043P17Rik|ADF|AU042046|Dsn|corn1|sid23p	destrin	protein-coding
mm_30361.1	chr3	151835968	151835979	-	1	NA	intron (NM_008966, intron 1 of 2)	intron (NM_008966, intron 1 of 2)	1555	NM_008966	19220	Mm.331442	NM_008966	ENSMUSG00000028036	Ptgfr	AI957154|PGF|fp	prostaglandin F receptor	protein-coding
mm_85744.1	chr9	108567363	108567449	-	1	NA	promoter-TSS (NR_029577)	promoter-TSS (NR_029577)	-64	NM_023247	66706	Mm.29471	NM_023247	ENSMUSG00000070283	Ndufaf3	4733401H18Rik	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, assembly factor 3	protein-coding
mm_92662.1	chr10	80419684	80419700	-	1	NA	intron (NM_001164148, intron 6 of 18)	intron (NM_001164148, intron 6 of 18)	-12871	NM_025650	66594	Mm.379119	NM_025650	ENSMUSG00000020163	Uqcr11	0710008D09Rik|AL022707|Uqcr	ubiquinol-cytochrome c reductase, complex III subunit XI	protein-coding
mm_172137.1	chr6	35395605	35395605	-	1	NA	Intergenic	L1Md_T|LINE|L1	64759	NR_040526	73409	Mm.69443	NR_040526	ENSMUSG00000107341	1700065J11Rik	-	RIKEN cDNA 1700065J11 gene	ncRNA
mm_6208.1	chr1	66816886	66816922	-	1	NA	intron (NM_177645, intron 1 of 13)	CpG	691	NM_177645	68691	Mm.240912	NM_177645	ENSMUSG00000026004	Kansl1l	1110028C15Rik|1190030G24|AI427598|C430010P07Rik|mKIAA4189	KAT8 regulatory NSL complex subunit 1-like	protein-coding
mm_41033.1	chr5	86071568	86071586	+	1	NA	promoter-TSS (NM_019992)	promoter-TSS (NM_019992)	-169	NM_019992	56792	Mm.131237	NM_019992	ENSMUSG00000029254	Stap1	AI586015|Brdg1|STAP-1	signal transducing adaptor family member 1	protein-coding
mm_88437.1	chr10	77535954	77535958	+	1	NA	intron (NM_008404, intron 1 of 15)	intron (NM_008404, intron 1 of 15)	5608	NM_008404	16414	Mm.1137	NM_008404	ENSMUSG00000000290	Itgb2	2E6|AI528527|Cd18|LAD|LCAMB|Lfa1|MF17	integrin beta 2	protein-coding
mm_24426.1	chr3	90537307	90537326	+	1	NA	Intergenic	Intergenic	-3907	NM_026416	67860	Mm.331185	NM_026416	ENSMUSG00000074457	S100a16	2300002L21Rik|AI325039|AI663996|DT1P1A7|S100F	S100 calcium binding protein A16	protein-coding
mm_171402.1	chr4	123718160	123718162	-	1	NA	promoter-TSS (NR_002445).2	promoter-TSS (NR_002445).2	0	NR_002445	170658	Mm.375824	NR_002445		BC002163	-	NADH dehydrogenase Fe-S protein 5 pseudogene	pseudo
mm_63021.1	chr7	121034543	121034580	+	1	NA	5' UTR (NM_021554, exon 1 of 5)	5' UTR (NM_021554, exon 1 of 5)	116	NM_021554	59052	Mm.29122	NM_021554	ENSMUSG00000030876	Mettl9	0610012D09Rik|AA517660|Drev|MNCb-5680	methyltransferase like 9	protein-coding
mm_128794.1	chr15	66812638	66812649	-	1	NA	5' UTR (NM_009192, exon 2 of 9)	5' UTR (NM_009192, exon 2 of 9)	19186	NM_001029841	20491	Mm.7601	NM_009192	ENSMUSG00000022372	Sla	Slap|Slap-1	src-like adaptor	protein-coding
mm_87502.1	chr10	52233613	52233672	+	1	NA	promoter-TSS (NM_025705)	promoter-TSS (NM_025705)	23	NM_025705	66686	Mm.62982	NM_025705	ENSMUSG00000019891	Dcbld1	4631413K11Rik	discoidin, CUB and LCCL domain containing 1	protein-coding
mm_27110.1	chr3	30793206	30793232	-	1	NA	5' UTR (NM_027016, exon 1 of 8)	5' UTR (NM_027016, exon 1 of 8)	343	NM_027016	69276	Mm.26017	NM_027016	ENSMUSG00000027706	Sec62	3100002M17Rik|AI844545|AW545092|Dtrp1|HTP1|Tloc1	SEC62 homolog (S. cerevisiae)	protein-coding
mm_113154.1	chr13	24801195	24801213	+	1	NA	promoter-TSS (NM_024473)	promoter-TSS (NM_024473)	-453	NM_024473	79555	Mm.266668	NM_024473	ENSMUSG00000019132	BC005537	8030460C05Rik|C78201	cDNA sequence BC005537	protein-coding
mm_131981.1	chr16	25024171	25024175	+	1	NA	Intergenic	Intergenic	-35466	NR_040374	319487	Mm.137341	NR_040374	ENSMUSG00000096960	A230028O05Rik	-	RIKEN cDNA A230028O05 gene	ncRNA
mm_132430.1	chr16	35775792	35775795	+	1	NA	intron (NM_175111, intron 1 of 7)	intron (NM_175111, intron 1 of 7)	5407	NM_175111	66667	Mm.45272	NM_175111	ENSMUSG00000022849	Hspbap1	3830421G21Rik	Hspb associated protein 1	protein-coding
mm_122009.1	chr14	26981626	26981630	-	1	NA	Intergenic	RMER17B2|LTR|ERVK	-11077	NM_145221	72993	Mm.202322	NM_145221	ENSMUSG00000040760	Appl1	2900057D21Rik|7330406P05Rik|AI585782|AW209077|BB022931|C88264|DIP13	adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 1	protein-coding
mm_132045.1	chr16	28929039	28929054	+	1	NA	intron (NM_177718, intron 1 of 1)	CpG	652	NM_177718	239796	Mm.155887	NM_177718	ENSMUSG00000051065	Mb21d2	1600021P15Rik|A430031N04|C87006	Mab-21 domain containing 2	protein-coding
mm_30565.1	chr4	3790291	3790301	+	1	NA	3' UTR (NM_001111096, exon 13 of 13)	3' UTR (NM_001111096, exon 13 of 13)	45359	NM_026147	67427	Mm.21938	NM_026147	ENSMUSG00000028234	Rps20	4632426K06Rik|Dsk4	ribosomal protein S20	protein-coding
mm_117095.1	chr13	59822650	59822678	-	1	NA	intron (NM_153538, intron 1 of 27)	CpG	483	NM_153538	214290	Mm.233082	NM_153538	ENSMUSG00000035248	Zcchc6	6030448M23Rik|AA420405	zinc finger, CCHC domain containing 6	protein-coding
mm_37862.1	chr4	132303182	132303210	-	1	NA	exon (NM_001081651, exon 1 of 2)	exon (NM_001081651, exon 1 of 2)	160	NM_001081651	242681	Mm.331927	NM_001081651	ENSMUSG00000089687	Rab42	9530096D07Rik|Rab42-ps	RAB42, member RAS oncogene family	protein-coding
mm_117897.1	chr13	99425221	99425236	-	1	NA	3' UTR (NM_008634, exon 7 of 7)	3' UTR (NM_008634, exon 7 of 7)	-12402	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_45486.1	chr5	71095766	71095862	-	1	NA	promoter-TSS (NM_008066)	promoter-TSS (NM_008066)	35	NM_008066	14395	Mm.5304	NM_008066	ENSMUSG00000000560	Gabra2	C630048P16Rik|Gabra-2	gamma-aminobutyric acid (GABA) A receptor, subunit alpha 2	protein-coding
mm_87194.1	chr10	39527559	39527606	+	1	NA	intron (NM_001122892, intron 7 of 12)	PB1D9|SINE|Alu	-85352	NM_134000	103213	Mm.436686	NM_134000	ENSMUSG00000019842	Traf3ip2	AI429613|Act1|CIKS	TRAF3 interacting protein 2	protein-coding
mm_139448.1	chr17	55446239	55446257	+	1	NA	intron (NM_001347403, intron 1 of 5)	intron (NM_001347403, intron 1 of 5)	531	NM_172829	240119	Mm.311687	NM_172829	ENSMUSG00000024172	St6gal2	C230064G14Rik|St6galII|mKIAA1877	beta galactoside alpha 2,6 sialyltransferase 2	protein-coding
mm_116457.1	chr13	43304119	43304130	-	1	NA	promoter-TSS (NM_001033399)	promoter-TSS (NM_001033399)	48	NM_001033399	328232	Mm.441399	NM_001033399	ENSMUSG00000051335	Gfod1	9630032O13|AI850995	glucose-fructose oxidoreductase domain containing 1	protein-coding
mm_37419.1	chr4	122869728	122869773	-	1	NA	exon (NM_007598, exon 4 of 13)	exon (NM_007598, exon 4 of 13)	16307	NM_007598	12331	Mm.8687	NM_007598	ENSMUSG00000028656	Cap1	-	CAP, adenylate cyclase-associated protein 1 (yeast)	protein-coding
mm_104161.1	chr11	87320401	87320404	-	1	NA	intron (NR_106195, intron 6 of 8)	intron (NR_106195, intron 6 of 8)	38592	NM_177167	320472	Mm.341988	NM_177167	ENSMUSG00000046442	Ppm1e	AW049266|B930008A12Rik|POPX1|PP2CH|mKIAA1072	protein phosphatase 1E (PP2C domain containing)	protein-coding
mm_56793.1	chr6	116647782	116647805	-	1	NA	intron (NM_178045, intron 3 of 10)	intron (NM_178045, intron 3 of 10)	-1746	NR_106010	102466793		NR_106010	ENSMUSG00000098334	Mir7043	Gm27776|mmu-mir-7043	microRNA 7043	ncRNA
mm_144453.1	chr18	23333720	23333731	+	1	NA	intron (NM_001285813, intron 1 of 21)	intron (NM_001285813, intron 1 of 21)	23705	NM_001285813	13527	Mm.94371	NM_010087	ENSMUSG00000024302	Dtna	2210407P21Rik|DTN-A|Dtn|Gm19389|a-DB-1|adbn	dystrobrevin alpha	protein-coding
mm_118.1	chr1	9797813	9797823	+	1	NA	promoter-TSS (NM_133220)	promoter-TSS (NM_133220)	-312	NM_133220	170755	Mm.336410	NM_133220	ENSMUSG00000025915	Sgk3	2510015P22Rik|A330005P07Rik|Cisk|fy|fz	serum/glucocorticoid regulated kinase 3	protein-coding
mm_11231.1	chr2	29802732	29802745	+	1	NA	promoter-TSS (NM_011989)	promoter-TSS (NM_011989)	58	NM_011989	26569	Mm.330113	NM_011989	ENSMUSG00000059316	Slc27a4	BB144259|FATP4	solute carrier family 27 (fatty acid transporter), member 4	protein-coding
mm_70125.1	chr7	143087116	143087155	-	1	NA	intron (NM_020277, intron 4 of 24)	intron (NM_020277, intron 4 of 24)	7507	NM_020277	56843	Mm.286668	NM_020277	ENSMUSG00000009246	Trpm5	9430099A16Rik|LTrpC-5|Ltrpc5|Mtr1	transient receptor potential cation channel, subfamily M, member 5	protein-coding
mm_119331.1	chr14	39220140	39220141	+	1	NA	intron (NM_001190187, intron 1 of 9)	MTB_Mm-int|LTR|ERVL-MaLR	-252289	NR_131973	432842	Mm.352566	NR_131973		LOC432842	-	uncharacterized LOC432842	ncRNA
mm_117306.1	chr13	67399739	67399764	-	1	NA	promoter-TSS (NM_001080941)	promoter-TSS (NM_001080941)	16	NM_001080941	72807	Mm.303790	NM_001080941	ENSMUSG00000078994	Zfp429	2810487A22Rik|AI929863|Rsl2	zinc finger protein 429	protein-coding
mm_33891.1	chr4	136180793	136180809	+	1	NA	promoter-TSS (NM_001305399)	promoter-TSS (NM_001305399)	19	NM_001305399	242705	Mm.307932	NM_177733	ENSMUSG00000018983	E2f2	E2F-2	E2F transcription factor 2	protein-coding
mm_54833.1	chr6	42586002	42586006	-	1	NA	Intergenic	Intergenic	11368	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_37920.1	chr4	132789896	132789911	-	1	NA	exon (NM_001033308, exon 3 of 6)	exon (NM_001033308, exon 3 of 6)	6461	NM_001033308	230787	Mm.290912	NM_001033308	ENSMUSG00000037731	Themis2	ICB-1	thymocyte selection associated family member 2	protein-coding
mm_51513.1	chr6	83137839	83137846	+	1	NA	5' UTR (NM_133641, exon 1 of 12)	5' UTR (NM_133641, exon 1 of 12)	758	NM_009106	20166	Mm.4139	NM_009106	ENSMUSG00000034930	Rtkn	-	rhotekin	protein-coding
mm_52776.1	chr6	121226328	121226334	+	1	NA	TTS (NM_017379)	TTS (NM_017379)	15597	NM_017379	53857	Mm.32884	NM_017379	ENSMUSG00000030137	Tuba8	-	tubulin, alpha 8	protein-coding
mm_169704.1	chr15	75086994	75086995	+	1	NA	Intergenic	RLTR11A|LTR|ERVK	24955	NM_001099217	100041546	Mm.482110	NM_001099217	ENSMUSG00000022584	Ly6c2	Ly-6C.2|Ly-6C2	lymphocyte antigen 6 complex, locus C2	protein-coding
mm_93524.1	chr10	115314876	115314887	-	1	NA	intron (NM_024454, intron 1 of 6)	intron (NM_024454, intron 1 of 6)	710	NM_024454	216344	Mm.21936	NM_024454	ENSMUSG00000020132	Rab21	9630024B22	RAB21, member RAS oncogene family	protein-coding
mm_106339.1	chr11	118393144	118393158	-	1	NA	exon (NM_011150, exon 6 of 6)	exon (NM_011150, exon 6 of 6)	8780	NM_011150	19039	Mm.3152	NM_011150	ENSMUSG00000033880	Lgals3bp	90K|CyCAP|MAC-2BP|Ppicap|Tango10b	lectin, galactoside-binding, soluble, 3 binding protein	protein-coding
mm_78690.1	chr9	40802626	40802656	+	1	NA	intron (NM_031165, intron 3 of 8)	intron (NM_031165, intron 3 of 8)	1368	NM_031165	15481	Mm.290774	NM_031165	ENSMUSG00000015656	Hspa8	2410008N15Rik|Hsc70|Hsc71|Hsc73|Hsp73|Hspa10	heat shock protein 8	protein-coding
mm_73404.1	chr8	105900422	105900467	+	1	NA	promoter-TSS (NM_173432)	promoter-TSS (NM_173432)	-30	NM_173432	244631	Mm.27627	NM_173432	ENSMUSG00000048310	Pskh1	AW539964|E130013P03Rik|b2b1230Clo	protein serine kinase H1	protein-coding
mm_147419.1	chr18	46179921	46179968	-	1	NA	intron (NM_178872, intron 4 of 9)	intron (NM_178872, intron 4 of 9)	18874	NM_001170855	28105	Mm.277382	NM_178872	ENSMUSG00000033949	Trim36	D18Wsu100e|haprin	tripartite motif-containing 36	protein-coding
mm_2048.1	chr1	87360278	87360280	+	1	NA	intron (NM_146112, intron 3 of 28)	intron (NM_146112, intron 3 of 28)	33281	NM_001110212	227331	Mm.23065	NM_146112	ENSMUSG00000048000	Gigyf2	2610016F01Rik|A830080H02Rik|AI852361|AW259676|BC006835|Tnrc15|mKIAA0642	GRB10 interacting GYF protein 2	protein-coding
mm_1610.1	chr1	74385475	74385509	+	1	NA	exon (NM_013612, exon 15 of 15)	exon (NM_013612, exon 15 of 15)	-6117	NM_153088	227292	Mm.165042	NM_153088	ENSMUSG00000026176	Ctdsp1	GIP|NLIIF|Nif3|SCP1	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 1	protein-coding
mm_138836.1	chr17	39848506	39848510	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	5511	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_100817.1	chr11	5150063	5150094	-	1	NA	intron (NM_080595, intron 1 of 14)	intron (NM_080595, intron 1 of 14)	2144	NM_080595	140703	Mm.840	NM_080595	ENSMUSG00000034164	Emid1	AW122071|CO-5|Emu1	EMI domain containing 1	protein-coding
mm_45101.1	chr5	44741224	44741227	-	1	NA	intron (NM_001347349, intron 1 of 7)	intron (NM_001347349, intron 1 of 7)	58521	NM_001347349	16826	Mm.25785	NM_010698	ENSMUSG00000039706	Ldb2	AI035351|AW146358|CLIM1|CLP-36|Ldb3	LIM domain binding 2	protein-coding
mm_72567.1	chr8	84127126	84127139	+	1	NA	intron (NM_001013384, intron 2 of 9)	tRNA-Ala-GCY_|tRNA|tRNA	1143	NM_001013384	244550	Mm.334654	NM_001013384	ENSMUSG00000012889	Podnl1	5832418A03Rik|Gm506	podocan-like 1	protein-coding
mm_66631.1	chr7	45510401	45510413	-	1	NA	promoter-TSS (NM_008749)	promoter-TSS (NM_008749)	1	NM_008749	18220	Mm.258923	NM_008749	ENSMUSG00000030824	Nucb1	B230337F23Rik|C77483|Calnuc|MTEST82|Nucb	nucleobindin 1	protein-coding
mm_120415.1	chr14	65358488	65358535	+	1	NA	promoter-TSS (NM_199029)	promoter-TSS (NM_199029)	-165	NM_199029	380912	Mm.270087	NM_199029	ENSMUSG00000034522	Zfp395	BC053701|Gm910	zinc finger protein 395	protein-coding
mm_147137.1	chr18	36321527	36321537	-	1	NA	Intergenic	Intergenic	21431	NM_001267796	109169	Mm.426423	NM_001267796	ENSMUSG00000110185	Igip	6330403M23Rik	IgA inducing protein	protein-coding
mm_117552.1	chr13	84064786	84064808	-	1	NA	promoter-TSS (NR_131220)	promoter-TSS (NR_131220)	-23	NR_131220	553095	Mm.39702	NR_131220	ENSMUSG00000098087	Gm17750	-	predicted gene, 17750	ncRNA
mm_100539.1	chr11	120672968	120672978	+	1	NA	promoter-TSS (NM_026877)	promoter-TSS (NM_026877)	0	NM_026877	68938	Mm.294020	NM_026877	ENSMUSG00000025142	Aspscr1	1190006K01Rik|ASPC|ASPCR1|ASPL|ASPS|RCC17|TUG	alveolar soft part sarcoma chromosome region, candidate 1 (human)	protein-coding
mm_233.1	chr1	19104132	19104138	+	1	NA	intron (NM_153154, intron 1 of 7)	intron (NM_153154, intron 1 of 7)	1113	NM_153154	226896	Mm.244858	NM_153154	ENSMUSG00000042596	Tfap2d	Tcfap2d	transcription factor AP-2, delta	protein-coding
mm_71647.1	chr8	58913697	58913704	+	1	NA	3' UTR (NM_173411, exon 3 of 3)	3' UTR (NM_173411, exon 3 of 3)	1945	NM_173411	234290	Mm.39244	NM_173411	ENSMUSG00000049946	BC030500	-	cDNA sequence BC030500	protein-coding
mm_134589.1	chr16	20426318	20426320	-	1	NA	promoter-TSS (NM_013790)	promoter-TSS (NM_013790)	75	NM_013790	27416	Mm.20845	NM_013790	ENSMUSG00000022822	Abcc5	2900011L11Rik|AI132311|Abcc5a|Abcc5b|Mrp5	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	protein-coding
mm_24128.1	chr3	88207101	88207135	+	1	NA	Intergenic	Intergenic	-8053	NR_037276	100526540		NR_037276	ENSMUSG00000092988	Mir3093	mir-3093|mmu-mir-3093	microRNA 3093	ncRNA
mm_56647.1	chr6	113377556	113377577	-	1	NA	promoter-TSS (NM_026552)	promoter-TSS (NM_026552)	-46	NM_133932	101206	Mm.266811	NM_133932	ENSMUSG00000048930	Tada3	1110004B19Rik|ADA3|AI987856|Tada3l	transcriptional adaptor 3	protein-coding
mm_161225.1	chr13	73944063	73944063	+	1	NA	intron (NM_001308041, intron 7 of 15)	intron (NM_001308041, intron 7 of 15)	6252	NM_001308041	105246	Mm.278509	NM_001024508	ENSMUSG00000057649	Brd9	AL022779	bromodomain containing 9	protein-coding
mm_165789.1	chr3	132592304	132592306	+	1	NA	Intergenic	ORR1D2|LTR|ERVL-MaLR	-37886	NM_001270430	433653		NM_001270430	ENSMUSG00000091721	Gimd1	EG433653|Gm5549	GIMAP family P-loop NTPase domain containing 1	protein-coding
mm_101663.1	chr11	36678535	36678540	-	1	NA	intron (NM_011856, intron 2 of 28)	intron (NM_011856, intron 2 of 28)	265704	NM_001290702	23964	Mm.439889	NM_011856	ENSMUSG00000049336	Tenm2	Odz2|Odz3|Ten-2|Ten-m2	teneurin transmembrane protein 2	protein-coding
mm_38911.1	chr4	149995806	149995811	-	1	NA	exon (NM_173371, exon 2 of 5)	exon (NM_173371, exon 2 of 5)	7428	NM_001291004	100198	Mm.22183	NM_173371	ENSMUSG00000028980	H6pd	AI785303|G6pd1|Gpd-1|Gpd1	hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase)	protein-coding
mm_36774.1	chr4	102572208	102572226	-	1	NA	intron (NM_019840, intron 6 of 14)	intron (NM_019840, intron 6 of 14)	2157	NM_001177980	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_171890.1	chr5	37338587	37338588	+	1	NA	exon (NM_145920, exon 1 of 20)	exon (NM_145920, exon 1 of 20)	109	NM_145920	68525	Mm.25506	NM_145920	ENSMUSG00000050248	Evc2	1110017L09Rik|Lbn|limbin	Ellis van Creveld syndrome 2	protein-coding
mm_170098.1	chr17	39843156	39843156	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	159	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_138647.1	chr17	35866856	35866877	+	1	NA	5' UTR (NM_175242, exon 1 of 3)	5' UTR (NM_175242, exon 1 of 3)	251	NM_175242	76448	Mm.359982	NM_175242	ENSMUSG00000034595	Ppp1r18	2310014H01Rik|AA407849|AI450394	protein phosphatase 1, regulatory subunit 18	protein-coding
mm_70443.1	chr8	11728041	11728068	+	1	NA	promoter-TSS (NM_001113517)	promoter-TSS (NM_001113517)	-51	NM_001113517	54126	Mm.244068	NM_017402	ENSMUSG00000031511	Arhgef7	Cool|PIX|Pak3bp|betaPix|betaPix-b|betaPix-c|cool-1|mKIAA0142|p85Cool1|p85SPR	Rho guanine nucleotide exchange factor (GEF7)	protein-coding
mm_168467.1	chr1	148378680	148378681	+	1	NA	Intergenic	Intergenic	1543759	NM_001305632	18783	Mm.4186	NM_008869	ENSMUSG00000056220	Pla2g4a	Pla2g4|cPLA2|cPLA2-alpha|cPLA2alpha	phospholipase A2, group IVA (cytosolic, calcium-dependent)	protein-coding
mm_78594.1	chr9	37401964	37401980	+	1	NA	promoter-TSS (NM_028783)	promoter-TSS (NM_028783)	75	NM_001309390	74144	Mm.485070	NM_028783	ENSMUSG00000032125	Robo4	1200012D01Rik|AI593217	roundabout guidance receptor 4	protein-coding
mm_103699.1	chr11	79516418	79516430	-	1	NA	exon (NM_001077496, exon 2 of 2)	exon (NM_001077496, exon 2 of 2)	7338	NM_001077496	216984	Mm.439665	NM_001077496	ENSMUSG00000093938	Evi2b	Evi-2|Evi2	ecotropic viral integration site 2b	protein-coding
mm_166112.1	chr4	149365783	149365790	-	1	NA	intron (NM_022022, intron 9 of 26)	intron (NM_022022, intron 9 of 26)	31147	NR_131918	74310	Mm.440455	NR_131918	ENSMUSG00000085286	Ube4bos3	1700121F15Rik	ubiquitination factor E4B, opposite strand 3	ncRNA
mm_57648.1	chr6	128438561	128438571	-	1	NA	promoter-TSS (NM_010219)	promoter-TSS (NM_010219)	65	NM_010219	14228	Mm.12758	NM_010219	ENSMUSG00000030357	Fkbp4	59kDa|AL022792|AW208983|FKBP-4|FKBP-52|FKBP52|FKPB52|p59	FK506 binding protein 4	protein-coding
mm_51158.1	chr6	70722839	70722851	+	1	NA	Intergenic	Intergenic	69330	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_62558.1	chr7	103812525	103812528	+	1	NA	TTS (NM_016956)	TTS (NM_016956)	1397	NM_016956	15130	Mm.288567	NM_016956		Hbb-b2	AI036344|Hbb2|Hbbt2|beta2	hemoglobin, beta adult minor chain	protein-coding
mm_93576.1	chr10	116729158	116729199	-	1	NA	promoter-TSS (NR_131036)	promoter-TSS (NR_131036)	-1	NR_045345	72286	Mm.396207	NR_045345	ENSMUSG00000100198	1700030O20Rik	-	RIKEN cDNA 1700030O20 gene	ncRNA
mm_170654.1	chr2	104590316	104590319	-	1	NA	promoter-TSS (NM_145529)	promoter-TSS (NM_145529)	-167	NM_177253	228410	Mm.259876	NM_145529	ENSMUSG00000027176	Cstf3	4732468G05Rik|C79532|CstF-77	cleavage stimulation factor, 3' pre-RNA, subunit 3	protein-coding
mm_29082.1	chr3	104220347	104220357	-	1	NA	promoter-TSS (NM_133853)	promoter-TSS (NM_133853)	54	NM_133853	99470	Mm.264849	NM_133853	ENSMUSG00000052539	Magi3	4732496O19Rik|6530407C02Rik|AA407180|AI120132|mKIAA1634	membrane associated guanylate kinase, WW and PDZ domain containing 3	protein-coding
mm_12976.1	chr2	90775878	90775883	+	1	NA	intron (NM_018828, intron 12 of 16)	intron (NM_018828, intron 12 of 16)	-6864	NM_178755	271813	Mm.61146	NM_178755	ENSMUSG00000040812	Agbl2	4930524K04|A430081C19Rik|CCP2	ATP/GTP binding protein-like 2	protein-coding
mm_25010.1	chr3	97901200	97901250	+	1	NA	promoter-TSS (NM_011342)	promoter-TSS (NM_011342)	-2	NM_011342	20333	Mm.2551	NM_011342	ENSMUSG00000027879	Sec22b	4930564D15Rik|AA517334|AI480645|C81333|ERS-24|Sec22l1	SEC22 homolog B, vesicle trafficking protein	protein-coding
mm_105031.1	chr11	100494187	100494204	-	1	NA	intron (NM_001199296, intron 17 of 28)	intron (NM_001199296, intron 17 of 28)	-15715	NR_130343	102465671		NR_130343	ENSMUSG00000104854	Mir7116	mmu-mir-7116	microRNA 7116	ncRNA
mm_65829.1	chr7	29179347	29179364	-	1	NA	intron (NM_026545, intron 1 of 6)	intron (NM_026545, intron 1 of 6)	1318	NM_026545	57296	Mm.273152	NM_026545	ENSMUSG00000030591	Psmd8	6720456J22Rik|AA407360|AL033291|AL033322|AL033323|C76433	proteasome (prosome, macropain) 26S subunit, non-ATPase, 8	protein-coding
mm_96684.1	chr11	69580386	69580388	+	1	NA	promoter-TSS (NM_011640)	promoter-TSS (NM_011640)	28	NM_001127233	22059	Mm.222	NM_011640	ENSMUSG00000059552	Trp53	Tp53|bbl|bfy|bhy|p44|p53	transformation related protein 53	protein-coding
mm_5672.1	chr1	42713750	42713755	-	1	NA	promoter-TSS (NR_110495)	promoter-TSS (NR_110495)	-298	NR_110495	66620	Mm.383631	NR_110495	ENSMUSG00000097063	Pantr2	2610207O16Rik|Pou3f3os2|linc-Brn1b	POU domain, class 3, transcription factor 3 adjacent noncoding transcript 2	ncRNA
mm_93443.1	chr10	109903831	109903845	-	1	NA	exon (NM_001081035, exon 2 of 39)	exon (NM_001081035, exon 2 of 39)	96381	NM_001081035	260315	Mm.225050	NM_177797	ENSMUSG00000020181	Nav3	4732483H20Rik|9630020C08Rik|POMFIL1|Pomfil1p|mKIAA0938|unc53H3	neuron navigator 3	protein-coding
mm_92387.1	chr10	76596019	76596090	-	1	NA	3' UTR (NM_146007, exon 28 of 28)	3' UTR (NM_146007, exon 28 of 28)	20406	NM_080845	14317	Mm.36278	NM_080845	ENSMUSG00000001155	Ftcd	-	formiminotransferase cyclodeaminase	protein-coding
mm_77095.1	chr8	110845026	110845030	-	1	NA	intron (NM_133953, intron 1 of 25)	intron (NM_133953, intron 1 of 25)	-1572	NM_001310607	102339	Mm.272930	NM_133973	ENSMUSG00000031753	Cog4	AW554810|D8Ertd515e	component of oligomeric golgi complex 4	protein-coding
mm_51798.1	chr6	88575989	88575989	+	1	NA	intron (NM_001278671, intron 5 of 5)	intron (NM_001278671, intron 5 of 5)	51459	NM_001278671	74589	Mm.196226	NM_029013	ENSMUSG00000033182	Kbtbd12	4833415F11Rik|4933428M03Rik|Klhdc6	kelch repeat and BTB (POZ) domain containing 12	protein-coding
mm_62440.1	chr7	101378111	101378133	+	1	NA	promoter-TSS (NM_001040112)	promoter-TSS (NM_001040112)	0	NM_001040112	69710	Mm.277687	NM_027180	ENSMUSG00000032812	Arap1	2410002L19Rik|Centd2|mKIAA0782	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	protein-coding
mm_167438.1	chr8	120041444	120041459	+	1	NA	intron (NM_030209, intron 14 of 14)	intron (NM_030209, intron 14 of 14)	49013	NM_001310635	78892	Mm.264680	NM_030209	ENSMUSG00000031825	Crispld2	1810049K24Rik|Lcrisp2|Lgl1|coffeecrisp	cysteine-rich secretory protein LCCL domain containing 2	protein-coding
mm_69513.1	chr7	134520102	134520131	-	1	NA	Intergenic	Intergenic	-143288	NM_001081331	71007	Mm.334285	NM_001081331	ENSMUSG00000030994	D7Ertd443e	4933400E14Rik|FATS|Gm497	DNA segment, Chr 7, ERATO Doi 443, expressed	protein-coding
mm_107858.1	chr12	69680867	69680877	+	1	NA	intron (NM_001135559, intron 1 of 22)	intron (NM_001135559, intron 1 of 22)	980	NM_001135559	20663	Mm.3770	NM_001135559	ENSMUSG00000034801	Sos2	SOS-2|mSOS-2	son of sevenless homolog 2 (Drosophila)	protein-coding
mm_31676.1	chr4	62281607	62281640	+	1	NA	Intergenic	Intergenic	-4806	NM_025286	20530	Mm.292539	NM_025286	ENSMUSG00000066152	Slc31a2	AI604396|CTR2	solute carrier family 31, member 2	protein-coding
mm_131085.1	chr16	4835407	4835422	+	1	NA	promoter-TSS (NM_030192)	promoter-TSS (NM_030192)	-2	NM_030192	78809	Mm.325551	NM_030192	ENSMUSG00000022518	4930562C15Rik	-	RIKEN cDNA 4930562C15 gene	protein-coding
mm_93167.1	chr10	93297834	93297839	-	1	NA	intron (NM_013508, intron 1 of 4)	intron (NM_013508, intron 1 of 4)	13323	NM_001322268	13713	Mm.4454	NM_013508	ENSMUSG00000008398	Elk3	D430049E23Rik|Erp|Etrp|Net|Sap-2	ELK3, member of ETS oncogene family	protein-coding
mm_93678.1	chr10	117746357	117746418	-	1	NA	promoter-TSS (NM_029875)	promoter-TSS (NM_029875)	-29	NM_029875	215436	Mm.256753	NM_029875	ENSMUSG00000060181	Slc35e3	9330166G04Rik|AI481200	solute carrier family 35, member E3	protein-coding
mm_86314.1	chr9	122865916	122865926	-	1	NA	promoter-TSS (NM_173364)	promoter-TSS (NM_173364)	85	NM_173364	235682	Mm.326477	NM_173364	ENSMUSG00000047036	Zfp445	AW610627|ZNF168|Znf445|mszf29|mszf50	zinc finger protein 445	protein-coding
mm_159334.1	chr3	40902496	40902496	-	1	NA	promoter-TSS (NR_045380)	promoter-TSS (NR_045380)	47	NR_045380	73297	Mm.422673	NM_028494	ENSMUSG00000074619	1700034I23Rik	-	FUN14 domain containing 2 pseudogene	pseudo
mm_81083.1	chr9	106247931	106247960	+	1	NA	promoter-TSS (NM_020559)	promoter-TSS (NM_020559)	9	NM_020559	11655	Mm.290578	NM_020559	ENSMUSG00000032786	Alas1	ALAS|ALAS-N|Alas-1|Alas-h	aminolevulinic acid synthase 1	protein-coding
mm_55738.1	chr6	77476712	77476742	-	1	NA	intron (NM_001109764, intron 8 of 19)	MLT1A0|LTR|ERVL-MaLR	-94252	NR_045141	70753	Mm.490700	NR_045141	ENSMUSG00000108077	6330415B21Rik	-	RIKEN cDNA 6330415B21 gene	ncRNA
mm_152686.1	chr19	16386110	16386122	-	1	NA	3' UTR (NM_008139, exon 7 of 7)	3' UTR (NM_008139, exon 7 of 7)	-49551	NM_008137	14675	Mm.313181	NM_008137	ENSMUSG00000024697	Gna14	AU023208	guanine nucleotide binding protein, alpha 14	protein-coding
mm_93513.1	chr10	115250507	115250517	-	1	NA	intron (NM_025706, intron 1 of 16)	intron (NM_025706, intron 1 of 16)	981	NM_025706	66687	Mm.22252	NM_025706	ENSMUSG00000020130	Tbc1d15	4432405K22Rik|AU022358|AU023730|AW557774|Ly6dl|Rab7-GAP	TBC1 domain family, member 15	protein-coding
mm_28896.1	chr3	97931721	97931746	-	1	NA	intron (NM_001033779, intron 1 of 1)	intron (NM_001033779, intron 1 of 1)	1560	NM_001033779	433632	Mm.212421	NM_001033779		Gm5544	EG433632	predicted gene 5544	protein-coding
mm_45342.1	chr5	65764412	65764422	-	1	NA	intron (NM_001024917, intron 1 of 19)	CpG	896	NM_001024917	333789	Mm.332398	NM_001024917	ENSMUSG00000037795	N4bp2	B3bp|E430014I16|Gm1791|Gm868	NEDD4 binding protein 2	protein-coding
mm_53152.1	chr6	125265559	125265585	+	1	NA	promoter-TSS (NR_015527)	promoter-TSS (NR_015527)	47	NR_015527	73870	Mm.440681	NR_015527	ENSMUSG00000108129	4930417O13Rik	-	RIKEN cDNA 4930417O13 gene	ncRNA
mm_168209.1	chr10	75034249	75034249	+	1	NA	Intergenic	Intergenic	-1663	NM_027730	71236	Mm.414817	NM_027730	ENSMUSG00000009070	Rsph14	4933431K05Rik|Rtdr1	radial spoke head homolog 14 (Chlamydomonas)	protein-coding
mm_167815.1	chr9	124273506	124273510	+	1	NA	Intergenic	RLTR30E_MM|LTR|ERV1	39186	NM_001243118	630836	Mm.458553	NM_001243117	ENSMUSG00000074829	2010315B03Rik	BC029716	RIKEN cDNA 2010315B03 gene	protein-coding
mm_99693.1	chr11	106085364	106085366	+	1	NA	intron (NM_011947, intron 1 of 15)	intron (NM_011947, intron 1 of 15)	463	NM_011947	26406	Mm.27041	NM_011947	ENSMUSG00000020700	Map3k3	AW548911|MAPKKK3|Mekk3|mKIAA4031	mitogen-activated protein kinase kinase kinase 3	protein-coding
mm_155180.1	chrX	53724837	53724844	+	1	NA	promoter-TSS (NM_029142)	promoter-TSS (NM_029142)	9	NM_029142	75013	Mm.336332	NM_029142	ENSMUSG00000055555	4930502E18Rik	Ct55	RIKEN cDNA 4930502E18 gene	protein-coding
mm_97938.1	chr11	83656076	83656089	+	1	NA	Intergenic	Intergenic	-6502	NM_013652	20303	Mm.244263	NM_013652	ENSMUSG00000018930	Ccl4	AT744.1|Act-2|MIP-1B|Mip1b|Scya4	chemokine (C-C motif) ligand 4	protein-coding
mm_147647.1	chr18	60499420	60499430	-	1	NA	intron (NM_134133, intron 1 of 1)	ORR1C2|LTR|ERVL-MaLR	2558	NM_134133	106878	Mm.273197	NM_134133	ENSMUSG00000038059	Smim3	2010002N04Rik|AI195350|AW561905|Nid67|cI-41	small integral membrane protein 3	protein-coding
mm_41063.1	chr5	86903863	86903869	+	1	NA	intron (NM_153598, intron 2 of 5)	intron (NM_153598, intron 2 of 5)	3071	NM_153598	100727	Mm.281844	NM_153598	ENSMUSG00000029260	Ugt2b34	AI788959	UDP glucuronosyltransferase 2 family, polypeptide B34	protein-coding
mm_83057.1	chr9	37545199	37545229	-	1	NA	3' UTR (NM_022029, exon 4 of 4)	3' UTR (NM_022029, exon 4 of 4)	5959	NM_020518	57276	Mm.27478	NM_020518	ENSMUSG00000001943	Vsig2	1190004B15Rik|2210413P10Rik|AU040484|CTX|Ctm	V-set and immunoglobulin domain containing 2	protein-coding
mm_130841.1	chr15	101869803	101869810	-	1	NA	promoter-TSS (NM_001003667)	promoter-TSS (NM_001003667)	-188	NM_001003667	406220	Mm.292992	NM_001003667	ENSMUSG00000067594	Krt77	4732484G22Rik|K1emb|Krt239|mK1b	keratin 77	protein-coding
mm_130265.1	chr15	96655533	96655534	-	1	NA	Intergenic	ORR1D2|LTR|ERVL-MaLR	-12620	NM_001166458	105727	Mm.103568	NM_134086	ENSMUSG00000023169	Slc38a1	AA408026|AA409865|AL022800|AU015942|NAT2	solute carrier family 38, member 1	protein-coding
mm_92264.1	chr10	71143530	71143554	-	1	NA	intron (NM_031397, intron 1 of 20)	L1M3|LINE|L1	16148	NM_031397	83675	Mm.286834	NM_031397	ENSMUSG00000014329	Bicc1	Bic-C|bpk|jcpk	BicC family RNA binding protein 1	protein-coding
mm_160111.1	chr7	25489515	25489515	-	1	NA	intron (NR_015569, intron 4 of 6)	MYSERV6-int|LTR|ERVK	-11890	NM_001039187	26365	Mm.322502	NM_011926	ENSMUSG00000074272	Ceacam1	Bgp|Bgp1|C-CAM|CD66a|Cc1|Cea-1|Cea-7|Cea1|Cea7|Hv-2|Hv2|MHVR|MHVR1|Mhv-1|bb-1|mCEA1|mmCGM1|mmCGM1a|mmCGM2	carcinoembryonic antigen-related cell adhesion molecule 1	protein-coding
mm_172598.1	chr8	15519810	15519812	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	462158	NM_008664	17930	Mm.272115	NM_008664	ENSMUSG00000031461	Myom2	AW146149	myomesin 2	protein-coding
mm_155696.1	chrX	94367148	94367165	+	1	NA	promoter-TSS (NM_026673)	promoter-TSS (NM_026673)	2	NM_001199338	68316	Mm.379156	NM_026673	ENSMUSG00000079508	Apoo	0610008C08Rik|1110019O03Rik	apolipoprotein O	protein-coding
mm_15424.1	chr2	156889521	156889540	+	1	NA	Intergenic	Intergenic	-2452	NM_029983	77799	Mm.29264	NM_029983	ENSMUSG00000027636	Sla2	A930009E21Rik|AI430952|SLAP-2|SLAP2	Src-like-adaptor 2	protein-coding
mm_65071.1	chr7	19004234	19004266	-	1	NA	5' UTR (NM_178757, exon 1 of 1)	5' UTR (NM_178757, exon 1 of 1)	185	NM_178757	272359	Mm.274237	NM_178757	ENSMUSG00000044030	Irf2bp1	6330414O09Rik|C530033F24	interferon regulatory factor 2 binding protein 1	protein-coding
mm_165052.1	chr19	41031212	41031216	-	1	NA	intron (NM_009345, intron 1 of 11)	intron (NM_009345, intron 1 of 11)	1939	NM_009345	21673	Mm.25620	NM_009345	ENSMUSG00000025014	Dntt	Tdt	deoxynucleotidyltransferase, terminal	protein-coding
mm_32021.1	chr4	95054678	95054681	+	1	NA	Intergenic	Intergenic	-2457	NM_010591	16476	Mm.275071	NM_010591	ENSMUSG00000052684	Jun	AP-1|Junc|c-jun	jun proto-oncogene	protein-coding
mm_30889.1	chr4	32252537	32252543	+	1	NA	Intergenic	Intergenic	-164895	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_45173.1	chr5	51526311	51526314	-	1	NA	intron (NR_132764, intron 2 of 12)	intron (NR_132764, intron 2 of 12)	27609	NR_027710	19017	Mm.259072	NM_008904	ENSMUSG00000029167	Ppargc1a	A830037N07Rik|ENSMUSG00000079510|Gm11133|PGC-1|PPARGC-1-alpha|Pgc-1alpha|Pgc1|Pgco1|Ppargc1	peroxisome proliferative activated receptor, gamma, coactivator 1 alpha	protein-coding
mm_61068.1	chr7	51510981	51510987	+	1	NA	promoter-TSS (NM_177694)	promoter-TSS (NM_177694)	-45	NR_073508	233246	Mm.254431	NM_177694	ENSMUSG00000055489	Ano5	9330162L24|Gdd1|Tmem16e	anoctamin 5	protein-coding
mm_76183.1	chr8	82402425	82402441	-	1	NA	5' UTR (NM_001254747, exon 1 of 8)	5' UTR (NM_001254747, exon 1 of 8)	153	NM_001254747	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_129636.1	chr15	80239891	80239901	-	1	NA	intron (NM_178719, intron 2 of 5)	intron (NM_178719, intron 2 of 5)	5816	NM_178719	239555	Mm.307163	NM_178719	ENSMUSG00000022412	Mief1	A230016E22|AI452372|Smcr7l	mitochondrial elongation factor 1	protein-coding
mm_424.1	chr1	34447032	34447041	+	1	NA	Intergenic	L1_Rod|LINE|L1	7207	NM_178601	27993	Mm.289667	NM_178601	ENSMUSG00000026127	Imp4	AA409888|AV031295|D1Wsu40e	IMP4, U3 small nucleolar ribonucleoprotein	protein-coding
mm_34814.1	chr4	154937151	154937168	+	1	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	-9082	NM_178931	230979	Mm.215147	NM_178931	ENSMUSG00000042333	Tnfrsf14	Atar|HveA|Hvem|Tnfrs14	tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)	protein-coding
mm_117184.1	chr13	63533585	63533605	-	1	NA	exon (NM_008957, exon 14 of 24)	exon (NM_008957, exon 14 of 24)	32140	NM_008957	19206	Mm.228798	NM_008957	ENSMUSG00000021466	Ptch1	A230106A15Rik|Ptc|Ptc1|Ptch|mes	patched 1	protein-coding
mm_98058.1	chr11	85830950	85830961	+	1	NA	intron (NR_077059, intron 1 of 4)	intron (NR_077059, intron 1 of 4)	1433	NR_077059	69909	Mm.440214	NR_077059	ENSMUSG00000087013	2610027K06Rik	-	RIKEN cDNA 2610027K06 gene	ncRNA
mm_139948.1	chr17	71204634	71204641	+	1	NA	promoter-TSS (NM_001164885)	promoter-TSS (NM_001164885)	-17	NM_001164885	64898	Mm.227924	NM_022882	ENSMUSG00000024052	Lpin2	2610511G02Rik|AI481352|AW742896	lipin 2	protein-coding
mm_82459.1	chr9	15627911	15627922	-	1	NA	promoter-TSS (NM_181816)	promoter-TSS (NM_181816)	17	NM_181816	234964	Mm.32237	NM_181816	ENSMUSG00000039977	Ccdc67	4933401K09Rik|Deup1	coiled-coil domain containing 67	protein-coding
mm_163307.1	chr12	4459595	4459618	+	1	NA	intron (NM_010881, intron 1 of 22)	intron (NM_010881, intron 1 of 22)	17576	NM_010881	17977	Mm.301039	NM_010881	ENSMUSG00000020647	Ncoa1	KAT13A|NCoA-1|NRC-1|SRC-1|SRC-a|SRC1|bHLHe74|mNRC-1	nuclear receptor coactivator 1	protein-coding
mm_171506.1	chr4	146270400	146270401	+	1	NA	promoter-TSS (NM_001083918).2	promoter-TSS (NM_001083918).2	15	NM_001083918	666532	Mm.392861	NM_001083918	ENSMUSG00000067916	Zfp991	Gm13139|OTTMUSG00000010657	zinc finger protein 991	protein-coding
mm_159826.1	chr5	124124702	124124702	-	1	NA	intron (NM_011256, intron 17 of 24)	intron (NM_011256, intron 17 of 24)	8594	NM_144509	65105	Mm.29430	NM_144509	ENSMUSG00000029404	Arl6ip4	AA408210|AA408365|Aip-4|Srp25	ADP-ribosylation factor-like 6 interacting protein 4	protein-coding
mm_143290.1	chr17	65884746	65884754	-	1	NA	5' UTR (NM_001198949, exon 1 of 10)	5' UTR (NM_001198949, exon 1 of 10)	173	NM_001198949	19765	Mm.17009	NM_009067	ENSMUSG00000024096	Ralbp1	RLIP76|Rip1	ralA binding protein 1	protein-coding
mm_165663.1	chr3	88282038	88282044	+	1	NA	TTS (NM_029801)	TTS (NM_029801)	14797	NM_029801	76927	Mm.273330	NM_029801	ENSMUSG00000010538	Tsacc	1700021C14Rik|SIP	TSSK6 activating co-chaperone	protein-coding
mm_10361.1	chr2	11705356	11705375	+	1	NA	promoter-TSS (NM_001271498)	promoter-TSS (NM_001271498)	72	NM_001271497	16169	Mm.200196	NM_008358	ENSMUSG00000023206	Il15ra	AA690181|IL-15RA	interleukin 15 receptor, alpha chain	protein-coding
mm_73494.1	chr8	107096919	107096935	+	1	NA	promoter-TSS (NM_001286200)	promoter-TSS (NM_001286200)	-382	NR_104410	21750	Mm.6402	NM_009353	ENSMUSG00000031921	Terf2	TRF2	telomeric repeat binding factor 2	protein-coding
mm_125863.1	chr15	75268380	75268402	+	1	NA	promoter-TSS (NM_008530)	promoter-TSS (NM_008530)	-30	NM_008530	17071	Mm.377095	NM_008530	ENSMUSG00000022583	Ly6f	-	lymphocyte antigen 6 complex, locus F	protein-coding
mm_164822.1	chr18	35572382	35572391	+	1	NA	exon (NM_010771, exon 2 of 15)	exon (NM_010771, exon 2 of 15)	10228	NM_010771	17184	Mm.215034	NM_010771	ENSMUSG00000037236	Matr3	1110061A14Rik|2810017I02Rik|AI841759|AW555618|D030046F20Rik|mKIAA0723	matrin 3	protein-coding
mm_14038.1	chr2	122161543	122161559	+	1	NA	intron (NM_080510, intron 1 of 6)	intron (NM_080510, intron 1 of 6)	851	NM_080510	70928	Mm.379188	NM_080510	ENSMUSG00000033368	Trim69	4921519C19Rik|Rnf36|Trif|Trimless	tripartite motif-containing 69	protein-coding
mm_101313.1	chr11	22800033	22800042	-	1	NA	Intergenic	Intergenic	59698	NM_016888	53625	Mm.395495	NM_016888	ENSMUSG00000051650	B3gnt2	AA408337|AA409404|AW260308|B3Galt6|B3gnt1|BGnT-1|BGnT-2|BGnT1|BGnT2|Beta3gnt	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 2	protein-coding
mm_40686.1	chr5	65763519	65763541	+	1	NA	promoter-TSS (NM_001024917)	promoter-TSS (NM_001024917)	9	NM_001024917	333789	Mm.332398	NM_001024917	ENSMUSG00000037795	N4bp2	B3bp|E430014I16|Gm1791|Gm868	NEDD4 binding protein 2	protein-coding
mm_108456.1	chr12	82707055	82707065	+	1	NA	intron (NM_001310478, intron 2 of 17)	L1MCb|LINE|L1	89561	NM_001282061	50779	Mm.126176	NM_015812	ENSMUSG00000021219	Rgs6	-	regulator of G-protein signaling 6	protein-coding
mm_159671.1	chr4	154856087	154856087	+	1	NA	promoter-TSS (NM_172878)	promoter-TSS (NM_172878)	-113	NM_172878	242800	Mm.72944	NM_172878	ENSMUSG00000046637	Ttc34	4932418L02|B230396O12Rik	tetratricopeptide repeat domain 34	protein-coding
mm_107427.1	chr12	35579306	35579310	+	1	NA	Intergenic	Intergenic	-44319	NM_001314027	11622	Mm.341377	NM_013464	ENSMUSG00000019256	Ahr	Ah|Ahh|Ahre|In|bHLHe76	aryl-hydrocarbon receptor	protein-coding
mm_50336.1	chr6	48504331	48504406	+	1	NA	promoter-TSS (NR_027808)	promoter-TSS (NR_027808)	29	NR_027808	58894	Mm.31983	NR_015597	ENSMUSG00000107476	Zfp862-ps	4732460K03Rik|AI448302|Zfp862|mKIAA0543	zinc finger protein 862, pseudogene	pseudo
mm_172781.1	chr8	98224815	98224825	-	1	NA	Intergenic	Intergenic	-787067	NR_110579	100873092	Mm.414599	NR_110579	ENSMUSG00000089819	Gm15679	OTTMUSG00000025218	predicted gene 15679	ncRNA
mm_151278.1	chr19	55253694	55253726	+	1	NA	5' UTR (NM_027976, exon 1 of 22)	5' UTR (NM_027976, exon 1 of 22)	341	NM_027976	433256	Mm.292056	NM_027976	ENSMUSG00000024981	Acsl5	1700030F05Rik|ACS2|ACS5|Facl5	acyl-CoA synthetase long-chain family member 5	protein-coding
mm_25447.1	chr3	108284104	108284142	+	1	NA	promoter-TSS (NM_019972)	promoter-TSS (NM_019972)	59	NM_019972	20661	Mm.157119	NM_019972	ENSMUSG00000068747	Sort1	2900053A11Rik|AI852375|Ntr3|Ntsr3	sortilin 1	protein-coding
mm_52438.1	chr6	113616215	113616226	+	1	NA	3' UTR (NM_133937, exon 3 of 3)	3' UTR (NM_133937, exon 3 of 3)	-7801	NM_009507	22346	Mm.29407	NM_009507	ENSMUSG00000033933	Vhl	Vhlh	von Hippel-Lindau tumor suppressor	protein-coding
mm_86405.1	chr9	123986686	123986688	-	1	NA	Intergenic	Intergenic	-8279	NM_007718	12770	Mm.423532	NM_007718	ENSMUSG00000064039	Ccr1l1	Cmkbr1l1	chemokine (C-C motif) receptor 1-like 1	protein-coding
mm_47079.1	chr5	117004703	117004713	-	1	NA	Intergenic	Intergenic	111285	NM_001122666	71954	Mm.34456	NM_178622	ENSMUSG00000066900	Suds3	2400003N08Rik|2410008L21Rik|AU067672|mSds3	suppressor of defective silencing 3 homolog (S. cerevisiae)	protein-coding
mm_28626.1	chr3	95133937	95133988	-	1	NA	promoter-TSS (NM_001163573)	promoter-TSS (NM_001163573)	50	NM_027013	69269	Mm.182944	NM_027013	ENSMUSG00000092607	Scnm1	3110001I17Rik|Scnm1-ps	sodium channel modifier 1	protein-coding
mm_116456.1	chr13	43292508	43292513	-	1	NA	intron (NM_001033399, intron 1 of 1)	intron (NM_001033399, intron 1 of 1)	11662	NM_001033399	328232	Mm.441399	NM_001033399	ENSMUSG00000051335	Gfod1	9630032O13|AI850995	glucose-fructose oxidoreductase domain containing 1	protein-coding
mm_21048.1	chr2	152580301	152580315	-	1	NA	promoter-TSS (NM_145157)	promoter-TSS (NM_145157)	4	NM_145157	246700	Mm.82820	NM_145157	ENSMUSG00000050645	Defb19	BD-19|Defb24|Tdl|mBD-19	defensin beta 19	protein-coding
mm_148145.1	chr18	77065039	77065069	-	1	NA	promoter-TSS (NM_001164168)	promoter-TSS (NM_001164168)	-154	NM_008602	17344	Mm.6370	NM_008602	ENSMUSG00000025423	Pias2	6330408K17Rik|AI462206|ARIP3|AU018068|Dib|Miz1|PIASxalpha|PIASxb|PIASxbeta|SIZ2	protein inhibitor of activated STAT 2	protein-coding
mm_69216.1	chr7	127512837	127512869	-	1	NA	promoter-TSS (NR_024331)	promoter-TSS (NR_024331)	16	NR_024331	629159	Mm.256720	NR_024331	ENSMUSG00000101225	1700008J07Rik	AW048743	RIKEN cDNA 1700008J07 gene	ncRNA
mm_156570.1	chrX	151910161	151910174	+	1	NA	exon (NM_021523, exon 58 of 83)	exon (NM_021523, exon 58 of 83)	-2179	NR_029732	387253		NR_029732	ENSMUSG00000065602	Mirlet7f-2	Mirlet7f2|Mirnlet7f2|let-7f-2	microRNA let7f-2	ncRNA
mm_37583.1	chr4	126325712	126325715	-	1	NA	promoter-TSS (NM_011902)	promoter-TSS (NM_011902)	-514	NM_011902	24084	Mm.23895	NM_011902	ENSMUSG00000028845	Tekt2	AU014974|tektin-t	tektin 2	protein-coding
mm_100821.1	chr11	5261531	5261543	-	1	NA	promoter-TSS (NM_032396)	promoter-TSS (NM_032396)	73	NM_032396	84035	Mm.209989	NM_032396	ENSMUSG00000020393	Kremen1	AV002070|Kremen|Krm1	kringle containing transmembrane protein 1	protein-coding
mm_75142.1	chr8	35430747	35430764	-	1	NA	Intergenic	Intergenic	55014	NM_177741	244416	Mm.247126	NM_177741	ENSMUSG00000046794	Ppp1r3b	6430576E21|AW821953|GL|PTG	protein phosphatase 1, regulatory (inhibitor) subunit 3B	protein-coding
mm_116692.1	chr13	49320200	49320218	-	1	NA	Intergenic	Intergenic	-11001	NM_015759	30938	Mm.291089	NM_015759	ENSMUSG00000037946	Fgd3	5830461L01Rik|ZFYVE5	FYVE, RhoGEF and PH domain containing 3	protein-coding
mm_75677.1	chr8	67974540	67974548	-	1	NA	promoter-TSS (NM_177698)	promoter-TSS (NM_177698)	30	NM_177698	234353	Mm.32525	NM_027626	ENSMUSG00000030465	Psd3	4931420C21Rik|AI661273|BC003498|D430018P08|EFA6D	pleckstrin and Sec7 domain containing 3	protein-coding
mm_61036.1	chr7	49609713	49609731	+	1	NA	3' UTR (NM_001111016, exon 39 of 39)	3' UTR (NM_001111016, exon 39 of 39)	27113	NM_001005232	13172	Mm.307176	NM_001005232	ENSMUSG00000030507	Dbx1	AI426026|Dbx	developing brain homeobox 1	protein-coding
mm_149045.1	chr19	8822856	8822870	+	1	NA	exon (NM_001081196, exon 2 of 14)	exon (NM_001081196, exon 2 of 14)	3462	NM_001081196	68693	Mm.476519	NM_001081196	ENSMUSG00000071659	Hnrnpul2	1110031M08Rik|AI465155|Hnrpul2	heterogeneous nuclear ribonucleoprotein U-like 2	protein-coding
mm_27608.1	chr3	59195096	59195110	-	1	NA	promoter-TSS (NM_001302203)	promoter-TSS (NM_001302203)	1	NM_001302203	84111	Mm.60267	NM_032399	ENSMUSG00000051431	Gpr87	-	G protein-coupled receptor 87	protein-coding
mm_87743.1	chr10	60266922	60266932	+	1	NA	Intergenic	Intergenic	-10701	NM_001146123	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_100536.1	chr11	120632682	120632714	+	1	NA	intron (NM_010756, intron 1 of 2)	CpG	849	NM_010756	17134	Mm.268010	NM_010756	ENSMUSG00000051510	Mafg	AA545192|C630022N07Rik	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein G (avian)	protein-coding
mm_167830.1	chr9	124424058	124424070	-	1	NA	non-coding (NR_015516, exon 1 of 1)	non-coding (NR_015516, exon 1 of 1)	277	NR_015516	75135	Mm.476814	NR_015516		4930526I15Rik	1600027J15Rik	RIKEN cDNA 4930526I15 gene	ncRNA
mm_65549.1	chr7	27131261	27131287	-	1	NA	exon (NM_007817, exon 8 of 10)	exon (NM_007817, exon 8 of 10)	11319	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_157774.1	chrX	73780106	73780126	-	1	NA	exon (NM_008323, exon 10 of 13)	exon (NM_008323, exon 10 of 13)	5711	NM_019684	56504	Mm.111904	NM_019684	ENSMUSG00000002007	Srpk3	Mssk1|Stk23	serine/arginine-rich protein specific kinase 3	protein-coding
mm_135173.1	chr16	35938886	35938908	-	1	NA	5' UTR (NM_030253, exon 1 of 11)	5' UTR (NM_030253, exon 1 of 11)	130	NM_001013371	209200	Mm.390852	NM_001013371	ENSMUSG00000049502	Dtx3l	AU042200|BC023741	deltex 3-like, E3 ubiquitin ligase	protein-coding
mm_5344.1	chr1	24613117	24613119	-	1	NA	Intergenic	Intergenic	-25681	NM_007733	12823	Mm.329196	NM_007733	ENSMUSG00000026141	Col19a1	-	collagen, type XIX, alpha 1	protein-coding
mm_145806.1	chr18	65386026	65386043	+	1	NA	intron (NM_001037294, intron 1 of 12)	ID4_|SINE|ID	7854	NM_001037294	225638	Mm.296528	NM_001037294	ENSMUSG00000032845	Alpk2	Gm549|Hak	alpha-kinase 2	protein-coding
mm_54944.1	chr6	48572767	48572777	-	1	NA	promoter-TSS (NM_001347168)	promoter-TSS (NM_001347168)	30	NM_001347168	71660	Mm.28231	NM_027852	ENSMUSG00000009281	Rarres2	0610007L05Rik|AI303516	retinoic acid receptor responder (tazarotene induced) 2	protein-coding
mm_84252.1	chr9	62476603	62476606	-	1	NA	intron (NM_175484, intron 2 of 11)	intron (NM_175484, intron 2 of 11)	60440	NM_175484	235431	Mm.335229	NM_175484	ENSMUSG00000041729	Coro2b	CLIPINC|E130012P22Rik	coronin, actin binding protein, 2B	protein-coding
mm_98107.1	chr11	86872875	86872885	+	1	NA	intron (NR_106195, intron 4 of 8)	intron (NR_106195, intron 4 of 8)	-65220	NM_026191	67487	Mm.260627	NM_026191	ENSMUSG00000018425	Dhx40	2410016C14Rik|ARG147|DDX40|PAD	DEAH (Asp-Glu-Ala-His) box polypeptide 40	protein-coding
mm_41612.1	chr5	96793414	96793424	+	1	NA	promoter-TSS (NM_013470)	promoter-TSS (NM_013470)	34	NM_013470	11745	Mm.7214	NM_013470	ENSMUSG00000029484	Anxa3	Anx3	annexin A3	protein-coding
mm_158012.1	chrX	95658380	95658390	-	1	NA	5' UTR (NM_001003916, exon 1 of 5)	5' UTR (NM_001003916, exon 1 of 5)	124	NM_001289696	245522	Mm.336158	NM_001003916	ENSMUSG00000035062	Zc4h2	Gm372|mKIAA1166	zinc finger, C4H2 domain containing	protein-coding
mm_147350.1	chr18	43328664	43328667	-	1	NA	intron (NM_009468, intron 11 of 13)	intron (NM_009468, intron 11 of 13)	44607	NM_001136086	22240	Mm.8180	NM_009468	ENSMUSG00000024501	Dpysl3	CRMP-4|DRP-3|TUC4|ULIP-1|Ulip|Ulip1	dihydropyrimidinase-like 3	protein-coding
mm_44743.1	chr5	31193106	31193134	-	1	NA	promoter-TSS (NM_001127356)	promoter-TSS (NM_001127356)	19	NM_001127355	13667	Mm.29394	NM_010122	ENSMUSG00000029145	Eif2b4	Eif2b	eukaryotic translation initiation factor 2B, subunit 4 delta	protein-coding
mm_170975.1	chr2	67707802	67707817	-	1	NA	Intergenic	Intergenic	32352	NR_106083	102465706		NR_106083	ENSMUSG00000098299	Mir7224	Gm27971|mmu-mir-7224	microRNA 7224	ncRNA
mm_32850.1	chr4	117977596	117977606	+	1	NA	intron (NM_009176, intron 5 of 11)	intron (NM_009176, intron 5 of 11)	-47838	NM_001284192	11876	Mm.56897	NM_009711	ENSMUSG00000028539	Artn	neublastin	artemin	protein-coding
mm_147074.1	chr18	35498817	35498829	-	1	NA	5' UTR (NM_030749, exon 1 of 10)	5' UTR (NM_030749, exon 1 of 10)	102	NM_030749	81500	Mm.291482	NM_030749	ENSMUSG00000024357	Sil1	1810057E01Rik|AI042831|wz	endoplasmic reticulum chaperone SIL1 homolog (S. cerevisiae)	protein-coding
mm_151793.1	chr19	5402494	5402528	-	1	NA	Intergenic	Intergenic	-4304	NR_015545	74931	Mm.388511	NR_015545	ENSMUSG00000086938	4930481A15Rik	-	RIKEN cDNA 4930481A15 gene	ncRNA
mm_170281.1	chr18	27599263	27599267	+	1	NA	Intergenic	(TGG)n|Simple_repeat|Simple_repeat	-960899	NR_045398	320624	Mm.50107	NR_045398		4930474G06Rik	-	RIKEN cDNA 4930474G06 gene	ncRNA
mm_114902.1	chr13	94731889	94731931	+	1	NA	Intergenic	Intergenic	-57033	NM_009321	21371	Mm.379025	NM_009321	ENSMUSG00000042043	Tbca	Tbca13	tubulin cofactor A	protein-coding
mm_32912.1	chr4	119133185	119133220	+	1	NA	exon (NM_011400, exon 5 of 10)	exon (NM_011400, exon 5 of 10)	24457	NM_011400	20525	Mm.21002	NM_011400	ENSMUSG00000028645	Slc2a1	Glut-1|Glut1	solute carrier family 2 (facilitated glucose transporter), member 1	protein-coding
mm_136686.1	chr17	6816587	6816606	+	1	NA	Intergenic	Intergenic	-33816	NM_009510	22350	Mm.277812	NM_009510	ENSMUSG00000052397	Ezr	AW146364|R75297|Vil2|p81	ezrin	protein-coding
mm_58605.1	chr7	5051604	5051632	+	1	NA	promoter-TSS (NM_026900)	promoter-TSS (NM_026900)	86	NM_026900	68992	Mm.41484	NM_026900	ENSMUSG00000055633	Zfp580	1500015O20Rik|AI838225|Znf580	zinc finger protein 580	protein-coding
mm_143602.1	chr17	76886869	76886873	-	1	NA	Intergenic	L1_Mus3|LINE|L1	1025848	NR_033456	100043885	Mm.127562	NR_033456		Gm4710	-	predicted gene 4710	ncRNA
mm_108574.1	chr12	84996310	84996419	+	1	NA	promoter-TSS (NM_001347421)	promoter-TSS (NM_001347421)	43	NM_178363	56531	Mm.153183	NM_178363	ENSMUSG00000021244	Ylpm1	A930013E17Rik|ZAP|Zap3	YLP motif containing 1	protein-coding
mm_61385.1	chr7	72672778	72672792	+	1	NA	Intergenic	Intergenic	-366190	NM_001024703	244049	Mm.217412	NM_001024703	ENSMUSG00000032776	Mctp2	Gm489	multiple C2 domains, transmembrane 2	protein-coding
mm_26079.1	chr3	136670587	136670602	+	1	NA	5' UTR (NM_001293622, exon 1 of 13)	5' UTR (NM_001293622, exon 1 of 13)	528	NM_001293622	19055	Mm.331389	NM_008913	ENSMUSG00000028161	Ppp3ca	2900074D19Rik|CN|Caln|Calna|CnA	protein phosphatase 3, catalytic subunit, alpha isoform	protein-coding
mm_68078.1	chr7	101869350	101869358	-	1	NA	intron (NM_001252553, intron 1 of 6)	intron (NM_001252553, intron 1 of 6)	1434	NM_001252554	14275	Mm.2135	NM_008034	ENSMUSG00000001827	Folr1	FBP1|Folbp-1|Folbp1	folate receptor 1 (adult)	protein-coding
mm_25954.1	chr3	132085451	132085455	+	1	NA	5' UTR (NM_020265, exon 1 of 4)	5' UTR (NM_020265, exon 1 of 4)	161	NM_020265	56811	Mm.103593	NM_020265	ENSMUSG00000028031	Dkk2	-	dickkopf WNT signaling pathway inhibitor 2	protein-coding
mm_102132.1	chr11	53430498	53430507	-	1	NA	intron (NM_001326614, intron 2 of 2)	CpG	329	NM_025352	22272	Mm.251621	NM_025352	ENSMUSG00000044894	Uqcrq	1100001F06Rik|1500040F11Rik|5830407L17Rik|9.5kDa|AA959903|QP-C|Qpc|Uqcrb|c1502	ubiquinol-cytochrome c reductase, complex III subunit VII	protein-coding
mm_92967.1	chr10	86102162	86102166	-	1	NA	intron (NR_038024, intron 1 of 2)	intron (NR_038024, intron 1 of 2)	6310	NR_038024	78170	Mm.444790	NR_038024		4930486F22Rik	-	RIKEN cDNA 4930486F22 gene	ncRNA
mm_65055.1	chr7	18735138	18735140	-	1	NA	Intergenic	RMER2|LTR|ERV1	17049	NM_001004152	243862	Mm.389833	NM_001004152	ENSMUSG00000044903	Psg22	AA408604|cea9	pregnancy-specific glycoprotein 22	protein-coding
mm_132879.1	chr16	48786650	48786678	+	1	NA	Intergenic	Intergenic	-14708	NM_198297	77647	Mm.167298	NM_198297	ENSMUSG00000030775	Trat1	C030046M14Rik|Tcrim|Trim	T cell receptor associated transmembrane adaptor 1	protein-coding
mm_989.1	chr1	58586592	58586625	+	1	NA	promoter-TSS (NM_172513)	promoter-TSS (NM_172513)	211	NM_025597	66495	Mm.2033	NM_025597	ENSMUSG00000026032	Ndufb3	2700033I16Rik|CI-B12	NADH dehydrogenase (ubiquinone) 1 beta subcomplex 3	protein-coding
mm_140958.1	chr17	24632609	24632632	-	1	NA	promoter-TSS (NM_008743)	promoter-TSS (NM_008743)	7	NM_011647	22084	Mm.30435	NM_011647	ENSMUSG00000002496	Tsc2	Nafld|Tcs2	tuberous sclerosis 2	protein-coding
mm_3456.1	chr1	150103861	150103903	+	1	NA	exon (NM_011198, exon 7 of 10)	exon (NM_011198, exon 7 of 10)	3851	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_149296.1	chr19	10689257	10689279	+	1	NA	intron (NM_181403, intron 1 of 4)	intron (NM_181403, intron 1 of 4)	453	NM_181403	107305	Mm.19091	NM_181403	ENSMUSG00000048832	Vps37c	5730409F24Rik|AU042646	vacuolar protein sorting 37C	protein-coding
mm_54413.1	chr6	32588216	32588238	-	1	NA	promoter-TSS (NM_175750)	promoter-TSS (NM_175750)	-35	NM_175750	243743	Mm.444029	NM_175750	ENSMUSG00000029765	Plxna4	9330117B14|Plxa4|mKIAA1550	plexin A4	protein-coding
mm_12709.1	chr2	76675323	76675349	+	1	NA	promoter-TSS (NM_031256)	promoter-TSS (NM_031256)	21	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_126173.1	chr15	78564909	78564968	+	1	NA	exon (NM_009008, exon 5 of 7)	exon (NM_009008, exon 5 of 7)	7845	NM_009008	19354	Mm.1972	NM_009008	ENSMUSG00000033220	Rac2	AI323801|AI452260	RAS-related C3 botulinum substrate 2	protein-coding
mm_111421.1	chr12	91589700	91589702	-	1	NA	promoter-TSS (NM_031391)	promoter-TSS (NM_031391)	-52	NM_031391	83602	Mm.275728	NM_031391	ENSMUSG00000020962	Gtf2a1	6330549H03Rik|AA536742|AA959775|AW060250|TfIIAa/b|Tfiia1	general transcription factor II A, 1	protein-coding
mm_79080.1	chr9	46242390	46242442	+	1	NA	exon (NM_007468, exon 3 of 3)	exon (NM_007468, exon 3 of 3)	1572	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_67468.1	chr7	80417763	80417782	-	1	NA	Intergenic	Intergenic	-12336	NM_001081454	18550	Mm.5241	NM_011046	ENSMUSG00000030530	Furin	9130404I01Rik|Fur|PACE|Pcsk3|SPC1	furin (paired basic amino acid cleaving enzyme)	protein-coding
mm_20828.1	chr2	146511993	146512015	-	1	NA	promoter-TSS (NM_001033348)	promoter-TSS (NM_001033348)	0	NM_001033348	241694	Mm.222310	NM_001033348	ENSMUSG00000037110	Ralgapa2	A230067G21Rik|AS250|BC053994|RGC2|pp250	Ral GTPase activating protein, alpha subunit 2 (catalytic)	protein-coding
mm_120083.1	chr14	57798157	57798180	+	1	NA	promoter-TSS (NM_001142441)	promoter-TSS (NM_001142441)	-21	NM_009119	20220	Mm.30173	NM_009119	ENSMUSG00000021963	Sap18	C530046K05Rik|D11Ertd539e|EMegR4|Sap18a|Sinbp1	Sin3-associated polypeptide 18	protein-coding
mm_8652.1	chr1	156446582	156446607	-	1	NA	exon (NM_009230, exon 4 of 16)	exon (NM_009230, exon 4 of 16)	-25679	NM_001346967	77352	Mm.428709	NM_001033180	ENSMUSG00000026601	Axdnd1	9430070O13Rik|Gm979	axonemal dynein light chain domain containing 1	protein-coding
mm_83520.1	chr9	46229995	46230003	-	1	NA	exon (NM_009692, exon 4 of 4)	exon (NM_009692, exon 4 of 4)	1369	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2|apo-AI|apoA-I	apolipoprotein A-I	protein-coding
mm_17766.1	chr2	32788733	32788767	-	1	NA	3' UTR (NM_001113569, exon 20 of 20)	3' UTR (NM_001113569, exon 20 of 20)	-4345	NM_025619	227736	Mm.441499	NM_025619	ENSMUSG00000038987	Cfap157	1700019L03Rik	cilia and flagella associated protein 157	protein-coding
mm_93644.1	chr10	117350883	117350887	-	1	NA	intron (NM_001310609, intron 9 of 9)	intron (NM_001310609, intron 9 of 9)	26088	NM_001013391	432508	Mm.478881	NM_001013391	ENSMUSG00000055531	Cpsf6	4733401N12Rik|AI256641|CFIM|CFIM68|HPBRII-4|HPBRII-7	cleavage and polyadenylation specific factor 6	protein-coding
mm_24556.1	chr3	93443539	93443549	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	1214	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_42190.1	chr5	112269498	112269506	+	1	NA	TTS (NM_001312894)	TTS (NM_001312894)	-7189	NM_001326590	22022	Mm.250631	NM_009419	ENSMUSG00000029344	Tpst2	AI448750|D5Ucla3|Tango13b|grm|grt	protein-tyrosine sulfotransferase 2	protein-coding
mm_70428.1	chr8	11519236	11519238	+	1	NA	intron (NM_024248, intron 9 of 14)	intron (NM_024248, intron 9 of 14)	21669	NM_026995	69225	Mm.64911	NM_026995	ENSMUSG00000031505	Naxd	0710008K08Rik|2810407E01Rik|Carkd	NAD(P)HX dehydratase	protein-coding
mm_124416.1	chr14	118051997	118051999	-	1	NA	5' UTR (NM_010024, exon 1 of 8)	5' UTR (NM_010024, exon 1 of 8)	248	NM_010024	13190	Mm.19987	NM_010024	ENSMUSG00000022129	Dct	DT|TRP-2|TRP2|Tyrp-2|Tyrp2|slaty|slt	dopachrome tautomerase	protein-coding
mm_126392.1	chr15	80192163	80192182	+	1	NA	intron (NM_010795, intron 1 of 1)	intron (NM_010795, intron 1 of 1)	18451	NM_010795	17309	Mm.299693	NM_010795	ENSMUSG00000042428	Mgat3	1110038J12Rik|AI848272|GnT-III	mannoside acetylglucosaminyltransferase 3	protein-coding
mm_62031.1	chr7	91711664	91711687	+	1	NA	intron (NM_011807, intron 2 of 22)	intron (NM_011807, intron 2 of 22)	-350719	NM_001243046	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_71194.1	chr8	40877812	40877822	+	1	NA	intron (NM_007514, intron 1 of 11)	MLTR11A|LTR|ERVK	15450	NM_001044740	11988	Mm.4676	NM_007514	ENSMUSG00000031596	Slc7a2	20.5|AI158848|Atrc2|CAT-2|Cat2|Tea	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	protein-coding
mm_63076.1	chr7	122219632	122219638	+	1	NA	5' UTR (NM_027363, exon 1 of 7)	5' UTR (NM_027363, exon 1 of 7)	139	NM_027363	70261	Mm.96997	NM_027363	ENSMUSG00000030865	Chp2	2010110P09Rik|Cbhp2	calcineurin-like EF hand protein 2	protein-coding
mm_39842.1	chr5	30889152	30889192	+	1	NA	promoter-TSS (NM_001294262)	promoter-TSS (NM_001294262)	-162	NM_001294262	231093	Mm.440364	NM_174849	ENSMUSG00000029165	Agbl5	9430057O19Rik|CCP5	ATP/GTP binding protein-like 5	protein-coding
mm_66739.1	chr7	46672512	46672524	-	1	NA	promoter-TSS (NM_009414)	promoter-TSS (NM_009414)	19	NM_009414	21990	Mm.248684	NM_009414	ENSMUSG00000040046	Tph1	Tph	tryptophan hydroxylase 1	protein-coding
mm_144394.1	chr18	20673699	20673721	+	1	NA	exon (NM_013697, exon 4 of 4)	exon (NM_013697, exon 4 of 4)	8460	NM_013697	22139	Mm.2108	NM_013697	ENSMUSG00000061808	Ttr	AA408768|AI787086|D17860|prealbumin	transthyretin	protein-coding
mm_26407.1	chr3	142606967	142606975	+	1	NA	exon (NM_010259, exon 7 of 11)	exon (NM_010259, exon 7 of 11)	12124	NM_010259	14468	Mm.457978	NM_010259	ENSMUSG00000040264	Gbp2b	Gbp-1|Gbp1|Mag-1|Mpa-1|Mpa1	guanylate binding protein 2b	protein-coding
mm_147702.1	chr18	60810002	60810024	-	1	NA	exon (NM_010545, exon 5 of 8)	exon (NM_010545, exon 5 of 8)	-2063	NR_039567	100628611		NR_039567	ENSMUSG00000093327	Mir5107	mir-5107|mmu-mir-5107|mu-mir-5107	microRNA 5107	ncRNA
mm_158997.1	chr1	139781230	139781230	-	1	NA	promoter-TSS (NM_001160304)	promoter-TSS (NM_001160304)	9	NM_001029977	214403	Mm.337613	NM_001029977	ENSMUSG00000070594	Gm4788	Cfhrc|EG214403	predicted gene 4788	protein-coding
mm_148603.1	chr19	5298365	5298367	+	1	NA	promoter-TSS (NM_001024717)	promoter-TSS (NM_001024717)	35	NM_001024717	545276	Mm.447174	NM_001024717	ENSMUSG00000047658	Gal3st3	-	galactose-3-O-sulfotransferase 3	protein-coding
mm_152380.1	chr19	10240690	10240751	-	1	NA	promoter-TSS (NM_001033481)	promoter-TSS (NM_001033481)	28	NM_001033481	225908	Mm.329716	NM_001033481	ENSMUSG00000036098	Myrf	6030439E18|Gm1804|Gm98|Mrf	myelin regulatory factor	protein-coding
mm_50919.1	chr6	57605404	57605416	+	1	NA	intron (NM_025992, intron 6 of 22)	Lx8b|LINE|L1	24418	NM_025992	67138	Mm.297393	NM_025992	ENSMUSG00000029798	Herc6	1700121D12Rik|2510038N07Rik|4930427L17Rik|AI451296|CEB1|Herc5	hect domain and RLD 6	protein-coding
mm_94789.1	chr11	22621326	22621342	+	1	NA	Intergenic	RLTR11A|LTR|ERVK	109051	NM_153596	103765	Mm.221274	NM_153596	ENSMUSG00000049904	Tmem17	AI503894|AW049890	transmembrane protein 17	protein-coding
mm_55533.1	chr6	70726868	70726887	-	1	NA	Intergenic	(TCC)n|Simple_repeat|Simple_repeat	65298	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_79324.1	chr9	53286051	53286054	+	1	NA	Intergenic	Intergenic	-15618	NM_176846	320051	Mm.277540	NM_176846	ENSMUSG00000034584	Exph5	AC079869.22gm5|B130009M24Rik|E030050P12|Kiaa0624|Slac2b|slac2-b	exophilin 5	protein-coding
mm_172316.1	chr7	106215326	106215327	-	1	NA	promoter-TSS (NM_001243039).2	promoter-TSS (NM_001243039).2	11	NM_001243039	100042856	Mm.425473	NM_001243039	ENSMUSG00000078606	Gm4070	VLIG-1	predicted gene 4070	protein-coding
mm_32999.1	chr4	120517588	120517615	+	1	NA	intron (NM_001159630, intron 13 of 17)	intron (NM_001159630, intron 13 of 17)	-14630	NM_177570	194219	Mm.29788	NM_177570	ENSMUSG00000047518	Slfnl1	4933406A14Rik	schlafen like 1	protein-coding
mm_112218.1	chr12	113429109	113429133	-	1	NA	Intergenic	Intergenic	-60444	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_121710.1	chr14	16172447	16172465	-	1	NA	Intergenic	Intergenic	-76858	NM_021504	59007	Mm.258381	NM_021504	ENSMUSG00000021785	Ngly1	1110002C09Rik|PNGase|Png1	N-glycanase 1	protein-coding
mm_98098.1	chr11	86629631	86629658	+	1	NA	intron (NM_029478, intron 7 of 11)	intron (NM_029478, intron 7 of 11)	-26427	NR_106195	102465902		NR_106195	ENSMUSG00000099324	Mir8115	Gm28012|mmu-mir-8115	microRNA 8115	ncRNA
mm_9037.1	chr1	167237522	167237533	-	1	NA	exon (NM_030724, exon 2 of 7)	exon (NM_030724, exon 2 of 7)	47600	NM_030724	80914	Mm.280895	NM_030724	ENSMUSG00000026558	Uck2	AA407809|AI481316|AU018180|AU020720|TSA903|UK|UMK|Umpk	uridine-cytidine kinase 2	protein-coding
mm_71324.1	chr8	44938239	44938249	+	1	NA	Intergenic	CpG	-11964	NM_001081286	14107	Mm.27365	NM_001081286	ENSMUSG00000070047	Fat1	2310038E12Rik|AU023433|Fath|mFat1	FAT atypical cadherin 1	protein-coding
mm_66605.1	chr7	45460923	45460946	-	1	NA	TTS (NM_007527)	TTS (NM_007527)	-1048	NM_010240	14325	Mm.30357	NM_010240	ENSMUSG00000050708	Ftl1	Ftl|Ftl-1|L-ferritin	ferritin light polypeptide 1	protein-coding
mm_71722.1	chr8	61967491	61967514	+	1	NA	intron (NM_001293783, intron 13 of 37)	(TCC)n|Simple_repeat|Simple_repeat	39415	NM_001293783	234311	Mm.275233	NM_144928	ENSMUSG00000037921	Ddx60	9830118M07	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	protein-coding
mm_144941.1	chr18	37765959	37766008	+	1	NA	5' UTR (NM_033595, exon 1 of 4)	5' UTR (NM_033595, exon 1 of 4)	403	NM_033595	93724	Mm.247203	NM_033595	ENSMUSG00000102428	Pcdhga12	Pcdh13|pc2c	protocadherin gamma subfamily A, 12	protein-coding
mm_136516.1	chr16	97452869	97452878	-	1	NA	intron (NM_010846, intron 7 of 10)	intron (NM_010846, intron 7 of 10)	10032	NM_010846	17857	Mm.33996	NM_010846	ENSMUSG00000000386	Mx1	AI893580|Mx|Mx-1	MX dynamin-like GTPase 1	protein-coding
mm_124337.1	chr14	103844236	103844238	-	1	NA	promoter-TSS (NM_001276296)	promoter-TSS (NM_001276296)	239	NM_001136061	13618	Mm.229532	NM_007904	ENSMUSG00000022122	Ednrb	ET-B|ET-BR|ETR-b|ETb|Sox10m1	endothelin receptor type B	protein-coding
mm_102444.1	chr11	59644493	59644495	-	1	NA	Intergenic	ORR1A3|LTR|ERVL-MaLR	-18001	NM_201245	26936	Mm.2402	NM_012027	ENSMUSG00000005417	Mprip	9530046C02|AA536749|AI647711|C76423|RIP3|Rhoip3|mKIAA0864|p116Rip	myosin phosphatase Rho interacting protein	protein-coding
mm_13405.1	chr2	103981553	103981580	+	1	NA	3' UTR (NM_001142337, exon 4 of 4)	3' UTR (NM_001142337, exon 4 of 4)	11279	NM_001142335	16909	Mm.29266	NM_008505	ENSMUSG00000032698	Lmo2	Rbtn-2|Rbtn2|Rhom-2|Ttg2	LIM domain only 2	protein-coding
mm_135708.1	chr16	55522303	55522311	-	1	NA	Intergenic	Intergenic	27576	NR_039578	100628589		NR_039578	ENSMUSG00000093292	Mir5118	mmu-mir-5118|mu-mir-5118	microRNA 5118	ncRNA
mm_138146.1	chr17	34204585	34204593	+	1	NA	5' UTR (NM_011530, exon 1 of 12)	5' UTR (NM_011530, exon 1 of 12)	110	NM_011530	21355	Mm.14814	NM_011530	ENSMUSG00000024339	Tap2	ABC18|AI462429|APT2|Abcb3|Ham-2|Ham2|MTP2|PSF2|RING11|Tap-2|Y1|jas	transporter 2, ATP-binding cassette, sub-family B (MDR/TAP)	protein-coding
mm_11593.1	chr2	33228844	33228857	+	1	NA	exon (NM_011923, exon 2 of 5)	exon (NM_011923, exon 2 of 5)	12889	NM_011923	26360	Mm.208919	NM_011923	ENSMUSG00000004105	Angptl2	AI593246|AW260363|Arp2	angiopoietin-like 2	protein-coding
mm_67939.1	chr7	100121447	100121511	-	1	NA	promoter-TSS (NM_133692)	promoter-TSS (NM_133692)	21	NM_133692	67967	Mm.37562	NM_133692	ENSMUSG00000030726	Pold3	2410142G14Rik|C85233|P66|P68	polymerase (DNA-directed), delta 3, accessory subunit	protein-coding
mm_72566.1	chr8	84127103	84127113	+	1	NA	intron (NM_001013384, intron 2 of 9)	tRNA-Ala-GCY_|tRNA|tRNA	1119	NM_001013384	244550	Mm.334654	NM_001013384	ENSMUSG00000012889	Podnl1	5832418A03Rik|Gm506	podocan-like 1	protein-coding
mm_80199.1	chr9	72400425	72400434	+	1	NA	Intergenic	Intergenic	-38100	NM_008613	17427	Mm.387671	NM_008613	ENSMUSG00000032221	Mns1	AW546487	meiosis-specific nuclear structural protein 1	protein-coding
mm_156832.1	chrX	164373311	164373321	+	1	NA	promoter-TSS (NM_010216)	promoter-TSS (NM_010216)	-206	NM_001308489	14205	Mm.297978	NM_010216	ENSMUSG00000031380	Vegfd	AI325264|Figf|VEGF-D	vascular endothelial growth factor D	protein-coding
mm_43856.1	chr5	143407065	143407067	+	1	NA	intron (NM_025841, intron 1 of 4)	intron (NM_025841, intron 1 of 4)	3246	NM_025841	66913	Mm.181880	NM_025841	ENSMUSG00000079111	Kdelr2	1110007A14Rik	KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 2	protein-coding
mm_97497.1	chr11	78346684	78346709	+	1	NA	promoter-TSS (NM_001313987)	promoter-TSS (NM_001313987)	-14	NM_001313986	22248	Mm.284811	NM_011676	ENSMUSG00000002058	Unc119	D11Bhm52|HRG4|MRG4|Rg4|Rtg4|Unc119h	unc-119 lipid binding chaperone	protein-coding
mm_130269.1	chr15	96698700	96698706	-	1	NA	exon (NM_175121, exon 2 of 16)	exon (NM_175121, exon 2 of 16)	995	NM_175121	67760	Mm.46754	NM_175121	ENSMUSG00000022462	Slc38a2	5033402L14Rik|AI316867|ATA2|SAT2|mKIAA1382	solute carrier family 38, member 2	protein-coding
mm_125117.1	chr15	28576472	28576478	+	1	NA	Intergenic	Intergenic	372709	NM_133365	110082	Mm.248464	NM_133365	ENSMUSG00000022262	Dnah5	AU022615|Dnahc5|Mdnah5|b2b1134Clo|b2b1154Clo|b2b1537Clo|b2b1565Clo|b2b601Clo|mKIAA1603	dynein, axonemal, heavy chain 5	protein-coding
mm_128644.1	chr15	59524581	59524588	-	1	NA	intron (NM_026746, intron 4 of 6)	intron (NM_026746, intron 4 of 6)	-124070	NM_144549	211770	Mm.40298	NM_144549	ENSMUSG00000032501	Trib1	A530090O15Rik|TRB-1|Trb1	tribbles pseudokinase 1	protein-coding
mm_21850.1	chr2	165865951	165865967	-	1	NA	intron (NM_027230, intron 2 of 23)	(A)n|Simple_repeat|Simple_repeat	-7786	NM_001252585	228880	Mm.227598	NM_027230	ENSMUSG00000039671	Zmynd8	1110013E22Rik|2010005I16Rik|3632413B07Rik|AI316811|AL024039|Prkcbp1|RACK7	zinc finger, MYND-type containing 8	protein-coding
mm_124873.1	chr15	10216033	10216041	+	1	NA	intron (NM_011169, intron 1 of 9)	intron (NM_011169, intron 1 of 9)	-7869	NM_001253781	19116	Mm.10516	NM_011169	ENSMUSG00000005268	Prlr	AI987712|Pr-1|Pr-3|Prlr-rs1	prolactin receptor	protein-coding
mm_108742.1	chr12	88724971	88724999	+	1	NA	Intergenic	Intergenic	-69519	NM_001198587	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding
mm_44003.1	chr5	146948722	146948728	+	1	NA	promoter-TSS (NM_025652)	promoter-TSS (NM_025652)	68	NM_025652	66596	Mm.196528	NM_025652	ENSMUSG00000016503	Gtf3a	2010015D03Rik|2610111I01Rik|5330403M05Rik	general transcription factor III A	protein-coding
mm_132969.1	chr16	52031325	52031342	+	1	NA	promoter-TSS (NM_001033238)	promoter-TSS (NM_001033238)	-216	NM_001033238	208650	Mm.328206	NM_001033238	ENSMUSG00000022637	Cblb	AI429560|AI851073|Cbl-b	Casitas B-lineage lymphoma b	protein-coding
mm_157419.1	chrX	38564154	38564163	-	1	NA	exon (NM_028288, exon 4 of 23)	exon (NM_028288, exon 4 of 23)	12038	NM_028288	72584	Mm.327675	NM_028288	ENSMUSG00000031095	Cul4b	2700050M05Rik|AA409770|CUL-4B|mKIAA0695	cullin 4B	protein-coding
mm_109067.1	chr12	104345314	104345328	+	1	NA	exon (NM_011458, exon 5 of 5)	exon (NM_011458, exon 5 of 5)	6835	NM_011458	20714	Mm.291569	NM_011458	ENSMUSG00000058207	Serpina3k	1300001I07Rik|D12Rp54|MMCM2|MMSpi2|RP54|Spi-2|Spi2|contrapsin	serine (or cysteine) peptidase inhibitor, clade A, member 3K	protein-coding
mm_143866.1	chr17	84186701	84186717	-	1	NA	exon (NM_001001806, exon 2 of 2)	exon (NM_001001806, exon 2 of 2)	1238	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_13003.1	chr2	90904734	90904747	+	1	NA	promoter-TSS (NM_025991)	promoter-TSS (NM_025991)	0	NM_001311116	67136	Mm.330394	NM_025991	ENSMUSG00000005505	Kbtbd4	2510026C23Rik	kelch repeat and BTB (POZ) domain containing 4	protein-coding
mm_133048.1	chr16	57569853	57569866	+	1	NA	exon (NM_001040397, exon 5 of 5)	exon (NM_001040397, exon 5 of 5)	20617	NM_001177871	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding
mm_21072.1	chr2	152830267	152830279	-	1	NA	intron (NM_009743, intron 1 of 2)	intron (NM_009743, intron 1 of 2)	444	NM_001289716	12048	Mm.238213	NM_009743	ENSMUSG00000007659	Bcl2l1	Bcl(X)L|Bcl-XL|Bcl2l|BclX|bcl-x|bcl2-L-1	BCL2-like 1	protein-coding
mm_18261.1	chr2	52291159	52291169	-	1	NA	exon (NM_010889, exon 33 of 157)	exon (NM_010889, exon 33 of 157)	162	NR_040620	78049	Mm.243883	NR_040620		4930573O16Rik	-	RIKEN cDNA 4930573O16 gene	ncRNA
mm_128469.1	chr15	50821812	50821827	-	1	NA	intron (NM_001310485, intron 5 of 7)	intron (NM_001310485, intron 5 of 7)	67230	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_123721.1	chr14	70153204	70153206	-	1	NA	intron (NM_146055, intron 1 of 20)	CpG	586	NM_146055	219158	Mm.218284	NM_146055	ENSMUSG00000033712	Ccar2	2610301G19Rik|Dbc1|mKIAA1967	cell cycle activator and apoptosis regulator 2	protein-coding
mm_108631.1	chr12	85686649	85686702	+	1	NA	promoter-TSS (NM_016767)	promoter-TSS (NM_016767)	-45	NM_016767	53314	Mm.6672	NM_016767	ENSMUSG00000034266	Batf	B-ATF|SFA-2	basic leucine zipper transcription factor, ATF-like	protein-coding
mm_39188.1	chr4	155869395	155869455	-	1	NA	promoter-TSS (NM_024472)	promoter-TSS (NM_024472)	15	NM_024472	79554	Mm.25556	NM_024472	ENSMUSG00000029073	Cptp	Gltpd1	ceramide-1-phosphate transfer protein	protein-coding
mm_121403.1	chr14	119173049	119173069	+	1	NA	intron (NM_015820, intron 1 of 1)	MIRb|SINE|MIR	34794	NM_015820	50787	Mm.445777	NM_015820	ENSMUSG00000053465	Hs6st3	6OST3|HS6ST-3	heparan sulfate 6-O-sulfotransferase 3	protein-coding
mm_151302.1	chr19	55741909	55741919	+	1	NA	non-coding (NR_138565, exon 1 of 16)	non-coding (NR_138565, exon 1 of 16)	104	NM_001142923	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_67681.1	chr7	89338647	89338666	-	1	NA	5' UTR (NM_028343, exon 1 of 15)	5' UTR (NM_028343, exon 1 of 15)	131	NM_028343	72759	Mm.208477	NM_028343	ENSMUSG00000039428	Tmem135	2810439K08Rik|AW319712|PMP52	transmembrane protein 135	protein-coding
mm_105934.1	chr11	115133956	115133966	-	1	NA	promoter-TSS (NM_001169153)	promoter-TSS (NM_001169153)	31	NM_001347648	246746	Mm.277387	NM_145634	ENSMUSG00000047798	Cd300lf	CLIM1|CLM-1|CLM1|Digr2|F730004D16Rik|IREM1|IgSF13|LMIR3|Pigr3	CD300 molecule like family member F	protein-coding
mm_47197.1	chr5	120777629	120777664	-	1	NA	promoter-TSS (NM_145226)	promoter-TSS (NM_145226)	13	NM_145226	246727	Mm.204887	NM_145226	ENSMUSG00000032661	Oas3	Oasl10	2'-5' oligoadenylate synthetase 3	protein-coding
mm_8281.1	chr1	140096505	140096510	-	1	NA	intron (NM_009888, intron 20 of 21)	intron (NM_009888, intron 20 of 21)	86904	NM_009888	12628	Mm.8655	NM_009888	ENSMUSG00000026365	Cfh	Mud-1|NOM|Sas-1|Sas1	complement component factor h	protein-coding
mm_9650.1	chr1	177463029	177463030	-	1	NA	Intergenic	MLT1O|LTR|ERVL-MaLR	17208	NM_013915	30928	Mm.330700	NM_013915	ENSMUSG00000063659	Zbtb18	RP58|Zfp238|Znf238	zinc finger and BTB domain containing 18	protein-coding
mm_11718.1	chr2	36242787	36242789	+	1	NA	exon (NM_008969, exon 8 of 11)	exon (NM_008969, exon 8 of 11)	12362	NM_008969	19224	Mm.275434	NM_008969	ENSMUSG00000047250	Ptgs1	COX1|Cox-1|Cox-3|PGHS-1|PHS 1|Pghs1	prostaglandin-endoperoxide synthase 1	protein-coding
mm_74190.1	chr8	123653842	123653877	+	1	NA	promoter-TSS (NM_133955)	promoter-TSS (NM_133955)	-70	NM_133955	69581	Mm.168257	NM_133955	ENSMUSG00000039960	Rhou	2310026M05Rik|AI182090|Arhu|CDC42L1|G28K|WRCH-1|WRCH1|mG28K	ras homolog family member U	protein-coding
mm_113796.1	chr13	46418267	46418316	+	1	NA	promoter-TSS (NM_001081425)	promoter-TSS (NM_001081425)	-9	NM_001081425	666794	Mm.38269	NM_001081425	ENSMUSG00000038132	Rbm24	6330546B05Rik|AI606861	RNA binding motif protein 24	protein-coding
mm_17050.1	chr2	20968974	20968984	-	1	NA	non-coding (NR_033225, exon 1 of 2)	non-coding (NR_033225, exon 1 of 2)	105	NR_033225	433408	Mm.386941	NR_033225		Gm13375	OTTMUSG00000011664	predicted gene 13375	ncRNA
mm_56643.1	chr6	113343899	113343966	-	1	NA	promoter-TSS (NM_133926)	promoter-TSS (NM_133926)	-10	NM_133926	52163	Mm.277373	NM_133926	ENSMUSG00000030272	Camk1	AI505105|CaMKIalpha|D6Ertd263e	calcium/calmodulin-dependent protein kinase I	protein-coding
mm_29790.1	chr3	127553211	127553225	-	1	NA	promoter-TSS (NM_197997)	promoter-TSS (NM_197997)	131	NM_138593	28036	Mm.291032	NM_138593	ENSMUSG00000027968	Larp7	C330027G06Rik|D3Wsu161e	La ribonucleoprotein domain family, member 7	protein-coding
mm_71069.1	chr8	34146361	34146367	+	1	NA	intron (NM_026609, intron 1 of 3)	intron (NM_026609, intron 1 of 3)	375	NM_026609	68192	Mm.34212	NM_026609	ENSMUSG00000031513	Leprotl1	1110067H13Rik|1520402O14Rik|AI854296	leptin receptor overlapping transcript-like 1	protein-coding
mm_34307.1	chr4	141793819	141793848	+	1	NA	5' UTR (NM_015733, exon 1 of 9)	5' UTR (NM_015733, exon 1 of 9)	221	NM_001277932	12371	Mm.88829	NM_015733	ENSMUSG00000028914	Casp9	AI115399|APAF-3|AW493809|CASP-9|Caspase-9|ICE-LAP6|Mch6	caspase 9	protein-coding
mm_110499.1	chr12	54203845	54203857	-	1	NA	promoter-TSS (NM_028133)	promoter-TSS (NM_028133)	23	NM_028133	112407	Mm.133037	NM_028133	ENSMUSG00000035105	Egln3	2610021G09Rik|AI505553|AI648162|Hif-p4h-3|Phd3|SM-20	egl-9 family hypoxia-inducible factor 3	protein-coding
mm_54198.1	chr6	24664873	24664896	-	1	NA	5' UTR (NM_028459, exon 1 of 11)	5' UTR (NM_028459, exon 1 of 11)	111	NM_001167745	73178	Mm.1574	NM_028459	ENSMUSG00000029684	Wasl	2900021I12Rik|3110031I02Rik|N-WASP	Wiskott-Aldrich syndrome-like (human)	protein-coding
mm_61173.1	chr7	59314601	59314628	+	1	NA	intron (NR_015479, intron 2 of 2)	intron (NR_015479, intron 2 of 2)	9535	NR_015479	330544	Mm.9002	NR_015479	ENSMUSG00000100826	C230091D08Rik	-	RIKEN cDNA C230091D08 gene	ncRNA
mm_14863.1	chr2	148798651	148798658	+	1	NA	promoter-TSS (NM_009978)	promoter-TSS (NM_009978)	-185	NM_009978	13012	Mm.20435	NM_009978	ENSMUSG00000027442	Cst8	Cres|Cst-rs1	cystatin 8 (cystatin-related epididymal spermatogenic)	protein-coding
mm_92024.1	chr10	62422428	62422448	-	1	NA	promoter-TSS (NM_145419)	promoter-TSS (NM_145419)	19	NM_145419	216019	Mm.213213	NM_145419	ENSMUSG00000020080	Hkdc1	BC016235	hexokinase domain containing 1	protein-coding
mm_22148.1	chr2	172396011	172396050	-	1	NA	intron (NM_001080820, intron 1 of 6)	intron (NM_001080820, intron 1 of 6)	2236	NM_001276423	320664	Mm.210195	NM_001033538	ENSMUSG00000074570	Cass4	F730031O20Rik	Cas scaffolding protein family member 4	protein-coding
mm_165012.1	chr19	27322601	27322601	+	1	NA	promoter-TSS (NM_183179)	promoter-TSS (NM_183179)	-18	NM_183179	240595	Mm.269759	NM_183179	ENSMUSG00000047298	Kcnv2	KV11.1	potassium channel, subfamily V, member 2	protein-coding
mm_169041.1	chr13	14400073	14400075	+	1	NA	intron (NM_001081348, intron 2 of 28)	RLTR10|LTR|ERVK	123152	NM_001081348	94253	Mm.125298	NM_153130	ENSMUSG00000021301	Hecw1	9330116H24Rik|AV273951|E130207I19Rik|Nedl1	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	protein-coding
mm_70236.1	chr8	3353322	3353332	+	1	NA	promoter-TSS (NM_001033378)	promoter-TSS (NM_001033378)	-88	NM_001033378	319493	Mm.234565	NM_001033378	ENSMUSG00000074497	A430078G23Rik	-	RIKEN cDNA A430078G23 gene	protein-coding
mm_112133.1	chr12	112959531	112959549	-	1	NA	TTS (NM_028193)	TTS (NM_028193)	-16942	NM_001145900	399566	Mm.440140	NM_201646	ENSMUSG00000002803	Btbd6	-	BTB (POZ) domain containing 6	protein-coding
mm_157386.1	chrX	38224619	38224621	-	1	NA	exon (NM_001289728, exon 6 of 9)	exon (NM_001289728, exon 6 of 9)	14179	NR_037297	100526512		NR_037297	ENSMUSG00000092794	Mir3110	mmu-mir-3110	microRNA 3110	ncRNA
mm_9685.1	chr1	178333928	178333966	-	1	NA	exon (NM_016805, exon 4 of 14)	exon (NM_016805, exon 4 of 14)	3837	NM_016805	51810	Mm.86589	NM_016805	ENSMUSG00000039630	Hnrnpu	AA408410|AI256620|AL024194|AL024437|AW557595|C86794|Hnrpu|SAFA|Sp120|hnRNP U	heterogeneous nuclear ribonucleoprotein U	protein-coding
mm_157647.1	chrX	57305067	57305110	-	1	NA	intron (NM_152801, intron 2 of 21)	intron (NM_152801, intron 2 of 21)	33641	NM_152801	73341	Mm.261443	NM_152801	ENSMUSG00000031133	Arhgef6	1600028C08Rik|1700038J06Rik|4930592P22Rik|alpha-PIX	Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_56480.1	chr6	99096182	99096186	-	1	NA	intron (NM_001347345, intron 5 of 19)	intron (NM_001347345, intron 5 of 19)	-67886	NM_001197322	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_103039.1	chr11	69761910	69761927	-	1	NA	promoter-TSS (NM_019871)	promoter-TSS (NM_019871)	-74	NM_019871	56293	Mm.6211	NM_019871	ENSMUSG00000018776	Slc35g3	Amac1	solute carrier family 35, member G3	protein-coding
mm_137288.1	chr17	24740038	24740053	+	1	NA	intron (NM_013759, intron 2 of 4)	intron (NM_013759, intron 2 of 4)	3452	NM_001346668	27361	Mm.28212	NM_013759	ENSMUSG00000075705	Msrb1	D17Wsu82e|SELX|SelR|Sepr|Sepx1	methionine sulfoxide reductase B1	protein-coding
mm_81315.1	chr9	108436464	108436470	+	1	NA	promoter-TSS (NM_001004192)	promoter-TSS (NM_001004192)	-15	NM_001004192	434439	Mm.78372	NM_001004192	ENSMUSG00000050641	BC048562	-	cDNA sequence BC048562	protein-coding
mm_165006.1	chr19	24200481	24200487	-	1	NA	intron (NM_011597, intron 1 of 22)	intron (NM_011597, intron 1 of 22)	24542	NM_011597	21873	Mm.104744	NM_011597	ENSMUSG00000024812	Tjp2	ZO-2	tight junction protein 2	protein-coding
mm_2548.1	chr1	107589998	107590040	+	1	NA	promoter-TSS (NM_001159748)	promoter-TSS (NM_001159748)	13	NM_001159748	20725	Mm.83909	NM_011459	ENSMUSG00000026315	Serpinb8	CAP-2|CAP2|NK10|Spi8|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 8	protein-coding
mm_139144.1	chr17	47512898	47512910	+	1	NA	intron (NM_001081635, intron 1 of 6)	intron (NM_001081635, intron 1 of 6)	7853	NM_001081635	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_153905.1	chr19	47131982	47132004	-	1	NA	TTS (NM_011053)	TTS (NM_011053)	6301	NM_133746	72691	Mm.31663	NM_133746	ENSMUSG00000033033	Calhm2	2810048G17Rik|Fam26b	calcium homeostasis modulator 2	protein-coding
mm_12684.1	chr2	75871960	75871963	+	1	NA	intron (NM_172666, intron 10 of 19)	intron (NM_172666, intron 10 of 19)	39784	NM_172666	228061	Mm.31227	NM_172666	ENSMUSG00000042410	Agps	5832437L22|9930035G10Rik|AW123847|Adaps|Adas|Adhaps|Adps|Aldhpsy|bs2	alkylglycerone phosphate synthase	protein-coding
mm_31402.1	chr4	48047267	48047279	+	1	NA	intron (NM_015743, intron 1 of 7)	CpG	1968	NM_015743	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_112518.1	chr13	9127965	9127986	+	1	NA	intron (NM_001311117, intron 3 of 16)	intron (NM_001311117, intron 3 of 16)	34094	NM_172585	217980	Mm.234944	NM_172585	ENSMUSG00000033499	Larp4b	A630096F19|AI256361|D13Wsu64e|Larp5	La ribonucleoprotein domain family, member 4B	protein-coding
mm_99966.1	chr11	113684534	113684551	+	1	NA	promoter-TSS (NM_138598)	promoter-TSS (NM_138598)	130	NM_177777	276852	Mm.239566	NM_177777	ENSMUSG00000041623	D11Wsu47e	-	DNA segment, Chr 11, Wayne State University 47, expressed	protein-coding
mm_24073.1	chr3	87919694	87919713	+	1	NA	5' UTR (NM_026591, exon 1 of 6)	5' UTR (NM_026591, exon 1 of 6)	159	NM_026591	67707	Mm.393802	NM_026591	ENSMUSG00000019710	Mrpl24	2010005E08Rik|2810470K06Rik|6720473G22Rik|AA407670	mitochondrial ribosomal protein L24	protein-coding
mm_72890.1	chr8	90493098	90493100	+	1	NA	Intergenic	Intergenic	-144847	NM_172913	244579	Mm.302755	NM_172913	ENSMUSG00000043668	Tox3	500-9|BC052044|C230068E13|CAGF9|Tnrc9	TOX high mobility group box family member 3	protein-coding
mm_5741.1	chr1	45502566	45502568	-	1	NA	intron (NM_007737, intron 1 of 53)	intron (NM_007737, intron 1 of 53)	715	NM_007737	12832	Mm.10299	NM_007737	ENSMUSG00000026042	Col5a2	1110014L14Rik	collagen, type V, alpha 2	protein-coding
mm_135236.1	chr16	36990146	36990150	-	1	NA	Intergenic	Intergenic	-11012	NM_001037321	207215	Mm.211899	NM_001037321	ENSMUSG00000047746	Fbxo40	9830003A13Rik|mKIAA1195	F-box protein 40	protein-coding
mm_116291.1	chr13	35212045	35212052	-	1	NA	promoter-TSS (NR_126478)	promoter-TSS (NR_126478)	0	NR_126478	75543	Mm.489052	NR_126478		1700019C18Rik	-	RIKEN cDNA 1700019C18 gene	ncRNA
mm_143868.1	chr17	84186809	84186820	-	1	NA	exon (NM_001001806, exon 2 of 2)	exon (NM_001001806, exon 2 of 2)	1133	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_46292.1	chr5	100414658	100414662	-	1	NA	intron (NM_026969, intron 1 of 27)	intron (NM_026969, intron 1 of 27)	1574	NM_026969	69162	Mm.18634	NM_026969	ENSMUSG00000035325	Sec31a	1810024J13Rik|ABP125|ABP130|AU042160|HSPC275|Sec31l1	Sec31 homolog A (S. cerevisiae)	protein-coding
mm_82585.1	chr9	21237154	21237165	-	1	NA	exon (NM_016679, exon 1 of 5)	exon (NM_016679, exon 1 of 5)	2173	NM_016679	50868	Mm.248266	NM_016679	ENSMUSG00000003308	Keap1	INRF2|mKIAA0132	kelch-like ECH-associated protein 1	protein-coding
mm_125683.1	chr15	66798698	66798706	+	1	NA	intron (NM_009192, intron 3 of 8)	intron (NM_009192, intron 3 of 8)	33127	NM_001029841	20491	Mm.7601	NM_009192	ENSMUSG00000022372	Sla	Slap|Slap-1	src-like adaptor	protein-coding
mm_107400.1	chr12	33337414	33337425	+	1	NA	intron (NM_001033436, intron 2 of 7)	intron (NM_001033436, intron 2 of 7)	34904	NM_001033436	380753	Mm.41540	NM_028139	ENSMUSG00000020564	Atxn7l1	2810423G08Rik|Atxn7l4	ataxin 7-like 1	protein-coding
mm_8471.1	chr1	153333022	153333028	-	1	NA	promoter-TSS (NM_010683)	promoter-TSS (NM_010683)	-239	NM_010683	226519	Mm.1249	NM_010683	ENSMUSG00000026478	Lamc1	Lamb2	laminin, gamma 1	protein-coding
mm_119221.1	chr14	33225439	33225441	+	1	NA	intron (NM_153800, intron 2 of 10)	L1M4|LINE|L1	8617	NM_153800	239027	Mm.318350	NM_153800	ENSMUSG00000063506	Arhgap22	B230341L19Rik|RHOGAP2|p68RacGAP	Rho GTPase activating protein 22	protein-coding
mm_48261.1	chr5	137871730	137871734	-	1	NA	promoter-TSS (NM_001024932)	promoter-TSS (NM_001024932)	26	NM_001024932	545812	Mm.332769	NM_001024932	ENSMUSG00000066682	Pilrb2	EG545812	paired immunoglobin-like type 2 receptor beta 2	protein-coding
mm_113038.1	chr13	23555024	23555039	+	1	NA	promoter-TSS (NM_145713)	promoter-TSS (NM_145713)	-1	NM_145713	14957	Mm.247046	NM_145713	ENSMUSG00000052565	Hist1h1d	H1.3|H1D|H1f3|H1s-4	histone cluster 1, H1d	protein-coding
mm_116765.1	chr13	52587887	52587898	-	1	NA	intron (NM_001198977, intron 1 of 13)	MLT1A1|LTR|ERVL-MaLR	4455	NM_001198977	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_95324.1	chr11	46480299	46480322	+	1	NA	3' UTR (NM_134250, exon 7 of 7)	3' UTR (NM_134250, exon 7 of 7)	25379	NM_134250	171285	Mm.72168	NM_134250	ENSMUSG00000020399	Havcr2	TIM-3|Tim3|Timd3	hepatitis A virus cellular receptor 2	protein-coding
mm_110638.1	chr12	57546782	57546793	-	1	NA	promoter-TSS (NM_008259)	promoter-TSS (NM_008259)	-666	NM_008259	15375	Mm.4578	NM_008259	ENSMUSG00000035451	Foxa1	Hnf-3a|Hnf3a|Tcf-3a|Tcf3a	forkhead box A1	protein-coding
mm_80901.1	chr9	100393317	100393322	+	1	NA	Intergenic	B4|SINE|B4	93154	NM_001033543	213208	Mm.242896	NM_001033543	ENSMUSG00000044244	Il20rb	AV228068|Fndc6|Gm186|Il20R2	interleukin 20 receptor beta	protein-coding
mm_130295.1	chr15	97013565	97013575	-	1	NA	intron (NM_027052, intron 4 of 15)	intron (NM_027052, intron 4 of 15)	42386	NM_027052	69354	Mm.250980	NM_027052	ENSMUSG00000022464	Slc38a4	1110012E16Rik|1700012A18Rik|Ata3|mATA3|mNAT3	solute carrier family 38, member 4	protein-coding
mm_133275.1	chr16	77389973	77389984	+	1	NA	intron (NR_015543, intron 2 of 4)	intron (NR_015543, intron 2 of 4)	60650	NR_015543	77994	Mm.394688	NR_015543	ENSMUSG00000090386	Mir99ahg	2810055G20Rik|D730043B02Rik	Mir99a and Mirlet7c-1 host gene (non-protein coding)	ncRNA
mm_64565.1	chr7	144896465	144896471	+	1	NA	promoter-TSS (NM_008003)	promoter-TSS (NM_008003)	-64	NM_008003	14170	Mm.3904	NM_008003	ENSMUSG00000031073	Fgf15	FGF19	fibroblast growth factor 15	protein-coding
mm_116776.1	chr13	52981028	52981083	-	1	NA	promoter-TSS (NM_017373)	promoter-TSS (NM_017373)	-16	NM_017373	18030	Mm.136604	NM_017373	ENSMUSG00000056749	Nfil3	AV225605|E4BP4	nuclear factor, interleukin 3, regulated	protein-coding
mm_147555.1	chr18	54961648	54961667	-	1	NA	intron (NM_175751, intron 2 of 9)	intron (NM_175751, intron 2 of 9)	28523	NM_175751	269023	Mm.192984	NM_175751	ENSMUSG00000052713	Zfp608	4932417D18Rik|D430007A19Rik|Znf608	zinc finger protein 608	protein-coding
mm_139850.1	chr17	69417442	69417465	+	1	NA	non-coding (NR_026848, exon 1 of 1)	non-coding (NR_026848, exon 1 of 1)	1006	NR_026848	77533	Mm.266592	NR_026848		C030034I22Rik	-	RIKEN cDNA C030034I22 gene	ncRNA
mm_158683.1	chrX	160338534	160338541	-	1	NA	Intergenic	Intergenic	-52153	NM_001079847	237175	Mm.213016	NM_178712	ENSMUSG00000031298	Adgrg2	AW212196|B830041D06Rik|Gpr64|Me6	adhesion G protein-coupled receptor G2	protein-coding
mm_103306.1	chr11	72795802	72795847	-	1	NA	promoter-TSS (NM_001045536)	promoter-TSS (NM_001045536)	15	NM_001024926	192986	Mm.194755	NM_001024926	ENSMUSG00000057778	Cyb5d2	9330151E16Rik|Gm2	cytochrome b5 domain containing 2	protein-coding
mm_37128.1	chr4	116685402	116685418	-	1	NA	promoter-TSS (NM_011034)	promoter-TSS (NM_011034)	-189	NM_011034	18477	Mm.30929	NM_011034	ENSMUSG00000028691	Prdx1	MSP23|NkefA|OSF-3|OSF3|PAG|Paga|PrdxI|PrxI|TDX2|TPxA|Tdpx2|prx1	peroxiredoxin 1	protein-coding
mm_142564.1	chr17	46646038	46646085	-	1	NA	promoter-TSS (NM_029091)	promoter-TSS (NM_029091)	-160	NM_001316742	27398	Mm.391007	NM_025302	ENSMUSG00000002767	Mrpl2	CGI-22|L2mt|MRP-L14|MRP-L2|Rpml14	mitochondrial ribosomal protein L2	protein-coding
mm_33657.1	chr4	133117189	133117203	+	1	NA	Intergenic	Intergenic	-13437	NM_153423	242687	Mm.23566	NM_153423	ENSMUSG00000028868	Wasf2	AW742646|D4Ertd13e|WAVE2	WAS protein family, member 2	protein-coding
mm_53630.1	chr6	140527014	140527018	+	1	NA	intron (NM_144920, intron 6 of 30)	intron (NM_144920, intron 6 of 30)	-95647	NM_178803	11569	Mm.86453	NM_009637	ENSMUSG00000030232	Aebp2	AU023766|B230313N05Rik	AE binding protein 2	protein-coding
mm_28666.1	chr3	95281711	95281748	-	1	NA	5' UTR (NM_173347, exon 1 of 8)	5' UTR (NM_173347, exon 1 of 8)	347	NM_173347	229589	Mm.14155	NM_173347	ENSMUSG00000015711	Prune1	9230112O05Rik|C130058A12|DRES-17|HTCD37|PRUNEM1|Prune|Prune-M1	prune exopolyphosphatase	protein-coding
mm_152950.1	chr19	29021864	29021903	-	1	NA	3' UTR (NM_021299, exon 5 of 5)	3' UTR (NM_021299, exon 5 of 5)	-25600	NR_028360	67329	Mm.394933	NR_028360		1700018L02Rik	-	RIKEN cDNA 1700018L02 gene	ncRNA
mm_125344.1	chr15	39112943	39112949	+	1	NA	promoter-TSS (NM_198606)	promoter-TSS (NM_198606)	72	NM_198606	223499	Mm.321937	NM_198606	ENSMUSG00000022300	Dcaf13	Gm83|Wdsof1	DDB1 and CUL4 associated factor 13	protein-coding
mm_93734.1	chr10	120112914	120112945	-	1	NA	promoter-TSS (NM_080446)	promoter-TSS (NM_080446)	36	NM_080446	117599	Mm.214703	NM_080446	ENSMUSG00000020228	Helb	AI447783|D10Ertd664e	helicase (DNA) B	protein-coding
mm_165358.1	chr2	122160697	122160697	+	1	NA	promoter-TSS (NM_080510)	promoter-TSS (NM_080510)	-3	NM_080510	70928	Mm.379188	NM_080510	ENSMUSG00000033368	Trim69	4921519C19Rik|Rnf36|Trif|Trimless	tripartite motif-containing 69	protein-coding
mm_167260.1	chr8	25976722	25976726	-	1	NA	promoter-TSS (NM_029884)	promoter-TSS (NM_029884)	20	NM_029884	52120	Mm.28326	NM_029884	ENSMUSG00000037260	Hgsnat	9430010M12Rik|AW208455|D8Ertd354e|Tmem76	heparan-alpha-glucosaminide N-acetyltransferase	protein-coding
mm_39450.1	chr5	17574541	17574549	+	1	NA	promoter-TSS (NM_013657)	promoter-TSS (NM_013657)	-271	NM_013657	20348	Mm.5071	NM_013657	ENSMUSG00000028780	Sema3c	1110036B02Rik|SemE|Semae	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	protein-coding
mm_36374.1	chr4	76559048	76559071	-	1	NA	intron (NM_011211, intron 10 of 39)	Lx2B|LINE|L1	-1280773	NM_025849	66928	Mm.24332	NM_025849	ENSMUSG00000028398	Tmem261	1700027K24Rik|3110001D03Rik	transmembrane protein 261	protein-coding
mm_31915.1	chr4	85205418	85205495	+	1	NA	promoter-TSS (NM_019535)	promoter-TSS (NM_019535)	0	NM_019535	20404	Mm.143603	NM_019535	ENSMUSG00000028488	Sh3gl2	9530001L19Rik|AI120490|AW555077|B930049H17Rik|EEN-B1|SH3PA|Sh3d2a	SH3-domain GRB2-like 2	protein-coding
mm_125323.1	chr15	38455370	38455383	+	1	NA	Intergenic	Intergenic	35171	NR_105916	102465574		NR_105916	ENSMUSG00000099110	Mir6951	Gm27765|mmu-mir-6951	microRNA 6951	ncRNA
mm_12127.1	chr2	61644303	61644314	+	1	NA	exon (NM_001164072, exon 6 of 8)	exon (NM_001164072, exon 6 of 8)	51211	NM_001164071	21353	Mm.244393	NM_011529	ENSMUSG00000064289	Tank	C86182|E430026L09Rik|I-TRAF	TRAF family member-associated Nf-kappa B activator	protein-coding
mm_118664.1	chr14	21838426	21838437	+	1	NA	exon (NM_011695, exon 7 of 10)	exon (NM_011695, exon 7 of 10)	6870	NM_011695	22334	Mm.262327	NM_011695	ENSMUSG00000021771	Vdac2	Vdac6|mVDAC2|mVDAC6	voltage-dependent anion channel 2	protein-coding
mm_149745.1	chr19	22448203	22448223	+	1	NA	promoter-TSS (NM_177341)	promoter-TSS (NM_177341)	5	NM_177341	226025	Mm.131943	NM_177341	ENSMUSG00000052387	Trpm3	6330504P12Rik|9330180E14|AU018608|B930001P07Rik|LTRPC3|MLSN2	transient receptor potential cation channel, subfamily M, member 3	protein-coding
mm_72813.1	chr8	87563847	87563869	+	1	NA	promoter-TSS (NM_177901)	promoter-TSS (NM_177901)	-49	NM_177901	330820	Mm.212913	NM_177901	ENSMUSG00000069971	4933402J07Rik	-	RIKEN cDNA 4933402J07 gene	protein-coding
mm_115221.1	chr13	109685499	109685543	+	1	NA	intron (NM_011056, intron 3 of 16)	intron (NM_011056, intron 3 of 16)	-218288	NR_035442	100316683		NR_035442	ENSMUSG00000084651	Mir1904	Mirn1904|mmu-mir-1904	microRNA 1904	ncRNA
mm_49243.1	chr6	17307273	17307287	+	1	NA	promoter-TSS (NM_001243064)	promoter-TSS (NM_001243064)	-360	NM_001243064	12389	Mm.28278	NM_007616	ENSMUSG00000007655	Cav1	Cav|Cav-1	caveolin 1, caveolae protein	protein-coding
mm_86047.1	chr9	114501214	114501254	-	1	NA	Intergenic	Intergenic	-4690	NM_009916	12773	Mm.1337	NM_009916	ENSMUSG00000047898	Ccr4	C-C CKR-4|CHEMR1|Cmkbr4|LESTR|Sdf1r	chemokine (C-C motif) receptor 4	protein-coding
mm_43407.1	chr5	135887941	135887970	+	1	NA	promoter-TSS (NM_013560)	promoter-TSS (NM_013560)	36	NM_013560	15507	Mm.13849	NM_013560	ENSMUSG00000004951	Hspb1	27kDa|Hsp25	heat shock protein 1	protein-coding
mm_142869.1	chr17	51815803	51815811	-	1	NA	intron (NM_001163632, intron 1 of 10)	intron (NM_001163632, intron 1 of 10)	-3753	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_108043.1	chr12	73902639	73902641	+	1	NA	intron (NM_001313920, intron 1 of 14)	B4A|SINE|B4	1316	NM_001313920	15251	Mm.3879	NM_010431	ENSMUSG00000021109	Hif1a	AA959795|HIF-1-alpha|HIF1-alpha|HIF1alpha|MOP1|bHLHe78	hypoxia inducible factor 1, alpha subunit	protein-coding
mm_23938.1	chr3	84335560	84335574	+	1	NA	Intergenic	Intergenic	-30792	NM_001271726	80890	Mm.44876	NM_030706	ENSMUSG00000027993	Trim2	mKIAA0517|narf	tripartite motif-containing 2	protein-coding
mm_33035.1	chr4	122836051	122836067	+	1	NA	promoter-TSS (NM_008917)	promoter-TSS (NM_008917)	-168	NM_008917	19063	Mm.277719	NM_008917	ENSMUSG00000028657	Ppt1	9530043G02Rik|AA960502|C77813|CLN1|D4Ertd184e|INCL|PPT	palmitoyl-protein thioesterase 1	protein-coding
mm_149670.1	chr19	18840641	18840649	+	1	NA	intron (NM_153417, intron 25 of 38)	intron (NM_153417, intron 25 of 38)	90662	NM_153417	225997	Mm.215171	NM_153417	ENSMUSG00000024727	Trpm6	CHAK2|TRPM6/CHAK2	transient receptor potential cation channel, subfamily M, member 6	protein-coding
mm_145067.1	chr18	40792715	40792716	+	1	NA	Intergenic	Intergenic	534354	NM_026135	383348	Mm.76366	NM_026135	ENSMUSG00000051401	Kctd16	4930434H12Rik|Gm1267	potassium channel tetramerisation domain containing 16	protein-coding
mm_109142.1	chr12	107124442	107124456	+	1	NA	Intergenic	Intergenic	-408125	NR_015512	71033	Mm.159404	NR_015512	ENSMUSG00000085820	4933406K04Rik	4930426M03Rik|4930485I22Rik|4933427G14Rik	RIKEN cDNA 4933406K04 gene	ncRNA
mm_29953.1	chr3	133092030	133092039	-	1	NA	promoter-TSS (NM_026231)	promoter-TSS (NM_026231)	179	NM_027927	71793	Mm.246726	NM_027927	ENSMUSG00000028016	Ints12	1110020M19Rik|2810027J24Rik|4930529N21Rik|A230056J18Rik|AI666778|Phf22|int12	integrator complex subunit 12	protein-coding
mm_99515.1	chr11	103104795	103104811	+	1	NA	exon (NM_025988, exon 7 of 10)	exon (NM_025988, exon 7 of 10)	3115	NM_025988	67131	Mm.390367	NM_025988	ENSMUSG00000056938	Acbd4	2010009P05Rik|2010015A21Rik|AI849317	acyl-Coenzyme A binding domain containing 4	protein-coding
mm_164758.1	chr17	84235861	84235877	+	1	NA	intron (NM_183021, intron 31 of 37)	intron (NM_183021, intron 31 of 37)	-47922	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_47976.1	chr5	135910782	135910794	-	1	NA	3' UTR (NM_018871, exon 2 of 2)	3' UTR (NM_018871, exon 2 of 2)	22869	NM_013560	15507	Mm.13849	NM_013560	ENSMUSG00000004951	Hspb1	27kDa|Hsp25	heat shock protein 1	protein-coding
mm_138057.1	chr17	33928156	33928250	+	1	NA	3' UTR (NM_009318, exon 8 of 8)	3' UTR (NM_009318, exon 8 of 8)	-1691	NM_009059	19732	Mm.43777	NM_009059	ENSMUSG00000041354	Rgl2	KE1.5|Rab2l|Rgt2|Rlf	ral guanine nucleotide dissociation stimulator-like 2	protein-coding
mm_50979.1	chr6	62057058	62057060	+	1	NA	intron (NM_001164316, intron 10 of 10)	MTEa|LTR|ERVL-MaLR	-876249	NR_040287	100504262	Mm.438066	NR_040287		A730020E08Rik	-	RIKEN cDNA A730020E08 gene	ncRNA
mm_80342.1	chr9	75081138	75081139	+	1	NA	intron (NM_010864, intron 1 of 40)	intron (NM_010864, intron 1 of 40)	9932	NM_010864	17918	Mm.3645	NM_010864	ENSMUSG00000034593	Myo5a	9630007J19Rik|AI413174|AI661011|Dbv|MVa|Myo5|MyoVA|Sev-1|d|d-120J|flail|flr	myosin VA	protein-coding
mm_152698.1	chr19	17166445	17166486	-	1	NA	intron (NM_181348, intron 9 of 19)	intron (NM_181348, intron 9 of 19)	173040	NM_001136484	14537	Mm.244825	NM_010265	ENSMUSG00000038843	Gcnt1	5630400D21Rik|B130048E03|C2 GlcNAcT|C2GNT|IGnT	glucosaminyl (N-acetyl) transferase 1, core 2	protein-coding
mm_170776.1	chr2	167631972	167631979	-	1	NA	promoter-TSS (NM_023230)	promoter-TSS (NM_023230)	30	NM_001311146	66589	Mm.278783	NM_023230	ENSMUSG00000078923	Ube2v1	0610011J09Rik|AI256840|CROC-1|CROC1|D7Bwg1382e|UEV-1	ubiquitin-conjugating enzyme E2 variant 1	protein-coding
mm_64690.1	chr7	4521877	4521903	-	1	NA	exon (NM_009406, exon 3 of 8)	exon (NM_009406, exon 3 of 8)	553	NM_009406	21954	Mm.27674	NM_009406	ENSMUSG00000035458	Tnni3	Tn1|cTnI	troponin I, cardiac 3	protein-coding
mm_114860.1	chr13	93340242	93340250	+	1	NA	intron (NM_152134, intron 1 of 8)	Tigger17a|DNA|TcMar-Tigger	32212	NM_152134	26556	Mm.37533	NM_011982	ENSMUSG00000007617	Homer1	PSD-Zip45|SYN47|Ves-1|homer-1|vesl-1	homer scaffolding protein 1	protein-coding
mm_38942.1	chr4	150198220	150198230	-	1	NA	exon (NM_009802, exon 2 of 8)	exon (NM_009802, exon 2 of 8)	2910	NM_009802	12353	Mm.232523	NM_009802	ENSMUSG00000028972	Car6	Ca6|DOC1	carbonic anhydrase 6	protein-coding
mm_62638.1	chr7	107664785	107664794	+	1	NA	intron (NM_001163557, intron 3 of 25)	intron (NM_001163557, intron 3 of 25)	57945	NM_001163557	19024	Mm.2817	NM_008905	ENSMUSG00000036528	Ppfibp2	Cclp1	PTPRF interacting protein, binding protein 2 (liprin beta 2)	protein-coding
mm_13755.1	chr2	118126682	118126714	+	1	NA	3' UTR (NM_011580, exon 22 of 22)	3' UTR (NM_011580, exon 22 of 22)	14822	NM_001313914	21825	Mm.4159	NM_011580	ENSMUSG00000040152	Thbs1	TSP-1|TSP1|Thbs-1|tbsp1	thrombospondin 1	protein-coding
mm_57513.1	chr6	125481815	125481822	-	1	NA	intron (NM_007657, intron 1 of 7)	intron (NM_007657, intron 1 of 7)	12937	NM_007657	12527	Mm.210676	NM_007657	ENSMUSG00000030342	Cd9	Tspan29	CD9 antigen	protein-coding
mm_22086.1	chr2	168767077	168767083	-	1	NA	5' UTR (NM_201396, exon 1 of 3)	5' UTR (NM_201396, exon 1 of 3)	121	NM_201395	99377	Mm.434054	NM_175303	ENSMUSG00000027547	Sall4	5730441M18Rik|AA407717|AL022809|AW536104|C330011P20Rik|C78083|C78563|Tex20	sal-like 4 (Drosophila)	protein-coding
mm_56341.1	chr6	92860432	92860447	-	1	NA	intron (NM_175314, intron 13 of 29)	intron (NM_175314, intron 13 of 29)	41002	NM_175314	101401	Mm.158235	NM_175314	ENSMUSG00000030022	Adamts9	1810011L16Rik|8430403M15Rik|AW743315|E030027K14Rik	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 9	protein-coding
mm_71856.1	chr8	68906325	68906331	+	1	NA	3' UTR (NM_008509, exon 10 of 10)	3' UTR (NM_008509, exon 10 of 10)	25773	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_113956.1	chr13	51132280	51132283	+	1	NA	intron (NM_146043, intron 3 of 5)	intron (NM_146043, intron 3 of 5)	-2037	NM_011462	20729	Mm.188432	NM_011462	ENSMUSG00000021395	Spin1	Spin	spindlin 1	protein-coding
mm_55466.1	chr6	67942550	67942565	-	1	NA	Intergenic	Intergenic	-376858	NR_003100	75070	Mm.463364	NR_003100		4930515G16Rik	-	myc induced nuclear antigen pseudogene	pseudo
mm_27016.1	chr3	26027282	26027294	-	1	NA	intron (NM_138666, intron 3 of 7)	B3A|SINE|B2	126019	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_126752.1	chr15	85772152	85772168	+	1	NA	intron (NM_001113418, intron 2 of 7)	intron (NM_001113418, intron 2 of 7)	36384	NM_011144	19013	Mm.212789	NM_011144	ENSMUSG00000022383	Ppara	4933429D07Rik|AW742785|Nr1c1|PPAR-alpha|PPARalpha|Ppar	peroxisome proliferator activated receptor alpha	protein-coding
mm_13938.1	chr2	121170179	121170180	+	1	NA	promoter-TSS (NR_110985)	promoter-TSS (NR_110985)	946	NM_001290819	99334	Mm.188422	NM_178889	ENSMUSG00000050619	Zscan29	AW125441|Zfp690	zinc finger SCAN domains 29	protein-coding
mm_121750.1	chr14	18894256	18894282	-	1	NA	promoter-TSS (NM_144839)	promoter-TSS (NM_144839)	-642	NM_144839	218793	Mm.23551	NM_144839	ENSMUSG00000058317	Ube2e2	BC016265	ubiquitin-conjugating enzyme E2E 2	protein-coding
mm_116191.1	chr13	31438311	31438319	-	1	NA	Intergenic	Intergenic	-119855	NM_008239	15220	Mm.44235	NM_008239	ENSMUSG00000038415	Foxq1	HFH-1|Hfh1|Hfh1l|sa	forkhead box Q1	protein-coding
mm_26235.1	chr3	141214476	141214479	+	1	NA	Intergenic	Intergenic	-2122	NM_008811	18598	Mm.4223	NM_008811	ENSMUSG00000047674	Pdha2	Pdhal	pyruvate dehydrogenase E1 alpha 2	protein-coding
mm_85743.1	chr9	108567337	108567359	-	1	NA	promoter-TSS (NR_029577)	promoter-TSS (NR_029577)	-6	NM_023247	66706	Mm.29471	NM_023247	ENSMUSG00000070283	Ndufaf3	4733401H18Rik	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, assembly factor 3	protein-coding
mm_138842.1	chr17	40298187	40298217	+	1	NA	exon (NM_009638, exon 7 of 8)	exon (NM_009638, exon 7 of 8)	21005	NM_009638	11571	Mm.16781	NM_009638	ENSMUSG00000025431	Crisp1	AW324342|Aeg1|CRISP-1	cysteine-rich secretory protein 1	protein-coding
mm_29527.1	chr3	116645719	116645730	-	1	NA	intron (NM_008246, intron 4 of 11)	intron (NM_008246, intron 4 of 11)	16953	NM_008246	15247	Mm.280077	NM_008246	ENSMUSG00000089911	Mfsd14a	Hiat1	major facilitator superfamily domain containing 14A	protein-coding
mm_123689.1	chr14	69636845	69636855	-	1	NA	intron (NM_033325, intron 2 of 13)	B4|SINE|B4	27374	NM_033325	94352	Mm.116714	NM_033325	ENSMUSG00000034205	Loxl2	1110004B06Rik|4930526G11Rik|9430067E15Rik	lysyl oxidase-like 2	protein-coding
mm_169045.1	chr1	3150879	3150886	+	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	520616	NM_001011874	497097	Mm.454496	NM_001011874	ENSMUSG00000051951	Xkr4	AY534250|Gm210|XRG4|mKIAA1889	X-linked Kx blood group related 4	protein-coding
mm_24195.1	chr3	88607743	88607757	+	1	NA	Intergenic	Intergenic	-8457	NM_001198911	16800	Mm.239329	NM_008487	ENSMUSG00000028059	Arhgef2	AA408978|GEF|GEF-H1|GEFH1|LFP40|Lbcl1|Lfc|P40|mKIAA0651	rho/rac guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_153269.1	chr19	37174922	37174935	-	1	NA	exon (NM_198300, exon 2 of 11)	exon (NM_198300, exon 2 of 11)	1085	NR_045329	319931	Mm.446730	NR_045329	ENSMUSG00000097591	A330032B11Rik	-	RIKEN cDNA A330032B11 gene	ncRNA
mm_17879.1	chr2	34961556	34961639	-	1	NA	5' UTR (NM_001326601, exon 1 of 10)	5' UTR (NM_001326601, exon 1 of 10)	175	NM_009421	22029	Mm.239514	NM_009421	ENSMUSG00000026875	Traf1	4732496E14Rik	TNF receptor-associated factor 1	protein-coding
mm_168261.1	chr10	87686215	87686225	+	1	NA	Intergenic	RLTR9E|LTR|ERVK	164425	NM_008777	18478	Mm.263539	NM_008777	ENSMUSG00000020051	Pah	AW106920	phenylalanine hydroxylase	protein-coding
mm_146602.1	chr18	9508208	9508243	-	1	NA	Intergenic	Intergenic	-58075	NM_026484	67974	Mm.86523	NM_026484	ENSMUSG00000024286	Ccny	1700025H17Rik|3110050L10Rik|4631402G10Rik|5730405I09Rik	cyclin Y	protein-coding
mm_99492.1	chr11	102775223	102775227	+	1	NA	intron (NM_001110778, intron 18 of 25)	intron (NM_001110778, intron 18 of 25)	13790	NM_001110778	11488	Mm.89854	NM_009613	ENSMUSG00000020926	Adam11	AW060611|Mdc	a disintegrin and metallopeptidase domain 11	protein-coding
mm_157736.1	chrX	71816651	71816666	-	1	NA	promoter-TSS (NM_001081356)	promoter-TSS (NM_001081356)	-100	NM_001081356	67048	Mm.41102	NM_001081356	ENSMUSG00000073131	Vma21	2610030H06Rik|AI840175	VMA21 vacuolar H+-ATPase homolog (S. cerevisiae)	protein-coding
mm_153584.1	chr19	43504585	43504595	-	1	NA	exon (NM_010324, exon 7 of 9)	exon (NM_010324, exon 7 of 9)	20015	NM_010324	14718	Mm.19039	NM_010324	ENSMUSG00000025190	Got1	AI789014|Got-1|cAspAT|cCAT	glutamic-oxaloacetic transaminase 1, soluble	protein-coding
mm_117641.1	chr13	92529984	92529987	-	1	NA	intron (NM_173392, intron 1 of 17)	intron (NM_173392, intron 1 of 17)	825	NM_173392	218441	Mm.259585	NM_173392	ENSMUSG00000021706	Zfyve16	AI035632|B130024H06Rik|B130031L15|mKIAA0305	zinc finger, FYVE domain containing 16	protein-coding
mm_78160.1	chr9	21027979	21027991	+	1	NA	3' UTR (NM_010493, exon 7 of 7)	3' UTR (NM_010493, exon 7 of 7)	-1388	NM_023892	78369	Mm.30220	NM_023892	ENSMUSG00000001014	Icam4	1810015M19Rik|Cd242|ICAM-4	intercellular adhesion molecule 4, Landsteiner-Wiener blood group	protein-coding
mm_59210.1	chr7	24530818	24530841	+	1	NA	5' UTR (NM_153134, exon 1 of 3)	5' UTR (NM_153134, exon 1 of 3)	181	NM_153134	210146	Mm.41108	NM_153134	ENSMUSG00000041037	Irgq	AF322649|FKSG27|Irgq1	immunity-related GTPase family, Q	protein-coding
mm_22571.1	chr3	10205231	10205242	+	1	NA	intron (NM_024406, intron 3 of 3)	intron (NM_024406, intron 3 of 3)	3340	NM_024406	11770	Mm.582	NM_024406	ENSMUSG00000062515	Fabp4	422/aP2|ALBP/Ap2|Ap2|Lbpl	fatty acid binding protein 4, adipocyte	protein-coding
mm_39161.1	chr4	155601792	155601841	-	1	NA	intron (NM_177186, intron 1 of 8)	CpG	400	NM_177186	320541	Mm.306018	NM_177186	ENSMUSG00000042202	Slc35e2	A530082C11Rik|AI957035	solute carrier family 35, member E2	protein-coding
mm_44203.1	chr5	3802859	3802875	-	1	NA	promoter-TSS (NM_001170552)	promoter-TSS (NM_001170552)	257	NM_001289528	70797	Mm.130148	NM_001003909	ENSMUSG00000040351	Ankib1	2310061P20Rik|4631416I11Rik|AW494740|C80642|mKIAA1386	ankyrin repeat and IBR domain containing 1	protein-coding
mm_30740.1	chr4	14284435	14284435	+	1	NA	intron (NR_131155, intron 1 of 2)	ID_B1|SINE|B4	6874	NR_131155	100040030	Mm.366499	NR_131155		Gm2560	-	predicted gene 2560	ncRNA
mm_78409.1	chr9	30427017	30427019	+	1	NA	promoter-TSS (NM_028874)	promoter-TSS (NM_028874)	-311	NM_028874	102607	Mm.35084	NM_028874	ENSMUSG00000031993	Snx19	3526401K03Rik|AI195321|AI848208|mKIAA0254	sorting nexin 19	protein-coding
mm_5492.1	chr1	36939555	36939565	-	1	NA	promoter-TSS (NM_018872)	promoter-TSS (NM_018872)	-33	NM_018872	56030	Mm.186943	NM_018872	ENSMUSG00000026116	Tmem131	2610524E03Rik|CC28|D1Bwg0491e|Neg|RW1|YR-23|mKIAA0257	transmembrane protein 131	protein-coding
mm_56136.1	chr6	87722787	87722801	-	1	NA	Intergenic	Intergenic	-8075	NM_001159697	58229	Mm.333229	NM_021418	ENSMUSG00000068263	Efcc1	Ccdc48	EF hand and coiled-coil domain containing 1	protein-coding
mm_131950.1	chr16	24393709	24393763	+	1	NA	promoter-TSS (NR_037954)	promoter-TSS (NR_037954)	-81	NR_037954	68841	Mm.361995	NR_037954		Lppos	1110054M08Rik|AI481106	LIM domain containing preferred translocation partner in lipoma, opposite strand	ncRNA
mm_102151.1	chr11	53656888	53656907	-	1	NA	intron (NM_009012, intron 21 of 24)	intron (NM_009012, intron 21 of 24)	-22195	NM_008355	16163	Mm.1284	NM_008355	ENSMUSG00000020383	Il13	Il-13	interleukin 13	protein-coding
mm_55992.1	chr6	86003596	86003625	-	1	NA	Intergenic	Intergenic	-13581	NM_012013	26910	Mm.8024	NM_012013	ENSMUSG00000030001	Figla	FIGalpha|bHLHc8	folliculogenesis specific basic helix-loop-helix	protein-coding
mm_42607.1	chr5	117841885	117841925	+	1	NA	Intergenic	CpG	-24934	NM_008712	18125	Mm.44249	NM_008712	ENSMUSG00000029361	Nos1	2310005C01Rik|N-NOS|NC-NOS|NO|NOS|NOS-I|Nos-1|bNOS|nNOS	nitric oxide synthase 1, neuronal	protein-coding
mm_151012.1	chr19	46707736	46707758	+	1	NA	intron (NM_020577, intron 1 of 10)	intron (NM_020577, intron 1 of 10)	304	NM_020577	57344	Mm.28566	NM_020577	ENSMUSG00000003559	As3mt	2310045H08Rik|Cyt19	arsenic (+3 oxidation state) methyltransferase	protein-coding
mm_18143.1	chr2	45059572	45059585	-	1	NA	intron (NM_001289521, intron 1 of 8)	intron (NM_001289521, intron 1 of 8)	-36401	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_104222.1	chr11	88456723	88456727	-	1	NA	intron (NM_054043, intron 7 of 13)	intron (NM_054043, intron 7 of 13)	103952	NR_039545	100628571		NR_039545	ENSMUSG00000092985	Mir378b	mir-378b|mmu-mir-378b	microRNA 378b	ncRNA
mm_23259.1	chr3	51415963	51415973	+	1	NA	promoter-TSS (NM_053089)	promoter-TSS (NM_053089)	-48	NM_053089	74838	Mm.275281	NM_053089	ENSMUSG00000063273	Naa15	5730450D16Rik|6330400I15|ASTBDN|Narg1|Tbdn-1|mNAT1	N(alpha)-acetyltransferase 15, NatA auxiliary subunit	protein-coding
mm_127727.1	chr15	103244004	103244019	+	1	NA	exon (NM_010447, exon 9 of 10)	exon (NM_010447, exon 9 of 10)	3557	NR_002883	434858	Mm.391346	NR_002883		Gm5643	EG434858	heterogeneous nuclear ribonucleoprotein A1 pseudogene	pseudo
mm_172850.1	chr9	36627028	36627028	+	1	NA	Intergenic	L1Md_F2|LINE|L1	11574	NM_001033325	235973	Mm.118804	NM_001033325	ENSMUSG00000070313	A630095E13Rik	Gm191|Pate14|Sslp-1|Sslp1	RIKEN cDNA A630095E13 gene	protein-coding
mm_104052.1	chr11	86358237	86358259	-	1	NA	promoter-TSS (NM_001080931)	promoter-TSS (NM_001080931)	-723	NM_001080931	327987	Mm.341886	NM_001080931	ENSMUSG00000034297	Med13	1110067M05Rik|D030023K18|Thrap1|Trap240	mediator complex subunit 13	protein-coding
mm_797.1	chr1	45347189	45347227	+	1	NA	exon (NM_009930, exon 49 of 51)	exon (NM_009930, exon 49 of 51)	35670	NM_009930	12825	Mm.249555	NM_009930	ENSMUSG00000026043	Col3a1	AW550625|Col3a-1|Tsk-2|Tsk2	collagen, type III, alpha 1	protein-coding
mm_143043.1	chr17	56830917	56831005	-	1	NA	promoter-TSS (NM_009056)	promoter-TSS (NM_009056)	47	NM_009056	19725	Mm.102	NM_009056	ENSMUSG00000024206	Rfx2	5430432H19Rik	regulatory factor X, 2 (influences HLA class II expression)	protein-coding
mm_105141.1	chr11	101459774	101459807	-	1	NA	3' UTR (NM_012037, exon 6 of 6)	3' UTR (NM_012037, exon 6 of 6)	6409	NM_012037	26949	Mm.29210	NM_012037	ENSMUSG00000034993	Vat1	VAT-1	vesicle amine transport 1	protein-coding
mm_142002.1	chr17	35199673	35199675	-	1	NA	3' UTR (NM_013693, exon 4 of 4)	3' UTR (NM_013693, exon 4 of 4)	2333	NM_013693	21926	Mm.1293	NM_013693	ENSMUSG00000024401	Tnf	DIF|TNF-a|TNF-alpha|TNFSF2|TNFalpha|Tnfa|Tnfsf1a|Tnlg1f	tumor necrosis factor	protein-coding
mm_20479.1	chr2	129629983	129630002	-	1	NA	exon (NM_001291022, exon 5 of 5)	exon (NM_001291022, exon 5 of 5)	36823	NM_001291022	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_172820.1	chr9	12808514	12808514	-	1	NA	Intergenic	L1Md_T|LINE|L1	297341	NR_040755	78219	Mm.414868	NR_040755	ENSMUSG00000111830	4930568E12Rik	-	RIKEN cDNA 4930568E12 gene	ncRNA
mm_4652.1	chr1	180334825	180334841	+	1	NA	intron (NM_001081175, intron 2 of 7)	intron (NM_001081175, intron 2 of 7)	-4284	NR_003623	277333	Mm.389223	NM_199472		Gm5069	EG277333	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_128277.1	chr15	36811246	36811278	-	1	NA	Intergenic	Intergenic	-14333	NM_001253806	22631	Mm.3360	NM_011740	ENSMUSG00000022285	Ywhaz	1110013I11Rik|14-3-3zeta|AI596267|AL022924|AU020854	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide	protein-coding
mm_33237.1	chr4	127023333	127023354	+	1	NA	exon (NM_023603, exon 3 of 10)	exon (NM_023603, exon 3 of 10)	2042	NM_023603	71514	Mm.257276	NM_023603	ENSMUSG00000028820	Sfpq	1110004P21Rik|2810416M14Rik|5730453G22Rik|9030402K04Rik|AU021830|D4Ertd314e|Gm12940|OTTMUSG00000009329|PSF|REP1	splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)	protein-coding
mm_53460.1	chr6	134831033	134831036	+	1	NA	intron (NM_177687, intron 1 of 4)	intron (NM_177687, intron 1 of 4)	835	NM_177687	232430	Mm.267010	NM_177687	ENSMUSG00000032652	Crebl2	AI046348|B230205M03	cAMP responsive element binding protein-like 2	protein-coding
mm_131006.1	chr15	103562837	103562846	-	1	NA	TTS (NM_008134)	TTS (NM_008134)	2240	NM_001289587	14663	Mm.219621	NM_008134	ENSMUSG00000022491	Glycam1	MC26|Sgp50|glyCAM-1	glycosylation dependent cell adhesion molecule 1	protein-coding
mm_41245.1	chr5	88781962	88781973	+	1	NA	3' UTR (NM_007832, exon 7 of 7)	3' UTR (NM_007832, exon 7 of 7)	16954	NM_007832	13178	Mm.298892	NM_007832	ENSMUSG00000029366	Dck	-	deoxycytidine kinase	protein-coding
mm_59208.1	chr7	24530646	24530693	+	1	NA	promoter-TSS (NM_153134)	promoter-TSS (NM_153134)	21	NM_153134	210146	Mm.41108	NM_153134	ENSMUSG00000041037	Irgq	AF322649|FKSG27|Irgq1	immunity-related GTPase family, Q	protein-coding
mm_172527.1	chr7	85023608	85023608	-	1	NA	Intergenic	L1Md_T|LINE|L1	-11588	NM_001033878	233437	Mm.424396	NM_001033878	ENSMUSG00000094950	Vmn2r66	F830104D24Rik	vomeronasal 2, receptor 66	protein-coding
mm_57153.1	chr6	122730098	122730119	-	1	NA	exon (NM_011401, exon 10 of 10)	exon (NM_011401, exon 10 of 10)	12637	NM_011401	20527	Mm.395108	NM_011401	ENSMUSG00000003153	Slc2a3	AA408729|AL023014|AL024341|AU040424|C78366|Glut-3|Glut3	solute carrier family 2 (facilitated glucose transporter), member 3	protein-coding
mm_170378.1	chr1	85598776	85598780	-	1	NA	promoter-TSS (NM_030194)	promoter-TSS (NM_030194)	32	NM_030194	109032	Mm.335802	NM_030194	ENSMUSG00000070034	Sp110	5031415C07Rik|52kDa|5830484A20Rik|ENSMUSG00000075603|Ifi75|Ipr1	Sp110 nuclear body protein	protein-coding
mm_93095.1	chr10	89686220	89686244	-	1	NA	promoter-TSS (NM_001310704)	promoter-TSS (NM_001310704)	53	NM_198021	213326	Mm.27651	NM_198021	ENSMUSG00000069539	Scyl2	AU015688|AW536445|BC030932|CVAK104|D10Ertd802e	SCY1-like 2 (S. cerevisiae)	protein-coding
mm_8650.1	chr1	156441401	156441454	-	1	NA	exon (NM_009230, exon 7 of 16)	exon (NM_009230, exon 7 of 16)	-20512	NM_001346967	77352	Mm.428709	NM_001033180	ENSMUSG00000026601	Axdnd1	9430070O13Rik|Gm979	axonemal dynein light chain domain containing 1	protein-coding
mm_113772.1	chr13	44840758	44840795	+	1	NA	intron (NM_001205044, intron 3 of 18)	C-rich|Low_complexity|Low_complexity	109505	NM_001205043	16468	Mm.25059	NM_021878	ENSMUSG00000038518	Jarid2	Jmj|jumonji	jumonji, AT rich interactive domain 2	protein-coding
mm_139445.1	chr17	55445672	55445701	+	1	NA	promoter-TSS (NM_172829)	promoter-TSS (NM_172829)	-31	NM_172829	240119	Mm.311687	NM_172829	ENSMUSG00000024172	St6gal2	C230064G14Rik|St6galII|mKIAA1877	beta galactoside alpha 2,6 sialyltransferase 2	protein-coding
mm_27449.1	chr3	52009134	52009157	-	1	NA	intron (NM_001004176, intron 1 of 4)	intron (NM_001004176, intron 1 of 4)	95861	NM_001004176	433586	Mm.234972	NM_001004176	ENSMUSG00000061143	Maml3	AV234550|BC049812|Mam-2|mKIAA1816	mastermind like 3 (Drosophila)	protein-coding
mm_173161.1	chrX	38668096	38668097	-	1	NA	Intergenic	Intergenic	-32953	NM_021550	59048	Mm.441410	NM_021550	ENSMUSG00000048970	C1galt1c1	1500002I11Rik|AB030184|C1GalT2|C81205|Cosmc	C1GALT1-specific chaperone 1	protein-coding
mm_164310.1	chr15	103897500	103897508	-	1	NA	exon (NM_009267, exon 3 of 4)	exon (NM_009267, exon 3 of 4)	1796	NM_009268	20771	Mm.30276	NM_009268		Mucl1	Spt-2|Spt2	mucin-like 1	protein-coding
mm_77730.1	chr8	126855890	126855917	-	1	NA	Intergenic	L1MB2|LINE|L1	90018	NM_024214	67952	Mm.6932	NM_024214	ENSMUSG00000093904	Tomm20	1810060K07Rik|BB284719|Gm19268|MAS20|MOM19|TOM20|mKIAA0016	translocase of outer mitochondrial membrane 20 homolog (yeast)	protein-coding
mm_92042.1	chr10	62494894	62494898	-	1	NA	exon (NM_011157, exon 3 of 3)	exon (NM_011157, exon 3 of 3)	-8091	NM_133672	30930	Mm.260703	NM_133672	ENSMUSG00000020078	Vps26a	AA407240|HB58|Vps26	VPS26 retromer complex component A	protein-coding
mm_3227.1	chr1	135848858	135848868	+	1	NA	exon (NM_001130176, exon 8 of 13)	exon (NM_001130176, exon 8 of 13)	8002	NM_001130176	21956	Mm.247470	NM_011619	ENSMUSG00000026414	Tnnt2	Tnt|cTnT	troponin T2, cardiac	protein-coding
mm_113941.1	chr13	49732445	49732464	+	1	NA	exon (NM_172015, exon 33 of 34)	exon (NM_172015, exon 33 of 34)	50324	NM_172015	105148	Mm.21118	NM_172015	ENSMUSG00000037851	Iars	2510016L12Rik|AI327140|AU044614|E430001P04Rik|ILRS	isoleucine-tRNA synthetase	protein-coding
mm_49459.1	chr6	29399199	29399211	+	1	NA	exon (NM_001347073, exon 3 of 10)	exon (NM_001347073, exon 3 of 10)	279	NM_001201378	232664	Mm.251303	NM_145574	ENSMUSG00000029769	Ccdc136	4921511K06Rik|BC006583	coiled-coil domain containing 136	protein-coding
mm_41196.1	chr5	88328129	88328141	+	1	NA	exon (NM_008644, exon 3 of 3)	exon (NM_008644, exon 3 of 3)	10823	NM_008644	17830	Mm.200411	NM_008644	ENSMUSG00000064156	Prol1	Muc10	proline rich, lacrimal 1	protein-coding
mm_4940.1	chr1	191183493	191183505	+	1	NA	promoter-TSS (NM_007498)	promoter-TSS (NM_007498)	-166	NM_007498	11910	Mm.2706	NM_007498	ENSMUSG00000026628	Atf3	LRG-21	activating transcription factor 3	protein-coding
mm_33722.1	chr4	134065697	134065704	+	1	NA	Intergenic	Intergenic	-2752	NM_001162970	230806	Mm.240080	NM_001162970	ENSMUSG00000012123	Aim1l	-	absent in melanoma 1-like	protein-coding
mm_134886.1	chr16	29378697	29378712	-	1	NA	promoter-TSS (NM_175650)	promoter-TSS (NM_175650)	28	NM_001284375	268878	Mm.9823	NM_175650	ENSMUSG00000048939	Atp13a5	C630015F21Rik	ATPase type 13A5	protein-coding
mm_151717.1	chr19	4774070	4774070	-	1	NA	Intergenic	Intergenic	17545	NM_025717	66704	Mm.396734	NM_025717	ENSMUSG00000033760	Rbm4b	4921506I22Rik|AI504630|AI506404|Lark2|Neosin	RNA binding motif protein 4B	protein-coding
mm_7624.1	chr1	127242245	127242274	-	1	NA	intron (NM_145128, intron 1 of 17)	intron (NM_145128, intron 1 of 17)	37273	NM_145128	107895	Mm.214682	NM_145128	ENSMUSG00000036155	Mgat5	4930471A21Rik|5330407H02Rik|AI480971|GlcNAc-TV	mannoside acetylglucosaminyltransferase 5	protein-coding
mm_56851.1	chr6	117937687	117937697	-	1	NA	promoter-TSS (NM_001173372)	promoter-TSS (NM_001173372)	-357	NM_001173372	108017	Mm.250392	NM_033648	ENSMUSG00000004988	Fxyd4	0610008I02Rik|AI267073|Chif	FXYD domain-containing ion transport regulator 4	protein-coding
mm_142687.1	chr17	47734345	47734364	-	1	NA	3' UTR (NM_025973, exon 9 of 9)	3' UTR (NM_025973, exon 9 of 9)	-2683	NM_001161722	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_104147.1	chr11	87074056	87074071	-	1	NA	promoter-TSS (NM_025638)	promoter-TSS (NM_025638)	74	NM_025638	66569	Mm.281887	NM_025638	ENSMUSG00000061666	Gdpd1	2610020H15Rik	glycerophosphodiester phosphodiesterase domain containing 1	protein-coding
mm_169019.1	chr13	111593639	111593655	-	1	NA	Intergenic	Intergenic	-92531	NM_172593	218613	Mm.31012	NM_172593	ENSMUSG00000032727	Mier3	5730509D14|AU015422|D130064H19Rik	MIER family member 3	protein-coding
mm_154965.1	chrX	37048808	37048814	+	1	NA	promoter-TSS (NM_173779)	promoter-TSS (NM_173779)	-34	NM_173779	245381	Mm.123697	NM_173779	ENSMUSG00000044400	Sowahd	A630014H24Rik|Ankrd58	sosondowah ankyrin repeat domain family member D	protein-coding
mm_58490.1	chr7	3693724	3693815	+	1	NA	promoter-TSS (NM_029934)	promoter-TSS (NM_029934)	159	NM_001164205	66078	Mm.379100	NM_024168	ENSMUSG00000035585	Tsen34	0610027F08Rik|Leng5	tRNA splicing endonuclease subunit 34	protein-coding
mm_77325.1	chr8	119424345	119424362	-	1	NA	Intergenic	Intergenic	-12809	NM_027950	71839	Mm.272357	NM_027950	ENSMUSG00000074063	Osgin1	1700012B18Rik|Okl38	oxidative stress induced growth inhibitor 1	protein-coding
mm_86482.1	chr10	4862316	4862319	+	1	NA	intron (NM_001302531, intron 5 of 8)	Lx9|LINE|L1	152159	NM_001302533	13982	Mm.9213	NM_007956	ENSMUSG00000019768	Esr1	ER|ER-alpha|ERa|ERalpha|ESR|Estr|Estra|Nr3a1	estrogen receptor 1 (alpha)	protein-coding
mm_45705.1	chr5	83355094	83355113	-	1	NA	promoter-TSS (NM_153801)	promoter-TSS (NM_153801)	92	NM_153801	243078	Mm.126783	NM_153801	ENSMUSG00000049537	Tecrl	D330017N19Rik|Srd5a2l2	trans-2,3-enoyl-CoA reductase-like	protein-coding
mm_41173.1	chr5	88002556	88002564	+	1	NA	promoter-TSS (NM_011422)	promoter-TSS (NM_011422)	35	NM_011422	20599	Mm.261199	NM_011422	ENSMUSG00000029280	Smr3a	AA589601|MSG1|MSG3|Smr1|Smr3	submaxillary gland androgen regulated protein 3A	protein-coding
mm_57399.1	chr6	124863878	124863996	-	1	NA	promoter-TSS (NM_013533)	promoter-TSS (NM_013533)	-20	NM_013533	14788	Mm.2514	NM_013533	ENSMUSG00000038390	Gpr162	A-2|BC031437|Grca	G protein-coupled receptor 162	protein-coding
mm_165279.1	chr2	81087326	81087329	+	1	NA	Intergenic	RMER19B|LTR|ERVK	448063	NM_001190179	69482	Mm.29200	NM_027091	ENSMUSG00000026999	Nup35	2310006I24Rik|35kDa|5330402E05Rik|MP44|NO44	nucleoporin 35	protein-coding
mm_44696.1	chr5	30408044	30408067	-	1	NA	intron (NM_001313767, intron 5 of 45)	intron (NM_001313767, intron 5 of 45)	53877	NM_001286421	83762	Mm.244502	NM_031875	ENSMUSG00000062372	Otof	-	otoferlin	protein-coding
mm_39066.1	chr4	154081547	154081586	-	1	NA	exon (NM_011642, exon 4 of 14)	exon (NM_011642, exon 4 of 14)	15607	NM_001126330	22062	Mm.78015	NM_011642	ENSMUSG00000029026	Trp73	TAp73|Tp73|deltaNp73|p73	transformation related protein 73	protein-coding
mm_23111.1	chr3	37481471	37481493	+	1	NA	intron (NM_001310473, intron 14 of 16)	LSU-rRNA_Hsa|rRNA|rRNA	61532	NM_021343	57815	Mm.172679	NM_021343	ENSMUSG00000027722	Spata5	2510048F20Rik|C78064|Spaf	spermatogenesis associated 5	protein-coding
mm_17431.1	chr2	27507605	27507620	-	1	NA	Intergenic	Intergenic	-7535	NM_080848	140858	Mm.28265	NM_080848	ENSMUSG00000026917	Wdr5	2410008O07Rik|AA408785|AA960360|Big|Big-3	WD repeat domain 5	protein-coding
mm_3660.1	chr1	153351345	153351350	+	1	NA	Intergenic	PB1D10|SINE|Alu	-18561	NM_010683	226519	Mm.1249	NM_010683	ENSMUSG00000026478	Lamc1	Lamb2	laminin, gamma 1	protein-coding
mm_23535.1	chr3	60806024	60806062	+	1	NA	Intergenic	Intergenic	-196742	NM_008772	18441	Mm.281452	NM_008772	ENSMUSG00000027765	P2ry1	P2Y1	purinergic receptor P2Y, G-protein coupled 1	protein-coding
mm_45386.1	chr5	66142944	66142965	-	1	NA	intron (NM_001127382, intron 2 of 7)	B2_Mm2|SINE|B2	8024	NM_001291226	245945	Mm.36863	NM_139065	ENSMUSG00000070780	Rbm47	9530077J19Rik	RNA binding motif protein 47	protein-coding
mm_54113.1	chr6	17634970	17634973	-	1	NA	Intergenic	Intergenic	-2127	NM_007604	12343	Mm.392504	NM_007604	ENSMUSG00000015733	Capza2	1110053K06Rik|AW208808|Cappa2	capping protein (actin filament) muscle Z-line, alpha 2	protein-coding
mm_22694.1	chr3	17794297	17794339	+	1	NA	intron (NR_033490, intron 1 of 2)	intron (NR_033490, intron 1 of 2)	-1344	NR_029814	723950		NR_029814	ENSMUSG00000093073	Mir124a-2	Mirn124a-2|mir-124-2|mir-124a-2	microRNA 124a-2	ncRNA
mm_162783.1	chr10	70097238	70097250	+	1	NA	5' UTR (NM_001111121, exon 1 of 9)	5' UTR (NM_001111121, exon 1 of 9)	123	NM_001111121	76551	Mm.281741	NM_001111121	ENSMUSG00000048701	Ccdc6	2810012H18Rik|AA536681|AA960498|AW061011	coiled-coil domain containing 6	protein-coding
mm_89658.1	chr10	97483338	97483347	+	1	NA	5' UTR (NM_007833, exon 2 of 8)	5' UTR (NM_007833, exon 2 of 8)	1011	NM_007833	13179	Mm.56769	NM_007833	ENSMUSG00000019929	Dcn	DC|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding
mm_59552.1	chr7	28075178	28075188	+	1	NA	exon (NM_001122603, exon 3 of 20)	exon (NM_001122603, exon 3 of 20)	3947	NM_001122603	215384	Mm.292276	NM_175444	ENSMUSG00000047730	Fcgbp	A430096B05Rik	Fc fragment of IgG binding protein	protein-coding
mm_18936.1	chr2	76752488	76752499	-	1	NA	exon (NM_011652, exon 275 of 313)	exon (NM_011652, exon 275 of 313)	77178	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_143439.1	chr17	70852796	70852808	-	1	NA	intron (NM_001164074, intron 1 of 2)	CpG	730	NM_001164074	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_107064.1	chr12	16810941	16810978	+	1	NA	promoter-TSS (NM_033270)	promoter-TSS (NM_033270)	-6	NR_027677	50496	Mm.23296	NM_033270	ENSMUSG00000057469	E2f6	AI462434|E2F6a|E2F6b|EMA	E2F transcription factor 6	protein-coding
mm_96050.1	chr11	59564606	59564619	+	1	NA	intron (NM_145827, intron 7 of 9)	ORR1A4|LTR|ERVL-MaLR	7126	NM_001011789	257962	Mm.377316	NM_001011789	ENSMUSG00000059610	Olfr222	MOR256-45P	olfactory receptor 222	protein-coding
mm_42352.1	chr5	114911541	114911579	+	1	NA	3' UTR (NM_011854, exon 6 of 6)	3' UTR (NM_011854, exon 6 of 6)	-11680	NM_145209	231655	Mm.95479	NM_145209	ENSMUSG00000041827	Oasl1	7530414C13Rik|oasl9	2'-5' oligoadenylate synthetase-like 1	protein-coding
mm_18101.1	chr2	44988082	44988124	-	1	NA	3' UTR (NM_015753, exon 10 of 10)	3' UTR (NM_015753, exon 10 of 10)	35074	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_107817.1	chr12	65225748	65225757	+	1	NA	5' UTR (NM_027614, exon 1 of 2)	5' UTR (NM_027614, exon 1 of 2)	235	NM_027614	70948	Mm.219475	NM_027614	ENSMUSG00000035560	Wdr20rt	4921538B03Rik|4930427E19Rik|Wdr20|Wdr20b	WD repeat domain 20, retrogene	protein-coding
mm_31878.1	chr4	80932142	80932145	+	1	NA	intron (NM_026821, intron 1 of 1)	intron (NM_026821, intron 1 of 1)	21457	NM_026821	52829	Mm.273986	NM_026821	ENSMUSG00000048706	Lurap1l	1110029A09Rik|AV077978|AV175137|D4Bwg0951e|WI-13707|bM350F23.1	leucine rich adaptor protein 1-like	protein-coding
mm_118911.1	chr14	26673177	26673184	+	1	NA	Intergenic	Intergenic	-3334	NM_178668	211948	Mm.290758	NM_178668	ENSMUSG00000043702	Pde12	2'-PDE|E430028B21Rik	phosphodiesterase 12	protein-coding
mm_1406.1	chr1	67152673	67152718	+	1	NA	intron (NM_001080809, intron 7 of 37)	intron (NM_001080809, intron 7 of 37)	29668	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_114076.1	chr13	54503763	54503769	+	1	NA	promoter-TSS (NM_176987)	promoter-TSS (NM_176987)	-39	NM_176987	319719	Mm.376151	NM_176987	ENSMUSG00000043183	Simc1	4732471D19Rik	SUMO-interacting motifs containing 1	protein-coding
mm_47704.1	chr5	129887140	129887157	-	1	NA	intron (NM_024166, intron 1 of 3)	CpG	322	NM_024166	14004	Mm.30133	NM_024166	ENSMUSG00000070493	Chchd2	AL033347|Etohi6	coiled-coil-helix-coiled-coil-helix domain containing 2	protein-coding
mm_53092.1	chr6	125008999	125009043	+	1	NA	promoter-TSS (NM_175557)	promoter-TSS (NM_175557)	-217	NM_001252083	269800	Mm.108677	NM_175557	ENSMUSG00000038346	Zfp384	BB163993|C130073D16Rik|Ciz|NP|Nmp4	zinc finger protein 384	protein-coding
mm_163053.1	chr11	58421672	58421672	+	1	NA	intron (NM_027239, intron 1 of 5)	intron (NM_027239, intron 1 of 5)	561	NM_027239	69864	Mm.45641	NM_027239	ENSMUSG00000013653	1810065E05Rik	AV047390	RIKEN cDNA 1810065E05 gene	protein-coding
mm_141202.1	chr17	27028916	27028932	-	1	NA	promoter-TSS (NM_027544)	promoter-TSS (NM_027544)	-298	NM_007523	12018	Mm.2443	NM_007523	ENSMUSG00000057789	Bak1	Bak|N-BAK1|N-Bak	BCL2-antagonist/killer 1	protein-coding
mm_42157.1	chr5	112195497	112195499	+	1	NA	Intergenic	Intergenic	-11265	NR_045377	75569	Mm.243721	NR_045377	ENSMUSG00000101683	1700028D13Rik	-	RIKEN cDNA 1700028D13 gene	ncRNA
mm_64251.1	chr7	141704465	141704532	+	1	NA	intron (NM_023566, intron 27 of 45)	intron (NM_023566, intron 27 of 45)	14158	NM_023566	17831	Mm.2041	NM_023566		Muc2	2010015E03Rik|MCM|wnn	mucin 2	protein-coding
mm_120238.1	chr14	62917837	62917841	+	1	NA	intron (NM_175546, intron 3 of 11)	intron (NM_175546, intron 3 of 11)	52297	NR_105860	102465311		NR_105860	ENSMUSG00000098858	Mir6541	Gm27311|mmu-mir-6541	microRNA 6541	ncRNA
mm_167196.1	chr7	142660886	142660921	-	1	NA	non-coding (NR_002855, exon 1 of 4)	non-coding (NR_002855, exon 1 of 4)	368	NM_001122736	16002	Mm.3862	NM_010514	ENSMUSG00000048583	Igf2	AL033362|Igf-2|Igf-II|M6pr|Mpr|Peg2	insulin-like growth factor 2	protein-coding
mm_108293.1	chr12	79168463	79168463	+	1	NA	intron (NM_016800, intron 1 of 5)	intron (NM_016800, intron 1 of 5)	3995	NM_016800	53612	Mm.265929	NM_016800	ENSMUSG00000021124	Vti1b	AU015348|GES30|MVti1b|SNARE|Vti1-rp1	vesicle transport through interaction with t-SNAREs 1B	protein-coding
mm_131787.1	chr16	22898783	22898804	+	1	NA	intron (NR_075099, intron 5 of 5)	intron (NR_075099, intron 5 of 5)	-4407	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_71888.1	chr8	69822647	69822657	+	1	NA	promoter-TSS (NM_020028)	promoter-TSS (NM_020028)	87	NM_020028	53978	Mm.23253	NM_020028	ENSMUSG00000031861	Lpar2	Edg4|IPA2|LPA2	lysophosphatidic acid receptor 2	protein-coding
mm_46633.1	chr5	108519411	108519420	-	1	NA	3' UTR (NM_007756, exon 4 of 4)	3' UTR (NM_007756, exon 4 of 4)	30612	NM_007756	12889	Mm.5195	NM_007756	ENSMUSG00000033615	Cplx1	921-S	complexin 1	protein-coding
mm_70733.1	chr8	18846581	18846593	+	1	NA	exon (NM_026792, exon 1 of 8)	exon (NM_026792, exon 1 of 8)	308	NM_026792	52123	Mm.24117	NM_026792	ENSMUSG00000031467	Agpat5	1110013A05Rik|D8Ertd319e	1-acylglycerol-3-phosphate O-acyltransferase 5 (lysophosphatidic acid acyltransferase, epsilon)	protein-coding
mm_57499.1	chr6	125351401	125351422	-	1	NA	intron (NM_011609, intron 1 of 9)	intron (NM_011609, intron 1 of 9)	1688	NM_011609	21937	Mm.1258	NM_011609	ENSMUSG00000030341	Tnfrsf1a	CD120a|FPF|TNF-R|TNF-R-I|TNF-R1|TNF-R55|TNF-alphaR1|TNFAR|TNFR60|TNFRI|TNFRp55|TNFalpha-R1|Tnfr-2|Tnfr1|p55|p55-R	tumor necrosis factor receptor superfamily, member 1a	protein-coding
mm_67422.1	chr7	80340140	80340150	-	1	NA	promoter-TSS (NM_133952)	promoter-TSS (NM_133952)	74	NM_133952	101869	Mm.243024	NM_133952	ENSMUSG00000030533	Unc45a	AW538196	unc-45 myosin chaperone A	protein-coding
mm_98691.1	chr11	96299113	96299129	+	1	NA	promoter-TSS (NM_008269)	promoter-TSS (NM_008269)	-50	NM_008269	15414	Mm.215	NM_008269	ENSMUSG00000000690	Hoxb6	Hox-2.2	homeobox B6	protein-coding
mm_23358.1	chr3	55182008	55182012	+	1	NA	promoter-TSS (NM_028937)	promoter-TSS (NM_028937)	-34	NM_028937	74434	Mm.25514	NM_028937	ENSMUSG00000027794	Sohlh2	4933406N12Rik|AI413378|Sosf2	spermatogenesis and oogenesis specific basic helix-loop-helix 2	protein-coding
mm_47240.1	chr5	121521561	121521563	-	1	NA	5' UTR (NM_172126, exon 1 of 1)	5' UTR (NM_172126, exon 1 of 1)	133	NM_172126	280668	Mm.1453	NM_172126	ENSMUSG00000072647	Adam1a	Adam1|Ftna	a disintegrin and metallopeptidase domain 1a	protein-coding
mm_110568.1	chr12	56275704	56275729	-	1	NA	Intergenic	Intergenic	22473	NR_045048	100503961	Mm.136732	NR_045048		Gm19990	-	predicted gene, 19990	ncRNA
mm_121635.1	chr14	8368150	8368157	-	1	NA	intron (NM_146050, intron 1 of 9)	intron (NM_146050, intron 1 of 9)	10610	NM_146050	18300	Mm.25351	NM_146050	ENSMUSG00000021749	Oit1	2310076N21Rik|AV067083|EF-7|Fam3d	oncoprotein induced transcript 1	protein-coding
mm_88989.1	chr10	81565707	81565733	+	1	NA	non-coding (NR_074087, exon 7 of 7)	non-coding (NR_074087, exon 7 of 7)	6276	NM_001276288	14797	Mm.180013	NM_010347	ENSMUSG00000054452	Aes	AL024115|Esp1|Grg|Grg-5|Grg5|Tle5	amino-terminal enhancer of split	protein-coding
mm_68197.1	chr7	104380006	104380020	-	1	NA	Intergenic	Intergenic	-21367	NM_175648	244183	Mm.347647	NM_175648	ENSMUSG00000052749	Trim30b	A530023O14Rik|Trim30-1	tripartite motif-containing 30B	protein-coding
mm_62408.1	chr7	101205396	101205407	+	1	NA	intron (NM_199012, intron 8 of 20)	MER58A|DNA|hAT-Charlie	96626	NM_199012	207278	Mm.263041	NM_199012	ENSMUSG00000030691	Fchsd2	BC034086|R74866|Sh3md3|mKIAA0769	FCH and double SH3 domains 2	protein-coding
mm_146629.1	chr18	10182096	10182107	-	1	NA	promoter-TSS (NM_009071)	promoter-TSS (NM_009071)	-309	NM_009071	19877	Mm.6710	NM_009071	ENSMUSG00000024290	Rock1	1110055K06Rik|Rock-I	Rho-associated coiled-coil containing protein kinase 1	protein-coding
mm_99720.1	chr11	106300271	106300276	+	1	NA	TTS (NM_008117)	TTS (NM_008117)	1623	NM_008117	14599	Mm.343934	NM_008117	ENSMUSG00000020713	Gh	Gh1|Ghb1	growth hormone	protein-coding
mm_120294.1	chr14	63138348	63138360	+	1	NA	exon (NM_007798, exon 7 of 10)	exon (NM_007798, exon 7 of 10)	15892	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_41005.1	chr5	81019717	81019732	+	1	NA	promoter-TSS (NM_001347367)	promoter-TSS (NM_001347367)	-847	NM_001347367	319387	Mm.273631	NM_198702	ENSMUSG00000037605	Adgrl3	5430402I23Rik|CIRL-3|D130075K09Rik|Gm1379|LEC3|Lphn3|mKIAA0768	adhesion G protein-coupled receptor L3	protein-coding
mm_42789.1	chr5	121506909	121506912	+	1	NA	Intergenic	ID_B1|SINE|B4	-3930	NM_172125	280667	Mm.444773	NM_172125	ENSMUSG00000062438	Adam1b	Adam1|Ftna	a disintegrin and metallopeptidase domain 1b	protein-coding
mm_171881.1	chr5	32854288	32854290	-	1	NA	promoter-TSS (NM_194340)	promoter-TSS (NM_194340)	-59	NM_194340	215476	Mm.248721	NM_194340	ENSMUSG00000054280	Prr14l	6030436E02Rik|C330019G07Rik|Prl14l	proline rich 14-like	protein-coding
mm_76780.1	chr8	97429197	97429200	-	1	NA	Intergenic	Intergenic	-883225	NR_039538	100628567		NR_039538	ENSMUSG00000104794	Mir28c	mmu-mir-28c	microRNA 28c	ncRNA
mm_151822.1	chr19	5560601	5560617	-	1	NA	promoter-TSS (NM_019935)	promoter-TSS (NM_019935)	-34	NM_019935	18426	Mm.280225	NM_019935	ENSMUSG00000024922	Ovol1	BB147136|Ovo1|movo1	ovo like zinc finger 1	protein-coding
mm_135590.1	chr16	50721441	50721476	-	1	NA	Intergenic	Intergenic	-5674	NR_105782	102466634		NR_105782	ENSMUSG00000098482	Mir6363	Gm28026|mmu-mir-6363	microRNA 6363	ncRNA
mm_101989.1	chr11	50887464	50887525	-	1	NA	promoter-TSS (NM_172794)	promoter-TSS (NM_172794)	-51	NM_172794	237758	Mm.74335	NM_172794	ENSMUSG00000048728	Zfp454	B230342N19	zinc finger protein 454	protein-coding
mm_14535.1	chr2	132781663	132781678	+	1	NA	5' UTR (NM_007694, exon 1 of 5)	5' UTR (NM_007694, exon 1 of 5)	392	NM_007694	12653	Mm.255241	NM_007694	ENSMUSG00000027350	Chgb	Scg-1	chromogranin B	protein-coding
mm_84439.1	chr9	66124710	66124720	-	1	NA	exon (NM_019727, exon 1 of 15)	exon (NM_019727, exon 1 of 15)	171	NM_019727	56440	Mm.271891	NM_019727	ENSMUSG00000032382	Snx1	-	sorting nexin 1	protein-coding
mm_69596.1	chr7	135716316	135716320	-	1	NA	promoter-TSS (NM_001081117)	promoter-TSS (NM_001081117)	61	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_165640.1	chr3	75143770	75143773	-	1	NA	promoter-TSS (NM_172515)	promoter-TSS (NM_172515)	1	NM_001310529	213234	Mm.80075	NM_172515	ENSMUSG00000034151	Zbbx	4931432L23	zinc finger, B-box domain containing	protein-coding
mm_51866.1	chr6	90550754	90550764	+	1	NA	promoter-TSS (NM_027406)	promoter-TSS (NM_027406)	-89	NM_027406	107747	Mm.30035	NM_027406	ENSMUSG00000030088	Aldh1l1	1810048F20Rik|FDH|Fthfd|Neut2	aldehyde dehydrogenase 1 family, member L1	protein-coding
mm_9683.1	chr1	178333572	178333605	-	1	NA	exon (NM_016805, exon 5 of 14)	exon (NM_016805, exon 5 of 14)	4196	NM_016805	51810	Mm.86589	NM_016805	ENSMUSG00000039630	Hnrnpu	AA408410|AI256620|AL024194|AL024437|AW557595|C86794|Hnrpu|SAFA|Sp120|hnRNP U	heterogeneous nuclear ribonucleoprotein U	protein-coding
mm_171556.1	chr4	147132108	147132109	+	1	NA	Intergenic	Intergenic	-43758	NM_001039209	195531	Mm.270762	NM_001039209	ENSMUSG00000078496	Zfp982	Gm13152|OTTMUSG00000010671	zinc finger protein 982	protein-coding
mm_114547.1	chr13	73938123	73938147	+	1	NA	promoter-TSS (NM_027182)	promoter-TSS (NM_027182)	324	NM_001308041	105246	Mm.278509	NM_001024508	ENSMUSG00000057649	Brd9	AL022779	bromodomain containing 9	protein-coding
mm_116688.1	chr13	49298803	49298813	-	1	NA	intron (NM_015759, intron 1 of 17)	intron (NM_015759, intron 1 of 17)	10400	NM_015759	30938	Mm.291089	NM_015759	ENSMUSG00000037946	Fgd3	5830461L01Rik|ZFYVE5	FYVE, RhoGEF and PH domain containing 3	protein-coding
mm_21568.1	chr2	164236099	164236118	-	1	NA	3' UTR (NM_017390, exon 3 of 3)	3' UTR (NM_017390, exon 3 of 3)	2233	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_48814.1	chr5	148996609	148996620	-	1	NA	Intergenic	Intergenic	-1399	NR_102384	319982	Mm.33303	NR_102383	ENSMUSG00000106951	5930430L01Rik	-	RIKEN cDNA 5930430L01 gene	ncRNA
mm_119959.1	chr14	55371166	55371174	+	1	NA	Intergenic	Intergenic	-107588	NM_001037938	28200	Mm.27427	NM_030686	ENSMUSG00000022210	Dhrs4	AI043103|AI790593|CR|D14Ucla2|NDRD|PHCR|PSCD|RRD|mouNRDR	dehydrogenase/reductase (SDR family) member 4	protein-coding
mm_109633.1	chr12	112767825	112767852	+	1	NA	exon (NM_178911, exon 9 of 11)	exon (NM_178911, exon 9 of 11)	7183	NM_178911	104759	Mm.203915	NM_178911	ENSMUSG00000052160	Pld4	AI132321|thss	phospholipase D family, member 4	protein-coding
mm_141850.1	chr17	34801787	34801797	-	1	NA	exon (NM_009995, exon 10 of 10)	exon (NM_009995, exon 10 of 10)	2634	NM_009995	13079	Mm.440407	NM_009995	ENSMUSG00000024365	Cyp21a1	21-OH|21OH|21OHA|21OHB|CYP21OH-A|Cyp21|Cyp21-ps1|Cyp21B|Cyp21a2-ps|Cyp21a2ps|Oh21-1|Oh21-2	cytochrome P450, family 21, subfamily a, polypeptide 1	protein-coding
mm_157063.1	chrX	8145697	8145707	-	1	NA	non-coding (NR_033561, exon 1 of 3)	non-coding (NR_033561, exon 1 of 3)	178	NM_001166410	19652	Mm.128512	NM_016809	ENSMUSG00000031167	Rbm3	2600016C11Rik	RNA binding motif protein 3	protein-coding
mm_47242.1	chr5	121527225	121527258	-	1	NA	intron (NM_010765, intron 10 of 13)	intron (NM_010765, intron 10 of 13)	-5546	NM_172126	280668	Mm.1453	NM_172126	ENSMUSG00000072647	Adam1a	Adam1|Ftna	a disintegrin and metallopeptidase domain 1a	protein-coding
mm_109704.1	chr12	113359911	113359956	+	1	NA	Intergenic	Intergenic	-129632	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_145079.1	chr18	42325977	42325987	+	1	NA	exon (NM_172626, exon 14 of 20)	exon (NM_172626, exon 14 of 20)	50629	NM_172626	225432	Mm.329400	NM_172626	ENSMUSG00000024491	Rbm27	A730010I06|AI043120|Psc1|mKIAA1311	RNA binding motif protein 27	protein-coding
mm_92732.1	chr10	80900750	80900819	-	1	NA	TTS (NM_010722)	TTS (NM_010722)	185	NM_013895	30055	Mm.142132	NM_013895	ENSMUSG00000020219	Timm13	D10Ertd378e|Tim9|Timm9	translocase of inner mitochondrial membrane 13	protein-coding
mm_100140.1	chr11	115982714	115982727	+	1	NA	exon (NM_133663, exon 8 of 39)	exon (NM_133663, exon 8 of 39)	7995	NM_133663	192897	Mm.213873	NM_133663	ENSMUSG00000020758	Itgb4	AA407042|C230078O20|CD104	integrin beta 4	protein-coding
mm_75184.1	chr8	36953083	36953127	-	1	NA	promoter-TSS (NM_001194940)	promoter-TSS (NM_001194940)	-663	NM_001194940	50768	Mm.125155	NM_015802	ENSMUSG00000031523	Dlc1	A730069N07Rik|Arhgap7|HP|STARD12|dlc-1	deleted in liver cancer 1	protein-coding
mm_150518.1	chr19	39035633	39035644	+	1	NA	intron (NM_028089, intron 7 of 8)	intron (NM_028089, intron 7 of 8)	-25368	NM_028191	72303	Mm.482578	NM_028191	ENSMUSG00000067231	Cyp2c65	2210009K14Rik	cytochrome P450, family 2, subfamily c, polypeptide 65	protein-coding
mm_47889.1	chr5	134703813	134703824	-	1	NA	exon (NM_007925, exon 37 of 37)	exon (NM_007925, exon 37 of 37)	-15228	NM_010717	16885	Mm.15409	NM_010717	ENSMUSG00000029674	Limk1	KIZ-1|LIMK-1|Limk	LIM-domain containing, protein kinase	protein-coding
mm_79330.1	chr9	53340632	53340646	+	1	NA	intron (NM_176846, intron 3 of 5)	intron (NM_176846, intron 3 of 5)	38969	NM_176846	320051	Mm.277540	NM_176846	ENSMUSG00000034584	Exph5	AC079869.22gm5|B130009M24Rik|E030050P12|Kiaa0624|Slac2b|slac2-b	exophilin 5	protein-coding
mm_63000.1	chr7	120740038	120740051	+	1	NA	5' UTR (NM_177697, exon 2 of 34)	5' UTR (NM_177697, exon 2 of 34)	487	NM_177697	233813	Mm.389939	NM_177697	ENSMUSG00000030889	Vwa3a	E030013G06Rik	von Willebrand factor A domain containing 3A	protein-coding
mm_115245.1	chr13	110395973	110395979	+	1	NA	intron (NM_152804, intron 1 of 13)	intron (NM_152804, intron 1 of 13)	932	NM_152804	20620	Mm.380	NM_152804	ENSMUSG00000021701	Plk2	Snk	polo-like kinase 2	protein-coding
mm_9336.1	chr1	172004452	172004458	-	1	NA	3' UTR (NM_033509, exon 8 of 8)	3' UTR (NM_033509, exon 8 of 8)	22840	NM_033509	93840	Mm.36148	NM_033509	ENSMUSG00000026556	Vangl2	C530001F03Rik|Lootl|Lp|Lpp1|Ltap|Vang1l2|loop-tail|ska17|ska<m17Jus>|stbm|strabismus	vang-like 2 (van gogh, Drosophila)	protein-coding
mm_162344.1	chr1	51250065	51250080	-	1	NA	intron (NR_045151, intron 4 of 4)	intron (NR_045151, intron 4 of 4)	-39054	NM_138741	20324	Mm.398690	NM_138741	ENSMUSG00000045954	Sdpr	-	serum deprivation response	protein-coding
mm_149933.1	chr19	26781758	26781760	+	1	NA	intron (NR_045306, intron 1 of 3)	intron (NR_045306, intron 1 of 3)	33356	NM_026003	67155	Mm.342988	NM_011416	ENSMUSG00000024921	Smarca2	2610209L14Rik|SNF2alpha|Snf2l2|brahma|brm	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	protein-coding
mm_99898.1	chr11	109650575	109650579	+	1	NA	promoter-TSS (NM_021880)	promoter-TSS (NM_021880)	-344	NM_021880	19084	Mm.30039	NM_021880	ENSMUSG00000020612	Prkar1a	1300018C22Rik|RIalpha|Tse-1|Tse1	protein kinase, cAMP dependent regulatory, type I, alpha	protein-coding
mm_92826.1	chr10	81464440	81464476	-	1	NA	intron (NM_001311124, intron 9 of 11)	CpG-1367	8673	NM_001311127	319586	Mm.152689	NM_176954	ENSMUSG00000034818	Celf5	4930565A21Rik|Brunol5	CUGBP, Elav-like family member 5	protein-coding
mm_40278.1	chr5	41767660	41767663	+	1	NA	Intergenic	Intergenic	-3441	NM_007524	12020	Mm.2530	NM_007524	ENSMUSG00000049691	Nkx3-2	Bapx1|NKX3.2|Nkx-3.2	NK3 homeobox 2	protein-coding
mm_143183.1	chr17	57292397	57292425	-	1	NA	intron (NM_001163816, intron 1 of 25)	B4A|SINE|B4	13311	NM_001163815	22324	Mm.248172	NM_011691	ENSMUSG00000034116	Vav1	Vav|vav-T	vav 1 oncogene	protein-coding
mm_9445.1	chr1	172590492	172590581	-	1	NA	promoter-TSS (NM_029084)	promoter-TSS (NM_029084)	32	NM_029084	74748	Mm.179812	NM_029084	ENSMUSG00000053318	Slamf8	5830408F06Rik|Blame|SBBI42	SLAM family member 8	protein-coding
mm_20391.1	chr2	129065901	129065916	-	1	NA	promoter-TSS (NM_027192)	promoter-TSS (NM_027192)	-39	NM_027192	69737	Mm.33909	NM_027192	ENSMUSG00000027394	Ttl	2410003M22Rik|2700049H19Rik|AI848570	tubulin tyrosine ligase	protein-coding
mm_116983.1	chr13	56296328	56296347	-	1	NA	5' UTR (NM_019568, exon 1 of 4)	5' UTR (NM_019568, exon 1 of 4)	214	NM_019568	57266	Mm.30211	NM_019568	ENSMUSG00000021508	Cxcl14	1110031L23Rik|1200006I23Rik|AI414372|BMAC|BRAK|KS1|Kec|MIP-2g|MIP2gamma|NJAC|Scyb14|bolekine	chemokine (C-X-C motif) ligand 14	protein-coding
mm_48053.1	chr5	136546836	136546840	-	1	NA	intron (NM_001291234, intron 1 of 22)	B4A|SINE|B4	19143	NM_001291239	13047	Mm.320317	NM_009986	ENSMUSG00000029705	Cux1	CDP|Cutl1|Cux|Cux-1	cut-like homeobox 1	protein-coding
mm_73874.1	chr8	119095003	119095032	+	1	NA	intron (NM_019707, intron 6 of 13)	intron (NM_019707, intron 6 of 13)	-249521	NM_024219	68196	Mm.358714	NM_024219	ENSMUSG00000031839	Hsbp1	0610007A03Rik|AA408769|Hsp25	heat shock factor binding protein 1	protein-coding
mm_130457.1	chr15	98567631	98567748	-	1	NA	promoter-TSS (NM_009833)	promoter-TSS (NM_009833)	-53	NM_009833	12455	Mm.29941	NM_009833	ENSMUSG00000011960	Ccnt1	2810478G24Rik|AI115585|CycT1	cyclin T1	protein-coding
mm_151530.1	chr19	58744132	58744142	+	1	NA	TTS (NM_018874)	TTS (NM_018874)	15250	NM_018874	18946	Mm.10753	NM_018874	ENSMUSG00000042179	Pnliprp1	Plrp1	pancreatic lipase related protein 1	protein-coding
mm_140657.1	chr17	12769606	12769700	-	1	NA	promoter-TSS (NM_010515)	promoter-TSS (NM_010515)	53	NM_010515	16004	Mm.26553	NM_010515	ENSMUSG00000023830	Igf2r	AI661837|CD222|CI-MPR|M6P/IGF2R|Mpr300	insulin-like growth factor 2 receptor	protein-coding
mm_66766.1	chr7	46728984	46728990	-	1	NA	3' UTR (NM_011316, exon 4 of 4)	3' UTR (NM_011316, exon 4 of 4)	3616	NM_011316	20211	Mm.3489	NM_011316	ENSMUSG00000040017	Saa4	Saa-4|Saa-5	serum amyloid A 4	protein-coding
mm_84095.1	chr9	58247451	58247465	-	1	NA	intron (NM_001311088, intron 1 of 8)	intron (NM_001311088, intron 1 of 8)	2328	NM_178087	18854	Mm.392123	NM_008884	ENSMUSG00000036986	Pml	1200009E24Rik|AI661194|Trim19	promyelocytic leukemia	protein-coding
mm_160407.1	chr8	71703534	71703534	-	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	-1734	NM_028189	72297	Mm.290837	NM_028189	ENSMUSG00000031803	B3gnt3	2210008L19Rik	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 3	protein-coding
mm_167328.1	chr8	70310378	70310397	+	1	NA	exon (NM_021538, exon 7 of 10)	exon (NM_021538, exon 7 of 10)	-5388	NM_138647	93898	Mm.258280	NM_138647	ENSMUSG00000087408	Cers1	Lass1|Uog-1|to	ceramide synthase 1	protein-coding
mm_57645.1	chr6	128434784	128434799	-	1	NA	exon (NM_010219, exon 4 of 10)	exon (NM_010219, exon 4 of 10)	3840	NM_010219	14228	Mm.12758	NM_010219	ENSMUSG00000030357	Fkbp4	59kDa|AL022792|AW208983|FKBP-4|FKBP-52|FKBP52|FKPB52|p59	FK506 binding protein 4	protein-coding
mm_107397.1	chr12	33315514	33315526	+	1	NA	intron (NM_001033436, intron 1 of 7)	intron (NM_001033436, intron 1 of 7)	13005	NM_001033436	380753	Mm.41540	NM_028139	ENSMUSG00000020564	Atxn7l1	2810423G08Rik|Atxn7l4	ataxin 7-like 1	protein-coding
mm_162811.1	chr10	79681015	79681040	+	1	NA	Intergenic	Intergenic	-1168	NM_177613	216150	Mm.21981	NM_177613	ENSMUSG00000020307	Cdc34	AI327276|UBE2R1	cell division cycle 34	protein-coding
mm_108000.1	chr12	73353144	73353149	+	1	NA	3' UTR (NM_001037717, exon 16 of 16)	3' UTR (NM_001037717, exon 16 of 16)	56417	NR_046013	380765	Mm.490476	NR_046013		D830013O20Rik	Gm891	RIKEN cDNA D830013O20 gene	ncRNA
mm_75871.1	chr8	70764152	70764184	-	1	NA	intron (NM_023065, intron 5 of 7)	intron (NM_023065, intron 5 of 7)	2495	NM_023065	65972	Mm.30241	NM_023065	ENSMUSG00000031838	Ifi30	GILT|IP30	interferon gamma inducible protein 30	protein-coding
mm_123851.1	chr14	70766599	70766644	-	1	NA	promoter-TSS (NM_023045)	promoter-TSS (NM_023045)	7	NM_023045	65246	Mm.152987	NM_023045	ENSMUSG00000022100	Xpo7	4930506C02Rik|BB164534|Ranbp16|mKIAA0745	exportin 7	protein-coding
mm_96893.1	chr11	70437316	70437326	+	1	NA	promoter-TSS (NR_106064)	promoter-TSS (NR_106064)	-934	NR_106064	102465670		NR_106064	ENSMUSG00000099109	Mir7115	Gm27902|mmu-mir-7115	microRNA 7115	ncRNA
mm_118636.1	chr14	21356318	21356321	+	1	NA	intron (NM_001243041, intron 7 of 10)	intron (NM_001243041, intron 7 of 10)	-143451	NM_001205241	54169	Mm.248967	NM_017479	ENSMUSG00000021767	Kat6b	AI507552|B130044K16Rik|MYST-4|Morf|Myst4|mKIAA0383|qkf|querkopf	K(lysine) acetyltransferase 6B	protein-coding
mm_170608.1	chr19	5845348	5845367	-	1	NA	non-coding (NR_003513, exon 1 of 1)	non-coding (NR_003513, exon 1 of 1)	121	NR_131212	66961	Mm.281895	NR_003513	ENSMUSG00000092274	Neat1	2310043N10Rik|VINC	nuclear paraspeckle assembly transcript 1 (non-protein coding)	ncRNA
mm_156629.1	chrX	155262532	155262544	+	1	NA	promoter-TSS (NM_019736)	promoter-TSS (NM_019736)	95	NM_019736	56360	Mm.268710	NM_019736	ENSMUSG00000025287	Acot9	0610041P13Rik|Acate2|C76421|MT-ACT48|MTE-2|U8|p48	acyl-CoA thioesterase 9	protein-coding
mm_152791.1	chr19	21471161	21471174	-	1	NA	intron (NM_010266, intron 1 of 13)	intron (NM_010266, intron 1 of 13)	1494	NM_010266	14544	Mm.45054	NM_010266	ENSMUSG00000058624	Gda	AU015411|AW047581|GAH	guanine deaminase	protein-coding
mm_2163.1	chr1	88227071	88227071	+	1	NA	promoter-TSS (NM_001281466)	promoter-TSS (NM_001281466)	51	NM_001281466	100040766	Mm.386915	NM_001177364	ENSMUSG00000079429	Mroh2a	ENSMUSG00000044873|Heatr7b1|OTTMUSG00000020804	maestro heat-like repeat family member 2A	protein-coding
mm_126664.1	chr15	84324193	84324204	+	1	NA	promoter-TSS (NM_022321)	promoter-TSS (NM_022321)	-522	NM_022321	64099	Mm.251356	NM_022321	ENSMUSG00000022439	Parvg	AI413459	parvin, gamma	protein-coding
mm_46092.1	chr5	92347103	92347118	-	1	NA	3' UTR (NM_021274, exon 4 of 4)	3' UTR (NM_021274, exon 4 of 4)	1779	NM_021274	15945	Mm.877	NM_021274	ENSMUSG00000034855	Cxcl10	C7|CRG-2|INP10|IP-10|IP10|Ifi10|Scyb10|gIP-10|mob-1	chemokine (C-X-C motif) ligand 10	protein-coding
mm_160512.1	chr9	21635363	21635363	+	1	NA	intron (NM_001174079, intron 3 of 33)	intron (NM_001174079, intron 3 of 33)	19194	NM_001174078	20586	Mm.286593	NM_011417	ENSMUSG00000032187	Smarca4	Brg1|HP1-BP72|SNF2beta|SW1/SNF|b2b508.1Clo|b2b692Clo	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	protein-coding
mm_59642.1	chr7	28159427	28159431	+	1	NA	exon (NM_001164655, exon 17 of 20)	exon (NM_001164655, exon 17 of 20)	-10319	NM_007991	14113	Mm.4595	NM_007991	ENSMUSG00000046865	Fbl	AL022665|FIB|FLRN|RNU3IP1	fibrillarin	protein-coding
mm_22313.1	chr2	180439523	180439528	-	1	NA	Intergenic	B4|SINE|B4	-21453	NM_148933	108115	Mm.133687	NM_148933	ENSMUSG00000038963	Slco4a1	OATP-E|Slc21a12	solute carrier organic anion transporter family, member 4a1	protein-coding
mm_132445.1	chr16	35981594	35981631	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-1751	NM_008465	16646	Mm.3991	NM_008465	ENSMUSG00000022905	Kpna1	AW494490|IPOA5|NPI1|Rch2|mSRP1	karyopherin (importin) alpha 1	protein-coding
mm_119259.1	chr14	33953978	33954016	+	1	NA	promoter-TSS (NM_015745)	promoter-TSS (NM_015745)	-25	NM_015745	19661	Mm.436622	NM_015745	ENSMUSG00000041534	Rbp3	Irbp|Rbp-3	retinol binding protein 3, interstitial	protein-coding
mm_14434.1	chr2	130589453	130589464	+	1	NA	TTS (NM_001255994)	TTS (NM_001255994)	-6870	NM_009732	11998	Mm.6190	NM_009732	ENSMUSG00000037727	Avp	Vp|Vsp	arginine vasopressin	protein-coding
mm_66566.1	chr7	45239376	45239387	-	1	NA	promoter-TSS (NM_007645)	promoter-TSS (NM_007645)	-266	NM_001290804	12493	Mm.3689	NM_007645	ENSMUSG00000030798	Cd37	Tspan26	CD37 antigen	protein-coding
mm_132196.1	chr16	32496260	32496267	+	1	NA	promoter-TSS (NM_199309)	promoter-TSS (NM_199309)	-18	NM_199309	245308	Mm.76859	NM_199309	ENSMUSG00000052363	Zdhhc19	Gm1744|Gm616	zinc finger, DHHC domain containing 19	protein-coding
mm_69246.1	chr7	127810935	127810951	-	1	NA	exon (NM_024414, exon 6 of 10)	exon (NM_024414, exon 6 of 10)	10334	NM_001040684	101502	Mm.157103	NM_133943	ENSMUSG00000042289	Hsd3b7	AI195443|BB098564	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 7	protein-coding
mm_57717.1	chr6	128788567	128788574	-	1	NA	promoter-TSS (NM_001159904)	promoter-TSS (NM_001159904)	71	NM_008527	17059	Mm.480764	NM_008527	ENSMUSG00000030325	Klrb1c	AI462337|CD161|Ly-59|Ly55c|Ly59|NK-RP1|NK1.1|NKR-P1.9|NKRP1|NKRP140|Nk-1|Nk-1.2|Nk1|Nk1.2|Nkrp1c|ly-55c	killer cell lectin-like receptor subfamily B member 1C	protein-coding
mm_114759.1	chr13	85189493	85189508	+	1	NA	5' UTR (NM_001347588, exon 1 of 9)	5' UTR (NM_001347588, exon 1 of 9)	115	NM_023243	66671	Mm.18474	NM_023243	ENSMUSG00000021548	Ccnh	6330408H09Rik|AI661354|AV102684|AW538719	cyclin H	protein-coding
mm_79913.1	chr9	65462666	65462672	+	1	NA	intron (NM_138584, intron 1 of 8)	intron (NM_138584, intron 1 of 8)	1732	NM_138584	27965	Mm.272475	NM_138584	ENSMUSG00000032388	Spg21	ACP33|BM-019|C78576|D9Wsu18e|GL010|MAST	spastic paraplegia 21 homolog (human)	protein-coding
mm_135856.1	chr16	59632526	59632541	-	1	NA	intron (NM_001347244, intron 1 of 8)	intron (NM_001347244, intron 1 of 8)	-4412	NR_040564	75145	Mm.399348	NR_040564		4930547E14Rik	-	RIKEN cDNA 4930547E14 gene	ncRNA
mm_107484.1	chr12	38545293	38545296	+	1	NA	intron (NM_178681, intron 22 of 24)	intron (NM_178681, intron 22 of 24)	69227	NR_045943	73867	Mm.78933	NR_045943		4930428E07Rik	-	RIKEN cDNA 4930428E07 gene	ncRNA
mm_136685.1	chr17	6782852	6782877	+	1	NA	promoter-TSS (NM_009510)	promoter-TSS (NM_009510)	-84	NM_009510	22350	Mm.277812	NM_009510	ENSMUSG00000052397	Ezr	AW146364|R75297|Vil2|p81	ezrin	protein-coding
mm_116656.1	chr13	49190152	49190167	-	1	NA	intron (NM_013610, intron 1 of 3)	intron (NM_013610, intron 1 of 3)	2612	NM_013610	18081	Mm.18503	NM_013610	ENSMUSG00000037966	Ninj1	AU024536	ninjurin 1	protein-coding
mm_168442.1	chr11	40420522	40420541	-	1	NA	Intergenic	Intergenic	272151	NM_134017	108645	Mm.293771	NM_134017	ENSMUSG00000042032	Mat2b	1110064C04Rik|2410018D16Rik|AI182287|AU022853|MAT-II|MATIIbeta|TGR	methionine adenosyltransferase II, beta	protein-coding
mm_62534.1	chr7	102249621	102249693	+	1	NA	intron (NM_019566, intron 1 of 1)	intron (NM_019566, intron 1 of 1)	461	NM_019566	56212	Mm.259795	NM_019566	ENSMUSG00000073982	Rhog	2810426G09Rik|Arhg|Sid10750	ras homolog family member G	protein-coding
mm_66569.1	chr7	45308684	45308702	-	1	NA	exon (NM_175130, exon 19 of 25)	exon (NM_175130, exon 19 of 25)	-16265	NR_110499	100040970	Mm.289810	NR_110499	ENSMUSG00000046721	Rpl14-ps1	ENSMUSG00000046721|Gm9811	ribosomal protein L14, pseudogene 1	pseudo
mm_132072.1	chr16	30065624	30065638	+	1	NA	exon (NM_008235, exon 1 of 4)	exon (NM_008235, exon 1 of 4)	274	NM_008235	15205	Mm.390859	NM_008235	ENSMUSG00000022528	Hes1	Hry|bHLHb39	hairy and enhancer of split 1 (Drosophila)	protein-coding
mm_31222.1	chr4	44018797	44018816	+	1	NA	intron (NM_016760, intron 1 of 5)	intron (NM_016760, intron 1 of 5)	6156	NM_001290470	12757	Mm.298875	NM_016760	ENSMUSG00000028478	Clta	AV026556|Lca	clathrin, light polypeptide (Lca)	protein-coding
mm_46362.1	chr5	103347904	103347912	-	1	NA	Intergenic	Intergenic	-48879	NR_040699	74624	Mm.389662	NR_040699	ENSMUSG00000104956	4930429D17Rik	-	RIKEN cDNA 4930429D17 gene	ncRNA
mm_31640.1	chr4	59581544	59581554	+	1	NA	promoter-TSS (NM_024255)	promoter-TSS (NM_024255)	-14	NM_001301367	72479	Mm.272905	NM_024255	ENSMUSG00000028383	Hsdl2	2610207I16Rik	hydroxysteroid dehydrogenase like 2	protein-coding
mm_20354.1	chr2	127975631	127975653	-	1	NA	intron (NM_028765, intron 10 of 17)	intron (NM_028765, intron 10 of 17)	121014	NM_028765	74121	Mm.244835	NM_028765	ENSMUSG00000027380	Acoxl	1200014P05Rik|AV025673	acyl-Coenzyme A oxidase-like	protein-coding
mm_129365.1	chr15	77970731	77970743	-	1	NA	promoter-TSS (NM_018749)	promoter-TSS (NM_018749)	87	NM_018749	55944	Mm.3955	NM_018749	ENSMUSG00000016554	Eif3d	66/67kDa|AA407891|Eif3s7|eIF3p66	eukaryotic translation initiation factor 3, subunit D	protein-coding
mm_49653.1	chr6	31023558	31023559	+	1	NA	Intergenic	L1_Mur3|LINE|L1	39189	NR_029744	387222		NR_029744	ENSMUSG00000065610	Mir29a	Mirn29a|mir-29a|mmu-mir-29a	microRNA 29a	ncRNA
mm_58234.1	chr6	145032809	145032847	-	1	NA	exon (NM_001024468, exon 5 of 11)	exon (NM_001024468, exon 5 of 11)	15984	NM_001024468	12035	Mm.4606	NM_007532	ENSMUSG00000030268	Bcat1	BCATc|Eca39	branched chain aminotransferase 1, cytosolic	protein-coding
mm_137045.1	chr17	17916185	17916196	+	1	NA	Intergenic	ID_B1|SINE|B4	28366	NM_008039	14289	Mm.378918	NM_008039	ENSMUSG00000052270	Fpr2	E330010I07Rik|Fpr-rs2	formyl peptide receptor 2	protein-coding
mm_26399.1	chr3	142602342	142602352	+	1	NA	intron (NM_010259, intron 4 of 10)	RLTR34B_MM|LTR|ERVK	7500	NM_010259	14468	Mm.457978	NM_010259	ENSMUSG00000040264	Gbp2b	Gbp-1|Gbp1|Mag-1|Mpa-1|Mpa1	guanylate binding protein 2b	protein-coding
mm_98486.1	chr11	94951230	94951240	+	1	NA	exon (NM_007742, exon 50 of 51)	exon (NM_007742, exon 50 of 51)	15011	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_140317.1	chr17	86338603	86338613	+	1	NA	intron (NM_011104, intron 1 of 14)	intron (NM_011104, intron 1 of 14)	-51430	NR_045435	72104	Mm.443401	NR_045435	ENSMUSG00000100738	2010106C02Rik	-	RIKEN cDNA 2010106C02 gene	ncRNA
mm_67005.1	chr7	65213445	65213449	-	1	NA	Intergenic	Intergenic	-56919	NM_183087	70638	Mm.441986	NM_183087	ENSMUSG00000030518	Fam189a1	5730507A09Rik|AW047451	family with sequence similarity 189, member A1	protein-coding
mm_15172.1	chr2	154015948	154015969	+	1	NA	3' UTR (NM_008953, exon 9 of 9)	3' UTR (NM_008953, exon 9 of 9)	7682	NM_008953	19194	Mm.29197	NM_008953	ENSMUSG00000042459	Bpifa2	Bpifa2e|Psp	BPI fold containing family A, member 2	protein-coding
mm_127624.1	chr15	102462253	102462263	+	1	NA	3' UTR (NM_025385, exon 5 of 5)	3' UTR (NM_025385, exon 5 of 5)	3088	NM_025385	66151	Mm.393955	NM_025385	ENSMUSG00000023048	Prr13	1110020C13Rik|2010324E22Rik	proline rich 13	protein-coding
mm_28330.1	chr3	89365234	89365244	-	1	NA	promoter-TSS (NM_029974)	promoter-TSS (NM_029974)	14	NM_029974	77772	Mm.164013	NM_029974	ENSMUSG00000042672	Dcst1	A330106H01Rik	DC-STAMP domain containing 1	protein-coding
mm_42644.1	chr5	118614975	118614977	+	1	NA	intron (NM_001347445, intron 2 of 30)	intron (NM_001347445, intron 2 of 30)	54257	NM_172424	76199	Mm.206238	NM_172424	ENSMUSG00000018076	Med13l	2210413I17Rik|6330591G05Rik|9030618F05Rik|Thrap2|Trap240L|mKIAA1025	mediator complex subunit 13-like	protein-coding
mm_107940.1	chr12	71889502	71889515	+	1	NA	promoter-TSS (NM_001286452)	promoter-TSS (NM_001286452)	-35	NM_001286452	208846	Mm.87417	NM_026102	ENSMUSG00000034574	Daam1	-	dishevelled associated activator of morphogenesis 1	protein-coding
mm_110242.1	chr12	31090553	31090569	-	1	NA	Intergenic	Intergenic	16593	NM_027828	104943	Mm.248938	NM_027828	ENSMUSG00000036136	Fam110c	9030611O19Rik|AU019489	family with sequence similarity 110, member C	protein-coding
mm_155844.1	chrX	101254560	101254574	+	1	NA	promoter-TSS (NM_018789)	promoter-TSS (NM_018789)	39	NM_018789	54601	Mm.240299	NM_018789	ENSMUSG00000042903	Foxo4	Afxh|Mllt7|afx	forkhead box O4	protein-coding
mm_147294.1	chr18	39491554	39491563	-	1	NA	Intergenic	CpG	-4313	NM_008173	14815	Mm.129481	NM_008173	ENSMUSG00000024431	Nr3c1	GR|Grl-1|Grl1	nuclear receptor subfamily 3, group C, member 1	protein-coding
mm_117174.1	chr13	63246247	63246250	-	1	NA	intron (NR_110520, intron 2 of 5)	intron (NR_110520, intron 2 of 5)	6219	NR_110521	72061	Mm.188105	NM_028079	ENSMUSG00000021458	2010111I01Rik	2300006M17Rik|AP-O|AW742919|Aopep|ApO|mir-23b|mir-24-1|mir-27b	RIKEN cDNA 2010111I01 gene	protein-coding
mm_5208.1	chr1	13566098	13566178	-	1	NA	3' UTR (NM_028173, exon 11 of 11)	3' UTR (NM_028173, exon 11 of 11)	23772	NM_028173	72265	Mm.28765	NM_028173	ENSMUSG00000025935	Tram1	1810049E02Rik|TRAMP	translocating chain-associating membrane protein 1	protein-coding
mm_162029.1	chr19	53330305	53330305	+	1	NA	promoter-TSS (NM_001008543)	promoter-TSS (NM_001008543)	-141	NM_001008543	17859	Mm.2154	NM_010847	ENSMUSG00000025025	Mxi1	ENSMUSG00000067085|Gm10197|Mad2|bHLHc11	MAX interactor 1, dimerization protein	protein-coding
mm_165257.1	chr2	72634044	72634060	+	1	NA	Intergenic	CpG	-69458	NR_040503	74541	Mm.410774	NR_040503	ENSMUSG00000085252	8430437L04Rik	-	RIKEN cDNA 8430437L04 gene	ncRNA
mm_41693.1	chr5	100650542	100650553	+	1	NA	Intergenic	Intergenic	23709	NM_027978	71883	Mm.260661	NM_027978	ENSMUSG00000029319	Coq2	2310002F18Rik|PHB:PPT	coenzyme Q2 4-hydroxybenzoate polyprenyltransferase	protein-coding
mm_27696.1	chr3	66296919	66296930	-	1	NA	promoter-TSS (NM_145820)	promoter-TSS (NM_145820)	-87	NM_145820	72789	Mm.443526	NM_028357	ENSMUSG00000027831	Veph1	2810471M23Rik|Veph	ventricular zone expressed PH domain-containing 1	protein-coding
mm_5280.1	chr1	20586910	20586913	-	1	NA	intron (NM_153179, intron 7 of 66)	intron (NM_153179, intron 7 of 66)	31146	NM_153179	241035	Mm.249253	NM_153179	ENSMUSG00000043760	Pkhd1	AI118496|AI182499|FPC|Tigm1	polycystic kidney and hepatic disease 1	protein-coding
mm_116171.1	chr13	30794019	30794063	-	1	NA	Intergenic	Intergenic	44808	NM_013674	16364	Mm.4677	NM_013674	ENSMUSG00000021356	Irf4	AI385587|IRF-4|LSIRF|NF-EM5|Spip	interferon regulatory factor 4	protein-coding
mm_99990.1	chr11	114727385	114727435	+	1	NA	promoter-TSS (NM_001034878)	promoter-TSS (NM_001034878)	-2	NM_001034878	432611	Mm.212764	NM_001034878	ENSMUSG00000034706	Dnaic2	C030015H18Rik|Dnai2|Gm728	dynein, axonemal, intermediate chain 2	protein-coding
mm_84951.1	chr9	83146602	83146614	-	1	NA	promoter-TSS (NM_026122)	promoter-TSS (NM_026122)	-1	NM_026122	94353	Mm.244426	NM_026122	ENSMUSG00000066456	Hmgn3	1110002A15Rik|6330514M13Rik|BB071015|TRIP7	high mobility group nucleosomal binding domain 3	protein-coding
mm_121923.1	chr14	23554757	23554769	-	1	NA	intron (NM_001253366, intron 5 of 29)	intron (NM_001253366, intron 5 of 29)	449442	NM_001253375	16531	Mm.343607	NM_010610	ENSMUSG00000063142	Kcnma1	5730414M22Rik|BKCa|MaxiK|Slo|Slo1|mSlo|mSlo1	potassium large conductance calcium-activated channel, subfamily M, alpha member 1	protein-coding
mm_29376.1	chr3	108722282	108722311	-	1	NA	promoter-TSS (NM_029522)	promoter-TSS (NM_029522)	3	NM_029522	76123	Mm.226941	NM_029522	ENSMUSG00000027883	Gpsm2	6230410J09Rik|LGN|Pins	G-protein signalling modulator 2 (AGS3-like, C. elegans)	protein-coding
mm_31972.1	chr4	88179554	88179568	+	1	NA	intron (NM_001081184, intron 8 of 43)	intron (NM_001081184, intron 8 of 43)	57521	NR_030478	735282		NR_030478	ENSMUSG00000070077	Mir491	Mirn491|mir-491|mmu-mir-491	microRNA 491	ncRNA
mm_66881.1	chr7	58740521	58740528	-	1	NA	intron (NM_009728, intron 2 of 20)	intron (NM_009728, intron 2 of 20)	82322	NM_009728	11982	Mm.135129	NM_009728	ENSMUSG00000025324	Atp10a	Atp10c|pfatp	ATPase, class V, type 10A	protein-coding
mm_50836.1	chr6	54816766	54816776	+	1	NA	promoter-TSS (NM_199143)	promoter-TSS (NM_199143)	-145	NM_199143	387524	Mm.286149	NM_199143	ENSMUSG00000058446	Znrf2	1190002C14Rik|AU044205|D6Ertd365e	zinc and ring finger 2	protein-coding
mm_137769.1	chr17	29490824	29490839	+	1	NA	promoter-TSS (NM_008842)	promoter-TSS (NM_008842)	-214	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_139416.1	chr17	53421934	53421939	+	1	NA	exon (NM_172497, exon 9 of 13)	exon (NM_172497, exon 9 of 13)	41385	NM_172497	211482	Mm.60887	NM_172497	ENSMUSG00000023931	Efhb	4921525D22Rik	EF hand domain family, member B	protein-coding
mm_87625.1	chr10	57807352	57807370	+	1	NA	exon (NM_020561, exon 5 of 8)	exon (NM_020561, exon 5 of 8)	12817	NM_020561	57319	Mm.2379	NM_020561	ENSMUSG00000019872	Smpdl3a	0610010C24Rik|AI529588|ASM3A|ASML3|ASML3A	sphingomyelin phosphodiesterase, acid-like 3A	protein-coding
mm_75662.1	chr8	66486453	66486469	-	1	NA	promoter-TSS (NM_025465)	promoter-TSS (NM_025465)	46	NM_025465	66282	Mm.294985	NM_025465	ENSMUSG00000025591	Tma16	1810029B16Rik	translation machinery associated 16	protein-coding
mm_103691.1	chr11	79504079	79504089	-	1	NA	promoter-TSS (NM_019409)	promoter-TSS (NM_019409)	-2	NM_019409	18377	Mm.93335	NM_019409	ENSMUSG00000049612	Omg	-	oligodendrocyte myelin glycoprotein	protein-coding
mm_93917.1	chr10	127067733	127067760	-	1	NA	TTS (NM_009870)	TTS (NM_009870)	2515	NM_025982	67125	Mm.35650	NM_025982	ENSMUSG00000006736	Tspan31	2700085A14Rik|AW742554|Sas	tetraspanin 31	protein-coding
mm_85082.1	chr9	91365346	91365362	-	1	NA	5' UTR (NM_009573, exon 1 of 3)	5' UTR (NM_009573, exon 1 of 3)	445	NM_009573	22771	Mm.335350	NM_009573	ENSMUSG00000032368	Zic1	ZIC|ZNF201	zinc finger protein of the cerebellum 1	protein-coding
mm_76578.1	chr8	89006698	89006711	-	1	NA	Intergenic	CpG	-18031	NR_106190	102465899		NR_106190	ENSMUSG00000099078	Mir8110	Gm27571|mmu-mir-8110	microRNA 8110	ncRNA
mm_60626.1	chr7	44748504	44748560	+	1	NA	promoter-TSS (NM_178734)	promoter-TSS (NM_178734)	85	NM_178734	243963	Mm.382935	NM_178734	ENSMUSG00000048012	Zfp473	D030014N22Rik|Znf473|zfp-100	zinc finger protein 473	protein-coding
mm_35871.1	chr4	49536633	49536643	-	1	NA	3' UTR (NM_144903, exon 9 of 9)	3' UTR (NM_144903, exon 9 of 9)	12908	NM_144903	230163	Mm.482116	NM_144903	ENSMUSG00000028307	Aldob	Aldo-2|Aldo2|BC016435	aldolase B, fructose-bisphosphate	protein-coding
mm_160307.1	chr7	140704389	140704389	+	1	NA	exon (NM_146962, exon 1 of 1)	exon (NM_146962, exon 1 of 1)	136	NM_146962	258964	Mm.389986	NM_146962	ENSMUSG00000057997	Olfr541	MOR253-3	olfactory receptor 541	protein-coding
mm_90392.1	chr10	127322283	127322297	+	1	NA	exon (NM_001285785, exon 1 of 16)	exon (NM_001285785, exon 1 of 16)	326	NM_001285785	216445	Mm.227198	NM_146011	ENSMUSG00000040345	Arhgap9	AU043488	Rho GTPase activating protein 9	protein-coding
mm_131000.1	chr15	103534393	103534404	-	1	NA	exon (NM_021391, exon 2 of 7)	exon (NM_021391, exon 2 of 7)	3594	NM_021391	58200	Mm.143788	NM_021391	ENSMUSG00000022490	Ppp1r1a	0610038N18Rik|I-1	protein phosphatase 1, regulatory (inhibitor) subunit 1A	protein-coding
mm_73808.1	chr8	117340473	117340494	+	1	NA	intron (NM_001163262, intron 1 of 20)	intron (NM_001163262, intron 1 of 20)	-8687	NM_028941	74440	Mm.233181	NM_028941	ENSMUSG00000034390	Cmip	4933407C03Rik|5830471E12Rik|AI314065|AI464126	c-Maf inducing protein	protein-coding
mm_30125.1	chr3	141931485	141931498	-	1	NA	promoter-TSS (NM_001277220)	promoter-TSS (NM_001277220)	97	NM_001277218	12167	Mm.39089	NM_007560	ENSMUSG00000052430	Bmpr1b	AI385617|ALK-6|AV355320|Acvrlk6|Alk6|BMPR-1B|BMPR-IB|CFK-43a|SKR6	bone morphogenetic protein receptor, type 1B	protein-coding
mm_126223.1	chr15	78928369	78928399	+	1	NA	intron (NM_008495, intron 2 of 3)	intron (NM_008495, intron 2 of 3)	1659	NM_008495	16852	Mm.43831	NM_008495	ENSMUSG00000068220	Lgals1	AA410090|Gal-1|Galbp|L-14.5|L14|Lect14|galectin-1	lectin, galactose binding, soluble 1	protein-coding
mm_102772.1	chr11	68271246	68271254	-	1	NA	intron (NM_008744, intron 3 of 6)	intron (NM_008744, intron 3 of 6)	50358	NR_105833	102465219		NR_105833	ENSMUSG00000099174	Mir6406	Gm27981|mmu-mir-6406	microRNA 6406	ncRNA
mm_16886.1	chr2	13011601	13011629	-	1	NA	promoter-TSS (NM_153155)	promoter-TSS (NM_153155)	-751	NM_153155	227580	Mm.229322	NM_153155	ENSMUSG00000049630	C1ql3	1110065A22Rik|AI661623|C1ql|C1qtnf13|CTRP13|K100	C1q-like 3	protein-coding
mm_52754.1	chr6	120773585	120773586	+	1	NA	promoter-TSS (NM_001081048)	promoter-TSS (NM_001081048)	-183	NM_001081048	71803	Mm.425340	NM_001081048	ENSMUSG00000004902	Slc25a18	1500015I14Rik|AW125787	solute carrier family 25 (mitochondrial carrier), member 18	protein-coding
mm_76625.1	chr8	91801476	91801486	-	1	NA	5' UTR (NM_001253822, exon 1 of 4)	5' UTR (NM_001253822, exon 1 of 4)	173	NM_001253822	16373	Mm.238044	NM_008393	ENSMUSG00000031734	Irx3	AI894186	Iroquois related homeobox 3	protein-coding
mm_123013.1	chr14	55092362	55092421	-	1	NA	promoter-TSS (NM_001039198)	promoter-TSS (NM_001039198)	-343	NM_001039198	239102	Mm.441113	NM_001039198	ENSMUSG00000040721	Zfhx2	ZFH-5	zinc finger homeobox 2	protein-coding
mm_72059.1	chr8	71396854	71396891	+	1	NA	promoter-TSS (NM_026636)	promoter-TSS (NM_026636)	17	NM_026636	68251	Mm.21749	NM_026636	ENSMUSG00000031820	Babam1	5430437P03Rik|Merit40	BRISC and BRCA1 A complex member 1	protein-coding
mm_84683.1	chr9	72110989	72110997	-	1	NA	intron (NM_001253865, intron 1 of 14)	CpG	208	NM_001253862	21406	Mm.171615	NM_011544	ENSMUSG00000032228	Tcf12	A130037E08Rik|ALF1|HEB|HEBAlt|HTF-4|HTF4|ME1|REB|bHLHb20	transcription factor 12	protein-coding
mm_14131.1	chr2	126034796	126034808	+	1	NA	5' UTR (NM_008008, exon 1 of 4)	5' UTR (NM_008008, exon 1 of 4)	144	NM_008008	14178	Mm.330557	NM_008008	ENSMUSG00000027208	Fgf7	Kgf	fibroblast growth factor 7	protein-coding
mm_93362.1	chr10	103145478	103145492	-	1	NA	exon (NM_001163559, exon 20 of 26)	exon (NM_001163559, exon 20 of 26)	90837	NM_001163559	74978	Mm.483817	NM_029134	ENSMUSG00000019892	Lrriq1	4930503E15Rik|Gm1557	leucine-rich repeats and IQ motif containing 1	protein-coding
mm_91374.1	chr10	30200493	30200542	-	1	NA	promoter-TSS (NM_001109747)	promoter-TSS (NM_001109747)	23	NM_001109747	66311	Mm.251779	NM_001109747	ENSMUSG00000075266	Cenpw	2610036L11Rik|Cug2	centromere protein W	protein-coding
mm_86974.1	chr10	25408347	25408395	+	1	NA	promoter-TSS (NM_013511)	promoter-TSS (NM_013511)	3	NM_013511	13822	Mm.306026	NM_013511	ENSMUSG00000019978	Epb41l2	4.1G|AW555191|D10Ertd398e|Epb4.1l2|NBL2	erythrocyte membrane protein band 4.1 like 2	protein-coding
mm_97517.1	chr11	78499833	78499842	+	1	NA	exon (NM_011707, exon 3 of 8)	exon (NM_011707, exon 3 of 8)	717	NM_011707	22370	Mm.3667	NM_011707	ENSMUSG00000017344	Vtn	AI256434|Vn	vitronectin	protein-coding
mm_139005.1	chr17	45570296	45570317	+	1	NA	exon (NM_008302, exon 6 of 11)	exon (NM_008302, exon 6 of 11)	2955	NM_008302	15516	Mm.2180	NM_008302	ENSMUSG00000023944	Hsp90ab1	90kDa|AL022974|C81438|Hsp84|Hsp84-1|Hsp90|Hspcb	heat shock protein 90 alpha (cytosolic), class B member 1	protein-coding
mm_125536.1	chr15	58033969	58033987	+	1	NA	intron (NM_029418, intron 1 of 5)	CpG	316	NM_029418	75758	Mm.455792	NM_029418	ENSMUSG00000101892	9130401M01Rik	AI849328	RIKEN cDNA 9130401M01 gene	protein-coding
mm_119799.1	chr14	54208177	54208220	+	1	NA	Intergenic	MIR3|SINE|MIR	45731	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_138027.1	chr17	33916183	33916196	+	1	NA	promoter-TSS (NM_020625)	promoter-TSS (NM_020625)	13	NM_020625	81630	Mm.482096	NM_020625	ENSMUSG00000051390	Zbtb22	1110008J20Rik|AI265210|AI415166|Bing1|Zfp297	zinc finger and BTB domain containing 22	protein-coding
mm_40628.1	chr5	64822079	64822108	+	1	NA	exon (NM_008453, exon 3 of 6)	exon (NM_008453, exon 3 of 6)	18570	NM_008453	16599	Mm.392759	NM_008453	ENSMUSG00000029178	Klf3	9930027G08Rik|AL024007|Bklf|Tef-2	Kruppel-like factor 3 (basic)	protein-coding
mm_19695.1	chr2	103605821	103605840	-	1	NA	intron (NM_178890, intron 1 of 16)	MIR|SINE|MIR	39520	NM_178890	99382	Mm.35850	NM_178890	ENSMUSG00000032724	Abtb2	AW539457|BPOZ-2	ankyrin repeat and BTB (POZ) domain containing 2	protein-coding
mm_147479.1	chr18	47248051	47248073	-	1	NA	3' UTR (NM_018744, exon 19 of 19)	3' UTR (NM_018744, exon 19 of 19)	120806	NM_018744	20358	Mm.40909	NM_018744	ENSMUSG00000019647	Sema6a	A730020P05Rik|AI851735|Sema6A-1|Semaq|VIa	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A	protein-coding
mm_5875.1	chr1	53823859	53823892	-	1	NA	intron (NM_001001883, intron 28 of 28)	intron (NM_001001883, intron 28 of 28)	-25549	NR_106149	102465783		NR_106149	ENSMUSG00000098443	Mir7681	Gm27806|mmu-mir-7681	microRNA 7681	ncRNA
mm_2428.1	chr1	95529024	95529032	+	1	NA	Intergenic	Intergenic	138566	NM_009183	20452	Mm.306228	NM_009183	ENSMUSG00000040710	St8sia4	PST|PST-1|SIAT8-D|ST8SiaIV|Siat8d	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4	protein-coding
mm_85399.1	chr9	103364783	103364845	-	1	NA	5' UTR (NM_001134427, exon 1 of 5)	5' UTR (NM_001134427, exon 1 of 5)	165	NM_001134427	321022	Mm.261025	NM_175565	ENSMUSG00000032803	Cdv3	2510010F10Rik|C230084J24Rik|C79446|TPP36	carnitine deficiency-associated gene expressed in ventricle 3	protein-coding
mm_72706.1	chr8	84980204	84980249	+	1	NA	Intergenic	Intergenic	-1478	NM_008416	16477	Mm.1167	NM_008416	ENSMUSG00000052837	Junb	-	jun B proto-oncogene	protein-coding
mm_159006.1	chr1	161034475	161034475	-	1	NA	promoter-TSS (NM_173424)	promoter-TSS (NM_173424)	-216	NM_173424	240869	Mm.296127	NM_173424	ENSMUSG00000043467	Zbtb37	D430004I08Rik	zinc finger and BTB domain containing 37	protein-coding
mm_165861.1	chr4	28813077	28813079	+	1	NA	promoter-TSS (NM_010141)	promoter-TSS (NM_010141)	-53	NM_001290434	13841	Mm.257266	NM_010141	ENSMUSG00000028289	Epha7	Cek11|Ebk|Ehk3|Hek11|Mdk1	Eph receptor A7	protein-coding
mm_68477.1	chr7	110862945	110862960	-	1	NA	promoter-TSS (NM_053247)	promoter-TSS (NM_053247)	1	NM_053247	114332	Mm.396078	NM_053247	ENSMUSG00000030787	Lyve1	1200012G08Rik|Crsbp-1|Lyve-1|Xlkd1	lymphatic vessel endothelial hyaluronan receptor 1	protein-coding
mm_65479.1	chr7	25539951	25539955	-	1	NA	promoter-TSS (NM_001113369)	promoter-TSS (NM_001113369)	51	NM_001113368	26367	Mm.439731	NM_007543	ENSMUSG00000054385	Ceacam2	AI267129|Bgp2|Ceacam2-L	carcinoembryonic antigen-related cell adhesion molecule 2	protein-coding
mm_143160.1	chr17	57224173	57224188	-	1	NA	intron (NM_009778, intron 9 of 40)	intron (NM_009778, intron 9 of 40)	3956	NM_009778	12266	Mm.19131	NM_009778	ENSMUSG00000024164	C3	AI255234|ASP|HSE-MSF|Plp	complement component 3	protein-coding
mm_60191.1	chr7	43408215	43408220	+	1	NA	promoter-TSS (NM_172900)	promoter-TSS (NM_172900)	-63	NM_172900	243958	Mm.24444	NM_172900	ENSMUSG00000030468	Siglecg	9830164H23|A630096C01Rik|Siglec-G|Siglec10|mSiglec-G	sialic acid binding Ig-like lectin G	protein-coding
mm_160185.1	chr7	48499200	48499200	-	1	NA	promoter-TSS (NM_001034868)	promoter-TSS (NM_001034868)	70	NM_001034868	243978	Mm.333873	NM_001034868	ENSMUSG00000074109	Mrgprx2	G370024M05Rik|MrgB10|Mrgprb10	MAS-related GPR, member X2	protein-coding
mm_24086.1	chr3	87971155	87971165	+	1	NA	promoter-TSS (NM_016701)	promoter-TSS (NM_016701)	67	NM_016701	18008	Mm.331129	NM_016701	ENSMUSG00000004891	Nes	AA166324|C78523|ESTM46	nestin	protein-coding
mm_98203.1	chr11	87796254	87796263	+	1	NA	exon (NM_010824, exon 7 of 14)	exon (NM_010824, exon 7 of 14)	2474	NM_010824	17523	Mm.4668	NM_010824	ENSMUSG00000009350	Mpo	mKIAA4033	myeloperoxidase	protein-coding
mm_104575.1	chr11	96953689	96953711	-	1	NA	3' UTR (NM_030220, exon 7 of 7)	3' UTR (NM_030220, exon 7 of 7)	9554	NR_003293	319371	Mm.436865	NR_003293	ENSMUSG00000078700	D030028A08Rik	-	RIKEN cDNA D030028A08 gene	ncRNA
mm_60938.1	chr7	46873013	46873031	+	1	NA	exon (NM_013580, exon 5 of 8)	exon (NM_013580, exon 5 of 8)	11759	NM_013580	16833	Mm.16563	NM_013580	ENSMUSG00000030851	Ldhc	LDH-C4|Ldh-3|Ldh-x|Ldh3|Ldhc4	lactate dehydrogenase C	protein-coding
mm_57351.1	chr6	124756850	124756883	-	1	NA	promoter-TSS (NM_007881)	promoter-TSS (NM_007881)	-379	NM_007881	13498	Mm.333380	NM_007881	ENSMUSG00000004263	Atn1	Atr1|Drpla|atrophin-1	atrophin 1	protein-coding
mm_49157.1	chr6	13069759	13069866	+	1	NA	promoter-TSS (NM_027992)	promoter-TSS (NM_027992)	53	NM_027992	71900	Mm.27742	NM_027992	ENSMUSG00000029571	Tmem106b	2310036D22Rik|5830455K21Rik|6430519M21Rik|AI428776|AI661344	transmembrane protein 106B	protein-coding
mm_65811.1	chr7	29019976	29020036	-	1	NA	exon (NM_009109, exon 91 of 106)	exon (NM_009109, exon 91 of 106)	37152	NM_008279	26411	Mm.148278	NM_008279	ENSMUSG00000037337	Map4k1	Hpk1|mHPK1	mitogen-activated protein kinase kinase kinase kinase 1	protein-coding
mm_124568.1	chr14	124192490	124192499	-	1	NA	promoter-TSS (NM_010201)	promoter-TSS (NM_010201)	52	NM_010201	14169	Mm.206362	NM_010201	ENSMUSG00000025551	Fgf14	FHF-4|Fhf4|mFHF-4(1B)	fibroblast growth factor 14	protein-coding
mm_8425.1	chr1	152497646	152497657	-	1	NA	intron (NM_177756, intron 7 of 11)	intron (NM_177756, intron 7 of 11)	97784	NM_177756	269132	Mm.23782	NM_177756	ENSMUSG00000032649	Colgalt2	AI427652|D730024P12|Glt25d2	collagen beta(1-O)galactosyltransferase 2	protein-coding
mm_4161.1	chr1	171029367	171029385	+	1	NA	3' UTR (NM_144559, exon 5 of 5)	3' UTR (NM_144559, exon 5 of 5)	10450	NM_144559	246256	Mm.251254	NM_144559	ENSMUSG00000059089	Fcgr4	4833442P21Rik|CD16-2|FcgRIV|FcgammaRIV|Fcgr3a|Fcrl3	Fc receptor, IgG, low affinity IV	protein-coding
mm_142637.1	chr17	47421874	47421885	-	1	NA	promoter-TSS (NM_001347584)	promoter-TSS (NM_001347584)	1	NM_001347584	75462	Mm.46129	NM_029296	ENSMUSG00000047150	1700001C19Rik	-	RIKEN cDNA 1700001C19 gene	protein-coding
mm_127998.1	chr15	12739871	12739906	-	1	NA	Intergenic	CpG	84769	NM_029998	77877	Mm.207311	NM_029998	ENSMUSG00000022195	6030458C11Rik	-	RIKEN cDNA 6030458C11 gene	protein-coding
mm_30010.1	chr3	135663295	135663313	-	1	NA	intron (NM_008689, intron 3 of 24)	intron (NM_008689, intron 3 of 24)	28243	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_68133.1	chr7	102210410	102210435	-	1	NA	promoter-TSS (NM_001291358)	promoter-TSS (NM_001291358)	87	NM_001291358	233575	Mm.302013	NM_145583	ENSMUSG00000030990	Pgap2	1810006G21Rik|C76649|Frag1	post-GPI attachment to proteins 2	protein-coding
mm_122216.1	chr14	32202309	32202322	-	1	NA	promoter-TSS (NM_016897)	promoter-TSS (NM_016897)	344	NM_011960	26430	Mm.15962	NM_011960	ENSMUSG00000021911	Parg	AI413217	poly (ADP-ribose) glycohydrolase	protein-coding
mm_95897.1	chr11	58199728	58199755	+	1	NA	5' UTR (NM_018738, exon 1 of 3)	5' UTR (NM_018738, exon 1 of 3)	185	NM_018738	16145	Mm.33902	NM_018738	ENSMUSG00000078853	Igtp	AW558444|Irgm3	interferon gamma induced GTPase	protein-coding
mm_17265.1	chr2	26021548	26021558	-	1	NA	5' UTR (NM_133835, exon 1 of 10)	5' UTR (NM_133835, exon 1 of 10)	207	NM_133835	98766	Mm.247824	NM_133835	ENSMUSG00000036352	Ubac1	1110033G07Rik|AA407978|GBDR1|Gdbr1|Kpc2|Ubadc1	ubiquitin associated domain containing 1	protein-coding
mm_48475.1	chr5	140995769	140995786	-	1	NA	intron (NM_175362, intron 1 of 24)	B4|SINE|B4	4819	NM_175362	108723	Mm.46187	NM_175362	ENSMUSG00000036526	Card11	0610008L17Rik|2410011D02Rik|BIMP3|CARMA1	caspase recruitment domain family, member 11	protein-coding
mm_137906.1	chr17	32007101	32007133	+	1	NA	intron (NM_028902, intron 6 of 7)	intron (NM_028902, intron 6 of 7)	27391	NM_028902	74377	Mm.75856	NM_028902	ENSMUSG00000002076	Hsf2bp	4932437G14Rik	heat shock transcription factor 2 binding protein	protein-coding
mm_165478.1	chr2	164333384	164333384	+	1	NA	exon (NM_009301, exon 2 of 3)	exon (NM_009301, exon 2 of 3)	619	NM_009301	20944	Mm.140154	NM_009301	ENSMUSG00000017004	Svs5	BB115186|Semg1|Svp-1|Svp1|Svp5	seminal vesicle secretory protein 5	protein-coding
mm_21098.1	chr2	153231711	153231728	-	1	NA	exon (NM_018807, exon 3 of 3)	exon (NM_018807, exon 3 of 3)	-6278	NM_198617	241732	Mm.277243	NM_198617	ENSMUSG00000074671	Tspyl3	AW212607|Gm36	TSPY-like 3	protein-coding
mm_78246.1	chr9	21660578	21660594	+	1	NA	intron (NM_001174079, intron 15 of 33)	intron (NM_001174079, intron 15 of 33)	44417	NM_001174078	20586	Mm.286593	NM_011417	ENSMUSG00000032187	Smarca4	Brg1|HP1-BP72|SNF2beta|SW1/SNF|b2b508.1Clo|b2b692Clo	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	protein-coding
mm_125090.1	chr15	27466813	27466828	+	1	NA	5' UTR (NM_020332, exon 1 of 12)	5' UTR (NM_020332, exon 1 of 12)	143	NM_020332	11732	Mm.265264	NM_020332	ENSMUSG00000022265	Ank	Ankh|D15Ertd221e|ank|mKIAA1581	progressive ankylosis	protein-coding
mm_110695.1	chr12	69197128	69197157	-	1	NA	promoter-TSS (NR_033222)	promoter-TSS (NR_033222)	-69	NR_033222	414085	Mm.256223	NR_033222	ENSMUSG00000097061	9330151L19Rik	-	RIKEN cDNA 9330151L19 gene	ncRNA
mm_24533.1	chr3	93279393	93279403	+	1	NA	Intergenic	Intergenic	-40351	NM_133698	68723	Mm.208047	NM_133698	ENSMUSG00000041991	Hrnr	1110033K19Rik|A530063N20Rik|S100a18	hornerin	protein-coding
mm_55531.1	chr6	70726819	70726848	-	1	NA	Intergenic	Intergenic	65342	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_119415.1	chr14	45219712	45219725	+	1	NA	promoter-TSS (NM_027518)	promoter-TSS (NM_027518)	1	NM_027518	70713	Mm.343793	NM_027518	ENSMUSG00000049092	Gpr137c	6330416L11Rik|Gm908|TM7SF1L2	G protein-coupled receptor 137C	protein-coding
mm_82406.1	chr9	14771172	14771178	-	1	NA	promoter-TSS (NM_029306)	promoter-TSS (NM_029306)	-145	NM_029306	69325	Mm.440453	NM_029306	ENSMUSG00000031927	1700012B09Rik	1700007P19Rik	RIKEN cDNA 1700012B09 gene	protein-coding
mm_131969.1	chr16	24733636	24733650	+	1	NA	intron (NM_001145954, intron 2 of 7)	intron (NM_001145954, intron 2 of 7)	11788	NM_001145954	210126	Mm.209385	NM_178665	ENSMUSG00000033306	Lpp	9430020K16Rik|AA959454|AU024130|B130055L10Rik|C79715|D630048H16	LIM domain containing preferred translocation partner in lipoma	protein-coding
mm_104153.1	chr11	87108737	87108759	-	1	NA	promoter-TSS (NM_175563)	promoter-TSS (NM_175563)	-34	NM_175563	270906	Mm.132381	NM_175563	ENSMUSG00000020493	Prr11	B930067F20Rik	proline rich 11	protein-coding
mm_161422.1	chr15	37961048	37961048	-	1	NA	promoter-TSS (NM_199476)	promoter-TSS (NM_199476)	7	NM_199476	382985	Mm.24738	NM_199476	ENSMUSG00000022292	Rrm2b	p53R2	ribonucleotide reductase M2 B (TP53 inducible)	protein-coding
mm_37197.1	chr4	117682234	117682279	-	1	NA	promoter-TSS (NM_023178)	promoter-TSS (NM_023178)	-31	NM_023178	66233	Mm.29142	NM_023178	ENSMUSG00000009640	Dmap1	1500016M21Rik|DNMAP1|DNMTAP1|Dmtap1|mKIAA1425	DNA methyltransferase 1-associated protein 1	protein-coding
mm_134738.1	chr16	23029013	23029026	-	1	NA	promoter-TSS (NM_201375)	promoter-TSS (NM_201375)	82	NM_201375	385643	Mm.440414	NM_201375	ENSMUSG00000060459	Kng2	-	kininogen 2	protein-coding
mm_17954.1	chr2	37359202	37359230	-	1	NA	5' UTR (NM_026176, exon 1 of 4)	5' UTR (NM_026176, exon 1 of 4)	116	NM_026176	67466	Mm.30709	NM_026176	ENSMUSG00000009030	Pdcl	1200011E13Rik|AW108059|PhLP1	phosducin-like	protein-coding
mm_147787.1	chr18	61635390	61635396	-	1	NA	Intergenic	Intergenic	-4260	NR_045420	545261	Mm.426593	NR_045420	ENSMUSG00000098098	Bvht	Braveheart|Gm20748	braveheart long non-coding RNA	ncRNA
mm_94316.1	chr11	4236412	4236433	+	1	NA	promoter-TSS (NM_001013365)	promoter-TSS (NM_001013365)	-363	NM_001013365	18413	Mm.131422	NM_001013365	ENSMUSG00000058755	Osm	OncoM	oncostatin M	protein-coding
mm_28462.1	chr3	90695125	90695134	-	1	NA	intron (NM_009114, intron 2 of 2)	intron (NM_009114, intron 2 of 2)	592	NM_001281852	20202	Mm.2128	NM_009114	ENSMUSG00000056071	S100a9	60B8Ag|AW546964|BEE22|Cagb|GAGB|L1Ag|MRP14|p14	S100 calcium binding protein A9 (calgranulin B)	protein-coding
mm_157239.1	chrX	17572178	17572213	-	1	NA	promoter-TSS (NM_001313746)	promoter-TSS (NM_001313746)	130	NM_001313745	72018	Mm.41558	NM_028058	ENSMUSG00000025040	Fundc1	1500005J14Rik|1810033P05Rik	FUN14 domain containing 1	protein-coding
mm_27166.1	chr3	33143276	33143292	-	1	NA	promoter-TSS (NM_001163516)	promoter-TSS (NM_001163516)	-93	NM_001163516	58869	Mm.151332	NM_021483	ENSMUSG00000027674	Pex5l	1700016J08Rik|PXR2|Pex2|TRIP8b|pex5Rp	peroxisomal biogenesis factor 5-like	protein-coding
mm_125438.1	chr15	44619225	44619242	+	1	NA	promoter-TSS (NM_019480)	promoter-TSS (NM_019480)	-408	NM_019480	55960	Mm.287896	NM_019480	ENSMUSG00000022339	Ebag9	AI835379|Rcas1	estrogen receptor-binding fragment-associated gene 9	protein-coding
mm_65136.1	chr7	19562202	19562248	-	1	NA	5' UTR (NM_199149, exon 1 of 13)	5' UTR (NM_199149, exon 1 of 13)	173	NM_199149	232947	Mm.219662	NM_199149	ENSMUSG00000051403	Ppp1r37	Gm158|Lrrc68	protein phosphatase 1, regulatory subunit 37	protein-coding
mm_120180.1	chr14	61305406	61305417	+	1	NA	promoter-TSS (NR_033788)	promoter-TSS (NR_033788)	-77	NR_033788	67355	Mm.193728	NR_033788	ENSMUSG00000101505	1700109G14Rik	1700126G13Rik	RIKEN cDNA 1700109G14 gene	ncRNA
mm_98620.1	chr11	95843867	95843875	+	1	NA	5' UTR (NM_001284397, exon 2 of 4)	5' UTR (NM_001284397, exon 2 of 4)	626	NM_001284397	14710	Mm.46299	NM_023121	ENSMUSG00000038811	Gngt2	AV096488	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 2	protein-coding
mm_44772.1	chr5	31967982	31967991	-	1	NA	intron (NM_144541, intron 7 of 11)	intron (NM_144541, intron 7 of 11)	-168486	NM_008037	14284	Mm.24684	NM_008037	ENSMUSG00000029135	Fosl2	Fra-2	fos-like antigen 2	protein-coding
mm_47025.1	chr5	115520642	115520646	-	1	NA	intron (NM_133915, intron 1 of 11)	intron (NM_133915, intron 1 of 11)	13968	NM_133915	19303	Mm.18714	NM_011223	ENSMUSG00000029528	Pxn	AW108311|AW123232|Pax	paxillin	protein-coding
mm_160162.1	chr7	44442276	44442276	+	1	NA	promoter-TSS (NM_198250)	promoter-TSS (NM_198250)	-211	NM_198250	272381	Mm.44173	NM_198250	ENSMUSG00000047085	Lrrc4b	A830007M12|Lrig4	leucine rich repeat containing 4B	protein-coding
mm_121369.1	chr14	117679970	117679973	+	1	NA	intron (NM_001079844, intron 4 of 9)	intron (NM_001079844, intron 4 of 9)	273876	NR_105747	102465148		NR_105747	ENSMUSG00000098648	Mir6239	Gm28025|mmu-mir-6239	microRNA 6239	ncRNA
mm_43473.1	chr5	136694214	136694255	+	1	NA	promoter-TSS (NM_001085387)	promoter-TSS (NM_001085387)	57	NM_001085387	59310	Mm.5178	NM_021611	ENSMUSG00000005474	Myl10	1700027I08Rik|Mylc2pl|PLRLC	myosin, light chain 10, regulatory	protein-coding
mm_139466.1	chr17	55959147	55959182	+	1	NA	promoter-TSS (NM_028381)	promoter-TSS (NM_028381)	-23	NM_028381	72886	Mm.22796	NM_028381	ENSMUSG00000003208	Ccdc94	2900016D05Rik|AI413813	coiled-coil domain containing 94	protein-coding
mm_73234.1	chr8	104131111	104131126	+	1	NA	exon (NM_009868, exon 7 of 12)	exon (NM_009868, exon 7 of 12)	-25245	NR_131138	546096	Mm.252264	NR_131138	ENSMUSG00000110053	Gm29682	-	predicted gene, 29682	ncRNA
mm_97874.1	chr11	83185377	83185410	+	1	NA	exon (NM_011410, exon 6 of 8)	exon (NM_011410, exon 6 of 8)	-5937	NM_011409	20557	Mm.290922	NM_011409	ENSMUSG00000018986	Slfn3	-	schlafen 3	protein-coding
mm_48594.1	chr5	143992632	143992648	-	1	NA	intron (NM_177682, intron 11 of 14)	intron (NM_177682, intron 11 of 14)	22213	NM_177682	231874	Mm.320432	NM_177682	ENSMUSG00000029617	Ccz1	AU022870	CCZ1 vacuolar protein trafficking and biogenesis associated	protein-coding
mm_14712.1	chr2	143546219	143546231	+	1	NA	promoter-TSS (NM_008792)	promoter-TSS (NM_008792)	92	NM_008792	18549	Mm.294493	NM_008792	ENSMUSG00000027419	Pcsk2	6330411F23Rik|AI839700|Nec-2|Nec2|PC2|Phpp-2|SPC2	proprotein convertase subtilisin/kexin type 2	protein-coding
mm_165197.1	chr2	32493401	32493407	-	1	NA	Intergenic	Intergenic	-41934	NM_146118	227731	Mm.37395	NM_146118	ENSMUSG00000026819	Slc25a25	1110030N17Rik|MCSC|mKIAA1896	solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 25	protein-coding
mm_87973.1	chr10	63480295	63480308	+	1	NA	intron (NM_001164376, intron 1 of 17)	intron (NM_001164376, intron 1 of 17)	22790	NM_001164376	216033	Mm.444692	NM_177612	ENSMUSG00000060843	Ctnna3	4930429L08Rik|4933408A16|Catna3|Vr22	catenin (cadherin associated protein), alpha 3	protein-coding
mm_150481.1	chr19	38931009	38931029	+	1	NA	promoter-TSS (NM_008234)	promoter-TSS (NM_008234)	29	NM_008234	15201	Mm.57223	NM_008234	ENSMUSG00000025001	Hells	AI323785|E130115I21Rik|LSH|Lysh|PASG|YFK8	helicase, lymphoid specific	protein-coding
mm_12697.1	chr2	76499045	76499077	+	1	NA	promoter-TSS (NM_001290735)	promoter-TSS (NM_001290735)	55	NM_001290735	99031	Mm.240435	NM_145525	ENSMUSG00000042359	Osbpl6	1110062M20Rik|AI596402|ORP-6|mKIAA4128	oxysterol binding protein-like 6	protein-coding
mm_166841.1	chr7	19319708	19319725	-	1	NA	Intergenic	Intergenic	-9671	NM_001347586	14282	Mm.248335	NM_008036	ENSMUSG00000003545	Fosb	-	FBJ osteosarcoma oncogene B	protein-coding
mm_139629.1	chr17	57367338	57367381	+	1	NA	intron (NM_010130, intron 2 of 21)	Lx8b|LINE|L1	8673	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_86026.1	chr9	112235967	112235975	-	1	NA	TTS (NR_015468)	TTS (NR_015468)	-1130	NM_001177619	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_172738.1	chr8	78516847	78516852	+	1	NA	intron (NM_001009981, intron 2 of 10)	ORR1D1|LTR|ERVL-MaLR	7521	NM_001282108	76775	Mm.334631	NM_029736	ENSMUSG00000031684	Slc10a7	2410193C02Rik|P7	solute carrier family 10 (sodium/bile acid cotransporter family), member 7	protein-coding
mm_157655.1	chrX	57338500	57338512	-	1	NA	exon (NM_152801, exon 1 of 22)	exon (NM_152801, exon 1 of 22)	223	NM_152801	73341	Mm.261443	NM_152801	ENSMUSG00000031133	Arhgef6	1600028C08Rik|1700038J06Rik|4930592P22Rik|alpha-PIX	Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_162830.1	chr10	81559615	81559619	+	1	NA	non-coding (NR_074087, exon 1 of 7)	non-coding (NR_074087, exon 1 of 7)	173	NM_001276288	14797	Mm.180013	NM_010347	ENSMUSG00000054452	Aes	AL024115|Esp1|Grg|Grg-5|Grg5|Tle5	amino-terminal enhancer of split	protein-coding
mm_143921.1	chr17	85618414	85618420	-	1	NA	promoter-TSS (NR_015387)	promoter-TSS (NR_015387)	-21	NR_038082	100043902	Mm.150838	NR_015385	ENSMUSG00000093460	Six3os1	D17Mgi26|E130112H22Rik|Rncr1|Six3os	SIX homeobox 3, opposite strand 1	ncRNA
mm_127141.1	chr15	98265583	98265602	+	1	NA	Intergenic	RLTR22_Mur|LTR|ERVK	-8285	NM_027304	70069	Mm.107718	NM_027304	ENSMUSG00000048077	H1fnt	1700026P10Rik|H1.7|H1t2|Hanp1|mH1t2	H1 histone family, member N, testis-specific	protein-coding
mm_93739.1	chr10	120142426	120142448	-	1	NA	3' UTR (NM_028679, exon 12 of 12)	3' UTR (NM_028679, exon 12 of 12)	-29472	NM_080446	117599	Mm.214703	NM_080446	ENSMUSG00000020228	Helb	AI447783|D10Ertd664e	helicase (DNA) B	protein-coding
mm_98031.1	chr11	85311290	85311325	+	1	NA	promoter-TSS (NM_016910)	promoter-TSS (NM_016910)	53	NM_016910	53892	Mm.45609	NM_016910	ENSMUSG00000020525	Ppm1d	AV338790|Wip1	protein phosphatase 1D magnesium-dependent, delta isoform	protein-coding
mm_99703.1	chr11	106160236	106160250	+	1	NA	promoter-TSS (NM_172397)	promoter-TSS (NM_172397)	-101	NM_172397	67803	Mm.21687	NM_172397	ENSMUSG00000040699	Limd2	0610025L06Rik|AI413966	LIM domain containing 2	protein-coding
mm_170996.1	chr2	75659303	75659308	+	1	NA	promoter-TSS (NM_198090)	promoter-TSS (NM_198090)	15	NR_033513	627828	Mm.459502	NR_033513	ENSMUSG00000092086	Gm6793	EG627828	heterogeneous nuclear ribonucleoprotein A3 pseudogene	pseudo
mm_131434.1	chr16	15887777	15887800	+	1	NA	exon (NM_007679, exon 1 of 1)	exon (NM_007679, exon 1 of 1)	502	NM_007679	12609	Mm.347407	NM_007679	ENSMUSG00000071637	Cebpd	c/EBPdelta	CCAAT/enhancer binding protein (C/EBP), delta	protein-coding
mm_44401.1	chr5	17836044	17836060	-	1	NA	promoter-TSS (NM_001159555)	promoter-TSS (NM_001159555)	-156	NM_007643	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_39960.1	chr5	32136589	32136599	+	1	NA	5' UTR (NM_008037, exon 1 of 4)	5' UTR (NM_008037, exon 1 of 4)	122	NM_008037	14284	Mm.24684	NM_008037	ENSMUSG00000029135	Fosl2	Fra-2	fos-like antigen 2	protein-coding
mm_167608.1	chr9	54772932	54772943	+	1	NA	3' UTR (NM_001284507, exon 3 of 3)	3' UTR (NM_001284507, exon 3 of 3)	8189	NM_013496	12903	Mm.34797	NM_013496	ENSMUSG00000032291	Crabp1	AI326249|CRABP-I|Crabp-1|CrabpI|Rbp-5	cellular retinoic acid binding protein I	protein-coding
mm_51626.1	chr6	85452006	85452026	+	1	NA	promoter-TSS (NM_001163427)	promoter-TSS (NM_001163427)	-46	NR_028081	73327	Mm.379221	NM_028505	ENSMUSG00000030008	Pradc1	1700040I03Rik|Pap21	protease-associated domain containing 1	protein-coding
mm_170486.1	chr19	16164841	16164857	-	1	NA	non-coding (NR_033228, exon 1 of 1)	non-coding (NR_033228, exon 1 of 1)	751	NR_033228	595139	Mm.405662	NR_033228		E030024N20Rik	9030417F11Rik|Ppia-ps8	peptidylprolyl isomerase A pseudogene 8	pseudo
mm_110590.1	chr12	56532901	56532912	-	1	NA	3' UTR (NM_009385, exon 3 of 3)	3' UTR (NM_009385, exon 3 of 3)	-3486	NR_045082	104798	Mm.310950	NR_045082		E030019B13Rik	AI413669	RIKEN cDNA E030019B13 gene	ncRNA
mm_5294.1	chr1	21079163	21079243	-	1	NA	promoter-TSS (NM_177409)	promoter-TSS (NM_177409)	22	NM_177409	170829	Mm.185680	NM_177409	ENSMUSG00000041779	Tram2	C330003D03Rik	translocating chain-associating membrane protein 2	protein-coding
mm_96610.1	chr11	69097223	69097253	+	1	NA	Intergenic	Intergenic	-1718	NM_011065	18626	Mm.7373	NM_011065	ENSMUSG00000020893	Per1	Hftm|Per|m-rigui|mPer1	period circadian clock 1	protein-coding
mm_51234.1	chr6	71493851	71493918	+	1	NA	promoter-TSS (NM_009543)	promoter-TSS (NM_009543)	7	NM_001308303	22644	Mm.422969	NM_009543	ENSMUSG00000052656	Rnf103	AW146237|AW212918|Zfp103|kf-1	ring finger protein 103	protein-coding
mm_127976.1	chr15	12397478	12397481	-	1	NA	intron (NM_001081064, intron 13 of 23)	intron (NM_001081064, intron 13 of 23)	75983	NM_025673	66629	Mm.157655	NM_025673	ENSMUSG00000022200	Golph3	4733401N08Rik|5730410D03Rik|AW413496	golgi phosphoprotein 3	protein-coding
mm_76325.1	chr8	84705191	84705202	-	1	NA	TTS (NM_008535)	TTS (NM_008535)	3739	NM_008535	17095	Mm.4925	NM_008535	ENSMUSG00000034041	Lyl1	Lyl-1|bHLHa18	lymphoblastomic leukemia 1	protein-coding
mm_24949.1	chr3	96629920	96629955	+	1	NA	promoter-TSS (NR_003619)	promoter-TSS (NR_003619)	9	NM_001102407	60365	Mm.261972	NM_025875	ENSMUSG00000038374	Rbm8a	2310057C03Rik|AA673428|Rbm8	RNA binding motif protein 8a	protein-coding
mm_49733.1	chr6	34745636	34745640	+	1	NA	exon (NM_145575, exon 3 of 12)	exon (NM_145575, exon 3 of 12)	-34794	NM_001289657	76223	Mm.150047	NM_178630	ENSMUSG00000038836	Agbl3	2900053G10Rik|4930431N21Rik|6530406M24Rik|CCP3	ATP/GTP binding protein-like 3	protein-coding
mm_135984.1	chr16	75092697	75092706	-	1	NA	Intergenic	Intergenic	493360	NM_001252513	320355	Mm.99517	NM_177142	ENSMUSG00000032948	Lipi	D930038D03Rik|lpd1	lipase, member I	protein-coding
mm_137529.1	chr17	27554581	27554626	+	1	NA	Intergenic	Intergenic	-1971	NM_001166536	15361	Mm.4438	NM_016660	ENSMUSG00000046711	Hmga1	AL023995|Hmga1a|Hmga1b|Hmgi|Hmgiy|Hmgy	high mobility group AT-hook 1	protein-coding
mm_80005.1	chr9	67757516	67757518	+	1	NA	Intergenic	MLTR18B_MM|LTR|ERVK	-1920	NM_001081314	75697	Mm.105353	NM_001081314	ENSMUSG00000091956	C2cd4b	3300001A09Rik|Fam148b	C2 calcium-dependent domain containing 4B	protein-coding
mm_59524.1	chr7	27608076	27608096	+	1	NA	intron (NM_001331109, intron 1 of 13)	intron (NM_001331109, intron 1 of 13)	750	NM_001331109	11652	Mm.177194	NM_007434	ENSMUSG00000004056	Akt2	2410016A19Rik|AW554154|PKB|PKBbeta	thymoma viral proto-oncogene 2	protein-coding
mm_51401.1	chr6	78372141	78372184	+	1	NA	exon (NM_011036, exon 4 of 6)	exon (NM_011036, exon 4 of 6)	1277	NM_011036	18489	Mm.2553	NM_011036	ENSMUSG00000071356	Reg3b	HIP|PAP1|Pap|REG-III	regenerating islet-derived 3 beta	protein-coding
mm_44087.1	chr5	149184683	149184740	+	1	NA	5' UTR (NM_001115151, exon 1 of 9)	5' UTR (NM_001115151, exon 1 of 9)	151	NM_001115149	231915	Mm.29402	NM_001013378	ENSMUSG00000041264	Uspl1	E430026A01Rik	ubiquitin specific peptidase like 1	protein-coding
mm_172982.1	chr9	97228956	97228964	-	1	NA	Intergenic	Intergenic	-117919	NM_138756	192287	Mm.228067	NM_138756	ENSMUSG00000032449	Slc25a36	C330005L02Rik	solute carrier family 25, member 36	protein-coding
mm_134043.1	chr16	5195936	5195949	-	1	NA	exon (NM_013796, exon 10 of 10)	exon (NM_013796, exon 10 of 10)	8070	NM_013796	27426	Mm.215641	NM_013796	ENSMUSG00000023143	Nagpa	AI596180|UCE	N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase	protein-coding
mm_77159.1	chr8	111687149	111687179	-	1	NA	exon (NM_025583, exon 6 of 7)	exon (NM_025583, exon 6 of 7)	2510	NR_106044	102466993		NR_106044	ENSMUSG00000099129	Mir7076	Gm27318|mmu-mir-7076	microRNA 7076	ncRNA
mm_108775.1	chr12	89812810	89812818	+	1	NA	5' UTR (NM_001252074, exon 1 of 7)	5' UTR (NM_001252074, exon 1 of 7)	331	NM_001252074	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding
mm_3993.1	chr1	164453493	164453524	+	1	NA	exon (NM_009721, exon 2 of 6)	exon (NM_009721, exon 2 of 6)	4847	NM_009721	11931	Mm.4550	NM_009721	ENSMUSG00000026576	Atp1b1	Atp4b|Atpb|Atpb-1|NKbeta1	ATPase, Na+/K+ transporting, beta 1 polypeptide	protein-coding
mm_40626.1	chr5	64820956	64820959	+	1	NA	intron (NM_008453, intron 2 of 5)	intron (NM_008453, intron 2 of 5)	17434	NM_008453	16599	Mm.392759	NM_008453	ENSMUSG00000029178	Klf3	9930027G08Rik|AL024007|Bklf|Tef-2	Kruppel-like factor 3 (basic)	protein-coding
mm_154596.1	chrX	7593146	7593172	+	1	NA	TTS (NM_138603)	TTS (NM_138603)	12261	NM_138603	54638	Mm.288192	NM_138603	ENSMUSG00000031143	Ccdc22	AI481216|DXImx40e|Ppp1r3f|Sfc22	coiled-coil domain containing 22	protein-coding
mm_56473.1	chr6	99028875	99028924	-	1	NA	promoter-TSS (NM_001197322)	promoter-TSS (NM_001197322)	-601	NM_001197322	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_77377.1	chr8	119836682	119836704	-	1	NA	intron (NM_028071, intron 2 of 3)	intron (NM_028071, intron 2 of 3)	3886	NM_028071	72042	Mm.393405	NM_028071	ENSMUSG00000031827	Cotl1	1810074P22Rik|2010004C08Rik|Clp	coactosin-like 1 (Dictyostelium)	protein-coding
mm_160170.1	chr7	45053054	45053054	-	1	NA	promoter-TSS (NM_175022)	promoter-TSS (NM_175022)	-173	NM_175022	233210	Mm.219137	NM_175022	ENSMUSG00000046574	Prr12	6720469B10|BC058674	proline rich 12	protein-coding
mm_37910.1	chr4	132757163	132757187	-	1	NA	promoter-TSS (NM_133888)	promoter-TSS (NM_133888)	-4	NM_133888	100340	Mm.287187	NM_133888	ENSMUSG00000028885	Smpdl3b	1110054A24Rik|AU045240|Asml3b	sphingomyelin phosphodiesterase, acid-like 3B	protein-coding
mm_171663.1	chr4	44710863	44710864	-	1	NA	promoter-TSS (NM_008782)	promoter-TSS (NM_008782)	-423	NM_008782	18507	Mm.439659	NM_008782	ENSMUSG00000014030	Pax5	BSAP|EBB-1|KLP|Pax-5	paired box 5	protein-coding
mm_8055.1	chr1	135374937	135374946	-	1	NA	exon (NM_175259, exon 1 of 5)	exon (NM_175259, exon 1 of 5)	122	NM_175259	77552	Mm.41407	NM_175259	ENSMUSG00000041889	Shisa4	9330132O05Rik|Tmem58|mShisa4	shisa family member 4	protein-coding
mm_143167.1	chr17	57226055	57226076	-	1	NA	exon (NM_009778, exon 4 of 41)	exon (NM_009778, exon 4 of 41)	2071	NM_009778	12266	Mm.19131	NM_009778	ENSMUSG00000024164	C3	AI255234|ASP|HSE-MSF|Plp	complement component 3	protein-coding
mm_165119.1	chr2	3411985	3412003	-	1	NA	5' UTR (NM_008579, exon 2 of 3)	5' UTR (NM_008579, exon 2 of 3)	10654	NM_008579	104362	Mm.2688	NM_008579	ENSMUSG00000026650	Meig1	MLZ-278|Meg1	meiosis expressed gene 1	protein-coding
mm_165865.1	chr4	34209164	34209166	-	1	NA	Intergenic	MERV1_LTR|LTR|ERV1	-159098	NM_026293	67652	Mm.55848	NM_026293	ENSMUSG00000028264	Spaca1	1700124L11Rik|4930540L03Rik	sperm acrosome associated 1	protein-coding
mm_19915.1	chr2	115344288	115344297	-	1	NA	promoter-TSS (NR_040516)	promoter-TSS (NR_040516)	-12	NR_040516	78193	Mm.189508	NR_040516	ENSMUSG00000087309	4930528P14Rik	-	RIKEN cDNA 4930528P14 gene	ncRNA
mm_136223.1	chr16	90143782	90143794	-	1	NA	non-coding (NR_033476, exon 1 of 1)	non-coding (NR_033476, exon 1 of 1)	1551	NR_033476	100038709	Mm.484070	NR_033476		Gm10789	ENSMUSG00000074924	predicted gene 10789	ncRNA
mm_111149.1	chr12	82245399	82245408	-	1	NA	intron (NM_001167983, intron 2 of 23)	L1M4c|LINE|L1	-65946	NM_172579	217692	Mm.261333	NM_172579	ENSMUSG00000042700	Sipa1l1	4931426N11Rik|AW213287|Spar|mKIAA0440	signal-induced proliferation-associated 1 like 1	protein-coding
mm_158281.1	chrX	111536326	111536341	-	1	NA	intron (NM_025949, intron 1 of 24)	intron (NM_025949, intron 1 of 24)	1626	NM_025949	67071	Mm.37617	NM_025949	ENSMUSG00000025665	Rps6ka6	2610524K04Rik|RSK4|S6K-alpha-6	ribosomal protein S6 kinase polypeptide 6	protein-coding
mm_134707.1	chr16	22892133	22892149	-	1	NA	exon (NM_001276450, exon 1 of 7)	exon (NM_001276450, exon 1 of 7)	126	NM_001276449	11625	Mm.197554	NM_013465	ENSMUSG00000022868	Ahsg	-	alpha-2-HS-glycoprotein	protein-coding
mm_112919.1	chr13	20923892	20923899	+	1	NA	intron (NM_012054, intron 11 of 20)	Lx8b|LINE|L1	129782	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_91511.1	chr10	37137313	37137335	-	1	NA	intron (NM_008538, intron 1 of 1)	intron (NM_008538, intron 1 of 1)	1602	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_77227.1	chr8	115703798	115703813	-	1	NA	3' UTR (NM_001025577, exon 1 of 1)	3' UTR (NM_001025577, exon 1 of 1)	3089	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_152985.1	chr19	29523167	29523175	-	1	NA	intron (NM_001081319, intron 1 of 25)	CpG	889	NM_001081319	226089	Mm.353838	NM_177641	ENSMUSG00000038658	Ric1	C030046E11Rik|C130057E09Rik|Kiaa1432	RAB6A GEF complex partner 1	protein-coding
mm_171036.1	chr2	91584981	91584991	-	1	NA	intron (NM_029437, intron 23 of 42)	(A)n|Simple_repeat|Simple_repeat	-11095	NR_028553	100217458		NR_028553	ENSMUSG00000077221	Snord67	MBII-166	small nucleolar RNA, C/D box 67	snoRNA
mm_140353.1	chr17	86831345	86831351	+	1	NA	3' UTR (NM_010137, exon 16 of 16)	3' UTR (NM_010137, exon 16 of 16)	77484	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_45568.1	chr5	73256556	73256636	-	1	NA	promoter-TSS (NM_028194)	promoter-TSS (NM_028194)	22	NM_028194	72313	Mm.260594	NM_028194	ENSMUSG00000070733	Fryl	2010313D22Rik|2310004H21Rik|2510002A14Rik|9030227G01Rik|mKIAA0826	FRY like transcription coactivator	protein-coding
mm_65991.1	chr7	30535057	30535066	-	1	NA	promoter-TSS (NM_001289670)	promoter-TSS (NM_001289670)	-1	NM_001289682	233071	Mm.190704	NM_178252	ENSMUSG00000036882	Arhgap33	AW324378|NOMA-GAP|Snx26|TCGAP	Rho GTPase activating protein 33	protein-coding
mm_139395.1	chr17	52304473	52304498	+	1	NA	Intergenic	Intergenic	-298224	NM_001031811	211468	Mm.399068	NM_001031811	ENSMUSG00000035580	Kcnh8	C130090D05Rik|ELK|ELK1|ELK3|Kv12.1	potassium voltage-gated channel, subfamily H (eag-related), member 8	protein-coding
mm_134910.1	chr16	30267504	30267522	-	1	NA	promoter-TSS (NM_027904)	promoter-TSS (NM_027904)	19	NM_027904	71756	Mm.290614	NM_027904	ENSMUSG00000023176	Cpn2	1300018K11Rik	carboxypeptidase N, polypeptide 2	protein-coding
mm_111713.1	chr12	103701178	103701184	-	1	NA	Intergenic	Intergenic	-5652	NM_026687	68348	Mm.20149	NM_026687	ENSMUSG00000021081	Serpina1f	0610012A11Rik|AI327419|Serpina2|epserin	serine (or cysteine) peptidase inhibitor, clade A, member 1F	protein-coding
mm_74700.1	chr8	16421872	16421874	-	1	NA	intron (NM_053171, intron 7 of 69)	B3A|SINE|B2	-253035	NR_037214	100526464		NR_037214	ENSMUSG00000093142	Mir3106	mir-3106|mmu-mir-3106	microRNA 3106	ncRNA
mm_55678.1	chr6	72610252	72610255	-	1	NA	TTS (NM_009444)	TTS (NM_009444)	6495	NM_009444	22135	Mm.246563	NM_009444		Tgoln2	TGN38B|TGN41|TGN46|Ttgn2	trans-golgi network protein 2	protein-coding
mm_91306.1	chr10	24917986	24918017	-	1	NA	exon (NM_007482, exon 4 of 8)	exon (NM_007482, exon 4 of 8)	7337	NR_105870	102465545		NR_105870	ENSMUSG00000099181	Mir6905	Gm27879|mmu-mir-6905	microRNA 6905	ncRNA
mm_99538.1	chr11	103193606	103193651	+	1	NA	exon (NM_001077698, exon 15 of 26)	exon (NM_001077698, exon 15 of 26)	14920	NM_001254724	69441	Mm.380648	NM_027082	ENSMUSG00000020940	1700023F06Rik	-	RIKEN cDNA 1700023F06 gene	protein-coding
mm_135575.1	chr16	50420124	50420133	-	1	NA	intron (NM_001347240, intron 2 of 16)	B1_Mus1|SINE|Alu	12261	NM_027444	70508	Mm.28940	NM_027444	ENSMUSG00000022641	Bbx	5530401J07Rik|5730403O13Rik	bobby sox HMG box containing	protein-coding
mm_90049.1	chr10	116018445	116018454	+	1	NA	promoter-TSS (NM_011217)	promoter-TSS (NM_011217)	86	NM_011217	19279	Mm.336316	NM_011217	ENSMUSG00000020151	Ptprr	Gmcp1|PTP-SL|PTPBR7|RPTPRR|mPTP213	protein tyrosine phosphatase, receptor type, R	protein-coding
mm_11406.1	chr2	31511079	31511089	+	1	NA	intron (NR_002687, intron 13 of 15)	PB1D9|SINE|Alu	40776	NR_002687	432466	Mm.333323	NR_002687	ENSMUSG00000046687	Gm5424	EG432466	argininosuccinate synthase pseudogene	pseudo
mm_143243.1	chr17	64269696	64269713	-	1	NA	Intergenic	Intergenic	62179	NM_144859	224938	Mm.489681	NM_144859	ENSMUSG00000024083	Pja2	AI447901|AL022700|Neurodap1|mKIAA0438	praja 2, RING-H2 motif containing	protein-coding
mm_67543.1	chr7	81493668	81493683	-	1	NA	TTS (NM_183143)	TTS (NM_183143)	250	NM_021492	11775	Mm.322894	NM_021492	ENSMUSG00000062444	Ap3b2	AI549966|AU042881|Naptb|[b]-NAP|beta-NAP|beta3B	adaptor-related protein complex 3, beta 2 subunit	protein-coding
mm_20903.1	chr2	150136481	150136501	-	1	NA	intron (NM_181266, intron 1 of 3)	intron (NM_181266, intron 1 of 3)	187	NM_023266	104348	Mm.485851	NM_023266	ENSMUSG00000068134	Zfp120	AI315103|E030042N05Rik|F80|MZF31|Zfp844	zinc finger protein 120	protein-coding
mm_5464.1	chr1	36445249	36445264	-	1	NA	promoter-TSS (NM_001310517)	promoter-TSS (NM_001310517)	15	NM_001310517	214895	Mm.287854	NM_001013374	ENSMUSG00000001143	Lman2l	A630028F14Rik|VIP36-like|VIPL	lectin, mannose-binding 2-like	protein-coding
mm_42481.1	chr5	115470812	115470828	+	1	NA	exon (NM_011107, exon 2 of 4)	exon (NM_011107, exon 2 of 4)	4554	NM_011107	18778	Mm.20190	NM_011107	ENSMUSG00000029522	Pla2g1b	Pla2a|sPLA2IB	phospholipase A2, group IB, pancreas	protein-coding
mm_170141.1	chr17	40127114	40127114	-	1	NA	Intergenic	Intergenic	81495	NM_031190	18663	Mm.717	NM_031190	ENSMUSG00000031233	Pgk2	Pgk-2|Tcp-2	phosphoglycerate kinase 2	protein-coding
mm_32203.1	chr4	101507478	101507495	+	1	NA	promoter-TSS (NM_001164585)	promoter-TSS (NM_001164585)	-490	NM_001164585	72685	Mm.76494	NM_198412	ENSMUSG00000028528	Dnajc6	2810027M23Rik|mKIAA0473	DnaJ heat shock protein family (Hsp40) member C6	protein-coding
mm_3116.1	chr1	134613327	134613356	+	1	NA	exon (NM_152895, exon 15 of 27)	exon (NM_152895, exon 15 of 27)	-33340	NM_009307	20980	Mm.5102	NM_009307	ENSMUSG00000026452	Syt2	IP4BP|R74640|mKIAA4194	synaptotagmin II	protein-coding
mm_149587.1	chr19	16132775	16132795	+	1	NA	promoter-TSS (NM_008139)	promoter-TSS (NM_008139)	-46	NM_008139	14682	Mm.439701	NM_008139	ENSMUSG00000024639	Gnaq	1110005L02Rik|6230401I02Rik|AA408290|AW060788|Dsk1|Dsk10|Galphaq|Gq|GqI	guanine nucleotide binding protein, alpha q polypeptide	protein-coding
mm_27473.1	chr3	53017196	53017247	-	1	NA	promoter-TSS (NM_026225)	promoter-TSS (NM_026225)	2	NM_026225	67542	Mm.249548	NM_026225	ENSMUSG00000027742	Cog6	4933405E16Rik|AU018618|mKIAA1134	component of oligomeric golgi complex 6	protein-coding
mm_69026.1	chr7	126792486	126792539	-	1	NA	promoter-TSS (NM_019674)	promoter-TSS (NM_019674)	-41	NM_019674	56420	Mm.41998	NM_019674	ENSMUSG00000030697	Ppp4c	1110002D08Rik|AU016079|Ppx	protein phosphatase 4, catalytic subunit	protein-coding
mm_156327.1	chrX	138914423	138914438	+	1	NA	promoter-TSS (NM_013724)	promoter-TSS (NM_013724)	0	NM_013724	27206	Mm.482319	NM_013724	ENSMUSG00000052854	Nrk	AA407323|AA409510|AI225895|AV168563|AW538185|Nesk	Nik related kinase	protein-coding
mm_153557.1	chr19	42135973	42136008	-	1	NA	Intergenic	RLTR12G|LTR|ERVK	-6997	NM_027106	69534	Mm.30060	NM_027106	ENSMUSG00000018821	Avpi1	2310008N12Rik|AA410041|VIT32|esu|mVIT32	arginine vasopressin-induced 1	protein-coding
mm_66171.1	chr7	33944393	33944401	-	1	NA	exon (NM_178308, exon 2 of 3)	exon (NM_178308, exon 2 of 3)	588	NM_178308	110187	Mm.155750	NM_178308	ENSMUSG00000066586	Scgb2b26	Abpbg26|Abpbg4|Abpg|C2d|Scgb2b4	secretoglobin, family 2B, member 26	protein-coding
mm_41360.1	chr5	90506601	90506604	+	1	NA	exon (NM_007423, exon 12 of 15)	exon (NM_007423, exon 12 of 15)	-12347	NM_145146	280662	Mm.348786	NM_145146	ENSMUSG00000029369	Afm	Alf|alpha-Alb	afamin	protein-coding
mm_30126.1	chr3	141931555	141931565	-	1	NA	promoter-TSS (NM_001277220)	promoter-TSS (NM_001277220)	28	NM_001277218	12167	Mm.39089	NM_007560	ENSMUSG00000052430	Bmpr1b	AI385617|ALK-6|AV355320|Acvrlk6|Alk6|BMPR-1B|BMPR-IB|CFK-43a|SKR6	bone morphogenetic protein receptor, type 1B	protein-coding
mm_151121.1	chr19	47865544	47865548	+	1	NA	promoter-TSS (NM_026619)	promoter-TSS (NM_026619)	1	NM_030051	68214	Mm.63791	NM_026619	ENSMUSG00000025069	Gsto2	1700020F09Rik|4930425C18Rik|GSTO 2-2	glutathione S-transferase omega 2	protein-coding
mm_61965.1	chr7	90426495	90426502	+	1	NA	5' UTR (NM_027298, exon 1 of 1)	5' UTR (NM_027298, exon 1 of 1)	186	NM_027298	70054	Mm.307198	NM_027298	ENSMUSG00000044362	Ccdc89	1700019B01Rik|AU022100|BOIP	coiled-coil domain containing 89	protein-coding
mm_48164.1	chr5	137152863	137152902	-	1	NA	Intergenic	Intergenic	-36675	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_124987.1	chr15	21367465	21367468	+	1	NA	intron (NM_001008420, intron 3 of 11)	L1_Mur2|LINE|L1	256014	NM_001008420	215654	Mm.300909	NM_001008420	ENSMUSG00000040452	Cdh12	Cdhb	cadherin 12	protein-coding
mm_6125.1	chr1	64305450	64305472	-	1	NA	Intergenic	Intergenic	-184072	NM_033563	93691	Mm.29466	NM_033563	ENSMUSG00000025959	Klf7	9830124P08Rik	Kruppel-like factor 7 (ubiquitous)	protein-coding
mm_46793.1	chr5	112771201	112771219	-	1	NA	intron (NM_028901, intron 34 of 43)	intron (NM_028901, intron 34 of 43)	-22082	NR_040675	67360	Mm.59218	NR_040675	ENSMUSG00000098230	1700095B10Rik	-	RIKEN cDNA 1700095B10 gene	ncRNA
mm_135420.1	chr16	45173920	45173937	-	1	NA	intron (NM_026402, intron 5 of 11)	Lx8|LINE|L1	15099	NM_026402	67841	Mm.41775	NM_026402	ENSMUSG00000022663	Atg3	2610016C12Rik|APG3|Apg3l|Atg3l|PC3-96	autophagy related 3	protein-coding
mm_130164.1	chr15	91643085	91643087	-	1	NA	Intergenic	Intergenic	-30138	NM_025730	66725	Mm.37558	NM_025730	ENSMUSG00000036273	Lrrk2	4921513O20Rik|9330188B09Rik|AW561911|D630001M17Rik|Gm927|cI-46	leucine-rich repeat kinase 2	protein-coding
mm_22317.1	chr2	180443887	180443933	-	1	NA	Intergenic	Intergenic	-17068	NM_148933	108115	Mm.133687	NM_148933	ENSMUSG00000038963	Slco4a1	OATP-E|Slc21a12	solute carrier organic anion transporter family, member 4a1	protein-coding
mm_77546.1	chr8	123212781	123212789	-	1	NA	promoter-TSS (NM_145606)	promoter-TSS (NM_145606)	3	NM_145606	234852	Mm.41596	NM_145606	ENSMUSG00000000743	Chmp1a	2900018H07Rik|Pcoln3	charged multivesicular body protein 1A	protein-coding
mm_29249.1	chr3	107218645	107218745	-	1	NA	exon (NM_001111143, exon 3 of 9)	exon (NM_001111143, exon 3 of 9)	3037	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_70008.1	chr7	142399385	142399391	-	1	NA	Intergenic	Intergenic	-11518	NM_009983	13033	Mm.231395	NM_009983	ENSMUSG00000007891	Ctsd	CD|CatD	cathepsin D	protein-coding
mm_64164.1	chr7	141393184	141393186	+	1	NA	intron (NM_011528, intron 1 of 7)	intron (NM_011528, intron 1 of 7)	1025	NM_011528	21351	Mm.29182	NM_011528	ENSMUSG00000025503	Taldo1	-	transaldolase 1	protein-coding
mm_66222.1	chr7	34748290	34748294	-	1	NA	intron (NM_175140, intron 1 of 3)	intron (NM_175140, intron 1 of 3)	64419	NM_175140	68947	Mm.29380	NM_175140	ENSMUSG00000060402	Chst8	1500011J21Rik|AI426009	carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 8	protein-coding
mm_102903.1	chr11	69546485	69546528	-	1	NA	intron (NM_001081330, intron 1 of 85)	intron (NM_001081330, intron 1 of 85)	2602	NM_001081330	327954	Mm.247478	NM_177617	ENSMUSG00000005237	Dnah2	2900022L05Rik|4930564A01|D130094J20|D330014H01Rik|Dnahc2|Dnhd3	dynein, axonemal, heavy chain 2	protein-coding
mm_25638.1	chr3	121021473	121021479	+	1	NA	Intergenic	Intergenic	-134744	NR_130170	320739	Mm.388474	NR_130170		6530403H02Rik	-	RIKEN cDNA 6530403H02 gene	ncRNA
mm_123595.1	chr14	67715344	67715425	-	1	NA	promoter-TSS (NM_001111028)	promoter-TSS (NM_001111028)	226	NM_001110162	108912	Mm.33831	NM_175384	ENSMUSG00000048922	Cdca2	2610311M19Rik|AI586158	cell division cycle associated 2	protein-coding
mm_79161.1	chr9	47813832	47813843	+	1	NA	exon (NM_018770, exon 7 of 10)	exon (NM_018770, exon 7 of 10)	4371	NR_046048	100038460	Mm.447649	NR_046048		Gm10677	ENSMUSG00000074363	predicted gene 10677	ncRNA
mm_57365.1	chr6	124769483	124769501	-	1	NA	TTS (NM_001302555)	TTS (NM_001302555)	181	NM_001302642	13807	Mm.3913	NM_013509	ENSMUSG00000004267	Eno2	AI837106|D6Ertd375e|Eno-2|NSE	enolase 2, gamma neuronal	protein-coding
mm_136683.1	chr17	6746287	6746292	+	1	NA	intron (NM_009510, intron 7 of 12)	intron (NM_009510, intron 7 of 12)	36491	NM_009510	22350	Mm.277812	NM_009510	ENSMUSG00000052397	Ezr	AW146364|R75297|Vil2|p81	ezrin	protein-coding
mm_151007.1	chr19	46669273	46669274	+	1	NA	exon (NM_007809, exon 5 of 8)	exon (NM_007809, exon 5 of 8)	3727	NM_007809	13074	Mm.1262	NM_007809	ENSMUSG00000003555	Cyp17a1	Cyp17|p450c17	cytochrome P450, family 17, subfamily a, polypeptide 1	protein-coding
mm_141598.1	chr17	32524046	32524057	-	1	NA	exon (NM_001101445, exon 7 of 13)	exon (NM_001101445, exon 7 of 13)	-12578	NM_024442	70101	Mm.30504	NM_024442	ENSMUSG00000048440	Cyp4f16	2310021J05Rik|AI746515	cytochrome P450, family 4, subfamily f, polypeptide 16	protein-coding
mm_46174.1	chr5	96921226	96921238	-	1	NA	promoter-TSS (NR_131152)	promoter-TSS (NR_131152)	-40	NR_131152	666266	Mm.32442	NR_131152	ENSMUSG00000106357	Gm8013	EG666266	predicted gene 8013	ncRNA
mm_106623.1	chr11	120824525	120824576	-	1	NA	promoter-TSS (NM_007988)	promoter-TSS (NM_007988)	-3	NM_007988	14104	Mm.236443	NM_007988	ENSMUSG00000025153	Fasn	A630082H08Rik|FAS	fatty acid synthase	protein-coding
mm_12604.1	chr2	74680631	74680661	+	1	NA	intron (NR_073086, intron 1 of 1)	intron (NR_073086, intron 1 of 1)	1088	NR_073086	15431	Mm.207763	NM_008273	ENSMUSG00000042499	Hoxd11	E230017H14Rik|Hox-4.6|Hox-5.4|Hox-5.5	homeobox D11	protein-coding
mm_79597.1	chr9	58488084	58488110	+	1	NA	promoter-TSS (NM_176921)	promoter-TSS (NM_176921)	-506	NM_176921	319477	Mm.153674	NM_176921	ENSMUSG00000066607	6030419C18Rik	-	RIKEN cDNA 6030419C18 gene	protein-coding
mm_116509.1	chr13	45556316	45556320	-	1	NA	3' UTR (NM_009124, exon 8 of 8)	3' UTR (NM_009124, exon 8 of 8)	48874	NM_025508	66355	Mm.290802	NM_025508	ENSMUSG00000000253	Gmpr	2310004P21Rik|AV028449|GMPR 1	guanosine monophosphate reductase	protein-coding
mm_4357.1	chr1	171917669	171917708	+	1	NA	5' UTR (NM_030710, exon 1 of 8)	5' UTR (NM_030710, exon 1 of 8)	151	NM_030710	30925	Mm.486404	NM_030710	ENSMUSG00000015314	Slamf6	KAL1|KAL1b|Ly108|NTB-A|NTBA|SF2000	SLAM family member 6	protein-coding
mm_104464.1	chr11	95080927	95080940	-	1	NA	Intergenic	Intergenic	-4122	NM_001306162	16400	Mm.57035	NM_013565	ENSMUSG00000001507	Itga3	AA407068|CD49C|GAPB3	integrin alpha 3	protein-coding
mm_7863.1	chr1	132567004	132567016	-	1	NA	3' UTR (NM_001160317, exon 28 of 28)	3' UTR (NM_001160317, exon 28 of 28)	-24070	NM_177129	21367	Mm.260861	NM_011531	ENSMUSG00000053024	Cntn2	D130012K04Rik|TAG-1|Tax	contactin 2	protein-coding
mm_33414.1	chr4	129928768	129928770	+	1	NA	Intergenic	Intergenic	22543	NR_045190	319894	Mm.59196	NR_045190	ENSMUSG00000086369	E330017L17Rik	-	RIKEN cDNA E330017L17 gene	ncRNA
mm_132223.1	chr16	32643848	32643916	+	1	NA	promoter-TSS (NM_001110147)	promoter-TSS (NM_001110147)	-761	NM_001110147	51789	Mm.251115	NM_016788	ENSMUSG00000022791	Tnk2	Ack|Ack-1|Ack1|Cdgip|Pyk1	tyrosine kinase, non-receptor, 2	protein-coding
mm_50856.1	chr6	55203382	55203459	+	1	NA	promoter-TSS (NM_001142781)	promoter-TSS (NM_001142781)	37	NM_001142781	330323	Mm.268997	NM_177883	ENSMUSG00000038022	Fam188b	C330043M08Rik|Gm1406	family with sequence similarity 188, member B	protein-coding
mm_21963.1	chr2	167240589	167240610	-	1	NA	promoter-TSS (NM_008968)	promoter-TSS (NM_008968)	-62	NM_008968	19223	Mm.2339	NM_008968	ENSMUSG00000017969	Ptgis	Cyp8|Cyp8a1|Pgis	prostaglandin I2 (prostacyclin) synthase	protein-coding
mm_45374.1	chr5	66050358	66050369	-	1	NA	intron (NM_178446, intron 2 of 6)	B1F1|SINE|Alu	-46078	NR_027961	231253	Mm.436542	NM_177679	ENSMUSG00000054598	9130230L23Rik	-	RIKEN cDNA 9130230L23 gene	ncRNA
mm_39139.1	chr4	155223207	155223218	-	1	NA	promoter-TSS (NM_011385)	promoter-TSS (NM_011385)	-677	NM_011385	20481	Mm.28520	NM_011385	ENSMUSG00000029050	Ski	2310012I02Rik|2610001A11Rik|AA062172|AA589460|BC004088	ski sarcoma viral oncogene homolog (avian)	protein-coding
mm_835.1	chr1	51478662	51478680	+	1	NA	promoter-TSS (NM_001310549)	promoter-TSS (NM_001310549)	-272	NM_001310549	109019	Mm.196290	NM_028696	ENSMUSG00000026107	Nabp1	4930434H03Rik|4930442A21Rik|4930488J04Rik|4933440J18Rik|5830411E10Rik|AI852561|Nbp1|Obfc2a|Ssb2	nucleic acid binding protein 1	protein-coding
mm_164934.1	chr18	83559734	83559741	+	1	NA	Intergenic	Lx7|LINE|L1	-233853	NR_045361	70960	Mm.410834	NR_045361		4921531P14Rik	1700108N05Rik	RIKEN cDNA 4921531P14 gene	ncRNA
mm_45205.1	chr5	52669733	52669743	-	1	NA	promoter-TSS (NM_172490)	promoter-TSS (NM_172490)	-37	NM_172490	211006	Mm.244719	NM_172490	ENSMUSG00000029173	Sepsecs	AA986712|D5Ertd135e|SLA|SecS	Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase	protein-coding
mm_170364.1	chr1	85272355	85272356	+	1	NA	Intergenic	Intergenic	-1789	NM_001037909	620078	Mm.386456	NM_175219	ENSMUSG00000052477	C130026I21Rik	4930565N07Rik|OTTMUSG00000029174	RIKEN cDNA C130026I21 gene	protein-coding
mm_109739.1	chr12	117220368	117220369	+	1	NA	intron (NM_011215, intron 15 of 22)	MTEa-int|LTR|ERVL-MaLR	-30449	NR_029563	387171		NR_029563	ENSMUSG00000065538	Mir153	Mirn153|mir-153|mmu-mir-153	microRNA 153	ncRNA
mm_162383.1	chr1	74178641	74178646	-	1	NA	Intergenic	(TATG)n|Simple_repeat|Simple_repeat	15988	NM_178241	227288	Mm.337035	NM_178241	ENSMUSG00000048480	Cxcr1	Il8ra	chemokine (C-X-C motif) receptor 1	protein-coding
mm_44760.1	chr5	31571406	31571429	-	1	NA	promoter-TSS (NR_102275)	promoter-TSS (NR_102275)	-20	NR_102275	100740	Mm.23370	NR_102275		AI839979	-	expressed sequence AI839979	ncRNA
mm_90075.1	chr10	116418049	116418103	+	1	NA	promoter-TSS (NR_028107)	promoter-TSS (NR_028107)	-45	NR_028107	67342	Mm.245800	NM_026098	ENSMUSG00000020164	Kcnmb4os1	1700058G18Rik	potassium large conductance calcium-activated channel, subfamily M, beta member 4, opposite strand 1	ncRNA
mm_53299.1	chr6	129045911	129045932	+	1	NA	promoter-TSS (NM_153094)	promoter-TSS (NM_153094)	20	NR_024263	232408	Mm.259262	NM_153094	ENSMUSG00000030154	Klrb1f	A630024B12Rik|Nkr-p1f|Nkrp1-f|Nkrp1f	killer cell lectin-like receptor subfamily B member 1F	protein-coding
mm_23472.1	chr3	60480582	60480598	+	1	NA	intron (NM_001253713, intron 2 of 9)	intron (NM_001253713, intron 2 of 9)	7760	NM_001253713	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_146517.1	chr18	4239212	4239220	-	1	NA	Intergenic	Intergenic	73384	NM_026092	67328	Mm.158148	NM_026092	ENSMUSG00000024233	Lyzl1	1700038F02Rik|Lyc2|Lyzd1	lysozyme-like 1	protein-coding
mm_82278.1	chr9	7358262	7358283	-	1	NA	exon (NM_008605, exon 10 of 10)	exon (NM_008605, exon 10 of 10)	10898	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_44253.1	chr5	5380608	5380682	-	1	NA	promoter-TSS (NM_011074)	promoter-TSS (NM_011074)	-394	NM_011074	18647	Mm.389061	NM_011074	ENSMUSG00000028926	Cdk14	Pftk1|mKIAA0834	cyclin-dependent kinase 14	protein-coding
mm_71104.1	chr8	35495296	35495296	+	1	NA	exon (NM_026067, exon 1 of 7)	exon (NM_026067, exon 1 of 7)	237	NM_026067	67276	Mm.207534	NM_026067	ENSMUSG00000031527	Eri1	3'hexo|3110010F15Rik|Thex1|eri-1	exoribonuclease 1	protein-coding
mm_24856.1	chr3	95882571	95882575	+	1	NA	promoter-TSS (NM_001033302)	promoter-TSS (NM_001033302)	-345	NM_001033302	229599	Mm.331218	NM_001033302	ENSMUSG00000038550	Ciart	Chrono|Gm129	circadian associated repressor of transcription	protein-coding
mm_16915.1	chr2	13544652	13544673	-	1	NA	promoter-TSS (NM_010067)	promoter-TSS (NM_010067)	2	NM_010067	13434	Mm.6979	NM_010067	ENSMUSG00000026723	Trdmt1	Dnmt2|Rnmt2	tRNA aspartic acid methyltransferase 1	protein-coding
mm_155309.1	chrX	61288189	61288199	+	1	NA	Intergenic	Intergenic	96901	NR_033502	320247	Mm.447372	NR_033502		C030023E24Rik	-	RIKEN cDNA C030023E24 gene	ncRNA
mm_20143.1	chr2	121456741	121456761	-	1	NA	promoter-TSS (NM_001025371)	promoter-TSS (NM_001025371)	13	NM_001025371	574418	Mm.459165	NM_001025371	ENSMUSG00000046110	Serinc4	-	serine incorporator 4	protein-coding
mm_131475.1	chr16	17070282	17070320	+	1	NA	5' UTR (NM_023249, exon 1 of 5)	5' UTR (NM_023249, exon 1 of 5)	162	NM_001291047	106369	Mm.237941	NM_023249	ENSMUSG00000022773	Ypel1	0610009L05Rik|1700016N17Rik|1700019O22Rik|4921520K19Rik|4930511F14Rik|AV118478|DGL-1|Dgl1|Ppil2|mdgl-1	yippee-like 1 (Drosophila)	protein-coding
mm_23434.1	chr3	59131866	59131866	+	1	NA	promoter-TSS (NM_001287123)	promoter-TSS (NM_001287123)	-538	NM_001287123	140795	Mm.439021	NM_133200	ENSMUSG00000036381	P2ry14	A330108O13Rik|Gpr105|P2Y14	purinergic receptor P2Y, G-protein coupled, 14	protein-coding
mm_167449.1	chr8	122567977	122567983	+	1	NA	promoter-TSS (NM_026014)	promoter-TSS (NM_026014)	-35	NM_026014	67177	Mm.21873	NM_026014	ENSMUSG00000006585	Cdt1	2610318F11Rik|AW545653|C76791|Ris2	chromatin licensing and DNA replication factor 1	protein-coding
mm_80924.1	chr9	101989194	101989201	+	1	NA	intron (NM_173447, intron 9 of 15)	intron (NM_173447, intron 9 of 15)	315778	NR_106163	102466241		NR_106163	ENSMUSG00000098521	Mir7243	Gm27363|mmu-mir-7243	microRNA 7243	ncRNA
mm_135900.1	chr16	66865430	66865432	-	1	NA	intron (NM_001347247, intron 2 of 9)	Lx2B|LINE|L1	208313	NR_040512	75501	Mm.394300	NR_040512	ENSMUSG00000092599	1700010K23Rik	-	RIKEN cDNA 1700010K23 gene	ncRNA
mm_100250.1	chr11	117326387	117326398	+	1	NA	intron (NM_001113487, intron 2 of 10)	intron (NM_001113487, intron 2 of 10)	-5323	NM_017380	53860	Mm.38450	NM_017380	ENSMUSG00000059248	Sept9	MSF1|Msf|PNUTL4|Sint1	septin 9	protein-coding
mm_70609.1	chr8	13405117	13405122	+	1	NA	promoter-TSS (NM_011881)	promoter-TSS (NM_011881)	38	NM_011881	24013	Mm.257501	NM_011881	ENSMUSG00000031450	Grk1	Gprk1|Rhok|Rk	G protein-coupled receptor kinase 1	protein-coding
mm_20276.1	chr2	126876180	126876205	-	1	NA	promoter-TSS (NM_001164325)	promoter-TSS (NM_001164325)	69	NM_001164325	58800	Mm.244705	NM_021450	ENSMUSG00000027365	Trpm7	2310022G15Rik|4833414K03Rik|5033407O22Rik|CHAK|CHAK1|LTrpC-7|Ltpr7|Ltrpc7|TRPPLIK	transient receptor potential cation channel, subfamily M, member 7	protein-coding
mm_141813.1	chr17	34603739	34603749	-	1	NA	promoter-TSS (NM_019403)	promoter-TSS (NM_019403)	-183	NM_019403	54197	Mm.274542	NM_019403	ENSMUSG00000015478	Rnf5	2410131O05Rik|AA407576|NG2	ring finger protein 5	protein-coding
mm_1624.1	chr1	74396557	74396573	+	1	NA	3' UTR (NM_153088, exon 7 of 7)	3' UTR (NM_153088, exon 7 of 7)	2255	NR_029743	387219		NR_029743	ENSMUSG00000065468	Mir26b	Mirn26b|mir-26b|mmu-mir-26b	microRNA 26b	ncRNA
mm_170902.1	chr2	30069576	30069586	+	1	NA	exon (NM_001204875, exon 5 of 8)	exon (NM_001204875, exon 5 of 8)	3107	NM_001204875	56086	Mm.326055	NM_023871	ENSMUSG00000054766	Set	2610030F17Rik|5730420M11Rik|AA407739|I-2PP2A|StF-IT-1|TAF-I	SET nuclear oncogene	protein-coding
mm_36279.1	chr4	63745108	63745118	-	1	NA	promoter-TSS (NM_177371)	promoter-TSS (NM_177371)	0	NM_177371	326623	Mm.208152	NM_177371	ENSMUSG00000050395	Tnfsf15	Tl1|Tl1a|Tnlg1b|Vegi	tumor necrosis factor (ligand) superfamily, member 15	protein-coding
mm_168740.1	chr12	115208545	115208545	-	1	NA	Intergenic	Intergenic	487249	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
mm_138722.1	chr17	36870103	36870142	+	1	NA	exon (NM_011280, exon 1 of 7)	exon (NM_011280, exon 1 of 7)	548	NM_011280	19824	Mm.299155	NM_011280	ENSMUSG00000073400	Trim10	AI324236|BB139825|Herf1|Rnf9	tripartite motif-containing 10	protein-coding
mm_75692.1	chr8	68212008	68212016	-	1	NA	Intergenic	Intergenic	-64516	NM_028182	72281	Mm.40974	NM_028182	ENSMUSG00000053886	Sh2d4a	2210402M20Rik|SH2A	SH2 domain containing 4A	protein-coding
mm_140756.1	chr17	17521643	17521652	-	1	NA	Intergenic	Intergenic	102842	NM_172827	240028	Mm.328807	NM_172827	ENSMUSG00000023845	Lnpep	2010309L07Rik|4732490P18Rik|CAP|IRAP|PLAP|gp160|vp165	leucyl/cystinyl aminopeptidase	protein-coding
mm_98559.1	chr11	95310305	95310338	+	1	NA	promoter-TSS (NM_001195004)	promoter-TSS (NM_001195004)	-75	NM_001195003	217127	Mm.90213	NM_177619	ENSMUSG00000038909	Kat7	Hbo1|Hboa|Myst2	K(lysine) acetyltransferase 7	protein-coding
mm_153686.1	chr19	44396771	44396783	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	10932	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_13757.1	chr2	118126776	118126822	+	1	NA	3' UTR (NM_011580, exon 22 of 22)	3' UTR (NM_011580, exon 22 of 22)	14923	NM_001313914	21825	Mm.4159	NM_011580	ENSMUSG00000040152	Thbs1	TSP-1|TSP1|Thbs-1|tbsp1	thrombospondin 1	protein-coding
mm_138417.1	chr17	35069403	35069416	+	1	NA	exon (NM_023463, exon 3 of 3)	exon (NM_023463, exon 3 of 3)	2084	NM_023463	68468	Mm.215096	NM_023463	ENSMUSG00000092586	Ly6g6c	1110003M04Rik|AU016360|G6c|NG24	lymphocyte antigen 6 complex, locus G6C	protein-coding
mm_173104.1	chrX	152923760	152923761	-	1	NA	Intergenic	7SK|RNA|RNA	-82709	NM_001137547	635253	Mm.426169	NM_001137547	ENSMUSG00000067215	Usp51	AV136873	ubiquitin specific protease 51	protein-coding
mm_91877.1	chr10	59583329	59583341	-	1	NA	intron (NM_001033259, intron 1 of 7)	(TG)n|Simple_repeat|Simple_repeat	33357	NM_001033259	215999	Mm.296470	NM_001033259	ENSMUSG00000009647	Mcu	2010012O16Rik|AV064928|C10orf42|Ccdc109a|D130073L02Rik|Gm64	mitochondrial calcium uniporter	protein-coding
mm_99142.1	chr11	100415716	100415720	+	1	NA	promoter-TSS (NM_010221)	promoter-TSS (NM_010221)	24	NM_001163481	14230	Mm.3894	NM_010221	ENSMUSG00000001555	Fkbp10	AI325255|FKBP-10|FKBP-65|FKBP65|Fkbp-rs1|Fkbp1-rs|Fkbp6|Fkbprp	FK506 binding protein 10	protein-coding
mm_13712.1	chr2	117162568	117162575	+	1	NA	intron (NM_033524, intron 2 of 6)	intron (NM_033524, intron 2 of 6)	-22556	NR_030440	732489		NR_030440	ENSMUSG00000076376	Mir674	Mirn674|mir-674|mmu-mir-674	microRNA 674	ncRNA
mm_68288.1	chr7	105633526	105633601	-	1	NA	promoter-TSS (NM_001285871)	promoter-TSS (NM_001285871)	8	NM_018880	55992	Mm.29290	NM_018880	ENSMUSG00000036989	Trim3	BERP1|HAC1|Rnf22	tripartite motif-containing 3	protein-coding
mm_128079.1	chr15	27670943	27670955	-	1	NA	intron (NM_001242423, intron 1 of 7)	intron (NM_001242423, intron 1 of 7)	10593	NM_001242424	223433	Mm.266485	NM_198301	ENSMUSG00000056069	Fam105a	9830126M18	family with sequence similarity 105, member A	protein-coding
mm_44670.1	chr5	29478631	29478638	-	1	NA	promoter-TSS (NM_019944)	promoter-TSS (NM_019944)	-164	NM_019944	15285	Mm.103760	NM_019944	ENSMUSG00000001566	Mnx1	HB9|Hlxb9|MNR2	motor neuron and pancreas homeobox 1	protein-coding
mm_15167.1	chr2	154011453	154011458	+	1	NA	exon (NM_008953, exon 5 of 9)	exon (NM_008953, exon 5 of 9)	3179	NM_008953	19194	Mm.29197	NM_008953	ENSMUSG00000042459	Bpifa2	Bpifa2e|Psp	BPI fold containing family A, member 2	protein-coding
mm_28293.1	chr3	89093359	89093367	-	1	NA	promoter-TSS (NM_001083807)	promoter-TSS (NM_001083807)	0	NM_001083807	72296	Mm.27687	NM_028188	ENSMUSG00000041263	Rusc1	2210403N08Rik|AA408288|NESCA	RUN and SH3 domain containing 1	protein-coding
mm_93601.1	chr10	117217337	117217362	-	1	NA	intron (NM_026570, intron 5 of 6)	intron (NM_026570, intron 5 of 6)	7158	NM_026570	64050	Mm.233529	NM_026570	ENSMUSG00000020171	Yeats4	4930573H17Rik|B230215M10Rik|GAS41|NuBI-1	YEATS domain containing 4	protein-coding
mm_90986.1	chr10	13832736	13832748	-	1	NA	intron (NM_001347362, intron 1 of 5)	intron (NM_001347362, intron 1 of 5)	36215	NM_025446	66253	Mm.45755	NM_025446	ENSMUSG00000019806	Aig1	1500031O19Rik|AV064870|AW413422|CGI-103	androgen-induced 1	protein-coding
mm_150879.1	chr19	45076637	45076644	+	1	NA	intron (NM_178929, intron 1 of 4)	intron (NM_178929, intron 1 of 4)	501	NM_178929	107250	Mm.24417	NM_178929	ENSMUSG00000025213	Kazald1	AI842353|Bono1|IGFBP-rP10	Kazal-type serine peptidase inhibitor domain 1	protein-coding
mm_12904.1	chr2	84809680	84809711	+	1	NA	3' UTR (NM_019949, exon 4 of 4)	3' UTR (NM_019949, exon 4 of 4)	10867	NM_019949	56791	Mm.38261	NM_019949	ENSMUSG00000027078	Ube2l6	2810489I21Rik|RIG-B|UBCH8|Ubce8|Ubcm8	ubiquitin-conjugating enzyme E2L 6	protein-coding
mm_21999.1	chr2	167744093	167744107	-	1	NA	Intergenic	Intergenic	52923	NR_015500	329562	Mm.123101	NM_177851	ENSMUSG00000006462	A530013C23Rik	-	RIKEN cDNA A530013C23 gene	ncRNA
mm_171227.1	chr3	6462020	6462029	-	1	NA	Intergenic	L1Md_T|LINE|L1	158419	NM_027048	69347	Mm.45822	NM_027048	ENSMUSG00000069118	1700008P02Rik	-	RIKEN cDNA 1700008P02 gene	protein-coding
mm_115277.1	chr13	111687765	111687774	+	1	NA	intron (NM_172593, intron 1 of 12)	intron (NM_172593, intron 1 of 12)	1591	NM_172593	218613	Mm.31012	NM_172593	ENSMUSG00000032727	Mier3	5730509D14|AU015422|D130064H19Rik	MIER family member 3	protein-coding
mm_138233.1	chr17	34398803	34398830	+	1	NA	promoter-TSS (NM_001163855)	promoter-TSS (NM_001163855)	-4	NM_001001177	407788	Mm.73205	NM_001001177	ENSMUSG00000057246	BC051142	NG8|TSBP|Tesb|Tesbp	cDNA sequence BC051142	protein-coding
mm_111677.1	chr12	103355799	103355825	-	1	NA	5' UTR (NM_023049, exon 1 of 10)	5' UTR (NM_023049, exon 1 of 10)	189	NM_023049	65256	Mm.27159	NM_023049	ENSMUSG00000021200	Asb2	1110008E15Rik	ankyrin repeat and SOCS box-containing 2	protein-coding
mm_111900.1	chr12	108710973	108710995	-	1	NA	Intergenic	MTEb|LTR|ERVL-MaLR	-8678	NM_027299	70059	Mm.207605	NM_027299	ENSMUSG00000021263	Degs2	2210008A03Rik|AI852933|DES2	delta(4)-desaturase, sphingolipid 2	protein-coding
mm_87357.1	chr10	43695451	43695469	+	1	NA	Intergenic	PB1D10|SINE|Alu	-50698	NR_040581	69443	Mm.484042	NR_040581	ENSMUSG00000111422	1700027J07Rik	-	RIKEN cDNA 1700027J07 gene	ncRNA
mm_94688.1	chr11	19924355	19924368	+	1	NA	promoter-TSS (NM_033523)	promoter-TSS (NM_033523)	-81	NM_033523	114716	Mm.266627	NM_033523	ENSMUSG00000045671	Spred2	C79158	sprouty-related, EVH1 domain containing 2	protein-coding
mm_34422.1	chr4	145274640	145274643	+	1	NA	intron (NM_009401, intron 11 of 12)	AT_rich|Low_complexity|Low_complexity	-27771	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_65263.1	chr7	19921127	19921136	-	1	NA	promoter-TSS (NM_027514)	promoter-TSS (NM_027514)	12	NM_027514	52118	Mm.227506	NM_027514	ENSMUSG00000040511	Pvr	3830421F03Rik|CD155|D7Ertd458e|HVED|PVS|Taa1|Tage4|mE4|necl-5	poliovirus receptor	protein-coding
mm_138649.1	chr17	35867042	35867058	+	1	NA	5' UTR (NM_175242, exon 1 of 3)	5' UTR (NM_175242, exon 1 of 3)	435	NM_175242	76448	Mm.359982	NM_175242	ENSMUSG00000034595	Ppp1r18	2310014H01Rik|AA407849|AI450394	protein phosphatase 1, regulatory subunit 18	protein-coding
mm_62642.1	chr7	107665586	107665606	+	1	NA	intron (NM_001163557, intron 3 of 25)	intron (NM_001163557, intron 3 of 25)	58752	NM_001163557	19024	Mm.2817	NM_008905	ENSMUSG00000036528	Ppfibp2	Cclp1	PTPRF interacting protein, binding protein 2 (liprin beta 2)	protein-coding
mm_87852.1	chr10	61089349	61089396	+	1	NA	promoter-TSS (NM_025273)	promoter-TSS (NM_025273)	41	NM_025273	13180	Mm.39473	NM_025273	ENSMUSG00000020098	Pcbd1	Dcoh|Pcbd|Pcd|Phs	pterin 4 alpha carbinolamine dehydratase/dimerization cofactor of hepatocyte nuclear factor 1 alpha (TCF1) 1	protein-coding
mm_91117.1	chr10	19188652	19188660	-	1	NA	intron (NR_038022, intron 1 of 1)	intron (NR_038022, intron 1 of 1)	21418	NR_038022	100504265	Mm.383417	NR_038021		Gm20139	-	predicted gene, 20139	ncRNA
mm_167925.1	chrX	102928370	102928374	+	1	NA	promoter-TSS (NR_045422)	promoter-TSS (NR_045422)	0	NR_045422	69388	Mm.138009	NR_045422	ENSMUSG00000109745	1700018G05Rik	-	RIKEN cDNA 1700018G05 gene	ncRNA
mm_140557.1	chr17	7874872	7874880	-	1	NA	Intergenic	Intergenic	-51124	NM_145968	72536	Mm.119680	NM_145968	ENSMUSG00000033450	Tagap	2610315E15Rik	T cell activation Rho GTPase activating protein	protein-coding
mm_130492.1	chr15	98804091	98804114	-	1	NA	3' UTR (NM_001013741, exon 2 of 2)	3' UTR (NM_001013741, exon 2 of 2)	3823	NM_001013741	13199	Mm.390810	NM_001013741	ENSMUSG00000059213	Ddn	Gm748	dendrin	protein-coding
mm_154933.1	chrX	35888783	35888792	+	1	NA	promoter-TSS (NM_001009947)	promoter-TSS (NM_001009947)	-45	NM_001009947	75974	Mm.32873	NM_177745	ENSMUSG00000031093	Dock11	5033414A21Rik|8030476J24|Zizimin2|sph238	dedicator of cytokinesis 11	protein-coding
mm_70706.1	chr8	15057668	15057691	+	1	NA	promoter-TSS (NM_008664)	promoter-TSS (NM_008664)	26	NM_008664	17930	Mm.272115	NM_008664	ENSMUSG00000031461	Myom2	AW146149	myomesin 2	protein-coding
mm_59511.1	chr7	27580906	27580918	+	1	NA	3' UTR (NM_175107, exon 10 of 10)	3' UTR (NM_175107, exon 10 of 10)	-10640	NM_001110208	11652	Mm.177194	NM_007434	ENSMUSG00000004056	Akt2	2410016A19Rik|AW554154|PKB|PKBbeta	thymoma viral proto-oncogene 2	protein-coding
mm_65384.1	chr7	25091239	25091250	-	1	NA	3' UTR (NM_001163556, exon 14 of 14)	3' UTR (NM_001163556, exon 14 of 14)	5931	NR_105855	102465968		NR_105855	ENSMUSG00000098441	Mir6537	Gm27808|mmu-mir-6537	microRNA 6537	ncRNA
mm_131848.1	chr16	23060386	23060393	+	1	NA	exon (NM_001102411, exon 2 of 10)	exon (NM_001102411, exon 2 of 10)	2089	NM_001102412	16644	Mm.2160	NM_023125	ENSMUSG00000022875	Kng1	Kng	kininogen 1	protein-coding
mm_171531.1	chr4	146750589	146750591	-	1	NA	Intergenic	CpG	-203717	NR_045468	67524	Mm.444300	NR_045468	ENSMUSG00000086046	1700095A21Rik	-	RIKEN cDNA 1700095A21 gene	ncRNA
mm_16484.1	chr2	180893122	180893138	+	1	NA	promoter-TSS (NR_029538)	promoter-TSS (NR_029538)	-910	NR_029538	723951		NR_029538	ENSMUSG00000065454	Mir124a-3	Mirn124a-3|mir-124-3|mir-124a-3	microRNA 124a-3	ncRNA
mm_154128.1	chr19	57251682	57251685	-	1	NA	Intergenic	Intergenic	-22277	NR_045319	78120	Mm.445892	NR_045319		4930449E18Rik	-	RIKEN cDNA 4930449E18 gene	ncRNA
mm_48057.1	chr5	136565704	136565724	-	1	NA	5' UTR (NM_001291240, exon 1 of 23)	5' UTR (NM_001291240, exon 1 of 23)	267	NM_001291239	13047	Mm.320317	NM_009986	ENSMUSG00000029705	Cux1	CDP|Cutl1|Cux|Cux-1	cut-like homeobox 1	protein-coding
mm_167013.1	chr7	62423269	62423292	-	1	NA	Intergenic	Intergenic	-3141	NM_011746	22652	Mm.146	NM_011746	ENSMUSG00000070527	Mkrn3	D7H15S9-1|Zfp127	makorin, ring finger protein, 3	protein-coding
mm_8512.1	chr1	154726661	154726668	-	1	NA	promoter-TSS (NM_009782)	promoter-TSS (NM_009782)	-744	NM_009782	12290	Mm.267517	NM_009782	ENSMUSG00000004110	Cacna1e	A430040I15|BII|Cach6|Cacnl1a6|Cav2.3|Cchra1|alpha1E	calcium channel, voltage-dependent, R type, alpha 1E subunit	protein-coding
mm_131491.1	chr16	17276292	17276330	+	1	NA	promoter-TSS (NM_177473)	promoter-TSS (NM_177473)	11	NM_177473	224019	Mm.246388	NM_177473	ENSMUSG00000055692	Tmem191c	4933405M22Rik|D16Bwg1494e|MNCb-4137	transmembrane protein 191C	protein-coding
mm_105008.1	chr11	100386759	100386791	-	1	NA	intron (NM_010593, intron 1 of 13)	intron (NM_010593, intron 1 of 13)	11015	NM_010593	16480	Mm.299774	NM_010593	ENSMUSG00000001552	Jup	Ctnng|D930025P04Rik|PG	junction plakoglobin	protein-coding
mm_90000.1	chr10	112270094	112270145	+	1	NA	Intergenic	Intergenic	-1004	NM_001025581	268345	Mm.336242	NM_001025581	ENSMUSG00000035681	Kcnc2	AW047325|B230117I07|KShIIIA|Kv3.2	potassium voltage gated channel, Shaw-related subfamily, member 2	protein-coding
mm_31088.1	chr4	41633287	41633297	+	1	NA	intron (NM_175138, intron 18 of 19)	L1MB8|LINE|L1	7010	NM_027147	69638	Mm.372459	NM_027147	ENSMUSG00000028445	Enho	1110065P19Rik|2310040A07Rik	energy homeostasis associated	protein-coding
mm_78433.1	chr9	32032264	32032274	+	1	NA	Intergenic	CpG	-83867	NM_001195632	330914	Mm.46683	NM_177379	ENSMUSG00000041444	Arhgap32	3426406O18Rik|Gc-gap|Grit|Px-rics|Rics|mKIAA0712|p200Rhogap|p250Gap	Rho GTPase activating protein 32	protein-coding
mm_68663.1	chr7	118855650	118855695	-	1	NA	promoter-TSS (NM_001168220)	promoter-TSS (NM_001168220)	-59	NM_001168220	66356	Mm.482278	NM_023197	ENSMUSG00000030980	Knop1	2310008H09Rik|Tsg118	lysine rich nucleolar protein 1	protein-coding
mm_53089.1	chr6	125002171	125002182	+	1	NA	3' UTR (NM_001145926, exon 6 of 6)	3' UTR (NM_001145926, exon 6 of 6)	3566	NM_001145926	319352	Mm.295327	NM_175696	ENSMUSG00000030329	Pianp	AI255183|AU067746|C530028O21Rik|Panp	PILR alpha associated neural protein	protein-coding
mm_109127.1	chr12	105776450	105776454	+	1	NA	intron (NM_030187, intron 16 of 17)	B4A|SINE|B4	-8245	NM_011112	18789	Mm.255877	NM_011112	ENSMUSG00000021111	Papola	Pap|PapIII|Plap	poly (A) polymerase alpha	protein-coding
mm_68068.1	chr7	101868510	101868522	-	1	NA	5' UTR (NM_008034, exon 3 of 7)	5' UTR (NM_008034, exon 3 of 7)	2272	NM_001252554	14275	Mm.2135	NM_008034	ENSMUSG00000001827	Folr1	FBP1|Folbp-1|Folbp1	folate receptor 1 (adult)	protein-coding
mm_173251.1	chrX	92801274	92801292	+	1	NA	Intergenic	L1Md_T|LINE|L1	-201711	NM_173783	215641	Mm.327999	NM_173783	ENSMUSG00000067649	Mageb18	B430216B18Rik	melanoma antigen family B, 18	protein-coding
mm_99663.1	chr11	105913981	105914009	+	1	NA	intron (NM_181071, intron 22 of 25)	intron (NM_181071, intron 22 of 25)	30152	NM_007805	13056	Mm.149403	NM_007805	ENSMUSG00000019590	Cyb561	-	cytochrome b-561	protein-coding
mm_24103.1	chr3	88140838	88140855	+	1	NA	Intergenic	Intergenic	-1526	NM_001310587	17261	Mm.28184	NM_133665	ENSMUSG00000001419	Mef2d	C80750	myocyte enhancer factor 2D	protein-coding
mm_154374.1	chrM	11084	11106	+	1	NA	NA	Intergenic	NA	NA								
mm_7848.1	chr1	132367880	132367894	-	1	NA	promoter-TSS (NM_001311108)	promoter-TSS (NM_001311108)	61	NM_001311108	68875	Mm.273785	NM_178874	ENSMUSG00000042066	Tmcc2	1110063G11Rik	transmembrane and coiled-coil domains 2	protein-coding
mm_141565.1	chr17	32272431	32272433	-	1	NA	intron (NM_198094, intron 1 of 12)	intron (NM_198094, intron 1 of 12)	11691	NM_198094	57261	Mm.253518	NM_020508	ENSMUSG00000024002	Brd4	Brd5|HUNK1|MCAP|WI-11513	bromodomain containing 4	protein-coding
mm_147121.1	chr18	35740440	35740492	-	1	NA	promoter-TSS (NM_001289592)	promoter-TSS (NM_001289592)	88	NM_001289592	72512	Mm.45995	NM_028261	ENSMUSG00000024349	Tmem173	2610307O08Rik|ERIS|MPYS|Mita|STING	transmembrane protein 173	protein-coding
mm_34617.1	chr4	150416921	150416925	+	1	NA	intron (NM_001085492, intron 2 of 22)	intron (NM_001085492, intron 2 of 22)	135007	NM_001085492	68703	Mm.291274	NM_001085492	ENSMUSG00000039852	Rere	1110033A15Rik|AI414665|ARG|ARP|ATN1L|AW742570|Atr2|DNB1|eye<m03Jus>|eyes3|mKIAA0458	arginine glutamic acid dipeptide (RE) repeats	protein-coding
mm_87380.1	chr10	44611822	44611841	+	1	NA	Intergenic	RSINE1|SINE|B4	-153083	NM_007548	12142	Mm.4800	NM_007548	ENSMUSG00000038151	Prdm1	Blimp-1|Blimp1|PRDI-BF1|ZNFPR1A1|b2b1765Clo	PR domain containing 1, with ZNF domain	protein-coding
mm_162707.1	chr10	23350330	23350342	-	1	NA	promoter-TSS (NM_001347372)	promoter-TSS (NM_001347372)	-393	NM_010167	14051	Mm.332128	NM_010167	ENSMUSG00000010461	Eya4	B130023L16Rik	EYA transcriptional coactivator and phosphatase 4	protein-coding
mm_127527.1	chr15	102089970	102089988	+	1	NA	exon (NM_145625, exon 9 of 15)	exon (NM_145625, exon 9 of 15)	-13009	NM_153533	209039	Mm.29389	NM_153533	ENSMUSG00000037003	Tns2	C1-ten|Tenc1|nep|nph	tensin 2	protein-coding
mm_98538.1	chr11	95009961	95009963	+	1	NA	promoter-TSS (NM_146025)	promoter-TSS (NM_146025)	83	NM_146025	217125	Mm.297199	NM_146025	ENSMUSG00000047181	Samd14	AI839049|AI854782|BC034054	sterile alpha motif domain containing 14	protein-coding
mm_144691.1	chr18	34855563	34855601	+	1	NA	Intergenic	Intergenic	-5625	NM_007913	13653	Mm.181959	NM_007913	ENSMUSG00000038418	Egr1	A530045N19Rik|ETR103|Egr-1|Krox-1|Krox-24|Krox24|NGF1-A|NGFI-A|NGFIA|TIS8|Zenk|Zfp-6|Zif268|egr	early growth response 1	protein-coding
mm_110254.1	chr12	31634526	31634543	-	1	NA	promoter-TSS (NM_007530)	promoter-TSS (NM_007530)	63	NM_007530	12033	Mm.242379	NM_007530	ENSMUSG00000020650	Bcap29	AW208404|Bap29	B cell receptor associated protein 29	protein-coding
mm_138665.1	chr17	35874935	35874941	+	1	NA	3' UTR (NM_001146711, exon 4 of 4)	3' UTR (NM_001146711, exon 4 of 4)	-4840	NM_026987	69192	Mm.390986	NM_026987	ENSMUSG00000024422	Dhx16	2410006N22Rik|DBP2|Ddx16|mKIAA0577	DEAH (Asp-Glu-Ala-His) box polypeptide 16	protein-coding
mm_168286.1	chr11	100534562	100534568	-	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	-6565	NM_001199296	104112	Mm.282039	NM_134037	ENSMUSG00000020917	Acly	A730098H14Rik|AW538652	ATP citrate lyase	protein-coding
mm_44888.1	chr5	34942071	34942073	-	1	NA	Intergenic	Intergenic	-7376	NM_173402	71729	Mm.196208	NM_173402	ENSMUSG00000029101	Rgs12	1200016K18Rik|4632412M04Rik|AI481290|E130309H11	regulator of G-protein signaling 12	protein-coding
mm_100266.1	chr11	117361306	117361329	+	1	NA	3' UTR (NM_001113486, exon 12 of 12)	3' UTR (NM_001113486, exon 12 of 12)	29004	NM_001113488	53860	Mm.38450	NM_017380	ENSMUSG00000059248	Sept9	MSF1|Msf|PNUTL4|Sint1	septin 9	protein-coding
mm_152230.1	chr19	8708045	8708055	-	1	NA	exon (NM_008577, exon 9 of 9)	exon (NM_008577, exon 9 of 9)	5847	NM_008577	17254	Mm.4114	NM_008577	ENSMUSG00000010095	Slc3a2	4F2|4F2HC|AI314110|Cd98|Ly-10|Ly-m10|Ly10|Mdu1|Mgp-2hc|NACAE	solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2	protein-coding
mm_61407.1	chr7	73418626	73418638	+	1	NA	3' UTR (NM_177740, exon 4 of 4)	3' UTR (NM_177740, exon 4 of 4)	-42858	NR_040324	319783	Mm.349813	NR_040324	ENSMUSG00000097756	A730056A06Rik	C76391	RIKEN cDNA A730056A06 gene	ncRNA
mm_111828.1	chr12	107131515	107131523	-	1	NA	Intergenic	Intergenic	-415195	NR_015512	71033	Mm.159404	NR_015512	ENSMUSG00000085820	4933406K04Rik	4930426M03Rik|4930485I22Rik|4933427G14Rik	RIKEN cDNA 4933406K04 gene	ncRNA
mm_165791.1	chr3	136061408	136061409	+	1	NA	intron (NM_001310749, intron 12 of 15)	intron (NM_001310749, intron 12 of 15)	-221139	NR_040540	71038	Mm.410798	NR_040540	ENSMUSG00000106306	4933401H06Rik	-	RIKEN cDNA 4933401H06 gene	ncRNA
mm_2027.1	chr1	87181262	87181279	+	1	NA	Intergenic	Intergenic	-2044	NM_027084	69453	Mm.84618	NM_027084	ENSMUSG00000036480	Prss56	1700027L20Rik	protease, serine 56	protein-coding
mm_147255.1	chr18	38631611	38631619	-	1	NA	Intergenic	Intergenic	-30347	NM_011898	24066	Mm.42038	NM_011898	ENSMUSG00000024427	Spry4	A030006O18Rik|sprouty4	sprouty homolog 4 (Drosophila)	protein-coding
mm_146382.1	chr18	82585399	82585412	+	1	NA	3' UTR (NM_010777, exon 7 of 7)	3' UTR (NM_010777, exon 7 of 7)	30897	NM_001025254	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_163072.1	chr11	67292901	67292916	+	1	NA	exon (NM_177369, exon 21 of 40)	exon (NM_177369, exon 21 of 40)	15784	NM_177369	17885	Mm.340163	NM_177369	ENSMUSG00000055775	Myh8	4832426G23Rik|AI327267|MHCp|MyHC-pn|Myhs-p|Myhsp	myosin, heavy polypeptide 8, skeletal muscle, perinatal	protein-coding
mm_132590.1	chr16	38444306	38444319	+	1	NA	Intergenic	ORR1C1|LTR|ERVL-MaLR	8377	NM_007414	11544	Mm.20047	NM_007414	ENSMUSG00000002844	Adprh	Arh1	ADP-ribosylarginine hydrolase	protein-coding
mm_143377.1	chr17	67868261	67868264	-	1	NA	intron (NM_172964, intron 10 of 17)	intron (NM_172964, intron 10 of 17)	82678	NM_001347410	268970	Mm.9935	NM_172964	ENSMUSG00000024043	Arhgap28	AU044757|AW550892|E130310N06	Rho GTPase activating protein 28	protein-coding
mm_22079.1	chr2	168765246	168765261	-	1	NA	intron (NM_201395, intron 1 of 3)	CpG	1948	NM_201395	99377	Mm.434054	NM_175303	ENSMUSG00000027547	Sall4	5730441M18Rik|AA407717|AL022809|AW536104|C330011P20Rik|C78083|C78563|Tex20	sal-like 4 (Drosophila)	protein-coding
mm_36128.1	chr4	58987118	58987131	-	1	NA	promoter-TSS (NM_025968)	promoter-TSS (NM_025968)	-46	NM_025968	67103	Mm.34497	NM_025968	ENSMUSG00000028378	Ptgr1	2510002C21Rik|Ltb4dh|Zadh3	prostaglandin reductase 1	protein-coding
mm_112153.1	chr12	113265133	113265147	-	1	NA	Intergenic	Intergenic	79237	NM_153776	69195	Mm.313244	NM_153776	ENSMUSG00000049036	Tmem121	2410008J05Rik|Hole	transmembrane protein 121	protein-coding
mm_148169.1	chr18	78057361	78057371	-	1	NA	promoter-TSS (NM_001101038)	promoter-TSS (NM_001101038)	-98	NM_001101038	620235	Mm.35607	NM_001101038	ENSMUSG00000091055	Siglec15	Cd33l3|EG620235|SIGLEC-I	sialic acid binding Ig-like lectin 15	protein-coding
mm_48750.1	chr5	147894842	147894849	-	1	NA	promoter-TSS (NM_027872)	promoter-TSS (NM_027872)	-43	NM_027872	71706	Mm.153218	NM_027872	ENSMUSG00000029650	Slc46a3	1200006F02Rik	solute carrier family 46, member 3	protein-coding
mm_29351.1	chr3	108439682	108439686	-	1	NA	intron (NM_001204979, intron 1 of 10)	B1_Mur2|SINE|Alu	5575	NM_011319	20226	Mm.28688	NM_011319	ENSMUSG00000068739	Sars	Sars1|Strs|serRS	seryl-aminoacyl-tRNA synthetase	protein-coding
mm_40729.1	chr5	66053139	66053149	+	1	NA	intron (NM_178446, intron 2 of 6)	intron (NM_178446, intron 2 of 6)	45035	NM_139065	245945	Mm.36863	NM_139065	ENSMUSG00000070780	Rbm47	9530077J19Rik	RNA binding motif protein 47	protein-coding
mm_42387.1	chr5	114936035	114936047	+	1	NA	exon (NM_145209, exon 6 of 7)	exon (NM_145209, exon 6 of 7)	-6161	NM_028211	72357	Mm.292672	NM_028211	ENSMUSG00000029559	2210016L21Rik	-	RIKEN cDNA 2210016L21 gene	protein-coding
mm_36176.1	chr4	62205120	62205135	-	1	NA	intron (NM_001290351, intron 1 of 3)	MurSatRep1|Unknown|Unknown	3075	NM_001290353	22696	Mm.5011	NM_009554	ENSMUSG00000028389	Zfp37	Tzn|Zfp-37	zinc finger protein 37	protein-coding
mm_84736.1	chr9	75160675	75160710	-	1	NA	intron (NM_010864, intron 15 of 40)	intron (NM_010864, intron 15 of 40)	-71322	NM_001081322	208943	Mm.41339	NM_001081322	ENSMUSG00000033590	Myo5c	9130003O20Rik|BB085560|C330029I24	myosin VC	protein-coding
mm_126968.1	chr15	93341241	93341263	+	1	NA	Intergenic	ERVL-E-int|LTR|ERVL	-4317	NM_024189	67057	Mm.4714	NM_024189	ENSMUSG00000022634	Yaf2	2810021M11Rik	YY1 associated factor 2	protein-coding
mm_127872.1	chr15	8444436	8444448	-	1	NA	promoter-TSS (NM_027707)	promoter-TSS (NM_027707)	21	NM_027707	71175	Mm.240329	NM_027707	ENSMUSG00000022141	Nipbl	Idn3	Nipped-B homolog (Drosophila)	protein-coding
mm_89133.1	chr10	85185137	85185161	+	1	NA	promoter-TSS (NM_007771)	promoter-TSS (NM_007771)	-95	NM_007771	12952	Mm.26237	NM_007771	ENSMUSG00000020038	Cry1	AU020726|AU021000|Phll1	cryptochrome 1 (photolyase-like)	protein-coding
mm_165106.1	chr19	56424644	56424660	-	1	NA	intron (NM_007611, intron 2 of 6)	intron (NM_007611, intron 2 of 6)	27523	NM_007611	12369	Mm.35687	NM_007611	ENSMUSG00000025076	Casp7	AI314680|CMH-1|ICE-IAP3|Mch3|caspase-7|mCASP-7	caspase 7	protein-coding
mm_57677.1	chr6	128495261	128495268	-	1	NA	exon (NM_007376, exon 20 of 36)	exon (NM_007376, exon 20 of 36)	31456	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_169143.1	chr13	62129874	62129889	+	1	NA	promoter-TSS (NM_001039239)	promoter-TSS (NM_001039239)	-9	NM_001039239	630579	Mm.440905	NM_001039239	ENSMUSG00000074867	Zfp808	EG630579|Gm7036	zinc finger protein 80	protein-coding
mm_18968.1	chr2	76810699	76810703	-	1	NA	exon (NM_011652, exon 183 of 313)	exon (NM_011652, exon 183 of 313)	135386	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_54633.1	chr6	38703533	38703544	-	1	NA	exon (NM_010433, exon 13 of 15)	exon (NM_010433, exon 13 of 15)	40469	NM_001101507	665180	Mm.349066	NM_001101507	ENSMUSG00000079598	Clec2l	AI414054|AW122724|Gm1064	C-type lectin domain family 2, member L	protein-coding
mm_88315.1	chr10	75518043	75518046	+	1	NA	promoter-TSS (NM_026095)	promoter-TSS (NM_026095)	2	NM_026095	67332	Mm.45151	NM_026095	ENSMUSG00000020180	Snrpd3	1700043E15Rik|2310009E13Rik|AW046420|SMD3	small nuclear ribonucleoprotein D3	protein-coding
mm_6115.1	chr1	64121278	64121312	-	1	NA	promoter-TSS (NM_033563)	promoter-TSS (NM_033563)	94	NM_033563	93691	Mm.29466	NM_033563	ENSMUSG00000025959	Klf7	9830124P08Rik	Kruppel-like factor 7 (ubiquitous)	protein-coding
mm_155067.1	chrX	42504770	42504787	+	1	NA	promoter-TSS (NM_001313691)	promoter-TSS (NM_001313691)	-544	NM_001313691	20400	Mm.441197	NM_011364	ENSMUSG00000005696	Sh2d1a	Gm686|SAP	SH2 domain containing 1A	protein-coding
mm_131129.1	chr16	5885454	5885509	+	1	NA	5' UTR (NM_021477, exon 1 of 17)	5' UTR (NM_021477, exon 1 of 17)	688	NM_021477	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_163834.1	chr14	19417747	19417789	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	184819	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_65409.1	chr7	25237867	25237877	-	1	NA	promoter-TSS (NM_001031667)	promoter-TSS (NM_001031667)	-21	NM_001031667	606496	Mm.491101	NM_001031667	ENSMUSG00000057177	Gsk3a	2700086H06Rik	glycogen synthase kinase 3 alpha	protein-coding
mm_139676.1	chr17	57414267	57414281	+	1	NA	intron (NM_010130, intron 10 of 21)	Lx8|LINE|L1	55588	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_72614.1	chr8	84601464	84601477	+	1	NA	exon (NM_001252060, exon 32 of 48)	exon (NM_001252060, exon 32 of 48)	61382	NM_010499	15936	Mm.399	NM_010499	ENSMUSG00000053560	Ier2	AI317238|Ch1|Pip92	immediate early response 2	protein-coding
mm_105724.1	chr11	109011861	109011871	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	91517	NM_015732	12006	Mm.71710	NM_015732	ENSMUSG00000000142	Axin2	Axi1|Axil|Conductin	axin 2	protein-coding
mm_9753.1	chr1	180812329	180812332	-	1	NA	intron (NM_008210, intron 1 of 3)	intron (NM_008210, intron 1 of 3)	1275	NM_008210	15078	Mm.138832	NM_008210	ENSMUSG00000060743	H3f3a	H3.3A	H3 histone, family 3A	protein-coding
mm_13809.1	chr2	119112810	119112882	+	1	NA	promoter-TSS (NM_011234)	promoter-TSS (NM_011234)	29	NM_011234	19361	Mm.330492	NM_011234	ENSMUSG00000027323	Rad51	AV304093|Rad51a|Reca	RAD51 recombinase	protein-coding
mm_36758.1	chr4	101355297	101355302	-	1	NA	intron (NR_040640, intron 1 of 3)	intron (NR_040640, intron 1 of 3)	949	NR_040708	77866	Mm.137053	NR_040708	ENSMUSG00000086782	E130102H24Rik	-	RIKEN cDNA E130102H24 gene	ncRNA
mm_119864.1	chr14	54476184	54476190	+	1	NA	promoter-TSS (NM_080726)	promoter-TSS (NM_080726)	87	NM_080726	140743	Mm.274727	NM_080726	ENSMUSG00000022176	Rem2	AW411893	rad and gem related GTP binding protein 2	protein-coding
mm_149473.1	chr19	11697050	11697057	+	1	NA	promoter-TSS (NM_001033283)	promoter-TSS (NM_001033283)	-2	NM_001033283	225923	Mm.297596	NM_001033283	ENSMUSG00000055933	Oosp3	Gm97	oocyte secreted protein 3	protein-coding
mm_127561.1	chr15	102203481	102203538	+	1	NA	promoter-TSS (NM_001289691)	promoter-TSS (NM_001289691)	-136	NM_001289694	68744	Mm.352945	NM_153194	ENSMUSG00000046897	Zfp740	1110034O07Rik|AW548228|Znf740	zinc finger protein 740	protein-coding
mm_45653.1	chr5	77095175	77095185	-	1	NA	promoter-TSS (NM_001159901)	promoter-TSS (NM_001159901)	87	NM_001159901	74318	Mm.181852	NM_175606	ENSMUSG00000059325	Hopx	1110018K11Rik|1200015P04Rik|2300002F06Rik|AI848177|AW490897|Cameo|Hdop|Hod|Hop|Ob1|Obl|Toto	HOP homeobox	protein-coding
mm_54296.1	chr6	29380469	29380485	-	1	NA	promoter-TSS (NM_007538)	promoter-TSS (NM_007538)	36	NM_007538	12057	Mm.56987	NM_007538	ENSMUSG00000058831	Opn1sw	AW551857|Bcp	opsin 1 (cone pigments), short-wave-sensitive (color blindness, tritan)	protein-coding
mm_42746.1	chr5	120753892	120753921	+	1	NA	3' UTR (NM_145226, exon 16 of 16)	3' UTR (NM_145226, exon 16 of 16)	-4058	NM_001347448	246728	Mm.260926	NM_145227	ENSMUSG00000032690	Oas2	Oasl11	2'-5' oligoadenylate synthetase 2	protein-coding
mm_73483.1	chr8	107031139	107031149	+	1	NA	promoter-TSS (NM_126165)	promoter-TSS (NM_126165)	-182	NM_126165	116733	Mm.236004	NM_126165	ENSMUSG00000031913	Vps4a	4930589C15Rik|AI325971|AW553189	vacuolar protein sorting 4A	protein-coding
mm_166424.1	chr5	137152063	137152075	-	1	NA	Intergenic	Intergenic	-35862	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_119203.1	chr14	32833969	32834003	+	1	NA	promoter-TSS (NM_001164485)	promoter-TSS (NM_001164485)	24	NM_001164485	105511	Mm.32231	NM_001164485	ENSMUSG00000078127	Fam170b	4922501K12Rik|AI449756	family with sequence similarity 170, member B	protein-coding
mm_101236.1	chr11	20631835	20631841	-	1	NA	promoter-TSS (NM_001038625)	promoter-TSS (NM_001038625)	-139	NM_001038625	58172	Mm.339676	NM_021372	ENSMUSG00000049800	Sertad2	AB041541|AU021878|Kiaa0127|MNCb-1504|SEI-2|Sei2|TRIP-Br2|mKIAA0127	SERTA domain containing 2	protein-coding
mm_9160.1	chr1	170960857	170960867	-	1	NA	3' UTR (NM_001077189, exon 8 of 8)	3' UTR (NM_001077189, exon 8 of 8)	15209	NM_001077189	14130	Mm.425062	NM_010187	ENSMUSG00000026656	Fcgr2b	AI528646|CD32|F630109E10Rik|Fc[g]RII|FcgRII|Fcgr2|Fcgr2a|Fcr-2|Fcr-3|Ly-17|Ly-m20|LyM-1|Lym-1|fcRII	Fc receptor, IgG, low affinity IIb	protein-coding
mm_63962.1	chr7	139943879	139943915	+	1	NA	promoter-TSS (NM_009482)	promoter-TSS (NM_009482)	41	NM_009482	22286	Mm.10205	NM_009482	ENSMUSG00000047751	Utf1	AI505934	undifferentiated embryonic cell transcription factor 1	protein-coding
mm_151787.1	chr19	5388657	5388691	-	1	NA	promoter-TSS (NM_016882)	promoter-TSS (NM_016882)	29	NM_016882	20227	Mm.34562	NM_016882	ENSMUSG00000039148	Sart1	U5-110K	squamous cell carcinoma antigen recognized by T cells 1	protein-coding
mm_32220.1	chr4	101717455	101717462	+	1	NA	promoter-TSS (NM_001122899)	promoter-TSS (NM_001122899)	51	NM_010704	16847	Mm.259282	NM_010704	ENSMUSG00000057722	Lepr	LEPROT|Leprb|Modb1|OB-RGRP|Obr|db|diabetes|obese-like|obl	leptin receptor	protein-coding
mm_6121.1	chr1	64122257	64122321	-	1	NA	promoter-TSS (NM_033563)	promoter-TSS (NM_033563)	-900	NM_033563	93691	Mm.29466	NM_033563	ENSMUSG00000025959	Klf7	9830124P08Rik	Kruppel-like factor 7 (ubiquitous)	protein-coding
mm_114825.1	chr13	91861431	91861443	+	1	NA	intron (NM_198415, intron 4 of 9)	intron (NM_198415, intron 4 of 9)	15448	NM_198415	76722	Mm.316438	NM_198415	ENSMUSG00000021622	Ckmt2	2300008A19Rik|ScCKmit	creatine kinase, mitochondrial 2	protein-coding
mm_18182.1	chr2	45111140	45111155	-	1	NA	promoter-TSS (NM_001289521)	promoter-TSS (NM_001289521)	9	NR_110572	433424	Mm.441408	NR_110571	ENSMUSG00000052248	Zeb2os	Gm13476|OTTMUSG00000012358|Zeb2nat	zinc finger E-box binding homeobox 2, opposite strand	ncRNA
mm_96784.1	chr11	69941325	69941329	+	1	NA	TTS (NM_009204)	TTS (NM_009204)	4999	NM_001347634	53422	Mm.29286	NM_016875	ENSMUSG00000018554	Ybx2	Msy2	Y box protein 2	protein-coding
mm_49583.1	chr6	30642886	30642888	+	1	NA	exon (NM_025350, exon 8 of 10)	exon (NM_025350, exon 8 of 10)	3669	NM_025350	109697	Mm.25377	NM_025350	ENSMUSG00000054446	Cpa1	0910001L12Rik|Cpa	carboxypeptidase A1, pancreatic	protein-coding
mm_77492.1	chr8	122575449	122575478	-	1	NA	exon (NM_009698, exon 3 of 5)	exon (NM_009698, exon 3 of 5)	1444	NM_009698	11821	Mm.1786	NM_009698	ENSMUSG00000006589	Aprt	C85684	adenine phosphoribosyl transferase	protein-coding
mm_115067.1	chr13	101442445	101442448	+	1	NA	Intergenic	Intergenic	-44866	NR_046187	78136	Mm.399065	NR_046187		4922502H24Rik	-	RIKEN cDNA 4922502H24 gene	ncRNA
mm_64250.1	chr7	141704413	141704462	+	1	NA	intron (NM_023566, intron 27 of 45)	intron (NM_023566, intron 27 of 45)	14097	NM_023566	17831	Mm.2041	NM_023566		Muc2	2010015E03Rik|MCM|wnn	mucin 2	protein-coding
mm_51570.1	chr6	83742985	83742995	+	1	NA	promoter-TSS (NM_134157)	promoter-TSS (NM_134157)	-27	NM_134157	110935	Mm.220823	NM_134157	ENSMUSG00000006269	Atp6v1b1	AW208839|Atp6b1|D630003L15|D630030L16Rik|D630039P21Rik|Vpp-3|Vpp3	ATPase, H+ transporting, lysosomal V1 subunit B1	protein-coding
mm_58941.1	chr7	18245236	18245236	+	1	NA	promoter-TSS (NM_153749)	promoter-TSS (NM_153749)	-111	NM_153749	266815	Mm.106769	NM_153749	ENSMUSG00000054005	Mill1	5530400I18Rik	MHC I like leukocyte 1	protein-coding
mm_170665.1	chr2	114895115	114895115	-	1	NA	Intergenic	L1Md_A|LINE|L1	-240187	NM_025675	66632	Mm.117809	NM_025675	ENSMUSG00000057147	Dph6	5730421E18Rik|Atpbd4	diphthamine biosynthesis 6	protein-coding
mm_353.1	chr1	33578987	33579003	+	1	NA	intron (NM_008922, intron 7 of 13)	intron (NM_008922, intron 7 of 13)	90799	NM_008922	19076	Mm.27705	NM_008922	ENSMUSG00000026134	Prim2	AI323589	DNA primase, p58 subunit	protein-coding
mm_127184.1	chr15	98992801	98992814	+	1	NA	Intergenic	Intergenic	6842	NR_045991	75951	Mm.441657	NR_045991	ENSMUSG00000097587	4930578M01Rik	3010001K12Rik	RIKEN cDNA 4930578M01 gene	ncRNA
mm_22474.1	chr3	5218591	5218614	+	1	NA	promoter-TSS (NM_030708)	promoter-TSS (NM_030708)	48	NM_030708	80892	Mm.41522	NM_030708	ENSMUSG00000025255	Zfhx4	A930021B15|C130041O22Rik|Zfh-4|Zfh4	zinc finger homeodomain 4	protein-coding
mm_7063.1	chr1	87573826	87573871	-	1	NA	promoter-TSS (NM_001160164)	promoter-TSS (NM_001160164)	22	NM_001111314	53972	Mm.435439	NM_019867	ENSMUSG00000026259	Ngef	Tims2|ephexin	neuronal guanine nucleotide exchange factor	protein-coding
mm_140500.1	chr17	4122089	4122137	-	1	NA	promoter-TSS (NR_045462)	promoter-TSS (NR_045462)	-11	NR_045462	78043	Mm.398313	NR_045462		4930548J01Rik	1700113K09Rik	RIKEN cDNA 4930548J01 gene	ncRNA
mm_12081.1	chr2	59811945	59811973	+	1	NA	intron (NM_198294, intron 16 of 26)	intron (NM_198294, intron 16 of 26)	70647	NM_001159636	72137	Mm.288734	NM_028118	ENSMUSG00000026988	Wdsub1	1700048E19Rik|2610014F08Rik	WD repeat, SAM and U-box domain containing 1	protein-coding
mm_128204.1	chr15	35938187	35938203	-	1	NA	promoter-TSS (NM_053071)	promoter-TSS (NM_053071)	51	NM_053071	12864	Mm.548	NM_053071	ENSMUSG00000014313	Cox6c	-	cytochrome c oxidase subunit VIc	protein-coding
mm_9907.1	chr1	187215431	187215451	-	1	NA	promoter-TSS (NM_029067)	promoter-TSS (NM_029067)	5	NM_029067	74717	Mm.250430	NM_028848	ENSMUSG00000026611	Spata17	1700065F16Rik|4930504I07Rik|4930513F16Rik|MSRG-11	spermatogenesis associated 17	protein-coding
mm_4055.1	chr1	165825761	165825777	+	1	NA	intron (NM_001113391, intron 1 of 7)	intron (NM_001113391, intron 1 of 7)	37088	NM_001113392	12503	Mm.217308	NM_031162	ENSMUSG00000005763	Cd247	4930549J05Rik|A430104F18Rik|AW552088|Cd3|Cd3-eta|Cd3-zeta|Cd3h|Cd3z|Cd3zeta|T3z|Tcrk|Tcrz	CD247 antigen	protein-coding
mm_85788.1	chr9	109082373	109082414	-	1	NA	promoter-TSS (NM_183250)	promoter-TSS (NM_183250)	-12	NM_183250	66167	Mm.2395	NM_183250	ENSMUSG00000091537	Tma7	1110017O22Rik|Ccdc72	translational machinery associated 7	protein-coding
mm_51430.1	chr6	78466398	78466416	+	1	NA	3' UTR (NM_011260, exon 6 of 6)	3' UTR (NM_011260, exon 6 of 6)	2467	NM_011260	19695	Mm.252385	NM_011260	ENSMUSG00000030017	Reg3g	AI449515|REG-3-gamma|reg III-gamma	regenerating islet-derived 3 gamma	protein-coding
mm_55869.1	chr6	83506257	83506260	-	1	NA	intron (NM_013764, intron 1 of 6)	B1_Mur4|SINE|Alu	711	NM_013764	27369	Mm.42234	NM_013764	ENSMUSG00000014554	Dguok	dGK|dGK1|dGK2|dGK3	deoxyguanosine kinase	protein-coding
mm_56302.1	chr6	91758602	91758634	-	1	NA	3' UTR (NM_009320, exon 15 of 15)	3' UTR (NM_009320, exon 15 of 15)	48775	NM_001159507	243547	Mm.333264	NM_001033353	ENSMUSG00000030098	Grip2	-	glutamate receptor interacting protein 2	protein-coding
mm_140564.1	chr17	8299670	8299680	-	1	NA	intron (NR_073374, intron 1 of 4)	intron (NR_073374, intron 1 of 4)	-11428	NM_134114	106489	Mm.311080	NM_134114	ENSMUSG00000073468	Sft2d1	5630401J11Rik|AA409698	SFT2 domain containing 1	protein-coding
mm_153016.1	chr19	30625516	30625537	-	1	NA	intron (NM_011160, intron 9 of 17)	intron (NM_011160, intron 9 of 17)	-76030	NM_010051	13380	Mm.214717	NM_010051	ENSMUSG00000024868	Dkk1	mdkk-1	dickkopf WNT signaling pathway inhibitor 1	protein-coding
mm_172661.1	chr8	41936833	41936833	+	1	NA	intron (NR_045497, intron 3 of 5)	L1Md_F2|LINE|L1	109566	NR_045497	69966	Mm.416903	NR_045497	ENSMUSG00000102046	2810404M03Rik	-	RIKEN cDNA 2810404M03 gene	ncRNA
mm_171286.1	chr3	90079574	90079576	+	1	NA	promoter-TSS (NM_001253740)	promoter-TSS (NM_001253740)	54	NM_001293749	59069	Mm.240839	NM_022314	ENSMUSG00000027940	Tpm3	TM30nm|TMnm|Tm5NM|Tpm-5|Tpm5|Trop-5|gamma-TM|hTM30nm|hTMnm	tropomyosin 3, gamma	protein-coding
mm_11551.1	chr2	32721081	32721108	+	1	NA	promoter-TSS (NM_013781)	promoter-TSS (NM_013781)	39	NM_013781	27387	Mm.9593	NM_013781	ENSMUSG00000059013	Sh2d3c	Chat|Nsp3|Shep1	SH2 domain containing 3C	protein-coding
mm_47999.1	chr5	136160949	136160963	-	1	NA	intron (NM_178751, intron 2 of 2)	B4A|SINE|B4	9700	NM_178751	269717	Mm.308396	NM_178751	ENSMUSG00000039747	Orai2	A730041O15Rik|Tmem142b	ORAI calcium release-activated calcium modulator 2	protein-coding
mm_3107.1	chr1	134494987	134495016	+	1	NA	intron (NM_145510, intron 1 of 1)	intron (NM_145510, intron 1 of 1)	341	NM_145510	98710	Mm.198119	NM_145510	ENSMUSG00000042229	Rabif	AI842864|AW549708|E130318E12Rik|MSS4|RASGFR3	RAB interacting factor	protein-coding
mm_81326.1	chr9	108497917	108497934	+	1	NA	exon (NM_001168373, exon 18 of 27)	exon (NM_001168373, exon 18 of 27)	7249	NM_027804	71472	Mm.289706	NM_027804	ENSMUSG00000006676	Usp19	8430421I07Rik|AI047774|Zmynd9	ubiquitin specific peptidase 19	protein-coding
mm_69816.1	chr7	141263998	141264010	-	1	NA	exon (NM_001252601, exon 8 of 10)	exon (NM_001252601, exon 8 of 10)	2420	NM_001252601	54123	Mm.3233	NM_016850	ENSMUSG00000025498	Irf7	-	interferon regulatory factor 7	protein-coding
mm_112943.1	chr13	20993371	20993374	+	1	NA	intron (NM_012054, intron 13 of 20)	intron (NM_012054, intron 13 of 20)	79927	NM_146535	258528	Mm.377554	NM_146535	ENSMUSG00000042869	Olfr1370	MOR256-14	olfactory receptor 1370	protein-coding
mm_34262.1	chr4	141421695	141421710	+	1	NA	5' UTR (NM_013868, exon 1 of 3)	5' UTR (NM_013868, exon 1 of 3)	923	NM_013868	29818	Mm.46181	NM_013868	ENSMUSG00000006221	Hspb7	27kDa|Hsp25-2|cvHsp	heat shock protein family, member 7 (cardiovascular)	protein-coding
mm_127713.1	chr15	103014130	103014145	+	1	NA	promoter-TSS (NR_030526)	promoter-TSS (NR_030526)	129	NM_175730	15424	Mm.103825	NM_175730	ENSMUSG00000022485	Hoxc5	AI181837|Hox-3.4|Hox-6.2	homeobox C5	protein-coding
mm_115392.1	chr13	113615779	113615789	+	1	NA	intron (NM_130796, intron 1 of 1)	intron (NM_130796, intron 1 of 1)	2780	NM_130796	170625	Mm.33721	NM_130796	ENSMUSG00000042364	Snx18	Snag1	sorting nexin 18	protein-coding
mm_82045.1	chr9	122351724	122351738	+	1	NA	5' UTR (NM_026179, exon 1 of 7)	5' UTR (NM_026179, exon 1 of 7)	115	NM_026179	67469	Mm.280254	NM_026179	ENSMUSG00000032540	Abhd5	1300003D03Rik|2010002J10Rik|CDS|CGI-58|IECN5|NCIE2	abhydrolase domain containing 5	protein-coding
mm_155584.1	chrX	78737775	78737783	+	1	NA	promoter-TSS (NM_001164739)	promoter-TSS (NM_001164739)	16	NM_001164739	70864	Mm.66681	NM_001164739	ENSMUSG00000078315	Fam47c	4921509A18Rik|Fam47a|Fam47a-ps	family with sequence similarity 47, member C	protein-coding
mm_70033.1	chr7	142576744	142576756	-	1	NA	TTS (NR_030416)	TTS (NR_030416)	397	NR_030416	735280		NR_030416	ENSMUSG00000076275	Mir675	Mirn675|mir-675|mmu-mir-675	microRNA 675	ncRNA
mm_12004.1	chr2	57265138	57265158	+	1	NA	intron (NM_010274, intron 1 of 16)	intron (NM_010274, intron 1 of 16)	26766	NM_010274	14571	Mm.3711	NM_010274	ENSMUSG00000026827	Gpd2	AA408484|AI448216|AU021455|AW494132|GPDH|Gdm1|Gpd-m|Gpdh-m|TISP38	glycerol phosphate dehydrogenase 2, mitochondrial	protein-coding
mm_22533.1	chr3	8541853	8541875	+	1	NA	exon (NM_025285, exon 2 of 5)	exon (NM_025285, exon 2 of 5)	32337	NM_025285	20257	Mm.29580	NM_025285	ENSMUSG00000027500	Stmn2	AI159727|SCG10|Scgn10|Stmb2	stathmin-like 2	protein-coding
mm_169506.1	chr14	7963420	7963427	+	1	NA	Intergenic	B4A|SINE|B4	30759	NM_007870	13421	Mm.272258	NM_007870	ENSMUSG00000025279	Dnase1l3	DNasegamma|Dhp2|Lsd	deoxyribonuclease 1-like 3	protein-coding
mm_13423.1	chr2	104586076	104586078	+	1	NA	Intergenic	Intergenic	-4407	NM_177253	228410	Mm.259876	NM_145529	ENSMUSG00000027176	Cstf3	4732468G05Rik|C79532|CstF-77	cleavage stimulation factor, 3' pre-RNA, subunit 3	protein-coding
mm_78988.1	chr9	45399703	45399718	+	1	NA	promoter-TSS (NR_028499)	promoter-TSS (NR_028499)	1	NR_028499	11936	Mm.22742	NM_007503	ENSMUSG00000059412	Fxyd2	Atp1g1	FXYD domain-containing ion transport regulator 2	protein-coding
mm_69557.1	chr7	135700043	135700053	-	1	NA	exon (NM_001081117, exon 12 of 14)	exon (NM_001081117, exon 12 of 14)	16331	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_132785.1	chr16	44943716	44943734	+	1	NA	promoter-TSS (NM_029018)	promoter-TSS (NM_029018)	47	NM_001128132	74603	Mm.297337	NM_027578	ENSMUSG00000036172	Cd200r3	4733401I18Rik|4833409J19Rik|AI505817|BB106877|mCD200RLb	CD200 receptor 3	protein-coding
mm_170392.1	chr1	86356957	86356968	-	1	NA	promoter-TSS (NR_002851)	promoter-TSS (NR_002851)	-635	NR_002851	80828		NR_002851	ENSMUSG00000064823	Snord82	Rnu82|U82|Z25	small nucleolar RNA, C/D box 82	snoRNA
mm_41048.1	chr5	86104100	86104110	+	1	NA	TTS (NM_019992)	TTS (NM_019992)	32359	NM_001310639	56792	Mm.131237	NM_019992	ENSMUSG00000029254	Stap1	AI586015|Brdg1|STAP-1	signal transducing adaptor family member 1	protein-coding
mm_115134.1	chr13	104430897	104430900	+	1	NA	intron (NR_136938, intron 18 of 26)	intron (NR_136938, intron 18 of 26)	143063	NM_001081020	108154	Mm.208125	NM_175496	ENSMUSG00000046169	Adamts6	A930019D11Rik|ADAM-TS6|b2b1879.1Clo|b2b2029Clo|b2b2182Clo|b2b2187.1Clo|b2b2228Clo	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 6	protein-coding
mm_148630.1	chr19	5455050	5455068	+	1	NA	exon (NM_010235, exon 4 of 4)	exon (NM_010235, exon 4 of 4)	2504	NM_198616	240514	Mm.329657	NM_198616	ENSMUSG00000095098	Ccdc85b	AI842788|BB115872	coiled-coil domain containing 85B	protein-coding
mm_91014.1	chr10	15520805	15520822	-	1	NA	Intergenic	Intergenic	-270964	NR_131087	77538	Mm.128235	NR_131087		C330004P14Rik	-	RIKEN cDNA C330004P14 gene	ncRNA
mm_128916.1	chr15	73677339	73677355	-	1	NA	Intergenic	PB1D7|SINE|Alu	30158	NM_173365	239530	Mm.122997	NM_173365	ENSMUSG00000045281	Gpr20	A430106B11Rik	G protein-coupled receptor 20	protein-coding
mm_25130.1	chr3	102262393	102262446	+	1	NA	promoter-TSS (NR_040391)	promoter-TSS (NR_040391)	14	NR_040391	319951	Mm.225196	NR_040391	ENSMUSG00000105891	A230001M10Rik	-	RIKEN cDNA A230001M10 gene	ncRNA
mm_115687.1	chr13	13590125	13590132	-	1	NA	promoter-TSS (NM_010748)	promoter-TSS (NM_010748)	-281	NM_010748	17101	Mm.342337	NM_010748	ENSMUSG00000019726	Lyst	D13Sfk13|beige|bg	lysosomal trafficking regulator	protein-coding
mm_74049.1	chr8	122230183	122230217	+	1	NA	Intergenic	CpG	-51941	NM_009569	22761	Mm.3105	NM_009569	ENSMUSG00000049577	Zfpm1	FOG|Fog1	zinc finger protein, multitype 1	protein-coding
mm_11750.1	chr2	38432532	38432534	+	1	NA	Intergenic	Intergenic	-79164	NM_021606	59126	Mm.143818	NM_021606	ENSMUSG00000026749	Nek6	1300007C09Rik	NIMA (never in mitosis gene a)-related expressed kinase 6	protein-coding
mm_35384.1	chr4	33248016	33248027	-	1	NA	exon (NM_001033225, exon 1 of 2)	exon (NM_001033225, exon 1 of 2)	766	NM_001033225	108767	Mm.27769	NM_001033225	ENSMUSG00000040128	Pnrc1	5730463C12Rik|B4-2|PRR2|Prol2	proline-rich nuclear receptor coactivator 1	protein-coding
mm_128576.1	chr15	57892313	57892323	-	1	NA	promoter-TSS (NM_024207)	promoter-TSS (NM_024207)	100	NM_024207	67819	Mm.289387	NM_024207	ENSMUSG00000022365	Derl1	1110021N07Rik|AI195141|AW551338|Derlin-1	Der1-like domain family, member 1	protein-coding
mm_29444.1	chr3	110143699	110143715	-	1	NA	promoter-TSS (NM_001163350)	promoter-TSS (NM_001163350)	-235	NM_030699	80883	Mm.39262	NM_030699	ENSMUSG00000059857	Ntng1	A930010C08Rik|AI853992|Lmnt1	netrin G1	protein-coding
mm_121199.1	chr14	103051837	103051846	+	1	NA	intron (NM_008392, intron 4 of 4)	intron (NM_008392, intron 4 of 4)	4829	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_114937.1	chr13	96011516	96011523	+	1	NA	intron (NM_029210, intron 4 of 12)	intron (NM_029210, intron 4 of 12)	-119597	NM_027711	544963	Mm.38878	NM_027711	ENSMUSG00000021676	Iqgap2	4933417J23Rik|A630053O10|AI788777	IQ motif containing GTPase activating protein 2	protein-coding
mm_120819.1	chr14	75136304	75136325	+	1	NA	promoter-TSS (NM_008879)	promoter-TSS (NM_008879)	-111	NM_008879	18826	Mm.153911	NM_008879	ENSMUSG00000021998	Lcp1	AW536232|D14Ertd310e|LCP-1|Pls2|pp65	lymphocyte cytosolic protein 1	protein-coding
mm_94555.1	chr11	11557389	11557398	+	1	NA	Intergenic	Intergenic	68127	NM_028669	73862	Mm.159077	NM_028669	ENSMUSG00000020191	4930415F15Rik	-	RIKEN cDNA 4930415F15 gene	protein-coding
mm_93530.1	chr10	115361871	115361876	-	1	NA	exon (NM_133683, exon 2 of 7)	exon (NM_133683, exon 2 of 7)	389	NM_133683	67226	Mm.29647	NM_133683	ENSMUSG00000069520	Tmem19	2810428F02Rik|AW125171	transmembrane protein 19	protein-coding
mm_101977.1	chr11	50376959	50376967	-	1	NA	promoter-TSS (NM_021510)	promoter-TSS (NM_021510)	-756	NM_021510	59013	Mm.21740	NM_021510	ENSMUSG00000007850	Hnrnph1	AI642080|E430005G16Rik|Hnrnph|Hnrph1	heterogeneous nuclear ribonucleoprotein H1	protein-coding
mm_91095.1	chr10	19062167	19062183	-	1	NA	Intergenic	Intergenic	-46765	NM_009397	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_26390.1	chr3	142570972	142570990	+	1	NA	exon (NM_018734, exon 10 of 11)	exon (NM_018734, exon 10 of 11)	10485	NM_001289493	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_63782.1	chr7	131619406	131619420	+	1	NA	Intergenic	Intergenic	58919	NM_001317350	12237	Mm.927	NM_009774	ENSMUSG00000066979	Bub3	AU019800|AU021329|AU043350|AW146323|C78067	BUB3 mitotic checkpoint protein	protein-coding
mm_147340.1	chr18	43059419	43059466	-	1	NA	promoter-TSS (NM_028392)	promoter-TSS (NM_028392)	29	NM_028392	72930	Mm.26134	NM_027531	ENSMUSG00000024500	Ppp2r2b	2900026H06Rik|6330404L05Rik|E130009M08Rik|PP2A-PR55B|PR55-BETA|SCA12	protein phosphatase 2, regulatory subunit B, beta	protein-coding
mm_88258.1	chr10	73821858	73821871	+	1	NA	promoter-TSS (NM_001142743)	promoter-TSS (NM_001142743)	-3	NM_001142760	11994	Mm.338933	NM_023115	ENSMUSG00000052613	Pcdh15	BB078305|ENSMUSG00000046980|Gm9815|Ush1f|av|nmf19|roda	protocadherin 15	protein-coding
mm_94959.1	chr11	30771796	30771812	+	1	NA	promoter-TSS (NM_134013)	promoter-TSS (NM_134013)	29	NM_134013	103554	Mm.240066	NM_134013	ENSMUSG00000040850	Psme4	AA409398|AU041366|TEMO|mKIAA0077	proteasome (prosome, macropain) activator subunit 4	protein-coding
mm_85993.1	chr9	112200248	112200249	-	1	NA	intron (NM_001177619, intron 1 of 10)	intron (NM_001177619, intron 1 of 10)	-12319	NM_028755	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_69280.1	chr7	127993832	127993845	-	1	NA	promoter-TSS (NM_023258)	promoter-TSS (NM_023258)	29	NM_023258	66824	Mm.24163	NM_023258	ENSMUSG00000030793	Pycard	9130417A21Rik|Asc|CARD5|TMS-1|TNS1|masc	PYD and CARD domain containing	protein-coding
mm_129637.1	chr15	80254964	80255000	-	1	NA	promoter-TSS (NM_009716)	promoter-TSS (NM_009716)	-202	NM_001287180	11911	Mm.641	NM_009716	ENSMUSG00000042406	Atf4	Atf-4|C/ATF|CREB2|TAXREB67	activating transcription factor 4	protein-coding
mm_28859.1	chr3	97208905	97208915	-	1	NA	exon (NM_029933, exon 8 of 10)	exon (NM_029933, exon 8 of 10)	18454	NM_029933	77578	Mm.226175	NM_029933	ENSMUSG00000038256	Bcl9	2610202E01Rik|8030475K17Rik|A330041G23Rik|Gm130	B cell CLL/lymphoma 9	protein-coding
mm_59919.1	chr7	30419916	30419949	+	1	NA	promoter-TSS (NM_011827)	promoter-TSS (NM_011827)	-78	NM_011827	23900	Mm.379050	NM_011827	ENSMUSG00000064109	Hcst	DAP10|KAP10	hematopoietic cell signal transducer	protein-coding
mm_19581.1	chr2	101650677	101650680	-	1	NA	Intergenic	Intergenic	-1146	NM_009019	19373	Mm.828	NM_009019	ENSMUSG00000061311	Rag1	Rag-1	recombination activating gene 1	protein-coding
mm_18144.1	chr2	45064518	45064561	-	1	NA	intron (NM_001289521, intron 1 of 8)	(CCA)n|Simple_repeat|Simple_repeat	-41362	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_123660.1	chr14	69244227	69244263	-	1	NA	3' UTR (NM_026331, exon 4 of 4)	3' UTR (NM_026331, exon 4 of 4)	40858	NM_026331	67712	Mm.293635	NM_026331	ENSMUSG00000034248	Slc25a37	1700020E22Rik|4930513O14Rik|4930526G11Rik|AI848481|C330015G08Rik|Mfrn|Mfrn1|Mscp|frascati|mitoferrin	solute carrier family 25, member 37	protein-coding
mm_163580.1	chr13	33985339	33985357	+	1	NA	exon (NM_001163242, exon 7 of 7)	exon (NM_001163242, exon 7 of 7)	17446	NM_001243192	20719	Mm.252210	NM_009254	ENSMUSG00000060147	Serpinb6a	4930482L21Rik|D330015H01Rik|PI-6|Serpinb6|Spi3|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 6a	protein-coding
mm_6109.1	chr1	64042330	64042350	-	1	NA	TTS (NR_105864)	TTS (NR_105864)	161	NR_105864	102466760		NR_105864	ENSMUSG00000098487	Mir6899	Gm27384|mmu-mir-6899	microRNA 6899	ncRNA
mm_59012.1	chr7	19228926	19228944	+	1	NA	intron (NM_207525, intron 1 of 1)	intron (NM_207525, intron 1 of 1)	546	NM_207525	403187	Mm.239583	NM_207525	ENSMUSG00000052214	Opa3	D630048P19Rik|Gm1425|Gm472	optic atrophy 3	protein-coding
mm_160405.1	chr8	71566600	71566600	-	1	NA	promoter-TSS (NM_145598)	promoter-TSS (NM_145598)	49	NM_145598	234404	Mm.213208	NM_145598	ENSMUSG00000034829	Nxnl1	A930031O08Rik|RdCVF|Txnl6	nucleoredoxin-like 1	protein-coding
mm_145933.1	chr18	67243490	67243513	+	1	NA	intron (NM_172630, intron 2 of 10)	intron (NM_172630, intron 2 of 10)	2329	NM_172630	225651	Mm.235792	NM_172630	ENSMUSG00000062526	Mppe1	A530095G11	metallophosphoesterase 1	protein-coding
mm_76704.1	chr8	94532919	94532932	-	1	NA	promoter-TSS (NM_153507)	promoter-TSS (NM_153507)	-103	NM_153507	234577	Mm.291815	NM_153507	ENSMUSG00000034361	Cpne2	3322401K10Rik	copine II	protein-coding
mm_111643.1	chr12	102657893	102657906	-	1	NA	intron (NM_172584, intron 2 of 9)	intron (NM_172584, intron 2 of 9)	27121	NR_035457	100316812		NR_035457	ENSMUSG00000089324	Mir1936	mir-1936|mmu-mir-1936	microRNA 1936	ncRNA
mm_97644.1	chr11	79339583	79339635	+	1	NA	promoter-TSS (NM_010897)	promoter-TSS (NM_010897)	-283	NM_010897	18015	Mm.255596	NM_010897	ENSMUSG00000020716	Nf1	AW494271|Dsk9|E030030H24Rik|Mhdadsk9|Nf-1	neurofibromin 1	protein-coding
mm_67673.1	chr7	88302215	88302233	-	1	NA	exon (NM_009982, exon 5 of 7)	exon (NM_009982, exon 5 of 7)	24139	NM_001311790	13032	Mm.89295	NM_009982	ENSMUSG00000030560	Ctsc	AI047818|CatC|DPP1|DPPI	cathepsin C	protein-coding
mm_16.1	chr1	4858285	4858308	+	1	NA	promoter-TSS (NM_001159751)	promoter-TSS (NM_001159751)	-32	NM_001159751	21399	Mm.207263	NM_011541	ENSMUSG00000033813	Tcea1	S-II	transcription elongation factor A (SII) 1	protein-coding
mm_96443.1	chr11	67454964	67454980	+	1	NA	Intergenic	CpG	-78026	NM_008088	14457	Mm.40338	NM_008088	ENSMUSG00000033066	Gas7	AW124766|B230343A10Rik|Gas7-cb	growth arrest specific 7	protein-coding
mm_128378.1	chr15	42676813	42676827	-	1	NA	5' UTR (NM_001286062, exon 1 of 9)	5' UTR (NM_001286062, exon 1 of 9)	157	NM_001286062	11600	Mm.309336	NM_009640	ENSMUSG00000022309	Angpt1	1110046O21Rik|Ang-1|Ang1	angiopoietin 1	protein-coding
mm_88543.1	chr10	78574991	78575063	+	1	NA	intron (NM_173751, intron 1 of 15)	CpG	527	NM_173751	216136	Mm.2644	NM_173751	ENSMUSG00000032763	Ilvbl	5830463I21|AI415009	ilvB (bacterial acetolactate synthase)-like	protein-coding
mm_13760.1	chr2	118388591	118388606	+	1	NA	promoter-TSS (NM_013719)	promoter-TSS (NM_013719)	-19	NM_013719	27103	Mm.217616	NM_013719	ENSMUSG00000005102	Eif2ak4	2610011M03|GCN2|MGCN2	eukaryotic translation initiation factor 2 alpha kinase 4	protein-coding
mm_108715.1	chr12	87147971	87147997	+	1	NA	promoter-TSS (NM_153415)	promoter-TSS (NM_153415)	-82	NM_153415	217734	Mm.388249	NM_153415	ENSMUSG00000034126	Pomt2	-	protein-O-mannosyltransferase 2	protein-coding
mm_39792.1	chr5	30588079	30588171	+	1	NA	promoter-TSS (NM_010608)	promoter-TSS (NM_010608)	-45	NM_010608	16527	Mm.439936	NM_010608	ENSMUSG00000049265	Kcnk3	TASK|Task-1|cTBAK-1	potassium channel, subfamily K, member 3	protein-coding
mm_52155.1	chr6	98018441	98018461	+	1	NA	3' UTR (NM_001178049, exon 10 of 10)	3' UTR (NM_001178049, exon 10 of 10)	26668	NM_008601	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_137084.1	chr17	21474250	21474273	+	1	NA	Intergenic	(TCTG)n|Simple_repeat|Simple_repeat	-14727	NM_013843	24132	Mm.42140	NM_013843	ENSMUSG00000057409	Zfp53	D030067O06Rik|KRAZ1|Zfp-53|Zfp118|zfas8	zinc finger protein 53	protein-coding
mm_143873.1	chr17	84187117	84187166	-	1	NA	exon (NM_001001806, exon 2 of 2)	exon (NM_001001806, exon 2 of 2)	806	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_12139.1	chr2	61727029	61727050	+	1	NA	intron (NM_021526, intron 3 of 11)	Lx7|LINE|L1	15345	NM_021526	59029	Mm.218198	NM_021526	ENSMUSG00000026914	Psmd14	2610312C03Rik|3200001M20Rik|AA986732|Pad1|Poh1|rpm11	proteasome (prosome, macropain) 26S subunit, non-ATPase, 14	protein-coding
mm_117260.1	chr13	64368757	64368768	-	1	NA	intron (NM_009984, intron 2 of 7)	intron (NM_009984, intron 2 of 7)	1758	NM_009984	13039	Mm.930	NM_009984	ENSMUSG00000021477	Ctsl	1190035F06Rik|CatL|Ctsl1|MEP|fs|nkt	cathepsin L	protein-coding
mm_140191.1	chr17	83350926	83350998	+	1	NA	promoter-TSS (NM_001114361)	promoter-TSS (NM_001114361)	31	NM_001114362	78798	Mm.295565	NM_199466	ENSMUSG00000032624	Eml4	4930443C24Rik|AI644019	echinoderm microtubule associated protein like 4	protein-coding
mm_44181.1	chr5	151252520	151252533	+	1	NA	Intergenic	Intergenic	-62333	NM_146258	243362	Mm.209272	NM_146258	ENSMUSG00000016128	Stard13	DLC2|GT650	StAR-related lipid transfer (START) domain containing 13	protein-coding
mm_133551.1	chr16	91372883	91372893	+	1	NA	5' UTR (NM_010509, exon 1 of 9)	5' UTR (NM_010509, exon 1 of 9)	105	NM_001110498	15976	Mm.6834	NM_010509	ENSMUSG00000022971	Ifnar2	AI747302|Ifnar-2	interferon (alpha and beta) receptor 2	protein-coding
mm_128194.1	chr15	35062368	35062390	-	1	NA	intron (NM_019635, intron 6 of 10)	B1_Mus1|SINE|Alu	93427	NM_019635	56274	Mm.262330	NM_019635	ENSMUSG00000022329	Stk3	0610042I06Rik|MST|Mst2|Mst3|Ste20|mess1	serine/threonine kinase 3	protein-coding
mm_88896.1	chr10	81150702	81150738	+	1	NA	3' UTR (NM_010731, exon 3 of 3)	3' UTR (NM_010731, exon 3 of 3)	14449	NM_010731	16969	Mm.20920	NM_010731	ENSMUSG00000035011	Zbtb7a	9030619K07Rik|9130006G12Rik|AI452336|FBI-1|Lrf|Pokemon|Zbtb7	zinc finger and BTB domain containing 7a	protein-coding
mm_44048.1	chr5	147860686	147860694	+	1	NA	promoter-TSS (NM_025624)	promoter-TSS (NM_025624)	62	NM_025624	66537	Mm.332855	NM_025624	ENSMUSG00000029649	Pomp	2510048O06Rik|Ump1	proteasome maturation protein	protein-coding
mm_4290.1	chr1	171766896	171766913	+	1	NA	promoter-TSS (NM_013730)	promoter-TSS (NM_013730)	-228	NM_013730	27218	Mm.103648	NM_013730	ENSMUSG00000015316	Slamf1	4933415F16|AA177906|CD150|CDw150|ESTM51|IPO-3|Slam	signaling lymphocytic activation molecule family member 1	protein-coding
mm_141397.1	chr17	29238207	29238252	-	1	NA	promoter-TSS (NM_153166)	promoter-TSS (NM_153166)	-439	NM_153166	240058	Mm.39905	NM_153166	ENSMUSG00000024008	Cpne5	A830083G22Rik	copine V	protein-coding
mm_154555.1	chrM	15381	15441	-	1	NA	NA	Intergenic	NA	NA								
mm_167604.1	chr9	52048157	52048202	+	1	NA	5' UTR (NM_009041, exon 1 of 14)	5' UTR (NM_009041, exon 1 of 14)	238	NM_001104617	19684	Mm.245746	NM_009041	ENSMUSG00000032050	Rdx	AA516625	radixin	protein-coding
mm_17336.1	chr2	26593421	26593431	-	1	NA	TTS (NM_001164564)	TTS (NM_001164564)	-2006	NR_106155	102465787		NR_106155	ENSMUSG00000105799	Mir126b	mmu-mir-126b	microRNA 126b	ncRNA
mm_72203.1	chr8	72573644	72573650	+	1	NA	intron (NM_144534, intron 1 of 5)	intron (NM_144534, intron 1 of 5)	1544	NM_144534	74166	Mm.212927	NM_144534	ENSMUSG00000031791	Tmem38a	1110001E17Rik|AI413399|TRIC-A|mg33a	transmembrane protein 38A	protein-coding
mm_135238.1	chr16	36990176	36990185	-	1	NA	Intergenic	Intergenic	-11044	NM_001037321	207215	Mm.211899	NM_001037321	ENSMUSG00000047746	Fbxo40	9830003A13Rik|mKIAA1195	F-box protein 40	protein-coding
mm_164183.1	chr15	76270986	76270988	+	1	NA	intron (NM_028852, intron 1 of 4)	B1F|SINE|Alu	-1148	NR_045747	100038659	Mm.448549	NR_045747		Mirt2	ENSMUSG00000075583|Gm10872|Gm24562	myocardial infraction associated transcript 2	ncRNA
mm_9681.1	chr1	178332305	178332317	-	1	NA	exon (NM_016805, exon 7 of 14)	exon (NM_016805, exon 7 of 14)	5473	NM_016805	51810	Mm.86589	NM_016805	ENSMUSG00000039630	Hnrnpu	AA408410|AI256620|AL024194|AL024437|AW557595|C86794|Hnrpu|SAFA|Sp120|hnRNP U	heterogeneous nuclear ribonucleoprotein U	protein-coding
mm_86306.1	chr9	122351601	122351610	-	1	NA	promoter-TSS (NM_026179)	promoter-TSS (NM_026179)	-11	NM_026179	67469	Mm.280254	NM_026179	ENSMUSG00000032540	Abhd5	1300003D03Rik|2010002J10Rik|CDS|CGI-58|IECN5|NCIE2	abhydrolase domain containing 5	protein-coding
mm_88049.1	chr10	67539939	67539952	+	1	NA	exon (NM_010118, exon 2 of 2)	exon (NM_010118, exon 2 of 2)	2015	NM_001347458	13654	Mm.290421	NM_010118	ENSMUSG00000037868	Egr2	Egr-2|Krox-20|Krox20|NGF1-B|Zfp-25|Zfp-6	early growth response 2	protein-coding
mm_127446.1	chr15	101270635	101270645	+	1	NA	exon (NM_010444, exon 2 of 7)	exon (NM_010444, exon 2 of 7)	3794	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_8609.1	chr1	156035968	156035980	-	1	NA	promoter-TSS (NM_001160182)	promoter-TSS (NM_001160182)	-62	NM_001160182	240832	Mm.253335	NM_022329	ENSMUSG00000050565	Tor1aip2	1110020D10Rik|15kDa|A130072J07|AA103493|AW060462|AW610675|C77739|Ifrg15|Lull1	torsin A interacting protein 2	protein-coding
mm_4345.1	chr1	171856990	171857026	+	1	NA	intron (NM_001289470, intron 3 of 8)	L1_Mur3|LINE|L1	17311	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_71455.1	chr8	46521794	46521804	+	1	NA	intron (NM_001302163, intron 11 of 20)	Lx7|LINE|L1	-30270	NM_027973	71876	Mm.22108	NM_027973	ENSMUSG00000031629	Cenpu	1700029A22Rik|Mlf1ip	centromere protein U	protein-coding
mm_24824.1	chr3	95651474	95651511	+	1	NA	Intergenic	Intergenic	-7229	NM_008562	17210	Mm.1639	NM_008562	ENSMUSG00000038612	Mcl1	AW556805|Mcl-1	myeloid cell leukemia sequence 1	protein-coding
mm_10037.1	chr1	192855651	192855679	-	1	NA	promoter-TSS (NM_198247)	promoter-TSS (NM_198247)	87	NM_198247	214791	Mm.22806	NM_198247	ENSMUSG00000016262	Sertad4	4833404A09|C130018M11Rik	SERTA domain containing 4	protein-coding
mm_37906.1	chr4	132734838	132734856	-	1	NA	intron (NM_133888, intron 7 of 7)	intron (NM_133888, intron 7 of 7)	-2301	NM_201368	381560	Mm.44558	NM_201368	ENSMUSG00000037752	Xkr8	4931440N07Rik|AI597014|Gm1031|XRG8|mXkr8	X-linked Kx blood group related 8	protein-coding
mm_112294.1	chr12	114565046	114565056	-	1	NA	Intergenic	Intergenic	-51357	NR_106063	102465664		NR_106063	ENSMUSG00000098357	Mir7094-2	Gm27508|mmu-mir-7094-2	microRNA 7094-2	ncRNA
mm_99630.1	chr11	105156946	105156956	+	1	NA	Intergenic	RMER19C|LTR|ERVK	-21856	NM_001294331	24086	Mm.126976	NM_011903	ENSMUSG00000020694	Tlk2	4933403M19Rik|PKU-alpha|PKUalpha|Tlk	tousled-like kinase 2 (Arabidopsis)	protein-coding
mm_54904.1	chr6	47594778	47594788	-	1	NA	intron (NM_007971, intron 1 of 19)	CpG	247	NM_007971	14056	Mm.246688	NM_007971	ENSMUSG00000029687	Ezh2	Enx-1|Enx1h|KMT6|mKIAA4065	enhancer of zeste 2 polycomb repressive complex 2 subunit	protein-coding
mm_56378.1	chr6	94283516	94283541	-	1	NA	5' UTR (NM_010367, exon 1 of 22)	5' UTR (NM_010367, exon 1 of 22)	389	NM_001286786	14924	Mm.217216	NM_010367	ENSMUSG00000045095	Magi1	AIP3|BAP1|Baiap1|Gukmi1|MAGI1c|Magi-1|TNRC19|WWP3|mKIAA4129	membrane associated guanylate kinase, WW and PDZ domain containing 1	protein-coding
mm_14880.1	chr2	148835117	148835125	+	1	NA	promoter-TSS (NM_009979)	promoter-TSS (NM_009979)	-26	NM_009979	13013	Mm.21005	NM_009979	ENSMUSG00000027445	Cst9	M12|cresp|testatin	cystatin 9	protein-coding
mm_29763.1	chr3	127194657	127194658	-	1	NA	intron (NM_001327938, intron 1 of 47)	intron (NM_001327938, intron 1 of 47)	33352	NR_105029	100862268	Mm.444603	NR_105029	ENSMUSG00000097456	LOC100862268	-	uncharacterized LOC100862268	ncRNA
mm_67772.1	chr7	96951843	96951881	-	1	NA	exon (NM_153591, exon 1 of 14)	exon (NM_153591, exon 1 of 14)	335	NM_153591	244141	Mm.274864	NM_153591	ENSMUSG00000018995	Nars2	AI875199	asparaginyl-tRNA synthetase 2 (mitochondrial)(putative)	protein-coding
mm_79042.1	chr9	46215963	46215972	+	1	NA	intron (NM_027498, intron 21 of 24)	intron (NM_027498, intron 21 of 24)	-12663	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2|apo-AI|apoA-I	apolipoprotein A-I	protein-coding
mm_334.1	chr1	27884031	27884051	+	1	NA	Intergenic	Intergenic	896211	NM_001013750	210962	Mm.214178	NM_001013750	ENSMUSG00000048411	Gm597	-	predicted gene 597	protein-coding
mm_104658.1	chr11	97628611	97628623	-	1	NA	exon (NM_175332, exon 1 of 1)	exon (NM_175332, exon 1 of 1)	1099	NM_175332	103551	Mm.24506	NM_175332	ENSMUSG00000043439	Epop	AA409164|AI413509|AW539173|E13|E130012A19Rik|esPRC2p48	elongin BC and polycomb repressive complex 2 associated protein	protein-coding
mm_17309.1	chr2	26380601	26380654	-	1	NA	promoter-TSS (NM_172339)	promoter-TSS (NM_172339)	26	NM_172339	227644	Mm.207460	NM_172339	ENSMUSG00000036281	Snapc4	5730436L13Rik	small nuclear RNA activating complex, polypeptide 4	protein-coding
mm_134508.1	chr16	19067060	19067094	-	1	NA	Intergenic	Intergenic	190327	NM_010435	15260	Mm.15694	NM_010435	ENSMUSG00000022702	Hira	AA138857|D16Ertd95e|Gm15797|N28177|OTTMUSG00000026264|Tuple1	histone cell cycle regulator	protein-coding
mm_46537.1	chr5	105702006	105702012	-	1	NA	intron (NM_178701, intron 1 of 2)	intron (NM_178701, intron 1 of 2)	1199	NM_178701	231549	Mm.23837	NM_178701	ENSMUSG00000046079	Lrrc8d	2810473G09Rik|4930525N13Rik|A930019F03|Lrrc5	leucine rich repeat containing 8D	protein-coding
mm_109201.1	chr12	108658680	108658708	+	1	NA	promoter-TSS (NR_029771)	promoter-TSS (NR_029771)	74	NR_029771	723909		NR_029771	ENSMUSG00000065436	Mir342	Mirn342|mmu-mir-342	microRNA 342	ncRNA
mm_75554.1	chr8	57699444	57699454	-	1	NA	Intergenic	LTR33|LTR|ERVL	-46394	NM_144731	108150	Mm.62886	NM_144731	ENSMUSG00000031608	Galnt7	AI225872	UDP-N-acetyl-alpha-D-galactosamine: polypeptide N-acetylgalactosaminyltransferase 7	protein-coding
mm_65855.1	chr7	29282034	29282040	-	1	NA	promoter-TSS (NM_001082548)	promoter-TSS (NM_001082548)	-60	NM_011464	20733	Mm.295230	NM_011464	ENSMUSG00000074227	Spint2	AL024025|C76321|HAI-2	serine protease inhibitor, Kunitz type 2	protein-coding
mm_4695.1	chr1	180748916	180748923	+	1	NA	intron (NM_133225, intron 7 of 7)	B3A|SINE|B2	22876	NM_133225	170760	Mm.272981	NM_133225	ENSMUSG00000026499	Acbd3	60kDa|8430407O11Rik|D1Ertd10e|GCP60|GOLPH1|Gocap1|Pap7	acyl-Coenzyme A binding domain containing 3	protein-coding
mm_82181.1	chr9	123931747	123931770	+	1	NA	Intergenic	Intergenic	36934	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_38825.1	chr4	148952996	148953019	-	1	NA	3' UTR (NM_001159344, exon 21 of 21)	3' UTR (NM_001159344, exon 21 of 21)	146805	NM_019781	56273	Mm.184172	NM_019781	ENSMUSG00000028975	Pex14	Pex14p|R75137	peroxisomal biogenesis factor 14	protein-coding
mm_25172.1	chr3	103102649	103102711	+	1	NA	Intergenic	CpG	-24876	NM_177857	329727	Mm.293641	NM_177857	ENSMUSG00000007379	Dennd2c	A930010I20Rik	DENN/MADD domain containing 2C	protein-coding
mm_59154.1	chr7	24370256	24370312	+	1	NA	promoter-TSS (NM_001163510)	promoter-TSS (NM_001163510)	21	NM_008433	16534	Mm.9911	NM_008433	ENSMUSG00000054342	Kcnn4	IK1|IKCA1|KCA4|KCa3.1|SK4|SKCas|mIKCa1	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4	protein-coding
mm_126861.1	chr15	89322970	89322986	+	1	NA	5' UTR (NM_182928, exon 1 of 3)	5' UTR (NM_182928, exon 1 of 3)	258	NM_182928	223780	Mm.210541	NM_182928	ENSMUSG00000054136	Adm2	Am2|IMD|Imdn	adrenomedullin 2	protein-coding
mm_10702.1	chr2	22773971	22773986	+	1	NA	promoter-TSS (NM_019456)	promoter-TSS (NM_019456)	-349	NM_019456	54519	Mm.14255	NM_019456	ENSMUSG00000026786	Apbb1ip	9930118P07Rik|Prp48	amyloid beta (A4) precursor protein-binding, family B, member 1 interacting protein	protein-coding
mm_100323.1	chr11	118146027	118146037	+	1	NA	Intergenic	Intergenic	-16813	NM_001167746	69926	Mm.473893	NM_001167746	ENSMUSG00000033987	Dnah17	2810003K23Rik|Dnahc17|Dnahcl1|Gm1178|mKIAA3028	dynein, axonemal, heavy chain 17	protein-coding
mm_52908.1	chr6	122819889	122819938	+	1	NA	promoter-TSS (NM_021899)	promoter-TSS (NM_021899)	-271	NM_021899	60611	Mm.87142	NM_021899	ENSMUSG00000003154	Foxj2	Fhx	forkhead box J2	protein-coding
mm_85151.1	chr9	96119192	96119225	-	1	NA	promoter-TSS (NM_177352)	promoter-TSS (NM_177352)	-221	NM_177352	235533	Mm.213651	NM_177352	ENSMUSG00000041440	Gk5	AV095337|C330018K18Rik|G630067D24Rik	glycerol kinase 5 (putative)	protein-coding
mm_100007.1	chr11	114852029	114852042	+	1	NA	promoter-TSS (NM_147217)	promoter-TSS (NM_147217)	5	NM_147217	70355	Mm.242413	NM_147217	ENSMUSG00000051043	Gprc5c	1110028I06Rik|3200002M13Rik|Raig3	G protein-coupled receptor, family C, group 5, member C	protein-coding
mm_125871.1	chr15	75596646	75596662	+	1	NA	promoter-TSS (NM_026730)	promoter-TSS (NM_026730)	-4	NM_026730	68453	Mm.46367	NM_026730	ENSMUSG00000022579	Gpihbp1	1110002J19Rik|GPI-HBP1	GPI-anchored HDL-binding protein 1	protein-coding
mm_83504.1	chr9	45955254	45955278	-	1	NA	promoter-TSS (NM_001289668)	promoter-TSS (NM_001289668)	-17	NM_001289668	214597	Mm.379345	NM_172257	ENSMUSG00000034908	Sidt2	B930096O19|BC023957|CGI-40	SID1 transmembrane family, member 2	protein-coding
mm_141054.1	chr17	25751114	25751132	-	1	NA	exon (NM_018857, exon 9 of 16)	exon (NM_018857, exon 9 of 16)	3204	NM_018857	56047	Mm.17510	NM_018857	ENSMUSG00000063011	Msln	MPF	mesothelin	protein-coding
mm_106369.1	chr11	118398412	118398460	-	1	NA	exon (NM_011150, exon 3 of 6)	exon (NM_011150, exon 3 of 6)	3495	NM_011150	19039	Mm.3152	NM_011150	ENSMUSG00000033880	Lgals3bp	90K|CyCAP|MAC-2BP|Ppicap|Tango10b	lectin, galactoside-binding, soluble, 3 binding protein	protein-coding
mm_99746.1	chr11	106549626	106549626	+	1	NA	intron (NM_198292, intron 2 of 11)	intron (NM_198292, intron 2 of 11)	48635	NR_030703	100216537		NR_030703	ENSMUSG00000065126	Snord104	-	small nucleolar RNA, C/D box 104	snoRNA
mm_54120.1	chr6	18109064	18109084	-	1	NA	promoter-TSS (NM_023729)	promoter-TSS (NM_023729)	-13	NM_023729	74068	Mm.73091	NM_023729	ENSMUSG00000010796	Asz1	4933400N19Rik|Gasz|ORF3	ankyrin repeat, SAM and basic leucine zipper domain containing 1	protein-coding
mm_102942.1	chr11	69602849	69602860	-	1	NA	exon (NM_013415, exon 4 of 7)	exon (NM_013415, exon 4 of 7)	3106	NM_013415	11932	Mm.235204	NM_013415	ENSMUSG00000041329	Atp1b2	Amog|Atpb-2	ATPase, Na+/K+ transporting, beta 2 polypeptide	protein-coding
mm_166861.1	chr7	24450842	24450847	+	1	NA	Intergenic	Intergenic	-5162	NM_199013	210145	Mm.33811	NM_199013	ENSMUSG00000062028	Irgc1	F630044M05Rik|Gm1102|Gm474|Ifgge|Iigp5|Irgc	immunity-related GTPase family, cinema 1	protein-coding
mm_29806.1	chr3	127789844	127789868	-	1	NA	promoter-TSS (NM_145133)	promoter-TSS (NM_145133)	-57	NM_145133	211550	Mm.31852	NM_145133	ENSMUSG00000046688	Tifa	T2bp	TRAF-interacting protein with forkhead-associated domain	protein-coding
mm_58522.1	chr7	4147193	4147205	+	1	NA	TTS (NM_175529)	TTS (NM_175529)	2673	NM_175529	243813	Mm.347643	NM_175529	ENSMUSG00000043432	Leng9	9530024C23Rik|F630035L11Rik	leukocyte receptor cluster (LRC) member 9	protein-coding
mm_100734.1	chr11	3983974	3983985	-	1	NA	intron (NM_001177703, intron 1 of 2)	intron (NM_001177703, intron 1 of 2)	343	NM_016922	53897	Mm.103414	NM_016922	ENSMUSG00000049721	Gal3st1	Cst|Gcst	galactose-3-O-sulfotransferase 1	protein-coding
mm_76954.1	chr8	106011404	106011421	-	1	NA	promoter-TSS (NM_025518)	promoter-TSS (NM_025518)	-66	NM_025518	66369	Mm.287500	NM_025518	ENSMUSG00000031901	Dus2	2310016K04Rik|Dus2l	dihydrouridine synthase 2	protein-coding
mm_90918.1	chr10	12586298	12586327	-	1	NA	intron (NM_011682, intron 50 of 73)	ORR1B1|LTR|ERVL-MaLR	275423	NM_011682	22288	Mm.331784	NM_011682	ENSMUSG00000019820	Utrn	AA589569|DRP|Dmdl	utrophin	protein-coding
mm_32534.1	chr4	109000899	109000909	+	1	NA	promoter-TSS (NM_146150)	promoter-TSS (NM_146150)	99	NM_146150	230598	Mm.274950	NM_146150	ENSMUSG00000053510	Nrd1	2600011I06Rik|AI875733|NRD-C|Nrdc	nardilysin, N-arginine dibasic convertase, NRD convertase 1	protein-coding
mm_170612.1	chr19	5849739	5849749	+	1	NA	Intergenic	B1_Mur3|SINE|Alu	-4264	NR_003513	66961	Mm.281895	NR_003513	ENSMUSG00000092274	Neat1	2310043N10Rik|VINC	nuclear paraspeckle assembly transcript 1 (non-protein coding)	ncRNA
mm_41335.1	chr5	90495991	90496029	+	1	NA	exon (NM_007423, exon 4 of 15)	exon (NM_007423, exon 4 of 15)	5296	NM_007423	11576	Mm.358570	NM_007423	ENSMUSG00000054932	Afp	-	alpha fetoprotein	protein-coding
mm_113672.1	chr13	42728993	42728995	+	1	NA	intron (NM_001005740, intron 1 of 12)	Lx5b|LINE|L1	19413	NM_001005740	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding
mm_89802.1	chr10	102519578	102519582	+	1	NA	intron (NM_146240, intron 1 of 1)	intron (NM_146240, intron 1 of 1)	7358	NM_146240	237504	Mm.282672	NM_146240	ENSMUSG00000044921	Rassf9	AW322107|Pamci	Ras association (RalGDS/AF-6) domain family (N-terminal) member 9	protein-coding
mm_142091.1	chr17	35834327	35834341	-	1	NA	3' UTR (NM_011655, exon 4 of 4)	3' UTR (NM_011655, exon 4 of 4)	3967	NM_011655	22154	Mm.273538	NM_011655	ENSMUSG00000001525	Tubb5	AA408537|AI596182|B130022C14Rik|M(beta)5	tubulin, beta 5 class I	protein-coding
mm_52862.1	chr6	122308657	122308683	+	1	NA	promoter-TSS (NM_010749)	promoter-TSS (NM_010749)	-340	NM_010749	17113	Mm.249225	NM_010749	ENSMUSG00000007458	M6pr	CD-MPR|Mpr46	mannose-6-phosphate receptor, cation dependent	protein-coding
mm_122100.1	chr14	30915478	30915481	-	1	NA	exon (NM_008407, exon 13 of 21)	exon (NM_008407, exon 13 of 21)	8108	NM_008407	16426	Mm.4517	NM_008407	ENSMUSG00000006522	Itih3	AW108094|ITI-HC3|Intin3|Itih-3	inter-alpha trypsin inhibitor, heavy chain 3	protein-coding
mm_157139.1	chrX	9459371	9459381	-	1	NA	intron (NM_007807, intron 3 of 12)	intron (NM_007807, intron 3 of 12)	9948	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_113325.1	chr13	30786538	30786550	+	1	NA	Intergenic	Intergenic	37311	NM_013674	16364	Mm.4677	NM_013674	ENSMUSG00000021356	Irf4	AI385587|IRF-4|LSIRF|NF-EM5|Spip	interferon regulatory factor 4	protein-coding
mm_118705.1	chr14	22164906	22164930	+	1	NA	intron (NM_028275, intron 2 of 6)	Lx8b|LINE|L1	145206	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_105188.1	chr11	101984750	101984798	-	1	NA	promoter-TSS (NM_028207)	promoter-TSS (NM_028207)	17	NM_028207	72349	Mm.196295	NM_028207	ENSMUSG00000003518	Dusp3	2210015O03Rik|5031436O03Rik|T-DSP11|VHR	dual specificity phosphatase 3 (vaccinia virus phosphatase VH1-related)	protein-coding
mm_44017.1	chr5	147341269	147341273	+	1	NA	exon (NM_010229, exon 20 of 24)	exon (NM_010229, exon 20 of 24)	-18831	NM_001039678	231903	Mm.291286	NM_001039678	ENSMUSG00000075543	Urad	EG231903|Prhoxnb	ureidoimidazoline (2-oxo-4-hydroxy-4-carboxy-5) decarboxylase	protein-coding
mm_171318.1	chr3	96119334	96119334	-	1	NA	intron (NM_001025613, intron 2 of 12)	intron (NM_001025613, intron 2 of 12)	14807	NM_001025614	229603	Mm.272336	NM_001025613	ENSMUSG00000038495	Otud7b	2900060B22Rik|4930463P07Rik|AI462125|CEZANNE|Trabid2|Za20d1	OTU domain containing 7B	protein-coding
mm_26296.1	chr3	142507917	142507921	+	1	NA	exon (NM_153564, exon 10 of 11)	exon (NM_153564, exon 10 of 11)	10985	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_132337.1	chr16	33829625	33829667	+	1	NA	promoter-TSS (NM_001145884)	promoter-TSS (NM_001145884)	-19	NM_010580	16419	Mm.6424	NM_010580	ENSMUSG00000022817	Itgb5	AA475909|AI874634|ESTM23|[b]-5|[b]5|[b]5A|[b]5B|beta-5|beta5	integrin beta 5	protein-coding
mm_24650.1	chr3	94388295	94388301	+	1	NA	intron (NR_121656, intron 3 of 9)	intron (NR_121656, intron 3 of 9)	10866	NR_121656	19885	Mm.4372	NM_011281	ENSMUSG00000028150	Rorc	Nr1f3|RORgamma|TOR|Thor	RAR-related orphan receptor gamma	protein-coding
mm_109890.1	chr12	5943596	5943621	-	1	NA	Intergenic	Intergenic	567106	NR_015579	72669	Mm.10434	NM_028318		2810032G03Rik	AI461720	RIKEN cDNA 2810032G03 gene	ncRNA
mm_170123.1	chr17	39846941	39846944	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	3945	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_8132.1	chr1	136234054	136234080	-	1	NA	exon (NM_028872, exon 1 of 10)	exon (NM_028872, exon 1 of 10)	213	NM_028872	67313	Mm.36763	NM_028872	ENSMUSG00000041605	5730559C18Rik	1700034M08Rik|4933426C09Rik|AI586180|D1Mgi54	RIKEN cDNA 5730559C18 gene	protein-coding
mm_33913.1	chr4	136424057	136424067	+	1	NA	promoter-TSS (NM_001285484)	promoter-TSS (NM_001285484)	538	NM_001285483	15552	Mm.40573	NM_008309	ENSMUSG00000070687	Htr1d	5-HT-1D|5-HT1D|AI853647|Gpcr14|Htr1db	5-hydroxytryptamine (serotonin) receptor 1D	protein-coding
mm_122261.1	chr14	34274278	34274294	-	1	NA	intron (NM_029389, intron 2 of 10)	intron (NM_029389, intron 2 of 10)	36217	NM_029389	75698	Mm.45406	NM_029389	ENSMUSG00000041471	Fam35a	3110001K24Rik	family with sequence similarity 35, member A	protein-coding
mm_110079.1	chr12	24639034	24639072	-	1	NA	Intergenic	Intergenic	-12318	NM_178357	194655	Mm.9616	NM_178357	ENSMUSG00000020653	Klf11	9830142A17|D12Ertd427e|Tieg2|Tieg2b|Tieg3	Kruppel-like factor 11	protein-coding
mm_420.1	chr1	34435093	34435106	+	1	NA	Intergenic	Intergenic	-1900	NR_039562	100628580		NR_039562	ENSMUSG00000092852	Mir5103	mir-5103|mmu-mir-5103|mu-mir-5103	microRNA 5103	ncRNA
mm_37294.1	chr4	119189950	119189964	-	1	NA	promoter-TSS (NM_013848)	promoter-TSS (NM_013848)	54	NM_013848	27028	Mm.290753	NM_013848	ENSMUSG00000028644	Ermap	AA409279|AI666418	erythroblast membrane-associated protein	protein-coding
mm_110007.1	chr12	16221260	16221277	-	1	NA	Intergenic	MLT1J2|LTR|ERVL-MaLR	368502	NM_015763	14245	Mm.153625	NM_015763	ENSMUSG00000020593	Lpin1	4631420P06|Kiaa0188|Lipin1|fld|mKIAA0188	lipin 1	protein-coding
mm_130597.1	chr15	99772532	99772542	-	1	NA	promoter-TSS (NM_028015)	promoter-TSS (NM_028015)	-22	NM_028015	71949	Mm.390821	NM_028015	ENSMUSG00000023021	Cers5	2310081H14Rik|AU045339|AW544927|Lass5|Trh4	ceramide synthase 5	protein-coding
mm_43898.1	chr5	144190409	144190421	+	1	NA	intron (NM_010800, intron 1 of 1)	intron (NM_010800, intron 1 of 1)	129	NM_010800	17341	Mm.386767	NM_010800	ENSMUSG00000052271	Bhlha15	1810009C13Rik|Bhlhb8|MIST-1|Mist1	basic helix-loop-helix family, member a15	protein-coding
mm_76727.1	chr8	94973328	94973330	-	1	NA	Intergenic	Intergenic	-3780	NM_001198894	14766	Mm.290834	NM_018882	ENSMUSG00000031785	Adgrg1	Cyt28|Gpr56|TM7LN4|TM7XN1	adhesion G protein-coupled receptor G1	protein-coding
mm_166194.1	chr5	36553291	36553297	-	1	NA	intron (NM_133910, intron 2 of 13)	intron (NM_133910, intron 2 of 13)	-22671	NM_001113364	100855	Mm.486203	NM_133910	ENSMUSG00000029192	Tbc1d14	2810413P16Rik|AU043625|C86258|D5Ertd110e|mKIAA1322	TBC1 domain family, member 14	protein-coding
mm_122713.1	chr14	52256333	52256339	-	1	NA	Intergenic	Intergenic	-18764	NM_201637	67772	Mm.289934	NM_201637	ENSMUSG00000053754	Chd8	5830451P18Rik|AU015341|Duplin|HELSNF1|mKIAA1564	chromodomain helicase DNA binding protein 8	protein-coding
mm_6206.1	chr1	66815875	66815883	-	1	NA	intron (NM_177645, intron 1 of 13)	intron (NM_177645, intron 1 of 13)	1716	NM_177645	68691	Mm.240912	NM_177645	ENSMUSG00000026004	Kansl1l	1110028C15Rik|1190030G24|AI427598|C430010P07Rik|mKIAA4189	KAT8 regulatory NSL complex subunit 1-like	protein-coding
mm_29767.1	chr3	127225918	127225959	-	1	NA	intron (NM_001327938, intron 1 of 47)	intron (NM_001327938, intron 1 of 47)	64633	NR_105029	100862268	Mm.444603	NR_105029	ENSMUSG00000097456	LOC100862268	-	uncharacterized LOC100862268	ncRNA
mm_62333.1	chr7	100493940	100493955	+	1	NA	intron (NM_011671, intron 1 of 7)	intron (NM_011671, intron 1 of 7)	589	NM_011671	22228	Mm.171378	NM_011671	ENSMUSG00000033685	Ucp2	Slc25a8	uncoupling protein 2 (mitochondrial, proton carrier)	protein-coding
mm_80662.1	chr9	90064508	90064549	+	1	NA	exon (NM_007801, exon 6 of 12)	exon (NM_007801, exon 6 of 12)	10261	NM_001312649	13036	Mm.2277	NM_007801	ENSMUSG00000032359	Ctsh	AL022844	cathepsin H	protein-coding
mm_133080.1	chr16	59471779	59471861	+	1	NA	promoter-TSS (NM_025910)	promoter-TSS (NM_025910)	45	NM_025910	67014	Mm.289150	NM_025910	ENSMUSG00000022724	Mina	1810047J07Rik|2410057H13Rik|3830408E23Rik|AI449204	myc induced nuclear antigen	protein-coding
mm_65220.1	chr7	19699595	19699607	-	1	NA	promoter-TSS (NM_009696)	promoter-TSS (NM_009696)	-413	NM_009696	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_152588.1	chr19	11604750	11604766	-	1	NA	promoter-TSS (NM_026835)	promoter-TSS (NM_026835)	46	NM_026835	68774	Mm.290390	NM_026835	ENSMUSG00000024679	Ms4a6d	1110058E16Rik|AI447446|Ms4a11	membrane-spanning 4-domains, subfamily A, member 6D	protein-coding
mm_80297.1	chr9	73113659	73113668	+	1	NA	intron (NM_198609, intron 1 of 5)	CpG	194	NM_198609	225215	Mm.379366	NM_198609	ENSMUSG00000032215	Rsl24d1	2410159K22Rik	ribosomal L24 domain containing 1	protein-coding
mm_97223.1	chr11	75650502	75650544	+	1	NA	promoter-TSS (NM_008659)	promoter-TSS (NM_008659)	-986	NM_008659	17913	Mm.234502	NM_008659	ENSMUSG00000017774	Myo1c	C80397|MMIb|MYO1E|NMI|mm1beta|myr2	myosin IC	protein-coding
mm_142496.1	chr17	46030598	46030621	-	1	NA	intron (NM_001317041, intron 1 of 6)	CpG	1768	NM_001287058	22339	Mm.282184	NM_009505	ENSMUSG00000023951	Vegfa	Vegf|Vpf	vascular endothelial growth factor A	protein-coding
mm_65908.1	chr7	30193795	30193819	-	1	NA	intron (NM_009795, intron 2 of 10)	intron (NM_009795, intron 2 of 10)	1241	NM_009795	12336	Mm.439782	NM_009795	ENSMUSG00000001794	Capns1	Capa-4|Capa4|Capn4|D7Ertd146e	calpain, small subunit 1	protein-coding
mm_131207.1	chr16	8680759	8680790	+	1	NA	promoter-TSS (NM_001324517)	promoter-TSS (NM_001324517)	4	NM_001324517	436336	Mm.357666	NM_001324517		Gm5767	EG436336	predicted gene 5767	protein-coding
mm_83803.1	chr9	53248064	53248105	-	1	NA	promoter-TSS (NM_029936)	promoter-TSS (NM_029936)	28	NM_029936	77591	Mm.133560	NM_029936	ENSMUSG00000053289	Ddx10	4632415A01Rik|AI646054	DEAD (Asp-Glu-Ala-Asp) box polypeptide 10	protein-coding
mm_71879.1	chr8	69811660	69811672	+	1	NA	intron (NM_198101, intron 7 of 20)	intron (NM_198101, intron 7 of 20)	2979	NM_198101	78816	Mm.324305	NM_198101	ENSMUSG00000036246	Gmip	5031419I10Rik	Gem-interacting protein	protein-coding
mm_147727.1	chr18	61014069	61014099	-	1	NA	5' UTR (NM_201353, exon 1 of 14)	5' UTR (NM_201353, exon 1 of 14)	115	NM_201353	240332	Mm.39846	NM_201353	ENSMUSG00000052026	Slc6a7	AW455934|PROT	solute carrier family 6 (neurotransmitter transporter, L-proline), member 7	protein-coding
mm_28367.1	chr3	89904374	89904382	-	1	NA	intron (NM_001310676, intron 1 of 9)	intron (NM_001310676, intron 1 of 9)	8818	NM_001310676	16194	Mm.2856	NM_010559	ENSMUSG00000027947	Il6ra	CD126|IL-6R|IL-6R-alpha|IL-6RA|Il6r	interleukin 6 receptor, alpha	protein-coding
mm_37822.1	chr4	131920703	131920707	-	1	NA	promoter-TSS (NR_102393)	promoter-TSS (NR_102393)	-676	NR_102393	545681	Mm.2478	NR_102393	ENSMUSG00000085667	Gm12992	OTTMUSG00000009742	predicted gene 12992	ncRNA
mm_24445.1	chr3	90605942	90605974	+	1	NA	TTS (NM_011311)	TTS (NM_011311)	2188	NM_011311	20198	Mm.3925	NM_011311	ENSMUSG00000001020	S100a4	18A2|42a|Capl|FSp1|Mts1|PeL98|metastasin|pk9a	S100 calcium binding protein A4	protein-coding
mm_5422.1	chr1	34144576	34144578	-	1	NA	intron (NM_001276764, intron 9 of 102)	(CTG)n|Simple_repeat|Simple_repeat	-15753	NM_010081	13518	Mm.336625	NM_010081	ENSMUSG00000026131	Dst	2310001O04Rik|A830042E19Rik|AW554249|BP230|BPAG1-n|Bpag|Bpag1|Macf2|ah|athetoid|dt|mKIAA0728|nmf203|nmf339	dystonin	protein-coding
mm_33235.1	chr4	127021312	127021339	+	1	NA	promoter-TSS (NM_023603)	promoter-TSS (NM_023603)	24	NM_023603	71514	Mm.257276	NM_023603	ENSMUSG00000028820	Sfpq	1110004P21Rik|2810416M14Rik|5730453G22Rik|9030402K04Rik|AU021830|D4Ertd314e|Gm12940|OTTMUSG00000009329|PSF|REP1	splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)	protein-coding
mm_89670.1	chr10	97506554	97506584	+	1	NA	exon (NM_007833, exon 4 of 8)	exon (NM_007833, exon 4 of 8)	24238	NM_007833	13179	Mm.56769	NM_007833	ENSMUSG00000019929	Dcn	DC|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding
mm_129709.1	chr15	81843750	81843755	-	1	NA	Intergenic	Intergenic	14574	NM_020507	57259	Mm.323595	NM_020507	ENSMUSG00000048546	Tob2	2900090N22Rik|4930545K18Rik|AV071822|mKIAA1663	transducer of ERBB2, 2	protein-coding
mm_84969.1	chr9	85096590	85096625	-	1	NA	Intergenic	Intergenic	230517	NM_001160378	212943	Mm.74610	NM_001160378	ENSMUSG00000032265	Fam46a	BAP014|D930050G01Rik	family with sequence similarity 46, member A	protein-coding
mm_58102.1	chr6	137570813	137570831	-	1	NA	5' UTR (NM_001271587, exon 1 of 21)	5' UTR (NM_001271587, exon 1 of 21)	187	NM_001271595	13860	Mm.235346	NM_007945	ENSMUSG00000015766	Eps8	AW261790	epidermal growth factor receptor pathway substrate 8	protein-coding
mm_6732.1	chr1	82810607	82810611	-	1	NA	Intergenic	RMER17C|LTR|ERVK	-28851	NM_001310713	15463	Mm.392569	NM_010472	ENSMUSG00000026159	Agfg1	AU045498|C130049H11Rik|C85612|D730048C23Rik|Hrb|RAB|Rip	ArfGAP with FG repeats 1	protein-coding
mm_42653.1	chr5	119133645	119133673	+	1	NA	Intergenic	Intergenic	25423	NR_040693	73477	Mm.410863	NR_040693	ENSMUSG00000100573	1700081H04Rik	-	RIKEN cDNA 1700081H04 gene	ncRNA
mm_47662.1	chr5	125849883	125849893	-	1	NA	Intergenic	Intergenic	317470	NM_001190352	208151	Mm.40397	NM_001190352	ENSMUSG00000070498	Tmem132b	AK220418|mKIAA1786	transmembrane protein 132B	protein-coding
mm_34990.1	chr4	156027527	156027535	+	1	NA	intron (NM_021985, intron 2 of 3)	intron (NM_021985, intron 2 of 3)	1189	NM_021985	21936	Mm.3180	NM_009400	ENSMUSG00000041954	Tnfrsf18	AITR|Gitr	tumor necrosis factor receptor superfamily, member 18	protein-coding
mm_113781.1	chr13	45410766	45410768	+	1	NA	3' UTR (NM_153789, exon 7 of 7)	3' UTR (NM_153789, exon 7 of 7)	21025	NM_153789	218203	Mm.212855	NM_153789	ENSMUSG00000038175	Mylip	9430057C20Rik|Mir	myosin regulatory light chain interacting protein	protein-coding
mm_151658.1	chr19	4125838	4125863	-	1	NA	promoter-TSS (NM_016666)	promoter-TSS (NM_016666)	8	NM_016666	11632	Mm.10433	NM_016666	ENSMUSG00000024847	Aip	AA408703|AW476050|Ara9|D19Bwg1412e|Fkbp16|Xap2	aryl-hydrocarbon receptor-interacting protein	protein-coding
mm_149173.1	chr19	9102473	9102479	+	1	NA	Intergenic	B1F|SINE|Alu	-14520	NM_011681	22287	Mm.2258	NM_011681	ENSMUSG00000024653	Scgb1a1	CC10|CC16|CCSP|PCB-BP|UG|UGB|Utg	secretoglobin, family 1A, member 1 (uteroglobin)	protein-coding
mm_97946.1	chr11	83664306	83664339	+	1	NA	exon (NM_013652, exon 3 of 3)	exon (NM_013652, exon 3 of 3)	1738	NM_013652	20303	Mm.244263	NM_013652	ENSMUSG00000018930	Ccl4	AT744.1|Act-2|MIP-1B|Mip1b|Scya4	chemokine (C-C motif) ligand 4	protein-coding
mm_59774.1	chr7	28834478	28834505	+	1	NA	exon (NM_010707, exon 2 of 9)	exon (NM_010707, exon 2 of 9)	321	NM_010707	16857	Mm.210336	NM_010707		Lgals6	galectin-6	lectin, galactose binding, soluble 6	protein-coding
mm_129402.1	chr15	78284378	78284412	-	1	NA	TTS (NR_106137).2	TTS (NR_106137).2	454	NR_106138	102466845		NR_106138	ENSMUSG00000099059	Mir7676-2	Gm27790|mmu-mir-7676-2	microRNA 7676-2	ncRNA
mm_169028.1	chr13	118362840	118362843	+	1	NA	Intergenic	Intergenic	24411	NM_021556	59054	Mm.143810	NM_021556	ENSMUSG00000021731	Mrps30	2610020A16Rik|AA968347|PAP|Pdcd9	mitochondrial ribosomal protein S30	protein-coding
mm_149528.1	chr19	12461033	12461043	+	1	NA	5' UTR (NM_010821, exon 2 of 2)	5' UTR (NM_010821, exon 2 of 2)	259	NM_010821	17476	Mm.3999	NM_010821	ENSMUSG00000046805	Mpeg1	MPS1|Mpg-1	macrophage expressed gene 1	protein-coding
mm_14405.1	chr2	130171884	130171905	+	1	NA	3' UTR (NM_009225, exon 7 of 7)	3' UTR (NM_009225, exon 7 of 7)	7470	NM_009225	20638	Mm.88216	NM_009225	ENSMUSG00000027404	Snrpb	AL024368|AU018828|SM-B|SM11|SMB|SNRNP-B	small nuclear ribonucleoprotein B	protein-coding
mm_78661.1	chr9	40575334	40575378	+	1	NA	Intergenic	Intergenic	-110608	NM_133733	71566	Mm.280560	NM_133733	ENSMUSG00000032024	Clmp	9030425E11Rik|ACAM|ASP5|AW557819	CXADR-like membrane protein	protein-coding
mm_166684.1	chr6	99750311	99750311	+	1	NA	Intergenic	Intergenic	-23919	NM_001170419	50501	Mm.87365	NM_015768	ENSMUSG00000030069	Prok2	Bv8|PK2|Prok1	prokineticin 2	protein-coding
mm_16682.1	chr2	6876702	6876718	-	1	NA	intron (NM_001110229, intron 2 of 14)	intron (NM_001110229, intron 2 of 14)	-4675	NM_001347094	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_7410.1	chr1	119422166	119422172	-	1	NA	promoter-TSS (NM_008381)	promoter-TSS (NM_008381)	79	NM_008381	16324	Mm.3092	NM_008381	ENSMUSG00000037035	Inhbb	-	inhibin beta-B	protein-coding
mm_106391.1	chr11	118650995	118650997	-	1	NA	intron (NM_001039168, intron 3 of 14)	intron (NM_001039168, intron 3 of 14)	110045	NM_001285438	52897	Mm.341103	NM_001024931	ENSMUSG00000025576	Rbfox3	Fox-3|Hrnbp3|NeuN|Neuna60	RNA binding protein, fox-1 homolog (C. elegans) 3	protein-coding
mm_70395.1	chr8	11071466	11071479	+	1	NA	Intergenic	Intergenic	-63042	NM_001081212	384783	Mm.407207	NM_001081212	ENSMUSG00000038894	Irs2	Irs-2	insulin receptor substrate 2	protein-coding
mm_41535.1	chr5	92825902	92825925	+	1	NA	intron (NM_001077595, intron 1 of 9)	(CA)n|Simple_repeat|Simple_repeat	16531	NM_001077595	27428	Mm.46014	NM_015756	ENSMUSG00000029381	Shroom3	AL022960|D5Ertd287e|Shrm|Shrm3	shroom family member 3	protein-coding
mm_120837.1	chr14	75179579	75179590	+	1	NA	intron (NM_008879, intron 2 of 16)	intron (NM_008879, intron 2 of 16)	43159	NM_008879	18826	Mm.153911	NM_008879	ENSMUSG00000021998	Lcp1	AW536232|D14Ertd310e|LCP-1|Pls2|pp65	lymphocyte cytosolic protein 1	protein-coding
mm_141715.1	chr17	34028017	34028023	-	1	NA	promoter-TSS (NM_013543)	promoter-TSS (NM_013543)	35	NM_013543	14979	Mm.275452	NM_013543	ENSMUSG00000073422	H2-Ke6	D17H6S112E|H-2Ke6|Hsd17b8|Ke-6|Ke6|Ring2	H2-K region expressed gene 6	protein-coding
mm_21494.1	chr2	163397914	163397944	-	1	NA	promoter-TSS (NM_001205076)	promoter-TSS (NM_001205076)	44	NM_021566	59091	Mm.34459	NM_021566	ENSMUSG00000017817	Jph2	1110002E14Rik|JP-2|Jp2	junctophilin 2	protein-coding
mm_17435.1	chr2	27548089	27548114	-	1	NA	Intergenic	ORR1C1|LTR|ERVL-MaLR	32954	NM_080848	140858	Mm.28265	NM_080848	ENSMUSG00000026917	Wdr5	2410008O07Rik|AA408785|AA960360|Big|Big-3	WD repeat domain 5	protein-coding
mm_110847.1	chr12	73046874	73046901	-	1	NA	promoter-TSS (NM_009189)	promoter-TSS (NM_009189)	-175	NM_009189	20471	Mm.4645	NM_009189	ENSMUSG00000051367	Six1	BB138287	sine oculis-related homeobox 1	protein-coding
mm_122318.1	chr14	36922415	36922417	-	1	NA	intron (NM_001347502, intron 3 of 8)	B1_Mur1|SINE|Alu	-2881	NM_001347503	72972	Mm.27621	NM_027045	ENSMUSG00000058690	Ccser2	1700012P13Rik|2900054P12Rik|AI035535|AW108503|Fam190b|Gcap14	coiled-coil serine rich 2	protein-coding
mm_89349.1	chr10	88147041	88147053	+	1	NA	promoter-TSS (NM_027191)	promoter-TSS (NM_027191)	-24	NM_028334	69736	Mm.222184	NM_027191	ENSMUSG00000035351	Nup37	2410003L22Rik|2810039M17Rik	nucleoporin 37	protein-coding
mm_170032.1	chr17	22361365	22361370	-	1	NA	promoter-TSS (NM_176962)	promoter-TSS (NM_176962)	33	NM_176962	319615	Mm.442162	NM_176962	ENSMUSG00000033972	Zfp944	6330416L07Rik	zinc finger protein 944	protein-coding
mm_117418.1	chr13	74333646	74333649	-	1	NA	intron (NM_023281, intron 7 of 14)	intron (NM_023281, intron 7 of 14)	-16321	NM_011051	18570	Mm.24254	NM_011051	ENSMUSG00000021576	Pdcd6	AV299538|Alg2|MA-3|PS2|alg-2	programmed cell death 6	protein-coding
mm_139268.1	chr17	47862276	47862287	+	1	NA	Intergenic	Intergenic	-27590	NM_001109973	17240	Mm.329100	NM_010783	ENSMUSG00000032717	Mdfi	I-mf|I-mfa	MyoD family inhibitor	protein-coding
mm_31696.1	chr4	62408771	62408865	+	1	NA	promoter-TSS (NM_027297)	promoter-TSS (NM_027297)	35	NM_027297	70052	Mm.30660	NM_027297	ENSMUSG00000066148	Prpf4	1600015H11Rik|AI874830|AW047464|bN189G18.1	pre-mRNA processing factor 4	protein-coding
mm_73876.1	chr8	119277397	119277428	+	1	NA	intron (NM_019707, intron 10 of 13)	intron (NM_019707, intron 10 of 13)	-67126	NM_024219	68196	Mm.358714	NM_024219	ENSMUSG00000031839	Hsbp1	0610007A03Rik|AA408769|Hsp25	heat shock factor binding protein 1	protein-coding
mm_103318.1	chr11	73177012	73177047	-	1	NA	promoter-TSS (NM_025318)	promoter-TSS (NM_025318)	13	NM_025318	66048	Mm.73608	NM_025318	ENSMUSG00000047260	Emc6	0610009E20Rik|0610025L18Rik|Tmem93	ER membrane protein complex subunit 6	protein-coding
mm_9199.1	chr1	171226272	171226309	-	1	NA	TTS (NM_013474)	TTS (NM_013474)	1236	NM_013474	11807	Mm.389209	NM_013474	ENSMUSG00000005681	Apoa2	Alp-2|Apo-AII|ApoA-II|ApoAII|Apoa-2|Hdl-1	apolipoprotein A-II	protein-coding
mm_27454.1	chr3	52056406	52056428	-	1	NA	intron (NM_001004176, intron 1 of 4)	B4|SINE|B4	48589	NM_001004176	433586	Mm.234972	NM_001004176	ENSMUSG00000061143	Maml3	AV234550|BC049812|Mam-2|mKIAA1816	mastermind like 3 (Drosophila)	protein-coding
mm_161439.1	chr15	65976784	65976784	-	1	NA	promoter-TSS (NM_001145096)	promoter-TSS (NM_001145096)	20	NM_001145096	654498	Mm.364550	NM_001145096	ENSMUSG00000072511	Hhla1	F930104E18Rik	HERV-H LTR-associating 1	protein-coding
mm_83974.1	chr9	57261710	57261710	-	1	NA	intron (NM_028820, intron 1 of 2)	CpG	889	NM_028820	74211	Mm.428905	NM_028820	ENSMUSG00000032300	1700017B05Rik	AA682102|D9Ertd278e	RIKEN cDNA 1700017B05 gene	protein-coding
mm_9111.1	chr1	170111417	170111427	-	1	NA	Intergenic	Intergenic	-22478	NM_022563	18214	Mm.229249	NM_022563	ENSMUSG00000026674	Ddr2	AW495251|Ntrkr3|tyro10	discoidin domain receptor family, member 2	protein-coding
mm_74815.1	chr8	22706508	22706580	-	1	NA	promoter-TSS (NM_010546)	promoter-TSS (NM_010546)	39	NM_010546	16150	Mm.277886	NM_010546	ENSMUSG00000031537	Ikbkb	AI132552|IKK-2|IKK-beta|IKK2|IKK[b]|IKKbeta	inhibitor of kappaB kinase beta	protein-coding
mm_157780.1	chrX	73787034	73787059	-	1	NA	promoter-TSS (NM_008323)	promoter-TSS (NM_008323)	18	NM_001166480	20832	Mm.831	NM_009279	ENSMUSG00000002014	Ssr4	AW743063|C78062|Trap	signal sequence receptor, delta	protein-coding
mm_95904.1	chr11	58203266	58203286	+	1	NA	intron (NM_018738, intron 2 of 2)	B1_Mus2|SINE|Alu	3720	NM_018738	16145	Mm.33902	NM_018738	ENSMUSG00000078853	Igtp	AW558444|Irgm3	interferon gamma induced GTPase	protein-coding
mm_88327.1	chr10	75568642	75568645	+	1	NA	promoter-TSS (NM_001305992)	promoter-TSS (NM_001305992)	-19	NM_001305992	14598	Mm.4559	NM_008116	ENSMUSG00000006345	Ggt1	CD224|GGT|GGT 1|GGT-1|Ggtp|dwg	gamma-glutamyltransferase 1	protein-coding
mm_132720.1	chr16	43522584	43522585	+	1	NA	intron (NM_181058, intron 3 of 6)	intron (NM_181058, intron 3 of 6)	-102388	NR_046026	626693	Mm.447083	NR_046026	ENSMUSG00000085499	Gm15713	OTTMUSG00000025617	predicted gene 15713	ncRNA
mm_110461.1	chr12	51762102	51762105	-	1	NA	intron (NM_144788, intron 28 of 42)	intron (NM_144788, intron 28 of 42)	67433	NM_144788	207304	Mm.249391	NM_144788	ENSMUSG00000035247	Hectd1	A630086P08Rik|AI844876|b2b327Clo|opm	HECT domain containing 1	protein-coding
mm_156303.1	chrX	136837968	136837974	+	1	NA	3' UTR (NM_011123, exon 7 of 7)	3' UTR (NM_011123, exon 7 of 7)	15225	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_147447.1	chr18	46526036	46526046	-	1	NA	promoter-TSS (NM_173423)	promoter-TSS (NM_173423)	-70	NM_173423	240263	Mm.38249	NM_173423	ENSMUSG00000033319	Fem1c	2610312A07Rik|3632443A22Rik|AI646567	fem-1 homolog c (C.elegans)	protein-coding
mm_153617.1	chr19	43986367	43986377	-	1	NA	5' UTR (NM_030703, exon 1 of 9)	5' UTR (NM_030703, exon 1 of 9)	148	NM_030703	93721	Mm.206774	NM_030703	ENSMUSG00000025196	Cpn1	0610011F20Rik|CPN	carboxypeptidase N, polypeptide 1	protein-coding
mm_56183.1	chr6	88446492	88446539	-	1	NA	promoter-TSS (NM_023060)	promoter-TSS (NM_023060)	24	NM_023060	65967	Mm.333237	NM_023060	ENSMUSG00000033216	Eefsec	Selb|sec	eukaryotic elongation factor, selenocysteine-tRNA-specific	protein-coding
mm_15557.1	chr2	158502578	158502586	+	1	NA	promoter-TSS (NM_145635)	promoter-TSS (NM_145635)	-30	NM_145635	246747	Mm.28800	NM_145635	ENSMUSG00000044405	Adig	SMAF-1|Smaf1	adipogenin	protein-coding
mm_55026.1	chr6	48841516	48841559	-	1	NA	promoter-TSS (NM_001164209)	promoter-TSS (NM_001164209)	54	NM_025326	66058	Mm.27061	NM_025326	ENSMUSG00000023367	Tmem176a	0610011I04Rik|AU040201|AU041743|Keg2	transmembrane protein 176A	protein-coding
mm_82115.1	chr9	123461929	123461984	+	1	NA	3' UTR (NM_153168, exon 21 of 21)	3' UTR (NM_153168, exon 21 of 21)	-16745	NM_013860	29806	Mm.10987	NM_013860	ENSMUSG00000025239	Limd1	AW822033|D9Ertd192e	LIM domains containing 1	protein-coding
mm_163999.1	chr14	65675893	65675896	+	1	NA	intron (NM_028903, intron 2 of 8)	intron (NM_028903, intron 2 of 8)	9491	NM_001168318	71145	Mm.83840	NM_028903	ENSMUSG00000022032	Scara5	4932433F15Rik|4933425F03Rik|AV278087|Tesr	scavenger receptor class A, member 5	protein-coding
mm_123328.1	chr14	63008720	63008727	-	1	NA	Intergenic	Lx5|LINE|L1	-3048	NM_001039121	654458	Mm.390737	NM_001039121	ENSMUSG00000075572	Defb43	BD-43|EG654458|mBD-43	defensin beta 43	protein-coding
mm_7156.1	chr1	91458242	91458251	-	1	NA	intron (NM_011066, intron 1 of 22)	intron (NM_011066, intron 1 of 22)	1082	NM_011066	18627	Mm.482463	NM_011066	ENSMUSG00000055866	Per2	mKIAA0347|mPer2	period circadian clock 2	protein-coding
mm_125881.1	chr15	75642453	75642496	+	1	NA	Intergenic	CpG	25790	NM_011759	22701	Mm.87210	NM_011759	ENSMUSG00000047003	Zfp41	CTfin92|Zfp-41	zinc finger protein 41	protein-coding
mm_133480.1	chr16	90140001	90140011	+	1	NA	Intergenic	Intergenic	-2231	NR_033476	100038709	Mm.484070	NR_033476		Gm10789	ENSMUSG00000074924	predicted gene 10789	ncRNA
mm_82807.1	chr9	29963093	29963103	-	1	NA	promoter-TSS (NM_172290)	promoter-TSS (NM_172290)	31	NM_172290	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding
mm_163630.1	chr13	58281175	58281180	+	1	NA	Intergenic	Intergenic	-6989	NM_019832	56278	Mm.296625	NM_019832	ENSMUSG00000021552	Gkap1	42kDa|4933400B15Rik|D13Ertd340e|Gkap42	G kinase anchoring protein 1	protein-coding
mm_83270.1	chr9	42968196	42968200	-	1	NA	3' UTR (NM_027144, exon 41 of 41)	3' UTR (NM_027144, exon 41 of 41)	-23827	NM_175481	110637	Mm.370291	NM_175481	ENSMUSG00000032017	Grik4	6330551K01Rik|GluK4|GluRgamma1|KA-1|KA1	glutamate receptor, ionotropic, kainate 4	protein-coding
mm_64420.1	chr7	142576612	142576653	+	1	NA	TTS (NR_030416)	TTS (NR_030416)	515	NR_030416	735280		NR_030416	ENSMUSG00000076275	Mir675	Mirn675|mir-675|mmu-mir-675	microRNA 675	ncRNA
mm_11014.1	chr2	26583859	26583874	+	1	NA	promoter-TSS (NM_198724)	promoter-TSS (NM_198724)	2	NM_198725	353156	Mm.268933	NM_178444	ENSMUSG00000026921	Egfl7	VE-statin|Zneu1	EGF-like domain 7	protein-coding
mm_42438.1	chr5	115429623	115429683	+	1	NA	promoter-TSS (NM_008629)	promoter-TSS (NM_008629)	-32	NM_008629	17690	Mm.5077	NM_008629	ENSMUSG00000054256	Msi1	Msi1h|Musahi1|m-Msi-1	musashi RNA-binding protein 1	protein-coding
mm_156210.1	chrX	134681470	134681492	+	1	NA	Intergenic	Intergenic	4981	NR_045454	77983	Mm.153204	NR_045454	ENSMUSG00000087024	B230119M05Rik	-	RIKEN cDNA B230119M05 gene	ncRNA
mm_134681.1	chr16	22411877	22411896	-	1	NA	exon (NM_023794, exon 7 of 13)	exon (NM_023794, exon 7 of 13)	27684	NM_023794	104156	Mm.155708	NM_023794	ENSMUSG00000013089	Etv5	1110005E01Rik|8430401F14Rik|ERM	ets variant 5	protein-coding
mm_128650.1	chr15	59648096	59648136	-	1	NA	promoter-TSS (NM_144549)	promoter-TSS (NM_144549)	-538	NM_144549	211770	Mm.40298	NM_144549	ENSMUSG00000032501	Trib1	A530090O15Rik|TRB-1|Trb1	tribbles pseudokinase 1	protein-coding
mm_22415.1	chr2	181492964	181493004	-	1	NA	promoter-TSS (NM_183181)	promoter-TSS (NM_183181)	-222	NM_183181	241850	Mm.87455	NM_183181	ENSMUSG00000055882	Abhd16b	1700095H12	abhydrolase domain containing 16B	protein-coding
mm_80374.1	chr9	75408055	75408079	+	1	NA	intron (NM_015806, intron 1 of 5)	intron (NM_015806, intron 1 of 5)	1292	NM_027418	50772	Mm.480076	NM_015806	ENSMUSG00000042688	Mapk6	2610021I23Rik|D130053K17Rik|Erk3|Mapk4|Mapk63|Prkm4|Prkm6	mitogen-activated protein kinase 6	protein-coding
mm_105756.1	chr11	109473221	109473278	-	1	NA	promoter-TSS (NM_028710)	promoter-TSS (NM_028710)	-20	NM_134038	104681	Mm.265874	NM_134038	ENSMUSG00000041920	Slc16a6	AW743111|ESTM12|MCT 6|MCT 7|MCT6	solute carrier family 16 (monocarboxylic acid transporters), member 6	protein-coding
mm_61118.1	chr7	54835793	54835801	+	1	NA	5' UTR (NM_178705, exon 1 of 12)	5' UTR (NM_178705, exon 1 of 12)	552	NM_178705	233271	Mm.387344	NM_178705	ENSMUSG00000063297	Luzp2	9330154K17Rik|D130073E01	leucine zipper protein 2	protein-coding
mm_76830.1	chr8	104641667	104641736	-	1	NA	promoter-TSS (NM_026753)	promoter-TSS (NM_026753)	27	NM_026753	68523	Mm.279	NM_026753	ENSMUSG00000031879	Fam96b	1110019N10Rik	family with sequence similarity 96, member B	protein-coding
mm_50655.1	chr6	51470495	51470497	+	1	NA	promoter-TSS (NM_007624)	promoter-TSS (NM_007624)	-120	NM_007624	12417	Mm.280968	NM_007624	ENSMUSG00000029836	Cbx3	HP1g|M32	chromobox 3	protein-coding
mm_81921.1	chr9	120127780	120127793	+	1	NA	promoter-TSS (NM_011029)	promoter-TSS (NM_011029)	20	NM_011029	16785	Mm.4071	NM_011029	ENSMUSG00000032518	Rpsa	67kDa|67lr|AL022858|Lamr|Lamr1|Lamrl1|MLR|P40|P40-3|P40-8	ribosomal protein SA	protein-coding
mm_18919.1	chr2	76740812	76740823	-	1	NA	exon (NM_011652, exon 275 of 313)	exon (NM_011652, exon 275 of 313)	65502	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_7803.1	chr1	131525837	131525847	-	1	NA	intron (NM_001081011, intron 1 of 22)	CpG	1519	NM_001081011	14270	Mm.276259	NM_019520	ENSMUSG00000026425	Srgap2	9930124L22Rik|AI448945|FBP2|Fnbp2|srGAP3	SLIT-ROBO Rho GTPase activating protein 2	protein-coding
mm_73541.1	chr8	108704262	108704283	+	1	NA	Intergenic	Intergenic	-10372	NM_007496	11906	Mm.416972	NM_007496	ENSMUSG00000038872	Zfhx3	A230102L03Rik|Atbf1|Sci|WBP9|mKIAA4228	zinc finger homeobox 3	protein-coding
mm_63207.1	chr7	126248365	126248375	+	1	NA	promoter-TSS (NR_131046)	promoter-TSS (NR_131046)	-132	NR_131046	76728	Mm.76920	NR_131046	ENSMUSG00000108676	1700123J17Rik	-	RIKEN cDNA 1700123J17 gene	ncRNA
mm_138624.1	chr17	35841604	35841659	+	1	NA	5' UTR (NM_001010833, exon 1 of 16)	5' UTR (NM_001010833, exon 1 of 16)	133	NM_001010833	240087	Mm.218511	NM_001010833	ENSMUSG00000061607	Mdc1	6820401C03|AA413496|Nfbd1|mKIAA0170	mediator of DNA damage checkpoint 1	protein-coding
mm_157439.1	chrX	38635096	38635148	-	1	NA	promoter-TSS (NM_021550)	promoter-TSS (NM_021550)	21	NM_021550	59048	Mm.441410	NM_021550	ENSMUSG00000048970	C1galt1c1	1500002I11Rik|AB030184|C1GalT2|C81205|Cosmc	C1GALT1-specific chaperone 1	protein-coding
mm_163583.1	chr13	34627756	34627759	+	1	NA	TTS (NM_025831)	TTS (NM_025831)	24924	NM_025831	66895	Mm.28943	NM_025831	ENSMUSG00000021411	Pxdc1	1300014I06Rik	PX domain containing 1	protein-coding
mm_9525.1	chr1	173767027	173767044	-	1	NA	promoter-TSS (NM_008329)	promoter-TSS (NM_008329)	-116	NM_008329	15951	Mm.261270	NM_008329	ENSMUSG00000073489	Ifi204	Ifi16|p204	interferon activated gene 204	protein-coding
mm_67619.1	chr7	83995317	83995320	-	1	NA	intron (NM_030728, intron 5 of 28)	intron (NM_030728, intron 5 of 28)	91187	NM_030728	80982	Mm.160389	NM_030728	ENSMUSG00000052353	Cemip	12H19.01.T7|6330404C01Rik|9930013L23Rik|AY007814|Kiaa1199	cell migration inducing protein, hyaluronan binding	protein-coding
mm_129000.1	chr15	74842597	74842609	-	1	NA	promoter-TSS (NM_001033229)	promoter-TSS (NM_001033229)	-960	NM_001033229	110115	Mm.322606	NM_001033229	ENSMUSG00000075604	Cyp11b1	AA389061|CPN1|Cyp11b|Cyp11b-1|FHI	cytochrome P450, family 11, subfamily b, polypeptide 1	protein-coding
mm_168864.1	chr12	30911568	30911570	-	1	NA	promoter-TSS (NM_013709)	promoter-TSS (NM_013709)	43	NM_021330	11431	Mm.359831	NM_021330	ENSMUSG00000044573	Acp1	4632432E04Rik|AI427468|Acp-1|LMW-PTP|Lmptp	acid phosphatase 1, soluble	protein-coding
mm_157076.1	chrX	8892939	8892956	-	1	NA	non-coding (NR_045448, exon 1 of 1)	non-coding (NR_045448, exon 1 of 1)	594	NR_045448	102941	Mm.41588	NM_175327	ENSMUSG00000052364	B630019K06Rik	AI843180	novel protein similar to F-box and leucine-rich repeat protein 17 (Fbxl17)	pseudo
mm_18741.1	chr2	73023863	73023871	-	1	NA	Intergenic	Intergenic	-43421	NM_001018042	20687	Mm.124328	NM_011450	ENSMUSG00000027109	Sp3	D130027J01Rik	trans-acting transcription factor 3	protein-coding
mm_64063.1	chr7	140856515	140856530	+	1	NA	promoter-TSS (NM_053194)	promoter-TSS (NM_053194)	-139	NM_018742	54399	Mm.155696	NM_018742	ENSMUSG00000025484	Bet1l	2610021K23Rik|Gs15	Bet1 golgi vesicular membrane trafficking protein like	protein-coding
mm_23269.1	chr3	51559770	51559781	+	1	NA	promoter-TSS (NR_033624)	promoter-TSS (NR_033624)	18	NR_033624	100039684	Mm.387178	NR_033624		5031434O11Rik	AI481280|Gm2370	RIKEN cDNA 5031434O11 gene	ncRNA
mm_98901.1	chr11	98022702	98022730	+	1	NA	promoter-TSS (NM_031173)	promoter-TSS (NM_031173)	-89	NM_001282978	12295	Mm.41252	NM_031173	ENSMUSG00000020882	Cacnb1	CAB1|Cchb1|Cchlb1	calcium channel, voltage-dependent, beta 1 subunit	protein-coding
mm_17011.1	chr2	18878457	18878460	-	1	NA	intron (NM_008845, intron 4 of 9)	A-rich|Low_complexity|Low_complexity	-76640	NR_131254	66774	Mm.87075	NR_131254	ENSMUSG00000097638	Carlr	4933439G12Rik|Carl	cardiac and apoptosis-related long non-coding RNA	ncRNA
mm_5960.1	chr1	56971763	56971781	-	1	NA	promoter-TSS (NM_139146)	promoter-TSS (NM_139146)	303	NR_024325	329160	Mm.419039	NR_024325	ENSMUSG00000087022	9130024F11Rik	B530002L08|EG329160	RIKEN cDNA 9130024F11 gene	ncRNA
mm_140186.1	chr17	81705121	81705146	+	1	NA	intron (NR_104580, intron 1 of 8)	intron (NR_104580, intron 1 of 8)	33254	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_109526.1	chr12	111538150	111538243	+	1	NA	promoter-TSS (NM_178041)	promoter-TSS (NM_178041)	95	NM_173363	217869	Mm.271222	NM_173363	ENSMUSG00000021282	Eif5	2810011H21Rik|D12Ertd549e	eukaryotic translation initiation factor 5	protein-coding
mm_34330.1	chr4	142089142	142089153	+	1	NA	Intergenic	Intergenic	-4843	NM_145402	214359	Mm.27587	NM_145402	ENSMUSG00000040616	Tmem51	BC003277	transmembrane protein 51	protein-coding
mm_121728.1	chr14	17172883	17172910	-	1	NA	Intergenic	CpG	67338	NR_144493	100417973		NR_144493		Pou5f1-rs6	Gm18927|Oct4P3|Otf3-rs6|Otf3f	POU domain, class 5, transcription factor 1, related sequence 6	pseudo
mm_57657.1	chr6	128486179	128486197	-	1	NA	intron (NM_007376, intron 32 of 35)	intron (NM_007376, intron 32 of 35)	40532	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_22780.1	chr3	21953184	21953192	+	1	NA	Intergenic	Intergenic	-123464	NM_030732	81004	Mm.202966	NM_030732	ENSMUSG00000027630	Tbl1xr1	8030499H02Rik|A630076E03Rik|AW539987|C21|C230089I12Rik|DC42|Ira1|TBLR1	transducin (beta)-like 1X-linked receptor 1	protein-coding
mm_31877.1	chr4	80910845	80910859	+	1	NA	5' UTR (NM_026821, exon 1 of 2)	5' UTR (NM_026821, exon 1 of 2)	166	NM_026821	52829	Mm.273986	NM_026821	ENSMUSG00000048706	Lurap1l	1110029A09Rik|AV077978|AV175137|D4Bwg0951e|WI-13707|bM350F23.1	leucine rich adaptor protein 1-like	protein-coding
mm_10721.1	chr2	22823506	22823538	+	1	NA	exon (NM_019456, exon 4 of 14)	exon (NM_019456, exon 4 of 14)	49195	NM_019456	54519	Mm.14255	NM_019456	ENSMUSG00000026786	Apbb1ip	9930118P07Rik|Prp48	amyloid beta (A4) precursor protein-binding, family B, member 1 interacting protein	protein-coding
mm_62113.1	chr7	96603475	96603513	+	1	NA	intron (NM_011858, intron 5 of 32)	intron (NM_011858, intron 5 of 32)	198055	NR_045874	791381	Mm.402112	NR_045874	ENSMUSG00000053049	Gm15413	ENSMUSG00000053049|OTTMUSG00000021246	predicted gene 15413	ncRNA
mm_156375.1	chrX	139671852	139671862	+	1	NA	exon (NM_023270, exon 7 of 7)	exon (NM_023270, exon 7 of 7)	-13139	NM_001081499	245638	Mm.275869	NM_001081499	ENSMUSG00000042473	Tbc1d8b	4921505D17Rik|9030605E16Rik	TBC1 domain family, member 8B	protein-coding
mm_101193.1	chr11	18885820	18885845	-	1	NA	intron (NM_001193271, intron 9 of 12)	intron (NM_001193271, intron 9 of 12)	133137	NM_001193271	17268	Mm.356578	NM_010789	ENSMUSG00000020160	Meis1	C530044H18Rik|Evi8	Meis homeobox 1	protein-coding
mm_99532.1	chr11	103192618	103192690	+	1	NA	intron (NM_019679, intron 12 of 26)	intron (NM_019679, intron 12 of 26)	15894	NM_001254724	69441	Mm.380648	NM_027082	ENSMUSG00000020940	1700023F06Rik	-	RIKEN cDNA 1700023F06 gene	protein-coding
mm_136916.1	chr17	13230211	13230214	+	1	NA	promoter-TSS (NM_001167913)	promoter-TSS (NM_001167913)	-51	NM_001167913	236574		NM_001167913	ENSMUSG00000073457	Smok2b	Gm1847|Smok+129	sperm motility kinase 2B	protein-coding
mm_32891.1	chr4	118964209	118964219	+	1	NA	exon (NM_133892, exon 3 of 7)	exon (NM_133892, exon 3 of 7)	2247	NM_133892	100470	Mm.26698	NM_133892	ENSMUSG00000024903	Lao1	AW990848	L-amino acid oxidase 1	protein-coding
mm_5135.1	chr1	9700394	9700412	-	1	NA	promoter-TSS (NM_001290397)	promoter-TSS (NM_001290397)	-194	NM_008651	17864	Mm.479	NM_008651	ENSMUSG00000025912	Mybl1	A-myb|G1-419-6|repro9	myeloblastosis oncogene-like 1	protein-coding
mm_45028.1	chr5	38771891	38771895	-	1	NA	intron (NM_013748, intron 5 of 18)	intron (NM_013748, intron 5 of 18)	-87067	NM_001081144	100515	Mm.38277	NM_001081144	ENSMUSG00000046572	Zfp518b	6820424L24Rik|AA410078|AI661722|Znf518b	zinc finger protein 518B	protein-coding
mm_48110.1	chr5	137109205	137109213	-	1	NA	Intergenic	PB1D10|SINE|Alu	6998	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_147412.1	chr18	45559326	45559339	-	1	NA	promoter-TSS (NM_080465)	promoter-TSS (NM_080465)	-822	NM_080465	140492	Mm.411614	NM_080465	ENSMUSG00000054477	Kcnn2	KCa2.2|SK2|SKCA2|bc|fri	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2	protein-coding
mm_126919.1	chr15	91641922	91641940	+	1	NA	Intergenic	Intergenic	-31293	NM_025730	66725	Mm.37558	NM_025730	ENSMUSG00000036273	Lrrk2	4921513O20Rik|9330188B09Rik|AW561911|D630001M17Rik|Gm927|cI-46	leucine-rich repeat kinase 2	protein-coding
mm_109352.1	chr12	109608869	109608882	+	1	NA	intron (NR_028261, intron 2 of 20)	intron (NR_028261, intron 2 of 20)	-2625	NR_029770	723846		NR_029770	ENSMUSG00000070101	Mir341	Mirn341|mmu-mir-341	microRNA 341	ncRNA
mm_168147.1	chr10	35711873	35711892	-	1	NA	Intergenic	Intergenic	-794925	NM_001253355	319415	Mm.332442	NM_001081208	ENSMUSG00000044499	Hs3st5	D930005L05Rik|Gm1151|Hs3ost5	heparan sulfate (glucosamine) 3-O-sulfotransferase 5	protein-coding
mm_99444.1	chr11	102433319	102433329	+	1	NA	exon (NM_008175, exon 3 of 13)	exon (NM_008175, exon 3 of 13)	3002	NM_008175	14824	Mm.1568	NM_008175	ENSMUSG00000034708	Grn	Pgrn|epithelin	granulin	protein-coding
mm_118467.1	chr14	11553556	11553564	+	1	NA	promoter-TSS (NM_008981)	promoter-TSS (NM_008981)	7	NM_008981	19270	Mm.431266	NM_008981	ENSMUSG00000021745	Ptprg	5430405N12Rik|AW046354|AW549872|RPTPgamma	protein tyrosine phosphatase, receptor type, G	protein-coding
mm_122204.1	chr14	31781914	31781935	-	1	NA	intron (NM_001024604, intron 1 of 27)	intron (NM_001024604, intron 1 of 27)	48491	NM_001024604	105522	Mm.37660	NM_001024604	ENSMUSG00000014496	Ankrd28	AI465466|AI604979|E430019N21Rik|mKIAA0379	ankyrin repeat domain 28	protein-coding
mm_126212.1	chr15	78899784	78899815	+	1	NA	promoter-TSS (NM_009164)	promoter-TSS (NM_009164)	31	NM_009164	20401	Mm.4462	NM_009164	ENSMUSG00000022436	Sh3bp1	3BP-1	SH3-domain binding protein 1	protein-coding
mm_119923.1	chr14	54964006	54964019	+	1	NA	exon (NM_010856, exon 4 of 39)	exon (NM_010856, exon 4 of 39)	2595	NM_001164171	17888	Mm.290003	NM_010856	ENSMUSG00000040752	Myh6	A830009F23Rik|AA517445|Myhc-a|Myhca|alpha-MHC	myosin, heavy polypeptide 6, cardiac muscle, alpha	protein-coding
mm_109805.1	chr12	3309913	3309975	-	1	NA	promoter-TSS (NM_016676)	promoter-TSS (NM_016676)	25	NM_016676	19325	Mm.378993	NM_016676	ENSMUSG00000020671	Rab10	AW107754	RAB10, member RAS oncogene family	protein-coding
mm_12350.1	chr2	69749263	69749273	+	1	NA	intron (NM_001081086, intron 13 of 13)	intron (NM_001081086, intron 13 of 13)	26180	NM_001081086	228005	Mm.11815	NM_001081086	ENSMUSG00000042133	Ppig	AU019516|AU022200|B230312B02Rik|CYP|SRCyp	peptidyl-prolyl isomerase G (cyclophilin G)	protein-coding
mm_22404.1	chr2	181242021	181242048	-	1	NA	promoter-TSS (NM_183162)	promoter-TSS (NM_183162)	-7	NM_183162	229003	Mm.315872	NM_183162	ENSMUSG00000027580	Helz2	PDIP1|Pric285|mKIAA1769|mPDIP1	helicase with zinc finger 2, transcriptional coactivator	protein-coding
mm_88006.1	chr10	67096457	67096534	+	1	NA	intron (NM_178606, intron 1 of 7)	CpG	493	NM_001204915	28193	Mm.41272	NM_178606	ENSMUSG00000019873	Reep3	D10Ucla1	receptor accessory protein 3	protein-coding
mm_119492.1	chr14	47378128	47378143	+	1	NA	intron (NM_001145953, intron 1 of 5)	B1F|SINE|Alu	4275	NM_001145953	16854	Mm.248615	NM_010705	ENSMUSG00000050335	Lgals3	GBP|L-34|Mac-2|gal3	lectin, galactose binding, soluble 3	protein-coding
mm_119341.1	chr14	41072906	41072922	+	1	NA	promoter-TSS (NM_027094)	promoter-TSS (NM_027094)	3	NM_027094	69496	Mm.55734	NM_027094	ENSMUSG00000021790	Dydc1	1700029M23Rik	DPY30 domain containing 1	protein-coding
mm_48768.1	chr5	148399874	148399889	-	1	NA	promoter-TSS (NM_007513)	promoter-TSS (NM_007513)	23	NM_007513	11987	Mm.275489	NM_007513	ENSMUSG00000041313	Slc7a1	4831426K01Rik|AI447493|Atrc-1|Atrc1|Cat1|Rec-1|Rev-1|mCAT-1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 1	protein-coding
mm_50489.1	chr6	48988795	48988807	+	1	NA	exon (NM_172888, exon 1 of 5)	exon (NM_172888, exon 1 of 5)	1940	NM_172888	243377	Mm.446302	NM_172888	ENSMUSG00000039215	Svs1	9530003A11	seminal vesicle secretory protein 1	protein-coding
mm_39851.1	chr5	30913575	30913585	+	1	NA	promoter-TSS (NM_133918)	promoter-TSS (NM_133918)	-206	NM_133918	100952	Mm.286375	NM_133918	ENSMUSG00000029163	Emilin1	5830419M17Rik|AW229038|BB105748|EMILIN-1|gp115	elastin microfibril interfacer 1	protein-coding
mm_153771.1	chr19	45660497	45660520	-	1	NA	promoter-TSS (NM_013907)	promoter-TSS (NM_013907)	-315	NM_013907	30838	Mm.254739	NM_013907	ENSMUSG00000040913	Fbxw4	Dac|Fbw4|SHFM3|SHSF3|dactylin|dactylyn	F-box and WD-40 domain protein 4	protein-coding
mm_147936.1	chr18	66022491	66022505	-	1	NA	Intergenic	Intergenic	-19863	NM_001172062	70361	Mm.290857	NM_027400	ENSMUSG00000041891	Lman1	2610020P13Rik|AI326273|AU043785|C730041J05|ERGIC53|F5F8D|MCFD1|MR60|P58|gp58	lectin, mannose-binding, 1	protein-coding
mm_72739.1	chr8	85085433	85085449	+	1	NA	exon (NM_010764, exon 4 of 24)	exon (NM_010764, exon 4 of 24)	2172	NM_010764	17159	Mm.4219	NM_010764	ENSMUSG00000005142	Man2b1	AW107687|LAMAN	mannosidase 2, alpha B1	protein-coding
mm_138564.1	chr17	35343173	35343190	+	1	NA	exon (NM_010392, exon 3 of 7)	exon (NM_010392, exon 3 of 7)	848	NM_010392	15013	Mm.427969	NM_010392	ENSMUSG00000091705	H2-Q2	BE136769|ENSMUSG00000079507|Gm11132|H-2Q2|gs14-2	histocompatibility 2, Q region locus 2	protein-coding
mm_144292.1	chr18	12158858	12158867	+	1	NA	Intergenic	Intergenic	-9868	NM_029623	76482	Mm.196596	NM_029623	ENSMUSG00000024410	3110002H16Rik	2400010D15Rik|Mic-1|Mic1	RIKEN cDNA 3110002H16 gene	protein-coding
mm_19943.1	chr2	116067392	116067409	-	1	NA	promoter-TSS (NM_001346047)	promoter-TSS (NM_001346047)	44	NM_001346047	17536	Mm.247566	NM_010825	ENSMUSG00000027210	Meis2	A430109D20Rik|Mrg1|Stra10	Meis homeobox 2	protein-coding
mm_813.1	chr1	45860607	45860613	+	1	NA	Intergenic	Intergenic	64984	NM_016917	53945	Mm.28756	NM_016917	ENSMUSG00000025993	Slc40a1	Dusg|Fpn1|IREG1|MTP|MTP1|Ol5|Pcm|Slc11a3|Slc39a1	solute carrier family 40 (iron-regulated transporter), member 1	protein-coding
mm_3252.1	chr1	136145229	136145235	+	1	NA	exon (NM_001039472, exon 3 of 35)	exon (NM_001039472, exon 3 of 35)	13831	NM_001039472	16565	Mm.276135	NM_019962	ENSMUSG00000041642	Kif21b	2610511N21Rik|mKIAA0449	kinesin family member 21B	protein-coding
mm_99307.1	chr11	101376635	101376643	+	1	NA	exon (NM_008061, exon 5 of 5)	exon (NM_008061, exon 5 of 5)	8923	NM_008061	14377	Mm.18064	NM_008061	ENSMUSG00000078650	G6pc	AW107337|G6Pase|G6pt|Glc-6-Pase	glucose-6-phosphatase, catalytic	protein-coding
mm_125378.1	chr15	40654995	40655004	+	1	NA	promoter-TSS (NM_011766)	promoter-TSS (NM_011766)	-43	NM_011766	22762	Mm.39496	NM_011766	ENSMUSG00000022306	Zfpm2	B330005D23Rik|FOG-2|FOG2	zinc finger protein, multitype 2	protein-coding
mm_20390.1	chr2	129055811	129055817	-	1	NA	Intergenic	Intergenic	-10133	NM_027192	69737	Mm.33909	NM_027192	ENSMUSG00000027394	Ttl	2410003M22Rik|2700049H19Rik|AI848570	tubulin tyrosine ligase	protein-coding
mm_48608.1	chr5	144357993	144358001	-	1	NA	promoter-TSS (NR_102374)	promoter-TSS (NR_102374)	74	NR_102374	100579137		NR_102372	ENSMUSG00000104600	Dmrt1i	Dmr	Dmrt1 interacting ncRNA	ncRNA
mm_120560.1	chr14	68120822	68120915	+	1	NA	exon (NM_008691, exon 3 of 3)	exon (NM_008691, exon 3 of 3)	-2884	NR_045897	100043072	Mm.242832	NR_045897		A230070E04Rik	Gm4210	RIKEN cDNA A230070E04 gene	ncRNA
mm_107795.1	chr12	62687787	62687814	+	1	NA	promoter-TSS (NR_131949)	promoter-TSS (NR_131949)	13	NR_131949	73309	Mm.276558	NR_131949		Spanxn4	1700047L15Rik	SPANX family, member N4	ncRNA
mm_35687.1	chr4	44067045	44067061	-	1	NA	intron (NM_015828, intron 1 of 11)	intron (NM_015828, intron 1 of 11)	5620	NM_001190414	50798	Mm.256718	NM_015828	ENSMUSG00000028479	Gne	2310066H07Rik|DMRV|GLCNE|IBM2|NM|Uae1	glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase	protein-coding
mm_127246.1	chr15	99601373	99601382	+	1	NA	promoter-TSS (NM_175087)	promoter-TSS (NM_175087)	-23	NM_175087	11831	Mm.202309	NM_175087	ENSMUSG00000043144	Aqp6	AI790337	aquaporin 6	protein-coding
mm_169307.1	chr14	104715862	104715875	-	1	NA	intron (NR_015593, intron 1 of 5)	LSU-rRNA_Hsa|rRNA|rRNA	76721	NR_015593	320249	Mm.320725	NR_015593		D130009I18Rik	-	RIKEN cDNA D130009I18 gene	ncRNA
mm_164450.1	chr16	49913716	49913756	+	1	NA	Intergenic	Intergenic	58082	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_112493.1	chr13	6559388	6559427	+	1	NA	exon (NM_145131, exon 10 of 27)	exon (NM_145131, exon 10 of 27)	11250	NM_145131	69617	Mm.41933	NM_145131	ENSMUSG00000021193	Pitrm1	2310012C15Rik|AA410010|MP-1|MP1|Ntup1|PreP|mKIAA1104	pitrilysin metallepetidase 1	protein-coding
mm_89579.1	chr10	95730284	95730303	+	1	NA	Intergenic	LTR72_RN|LTR|ERV1	-166126	NM_027722	71207	Mm.24397	NM_027722	ENSMUSG00000020029	Nudt4	4933436C10Rik|DIPP2|DIPP2alpha|DIPP2beta|HDCMB47P	nudix (nucleoside diphosphate linked moiety X)-type motif 4	protein-coding
mm_65599.1	chr7	27355945	27355977	-	1	NA	promoter-TSS (NM_138676)	promoter-TSS (NM_138676)	47	NM_138676	192192	Mm.21297	NM_138676	ENSMUSG00000089832	Shkbp1	B930062H15Rik|Sb1	Sh3kbp1 binding protein 1	protein-coding
mm_36310.1	chr4	69758476	69758481	-	1	NA	Intergenic	Intergenic	651957	NM_001313762	214444	Mm.370777	NM_145990	ENSMUSG00000039298	Cdk5rap2	2900018K03Rik|an|mKIAA1633	CDK5 regulatory subunit associated protein 2	protein-coding
mm_151688.1	chr19	4318696	4318710	-	1	NA	3' UTR (NM_001001984, exon 21 of 21)	3' UTR (NM_001001984, exon 21 of 21)	-12481	NM_001290818	110355	Mm.254144	NM_130863	ENSMUSG00000024858	Grk2	Adrbk-1|Adrbk1|Bark-1|beta ARK|betaARK1	G protein-coupled receptor kinase 2	protein-coding
mm_111348.1	chr12	86897018	86897028	-	1	NA	Intergenic	Intergenic	-12209	NM_145836	238330	Mm.248358	NM_145836	ENSMUSG00000034168	Irf2bpl	6430527G18Rik|Eap1	interferon regulatory factor 2 binding protein-like	protein-coding
mm_61030.1	chr7	49523847	49523863	+	1	NA	intron (NM_175272, intron 11 of 37)	intron (NM_175272, intron 11 of 37)	112980	NM_001005232	13172	Mm.307176	NM_001005232	ENSMUSG00000030507	Dbx1	AI426026|Dbx	developing brain homeobox 1	protein-coding
mm_27752.1	chr3	69596243	69596246	-	1	NA	intron (NM_020026, intron 1 of 2)	ORR1A4|LTR|ERVL-MaLR	2716	NM_020026	26879	Mm.153710	NM_020026	ENSMUSG00000043300	B3galnt1	B3galt3|b3GT3	UDP-GalNAc:betaGlcNAc beta 1,3-galactosaminyltransferase, polypeptide 1	protein-coding
mm_167877.1	chrX	37804761	37804778	+	1	NA	intron (NM_008818, intron 1 of 4)	intron (NM_008818, intron 1 of 4)	-22286	NM_008955	19202	Mm.10105	NM_008955	ENSMUSG00000006200	Rhox6	AV213605|AW548842|Psx1	reproductive homeobox 6	protein-coding
mm_92300.1	chr10	74863510	74863513	-	1	NA	Intergenic	Intergenic	-103720	NM_010311	14687	Mm.32595	NM_010311	ENSMUSG00000040009	Gnaz	AI847979|Gz	guanine nucleotide binding protein, alpha z subunit	protein-coding
mm_28683.1	chr3	95357218	95357244	-	1	NA	promoter-TSS (NM_001163642)	promoter-TSS (NM_001163642)	-29	NM_001163642	84505	Mm.490259	NM_018877	ENSMUSG00000015697	Setdb1	AU022152|ESET|KMT1E|mKIAA0067	SET domain, bifurcated 1	protein-coding
mm_26580.1	chr3	147399090	147399093	+	1	NA	Intergenic	Intergenic	546724	NM_001302958	70892	Mm.187793	NM_027594	ENSMUSG00000036745	Ttll7	1110049N09Rik|4921517B04Rik|C630030B20|mTTLL7	tubulin tyrosine ligase-like family, member 7	protein-coding
mm_104937.1	chr11	100105639	100105645	-	1	NA	promoter-TSS (NM_001174099)	promoter-TSS (NM_001174099)	-16	NM_001174099	16673	Mm.306829	NM_008472	ENSMUSG00000020916	Krt36	HRa-1|K36|Krt1-22|Krt1-5|MHRa-1	keratin 36	protein-coding
mm_54072.1	chr6	14755087	14755095	-	1	NA	exon (NM_080464, exon 1 of 4)	exon (NM_080464, exon 1 of 4)	183	NM_080464	140491	Mm.209429	NM_080464	ENSMUSG00000042717	Ppp1r3a	GM|RG1|RGL	protein phosphatase 1, regulatory (inhibitor) subunit 3A	protein-coding
mm_102181.1	chr11	54028790	54028803	-	1	NA	promoter-TSS (NM_001330304)	promoter-TSS (NM_001330304)	-692	NM_001330304	30805	Mm.274590	NM_019687	ENSMUSG00000020334	Slc22a4	Octn1	solute carrier family 22 (organic cation transporter), member 4	protein-coding
mm_113303.1	chr13	30749529	30749576	+	1	NA	intron (NM_001347508, intron 1 of 8)	intron (NM_001347508, intron 1 of 8)	319	NM_013674	16364	Mm.4677	NM_013674	ENSMUSG00000021356	Irf4	AI385587|IRF-4|LSIRF|NF-EM5|Spip	interferon regulatory factor 4	protein-coding
mm_43322.1	chr5	134986303	134986323	+	1	NA	promoter-TSS (NM_009902)	promoter-TSS (NM_009902)	99	NM_009902	12739	Mm.158662	NM_009902	ENSMUSG00000070473	Cldn3	AI182374|Cpetr2|mRVP1	claudin 3	protein-coding
mm_83759.1	chr9	51956934	51956936	-	1	NA	intron (NM_001301728, intron 2 of 3)	intron (NM_001301728, intron 2 of 3)	6667	NM_007996	14148	Mm.1061	NM_007996	ENSMUSG00000032051	Fdx1	-	ferredoxin 1	protein-coding
mm_164325.1	chr16	5608214	5608214	+	1	NA	Intergenic	Intergenic	-276579	NM_021477	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_68835.1	chr7	126285408	126285418	-	1	NA	intron (NM_145587, intron 1 of 3)	intron (NM_145587, intron 1 of 3)	12794	NM_145587	104175	Mm.29660	NM_145587	ENSMUSG00000042978	Sbk1	Sbk	SH3-binding kinase 1	protein-coding
mm_4309.1	chr1	171844431	171844471	+	1	NA	intron (NM_001289470, intron 2 of 8)	intron (NM_001289470, intron 2 of 8)	4754	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_34373.1	chr4	144893483	144893512	+	1	NA	5' UTR (NM_011303, exon 1 of 6)	5' UTR (NM_011303, exon 1 of 6)	360	NM_011303	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding
mm_167845.1	chrX	5824089	5824090	+	1	NA	Intergenic	L1_Mur3|LINE|L1	155022	NM_001085523	434725	Mm.457958	NM_001085523	ENSMUSG00000095814	Btbd35f7	Gm14374|OTTMUSG00000016453	BTB domain containing 35, family member 7	protein-coding
mm_1475.1	chr1	70725815	70725830	+	1	NA	TTS (NM_025728)	TTS (NM_025728)	107	NM_001310658	320460	Mm.360649	NM_177164	ENSMUSG00000045648	Vwc2l	A830006F12Rik|Brl	von Willebrand factor C domain-containing protein 2-like	protein-coding
mm_55121.1	chr6	50456086	50456174	-	1	NA	promoter-TSS (NM_001163645)	promoter-TSS (NM_001163645)	40	NM_001163645	71720	Mm.44153	NM_027881	ENSMUSG00000029822	Osbpl3	1200014M06Rik|6720421I08Rik|A530055M08|ORP-3|ORP3|OSBP3	oxysterol binding protein-like 3	protein-coding
mm_99181.1	chr11	100860293	100860302	+	1	NA	promoter-TSS (NM_001164062)	promoter-TSS (NM_001164062)	-187	NM_001164062	20850	Mm.277403	NM_011488	ENSMUSG00000004043	Stat5a	AA959963|STAT5	signal transducer and activator of transcription 5A	protein-coding
mm_138800.1	chr17	37995894	37995913	+	1	NA	Intergenic	Intergenic	-42881	NM_001011829	258094	Mm.377348	NM_001011829	ENSMUSG00000109376	Olfr761	MOR218-12|MOR218-5P|MOR218-6P|Olfr1552-ps1	olfactory receptor 761	protein-coding
mm_62822.1	chr7	113419736	113419738	+	1	NA	Intergenic	RMER17C|LTR|ERVK	-31164	NM_020623	19226	Mm.284168	NM_020623	ENSMUSG00000059077	Pth	Pthp	parathyroid hormone	protein-coding
mm_19335.1	chr2	90580439	90580461	-	1	NA	exon (NM_008982, exon 1 of 24)	exon (NM_008982, exon 1 of 24)	197	NM_008982	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_69888.1	chr7	141637209	141637225	-	1	NA	intron (NM_001330001, intron 31 of 33)	intron (NM_001330001, intron 31 of 33)	16516	NR_106030	102466798		NR_106030	ENSMUSG00000098759	Mir7063	Gm27654|mmu-mir-7063	microRNA 7063	ncRNA
mm_63210.1	chr7	126272445	126272455	+	1	NA	promoter-TSS (NM_145587)	promoter-TSS (NM_145587)	-169	NM_145587	104175	Mm.29660	NM_145587	ENSMUSG00000042978	Sbk1	Sbk	SH3-binding kinase 1	protein-coding
mm_109100.1	chr12	105019497	105019506	+	1	NA	Intergenic	Intergenic	-9692	NM_172500	212073	Mm.212688	NM_172500	ENSMUSG00000054150	Syne3	nesprin-3	spectrin repeat containing, nuclear envelope family member 3	protein-coding
mm_36562.1	chr4	87227591	87227596	-	1	NA	exon (NM_001110240, exon 1 of 10)	exon (NM_001110240, exon 1 of 10)	370	NM_001110240	76376	Mm.490487	NM_172426	ENSMUSG00000037996	Slc24a2	2810021B17Rik|6330417K15Rik|AI847460|Nckx2	solute carrier family 24 (sodium/potassium/calcium exchanger), member 2	protein-coding
mm_34560.1	chr4	149647882	149647913	+	1	NA	3' UTR (NM_023051, exon 19 of 19)	3' UTR (NM_023051, exon 19 of 19)	7670	NR_105990	102465983		NR_105990	ENSMUSG00000098580	Mir7023	Gm27912|mmu-mir-7023	microRNA 7023	ncRNA
mm_121425.1	chr14	120303322	120303347	+	1	NA	intron (NM_175341, intron 1 of 8)	intron (NM_175341, intron 1 of 8)	27665	NM_175341	105559	Mm.238266	NM_175341	ENSMUSG00000022139	Mbnl2	1110002M11Rik|AI047808|AI837313|AI849185|AL118326|MBLL|R75232|mKIAA4072	muscleblind-like 2	protein-coding
mm_30675.1	chr4	11165260	11165286	+	1	NA	exon (NM_001199105, exon 3 of 5)	exon (NM_001199105, exon 3 of 5)	8832	NM_021897	60599	Mm.393018	NM_021897	ENSMUSG00000028211	Trp53inp1	2700057G22Rik|SIP|SIP18|SIP27|Stinp|Teap	transformation related protein 53 inducible nuclear protein 1	protein-coding
mm_41234.1	chr5	88758638	88758642	+	1	NA	TTS (NM_026735)	TTS (NM_026735)	-6373	NM_007832	13178	Mm.298892	NM_007832	ENSMUSG00000029366	Dck	-	deoxycytidine kinase	protein-coding
mm_26720.1	chr3	159495409	159495438	+	1	NA	promoter-TSS (NM_001172093)	promoter-TSS (NM_001172093)	-10	NM_001172092	76131	Mm.371655	NM_029523	ENSMUSG00000028175	Depdc1a	5830484J08Rik|Depdc1	DEP domain containing 1a	protein-coding
mm_83532.1	chr9	46230341	46230349	-	1	NA	exon (NM_009692, exon 4 of 4)	exon (NM_009692, exon 4 of 4)	1715	NM_009692	11806	Mm.26743	NM_009692	ENSMUSG00000032083	Apoa1	Alp-1|Apoa-1|Brp-14|Ltw-1|Lvtw-1|Sep-1|Sep-2|Sep2|apo-AI|apoA-I	apolipoprotein A-I	protein-coding
mm_22477.1	chr3	5219026	5219036	+	1	NA	intron (NM_030708, intron 1 of 10)	intron (NM_030708, intron 1 of 10)	477	NM_030708	80892	Mm.41522	NM_030708	ENSMUSG00000025255	Zfhx4	A930021B15|C130041O22Rik|Zfh-4|Zfh4	zinc finger homeodomain 4	protein-coding
mm_139452.1	chr17	55750030	55750046	+	1	NA	promoter-TSS (NM_139138)	promoter-TSS (NM_139138)	54	NM_139138	52614	Mm.210497	NM_139138	ENSMUSG00000032915	Adgre4	D17Ertd479e|Egf-tm7|Emr4|Fire|Gpr127	adhesion G protein-coupled receptor E4	protein-coding
mm_62214.1	chr7	97919972	97919991	+	1	NA	promoter-TSS (NM_177696)	promoter-TSS (NM_177696)	23	NM_177696	233537	Mm.375772	NM_177696	ENSMUSG00000035582	Gdpd4	4921513O04	glycerophosphodiester phosphodiesterase domain containing 4	protein-coding
mm_39744.1	chr5	29569450	29569459	+	1	NA	5' UTR (NM_133907, exon 1 of 23)	5' UTR (NM_133907, exon 1 of 23)	212	NM_133907	100763	Mm.137746	NM_133907	ENSMUSG00000039000	Ube3c	AI853514|mKIAA0010	ubiquitin protein ligase E3C	protein-coding
mm_104441.1	chr11	94976349	94976359	-	1	NA	promoter-TSS (NM_009161)	promoter-TSS (NM_009161)	-27	NM_009161	20391	Mm.18709	NM_009161	ENSMUSG00000001508	Sgca	50DAG|Asg	sarcoglycan, alpha (dystrophin-associated glycoprotein)	protein-coding
mm_149114.1	chr19	8967065	8967077	+	1	NA	promoter-TSS (NM_026007)	promoter-TSS (NM_026007)	30	NM_026007	67160	Mm.247762	NM_026007	ENSMUSG00000071644	Eef1g	2610301D06Rik|AA407312|EF1G	eukaryotic translation elongation factor 1 gamma	protein-coding
mm_62049.1	chr7	92402699	92402706	+	1	NA	intron (NM_011807, intron 16 of 22)	intron (NM_011807, intron 16 of 22)	-158447	NM_025515	66365	Mm.21173	NM_025515	ENSMUSG00000030613	Ccdc90b	2310015N07Rik|C86558	coiled-coil domain containing 90B	protein-coding
mm_26781.1	chr3	9004687	9004750	-	1	NA	promoter-TSS (NM_009412)	promoter-TSS (NM_009412)	-203	NM_001025264	21985	Mm.371590	NM_009412	ENSMUSG00000027506	Tpd52	AI043038|mD52	tumor protein D52	protein-coding
mm_46550.1	chr5	106614308	106614311	-	1	NA	Intergenic	Intergenic	82521	NM_026856	52397	Mm.249474	NM_026856	ENSMUSG00000049606	Zfp644	1110068L01Rik|AA408882|BM-005|D5Ertd689e|Zep-2	zinc finger protein 644	protein-coding
mm_134744.1	chr16	23098018	23098021	-	1	NA	Intergenic	LTRIS2|LTR|ERV1	-9378	NM_001347179	13682	Mm.260084	NM_013506	ENSMUSG00000022884	Eif4a2	4833432N07Rik|BM-010|Ddx2b|Eif4|eIF-4A-II|eIF4A-II	eukaryotic translation initiation factor 4A2	protein-coding
mm_62702.1	chr7	110237740	110237741	+	1	NA	intron (NM_009302, intron 1 of 11)	intron (NM_009302, intron 1 of 11)	16037	NM_009302	20947	Mm.334144	NM_009302	ENSMUSG00000031015	Swap70	70kDa|AV235546	SWA-70 protein	protein-coding
mm_86.1	chr1	7088918	7088993	+	1	NA	promoter-TSS (NM_183028)	promoter-TSS (NM_183028)	35	NM_183028	319263	Mm.21539	NM_183028	ENSMUSG00000051285	Pcmtd1	8430411F12Rik|A030012M09Rik	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding
mm_154702.1	chrX	8271681	8271790	+	1	NA	intron (NM_172479, intron 1 of 15)	intron (NM_172479, intron 1 of 15)	354	NM_172479	209837	Mm.6055	NM_172479	ENSMUSG00000031170	Slc38a5	C81234|E330031E14|JM24|SN2	solute carrier family 38, member 5	protein-coding
mm_108231.1	chr12	77239037	77239074	+	1	NA	non-coding (NR_045554, exon 1 of 12)	non-coding (NR_045554, exon 1 of 12)	316	NR_045554	53618	Mm.35628	NM_016893	ENSMUSG00000021065	Fut8	-	fucosyltransferase 8	protein-coding
mm_173269.1	chrX	95956885	95956885	-	1	NA	promoter-TSS (NM_152822)	promoter-TSS (NM_152822)	89	NM_152822	76130	Mm.274318	NM_152822	ENSMUSG00000057421	Las1l	1810030A06Rik|5830482G23Rik	LAS1-like (S. cerevisiae)	protein-coding
mm_96676.1	chr11	69411966	69411986	+	1	NA	intron (NM_001017426, intron 1 of 22)	intron (NM_001017426, intron 1 of 22)	1699	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_43113.1	chr5	124579116	124579124	+	1	NA	promoter-TSS (NM_145371)	promoter-TSS (NM_145371)	11	NM_145371	209354	Mm.28839	NM_145371	ENSMUSG00000029388	Eif2b1	D5Ertd406e|EIF2BA	eukaryotic translation initiation factor 2B, subunit 1 (alpha)	protein-coding
mm_36570.1	chr4	87829520	87829524	-	1	NA	intron (NM_027326, intron 5 of 10)	intron (NM_027326, intron 5 of 10)	-23199	NM_029931	70122	Mm.288898	NM_027326	ENSMUSG00000028496	Mllt3	2210011H10Rik|2610012I03Rik|3830408D16Rik|Af9|D4Ertd321e	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 3	protein-coding
mm_170534.1	chr1	93845624	93845624	-	1	NA	intron (NM_178882, intron 8 of 9)	L1Md_T|LINE|L1	-15720	NM_199366	381334	Mm.482878	NM_199366	ENSMUSG00000094651	Gal3st2	GP3ST|Gm988	galactose-3-O-sulfotransferase 2	protein-coding
mm_90707.1	chr10	130544776	130544780	+	1	NA	Intergenic	RMER16B2|LTR|ERVK	-47399	NM_001103366	625131	Mm.469844	NM_001103366	ENSMUSG00000091511	Vmn2r87	EG625131	vomeronasal 2, receptor 87	protein-coding
mm_169670.1	chr15	62770874	62770874	-	1	NA	Intergenic	L1Md_Gf|LINE|L1	-551423	NR_003523	67552	Mm.484027	NM_026230		H2afy3	4933432H23Rik	H2A histone family, member Y3	pseudo
mm_90724.1	chr10	5185527	5185546	-	1	NA	exon (NM_001079686, exon 4 of 55)	exon (NM_001079686, exon 4 of 55)	9171	NM_001079686	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_86218.1	chr9	120068293	120068301	-	1	NA	promoter-TSS (NM_009987)	promoter-TSS (NM_009987)	-1	NM_009987	13051	Mm.44065	NM_009987	ENSMUSG00000052336	Cx3cr1	-	chemokine (C-X3-C motif) receptor 1	protein-coding
mm_169723.1	chr15	79542535	79542539	-	1	NA	exon (NM_001040187, exon 3 of 13)	exon (NM_001040187, exon 3 of 13)	4022	NM_199079	67040	Mm.29644	NM_152806	ENSMUSG00000055065	Ddx17	2610007K22Rik|A430025E01Rik|AI047725|C80929|Gm926|p72	DEAD (Asp-Glu-Ala-Asp) box polypeptide 17	protein-coding
mm_33596.1	chr4	132568323	132568367	+	1	NA	intron (NM_001081211, intron 1 of 1)	PB1D7|SINE|Alu	4278	NM_001081211	19204	Mm.89389	NM_001081211	ENSMUSG00000056529	Ptafr	PAFR	platelet-activating factor receptor	protein-coding
mm_114335.1	chr13	60729381	60729385	+	1	NA	exon (NM_134062, exon 16 of 27)	exon (NM_134062, exon 16 of 27)	56981	NM_199148	218275	Mm.222427	NM_199148	ENSMUSG00000042243	BC051665	-	cDNA sequence BC051665	protein-coding
mm_84007.1	chr9	57644238	57644240	-	1	NA	intron (NM_001304761, intron 2 of 14)	intron (NM_001304761, intron 2 of 14)	1414	NM_007783	12988	Mm.21974	NM_007783	ENSMUSG00000032312	Csk	AW212630|p50CSK	c-src tyrosine kinase	protein-coding
mm_146308.1	chr18	80256336	80256347	+	1	NA	promoter-TSS (NM_025861)	promoter-TSS (NM_025861)	35	NM_001164423	66943	Mm.29247	NM_025861	ENSMUSG00000034006	Pqlc1	2310009N05Rik|4933425L21Rik|5730564E11Rik|C78974	PQ loop repeat containing 1	protein-coding
mm_30012.1	chr3	135665094	135665100	-	1	NA	intron (NM_008689, intron 3 of 24)	(TG)n|Simple_repeat|Simple_repeat	26450	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_126183.1	chr15	78615741	78615749	+	1	NA	exon (NM_028195, exon 9 of 13)	exon (NM_028195, exon 9 of 13)	18698	NM_028195	72318	Mm.32911	NM_028195	ENSMUSG00000018008	Cyth4	2510004M07Rik|5830469K17Rik|AI467541|Pscd4|mFLJ00017	cytohesin 4	protein-coding
mm_66050.1	chr7	30729469	30729501	-	1	NA	promoter-TSS (NM_027215)	promoter-TSS (NM_027215)	49	NM_027215	69804	Mm.27499	NM_027215	ENSMUSG00000006315	Tmem147	2010004E11Rik|5033425B17Rik|Nifie14	transmembrane protein 147	protein-coding
mm_18874.1	chr2	76240133	76240136	-	1	NA	intron (NM_001081033, intron 2 of 19)	B3|SINE|B2	98519	NM_001081033	241489	Mm.246613	NM_001081033	ENSMUSG00000075270	Pde11a	6330414F14Rik|A630086N24Rik|Gm350|PDE11A1	phosphodiesterase 11A	protein-coding
mm_116889.1	chr13	55321929	55321974	-	1	NA	promoter-TSS (NM_025596)	promoter-TSS (NM_025596)	29	NM_009000	19336	Mm.220923	NM_009000	ENSMUSG00000034789	Rab24	6530406O07Rik	RAB24, member RAS oncogene family	protein-coding
mm_148636.1	chr19	5474682	5474775	+	1	NA	promoter-TSS (NM_021474)	promoter-TSS (NM_021474)	-7	NM_001164352	58859	Mm.276367	NM_021474	ENSMUSG00000024909	Efemp2	0610011K11Rik|Fbln4|MBP1	epidermal growth factor-containing fibulin-like extracellular matrix protein 2	protein-coding
mm_5706.1	chr1	43521846	43521850	-	1	NA	intron (NM_010879, intron 2 of 4)	intron (NM_010879, intron 2 of 4)	76097	NM_010879	17974	Mm.389903	NM_010879	ENSMUSG00000066877	Nck2	4833426I10Rik|Grb4|NCKbeta|Nck-2	non-catalytic region of tyrosine kinase adaptor protein 2	protein-coding
mm_13506.1	chr2	109280810	109280863	+	1	NA	promoter-TSS (NM_139303)	promoter-TSS (NM_139303)	98	NM_139303	228421	Mm.274086	NM_139303	ENSMUSG00000027115	Kif18a	AU024633|B130001M12Rik|gcd2	kinesin family member 18A	protein-coding
mm_139848.1	chr17	69383769	69383789	+	1	NA	promoter-TSS (NM_009547)	promoter-TSS (NM_009547)	-199	NM_009547	22666	Mm.29434	NM_009547	ENSMUSG00000049672	Zbtb14	ZF5|Zfp161|b2b1982Clo	zinc finger and BTB domain containing 14	protein-coding
mm_37922.1	chr4	132794103	132794112	-	1	NA	intron (NM_001033308, intron 1 of 5)	intron (NM_001033308, intron 1 of 5)	2257	NM_001033308	230787	Mm.290912	NM_001033308	ENSMUSG00000037731	Themis2	ICB-1	thymocyte selection associated family member 2	protein-coding
mm_31699.1	chr4	62525619	62525622	+	1	NA	promoter-TSS (NM_021498)	promoter-TSS (NM_021498)	251	NM_177607	214106	Mm.73212	NM_177607	ENSMUSG00000058046	4933430I17Rik	bN189G18.7	RIKEN cDNA 4933430I17 gene	protein-coding
mm_33313.1	chr4	129070505	129070517	+	1	NA	intron (NM_029219, intron 1 of 8)	B3|SINE|B2	12240	NM_029219	75234	Mm.259672	NM_029219	ENSMUSG00000028793	Rnf19b	4930534K13Rik|4930555L03Rik|Ibrdc3	ring finger protein 19B	protein-coding
mm_162084.1	chrX	33956602	33956602	-	1	NA	Intergenic	Intergenic	204982	NM_001085552	668960		NM_001085552	ENSMUSG00000095716	Btbd35f10	Gm14351|OTTMUSG00000016411	BTB domain containing 35, family member 10	protein-coding
mm_123261.1	chr14	61258485	61258493	-	1	NA	promoter-TSS (NM_011892)	promoter-TSS (NM_011892)	1	NM_011892	24053	Mm.72173	NM_011892	ENSMUSG00000035296	Sgcg	35kDa|5430420E18Rik|AI642964|gamma-SG	sarcoglycan, gamma (dystrophin-associated glycoprotein)	protein-coding
mm_169515.1	chr1	4857827	4857827	+	1	NA	promoter-TSS (NM_001159751)	promoter-TSS (NM_001159751)	133	NM_011541	21399	Mm.207263	NM_011541	ENSMUSG00000033813	Tcea1	S-II	transcription elongation factor A (SII) 1	protein-coding
mm_163387.1	chr12	54559234	54559246	+	1	NA	Intergenic	Intergenic	86772	NR_035439	100316682		NR_035439	ENSMUSG00000106344	Mir1892	Mirn1892|mir-1892|mmu-mir-1892	microRNA 1892	ncRNA
mm_131420.1	chr16	14708116	14708123	+	1	NA	exon (NM_011415, exon 3 of 3)	exon (NM_011415, exon 3 of 3)	2260	NM_011415	20583	Mm.4272	NM_011415	ENSMUSG00000022676	Snai2	Slug|Slugh|Snail2	snail family zinc finger 2	protein-coding
mm_97562.1	chr11	78935423	78935433	+	1	NA	exon (NM_010927, exon 6 of 27)	exon (NM_010927, exon 6 of 27)	10137	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_82024.1	chr9	121777713	121777723	+	1	NA	5' UTR (NM_028202, exon 1 of 6)	5' UTR (NM_028202, exon 1 of 6)	111	NM_028202	72330	Mm.45734	NM_028202	ENSMUSG00000074001	Klhl40	2310024D23Rik|Kbtbd5	kelch-like 40	protein-coding
mm_19295.1	chr2	90460696	90460718	-	1	NA	exon (NM_008982, exon 8 of 24)	exon (NM_008982, exon 8 of 24)	18467	NM_001135657	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_1166.1	chr1	60911082	60911094	+	1	NA	intron (NM_001281976, intron 1 of 2)	intron (NM_001281976, intron 1 of 2)	2063	NM_001281976	12477	Mm.390	NM_009843	ENSMUSG00000026011	Ctla4	Cd152|Ctla-4|Ly-56	cytotoxic T-lymphocyte-associated protein 4	protein-coding
mm_141530.1	chr17	31844511	31844515	-	1	NA	3' UTR (NM_010831, exon 14 of 14)	3' UTR (NM_010831, exon 14 of 14)	11279	NM_010831	17691	Mm.290941	NM_010831	ENSMUSG00000024042	Sik1	Msk|Sik|Snf1lk	salt inducible kinase 1	protein-coding
mm_152638.1	chr19	12501936	12501973	-	1	NA	promoter-TSS (NM_172442)	promoter-TSS (NM_172442)	42	NM_172442	207521	Mm.247695	NM_172442	ENSMUSG00000039982	Dtx4	AI449438|BC044798|D930042H13|RNF155	deltex 4, E3 ubiquitin ligase	protein-coding
mm_60439.1	chr7	44476976	44476992	+	1	NA	Intergenic	L1MEd|LINE|L1	6637	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_96459.1	chr11	67586645	67586662	+	1	NA	5' UTR (NM_001109657, exon 1 of 14)	5' UTR (NM_001109657, exon 1 of 14)	153	NM_001109657	14457	Mm.40338	NM_008088	ENSMUSG00000033066	Gas7	AW124766|B230343A10Rik|Gas7-cb	growth arrest specific 7	protein-coding
mm_147660.1	chr18	60596767	60596768	-	1	NA	intron (NM_177340, intron 2 of 2)	intron (NM_177340, intron 2 of 2)	-5051	NM_133363	170947	Mm.159257	NM_133363	ENSMUSG00000049173	Myoz3	4833419K08Rik|Fatz-3	myozenin 3	protein-coding
mm_155741.1	chrX	96166619	96166629	+	1	NA	exon (NM_010833, exon 13 of 13)	exon (NM_010833, exon 13 of 13)	70579	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_18508.1	chr2	62617256	62617264	-	1	NA	intron (NM_001164477, intron 4 of 14)	intron (NM_001164477, intron 4 of 14)	28995	NM_027835	71586	Mm.136224	NM_027835	ENSMUSG00000026896	Ifih1	9130009C22Rik|Helicard|Hlcd|MDA5|RLR-2	interferon induced with helicase C domain 1	protein-coding
mm_163869.1	chr14	19419088	19419103	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	183492	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_150561.1	chr19	39510821	39510823	+	1	NA	promoter-TSS (NM_010003)	promoter-TSS (NM_010003)	0	NM_010003	13098	Mm.42101	NM_010003	ENSMUSG00000025003	Cyp2c39	CYPIIC39	cytochrome P450, family 2, subfamily c, polypeptide 39	protein-coding
mm_158677.1	chrX	158043406	158043425	-	1	NA	promoter-TSS (NM_177751)	promoter-TSS (NM_177751)	-218	NM_177751	245684	Mm.197074	NM_177751	ENSMUSG00000025658	Cnksr2	Cnk2|Ksr2	connector enhancer of kinase suppressor of Ras 2	protein-coding
mm_87082.1	chr10	29313526	29313594	+	1	NA	promoter-TSS (NM_025855)	promoter-TSS (NM_025855)	60	NM_025855	52665	Mm.28930	NM_025855	ENSMUSG00000019883	Echdc1	1700028A24Rik|AI314462|AI930038|D10Ertd667e|MMCD	enoyl Coenzyme A hydratase domain containing 1	protein-coding
mm_691.1	chr1	40580069	40580092	+	1	NA	promoter-TSS (NM_177084)	promoter-TSS (NM_177084)	-147	NM_177084	110895	Mm.108602	NM_177084	ENSMUSG00000026065	Slc9a4	AW990558|D730009J23Rik|NHE4	solute carrier family 9 (sodium/hydrogen exchanger), member 4	protein-coding
mm_88832.1	chr10	80806400	80806410	+	1	NA	exon (NM_007445, exon 3 of 5)	exon (NM_007445, exon 3 of 5)	1157	NM_007445	11705	Mm.376094	NM_007445	ENSMUSG00000035262	Amh	MIS	anti-Mullerian hormone	protein-coding
mm_146586.1	chr18	8138054	8138056	-	1	NA	Intergenic	RLTR13D6|LTR|ERVK	268858	NM_153085	225131	Mm.204524	NM_153085	ENSMUSG00000024283	Wac	1110067P07Rik|A230035H12Rik|AI256735|AI256776|Wwp4	WW domain containing adaptor with coiled-coil	protein-coding
mm_97033.1	chr11	72267241	72267247	+	1	NA	promoter-TSS (NM_001004148)	promoter-TSS (NM_001004148)	400	NR_045922	73366	Mm.396157	NR_045922	ENSMUSG00000086951	1700051A21Rik	-	RIKEN cDNA 1700051A21 gene	ncRNA
mm_76682.1	chr8	94012842	94012851	-	1	NA	promoter-TSS (NM_011787)	promoter-TSS (NM_011787)	-206	NM_011787	23802	Mm.34641	NM_011787	ENSMUSG00000031751	Amfr	gp78	autocrine motility factor receptor	protein-coding
mm_48029.1	chr5	136246519	136246542	-	1	NA	Intergenic	Intergenic	-1590	NM_018825	23921	Mm.425294	NM_018825	ENSMUSG00000005057	Sh2b2	Aps	SH2B adaptor protein 2	protein-coding
mm_132773.1	chr16	44771788	44771815	+	1	NA	intron (NM_021325, intron 1 of 6)	B1_Mus2|SINE|Alu	6065	NM_021325	57781	Mm.416152	NM_021325	ENSMUSG00000022667	Cd200r1	CD200R|Mox2r|OX2R	CD200 receptor 1	protein-coding
mm_118448.1	chr14	8214200	8214209	+	1	NA	promoter-TSS (NM_001305936)	promoter-TSS (NM_001305936)	123	NM_027782	71393	Mm.292712	NM_027782	ENSMUSG00000021752	Kctd6	5430433B02Rik|AU044285	potassium channel tetramerisation domain containing 6	protein-coding
mm_102516.1	chr11	60811106	60811210	-	1	NA	5' UTR (NM_009171, exon 1 of 12)	5' UTR (NM_009171, exon 1 of 12)	107	NM_009171	20425	Mm.364956	NM_009171	ENSMUSG00000020534	Shmt1	AI324848|AI385541|C81125|Shmt|mshmt|mshmt1|mshmt2	serine hydroxymethyltransferase 1 (soluble)	protein-coding
mm_100071.1	chr11	115420139	115420164	+	1	NA	promoter-TSS (NM_027862)	promoter-TSS (NM_027862)	25	NM_183285	70382	Mm.276299	NM_183285	ENSMUSG00000016940	Kctd2	2310012I15Rik	potassium channel tetramerisation domain containing 2	protein-coding
mm_4542.1	chr1	176902892	176902895	+	1	NA	intron (NM_029756, intron 12 of 17)	intron (NM_029756, intron 12 of 17)	-66760	NR_037996	15365	Mm.441435	NR_037996		Hmga2-ps1	EG666235|Gm7996|Hmgic-ps1|[y]i-c	high mobility group AT-hook 2, pseudogene 1	pseudo
mm_42662.1	chr5	119670799	119670801	+	1	NA	promoter-TSS (NM_011535)	promoter-TSS (NM_011535)	-62	NM_198052	21386	Mm.219139	NM_011535	ENSMUSG00000018604	Tbx3	D5Ertd189e	T-box 3	protein-coding
mm_139814.1	chr17	66518778	66518795	+	1	NA	intron (NM_024448, intron 1 of 5)	intron (NM_024448, intron 1 of 5)	884	NM_024448	19328	Mm.248313	NM_024448	ENSMUSG00000023460	Rab12	2900054P15Rik|AW555448|C77700	RAB12, member RAS oncogene family	protein-coding
mm_34144.1	chr4	139338205	139338230	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	14359	NM_001290810	69902	Mm.27871	NM_023536	ENSMUSG00000028741	Mrto4	2610012O22Rik|Mg684|Mrt4	mRNA turnover 4, ribosome maturation factor	protein-coding
mm_81014.1	chr9	104074065	104074070	+	1	NA	intron (NM_175324, intron 2 of 19)	intron (NM_175324, intron 2 of 19)	10364	NM_175324	102632	Mm.41274	NM_175324	ENSMUSG00000090150	Acad11	5730439E10Rik|AI987948	acyl-Coenzyme A dehydrogenase family, member 11	protein-coding
mm_137919.1	chr17	32452720	32452731	+	1	NA	promoter-TSS (NM_177307)	promoter-TSS (NM_177307)	2	NM_177307	320997	Mm.130900	NM_177307	ENSMUSG00000061126	Cyp4f39	4732474A20Rik	cytochrome P450, family 4, subfamily f, polypeptide 39	protein-coding
mm_24643.1	chr3	94377506	94377527	+	1	NA	promoter-TSS (NM_001293734)	promoter-TSS (NM_001293734)	84	NR_121656	19885	Mm.4372	NM_011281	ENSMUSG00000028150	Rorc	Nr1f3|RORgamma|TOR|Thor	RAR-related orphan receptor gamma	protein-coding
mm_59504.1	chr7	27560452	27560468	+	1	NA	promoter-TSS (NM_001122767)	promoter-TSS (NM_001122767)	-16	NM_001122767	66367	Mm.29831	NM_175107	ENSMUSG00000049643	2310022A10Rik	-	RIKEN cDNA 2310022A10 gene	protein-coding
mm_120859.1	chr14	75229312	75229322	+	1	NA	exon (NM_001247984, exon 16 of 16)	exon (NM_001247984, exon 16 of 16)	-12970	NM_019775	56373	Mm.24242	NM_019775	ENSMUSG00000021999	Cpb2	1110032P04Rik|4930405E17Rik|AI255929|CPR|Cpu|TAFI	carboxypeptidase B2 (plasma)	protein-coding
mm_140382.1	chr17	87116931	87116933	+	1	NA	intron (NM_019654, intron 1 of 2)	B2_Mm2|SINE|B2	9253	NM_019654	56468	Mm.126885	NM_019654	ENSMUSG00000037104	Socs5	1810018L08Rik|Cish5|mKIAA0671	suppressor of cytokine signaling 5	protein-coding
mm_106957.1	chr12	8921599	8921671	+	1	NA	5' UTR (NM_008640, exon 1 of 7)	5' UTR (NM_008640, exon 1 of 7)	328	NM_008640	17775	Mm.30071	NM_008640	ENSMUSG00000020585	Laptm4a	AA286466|LAPTM4|MTP|Mtrp|mKIAA0108	lysosomal-associated protein transmembrane 4A	protein-coding
mm_77366.1	chr8	119810186	119810203	-	1	NA	3' UTR (NM_028071, exon 4 of 4)	3' UTR (NM_028071, exon 4 of 4)	30385	NM_028071	72042	Mm.393405	NM_028071	ENSMUSG00000031827	Cotl1	1810074P22Rik|2010004C08Rik|Clp	coactosin-like 1 (Dictyostelium)	protein-coding
mm_94280.1	chr11	3963988	3964021	+	1	NA	promoter-TSS (NM_022889)	promoter-TSS (NM_022889)	29	NM_022889	64934	Mm.28659	NM_022889	ENSMUSG00000020430	Pes1	-	pescadillo ribosomal biogenesis factor 1	protein-coding
mm_19649.1	chr2	102866683	102866684	-	1	NA	intron (NM_001039150, intron 1 of 13)	intron (NM_001039150, intron 1 of 13)	34982	NM_001177785	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_77313.1	chr8	117692256	117692278	-	1	NA	non-coding (NR_131057, exon 8 of 8)	non-coding (NR_131057, exon 8 of 8)	-9679	NM_008290	15486	Mm.276466	NM_008290	ENSMUSG00000031844	Hsd17b2	AI194836|AI194967|AI255511	hydroxysteroid (17-beta) dehydrogenase 2	protein-coding
mm_133594.1	chr16	91462140	91462152	+	1	NA	Intergenic	Intergenic	-2958	NR_077219	100503120	Mm.387130	NR_077219	ENSMUSG00000084866	A930006K02Rik	-	RIKEN cDNA A930006K02 gene	ncRNA
mm_93462.1	chr10	110856681	110856691	-	1	NA	intron (NR_045979, intron 2 of 2)	Lx4A|LINE|L1	39821	NR_045979	75630	Mm.392786	NR_045979	ENSMUSG00000101801	1700020G17Rik	4930480D05Rik	RIKEN cDNA 1700020G17 gene	ncRNA
mm_132496.1	chr16	36946659	36946671	+	1	NA	exon (NM_008225, exon 4 of 14)	exon (NM_008225, exon 4 of 14)	11682	NM_008225	15163	Mm.4091	NM_008225	ENSMUSG00000022831	Hcls1	AW213261|HS1	hematopoietic cell specific Lyn substrate 1	protein-coding
mm_158007.1	chrX	95444766	95444777	-	1	NA	promoter-TSS (NM_175179)	promoter-TSS (NM_175179)	69	NM_175179	72345	Mm.182867	NM_175179	ENSMUSG00000050332	Amer1	2810002O09Rik|AW492303|Fam123b|Wtx	APC membrane recruitment 1	protein-coding
mm_25203.1	chr3	103803122	103803129	+	1	NA	promoter-TSS (NR_040412)	promoter-TSS (NR_040412)	-4	NR_040412	100503157	Mm.445554	NR_040412	ENSMUSG00000084997	Gm15471	OTTMUSG00000022448	predicted gene 15471	ncRNA
mm_53433.1	chr6	134079612	134079615	+	1	NA	intron (NM_001303102, intron 2 of 8)	intron (NM_001303102, intron 2 of 8)	43913	NM_007961	14011	Mm.269995	NM_007961	ENSMUSG00000030199	Etv6	AW123102|AW557856|Tel	ets variant 6	protein-coding
mm_141234.1	chr17	27436755	27436767	-	1	NA	intron (NM_001013385, intron 7 of 8)	(TCTG)n|Simple_repeat|Simple_repeat	66772	NM_001013385	268934	Mm.358940	NM_001013385	ENSMUSG00000063239	Grm4	Gprc1d|mGluR4	glutamate receptor, metabotropic 4	protein-coding
mm_36590.1	chr4	88438128	88438131	-	1	NA	intron (NM_025760, intron 1 of 6)	intron (NM_025760, intron 1 of 6)	797	NM_025760	66775	Mm.386788	NM_025760	ENSMUSG00000028497	Hacd4	4933428I03Rik|Hcad4|Ptplad2	3-hydroxyacyl-CoA dehydratase 4	protein-coding
mm_59671.1	chr7	28379353	28379390	+	1	NA	promoter-TSS (NM_011756)	promoter-TSS (NM_011756)	-143	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_40676.1	chr5	65537210	65537214	+	1	NA	promoter-TSS (NM_016786)	promoter-TSS (NM_016786)	-33	NM_016786	53323	Mm.319512	NM_016786	ENSMUSG00000029203	Ube2k	AW492011|D5Ertd601e|E2-25k|HIP-2|Hip2|Hypg|Lig	ubiquitin-conjugating enzyme E2K	protein-coding
mm_88667.1	chr10	80016970	80016978	+	1	NA	promoter-TSS (NM_001347074)	promoter-TSS (NM_001347074)	59	NM_001347074	70719	Mm.243954	NM_027521	ENSMUSG00000035697	Hmha1	6330406L22Rik|AW539505|Ha-1	histocompatibility (minor) HA-1	protein-coding
mm_138383.1	chr17	35046901	35046940	+	1	NA	promoter-TSS (NR_130641)	promoter-TSS (NR_130641)	-175	NM_001146215	17687	Mm.24192	NM_013600	ENSMUSG00000007035	Msh5	Mut5	mutS homolog 5	protein-coding
mm_39203.1	chr4	156031619	156031635	-	1	NA	Intergenic	RLTR20B4_MM|LTR|ERVK	5285	NM_021985	21936	Mm.3180	NM_009400	ENSMUSG00000041954	Tnfrsf18	AITR|Gitr	tumor necrosis factor receptor superfamily, member 18	protein-coding
mm_158568.1	chrX	150559780	150559782	-	1	NA	intron (NM_001102446, intron 6 of 10)	PB1D11|SINE|Alu	-12336	NR_106147	102465782		NR_106147	ENSMUSG00000099172	Mir3620	Gm27984|mmu-mir-3620	microRNA 3620	ncRNA
mm_89867.1	chr10	108177300	108177303	+	1	NA	intron (NM_027892, intron 1 of 25)	intron (NM_027892, intron 1 of 25)	14901	NM_027892	17931	Mm.422959	NM_027892	ENSMUSG00000019907	Ppp1r12a	1200015F06Rik|5730577I22Rik|AA792106|AV099298|D10Ertd625e|Mypt1	protein phosphatase 1, regulatory (inhibitor) subunit 12A	protein-coding
mm_86611.1	chr10	13964850	13964875	+	1	NA	Intergenic	CpG	-1517	NM_010437	15273	Mm.42157	NM_010437	ENSMUSG00000015501	Hivep2	Gm20114|MIBP1|Schnurri-2|Shn-2	human immunodeficiency virus type I enhancer binding protein 2	protein-coding
mm_71971.1	chr8	70539686	70539710	+	1	NA	promoter-TSS (NM_007924)	promoter-TSS (NM_007924)	23	NM_007924	13716	Mm.271973	NM_007924	ENSMUSG00000070002	Ell	Ell1|Men	elongation factor RNA polymerase II	protein-coding
mm_143678.1	chr17	80055370	80055378	-	1	NA	intron (NM_144802, intron 1 of 12)	intron (NM_144802, intron 1 of 12)	6894	NM_144802	72692	Mm.64579	NM_144802	ENSMUSG00000024095	Hnrnpll	2510028H02Rik|2810036L13Rik|AI256697|AI852082|Hnrpll	heterogeneous nuclear ribonucleoprotein L-like	protein-coding
mm_22272.1	chr2	178546411	178546451	-	1	NA	Intergenic	Intergenic	115916	NM_198656	381409	Mm.330860	NM_198656	ENSMUSG00000039155	Cdh26	Gm1010	cadherin-like 26	protein-coding
mm_148193.1	chr18	79033358	79033371	-	1	NA	intron (NM_053099, intron 2 of 5)	intron (NM_053099, intron 2 of 5)	76027	NM_053099	240427	Mm.312871	NM_053099	ENSMUSG00000024548	Setbp1	C130092E12|Seb|mKIAA0437	SET binding protein 1	protein-coding
mm_102190.1	chr11	54249641	54249644	-	1	NA	5' UTR (NM_009969, exon 1 of 4)	5' UTR (NM_009969, exon 1 of 4)	257	NM_009969	12981	Mm.4922	NM_009969	ENSMUSG00000018916	Csf2	Csfgm|GMCSF|Gm-CSf|MGI-IGM	colony stimulating factor 2 (granulocyte-macrophage)	protein-coding
mm_167505.1	chr9	13302914	13302915	+	1	NA	Intergenic	Intergenic	55958	NM_025534	66396	Mm.290620	NM_025534	ENSMUSG00000079084	Ccdc82	2310043N13Rik	coiled-coil domain containing 82	protein-coding
mm_98549.1	chr11	95040723	95040735	+	1	NA	intron (NM_133667, intron 1 of 10)	intron (NM_133667, intron 1 of 10)	642	NM_133667	18604	Mm.29768	NM_133667	ENSMUSG00000038967	Pdk2	-	pyruvate dehydrogenase kinase, isoenzyme 2	protein-coding
mm_154136.1	chr19	57358466	57358485	-	1	NA	intron (NR_040316, intron 1 of 2)	ORR1E|LTR|ERVL-MaLR	2424	NR_040316	320879	Mm.375089	NR_040316	ENSMUSG00000097785	B230217O12Rik	-	RIKEN cDNA B230217O12 gene	ncRNA
mm_124134.1	chr14	84758682	84758723	-	1	NA	Intergenic	Intergenic	-282278	NR_015539	319903	Mm.440481	NR_015539		9630013A20Rik	-	RIKEN cDNA 9630013A20 gene	ncRNA
mm_11299.1	chr2	30171530	30171536	+	1	NA	promoter-TSS (NM_007931)	promoter-TSS (NM_007931)	9	NM_007931	13804	Mm.474473	NM_007931	ENSMUSG00000015337	Endog	-	endonuclease G	protein-coding
mm_12630.1	chr2	74704918	74704929	+	1	NA	promoter-TSS (NM_001290730)	promoter-TSS (NM_001290730)	308	NM_001290731	15437	Mm.280673	NM_008276	ENSMUSG00000027102	Hoxd8	4921540P06Rik|AI047735|Hox-4.3|Hox-5.4	homeobox D8	protein-coding
mm_39639.1	chr5	24577719	24577760	+	1	NA	promoter-TSS (NM_001190443)	promoter-TSS (NM_001190443)	-272	NM_001190443	27407	Mm.21629	NM_013853	ENSMUSG00000028953	Abcf2	0710005O05Rik|Drr3|E430001O06	ATP-binding cassette, sub-family F (GCN20), member 2	protein-coding
mm_81535.1	chr9	110131990	110131998	+	1	NA	promoter-TSS (NM_009211)	promoter-TSS (NM_009211)	-30	NM_009211	20588	Mm.85410	NM_009211	ENSMUSG00000032481	Smarcc1	AI115498|BAF155|Rsc8|SRG3|msp3	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 1	protein-coding
mm_134258.1	chr16	13731007	13731013	-	1	NA	promoter-TSS (NM_011987)	promoter-TSS (NM_011987)	-526	NM_011987	26565	Mm.4214	NM_011987	ENSMUSG00000022683	Pla2g10	GX sPLA2|PLA2GX|sPLA2-X	phospholipase A2, group X	protein-coding
mm_138039.1	chr17	33920243	33920337	+	1	NA	TTS (NM_020625)	TTS (NM_020625)	812	NM_009318	21356	Mm.154457	NM_009318	ENSMUSG00000024308	Tapbp	D17Wsu91e|TPN	TAP binding protein	protein-coding
mm_170756.1	chr2	157034954	157034957	+	1	NA	intron (NM_001164663, intron 6 of 14)	MT2_Mm|LTR|ERVL	-27880	NM_025853	66934	Mm.25410	NM_025853	ENSMUSG00000027635	Dsn1	1700022L09Rik|AW552447	DSN1 homolog, MIS12 kinetochore complex component	protein-coding
mm_75736.1	chr8	69625504	69625559	-	1	NA	promoter-TSS (NM_001045553)	promoter-TSS (NM_001045553)	17	NM_172754	234362	Mm.458487	NM_172754	ENSMUSG00000060427	Zfp868	AI449175|AW108241|C530032E20|mszf62	zinc finger protein 868	protein-coding
mm_169647.1	chr15	52544574	52544580	-	1	NA	Intergenic	RLTR10D|LTR|ERVK	-167868	NM_027212	69790	Mm.195562	NM_027212	ENSMUSG00000038622	Med30	1810038N03Rik|2510044J04Rik|TRAP25|Thrap6	mediator complex subunit 30	protein-coding
mm_93236.1	chr10	95413594	95413601	-	1	NA	intron (NM_001168655, intron 2 of 2)	(A)n|Simple_repeat|Simple_repeat	1686	NM_001168657	216233	Mm.474283	NM_007706	ENSMUSG00000020027	Socs2	8030460M17|AI527257|AW108012|CIS2|Cish2|D130043N08Rik|JAB|SOCS-2|SSI-2|hg	suppressor of cytokine signaling 2	protein-coding
mm_32086.1	chr4	98436860	98436877	+	1	NA	intron (NM_001005784, intron 11 of 19)	intron (NM_001005784, intron 11 of 19)	41042	NM_172696	12695	Mm.90218	NM_007704	ENSMUSG00000061859	Patj	Cipp|Inadl	PATJ, crumbs cell polarity complex component	protein-coding
mm_28991.1	chr3	101290740	101290754	-	1	NA	Intergenic	RLTR10|LTR|ERVK	-2808	NM_013486	12481	Mm.22842	NM_013486	ENSMUSG00000027863	Cd2	LFA-2|Ly-37|Ly37	CD2 antigen	protein-coding
mm_62606.1	chr7	105742544	105742560	+	1	NA	TTS (NM_020024)	TTS (NM_020024)	1786	NM_020024	24075	Mm.274846	NM_020024	ENSMUSG00000043866	Taf10	30kDa|AU041226|TAFII30|Taf2h	TATA-box binding protein associated factor 10	protein-coding
mm_112348.1	chr12	118198918	118198951	-	1	NA	5' UTR (NM_010060, exon 1 of 82)	5' UTR (NM_010060, exon 1 of 82)	109	NM_010060	13411	Mm.390540	NM_010060	ENSMUSG00000018581	Dnah11	Dnahc11|b2b1203Clo|b2b1279Clo|b2b1289Clo|b2b1727Clo|b2b598Clo|iv|lrd	dynein, axonemal, heavy chain 11	protein-coding
mm_67063.1	chr7	67645196	67645273	-	1	NA	promoter-TSS (NR_028144)	promoter-TSS (NR_028144)	2	NM_175124	67867	Mm.31247	NM_027413	ENSMUSG00000030556	Lrrc28	1300004K21Rik|2210012C09Rik|2310058O11Rik	leucine rich repeat containing 28	protein-coding
mm_128707.1	chr15	63808734	63808745	-	1	NA	promoter-TSS (NM_031378)	promoter-TSS (NM_031378)	0	NM_031378	83492	Mm.335619	NM_031378	ENSMUSG00000079025	Gsdmc	Gsdmc1|Mlze	gasdermin C	protein-coding
mm_60187.1	chr7	43267669	43267682	+	1	NA	Intergenic	RLTR44E|LTR|ERVK	45586	NM_027264	69930	Mm.45367	NM_027264	ENSMUSG00000012640	Zfp715	2610041B18Rik|mszf15	zinc finger protein 715	protein-coding
mm_3918.1	chr1	162218853	162218856	+	1	NA	TTS (NR_029810)	TTS (NR_029810)	1040	NR_029810	723821		NR_029810	ENSMUSG00000070126	Mir199a-2	Mirn199a-2|mir-199a-2	microRNA 199a-2	ncRNA
mm_73496.1	chr8	107153738	107153742	+	1	NA	intron (NM_025558, intron 1 of 4)	intron (NM_025558, intron 1 of 4)	3079	NM_025558	66427	Mm.20242	NM_025558	ENSMUSG00000031924	Cyb5b	1810044O22Rik|AU015618|Cyb5m	cytochrome b5 type B	protein-coding
mm_68675.1	chr7	118976802	118976828	-	1	NA	intron (NM_022420, intron 2 of 3)	intron (NM_022420, intron 2 of 3)	18396	NM_022420	64297	Mm.103439	NM_022420	ENSMUSG00000008734	Gprc5b	AW125761|Raig2	G protein-coupled receptor, family C, group 5, member B	protein-coding
mm_49195.1	chr6	15186903	15186913	+	1	NA	intron (NM_212435, intron 1 of 16)	intron (NM_212435, intron 1 of 16)	1402	NM_001286607	114142	Mm.332919	NM_053242	ENSMUSG00000029563	Foxp2	2810043D05Rik|AI449000|CAG-16|D0Kist7	forkhead box P2	protein-coding
mm_6611.1	chr1	75479162	75479168	-	1	NA	promoter-TSS (NM_177056)	promoter-TSS (NM_177056)	306	NM_001001565	74241	Mm.260577	NM_001001565	ENSMUSG00000032997	Chpf	1700028N03Rik|AI414328|D1Bwg1363e	chondroitin polymerizing factor	protein-coding
mm_32735.1	chr4	116596673	116596703	+	1	NA	promoter-TSS (NM_001037916)	promoter-TSS (NM_001037916)	-42	NM_001037916	622665	Mm.388905	NM_001037916	ENSMUSG00000034035	Ccdc17	-	coiled-coil domain containing 17	protein-coding
mm_7880.1	chr1	133019481	133019496	-	1	NA	intron (NM_008575, intron 1 of 11)	intron (NM_008575, intron 1 of 11)	5928	NR_126506	17248	Mm.426531	NM_008575	ENSMUSG00000054387	Mdm4	4933417N07Rik|AA414968|AL023055|AU018793|AU021806|C85810|Mdmx	transformed mouse 3T3 cell double minute 4	protein-coding
mm_93022.1	chr10	87915322	87915354	-	1	NA	exon (NM_010512, exon 4 of 5)	exon (NM_010512, exon 4 of 5)	-51333	NR_000040	22172	Mm.391420	NR_000040		Tyms-ps	-	thymidylate synthase, pseudogene	pseudo
mm_64429.1	chr7	142577774	142577796	+	1	NA	promoter-TSS (NR_030416)	promoter-TSS (NR_030416)	361	NR_130974	14955	Mm.14802	NR_001592	ENSMUSG00000000031	H19	AI747191	H19, imprinted maternally expressed transcript	ncRNA
mm_160087.1	chr7	14622704	14622704	-	1	NA	promoter-TSS (NR_045120)	promoter-TSS (NR_045120)	-226	NR_045120	100417675	Mm.372763	NR_045119	ENSMUSG00000041596	Nlrp5-ps	Gm18756	NLR family, pyrin domain containing 5, pseudogene	pseudo
mm_109624.1	chr12	112766743	112766753	+	1	NA	exon (NM_178911, exon 7 of 11)	exon (NM_178911, exon 7 of 11)	6093	NM_178911	104759	Mm.203915	NM_178911	ENSMUSG00000052160	Pld4	AI132321|thss	phospholipase D family, member 4	protein-coding
mm_44676.1	chr5	29795215	29795220	-	1	NA	intron (NR_105781, intron 1 of 2)	intron (NR_105781, intron 1 of 2)	6206	NR_105781	102465962		NR_105781	ENSMUSG00000098448	Mir6362	Gm27812|mmu-mir-6362	microRNA 6362	ncRNA
mm_2344.1	chr1	92865179	92865210	+	1	NA	Intergenic	Intergenic	14816	NR_029559	387167		NR_029559	ENSMUSG00000065470	Mir149	Mirn149|mir-149|mmu-mir-149	microRNA 149	ncRNA
mm_38659.1	chr4	144162647	144162651	-	1	NA	promoter-TSS (NM_201258)	promoter-TSS (NM_201258)	2	NM_201258	100012	Mm.28722	NM_201258	ENSMUSG00000050810	Oog3	AA617276|C86881	oogenesin 3	protein-coding
mm_50128.1	chr6	41541891	41541903	+	1	NA	Intergenic	Intergenic	20121	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_13498.1	chr2	107290579	107290586	+	1	NA	promoter-TSS (NM_021275)	promoter-TSS (NM_021275)	-7	NM_021275	16492	Mm.142718	NM_021275	ENSMUSG00000042604	Kcna4	Kv1.4	potassium voltage-gated channel, shaker-related subfamily, member 4	protein-coding
mm_34060.1	chr4	138440572	138440574	+	1	NA	3' UTR (NM_026689, exon 4 of 4)	3' UTR (NM_026689, exon 4 of 4)	5901	NM_026689	68350	Mm.103413	NM_026689	ENSMUSG00000041241	Mul1	0610009K11Rik|AV000801|Gide	mitochondrial ubiquitin ligase activator of NFKB 1	protein-coding
mm_3005.1	chr1	133309779	133309829	+	1	NA	promoter-TSS (NM_026680)	promoter-TSS (NM_026680)	-19	NM_026680	68338	Mm.247935	NM_026680	ENSMUSG00000098306	Golt1a	0610012C01Rik|Kiss1|metastatin	golgi transport 1A	protein-coding
mm_168559.1	chr1	167340360	167340378	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-9622	NM_019993	56752	Mm.292539	NM_019993	ENSMUSG00000026687	Aldh9a1	AA139417|Abaldh|ESTM40|TMABA-DH|Tmabadh	aldehyde dehydrogenase 9, subfamily A1	protein-coding
mm_148865.1	chr19	6413106	6413130	+	1	NA	exon (NM_011242, exon 13 of 17)	exon (NM_011242, exon 13 of 17)	-5620	NM_001205235	18190	Mm.329616	NM_020253	ENSMUSG00000033768	Nrxn2	6430591O13Rik|mKIAA0921	neurexin II	protein-coding
mm_2215.1	chr1	89783464	89783468	+	1	NA	intron (NM_178119, intron 12 of 17)	intron (NM_178119, intron 12 of 17)	-99574	NR_015540	74403	Mm.444291	NR_015540		4933400F21Rik	1700091C04Rik|4930565K10Rik	RIKEN cDNA 4933400F21 gene	ncRNA
mm_115906.1	chr13	23430727	23430776	-	1	NA	non-coding (NR_015492, exon 1 of 4)	non-coding (NR_015492, exon 1 of 4)	266	NR_015492	320842	Mm.487476	NR_015492	ENSMUSG00000085024	C230035I16Rik	-	RIKEN cDNA C230035I16 gene	ncRNA
mm_71981.1	chr8	70595045	70595073	+	1	NA	intron (NM_023627, intron 3 of 10)	CpG-14104	578	NM_023627	71780	Mm.29357	NM_023627	ENSMUSG00000019139	Isyna1	1300017C10Rik|AU018670	myo-inositol 1-phosphate synthase A1	protein-coding
mm_60428.1	chr7	44476696	44476723	+	1	NA	Intergenic	L1MEd|LINE|L1	6362	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_28816.1	chr3	96262317	96262327	-	1	NA	TTS (NM_033596)	TTS (NM_033596)	995	NM_033596	97122	Mm.227295	NM_033596	ENSMUSG00000091405	Hist2h4	H4|X04652	histone cluster 2, H4	protein-coding
mm_173336.1	chrY	90811298	90811301	+	1	NA	intron (NM_133362, intron 2 of 3)	RLTR40|LTR|ERVK	25857	NM_133362	170942	Mm.76062	NM_133362	ENSMUSG00000096768	Erdr1	edr	erythroid differentiation regulator 1	protein-coding
mm_65137.1	chr7	19562378	19562401	-	1	NA	promoter-TSS (NM_199149)	promoter-TSS (NM_199149)	9	NM_199149	232947	Mm.219662	NM_199149	ENSMUSG00000051403	Ppp1r37	Gm158|Lrrc68	protein phosphatase 1, regulatory subunit 37	protein-coding
mm_82744.1	chr9	26802600	26802606	-	1	NA	intron (NM_153803, intron 1 of 19)	intron (NM_153803, intron 1 of 19)	3814	NM_153803	244757	Mm.293696	NM_153803	ENSMUSG00000036395	Glb1l2	-	galactosidase, beta 1-like 2	protein-coding
mm_113789.1	chr13	45936036	45936053	+	1	NA	intron (NM_001199304, intron 2 of 6)	ORR1E|LTR|ERVL-MaLR	28947	NM_001199304	20238	Mm.342683	NM_009124	ENSMUSG00000046876	Atxn1	2900016G23Rik|Atx1|C85907|ENSMUSG00000074917|Gm10786|Sca1	ataxin 1	protein-coding
mm_53133.1	chr6	125191804	125191850	+	1	NA	promoter-TSS (NM_025595)	promoter-TSS (NM_025595)	-241	NM_146171	68298	Mm.257590	NM_146171	ENSMUSG00000038252	Ncapd2	2810406C15Rik|2810465G24Rik|CAP-D2|CNAP1|mKIAA0159	non-SMC condensin I complex, subunit D2	protein-coding
mm_59283.1	chr7	24917916	24917928	+	1	NA	exon (NM_008488, exon 13 of 29)	exon (NM_008488, exon 13 of 29)	13576	NM_001130152	16801	Mm.3181	NM_008488	ENSMUSG00000040940	Arhgef1	Lbcl2|Lsc	Rho guanine nucleotide exchange factor (GEF) 1	protein-coding
mm_133913.1	chr16	97557748	97557760	+	1	NA	intron (NM_013606, intron 12 of 13)	MTEb|LTR|ERVL-MaLR	21671	NM_013606	17858	Mm.14157	NM_013606	ENSMUSG00000023341	Mx2	AI528743|Mx-2	MX dynamin-like GTPase 2	protein-coding
mm_13702.1	chr2	117139384	117139386	+	1	NA	intron (NM_033524, intron 1 of 6)	intron (NM_033524, intron 1 of 6)	18314	NM_033524	114715	Mm.245890	NM_033524	ENSMUSG00000027351	Spred1	5730461F13Rik|AL024345|AW047647	sprouty protein with EVH-1 domain 1, related sequence	protein-coding
mm_84857.1	chr9	78527464	78527472	-	1	NA	Intergenic	Intergenic	-45744	NM_010106	13627	Mm.138471	NM_010106	ENSMUSG00000037742	Eef1a1	-	eukaryotic translation elongation factor 1 alpha 1	protein-coding
mm_97448.1	chr11	78189112	78189126	+	1	NA	5' UTR (NM_033475, exon 1 of 10)	5' UTR (NM_033475, exon 1 of 10)	371	NM_033475	19376	Mm.275864	NM_033475	ENSMUSG00000002059	Rab34	AI326479|Narr|Rah|Rah1	RAB34, member RAS oncogene family	protein-coding
mm_29926.1	chr3	131491054	131491057	-	1	NA	Intergenic	Intergenic	-73713	NM_001289479	23971	Mm.244912	NM_011863	ENSMUSG00000028032	Papss1	AI325286|Asapk|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding
mm_126910.1	chr15	90224449	90224461	+	1	NA	promoter-TSS (NR_106106)	promoter-TSS (NR_106106)	95	NR_106106	102466838		NR_106106	ENSMUSG00000099319	Mir7648	Gm27736|mmu-mir-7648	microRNA 7648	ncRNA
mm_159073.1	chr2	25500649	25500649	-	1	NA	promoter-TSS (NM_027062)	promoter-TSS (NM_027062)	-129	NM_013908	30839	Mm.29170	NM_013908	ENSMUSG00000015095	Fbxw5	AI159739|Fbw5	F-box and WD-40 domain protein 5	protein-coding
mm_19617.1	chr2	102812379	102812400	-	1	NA	3' UTR (NM_009851, exon 19 of 19)	3' UTR (NM_009851, exon 19 of 19)	89276	NM_001177785	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_130204.1	chr15	95528079	95528123	-	1	NA	intron (NM_001289653, intron 1 of 20)	CpG-5276	151	NM_001289653	54003	Mm.3959	NM_016743	ENSMUSG00000022454	Nell2	A330108N19Rik|R75516|mel91	NEL-like 2	protein-coding
mm_10849.1	chr2	24977922	24977931	+	1	NA	intron (NM_146251, intron 1 of 34)	intron (NM_146251, intron 1 of 34)	1893	NM_146251	241274	Mm.389243	NM_146251	ENSMUSG00000036833	Pnpla7	BC027342|E430013P11Rik|Nre	patatin-like phospholipase domain containing 7	protein-coding
mm_77417.1	chr8	120668059	120668098	-	1	NA	promoter-TSS (NM_009941)	promoter-TSS (NM_009941)	34	NM_010926	18117	Mm.2136	NM_010926	ENSMUSG00000031819	Emc8	Cox4nb|Fam158b|Noc4	ER membrane protein complex subunit 8	protein-coding
mm_74072.1	chr8	122438150	122438175	+	1	NA	intron (NR_028354, intron 5 of 10)	intron (NR_028354, intron 5 of 10)	-5222	NM_007806	13057	Mm.271671	NM_007806	ENSMUSG00000006519	Cyba	b558|nmf333|p22-phox|p22phox	cytochrome b-245, alpha polypeptide	protein-coding
mm_105960.1	chr11	115461913	115461932	-	1	NA	promoter-TSS (NM_001080934)	promoter-TSS (NM_001080934)	-551	NM_001080934	217316	Mm.25773	NM_001080934	ENSMUSG00000045775	Slc16a5	A130015N09Rik|MCT 5|MCT 6|MCT5	solute carrier family 16 (monocarboxylic acid transporters), member 5	protein-coding
mm_102741.1	chr11	67252693	67252710	-	1	NA	intron (NM_010855, intron 25 of 39)	intron (NM_010855, intron 25 of 39)	14889	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_161019.1	chr11	120643475	120643475	-	1	NA	5' UTR (NM_144795, exon 1 of 8)	5' UTR (NM_144795, exon 1 of 8)	195	NM_144795	209027	Mm.127731	NM_144795	ENSMUSG00000025140	Pycr1	-	pyrroline-5-carboxylate reductase 1	protein-coding
mm_111392.1	chr12	90071029	90071029	-	1	NA	intron (NM_001252074, intron 2 of 6)	intron (NM_001252074, intron 2 of 6)	258546	NM_001252074	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding
mm_137057.1	chr17	17932293	17932319	+	1	NA	Intergenic	Intergenic	-38152	NM_008042	14294	Mm.378918	NM_008042	ENSMUSG00000079700	Fpr3	ALX|Fpr-rs1|Fpr-s1|Fprl1|LXA4-R|Lxa4r	formyl peptide receptor 3	protein-coding
mm_151590.1	chr19	3323721	3323721	-	1	NA	intron (NM_013495, intron 1 of 18)	CpG	420	NM_013495	12894	Mm.18522	NM_013495	ENSMUSG00000024900	Cpt1a	C730027G07|CPTI|Cpt1	carnitine palmitoyltransferase 1a, liver	protein-coding
mm_67668.1	chr7	87493328	87493340	-	1	NA	exon (NM_011661, exon 1 of 5)	exon (NM_011661, exon 1 of 5)	178	NM_011661	22173	Mm.238127	NM_011661	ENSMUSG00000004651	Tyr	Oca1|albino|c|skc35	tyrosinase	protein-coding
mm_56900.1	chr6	119196392	119196422	-	1	NA	promoter-TSS (NM_009781)	promoter-TSS (NM_009781)	2	NM_001255997	12288	Mm.41628	NM_009781	ENSMUSG00000051331	Cacna1c	Cav1.2|Cchl1a1|D930026N18Rik|MBC|MELC-CC	calcium channel, voltage-dependent, L type, alpha 1C subunit	protein-coding
mm_70555.1	chr8	13060922	13060960	+	1	NA	promoter-TSS (NM_025834)	promoter-TSS (NM_025834)	33	NM_025834	66901	Mm.441140	NM_025834	ENSMUSG00000031445	Proz	1300015B06Rik	protein Z, vitamin K-dependent plasma glycoprotein	protein-coding
mm_166772.1	chr6	136234058	136234063	+	1	NA	Intergenic	(CACTA)n|Simple_repeat|Simple_repeat	-60549	NM_008171	14812	Mm.436649	NM_008171	ENSMUSG00000030209	Grin2b	AW490526|GluN2B|NR2B|Nmdar2b	glutamate receptor, ionotropic, NMDA2B (epsilon 2)	protein-coding
mm_60217.1	chr7	43506922	43506949	+	1	NA	promoter-TSS (NM_028737)	promoter-TSS (NM_028737)	-997	NM_028737	74054	Mm.195732	NM_028737	ENSMUSG00000013353	4931406B18Rik	4930538L19Rik	RIKEN cDNA 4931406B18 gene	protein-coding
mm_73400.1	chr8	105860598	105860608	+	1	NA	promoter-TSS (NM_026532)	promoter-TSS (NM_026532)	-31	NM_026532	68051	Mm.455474	NM_026532	ENSMUSG00000008450	Nutf2	2700067I02Rik|AI115459|AI413596|AW546000|Ntf2|Ntf3|PP15	nuclear transport factor 2	protein-coding
mm_30370.1	chr3	152193748	152193768	-	1	NA	promoter-TSS (NM_025926)	promoter-TSS (NM_025926)	87	NM_025926	67035	Mm.46746	NM_025926	ENSMUSG00000028035	Dnajb4	1700029A20Rik|2010306G19Rik|5730460G06Rik	DnaJ heat shock protein family (Hsp40) member B4	protein-coding
mm_82109.1	chr9	123113228	123113264	+	1	NA	promoter-TSS (NM_026917)	promoter-TSS (NM_026917)	15	NM_001081188	66446	Mm.41562	NM_001081188	ENSMUSG00000025785	Exosc7	2610002K22Rik|AV212732|mKIAA0116	exosome component 7	protein-coding
mm_41996.1	chr5	107830245	107830259	+	1	NA	promoter-TSS (NM_001276397)	promoter-TSS (NM_001276397)	90	NM_001276397	73318	Mm.441500	NM_028502	ENSMUSG00000063447	Ube2d2b	1700013N18Rik	ubiquitin-conjugating enzyme E2D 2B	protein-coding
mm_10982.1	chr2	25877888	25877898	+	1	NA	exon (NM_001302351, exon 1 of 31)	exon (NM_001302351, exon 1 of 31)	110	NM_001302351	227632	Mm.119462	NM_175462	ENSMUSG00000058740	Kcnt1	C030030G16Rik|Slack|Slo2.2|slo2	potassium channel, subfamily T, member 1	protein-coding
mm_39269.1	chr5	3657173	3657186	+	1	NA	5' UTR (NM_029154, exon 1 of 11)	5' UTR (NM_029154, exon 1 of 11)	175	NM_029154	75010	Mm.85064	NM_029141	ENSMUSG00000014529	Tmbim7	4930403J02Rik|4930500J03Rik|4930511M11Rik|Lfg5|Lgf5|Tmbim1b	transmembrane BAX inhibitor motif containing 7	protein-coding
mm_86231.1	chr9	120306038	120306049	-	1	NA	intron (NM_144557, intron 1 of 16)	intron (NM_144557, intron 1 of 16)	1970	NM_144557	245049	Mm.100936	NM_144557	ENSMUSG00000041794	Myrip	A230081N12Rik|Slac2-c|Slac2c	myosin VIIA and Rab interacting protein	protein-coding
mm_81194.1	chr9	107554607	107554631	+	1	NA	promoter-TSS (NM_019713)	promoter-TSS (NM_019713)	36	NM_019713	56289	Mm.12091	NM_019713	ENSMUSG00000010067	Rassf1	123F2|AA536941|AU044980|NORE2A|RDA32|REH3P21|Rassf1A|Rassf1B|Rassf1C	Ras association (RalGDS/AF-6) domain family member 1	protein-coding
mm_68213.1	chr7	104409437	104409450	-	1	NA	3' UTR (NM_009099, exon 8 of 8)	3' UTR (NM_009099, exon 8 of 8)	-50797	NM_175648	244183	Mm.347647	NM_175648	ENSMUSG00000052749	Trim30b	A530023O14Rik|Trim30-1	tripartite motif-containing 30B	protein-coding
mm_141.1	chr1	10993453	10993478	+	1	NA	promoter-TSS (NM_029525)	promoter-TSS (NM_029525)	0	NM_029525	109294	Mm.123247	NM_029525	ENSMUSG00000048960	Prex2	6230420N16Rik|AI316880|AI553603|C030045D06Rik|D430013K02|Depdc2|P-Rex2	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	protein-coding
mm_92608.1	chr10	80121755	80121767	-	1	NA	intron (NR_126043, intron 1 of 10)	MTEb|LTR|ERVL-MaLR	5958	NM_001301854	20869	Mm.44231	NM_011492	ENSMUSG00000003068	Stk11	AA408040|Lkb1|Par-4|R75140	serine/threonine kinase 11	protein-coding
mm_3815.1	chr1	159232160	159232232	+	1	NA	promoter-TSS (NM_011931)	promoter-TSS (NM_011931)	-130	NM_011931	26374	Mm.328135	NM_011931	ENSMUSG00000040782	Rfwd2	AI316802|C80879|Cop1	ring finger and WD repeat domain 2	protein-coding
mm_109019.1	chr12	103532436	103532485	+	1	NA	promoter-TSS (NM_028980)	promoter-TSS (NM_028980)	-105	NM_028980	74521	Mm.248619	NM_028980	ENSMUSG00000021209	Ppp4r4	8430415E04Rik|mKIAA1622	protein phosphatase 4, regulatory subunit 4	protein-coding
mm_161402.1	chr14	120324863	120324863	+	1	NA	5' UTR (NM_207515, exon 2 of 8)	5' UTR (NM_207515, exon 2 of 8)	49194	NM_175341	105559	Mm.238266	NM_175341	ENSMUSG00000022139	Mbnl2	1110002M11Rik|AI047808|AI837313|AI849185|AL118326|MBLL|R75232|mKIAA4072	muscleblind-like 2	protein-coding
mm_109929.1	chr12	8762067	8762070	-	1	NA	Intergenic	Intergenic	-9328	NM_011519	20969	Mm.2580	NM_011519	ENSMUSG00000020592	Sdc1	AA408134|AA409076|CD138|Sstn|Synd|Synd1|syn-1	syndecan 1	protein-coding
mm_142476.1	chr17	45686211	45686213	-	1	NA	promoter-TSS (NM_026732)	promoter-TSS (NM_026732)	6	NM_198167	224807	Mm.157904	NM_198167	ENSMUSG00000036026	Tmem63b	BC026370	transmembrane protein 63b	protein-coding
mm_23416.1	chr3	58526034	58526061	+	1	NA	promoter-TSS (NM_030685)	promoter-TSS (NM_030685)	-163	NM_030685	28146	Mm.29702	NM_030685	ENSMUSG00000027808	Serp1	D3Ucla1|Ramp4	stress-associated endoplasmic reticulum protein 1	protein-coding
mm_118683.1	chr14	22113447	22113454	+	1	NA	intron (NM_028275, intron 2 of 6)	T-rich|Low_complexity|Low_complexity	93738	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_147115.1	chr18	35739996	35740021	-	1	NA	5' UTR (NM_001289592, exon 2 of 8)	5' UTR (NM_001289592, exon 2 of 8)	546	NM_001289592	72512	Mm.45995	NM_028261	ENSMUSG00000024349	Tmem173	2610307O08Rik|ERIS|MPYS|Mita|STING	transmembrane protein 173	protein-coding
mm_122518.1	chr14	47189407	47189419	-	1	NA	promoter-TSS (NM_008102)	promoter-TSS (NM_008102)	-11	NM_008102	14528	Mm.10651	NM_008102	ENSMUSG00000037580	Gch1	GTP-CH|GTPCH|Gch	GTP cyclohydrolase 1	protein-coding
mm_124370.1	chr14	105897311	105897358	-	1	NA	promoter-TSS (NM_011897)	promoter-TSS (NM_011897)	-515	NM_011897	24064	Mm.89982	NM_011897	ENSMUSG00000022114	Spry2	sprouty2	sprouty homolog 2 (Drosophila)	protein-coding
mm_77046.1	chr8	109575921	109575931	-	1	NA	exon (NM_017370, exon 5 of 5)	exon (NM_017370, exon 5 of 5)	3246	NM_017370	15439	Mm.26730	NM_017370	ENSMUSG00000031722	Hp	HP-1|preHP2	haptoglobin	protein-coding
mm_58099.1	chr6	137563573	137563577	-	1	NA	intron (NM_001271588, intron 1 of 20)	intron (NM_001271588, intron 1 of 20)	7434	NM_001271595	13860	Mm.235346	NM_007945	ENSMUSG00000015766	Eps8	AW261790	epidermal growth factor receptor pathway substrate 8	protein-coding
mm_141489.1	chr17	31277328	31277352	-	1	NA	promoter-TSS (NM_025290)	promoter-TSS (NM_025290)	16	NM_025290	22092	Mm.12743	NM_025290	ENSMUSG00000024033	Rsph1	MCA|Tsga2	radial spoke head 1 homolog (Chlamydomonas)	protein-coding
mm_26724.1	chr3	159839730	159839745	+	1	NA	promoter-TSS (NR_037590)	promoter-TSS (NR_037590)	42	NM_026582	68151	Mm.6766	NM_026582	ENSMUSG00000028173	Wls	5031439A09Rik|AI173978|AI987742|Gpr177	wntless homolog (Drosophila)	protein-coding
mm_112529.1	chr13	9280650	9280653	+	1	NA	intron (NM_001081426, intron 1 of 36)	intron (NM_001081426, intron 1 of 36)	4126	NM_001081426	208440	Mm.217326	NM_172459	ENSMUSG00000048264	Dip2c	2900024P20Rik|9630044M06|mKIAA0934	disco interacting protein 2 homolog C	protein-coding
mm_134108.1	chr16	9995527	9995549	-	1	NA	Intergenic	CpG	-3005	NM_008170	14811	Mm.2953	NM_008170	ENSMUSG00000059003	Grin2a	GluN2A|NMDAR2A|NR2A	glutamate receptor, ionotropic, NMDA2A (epsilon 1)	protein-coding
mm_32336.1	chr4	104463975	104463977	+	1	NA	intron (NM_010014, intron 1 of 6)	intron (NM_010014, intron 1 of 6)	96438	NM_177259	13131	Mm.289682	NM_010014	ENSMUSG00000028519	Dab1	AI956902|C630028C02Rik|scm|scr|scrambler|yot	disabled 1	protein-coding
mm_171965.1	chr5	86369563	86369565	-	1	NA	intron (NM_145561, intron 1 of 9)	intron (NM_145561, intron 1 of 9)	3823	NM_145561	231382	Mm.240139	NM_145561	ENSMUSG00000061259	Tmprss11d	AST|AsP|BC020151	transmembrane protease, serine 11d	protein-coding
mm_68482.1	chr7	110982050	110982108	-	1	NA	5' UTR (NM_194464, exon 1 of 21)	5' UTR (NM_194464, exon 1 of 21)	382	NM_194464	17540	Mm.250023	NM_010826	ENSMUSG00000005611	Mrvi1	BB115629|Irag|Ris1	MRV integration site 1	protein-coding
mm_88911.1	chr10	81179682	81179739	+	1	NA	TTS (NR_028549)	TTS (NR_028549)	749	NR_028549	100217454		NR_028549	ENSMUSG00000064441	Snord37	MBII-376	small nucleolar RNA, C/D box 37	snoRNA
mm_78401.1	chr9	28921001	28921008	+	1	NA	3' UTR (NM_177906, exon 8 of 8)	3' UTR (NM_177906, exon 8 of 8)	1042125	NM_172290	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding
mm_37003.1	chr4	110356032	110356037	-	1	NA	Intergenic	Intergenic	-4123	NM_001163397	15572	Mm.3970	NM_010488	ENSMUSG00000028546	Elavl4	Elav|Hud|PNEM	ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4 (Hu antigen D)	protein-coding
mm_82760.1	chr9	26880573	26880574	-	1	NA	intron (NM_001281475, intron 20 of 20)	intron (NM_001281475, intron 20 of 20)	-19750	NM_001113323	70893	Mm.78118	NM_001113323	ENSMUSG00000031966	Glb1l3	4921509F24Rik	galactosidase, beta 1 like 3	protein-coding
mm_153007.1	chr19	30175444	30175466	-	1	NA	promoter-TSS (NM_138595)	promoter-TSS (NM_138595)	-14	NM_138595	104174	Mm.274852	NM_138595	ENSMUSG00000024827	Gldc	D030049L12Rik|D19Wsu57e	glycine decarboxylase	protein-coding
mm_75283.1	chr8	41016786	41016807	-	1	NA	promoter-TSS (NR_015457)	promoter-TSS (NR_015457)	-672	NR_015457	78849	Mm.440930	NR_015457	ENSMUSG00000084960	B430010I23Rik	-	RIKEN cDNA B430010I23 gene	ncRNA
mm_130770.1	chr15	101418349	101418367	-	1	NA	exon (NM_033073, exon 4 of 9)	exon (NM_033073, exon 4 of 9)	5955	NM_033073	110310	Mm.486285	NM_033073	ENSMUSG00000023039	Krt7	D15Wsu77e|K7|Krt2-7	keratin 7	protein-coding
mm_103290.1	chr11	72410308	72410320	-	1	NA	intron (NM_177776, intron 1 of 7)	intron (NM_177776, intron 1 of 7)	1399	NM_177776	276829	Mm.46732	NM_177776	ENSMUSG00000045667	Smtnl2	D130058I21Rik	smoothelin-like 2	protein-coding
mm_145454.1	chr18	60226143	60226152	+	1	NA	intron (NM_001033767, intron 2 of 2)	L1_Rod|LINE|L1	14070	NM_001033767	240327	Mm.357104	NM_001033767	ENSMUSG00000073555	Gm4951	EG240327|Ifgga2	predicted gene 4951	protein-coding
mm_158389.1	chrX	136172196	136172228	-	1	NA	promoter-TSS (NM_025703)	promoter-TSS (NM_025703)	39	NM_001168578	66684	Mm.182094	NM_025703	ENSMUSG00000051579	Tceal8	3930402F23Rik	transcription elongation factor A (SII)-like 8	protein-coding
mm_55903.1	chr6	83677808	83677812	-	1	NA	promoter-TSS (NM_144943)	promoter-TSS (NM_144943)	47	NM_144943	246278	Mm.136079	NM_144943	ENSMUSG00000034783	Cd207	-	CD207 antigen	protein-coding
mm_112679.1	chr13	16028300	16028308	+	1	NA	3' UTR (NM_008380, exon 5 of 5)	3' UTR (NM_008380, exon 5 of 5)	16453	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_8679.1	chr1	156814811	156814815	-	1	NA	intron (NR_027640, intron 17 of 19)	intron (NR_027640, intron 17 of 19)	-24210	NM_028333	72713	Mm.389206	NM_028333	ENSMUSG00000033544	Angptl1	2810039D03Rik|ANG3|ANGPT3|ANGY|ARP1	angiopoietin-like 1	protein-coding
mm_35738.1	chr4	45320377	45320438	-	1	NA	exon (NM_025513, exon 1 of 4)	exon (NM_025513, exon 1 of 4)	196	NM_025513	66362	Mm.275788	NM_025513	ENSMUSG00000028322	Exosc3	2310005D06Rik|AI593501|Rrp40	exosome component 3	protein-coding
mm_10497.1	chr2	14959758	14959761	+	1	NA	intron (NM_023116, intron 4 of 13)	intron (NM_023116, intron 4 of 13)	86103	NM_001309519	12296	Mm.313930	NM_023116	ENSMUSG00000057914	Cacnb2	AW060387|CAB2|Cavbeta2|Cchb2	calcium channel, voltage-dependent, beta 2 subunit	protein-coding
mm_18472.1	chr2	62411958	62411974	-	1	NA	5' UTR (NM_010074, exon 1 of 26)	5' UTR (NM_010074, exon 1 of 26)	265	NM_010074	13482	Mm.1151	NM_010074	ENSMUSG00000035000	Dpp4	Cd26|Dpp-4|THAM	dipeptidylpeptidase 4	protein-coding
mm_95854.1	chr11	57831708	57831720	+	1	NA	exon (NM_008213, exon 1 of 2)	exon (NM_008213, exon 1 of 2)	433	NM_008213	15110	Mm.4746	NM_008213	ENSMUSG00000037335	Hand1	Ehand1|Hxt|Th1|Thing1|bHLHa27|eHAND	heart and neural crest derivatives expressed transcript 1	protein-coding
mm_24179.1	chr3	88579603	88579727	+	1	NA	promoter-TSS (NM_025448)	promoter-TSS (NM_025448)	-6	NM_025448	66256	Mm.7091	NM_025448	ENSMUSG00000041355	Ssr2	1500032E05Rik|AI315033|AU020133|TLAP|TRAPB|TRAPbeta	signal sequence receptor, beta	protein-coding
mm_83093.1	chr9	40321182	40321190	-	1	NA	intron (NM_172768, intron 4 of 19)	intron (NM_172768, intron 4 of 19)	-12286	NR_040728	73558	Mm.398307	NR_040728		1700110K17Rik	-	RIKEN cDNA 1700110K17 gene	ncRNA
mm_56663.1	chr6	113531502	113531512	-	1	NA	promoter-TSS (NM_001033244)	promoter-TSS (NM_001033244)	131	NM_175101	66087	Mm.275989	NM_175101	ENSMUSG00000030286	Emc3	0610039A15Rik|AI225901|AW260416|Pob|Tmem111	ER membrane protein complex subunit 3	protein-coding
mm_9288.1	chr1	171634915	171634932	-	1	NA	3' UTR (NM_144539, exon 8 of 8)	3' UTR (NM_144539, exon 8 of 8)	6977	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_101712.1	chr11	42133493	42133531	-	1	NA	exon (NM_010250, exon 10 of 10)	exon (NM_010250, exon 10 of 10)	49418	NM_010250	14394	Mm.439668	NM_010250	ENSMUSG00000010803	Gabra1	Gabra-1	gamma-aminobutyric acid (GABA) A receptor, subunit alpha 1	protein-coding
mm_133711.1	chr16	93591160	93591185	+	1	NA	exon (NM_145482, exon 7 of 12)	exon (NM_145482, exon 7 of 12)	12643	NM_145482	224440	Mm.10628	NM_145482	ENSMUSG00000022948	Setd4	AY037804|C21orf18|ORF21	SET domain containing 4	protein-coding
mm_5573.1	chr1	39478681	39478733	-	1	NA	promoter-TSS (NM_018775)	promoter-TSS (NM_018775)	40	NM_018775	54610	Mm.387293	NM_018775	ENSMUSG00000003134	Tbc1d8	AD3|HBLP1|VRP	TBC1 domain family, member 8	protein-coding
mm_1660.1	chr1	74713304	74713332	+	1	NA	promoter-TSS (NM_024264)	promoter-TSS (NM_024264)	-217	NM_024264	104086	Mm.85083	NM_024264	ENSMUSG00000026170	Cyp27a1	1300013A03Rik|Cyp27	cytochrome P450, family 27, subfamily a, polypeptide 1	protein-coding
mm_81821.1	chr9	118047389	118047398	+	1	NA	intron (NM_001286507, intron 1 of 6)	intron (NM_001286507, intron 1 of 6)	6871	NM_013727	27215	Mm.92705	NM_013727	ENSMUSG00000039285	Azi2	AA410145|AZ2	5-azacytidine induced gene 2	protein-coding
mm_8776.1	chr1	161071406	161071417	-	1	NA	promoter-TSS (NM_172644)	promoter-TSS (NM_172644)	644	NR_131028	70454	Mm.248212	NM_027429	ENSMUSG00000026708	Cenpl	2610300B10Rik|AW121806|AW550697|CENP-L	centromere protein L	protein-coding
mm_145009.1	chr18	38542879	38542906	+	1	NA	Intergenic	Intergenic	58376	NM_011898	24066	Mm.42038	NM_011898	ENSMUSG00000024427	Spry4	A030006O18Rik|sprouty4	sprouty homolog 4 (Drosophila)	protein-coding
mm_161155.1	chr13	23934709	23934709	+	1	NA	promoter-TSS (NM_175663)	promoter-TSS (NM_175663)	247	NM_175658	319163	Mm.377876	NM_175658	ENSMUSG00000060081	Hist1h2aa	Th2a	histone cluster 1, H2aa	protein-coding
mm_45472.1	chr5	69483945	69483947	-	1	NA	Intergenic	L2a|LINE|L2	58701	NM_023784	75581	Mm.154776	NM_023784	ENSMUSG00000029158	Yipf7	2310016N21Rik|Yip1b	Yip1 domain family, member 7	protein-coding
mm_121928.1	chr14	23835542	23835567	-	1	NA	intron (NM_001253366, intron 1 of 29)	intron (NM_001253366, intron 1 of 29)	168651	NM_001253375	16531	Mm.343607	NM_010610	ENSMUSG00000063142	Kcnma1	5730414M22Rik|BKCa|MaxiK|Slo|Slo1|mSlo|mSlo1	potassium large conductance calcium-activated channel, subfamily M, alpha member 1	protein-coding
mm_141187.1	chr17	26939414	26939427	-	1	NA	promoter-TSS (NR_104458)	promoter-TSS (NR_104458)	38	NR_104458	67675	Mm.439919	NM_026307	ENSMUSG00000024194	Cuta	0610039D01Rik|1810022E02Rik|1810060C03Rik|2700094G22Rik|AI326454	cutA divalent cation tolerance homolog	protein-coding
mm_125660.1	chr15	64098317	64098351	+	1	NA	intron (NM_010026, intron 28 of 30)	intron (NM_010026, intron 28 of 30)	-37886	NM_144846	223601	Mm.246108	NM_144846	ENSMUSG00000022378	Fam49b	0910001A06Rik|AW122079	family with sequence similarity 49, member B	protein-coding
mm_152141.1	chr19	7094862	7094866	-	1	NA	3' UTR (NM_201411, exon 2 of 2)	3' UTR (NM_201411, exon 2 of 2)	10865	NM_201411	396184	Mm.386930	NM_201411	ENSMUSG00000047787	Flrt1	AW742165|D630040I23Rik	fibronectin leucine rich transmembrane protein 1	protein-coding
mm_11140.1	chr2	28480175	28480185	+	1	NA	Intergenic	RMER17B|LTR|ERVK	12114	NM_001166031	118451	Mm.294951	NM_080452	ENSMUSG00000035772	Mrps2	1500019M10Rik	mitochondrial ribosomal protein S2	protein-coding
mm_6453.1	chr1	74016583	74016593	-	1	NA	intron (NM_027884, intron 3 of 34)	intron (NM_027884, intron 3 of 34)	107859	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_117031.1	chr13	58274264	58274338	-	1	NA	promoter-TSS (NM_019832)	promoter-TSS (NM_019832)	-113	NM_019832	56278	Mm.296625	NM_019832	ENSMUSG00000021552	Gkap1	42kDa|4933400B15Rik|D13Ertd340e|Gkap42	G kinase anchoring protein 1	protein-coding
mm_48861.1	chr5	149814634	149814636	-	1	NA	Intergenic	L1MEg|LINE|L1	-2884	NR_077242	100861794	Mm.402054	NR_077242	ENSMUSG00000106740	Gm21221	-	predicted gene, 21221	ncRNA
mm_140233.1	chr17	84103635	84103648	+	1	NA	Intergenic	Intergenic	24981	NR_045458	74473	Mm.399575	NR_045458		4933433H22Rik	-	RIKEN cDNA 4933433H22 gene	ncRNA
mm_136568.1	chr17	3397190	3397204	+	1	NA	promoter-TSS (NM_011878)	promoter-TSS (NM_011878)	-10	NM_011878	24001	Mm.137134	NM_011878	ENSMUSG00000023800	Tiam2	3000002F19Rik|STEF|mKIAA2016	T cell lymphoma invasion and metastasis 2	protein-coding
mm_144161.1	chr18	5669263	5669269	+	1	NA	intron (NM_011546, intron 1 of 7)	RMER17D2|LTR|ERVK	-76829	NR_033552	791318	Mm.84339	NR_033552	ENSMUSG00000063087	Gm10125	ENSMUSG00000063087|Zeb1os	predicted gene 10125	ncRNA
mm_114106.1	chr13	54789427	54789497	+	1	NA	promoter-TSS (NM_028841)	promoter-TSS (NM_028841)	57	NM_028841	74257	Mm.32883	NM_028841	ENSMUSG00000025875	Tspan17	2210021G21Rik|AI047581|Fbxo23|Tm4sf17	tetraspanin 17	protein-coding
mm_159013.1	chr1	167466712	167466712	-	1	NA	promoter-TSS (NM_001013382)	promoter-TSS (NM_001013382)	68	NM_001013382	240899	Mm.159799	NM_001013382	ENSMUSG00000040485	Lrrc52	4930413P14Rik	leucine rich repeat containing 52	protein-coding
mm_95031.1	chr11	32057670	32057683	+	1	NA	3' UTR (NM_008741, exon 5 of 5)	3' UTR (NM_008741, exon 5 of 5)	43552	NR_130637	104692	Mm.414035	NR_130637	ENSMUSG00000086386	Gm12108	BB052462|OTTMUSG00000005365	predicted gene 12108	ncRNA
mm_133760.1	chr16	94468498	94468501	+	1	NA	3' UTR (NM_009441, exon 46 of 46)	3' UTR (NM_009441, exon 46 of 46)	58130	NM_007834	13185	Mm.7472	NM_007834	ENSMUSG00000022898	Dscr3	AW538125|Dcra	Down syndrome critical region gene 3	protein-coding
mm_63092.1	chr7	122366140	122366155	+	1	NA	intron (NM_001316672, intron 2 of 16)	intron (NM_001316672, intron 2 of 16)	77022	NM_008855	18751	Mm.207496	NM_008855	ENSMUSG00000052889	Prkcb	PKC-B|PKC-Beta|Pkcb|Prkcb1|Prkcb2	protein kinase C, beta	protein-coding
mm_47204.1	chr5	120907511	120907533	-	1	NA	promoter-TSS (NM_145211)	promoter-TSS (NM_145211)	3	NM_145211	246730	Mm.14301	NM_145211	ENSMUSG00000052776	Oas1a	L3	2'-5' oligoadenylate synthetase 1A	protein-coding
mm_98051.1	chr11	85739949	85739965	+	1	NA	intron (NM_138681, intron 24 of 25)	intron (NM_138681, intron 24 of 25)	-20213	NR_045875	71489	Mm.442482	NR_045875	ENSMUSG00000086199	Bcas3os1	8430403D17Rik	breast carcinoma amplified sequence 3, opposite strand 1	ncRNA
mm_147593.1	chr18	56675543	56675553	-	1	NA	Intergenic	Intergenic	-32265	NM_010721	16906	Mm.4105	NM_010721	ENSMUSG00000024590	Lmnb1	-	lamin B1	protein-coding
mm_47505.1	chr5	124035769	124035773	-	1	NA	Intergenic	Intergenic	-3511	NM_177876	330192	Mm.4079	NM_177876	ENSMUSG00000066278	Vps37b	2300007F24Rik|AI415429|BC026744	vacuolar protein sorting 37B	protein-coding
mm_91058.1	chr10	18848022	18848032	-	1	NA	intron (NM_022032, intron 1 of 2)	intron (NM_022032, intron 1 of 2)	2956	NM_022032	64058	Mm.28209	NM_022032	ENSMUSG00000019851	Perp	1110017A08Rik|KCP1|KRTCAP1|PIGPC1|THW	PERP, TP53 apoptosis effector	protein-coding
mm_77738.1	chr8	126937365	126937390	-	1	NA	intron (NM_024214, intron 3 of 4)	intron (NM_024214, intron 3 of 4)	8544	NM_024214	67952	Mm.6932	NM_024214	ENSMUSG00000093904	Tomm20	1810060K07Rik|BB284719|Gm19268|MAS20|MOM19|TOM20|mKIAA0016	translocase of outer mitochondrial membrane 20 homolog (yeast)	protein-coding
mm_154264.1	chr19	60771036	60771072	-	1	NA	exon (NM_010123, exon 15 of 22)	exon (NM_010123, exon 15 of 22)	3331	NR_034047	100217439		NR_034047		Snora19	MBI-51	small nucleolar RNA, H/ACA box 19	snoRNA
mm_166765.1	chr6	134020861	134020869	-	1	NA	Intergenic	LTR33C|LTR|ERVL	-14835	NM_001303102	14011	Mm.269995	NM_007961	ENSMUSG00000030199	Etv6	AW123102|AW557856|Tel	ets variant 6	protein-coding
mm_45989.1	chr5	90498328	90498367	-	1	NA	exon (NM_007423, exon 6 of 15)	exon (NM_007423, exon 6 of 15)	7633	NM_007423	11576	Mm.358570	NM_007423	ENSMUSG00000054932	Afp	-	alpha fetoprotein	protein-coding
mm_154412.1	chrM	15395	15430	+	1	NA	NA	Intergenic	NA	NA								
mm_133529.1	chr16	91011241	91011267	+	1	NA	promoter-TSS (NM_001045515)	promoter-TSS (NM_001045515)	5	NR_028368	67394	Mm.491293	NR_028368	ENSMUSG00000087354	4930404I05Rik	-	RIKEN cDNA 4930404I05 gene	ncRNA
mm_81256.1	chr9	107992464	107992522	+	1	NA	Intergenic	Intergenic	-6577	NM_026597	68176	Mm.76166	NM_026597	ENSMUSG00000042106	Fam212a	6230427J02Rik|Inka1	family with sequence similarity 212, member A	protein-coding
mm_26773.1	chr3	8964223	8964240	-	1	NA	promoter-TSS (NM_001025262)	promoter-TSS (NM_001025262)	-177	NM_001025261	21985	Mm.371590	NM_009412	ENSMUSG00000027506	Tpd52	AI043038|mD52	tumor protein D52	protein-coding
mm_98848.1	chr11	97659795	97659813	+	1	NA	Intergenic	Intergenic	-3608	NM_139311	246198	Mm.23685	NM_139311	ENSMUSG00000038437	Mllt6	AI315037|Af17	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 6	protein-coding
mm_115640.1	chr13	12260164	12260204	-	1	NA	Intergenic	Intergenic	-2071	NM_001081128	238505	Mm.40335	NM_001081128	ENSMUSG00000021311	Mtr	AI894170|D830038K18Rik|MS	5-methyltetrahydrofolate-homocysteine methyltransferase	protein-coding
mm_14297.1	chr2	128967350	128967380	+	1	NA	promoter-TSS (NM_178404)	promoter-TSS (NM_178404)	-37	NM_178404	78751	Mm.26377	NM_178404	ENSMUSG00000042851	Zc3h6	4631426G04Rik|4833425H18Rik|AU024389|AW060453|Zc3hdc6|mKIAA2035	zinc finger CCCH type containing 6	protein-coding
mm_160249.1	chr7	105404536	105404536	+	1	NA	promoter-TSS (NM_001033317)	promoter-TSS (NM_001033317)	-32	NM_001033317	233649	Mm.99556	NM_001033317	ENSMUSG00000030897	Cnga4	-	cyclic nucleotide gated channel alpha 4	protein-coding
mm_22606.1	chr3	14506638	14506655	+	1	NA	TTS (NM_080852)	TTS (NM_080852)	25947	NM_080852	140918	Mm.215250	NM_080852	ENSMUSG00000039710	Slc7a12	Asc-2|XAT1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 12	protein-coding
mm_165184.1	chr2	29889710	29889716	+	1	NA	promoter-TSS (NM_001113213)	promoter-TSS (NM_001113213)	-7	NM_001177661	18286	Mm.330116	NM_013615	ENSMUSG00000026790	Odf2	AI848335|MMTEST29	outer dense fiber of sperm tails 2	protein-coding
mm_42337.1	chr5	114903494	114903503	+	1	NA	intron (NM_011854, intron 3 of 5)	L1M5|LINE|L1	6564	NM_011854	23962	Mm.228363	NM_011854	ENSMUSG00000029561	Oasl2	M1204|Mmu-OASL|Oasl	2'-5' oligoadenylate synthetase-like 2	protein-coding
mm_102204.1	chr11	54778908	54778911	-	1	NA	intron (NM_178626, intron 1 of 5)	intron (NM_178626, intron 1 of 5)	8794	NM_178626	72729	Mm.29476	NM_178626	ENSMUSG00000052298	Cdc42se2	2810404F18Rik|AA408783|AA536669|SPEC2	CDC42 small effector 2	protein-coding
mm_83762.1	chr9	51963549	51963563	-	1	NA	promoter-TSS (NM_007996)	promoter-TSS (NM_007996)	46	NM_007996	14148	Mm.1061	NM_007996	ENSMUSG00000032051	Fdx1	-	ferredoxin 1	protein-coding
mm_95821.1	chr11	55394978	55395009	+	1	NA	3' UTR (NM_009242, exon 10 of 10)	3' UTR (NM_009242, exon 10 of 10)	25087	NM_009242	20692	Mm.291442	NM_009242	ENSMUSG00000018593	Sparc	BM-40|ON	secreted acidic cysteine rich glycoprotein	protein-coding
mm_99045.1	chr11	98974589	98974603	+	1	NA	3' UTR (NM_009024, exon 9 of 9)	3' UTR (NM_009024, exon 9 of 9)	8420	NM_178596	353155	Mm.453253	NM_178596	ENSMUSG00000047197	Gjd3	Gja11|Gjc1|cx30.2	gap junction protein, delta 3	protein-coding
mm_71174.1	chr8	40633581	40633610	+	1	NA	intron (NM_001040699, intron 1 of 13)	intron (NM_001040699, intron 1 of 13)	1197	NM_001040699	54384	Mm.294871	NM_019433	ENSMUSG00000039431	Mtmr7	-	myotubularin related protein 7	protein-coding
mm_68157.1	chr7	102481690	102481696	-	1	NA	Intergenic	Intergenic	-3791	NM_001011782	257947	Mm.376117	NM_001011782	ENSMUSG00000044814	Olfr543	MOR42-2	olfactory receptor 543	protein-coding
mm_88070.1	chr10	67797936	67797937	+	1	NA	Intergenic	Intergenic	114726	NM_178679	216049	Mm.268346	NM_178679	ENSMUSG00000037855	Zfp365	AI839779|AV340892|DBZ|Su48|Znf365|talanin	zinc finger protein 365	protein-coding
mm_80836.1	chr9	97111303	97111319	+	1	NA	promoter-TSS (NM_138756)	promoter-TSS (NM_138756)	-270	NM_138756	192287	Mm.228067	NM_138756	ENSMUSG00000032449	Slc25a36	C330005L02Rik	solute carrier family 25, member 36	protein-coding
mm_11170.1	chr2	28560949	28560963	+	1	NA	exon (NM_009885, exon 3 of 11)	exon (NM_009885, exon 3 of 11)	2447	NM_009885	12613	Mm.236017	NM_009885	ENSMUSG00000026818	Cel	1810036E18Rik|BAL	carboxyl ester lipase	protein-coding
mm_39076.1	chr4	154300030	154300079	-	1	NA	promoter-TSS (NM_001112744)	promoter-TSS (NM_001112744)	-159	NM_001112744	230972	Mm.38481	NM_001112744	ENSMUSG00000029032	Arhgef16	-	Rho guanine nucleotide exchange factor (GEF) 16	protein-coding
mm_90604.1	chr10	128322608	128322621	+	1	NA	5' UTR (NM_019953, exon 1 of 6)	5' UTR (NM_019953, exon 1 of 6)	155	NM_019953	56530	Mm.44220	NM_019953	ENSMUSG00000025381	Cnpy2	5330432A10Rik|AW229003|D10Bwg1546e|Tmem4|Zsig9	canopy FGF signaling regulator 2	protein-coding
mm_19115.1	chr2	79908429	79908438	-	1	NA	promoter-TSS (NM_001009978)	promoter-TSS (NM_001009978)	-34	NM_001009978	18573	Mm.40678	NM_016744	ENSMUSG00000059173	Pde1a	AI987702|AW125737	phosphodiesterase 1A, calmodulin-dependent	protein-coding
mm_15905.1	chr2	164968321	164968323	+	1	NA	5' UTR (NM_020333, exon 1 of 26)	5' UTR (NM_020333, exon 1 of 26)	334	NM_020333	57138	Mm.252987	NM_020333	ENSMUSG00000017740	Slc12a5	KCC2|mKIAA1176	solute carrier family 12, member 5	protein-coding
mm_161574.1	chr16	23107433	23107433	+	1	NA	promoter-TSS (NM_001123037)	promoter-TSS (NM_001123037)	-35	NM_001123038	13682	Mm.260084	NM_013506	ENSMUSG00000022884	Eif4a2	4833432N07Rik|BM-010|Ddx2b|Eif4|eIF-4A-II|eIF4A-II	eukaryotic translation initiation factor 4A2	protein-coding
mm_68944.1	chr7	126503604	126503613	-	1	NA	promoter-TSS (NM_183020)	promoter-TSS (NM_183020)	-306	NM_183020	233871	Mm.231450	NM_183020	ENSMUSG00000032637	Atxn2l	A2D|A2LG|A2RP|A2lp|Atxnl2	ataxin 2-like	protein-coding
mm_53443.1	chr6	134396322	134396338	+	1	NA	promoter-TSS (NM_025778)	promoter-TSS (NM_025778)	1	NM_025778	66813	Mm.474472	NM_025778	ENSMUSG00000030200	Bcl2l14	4930452K23Rik|4933405K19Rik|9030625M01Rik|AI429211|Bclg	BCL2-like 14 (apoptosis facilitator)	protein-coding
mm_169027.1	chr13	117966540	117966556	-	1	NA	intron (NM_010408, intron 6 of 7)	CT-rich|Low_complexity|Low_complexity	-246537	NR_045508	71100	Mm.414841	NR_045508	ENSMUSG00000079048	4933413L06Rik	-	RIKEN cDNA 4933413L06 gene	ncRNA
mm_140794.1	chr17	20945063	20945128	-	1	NA	promoter-TSS (NM_016891)	promoter-TSS (NM_016891)	-359	NM_016891	51792	Mm.294138	NM_016891	ENSMUSG00000007564	Ppp2r1a	6330556D22Rik|PP2A|PR65	protein phosphatase 2, regulatory subunit A, alpha	protein-coding
mm_110082.1	chr12	24681777	24681812	-	1	NA	promoter-TSS (NM_001161807)	promoter-TSS (NM_001161807)	1	NM_138686	12879	Mm.52265	NM_138686	ENSMUSG00000062563	Cys1	2900006B19Rik|AV218859|Ccap|ck|cpk	cystin 1	protein-coding
mm_161854.1	chr18	15410935	15410935	-	1	NA	promoter-TSS (NM_001308646)	promoter-TSS (NM_001308646)	47	NM_001308643	11829	Mm.250786	NM_009700	ENSMUSG00000024411	Aqp4	WCH4	aquaporin 4	protein-coding
mm_27503.1	chr3	55403212	55403225	-	1	NA	intron (NM_019978, intron 4 of 16)	intron (NM_019978, intron 4 of 16)	-58540	NM_001195539	13175	Mm.393242	NM_019978	ENSMUSG00000027797	Dclk1	1700113D08Rik|2810480F11Rik|AI836758|Click-I|Cpg16|Dcamkl1|Dcl|Dclk|mKIAA0369	doublecortin-like kinase 1	protein-coding
mm_64548.1	chr7	144407111	144407131	+	1	NA	exon (NM_001081370, exon 8 of 11)	exon (NM_001081370, exon 8 of 11)	36312	NR_037302	100499519		NR_037302	ENSMUSG00000093912	Mir3470b	mmu-mir-3470b	microRNA 3470b	ncRNA
mm_87098.1	chr10	33091413	33091417	+	1	NA	intron (NM_029726, intron 1 of 37)	intron (NM_029726, intron 1 of 37)	7932	NM_029726	76757	Mm.338508	NM_029726	ENSMUSG00000019787	Trdn	2310045H21Rik|EG432451|TDN	triadin	protein-coding
mm_66551.1	chr7	45211878	45211887	-	1	NA	promoter-TSS (NM_015789)	promoter-TSS (NM_015789)	1	NM_015789	50722	Mm.27287	NM_015789	ENSMUSG00000030792	Dkkl1	AI414495|SGY|SGY-1|SGY1|Soggy|mSgy	dickkopf-like 1	protein-coding
mm_47382.1	chr5	122990405	122990407	-	1	NA	intron (NR_045820, intron 1 of 2)	intron (NR_045820, intron 1 of 2)	1052	NR_045820	109202	Mm.30769	NM_175405	ENSMUSG00000056735	A930024E05Rik	-	RIKEN cDNA A930024E05 gene	ncRNA
mm_135853.1	chr16	59557403	59557441	-	1	NA	Intergenic	Intergenic	-1670	NM_174848	224273	Mm.246424	NM_174848	ENSMUSG00000022723	Crybg3	5031404N19|AU022790|Gm9581	beta-gamma crystallin domain containing 3	protein-coding
mm_17430.1	chr2	27507568	27507591	-	1	NA	Intergenic	Intergenic	-7568	NM_080848	140858	Mm.28265	NM_080848	ENSMUSG00000026917	Wdr5	2410008O07Rik|AA408785|AA960360|Big|Big-3	WD repeat domain 5	protein-coding
mm_145404.1	chr18	57405398	57405432	+	1	NA	Intergenic	Intergenic	50682	NM_028447	73137	Mm.29889	NM_028447	ENSMUSG00000024594	Prrc1	1190002C06Rik|2310058D16Rik|3110038B19Rik|9430085A19Rik	proline-rich coiled-coil 1	protein-coding
mm_31137.1	chr4	43264250	43264256	+	1	NA	3' UTR (NM_021468, exon 40 of 40)	3' UTR (NM_021468, exon 40 of 40)	-2906	NM_177195	320571	Mm.74465	NM_177195	ENSMUSG00000028457	Atp8b5	4930417M19Rik|Feta	ATPase, class I, type 8B, member 5	protein-coding
mm_82804.1	chr9	29834435	29834439	-	1	NA	intron (NM_172290, intron 1 of 7)	intron (NM_172290, intron 1 of 7)	128692	NM_172290	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding
mm_7135.1	chr1	91053847	91053850	-	1	NA	intron (NM_001310732, intron 1 of 24)	intron (NM_001310732, intron 1 of 24)	404	NM_008515	16978	Mm.45039	NM_008515	ENSMUSG00000026305	Lrrfip1	AU024550|Fliiap1	leucine rich repeat (in FLII) interacting protein 1	protein-coding
mm_107069.1	chr12	16895083	16895090	+	1	NA	5' UTR (NM_009072, exon 1 of 33)	5' UTR (NM_009072, exon 1 of 33)	108	NM_009072	19878	Mm.276024	NM_009072	ENSMUSG00000020580	Rock2	B230113H15Rik|ROKalpha|Rho-kinase|Rock-II|Rock2m|mKIAA0619	Rho-associated coiled-coil containing protein kinase 2	protein-coding
mm_111334.1	chr12	86824915	86824956	-	1	NA	Intergenic	Intergenic	59879	NM_145836	238330	Mm.248358	NM_145836	ENSMUSG00000034168	Irf2bpl	6430527G18Rik|Eap1	interferon regulatory factor 2 binding protein-like	protein-coding
mm_130422.1	chr15	98093275	98093294	-	1	NA	5' UTR (NM_144851, exon 1 of 18)	5' UTR (NM_144851, exon 1 of 18)	285	NM_144851	223870	Mm.384023	NM_144851	ENSMUSG00000033075	Senp1	2310046A20Rik|D15Ertd528e|E330036L07Rik|suPr-2	SUMO1/sentrin specific peptidase 1	protein-coding
mm_82693.1	chr9	22376232	22376241	-	1	NA	exon (NM_028390, exon 4 of 24)	exon (NM_028390, exon 4 of 24)	2987	NR_030448	751551		NR_030448	ENSMUSG00000076117	Mir680-2	Mirn680-2	microRNA 680-2	ncRNA
mm_45438.1	chr5	67269478	67269490	-	1	NA	intron (NM_001285452, intron 5 of 6)	MTC|LTR|ERVL-MaLR	8919	NM_030108	67878	Mm.23217	NM_028975	ENSMUSG00000037720	Tmem33	1110006G02Rik|1600019D15Rik|2410089A21Rik|2700052H22Rik|5430406L04Rik|AA388285|AI314185|AI426615|db83	transmembrane protein 33	protein-coding
mm_173172.1	chrX	4899401	4899409	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-52730	NM_001243024	100042275	Mm.427352	NM_001243024	ENSMUSG00000094860	Btbd35f27	Gm3763	BTB domain containing 35, family member 27	protein-coding
mm_171068.1	chr3	114094556	114094558	+	1	NA	exon (NM_007729, exon 6 of 67)	exon (NM_007729, exon 6 of 67)	64017	NM_007729	12814	Mm.209715	NM_007729	ENSMUSG00000027966	Col11a1	C530001D20Rik|cho	collagen, type XI, alpha 1	protein-coding
mm_123418.1	chr14	64403663	64403665	-	1	NA	intron (NM_001253712, intron 1 of 5)	intron (NM_001253712, intron 1 of 5)	13292	NM_001253716	110265	Mm.26713	NM_026322	ENSMUSG00000054733	Msra	2310045J23Rik|6530413P12Rik|MSR-A	methionine sulfoxide reductase A	protein-coding
mm_74426.1	chr8	3672291	3672364	-	1	NA	Intergenic	Intergenic	-4150	NM_025701	66682	Mm.29090	NM_025701	ENSMUSG00000040236	Trappc5	4021401A16Rik|TRS31	trafficking protein particle complex 5	protein-coding
mm_64666.1	chr7	4426798	4426801	-	1	NA	3' UTR (NM_001290411, exon 7 of 7)	3' UTR (NM_001290411, exon 7 of 7)	18858	NM_175372	108841	Mm.413106	NM_175372	ENSMUSG00000008435	Rdh13	8430425D21Rik	retinol dehydrogenase 13 (all-trans and 9-cis)	protein-coding
mm_23667.1	chr3	68506910	68506915	+	1	NA	intron (NM_001113419, intron 5 of 10)	MamRep1879|DNA|hAT-Tip100?	12731	NM_001282044	30953	Mm.331064	NM_013928	ENSMUSG00000027777	Schip1	Nf2ip|Schip-1	schwannomin interacting protein 1	protein-coding
mm_55850.1	chr6	83416619	83416623	-	1	NA	intron (NM_001347313, intron 3 of 11)	intron (NM_001347313, intron 3 of 11)	-15519	NR_105793	102465194		NR_105793	ENSMUSG00000099045	Mir6374	Gm27292|mmu-mir-6374	microRNA 6374	ncRNA
mm_43263.1	chr5	130280943	130280952	+	1	NA	intron (NM_001015876, intron 8 of 15)	MTD|LTR|ERVL-MaLR	23910	NM_001015876	100929	Mm.271296	NM_178897	ENSMUSG00000056310	Tyw1	AW125391|Rsafd1	tRNA-yW synthesizing protein 1 homolog (S. cerevisiae)	protein-coding
mm_92556.1	chr10	79766995	79767017	-	1	NA	promoter-TSS (NM_144528)	promoter-TSS (NM_144528)	-54	NR_027505	70294	Mm.466670	NM_144528	ENSMUSG00000035890	Rnf126	2610010O19Rik	ring finger protein 126	protein-coding
mm_123599.1	chr14	67780463	67780476	-	1	NA	intron (NM_177780, intron 36 of 51)	intron (NM_177780, intron 36 of 51)	35288	NR_133010	14714	Mm.358309	NM_008145	ENSMUSG00000015812	Gnrh1	Gnrh|Gnrh2|LHRH|Lhrh1|Lnrh|hpg	gonadotropin releasing hormone 1	protein-coding
mm_100392.1	chr11	119390059	119390104	+	1	NA	promoter-TSS (NR_035453)	promoter-TSS (NR_035453)	-391	NR_035453	100316690		NR_035453	ENSMUSG00000088015	Mir1932	mir-1932|mmu-mir-1932	microRNA 1932	ncRNA
mm_19926.1	chr2	116063849	116063900	-	1	NA	intron (NM_001346047, intron 2 of 13)	intron (NM_001346047, intron 2 of 13)	745	NM_001346044	17536	Mm.247566	NM_010825	ENSMUSG00000027210	Meis2	A430109D20Rik|Mrg1|Stra10	Meis homeobox 2	protein-coding
mm_25187.1	chr3	103385175	103385191	+	1	NA	Intergenic	Intergenic	105890	NM_001079830	94093	Mm.195036	NM_053170	ENSMUSG00000033014	Trim33	8030451N04Rik|AI413936|Ecto|Tif1g	tripartite motif-containing 33	protein-coding
mm_165763.1	chr3	118756291	118756291	+	1	NA	intron (NM_170778, intron 3 of 22)	intron (NM_170778, intron 3 of 22)	194113	NM_170778	99586	Mm.27907	NM_170778	ENSMUSG00000033308	Dpyd	AI315208|DPD|E330028L06Rik	dihydropyrimidine dehydrogenase	protein-coding
mm_56431.1	chr6	97312523	97312559	-	1	NA	intron (NM_001346639, intron 11 of 22)	intron (NM_001346639, intron 11 of 22)	-59761	NM_001081157	320502	Mm.68163	NM_001081157	ENSMUSG00000044086	Lmod3	5430424A14Rik	leiomodin 3 (fetal)	protein-coding
mm_130642.1	chr15	100580205	100580236	-	1	NA	intron (NM_001304965, intron 9 of 10)	intron (NM_001304965, intron 9 of 10)	6145	NM_010127	19009	Mm.28825	NM_010127	ENSMUSG00000009739	Pou6f1	2310038G18Rik|C79593|Emb|cns-1	POU domain, class 6, transcription factor 1	protein-coding
mm_139761.1	chr17	64600769	64600780	+	1	NA	promoter-TSS (NM_008549)	promoter-TSS (NM_008549)	-875	NM_008549	17158	Mm.2433	NM_008549	ENSMUSG00000024085	Man2a1	Mana-2|Mana2|Map-2	mannosidase 2, alpha 1	protein-coding
mm_56383.1	chr6	94283849	94283936	-	1	NA	promoter-TSS (NM_010367)	promoter-TSS (NM_010367)	25	NM_001286786	14924	Mm.217216	NM_010367	ENSMUSG00000045095	Magi1	AIP3|BAP1|Baiap1|Gukmi1|MAGI1c|Magi-1|TNRC19|WWP3|mKIAA4129	membrane associated guanylate kinase, WW and PDZ domain containing 1	protein-coding
mm_103276.1	chr11	72135989	72136009	-	1	NA	promoter-TSS (NM_001081641)	promoter-TSS (NM_001081641)	-110	NM_001081641	327958	Mm.351793	NM_001024927	ENSMUSG00000040543	Pitpnm3	A330068P14Rik|AI848332|Ackr6|Gm880	PITPNM family member 3	protein-coding
mm_116781.1	chr13	53163477	53163480	-	1	NA	intron (NM_013846, intron 1 of 8)	intron (NM_013846, intron 1 of 8)	122631	NM_013846	26564	Mm.342774	NM_013846	ENSMUSG00000021464	Ror2	Ntrkr2|mRor2	receptor tyrosine kinase-like orphan receptor 2	protein-coding
mm_82282.1	chr9	7572742	7572752	-	1	NA	intron (NM_001310717, intron 2 of 9)	(A)n|Simple_repeat|Simple_repeat	1351	NM_001310717	234911	Mm.334940	NM_001030289	ENSMUSG00000070323	Mmp27	Gm180	matrix metallopeptidase 27	protein-coding
mm_81288.1	chr9	108306823	108306847	+	1	NA	promoter-TSS (NM_133986)	promoter-TSS (NM_133986)	38	NM_001313962	11848	Mm.757	NM_016802	ENSMUSG00000007815	Rhoa	Arha|Arha1|Arha2	ras homolog family member A	protein-coding
mm_27888.1	chr3	79269759	79269763	-	1	NA	Intergenic	Intergenic	56842	NR_045502	70924	Mm.444622	NR_045502	ENSMUSG00000104585	4921511C10Rik	-	RIKEN cDNA 4921511C10 gene	ncRNA
mm_85558.1	chr9	106887104	106887112	-	1	NA	promoter-TSS (NM_175402)	promoter-TSS (NM_175402)	-108	NM_175402	109095	Mm.431589	NM_175402	ENSMUSG00000074102	Rbm15b	1810017N16Rik	RNA binding motif protein 15B	protein-coding
mm_137179.1	chr17	23816212	23816231	+	1	NA	exon (NM_175229, exon 10 of 14)	exon (NM_175229, exon 10 of 14)	12888	NM_026305	67673	Mm.153758	NM_026305	ENSMUSG00000055839	Elob	0610040H15Rik|Tceb2	elongin B	protein-coding
mm_84354.1	chr9	64341293	64341311	-	1	NA	promoter-TSS (NM_001177784)	promoter-TSS (NM_001177784)	-45	NM_001001295	213550	Mm.268341	NM_172519	ENSMUSG00000032396	Dis3l	AV340375	DIS3 like exosome 3'-5' exoribonuclease	protein-coding
mm_41714.1	chr5	101897931	101897931	+	1	NA	intron (NM_172882, intron 34 of 66)	MIRb|SINE|MIR	132801	NM_173370	74596	Mm.46764	NM_173370	ENSMUSG00000029330	Cds1	4833409J18Rik|AI314024|AW125888	CDP-diacylglycerol synthase 1	protein-coding
mm_1224.1	chr1	62743575	62743602	+	1	NA	intron (NM_001077405, intron 3 of 15)	intron (NM_001077405, intron 3 of 15)	40271	NM_001077405	18187	Mm.266341	NM_010939	ENSMUSG00000025969	Nrp2	1110048P06Rik|Np-2|Np2|Npn-2|Npn2	neuropilin 2	protein-coding
mm_36301.1	chr4	68882672	68882677	-	1	NA	intron (NM_019967, intron 2 of 7)	intron (NM_019967, intron 2 of 7)	71723	NM_019967	56710	Mm.248788	NM_019967	ENSMUSG00000028351	Brinp1	BRINP|Dbc1|Dbccr1|Fam5a	bone morphogenic protein/retinoic acid inducible neural specific 1	protein-coding
mm_133409.1	chr16	84852892	84852897	+	1	NA	intron (NM_008065, intron 6 of 9)	intron (NM_008065, intron 6 of 9)	-17269	NM_001302213	11957	Mm.353	NM_016755	ENSMUSG00000022890	Atp5j	CF6	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit F	protein-coding
mm_112677.1	chr13	16027985	16027995	+	1	NA	3' UTR (NM_008380, exon 5 of 5)	3' UTR (NM_008380, exon 5 of 5)	16139	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_51011.1	chr6	65017863	65017869	+	1	NA	Intergenic	RLTR1B|LTR|ERV1	-24801	NM_007958	13990	Mm.99113	NM_007958	ENSMUSG00000029920	Smarcad1	AV081750|AW226546|D6Pas1|Etl1|mKIAA1122	SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1	protein-coding
mm_14122.1	chr2	125941755	125941762	+	1	NA	intron (NM_175154, intron 7 of 9)	intron (NM_175154, intron 7 of 9)	75535	NM_001291002	69976	Mm.20216	NM_175154	ENSMUSG00000027207	Galk2	2810017M24Rik|AI327030|Gk2	galactokinase 2	protein-coding
mm_14491.1	chr2	131936793	131936804	+	1	NA	exon (NM_001278256, exon 4 of 4)	exon (NM_001278256, exon 4 of 4)	-14063	NM_001278257	26434	Mm.180750	NM_023043	ENSMUSG00000027338	Prnd	AI450264|Dpl|PrPLP|doppel	prion protein dublet	protein-coding
mm_21324.1	chr2	157101211	157101228	-	1	NA	intron (NM_018851, intron 15 of 15)	(TG)n|Simple_repeat|Simple_repeat	14164	NM_001177439	383766	Mm.480305	NM_001177439	ENSMUSG00000074628	Tldc2	Gm1332	TBC/LysM associated domain containing 2	protein-coding
mm_80947.1	chr9	102834962	102834972	+	1	NA	promoter-TSS (NM_013649)	promoter-TSS (NM_013649)	47	NM_001042607	20187	Mm.335391	NM_013649	ENSMUSG00000032547	Ryk	AW536699|ERK-3|Vik	receptor-like tyrosine kinase	protein-coding
mm_129023.1	chr15	74958613	74958626	-	1	NA	exon (NM_001164036, exon 4 of 4)	exon (NM_001164036, exon 4 of 4)	3513	NM_001164040	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_173246.1	chrX	89488502	89488506	+	1	NA	Intergenic	L1Md_T|LINE|L1	-78815	NM_008821	18630	Mm.3086	NM_008821	ENSMUSG00000035395	Pet2	PC231|PC326|Pex3	plasmacytoma expressed transcript 2	protein-coding
mm_170867.1	chr2	18453769	18453769	+	1	NA	Intergenic	RLTR9E|LTR|ERVK	-60939	NM_007869	13418	Mm.246674	NM_007869	ENSMUSG00000026740	Dnajc1	4733401K02Rik|AA960110|D230036H06Rik|Dnajl1|ERdj1|ERj1p|MTJ1	DnaJ heat shock protein family (Hsp40) member C1	protein-coding
mm_155896.1	chrX	101652705	101652731	+	1	NA	intron (NM_139144, intron 4 of 21)	intron (NM_139144, intron 4 of 21)	12500	NM_001290535	108155	Mm.487332	NM_139144	ENSMUSG00000034160	Ogt	1110038P24Rik|4831420N21Rik|AI115525|Ogtl	O-linked N-acetylglucosamine (GlcNAc) transferase (UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase)	protein-coding
mm_82993.1	chr9	36599488	36599495	-	1	NA	Intergenic	Intergenic	-16856	NM_001167584	100312948	Mm.475849	NM_001167584	ENSMUSG00000091248	Gm17689	Pate-g|Pate8	predicted gene, 17689	protein-coding
mm_89145.1	chr10	85929083	85929087	+	1	NA	3' UTR (NM_001163614, exon 1 of 1)	3' UTR (NM_001163614, exon 1 of 1)	594	NM_001163614	67341	Mm.382315	NM_001163614	ENSMUSG00000085111	Ascl4	1700054F16Rik|bHLHa44	achaete-scute family bHLH transcription factor 4	protein-coding
mm_109564.1	chr12	111966786	111966791	+	1	NA	intron (NM_027360, intron 1 of 3)	CpG	189	NM_027360	70257	Mm.318	NM_027360	ENSMUSG00000021290	2010107E04Rik	9430003J03Rik|AU043134|AV124504|Mp68	RIKEN cDNA 2010107E04 gene	protein-coding
mm_36694.1	chr4	96658671	96658681	-	1	NA	exon (NM_010007, exon 4 of 9)	exon (NM_010007, exon 4 of 9)	5443	NM_010007	13109	Mm.12838	NM_010007	ENSMUSG00000052520	Cyp2j5	-	cytochrome P450, family 2, subfamily j, polypeptide 5	protein-coding
mm_54779.1	chr6	41541783	41541799	-	1	NA	Intergenic	Intergenic	20015	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_38947.1	chr4	150544992	150545032	-	1	NA	intron (NM_001085492, intron 11 of 22)	intron (NM_001085492, intron 11 of 22)	107162	NM_173774	242773	Mm.29280	NM_173774	ENSMUSG00000039838	Slc45a1	C230078B22|Dnb5	solute carrier family 45, member 1	protein-coding
mm_104692.1	chr11	97829916	97829944	-	1	NA	intron (NM_010688, intron 4 of 6)	intron (NM_010688, intron 4 of 6)	-10850	NM_001080935	68127	Mm.110270	NM_001080935	ENSMUSG00000050538	B230217C12Rik	AI840637	RIKEN cDNA B230217C12 gene	protein-coding
mm_110026.1	chr12	16800675	16800705	-	1	NA	5' UTR (NM_015764, exon 1 of 35)	5' UTR (NM_015764, exon 1 of 35)	196	NM_015764	268527	Mm.428062	NM_015764	ENSMUSG00000036523	Greb1	5730583K22Rik|9130004E13|AF180470|AU023194|mKIAA0575	gene regulated by estrogen in breast cancer protein	protein-coding
mm_319.1	chr1	24678537	24678609	+	1	NA	promoter-TSS (NM_026719)	promoter-TSS (NM_026719)	29	NM_026719	68421	Mm.336563	NM_026719	ENSMUSG00000073725	Lmbrd1	0910001K20Rik|AV347960	LMBR1 domain containing 1	protein-coding
mm_97595.1	chr11	78948329	78948337	+	1	NA	exon (NM_010927, exon 17 of 27)	exon (NM_010927, exon 17 of 27)	23042	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_159595.1	chr4	126325411	126325411	-	1	NA	promoter-TSS (NM_011902)	promoter-TSS (NM_011902)	-212	NM_011902	24084	Mm.23895	NM_011902	ENSMUSG00000028845	Tekt2	AU014974|tektin-t	tektin 2	protein-coding
mm_5504.1	chr1	37429990	37430000	-	1	NA	promoter-TSS (NM_026123)	promoter-TSS (NM_026123)	108	NM_198006	76178	Mm.28085	NM_198006	ENSMUSG00000026112	Coa5	1700001A24Rik|6330578E17Rik|Pet191	cytochrome C oxidase assembly factor 5	protein-coding
mm_25290.1	chr3	105815531	105815555	+	1	NA	promoter-TSS (NR_045845)	promoter-TSS (NR_045845)	-24	NR_045845	433637	Mm.331285	NR_045845	ENSMUSG00000104835	Gm5547	EG433637	predicted gene 5547	ncRNA
mm_172650.1	chr8	33488464	33488467	+	1	NA	Intergenic	RLTR10A|LTR|ERVK	4154	NR_033589	628431	Mm.376526	NR_033589		Hmgb1-rs17	Hmg1-rs17	high mobility group box 1, related sequence 17	pseudo
mm_38352.1	chr4	137782183	137782229	-	1	NA	intron (NM_007431, intron 1 of 11)	intron (NM_007431, intron 1 of 11)	14178	NM_007431	11647	Mm.288186	NM_007431	ENSMUSG00000028766	Alpl	ALP|APTNAP|Akp-2|Akp2|TNAP|TNSALP	alkaline phosphatase, liver/bone/kidney	protein-coding
mm_67460.1	chr7	80403316	80403339	-	1	NA	promoter-TSS (NM_011046)	promoter-TSS (NM_011046)	-515	NM_011046	18550	Mm.5241	NM_011046	ENSMUSG00000030530	Furin	9130404I01Rik|Fur|PACE|Pcsk3|SPC1	furin (paired basic amino acid cleaving enzyme)	protein-coding
mm_20820.1	chr2	144720601	144720607	-	1	NA	intron (NM_025314, intron 4 of 5)	intron (NM_025314, intron 4 of 5)	-103062	NM_025490	66328	Mm.45377	NM_025490	ENSMUSG00000027431	Scp2d1	1700010M22Rik	SCP2 sterol-binding domain containing 1	protein-coding
mm_65652.1	chr7	28131665	28131669	-	1	NA	exon (NM_001164655, exon 3 of 20)	exon (NM_001164655, exon 3 of 20)	2201	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_11039.1	chr2	27009933	27009935	+	1	NA	promoter-TSS (NM_029862)	promoter-TSS (NM_029862)	8	NM_001243239	381356	Mm.150270	NM_029862	ENSMUSG00000015488	Cacfd1	5930434B04Rik|mFwe	calcium channel flower domain containing 1	protein-coding
mm_90130.1	chr10	117711715	117711756	+	1	NA	promoter-TSS (NM_010786)	promoter-TSS (NM_010786)	-977	NM_001288586	17246	Mm.22670	NM_010786	ENSMUSG00000020184	Mdm2	1700007J15Rik|AA415488|Mdm-2	transformed mouse 3T3 cell double minute 2	protein-coding
mm_89782.1	chr10	101681696	101681720	+	1	NA	5' UTR (NM_001205098, exon 1 of 8)	5' UTR (NM_001205098, exon 1 of 8)	221	NM_001205098	67569	Mm.25252	NM_026243	ENSMUSG00000019888	Mgat4c	9130411I17Rik|GntIVh	MGAT4 family, member C	protein-coding
mm_28767.1	chr3	95899492	95899529	-	1	NA	TTS (NM_146104)	TTS (NM_146104)	5129	NM_011797	23831	Mm.489647	NM_011797	ENSMUSG00000038526	Car14	AW536446|Ca14	carbonic anhydrase 14	protein-coding
mm_153058.1	chr19	32181326	32181332	-	1	NA	intron (NM_001168525, intron 5 of 9)	intron (NM_001168525, intron 5 of 9)	29684	NM_001168526	208449	Mm.329810	NM_144792	ENSMUSG00000040451	Sgms1	9530058O11Rik|AI841905|C80702|Mob|Sms1|Sor1|Tmem23	sphingomyelin synthase 1	protein-coding
mm_122411.1	chr14	41013754	41013817	-	1	NA	promoter-TSS (NM_001316734)	promoter-TSS (NM_001316734)	48	NM_001316734	70564	Mm.27227	NM_027464	ENSMUSG00000021792	Fam213a	5730469M10Rik|AU040822|Adrx|Pamm	family with sequence similarity 213, member A	protein-coding
mm_92473.1	chr10	78043661	78043696	-	1	NA	promoter-TSS (NM_001271556)	promoter-TSS (NM_001271556)	-68	NM_001271550	11634	Mm.35300	NM_009646	ENSMUSG00000000731	Aire	-	autoimmune regulator (autoimmune polyendocrinopathy candidiasis ectodermal dystrophy)	protein-coding
mm_12405.1	chr2	70508663	70508680	+	1	NA	promoter-TSS (NM_025744)	promoter-TSS (NM_025744)	-148	NM_025744	66748	Mm.423014	NM_025744	ENSMUSG00000075302	Erich2	4933404M02Rik	glutamate rich 2	protein-coding
mm_24452.1	chr3	90613147	90613157	+	1	NA	5' UTR (NM_011313, exon 1 of 3)	5' UTR (NM_011313, exon 1 of 3)	258	NM_011313	20200	Mm.100144	NM_011313	ENSMUSG00000001025	S100a6	2A9|5B10|CALCYCLIN|Cacy|PRA	S100 calcium binding protein A6 (calcyclin)	protein-coding
mm_36633.1	chr4	92339843	92339848	-	1	NA	Intergenic	Intergenic	-192624	NM_027034	69314	Mm.55891	NM_027034	ENSMUSG00000028533	Izumo3	1700011H22Rik	IZUMO family member 3	protein-coding
mm_9764.1	chr1	180906894	180906900	-	1	NA	exon (NM_133705, exon 6 of 7)	exon (NM_133705, exon 6 of 7)	2623	NM_133705	69051	Mm.274180	NM_133705	ENSMUSG00000026520	Pycr2	1810018M05Rik|P5cr2	pyrroline-5-carboxylate reductase family, member 2	protein-coding
mm_36673.1	chr4	96141150	96141158	-	1	NA	promoter-TSS (NM_001100182)	promoter-TSS (NM_001100182)	-2	NM_001100182	242546	Mm.302562	NM_001100182	ENSMUSG00000081225	Cyp2j12	BB197342|Cyp2j12-ps|OTTMUSG00000007939	cytochrome P450, family 2, subfamily j, polypeptide 12	protein-coding
mm_74660.1	chr8	13550247	13550254	-	1	NA	TTS (NM_025601)	TTS (NM_025601)	12211	NM_025601	66501	Mm.46136	NM_025601	ENSMUSG00000031452	1700029H14Rik	-	RIKEN cDNA 1700029H14 gene	protein-coding
mm_172307.1	chr7	104353528	104353536	+	1	NA	promoter-TSS (NM_175677)	promoter-TSS (NM_175677)	-174	NM_001146007	319236	Mm.425502	NM_175677	ENSMUSG00000057143	Trim12c	9230105E10Rik|Trim12-2	tripartite motif-containing 12C	protein-coding
mm_125141.1	chr15	30539584	30539596	+	1	NA	intron (NM_008729, intron 3 of 22)	intron (NM_008729, intron 3 of 22)	366997	NM_008729	18163	Mm.321648	NM_008729	ENSMUSG00000022240	Ctnnd2	Catnd2|Nprap|neurojugin	catenin (cadherin associated protein), delta 2	protein-coding
mm_172402.1	chr7	144791952	144791971	+	1	NA	Intergenic	Intergenic	-46651	NM_008007	14174	Mm.4947	NM_008007	ENSMUSG00000031074	Fgf3	Fgf-3|Int-2|Int-P	fibroblast growth factor 3	protein-coding
mm_62691.1	chr7	110061804	110061817	+	1	NA	intron (NM_009281, intron 1 of 15)	CpG	108	NM_009281	20841	Mm.10815	NM_009281	ENSMUSG00000061079	Zfp143	AA959806|AU015869|D7Ertd805e|KRAB14|SBF|Staf|Zfp79|Zfp80-rs1|Znf143|pHZ-1	zinc finger protein 143	protein-coding
mm_161896.1	chr18	44159058	44159058	-	1	NA	intron (NM_001281470, intron 2 of 4)	intron (NM_001281470, intron 2 of 4)	827	NM_001281470	100042855	Mm.479515	NM_001165950	ENSMUSG00000069385	Gm10267	ENSMUSG00000069385|Vtlgl1	predicted gene 10267	protein-coding
mm_78345.1	chr9	25299481	25299519	+	1	NA	exon (NM_001205367, exon 9 of 13)	exon (NM_001205367, exon 9 of 13)	47061	NM_001205367	235072	Mm.270259	NM_009859	ENSMUSG00000001833	Sept7	Cdc10|E430034N22	septin 7	protein-coding
mm_85882.1	chr9	111017161	111017167	-	1	NA	Intergenic	Intergenic	-2128	NM_008522	17002	Mm.282359	NM_008522	ENSMUSG00000032496	Ltf	Csp82|Lf|MMS10R|Ms10r	lactotransferrin	protein-coding
mm_114927.1	chr13	95696896	95696921	+	1	NA	promoter-TSS (NM_010170)	promoter-TSS (NM_010170)	-12	NM_010170	14064	Mm.440952	NM_010170	ENSMUSG00000021675	F2rl2	F730031A08|PAR3	coagulation factor II (thrombin) receptor-like 2	protein-coding
mm_50188.1	chr6	41684379	41684402	+	1	NA	promoter-TSS (NM_029671)	promoter-TSS (NM_029671)	-41	NM_029671	76606	Mm.272520	NM_029671	ENSMUSG00000029867	1700034O15Rik	-	RIKEN cDNA 1700034O15 gene	protein-coding
mm_151000.1	chr19	46654034	46654041	+	1	NA	exon (NM_001177813, exon 4 of 4)	exon (NM_001177813, exon 4 of 4)	18963	NM_007809	13074	Mm.1262	NM_007809	ENSMUSG00000003555	Cyp17a1	Cyp17|p450c17	cytochrome P450, family 17, subfamily a, polypeptide 1	protein-coding
mm_95617.1	chr11	53519921	53519933	+	1	NA	5' UTR (NM_001252332, exon 1 of 10)	5' UTR (NM_001252332, exon 1 of 10)	191	NM_001347496	20362	Mm.274399	NM_033144	ENSMUSG00000018398	Sept8	AW046166|Sepl	septin 8	protein-coding
mm_59376.1	chr7	25754896	25754933	+	1	NA	promoter-TSS (NM_178089)	promoter-TSS (NM_178089)	-194	NM_144922	232989	Mm.254223	NM_144922	ENSMUSG00000040725	Hnrnpul1	E130317O14Rik|E1B-AP5|E1BAP5|Hnrnpul|Hnrpul1	heterogeneous nuclear ribonucleoprotein U-like 1	protein-coding
mm_76347.1	chr8	84727633	84727644	-	1	NA	exon (NM_010906, exon 4 of 9)	exon (NM_010906, exon 4 of 9)	26181	NM_008535	17095	Mm.4925	NM_008535	ENSMUSG00000034041	Lyl1	Lyl-1|bHLHa18	lymphoblastomic leukemia 1	protein-coding
mm_165486.1	chr2	164334265	164334269	+	1	NA	3' UTR (NM_009301, exon 3 of 3)	3' UTR (NM_009301, exon 3 of 3)	1502	NM_009301	20944	Mm.140154	NM_009301	ENSMUSG00000017004	Svs5	BB115186|Semg1|Svp-1|Svp1|Svp5	seminal vesicle secretory protein 5	protein-coding
mm_134648.1	chr16	21947537	21947577	-	1	NA	promoter-TSS (NR_037773)	promoter-TSS (NR_037773)	-5	NR_037773	66664	Mm.46480	NM_025693	ENSMUSG00000022856	Tmem41a	2900010K02Rik|5730578N08Rik	transmembrane protein 41a	protein-coding
mm_109774.1	chr12	118848389	118848412	+	1	NA	5' UTR (NM_177082, exon 3 of 3)	5' UTR (NM_177082, exon 3 of 3)	2071	NM_177082	320145	Mm.51682	NM_177082	ENSMUSG00000048562	Sp8	D930049B17Rik|mBtd	trans-acting transcription factor 8	protein-coding
mm_127511.1	chr15	101711595	101711607	+	1	NA	exon (NM_027011, exon 2 of 9)	exon (NM_027011, exon 2 of 9)	1290	NM_027011	110308	Mm.451847	NM_027011	ENSMUSG00000061527	Krt5	3300001P10Rik|AW146334|CK5|K5|Krt2-5|Tfip8	keratin 5	protein-coding
mm_25040.1	chr3	98290892	98290907	+	1	NA	exon (NM_008256, exon 2 of 10)	exon (NM_008256, exon 2 of 10)	10468	NM_008256	15360	Mm.289131	NM_008256	ENSMUSG00000027875	Hmgcs2	1300002P16|mHS	3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2	protein-coding
mm_129979.1	chr15	86019798	86019801	-	1	NA	intron (NM_009886, intron 1 of 34)	intron (NM_009886, intron 1 of 34)	13978	NM_009886	12614	Mm.22680	NM_009886	ENSMUSG00000016028	Celsr1	Adgrc1|Crsh|Scy|crash	cadherin, EGF LAG seven-pass G-type receptor 1	protein-coding
mm_4871.1	chr1	187803504	187803528	+	1	NA	intron (NM_001243792, intron 2 of 7)	(T)n|Simple_repeat|Simple_repeat	-194311	NM_011935	26381	Mm.89989	NM_011935	ENSMUSG00000026610	Esrrg	ERR3|Errg|NR3B3|mKIAA0832	estrogen-related receptor gamma	protein-coding
mm_100340.1	chr11	118393418	118393470	+	1	NA	exon (NM_011150, exon 6 of 6)	exon (NM_011150, exon 6 of 6)	8487	NM_011150	19039	Mm.3152	NM_011150	ENSMUSG00000033880	Lgals3bp	90K|CyCAP|MAC-2BP|Ppicap|Tango10b	lectin, galactoside-binding, soluble, 3 binding protein	protein-coding
mm_24050.1	chr3	87906363	87906414	+	1	NA	promoter-TSS (NM_008231)	promoter-TSS (NM_008231)	67	NM_008231	15191	Mm.292208	NM_008231	ENSMUSG00000004897	Hdgf	AI118077|D3Ertd299e	hepatoma-derived growth factor	protein-coding
mm_6345.1	chr1	71640405	71640418	-	1	NA	exon (NM_001276413, exon 10 of 44)	exon (NM_001276413, exon 10 of 44)	12823	NM_010233	14268	Mm.193099	NM_010233	ENSMUSG00000026193	Fn1	E330027I09|Fn|Fn-1	fibronectin 1	protein-coding
mm_94460.1	chr11	6416259	6416317	+	1	NA	intron (NM_008907, intron 1 of 4)	CpG	418	NM_008907	268373	Mm.5246	NM_008907	ENSMUSG00000071866	Ppia	2700098C05|Cphn|CyP-18|CypA	peptidylprolyl isomerase A	protein-coding
mm_42917.1	chr5	122707960	122707988	+	1	NA	intron (NM_001310718, intron 1 of 10)	intron (NM_001310718, intron 1 of 10)	430	NM_001310718	18438	Mm.290884	NM_011026	ENSMUSG00000029470	P2rx4	AI504491|AW555605|D5Ertd444e|P2X4	purinergic receptor P2X, ligand-gated ion channel 4	protein-coding
mm_168862.1	chr12	30911540	30911541	-	1	NA	promoter-TSS (NM_013709)	promoter-TSS (NM_013709)	72	NM_021330	11431	Mm.359831	NM_021330	ENSMUSG00000044573	Acp1	4632432E04Rik|AI427468|Acp-1|LMW-PTP|Lmptp	acid phosphatase 1, soluble	protein-coding
mm_91771.1	chr10	51590474	51590497	-	1	NA	promoter-TSS (NM_029894)	promoter-TSS (NM_029894)	-25	NM_029894	77296	Mm.30588	NM_029894	ENSMUSG00000019909	Fam162b	9430073N08Rik	family with sequence similarity 162, member B	protein-coding
mm_62115.1	chr7	96644114	96644135	+	1	NA	exon (NM_001310762, exon 7 of 33)	exon (NM_001310762, exon 7 of 33)	157425	NR_045874	791381	Mm.402112	NR_045874	ENSMUSG00000053049	Gm15413	ENSMUSG00000053049|OTTMUSG00000021246	predicted gene 15413	ncRNA
mm_88099.1	chr10	68723944	68723960	+	1	NA	exon (NM_177794, exon 1 of 6)	exon (NM_177794, exon 1 of 6)	206	NM_177794	327766	Mm.2479	NM_177794	ENSMUSG00000060044	Tmem26	3230401A06|AI195372	transmembrane protein 26	protein-coding
mm_122409.1	chr14	41008288	41008298	-	1	NA	promoter-TSS (NM_001316740)	promoter-TSS (NM_001316740)	-27	NM_001316740	70564	Mm.27227	NM_027464	ENSMUSG00000021792	Fam213a	5730469M10Rik|AU040822|Adrx|Pamm	family with sequence similarity 213, member A	protein-coding
mm_83681.1	chr9	50475710	50475727	-	1	NA	Intergenic	Intergenic	-18807	NM_029639	76509	Mm.29959	NM_029639	ENSMUSG00000032068	Plet1	0610037B23Rik|1600029D21Rik|AA407923|AU043048	placenta expressed transcript 1	protein-coding
mm_63928.1	chr7	139403786	139403804	+	1	NA	intron (NM_183144, intron 1 of 15)	intron (NM_183144, intron 1 of 15)	14686	NM_001127363	212111	Mm.28308	NM_183144	ENSMUSG00000025477	Inpp5a	-	inositol polyphosphate-5-phosphatase A	protein-coding
mm_164397.1	chr16	33819128	33819158	+	1	NA	3' UTR (NM_010739, exon 13 of 13)	3' UTR (NM_010739, exon 13 of 13)	-10522	NM_010580	16419	Mm.6424	NM_010580	ENSMUSG00000022817	Itgb5	AA475909|AI874634|ESTM23|[b]-5|[b]5|[b]5A|[b]5B|beta-5|beta5	integrin beta 5	protein-coding
mm_118404.1	chr13	119409007	119409018	-	1	NA	promoter-TSS (NM_008710)	promoter-TSS (NM_008710)	-1	NM_008710	18115	Mm.132584	NM_008710	ENSMUSG00000025453	Nnt	4930423F13Rik|AI323702|BB168308	nicotinamide nucleotide transhydrogenase	protein-coding
mm_138061.1	chr17	33929895	33929917	+	1	NA	promoter-TSS (NM_009059)	promoter-TSS (NM_009059)	12	NM_009059	19732	Mm.43777	NM_009059	ENSMUSG00000041354	Rgl2	KE1.5|Rab2l|Rgt2|Rlf	ral guanine nucleotide dissociation stimulator-like 2	protein-coding
mm_148431.1	chr19	3941933	3941946	+	1	NA	exon (NM_019449, exon 5 of 11)	exon (NM_019449, exon 5 of 11)	6753	NM_001161428	54445	Mm.262094	NM_019449	ENSMUSG00000036908	Unc93b1	Unc-93B1|Unc93b	unc-93 homolog B1 (C. elegans)	protein-coding
mm_33798.1	chr4	134926069	134926073	+	1	NA	intron (NM_023665, intron 3 of 4)	intron (NM_023665, intron 3 of 4)	2446	NM_023665	27981	Mm.331964	NM_023665	ENSMUSG00000037266	Rsrp1	2700043I21Rik|D4Ucla2|D4Wsu53e	arginine/serine rich protein 1	protein-coding
mm_171471.1	chr4	145781517	145781521	+	1	NA	promoter-TSS (NM_001083918)	promoter-TSS (NM_001083918)	-24	NM_001083918	666532	Mm.392861	NM_001083918	ENSMUSG00000067916	Zfp991	Gm13139|OTTMUSG00000010657	zinc finger protein 991	protein-coding
mm_149071.1	chr19	8871606	8871616	+	1	NA	promoter-TSS (NM_146093)	promoter-TSS (NM_146093)	52	NM_146093	225896	Mm.27839	NM_146093	ENSMUSG00000071655	Ubxn1	2B28|4930455J02Rik|D19Ertd721e|T25529	UBX domain protein 1	protein-coding
mm_52453.1	chr6	113684097	113684116	+	1	NA	intron (NM_001113553, intron 9 of 11)	PB1|SINE|Alu	-12944	NM_001347356	381801	Mm.333322	NM_001033463	ENSMUSG00000056952	Tatdn2	AI646012|mKIAA0218	TatD DNase domain containing 2	protein-coding
mm_138557.1	chr17	35267094	35267108	+	1	NA	TTS (NM_001267808)	TTS (NM_001267808)	3978	NM_001267808	14980	Mm.439675	NM_001267808		H2-L	H-2L	histocompatibility 2, D region locus L	protein-coding
mm_54400.1	chr6	31528642	31528666	-	1	NA	exon (NM_013723, exon 2 of 8)	exon (NM_013723, exon 2 of 8)	35283	NM_013723	27205	Mm.89918	NM_013723	ENSMUSG00000025608	Podxl	AW121214|Ly102|PC|PCLP-1|Pclp1	podocalyxin-like	protein-coding
mm_168024.1	chrY	90738264	90738277	+	1	NA	Intergenic	IMPB_01|Satellite|Satellite	16780	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_127660.1	chr15	102518406	102518496	+	1	NA	5' UTR (NM_009319, exon 1 of 9)	5' UTR (NM_009319, exon 1 of 9)	259	NM_009319	21357	Mm.291485	NM_009319	ENSMUSG00000023051	Tarbp2	Prbp|TRBP	TARBP2, RISC loading complex RNA binding subunit	protein-coding
mm_34027.1	chr4	138058015	138058026	+	1	NA	5' UTR (NM_001256198, exon 4 of 33)	5' UTR (NM_001256198, exon 4 of 33)	64564	NM_172703	230861	Mm.268903	NM_172703	ENSMUSG00000028760	Eif4g3	1500002J22Rik|4930523M17Rik|G1-419-52|eIF4GII|repro8	eukaryotic translation initiation factor 4 gamma, 3	protein-coding
mm_75988.1	chr8	72377923	72377945	-	1	NA	3' UTR (NM_001122832, exon 16 of 16)	3' UTR (NM_001122832, exon 16 of 16)	43540	NM_001122832	13859	Mm.288894	NM_007944	ENSMUSG00000006276	Eps15l1	9830147J04Rik|AI593686|Eps15-rs|Eps15R	epidermal growth factor receptor pathway substrate 15-like 1	protein-coding
mm_11552.1	chr2	32721110	32721140	+	1	NA	promoter-TSS (NM_013781)	promoter-TSS (NM_013781)	70	NM_013781	27387	Mm.9593	NM_013781	ENSMUSG00000059013	Sh2d3c	Chat|Nsp3|Shep1	SH2 domain containing 3C	protein-coding
mm_82341.1	chr9	10904854	10904864	-	1	NA	promoter-TSS (NM_001170787)	promoter-TSS (NM_001170787)	-84	NM_001170787	244682	Mm.187021	NM_001033359	ENSMUSG00000039488	Cntn5	6720426O10Rik|A830025P08Rik|Gm507|NB-2	contactin 5	protein-coding
mm_139128.1	chr17	47505118	47505132	+	1	NA	promoter-TSS (NM_001081636)	promoter-TSS (NM_001081636)	74	NM_001081635	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_145940.1	chr18	67343595	67343605	+	1	NA	promoter-TSS (NM_007702)	promoter-TSS (NM_007702)	36	NM_007702	12683	Mm.449	NM_007702	ENSMUSG00000024526	Cidea	AW212747	cell death-inducing DNA fragmentation factor, alpha subunit-like effector A	protein-coding
mm_153264.1	chr19	37023208	37023217	-	1	NA	3' UTR (NM_198300, exon 11 of 11)	3' UTR (NM_198300, exon 11 of 11)	97133	NM_001080706	107182	Mm.295062	NM_001080706	ENSMUSG00000040565	Btaf1	AI414500|AI447930|E430027O22Rik|TAF170	B-TFIID TATA-box binding protein associated factor 1	protein-coding
mm_8208.1	chr1	138124040	138124062	-	1	NA	intron (NM_001111316, intron 2 of 31)	B2_Mm2|SINE|B2	51075	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_98363.1	chr11	93924483	93924499	+	1	NA	exon (NM_134012, exon 9 of 16)	exon (NM_134012, exon 9 of 16)	31292	NM_001077529	18103	Mm.1260	NM_008705	ENSMUSG00000020857	Nme2	NM23-H2|NM23B|nm23-M2	NME/NM23 nucleoside diphosphate kinase 2	protein-coding
mm_114643.1	chr13	76579682	76579686	+	1	NA	intron (NM_030174, intron 1 of 20)	intron (NM_030174, intron 1 of 20)	194723	NM_030174	78771	Mm.316249	NM_030174	ENSMUSG00000021596	Mctp1	2810465F10Rik	multiple C2 domains, transmembrane 1	protein-coding
mm_113528.1	chr13	37826793	37826804	+	1	NA	promoter-TSS (NM_001039188)	promoter-TSS (NM_001039188)	-114	NM_001177868	68750	Mm.491109	NM_026830	ENSMUSG00000039087	Rreb1	1110037N09Rik|AA414966|B930013M22Rik	ras responsive element binding protein 1	protein-coding
mm_92288.1	chr10	71344883	71344893	-	1	NA	promoter-TSS (NM_134007)	promoter-TSS (NM_134007)	-39	NM_134007	52637	Mm.254114	NM_134007	ENSMUSG00000037710	Cisd1	AU043990|AW743335|D10Ertd214e|Zcd1|mitoNEET	CDGSH iron sulfur domain 1	protein-coding
mm_82044.1	chr9	122351556	122351565	+	1	NA	promoter-TSS (NM_026179)	promoter-TSS (NM_026179)	-56	NM_026179	67469	Mm.280254	NM_026179	ENSMUSG00000032540	Abhd5	1300003D03Rik|2010002J10Rik|CDS|CGI-58|IECN5|NCIE2	abhydrolase domain containing 5	protein-coding
mm_99176.1	chr11	100859493	100859506	+	1	NA	promoter-TSS (NM_001164062)	promoter-TSS (NM_001164062)	148	NM_011488	20850	Mm.277403	NM_011488	ENSMUSG00000004043	Stat5a	AA959963|STAT5	signal transducer and activator of transcription 5A	protein-coding
mm_30918.1	chr4	32657108	32657166	+	1	NA	promoter-TSS (NM_001081392)	promoter-TSS (NM_001081392)	18	NM_001081392	100019	Mm.24627	NM_133874	ENSMUSG00000058006	Mdn1	4833432B22Rik|A130070M06|AA958993|D4Abb1e|Gm135	midasin AAA ATPase 1	protein-coding
mm_81722.1	chr9	112227444	112227461	+	1	NA	promoter-TSS (NR_131053)	promoter-TSS (NR_131053)	-4	NR_131053	70194	Mm.452769	NR_131053		2310075C17Rik	-	RIKEN cDNA 2310075C17 gene	ncRNA
mm_14551.1	chr2	133199574	133199574	+	1	NA	Intergenic	ORR1D2|LTR|ERVL-MaLR	-253538	NM_198029	241639	Mm.209784	NM_198029	ENSMUSG00000027356	Fermt1	5830467P10Rik|Kindlin-1	fermitin family member 1	protein-coding
mm_50013.1	chr6	41062343	41062356	+	1	NA	Intergenic	Intergenic	-26840	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_116372.1	chr13	40733969	40733991	-	1	NA	promoter-TSS (NM_011547)	promoter-TSS (NM_011547)	-157	NM_011547	21418	Mm.85544	NM_011547	ENSMUSG00000021359	Tfap2a	AP-2|AP2alpha|Ap-2 (a)|Ap2|Ap2tf|Tcfap2a	transcription factor AP-2, alpha	protein-coding
mm_151356.1	chr19	55908434	55908479	+	1	NA	exon (NM_001142918, exon 5 of 15)	exon (NM_001142918, exon 5 of 15)	13135	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_96988.1	chr11	70657817	70657831	+	1	NA	5' UTR (NM_007933, exon 2 of 12)	5' UTR (NM_007933, exon 2 of 12)	648	NM_007933	13808	Mm.251322	NM_007933	ENSMUSG00000060600	Eno3	Eno-3|MSE	enolase 3, beta muscle	protein-coding
mm_132747.1	chr16	44156422	44156443	+	1	NA	exon (NM_028108, exon 2 of 5)	exon (NM_028108, exon 2 of 5)	16623	NM_028108	72117	Mm.278726	NM_028108	ENSMUSG00000022698	Naa50	2600005K24Rik|2810441M03Rik|AW112078|Mak3|Mak3p|Nat13|Nat5|San	N(alpha)-acetyltransferase 50, NatE catalytic subunit	protein-coding
mm_27991.1	chr3	82145759	82145843	-	1	NA	promoter-TSS (NM_021896)	promoter-TSS (NM_021896)	76	NM_021896	60596	Mm.143831	NM_021896	ENSMUSG00000033910	Gucy1a3	1200016O07Rik|sGC-alpha1	guanylate cyclase 1, soluble, alpha 3	protein-coding
mm_53427.1	chr6	134036071	134036104	+	1	NA	5' UTR (NM_007961, exon 1 of 8)	5' UTR (NM_007961, exon 1 of 8)	387	NM_007961	14011	Mm.269995	NM_007961	ENSMUSG00000030199	Etv6	AW123102|AW557856|Tel	ets variant 6	protein-coding
mm_95072.1	chr11	32611065	32611083	+	1	NA	intron (NM_009288, intron 13 of 18)	intron (NM_009288, intron 13 of 18)	-31481	NM_001271348	103583	Mm.28017	NM_134015	ENSMUSG00000020271	Fbxw11	2310065A07Rik|AA536858|BTRC2|BTRCP2|Fbxw1b|HOS	F-box and WD-40 domain protein 11	protein-coding
mm_15621.1	chr2	161537137	161537138	+	1	NA	intron (NM_001291151, intron 27 of 30)	intron (NM_001291151, intron 27 of 30)	-428051	NR_126509	71389	Mm.122738	NM_173368	ENSMUSG00000057133	Chd6	5430439G14Rik|6330406J24Rik|CHD-6	chromodomain helicase DNA binding protein 6	protein-coding
mm_80487.1	chr9	78366048	78366074	+	1	NA	TTS (NM_025274)	TTS (NM_025274)	2138	NM_025274	434423	Mm.139314	NM_025274	ENSMUSG00000060461	Dppa5a	AA536857|Dppa5|Esg1|ecat2	developmental pluripotency associated 5A	protein-coding
mm_4433.1	chr1	172506666	172506704	+	1	NA	exon (NM_178598, exon 5 of 5)	exon (NM_178598, exon 5 of 5)	6439	NM_178598	21346	Mm.271711	NM_178598	ENSMUSG00000026547	Tagln2	2700094C18Rik|SM22beta|Sm22B|Sm22a	transgelin 2	protein-coding
mm_159842.1	chr5	135064764	135064764	-	1	NA	promoter-TSS (NM_025375)	promoter-TSS (NM_025375)	-98	NM_025375	66138	Mm.439878	NM_025375	ENSMUSG00000005378	Wbscr22	1110003N24Rik	Williams Beuren syndrome chromosome region 22	protein-coding
mm_86154.1	chr9	118040314	118040333	-	1	NA	promoter-TSS (NM_013727)	promoter-TSS (NM_013727)	-199	NM_001286508	27215	Mm.92705	NM_013727	ENSMUSG00000039285	Azi2	AA410145|AZ2	5-azacytidine induced gene 2	protein-coding
mm_134519.1	chr16	19235622	19235630	-	1	NA	Intergenic	Lx3_Mus|LINE|L1	51115	NM_146451	258443	Mm.377506	NM_146451	ENSMUSG00000050742	Olfr164	MOR279-2	olfactory receptor 164	protein-coding
mm_43514.1	chr5	137103206	137103216	+	1	NA	Intergenic	Intergenic	12996	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_89737.1	chr10	99013911	99013959	+	1	NA	intron (NM_026482, intron 15 of 20)	HAL1|LINE|L1	-93236	NM_027740	382406	Mm.440656	NM_027740	ENSMUSG00000019952	Poc1b	4933430F16Rik|Wdr51b	POC1 centriolar protein B	protein-coding
mm_6043.1	chr1	59710545	59710620	-	1	NA	exon (NM_018868, exon 14 of 15)	exon (NM_018868, exon 14 of 15)	5774	NR_028521	100217421		NR_028521		Snord11	MBII-95	small nucleolar RNA, C/D box 11	snoRNA
mm_79101.1	chr9	46243162	46243172	+	1	NA	exon (NM_007468, exon 3 of 3)	exon (NM_007468, exon 3 of 3)	2323	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_158825.1	chrX	167855062	167855081	-	1	NA	promoter-TSS (NM_001290428)	promoter-TSS (NM_001290428)	6	NM_001290428	333605	Mm.426168	NM_001033330	ENSMUSG00000049176	Frmpd4	Gm196|PKAP1|Pdzd10|Pdzk10|Preso1|preso	FERM and PDZ domain containing 4	protein-coding
mm_53637.1	chr6	140621089	140621108	+	1	NA	Intergenic	LTR88b|LTR|Gypsy?	-1565	NM_178803	11569	Mm.86453	NM_009637	ENSMUSG00000030232	Aebp2	AU023766|B230313N05Rik	AE binding protein 2	protein-coding
mm_65508.1	chr7	25754567	25754577	-	1	NA	exon (NM_178089, exon 1 of 8)	exon (NM_178089, exon 1 of 8)	129	NM_178089	232989	Mm.254223	NM_144922	ENSMUSG00000040725	Hnrnpul1	E130317O14Rik|E1B-AP5|E1BAP5|Hnrnpul|Hnrpul1	heterogeneous nuclear ribonucleoprotein U-like 1	protein-coding
mm_58751.1	chr7	13309618	13309626	+	1	NA	intron (NM_001199310, intron 27 of 28)	intron (NM_001199310, intron 27 of 28)	-16045	NM_001168504	232889	Mm.223639	NM_001004762	ENSMUSG00000033847	Pla2g4c	D7Ertd445e	phospholipase A2, group IVC (cytosolic, calcium-independent)	protein-coding
mm_135654.1	chr16	52400465	52400475	-	1	NA	intron (NM_009655, intron 1 of 15)	intron (NM_009655, intron 1 of 15)	52611	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_67188.1	chr7	73940421	73940435	-	1	NA	3' UTR (NM_009181, exon 6 of 6)	3' UTR (NM_009181, exon 6 of 6)	73254	NM_009181	20450	Mm.4954	NM_009181	ENSMUSG00000025789	St8sia2	AI323367|ST8SiaII|STX|Siat8b	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 2	protein-coding
mm_20548.1	chr2	131068898	131068916	-	1	NA	TTS (NM_011426)	TTS (NM_011426)	-5093	NM_001163529	110751	Mm.108550	NM_033615	ENSMUSG00000027318	Adam33	Adaml	a disintegrin and metallopeptidase domain 33	protein-coding
mm_18699.1	chr2	71546746	71546758	-	1	NA	promoter-TSS (NM_010054)	promoter-TSS (NM_010054)	2	NM_010054	13392	Mm.3896	NM_010054	ENSMUSG00000023391	Dlx2	AW121999|Dlx-2|Tes-1	distal-less homeobox 2	protein-coding
mm_14128.1	chr2	126034648	126034665	+	1	NA	promoter-TSS (NM_008008)	promoter-TSS (NM_008008)	-2	NM_008008	14178	Mm.330557	NM_008008	ENSMUSG00000027208	Fgf7	Kgf	fibroblast growth factor 7	protein-coding
mm_57639.1	chr6	128362693	128362724	-	1	NA	promoter-TSS (NM_008021)	promoter-TSS (NM_008021)	114	NM_001326583	72440	Mm.143908	NM_197981	ENSMUSG00000048668	Rhno1	2510047L19Rik|5930416I19Rik	RAD9-HUS1-RAD1 interacting nuclear orphan 1	protein-coding
mm_101886.1	chr11	48992258	48992279	-	1	NA	promoter-TSS (NM_011579)	promoter-TSS (NM_011579)	-22	NM_011579	21822	Mm.15793	NM_011579	ENSMUSG00000078922	Tgtp1	Gtp2|Irgb6|Mg21|Tgtp	T cell specific GTPase 1	protein-coding
mm_121793.1	chr14	20082760	20082792	-	1	NA	intron (NM_026209, intron 1 of 1)	intron (NM_026209, intron 1 of 1)	396	NM_026209	67509	Mm.292423	NM_026209	ENSMUSG00000045107	Saysd1	1810063B07Rik|4930488P03Rik	SAYSVFN motif domain containing 1	protein-coding
mm_145032.1	chr18	39306726	39306736	+	1	NA	exon (NM_175164, exon 20 of 23)	exon (NM_175164, exon 20 of 23)	180514	NM_008173	14815	Mm.129481	NM_008173	ENSMUSG00000024431	Nr3c1	GR|Grl-1|Grl1	nuclear receptor subfamily 3, group C, member 1	protein-coding
mm_65900.1	chr7	30190120	30190140	-	1	NA	exon (NM_009795, exon 9 of 11)	exon (NM_009795, exon 9 of 11)	4918	NM_009795	12336	Mm.439782	NM_009795	ENSMUSG00000001794	Capns1	Capa-4|Capa4|Capn4|D7Ertd146e	calpain, small subunit 1	protein-coding
mm_30089.1	chr3	138186701	138186732	-	1	NA	promoter-TSS (NM_001163386)	promoter-TSS (NM_001163386)	-3	NM_001163386	67741	Mm.383221	NM_001163385	ENSMUSG00000012042	4930579F01Rik	-	RIKEN cDNA 4930579F01 gene	protein-coding
mm_103354.1	chr11	74832183	74832205	-	1	NA	intron (NM_010813, intron 1 of 5)	CpG-2219	1270	NM_010813	17428	Mm.3759	NM_010813	ENSMUSG00000000282	Mnt	Rox|bHLHd3	max binding protein	protein-coding
mm_51956.1	chr6	91756494	91756520	+	1	NA	3' UTR (NM_009320, exon 15 of 15)	3' UTR (NM_009320, exon 15 of 15)	50886	NM_001159507	243547	Mm.333264	NM_001033353	ENSMUSG00000030098	Grip2	-	glutamate receptor interacting protein 2	protein-coding
mm_119487.1	chr14	47374297	47374323	+	1	NA	intron (NM_001145953, intron 1 of 5)	intron (NM_001145953, intron 1 of 5)	450	NM_001145953	16854	Mm.248615	NM_010705	ENSMUSG00000050335	Lgals3	GBP|L-34|Mac-2|gal3	lectin, galactose binding, soluble 3	protein-coding
mm_71880.1	chr8	69811895	69811908	+	1	NA	intron (NM_198101, intron 7 of 20)	RMER4A|LTR|ERVK	3214	NM_198101	78816	Mm.324305	NM_198101	ENSMUSG00000036246	Gmip	5031419I10Rik	Gem-interacting protein	protein-coding
mm_120285.1	chr14	63133337	63133360	+	1	NA	exon (NM_007798, exon 2 of 10)	exon (NM_007798, exon 2 of 10)	10886	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_6990.1	chr1	86357382	86357405	-	1	NA	exon (NM_010880, exon 3 of 14)	exon (NM_010880, exon 3 of 14)	-1066	NR_002851	80828		NR_002851	ENSMUSG00000064823	Snord82	Rnu82|U82|Z25	small nucleolar RNA, C/D box 82	snoRNA
mm_150935.1	chr19	46305910	46305927	+	1	NA	promoter-TSS (NM_001177370)	promoter-TSS (NM_001177370)	-12	NM_001177370	18034	Mm.102365	NM_019408	ENSMUSG00000025225	Nfkb2	NF-kappaB2|lyt|p49|p49/p100|p50B|p52	nuclear factor of kappa light polypeptide gene enhancer in B cells 2, p49/p100	protein-coding
mm_15636.1	chr2	163017451	163017513	+	1	NA	promoter-TSS (NM_172150)	promoter-TSS (NM_172150)	10	NM_172150	245866	Mm.34034	NM_172150	ENSMUSG00000017858	Ift52	BC037708|NGD5	intraflagellar transport 52	protein-coding
mm_123794.1	chr14	70443397	70443407	-	1	NA	promoter-TSS (NM_025945)	promoter-TSS (NM_025945)	69	NM_025945	67065	Mm.20420	NM_025945	ENSMUSG00000000776	Polr3d	2810426M17Rik|44kDa|AI326118|AW489084|BN51T|RPC4|TSBN51	polymerase (RNA) III (DNA directed) polypeptide D	protein-coding
mm_7781.1	chr1	131276915	131276925	-	1	NA	intron (NM_019777, intron 2 of 21)	intron (NM_019777, intron 2 of 21)	2643	NM_019777	56489	Mm.386783	NM_019777	ENSMUSG00000042349	Ikbke	AW558201|IKK-i|IKKepsilon|Ikki	inhibitor of kappaB kinase epsilon	protein-coding
mm_153355.1	chr19	40159469	40159472	-	1	NA	intron (NM_145499, intron 7 of 8)	intron (NM_145499, intron 7 of 8)	27816	NM_145499	226105	Mm.29119	NM_145499	ENSMUSG00000060613	Cyp2c70	-	cytochrome P450, family 2, subfamily c, polypeptide 70	protein-coding
mm_5220.1	chr1	14227914	14227917	-	1	NA	intron (NM_001310459, intron 11 of 17)	intron (NM_001310459, intron 11 of 17)	82284	NM_001310459	14048	Mm.250185	NM_010164	ENSMUSG00000025932	Eya1	bor	EYA transcriptional coactivator and phosphatase 1	protein-coding
mm_149252.1	chr19	10389271	10389291	+	1	NA	5' UTR (NM_018801, exon 1 of 9)	5' UTR (NM_018801, exon 1 of 9)	191	NM_173068	54525	Mm.182654	NM_018801	ENSMUSG00000024743	Syt7	AI851541|B230112P13Rik	synaptotagmin VII	protein-coding
mm_121237.1	chr14	103056166	103056183	+	1	NA	3' UTR (NM_008392, exon 5 of 5)	3' UTR (NM_008392, exon 5 of 5)	9162	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_55348.1	chr6	56797496	56797553	-	1	NA	5' UTR (NM_145958, exon 1 of 4)	5' UTR (NM_145958, exon 1 of 4)	289	NM_145958	210973	Mm.57295	NM_145958	ENSMUSG00000059486	Kbtbd2	BC022962|Bklhd1|mKIAA1489	kelch repeat and BTB (POZ) domain containing 2	protein-coding
mm_147951.1	chr18	66860459	66860485	-	1	NA	promoter-TSS (NM_016977)	promoter-TSS (NM_016977)	15	NM_016977	17202	Mm.229447	NM_016977	ENSMUSG00000047259	Mc4r	Mc4-r	melanocortin 4 receptor	protein-coding
mm_33263.1	chr4	127210308	127210329	+	1	NA	intron (NM_001302081, intron 5 of 11)	ID_B1|SINE|B4	-33466	NM_030252	80284	Mm.139607	NM_030252	ENSMUSG00000042380	Smim12	BC003266	small integral membrane protein 12	protein-coding
mm_121708.1	chr14	15438975	15439002	-	1	NA	promoter-TSS (NM_146052)	promoter-TSS (NM_146052)	-1	NM_146052	218763	Mm.138039	NM_146052	ENSMUSG00000045201	Lrrc3b	BC019794|LRP15	leucine rich repeat containing 3B	protein-coding
mm_97051.1	chr11	72450704	72450707	+	1	NA	TTS (NM_001276383)	TTS (NM_001276383)	9327	NM_016776	18432	Mm.147946	NM_016776	ENSMUSG00000040463	Mybbp1a	AL024407|AU019902|P160|p160MBP|p67MBP	MYB binding protein (P160) 1a	protein-coding
mm_47330.1	chr5	122500333	122500341	-	1	NA	intron (NM_001110140, intron 3 of 19)	intron (NM_001110140, intron 3 of 19)	1888	NM_001110140	11938	Mm.227583	NM_009722	ENSMUSG00000029467	Atp2a2	9530097L16Rik|D5Wsu150e|SERCA2|SERCA2B|Serca2a|mKIAA4195	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	protein-coding
mm_81465.1	chr9	109875542	109875591	+	1	NA	promoter-TSS (NM_007658)	promoter-TSS (NM_007658)	-13	NM_007658	12530	Mm.307103	NM_007658	ENSMUSG00000032477	Cdc25a	D9Ertd393e	cell division cycle 25A	protein-coding
mm_160852.1	chr11	55312241	55312241	-	1	NA	promoter-TSS (NM_001029988)	promoter-TSS (NM_001029988)	16	NM_001029988	245827	Mm.339363	NM_001029988	ENSMUSG00000055333	Fat2	EMI2|Fath2|Gm523|mKIAA0811	FAT atypical cadherin 2	protein-coding
mm_154272.1	chr19	60775810	60775823	-	1	NA	exon (NM_010123, exon 8 of 22)	exon (NM_010123, exon 8 of 22)	-1419	NR_037245	100526521		NR_037245	ENSMUSG00000104890	Mir3084-1	Mir3084|mmu-mir-3084|mmu-mir-3084-1	microRNA 3084-1	ncRNA
mm_70157.1	chr7	143521578	143521614	-	1	NA	intron (NM_001285489, intron 12 of 14)	intron (NM_001285489, intron 12 of 14)	-19072	NM_009434	22113	Mm.334344	NM_009434	ENSMUSG00000010760	Phlda2	Ipl|Tssc3	pleckstrin homology like domain, family A, member 2	protein-coding
mm_63660.1	chr7	129591779	129591784	+	1	NA	promoter-TSS (NM_172255)	promoter-TSS (NM_172255)	-82	NM_172255	207425	Mm.229323	NM_172255	ENSMUSG00000042055	Wdr11	2900055P10Rik|AW489876|Brwd2|mKIAA1351	WD repeat domain 11	protein-coding
mm_38075.1	chr4	134127799	134127811	-	1	NA	exon (NM_080559, exon 3 of 3)	exon (NM_080559, exon 3 of 3)	948	NM_080559	73723	Mm.22240	NM_080559	ENSMUSG00000028843	Sh3bgrl3	1110004L05Rik|AU022188	SH3 domain binding glutamic acid-rich protein-like 3	protein-coding
mm_42669.1	chr5	119671438	119671452	+	1	NA	5' UTR (NM_011535, exon 1 of 8)	5' UTR (NM_011535, exon 1 of 8)	212	NM_011535	21386	Mm.219139	NM_011535	ENSMUSG00000018604	Tbx3	D5Ertd189e	T-box 3	protein-coding
mm_136879.1	chr17	13008159	13008188	+	1	NA	intron (NM_013671, intron 1 of 4)	CpG	334	NM_013671	20656	Mm.290876	NM_013671	ENSMUSG00000006818	Sod2	MnSOD|Sod-2	superoxide dismutase 2, mitochondrial	protein-coding
mm_34375.1	chr4	144893656	144893666	+	1	NA	exon (NM_001172424, exon 2 of 7)	exon (NM_001172424, exon 2 of 7)	524	NM_011303	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding
mm_133466.1	chr16	89205859	89205862	+	1	NA	promoter-TSS (NM_001163615)	promoter-TSS (NM_001163615)	-1	NM_001163615	622935	Mm.459837	NM_001163615	ENSMUSG00000091039	Krtap20-2	1190004K03Rik|EG622935|Gm6371	keratin associated protein 20-2	protein-coding
mm_99008.1	chr11	98836763	98836771	+	1	NA	promoter-TSS (NM_001080925)	promoter-TSS (NM_001080925)	-18	NM_001080925	268480	Mm.340766	NM_001080925	ENSMUSG00000038020	Rapgefl1	B230105J10	Rap guanine nucleotide exchange factor (GEF)-like 1	protein-coding
mm_99811.1	chr11	108395877	108395898	+	1	NA	exon (NM_013475, exon 2 of 8)	exon (NM_013475, exon 2 of 8)	590	NM_013475	11818	Mm.2266	NM_013475	ENSMUSG00000000049	Apoh	B2GPI|beta-2-GPI|beta2-GPI	apolipoprotein H	protein-coding
mm_120191.1	chr14	61598265	61598286	+	1	NA	promoter-TSS (NM_001164220)	promoter-TSS (NM_001164220)	49	NM_001164220	66597	Mm.491258	NM_023233	ENSMUSG00000035235	Trim13	3110001L12Rik|CAR|LEU5|RNF77|Rfp2	tripartite motif-containing 13	protein-coding
mm_156.1	chr1	12692434	12692485	+	1	NA	promoter-TSS (NM_001198566)	promoter-TSS (NM_001198566)	29	NM_001198566	240725	Mm.45563	NM_172294	ENSMUSG00000016918	Sulf1	AI467640|AW121680|mKIAA1077	sulfatase 1	protein-coding
mm_93405.1	chr10	107912323	107912334	-	1	NA	promoter-TSS (NM_001177567)	promoter-TSS (NM_001177567)	-194	NM_001177567	628870	Mm.336090	NM_001177567	ENSMUSG00000091455	Otogl	EG628870|Gm6924	otogelin-like	protein-coding
mm_161697.1	chr17	23811944	23811944	+	1	NA	intron (NM_175229, intron 8 of 13)	intron (NM_175229, intron 8 of 13)	8757	NM_175229	75956	Mm.5222	NM_175229	ENSMUSG00000039218	Srrm2	5033413A03Rik|AA410130|SRm300|mKIAA0324	serine/arginine repetitive matrix 2	protein-coding
mm_152736.1	chr19	19001071	19001075	-	1	NA	promoter-TSS (NM_001289921)	promoter-TSS (NM_001289921)	44	NM_146095	225998	Mm.234641	NM_146095	ENSMUSG00000036192	Rorb	Nr1f2|RZR-beta|RZRB|Rorbeta|hstp	RAR-related orphan receptor beta	protein-coding
mm_34095.1	chr4	138863553	138863577	+	1	NA	promoter-TSS (NM_001122954)	promoter-TSS (NM_001122954)	-96	NM_001122954	18784	Mm.486532	NM_011110	ENSMUSG00000041193	Pla2g5	PLA2|sPLA2	phospholipase A2, group V	protein-coding
mm_101988.1	chr11	50827682	50827742	-	1	NA	promoter-TSS (NM_013922)	promoter-TSS (NM_013922)	19	NM_013922	30944	Mm.103674	NM_013922	ENSMUSG00000044807	Zfp354c	5330421P20Rik|AJ18|AW743325|Kid3|Tcf17l2|Znf354c|mKIAA4218	zinc finger protein 354C	protein-coding
mm_82237.1	chr9	3258605	3258629	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-58804	NR_027988	114673	Mm.422774	NM_053265	ENSMUSG00000042360	4930433N12Rik	-	RIKEN cDNA 4930433N12 gene	ncRNA
mm_142610.1	chr17	46832289	46832316	-	1	NA	promoter-TSS (NM_001100452)	promoter-TSS (NM_001100452)	-889	NM_001100452	210982	Mm.37642	NM_001100452	ENSMUSG00000036568	Gltscr1l	mKIAA0240	GLTSCR1-like	protein-coding
mm_79992.1	chr9	67033867	67033886	+	1	NA	exon (NM_001164251, exon 4 of 10)	exon (NM_001164251, exon 4 of 10)	9995	NM_001164252	22003	Mm.121878	NM_024427	ENSMUSG00000032366	Tpm1	AA986836|AI854628|TM2|Tm3|Tmpa|Tpm-1|alpha-TM	tropomyosin 1, alpha	protein-coding
mm_115744.1	chr13	17939983	17940012	-	1	NA	intron (NM_019491, intron 1 of 4)	(A)n|Simple_repeat|Simple_repeat	4220	NM_019491	56044	Mm.27348	NM_019491	ENSMUSG00000008859	Rala	3010001O15Rik|AW322615|Ral|Rasl1	v-ral simian leukemia viral oncogene A (ras related)	protein-coding
mm_164150.1	chr15	63530301	63530302	+	1	NA	Intergenic	Lx10|LINE|L1	-50693	NR_045279	432958	Mm.255105	NR_045279		Gm20740	-	predicted gene, 20740	ncRNA
mm_3435.1	chr1	150101318	150101326	+	1	NA	exon (NM_011198, exon 3 of 10)	exon (NM_011198, exon 3 of 10)	1291	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_46034.1	chr5	91961448	91961462	-	1	NA	intron (NR_073442, intron 1 of 9)	intron (NR_073442, intron 1 of 9)	1101	NR_073442	68098	Mm.159453	NM_026557	ENSMUSG00000029397	Rchy1	ARNIP|CHIMP|Pirh2|Zfp363|Znf363	ring finger and CHY zinc finger domain containing 1	protein-coding
mm_28951.1	chr3	100476441	100476445	-	1	NA	intron (NM_001142952, intron 1 of 1)	(A)n|Simple_repeat|Simple_repeat	12749	NM_001142952	74645	Mm.226900	NM_001142952	ENSMUSG00000044468	Fam46c	4930431B09Rik|AI449797	family with sequence similarity 46, member C	protein-coding
mm_157592.1	chrX	53121705	53121754	-	1	NA	Intergenic	Intergenic	-7324	NM_019538	56096	Mm.274842	NM_019538	ENSMUSG00000061082	Plac1	DXWsu72e|Epcs26|Oosp2l	placental specific protein 1	protein-coding
mm_126755.1	chr15	85804046	85804060	+	1	NA	3' UTR (NM_011144, exon 8 of 8)	3' UTR (NM_011144, exon 8 of 8)	7644	NM_001164626	72355	Mm.33706	NM_197998	ENSMUSG00000064284	Cdpf1	2210021J22Rik	cysteine rich, DPF motif domain containing 1	protein-coding
mm_8737.1	chr1	160212717	160212858	-	1	NA	5' UTR (NM_009786, exon 1 of 6)	5' UTR (NM_009786, exon 1 of 6)	105	NM_009786	12301	Mm.10702	NM_009786	ENSMUSG00000014226	Cacybp	SIP	calcyclin binding protein	protein-coding
mm_103079.1	chr11	69900881	69900881	-	1	NA	promoter-TSS (NM_001291119)	promoter-TSS (NM_001291119)	105	NM_001316696	70419	Mm.272859	NM_027419	ENSMUSG00000018570	2810408A11Rik	1700019L01Rik|4930470J18Rik	RIKEN cDNA 2810408A11 gene	protein-coding
mm_2799.1	chr1	130851626	130851657	+	1	NA	3' UTR (NM_011082, exon 11 of 11)	3' UTR (NM_011082, exon 11 of 11)	-14136	NM_026976	69169	Mm.46042	NM_026976	ENSMUSG00000042474	Fcmr	1810037B05Rik|Faim3|FcmuR|Toso	Fc fragment of IgM receptor	protein-coding
mm_152319.1	chr19	9931148	9931163	-	1	NA	Intergenic	Intergenic	-31622	NM_016692	16319	Mm.29755	NM_016692	ENSMUSG00000024660	Incenp	2700067E22Rik|AU019509|C130081E20|C77457	inner centromere protein	protein-coding
mm_104812.1	chr11	98941908	98941932	-	1	NA	intron (NM_001177303, intron 1 of 8)	intron (NM_001177303, intron 1 of 8)	2209	NM_001177303	19401	Mm.439744	NM_009024	ENSMUSG00000037992	Rara	Nr1b1|RAR|RARalpha1	retinoic acid receptor, alpha	protein-coding
mm_42154.1	chr5	111793362	111793404	+	1	NA	Intergenic	Intergenic	-31655	NR_045833	269683	Mm.136946	NM_207252	ENSMUSG00000085271	E130006D01Rik	Gm16018|Gm681|OTTMUSG00000029083	RIKEN cDNA E130006D01 gene	ncRNA
mm_30466.1	chr3	154094154	154094160	-	1	NA	intron (NM_001081263, intron 1 of 21)	intron (NM_001081263, intron 1 of 21)	120721	NM_001081263	242259	Mm.239962	NM_001081263	ENSMUSG00000028360	Slc44a5	AA117069|Gm422	solute carrier family 44, member 5	protein-coding
mm_127318.1	chr15	100279952	100279955	+	1	NA	promoter-TSS (NM_183109)	promoter-TSS (NM_183109)	-884	NM_183109	75002	Mm.261400	NM_183109	ENSMUSG00000045631	Tmprss12	4930478A21Rik	transmembrane (C-terminal) protease, serine 12	protein-coding
mm_101366.1	chr11	23746797	23746807	-	1	NA	intron (NM_009044, intron 5 of 9)	B4|SINE|B4	24168	NM_009044	19696	Mm.4869	NM_009044	ENSMUSG00000020275	Rel	c-Rel	reticuloendotheliosis oncogene	protein-coding
mm_9292.1	chr1	171636341	171636380	-	1	NA	exon (NM_144539, exon 7 of 8)	exon (NM_144539, exon 7 of 8)	5540	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_24228.1	chr3	88914049	88914067	+	1	NA	promoter-TSS (NM_144898)	promoter-TSS (NM_144898)	-108	NM_144898	229524	Mm.440405	NM_144898	ENSMUSG00000068922	Msto1	BC008103|mst	misato 1, mitochondrial distribution and morphology regulator	protein-coding
mm_38244.1	chr4	136602578	136602602	-	1	NA	5' UTR (NM_133872, exon 1 of 19)	5' UTR (NM_133872, exon 1 of 19)	133	NM_133872	99982	Mm.28540	NM_133872	ENSMUSG00000036940	Kdm1a	1810043O07Rik|AA408884|Aof2|D4Ertd478e|Kdm1|Lsd1|mKIAA0601	lysine (K)-specific demethylase 1A	protein-coding
mm_17238.1	chr2	25587578	25587607	-	1	NA	exon (NM_001024616, exon 9 of 15)	exon (NM_001024616, exon 9 of 15)	-7493	NM_001005424	381353	Mm.379511	NM_001005424	ENSMUSG00000029419	Gm996	-	predicted gene 996	protein-coding
mm_158074.1	chrX	101264795	101264815	-	1	NA	promoter-TSS (NM_001317221)	promoter-TSS (NM_001317221)	-813	NM_001317221	245536	Mm.212463	NM_001033362	ENSMUSG00000090141	Gm614	-	predicted gene 614	protein-coding
mm_109909.1	chr12	8480058	8480060	-	1	NA	Intergenic	Intergenic	19926	NM_007483	11852	Mm.687	NM_007483	ENSMUSG00000054364	Rhob	AA017882|Arh6|Arhb	ras homolog family member B	protein-coding
mm_152938.1	chr19	28680203	28680267	-	1	NA	promoter-TSS (NM_175459)	promoter-TSS (NM_175459)	-158	NM_175459	226075	Mm.223508	NM_175459	ENSMUSG00000052942	Glis3	4833409N03Rik|E330013K21Rik	GLIS family zinc finger 3	protein-coding
mm_70275.1	chr8	3598444	3598454	+	1	NA	intron (NM_001347112, intron 2 of 17)	intron (NM_001347112, intron 2 of 17)	10999	NM_001347111	69697	Mm.390010	NM_027171	ENSMUSG00000044433	Camsap3	2310057J16Rik|Kiaa1543|Nezha	calmodulin regulated spectrin-associated protein family, member 3	protein-coding
mm_145653.1	chr18	61129329	61129353	+	1	NA	exon (NM_001037859, exon 19 of 22)	exon (NM_001037859, exon 19 of 22)	11873	NR_105949	102466212		NR_105949	ENSMUSG00000098389	Mir6983	Gm27496|mmu-mir-6983	microRNA 6983	ncRNA
mm_149699.1	chr19	21277701	21277723	+	1	NA	exon (NM_009551, exon 4 of 6)	exon (NM_009551, exon 4 of 6)	5434	NM_009551	22682	Mm.292405	NM_009551	ENSMUSG00000024750	Zfand5	2310057A04Rik|5830475F03Rik|AA415485|Za20d2|Zfp216	zinc finger, AN1-type domain 5	protein-coding
mm_57170.1	chr6	122820855	122820857	-	1	NA	5' UTR (NM_021899, exon 1 of 11)	5' UTR (NM_021899, exon 1 of 11)	672	NM_021899	60611	Mm.87142	NM_021899	ENSMUSG00000003154	Foxj2	Fhx	forkhead box J2	protein-coding
mm_155065.1	chrX	42502534	42502543	+	1	NA	promoter-TSS (NM_011364)	promoter-TSS (NM_011364)	-27	NM_011364	20400	Mm.441197	NM_011364	ENSMUSG00000005696	Sh2d1a	Gm686|SAP	SH2 domain containing 1A	protein-coding
mm_123598.1	chr14	67780418	67780441	-	1	NA	intron (NM_177780, intron 36 of 51)	intron (NM_177780, intron 36 of 51)	35248	NR_133010	14714	Mm.358309	NM_008145	ENSMUSG00000015812	Gnrh1	Gnrh|Gnrh2|LHRH|Lhrh1|Lnrh|hpg	gonadotropin releasing hormone 1	protein-coding
mm_168529.1	chr1	161035466	161035469	+	1	NA	non-coding (NR_002840, exon 1 of 4)	non-coding (NR_002840, exon 1 of 4)	301	NR_002840	14455	Mm.270065	NR_002840	ENSMUSG00000053332	Gas5	Gas-5|Mir5117|Snhg2	growth arrest specific 5	ncRNA
mm_10303.1	chr2	10893276	10893283	+	1	NA	Intergenic	Intergenic	-279103	NM_008859	18761	Mm.329993	NM_008859	ENSMUSG00000026778	Prkcq	A130035A12Rik|AW494342|PKC-0|PKC-theta|PKCtheta|Pkcq	protein kinase C, theta	protein-coding
mm_154268.1	chr19	60772716	60772726	-	1	NA	exon (NM_010123, exon 12 of 22)	exon (NM_010123, exon 12 of 22)	1664	NR_034047	100217439		NR_034047		Snora19	MBI-51	small nucleolar RNA, H/ACA box 19	snoRNA
mm_7570.1	chr1	124830701	124830748	-	1	NA	Intergenic	Intergenic	605003	NM_023735	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding
mm_168364.1	chr1	11626484	11626488	-	1	NA	intron (NM_001310451, intron 7 of 12)	L1Md_Gf|LINE|L1	212381	NM_001160371	320492	Mm.52021	NM_177173	ENSMUSG00000057715	A830018L16Rik	-	RIKEN cDNA A830018L16 gene	protein-coding
mm_66378.1	chr7	43756164	43756168	-	1	NA	promoter-TSS (NR_077063)	promoter-TSS (NR_077063)	-230	NR_077063	100504720	Mm.226595	NR_077063		2310002F09Rik	-	RIKEN cDNA 2310002F09 gene	ncRNA
mm_55346.1	chr6	56784424	56784426	-	1	NA	intron (NM_145958, intron 2 of 3)	intron (NM_145958, intron 2 of 3)	13388	NM_145958	210973	Mm.57295	NM_145958	ENSMUSG00000059486	Kbtbd2	BC022962|Bklhd1|mKIAA1489	kelch repeat and BTB (POZ) domain containing 2	protein-coding
mm_157841.1	chrX	74368548	74368571	-	1	NA	promoter-TSS (NM_145405)	promoter-TSS (NM_145405)	-11	NM_145405	27643	Mm.3979	NM_145405	ENSMUSG00000015290	Ubl4a	DXHXS254E|DXS254E|DXS254Eh|Gdx|Ubl4	ubiquitin-like 4A	protein-coding
mm_25934.1	chr3	131369002	131369016	+	1	NA	Intergenic	Intergenic	-24086	NM_028943	74442	Mm.273360	NM_028943	ENSMUSG00000050931	Sgms2	4933405A16Rik|5133401H06Rik|AI854299	sphingomyelin synthase 2	protein-coding
mm_76031.1	chr8	77286903	77286906	-	1	NA	intron (NM_030113, intron 19 of 22)	intron (NM_030113, intron 19 of 22)	-230152	NR_028125	70345	Mm.411813	NR_028125	ENSMUSG00000097882	0610038B21Rik	-	RIKEN cDNA 0610038B21 gene	ncRNA
mm_143647.1	chr17	79355624	79355708	-	1	NA	promoter-TSS (NM_026514)	promoter-TSS (NM_026514)	-575	NM_026514	260409	Mm.140601	NM_026514	ENSMUSG00000036533	Cdc42ep3	3200001F04Rik|AA986861|Borg2|Cep3|UB1	CDC42 effector protein (Rho GTPase binding) 3	protein-coding
mm_150972.1	chr19	46501432	46501471	+	1	NA	promoter-TSS (NM_053100)	promoter-TSS (NM_053100)	-197	NM_053100	93679	Mm.392177	NM_053100	ENSMUSG00000025034	Trim8	AA408830|BB006755|GERP|Rnf27	tripartite motif-containing 8	protein-coding
mm_1932.1	chr1	86110989	86110999	+	1	NA	5' UTR (NM_008311, exon 2 of 4)	5' UTR (NM_008311, exon 2 of 4)	976	NM_008311	15559	Mm.439747	NM_008311	ENSMUSG00000026228	Htr2b	5-HT2B|AJ012488|AV377389	5-hydroxytryptamine (serotonin) receptor 2B	protein-coding
mm_77800.1	chr9	3032000	3032033	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	6727	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_73523.1	chr8	107545012	107545026	+	1	NA	intron (NM_025830, intron 10 of 23)	intron (NM_025830, intron 10 of 23)	-6225	NR_029553	387158		NR_029553	ENSMUSG00000065439	Mir140	Mirn140|mir-140|mmu-mir-140	microRNA 140	ncRNA
mm_124857.1	chr15	9547826	9547831	+	1	NA	Intergenic	Intergenic	-17952	NM_008372	16197	Mm.389	NM_008372	ENSMUSG00000003882	Il7r	CD127|IL-7Ralpha	interleukin 7 receptor	protein-coding
mm_85824.1	chr9	110420909	110420919	-	1	NA	exon (NM_008694, exon 2 of 4)	exon (NM_008694, exon 2 of 4)	1106	NM_008694	18054	Mm.236225	NM_008694	ENSMUSG00000032484	Ngp	bectenecin	neutrophilic granule protein	protein-coding
mm_146412.1	chr18	84088681	84088693	+	1	NA	intron (NM_146090, intron 1 of 1)	CpG	529	NM_146090	225791	Mm.147052	NM_146090	ENSMUSG00000049090	Zadh2	C530046K17Rik|PTGR-3|Pthr3	zinc binding alcohol dehydrogenase, domain containing 2	protein-coding
mm_146555.1	chr18	6224046	6224065	-	1	NA	exon (NM_008448, exon 9 of 26)	exon (NM_008448, exon 9 of 26)	17469	NM_008448	16573	Mm.223744	NM_008448	ENSMUSG00000006740	Kif5b	AL022807|Khc|Khcs|Kns1|Ukhc	kinesin family member 5B	protein-coding
mm_152508.1	chr19	11266106	11266114	-	1	NA	promoter-TSS (NM_007641)	promoter-TSS (NM_007641)	41	NM_007641	12482	Mm.4046	NM_007641	ENSMUSG00000024673	Ms4a1	AA960661|Cd20|Ly-44|Ms4a2	membrane-spanning 4-domains, subfamily A, member 1	protein-coding
mm_118307.1	chr13	113101191	113101197	-	1	NA	promoter-TSS (NM_010370)	promoter-TSS (NM_010370)	-213	NM_010370	14938	Mm.15510	NM_010370	ENSMUSG00000023132	Gzma	AW494114|Ctla-3|Ctla3|Hf|Hf1|SE1|TSP-1|TSP1	granzyme A	protein-coding
mm_160231.1	chr7	102698122	102698122	+	1	NA	promoter-TSS (NM_146361)	promoter-TSS (NM_146361)	-94	NM_146361	258358	Mm.377455	NM_146361	ENSMUSG00000073967	Olfr557	MOR18-3	olfactory receptor 557	protein-coding
mm_163371.1	chr12	40446120	40446128	+	1	NA	promoter-TSS (NM_178845)	promoter-TSS (NM_178845)	71	NM_172803	238130	Mm.341423	NM_172803	ENSMUSG00000035954	Dock4	5330406C03|6330411N01Rik|AF263288|C030023J22|mKIAA0716	dedicator of cytokinesis 4	protein-coding
mm_104797.1	chr11	98773743	98773764	-	1	NA	intron (NM_145434, intron 1 of 7)	intron (NM_145434, intron 1 of 7)	1624	NM_145434	217166	Mm.390397	NM_145434	ENSMUSG00000020889	Nr1d1	A530070C09Rik|R75201	nuclear receptor subfamily 1, group D, member 1	protein-coding
mm_155897.1	chrX	101653225	101653237	+	1	NA	intron (NM_139144, intron 4 of 21)	intron (NM_139144, intron 4 of 21)	13013	NM_001290535	108155	Mm.487332	NM_139144	ENSMUSG00000034160	Ogt	1110038P24Rik|4831420N21Rik|AI115525|Ogtl	O-linked N-acetylglucosamine (GlcNAc) transferase (UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase)	protein-coding
mm_166946.1	chr7	43554606	43554619	-	1	NA	Intergenic	Intergenic	-7758	NM_001008549	210104	Mm.333821	NM_001008549	ENSMUSG00000056592	Zfp658	-	zinc finger protein 658	protein-coding
mm_47528.1	chr5	124187004	124187060	-	1	NA	5' UTR (NM_001289472, exon 1 of 25)	5' UTR (NM_001289472, exon 1 of 25)	150	NM_001289472	19679	Mm.44261	NM_011256	ENSMUSG00000029406	Pitpnm2	NIR3|RDGBA2|Rdgb2|mKIAA1457	phosphatidylinositol transfer protein, membrane-associated 2	protein-coding
mm_61423.1	chr7	73618820	73618824	+	1	NA	Intergenic	CpG	-60427	NR_037569	69170	Mm.34539	NR_037569	ENSMUSG00000101970	1810026B05Rik	-	RIKEN cDNA 1810026B05 gene	ncRNA
mm_8657.1	chr1	156474232	156474248	-	1	NA	promoter-TSS (NM_009230)	promoter-TSS (NM_009230)	88	NM_009230	20652	Mm.28099	NM_009230	ENSMUSG00000026600	Soat1	8430426K15Rik|ACAT-1|AW550831|Acact|ald|hid	sterol O-acyltransferase 1	protein-coding
mm_91668.1	chr10	43174497	43174516	-	1	NA	promoter-TSS (NR_102361)	promoter-TSS (NR_102361)	24	NM_175407	109205	Mm.153750	NM_175407	ENSMUSG00000038248	Sobp	2900009C16Rik|5330439J01Rik|JXC1|jc	sine oculis-binding protein homolog (Drosophila)	protein-coding
mm_153276.1	chr19	37178012	37178048	-	1	NA	intron (NR_045329, intron 2 of 2)	intron (NR_045329, intron 2 of 2)	-1967	NM_001290826	208922	Mm.391176	NM_198300	ENSMUSG00000039652	Cpeb3	4831444O18Rik|CPE-BP3|mKIAA0940	cytoplasmic polyadenylation element binding protein 3	protein-coding
mm_85962.1	chr9	112139345	112139365	-	1	NA	intron (NM_001177617, intron 10 of 14)	L1MB7|LINE|L1	-20644	NR_029823	723815		NR_029823	ENSMUSG00000065441	Mir128-2	Mirn128-2|Mirn128b|mir-128-2|mir-128b	microRNA 128-2	ncRNA
mm_35832.1	chr4	48039811	48039817	-	1	NA	Intergenic	Intergenic	-5491	NM_015743	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_146608.1	chr18	9866768	9866779	-	1	NA	exon (NM_130449, exon 8 of 10)	exon (NM_130449, exon 8 of 10)	-91407	NM_153552	225160	Mm.219648	NM_153552	ENSMUSG00000024287	Thoc1	3110002N20Rik|AW107452|NMP-84	THO complex 1	protein-coding
mm_40661.1	chr5	65250798	65250808	+	1	NA	intron (NM_153391, intron 29 of 36)	intron (NM_153391, intron 29 of 36)	51107	NM_153391	213081	Mm.127550	NM_153391	ENSMUSG00000037890	Wdr19	C330027H04Rik|D330023L08Rik|DYF2|Ift144|PWDMP|mKIAA1638	WD repeat domain 19	protein-coding
mm_58736.1	chr7	13030463	13030473	+	1	NA	exon (NM_011588, exon 16 of 17)	exon (NM_011588, exon 16 of 17)	4309	NM_026885	68953	Mm.295670	NM_026885	ENSMUSG00000033916	Chmp2a	1500016L11Rik	charged multivesicular body protein 2A	protein-coding
mm_25430.1	chr3	107895850	107895901	+	1	NA	promoter-TSS (NM_010360)	promoter-TSS (NM_010360)	21	NM_010360	14866	Mm.282351	NM_010360	ENSMUSG00000004032	Gstm5	-	glutathione S-transferase, mu 5	protein-coding
mm_119314.1	chr14	36968865	36968882	+	1	NA	promoter-TSS (NM_027045)	promoter-TSS (NM_027045)	-109	NM_027045	72972	Mm.27621	NM_027045	ENSMUSG00000058690	Ccser2	1700012P13Rik|2900054P12Rik|AI035535|AW108503|Fam190b|Gcap14	coiled-coil serine rich 2	protein-coding
mm_98169.1	chr11	87751793	87751810	+	1	NA	Intergenic	Intergenic	-5063	NR_029555	387160		NR_029555	ENSMUSG00000105196	Mir142	Mirn142|miR-142|mir-142a|mmu-mir-142|mmu-mir-142a	microRNA 142	ncRNA
mm_84090.1	chr9	58227035	58227049	-	1	NA	intron (NM_001311088, intron 7 of 8)	intron (NM_001311088, intron 7 of 8)	5892	NR_105806	102466639		NR_105806	ENSMUSG00000098886	Mir6385	Gm28021|mmu-mir-6385	microRNA 6385	ncRNA
mm_104479.1	chr11	95569947	95569960	-	1	NA	3' UTR (NM_033217, exon 6 of 6)	3' UTR (NM_033217, exon 6 of 6)	17745	NM_033217	18053	Mm.283893	NM_033217	ENSMUSG00000000120	Ngfr	LNGFR|Tnfrsf16|p75|p75NGFR|p75NTR	nerve growth factor receptor (TNFR superfamily, member 16)	protein-coding
mm_13085.1	chr2	91208870	91208884	+	1	NA	intron (NM_007387, intron 10 of 10)	L2a|LINE|L2	5965	NM_007387	11432	Mm.45570	NM_007387	ENSMUSG00000002103	Acp2	Acp-2|LAP	acid phosphatase 2, lysosomal	protein-coding
mm_103970.1	chr11	84519048	84519059	-	1	NA	TTS (NM_008498)	TTS (NM_008498)	-5552	NM_019816	56321	Mm.257482	NM_019816	ENSMUSG00000018697	Aatf	4933415H02Rik|5830465M17Rik|Che-1|Trb	apoptosis antagonizing transcription factor	protein-coding
mm_142060.1	chr17	35670482	35670510	-	1	NA	intron (NM_010364, intron 6 of 13)	intron (NM_010364, intron 6 of 13)	-2904	NM_175137	68915	Mm.32002	NM_175137	ENSMUSG00000038838	Vars2	1190004I24Rik|Vars2l|mKIAA1885	valyl-tRNA synthetase 2, mitochondrial	protein-coding
mm_42876.1	chr5	122241158	122241176	+	1	NA	non-coding (NR_104441, exon 13 of 13)	non-coding (NR_104441, exon 13 of 13)	23293	NR_104441	654470	Mm.28804	NM_001039153	ENSMUSG00000038593	Tctn1	G730031O11Rik|Tect1	tectonic family member 1	protein-coding
mm_98020.1	chr11	84957776	84957799	+	1	NA	promoter-TSS (NM_007607)	promoter-TSS (NM_007607)	33	NM_007607	12351	Mm.1641	NM_007607	ENSMUSG00000000805	Car4	AW456718|Ca4	carbonic anhydrase 4	protein-coding
mm_53345.1	chr6	129349739	129349750	+	1	NA	promoter-TSS (NM_177686)	promoter-TSS (NM_177686)	-500	NM_177686	232413	Mm.90241	NM_177686	ENSMUSG00000053063	Clec12a	CLL-1|D230024O04|KLRL1|Micl	C-type lectin domain family 12, member a	protein-coding
mm_132361.1	chr16	34690704	34690720	+	1	NA	promoter-TSS (NM_172824)	promoter-TSS (NM_172824)	96	NM_172824	239839	Mm.272045	NM_172824	ENSMUSG00000022833	Ccdc14	G630039H03Rik	coiled-coil domain containing 14	protein-coding
mm_139999.1	chr17	72941276	72941340	+	1	NA	3' UTR (NM_029999, exon 3 of 3)	3' UTR (NM_029999, exon 3 of 3)	23003	NM_029999	77889	Mm.154109	NM_029999	ENSMUSG00000024063	Lbh	1810009F10Rik|6720416L16Rik	limb-bud and heart	protein-coding
mm_122674.1	chr14	52008861	52008893	-	1	NA	exon (NM_001253694, exon 4 of 6)	exon (NM_001253694, exon 4 of 6)	5681	NM_001253695	69890	Mm.475652	NM_027248	ENSMUSG00000049295	Zfp219	2010302A17Rik	zinc finger protein 219	protein-coding
mm_110470.1	chr12	51829596	51829610	-	1	NA	promoter-TSS (NM_144788)	promoter-TSS (NM_144788)	-67	NM_144788	207304	Mm.249391	NM_144788	ENSMUSG00000035247	Hectd1	A630086P08Rik|AI844876|b2b327Clo|opm	HECT domain containing 1	protein-coding
mm_136752.1	chr17	8526997	8527025	+	1	NA	5' UTR (NM_001290707, exon 1 of 23)	5' UTR (NM_001290707, exon 1 of 23)	210	NM_001290707	23984	Mm.87161	NM_011866	ENSMUSG00000023868	Pde10a	-	phosphodiesterase 10A	protein-coding
mm_111520.1	chr12	100159602	100159672	-	1	NA	promoter-TSS (NM_001290303)	promoter-TSS (NM_001290303)	16	NM_001290303	217827	Mm.224076	NM_183155	ENSMUSG00000021179	Nrde2	6720454P05Rik	nrde-2 necessary for RNA interference, domain containing	protein-coding
mm_76312.1	chr8	84661591	84661605	-	1	NA	3' UTR (NM_010499, exon 1 of 1)	3' UTR (NM_010499, exon 1 of 1)	1254	NM_010499	15936	Mm.399	NM_010499	ENSMUSG00000053560	Ier2	AI317238|Ch1|Pip92	immediate early response 2	protein-coding
mm_67218.1	chr7	74482119	74482132	-	1	NA	intron (NM_001038643, intron 2 of 10)	intron (NM_001038643, intron 2 of 10)	72655	NM_023908	108116	Mm.425467	NM_023908	ENSMUSG00000025790	Slco3a1	5830414C08Rik|Anr1|MJAM|OATP-D|R75096|Slc21a11	solute carrier organic anion transporter family, member 3a1	protein-coding
mm_101794.1	chr11	46196031	46196041	-	1	NA	3' UTR (NM_001252459, exon 31 of 31)	3' UTR (NM_001252459, exon 31 of 31)	25949	NR_106098	102465715		NR_106098	ENSMUSG00000099331	Mir7239	Gm27504|mmu-mir-7239	microRNA 7239	ncRNA
mm_78384.1	chr9	28256986	28256989	+	1	NA	intron (NM_177906, intron 1 of 7)	ORR1B2|LTR|ERVL-MaLR	465718	NM_177906	330908	Mm.379474	NM_177906	ENSMUSG00000062257	Opcml	2900075O15Rik|3732419F12|AI844366|B930023M13Rik|C230027C17|Gm181|Obcam	opioid binding protein/cell adhesion molecule-like	protein-coding
mm_162326.1	chr1	40084711	40084717	+	1	NA	promoter-TSS (NM_010555)	promoter-TSS (NM_010555)	-54	NM_010555	16178	Mm.1349	NM_010555	ENSMUSG00000026073	Il1r2	CD121b|Il1r-2	interleukin 1 receptor, type II	protein-coding
mm_144594.1	chr18	32163063	32163069	+	1	NA	promoter-TSS (NM_011946)	promoter-TSS (NM_011946)	-23	NM_011946	26405	Mm.211762	NM_011946	ENSMUSG00000024383	Map3k2	9630061B06Rik|AI585793|Mekk2|Mekk2b	mitogen-activated protein kinase kinase kinase 2	protein-coding
mm_103188.1	chr11	70615646	70615656	-	1	NA	promoter-TSS (NM_001145537)	promoter-TSS (NM_001145537)	-243	NM_001145537	668433	Mm.425687	NM_001145537	ENSMUSG00000087279	4930544D05Rik	-	RIKEN cDNA 4930544D05 gene	protein-coding
mm_71810.1	chr8	68880715	68880717	+	1	NA	5' UTR (NM_008509, exon 1 of 10)	5' UTR (NM_008509, exon 1 of 10)	161	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_109944.1	chr12	11326423	11326436	-	1	NA	exon (NM_012038, exon 4 of 4)	exon (NM_012038, exon 4 of 4)	26542	NR_106136	102465775		NR_106136	ENSMUSG00000098879	Mir7675	Gm27965|mmu-mir-7675	microRNA 7675	ncRNA
mm_136885.1	chr17	13008701	13008712	+	1	NA	intron (NM_013671, intron 2 of 4)	intron (NM_013671, intron 2 of 4)	867	NM_013671	20656	Mm.290876	NM_013671	ENSMUSG00000006818	Sod2	MnSOD|Sod-2	superoxide dismutase 2, mitochondrial	protein-coding
mm_57889.1	chr6	131368100	131368110	-	1	NA	intron (NM_139117, intron 8 of 9)	intron (NM_139117, intron 8 of 9)	20345	NM_139117	56449	Mm.458000	NM_011733	ENSMUSG00000030189	Ybx3	Csda|Dpba|MSY3|MSY4|Yb2|dbpA|oxyR	Y box protein 3	protein-coding
mm_719.1	chr1	42695810	42695820	+	1	NA	promoter-TSS (NR_027826)	promoter-TSS (NR_027826)	-990	NR_027826	66297	Mm.45203	NM_183252	ENSMUSG00000060424	Pantr1	2610017I09Rik|Pou3f3os|linc-Brn1a	POU domain, class 3, transcription factor 3 adjacent noncoding transcript 1	ncRNA
mm_76897.1	chr8	105774325	105774357	-	1	NA	exon (NM_145824, exon 9 of 14)	exon (NM_145824, exon 9 of 14)	-15734	NM_027469	70575	Mm.40954	NM_027469	ENSMUSG00000013150	Gfod2	5730466C23Rik	glucose-fructose oxidoreductase domain containing 2	protein-coding
mm_65754.1	chr7	28598141	28598176	-	1	NA	promoter-TSS (NM_027470)	promoter-TSS (NM_027470)	26	NM_027470	70584	Mm.21876	NM_027470	ENSMUSG00000030602	Pak4	5730488L07Rik|AW555722|mKIAA1142	p21 protein (Cdc42/Rac)-activated kinase 4	protein-coding
mm_101462.1	chr11	30279443	30279465	-	1	NA	Intergenic	Intergenic	-59682	NM_175836	20742	Mm.123110	NM_009260	ENSMUSG00000020315	Sptbn1	9930031C03Rik|AL033301|SPTB2|Spnb-2|Spnb2|elf1|elf3|mKIAA4049	spectrin beta, non-erythrocytic 1	protein-coding
mm_58557.1	chr7	4740976	4740982	+	1	NA	intron (NM_146177, intron 1 of 8)	intron (NM_146177, intron 1 of 8)	852	NM_001115018	232811	Mm.247844	NM_146177	ENSMUSG00000059851	Kmt5c	BC024816|Suv4-20h2|Suv420h2	lysine methyltransferase 5C	protein-coding
mm_31857.1	chr4	78773691	78773724	+	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	179660	NR_131142	623726		NR_131142		A430085M09Rik	EG623726	RIKEN cDNA A430085M09 gene	ncRNA
mm_59817.1	chr7	29179573	29179579	+	1	NA	intron (NM_026545, intron 1 of 6)	PB1D10|SINE|Alu	1097	NM_026545	57296	Mm.273152	NM_026545	ENSMUSG00000030591	Psmd8	6720456J22Rik|AA407360|AL033291|AL033322|AL033323|C76433	proteasome (prosome, macropain) 26S subunit, non-ATPase, 8	protein-coding
mm_171683.1	chr4	57956429	57956443	-	1	NA	promoter-TSS (NM_011660)	promoter-TSS (NM_011660)	-25	NM_011660	22166	Mm.260618	NM_011660	ENSMUSG00000028367	Txn1	ADF|AW550880|Trx1|Txn	thioredoxin 1	protein-coding
mm_127801.1	chr15	3995245	3995245	-	1	NA	promoter-TSS (NR_045740)	promoter-TSS (NR_045740)	507	NM_145930	106064	Mm.21299	NM_145930	ENSMUSG00000041935	AW549877	AI195826	expressed sequence AW549877	protein-coding
mm_92267.1	chr10	71158972	71158972	-	1	NA	intron (NM_031397, intron 1 of 20)	intron (NM_031397, intron 1 of 20)	718	NM_031397	83675	Mm.286834	NM_031397	ENSMUSG00000014329	Bicc1	Bic-C|bpk|jcpk	BicC family RNA binding protein 1	protein-coding
mm_52828.1	chr6	121359495	121359511	+	1	NA	intron (NM_001347433, intron 9 of 14)	intron (NM_001347433, intron 9 of 14)	12806	NM_133661	14411	Mm.274506	NM_133661	ENSMUSG00000030109	Slc6a12	BGT1|GAT-2|GAT2|Gabt2	solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12	protein-coding
mm_146404.1	chr18	83124716	83124722	+	1	NA	Intergenic	RLTR12G|LTR|ERVK	201165	NR_045361	70960	Mm.410834	NR_045361		4921531P14Rik	1700108N05Rik	RIKEN cDNA 4921531P14 gene	ncRNA
mm_80159.1	chr9	70956918	70956927	+	1	NA	Intergenic	IMPB_01|Satellite|Satellite	-4701	NM_001324472	15450	Mm.390187	NM_008280	ENSMUSG00000032207	Lipc	AI256194|HL|Hpl	lipase, hepatic	protein-coding
mm_168338.1	chr11	11932452	11932469	-	1	NA	3' UTR (NM_010345, exon 17 of 17)	3' UTR (NM_010345, exon 17 of 17)	-34316	NM_001190448	13195	Mm.12906	NM_016672	ENSMUSG00000020182	Ddc	Aadc	dopa decarboxylase	protein-coding
mm_64637.1	chr7	3898130	3898142	-	1	NA	promoter-TSS (NM_001166672)	promoter-TSS (NM_001166672)	14	NM_001289428	18729	Mm.326531	NM_008848		Pira6	12M1|Pira10|p91B	paired-Ig-like receptor A6	protein-coding
mm_102248.1	chr11	55109725	55109751	-	1	NA	3' UTR (NM_010299, exon 4 of 4)	3' UTR (NM_010299, exon 4 of 4)	11753	NM_010299	14667	Mm.287807	NM_010299	ENSMUSG00000000594	Gm2a	AA408702|AW215435|GM2-AP|SAP-3	GM2 ganglioside activator protein	protein-coding
mm_72910.1	chr8	90955080	90955096	+	1	NA	intron (NM_001310530, intron 1 of 37)	intron (NM_001310530, intron 1 of 37)	22839	NM_001310530	109151	Mm.100615	NM_177224	ENSMUSG00000056608	Chd9	1810014J18Rik|9030205D12Rik|A330063D19Rik|AD013|PRIC320|mKIAA0308	chromodomain helicase DNA binding protein 9	protein-coding
mm_158829.1	chrX	168123257	168123267	-	1	NA	promoter-TSS (NM_001290427)	promoter-TSS (NM_001290427)	-265	NM_001290427	333605	Mm.426168	NM_001033330	ENSMUSG00000049176	Frmpd4	Gm196|PKAP1|Pdzd10|Pdzk10|Preso1|preso	FERM and PDZ domain containing 4	protein-coding
mm_61611.1	chr7	80040240	80040261	+	1	NA	intron (NM_175433, intron 1 of 4)	B3|SINE|B2	14022	NM_175433	209225	Mm.290925	NM_175433	ENSMUSG00000048897	Zfp710	5430400N05Rik|9830165K13|AI324798|Znf710	zinc finger protein 710	protein-coding
mm_36270.1	chr4	63728810	63728819	-	1	NA	3' UTR (NM_177371, exon 4 of 4)	3' UTR (NM_177371, exon 4 of 4)	16299	NM_177371	326623	Mm.208152	NM_177371	ENSMUSG00000050395	Tnfsf15	Tl1|Tl1a|Tnlg1b|Vegi	tumor necrosis factor (ligand) superfamily, member 15	protein-coding
mm_54094.1	chr6	16836979	16837005	-	1	NA	intron (NM_031198, intron 5 of 6)	Lx8|LINE|L1	61449	NM_031198	21426	Mm.36217	NM_031198	ENSMUSG00000029553	Tfec	BB107417|Tcfec|bHLHe34	transcription factor EC	protein-coding
mm_54714.1	chr6	39810866	39810876	-	1	NA	promoter-TSS (NM_010270)	promoter-TSS (NM_010270)	65	NM_010270	14548	Mm.377071	NM_010270	ENSMUSG00000029918	Mrps33	AI841153|CGI-139|Gdap3|MRP-S33|PTD003	mitochondrial ribosomal protein S33	protein-coding
mm_109033.1	chr12	104101021	104101028	+	1	NA	promoter-TSS (NM_172953)	promoter-TSS (NM_172953)	-89	NM_172953	268591	Mm.73172	NM_172953	ENSMUSG00000041550	Serpina5	4933415L04|PAI-3|Pci	serine (or cysteine) peptidase inhibitor, clade A, member 5	protein-coding
mm_24924.1	chr3	96525193	96525219	+	1	NA	promoter-TSS (NM_027126)	promoter-TSS (NM_027126)	21	NM_027126	69585	Mm.171314	NM_027126	ENSMUSG00000038403	Hfe2	2310035L15Rik|5230400G09Rik|AI414844|AI789733|DL-M|HJV|Rgmc|hemojuvelin	hemochromatosis type 2 (juvenile)	protein-coding
mm_69381.1	chr7	131322071	131322094	-	1	NA	5' UTR (NM_008411, exon 1 of 9)	5' UTR (NM_008411, exon 1 of 9)	210	NM_008411	16433	Mm.142717	NM_008411	ENSMUSG00000040205	Cuzd1	Erg-1|Itmap1|Uo-44|Usg|Utczp	CUB and zona pellucida-like domains 1	protein-coding
mm_154258.1	chr19	60768840	60768865	-	1	NA	exon (NM_010123, exon 17 of 22)	exon (NM_010123, exon 17 of 22)	5533	NR_034047	100217439		NR_034047		Snora19	MBI-51	small nucleolar RNA, H/ACA box 19	snoRNA
mm_94487.1	chr11	6637232	6637250	+	1	NA	exon (NM_011709, exon 2 of 4)	exon (NM_011709, exon 2 of 4)	1408	NM_011709	22373	Mm.268094	NM_011709	ENSMUSG00000000381	Wap	-	whey acidic protein	protein-coding
mm_47111.1	chr5	119527946	119527962	-	1	NA	Intergenic	Intergenic	52404	NR_045702	100993	Mm.381453	NR_045702	ENSMUSG00000087516	AW549542	-	expressed sequence AW549542	ncRNA
mm_92519.1	chr10	78574901	78574912	-	1	NA	intron (NM_173751, intron 1 of 15)	CpG	406	NM_173751	216136	Mm.2644	NM_173751	ENSMUSG00000032763	Ilvbl	5830463I21|AI415009	ilvB (bacterial acetolactate synthase)-like	protein-coding
mm_114597.1	chr13	75765119	75765124	+	1	NA	intron (NM_138953, intron 8 of 11)	intron (NM_138953, intron 8 of 11)	57637	NM_138953	192657	Mm.21288	NM_138953	ENSMUSG00000001542	Ell2	-	elongation factor RNA polymerase II 2	protein-coding
mm_59295.1	chr7	25077551	25077564	+	1	NA	intron (NM_175477, intron 1 of 1)	CpG	311	NM_175477	232976	Mm.41568	NM_175477	ENSMUSG00000045252	Zfp574	A630056B21Rik|Znf574	zinc finger protein 574	protein-coding
mm_164724.1	chr17	57080220	57080244	+	1	NA	3' UTR (NM_009451, exon 4 of 4)	3' UTR (NM_009451, exon 4 of 4)	-1722	NM_153551	70785	Mm.284447	NM_153551	ENSMUSG00000002668	Dennd1c	4432409M07Rik	DENN/MADD domain containing 1C	protein-coding
mm_46806.1	chr5	113077151	113077164	-	1	NA	intron (NM_001159650, intron 5 of 5)	GA-rich|Low_complexity|Low_complexity	4427	NM_001159650	12962	Mm.378899	NM_021352	ENSMUSG00000029352	Crybb3	AI852419	crystallin, beta B3	protein-coding
mm_71521.1	chr8	46847203	46847213	+	1	NA	3' UTR (NM_008391, exon 9 of 9)	3' UTR (NM_008391, exon 9 of 9)	107463	NM_008391	16363	Mm.1149	NM_008391	ENSMUSG00000031627	Irf2	9830146E22Rik|AI646973|Irf-2	interferon regulatory factor 2	protein-coding
mm_70647.1	chr8	14270725	14270726	+	1	NA	intron (NM_172910, intron 3 of 15)	L1_Mus3|LINE|L1	174850	NM_172910	244310	Mm.404697	NM_172910	ENSMUSG00000047495	Dlgap2	6430596N04Rik|Dap-2|Dap2|Sapap2	discs, large (Drosophila) homolog-associated protein 2	protein-coding
mm_135198.1	chr16	36532170	36532184	-	1	NA	intron (NM_013803, intron 1 of 6)	intron (NM_013803, intron 1 of 6)	29957	NM_013803	12374	Mm.103619	NM_013803	ENSMUSG00000051980	Casr	CaR|Gprc2a	calcium-sensing receptor	protein-coding
mm_85710.1	chr9	108190353	108190420	-	1	NA	promoter-TSS (NM_007567)	promoter-TSS (NM_007567)	-3	NM_007567	12217	Mm.20425	NM_007567	ENSMUSG00000032589	Bsn	-	bassoon	protein-coding
mm_40453.1	chr5	53603962	53603976	+	1	NA	intron (NM_001277116, intron 3 of 12)	intron (NM_001277116, intron 3 of 12)	13483	NM_001080927	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_62149.1	chr7	97131176	97131187	+	1	NA	intron (NM_001162477, intron 1 of 9)	L1_Mur1|LINE|L1	49430	NM_010248	14389	Mm.42033	NM_010248	ENSMUSG00000004508	Gab2	AI463667|D130058I17Rik|p97	growth factor receptor bound protein 2-associated protein 2	protein-coding
mm_140553.1	chr17	7765229	7765302	-	1	NA	exon (NM_001081416, exon 11 of 20)	exon (NM_001081416, exon 11 of 20)	39709	NM_001081416	68655	Mm.379161	NM_001081416	ENSMUSG00000071984	Fndc1	1110027O12Rik|1110051A18Rik|mKIAA1866	fibronectin type III domain containing 1	protein-coding
mm_56342.1	chr6	92860495	92860509	-	1	NA	intron (NM_175314, intron 13 of 29)	intron (NM_175314, intron 13 of 29)	40939	NM_175314	101401	Mm.158235	NM_175314	ENSMUSG00000030022	Adamts9	1810011L16Rik|8430403M15Rik|AW743315|E030027K14Rik	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 9	protein-coding
mm_126859.1	chr15	89286954	89286957	+	1	NA	TTS (NM_026813)	TTS (NM_026813)	18777	NR_105924	102465981		NR_105924	ENSMUSG00000098442	Mir6959	Gm27807|mmu-mir-6959	microRNA 6959	ncRNA
mm_155204.1	chrX	56731757	56731767	+	1	NA	promoter-TSS (NM_010211)	promoter-TSS (NM_010211)	1	NM_010211	14199	Mm.3126	NM_010211	ENSMUSG00000023092	Fhl1	FHL-1|KyoT|RAM14-1|SLIM|SLIM-1	four and a half LIM domains 1	protein-coding
mm_73490.1	chr8	107056923	107056927	+	1	NA	promoter-TSS (NM_139229)	promoter-TSS (NM_139229)	48	NR_028367	66164	Mm.334789	NM_025391	ENSMUSG00000031917	Nip7	1110017C15Rik|6330509M23Rik|AA408773|AA410017|PEachy	NIP7, nucleolar pre-rRNA processing protein	protein-coding
mm_117412.1	chr13	74062263	74062315	-	1	NA	promoter-TSS (NM_028959)	promoter-TSS (NM_028959)	-4	NM_028959	74470	Mm.73234	NM_028959	ENSMUSG00000021572	Cep72	2610029E11Rik|4933440J22Rik	centrosomal protein 72	protein-coding
mm_131384.1	chr16	14172265	14172267	+	1	NA	intron (NM_001285504, intron 3 of 7)	intron (NM_001285504, intron 3 of 7)	8991	NM_001114085	67203	Mm.24105	NM_023317	ENSMUSG00000022678	Nde1	2810027M15Rik|AU042936|AW822251|Nude|mNudE	nudE neurodevelopment protein 1	protein-coding
mm_44112.1	chr5	149412099	149412138	+	1	NA	exon (NM_027519, exon 1 of 5)	exon (NM_027519, exon 1 of 5)	312	NM_027519	70717	Mm.252139	NM_027519	ENSMUSG00000029659	Medag	6330406I15Rik|Awms3|MEDA-4|Meda4|mAWMS3	mesenteric estrogen dependent adipogenesis	protein-coding
mm_17092.1	chr2	23036146	23036159	-	1	NA	intron (NM_001331043, intron 1 of 10)	intron (NM_001331043, intron 1 of 10)	4089	NM_001077192	11308	Mm.205647	NM_007380	ENSMUSG00000058835	Abi1	E3B1|NAP1|Ssh3bp1|abi-1	abl-interactor 1	protein-coding
mm_68987.1	chr7	126592874	126592884	-	1	NA	exon (NM_145636, exon 2 of 5)	exon (NM_145636, exon 2 of 5)	2031	NM_145636	246779	Mm.222632	NM_145636	ENSMUSG00000044701	Il27	IL-27|IL-27p28|Il30|p28	interleukin 27	protein-coding
mm_74487.1	chr8	4779452	4779458	-	1	NA	promoter-TSS (NM_011369)	promoter-TSS (NM_011369)	79	NM_011369	20419	Mm.37801	NM_011369	ENSMUSG00000022322	Shcbp1	mPAL	Shc SH2-domain binding protein 1	protein-coding
mm_95067.1	chr11	32554286	32554334	+	1	NA	intron (NM_009288, intron 1 of 18)	URR1B|DNA|hAT-Charlie	21044	NM_009288	20868	Mm.8235	NM_009288	ENSMUSG00000020272	Stk10	Gek1|Lok|mKIAA4026	serine/threonine kinase 10	protein-coding
mm_148538.1	chr19	4603127	4603145	+	1	NA	exon (NM_001162946, exon 8 of 21)	exon (NM_001162946, exon 8 of 21)	8817	NM_008797	18563	Mm.1845	NM_008797	ENSMUSG00000024892	Pcx	Pc|Pcb	pyruvate carboxylase	protein-coding
mm_155565.1	chrX	75915105	75915112	+	1	NA	Intergenic	RSINE1|SINE|B4	-39926	NM_001346519	102866	Mm.28777	NM_145629	ENSMUSG00000016382	Pls3	AI115446|AL024105	plastin 3 (T-isoform)	protein-coding
mm_79725.1	chr9	62122989	62122991	+	1	NA	promoter-TSS (NR_039595)	promoter-TSS (NR_039595)	-396	NR_039595	100628602		NR_039595	ENSMUSG00000092696	Mir5133	mir-5133|mmu-mir-5133|mu-mir-5133	microRNA 5133	ncRNA
mm_75602.1	chr8	61760420	61760422	-	1	NA	promoter-TSS (NM_001293773)	promoter-TSS (NM_001293773)	-323	NM_001293773	72333	Mm.29933	NM_001081390	ENSMUSG00000058056	Palld	2410003B16Rik|6030492A02	palladin, cytoskeletal associated protein	protein-coding
mm_61640.1	chr7	80294558	80294565	+	1	NA	5' UTR (NM_145150, exon 1 of 14)	5' UTR (NM_145150, exon 1 of 14)	110	NM_001285998	233406	Mm.227274	NM_145150	ENSMUSG00000038943	Prc1	D7Ertd348e	protein regulator of cytokinesis 1	protein-coding
mm_30703.1	chr4	11765269	11765285	+	1	NA	intron (NM_019753, intron 1 of 17)	intron (NM_019753, intron 1 of 17)	7120	NM_019753	12557	Mm.33402	NM_019753	ENSMUSG00000028217	Cdh17	HPT-1|HPT-1/LI	cadherin 17	protein-coding
mm_147554.1	chr18	54957775	54957789	-	1	NA	intron (NM_175751, intron 2 of 9)	intron (NM_175751, intron 2 of 9)	32398	NM_175751	269023	Mm.192984	NM_175751	ENSMUSG00000052713	Zfp608	4932417D18Rik|D430007A19Rik|Znf608	zinc finger protein 608	protein-coding
mm_113831.1	chr13	47102007	47102054	+	1	NA	exon (NM_025900, exon 3 of 11)	exon (NM_025900, exon 3 of 11)	4191	NM_025900	110052	Mm.131150	NM_025900	ENSMUSG00000021377	Dek	1810019E15Rik|D13H6S231E	DEK oncogene (DNA binding)	protein-coding
mm_156967.1	chrX	169997065	169997076	+	1	NA	Intergenic	CpG	-18153	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_2840.1	chr1	131573844	131573847	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-25269	NM_011924	26361	Mm.89986	NM_011924	ENSMUSG00000026432	Avpr1b	AVPR3|V3/V1b|VIBR|VPR3	arginine vasopressin receptor 1B	protein-coding
mm_817.1	chr1	46088875	46088881	+	1	NA	intron (NM_001160386, intron 6 of 65)	intron (NM_001160386, intron 6 of 65)	22140	NM_001160386	227058	Mm.296880	NM_001160386	ENSMUSG00000041144	Dnah7b	Dnahc7b|Gm107	dynein, axonemal, heavy chain 7B	protein-coding
mm_96720.1	chr11	69665683	69665704	+	1	NA	exon (NM_001291058, exon 2 of 6)	exon (NM_001291058, exon 2 of 6)	477	NM_001291058	12514	Mm.15819	NM_009853	ENSMUSG00000018774	Cd68	Lamp4|Scard1|gp110	CD68 antigen	protein-coding
mm_92438.1	chr10	77211126	77211169	-	1	NA	Intergenic	Intergenic	-44617	NM_009929	12822	Mm.4352	NM_009929	ENSMUSG00000001435	Col18a1	-	collagen, type XVIII, alpha 1	protein-coding
mm_4438.1	chr1	172506896	172506924	+	1	NA	3' UTR (NM_178598, exon 5 of 5)	3' UTR (NM_178598, exon 5 of 5)	6664	NM_178598	21346	Mm.271711	NM_178598	ENSMUSG00000026547	Tagln2	2700094C18Rik|SM22beta|Sm22B|Sm22a	transgelin 2	protein-coding
mm_137181.1	chr17	23816273	23816289	+	1	NA	exon (NM_175229, exon 10 of 14)	exon (NM_175229, exon 10 of 14)	12828	NM_026305	67673	Mm.153758	NM_026305	ENSMUSG00000055839	Elob	0610040H15Rik|Tceb2	elongin B	protein-coding
mm_44987.1	chr5	37624831	37624850	-	1	NA	intron (NM_022416, intron 3 of 11)	intron (NM_022416, intron 3 of 11)	92313	NM_022416	64293	Mm.103714	NM_022416	ENSMUSG00000029123	Stk32b	2510009F08Rik|STKG6|Stk32|YANK2	serine/threonine kinase 32B	protein-coding
mm_104726.1	chr11	98326061	98326082	-	1	NA	3' UTR (NM_010895, exon 2 of 2)	3' UTR (NM_010895, exon 2 of 2)	3574	NM_010895	18013	Mm.4814	NM_010895	ENSMUSG00000038255	Neurod2	Ndrf|bHLHa1	neurogenic differentiation 2	protein-coding
mm_149735.1	chr19	22040853	22040883	+	1	NA	Intergenic	Intergenic	-98249	NM_001035239	226025	Mm.131943	NM_177341	ENSMUSG00000052387	Trpm3	6330504P12Rik|9330180E14|AU018608|B930001P07Rik|LTRPC3|MLSN2	transient receptor potential cation channel, subfamily M, member 3	protein-coding
mm_86125.1	chr9	116175198	116175261	-	1	NA	5' UTR (NM_029575, exon 1 of 7)	5' UTR (NM_029575, exon 1 of 7)	134	NM_029575	21813	Mm.172346	NM_009371	ENSMUSG00000032440	Tgfbr2	1110020H15Rik|AU042018|DNIIR|RIIDN|TBR-II|TbetaR-II|TbetaRII	transforming growth factor, beta receptor II	protein-coding
mm_44521.1	chr5	24391946	24391961	-	1	NA	5' UTR (NM_001002897, exon 1 of 14)	5' UTR (NM_001002897, exon 1 of 14)	190	NM_001002897	213948	Mm.332252	NM_001002897	ENSMUSG00000038295	Atg9b	Apg912|Apg9l2|Apgdc2|Gm574|Nos3as|eONE|sONE	autophagy related 9B	protein-coding
mm_44978.1	chr5	36827917	36827927	-	1	NA	exon (NM_008550, exon 3 of 19)	exon (NM_008550, exon 3 of 19)	2727	NM_008550	17160	Mm.761	NM_008550	ENSMUSG00000029119	Man2b2	mKIAA0935	mannosidase 2, alpha B2	protein-coding
mm_3747.1	chr1	155742510	155742515	+	1	NA	promoter-TSS (NM_010712)	promoter-TSS (NM_010712)	-485	NM_010712	16872	Mm.103624	NM_010712	ENSMUSG00000026468	Lhx4	A330062J17Rik|Gsh-4|Gsh4	LIM homeobox protein 4	protein-coding
mm_98409.1	chr11	94352201	94352211	+	1	NA	exon (NM_029600, exon 27 of 31)	exon (NM_029600, exon 27 of 31)	24205	NM_146024	71452	Mm.141054	NM_027799	ENSMUSG00000020864	Ankrd40	1110011C06Rik|5530600A18Rik|Gcap15	ankyrin repeat domain 40	protein-coding
mm_161134.1	chr13	3837858	3837858	+	1	NA	5' UTR (NM_020036, exon 1 of 1)	5' UTR (NM_020036, exon 1 of 1)	101	NM_020036	80796	Mm.21075	NM_020036	ENSMUSG00000033765	Calm4	2310037J09Rik|AI649108|DD112|Scarf	calmodulin 4	protein-coding
mm_164392.1	chr16	33725587	33725609	+	1	NA	exon (NM_175256, exon 3 of 15)	exon (NM_175256, exon 3 of 15)	41132	NM_175256	77446	Mm.245741	NM_172934	ENSMUSG00000075254	Heg1	4632417D23Rik|5530401I02Rik|9530025L16Rik|BC038614|Gm629|OTTMUSG00000027315	heart development protein with EGF-like domains 1	protein-coding
mm_105275.1	chr11	102407456	102407528	-	1	NA	promoter-TSS (NM_026542)	promoter-TSS (NM_026542)	25	NM_026542	68066	Mm.44226	NM_026542	ENSMUSG00000018677	Slc25a39	3010027G13Rik|D11Ertd333e	solute carrier family 25, member 39	protein-coding
mm_164655.1	chr17	36058452	36058457	-	1	NA	promoter-TSS (NM_001199967)	promoter-TSS (NM_001199967)	-83	NM_001199967	100529082	Mm.484641	NM_001199967	ENSMUSG00000079492	Gm11127	ENSMUSG00000079492	predicted gene 11127	protein-coding
mm_24909.1	chr3	96221112	96221134	+	1	NA	promoter-TSS (NM_178214)	promoter-TSS (NM_178214)	51	NM_178214	319190	Mm.439791	NM_178214	ENSMUSG00000068854	Hist2h2be	AV127319|H2b-613|T25626	histone cluster 2, H2be	protein-coding
mm_81911.1	chr9	120091380	120091427	+	1	NA	promoter-TSS (NM_007720)	promoter-TSS (NM_007720)	-730	NM_007720	12776	Mm.442098	NM_007720	ENSMUSG00000042262	Ccr8	C-C|C-C CKR-8|CC-CKR-8|CCR-8|CKR-8|Cmkbr8|mCCR8	chemokine (C-C motif) receptor 8	protein-coding
mm_32629.1	chr4	114986665	114986684	+	1	NA	intron (NM_025647, intron 1 of 5)	intron (NM_025647, intron 1 of 5)	554	NM_025647	66588	Mm.294159	NM_025647	ENSMUSG00000028719	Cmpk1	0610011D08Rik|CK|Cmpk|UMP-CMPk	cytidine monophosphate (UMP-CMP) kinase 1	protein-coding
mm_71110.1	chr8	35672360	35672366	+	1	NA	intron (NM_001081279, intron 2 of 2)	intron (NM_001081279, intron 2 of 2)	-83343	NR_040376	100504714	Mm.381744	NR_040376	ENSMUSG00000097357	Gm16793	-	predicted gene, 16793	ncRNA
mm_28773.1	chr3	95928871	95928889	-	1	NA	promoter-TSS (NM_001253757)	promoter-TSS (NM_001253757)	-377	NM_001253758	66471	Mm.218657	NM_023210	ENSMUSG00000015749	Anp32e	2810018A15Rik|AI047746|AI326868|CPD1|LANP-L|LANPL|mLANP-L	acidic (leucine-rich) nuclear phosphoprotein 32 family, member E	protein-coding
mm_69933.1	chr7	142061022	142061071	-	1	NA	promoter-TSS (NM_028308)	promoter-TSS (NM_028308)	-12	NM_028308	101513	Mm.53259	NM_028308	ENSMUSG00000025147	Mob2	1110017M21Rik|2700078K21Rik|AI256456|Mmh	MOB kinase activator 2	protein-coding
mm_95242.1	chr11	44617614	44617630	+	1	NA	promoter-TSS (NM_001290711)	promoter-TSS (NM_001290711)	-478	NM_001290711	13591	Mm.439662	NM_007897	ENSMUSG00000057098	Ebf1	Ebf|O/E-1|OE-1|Olf-1|Olf1	early B cell factor 1	protein-coding
mm_66452.1	chr7	44869629	44869724	-	1	NA	5' UTR (NM_133949, exon 1 of 12)	5' UTR (NM_133949, exon 1 of 12)	112	NM_133949	84113	Mm.42855	NM_133949	ENSMUSG00000038502	Ptov1	1110030G05Rik|AU041779|Gcap3	prostate tumor over expressed gene 1	protein-coding
mm_34705.1	chr4	152108162	152108206	+	1	NA	exon (NM_001285999, exon 14 of 21)	exon (NM_001285999, exon 14 of 21)	-7750	NM_001291010	85030	Mm.101198	NM_033042	ENSMUSG00000024793	Tnfrsf25	APO-3|DDR3|DR3|LARD|TR3|TRAMP|Tnfrsf12|WSL-1|WSL-LR|Wsl	tumor necrosis factor receptor superfamily, member 25	protein-coding
mm_132714.1	chr16	43506433	43506455	+	1	NA	intron (NM_181058, intron 3 of 6)	intron (NM_181058, intron 3 of 6)	-86248	NR_046026	626693	Mm.447083	NR_046026	ENSMUSG00000085499	Gm15713	OTTMUSG00000025617	predicted gene 15713	ncRNA
mm_101220.1	chr11	20153701	20153745	-	1	NA	Intergenic	RMER16-int|LTR|ERVK	-40772	NM_146243	66713	Mm.259045	NM_146243	ENSMUSG00000020152	Actr2	4921510D23Rik|AA409782|Arp2|D6Ertd746e	ARP2 actin-related protein 2	protein-coding
mm_18457.1	chr2	61593573	61593613	-	1	NA	intron (NM_001164072, intron 1 of 7)	intron (NM_001164072, intron 1 of 7)	496	NM_001164071	21353	Mm.244393	NM_011529	ENSMUSG00000064289	Tank	C86182|E430026L09Rik|I-TRAF	TRAF family member-associated Nf-kappa B activator	protein-coding
mm_45602.1	chr5	75043258	75043263	-	1	NA	intron (NM_028850, intron 1 of 5)	intron (NM_028850, intron 1 of 5)	1381	NM_028850	74277	Mm.239814	NM_028850	ENSMUSG00000029229	Chic2	1700081B18Rik|4930502K01Rik|BTL	cysteine-rich hydrophobic domain 2	protein-coding
mm_72527.1	chr8	83980513	83980552	+	1	NA	intron (NM_001277898, intron 1 of 9)	intron (NM_001277898, intron 1 of 9)	3649	NM_001277898	18747	Mm.19111	NM_008854	ENSMUSG00000005469	Prkaca	PKCD|Pkaca	protein kinase, cAMP dependent, catalytic, alpha	protein-coding
mm_111145.1	chr12	81817260	81817280	-	1	NA	Intergenic	Intergenic	-36100	NM_001174107	338372	Mm.35284	NM_177395	ENSMUSG00000042724	Map3k9	E130314H24Rik|Mlk1|Prke1	mitogen-activated protein kinase kinase kinase 9	protein-coding
mm_10945.1	chr2	25543427	25543439	+	1	NA	intron (NM_009422, intron 1 of 10)	intron (NM_009422, intron 1 of 10)	3507	NM_001290413	22030	Mm.3399	NM_009422	ENSMUSG00000026942	Traf2	AI325259	TNF receptor-associated factor 2	protein-coding
mm_156883.1	chrX	166344785	166344914	+	1	NA	5' UTR (NM_001177959, exon 1 of 7)	5' UTR (NM_001177959, exon 1 of 7)	296	NM_001177960	14758	Mm.222320	NM_023122	ENSMUSG00000031342	Gpm6b	AI593561|Gpm6|M6B	glycoprotein m6b	protein-coding
mm_148500.1	chr19	4193102	4193130	+	1	NA	exon (NM_031868, exon 3 of 7)	exon (NM_031868, exon 3 of 7)	942	NM_031868	19045	Mm.1970	NM_031868	ENSMUSG00000040385	Ppp1ca	Ppp1c|dism2	protein phosphatase 1, catalytic subunit, alpha isoform	protein-coding
mm_125500.1	chr15	55255777	55255787	+	1	NA	3' UTR (NM_145470, exon 9 of 9)	3' UTR (NM_145470, exon 9 of 9)	-51968	NM_181277	12818	Mm.297859	NM_181277	ENSMUSG00000022371	Col14a1	5730412L22Rik|AW108078	collagen, type XIV, alpha 1	protein-coding
mm_10064.1	chr1	193510025	193510034	-	1	NA	Intergenic	Intergenic	-2499	NR_029592	387201		NR_029592	ENSMUSG00000065533	Mir205	Mirn205|mir-205|mmu-mir-205	microRNA 205	ncRNA
mm_107175.1	chr12	24831584	24831658	+	1	NA	promoter-TSS (NM_026037)	promoter-TSS (NM_026037)	22	NM_001083341	67216	Mm.167671	NM_026037	ENSMUSG00000020646	Mboat2	2810049G06Rik|AU022889|AW547221|LPCAT4|Moact2|Oact2	membrane bound O-acyltransferase domain containing 2	protein-coding
mm_167175.1	chr7	140093263	140093274	+	1	NA	promoter-TSS (NM_009475)	promoter-TSS (NM_009475)	-128	NM_009475	22264	Mm.439707	NM_009475	ENSMUSG00000025467	Prap1	Upa	proline-rich acidic protein 1	protein-coding
mm_157477.1	chrX	48143683	48143694	-	1	NA	Intergenic	Intergenic	-2748	NM_001313749	74131	Mm.276131	NM_028773	ENSMUSG00000031101	Sash3	1200013B08Rik|AW413946|SLY1	SAM and SH3 domain containing 3	protein-coding
mm_142702.1	chr17	47878512	47878528	-	1	NA	intron (NM_001110824, intron 6 of 16)	intron (NM_001110824, intron 6 of 16)	-43829	NM_001109973	17240	Mm.329100	NM_010783	ENSMUSG00000032717	Mdfi	I-mf|I-mfa	MyoD family inhibitor	protein-coding
mm_29031.1	chr3	102167022	102167037	-	1	NA	intron (NM_177545, intron 4 of 7)	intron (NM_177545, intron 4 of 7)	37664	NM_177545	229658	Mm.118004	NM_177545	ENSMUSG00000027860	Vangl1	Kitenin|Lpp2|Stb2|Stbm	vang-like 1 (van gogh, Drosophila)	protein-coding
mm_141586.1	chr17	32403552	32403590	-	1	NA	promoter-TSS (NM_178785)	promoter-TSS (NM_178785)	10	NM_178785	320484	Mm.122284	NM_178785	ENSMUSG00000052142	Rasal3	A430107D22Rik	RAS protein activator like 3	protein-coding
mm_171052.1	chr3	103040015	103040015	-	1	NA	exon (NM_001161854, exon 4 of 19)	exon (NM_001161854, exon 4 of 19)	-18270	NM_010937	18176	Mm.400954	NM_010937	ENSMUSG00000027852	Nras	AV095280|N-ras	neuroblastoma ras oncogene	protein-coding
mm_114956.1	chr13	97067267	97067281	+	1	NA	promoter-TSS (NM_001146045)	promoter-TSS (NM_001146045)	-13	NM_001146045	320557	Mm.458280	NM_001100458	ENSMUSG00000041817	Fam169a	B230112C05Rik|SLAP75	family with sequence similarity 169, member A	protein-coding
mm_136915.1	chr17	13061100	13061112	+	1	NA	promoter-TSS (NM_009341)	promoter-TSS (NM_009341)	-5	NM_009341	21462	Mm.264651	NM_009341	ENSMUSG00000055602	Tcp10b	D17Leh66B|D17Leh66ba|T66B-a|Tcp-10b|Tcp-10bt	t-complex protein 10b	protein-coding
mm_155192.1	chrX	56454852	56454869	+	1	NA	promoter-TSS (NM_172779)	promoter-TSS (NM_172779)	21	NM_172779	236790	Mm.474772	NM_172779	ENSMUSG00000035967	Ints6l	4930535D10Rik|6330505F04Rik|D130066O12|Ddx26b	integrator complex subunit 6 like	protein-coding
mm_164303.1	chr15	103897402	103897422	+	1	NA	exon (NM_009267, exon 3 of 4)	exon (NM_009267, exon 3 of 4)	1888	NM_009268	20771	Mm.30276	NM_009268		Mucl1	Spt-2|Spt2	mucin-like 1	protein-coding
mm_101341.1	chr11	23520134	23520147	-	1	NA	promoter-TSS (NM_026105)	promoter-TSS (NM_026105)	-198	NM_001110133	67358	Mm.87328	NM_026105	ENSMUSG00000020286	1700093K21Rik	-	RIKEN cDNA 1700093K21 gene	protein-coding
mm_138819.1	chr17	39847563	39847592	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	4580	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_30206.1	chr3	144760730	144760746	-	1	NA	non-coding (NR_130895, exon 1 of 13)	non-coding (NR_130895, exon 1 of 13)	239	NR_130895	12722	Mm.454553	NM_009899	ENSMUSG00000056025	Clca3a1	Cacc|Clca1	chloride channel accessory 3A1	protein-coding
mm_157807.1	chrX	73930752	73930823	-	1	NA	promoter-TSS (NM_001164704)	promoter-TSS (NM_001164704)	63	NM_023132	19703	Mm.236969	NM_023132	ENSMUSG00000031387	Renbp	Age|Rnbp	renin binding protein	protein-coding
mm_124611.1	chr15	3279460	3279475	+	1	NA	exon (NM_009155, exon 5 of 5)	exon (NM_009155, exon 5 of 5)	8490	NM_009155	20363	Mm.392203	NM_009155	ENSMUSG00000064373	Selenop	AU018766|D15Ucla1|Se-P|Sepp1|selp	selenoprotein P	protein-coding
mm_124223.1	chr14	100284857	100284879	-	1	NA	Intergenic	(CGGGGG)n|Simple_repeat|Simple_repeat	-135072	NM_010636	16597	Mm.396499	NM_010636	ENSMUSG00000072294	Klf12	2700063E05Rik|AI225908|AI315654|AP-2rep|B130052C06Rik|D530033K05Rik	Kruppel-like factor 12	protein-coding
mm_60851.1	chr7	45830890	45830901	+	1	NA	promoter-TSS (NM_153419)	promoter-TSS (NM_153419)	-106	NM_153419	101612	Mm.274847	NM_153419	ENSMUSG00000053801	Grwd1	A301|AI504353|Grwd|Wdr28	glutamate-rich WD repeat containing 1	protein-coding
mm_169018.1	chr13	111140331	111140333	-	1	NA	Intergenic	LTR28B|LTR|ERV1	89099	NR_045908	73129	Mm.417826	NR_045908		3110015C05Rik	-	RIKEN cDNA 3110015C05 gene	ncRNA
mm_155957.1	chrX	105140754	105140758	+	1	NA	Intergenic	Intergenic	20378	NM_053201	107528	Mm.24341	NM_053201	ENSMUSG00000031227	Magee1	AI847422|DAMAGE|mMage-e1	melanoma antigen, family E, 1	protein-coding
mm_134293.1	chr16	14248984	14248992	-	1	NA	intron (NM_001161775, intron 5 of 40)	(TCCC)n|Simple_repeat|Simple_repeat	42420	NM_001161775	17880	Mm.250705	NM_013607	ENSMUSG00000018830	Myh11	AV071570|SM1|SM2|smMHC	myosin, heavy polypeptide 11, smooth muscle	protein-coding
mm_21791.1	chr2	164857199	164857239	-	1	NA	intron (NM_011125, intron 1 of 15)	CpG-8831	489	NM_011125	18830	Mm.6105	NM_011125	ENSMUSG00000017754	Pltp	Bpife|OD107	phospholipid transfer protein	protein-coding
mm_147338.1	chr18	42899471	42899539	-	1	NA	promoter-TSS (NR_073583)	promoter-TSS (NR_073583)	1	NR_073583	72930	Mm.26134	NM_027531	ENSMUSG00000024500	Ppp2r2b	2900026H06Rik|6330404L05Rik|E130009M08Rik|PP2A-PR55B|PR55-BETA|SCA12	protein phosphatase 2, regulatory subunit B, beta	protein-coding
mm_145504.1	chr18	60391517	60391527	+	1	NA	3' UTR (NM_001146275, exon 3 of 3)	3' UTR (NM_001146275, exon 3 of 3)	15493	NM_001146275	60440	Mm.261140	NM_021792	ENSMUSG00000054072	Iigp1	2900074L10Rik|AI046432|AW111922|Ifgga1|Iigp|Irga6	interferon inducible GTPase 1	protein-coding
mm_16677.1	chr2	6872393	6872496	-	1	NA	promoter-TSS (NM_001347094)	promoter-TSS (NM_001347094)	-409	NM_001347094	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_71204.1	chr8	40888402	40888412	+	1	NA	intron (NM_007514, intron 1 of 11)	intron (NM_007514, intron 1 of 11)	26040	NM_001044740	11988	Mm.4676	NM_007514	ENSMUSG00000031596	Slc7a2	20.5|AI158848|Atrc2|CAT-2|Cat2|Tea	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	protein-coding
mm_151419.1	chr19	56758196	56758209	+	1	NA	Intergenic	B4A|SINE|B4	35830	NM_007419	11554	Mm.46797	NM_007419	ENSMUSG00000035283	Adrb1	Adrb-1|beta-AR	adrenergic receptor, beta 1	protein-coding
mm_62785.1	chr7	112500013	112500014	+	1	NA	intron (NM_020606, intron 1 of 12)	intron (NM_020606, intron 1 of 12)	72307	NM_020606	57342	Mm.143763	NM_020606	ENSMUSG00000030770	Parva	2010012A22Rik|5430400F08Rik|AI225929|AU042898|Actp|CH-ILKBP|Parvin	parvin, alpha	protein-coding
mm_106377.1	chr11	118419117	118419131	-	1	NA	promoter-TSS (NM_029502)	promoter-TSS (NM_029502)	-6	NM_001267592	76025	Mm.177551	NM_029502	ENSMUSG00000025575	Cant1	5830420C20Rik|Apy1h|D11Bwg0554e|Entpd8|SCAN-1|Shapy	calcium activated nucleotidase 1	protein-coding
mm_32327.1	chr4	104175155	104175188	+	1	NA	Intergenic	Intergenic	-192367	NR_104385	13131	Mm.289682	NM_010014	ENSMUSG00000028519	Dab1	AI956902|C630028C02Rik|scm|scr|scrambler|yot	disabled 1	protein-coding
mm_59937.1	chr7	30424313	30424316	+	1	NA	5' UTR (NM_172142, exon 3 of 11)	5' UTR (NM_172142, exon 3 of 11)	1010	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_15739.1	chr2	164237287	164237299	+	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	1048	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_8298.1	chr1	143702805	143702829	-	1	NA	promoter-TSS (NM_145991)	promoter-TSS (NM_145991)	76	NM_145991	214498	Mm.156727	NM_145991	ENSMUSG00000026361	Cdc73	8430414L16Rik|C130030P16Rik|C81219|Hrpt2	cell division cycle 73, Paf1/RNA polymerase II complex component	protein-coding
mm_63171.1	chr7	125318335	125318343	+	1	NA	Intergenic	Intergenic	31447	NR_045804	71208	Mm.159465	NM_172408	ENSMUSG00000045928	4933440M02Rik	-	RIKEN cDNA 4933440M02 gene	ncRNA
mm_131546.1	chr16	17891927	17891935	+	1	NA	promoter-TSS (NM_001109750)	promoter-TSS (NM_001109750)	-203	NM_001109750	13356	Mm.254515	NM_010048	ENSMUSG00000003166	Dgcr2	9930034O06Rik|DGS-C|Dgsc|Idd|Lan|Sez12|mKIAA0163	DiGeorge syndrome critical region gene 2	protein-coding
mm_131458.1	chr16	16983396	16983416	+	1	NA	promoter-TSS (NM_001038663)	promoter-TSS (NM_001038663)	24	NM_001038663	26413	Mm.196581	NM_011949	ENSMUSG00000063358	Mapk1	9030612K14Rik|AA407128|AU018647|C78273|ERK|Erk2|MAPK2|PRKM2|Prkm1|p41mapk|p42mapk	mitogen-activated protein kinase 1	protein-coding
mm_122495.1	chr14	46634490	46634494	-	1	NA	intron (NR_046460, intron 1 of 4)	intron (NR_046460, intron 1 of 4)	2931	NR_046460	74458	Mm.390708	NR_046460		4933425B07Rik	-	RIKEN cDNA 4933425B07 gene	ncRNA
mm_84335.1	chr9	64022985	64022998	-	1	NA	promoter-TSS (NM_008542)	promoter-TSS (NM_008542)	-932	NM_008542	17130	Mm.325757	NM_008542	ENSMUSG00000036867	Smad6	Madh6|b2b390Clo	SMAD family member 6	protein-coding
mm_55444.1	chr6	67186647	67186676	-	1	NA	Intergenic	Intergenic	-80318	NM_001113564	66870	Mm.240490	NM_025814	ENSMUSG00000036371	Serbp1	1200009K13Rik|9330147J08Rik|AL022786|Pairbp1	serpine1 mRNA binding protein 1	protein-coding
mm_137272.1	chr17	24718089	24718118	+	1	NA	promoter-TSS (NM_026205)	promoter-TSS (NM_026205)	-46	NM_026205	67504	Mm.46159	NM_026205	ENSMUSG00000008482	Rnf151	1700010O16Rik|AV047371	ring finger protein 151	protein-coding
mm_5424.1	chr1	34439338	34439379	-	1	NA	promoter-TSS (NM_178601)	promoter-TSS (NM_178601)	314	NM_027159	69668	Mm.379170	NM_027159	ENSMUSG00000042111	Ccdc115	2310061I09Rik|Ccp1	coiled-coil domain containing 115	protein-coding
mm_146021.1	chr18	69519684	69519700	+	1	NA	intron (NM_013685, intron 5 of 19)	intron (NM_013685, intron 5 of 19)	173971	NM_001083967	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding
mm_165825.1	chr3	151294520	151294529	+	1	NA	Intergenic	Intergenic	-143358	NM_133222	170757	Mm.317261	NM_133222	ENSMUSG00000039167	Adgrl4	1110033N21Rik|ETL1|Eltd1|Etl	adhesion G protein-coupled receptor L4	protein-coding
mm_66403.1	chr7	44474010	44474017	-	1	NA	Intergenic	Intergenic	3666	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_27344.1	chr3	50414828	50414841	-	1	NA	intron (NM_011990, intron 6 of 11)	intron (NM_011990, intron 6 of 11)	28779	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_5150.1	chr1	9799352	9799373	-	1	NA	intron (NM_177547, intron 1 of 16)	intron (NM_177547, intron 1 of 16)	1232	NM_177547	170755	Mm.336410	NM_133220	ENSMUSG00000025915	Sgk3	2510015P22Rik|A330005P07Rik|Cisk|fy|fz	serum/glucocorticoid regulated kinase 3	protein-coding
mm_12642.1	chr2	74712122	74712157	+	1	NA	5' UTR (NM_010468, exon 1 of 3)	5' UTR (NM_010468, exon 1 of 3)	146	NM_010468	15434	Mm.430708	NM_010468	ENSMUSG00000079277	Hoxd3	Hox-4.1|Hox-5.5	homeobox D3	protein-coding
mm_6087.1	chr1	63114517	63114539	-	1	NA	promoter-TSS (NM_001114609)	promoter-TSS (NM_001114609)	57	NR_045915	100380944	Mm.392955	NR_045914	ENSMUSG00000084799	Ino80dos	Gm11602|OTTMUSG00000002611	INO80 complex subunit D, opposite strand	ncRNA
mm_98347.1	chr11	93320283	93320285	+	1	NA	intron (NM_028296, intron 3 of 8)	T-rich|Low_complexity|Low_complexity	220994	NM_028296	72605	Mm.342160	NM_028296	ENSMUSG00000056158	Car10	2700029L05Rik|BB085816|Ca10	carbonic anhydrase 10	protein-coding
mm_68859.1	chr7	126396716	126396762	-	1	NA	promoter-TSS (NM_010900)	promoter-TSS (NM_010900)	-2	NM_010900	18020	Mm.1389	NM_010900	ENSMUSG00000030722	Nfatc2ip	D7Ertd304e|NIP45	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 2 interacting protein	protein-coding
mm_30783.1	chr4	19575051	19575092	+	1	NA	promoter-TSS (NM_025476)	promoter-TSS (NM_025476)	5	NM_025476	66302	Mm.440686	NM_025476	ENSMUSG00000028229	Rmdn1	Fam82b|RMD-1	regulator of microtubule dynamics 1	protein-coding
mm_125636.1	chr15	62056800	62056803	+	1	NA	intron (NR_132746, intron 1 of 6)	intron (NR_132746, intron 1 of 6)	17544	NR_132746	19296	Mm.4608	NM_011222	ENSMUSG00000097039	Pvt1	Ayu21-84Imeg|Gt(pU21)84Imeg|Mis-1|Mlvi-1|Pvt-1	plasmacytoma variant translocation 1	ncRNA
mm_154084.1	chr19	56666049	56666058	-	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	-56319	NM_007419	11554	Mm.46797	NM_007419	ENSMUSG00000035283	Adrb1	Adrb-1|beta-AR	adrenergic receptor, beta 1	protein-coding
mm_118009.1	chr13	100651254	100651264	-	1	NA	promoter-TSS (NM_001015889)	promoter-TSS (NM_001015889)	-84	NM_027139	108143	Mm.301148	NM_027139	ENSMUSG00000052293	Taf9	2310012M09Rik|AA673500|AU045423|TAFII31|TAFII32|Taf2g	TATA-box binding protein associated factor 9	protein-coding
mm_94332.1	chr11	4424091	4424104	+	1	NA	intron (NM_029458, intron 5 of 10)	intron (NM_029458, intron 5 of 10)	16985	NM_029458	75828	Mm.159592	NM_029458	ENSMUSG00000020419	Hormad2	4930529M09Rik	HORMA domain containing 2	protein-coding
mm_40788.1	chr5	67450470	67450506	+	1	NA	Intergenic	Intergenic	-13410	NR_110363	320479	Mm.387187	NR_015582	ENSMUSG00000107385	C330024D21Rik	-	RIKEN cDNA C330024D21 gene	ncRNA
mm_95841.1	chr11	57012748	57012785	+	1	NA	promoter-TSS (NM_001252403)	promoter-TSS (NM_001252403)	-280	NM_001252403	14799	Mm.4920	NM_008165	ENSMUSG00000020524	Gria1	2900051M01Rik|Glr-1|Glr1|GluA1|GluR-A|GluRA|Glur-1|Glur1|HIPA1|gluR-K1	glutamate receptor, ionotropic, AMPA1 (alpha 1)	protein-coding
mm_103217.1	chr11	70655131	70655150	-	1	NA	promoter-TSS (NM_011072)	promoter-TSS (NM_011072)	-490	NM_011072	18643	Mm.2647	NM_011072	ENSMUSG00000018293	Pfn1	Pfn	profilin 1	protein-coding
mm_85954.1	chr9	112121334	112121346	-	1	NA	intron (NM_001177617, intron 13 of 14)	B3|SINE|B2	-2629	NR_029823	723815		NR_029823	ENSMUSG00000065441	Mir128-2	Mirn128-2|Mirn128b|mir-128-2|mir-128b	microRNA 128-2	ncRNA
mm_55967.1	chr6	85820966	85820977	-	1	NA	promoter-TSS (NM_023493)	promoter-TSS (NM_023493)	1	NM_023493	69049	Mm.441449	NM_023493	ENSMUSG00000079494	Nat8f5	1810018F03Rik|Cml5	N-acetyltransferase 8 (GCN5-related) family member 5	protein-coding
mm_121084.1	chr14	99201608	99201612	+	1	NA	intron (NM_029320, intron 14 of 17)	intron (NM_029320, intron 14 of 17)	-97081	NM_009769	12224	Mm.30262	NM_009769	ENSMUSG00000005148	Klf5	4930520J07Rik|Bteb2|CKLF|IKLF	Kruppel-like factor 5	protein-coding
mm_21439.1	chr2	158610658	158610665	-	1	NA	promoter-TSS (NM_009508)	promoter-TSS (NM_009508)	62	NR_040358	100045469	Mm.143404	NR_040358	ENSMUSG00000086496	Gm14204	OTTMUSG00000015935	predicted gene 14204	ncRNA
mm_84387.1	chr9	65423012	65423022	-	1	NA	promoter-TSS (NM_178933)	promoter-TSS (NM_178933)	-244	NM_178933	330962	Mm.335247	NM_178933	ENSMUSG00000053862	Slc51b	Ostb	solute carrier family 51, beta subunit	protein-coding
mm_41747.1	chr5	102845111	102845115	+	1	NA	5' UTR (NM_001346585, exon 1 of 7)	5' UTR (NM_001346585, exon 1 of 7)	106	NM_001346585	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding
mm_167338.1	chr8	72318901	72318908	-	1	NA	promoter-TSS (NM_008452)	promoter-TSS (NM_008452)	-158	NM_008452	16598	Mm.26938	NM_008452	ENSMUSG00000055148	Klf2	Lklf	Kruppel-like factor 2 (lung)	protein-coding
mm_134800.1	chr16	24296222	24296231	-	1	NA	Intergenic	Intergenic	-97124	NM_178665	210126	Mm.209385	NM_178665	ENSMUSG00000033306	Lpp	9430020K16Rik|AA959454|AU024130|B130055L10Rik|C79715|D630048H16	LIM domain containing preferred translocation partner in lipoma	protein-coding
mm_70387.1	chr8	10634750	10634762	+	1	NA	TTS (NM_001319151)	TTS (NM_001319151)	247698	NR_040705	320014	Mm.403203	NR_040705	ENSMUSG00000109473	B930025P03Rik	-	RIKEN cDNA B930025P03 gene	ncRNA
mm_94467.1	chr11	6475267	6475307	+	1	NA	exon (NM_011221, exon 1 of 1)	exon (NM_011221, exon 1 of 1)	789	NM_011221	19291	Mm.296150	NM_011221	ENSMUSG00000094483	Purb	2310015K15Rik|AA114818|Cager-2|D11Bwg0414e	purine rich element binding protein B	protein-coding
mm_29769.1	chr3	127226076	127226096	-	1	NA	intron (NM_001327938, intron 1 of 47)	intron (NM_001327938, intron 1 of 47)	64781	NR_105029	100862268	Mm.444603	NR_105029	ENSMUSG00000097456	LOC100862268	-	uncharacterized LOC100862268	ncRNA
mm_57695.1	chr6	128522084	128522117	-	1	NA	exon (NM_007376, exon 6 of 36)	exon (NM_007376, exon 6 of 36)	4620	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_60719.1	chr7	45335257	45335297	+	1	NA	promoter-TSS (NM_010473)	promoter-TSS (NM_010473)	8	NM_010473	15464	Mm.39968	NM_010473	ENSMUSG00000038239	Hrc	-	histidine rich calcium binding protein	protein-coding
mm_138395.1	chr17	35052482	35052515	+	1	NA	exon (NM_033444, exon 2 of 6)	exon (NM_033444, exon 2 of 6)	2255	NM_033444	114584	Mm.29524	NM_033444	ENSMUSG00000007041	Clic1	Clcp|G6	chloride intracellular channel 1	protein-coding
mm_52845.1	chr6	121838626	121838639	+	1	NA	promoter-TSS (NM_008645)	promoter-TSS (NM_008645)	91	NM_008645	17836	Mm.1311	NM_008645	ENSMUSG00000059908	Mug1	-	murinoglobulin 1	protein-coding
mm_8768.1	chr1	160813148	160813152	-	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-20212	NM_013862	29809	Mm.25833	NM_013862	ENSMUSG00000026721	Rabgap1l	5830411O09Rik|8430421H08Rik|9630005B12Rik|AW049894|HHL|Hh1|mKIAA0471	RAB GTPase activating protein 1-like	protein-coding
mm_105521.1	chr11	106300375	106300396	-	1	NA	exon (NM_008117, exon 5 of 5)	exon (NM_008117, exon 5 of 5)	1511	NM_008117	14599	Mm.343934	NM_008117	ENSMUSG00000020713	Gh	Gh1|Ghb1	growth hormone	protein-coding
mm_12176.1	chr2	62692725	62692766	+	1	NA	3' UTR (NM_145523, exon 8 of 8)	3' UTR (NM_145523, exon 8 of 8)	28418	NM_145523	227960	Mm.219877	NM_145523	ENSMUSG00000026893	Gca	5133401E04Rik|AI573844	grancalcin	protein-coding
mm_66146.1	chr7	31127165	31127177	-	1	NA	promoter-TSS (NM_011322)	promoter-TSS (NM_011322)	-148	NM_011322	20266	Mm.1418	NM_011322	ENSMUSG00000019194	Scn1b	-	sodium channel, voltage-gated, type I, beta	protein-coding
mm_103821.1	chr11	83004390	83004402	-	1	NA	exon (NM_181545, exon 5 of 6)	exon (NM_181545, exon 5 of 6)	-12566	NM_172796	237886	Mm.270253	NM_172796	ENSMUSG00000069793	Slfn9	9830137M10Rik	schlafen 9	protein-coding
mm_131469.1	chr16	17044540	17044559	+	1	NA	3' UTR (NM_011949, exon 9 of 9)	3' UTR (NM_011949, exon 9 of 9)	-25590	NM_023249	106369	Mm.237941	NM_023249	ENSMUSG00000022773	Ypel1	0610009L05Rik|1700016N17Rik|1700019O22Rik|4921520K19Rik|4930511F14Rik|AV118478|DGL-1|Dgl1|Ppil2|mdgl-1	yippee-like 1 (Drosophila)	protein-coding
mm_102685.1	chr11	65345224	65345227	-	1	NA	Intergenic	Intergenic	-57392	NR_040280	327946	Mm.383301	NR_040280	ENSMUSG00000085162	Gm12295	A730013G04|OTTMUSG00000005904	predicted gene 12295	ncRNA
mm_70261.1	chr8	3516940	3516951	+	1	NA	intron (NM_001122818, intron 3 of 34)	CpG	1561	NM_015801	50767	Mm.23085	NM_015801	ENSMUSG00000004565	Pnpla6	AI661849|MSws|Nte	patatin-like phospholipase domain containing 6	protein-coding
mm_80433.1	chr9	77923318	77923328	+	1	NA	intron (NM_134255, intron 1 of 7)	intron (NM_134255, intron 1 of 7)	5958	NM_134255	68801	Mm.430736	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	ELOVL family member 5, elongation of long chain fatty acids (yeast)	protein-coding
mm_88110.1	chr10	69151397	69151406	+	1	NA	Intergenic	Intergenic	-57151	NM_001252636	69288	Mm.26659	NM_001081347	ENSMUSG00000019944	Rhobtb1	1700008H16Rik|3110048G13Rik|AI173445|AI573858|AV350930	Rho-related BTB domain containing 1	protein-coding
mm_146671.1	chr18	12425255	12425275	-	1	NA	intron (NM_010680, intron 11 of 74)	MER34A|LTR|ERV1	-78934	NM_001347461	16774	Mm.42012	NM_010680	ENSMUSG00000024421	Lama3	Lama3B|[a]3B	laminin, alpha 3	protein-coding
mm_125609.1	chr15	61157830	61157848	+	1	NA	Intergenic	Intergenic	-236569	NM_001081067	117586	Mm.291499	NM_001081067	ENSMUSG00000022347	A1bg	C44	alpha-1-B glycoprotein	protein-coding
mm_100647.1	chr11	3104784	3104799	-	1	NA	Intergenic	IAPLTR4|LTR|ERVK	-19230	NR_003517	236604	Mm.247625	NM_001004146		Pisd-ps1	-	phosphatidylserine decarboxylase, pseudogene 1	pseudo
mm_34073.1	chr4	138457606	138457619	+	1	NA	3' UTR (NM_025451, exon 2 of 2)	3' UTR (NM_025451, exon 2 of 2)	2464	NM_025451	66259	Mm.41603	NM_025451	ENSMUSG00000046447	Camk2n1	1810006K23Rik|AI848599|AI891706	calcium/calmodulin-dependent protein kinase II inhibitor 1	protein-coding
mm_77486.1	chr8	122556735	122556755	-	1	NA	Intergenic	Intergenic	-5416	NM_001037298	234839	Mm.37324	NM_001037298	ENSMUSG00000014444	Piezo1	9630020g22|Fam38a|mKIAA0233	piezo-type mechanosensitive ion channel component 1	protein-coding
mm_51143.1	chr6	70518241	70518252	+	1	NA	Intergenic	Intergenic	273929	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_121034.1	chr14	79875569	79875600	+	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-6408	NR_033535	100038734	Mm.387484	NR_033535		Gm10845	ENSMUSG00000075496	predicted gene 10845	ncRNA
mm_127738.1	chr15	103298870	103298888	+	1	NA	3' UTR (NM_019817, exon 9 of 9)	3' UTR (NM_019817, exon 9 of 9)	11559	NM_030720	80910	Mm.160369	NM_030720	ENSMUSG00000063234	Gpr84	EX33	G protein-coupled receptor 84	protein-coding
mm_64808.1	chr7	6706612	6706626	-	1	NA	promoter-TSS (NR_023846)	promoter-TSS (NR_023846)	-141	NR_023846	100169889	Mm.491213	NR_023846		Peg3os	Apeg3|Peg3as	Peg3 opposite strand	ncRNA
mm_96543.1	chr11	68704507	68704507	+	1	NA	intron (NM_175260, intron 2 of 40)	ID_B1|SINE|B4	12592	NM_175260	77579	Mm.218233	NM_175260	ENSMUSG00000020900	Myh10	5730504C04Rik|9330167F11Rik|Fltn|Myhn-2|Myhn2|NMHC II-B|NMHC-B|NMHCII-B|NMMHC II-b|NMMHC-B|NMMHC-IIB|SMemb|mKIAA3005	myosin, heavy polypeptide 10, non-muscle	protein-coding
mm_100966.1	chr11	6660210	6660223	-	1	NA	promoter-TSS (NR_028586)	promoter-TSS (NR_028586)	20	NR_028586	100041311	Mm.388018	NR_028586	ENSMUSG00000086373	Gm11978	OTTMUSG00000005125|OTTMUSG00000005127	predicted gene 11978	pseudo
mm_124718.1	chr15	6579885	6579900	+	1	NA	promoter-TSS (NM_001278269)	promoter-TSS (NM_001278269)	45	NM_011815	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_113562.1	chr13	38190433	38190443	+	1	NA	exon (NM_023842, exon 22 of 24)	exon (NM_023842, exon 22 of 24)	-14501	NM_026382	67797	Mm.250783	NM_026382	ENSMUSG00000021431	Snrnp48	1110050F08Rik|6530403A03Rik|C6orf151	small nuclear ribonucleoprotein 48 (U11/U12)	protein-coding
mm_77913.1	chr9	7350066	7350076	+	1	NA	exon (NM_008605, exon 4 of 10)	exon (NM_008605, exon 4 of 10)	2697	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_10153.1	chr2	4300909	4300931	+	1	NA	intron (NM_172475, intron 1 of 22)	intron (NM_172475, intron 1 of 22)	-100056	NM_001177843	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding
mm_152586.1	chr19	11604715	11604724	-	1	NA	promoter-TSS (NM_026835)	promoter-TSS (NM_026835)	85	NM_026835	68774	Mm.290390	NM_026835	ENSMUSG00000024679	Ms4a6d	1110058E16Rik|AI447446|Ms4a11	membrane-spanning 4-domains, subfamily A, member 6D	protein-coding
mm_80912.1	chr9	100645008	100645011	+	1	NA	intron (NM_009282, intron 1 of 33)	intron (NM_009282, intron 1 of 33)	1386	NM_009282	20842	Mm.42135	NM_009282	ENSMUSG00000037286	Stag1	AU045003|SA-1|Scc3	stromal antigen 1	protein-coding
mm_121082.1	chr14	99099989	99100012	+	1	NA	promoter-TSS (NM_028315)	promoter-TSS (NM_028315)	-230	NM_028315	72662	Mm.163339	NM_028315	ENSMUSG00000033166	Dis3	2810028N01Rik	DIS3 homolog, exosome endoribonuclease and 3'-5' exoribonuclease	protein-coding
mm_160280.1	chr7	122219460	122219460	+	1	NA	promoter-TSS (NM_027363)	promoter-TSS (NM_027363)	-36	NM_027363	70261	Mm.96997	NM_027363	ENSMUSG00000030865	Chp2	2010110P09Rik|Cbhp2	calcineurin-like EF hand protein 2	protein-coding
mm_119011.1	chr14	29968370	29968462	+	1	NA	promoter-TSS (NM_019979)	promoter-TSS (NM_019979)	36	NM_019979	80795	Mm.104491	NM_019979	ENSMUSG00000042682	Selenok	1110001C03Rik|AA673253|HSPC030|Hsp30|Selk	selenoprotein K	protein-coding
mm_9886.1	chr1	186625211	186625216	-	1	NA	3' UTR (NM_009367, exon 7 of 7)	3' UTR (NM_009367, exon 7 of 7)	-66532	NR_131158	320449	Mm.404477	NR_131124	ENSMUSG00000103690	A730004F24Rik	-	RIKEN cDNA A730004F24 gene	ncRNA
mm_34916.1	chr4	155721732	155721734	+	1	NA	intron (NM_026899, intron 2 of 4)	B2_Mm2|SINE|B2	-13071	NM_001101506	381582	Mm.379515	NM_001101506	ENSMUSG00000084845	Tmem240	EG381582|Gm5151	transmembrane protein 240	protein-coding
mm_172256.1	chr6	70387263	70387277	-	1	NA	Intergenic	Intergenic	404905	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_153768.1	chr19	45631087	45631106	-	1	NA	intron (NM_013907, intron 4 of 8)	intron (NM_013907, intron 4 of 8)	29097	NM_013907	30838	Mm.254739	NM_013907	ENSMUSG00000040913	Fbxw4	Dac|Fbw4|SHFM3|SHSF3|dactylin|dactylyn	F-box and WD-40 domain protein 4	protein-coding
mm_90290.1	chr10	123434713	123434722	+	1	NA	intron (NM_182807, intron 2 of 5)	intron (NM_182807, intron 2 of 5)	170641	NM_001252387	268354	Mm.51939	NM_182807	ENSMUSG00000044071	Fam19a2	6330575M02|FAM19A2 TAFA-2|TAFA2|Tafa-2	family with sequence similarity 19, member A2	protein-coding
mm_141137.1	chr17	26244191	26244199	-	1	NA	promoter-TSS (NM_001206335)	promoter-TSS (NM_001206335)	47	NM_207217	106581	Mm.28844	NM_207217	ENSMUSG00000024187	Fam234a	Itfg3	family with sequence similarity 234, member A	protein-coding
mm_13514.1	chr2	109917597	109917638	+	1	NA	promoter-TSS (NM_172671)	promoter-TSS (NM_172671)	-30	NM_172671	107515	Mm.277351	NM_172671	ENSMUSG00000050199	Lgr4	9130225G07|A330106J01Rik|A930009A08Rik|Gpr48	leucine-rich repeat-containing G protein-coupled receptor 4	protein-coding
mm_152528.1	chr19	11324226	11324241	-	1	NA	intron (NM_001025610, intron 4 of 5)	intron (NM_001025610, intron 4 of 5)	10462	NM_001276398	109225	Mm.491251	NM_027836	ENSMUSG00000024672	Ms4a7	9130422I10Rik|A430103C15Rik|CD20l4|CFFMA	membrane-spanning 4-domains, subfamily A, member 7	protein-coding
mm_10723.1	chr2	22853144	22853161	+	1	NA	exon (NM_019456, exon 9 of 14)	exon (NM_019456, exon 9 of 14)	-42370	NM_019501	56075	Mm.249752	NM_019501	ENSMUSG00000026784	Pdss1	2610203G20Rik|2700031G06Rik|TPT|TPT 1|Tprt|mDLP1|mSPS1	prenyl (solanesyl) diphosphate synthase, subunit 1	protein-coding
mm_73205.1	chr8	95678290	95678296	+	1	NA	Intergenic	CpG	-24744	NM_001195006	234593	Mm.29846	NM_145602	ENSMUSG00000036564	Ndrg4	D8Bwg1337e|Ndr1-rs|Ndr4|R74996|SMAP-8	N-myc downstream regulated gene 4	protein-coding
mm_14924.1	chr2	151485982	151485984	+	1	NA	Intergenic	Intergenic	-8199	NM_001291074	386649	Mm.419479	NM_198326	ENSMUSG00000027455	Nsfl1c	Munc-18c|Stxbp3a|p47	NSFL1 (p97) cofactor (p47)	protein-coding
mm_72938.1	chr8	91384693	91384710	+	1	NA	intron (NM_011936, intron 1 of 8)	intron (NM_011936, intron 1 of 8)	71176	NM_011936	26383	Mm.4375	NM_011936	ENSMUSG00000055932	Fto	AW743446|mKIAA1752	fat mass and obesity associated	protein-coding
mm_166497.1	chr6	3494606	3494612	-	1	NA	promoter-TSS (NM_178899)	promoter-TSS (NM_178899)	-111	NM_178899	101202	Mm.206911	NM_178899	ENSMUSG00000044156	Hepacam2	AI987662	HEPACAM family member 2	protein-coding
mm_69665.1	chr7	139980862	139980869	-	1	NA	intron (NM_007403, intron 22 of 23)	intron (NM_007403, intron 22 of 23)	-2110	NM_001347613	381933	Mm.440431	NM_001033465	ENSMUSG00000073795	6430531B16Rik	Gm1093	RIKEN cDNA 6430531B16 gene	protein-coding
mm_87520.1	chr10	52823764	52823767	+	1	NA	intron (NM_178675, intron 1 of 7)	intron (NM_178675, intron 1 of 7)	133264	NM_178675	215085	Mm.338690	NM_178675	ENSMUSG00000038602	Slc35f1	Duf6|E130016L02	solute carrier family 35, member F1	protein-coding
mm_12261.1	chr2	68941830	68941840	+	1	NA	intron (NM_172856, intron 2 of 9)	L1_Mus3|LINE|L1	80394	NM_001347161	241447	Mm.222222	NM_172856	ENSMUSG00000027035	Cers6	4732462C07Rik|AW544719|Lass6|T1L	ceramide synthase 6	protein-coding
mm_132869.1	chr16	48611783	48611785	+	1	NA	intron (NM_010816, intron 20 of 26)	intron (NM_010816, intron 20 of 26)	160172	NM_198297	77647	Mm.167298	NM_198297	ENSMUSG00000030775	Trat1	C030046M14Rik|Tcrim|Trim	T cell receptor associated transmembrane adaptor 1	protein-coding
mm_117261.1	chr13	64368820	64368831	-	1	NA	intron (NM_009984, intron 2 of 7)	intron (NM_009984, intron 2 of 7)	1695	NM_009984	13039	Mm.930	NM_009984	ENSMUSG00000021477	Ctsl	1190035F06Rik|CatL|Ctsl1|MEP|fs|nkt	cathepsin L	protein-coding
mm_158330.1	chrX	133961748	133961754	-	1	NA	exon (NM_001290718, exon 3 of 14)	exon (NM_001290718, exon 3 of 14)	20061	NM_001290718	27359	Mm.38674	NM_013757	ENSMUSG00000031255	Sytl4	Gph|Slp4	synaptotagmin-like 4	protein-coding
mm_140587.1	chr17	10216272	10216307	-	1	NA	exon (NM_001159517, exon 6 of 8)	exon (NM_001159517, exon 6 of 8)	103072	NM_021881	19317	Mm.130694	NM_021881	ENSMUSG00000062078	Qk	1110003F05Rik|1500005P18|QkI|l(17)-1Wis|l17Wis1	quaking	protein-coding
mm_112403.1	chr13	3538479	3538484	+	1	NA	intron (NM_008112, intron 1 of 10)	CpG	406	NM_008112	14569	Mm.153226	NM_008112	ENSMUSG00000021218	Gdi2	GDI-B|GDIB|Gdi3	guanosine diphosphate (GDP) dissociation inhibitor 2	protein-coding
mm_67755.1	chr7	92667958	92667966	-	1	NA	intron (NM_029078, intron 1 of 15)	intron (NM_029078, intron 1 of 15)	1950	NM_029078	74737	Mm.288645	NM_029078	ENSMUSG00000041328	Pcf11	2500001H09Rik|5730417B17Rik|C77803	PCF11 cleavage and polyadenylation factor subunit	protein-coding
mm_36267.1	chr4	63605127	63605165	-	1	NA	non-coding (NR_028583, exon 1 of 2)	non-coding (NR_028583, exon 1 of 2)	115	NR_028583	670833	Mm.32213	NR_028583	ENSMUSG00000084782	Gm11213	OTTMUSG00000000252	predicted gene 11213	ncRNA
mm_26779.1	chr3	9004473	9004515	-	1	NA	promoter-TSS (NM_009412)	promoter-TSS (NM_009412)	21	NM_009412	21985	Mm.371590	NM_009412	ENSMUSG00000027506	Tpd52	AI043038|mD52	tumor protein D52	protein-coding
mm_95.1	chr1	7204212	7204213	+	1	NA	Intergenic	Intergenic	115292	NM_183028	319263	Mm.21539	NM_183028	ENSMUSG00000051285	Pcmtd1	8430411F12Rik|A030012M09Rik	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding
mm_63365.1	chr7	127083820	127083846	+	1	NA	Intergenic	ID_B1|SINE|B4	-7603	NM_178901	101602	Mm.490357	NM_178901	ENSMUSG00000045165	AI467606	-	expressed sequence AI467606	protein-coding
mm_32054.1	chr4	97772829	97772848	+	1	NA	intron (NM_001122952, intron 1 of 10)	intron (NM_001122952, intron 1 of 10)	-4788	NM_001122953	18027	Mm.31274	NM_010905	ENSMUSG00000028565	Nfia	1110047K16Rik|9430022M17Rik|CTF|NF1-A|NF1A	nuclear factor I/A	protein-coding
mm_77699.1	chr8	126589890	126589904	-	1	NA	3' UTR (NM_001164598, exon 2 of 2)	3' UTR (NM_001164598, exon 2 of 2)	3539	NM_001164598	270110	Mm.334918	NM_001164598	ENSMUSG00000051495	Irf2bp2	E130305N23Rik|IRF-2BP2	interferon regulatory factor 2 binding protein 2	protein-coding
mm_122038.1	chr14	30008837	30008846	-	1	NA	promoter-TSS (NM_001136240)	promoter-TSS (NM_001136240)	55	NM_019583	50905	Mm.269363	NM_019583	ENSMUSG00000015966	Il17rb	Evi27|IL-17ER|IL-17Rh1|IL17RH1|Il17br	interleukin 17 receptor B	protein-coding
mm_113342.1	chr13	31785244	31785253	+	1	NA	Intergenic	Intergenic	-21398	NM_008592	17300	Mm.12949	NM_008592	ENSMUSG00000050295	Foxc1	FREAC3|Fkh1|Mf1|Mf4|ch|fkh-1|frkhda	forkhead box C1	protein-coding
mm_16574.1	chr2	3474955	3474975	-	1	NA	promoter-TSS (NM_022724)	promoter-TSS (NM_022724)	21	NM_022724	64707	Mm.23483	NM_022724	ENSMUSG00000026646	Suv39h2	4930507K23Rik|AA536750|D030054H19Rik|D2Ertd544e|KMT1B	suppressor of variegation 3-9 homolog 2 (Drosophila)	protein-coding
mm_46416.1	chr5	104097743	104097775	-	1	NA	exon (NM_010097, exon 2 of 11)	exon (NM_010097, exon 2 of 11)	16329	NM_010097	13602	Mm.29027	NM_010097	ENSMUSG00000029309	Sparcl1	Ecm2|Sc1|hevin|mast9	SPARC-like 1	protein-coding
mm_126990.1	chr15	94567075	94567080	+	1	NA	3' UTR (NM_029926, exon 12 of 12)	3' UTR (NM_029926, exon 12 of 12)	22747	NM_008971	19230	Mm.490250	NM_008971	ENSMUSG00000022451	Twf1	A6|Ptk9|twinfilin	twinfilin actin binding protein 1	protein-coding
mm_58976.1	chr7	19037346	19037363	+	1	NA	intron (NM_026605, intron 8 of 26)	MLT1K|LTR|ERVL-MaLR	12977	NM_026605	68188	Mm.130902	NM_026605	ENSMUSG00000023118	Sympk	1500016F02Rik|4632415H16Rik|AA125406|AI449890|SPK|SYM	symplekin	protein-coding
mm_105412.1	chr11	103638840	103638850	-	1	NA	promoter-TSS (NM_027083)	promoter-TSS (NM_027083)	29	NM_027083	69444	Mm.275677	NM_027083	ENSMUSG00000020945	Lyzl6	1700023H08Rik|Lyc1|Lyzb	lysozyme-like 6	protein-coding
mm_81164.1	chr9	107299153	107299156	+	1	NA	intron (NM_001317354, intron 1 of 1)	intron (NM_001317354, intron 1 of 1)	2495	NM_009895	12700	Mm.4592	NM_009895	ENSMUSG00000032578	Cish	CIS-1|CIS1|Cis|F17|F23|SOCS	cytokine inducible SH2-containing protein	protein-coding
mm_710.1	chr1	41743677	41743698	+	1	NA	Intergenic	Intergenic	-562435	NR_040475	74897	Mm.243822	NR_040475	ENSMUSG00000104072	4930448I06Rik	-	RIKEN cDNA 4930448I06 gene	ncRNA
mm_126403.1	chr15	80242573	80242576	+	1	NA	intron (NM_178719, intron 2 of 5)	intron (NM_178719, intron 2 of 5)	8494	NM_178719	239555	Mm.307163	NM_178719	ENSMUSG00000022412	Mief1	A230016E22|AI452372|Smcr7l	mitochondrial elongation factor 1	protein-coding
mm_123853.1	chr14	70924165	70924169	-	1	NA	intron (NM_001302094, intron 2 of 7)	MIR|SINE|MIR	34060	NM_001302094	14586	Mm.32619	NM_008115	ENSMUSG00000022103	Gfra2	-	glial cell line derived neurotrophic factor family receptor alpha 2	protein-coding
mm_129063.1	chr15	75567652	75567700	-	1	NA	promoter-TSS (NM_011837)	promoter-TSS (NM_011837)	-494	NM_011837	23934	Mm.22154	NM_011837	ENSMUSG00000022577	Ly6h	-	lymphocyte antigen 6 complex, locus H	protein-coding
mm_130214.1	chr15	95654780	95654794	-	1	NA	promoter-TSS (NM_207533)	promoter-TSS (NM_207533)	-16	NM_207533	223843	Mm.152937	NM_207533	ENSMUSG00000045608	Dbx2	9430056A22Rik|9630005K15|AI846217|Gm1229	developing brain homeobox 2	protein-coding
mm_67791.1	chr7	97729070	97729080	-	1	NA	exon (NM_175105, exon 2 of 3)	exon (NM_175105, exon 2 of 3)	9172	NM_175105	66333	Mm.29756	NM_175105	ENSMUSG00000042797	Aqp11	1700015P13Rik|AI648923|sjds	aquaporin 11	protein-coding
mm_31466.1	chr4	49536646	49536665	+	1	NA	3' UTR (NM_144903, exon 9 of 9)	3' UTR (NM_144903, exon 9 of 9)	12891	NM_144903	230163	Mm.482116	NM_144903	ENSMUSG00000028307	Aldob	Aldo-2|Aldo2|BC016435	aldolase B, fructose-bisphosphate	protein-coding
mm_5528.1	chr1	37916486	37916499	-	1	NA	promoter-TSS (NM_001033427)	promoter-TSS (NM_001033427)	1	NM_001033427	332427	Mm.332981	NM_001033427	ENSMUSG00000061584	Lyg2	Gm776	lysozyme G-like 2	protein-coding
mm_97311.1	chr11	76697502	76697505	+	1	NA	3' UTR (NM_177709, exon 3 of 3)	3' UTR (NM_177709, exon 3 of 3)	17630	NM_177709	237858	Mm.127006	NM_177709	ENSMUSG00000046275	Tusc5	C130069F04Rik|DSPB1|Lost1	tumor suppressor candidate 5	protein-coding
mm_29432.1	chr3	109051820	109051831	-	1	NA	Intergenic	Intergenic	-24218	NM_001163567	329739	Mm.69013	NM_001163567	ENSMUSG00000040339	Fam102b	1600010D10Rik|B430201A12Rik	family with sequence similarity 102, member B	protein-coding
mm_32045.1	chr4	95969920	95969928	+	1	NA	intron (NM_030014, intron 1 of 21)	Lx2B2|LINE|L1	-2269	NR_045776	319247	Mm.473527	NM_175680	ENSMUSG00000044125	9530080O11Rik	-	RIKEN cDNA 9530080O11 gene	ncRNA
mm_24991.1	chr3	97158824	97158845	+	1	NA	promoter-TSS (NM_019800)	promoter-TSS (NM_019800)	57	NM_019800	66659	Mm.101368	NM_019800	ENSMUSG00000028093	Acp6	5730559A09Rik|ACPL1|AU022842|mPACPL1	acid phosphatase 6, lysophosphatidic	protein-coding
mm_55939.1	chr6	84970856	84970858	-	1	NA	intron (NM_177077, intron 6 of 21)	HAL1|LINE|L1	98656	NM_177077	75914	Mm.159621	NM_177077	ENSMUSG00000033769	Exoc6b	4930569O18Rik|G430127E12Rik|Sec15b|Sec15l2|mKIAA0919	exocyst complex component 6B	protein-coding
mm_161706.1	chr17	24732567	24732567	+	1	NA	promoter-TSS (NM_025425)	promoter-TSS (NM_025425)	-118	NM_025425	66211	Mm.46198	NM_025425	ENSMUSG00000002500	Rpl3l	1110057H16Rik	ribosomal protein L3-like	protein-coding
mm_92322.1	chr10	75667580	75667616	-	1	NA	intron (NM_172549, intron 29 of 36)	CpG	-23590	NM_027890	71733	Mm.247956	NM_027890	ENSMUSG00000006342	Susd2	1200011D11Rik	sushi domain containing 2	protein-coding
mm_89381.1	chr10	89443496	89443520	+	1	NA	intron (NM_001079876, intron 1 of 10)	intron (NM_001079876, intron 1 of 10)	459	NM_001284344	237436	Mm.11982	NM_001033331	ENSMUSG00000074802	Gas2l3	8430435B07Rik|Gm240	growth arrest-specific 2 like 3	protein-coding
mm_113616.1	chr13	41569293	41569293	+	1	NA	Intergenic	Intergenic	-36923	NM_001163572	621976	Mm.259830	NM_001163572	ENSMUSG00000087370	Tmem170b	EG621976	transmembrane protein 170B	protein-coding
mm_143601.1	chr17	75701118	75701118	-	1	NA	Intergenic	Intergenic	-149172	NM_133747	72722	Mm.24641	NM_133747	ENSMUSG00000002017	Fam98a	2810405J04Rik|AL024114	family with sequence similarity 98, member A	protein-coding
mm_102716.1	chr11	67114827	67114831	-	1	NA	non-coding (NR_038055, exon 4 of 5)	non-coding (NR_038055, exon 4 of 5)	5251	NR_038055	74184	Mm.162554	NR_038055	ENSMUSG00000087410	2310065F04Rik	linc-Myh	RIKEN cDNA 2310065F04 gene	ncRNA
mm_120616.1	chr14	70289589	70289595	+	1	NA	promoter-TSS (NM_001304992)	promoter-TSS (NM_001304992)	-95	NM_001304992	19057	Mm.439683	NM_008915	ENSMUSG00000022092	Ppp3cc	Calnc|PP2BA gamma	protein phosphatase 3, catalytic subunit, gamma isoform	protein-coding
mm_28524.1	chr3	92589038	92589043	-	1	NA	promoter-TSS (NM_008574)	promoter-TSS (NM_008574)	-16	NM_008574	17235	Mm.331192	NM_008574		Smcp	Mcs|Mcsp	sperm mitochondria-associated cysteine-rich protein	protein-coding
mm_26038.1	chr3	135547586	135547598	+	1	NA	exon (NM_027288, exon 10 of 17)	exon (NM_027288, exon 10 of 17)	61981	NM_027288	110173	Mm.280536	NM_027288	ENSMUSG00000028164	Manba	2410030O07Rik|B930014J03Rik|Bmn	mannosidase, beta A, lysosomal	protein-coding
mm_118838.1	chr14	25635935	25635961	+	1	NA	exon (NM_183208, exon 7 of 24)	exon (NM_183208, exon 7 of 24)	32435	NM_001309430	100188919	Mm.473810	NM_001309430		Israa	-	immune system released activating agent	protein-coding
mm_28543.1	chr3	92851285	92851286	-	1	NA	promoter-TSS (NM_028628)	promoter-TSS (NM_028628)	1	NM_028628	73730	Mm.291773	NM_028628	ENSMUSG00000046676	Lce1l	1110008K04Rik|AI415426	late cornified envelope 1L	protein-coding
mm_111695.1	chr12	103655858	103655896	-	1	NA	intron (NM_007618, intron 1 of 4)	intron (NM_007618, intron 1 of 4)	1341	NM_007618	12401	Mm.290079	NM_007618	ENSMUSG00000060807	Serpina6	Cbg	serine (or cysteine) peptidase inhibitor, clade A, member 6	protein-coding
mm_129099.1	chr15	76009441	76009479	-	1	NA	promoter-TSS (NM_001168253)	promoter-TSS (NM_001168253)	38	NM_001168253	105732	Mm.267178	NM_134087	ENSMUSG00000046761	Fam83h	AA409316	family with sequence similarity 83, member H	protein-coding
mm_172407.1	chr7	16661861	16661876	+	1	NA	Intergenic	L1Md_T|LINE|L1	-4390	NR_003247	100038912	Mm.389813	NR_003247	ENSMUSG00000108307	Ceacam-ps1	Gm1978	carcinoembryonic antigen-related cell adhesion molecule pseudogene 1	pseudo
mm_30553.1	chr4	3694105	3694114	+	1	NA	intron (NM_010747, intron 1 of 12)	intron (NM_010747, intron 1 of 12)	15988	NM_010747	17096	Mm.317331	NM_010747	ENSMUSG00000042228	Lyn	AA407514|Hck-2|p53Lyn|p56Lyn	LYN proto-oncogene, Src family tyrosine kinase	protein-coding
mm_67595.1	chr7	83706769	83706773	-	1	NA	intron (NM_010551, intron 2 of 18)	intron (NM_010551, intron 2 of 18)	28719	NM_010551	16170	Mm.10137	NM_010551	ENSMUSG00000001741	Il16	mKIAA4048	interleukin 16	protein-coding
mm_20955.1	chr2	151741209	151741218	-	1	NA	promoter-TSS (NM_001305244)	promoter-TSS (NM_001305244)	97	NM_212446	228769	Mm.146984	NM_144889	ENSMUSG00000032869	Psmf1	AW048666|BC012260|PI31	proteasome (prosome, macropain) inhibitor subunit 1	protein-coding
mm_34380.1	chr4	144904312	144904313	+	1	NA	intron (NM_011303, intron 1 of 5)	intron (NM_011303, intron 1 of 5)	11175	NM_011303	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding
mm_51288.1	chr6	72305041	72305047	+	1	NA	exon (NM_001282071, exon 2 of 11)	exon (NM_001282071, exon 2 of 11)	434	NM_147779	20388	Mm.46033	NM_147779	ENSMUSG00000056370	Sftpb	AI562151|SF-B|SP-B|Sftp-3|Sftp3	surfactant associated protein B	protein-coding
mm_27792.1	chr3	75556790	75556871	-	1	NA	promoter-TSS (NM_009250)	promoter-TSS (NM_009250)	22	NM_019745	56426	Mm.316473	NM_019745	ENSMUSG00000027835	Pdcd10	2410003B13Rik|Ccm3|Tfa15|Tfar15	programmed cell death 10	protein-coding
mm_15155.1	chr2	154008330	154008343	+	1	NA	promoter-TSS (NM_008953)	promoter-TSS (NM_008953)	60	NM_008953	19194	Mm.29197	NM_008953	ENSMUSG00000042459	Bpifa2	Bpifa2e|Psp	BPI fold containing family A, member 2	protein-coding
mm_1435.1	chr1	67200968	67200970	+	1	NA	intron (NM_001080809, intron 25 of 37)	intron (NM_001080809, intron 25 of 37)	77942	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_8076.1	chr1	135585315	135585364	-	1	NA	promoter-TSS (NM_173437)	promoter-TSS (NM_173437)	16	NM_173437	215690	Mm.34977	NM_173437	ENSMUSG00000009418	Nav1	9530089B19|9930003A20Rik|C230080M11Rik|Pomfil3|Unc53h1|mKIAA1151|steerin-1	neuron navigator 1	protein-coding
mm_13824.1	chr2	119237679	119237710	+	1	NA	intron (NM_016907, intron 1 of 10)	CpG	334	NM_016907	20732	Mm.104955	NM_016907	ENSMUSG00000027315	Spint1	HAI-1	serine protease inhibitor, Kunitz type 1	protein-coding
mm_76498.1	chr8	86728716	86728726	-	1	NA	intron (NM_009172, intron 1 of 1)	intron (NM_009172, intron 1 of 1)	-16978	NR_027829	666945	Mm.391806	NR_027829		Gm10638	ENSMUSG00000074178	predicted gene 10638	ncRNA
mm_95604.1	chr11	53352063	53352097	+	1	NA	intron (NM_033565, intron 1 of 20)	intron (NM_033565, intron 1 of 20)	1313	NM_033565	93736	Mm.395281	NM_033565	ENSMUSG00000049470	Aff4	AF5Q31|Alf4|Laf4l|MCEF	AF4/FMR2 family, member 4	protein-coding
mm_161543.1	chr16	3747751	3747751	+	1	NA	intron (NM_148924, intron 4 of 5)	intron (NM_148924, intron 4 of 5)	3652	NM_148924	74120	Mm.29081	NM_148924	ENSMUSG00000022529	Zfp263	1200014J04Rik|AI326880|AU020888|NT2|mFPM315	zinc finger protein 263	protein-coding
mm_20101.1	chr2	121037049	121037067	-	1	NA	promoter-TSS (NM_013513)	promoter-TSS (NM_013513)	-181	NM_013513	13828	Mm.240051	NM_013513	ENSMUSG00000023216	Epb42	Epb4.2	erythrocyte membrane protein band 4.2	protein-coding
mm_30103.1	chr3	138493813	138493851	-	1	NA	Intergenic	Intergenic	-4450	NM_175224	75624	Mm.26833	NM_175224	ENSMUSG00000005813	Metap1	1700029C17Rik|AW047992|mKIAA0094	methionyl aminopeptidase 1	protein-coding
mm_143300.1	chr17	65985369	65985406	-	1	NA	exon (NM_001025572, exon 9 of 13)	exon (NM_001025572, exon 9 of 13)	-34200	NM_023053	65960	Mm.10153	NM_023053	ENSMUSG00000024098	Twsg1	1810013J15Rik|9030422N06Rik|AW552143|D17Ertd403e|Tsg|Twg	twisted gastrulation BMP signaling modulator 1	protein-coding
mm_32489.1	chr4	107968435	107968446	+	1	NA	5' UTR (NM_146255, exon 1 of 11)	5' UTR (NM_146255, exon 1 of 11)	106	NM_146255	242607	Mm.192040	NM_146255	ENSMUSG00000008932	Slc1a7	A930031E15Rik|Eaat5	solute carrier family 1 (glutamate transporter), member 7	protein-coding
mm_24498.1	chr3	92385684	92385687	+	1	NA	promoter-TSS (NM_011474)	promoter-TSS (NM_011474)	0	NM_011474	20762	Mm.10693	NM_011474	ENSMUSG00000046259	Sprr2h	AI661967	small proline-rich protein 2H	protein-coding
mm_148498.1	chr19	4192121	4192125	+	1	NA	promoter-TSS (NM_031868)	promoter-TSS (NM_031868)	-51	NM_031868	19045	Mm.1970	NM_031868	ENSMUSG00000040385	Ppp1ca	Ppp1c|dism2	protein phosphatase 1, catalytic subunit, alpha isoform	protein-coding
mm_139958.1	chr17	71552084	71552094	+	1	NA	promoter-TSS (NM_029254)	promoter-TSS (NM_029254)	28	NM_029254	70891	Mm.477599	NM_029254	ENSMUSG00000052525	Spdya	4921517J08Rik|4930548B21Rik|GS4|MLZ-465|Spdy1	speedy/RINGO cell cycle regulator family, member A	protein-coding
mm_125280.1	chr15	36283247	36283306	+	1	NA	promoter-TSS (NM_013923)	promoter-TSS (NM_013923)	-129	NM_013923	30945	Mm.5181	NM_013923	ENSMUSG00000022280	Rnf19a	AA032313|Dorfin|Rnf19|UIP117|Ubce7ip2|XYbp	ring finger protein 19A	protein-coding
mm_91099.1	chr10	19065206	19065217	-	1	NA	Intergenic	Intergenic	-49801	NM_009397	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_42670.1	chr5	119671591	119671613	+	1	NA	5' UTR (NM_011535, exon 1 of 8)	5' UTR (NM_011535, exon 1 of 8)	369	NM_011535	21386	Mm.219139	NM_011535	ENSMUSG00000018604	Tbx3	D5Ertd189e	T-box 3	protein-coding
mm_69205.1	chr7	127406808	127406831	-	1	NA	promoter-TSS (NM_001167832)	promoter-TSS (NM_001167832)	3	NM_146203	233893	Mm.297097	NM_146203	ENSMUSG00000045757	Zfp764	8030466O12Rik	zinc finger protein 764	protein-coding
mm_138635.1	chr17	35861326	35861339	+	1	NA	promoter-TSS (NM_134122)	promoter-TSS (NM_134122)	14	NM_134122	106582	Mm.390992	NM_134122	ENSMUSG00000059791	Nrm	2610307M02Rik|AI429796	nurim (nuclear envelope membrane protein)	protein-coding
mm_89237.1	chr10	87753810	87753856	+	1	NA	Intergenic	Intergenic	-104432	NM_001314010	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_47628.1	chr5	125289726	125289761	-	1	NA	exon (NM_001205082, exon 8 of 12)	exon (NM_001205082, exon 8 of 12)	51351	NM_016741	20778	Mm.282242	NM_016741	ENSMUSG00000037936	Scarb1	AI120173|CD36|Cd36l1|Chohd1|Cla-1|Cla1|D5Ertd460e|Hdlq1|Hlb398|SR-B1|SR-BI|SRBI|Srb1|mSR-BI	scavenger receptor class B, member 1	protein-coding
mm_60460.1	chr7	44477707	44477750	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-6789	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_53230.1	chr6	127153643	127153652	+	1	NA	intron (NR_040275, intron 1 of 1)	intron (NR_040275, intron 1 of 1)	-2599	NM_009829	12444	Mm.333406	NM_009829	ENSMUSG00000000184	Ccnd2	2600016F06Rik|AI256817|BF642806|C86853|Vin-1|Vin1|cD2	cyclin D2	protein-coding
mm_94101.1	chr10	128565905	128565999	-	1	NA	promoter-TSS (NM_011119)	promoter-TSS (NM_011119)	-18	NM_011119	18813	Mm.4742	NM_011119	ENSMUSG00000025364	Pa2g4	38kDa|AA672939|Ebp1|Plfap	proliferation-associated 2G4	protein-coding
mm_23378.1	chr3	55707508	55707525	+	1	NA	intron (NM_030595, intron 45 of 57)	intron (NM_030595, intron 45 of 57)	-74994	NM_010750	17116	Mm.440209	NM_010750	ENSMUSG00000056947	Mab21l1	AW047968	mab-21-like 1 (C. elegans)	protein-coding
mm_46126.1	chr5	92500523	92500525	-	1	NA	intron (NM_007644, intron 1 of 11)	intron (NM_007644, intron 1 of 11)	5133	NM_007644	12492	Mm.297964	NM_007644	ENSMUSG00000029426	Scarb2	9330185J12Rik|Cd36l2|LGP85|LIMP II|LIMP-2|MLGP85	scavenger receptor class B, member 2	protein-coding
mm_62061.1	chr7	92447651	92447657	+	1	NA	3' UTR (NM_001243047, exon 11 of 11)	3' UTR (NM_001243047, exon 11 of 11)	-113495	NM_025515	66365	Mm.21173	NM_025515	ENSMUSG00000030613	Ccdc90b	2310015N07Rik|C86558	coiled-coil domain containing 90B	protein-coding
mm_31890.1	chr4	82513367	82513408	+	1	NA	intron (NR_137202, intron 1 of 1)	CpG	5398	NR_137202	102635783	Mm.41666	NR_137202		Gm11266	OTTMUSG00000000396	predicted gene 11266	ncRNA
mm_45418.1	chr5	66514816	66514837	-	1	NA	intron (NM_001310626, intron 2 of 15)	intron (NM_001310626, intron 2 of 15)	103991	NM_009686	11787	Mm.5159	NM_009686	ENSMUSG00000029207	Apbb2	2310007D03Rik|FE65L1|Rirl1|TR2L|Zfra	amyloid beta (A4) precursor protein-binding, family B, member 2	protein-coding
mm_61871.1	chr7	89426281	89426293	+	1	NA	promoter-TSS (NR_102276)	promoter-TSS (NR_102276)	-19	NR_102276	101521	Mm.26902	NR_102276	ENSMUSG00000109311	AI314278	-	expressed sequence AI314278	ncRNA
mm_3923.1	chr1	162570688	162570755	+	1	NA	promoter-TSS (NM_016796)	promoter-TSS (NM_016796)	-107	NM_016796	53330	Mm.10699	NM_016796	ENSMUSG00000026696	Vamp4	D1Ertd147e	vesicle-associated membrane protein 4	protein-coding
mm_148123.1	chr18	75367071	75367095	-	1	NA	promoter-TSS (NM_001042660)	promoter-TSS (NM_001042660)	-282	NM_001042660	17131	Mm.34407	NM_008543	ENSMUSG00000025880	Smad7	Madh7	SMAD family member 7	protein-coding
mm_83701.1	chr9	50659571	50659573	-	1	NA	5' UTR (NM_145614, exon 1 of 14)	5' UTR (NM_145614, exon 1 of 14)	208	NM_145614	235339	Mm.285076	NM_145614	ENSMUSG00000000168	Dlat	6332404G05Rik|DLTA|PDC-E2	dihydrolipoamide S-acetyltransferase (E2 component of pyruvate dehydrogenase complex)	protein-coding
mm_22911.1	chr3	31091713	31091729	+	1	NA	Intergenic	ORR1C2|LTR|ERVL-MaLR	-3337	NM_011386	20482	Mm.15406	NM_011386	ENSMUSG00000027660	Skil	Skir|SnoN|sno	SKI-like	protein-coding
mm_17271.1	chr2	26091832	26091855	-	1	NA	5' UTR (NM_001037098, exon 1 of 6)	5' UTR (NM_001037098, exon 1 of 6)	553	NM_001037098	67991	Mm.131074	NM_026495	ENSMUSG00000026932	Nacc2	0610020I02Rik|AI448087|Btbd14a|C030048H19Rik	nucleus accumbens associated 2, BEN and BTB (POZ) domain containing	protein-coding
mm_49982.1	chr6	41031626	41031667	+	1	NA	exon (NM_023333, exon 5 of 5)	exon (NM_023333, exon 5 of 5)	3863	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_70966.1	chr8	27023813	27023937	+	1	NA	promoter-TSS (NM_153592)	promoter-TSS (NM_153592)	76	NM_153592	244373	Mm.277699	NM_153592	ENSMUSG00000031483	Erlin2	BC036333|C87251|Spfh2	ER lipid raft associated 2	protein-coding
mm_153613.1	chr19	43986107	43986120	-	1	NA	exon (NM_030703, exon 1 of 9)	exon (NM_030703, exon 1 of 9)	407	NM_030703	93721	Mm.206774	NM_030703	ENSMUSG00000025196	Cpn1	0610011F20Rik|CPN	carboxypeptidase N, polypeptide 1	protein-coding
mm_35005.1	chr4	156254342	156254354	+	1	NA	intron (NM_001110516, intron 2 of 10)	intron (NM_001110516, intron 2 of 10)	990	NM_001110516	231004	Mm.406833	NM_173736	ENSMUSG00000096351	Samd11	BC026991|mr-s	sterile alpha motif domain containing 11	protein-coding
mm_27227.1	chr3	36406378	36406388	-	1	NA	Intergenic	Intergenic	69141	NR_105976	102466786		NR_105976	ENSMUSG00000098808	Mir7009	Gm27472|mmu-mir-7009	microRNA 7009	ncRNA
mm_117025.1	chr13	58215559	58215612	-	1	NA	promoter-TSS (NM_152234)	promoter-TSS (NM_152234)	68	NM_152234	56085	Mm.182053	NM_026842	ENSMUSG00000005312	Ubqln1	1110046H03Rik|1810030E05Rik|AU019746|C77538|D13Ertd372e|Da41|Dsk2|Plic-1|Plic1|Xdrp1	ubiquilin 1	protein-coding
mm_2377.1	chr1	93373811	93373839	+	1	NA	promoter-TSS (NM_207031)	promoter-TSS (NM_207031)	-71	NM_207031	404545	Mm.297411	NM_207031	ENSMUSG00000034107	Ano7	Ngep|Ngep-L|Pcanap5|Tmem16g	anoctamin 7	protein-coding
mm_171516.1	chr4	146514891	146514893	+	1	NA	promoter-TSS (NM_001243139)	promoter-TSS (NM_001243139)	-28	NM_001243139	100041433	Mm.441741	NM_001243138	ENSMUSG00000056300	Zfp981	Gm13247|OTTMUSG00000011075	zinc finger protein 981	protein-coding
mm_49922.1	chr6	39205537	39205547	+	1	NA	intron (NM_001033430, intron 1 of 19)	CpG	1231	NM_001033430	338523	Mm.293175	NM_001033430	ENSMUSG00000042599	Kdm7a	A630082K20Rik|BB041802|ENSMUSG00000073143|Jhdm1d|mKIAA1718	lysine (K)-specific demethylase 7A	protein-coding
mm_133956.1	chr16	4037865	4037882	-	1	NA	intron (NM_010061, intron 2 of 8)	intron (NM_010061, intron 2 of 8)	728	NM_010061	13419	Mm.291048	NM_010061	ENSMUSG00000005980	Dnase1	AI788650|DNaseI|Dnl1	deoxyribonuclease I	protein-coding
mm_124629.1	chr15	4026461	4026471	+	1	NA	promoter-TSS (NM_024188)	promoter-TSS (NM_024188)	38	NM_024188	67041	Mm.13445	NM_024188	ENSMUSG00000022186	Oxct1	2610008O03Rik|Oxct|Oxct2a|Scot-s	3-oxoacid CoA transferase 1	protein-coding
mm_142199.1	chr17	36958418	36958433	-	1	NA	promoter-TSS (NM_029602)	promoter-TSS (NM_029602)	3	NM_023162	66136	Mm.486229	NM_023162	ENSMUSG00000036315	Znrd1	1110014N07Rik|Rpa12	zinc ribbon domain containing, 1	protein-coding
mm_123243.1	chr14	60251376	60251445	-	1	NA	promoter-TSS (NM_170591)	promoter-TSS (NM_170591)	-32	NM_170591	71844	Mm.258051	NM_170591	ENSMUSG00000063895	Nupl1	1700017F11Rik|Nup58|mKIAA0410	nucleoporin like 1	protein-coding
mm_52117.1	chr6	97922752	97922757	+	1	NA	intron (NM_001113198, intron 1 of 9)	intron (NM_001113198, intron 1 of 9)	-7063	NM_001178049	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_51831.1	chr6	89643983	89644007	+	1	NA	promoter-TSS (NM_001178058)	promoter-TSS (NM_001178058)	7	NM_001178058	232223	Mm.229332	NM_153162	ENSMUSG00000000811	Txnrd3	AI196535|TR2|Tgr	thioredoxin reductase 3	protein-coding
mm_130108.1	chr15	89456678	89456689	-	1	NA	exon (NM_021921, exon 3 of 12)	exon (NM_021921, exon 3 of 12)	2772	NM_021921	60597	Mm.173337	NM_021921	ENSMUSG00000022619	Mapk8ip2	3230402N03Rik|AI847694|AW049958|IB2|Jip2|R75148	mitogen-activated protein kinase 8 interacting protein 2	protein-coding
mm_140709.1	chr17	14943039	14943055	-	1	NA	promoter-TSS (NM_001083881)	promoter-TSS (NM_001083881)	77	NM_175173	71682	Mm.122698	NM_175173	ENSMUSG00000046991	Wdr27	0610012K18Rik	WD repeat domain 27	protein-coding
mm_103018.1	chr11	69734924	69734943	-	1	NA	exon (NM_001291068, exon 29 of 29)	exon (NM_001291068, exon 29 of 29)	23700	NM_001291068	20020	Mm.16533	NM_009089	ENSMUSG00000005198	Polr2a	220kDa|Rpb1|Rpo2-1	polymerase (RNA) II (DNA directed) polypeptide A	protein-coding
mm_145521.1	chr18	60557739	60557759	+	1	NA	3' UTR (NM_026302, exon 13 of 13)	3' UTR (NM_026302, exon 13 of 13)	-3037	NM_025776	66810	Mm.275106	NM_025776	ENSMUSG00000024604	Rbm22	8430430L24Rik	RNA binding motif protein 22	protein-coding
mm_148534.1	chr19	4594364	4594394	+	1	NA	promoter-TSS (NM_008797)	promoter-TSS (NM_008797)	60	NM_008797	18563	Mm.1845	NM_008797	ENSMUSG00000024892	Pcx	Pc|Pcb	pyruvate carboxylase	protein-coding
mm_42783.1	chr5	121452607	121452665	+	1	NA	promoter-TSS (NM_029912)	promoter-TSS (NM_029912)	-73	NM_029912	77462	Mm.358781	NM_029912	ENSMUSG00000029452	Tmem116	4930406A18Rik|4930513P12Rik|C030022K24Rik	transmembrane protein 116	protein-coding
mm_75087.1	chr8	33929799	33929816	-	1	NA	promoter-TSS (NM_019733)	promoter-TSS (NM_019733)	56	NM_019733	19663	Mm.323997	NM_019733	ENSMUSG00000031586	Rbpms	2010300K22Rik|2700019M19Rik|AU017537|RBP-MS|hermes	RNA binding protein gene with multiple splicing	protein-coding
mm_151136.1	chr19	52264445	52264455	+	1	NA	5' UTR (NM_008386, exon 1 of 2)	5' UTR (NM_008386, exon 1 of 2)	153	NM_008386	16333	Mm.46269	NM_008386	ENSMUSG00000035804	Ins1	Ins-1|Ins2-rs1	insulin I	protein-coding
mm_95686.1	chr11	54303803	54303844	+	1	NA	promoter-TSS (NM_144823)	promoter-TSS (NM_144823)	-1	NM_001033598	216739	Mm.267478	NM_144823	ENSMUSG00000020333	Acsl6	A330035H04Rik|AW050338|Facl6|LACS|Lacsl|mKIAA0837	acyl-CoA synthetase long-chain family member 6	protein-coding
mm_35874.1	chr4	49536736	49536753	-	1	NA	3' UTR (NM_144903, exon 9 of 9)	3' UTR (NM_144903, exon 9 of 9)	12802	NM_144903	230163	Mm.482116	NM_144903	ENSMUSG00000028307	Aldob	Aldo-2|Aldo2|BC016435	aldolase B, fructose-bisphosphate	protein-coding
mm_12378.1	chr2	69822976	69822998	+	1	NA	intron (NM_177784, intron 1 of 3)	CpG	617	NM_177784	277396	Mm.138073	NM_177784	ENSMUSG00000042155	Klhl23	C130068N17Rik	kelch-like 23	protein-coding
mm_28009.1	chr3	83041018	83041024	-	1	NA	Intergenic	Intergenic	8842	NM_181849	110135	Mm.30063	NM_181849	ENSMUSG00000033831	Fgb	2510049G14Rik	fibrinogen beta chain	protein-coding
mm_99961.1	chr11	113683435	113683471	+	1	NA	promoter-TSS (NM_177777)	promoter-TSS (NM_177777)	698	NM_138598	28081	Mm.351688	NM_138598	ENSMUSG00000041629	Fam104a	D11Wsu99e	family with sequence similarity 104, member A	protein-coding
mm_111414.1	chr12	91556728	91556736	-	1	NA	3' UTR (NM_031391, exon 9 of 9)	3' UTR (NM_031391, exon 9 of 9)	32917	NM_031391	83602	Mm.275728	NM_031391	ENSMUSG00000020962	Gtf2a1	6330549H03Rik|AA536742|AA959775|AW060250|TfIIAa/b|Tfiia1	general transcription factor II A, 1	protein-coding
mm_94581.1	chr11	11690409	11690421	+	1	NA	intron (NM_001301866, intron 1 of 5)	intron (NM_001301866, intron 1 of 5)	238	NM_001301863	22778	Mm.103545	NM_009578	ENSMUSG00000018654	Ikzf1	5832432G11Rik|Ikaros|LyF-1|Zfpn1a1|Znfn1a1|hlk-1|mKIAA4227	IKAROS family zinc finger 1	protein-coding
mm_26982.1	chr3	25661906	25661921	-	1	NA	intron (NM_001163387, intron 3 of 5)	intron (NM_001163387, intron 3 of 5)	491394	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_101885.1	chr11	48946149	48946150	-	1	NA	TTS (NM_001114679)	TTS (NM_001114679)	261	NM_001281472	621823	Mm.440151	NM_001281472	ENSMUSG00000078153	Psme2b	PA28b-p|PA28b2|Psme2-like|Psme2b-ps	protease (prosome, macropain) activator subunit 2B	protein-coding
mm_2746.1	chr1	128592446	128592458	+	1	NA	promoter-TSS (NM_009911)	promoter-TSS (NM_009911)	-153	NM_009911	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding
mm_47021.1	chr5	115490186	115490204	-	1	NA	Intergenic	CpG	-5711	NM_133760	75387	Mm.332616	NM_133760	ENSMUSG00000029524	Sirt4	4930596O17Rik	sirtuin 4	protein-coding
mm_104866.1	chr11	99387316	99387332	-	1	NA	exon (NM_010660, exon 4 of 8)	exon (NM_010660, exon 4 of 8)	2040	NM_010660	16661	Mm.22662	NM_010660	ENSMUSG00000019761	Krt10	D130054E02Rik|K10|K1C1|Krt-1.10|Krt1-10	keratin 10	protein-coding
mm_173260.1	chrX	9487717	9487721	-	1	NA	Intergenic	ETnERV2-int|LTR|ERVK	-18395	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_52749.1	chr6	120644404	120644419	+	1	NA	Intergenic	Intergenic	-22010	NM_001128151	330409	Mm.333357	NM_001128151	ENSMUSG00000071226	Cecr2	2610101O16Rik|2810409N01Rik|Gtl4|mKIAA1740	cat eye syndrome chromosome region, candidate 2	protein-coding
mm_18173.1	chr2	45110143	45110165	-	1	NA	promoter-TSS (NR_110572)	promoter-TSS (NR_110572)	123	NM_001289521	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_137752.1	chr17	29429078	29429099	+	1	NA	Intergenic	Charlie16a|DNA|hAT-Charlie	-61957	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_25486.1	chr3	109250980	109251017	+	1	NA	Intergenic	Intergenic	-89685	NM_020505	57257	Mm.282257	NM_020505	ENSMUSG00000033721	Vav3	A530094I06Rik|AA986410|Idd18.1	vav 3 oncogene	protein-coding
mm_77249.1	chr8	115705663	115705673	-	1	NA	3' UTR (NM_001025577, exon 1 of 1)	3' UTR (NM_001025577, exon 1 of 1)	1226	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_62612.1	chr7	107187167	107187171	+	1	NA	intron (NM_001002894, intron 5 of 10)	intron (NM_001002894, intron 5 of 10)	20179	NM_001002894	76858	Mm.35644	NM_001002894	ENSMUSG00000016626	Nlrp14	4921520L01Rik|GC-LRR|Nalp-iota|Nalp14|Nalp14l	NLR family, pyrin domain containing 14	protein-coding
mm_96601.1	chr11	69091110	69091116	+	1	NA	3' UTR (NM_009497, exon 5 of 5)	3' UTR (NM_009497, exon 5 of 5)	2585	NM_009497	22318	Mm.28643	NM_009497	ENSMUSG00000020894	Vamp2	Syb-2|Syb2|sybII	vesicle-associated membrane protein 2	protein-coding
mm_171737.1	chr4	94932818	94932822	-	1	NA	Intergenic	RMER19C|LTR|ERVK	-3977	NM_001290623	67753	Mm.25097	NM_027089	ENSMUSG00000028575	Eqtn	1700028B15Rik|4930579C15Rik|Afaf|C81058|Eqtl|Eqts	equatorin, sperm acrosome associated	protein-coding
mm_112446.1	chr13	5861554	5861564	+	1	NA	promoter-TSS (NM_011803)	promoter-TSS (NM_011803)	70	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_148459.1	chr19	4046473	4046481	+	1	NA	Intergenic	Intergenic	-4256	NM_181796	14869	Mm.441542	NM_181796	ENSMUSG00000038155	Gstp2	GSTpiA|Gst-3|Gst3	glutathione S-transferase, pi 2	protein-coding
mm_15890.1	chr2	164880017	164880039	+	1	NA	intron (NM_146129, intron 1 of 16)	CpG	660	NM_146129	228866	Mm.241134	NM_146129	ENSMUSG00000039849	Pcif1	2310022K11Rik|C20orf67|F730014I05Rik	PDX1 C-terminal inhibiting factor 1	protein-coding
mm_6132.1	chr1	64690579	64690587	-	1	NA	promoter-TSS (NM_001097644)	promoter-TSS (NM_001097644)	76	NR_038009	69941	Mm.69044	NR_038009	ENSMUSG00000087213	2810408I11Rik	-	RIKEN cDNA 2810408I11 gene	ncRNA
mm_72996.1	chr8	93398916	93398934	+	1	NA	Intergenic	Intergenic	-61716	NM_021456	12623	Mm.22720	NM_021456	ENSMUSG00000057074	Ces1g	Ces-1|Ces1|Ses-1	carboxylesterase 1G	protein-coding
mm_100567.1	chr11	120730824	120730866	+	1	NA	exon (NM_007621, exon 3 of 8)	exon (NM_007621, exon 3 of 8)	1176	NM_007621	12409	Mm.21454	NM_007621	ENSMUSG00000025150	Cbr2	MLCR	carbonyl reductase 2	protein-coding
mm_149674.1	chr19	20389539	20389548	+	1	NA	intron (NM_010730, intron 1 of 12)	intron (NM_010730, intron 1 of 12)	1128	NM_010730	16952	Mm.248360	NM_010730	ENSMUSG00000024659	Anxa1	Anx-1|Anx-A1|C430014K04Rik|Lpc-1|Lpc1	annexin A1	protein-coding
mm_56042.1	chr6	86733219	86733256	-	1	NA	5' UTR (NM_011818, exon 1 of 14)	5' UTR (NM_011818, exon 1 of 14)	141	NM_011818	23885	Mm.321452	NM_011818	ENSMUSG00000001157	Gmcl1	2810049L19Rik|Btbd13|DIP|Gcl|Gcl-1|glc-1|mglc-1	germ cell-less, spermatogenesis associated 1	protein-coding
mm_127662.1	chr15	102520740	102520747	+	1	NA	intron (NM_009319, intron 3 of 8)	intron (NM_009319, intron 3 of 8)	2551	NM_009319	21357	Mm.291485	NM_009319	ENSMUSG00000023051	Tarbp2	Prbp|TRBP	TARBP2, RISC loading complex RNA binding subunit	protein-coding
mm_118765.1	chr14	22455892	22455896	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	86904	NR_046307	74896	Mm.444661	NR_046307		4930405A10Rik	4930456G20Rik	RIKEN cDNA 4930405A10 gene	ncRNA
mm_166435.1	chr5	137207568	137207599	-	1	NA	Intergenic	Intergenic	-80671	NM_009599	11423	Mm.255464	NM_009599	ENSMUSG00000023328	Ache	-	acetylcholinesterase	protein-coding
mm_91011.1	chr10	15263206	15263208	-	1	NA	Intergenic	RLTR13D6|LTR|ERVK	502918	NM_008703	18101	Mm.487342	NM_008703	ENSMUSG00000019865	Nmbr	BB182387	neuromedin B receptor	protein-coding
mm_51069.1	chr6	66535419	66535482	+	1	NA	promoter-TSS (NM_019499)	promoter-TSS (NM_019499)	-18	NM_019499	56150	Mm.489653	NM_019499	ENSMUSG00000029910	Mad2l1	AA673185|MAD2	MAD2 mitotic arrest deficient-like 1	protein-coding
mm_147219.1	chr18	37998715	37998771	-	1	NA	5' UTR (NM_001205336, exon 1 of 33)	5' UTR (NM_001205336, exon 1 of 33)	226	NM_001205336	106952	Mm.247642	NM_139206	ENSMUSG00000024451	Arap3	Centd3|Drag1|E030006K04Rik|cnt-d3	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3	protein-coding
mm_38799.1	chr4	148151976	148152002	-	1	NA	promoter-TSS (NM_001163706)	promoter-TSS (NM_001163706)	40	NM_001163706	50762	Mm.27445	NM_015797	ENSMUSG00000055401	Fbxo6	AA408845|FBG2|Fbs2|Fbx6b|Fbxo6b	F-box protein 6	protein-coding
mm_19509.1	chr2	93869102	93869103	-	1	NA	promoter-TSS (NM_001033452)	promoter-TSS (NM_001033452)	55	NM_001033452	381411	Mm.9889	NM_001033452	ENSMUSG00000075023	Accsl	Gm1967	1-aminocyclopropane-1-carboxylate synthase (non-functional)-like	protein-coding
mm_135187.1	chr16	36131090	36131102	-	1	NA	promoter-TSS (NM_001033239)	promoter-TSS (NM_001033239)	93	NM_001033239	209294	Mm.300592	NM_001033239	ENSMUSG00000034362	Csta1	Csta	cystatin A1	protein-coding
mm_108752.1	chr12	88953439	88953461	+	1	NA	promoter-TSS (NM_172544)	promoter-TSS (NM_172544)	60	NM_172544	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding
mm_59648.1	chr7	28164748	28164778	+	1	NA	TTS (NM_001164655)	TTS (NM_001164655)	-4985	NM_007991	14113	Mm.4595	NM_007991	ENSMUSG00000046865	Fbl	AL022665|FIB|FLRN|RNU3IP1	fibrillarin	protein-coding
mm_95510.1	chr11	52004192	52004217	+	1	NA	promoter-TSS (NM_001166657)	promoter-TSS (NM_001166657)	-17	NM_001166657	213084	Mm.280557	NM_153785	ENSMUSG00000020389	Cdkl3	AI852479|B230379H01Rik	cyclin-dependent kinase-like 3	protein-coding
mm_11083.1	chr2	27728846	27728862	+	1	NA	intron (NM_001290482, intron 1 of 9)	intron (NM_001290482, intron 1 of 9)	18271	NM_001290482	20181	Mm.24624	NM_011305	ENSMUSG00000015846	Rxra	9530071D11Rik|Nr2b1|RXRalpha1	retinoid X receptor alpha	protein-coding
mm_142256.1	chr17	38420181	38420190	-	1	NA	promoter-TSS (NM_001177587)	promoter-TSS (NM_001177587)	0	NM_001177587	100126765	Mm.471586	NM_001177587	ENSMUSG00000092322	Esp36	Gm20408	exocrine gland secreted peptide 36	protein-coding
mm_158247.1	chrX	107403296	107403404	-	1	NA	promoter-TSS (NM_008409)	promoter-TSS (NM_008409)	10	NM_008409	16431	Mm.193	NM_008409	ENSMUSG00000031239	Itm2a	AW108051|Bricd2a|E25|Itm2	integral membrane protein 2A	protein-coding
mm_68505.1	chr7	111082216	111082251	-	1	NA	intron (NM_001040131, intron 1 of 20)	CpG	797	NM_001040131	13690	Mm.185453	NM_013507	ENSMUSG00000005610	Eif4g2	DAP-5|E130105L11Rik|Nat1|Natm1|p97	eukaryotic translation initiation factor 4, gamma 2	protein-coding
mm_171511.1	chr4	146431100	146431100	+	1	NA	intron (NM_001083918, intron 3 of 6).2	intron (NM_001083918, intron 3 of 6).2	-17930	NM_001085522	433791	Mm.276881	NM_001085522	ENSMUSG00000070605	Zfp992	Gm13251|OTTMUSG00000011097	zinc finger protein 992	protein-coding
mm_172749.1	chr8	83666816	83666827	+	1	NA	5' UTR (NM_013641, exon 1 of 3)	5' UTR (NM_013641, exon 1 of 3)	181	NM_013641	19216	Mm.213000	NM_013641	ENSMUSG00000019464	Ptger1	42kDa|EP1|Ptgerep1	prostaglandin E receptor 1 (subtype EP1)	protein-coding
mm_87152.1	chr10	36148966	36148969	+	1	NA	Intergenic	B4A|SINE|B4	-357840	NM_001253355	319415	Mm.332442	NM_001081208	ENSMUSG00000044499	Hs3st5	D930005L05Rik|Gm1151|Hs3ost5	heparan sulfate (glucosamine) 3-O-sulfotransferase 5	protein-coding
mm_30535.1	chr4	3574918	3574933	+	1	NA	promoter-TSS (NM_028097)	promoter-TSS (NM_028097)	46	NM_054089	116940	Mm.171323	NM_054089	ENSMUSG00000028233	Tgs1	D4Ertd800e|Ncoa6ip|Pimt	trimethylguanosine synthase 1	protein-coding
mm_44717.1	chr5	30949922	30949941	-	1	NA	promoter-TSS (NR_003522)	promoter-TSS (NR_003522)	-135	NR_003522	57742	Mm.389615	NM_021304	ENSMUSG00000006638	Abhd1	LABH-1|LABH1	abhydrolase domain containing 1	protein-coding
mm_135953.1	chr16	74502587	74502588	-	1	NA	Intergenic	L1_Mus2|LINE|L1	-91675	NM_175549	268902	Mm.171736	NM_175549	ENSMUSG00000052516	Robo2	2600013A04Rik|9430089E08Rik|BB097918|D230004I22Rik|mKIAA1568	roundabout guidance receptor 2	protein-coding
mm_125300.1	chr15	37233042	37233073	+	1	NA	promoter-TSS (NM_026496)	promoter-TSS (NM_026496)	21	NM_026496	252973	Mm.244612	NM_026496	ENSMUSG00000022286	Grhl2	0610015A08Rik|BOM|Tcfcp2l3|clft3	grainyhead-like 2 (Drosophila)	protein-coding
mm_156120.1	chrX	114907589	114907600	+	1	NA	promoter-TSS (NM_001081661)	promoter-TSS (NM_001081661)	12	NM_001081661	75097	Mm.50414	NM_001081661	ENSMUSG00000047079	Ube2dnl2	4930524E20Rik	ubiquitin-conjugating enzyme E2D N-terminal like 2	protein-coding
mm_53178.1	chr6	125361298	125361335	+	1	NA	exon (NM_011609, exon 9 of 10)	exon (NM_011609, exon 9 of 10)	11593	NM_011609	21937	Mm.1258	NM_011609	ENSMUSG00000030341	Tnfrsf1a	CD120a|FPF|TNF-R|TNF-R-I|TNF-R1|TNF-R55|TNF-alphaR1|TNFAR|TNFR60|TNFRI|TNFRp55|TNFalpha-R1|Tnfr-2|Tnfr1|p55|p55-R	tumor necrosis factor receptor superfamily, member 1a	protein-coding
mm_108342.1	chr12	80272065	80272107	+	1	NA	Intergenic	Charlie29a|DNA|hAT-Charlie	-11705	NM_001346669	109711	Mm.253564	NM_134156	ENSMUSG00000015143	Actn1	3110023F10Rik|Actn1a	actinin, alpha 1	protein-coding
mm_40849.1	chr5	73406219	73406268	+	1	NA	5' UTR (NM_181323, exon 1 of 16)	5' UTR (NM_181323, exon 1 of 16)	165	NM_181323	231293	Mm.280211	NM_181323	ENSMUSG00000029154	Cwh43	C130090K23Rik|imds-60	cell wall biogenesis 43 C-terminal homolog	protein-coding
mm_82718.1	chr9	24724790	24724793	-	1	NA	3' UTR (NM_194263, exon 8 of 8)	3' UTR (NM_194263, exon 8 of 8)	-28498	NM_001166207	320752	Mm.46158	NM_001166207	ENSMUSG00000085576	Dpy19l2	4932443J21Rik|Gm18376	dpy-19-like 2 (C. elegans)	protein-coding
mm_123399.1	chr14	63436432	63436440	-	1	NA	promoter-TSS (NM_177628)	promoter-TSS (NM_177628)	42	NM_177628	219148	Mm.37882	NM_177628	ENSMUSG00000035095	Fam167a	A030013D21	family with sequence similarity 167, member A	protein-coding
mm_92674.1	chr10	80546779	80546835	-	1	NA	intron (NM_025852, intron 4 of 14)	intron (NM_025852, intron 4 of 14)	-7683	NM_026094	67331	Mm.52511	NM_026094	ENSMUSG00000003341	Atp8b3	1700042F02Rik|1700056N23Rik|ATPIK|SAPLT	ATPase, class I, type 8B, member 3	protein-coding
mm_100311.1	chr11	117978093	117978101	+	1	NA	Intergenic	Intergenic	-8731	NM_007707	12702	Mm.3468	NM_007707	ENSMUSG00000053113	Socs3	Cis3|Cish3|EF-10|Ef10|SSI-3|Ssi3	suppressor of cytokine signaling 3	protein-coding
mm_145231.1	chr18	50131366	50131369	+	1	NA	intron (NM_008292, intron 2 of 23)	intron (NM_008292, intron 2 of 23)	3166	NM_008292	15488	Mm.277857	NM_008292	ENSMUSG00000024507	Hsd17b4	17-beta-HSD|17[b]-HSD|DBP|MFE-2|MFP2|MPF-2|Mfp-2|perMFE-2	hydroxysteroid (17-beta) dehydrogenase 4	protein-coding
mm_9169.1	chr1	170976045	170976106	-	1	NA	promoter-TSS (NM_001077189)	promoter-TSS (NM_001077189)	-4	NM_010187	14130	Mm.425062	NM_010187	ENSMUSG00000026656	Fcgr2b	AI528646|CD32|F630109E10Rik|Fc[g]RII|FcgRII|Fcgr2|Fcgr2a|Fcr-2|Fcr-3|Ly-17|Ly-m20|LyM-1|Lym-1|fcRII	Fc receptor, IgG, low affinity IIb	protein-coding
mm_72987.1	chr8	92961344	92961354	+	1	NA	exon (NM_009209, exon 1 of 14)	exon (NM_009209, exon 1 of 14)	302	NM_009209	20538	Mm.57040	NM_009209	ENSMUSG00000055368	Slc6a2	NE-T|NET|Slc6a5	solute carrier family 6 (neurotransmitter transporter, noradrenalin), member 2	protein-coding
mm_83610.1	chr9	48605148	48605158	-	1	NA	promoter-TSS (NM_001311062)	promoter-TSS (NM_001311062)	-30	NM_010924	18113	Mm.8362	NM_010924	ENSMUSG00000032271	Nnmt	-	nicotinamide N-methyltransferase	protein-coding
mm_152331.1	chr19	9955034	9955046	-	1	NA	Intergenic	Intergenic	-25560	NR_073181	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
mm_56115.1	chr6	87512284	87512303	-	1	NA	intron (NM_001037727, intron 1 of 10)	L1M5|LINE|L1	-15966	NM_175476	232201	Mm.119564	NM_175476	ENSMUSG00000030047	Arhgap25	A130039I20Rik	Rho GTPase activating protein 25	protein-coding
mm_90445.1	chr10	127667118	127667142	+	1	NA	promoter-TSS (NM_008668)	promoter-TSS (NM_008668)	7	NR_045171	72243	Mm.482902	NR_045171	ENSMUSG00000040195	1700012D01Rik	-	RIKEN cDNA 1700012D01 gene	ncRNA
mm_39569.1	chr5	23432824	23432828	+	1	NA	non-coding (NR_040469, exon 1 of 1)	non-coding (NR_040469, exon 1 of 1)	1527	NR_040469	269630	Mm.425231	NR_040469	ENSMUSG00000073147	5031425E22Rik	-	RIKEN cDNA 5031425E22 gene	ncRNA
mm_45238.1	chr5	53707313	53707328	-	1	NA	exon (NM_009827, exon 1 of 5)	exon (NM_009827, exon 1 of 5)	384	NM_009827	12425	Mm.3521	NM_009827	ENSMUSG00000029193	Cckar	AW106902	cholecystokinin A receptor	protein-coding
mm_46147.1	chr5	93206443	93206470	-	1	NA	promoter-TSS (NM_017367)	promoter-TSS (NM_017367)	39	NM_017367	12453	Mm.250419	NM_017367	ENSMUSG00000063015	Ccni	-	cyclin I	protein-coding
mm_165590.1	chr3	33720116	33720120	+	1	NA	Intergenic	L1ME1|LINE|L1	-80065	NM_027619	67120	Mm.275710	NM_025978	ENSMUSG00000027677	Ttc14	2700016E08Rik|4930434D01Rik|4931403I22Rik|4933402I15Rik|AI662468|AU014779|AW561908|cI-44|mKIAA1980	tetratricopeptide repeat domain 14	protein-coding
mm_46735.1	chr5	110810019	110810027	-	1	NA	promoter-TSS (NM_009469)	promoter-TSS (NM_009469)	58	NM_009469	22241	Mm.271898	NM_009469	ENSMUSG00000029512	Ulk1	AU041434|Unc51.1|mKIAA0722	unc-51 like kinase 1	protein-coding
mm_147308.1	chr18	40219325	40219369	-	1	NA	promoter-TSS (NM_023311)	promoter-TSS (NM_023311)	52	NM_023311	67180	Mm.270382	NM_023311	ENSMUSG00000024487	Yipf5	2610311I19Rik|AA408236|Yip1a	Yip1 domain family, member 5	protein-coding
mm_72986.1	chr8	92961028	92961044	+	1	NA	promoter-TSS (NM_009209)	promoter-TSS (NM_009209)	-11	NM_009209	20538	Mm.57040	NM_009209	ENSMUSG00000055368	Slc6a2	NE-T|NET|Slc6a5	solute carrier family 6 (neurotransmitter transporter, noradrenalin), member 2	protein-coding
mm_64650.1	chr7	4063196	4063210	-	1	NA	promoter-TSS (NM_178611)	promoter-TSS (NM_178611)	1	NM_001302677	52855	Mm.290880	NM_178611	ENSMUSG00000055541	Lair1	5133400O11Rik|BB115266|D7Bwg0421e|Lair-1	leukocyte-associated Ig-like receptor 1	protein-coding
mm_142160.1	chr17	36129436	36129463	-	1	NA	promoter-TSS (NM_001177467)	promoter-TSS (NM_001177467)	-24	NM_001177467	630294	Mm.484916	NM_001177467	ENSMUSG00000092243	Gm7030	EG630294|H2-t9	predicted gene 7030	protein-coding
mm_144173.1	chr18	6733780	6733788	+	1	NA	Intergenic	Intergenic	-31383	NM_181070	19330	Mm.132802	NM_181070	ENSMUSG00000073639	Rab18	AA959686	RAB18, member RAS oncogene family	protein-coding
mm_8630.1	chr1	156303391	156303438	-	1	NA	promoter-TSS (NM_001134741)	promoter-TSS (NM_001134741)	-66	NM_001134741	214575	Mm.252800	NM_001134741	ENSMUSG00000060985	Tdrd5	Gm103	tudor domain containing 5	protein-coding
mm_130052.1	chr15	89169563	89169573	-	1	NA	intron (NM_138749, intron 3 of 37)	intron (NM_138749, intron 3 of 37)	4383	NM_001159521	140570	Mm.267514	NM_138749	ENSMUSG00000036606	Plxnb2	Debt|plexin-B2	plexin B2	protein-coding
mm_25018.1	chr3	98013551	98013574	+	1	NA	promoter-TSS (NM_010928)	promoter-TSS (NM_010928)	24	NM_010928	18129	Mm.485843	NM_010928	ENSMUSG00000027878	Notch2	AI853703|N2	notch 2	protein-coding
mm_80263.1	chr9	72912773	72912777	+	1	NA	3' UTR (NM_175485, exon 20 of 20)	3' UTR (NM_175485, exon 20 of 20)	-12875	NM_028116	72135	Mm.273605	NM_028116	ENSMUSG00000034910	Pygo1	2600014C22Rik	pygopus 1	protein-coding
mm_93308.1	chr10	98744287	98744291	-	1	NA	Intergenic	Intergenic	-170863	NM_026482	67972	Mm.166944	NM_026482	ENSMUSG00000019943	Atp2b1	2810442I22Rik|E130111D10Rik|Pmca1	ATPase, Ca++ transporting, plasma membrane 1	protein-coding
mm_46312.1	chr5	100572169	100572179	-	1	NA	promoter-TSS (NM_139198)	promoter-TSS (NM_139198)	31	NM_139198	231507	Mm.34609	NM_139198	ENSMUSG00000029322	Plac8	C15|D5Wsu111e	placenta-specific 8	protein-coding
mm_102249.1	chr11	55118851	55118888	-	1	NA	Intergenic	Intergenic	20884	NM_010299	14667	Mm.287807	NM_010299	ENSMUSG00000000594	Gm2a	AA408702|AW215435|GM2-AP|SAP-3	GM2 ganglioside activator protein	protein-coding
mm_159491.1	chr4	42655250	42655250	+	1	NA	promoter-TSS (NM_001199959).2	promoter-TSS (NM_001199959).2	-1	NM_001199959	100040048	Mm.6660	NM_001199959	ENSMUSG00000096826	Ccl27b	Ctack|ENSMUSG00000066202|Scya27b	chemokine (C-C motif) ligand 27b	protein-coding
mm_148941.1	chr19	7056868	7056933	+	1	NA	exon (NM_134147, exon 1 of 11)	exon (NM_134147, exon 1 of 11)	132	NM_134147	107227	Mm.439977	NM_134147	ENSMUSG00000036278	Macrod1	AI604841|AW743046|D930010J01Rik|Lrp16	MACRO domain containing 1	protein-coding
mm_23272.1	chr3	51652911	51652931	+	1	NA	Intergenic	Intergenic	-8258	NM_174995	211666	Mm.24679	NM_174995	ENSMUSG00000074604	Mgst2	GST2|MGST-II	microsomal glutathione S-transferase 2	protein-coding
mm_117149.1	chr13	61202190	61202227	-	1	NA	exon (NM_021445, exon 2 of 8)	exon (NM_021445, exon 2 of 8)	1184	NM_021445	58518	Mm.143794	NM_021445	ENSMUSG00000021441	Cts6	1600022N02Rik	cathepsin 6	protein-coding
mm_144105.1	chr18	3542488	3542504	+	1	NA	Intergenic	RLTR1B-int|LTR|ERV1	34539	NM_026505	68010	Mm.284863	NM_026505	ENSMUSG00000024232	Bambi	2610003H06Rik	BMP and activin membrane-bound inhibitor	protein-coding
mm_74915.1	chr8	25499585	25499585	-	1	NA	Intergenic	Intergenic	-19174	NM_001079909	14182	Mm.265716	NM_010206	ENSMUSG00000031565	Fgfr1	AW208770|Eask|FGFR-I|FLG|Fgfr-1|Flt-2|Hspy|MFR|bFGF-R-1|c-fgr	fibroblast growth factor receptor 1	protein-coding
mm_5065.1	chr1	195017151	195017181	+	1	NA	promoter-TSS (NR_015566)	promoter-TSS (NR_015566)	-233	NR_015566	320977	Mm.99905	NR_015566	ENSMUSG00000096929	A330023F24Rik	C030002C11Rik	RIKEN cDNA A330023F24 gene	ncRNA
mm_166846.1	chr7	19696592	19696617	+	1	NA	exon (NM_009696, exon 4 of 4)	exon (NM_009696, exon 4 of 4)	1794	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_43565.1	chr5	137630857	137630883	+	1	NA	intron (NR_033148, intron 1 of 21)	intron (NR_033148, intron 1 of 21)	1747	NR_033148	100316903	Mm.200763	NR_033148		Gm20605	Lrch4-sap25	predicted gene 20605	ncRNA
mm_81610.1	chr9	110709985	110710028	+	1	NA	intron (NM_028312, intron 4 of 6)	intron (NM_028312, intron 4 of 6)	32604	NM_001083936	19228	Mm.3542	NM_011199	ENSMUSG00000032492	Pth1r	PPR|Pthr|Pthr1	parathyroid hormone 1 receptor	protein-coding
mm_77771.1	chr9	3007411	3007440	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	31318	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_128308.1	chr15	37792020	37792036	-	1	NA	promoter-TSS (NM_001170866)	promoter-TSS (NM_001170866)	-28	NM_001170866	52589	Mm.283370	NM_134094	ENSMUSG00000051359	Ncald	AI848120|D030020D09Rik|D15Ertd412e	neurocalcin delta	protein-coding
mm_99364.1	chr11	101732901	101732903	+	1	NA	promoter-TSS (NM_144831)	promoter-TSS (NM_144831)	-54	NM_144831	217207	Mm.28186	NM_144831	ENSMUSG00000034931	Dhx8	Ddx8|mDEAH6|mKIAA4096	DEAH (Asp-Glu-Ala-His) box polypeptide 8	protein-coding
mm_35628.1	chr4	43483589	43483598	-	1	NA	5' UTR (NM_019436, exon 1 of 5)	5' UTR (NM_019436, exon 1 of 5)	116	NM_019436	54390	Mm.31775	NM_019436	ENSMUSG00000028460	Sit1	Sit	suppression inducing transmembrane adaptor 1	protein-coding
mm_61882.1	chr7	89632557	89632567	+	1	NA	promoter-TSS (NM_181407)	promoter-TSS (NM_181407)	-256	NM_181407	109264	Mm.334011	NM_181407	ENSMUSG00000030621	Me3	1700020C08Rik|B230207H15Rik	malic enzyme 3, NADP(+)-dependent, mitochondrial	protein-coding
mm_102851.1	chr11	69395136	69395139	-	1	NA	promoter-TSS (NM_030083)	promoter-TSS (NM_030083)	209	NM_001045525	327951	Mm.415669	NM_001045525	ENSMUSG00000044795	Cyb5d1	Gm740	cytochrome b5 domain containing 1	protein-coding
mm_26920.1	chr3	20249513	20249533	-	1	NA	TTS (NM_029706)	TTS (NM_029706)	-7342	NM_007753	12873	Mm.1135	NM_007753	ENSMUSG00000001865	Cpa3	MC-CPA	carboxypeptidase A3, mast cell	protein-coding
mm_115630.1	chr13	12106870	12106881	-	1	NA	promoter-TSS (NM_023868)	promoter-TSS (NM_023868)	70	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding
mm_127322.1	chr15	100304182	100304190	+	1	NA	promoter-TSS (NM_027334)	promoter-TSS (NM_027334)	-631	NM_027334	70152	Mm.488086	NM_027334	ENSMUSG00000054619	Mettl7a1	2210414H16Rik|3300001H21Rik|Aam-B|Mettl7a|UbiE1	methyltransferase like 7A1	protein-coding
mm_74926.1	chr8	25597612	25597614	-	1	NA	promoter-TSS (NM_173012)	promoter-TSS (NM_173012)	-126	NM_173012	270035	Mm.268349	NM_173012	ENSMUSG00000037363	Letm2	6030453H13|D030041N04Rik	leucine zipper-EF-hand containing transmembrane protein 2	protein-coding
mm_145254.1	chr18	52528767	52528791	+	1	NA	exon (NM_010728, exon 1 of 7)	exon (NM_010728, exon 1 of 7)	942	NM_001286181	16948	Mm.172	NM_010728	ENSMUSG00000024529	Lox	AI893619|TSC-160|rrg	lysyl oxidase	protein-coding
mm_3905.1	chr1	161876012	161876041	+	1	NA	intron (NM_172645, intron 1 of 23)	intron (NM_172645, intron 1 of 23)	635	NM_172645	226551	Mm.170002	NM_172645	ENSMUSG00000040297	Suco	4732491B11|AI848100|AU016931|Opt	SUN domain containing ossification factor	protein-coding
mm_140171.1	chr17	80307460	80307469	+	1	NA	promoter-TSS (NM_001145452)	promoter-TSS (NM_001145452)	57	NM_001145452	381112	Mm.360004	NM_001145452	ENSMUSG00000054901	Arhgef33	Gm941	Rho guanine nucleotide exchange factor (GEF) 33	protein-coding
mm_6138.1	chr1	64737596	64737612	-	1	NA	5' UTR (NM_001042659, exon 1 of 2)	5' UTR (NM_001042659, exon 1 of 2)	146	NM_001042659	14367	Mm.150813	NM_022721	ENSMUSG00000045005	Fzd5	5330434N09Rik|AI427138|Fz-5|Fz5|mFz5	frizzled class receptor 5	protein-coding
mm_15134.1	chr2	153943920	153943934	+	1	NA	intron (NM_001034875, intron 3 of 15)	intron (NM_001034875, intron 3 of 15)	3065	NM_001034875	381399	Mm.315572	NM_001034875	ENSMUSG00000074665	Bpifb4	Gm1006|Lplunc4	BPI fold containing family B, member 4	protein-coding
mm_155270.1	chrX	59589284	59589294	+	1	NA	Intergenic	Intergenic	-3717	NM_001290414	14168	Mm.7995	NM_010200	ENSMUSG00000031137	Fgf13	Fhf2	fibroblast growth factor 13	protein-coding
mm_169353.1	chr14	22835828	22835838	-	1	NA	intron (NM_028275, intron 6 of 6)	L1Md_T|LINE|L1	258738	NR_033550	791307	Mm.364384	NR_033550	ENSMUSG00000068680	Gm10248	ENSMUSG00000068680	predicted gene 10248	ncRNA
mm_147966.1	chr18	67228876	67228878	-	1	NA	intron (NM_172630, intron 6 of 10)	intron (NM_172630, intron 6 of 10)	16953	NM_172630	225651	Mm.235792	NM_172630	ENSMUSG00000062526	Mppe1	A530095G11	metallophosphoesterase 1	protein-coding
mm_154310.1	chr19	61228387	61228395	-	1	NA	promoter-TSS (NM_009970)	promoter-TSS (NM_009970)	27	NM_009970	12982	Mm.287228	NM_009970	ENSMUSG00000059326	Csf2ra	CD116|Csfgmra|GM-CSF-Ra|GM-CSFR	colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)	protein-coding
mm_120283.1	chr14	63132615	63132651	+	1	NA	intron (NM_007798, intron 1 of 9)	intron (NM_007798, intron 1 of 9)	10171	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_51224.1	chr6	71372649	71372664	+	1	NA	promoter-TSS (NM_009857)	promoter-TSS (NM_009857)	-771	NM_009857	12525	Mm.1858	NM_009857	ENSMUSG00000053977	Cd8a	BB154331|Ly-2|Ly-35|Ly-B|Lyt-2	CD8 antigen, alpha chain	protein-coding
mm_111072.1	chr12	80132803	80132821	-	1	NA	promoter-TSS (NR_033514)	promoter-TSS (NR_033514)	32	NR_033514	69548	Mm.269712	NR_033514	ENSMUSG00000097729	2310015A10Rik	5330419I17Rik	RIKEN cDNA 2310015A10 gene	ncRNA
mm_169921.1	chr16	57391267	57391267	-	1	NA	intron (NM_001040397, intron 1 of 4)	LSU-rRNA_Hsa|rRNA|rRNA	37990	NM_001040397	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding
mm_65269.1	chr7	23357763	23357773	-	1	NA	intron (NM_001004194, intron 8 of 8)	intron (NM_001004194, intron 8 of 8)	-28121	NM_001039143	23968	Mm.333653	NM_011860	ENSMUSG00000015721	Nlrp5	Mater|Nalp5|Op1|PAN11	NLR family, pyrin domain containing 5	protein-coding
mm_124450.1	chr14	118925301	118925319	-	1	NA	5' UTR (NM_025943, exon 1 of 22)	5' UTR (NM_025943, exon 1 of 22)	160	NM_025943	66573	Mm.87456	NM_025943	ENSMUSG00000042156	Dzip1	2510025K24Rik|2810422M04Rik	DAZ interacting protein 1	protein-coding
mm_147992.1	chr18	67641330	67641349	-	1	NA	promoter-TSS (NM_001081073)	promoter-TSS (NM_001081073)	-3	NM_001081073	225659	Mm.111928	NM_001081073	ENSMUSG00000073542	Cep76	6230425F05Rik|9630013E05	centrosomal protein 76	protein-coding
mm_15188.1	chr2	154202568	154202580	+	1	NA	5' UTR (NM_153418, exon 2 of 16)	5' UTR (NM_153418, exon 2 of 16)	2194	NM_153418	228801	Mm.3783	NM_153418	ENSMUSG00000027485	Bpifb1	Lplunc1	BPI fold containing family B, member 1	protein-coding
mm_48005.1	chr5	136161396	136161407	-	1	NA	intron (NM_178751, intron 2 of 2)	intron (NM_178751, intron 2 of 2)	9255	NM_178751	269717	Mm.308396	NM_178751	ENSMUSG00000039747	Orai2	A730041O15Rik|Tmem142b	ORAI calcium release-activated calcium modulator 2	protein-coding
mm_88933.1	chr10	81266694	81266716	+	1	NA	intron (NM_025317, intron 1 of 2)	CpG	221	NM_025317	66047	Mm.43397	NM_025317	ENSMUSG00000034932	Mrpl54	0610008M19Rik|D10Sut1e	mitochondrial ribosomal protein L54	protein-coding
mm_142277.1	chr17	39848309	39848332	-	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	5323	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_162167.1	chrX	99821103	99821103	+	1	NA	promoter-TSS (NM_001081283)	promoter-TSS (NM_001081283)	34	NM_001081283	620592	Mm.388976	NM_001081283	ENSMUSG00000071719	Tmem28	EG620592|Fam155b|Tnen28	transmembrane protein 28	protein-coding
mm_44308.1	chr5	8997166	8997172	-	1	NA	promoter-TSS (NM_023733)	promoter-TSS (NM_023733)	-23	NM_023733	74114	Mm.28197	NM_023733	ENSMUSG00000003623	Crot	1200003H03Rik	carnitine O-octanoyltransferase	protein-coding
mm_7780.1	chr1	131276896	131276906	-	1	NA	intron (NM_019777, intron 2 of 21)	intron (NM_019777, intron 2 of 21)	2662	NM_019777	56489	Mm.386783	NM_019777	ENSMUSG00000042349	Ikbke	AW558201|IKK-i|IKKepsilon|Ikki	inhibitor of kappaB kinase epsilon	protein-coding
mm_89248.1	chr10	87859063	87859094	+	1	NA	promoter-TSS (NM_010512)	promoter-TSS (NM_010512)	26	NM_010512	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_118017.1	chr13	100780179	100780182	-	1	NA	intron (NM_172301, intron 7 of 8)	intron (NM_172301, intron 7 of 8)	-4281	NM_021886	26886	Mm.273502	NM_021886	ENSMUSG00000045273	Cenph	1700021I11Rik|2410018A12Rik|2610042E16Rik|2810046K12Rik|AU044255|CENP-H|ENP	centromere protein H	protein-coding
mm_166651.1	chr6	86607780	86607786	+	1	NA	Intergenic	Intergenic	-20391	NM_026414	67855	Mm.183043	NM_026414	ENSMUSG00000033508	Asprv1	2300003P22Rik|AA986851|SASP|SASPase|Taps	aspartic peptidase, retroviral-like 1	protein-coding
mm_91600.1	chr10	41072280	41072290	-	1	NA	promoter-TSS (NM_199058)	promoter-TSS (NM_199058)	-701	NM_199058	140741	Mm.290693	NM_199058	ENSMUSG00000046922	Gpr6	AI852874|Gm233	G protein-coupled receptor 6	protein-coding
mm_132241.1	chr16	32750915	32750931	+	1	NA	exon (NM_080457, exon 2 of 27)	exon (NM_080457, exon 2 of 27)	15037	NM_080457	140474	Mm.214599	NM_080457	ENSMUSG00000079620	Muc4	4933405I11Rik|Asgp	mucin 4	protein-coding
mm_139941.1	chr17	71183546	71183570	+	1	NA	promoter-TSS (NM_022882)	promoter-TSS (NM_022882)	-420	NM_022882	64898	Mm.227924	NM_022882	ENSMUSG00000024052	Lpin2	2610511G02Rik|AI481352|AW742896	lipin 2	protein-coding
mm_30181.1	chr3	144232096	144232118	-	1	NA	Intergenic	Intergenic	-26852	NM_010723	16911	Mm.29187	NM_010723	ENSMUSG00000028266	Lmo4	A730077C12Rik|Crp3|Etohi4	LIM domain only 4	protein-coding
mm_98.1	chr1	9377650	9377653	+	1	NA	Intergenic	Intergenic	-77774	NM_001290392	71096	Mm.336395	NM_027671	ENSMUSG00000025909	Sntg1	4933426D16Rik|G1SYN|SYN4	syntrophin, gamma 1	protein-coding
mm_118094.1	chr13	103850779	103850795	-	1	NA	exon (NM_001289475, exon 15 of 26)	exon (NM_001289475, exon 15 of 26)	69799	NM_001289473	59079	Mm.277354	NM_021563	ENSMUSG00000021709	Erbin	1700028E05Rik|Erbb2ip|mKIAA1225	Erbb2 interacting protein	protein-coding
mm_20996.1	chr2	152332354	152332422	-	1	NA	promoter-TSS (NM_001083921)	promoter-TSS (NM_001083921)	37	NM_001083921	24105	Mm.182145	NM_019705	ENSMUSG00000027466	Rbck1	AL033326|HOIL-1|HOIL-1L|UIP28|Ubce7ip3	RanBP-type and C3HC4-type zinc finger containing 1	protein-coding
mm_151498.1	chr19	58728061	58728069	+	1	NA	promoter-TSS (NM_018874)	promoter-TSS (NM_018874)	-822	NM_018874	18946	Mm.10753	NM_018874	ENSMUSG00000042179	Pnliprp1	Plrp1	pancreatic lipase related protein 1	protein-coding
mm_41472.1	chr5	91517702	91517719	+	1	NA	promoter-TSS (NM_145562)	promoter-TSS (NM_145562)	10	NM_145562	231440	Mm.5002	NM_145562	ENSMUSG00000034981	Parm1	2210012L08Rik|9130213B05Rik|W91666	prostate androgen-regulated mucin-like protein 1	protein-coding
mm_112561.1	chr13	13275693	13275736	+	1	NA	Intergenic	Intergenic	92998	NM_001311129	107849	Mm.392548	NM_181852	ENSMUSG00000055360	Prl2c5	Ghd3|MRP-4|Mrpplf4|PLF-4	prolactin family 2, subfamily c, member 5	protein-coding
mm_57403.1	chr6	124864920	124864934	-	1	NA	3' UTR (NM_013488, exon 10 of 10)	3' UTR (NM_013488, exon 10 of 10)	-1010	NM_013533	14788	Mm.2514	NM_013533	ENSMUSG00000038390	Gpr162	A-2|BC031437|Grca	G protein-coupled receptor 162	protein-coding
mm_76666.1	chr8	93379773	93379782	-	1	NA	Intergenic	Intergenic	-42568	NM_021456	12623	Mm.22720	NM_021456	ENSMUSG00000057074	Ces1g	Ces-1|Ces1|Ses-1	carboxylesterase 1G	protein-coding
mm_145535.1	chr18	60805079	60805088	+	1	NA	intron (NM_001042605, intron 1 of 8)	intron (NM_001042605, intron 1 of 8)	1234	NM_010545	16149	Mm.439737	NM_010545	ENSMUSG00000024610	Cd74	CLIP|DHLAG|HLADG|Ia-GAMMA|Ii	CD74 antigen (invariant polypeptide of major histocompatibility complex, class II antigen-associated)	protein-coding
mm_25741.1	chr3	122924354	122924402	+	1	NA	promoter-TSS (NM_024461)	promoter-TSS (NM_024461)	-19	NM_024461	67704	Mm.24219	NM_024461	ENSMUSG00000054091	1810037I17Rik	5730414I01Rik	RIKEN cDNA 1810037I17 gene	protein-coding
mm_95945.1	chr11	58386724	58386761	+	1	NA	exon (NM_001083884, exon 6 of 7)	exon (NM_001083884, exon 6 of 7)	6096	NM_001330197	70163	Mm.24119	NM_027339	ENSMUSG00000013643	Lypd8	2210415F13Rik	LY6/PLAUR domain containing 8	protein-coding
mm_139089.1	chr17	46832376	46832386	+	1	NA	promoter-TSS (NM_001100452)	promoter-TSS (NM_001100452)	-968	NM_001100452	210982	Mm.37642	NM_001100452	ENSMUSG00000036568	Gltscr1l	mKIAA0240	GLTSCR1-like	protein-coding
mm_150966.1	chr19	46500235	46500259	+	1	NA	Intergenic	CpG	-1401	NM_053100	93679	Mm.392177	NM_053100	ENSMUSG00000025034	Trim8	AA408830|BB006755|GERP|Rnf27	tripartite motif-containing 8	protein-coding
mm_35232.1	chr4	19709020	19709030	-	1	NA	promoter-TSS (NM_177327)	promoter-TSS (NM_177327)	-21	NR_074090	107568	Mm.78312	NM_177327	ENSMUSG00000041058	Wwp1	8030445B08Rik|AIP5|SDRP1|Tiul1	WW domain containing E3 ubiquitin protein ligase 1	protein-coding
mm_113356.1	chr13	32465447	32465460	+	1	NA	Intergenic	Intergenic	-126909	NM_146041	218138	Mm.247143	NM_146041	ENSMUSG00000038372	Gmds	BC031788|C87208	GDP-mannose 4, 6-dehydratase	protein-coding
mm_21487.1	chr2	163087815	163087834	-	1	NA	5' UTR (NM_026630, exon 2 of 2)	5' UTR (NM_026630, exon 2 of 2)	1777	NM_026630	68236	Mm.33648	NM_026630	ENSMUSG00000070708	Gtsf1l	2410116G06Rik	gametocyte specific factor 1-like	protein-coding
mm_134339.1	chr16	16542170	16542187	-	1	NA	intron (NM_001301817, intron 1 of 16)	Lx7|LINE|L1	-14767	NM_001301818	224014	Mm.256131	NM_139232	ENSMUSG00000022788	Fgd4	9030023J02Rik|9330209B17Rik|Frabp|ZFYVE6	FYVE, RhoGEF and PH domain containing 4	protein-coding
mm_75437.1	chr8	47352353	47352367	-	1	NA	promoter-TSS (NM_175162)	promoter-TSS (NM_175162)	-12	NM_175162	71069	Mm.23973	NM_175162	ENSMUSG00000038143	Stox2	4933409N07Rik|AI449080|AI835114|mKIAA1392	storkhead box 2	protein-coding
mm_113876.1	chr13	48870075	48870091	+	1	NA	intron (NM_011078, intron 1 of 21)	CpG	802	NM_011078	18676	Mm.486213	NM_011078	ENSMUSG00000038025	Phf2	GRC5	PHD finger protein 2	protein-coding
mm_91311.1	chr10	24921895	24921902	-	1	NA	intron (NM_007482, intron 2 of 7)	L1ME1|LINE|L1	5572	NM_007482	11846	Mm.154144	NM_007482	ENSMUSG00000019987	Arg1	AI|AI256583|Arg-1|PGIF	arginase, liver	protein-coding
mm_21240.1	chr2	156154295	156154295	-	1	NA	intron (NM_133242, intron 12 of 16)	intron (NM_133242, intron 12 of 16)	10062	NM_025946	67067	Mm.371623	NM_025946	ENSMUSG00000067847	Romo1	2010100O12Rik|AI853864	reactive oxygen species modulator 1	protein-coding
mm_166638.1	chr6	83179667	83179681	+	1	NA	promoter-TSS (NM_007835)	promoter-TSS (NM_007835)	85	NM_007835	13191	Mm.6919	NM_007835	ENSMUSG00000031865	Dctn1	AL022633|DAP-150|DP-150|Glued|p150|p150-glued|p150<glued>	dynactin 1	protein-coding
mm_166189.1	chr5	33105099	33105104	-	1	NA	intron (NM_019810, intron 1 of 14)	intron (NM_019810, intron 1 of 14)	882	NM_019810	20537	Mm.25237	NM_019810	ENSMUSG00000011034	Slc5a1	Sglt1	solute carrier family 5 (sodium/glucose cotransporter), member 1	protein-coding
mm_113148.1	chr13	24741199	24741203	+	1	NA	Intergenic	Intergenic	20736	NM_020567	57441	Mm.12239	NM_020567	ENSMUSG00000006715	Gmnn	AW546347|Gem	geminin	protein-coding
mm_68439.1	chr7	109960462	109960477	-	1	NA	promoter-TSS (NM_021494)	promoter-TSS (NM_021494)	1	NM_001311139	19347	Mm.21904	NM_021494	ENSMUSG00000035901	Dennd5a	1500012B19Rik|AJ245569|AW496491|ORF37|Rab6ip1|mKIAA1091	DENN/MADD domain containing 5A	protein-coding
mm_42878.1	chr5	122284373	122284397	+	1	NA	promoter-TSS (NM_177242)	promoter-TSS (NM_177242)	-13	NM_177242	320717	Mm.489670	NM_177242	ENSMUSG00000038582	Pptc7	9130017A15Rik|AA672638|AI848390|TA-PP2C	PTC7 protein phosphatase homolog	protein-coding
mm_13698.1	chr2	117123223	117123227	+	1	NA	intron (NM_033524, intron 1 of 6)	intron (NM_033524, intron 1 of 6)	2154	NM_033524	114715	Mm.245890	NM_033524	ENSMUSG00000027351	Spred1	5730461F13Rik|AL024345|AW047647	sprouty protein with EVH-1 domain 1, related sequence	protein-coding
mm_38228.1	chr4	136010535	136010545	-	1	NA	exon (NM_013736, exon 4 of 11)	exon (NM_013736, exon 4 of 11)	11109	NM_013736	27224	Mm.27663	NM_013736	ENSMUSG00000028668	Eloa	110kDa|AA408125|Tceb3|Tceb3a	elongin A	protein-coding
mm_164585.1	chr17	26087249	26087258	+	1	NA	intron (NM_011933, intron 4 of 8)	intron (NM_011933, intron 4 of 8)	2911	NM_011933	26378	Mm.292869	NM_011933	ENSMUSG00000036775	Decr2	-	2-4-dienoyl-Coenzyme A reductase 2, peroxisomal	protein-coding
mm_39919.1	chr5	31526990	31527034	+	1	NA	promoter-TSS (NM_009206)	promoter-TSS (NM_009206)	17	NM_001347328	20534	Mm.352407	NM_009206	ENSMUSG00000029141	Slc4a1ap	kanadaptin	solute carrier family 4 (anion exchanger), member 1, adaptor protein	protein-coding
mm_115242.1	chr13	110394481	110394498	+	1	NA	promoter-TSS (NM_152804)	promoter-TSS (NM_152804)	-555	NM_152804	20620	Mm.380	NM_152804	ENSMUSG00000021701	Plk2	Snk	polo-like kinase 2	protein-coding
mm_97147.1	chr11	75460694	75460704	+	1	NA	promoter-TSS (NR_030711)	promoter-TSS (NR_030711)	-840	NR_030711	100042498	Mm.482242	NR_030711	ENSMUSG00000085148	Mir22hg	2210403K04Rik|mir-22	Mir22 host gene (non-protein coding)	ncRNA
mm_28195.1	chr3	88143621	88143631	-	1	NA	intron (NM_133665, intron 1 of 10)	intron (NM_133665, intron 1 of 10)	1254	NM_001310593	17261	Mm.28184	NM_133665	ENSMUSG00000001419	Mef2d	C80750	myocyte enhancer factor 2D	protein-coding
mm_64558.1	chr7	144742110	144742116	+	1	NA	Intergenic	Intergenic	-3521	NM_001242349	101772	Mm.26700	NM_178642	ENSMUSG00000031075	Ano1	Tmem16a	anoctamin 1, calcium activated chloride channel	protein-coding
mm_59398.1	chr7	26764673	26764677	+	1	NA	intron (NM_007814, intron 6 of 8)	(TCCA)n|Simple_repeat|Simple_repeat	7533	NM_007814	13090	Mm.14098	NM_007814	ENSMUSG00000066704	Cyp2b19	CYPIIB19	cytochrome P450, family 2, subfamily b, polypeptide 19	protein-coding
mm_107690.1	chr12	55361349	55361391	+	1	NA	intron (NM_025373, intron 4 of 6)	intron (NM_025373, intron 4 of 6)	-9325	NR_035430	100316807		NR_035430	ENSMUSG00000080645	Mir1198	Mirn1198|mmu-mir-1198	microRNA 1198	ncRNA
mm_160191.1	chr7	57387086	57387086	-	1	NA	promoter-TSS (NM_008074)	promoter-TSS (NM_008074)	-186	NR_033504	791383	Mm.403104	NR_033504	ENSMUSG00000055048	Gm9962	ENSMUSG00000055048	predicted gene 9962	ncRNA
mm_115086.1	chr13	102698500	102698515	+	1	NA	intron (NM_008533, intron 1 of 2)	intron (NM_008533, intron 1 of 2)	4949	NM_008533	17079	Mm.373974	NM_008533	ENSMUSG00000021624	Cd180	F630107B15|Ly78|RP105	CD180 antigen	protein-coding
mm_75729.1	chr8	69184250	69184257	-	1	NA	Intergenic	(CGGGG)n|Simple_repeat|Simple_repeat	-24793	NM_001013379	234358	Mm.334577	NM_001013379	ENSMUSG00000059897	Zfp930	-	zinc finger protein 930	protein-coding
mm_147443.1	chr18	46525852	46525871	-	1	NA	5' UTR (NM_173423, exon 1 of 3)	5' UTR (NM_173423, exon 1 of 3)	110	NM_173423	240263	Mm.38249	NM_173423	ENSMUSG00000033319	Fem1c	2610312A07Rik|3632443A22Rik|AI646567	fem-1 homolog c (C.elegans)	protein-coding
mm_33737.1	chr4	134118590	134118605	+	1	NA	intron (NR_045571, intron 8 of 13)	intron (NR_045571, intron 8 of 13)	10156	NM_080559	73723	Mm.22240	NM_080559	ENSMUSG00000028843	Sh3bgrl3	1110004L05Rik|AU022188	SH3 domain binding glutamic acid-rich protein-like 3	protein-coding
mm_22459.1	chr3	3188125	3188132	+	1	NA	Intergenic	Intergenic	-319902	NM_013920	30942	Mm.330897	NM_013920	ENSMUSG00000017688	Hnf4g	NR2A2	hepatocyte nuclear factor 4, gamma	protein-coding
mm_25812.1	chr3	127790801	127790825	+	1	NA	intron (NM_145133, intron 1 of 2)	CpG	900	NM_145133	211550	Mm.31852	NM_145133	ENSMUSG00000046688	Tifa	T2bp	TRAF-interacting protein with forkhead-associated domain	protein-coding
mm_54663.1	chr6	39202995	39202998	-	1	NA	intron (NM_001033430, intron 1 of 19)	intron (NM_001033430, intron 1 of 19)	3777	NM_001033430	338523	Mm.293175	NM_001033430	ENSMUSG00000042599	Kdm7a	A630082K20Rik|BB041802|ENSMUSG00000073143|Jhdm1d|mKIAA1718	lysine (K)-specific demethylase 7A	protein-coding
mm_100798.1	chr11	4947106	4947134	-	1	NA	promoter-TSS (NM_001243043)	promoter-TSS (NM_001243043)	-401	NM_001243043	11764	Mm.274816	NM_007454	ENSMUSG00000009090	Ap1b1	Adtb1|b2b1660Clo	adaptor protein complex AP-1, beta 1 subunit	protein-coding
mm_16780.1	chr2	9887825	9887842	-	1	NA	intron (NR_040511, intron 1 of 3)	intron (NR_040511, intron 1 of 3)	1707	NR_040511	77682	Mm.488621	NR_040511	ENSMUSG00000079602	9230102O04Rik	-	RIKEN cDNA 9230102O04 gene	ncRNA
mm_57356.1	chr6	124757240	124757266	-	1	NA	promoter-TSS (NM_007881)	promoter-TSS (NM_007881)	-766	NM_007881	13498	Mm.333380	NM_007881	ENSMUSG00000004263	Atn1	Atr1|Drpla|atrophin-1	atrophin 1	protein-coding
mm_135089.1	chr16	34566508	34566510	-	1	NA	Intergenic	MER20|DNA|hAT-Charlie	-52482	NM_177357	545156	Mm.82274	NM_177357	ENSMUSG00000061751	Kalrn	2210407G14Rik|AV235988|DUET|E530005C20Rik|Gm539|Hapip|TRAD	kalirin, RhoGEF kinase	protein-coding
mm_70604.1	chr8	13354437	13354448	+	1	NA	intron (NM_001291766, intron 2 of 10)	intron (NM_001291766, intron 2 of 10)	15638	NM_009361	21781	Mm.925	NM_009361	ENSMUSG00000038482	Tfdp1	Dp1|Drtf1	transcription factor Dp 1	protein-coding
mm_136129.1	chr16	85901793	85901828	-	1	NA	promoter-TSS (NM_011782)	promoter-TSS (NM_011782)	-685	NM_011782	23794	Mm.112933	NM_011782	ENSMUSG00000022894	Adamts5	9530092O11Rik|ADAM-TS5|ADAMTS1|ADAMTS11|ADMP-2|AI481094|ASMP-2	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)	protein-coding
mm_19248.1	chr2	84773242	84773252	-	1	NA	exon (NM_009776, exon 3 of 8)	exon (NM_009776, exon 3 of 8)	2182	NM_009776	12258	Mm.38888	NM_009776	ENSMUSG00000023224	Serping1	C1INH|C1nh	serine (or cysteine) peptidase inhibitor, clade G, member 1	protein-coding
mm_41101.1	chr5	87694867	87694885	+	1	NA	exon (NM_001286023, exon 5 of 7)	exon (NM_001286023, exon 5 of 7)	4549	NM_001286020	12991	Mm.268737	NM_009972	ENSMUSG00000063157	Csn2	Csnb	casein beta	protein-coding
mm_54051.1	chr6	13838653	13838689	-	1	NA	5' UTR (NM_001330667, exon 2 of 3)	5' UTR (NM_001330667, exon 2 of 3)	1271	NM_001330666	64450	Mm.167625	NM_145066	ENSMUSG00000048216	Gpr85	2900026B03Rik	G protein-coupled receptor 85	protein-coding
mm_130963.1	chr15	103315073	103315084	-	1	NA	exon (NM_013866, exon 8 of 8)	exon (NM_013866, exon 8 of 8)	-4640	NM_030720	80910	Mm.160369	NM_030720	ENSMUSG00000063234	Gpr84	EX33	G protein-coupled receptor 84	protein-coding
mm_25264.1	chr3	104788843	104788855	+	1	NA	promoter-TSS (NM_007484)	promoter-TSS (NM_007484)	-185	NM_001291859	11853	Mm.262	NM_007484	ENSMUSG00000002233	Rhoc	AI324259|Arh9|Arhc	ras homolog family member C	protein-coding
mm_54683.1	chr6	39419968	39420074	-	1	NA	promoter-TSS (NM_001311109)	promoter-TSS (NM_001311109)	-245	NM_001311109	54484	Mm.270484	NM_018810	ENSMUSG00000029922	Mkrn1	RFP	makorin, ring finger protein, 1	protein-coding
mm_95429.1	chr11	50200656	50200676	+	1	NA	TTS (NM_026543)	TTS (NM_026543)	10154	NM_001290769	18412	Mm.40828	NM_011018	ENSMUSG00000015837	Sqstm1	A170|OSF-6|Osi|STAP|STONE14|p62	sequestosome 1	protein-coding
mm_10032.1	chr1	192137999	192138047	-	1	NA	promoter-TSS (NM_144814)	promoter-TSS (NM_144814)	17	NM_001290278	214742	Mm.207457	NM_144814	ENSMUSG00000037395	Rcor3	4921514E24Rik|C730034D20Rik|E130101E15Rik	REST corepressor 3	protein-coding
mm_78861.1	chr9	44397339	44397396	+	1	NA	promoter-TSS (NM_008063)	promoter-TSS (NM_008063)	272	NM_001293630	14385	Mm.30087	NM_008063	ENSMUSG00000032114	Slc37a4	100043178|G6PT|G6pt1|GSD-1b|mG6PT	solute carrier family 37 (glucose-6-phosphate transporter), member 4	protein-coding
mm_8680.1	chr1	156937837	156937842	-	1	NA	intron (NR_027640, intron 1 of 19)	B1_Mur2|SINE|Alu	1548	NM_001159966	78255	Mm.28376	NM_023884	ENSMUSG00000026594	Ralgps2	1810020P17Rik|2210408F11Rik|4921528G01Rik|9130014M22Rik|AU043409|AW046161	Ral GEF with PH domain and SH3 binding motif 2	protein-coding
mm_35522.1	chr4	41207059	41207066	-	1	NA	exon (NM_026872, exon 14 of 29)	exon (NM_026872, exon 14 of 29)	68073	NM_026872	68926	Mm.41864	NM_026872	ENSMUSG00000028433	Ubap2	1190005K07Rik|AA408600|AU045235|UBAP-2|mKIAA1491	ubiquitin-associated protein 2	protein-coding
mm_53226.1	chr6	127149390	127149425	+	1	NA	promoter-TSS (NR_040275)	promoter-TSS (NR_040275)	18	NR_040274	77558	Mm.358918	NR_040273	ENSMUSG00000097166	9330179D12Rik	-	RIKEN cDNA 9330179D12 gene	ncRNA
mm_7194.1	chr1	92950701	92950731	-	1	NA	promoter-TSS (NR_015525)	promoter-TSS (NR_015525)	-126	NR_015525	100037260	Mm.442236	NR_015525	ENSMUSG00000100632	9430060I03Rik	-	RIKEN cDNA 9430060I03 gene	ncRNA
mm_102352.1	chr11	58207590	58207591	-	1	NA	TTS (NM_018738)	TTS (NM_018738)	-7387	NM_019440	54396	Mm.458517	NM_019440	ENSMUSG00000069874	Irgm2	AI481100|GTPI|Ifggd2|Iigp2	immunity-related GTPase family M member 2	protein-coding
mm_8986.1	chr1	165697459	165697466	-	1	NA	intron (NM_178593, intron 1 of 6)	RLTR17B_Mm|LTR|ERVK	10632	NM_178593	226594	Mm.265552	NM_178593	ENSMUSG00000040723	Rcsd1	A430105K13Rik|BC025872|CapZIP	RCSD domain containing 1	protein-coding
mm_36472.1	chr4	82705901	82705909	-	1	NA	Intergenic	Intergenic	153756	NM_026647	68268	Mm.32047	NM_026647	ENSMUSG00000028403	Zdhhc21	9130404H11Rik|AL024349|D130004H04Rik|dep	zinc finger, DHHC domain containing 21	protein-coding
mm_147323.1	chr18	42261979	42262013	-	1	NA	promoter-TSS (NM_134137)	promoter-TSS (NM_134137)	75	NM_134137	107045	Mm.312170	NM_134137	ENSMUSG00000024493	Lars	2310045K21Rik|3110009L02Rik|AW536573|mKIAA1352	leucyl-tRNA synthetase	protein-coding
mm_111326.1	chr12	86470037	86470057	-	1	NA	intron (NM_011934, intron 1 of 6)	CpG	48403	NM_011934	26380	Mm.235550	NM_011934	ENSMUSG00000021255	Esrrb	Err2|Errb|Estrrb|Nr3b2	estrogen related receptor, beta	protein-coding
mm_168929.1	chr12	64786191	64786201	+	1	NA	Intergenic	Intergenic	-131715	NM_001025605	217648	Mm.341586	NM_001025605	ENSMUSG00000047227	Gm527	-	predicted gene 527	protein-coding
mm_5513.1	chr1	37536233	37536236	-	1	NA	5' UTR (NM_173870, exon 2 of 16)	5' UTR (NM_173870, exon 2 of 16)	170	NM_001290801	269181	Mm.25861	NM_173870	ENSMUSG00000026110	Mgat4a	9530018I07Rik|GnT-IVa|glcNAc-T-IVa	mannoside acetylglucosaminyltransferase 4, isoenzyme A	protein-coding
mm_64930.1	chr7	16285993	16286005	-	1	NA	intron (NM_001136471, intron 1 of 13)	intron (NM_001136471, intron 1 of 13)	796	NM_001136471	243846	Mm.482401	NM_172297	ENSMUSG00000041375	Ccdc9	2600011L02Rik	coiled-coil domain containing 9	protein-coding
mm_166079.1	chr4	137484695	137484697	+	1	NA	intron (NM_008305, intron 1 of 96)	intron (NM_008305, intron 1 of 96)	15893	NM_008305	15530	Mm.273662	NM_008305	ENSMUSG00000028763	Hspg2	AI852380|Pcn|Plc|per	perlecan (heparan sulfate proteoglycan 2)	protein-coding
mm_139580.1	chr17	57080689	57080721	+	1	NA	exon (NM_009451, exon 4 of 4)	exon (NM_009451, exon 4 of 4)	-2195	NM_153551	70785	Mm.284447	NM_153551	ENSMUSG00000002668	Dennd1c	4432409M07Rik	DENN/MADD domain containing 1C	protein-coding
mm_104012.1	chr11	85234868	85234914	-	1	NA	promoter-TSS (NR_028329)	promoter-TSS (NR_028329)	229	NM_025825	66884	Mm.271997	NM_025825	ENSMUSG00000018481	Appbp2	1300003O07Rik|AI465480|PAT1	amyloid beta precursor protein (cytoplasmic tail) binding protein 2	protein-coding
mm_80992.1	chr9	103368532	103368533	+	1	NA	Intergenic	B4A|SINE|B4	-2752	NM_001134426	321022	Mm.261025	NM_175565	ENSMUSG00000032803	Cdv3	2510010F10Rik|C230084J24Rik|C79446|TPP36	carnitine deficiency-associated gene expressed in ventricle 3	protein-coding
mm_151923.1	chr19	5799985	5800002	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	2679	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_86327.1	chr9	123061787	123061789	-	1	NA	exon (NM_177911, exon 11 of 14)	exon (NM_177911, exon 11 of 14)	27047	NM_177911	331046	Mm.195309	NM_177911	ENSMUSG00000025787	Tgm4	9530008N10Rik|Eapa1|TGP	transglutaminase 4 (prostate)	protein-coding
mm_143380.1	chr17	67950985	67950996	-	1	NA	promoter-TSS (NM_001347410)	promoter-TSS (NM_001347410)	-50	NM_001347410	268970	Mm.9935	NM_172964	ENSMUSG00000024043	Arhgap28	AU044757|AW550892|E130310N06	Rho GTPase activating protein 28	protein-coding
mm_149661.1	chr19	18730631	18730649	+	1	NA	Intergenic	Intergenic	17404	NM_177640	225995	Mm.28101	NM_177640	ENSMUSG00000047044	D030056L22Rik	-	RIKEN cDNA D030056L22 gene	protein-coding
mm_88245.1	chr10	72657325	72657339	+	1	NA	exon (NM_025635, exon 7 of 8)	exon (NM_025635, exon 7 of 8)	2486	NM_001293683	52696	Mm.62876	NM_025635	ENSMUSG00000019923	Zwint	2010007E07Rik|2600001N01Rik|D10Ertd749e|Zwint-1	ZW10 interactor	protein-coding
mm_121603.1	chr14	8114397	8114436	-	1	NA	intron (NM_178279, intron 1 of 18)	intron (NM_178279, intron 1 of 18)	16203	NM_178279	218699	Mm.29515	NM_145458	ENSMUSG00000033885	Pxk	C230080L11Rik|D14Ertd813e|MONaKA	PX domain containing serine/threonine kinase	protein-coding
mm_146679.1	chr18	12819843	12819863	-	1	NA	promoter-TSS (NR_045524)	promoter-TSS (NR_045524)	54	NR_045524	64291	Mm.259470	NM_020573	ENSMUSG00000044252	Osbpl1a	G430090F17Rik|Gm753|ORP-1|Osbpl1b	oxysterol binding protein-like 1A	protein-coding
mm_239.1	chr1	19209015	19209033	+	1	NA	5' UTR (NM_009334, exon 1 of 7)	5' UTR (NM_009334, exon 1 of 7)	110	NM_001286340	21419	Mm.137021	NM_009334	ENSMUSG00000025927	Tfap2b	AI606113|AP-2(beta)|E130018K07Rik|Tcfap2b	transcription factor AP-2 beta	protein-coding
mm_13378.1	chr2	103795949	103795962	+	1	NA	intron (NM_001111289, intron 1 of 17)	intron (NM_001111289, intron 1 of 17)	1123	NM_001111290	53872	Mm.427589	NM_016739	ENSMUSG00000027184	Caprin1	AL022980|Caprin-1|Gpiap|Gpiap1|Mmgpip137|P137|rng105	cell cycle associated protein 1	protein-coding
mm_83583.1	chr9	48340793	48340809	-	1	NA	promoter-TSS (NM_030069)	promoter-TSS (NM_030069)	97	NM_030069	78252	Mm.31626	NM_030069	ENSMUSG00000032028	Nxpe2	4432416J03Rik|AI323362|Fam55b	neurexophilin and PC-esterase domain family, member 2	protein-coding
mm_21515.1	chr2	163627976	163627996	-	1	NA	exon (NM_012032, exon 8 of 10)	exon (NM_012032, exon 8 of 10)	-16864	NR_028113	68386	Mm.410649	NR_028113	ENSMUSG00000058812	0610039K10Rik	-	RIKEN cDNA 0610039K10 gene	ncRNA
mm_78112.1	chr9	20642703	20642712	+	1	NA	promoter-TSS (NM_013911)	promoter-TSS (NM_013911)	99	NM_013911	30843	Mm.24608	NM_013911	ENSMUSG00000066892	Fbxl12	3110048D16Rik|Fbl12	F-box and leucine-rich repeat protein 12	protein-coding
mm_66701.1	chr7	45920682	45920694	-	1	NA	5' UTR (NM_001146346, exon 1 of 5)	5' UTR (NM_001146346, exon 1 of 5)	161	NM_001146346	13732	Mm.20829	NM_010129	ENSMUSG00000040212	Emp3	H-4|H4|HNMP-1|MI-35|Ymp	epithelial membrane protein 3	protein-coding
mm_74000.1	chr8	120756306	120756346	+	1	NA	3' UTR (NM_008320, exon 9 of 9)	3' UTR (NM_008320, exon 9 of 9)	17687	NM_001301811	15900	Mm.334861	NM_008320	ENSMUSG00000041515	Irf8	AI893568|ICSBP|IRF-8|Icsbp1|Myls	interferon regulatory factor 8	protein-coding
mm_19140.1	chr2	80447248	80447266	-	1	NA	5' UTR (NM_011356, exon 1 of 6)	5' UTR (NM_011356, exon 1 of 6)	139	NM_011356	20378	Mm.427436	NM_011356	ENSMUSG00000027004	Frzb	Frp|Sfrp3|frezzled|fritz|frzb-1	frizzled-related protein	protein-coding
mm_71730.1	chr8	61984715	61984720	+	1	NA	intron (NM_001293783, intron 22 of 37)	intron (NM_001293783, intron 22 of 37)	56630	NM_001293783	234311	Mm.275233	NM_144928	ENSMUSG00000037921	Ddx60	9830118M07	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	protein-coding
mm_18364.1	chr2	59160625	59160635	-	1	NA	promoter-TSS (NM_026361)	promoter-TSS (NM_026361)	-220	NM_026361	227937	Mm.260938	NM_026361	ENSMUSG00000026991	Pkp4	5031422I09Rik|9430019K17Rik|Armrp|p0071	plakophilin 4	protein-coding
mm_25458.1	chr3	108534127	108534133	+	1	NA	intron (NM_001346518, intron 1 of 21)	intron (NM_001346518, intron 1 of 21)	2392	NM_001033304	229722	Mm.316890	NM_001033304	ENSMUSG00000040412	5330417C22Rik	BB183350	RIKEN cDNA 5330417C22 gene	protein-coding
mm_67883.1	chr7	99348999	99349049	-	1	NA	exon (NM_009825, exon 2 of 5)	exon (NM_009825, exon 2 of 5)	4215	NM_009825	12406	Mm.22708	NM_009825	ENSMUSG00000070436	Serpinh1	BERF-1|Cbp1|Cbp2|Hsp47|J6|Serpinh2|gp46	serine (or cysteine) peptidase inhibitor, clade H, member 1	protein-coding
mm_12915.1	chr2	84936584	84936606	+	1	NA	promoter-TSS (NM_021398)	promoter-TSS (NM_021398)	-51	NM_021398	58207	Mm.290729	NM_021398	ENSMUSG00000027074	Slc43a3	Eeg1|SEEEG-1	solute carrier family 43, member 3	protein-coding
mm_130777.1	chr15	101488212	101488220	-	1	NA	exon (NM_016879, exon 4 of 10)	exon (NM_016879, exon 4 of 10)	3087	NM_016879	53622	Mm.347934	NM_016879		Krt85	AA589597|BB007925|Hb5|Krt2-18	keratin 85	protein-coding
mm_37821.1	chr4	131873418	131873445	-	1	NA	promoter-TSS (NM_020587)	promoter-TSS (NM_020587)	-208	NM_020587	57317	Mm.2478	NM_020587	ENSMUSG00000028911	Srsf4	5730499P16Rik|AW550192|MNCb-2616|SRp75|Sfrs4	serine/arginine-rich splicing factor 4	protein-coding
mm_83630.1	chr9	49079359	49079378	-	1	NA	TTS (NM_012039)	TTS (NM_012039)	-23411	NM_030709	80893	Mm.72799	NM_030709	ENSMUSG00000032268	Tmprss5	spinesin	transmembrane protease, serine 5 (spinesin)	protein-coding
mm_164256.1	chr15	99692190	99692199	+	1	NA	5' UTR (NM_001289791, exon 1 of 10)	5' UTR (NM_001289791, exon 1 of 10)	439	NM_001289791	11419	Mm.440107	NM_009597	ENSMUSG00000023017	Asic1	AI843610|ASIC|ASIC1a|Accn2|B530003N02Rik|BNaC2	acid-sensing (proton-gated) ion channel 1	protein-coding
mm_10115.1	chr2	3723198	3723202	+	1	NA	intron (NM_025626, intron 1 of 3)	intron (NM_025626, intron 1 of 3)	9742	NM_025626	66540	Mm.277864	NM_025626	ENSMUSG00000026655	Fam107b	3110001A13Rik|AA589595|AA959793|AI132312	family with sequence similarity 107, member B	protein-coding
mm_2021.1	chr1	87128147	87128162	+	1	NA	TTS (NM_007432)	TTS (NM_007432)	3146	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_88418.1	chr10	77191525	77191543	+	1	NA	Intergenic	Intergenic	-25004	NM_009929	12822	Mm.4352	NM_009929	ENSMUSG00000001435	Col18a1	-	collagen, type XVIII, alpha 1	protein-coding
mm_170529.1	chr19	34583574	34583574	+	1	NA	promoter-TSS (NM_010501)	promoter-TSS (NM_010501)	45	NM_010501	15959	Mm.426079	NM_010501	ENSMUSG00000074896	Ifit3	Ifi49|P49	interferon-induced protein with tetratricopeptide repeats 3	protein-coding
mm_36567.1	chr4	87806277	87806292	-	1	NA	promoter-TSS (NM_029931)	promoter-TSS (NM_029931)	39	NM_001286158	70122	Mm.288898	NM_027326	ENSMUSG00000028496	Mllt3	2210011H10Rik|2610012I03Rik|3830408D16Rik|Af9|D4Ertd321e	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 3	protein-coding
mm_99464.1	chr11	102435346	102435370	+	1	NA	exon (NM_008175, exon 10 of 13)	exon (NM_008175, exon 10 of 13)	5036	NM_008175	14824	Mm.1568	NM_008175	ENSMUSG00000034708	Grn	Pgrn|epithelin	granulin	protein-coding
mm_68704.1	chr7	119720743	119720803	-	1	NA	promoter-TSS (NM_145585)	promoter-TSS (NM_145585)	25	NM_145585	233802	Mm.26392	NM_145585	ENSMUSG00000030942	Thumpd1	6330575P11Rik	THUMP domain containing 1	protein-coding
mm_65948.1	chr7	30419803	30419872	-	1	NA	promoter-TSS (NM_011827)	promoter-TSS (NM_011827)	17	NM_011827	23900	Mm.379050	NM_011827	ENSMUSG00000064109	Hcst	DAP10|KAP10	hematopoietic cell signal transducer	protein-coding
mm_140036.1	chr17	74339128	74339160	+	1	NA	exon (NM_001162870, exon 1 of 17)	exon (NM_001162870, exon 1 of 17)	157	NM_016962	50850	Mm.19804	NM_016962	ENSMUSG00000024068	Spast	Spg4|mKIAA1083	spastin	protein-coding
mm_125969.1	chr15	76274391	76274402	+	1	NA	intron (NM_028852, intron 1 of 4)	B1_Mur4|SINE|Alu	-4557	NR_045747	100038659	Mm.448549	NR_045747		Mirt2	ENSMUSG00000075583|Gm10872|Gm24562	myocardial infraction associated transcript 2	ncRNA
mm_145726.1	chr18	64075296	64075299	+	1	NA	Intergenic	Intergenic	-179062	NM_009182	20451	Mm.252110	NM_009182	ENSMUSG00000056812	St8sia3	AI847333|ST8SiaIII|Siat8c	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3	protein-coding
mm_84039.1	chr9	57765912	57765922	-	1	NA	promoter-TSS (NM_007713)	promoter-TSS (NM_007713)	-57	NM_007713	102414	Mm.25720	NM_007713	ENSMUSG00000032316	Clk3	AI256811	CDC-like kinase 3	protein-coding
mm_29952.1	chr3	133091799	133091847	-	1	NA	promoter-TSS (NM_026231)	promoter-TSS (NM_026231)	-32	NM_027927	71793	Mm.246726	NM_027927	ENSMUSG00000028016	Ints12	1110020M19Rik|2810027J24Rik|4930529N21Rik|A230056J18Rik|AI666778|Phf22|int12	integrator complex subunit 12	protein-coding
mm_61603.1	chr7	80027486	80027507	+	1	NA	intron (NM_175433, intron 1 of 4)	CpG	1268	NM_175433	209225	Mm.290925	NM_175433	ENSMUSG00000048897	Zfp710	5430400N05Rik|9830165K13|AI324798|Znf710	zinc finger protein 710	protein-coding
mm_160169.1	chr7	45014344	45014344	-	1	NA	intron (NM_001008422, intron 1 of 10)	MLT1G3|LTR|ERVL-MaLR	-1857	NR_106021	102466218		NR_106021	ENSMUSG00000098839	Mir7054	Gm27557|mmu-mir-7054	microRNA 7054	ncRNA
mm_17694.1	chr2	32338046	32338066	-	1	NA	non-coding (NR_125959, exon 5 of 22)	non-coding (NR_125959, exon 5 of 22)	15273	NM_001301737	13429	Mm.44736	NM_010065	ENSMUSG00000026825	Dnm1	AI838169|Dnm|Ftfl|mKIAA4093	dynamin 1	protein-coding
mm_91812.1	chr10	54014546	54014556	-	1	NA	intron (NM_008548, intron 4 of 12)	intron (NM_008548, intron 4 of 12)	61245	NM_008548	17155	Mm.117294	NM_008548	ENSMUSG00000003746	Man1a	Man1a1|PCR1	mannosidase 1, alpha	protein-coding
mm_77438.1	chr8	121580508	121580541	-	1	NA	Intergenic	Intergenic	-1718	NM_133765	76454	Mm.24829	NM_133765	ENSMUSG00000052934	Fbxo31	1110003O08Rik|2310046N15Rik|Fbx14|Fbxo14	F-box protein 31	protein-coding
mm_143812.1	chr17	83706841	83706884	-	1	NA	intron (NM_001171053, intron 1 of 13)	intron (NM_001171053, intron 1 of 13)	699	NM_001171052	116871	Mm.277668	NM_054082	ENSMUSG00000055817	Mta3	1110002J22Rik|mKIAA1266	metastasis associated 3	protein-coding
mm_137478.1	chr17	26885157	26885184	+	1	NA	Intergenic	Intergenic	-31921	NM_053173	16580	Mm.491138	NM_016761	ENSMUSG00000024301	Kifc5b	Hset|KNSL2|Kifc5a	kinesin family member C5B	protein-coding
mm_166430.1	chr5	137166031	137166052	-	1	NA	Intergenic	Intergenic	-49834	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_7295.1	chr1	97908616	97908619	-	1	NA	intron (NM_013626, intron 7 of 25)	(A)n|Simple_repeat|Simple_repeat	138445	NM_026250	252876	Mm.86090	NM_026250	ENSMUSG00000026333	Gin1	4930429M06Rik|8430411H10Rik|Gin-1|Zh2c2	gypsy retrotransposon integrase 1	protein-coding
mm_101026.1	chr11	8579406	8579430	-	1	NA	intron (NM_001083587, intron 3 of 30)	intron (NM_001083587, intron 3 of 30)	85117	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_80229.1	chr9	72669985	72670004	+	1	NA	exon (NM_010890, exon 2 of 29)	exon (NM_010890, exon 2 of 29)	7647	NM_010890	17999	Mm.279923	NM_010890	ENSMUSG00000032216	Nedd4	AA959633|AL023035|AU019897|E430025J12Rik|Nedd4-1|Nedd4a|mKIAA0093	neural precursor cell expressed, developmentally down-regulated 4	protein-coding
mm_86582.1	chr10	13008424	13008437	+	1	NA	promoter-TSS (NM_175102)	promoter-TSS (NM_175102)	-20	NM_175102	66125	Mm.29743	NM_175102	ENSMUSG00000078348	Sf3b5	10kDa|1110005L13Rik|AU043053|Sf3b10	splicing factor 3b, subunit 5	protein-coding
mm_148737.1	chr19	5924961	5924996	+	1	NA	promoter-TSS (NM_026772)	promoter-TSS (NM_026772)	-162	NM_026772	104252	Mm.491103	NM_026772	ENSMUSG00000045664	Cdc42ep2	1110008C05Rik|Borg1|Cep2|D19Bwg1013e	CDC42 effector protein (Rho GTPase binding) 2	protein-coding
mm_98653.1	chr11	96263892	96263911	+	1	NA	intron (NR_037977, intron 2 of 2)	intron (NR_037977, intron 2 of 2)	-1263	NR_029721	387191		NR_029721	ENSMUSG00000065546	Mir196a-1	Mirn196|Mirn196a-1|miR-196|mir-196a-1	microRNA 196a-1	ncRNA
mm_38213.1	chr4	135946366	135946382	-	1	NA	promoter-TSS (NM_008254)	promoter-TSS (NM_008254)	-79	NM_008254	15356	Mm.482102	NM_008254	ENSMUSG00000028672	Hmgcl	AW476067|HL	3-hydroxy-3-methylglutaryl-Coenzyme A lyase	protein-coding
mm_102725.1	chr11	67237572	67237609	-	1	NA	promoter-TSS (NM_010855)	promoter-TSS (NM_010855)	-222	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_22577.1	chr3	10366928	10366963	+	1	NA	promoter-TSS (NM_025519)	promoter-TSS (NM_025519)	-28	NM_025519	66371	Mm.366147	NM_025519	ENSMUSG00000027536	Chmp4c	2010012P02Rik|2210015K02Rik|2310010I16Rik|Shax3|Snf7-3	charged multivesicular body protein 4C	protein-coding
mm_83427.1	chr9	44980391	44980437	-	1	NA	promoter-TSS (NM_009850)	promoter-TSS (NM_009850)	17	NM_009850	12502	Mm.335106	NM_009850	ENSMUSG00000002033	Cd3g	Ctg-3|Ctg3|T3g	CD3 antigen, gamma polypeptide	protein-coding
mm_84890.1	chr9	79770388	79770428	-	1	NA	3' UTR (NM_133718, exon 7 of 7)	3' UTR (NM_133718, exon 7 of 7)	-10555	NM_009945	12866	Mm.152627	NM_009945	ENSMUSG00000032330	Cox7a2	COX7AL|Cox7a3|CoxVIIa-L	cytochrome c oxidase subunit VIIa 2	protein-coding
mm_160493.1	chr8	129065492	129065492	-	1	NA	promoter-TSS (NM_029061)	promoter-TSS (NM_029061)	0	NM_029061	74703	Mm.196017	NM_029061	ENSMUSG00000025808	Ccdc7a	4930517G15Rik|4930540C21Rik|Biot2|Ccdc7	coiled-coil domain containing 7A	protein-coding
mm_138891.1	chr17	43567988	43568005	+	1	NA	promoter-TSS (NM_013737)	promoter-TSS (NM_013737)	-455	NM_013737	27226	Mm.9277	NM_013737	ENSMUSG00000023913	Pla2g7	PAF-AH|R75400	phospholipase A2, group VII (platelet-activating factor acetylhydrolase, plasma)	protein-coding
mm_30619.1	chr4	8553748	8553751	+	1	NA	intron (NM_021518, intron 1 of 7)	intron (NM_021518, intron 1 of 7)	18105	NM_021518	59021	Mm.397471	NM_021518	ENSMUSG00000047187	Rab2a	9330148M11Rik|C80220|Rab2	RAB2A, member RAS oncogene family	protein-coding
mm_57060.1	chr6	122494211	122494213	-	1	NA	Intergenic	Intergenic	-7907	NM_027664	108653	Mm.277939	NM_027664	ENSMUSG00000040649	Rimklb	4931417E21Rik|4933426K21Rik|AA097693|AI325948|AU015629|Naags	ribosomal modification protein rimK-like family member B	protein-coding
mm_163792.1	chr14	13284625	13284643	-	1	NA	promoter-TSS (NM_028052)	promoter-TSS (NM_028052)	4	NR_121589	328354	Mm.252404	NM_177813	ENSMUSG00000051729	Gm5087	C630025C03|EG328354	predicted gene 5087	ncRNA
mm_112896.1	chr13	20885358	20885367	+	1	NA	intron (NM_012054, intron 4 of 20)	MLT1D|LTR|ERVL-MaLR	91249	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_85502.1	chr9	106199139	106199155	-	1	NA	promoter-TSS (NM_026447)	promoter-TSS (NM_026447)	86	NM_026447	67905	Mm.23018	NM_026447	ENSMUSG00000020253	Ppm1m	2810423O19Rik|AW610647|C77250|PP2Ceta	protein phosphatase 1M	protein-coding
mm_10133.1	chr2	4017728	4017745	+	1	NA	promoter-TSS (NM_001347086)	promoter-TSS (NM_001347086)	53	NM_001347086	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding
mm_18133.1	chr2	45017062	45017076	-	1	NA	intron (NM_001289521, intron 3 of 8)	intron (NM_001289521, intron 3 of 8)	6108	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_6467.1	chr1	74036203	74036224	-	1	NA	intron (NM_027884, intron 3 of 34)	intron (NM_027884, intron 3 of 34)	88234	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_37158.1	chr4	117131438	117131468	-	1	NA	exon (NM_013807, exon 8 of 15)	exon (NM_013807, exon 8 of 15)	2510	NM_013807	12795	Mm.259022	NM_013807	ENSMUSG00000028680	Plk3	Cnk|Fnk|PLK-3|PRK	polo-like kinase 3	protein-coding
mm_76023.1	chr8	75085087	75085097	-	1	NA	Intergenic	Intergenic	-8526	NM_010442	15368	Mm.276389	NM_010442	ENSMUSG00000005413	Hmox1	D8Wsu38e|HO-1|HO1|Hemox|Hmox|Hsp32	heme oxygenase 1	protein-coding
mm_131504.1	chr16	17421297	17421304	+	1	NA	intron (NM_023348, intron 2 of 4)	intron (NM_023348, intron 2 of 4)	-14986	NM_001001983	224020	Mm.5718	NM_001001983	ENSMUSG00000041720	Pi4ka	Pik4ca	phosphatidylinositol 4-kinase, catalytic, alpha polypeptide	protein-coding
mm_49464.1	chr6	29433132	29433165	+	1	NA	promoter-TSS (NM_001081185)	promoter-TSS (NM_001081185)	-5	NM_001081185	68794	Mm.39046	NM_026839	ENSMUSG00000068699	Flnc	1110055E19Rik|ABP-280|ABPL|Fln2	filamin C, gamma	protein-coding
mm_145641.1	chr18	61117630	61117646	+	1	NA	TTS (NR_105949)	TTS (NR_105949)	170	NR_105949	102466212		NR_105949	ENSMUSG00000098389	Mir6983	Gm27496|mmu-mir-6983	microRNA 6983	ncRNA
mm_76344.1	chr8	84723831	84723864	-	1	NA	exon (NM_001081982, exon 7 of 10)	exon (NM_001081982, exon 7 of 10)	22390	NM_008535	17095	Mm.4925	NM_008535	ENSMUSG00000034041	Lyl1	Lyl-1|bHLHa18	lymphoblastomic leukemia 1	protein-coding
mm_43321.1	chr5	134986277	134986292	+	1	NA	promoter-TSS (NM_009902)	promoter-TSS (NM_009902)	70	NM_009902	12739	Mm.158662	NM_009902	ENSMUSG00000070473	Cldn3	AI182374|Cpetr2|mRVP1	claudin 3	protein-coding
mm_18492.1	chr2	62606254	62606296	-	1	NA	exon (NM_027835, exon 10 of 16)	exon (NM_027835, exon 10 of 16)	-32254	NM_007986	14089	Mm.41816	NM_007986	ENSMUSG00000000392	Fap	SIMP	fibroblast activation protein	protein-coding
mm_28694.1	chr3	95529521	95529570	-	1	NA	exon (NM_021281, exon 2 of 8)	exon (NM_021281, exon 2 of 8)	2759	NM_001267695	13040	Mm.3619	NM_021281	ENSMUSG00000038642	Ctss	Cats	cathepsin S	protein-coding
mm_116361.1	chr13	40730417	40730429	-	1	NA	promoter-TSS (NM_001122948)	promoter-TSS (NM_001122948)	34	NM_001122948	21418	Mm.85544	NM_011547	ENSMUSG00000021359	Tfap2a	AP-2|AP2alpha|Ap-2 (a)|Ap2|Ap2tf|Tcfap2a	transcription factor AP-2, alpha	protein-coding
mm_139286.1	chr17	48300335	48300343	+	1	NA	5' UTR (NM_001033405, exon 1 of 5)	5' UTR (NM_001033405, exon 1 of 5)	301	NM_001033405	328833	Mm.329104	NM_001033405	ENSMUSG00000071068	Treml2	AW049306|Gm750|Tlt2	triggering receptor expressed on myeloid cells-like 2	protein-coding
mm_122120.1	chr14	31019005	31019042	-	1	NA	promoter-TSS (NM_001081251)	promoter-TSS (NM_001081251)	108	NM_153547	30877	Mm.88512	NM_153547	ENSMUSG00000042354	Gnl3	Ns	guanine nucleotide binding protein-like 3 (nucleolar)	protein-coding
mm_154701.1	chrX	8271569	8271578	+	1	NA	intron (NM_172479, intron 1 of 15)	intron (NM_172479, intron 1 of 15)	192	NM_172479	209837	Mm.6055	NM_172479	ENSMUSG00000031170	Slc38a5	C81234|E330031E14|JM24|SN2	solute carrier family 38, member 5	protein-coding
mm_96354.1	chr11	67010628	67010638	+	1	NA	Intergenic	Intergenic	-14521	NM_001291042	338369	Mm.128138	NM_177392	ENSMUSG00000050270	Tmem220	-	transmembrane protein 220	protein-coding
mm_74191.1	chr8	123653904	123653908	+	1	NA	promoter-TSS (NM_133955)	promoter-TSS (NM_133955)	-23	NM_133955	69581	Mm.168257	NM_133955	ENSMUSG00000039960	Rhou	2310026M05Rik|AI182090|Arhu|CDC42L1|G28K|WRCH-1|WRCH1|mG28K	ras homolog family member U	protein-coding
mm_79377.1	chr9	54699549	54699565	+	1	NA	promoter-TSS (NM_021422)	promoter-TSS (NM_021422)	-2	NM_021422	58233	Mm.489676	NM_021422	ENSMUSG00000032285	Dnaja4	1110021L12Rik|AV358213|Dj4|Hsj4|mmDjA4	DnaJ heat shock protein family (Hsp40) member A4	protein-coding
mm_170786.1	chr2	174980991	174981009	-	1	NA	Intergenic	Intergenic	86769	NM_001085546	664987		NM_001085546	ENSMUSG00000078905	Gm14393	OTTMUSG00000016546	predicted gene 14393	protein-coding
mm_132743.1	chr16	44139150	44139161	+	1	NA	promoter-TSS (NM_007508)	promoter-TSS (NM_007508)	-136	NM_007508	11964	Mm.217787	NM_007508	ENSMUSG00000052459	Atp6v1a	AI647066|Atp6a1|Atp6a2|Atp6v1a1|VA68|VPP2	ATPase, H+ transporting, lysosomal V1 subunit A	protein-coding
mm_32918.1	chr4	119136715	119136719	+	1	NA	3' UTR (NM_011400, exon 10 of 10)	3' UTR (NM_011400, exon 10 of 10)	27972	NM_011400	20525	Mm.21002	NM_011400	ENSMUSG00000028645	Slc2a1	Glut-1|Glut1	solute carrier family 2 (facilitated glucose transporter), member 1	protein-coding
mm_158429.1	chrX	139871479	139871489	-	1	NA	5' UTR (NM_001193309, exon 1 of 17)	5' UTR (NM_001193309, exon 1 of 17)	170	NM_029413	75746	Mm.23269	NM_029413	ENSMUSG00000031434	Morc4	1600017G11Rik|5630401M14Rik|AA117449|Zcwcc2	microrchidia 4	protein-coding
mm_167019.1	chr7	64971457	64971457	+	1	NA	intron (NM_183087, intron 2 of 9)	Lx8b|LINE|L1	-98417	NM_023239	66647	Mm.19944	NM_023239	ENSMUSG00000070520	Ndnl2	5730494G16Rik|AI642138|BB044375|HCA4|Mageg1|Nsmce3|mage-g1	necdin-like 2	protein-coding
mm_102855.1	chr11	69398946	69398999	-	1	NA	promoter-TSS (NM_025915)	promoter-TSS (NM_025915)	-738	NM_025915	67020	Mm.390406	NM_025915	ENSMUSG00000045377	Tmem88	2600017H02Rik	transmembrane protein 88	protein-coding
mm_18898.1	chr2	76713862	76713899	-	1	NA	exon (NM_011652, exon 307 of 313)	exon (NM_011652, exon 307 of 313)	38565	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_112099.1	chr12	112785247	112785276	-	1	NA	Intergenic	Intergenic	-23714	NM_145450	217887	Mm.186678	NM_145450	ENSMUSG00000037594	BC022687	AW050009|C130001I08Rik|Flj20080	cDNA sequence BC022687	protein-coding
mm_150425.1	chr19	37436622	37436625	+	1	NA	intron (NM_008245, intron 1 of 3)	intron (NM_008245, intron 1 of 3)	1782	NM_008245	15242	Mm.33896	NM_008245	ENSMUSG00000024986	Hhex	Hex|Hex1|Hhex-rs2|Prh|Prhx	hematopoietically expressed homeobox	protein-coding
mm_173312.1	chrY	90735020	90735021	+	1	NA	Intergenic	IMPB_01|Satellite|Satellite	20030	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_21148.1	chr2	154407981	154408003	-	1	NA	promoter-TSS (NM_009228)	promoter-TSS (NM_009228)	92	NM_009228	20648	Mm.1541	NM_009228	ENSMUSG00000027488	Snta1	AW228934|Snt1	syntrophin, acidic 1	protein-coding
mm_110851.1	chr12	73198567	73198574	-	1	NA	intron (NM_008612, intron 6 of 7)	L1MA5A|LINE|L1	74853	NM_008612	17420	Mm.246750	NM_008612	ENSMUSG00000021103	Mnat1	E130115E11Rik|MAT1|P36	menage a trois 1	protein-coding
mm_139610.1	chr17	57316620	57316632	+	1	NA	intron (NM_001163816, intron 23 of 25)	RSINE1|SINE|B4	37526	NM_001163815	22324	Mm.248172	NM_011691	ENSMUSG00000034116	Vav1	Vav|vav-T	vav 1 oncogene	protein-coding
mm_172813.1	chr9	123689606	123689610	-	1	NA	Intergenic	Intergenic	-10776	NM_139142	102680	Mm.440867	NM_139142	ENSMUSG00000036814	Slc6a20a	A730081N20Rik|AU022428|Xt3s1|Xtrp3s1	solute carrier family 6 (neurotransmitter transporter), member 20A	protein-coding
mm_60942.1	chr7	46920039	46920052	+	1	NA	promoter-TSS (NM_021884)	promoter-TSS (NM_021884)	-115	NM_021884	22088	Mm.241334	NM_021884	ENSMUSG00000014402	Tsg101	AI255943|CC2	tumor susceptibility gene 101	protein-coding
mm_32697.1	chr4	116067194	116067208	+	1	NA	intron (NM_025641, intron 3 of 3)	intron (NM_025641, intron 3 of 3)	7869	NM_025641	66576	Mm.181721	NM_025641	ENSMUSG00000063882	Uqcrh	2210416J04Rik|2310021J10Rik|2610041P16Rik	ubiquinol-cytochrome c reductase hinge protein	protein-coding
mm_66127.1	chr7	31054769	31054779	-	1	NA	promoter-TSS (NM_194321)	promoter-TSS (NM_194321)	79	NM_052991	56188	Mm.1491	NM_019503	ENSMUSG00000036570	Fxyd1	0610012C17Rik|1110006M24Rik|Plm|Pml	FXYD domain-containing ion transport regulator 1	protein-coding
mm_25008.1	chr3	97658617	97658628	+	1	NA	exon (NM_182997, exon 2 of 8)	exon (NM_182997, exon 2 of 8)	410	NM_182997	108097	Mm.31175	NM_182997	ENSMUSG00000038205	Prkab2	5730553K21Rik|AW049591|BB124140	protein kinase, AMP-activated, beta 2 non-catalytic subunit	protein-coding
mm_157873.1	chrX	75475630	75475663	-	1	NA	Intergenic	CpG	-38651	NM_011692	22327	Mm.8294	NM_011692	ENSMUSG00000031197	Vbp1	VBP-1	von Hippel-Lindau binding protein 1	protein-coding
mm_18613.1	chr2	68409335	68409338	-	1	NA	intron (NM_016866, intron 2 of 17)	intron (NM_016866, intron 2 of 17)	62645	NM_016866	53416	Mm.198414	NM_016866	ENSMUSG00000027030	Stk39	AW227544|AW556857|DCHT|RF005|Rnl5|SPAK	serine/threonine kinase 39	protein-coding
mm_96590.1	chr11	69090693	69090757	+	1	NA	3' UTR (NM_009497, exon 5 of 5)	3' UTR (NM_009497, exon 5 of 5)	2197	NM_009497	22318	Mm.28643	NM_009497	ENSMUSG00000020894	Vamp2	Syb-2|Syb2|sybII	vesicle-associated membrane protein 2	protein-coding
mm_62608.1	chr7	106511253	106511318	+	1	NA	Intergenic	Intergenic	-70212	NR_003967	209380	Mm.461779	NM_001001318		Gm4759	EG209380	GTPase, very large interferon inducible 1 pseudogene	pseudo
mm_89551.1	chr10	94719694	94719717	+	1	NA	exon (NM_029852, exon 3 of 16)	exon (NM_029852, exon 3 of 16)	30915	NM_029852	77048	Mm.296971	NM_029852	ENSMUSG00000020024	Cep83	2600001G24Rik|4921537D05Rik|5730513H21Rik|Ccdc41	centrosomal protein 83	protein-coding
mm_98908.1	chr11	98058277	98058307	+	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-4830	NM_146028	217154	Mm.181008	NM_146028	ENSMUSG00000017400	Stac2	24b2|24b2/STAC2|AW240854	SH3 and cysteine rich domain 2	protein-coding
mm_46675.1	chr5	109529547	109529548	-	1	NA	Intergenic	Intergenic	29446	NM_016715	57914	Mm.35771	NM_016715	ENSMUSG00000033467	Crlf2	CRLM2|Ly114|Tpte2|Tslpr	cytokine receptor-like factor 2	protein-coding
mm_133597.1	chr16	91465034	91465051	+	1	NA	promoter-TSS (NR_077219)	promoter-TSS (NR_077219)	-62	NR_077219	100503120	Mm.387130	NR_077219	ENSMUSG00000084866	A930006K02Rik	-	RIKEN cDNA A930006K02 gene	ncRNA
mm_151096.1	chr19	47854247	47854274	+	1	NA	promoter-TSS (NM_010362)	promoter-TSS (NM_010362)	-713	NM_010362	14873	Mm.378931	NM_010362	ENSMUSG00000025068	Gsto1	AA407097|AI194287|AU018802|Gsto-1|Gstx|Spg-r|p28	glutathione S-transferase omega 1	protein-coding
mm_52552.1	chr6	115989990	115990000	+	1	NA	intron (NM_026376, intron 1 of 35)	MIR|SINE|MIR	5010	NM_026376	67784	Mm.3085	NM_026376	ENSMUSG00000030123	Plxnd1	6230425C21Rik|b2b1863Clo|b2b553Clo	plexin D1	protein-coding
mm_24818.1	chr3	95628632	95628651	+	1	NA	exon (NM_019561, exon 3 of 4)	exon (NM_019561, exon 3 of 4)	3661	NM_001026212	56205	Mm.241365	NM_019561	ENSMUSG00000038619	Ensa	1700020C18Rik|2610007F17Rik|AI451924	endosulfine alpha	protein-coding
mm_162056.1	chrX	8074303	8074303	-	1	NA	promoter-TSS (NM_001290716)	promoter-TSS (NM_001290716)	10	NM_001290716	20937	Mm.9244	NM_011514	ENSMUSG00000039231	Suv39h1	AI852103|AL022883|DXHXS7466e|H3-K9-HMTase 1|KMT1A|mIS6	suppressor of variegation 3-9 homolog 1 (Drosophila)	protein-coding
mm_59433.1	chr7	27130285	27130353	+	1	NA	exon (NM_007817, exon 7 of 10)	exon (NM_007817, exon 7 of 10)	10364	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_105353.1	chr11	103018712	103018716	-	1	NA	Intergenic	B1_Mur4|SINE|Alu	-1567	NM_026551	68087	Mm.277449	NM_026551	ENSMUSG00000020935	Dcakd	3010024O21Rik|6720485C15Rik|AI849483	dephospho-CoA kinase domain containing	protein-coding
mm_106102.1	chr11	116273336	116273342	-	1	NA	intron (NM_146032, intron 1 of 15)	intron (NM_146032, intron 1 of 15)	878	NM_146032	217337	Mm.29655	NM_146032	ENSMUSG00000020780	Srp68	2610024I03Rik	signal recognition particle 68	protein-coding
mm_31359.1	chr4	47208281	47208292	+	1	NA	5' UTR (NM_009928, exon 1 of 40)	5' UTR (NM_009928, exon 1 of 40)	274	NM_009928	12819	Mm.233547	NM_009928	ENSMUSG00000028339	Col15a1	-	collagen, type XV, alpha 1	protein-coding
mm_124533.1	chr14	122451097	122451107	-	1	NA	promoter-TSS (NR_033325)	promoter-TSS (NR_033325)	13	NR_033325	328479	Mm.86095	NR_033325	ENSMUSG00000064052	Gm5089	6530402A20|C030005G22Rik|EG328479	predicted gene 5089	ncRNA
mm_128028.1	chr15	25332633	25332670	-	1	NA	Intergenic	RMER5|LTR|ERV1	81113	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	brain abundant, membrane attached signal protein 1	protein-coding
mm_120101.1	chr14	58085614	58085617	+	1	NA	intron (NM_013518, intron 2 of 2)	intron (NM_013518, intron 2 of 2)	12929	NM_013518	14180	Mm.8846	NM_013518	ENSMUSG00000021974	Fgf9	Eks	fibroblast growth factor 9	protein-coding
mm_107601.1	chr12	49383918	49383963	+	1	NA	5' UTR (NM_001160112, exon 1 of 1)	5' UTR (NM_001160112, exon 1 of 1)	933	NM_008241	15228	Mm.4704	NM_008241	ENSMUSG00000020950	Foxg1	2900064B05Rik|BF-1|Bf1|Hfh9|Hfhbf1	forkhead box G1	protein-coding
mm_46521.1	chr5	105343243	105343251	-	1	NA	intron (NR_132129, intron 2 of 10)	B3|SINE|B2	3225	NM_001039647	634650	Mm.458435	NM_001039647	ENSMUSG00000092021	Gbp11	EG634650|Gm7141	guanylate binding protein 11	protein-coding
mm_11803.1	chr2	43867108	43867110	+	1	NA	intron (NM_001301832, intron 6 of 14)	Lx8b|LINE|L1	118285	NM_001301831	76117	Mm.217350	NM_153820	ENSMUSG00000049744	Arhgap15	5830480G12Rik	Rho GTPase activating protein 15	protein-coding
mm_79994.1	chr9	67033908	67033961	+	1	NA	exon (NM_001164251, exon 4 of 10)	exon (NM_001164251, exon 4 of 10)	9937	NM_001164252	22003	Mm.121878	NM_024427	ENSMUSG00000032366	Tpm1	AA986836|AI854628|TM2|Tm3|Tmpa|Tpm-1|alpha-TM	tropomyosin 1, alpha	protein-coding
mm_141552.1	chr17	32189440	32189450	-	1	NA	promoter-TSS (NM_001033163)	promoter-TSS (NM_001033163)	18	NM_001033163	71932	Mm.176240	NM_001033163	ENSMUSG00000037577	Ephx3	2310063B19Rik|Abhd9	epoxide hydrolase 3	protein-coding
mm_162142.1	chrX	74283917	74283917	+	1	NA	intron (NM_001290738, intron 3 of 7)	intron (NM_001290738, intron 3 of 7)	1199	NM_001242615	66826	Mm.268483	NM_181516	ENSMUSG00000009995	Taz	5031411C02Rik|9130012G04Rik|AW107266|AW552613|G4.5	tafazzin	protein-coding
mm_68551.1	chr7	114317518	114317528	-	1	NA	intron (NR_029437, intron 3 of 3)	intron (NR_029437, intron 3 of 3)	-41407	NM_011965	26440	Mm.121265	NM_011965	ENSMUSG00000030751	Psma1	C2|HC2|Pros-30|alpha-type	proteasome (prosome, macropain) subunit, alpha type 1	protein-coding
mm_145045.1	chr18	39773601	39773605	+	1	NA	5' UTR (NM_011033, exon 1 of 1)	5' UTR (NM_011033, exon 1 of 1)	106	NM_011033	18459	Mm.9493	NM_011033	ENSMUSG00000051732	Pabpc2	Pabp|Pabp+|Pabp2	poly(A) binding protein, cytoplasmic 2	protein-coding
mm_53916.1	chr6	4047558	4047569	-	1	NA	promoter-TSS (NR_131108)	promoter-TSS (NR_131108)	21	NR_131108	78034	Mm.243851	NR_131108	ENSMUSG00000107681	4930528H21Rik	-	RIKEN cDNA 4930528H21 gene	ncRNA
mm_61972.1	chr7	90476661	90476681	+	1	NA	promoter-TSS (NM_026734)	promoter-TSS (NM_026734)	-676	NM_026734	68472	Mm.289791	NM_026734	ENSMUSG00000030614	Tmem126b	1110001A23Rik	transmembrane protein 126B	protein-coding
mm_9194.1	chr1	171196230	171196246	-	1	NA	promoter-TSS (NM_025557)	promoter-TSS (NM_025557)	30	NM_025557	66425	Mm.482117	NM_025557	ENSMUSG00000038370	Pcp4l1	1500036F01Rik	Purkinje cell protein 4-like 1	protein-coding
mm_105424.1	chr11	103697938	103697948	-	1	NA	promoter-TSS (NM_019650)	promoter-TSS (NM_019650)	219	NR_102396	399609	Mm.351922	NR_102388		C130046K22Rik	-	RIKEN cDNA C130046K22 gene	ncRNA
mm_23698.1	chr3	68694079	68694089	+	1	NA	intron (NM_001159424, intron 3 of 7)	intron (NM_001159424, intron 3 of 7)	2660	NM_008351	16159	Mm.103783	NM_008351	ENSMUSG00000027776	Il12a	IL-12p35|Il-12a|Ll12a|p35	interleukin 12a	protein-coding
mm_146038.1	chr18	69575369	69575370	+	1	NA	intron (NM_013685, intron 8 of 19)	intron (NM_013685, intron 8 of 19)	229648	NM_001083967	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding
mm_90574.1	chr10	128238035	128238069	+	1	NA	promoter-TSS (NM_011589)	promoter-TSS (NM_011589)	-14	NM_011589	21853	Mm.6458	NM_011589	ENSMUSG00000039994	Timeless	C77407|Debt69|tim	timeless circadian clock 1	protein-coding
mm_159294.1	chr2	175067765	175067765	-	1	NA	promoter-TSS (NM_001085546)	promoter-TSS (NM_001085546)	4	NM_001085546	664987		NM_001085546	ENSMUSG00000078905	Gm14393	OTTMUSG00000016546	predicted gene 14393	protein-coding
mm_95992.1	chr11	59192130	59192145	+	1	NA	promoter-TSS (NM_008193)	promoter-TSS (NM_008193)	-185	NM_008193	14923	Mm.3624	NM_008193	ENSMUSG00000020444	Guk1	AA409738|AL033299|AL033300|AV026611|Gmk|Guk-1	guanylate kinase 1	protein-coding
mm_81901.1	chr9	119981646	119981655	+	1	NA	intron (NM_153287, intron 1 of 4)	intron (NM_153287, intron 1 of 4)	3008	NM_153287	215418	Mm.491094	NM_153287	ENSMUSG00000032515	Csrnp1	4931429D10Rik|Axud1|CSRNP-1|URAX1|taip-3	cysteine-serine-rich nuclear protein 1	protein-coding
mm_144185.1	chr18	7868824	7868862	+	1	NA	promoter-TSS (NM_001146298)	promoter-TSS (NM_001146298)	11	NM_001282093	225131	Mm.204524	NM_153085	ENSMUSG00000024283	Wac	1110067P07Rik|A230035H12Rik|AI256735|AI256776|Wwp4	WW domain containing adaptor with coiled-coil	protein-coding
mm_36731.1	chr4	99121247	99121255	-	1	NA	promoter-TSS (NM_026082)	promoter-TSS (NM_026082)	-336	NM_026082	67299	Mm.260623	NM_026082	ENSMUSG00000028556	Dock7	3110056M06Rik|Gm430	dedicator of cytokinesis 7	protein-coding
mm_101070.1	chr11	11462416	11462426	-	1	NA	promoter-TSS (NM_015785)	promoter-TSS (NM_015785)	-2	NM_001185153	53604	Mm.9500	NM_015785	ENSMUSG00000020193	Zpbp	4930486K01Rik|Iam38|Sp38	zona pellucida binding protein	protein-coding
mm_138574.1	chr17	35424871	35424885	+	1	NA	promoter-TSS (NM_207648)	promoter-TSS (NM_207648)	1	NM_207648	110557	Mm.439827	NM_207648	ENSMUSG00000073409	H2-Q6	0610037M15Rik|H-2Q6|Qa-6|Qa6	histocompatibility 2, Q region locus 6	protein-coding
mm_76790.1	chr8	102739264	102739275	-	1	NA	intron (NM_009866, intron 1 of 12)	intron (NM_009866, intron 1 of 12)	45842	NM_009866	12552	Mm.1571	NM_009866	ENSMUSG00000031673	Cdh11	Cad11|OSF-4	cadherin 11	protein-coding
mm_58406.1	chr7	3220813	3220817	+	1	NA	promoter-TSS (NR_029645)	promoter-TSS (NR_029645)	42	NR_029645	100049713		NR_029645	ENSMUSG00000077886	Mir295	Mirn295|mir-295|mmu-miR-295	microRNA 295	ncRNA
mm_104506.1	chr11	95969964	95969987	-	1	NA	exon (NM_009951, exon 9 of 15)	exon (NM_009951, exon 9 of 15)	-6592	NR_037223	100526468		NR_037223	ENSMUSG00000093358	Mir3063	mmu-mir-3063	microRNA 3063	ncRNA
mm_25522.1	chr3	114030867	114030880	+	1	NA	5' UTR (NM_007729, exon 1 of 67)	5' UTR (NM_007729, exon 1 of 67)	333	NM_007729	12814	Mm.209715	NM_007729	ENSMUSG00000027966	Col11a1	C530001D20Rik|cho	collagen, type XI, alpha 1	protein-coding
mm_112283.1	chr12	114407026	114407033	-	1	NA	Intergenic	Intergenic	62437	NR_106062	102465663		NR_106062	ENSMUSG00000105438	Mir7094-1	mmu-mir-7094-1	microRNA 7094-1	ncRNA
mm_99003.1	chr11	98798703	98798711	+	1	NA	non-coding (NR_033551, exon 3 of 3)	non-coding (NR_033551, exon 3 of 3)	2938	NM_028722	74026	Mm.258352	NM_028722	ENSMUSG00000052915	Msl1	2810017F12Rik|4121402D02Rik|4930463F05Rik|AA682082|Msl-1	male-specific lethal 1 homolog (Drosophila)	protein-coding
mm_21616.1	chr2	164276002	164276026	-	1	NA	TTS (NM_009300)	TTS (NM_009300)	2293	NM_009300	20941	Mm.1286	NM_009300	ENSMUSG00000016998	Svs4	SVS-IV|Svp-2|Svp-4|Svp2|Svp4	seminal vesicle secretory protein 4	protein-coding
mm_109942.1	chr12	11326316	11326351	-	1	NA	exon (NM_012038, exon 4 of 4)	exon (NM_012038, exon 4 of 4)	26446	NR_106136	102465775		NR_106136	ENSMUSG00000098879	Mir7675	Gm27965|mmu-mir-7675	microRNA 7675	ncRNA
mm_17055.1	chr2	21205311	21205324	-	1	NA	promoter-TSS (NM_027728)	promoter-TSS (NM_027728)	48	NM_027728	71233	Mm.27658	NM_027728	ENSMUSG00000026679	Enkur	4933434I06Rik|AU016229	enkurin, TRPC channel interacting protein	protein-coding
mm_62370.1	chr7	100607913	100607992	+	1	NA	promoter-TSS (NR_003559)	promoter-TSS (NR_003559)	44	NR_003559	52443	Mm.473730	NM_198831	ENSMUSG00000030706	Mrpl48	1810030E20Rik|2610028L11Rik|CGI-118|D4Ertd786e	mitochondrial ribosomal protein L48	protein-coding
mm_48569.1	chr5	143315267	143315291	-	1	NA	promoter-TSS (NM_172726)	promoter-TSS (NM_172726)	81	NM_172726	231868	Mm.440105	NM_172726	ENSMUSG00000039244	E130309D02Rik	A630028N22	RIKEN cDNA E130309D02 gene	protein-coding
mm_49225.1	chr6	15794301	15794311	+	1	NA	intron (NM_175088, intron 4 of 4)	intron (NM_175088, intron 4 of 4)	73645	NM_175088	16543	Mm.1314	NM_175088	ENSMUSG00000041390	Mdfic	Kdt1|Mdfid	MyoD family inhibitor domain containing	protein-coding
mm_159263.1	chr2	155962017	155962017	+	1	NA	exon (NM_008383, exon 2 of 34)	exon (NM_008383, exon 2 of 34)	5459	NM_177217	16328	Mm.288729	NM_008383	ENSMUSG00000038241	Cep250	AW490617|B230210E21Rik|Cep2|Inmp	centrosomal protein 250	protein-coding
mm_31223.1	chr4	44019865	44019891	+	1	NA	exon (NM_001080385, exon 3 of 7)	exon (NM_001080385, exon 3 of 7)	7228	NM_001290470	12757	Mm.298875	NM_016760	ENSMUSG00000028478	Clta	AV026556|Lca	clathrin, light polypeptide (Lca)	protein-coding
mm_47556.1	chr5	124392606	124392644	-	1	NA	exon (NM_001081203, exon 19 of 32)	exon (NM_001081203, exon 19 of 32)	33289	NM_001081203	243272	Mm.23879	NM_001081203	ENSMUSG00000038095	Sbno1	9330180L10Rik|AI849128|AW557836|BC021875|Sbno|mSno1|sno	strawberry notch homolog 1 (Drosophila)	protein-coding
mm_158494.1	chrX	142346942	142346981	-	1	NA	intron (NM_019477, intron 5 of 15)	intron (NM_019477, intron 5 of 15)	-40763	NM_021487	66240	Mm.58507	NM_021487	ENSMUSG00000090122	Kcne1l	1500015C14Rik|Kcne5|Mink	potassium voltage-gated channel, Isk-related family, member 1-like, pseudogene	protein-coding
mm_112340.1	chr12	116262947	116263046	-	1	NA	promoter-TSS (NM_146039)	promoter-TSS (NM_146039)	29	NM_146039	217935	Mm.31382	NM_146039	ENSMUSG00000042050	Wdr60	D430033N04Rik	WD repeat domain 60	protein-coding
mm_147154.1	chr18	36679259	36679279	-	1	NA	promoter-TSS (NM_146085)	promoter-TSS (NM_146085)	54	NM_026404	67843	Mm.273350	NM_026404	ENSMUSG00000033272	Slc35a4	2610030J16Rik	solute carrier family 35, member A4	protein-coding
mm_26345.1	chr3	142547397	142547407	+	1	NA	3' UTR (NM_001083312, exon 11 of 11)	3' UTR (NM_001083312, exon 11 of 11)	-12650	NM_018734	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_2312.1	chr1	91720882	91720911	+	1	NA	Intergenic	Intergenic	-80565	NM_007855	13345	Mm.9474	NM_007855	ENSMUSG00000007805	Twist2	Dermo1|bHLHa39	twist basic helix-loop-helix transcription factor 2	protein-coding
mm_53967.1	chr6	5977397	5977408	-	1	NA	promoter-TSS (NR_040255)	promoter-TSS (NR_040255)	-9	NR_040255	72249	Mm.443268	NR_040255	ENSMUSG00000085416	1700019G24Rik	-	RIKEN cDNA 1700019G24 gene	ncRNA
mm_11052.1	chr2	27182138	27182148	+	1	NA	intron (NM_138942, intron 11 of 11)	intron (NM_138942, intron 11 of 11)	16636	NM_138942	13166	Mm.167781	NM_138942	ENSMUSG00000000889	Dbh	-	dopamine beta hydroxylase	protein-coding
mm_42970.1	chr5	123141225	123141240	+	1	NA	promoter-TSS (NM_001040398)	promoter-TSS (NM_001040398)	-961	NM_001040398	208043	Mm.250391	NM_177581	ENSMUSG00000038384	Setd1b	AA516740|BC035291|KMT2G|mKIAA1076	SET domain containing 1B	protein-coding
mm_76834.1	chr8	105264579	105264585	-	1	NA	promoter-TSS (NM_015821)	promoter-TSS (NM_015821)	12	NM_001033161	71609	Mm.264255	NM_001033161	ENSMUSG00000031887	Tradd	9130005N23Rik|AA930854	TNFRSF1A-associated via death domain	protein-coding
mm_28380.1	chr3	89998244	89998251	-	1	NA	promoter-TSS (NR_045749)	promoter-TSS (NR_045749)	-144	NM_001310681	23897	Mm.256035	NM_011826	ENSMUSG00000027944	Hax1	HAX-1|HSP1BP-1|Hs1bp1|SIG-111|Silg111|mHAX-1s	HCLS1 associated X-1	protein-coding
mm_100611.1	chr11	121451955	121451970	+	1	NA	promoter-TSS (NM_029878)	promoter-TSS (NM_029878)	13	NM_029878	108903	Mm.23686	NM_029878	ENSMUSG00000039230	Tbcd	2310057L06Rik|A030005L14Rik|mKIAA0988	tubulin-specific chaperone d	protein-coding
mm_9338.1	chr1	172004541	172004553	-	1	NA	3' UTR (NM_033509, exon 8 of 8)	3' UTR (NM_033509, exon 8 of 8)	22748	NM_033509	93840	Mm.36148	NM_033509	ENSMUSG00000026556	Vangl2	C530001F03Rik|Lootl|Lp|Lpp1|Ltap|Vang1l2|loop-tail|ska17|ska<m17Jus>|stbm|strabismus	vang-like 2 (van gogh, Drosophila)	protein-coding
mm_157242.1	chrX	17572283	17572296	-	1	NA	promoter-TSS (NM_028058)	promoter-TSS (NM_028058)	36	NM_001313745	72018	Mm.41558	NM_028058	ENSMUSG00000025040	Fundc1	1500005J14Rik|1810033P05Rik	FUN14 domain containing 1	protein-coding
mm_101637.1	chr11	36432884	36432895	-	1	NA	intron (NM_011856, intron 2 of 28)	intron (NM_011856, intron 2 of 28)	-452800	NM_170779	211652	Mm.31267	NM_170779	ENSMUSG00000018849	Wwc1	AA408228|AU017197|BC037006|Kibra|mKIAA0869	WW, C2 and coiled-coil domain containing 1	protein-coding
mm_133136.1	chr16	66657108	66657142	+	1	NA	promoter-TSS (NR_040512)	promoter-TSS (NR_040512)	7	NR_040512	75501	Mm.394300	NR_040512	ENSMUSG00000092599	1700010K23Rik	-	RIKEN cDNA 1700010K23 gene	ncRNA
mm_16386.1	chr2	178455432	178455446	+	1	NA	intron (NM_001291189, intron 3 of 13)	intron (NM_001291189, intron 3 of 13)	24924	NM_198656	381409	Mm.330860	NM_198656	ENSMUSG00000039155	Cdh26	Gm1010	cadherin-like 26	protein-coding
mm_145295.1	chr18	53268550	53268565	+	1	NA	intron (NM_029394, intron 1 of 6)	intron (NM_029394, intron 1 of 6)	22895	NM_029394	69226	Mm.32414	NM_029394	ENSMUSG00000024535	Snx24	2810011K15Rik|5730433I16Rik|AI451341	sorting nexing 24	protein-coding
mm_136735.1	chr17	8340349	8340369	+	1	NA	promoter-TSS (NM_178774)	promoter-TSS (NM_178774)	-47	NR_028280	320111	Mm.442510	NM_178774	ENSMUSG00000055945	Prr18	9630019K15Rik	proline rich 18	protein-coding
mm_141015.1	chr17	25015799	25015821	-	1	NA	promoter-TSS (NM_020608)	promoter-TSS (NM_020608)	-276	NM_134126	106633	Mm.32802	NM_134126	ENSMUSG00000024169	Ift140	AI661311|Tce5|Wdtc2|mKIAA0590	intraflagellar transport 140	protein-coding
mm_122825.1	chr14	54686170	54686198	-	1	NA	promoter-TSS (NM_021437)	promoter-TSS (NM_021437)	13	NM_021437	58248	Mm.197509	NM_021437	ENSMUSG00000040822	1700123O20Rik	MNCb-2990	RIKEN cDNA 1700123O20 gene	protein-coding
mm_34936.1	chr4	155841122	155841138	+	1	NA	exon (NM_024263, exon 3 of 10)	exon (NM_024263, exon 3 of 10)	1450	NM_024263	74761	Mm.159028	NM_024263	ENSMUSG00000029070	Mxra8	1200013A08Rik|1700095D18Rik|AI131686|Asp3|Dicam	matrix-remodelling associated 8	protein-coding
mm_166119.1	chr4	151057614	151057627	+	1	NA	intron (NM_009498, intron 1 of 4)	CpG	333	NM_009498	22319	Mm.273930	NM_009498	ENSMUSG00000028955	Vamp3	D130027G05Rik|VAMP-3|ceb	vesicle-associated membrane protein 3	protein-coding
mm_51783.1	chr6	88199646	88199682	+	1	NA	exon (NM_008090, exon 2 of 6)	exon (NM_008090, exon 2 of 6)	1000	NM_008090	14461	Mm.491156	NM_008090	ENSMUSG00000015053	Gata2	Gata-2	GATA binding protein 2	protein-coding
mm_89298.1	chr10	87913692	87913702	+	1	NA	exon (NM_010512, exon 3 of 5)	exon (NM_010512, exon 3 of 5)	52586	NM_001111276	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_122677.1	chr14	52009620	52009635	-	1	NA	exon (NM_001253694, exon 4 of 6)	exon (NM_001253694, exon 4 of 6)	4931	NM_001253695	69890	Mm.475652	NM_027248	ENSMUSG00000049295	Zfp219	2010302A17Rik	zinc finger protein 219	protein-coding
mm_18547.1	chr2	64975763	64975795	-	1	NA	intron (NM_016719, intron 2 of 13)	intron (NM_016719, intron 2 of 13)	46987	NM_016719	50915	Mm.214554	NM_016719	ENSMUSG00000026888	Grb14	AI505286	growth factor receptor bound protein 14	protein-coding
mm_27159.1	chr3	33142986	33143000	-	1	NA	5' UTR (NM_001163516, exon 1 of 13)	5' UTR (NM_001163516, exon 1 of 13)	198	NM_001163516	58869	Mm.151332	NM_021483	ENSMUSG00000027674	Pex5l	1700016J08Rik|PXR2|Pex2|TRIP8b|pex5Rp	peroxisomal biogenesis factor 5-like	protein-coding
mm_118623.1	chr14	21111249	21111256	+	1	NA	intron (NM_001243041, intron 3 of 10)	intron (NM_001243041, intron 3 of 10)	35100	NM_001243041	11534	Mm.188734	NM_134079	ENSMUSG00000039197	Adk	2310026J05Rik|5033405D03Rik|AI255373|AI987814|Ak	adenosine kinase	protein-coding
mm_168219.1	chr10	77166533	77166534	-	1	NA	promoter-TSS (NM_009929)	promoter-TSS (NM_009929)	-3	NM_009929	12822	Mm.4352	NM_009929	ENSMUSG00000001435	Col18a1	-	collagen, type XVIII, alpha 1	protein-coding
mm_91596.1	chr10	40502862	40502905	-	1	NA	Intergenic	Intergenic	-67479	NM_027572	70840	Mm.332570	NM_027572	ENSMUSG00000019834	Slc22a16	4921504E14Rik|CT2|FLIPT2|OCT6|OKB1	solute carrier family 22 (organic cation transporter), member 16	protein-coding
mm_107845.1	chr12	69364339	69364360	+	1	NA	Intergenic	Intergenic	-7173	NM_025441	66244	Mm.46705	NM_025441	ENSMUSG00000020982	Nemf	1500011I12Rik|4933405E14Rik|Sdccag1	nuclear export mediator factor	protein-coding
mm_142754.1	chr17	48682970	48682970	-	1	NA	Intergenic	Intergenic	228069	NM_152823	76589	Mm.311629	NM_152823	ENSMUSG00000043592	Unc5cl	2510009H09Rik|BB155270|Zud	unc-5 family C-terminal like	protein-coding
mm_66829.1	chr7	48843664	48843674	-	1	NA	promoter-TSS (NM_013808)	promoter-TSS (NM_013808)	2	NM_013808	13009	Mm.17235	NM_013808	ENSMUSG00000030470	Csrp3	CRP3|MLP|MMLP	cysteine and glycine-rich protein 3	protein-coding
mm_164766.1	chr17	86223575	86223591	+	1	NA	intron (NM_011104, intron 1 of 14)	intron (NM_011104, intron 1 of 14)	55798	NM_011104	18754	Mm.24614	NM_011104	ENSMUSG00000045038	Prkce	5830406C15Rik|PKC[e]|PKCepsilon|Pkce|R75156	protein kinase C, epsilon	protein-coding
mm_3186.1	chr1	135783134	135783143	+	1	NA	Intergenic	Intergenic	-16283	NM_021467	21952	Mm.44379	NM_021467	ENSMUSG00000026418	Tnni1	2700018B22Rik|AI747285|ssTnI	troponin I, skeletal, slow 1	protein-coding
mm_138036.1	chr17	33919726	33919736	+	1	NA	TTS (NM_020625)	TTS (NM_020625)	253	NM_009318	21356	Mm.154457	NM_009318	ENSMUSG00000024308	Tapbp	D17Wsu91e|TPN	TAP binding protein	protein-coding
mm_149572.1	chr19	12805349	12805380	+	1	NA	intron (NM_134152, intron 2 of 8)	intron (NM_134152, intron 2 of 8)	6755	NM_134152	107321	Mm.313136	NM_134152	ENSMUSG00000024696	Lpxn	4933402K05Rik|A530083L21Rik|AV278559|LDPL	leupaxin	protein-coding
mm_95677.1	chr11	54101582	54101590	+	1	NA	5' UTR (NM_001136076, exon 2 of 16)	5' UTR (NM_001136076, exon 2 of 16)	662	NM_011031	18452	Mm.3705	NM_011031	ENSMUSG00000018906	P4ha2	AA407196|C76437|P4hl	procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha II polypeptide	protein-coding
mm_110794.1	chr12	72085394	72085418	-	1	NA	promoter-TSS (NM_024205)	promoter-TSS (NM_024205)	-93	NM_026038	67217	Mm.286120	NM_026038	ENSMUSG00000019718	L3hypdh	2810055F11Rik	L-3-hydroxyproline dehydratase (trans-)	protein-coding
mm_170912.1	chr2	34964910	34964921	-	1	NA	Intergenic	Intergenic	-3143	NM_001326601	22029	Mm.239514	NM_009421	ENSMUSG00000026875	Traf1	4732496E14Rik	TNF receptor-associated factor 1	protein-coding
mm_33955.1	chr4	137454762	137454772	+	1	NA	exon (NM_027063, exon 2 of 2)	exon (NM_027063, exon 2 of 2)	1471	NM_027063	69380	Mm.272519	NM_027063	ENSMUSG00000041399	1700013G24Rik	AI507018	RIKEN cDNA 1700013G24 gene	protein-coding
mm_169522.1	chr1	48928251	48928253	-	1	NA	Intergenic	L1Md_T|LINE|L1	-1461127	NR_105768	102466969		NR_105768	ENSMUSG00000098876	Mir6350	Gm27958|mmu-mir-6350	microRNA 6350	ncRNA
mm_86149.1	chr9	117252346	117252383	-	1	NA	5' UTR (NM_001172126, exon 1 of 13)	5' UTR (NM_001172126, exon 1 of 13)	119	NM_001172123	207181	Mm.326411	NM_178660	ENSMUSG00000039607	Rbms3	6720477E09Rik|8430436O14Rik	RNA binding motif, single stranded interacting protein	protein-coding
mm_105548.1	chr11	106365530	106365567	-	1	NA	Intergenic	Intergenic	-9278	NM_029345	75573	Mm.159539	NM_029345	ENSMUSG00000009210	Prr29	2310007L24Rik	proline rich 29	protein-coding
mm_43285.1	chr5	134099693	134099695	+	1	NA	promoter-TSS (NM_030719)	promoter-TSS (NM_030719)	-54	NM_030719	80909	Mm.45218	NM_030719	ENSMUSG00000015944	Gatsl2	7530428J21Rik|AW742413|Gats|Gatsl1	GATS protein-like 2	protein-coding
mm_43509.1	chr5	137025316	137025338	+	1	NA	Intergenic	Intergenic	-4968	NM_001039385	381677	Mm.389697	NM_001039385	ENSMUSG00000037428	Vgf	Gm1052	VGF nerve growth factor inducible	protein-coding
mm_96134.1	chr11	60878945	60878999	+	1	NA	promoter-TSS (NM_001168507)	promoter-TSS (NM_001168507)	66	NM_173453	216821	Mm.28063	NM_173453	ENSMUSG00000043284	Tmem11	5730466P16Rik|AA409091	transmembrane protein 11	protein-coding
mm_93888.1	chr10	125328531	125328541	-	1	NA	promoter-TSS (NM_011391)	promoter-TSS (NM_011391)	-1	NM_011391	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|Mct2	solute carrier family 16 (monocarboxylic acid transporters), member 7	protein-coding
mm_11017.1	chr2	26604060	26604074	+	1	NA	exon (NM_026212, exon 1 of 6)	exon (NM_026212, exon 1 of 6)	350	NM_026212	67512	Mm.24244	NM_026212	ENSMUSG00000026922	Agpat2	2510002J07Rik|AV000834|BSCL|BSCL1|LPAAB|LPAAT-beta	1-acylglycerol-3-phosphate O-acyltransferase 2 (lysophosphatidic acid acyltransferase, beta)	protein-coding
mm_131331.1	chr16	13256486	13256526	+	1	NA	promoter-TSS (NM_001122667)	promoter-TSS (NM_001122667)	25	NM_001122667	239719	Mm.270643	NM_153588	ENSMUSG00000009569	Mkl2	ENSMUSG00000075401|Gt4-1|MRTF-B|Mrtfb|mKIAA1243	MKL/myocardin-like 2	protein-coding
mm_21945.1	chr2	167061070	167061076	-	1	NA	intron (NM_001033196, intron 1 of 13)	intron (NM_001033196, intron 1 of 13)	-1861	NR_138563	68949	Mm.391959	NM_001081005		Zfas1	1500012F01Rik|Zfos1	zinc finger, NFX1-type containing 1, antisense RNA 1	ncRNA
mm_19433.1	chr2	91950387	91950406	-	1	NA	promoter-TSS (NM_001166597)	promoter-TSS (NM_001166597)	-48	NM_001166597	104418	Mm.314923	NM_138306	ENSMUSG00000040479	Dgkz	E130307B02Rik|ENSMUSG00000075035|F730209L11Rik|mDGK[z]	diacylglycerol kinase zeta	protein-coding
mm_102804.1	chr11	68863982	68863988	-	1	NA	Intergenic	Intergenic	-10854	NM_023668	83431	Mm.31979	NM_023668	ENSMUSG00000018736	Ndel1	2600006O07Rik|MITAP1|NUDEL|mNudel	nudE neurodevelopment protein 1 like 1	protein-coding
mm_138991.1	chr17	45523500	45523532	+	1	NA	promoter-TSS (NM_013688)	promoter-TSS (NM_013688)	82	NM_013688	21645	Mm.491193	NM_013688	ENSMUSG00000023949	Tcte1	D17Sil1|Tcte-1	t-complex-associated testis expressed 1	protein-coding
mm_150086.1	chr19	29410913	29410948	+	1	NA	promoter-TSS (NM_021396)	promoter-TSS (NM_021396)	11	NM_021396	58205	Mm.116737	NM_021396	ENSMUSG00000016498	Pdcd1lg2	B7-DC|Btdc|F730015O22Rik|PD-L2	programmed cell death 1 ligand 2	protein-coding
mm_166078.1	chr4	137388695	137388704	+	1	NA	Intergenic	Intergenic	21092	NM_001126318	242711	Mm.475541	NM_001126318	ENSMUSG00000078520	Cela3a	Gm13011|OTTMUSG00000009877	chymotrypsin-like elastase family, member 3A	protein-coding
mm_75110.1	chr8	34154440	34154449	-	1	NA	promoter-TSS (NM_026432)	promoter-TSS (NM_026432)	-119	NM_026432	67887	Mm.290353	NM_026432	ENSMUSG00000031532	Saraf	1810045K07Rik|Tmem66	store-operated calcium entry-associated regulatory factor	protein-coding
mm_135224.1	chr16	36784785	36784825	-	1	NA	5' UTR (NM_021301, exon 1 of 22)	5' UTR (NM_021301, exon 1 of 22)	157	NM_001145899	57738	Mm.281804	NM_021301	ENSMUSG00000022899	Slc15a2	8430408C16Rik|C78862|Pept2	solute carrier family 15 (H+/peptide transporter), member 2	protein-coding
mm_2855.1	chr1	131675031	131675058	+	1	NA	3' UTR (NM_007799, exon 10 of 10)	3' UTR (NM_007799, exon 10 of 10)	-13651	NM_145509	226421	Mm.44508	NM_145509	ENSMUSG00000052688	Rab7b	5430435G22Rik	RAB7B, member RAS oncogene family	protein-coding
mm_16481.1	chr2	180890688	180890698	+	1	NA	Intergenic	Intergenic	-3347	NR_029538	723951		NR_029538	ENSMUSG00000065454	Mir124a-3	Mirn124a-3|mir-124-3|mir-124a-3	microRNA 124a-3	ncRNA
mm_11347.1	chr2	30845311	30845323	+	1	NA	promoter-TSS (NM_009116)	promoter-TSS (NM_009116)	-50	NM_009116	20204	Mm.1802	NM_009116	ENSMUSG00000039476	Prrx2	Prx2|S8	paired related homeobox 2	protein-coding
mm_16905.1	chr2	13491892	13491896	-	1	NA	promoter-TSS (NM_001081084)	promoter-TSS (NM_001081084)	-18	NM_001081084	65969	Mm.313915	NM_001081084	ENSMUSG00000026726	Cubn	AA408369|AL022750|D2Wsu88e	cubilin (intrinsic factor-cobalamin receptor)	protein-coding
mm_98943.1	chr11	98400538	98400562	+	1	NA	promoter-TSS (NM_001033537)	promoter-TSS (NM_001033537)	-60	NM_001033537	320655	Mm.86519	NM_001033537	ENSMUSG00000038208	Pgap3	CAB2|D430035D22Rik|Perld1	post-GPI attachment to proteins 3	protein-coding
mm_75768.1	chr8	69974368	69974407	-	1	NA	promoter-TSS (NM_001113346)	promoter-TSS (NM_001113346)	-4	NM_001113346	234366	Mm.270044	NM_145596	ENSMUSG00000036180	Gatad2a	1110066C11Rik|BC031407|C80248	GATA zinc finger domain containing 2A	protein-coding
mm_70222.1	chr7	145137214	145137241	-	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	70892	NR_033626	100040049	Mm.102235	NR_033626	ENSMUSG00000109305	1810010D01Rik	Gm2572	RIKEN cDNA 1810010D01 gene	ncRNA
mm_26109.1	chr3	137623717	137623727	+	1	NA	promoter-TSS (NM_030143)	promoter-TSS (NM_030143)	50	NM_030143	73284	Mm.250841	NM_030143	ENSMUSG00000046818	Ddit4l	1700037B15Rik|1700108M02Rik|REDD2|RTP801L|Smhs1	DNA-damage-inducible transcript 4-like	protein-coding
mm_154762.1	chrX	12079209	12079223	+	1	NA	intron (NM_001168321, intron 1 of 13)	CpG	1337	NM_175045	71458	Mm.196328	NM_029510	ENSMUSG00000040363	Bcor	2900008C10Rik|5830466J11Rik|8430401K06Rik|BcorR|D930024N20Rik|mKIAA1575	BCL6 interacting corepressor	protein-coding
mm_133033.1	chr16	57352983	57353002	+	1	NA	promoter-TSS (NM_001040397)	promoter-TSS (NM_001040397)	-285	NM_001040397	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding
mm_140625.1	chr17	12318705	12318713	-	1	NA	promoter-TSS (NR_045290)	promoter-TSS (NR_045290)	-49	NM_011948	26407	Mm.28587	NM_011948	ENSMUSG00000014426	Map3k4	D17Rp17|D17Rp17e|MAPKKK4|MEKK 4|MTK1|Mek4b|Mekk4|RP17|Rp17a|Tas|mKIAA0213	mitogen-activated protein kinase kinase kinase 4	protein-coding
mm_35394.1	chr4	34050078	34050089	-	1	NA	promoter-TSS (NM_026293)	promoter-TSS (NM_026293)	-16	NM_026293	67652	Mm.55848	NM_026293	ENSMUSG00000028264	Spaca1	1700124L11Rik|4930540L03Rik	sperm acrosome associated 1	protein-coding
mm_137577.1	chr17	27909288	27909314	+	1	NA	promoter-TSS (NM_001286041)	promoter-TSS (NM_001286041)	-5	NM_001286040	224650	Mm.32556	NM_181413	ENSMUSG00000024219	Anks1	Anks1a|mKIAA0229	ankyrin repeat and SAM domain containing 1	protein-coding
mm_52471.1	chr6	114248162	114248174	+	1	NA	3' UTR (NM_172890, exon 14 of 14)	3' UTR (NM_172890, exon 14 of 14)	-34467	NM_178703	232333	Mm.5260	NM_178703	ENSMUSG00000030310	Slc6a1	A730043E01|GABATHG|GABATR|GAT-1|Gabt|Gabt1|Gat1|XT-1|Xtrp1	solute carrier family 6 (neurotransmitter transporter, GABA), member 1	protein-coding
mm_96500.1	chr11	68431928	68431947	+	1	NA	promoter-TSS (NM_177320)	promoter-TSS (NM_177320)	-188	NM_177320	320207	Mm.244960	NM_177320	ENSMUSG00000020901	Pik3r5	AV230647|F730038I15Rik	phosphoinositide-3-kinase, regulatory subunit 5, p101	protein-coding
mm_21419.1	chr2	158129410	158129432	-	1	NA	exon (NM_009373, exon 7 of 13)	exon (NM_009373, exon 7 of 13)	16971	NM_009373	21817	Mm.330731	NM_009373	ENSMUSG00000037820	Tgm2	G[a]h|TG2|TGase2|tTG|tTGas	transglutaminase 2, C polypeptide	protein-coding
mm_130045.1	chr15	89128635	89128693	-	1	NA	promoter-TSS (NR_028449)	promoter-TSS (NR_028449)	36	NR_028448	170787	Mm.203954	NM_199198	ENSMUSG00000062906	Hdac10	AW548891|Hd10	histone deacetylase 10	protein-coding
mm_75663.1	chr8	66486495	66486539	-	1	NA	promoter-TSS (NM_025465)	promoter-TSS (NM_025465)	-10	NM_025465	66282	Mm.294985	NM_025465	ENSMUSG00000025591	Tma16	1810029B16Rik	translation machinery associated 16	protein-coding
mm_58884.1	chr7	17087988	17087995	+	1	NA	intron (NM_001310628, intron 1 of 5)	intron (NM_001310628, intron 1 of 5)	13951	NM_007676	26436	Mm.143686	NM_007676	ENSMUSG00000066760	Psg16	Cea11|PSG|bCEA	pregnancy specific glycoprotein 16	protein-coding
mm_86538.1	chr10	8214264	8214274	+	1	NA	intron (NM_177387, intron 7 of 7)	intron (NM_177387, intron 7 of 7)	-258146	NM_138667	68652	Mm.193041	NM_138667	ENSMUSG00000015755	Tab2	1110030N06Rik|A530078N03Rik|Map3k7ip2|mKIAA0733	TGF-beta activated kinase 1/MAP3K7 binding protein 2	protein-coding
mm_172941.1	chr9	79902577	79902578	+	1	NA	intron (NM_001081243, intron 1 of 5)	L1Md_A|LINE|L1	75305	NM_001081243	70598	Mm.23049	NM_001081243	ENSMUSG00000034898	Filip1	5730485H21Rik|AI843021	filamin A interacting protein 1	protein-coding
mm_91232.1	chr10	22302495	22302548	-	1	NA	intron (NM_009018, intron 5 of 5)	intron (NM_009018, intron 5 of 5)	-4199	NR_015465	606736	Mm.387042	NR_015465	ENSMUSG00000097352	C920009B18Rik	-	RIKEN cDNA C920009B18 gene	ncRNA
mm_144964.1	chr18	37824072	37824080	+	1	NA	intron (NM_033583, intron 1 of 3)	intron (NM_033583, intron 1 of 3)	4530	NM_033583	93708	Mm.247203	NM_033583	ENSMUSG00000102543	Pcdhgc5	-	protocadherin gamma subfamily C, 5	protein-coding
mm_153009.1	chr19	30363316	30363319	-	1	NA	Intergenic	Intergenic	130360	NM_010776	17195	Mm.30045	NM_010776	ENSMUSG00000024863	Mbl2	L-MBP|MBL|MBL-C|MBP-C	mannose-binding lectin (protein C) 2	protein-coding
mm_157717.1	chrX	70143575	70143591	-	1	NA	promoter-TSS (NR_033213)	promoter-TSS (NR_033213)	5	NR_033213	74305	Mm.410860	NR_033213	ENSMUSG00000100511	1700111N16Rik	-	RIKEN cDNA 1700111N16 gene	ncRNA
mm_4556.1	chr1	177444690	177444700	+	1	NA	promoter-TSS (NM_001012330)	promoter-TSS (NM_001012330)	34	NM_001012330	30928	Mm.330700	NM_013915	ENSMUSG00000063659	Zbtb18	RP58|Zfp238|Znf238	zinc finger and BTB domain containing 18	protein-coding
mm_55234.1	chr6	52240860	52240874	-	1	NA	promoter-TSS (NM_001122950)	promoter-TSS (NM_001122950)	-13	NM_001122950	15395	Mm.5	NM_008263	ENSMUSG00000000938	Hoxa10	Hox-1.8|Hoxa-10	homeobox A10	protein-coding
mm_38740.1	chr4	145246856	145246879	-	1	NA	promoter-TSS (NM_011610)	promoter-TSS (NM_011610)	3	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_173045.1	chrX	118200200	118200208	+	1	NA	Intergenic	L1Md_T|LINE|L1	-227023	NM_001142750	100039551	Mm.272850	NM_001142750	ENSMUSG00000100194	Tgif2lx2	-	TGFB-induced factor homeobox 2-like, X-linked 2	protein-coding
mm_87838.1	chr10	60390784	60390800	+	1	NA	intron (NR_045556, intron 30 of 68)	intron (NR_045556, intron 30 of 68)	-8934	NM_001164374	100302688	Mm.444135	NM_001164374	ENSMUSG00000090439	Gm17455	-	predicted gene, 17455	protein-coding
mm_103167.1	chr11	70458813	70458848	-	1	NA	promoter-TSS (NM_001029929)	promoter-TSS (NM_001029929)	-792	NM_001029929	574428	Mm.472771	NM_001029929	ENSMUSG00000040829	Zmynd15	-	zinc finger, MYND-type containing 15	protein-coding
mm_157949.1	chrX	86997673	86997676	-	1	NA	intron (NM_001160403, intron 6 of 10)	intron (NM_001160403, intron 6 of 10)	-642680	NR_036689	245502	Mm.490821	NR_036689		Gm41	-	melanoma antigen, family B, 4 pseudogene	pseudo
mm_108659.1	chr12	86421668	86421672	+	1	NA	promoter-TSS (NM_011934)	promoter-TSS (NM_011934)	26	NM_011934	26380	Mm.235550	NM_011934	ENSMUSG00000021255	Esrrb	Err2|Errb|Estrrb|Nr3b2	estrogen related receptor, beta	protein-coding
mm_102750.1	chr11	67256295	67256315	-	1	NA	exon (NM_010855, exon 34 of 40)	exon (NM_010855, exon 34 of 40)	18493	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_13390.1	chr2	103969634	103969640	+	1	NA	promoter-TSS (NM_008505)	promoter-TSS (NM_008505)	80	NM_001142336	16909	Mm.29266	NM_008505	ENSMUSG00000032698	Lmo2	Rbtn-2|Rbtn2|Rhom-2|Ttg2	LIM domain only 2	protein-coding
mm_93964.1	chr10	127288760	127288774	-	1	NA	5' UTR (NM_001347171, exon 1 of 13)	5' UTR (NM_001347171, exon 1 of 13)	251	NM_001347171	110962	Mm.372826	NM_033072	ENSMUSG00000025409	Mbd6	D10Wsu93e	methyl-CpG binding domain protein 6	protein-coding
mm_103360.1	chr11	74908057	74908070	-	1	NA	exon (NM_177325, exon 14 of 15)	exon (NM_177325, exon 14 of 15)	2617	NR_028562	100217469		NR_028562		Snord91a	MBII-296	small nucleolar RNA, C/D box 91A	snoRNA
mm_74882.1	chr8	25091365	25091372	-	1	NA	intron (NM_031257, intron 1 of 11)	intron (NM_031257, intron 1 of 11)	10443	NM_031257	83436	Mm.261122	NM_031257	ENSMUSG00000031557	Plekha2	6430512N22Rik|AI851530|AU041791|TAPP2|W91773	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 2	protein-coding
mm_85014.1	chr9	87731249	87731273	-	1	NA	promoter-TSS (NM_023814)	promoter-TSS (NM_023814)	-1	NM_023814	76365	Mm.158789	NM_023814	ENSMUSG00000032419	Tbx18	2810012F10Rik|2810404D13Rik	T-box18	protein-coding
mm_125673.1	chr15	66541588	66541608	+	1	NA	exon (NM_172514, exon 6 of 10)	exon (NM_172514, exon 6 of 10)	19448	NM_172514	213068	Mm.132299	NM_172514	ENSMUSG00000036944	Tmem71	AI661017|E430024D12	transmembrane protein 71	protein-coding
mm_107198.1	chr12	25318151	25318163	+	1	NA	Intergenic	Intergenic	188983	NR_045844	432641	Mm.112955	NR_045844		Gm17746	-	predicted gene, 17746	ncRNA
mm_54213.1	chr6	25689837	25689854	-	1	NA	5' UTR (NM_010338, exon 1 of 2)	5' UTR (NM_010338, exon 1 of 2)	135	NM_010338	14763	Mm.409670	NM_010338	ENSMUSG00000039904	Gpr37	AI848630|Pael-R	G protein-coupled receptor 37	protein-coding
mm_81519.1	chr9	110052017	110052111	+	1	NA	promoter-TSS (NM_001311164)	promoter-TSS (NM_001311164)	43	NM_001311164	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_119540.1	chr14	48120811	48120828	+	1	NA	promoter-TSS (NM_033602)	promoter-TSS (NM_033602)	-50	NM_033602	93834	Mm.296457	NM_033602	ENSMUSG00000021846	Peli2	AW047589|BB129927	pellino 2	protein-coding
mm_25685.1	chr3	122245564	122245578	+	1	NA	promoter-TSS (NM_008129)	promoter-TSS (NM_008129)	14	NM_008129	14630	Mm.292676	NM_008129	ENSMUSG00000028124	Gclm	AI649393|Gcmc|Glclr	glutamate-cysteine ligase, modifier subunit	protein-coding
mm_96783.1	chr11	69941241	69941271	+	1	NA	3' UTR (NM_016875, exon 9 of 9)	3' UTR (NM_016875, exon 9 of 9)	4928	NM_001347634	53422	Mm.29286	NM_016875	ENSMUSG00000018554	Ybx2	Msy2	Y box protein 2	protein-coding
mm_116277.1	chr13	34916978	34917038	-	1	NA	intron (NM_027967, intron 1 of 7)	intron (NM_027967, intron 1 of 7)	2984	NM_027967	71864	Mm.380836	NM_027967	ENSMUSG00000021414	Fam217a	1700026J04Rik	family with sequence similarity 217, member A	protein-coding
mm_12199.1	chr2	65845786	65845799	+	1	NA	promoter-TSS (NM_153409)	promoter-TSS (NM_153409)	25	NM_178634	77771	Mm.102025	NM_153409	ENSMUSG00000044647	Csrnp3	A330102K23Rik|CSRNP-3|Csnrp3|Mbu1|taip-2	cysteine-serine-rich nuclear protein 3	protein-coding
mm_128586.1	chr15	58076437	58076455	-	1	NA	promoter-TSS (NM_001042438)	promoter-TSS (NM_001042438)	62	NM_001042438	22770	Mm.244931	NM_009572	ENSMUSG00000022361	Zhx1	-	zinc fingers and homeoboxes 1	protein-coding
mm_5999.1	chr1	58962507	58962517	-	1	NA	intron (NM_172406, intron 1 of 15)	intron (NM_172406, intron 1 of 15)	10970	NM_172406	70827	Mm.222887	NM_172406	ENSMUSG00000026028	Trak2	2900022D04Rik|4733401O11Rik|AI480836|AW046271|Als2cr3|CALS-C|GRIF-1|GRIF1|OIP98|mKIAA0549	trafficking protein, kinesin binding 2	protein-coding
mm_33903.1	chr4	136286062	136286114	+	1	NA	promoter-TSS (NM_009557)	promoter-TSS (NM_009557)	19	NM_009557	22704	Mm.1504	NM_009557	ENSMUSG00000051351	Zfp46	AI426962|Mlz-4|Zfp-46|Znf436	zinc finger protein 46	protein-coding
mm_166635.1	chr6	82780501	82780541	-	1	NA	Intergenic	MTEb|LTR|ERVL-MaLR	-6067	NM_013820	15277	Mm.255848	NM_013820	ENSMUSG00000000628	Hk2	AI642394|HKII	hexokinase 2	protein-coding
mm_115022.1	chr13	98816723	98816738	+	1	NA	Intergenic	Intergenic	-1281	NM_172591	218503	Mm.23928	NM_172591	ENSMUSG00000041685	Fcho2	5832424M12Rik|AA387320	FCH domain only 2	protein-coding
mm_115478.1	chr13	3139683	3139718	-	1	NA	Intergenic	Intergenic	-9775	NR_001581	73266	Mm.335891	NR_001581		Speer6-ps1	1700039A02Rik|SPEER-6	spermatogenesis associated glutamate (E)-rich protein 6, pseudogene 1	pseudo
mm_87356.1	chr10	43656471	43656476	+	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	63046	NR_033558	414125	Mm.244305	NR_033558	ENSMUSG00000075184	F830002L21Rik	F930017D23Rik	RIKEN cDNA F830002L21 gene	ncRNA
mm_82117.1	chr9	123462076	123462090	+	1	NA	3' UTR (NM_153168, exon 21 of 21)	3' UTR (NM_153168, exon 21 of 21)	-16618	NM_013860	29806	Mm.10987	NM_013860	ENSMUSG00000025239	Limd1	AW822033|D9Ertd192e	LIM domains containing 1	protein-coding
mm_96138.1	chr11	60932046	60932123	+	1	NA	promoter-TSS (NR_027800)	promoter-TSS (NR_027800)	27	NM_008928	26397	Mm.18494	NM_008928	ENSMUSG00000018932	Map2k3	AW212142|MEK3|MKK3|Prkmk3|mMKK3b	mitogen-activated protein kinase kinase 3	protein-coding
mm_114778.1	chr13	88821883	88821914	+	1	NA	5' UTR (NM_001037987, exon 1 of 11)	5' UTR (NM_001037987, exon 1 of 11)	426	NM_001037987	13612	Mm.125580	NM_010103	ENSMUSG00000034488	Edil3	Del-1|Del1	EGF-like repeats and discoidin I-like domains 3	protein-coding
mm_98325.1	chr11	90259404	90259435	+	1	NA	intron (NM_026178, intron 2 of 6)	intron (NM_026178, intron 2 of 6)	9943	NM_026178	67468	Mm.277518	NM_026178	ENSMUSG00000003948	Mmd	1200017E07Rik|1810073C06Rik|AA690185	monocyte to macrophage differentiation-associated	protein-coding
mm_144556.1	chr18	31634375	31634390	+	1	NA	promoter-TSS (NM_172965)	promoter-TSS (NM_172965)	-1	NM_172965	269003	Mm.194538	NM_172965	ENSMUSG00000024260	Sap130	2610304F09Rik|6720406D06	Sin3A associated protein	protein-coding
mm_122164.1	chr14	31402055	31402064	-	1	NA	intron (NM_011894, intron 3 of 8)	intron (NM_011894, intron 3 of 8)	15618	NM_001347585	24056	Mm.383198	NM_011894	ENSMUSG00000021892	Sh3bp5	AI606498|SH3BP-5|Sab	SH3-domain binding protein 5 (BTK-associated)	protein-coding
mm_46928.1	chr5	114690975	114690999	-	1	NA	promoter-TSS (NM_019821)	promoter-TSS (NM_019821)	-52	NM_019821	56356	Mm.275766	NM_019821	ENSMUSG00000011884	Gltp	1110001F24Rik|C76925|C77564	glycolipid transfer protein	protein-coding
mm_101926.1	chr11	50202505	50202513	-	1	NA	exon (NM_011018, exon 7 of 8)	exon (NM_011018, exon 7 of 8)	8311	NM_001290769	18412	Mm.40828	NM_011018	ENSMUSG00000015837	Sqstm1	A170|OSF-6|Osi|STAP|STONE14|p62	sequestosome 1	protein-coding
mm_156569.1	chrX	151909852	151909866	+	1	NA	intron (NM_021523, intron 56 of 82)	intron (NM_021523, intron 56 of 82)	-2487	NR_029732	387253		NR_029732	ENSMUSG00000065602	Mirlet7f-2	Mirlet7f2|Mirnlet7f2|let-7f-2	microRNA let7f-2	ncRNA
mm_123026.1	chr14	55116945	55116980	-	1	NA	promoter-TSS (NM_177049)	promoter-TSS (NM_177049)	-27	NM_177049	319984	Mm.19047	NM_177049	ENSMUSG00000022208	Jph4	9330157P13Rik|JP-4|JPHL1	junctophilin 4	protein-coding
mm_56099.1	chr6	87459216	87459229	-	1	NA	non-coding (NR_104483, exon 11 of 11)	non-coding (NR_104483, exon 11 of 11)	30228	NM_009756	12154	Mm.483321	NM_009756	ENSMUSG00000030046	Bmp10	-	bone morphogenetic protein 10	protein-coding
mm_135210.1	chr16	36618565	36618575	-	1	NA	exon (NM_019388, exon 4 of 8)	exon (NM_019388, exon 4 of 8)	47507	NM_019388	12524	Mm.1452	NM_019388	ENSMUSG00000022901	Cd86	B7|B7-2|B7.2|B70|CLS1|Cd28l2|ETC-1|Ly-58|Ly58|MB7|MB7-2|TS/A-2	CD86 antigen	protein-coding
mm_141253.1	chr17	27580424	27580425	-	1	NA	3' UTR (NM_001291046, exon 5 of 5)	3' UTR (NM_001291046, exon 5 of 5)	-14697	NM_001002895	106672	Mm.61488	NM_001002895	ENSMUSG00000062753	AI413582	AI854251	expressed sequence AI413582	protein-coding
mm_81978.1	chr9	121314252	121314268	+	1	NA	Intergenic	Intergenic	-37088	NM_177589	209012	Mm.371804	NM_177589	ENSMUSG00000040936	Ulk4	4932415A06Rik|A730098P15	unc-51-like kinase 4	protein-coding
mm_164353.1	chr16	20590089	20590115	+	1	NA	intron (NM_001144953, intron 1 of 22)	intron (NM_001144953, intron 1 of 22)	520	NM_001144953	328643	Mm.40539	NM_182636	ENSMUSG00000046613	Vwa5b2	BB182430|EG328644|Gm1738|Gm931	von Willebrand factor A domain containing 5B2	protein-coding
mm_148981.1	chr19	7612497	7612507	+	1	NA	promoter-TSS (NM_025731)	promoter-TSS (NM_025731)	-67	NM_025731	66727	Mm.116803	NM_025731	ENSMUSG00000024973	Hrasls5	1700055A14Rik|1700086E08Rik|4921526K24Rik|HRSL5|iNAT	HRAS-like suppressor family, member 5	protein-coding
mm_167760.1	chr9	110422688	110422701	-	1	NA	3' UTR (NM_008694, exon 4 of 4)	3' UTR (NM_008694, exon 4 of 4)	2886	NM_008694	18054	Mm.236225	NM_008694	ENSMUSG00000032484	Ngp	bectenecin	neutrophilic granule protein	protein-coding
mm_75167.1	chr8	36613938	36613948	-	1	NA	promoter-TSS (NM_015802)	promoter-TSS (NM_015802)	0	NM_015802	50768	Mm.125155	NM_015802	ENSMUSG00000031523	Dlc1	A730069N07Rik|Arhgap7|HP|STARD12|dlc-1	deleted in liver cancer 1	protein-coding
mm_171578.1	chr4	147449178	147449183	+	1	NA	intron (NM_001039209, intron 1 of 2)	intron (NM_001039209, intron 1 of 2)	-104097	NM_001014397	433804	Mm.332047	NM_001014397	ENSMUSG00000065999	Zfp985	Gm13154|OTTMUSG00000010673	zinc finger protein 985	protein-coding
mm_92929.1	chr10	84526834	84526844	-	1	NA	3' UTR (NM_175451, exon 2 of 2)	3' UTR (NM_175451, exon 2 of 2)	7049	NM_175451	216197	Mm.334999	NM_175451	ENSMUSG00000046841	Ckap4	5630400A09Rik|CLIMP-63|P63	cytoskeleton-associated protein 4	protein-coding
mm_33682.1	chr4	133369721	133369743	+	1	NA	promoter-TSS (NM_016981)	promoter-TSS (NM_016981)	-40	NM_016981	20544	Mm.4312	NM_016981	ENSMUSG00000028854	Slc9a1	AW554487|Apnh|Mir5122|Nhe1|mir-5122|swe	solute carrier family 9 (sodium/hydrogen exchanger), member 1	protein-coding
mm_30916.1	chr4	32623986	32623989	+	1	NA	intron (NM_011997, intron 1 of 10)	intron (NM_011997, intron 1 of 10)	8517	NM_011997	26885	Mm.22279	NM_011997	ENSMUSG00000028282	Casp8ap2	D4Ertd659e|FLASH	caspase 8 associated protein 2	protein-coding
mm_160897.1	chr11	73371006	73371006	+	1	NA	promoter-TSS (NM_001172686)	promoter-TSS (NM_001172686)	-240	NM_001172686	258924	Mm.236410	NM_146922	ENSMUSG00000063881	Olfr376	MOR135-12	olfactory receptor 376	protein-coding
mm_132530.1	chr16	37835448	37835460	+	1	NA	3' UTR (NM_008047, exon 11 of 11)	3' UTR (NM_008047, exon 11 of 11)	-32946	NM_177093	320184	Mm.390882	NM_177093	ENSMUSG00000034158	Lrrc58	1810012N18Rik|C330018J07Rik	leucine rich repeat containing 58	protein-coding
mm_98966.1	chr11	98682559	98682573	+	1	NA	promoter-TSS (NM_009439)	promoter-TSS (NM_009439)	12	NM_009439	22123	Mm.12194	NM_009439	ENSMUSG00000017221	Psmd3	AI255837|AntP91a|D11Bwg1349e|Psd3|Tstap91a	proteasome (prosome, macropain) 26S subunit, non-ATPase, 3	protein-coding
mm_82281.1	chr9	7556271	7556278	-	1	NA	Intergenic	Intergenic	-2155	NM_008611	17394	Mm.16415	NM_008611	ENSMUSG00000005800	Mmp8	BB138268	matrix metallopeptidase 8	protein-coding
mm_119758.1	chr14	54168597	54168605	+	1	NA	Intergenic	Intergenic	85328	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_143487.1	chr17	71310900	71310917	-	1	NA	promoter-TSS (NM_145158)	promoter-TSS (NM_145158)	57	NM_145158	246707	Mm.23462	NM_145158	ENSMUSG00000024053	Emilin2	FOAP-10	elastin microfibril interfacer 2	protein-coding
mm_70341.1	chr8	4613153	4613177	+	1	NA	promoter-TSS (NM_145591)	promoter-TSS (NM_145591)	-5	NM_145591	233987	Mm.102799	NM_145591	ENSMUSG00000058748	Zfp958	-	zinc finger protein 958	protein-coding
mm_53628.1	chr6	140514917	140514950	+	1	NA	intron (NM_144920, intron 3 of 30)	intron (NM_144920, intron 3 of 30)	90834	NM_144920	109135	Mm.247670	NM_144920	ENSMUSG00000030231	Plekha5	2810431N21Rik|AI428202|AK129423|AMH-Cre|Ayu21-9|Gt(pU21)9Imeg|Pepp2|Tg(AMH-cre)1Flor	pleckstrin homology domain containing, family A member 5	protein-coding
mm_145528.1	chr18	60747080	60747139	+	1	NA	Intergenic	Intergenic	-27487	NM_020600	20044	Mm.43778	NM_020600	ENSMUSG00000024608	Rps14	2600014J02Rik|AL023078	ribosomal protein S14	protein-coding
mm_156773.1	chrX	160794752	160794758	+	1	NA	3' UTR (NM_011302, exon 6 of 6)	3' UTR (NM_011302, exon 6 of 6)	26742	NM_011302	20147	Mm.41982	NM_011302	ENSMUSG00000031293	Rs1	Rs1h|Xlrs1|tmgc1	retinoschisis (X-linked, juvenile) 1 (human)	protein-coding
mm_94211.1	chr11	3124044	3124054	+	1	NA	promoter-TSS (NR_003517)	promoter-TSS (NR_003517)	28	NR_003517	236604	Mm.247625	NM_001004146		Pisd-ps1	-	phosphatidylserine decarboxylase, pseudogene 1	pseudo
mm_61951.1	chr7	90207636	90207652	+	1	NA	3' UTR (NM_001252521, exon 20 of 20)	3' UTR (NM_001252521, exon 20 of 20)	57788	NM_029256	75338	Mm.487222	NM_029256	ENSMUSG00000030617	Ccdc83	4930549K11Rik|4930554C01Rik|4932423M01Rik	coiled-coil domain containing 83	protein-coding
mm_144617.1	chr18	32837272	32837307	+	1	NA	promoter-TSS (NM_001110015)	promoter-TSS (NM_001110015)	-2	NR_045381	75795	Mm.382634	NR_045381	ENSMUSG00000097553	4930455D15Rik	-	RIKEN cDNA 4930455D15 gene	ncRNA
mm_10970.1	chr2	25706796	25706824	+	1	NA	promoter-TSS (NM_023326)	promoter-TSS (NM_023326)	-69	NM_023326	107771	Mm.330057	NM_023326	ENSMUSG00000049086	Bmyc	2900002K07Rik|AW060705|Mycb	brain expressed myelocytomatosis oncogene	protein-coding
mm_11441.1	chr2	32034433	32034454	+	1	NA	exon (NM_172268, exon 29 of 36)	exon (NM_172268, exon 29 of 36)	-16503	NR_106135	102466844		NR_106135	ENSMUSG00000099075	Mir7674	Gm27563|mmu-mir-7674	microRNA 7674	ncRNA
mm_130536.1	chr15	98937328	98937351	-	1	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	-2949	NM_011654	22143	Mm.392113	NM_011654	ENSMUSG00000023004	Tuba1b	Tuba2	tubulin, alpha 1B	protein-coding
mm_118139.1	chr13	104975981	104975982	-	1	NA	intron (NM_029879, intron 3 of 5)	intron (NM_029879, intron 3 of 5)	78949	NM_029879	52882	Mm.100348	NM_029879	ENSMUSG00000021719	Rgs7bp	A930030I01Rik|AI842293|D13Bwg1146e|R7bp	regulator of G-protein signalling 7 binding protein	protein-coding
mm_36856.1	chr4	106855831	106855842	-	1	NA	Intergenic	Intergenic	-50829	NM_001347159	329910	Mm.222956	NM_025590	ENSMUSG00000034853	Acot11	1110020M10Rik|2010309H15Rik|AW060409|BFIT|BFIT1|Thea|Them1|mKIAA0707	acyl-CoA thioesterase 11	protein-coding
mm_71638.1	chr8	57490332	57490359	+	1	NA	non-coding (NR_126555, exon 2 of 3)	non-coding (NR_126555, exon 2 of 3)	2382	NR_126555	78353	Mm.426240	NR_126553	ENSMUSG00000096917	2500002B13Rik	-	RIKEN cDNA 2500002B13 gene	ncRNA
mm_94722.1	chr11	20632098	20632108	+	1	NA	5' UTR (NM_001038625, exon 1 of 2)	5' UTR (NM_001038625, exon 1 of 2)	126	NM_001038625	58172	Mm.339676	NM_021372	ENSMUSG00000049800	Sertad2	AB041541|AU021878|Kiaa0127|MNCb-1504|SEI-2|Sei2|TRIP-Br2|mKIAA0127	SERTA domain containing 2	protein-coding
mm_2192.1	chr1	89103769	89103783	+	1	NA	intron (NM_133816, intron 1 of 5)	intron (NM_133816, intron 1 of 5)	33314	NM_133816	98402	Mm.170983	NM_133816	ENSMUSG00000036206	Sh3bp4	AI594717|AW227605|BOG25	SH3-domain binding protein 4	protein-coding
mm_32862.1	chr4	118411737	118411758	+	1	NA	exon (NM_173719, exon 4 of 8)	exon (NM_173719, exon 4 of 8)	2410	NM_020000	80509	Mm.259567	NM_020000	ENSMUSG00000006392	Med8	2210021A15Rik|AB041805|ARC32	mediator complex subunit 8	protein-coding
mm_50490.1	chr6	48988819	48988819	+	1	NA	exon (NM_172888, exon 1 of 5)	exon (NM_172888, exon 1 of 5)	1958	NM_172888	243377	Mm.446302	NM_172888	ENSMUSG00000039215	Svs1	9530003A11	seminal vesicle secretory protein 1	protein-coding
mm_3508.1	chr1	150107256	150107257	+	1	NA	3' UTR (NM_011198, exon 10 of 10)	3' UTR (NM_011198, exon 10 of 10)	7225	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_7479.1	chr1	120504941	120504952	-	1	NA	5' UTR (NM_010766, exon 1 of 17)	5' UTR (NM_010766, exon 1 of 17)	138	NM_010766	17167	Mm.1856	NM_010766	ENSMUSG00000026390	Marco	AI323439|Ly112|Scara2	macrophage receptor with collagenous structure	protein-coding
mm_97341.1	chr11	77456433	77456444	+	1	NA	3' UTR (NM_001291190, exon 14 of 14)	3' UTR (NM_001291190, exon 14 of 14)	-7475	NM_139129	216961	Mm.33477	NM_139128	ENSMUSG00000020836	Coro6	-	coronin 6	protein-coding
mm_53420.1	chr6	134035640	134035689	+	1	NA	promoter-TSS (NM_007961)	promoter-TSS (NM_007961)	-36	NM_001303102	14011	Mm.269995	NM_007961	ENSMUSG00000030199	Etv6	AW123102|AW557856|Tel	ets variant 6	protein-coding
mm_11227.1	chr2	29788322	29788335	+	1	NA	promoter-TSS (NM_178693)	promoter-TSS (NM_178693)	65	NM_178693	227683	Mm.245948	NM_178693	ENSMUSG00000026798	Coq4	A330041N06|D2Ertd97e	coenzyme Q4	protein-coding
mm_39982.1	chr5	32459239	32459249	+	1	NA	5' UTR (NM_172707, exon 1 of 8)	5' UTR (NM_172707, exon 1 of 8)	274	NM_172707	19046	Mm.241931	NM_172707	ENSMUSG00000014956	Ppp1cb	1200010B19	protein phosphatase 1, catalytic subunit, beta isoform	protein-coding
mm_154378.1	chrM	11195	11230	+	1	NA	NA	Intergenic	NA	NA								
mm_167463.1	chr8	124562827	124562832	-	1	NA	intron (NM_007428, intron 2 of 4)	intron (NM_007428, intron 2 of 4)	6878	NM_007428	11606	Mm.301626	NM_007428	ENSMUSG00000031980	Agt	AI265500|AngI|AngII|Aogen|Serpina8	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	protein-coding
mm_87497.1	chr10	51526402	51526439	+	1	NA	Intergenic	LTRIS2|LTR|ERV1	35522	NM_013532	14728	Mm.34408	NM_013532	ENSMUSG00000062593	Lilrb4a	CD85K|Gp49b|HM18|ILT3|LIR-5|Lilrb4|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4A	protein-coding
mm_163917.1	chr14	37049024	37049028	-	1	NA	promoter-TSS (NM_021340)	promoter-TSS (NM_021340)	-12	NM_001301692	57811	Mm.20460	NM_021340	ENSMUSG00000021804	Rgr	-	retinal G protein coupled receptor	protein-coding
mm_106521.1	chr11	120560338	120560376	-	1	NA	TTS (NM_011032)	TTS (NM_011032)	-9225	NM_026814	68701	Mm.46477	NM_026814	ENSMUSG00000025129	Ppp1r27	1110033I14Rik|Dysfip1|toonin	protein phosphatase 1, regulatory subunit 27	protein-coding
mm_98828.1	chr11	97404389	97404440	+	1	NA	Intergenic	Intergenic	41863	NM_138657	192157	Mm.34339	NM_138657	ENSMUSG00000038485	Socs7	2310063P06Rik|C85125|Nap4	suppressor of cytokine signaling 7	protein-coding
mm_10525.1	chr2	16396578	16396597	+	1	NA	intron (NM_026162, intron 1 of 13)	intron (NM_026162, intron 1 of 13)	40283	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding
mm_78069.1	chr9	15311164	15311167	+	1	NA	intron (NM_029248, intron 5 of 6)	intron (NM_029248, intron 5 of 6)	-1446	NR_106108	102465758		NR_106108	ENSMUSG00000105847	Gm25500	Mir7650|mmu-mir-7650	predicted gene, 25500	ncRNA
mm_64101.1	chr7	141010544	141010566	+	1	NA	exon (NM_025378, exon 1 of 2)	exon (NM_025378, exon 1 of 2)	189	NM_025378	66141	Mm.141021	NM_025378	ENSMUSG00000025492	Ifitm3	1110004C05Rik|Cd225|Cdw217|DSPA2b|Fgls|IP15|mil-1	interferon induced transmembrane protein 3	protein-coding
mm_106918.1	chr12	8220027	8220033	+	1	NA	intron (NM_001167767, intron 1 of 5)	intron (NM_001167767, intron 1 of 5)	11903	NM_001167767	68832	Mm.25608	NM_172401	ENSMUSG00000037669	Ldah	1110057K04Rik|mLDAH	lipid droplet associated hydrolase	protein-coding
mm_31906.1	chr4	84698133	84698161	+	1	NA	Intergenic	Intergenic	-23061	NM_172870	242509	Mm.190774	NM_172870	ENSMUSG00000028487	Bnc2	5031434M05Rik|8430420F16Rik	basonuclin 2	protein-coding
mm_36909.1	chr4	108031939	108031961	-	1	NA	promoter-TSS (NM_001285956)	promoter-TSS (NM_001285956)	140	NM_001285958	242608	Mm.74710	NM_172874	ENSMUSG00000028600	Podn	9430070G18|Pcan|SLRR5A	podocan	protein-coding
mm_35104.1	chr4	9526215	9526223	-	1	NA	intron (NM_023066, intron 17 of 23)	ID_B1|SINE|B4	117498	NM_001177853	65973	Mm.222206	NM_023066	ENSMUSG00000028207	Asph	2310005F16Rik|3110001L23Rik|AI848629|AW261690|AW561901|BAH|C79816|cI-37	aspartate-beta-hydroxylase	protein-coding
mm_34414.1	chr4	145258444	145258451	+	1	NA	Intergenic	Intergenic	-11577	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_154431.1	chrM	680	688	-	1	NA	NA	Intergenic	NA	NA								
mm_146935.1	chr18	32135953	32135954	-	1	NA	intron (NM_001042767, intron 1 of 8)	intron (NM_001042767, intron 1 of 8)	2252	NM_008934	19123	Mm.2786	NM_008934	ENSMUSG00000024386	Proc	PC	protein C	protein-coding
mm_157840.1	chrX	74368473	74368543	-	1	NA	promoter-TSS (NM_145405)	promoter-TSS (NM_145405)	40	NR_045779	27643	Mm.3979	NM_145405	ENSMUSG00000015290	Ubl4a	DXHXS254E|DXS254E|DXS254Eh|Gdx|Ubl4	ubiquitin-like 4A	protein-coding
mm_87921.1	chr10	62506565	62506593	+	1	NA	intron (NM_011157, intron 1 of 2)	intron (NM_011157, intron 1 of 2)	1176	NM_011157	19073	Mm.338790	NM_011157	ENSMUSG00000020077	Srgn	Prg|Prg1|Sgc	serglycin	protein-coding
mm_72352.1	chr8	79663738	79663755	+	1	NA	exon (NM_001256033, exon 12 of 21)	exon (NM_001256033, exon 12 of 21)	24070	NM_001081164	73945	Mm.34348	NM_001081164	ENSMUSG00000036990	Otud4	4930431L18Rik|AI449692|D8Ertd69e|mKIAA1046	OTU domain containing 4	protein-coding
mm_78820.1	chr9	44086207	44086219	+	1	NA	intron (NM_198091, intron 1 of 11)	intron (NM_198091, intron 1 of 11)	1293	NM_198091	53376	Mm.272770	NM_016808	ENSMUSG00000032010	Usp2	B930035K21Rik|Ubp41	ubiquitin specific peptidase 2	protein-coding
mm_123748.1	chr14	70192719	70192738	-	1	NA	promoter-TSS (NM_001271409)	promoter-TSS (NM_001271409)	-482	NM_001271409	20410	Mm.5068	NM_011366	ENSMUSG00000022091	Sorbs3	SCAM-1|SH3P3|Sh3d4|vinexin-g	sorbin and SH3 domain containing 3	protein-coding
mm_53368.1	chr6	129408855	129408876	+	1	NA	promoter-TSS (NM_001205364)	promoter-TSS (NM_001205364)	3	NM_172732	232414	Mm.391518	NM_172732	ENSMUSG00000046080	Clec9a	9830005G06Rik|DNGR-1	C-type lectin domain family 9, member a	protein-coding
mm_124610.1	chr15	3279440	3279457	+	1	NA	exon (NM_009155, exon 5 of 5)	exon (NM_009155, exon 5 of 5)	8471	NM_009155	20363	Mm.392203	NM_009155	ENSMUSG00000064373	Selenop	AU018766|D15Ucla1|Se-P|Sepp1|selp	selenoprotein P	protein-coding
mm_100064.1	chr11	115381868	115381899	+	1	NA	promoter-TSS (NM_001080929)	promoter-TSS (NM_001080929)	-33	NM_001080929	237988	Mm.102872	NM_001080929	ENSMUSG00000050910	Cdr2l	D030068L24Rik|Gm21	cerebellar degeneration-related protein 2-like	protein-coding
mm_81138.1	chr9	106656403	106656403	+	1	NA	promoter-TSS (NM_001160353)	promoter-TSS (NM_001160353)	-294	NM_001160353	108068	Mm.410822	NM_001160353	ENSMUSG00000023192	Grm2	4930441L02Rik|Gprc1b|mGluR2|mGluR7	glutamate receptor, metabotropic 2	protein-coding
mm_83420.1	chr9	44945930	44945937	-	1	NA	intron (NM_001346698, intron 10 of 20)	intron (NM_001346698, intron 10 of 20)	19667	NM_001346698	140630	Mm.215069	NM_145400	ENSMUSG00000059890	Ube4a	4732444G18Rik|9930123J21Rik|UFD2b	ubiquitination factor E4A	protein-coding
mm_63638.1	chr7	128540028	128540053	+	1	NA	exon (NM_013863, exon 2 of 4)	exon (NM_013863, exon 2 of 4)	16457	NM_013863	29810	Mm.84073	NM_013863	ENSMUSG00000030847	Bag3	AA407278|Bis|mg638	BCL2-associated athanogene 3	protein-coding
mm_90744.1	chr10	5368486	5368497	-	1	NA	intron (NM_001347732, intron 13 of 145)	intron (NM_001347732, intron 13 of 145)	119823	NM_001347711	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_19778.1	chr2	106964303	106964305	-	1	NA	3' UTR (NM_173750, exon 5 of 5)	3' UTR (NM_173750, exon 5 of 5)	6087	NM_173750	212772	Mm.381231	NM_173750	ENSMUSG00000027122	Arl14ep	2700007P21Rik|4930448O08Rik|ARF7EP	ADP-ribosylation factor-like 14 effector protein	protein-coding
mm_76300.1	chr8	84249631	84249641	-	1	NA	TTS (NM_026423)	TTS (NM_026423)	125	NM_001007571	101966	Mm.200723	NM_001007571	ENSMUSG00000019362	D8Ertd738e	AA589584	DNA segment, Chr 8, ERATO Doi 738, expressed	protein-coding
mm_148404.1	chr19	3851940	3851948	+	1	NA	non-coding (NR_073190, exon 1 of 13)	non-coding (NR_073190, exon 1 of 13)	171	NR_073190	12660	Mm.225505	NM_013490	ENSMUSG00000024843	Chka	CK|CK/EK-alpha|Chetk-alpha|Chk|ChoK|EK|EtnK-alpha	choline kinase alpha	protein-coding
mm_86083.1	chr9	114819034	114819042	-	1	NA	intron (NM_027294, intron 1 of 3)	Charlie29a|DNA|hAT-Charlie	25114	NM_027294	70031	Mm.150064	NM_027294	ENSMUSG00000041012	Cmtm8	2700018N07Rik|AA408515|Cklfsf8	CKLF-like MARVEL transmembrane domain containing 8	protein-coding
mm_43443.1	chr5	136102324	136102378	+	1	NA	exon (NM_133914, exon 13 of 21)	exon (NM_133914, exon 13 of 21)	-3171	NR_106002	102465626		NR_106002	ENSMUSG00000099003	Mir7035	Gm27661|mmu-mir-7035	microRNA 7035	ncRNA
mm_71102.1	chr8	35376681	35376696	+	1	NA	intron (NM_177741, intron 1 of 1)	CpG	947	NM_177741	244416	Mm.247126	NM_177741	ENSMUSG00000046794	Ppp1r3b	6430576E21|AW821953|GL|PTG	protein phosphatase 1, regulatory (inhibitor) subunit 3B	protein-coding
mm_42284.1	chr5	114289269	114289278	+	1	NA	Intergenic	Intergenic	-15512	NM_148935	116810	Mm.17709	NM_148935	ENSMUSG00000042002	Foxn4	-	forkhead box N4	protein-coding
mm_98455.1	chr11	94946770	94946804	+	1	NA	exon (NM_007742, exon 35 of 51)	exon (NM_007742, exon 35 of 51)	10563	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_166197.1	chr5	37276269	37276304	+	1	NA	exon (NM_001136058, exon 5 of 14)	exon (NM_001136058, exon 5 of 14)	30522	NM_007765	12933	Mm.290995	NM_007765	ENSMUSG00000029121	Crmp1	CRMP-1|DRP-1|Dpysl1|ULIP-3|Ulip3	collapsin response mediator protein 1	protein-coding
mm_51001.1	chr6	63579837	63579839	+	1	NA	intron (NM_008167, intron 2 of 15)	intron (NM_008167, intron 2 of 15)	322981	NM_008167	14804	Mm.439651	NM_008167	ENSMUSG00000071424	Grid2	B230104L07Rik|GluD2|GluRdelta2|Lc|Lc<J>|MMS10-AC|Ms10ac|cpr|ho|nmf408|tpr	glutamate receptor, ionotropic, delta 2	protein-coding
mm_93014.1	chr10	87492760	87492771	-	1	NA	exon (NM_008553, exon 1 of 2)	exon (NM_008553, exon 1 of 2)	895	NM_008553	17172	Mm.136217	NM_008553	ENSMUSG00000020052	Ascl1	AI225900|ASH1|Mash1|bHLHa46	achaete-scute family bHLH transcription factor 1	protein-coding
mm_142593.1	chr17	46752155	46752167	-	1	NA	promoter-TSS (NM_001305990)	promoter-TSS (NM_001305990)	53	NM_001305989	72029	Mm.240325	NM_028065	ENSMUSG00000023973	Cnpy3	1600025D17Rik|2410050O22Rik|AI413153|CAG4A|ERDA5|PRAT4A|Tnrc5	canopy FGF signaling regulator 3	protein-coding
mm_104241.1	chr11	88718224	88718294	-	1	NA	promoter-TSS (NM_054043)	promoter-TSS (NM_054043)	8	NM_001201341	76626	Mm.400451	NM_054043	ENSMUSG00000069769	Msi2	1700105C15Rik|AI451722|AI563628|AW489193|Msi2h	musashi RNA-binding protein 2	protein-coding
mm_31816.1	chr4	66841063	66841071	+	1	NA	exon (NM_021297, exon 3 of 3)	exon (NM_021297, exon 3 of 3)	13516	NM_021297	21898	Mm.38049	NM_021297	ENSMUSG00000039005	Tlr4	Lps|Ly87|Ran/M1|Rasl2-8	toll-like receptor 4	protein-coding
mm_64015.1	chr7	140218388	140218403	+	1	NA	5' UTR (NM_172909, exon 1 of 14)	5' UTR (NM_172909, exon 1 of 14)	128	NM_172909	244233	Mm.19283	NM_172909	ENSMUSG00000025461	Cd163l1	B430307C05|E430002D04Rik|Scart1	CD163 molecule-like 1	protein-coding
mm_25212.1	chr3	103836069	103836079	+	1	NA	exon (NM_001142960, exon 3 of 4)	exon (NM_001142960, exon 3 of 4)	3378	NM_001142960	229672	Mm.297245	NM_001142959	ENSMUSG00000044165	Bcl2l15	Bfk|Gm566	BCLl2-like 15	protein-coding
mm_78776.1	chr9	43744400	43744437	+	1	NA	promoter-TSS (NM_021424)	promoter-TSS (NM_021424)	-158	NM_021424	58235	Mm.335096	NM_021424	ENSMUSG00000032012	Nectin1	AI835281|AW549174|Cd111|HIgR|HveC|PRR|PRR1|Pvrl1|nectin-1	nectin cell adhesion molecule 1	protein-coding
mm_119254.1	chr14	33923801	33923812	+	1	NA	5' UTR (NM_145741, exon 1 of 3)	5' UTR (NM_145741, exon 1 of 3)	219	NM_145741	14560	Mm.432071	NM_145741	ENSMUSG00000021943	Gdf10	Bmp3b	growth differentiation factor 10	protein-coding
mm_112422.1	chr13	4059672	4059672	+	1	NA	promoter-TSS (NM_134072)	promoter-TSS (NM_134072)	81	NM_134072	105387	Mm.26838	NM_134072	ENSMUSG00000033715	Akr1c14	9030611N15Rik|AW557061	aldo-keto reductase family 1, member C14	protein-coding
mm_126757.1	chr15	85811324	85811334	+	1	NA	intron (NM_197998, intron 1 of 4)	CpG	368	NM_001164626	72355	Mm.33706	NM_197998	ENSMUSG00000064284	Cdpf1	2210021J22Rik	cysteine rich, DPF motif domain containing 1	protein-coding
mm_103993.1	chr11	84846482	84846502	-	1	NA	intron (NM_153144, intron 6 of 13)	RSINE1|SINE|B4	17314	NR_046281	74995	Mm.84413	NR_046281	ENSMUSG00000086799	4930502E09Rik	-	RIKEN cDNA 4930502E09 gene	ncRNA
mm_51691.1	chr6	86526737	86526796	+	1	NA	promoter-TSS (NM_011865)	promoter-TSS (NM_011865)	-564	NR_037960	72012	Mm.349174	NR_037960	ENSMUSG00000097048	1600020E01Rik	-	RIKEN cDNA 1600020E01 gene	ncRNA
mm_170332.1	chr18	44724669	44724682	-	1	NA	exon (NM_001085373, exon 3 of 19)	exon (NM_001085373, exon 3 of 19)	-62409	NM_001085374	328949	Mm.312511	NM_001033406	ENSMUSG00000071856	Mcc	D18Ertd451e|E330037C19	mutated in colorectal cancers	protein-coding
mm_89321.1	chr10	87931141	87931169	+	1	NA	3' UTR (NM_010512, exon 5 of 5)	3' UTR (NM_010512, exon 5 of 5)	-35516	NR_000040	22172	Mm.391420	NR_000040		Tyms-ps	-	thymidylate synthase, pseudogene	pseudo
mm_16028.1	chr2	167589549	167589559	+	1	NA	Intergenic	L2a|LINE|L2	42451	NM_001311146	66589	Mm.278783	NM_023230	ENSMUSG00000078923	Ube2v1	0610011J09Rik|AI256840|CROC-1|CROC1|D7Bwg1382e|UEV-1	ubiquitin-conjugating enzyme E2 variant 1	protein-coding
mm_83334.1	chr9	44251466	44251491	-	1	NA	promoter-TSS (NM_133226)	promoter-TSS (NM_133226)	-14	NM_133226	170761	Mm.29872	NM_133226	ENSMUSG00000032105	Pdzd3	NaPi-Cap2|Pdzk2	PDZ domain containing 3	protein-coding
mm_43236.1	chr5	129989020	129989040	+	1	NA	TTS (NM_010368)	TTS (NM_010368)	13798	NM_010368	110006	Mm.3317	NM_010368	ENSMUSG00000025534	Gusb	AI747421|Gur|Gus|Gus-r|Gus-s|Gus-t|Gus-u|Gut|asd|g	glucuronidase, beta	protein-coding
mm_129600.1	chr15	79834324	79834334	-	1	NA	promoter-TSS (NM_001013360)	promoter-TSS (NM_001013360)	4	NM_001013360	504193	Mm.38438	NM_029079	ENSMUSG00000089837	Npcd	Cbx6-Nptxr	neuronal pentraxin chromo domain	protein-coding
mm_95315.1	chr11	46404721	46404730	+	1	NA	promoter-TSS (NM_001013783)	promoter-TSS (NM_001013783)	-3	NM_001013783	432552	Mm.443244	NM_001013783	ENSMUSG00000020401	Fam71b	Gari-l3|OTTMUSG00000005491	family with sequence similarity 71, member B	protein-coding
mm_65024.1	chr7	18404037	18404041	-	1	NA	Intergenic	RLTR46A2|LTR|ERVK	28016	NM_054063	114871	Mm.362025	NM_054063	ENSMUSG00000030373	Psg28	cea16	pregnancy-specific glycoprotein 28	protein-coding
mm_51582.1	chr6	83794975	83794985	+	1	NA	promoter-TSS (NM_001164187)	promoter-TSS (NM_001164187)	-20	NM_001347315	56174	Mm.190650	NM_019542	ENSMUSG00000034744	Nagk	Gnk	N-acetylglucosamine kinase	protein-coding
mm_162906.1	chr10	117287849	117287881	+	1	NA	TTS (NM_013590)	TTS (NM_013590)	5003	NM_013590	17110	Mm.177539	NM_013590	ENSMUSG00000069515	Lyz1	Lyz|Lyzf3|Lzp-s	lysozyme 1	protein-coding
mm_150226.1	chr19	33968764	33968774	+	1	NA	exon (NM_026334, exon 6 of 10)	exon (NM_026334, exon 6 of 10)	7521	NM_026334	67717	Mm.329816	NM_026334	ENSMUSG00000024768	Lipf	2310051B21Rik|AV082900	lipase, gastric	protein-coding
mm_165096.1	chr19	54728347	54728351	+	1	NA	Intergenic	Intergenic	371098	NM_008149	14732	Mm.210196	NM_008149	ENSMUSG00000024978	Gpam	GPAT|GPAT1	glycerol-3-phosphate acyltransferase, mitochondrial	protein-coding
mm_50220.1	chr6	42349827	42349837	+	1	NA	promoter-TSS (NM_001289618)	promoter-TSS (NM_001289618)	4	NM_001289619	22793	Mm.282303	NM_011777	ENSMUSG00000029860	Zyx	9530098H06Rik|R75157	zyxin	protein-coding
mm_110322.1	chr12	34770639	34770641	-	1	NA	intron (NM_001271386, intron 3 of 27)	ID_B1|SINE|B4	146455	NM_001271386	79221	Mm.310551	NM_024124	ENSMUSG00000004698	Hdac9	AV022454|D030072B18Rik|HD7B|HD9|HDRP|Hdac7b|Mitr|mKIAA0744	histone deacetylase 9	protein-coding
mm_132996.1	chr16	55818140	55818190	+	1	NA	exon (NM_030612, exon 7 of 14)	exon (NM_030612, exon 7 of 14)	3973	NM_001159394	80859	Mm.247272	NM_030612	ENSMUSG00000035356	Nfkbiz	AA408868|INAP|Mail	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, zeta	protein-coding
mm_163367.1	chr12	35772846	35772846	+	1	NA	Intergenic	Intergenic	-77728	NR_045050	71581	Mm.100110	NR_045050		9130015A21Rik	100043575|Gm4527	RIKEN cDNA 9130015A21 gene	ncRNA
mm_133067.1	chr16	58670236	58670246	+	1	NA	promoter-TSS (NM_007757)	promoter-TSS (NM_007757)	33	NM_007757	12892	Mm.291519	NM_007757	ENSMUSG00000022742	Cpox	CPX|Cpo|HCP|cac|nct	coproporphyrinogen oxidase	protein-coding
mm_95871.1	chr11	58049648	58049659	+	1	NA	intron (NM_028451, intron 10 of 18)	intron (NM_028451, intron 10 of 18)	40589	NM_028451	73158	Mm.248843	NM_028451	ENSMUSG00000037331	Larp1	1810024J12Rik|3110040D16Rik|Larp|mKIAA0731	La ribonucleoprotein domain family, member 1	protein-coding
mm_128115.1	chr15	28026011	28026021	-	1	NA	promoter-TSS (NM_001081302)	promoter-TSS (NM_001081302)	-168	NM_001081302	223435	Mm.485422	NM_001081302	ENSMUSG00000022263	Trio	6720464I07Rik|AA408740|Solo	triple functional domain (PTPRF interacting)	protein-coding
mm_82040.1	chr9	122128955	122128963	+	1	NA	intron (NM_001164572, intron 1 of 5)	intron (NM_001164572, intron 1 of 5)	11693	NM_133741	20623	Mm.257989	NM_133741	ENSMUSG00000038145	Snrk	2010012F07Rik|AI448042|AW547029|E030034B15|R74830|mKIAA0096	SNF related kinase	protein-coding
mm_69106.1	chr7	127021142	127021152	-	1	NA	promoter-TSS (NM_001102563)	promoter-TSS (NM_001102563)	64	NM_001102563	69017	Mm.392047	NM_001102563	ENSMUSG00000045114	Prrt2	1500031I19Rik|AI195361|DSPB3	proline-rich transmembrane protein 2	protein-coding
mm_58621.1	chr7	5069094	5069110	+	1	NA	intron (NM_133671, intron 5 of 11)	intron (NM_133671, intron 5 of 11)	6959	NM_001205231	22185	Mm.360389	NM_133671	ENSMUSG00000030435	U2af2	65kDa	U2 small nuclear ribonucleoprotein auxiliary factor (U2AF) 2	protein-coding
mm_104915.1	chr11	99759226	99759230	-	1	NA	Intergenic	Intergenic	13685	NM_001126322	100040276	Mm.475095	NM_001126322	ENSMUSG00000078668	Gm11595	OTTMUSG00000002543	predicted gene 11595	protein-coding
mm_149591.1	chr19	16141083	16141083	+	1	NA	intron (NM_008139, intron 1 of 6)	intron (NM_008139, intron 1 of 6)	8252	NM_008139	14682	Mm.439701	NM_008139	ENSMUSG00000024639	Gnaq	1110005L02Rik|6230401I02Rik|AA408290|AW060788|Dsk1|Dsk10|Galphaq|Gq|GqI	guanine nucleotide binding protein, alpha q polypeptide	protein-coding
mm_107881.1	chr12	69987191	69987199	+	1	NA	promoter-TSS (NM_022028)	promoter-TSS (NM_022028)	-193	NM_022028	64010	Mm.390480	NM_022028	ENSMUSG00000021067	Sav1	1700040G09Rik|Salv|Sav|WW45|Wwp3|Wwp4	salvador family WW domain containing 1	protein-coding
mm_28440.1	chr3	90490976	90491038	-	1	NA	promoter-TSS (NM_133854)	promoter-TSS (NM_133854)	6	NM_133854	20615	Mm.331182	NM_133854	ENSMUSG00000001018	Snapin	25kDa|AA407989|AV026596|Bloc1s7|Snap25bp|Snapap	SNAP-associated protein	protein-coding
mm_117629.1	chr13	92131608	92131680	-	1	NA	Intergenic	CpG	-143602	NM_009027	19418	Mm.248630	NM_009027	ENSMUSG00000021708	Rasgrf2	6330417G04Rik|AW048350|Grf2|Ras-GRF2	RAS protein-specific guanine nucleotide-releasing factor 2	protein-coding
mm_1821.1	chr1	82586910	82586938	+	1	NA	promoter-TSS (NM_007735)	promoter-TSS (NM_007735)	3	NM_007734	12828	Mm.389135	NM_007734	ENSMUSG00000079465	Col4a3	[a]3(IV)|alpha3(IV)	collagen, type IV, alpha 3	protein-coding
mm_80681.1	chr9	91362096	91362116	+	1	NA	intron (NM_009573, intron 2 of 2)	intron (NM_009573, intron 2 of 2)	3693	NM_009573	22771	Mm.335350	NM_009573	ENSMUSG00000032368	Zic1	ZIC|ZNF201	zinc finger protein of the cerebellum 1	protein-coding
mm_100008.1	chr11	114852054	114852075	+	1	NA	promoter-TSS (NM_147217)	promoter-TSS (NM_147217)	34	NM_147217	70355	Mm.242413	NM_147217	ENSMUSG00000051043	Gprc5c	1110028I06Rik|3200002M13Rik|Raig3	G protein-coupled receptor, family C, group 5, member C	protein-coding
mm_82166.1	chr9	123806492	123806504	+	1	NA	promoter-TSS (NM_030712)	promoter-TSS (NM_030712)	21	NM_030712	80901	Mm.124289	NM_030712	ENSMUSG00000048521	Cxcr6	BB217514|BONZO|STRL33	chemokine (C-X-C motif) receptor 6	protein-coding
mm_1061.1	chr1	58973691	58973701	+	1	NA	promoter-TSS (NM_172406)	promoter-TSS (NM_172406)	125	NM_172656	227154	Mm.286006	NM_172656	ENSMUSG00000026027	Stradb	AA792893|Als2cr2|B830008M19|D1Ucla2|ILPIP|ILPIPA|PRO1038|Papk|Syradb	STE20-related kinase adaptor beta	protein-coding
mm_142733.1	chr17	48352266	48352272	-	1	NA	TTS (NM_031254)	TTS (NM_031254)	5868	NM_001272078	83433	Mm.261623	NM_031254	ENSMUSG00000023992	Trem2	TREM-2|Trem2a|Trem2b|Trem2c	triggering receptor expressed on myeloid cells 2	protein-coding
mm_127204.1	chr15	99126783	99126822	+	1	NA	promoter-TSS (NM_139140)	promoter-TSS (NM_139140)	-43	NM_139140	72572	Mm.276650	NM_139140	ENSMUSG00000051934	Spats2	2700012F11Rik|59kDa|Scr59|p59	spermatogenesis associated, serine-rich 2	protein-coding
mm_48900.1	chr6	3201427	3201427	+	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	-87092	NR_036696	667335	Mm.380219	NR_036696	ENSMUSG00000106779	Gm8579	EG667335	spermatogenesis associated glutamate (E)-rich protein 4a pseudogene	pseudo
mm_115712.1	chr13	15853106	15853114	-	1	NA	Intergenic	Intergenic	45867	NR_046131	328190	Mm.446957	NR_046131		A530046M15Rik	A530046M15	RIKEN cDNA A530046M15 gene	ncRNA
mm_171588.1	chr4	147642305	147642305	-	1	NA	intron (NM_145078, intron 1 of 4)	intron (NM_145078, intron 1 of 4)	203	NM_145078	112422	Mm.327194	NM_145078	ENSMUSG00000066000	Zfp979	2610305D13Rik|Ssm1b	zinc finger protein 979	protein-coding
mm_101847.1	chr11	48826302	48826323	-	1	NA	intron (NM_053166, intron 1 of 6)	intron (NM_053166, intron 1 of 6)	174	NM_053166	94089	Mm.390335	NM_053166	ENSMUSG00000040350	Trim7	AI790312	tripartite motif-containing 7	protein-coding
mm_70732.1	chr8	18846525	18846544	+	1	NA	5' UTR (NM_026792, exon 1 of 8)	5' UTR (NM_026792, exon 1 of 8)	255	NM_026792	52123	Mm.24117	NM_026792	ENSMUSG00000031467	Agpat5	1110013A05Rik|D8Ertd319e	1-acylglycerol-3-phosphate O-acyltransferase 5 (lysophosphatidic acid acyltransferase, epsilon)	protein-coding
mm_62609.1	chr7	106814136	106814160	+	1	NA	promoter-TSS (NM_028910)	promoter-TSS (NM_028910)	4	NM_028910	66786	Mm.159186	NM_028910	ENSMUSG00000036744	Olfr701	4932441H21Rik|4933433E02Rik|MOR283-1	olfactory receptor 701	protein-coding
mm_109017.1	chr12	103442318	103442346	+	1	NA	exon (NM_029803, exon 4 of 4)	exon (NM_029803, exon 4 of 4)	1348	NM_029803	76933	Mm.271275	NM_029803	ENSMUSG00000079017	Ifi27l2a	2310061N23Rik|Ifi27|Isg12|Isg12(b1)	interferon, alpha-inducible protein 27 like 2A	protein-coding
mm_123437.1	chr14	64813056	64813073	-	1	NA	3' UTR (NM_001347627, exon 11 of 11)	3' UTR (NM_001347627, exon 11 of 11)	136793	NM_177338	219150	Mm.344074	NM_177338	ENSMUSG00000021972	Hmbox1	AI451877|AI604847|F830020C16Rik	homeobox containing 1	protein-coding
mm_118171.1	chr13	106836296	106836323	-	1	NA	intron (NM_029665, intron 27 of 29)	intron (NM_029665, intron 27 of 29)	100606	NM_029665	76582	Mm.132208	NM_029665	ENSMUSG00000042590	Ipo11	1700081H05Rik|2510001A17Rik|AI314624|AW555235|E330021B14Rik|Ranbp11	importin 11	protein-coding
mm_80853.1	chr9	98424863	98424905	+	1	NA	5' UTR (NM_011254, exon 1 of 4)	5' UTR (NM_011254, exon 1 of 4)	1923	NM_011254	19659	Mm.279741	NM_011254	ENSMUSG00000046402	Rbp1	CRBPI|Crbp|Rbp-1	retinol binding protein 1, cellular	protein-coding
mm_167733.1	chr9	105829960	105829960	-	1	NA	Intergenic	Intergenic	-1875	NM_001102607	245026	Mm.482507	NM_172927	ENSMUSG00000043719	Col6a6	E330019B14|E330026B02Rik	collagen, type VI, alpha 6	protein-coding
mm_113078.1	chr13	23819869	23819870	+	1	NA	exon (NM_144836, exon 9 of 12)	exon (NM_144836, exon 9 of 12)	12842	NM_144836	218103	Mm.24030	NM_144836	ENSMUSG00000036110	Slc17a2	C730032N17Rik|NPT3	solute carrier family 17 (sodium phosphate), member 2	protein-coding
mm_171051.1	chr3	102983889	102983896	+	1	NA	Intergenic	L1Md_T|LINE|L1	-11848	NM_025679	66641	Mm.33937	NM_025679	ENSMUSG00000027854	Sike1	2810005O12Rik|5730470L24Rik|AI450236|AI839862|Sike|Sikeb	suppressor of IKBKE 1	protein-coding
mm_12087.1	chr2	60211979	60211987	+	1	NA	intron (NM_020575, intron 1 of 9)	intron (NM_020575, intron 1 of 9)	2047	NM_020575	57438	Mm.260635	NM_020575	ENSMUSG00000026977	March7	Axo|Axot|Gtrgeo17	membrane-associated ring finger (C3HC4) 7	protein-coding
mm_117654.1	chr13	93188846	93188850	-	1	NA	intron (NM_133905, intron 1 of 14)	intron (NM_133905, intron 1 of 14)	3435	NM_133905	100715	Mm.242865	NM_133905	ENSMUSG00000042167	Papd4	8030446C20Rik|AI649009|GLD-2|Gld2	PAP associated domain containing 4	protein-coding
mm_45870.1	chr5	88008225	88008229	-	1	NA	exon (NM_011422, exon 3 of 3)	exon (NM_011422, exon 3 of 3)	5702	NM_011422	20599	Mm.261199	NM_011422	ENSMUSG00000029280	Smr3a	AA589601|MSG1|MSG3|Smr1|Smr3	submaxillary gland androgen regulated protein 3A	protein-coding
mm_121431.1	chr14	120397150	120397153	+	1	NA	intron (NM_175341, intron 7 of 8)	intron (NM_175341, intron 7 of 8)	-81310	NM_029519	76108	Mm.261448	NM_029519	ENSMUSG00000051615	Rap2a	5830461H18Rik	RAS related protein 2a	protein-coding
mm_115259.1	chr13	110400614	110400638	+	1	NA	3' UTR (NM_152804, exon 14 of 14)	3' UTR (NM_152804, exon 14 of 14)	5582	NM_152804	20620	Mm.380	NM_152804	ENSMUSG00000021701	Plk2	Snk	polo-like kinase 2	protein-coding
mm_115316.1	chr13	112366145	112366147	+	1	NA	intron (NM_001168403, intron 9 of 11)	intron (NM_001168403, intron 9 of 11)	77628	NM_001168404	77318	Mm.159895	NM_029898	ENSMUSG00000049985	Ankrd55	C030011J08Rik	ankyrin repeat domain 55	protein-coding
mm_11763.1	chr2	38533690	38533695	+	1	NA	intron (NM_001159631, intron 1 of 9)	intron (NM_001159631, intron 1 of 9)	21816	NM_001159631	59126	Mm.143818	NM_021606	ENSMUSG00000026749	Nek6	1300007C09Rik	NIMA (never in mitosis gene a)-related expressed kinase 6	protein-coding
mm_65231.1	chr7	19733127	19733137	-	1	NA	exon (NM_001159724, exon 3 of 6)	exon (NM_001159724, exon 3 of 6)	16441	NM_008990	19294	Mm.4341	NM_008990	ENSMUSG00000062300	Nectin2	AI325026|AI987993|Cd112|MPH|Pvr|Pvrl2|Pvs|nectin-2	nectin cell adhesion molecule 2	protein-coding
mm_44849.1	chr5	34196597	34196637	-	1	NA	exon (NM_001015039, exon 12 of 13)	exon (NM_001015039, exon 12 of 13)	-8907	NM_010753	17122	Mm.259260	NM_010753	ENSMUSG00000037235	Mxd4	2810410A03Rik|Mad4|bHLHc12	Max dimerization protein 4	protein-coding
mm_75409.1	chr8	46430156	46430175	-	1	NA	Intergenic	Intergenic	-40872	NM_007981	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_147332.1	chr18	42877934	42877938	-	1	NA	intron (NM_028392, intron 1 of 8)	intron (NM_028392, intron 1 of 8)	21570	NR_073583	72930	Mm.26134	NM_027531	ENSMUSG00000024500	Ppp2r2b	2900026H06Rik|6330404L05Rik|E130009M08Rik|PP2A-PR55B|PR55-BETA|SCA12	protein phosphatase 2, regulatory subunit B, beta	protein-coding
mm_34017.1	chr4	137995829	137995837	+	1	NA	intron (NM_172703, intron 2 of 34)	intron (NM_172703, intron 2 of 34)	2377	NM_172703	230861	Mm.268903	NM_172703	ENSMUSG00000028760	Eif4g3	1500002J22Rik|4930523M17Rik|G1-419-52|eIF4GII|repro8	eukaryotic translation initiation factor 4 gamma, 3	protein-coding
mm_76617.1	chr8	91313377	91313388	-	1	NA	promoter-TSS (NM_173431)	promoter-TSS (NM_173431)	-143	NM_011936	26383	Mm.4375	NM_011936	ENSMUSG00000055932	Fto	AW743446|mKIAA1752	fat mass and obesity associated	protein-coding
mm_169377.1	chr14	37236027	37236027	-	1	NA	Intergenic	IAPLTR1_Mm|LTR|ERVK	-100705	NM_078478	66092	Mm.182912	NM_078478	ENSMUSG00000041028	Ghitm	1010001P14Rik|C77840|MICS1|PTD010|Tmbim5	growth hormone inducible transmembrane protein	protein-coding
mm_96273.1	chr11	62847063	62847087	+	1	NA	promoter-TSS (NM_001291441)	promoter-TSS (NM_001291441)	-48	NM_001033669	213980	Mm.482259	NM_001033669	ENSMUSG00000090173	Fbxw10	Fbw10|HREP|SM25H2|SM2SH2	F-box and WD-40 domain protein 10	protein-coding
mm_118426.1	chr14	7941649	7941659	+	1	NA	intron (NM_134080, intron 42 of 45)	intron (NM_134080, intron 42 of 45)	52528	NM_007870	13421	Mm.272258	NM_007870	ENSMUSG00000025279	Dnase1l3	DNasegamma|Dhp2|Lsd	deoxyribonuclease 1-like 3	protein-coding
mm_166766.1	chr6	134034087	134034103	+	1	NA	Intergenic	PB1D10|SINE|Alu	-1605	NM_001303102	14011	Mm.269995	NM_007961	ENSMUSG00000030199	Etv6	AW123102|AW557856|Tel	ets variant 6	protein-coding
mm_7307.1	chr1	97977339	97977398	-	1	NA	intron (NM_013626, intron 1 of 25)	intron (NM_013626, intron 1 of 25)	70425	NR_037993	78603	Mm.442597	NR_037993	ENSMUSG00000089706	B230216N24Rik	-	RIKEN cDNA B230216N24 gene	ncRNA
mm_41226.1	chr5	88650746	88650749	+	1	NA	3' UTR (NM_001289774, exon 18 of 18)	3' UTR (NM_001289774, exon 18 of 18)	24833	NM_001098476	231413	Mm.332474	NM_178700	ENSMUSG00000044221	Grsf1	BB232551|C80280|D5Wsu31e	G-rich RNA sequence binding factor 1	protein-coding
mm_72363.1	chr8	80770593	80770597	+	1	NA	intron (NM_021356, intron 8 of 9)	intron (NM_021356, intron 8 of 9)	-31136	NM_053124	93762	Mm.246803	NM_053124	ENSMUSG00000031715	Smarca5	4933427E24Rik|D030040M08Rik|D330027N15Rik|MommeD4|Snf2h	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5	protein-coding
mm_69738.1	chr7	140900402	140900419	-	1	NA	promoter-TSS (NM_007751)	promoter-TSS (NM_007751)	36	NM_007751	12869	Mm.3841	NM_007751	ENSMUSG00000025488	Cox8b	Cox8h|CoxVIII-H	cytochrome c oxidase subunit VIIIb	protein-coding
mm_124025.1	chr14	76575971	76576006	-	1	NA	Intergenic	RMER21B|LTR|ERV1	-19099	NR_027699	72661	Mm.320384	NM_001160326	ENSMUSG00000052584	Serp2	2810032E02Rik	stress-associated endoplasmic reticulum protein family member 2	protein-coding
mm_139758.1	chr17	64600488	64600496	+	1	NA	Intergenic	Intergenic	-1157	NM_008549	17158	Mm.2433	NM_008549	ENSMUSG00000024085	Man2a1	Mana-2|Mana2|Map-2	mannosidase 2, alpha 1	protein-coding
mm_85956.1	chr9	112124354	112124381	-	1	NA	intron (NM_001177617, intron 13 of 14)	B4|SINE|B4	-5656	NR_029823	723815		NR_029823	ENSMUSG00000065441	Mir128-2	Mirn128-2|Mirn128b|mir-128-2|mir-128b	microRNA 128-2	ncRNA
mm_63792.1	chr7	132664750	132664754	+	1	NA	intron (NM_029609, intron 6 of 6)	intron (NM_029609, intron 6 of 6)	54109	NM_029609	76429	Mm.276721	NM_029609	ENSMUSG00000030946	Lhpp	2310007H09Rik	phospholysine phosphohistidine inorganic pyrophosphate phosphatase	protein-coding
mm_17659.1	chr2	32065439	32065457	-	1	NA	Intergenic	Intergenic	14502	NR_106135	102466844		NR_106135	ENSMUSG00000099075	Mir7674	Gm27563|mmu-mir-7674	microRNA 7674	ncRNA
mm_139583.1	chr17	57222191	57222231	+	1	NA	exon (NM_009778, exon 14 of 41)	exon (NM_009778, exon 14 of 41)	-4983	NR_105944	102465591		NR_105944	ENSMUSG00000099066	Mir6978	Gm27858|mmu-mir-6978	microRNA 6978	ncRNA
mm_148152.1	chr18	77565174	77565183	-	1	NA	promoter-TSS (NM_001164504)	promoter-TSS (NM_001164504)	-42	NM_001164504	225743	Mm.23293	NM_001164504	ENSMUSG00000025427	Rnf165	2900024M11Rik|AI427432|Akd2|Ark2c|G630064H08Rik|Gm96	ring finger protein 165	protein-coding
mm_156437.1	chrX	142060785	142060799	+	1	NA	Intergenic	Intergenic	136144	NM_001007576	245650	Mm.208511	NM_001007576	ENSMUSG00000042282	Gucy2f	A930002I06|GC-F|GC2	guanylate cyclase 2f	protein-coding
mm_69815.1	chr7	141263973	141263989	-	1	NA	exon (NM_001252601, exon 8 of 10)	exon (NM_001252601, exon 8 of 10)	2443	NM_001252601	54123	Mm.3233	NM_016850	ENSMUSG00000025498	Irf7	-	interferon regulatory factor 7	protein-coding
mm_131604.1	chr16	19179507	19179547	+	1	NA	Intergenic	Intergenic	107214	NM_146451	258443	Mm.377506	NM_146451	ENSMUSG00000050742	Olfr164	MOR279-2	olfactory receptor 164	protein-coding
mm_162831.1	chr10	81596700	81596714	-	1	NA	intron (NM_001346695, intron 4 of 13)	(CCG)n|Simple_repeat|Simple_repeat	4193	NM_053254	114606	Mm.206764	NM_053254	ENSMUSG00000034758	Tle6	1810057E06Rik|Grg6	transducin-like enhancer of split 6	protein-coding
mm_161338.1	chr14	51203464	51203464	+	1	NA	promoter-TSS (NM_001017422)	promoter-TSS (NM_001017422)	-226	NM_001017422	53877	Mm.377124	NM_001017422		Ear4	RNS2|Rnase2|mR4	eosinophil-associated, ribonuclease A family, member 4	protein-coding
mm_93789.1	chr10	120636103	120636107	-	1	NA	Intergenic	Intergenic	-129627	NR_038000	70874	Mm.427286	NR_038000	ENSMUSG00000044544	4921513I03Rik	-	RIKEN cDNA 4921513I03 gene	ncRNA
mm_26582.1	chr3	149334840	149334869	+	1	NA	Intergenic	Intergenic	60117	NR_040591	381482	Mm.393866	NR_040591		Gm1653	-	predicted gene 1653	ncRNA
mm_32283.1	chr4	102989595	102989632	+	1	NA	non-coding (NR_040444, exon 1 of 4)	non-coding (NR_040444, exon 1 of 4)	142	NR_040444	100504717	Mm.394445	NR_040444	ENSMUSG00000085181	Gm12709	OTTMUSG00000008056	predicted gene 12709	ncRNA
mm_9158.1	chr1	170960075	170960085	-	1	NA	TTS (NM_001077189)	TTS (NM_001077189)	15991	NM_001077189	14130	Mm.425062	NM_010187	ENSMUSG00000026656	Fcgr2b	AI528646|CD32|F630109E10Rik|Fc[g]RII|FcgRII|Fcgr2|Fcgr2a|Fcr-2|Fcr-3|Ly-17|Ly-m20|LyM-1|Lym-1|fcRII	Fc receptor, IgG, low affinity IIb	protein-coding
mm_88381.1	chr10	76447380	76447386	+	1	NA	Intergenic	Intergenic	-1698	NM_029816	76964	Mm.472489	NM_029816	ENSMUSG00000009114	2610028H24Rik	ORF67	RIKEN cDNA 2610028H24 gene	protein-coding
mm_45316.1	chr5	65435882	65435929	-	1	NA	promoter-TSS (NM_009466)	promoter-TSS (NM_009466)	-63	NM_009466	22235	Mm.344831	NM_009466	ENSMUSG00000029201	Ugdh	Udpgdh	UDP-glucose dehydrogenase	protein-coding
mm_157494.1	chrX	48454153	48454193	-	1	NA	intron (NM_019680, intron 1 of 8)	CpG	8959	NM_019680	56501	Mm.36808	NM_019680	ENSMUSG00000031103	Elf4	AV314029|BC042423|ENSMUSG00000053512|Gm9907|Mef	E74-like factor 4 (ets domain transcription factor)	protein-coding
mm_77732.1	chr8	126881822	126881843	-	1	NA	Intergenic	Intergenic	64089	NM_024214	67952	Mm.6932	NM_024214	ENSMUSG00000093904	Tomm20	1810060K07Rik|BB284719|Gm19268|MAS20|MOM19|TOM20|mKIAA0016	translocase of outer mitochondrial membrane 20 homolog (yeast)	protein-coding
mm_66564.1	chr7	45239305	45239320	-	1	NA	promoter-TSS (NM_007645)	promoter-TSS (NM_007645)	-197	NM_001290804	12493	Mm.3689	NM_007645	ENSMUSG00000030798	Cd37	Tspan26	CD37 antigen	protein-coding
mm_39496.1	chr5	21055036	21055046	+	1	NA	intron (NM_011203, intron 1 of 17)	intron (NM_011203, intron 1 of 17)	756	NM_011203	19248	Mm.319117	NM_011203	ENSMUSG00000028771	Ptpn12	P19-PTP|PTP-P19|PTP-PEST|PTPG1	protein tyrosine phosphatase, non-receptor type 12	protein-coding
mm_147186.1	chr18	37178494	37178531	-	1	NA	intron (NM_001003671, intron 3 of 3)	(GCTG)n|Simple_repeat|Simple_repeat	34543	NM_001003672	353237	Mm.308500	NM_001003672	ENSMUSG00000102697	Pcdhac2	CNRc2	protocadherin alpha subfamily C, 2	protein-coding
mm_172398.1	chr7	141924199	141924203	-	1	NA	Intergenic	RLTR27|LTR|ERVK	-21740	NM_001347562	54473	Mm.103551	NM_023764	ENSMUSG00000025139	Tollip	4930403G24Rik|4931428G15Rik	toll interacting protein	protein-coding
mm_63668.1	chr7	129831924	129831927	+	1	NA	Intergenic	Intergenic	-130240	NR_046077	100043150	Mm.334264	NR_046077	ENSMUSG00000108504	Gm4265	-	predicted gene 4265	ncRNA
mm_85711.1	chr9	108190422	108190430	-	1	NA	promoter-TSS (NM_007567)	promoter-TSS (NM_007567)	-43	NM_007567	12217	Mm.20425	NM_007567	ENSMUSG00000032589	Bsn	-	bassoon	protein-coding
mm_82083.1	chr9	123034661	123034682	+	1	NA	promoter-TSS (NM_177911)	promoter-TSS (NM_177911)	-70	NM_177911	331046	Mm.195309	NM_177911	ENSMUSG00000025787	Tgm4	9530008N10Rik|Eapa1|TGP	transglutaminase 4 (prostate)	protein-coding
mm_123548.1	chr14	66831463	66831503	-	1	NA	intron (NM_009955, intron 4 of 13)	intron (NM_009955, intron 4 of 13)	37117	NM_009955	12934	Mm.352648	NM_009955	ENSMUSG00000022048	Dpysl2	AI851130|Crmp2|DRP2|Musunc33|TOAD-64|Ulip2	dihydropyrimidinase-like 2	protein-coding
mm_101127.1	chr11	12309733	12309746	-	1	NA	exon (NM_001282994, exon 8 of 15)	exon (NM_001282994, exon 8 of 15)	102401	NM_001282994	12808	Mm.22847	NM_172496	ENSMUSG00000020173	Cobl	-	cordon-bleu WH2 repeat	protein-coding
mm_148591.1	chr19	5069432	5069446	+	1	NA	exon (NM_054042, exon 1 of 1)	exon (NM_054042, exon 1 of 1)	1361	NM_054042	70445	Mm.29597	NM_054042	ENSMUSG00000056481	Cd248	2610111G01Rik|AI842296|Cd164l1|Tem1	CD248 antigen, endosialin	protein-coding
mm_58244.1	chr6	145048657	145048670	-	1	NA	exon (NM_001024468, exon 1 of 11)	exon (NM_001024468, exon 1 of 11)	149	NM_001024468	12035	Mm.4606	NM_007532	ENSMUSG00000030268	Bcat1	BCATc|Eca39	branched chain aminotransferase 1, cytosolic	protein-coding
mm_37459.1	chr4	123444904	123444916	-	1	NA	exon (NM_001199137, exon 46 of 93)	exon (NM_001199137, exon 46 of 93)	-32999	NM_001167918	442834	Mm.483803	NM_001167918		D830031N03Rik	Kiaa0754|mKIAA0754	RIKEN cDNA D830031N03 gene	protein-coding
mm_3464.1	chr1	150104325	150104337	+	1	NA	exon (NM_011198, exon 8 of 10)	exon (NM_011198, exon 8 of 10)	4300	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_151055.1	chr19	47179005	47179030	+	1	NA	5' UTR (NM_021360, exon 1 of 6)	5' UTR (NM_021360, exon 1 of 6)	197	NM_021360	18011	Mm.313651	NM_021360	ENSMUSG00000006435	Neurl1a	2410129E16Rik|AI450910|AI481072|Neu1|Neur1|Neurl|Neurl1|Nlz|Rnf67	neuralized E3 ubiquitin protein ligase 1A	protein-coding
mm_90683.1	chr10	128911474	128911518	+	1	NA	exon (NM_007653, exon 3 of 8)	exon (NM_007653, exon 3 of 8)	1630	NM_007653	12512	Mm.371552	NM_007653	ENSMUSG00000025351	Cd63	C75951|ME491|Tspan30	CD63 antigen	protein-coding
mm_115041.1	chr13	99550941	99550945	+	1	NA	Intergenic	Intergenic	-34341	NM_008634	17755	Mm.4173	NM_008634	ENSMUSG00000052727	Map1b	A230055D22|AI843217|LC1|MAP5|Mtap-5|Mtap1b|Mtap5	microtubule-associated protein 1B	protein-coding
mm_32323.1	chr4	103685761	103685765	+	1	NA	Intergenic	Intergenic	303263	NR_040673	622167	Mm.244115	NR_040673	ENSMUSG00000086136	Gm12718	OTTMUSG00000008109	predicted gene 12718	ncRNA
mm_14068.1	chr2	122738623	122738627	+	1	NA	exon (NM_019788, exon 1 of 5)	exon (NM_019788, exon 1 of 5)	120	NM_019788	18457	Mm.268921	NM_019788	ENSMUSG00000005804	Bloc1s6	BLOC-1|Pldn|Stx13bp1|pa	biogenesis of lysosomal organelles complex-1, subunit 6, pallidin	protein-coding
mm_26617.1	chr3	152395992	152396059	+	1	NA	promoter-TSS (NM_001080755)	promoter-TSS (NM_001080755)	22	NM_001080755	108946	Mm.379292	NM_198416	ENSMUSG00000039068	Zzz3	3110065C23Rik|6430567E01Rik|AA408566|AI481057|AW556059|R75514	zinc finger, ZZ domain containing 3	protein-coding
mm_16437.1	chr2	180394519	180394536	+	1	NA	intron (NR_045331, intron 3 of 3)	intron (NR_045331, intron 3 of 3)	-3852	NR_029901	723954		NR_029901	ENSMUSG00000065460	Mir133a-2	Mirn133a-2|mir-133a-2	microRNA 133a-2	ncRNA
mm_145908.1	chr18	65806127	65806137	+	1	NA	intron (NM_025468, intron 1 of 5)	L2b|LINE|L2	5554	NM_025468	66286	Mm.27800	NM_025468	ENSMUSG00000024516	Sec11c	1810029G24Rik|Sec11l3	SEC11 homolog C, signal peptidase complex subunit	protein-coding
mm_73596.1	chr8	109998772	109998786	+	1	NA	exon (NM_146214, exon 12 of 12)	exon (NM_146214, exon 12 of 12)	8343	NM_146214	234724	Mm.28110	NM_146214	ENSMUSG00000001670	Tat	-	tyrosine aminotransferase	protein-coding
mm_86616.1	chr10	13965329	13965339	+	1	NA	Intergenic	CpG	-1045	NM_010437	15273	Mm.42157	NM_010437	ENSMUSG00000015501	Hivep2	Gm20114|MIBP1|Schnurri-2|Shn-2	human immunodeficiency virus type I enhancer binding protein 2	protein-coding
mm_54690.1	chr6	39423454	39423466	-	1	NA	Intergenic	Intergenic	-3091	NM_018810	54484	Mm.270484	NM_018810	ENSMUSG00000029922	Mkrn1	RFP	makorin, ring finger protein, 1	protein-coding
mm_5078.1	chr1	4360238	4360246	-	1	NA	promoter-TSS (NM_011283)	promoter-TSS (NM_011283)	72	NM_011283	19888	Mm.294263	NM_011283	ENSMUSG00000025900	Rp1	Dcdc3|Orp1|Rp1h|mG145	retinitis pigmentosa 1 (human)	protein-coding
mm_23941.1	chr3	84480272	84480298	+	1	NA	promoter-TSS (NM_001205355)	promoter-TSS (NM_001205355)	154	NM_001033301	229474	Mm.331107	NM_001033301	ENSMUSG00000041842	Fhdc1	6330505N24Rik|Gm126	FH2 domain containing 1	protein-coding
mm_69347.1	chr7	130216895	130216898	-	1	NA	intron (NM_001347638, intron 4 of 15)	ID_B1|SINE|B4	49912	NM_010207	14183	Mm.16340	NM_010207	ENSMUSG00000030849	Fgfr2	AU043015|AW556123|Bek|Fgfr-2|Fgfr-7|Fgfr7|KGFR|KGFRTr|svs	fibroblast growth factor receptor 2	protein-coding
mm_87035.1	chr10	28668546	28668552	+	1	NA	non-coding (NR_131208, exon 1 of 4)	non-coding (NR_131208, exon 1 of 4)	189	NM_178666	210757	Mm.123021	NM_178666	ENSMUSG00000049109	Themis	E430004N04Rik|Gasp|Spot|Tsepa|thylex	thymocyte selection associated	protein-coding
mm_105688.1	chr11	107734018	107734040	-	1	NA	TTS (NM_019431)	TTS (NM_019431)	-17553	NM_007582	12299	Mm.57093	NM_007582	ENSMUSG00000020722	Cacng1	-	calcium channel, voltage-dependent, gamma subunit 1	protein-coding
mm_77100.1	chr8	111027725	111027745	-	1	NA	promoter-TSS (NM_001190800)	promoter-TSS (NM_001190800)	35	NM_172284	234733	Mm.482176	NM_172284	ENSMUSG00000033658	Ddx19b	2810457M08Rik|4921519L13Rik|AW260119	DEAD (Asp-Glu-Ala-Asp) box polypeptide 19b	protein-coding
mm_68657.1	chr7	118695075	118695092	-	1	NA	exon (NM_019580, exon 3 of 6)	exon (NM_019580, exon 3 of 6)	10655	NM_019580	56209	Mm.273142	NM_019580	ENSMUSG00000033917	Gde1	1200003M13Rik|Mir16|RGS16	glycerophosphodiester phosphodiesterase 1	protein-coding
mm_124851.1	chr15	9527069	9527076	+	1	NA	intron (NM_008372, intron 1 of 7)	L1Md_A|LINE|L1	2804	NM_008372	16197	Mm.389	NM_008372	ENSMUSG00000003882	Il7r	CD127|IL-7Ralpha	interleukin 7 receptor	protein-coding
mm_148068.1	chr18	72340202	72340211	-	1	NA	intron (NM_007831, intron 1 of 28)	intron (NM_007831, intron 1 of 28)	10863	NM_007831	13176	Mm.167882	NM_007831	ENSMUSG00000060534	Dcc	C030036D22Rik|Igdcc1	deleted in colorectal carcinoma	protein-coding
mm_37962.1	chr4	133353448	133353474	-	1	NA	Intergenic	B1F1|SINE|Alu	-14146	NM_199306	230796	Mm.226576	NM_199306	ENSMUSG00000037622	Wdtc1	Gm695|adipose|adp	WD and tetratricopeptide repeats 1	protein-coding
mm_156172.1	chrX	130213196	130213208	+	1	NA	intron (NM_172493, intron 23 of 26)	intron (NM_172493, intron 23 of 26)	463460	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diaph2	Dia3|Diap2|Drf2|E430022I22Rik	diaphanous related formin 2	protein-coding
mm_94158.1	chr10	128745083	128745085	-	1	NA	Intergenic	Intergenic	-1028	NM_016811	13139	Mm.291235	NM_016811	ENSMUSG00000025357	Dgka	80kDa|AW146112|Dagk1	diacylglycerol kinase, alpha	protein-coding
mm_89.1	chr1	7089131	7089178	+	1	NA	5' UTR (NM_183028, exon 1 of 6)	5' UTR (NM_183028, exon 1 of 6)	234	NM_183028	319263	Mm.21539	NM_183028	ENSMUSG00000051285	Pcmtd1	8430411F12Rik|A030012M09Rik	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding
mm_26932.1	chr3	20262573	20262581	-	1	NA	exon (NM_029706, exon 9 of 11)	exon (NM_029706, exon 9 of 11)	13156	NM_029706	76703	Mm.34692	NM_029706	ENSMUSG00000011463	Cpb1	0910001A18Rik|1810063F02Rik|2210008M23Rik|AI504870	carboxypeptidase B1 (tissue)	protein-coding
mm_76782.1	chr8	99416330	99416348	-	1	NA	promoter-TSS (NR_132435)	promoter-TSS (NR_132435)	132	NM_001285913	12564	Mm.441131	NM_007667	ENSMUSG00000036510	Cdh8	AI851472|cad8	cadherin 8	protein-coding
mm_43966.1	chr5	145345255	145345270	+	1	NA	promoter-TSS (NM_001100180)	promoter-TSS (NM_001100180)	-8	NM_001100180	622127	Mm.359379	NM_001100180	ENSMUSG00000070419	Cyp3a57	EG622127	cytochrome P450, family 3, subfamily a, polypeptide 57	protein-coding
mm_32457.1	chr4	107368322	107368340	+	1	NA	intron (NM_028355, intron 1 of 17)	intron (NM_028355, intron 1 of 17)	547	NM_028355	72787	Mm.28478	NM_028355	ENSMUSG00000028614	Ndc1	2810475A17Rik|AI450313|Tmem48|sks	NDC1 transmembrane nucleoporin	protein-coding
mm_23279.1	chr3	51661168	51661189	+	1	NA	promoter-TSS (NM_174995)	promoter-TSS (NM_174995)	-1	NM_174995	211666	Mm.24679	NM_174995	ENSMUSG00000074604	Mgst2	GST2|MGST-II	microsomal glutathione S-transferase 2	protein-coding
mm_50616.1	chr6	49823754	49823762	+	1	NA	exon (NM_023456, exon 2 of 4)	exon (NM_023456, exon 2 of 4)	1048	NM_023456	109648	Mm.154796	NM_023456	ENSMUSG00000029819	Npy	0710005A05Rik	neuropeptide Y	protein-coding
mm_164500.1	chr16	91534685	91534699	-	1	NA	Intergenic	Intergenic	-12402	NM_008338	15980	Mm.249364	NM_008338	ENSMUSG00000022965	Ifngr2	Ifgr2|Ifgt	interferon gamma receptor 2	protein-coding
mm_116681.1	chr13	49248147	49248168	-	1	NA	promoter-TSS (NM_025491)	promoter-TSS (NM_025491)	6	NM_025491	66329	Mm.34308	NM_025491	ENSMUSG00000021384	Susd3	1700017I11Rik|2810440J20Rik	sushi domain containing 3	protein-coding
mm_143867.1	chr17	84186750	84186780	-	1	NA	exon (NM_001001806, exon 2 of 2)	exon (NM_001001806, exon 2 of 2)	1182	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_109847.1	chr12	4593777	4593790	-	1	NA	intron (NM_011365, intron 1 of 38)	intron (NM_011365, intron 1 of 38)	775	NM_001198968	20403	Mm.341204	NM_011365	ENSMUSG00000020640	Itsn2	AI327390|Ese2|Sh3d1B|Sh3p18|mKIAA1256	intersectin 2	protein-coding
mm_137586.1	chr17	28007992	28008028	+	1	NA	exon (NM_001286041, exon 11 of 24)	exon (NM_001286041, exon 11 of 24)	72574	NM_013687	21463	Mm.29758	NM_013687	ENSMUSG00000062859	Tcp11	D17Ken1|Tcp-11	t-complex protein 11	protein-coding
mm_80120.1	chr9	70573608	70573616	+	1	NA	exon (NM_025690, exon 7 of 21)	exon (NM_025690, exon 7 of 21)	30742	NM_025690	66660	Mm.22379	NM_025690	ENSMUSG00000032212	Sltm	5730455C01Rik|5730555F13Rik|9130215G10Rik|Met	SAFB-like, transcription modulator	protein-coding
mm_56293.1	chr6	91493232	91493248	-	1	NA	intron (NM_009531, intron 11 of 15)	intron (NM_009531, intron 11 of 15)	19489	NM_028766	74122	Mm.38801	NM_028766	ENSMUSG00000030095	Tmem43	1200015A22Rik|LUMA	transmembrane protein 43	protein-coding
mm_18882.1	chr2	76647993	76648043	-	1	NA	promoter-TSS (NM_011871)	promoter-TSS (NM_011871)	-24	NM_011871	23992	Mm.277250	NM_011871	ENSMUSG00000002731	Prkra	AV120107|PRK|Pact|RAX|lear	protein kinase, interferon inducible double stranded RNA dependent activator	protein-coding
mm_88948.1	chr10	81357504	81357585	+	1	NA	promoter-TSS (NM_028657)	promoter-TSS (NM_028657)	-26	NM_028657	73822	Mm.182281	NM_028657	ENSMUSG00000034854	Mfsd12	C19orf28|F630110N24Rik|Wdt1	major facilitator superfamily domain containing 12	protein-coding
mm_113384.1	chr13	33027503	33027513	+	1	NA	promoter-TSS (NM_011452)	promoter-TSS (NM_011452)	94	NM_011452	20706	Mm.45371	NM_011452	ENSMUSG00000021403	Serpinb9b	1600019A21Rik|R86|SPI-CI|Spi10|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 9b	protein-coding
mm_58366.1	chr6	148831396	148831407	-	1	NA	promoter-TSS (NM_001081113)	promoter-TSS (NM_001081113)	66	NM_001081113	320727	Mm.260105	NM_001081113	ENSMUSG00000040029	Ipo8	6230418K12Rik|Abcc10|C130009K11Rik|MRP7|OM-1|Om1|Ranbp8	importin 8	protein-coding
mm_134132.1	chr16	10543029	10543096	-	1	NA	promoter-TSS (NM_021428)	promoter-TSS (NM_021428)	-8	NM_021428	58239	Mm.353006	NM_021428	ENSMUSG00000038055	Dexi	1810029J14Rik|AI836170|AW413143|D16Bwg0586e|Myle	dexamethasone-induced transcript	protein-coding
mm_1054.1	chr1	58846804	58846818	+	1	NA	3' UTR (NM_001277926, exon 10 of 10)	3' UTR (NM_001277926, exon 10 of 10)	44309	NM_001080126	12370	Mm.336851	NM_009812	ENSMUSG00000026029	Casp8	CASP-8|FLICE|MACH|Mch5	caspase 8	protein-coding
mm_35130.1	chr4	11254195	11254246	-	1	NA	promoter-TSS (NM_001159595)	promoter-TSS (NM_001159595)	39	NM_178112	72656	Mm.246713	NM_178112	ENSMUSG00000040738	Ints8	2810013E07Rik|AV063769|D130008D20Rik	integrator complex subunit 8	protein-coding
mm_5782.1	chr1	51585263	51585267	-	1	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	-106866	NM_001310549	109019	Mm.196290	NM_028696	ENSMUSG00000026107	Nabp1	4930434H03Rik|4930442A21Rik|4930488J04Rik|4933440J18Rik|5830411E10Rik|AI852561|Nbp1|Obfc2a|Ssb2	nucleic acid binding protein 1	protein-coding
mm_49345.1	chr6	21985904	21985972	+	1	NA	promoter-TSS (NM_001081351)	promoter-TSS (NM_001081351)	28	NM_001081351	214642	Mm.221404	NM_001081351	ENSMUSG00000062980	Cped1	6720481P07|A430107O13Rik|AI552584	cadherin-like and PC-esterase domain containing 1	protein-coding
mm_129526.1	chr15	79261278	79261309	-	1	NA	intron (NM_177580, intron 9 of 13)	CpG-5083	-6545	NM_020516	57274	Mm.441697	NM_020516	ENSMUSG00000032988	Slc16a8	Mct3	solute carrier family 16 (monocarboxylic acid transporters), member 8	protein-coding
mm_36789.1	chr4	103114211	103114221	-	1	NA	promoter-TSS (NM_027696)	promoter-TSS (NM_027696)	83	NM_146254	242584	Mm.374877	NM_146254	ENSMUSG00000035126	Wdr78	BC028975	WD repeat domain 78	protein-coding
mm_110306.1	chr12	33061765	33061802	-	1	NA	exon (NM_001024478, exon 7 of 20)	exon (NM_001024478, exon 7 of 20)	31092	NM_001024478	68764	Mm.60083	NM_001024478	ENSMUSG00000035860	Cdhr3	1110049B09Rik|BB172694|Cdh28	cadherin-related family member 3	protein-coding
mm_32893.1	chr4	118965327	118965337	+	1	NA	exon (NM_133892, exon 4 of 7)	exon (NM_133892, exon 4 of 7)	3365	NM_133892	100470	Mm.26698	NM_133892	ENSMUSG00000024903	Lao1	AW990848	L-amino acid oxidase 1	protein-coding
mm_142254.1	chr17	37713853	37713888	-	1	NA	Intergenic	Intergenic	-12129	NM_146631	258624	Mm.272073	NM_146631	ENSMUSG00000063994	Olfr120	MOR263-3	olfactory receptor 120	protein-coding
mm_80382.1	chr9	75438126	75438130	+	1	NA	Intergenic	RMER17C|LTR|ERVK	-3396	NM_001039522	235497	Mm.41508	NM_001006122	ENSMUSG00000042487	Leo1	Gm185	Leo1, Paf1/RNA polymerase II complex component	protein-coding
mm_133487.1	chr16	90220637	90220641	+	1	NA	promoter-TSS (NM_011434)	promoter-TSS (NM_011434)	-103	NM_011434	20655	Mm.276325	NM_011434	ENSMUSG00000022982	Sod1	B430204E11Rik|Cu/Zn-SOD|CuZnSOD|Ipo-1|Ipo1|SODC|Sod-1	superoxide dismutase 1, soluble	protein-coding
mm_170876.1	chr2	20900021	20900026	+	1	NA	intron (NM_001128084, intron 3 of 24)	LSU-rRNA_Hsa|rRNA|rRNA	67698	NM_001081364	71435	Mm.28507	NM_001081364	ENSMUSG00000036591	Arhgap21	5530401C11Rik|AA416458|ARHGAP10	Rho GTPase activating protein 21	protein-coding
mm_14319.1	chr2	129314146	129314191	+	1	NA	Intergenic	MIRb|SINE|MIR	-4196	NM_010554	16175	Mm.15534	NM_010554	ENSMUSG00000027399	Il1a	Il-1a	interleukin 1 alpha	protein-coding
mm_160453.1	chr8	106212314	106212314	+	1	NA	intron (NM_145404, intron 1 of 17)	T-rich|Low_complexity|Low_complexity	1260	NM_145404	214572	Mm.251804	NM_145404	ENSMUSG00000060098	Prmt7	4933402B05Rik|BC006705	protein arginine N-methyltransferase 7	protein-coding
mm_102564.1	chr11	61488219	61488277	-	1	NA	TTS (NM_001291037)	TTS (NM_001291037)	2804	NM_029568	76293	Mm.272278	NM_029568	ENSMUSG00000042436	Mfap4	1110007F23Rik	microfibrillar-associated protein 4	protein-coding
mm_23338.1	chr3	54692806	54692836	+	1	NA	promoter-TSS (NM_019995)	promoter-TSS (NM_019995)	-284	NM_019995	56790	Mm.486375	NM_019995	ENSMUSG00000027751	Supt20	AA667204|AI450544|D3Ertd300e|Fam48a|Supt20h|p38IP	suppressor of Ty 20	protein-coding
mm_116780.1	chr13	53146643	53146644	-	1	NA	exon (NM_013846, exon 2 of 9)	exon (NM_013846, exon 2 of 9)	139466	NM_013846	26564	Mm.342774	NM_013846	ENSMUSG00000021464	Ror2	Ntrkr2|mRor2	receptor tyrosine kinase-like orphan receptor 2	protein-coding
mm_165444.1	chr2	155250004	155250014	+	1	NA	non-coding (NR_111891, exon 4 of 4)	non-coding (NR_111891, exon 4 of 4)	13401	NM_001291108	67068	Mm.23693	NM_025947	ENSMUSG00000047459	Dynlrb1	2010012N15Rik|2010320M17Rik|9430076K19Rik|AV124457|DNLC2A|Dncl2a|km23-1	dynein light chain roadblock-type 1	protein-coding
mm_147960.1	chr18	67066454	67066468	-	1	NA	Intergenic	Intergenic	-21837	NM_177137	14680	Mm.440746	NM_010307	ENSMUSG00000024524	Gnal	2610011C15Rik|9630020G10Rik|Galphaolf|Gna10|Golf	guanine nucleotide binding protein, alpha stimulating, olfactory type	protein-coding
mm_32894.1	chr4	118967834	118967838	+	1	NA	exon (NM_133892, exon 7 of 7)	exon (NM_133892, exon 7 of 7)	5869	NM_133892	100470	Mm.26698	NM_133892	ENSMUSG00000024903	Lao1	AW990848	L-amino acid oxidase 1	protein-coding
mm_121000.1	chr14	79481165	79481185	+	1	NA	promoter-TSS (NM_007920)	promoter-TSS (NM_007920)	-19	NM_007920	13709	Mm.20938	NM_007920	ENSMUSG00000036461	Elf1	Elf-1|Sts1|mElf-1|p70	E74-like factor 1	protein-coding
mm_1024.1	chr1	58754743	58754758	+	1	NA	3' UTR (NM_207653, exon 10 of 10)	3' UTR (NM_207653, exon 10 of 10)	24198	NM_001293805	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_159343.1	chr3	59925232	59925232	+	1	NA	promoter-TSS (NM_177661)	promoter-TSS (NM_177661)	18	NM_177661	229333	Mm.75765	NM_177661	ENSMUSG00000036951	C130079G13Rik	-	RIKEN cDNA C130079G13 gene	protein-coding
mm_59965.1	chr7	30428373	30428380	+	1	NA	3' UTR (NM_172142, exon 11 of 11)	3' UTR (NM_172142, exon 11 of 11)	5072	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_39020.1	chr4	152131491	152131505	-	1	NA	intron (NM_207688, intron 3 of 10)	CpG-10714	-2573	NM_019585	56226	Mm.264215	NM_019585	ENSMUSG00000028943	Espn	je	espin	protein-coding
mm_1015.1	chr1	58729558	58729559	+	1	NA	promoter-TSS (NM_001293805)	promoter-TSS (NM_001293805)	-994	NM_001293805	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_36417.1	chr4	78211828	78211889	-	1	NA	promoter-TSS (NM_011211)	promoter-TSS (NM_011211)	37	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding
mm_68493.1	chr7	111076156	111076176	-	1	NA	intron (NM_001040131, intron 13 of 20)	GA-rich|Low_complexity|Low_complexity	6864	NM_001040131	13690	Mm.185453	NM_013507	ENSMUSG00000005610	Eif4g2	DAP-5|E130105L11Rik|Nat1|Natm1|p97	eukaryotic translation initiation factor 4, gamma 2	protein-coding
mm_127783.1	chr15	3542412	3542421	-	1	NA	intron (NM_001048178, intron 1 of 8)	Tigger7|DNA|TcMar-Tigger	39426	NM_001286370	14600	Mm.3986	NM_010284	ENSMUSG00000055737	Ghr	GHBP|GHR/BP	growth hormone receptor	protein-coding
mm_9042.1	chr1	167269608	167269618	-	1	NA	intron (NM_030724, intron 1 of 6)	intron (NM_030724, intron 1 of 6)	15514	NM_030724	80914	Mm.280895	NM_030724	ENSMUSG00000026558	Uck2	AA407809|AI481316|AU018180|AU020720|TSA903|UK|UMK|Umpk	uridine-cytidine kinase 2	protein-coding
mm_117120.1	chr13	60864374	60864437	-	1	NA	promoter-TSS (NM_178098)	promoter-TSS (NM_178098)	11	NM_178098	214639	Mm.19839	NM_178098	ENSMUSG00000050345	4930486L24Rik	AW545031	RIKEN cDNA 4930486L24 gene	protein-coding
mm_87179.1	chr10	39133959	39133980	+	1	NA	promoter-TSS (NM_028006)	promoter-TSS (NM_028006)	-54	NM_028006	71924	Mm.297956	NM_028006	ENSMUSG00000019845	Tube1	2310061K05Rik|AI551343|Tube	epsilon-tubulin 1	protein-coding
mm_66653.1	chr7	45712308	45712323	-	1	NA	exon (NM_001172561, exon 4 of 6)	exon (NM_001172561, exon 4 of 6)	2892	NM_020011	56632	Mm.24222	NM_020011	ENSMUSG00000057342	Sphk2	C76851	sphingosine kinase 2	protein-coding
mm_114911.1	chr13	94976365	94976422	+	1	NA	promoter-TSS (NM_172590)	promoter-TSS (NM_172590)	49	NM_172590	218460	Mm.33856	NM_172590	ENSMUSG00000042015	Wdr41	B830029I03Rik|MSTP048	WD repeat domain 41	protein-coding
mm_147812.1	chr18	61719796	61719833	-	1	NA	exon (NM_021296, exon 2 of 4)	exon (NM_021296, exon 2 of 4)	6517	NM_021296	17714	Mm.269657	NM_021296	ENSMUSG00000024580	Grpel2	mt-GrpE#2|mt-Grpel2	GrpE-like 2, mitochondrial	protein-coding
mm_91084.1	chr10	19014550	19014589	-	1	NA	intron (NM_009397, intron 1 of 8)	intron (NM_009397, intron 1 of 8)	841	NM_009397	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_14654.1	chr2	136935028	136935030	+	1	NA	intron (NM_001038641, intron 2 of 7)	Lx8|LINE|L1	35678	NM_001038641	74243	Mm.330612	NM_028201	ENSMUSG00000027281	Slx4ip	2210009G21Rik|2410004I22Rik|C85661|Slxip	SLX4 interacting protein	protein-coding
mm_128338.1	chr15	38518214	38518230	-	1	NA	intron (NR_125913, intron 1 of 11)	intron (NR_125913, intron 1 of 11)	1044	NM_001301688	54375	Mm.250214	NM_018745	ENSMUSG00000037458	Azin1	1700085L02Rik|AZI|Oazi|Oazin	antizyme inhibitor 1	protein-coding
mm_39898.1	chr5	31205047	31205094	+	1	NA	exon (NM_008014, exon 6 of 10)	exon (NM_008014, exon 6 of 10)	-2767	NM_175311	101023	Mm.45033	NM_175311	ENSMUSG00000043059	Zfp513	AW990386|D430028M17Rik|Znf513	zinc finger protein 513	protein-coding
mm_91288.1	chr10	24828706	24828708	-	1	NA	intron (NM_134005, intron 2 of 24)	intron (NM_134005, intron 2 of 24)	7488	NM_134005	209558	Mm.338425	NM_134005	ENSMUSG00000019989	Enpp3	AI876438|CD203c	ectonucleotide pyrophosphatase/phosphodiesterase 3	protein-coding
mm_113814.1	chr13	46669518	46669545	+	1	NA	promoter-TSS (NM_001033192)	promoter-TSS (NM_001033192)	9	NM_001033192	97863	Mm.275934	NM_001033192	ENSMUSG00000069237	Fam8a1	C78339	family with sequence similarity 8, member A1	protein-coding
mm_172613.1	chr8	19492911	19492933	+	1	NA	Intergenic	Intergenic	-2175	NM_139220	246080	Mm.207067	NM_139220	ENSMUSG00000037790	Defb7	BD-7|Defb15	defensin beta 7	protein-coding
mm_4787.1	chr1	184118273	184118277	+	1	NA	Intergenic	B4A|SINE|B4	83814	NM_022019	63953	Mm.404024	NM_022019	ENSMUSG00000039384	Dusp10	2610306G15Rik|AI158871|MKP-5|MKP5	dual specificity phosphatase 10	protein-coding
mm_113567.1	chr13	38328767	38328780	+	1	NA	Intergenic	Intergenic	-16943	NM_007556	12161	Mm.385759	NM_007556	ENSMUSG00000039004	Bmp6	D13Wsu115e|Vgr1	bone morphogenetic protein 6	protein-coding
mm_13500.1	chr2	107290668	107290678	+	1	NA	promoter-TSS (NM_021275)	promoter-TSS (NM_021275)	84	NM_021275	16492	Mm.142718	NM_021275	ENSMUSG00000042604	Kcna4	Kv1.4	potassium voltage-gated channel, shaker-related subfamily, member 4	protein-coding
mm_170841.1	chr2	177294456	177294471	+	1	NA	Intergenic	Intergenic	-170279	NM_001177568	628308	Mm.460436	NM_001177568	ENSMUSG00000078866	Zfp970	Gm14420|OTTMUSG00000016588	zinc finger protein 970	protein-coding
mm_150606.1	chr19	40831249	40831292	+	1	NA	promoter-TSS (NM_172839)	promoter-TSS (NM_172839)	-9	NM_172839	240665	Mm.309	NM_172839	ENSMUSG00000025010	Ccnj	D430039C20Rik	cyclin J	protein-coding
mm_117135.1	chr13	60939990	60939995	-	1	NA	exon (NM_009411, exon 4 of 5)	exon (NM_009411, exon 4 of 5)	1943	NM_009411	21984	Mm.2372	NM_009411	ENSMUSG00000033834	Tpbpa	AV033951|Tb-1|Tb1|Tpbp|b2b1247Clo	trophoblast specific protein alpha	protein-coding
mm_5500.1	chr1	37169944	37169944	-	1	NA	Intergenic	Intergenic	-48334	NM_001282010	12790	Mm.214224	NM_009918	ENSMUSG00000026114	Cnga3	CNG3	cyclic nucleotide gated channel alpha 3	protein-coding
mm_168438.1	chr1	136696074	136696086	+	1	NA	promoter-TSS (NR_037986)	promoter-TSS (NR_037986)	-131	NR_037986	100503474	Mm.428276	NR_037986		Platr22	Gm16880	pluripotency associated transcript 22	ncRNA
mm_79455.1	chr9	56166444	56166453	+	1	NA	Intergenic	Intergenic	-5378	NM_019793	56434	Mm.28484	NM_019793	ENSMUSG00000032324	Tspan3	1700055K04Rik|TM4-A|Tm4sf8	tetraspanin 3	protein-coding
mm_23555.1	chr3	62159294	62159334	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-179463	NM_001081295	622434	Mm.153974	NM_001081295	ENSMUSG00000036885	Arhgef26	4631416L12Rik|8430436L14Rik|AI303572|AW491953|SGEF	Rho guanine nucleotide exchange factor (GEF) 26	protein-coding
mm_40201.1	chr5	36954054	36954058	+	1	NA	3' UTR (NM_172994, exon 9 of 9)	3' UTR (NM_172994, exon 9 of 9)	34926	NM_011716	22393	Mm.20916	NM_011716	ENSMUSG00000039474	Wfs1	AI481085|wolframin	Wolfram syndrome 1 homolog (human)	protein-coding
mm_68009.1	chr7	100939107	100939125	-	1	NA	exon (NM_183168, exon 3 of 3)	exon (NM_183168, exon 3 of 3)	-6955	NM_001081116	207212	Mm.29954	NM_001081116	ENSMUSG00000032875	Arhgef17	8030463K16|AI428794|AW558066|BC035332|mKIAA0337	Rho guanine nucleotide exchange factor (GEF) 17	protein-coding
mm_79262.1	chr9	50753152	50753155	+	1	NA	promoter-TSS (NM_024441)	promoter-TSS (NM_024441)	182	NM_009964	12955	Mm.178	NM_009964	ENSMUSG00000032060	Cryab	Crya-2|Crya2|HspB5|P23	crystallin, alpha B	protein-coding
mm_155953.1	chrX	105086960	105086964	+	1	NA	intron (NM_001281871, intron 5 of 5)	Lx3_Mus|LINE|L1	7206	NM_026312	67683	Mm.273405	NM_026312	ENSMUSG00000031226	Pbdc1	2610029G23Rik	polysaccharide biosynthesis domain containing 1	protein-coding
mm_163715.1	chr13	111578041	111578043	+	1	NA	Intergenic	B3A|SINE|B2	-88001	NM_001122963	73274	Mm.57286	NM_028487	ENSMUSG00000032745	Gpbp1	1700034P14Rik|AU019836|D230035M11Rik|Gpbp|mGPBP	GC-rich promoter binding protein 1	protein-coding
mm_131158.1	chr16	6914403	6914413	+	1	NA	intron (NM_021477, intron 5 of 16)	intron (NM_021477, intron 5 of 16)	-155427	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_46278.1	chr5	100039623	100039657	-	1	NA	promoter-TSS (NM_016690)	promoter-TSS (NM_016690)	-354	NM_026421	67870	Mm.11311	NM_026421	ENSMUSG00000029326	Enoph1	2310057D15Rik|BB183658|C81437	enolase-phosphatase 1	protein-coding
mm_82878.1	chr9	32452046	32452061	-	1	NA	intron (NM_008026, intron 5 of 8)	intron (NM_008026, intron 5 of 8)	58068	NM_001168354	56379	Mm.390168	NM_019659	ENSMUSG00000041248	Kcnj1	Kir1.1|ROMK|Romk2	potassium inwardly-rectifying channel, subfamily J, member 1	protein-coding
mm_98491.1	chr11	94951556	94951567	+	1	NA	exon (NM_007742, exon 51 of 51)	exon (NM_007742, exon 51 of 51)	15337	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_129256.1	chr15	76710487	76710511	-	1	NA	promoter-TSS (NM_058214)	promoter-TSS (NM_058214)	60	NM_058214	79456	Mm.18373	NM_058214	ENSMUSG00000033762	Recql4	RecQ4	RecQ protein-like 4	protein-coding
mm_121693.1	chr14	13961379	13961442	-	1	NA	promoter-TSS (NM_025435)	promoter-TSS (NM_025435)	-97	NM_025435	66231	Mm.295875	NM_025435	ENSMUSG00000053453	Thoc7	Nif3l1bp1	THO complex 7	protein-coding
mm_119078.1	chr14	30880487	30880499	+	1	NA	intron (NM_181390, intron 1 of 2)	intron (NM_181390, intron 1 of 2)	1236	NM_181390	66175	Mm.220895	NM_181390	ENSMUSG00000042485	Mustn1	1110028G01Rik|Mustang	musculoskeletal, embryonic nuclear protein 1	protein-coding
mm_161029.1	chr12	8599065	8599065	-	1	NA	promoter-TSS (NM_177802)	promoter-TSS (NM_177802)	1	NM_177802	328059	Mm.46326	NM_177802	ENSMUSG00000020600	Slc7a15	Arpat	solute carrier family 7 (cationic amino acid transporter, y+ system), member 15	protein-coding
mm_112813.1	chr13	20794446	20794452	+	1	NA	exon (NM_001281854, exon 1 of 5)	exon (NM_001281854, exon 1 of 5)	336	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_20778.1	chr2	143983165	143983172	-	1	NA	intron (NM_024281, intron 2 of 23)	intron (NM_024281, intron 2 of 23)	28095	NM_133626	81910	Mm.13705	NM_024281	ENSMUSG00000027422	Rrbp1	1700087N07Rik|5730465C04Rik|ES/130|mKIAA1398|mRRp0|mRRp1.8|mRRp10|mRRp15a|mRRp15b|mRRp16.8|mRRp2|mRRp41|mRRp47|mRRp5.4|p180	ribosome binding protein 1	protein-coding
mm_96523.1	chr11	68496613	68496625	+	1	NA	3' UTR (NM_177320, exon 19 of 19)	3' UTR (NM_177320, exon 19 of 19)	-6400	NM_001004435	104709	Mm.234573	NM_001004435	ENSMUSG00000046207	Pik3r6	BB220380|p84|p84 PIKAP|p87(PIKAP)|p87PIKAP	phosphoinositide-3-kinase, regulatory subunit 6	protein-coding
mm_147371.1	chr18	43438372	43438382	-	1	NA	promoter-TSS (NM_001291455)	promoter-TSS (NM_001291455)	-91	NM_001291455	22240	Mm.8180	NM_009468	ENSMUSG00000024501	Dpysl3	CRMP-4|DRP-3|TUC4|ULIP-1|Ulip|Ulip1	dihydropyrimidinase-like 3	protein-coding
mm_65145.1	chr7	19584355	19584364	-	1	NA	intron (NM_016680, intron 16 of 20)	intron (NM_016680, intron 16 of 20)	7072	NM_022409	63872	Mm.23310	NM_022409	ENSMUSG00000011267	Zfp296	2210018A16Rik|Znf296	zinc finger protein 296	protein-coding
mm_22828.1	chr3	27241621	27241665	+	1	NA	exon (NM_178772, exon 5 of 5)	exon (NM_178772, exon 5 of 5)	58639	NM_178772	320024	Mm.24576	NM_178772	ENSMUSG00000027698	Nceh1	Aadacl1|B230106I24Rik|CPO-BP|Nceh	neutral cholesterol ester hydrolase 1	protein-coding
mm_84680.1	chr9	72110821	72110831	-	1	NA	5' UTR (NM_011544, exon 2 of 21)	5' UTR (NM_011544, exon 2 of 21)	375	NM_001253862	21406	Mm.171615	NM_011544	ENSMUSG00000032228	Tcf12	A130037E08Rik|ALF1|HEB|HEBAlt|HTF-4|HTF4|ME1|REB|bHLHb20	transcription factor 12	protein-coding
mm_41208.1	chr5	88554426	88554442	+	1	NA	promoter-TSS (NM_023054)	promoter-TSS (NM_023054)	-49	NM_023054	65961	Mm.490364	NM_023054	ENSMUSG00000070697	Utp3	2400011K09Rik|AW557551|C87704|Crl1|Crlz1|Sas10	UTP3 small subunit processome component	protein-coding
mm_148595.1	chr19	5088535	5088575	+	1	NA	promoter-TSS (NM_026553)	promoter-TSS (NM_026553)	17	NM_026553	68090	Mm.44202	NM_026553	ENSMUSG00000024875	Yif1a	5330422J23Rik|54TM|Yif1|Yif1p	Yip1 interacting factor homolog A (S. cerevisiae)	protein-coding
mm_143694.1	chr17	80424778	80424781	-	1	NA	intron (NM_009231, intron 10 of 21)	intron (NM_009231, intron 10 of 21)	-51237	NR_028385	791338	Mm.204722	NR_028385		Gm10190	ENSMUSG00000066938	predicted gene 10190	ncRNA
mm_140806.1	chr17	22219478	22219481	-	1	NA	intron (NM_001205095, intron 2 of 4)	intron (NM_001205095, intron 2 of 4)	6135	NM_001205095	240038	Mm.227945	NM_001205095	ENSMUSG00000096433	Zfp994	EG240038|Gm4944	zinc finger protein 994	protein-coding
mm_30602.1	chr4	6393167	6393171	+	1	NA	intron (NM_001098227, intron 7 of 8)	intron (NM_001098227, intron 7 of 8)	27489	NM_001098227	53378	Mm.247473	NM_016807	ENSMUSG00000028249	Sdcbp	MDA-9|Sycl|syntenin-1	syndecan binding protein	protein-coding
mm_123980.1	chr14	75327840	75327929	-	1	NA	exon (NM_026083, exon 12 of 19)	exon (NM_026083, exon 12 of 19)	43511	NM_026083	67302	Mm.74704	NM_026083	ENSMUSG00000022000	Zc3h13	2600010B19Rik|3110050K21Rik|4930570G11Rik|C87618	zinc finger CCCH type containing 13	protein-coding
mm_136550.1	chr16	98081982	98082012	-	1	NA	intron (NR_015491, intron 1 of 4)	intron (NR_015491, intron 1 of 4)	442	NR_015491	320586	Mm.442230	NR_015491		A630089N07Rik	-	RIKEN cDNA A630089N07 gene	ncRNA
mm_73738.1	chr8	114133602	114133630	+	1	NA	promoter-TSS (NM_024446)	promoter-TSS (NM_024446)	42	NM_024437	67528	Mm.27889	NM_024437	ENSMUSG00000031767	Nudt7	1300007B24Rik|2210404C19Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 7	protein-coding
mm_32840.1	chr4	117835339	117835349	+	1	NA	promoter-TSS (NM_008135)	promoter-TSS (NM_008135)	86	NM_008135	14664	Mm.244549	NM_008135	ENSMUSG00000028542	Slc6a9	Glyt-1|Glyt1	solute carrier family 6 (neurotransmitter transporter, glycine), member 9	protein-coding
mm_43463.1	chr5	136692821	136692837	+	1	NA	promoter-TSS (NM_021611)	promoter-TSS (NM_021611)	-317	NM_001303019	59310	Mm.5178	NM_021611	ENSMUSG00000005474	Myl10	1700027I08Rik|Mylc2pl|PLRLC	myosin, light chain 10, regulatory	protein-coding
mm_77825.1	chr9	3532296	3532354	+	1	NA	promoter-TSS (NM_001033322)	promoter-TSS (NM_001033322)	-24	NM_001033322	234889	Mm.91240	NM_001033322	ENSMUSG00000041624	Gucy1a2	6330407I18Rik|A230060L24Rik	guanylate cyclase 1, soluble, alpha 2	protein-coding
mm_135346.1	chr16	43663200	43663231	-	1	NA	intron (NM_001146325, intron 1 of 3)	G-rich|Low_complexity|Low_complexity	969	NM_001146325	100043314	Mm.390896	NM_001146325	ENSMUSG00000071552	Tigit	ENSMUSG00000071552|Vstm3	T cell immunoreceptor with Ig and ITIM domains	protein-coding
mm_163904.1	chr14	30605842	30605909	-	1	NA	exon (NM_001310682, exon 6 of 17)	exon (NM_001310682, exon 6 of 17)	4435	NM_001310682	18753	Mm.2314	NM_011103	ENSMUSG00000021948	Prkcd	AI385711|D14Ertd420e|PKC[d]|PKCdelta|Pkcd	protein kinase C, delta	protein-coding
mm_157638.1	chrX	57200397	57200425	-	1	NA	promoter-TSS (NR_038463)	promoter-TSS (NR_038463)	-226	NR_038463	100502842	Mm.164733	NR_038463	ENSMUSG00000085808	Gm14718	OTTMUSG00000017790	predicted gene 14718	ncRNA
mm_159396.1	chr3	95134169	95134169	+	1	NA	promoter-TSS (NM_001163573)	promoter-TSS (NM_001163573)	81	NM_153121	217779	Mm.341945	NM_153121	ENSMUSG00000053769	Lysmd1	2610022K04Rik|AI415311	LysM, putative peptidoglycan-binding, domain containing 1	protein-coding
mm_94713.1	chr11	20542890	20542900	+	1	NA	promoter-TSS (NM_021372)	promoter-TSS (NM_021372)	-358	NM_021372	58172	Mm.339676	NM_021372	ENSMUSG00000049800	Sertad2	AB041541|AU021878|Kiaa0127|MNCb-1504|SEI-2|Sei2|TRIP-Br2|mKIAA0127	SERTA domain containing 2	protein-coding
mm_111974.1	chr12	110023812	110023838	-	1	NA	Intergenic	Intergenic	134248	NR_045466	67280	Mm.390495	NR_045466		3110009F21Rik	-	RIKEN cDNA 3110009F21 gene	ncRNA
mm_71281.1	chr8	40919832	40919849	+	1	NA	3' UTR (NM_001044740, exon 12 of 12)	3' UTR (NM_001044740, exon 12 of 12)	-6393	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_67064.1	chr7	67645281	67645332	-	1	NA	promoter-TSS (NR_028144)	promoter-TSS (NR_028144)	-70	NR_028143	67867	Mm.31247	NM_027413	ENSMUSG00000030556	Lrrc28	1300004K21Rik|2210012C09Rik|2310058O11Rik	leucine rich repeat containing 28	protein-coding
mm_130027.1	chr15	88891521	88891530	-	1	NA	Intergenic	Intergenic	29331	NM_145478	223775	Mm.400129	NM_145478	ENSMUSG00000035828	Pim3	BC026639|Kid1	proviral integration site 3	protein-coding
mm_158592.1	chrX	150954887	150954898	-	1	NA	Intergenic	MLT1M|LTR|ERVL-MaLR	62401	NM_001168600	237107	Mm.45987	NM_198110	ENSMUSG00000025266	Gnl3l	BC020354	guanine nucleotide binding protein-like 3 (nucleolar)-like	protein-coding
mm_133381.1	chr16	84715074	84715087	+	1	NA	TTS (NR_029565)	TTS (NR_029565)	940	NR_029565	387173		NR_029565	ENSMUSG00000065397	Mir155	Mirn155|mir-155|mmu-mir-155	microRNA 155	ncRNA
mm_83157.1	chr9	40465635	40465664	-	1	NA	Intergenic	Intergenic	-9885	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_51003.1	chr6	63605436	63605440	+	1	NA	intron (NM_008167, intron 2 of 15)	intron (NM_008167, intron 2 of 15)	348581	NM_008167	14804	Mm.439651	NM_008167	ENSMUSG00000071424	Grid2	B230104L07Rik|GluD2|GluRdelta2|Lc|Lc<J>|MMS10-AC|Ms10ac|cpr|ho|nmf408|tpr	glutamate receptor, ionotropic, delta 2	protein-coding
mm_87800.1	chr10	60300167	60300195	+	1	NA	exon (NM_011179, exon 12 of 15)	exon (NM_011179, exon 12 of 15)	15720	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_145637.1	chr18	61114788	61114874	+	1	NA	exon (NM_001037859, exon 7 of 22)	exon (NM_001037859, exon 7 of 22)	-2637	NR_105949	102466212		NR_105949	ENSMUSG00000098389	Mir6983	Gm27496|mmu-mir-6983	microRNA 6983	ncRNA
mm_47805.1	chr5	132543364	132543379	-	1	NA	Intergenic	CpG	-1028	NM_177047	319974	Mm.409595	NM_177047	ENSMUSG00000029673	Auts2	2700063G02Rik|A730011F23Rik|D830032G16Rik	autism susceptibility candidate 2	protein-coding
mm_164277.1	chr15	102009125	102009143	-	1	NA	Intergenic	Intergenic	-4792	NM_031170	16691	Mm.358618	NM_031170	ENSMUSG00000049382	Krt8	AA960620|AL022697|AU019895|Card2|EndoA|K8|Krt-2.8|Krt2-8	keratin 8	protein-coding
mm_111948.1	chr12	109073393	109073410	-	1	NA	Intergenic	Intergenic	-5184	NM_001163175	380785	Mm.342085	NM_001163175	ENSMUSG00000040867	Begain	BM948371|Gm897	brain-enriched guanylate kinase-associated	protein-coding
mm_58477.1	chr7	3423590	3423594	+	1	NA	promoter-TSS (NR_126426)	promoter-TSS (NR_126426)	-147	NR_126426	70230	Mm.458356	NR_126426	ENSMUSG00000107585	3300002P13Rik	-	RIKEN cDNA 3300002P13 gene	ncRNA
mm_135554.1	chr16	49855298	49855312	-	1	NA	promoter-TSS (NM_010581)	promoter-TSS (NM_010581)	-349	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_156804.1	chrX	163909204	163909210	+	1	NA	5' UTR (NM_026887, exon 1 of 5)	5' UTR (NM_026887, exon 1 of 5)	190	NM_001290379	108012	Mm.426783	NM_026887	ENSMUSG00000031367	Ap1s2	1500012A13Rik|AI853648|EST1	adaptor-related protein complex 1, sigma 2 subunit	protein-coding
mm_92848.1	chr10	81524107	81524127	-	1	NA	5' UTR (NM_010304, exon 1 of 7)	5' UTR (NM_010304, exon 1 of 7)	108	NM_010304	14676	Mm.1546	NM_010304	ENSMUSG00000034792	Gna15	G[a]15|Galpha15	guanine nucleotide binding protein, alpha 15	protein-coding
mm_10742.1	chr2	23069414	23069424	+	1	NA	intron (NM_001102437, intron 1 of 12)	intron (NM_001102437, intron 1 of 12)	347	NM_001102438	74159	Mm.181973	NM_028793	ENSMUSG00000026781	Acbd5	1300014E15Rik	acyl-Coenzyme A binding domain containing 5	protein-coding
mm_129196.1	chr15	76507722	76507725	-	1	NA	intron (NM_010046, intron 1 of 16)	intron (NM_010046, intron 1 of 16)	4095	NM_010046	13350	Mm.22633	NM_010046	ENSMUSG00000022555	Dgat1	ARAT|C75990|D15Ertd23e|Dgat	diacylglycerol O-acyltransferase 1	protein-coding
mm_6140.1	chr1	64737736	64737756	-	1	NA	promoter-TSS (NM_001042659)	promoter-TSS (NM_001042659)	4	NM_001042659	14367	Mm.150813	NM_022721	ENSMUSG00000045005	Fzd5	5330434N09Rik|AI427138|Fz-5|Fz5|mFz5	frizzled class receptor 5	protein-coding
mm_53942.1	chr6	5178285	5178291	-	1	NA	intron (NM_011134, intron 5 of 8)	intron (NM_011134, intron 5 of 8)	15658	NM_011134	18979	Mm.237657	NM_011134	ENSMUSG00000002588	Pon1	Pon	paraoxonase 1	protein-coding
mm_111028.1	chr12	79134537	79134537	-	1	NA	intron (NM_009705, intron 2 of 7)	intron (NM_009705, intron 2 of 7)	3749	NM_009705	11847	Mm.3506	NM_009705	ENSMUSG00000021125	Arg2	AII|AU022422	arginase type II	protein-coding
mm_158777.1	chrX	167102060	167102076	-	1	NA	Intergenic	Intergenic	-31698	NM_001101606	667794	Mm.302232	NM_001101606		Gm8817	EG667794	predicted gene 8817	protein-coding
mm_52103.1	chr6	97875949	97875959	+	1	NA	intron (NM_001113198, intron 1 of 9)	intron (NM_001113198, intron 1 of 9)	-53863	NM_001178049	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_95640.1	chr11	53719991	53720004	+	1	NA	promoter-TSS (NM_010558)	promoter-TSS (NM_010558)	-797	NM_010558	16191	Mm.4461	NM_010558	ENSMUSG00000036117	Il5	Il-5	interleukin 5	protein-coding
mm_137499.1	chr17	26972252	26972266	+	1	NA	promoter-TSS (NM_001005916)	promoter-TSS (NM_001005916)	-920	NM_001005916	474156	Mm.328890	NM_001005916	ENSMUSG00000079605	Zbtb9	3930402F13Rik	zinc finger and BTB domain containing 9	protein-coding
mm_83623.1	chr9	48836180	48836200	-	1	NA	promoter-TSS (NM_001033324)	promoter-TSS (NM_001033324)	-245	NM_001033324	235320	Mm.457803	NM_001033324	ENSMUSG00000066687	Zbtb16	AI467657|PLZF|Zfp145|lu	zinc finger and BTB domain containing 16	protein-coding
mm_129663.1	chr15	81190702	81190719	-	1	NA	promoter-TSS (NM_001082536)	promoter-TSS (NM_001082536)	47	NM_001082536	223701	Mm.439814	NM_153049	ENSMUSG00000042292	Mkl1	AMKL|Bsac|Mal|Mrtf-A	MKL (megakaryoblastic leukemia)/myocardin-like 1	protein-coding
mm_38148.1	chr4	134897237	134897245	-	1	NA	TTS (NM_027935)	TTS (NM_027935)	17675	NM_027935	71817	Mm.88349	NM_027935	ENSMUSG00000028822	Tmem50a	3200001F09Rik|CAM|Smp1	transmembrane protein 50A	protein-coding
mm_71703.1	chr8	61928082	61928094	+	1	NA	promoter-TSS (NM_001293783)	promoter-TSS (NM_001293783)	1	NM_001293783	234311	Mm.275233	NM_144928	ENSMUSG00000037921	Ddx60	9830118M07	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	protein-coding
mm_4757.1	chr1	182300944	182300989	+	1	NA	non-coding (NR_015458, exon 1 of 2)	non-coding (NR_015458, exon 1 of 2)	132	NR_015458	67330	Mm.331019	NR_015458	ENSMUSG00000100147	1700047M11Rik	-	RIKEN cDNA 1700047M11 gene	ncRNA
mm_119298.1	chr14	34694288	34694310	+	1	NA	intron (NM_001301330, intron 3 of 18)	RLTR12E|LTR|ERVK	20371	NM_001301330	218914	Mm.27957	NM_001004436	ENSMUSG00000041408	Wapl	A530089A20Rik|BC037674|DIF-2|FOE|Wapal	WAPL cohesin release factor	protein-coding
mm_156754.1	chrX	160404473	160404476	+	1	NA	intron (NM_001079847, intron 1 of 26)	Lx6|LINE|L1	13784	NM_001290445	237175	Mm.213016	NM_178712	ENSMUSG00000031298	Adgrg2	AW212196|B830041D06Rik|Gpr64|Me6	adhesion G protein-coupled receptor G2	protein-coding
mm_66387.1	chr7	44055748	44055784	-	1	NA	exon (NM_020268, exon 3 of 5)	exon (NM_020268, exon 3 of 5)	3476	NM_020268	16619	Mm.445911	NM_020268	ENSMUSG00000063177	Klk1b27	Gk27|Klk21l|Klk27|mGK-27	kallikrein 1-related peptidase b27	protein-coding
mm_3555.1	chr1	150423518	150423539	+	1	NA	exon (NM_133780, exon 26 of 52)	exon (NM_133780, exon 26 of 52)	-30473	NM_145511	226499	Mm.222093	NM_145511	ENSMUSG00000006010	BC003331	1810053E15Rik|Odr4|odr-4	cDNA sequence BC003331	protein-coding
mm_162045.1	chr19	60889839	60889839	+	1	NA	promoter-TSS (NM_018869)	promoter-TSS (NM_018869)	90	NM_018869	14773	Mm.279400	NM_018869	ENSMUSG00000003228	Grk5	Gprk5	G protein-coupled receptor kinase 5	protein-coding
mm_95764.1	chr11	54907168	54907177	+	1	NA	exon (NM_008161, exon 2 of 5)	exon (NM_008161, exon 2 of 5)	4318	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_119039.1	chr14	30565607	30565635	+	1	NA	exon (NM_009388, exon 5 of 14)	exon (NM_009388, exon 5 of 14)	-6528	NR_037237	100526475		NR_037237	ENSMUSG00000093156	Mir3076	mir-3076|mmu-mir-3076	microRNA 3076	ncRNA
mm_19157.1	chr2	80717991	80717996	-	1	NA	Intergenic	Intergenic	78729	NM_001190179	69482	Mm.29200	NM_027091	ENSMUSG00000026999	Nup35	2310006I24Rik|35kDa|5330402E05Rik|MP44|NO44	nucleoporin 35	protein-coding
mm_53229.1	chr6	127153260	127153263	+	1	NA	intron (NR_040275, intron 1 of 1)	intron (NR_040275, intron 1 of 1)	-2213	NM_009829	12444	Mm.333406	NM_009829	ENSMUSG00000000184	Ccnd2	2600016F06Rik|AI256817|BF642806|C86853|Vin-1|Vin1|cD2	cyclin D2	protein-coding
mm_90155.1	chr10	118441045	118441050	+	1	NA	promoter-TSS (NM_008337)	promoter-TSS (NM_008337)	1	NM_008337	15978	Mm.240327	NM_008337	ENSMUSG00000055170	Ifng	IFN-g|Ifg	interferon gamma	protein-coding
mm_97973.1	chr11	83859322	83859328	+	1	NA	intron (NM_001291268, intron 2 of 8)	intron (NM_001291268, intron 2 of 8)	6365	NM_001291269	21410	Mm.7226	NM_009330	ENSMUSG00000020679	Hnf1b	HNF-1-beta|HNF-1B|HNF-1Beta|Hnf1beta|LFB3|Tcf-2|Tcf2|vHNF1	HNF1 homeobox B	protein-coding
mm_39547.1	chr5	21645979	21646032	+	1	NA	promoter-TSS (NM_026034)	promoter-TSS (NM_026034)	21	NM_026034	67211	Mm.260782	NM_026034	ENSMUSG00000038525	Armc10	2810037C14Rik|Svh	armadillo repeat containing 10	protein-coding
mm_60058.1	chr7	31155679	31155689	+	1	NA	Intergenic	Intergenic	-4634	NM_027898	52857	Mm.27366	NM_027898	ENSMUSG00000001248	Gramd1a	1300003M23Rik|AI415002|AW547240|D7Bwg0611e	GRAM domain containing 1A	protein-coding
mm_97032.1	chr11	72266470	72266479	+	1	NA	promoter-TSS (NR_045922)	promoter-TSS (NR_045922)	130	NM_001004148	237831	Mm.340778	NM_001004148	ENSMUSG00000020805	Slc13a5	Indy|NaC2/NaCT|Nact|mINDY	solute carrier family 13 (sodium-dependent citrate transporter), member 5	protein-coding
mm_50419.1	chr6	48768750	48768769	+	1	NA	5' UTR (NM_031247, exon 2 of 5)	5' UTR (NM_031247, exon 2 of 5)	2092	NM_031247	83408	Mm.333050	NM_031247	ENSMUSG00000039264	Gimap3	2010110D23Rik|Gimap5|Ian4	GTPase, IMAP family member 3	protein-coding
mm_108130.1	chr12	76072030	76072079	+	1	NA	intron (NM_001005510, intron 96 of 115)	intron (NM_001005510, intron 96 of 115)	105205	NM_010157	13983	Mm.2561	NM_010157	ENSMUSG00000021055	Esr2	ER[b]|ERbeta|Estrb	estrogen receptor 2 (beta)	protein-coding
mm_12591.1	chr2	73764865	73764872	+	1	NA	intron (NM_001166603, intron 1 of 11)	intron (NM_001166603, intron 1 of 11)	10478	NM_001166603	108699	Mm.257073	NM_029716	ENSMUSG00000056486	Chn1	0610007I19Rik|0710001E19Rik|1700112L09Rik|2900046J01Rik|AI413815|ARHGAP2	chimerin 1	protein-coding
mm_160178.1	chr7	45694165	45694165	-	1	NA	exon (NM_001289693, exon 7 of 7)	exon (NM_001289693, exon 7 of 7)	237	NM_001271578	56546	Mm.56914	NM_019934	ENSMUSG00000040364	Sec1	Fut10|Fut3	secretory blood group 1	protein-coding
mm_92116.1	chr10	63243635	63243672	-	1	NA	promoter-TSS (NM_026101)	promoter-TSS (NM_026101)	-144	NM_030114	67345	Mm.234437	NM_026101	ENSMUSG00000020064	Herc4	1700056O17Rik|4921531D01Rik|9530080M15Rik|mKIAA1593	hect domain and RLD 4	protein-coding
mm_54546.1	chr6	36810039	36810057	-	1	NA	5' UTR (NM_008973, exon 1 of 5)	5' UTR (NM_008973, exon 1 of 5)	1313	NM_008973	19242	Mm.279690	NM_008973	ENSMUSG00000029838	Ptn	HARP|HB-GAM|HBBN|HBGF-8|HBNF|OSF|Osf-1|Osf1	pleiotrophin	protein-coding
mm_113857.1	chr13	47246937	47246951	+	1	NA	3' UTR (NM_146042, exon 8 of 8)	3' UTR (NM_146042, exon 8 of 8)	52941	NM_001170643	218215	Mm.287609	NM_146042	ENSMUSG00000038068	Rnf144b	BC025007|E130105P19Rik|Ibrdc2|Pir2	ring finger protein 144B	protein-coding
mm_163132.1	chr11	78772813	78772817	+	1	NA	Intergenic	Intergenic	-21086	NM_197989	69109	Mm.341420	NM_197989	ENSMUSG00000049489	Fam58b	1810009O10Rik|Fam58a	family with sequence similarity 58, member B	protein-coding
mm_160506.1	chr9	20171417	20171417	-	1	NA	exon (NM_146904, exon 1 of 1)	exon (NM_146904, exon 1 of 1)	152	NM_146904	57251	Mm.377130	NM_146904	ENSMUSG00000066899	Olfr870	MOR141-1|Olfr72	olfactory receptor 870	protein-coding
mm_64277.1	chr7	141808623	141808643	+	1	NA	intron (NM_010844, intron 31 of 49)	intron (NM_010844, intron 31 of 49)	19622	NM_010844	17833	Mm.334332	NM_010844	ENSMUSG00000037974	Muc5ac	2210005L13Rik|MGM	mucin 5, subtypes A and C, tracheobronchial/gastric	protein-coding
mm_15659.1	chr2	163225446	163225469	+	1	NA	promoter-TSS (NM_001098799)	promoter-TSS (NM_001098799)	3	NM_001098799	269389	Mm.207709	NM_001098799	ENSMUSG00000074607	Tox2	AI851523|AV026525|BI987407|Gcx1|RxHMG1	TOX high mobility group box family member 2	protein-coding
mm_127491.1	chr15	101364763	101364768	+	1	NA	intron (NM_028770, intron 1 of 8)	intron (NM_028770, intron 1 of 8)	-4587	NR_035462	100316694		NR_035462	ENSMUSG00000088459	Mir1941	mmu-mir-1941	microRNA 1941	ncRNA
mm_6615.1	chr1	75506332	75506402	-	1	NA	promoter-TSS (NM_178884)	promoter-TSS (NM_178884)	85	NM_178884	98733	Mm.236454	NM_178884	ENSMUSG00000026211	Obsl1	AW822216	obscurin-like 1	protein-coding
mm_170533.1	chr19	38325988	38325997	-	1	NA	Intergenic	RLTR17|LTR|ERVK	61210	NM_020278	56839	Mm.298251	NM_020278	ENSMUSG00000067242	Lgi1	BB130740	leucine-rich repeat LGI family, member 1	protein-coding
mm_26541.1	chr3	146149859	146149868	+	1	NA	promoter-TSS (NM_026656)	promoter-TSS (NM_026656)	30	NM_026656	68279	Mm.116862	NM_026656	ENSMUSG00000011008	Mcoln2	3300002C04Rik|AI549968|C86638|TRPML2	mucolipin 2	protein-coding
mm_37656.1	chr4	128947705	128947748	-	1	NA	intron (NM_001301841, intron 5 of 8)	intron (NM_001301841, intron 5 of 8)	14729	NM_172875	242669	Mm.215814	NM_172875	ENSMUSG00000028789	Azin2	4933429I20Rik|Adc|Azi2|B930082O19|ODC-p|Odcp	antizyme inhibitor 2	protein-coding
mm_67269.1	chr7	75780746	75780757	-	1	NA	Intergenic	Intergenic	-67587	NM_001122780	207952	Mm.206223	NM_029652	ENSMUSG00000055652	Klhl25	2810402K13Rik|BC027373|Enc-1	kelch-like 25	protein-coding
mm_60275.1	chr7	43931673	43931679	+	1	NA	Intergenic	Intergenic	-2095	NM_174865	317652	Mm.389896	NM_174865	ENSMUSG00000055193	Klk15	-	kallikrein related-peptidase 15	protein-coding
mm_20629.1	chr2	131993590	131993601	-	1	NA	3' UTR (NM_175445, exon 11 of 11)	3' UTR (NM_175445, exon 11 of 11)	36393	NM_175445	215653	Mm.204737	NM_175445	ENSMUSG00000027339	Rassf2	3830431H01Rik|9030412M04Rik|AI852669|AW495050	Ras association (RalGDS/AF-6) domain family member 2	protein-coding
mm_159523.1	chr4	61595826	61595826	-	1	NA	promoter-TSS (NM_001134644).5	promoter-TSS (NM_001134644).5	-1	NM_001134644	100048885	Mm.422695	NM_001134644		Gm2083	-	major urinary protein LOC100048885	protein-coding
mm_163678.1	chr13	91374878	91374883	+	1	NA	intron (NR_045161, intron 1 of 2)	intron (NR_045161, intron 1 of 2)	13205	NR_045161	320297	Mm.375866	NR_045161	ENSMUSG00000097182	A830009L08Rik	-	RIKEN cDNA A830009L08 gene	ncRNA
mm_5973.1	chr1	57406447	57406507	-	1	NA	promoter-TSS (NM_001081181)	promoter-TSS (NM_001081181)	-71	NM_001081181	68115	Mm.275428	NM_001081181	ENSMUSG00000025971	Maip1	9430016H08Rik|AA409999|C78988	matrix AAA peptidase interacting protein 1	protein-coding
mm_10118.1	chr2	3730958	3730996	+	1	NA	intron (NM_025626, intron 1 of 3)	intron (NM_025626, intron 1 of 3)	17519	NM_025626	66540	Mm.277864	NM_025626	ENSMUSG00000026655	Fam107b	3110001A13Rik|AA589595|AA959793|AI132312	family with sequence similarity 107, member B	protein-coding
mm_156209.1	chrX	134601273	134601281	+	1	NA	promoter-TSS (NM_001313716)	promoter-TSS (NM_001313716)	98	NM_001313717	56258	Mm.315909	NM_019868	ENSMUSG00000045427	Hnrnph2	DXHXS1271E|Ftp-3|Ftp3|H'|HNRNP|Hnrph2	heterogeneous nuclear ribonucleoprotein H2	protein-coding
mm_57870.1	chr6	129678845	129678853	-	1	NA	exon (NM_001288664, exon 1 of 6)	exon (NM_001288664, exon 1 of 6)	124	NM_001288664	16641	Mm.56899	NM_010652	ENSMUSG00000030167	Klrc1	CD159a|NKG2A|NKG2B	killer cell lectin-like receptor subfamily C, member 1	protein-coding
mm_126513.1	chr15	81811513	81811521	+	1	NA	5' UTR (NM_017376, exon 1 of 4)	5' UTR (NM_017376, exon 1 of 4)	103	NM_017376	21685	Mm.270278	NM_017376	ENSMUSG00000022389	Tef	2310028D20Rik	thyrotroph embryonic factor	protein-coding
mm_146351.1	chr18	82561735	82561740	+	1	NA	intron (NM_001025258, intron 1 of 4)	intron (NM_001025258, intron 1 of 4)	7229	NM_001025254	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_78297.1	chr9	22411580	22411594	+	1	NA	promoter-TSS (NM_026739)	promoter-TSS (NM_026739)	10	NM_026739	68283	Mm.280669	NM_026739	ENSMUSG00000036411	9530077C05Rik	1110003N12Rik|Kiaa0895|mKIAA0895	RIKEN cDNA 9530077C05 gene	protein-coding
mm_58091.1	chr6	137505428	137505440	-	1	NA	exon (NM_001271587, exon 15 of 21)	exon (NM_001271587, exon 15 of 21)	14461	NM_001271589	13860	Mm.235346	NM_007945	ENSMUSG00000015766	Eps8	AW261790	epidermal growth factor receptor pathway substrate 8	protein-coding
mm_75221.1	chr8	39607548	39607559	-	1	NA	intron (NM_031195, intron 8 of 8)	intron (NM_031195, intron 8 of 8)	35125	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_169451.1	chr1	46076149	46076161	-	1	NA	intron (NM_001160386, intron 2 of 65)	L1Md_F2|LINE|L1	9417	NM_001160386	227058	Mm.296880	NM_001160386	ENSMUSG00000041144	Dnah7b	Dnahc7b|Gm107	dynein, axonemal, heavy chain 7B	protein-coding
mm_45058.1	chr5	41821439	41821461	-	1	NA	exon (NM_001081422, exon 10 of 27)	exon (NM_001081422, exon 10 of 27)	22865	NM_001310601	665775	Mm.158726	NM_001081422	ENSMUSG00000061755	Bod1l	A230054D04Rik|AI853319|FAM44A|mKIAA1327	biorientation of chromosomes in cell division 1-like	protein-coding
mm_44218.1	chr5	4757978	4757995	-	1	NA	5' UTR (NM_021457, exon 1 of 1)	5' UTR (NM_021457, exon 1 of 1)	230	NM_021457	14362	Mm.246003	NM_021457	ENSMUSG00000044674	Fzd1	AW227548|FZ-1|Fz1	frizzled class receptor 1	protein-coding
mm_35388.1	chr4	33290095	33290102	-	1	NA	Intergenic	Intergenic	-20213	NM_011884	24018	Mm.240024	NM_011884	ENSMUSG00000028274	Rngtt	AU020997|HCE|MCE1	RNA guanylyltransferase and 5'-phosphatase	protein-coding
mm_12247.1	chr2	68877953	68877967	+	1	NA	intron (NM_172856, intron 1 of 9)	intron (NM_172856, intron 1 of 9)	16519	NM_001347161	241447	Mm.222222	NM_172856	ENSMUSG00000027035	Cers6	4732462C07Rik|AW544719|Lass6|T1L	ceramide synthase 6	protein-coding
mm_142385.1	chr17	44814483	44814496	-	1	NA	5' UTR (NM_001146038, exon 1 of 9)	5' UTR (NM_001146038, exon 1 of 9)	138	NM_009820	12393	Mm.391013	NM_009820	ENSMUSG00000039153	Runx2	AML3|Cbf|Cbfa-1|Cbfa1|LS3|Osf2|PEBP2aA|Pebp2a1|Pebpa2a	runt related transcription factor 2	protein-coding
mm_157289.1	chrX	20861444	20861465	-	1	NA	TTS (NM_009703)	TTS (NM_009703)	1728	NR_049190	100885829		NR_049190	ENSMUSG00000093408	Mir5617	Gm25192|mir-5617|mmu-mir-5617	microRNA 5617	ncRNA
mm_137616.1	chr17	28272173	28272188	+	1	NA	intron (NR_045427, intron 1 of 2)	intron (NR_045427, intron 1 of 2)	472	NR_045427	69050	Mm.486938	NR_045427	ENSMUSG00000002250	1810013A23Rik	-	RIKEN cDNA 1810013A23 gene	ncRNA
mm_58729.1	chr7	13029675	13029717	+	1	NA	exon (NM_011588, exon 13 of 17)	exon (NM_011588, exon 13 of 17)	5081	NM_026885	68953	Mm.295670	NM_026885	ENSMUSG00000033916	Chmp2a	1500016L11Rik	charged multivesicular body protein 2A	protein-coding
mm_81305.1	chr9	108340299	108340316	+	1	NA	TTS (NM_008160)	TTS (NM_008160)	1227	NM_001329528	14775	Mm.1090	NM_008160	ENSMUSG00000063856	Gpx1	AI195024|AL033363|CGPx|GPx-1|GSHPx-1|Gpx	glutathione peroxidase 1	protein-coding
mm_159831.1	chr5	125388067	125388067	-	1	NA	exon (NM_019639, exon 2 of 2)	exon (NM_019639, exon 2 of 2)	1950	NM_019639	22190	Mm.331	NM_019639	ENSMUSG00000008348	Ubc	2700054O04Rik|AI194771|Rps27a|TI-225|Uba52|Ubb	ubiquitin C	protein-coding
mm_166836.1	chr7	19271753	19271757	-	1	NA	promoter-TSS (NM_001282022)	promoter-TSS (NM_001282022)	99	NM_001282021	22323	Mm.9684	NM_009499	ENSMUSG00000030403	Vasp	-	vasodilator-stimulated phosphoprotein	protein-coding
mm_46529.1	chr5	105651068	105651070	-	1	NA	Intergenic	ID_B1|SINE|B4	-48900	NM_001122768	231549	Mm.23837	NM_178701	ENSMUSG00000046079	Lrrc8d	2810473G09Rik|4930525N13Rik|A930019F03|Lrrc5	leucine rich repeat containing 8D	protein-coding
mm_113978.1	chr13	51846674	51846683	+	1	NA	promoter-TSS (NM_011817)	promoter-TSS (NM_011817)	3	NM_011817	23882	Mm.281298	NM_011817	ENSMUSG00000021453	Gadd45g	AI327420|C86281|CR6|DDIT2|OIG37	growth arrest and DNA-damage-inducible 45 gamma	protein-coding
mm_138766.1	chr17	37057159	37057183	+	1	NA	intron (NM_019439, intron 11 of 22)	intron (NM_019439, intron 11 of 22)	11205	NM_019439	54393	Mm.32191	NM_019439	ENSMUSG00000024462	Gabbr1	GABAB1|GABAbR1|bM573K1.1	gamma-aminobutyric acid (GABA) B receptor, 1	protein-coding
mm_154099.1	chr19	57008547	57008560	-	1	NA	promoter-TSS (NM_001177797)	promoter-TSS (NM_001177797)	22	NM_146102	226250	Mm.226284	NM_146102	ENSMUSG00000025083	Afap1l2	AU041783|C86904|mKIAA1914	actin filament associated protein 1-like 2	protein-coding
mm_42755.1	chr5	120847365	120847391	+	1	NA	promoter-TSS (NM_145153)	promoter-TSS (NM_145153)	11	NM_145153	243262	Mm.105369	NM_145153	ENSMUSG00000053765	Oas1f	-	2'-5' oligoadenylate synthetase 1F	protein-coding
mm_67036.1	chr7	67044308	67044331	-	1	NA	intron (NM_001033877, intron 13 of 22)	intron (NM_001033877, intron 13 of 22)	178139	NR_131044	76628	Mm.384589	NR_131043	ENSMUSG00000097527	1700112J16Rik	-	RIKEN cDNA 1700112J16 gene	ncRNA
mm_121358.1	chr14	117063130	117063133	+	1	NA	intron (NM_001079844, intron 1 of 9)	intron (NM_001079844, intron 1 of 9)	137834	NM_011821	23888	Mm.440025	NM_011821	ENSMUSG00000058571	Gpc6	-	glypican 6	protein-coding
mm_134798.1	chr16	24296174	24296186	-	1	NA	Intergenic	Intergenic	-97170	NM_178665	210126	Mm.209385	NM_178665	ENSMUSG00000033306	Lpp	9430020K16Rik|AA959454|AU024130|B130055L10Rik|C79715|D630048H16	LIM domain containing preferred translocation partner in lipoma	protein-coding
mm_7563.1	chr1	124756316	124756324	-	1	NA	Intergenic	B3A|SINE|B2	679407	NM_023735	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding
mm_62039.1	chr7	92234941	92234970	+	1	NA	promoter-TSS (NM_001243047)	promoter-TSS (NM_001243047)	-15	NM_001243047	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_13555.1	chr2	112261958	112261974	+	1	NA	promoter-TSS (NM_025403)	promoter-TSS (NM_025403)	40	NM_025403	66181	Mm.272346	NM_025403	ENSMUSG00000027133	Nop10	1110036B12Rik|NOP10P|Nola3	NOP10 ribonucleoprotein	protein-coding
mm_39087.1	chr4	154636774	154636780	-	1	NA	promoter-TSS (NM_027504)	promoter-TSS (NM_027504)	96	NM_001177995	70673	Mm.257785	NM_027504	ENSMUSG00000039410	Prdm16	5730557K01Rik|csp1|mel1	PR domain containing 16	protein-coding
mm_47187.1	chr5	120754059	120754152	-	1	NA	3' UTR (NM_145226, exon 16 of 16)	3' UTR (NM_145226, exon 16 of 16)	-4257	NM_001347448	246728	Mm.260926	NM_145227	ENSMUSG00000032690	Oas2	Oasl11	2'-5' oligoadenylate synthetase 2	protein-coding
mm_85873.1	chr9	110920835	110920844	-	1	NA	Intergenic	Intergenic	-3978	NM_001195437	235634	Mm.31788	NM_001195437	ENSMUSG00000096393	Gm590	-	predicted gene 590	protein-coding
mm_127915.1	chr15	9530135	9530185	-	1	NA	promoter-TSS (NM_008372)	promoter-TSS (NM_008372)	-284	NM_008372	16197	Mm.389	NM_008372	ENSMUSG00000003882	Il7r	CD127|IL-7Ralpha	interleukin 7 receptor	protein-coding
mm_124122.1	chr14	79642141	79642151	-	1	NA	intron (NM_001310655, intron 5 of 6)	intron (NM_001310655, intron 5 of 6)	20037	NM_001310655	16840	Mm.46561	NM_010701	ENSMUSG00000022025	Cnmd	Bricd3|ChM-I|Chmd|Lect1	chondromodulin	protein-coding
mm_145562.1	chr18	60812391	60812391	+	1	NA	TTS (NR_039567)	TTS (NR_039567)	315	NR_039567	100628611		NR_039567	ENSMUSG00000093327	Mir5107	mir-5107|mmu-mir-5107|mu-mir-5107	microRNA 5107	ncRNA
mm_27523.1	chr3	57301944	57301956	-	1	NA	promoter-TSS (NM_008536)	promoter-TSS (NM_008536)	-31	NM_008536	17112	Mm.856	NM_008536	ENSMUSG00000027800	Tm4sf1	L6|M3s1	transmembrane 4 superfamily member 1	protein-coding
mm_68765.1	chr7	121841079	121841081	-	1	NA	Intergenic	L1MB5|LINE|L1	-23958	NM_001272023	20277	Mm.7709	NM_011325	ENSMUSG00000030873	Scnn1b	-	sodium channel, nonvoltage-gated 1 beta	protein-coding
mm_42677.1	chr5	119681013	119681013	+	1	NA	exon (NM_011535, exon 7 of 8)	exon (NM_011535, exon 7 of 8)	9780	NM_011535	21386	Mm.219139	NM_011535	ENSMUSG00000018604	Tbx3	D5Ertd189e	T-box 3	protein-coding
mm_105614.1	chr11	106788061	106788063	-	1	NA	intron (NM_007840, intron 1 of 12)	CpG	432	NM_007840	13207	Mm.491096	NM_007840	ENSMUSG00000020719	Ddx5	2600009A06Rik|G17P1|HUMP68|Hlr1|p68	DEAD (Asp-Glu-Ala-Asp) box polypeptide 5	protein-coding
mm_147465.1	chr18	46673469	46673472	-	1	NA	Intergenic	RLTR24|LTR|ERV1	54872	NM_033037	12583	Mm.241056	NM_033037	ENSMUSG00000033022	Cdo1	1300002L19Rik|Cdo|D18Ucla3	cysteine dioxygenase 1, cytosolic	protein-coding
mm_11865.1	chr2	48949525	48949543	+	1	NA	promoter-TSS (NM_001177313)	promoter-TSS (NM_001177313)	26	NM_029924	109241	Mm.440436	NM_029924	ENSMUSG00000036792	Mbd5	9430004D19Rik|AA536666|AI426407|C030040A15Rik|Gm1630|OTTMUSG00000012483	methyl-CpG binding domain protein 5	protein-coding
mm_167918.1	chrX	100796582	100796620	+	1	NA	intron (NM_001177780, intron 1 of 11)	intron (NM_001177780, intron 1 of 11)	19330	NM_001177780	53310	Mm.4615	NM_016747	ENSMUSG00000000881	Dlg3	Dlgh3|SAP102|mKIAA1232	discs, large homolog 3 (Drosophila)	protein-coding
mm_130213.1	chr15	95654693	95654713	-	1	NA	promoter-TSS (NM_207533)	promoter-TSS (NM_207533)	68	NM_207533	223843	Mm.152937	NM_207533	ENSMUSG00000045608	Dbx2	9430056A22Rik|9630005K15|AI846217|Gm1229	developing brain homeobox 2	protein-coding
mm_117329.1	chr13	68582088	68582147	-	1	NA	promoter-TSS (NR_131892)	promoter-TSS (NR_131892)	-13	NM_001308475	210009	Mm.205514	NM_172480	ENSMUSG00000034617	Mtrr	4732420G08|MSR	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	protein-coding
mm_107406.1	chr12	33395051	33395090	+	1	NA	promoter-TSS (NR_131031)	promoter-TSS (NR_131031)	216	NM_029152	75040	Mm.156068	NM_029152	ENSMUSG00000020562	Efcab10	4930504H06Rik	EF-hand calcium binding domain 10	protein-coding
mm_85500.1	chr9	106159895	106159916	-	1	NA	Intergenic	CpG	-1767	NM_174846	235582	Mm.335420	NM_174846	ENSMUSG00000020258	Glyctk	6230410P16Rik|C430006L12	glycerate kinase	protein-coding
mm_7345.1	chr1	105990094	105990113	-	1	NA	promoter-TSS (NM_001122675)	promoter-TSS (NM_001122675)	-303	NM_001122676	227449	Mm.210188	NM_001122675	ENSMUSG00000038866	Zcchc2	9930114B20Rik|AW212015	zinc finger, CCHC domain containing 2	protein-coding
mm_96683.1	chr11	69580367	69580382	+	1	NA	promoter-TSS (NM_011640)	promoter-TSS (NM_011640)	15	NM_001127233	22059	Mm.222	NM_011640	ENSMUSG00000059552	Trp53	Tp53|bbl|bfy|bhy|p44|p53	transformation related protein 53	protein-coding
mm_86431.1	chr10	3863794	3863811	+	1	NA	intron (NM_001159942, intron 2 of 16)	intron (NM_001159942, intron 2 of 16)	-8865	NM_001033253	213783	Mm.150831	NM_001033253	ENSMUSG00000040624	Plekhg1	D10Ertd733e|Gm521|mKIAA1209	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	protein-coding
mm_138089.1	chr17	34031788	34031821	+	1	NA	promoter-TSS (NM_001205216)	promoter-TSS (NM_001205216)	-8	NM_011306	20182	Mm.1243	NM_011306	ENSMUSG00000039656	Rxrb	AL023085|H-2RIIBP|Nr2b2|RCoR-1|Rub	retinoid X receptor beta	protein-coding
mm_122525.1	chr14	47378737	47378758	-	1	NA	intron (NM_001145953, intron 1 of 5)	A-rich|Low_complexity|Low_complexity	4887	NM_001145953	16854	Mm.248615	NM_010705	ENSMUSG00000050335	Lgals3	GBP|L-34|Mac-2|gal3	lectin, galactose binding, soluble 3	protein-coding
mm_170540.1	chr19	39821729	39821731	+	1	NA	Intergenic	RLTR9D|LTR|ERVK	-8916	NM_010004	13099	Mm.353875	NM_010004	ENSMUSG00000025004	Cyp2c40	AI265721|AI662255	cytochrome P450, family 2, subfamily c, polypeptide 40	protein-coding
mm_32995.1	chr4	120450410	120450412	+	1	NA	intron (NM_001159630, intron 2 of 17)	intron (NM_001159630, intron 2 of 17)	45130	NM_013883	29871	Mm.427014	NM_013883	ENSMUSG00000000085	Scmh1	AI315320|AI851618|Scml1|Scml3	sex comb on midleg homolog 1	protein-coding
mm_84578.1	chr9	69349726	69349755	-	1	NA	intron (NR_136934, intron 2 of 2)	intron (NR_136934, intron 2 of 2)	14507	NR_136934	102642202	Mm.415363	NR_136934	ENSMUSG00000086648	Gm15511	OTTMUSG00000023029	predicted gene 15511	ncRNA
mm_6231.1	chr1	66937581	66937621	-	1	NA	intron (NM_021285, intron 1 of 6)	intron (NM_021285, intron 1 of 6)	-2235	NM_001113387	17901	Mm.1000	NM_021285	ENSMUSG00000061816	Myl1	AI325107|MLC1f|MLC3f|Mylf	myosin, light polypeptide 1	protein-coding
mm_38062.1	chr4	134018799	134018823	-	1	NA	promoter-TSS (NM_145833)	promoter-TSS (NM_145833)	5	NM_145833	83557	Mm.302567	NM_145833	ENSMUSG00000050966	Lin28a	AL024421|ENSMUSG00000070700|Gm10299|Lin-28|Lin28|Tex17|lin-28A	lin-28 homolog A (C. elegans)	protein-coding
mm_41938.1	chr5	105718659	105718697	+	1	NA	intron (NM_178701, intron 1 of 2)	intron (NM_178701, intron 1 of 2)	17868	NM_178701	231549	Mm.23837	NM_178701	ENSMUSG00000046079	Lrrc8d	2810473G09Rik|4930525N13Rik|A930019F03|Lrrc5	leucine rich repeat containing 8D	protein-coding
mm_171499.1	chr4	146224808	146224822	-	1	NA	Intergenic	Intergenic	-45570	NM_001083918	666532	Mm.392861	NM_001083918	ENSMUSG00000067916	Zfp991	Gm13139|OTTMUSG00000010657	zinc finger protein 991	protein-coding
mm_93998.1	chr10	127563877	127563883	-	1	NA	intron (NM_008512, intron 41 of 88)	intron (NM_008512, intron 41 of 88)	-29321	NM_183297	104080	Mm.437200	NM_183297	ENSMUSG00000040258	Nxph4	1110036M10Rik|AI851051	neurexophilin 4	protein-coding
mm_128653.1	chr15	59652832	59652842	-	1	NA	intron (NM_144549, intron 2 of 2)	intron (NM_144549, intron 2 of 2)	4183	NM_144549	211770	Mm.40298	NM_144549	ENSMUSG00000032501	Trib1	A530090O15Rik|TRB-1|Trb1	tribbles pseudokinase 1	protein-coding
mm_30608.1	chr4	6453496	6453509	+	1	NA	intron (NM_010945, intron 1 of 30)	intron (NM_010945, intron 1 of 30)	769	NM_010945	18201	Mm.3059	NM_010945	ENSMUSG00000028245	Nsmaf	AA959567|C630007J05|Fan	neutral sphingomyelinase (N-SMase) activation associated factor	protein-coding
mm_36085.1	chr4	58206687	58206697	-	1	NA	promoter-TSS (NM_022814)	promoter-TSS (NM_022814)	-96	NM_022814	64817	Mm.261024	NM_022814	ENSMUSG00000028369	Svep1	1110021D17Rik|4833413O10Rik|AA387071|D430029O09Rik|Polydom	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	protein-coding
mm_4874.1	chr1	187843309	187843321	+	1	NA	intron (NM_001243792, intron 2 of 7)	B4A|SINE|B4	-154512	NM_011935	26381	Mm.89989	NM_011935	ENSMUSG00000026610	Esrrg	ERR3|Errg|NR3B3|mKIAA0832	estrogen-related receptor gamma	protein-coding
mm_139864.1	chr17	70521760	70521768	+	1	NA	promoter-TSS (NM_001128180)	promoter-TSS (NM_001128180)	-130	NM_001347414	224997	Mm.311840	NM_027712	ENSMUSG00000003279	Dlgap1	4933422O14Rik|9630002F18|AI845682|AI848168|BB075781|D17Bwg0511e|GKAP/SAPAP|GKPA/SAPAP|Gkap|Sapap1|mKIAA4162	discs, large (Drosophila) homolog-associated protein 1	protein-coding
mm_156383.1	chrX	139672348	139672361	+	1	NA	3' UTR (NM_023270, exon 7 of 7)	3' UTR (NM_023270, exon 7 of 7)	-12642	NM_001081499	245638	Mm.275869	NM_001081499	ENSMUSG00000042473	Tbc1d8b	4921505D17Rik|9030605E16Rik	TBC1 domain family, member 8B	protein-coding
mm_82575.1	chr9	21131182	21131221	-	1	NA	promoter-TSS (NM_018793)	promoter-TSS (NM_018793)	74	NM_018793	54721	Mm.20249	NM_018793	ENSMUSG00000032175	Tyk2	JTK1	tyrosine kinase 2	protein-coding
mm_139523.1	chr17	56628119	56628148	+	1	NA	promoter-TSS (NM_175350)	promoter-TSS (NM_175350)	-10	NM_175350	106757	Mm.23401	NM_175350	ENSMUSG00000040828	Catsperd	4921529N20Rik|4933402B14Rik|619718|AW045609|Gm6095|Tmem146	catsper channel auxiliary subunit delta	protein-coding
mm_37263.1	chr4	118457468	118457507	-	1	NA	promoter-TSS (NM_001122949)	promoter-TSS (NM_001122949)	26	NM_001285496	17480	Mm.4864	NM_010823	ENSMUSG00000006389	Mpl	CD110|TPO-R|c-mpl|hlb219	myeloproliferative leukemia virus oncogene	protein-coding
mm_149776.1	chr19	23096861	23096883	+	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	-44354	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_81147.1	chr9	106886422	106886437	+	1	NA	TTS (NM_029103)	TTS (NM_029103)	571	NM_175402	109095	Mm.431589	NM_175402	ENSMUSG00000074102	Rbm15b	1810017N16Rik	RNA binding motif protein 15B	protein-coding
mm_24625.1	chr3	93555112	93555122	+	1	NA	promoter-TSS (NM_009112)	promoter-TSS (NM_009112)	0	NM_009112	20194	Mm.1	NM_009112	ENSMUSG00000041959	S100a10	42C|AA409961|AL024248|CAL12|CLP11|Cal1l|p10|p11	S100 calcium binding protein A10 (calpactin)	protein-coding
mm_121711.1	chr14	16172467	16172488	-	1	NA	Intergenic	Intergenic	-76837	NM_021504	59007	Mm.258381	NM_021504	ENSMUSG00000021785	Ngly1	1110002C09Rik|PNGase|Png1	N-glycanase 1	protein-coding
mm_35662.1	chr4	43562188	43562199	-	1	NA	promoter-TSS (NM_013497)	promoter-TSS (NM_013497)	390	NM_011602	21894	Mm.208601	NM_011602	ENSMUSG00000028465	Tln1	Tln	talin 1	protein-coding
mm_43309.1	chr5	134755460	134755462	+	1	NA	Intergenic	PB1D10|SINE|Alu	-8138	NM_007925	13717	Mm.275320	NM_007925	ENSMUSG00000029675	Eln	AI385707|AI480567|E030024M20Rik	elastin	protein-coding
mm_52945.1	chr6	122952685	122952697	+	1	NA	promoter-TSS (NM_153197)	promoter-TSS (NM_153197)	47	NM_153197	73149	Mm.25684	NM_153197	ENSMUSG00000043832	Clec4a3	3110037K17Rik|Dcir3	C-type lectin domain family 4, member a3	protein-coding
mm_148066.1	chr18	72327780	72327817	-	1	NA	intron (NM_007831, intron 1 of 28)	intron (NM_007831, intron 1 of 28)	23271	NM_007831	13176	Mm.167882	NM_007831	ENSMUSG00000060534	Dcc	C030036D22Rik|Igdcc1	deleted in colorectal carcinoma	protein-coding
mm_39028.1	chr4	152138775	152138803	-	1	NA	exon (NM_207687, exon 4 of 16)	exon (NM_207687, exon 4 of 16)	-2464	NM_207690	56226	Mm.264215	NM_019585	ENSMUSG00000028943	Espn	je	espin	protein-coding
mm_73648.1	chr8	110919917	110919994	+	1	NA	promoter-TSS (NM_009179)	promoter-TSS (NM_009179)	90	NM_009179	20444	Mm.200388	NM_009179	ENSMUSG00000031749	St3gal2	AI429591|AW822065|ST3GalII|Siat5	ST3 beta-galactoside alpha-2,3-sialyltransferase 2	protein-coding
mm_168071.1	chr10	105881003	105881017	+	1	NA	Intergenic	IAP1-MM_LTR|LTR|ERVK	39531	NM_025602	52713	Mm.339224	NM_025602	ENSMUSG00000019897	Ccdc59	2300004H16Rik|D10Ertd718e	coiled-coil domain containing 59	protein-coding
mm_158861.1	chrY	1010588	1010613	+	1	NA	promoter-TSS (NM_012011)	promoter-TSS (NM_012011)	-12	NM_012011	26908	Mm.250909	NM_012011	ENSMUSG00000069049	Eif2s3y	Eif-2gy|Spy|Tfy	eukaryotic translation initiation factor 2, subunit 3, structural gene Y-linked	protein-coding
mm_101170.1	chr11	16981849	16981933	-	1	NA	exon (NM_019549, exon 9 of 10)	exon (NM_019549, exon 9 of 10)	26827	NM_019549	56193	Mm.98232	NM_019549	ENSMUSG00000020120	Plek	2010300B13Rik	pleckstrin	protein-coding
mm_106716.1	chr12	3834851	3834864	+	1	NA	intron (NM_001271753, intron 1 of 22)	intron (NM_001271753, intron 1 of 22)	27387	NR_045884	100038522	Mm.417270	NR_045884	ENSMUSG00000073242	Dnmt3aos	ENSMUSG00000073242|Gm10485	DNA methyltransferase 3A, opposite strand	ncRNA
mm_50441.1	chr6	48872872	48872885	+	1	NA	Intergenic	Intergenic	-22377	NM_029638	76507	Mm.213898	NM_029638	ENSMUSG00000029811	Aoc1	1600012D06Rik|Abp1|DAO	amine oxidase, copper-containing 1	protein-coding
mm_157748.1	chrX	73458946	73458980	-	1	NA	promoter-TSS (NM_028633)	promoter-TSS (NM_028633)	66	NM_028633	73738	Mm.264899	NM_028633	ENSMUSG00000031371	Haus7	1110020L19Rik|Uchl5ip|Uip1	HAUS augmin-like complex, subunit 7	protein-coding
mm_104711.1	chr11	98043592	98043616	-	1	NA	exon (NM_146028, exon 2 of 11)	exon (NM_146028, exon 2 of 11)	9858	NM_146028	217154	Mm.181008	NM_146028	ENSMUSG00000017400	Stac2	24b2|24b2/STAC2|AW240854	SH3 and cysteine rich domain 2	protein-coding
mm_13897.1	chr2	120450889	120450917	+	1	NA	intron (NM_172672, intron 19 of 23)	intron (NM_172672, intron 19 of 23)	-12690	NM_001177799	12335	Mm.458021	NM_007601	ENSMUSG00000079110	Capn3	AI323605|Capa-3|Capa3|Lp82|p94	calpain 3	protein-coding
mm_17859.1	chr2	34799833	34799884	-	1	NA	promoter-TSS (NM_145522)	promoter-TSS (NM_145522)	54	NM_145522	227746	Mm.158705	NM_145522	ENSMUSG00000070953	Rabepk	8430412M01Rik|9530020D24Rik|AV073337|C87311|Rab9p40	Rab9 effector protein with kelch motifs	protein-coding
mm_159481.1	chr4	35845201	35845201	-	1	NA	promoter-TSS (NM_175516)	promoter-TSS (NM_175516)	3	NM_001166001	242384	Mm.132507	NM_175516	ENSMUSG00000045083	Lingo2	B230217C06Rik|Lern3|Lrrn6c	leucine rich repeat and Ig domain containing 2	protein-coding
mm_112059.1	chr12	111909131	111909137	-	1	NA	Intergenic	Intergenic	-1079	NM_011625	21981	Mm.313076	NM_011625	ENSMUSG00000021285	Ppp1r13b	AI449786|ASPP1|AW545810|Tp53bp2|Trp53bp2|p85	protein phosphatase 1, regulatory (inhibitor) subunit 13B	protein-coding
mm_61043.1	chr7	49759580	49759590	+	1	NA	promoter-TSS (NM_001146052)	promoter-TSS (NM_001146052)	73	NM_001146052	53415	Mm.20801	NM_016865	ENSMUSG00000039745	Htatip2	AW111545|Cc3|Tip30	HIV-1 Tat interactive protein 2	protein-coding
mm_34483.1	chr4	148496491	148496494	+	1	NA	intron (NM_001039554, intron 4 of 4)	intron (NM_001039554, intron 4 of 4)	3970	NM_001039554	654812	Mm.388929	NM_001039554	ENSMUSG00000028989	Angptl7	-	angiopoietin-like 7	protein-coding
mm_87697.1	chr10	59702630	59702643	+	1	NA	promoter-TSS (NM_001291442)	promoter-TSS (NM_001291442)	73	NM_001291443	216001	Mm.27199	NM_144822	ENSMUSG00000020111	Micu1	C730016L05Rik|Calc|Cbara1	mitochondrial calcium uptake 1	protein-coding
mm_43872.1	chr5	143622441	143622459	+	1	NA	promoter-TSS (NM_011182)	promoter-TSS (NM_011182)	3	NM_011182	19159	Mm.281003	NM_011182	ENSMUSG00000018001	Cyth3	AI648983|ARNO3|CLM3|Grp1|Pscd3	cytohesin 3	protein-coding
mm_74901.1	chr8	25201537	25201603	-	1	NA	promoter-TSS (NM_177089)	promoter-TSS (NM_177089)	-28	NM_177089	320165	Mm.308452	NM_177089	ENSMUSG00000065954	Tacc1	4833447E04Rik|AA960202|B230378H13Rik	transforming, acidic coiled-coil containing protein 1	protein-coding
mm_157972.1	chrX	93831894	93831904	-	1	NA	exon (NM_145630, exon 1 of 12)	exon (NM_145630, exon 1 of 12)	196	NM_145630	236900	Mm.12775	NM_145630	ENSMUSG00000035232	Pdk3	2610001M10Rik|AI035637	pyruvate dehydrogenase kinase, isoenzyme 3	protein-coding
mm_125114.1	chr15	28203727	28203742	+	1	NA	promoter-TSS (NM_133365)	promoter-TSS (NM_133365)	-32	NM_133365	110082	Mm.248464	NM_133365	ENSMUSG00000022262	Dnah5	AU022615|Dnahc5|Mdnah5|b2b1134Clo|b2b1154Clo|b2b1537Clo|b2b1565Clo|b2b601Clo|mKIAA1603	dynein, axonemal, heavy chain 5	protein-coding
mm_47735.1	chr5	130172597	130172606	-	1	NA	intron (NM_001199059, intron 1 of 8)	intron (NM_001199059, intron 1 of 8)	782	NM_001199059	56715	Mm.288639	NM_019983	ENSMUSG00000025340	Rabgef1	Rab5ef|Rabex5|Rin2	RAB guanine nucleotide exchange factor (GEF) 1	protein-coding
mm_136362.1	chr16	92789348	92789352	-	1	NA	intron (NM_001111022, intron 2 of 6)	intron (NM_001111022, intron 2 of 6)	36724	NM_001111021	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_58774.1	chr7	16046603	16046617	+	1	NA	Intergenic	Intergenic	-25235	NM_001347559	666528	Mm.290718	NM_001099277	ENSMUSG00000078796	Zfp541	EG666528|Znf541	zinc finger protein 541	protein-coding
mm_115684.1	chr13	13537660	13537666	-	1	NA	Intergenic	Intergenic	-52746	NM_010748	17101	Mm.342337	NM_010748	ENSMUSG00000019726	Lyst	D13Sfk13|beige|bg	lysosomal trafficking regulator	protein-coding
mm_140424.1	chr17	87984529	87984535	+	1	NA	exon (NM_010830, exon 4 of 10)	exon (NM_010830, exon 4 of 10)	9482	NM_010830	17688	Mm.18210	NM_010830	ENSMUSG00000005370	Msh6	AU044881|AW550279|GTBP|Gtmbp	mutS homolog 6	protein-coding
mm_163319.1	chr12	7977690	7977703	+	1	NA	promoter-TSS (NM_009693)	promoter-TSS (NM_009693)	19	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_89077.1	chr10	83338686	83338690	+	1	NA	promoter-TSS (NM_177388)	promoter-TSS (NM_177388)	-871	NM_177388	338365	Mm.67073	NM_177388	ENSMUSG00000034591	Slc41a2	A230035L05Rik|SLC41A1-L1	solute carrier family 41, member 2	protein-coding
mm_101532.1	chr11	33203564	33203583	-	1	NA	promoter-TSS (NM_019916)	promoter-TSS (NM_019916)	15	NM_019916	27140	Mm.25362	NM_019916	ENSMUSG00000040610	Tlx3	Hox11l2|Rnx|Tlx1l2	T cell leukemia, homeobox 3	protein-coding
mm_10792.1	chr2	24349458	24349466	+	1	NA	exon (NM_031167, exon 5 of 5)	exon (NM_031167, exon 5 of 5)	4091	NM_001039701	16181	Mm.882	NM_031167	ENSMUSG00000026981	Il1rn	F630041P17Rik|IL-1ra	interleukin 1 receptor antagonist	protein-coding
mm_38131.1	chr4	134703327	134703411	-	1	NA	exon (NM_207237, exon 1 of 12)	exon (NM_207237, exon 1 of 12)	921	NM_207237	230815	Mm.18905	NM_207237	ENSMUSG00000037306	Man1c1	AI593348	mannosidase, alpha, class 1C, member 1	protein-coding
mm_78941.1	chr9	45138315	45138321	+	1	NA	promoter-TSS (NM_001013390)	promoter-TSS (NM_001013390)	-724	NM_001013390	399548	Mm.335112	NM_001013390	ENSMUSG00000046480	Scn4b	Gm1471	sodium channel, type IV, beta	protein-coding
mm_135340.1	chr16	42340596	42340630	-	1	NA	promoter-TSS (NM_008083)	promoter-TSS (NM_008083)	38	NM_008083	14432	Mm.1222	NM_008083	ENSMUSG00000047261	Gap43	B-50|Basp2|GAP-43	growth associated protein 43	protein-coding
mm_171816.1	chr5	138161071	138161071	+	1	NA	promoter-TSS (NM_012002)	promoter-TSS (NM_012002)	-31	NM_012002	26893	Mm.3981	NM_012002	ENSMUSG00000019494	Cops6	Sgn3|VIP/MOV34	COP9 signalosome subunit 6	protein-coding
mm_85054.1	chr9	90114789	90114797	-	1	NA	promoter-TSS (NM_024431)	promoter-TSS (NM_024431)	27	NM_001039147	21761	Mm.426209	NM_024431	ENSMUSG00000062270	Morf4l1	MORFRG15|MRG15|TEG-189|Tex189|mKIAA4002	mortality factor 4 like 1	protein-coding
mm_83194.1	chr9	41014330	41014371	-	1	NA	3' UTR (NM_176860, exon 14 of 14)	3' UTR (NM_176860, exon 14 of 14)	-9722	NM_019465	54698	Mm.42791	NM_019465	ENSMUSG00000032021	Crtam	-	cytotoxic and regulatory T cell molecule	protein-coding
mm_73204.1	chr8	95678265	95678288	+	1	NA	Intergenic	CpG	-24761	NM_001195006	234593	Mm.29846	NM_145602	ENSMUSG00000036564	Ndrg4	D8Bwg1337e|Ndr1-rs|Ndr4|R74996|SMAP-8	N-myc downstream regulated gene 4	protein-coding
mm_107973.1	chr12	72939730	72939758	+	1	NA	promoter-TSS (NM_011384)	promoter-TSS (NM_011384)	-138	NM_011384	20476	Mm.57138	NM_011384	ENSMUSG00000021099	Six6	Optx2|Six9	sine oculis-related homeobox 6	protein-coding
mm_168085.1	chr10	12445280	12445280	+	1	NA	intron (NM_011682, intron 61 of 73)	intron (NM_011682, intron 61 of 73)	416455	NM_011682	22288	Mm.331784	NM_011682	ENSMUSG00000019820	Utrn	AA589569|DRP|Dmdl	utrophin	protein-coding
mm_114504.1	chr13	70574505	70574515	+	1	NA	intron (NR_045934, intron 1 of 2)	intron (NR_045934, intron 1 of 2)	1269	NR_045934	73584	Mm.442491	NR_045934	ENSMUSG00000101051	1700100L14Rik	-	RIKEN cDNA 1700100L14 gene	ncRNA
mm_127944.1	chr15	10714613	10714637	-	1	NA	promoter-TSS (NM_001166408)	promoter-TSS (NM_001166408)	6	NM_001166408	75646	Mm.212395	NM_030690	ENSMUSG00000022246	Rai14	1700008J19Rik|1700020L11Rik|Ankycorbin|Norpeg|mKIAA1334	retinoic acid induced 14	protein-coding
mm_87517.1	chr10	52690596	52690602	+	1	NA	promoter-TSS (NM_178675)	promoter-TSS (NM_178675)	98	NM_178675	215085	Mm.338690	NM_178675	ENSMUSG00000038602	Slc35f1	Duf6|E130016L02	solute carrier family 35, member F1	protein-coding
mm_89827.1	chr10	105841455	105841512	+	1	NA	promoter-TSS (NM_207522)	promoter-TSS (NM_207522)	4	NM_025602	52713	Mm.339224	NM_025602	ENSMUSG00000019897	Ccdc59	2300004H16Rik|D10Ertd718e	coiled-coil domain containing 59	protein-coding
mm_88227.1	chr10	70440845	70440937	+	1	NA	promoter-TSS (NM_001143776)	promoter-TSS (NM_001143776)	-19	NM_024244	71721	Mm.477813	NM_024244	ENSMUSG00000043259	Fam13c	1200015N20Rik|C030038O19Rik|mKIAA1796	family with sequence similarity 13, member C	protein-coding
mm_123668.1	chr14	69247475	69247486	-	1	NA	intron (NM_026331, intron 3 of 3)	intron (NM_026331, intron 3 of 3)	37623	NM_026331	67712	Mm.293635	NM_026331	ENSMUSG00000034248	Slc25a37	1700020E22Rik|4930513O14Rik|4930526G11Rik|AI848481|C330015G08Rik|Mfrn|Mfrn1|Mscp|frascati|mitoferrin	solute carrier family 25, member 37	protein-coding
mm_169917.1	chr16	57391174	57391187	-	1	NA	intron (NM_001040397, intron 1 of 4)	LSU-rRNA_Hsa|rRNA|rRNA	37903	NM_001040397	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding
mm_16555.1	chr2	181837921	181837934	+	1	NA	promoter-TSS (NM_153594)	promoter-TSS (NM_153594)	73	NM_001291211	245867	Mm.491085	NM_153594	ENSMUSG00000027589	Pcmtd2	5330414D10Rik|AI314201	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 2	protein-coding
mm_40555.1	chr5	58828022	58828036	+	1	NA	Intergenic	RLTR12E|LTR|ERVK	-375031	NR_046190	78163	Mm.243828	NR_046190	ENSMUSG00000105234	4930459L07Rik	-	RIKEN cDNA 4930459L07 gene	ncRNA
mm_129963.1	chr15	85578137	85578154	-	1	NA	promoter-TSS (NM_001163634)	promoter-TSS (NM_001163634)	-75	NM_001163634	22422	Mm.306946	NM_009528	ENSMUSG00000022382	Wnt7b	Wnt-7b	wingless-type MMTV integration site family, member 7B	protein-coding
mm_38944.1	chr4	150201126	150201141	-	1	NA	promoter-TSS (NM_009802)	promoter-TSS (NM_009802)	2	NM_009802	12353	Mm.232523	NM_009802	ENSMUSG00000028972	Car6	Ca6|DOC1	carbonic anhydrase 6	protein-coding
mm_78058.1	chr9	14902673	14902692	+	1	NA	intron (NM_022888, intron 1 of 4)	intron (NM_022888, intron 1 of 4)	1269	NM_176807	64931	Mm.86738	NM_022888	ENSMUSG00000031933	Izumo1r	0910001L11Rik|C86255|Folbp3|Folr4|Juno	IZUMO1 receptor, JUNO	protein-coding
mm_87586.1	chr10	56795681	56795690	+	1	NA	Intergenic	Intergenic	418385	NM_010288	14609	Mm.378921	NM_010288	ENSMUSG00000050953	Gja1	AU042049|AW546267|Cnx43|Cx43|Cx43alpha1|Gja-1|Npm1|connexin43	gap junction protein, alpha 1	protein-coding
mm_126108.1	chr15	78250616	78250629	+	1	NA	intron (NM_008677, intron 2 of 9)	intron (NM_008677, intron 2 of 9)	5811	NM_008677	17972	Mm.2068	NM_008677	ENSMUSG00000071715	Ncf4	AI451400|p40phox	neutrophil cytosolic factor 4	protein-coding
mm_159913.1	chr6	48448357	48448357	+	1	NA	intron (NM_173428, intron 1 of 102)	intron (NM_173428, intron 1 of 102)	128	NM_173428	243369	Mm.25039	NM_173428	ENSMUSG00000029797	Sspo	C79529|Scospondin	SCO-spondin	protein-coding
mm_7968.1	chr1	134040390	134040398	-	1	NA	exon (NM_021355, exon 2 of 3)	exon (NM_021355, exon 2 of 3)	2879	NM_021355	14264	Mm.287146	NM_021355	ENSMUSG00000041559	Fmod	AI131919|AU041740|SLRR2E	fibromodulin	protein-coding
mm_129096.1	chr15	75929782	75929792	-	1	NA	promoter-TSS (NM_031201)	promoter-TSS (NM_031201)	-57	NM_031201	22122	Mm.22596	NM_031201	ENSMUSG00000022570	Tsta3	AI256181|FX|Tstap35b	tissue specific transplantation antigen P35B	protein-coding
mm_102599.1	chr11	62344847	62344887	-	1	NA	exon (NM_001252313, exon 29 of 45)	exon (NM_001252313, exon 29 of 45)	63394	NM_029704	72795	Mm.489722	NM_028360	ENSMUSG00000042298	Ttc19	2010204O13Rik|2810460C24Rik|AI505442	tetratricopeptide repeat domain 19	protein-coding
mm_93583.1	chr10	116931852	116931867	-	1	NA	intron (NM_001003950, intron 3 of 9)	intron (NM_001003950, intron 3 of 9)	18521	NM_001003950	216363	Mm.336394	NM_001003950	ENSMUSG00000064181	Rab3ip	B230311A06|Gtpat12|Rabin3	RAB3A interacting protein	protein-coding
mm_108501.1	chr12	83950020	83950032	+	1	NA	promoter-TSS (NM_023633)	promoter-TSS (NM_023633)	-582	NM_023633	71952	Mm.251483	NM_023633	ENSMUSG00000046791	2410016O06Rik	MAPJD|NO66	RIKEN cDNA 2410016O06 gene	protein-coding
mm_170794.1	chr2	175338230	175338249	-	1	NA	promoter-TSS (NM_001177543)	promoter-TSS (NM_001177543)	-27	NM_001099349	100043381		NM_001099349	ENSMUSG00000078880	Gm14308	OTTMUSG00000016254	predicted gene 14308	protein-coding
mm_168225.1	chr10	79497233	79497242	+	1	NA	Intergenic	MMERVK9C_I-int|LTR|ERVK	28279	NM_001104537	625029	Mm.469865	NM_001104537	ENSMUSG00000091381	Vmn2r83	EG625029	vomeronasal 2, receptor 83	protein-coding
mm_1756.1	chr1	75521522	75521602	+	1	NA	promoter-TSS (NM_027886)	promoter-TSS (NM_027886)	33	NM_027886	71728	Mm.312650	NM_027886	ENSMUSG00000026213	Stk11ip	1200014D22Rik|BB131189|LIP1|LKB1IP	serine/threonine kinase 11 interacting protein	protein-coding
mm_102312.1	chr11	55659131	55659133	-	1	NA	Intergenic	Intergenic	-50934	NM_020492	14654	Mm.89320	NM_020492	ENSMUSG00000000263	Glra1	nmf11|oscillator|ot|spasmodic|spd	glycine receptor, alpha 1 subunit	protein-coding
mm_124580.1	chr14	124663647	124663661	-	1	NA	intron (NM_207667, intron 1 of 4)	intron (NM_207667, intron 1 of 4)	13473	NM_207667	14169	Mm.206362	NM_010201	ENSMUSG00000025551	Fgf14	FHF-4|Fhf4|mFHF-4(1B)	fibroblast growth factor 14	protein-coding
mm_32125.1	chr4	99037381	99037394	+	1	NA	exon (NM_013913, exon 6 of 7)	exon (NM_013913, exon 6 of 7)	6433	NM_013913	30924	Mm.28341	NM_013913	ENSMUSG00000028553	Angptl3	hypl	angiopoietin-like 3	protein-coding
mm_107468.1	chr12	37242031	37242039	+	1	NA	5' UTR (NM_178767, exon 1 of 13)	5' UTR (NM_178767, exon 1 of 13)	396	NM_178767	319660	Mm.485540	NM_178767	ENSMUSG00000050103	Agmo	A530016O06Rik|AI790538|Tmem195	alkylglycerol monooxygenase	protein-coding
mm_13829.1	chr2	119288774	119288796	+	1	NA	promoter-TSS (NM_172269)	promoter-TSS (NM_172269)	43	NM_172269	228545	Mm.294761	NM_172269	ENSMUSG00000034216	Vps18	9930024E13Rik	VPS18 CORVET/HOPS core subunit	protein-coding
mm_162300.1	chr1	34485313	34485329	+	1	NA	Intergenic	Intergenic	-13109	NM_009355	21755	Mm.10725	NM_009355	ENSMUSG00000026125	Prss39	Tesp1	protease, serine 39	protein-coding
mm_69831.1	chr7	141271811	141271821	-	1	NA	exon (NM_001114322, exon 13 of 15)	exon (NM_001114322, exon 13 of 15)	4970	NM_028069	72040	Mm.29080	NM_028069	ENSMUSG00000025497	Cdhr5	1810074H01Rik|AI481143|Mucdhl|Mupcdh	cadherin-related family member 5	protein-coding
mm_158376.1	chrX	135210673	135210700	-	1	NA	promoter-TSS (NM_025355)	promoter-TSS (NM_025355)	1	NM_025355	66104	Mm.336239	NM_025355	ENSMUSG00000031409	Tceal6	1500026B10Rik	transcription elongation factor A (SII)-like 6	protein-coding
mm_107666.1	chr12	53149212	53149213	+	1	NA	3' UTR (NM_198111, exon 14 of 14)	3' UTR (NM_198111, exon 14 of 14)	-99465	NM_013780	27386	Mm.247044	NM_013780	ENSMUSG00000021010	Npas3	4930423H22Rik|bHLHe12	neuronal PAS domain protein 3	protein-coding
mm_117203.1	chr13	64066179	64066201	-	1	NA	intron (NM_008291, intron 6 of 10)	B4A|SINE|B4	23011	NM_008291	15487	Mm.5109	NM_008291	ENSMUSG00000033122	Hsd17b3	-	hydroxysteroid (17-beta) dehydrogenase 3	protein-coding
mm_44162.1	chr5	150673847	150673877	+	1	NA	promoter-TSS (NM_175310)	promoter-TSS (NM_175310)	35	NM_001346503	100710	Mm.32959	NM_175310	ENSMUSG00000034021	Pds5b	AI646570|AS3|AW212954|Aprin|Tg(Wap-ERBB2)229Wzw|WAP-Her-2|mKIAA0979	PDS5 cohesin associated factor B	protein-coding
mm_171585.1	chr4	147639223	147639239	-	1	NA	intron (NM_145078, intron 2 of 4)	intron (NM_145078, intron 2 of 4)	3277	NM_145078	112422	Mm.327194	NM_145078	ENSMUSG00000066000	Zfp979	2610305D13Rik|Ssm1b	zinc finger protein 979	protein-coding
mm_45915.1	chr5	89438443	89438455	-	1	NA	intron (NM_008096, intron 7 of 12)	intron (NM_008096, intron 7 of 12)	19449	NM_008096	14473	Mm.196595	NM_008096	ENSMUSG00000035540	Gc	DBP|VDB	group specific component	protein-coding
mm_14150.1	chr2	126553581	126553598	+	1	NA	exon (NM_011978, exon 1 of 10)	exon (NM_011978, exon 1 of 10)	565	NM_011978	26458	Mm.290044	NM_011978	ENSMUSG00000027359	Slc27a2	ACSVL1|FATP2|VLCS|Vlac|Vlacs	solute carrier family 27 (fatty acid transporter), member 2	protein-coding
mm_59403.1	chr7	26816316	26816337	+	1	NA	intron (NM_013809, intron 5 of 8)	intron (NM_013809, intron 5 of 8)	7399	NM_013809	13108	Mm.102312	NM_013809	ENSMUSG00000049685	Cyp2g1	-	cytochrome P450, family 2, subfamily g, polypeptide 1	protein-coding
mm_15026.1	chr2	152687138	152687158	+	1	NA	promoter-TSS (NM_025543)	promoter-TSS (NM_025543)	0	NM_025543	66405	Mm.440291	NM_025543	ENSMUSG00000042814	Mcts2	2400002F11Rik|MCT-2	malignant T cell amplified sequence 2	protein-coding
mm_13107.1	chr2	91526771	91526828	+	1	NA	Intergenic	CpG	-19523	NM_001165989	75786	Mm.168478	NM_029437	ENSMUSG00000040549	Ckap5	3110043H24Rik|4930432B04Rik|D730027C18Rik|T25636|mKIAA0097	cytoskeleton associated protein 5	protein-coding
mm_120214.1	chr14	62555739	62555812	+	1	NA	promoter-TSS (NM_001243857)	promoter-TSS (NM_001243857)	38	NM_001243857	629059	Mm.291864	NM_001243857	ENSMUSG00000035184	Fam124a	EG629059	family with sequence similarity 124, member A	protein-coding
mm_94971.1	chr11	30954451	30954480	+	1	NA	promoter-TSS (NM_023906)	promoter-TSS (NM_023906)	67	NM_023906	65257	Mm.440539	NM_023906	ENSMUSG00000020305	Asb3	2400011J03Rik|Asb-3	ankyrin repeat and SOCS box-containing 3	protein-coding
mm_91331.1	chr10	25297056	25297101	-	1	NA	intron (NM_018747, intron 1 of 7)	CpG	2085	NM_018747	432442	Mm.485937	NM_018747	ENSMUSG00000039166	Akap7	6430401D08|AI662165|AKAP15|Akap18|BB170514	A kinase (PRKA) anchor protein 7	protein-coding
mm_97508.1	chr11	78499044	78499065	+	1	NA	promoter-TSS (NM_011707)	promoter-TSS (NM_011707)	-66	NM_011707	22370	Mm.3667	NM_011707	ENSMUSG00000017344	Vtn	AI256434|Vn	vitronectin	protein-coding
mm_168000.1	chrX	170022299	170022315	+	1	NA	Intergenic	Intergenic	-43390	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_85412.1	chr9	103426439	103426451	-	1	NA	intron (NM_001002896, intron 6 of 6)	ID_B1|SINE|B4	2867	NR_040466	100529079	Mm.437003	NR_040466	ENSMUSG00000086236	5830418P13Rik	-	RIKEN cDNA 5830418P13 gene	ncRNA
mm_4244.1	chr1	171389182	171389197	+	1	NA	TTS (NM_027893)	TTS (NM_027893)	229	NM_001005508	226652	Mm.251048	NM_001005508	ENSMUSG00000048865	Arhgap30	6030405P05Rik|Gm102|mFLJ00267	Rho GTPase activating protein 30	protein-coding
mm_166227.1	chr5	65860748	65860759	+	1	NA	Intergenic	Intergenic	-2816	NM_001081105	74734	Mm.20323	NM_001081105	ENSMUSG00000029204	Rhoh	5830400A04Rik|AU019774|Arhh	ras homolog family member H	protein-coding
mm_86560.1	chr10	11281305	11281357	+	1	NA	promoter-TSS (NM_027968)	promoter-TSS (NM_027968)	1	NM_027968	71865	Mm.276229	NM_027968	ENSMUSG00000047648	Fbxo30	1700026A16Rik|MUSA1	F-box protein 30	protein-coding
mm_85471.1	chr9	105764713	105764740	-	1	NA	intron (NM_001102607, intron 10 of 36)	intron (NM_001102607, intron 10 of 36)	44922	NM_172927	245026	Mm.482507	NM_172927	ENSMUSG00000043719	Col6a6	E330019B14|E330026B02Rik	collagen, type VI, alpha 6	protein-coding
mm_119866.1	chr14	54549551	54549598	+	1	NA	intron (NM_145462, intron 4 of 9)	PB1|SINE|Alu	4787	NM_145462	219072	Mm.202152	NM_145462	ENSMUSG00000022177	Haus4	9430093H08Rik|AU016300|D14Ertd500e	HAUS augmin-like complex, subunit 4	protein-coding
mm_37917.1	chr4	132785252	132785291	-	1	NA	exon (NM_001033308, exon 4 of 6)	exon (NM_001033308, exon 4 of 6)	11093	NM_001033308	230787	Mm.290912	NM_001033308	ENSMUSG00000037731	Themis2	ICB-1	thymocyte selection associated family member 2	protein-coding
mm_167354.1	chr8	83918904	83918912	+	1	NA	exon (NM_181039, exon 3 of 23)	exon (NM_181039, exon 3 of 23)	18810	NM_181039	330814	Mm.260733	NM_181039	ENSMUSG00000013033	Adgrl1	2900070I05Rik|AI182398|CLIBA|Lec2|Lphn1|mKIAA0821	adhesion G protein-coupled receptor L1	protein-coding
mm_152825.1	chr19	23136548	23136592	-	1	NA	Intergenic	Intergenic	-4656	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_161034.1	chr12	17266545	17266545	+	1	NA	promoter-TSS (NM_027959)	promoter-TSS (NM_027959)	-50	NM_027959	71853	Mm.222825	NM_027959	ENSMUSG00000020571	Pdia6	1700015E05Rik|AL023058|C77895|CaBP5|P5|Txndc7	protein disulfide isomerase associated 6	protein-coding
mm_74662.1	chr8	13584016	13584016	-	1	NA	intron (NM_009025, intron 14 of 23)	(TCTCTG)n|Simple_repeat|Simple_repeat	-21555	NM_001080781	66501	Mm.46136	NM_025601	ENSMUSG00000031452	1700029H14Rik	-	RIKEN cDNA 1700029H14 gene	protein-coding
mm_148000.1	chr18	67718676	67718713	-	1	NA	intron (NM_008977, intron 1 of 9)	intron (NM_008977, intron 1 of 9)	5927	NM_001127177	19255	Mm.260433	NM_008977	ENSMUSG00000024539	Ptpn2	AI325124|Ptpt|TC-PTP	protein tyrosine phosphatase, non-receptor type 2	protein-coding
mm_9728.1	chr1	180195982	180196005	-	1	NA	promoter-TSS (NM_023341)	promoter-TSS (NM_023341)	27	NM_023341	67426	Mm.38330	NM_023341	ENSMUSG00000026489	Coq8a	4632432J16Rik|AI462003|Adck3|Cabc1|mKIAA0451	coenzyme Q8A	protein-coding
mm_170963.1	chr2	58108043	58108056	+	1	NA	Intergenic	Intergenic	52073	NM_139200	227929	Mm.273905	NM_139200	ENSMUSG00000026832	Cytip	A130053M09Rik|AI462064|C80816|Cbp|Cybr|Pscdbp	cytohesin 1 interacting protein	protein-coding
mm_125547.1	chr15	58449662	58449673	+	1	NA	intron (NM_145959, intron 20 of 23)	intron (NM_145959, intron 20 of 23)	34199	NM_145959	210998	Mm.3224	NM_145959	ENSMUSG00000037119	Fam91a1	AV220772|BC033609|D15Ertd621e|SKIN|mKIAA0493	family with sequence similarity 91, member A1	protein-coding
mm_53889.1	chr6	3376991	3377002	-	1	NA	exon (NM_010156, exon 2 of 2)	exon (NM_010156, exon 2 of 2)	22575	NM_010156	209086	Mm.196013	NM_010156	ENSMUSG00000047735	Samd9l	AA175286|ESTM25|mKIAA2005	sterile alpha motif domain containing 9-like	protein-coding
mm_83345.1	chr9	44305596	44305688	-	1	NA	promoter-TSS (NM_172162)	promoter-TSS (NM_172162)	29	NM_172162	102423	Mm.24570	NM_172162	ENSMUSG00000032119	Hinfp	AA589481|HiNF-P|Mizf	histone H4 transcription factor	protein-coding
mm_25025.1	chr3	98127010	98127031	+	1	NA	intron (NM_010928, intron 22 of 33)	intron (NM_010928, intron 22 of 33)	-33614	NM_027665	71078	Mm.50711	NM_027665	ENSMUSG00000043468	Adam30	4933424D07Rik|svph4	a disintegrin and metallopeptidase domain 30	protein-coding
mm_144361.1	chr18	20310924	20310929	+	1	NA	promoter-TSS (NM_010079)	promoter-TSS (NM_010079)	53	NM_010079	13510	Mm.37953	NM_010079	ENSMUSG00000069441	Dsg1a	DG1|DGI|Dsg1|dsg1-alpha	desmoglein 1 alpha	protein-coding
mm_104148.1	chr11	87074074	87074116	-	1	NA	promoter-TSS (NM_025638)	promoter-TSS (NM_025638)	42	NM_025638	66569	Mm.281887	NM_025638	ENSMUSG00000061666	Gdpd1	2610020H15Rik	glycerophosphodiester phosphodiesterase domain containing 1	protein-coding
mm_30489.1	chr3	155093347	155093385	-	1	NA	promoter-TSS (NM_028938)	promoter-TSS (NM_028938)	12	NM_029330	75540	Mm.35218	NM_029330	ENSMUSG00000053870	Fpgt	1700016E03Rik	fucose-1-phosphate guanylyltransferase	protein-coding
mm_116604.1	chr13	48625597	48625618	-	1	NA	promoter-TSS (NM_207232)	promoter-TSS (NM_207232)	65	NM_207232	218232	Mm.315089	NM_207232	ENSMUSG00000038042	Ptpdc1	AI843923|AW456874|Naa-1|Ptpcd1	protein tyrosine phosphatase domain containing 1	protein-coding
mm_3049.1	chr1	134040870	134040895	+	1	NA	exon (NM_021355, exon 2 of 3)	exon (NM_021355, exon 2 of 3)	3367	NM_021355	14264	Mm.287146	NM_021355	ENSMUSG00000041559	Fmod	AI131919|AU041740|SLRR2E	fibromodulin	protein-coding
mm_39467.1	chr5	19227205	19227244	+	1	NA	promoter-TSS (NR_102342)	promoter-TSS (NR_102342)	178	NM_001170746	50791	Mm.332231	NM_015823	ENSMUSG00000040003	Magi2	AIP-1|Acvri1|Acvrinp1|Acvrip1|Magi-2|S-SCAM|mKIAA0705	membrane associated guanylate kinase, WW and PDZ domain containing 2	protein-coding
mm_126685.1	chr15	84906638	84906645	+	1	NA	Intergenic	LFSINE_Vert|SINE|tRNA	-16787	NM_016714	18141	Mm.28379	NM_016714	ENSMUSG00000016619	Nup50	1700030K07Rik|AI413123|Npap60	nucleoporin 50	protein-coding
mm_113374.1	chr13	33004529	33004553	+	1	NA	promoter-TSS (NM_009256)	promoter-TSS (NM_009256)	0	NM_009256	20723	Mm.245041	NM_009256	ENSMUSG00000045827	Serpinb9	BB283241|CAP-3|CAP3|PI-9|PI9|Spi6|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 9	protein-coding
mm_145406.1	chr18	57468479	57468541	+	1	NA	promoter-TSS (NM_001134697)	promoter-TSS (NM_001134697)	24	NM_001134697	629147	Mm.57415	NM_001134697	ENSMUSG00000069372	Ctxn3	ENSMUSG00000069372	cortexin 3	protein-coding
mm_92333.1	chr10	75797729	75797757	-	1	NA	intron (NM_008185, intron 1 of 4)	intron (NM_008185, intron 1 of 4)	841	NM_008185	14871	Mm.2746	NM_008185	ENSMUSG00000001663	Gstt1	AI255817|Gstt1-1	glutathione S-transferase, theta 1	protein-coding
mm_21380.1	chr2	157425675	157425696	-	1	NA	intron (NM_009271, intron 1 of 14)	intron (NM_009271, intron 1 of 14)	1392	NM_001025395	20779	Mm.22845	NM_009271	ENSMUSG00000027646	Src	AW259666|pp60c-src	Rous sarcoma oncogene	protein-coding
mm_150815.1	chr19	44397352	44397358	+	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	10354	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_30343.1	chr3	151742275	151742285	-	1	NA	intron (NM_133871, intron 5 of 7)	intron (NM_133871, intron 5 of 7)	7679	NM_133871	99899	Mm.30756	NM_133871	ENSMUSG00000028037	Ifi44	A430056A10Rik|AW261460|MTAP44|p44	interferon-induced protein 44	protein-coding
mm_136464.1	chr16	95459018	95459023	-	1	NA	intron (NM_001302152, intron 3 of 10)	intron (NM_001302152, intron 3 of 10)	328	NM_001302154	13876	Mm.164531	NM_133659	ENSMUSG00000040732	Erg	D030036I24Rik	avian erythroblastosis virus E-26 (v-ets) oncogene related	protein-coding
mm_74260.1	chr8	124897847	124897869	+	1	NA	promoter-TSS (NM_198103)	promoter-TSS (NM_198103)	-28	NM_001111141	244666	Mm.482915	NM_001111141	ENSMUSG00000031986	Sprtn	Gm505	SprT-like N-terminal domain	protein-coding
mm_23568.1	chr3	63295816	63295830	+	1	NA	promoter-TSS (NM_008604)	promoter-TSS (NM_008604)	-49	NM_008604	17380	Mm.296022	NM_008604	ENSMUSG00000027820	Mme	6030454K05Rik|C85356|CALLA|CD10|NEP|SFE	membrane metallo endopeptidase	protein-coding
mm_151361.1	chr19	55912590	55912608	+	1	NA	exon (NM_001142918, exon 7 of 15)	exon (NM_001142918, exon 7 of 15)	17278	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_68559.1	chr7	114562946	114562989	-	1	NA	promoter-TSS (NM_177382)	promoter-TSS (NM_177382)	5	NR_110407	244209	Mm.108037	NM_177382	ENSMUSG00000030670	Cyp2r1	-	cytochrome P450, family 2, subfamily r, polypeptide 1	protein-coding
mm_7628.1	chr1	127677746	127677798	-	1	NA	5' UTR (NM_028135, exon 1 of 8)	5' UTR (NM_028135, exon 1 of 8)	249	NM_028135	72160	Mm.281287	NM_028135	ENSMUSG00000026347	Tmem163	2610024A01Rik|SV31	transmembrane protein 163	protein-coding
mm_81791.1	chr9	114998945	114998990	+	1	NA	Intergenic	Intergenic	-64980	NM_175380	333433	Mm.38198	NM_175380	ENSMUSG00000050627	Gpd1l	2210409H23Rik|D9Ertd660e	glycerol-3-phosphate dehydrogenase 1-like	protein-coding
mm_62680.1	chr7	109752308	109752342	+	1	NA	promoter-TSS (NM_020050)	promoter-TSS (NM_020050)	-62	NM_020050	56786	Mm.240668	NM_020050	ENSMUSG00000031021	Tmem9b	2310004K06Rik|AW539847|D7H11orf15|ICRFP703B1614Q5.3	TMEM9 domain family, member B	protein-coding
mm_106902.1	chr12	8015038	8015050	+	1	NA	exon (NM_009693, exon 29 of 29)	exon (NM_009693, exon 29 of 29)	37367	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_6892.1	chr1	84696134	84696138	-	1	NA	promoter-TSS (NM_152915)	promoter-TSS (NM_152915)	85	NM_152915	227325	Mm.292560	NM_152915	ENSMUSG00000036766	Dner	A930026D19Rik|BET|Bret	delta/notch-like EGF repeat containing	protein-coding
mm_151969.1	chr19	5803572	5803582	-	1	NA	promoter-TSS (NR_002847)	promoter-TSS (NR_002847)	-905	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_20974.1	chr2	151973401	151973423	-	1	NA	promoter-TSS (NM_001289151)	promoter-TSS (NM_001289151)	-18	NM_001289151	73847	Mm.272444	NM_028666	ENSMUSG00000027459	Fam110a	1700008J10Rik|5430432M24Rik|AI747080	family with sequence similarity 110, member A	protein-coding
mm_170944.1	chr2	51871649	51871668	-	1	NA	Intergenic	Intergenic	62986	NM_001141982	71684	Mm.28309	NM_030243	ENSMUSG00000036249	Rbm43	0610033I05Rik	RNA binding motif protein 43	protein-coding
mm_65464.1	chr7	25472021	25472023	-	1	NA	exon (NM_001039186, exon 5 of 8)	exon (NM_001039186, exon 5 of 8)	5603	NM_001039185	26365	Mm.322502	NM_011926	ENSMUSG00000074272	Ceacam1	Bgp|Bgp1|C-CAM|CD66a|Cc1|Cea-1|Cea-7|Cea1|Cea7|Hv-2|Hv2|MHVR|MHVR1|Mhv-1|bb-1|mCEA1|mmCGM1|mmCGM1a|mmCGM2	carcinoembryonic antigen-related cell adhesion molecule 1	protein-coding
mm_77797.1	chr9	3031069	3031097	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	7660	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_89191.1	chr10	86347364	86347379	+	1	NA	3' UTR (NM_011595, exon 5 of 5)	3' UTR (NM_011595, exon 5 of 5)	46959	NM_011595	21859	Mm.4871	NM_011595	ENSMUSG00000020044	Timp3	Timp-3	tissue inhibitor of metalloproteinase 3	protein-coding
mm_38527.1	chr4	141538435	141538525	-	1	NA	5' UTR (NM_019763, exon 1 of 16)	5' UTR (NM_019763, exon 1 of 16)	117	NM_001347235	56381	Mm.299906	NM_019763	ENSMUSG00000040761	Spen	Mint|mKIAA0929	SPEN homolog, transcriptional regulator (Drosophila)	protein-coding
mm_24506.1	chr3	92484233	92484279	+	1	NA	3' UTR (NM_009264, exon 2 of 2)	3' UTR (NM_009264, exon 2 of 2)	1625	NM_009264	20753	Mm.331191	NM_009264	ENSMUSG00000050359	Sprr1a	AI528815|SPR1a|mSPRR1A	small proline-rich protein 1A	protein-coding
mm_160097.1	chr7	18431847	18431847	-	1	NA	exon (NM_054063, exon 1 of 5)	exon (NM_054063, exon 1 of 5)	208	NM_054063	114871	Mm.362025	NM_054063	ENSMUSG00000030373	Psg28	cea16	pregnancy-specific glycoprotein 28	protein-coding
mm_10759.1	chr2	24153149	24153165	+	1	NA	promoter-TSS (NM_027163)	promoter-TSS (NM_027163)	-15	NM_027163	69677	Mm.45901	NM_027163	ENSMUSG00000026985	Il1f8	2310043N20Rik|Il36b	interleukin 1 family, member 8	protein-coding
mm_99441.1	chr11	102433070	102433082	+	1	NA	exon (NM_008175, exon 2 of 13)	exon (NM_008175, exon 2 of 13)	2754	NM_008175	14824	Mm.1568	NM_008175	ENSMUSG00000034708	Grn	Pgrn|epithelin	granulin	protein-coding
mm_159217.1	chr2	127142551	127142551	-	1	NA	promoter-TSS (NM_001163528)	promoter-TSS (NM_001163528)	39	NM_001163528	73338	Mm.57559	NM_001163527	ENSMUSG00000074825	Itpripl1	1700041B20Rik	inositol 1,4,5-triphosphate receptor interacting protein-like 1	protein-coding
mm_81269.1	chr9	108080447	108080462	+	1	NA	promoter-TSS (NM_008243)	promoter-TSS (NM_008243)	18	NM_008243	15235	Mm.8369	NM_008243	ENSMUSG00000032591	Mst1	D3F15S2h|D9H3F15S2|DNF15S2h|Hgfl	macrophage stimulating 1 (hepatocyte growth factor-like)	protein-coding
mm_117321.1	chr13	67729110	67729145	-	1	NA	promoter-TSS (NM_145622)	promoter-TSS (NM_145622)	46	NM_145622	235907	Mm.440123	NM_145622	ENSMUSG00000071281	Zfp65	KRAB5|Zfp71-rs1|pz114	zinc finger protein 65	protein-coding
mm_61013.1	chr7	49364991	49365005	+	1	NA	intron (NM_175272, intron 2 of 37)	intron (NM_175272, intron 2 of 37)	118809	NM_175272	78286	Mm.333881	NM_175272	ENSMUSG00000052512	Nav2	5330421F07Rik|AU067780|BQ960892|HELAD1|POMFIL2|RAINB1|RAINB2|Unc53H2|mKIAA3015	neuron navigator 2	protein-coding
mm_101863.1	chr11	48871409	48871424	-	1	NA	promoter-TSS (NM_008326)	promoter-TSS (NM_008326)	-70	NM_008326	15944	Mm.29938	NM_008326	ENSMUSG00000046879	Irgm1	Ifggd3|Ifi1|Iigp3|Iipg3|Irgm|LRG-47	immunity-related GTPase family M member 1	protein-coding
mm_74904.1	chr8	25203820	25203843	-	1	NA	Intergenic	Intergenic	-2289	NM_177089	320165	Mm.308452	NM_177089	ENSMUSG00000065954	Tacc1	4833447E04Rik|AA960202|B230378H13Rik	transforming, acidic coiled-coil containing protein 1	protein-coding
mm_133417.1	chr16	85819247	85819257	+	1	NA	promoter-TSS (NR_040506)	promoter-TSS (NR_040506)	41	NR_040506	75310	Mm.108627	NR_040506		4930556C24Rik	-	RIKEN cDNA 4930556C24 gene	ncRNA
mm_26836.1	chr3	11904910	11904924	-	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	-60558	NR_040751	100038545	Mm.388494	NR_040751	ENSMUSG00000104015	Gm10745	ENSMUSG00000074696	predicted gene 10745	ncRNA
mm_86378.1	chr9	123844589	123844620	-	1	NA	intron (NM_001110253, intron 1 of 17)	intron (NM_001110253, intron 1 of 17)	7057	NM_148925	17281	Mm.252941	NM_148925	ENSMUSG00000025241	Fyco1	2810409M01Rik|Mem2|RUFY3|ZFYVE7	FYVE and coiled-coil domain containing 1	protein-coding
mm_90696.1	chr10	130322870	130322905	+	1	NA	promoter-TSS (NM_183264)	promoter-TSS (NM_183264)	35	NM_183264	67596	Mm.131264	NM_183264	ENSMUSG00000034833	Tespa1	5830405N20Rik|A430001F24Rik|AI450549	thymocyte expressed, positive selection associated 1	protein-coding
mm_43738.1	chr5	139822311	139822345	+	1	NA	Intergenic	Intergenic	4515	NM_025604	66506	Mm.29070	NM_025604	ENSMUSG00000029551	Psmg3	1810042K04Rik|4930403H09Rik|AI303239	proteasome (prosome, macropain) assembly chaperone 3	protein-coding
mm_66945.1	chr7	61982349	61982364	-	1	NA	promoter-TSS (NR_037287)	promoter-TSS (NR_037287)	3	NR_037287	100526507		NR_037287	ENSMUSG00000092850	Mir344g	mir-344g|mmu-mir-344g	microRNA 344g	ncRNA
mm_159203.1	chr2	121109961	121109961	-	1	NA	promoter-TSS (NM_001160424)	promoter-TSS (NM_001160424)	-170	NM_001160424	640543	Mm.478785	NM_001160424	ENSMUSG00000079103	Tgm7	TGMZ|TGz	transglutaminase 7	protein-coding
mm_137982.1	chr17	33594495	33594506	+	1	NA	intron (NM_053214, intron 19 of 27)	RSINE1|SINE|B4	-34592	NR_034153	328801	Mm.181488	NM_026712	ENSMUSG00000073423	Zfp414	0610030H11Rik|Znf414	zinc finger protein 414	protein-coding
mm_64797.1	chr7	6685520	6685539	-	1	NA	intron (NM_011769, intron 5 of 7)	intron (NM_011769, intron 5 of 7)	10903	NM_011769	22776	Mm.89976	NM_011769	ENSMUSG00000002266	Zim1	-	zinc finger, imprinted 1	protein-coding
mm_167666.1	chr9	72970209	72970217	+	1	NA	intron (NM_026314, intron 7 of 8)	intron (NM_026314, intron 7 of 8)	11428	NM_001163725	67685	Mm.31817	NM_026314	ENSMUSG00000089865	Dyx1c1	1700010I24Rik|Dnaaf4|EKN1|b2b811.1Clo|b2b811Clo	dyslexia susceptibility 1 candidate 1	protein-coding
mm_150197.1	chr19	32754917	32754921	+	1	NA	Intergenic	Intergenic	-2658	NM_008960	19211	Mm.245395	NM_008960	ENSMUSG00000013663	Pten	2310035O07Rik|A130070J02Rik|AI463227|B430203M17Rik|MMAC1|TEP1	phosphatase and tensin homolog	protein-coding
mm_117411.1	chr13	74020203	74020206	-	1	NA	intron (NM_182839, intron 1 of 3)	intron (NM_182839, intron 1 of 3)	10785	NM_182839	72948	Mm.39752	NM_182839	ENSMUSG00000021573	Tppp	2900041A09Rik|AI849835	tubulin polymerization promoting protein	protein-coding
mm_144221.1	chr18	9799144	9799178	+	1	NA	intron (NM_130449, intron 2 of 9)	intron (NM_130449, intron 2 of 9)	91513	NM_130449	140792	Mm.218571	NM_130449	ENSMUSG00000036103	Colec12	CL-P1|SRCL|Scara4	collectin sub-family member 12	protein-coding
mm_17514.1	chr2	29194197	29194197	-	1	NA	TTS (NM_133500)	TTS (NM_133500)	53902	NM_001305805	171171	Mm.442448	NM_133500	ENSMUSG00000035513	Ntng2	2610016D08Rik|Lmnt2	netrin G2	protein-coding
mm_144672.1	chr18	34624635	34624662	+	1	NA	promoter-TSS (NM_009004)	promoter-TSS (NM_009004)	24	NM_001166407	19348	Mm.258846	NM_009004	ENSMUSG00000003779	Kif20a	AA415432|Rab6kifl	kinesin family member 20A	protein-coding
mm_86210.1	chr9	120009185	120009190	-	1	NA	Intergenic	Intergenic	14411	NM_011724	22437	Mm.10117	NM_011724	ENSMUSG00000079243	Xirp1	AI415219|Cmya1	xin actin-binding repeat containing 1	protein-coding
mm_80962.1	chr9	103085879	103085898	+	1	NA	3' UTR (NM_033314, exon 14 of 14)	3' UTR (NM_033314, exon 14 of 14)	-26186	NM_173781	270192	Mm.490252	NM_173781	ENSMUSG00000032549	Rab6b	9630015C03|AI844641|C330006L04Rik|D9Bwg0185e	RAB6B, member RAS oncogene family	protein-coding
mm_151849.1	chr19	5771413	5771423	-	1	NA	promoter-TSS (NM_023912)	promoter-TSS (NM_023912)	-17	NM_023912	78891	Mm.276063	NM_023912	ENSMUSG00000024941	Scyl1	2810011O19Rik|C85140|Ntkl|mdf|mfd|p105	SCY1-like 1 (S. cerevisiae)	protein-coding
mm_42045.1	chr5	108461309	108461342	+	1	NA	promoter-TSS (NM_172716)	promoter-TSS (NM_172716)	-7	NM_172716	69587	Mm.261218	NM_172716	ENSMUSG00000033623	Pcgf3	2310035N15Rik|AI662857|D630042K08Rik|DONG1|E430039C14|RNF3A|Rnf3	polycomb group ring finger 3	protein-coding
mm_95062.1	chr11	32455363	32455438	+	1	NA	promoter-TSS (NM_173784)	promoter-TSS (NM_173784)	28	NM_173784	327900	Mm.260956	NM_173784	ENSMUSG00000044949	Ubtd2	4930571L24|9630054F20Rik|AI645720	ubiquitin domain containing 2	protein-coding
mm_81160.1	chr9	107296683	107296737	+	1	NA	promoter-TSS (NM_009895)	promoter-TSS (NM_009895)	51	NM_009895	12700	Mm.4592	NM_009895	ENSMUSG00000032578	Cish	CIS-1|CIS1|Cis|F17|F23|SOCS	cytokine inducible SH2-containing protein	protein-coding
mm_166945.1	chr7	43553632	43553638	+	1	NA	Intergenic	Intergenic	-8735	NM_001008549	210104	Mm.333821	NM_001008549	ENSMUSG00000056592	Zfp658	-	zinc finger protein 658	protein-coding
mm_163931.1	chr14	47384700	47384708	+	1	NA	exon (NM_010705, exon 5 of 6)	exon (NM_010705, exon 5 of 6)	10844	NM_001145953	16854	Mm.248615	NM_010705	ENSMUSG00000050335	Lgals3	GBP|L-34|Mac-2|gal3	lectin, galactose binding, soluble 3	protein-coding
mm_114401.1	chr13	63815291	63815379	+	1	NA	promoter-TSS (NM_023507)	promoter-TSS (NM_023507)	1	NM_023507	76251	Mm.186610	NM_023507	ENSMUSG00000021470	Ercc6l2	0610007P08Rik|1700019D06Rik|9330134C04Rik|Rad26l|Sr278	excision repair cross-complementing rodent repair deficiency, complementation group 6 like 2	protein-coding
mm_98628.1	chr11	96034907	96034952	+	1	NA	promoter-TSS (NM_033568)	promoter-TSS (NM_033568)	12	NM_033568	27681	Mm.372235	NM_033568	ENSMUSG00000006058	Snf8	D11Moh34	SNF8, ESCRT-II complex subunit, homolog (S. cerevisiae)	protein-coding
mm_33281.1	chr4	128744991	128745009	+	1	NA	intron (NM_001195083, intron 2 of 6)	intron (NM_001195083, intron 2 of 6)	-14258	NM_001009819	215493	Mm.300900	NM_001009819	ENSMUSG00000028794	A3galt2	Gm433|iGb3|iGb3S	alpha 1,3-galactosyltransferase 2 (isoglobotriaosylceramide synthase)	protein-coding
mm_135151.1	chr16	35857771	35857794	-	1	NA	exon (NM_001039530, exon 6 of 17)	exon (NM_001039530, exon 6 of 17)	13600	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_131909.1	chr16	23269638	23269659	+	1	NA	intron (NM_001252505, intron 2 of 7)	intron (NM_001252505, intron 2 of 7)	-20822	NM_001252506	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_67863.1	chr7	99131746	99131747	-	1	NA	intron (NM_178635, intron 1 of 14)	intron (NM_178635, intron 1 of 14)	9398	NM_178635	78610	Mm.323072	NM_178635	ENSMUSG00000035354	Uvrag	9530039D02Rik|AI648770|BB124205|Uvrag1|Uvragl	UV radiation resistance associated gene	protein-coding
mm_24283.1	chr3	89230826	89230878	+	1	NA	exon (NM_013605, exon 2 of 7)	exon (NM_013605, exon 2 of 7)	1796	NM_013605	17829	Mm.16193	NM_013605	ENSMUSG00000042784	Muc1	CD227|EMA|Muc-1	mucin 1, transmembrane	protein-coding
mm_5843.1	chr1	52953597	52953627	-	1	NA	promoter-TSS (NM_144953)	promoter-TSS (NM_144953)	-772	NM_144953	67080	Mm.236287	NM_144953	ENSMUSG00000043629	1700019D03Rik	2410136C24Rik|AA410151|smAKAP	RIKEN cDNA 1700019D03 gene	protein-coding
mm_172992.1	chrM	1381	1395	+	1	NA	NA	Intergenic	NA	NA								
mm_40751.1	chr5	66853405	66853432	+	1	NA	intron (NM_001001980, intron 1 of 25)	(CAGT)n|Simple_repeat|Simple_repeat	107578	NM_001001980	77569	Mm.374778	NM_001001980	ENSMUSG00000037736	Limch1	3732412D22Rik|mKIAA1102	LIM and calponin homology domains 1	protein-coding
mm_52999.1	chr6	123269206	123269224	+	1	NA	intron (NM_001163161, intron 4 of 5)	intron (NM_001163161, intron 4 of 5)	7108	NM_010819	17474	Mm.441101	NM_010819	ENSMUSG00000030144	Clec4d	Clecsf8|Mpcl|mcl	C-type lectin domain family 4, member d	protein-coding
mm_47402.1	chr5	123130846	123130852	-	1	NA	intron (NM_175092, intron 2 of 4)	intron (NM_175092, intron 2 of 4)	1780	NM_175092	23912	Mm.253876	NM_175092	ENSMUSG00000029449	Rhof	AI845056|AV026554|Arhf|Ifld1|Rif	ras homolog family member F (in filopodia)	protein-coding
mm_104226.1	chr11	88552559	88552566	-	1	NA	intron (NM_054043, intron 6 of 13)	intron (NM_054043, intron 6 of 13)	-66689	NR_131025	68397	Mm.426889	NR_131025		0610039H22Rik	-	RIKEN cDNA 0610039H22 gene	ncRNA
mm_160841.1	chr11	49317642	49317642	+	1	NA	promoter-TSS (NM_206822)	promoter-TSS (NM_206822)	94	NM_206822	18307	Mm.377101	NM_206822	ENSMUSG00000100923	Olfr10	GA_x6K02T2QP88-6117098-6116163|L45|MOR256-55	olfactory receptor 10	protein-coding
mm_17928.1	chr2	35462520	35462574	-	1	NA	Intergenic	CpG	-1098	NM_001145821	14594	Mm.281124	NM_010283	ENSMUSG00000035778	Ggta1	AW108479|GALT|Gal|Ggta|Ggta-1|alpha Gal|alpha3GalT	glycoprotein galactosyltransferase alpha 1, 3	protein-coding
mm_69521.1	chr7	135626432	135626441	-	1	NA	intron (NM_001316679, intron 1 of 19)	MTEa|LTR|ERVL-MaLR	20608	NM_001316679	19267	Mm.945	NM_011212	ENSMUSG00000041836	Ptpre	PTPe|PTPepsilon|RPTPepsilon	protein tyrosine phosphatase, receptor type, E	protein-coding
mm_121074.1	chr14	98577414	98577420	+	1	NA	Intergenic	Intergenic	-407652	NM_007826	13134	Mm.320593	NM_007826	ENSMUSG00000055639	Dach1	Dac|Dach	dachshund 1 (Drosophila)	protein-coding
mm_136557.1	chr17	3115121	3115134	+	1	NA	5' UTR (NM_134123, exon 1 of 20)	5' UTR (NM_134123, exon 1 of 20)	155	NM_134123	106583	Mm.124373	NM_134123	ENSMUSG00000046201	Scaf8	A630086M08Rik|A930036P18Rik|AA408306|AI447644|AI448652|AU015035|Rbm16|mKIAA1116	SR-related CTD-associated factor 8	protein-coding
mm_120542.1	chr14	67237709	67237745	+	1	NA	intron (NM_010095, intron 3 of 16)	intron (NM_010095, intron 3 of 16)	4435	NM_001276387	13592	Mm.319947	NM_010095	ENSMUSG00000022053	Ebf2	D14Ggc1e|EBF-2|Mmot1|O/E-3|OE-3	early B cell factor 2	protein-coding
mm_11217.1	chr2	29643764	29643782	+	1	NA	intron (NM_001039087, intron 1 of 25)	intron (NM_001039087, intron 1 of 25)	24053	NM_001039086	107746	Mm.298274	NM_054050	ENSMUSG00000039844	Rapgef1	4932418O06Rik|C3G|Grf2	Rap guanine nucleotide exchange factor (GEF) 1	protein-coding
mm_120328.1	chr14	63269169	63269180	+	1	NA	Intergenic	Intergenic	-23903	NM_001310610	14463	Mm.247669	NM_008092	ENSMUSG00000021944	Gata4	Gata-4	GATA binding protein 4	protein-coding
mm_93817.1	chr10	121439052	121439056	-	1	NA	intron (NM_138956, intron 1 of 4)	intron (NM_138956, intron 1 of 4)	37196	NM_138956	192678	Mm.41265	NM_138956	ENSMUSG00000025795	Rassf3	AW212023|AW322379	Ras association (RalGDS/AF-6) domain family member 3	protein-coding
mm_153916.1	chr19	47266881	47266886	-	1	NA	3' UTR (NM_008018, exon 15 of 15)	3' UTR (NM_008018, exon 15 of 15)	6706	NR_105961	102466782		NR_105961	ENSMUSG00000098786	Mir6995	Gm27576|mmu-mir-6995	microRNA 6995	ncRNA
mm_158304.1	chrX	122397193	122397236	-	1	NA	5' UTR (NM_138742, exon 1 of 1)	5' UTR (NM_138742, exon 1 of 1)	171	NM_138742	54561	Mm.490573	NM_138742	ENSMUSG00000055733	Nap1l3	MB20	nucleosome assembly protein 1-like 3	protein-coding
mm_57660.1	chr6	128487435	128487445	-	1	NA	exon (NM_007376, exon 31 of 36)	exon (NM_007376, exon 31 of 36)	39280	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_153710.1	chr19	44397981	44398012	-	1	NA	exon (NM_009127, exon 6 of 6)	exon (NM_009127, exon 6 of 6)	9713	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_106495.1	chr11	120348205	120348245	-	1	NA	promoter-TSS (NR_105900)	promoter-TSS (NR_105900)	270	NM_001313923	11465	Mm.196173	NM_009609	ENSMUSG00000062825	Actg1	AL023024|Actg|Actl|E51	actin, gamma, cytoplasmic 1	protein-coding
mm_166709.1	chr6	116459436	116459471	+	1	NA	intron (NM_009662, intron 1 of 13)	intron (NM_009662, intron 1 of 13)	1725	NM_009662	11689	Mm.41072	NM_009662	ENSMUSG00000025701	Alox5	5-LO|5-LOX|5LO|5LX|AI850497|F730011J02	arachidonate 5-lipoxygenase	protein-coding
mm_12587.1	chr2	73485328	73485331	+	1	NA	intron (NM_153138, intron 1 of 7)	ID_B1|SINE|B4	424	NM_001289723	215280	Mm.223504	NM_153138	ENSMUSG00000075284	Wipf1	AI115543|D2Ertd120e|WIP|Waspip	WAS/WASL interacting protein family, member 1	protein-coding
mm_8122.1	chr1	136135109	136135124	-	1	NA	intron (NM_001039472, intron 1 of 34)	intron (NM_001039472, intron 1 of 34)	3715	NM_001039472	16565	Mm.276135	NM_019962	ENSMUSG00000041642	Kif21b	2610511N21Rik|mKIAA0449	kinesin family member 21B	protein-coding
mm_136884.1	chr17	13008396	13008399	+	1	NA	intron (NM_013671, intron 2 of 4)	CpG-5970	558	NM_013671	20656	Mm.290876	NM_013671	ENSMUSG00000006818	Sod2	MnSOD|Sod-2	superoxide dismutase 2, mitochondrial	protein-coding
mm_71077.1	chr8	34507159	34507171	+	1	NA	Intergenic	Intergenic	133151	NR_040706	330734	Mm.149998	NR_040706	ENSMUSG00000109819	B930018H19Rik	B930018H19	RIKEN cDNA B930018H19 gene	ncRNA
mm_58642.1	chr7	6172534	6172556	+	1	NA	promoter-TSS (NM_001146024)	promoter-TSS (NM_001146024)	32	NM_001146024	72667	Mm.274089	NM_028316	ENSMUSG00000044876	Zfp444	2810031J10Rik|6230401O10Rik|mFLJ00134	zinc finger protein 444	protein-coding
mm_47763.1	chr5	131495773	131495779	-	1	NA	intron (NM_177047, intron 6 of 18)	intron (NM_177047, intron 6 of 18)	-188254	NM_145218	212996	Mm.299204	NM_145218	ENSMUSG00000034040	Wbscr17	AA388321|E330012B09Rik	Williams-Beuren syndrome chromosome region 17 homolog (human)	protein-coding
mm_92836.1	chr10	81496330	81496387	-	1	NA	promoter-TSS (NM_134009)	promoter-TSS (NM_134009)	5	NM_134009	103425	Mm.302791	NM_134009	ENSMUSG00000020238	Ncln	3100002P13Rik|AW120537	nicalin	protein-coding
mm_97289.1	chr11	76217618	76217636	+	1	NA	promoter-TSS (NM_177367)	promoter-TSS (NM_177367)	14	NM_021294	13168	Mm.347413	NM_021294	ENSMUSG00000038057	Dbil5	ELP	diazepam binding inhibitor-like 5	protein-coding
mm_95873.1	chr11	58051336	58051345	+	1	NA	intron (NM_028451, intron 13 of 18)	intron (NM_028451, intron 13 of 18)	42276	NM_028451	73158	Mm.248843	NM_028451	ENSMUSG00000037331	Larp1	1810024J12Rik|3110040D16Rik|Larp|mKIAA0731	La ribonucleoprotein domain family, member 1	protein-coding
mm_170684.1	chr2	127210824	127210826	+	1	NA	exon (NM_177214, exon 3 of 45)	exon (NM_177214, exon 3 of 45)	2421	NM_177214	320632	Mm.215860	NM_177214	ENSMUSG00000003660	Snrnp200	A330064G03Rik|Ascc3l1|BC011390|HELIC2|U5-200-KD|U5-200KD	small nuclear ribonucleoprotein 200 (U5)	protein-coding
mm_42555.1	chr5	116802762	116802772	+	1	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	-210950	NM_026886	68955	Mm.146779	NM_026886	ENSMUSG00000063919	Srrm4	1500001A10Rik|B230202K19Rik|bv|mKIAA1853|nSR100	serine/arginine repetitive matrix 4	protein-coding
mm_73198.1	chr8	95601510	95601533	+	1	NA	Intergenic	Intergenic	-25914	NM_001310539	70993	Mm.486561	NM_027640	ENSMUSG00000048400	Prss54	4931432M23Rik|Klkbl4	protease, serine 54	protein-coding
mm_155014.1	chrX	41604796	41604799	+	1	NA	intron (NR_104053, intron 10 of 16)	intron (NR_104053, intron 10 of 16)	203268	NM_001290451	53623	Mm.327681	NM_016886	ENSMUSG00000001986	Gria3	2900064I19Rik|GluA3|GluR-C|GluR-K3|Glur-3|Glur3|Gluralpha3	glutamate receptor, ionotropic, AMPA3 (alpha 3)	protein-coding
mm_64719.1	chr7	4657745	4657783	-	1	NA	intron (NM_172894, intron 1 of 23)	L2c|LINE|L2	1186	NM_172894	243819	Mm.258670	NM_172894	ENSMUSG00000052296	Ppp6r1	2010309P17Rik|AI836219|B430201G11Rik|D030074N20Rik|Pp6r1|Saps1|mKIAA1115	protein phosphatase 6, regulatory subunit 1	protein-coding
mm_140928.1	chr17	24251323	24251381	-	1	NA	promoter-TSS (NM_007634)	promoter-TSS (NM_007634)	57	NM_007634	12449	Mm.77695	NM_007634	ENSMUSG00000072082	Ccnf	CycF|Fbxo1	cyclin F	protein-coding
mm_82003.1	chr9	121706798	121706799	+	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	-1769	NM_178677	215474	Mm.31421	NM_178677	ENSMUSG00000061536	Sec22c	4932412K21|5930407I15Rik|C530046H07|Sec22l3	SEC22 homolog C, vesicle trafficking protein	protein-coding
mm_78921.1	chr9	45042536	45042551	+	1	NA	5' UTR (NM_007962, exon 1 of 6)	5' UTR (NM_007962, exon 1 of 6)	199	NM_007962	14012	Mm.33240	NM_007962	ENSMUSG00000032092	Mpzl2	Eva|Eva1	myelin protein zero-like 2	protein-coding
mm_86225.1	chr9	120135815	120135826	-	1	NA	Intergenic	Intergenic	5386	NR_002902	104433	Mm.453530	NR_002902	ENSMUSG00000064925	Snora62	E2|MBI-13|MBI-136|Rnu108	small nucleolar RNA, H/ACA box 62	snoRNA
mm_153855.1	chr19	46380966	46380969	-	1	NA	exon (NM_016860, exon 6 of 11)	exon (NM_016860, exon 6 of 11)	14768	NM_016860	54130	Mm.3118	NM_016860	ENSMUSG00000025228	Actr1a	Arp1|alpha-Arp1	ARP1 actin-related protein 1A, centractin alpha	protein-coding
mm_166285.1	chr5	97710195	97710195	+	1	NA	Intergenic	Lx8b|LINE|L1	-253187	NM_010294	14626	Mm.61206	NM_010294	ENSMUSG00000050553	Gk2	GKTA|Gk-rs2	glycerol kinase 2	protein-coding
mm_70227.1	chr7	145283949	145283962	-	1	NA	promoter-TSS (NM_146206)	promoter-TSS (NM_146206)	56	NR_132644	233979	Mm.102235	NM_146206	ENSMUSG00000048677	Tpcn2	D830047E22Rik|Gm35086	two pore segment channel 2	protein-coding
mm_117843.1	chr13	98692790	98692807	-	1	NA	intron (NM_001025606, intron 1 of 3)	intron (NM_001025606, intron 1 of 3)	2033	NM_001025606	380863	Mm.28264	NM_001025606	ENSMUSG00000052485	Tmem171	Gm905	transmembrane protein 171	protein-coding
mm_109271.1	chr12	109545737	109545759	+	1	NA	non-coding (NR_003633, exon 1 of 5)	non-coding (NR_003633, exon 1 of 5)	350	NR_003633	17263	Mm.289645	NM_144513	ENSMUSG00000021268	Meg3	2900016C05Rik|3110050O07Rik|6330408G06Rik|AI425946|AW108224|D12Bwg1266e|Gtl2|R74756|R75394	maternally expressed 3	ncRNA
mm_105931.1	chr11	115133907	115133916	-	1	NA	promoter-TSS (NM_001169153)	promoter-TSS (NM_001169153)	81	NM_001347648	246746	Mm.277387	NM_145634	ENSMUSG00000047798	Cd300lf	CLIM1|CLM-1|CLM1|Digr2|F730004D16Rik|IREM1|IgSF13|LMIR3|Pigr3	CD300 molecule like family member F	protein-coding
mm_93877.1	chr10	125242165	125242169	-	1	NA	intron (NM_011391, intron 4 of 6)	intron (NM_011391, intron 4 of 6)	86368	NM_011391	20503	Mm.29161	NM_011391	ENSMUSG00000020102	Slc16a7	4921534N07Rik|Mct2	solute carrier family 16 (monocarboxylic acid transporters), member 7	protein-coding
mm_43461.1	chr5	136689299	136689300	+	1	NA	Intergenic	Intergenic	-3847	NM_001303019	59310	Mm.5178	NM_021611	ENSMUSG00000005474	Myl10	1700027I08Rik|Mylc2pl|PLRLC	myosin, light chain 10, regulatory	protein-coding
mm_38377.1	chr4	138623979	138623999	-	1	NA	promoter-TSS (NM_029401)	promoter-TSS (NM_029401)	3	NM_029401	75718	Mm.251530	NM_029401	ENSMUSG00000028753	Vwa5b1	4931403E03Rik	von Willebrand factor A domain containing 5B1	protein-coding
mm_139793.1	chr17	65950991	65950999	+	1	NA	intron (NM_023053, intron 1 of 4)	CpG	192	NM_023053	65960	Mm.10153	NM_023053	ENSMUSG00000024098	Twsg1	1810013J15Rik|9030422N06Rik|AW552143|D17Ertd403e|Tsg|Twg	twisted gastrulation BMP signaling modulator 1	protein-coding
mm_103384.1	chr11	75415626	75415648	-	1	NA	exon (NM_011340, exon 4 of 8)	exon (NM_011340, exon 4 of 8)	6986	NM_011340	20317	Mm.2044	NM_011340	ENSMUSG00000000753	Serpinf1	AI195227|EPC-1|Pedf|Pedfl|Sdf3	serine (or cysteine) peptidase inhibitor, clade F, member 1	protein-coding
mm_136528.1	chr16	97462904	97462908	-	1	NA	promoter-TSS (NM_010846)	promoter-TSS (NM_010846)	0	NR_003520	17857	Mm.33996	NM_010846	ENSMUSG00000000386	Mx1	AI893580|Mx|Mx-1	MX dynamin-like GTPase 1	protein-coding
mm_139731.1	chr17	57477300	57477331	+	1	NA	intron (NM_010130, intron 19 of 21)	intron (NM_010130, intron 19 of 21)	67999	NM_001104591	224916	Mm.469889	NM_001104591	ENSMUSG00000090655	Vmn2r120	EG224916	vomeronasal 2, receptor 120	protein-coding
mm_115010.1	chr13	98354282	98354288	+	1	NA	promoter-TSS (NM_008242)	promoter-TSS (NM_008242)	40	NM_008242	15229	Mm.347441	NM_008242	ENSMUSG00000078302	Foxd1	AI385632|BF-2|FREAC4|Hfh10|Hfhbf2	forkhead box D1	protein-coding
mm_108197.1	chr12	76837409	76837466	+	1	NA	promoter-TSS (NM_145927)	promoter-TSS (NM_145927)	-30	NM_145927	110606	Mm.151174	NM_145927	ENSMUSG00000033373	Fntb	2010013E13Rik|AA409500	farnesyltransferase, CAAX box, beta	protein-coding
mm_90636.1	chr10	128498771	128498819	+	1	NA	promoter-TSS (NM_172259)	promoter-TSS (NM_172259)	-110	NM_172259	216459	Mm.291688	NM_172259	ENSMUSG00000039824	Myl6b	5730437E04Rik|BC037527|MLC1SA	myosin, light polypeptide 6B	protein-coding
mm_81075.1	chr9	106222639	106222666	+	1	NA	promoter-TSS (NM_031178)	promoter-TSS (NM_031178)	54	NM_031178	81897	Mm.44889	NM_031178	ENSMUSG00000045322	Tlr9	-	toll-like receptor 9	protein-coding
mm_151206.1	chr19	53600161	53600174	+	1	NA	promoter-TSS (NM_007790)	promoter-TSS (NM_007790)	-229	NM_007790	13006	Mm.14910	NM_007790	ENSMUSG00000024974	Smc3	Bamacan|Cspg6|HCAP|Mmip1|SMC-3|SmcD	structural maintenance of chromosomes 3	protein-coding
mm_57995.1	chr6	136172432	136172436	-	1	NA	intron (NM_008171, intron 2 of 14)	intron (NM_008171, intron 2 of 14)	1077	NM_008171	14812	Mm.436649	NM_008171	ENSMUSG00000030209	Grin2b	AW490526|GluN2B|NR2B|Nmdar2b	glutamate receptor, ionotropic, NMDA2B (epsilon 2)	protein-coding
mm_20674.1	chr2	132253175	132253217	-	1	NA	promoter-TSS (NM_011045)	promoter-TSS (NM_011045)	-16	NM_011045	18538	Mm.7141	NM_011045	ENSMUSG00000027342	Pcna	-	proliferating cell nuclear antigen	protein-coding
mm_130140.1	chr15	90898486	90898497	-	1	NA	promoter-TSS (NR_033583)	promoter-TSS (NR_033583)	-15	NR_033583	20738	Mm.431547	NR_033583		Spn-ps	Cd43-ps	sialophorin, pseudogene	pseudo
mm_10798.1	chr2	24349602	24349602	+	1	NA	exon (NM_031167, exon 5 of 5)	exon (NM_031167, exon 5 of 5)	4231	NM_001039701	16181	Mm.882	NM_031167	ENSMUSG00000026981	Il1rn	F630041P17Rik|IL-1ra	interleukin 1 receptor antagonist	protein-coding
mm_170149.1	chr17	45569504	45569504	-	1	NA	exon (NM_008302, exon 7 of 11)	exon (NM_008302, exon 7 of 11)	3757	NM_008302	15516	Mm.2180	NM_008302	ENSMUSG00000023944	Hsp90ab1	90kDa|AL022974|C81438|Hsp84|Hsp84-1|Hsp90|Hspcb	heat shock protein 90 alpha (cytosolic), class B member 1	protein-coding
mm_155908.1	chrX	101747607	101747607	+	1	NA	Intergenic	Intergenic	-13460	NM_009910	12766	Mm.12876	NM_009910	ENSMUSG00000050232	Cxcr3	Cd183|Cmkar3	chemokine (C-X-C motif) receptor 3	protein-coding
mm_68222.1	chr7	104420775	104420812	-	1	NA	intron (NM_009099, intron 5 of 7)	intron (NM_009099, intron 5 of 7)	44400	NM_009099	20128	Mm.295578	NM_009099	ENSMUSG00000030921	Trim30a	Rpt-1|Rpt1|Trim30	tripartite motif-containing 30A	protein-coding
mm_102862.1	chr11	69404973	69404996	-	1	NA	exon (NM_001017426, exon 11 of 23)	exon (NM_001017426, exon 11 of 23)	-6750	NM_025915	67020	Mm.390406	NM_025915	ENSMUSG00000045377	Tmem88	2600017H02Rik	transmembrane protein 88	protein-coding
mm_31252.1	chr4	45011729	45011748	+	1	NA	5' UTR (NM_001163284, exon 1 of 2)	5' UTR (NM_001163284, exon 1 of 2)	674	NM_001163284	230119	Mm.44222	NM_173399	ENSMUSG00000049657	Zbtb5	5930421I10|9430083K24Rik|AI646847|mKIAA0354	zinc finger and BTB domain containing 5	protein-coding
mm_121703.1	chr14	15438744	15438767	-	1	NA	5' UTR (NM_146052, exon 1 of 2)	5' UTR (NM_146052, exon 1 of 2)	232	NM_146052	218763	Mm.138039	NM_146052	ENSMUSG00000045201	Lrrc3b	BC019794|LRP15	leucine rich repeat containing 3B	protein-coding
mm_136692.1	chr17	6978894	6978912	+	1	NA	promoter-TSS (NM_026611)	promoter-TSS (NM_026611)	43	NM_026611	68195	Mm.181237	NM_026611	ENSMUSG00000094724	Rnaset2b	0610007O07Rik|4833423A10Rik|4930532K22Rik|C79750|RNASE6PL|Rnaset2	ribonuclease T2B	protein-coding
mm_21294.1	chr2	157007016	157007038	-	1	NA	promoter-TSS (NM_025853)	promoter-TSS (NM_025853)	48	NM_025853	66934	Mm.25410	NM_025853	ENSMUSG00000027635	Dsn1	1700022L09Rik|AW552447	DSN1 homolog, MIS12 kinetochore complex component	protein-coding
mm_27299.1	chr3	48609064	48609074	-	1	NA	promoter-TSS (NR_003617)	promoter-TSS (NR_003617)	31	NR_003617	66332	Mm.46124	NM_025493		1700018B24Rik	-	enhancer of rudimentary homolog pseudogene	pseudo
mm_87491.1	chr10	51495282	51495300	+	1	NA	intron (NM_001291894, intron 7 of 8)	intron (NM_001291894, intron 7 of 8)	4393	NM_013532	14728	Mm.34408	NM_013532	ENSMUSG00000062593	Lilrb4a	CD85K|Gp49b|HM18|ILT3|LIR-5|Lilrb4|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4A	protein-coding
mm_124555.1	chr14	122913205	122913213	-	1	NA	promoter-TSS (NM_145466)	promoter-TSS (NM_145466)	-44	NM_145466	223267	Mm.379358	NM_145466	ENSMUSG00000041625	Ggact	A2ld1	gamma-glutamylamine cyclotransferase	protein-coding
mm_31887.1	chr4	82507947	82508000	+	1	NA	promoter-TSS (NR_137202)	promoter-TSS (NR_137202)	-16	NR_137202	102635783	Mm.41666	NR_137202		Gm11266	OTTMUSG00000000396	predicted gene 11266	ncRNA
mm_37192.1	chr4	117495662	117495665	-	1	NA	intron (NM_025739, intron 1 of 14)	CpG	1389	NM_025739	66743	Mm.318331	NM_025739	ENSMUSG00000028677	Rnf220	4732477A13|4931406I20Rik|5730503K05Rik|AV302541	ring finger protein 220	protein-coding
mm_57624.1	chr6	128244430	128244433	-	1	NA	intron (NM_011567, intron 7 of 11)	intron (NM_011567, intron 7 of 11)	56382	NM_001080979	21679	Mm.14774	NM_011567	ENSMUSG00000030353	Tead4	ETFR-2|Etfr2|FR-19|Rtef1|TEAD-4|TEF-3|Tcf13r1|Tef3|Tefr|Tefr1|Tefr1a	TEA domain family member 4	protein-coding
mm_31351.1	chr4	46787604	46787624	+	1	NA	exon (NM_001081141, exon 7 of 19)	exon (NM_001081141, exon 7 of 19)	-137415	NM_198664	381605	Mm.331595	NM_198664	ENSMUSG00000039813	Tbc1d2	A630005A06Rik|BC022630|Gm1037|PARIS-1|PARIS1	TBC1 domain family, member 2	protein-coding
mm_128250.1	chr15	36770364	36770368	-	1	NA	3' UTR (NM_001253807, exon 5 of 5)	3' UTR (NM_001253807, exon 5 of 5)	20566	NM_001253807	22631	Mm.3360	NM_011740	ENSMUSG00000022285	Ywhaz	1110013I11Rik|14-3-3zeta|AI596267|AL022924|AU020854	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide	protein-coding
mm_166418.1	chr5	137151634	137151638	-	1	NA	Intergenic	Intergenic	-35429	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_123986.1	chr14	75593185	75593192	-	1	NA	promoter-TSS (NM_001164139)	promoter-TSS (NM_001164139)	-72	NM_001164139	67926	Mm.23361	NM_026457	ENSMUSG00000034913	Spert	1700086N05Rik|AI596460|Nurit	spermatid associated	protein-coding
mm_137773.1	chr17	29491643	29491673	+	1	NA	intron (NM_008842, intron 3 of 5)	CpG-6203	613	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_26502.1	chr3	145758690	145758694	+	1	NA	promoter-TSS (NM_026993)	promoter-TSS (NM_026993)	0	NM_026993	69219	Mm.234247	NM_026993	ENSMUSG00000028194	Ddah1	2410006N07Rik|2510015N06Rik|AI987801|AW050362	dimethylarginine dimethylaminohydrolase 1	protein-coding
mm_68054.1	chr7	101832926	101832963	-	1	NA	exon (NM_010567, exon 5 of 29)	exon (NM_010567, exon 5 of 29)	4880	NM_001122739	16332	Mm.476000	NM_010567	ENSMUSG00000032737	Inppl1	51C|SHIP2	inositol polyphosphate phosphatase-like 1	protein-coding
mm_111410.1	chr12	91384312	91384336	-	1	NA	promoter-TSS (NM_181815)	promoter-TSS (NM_181815)	85	NM_181815	75216	Mm.312204	NM_181815	ENSMUSG00000061533	Cep128	4930534B04Rik|5430424K18Rik|AI449708|AI480494|E230024F20	centrosomal protein 128	protein-coding
mm_25279.1	chr3	105452327	105452365	+	1	NA	promoter-TSS (NM_001039347)	promoter-TSS (NM_001039347)	16	NM_001039347	56543	Mm.44530	NM_019931	ENSMUSG00000040896	Kcnd3	AW045978|Kncd3|Kv4.3	potassium voltage-gated channel, Shal-related family, member 3	protein-coding
mm_55003.1	chr6	48835943	48835971	-	1	NA	exon (NM_001164209, exon 5 of 8)	exon (NM_001164209, exon 5 of 8)	5031	NM_023056	65963	Mm.28385	NM_023056	ENSMUSG00000029810	Tmem176b	1810009M01Rik|Clast1|Lr8	transmembrane protein 176B	protein-coding
mm_105372.1	chr11	103218422	103218438	-	1	NA	promoter-TSS (NM_177801)	promoter-TSS (NM_177801)	2	NM_177801	328019	Mm.189646	NM_177801	ENSMUSG00000044787	Spata32	4933400C05Rik|VAD1.2	spermatogenesis associated 32	protein-coding
mm_54963.1	chr6	48708865	48708898	-	1	NA	promoter-TSS (NM_153175)	promoter-TSS (NM_153175)	-637	NM_153175	231931	Mm.321047	NM_153175	ENSMUSG00000047867	Gimap6	4833419H03Rik|Ian6|mFLJ00102	GTPase, IMAP family member 6	protein-coding
mm_164157.1	chr15	67107396	67107396	+	1	NA	intron (NM_009177, intron 8 of 8)	intron (NM_009177, intron 8 of 8)	69486	NM_009177	20442	Mm.248334	NM_009177	ENSMUSG00000013846	St3gal1	5330418N22Rik|AI467004|ST3GalI|Siat4|Siat4a|St3gal-1	ST3 beta-galactoside alpha-2,3-sialyltransferase 1	protein-coding
mm_169251.1	chr13	78202552	78202571	+	1	NA	intron (NR_045195, intron 1 of 2)	(GGAA)n|Simple_repeat|Simple_repeat	-3688	NM_010151	13865	Mm.439653	NM_010151	ENSMUSG00000069171	Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR-3|EAR3|Erbal3|SVP44|Tcfcoup1	nuclear receptor subfamily 2, group F, member 1	protein-coding
mm_113101.1	chr13	24376169	24376197	+	1	NA	intron (NM_001284519, intron 2 of 17)	intron (NM_001284519, intron 2 of 17)	-38939	NM_007717	12763	Mm.8396	NM_007717	ENSMUSG00000016756	Cmah	-	cytidine monophospho-N-acetylneuraminic acid hydroxylase	protein-coding
mm_97537.1	chr11	78676620	78676624	+	1	NA	intron (NM_008702, intron 1 of 10)	intron (NM_008702, intron 1 of 10)	20803	NM_008702	18099	Mm.9001	NM_008702	ENSMUSG00000017376	Nlk	AI194375	nemo like kinase	protein-coding
mm_15757.1	chr2	164277103	164277135	+	1	NA	exon (NM_009300, exon 2 of 3)	exon (NM_009300, exon 2 of 3)	1188	NM_009300	20941	Mm.1286	NM_009300	ENSMUSG00000016998	Svs4	SVS-IV|Svp-2|Svp-4|Svp2|Svp4	seminal vesicle secretory protein 4	protein-coding
mm_130388.1	chr15	97867198	97867220	-	1	NA	exon (NM_009504, exon 7 of 10)	exon (NM_009504, exon 7 of 10)	-22707	NM_001204278	56233	Mm.384027	NM_019572	ENSMUSG00000022475	Hdac7	5830434K02Rik|HD7|HD7a|Hdac7a|mFLJ00062	histone deacetylase 7	protein-coding
mm_61831.1	chr7	88280495	88280538	+	1	NA	intron (NM_001311790, intron 1 of 3)	B1_Mus2|SINE|Alu	2431	NM_001311790	13032	Mm.89295	NM_009982	ENSMUSG00000030560	Ctsc	AI047818|CatC|DPP1|DPPI	cathepsin C	protein-coding
mm_171977.1	chr5	89499873	89499877	-	1	NA	Intergenic	Intergenic	-27554	NM_133192	104443	Mm.447881	NM_133192	ENSMUSG00000035528	Npffr2	Gpr74|HG31|NPFF2	neuropeptide FF receptor 2	protein-coding
mm_44065.1	chr5	148400017	148400029	+	1	NA	promoter-TSS (NM_007513)	promoter-TSS (NM_007513)	-119	NM_007513	11987	Mm.275489	NM_007513	ENSMUSG00000041313	Slc7a1	4831426K01Rik|AI447493|Atrc-1|Atrc1|Cat1|Rec-1|Rev-1|mCAT-1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 1	protein-coding
mm_143641.1	chr17	79354869	79354875	-	1	NA	5' UTR (NM_026514, exon 1 of 2)	5' UTR (NM_026514, exon 1 of 2)	219	NM_026514	260409	Mm.140601	NM_026514	ENSMUSG00000036533	Cdc42ep3	3200001F04Rik|AA986861|Borg2|Cep3|UB1	CDC42 effector protein (Rho GTPase binding) 3	protein-coding
mm_68869.1	chr7	126446020	126446054	-	1	NA	TTS (NM_030566)	TTS (NM_030566)	17036	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_59231.1	chr7	24709238	24709271	+	1	NA	promoter-TSS (NM_199150)	promoter-TSS (NM_199150)	-5	NM_199150	232972	Mm.293074	NM_199150	ENSMUSG00000045587	BC049730	Lypd10	cDNA sequence BC049730	protein-coding
mm_91674.1	chr10	43221373	43221388	-	1	NA	promoter-TSS (NM_001168289)	promoter-TSS (NM_001168289)	-106	NM_027772	71365	Mm.490430	NM_027772	ENSMUSG00000038240	Pdss2	5430420P03Rik|Gm60|Plmp|kd|mDLP1	prenyl (solanesyl) diphosphate synthase, subunit 2	protein-coding
mm_47509.1	chr5	124052214	124052227	-	1	NA	Intergenic	Intergenic	-19960	NM_177876	330192	Mm.4079	NM_177876	ENSMUSG00000066278	Vps37b	2300007F24Rik|AI415429|BC026744	vacuolar protein sorting 37B	protein-coding
mm_16496.1	chr2	181187598	181187618	+	1	NA	5' UTR (NM_025598, exon 2 of 5)	5' UTR (NM_025598, exon 2 of 5)	265	NM_025598	66496	Mm.213943	NM_025598	ENSMUSG00000016344	Ppdpf	0610012G23Rik|2610317A05Rik|2700038C09Rik|3110053G12Rik	pancreatic progenitor cell differentiation and proliferation factor	protein-coding
mm_30049.1	chr3	136325929	136325947	-	1	NA	exon (NM_001033350, exon 1 of 17)	exon (NM_001033350, exon 1 of 17)	128	NM_001310749	242248	Mm.30832	NM_001033350	ENSMUSG00000037922	Bank1	A530094C12Rik|AI451642|AVIEF|BANK	B cell scaffold protein with ankyrin repeats 1	protein-coding
mm_10245.1	chr2	8950152	8950157	+	1	NA	Intergenic	Intergenic	-239361	NR_038180	73438	Mm.23558	NR_038180	ENSMUSG00000085580	1700061F12Rik	-	RIKEN cDNA 1700061F12 gene	ncRNA
mm_172269.1	chr6	79284963	79284964	-	1	NA	Intergenic	BGLII_Mus|LTR|ERVK	252921	NR_040301	100504701	Mm.400420	NR_040301	ENSMUSG00000108072	Gm20362	-	predicted gene, 20362	ncRNA
mm_7807.1	chr1	131527267	131527293	-	1	NA	promoter-TSS (NM_001081011)	promoter-TSS (NM_001081011)	81	NM_001081011	14270	Mm.276259	NM_019520	ENSMUSG00000026425	Srgap2	9930124L22Rik|AI448945|FBP2|Fnbp2|srGAP3	SLIT-ROBO Rho GTPase activating protein 2	protein-coding
mm_123051.1	chr14	55628358	55628373	-	1	NA	intron (NM_024267, intron 24 of 29)	intron (NM_024267, intron 24 of 29)	7313	NM_024267	75751	Mm.27546	NM_024267	ENSMUSG00000002319	Ipo4	8430408O15Rik|AA409693|Imp4a|RanBP4	importin 4	protein-coding
mm_133004.1	chr16	55967130	55967143	+	1	NA	exon (NM_024218, exon 3 of 6)	exon (NM_024218, exon 3 of 6)	861	NM_024218	68193	Mm.29221	NM_024218	ENSMUSG00000098274	Rpl24	0610008L05Rik|Bst	ribosomal protein L24	protein-coding
mm_35557.1	chr4	41569435	41569465	-	1	NA	promoter-TSS (NM_027993)	promoter-TSS (NM_027993)	77	NM_001159583	71901	Mm.39215	NM_027993	ENSMUSG00000028439	Fam219a	2310028H24Rik	family with sequence similarity 219, member A	protein-coding
mm_86954.1	chr10	24920052	24920057	+	1	NA	intron (NM_007482, intron 3 of 7)	intron (NM_007482, intron 3 of 7)	7416	NM_007482	11846	Mm.154144	NM_007482	ENSMUSG00000019987	Arg1	AI|AI256583|Arg-1|PGIF	arginase, liver	protein-coding
mm_28338.1	chr3	89387881	89387902	-	1	NA	intron (NM_009565, intron 1 of 2)	intron (NM_009565, intron 1 of 2)	-3973	NR_040403	545539	Mm.393389	NR_040403	ENSMUSG00000074466	Gm15417	ENSMUSG00000074466|OTTMUSG00000021274	predicted gene 15417	ncRNA
mm_51366.1	chr6	72636376	72636378	+	1	NA	non-coding (NR_040422, exon 4 of 5)	non-coding (NR_040422, exon 4 of 5)	6546	NR_040421	100038714	Mm.321330	NR_040421		Gm15401	ENSMUSG00000072999|OTTMUSG00000021199	predicted gene 15401	ncRNA
mm_135390.1	chr16	44332843	44332868	-	1	NA	promoter-TSS (NM_001159419)	promoter-TSS (NM_001159419)	-17	NM_001159419	320007	Mm.242144	NM_198034	ENSMUSG00000022696	Sidt1	AW045928|B830021E24Rik	SID1 transmembrane family, member 1	protein-coding
mm_168679.1	chr1	195279287	195279288	-	1	NA	Intergenic	L1Md_F2|LINE|L1	-102572	NM_007758	12902	Mm.235387	NM_007758	ENSMUSG00000026616	Cr2	C3DR|CD21|CD35|Cr-1|Cr-2|Cr1	complement receptor 2	protein-coding
mm_91148.1	chr10	20175330	20175346	-	1	NA	intron (NM_001198635, intron 1 of 17)	intron (NM_001198635, intron 1 of 17)	26418	NM_001198635	17761	Mm.20928	NM_008635	ENSMUSG00000019996	Map7	E-MAP-115|MAP-7|Mtap7|R75000|mshi|mste|ste	microtubule-associated protein 7	protein-coding
mm_108453.1	chr12	82616886	82616971	+	1	NA	promoter-TSS (NM_001282061)	promoter-TSS (NM_001282061)	3	NM_015812	50779	Mm.126176	NM_015812	ENSMUSG00000021219	Rgs6	-	regulator of G-protein signaling 6	protein-coding
mm_54152.1	chr6	22356177	22356190	-	1	NA	promoter-TSS (NM_138587)	promoter-TSS (NM_138587)	-102	NM_138587	27999	Mm.490307	NM_138587	ENSMUSG00000029672	Fam3c	D6Wsu176e|Ilei	family with sequence similarity 3, member C	protein-coding
mm_62507.1	chr7	102101737	102101752	+	1	NA	promoter-TSS (NM_009710)	promoter-TSS (NM_009710)	1	NM_009710	11870	Mm.261071	NM_009710	ENSMUSG00000030996	Art1	ADPRT|ARTC1|Yac-1	ADP-ribosyltransferase 1	protein-coding
mm_164903.1	chr18	67610785	67610800	-	1	NA	Intergenic	CpG	30544	NM_001081073	225659	Mm.111928	NM_001081073	ENSMUSG00000073542	Cep76	6230425F05Rik|9630013E05	centrosomal protein 76	protein-coding
mm_97227.1	chr11	75651222	75651246	+	1	NA	promoter-TSS (NM_001080774)	promoter-TSS (NM_001080774)	-275	NM_008659	17913	Mm.234502	NM_008659	ENSMUSG00000017774	Myo1c	C80397|MMIb|MYO1E|NMI|mm1beta|myr2	myosin IC	protein-coding
mm_94600.1	chr11	12037645	12037659	+	1	NA	promoter-TSS (NM_010345)	promoter-TSS (NM_010345)	-232	NM_010345	14783	Mm.273117	NM_010345	ENSMUSG00000020176	Grb10	5730571D09Rik|AI325020|Meg1|mKIAA0207	growth factor receptor bound protein 10	protein-coding
mm_79148.1	chr9	47712780	47712787	+	1	NA	intron (NM_001025600, intron 1 of 8)	intron (NM_001025600, intron 1 of 8)	105425	NR_046048	100038460	Mm.447649	NR_046048		Gm10677	ENSMUSG00000074363	predicted gene 10677	ncRNA
mm_139371.1	chr17	51829666	51829684	+	1	NA	intron (NM_001163632, intron 1 of 10)	intron (NM_001163632, intron 1 of 10)	2972	NM_009122	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_166048.1	chr4	131046575	131046576	+	1	NA	Intergenic	Intergenic	-36101	NR_130167	77835	Mm.348412	NR_130167	ENSMUSG00000086262	A930031H19Rik	A930004I12Rik	RIKEN cDNA A930031H19 gene	ncRNA
mm_49094.1	chr6	7562363	7562373	+	1	NA	intron (NM_009311, intron 6 of 6)	intron (NM_009311, intron 6 of 6)	7297	NM_009311	21333	Mm.1440	NM_009311	ENSMUSG00000061762	Tac1	4930528L02Rik|NK-1|NK1|Nkna|PPT-A|PPTA|SP	tachykinin 1	protein-coding
mm_153791.1	chr19	45903818	45903821	-	1	NA	intron (NM_198296, intron 20 of 25)	intron (NM_198296, intron 20 of 25)	-87756	NM_145703	80906	Mm.213204	NM_030716	ENSMUSG00000025221	Kcnip2	KChIP2	Kv channel-interacting protein 2	protein-coding
mm_159019.1	chr1	171360818	171360818	-	1	NA	promoter-TSS (NM_001033039)	promoter-TSS (NM_001033039)	-20	NM_001033039	68874	Mm.10756	NM_001033039	ENSMUSG00000045259	Klhdc9	1190002J23Rik|AA087357|ESTM31	kelch domain containing 9	protein-coding
mm_65863.1	chr7	29397679	29397709	-	1	NA	intron (NM_001081028, intron 4 of 22)	intron (NM_001081028, intron 4 of 22)	93689	NM_013874	29861	Mm.101885	NM_013874	ENSMUSG00000030584	Dpf1	Neud4	D4, zinc and double PHD fingers family 1	protein-coding
mm_97483.1	chr11	78324467	78324479	+	1	NA	exon (NM_009657, exon 1 of 8)	exon (NM_009657, exon 1 of 8)	275	NM_009657	11676	Mm.7729	NM_009657	ENSMUSG00000017390	Aldoc	AI847350|AU040929|Aldo3|Scrg2	aldolase C, fructose-bisphosphate	protein-coding
mm_110484.1	chr12	51925430	51925438	-	1	NA	intron (NM_177171, intron 14 of 35)	intron (NM_177171, intron 14 of 35)	45887	NM_177171	320487	Mm.131941	NM_177171	ENSMUSG00000035181	Heatr5a	C230081H03Rik|D930036F22Rik|mKIAA1316	HEAT repeat containing 5A	protein-coding
mm_151732.1	chr19	4877883	4877899	-	1	NA	promoter-TSS (NM_001168517)	promoter-TSS (NM_001168517)	18	NM_013456	11474	Mm.5316	NM_013456	ENSMUSG00000006457	Actn3	-	actinin alpha 3	protein-coding
mm_105981.1	chr11	115612492	115612503	-	1	NA	promoter-TSS (NM_027162)	promoter-TSS (NM_027162)	6	NM_027162	69674	Mm.390387	NM_027162	ENSMUSG00000020743	Mif4gd	1110014L05Rik|2310075G12Rik	MIF4G domain containing	protein-coding
mm_2139.1	chr1	88087853	88087867	+	1	NA	intron (NM_201644, intron 1 of 4)	intron (NM_201644, intron 1 of 4)	-7141	NM_201642	394432	Mm.300095	NM_201642	ENSMUSG00000090124	Ugt1a7c	A10'|A13|Ugt1a10	UDP glucuronosyltransferase 1 family, polypeptide A7C	protein-coding
mm_98050.1	chr11	85739932	85739947	+	1	NA	intron (NM_138681, intron 24 of 25)	intron (NM_138681, intron 24 of 25)	-20195	NR_045875	71489	Mm.442482	NR_045875	ENSMUSG00000086199	Bcas3os1	8430403D17Rik	breast carcinoma amplified sequence 3, opposite strand 1	ncRNA
mm_146275.1	chr18	77882352	77882362	+	1	NA	3' UTR (NM_013831, exon 15 of 15)	3' UTR (NM_013831, exon 15 of 15)	-56110	NM_001195633	100502841	Mm.297782	NM_001195633	ENSMUSG00000039840	Epg5	4732475F16|5430411K18Rik|AI661957|AW456499|mKIAA1632	ectopic P-granules autophagy protein 5 homolog (C. elegans)	protein-coding
mm_155928.1	chrX	103447743	103447758	+	1	NA	non-coding (NR_002844, exon 2 of 4)	non-coding (NR_002844, exon 2 of 4)	16233	NR_002844	22097	Mm.472939	NR_002844	ENSMUSG00000085715	Tsix	-	X (inactive)-specific transcript, opposite strand	ncRNA
mm_84191.1	chr9	60511004	60511016	-	1	NA	promoter-TSS (NM_001040426)	promoter-TSS (NM_001040426)	25	NM_001040426	207596	Mm.28791	NM_172444	ENSMUSG00000032289	Thsd4	ADAMTSL-6|ADAMTSL6|AI585901|Adamtsl4|B230114P05Rik	thrombospondin, type I, domain containing 4	protein-coding
mm_113790.1	chr13	45965212	45965231	+	1	NA	promoter-TSS (NM_009124)	promoter-TSS (NM_009124)	-230	NM_009124	20238	Mm.342683	NM_009124	ENSMUSG00000046876	Atxn1	2900016G23Rik|Atx1|C85907|ENSMUSG00000074917|Gm10786|Sca1	ataxin 1	protein-coding
mm_10649.1	chr2	20665853	20665885	+	1	NA	intron (NM_029895, intron 4 of 18)	intron (NM_029895, intron 4 of 18)	146356	NM_001177631	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding
mm_120123.1	chr14	59626310	59626320	+	1	NA	exon (NM_145463, exon 1 of 2)	exon (NM_145463, exon 1 of 2)	1034	NM_145463	219134	Mm.275409	NM_145463	ENSMUSG00000044461	Shisa2	9430059P22Rik|MAd2|Tmem46|mShisa|shisa	shisa family member 2	protein-coding
mm_162287.1	chr1	24613176	24613194	+	1	NA	Intergenic	Intergenic	-25748	NM_007733	12823	Mm.329196	NM_007733	ENSMUSG00000026141	Col19a1	-	collagen, type XIX, alpha 1	protein-coding
mm_8545.1	chr1	155099631	155099633	-	1	NA	promoter-TSS (NM_010500)	promoter-TSS (NM_010500)	4	NM_010500	15939	Mm.12246	NM_010500	ENSMUSG00000056708	Ier5	-	immediate early response 5	protein-coding
mm_147123.1	chr18	35822866	35822875	-	1	NA	Intergenic	Intergenic	-6948	NM_133687	67393	Mm.94560	NM_133687	ENSMUSG00000046668	Cxxc5	4930415K17Rik	CXXC finger 5	protein-coding
mm_17129.1	chr2	24834580	24834584	-	1	NA	intron (NM_001012518, intron 15 of 26)	intron (NM_001012518, intron 15 of 26)	-71430	NM_007579	12287	Mm.4424	NM_007579	ENSMUSG00000004113	Cacna1b	AW050276|AW060892|AW822256|BIII|Cav2.2|Cchn1a|alpha(1B)	calcium channel, voltage-dependent, N type, alpha 1B subunit	protein-coding
mm_148931.1	chr19	7018310	7018333	+	1	NA	intron (NM_153795, intron 2 of 14)	intron (NM_153795, intron 2 of 14)	1148	NM_153795	108101	Mm.157591	NM_153795	ENSMUSG00000024965	Fermt3	C79673|Kindlin3	fermitin family member 3	protein-coding
mm_171686.1	chr4	58391622	58391636	-	1	NA	Intergenic	L1Md_T|LINE|L1	49469	NR_037278	100526502		NR_037278	ENSMUSG00000093293	Mir3095	mir-3095|mmu-mir-3095	microRNA 3095	ncRNA
mm_143493.1	chr17	71475286	71475340	-	1	NA	promoter-TSS (NM_028887)	promoter-TSS (NM_028887)	30	NM_028887	74355	Mm.194450	NM_028887	ENSMUSG00000024054	Smchd1	4931400A14Rik|AW554188|MommeD1|mKIAA0650	SMC hinge domain containing 1	protein-coding
mm_51176.1	chr6	70726710	70726720	+	1	NA	Intergenic	Intergenic	65460	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_163780.1	chr13	120044352	120044364	-	1	NA	intron (NM_001302966, intron 4 of 5)	intron (NM_001302966, intron 4 of 5)	7846	NM_001302966	100861753	Mm.165042	NM_001302966	ENSMUSG00000095609	Gm21188	-	predicted gene, 21188	protein-coding
mm_16936.1	chr2	14056030	14056044	-	1	NA	promoter-TSS (NM_013935)	promoter-TSS (NM_013935)	-2	NM_013935	30963	Mm.241205	NM_013935	ENSMUSG00000063275	Hacd1	Ptpla	3-hydroxyacyl-CoA dehydratase 1	protein-coding
mm_37793.1	chr4	130519978	130519983	-	1	NA	Intergenic	Intergenic	54056	NM_025998	67149	Mm.423029	NM_025998	ENSMUSG00000078532	Nkain1	2610200G18Rik|2810426C15Rik	Na+/K+ transporting ATPase interacting 1	protein-coding
mm_94609.1	chr11	16257707	16257808	+	1	NA	promoter-TSS (NM_001290539)	promoter-TSS (NM_001290539)	33	NM_145967	211739	Mm.284015	NM_145967	ENSMUSG00000048834	Vstm2a	Vstm2	V-set and transmembrane domain containing 2A	protein-coding
mm_139119.1	chr17	47436617	47436639	+	1	NA	promoter-TSS (NM_145489)	promoter-TSS (NM_145489)	-11	NM_145489	224833	Mm.218444	NM_145489	ENSMUSG00000034382	AI661453	-	expressed sequence AI661453	protein-coding
mm_144020.1	chr17	89910440	89910446	-	1	NA	Intergenic	Lx2A1|LINE|L1	177925	NM_001346962	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_61239.1	chr7	65644871	65644878	+	1	NA	promoter-TSS (NM_172310)	promoter-TSS (NM_172310)	-24	NM_172310	272396	Mm.35127	NM_172310	ENSMUSG00000030515	Tarsl2	A530046H20Rik	threonyl-tRNA synthetase-like 2	protein-coding
mm_85281.1	chr9	99692180	99692204	-	1	NA	3' UTR (NM_001194922, exon 5 of 5)	3' UTR (NM_001194922, exon 5 of 5)	17871	NM_019815	56492	Mm.386784	NM_019815	ENSMUSG00000032473	Cldn18	-	claudin 18	protein-coding
mm_93995.1	chr10	127534571	127534594	-	1	NA	promoter-TSS (NM_183297)	promoter-TSS (NM_183297)	-23	NM_183297	104080	Mm.437200	NM_183297	ENSMUSG00000040258	Nxph4	1110036M10Rik|AI851051	neurexophilin 4	protein-coding
mm_16257.1	chr2	173273017	173273019	+	1	NA	intron (NM_022995, intron 1 of 3)	B4|SINE|B4	3515	NM_022995	65112	Mm.73682	NM_022995	ENSMUSG00000038400	Pmepa1	2210418I02Rik|AW455466|Erg1.2|N4wbp4|Stag1|Tmepai	prostate transmembrane protein, androgen induced 1	protein-coding
mm_102523.1	chr11	60913758	60913771	-	1	NA	promoter-TSS (NM_025294)	promoter-TSS (NM_025294)	28	NM_025294	24083	Mm.22780	NM_025294	ENSMUSG00000018931	Natd1	AI256713|F3-2|Gm16515|Gtlf3b	N-acetyltransferase domain containing 1	protein-coding
mm_161315.1	chr14	43819634	43819634	-	1	NA	promoter-TSS (NM_007894)	promoter-TSS (NM_007894)	5	NM_007894	13586	Mm.86948	NM_007894	ENSMUSG00000072601	Ear1	EAR-1|ECP 1|Raf1	eosinophil-associated, ribonuclease A family, member 1	protein-coding
mm_129049.1	chr15	75352124	75352126	-	1	NA	Intergenic	Intergenic	79704	NR_108041	105892	Mm.38909	NM_001039720	ENSMUSG00000053168	9030619P08Rik	-	lymphocyte antigen 6 complex pseudogene	pseudo
mm_120862.1	chr14	75229448	75229519	+	1	NA	3' UTR (NM_001247984, exon 16 of 16)	3' UTR (NM_001247984, exon 16 of 16)	-12804	NM_019775	56373	Mm.24242	NM_019775	ENSMUSG00000021999	Cpb2	1110032P04Rik|4930405E17Rik|AI255929|CPR|Cpu|TAFI	carboxypeptidase B2 (plasma)	protein-coding
mm_109278.1	chr12	109547113	109547123	+	1	NA	intron (NR_027651, intron 5 of 8)	intron (NR_027651, intron 5 of 8)	1720	NR_003633	17263	Mm.289645	NM_144513	ENSMUSG00000021268	Meg3	2900016C05Rik|3110050O07Rik|6330408G06Rik|AI425946|AW108224|D12Bwg1266e|Gtl2|R74756|R75394	maternally expressed 3	ncRNA
mm_79864.1	chr9	65032767	65032790	+	1	NA	intron (NM_028906, intron 1 of 20)	CpG	320	NM_028906	74388	Mm.202749	NM_028906	ENSMUSG00000032393	Dpp8	2310004I03Rik|4932434F09Rik|AI666706|DPP VIII	dipeptidylpeptidase 8	protein-coding
mm_160535.1	chr9	39669131	39669131	+	1	NA	promoter-TSS (NM_001011827)	promoter-TSS (NM_001011827)	72	NM_001011827	258087	Mm.377346	NM_001011827	ENSMUSG00000064110	Olfr963	MOR224-13|MOR224-7P	olfactory receptor 963	protein-coding
mm_155657.1	chrX	86044187	86044203	+	1	NA	promoter-TSS (NM_028554)	promoter-TSS (NM_028554)	-4	NM_028554	73495	Mm.159020	NM_028554	ENSMUSG00000035454	Samt3	1700072E05Rik	spermatogenesis associated multipass transmembrane protein 3	protein-coding
mm_89121.1	chr10	84838144	84838153	+	1	NA	promoter-TSS (NM_027689)	promoter-TSS (NM_027689)	0	NM_027689	71137	Mm.79070	NM_027689	ENSMUSG00000020037	Rfx4	4933412G19Rik|NYD-sp10	regulatory factor X, 4 (influences HLA class II expression)	protein-coding
mm_156188.1	chrX	133908607	133908634	+	1	NA	5' UTR (NM_026838, exon 1 of 12)	5' UTR (NM_026838, exon 1 of 12)	195	NM_001083895	68792	Mm.263553	NM_026838	ENSMUSG00000031253	Srpx2	1110039C07Rik|SRP|SRPUL	sushi-repeat-containing protein, X-linked 2	protein-coding
mm_47942.1	chr5	135394175	135394196	-	1	NA	exon (NM_148932, exon 1 of 13)	exon (NM_148932, exon 1 of 13)	361	NM_148932	107939	Mm.28399	NM_148932	ENSMUSG00000053293	Pom121	2610027A18Rik|C80273|mKIAA0618	nuclear pore membrane protein 121	protein-coding
mm_132440.1	chr16	35938973	35939072	+	1	NA	promoter-TSS (NM_001013371)	promoter-TSS (NM_001013371)	5	NM_001013371	209200	Mm.390852	NM_001013371	ENSMUSG00000049502	Dtx3l	AU042200|BC023741	deltex 3-like, E3 ubiquitin ligase	protein-coding
mm_111416.1	chr12	91558019	91558039	-	1	NA	3' UTR (NM_031391, exon 9 of 9)	3' UTR (NM_031391, exon 9 of 9)	31620	NM_031391	83602	Mm.275728	NM_031391	ENSMUSG00000020962	Gtf2a1	6330549H03Rik|AA536742|AA959775|AW060250|TfIIAa/b|Tfiia1	general transcription factor II A, 1	protein-coding
mm_49446.1	chr6	29348115	29348123	+	1	NA	promoter-TSS (NM_184053)	promoter-TSS (NM_184053)	13	NM_184053	12321	Mm.392075	NM_007594	ENSMUSG00000029767	Calu	9530075H20Rik	calumenin	protein-coding
mm_65047.1	chr7	18646988	18647006	-	1	NA	3' UTR (NM_027403, exon 5 of 5)	3' UTR (NM_027403, exon 5 of 5)	9728	NM_027403	72242	Mm.326858	NM_027403	ENSMUSG00000070796	Psg21	1600019C01Rik|1600025N01Rik|1600026N13Rik|cea8	pregnancy-specific glycoprotein 21	protein-coding
mm_25278.1	chr3	105452150	105452177	+	1	NA	promoter-TSS (NM_001039347)	promoter-TSS (NM_001039347)	-167	NM_001039347	56543	Mm.44530	NM_019931	ENSMUSG00000040896	Kcnd3	AW045978|Kncd3|Kv4.3	potassium voltage-gated channel, Shal-related family, member 3	protein-coding
mm_146497.1	chr18	3281037	3281106	-	1	NA	promoter-TSS (NM_001311067)	promoter-TSS (NM_001311067)	61	NM_001311066	12916	Mm.5244	NM_013498	ENSMUSG00000063889	Crem	ICER|ICERI	cAMP responsive element modulator	protein-coding
mm_46632.1	chr5	108519131	108519141	-	1	NA	3' UTR (NM_007756, exon 4 of 4)	3' UTR (NM_007756, exon 4 of 4)	30891	NM_007756	12889	Mm.5195	NM_007756	ENSMUSG00000033615	Cplx1	921-S	complexin 1	protein-coding
mm_161393.1	chr14	99099422	99099422	+	1	NA	promoter-TSS (NM_029320)	promoter-TSS (NM_029320)	-2	NM_029320	52023	Mm.22835	NM_029320	ENSMUSG00000022064	Pibf1	-	progesterone immunomodulatory binding factor 1	protein-coding
mm_104177.1	chr11	87749407	87749423	-	1	NA	Intergenic	Intergenic	-7449	NR_029555	387160		NR_029555	ENSMUSG00000105196	Mir142	Mirn142|miR-142|mir-142a|mmu-mir-142|mmu-mir-142a	microRNA 142	ncRNA
mm_12967.1	chr2	90732740	90732758	+	1	NA	intron (NM_021512, intron 34 of 36)	intron (NM_021512, intron 34 of 36)	-12621	NM_018828	55935	Mm.489638	NM_018828	ENSMUSG00000008200	Fnbp4	FBP30|Fnbp30|mKIAA1014	formin binding protein 4	protein-coding
mm_56214.1	chr6	89362554	89362574	-	1	NA	promoter-TSS (NM_008881)	promoter-TSS (NM_008881)	49	NM_008881	18844	Mm.3789	NM_008881	ENSMUSG00000030084	Plxna1	2600013D04Rik|NOV|PlexA1|Plxn1|mKIAA4053	plexin A1	protein-coding
mm_63495.1	chr7	127777316	127777367	+	1	NA	promoter-TSS (NM_178029)	promoter-TSS (NM_178029)	-48	NM_178029	233904	Mm.435494	NM_010940	ENSMUSG00000042308	Setd1a	BC010250|KMT2F|Nsccn1|mKIAA0339|mNSC1	SET domain containing 1A	protein-coding
mm_65242.1	chr7	19820205	19820214	-	1	NA	intron (NM_033601, intron 1 of 8)	intron (NM_033601, intron 1 of 8)	2546	NM_033601	12051	Mm.439658	NM_033601	ENSMUSG00000053175	Bcl3	AI528691|Bcl-3	B cell leukemia/lymphoma 3	protein-coding
mm_7316.1	chr1	98095597	98095648	-	1	NA	promoter-TSS (NM_013626)	promoter-TSS (NM_013626)	10	NM_013626	18484	Mm.5121	NM_013626	ENSMUSG00000026335	Pam	PHM	peptidylglycine alpha-amidating monooxygenase	protein-coding
mm_162216.1	chrX	136957991	136957991	-	1	NA	promoter-TSS (NM_001080967)	promoter-TSS (NM_001080967)	-12	NM_001080967	100034363	Mm.381904	NM_001080967	ENSMUSG00000089996	Tmsb15b2	Tb15c	thymosin beta 15b2	protein-coding
mm_153509.1	chr19	41363941	41363957	-	1	NA	intron (NM_031376, intron 2 of 16)	B2_Mm2|SINE|B2	21121	NM_031376	83490	Mm.222266	NM_031376	ENSMUSG00000025017	Pik3ap1	1810044J04Rik|BCAP	phosphoinositide-3-kinase adaptor protein 1	protein-coding
mm_134008.1	chr16	4870691	4870697	-	1	NA	Intergenic	B3|SINE|B2	9157	NM_145359	207740	Mm.268895	NM_145359	ENSMUSG00000039568	Ubald1	1500031H01Rik|BC013706|Fam100a	UBA-like domain containing 1	protein-coding
mm_153430.1	chr19	40940218	40940229	-	1	NA	exon (NM_008528, exon 12 of 17)	exon (NM_008528, exon 12 of 17)	45518	NM_028319	72672	Mm.313523	NM_028319	ENSMUSG00000049164	Zfp518a	2810401C22Rik|6330417C12Rik|AI426493|Zfp518|Znf518|Znf518a|mKIAA0335	zinc finger protein 518A	protein-coding
mm_10458.1	chr2	14294814	14294826	+	1	NA	exon (NM_008625, exon 15 of 30)	exon (NM_008625, exon 15 of 30)	33817	NR_030609	100124488		NR_030609	ENSMUSG00000077897	Mir511	Mirn511|mir-511|mmu-mir-511	microRNA 511	ncRNA
mm_68894.1	chr7	126448753	126448759	-	1	NA	exon (NM_007504, exon 15 of 23)	exon (NM_007504, exon 15 of 23)	14317	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_161092.1	chr12	88181668	88181668	-	1	NA	intron (NM_001105254, intron 1 of 3)	intron (NM_001105254, intron 1 of 3)	226	NM_001105254	100039315	Mm.426539	NM_001105254	ENSMUSG00000066027	Gm10436	ENSMUSG00000072907	predicted gene 10436	protein-coding
mm_45098.1	chr5	44634380	44634382	-	1	NA	intron (NM_001347349, intron 2 of 7)	intron (NM_001347349, intron 2 of 7)	165365	NM_001347349	16826	Mm.25785	NM_010698	ENSMUSG00000039706	Ldb2	AI035351|AW146358|CLIM1|CLP-36|Ldb3	LIM domain binding 2	protein-coding
mm_38450.1	chr4	140236824	140236837	-	1	NA	intron (NM_198610, intron 1 of 9)	intron (NM_198610, intron 1 of 9)	9981	NM_198610	230868	Mm.298731	NM_198610	ENSMUSG00000040972	Igsf21	BC055811|Gm141	immunoglobulin superfamily, member 21	protein-coding
mm_119817.1	chr14	54225947	54225958	+	1	NA	Intergenic	Intergenic	27977	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_147300.1	chr18	39519266	39519274	-	1	NA	Intergenic	Intergenic	-32025	NM_008173	14815	Mm.129481	NM_008173	ENSMUSG00000024431	Nr3c1	GR|Grl-1|Grl1	nuclear receptor subfamily 3, group C, member 1	protein-coding
mm_127791.1	chr15	3582330	3582351	-	1	NA	promoter-TSS (NM_001286370)	promoter-TSS (NM_001286370)	-498	NM_001286370	14600	Mm.3986	NM_010284	ENSMUSG00000055737	Ghr	GHBP|GHR/BP	growth hormone receptor	protein-coding
mm_98371.1	chr11	94044125	94044136	+	1	NA	promoter-TSS (NM_001199205)	promoter-TSS (NM_001199205)	-75	NM_001025430	70834	Mm.260737	NM_027569	ENSMUSG00000020859	Spag9	3110018C07Rik|4733401I23Rik|4831406C20Rik|AW552012|JLP|JSAP2|JSAP2a|Jip4|Mapk8ip4|syd1	sperm associated antigen 9	protein-coding
mm_140072.1	chr17	75005808	75005823	+	1	NA	5' UTR (NM_019919, exon 1 of 34)	5' UTR (NM_019919, exon 1 of 34)	286	NM_019919	268977	Mm.269747	NM_019919	ENSMUSG00000001870	Ltbp1	9430031G15Rik|9830146M04|Ltbp-1|Ltbp1L|TGF-beta1-BP-1|Tgfb|b2b1000Clo	latent transforming growth factor beta binding protein 1	protein-coding
mm_19937.1	chr2	116065799	116065853	-	1	NA	promoter-TSS (NM_010825)	promoter-TSS (NM_010825)	-768	NM_010825	17536	Mm.247566	NM_010825	ENSMUSG00000027210	Meis2	A430109D20Rik|Mrg1|Stra10	Meis homeobox 2	protein-coding
mm_159083.1	chr2	28916267	28916267	-	1	NA	5' UTR (NM_019446, exon 1 of 3)	5' UTR (NM_019446, exon 1 of 3)	154	NM_019446	54422	Mm.21390	NM_019446	ENSMUSG00000026805	Barhl1	Dres115|MBH2	BarH-like 1 (Drosophila)	protein-coding
mm_19986.1	chr2	118547542	118547567	-	1	NA	promoter-TSS (NM_001311140)	promoter-TSS (NM_001311140)	45	NM_001331221	171543	Mm.210125	NM_138313	ENSMUSG00000040093	Bmf	AW260063|AW411872	BCL2 modifying factor	protein-coding
mm_70828.1	chr8	23142980	23142998	+	1	NA	promoter-TSS (NR_037293)	promoter-TSS (NR_037293)	-327	NR_037293	100526510		NR_037293	ENSMUSG00000106471	Mir3107	mir-486b|mmu-mir-3107|mmu-mir-486b	microRNA 3107	ncRNA
mm_166450.1	chr5	137268727	137268751	-	1	NA	Intergenic	Intergenic	-19515	NM_009599	11423	Mm.255464	NM_009599	ENSMUSG00000023328	Ache	-	acetylcholinesterase	protein-coding
mm_25857.1	chr3	129757916	129757925	+	1	NA	intron (NR_040589, intron 3 of 4)	ERVB3_1-LTR_MM|LTR|ERVK	-2598	NM_010113	13645	Mm.252481	NM_010113	ENSMUSG00000028017	Egf	AI790464	epidermal growth factor	protein-coding
mm_144430.1	chr18	21001795	21001810	+	1	NA	promoter-TSS (NM_207623)	promoter-TSS (NM_207623)	-155	NM_001303011	56515	Mm.253542	NM_019706	ENSMUSG00000024317	Rnf138	2410015A17Rik|2810480D20Rik|STRIN|Trif|Trif-d	ring finger protein 138	protein-coding
mm_12412.1	chr2	70533025	70533034	+	1	NA	intron (NM_025744, intron 9 of 12)	intron (NM_025744, intron 9 of 12)	24210	NM_025744	66748	Mm.423014	NM_025744	ENSMUSG00000075302	Erich2	4933404M02Rik	glutamate rich 2	protein-coding
mm_106977.1	chr12	9574438	9574448	+	1	NA	promoter-TSS (NM_011859)	promoter-TSS (NM_011859)	1	NM_011859	23967	Mm.45055	NM_011859	ENSMUSG00000048387	Osr1	Odd1|Osr	odd-skipped related 1 (Drosophila)	protein-coding
mm_171974.1	chr5	89148381	89148381	+	1	NA	intron (NM_001197147, intron 12 of 25)	(CAG)n|Simple_repeat|Simple_repeat	261121	NM_018760	54403	Mm.41044	NM_018760	ENSMUSG00000060961	Slc4a4	AI835705|NBC|NBC1	solute carrier family 4 (anion exchanger), member 4	protein-coding
mm_106287.1	chr11	118202754	118202772	-	1	NA	intron (NM_001112699, intron 1 of 12)	intron (NM_001112699, intron 1 of 12)	9979	NM_001112700	19157	Mm.86413	NM_011180	ENSMUSG00000017132	Cyth1	CLM1|CTH-1|CYTIP|Pscd1	cytohesin 1	protein-coding
mm_139813.1	chr17	66485985	66486022	+	1	NA	Intergenic	Intergenic	33667	NM_024448	19328	Mm.248313	NM_024448	ENSMUSG00000023460	Rab12	2900054P15Rik|AW555448|C77700	RAB12, member RAS oncogene family	protein-coding
mm_25537.1	chr3	115683144	115683170	+	1	NA	Intergenic	Intergenic	31898	NM_007901	13609	Mm.982	NM_007901	ENSMUSG00000045092	S1pr1	AI849002|Edg1|Lpb1|S1p|S1p1	sphingosine-1-phosphate receptor 1	protein-coding
mm_132315.1	chr16	33726740	33726779	+	1	NA	exon (NM_175256, exon 4 of 15)	exon (NM_175256, exon 4 of 15)	42293	NM_175256	77446	Mm.245741	NM_172934	ENSMUSG00000075254	Heg1	4632417D23Rik|5530401I02Rik|9530025L16Rik|BC038614|Gm629|OTTMUSG00000027315	heart development protein with EGF-like domains 1	protein-coding
mm_81349.1	chr9	108568019	108568059	+	1	NA	promoter-TSS (NR_029577)	promoter-TSS (NR_029577)	-280	NR_029577	387186		NR_029577	ENSMUSG00000105497	Mir191	Mirn191|mir-191|mmu-mir-191	microRNA 191	ncRNA
mm_39533.1	chr5	21375721	21375731	+	1	NA	exon (NM_008013, exon 2 of 2)	exon (NM_008013, exon 2 of 2)	3053	NM_008013	14190	Mm.292100	NM_008013	ENSMUSG00000039899	Fgl2	AI385601|musfiblp	fibrinogen-like protein 2	protein-coding
mm_84441.1	chr9	66124825	66124846	-	1	NA	promoter-TSS (NM_019727)	promoter-TSS (NM_019727)	51	NM_019727	56440	Mm.271891	NM_019727	ENSMUSG00000032382	Snx1	-	sorting nexin 1	protein-coding
mm_41801.1	chr5	103753925	103753935	+	1	NA	promoter-TSS (NM_133919)	promoter-TSS (NM_133919)	-232	NM_133919	17355	Mm.6949	NM_133919	ENSMUSG00000029313	Aff1	9630032B01Rik|AW319193|Af4|Mllt2h|Rob	AF4/FMR2 family, member 1	protein-coding
mm_95554.1	chr11	52309664	52309672	+	1	NA	Intergenic	Intergenic	-26654	NM_001313981	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_130226.1	chr15	96273335	96273337	-	1	NA	non-coding (NR_030690, exon 1 of 1)	non-coding (NR_030690, exon 1 of 1)	1939	NR_030690	319722	Mm.103823	NR_030690		E330033B04Rik	-	RIKEN cDNA E330033B04 gene	ncRNA
mm_56202.1	chr6	88897381	88897397	-	1	NA	exon (NM_008564, exon 2 of 16)	exon (NM_008564, exon 2 of 16)	1391	NM_008564	17216	Mm.16711	NM_008564	ENSMUSG00000002870	Mcm2	AA959861|AW476101|BM28|CDCL1|Mcmd2|mKIAA0030	minichromosome maintenance complex component 2	protein-coding
mm_692.1	chr1	40580294	40580302	+	1	NA	promoter-TSS (NM_177084)	promoter-TSS (NM_177084)	71	NM_177084	110895	Mm.108602	NM_177084	ENSMUSG00000026065	Slc9a4	AW990558|D730009J23Rik|NHE4	solute carrier family 9 (sodium/hydrogen exchanger), member 4	protein-coding
mm_46854.1	chr5	113654913	113654917	-	1	NA	Intergenic	Intergenic	-4525	NM_008153	14747	Mm.5196	NM_008153	ENSMUSG00000042190	Cmklr1	ChemR23|DEZ|Gpcr27|mcmklr1	chemokine-like receptor 1	protein-coding
mm_163661.1	chr13	75825177	75825190	+	1	NA	Intergenic	Intergenic	-14703	NM_053108	93692	Mm.25844	NM_053108	ENSMUSG00000021591	Glrx	C86710|D13Wsu156e|Glrx1|Grx1|TTase	glutaredoxin	protein-coding
mm_25680.1	chr3	122131989	122132002	+	1	NA	intron (NM_007378, intron 24 of 49)	PB1D7|SINE|Alu	87535	NM_007378	11304	Mm.3918	NM_007378	ENSMUSG00000028125	Abca4	AW050280|Abc10|Abcr|D430003I15Rik|RmP	ATP-binding cassette, sub-family A (ABC1), member 4	protein-coding
mm_79259.1	chr9	50753094	50753098	+	1	NA	promoter-TSS (NM_024441)	promoter-TSS (NM_024441)	125	NM_009964	12955	Mm.178	NM_009964	ENSMUSG00000032060	Cryab	Crya-2|Crya2|HspB5|P23	crystallin, alpha B	protein-coding
mm_160863.1	chr11	59752458	59752458	+	1	NA	intron (NM_012027, intron 13 of 23)	intron (NM_012027, intron 13 of 23)	-12304	NR_045476	69320	Mm.443242	NR_045476	ENSMUSG00000086330	1700007J10Rik	4930573L17Rik	RIKEN cDNA 1700007J10 gene	ncRNA
mm_149432.1	chr19	11470741	11470754	+	1	NA	intron (NM_001166376, intron 1 of 2)	intron (NM_001166376, intron 1 of 2)	1379	NM_028595	73656	Mm.440719	NM_028595	ENSMUSG00000079419	Ms4a6c	2200009H22Rik|2210417N07Rik	membrane-spanning 4-domains, subfamily A, member 6C	protein-coding
mm_33129.1	chr4	124850791	124850809	+	1	NA	promoter-TSS (NM_001142727)	promoter-TSS (NM_001142727)	41	NM_153566	230734	Mm.258568	NM_153566	ENSMUSG00000028889	Yrdc	AV303379|BC023823|IRIP|ITIP	yrdC domain containing (E.coli)	protein-coding
mm_142915.1	chr17	53568319	53568332	-	1	NA	intron (NM_020005, intron 1 of 17)	intron (NM_020005, intron 1 of 17)	1354	NM_020005	18519	Mm.255025	NM_020005	ENSMUSG00000000708	Kat2b	A930006P13Rik|AI461839|AW536563|Pcaf|p/CAF	K(lysine) acetyltransferase 2B	protein-coding
mm_111040.1	chr12	79192249	79192284	-	1	NA	promoter-TSS (NM_021557)	promoter-TSS (NM_021557)	-447	NM_021557	17252	Mm.291799	NM_021557	ENSMUSG00000066441	Rdh11	2610319N22Rik|AI428145|AU045252|Arsdr1|C85936|CGI-82|HCBP12|M42C60|Mdt1|Psdr1|SCALD|UBE-1c1|Ube-1c	retinol dehydrogenase 11	protein-coding
mm_94353.1	chr11	4941151	4941166	+	1	NA	exon (NM_010904, exon 4 of 4)	exon (NM_010904, exon 4 of 4)	-6363	NM_001243043	11764	Mm.274816	NM_007454	ENSMUSG00000009090	Ap1b1	Adtb1|b2b1660Clo	adaptor protein complex AP-1, beta 1 subunit	protein-coding
mm_139239.1	chr17	47733060	47733060	+	1	NA	exon (NM_025973, exon 7 of 9)	exon (NM_025973, exon 7 of 9)	-3977	NM_001161722	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_23340.1	chr3	54692884	54692892	+	1	NA	promoter-TSS (NM_019995)	promoter-TSS (NM_019995)	-217	NM_019995	56790	Mm.486375	NM_019995	ENSMUSG00000027751	Supt20	AA667204|AI450544|D3Ertd300e|Fam48a|Supt20h|p38IP	suppressor of Ty 20	protein-coding
mm_62629.1	chr7	107595185	107595233	+	1	NA	5' UTR (NM_008905, exon 1 of 25)	5' UTR (NM_008905, exon 1 of 25)	158	NM_008905	19024	Mm.2817	NM_008905	ENSMUSG00000036528	Ppfibp2	Cclp1	PTPRF interacting protein, binding protein 2 (liprin beta 2)	protein-coding
mm_119908.1	chr14	54950524	54950541	+	1	NA	exon (NM_010856, exon 26 of 39)	exon (NM_010856, exon 26 of 39)	-1390	NR_029724	387204		NR_029724	ENSMUSG00000065432	Mir208a	Mirn208|Mirn208a|mir-208|mir-208a|mmu-mir-208	microRNA 208a	ncRNA
mm_87132.1	chr10	34283622	34283644	+	1	NA	3' UTR (NM_009433, exon 1 of 1)	3' UTR (NM_009433, exon 1 of 1)	1443	NM_009433	22110	Mm.20445	NM_009433	ENSMUSG00000047514	Tspyl1	Tspyl	testis-specific protein, Y-encoded-like 1	protein-coding
mm_170386.1	chr18	60376644	60376644	+	1	NA	intron (NM_021792, intron 1 of 1)	RMER17A|LTR|ERVK	615	NM_001146275	60440	Mm.261140	NM_021792	ENSMUSG00000054072	Iigp1	2900074L10Rik|AI046432|AW111922|Ifgga1|Iigp|Irga6	interferon inducible GTPase 1	protein-coding
mm_4647.1	chr1	180330471	180330493	+	1	NA	promoter-TSS (NR_003623)	promoter-TSS (NR_003623)	6	NM_001081175	320404	Mm.132535	NM_001081175	ENSMUSG00000038855	Itpkb	1110033J02Rik|E130307H12Rik	inositol 1,4,5-trisphosphate 3-kinase B	protein-coding
mm_25011.1	chr3	97922189	97922242	+	1	NA	3' UTR (NM_011342, exon 5 of 5)	3' UTR (NM_011342, exon 5 of 5)	-7958	NM_001033779	433632	Mm.212421	NM_001033779		Gm5544	EG433632	predicted gene 5544	protein-coding
mm_136083.1	chr16	84835485	84835534	-	1	NA	promoter-TSS (NM_001302216)	promoter-TSS (NM_001302216)	116	NM_016755	11957	Mm.353	NM_016755	ENSMUSG00000022890	Atp5j	CF6	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit F	protein-coding
mm_111838.1	chr12	107913605	107913609	-	1	NA	3' UTR (NM_021399, exon 3 of 3)	3' UTR (NM_021399, exon 3 of 3)	89807	NM_001079883	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_16160.1	chr2	172440651	172440657	+	1	NA	promoter-TSS (NM_025542)	promoter-TSS (NM_025542)	76	NM_025542	66404	Mm.25157	NM_025542	ENSMUSG00000027502	Rtfdc1	1700067C04Rik|2410001C21Rik|5730427M17Rik|AA589417	replication termination factor 2 domain containing 1	protein-coding
mm_119142.1	chr14	31217851	31217866	+	1	NA	promoter-TSS (NM_001025379)	promoter-TSS (NM_001025379)	-15	NM_001025379	218877	Mm.27812	NM_001025379	ENSMUSG00000021904	Sema3g	AK129018	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3G	protein-coding
mm_98248.1	chr11	88204397	88204437	+	1	NA	promoter-TSS (NM_024174)	promoter-TSS (NM_024174)	29	NM_001291271	64656	Mm.168680	NM_024174	ENSMUSG00000023723	Mrps23	D11Bwg1153e|MRP-S23|Rpms23|S23mt	mitochondrial ribosomal protein S23	protein-coding
mm_139831.1	chr17	69127415	69127445	+	1	NA	Intergenic	Intergenic	-29380	NM_013813	13823	Mm.131135	NM_013813	ENSMUSG00000024044	Epb41l3	4.1B|DAL1P|Dal1|Epb4.1l3|NBL3	erythrocyte membrane protein band 4.1 like 3	protein-coding
mm_28418.1	chr3	90433465	90433499	-	1	NA	5' UTR (NM_178876, exon 1 of 31)	5' UTR (NM_178876, exon 1 of 31)	154	NM_145540	229543	Mm.268564	NM_145540	ENSMUSG00000027933	Ints3	C77668	integrator complex subunit 3	protein-coding
mm_1682.1	chr1	74856346	74856365	+	1	NA	3' UTR (NM_009872, exon 1 of 1)	3' UTR (NM_009872, exon 1 of 1)	1326	NM_009872	12570	Mm.153833	NM_009872	ENSMUSG00000090071	Cdk5r2	B230310J22Rik|p39	cyclin-dependent kinase 5, regulatory subunit 2 (p39)	protein-coding
mm_87174.1	chr10	38965560	38965576	+	1	NA	promoter-TSS (NM_010681)	promoter-TSS (NM_010681)	53	NM_010681	16775	Mm.258065	NM_010681	ENSMUSG00000019846	Lama4	-	laminin, alpha 4	protein-coding
mm_93077.1	chr10	89434889	89434894	-	1	NA	intron (NM_001079876, intron 2 of 10)	intron (NM_001079876, intron 2 of 10)	9076	NM_001284344	237436	Mm.11982	NM_001033331	ENSMUSG00000074802	Gas2l3	8430435B07Rik|Gm240	growth arrest-specific 2 like 3	protein-coding
mm_140185.1	chr17	81046982	81046996	+	1	NA	intron (NM_028138, intron 5 of 9)	ORR1D1|LTR|ERVL-MaLR	18096	NM_028138	72167	Mm.273257	NM_028138	ENSMUSG00000024246	Thumpd2	2810025A12Rik	THUMP domain containing 2	protein-coding
mm_52126.1	chr6	97943271	97943297	+	1	NA	intron (NM_001113198, intron 2 of 9)	intron (NM_001113198, intron 2 of 9)	13467	NM_001178049	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_16692.1	chr2	6884941	6884957	-	1	NA	promoter-TSS (NM_001110228)	promoter-TSS (NM_001110228)	47	NM_010160	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_169419.1	chr1	45311664	45311667	+	1	NA	5' UTR (NM_009930, exon 1 of 51)	5' UTR (NM_009930, exon 1 of 51)	127	NM_009930	12825	Mm.249555	NM_009930	ENSMUSG00000026043	Col3a1	AW550625|Col3a-1|Tsk-2|Tsk2	collagen, type III, alpha 1	protein-coding
mm_50552.1	chr6	49047362	49047395	+	1	NA	exon (NM_053110, exon 5 of 11)	exon (NM_053110, exon 5 of 11)	10860	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_142347.1	chr17	43612134	43612157	-	1	NA	TTS (NM_013737)	TTS (NM_013737)	18154	NM_001161366	210510	Mm.329058	NM_198418	ENSMUSG00000040140	Tdrd6	AB097085|Tdr2	tudor domain containing 6	protein-coding
mm_137701.1	chr17	29090970	29091020	+	1	NA	promoter-TSS (NM_001111099)	promoter-TSS (NM_001111099)	16	NM_001111099	12575	Mm.195663	NM_007669	ENSMUSG00000023067	Cdkn1a	CAP20|CDKI|CIP1|Cdkn1|P21|SDI1|Waf1|mda6|p21Cip1|p21WAF	cyclin-dependent kinase inhibitor 1A (P21)	protein-coding
mm_152517.1	chr19	11283867	11283879	-	1	NA	promoter-TSS (NM_183190)	promoter-TSS (NM_183190)	-60	NM_183190	269063	Mm.268940	NM_183190	ENSMUSG00000054523	Ms4a5	-	membrane-spanning 4-domains, subfamily A, member 5	protein-coding
mm_106276.1	chr11	117991866	117991876	-	1	NA	intron (NM_133757, intron 1 of 9)	intron (NM_133757, intron 1 of 9)	5014	NM_133757	74451	Mm.28864	NM_133757	ENSMUSG00000017715	Pgs1	2610019F11Rik|4933424M23Rik|SAF	phosphatidylglycerophosphate synthase 1	protein-coding
mm_8347.1	chr1	150197476	150197492	-	1	NA	Intergenic	ID_B1|SINE|B4	-32536	NR_110420	102639566	Mm.417208	NR_110420	ENSMUSG00000097754	Ptgs2os2	Gm26687|Linc-cox2|Lincrna-cox2	prostaglandin-endoperoxide synthase 2, opposite strand 2	ncRNA
mm_116086.1	chr13	28554869	28554914	-	1	NA	intron (NR_045053, intron 7 of 8)	intron (NR_045053, intron 7 of 8)	155982	NR_105787	102466635		NR_105787	ENSMUSG00000099158	Mir6368	Gm27800|mmu-mir-6368	microRNA 6368	ncRNA
mm_20316.1	chr2	127314515	127314523	-	1	NA	Intergenic	Intergenic	-21640	NM_010090	13537	Mm.4729	NM_010090	ENSMUSG00000027368	Dusp2	PAC1	dual specificity phosphatase 2	protein-coding
mm_131898.1	chr16	23239355	23239357	+	1	NA	intron (NM_001252505, intron 1 of 7)	B1_Mus1|SINE|Alu	13335	NM_001252505	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_13195.1	chr2	93201578	93201615	+	1	NA	TTS (NM_183180)	TTS (NM_183180)	14012	NM_001025246	277414	Mm.41033	NM_001025246	ENSMUSG00000068735	Trp53i11	Tp53i11	transformation related protein 53 inducible protein 11	protein-coding
mm_106996.1	chr12	11266566	11266572	+	1	NA	promoter-TSS (NM_177331)	promoter-TSS (NM_177331)	683	NM_025695	67241	Mm.173953	NM_025695	ENSMUSG00000020608	Smc6	2810489L22Rik|3830418C19Rik|AA990493|AU018782|AW742439|SMC-6|Smc6l1|mKIAA4103	structural maintenance of chromosomes 6	protein-coding
mm_109982.1	chr12	12943101	12943112	-	1	NA	Intergenic	Intergenic	-1270	NM_008709	18109	Mm.16469	NM_008709	ENSMUSG00000037169	Mycn	N-myc|Nmyc|Nmyc-1|Nmyc1|bHLHe37|c-nmyc	v-myc avian myelocytomatosis viral related oncogene, neuroblastoma derived	protein-coding
mm_143789.1	chr17	81732973	81732975	-	1	NA	intron (NR_104580, intron 1 of 8)	B3|SINE|B2	5413	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_5162.1	chr1	10037923	10037931	-	1	NA	promoter-TSS (NM_026493)	promoter-TSS (NM_026493)	232	NR_102282	26754	Mm.402384	NM_013715	ENSMUSG00000025917	Cops5	AI303502|CSN5|Jab1|Mov34|Sgn5	COP9 signalosome subunit 5	protein-coding
mm_96615.1	chr11	69098938	69098985	+	1	NA	promoter-TSS (NM_011065)	promoter-TSS (NM_011065)	5	NM_011065	18626	Mm.7373	NM_011065	ENSMUSG00000020893	Per1	Hftm|Per|m-rigui|mPer1	period circadian clock 1	protein-coding
mm_126046.1	chr15	76904927	76904936	+	1	NA	exon (NM_012053, exon 4 of 6)	exon (NM_012053, exon 4 of 6)	860	NM_012053	26961	Mm.30066	NM_012053	ENSMUSG00000003970	Rpl8	-	ribosomal protein L8	protein-coding
mm_68540.1	chr7	113699770	113699771	-	1	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	-66228	NM_145584	233744	Mm.334160	NM_145584	ENSMUSG00000038156	Spon1	AI666765|AW455831|BC020531|D330035F22Rik|FSP	spondin 1, (f-spondin) extracellular matrix protein	protein-coding
mm_17837.1	chr2	34326684	34326692	-	1	NA	intron (NM_016768, intron 2 of 8)	AT_rich|Low_complexity|Low_complexity	45357	NM_001290576	18516	Mm.239941	NM_016768	ENSMUSG00000038718	Pbx3	-	pre B cell leukemia homeobox 3	protein-coding
mm_75033.1	chr8	32009529	32009541	-	1	NA	Intergenic	CpG	-91332	NM_178591	211323	Mm.153432	NM_178591	ENSMUSG00000062991	Nrg1	6030402G23Rik|ARIA|D230005F13Rik|GGF|GGFII|HRG|HRGalpha|Hgl|NDF|SMDF	neuregulin 1	protein-coding
mm_79945.1	chr9	65965938	65965940	+	1	NA	intron (NM_173185, intron 3 of 13)	intron (NM_173185, intron 3 of 13)	56929	NM_173185	214897	Mm.325816	NM_173185	ENSMUSG00000032384	Csnk1g1	9130020E21Rik	casein kinase 1, gamma 1	protein-coding
mm_130686.1	chr15	100681921	100681931	-	1	NA	intron (NM_033612, intron 5 of 7)	B1_Mur2|SINE|Alu	5994	NM_033612	109901	Mm.2131	NM_033612	ENSMUSG00000023031	Cela1	1810009A17Rik|1810062B19Rik|Ela-1|Ela1|PC-TsF	chymotrypsin-like elastase family, member 1	protein-coding
mm_119417.1	chr14	45276053	45276069	+	1	NA	intron (NM_027518, intron 3 of 6)	intron (NM_027518, intron 3 of 6)	42511	NM_015774	50527	Mm.387108	NM_015774	ENSMUSG00000021831	Ero1l	ERO1-L|Ero1a	ERO1-like (S. cerevisiae)	protein-coding
mm_21745.1	chr2	164804825	164804837	-	1	NA	promoter-TSS (NM_178375)	promoter-TSS (NM_178375)	50	NM_133240	170789	Mm.277878	NM_133240	ENSMUSG00000017307	Acot8	PTE-2|Pte1	acyl-CoA thioesterase 8	protein-coding
mm_42748.1	chr5	120753957	120754029	+	1	NA	3' UTR (NM_145226, exon 16 of 16)	3' UTR (NM_145226, exon 16 of 16)	-4145	NM_001347448	246728	Mm.260926	NM_145227	ENSMUSG00000032690	Oas2	Oasl11	2'-5' oligoadenylate synthetase 2	protein-coding
mm_89019.1	chr10	82127999	82128020	+	1	NA	promoter-TSS (NM_001163064)	promoter-TSS (NM_001163064)	-4	NM_001163064	216177	Mm.482395	NM_001163064	ENSMUSG00000078435	AU041133	-	expressed sequence AU041133	protein-coding
mm_169879.1	chr16	37834091	37834099	+	1	NA	3' UTR (NM_008047, exon 11 of 11)	3' UTR (NM_008047, exon 11 of 11)	-34305	NM_177093	320184	Mm.390882	NM_177093	ENSMUSG00000034158	Lrrc58	1810012N18Rik|C330018J07Rik	leucine rich repeat containing 58	protein-coding
mm_140135.1	chr17	79626670	79626697	+	1	NA	intron (NM_201361, intron 2 of 10)	intron (NM_201361, intron 2 of 10)	11783	NM_201361	381110	Mm.209801	NM_201361	ENSMUSG00000036368	Rmdn2	AW061290|Fam82a1|RMD-2|mRMD-2	regulator of microtubule dynamics 2	protein-coding
mm_10247.1	chr2	9178032	9178042	+	1	NA	Intergenic	Intergenic	-11478	NR_038180	73438	Mm.23558	NR_038180	ENSMUSG00000085580	1700061F12Rik	-	RIKEN cDNA 1700061F12 gene	ncRNA
mm_170948.1	chr2	53191183	53191184	-	1	NA	promoter-TSS (NM_018785)	promoter-TSS (NM_018785)	4	NM_018785	56194	Mm.257474	NM_018785	ENSMUSG00000061136	Prpf40a	2810012K09Rik|FBP-11|FBP11|Fnbp11|Fnbp3	pre-mRNA processing factor 40A	protein-coding
mm_134242.1	chr16	12945927	12945939	-	1	NA	Intergenic	Lx8|LINE|L1	134543	NR_040507	75493	Mm.396146	NR_040507	ENSMUSG00000101565	1700003L19Rik	-	RIKEN cDNA 1700003L19 gene	ncRNA
mm_16520.1	chr2	181497224	181497244	+	1	NA	promoter-TSS (NM_001291200)	promoter-TSS (NM_001291200)	92	NM_001291204	66314	Mm.136648	NM_025482	ENSMUSG00000000827	Tpd52l2	2810411G23Rik|AU016537|C86069|D54	tumor protein D52-like 2	protein-coding
mm_53468.1	chr6	134920713	134920726	+	1	NA	5' UTR (NM_009875, exon 1 of 3)	5' UTR (NM_009875, exon 1 of 3)	318	NM_009875	12576	Mm.2958	NM_009875	ENSMUSG00000003031	Cdkn1b	AA408329|AI843786|Kip1|p27|p27Kip1	cyclin-dependent kinase inhibitor 1B	protein-coding
mm_121460.1	chr14	120506195	120506203	+	1	NA	3' UTR (NM_029519, exon 2 of 2)	3' UTR (NM_029519, exon 2 of 2)	27738	NM_029519	76108	Mm.261448	NM_029519	ENSMUSG00000051615	Rap2a	5830461H18Rik	RAS related protein 2a	protein-coding
mm_147120.1	chr18	35740392	35740438	-	1	NA	exon (NM_001289591, exon 1 of 7)	exon (NM_001289591, exon 1 of 7)	139	NM_001289592	72512	Mm.45995	NM_028261	ENSMUSG00000024349	Tmem173	2610307O08Rik|ERIS|MPYS|Mita|STING	transmembrane protein 173	protein-coding
mm_64229.1	chr7	141691295	141691324	+	1	NA	exon (NM_023566, exon 2 of 46)	exon (NM_023566, exon 2 of 46)	969	NM_023566	17831	Mm.2041	NM_023566		Muc2	2010015E03Rik|MCM|wnn	mucin 2	protein-coding
mm_98154.1	chr11	87617177	87617200	+	1	NA	promoter-TSS (NM_001045527)	promoter-TSS (NM_001045527)	24	NM_001045527	327992	Mm.390371	NM_001045527	ENSMUSG00000070345	Hsf5	Gm739|MLZ-220	heat shock transcription factor family member 5	protein-coding
mm_89838.1	chr10	106879006	106879012	+	1	NA	intron (NM_001205341, intron 21 of 31)	intron (NM_001205341, intron 21 of 31)	244655	NM_001142804	380660	Mm.336072	NM_198636	ENSMUSG00000035948	Acss3	8430416H19Rik|Gm874	acyl-CoA synthetase short-chain family member 3	protein-coding
mm_163268.1	chr11	115037720	115037748	-	1	NA	promoter-TSS (NM_199201).2	promoter-TSS (NM_199201).2	-44	NM_001101656	100043123		NM_001101656	ENSMUSG00000069609	Cd300ld4	Gm11710|OTTMUSG00000003605	CD300 molecule like family member D4	protein-coding
mm_81589.1	chr9	110477017	110477025	+	1	NA	promoter-TSS (NM_001163569)	promoter-TSS (NM_001163569)	27	NM_001163569	16578	Mm.42170	NM_010628	ENSMUSG00000032489	Kif9	-	kinesin family member 9	protein-coding
mm_81217.1	chr9	107587758	107587801	+	1	NA	promoter-TSS (NM_025903)	promoter-TSS (NM_025903)	61	NM_025903	15983	Mm.215335	NM_025903	ENSMUSG00000010048	Ifrd2	1810034A24Rik|AA470234|AI838527|SKMc15	interferon-related developmental regulator 2	protein-coding
mm_67129.1	chr7	70366737	70366771	-	1	NA	promoter-TSS (NM_183261)	promoter-TSS (NM_183261)	-8	NM_183261	11819	Mm.158143	NM_009697	ENSMUSG00000030551	Nr2f2	2700033K02Rik|9430015G03Rik|ARP-1|Aporp1|COUP-TF2|COUP-TFII|COUPTFB|EAR3|SVP40|Tcfcoup2	nuclear receptor subfamily 2, group F, member 2	protein-coding
mm_68586.1	chr7	116033812	116033822	-	1	NA	intron (NM_001025559, intron 1 of 15)	CpG	-2770	NM_001025560	20679	Mm.323365	NM_011445	ENSMUSG00000051910	Sox6	AI987981|SOX-LZ	SRY (sex determining region Y)-box 6	protein-coding
mm_156030.1	chrX	107256032	107256064	+	1	NA	promoter-TSS (NM_001033251)	promoter-TSS (NM_001033251)	20	NM_001033251	213439	Mm.383562	NM_001033251	ENSMUSG00000073008	Gpr174	Gm376|Lypsr3	G protein-coupled receptor 174	protein-coding
mm_3345.1	chr1	138137386	138137388	+	1	NA	intron (NM_001111316, intron 1 of 31)	intron (NM_001111316, intron 1 of 31)	37739	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_106645.1	chr11	121054426	121054444	-	1	NA	3' UTR (NM_026907, exon 5 of 5)	3' UTR (NM_026907, exon 5 of 5)	9134	NM_026907	58210	Mm.116986	NM_026907	ENSMUSG00000039364	Sectm1b	1810003C24Rik|K12|Sectm1	secreted and transmembrane 1B	protein-coding
mm_36620.1	chr4	89859314	89859316	-	1	NA	Intergenic	Intergenic	171117	NM_175647	242523	Mm.130167	NM_175647	ENSMUSG00000043753	Dmrta1	Dmrt4	doublesex and mab-3 related transcription factor like family A1	protein-coding
mm_61888.1	chr7	89721402	89721405	+	1	NA	intron (NM_181407, intron 1 of 13)	intron (NM_181407, intron 1 of 13)	88585	NM_181407	109264	Mm.334011	NM_181407	ENSMUSG00000030621	Me3	1700020C08Rik|B230207H15Rik	malic enzyme 3, NADP(+)-dependent, mitochondrial	protein-coding
mm_134696.1	chr16	22657010	22657045	-	1	NA	5' UTR (NM_138650, exon 1 of 25)	5' UTR (NM_138650, exon 1 of 25)	204	NM_138650	110197	Mm.194986	NM_138650	ENSMUSG00000022861	Dgkg	2900055E17Rik|90kDa|AI854428|Dagk3|E430001K23Rik|mKIAA4131	diacylglycerol kinase, gamma	protein-coding
mm_111793.1	chr12	104865039	104865052	-	1	NA	promoter-TSS (NR_104437)	promoter-TSS (NR_104437)	31	NR_104436	94040	Mm.244078	NM_053155	ENSMUSG00000021097	Clmn	9330188N17Rik|AI428889|AI788815|mKIAA1188	calmin	protein-coding
mm_140172.1	chr17	80373611	80373644	+	1	NA	promoter-TSS (NR_028385)	promoter-TSS (NR_028385)	-85	NR_028385	791338	Mm.204722	NR_028385		Gm10190	ENSMUSG00000066938	predicted gene 10190	ncRNA
mm_105330.1	chr11	102925087	102925130	-	1	NA	promoter-TSS (NM_197959)	promoter-TSS (NM_197959)	16	NM_197959	70218	Mm.32084	NM_197959	ENSMUSG00000051378	Kif18b	3000004C01Rik	kinesin family member 18B	protein-coding
mm_124636.1	chr15	4112804	4112844	+	1	NA	intron (NM_024188, intron 13 of 16)	intron (NM_024188, intron 13 of 16)	-85418	NR_028266	414066	Mm.394461	NR_028266		BC037032	-	cDNA Sequence BC037032	ncRNA
mm_38935.1	chr4	150196080	150196086	-	1	NA	exon (NM_009802, exon 4 of 8)	exon (NM_009802, exon 4 of 8)	5052	NM_009802	12353	Mm.232523	NM_009802	ENSMUSG00000028972	Car6	Ca6|DOC1	carbonic anhydrase 6	protein-coding
mm_49698.1	chr6	34029422	34029456	+	1	NA	promoter-TSS (NM_028886)	promoter-TSS (NM_028886)	-9	NM_028886	74354	Mm.127952	NM_028886	ENSMUSG00000056215	Lrguk	4921528H16Rik	leucine-rich repeats and guanylate kinase domain containing	protein-coding
mm_144271.1	chr18	11084123	11084131	+	1	NA	intron (NM_010258, intron 6 of 6)	intron (NM_010258, intron 6 of 6)	-31560	NR_105023	68434	Mm.57626	NR_105022	ENSMUSG00000097222	1010001N08Rik	Gata6as	RIKEN cDNA 1010001N08 gene	ncRNA
mm_21950.1	chr2	167062982	167063048	-	1	NA	promoter-TSS (NM_001033196)	promoter-TSS (NM_001033196)	0	NM_001033196	98999	Mm.297074	NM_001033196	ENSMUSG00000039501	Znfx1	AI481105|Astx3	zinc finger, NFX1-type containing 1	protein-coding
mm_28345.1	chr3	89418256	89418286	-	1	NA	promoter-TSS (NM_011368)	promoter-TSS (NM_011368)	20	NM_016904	54124	Mm.3049	NM_016904	ENSMUSG00000028044	Cks1b	2410005G18Rik|2610005D03Rik|AA407784|Cks1|sid1334	CDC28 protein kinase 1b	protein-coding
mm_117236.1	chr13	64289157	64289158	-	1	NA	Intergenic	MLTR25A|LTR|ERVK	-14169	NM_172587	218294	Mm.25335	NM_172587	ENSMUSG00000033102	Cdc14b	2810432N10Rik|A530086E13Rik|AA472821|CDC14B3|Cdc14B1	CDC14 cell division cycle 14B	protein-coding
mm_59696.1	chr7	28543928	28543944	+	1	NA	3' UTR (NM_001081115, exon 6 of 6)	3' UTR (NM_001081115, exon 6 of 6)	3051	NM_026716	68416	Mm.25210	NM_026716	ENSMUSG00000084174	Sycn	0910001K16Rik|1810038B08Rik|SYL	syncollin	protein-coding
mm_169072.1	chr13	29255245	29255249	+	1	NA	intron (NR_131896, intron 15 of 16)	L1Md_T|LINE|L1	238992	NR_045075	77920	Mm.197051	NR_045073	ENSMUSG00000086363	A330102I10Rik	-	RIKEN cDNA A330102I10 gene	ncRNA
mm_150999.1	chr19	46654004	46654027	+	1	NA	exon (NM_001177813, exon 4 of 4)	exon (NM_001177813, exon 4 of 4)	18985	NM_007809	13074	Mm.1262	NM_007809	ENSMUSG00000003555	Cyp17a1	Cyp17|p450c17	cytochrome P450, family 17, subfamily a, polypeptide 1	protein-coding
mm_102494.1	chr11	60296591	60296624	-	1	NA	intron (NM_153080, intron 1 of 14)	intron (NM_153080, intron 1 of 14)	56298	NM_153080	216810	Mm.218875	NM_153080	ENSMUSG00000000538	Tom1l2	2900016I08Rik|A730055F12Rik|AU042072|Srebf1	target of myb1-like 2 (chicken)	protein-coding
mm_73296.1	chr8	105000825	105000832	+	1	NA	promoter-TSS (NM_001272045)	promoter-TSS (NM_001272045)	-25	NM_001272045	436059	Mm.491825	NM_001272045	ENSMUSG00000091813	Ces2h	Ces2|EG436059|Gm5744	carboxylesterase 2H	protein-coding
mm_11086.1	chr2	27761572	27761584	+	1	NA	3' UTR (NM_001290481, exon 10 of 10)	3' UTR (NM_001290481, exon 10 of 10)	50995	NM_001290482	20181	Mm.24624	NM_011305	ENSMUSG00000015846	Rxra	9530071D11Rik|Nr2b1|RXRalpha1	retinoid X receptor alpha	protein-coding
mm_96771.1	chr11	69935819	69935843	+	1	NA	promoter-TSS (NM_016875)	promoter-TSS (NM_016875)	-68	NM_016875	53422	Mm.29286	NM_016875	ENSMUSG00000018554	Ybx2	Msy2	Y box protein 2	protein-coding
mm_57225.1	chr6	123281529	123281572	-	1	NA	TTS (NM_019948)	TTS (NM_019948)	8321	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_12983.1	chr2	90847150	90847160	+	1	NA	promoter-TSS (NM_001317241)	promoter-TSS (NM_001317241)	0	NM_001317241	56428	Mm.28023	NM_019758	ENSMUSG00000027282	Mtch2	2310034D24Rik|4930539J07Rik|HSPC032	mitochondrial carrier 2	protein-coding
mm_22044.1	chr2	168230324	168230334	-	1	NA	promoter-TSS (NM_010072)	promoter-TSS (NM_010072)	50	NM_010072	13480	Mm.422657	NM_010072	ENSMUSG00000078919	Dpm1	AI118379|AI194292	dolichol-phosphate (beta-D) mannosyltransferase 1	protein-coding
mm_42865.1	chr5	122231028	122231040	+	1	NA	intron (NM_028752, intron 2 of 6)	B4A|SINE|B4	20747	NM_028752	74096	Mm.28804	NM_028752	ENSMUSG00000064267	Hvcn1	0610039P13Rik|AI450555|BTS|HV1|Vsop.|mVSOP	hydrogen voltage-gated channel 1	protein-coding
mm_39566.1	chr5	23387274	23387297	+	1	NA	Intergenic	Intergenic	47068	NR_040469	269630	Mm.425231	NR_040469	ENSMUSG00000073147	5031425E22Rik	-	RIKEN cDNA 5031425E22 gene	ncRNA
mm_133479.1	chr16	90089927	90089931	+	1	NA	Intergenic	Intergenic	-52308	NR_033476	100038709	Mm.484070	NR_033476		Gm10789	ENSMUSG00000074924	predicted gene 10789	ncRNA
mm_169708.1	chr15	75882515	75882518	-	1	NA	TTS (NM_001282443)	TTS (NM_001282443)	6207	NM_001282443	223645		NM_001282443	ENSMUSG00000098678	Mroh6	Gm19570	maestro heat-like repeat family member 6	protein-coding
mm_150673.1	chr19	42051842	42051846	+	1	NA	promoter-TSS (NM_025752)	promoter-TSS (NM_025752)	-384	NM_025752	66765	Mm.440412	NM_025752	ENSMUSG00000090369	4933411K16Rik	-	RIKEN cDNA 4933411K16 gene	protein-coding
mm_81318.1	chr9	108460530	108460571	+	1	NA	promoter-TSS (NM_133744)	promoter-TSS (NM_133744)	32	NM_133744	72454	Mm.46488	NM_133744	ENSMUSG00000049305	Ccdc71	2600016J21Rik	coiled-coil domain containing 71	protein-coding
mm_14204.1	chr2	127247940	127247997	+	1	NA	promoter-TSS (NM_175145)	promoter-TSS (NM_175145)	-7	NM_175145	69470	Mm.200889	NM_175145	ENSMUSG00000034850	Tmem127	2310003P10Rik|AI314202|AI317350	transmembrane protein 127	protein-coding
mm_98374.1	chr11	94044242	94044273	+	1	NA	promoter-TSS (NM_001199205)	promoter-TSS (NM_001199205)	52	NM_001025429	70834	Mm.260737	NM_027569	ENSMUSG00000020859	Spag9	3110018C07Rik|4733401I23Rik|4831406C20Rik|AW552012|JLP|JSAP2|JSAP2a|Jip4|Mapk8ip4|syd1	sperm associated antigen 9	protein-coding
mm_108213.1	chr12	77001484	77001488	+	1	NA	Intergenic	Intergenic	-39238	NM_001146176	17187	Mm.268548	NM_008558	ENSMUSG00000059436	Max	AA960152|AI875693|bHLHd4|bHLHd5|bHLHd6|bHLHd7|bHLHd8	Max protein	protein-coding
mm_78778.1	chr9	43796254	43796264	+	1	NA	intron (NM_021424, intron 5 of 5)	intron (NM_021424, intron 5 of 5)	51683	NM_021424	58235	Mm.335096	NM_021424	ENSMUSG00000032012	Nectin1	AI835281|AW549174|Cd111|HIgR|HveC|PRR|PRR1|Pvrl1|nectin-1	nectin cell adhesion molecule 1	protein-coding
mm_110107.1	chr12	26415258	26415303	-	1	NA	promoter-TSS (NR_105856)	promoter-TSS (NR_105856)	-18	NM_080563	108089	Mm.214932	NM_080563	ENSMUSG00000020642	Rnf144a	Rnf144|UIP4|Ubce7ip4	ring finger protein 144A	protein-coding
mm_109827.1	chr12	3894640	3894660	-	1	NA	intron (NM_153743, intron 1 of 17)	intron (NM_153743, intron 1 of 17)	2906	NM_153743	13435	Mm.5001	NM_007872	ENSMUSG00000020661	Dnmt3a	MmuIIIA	DNA methyltransferase 3A	protein-coding
mm_31991.1	chr4	89477635	89477639	+	1	NA	intron (NR_132431, intron 7 of 9)	ORR1A2|LTR|ERVL-MaLR	-166605	NM_007670	12579	Mm.423094	NM_007670	ENSMUSG00000073802	Cdkn2b	AV083695|INK4b|MTS2|p15|p15(INK4b)|p15INK4b	cyclin-dependent kinase inhibitor 2B (p15, inhibits CDK4)	protein-coding
mm_116195.1	chr13	31625550	31625564	-	1	NA	promoter-TSS (NM_010225)	promoter-TSS (NM_010225)	-259	NM_010225	14238	Mm.125548	NM_010225	ENSMUSG00000038402	Foxf2	FREAC2|Fkh20|LUN	forkhead box F2	protein-coding
mm_72547.1	chr8	84001496	84001500	+	1	NA	promoter-TSS (NM_183097)	promoter-TSS (NM_183097)	-208	NM_183097	73453	Mm.75101	NM_183097	ENSMUSG00000046408	1700067K01Rik	-	RIKEN cDNA 1700067K01 gene	protein-coding
mm_159479.1	chr4	34716513	34716513	-	1	NA	intron (NM_001347062, intron 8 of 12)	CpG	13693	NM_027041	69329	Mm.389548	NM_027041	ENSMUSG00000028294	Cfap206	1700003M02Rik|AU024269	cilia and flagella associated protein 206	protein-coding
mm_125003.1	chr15	24945483	24945485	+	1	NA	Intergenic	RMER13B|LTR|ERVK	468280	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	brain abundant, membrane attached signal protein 1	protein-coding
mm_112734.1	chr13	19255557	19255579	+	1	NA	Intergenic	Intergenic	140245	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_128186.1	chr15	34678877	34678892	-	1	NA	promoter-TSS (NM_145469)	promoter-TSS (NM_145469)	-178	NM_145469	223473	Mm.258402	NM_145469	ENSMUSG00000038879	Nipal2	9330161F08Rik|Npal2	NIPA-like domain containing 2	protein-coding
mm_53023.1	chr6	124304647	124304671	+	1	NA	promoter-TSS (NM_001170395)	promoter-TSS (NM_001170395)	8	NM_053094	93671	Mm.37426	NM_053094	ENSMUSG00000008845	Cd163	CD163v2|CD163v3	CD163 antigen	protein-coding
mm_73909.1	chr8	119575263	119575340	+	1	NA	promoter-TSS (NM_026648)	promoter-TSS (NM_026648)	66	NM_026648	68270	Mm.41977	NM_026648	ENSMUSG00000031831	Dnaaf1	4930457P18Rik|Lrrc50	dynein, axonemal assembly factor 1	protein-coding
mm_74198.1	chr8	123806043	123806063	+	1	NA	promoter-TSS (NM_009003)	promoter-TSS (NM_009003)	57	NM_009003	19341	Mm.9221	NM_009003	ENSMUSG00000019478	Rab4a	AI848268|Rab4	RAB4A, member RAS oncogene family	protein-coding
mm_152941.1	chr19	28863767	28863767	-	1	NA	intron (NM_009199, intron 1 of 11)	intron (NM_009199, intron 1 of 11)	28601	NM_009199	20510	Mm.246670	NM_009199	ENSMUSG00000024935	Slc1a1	D130048G10Rik|EAAC1|EAAC2|EAAT3|MEAAC1	solute carrier family 1 (neuronal/epithelial high affinity glutamate transporter, system Xag), member 1	protein-coding
mm_67694.1	chr7	89518100	89518108	-	1	NA	promoter-TSS (NM_029614)	promoter-TSS (NM_029614)	-518	NM_029614	76453	Mm.250438	NM_029614	ENSMUSG00000039405	Prss23	2310046G15Rik|4930479H08Rik|AI790574|Spuve	protease, serine 23	protein-coding
mm_159517.1	chr4	60501924	60501924	-	1	NA	promoter-TSS (NM_031188)	promoter-TSS (NM_031188)	36	NM_001163011	17840	Mm.335875	NM_031188	ENSMUSG00000078683	Mup1	Ltn-1|Lvtn-1|Mup-1|Mup-a|Mup10|Mup7|Up-1	major urinary protein 1	protein-coding
mm_733.1	chr1	43410947	43410949	+	1	NA	Intergenic	Intergenic	-34803	NM_010879	17974	Mm.389903	NM_010879	ENSMUSG00000066877	Nck2	4833426I10Rik|Grb4|NCKbeta|Nck-2	non-catalytic region of tyrosine kinase adaptor protein 2	protein-coding
mm_170938.1	chr2	47669668	47669676	-	1	NA	Intergenic	L1Md_T|LINE|L1	-1144437	NM_007396	11480	Mm.314338	NM_007396	ENSMUSG00000052155	Acvr2a	ActrIIa|Acvr2|TactrII	activin receptor IIA	protein-coding
mm_32004.1	chr4	94614590	94614598	+	1	NA	5' UTR (NM_001290568, exon 1 of 14)	5' UTR (NM_001290568, exon 1 of 14)	103	NM_026319	67694	Mm.240619	NM_026319	ENSMUSG00000028576	Ift74	1700029H06Rik|Ccdc2|Cmg1|b2b796Clo	intraflagellar transport 74	protein-coding
mm_40337.1	chr5	43948708	43948712	+	1	NA	Intergenic	Intergenic	33089	NM_008009	14181	Mm.46053	NM_008009	ENSMUSG00000048373	Fgfbp1	FGF-BP|FGF-BP1|FGFBP-1	fibroblast growth factor binding protein 1	protein-coding
mm_3477.1	chr1	150105449	150105459	+	1	NA	exon (NM_011198, exon 10 of 10)	exon (NM_011198, exon 10 of 10)	5423	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_71215.1	chr8	40893698	40893708	+	1	NA	intron (NM_007514, intron 1 of 11)	intron (NM_007514, intron 1 of 11)	31336	NM_001044740	11988	Mm.4676	NM_007514	ENSMUSG00000031596	Slc7a2	20.5|AI158848|Atrc2|CAT-2|Cat2|Tea	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	protein-coding
mm_106314.1	chr11	118302788	118302800	-	1	NA	3' UTR (NM_011594, exon 5 of 5)	3' UTR (NM_011594, exon 5 of 5)	-12550	NM_001033528	72344	Mm.232293	NM_001033528	ENSMUSG00000033909	Usp36	2700002L06Rik|mKIAA1453	ubiquitin specific peptidase 36	protein-coding
mm_72350.1	chr8	79640196	79640218	+	1	NA	intron (NM_001081164, intron 1 of 20)	CpG	531	NM_001081164	73945	Mm.34348	NM_001081164	ENSMUSG00000036990	Otud4	4930431L18Rik|AI449692|D8Ertd69e|mKIAA1046	OTU domain containing 4	protein-coding
mm_57121.1	chr6	122596889	122596899	-	1	NA	intron (NM_001134391, intron 2 of 7)	intron (NM_001134391, intron 2 of 7)	5550	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_107155.1	chr12	24572312	24572325	+	1	NA	promoter-TSS (NM_001161406)	promoter-TSS (NM_001161406)	31	NM_001161406	195733	Mm.263068	NM_145890	ENSMUSG00000020656	Grhl1	LBP-32|MGR|Tcfcp2l2	grainyhead-like 1 (Drosophila)	protein-coding
mm_70354.1	chr8	5578316	5578324	+	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-473033	NM_011388	20494	Mm.3500	NM_011388	ENSMUSG00000023073	Slc10a2	9130221J18Rik|AI605518|ASBT|IBAT|ISBT	solute carrier family 10, member 2	protein-coding
mm_75991.1	chr8	72388960	72388961	-	1	NA	intron (NM_001122832, intron 8 of 15)	PB1D9|SINE|Alu	32514	NM_001122832	13859	Mm.288894	NM_007944	ENSMUSG00000006276	Eps15l1	9830147J04Rik|AI593686|Eps15-rs|Eps15R	epidermal growth factor receptor pathway substrate 15-like 1	protein-coding
mm_77504.1	chr8	122699067	122699119	-	1	NA	promoter-TSS (NM_009824)	promoter-TSS (NM_009824)	16	NM_009824	12398	Mm.194339	NM_009824	ENSMUSG00000006362	Cbfa2t3	A630044F12Rik|AI465270|AW229127|Cbfa2t3h|ETO-2|Eto2|MTGR2	core-binding factor, runt domain, alpha subunit 2, translocated to, 3 (human)	protein-coding
mm_149263.1	chr19	10577148	10577175	+	1	NA	promoter-TSS (NM_201351)	promoter-TSS (NM_201351)	4	NM_001282067	225912	Mm.252701	NM_201351	ENSMUSG00000034445	Cyb561a3	2310004G04Rik|Cybasc3|Lcytb	cytochrome b561 family, member A3	protein-coding
mm_138518.1	chr17	35237966	35237981	+	1	NA	3' UTR (NM_023179, exon 3 of 3)	3' UTR (NM_023179, exon 3 of 3)	1377	NM_023179	66237	Mm.396107	NM_023179	ENSMUSG00000024403	Atp6v1g2	1500002D01Rik|Atp6g2|NG38|VAG2	ATPase, H+ transporting, lysosomal V1 subunit G2	protein-coding
mm_111719.1	chr12	103730403	103730424	-	1	NA	exon (NM_009244, exon 3 of 5)	exon (NM_009244, exon 3 of 5)	7776	NM_009244	20701	Mm.439692	NM_009244	ENSMUSG00000071178	Serpina1b	D12Ucla2|Dom2|PI2|Spi1-2	serine (or cysteine) preptidase inhibitor, clade A, member 1B	protein-coding
mm_87044.1	chr10	28791581	28791603	+	1	NA	intron (NM_001305663, intron 5 of 5)	L1_Mur1|LINE|L1	123232	NM_178666	210757	Mm.123021	NM_178666	ENSMUSG00000049109	Themis	E430004N04Rik|Gasp|Spot|Tsepa|thylex	thymocyte selection associated	protein-coding
mm_120219.1	chr14	62761758	62761782	+	1	NA	promoter-TSS (NM_008715)	promoter-TSS (NM_008715)	-658	NM_008715	18130	Mm.319684	NM_008715	ENSMUSG00000035161	Ints6	2900075H24Rik|AI480962|DICE1|Ddx26|HDB|Notch2l	integrator complex subunit 6	protein-coding
mm_28323.1	chr3	89340141	89340185	-	1	NA	exon (NM_001037722, exon 22 of 23)	exon (NM_001037722, exon 22 of 23)	-2135	NM_007910	13639	Mm.16332	NM_007910	ENSMUSG00000028040	Efna4	EFL-4|Epl4|LERK-4	ephrin A4	protein-coding
mm_89097.1	chr10	84517988	84518005	+	1	NA	Intergenic	Intergenic	15892	NM_175451	216197	Mm.334999	NM_175451	ENSMUSG00000046841	Ckap4	5630400A09Rik|CLIMP-63|P63	cytoskeleton-associated protein 4	protein-coding
mm_17834.1	chr2	34291410	34291413	-	1	NA	intron (NM_016768, intron 2 of 8)	intron (NM_016768, intron 2 of 8)	80634	NM_001290576	18516	Mm.239941	NM_016768	ENSMUSG00000038718	Pbx3	-	pre B cell leukemia homeobox 3	protein-coding
mm_74763.1	chr8	20902453	20902459	-	1	NA	promoter-TSS (NM_001177471)	promoter-TSS (NM_001177471)	-483	NM_001177471	100504014	Mm.490239	NM_001177471	ENSMUSG00000082976	Gm15056	Defb52|OTTMUSG00000018888	predicted gene 15056	protein-coding
mm_120074.1	chr14	57424055	57424093	+	1	NA	promoter-TSS (NM_009376)	promoter-TSS (NM_009376)	3	NM_009376	21821	Mm.4653	NM_009376	ENSMUSG00000040040	Ift88	AW552028|Tg737|Tg737Rpw|TgN737Rpw|Ttc10|flexo|fxo|orpk|polaris	intraflagellar transport 88	protein-coding
mm_47921.1	chr5	135008810	135008830	-	1	NA	promoter-TSS (NM_001190437)	promoter-TSS (NM_001190437)	-332	NM_001190437	68758	Mm.389700	NM_145215	ENSMUSG00000040532	Abhd11	1110054D16Rik|A630008N09Rik|Wbscr21	abhydrolase domain containing 11	protein-coding
mm_91464.1	chr10	34127956	34127980	-	1	NA	promoter-TSS (NM_175449)	promoter-TSS (NM_175449)	4	NM_175449	215900	Mm.34479	NM_175449	ENSMUSG00000046031	Fam26f	A630077B13Rik	family with sequence similarity 26, member F	protein-coding
mm_105185.1	chr11	101972943	101972959	-	1	NA	3' UTR (NM_028207, exon 3 of 3)	3' UTR (NM_028207, exon 3 of 3)	-5936	NM_024449	74499	Mm.265602	NM_024449	ENSMUSG00000001494	Sost	5430411E23Rik	sclerostin	protein-coding
mm_130541.1	chr15	98953529	98953533	-	1	NA	promoter-TSS (NM_011653)	promoter-TSS (NM_011653)	-30	NM_011653	22142	Mm.405359	NM_011653	ENSMUSG00000072235	Tuba1a	Tuba-1|Tuba1	tubulin, alpha 1A	protein-coding
mm_118523.1	chr14	14718827	14718829	+	1	NA	intron (NM_001033270, intron 1 of 24)	intron (NM_001033270, intron 1 of 24)	15803	NM_001033270	218756	Mm.258893	NM_001033270	ENSMUSG00000021733	Slc4a7	E430014N10Rik|NBC3|NBCn1|NBCn1-G	solute carrier family 4, sodium bicarbonate cotransporter, member 7	protein-coding
mm_142956.1	chr17	56120117	56120131	-	1	NA	exon (NM_029796, exon 2 of 2)	exon (NM_029796, exon 2 of 2)	1822	NM_029796	76905	Mm.348025	NM_029796	ENSMUSG00000037095	Lrg1	1300008B03Rik|2310031E04Rik|Lrg|Lrhg	leucine-rich alpha-2-glycoprotein 1	protein-coding
mm_787.1	chr1	45332160	45332184	+	1	NA	exon (NM_009930, exon 20 of 51)	exon (NM_009930, exon 20 of 51)	20634	NM_009930	12825	Mm.249555	NM_009930	ENSMUSG00000026043	Col3a1	AW550625|Col3a-1|Tsk-2|Tsk2	collagen, type III, alpha 1	protein-coding
mm_102371.1	chr11	58611478	58611500	-	1	NA	intron (NM_144544, intron 4 of 5)	intron (NM_144544, intron 4 of 5)	2003	NM_144544	78354	Mm.58038	NM_144544	ENSMUSG00000037145	2210407C18Rik	Ep1	RIKEN cDNA 2210407C18 gene	protein-coding
mm_78761.1	chr9	43303279	43303289	+	1	NA	Intergenic	Intergenic	-7479	NM_023655	72169	Mm.273277	NM_023655	ENSMUSG00000032013	Trim29	1110047J21Rik|2810431N19Rik|4732461M22Rik|AI119726	tripartite motif-containing 29	protein-coding
mm_172505.1	chr7	68250050	68250053	-	1	NA	intron (NM_030101, intron 1 of 3)	ORR1B1-int|LTR|ERVL-MaLR	14182	NM_030101	78444	Mm.425468	NM_030101	ENSMUSG00000030553	Pgpep1l	C330024D12Rik	pyroglutamyl-peptidase I-like	protein-coding
mm_163564.1	chr13	25910059	25910088	-	1	NA	Intergenic	L1M2|LINE|L1	56243	NR_045062	100503530	Mm.86763	NR_045062	ENSMUSG00000086531	Gm11351	OTTMUSG00000000620	predicted gene 11351	ncRNA
mm_97009.1	chr11	70970182	70970196	+	1	NA	promoter-TSS (NM_001276406)	promoter-TSS (NM_001276406)	-11	NM_027186	69723	Mm.275691	NM_027186	ENSMUSG00000018449	Rpain	2400006N03Rik|Rip	RPA interacting protein	protein-coding
mm_86011.1	chr9	112234592	112234619	-	1	NA	5' UTR (NM_001177619, exon 1 of 11)	5' UTR (NM_001177619, exon 1 of 11)	224	NR_015468	620760	Mm.259863	NR_015468	ENSMUSG00000087038	2900079G21Rik	C130083B14|Gm6179	RIKEN cDNA 2900079G21 gene	ncRNA
mm_167225.1	chr8	12672427	12672457	+	1	NA	promoter-TSS (NM_198031)	promoter-TSS (NM_198031)	-342	NM_198031	259279	Mm.142095	NM_198031	ENSMUSG00000000759	Tubgcp3	GCP3|Spc98p	tubulin, gamma complex associated protein 3	protein-coding
mm_146957.1	chr18	33205122	33205154	-	1	NA	exon (NM_133774, exon 5 of 6)	exon (NM_133774, exon 5 of 6)	8724	NM_001347624	170459	Mm.127058	NM_133774	ENSMUSG00000024378	Stard4	4632419C16Rik|9030213J02Rik	StAR-related lipid transfer (START) domain containing 4	protein-coding
mm_90706.1	chr10	130542326	130542359	+	1	NA	Intergenic	Intergenic	-44963	NM_001103366	625131	Mm.469844	NM_001103366	ENSMUSG00000091511	Vmn2r87	EG625131	vomeronasal 2, receptor 87	protein-coding
mm_50341.1	chr6	48537756	48537768	+	1	NA	promoter-TSS (NR_130985)	promoter-TSS (NR_130985)	193	NM_133764	76252	Mm.30214	NM_133764	ENSMUSG00000039347	Atp6v0e2	0610006O14Rik|NM9.2	ATPase, H+ transporting, lysosomal V0 subunit E2	protein-coding
mm_72638.1	chr8	84699161	84699178	+	1	NA	exon (NM_198020, exon 15 of 17)	exon (NM_198020, exon 15 of 17)	-2288	NM_008535	17095	Mm.4925	NM_008535	ENSMUSG00000034041	Lyl1	Lyl-1|bHLHa18	lymphoblastomic leukemia 1	protein-coding
mm_101439.1	chr11	30150076	30150079	-	1	NA	intron (NM_175836, intron 4 of 34)	intron (NM_175836, intron 4 of 34)	48180	NM_009260	20742	Mm.123110	NM_009260	ENSMUSG00000020315	Sptbn1	9930031C03Rik|AL033301|SPTB2|Spnb-2|Spnb2|elf1|elf3|mKIAA4049	spectrin beta, non-erythrocytic 1	protein-coding
mm_29143.1	chr3	105931246	105931277	-	1	NA	intron (NM_001033780, intron 1 of 5)	intron (NM_001033780, intron 1 of 5)	1403	NM_001033780	433638	Mm.239081	NM_001033780	ENSMUSG00000074342	I830077J02Rik	-	RIKEN cDNA I830077J02 gene	protein-coding
mm_139378.1	chr17	51834463	51834471	+	1	NA	Intergenic	Intergenic	-1177	NM_001163632	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_153917.1	chr19	47268783	47268806	-	1	NA	exon (NM_008018, exon 15 of 15)	exon (NM_008018, exon 15 of 15)	4795	NR_105961	102466782		NR_105961	ENSMUSG00000098786	Mir6995	Gm27576|mmu-mir-6995	microRNA 6995	ncRNA
mm_7198.1	chr1	92997077	92997084	-	1	NA	Intergenic	Intergenic	-9254	NM_177587	208760	Mm.235537	NM_177587	ENSMUSG00000045091	Aqp12	AB084104|mAQP12	aquaporin 12	protein-coding
mm_31802.1	chr4	64154362	64154405	+	1	NA	Intergenic	Intergenic	-107368	NM_011607	21923	Mm.980	NM_011607	ENSMUSG00000028364	Tnc	AI528729|C130033P17Rik|Hxb|TN|TN-C|Ten|cytotactin|tenascin-C	tenascin C	protein-coding
mm_166639.1	chr6	83248648	83248649	+	1	NA	intron (NM_001166067, intron 2 of 24)	intron (NM_001166067, intron 2 of 24)	11273	NM_001166067	232156	Mm.333189	NM_001166067	ENSMUSG00000068323	Slc4a5	C330006M16|C330016K18Rik	solute carrier family 4, sodium bicarbonate cotransporter, member 5	protein-coding
mm_90418.1	chr10	127471829	127471837	+	1	NA	exon (NM_001168293, exon 12 of 24)	exon (NM_001168293, exon 12 of 24)	-29884	NM_177707	237611	Mm.32087	NM_177707	ENSMUSG00000040287	Stac3	9830125E18	SH3 and cysteine rich domain 3	protein-coding
mm_36134.1	chr4	59336136	59336163	-	1	NA	intron (NM_001163288, intron 12 of 16)	MLT1O|LTR|ERVL-MaLR	76098	NR_105031	101055769	Mm.421401	NR_105031		Gm12596	OTTMUSG00000007649	predicted gene 12596	ncRNA
mm_156537.1	chrX	151120880	151120883	+	1	NA	Intergenic	RMER13A2|LTR|ERVK	-24338	NR_028392	69499	Mm.8142	NM_175146	ENSMUSG00000025264	Tsr2	2310007F12Rik	TSR2 20S rRNA accumulation	protein-coding
mm_108578.1	chr12	84997016	84997026	+	1	NA	exon (NM_001347421, exon 1 of 20)	exon (NM_001347421, exon 1 of 20)	700	NM_178363	56531	Mm.153183	NM_178363	ENSMUSG00000021244	Ylpm1	A930013E17Rik|ZAP|Zap3	YLP motif containing 1	protein-coding
mm_3902.1	chr1	161747541	161747551	+	1	NA	Intergenic	Intergenic	40949	NM_001205243	14103	Mm.3355	NM_010177	ENSMUSG00000000817	Fasl	APT1LG1|CD178|CD95-L|CD95L|Fas-L|Faslg|Tnfsf6|Tnlg1a|gld	Fas ligand (TNF superfamily, member 6)	protein-coding
mm_86654.1	chr10	17724260	17724276	+	1	NA	exon (NM_010828, exon 2 of 2)	exon (NM_010828, exon 2 of 2)	1040	NM_010828	17684	Mm.272321	NM_010828	ENSMUSG00000039910	Cited2	AI835299|ER154-like|Mrg1|Msg2|p35srj	Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 2	protein-coding
mm_2871.1	chr1	131760320	131760327	+	1	NA	intron (NM_177243, intron 12 of 20)	intron (NM_177243, intron 12 of 20)	16301	NM_177243	320718	Mm.482704	NM_177243	ENSMUSG00000042268	Slc26a9	E030002L01Rik	solute carrier family 26, member 9	protein-coding
mm_159889.1	chr6	28449339	28449339	-	1	NA	promoter-TSS (NM_011038)	promoter-TSS (NM_011038)	1	NM_001159925	18506	Mm.8026	NM_011038	ENSMUSG00000029706	Pax4	Pax-4	paired box 4	protein-coding
mm_74894.1	chr8	25119080	25119095	-	1	NA	Intergenic	Intergenic	-17276	NM_031257	83436	Mm.261122	NM_031257	ENSMUSG00000031557	Plekha2	6430512N22Rik|AI851530|AU041791|TAPP2|W91773	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 2	protein-coding
mm_69079.1	chr7	127003764	127003786	-	1	NA	intron (NM_080638, intron 1 of 14)	intron (NM_080638, intron 1 of 14)	10819	NM_080638	78388	Mm.228797	NM_080638	ENSMUSG00000030681	Mvp	2310009M24Rik|LRP|VAULT1	major vault protein	protein-coding
mm_51087.1	chr6	67037200	67037201	+	1	NA	intron (NM_007836, intron 1 of 3)	CpG-12134	207	NM_007836	13197	Mm.72235	NM_007836	ENSMUSG00000036390	Gadd45a	AA545191|Ddit1|GADD45	growth arrest and DNA-damage-inducible 45 alpha	protein-coding
mm_96454.1	chr11	67586521	67586546	+	1	NA	promoter-TSS (NM_001109657)	promoter-TSS (NM_001109657)	33	NM_001109657	14457	Mm.40338	NM_008088	ENSMUSG00000033066	Gas7	AW124766|B230343A10Rik|Gas7-cb	growth arrest specific 7	protein-coding
mm_150984.1	chr19	46515715	46515762	+	1	NA	3' UTR (NM_053100, exon 6 of 6)	3' UTR (NM_053100, exon 6 of 6)	14090	NM_053100	93679	Mm.392177	NM_053100	ENSMUSG00000025034	Trim8	AA408830|BB006755|GERP|Rnf27	tripartite motif-containing 8	protein-coding
mm_147877.1	chr18	64516493	64516545	-	1	NA	promoter-TSS (NM_027350)	promoter-TSS (NM_027350)	38	NM_027350	70223	Mm.29192	NM_027350	ENSMUSG00000024587	Nars	3010001M15Rik|AA960128|ASNRS|C78150	asparaginyl-tRNA synthetase	protein-coding
mm_28070.1	chr3	84270783	84270794	-	1	NA	promoter-TSS (NM_001271725)	promoter-TSS (NM_001271725)	-5	NM_001271725	80890	Mm.44876	NM_030706	ENSMUSG00000027993	Trim2	mKIAA0517|narf	tripartite motif-containing 2	protein-coding
mm_74382.1	chr8	128685913	128685923	+	1	NA	5' UTR (NM_010578, exon 1 of 16)	5' UTR (NM_010578, exon 1 of 16)	264	NM_010578	16412	Mm.263396	NM_010578	ENSMUSG00000025809	Itgb1	4633401G24Rik|AA409975|AA960159|CD29|ENSMUSG00000051907|Fnrb|Gm9863|gpIIa	integrin beta 1 (fibronectin receptor beta)	protein-coding
mm_28537.1	chr3	92752338	92752338	-	1	NA	promoter-TSS (NM_025413)	promoter-TSS (NM_025413)	0	NM_025413	66195	Mm.158107	NM_025413	ENSMUSG00000027919	Lce1g	1110058A15Rik|AI604448	late cornified envelope 1G	protein-coding
mm_61569.1	chr7	79710409	79710423	+	1	NA	exon (NM_010626, exon 4 of 18)	exon (NM_010626, exon 4 of 18)	3770	NM_010626	16576	Mm.101633	NM_010626	ENSMUSG00000050382	Kif7	-	kinesin family member 7	protein-coding
mm_113309.1	chr13	30753449	30753454	+	1	NA	exon (NM_013674, exon 5 of 9)	exon (NM_013674, exon 5 of 9)	4218	NM_013674	16364	Mm.4677	NM_013674	ENSMUSG00000021356	Irf4	AI385587|IRF-4|LSIRF|NF-EM5|Spip	interferon regulatory factor 4	protein-coding
mm_1249.1	chr1	62810114	62810144	+	1	NA	intron (NM_010939, intron 15 of 15)	intron (NM_010939, intron 15 of 15)	-15397	NR_040601	74992	Mm.401979	NR_040601		4930487H11Rik	-	RIKEN cDNA 4930487H11 gene	ncRNA
mm_8775.1	chr1	161071196	161071232	-	1	NA	promoter-TSS (NM_172644)	promoter-TSS (NM_172644)	447	NR_131028	70454	Mm.248212	NM_027429	ENSMUSG00000026708	Cenpl	2610300B10Rik|AW121806|AW550697|CENP-L	centromere protein L	protein-coding
mm_35709.1	chr4	44168357	44168371	-	1	NA	promoter-TSS (NM_175201)	promoter-TSS (NM_175201)	-81	NM_001038993	73469	Mm.262859	NM_175201	ENSMUSG00000035696	Rnf38	1700065B19Rik|2610202O07Rik|AA673263|Oip1	ring finger protein 38	protein-coding
mm_56980.1	chr6	120357423	120357435	-	1	NA	promoter-TSS (NM_026028)	promoter-TSS (NM_026028)	40	NM_026028	67200	Mm.45767	NM_026028	ENSMUSG00000030177	Ccdc77	2400002C23Rik|2700091N06Rik|AV168274	coiled-coil domain containing 77	protein-coding
mm_47211.1	chr5	121009383	121009394	-	1	NA	promoter-TSS (NM_001302345)	promoter-TSS (NM_001302345)	150	NM_011286	19894	Mm.181166	NM_011286	ENSMUSG00000029608	Rph3a	2900002P20Rik|AU022689|AW108370	rabphilin 3A	protein-coding
mm_105386.1	chr11	103363342	103363406	-	1	NA	5' UTR (NM_183288, exon 1 of 3)	5' UTR (NM_183288, exon 1 of 3)	318	NM_183288	544817	Mm.259113	NM_133715	ENSMUSG00000034255	Arhgap27	2310069I04Rik|5730442P18Rik|Gm21552|Sh3d20	Rho GTPase activating protein 27	protein-coding
mm_68409.1	chr7	109637380	109637407	-	1	NA	Intergenic	Intergenic	-20246	NM_029811	76954	Mm.252009	NM_029811	ENSMUSG00000031024	St5	2010004M01Rik|2610305K15Rik	suppression of tumorigenicity 5	protein-coding
mm_139343.1	chr17	50239135	50239140	+	1	NA	promoter-TSS (NR_131975)	promoter-TSS (NR_131975)	-71	NR_131975	446210	Mm.378184	NM_001004437	ENSMUSG00000067103	AY702103	STDP2	cDNA sequence AY702103	ncRNA
mm_10597.1	chr2	18677079	18677101	+	1	NA	promoter-TSS (NM_007552)	promoter-TSS (NM_007552)	72	NM_007552	12151	Mm.289584	NM_007552	ENSMUSG00000026739	Bmi1	AW546694|Bmi-1|Pcgf4	Bmi1 polycomb ring finger oncogene	protein-coding
mm_102374.1	chr11	58613482	58613495	-	1	NA	promoter-TSS (NM_144544)	promoter-TSS (NM_144544)	4	NM_144544	78354	Mm.58038	NM_144544	ENSMUSG00000037145	2210407C18Rik	Ep1	RIKEN cDNA 2210407C18 gene	protein-coding
mm_94310.1	chr11	4218256	4218279	+	1	NA	promoter-TSS (NM_028022)	promoter-TSS (NM_028022)	16	NM_028022	71962	Mm.7852	NM_028022	ENSMUSG00000020424	Gatsl3	2410008K03Rik	GATS protein-like 3	protein-coding
mm_38955.1	chr4	150570266	150570308	-	1	NA	exon (NM_001085492, exon 12 of 23)	exon (NM_001085492, exon 12 of 23)	81887	NM_173774	242773	Mm.29280	NM_173774	ENSMUSG00000039838	Slc45a1	C230078B22|Dnb5	solute carrier family 45, member 1	protein-coding
mm_62517.1	chr7	102225813	102225823	+	1	NA	intron (NR_111938, intron 2 of 4)	intron (NR_111938, intron 2 of 4)	2790	NR_111937	233575	Mm.302013	NM_145583	ENSMUSG00000030990	Pgap2	1810006G21Rik|C76649|Frag1	post-GPI attachment to proteins 2	protein-coding
mm_73802.1	chr8	117275198	117275215	+	1	NA	intron (NM_001163262, intron 1 of 20)	(CA)n|Simple_repeat|Simple_repeat	18187	NM_001163262	74440	Mm.233181	NM_028941	ENSMUSG00000034390	Cmip	4933407C03Rik|5830471E12Rik|AI314065|AI464126	c-Maf inducing protein	protein-coding
mm_91247.1	chr10	22731307	22731330	-	1	NA	5' UTR (NM_011603, exon 1 of 7)	5' UTR (NM_011603, exon 1 of 7)	129	NM_011603	237336	Mm.86670	NM_011603	ENSMUSG00000071359	Tbpl1	4732475G08|AW011832|AW491032|D18347|STD|TLF|TRF2|TRP|Tlp	TATA box binding protein-like 1	protein-coding
mm_84088.1	chr9	58204377	58204381	-	1	NA	promoter-TSS (NM_001161541)	promoter-TSS (NM_001161541)	-60	NM_001161541	320563	Mm.186499	NM_177193	ENSMUSG00000051243	Islr2	B930052A04Rik|Linx|Mbu-3|mKIAA1465	immunoglobulin superfamily containing leucine-rich repeat 2	protein-coding
mm_164569.1	chr17	21423233	21423264	+	1	NA	promoter-TSS (NM_011760)	promoter-TSS (NM_011760)	21	NM_011760	22712	Mm.12916	NM_011760	ENSMUSG00000023882	Zfp54	2810034D10Rik|KRAB10|Zfp-54|Zfp76|mszf83	zinc finger protein 54	protein-coding
mm_13816.1	chr2	119237352	119237374	+	1	NA	promoter-TSS (NM_016907)	promoter-TSS (NM_016907)	3	NM_016907	20732	Mm.104955	NM_016907	ENSMUSG00000027315	Spint1	HAI-1	serine protease inhibitor, Kunitz type 1	protein-coding
mm_140081.1	chr17	75178948	75178961	+	1	NA	5' UTR (NM_001331237, exon 1 of 30)	5' UTR (NM_001331237, exon 1 of 30)	173	NM_001331235	268977	Mm.269747	NM_019919	ENSMUSG00000001870	Ltbp1	9430031G15Rik|9830146M04|Ltbp-1|Ltbp1L|TGF-beta1-BP-1|Tgfb|b2b1000Clo	latent transforming growth factor beta binding protein 1	protein-coding
mm_86903.1	chr10	22343403	22343414	+	1	NA	intron (NM_009018, intron 5 of 5)	ETnERV-int|LTR|ERVK	-18486	NM_020030	56554	Mm.458004	NM_020030	ENSMUSG00000078452	Raet1d	RAE-1delta	retinoic acid early transcript delta	protein-coding
mm_76057.1	chr8	77724333	77724359	-	1	NA	5' UTR (NM_010332, exon 1 of 8)	5' UTR (NM_010332, exon 1 of 8)	106	NM_010332	13617	Mm.283168	NM_010332	ENSMUSG00000031616	Ednra	ET-AR|ETa|Gpcr10	endothelin receptor type A	protein-coding
mm_134612.1	chr16	20803258	20803260	-	1	NA	Intergenic	MER90a|LTR|ERV1	-68748	NM_009379	21832	Mm.3943	NM_009379	ENSMUSG00000022847	Thpo	Mgdf|Ml|Mpllg|Tpo	thrombopoietin	protein-coding
mm_139277.1	chr17	48247745	48247751	+	1	NA	promoter-TSS (NM_021407)	promoter-TSS (NM_021407)	19	NM_021407	58218	Mm.302438	NM_021407	ENSMUSG00000041754	Trem3	BB134760	triggering receptor expressed on myeloid cells 3	protein-coding
mm_69497.1	chr7	134225176	134225189	-	1	NA	promoter-TSS (NM_007400)	promoter-TSS (NM_007400)	-85	NM_007400	11489	Mm.439714	NM_007400	ENSMUSG00000054555	Adam12	Mltna	a disintegrin and metallopeptidase domain 12 (meltrin alpha)	protein-coding
mm_35806.1	chr4	46650050	46650078	-	1	NA	5' UTR (NM_198664, exon 1 of 13)	5' UTR (NM_198664, exon 1 of 13)	135	NM_198664	381605	Mm.331595	NM_198664	ENSMUSG00000039813	Tbc1d2	A630005A06Rik|BC022630|Gm1037|PARIS-1|PARIS1	TBC1 domain family, member 2	protein-coding
mm_111295.1	chr12	85475937	85475973	-	1	NA	exon (NM_010234, exon 4 of 4)	exon (NM_010234, exon 4 of 4)	2054	NM_010234	14281	Mm.246513	NM_010234	ENSMUSG00000021250	Fos	D12Rfj1|c-fos|cFos	FBJ osteosarcoma oncogene	protein-coding
mm_108306.1	chr12	79383811	79383831	+	1	NA	intron (NM_009014, intron 7 of 10)	Lx7|LINE|L1	86470	NM_001252562	19363	Mm.341756	NM_009014	ENSMUSG00000059060	Rad51b	AI553500|R51H2|Rad51l1|mREC2	RAD51 paralog B	protein-coding
mm_18274.1	chr2	52372537	52372550	-	1	NA	Intergenic	Intergenic	-33745	NM_010889	17996	Mm.389247	NM_010889	ENSMUSG00000026950	Neb	AI595938	nebulin	protein-coding
mm_10154.1	chr2	4389456	4389467	+	1	NA	intron (NM_172475, intron 1 of 22)	intron (NM_172475, intron 1 of 22)	-11515	NM_001177843	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding
mm_21865.1	chr2	165898952	165898988	-	1	NA	Intergenic	Intergenic	-14132	NM_001252587	228880	Mm.227598	NM_027230	ENSMUSG00000039671	Zmynd8	1110013E22Rik|2010005I16Rik|3632413B07Rik|AI316811|AL024039|Prkcbp1|RACK7	zinc finger, MYND-type containing 8	protein-coding
mm_8823.1	chr1	162387216	162387216	-	1	NA	intron (NM_001038619, intron 2 of 20)	intron (NM_001038619, intron 2 of 20)	90814	NM_001038619	103967	Mm.441620	NM_172646	ENSMUSG00000040265	Dnm3	9630020E24Rik|AW061159|B230343F03Rik|C530045C17|mKIAA0820	dynamin 3	protein-coding
mm_27144.1	chr3	32736780	32736782	-	1	NA	promoter-TSS (NM_025316)	promoter-TSS (NM_025316)	-26	NM_029017	74600	Mm.288960	NM_029017	ENSMUSG00000037531	Mrpl47	4833424P18Rik|CGI-204|ENSMUSG00000051761|Gm9859|L47mt|MRP-L47|MTF/L47|NCM1	mitochondrial ribosomal protein L47	protein-coding
mm_79139.1	chr9	47644443	47644446	+	1	NA	intron (NM_001025600, intron 1 of 8)	L1MC4a|LINE|L1	114092	NM_018770	54725	Mm.234832	NM_018770	ENSMUSG00000032076	Cadm1	2900073G06Rik|3100001I08Rik|AI987920|Bl2|Igsf4|Igsf4a|Necl2|RA175|RA175A|RA175B|RA175C|RA175N|ST17|SgIGSF|SynCam|Tslc1	cell adhesion molecule 1	protein-coding
mm_51723.1	chr6	86946859	86946881	+	1	NA	exon (NM_177762, exon 7 of 20)	exon (NM_177762, exon 7 of 20)	-62966	NM_001170591	56748	Mm.23809	NM_020045	ENSMUSG00000029993	Nfu1	0610006G17Rik|CGI-33|Hirip5	NFU1 iron-sulfur cluster scaffold	protein-coding
mm_76200.1	chr8	82774171	82774181	-	1	NA	promoter-TSS (NM_145600)	promoter-TSS (NM_145600)	-50	NM_145600	30932	Mm.269248	NM_145600	ENSMUSG00000031711	Zfp330	BC008086|Noa36|Znf330	zinc finger protein 330	protein-coding
mm_24107.1	chr3	88142329	88142483	+	1	NA	promoter-TSS (NM_001310593)	promoter-TSS (NM_001310593)	34	NM_001310593	17261	Mm.28184	NM_133665	ENSMUSG00000001419	Mef2d	C80750	myocyte enhancer factor 2D	protein-coding
mm_341.1	chr1	30874000	30874013	+	1	NA	Intergenic	CpG	-10750	NM_001081080	213109	Mm.194486	NM_025871	ENSMUSG00000048874	Phf3	2310061N19Rik|mKIAA0244	PHD finger protein 3	protein-coding
mm_17284.1	chr2	26140290	26140344	-	1	NA	promoter-TSS (NM_001256522)	promoter-TSS (NM_001256522)	189	NM_001256521	109299	Mm.389259	NM_001256521		C330006A16Rik	AI551216	RIKEN cDNA C330006A16 gene	protein-coding
mm_86339.1	chr9	123216023	123216046	-	1	NA	promoter-TSS (NM_133974)	promoter-TSS (NM_133974)	4	NM_133974	109332	Mm.27519	NM_133974	ENSMUSG00000035498	Cdcp1	9030022E12Rik|AA409659|E030027H19Rik	CUB domain containing protein 1	protein-coding
mm_93090.1	chr10	89621430	89621464	-	1	NA	promoter-TSS (NM_182959)	promoter-TSS (NM_182959)	-198	NM_182959	216227	Mm.233921	NM_182959	ENSMUSG00000019935	Slc17a8	BC042593|Vglut3	solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 8	protein-coding
mm_112401.1	chr13	3538112	3538150	+	1	NA	promoter-TSS (NM_008112)	promoter-TSS (NM_008112)	56	NM_008112	14569	Mm.153226	NM_008112	ENSMUSG00000021218	Gdi2	GDI-B|GDIB|Gdi3	guanosine diphosphate (GDP) dissociation inhibitor 2	protein-coding
mm_106556.1	chr11	120624974	120624998	-	1	NA	promoter-TSS (NR_105901)	promoter-TSS (NR_105901)	16	NM_153056	209011	Mm.292957	NM_153056	ENSMUSG00000025138	Sirt7	-	sirtuin 7	protein-coding
mm_132143.1	chr16	32003221	32003266	+	1	NA	promoter-TSS (NM_177103)	promoter-TSS (NM_177103)	44	NM_177103	320213	Mm.152890	NM_023801	ENSMUSG00000022772	Senp5	6230429P13Rik|A730063F07Rik|AI851888|BB189556|SMT3IP3	SUMO/sentrin specific peptidase 5	protein-coding
mm_142271.1	chr17	39847759	39847784	-	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	4774	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_39891.1	chr5	31180183	31180210	+	1	NA	promoter-TSS (NM_027901)	promoter-TSS (NM_027901)	-52	NM_027901	71752	Mm.271923	NM_027901	ENSMUSG00000101678	Gtf3c2	1300004C11Rik|2610510G03Rik|AI225816|AU041069|TFIIIC110|mKIAA0011	general transcription factor IIIC, polypeptide 2, beta	protein-coding
mm_51012.1	chr6	65022122	65022132	+	1	NA	Intergenic	Intergenic	-20540	NM_007958	13990	Mm.99113	NM_007958	ENSMUSG00000029920	Smarcad1	AV081750|AW226546|D6Pas1|Etl1|mKIAA1122	SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1	protein-coding
mm_65822.1	chr7	29166902	29166905	-	1	NA	intron (NM_182927, intron 2 of 5)	intron (NM_182927, intron 2 of 5)	1744	NM_182927	101809	Mm.377262	NM_182927	ENSMUSG00000037239	Spred3	AW047143|D130060H24Rik|Spred-3	sprouty-related, EVH1 domain containing 3	protein-coding
mm_1905.1	chr1	85851436	85851460	+	1	NA	3' UTR (NM_133781, exon 9 of 9)	3' UTR (NM_133781, exon 9 of 9)	-43062	NM_022417	64294	Mm.29870	NM_022417	ENSMUSG00000026223	Itm2c	3110038L02Rik|BRI3|Bricd2c|E25|E25C|ITM3	integral membrane protein 2C	protein-coding
mm_104774.1	chr11	98545921	98545945	-	1	NA	promoter-TSS (NM_011771)	promoter-TSS (NM_011771)	98	NM_011771	22780	Mm.133367	NM_011771	ENSMUSG00000018168	Ikzf3	5830411O07Rik|Aiolos|Zfpn1a3|Znfn1a3	IKAROS family zinc finger 3	protein-coding
mm_61166.1	chr7	59229032	59229051	+	1	NA	5' UTR (NM_001033962, exon 1 of 11)	5' UTR (NM_001033962, exon 1 of 11)	289	NM_011668	22215	Mm.9002	NM_011668	ENSMUSG00000025326	Ube3a	4732496B02|5830462N02Rik|A130086L21Rik|Hpve6a|mKIAA4216	ubiquitin protein ligase E3A	protein-coding
mm_130684.1	chr15	100681570	100681585	-	1	NA	intron (NM_033612, intron 5 of 7)	(TCCC)n|Simple_repeat|Simple_repeat	6343	NM_033612	109901	Mm.2131	NM_033612	ENSMUSG00000023031	Cela1	1810009A17Rik|1810062B19Rik|Ela-1|Ela1|PC-TsF	chymotrypsin-like elastase family, member 1	protein-coding
mm_127643.1	chr15	102483205	102483239	+	1	NA	exon (NM_001174073, exon 7 of 13)	exon (NM_001174073, exon 7 of 13)	12590	NM_001174073	18521	Mm.236513	NM_011042	ENSMUSG00000056851	Pcbp2	AW412548|Hnrpx|alphaCP-2	poly(rC) binding protein 2	protein-coding
mm_103904.1	chr11	83578421	83578428	-	1	NA	exon (NM_011338, exon 1 of 4)	exon (NM_011338, exon 1 of 4)	212	NM_011338	20308	Mm.416125	NM_011338	ENSMUSG00000019122	Ccl9	CCF18|MRP-2|Scya10|Scya9	chemokine (C-C motif) ligand 9	protein-coding
mm_128681.1	chr15	60824858	60824872	-	1	NA	5' UTR (NM_001162926, exon 1 of 2)	5' UTR (NM_001162926, exon 1 of 2)	215	NM_001162926	399603	Mm.411968	NM_207269	ENSMUSG00000072568	Fam84b	BF642811|D330050I23Rik	family with sequence similarity 84, member B	protein-coding
mm_41426.1	chr5	90892616	90892640	+	1	NA	3' UTR (NM_008176, exon 4 of 4)	3' UTR (NM_008176, exon 4 of 4)	1383	NM_008176	14825	Mm.21013	NM_008176	ENSMUSG00000029380	Cxcl1	Fsp|Gro1|KC|Mgsa|N51|Scyb1|gro	chemokine (C-X-C motif) ligand 1	protein-coding
mm_139155.1	chr17	47540488	47540501	+	1	NA	intron (NM_001081635, intron 1 of 6)	intron (NM_001081635, intron 1 of 6)	35443	NM_001081635	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_29198.1	chr3	106766426	106766465	-	1	NA	intron (NM_007651, intron 5 of 7)	B3|SINE|B2	23704	NM_007651	12508	Mm.316861	NM_007651	ENSMUSG00000040747	Cd53	AI323659|Ox-44|Tspan25	CD53 antigen	protein-coding
mm_149443.1	chr19	11481192	11481290	+	1	NA	3' UTR (NM_028595, exon 7 of 7)	3' UTR (NM_028595, exon 7 of 7)	-10797	NM_001164202	666926	Mm.486382	NM_001164202	ENSMUSG00000058470	Gm8369	EG666926	predicted gene 8369	protein-coding
mm_11266.1	chr2	30018864	30018867	+	1	NA	intron (NM_001309460, intron 41 of 57)	intron (NM_001309460, intron 41 of 57)	22915	NR_105963	102465603		NR_105963	ENSMUSG00000098453	Mir6997	Gm27310|mmu-mir-6997	microRNA 6997	ncRNA
mm_35114.1	chr4	10797793	10797802	-	1	NA	promoter-TSS (NR_045185)	promoter-TSS (NR_045185)	5	NR_045185	73624	Mm.67392	NR_045185	ENSMUSG00000086080	1700123O12Rik	-	RIKEN cDNA 1700123O12 gene	ncRNA
mm_30697.1	chr4	11694804	11694809	+	1	NA	Intergenic	Intergenic	-9641	NM_010276	14579	Mm.247486	NM_010276	ENSMUSG00000028214	Gem	AV020497	GTP binding protein (gene overexpressed in skeletal muscle)	protein-coding
mm_4487.1	chr1	173631028	173631068	+	1	NA	5' UTR (NM_175026, exon 1 of 7)	5' UTR (NM_175026, exon 1 of 7)	189	NM_175026	236312	Mm.447	NM_175026	ENSMUSG00000043263	Ifi209	4930422C14|AI447904|Ifix|Pyhin-1|Pyhin1	interferon activated gene 209	protein-coding
mm_162809.1	chr10	79544322	79544343	-	1	NA	intron (NM_001316699, intron 10 of 13)	intron (NM_001316699, intron 10 of 13)	-10545	NM_001302389	50784	Mm.28873	NM_015817	ENSMUSG00000052151	Plpp2	Lpp2|PAP2-G|PAP2-gamma|PAP2c|Ppap2c	phospholipid phosphatase 2	protein-coding
mm_11389.1	chr2	31446761	31446775	+	1	NA	Intergenic	ORR1C2|LTR|ERVL-MaLR	-23502	NM_007494	11898	Mm.3217	NM_007494	ENSMUSG00000076441	Ass1	AA408052|ASS|Ass-1|fold	argininosuccinate synthetase 1	protein-coding
mm_44469.1	chr5	23402577	23402578	-	1	NA	Intergenic	Intergenic	31776	NR_040469	269630	Mm.425231	NR_040469	ENSMUSG00000073147	5031425E22Rik	-	RIKEN cDNA 5031425E22 gene	ncRNA
mm_54065.1	chr6	13872306	13872316	-	1	NA	promoter-TSS (NR_024619)	promoter-TSS (NR_024619)	742	NR_045995	76311	Mm.367129	NR_045995	ENSMUSG00000097616	1110019D14Rik	-	RIKEN cDNA 1110019D14 gene	ncRNA
mm_149155.1	chr19	9015497	9015545	+	1	NA	exon (NM_009643, exon 5 of 5)	exon (NM_009643, exon 5 of 5)	-2383	NR_105786	102465190		NR_105786	ENSMUSG00000099308	Mir6367	Gm27467|mmu-mir-6367	microRNA 6367	ncRNA
mm_144562.1	chr18	31759977	31760003	+	1	NA	promoter-TSS (NM_001242430)	promoter-TSS (NM_001242430)	166	NM_153515	225339	Mm.290804	NM_153515	ENSMUSG00000041915	Ammecr1l	5430429D03Rik|AU022236|AU040755|AW111353|E230022H04Rik	AMME chromosomal region gene 1-like	protein-coding
mm_97229.1	chr11	75651542	75651613	+	1	NA	promoter-TSS (NM_001080774)	promoter-TSS (NM_001080774)	68	NM_008659	17913	Mm.234502	NM_008659	ENSMUSG00000017774	Myo1c	C80397|MMIb|MYO1E|NMI|mm1beta|myr2	myosin IC	protein-coding
mm_141306.1	chr17	28224153	28224167	-	1	NA	exon (NM_027185, exon 7 of 11)	exon (NM_027185, exon 7 of 11)	-8594	NM_011145	19015	Mm.328914	NM_011145	ENSMUSG00000002250	Ppard	NUC-1|NUC1|Nr1c2|PPAR-beta|PPAR-delta|PPAR[b]|PPARdelta|Pparb|Pparb/d	peroxisome proliferator activator receptor delta	protein-coding
mm_13316.1	chr2	102659214	102659232	+	1	NA	5' UTR (NM_001077514, exon 1 of 11)	5' UTR (NM_001077514, exon 1 of 11)	540	NM_001077514	20511	Mm.267547	NM_011393	ENSMUSG00000005089	Slc1a2	1700091C19Rik|2900019G14Rik|AI159670|Eaat2|GLT-1|GLT1|MGLT1	solute carrier family 1 (glial high affinity glutamate transporter), member 2	protein-coding
mm_63839.1	chr7	135650344	135650354	+	1	NA	intron (NR_015548, intron 2 of 2)	intron (NR_015548, intron 2 of 2)	-1550	NM_001316681	19267	Mm.945	NM_011212	ENSMUSG00000041836	Ptpre	PTPe|PTPepsilon|RPTPepsilon	protein tyrosine phosphatase, receptor type, E	protein-coding
mm_97856.1	chr11	83078333	83078352	+	1	NA	Intergenic	Intergenic	13230	NM_011408	20556	Mm.278689	NM_011408	ENSMUSG00000072620	Slfn2	Shlf2	schlafen 2	protein-coding
mm_51343.1	chr6	72549253	72549264	+	1	NA	promoter-TSS (NM_001042534)	promoter-TSS (NM_001042534)	-15	NM_001042534	12332	Mm.18626	NM_007599	ENSMUSG00000056737	Capg	gCap39|mbh1	capping protein (actin filament), gelsolin-like	protein-coding
mm_163601.1	chr13	46669511	46669515	+	1	NA	promoter-TSS (NM_001033192)	promoter-TSS (NM_001033192)	-9	NM_001033192	97863	Mm.275934	NM_001033192	ENSMUSG00000069237	Fam8a1	C78339	family with sequence similarity 8, member A1	protein-coding
mm_31568.1	chr4	57594396	57594413	+	1	NA	intron (NM_001304544, intron 1 of 8)	RSINE1|SINE|B4	26156	NM_172868	242481	Mm.331630	NM_172868	ENSMUSG00000090053	Palm2	53-H12|B130066I24|R75368|pEN70	paralemmin 2	protein-coding
mm_95310.1	chr11	46372887	46372899	+	1	NA	intron (NM_010583, intron 1 of 16)	Lx8b|LINE|L1	16622	NM_001281968	16428	Mm.339927	NM_010583	ENSMUSG00000020395	Itk	Emt|Tcsk|Tsk	IL2 inducible T cell kinase	protein-coding
mm_66949.1	chr7	62046245	62046250	-	1	NA	promoter-TSS (NR_037288)	promoter-TSS (NR_037288)	1	NR_037288	100526527		NR_037288	ENSMUSG00000093108	Mir344f	mir-344f|mmu-mir-344f	microRNA Mir344f	ncRNA
mm_127992.1	chr15	12622334	12622345	-	1	NA	Intergenic	Intergenic	-29783	NM_001081064	68070	Mm.423205	NM_001081064	ENSMUSG00000022197	Pdzd2	4930537L06Rik|A930022H17Rik|Gm21706|Gm82|Pdzk3|mKIAA0300	PDZ domain containing 2	protein-coding
mm_44109.1	chr5	149369127	149369136	+	1	NA	Intergenic	Intergenic	-42675	NM_027519	70717	Mm.252139	NM_027519	ENSMUSG00000029659	Medag	6330406I15Rik|Awms3|MEDA-4|Meda4|mAWMS3	mesenteric estrogen dependent adipogenesis	protein-coding
mm_78957.1	chr9	45138930	45138939	+	1	NA	promoter-TSS (NM_001013390)	promoter-TSS (NM_001013390)	-108	NM_001013390	399548	Mm.335112	NM_001013390	ENSMUSG00000046480	Scn4b	Gm1471	sodium channel, type IV, beta	protein-coding
mm_114425.1	chr13	64432596	64432609	+	1	NA	promoter-TSS (NM_053180)	promoter-TSS (NM_053180)	49	NM_053180	105278	Mm.74982	NM_053180	ENSMUSG00000021483	Cdk20	4932702G04Rik|AU019450|AW558027|CDCH|Ccrk|PNQLARE|p42	cyclin-dependent kinase 20	protein-coding
mm_111025.1	chr12	79103914	79103950	-	1	NA	promoter-TSS (NR_110486)	promoter-TSS (NR_110486)	7	NR_110486	321017	Mm.311575	NR_110486		9230116L04Rik	-	RIKEN cDNA 9230116L04 gene	ncRNA
mm_89990.1	chr10	112002458	112002498	+	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-5214	NM_028608	73690	Mm.173790	NM_028608	ENSMUSG00000056888	Glipr1	2410114O14Rik|RTVP-1|RTVP1|mRTVP-1	GLI pathogenesis-related 1 (glioma)	protein-coding
mm_165506.1	chr2	167777997	167778007	-	1	NA	Intergenic	Intergenic	86825	NR_015500	329562	Mm.123101	NM_177851	ENSMUSG00000006462	A530013C23Rik	-	RIKEN cDNA A530013C23 gene	ncRNA
mm_95593.1	chr11	53332384	53332394	+	1	NA	exon (NM_026479, exon 4 of 4)	exon (NM_026479, exon 4 of 4)	7700	NM_026479	67966	Mm.288072	NM_026479	ENSMUSG00000018239	Zcchc10	2410141K03Rik|AA675321|D11Ertd416e	zinc finger, CCHC domain containing 10	protein-coding
mm_84106.1	chr9	58312991	58313004	-	1	NA	5' UTR (NM_010729, exon 1 of 7)	5' UTR (NM_010729, exon 1 of 7)	215	NM_010729	16949	Mm.250492	NM_010729	ENSMUSG00000032334	Loxl1	Loxl	lysyl oxidase-like 1	protein-coding
mm_77511.1	chr8	122893593	122893623	-	1	NA	non-coding (NR_037865, exon 10 of 14)	non-coding (NR_037865, exon 10 of 14)	45234	NM_007662	12555	Mm.1976	NM_007662	ENSMUSG00000031962	Cdh15	AI323380|Cdh14|Mcad	cadherin 15	protein-coding
mm_21870.1	chr2	165977010	165977015	-	1	NA	Intergenic	Intergenic	-15625	NM_008679	17979	Mm.469663	NM_008679	ENSMUSG00000027678	Ncoa3	2010305B15Rik|AW321064|Actr|Aib1|KAT13B|Rac3|Src3|Tram-1|Tram1|bHLHe42|p/Cip|pCip	nuclear receptor coactivator 3	protein-coding
mm_162816.1	chr10	79874065	79874082	+	1	NA	exon (NM_001170935, exon 1 of 9)	exon (NM_001170935, exon 1 of 9)	561	NM_181681	216152	Mm.29678	NM_181681	ENSMUSG00000035835	Plppr3	Lppr3|Prg2	phospholipid phosphatase related 3	protein-coding
mm_151665.1	chr19	4163288	4163338	-	1	NA	promoter-TSS (NM_021485)	promoter-TSS (NM_021485)	-68	NM_021485	58988	Mm.271937	NM_021485	ENSMUSG00000024830	Rps6kb2	70kDa|S6K2	ribosomal protein S6 kinase, polypeptide 2	protein-coding
mm_41898.1	chr5	105519435	105519472	+	1	NA	promoter-TSS (NM_133897)	promoter-TSS (NM_133897)	-18	NM_133897	100604	Mm.319847	NM_133897	ENSMUSG00000054720	Lrrc8c	AD158|AI326115|E430036I04Rik|fad158	leucine rich repeat containing 8 family, member C	protein-coding
mm_5247.1	chr1	16520068	16520095	-	1	NA	promoter-TSS (NM_025303)	promoter-TSS (NM_025303)	-779	NM_001111272	29819	Mm.216257	NM_025303	ENSMUSG00000025920	Stau2	-	staufen (RNA binding protein) homolog 2 (Drosophila)	protein-coding
mm_21631.1	chr2	164277319	164277323	-	1	NA	exon (NM_009300, exon 2 of 3)	exon (NM_009300, exon 2 of 3)	986	NM_009300	20941	Mm.1286	NM_009300	ENSMUSG00000016998	Svs4	SVS-IV|Svp-2|Svp-4|Svp2|Svp4	seminal vesicle secretory protein 4	protein-coding
mm_167904.1	chrX	77837947	77837953	-	1	NA	TTS (NM_017471)	TTS (NM_017471)	15550	NM_017471	54192	Mm.8034	NM_017471	ENSMUSG00000000003	Pbsn	PB|Prbs	probasin	protein-coding
mm_82101.1	chr9	123061806	123061810	+	1	NA	exon (NM_177911, exon 11 of 14)	exon (NM_177911, exon 11 of 14)	27067	NM_177911	331046	Mm.195309	NM_177911	ENSMUSG00000025787	Tgm4	9530008N10Rik|Eapa1|TGP	transglutaminase 4 (prostate)	protein-coding
mm_52647.1	chr6	117179209	117179235	+	1	NA	3' UTR (NM_001012477, exon 4 of 4)	3' UTR (NM_001012477, exon 4 of 4)	10687	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_117192.1	chr13	63566188	63566224	-	1	NA	promoter-TSS (NM_008957)	promoter-TSS (NM_008957)	-471	NM_008957	19206	Mm.228798	NM_008957	ENSMUSG00000021466	Ptch1	A230106A15Rik|Ptc|Ptc1|Ptch|mes	patched 1	protein-coding
mm_43668.1	chr5	138757871	138757884	+	1	NA	exon (NM_030565, exon 2 of 10)	exon (NM_030565, exon 2 of 10)	2796	NM_030565	80752	Mm.320355	NM_030565	ENSMUSG00000025854	Fam20c	C76981|DMP-4|DMP4|GEF-CK|mKIAA4081	family with sequence similarity 20, member C	protein-coding
mm_161889.1	chr18	39487015	39487015	-	1	NA	exon (NM_008173, exon 1 of 8)	exon (NM_008173, exon 1 of 8)	230	NM_008173	14815	Mm.129481	NM_008173	ENSMUSG00000024431	Nr3c1	GR|Grl-1|Grl1	nuclear receptor subfamily 3, group C, member 1	protein-coding
mm_72543.1	chr8	83997516	83997516	+	1	NA	promoter-TSS (NM_001081415)	promoter-TSS (NM_001081415)	-156	NM_001081415	666704	Mm.298091	NM_001081415	ENSMUSG00000079003	Samd1	AA589507	sterile alpha motif domain containing 1	protein-coding
mm_48192.1	chr5	137529676	137529692	-	1	NA	promoter-TSS (NR_105846)	promoter-TSS (NR_105846)	-90	NR_105846	102465227		NR_105846	ENSMUSG00000098597	Mir6418	Gm27629|mir-6418|mmu-mir-6418	microRNA 6418	ncRNA
mm_38704.1	chr4	145215364	145215395	-	1	NA	3' UTR (NM_011610, exon 10 of 10)	3' UTR (NM_011610, exon 10 of 10)	-20374	NM_001276465	230895	Mm.240310	NM_001033190	ENSMUSG00000020220	Vps13d	-	vacuolar protein sorting 13D	protein-coding
mm_78605.1	chr9	37539266	37539279	+	1	NA	promoter-TSS (NM_020518)	promoter-TSS (NM_020518)	17	NM_020518	57276	Mm.27478	NM_020518	ENSMUSG00000001943	Vsig2	1190004B15Rik|2210413P10Rik|AU040484|CTX|Ctm	V-set and immunoglobulin domain containing 2	protein-coding
mm_75689.1	chr8	68206013	68206026	-	1	NA	Intergenic	Intergenic	-70509	NM_028182	72281	Mm.40974	NM_028182	ENSMUSG00000053886	Sh2d4a	2210402M20Rik|SH2A	SH2 domain containing 4A	protein-coding
mm_146103.1	chr18	74216101	74216109	+	1	NA	promoter-TSS (NM_028868)	promoter-TSS (NM_028868)	-107	NM_028868	74322	Mm.17537	NM_028868	ENSMUSG00000024560	Cxxc1	2410002I16Rik|5830420C16Rik|AI426635|Cfp1|Cgbp|PHF18	CXXC finger 1 (PHD domain)	protein-coding
mm_55354.1	chr6	56888698	56888713	-	1	NA	intron (NM_001252374, intron 5 of 9)	intron (NM_001252374, intron 5 of 9)	13181	NM_001252374	107569	Mm.158936	NM_026004	ENSMUSG00000029780	Nt5c3	1600024P05Rik|2610206B05Rik|3110004A18Rik|AI842776|Nt5c3a|Nt5y|PN-1|PN-I|PSN1|UMPH|Umph-1|Umph1|cN-III|lupin|p36	5'-nucleotidase, cytosolic III	protein-coding
mm_62938.1	chr7	118912618	118912641	+	1	NA	intron (NM_001081446, intron 6 of 8)	intron (NM_001081446, intron 6 of 8)	-56631	NM_023197	66356	Mm.482278	NM_023197	ENSMUSG00000030980	Knop1	2310008H09Rik|Tsg118	lysine rich nucleolar protein 1	protein-coding
mm_49546.1	chr6	30460992	30461000	+	1	NA	promoter-TSS (NR_131049)	promoter-TSS (NR_131049)	11	NR_131049	69337	Mm.396168	NR_131049	ENSMUSG00000085470	1700012C14Rik	-	RIKEN cDNA 1700012C14 gene	ncRNA
mm_12472.1	chr2	71499585	71499603	+	1	NA	intron (NM_025633, intron 1 of 9)	intron (NM_025633, intron 1 of 9)	-29851	NM_010053	13390	Mm.475101	NM_010053	ENSMUSG00000041911	Dlx1	Dlx|Dlx-1	distal-less homeobox 1	protein-coding
mm_24651.1	chr3	94392742	94392748	+	1	NA	intron (NR_121656, intron 8 of 9)	intron (NR_121656, intron 8 of 9)	-6474	NM_177250	320747	Mm.213001	NM_177250	ENSMUSG00000044505	Lingo4	A530050P17Rik|LERN4|Lrrn6d	leucine rich repeat and Ig domain containing 4	protein-coding
mm_120394.1	chr14	64652504	64652521	+	1	NA	promoter-TSS (NM_001081177)	promoter-TSS (NM_001081177)	-19	NM_001081177	16554	Mm.23611	NM_001081177	ENSMUSG00000060012	Kif13b	5330429L19Rik|6030414C01|AI429803|C130021D12Rik|GAKIN	kinesin family member 13B	protein-coding
mm_152302.1	chr19	9085342	9085350	-	1	NA	exon (NM_011681, exon 2 of 3)	exon (NM_011681, exon 2 of 3)	2610	NM_011681	22287	Mm.2258	NM_011681	ENSMUSG00000024653	Scgb1a1	CC10|CC16|CCSP|PCB-BP|UG|UGB|Utg	secretoglobin, family 1A, member 1 (uteroglobin)	protein-coding
mm_97027.1	chr11	72207538	72207620	+	1	NA	promoter-TSS (NM_026559)	promoter-TSS (NM_026559)	25	NM_026559	52700	Mm.27670	NM_026559	ENSMUSG00000020803	Txndc17	4831443O22Rik|D11Ertd672e|TRP14|Txnl5	thioredoxin domain containing 17	protein-coding
mm_28906.1	chr3	98580551	98580555	-	1	NA	Intergenic	Intergenic	-16515	NM_008294	15495	Mm.14309	NM_008294	ENSMUSG00000095143	Hsd3b4	-	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 4	protein-coding
mm_58090.1	chr6	137487218	137487221	-	1	NA	intron (NM_001271589, intron 11 of 13)	intron (NM_001271589, intron 11 of 13)	32676	NM_001271589	13860	Mm.235346	NM_007945	ENSMUSG00000015766	Eps8	AW261790	epidermal growth factor receptor pathway substrate 8	protein-coding
mm_155429.1	chrX	73492971	73492982	+	1	NA	exon (NM_007542, exon 6 of 8)	exon (NM_007542, exon 6 of 8)	9375	NM_007542	12111	Mm.2608	NM_007542	ENSMUSG00000031375	Bgn	BG|DSPG1|PG-S1|PGI|SLRR1A	biglycan	protein-coding
mm_83224.1	chr9	42264205	42264219	-	1	NA	promoter-TSS (NM_172769)	promoter-TSS (NM_172769)	88	NM_172769	235293	Mm.32700	NM_172769	ENSMUSG00000032018	Sc5d	A830037K02|A830073K23Rik|Sc5dl	sterol-C5-desaturase	protein-coding
mm_52274.1	chr6	108658655	108658670	+	1	NA	intron (NR_104577, intron 1 of 6)	intron (NR_104577, intron 1 of 6)	-1967	NM_011498	20893	Mm.2436	NM_011498	ENSMUSG00000030103	Bhlhe40	Bhlhb2|C130042M06Rik|CR8|Clast5|Dec1|Sharp2|Stra13|Stra14	basic helix-loop-helix family, member e40	protein-coding
mm_132835.1	chr16	45535326	45535336	+	1	NA	promoter-TSS (NM_198106)	promoter-TSS (NM_198106)	65	NM_198106	208169	Mm.277437	NM_198106	ENSMUSG00000033210	Slc9c1	Gm610|NHE-10|Slc9a10|sNHE|spermNHE	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	protein-coding
mm_56279.1	chr6	91117009	91117023	-	1	NA	promoter-TSS (NM_018815)	promoter-TSS (NM_018815)	-190	NM_018815	54563	Mm.28162	NM_018815	ENSMUSG00000030091	Nup210	9830001L10|AI836801|Pom210|gp190|gp210	nucleoporin 210	protein-coding
mm_108090.1	chr12	74284349	74284353	+	1	NA	promoter-TSS (NR_030735)	promoter-TSS (NR_030735)	75	NR_030735	74284	Mm.287421	NR_030733	ENSMUSG00000071265	1700086L19Rik	1700006L05Rik|AU016007	RIKEN cDNA 1700086L19 gene	ncRNA
mm_85701.1	chr9	108104875	108104902	-	1	NA	exon (NM_007567, exon 8 of 12)	exon (NM_007567, exon 8 of 12)	-10408	NM_146226	235606	Mm.219639	NM_146226	ENSMUSG00000032590	Apeh	-	acylpeptide hydrolase	protein-coding
mm_56826.1	chr6	117173658	117173668	-	1	NA	3' UTR (NM_021704, exon 3 of 3)	3' UTR (NM_021704, exon 3 of 3)	5128	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_134861.1	chr16	28446779	28446834	-	1	NA	promoter-TSS (NM_183064)	promoter-TSS (NM_183064)	-731	NM_001276420	14167	Mm.7996	NM_010199	ENSMUSG00000022523	Fgf12	AV114868|B230343J05Rik|FGF-12|FHF-1|Fhf1	fibroblast growth factor 12	protein-coding
mm_68156.1	chr7	102250577	102250595	-	1	NA	promoter-TSS (NM_019566)	promoter-TSS (NM_019566)	-468	NM_019566	56212	Mm.259795	NM_019566	ENSMUSG00000073982	Rhog	2810426G09Rik|Arhg|Sid10750	ras homolog family member G	protein-coding
mm_114004.1	chr13	52591833	52591836	+	1	NA	intron (NM_001198977, intron 1 of 13)	intron (NM_001198977, intron 1 of 13)	-5048	NM_011518	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_107811.1	chr12	65075583	65075617	+	1	NA	promoter-TSS (NM_178912)	promoter-TSS (NM_178912)	-6	NM_178912	104806	Mm.374847	NM_178912	ENSMUSG00000055884	Fancm	AI427100|C730036B14Rik|D12Ertd364e	Fanconi anemia, complementation group M	protein-coding
mm_167561.1	chr9	38972372	38972375	+	1	NA	Intergenic	Intergenic	-3305	NM_146441	258433	Mm.271361	NM_146441	ENSMUSG00000058515	Olfr933	MOR171-22	olfactory receptor 933	protein-coding
mm_48911.1	chr6	3994002	3994016	+	1	NA	promoter-TSS (NM_010314)	promoter-TSS (NM_010314)	-3	NM_010314	14699	Mm.95398	NM_010314	ENSMUSG00000029663	Gngt1	G(y)1|Gng1	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1	protein-coding
mm_83213.1	chr9	42097981	42097983	-	1	NA	intron (NM_011436, intron 3 of 47)	intron (NM_011436, intron 3 of 47)	26307	NM_011436	20660	Mm.121920	NM_011436	ENSMUSG00000049313	Sorl1	2900010L19Rik|AI596264|AW261561|LR11|SorLA|gp250|mSorLA	sortilin-related receptor, LDLR class A repeats-containing	protein-coding
mm_60572.1	chr7	44481565	44481580	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-2945	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_43868.1	chr5	143503546	143503566	+	1	NA	3' UTR (NM_144915, exon 15 of 15)	3' UTR (NM_144915, exon 15 of 15)	24437	NM_009007	19353	Mm.292510	NM_009007	ENSMUSG00000001847	Rac1	AL023026|D5Ertd559e	RAS-related C3 botulinum substrate 1	protein-coding
mm_45507.1	chr5	72504062	72504066	-	1	NA	exon (NM_016869, exon 1 of 22)	exon (NM_016869, exon 1 of 22)	144	NM_016869	53419	Mm.332425	NM_016869	ENSMUSG00000005220	Corin	AV273130|Lrp4	corin	protein-coding
mm_95204.1	chr11	43528760	43528796	+	1	NA	promoter-TSS (NM_001045530)	promoter-TSS (NM_001045530)	29	NM_001045530	380694	Mm.247595	NM_001045530	ENSMUSG00000044707	Ccnjl	Gm877	cyclin J-like	protein-coding
mm_27021.1	chr3	26046297	26046317	-	1	NA	intron (NM_138666, intron 3 of 7)	intron (NM_138666, intron 3 of 7)	107000	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_69646.1	chr7	139020944	139020957	-	1	NA	intron (NM_028708, intron 7 of 19)	intron (NM_028708, intron 7 of 19)	-65051	NM_011993	26757	Mm.250414	NM_011993	ENSMUSG00000025478	Dpysl4	AI173505|CRMP-3|Crmp3|DPY4|Drp-4|Ulip4	dihydropyrimidinase-like 4	protein-coding
mm_118076.1	chr13	103047162	103047162	-	1	NA	intron (NM_175171, intron 3 of 28)	PB1D10|SINE|Alu	286907	NR_130171	76624	Mm.426384	NR_130171	ENSMUSG00000091906	1700099I09Rik	-	RIKEN cDNA 1700099I09 gene	ncRNA
mm_133830.1	chr16	95900514	95900524	+	1	NA	intron (NR_040484, intron 1 of 3)	L1MC5|LINE|L1	-1806	NR_040485	69776	Mm.120470	NR_040484	ENSMUSG00000086899	1600002D24Rik	-	RIKEN cDNA 1600002D24 gene	ncRNA
mm_79193.1	chr9	48452337	48452345	+	1	NA	Intergenic	Intergenic	-2003	NR_026561	667933	Mm.491076	NR_026561		Gm8884	EG667933	predicted gene 8884	ncRNA
mm_19501.1	chr2	93462390	93462435	-	1	NA	promoter-TSS (NM_007656)	promoter-TSS (NM_007656)	90	NM_001271430	12521	Mm.4261	NM_007656	ENSMUSG00000027215	Cd82	AA682076|AL023070|C33|IA4|Kai1|Tspan27	CD82 antigen	protein-coding
mm_123517.1	chr14	66280950	66280997	-	1	NA	promoter-TSS (NM_172498)	promoter-TSS (NM_172498)	79	NM_172498	19229	Mm.21613	NM_172498	ENSMUSG00000059456	Ptk2b	CADTK|CAKB|CAKbeta|E430023O05Rik|FADK2|FAK2|PYK2|Raftk	PTK2 protein tyrosine kinase 2 beta	protein-coding
mm_57319.1	chr6	124732387	124732433	-	1	NA	exon (NM_013545, exon 3 of 16)	exon (NM_013545, exon 3 of 16)	744	NM_013545	15170	Mm.271799	NM_013545	ENSMUSG00000004266	Ptpn6	70Z-SHP|Hcph|PTPTY-42|Ptp1C|SH-PTP1|SHP-1|hcp|me	protein tyrosine phosphatase, non-receptor type 6	protein-coding
mm_3069.1	chr1	134189126	134189146	+	1	NA	intron (NM_007695, intron 8 of 9)	intron (NM_007695, intron 8 of 9)	-4312	NM_016749	53311	Mm.379067	NM_016749	ENSMUSG00000042451	Mybph	AI385643|MyBP-H	myosin binding protein H	protein-coding
mm_81778.1	chr9	114688821	114688833	+	1	NA	promoter-TSS (NM_146229)	promoter-TSS (NM_146229)	-4	NM_146229	235661	Mm.128627	NM_146229	ENSMUSG00000032435	Dync1li1	1110053F02Rik|Dnclic1|LIC-1	dynein cytoplasmic 1 light intermediate chain 1	protein-coding
mm_84684.1	chr9	72111173	72111225	-	1	NA	promoter-TSS (NM_001253862)	promoter-TSS (NM_001253862)	2	NM_001253862	21406	Mm.171615	NM_011544	ENSMUSG00000032228	Tcf12	A130037E08Rik|ALF1|HEB|HEBAlt|HTF-4|HTF4|ME1|REB|bHLHb20	transcription factor 12	protein-coding
mm_76826.1	chr8	104624250	104624262	-	1	NA	5' UTR (NM_001252627, exon 1 of 17)	5' UTR (NM_001252627, exon 1 of 17)	140	NM_007663	12556	Mm.19423	NM_007663	ENSMUSG00000031881	Cdh16	-	cadherin 16	protein-coding
mm_575.1	chr1	38987807	38987827	+	1	NA	promoter-TSS (NM_026850)	promoter-TSS (NM_026850)	3	NM_026850	68833	Mm.28121	NM_026850	ENSMUSG00000026078	Pdcl3	1110061A19Rik|C80025|Viaf1	phosducin-like 3	protein-coding
mm_88009.1	chr10	67098038	67098040	+	1	NA	Intergenic	Intergenic	-1051	NM_178606	28193	Mm.41272	NM_178606	ENSMUSG00000019873	Reep3	D10Ucla1	receptor accessory protein 3	protein-coding
mm_108682.1	chr12	86734382	86734417	+	1	NA	promoter-TSS (NM_001195767)	promoter-TSS (NM_001195767)	30	NM_001195767	627607	Mm.341880	NM_001195767	ENSMUSG00000059114	Lrrc74a	EG627607|Gm6772|Lrrc74	leucine rich repeat containing 74A	protein-coding
mm_35669.1	chr4	43562515	43562517	-	1	NA	promoter-TSS (NM_013497)	promoter-TSS (NM_013497)	67	NM_011602	21894	Mm.208601	NM_011602	ENSMUSG00000028465	Tln1	Tln	talin 1	protein-coding
mm_114217.1	chr13	56372632	56372636	+	1	NA	Intergenic	Intergenic	9734	NR_046061	100038494	Mm.370447	NR_046061		Gm10782	ENSMUSG00000074885	predicted gene 10782	ncRNA
mm_143783.1	chr17	81730987	81730995	-	1	NA	intron (NR_104580, intron 1 of 8)	B4|SINE|B4	7396	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_45123.1	chr5	46007543	46007557	-	1	NA	Intergenic	Intergenic	-75141	NR_110478	78106	Mm.243807	NR_110478	ENSMUSG00000106602	4930405L22Rik	-	RIKEN cDNA 4930405L22 gene	ncRNA
mm_137746.1	chr17	29381750	29381755	+	1	NA	Intergenic	Intergenic	20838	NM_001159538	26382	Mm.279187	NM_013710	ENSMUSG00000024013	Fgd2	Tcd-2|Tcd2|ZFYVE4|tcs-2|tcs2	FYVE, RhoGEF and PH domain containing 2	protein-coding
mm_11350.1	chr2	30845464	30845464	+	1	NA	promoter-TSS (NM_009116)	promoter-TSS (NM_009116)	97	NM_009116	20204	Mm.1802	NM_009116	ENSMUSG00000039476	Prrx2	Prx2|S8	paired related homeobox 2	protein-coding
mm_58021.1	chr6	136661743	136661752	-	1	NA	5' UTR (NM_025806, exon 1 of 11)	5' UTR (NM_025806, exon 1 of 11)	146	NM_025806	66857	Mm.3311	NM_025806	ENSMUSG00000030214	Plbd1	1100001H23Rik	phospholipase B domain containing 1	protein-coding
mm_86834.1	chr10	21295988	21296013	+	1	NA	promoter-TSS (NM_001145209)	promoter-TSS (NM_001145209)	21	NM_001145209	56422	Mm.25527	NM_019702	ENSMUSG00000019977	Hbs1l	2810035F15Rik|AI326327|eRFS	Hbs1-like (S. cerevisiae)	protein-coding
mm_155090.1	chrX	48146460	48146482	+	1	NA	promoter-TSS (NM_028773)	promoter-TSS (NM_028773)	35	NM_028773	74131	Mm.276131	NM_028773	ENSMUSG00000031101	Sash3	1200013B08Rik|AW413946|SLY1	SAM and SH3 domain containing 3	protein-coding
mm_160223.1	chr7	101838212	101838212	-	1	NA	promoter-TSS (NM_010567)	promoter-TSS (NM_010567)	14	NM_010567	16332	Mm.476000	NM_010567	ENSMUSG00000032737	Inppl1	51C|SHIP2	inositol polyphosphate phosphatase-like 1	protein-coding
mm_59244.1	chr7	24784488	24784489	+	1	NA	3' UTR (NM_007675, exon 4 of 4)	3' UTR (NM_007675, exon 4 of 4)	7284	NM_007675	26366	Mm.30300	NM_007675	ENSMUSG00000054169	Ceacam10	Bgp3|Cea10	carcinoembryonic antigen-related cell adhesion molecule 10	protein-coding
mm_51467.1	chr6	82946899	82946924	+	1	NA	promoter-TSS (NM_033079)	promoter-TSS (NM_033079)	-11	NM_033079	110958	Mm.100652	NM_033079	ENSMUSG00000030041	M1ap	D6Mm5e	meiosis 1 associated protein	protein-coding
mm_19880.1	chr2	114049553	114049599	-	1	NA	exon (NM_009608, exon 4 of 7)	exon (NM_009608, exon 4 of 7)	3299	NM_009608	11464	Mm.686	NM_009608	ENSMUSG00000068614	Actc1	Actc-1	actin, alpha, cardiac muscle 1	protein-coding
mm_15256.1	chr2	154892936	154892944	+	1	NA	promoter-TSS (NM_026030)	promoter-TSS (NM_026030)	-34	NM_026030	67204	Mm.377134	NM_026030	ENSMUSG00000074656	Eif2s2	2810026E11Rik|38kDa|AA408636|AA571381|AA986487|AW822225|D2Ertd303e|EIF2|EIF2B	eukaryotic translation initiation factor 2, subunit 2 (beta)	protein-coding
mm_131800.1	chr16	22899250	22899258	+	1	NA	non-coding (NR_075099, exon 6 of 6)	non-coding (NR_075099, exon 6 of 6)	-4868	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_33057.1	chr4	123190942	123190949	+	1	NA	3' UTR (NM_174998, exon 5 of 5)	3' UTR (NM_174998, exon 5 of 5)	7441	NM_174998	170638	Mm.270641	NM_174998	ENSMUSG00000046093	Hpcal4	AI846570|NVP-2	hippocalcin-like 4	protein-coding
mm_33220.1	chr4	126677660	126677673	+	1	NA	promoter-TSS (NM_011970)	promoter-TSS (NM_011970)	23	NM_011970	26445	Mm.22233	NM_011970	ENSMUSG00000028837	Psmb2	AU045357|AW108089|C7-I|D4Wsu33e|HC7-I	proteasome (prosome, macropain) subunit, beta type 2	protein-coding
mm_100783.1	chr11	4833049	4833057	-	1	NA	promoter-TSS (NM_001252253)	promoter-TSS (NM_001252253)	82	NM_001252253	18016	Mm.297109	NM_010898	ENSMUSG00000009073	Nf2	merlin	neurofibromin 2	protein-coding
mm_104520.1	chr11	96065316	96065327	-	1	NA	promoter-TSS (NM_172300)	promoter-TSS (NM_172300)	43	NM_172300	268470	Mm.38802	NM_172300	ENSMUSG00000014349	Ube2z	AW049199|C030047H17Rik|D11Moh35	ubiquitin-conjugating enzyme E2Z	protein-coding
mm_164879.1	chr18	58210268	58210269	-	1	NA	promoter-TSS (NM_010181)	promoter-TSS (NM_010181)	-342	NM_010181	14119	Mm.20271	NM_010181	ENSMUSG00000024598	Fbn2	BC063774|Fib-2|mKIAA4226|sne|sy	fibrillin 2	protein-coding
mm_15353.1	chr2	156255184	156255191	+	1	NA	intron (NM_172674, intron 4 of 17)	PB1D9|SINE|Alu	-57286	NM_027585	70873	Mm.475234	NM_027585	ENSMUSG00000038085	Cnbd2	4921517L17Rik|5430421B09Rik|Cris	cyclic nucleotide binding domain containing 2	protein-coding
mm_59619.1	chr7	28152816	28152825	+	1	NA	exon (NM_001164655, exon 11 of 20)	exon (NM_001164655, exon 11 of 20)	-16928	NM_007991	14113	Mm.4595	NM_007991	ENSMUSG00000046865	Fbl	AL022665|FIB|FLRN|RNU3IP1	fibrillarin	protein-coding
mm_152512.1	chr19	11278690	11278699	-	1	NA	intron (NM_183190, intron 2 of 4)	intron (NM_183190, intron 2 of 4)	5119	NM_183190	269063	Mm.268940	NM_183190	ENSMUSG00000054523	Ms4a5	-	membrane-spanning 4-domains, subfamily A, member 5	protein-coding
mm_136369.1	chr16	92817927	92817940	-	1	NA	intron (NM_001111022, intron 2 of 6)	C-rich|Low_complexity|Low_complexity	8141	NM_001111021	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_27033.1	chr3	26317829	26317830	-	1	NA	intron (NM_138666, intron 1 of 7)	intron (NM_138666, intron 1 of 7)	14080	NM_138666	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_93073.1	chr10	89417710	89417713	-	1	NA	intron (NM_001079876, intron 9 of 10)	Lx8|LINE|L1	26256	NM_001284344	237436	Mm.11982	NM_001033331	ENSMUSG00000074802	Gas2l3	8430435B07Rik|Gm240	growth arrest-specific 2 like 3	protein-coding
mm_35105.1	chr4	9602045	9602080	-	1	NA	intron (NM_023066, intron 7 of 23)	B1_Mus1|SINE|Alu	41655	NM_001177853	65973	Mm.222206	NM_023066	ENSMUSG00000028207	Asph	2310005F16Rik|3110001L23Rik|AI848629|AW261690|AW561901|BAH|C79816|cI-37	aspartate-beta-hydroxylase	protein-coding
mm_23640.1	chr3	67092573	67092582	+	1	NA	intron (NM_025822, intron 4 of 9)	intron (NM_025822, intron 4 of 9)	106905	NM_025822	66880	Mm.316418	NM_025822	ENSMUSG00000034544	Rsrc1	1200013F24Rik|SRrp53	arginine/serine-rich coiled-coil 1	protein-coding
mm_171837.1	chr5	149053012	149053012	-	1	NA	promoter-TSS (NM_010439)	promoter-TSS (NM_010439)	45	NM_010439	15289	Mm.207047	NM_010439	ENSMUSG00000066551	Hmgb1	HMG-1|Hmg1|SBP-1|p30	high mobility group box 1	protein-coding
mm_129425.1	chr15	78468464	78468485	-	1	NA	5' UTR (NM_027902, exon 1 of 18)	5' UTR (NM_027902, exon 1 of 18)	160	NM_027902	71753	Mm.34056	NM_027902	ENSMUSG00000016942	Tmprss6	1300008A22Rik	transmembrane serine protease 6	protein-coding
mm_39439.1	chr5	16870215	16870215	+	1	NA	Intergenic	Intergenic	316314	NM_001289461	15234	Mm.267078	NM_010427	ENSMUSG00000028864	Hgf	C230052L06Rik|HGF/SF|NK1|NK2|SF|SF/HGF	hepatocyte growth factor	protein-coding
mm_29954.1	chr3	133092046	133092054	-	1	NA	promoter-TSS (NM_026231)	promoter-TSS (NM_026231)	195	NM_027927	71793	Mm.246726	NM_027927	ENSMUSG00000028016	Ints12	1110020M19Rik|2810027J24Rik|4930529N21Rik|A230056J18Rik|AI666778|Phf22|int12	integrator complex subunit 12	protein-coding
mm_116259.1	chr13	34130346	34130361	-	1	NA	promoter-TSS (NM_023716)	promoter-TSS (NM_023716)	1	NM_023716	73710	Mm.379227	NM_023716	ENSMUSG00000045136	Tubb2b	2410129E14Rik|brdp	tubulin, beta 2B class IIB	protein-coding
mm_45910.1	chr5	89434625	89434658	-	1	NA	intron (NM_008096, intron 10 of 12)	RLTR15|LTR|ERVK	23257	NM_008096	14473	Mm.196595	NM_008096	ENSMUSG00000035540	Gc	DBP|VDB	group specific component	protein-coding
mm_74013.1	chr8	121542066	121542072	+	1	NA	promoter-TSS (NM_029597)	promoter-TSS (NM_029597)	-115	NM_029597	76405	Mm.165697	NM_029597	ENSMUSG00000031809	1700018B08Rik	1700084O22Rik	RIKEN cDNA 1700018B08 gene	protein-coding
mm_105272.1	chr11	102406767	102406782	-	1	NA	intron (NM_026542, intron 1 of 11)	intron (NM_026542, intron 1 of 11)	743	NM_026542	68066	Mm.44226	NM_026542	ENSMUSG00000018677	Slc25a39	3010027G13Rik|D11Ertd333e	solute carrier family 25, member 39	protein-coding
mm_10712.1	chr2	22779533	22779605	+	1	NA	intron (NM_019456, intron 1 of 13)	intron (NM_019456, intron 1 of 13)	5242	NM_019456	54519	Mm.14255	NM_019456	ENSMUSG00000026786	Apbb1ip	9930118P07Rik|Prp48	amyloid beta (A4) precursor protein-binding, family B, member 1 interacting protein	protein-coding
mm_81747.1	chr9	113931139	113931188	+	1	NA	5' UTR (NM_001083319, exon 1 of 17)	5' UTR (NM_001083319, exon 1 of 17)	229	NM_013699	22221	Mm.28052	NM_013699	ENSMUSG00000009741	Ubp1	Cp2b|LBP-1a|LBP-1b|NF2d9	upstream binding protein 1	protein-coding
mm_20012.1	chr2	119229886	119229913	-	1	NA	promoter-TSS (NM_028104)	promoter-TSS (NM_028104)	-34	NM_001290796	72112	Mm.46317	NM_028104	ENSMUSG00000027317	Ppp1r14d	2010107K19Rik|GBPI-1|Ppp1r14	protein phosphatase 1, regulatory (inhibitor) subunit 14D	protein-coding
mm_160746.1	chr10	81183966	81183966	+	1	NA	promoter-TSS (NM_007828)	promoter-TSS (NM_007828)	48	NM_007828	13144	Mm.10294	NM_007828	ENSMUSG00000034974	Dapk3	ZIPK|dlk	death-associated protein kinase 3	protein-coding
mm_28488.1	chr3	92484138	92484148	-	1	NA	3' UTR (NM_009264, exon 2 of 2)	3' UTR (NM_009264, exon 2 of 2)	1738	NM_009264	20753	Mm.331191	NM_009264	ENSMUSG00000050359	Sprr1a	AI528815|SPR1a|mSPRR1A	small proline-rich protein 1A	protein-coding
mm_42929.1	chr5	122850155	122850165	+	1	NA	promoter-TSS (NM_030564)	promoter-TSS (NM_030564)	-28	NM_030564	80751	Mm.388529	NM_030564	ENSMUSG00000029474	Rnf34	AW061037|AW536122|BC004042|C88279|RIFF	ring finger protein 34	protein-coding
mm_122166.1	chr14	31434276	31434286	-	1	NA	intron (NM_011894, intron 1 of 8)	intron (NM_011894, intron 1 of 8)	1819	NM_011894	24056	Mm.383198	NM_011894	ENSMUSG00000021892	Sh3bp5	AI606498|SH3BP-5|Sab	SH3-domain binding protein 5 (BTK-associated)	protein-coding
mm_95198.1	chr11	43433721	43433783	+	1	NA	promoter-TSS (NM_198936)	promoter-TSS (NM_198936)	21	NM_198936	193116	Mm.28200	NM_148673	ENSMUSG00000020409	Slu7	AU018913|D11Ertd730e|D3Bwg0878e	SLU7 splicing factor homolog (S. cerevisiae)	protein-coding
mm_11773.1	chr2	38925491	38925497	+	1	NA	intron (NM_010264, intron 1 of 10)	CpG	967	NM_010264	14536	Mm.439703	NM_010264	ENSMUSG00000063972	Nr6a1	1700113M01Rik|Gcnf|NCNF|RTR	nuclear receptor subfamily 6, group A, member 1	protein-coding
mm_43929.1	chr5	145083892	145083915	+	1	NA	promoter-TSS (NM_019767)	promoter-TSS (NM_019767)	34	NM_019767	56443	Mm.371610	NM_019767	ENSMUSG00000029621	Arpc1a	0610010H08Rik|1110030K07Rik|41kDa|AA407347|Sid32|Sid329	actin related protein 2/3 complex, subunit 1A	protein-coding
mm_30146.1	chr3	142501832	142501882	-	1	NA	intron (NM_153564, intron 3 of 10)	RMER17C|LTR|ERVK	4923	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_10113.1	chr2	3713480	3713500	+	1	NA	promoter-TSS (NM_025626)	promoter-TSS (NM_025626)	32	NM_025626	66540	Mm.277864	NM_025626	ENSMUSG00000026655	Fam107b	3110001A13Rik|AA589595|AA959793|AI132312	family with sequence similarity 107, member B	protein-coding
mm_108075.1	chr12	73945684	73945716	+	1	NA	exon (NM_010431, exon 15 of 15)	exon (NM_010431, exon 15 of 15)	-18830	NM_178392	75627	Mm.25937	NM_178392	ENSMUSG00000021113	Snapc1	2700033G17Rik|AU015787	small nuclear RNA activating complex, polypeptide 1	protein-coding
mm_103043.1	chr11	69795931	69795947	-	1	NA	promoter-TSS (NM_009601)	promoter-TSS (NM_009601)	-2	NM_009601	11443	Mm.86425	NM_009601	ENSMUSG00000041189	Chrnb1	Achr-2|Acrb	cholinergic receptor, nicotinic, beta polypeptide 1 (muscle)	protein-coding
mm_70402.1	chr8	11312870	11312887	+	1	NA	promoter-TSS (NM_009932)	promoter-TSS (NM_009932)	-52	NM_009931	12826	Mm.738	NM_009931	ENSMUSG00000031502	Col4a1	Bru|Col4a-1|Raw|Svc	collagen, type IV, alpha 1	protein-coding
mm_171768.1	chr5	108077376	108077377	+	1	NA	promoter-TSS (NM_001253878)	promoter-TSS (NM_001253878)	-789	NM_001253878	17765	Mm.257149	NM_013827	ENSMUSG00000029267	Mtf2	9230112N11Rik|AA537621|C76717|M96|Pcl2	metal response element binding transcription factor 2	protein-coding
mm_69233.1	chr7	127708621	127708665	-	1	NA	TTS (NR_030428)	TTS (NR_030428)	123	NM_009746	12055	Mm.89667	NM_009746	ENSMUSG00000030814	Bcl7c	C230096E12Rik	B cell CLL/lymphoma 7C	protein-coding
mm_24016.1	chr3	87518713	87518715	+	1	NA	Intergenic	Intergenic	-6864	NM_001083318	27049	Mm.219460	NM_012051	ENSMUSG00000003382	Etv3	AI414410|METS|Pe1	ets variant 3	protein-coding
mm_50105.1	chr6	41533268	41533278	+	1	NA	Intergenic	Intergenic	11497	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_84412.1	chr9	65562165	65562180	-	1	NA	intron (NM_153119, intron 3 of 5)	intron (NM_153119, intron 3 of 5)	17915	NM_153119	102595	Mm.247303	NM_153119	ENSMUSG00000050721	Plekho2	AI840980|Plekhq1	pleckstrin homology domain containing, family O member 2	protein-coding
mm_7224.1	chr1	93342623	93342631	-	1	NA	5' UTR (NM_080850, exon 1 of 18)	5' UTR (NM_080850, exon 1 of 18)	161	NM_080850	269224	Mm.379454	NM_080850	ENSMUSG00000026274	Pask	mKIAA0135	PAS domain containing serine/threonine kinase	protein-coding
mm_158912.1	chr1	44120017	44120017	+	1	NA	promoter-TSS (NM_144558)	promoter-TSS (NM_144558)	49	NM_144558	246229	Mm.386883	NM_144558	ENSMUSG00000041684	Bivm	AI854267	basic, immunoglobulin-like variable motif containing	protein-coding
mm_140440.1	chr17	88530150	88530161	+	1	NA	promoter-TSS (NM_028658)	promoter-TSS (NM_028658)	31	NM_028658	73825	Mm.271817	NM_028658	ENSMUSG00000034709	Ppp1r21	1110018J12Rik|AI426045|AW550781|Ccdc128|Klraq1	protein phosphatase 1, regulatory subunit 21	protein-coding
mm_15429.1	chr2	157101640	157101651	+	1	NA	intron (NM_001139520, intron 15 of 16)	ID_B1|SINE|B4	14590	NM_001177439	383766	Mm.480305	NM_001177439	ENSMUSG00000074628	Tldc2	Gm1332	TBC/LysM associated domain containing 2	protein-coding
mm_139911.1	chr17	70901036	70901047	+	1	NA	Intergenic	Intergenic	-47509	NM_001164074	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_64471.1	chr7	143005739	143005757	+	1	NA	promoter-TSS (NM_001128082)	promoter-TSS (NM_001128082)	89	NM_001128081	27027	Mm.28172	NM_020286	ENSMUSG00000000244	Tspan32	AW208513|Art-1|BB235973|D7Wsu37e|Phemx|Tssc6	tetraspanin 32	protein-coding
mm_136643.1	chr17	5804622	5804633	+	1	NA	Intergenic	Intergenic	5137	NR_045080	78512	Mm.23696	NR_045079	ENSMUSG00000096965	3300005D01Rik	-	RIKEN cDNA 3300005D01 gene	ncRNA
mm_9100.1	chr1	169969144	169969218	-	1	NA	promoter-TSS (NM_010476)	promoter-TSS (NM_010476)	24	NM_010476	15490	Mm.12882	NM_010476	ENSMUSG00000026675	Hsd17b7	AI266814|ERG27	hydroxysteroid (17-beta) dehydrogenase 7	protein-coding
mm_15463.1	chr2	157455997	157456008	+	1	NA	intron (NM_009271, intron 3 of 14)	intron (NM_009271, intron 3 of 14)	31709	NM_001025395	20779	Mm.22845	NM_009271	ENSMUSG00000027646	Src	AW259666|pp60c-src	Rous sarcoma oncogene	protein-coding
mm_55647.1	chr6	72362366	72362379	-	1	NA	promoter-TSS (NM_001331169)	promoter-TSS (NM_001331169)	60	NR_138581	66510	Mm.170023	NM_025607	ENSMUSG00000055850	Rnf181	1700047F16Rik|2500002L14Rik|6230415N01Rik|C77350	ring finger protein 181	protein-coding
mm_169004.1	chr13	103160899	103160914	-	1	NA	intron (NM_175171, intron 2 of 28)	intron (NM_175171, intron 2 of 28)	173586	NM_175171	328329	Mm.202606	NM_175171	ENSMUSG00000034751	Mast4	4930420O11Rik|AI642422|mKIAA0303	microtubule associated serine/threonine kinase family member 4	protein-coding
mm_97327.1	chr11	76998596	76998600	+	1	NA	promoter-TSS (NM_010484)	promoter-TSS (NM_010484)	1	NM_010484	15567	Mm.300318	NM_010484	ENSMUSG00000020838	Slc6a4	5-HTT|AI323329|Htt|Sert	solute carrier family 6 (neurotransmitter transporter, serotonin), member 4	protein-coding
mm_82915.1	chr9	35054103	35054131	-	1	NA	exon (NM_009178, exon 6 of 11)	exon (NM_009178, exon 6 of 11)	-62611	NR_029475	78934	Mm.391688	NR_029475	ENSMUSG00000070315	4930581F22Rik	-	RIKEN cDNA 4930581F22 gene	ncRNA
mm_76833.1	chr8	105255101	105255157	-	1	NA	promoter-TSS (NM_178879)	promoter-TSS (NM_178879)	24	NM_001271915	97440	Mm.489600	NM_178879	ENSMUSG00000069920	B3gnt9	3-Gn-T9|B3gnt9-ps|BGnT-9|C76565|C76566|beta-1|beta3Gn-T9	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 9	protein-coding
mm_52920.1	chr6	122852936	122852956	+	1	NA	intron (NM_009779, intron 1 of 1)	MTD|LTR|ERVL-MaLR	3211	NM_009779	12267	Mm.2408	NM_009779	ENSMUSG00000040552	C3ar1	AZ3B|C3AR|HNFAG09	complement component 3a receptor 1	protein-coding
mm_121581.1	chr14	123660266	123660284	+	1	NA	5' UTR (NM_145467, exon 1 of 11)	5' UTR (NM_145467, exon 1 of 11)	135	NM_145467	223272	Mm.383176	NM_145467	ENSMUSG00000032925	Itgbl1	B930011D01Rik	integrin, beta-like 1	protein-coding
mm_6924.1	chr1	84840597	84840612	-	1	NA	intron (NM_025386, intron 1 of 3)	intron (NM_025386, intron 1 of 3)	763	NM_025386	66153	Mm.381192	NM_025386	ENSMUSG00000073633	Fbxo36	0610008D19Rik|1110020F21Rik|2410002G19Rik|D1Ertd757e	F-box protein 36	protein-coding
mm_118402.1	chr13	119408944	119408974	-	1	NA	promoter-TSS (NM_008710)	promoter-TSS (NM_008710)	52	NM_008710	18115	Mm.132584	NM_008710	ENSMUSG00000025453	Nnt	4930423F13Rik|AI323702|BB168308	nicotinamide nucleotide transhydrogenase	protein-coding
mm_126804.1	chr15	87625099	87625106	+	1	NA	promoter-TSS (NM_134096)	promoter-TSS (NM_134096)	-128	NM_134096	106014	Mm.244319	NM_134096	ENSMUSG00000054863	Fam19a5	TAFA5|Tafa-5|Tara-5	family with sequence similarity 19, member A5	protein-coding
mm_101047.1	chr11	8624724	8624774	-	1	NA	intron (NM_001083587, intron 1 of 30)	CpG	39786	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_19585.1	chr2	101820458	101820460	-	1	NA	intron (NM_001110849, intron 2 of 9)	L2b|LINE|L2	18521	NM_001110849	72446	Mm.24138	NM_175181	ENSMUSG00000032841	Prr5l	2600010E01Rik|4833411O04Rik|Protor-2|Protor2	proline rich 5 like	protein-coding
mm_14447.1	chr2	131086391	131086405	+	1	NA	5' UTR (NM_011426, exon 1 of 21)	5' UTR (NM_011426, exon 1 of 21)	367	NM_011426	20612	Mm.1374	NM_011426	ENSMUSG00000027322	Siglec1	Cd169|Siglec-1|Sn	sialic acid binding Ig-like lectin 1, sialoadhesin	protein-coding
mm_153271.1	chr19	37175025	37175049	-	1	NA	intron (NM_001290827, intron 1 of 10)	intron (NM_001290827, intron 1 of 10)	1026	NM_001290826	208922	Mm.391176	NM_198300	ENSMUSG00000039652	Cpeb3	4831444O18Rik|CPE-BP3|mKIAA0940	cytoplasmic polyadenylation element binding protein 3	protein-coding
mm_85127.1	chr9	95543127	95543140	-	1	NA	Intergenic	Intergenic	-16684	NM_198414	75552	Mm.151485	NM_198414	ENSMUSG00000064225	Paqr9	1700020G04Rik	progestin and adipoQ receptor family member IX	protein-coding
mm_104564.1	chr11	96880440	96880450	-	1	NA	Intergenic	RMER19C|LTR|ERVK	30052	NR_029562	387170		NR_029562	ENSMUSG00000065515	Mir152	Mirn152|mir-152|mmu-mir-152	microRNA 152	ncRNA
mm_153323.1	chr19	38118481	38118491	-	1	NA	intron (NM_001159487, intron 4 of 5)	intron (NM_001159487, intron 4 of 5)	6325	NM_011255	19662	Mm.2605	NM_011255	ENSMUSG00000024990	Rbp4	Rbp-4	retinol binding protein 4, plasma	protein-coding
mm_46921.1	chr5	114667574	114667587	-	1	NA	Intergenic	CpG	-9159	NM_022017	63873	Mm.266450	NM_022017	ENSMUSG00000014158	Trpv4	0610033B08Rik|OTRPC4|Trp12|VR-OAC|VRL-2|VROAC	transient receptor potential cation channel, subfamily V, member 4	protein-coding
mm_35980.1	chr4	54028747	54028753	-	1	NA	Intergenic	Intergenic	202705	NM_028053	52076	Mm.27184	NM_028053	ENSMUSG00000028420	Tmem38b	1600017F22Rik|AA437809|AV051057|D4Ertd89e|TRIC-B|mg33b	transmembrane protein 38B	protein-coding
mm_47003.1	chr5	115429496	115429509	-	1	NA	promoter-TSS (NM_008629)	promoter-TSS (NM_008629)	-183	NM_008629	17690	Mm.5077	NM_008629	ENSMUSG00000054256	Msi1	Msi1h|Musahi1|m-Msi-1	musashi RNA-binding protein 1	protein-coding
mm_115355.1	chr13	112800852	112800876	+	1	NA	promoter-TSS (NM_008903)	promoter-TSS (NM_008903)	87	NM_008247	19012	Mm.291029	NM_008247	ENSMUSG00000021759	Plpp1	Hic53|Hpic53|LPP-1|LPP1|PAP-2a|PAP2-alpha|PAP2a|Ppap2a|mPAP	phospholipid phosphatase 1	protein-coding
mm_27693.1	chr3	66253683	66253694	-	1	NA	intron (NM_145820, intron 3 of 13)	(A)n|Simple_repeat|Simple_repeat	33801	NM_008987	19288	Mm.276776	NM_008987	ENSMUSG00000027832	Ptx3	AI607804|TSG-14	pentraxin related gene	protein-coding
mm_148820.1	chr19	6299125	6299154	+	1	NA	3' UTR (NM_010119, exon 5 of 5)	3' UTR (NM_010119, exon 5 of 5)	-7318	NM_001033342	240505	Mm.329622	NM_001033342	ENSMUSG00000024769	Cdc42bpg	BC046418|MRCKgamma	CDC42 binding protein kinase gamma (DMPK-like)	protein-coding
mm_7274.1	chr1	97128250	97128256	-	1	NA	promoter-TSS (NM_028942)	promoter-TSS (NM_028942)	50	NM_028942	74441	Mm.60362	NM_028942	ENSMUSG00000026331	Slco6c1	4933404A18Rik|C79179	solute carrier organic anion transporter family, member 6c1	protein-coding
mm_154893.1	chrX	20853345	20853370	+	1	NA	TTS (NM_001159645)	TTS (NM_001159645)	4814	NM_001159645	11836	Mm.220946	NM_009703	ENSMUSG00000001127	Araf	1200013E08Rik|A-Raf|AW495444|Araf1	Araf proto-oncogene, serine/threonine kinase	protein-coding
mm_20214.1	chr2	125723525	125723537	-	1	NA	5' UTR (NM_199022, exon 1 of 12)	5' UTR (NM_199022, exon 1 of 12)	617	NM_199022	271849	Mm.425101	NM_199022	ENSMUSG00000035109	Shc4	6230417E10Rik|9930029B02Rik|Gm685|RaLP	SHC (Src homology 2 domain containing) family, member 4	protein-coding
mm_103182.1	chr11	70511169	70511182	-	1	NA	TTS (NM_029360)	TTS (NM_029360)	3441	NM_001013607	327956	Mm.244514	NM_001013607	ENSMUSG00000020830	Vmo1	Gm741	vitelline membrane outer layer 1 homolog (chicken)	protein-coding
mm_102647.1	chr11	62915533	62915535	-	1	NA	Intergenic	ORR1D2|LTR|ERVL-MaLR	-35659	NM_025496	66338	Mm.46166	NM_025496	ENSMUSG00000042200	Cdrt4	1700019I23Rik	CMT1A duplicated region transcript 4	protein-coding
mm_38265.1	chr4	136880554	136880569	-	1	NA	exon (NM_009777, exon 3 of 3)	exon (NM_009777, exon 3 of 3)	5616	NM_009777	12260	Mm.2570	NM_009777	ENSMUSG00000036905	C1qb	-	complement component 1, q subcomponent, beta polypeptide	protein-coding
mm_41116.1	chr5	87780153	87780155	+	1	NA	intron (NM_007785, intron 8 of 13)	intron (NM_007785, intron 8 of 13)	5704	NM_007785	12993	Mm.4908	NM_007785	ENSMUSG00000061937	Csn1s2a	Csng|PP22	casein alpha s2-like A	protein-coding
mm_100275.1	chr11	117782113	117782130	+	1	NA	promoter-TSS (NM_181856)	promoter-TSS (NM_181856)	-176	NM_001195090	217356	Mm.116675	NM_181856	ENSMUSG00000050106	Tmc8	EVIN2|Ever2|mFLJ00400	transmembrane channel-like gene family 8	protein-coding
mm_17352.1	chr2	26608173	26608193	-	1	NA	Intergenic	Intergenic	-3766	NM_026212	67512	Mm.24244	NM_026212	ENSMUSG00000026922	Agpat2	2510002J07Rik|AV000834|BSCL|BSCL1|LPAAB|LPAAT-beta	1-acylglycerol-3-phosphate O-acyltransferase 2 (lysophosphatidic acid acyltransferase, beta)	protein-coding
mm_22985.1	chr3	33313164	33313167	+	1	NA	Intergenic	Intergenic	-169974	NM_001163516	58869	Mm.151332	NM_021483	ENSMUSG00000027674	Pex5l	1700016J08Rik|PXR2|Pex2|TRIP8b|pex5Rp	peroxisomal biogenesis factor 5-like	protein-coding
mm_25134.1	chr3	102469636	102469643	+	1	NA	promoter-TSS (NM_013609)	promoter-TSS (NM_013609)	-280	NM_001112698	18049	Mm.1259	NM_013609	ENSMUSG00000027859	Ngf	Ngfb	nerve growth factor	protein-coding
mm_148267.1	chr18	81566215	81566215	-	1	NA	Intergenic	Intergenic	425865	NR_039589	100628596		NR_039589	ENSMUSG00000093036	Mir5127	mmu-mir-5127|mu-mir-5127	microRNA 5127	ncRNA
mm_158373.1	chrX	135210606	135210612	-	1	NA	promoter-TSS (NM_025355)	promoter-TSS (NM_025355)	78	NM_025355	66104	Mm.336239	NM_025355	ENSMUSG00000031409	Tceal6	1500026B10Rik	transcription elongation factor A (SII)-like 6	protein-coding
mm_82295.1	chr9	7836861	7836883	-	1	NA	promoter-TSS (NM_001291503)	promoter-TSS (NM_001291503)	-66	NM_001291503	11797	Mm.335659	NM_007465	ENSMUSG00000057367	Birc2	AW146227|Api1|Api2|Birc3|C-IAP1|C330006D17Rik|HIAP1|HIAP2|IAP1|IAP2|MIAP1|MIAP2|MIHB|MIHC|RNF48|cIAP1|cIAP2|mcIAP1	baculoviral IAP repeat-containing 2	protein-coding
mm_124917.1	chr15	12117585	12117612	+	1	NA	promoter-TSS (NM_011767)	promoter-TSS (NM_011767)	-253	NM_011767	22763	Mm.273496	NM_011767	ENSMUSG00000022201	Zfr	C920030H05Rik	zinc finger RNA binding protein	protein-coding
mm_53461.1	chr6	134858383	134858386	+	1	NA	TTS (NM_177687)	TTS (NM_177687)	28185	NM_177687	232430	Mm.267010	NM_177687	ENSMUSG00000032652	Crebl2	AI046348|B230205M03	cAMP responsive element binding protein-like 2	protein-coding
mm_68206.1	chr7	104400714	104400718	-	1	NA	Intergenic	Intergenic	-42070	NM_175648	244183	Mm.347647	NM_175648	ENSMUSG00000052749	Trim30b	A530023O14Rik|Trim30-1	tripartite motif-containing 30B	protein-coding
mm_38347.1	chr4	137769980	137769983	-	1	NA	intron (NM_007431, intron 1 of 11)	intron (NM_007431, intron 1 of 11)	-3506	NM_001287172	11647	Mm.288186	NM_007431	ENSMUSG00000028766	Alpl	ALP|APTNAP|Akp-2|Akp2|TNAP|TNSALP	alkaline phosphatase, liver/bone/kidney	protein-coding
mm_99974.1	chr11	113933988	113934001	+	1	NA	intron (NM_172800, intron 2 of 44)	intron (NM_172800, intron 2 of 44)	131957	NM_172800	237979	Mm.130504	NM_172800	ENSMUSG00000041592	Sdk2	4632412F08Rik|5330435L01Rik|Sdk-2|mKIAA1514	sidekick cell adhesion molecule 2	protein-coding
mm_102705.1	chr11	66526618	66526628	-	1	NA	promoter-TSS (NM_001034874)	promoter-TSS (NM_001034874)	-497	NM_001034874	380702	Mm.351764	NM_001034874	ENSMUSG00000053930	Shisa6	Gm879|ckamp52	shisa family member 6	protein-coding
mm_81727.1	chr9	113122493	113122514	+	1	NA	Intergenic	Intergenic	464649	NR_040760	102688	Mm.394901	NR_040760	ENSMUSG00000109890	AU023762	-	expressed sequence AU023762	ncRNA
mm_97963.1	chr11	83746367	83746386	+	1	NA	promoter-TSS (NM_183249)	promoter-TSS (NM_183249)	-564	NM_183249	66107	Mm.902	NM_183249	ENSMUSG00000051748	Wfdc21	1100001G20Rik|Wdnm1-like	WAP four-disulfide core domain 21	protein-coding
mm_99438.1	chr11	102432887	102432910	+	1	NA	intron (NM_008175, intron 1 of 12)	intron (NM_008175, intron 1 of 12)	2576	NM_008175	14824	Mm.1568	NM_008175	ENSMUSG00000034708	Grn	Pgrn|epithelin	granulin	protein-coding
mm_22530.1	chr3	8462420	8462438	+	1	NA	non-coding (NR_033512, exon 1 of 1)	non-coding (NR_033512, exon 1 of 1)	669	NR_033512	620966	Mm.301719	NR_033512		Gm6194	1700003N22Rik|EG620966	transmembrane protein 189 pseudogene	pseudo
mm_80686.1	chr9	91371424	91371444	+	1	NA	intron (NM_009576, intron 1 of 4)	intron (NM_009576, intron 1 of 4)	2462	NM_009576	22774	Mm.8062	NM_009576	ENSMUSG00000036972	Zic4	-	zinc finger protein of the cerebellum 4	protein-coding
mm_41768.1	chr5	103501439	103501449	+	1	NA	exon (NM_011204, exon 7 of 48)	exon (NM_011204, exon 7 of 48)	76252	NM_011204	19249	Mm.3414	NM_011204	ENSMUSG00000034573	Ptpn13	AI324989|PTP-BL|PTPL1|Ptpri|RIP	protein tyrosine phosphatase, non-receptor type 13	protein-coding
mm_136075.1	chr16	84834849	84834874	-	1	NA	promoter-TSS (NM_008065)	promoter-TSS (NM_008065)	137	NM_001302216	11957	Mm.353	NM_016755	ENSMUSG00000022890	Atp5j	CF6	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit F	protein-coding
mm_21960.1	chr2	167190288	167190312	-	1	NA	Intergenic	CpG	-1482	NM_008420	16500	Mm.205341	NM_008420	ENSMUSG00000050556	Kcnb1	Kcr1-1|Kv2.1|Shab	potassium voltage gated channel, Shab-related subfamily, member 1	protein-coding
mm_75654.1	chr8	65129525	65129540	-	1	NA	promoter-TSS (NR_033217)	promoter-TSS (NR_033217)	5	NR_033217	407795	Mm.387876	NR_033217	ENSMUSG00000074300	BC030870	-	cDNA sequence BC030870	ncRNA
mm_158727.1	chrX	163885477	163885484	-	1	NA	Intergenic	Intergenic	-23537	NM_001290378	108012	Mm.426783	NM_026887	ENSMUSG00000031367	Ap1s2	1500012A13Rik|AI853648|EST1	adaptor-related protein complex 1, sigma 2 subunit	protein-coding
mm_53371.1	chr6	129408931	129408937	+	1	NA	promoter-TSS (NM_001205364)	promoter-TSS (NM_001205364)	72	NM_172732	232414	Mm.391518	NM_172732	ENSMUSG00000046080	Clec9a	9830005G06Rik|DNGR-1	C-type lectin domain family 9, member a	protein-coding
mm_170988.1	chr2	7409174	7409186	+	1	NA	Intergenic	IAPLTR1_Mm|LTR|ERVK	-12982	NM_001110231	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_12280.1	chr2	69005310	69005319	+	1	NA	intron (NM_172856, intron 4 of 9)	intron (NM_172856, intron 4 of 9)	-130486	NM_181547	329416	Mm.90047	NM_181547	ENSMUSG00000034738	Nostrin	Daip2|mDaIP2	nitric oxide synthase trafficker	protein-coding
mm_76861.1	chr8	105471384	105471400	-	1	NA	promoter-TSS (NM_026481)	promoter-TSS (NM_026481)	30	NM_026481	67971	Mm.29358	NM_026481	ENSMUSG00000014846	Tppp3	2700055K07Rik|CGI-38|Ceacam9|mmCGM8	tubulin polymerization-promoting protein family member 3	protein-coding
mm_92488.1	chr10	78298163	78298184	-	1	NA	intron (NM_053014, intron 2 of 9)	intron (NM_053014, intron 2 of 9)	42034	NR_106119	102465765		NR_106119	ENSMUSG00000098885	Mir7659	Gm27433|mmu-mir-7659	microRNA 7659	ncRNA
mm_19471.1	chr2	92459712	92459781	-	1	NA	promoter-TSS (NM_211358)	promoter-TSS (NM_211358)	48	NM_211358	228368	Mm.273990	NM_145832	ENSMUSG00000049922	Slc35c1	E430007K15Rik|fuct1	solute carrier family 35, member C1	protein-coding
mm_86202.1	chr9	119981365	119981379	-	1	NA	intron (NM_153287, intron 1 of 4)	intron (NM_153287, intron 1 of 4)	3286	NM_153287	215418	Mm.491094	NM_153287	ENSMUSG00000032515	Csrnp1	4931429D10Rik|Axud1|CSRNP-1|URAX1|taip-3	cysteine-serine-rich nuclear protein 1	protein-coding
mm_94936.1	chr11	29706997	29707022	+	1	NA	exon (NM_194051, exon 3 of 9)	exon (NM_194051, exon 3 of 9)	-11554	NM_024226	68585	Mm.192580	NM_024226	ENSMUSG00000020458	Rtn4	1110020G17Rik|AA407876|AA409940|AA960376|ASY|C130026I10Rik|NOGO|NSP-CL|NgA|Nogo-A|Nogo-B|Nogo-C|mKIAA0886|mKIAA4153	reticulon 4	protein-coding
mm_34994.1	chr4	156060059	156060068	+	1	NA	promoter-TSS (NR_132444)	promoter-TSS (NR_132444)	-261	NR_132444	100415901	Mm.437006	NR_132444	ENSMUSG00000086549	Gm13648	OTTMUSG00000013217	predicted gene 13648	ncRNA
mm_172967.1	chr9	88858831	88858832	-	1	NA	promoter-TSS (NR_037983)	promoter-TSS (NR_037983)	-30	NR_037982	319673	Mm.149040	NR_037982	ENSMUSG00000097177	9330159M07Rik	1700096K11Rik|mU50hg-a	RIKEN cDNA 9330159M07 gene	ncRNA
mm_62989.1	chr7	120409636	120409699	+	1	NA	promoter-TSS (NM_001278943)	promoter-TSS (NM_001278943)	20	NM_001278943	233810		NM_001278943	ENSMUSG00000051900	Abca16	AY243472	ATP-binding cassette, sub-family A (ABC1), member 16	protein-coding
mm_23080.1	chr3	36613483	36613486	+	1	NA	promoter-TSS (NM_027810)	promoter-TSS (NM_027810)	-95	NM_027810	71492	Mm.286187	NM_027810	ENSMUSG00000037325	Bbs7	8430406N16Rik	Bardet-Biedl syndrome 7 (human)	protein-coding
mm_11224.1	chr2	29787483	29787511	+	1	NA	promoter-TSS (NM_178693)	promoter-TSS (NM_178693)	174	NM_001290496	227682	Mm.245739	NM_145520	ENSMUSG00000039826	Trub2	G430055L02Rik	TruB pseudouridine (psi) synthase family member 2	protein-coding
mm_63829.1	chr7	135171153	135171157	+	1	NA	intron (NM_001033420, intron 51 of 51)	B4A|SINE|B4	24847	NR_046050	74314	Mm.415339	NR_046050	ENSMUSG00000100717	1700120G07Rik	-	RIKEN cDNA 1700120G07 gene	ncRNA
mm_103532.1	chr11	77201000	77201004	-	1	NA	Intergenic	Intergenic	-12034	NM_176965	319634	Mm.108786	NM_176965	ENSMUSG00000050944	Efcab5	4930563A03Rik	EF-hand calcium binding domain 5	protein-coding
mm_121067.1	chr14	95881224	95881241	+	1	NA	promoter-TSS (NM_025733)	promoter-TSS (NM_025733)	-34	NM_025733	66732	Mm.75060	NM_025733	ENSMUSG00000034689	4921530L21Rik	-	RIKEN cDNA 4921530L21 gene	protein-coding
mm_19299.1	chr2	90466728	90466751	-	1	NA	intron (NM_001135657, intron 5 of 25)	intron (NM_001135657, intron 5 of 25)	12435	NM_001135657	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_156034.1	chrX	107397728	107397758	+	1	NA	3' UTR (NM_008409, exon 6 of 6)	3' UTR (NM_008409, exon 6 of 6)	5617	NM_008409	16431	Mm.193	NM_008409	ENSMUSG00000031239	Itm2a	AW108051|Bricd2a|E25|Itm2	integral membrane protein 2A	protein-coding
mm_44293.1	chr5	8422696	8422727	-	1	NA	promoter-TSS (NM_178766)	promoter-TSS (NM_178766)	5	NM_013726	27214	Mm.292470	NM_013726	ENSMUSG00000002297	Dbf4	AA545217|Ask	DBF4 zinc finger	protein-coding
mm_6137.1	chr1	64737521	64737541	-	1	NA	5' UTR (NM_001042659, exon 1 of 2)	5' UTR (NM_001042659, exon 1 of 2)	219	NM_001042659	14367	Mm.150813	NM_022721	ENSMUSG00000045005	Fzd5	5330434N09Rik|AI427138|Fz-5|Fz5|mFz5	frizzled class receptor 5	protein-coding
mm_62364.1	chr7	100539900	100539927	+	1	NA	TTS (NM_183270)	TTS (NM_183270)	2813	NM_183270	68185	Mm.228995	NM_183270	ENSMUSG00000044881	Coa4	5330414O08Rik|AI115477|AW047259|Chchd8|E2ig2	cytochrome c oxidase assembly factor 4	protein-coding
mm_126128.1	chr15	78335144	78335163	+	1	NA	5' UTR (NM_007780, exon 2 of 14)	5' UTR (NM_007780, exon 2 of 14)	9163	NM_007780	12983	Mm.235324	NM_007780	ENSMUSG00000071713	Csf2rb	AI848964|AIC2B|Bc|CDw131|Csf2rb1|Csfgmrb|Il3r|Il3rb|Il3rb1|Il5rb	colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage)	protein-coding
mm_140015.1	chr17	73332235	73332236	+	1	NA	intron (NM_001033444, intron 11 of 22)	intron (NM_001033444, intron 11 of 22)	67061	NM_001033444	381122	Mm.81496	NM_001033444	ENSMUSG00000043705	Capn13	CANP 13|Gm943	calpain 13	protein-coding
mm_13926.1	chr2	120850672	120850724	+	1	NA	promoter-TSS (NM_001024856)	promoter-TSS (NM_001024856)	42	NR_038350	100502700	Mm.330516	NR_038349	ENSMUSG00000087519	AV039307	-	expressed sequence AV039307	ncRNA
mm_117679.1	chr13	94154588	94154636	-	1	NA	intron (NM_172589, intron 2 of 3)	intron (NM_172589, intron 2 of 3)	96816	NM_172589	218454	Mm.316553	NM_172589	ENSMUSG00000045312	Lhfpl2	6030465B15|AI447312|AW050335|mKIAA0206|vgim	lipoma HMGIC fusion partner-like 2	protein-coding
mm_138507.1	chr17	35235898	35235913	+	1	NA	promoter-TSS (NM_010909)	promoter-TSS (NM_010909)	-90	NM_010909	18038	Mm.300795	NM_010909	ENSMUSG00000042419	Nfkbil1	Def-7|IKBL	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor like 1	protein-coding
mm_9666.1	chr1	177796694	177796700	-	1	NA	promoter-TSS (NM_007422)	promoter-TSS (NM_007422)	-188	NM_007422	11566	Mm.338021	NM_007422	ENSMUSG00000015961	Adss	AI314886|AS|Adss2	adenylosuccinate synthetase, non muscle	protein-coding
mm_107438.1	chr12	36196645	36196648	+	1	NA	3' UTR (NM_146033, exon 10 of 10)	3' UTR (NM_146033, exon 10 of 10)	21556	NM_027699	71156	Mm.250837	NM_027699	ENSMUSG00000020545	Lrrc72	1700108M19Rik|4933421E18Rik	leucine rich repeat containing 72	protein-coding
mm_96247.1	chr11	62575619	62575642	+	1	NA	intron (NM_011706, intron 1 of 15)	intron (NM_011706, intron 1 of 15)	1144	NM_011706	22368	Mm.288064	NM_011706	ENSMUSG00000018507	Trpv2	GRC|OTRPC2|VRL-1|Vrl1	transient receptor potential cation channel, subfamily V, member 2	protein-coding
mm_154225.1	chr19	59943075	59943100	-	1	NA	5' UTR (NM_001033172, exon 1 of 6)	5' UTR (NM_001033172, exon 1 of 6)	277	NM_001033172	74998	Mm.24167	NM_001033172	ENSMUSG00000040022	Rab11fip2	4930470G04Rik|A830046J09Rik|AW558126|Nrip11	RAB11 family interacting protein 2 (class I)	protein-coding
mm_29693.1	chr3	123113762	123113791	-	1	NA	exon (NM_080451, exon 4 of 5)	exon (NM_080451, exon 4 of 5)	-78789	NM_021503	59006	Mm.141157	NM_021503	ENSMUSG00000028116	Myoz2	1110012I24Rik|Fatz-2|Myozl2	myozenin 2	protein-coding
mm_45580.1	chr5	74009170	74009189	-	1	NA	intron (NM_177561, intron 5 of 8)	IMPB_01|Satellite|Satellite	59232	NM_177561	69727	Mm.48795	NM_177561	ENSMUSG00000054814	Usp46	1190009E20Rik|2410018I08Rik|AI451644	ubiquitin specific peptidase 46	protein-coding
mm_130436.1	chr15	98257297	98257312	-	1	NA	promoter-TSS (NM_027304)	promoter-TSS (NM_027304)	3	NM_027304	70069	Mm.107718	NM_027304	ENSMUSG00000048077	H1fnt	1700026P10Rik|H1.7|H1t2|Hanp1|mH1t2	H1 histone family, member N, testis-specific	protein-coding
mm_26464.1	chr3	144138931	144138947	+	1	NA	Intergenic	Intergenic	63393	NM_001161770	16911	Mm.29187	NM_010723	ENSMUSG00000028266	Lmo4	A730077C12Rik|Crp3|Etohi4	LIM domain only 4	protein-coding
mm_20291.1	chr2	126932994	126933090	-	1	NA	5' UTR (NM_023220, exon 1 of 15)	5' UTR (NM_023220, exon 1 of 15)	193	NM_023220	66552	Mm.269928	NM_023220	ENSMUSG00000027366	Sppl2a	2010106G01Rik|C130089K23Rik	signal peptide peptidase like 2A	protein-coding
mm_72845.1	chr8	88306452	88306470	+	1	NA	5' UTR (NM_001037724, exon 4 of 28)	5' UTR (NM_001037724, exon 4 of 28)	12257	NM_001037724	11513	Mm.288206	NM_007406	ENSMUSG00000031659	Adcy7	AA407758	adenylate cyclase 7	protein-coding
mm_118352.1	chr13	115052742	115052755	-	1	NA	intron (NM_001033228, intron 1 of 28)	intron (NM_001033228, intron 1 of 28)	37410	NM_134058	105083	Mm.486295	NM_134058	ENSMUSG00000042275	Pelo	AA409897|AI852218	pelota homolog (Drosophila)	protein-coding
mm_160389.1	chr8	54077606	54077606	+	1	NA	promoter-TSS (NM_009506)	promoter-TSS (NM_009506)	74	NM_009506	22341	Mm.1402	NM_009506	ENSMUSG00000031520	Vegfc	AW228853|VEGF-C	vascular endothelial growth factor C	protein-coding
mm_161570.1	chr16	20734530	20734530	-	1	NA	promoter-TSS (NM_009379)	promoter-TSS (NM_009379)	-19	NM_009379	21832	Mm.3943	NM_009379	ENSMUSG00000022847	Thpo	Mgdf|Ml|Mpllg|Tpo	thrombopoietin	protein-coding
mm_70249.1	chr8	3470842	3470858	+	1	NA	promoter-TSS (NM_029598)	promoter-TSS (NM_029598)	-12	NM_029598	76406	Mm.74996	NM_029598	ENSMUSG00000040340	1700019B03Rik	-	RIKEN cDNA 1700019B03 gene	protein-coding
mm_81361.1	chr9	108692117	108692193	+	1	NA	promoter-TSS (NM_008924)	promoter-TSS (NM_008924)	12	NM_008924	19087	Mm.253102	NM_008924	ENSMUSG00000032601	Prkar2a	1110061A24Rik|AI317181|AI836829|RII(alpha)	protein kinase, cAMP dependent regulatory, type II alpha	protein-coding
mm_55785.1	chr6	82652492	82652554	-	1	NA	intron (NM_025882, intron 1 of 3)	intron (NM_025882, intron 1 of 3)	342	NM_025882	66979	Mm.195753	NM_025882	ENSMUSG00000030042	Pole4	2400007P05Rik|5830430F06Rik	polymerase (DNA-directed), epsilon 4 (p12 subunit)	protein-coding
mm_121860.1	chr14	20674709	20674716	-	1	NA	intron (NM_001168273, intron 1 of 23)	intron (NM_001168273, intron 1 of 23)	391	NM_001168273	218811	Mm.173119	NM_172596	ENSMUSG00000039367	Sec24c	2610204K03Rik|mKIAA0079	Sec24 related gene family, member C (S. cerevisiae)	protein-coding
mm_61764.1	chr7	82771961	82772011	+	1	NA	intron (NM_175317, intron 18 of 19)	intron (NM_175317, intron 18 of 19)	-16342	NR_046004	77800	Mm.444811	NR_046004	ENSMUSG00000086690	4933406J10Rik	A930009F24Rik	RIKEN cDNA 4933406J10 gene	ncRNA
mm_164565.1	chr17	17871695	17871707	-	1	NA	Intergenic	Intergenic	12238	NM_013521	14293	Mm.56951	NM_013521	ENSMUSG00000045551	Fpr1	FPR|LXA4R|fMLF-R	formyl peptide receptor 1	protein-coding
mm_49166.1	chr6	14608328	14608350	+	1	NA	Intergenic	Intergenic	146935	NM_080464	140491	Mm.209429	NM_080464	ENSMUSG00000042717	Ppp1r3a	GM|RG1|RGL	protein phosphatase 1, regulatory (inhibitor) subunit 3A	protein-coding
mm_91447.1	chr10	33937614	33937655	-	1	NA	intron (NM_028287, intron 5 of 9)	B2_Mm2|SINE|B2	13578	NM_028287	72580	Mm.248081	NM_028287	ENSMUSG00000039531	Zufsp	2700019D07Rik	zinc finger with UFM1-specific peptidase domain	protein-coding
mm_123536.1	chr14	66807905	66807945	-	1	NA	exon (NM_009955, exon 12 of 14)	exon (NM_009955, exon 12 of 14)	60675	NM_009955	12934	Mm.352648	NM_009955	ENSMUSG00000022048	Dpysl2	AI851130|Crmp2|DRP2|Musunc33|TOAD-64|Ulip2	dihydropyrimidinase-like 2	protein-coding
mm_99415.1	chr11	102285162	102285251	+	1	NA	5' UTR (NM_001302505, exon 1 of 3)	5' UTR (NM_001302505, exon 1 of 3)	267	NM_001302505	72053	Mm.101274	NM_028076	ENSMUSG00000034757	Tmub2	2010008E23Rik	transmembrane and ubiquitin-like domain containing 2	protein-coding
mm_83425.1	chr9	44980331	44980341	-	1	NA	promoter-TSS (NM_009850)	promoter-TSS (NM_009850)	95	NM_009850	12502	Mm.335106	NM_009850	ENSMUSG00000002033	Cd3g	Ctg-3|Ctg3|T3g	CD3 antigen, gamma polypeptide	protein-coding
mm_45074.1	chr5	43868749	43868762	-	1	NA	promoter-TSS (NM_007646)	promoter-TSS (NM_007646)	-54	NM_007646	12494	Mm.249873	NM_007646	ENSMUSG00000029084	Cd38	ADPRC 1|Cd38-rs1|I-19	CD38 antigen	protein-coding
mm_42009.1	chr5	108065697	108065738	+	1	NA	promoter-TSS (NM_013827)	promoter-TSS (NM_013827)	43	NM_013827	17765	Mm.257149	NM_013827	ENSMUSG00000029267	Mtf2	9230112N11Rik|AA537621|C76717|M96|Pcl2	metal response element binding transcription factor 2	protein-coding
mm_26415.1	chr3	142610705	142610715	+	1	NA	intron (NM_010259, intron 8 of 10)	intron (NM_010259, intron 8 of 10)	-9953	NM_010260	14469	Mm.24038	NM_010260	ENSMUSG00000028270	Gbp2	-	guanylate binding protein 2	protein-coding
mm_48736.1	chr5	147592474	147592474	-	1	NA	intron (NM_010228, intron 18 of 29)	B3|SINE|B2	133514	NM_010228	14254	Mm.389712	NM_010228	ENSMUSG00000029648	Flt1	AI323757|Flt-1|VEGFR-1|VEGFR1|sFlt1	FMS-like tyrosine kinase 1	protein-coding
mm_1489.1	chr1	71714166	71714173	+	1	NA	Intergenic	Intergenic	60834	NR_040308	100042814	Mm.405775	NR_040308	ENSMUSG00000073652	Apol7d	ENSMUSG00000073652|Gm15456|OTTMUSG00000022136	apolipoprotein L 7d	ncRNA
mm_150813.1	chr19	44396733	44396747	+	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	10969	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_83452.1	chr9	45204025	45204048	-	1	NA	promoter-TSS (NM_145403)	promoter-TSS (NM_145403)	39	NM_145403	214523	Mm.436756	NM_145403	ENSMUSG00000032091	Tmprss4	mCAP2	transmembrane protease, serine 4	protein-coding
mm_93866.1	chr10	123147294	123147302	-	1	NA	intron (NM_001301628, intron 6 of 20)	intron (NM_001301628, intron 6 of 20)	49721	NM_027604	14479	Mm.244209	NM_027604	ENSMUSG00000020124	Usp15	4921514G19Rik|AI327321|E430033I05Rik|Gcap18	ubiquitin specific peptidase 15	protein-coding
mm_28968.1	chr3	101003811	101003829	-	1	NA	exon (NM_001167906, exon 8 of 9)	exon (NM_001167906, exon 8 of 9)	25675	NM_001167906	630146	Mm.190915	NM_001099332	ENSMUSG00000086564	Cd101	EWI-101|Gm1016|Gm734|Igsf2	CD101 antigen	protein-coding
mm_152975.1	chr19	29453997	29454008	-	1	NA	intron (NM_021396, intron 4 of 5)	intron (NM_021396, intron 4 of 5)	43083	NM_021396	58205	Mm.116737	NM_021396	ENSMUSG00000016498	Pdcd1lg2	B7-DC|Btdc|F730015O22Rik|PD-L2	programmed cell death 1 ligand 2	protein-coding
mm_134283.1	chr16	14205135	14205140	-	1	NA	exon (NM_013607, exon 34 of 42)	exon (NM_013607, exon 34 of 42)	41862	NM_001114085	67203	Mm.24105	NM_023317	ENSMUSG00000022678	Nde1	2810027M15Rik|AU042936|AW822251|Nude|mNudE	nudE neurodevelopment protein 1	protein-coding
mm_164842.1	chr18	42952480	42952480	+	1	NA	intron (NM_028392, intron 1 of 8)	intron (NM_028392, intron 1 of 8)	-52974	NR_073583	72930	Mm.26134	NM_027531	ENSMUSG00000024500	Ppp2r2b	2900026H06Rik|6330404L05Rik|E130009M08Rik|PP2A-PR55B|PR55-BETA|SCA12	protein phosphatase 2, regulatory subunit B, beta	protein-coding
mm_32399.1	chr4	106867055	106867062	+	1	NA	Intergenic	Intergenic	-44412	NM_198438	72475	Mm.195635	NM_023672	ENSMUSG00000061887	Ssbp3	2610021L12Rik|2610200M23Rik|5730488C10Rik|AI854733|AW551939|LAST|SSDP1	single-stranded DNA binding protein 3	protein-coding
mm_32771.1	chr4	116694112	116694128	+	1	NA	intron (NM_011034, intron 5 of 5)	B1_Mus2|SINE|Alu	-8098	NR_040442	100502959	Mm.395400	NR_040442		AV051173	-	expressed sequence AV051173	ncRNA
mm_11948.1	chr2	52927644	52927655	+	1	NA	intron (NM_172409, intron 1 of 26)	intron (NM_172409, intron 1 of 26)	69781	NM_172409	71409	Mm.394427	NM_172409	ENSMUSG00000036053	Fmnl2	5430425K04Rik|Man	formin-like 2	protein-coding
mm_31582.1	chr4	57782154	57782186	+	1	NA	intron (NM_001304544, intron 6 of 8)	CpG	-63078	NM_009649	11641	Mm.467752	NM_009649	ENSMUSG00000038729	Akap2	AA959716|AI649048|Akap-2|Akap-kl|B230340M18Rik|Prka2	A kinase (PRKA) anchor protein 2	protein-coding
mm_35699.1	chr4	44167394	44167424	-	1	NA	5' UTR (NM_175201, exon 1 of 11)	5' UTR (NM_175201, exon 1 of 11)	129	NM_175201	73469	Mm.262859	NM_175201	ENSMUSG00000035696	Rnf38	1700065B19Rik|2610202O07Rik|AA673263|Oip1	ring finger protein 38	protein-coding
mm_157050.1	chrX	8018494	8018502	-	1	NA	promoter-TSS (NM_027227)	promoter-TSS (NM_027227)	-6	NM_027227	69824	Mm.279756	NM_027227	ENSMUSG00000031163	Glod5	2010001H14Rik|AV061890	glyoxalase domain containing 5	protein-coding
mm_16151.1	chr2	172345596	172345626	+	1	NA	promoter-TSS (NM_025912)	promoter-TSS (NM_025912)	34	NM_025912	67017	Mm.30013	NM_025912	ENSMUSG00000027495	Fam210b	2010011I20Rik|AI430961|AV108736	family with sequence similarity 210, member B	protein-coding
mm_57491.1	chr6	125286063	125286075	-	1	NA	promoter-TSS (NM_009446)	promoter-TSS (NM_009446)	-27	NM_009446	22144	Mm.287784	NM_009446	ENSMUSG00000067702	Tuba3a	AI528779|M[a]3|Tuba3	tubulin, alpha 3A	protein-coding
mm_22900.1	chr3	30809818	30809860	+	1	NA	exon (NM_027016, exon 4 of 8)	exon (NM_027016, exon 4 of 8)	16963	NM_027016	69276	Mm.26017	NM_027016	ENSMUSG00000027706	Sec62	3100002M17Rik|AI844545|AW545092|Dtrp1|HTP1|Tloc1	SEC62 homolog (S. cerevisiae)	protein-coding
mm_129777.1	chr15	82792625	82792636	-	1	NA	intron (NM_029562, intron 3 of 8)	intron (NM_029562, intron 3 of 8)	1615	NM_029562	76279	Mm.439931	NM_029562	ENSMUSG00000022445	Cyp2d26	1300006E06Rik	cytochrome P450, family 2, subfamily d, polypeptide 26	protein-coding
mm_122849.1	chr14	54759673	54759683	-	1	NA	exon (NM_016972, exon 2 of 11)	exon (NM_016972, exon 2 of 11)	22208	NM_016972	50934	Mm.276831	NM_016972	ENSMUSG00000022180	Slc7a8	AA408822|LAT2	solute carrier family 7 (cationic amino acid transporter, y+ system), member 8	protein-coding
mm_51575.1	chr6	83758794	83758803	+	1	NA	TTS (NM_134157)	TTS (NM_134157)	3710	NR_105027	67934	Mm.126190	NR_105027	ENSMUSG00000099354	1700124L16Rik	-	RIKEN cDNA 1700124L16 gene	ncRNA
mm_127247.1	chr15	99670218	99670231	+	1	NA	promoter-TSS (NM_009597)	promoter-TSS (NM_009597)	-494	NM_009597	11419	Mm.440107	NM_009597	ENSMUSG00000023017	Asic1	AI843610|ASIC|ASIC1a|Accn2|B530003N02Rik|BNaC2	acid-sensing (proton-gated) ion channel 1	protein-coding
mm_47287.1	chr5	122131977	122131982	-	1	NA	intron (NM_001289809, intron 1 of 11)	intron (NM_001289809, intron 1 of 11)	2914	NM_001289811	330188	Mm.386907	NM_183307	ENSMUSG00000043036	Ccdc63	4921511C16Rik	coiled-coil domain containing 63	protein-coding
mm_15850.1	chr2	164777486	164777510	+	1	NA	exon (NM_009394, exon 5 of 6)	exon (NM_009394, exon 5 of 6)	2236	NM_009394	21925	Mm.1716	NM_009394	ENSMUSG00000017300	Tnnc2	Tncs	troponin C2, fast	protein-coding
mm_80170.1	chr9	71591486	71591498	+	1	NA	intron (NM_001033208, intron 1 of 12)	intron (NM_001033208, intron 1 of 12)	868	NM_001033208	102371	Mm.27585	NM_001033208	ENSMUSG00000041361	Myzap	AA407270|AV006038|Gcom1|Gm640|Grinl1a7|Myozap	myocardial zonula adherens protein	protein-coding
mm_93339.1	chr10	99759594	99759601	-	1	NA	promoter-TSS (NM_027945)	promoter-TSS (NM_027945)	61	NM_027945	71832	Mm.483162	NM_027945	ENSMUSG00000046934	Csl	1700007H16Rik	citrate synthase like	protein-coding
mm_16552.1	chr2	181767284	181767321	+	1	NA	5' UTR (NM_008665, exon 1 of 23)	5' UTR (NM_008665, exon 1 of 23)	273	NM_001171616	17932	Mm.458718	NM_008665	ENSMUSG00000010505	Myt1	Nzf2|Nzf2a|Nzf2b|Nztf2	myelin transcription factor 1	protein-coding
mm_27886.1	chr3	79181326	79181351	-	1	NA	Intergenic	Intergenic	-31581	NR_045502	70924	Mm.444622	NR_045502	ENSMUSG00000104585	4921511C10Rik	-	RIKEN cDNA 4921511C10 gene	ncRNA
mm_107984.1	chr12	73044529	73044537	+	1	NA	intron (NM_009189, intron 1 of 1)	intron (NM_009189, intron 1 of 1)	2179	NM_009189	20471	Mm.4645	NM_009189	ENSMUSG00000051367	Six1	BB138287	sine oculis-related homeobox 1	protein-coding
mm_110515.1	chr12	54795718	54795724	-	1	NA	promoter-TSS (NM_026998)	promoter-TSS (NM_026998)	-59	NM_026998	72183	Mm.28240	NM_026998	ENSMUSG00000005656	Snx6	2010006G21Rik|2610032J07Rik|2810425K19Rik|AU018928|C85963	sorting nexin 6	protein-coding
mm_170930.1	chr2	40555708	40555713	+	1	NA	Intergenic	Intergenic	-1329372	NM_024209	67857	Mm.389242	NM_024209	ENSMUSG00000026753	Ppp6c	2310003C10Rik	protein phosphatase 6, catalytic subunit	protein-coding
mm_137071.1	chr17	20955954	20955982	+	1	NA	exon (NM_016891, exon 4 of 15)	exon (NM_016891, exon 4 of 15)	10514	NM_016891	51792	Mm.294138	NM_016891	ENSMUSG00000007564	Ppp2r1a	6330556D22Rik|PP2A|PR65	protein phosphatase 2, regulatory subunit A, alpha	protein-coding
mm_145361.1	chr18	56676699	56676725	+	1	NA	Intergenic	RMER17C2|LTR|ERVK	-31101	NM_010721	16906	Mm.4105	NM_010721	ENSMUSG00000024590	Lmnb1	-	lamin B1	protein-coding
mm_95471.1	chr11	50793616	50793628	+	1	NA	intron (NM_175643, intron 19 of 21)	intron (NM_175643, intron 19 of 21)	34109	NM_013922	30944	Mm.103674	NM_013922	ENSMUSG00000044807	Zfp354c	5330421P20Rik|AJ18|AW743325|Kid3|Tcf17l2|Znf354c|mKIAA4218	zinc finger protein 354C	protein-coding
mm_59311.1	chr7	25282601	25282683	+	1	NA	5' UTR (NM_027882, exon 1 of 20)	5' UTR (NM_027882, exon 1 of 20)	463	NM_027882	71722	Mm.28833	NM_027882	ENSMUSG00000005442	Cic	1200010B10Rik|mKIAA0306	capicua transcriptional repressor	protein-coding
mm_60978.1	chr7	48959090	48959128	+	1	NA	promoter-TSS (NM_001111016)	promoter-TSS (NM_001111016)	36	NM_001111016	78286	Mm.333881	NM_175272	ENSMUSG00000052512	Nav2	5330421F07Rik|AU067780|BQ960892|HELAD1|POMFIL2|RAINB1|RAINB2|Unc53H2|mKIAA3015	neuron navigator 2	protein-coding
mm_125938.1	chr15	76247933	76247953	+	1	NA	promoter-TSS (NR_105918)	promoter-TSS (NR_105918)	-248	NR_105918	102465575		NR_105918	ENSMUSG00000098625	Mir6953	Gm27738|mmu-mir-6953	microRNA 6953	ncRNA
mm_117959.1	chr13	99447586	99447622	-	1	NA	intron (NM_008634, intron 2 of 6)	intron (NM_008634, intron 2 of 6)	-34778	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_3897.1	chr1	161701372	161701383	+	1	NA	Intergenic	Intergenic	87118	NM_001205243	14103	Mm.3355	NM_010177	ENSMUSG00000000817	Fasl	APT1LG1|CD178|CD95-L|CD95L|Fas-L|Faslg|Tnfsf6|Tnlg1a|gld	Fas ligand (TNF superfamily, member 6)	protein-coding
mm_102083.1	chr11	52280240	52280249	-	1	NA	intron (NM_001313981, intron 3 of 10)	RSINE1|SINE|B4	2351	NM_009331	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_74917.1	chr8	25548063	25548072	-	1	NA	TTS (NR_110510)	TTS (NR_110510)	8016	NR_110510	102633315	Mm.437828	NR_110510	ENSMUSG00000086134	Gm16159	OTTMUSG00000031030	predicted gene 16159	ncRNA
mm_34717.1	chr4	152127163	152127165	+	1	NA	intron (NM_207688, intron 8 of 10)	intron (NM_207688, intron 8 of 10)	1761	NM_019585	56226	Mm.264215	NM_019585	ENSMUSG00000028943	Espn	je	espin	protein-coding
mm_113263.1	chr13	28912026	28912026	+	1	NA	Intergenic	Intergenic	-26604	NR_045053	72518	Mm.37454	NR_045053		2610307P16Rik	AI666457	RIKEN cDNA 2610307P16 gene	ncRNA
mm_113706.1	chr13	43365617	43365657	+	1	NA	Intergenic	CpG	-5079	NM_178848	68346	Mm.35325	NM_178848	ENSMUSG00000054021	Sirt5	0610012J09Rik|1500032M05Rik|AV001953	sirtuin 5	protein-coding
mm_147021.1	chr18	34624773	34624815	-	1	NA	promoter-TSS (NM_009004)	promoter-TSS (NM_009004)	69	NM_030147	78656	Mm.45602	NM_030147	ENSMUSG00000003778	Brd8	2610007E11Rik|4432404P07Rik|SMAP	bromodomain containing 8	protein-coding
mm_49394.1	chr6	28421770	28421806	+	1	NA	promoter-TSS (NM_028900)	promoter-TSS (NM_028900)	-64	NM_028900	74375	Mm.332950	NM_028900	ENSMUSG00000029708	Gcc1	4932417P04Rik	golgi coiled coil 1	protein-coding
mm_105608.1	chr11	106782871	106782884	-	1	NA	promoter-TSS (NR_037224)	promoter-TSS (NR_037224)	-118	NR_037224	100526469		NR_037224	ENSMUSG00000093273	Mir3064	mir-3064|mmu-mir-3064	microRNA 3064	ncRNA
mm_146589.1	chr18	9315370	9315381	-	1	NA	3' UTR (NM_026484, exon 10 of 10)	3' UTR (NM_026484, exon 10 of 10)	-32566	NM_153086	225152	Mm.119273	NM_153086	ENSMUSG00000036855	Gjd4	9430022F06Rik|Cx39	gap junction protein, delta 4	protein-coding
mm_14085.1	chr2	125136599	125136623	+	1	NA	promoter-TSS (NM_001162934)	promoter-TSS (NM_001162934)	-81	NM_001162934	381418	Mm.295608	NM_001162934	ENSMUSG00000074872	Ctxn2	BB181834|Gm1638	cortexin 2	protein-coding
mm_127317.1	chr15	100275992	100275998	+	1	NA	Intergenic	Intergenic	-4842	NM_183109	75002	Mm.261400	NM_183109	ENSMUSG00000045631	Tmprss12	4930478A21Rik	transmembrane (C-terminal) protease, serine 12	protein-coding
mm_97593.1	chr11	78948208	78948233	+	1	NA	exon (NM_010927, exon 17 of 27)	exon (NM_010927, exon 17 of 27)	22929	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_72153.1	chr8	72152597	72152610	+	1	NA	3' UTR (NM_001001491, exon 8 of 8)	3' UTR (NM_001001491, exon 8 of 8)	-8597	NM_023126	17274	Mm.162811	NM_023126	ENSMUSG00000003037	Rab8a	AA409338|Mel	RAB8A, member RAS oncogene family	protein-coding
mm_22770.1	chr3	20249560	20249587	+	1	NA	TTS (NM_029706)	TTS (NM_029706)	-7392	NM_007753	12873	Mm.1135	NM_007753	ENSMUSG00000001865	Cpa3	MC-CPA	carboxypeptidase A3, mast cell	protein-coding
mm_133081.1	chr16	59538731	59538731	+	1	NA	intron (NM_174848, intron 8 of 18)	intron (NM_174848, intron 8 of 18)	17021	NM_174848	224273	Mm.246424	NM_174848	ENSMUSG00000022723	Crybg3	5031404N19|AU022790|Gm9581	beta-gamma crystallin domain containing 3	protein-coding
mm_118997.1	chr14	28510099	28510119	+	1	NA	intron (NM_009524, intron 1 of 4)	intron (NM_009524, intron 1 of 4)	-1296	NM_001256224	22418	Mm.287544	NM_009524	ENSMUSG00000021994	Wnt5a	8030457G12Rik|Wnt-5a	wingless-type MMTV integration site family, member 5A	protein-coding
mm_76145.1	chr8	82207374	82207383	-	1	NA	Intergenic	(GA)n|Simple_repeat|Simple_repeat	195208	NM_001254747	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_152509.1	chr19	11266123	11266161	-	1	NA	promoter-TSS (NM_007641)	promoter-TSS (NM_007641)	9	NM_007641	12482	Mm.4046	NM_007641	ENSMUSG00000024673	Ms4a1	AA960661|Cd20|Ly-44|Ms4a2	membrane-spanning 4-domains, subfamily A, member 1	protein-coding
mm_117152.1	chr13	61255346	61255350	-	1	NA	promoter-TSS (NM_019541)	promoter-TSS (NM_019541)	0	NM_019541	56094	Mm.342861	NM_019541	ENSMUSG00000057446	Cts8	CTS2|Epcs68|Epcs70	cathepsin 8	protein-coding
mm_113660.1	chr13	42681567	42681586	+	1	NA	intron (NM_001302635, intron 1 of 13)	intron (NM_001302635, intron 1 of 13)	777	NM_001302635	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding
mm_27940.1	chr3	79628637	79628647	-	1	NA	promoter-TSS (NM_029482)	promoter-TSS (NM_029482)	125	NM_025794	66841	Mm.28336	NM_025794	ENSMUSG00000027809	Etfdh	0610010I20Rik|AV001013	electron transferring flavoprotein, dehydrogenase	protein-coding
mm_76352.1	chr8	84771891	84771908	-	1	NA	exon (NM_010906, exon 2 of 9)	exon (NM_010906, exon 2 of 9)	2470	NM_001081981	18032	Mm.9394	NM_010906	ENSMUSG00000001911	Nfix	CTF|NF-I/X|NF1-X|NFI-X	nuclear factor I/X	protein-coding
mm_77573.1	chr8	123432614	123432619	-	1	NA	Intergenic	MuLV-int|LTR|ERV1	-10340	NM_001253784	23854	Mm.275127	NM_054046	ENSMUSG00000001482	Def8	AI449518|D8Ertd713e|DEF-8	differentially expressed in FDCP 8	protein-coding
mm_67137.1	chr7	72649350	72649359	-	1	NA	Intergenic	Intergenic	-342759	NM_001024703	244049	Mm.217412	NM_001024703	ENSMUSG00000032776	Mctp2	Gm489	multiple C2 domains, transmembrane 2	protein-coding
mm_124541.1	chr14	122464227	122464240	-	1	NA	exon (NM_022987, exon 1 of 2)	exon (NM_022987, exon 1 of 2)	1425	NM_022987	65100	Mm.390761	NM_022987	ENSMUSG00000041703	Zic5	1700049L20Rik|Opr	zinc finger protein of the cerebellum 5	protein-coding
mm_141570.1	chr17	32284716	32284738	-	1	NA	promoter-TSS (NM_001286630)	promoter-TSS (NM_001286630)	-594	NM_020508	57261	Mm.253518	NM_020508	ENSMUSG00000024002	Brd4	Brd5|HUNK1|MCAP|WI-11513	bromodomain containing 4	protein-coding
mm_45184.1	chr5	51910839	51910846	-	1	NA	Intergenic	Intergenic	225175	NR_105845	102466648		NR_105845	ENSMUSG00000098726	Mir6417	Gm27334|mmu-mir-6417	microRNA 6417	ncRNA
mm_62843.1	chr7	114276303	114276331	+	1	NA	promoter-TSS (NM_011965)	promoter-TSS (NM_011965)	-201	NM_011965	26440	Mm.121265	NM_011965	ENSMUSG00000030751	Psma1	C2|HC2|Pros-30|alpha-type	proteasome (prosome, macropain) subunit, alpha type 1	protein-coding
mm_4231.1	chr1	171370093	171370111	+	1	NA	promoter-TSS (NM_027893)	promoter-TSS (NM_027893)	-71	NM_027893	71740	Mm.263414	NM_027893	ENSMUSG00000006411	Nectin4	1200017F15Rik|Prr4|Pvrl4	nectin cell adhesion molecule 4	protein-coding
mm_5824.1	chr1	52794927	52794930	-	1	NA	intron (NM_008384, intron 3 of 5)	intron (NM_008384, intron 3 of 5)	22760	NM_008384	16329	Mm.917	NM_008384	ENSMUSG00000026102	Inpp1	2300002C06Rik|AV137389	inositol polyphosphate-1-phosphatase	protein-coding
mm_11250.1	chr2	29890699	29890710	+	1	NA	intron (NM_013615, intron 1 of 16)	CpG	641	NM_013615	18286	Mm.330116	NM_013615	ENSMUSG00000026790	Odf2	AI848335|MMTEST29	outer dense fiber of sperm tails 2	protein-coding
mm_65683.1	chr7	28350466	28350476	-	1	NA	promoter-TSS (NM_013647)	promoter-TSS (NM_013647)	-218	NM_013647	20055	Mm.702	NM_013647	ENSMUSG00000037563	Rps16	AA420385|AI317031	ribosomal protein S16	protein-coding
mm_146722.1	chr18	15064312	15064335	-	1	NA	promoter-TSS (NM_001142731)	promoter-TSS (NM_001142731)	-741	NM_001142731	106931	Mm.329299	NM_134112	ENSMUSG00000036225	Kctd1	4933402K10Rik|AI661543|AW553000	potassium channel tetramerisation domain containing 1	protein-coding
mm_52110.1	chr6	97893937	97893952	+	1	NA	intron (NM_001113198, intron 1 of 9)	RLTR20A4|LTR|ERVK	-35873	NM_001178049	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_7444.1	chr1	120120141	120120194	-	1	NA	intron (NM_007830, intron 1 of 3)	intron (NM_007830, intron 1 of 3)	752	NM_001037999	13167	Mm.2785	NM_007830	ENSMUSG00000026385	Dbi	ACBD1|Acbp|EP|endozepine	diazepam binding inhibitor	protein-coding
mm_16200.1	chr2	173021923	173021939	+	1	NA	promoter-TSS (NM_019547)	promoter-TSS (NM_019547)	29	NM_019547	56190	Mm.485782	NM_019547	ENSMUSG00000027510	Rbm38	Rnpc1|Seb4|Seb4l	RNA binding motif protein 38	protein-coding
mm_154274.1	chr19	60782211	60782221	-	1	NA	exon (NM_010123, exon 2 of 22)	exon (NM_010123, exon 2 of 22)	-7819	NR_037245	100526521		NR_037245	ENSMUSG00000104890	Mir3084-1	Mir3084|mmu-mir-3084|mmu-mir-3084-1	microRNA 3084-1	ncRNA
mm_142291.1	chr17	40319301	40319304	-	1	NA	promoter-TSS (NM_009638)	promoter-TSS (NM_009638)	-95	NM_009638	11571	Mm.16781	NM_009638	ENSMUSG00000025431	Crisp1	AW324342|Aeg1|CRISP-1	cysteine-rich secretory protein 1	protein-coding
mm_112150.1	chr12	113260047	113260062	-	1	NA	Intergenic	Intergenic	74151	NM_153776	69195	Mm.313244	NM_153776	ENSMUSG00000049036	Tmem121	2410008J05Rik|Hole	transmembrane protein 121	protein-coding
mm_137805.1	chr17	29948055	29948055	+	1	NA	Intergenic	Intergenic	-57032	NM_148926	21769	Mm.220972	NM_148926	ENSMUSG00000044477	Zfand3	AW539211|TEG-27|Tex27	zinc finger, AN1-type domain 3	protein-coding
mm_54419.1	chr6	32897064	32897079	-	1	NA	intron (NM_025336, intron 4 of 7)	intron (NM_025336, intron 4 of 7)	163081	NM_025336	66075	Mm.21501	NM_025336	ENSMUSG00000053768	Chchd3	0610041L09Rik|1700039J09Rik|AW558177	coiled-coil-helix-coiled-coil-helix domain containing 3	protein-coding
mm_117359.1	chr13	70573150	70573159	-	1	NA	promoter-TSS (NR_045934)	promoter-TSS (NR_045934)	-87	NR_045934	73584	Mm.442491	NR_045934	ENSMUSG00000101051	1700100L14Rik	-	RIKEN cDNA 1700100L14 gene	ncRNA
mm_125640.1	chr15	62152950	62152999	+	1	NA	intron (NR_003368, intron 3 of 8)	intron (NR_003368, intron 3 of 8)	66477	NR_003523	67552	Mm.484027	NM_026230		H2afy3	4933432H23Rik	H2A histone family, member Y3	pseudo
mm_39970.1	chr5	32156703	32156713	+	1	NA	3' UTR (NM_008037, exon 4 of 4)	3' UTR (NM_008037, exon 4 of 4)	20236	NM_008037	14284	Mm.24684	NM_008037	ENSMUSG00000029135	Fosl2	Fra-2	fos-like antigen 2	protein-coding
mm_107307.1	chr12	31073963	31073967	+	1	NA	promoter-TSS (NM_027828)	promoter-TSS (NM_027828)	-3	NM_027828	104943	Mm.248938	NM_027828	ENSMUSG00000036136	Fam110c	9030611O19Rik|AU019489	family with sequence similarity 110, member C	protein-coding
mm_172443.1	chr7	29965639	29965639	-	1	NA	Intergenic	Intergenic	-13746	NM_178384	72723	Mm.371648	NM_178384	ENSMUSG00000059975	Zfp74	2810054M15Rik|KRAB8|Zfp66|Znf569|mszf21|mszf77	zinc finger protein 74	protein-coding
mm_10226.1	chr2	6322622	6322647	+	1	NA	promoter-TSS (NM_001080548)	promoter-TSS (NM_001080548)	-123	NM_001080548	98910	Mm.40673	NM_181399	ENSMUSG00000039046	Usp6nl	AI316785|RNTRE|TRE2NL|mKIAA0019	USP6 N-terminal like	protein-coding
mm_152194.1	chr19	7483138	7483148	-	1	NA	5' UTR (NM_053076, exon 1 of 7)	5' UTR (NM_053076, exon 1 of 7)	148	NM_001271486	20168	Mm.246990	NM_053076	ENSMUSG00000024758	Rtn3	RTN3-A1	reticulon 3	protein-coding
mm_63739.1	chr7	130900547	130900557	+	1	NA	exon (NM_133942, exon 5 of 10)	exon (NM_133942, exon 5 of 10)	-7716	NR_106028	102466219		NR_106028	ENSMUSG00000104914	Mir7061	mmu-mir-7061	microRNA 7061	ncRNA
mm_136029.1	chr16	76373873	76373886	-	1	NA	promoter-TSS (NM_173440)	promoter-TSS (NM_173440)	-830	NM_173440	268903	Mm.74711	NM_173440	ENSMUSG00000048490	Nrip1	6030458L20Rik|8430438I05Rik|9630050P12|AA959574|AW456757|RIP140	nuclear receptor interacting protein 1	protein-coding
mm_127765.1	chr15	103562963	103562971	+	1	NA	exon (NM_008134, exon 4 of 4)	exon (NM_008134, exon 4 of 4)	2114	NM_001289587	14663	Mm.219621	NM_008134	ENSMUSG00000022491	Glycam1	MC26|Sgp50|glyCAM-1	glycosylation dependent cell adhesion molecule 1	protein-coding
mm_10846.1	chr2	24976047	24976110	+	1	NA	promoter-TSS (NM_001031808)	promoter-TSS (NM_001031808)	45	NM_146251	241274	Mm.389243	NM_146251	ENSMUSG00000036833	Pnpla7	BC027342|E430013P11Rik|Nre	patatin-like phospholipase domain containing 7	protein-coding
mm_155359.1	chrX	70385871	70385944	+	1	NA	promoter-TSS (NM_026787)	promoter-TSS (NM_026787)	-6	NM_026787	68618	Mm.293255	NM_026787	ENSMUSG00000045237	1110012L19Rik	-	RIKEN cDNA 1110012L19 gene	protein-coding
mm_130728.1	chr15	101224626	101224638	-	1	NA	promoter-TSS (NR_045326)	promoter-TSS (NR_045326)	145	NR_045327	380977	Mm.399924	NR_045326	ENSMUSG00000097915	A330009N23Rik	-	RIKEN cDNA A330009N23 gene	ncRNA
mm_2832.1	chr1	131275598	131275615	+	1	NA	intron (NM_019777, intron 4 of 21)	intron (NM_019777, intron 4 of 21)	3957	NM_019777	56489	Mm.386783	NM_019777	ENSMUSG00000042349	Ikbke	AW558201|IKK-i|IKKepsilon|Ikki	inhibitor of kappaB kinase epsilon	protein-coding
mm_94170.1	chr10	128804409	128804446	-	1	NA	promoter-TSS (NM_178066)	promoter-TSS (NM_178066)	-57	NM_178066	73827	Mm.24630	NM_178066	ENSMUSG00000047090	Tmem198b	1110012D08Rik	transmembrane protein 198b	protein-coding
mm_122102.1	chr14	30915765	30915773	-	1	NA	exon (NM_008407, exon 12 of 21)	exon (NM_008407, exon 12 of 21)	7818	NM_008407	16426	Mm.4517	NM_008407	ENSMUSG00000006522	Itih3	AW108094|ITI-HC3|Intin3|Itih-3	inter-alpha trypsin inhibitor, heavy chain 3	protein-coding
mm_47154.1	chr5	120629979	120629988	-	1	NA	intron (NM_001195094, intron 5 of 6)	intron (NM_001195094, intron 5 of 6)	4252	NM_001195094	546886	Mm.464847	NM_001195094	ENSMUSG00000094282	Cfap73	Ccdc42b|Gm5988	cilia and flagella associated protein 73	protein-coding
mm_163754.1	chr13	119790724	119790743	-	1	NA	promoter-TSS (NM_028245)	promoter-TSS (NM_028245)	-1	NM_001302548	72465	Mm.139115	NM_028245	ENSMUSG00000094870	Zfp131	2610109I01Rik|AW558871|Znf131	zinc finger protein 131	protein-coding
mm_35290.1	chr4	21772410	21772417	-	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-3857	NM_001290425	77593	Mm.154306	NM_152825	ENSMUSG00000040455	Usp45	3110003C05Rik|4930550B20Rik|AI843191|Gcap7	ubiquitin specific petidase 45	protein-coding
mm_32096.1	chr4	98546711	98546739	+	1	NA	promoter-TSS (NM_007704)	promoter-TSS (NM_007704)	91	NM_001005787	12695	Mm.90218	NM_007704	ENSMUSG00000061859	Patj	Cipp|Inadl	PATJ, crumbs cell polarity complex component	protein-coding
mm_109011.1	chr12	103346768	103346794	+	1	NA	intron (NM_023049, intron 1 of 9)	intron (NM_023049, intron 1 of 9)	9220	NM_023049	65256	Mm.27159	NM_023049	ENSMUSG00000021200	Asb2	1110008E15Rik	ankyrin repeat and SOCS box-containing 2	protein-coding
mm_94593.1	chr11	11771445	11771457	+	1	NA	3' UTR (NM_009578, exon 7 of 7)	3' UTR (NM_009578, exon 7 of 7)	37511	NM_021891	60530	Mm.236114	NM_021891	ENSMUSG00000035455	Fignl1	-	fidgetin-like 1	protein-coding
mm_91800.1	chr10	53629988	53630022	-	1	NA	exon (NM_027830, exon 2 of 14)	exon (NM_027830, exon 2 of 14)	434	NM_027830	71567	Mm.278221	NM_027830	ENSMUSG00000058298	Mcm9	9030408O17Rik|Gm235|Mcmdc1	minichromosome maintenance 9 homologous recombination repair factor	protein-coding
mm_29431.1	chr3	109027657	109027665	-	1	NA	promoter-TSS (NM_001163567)	promoter-TSS (NM_001163567)	-54	NM_001163567	329739	Mm.69013	NM_001163567	ENSMUSG00000040339	Fam102b	1600010D10Rik|B430201A12Rik	family with sequence similarity 102, member B	protein-coding
mm_104947.1	chr11	100121705	100121711	-	1	NA	promoter-TSS (NM_010662)	promoter-TSS (NM_010662)	-142	NM_010662	16663	Mm.4646	NM_010662	ENSMUSG00000044041	Krt13	CK13|K13|Krt-1.13|Krt1-13	keratin 13	protein-coding
mm_91450.1	chr10	33949490	33949502	-	1	NA	5' UTR (NM_028287, exon 3 of 10)	5' UTR (NM_028287, exon 3 of 10)	1716	NM_028287	72580	Mm.248081	NM_028287	ENSMUSG00000039531	Zufsp	2700019D07Rik	zinc finger with UFM1-specific peptidase domain	protein-coding
mm_87186.1	chr10	39369751	39369804	+	1	NA	promoter-TSS (NM_008054)	promoter-TSS (NM_008054)	-22	NM_001122892	14360	Mm.4848	NM_008054	ENSMUSG00000019843	Fyn	AI448320|AW552119	Fyn proto-oncogene	protein-coding
mm_68852.1	chr7	126369441	126369457	-	1	NA	TTS (NM_023712)	TTS (NM_023712)	119	NM_010689	16797	Mm.10280	NM_010689	ENSMUSG00000030742	Lat	p36-38|pp36	linker for activation of T cells	protein-coding
mm_46800.1	chr5	113069659	113069661	-	1	NA	5' UTR (NM_007773, exon 2 of 7)	5' UTR (NM_007773, exon 2 of 7)	457	NM_007773	12961	Mm.1215	NM_007773	ENSMUSG00000042240	Crybb2	Cryb-2	crystallin, beta B2	protein-coding
mm_117799.1	chr13	97207050	97207058	-	1	NA	Intergenic	RMER5|LTR|ERV1	-8697	NM_010422	15212	Mm.27816	NM_010422	ENSMUSG00000021665	Hexb	-	hexosaminidase B	protein-coding
mm_113488.1	chr13	37378535	37378545	+	1	NA	intron (NM_010745, intron 3 of 4)	MER2|DNA|TcMar-Tigger	33195	NM_010745	17084	Mm.2639	NM_010745	ENSMUSG00000021423	Ly86	MD-1|MD1|ly86_tv2	lymphocyte antigen 86	protein-coding
mm_145840.1	chr18	65446609	65446658	+	1	NA	intron (NM_172833, intron 3 of 15)	intron (NM_172833, intron 3 of 15)	15636	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_83094.1	chr9	40321192	40321202	-	1	NA	intron (NM_172768, intron 4 of 19)	intron (NM_172768, intron 4 of 19)	-12275	NR_040728	73558	Mm.398307	NR_040728		1700110K17Rik	-	RIKEN cDNA 1700110K17 gene	ncRNA
mm_122323.1	chr14	36968680	36968738	-	1	NA	promoter-TSS (NM_027045)	promoter-TSS (NM_027045)	55	NM_027045	72972	Mm.27621	NM_027045	ENSMUSG00000058690	Ccser2	1700012P13Rik|2900054P12Rik|AI035535|AW108503|Fam190b|Gcap14	coiled-coil serine rich 2	protein-coding
mm_83121.1	chr9	40408024	40408028	-	1	NA	intron (NM_172768, intron 2 of 19)	intron (NM_172768, intron 2 of 19)	47738	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_163542.1	chr13	15771572	15771578	+	1	NA	Intergenic	Intergenic	31055	NR_045507	71071	Mm.380845	NR_045507		4933412O06Rik	-	RIKEN cDNA 4933412O06 gene	ncRNA
mm_7687.1	chr1	128592285	128592307	-	1	NA	promoter-TSS (NM_009911)	promoter-TSS (NM_009911)	3	NM_009911	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding
mm_55322.1	chr6	55678526	55678539	-	1	NA	3' UTR (NM_009717, exon 2 of 2)	3' UTR (NM_009717, exon 2 of 2)	2731	NM_009717	11922	Mm.5106	NM_009717	ENSMUSG00000037984	Neurod6	Atoh2|Math-2|Math2|Nex|Nex1m|bHLHa2	neurogenic differentiation 6	protein-coding
mm_68151.1	chr7	102250128	102250138	-	1	NA	promoter-TSS (NM_019566)	promoter-TSS (NM_019566)	-15	NM_019566	56212	Mm.259795	NM_019566	ENSMUSG00000073982	Rhog	2810426G09Rik|Arhg|Sid10750	ras homolog family member G	protein-coding
mm_55594.1	chr6	71609086	71609108	-	1	NA	intron (NM_001038695, intron 11 of 26)	intron (NM_001038695, intron 11 of 26)	23589	NM_173001	104263	Mm.260479	NM_173001	ENSMUSG00000053470	Kdm3a	1700105C21Rik|C230043E16Rik|JHDM2a|Jmjd1|Jmjd1a|KDM2A|TGSA|Tsga	lysine (K)-specific demethylase 3A	protein-coding
mm_64469.1	chr7	143005678	143005703	+	1	NA	promoter-TSS (NM_001128082)	promoter-TSS (NM_001128082)	31	NM_001128081	27027	Mm.28172	NM_020286	ENSMUSG00000000244	Tspan32	AW208513|Art-1|BB235973|D7Wsu37e|Phemx|Tssc6	tetraspanin 32	protein-coding
mm_158762.1	chrX	166499008	166499020	-	1	NA	TTS (NM_001007577)	TTS (NM_001007577)	11464	NM_001007577	245695	Mm.336318	NM_001007577	ENSMUSG00000051224	Tceanc	A630018P17Rik|Gm390	transcription elongation factor A (SII) N-terminal and central domain containing	protein-coding
mm_162620.1	chr1	183418454	183418465	+	1	NA	promoter-TSS (NM_030175)	promoter-TSS (NM_030175)	-11	NM_030175	78772	Mm.29003	NM_030175	ENSMUSG00000053461	Hhipl2	4930507C10Rik|AW208802|Hhip3	hedgehog interacting protein-like 2	protein-coding
mm_77243.1	chr8	115705318	115705344	-	1	NA	3' UTR (NM_001025577, exon 1 of 1)	3' UTR (NM_001025577, exon 1 of 1)	1563	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_37430.1	chr4	122927458	122927463	-	1	NA	Intergenic	ORR1D1|LTR|ERVL-MaLR	33728	NM_029662	76574	Mm.331842	NM_029662	ENSMUSG00000028655	Mfsd2a	1700018O18Rik|Mfsd2|NLS1	major facilitator superfamily domain containing 2A	protein-coding
mm_21961.1	chr2	167221334	167221385	-	1	NA	exon (NM_008968, exon 5 of 10)	exon (NM_008968, exon 5 of 10)	19178	NM_008968	19223	Mm.2339	NM_008968	ENSMUSG00000017969	Ptgis	Cyp8|Cyp8a1|Pgis	prostaglandin I2 (prostacyclin) synthase	protein-coding
mm_97247.1	chr11	75747447	75747486	+	1	NA	intron (NM_009536, intron 1 of 5)	ID_B1|SINE|B4	14579	NM_009536	22627	Mm.234700	NM_009536	ENSMUSG00000020849	Ywhae	AU019196	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide	protein-coding
mm_140019.1	chr17	73804903	73804941	+	1	NA	promoter-TSS (NM_020578)	promoter-TSS (NM_020578)	81	NM_020578	57440	Mm.18526	NM_020578	ENSMUSG00000024065	Ehd3	Ehd2	EH-domain containing 3	protein-coding
mm_113061.1	chr13	23739191	23739198	+	1	NA	exon (NM_015786, exon 1 of 1)	exon (NM_015786, exon 1 of 1)	387	NM_015786	50708	Mm.193539	NM_015786	ENSMUSG00000036181	Hist1h1c	0610008C09Rik|H1.2|H1c|H1f2|H1var1|His1a	histone cluster 1, H1c	protein-coding
mm_107520.1	chr12	40455035	40455038	+	1	NA	intron (NM_172803, intron 1 of 52)	MLT1A|LTR|ERVL-MaLR	8983	NM_172803	238130	Mm.341423	NM_172803	ENSMUSG00000035954	Dock4	5330406C03|6330411N01Rik|AF263288|C030023J22|mKIAA0716	dedicator of cytokinesis 4	protein-coding
mm_138023.1	chr17	33911492	33911536	+	1	NA	exon (NM_001199733, exon 3 of 8)	exon (NM_001199733, exon 3 of 8)	1913	NM_001199733	13163	Mm.271809	NM_007829	ENSMUSG00000002307	Daxx	-	Fas death domain-associated protein	protein-coding
mm_47650.1	chr5	125390177	125390222	-	1	NA	promoter-TSS (NM_019639)	promoter-TSS (NM_019639)	-182	NM_019639	22190	Mm.331	NM_019639	ENSMUSG00000008348	Ubc	2700054O04Rik|AI194771|Rps27a|TI-225|Uba52|Ubb	ubiquitin C	protein-coding
mm_142576.1	chr17	46680787	46680834	-	1	NA	promoter-TSS (NM_010787)	promoter-TSS (NM_010787)	27	NM_001277311	17256	Mm.329083	NM_010787	ENSMUSG00000002768	Mea1	Mea-1	male enhanced antigen 1	protein-coding
mm_154680.1	chrX	7920008	7920020	+	1	NA	exon (NM_013892, exon 1 of 3)	exon (NM_013892, exon 1 of 3)	192	NM_013892	30052	Mm.4881	NM_013892	ENSMUSG00000039278	Pcsk1n	AI848336|KEP|PEN|PEN19|PEN20|Pan3|SAAS|SAASCT|bLEN|lLEN|proSAAS	proprotein convertase subtilisin/kexin type 1 inhibitor	protein-coding
mm_108863.1	chr12	98920621	98920634	+	1	NA	promoter-TSS (NM_198311)	promoter-TSS (NM_198311)	15	NM_198311	76260	Mm.282660	NM_029553	ENSMUSG00000021013	Ttc8	0610012F22Rik|AV001447|BBS8	tetratricopeptide repeat domain 8	protein-coding
mm_128107.1	chr15	28022188	28022190	-	1	NA	intron (NM_001081302, intron 1 of 56)	intron (NM_001081302, intron 1 of 56)	3659	NM_001081302	223435	Mm.485422	NM_001081302	ENSMUSG00000022263	Trio	6720464I07Rik|AA408740|Solo	triple functional domain (PTPRF interacting)	protein-coding
mm_141242.1	chr17	27467783	27467792	-	1	NA	intron (NM_001013385, intron 2 of 8)	RLTR20A4|LTR|ERVK	35746	NM_001013385	268934	Mm.358940	NM_001013385	ENSMUSG00000063239	Grm4	Gprc1d|mGluR4	glutamate receptor, metabotropic 4	protein-coding
mm_25839.1	chr3	129214270	129214305	+	1	NA	5' UTR (NM_001287048, exon 1 of 3)	5' UTR (NM_001287048, exon 1 of 3)	355	NM_001287048	18741	Mm.246804	NM_011098	ENSMUSG00000028023	Pitx2	9430085M16Rik|Brx1|Brx1b|Munc30|Otlx2|Ptx2|Rieg	paired-like homeodomain transcription factor 2	protein-coding
mm_95157.1	chr11	35838614	35838629	+	1	NA	TTS (NM_170779)	TTS (NM_170779)	-4093	NM_025936	104458	Mm.284906	NM_025936	ENSMUSG00000018848	Rars	2610011N19Rik|2610037E21Rik|AL033339|AW985894	arginyl-tRNA synthetase	protein-coding
mm_16660.1	chr2	6650948	6650955	-	1	NA	intron (NM_001347094, intron 3 of 12)	L1_Mur2|LINE|L1	70711	NM_001310447	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_62826.1	chr7	113513855	113513909	+	1	NA	promoter-TSS (NM_027379)	promoter-TSS (NM_027379)	48	NM_027379	67420	Mm.206919	NM_026143	ENSMUSG00000030759	Far1	2600011M19Rik|2900034E22Rik|3732409C05Rik|AI850429|Mlstd2	fatty acyl CoA reductase 1	protein-coding
mm_171571.1	chr4	147361305	147361305	+	1	NA	intron (NM_001039209, intron 1 of 2)	intron (NM_001039209, intron 1 of 2)	185439	NM_001039209	195531	Mm.270762	NM_001039209	ENSMUSG00000078496	Zfp982	Gm13152|OTTMUSG00000010671	zinc finger protein 982	protein-coding
mm_81314.1	chr9	108397929	108397934	+	1	NA	TTS (NM_053216)	TTS (NM_053216)	5097	NM_053216	112418	Mm.78287	NM_053216	ENSMUSG00000032611	1700102P08Rik	AI593206	RIKEN cDNA 1700102P08 gene	protein-coding
mm_80172.1	chr9	72060897	72060897	+	1	NA	intron (NM_001253862, intron 3 of 19)	intron (NM_001253862, intron 3 of 19)	50304	NM_001253862	21406	Mm.171615	NM_011544	ENSMUSG00000032228	Tcf12	A130037E08Rik|ALF1|HEB|HEBAlt|HTF-4|HTF4|ME1|REB|bHLHb20	transcription factor 12	protein-coding
mm_172561.1	chr8	107038211	107038231	-	1	NA	intron (NM_126165, intron 3 of 10)	intron (NM_126165, intron 3 of 10)	6895	NM_126165	116733	Mm.236004	NM_126165	ENSMUSG00000031913	Vps4a	4930589C15Rik|AI325971|AW553189	vacuolar protein sorting 4A	protein-coding
mm_125305.1	chr15	37264388	37264409	+	1	NA	intron (NM_026496, intron 1 of 15)	ORR1C2|LTR|ERVL-MaLR	31362	NM_026496	252973	Mm.244612	NM_026496	ENSMUSG00000022286	Grhl2	0610015A08Rik|BOM|Tcfcp2l3|clft3	grainyhead-like 2 (Drosophila)	protein-coding
mm_26902.1	chr3	19311244	19311263	-	1	NA	promoter-TSS (NM_001122759)	promoter-TSS (NM_001122759)	69	NM_001122759	18583	Mm.355614	NM_008802	ENSMUSG00000069094	Pde7a	AU015378|AW047537	phosphodiesterase 7A	protein-coding
mm_139530.1	chr17	56673322	56673328	+	1	NA	promoter-TSS (NM_027933)	promoter-TSS (NM_027933)	100	NM_027933	71810	Mm.29608	NM_027933	ENSMUSG00000002372	Ranbp3	2610024N24Rik|AA408221	RAN binding protein 3	protein-coding
mm_150690.1	chr19	42147374	42147388	+	1	NA	promoter-TSS (NM_183195)	promoter-TSS (NM_183195)	-8	NM_183195	277010	Mm.206250	NM_183195	ENSMUSG00000044345	Marveld1	AI504298|Mrvldc1	MARVEL (membrane-associating) domain containing 1	protein-coding
mm_91249.1	chr10	22731834	22731849	-	1	NA	promoter-TSS (NM_011603)	promoter-TSS (NM_011603)	-394	NM_011603	237336	Mm.86670	NM_011603	ENSMUSG00000071359	Tbpl1	4732475G08|AW011832|AW491032|D18347|STD|TLF|TRF2|TRP|Tlp	TATA box binding protein-like 1	protein-coding
mm_138218.1	chr17	34312113	34312116	+	1	NA	intron (NM_010382, intron 2 of 5)	intron (NM_010382, intron 2 of 5)	6247	NM_010382	14969	Mm.22564	NM_010382	ENSMUSG00000060586	H2-Eb1	Eb|H-2Eb|H2Eb|Ia-4|Ia4	histocompatibility 2, class II antigen E beta	protein-coding
mm_122271.1	chr14	34362362	34362377	-	1	NA	Intergenic	L1MC4|LINE|L1	-6976	NM_183278	69134	Mm.27156	NM_183278	ENSMUSG00000043681	Fam25c	2200001I15Rik|Fam25	family with sequence similarity 25, member C	protein-coding
mm_62626.1	chr7	107594106	107594130	+	1	NA	promoter-TSS (NM_008905)	promoter-TSS (NM_008905)	-933	NM_008905	19024	Mm.2817	NM_008905	ENSMUSG00000036528	Ppfibp2	Cclp1	PTPRF interacting protein, binding protein 2 (liprin beta 2)	protein-coding
mm_29476.1	chr3	115711187	115711198	-	1	NA	3' UTR (NM_007901, exon 2 of 2)	3' UTR (NM_007901, exon 2 of 2)	3863	NM_007901	13609	Mm.982	NM_007901	ENSMUSG00000045092	S1pr1	AI849002|Edg1|Lpb1|S1p|S1p1	sphingosine-1-phosphate receptor 1	protein-coding
mm_39372.1	chr5	12383157	12383177	+	1	NA	promoter-TSS (NM_028882)	promoter-TSS (NM_028882)	1	NM_028882	108151	Mm.89313	NM_028882	ENSMUSG00000040254	Sema3d	4631426B19Rik	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D	protein-coding
mm_135413.1	chr16	45031185	45031189	-	1	NA	Intergenic	Intergenic	-62866	NM_026439	67896	Mm.181074	NM_026439	ENSMUSG00000022665	Ccdc80	2610001E17Rik|DRO1|Ssg1|Urb	coiled-coil domain containing 80	protein-coding
mm_51031.1	chr6	65525323	65525335	+	1	NA	Intergenic	Intergenic	-65069	NM_001001495	414084	Mm.117558	NM_001001495	ENSMUSG00000044162	Tnip3	9030611K07Rik|ABIN-3|LIND	TNFAIP3 interacting protein 3	protein-coding
mm_123393.1	chr14	63417030	63417059	-	1	NA	5' UTR (NM_007549, exon 1 of 13)	5' UTR (NM_007549, exon 1 of 13)	143	NM_007549	12143	Mm.3962	NM_007549	ENSMUSG00000014453	Blk	-	B lymphoid kinase	protein-coding
mm_17545.1	chr2	29846477	29846494	-	1	NA	promoter-TSS (NR_029838)	promoter-TSS (NR_029838)	-758	NR_029838	723904		NR_029838	ENSMUSG00000065485	Mir219a-2	Mir219-2|Mirn219-2|mir-219a-2|mmu-mir-219a-2	microRNA 219a-2	ncRNA
mm_22686.1	chr3	17789728	17789763	+	1	NA	promoter-TSS (NR_033490)	promoter-TSS (NR_033490)	-176	NR_033490	70441	Mm.458192	NR_033490	ENSMUSG00000100252	Mir124-2hg	100040120|2610100L16Rik|6430547I21Rik|A930005K07Rik|AW125202|Gm2612	Mir124-2 host gene (non-protein coding)	ncRNA
mm_133304.1	chr16	77598028	77598038	+	1	NA	promoter-TSS (NR_029535)	promoter-TSS (NR_029535)	-903	NR_029535	387229		NR_029535	ENSMUSG00000065530	Mir99a	Mirn99a|mir-99a|mmu-mir-99a	microRNA 99a	ncRNA
mm_69651.1	chr7	139638989	139638992	-	1	NA	exon (NM_001302546, exon 30 of 59)	exon (NM_001302546, exon 30 of 59)	44825	NM_001302546	212124	Mm.425507	NM_177212	ENSMUSG00000049571	Cfap46	9330101J02Rik|E030019B06Rik|Gm170|Ttc40	cilia and flagella associated protein 46	protein-coding
mm_126938.1	chr15	91898094	91898100	+	1	NA	exon (NM_207243, exon 26 of 44)	exon (NM_207243, exon 26 of 44)	59769	NM_198927	223809	Mm.486225	NM_198927	ENSMUSG00000047295	Smgc	2310010P21Rik|DXImx49e|Muc19|Muc19/Smgc|Sfc21	submandibular gland protein C	protein-coding
mm_73694.1	chr8	111621687	111621692	+	1	NA	3' UTR (NM_133206, exon 4 of 4)	3' UTR (NM_133206, exon 4 of 4)	8633	NM_027570	52815	Mm.27589	NM_027570	ENSMUSG00000031958	Ldhd	4733401P21Rik|D8Bwg1320e	lactate dehydrogenase D	protein-coding
mm_111019.1	chr12	79017342	79017352	-	1	NA	Intergenic	Intergenic	-10070	NM_178745	268567	Mm.341747	NM_178745	ENSMUSG00000046157	Tmem229b	6330442E10Rik|9830138K24|AU019070	transmembrane protein 229B	protein-coding
mm_93377.1	chr10	105532578	105532581	-	1	NA	intron (NM_177368, intron 1 of 11)	intron (NM_177368, intron 1 of 11)	41900	NM_177368	278279	Mm.25225	NM_177368	ENSMUSG00000036019	Tmtc2	8430438D04Rik|D330034A10Rik	transmembrane and tetratricopeptide repeat containing 2	protein-coding
mm_46987.1	chr5	115326968	115326981	-	1	NA	promoter-TSS (NM_025573)	promoter-TSS (NM_025573)	-203	NM_025573	108014	Mm.287826	NM_025573	ENSMUSG00000029538	Srsf9	25kDa|2610029M16Rik|SRp30c|Sfrs9	serine/arginine-rich splicing factor 9	protein-coding
mm_169518.1	chr14	8800187	8800202	-	1	NA	Intergenic	Intergenic	133804	NR_045968	74859	Mm.84041	NR_045968	ENSMUSG00000097898	4930455B14Rik	1700027C12Rik	RIKEN cDNA 4930455B14 gene	ncRNA
mm_93508.1	chr10	114802263	114802282	-	1	NA	promoter-TSS (NM_146241)	promoter-TSS (NM_146241)	-902	NM_146241	237553	Mm.445550	NM_146241	ENSMUSG00000050663	Trhde	9330155P21Rik	TRH-degrading enzyme	protein-coding
mm_119997.1	chr14	55604551	55604564	+	1	NA	promoter-TSS (NM_001159418)	promoter-TSS (NM_001159418)	-22	NM_001159418	16391	Mm.2032	NM_008394	ENSMUSG00000002325	Irf9	Irf-9|Isgf3g|p48	interferon regulatory factor 9	protein-coding
mm_134244.1	chr16	13419848	13419851	-	1	NA	Intergenic	RLTR30D2_MM|LTR|ERV1	-29674	NR_030549	100124432		NR_030549	ENSMUSG00000076972	Mir193b	Mir193|Mirn193b|mir-193b	microRNA 193b	ncRNA
mm_157106.1	chrX	9437859	9437871	-	1	NA	3' UTR (NM_007807, exon 13 of 13)	3' UTR (NM_007807, exon 13 of 13)	31459	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_123526.1	chr14	66750119	66750123	-	1	NA	intron (NM_001271761, intron 2 of 2)	intron (NM_001271761, intron 2 of 2)	114870	NM_001271760	11549	Mm.57064	NM_013461	ENSMUSG00000045875	Adra1a	Adra1c	adrenergic receptor, alpha 1a	protein-coding
mm_90383.1	chr10	127288491	127288521	+	1	NA	intron (NM_033072, intron 1 of 12)	intron (NM_033072, intron 1 of 12)	512	NM_001347171	110962	Mm.372826	NM_033072	ENSMUSG00000025409	Mbd6	D10Wsu93e	methyl-CpG binding domain protein 6	protein-coding
mm_63191.1	chr7	125603444	125603474	+	1	NA	promoter-TSS (NM_021887)	promoter-TSS (NM_021887)	30	NM_021887	60504	Mm.155643	NM_021887	ENSMUSG00000030745	Il21r	NILR	interleukin 21 receptor	protein-coding
mm_43482.1	chr5	136908131	136908174	+	1	NA	promoter-TSS (NM_026073)	promoter-TSS (NM_026073)	2	NM_026073	67286	Mm.41779	NM_026073	ENSMUSG00000007987	Ift22	3110017O03Rik|AI835745|AI847427|Rabl5	intraflagellar transport 22	protein-coding
mm_85735.1	chr9	108460914	108460937	-	1	NA	intron (NM_133744, intron 1 of 1)	CpG	407	NM_133744	72454	Mm.46488	NM_133744	ENSMUSG00000049305	Ccdc71	2600016J21Rik	coiled-coil domain containing 71	protein-coding
mm_84999.1	chr9	86858407	86858411	-	1	NA	intron (NR_102729, intron 2 of 30)	intron (NR_102729, intron 2 of 30)	21988	NM_001277982	20616	Mm.281651	NM_013669	ENSMUSG00000033419	Snap91	91kDa|AP180|F1-20|mKIAA0656	synaptosomal-associated protein 91	protein-coding
mm_39310.1	chr5	8046123	8046152	+	1	NA	promoter-TSS (NM_025618)	promoter-TSS (NM_025618)	59	NM_025618	109552	Mm.96211	NM_025618	ENSMUSG00000003161	Sri	2210417O06Rik|2900070H08Rik|Sor	sorcin	protein-coding
mm_8361.1	chr1	150455978	150455985	-	1	NA	exon (NM_021400, exon 7 of 13)	exon (NM_021400, exon 7 of 13)	10184	NM_021400	96875	Mm.174256	NM_021400	ENSMUSG00000006014	Prg4	CACP|DOL54|JCAP|MSF|SZP|lubricin	proteoglycan 4 (megakaryocyte stimulating factor, articular superficial zone protein)	protein-coding
mm_116744.1	chr13	51777120	51777141	-	1	NA	intron (NM_013660, intron 1 of 15)	intron (NM_013660, intron 1 of 15)	16617	NM_001281880	20354	Mm.33903	NM_013660	ENSMUSG00000021451	Sema4d	CD100|Semacl2|Semaj|Semcl2|coll-4	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D	protein-coding
mm_117427.1	chr13	74462659	74462704	-	1	NA	Intergenic	Intergenic	31269	NM_146231	235956	Mm.296909	NM_146231	ENSMUSG00000069208	Zfp825	-	zinc finger protein 825	protein-coding
mm_44290.1	chr5	8368184	8368216	-	1	NA	promoter-TSS (NM_001007221)	promoter-TSS (NM_001007221)	-40	NM_001310439	11496	Mm.275895	NM_001007220	ENSMUSG00000040537	Adam22	2900022I03Rik|AI854032|MDC2	a disintegrin and metallopeptidase domain 22	protein-coding
mm_47174.1	chr5	120745706	120745716	-	1	NA	exon (NM_145227, exon 3 of 11)	exon (NM_145227, exon 3 of 11)	4137	NM_145227	246728	Mm.260926	NM_145227	ENSMUSG00000032690	Oas2	Oasl11	2'-5' oligoadenylate synthetase 2	protein-coding
mm_34854.1	chr4	155522530	155522543	+	1	NA	intron (NM_001160016, intron 2 of 11)	intron (NM_001160016, intron 2 of 11)	31175	NM_001160016	14688	Mm.2344	NM_008142	ENSMUSG00000029064	Gnb1	AA409223|C77571|Gnb-1	guanine nucleotide binding protein (G protein), beta 1	protein-coding
mm_27829.1	chr3	79097644	79097653	-	1	NA	intron (NM_001310536, intron 5 of 23)	L1M3|LINE|L1	47239	NM_001310536	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_133623.1	chr16	91563030	91563064	+	1	NA	3' UTR (NM_008338, exon 7 of 7)	3' UTR (NM_008338, exon 7 of 7)	15953	NM_008338	15980	Mm.249364	NM_008338	ENSMUSG00000022965	Ifngr2	Ifgr2|Ifgt	interferon gamma receptor 2	protein-coding
mm_165909.1	chr4	56802317	56802327	+	1	NA	promoter-TSS (NM_026079)	promoter-TSS (NM_026079)	-7	NM_001081420	230234	Mm.268148	NM_001081420	ENSMUSG00000038827	Fam206a	simiate	family with sequence similarity 206, member A	protein-coding
mm_167423.1	chr8	111687184	111687197	+	1	NA	exon (NM_025583, exon 6 of 7)	exon (NM_025583, exon 6 of 7)	2484	NR_106044	102466993		NR_106044	ENSMUSG00000099129	Mir7076	Gm27318|mmu-mir-7076	microRNA 7076	ncRNA
mm_30137.1	chr3	142249661	142249667	-	1	NA	intron (NM_001190852, intron 12 of 15)	intron (NM_001190852, intron 12 of 15)	-80436	NM_001277216	12167	Mm.39089	NM_007560	ENSMUSG00000052430	Bmpr1b	AI385617|ALK-6|AV355320|Acvrlk6|Alk6|BMPR-1B|BMPR-IB|CFK-43a|SKR6	bone morphogenetic protein receptor, type 1B	protein-coding
mm_22204.1	chr2	173578216	173578278	-	1	NA	promoter-TSS (NM_001199955)	promoter-TSS (NM_001199955)	94	NM_001199955	70065	Mm.425115	NM_027303	ENSMUSG00000027517	Ankrd60	1700019A24Rik|1700030G11Rik	ankyrin repeat domain 60	protein-coding
mm_100115.1	chr11	115834339	115834349	+	1	NA	intron (NM_145438, intron 1 of 25)	intron (NM_145438, intron 1 of 25)	10286	NM_001252532	217325	Mm.290450	NM_145438	ENSMUSG00000020782	Llgl2	9130006H11Rik|Llglh2	lethal giant larvae homolog 2 (Drosophila)	protein-coding
mm_172096.1	chr6	25557815	25557815	-	1	NA	Intergenic	Intergenic	132165	NM_010338	14763	Mm.409670	NM_010338	ENSMUSG00000039904	Gpr37	AI848630|Pael-R	G protein-coupled receptor 37	protein-coding
mm_140590.1	chr17	10231119	10231122	-	1	NA	intron (NM_021881, intron 4 of 6)	intron (NM_021881, intron 4 of 6)	88241	NM_021881	19317	Mm.130694	NM_021881	ENSMUSG00000062078	Qk	1110003F05Rik|1500005P18|QkI|l(17)-1Wis|l17Wis1	quaking	protein-coding
mm_145241.1	chr18	50398616	50398621	+	1	NA	Intergenic	Intergenic	120249	NM_001004061	225497	Mm.329435	NM_001004061	ENSMUSG00000035420	Fam170a	Gm93|Znfd	family with sequence similarity 170, member A	protein-coding
mm_29796.1	chr3	127734129	127734136	-	1	NA	intron (NM_027808, intron 1 of 13)	MusHAL1|LINE|L1	46395	NM_027808	71481	Mm.158704	NM_027808	ENSMUSG00000028028	Alpk1	8430410J10Rik|LAK	alpha-kinase 1	protein-coding
mm_162563.1	chr1	172428900	172428914	+	1	NA	Intergenic	MTB_Mm|LTR|ERVL-MaLR	-46453	NM_029612	98365	Mm.150050	NM_029612	ENSMUSG00000026548	Slamf9	2310026I04Rik|AI462096|CD2F-10|CD84-H1|Cd2f10|SF2001	SLAM family member 9	protein-coding
mm_6629.1	chr1	78197113	78197117	-	1	NA	promoter-TSS (NM_008781)	promoter-TSS (NM_008781)	21	NM_008781	18505	Mm.1371	NM_008781	ENSMUSG00000004872	Pax3	Pax-3|Sp|Splchl2|splotch	paired box 3	protein-coding
mm_129810.1	chr15	82995052	82995053	-	1	NA	Intergenic	Intergenic	28086	NM_028728	74039	Mm.32584	NM_028728	ENSMUSG00000058099	Nfam1	4921501M20Rik|Cnaip	Nfat activating molecule with ITAM motif 1	protein-coding
mm_68431.1	chr7	109840905	109840907	-	1	NA	intron (NM_020052, intron 7 of 21)	ID_B1|SINE|B4	24773	NM_020052	56788	Mm.40447	NM_020052	ENSMUSG00000007279	Scube2	4932442O19Rik|Cegf1|Cegp1	signal peptide, CUB domain, EGF-like 2	protein-coding
mm_121432.1	chr14	120408510	120408514	+	1	NA	intron (NM_175341, intron 8 of 8)	intron (NM_175341, intron 8 of 8)	-69949	NM_029519	76108	Mm.261448	NM_029519	ENSMUSG00000051615	Rap2a	5830461H18Rik	RAS related protein 2a	protein-coding
mm_30578.1	chr4	4138299	4138343	+	1	NA	5' UTR (NM_001002927, exon 1 of 2)	5' UTR (NM_001002927, exon 1 of 2)	124	NM_001002927	18619	Mm.475097	NM_001002927	ENSMUSG00000045573	Penk	AI326464|ENK|PPA|Penk1	preproenkephalin	protein-coding
mm_85915.1	chr9	111057509	111057523	-	1	NA	promoter-TSS (NM_017466)	promoter-TSS (NM_017466)	2	NM_001302376	54199	Mm.7336	NM_017466	ENSMUSG00000043953	Ccrl2	1810047I05Rik|Ackr5|CCR11|Cmkbr1l2|E01|L-CCR	chemokine (C-C motif) receptor-like 2	protein-coding
mm_32729.1	chr4	116557741	116557751	+	1	NA	promoter-TSS (NM_029868)	promoter-TSS (NM_029868)	19	NM_029868	77110	Mm.41715	NM_029868	ENSMUSG00000034042	Gpbp1l1	5330440M15Rik|BC002292	GC-rich promoter binding protein 1-like 1	protein-coding
mm_140296.1	chr17	85620954	85620978	+	1	NA	5' UTR (NM_011381, exon 1 of 2)	5' UTR (NM_011381, exon 1 of 2)	132	NM_011381	20473	Mm.370208	NM_011381	ENSMUSG00000038805	Six3	E130112M24Rik|Six3a|Six3alpha|Six3b|Six3beta	sine oculis-related homeobox 3	protein-coding
mm_115019.1	chr13	98613235	98613238	+	1	NA	Intergenic	Intergenic	24174	NM_026685	68344	Mm.28766	NM_026685	ENSMUSG00000046082	Tmem174	0610009B10Rik|AA986094	transmembrane protein 174	protein-coding
mm_156482.1	chrX	144318039	144318056	+	1	NA	promoter-TSS (NM_026247)	promoter-TSS (NM_026247)	81	NM_026247	67574	Mm.249084	NM_026247	ENSMUSG00000041718	Alg13	2810046O15Rik|4833435D08Rik|Glt28d1|MDS031|OTTMUSG00000018917	asparagine-linked glycosylation 13	protein-coding
mm_142923.1	chr17	53845935	53846000	-	1	NA	promoter-TSS (NM_026935)	promoter-TSS (NM_026935)	-9	NM_026935	69083	Mm.19320	NM_026935	ENSMUSG00000023122	Sult1c2	1810008N17Rik|ST1C1|ST1C2|Sult1c1	sulfotransferase family, cytosolic, 1C, member 2	protein-coding
mm_94436.1	chr11	6292631	6292650	+	1	NA	promoter-TSS (NM_001252288)	promoter-TSS (NM_001252288)	82	NM_001252288	18293	Mm.276348	NM_010956	ENSMUSG00000020456	Ogdh	2210403E04Rik|2210412K19Rik|AA409584|d1401|mKIAA4192	oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)	protein-coding
mm_144412.1	chr18	20961568	20961589	+	1	NA	intron (NM_026301, intron 1 of 5)	CpG	16953	NM_026301	67664	Mm.45980	NM_026301	ENSMUSG00000033107	Rnf125	4930553F04Rik	ring finger protein 125	protein-coding
mm_160149.1	chr7	41284300	41284300	+	1	NA	promoter-TSS (NM_001033782)	promoter-TSS (NM_001033782)	-27	NM_001033782	434172	Mm.247214	NM_001033782	ENSMUSG00000072259	Gm5592	EG434172	predicted gene 5592	protein-coding
mm_40313.1	chr5	43868533	43868546	+	1	NA	promoter-TSS (NM_007646)	promoter-TSS (NM_007646)	-270	NM_007646	12494	Mm.249873	NM_007646	ENSMUSG00000029084	Cd38	ADPRC 1|Cd38-rs1|I-19	CD38 antigen	protein-coding
mm_59757.1	chr7	28827523	28827524	+	1	NA	intron (NM_016772, intron 3 of 9)	intron (NM_016772, intron 3 of 9)	2185	NM_016772	51798	Mm.291776	NM_016772	ENSMUSG00000053898	Ech1	AA617331	enoyl coenzyme A hydratase 1, peroxisomal	protein-coding
mm_105686.1	chr11	107733667	107733683	-	1	NA	Intergenic	Intergenic	-17199	NM_007582	12299	Mm.57093	NM_007582	ENSMUSG00000020722	Cacng1	-	calcium channel, voltage-dependent, gamma subunit 1	protein-coding
mm_69670.1	chr7	139983880	139983897	-	1	NA	exon (NM_001291066, exon 20 of 24)	exon (NM_001291066, exon 20 of 24)	2986	NR_106029	102465643		NR_106029	ENSMUSG00000099092	Mir7062	Gm27339|mmu-mir-7062	microRNA 7062	ncRNA
mm_100084.1	chr11	115475646	115475727	+	1	NA	promoter-TSS (NM_177778)	promoter-TSS (NM_177778)	9	NM_177778	276905	Mm.38019	NM_177778	ENSMUSG00000057219	Armc7	A630084C13|BC023126	armadillo repeat containing 7	protein-coding
mm_136358.1	chr16	92776113	92776130	-	1	NA	intron (NM_001111022, intron 2 of 6)	intron (NM_001111022, intron 2 of 6)	49953	NM_001111021	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_132516.1	chr16	37580213	37580224	+	1	NA	promoter-TSS (NR_027778)	promoter-TSS (NR_027778)	65	NM_013547	15233	Mm.157442	NM_013547	ENSMUSG00000022821	Hgd	Hgo|aku	homogentisate 1, 2-dioxygenase	protein-coding
mm_91924.1	chr10	60331929	60331935	-	1	NA	intron (NR_045556, intron 40 of 68)	intron (NR_045556, intron 40 of 68)	-14919	NM_001159572	74048	Mm.273584	NM_028732	ENSMUSG00000020101	Vsir	4632428N05Rik|Dies1|PD-1H|VISTA	V-set immunoregulatory receptor	protein-coding
mm_23911.1	chr3	83043320	83043349	+	1	NA	exon (NM_181849, exon 7 of 8)	exon (NM_181849, exon 7 of 8)	6529	NM_181849	110135	Mm.30063	NM_181849	ENSMUSG00000033831	Fgb	2510049G14Rik	fibrinogen beta chain	protein-coding
mm_142560.1	chr17	46640124	46640134	-	1	NA	intron (NM_029091, intron 4 of 15)	intron (NM_029091, intron 4 of 15)	5015	NM_029091	74764	Mm.279599	NM_029091	ENSMUSG00000003546	Klc4	1200014P03Rik|AA408085|AW146303|Knsl8	kinesin light chain 4	protein-coding
mm_18230.1	chr2	51933334	51933340	-	1	NA	intron (NM_030243, intron 1 of 4)	B1_Mur4|SINE|Alu	1307	NM_001141982	71684	Mm.28309	NM_030243	ENSMUSG00000036249	Rbm43	0610033I05Rik	RNA binding motif protein 43	protein-coding
mm_120414.1	chr14	65358088	65358109	+	1	NA	promoter-TSS (NM_199029)	promoter-TSS (NM_199029)	-578	NM_199029	380912	Mm.270087	NM_199029	ENSMUSG00000034522	Zfp395	BC053701|Gm910	zinc finger protein 395	protein-coding
mm_73896.1	chr8	119425904	119425931	+	1	NA	Intergenic	Intergenic	-11245	NM_027950	71839	Mm.272357	NM_027950	ENSMUSG00000074063	Osgin1	1700012B18Rik|Okl38	oxidative stress induced growth inhibitor 1	protein-coding
mm_118365.1	chr13	115101892	115101907	-	1	NA	promoter-TSS (NM_001033228)	promoter-TSS (NM_001033228)	65	NM_001033228	109700	Mm.317280	NM_001033228	ENSMUSG00000042284	Itga1	CD49A|E130012M19Rik|Vla1	integrin alpha 1	protein-coding
mm_116603.1	chr13	48625572	48625594	-	1	NA	promoter-TSS (NM_207232)	promoter-TSS (NM_207232)	89	NM_207232	218232	Mm.315089	NM_207232	ENSMUSG00000038042	Ptpdc1	AI843923|AW456874|Naa-1|Ptpcd1	protein tyrosine phosphatase domain containing 1	protein-coding
mm_38489.1	chr4	140826545	140826590	-	1	NA	exon (NM_011059, exon 10 of 16)	exon (NM_011059, exon 10 of 16)	15574	NR_045944	100049161	Mm.20854	NR_045944	ENSMUSG00000085918	Gm13032	OTTMUSG00000010086	predicted gene 13032	ncRNA
mm_133835.1	chr16	95926852	95926852	+	1	NA	intron (NR_040484, intron 1 of 3)	intron (NR_040484, intron 1 of 3)	2225	NR_040484	69776	Mm.120470	NR_040484	ENSMUSG00000086899	1600002D24Rik	-	RIKEN cDNA 1600002D24 gene	ncRNA
mm_66289.1	chr7	37924341	37924342	-	1	NA	Intergenic	Intergenic	95211	NM_011274	19777	Mm.387220	NM_011274	ENSMUSG00000030421	Uri1	C80913|NNX3|Rmp	URI1, prefoldin-like chaperone	protein-coding
mm_65197.1	chr7	19696852	19696854	-	1	NA	exon (NM_009696, exon 4 of 4)	exon (NM_009696, exon 4 of 4)	1545	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_161130.1	chr12	112929741	112929741	-	1	NA	promoter-TSS (NM_010588)	promoter-TSS (NM_010588)	-246	NM_010588	16450	Mm.186146	NM_010588	ENSMUSG00000002799	Jag2	D12Ggc2e|Serh|mJagged2-1|sm	jagged 2	protein-coding
mm_103721.1	chr11	79530442	79530468	-	1	NA	5' UTR (NM_010161, exon 1 of 2)	5' UTR (NM_010161, exon 1 of 2)	154	NM_146023	101488212	Mm.439665	NM_146023	ENSMUSG00000070354	Gm21975	Evi2a-evi2b	predicted gene 21975	protein-coding
mm_83353.1	chr9	44361626	44361670	-	1	NA	promoter-TSS (NM_027889)	promoter-TSS (NM_027889)	22	NM_027889	71732	Mm.295013	NM_027889	ENSMUSG00000032127	Vps11	1200011A11Rik	VPS11, CORVET/HOPS core subunit	protein-coding
mm_151877.1	chr19	5798410	5798420	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	-2434	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_14821.1	chr2	146908364	146908367	+	1	NA	intron (NM_001033298, intron 6 of 13)	intron (NM_001033298, intron 6 of 13)	52476	NM_001033298	228730	Mm.292352	NM_001033298	ENSMUSG00000074749	Kiz	Gm114|Ncrna00153|Plk1s1	kizuna centrosomal protein	protein-coding
mm_56361.1	chr6	93893332	93893341	-	1	NA	intron (NM_001029850, intron 2 of 23)	(A)n|Simple_repeat|Simple_repeat	19627	NR_104594	14924	Mm.217216	NM_010367	ENSMUSG00000045095	Magi1	AIP3|BAP1|Baiap1|Gukmi1|MAGI1c|Magi-1|TNRC19|WWP3|mKIAA4129	membrane associated guanylate kinase, WW and PDZ domain containing 1	protein-coding
mm_78807.1	chr9	44067042	44067059	+	1	NA	promoter-TSS (NM_198092)	promoter-TSS (NM_198092)	29	NM_198092	53376	Mm.272770	NM_016808	ENSMUSG00000032010	Usp2	B930035K21Rik|Ubp41	ubiquitin specific peptidase 2	protein-coding
mm_136803.1	chr17	12378604	12378621	+	1	NA	promoter-TSS (NM_008877)	promoter-TSS (NM_008877)	3	NM_008877	18815	Mm.971	NM_008877	ENSMUSG00000059481	Plg	AI649309|Pg	plasminogen	protein-coding
mm_45097.1	chr5	44406345	44406352	-	1	NA	Intergenic	Intergenic	-179742	NM_173764	231225	Mm.30688	NM_173764	ENSMUSG00000046985	Tapt1	4932414K18Rik	transmembrane anterior posterior transformation 1	protein-coding
mm_157789.1	chrX	73824994	73825006	-	1	NA	promoter-TSS (NM_001290540)	promoter-TSS (NM_001290540)	-31	NM_001290540	245469	Mm.103782	NM_001029868	ENSMUSG00000002006	Pdzd4	B230341P03|D130075J17Rik|Kiaa1444-hp|LU1|PDZRN4L|Pdzk4|Pdzrnk4l|Xlu	PDZ domain containing 4	protein-coding
mm_123318.1	chr14	62531035	62531072	-	1	NA	Intergenic	Intergenic	-24684	NM_001243857	629059	Mm.291864	NM_001243857	ENSMUSG00000035184	Fam124a	EG629059	family with sequence similarity 124, member A	protein-coding
mm_105615.1	chr11	106788487	106788500	-	1	NA	promoter-TSS (NM_177088)	promoter-TSS (NM_177088)	1	NM_007840	13207	Mm.491096	NM_007840	ENSMUSG00000020719	Ddx5	2600009A06Rik|G17P1|HUMP68|Hlr1|p68	DEAD (Asp-Glu-Ala-Asp) box polypeptide 5	protein-coding
mm_124623.1	chr15	3290759	3290771	+	1	NA	intron (NM_001166063, intron 5 of 8)	ORR1E|LTR|ERVL-MaLR	12761	NM_001166063	100039139	Mm.455610	NM_001166063	ENSMUSG00000091119	Ccdc152	ENSMUSG00000071814	coiled-coil domain containing 152	protein-coding
mm_9955.1	chr1	191026014	191026036	-	1	NA	exon (NM_001081259, exon 1 of 10)	exon (NM_001081259, exon 1 of 10)	165	NM_001081259	226844	Mm.134053	NM_198025	ENSMUSG00000066595	Mfsd7b	9630055N22Rik|FLVCR|Flvcr1	major facilitator superfamily domain containing 7B	protein-coding
mm_66796.1	chr7	47132622	47132637	-	1	NA	promoter-TSS (NM_001163565)	promoter-TSS (NM_001163565)	-31	NM_001163565	19259	Mm.4654	NM_013643	ENSMUSG00000030854	Ptpn5	Step	protein tyrosine phosphatase, non-receptor type 5	protein-coding
mm_112022.1	chr12	111445189	111445206	-	1	NA	exon (NM_009396, exon 2 of 12)	exon (NM_009396, exon 2 of 12)	2536	NM_009396	21928	Mm.255332	NM_009396	ENSMUSG00000021281	Tnfaip2	B94|Exoc3l3|M-sec|Tnfip2|tnfb94	tumor necrosis factor, alpha-induced protein 2	protein-coding
mm_154509.1	chrM	12151	12168	-	1	NA	NA	Intergenic	NA	NA								
mm_94416.1	chr11	5863030	5863048	+	1	NA	intron (NM_001291857, intron 1 of 20)	intron (NM_001291857, intron 1 of 20)	1173	NM_001291857	11568	Mm.3317	NM_009636	ENSMUSG00000020473	Aebp1	ACLP	AE binding protein 1	protein-coding
mm_47028.1	chr5	115652827	115652829	-	1	NA	intron (NM_001080808, intron 7 of 8)	intron (NM_001080808, intron 7 of 8)	7255	NR_105997	102465623		NR_105997	ENSMUSG00000099254	Mir7030	Gm27267|mmu-mir-7030	microRNA 7030	ncRNA
mm_42856.1	chr5	122210329	122210353	+	1	NA	promoter-TSS (NM_028752)	promoter-TSS (NM_028752)	54	NM_028752	74096	Mm.28804	NM_028752	ENSMUSG00000064267	Hvcn1	0610039P13Rik|AI450555|BTS|HV1|Vsop.|mVSOP	hydrogen voltage-gated channel 1	protein-coding
mm_107532.1	chr12	40538839	40538843	+	1	NA	intron (NM_172803, intron 1 of 52)	intron (NM_172803, intron 1 of 52)	92788	NM_172803	238130	Mm.341423	NM_172803	ENSMUSG00000035954	Dock4	5330406C03|6330411N01Rik|AF263288|C030023J22|mKIAA0716	dedicator of cytokinesis 4	protein-coding
mm_96959.1	chr11	70640220	70640246	+	1	NA	exon (NM_010326, exon 2 of 2)	exon (NM_010326, exon 2 of 2)	1111	NM_010326	14723	Mm.377085	NM_010326	ENSMUSG00000050675	Gp1ba	GPIba|GPIbalpha	glycoprotein 1b, alpha polypeptide	protein-coding
mm_15445.1	chr2	157367587	157367599	+	1	NA	promoter-TSS (NM_026968)	promoter-TSS (NM_026968)	-1	NM_026968	69161	Mm.228619	NM_026968	ENSMUSG00000063019	Manbal	1810024K12Rik|AI836500	mannosidase, beta A, lysosomal-like	protein-coding
mm_10653.1	chr2	20669838	20669846	+	1	NA	intron (NM_029895, intron 4 of 18)	intron (NM_029895, intron 4 of 18)	150329	NM_001177631	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding
mm_19348.1	chr2	90917736	90917746	-	1	NA	exon (NM_025576, exon 1 of 5)	exon (NM_025576, exon 1 of 5)	309	NM_025576	66461	Mm.23926	NM_025576		Ptpmt1	1110001D10Rik|2810004N20Rik|PLIP	protein tyrosine phosphatase, mitochondrial 1	protein-coding
mm_115930.1	chr13	23571201	23571208	-	1	NA	promoter-TSS (NM_178196)	promoter-TSS (NM_178196)	16	NM_178187	319166	Mm.261665	NM_178187	ENSMUSG00000069272	Hist1h2ae	1190022L06	histone cluster 1, H2ae	protein-coding
mm_96738.1	chr11	69776083	69776110	+	1	NA	exon (NM_029348, exon 3 of 4)	exon (NM_029348, exon 3 of 4)	10184	NM_029348	75580	Mm.426361	NM_029348	ENSMUSG00000018750	Zbtb4	2310026P19Rik|9230111I22Rik|mKIAA1538	zinc finger and BTB domain containing 4	protein-coding
mm_84702.1	chr9	72663287	72663297	-	1	NA	intron (NM_010890, intron 1 of 28)	intron (NM_010890, intron 1 of 28)	945	NM_010890	17999	Mm.279923	NM_010890	ENSMUSG00000032216	Nedd4	AA959633|AL023035|AU019897|E430025J12Rik|Nedd4-1|Nedd4a|mKIAA0093	neural precursor cell expressed, developmentally down-regulated 4	protein-coding
mm_44875.1	chr5	34634886	34634933	-	1	NA	exon (NM_026660, exon 8 of 13)	exon (NM_026660, exon 8 of 13)	2205	NM_026660	68294	Mm.34564	NM_026660	ENSMUSG00000001082	Mfsd10	0610009O03Rik|Tetran	major facilitator superfamily domain containing 10	protein-coding
mm_139226.1	chr17	47730663	47730671	+	1	NA	exon (NM_025973, exon 5 of 9)	exon (NM_025973, exon 5 of 9)	3825	NM_025973	109820	Mm.22957	NM_025973	ENSMUSG00000023987	Pgc	2210410L06Rik|Upg-1|Upg1	progastricsin (pepsinogen C)	protein-coding
mm_26822.1	chr3	10335677	10335687	-	1	NA	promoter-TSS (NM_001010834)	promoter-TSS (NM_001010834)	-26	NM_001010834	241877	Mm.442146	NM_001010834	ENSMUSG00000058921	Slc10a5	Gm405|mP5	solute carrier family 10 (sodium/bile acid cotransporter family), member 5	protein-coding
mm_139673.1	chr17	57412348	57412373	+	1	NA	intron (NM_010130, intron 9 of 21)	intron (NM_010130, intron 9 of 21)	53674	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_146510.1	chr18	3337468	3337500	-	1	NA	5' UTR (NM_001110852, exon 1 of 4)	5' UTR (NM_001110852, exon 1 of 4)	105	NM_001110851	12916	Mm.5244	NM_013498	ENSMUSG00000063889	Crem	ICER|ICERI	cAMP responsive element modulator	protein-coding
mm_62127.1	chr7	96951535	96951548	+	1	NA	promoter-TSS (NM_153591)	promoter-TSS (NM_153591)	14	NM_153591	244141	Mm.274864	NM_153591	ENSMUSG00000018995	Nars2	AI875199	asparaginyl-tRNA synthetase 2 (mitochondrial)(putative)	protein-coding
mm_17831.1	chr2	34255471	34255473	-	1	NA	intron (NM_016768, intron 2 of 8)	PB1D9|SINE|Alu	116573	NM_001290576	18516	Mm.239941	NM_016768	ENSMUSG00000038718	Pbx3	-	pre B cell leukemia homeobox 3	protein-coding
mm_23634.1	chr3	66981353	66981407	+	1	NA	promoter-TSS (NM_001302359)	promoter-TSS (NM_001302359)	-239	NM_001302359	20429	Mm.39093	NM_013665	ENSMUSG00000027833	Shox2	6330543G17Rik|OG12|Og12x|Prx3|SHOT	short stature homeobox 2	protein-coding
mm_159810.1	chr5	118724005	118724005	+	1	NA	exon (NM_172424, exon 8 of 31)	exon (NM_172424, exon 8 of 31)	163286	NM_172424	76199	Mm.206238	NM_172424	ENSMUSG00000018076	Med13l	2210413I17Rik|6330591G05Rik|9030618F05Rik|Thrap2|Trap240L|mKIAA1025	mediator complex subunit 13-like	protein-coding
mm_172900.1	chr9	57477317	57477328	-	1	NA	Intergenic	RLTR1B|LTR|ERV1	-9262	NM_001301635	56807	Mm.102278	NM_020270	ENSMUSG00000040722	Scamp5	Sc5	secretory carrier membrane protein 5	protein-coding
mm_57955.1	chr6	135168132	135168161	-	1	NA	promoter-TSS (NM_013546)	promoter-TSS (NM_013546)	69	NM_013546	15199	Mm.378937	NM_013546	ENSMUSG00000042770	Hebp1	Hebp|p22HBP	heme binding protein 1	protein-coding
mm_118661.1	chr14	21831532	21831574	+	1	NA	promoter-TSS (NM_011695)	promoter-TSS (NM_011695)	-8	NM_011695	22334	Mm.262327	NM_011695	ENSMUSG00000021771	Vdac2	Vdac6|mVDAC2|mVDAC6	voltage-dependent anion channel 2	protein-coding
mm_8413.1	chr1	152090146	152090167	-	1	NA	5' UTR (NM_197990, exon 1 of 6)	5' UTR (NM_197990, exon 1 of 6)	164	NM_197990	69399	Mm.278031	NM_197990	ENSMUSG00000032666	1700025G04Rik	2610510E02Rik|2900042O04Rik|ENSMUSG00000073540	RIKEN cDNA 1700025G04 gene	protein-coding
mm_97923.1	chr11	83582074	83582090	+	1	NA	promoter-TSS (NR_036453)	promoter-TSS (NR_036453)	21	NR_036452	100504464	Mm.341706	NR_036452	ENSMUSG00000051832	E230016K23Rik	-	RIKEN cDNA E230016K23 gene	ncRNA
mm_112702.1	chr13	17944260	17944299	+	1	NA	promoter-TSS (NM_019491)	promoter-TSS (NM_019491)	-62	NM_019491	56044	Mm.27348	NM_019491	ENSMUSG00000008859	Rala	3010001O15Rik|AW322615|Ral|Rasl1	v-ral simian leukemia viral oncogene A (ras related)	protein-coding
mm_17462.1	chr2	28557968	28557992	-	1	NA	exon (NM_009885, exon 8 of 11)	exon (NM_009885, exon 8 of 11)	5423	NM_009885	12613	Mm.236017	NM_009885	ENSMUSG00000026818	Cel	1810036E18Rik|BAL	carboxyl ester lipase	protein-coding
mm_126323.1	chr15	79739575	79739594	+	1	NA	intron (NM_001205346, intron 2 of 17)	intron (NM_001205346, intron 2 of 17)	2952	NM_194342	223697	Mm.202715	NM_194342	ENSMUSG00000042524	Sun2	B230369L08Rik|C030011B15|Unc84b	Sad1 and UNC84 domain containing 2	protein-coding
mm_109590.1	chr12	112620093	112620095	+	1	NA	promoter-TSS (NM_007421)	promoter-TSS (NM_007421)	47	NM_007421	11565	Mm.3440	NM_007421	ENSMUSG00000011148	Adssl1	AI528595|Adss|Adss1	adenylosuccinate synthetase like 1	protein-coding
mm_108097.1	chr12	74804138	74804179	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	373174	NM_172805	238271	Mm.44465	NM_172805	ENSMUSG00000034402	Kcnh5	Eag2	potassium voltage-gated channel, subfamily H (eag-related), member 5	protein-coding
mm_47619.1	chr5	125245780	125245794	-	1	NA	Intergenic	CpG	-66573	NM_001253904	20602	Mm.278646	NM_011424	ENSMUSG00000029478	Ncor2	N-CoR|SMRT|SMRTe	nuclear receptor co-repressor 2	protein-coding
mm_113093.1	chr13	24105567	24105579	+	1	NA	intron (NM_026825, intron 17 of 37)	intron (NM_026825, intron 17 of 37)	-114359	NM_145399	214189	Mm.255667	NM_145399	ENSMUSG00000021337	Scgn	-	secretagogin, EF-hand calcium binding protein	protein-coding
mm_113401.1	chr13	33921312	33921323	+	1	NA	intron (NM_001243192, intron 6 of 7)	RLTR17|LTR|ERVK	-14715	NR_040707	68808	Mm.443347	NR_040707	ENSMUSG00000085457	1110046J04Rik	-	RIKEN cDNA 1110046J04 gene	ncRNA
mm_61448.1	chr7	75586180	75586188	+	1	NA	exon (NM_029332, exon 5 of 37)	exon (NM_029332, exon 5 of 37)	130650	NM_029332	75547	Mm.216107	NM_029332	ENSMUSG00000066406	Akap13	1700026G02Rik|5730522G15Rik|5830460E08Rik|AKAP-13|AKAP-Lbc|BRX|Ht31|LBC|PROTO-LB|PROTO-LBC	A kinase (PRKA) anchor protein 13	protein-coding
mm_35120.1	chr4	11007542	11007634	-	1	NA	promoter-TSS (NM_175175)	promoter-TSS (NM_175175)	31	NM_175175	71801	Mm.34351	NM_175175	ENSMUSG00000049969	Plekhf2	1110070J07Rik|AA673237|ZFYVE18	pleckstrin homology domain containing, family F (with FYVE domain) member 2	protein-coding
mm_133083.1	chr16	59639194	59639211	+	1	NA	5' UTR (NM_019665, exon 1 of 8)	5' UTR (NM_019665, exon 1 of 8)	137	NM_019665	56297	Mm.392505	NM_019665	ENSMUSG00000022722	Arl6	1110018H24Rik|2210411E14Rik|BBS3	ADP-ribosylation factor-like 6	protein-coding
mm_96652.1	chr11	69368317	69368326	+	1	NA	intron (NM_146019, intron 1 of 39)	intron (NM_146019, intron 1 of 39)	1105	NM_146019	216848	Mm.178246	NM_146019	ENSMUSG00000018474	Chd3	2600010P09Rik|AF020312|Chd7|Prp7|Prp9-1	chromodomain helicase DNA binding protein 3	protein-coding
mm_141227.1	chr17	27364471	27364487	-	1	NA	Intergenic	Intergenic	6382	NR_106077	102466228		NR_106077	ENSMUSG00000106215	Mir7218	mmu-mir-7218	microRNA 7218	ncRNA
mm_49667.1	chr6	31221801	31221846	+	1	NA	intron (NR_040260, intron 1 of 5)	intron (NR_040260, intron 1 of 5)	1472	NR_040261	73652	Mm.441297	NR_040257	ENSMUSG00000087380	2210408F21Rik	-	RIKEN cDNA 2210408F21 gene	ncRNA
mm_6046.1	chr1	59764830	59764838	-	1	NA	intron (NM_007561, intron 1 of 12)	intron (NM_007561, intron 1 of 12)	555	NM_007561	12168	Mm.7106	NM_007561	ENSMUSG00000067336	Bmpr2	2610024H22Rik|AL117858|AW546137|BB189135|BMP-2|BMPR-2|BMPR-II|BMPRII|BRK-3|Gm20272	bone morphogenetic protein receptor, type II (serine/threonine kinase)	protein-coding
mm_159132.1	chr2	75659267	75659267	+	1	NA	promoter-TSS (NM_198090)	promoter-TSS (NM_198090)	8	NM_053263	229279	Mm.316306	NM_053263	ENSMUSG00000059005	Hnrnpa3	2410013L13Rik|2610209F03Rik|2610510D13Rik|Hnrpa3	heterogeneous nuclear ribonucleoprotein A3	protein-coding
mm_111913.1	chr12	108835810	108835832	-	1	NA	promoter-TSS (NM_181328)	promoter-TSS (NM_181328)	55	NM_181328	214663	Mm.266264	NM_181328	ENSMUSG00000021265	Slc25a29	C030003J19Rik|CACL|mCACL	solute carrier family 25 (mitochondrial carrier, palmitoylcarnitine transporter), member 29	protein-coding
mm_64032.1	chr7	140769637	140769651	+	1	NA	exon (NM_021282, exon 4 of 9)	exon (NM_021282, exon 4 of 9)	5812	NM_021282	13106	Mm.21758	NM_021282	ENSMUSG00000025479	Cyp2e1	Cyp2e	cytochrome P450, family 2, subfamily e, polypeptide 1	protein-coding
mm_168604.1	chr11	75066848	75066849	-	1	NA	promoter-TSS (NR_030454)	promoter-TSS (NR_030454)	-857	NR_030454	735274		NR_030454	ENSMUSG00000106252	Mir684-1	Mirn684-1	microRNA 684-1	ncRNA
mm_173294.1	chrY	40026890	40026890	-	1	NA	Intergenic	RLTR6_Mm|LTR|ERV1	2069070	NM_207162	382133	Mm.463885	NM_207162	ENSMUSG00000094575	Gm20738	-	predicted gene, 20738	protein-coding
mm_60742.1	chr7	45447897	45447907	+	1	NA	exon (NM_030678, exon 11 of 16)	exon (NM_030678, exon 11 of 16)	11984	NM_010240	14325	Mm.30357	NM_010240	ENSMUSG00000050708	Ftl1	Ftl|Ftl-1|L-ferritin	ferritin light polypeptide 1	protein-coding
mm_92810.1	chr10	81394800	81394820	-	1	NA	exon (NM_001099917, exon 4 of 4)	exon (NM_001099917, exon 4 of 4)	1746	NM_001099917	72273	Mm.253147	NM_001099917	ENSMUSG00000078439	Smim24	2210404O07Rik	small integral membrane protein 24	protein-coding
mm_130369.1	chr15	97812252	97812268	-	1	NA	intron (NM_001204275, intron 1 of 24)	intron (NM_001204275, intron 1 of 24)	2603	NM_001204281	56233	Mm.384027	NM_019572	ENSMUSG00000022475	Hdac7	5830434K02Rik|HD7|HD7a|Hdac7a|mFLJ00062	histone deacetylase 7	protein-coding
mm_148665.1	chr19	5609841	5609860	+	1	NA	promoter-TSS (NR_037603)	promoter-TSS (NR_037603)	-143	NR_037603	81601	Mm.228930	NM_178637	ENSMUSG00000024926	Kat5	AI839539|CPLA2|Htatip|Htatip1|PLIP|Tip55|Tip60	K(lysine) acetyltransferase 5	protein-coding
mm_129585.1	chr15	79742519	79742562	-	1	NA	promoter-TSS (NM_194342)	promoter-TSS (NM_194342)	-4	NM_001205345	223697	Mm.202715	NM_194342	ENSMUSG00000042524	Sun2	B230369L08Rik|C030011B15|Unc84b	Sad1 and UNC84 domain containing 2	protein-coding
mm_158141.1	chrX	103311819	103311837	-	1	NA	Intergenic	Intergenic	-9570	NM_007674	12592	Mm.4353	NM_007674	ENSMUSG00000031326	Cdx4	Cdx-3|Cdx-4|Cdx3	caudal type homeobox 4	protein-coding
mm_63919.1	chr7	139254928	139254969	+	1	NA	exon (NM_001098636, exon 2 of 3)	exon (NM_001098636, exon 2 of 3)	6466	NM_001098636	101631	Mm.334300	NM_001033206	ENSMUSG00000060260	Pwwp2b	AI594893|D7Ertd517e|D930023J19Rik|Pwwp2	PWWP domain containing 2B	protein-coding
mm_124446.1	chr14	118876894	118876896	-	1	NA	non-coding (NR_130725, exon 21 of 21)	non-coding (NR_130725, exon 21 of 21)	21945	NM_001160099	58187	Mm.390755	NM_021386	ENSMUSG00000022132	Cldn10	6720456I16Rik|Cldn10a|Cldn10b|D14Ertd728e	claudin 10	protein-coding
mm_98764.1	chr11	96603777	96603778	+	1	NA	intron (NM_001033186, intron 4 of 12)	intron (NM_001033186, intron 4 of 12)	139186	NM_001177898	78473	Mm.395840	NM_001033186	ENSMUSG00000057058	Skap1	1700091G21Rik|Scap1|Skap-55	src family associated phosphoprotein 1	protein-coding
mm_169641.1	chr1	55084558	55084560	-	1	NA	exon (NM_010477, exon 3 of 12)	exon (NM_010477, exon 3 of 12)	3373	NM_010477	15510	Mm.1777	NM_010477	ENSMUSG00000025980	Hspd1	60kDa|Hsp60	heat shock protein 1 (chaperonin)	protein-coding
mm_18108.1	chr2	44989061	44989072	-	1	NA	exon (NM_015753, exon 10 of 10)	exon (NM_015753, exon 10 of 10)	34111	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_2305.1	chr1	91540055	91540057	+	1	NA	promoter-TSS (NM_001039126)	promoter-TSS (NM_001039126)	-509	NM_001039126	65247	Mm.234152	NM_023046	ENSMUSG00000026311	Asb1	1700029O08Rik|1700054C17Rik|AI426616|AI851378|mKIAA1146	ankyrin repeat and SOCS box-containing 1	protein-coding
mm_140079.1	chr17	75178798	75178824	+	1	NA	promoter-TSS (NM_001331237)	promoter-TSS (NM_001331237)	30	NM_001331235	268977	Mm.269747	NM_019919	ENSMUSG00000001870	Ltbp1	9430031G15Rik|9830146M04|Ltbp-1|Ltbp1L|TGF-beta1-BP-1|Tgfb|b2b1000Clo	latent transforming growth factor beta binding protein 1	protein-coding
mm_128427.1	chr15	49942848	49942852	-	1	NA	Intergenic	RLTR8|LTR|ERVK	946199	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_110941.1	chr12	76609412	76609417	-	1	NA	intron (NM_013675, intron 19 of 35)	intron (NM_013675, intron 19 of 35)	-61489	NR_046044	100504549	Mm.440349	NR_046044		AI463170	-	expressed sequence AI463170	ncRNA
mm_170579.1	chr1	95498659	95498660	+	1	NA	Intergenic	Intergenic	168935	NM_009183	20452	Mm.306228	NM_009183	ENSMUSG00000040710	St8sia4	PST|PST-1|SIAT8-D|ST8SiaIV|Siat8d	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4	protein-coding
mm_4639.1	chr1	179959973	179959981	+	1	NA	promoter-TSS (NM_001346804)	promoter-TSS (NM_001346804)	-783	NM_001346804	226751	Mm.259655	NM_001033285	ENSMUSG00000026490	Cdc42bpa	A930014J19Rik|DMPK-like	CDC42 binding protein kinase alpha	protein-coding
mm_13344.1	chr2	102899418	102899435	+	1	NA	intron (NM_001039150, intron 1 of 13)	intron (NM_001039150, intron 1 of 13)	2239	NM_001177785	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_124707.1	chr15	6552168	6552172	+	1	NA	Intergenic	Intergenic	-27677	NM_001278269	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_15413.1	chr2	156781145	156781237	+	1	NA	3' UTR (NM_172118, exon 4 of 4)	3' UTR (NM_172118, exon 4 of 4)	5727	NM_172118	98932	Mm.271770	NM_172118	ENSMUSG00000067818	Myl9	AI327049|MLC20|Mylc2c|RLC-C	myosin, light polypeptide 9, regulatory	protein-coding
mm_171726.1	chr4	88599867	88599876	-	1	NA	Intergenic	Intergenic	3505	NM_177361	242519	Mm.246618	NM_177361	ENSMUSG00000073811	Ifna12	-	interferon alpha 12	protein-coding
mm_69184.1	chr7	127260607	127260609	-	1	NA	promoter-TSS (NM_023203)	promoter-TSS (NM_023203)	59	NM_023203	66422	Mm.29898	NM_023203	ENSMUSG00000042462	Dctpp1	2410015N17Rik|AI854235|RS21-C6	dCTP pyrophosphatase 1	protein-coding
mm_156115.1	chrX	114474635	114474655	+	1	NA	exon (NM_001290478, exon 1 of 11)	exon (NM_001290478, exon 1 of 11)	312	NM_001290477	237010	Mm.132583	NM_172781	ENSMUSG00000025597	Klhl4	B130014A11|C130018J01Rik	kelch-like 4	protein-coding
mm_59589.1	chr7	28131656	28131662	+	1	NA	exon (NM_001164655, exon 3 of 20)	exon (NM_001164655, exon 3 of 20)	2193	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_75879.1	chr8	70776635	70776640	-	1	NA	promoter-TSS (NR_029440)	promoter-TSS (NR_029440)	75	NM_008841	18709	Mm.12945	NM_008841	ENSMUSG00000031834	Pik3r2	p85beta	phosphatidylinositol 3-kinase, regulatory subunit, polypeptide 2 (p85 beta)	protein-coding
mm_138897.1	chr17	43568503	43568541	+	1	NA	promoter-TSS (NM_013737)	promoter-TSS (NM_013737)	71	NM_013737	27226	Mm.9277	NM_013737	ENSMUSG00000023913	Pla2g7	PAF-AH|R75400	phospholipase A2, group VII (platelet-activating factor acetylhydrolase, plasma)	protein-coding
mm_62309.1	chr7	100227625	100227635	+	1	NA	promoter-TSS (NM_027629)	promoter-TSS (NM_027629)	23	NM_027629	70974	Mm.440524	NM_027629	ENSMUSG00000030729	Pgm2l1	4931406N15Rik|AI553438|BM32A	phosphoglucomutase 2-like 1	protein-coding
mm_11610.1	chr2	34406950	34406960	+	1	NA	5' UTR (NM_177345, exon 1 of 12)	5' UTR (NM_177345, exon 1 of 12)	104	NM_001290626	227743	Mm.270866	NM_177345	ENSMUSG00000038696	Mapkap1	AI591529|D230039K05Rik|Sin1	mitogen-activated protein kinase associated protein 1	protein-coding
mm_69811.1	chr7	141263684	141263764	-	1	NA	TTS (NM_001081118)	TTS (NM_001081118)	2700	NM_001252601	54123	Mm.3233	NM_016850	ENSMUSG00000025498	Irf7	-	interferon regulatory factor 7	protein-coding
mm_132164.1	chr16	32271531	32271544	+	1	NA	promoter-TSS (NM_183283)	promoter-TSS (NM_183283)	-72	NM_183283	69576	Mm.432545	NM_183283	ENSMUSG00000046345	Smco1	2310010M20Rik	single-pass membrane protein with coiled-coil domains 1	protein-coding
mm_71135.1	chr8	39005881	39005952	+	1	NA	promoter-TSS (NM_030254)	promoter-TSS (NM_030254)	49	NM_030254	80286	Mm.272722	NM_030254	ENSMUSG00000039530	Tusc3	AU022242|BC003311|N33	tumor suppressor candidate 3	protein-coding
mm_35988.1	chr4	55528575	55528578	-	1	NA	intron (NM_010637, intron 4 of 4)	intron (NM_010637, intron 4 of 4)	3899	NM_010637	16600	Mm.4325	NM_010637	ENSMUSG00000003032	Klf4	EZF|Gklf|Zie	Kruppel-like factor 4 (gut)	protein-coding
mm_7918.1	chr1	133753839	133753857	-	1	NA	promoter-TSS (NM_001167949)	promoter-TSS (NM_001167949)	-101	NM_213616	381290	Mm.188617	NM_213616	ENSMUSG00000026463	Atp2b4	Pmca4	ATPase, Ca++ transporting, plasma membrane 4	protein-coding
mm_75488.1	chr8	48843805	48843827	-	1	NA	Intergenic	Intergenic	-169126	NM_011857	23965	Mm.42191	NM_011857	ENSMUSG00000031561	Tenm3	2610100B16Rik|Odz1|Odz3|Ten-m3|mKIAA1455	teneurin transmembrane protein 3	protein-coding
mm_133075.1	chr16	58726340	58726349	+	1	NA	Intergenic	Intergenic	-1566	NR_045518	224250	Mm.29482	NM_171826	ENSMUSG00000022744	Cldnd1	1110019C08Rik|AA407103|AI849195|AW489850|Cldn25	claudin domain containing 1	protein-coding
mm_119638.1	chr14	51902977	51902978	+	1	NA	Intergenic	Intergenic	9367	NM_001039676	214922	Mm.281343	NM_001039676	ENSMUSG00000072572	Slc39a2	F730005G13Rik|Gm1789|Gm289|Zip2	solute carrier family 39 (zinc transporter), member 2	protein-coding
mm_172331.1	chr7	10846064	10846066	-	1	NA	Intergenic	Intergenic	-47000	NR_033707	434555	Mm.379679	NR_033707	ENSMUSG00000110097	Zscan4a	BQ559217	zinc finger and SCAN domain containing 4A	pseudo
mm_98687.1	chr11	96298785	96298798	+	1	NA	promoter-TSS (NM_008269)	promoter-TSS (NM_008269)	-380	NM_008269	15414	Mm.215	NM_008269	ENSMUSG00000000690	Hoxb6	Hox-2.2	homeobox B6	protein-coding
mm_84921.1	chr9	80265422	80265433	-	1	NA	intron (NM_001039546, intron 15 of 32)	intron (NM_001039546, intron 15 of 32)	100393	NM_001039546	17920	Mm.4040	NM_008662	ENSMUSG00000033577	Myo6	BC029719|Tlc|sv	myosin VI	protein-coding
mm_170650.1	chr2	10068647	10068659	-	1	NA	exon (NM_001112738, exon 3 of 10)	exon (NM_001112738, exon 3 of 10)	11857	NM_020615	11949	Mm.12677	NM_020615	ENSMUSG00000025781	Atp5c1	1700094F02Rik	ATP synthase, H+ transporting, mitochondrial F1 complex, gamma polypeptide 1	protein-coding
mm_14603.1	chr2	136501967	136501977	+	1	NA	Intergenic	Intergenic	-30349	NM_175667	319196	Mm.477841	NM_175667	ENSMUSG00000074771	Ankef1	AV276460|Ankrd5	ankyrin repeat and EF-hand domain containing 1	protein-coding
mm_135015.1	chr16	32487196	32487219	-	1	NA	intron (NM_145932, intron 1 of 8)	intron (NM_145932, intron 1 of 8)	672	NM_145932	106407	Mm.476915	NM_145932	ENSMUSG00000035699	Slc51a	AV001382|AW261577|D630035O19Rik|OSTalpha|Osta	solute carrier family 51, alpha subunit	protein-coding
mm_23517.1	chr3	60595589	60595604	+	1	NA	exon (NM_001253708, exon 3 of 9)	exon (NM_001253708, exon 3 of 9)	94417	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_53122.1	chr6	125113896	125113912	+	1	NA	exon (NM_145979, exon 24 of 39)	exon (NM_145979, exon 24 of 39)	16880	NR_106012	102466272		NR_106012	ENSMUSG00000098762	Mir7045	Gm27758|mmu-mir-7045	microRNA 7045	ncRNA
mm_32895.1	chr4	118968093	118968100	+	1	NA	exon (NM_133892, exon 7 of 7)	exon (NM_133892, exon 7 of 7)	6129	NM_133892	100470	Mm.26698	NM_133892	ENSMUSG00000024903	Lao1	AW990848	L-amino acid oxidase 1	protein-coding
mm_155951.1	chrX	105080209	105080231	+	1	NA	intron (NM_026312, intron 2 of 5)	MER5B|DNA|hAT-Charlie	464	NM_026312	67683	Mm.273405	NM_026312	ENSMUSG00000031226	Pbdc1	2610029G23Rik	polysaccharide biosynthesis domain containing 1	protein-coding
mm_172939.1	chr9	78821682	78821700	-	1	NA	Intergenic	CpG	206145	NM_153098	235505	Mm.32955	NM_153098	ENSMUSG00000046186	Cd109	9930012E15Rik|AI480638|GARP	CD109 antigen	protein-coding
mm_151253.1	chr19	53929281	53929291	+	1	NA	TTS (NM_001195338)	TTS (NM_001195338)	-15020	NM_001168505	56392	Mm.228669	NM_019658	ENSMUSG00000024976	Shoc2	AU017287|Sur8|mKIAA0862	soc-2 (suppressor of clear) homolog (C. elegans)	protein-coding
mm_103538.1	chr11	77490011	77490055	-	1	NA	promoter-TSS (NM_172945)	promoter-TSS (NM_172945)	-355	NM_172945	268445	Mm.39296	NM_172945	ENSMUSG00000037907	Ankrd13b	AW124583|B930093C12Rik	ankyrin repeat domain 13b	protein-coding
mm_24685.1	chr3	94974694	94974719	+	1	NA	promoter-TSS (NM_001293716)	promoter-TSS (NM_001293716)	-25	NM_001293715	107650	Mm.217222	NM_175356	ENSMUSG00000038861	Pi4kb	ESTM41|PI4K-beta|PI4Kbeta|Pik4cb	phosphatidylinositol 4-kinase, catalytic, beta polypeptide	protein-coding
mm_140889.1	chr17	23975184	23975235	-	1	NA	promoter-TSS (NM_013921)	promoter-TSS (NM_013921)	21	NM_013921	30943	Mm.142568	NM_013921	ENSMUSG00000024124	Prss30	2010015P21Rik|Disp|Disp1|Tmprss8	protease, serine 30	protein-coding
mm_14045.1	chr2	122264855	122264874	+	1	NA	3' UTR (NM_146126, exon 9 of 9)	3' UTR (NM_146126, exon 9 of 9)	30025	NM_146126	20322	Mm.371580	NM_146126	ENSMUSG00000027227	Sord	Sdh-1|Sdh1|Sodh-1	sorbitol dehydrogenase	protein-coding
mm_25578.1	chr3	116861642	116861695	+	1	NA	promoter-TSS (NM_009146)	promoter-TSS (NM_009146)	-12	NM_009146	20321	Mm.66293	NM_009146	ENSMUSG00000033386	Frrs1	AI131732|Sdfr2	ferric-chelate reductase 1	protein-coding
mm_8571.1	chr1	155527157	155527165	-	1	NA	promoter-TSS (NR_132128)	promoter-TSS (NR_132128)	-50	NR_132128	433367	Mm.359304	NR_132128	ENSMUSG00000073535	Gm5532	EG433367	predicted gene 5532	ncRNA
mm_172793.1	chr9	110940337	110940350	-	1	NA	3' UTR (NM_011562, exon 6 of 6)	3' UTR (NM_011562, exon 6 of 6)	5815	NM_011562	21667	Mm.5090	NM_011562	ENSMUSG00000032494	Tdgf1	CR1|cripto	teratocarcinoma-derived growth factor 1	protein-coding
mm_107348.1	chr12	32820366	32820381	+	1	NA	promoter-TSS (NM_021524)	promoter-TSS (NM_021524)	38	NM_021524	59027	Mm.202727	NM_021524	ENSMUSG00000020572	Nampt	1110035O14Rik|AI314458|AI480535|NAmPRTase|Pbef|Pbef1|Visfatin	nicotinamide phosphoribosyltransferase	protein-coding
mm_104582.1	chr11	96968706	96968718	-	1	NA	intron (NM_030220, intron 1 of 6)	intron (NM_030220, intron 1 of 6)	8976	NM_030220	78912	Mm.491183	NM_030220	ENSMUSG00000018678	Sp2	4930480I16Rik|mKIAA0048	Sp2 transcription factor	protein-coding
mm_89452.1	chr10	93160688	93160714	+	1	NA	promoter-TSS (NM_146239)	promoter-TSS (NM_146239)	-175	NM_146239	237459	Mm.217404	NM_146239	ENSMUSG00000020015	Cdk17	6430598J10Rik|Pctk2	cyclin-dependent kinase 17	protein-coding
mm_154194.1	chr19	58861014	58861022	-	1	NA	promoter-TSS (NM_175199)	promoter-TSS (NM_175199)	-34	NM_175199	73442	Mm.39739	NM_175199	ENSMUSG00000025092	Hspa12a	1700063D12Rik|AI118035|AI840429|AW048913|AW556406|D5Mgi40|Gm19925|mKIAA0417	heat shock protein 12A	protein-coding
mm_168042.1	chrY	90744365	90744389	-	1	NA	Intergenic	CpG	10673	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_8092.1	chr1	135813144	135813180	-	1	NA	Intergenic	Intergenic	-5436	NM_133664	16763	Mm.36726	NM_133664	ENSMUSG00000041782	Lad1	-	ladinin	protein-coding
mm_17044.1	chr2	20924902	20924905	-	1	NA	intron (NM_001128084, intron 1 of 24)	intron (NM_001128084, intron 1 of 24)	42818	NM_001081364	71435	Mm.28507	NM_001081364	ENSMUSG00000036591	Arhgap21	5530401C11Rik|AA416458|ARHGAP10	Rho GTPase activating protein 21	protein-coding
mm_14857.1	chr2	148713741	148713747	+	1	NA	intron (NM_019632, intron 1 of 10)	intron (NM_019632, intron 1 of 10)	18676	NM_019632	17957	Mm.274308	NM_019632	ENSMUSG00000027438	Napb	Brp14|E161|I47|SNARE|b-SNAP	N-ethylmaleimide sensitive fusion protein attachment protein beta	protein-coding
mm_58640.1	chr7	6155801	6155811	+	1	NA	intron (NM_001013012, intron 1 of 2)	CpG	165	NM_001013012	67109	Mm.3254	NM_001013012	ENSMUSG00000046792	Zfp787	2210018M03Rik|Znf787	zinc finger protein 787	protein-coding
mm_7145.1	chr1	91251373	91251409	-	1	NA	intron (NM_026454, intron 1 of 9)	intron (NM_026454, intron 1 of 9)	1072	NM_026454	67921	Mm.337238	NM_026454	ENSMUSG00000034343	Ube2f	2510010F15Rik|AI851109	ubiquitin-conjugating enzyme E2F (putative)	protein-coding
mm_56305.1	chr6	91796251	91796266	-	1	NA	intron (NM_001159507, intron 1 of 23)	intron (NM_001159507, intron 1 of 23)	11135	NM_001159507	243547	Mm.333264	NM_001033353	ENSMUSG00000030098	Grip2	-	glutamate receptor interacting protein 2	protein-coding
mm_85784.1	chr9	109059677	109059706	-	1	NA	promoter-TSS (NM_011637)	promoter-TSS (NM_011637)	32	NM_011637	22040	Mm.439964	NM_011637	ENSMUSG00000049734	Trex1	AU041952	three prime repair exonuclease 1	protein-coding
mm_162155.1	chrX	83487877	83487877	-	1	NA	promoter-TSS (NM_021898)	promoter-TSS (NM_021898)	47	NM_021898	100502723	Mm.383210	NM_021898	ENSMUSG00000035522	Tsga8	Halap-X|Halapx	testis specific gene A8	protein-coding
mm_57792.1	chr6	129274513	129274522	-	1	NA	intron (NM_001033122, intron 1 of 4)	intron (NM_001033122, intron 1 of 4)	852	NM_001033122	12515	Mm.74745	NM_001033122	ENSMUSG00000030156	Cd69	5830438K24Rik|AI452015|AIM|VEA	CD69 antigen	protein-coding
mm_35791.1	chr4	46509305	46509324	-	1	NA	intron (NM_029077, intron 5 of 5)	B1_Mus2|SINE|Alu	19985	NM_053179	94181	Mm.249349	NM_053179	ENSMUSG00000028334	Nans	4632418E04Rik|BB056474|Sas	N-acetylneuraminic acid synthase (sialic acid synthase)	protein-coding
mm_130357.1	chr15	97767645	97767679	-	1	NA	promoter-TSS (NM_001177811)	promoter-TSS (NM_001177811)	4	NM_001177810	223864	Mm.24028	NM_144850	ENSMUSG00000022469	Rapgef3	2310016P22Rik|9330170P05Rik|Epac|Epac1	Rap guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_35004.1	chr4	156236000	156236050	+	1	NA	promoter-TSS (NM_021303)	promoter-TSS (NM_021303)	15	NM_021303	57741	Mm.423051	NM_021303	ENSMUSG00000095567	Noc2l	AA410003|AF155546|NIR	NOC2 like nucleolar associated transcriptional repressor	protein-coding
mm_107518.1	chr12	40446149	40446159	+	1	NA	promoter-TSS (NM_178845)	promoter-TSS (NM_178845)	101	NM_172803	238130	Mm.341423	NM_172803	ENSMUSG00000035954	Dock4	5330406C03|6330411N01Rik|AF263288|C030023J22|mKIAA0716	dedicator of cytokinesis 4	protein-coding
mm_61857.1	chr7	88309459	88309477	+	1	NA	exon (NM_009982, exon 7 of 7)	exon (NM_009982, exon 7 of 7)	31383	NM_001311790	13032	Mm.89295	NM_009982	ENSMUSG00000030560	Ctsc	AI047818|CatC|DPP1|DPPI	cathepsin C	protein-coding
mm_9456.1	chr1	172894581	172894597	-	1	NA	exon (NM_011318, exon 2 of 2)	exon (NM_011318, exon 2 of 2)	465	NM_011318	20219	Mm.330510	NM_011318	ENSMUSG00000026542	Apcs	Sap	serum amyloid P-component	protein-coding
mm_98787.1	chr11	96929261	96929324	+	1	NA	promoter-TSS (NM_146026)	promoter-TSS (NM_146026)	-32	NM_146026	217138	Mm.342551	NM_146026	ENSMUSG00000047040	Prr15l	Atad4|BC022765|E230006A12Rik	proline rich 15-like	protein-coding
mm_95230.1	chr11	44519458	44519478	+	1	NA	promoter-TSS (NM_001166553)	promoter-TSS (NM_001166553)	91	NM_001166553	74315	Mm.156771	NM_028862	ENSMUSG00000019189	Rnf145	3732413I11Rik|TMRF1	ring finger protein 145	protein-coding
mm_50855.1	chr6	55037989	55038091	+	1	NA	promoter-TSS (NM_180678)	promoter-TSS (NM_180678)	39	NM_180678	353172	Mm.250004	NM_180678	ENSMUSG00000029777	Gars	GENA202|Gena201|Nmf249|Sgrp23	glycyl-tRNA synthetase	protein-coding
mm_82476.1	chr9	16502223	16502238	-	1	NA	Intergenic	CpG	-123999	NM_001080814	270120	Mm.195010	NM_001080814	ENSMUSG00000074505	Fat3	9430076A06Rik|D430038H04Rik|Gm1132|Gm510|MFAT3F	FAT atypical cadherin 3	protein-coding
mm_26270.1	chr3	142503385	142503395	+	1	NA	intron (NM_153564, intron 4 of 10)	B4A|SINE|B4	6456	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_135910.1	chr16	67545958	67545964	-	1	NA	intron (NM_178721, intron 1 of 9)	Lx2|LINE|L1	74947	NM_001347247	239857	Mm.394300	NM_178721	ENSMUSG00000064115	Cadm2	2900078E11Rik|9330131D06|A830029E02Rik|Igdf4d|Igsf4d|NECL3|SynCAM 2|SynCAM2	cell adhesion molecule 2	protein-coding
mm_153543.1	chr19	42053087	42053089	-	1	NA	exon (NM_025752, exon 1 of 1)	exon (NM_025752, exon 1 of 1)	860	NM_025752	66765	Mm.440412	NM_025752	ENSMUSG00000090369	4933411K16Rik	-	RIKEN cDNA 4933411K16 gene	protein-coding
mm_74898.1	chr8	25169262	25169276	-	1	NA	exon (NM_177089, exon 7 of 13)	exon (NM_177089, exon 7 of 13)	-10036	NR_106187	102467006		NR_106187	ENSMUSG00000099142	Mir8108	Gm27484|mmu-mir-8108	microRNA 8108	ncRNA
mm_158212.1	chrX	105875472	105875493	-	1	NA	exon (NM_009530, exon 9 of 35)	exon (NM_009530, exon 9 of 35)	53890	NM_009530	22589	Mm.10141	NM_009530	ENSMUSG00000031229	Atrx	4833408C14Rik|AI447451|ATR2|DXHXS6677E|HP1-BP38|Hp1bp2|Hp1bp38|MRXS3|RAD54L|Rad54|XH2|Xnp|ZNF-HX	alpha thalassemia/mental retardation syndrome X-linked	protein-coding
mm_30667.1	chr4	10946585	10946598	+	1	NA	Intergenic	Intergenic	61028	NM_175175	71801	Mm.34351	NM_175175	ENSMUSG00000049969	Plekhf2	1110070J07Rik|AA673237|ZFYVE18	pleckstrin homology domain containing, family F (with FYVE domain) member 2	protein-coding
mm_90676.1	chr10	128908967	128908978	+	1	NA	promoter-TSS (NM_007653)	promoter-TSS (NM_007653)	53	NM_001042580	12512	Mm.371552	NM_007653	ENSMUSG00000025351	Cd63	C75951|ME491|Tspan30	CD63 antigen	protein-coding
mm_115940.1	chr13	23683942	23683967	-	1	NA	promoter-TSS (NM_178189)	promoter-TSS (NM_178189)	5	NM_178189	319164	Mm.261973	NM_178189	ENSMUSG00000069270	Hist1h2ac	-	histone cluster 1, H2ac	protein-coding
mm_154694.1	chrX	8051583	8051603	+	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	22720	NM_001290716	20937	Mm.9244	NM_011514	ENSMUSG00000039231	Suv39h1	AI852103|AL022883|DXHXS7466e|H3-K9-HMTase 1|KMT1A|mIS6	suppressor of variegation 3-9 homolog 1 (Drosophila)	protein-coding
mm_159046.1	chr1	182765080	182765080	+	1	NA	exon (NM_144796, exon 1 of 8)	exon (NM_144796, exon 1 of 8)	174	NM_144796	96935	Mm.331052	NM_144796	ENSMUSG00000038576	Susd4	AI848994|E430021N18Rik|N28096	sushi domain containing 4	protein-coding
mm_51509.1	chr6	83137104	83137121	+	1	NA	promoter-TSS (NM_133641)	promoter-TSS (NM_133641)	28	NM_009106	20166	Mm.4139	NM_009106	ENSMUSG00000034930	Rtkn	-	rhotekin	protein-coding
mm_435.1	chr1	34579696	34579751	+	1	NA	promoter-TSS (NM_213727)	promoter-TSS (NM_213727)	30	NM_213727	211383	Mm.330696	NM_213727	ENSMUSG00000045174	Amer3	9430069J07Rik|Fam123c	APC membrane recruitment 3	protein-coding
mm_173133.1	chrX	19364163	19364170	-	1	NA	Intergenic	LTRIS2|LTR|ERV1	-217195	NR_029807	723828		NR_029807	ENSMUSG00000065471	Mir222	Mirn222|mir-222|mmu-mir-222	microRNA 222	ncRNA
mm_6211.1	chr1	66817602	66817617	-	1	NA	promoter-TSS (NM_001122738)	promoter-TSS (NM_001122738)	-14	NM_001122738	68691	Mm.240912	NM_177645	ENSMUSG00000026004	Kansl1l	1110028C15Rik|1190030G24|AI427598|C430010P07Rik|mKIAA4189	KAT8 regulatory NSL complex subunit 1-like	protein-coding
mm_137362.1	chr17	25369329	25369337	+	1	NA	Intergenic	Intergenic	-1220	NM_012034	26945	Mm.180108	NM_012034	ENSMUSG00000033200	Tpsg1	Prss31|Tmt	tryptase gamma 1	protein-coding
mm_3861.1	chr1	160978671	160978680	+	1	NA	promoter-TSS (NM_080844)	promoter-TSS (NM_080844)	69	NM_080844	11905	Mm.260770	NM_080844	ENSMUSG00000026715	Serpinc1	AI114908|ATIII|At-3|At3	serine (or cysteine) peptidase inhibitor, clade C (antithrombin), member 1	protein-coding
mm_127145.1	chr15	98492398	98492402	+	1	NA	Intergenic	Intergenic	-5074	NM_001001807	258502	Mm.377539	NM_001001807	ENSMUSG00000054036	Olfr279	MOR122-1|Olfr234|Olfr234-ps1|Olfr279-ps1	olfactory receptor 279	protein-coding
mm_151347.1	chr19	55895583	55895591	+	1	NA	5' UTR (NM_001142924, exon 1 of 12)	5' UTR (NM_001142924, exon 1 of 12)	266	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_54787.1	chr6	41557818	41557835	-	1	NA	Intergenic	Intergenic	36050	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_122839.1	chr14	54724067	54724086	-	1	NA	3' UTR (NM_016972, exon 11 of 11)	3' UTR (NM_016972, exon 11 of 11)	-11902	NM_207131	110794	Mm.236223	NM_207131	ENSMUSG00000052435	Cebpe	C/EBPe|CRP1|Gm294	CCAAT/enhancer binding protein (C/EBP), epsilon	protein-coding
mm_158035.1	chrX	98599452	98599458	-	1	NA	intron (NM_001313755, intron 18 of 23)	intron (NM_001313755, intron 18 of 23)	291570	NM_052976	94190	Mm.33536	NM_052976	ENSMUSG00000031214	Ophn1	C130037N19Rik|Wtgr	oligophrenin 1	protein-coding
mm_60909.1	chr7	46753440	46753450	+	1	NA	exon (NM_011314, exon 3 of 4)	exon (NM_011314, exon 3 of 4)	1612	NM_011314	20209	Mm.200941	NM_011314	ENSMUSG00000057465	Saa2	AW111173|Saa-2|Saa1	serum amyloid A 2	protein-coding
mm_34326.1	chr4	141901991	141901993	+	1	NA	intron (NM_177868, intron 29 of 31)	intron (NM_177868, intron 29 of 31)	-27072	NM_025994	27984	Mm.395598	NM_025994	ENSMUSG00000040659	Efhd2	2600015J22Rik|AA408606|D4Wsu27e	EF hand domain containing 2	protein-coding
mm_100240.1	chr11	117249096	117249099	+	1	NA	intron (NM_001113486, intron 2 of 11)	intron (NM_001113486, intron 2 of 11)	-17149	NM_001113487	53860	Mm.38450	NM_017380	ENSMUSG00000059248	Sept9	MSF1|Msf|PNUTL4|Sint1	septin 9	protein-coding
mm_72027.1	chr8	70758088	70758098	+	1	NA	TTS (NM_183170)	TTS (NM_183170)	2828	NM_183170	234384	Mm.213010	NM_183170	ENSMUSG00000035559	Mpv17l2	Fksg24	MPV17 mitochondrial membrane protein-like 2	protein-coding
mm_23981.1	chr3	86038838	86038891	+	1	NA	Intergenic	Intergenic	-36373	NM_001001650	368202	Mm.253822	NM_001001650	ENSMUSG00000049013	Prss48	Esspl|Gm1019	protease, serine 48	protein-coding
mm_110710.1	chr12	69357121	69357181	-	1	NA	promoter-TSS (NM_025441)	promoter-TSS (NM_025441)	25	NM_025441	66244	Mm.46705	NM_025441	ENSMUSG00000020982	Nemf	1500011I12Rik|4933405E14Rik|Sdccag1	nuclear export mediator factor	protein-coding
mm_4409.1	chr1	172481903	172481907	+	1	NA	promoter-TSS (NM_001145800)	promoter-TSS (NM_001145800)	-308	NM_001145800	93842	Mm.214530	NM_033608	ENSMUSG00000037995	Igsf9	644ETD8|Dasm1|Kiaa1355-hp|NRT1|Ncaml|mKIAA1355	immunoglobulin superfamily, member 9	protein-coding
mm_145324.1	chr18	54971293	54971294	+	1	NA	intron (NM_175751, intron 2 of 9)	intron (NM_175751, intron 2 of 9)	18887	NM_175751	269023	Mm.192984	NM_175751	ENSMUSG00000052713	Zfp608	4932417D18Rik|D430007A19Rik|Znf608	zinc finger protein 608	protein-coding
mm_79257.1	chr9	50752887	50752894	+	1	NA	promoter-TSS (NM_001289784)	promoter-TSS (NM_001289784)	-81	NM_001289785	12955	Mm.178	NM_009964	ENSMUSG00000032060	Cryab	Crya-2|Crya2|HspB5|P23	crystallin, alpha B	protein-coding
mm_136138.1	chr16	87354177	87354184	-	1	NA	promoter-TSS (NM_001159331)	promoter-TSS (NM_001159331)	-5	NM_001159331	67768	Mm.296532	NM_026366	ENSMUSG00000044442	N6amt1	5830445C04Rik|Hemk2|Pred28	N-6 adenine-specific DNA methyltransferase 1 (putative)	protein-coding
mm_3064.1	chr1	134182151	134182177	+	1	NA	promoter-TSS (NM_007695)	promoter-TSS (NM_007695)	-240	NM_007695	12654	Mm.38274	NM_007695	ENSMUSG00000064246	Chil1	AW208766|Brp39|Chi3l1|Gp39	chitinase-like 1	protein-coding
mm_112847.1	chr13	20836045	20836049	+	1	NA	intron (NM_012054, intron 2 of 20)	intron (NM_012054, intron 2 of 20)	41934	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_46116.1	chr5	92363301	92363309	-	1	NA	promoter-TSS (NM_019494)	promoter-TSS (NM_019494)	-9	NR_038116	56066	Mm.131723	NM_019494	ENSMUSG00000060183	Cxcl11	Cxc11|H174|I-tac|Ip9|Itac|Scyb11|Scyb9b|b-R1|betaR1	chemokine (C-X-C motif) ligand 11	protein-coding
mm_134666.1	chr16	22257827	22257833	-	1	NA	intron (NM_009186, intron 1 of 8)	intron (NM_009186, intron 1 of 8)	8175	NM_001330554	20462	Mm.210352	NM_009186	ENSMUSG00000022858	Tra2b	5730405G21Rik|D16Ertd266e|SIG-41|Sfrs10|Silg41|TRA2beta	transformer 2 beta homolog (Drosophila)	protein-coding
mm_12996.1	chr2	90885905	90885914	+	1	NA	5' UTR (NM_026161, exon 1 of 2)	5' UTR (NM_026161, exon 1 of 2)	123	NM_026161	67445	Mm.258993	NM_026161	ENSMUSG00000040794	C1qtnf4	0710001E10Rik|9430004J15Rik|CTRP4	C1q and tumor necrosis factor related protein 4	protein-coding
mm_132956.1	chr16	49970775	49970786	+	1	NA	Intergenic	Intergenic	-9680	NR_045001	628951	Mm.428032	NR_045001		Gm6936	-	predicted gene 6936	ncRNA
mm_81970.1	chr9	120960007	120960039	+	1	NA	3' UTR (NM_007614, exon 15 of 15)	3' UTR (NM_007614, exon 15 of 15)	4937	NR_106058	102465661		NR_106058	ENSMUSG00000106193	Mir7090	mmu-mir-7090	microRNA 7090	ncRNA
mm_100241.1	chr11	117266158	117266189	+	1	NA	promoter-TSS (NM_001113487)	promoter-TSS (NM_001113487)	-73	NM_001113487	53860	Mm.38450	NM_017380	ENSMUSG00000059248	Sept9	MSF1|Msf|PNUTL4|Sint1	septin 9	protein-coding
mm_49116.1	chr6	8509798	8509800	+	1	NA	promoter-TSS (NR_040452)	promoter-TSS (NR_040452)	199	NM_133236	170772	Mm.210787	NM_133236	ENSMUSG00000029638	Glcci1	2310047L21Rik|A130036A18Rik|Fam117c|Gig18|Tssn1	glucocorticoid induced transcript 1	protein-coding
mm_59871.1	chr7	30232311	30232350	+	1	NA	promoter-TSS (NM_025548)	promoter-TSS (NM_025548)	256	NM_027259	69920	Mm.440028	NM_027259	ENSMUSG00000019738	Polr2i	2810002B19Rik	polymerase (RNA) II (DNA directed) polypeptide I	protein-coding
mm_86636.1	chr10	14073865	14073866	+	1	NA	intron (NM_010437, intron 2 of 8)	intron (NM_010437, intron 2 of 8)	107486	NM_010437	15273	Mm.42157	NM_010437	ENSMUSG00000015501	Hivep2	Gm20114|MIBP1|Schnurri-2|Shn-2	human immunodeficiency virus type I enhancer binding protein 2	protein-coding
mm_131611.1	chr16	19241275	19241284	+	1	NA	Intergenic	Intergenic	45462	NM_146451	258443	Mm.377506	NM_146451	ENSMUSG00000050742	Olfr164	MOR279-2	olfactory receptor 164	protein-coding
mm_72445.1	chr8	83165503	83165523	+	1	NA	5' UTR (NM_001111304, exon 1 of 21)	5' UTR (NM_001111304, exon 1 of 21)	161	NM_027758	71310	Mm.24031	NM_027758	ENSMUSG00000031709	Tbc1d9	4933431N12Rik|AI847101|AW490653|C76116	TBC1 domain family, member 9	protein-coding
mm_165412.1	chr2	144698218	144698226	+	1	NA	intron (NM_025314, intron 4 of 5)	intron (NM_025314, intron 4 of 5)	98269	NM_025314	66044	Mm.28109	NM_025314	ENSMUSG00000027430	Dtd1	0610006H08Rik|DUE-B|Hars2	D-tyrosyl-tRNA deacylase 1	protein-coding
mm_81154.1	chr9	107289026	107289037	+	1	NA	intron (NM_001316691, intron 1 of 7)	intron (NM_001316691, intron 1 of 7)	365	NM_001316691	102626	Mm.222612	NM_178907	ENSMUSG00000032577	Mapkapk3	3PK|AI874665|MAPKAP-K3|MAPKAP3|MK-3|MK3|MapkKapk3	mitogen-activated protein kinase-activated protein kinase 3	protein-coding
mm_67857.1	chr7	98943354	98943359	-	1	NA	intron (NM_178635, intron 12 of 14)	PB1D10|SINE|Alu	104511	NM_001285795	22411	Mm.22182	NM_009519	ENSMUSG00000015957	Wnt11	-	wingless-type MMTV integration site family, member 11	protein-coding
mm_17747.1	chr2	32714924	32714942	-	1	NA	Intergenic	Intergenic	-1961	NR_039536	100628606		NR_039536	ENSMUSG00000105841	Mir3960	mmu-mir-3960	microRNA 3960	ncRNA
mm_159270.1	chr2	163918913	163918913	-	1	NA	promoter-TSS (NM_183023)	promoter-TSS (NM_183023)	-230	NM_183023	241770	Mm.330760	NM_183023	ENSMUSG00000035226	Rims4	6530406L02|Rim4	regulating synaptic membrane exocytosis 4	protein-coding
mm_117362.1	chr13	70750083	70750085	-	1	NA	intron (NM_172053, intron 18 of 22)	ORR1E|LTR|ERVL-MaLR	91727	NM_172053	271127	Mm.115970	NM_172053	ENSMUSG00000049538	Adamts16	-	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 16	protein-coding
mm_129309.1	chr15	77596111	77596131	-	1	NA	promoter-TSS (NM_177820)	promoter-TSS (NM_177820)	4	NM_177820	328561	Mm.379486	NM_177820	ENSMUSG00000050014	Apol10b	9130218O11Rik	apolipoprotein L 10B	protein-coding
mm_87461.1	chr10	51485001	51485019	+	1	NA	intron (NM_001291892, intron 7 of 8)	intron (NM_001291892, intron 7 of 8)	4398	NM_001291892	14727	Mm.439661	NM_008147	ENSMUSG00000062593	Lilr4b	Gp49a|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4B	protein-coding
mm_41147.1	chr5	87927571	87927591	+	1	NA	exon (NM_007786, exon 2 of 5)	exon (NM_007786, exon 2 of 5)	1948	NM_007786	12994	Mm.296303	NM_007786	ENSMUSG00000001622	Csn3	AW208918|CSN10|Csnk	casein kappa	protein-coding
mm_105232.1	chr11	102316692	102316708	-	1	NA	intron (NM_001302955, intron 1 of 19)	CpG	587	NM_001044383	21429	Mm.2845	NM_011551	ENSMUSG00000020923	Ubtf	A930005G04Rik|NOR-90|Tcfubf|UBF|UBF-1|UBF1	upstream binding transcription factor, RNA polymerase I	protein-coding
mm_5731.1	chr1	45332001	45332032	-	1	NA	exon (NM_009930, exon 19 of 51)	exon (NM_009930, exon 19 of 51)	20478	NM_009930	12825	Mm.249555	NM_009930	ENSMUSG00000026043	Col3a1	AW550625|Col3a-1|Tsk-2|Tsk2	collagen, type III, alpha 1	protein-coding
mm_17743.1	chr2	32713066	32713091	-	1	NA	promoter-TSS (NM_130860)	promoter-TSS (NM_130860)	-106	NR_039536	100628606		NR_039536	ENSMUSG00000105841	Mir3960	mmu-mir-3960	microRNA 3960	ncRNA
mm_160503.1	chr9	18397538	18397538	-	1	NA	Intergenic	Intergenic	-6880	NM_001033793	546118	Mm.380138	NM_001033793	ENSMUSG00000074502	Ubtfl1	B020006M18Rik|Hmgpi	upstream binding transcription factor, RNA polymerase I-like 1	protein-coding
mm_9064.1	chr1	167467013	167467024	-	1	NA	promoter-TSS (NM_001013382)	promoter-TSS (NM_001013382)	-238	NM_001013382	240899	Mm.159799	NM_001013382	ENSMUSG00000040485	Lrrc52	4930413P14Rik	leucine rich repeat containing 52	protein-coding
mm_3716.1	chr1	153909458	153909471	+	1	NA	3' UTR (NM_008131, exon 7 of 7)	3' UTR (NM_008131, exon 7 of 7)	9535	NM_008131	14645	Mm.210745	NM_008131	ENSMUSG00000026473	Glul	GS|Glns	glutamate-ammonia ligase (glutamine synthetase)	protein-coding
mm_88326.1	chr10	75568631	75568639	+	1	NA	promoter-TSS (NM_001305992)	promoter-TSS (NM_001305992)	-27	NM_001305992	14598	Mm.4559	NM_008116	ENSMUSG00000006345	Ggt1	CD224|GGT|GGT 1|GGT-1|Ggtp|dwg	gamma-glutamyltransferase 1	protein-coding
mm_48832.1	chr5	149184274	149184294	-	1	NA	promoter-TSS (NM_001115151)	promoter-TSS (NM_001115151)	-276	NM_001115153	231915	Mm.29402	NM_001013378	ENSMUSG00000041264	Uspl1	E430026A01Rik	ubiquitin specific peptidase like 1	protein-coding
mm_85835.1	chr9	110476638	110476648	-	1	NA	promoter-TSS (NM_001163569)	promoter-TSS (NM_001163569)	51	NM_177771	270201	Mm.41744	NM_177771	ENSMUSG00000054792	Klhl18	A930041K15|AW545966	kelch-like 18	protein-coding
mm_133944.1	chr16	3908640	3908686	-	1	NA	promoter-TSS (NM_029738)	promoter-TSS (NM_029738)	26	NM_028484	73261	Mm.486226	NM_028484	ENSMUSG00000005983	1700037C18Rik	2810022L20Rik	RIKEN cDNA 1700037C18 gene	protein-coding
mm_128884.1	chr15	73147862	73147879	-	1	NA	intron (NM_153178, intron 1 of 18)	B1F2|SINE|Alu	37077	NM_153178	239528	Mm.23095	NM_153178	ENSMUSG00000036698	Ago2	1110029L17Rik|2310051F07Rik|AI225898|AL022874|AW546247|ENSMUSG00000072493|Eif2c2|Gerp95|Gm10365|mKIAA4215	argonaute RISC catalytic subunit 2	protein-coding
mm_53265.1	chr6	128362795	128362803	+	1	NA	promoter-TSS (NM_008021)	promoter-TSS (NM_008021)	23	NM_001326583	72440	Mm.143908	NM_197981	ENSMUSG00000048668	Rhno1	2510047L19Rik|5930416I19Rik	RAD9-HUS1-RAD1 interacting nuclear orphan 1	protein-coding
mm_146529.1	chr18	5273322	5273325	-	1	NA	intron (NM_178722, intron 2 of 4)	intron (NM_178722, intron 2 of 4)	61116	NM_178722	240186	Mm.118257	NM_178722	ENSMUSG00000050945	Zfp438	9430031G09|9430091M14Rik|B830013J05Rik	zinc finger protein 438	protein-coding
mm_43879.1	chr5	143758294	143758363	+	1	NA	promoter-TSS (NR_015486)	promoter-TSS (NR_015486)	-26	NR_015486	320064	Mm.332820	NR_015486		D130017N08Rik	1700012G11Rik	RIKEN cDNA D130017N08 gene	ncRNA
mm_13707.1	chr2	117157574	117157588	+	1	NA	intron (NM_033524, intron 2 of 6)	intron (NM_033524, intron 2 of 6)	-27546	NR_030440	732489		NR_030440	ENSMUSG00000076376	Mir674	Mirn674|mir-674|mmu-mir-674	microRNA 674	ncRNA
mm_58485.1	chr7	3629986	3630037	+	1	NA	promoter-TSS (NM_001290381)	promoter-TSS (NM_001290381)	26	NM_027328	68988	Mm.246863	NM_027328	ENSMUSG00000008373	Prpf31	1500019O16Rik|2810404O06Rik|AW554706|PRP31|RP11	pre-mRNA processing factor 31	protein-coding
mm_8228.1	chr1	138175239	138175254	-	1	NA	promoter-TSS (NM_001268286)	promoter-TSS (NM_001268286)	59	NM_011210	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_54245.1	chr6	28259236	28259238	-	1	NA	intron (NM_001081678, intron 2 of 5)	intron (NM_001081678, intron 2 of 5)	2364	NM_001081678	627049	Mm.84441	NM_001081678	ENSMUSG00000039841	Zfp800	AA407452|Znf800	zinc finger protein 800	protein-coding
mm_59550.1	chr7	28071216	28071228	+	1	NA	promoter-TSS (NM_001122603)	promoter-TSS (NM_001122603)	-14	NM_001122603	215384	Mm.292276	NM_175444	ENSMUSG00000047730	Fcgbp	A430096B05Rik	Fc fragment of IgG binding protein	protein-coding
mm_164398.1	chr16	33959839	33959842	+	1	NA	intron (NM_009471, intron 4 of 5)	intron (NM_009471, intron 4 of 5)	7163	NM_009471	22247	Mm.13145	NM_009471	ENSMUSG00000022814	Umps	1700095D23Rik|AA408257|AL033308|BB164745	uridine monophosphate synthetase	protein-coding
mm_77009.1	chr8	107581146	107581160	-	1	NA	exon (NM_010817, exon 7 of 7)	exon (NM_010817, exon 7 of 7)	7329	NM_010817	17463	Mm.18347	NM_010817	ENSMUSG00000039067	Psmd7	AW107203|Mov-34|Mov34	proteasome (prosome, macropain) 26S subunit, non-ATPase, 7	protein-coding
mm_68028.1	chr7	101011985	101012004	-	1	NA	promoter-TSS (NM_001302347)	promoter-TSS (NM_001302347)	4	NM_001302347	18442	Mm.3000	NM_008773	ENSMUSG00000032860	P2ry2	P2U1|P2Y2	purinergic receptor P2Y, G-protein coupled 2	protein-coding
mm_35743.1	chr4	45408722	45408768	-	1	NA	promoter-TSS (NM_001009949)	promoter-TSS (NM_001009949)	21	NM_001009949	230125	Mm.260210	NM_001009949	ENSMUSG00000045973	Slc25a51	9130208E07Rik|D130005A03Rik|Gm138|Mcart1	solute carrier family 25, member 51	protein-coding
mm_52790.1	chr6	121263919	121263930	+	1	NA	intron (NM_011909, intron 8 of 10)	MTD|LTR|ERVL-MaLR	18018	NM_011909	24110	Mm.326911	NM_011909	ENSMUSG00000030107	Usp18	1110058H21Rik|AW047653|UBP43|Ubp15	ubiquitin specific peptidase 18	protein-coding
mm_101081.1	chr11	11725578	11725597	-	1	NA	intron (NM_001301866, intron 3 of 5)	intron (NM_001301866, intron 3 of 5)	35410	NM_001301863	22778	Mm.103545	NM_009578	ENSMUSG00000018654	Ikzf1	5832432G11Rik|Ikaros|LyF-1|Zfpn1a1|Znfn1a1|hlk-1|mKIAA4227	IKAROS family zinc finger 1	protein-coding
mm_165925.1	chr4	63344384	63344395	-	1	NA	promoter-TSS (NM_008768)	promoter-TSS (NM_008768)	-167	NM_008768	18405	Mm.4777	NM_008768	ENSMUSG00000039196	Orm1	Agp-1|Agp-2|Orm-1	orosomucoid 1	protein-coding
mm_131542.1	chr16	17797230	17797240	+	1	NA	promoter-TSS (NM_153790)	promoter-TSS (NM_153790)	-47	NM_153790	224024	Mm.194950	NM_153790	ENSMUSG00000012017	Scarf2	NSR1|SREC-II|SRECRP-1|Scatf1|Srec2|SrecII	scavenger receptor class F, member 2	protein-coding
mm_104136.1	chr11	86875976	86875978	-	1	NA	intron (NR_106195, intron 4 of 8)	B3|SINE|B2	-68317	NM_026191	67487	Mm.260627	NM_026191	ENSMUSG00000018425	Dhx40	2410016C14Rik|ARG147|DDX40|PAD	DEAH (Asp-Glu-Ala-His) box polypeptide 40	protein-coding
mm_152857.1	chr19	24175338	24175363	-	1	NA	intron (NM_011597, intron 1 of 22)	intron (NM_011597, intron 1 of 22)	-1210	NM_001198985	21873	Mm.104744	NM_011597	ENSMUSG00000024812	Tjp2	ZO-2	tight junction protein 2	protein-coding
mm_27936.1	chr3	79572459	79572473	-	1	NA	Intergenic	Intergenic	-4787	NM_001162999	329679	Mm.244005	NM_001162999	ENSMUSG00000061175	Fnip2	D630023B12Rik|mKIAA1450	folliculin interacting protein 2	protein-coding
mm_40410.1	chr5	53061398	53061408	+	1	NA	exon (NM_011402, exon 6 of 13)	exon (NM_011402, exon 6 of 13)	12050	NM_011402	20531	Mm.284891	NM_011402	ENSMUSG00000029188	Slc34a2	AA536683|D5Ertd227e|NaPi-2b|Npt2b	solute carrier family 34 (sodium phosphate), member 2	protein-coding
mm_85299.1	chr9	100506805	100506811	-	1	NA	promoter-TSS (NM_001324530)	promoter-TSS (NM_001324530)	48	NM_001324530	17973	Mm.181485	NM_010878	ENSMUSG00000032475	Nck1	6330586M15Rik|D230010O13Rik|Nck|Nck-1	non-catalytic region of tyrosine kinase adaptor protein 1	protein-coding
mm_1048.1	chr1	58802493	58802517	+	1	NA	promoter-TSS (NM_001277926)	promoter-TSS (NM_001277926)	3	NM_001080126	12370	Mm.336851	NM_009812	ENSMUSG00000026029	Casp8	CASP-8|FLICE|MACH|Mch5	caspase 8	protein-coding
mm_48375.1	chr5	139484476	139484496	-	1	NA	promoter-TSS (NM_001159908)	promoter-TSS (NM_001159908)	5	NM_133349	100494	Mm.24521	NM_133349	ENSMUSG00000053581	Zfand2a	AA407930|AU016206|Airap	zinc finger, AN1-type domain 2A	protein-coding
mm_143993.1	chr17	87798056	87798090	-	1	NA	promoter-TSS (NM_199251)	promoter-TSS (NM_199251)	-79	NM_199251	210741	Mm.312046	NM_199251	ENSMUSG00000050138	Kcnk12	mntk1	potassium channel, subfamily K, member 12	protein-coding
mm_40980.1	chr5	77098861	77098875	+	1	NA	intron (NM_175606, intron 1 of 2)	ORR1D1|LTR|ERVL-MaLR	-3601	NM_001159900	74318	Mm.181852	NM_175606	ENSMUSG00000059325	Hopx	1110018K11Rik|1200015P04Rik|2300002F06Rik|AI848177|AW490897|Cameo|Hdop|Hod|Hop|Ob1|Obl|Toto	HOP homeobox	protein-coding
mm_153252.1	chr19	36626046	36626061	-	1	NA	intron (NR_033510, intron 3 of 4)	RMER1B|Other|Other	63426	NR_033510	668215	Mm.394223	NR_033510	ENSMUSG00000087579	1500017E21Rik	-	RIKEN cDNA 1500017E21 gene	ncRNA
mm_85965.1	chr9	112141325	112141328	-	1	NA	intron (NM_001177617, intron 10 of 14)	AT_rich|Low_complexity|Low_complexity	-22615	NR_029823	723815		NR_029823	ENSMUSG00000065441	Mir128-2	Mirn128-2|Mirn128b|mir-128-2|mir-128b	microRNA 128-2	ncRNA
mm_92399.1	chr10	76614752	76614772	-	1	NA	exon (NM_146007, exon 3 of 28)	exon (NM_146007, exon 3 of 28)	8642	NM_146007	12834	Mm.1949	NM_146007	ENSMUSG00000020241	Col6a2	Col6a-2	collagen, type VI, alpha 2	protein-coding
mm_52508.1	chr6	115361066	115361101	+	1	NA	promoter-TSS (NM_001308352)	promoter-TSS (NM_001308352)	-61	NM_001308352	19016	Mm.3020	NM_011146	ENSMUSG00000000440	Pparg	Nr1c3|PPAR-gamma|PPAR-gamma2|PPARgamma|PPARgamma2	peroxisome proliferator activated receptor gamma	protein-coding
mm_134264.1	chr16	13750874	13750889	-	1	NA	Intergenic	B1_Mus2|SINE|Alu	-20397	NM_011987	26565	Mm.4214	NM_011987	ENSMUSG00000022683	Pla2g10	GX sPLA2|PLA2GX|sPLA2-X	phospholipase A2, group X	protein-coding
mm_47167.1	chr5	120743670	120743698	-	1	NA	intron (NM_001347448, intron 3 of 11)	RLTR17B_Mm|LTR|ERVK	6164	NM_145227	246728	Mm.260926	NM_145227	ENSMUSG00000032690	Oas2	Oasl11	2'-5' oligoadenylate synthetase 2	protein-coding
mm_74291.1	chr8	125919143	125919149	+	1	NA	intron (NM_145608, intron 1 of 9)	B3A|SINE|B2	8696	NM_145608	234878	Mm.216458	NM_145608	ENSMUSG00000031853	Map3k21	Mlk4|mKIAA1804	mitogen-activated protein kinase kinase kinase 21	protein-coding
mm_59583.1	chr7	28129481	28129490	+	1	NA	promoter-TSS (NM_001164655)	promoter-TSS (NM_001164655)	19	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_38236.1	chr4	136172602	136172604	-	1	NA	5' UTR (NM_177733, exon 1 of 7)	5' UTR (NM_177733, exon 1 of 7)	329	NM_177733	242705	Mm.307932	NM_177733	ENSMUSG00000018983	E2f2	E2F-2	E2F transcription factor 2	protein-coding
mm_24861.1	chr3	95894014	95894031	+	1	NA	5' UTR (NM_146104, exon 1 of 6)	5' UTR (NM_146104, exon 1 of 6)	101	NM_146134	226548	Mm.306954	NM_146104	ENSMUSG00000015750	Aph1a	6530402N02Rik|APH-1a	aph1 homolog A, gamma secretase subunit	protein-coding
mm_9289.1	chr1	171634944	171634961	-	1	NA	exon (NM_144539, exon 8 of 8)	exon (NM_144539, exon 8 of 8)	6948	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_137953.1	chr17	32965798	32965826	+	1	NA	promoter-TSS (NM_153063)	promoter-TSS (NM_153063)	-19	NM_153063	224691	Mm.328953	NM_153063	ENSMUSG00000053600	Zfp472	KRIM-1|Krim-1A|Krim-1B|Krim1	zinc finger protein 472	protein-coding
mm_127360.1	chr15	100674606	100674633	+	1	NA	3' UTR (NM_033612, exon 8 of 8)	3' UTR (NM_033612, exon 8 of 8)	-5119	NM_001270537	668218	Mm.451225	NM_001270537	ENSMUSG00000098112	Bin2	-	bridging integrator 2	protein-coding
mm_29482.1	chr3	115713718	115713747	-	1	NA	intron (NM_007901, intron 1 of 1)	intron (NM_007901, intron 1 of 1)	1323	NM_007901	13609	Mm.982	NM_007901	ENSMUSG00000045092	S1pr1	AI849002|Edg1|Lpb1|S1p|S1p1	sphingosine-1-phosphate receptor 1	protein-coding
mm_7354.1	chr1	106642214	106642216	-	1	NA	intron (NM_009741, intron 1 of 1)	intron (NM_009741, intron 1 of 1)	72075	NM_009741	12043	Mm.257460	NM_009741	ENSMUSG00000057329	Bcl2	AW986256|Bcl-2|C430015F12Rik|D630044D05Rik|D830018M01Rik	B cell leukemia/lymphoma 2	protein-coding
mm_48609.1	chr5	144358004	144358008	-	1	NA	promoter-TSS (NR_102374)	promoter-TSS (NR_102374)	83	NR_102374	100579137		NR_102372	ENSMUSG00000104600	Dmrt1i	Dmr	Dmrt1 interacting ncRNA	ncRNA
mm_93520.1	chr10	115288142	115288156	-	1	NA	Intergenic	Intergenic	27442	NM_024454	216344	Mm.21936	NM_024454	ENSMUSG00000020132	Rab21	9630024B22	RAB21, member RAS oncogene family	protein-coding
mm_40727.1	chr5	65991492	65991511	+	1	NA	intron (NR_027961, intron 4 of 6)	ORR1B1|LTR|ERVL-MaLR	12784	NR_027961	231253	Mm.436542	NM_177679	ENSMUSG00000054598	9130230L23Rik	-	RIKEN cDNA 9130230L23 gene	ncRNA
mm_68827.1	chr7	126200306	126200313	-	1	NA	promoter-TSS (NM_028816)	promoter-TSS (NM_028816)	99	NM_028816	74204	Mm.235663	NM_028816	ENSMUSG00000000131	Xpo6	2610005L19Rik|AL022631|C230091E20Rik|R75304|Ranbp20|mKIAA0370	exportin 6	protein-coding
mm_64423.1	chr7	142577043	142577057	+	1	NA	promoter-TSS (NR_030416)	promoter-TSS (NR_030416)	97	NR_030416	735280		NR_030416	ENSMUSG00000076275	Mir675	Mirn675|mir-675|mmu-mir-675	microRNA 675	ncRNA
mm_96599.1	chr11	69091022	69091038	+	1	NA	3' UTR (NM_009497, exon 5 of 5)	3' UTR (NM_009497, exon 5 of 5)	2502	NM_009497	22318	Mm.28643	NM_009497	ENSMUSG00000020894	Vamp2	Syb-2|Syb2|sybII	vesicle-associated membrane protein 2	protein-coding
mm_71044.1	chr8	33673904	33673943	+	1	NA	intron (NM_010344, intron 4 of 12)	ID_B1|SINE|B4	20685	NM_010344	14782	Mm.283573	NM_010344	ENSMUSG00000031584	Gsr	AI325518|D8Ertd238e|Gr-1|Gr1	glutathione reductase	protein-coding
mm_23281.1	chr3	51666115	51666130	+	1	NA	intron (NM_001310482, intron 2 of 3)	HAL1|LINE|L1	4943	NM_001310482	211666	Mm.24679	NM_174995	ENSMUSG00000074604	Mgst2	GST2|MGST-II	microsomal glutathione S-transferase 2	protein-coding
mm_69282.1	chr7	128140285	128140320	-	1	NA	exon (NM_021334, exon 16 of 30)	exon (NM_021334, exon 16 of 30)	10734	NM_021334	16411	Mm.22378	NM_021334	ENSMUSG00000030789	Itgax	AI449405|Cd11c|Cr4|N418	integrin alpha X	protein-coding
mm_28681.1	chr3	95339970	95339990	-	1	NA	exon (NM_001163642, exon 12 of 22)	exon (NM_001163642, exon 12 of 22)	17222	NM_001163641	84505	Mm.490259	NM_018877	ENSMUSG00000015697	Setdb1	AU022152|ESET|KMT1E|mKIAA0067	SET domain, bifurcated 1	protein-coding
mm_47034.1	chr5	115754916	115754930	-	1	NA	Intergenic	Intergenic	-23364	NM_001080808	75665	Mm.233914	NM_001080808	ENSMUSG00000041609	Ccdc64	2210403N09Rik|BICDR-1|Bicdl1	coiled-coil domain containing 64	protein-coding
mm_87059.1	chr10	28843982	28843997	+	1	NA	intron (NM_001305663, intron 5 of 5)	intron (NM_001305663, intron 5 of 5)	79518	NR_033601	114676	Mm.390292	NR_033601		4930519F09Rik	-	pyruvate dehydrogenase E1 alpha 1 pseudogene	pseudo
mm_139897.1	chr17	70852752	70852770	+	1	NA	intron (NM_001164074, intron 1 of 2)	intron (NM_001164074, intron 1 of 2)	771	NM_001164074	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_101420.1	chr11	29547362	29547364	-	1	NA	promoter-TSS (NM_028504)	promoter-TSS (NM_028504)	-587	NM_028504	73324	Mm.69388	NM_028504	ENSMUSG00000020461	Clhc1	1700034F02Rik	clathrin heavy chain linker domain containing 1	protein-coding
mm_117405.1	chr13	73937656	73937715	-	1	NA	promoter-TSS (NM_027182)	promoter-TSS (NM_027182)	82	NM_027182	69716	Mm.275095	NM_027182	ENSMUSG00000021569	Trip13	2410002G23Rik|D13Ertd328e	thyroid hormone receptor interactor 13	protein-coding
mm_170722.1	chr2	148978472	148978480	-	1	NA	Intergenic	L1Md_T|LINE|L1	-102964	NM_009976	13010	Mm.4263	NM_009976	ENSMUSG00000027447	Cst3	CysC	cystatin C	protein-coding
mm_119594.1	chr14	50952298	50952300	+	1	NA	3' UTR (NM_013632, exon 6 of 6)	3' UTR (NM_013632, exon 6 of 6)	-3842	NM_001123371	667034	Mm.482171	NM_001123371	ENSMUSG00000068417	Pnp2	-	purine-nucleoside phosphorylase 2	protein-coding
mm_53997.1	chr6	7441739	7441742	-	1	NA	Intergenic	ERVB7_3-LTR_MM|LTR|ERVK	-113145	NM_001311060	21333	Mm.1440	NM_009311	ENSMUSG00000061762	Tac1	4930528L02Rik|NK-1|NK1|Nkna|PPT-A|PPTA|SP	tachykinin 1	protein-coding
mm_12789.1	chr2	79621606	79621635	+	1	NA	Intergenic	ORR1D2|LTR|ERVL-MaLR	-13805	NM_080558	70599	Mm.272881	NM_080558	ENSMUSG00000027007	Ssfa2	5730488C15Rik|CS-1|CS1|KRAP|SPAG13|mKIAA1927	sperm specific antigen 2	protein-coding
mm_29174.1	chr3	106516136	106516173	-	1	NA	intron (NM_133869, intron 4 of 8)	B3|SINE|B2	30114	NM_028110	72121	Mm.14816	NM_028110	ENSMUSG00000027901	Dennd2d	2010308M01Rik|AI451421	DENN/MADD domain containing 2D	protein-coding
mm_154947.1	chrX	36336702	36336714	+	1	NA	intron (NM_028894, intron 3 of 10)	(T)n|Simple_repeat|Simple_repeat	8299	NM_028894	74365	Mm.327654	NM_028894	ENSMUSG00000016239	Lonrf3	4932412G04Rik|5730439E01Rik|A830039N02Rik|AU023707|Rnf127	LON peptidase N-terminal domain and ring finger 3	protein-coding
mm_37776.1	chr4	129853212	129853250	-	1	NA	Intergenic	B1_Mur4|SINE|Alu	32523	NM_001164745	19244	Mm.193688	NM_008974	ENSMUSG00000028788	Ptp4a2	Prl-2	protein tyrosine phosphatase 4a2	protein-coding
mm_1890.1	chr1	85682409	85682421	+	1	NA	3' UTR (NM_001313714, exon 12 of 12)	3' UTR (NM_001313714, exon 12 of 12)	32427	NM_001313714	20684	Mm.290906	NM_013673	ENSMUSG00000026222	Sp100	A430075G10Rik	nuclear antigen Sp100	protein-coding
mm_60584.1	chr7	44482712	44482720	+	1	NA	Intergenic	Intergenic	-1801	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_142030.1	chr17	35235694	35235709	-	1	NA	promoter-TSS (NM_023179)	promoter-TSS (NM_023179)	114	NM_010909	18038	Mm.300795	NM_010909	ENSMUSG00000042419	Nfkbil1	Def-7|IKBL	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor like 1	protein-coding
mm_112857.1	chr13	20842037	20842048	+	1	NA	intron (NM_012054, intron 3 of 20)	intron (NM_012054, intron 3 of 20)	47929	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_38041.1	chr4	133910731	133910735	-	1	NA	Intergenic	CpG	-22936	NM_009097	20111	Mm.301827	NM_009097	ENSMUSG00000003644	Rps6ka1	Mapkapk-1a|Rsk|Rsk-1|Rsk1|S6K-alpha-1|p90-Rsk1|p90Rsk1|p90S6K|p90rsk	ribosomal protein S6 kinase polypeptide 1	protein-coding
mm_42035.1	chr5	108388438	108388440	+	1	NA	promoter-TSS (NM_008806)	promoter-TSS (NM_008806)	66	NM_008806	18587	Mm.1372	NM_008806	ENSMUSG00000029491	Pde6b	Pdeb|r|rd|rd-1|rd1|rd10	phosphodiesterase 6B, cGMP, rod receptor, beta polypeptide	protein-coding
mm_110028.1	chr12	16800945	16800955	-	1	NA	promoter-TSS (NM_015764)	promoter-TSS (NM_015764)	-64	NM_015764	268527	Mm.428062	NM_015764	ENSMUSG00000036523	Greb1	5730583K22Rik|9130004E13|AF180470|AU023194|mKIAA0575	gene regulated by estrogen in breast cancer protein	protein-coding
mm_122575.1	chr14	50826881	50826894	-	1	NA	exon (NM_009351, exon 51 of 55)	exon (NM_009351, exon 51 of 55)	18941	NM_009632	11546	Mm.281482	NM_009632	ENSMUSG00000036023	Parp2	ARTD2|Adprt2|Adprtl2|Aspartl2|C78626|PARP-2	poly (ADP-ribose) polymerase family, member 2	protein-coding
mm_25602.1	chr3	116906374	116906378	+	1	NA	Intergenic	Intergenic	44696	NM_009146	20321	Mm.66293	NM_009146	ENSMUSG00000033386	Frrs1	AI131732|Sdfr2	ferric-chelate reductase 1	protein-coding
mm_125638.1	chr15	62080020	62080024	+	1	NA	intron (NR_132746, intron 1 of 6)	intron (NR_132746, intron 1 of 6)	40765	NR_132746	19296	Mm.4608	NM_011222	ENSMUSG00000097039	Pvt1	Ayu21-84Imeg|Gt(pU21)84Imeg|Mis-1|Mlvi-1|Pvt-1	plasmacytoma variant translocation 1	ncRNA
mm_168246.1	chr10	81997001	81997008	+	1	NA	Intergenic	Intergenic	-51119	NM_001319203	408062	Mm.391409	NM_001024626	ENSMUSG00000061371	Zfp873	-	zinc finger protein 873	protein-coding
mm_93480.1	chr10	111995555	111995562	-	1	NA	intron (NM_028608, intron 1 of 5)	A-rich|Low_complexity|Low_complexity	1706	NM_028608	73690	Mm.173790	NM_028608	ENSMUSG00000056888	Glipr1	2410114O14Rik|RTVP-1|RTVP1|mRTVP-1	GLI pathogenesis-related 1 (glioma)	protein-coding
mm_24543.1	chr3	93293133	93293147	+	1	NA	Intergenic	Intergenic	-26609	NM_133698	68723	Mm.208047	NM_133698	ENSMUSG00000041991	Hrnr	1110033K19Rik|A530063N20Rik|S100a18	hornerin	protein-coding
mm_52413.1	chr6	113390716	113390716	+	1	NA	TTS (NM_026552)	TTS (NM_026552)	1456	NM_001142732	101100	Mm.388573	NM_133923	ENSMUSG00000030276	Ttll3	4833441J24Rik|AI450050	tubulin tyrosine ligase-like family, member 3	protein-coding
mm_163008.1	chr11	40364697	40364701	+	1	NA	Intergenic	(T)n|Simple_repeat|Simple_repeat	327983	NM_134017	108645	Mm.293771	NM_134017	ENSMUSG00000042032	Mat2b	1110064C04Rik|2410018D16Rik|AI182287|AU022853|MAT-II|MATIIbeta|TGR	methionine adenosyltransferase II, beta	protein-coding
mm_162435.1	chr1	105981112	105981120	+	1	NA	Intergenic	Intergenic	-9290	NM_001122676	227449	Mm.210188	NM_001122675	ENSMUSG00000038866	Zcchc2	9930114B20Rik|AW212015	zinc finger, CCHC domain containing 2	protein-coding
mm_4029.1	chr1	165769393	165769436	+	1	NA	intron (NM_011804, intron 1 of 3)	intron (NM_011804, intron 1 of 3)	5634	NM_011804	433375	Mm.294885	NM_011804	ENSMUSG00000040713	Creg1	AA755314|Creg	cellular repressor of E1A-stimulated genes 1	protein-coding
mm_46994.1	chr5	115334480	115334498	-	1	NA	3' UTR (NM_029645, exon 3 of 3)	3' UTR (NM_029645, exon 3 of 3)	6672	NM_029645	384281	Mm.229308	NM_029645	ENSMUSG00000029536	Gatc	2010003O18Rik	glutamyl-tRNA(Gln) amidotransferase, subunit C	protein-coding
mm_34640.1	chr4	150615956	150615970	+	1	NA	exon (NM_001085492, exon 19 of 23)	exon (NM_001085492, exon 19 of 23)	36211	NM_173774	242773	Mm.29280	NM_173774	ENSMUSG00000039838	Slc45a1	C230078B22|Dnb5	solute carrier family 45, member 1	protein-coding
mm_160827.1	chr11	43149835	43149835	+	1	NA	promoter-TSS (NM_176999)	promoter-TSS (NM_176999)	-42	NM_176999	319767	Mm.252339	NM_176999	ENSMUSG00000055415	Atp10b	5930426O13Rik|9030605H24Rik	ATPase, class V, type 10B	protein-coding
mm_148954.1	chr19	7297711	7297722	+	1	NA	intron (NM_007928, intron 1 of 17)	intron (NM_007928, intron 1 of 17)	-2269	NM_001080390	13728	Mm.258986	NM_007928	ENSMUSG00000024969	Mark2	EMK-1|Emk|Par-1|Par-1b	MAP/microtubule affinity regulating kinase 2	protein-coding
mm_130565.1	chr15	99406656	99406678	-	1	NA	exon (NM_026669, exon 8 of 10)	exon (NM_026669, exon 8 of 10)	13448	NM_001171035	110213	Mm.16769	NM_026669	ENSMUSG00000023010	Tmbim6	5031406P05Rik|Bi1|Tegt	transmembrane BAX inhibitor motif containing 6	protein-coding
mm_108555.1	chr12	84451486	84451518	+	1	NA	promoter-TSS (NM_134042)	promoter-TSS (NM_134042)	-6	NM_173756	217708	Mm.311904	NM_173756	ENSMUSG00000085793	Lin52	5830457H20Rik	lin-52 homolog (C. elegans)	protein-coding
mm_169483.1	chr14	73528153	73528158	-	1	NA	intron (NM_172527, intron 2 of 4)	RLTR1B|LTR|ERV1	18106	NM_026119	67381	Mm.282888	NM_026119	ENSMUSG00000022109	Med4	2410046H15Rik|DRIP36|HSPC126|TRAP36|Vdirp|Vdrip	mediator complex subunit 4	protein-coding
mm_19040.1	chr2	76982540	76982553	-	1	NA	promoter-TSS (NM_011652)	promoter-TSS (NM_011652)	1	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_163178.1	chr11	87931947	87931950	+	1	NA	Intergenic	Intergenic	-16945	NM_146412	258407	Mm.271337	NM_146412	ENSMUSG00000060787	Olfr464	MOR240-2	olfactory receptor 464	protein-coding
mm_83042.1	chr9	37430883	37430898	-	1	NA	intron (NM_001164767, intron 1 of 27)	intron (NM_001164767, intron 1 of 27)	2285	NM_001164767	19649	Mm.212826	NM_011248	ENSMUSG00000032128	Robo3	Rbig1|Rig-1|Rig1|Robo3a|Robo3b	roundabout guidance receptor 3	protein-coding
mm_52967.1	chr6	123138410	123138427	+	1	NA	intron (NM_011999, intron 3 of 5)	L1Md_A|LINE|L1	15102	NM_001170333	26888	Mm.47384	NM_011999	ENSMUSG00000030148	Clec4a2	Clec4a|Clecsf6|DCIR|Dcir1	C-type lectin domain family 4, member a2	protein-coding
mm_128295.1	chr15	37368316	37368326	-	1	NA	3' UTR (NM_001170868, exon 4 of 4)	3' UTR (NM_001170868, exon 4 of 4)	-57233	NM_029113	74892	Mm.107630	NM_029113	ENSMUSG00000022288	4930447A16Rik	-	RIKEN cDNA 4930447A16 gene	protein-coding
mm_23477.1	chr3	60481095	60481136	+	1	NA	intron (NM_001253713, intron 2 of 9)	PB1D10|SINE|Alu	8285	NM_001253713	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_160626.1	chr9	98903302	98903302	+	1	NA	exon (NM_001033983, exon 1 of 1)	exon (NM_001033983, exon 1 of 1)	183	NM_001033983	546157	Mm.380145	NM_001033983	ENSMUSG00000074123	7420426K07Rik	-	RIKEN cDNA 7420426K07 gene	protein-coding
mm_67521.1	chr7	80929455	80929458	-	1	NA	intron (NM_019951, intron 2 of 5)	intron (NM_019951, intron 2 of 5)	18094	NM_019951	56529	Mm.43760	NM_019951	ENSMUSG00000025724	Sec11a	1810012E07Rik|18kDa|Sec11l1|Sid2895p|Spc18|sid2895	SEC11 homolog A, signal peptidase complex subunit	protein-coding
mm_92362.1	chr10	75940005	75940023	-	1	NA	exon (NM_001277132, exon 3 of 7)	exon (NM_001277132, exon 3 of 7)	658	NM_001277132	333670	Mm.291320	NM_001037714	ENSMUSG00000050157	Gm867	Gm736	predicted gene 867	protein-coding
mm_56746.1	chr6	115935530	115935550	-	1	NA	exon (NM_145383, exon 4 of 5)	exon (NM_145383, exon 4 of 5)	3613	NM_145383	212541	Mm.2965	NM_145383	ENSMUSG00000030324	Rho	Noerg1|Opn2|Ops|RP4	rhodopsin	protein-coding
mm_127785.1	chr15	3542458	3542484	-	1	NA	intron (NM_001048178, intron 1 of 8)	Tigger7|DNA|TcMar-Tigger	39371	NM_001286370	14600	Mm.3986	NM_010284	ENSMUSG00000055737	Ghr	GHBP|GHR/BP	growth hormone receptor	protein-coding
mm_165363.1	chr2	124610069	124610131	+	1	NA	promoter-TSS (NM_199238)	promoter-TSS (NM_199238)	-196	NM_199238	214968	Mm.330536	NM_172537	ENSMUSG00000027200	Sema6d	1110067B02Rik|AA409156|D330011G23|mKIAA1479	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	protein-coding
mm_97406.1	chr11	77884679	77884695	+	1	NA	intron (NM_008952, intron 2 of 7)	intron (NM_008952, intron 2 of 7)	9185	NM_008952	19193	Mm.8543	NM_008952	ENSMUSG00000017453	Pipox	LPIPOX|Pso	pipecolic acid oxidase	protein-coding
mm_167945.1	chrX	134583078	134583088	-	1	NA	promoter-TSS (NM_013482)	promoter-TSS (NM_013482)	57	NM_013482	12229	Mm.4475	NM_013482	ENSMUSG00000031264	Btk	AI528679|xid	Bruton agammaglobulinemia tyrosine kinase	protein-coding
mm_109194.1	chr12	108606940	108606943	+	1	NA	intron (NM_001163395, intron 1 of 12)	intron (NM_001163395, intron 1 of 12)	1175	NM_001163395	14026	Mm.238841	NM_007965	ENSMUSG00000021262	Evl	AI528774	Ena-vasodilator stimulated phosphoprotein	protein-coding
mm_126777.1	chr15	86182816	86182850	+	1	NA	intron (NM_145475, intron 1 of 12)	intron (NM_145475, intron 1 of 12)	3308	NM_145475	223753	Mm.222685	NM_145475	ENSMUSG00000035891	Cerk	AI848610|D330016D08Rik|mKIAA1646	ceramide kinase	protein-coding
mm_13121.1	chr2	91664334	91664350	+	1	NA	intron (NR_027371, intron 5 of 13)	intron (NR_027371, intron 5 of 13)	11134	NM_146124	228359	Mm.22413	NM_146124	ENSMUSG00000027247	Arhgap1	B230365D05Rik|C76222|Cdc42GAP|p50rhoGAP	Rho GTPase activating protein 1	protein-coding
mm_154912.1	chrX	21484562	21484573	+	1	NA	promoter-TSS (NM_007429)	promoter-TSS (NM_007429)	-57	NM_007429	11609	Mm.2679	NM_007429	ENSMUSG00000068122	Agtr2	AI316812|AW107640	angiotensin II receptor, type 2	protein-coding
mm_145412.1	chr18	57658039	57658041	+	1	NA	intron (NM_001311063, intron 5 of 5)	PB1|SINE|Alu	-19455	NR_045360	70157	Mm.490532	NR_045360		2210409D07Rik	-	RIKEN cDNA 2210409D07 gene	ncRNA
mm_28445.1	chr3	90509518	90509528	-	1	NA	promoter-TSS (NM_001293782)	promoter-TSS (NM_001293782)	-25	NM_001293782	66511	Mm.154136	NM_023215	ENSMUSG00000001017	Chtop	2500003M10Rik|Fop|Srag	chromatin target of PRMT1	protein-coding
mm_77618.1	chr8	123925930	123925940	-	1	NA	intron (NM_172288, intron 12 of 25)	intron (NM_172288, intron 12 of 25)	23330	NM_172288	234865	Mm.267812	NM_172288	ENSMUSG00000039509	Nup133	mermaid	nucleoporin 133	protein-coding
mm_83720.1	chr9	50765905	50765923	-	1	NA	promoter-TSS (NM_001311073)	promoter-TSS (NM_001311073)	19	NM_001311073	68721	Mm.171374	NM_023483	ENSMUSG00000037971	1110032A03Rik	4930500N06Rik|c11orf1	RIKEN cDNA 1110032A03 gene	protein-coding
mm_6233.1	chr1	66944979	66944989	-	1	NA	promoter-TSS (NM_021285)	promoter-TSS (NM_021285)	72	NM_021285	17901	Mm.1000	NM_021285	ENSMUSG00000061816	Myl1	AI325107|MLC1f|MLC3f|Mylf	myosin, light polypeptide 1	protein-coding
mm_5318.1	chr1	22783544	22783567	-	1	NA	intron (NM_001012623, intron 1 of 14).2	intron (NM_001012623, intron 1 of 14).2	22169	NM_001012625	116837	Mm.60061	NM_053270	ENSMUSG00000041670	Rims1	C030033M19Rik|RIM1|RIM1a|RIM1alpha|Rab3ip1|Rim|Serg1|mKIAA0340	regulating synaptic membrane exocytosis 1	protein-coding
mm_33413.1	chr4	129906206	129906244	+	1	NA	promoter-TSS (NR_045190)	promoter-TSS (NR_045190)	-1	NR_045190	319894	Mm.59196	NR_045190	ENSMUSG00000086369	E330017L17Rik	-	RIKEN cDNA E330017L17 gene	ncRNA
mm_138181.1	chr17	34267503	34267512	+	1	NA	exon (NM_207105, exon 3 of 6)	exon (NM_207105, exon 3 of 6)	4280	NM_207105	14961	Mm.254067	NM_207105	ENSMUSG00000073421	H2-Ab1	AI845868|Abeta|H-2Ab|H2-Ab|I-Abeta|IAb|Ia-2|Ia2|Rmcs1	histocompatibility 2, class II antigen A, beta 1	protein-coding
mm_71444.1	chr8	46518442	46518467	+	1	NA	exon (NM_007981, exon 9 of 21)	exon (NM_007981, exon 9 of 21)	27488	NM_001302163	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_133241.1	chr16	77077180	77077197	+	1	NA	exon (NM_013918, exon 14 of 24)	exon (NM_013918, exon 14 of 24)	63119	NM_013918	30940	Mm.40986	NM_013918	ENSMUSG00000022867	Usp25	-	ubiquitin specific peptidase 25	protein-coding
mm_33803.1	chr4	134930919	134930929	+	1	NA	promoter-TSS (NM_026780)	promoter-TSS (NM_026780)	-56	NM_026780	68592	Mm.29989	NM_026780	ENSMUSG00000028821	Syf2	1110018L13Rik|Cbpin|D4Bwg1551e|Gcipip|Ntc31|mp29|p29	SYF2 homolog, RNA splicing factor (S. cerevisiae)	protein-coding
mm_163120.1	chr11	75650489	75650493	+	1	NA	Intergenic	Intergenic	-1018	NM_008659	17913	Mm.234502	NM_008659	ENSMUSG00000017774	Myo1c	C80397|MMIb|MYO1E|NMI|mm1beta|myr2	myosin IC	protein-coding
mm_98489.1	chr11	94951462	94951477	+	1	NA	intron (NM_007742, intron 50 of 50)	intron (NM_007742, intron 50 of 50)	15245	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_81172.1	chr9	107300041	107300047	+	1	NA	exon (NM_009895, exon 2 of 3)	exon (NM_009895, exon 2 of 3)	3385	NM_009895	12700	Mm.4592	NM_009895	ENSMUSG00000032578	Cish	CIS-1|CIS1|Cis|F17|F23|SOCS	cytokine inducible SH2-containing protein	protein-coding
mm_99513.1	chr11	103104756	103104768	+	1	NA	intron (NM_025988, intron 6 of 9)	intron (NM_025988, intron 6 of 9)	3074	NM_025988	67131	Mm.390367	NM_025988	ENSMUSG00000056938	Acbd4	2010009P05Rik|2010015A21Rik|AI849317	acyl-Coenzyme A binding domain containing 4	protein-coding
mm_124366.1	chr14	105859181	105859191	-	1	NA	Intergenic	Intergenic	37633	NM_011897	24064	Mm.89982	NM_011897	ENSMUSG00000022114	Spry2	sprouty2	sprouty homolog 2 (Drosophila)	protein-coding
mm_23419.1	chr3	58576653	58576717	+	1	NA	promoter-TSS (NM_001040396)	promoter-TSS (NM_001040396)	27	NM_001040396	69227	Mm.270950	NM_001040396	ENSMUSG00000075700	Selenot	2810407C02Rik|5730408P04Rik|Selt	selenoprotein T	protein-coding
mm_96503.1	chr11	68442621	68442640	+	1	NA	intron (NM_177320, intron 1 of 18)	intron (NM_177320, intron 1 of 18)	10505	NM_177320	320207	Mm.244960	NM_177320	ENSMUSG00000020901	Pik3r5	AV230647|F730038I15Rik	phosphoinositide-3-kinase, regulatory subunit 5, p101	protein-coding
mm_162014.1	chr19	44757336	44757336	+	1	NA	promoter-TSS (NM_011037)	promoter-TSS (NM_011037)	-58	NM_011037	18504	Mm.192158	NM_011037	ENSMUSG00000004231	Pax2	Opdc|Pax-2	paired box 2	protein-coding
mm_33609.1	chr4	132581484	132581511	+	1	NA	3' UTR (NM_001081211, exon 2 of 2)	3' UTR (NM_001081211, exon 2 of 2)	17430	NM_001081211	19204	Mm.89389	NM_001081211	ENSMUSG00000056529	Ptafr	PAFR	platelet-activating factor receptor	protein-coding
mm_3170.1	chr1	135687075	135687088	+	1	NA	Intergenic	Intergenic	-42116	NM_007791	13007	Mm.196484	NM_007791	ENSMUSG00000026421	Csrp1	AA408841|AA959891|AW545626|CRP1|Csrp	cysteine and glycine-rich protein 1	protein-coding
mm_106883.1	chr12	8011927	8011937	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	34255	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_28443.1	chr3	90508728	90508731	-	1	NA	intron (NM_001293777, intron 1 of 5)	ID2|SINE|ID	769	NM_001293776	66511	Mm.154136	NM_023215	ENSMUSG00000001017	Chtop	2500003M10Rik|Fop|Srag	chromatin target of PRMT1	protein-coding
mm_14838.1	chr2	147373910	147373919	+	1	NA	3' UTR (NM_008780, exon 5 of 5)	3' UTR (NM_008780, exon 5 of 5)	8920	NM_008780	18503	Mm.315502	NM_008780	ENSMUSG00000037034	Pax1	Pax-1|hbs|hunchback|un|undulated|wt	paired box 1	protein-coding
mm_56142.1	chr6	87807540	87807576	-	1	NA	intron (NR_104478, intron 1 of 2)	RSINE1|SINE|B4	2199	NM_133717	69834	Mm.37380	NM_133717	ENSMUSG00000030055	Rab43	1810048P08Rik|2500004H21Rik|AW490415	RAB43, member RAS oncogene family	protein-coding
mm_149565.1	chr19	12798575	12798589	+	1	NA	promoter-TSS (NM_134152)	promoter-TSS (NM_134152)	-27	NM_134152	107321	Mm.313136	NM_134152	ENSMUSG00000024696	Lpxn	4933402K05Rik|A530083L21Rik|AV278559|LDPL	leupaxin	protein-coding
mm_115627.1	chr13	12106671	12106703	-	1	NA	5' UTR (NM_023868, exon 1 of 105)	5' UTR (NM_023868, exon 1 of 105)	258	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding
mm_65750.1	chr7	28561045	28561054	-	1	NA	promoter-TSS (NR_106016)	promoter-TSS (NR_106016)	-65	NR_106016	102466795		NR_106016	ENSMUSG00000098558	Mir7049	Gm27277|mmu-mir-7049	microRNA 7049	ncRNA
mm_606.1	chr1	39904009	39904035	+	1	NA	intron (NM_001252200, intron 2 of 31)	intron (NM_001252200, intron 2 of 31)	3109	NM_008696	26921	Mm.491139	NM_008696	ENSMUSG00000026074	Map4k4	9430080K19Rik|AU043147|AU045934|AW046177|HGK|Nik	mitogen-activated protein kinase kinase kinase kinase 4	protein-coding
mm_164096.1	chr15	11762917	11762918	+	1	NA	Intergenic	Intergenic	142757	NM_008728	18162	Mm.25259	NM_008728	ENSMUSG00000022206	Npr3	ANP-C|ANPR-C|EF-2|NPR-C|lgj|stri	natriuretic peptide receptor 3	protein-coding
mm_121399.1	chr14	119156037	119156040	+	1	NA	intron (NM_015820, intron 1 of 1)	intron (NM_015820, intron 1 of 1)	17773	NM_015820	50787	Mm.445777	NM_015820	ENSMUSG00000053465	Hs6st3	6OST3|HS6ST-3	heparan sulfate 6-O-sulfotransferase 3	protein-coding
mm_126676.1	chr15	84669566	84669609	+	1	NA	intron (NM_001346662, intron 1 of 8)	intron (NM_001346662, intron 1 of 8)	6381	NM_001346662	109270	Mm.291372	NM_146061	ENSMUSG00000036106	Prr5	AU043908|Arhgap8|C030017C09Rik|C78947|Protor-1|Protor1	proline rich 5 (renal)	protein-coding
mm_32533.1	chr4	109000810	109000864	+	1	NA	promoter-TSS (NM_146150)	promoter-TSS (NM_146150)	32	NM_146150	230598	Mm.274950	NM_146150	ENSMUSG00000053510	Nrd1	2600011I06Rik|AI875733|NRD-C|Nrdc	nardilysin, N-arginine dibasic convertase, NRD convertase 1	protein-coding
mm_83017.1	chr9	36785981	36785998	-	1	NA	exon (NM_001199494, exon 6 of 11)	exon (NM_001199494, exon 6 of 11)	11079	NM_007915	13663	Mm.4337	NM_007915	ENSMUSG00000062762	Ei24	AA536736|AI115355|PIG8	etoposide induced 2.4 mRNA	protein-coding
mm_87679.1	chr10	59221946	59221960	+	1	NA	promoter-TSS (NM_001024910)	promoter-TSS (NM_001024910)	31	NM_172939	268301	Mm.3036	NM_172939	ENSMUSG00000098188	Sowahc	4921515A04Rik|9430099J10Rik|Ankrd57|C820004L04Rik	sosondowah ankyrin repeat domain family member C	protein-coding
mm_95917.1	chr11	58220678	58220714	+	1	NA	3' UTR (NM_019440, exon 2 of 2)	3' UTR (NM_019440, exon 2 of 2)	5719	NM_019440	54396	Mm.458517	NM_019440	ENSMUSG00000069874	Irgm2	AI481100|GTPI|Ifggd2|Iigp2	immunity-related GTPase family M member 2	protein-coding
mm_38829.1	chr4	149137537	149137595	-	1	NA	promoter-TSS (NM_027263)	promoter-TSS (NM_027263)	34	NM_027263	69928	Mm.260893	NM_027263	ENSMUSG00000073705	Apitd1	2610040C18Rik|2810407L01Rik|CENP-S	apoptosis-inducing, TAF9-like domain 1	protein-coding
mm_119227.1	chr14	33250539	33250553	+	1	NA	intron (NM_153800, intron 2 of 10)	intron (NM_153800, intron 2 of 10)	33723	NM_153800	239027	Mm.318350	NM_153800	ENSMUSG00000063506	Arhgap22	B230341L19Rik|RHOGAP2|p68RacGAP	Rho GTPase activating protein 22	protein-coding
mm_103664.1	chr11	79059795	79059810	-	1	NA	intron (NM_013571, intron 2 of 17)	intron (NM_013571, intron 2 of 17)	36205	NR_045873	790910	Mm.440410	NR_045873		Gm11201	ENSMUSG00000072637|OTTMUSG00000000169	predicted gene 11201	ncRNA
mm_25869.1	chr3	129901469	129901490	+	1	NA	promoter-TSS (NM_009811)	promoter-TSS (NM_009811)	64	NM_009811	12368	Mm.281379	NM_009811	ENSMUSG00000027997	Casp6	CASP-6|Mch2	caspase 6	protein-coding
mm_69901.1	chr7	141639046	141639052	-	1	NA	intron (NM_001330001, intron 31 of 33)	intron (NM_001330001, intron 31 of 33)	16270	NM_001330001	353328	Mm.246621	NM_181729	ENSMUSG00000048191	Muc6	-	mucin 6, gastric	protein-coding
mm_61591.1	chr7	80025302	80025320	+	1	NA	promoter-TSS (NM_175433)	promoter-TSS (NM_175433)	497	NM_001146000	209225	Mm.290925	NM_175433	ENSMUSG00000048897	Zfp710	5430400N05Rik|9830165K13|AI324798|Znf710	zinc finger protein 710	protein-coding
mm_128109.1	chr15	28025835	28025879	-	1	NA	promoter-TSS (NM_001081302)	promoter-TSS (NM_001081302)	-9	NM_001081302	223435	Mm.485422	NM_001081302	ENSMUSG00000022263	Trio	6720464I07Rik|AA408740|Solo	triple functional domain (PTPRF interacting)	protein-coding
mm_35087.1	chr4	7912032	7912042	-	1	NA	Intergenic	Intergenic	327004	NM_007592	12319	Mm.119320	NM_007592	ENSMUSG00000041261	Car8	AW546993|Ca8|Cals|Cals1|Carp|wdl	carbonic anhydrase 8	protein-coding
mm_69584.1	chr7	135704641	135704661	-	1	NA	exon (NM_001081117, exon 8 of 14)	exon (NM_001081117, exon 8 of 14)	11728	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_58149.1	chr6	142322979	142323007	-	1	NA	promoter-TSS (NM_130861)	promoter-TSS (NM_130861)	-12	NM_130861	108096	Mm.206599	NM_130861	ENSMUSG00000063975	Slco1a5	Oatp-3|Oatp3|Slc21a7	solute carrier organic anion transporter family, member 1a5	protein-coding
mm_161892.1	chr18	42300358	42300358	+	1	NA	exon (NM_172626, exon 6 of 20)	exon (NM_172626, exon 6 of 20)	25005	NM_172626	225432	Mm.329400	NM_172626	ENSMUSG00000024491	Rbm27	A730010I06|AI043120|Psc1|mKIAA1311	RNA binding motif protein 27	protein-coding
mm_77449.1	chr8	121805327	121805338	-	1	NA	intron (NM_145605, intron 6 of 11)	intron (NM_145605, intron 6 of 11)	24237	NM_145605	234825	Mm.209329	NM_145605	ENSMUSG00000040263	Klhdc4	AA408426|AV352552|BC012312|G430025P05Rik	kelch domain containing 4	protein-coding
mm_65669.1	chr7	28291118	28291128	-	1	NA	promoter-TSS (NM_175033)	promoter-TSS (NM_175033)	11	NM_175033	280621	Mm.212777	NM_175033	ENSMUSG00000046750	Selenov	Selv	selenoprotein V	protein-coding
mm_147390.1	chr18	44175050	44175050	-	1	NA	promoter-TSS (NM_183123)	promoter-TSS (NM_183123)	23	NM_183123	77424	Mm.99224	NM_183123	ENSMUSG00000053729	Spinkl	9530002K18Rik	serine protease inhibitor, Kazal type-like	protein-coding
mm_43351.1	chr5	135168526	135168534	+	1	NA	exon (NM_009745, exon 1 of 6)	exon (NM_009745, exon 1 of 6)	158	NM_009745	12054	Mm.405834	NM_009745	ENSMUSG00000029681	Bcl7b	-	B cell CLL/lymphoma 7B	protein-coding
mm_74154.1	chr8	123381490	123381502	+	1	NA	exon (NM_001037877, exon 2 of 18)	exon (NM_001037877, exon 2 of 18)	7785	NM_001286363	66855	Mm.178818	NM_025804	ENSMUSG00000001472	Tcf25	1100001J13Rik|1810041K11Rik|D8Ertd325e|Nulp1|mKIAA1049	transcription factor 25 (basic helix-loop-helix)	protein-coding
mm_115234.1	chr13	109903367	109903381	+	1	NA	promoter-TSS (NR_035442)	promoter-TSS (NR_035442)	-435	NR_035442	100316683		NR_035442	ENSMUSG00000084651	Mir1904	Mirn1904|mmu-mir-1904	microRNA 1904	ncRNA
mm_105106.1	chr11	100969723	100969756	-	1	NA	intron (NM_008986, intron 1 of 1)	CpG	878	NM_008986	19285	Mm.21864	NM_008986	ENSMUSG00000004044	Ptrf	2310075E07Rik|AW546441|Cav-p60|Cavin	polymerase I and transcript release factor	protein-coding
mm_699.1	chr1	40600914	40600949	+	1	NA	exon (NM_177084, exon 3 of 12)	exon (NM_177084, exon 3 of 12)	20704	NM_177084	110895	Mm.108602	NM_177084	ENSMUSG00000026065	Slc9a4	AW990558|D730009J23Rik|NHE4	solute carrier family 9 (sodium/hydrogen exchanger), member 4	protein-coding
mm_31901.1	chr4	83597279	83597287	+	1	NA	intron (NM_001081012, intron 7 of 25)	intron (NM_001081012, intron 7 of 25)	71738	NM_001081012	320226	Mm.180032	NM_029117	ENSMUSG00000052407	Ccdc171	4930418J05Rik|4930473A06Rik|A330015D16Rik	coiled-coil domain containing 171	protein-coding
mm_44302.1	chr5	8996643	8996647	-	1	NA	intron (NM_023733, intron 1 of 17)	intron (NM_023733, intron 1 of 17)	501	NM_023733	74114	Mm.28197	NM_023733	ENSMUSG00000003623	Crot	1200003H03Rik	carnitine O-octanoyltransferase	protein-coding
mm_77496.1	chr8	122596093	122596111	-	1	NA	intron (NM_001193645, intron 8 of 11)	intron (NM_001193645, intron 8 of 11)	15385	NM_001193645	50917	Mm.1786	NM_016722	ENSMUSG00000015027	Galns	mFLJ00319	galactosamine (N-acetyl)-6-sulfate sulfatase	protein-coding
mm_130916.1	chr15	102625437	102625499	-	1	NA	promoter-TSS (NM_001310070)	promoter-TSS (NM_001310070)	-4	NM_001310066	223922	Mm.208714	NM_146065	ENSMUSG00000052414	Atf7	1110012F10Rik|9430065F09Rik|AI549878|C130020M04Rik	activating transcription factor 7	protein-coding
mm_142682.1	chr17	47733056	47733077	-	1	NA	exon (NM_025973, exon 7 of 9)	exon (NM_025973, exon 7 of 9)	-3971	NM_001161722	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_116391.1	chr13	41194793	41194803	-	1	NA	exon (NM_019423, exon 3 of 8)	exon (NM_019423, exon 3 of 8)	25364	NM_001311121	54326	Mm.2567	NM_019423	ENSMUSG00000021364	Elovl2	AI317360|Ssc2	elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 2	protein-coding
mm_85086.1	chr9	91368153	91368173	-	1	NA	promoter-TSS (NM_009576)	promoter-TSS (NM_009576)	-809	NM_009576	22774	Mm.8062	NM_009576	ENSMUSG00000036972	Zic4	-	zinc finger protein of the cerebellum 4	protein-coding
mm_22979.1	chr3	32817607	32817637	+	1	NA	promoter-TSS (NM_001013024)	promoter-TSS (NM_001013024)	-4	NM_001013024	72607	Mm.316153	NM_001013024	ENSMUSG00000056900	Usp13	2700071E21Rik|AI848077|ISOT3|IsoT-3	ubiquitin specific peptidase 13 (isopeptidase T-3)	protein-coding
mm_34492.1	chr4	148591924	148591975	+	1	NA	intron (NM_009272, intron 1 of 6)	CpG	436	NM_009272	20810	Mm.10	NM_009272	ENSMUSG00000006442	Srm	AA407669|SpdST|SpdSy	spermidine synthase	protein-coding
mm_155758.1	chrX	96167728	96167740	+	1	NA	3' UTR (NM_010833, exon 13 of 13)	3' UTR (NM_010833, exon 13 of 13)	71689	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_80517.1	chr9	80066940	80066983	+	1	NA	promoter-TSS (NM_146003)	promoter-TSS (NM_146003)	58	NM_146003	215351	Mm.28232	NM_146003	ENSMUSG00000034252	Senp6	2810017C20Rik|E130319N12Rik|Susp1|mKIAA0797	SUMO/sentrin specific peptidase 6	protein-coding
mm_60496.1	chr7	44478842	44478866	+	1	NA	Intergenic	L1M4c|LINE|L1	-5663	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_104391.1	chr11	94486225	94486234	-	1	NA	promoter-TSS (NM_144827)	promoter-TSS (NM_144827)	-919	NM_144827	217116	Mm.156123	NM_144827	ENSMUSG00000020867	Spata20	Tisp78	spermatogenesis associated 20	protein-coding
mm_165355.1	chr2	121405147	121405147	+	1	NA	intron (NM_153075, intron 7 of 12)	intron (NM_153075, intron 7 of 12)	8645	NM_153075	212670	Mm.384318	NM_153075	ENSMUSG00000033486	Catsper2	-	cation channel, sperm associated 2	protein-coding
mm_64198.1	chr7	141468333	141468393	+	1	NA	promoter-TSS (NM_001111050)	promoter-TSS (NM_001111050)	-426	NM_001111050	12476	Mm.30246	NM_009842	ENSMUSG00000025510	Cd151	PETA-3|SFA-1|Tspan24	CD151 antigen	protein-coding
mm_166140.1	chr4	156245454	156245470	+	1	NA	exon (NM_021303, exon 16 of 19)	exon (NM_021303, exon 16 of 19)	9452	NM_021303	57741	Mm.423051	NM_021303	ENSMUSG00000095567	Noc2l	AA410003|AF155546|NIR	NOC2 like nucleolar associated transcriptional repressor	protein-coding
mm_171644.1	chr4	32964835	32964835	+	1	NA	Intergenic	Intergenic	-14009	NM_001012451	140577	Mm.214766	NM_080471	ENSMUSG00000040183	Ankrd6	-	ankyrin repeat domain 6	protein-coding
mm_74835.1	chr8	23208408	23208412	-	1	NA	promoter-TSS (NM_018743)	promoter-TSS (NM_018743)	43	NM_018743	102247	Mm.200898	NM_018743	ENSMUSG00000031545	Gpat4	AU041707|AW545732|Agpat6|Tsarg7	glycerol-3-phosphate acyltransferase 4	protein-coding
mm_148847.1	chr19	6376539	6376558	+	1	NA	non-coding (NR_122118, exon 12 of 12)	non-coding (NR_122118, exon 12 of 12)	-7860	NM_011224	19309	Mm.27806	NM_011224	ENSMUSG00000032648	Pygm	AI115133|PG	muscle glycogen phosphorylase	protein-coding
mm_17853.1	chr2	34755230	34755252	-	1	NA	promoter-TSS (NM_025709)	promoter-TSS (NM_025709)	-9	NM_025709	66691	Mm.156452	NM_025709	ENSMUSG00000026867	Gapvd1	2010005B09Rik|4432404J10Rik|AW108497|Gapex-5|RAP6|RME-6|mKIAA1521	GTPase activating protein and VPS9 domains 1	protein-coding
mm_126284.1	chr15	79229141	79229162	+	1	NA	promoter-TSS (NM_008837)	promoter-TSS (NM_008837)	-22	NM_008837	18693	Mm.259464	NM_008837	ENSMUSG00000068206	Pick1	Prkcabp	protein interacting with C kinase 1	protein-coding
mm_19895.1	chr2	114052060	114052071	-	1	NA	intron (NM_009608, intron 1 of 6)	intron (NM_009608, intron 1 of 6)	810	NM_009608	11464	Mm.686	NM_009608	ENSMUSG00000068614	Actc1	Actc-1	actin, alpha, cardiac muscle 1	protein-coding
mm_131088.1	chr16	4886136	4886150	+	1	NA	promoter-TSS (NM_029657)	promoter-TSS (NM_029657)	43	NM_001252437	17237	Mm.291326	NM_029657	ENSMUSG00000022517	Mgrn1	2610042J20Rik|mKIAA0544|md|nc	mahogunin, ring finger 1	protein-coding
mm_113034.1	chr13	23533870	23533882	+	1	NA	promoter-TSS (NM_175661)	promoter-TSS (NM_175661)	-35	NM_175661	319173	Mm.377878	NM_175661	ENSMUSG00000061991	Hist1h2af	H2a-221	histone cluster 1, H2af	protein-coding
mm_173192.1	chrX	62072545	62072545	-	1	NA	Intergenic	Intergenic	-210954	NM_001199997	74437	Mm.85792	NM_001199996	ENSMUSG00000045330	4933402E13Rik	-	RIKEN cDNA 4933402E13 gene	protein-coding
mm_5917.1	chr1	55087826	55087885	-	1	NA	promoter-TSS (NM_010477)	promoter-TSS (NM_010477)	77	NM_010477	15510	Mm.1777	NM_010477	ENSMUSG00000025980	Hspd1	60kDa|Hsp60	heat shock protein 1 (chaperonin)	protein-coding
mm_169638.1	chr15	47548609	47548623	+	1	NA	Intergenic	L1Md_T|LINE|L1	925311	NR_045811	75281	Mm.159487	NR_045811	ENSMUSG00000051198	4930548G14Rik	-	RIKEN cDNA 4930548G14 gene	ncRNA
mm_13033.1	chr2	91054208	91054239	+	1	NA	5' UTR (NM_008948, exon 1 of 12)	5' UTR (NM_008948, exon 1 of 12)	207	NM_008948	19182	Mm.289832	NM_008948	ENSMUSG00000002102	Psmc3	TBP-1	proteasome (prosome, macropain) 26S subunit, ATPase 3	protein-coding
mm_75305.1	chr8	41133652	41133663	-	1	NA	promoter-TSS (NM_001005863)	promoter-TSS (NM_001005863)	69	NM_001005863	102103	Mm.149438	NM_001005863	ENSMUSG00000045636	Mtus1	AI481402|ATBP135|Atip1|B430010I23Rik|B430305I03Rik|C85752|Cctsg1-440|MD44|MTSG1|mKIAA1288	mitochondrial tumor suppressor 1	protein-coding
mm_50643.1	chr6	51432824	51432834	+	1	NA	5' UTR (NM_010903, exon 1 of 4)	5' UTR (NM_010903, exon 1 of 4)	159	NM_010903	18025	Mm.42138	NM_010903	ENSMUSG00000029832	Nfe2l3	Nrf3	nuclear factor, erythroid derived 2, like 3	protein-coding
mm_28320.1	chr3	89322884	89322946	-	1	NA	promoter-TSS (NM_010108)	promoter-TSS (NM_010108)	-36	NM_010108	13638	Mm.331159	NM_010108	ENSMUSG00000028039	Efna3	AW494418|EFL-2|Ehk1-L|Epl3|LERK-3	ephrin A3	protein-coding
mm_37160.1	chr4	117133954	117133969	-	1	NA	promoter-TSS (NM_013807)	promoter-TSS (NM_013807)	2	NM_013807	12795	Mm.259022	NM_013807	ENSMUSG00000028680	Plk3	Cnk|Fnk|PLK-3|PRK	polo-like kinase 3	protein-coding
mm_3162.1	chr1	135232537	135232559	+	1	NA	Intergenic	Intergenic	25924	NM_001163131	13710	Mm.441439	NM_007921	ENSMUSG00000003051	Elf3	ESE-1|ESX|jen	E74-like factor 3	protein-coding
mm_148025.1	chr18	68704412	68704433	-	1	NA	Intergenic	Intergenic	-34978	NR_105774	102465183		NR_105774	ENSMUSG00000099300	Mir6356	Gm27461|mmu-mir-6356	microRNA 6356	ncRNA
mm_92031.1	chr10	62477924	62477928	-	1	NA	intron (NM_133672, intron 2 of 8)	intron (NM_133672, intron 2 of 8)	8672	NM_001113355	30930	Mm.260703	NM_133672	ENSMUSG00000020078	Vps26a	AA407240|HB58|Vps26	VPS26 retromer complex component A	protein-coding
mm_39113.1	chr4	154928546	154928571	-	1	NA	promoter-TSS (NM_178931)	promoter-TSS (NM_178931)	-481	NM_178931	230979	Mm.215147	NM_178931	ENSMUSG00000042333	Tnfrsf14	Atar|HveA|Hvem|Tnfrs14	tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)	protein-coding
mm_86267.1	chr9	121705523	121705539	-	1	NA	promoter-TSS (NM_178677)	promoter-TSS (NM_178677)	-502	NM_178677	215474	Mm.31421	NM_178677	ENSMUSG00000061536	Sec22c	4932412K21|5930407I15Rik|C530046H07|Sec22l3	SEC22 homolog C, vesicle trafficking protein	protein-coding
mm_16007.1	chr2	167375342	167375354	+	1	NA	Intergenic	Intergenic	-26170	NM_019835	56336	Mm.200886	NM_019835	ENSMUSG00000017929	B4galt5	9430078I07Rik|AW049941|AW539721	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 5	protein-coding
mm_43627.1	chr5	138172142	138172188	+	1	NA	promoter-TSS (NM_008568)	promoter-TSS (NM_008568)	144	NM_021392	11781	Mm.113205	NM_021392	ENSMUSG00000019518	Ap4m1	4930443L05Rik|Ap4m4	adaptor-related protein complex AP-4, mu 1	protein-coding
mm_84778.1	chr9	75683993	75684046	-	1	NA	promoter-TSS (NM_001164790)	promoter-TSS (NM_001164790)	37	NM_001164790	20255	Mm.2386	NM_009130	ENSMUSG00000032181	Scg3	1B1075|AI385542|Chgd|SgIII	secretogranin III	protein-coding
mm_130802.1	chr15	101707582	101707593	-	1	NA	exon (NM_027011, exon 9 of 9)	exon (NM_027011, exon 9 of 9)	5304	NM_027011	110308	Mm.451847	NM_027011	ENSMUSG00000061527	Krt5	3300001P10Rik|AW146334|CK5|K5|Krt2-5|Tfip8	keratin 5	protein-coding
mm_56078.1	chr6	87228699	87228714	-	1	NA	intron (NM_054041, intron 12 of 17)	RSINE1|SINE|B4	107069	NM_054041	69538	Mm.232525	NM_054041	ENSMUSG00000033420	Antxr1	2310008J16Rik|2810405N18Rik|Antrx1|Tem8	anthrax toxin receptor 1	protein-coding
mm_80667.1	chr9	90163009	90163037	+	1	NA	promoter-TSS (NM_001326351)	promoter-TSS (NM_001326351)	45	NM_001311115	108153	Mm.102141	NM_001003911	ENSMUSG00000032363	Adamts7	ADAM-TS7|ADAMTS7B	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 7	protein-coding
mm_71909.1	chr8	70083471	70083473	+	1	NA	promoter-TSS (NM_177900)	promoter-TSS (NM_177900)	-57	NM_177900	330790	Mm.152048	NM_177900	ENSMUSG00000007594	Hapln4	9330174O11|Bral2|Lpr4	hyaluronan and proteoglycan link protein 4	protein-coding
mm_133934.1	chr16	3872287	3872315	-	1	NA	promoter-TSS (NM_001033159)	promoter-TSS (NM_001033159)	73	NM_001033159	71063	Mm.379190	NM_001033159	ENSMUSG00000039789	Zfp597	4933407K12Rik|AI462383|AI666357	zinc finger protein 597	protein-coding
mm_124447.1	chr14	118917508	118917534	-	1	NA	intron (NR_130725, intron 2 of 20)	intron (NR_130725, intron 2 of 20)	5646	NR_130725	66573	Mm.87456	NM_025943	ENSMUSG00000042156	Dzip1	2510025K24Rik|2810422M04Rik	DAZ interacting protein 1	protein-coding
mm_150570.1	chr19	40113435	40113477	+	1	NA	exon (NM_001167875, exon 8 of 8)	exon (NM_001167875, exon 8 of 8)	23777	NM_001167875	107141	Mm.474575	NM_134144	ENSMUSG00000054827	Cyp2c50	AI266900	cytochrome P450, family 2, subfamily c, polypeptide 50	protein-coding
mm_78493.1	chr9	32716760	32716761	+	1	NA	intron (NM_011808, intron 1 of 7)	L3|LINE|CR1	20718	NM_001038642	23871	Mm.292415	NM_011808	ENSMUSG00000032035	Ets1	AI196000|AI448617|D230050P06|Ets-1|Tpl1|vs	E26 avian leukemia oncogene 1, 5' domain	protein-coding
mm_147449.1	chr18	46557913	46557933	-	1	NA	TTS (NM_173394)	TTS (NM_173394)	16610	NM_173394	225471	Mm.149280	NM_173394	ENSMUSG00000056130	Ticam2	B430113A10|TICAM-2|TRAM|Tirp|Trif	toll-like receptor adaptor molecule 2	protein-coding
mm_1951.1	chr1	86356553	86356633	+	1	NA	promoter-TSS (NR_002851)	promoter-TSS (NR_002851)	-266	NR_002851	80828		NR_002851	ENSMUSG00000064823	Snord82	Rnu82|U82|Z25	small nucleolar RNA, C/D box 82	snoRNA
mm_170839.1	chr2	177272334	177272348	-	1	NA	Intergenic	Intergenic	-192401	NM_001177568	628308	Mm.460436	NM_001177568	ENSMUSG00000078866	Zfp970	Gm14420|OTTMUSG00000016588	zinc finger protein 970	protein-coding
mm_170286.1	chr18	29195645	29195662	+	1	NA	Intergenic	L1Md_T|LINE|L1	-246547	NR_045395	78199	Mm.243850	NR_045395		4930527G23Rik	-	RIKEN cDNA 4930527G23 gene	ncRNA
mm_149199.1	chr19	9975173	9975202	+	1	NA	Intergenic	Intergenic	-5413	NR_073181	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
mm_23580.1	chr3	63382959	63382964	+	1	NA	3' UTR (NM_008604, exon 23 of 23)	3' UTR (NM_008604, exon 23 of 23)	86866	NM_001289463	17380	Mm.296022	NM_008604	ENSMUSG00000027820	Mme	6030454K05Rik|C85356|CALLA|CD10|NEP|SFE	membrane metallo endopeptidase	protein-coding
mm_157388.1	chrX	38252448	38252465	-	1	NA	promoter-TSS (NM_001289728)	promoter-TSS (NM_001289728)	25	NM_001289727	245386	Mm.72979	NM_172930	ENSMUSG00000036502	Tmem255a	4933417N17|6430550H21Rik|Fam70a	transmembrane protein 255A	protein-coding
mm_108265.1	chr12	78723541	78723543	+	1	NA	intron (NM_027597, intron 6 of 7)	intron (NM_027597, intron 6 of 7)	-25405	NM_019579	56217	Mm.425777	NM_019579	ENSMUSG00000021112	Mpp5	3830420B02Rik|AI255216|AI644496|Pals1	membrane protein, palmitoylated 5 (MAGUK p55 subfamily member 5)	protein-coding
mm_29090.1	chr3	104638430	104638442	-	1	NA	promoter-TSS (NM_009196)	promoter-TSS (NM_009196)	-228	NM_009196	20501	Mm.9086	NM_009196	ENSMUSG00000032902	Slc16a1	AL022710|Mct1	solute carrier family 16 (monocarboxylic acid transporters), member 1	protein-coding
mm_868.1	chr1	52152292	52152303	+	1	NA	exon (NM_001205314, exon 21 of 25)	exon (NM_001205314, exon 21 of 25)	32675	NM_001205313	20846	Mm.277406	NM_009283	ENSMUSG00000026104	Stat1	2010005J02Rik|AA408197	signal transducer and activator of transcription 1	protein-coding
mm_11283.1	chr2	30066489	30066530	+	1	NA	promoter-TSS (NM_001204875)	promoter-TSS (NM_001204875)	35	NM_001204875	56086	Mm.326055	NM_023871	ENSMUSG00000054766	Set	2610030F17Rik|5730420M11Rik|AA407739|I-2PP2A|StF-IT-1|TAF-I	SET nuclear oncogene	protein-coding
mm_171827.1	chr5	14401668	14401668	-	1	NA	Intergenic	L1Md_T|LINE|L1	-113250	NM_011995	26875	Mm.146275	NM_011995	ENSMUSG00000061601	Pclo	Acz|Pico	piccolo (presynaptic cytomatrix protein)	protein-coding
mm_60063.1	chr7	31208371	31208390	+	1	NA	Intergenic	CpG	46022	NR_046062	100038516	Mm.387223	NR_046062	ENSMUSG00000100985	Gm10640	EG668322|ENSMUSG00000074193	predicted gene 10640	ncRNA
mm_139199.1	chr17	47658010	47658014	+	1	NA	intron (NM_198421, intron 2 of 6)	intron (NM_198421, intron 2 of 6)	27322	NM_198421	224836	Mm.59393	NM_198421	ENSMUSG00000090115	Usp49	C330046L10Rik|Gm545	ubiquitin specific peptidase 49	protein-coding
mm_106343.1	chr11	118393303	118393305	-	1	NA	exon (NM_011150, exon 6 of 6)	exon (NM_011150, exon 6 of 6)	8627	NM_011150	19039	Mm.3152	NM_011150	ENSMUSG00000033880	Lgals3bp	90K|CyCAP|MAC-2BP|Ppicap|Tango10b	lectin, galactoside-binding, soluble, 3 binding protein	protein-coding
mm_44027.1	chr5	147430291	147430302	+	1	NA	promoter-TSS (NM_028291)	promoter-TSS (NM_028291)	-284	NM_028291	72587	Mm.320469	NM_028291	ENSMUSG00000029647	Pan3	2700050F09Rik|A430027N15Rik|AU014670	PAN3 poly(A) specific ribonuclease subunit	protein-coding
mm_72523.1	chr8	83976867	83976878	+	1	NA	promoter-TSS (NM_001277898)	promoter-TSS (NM_001277898)	-11	NM_001277898	18747	Mm.19111	NM_008854	ENSMUSG00000005469	Prkaca	PKCD|Pkaca	protein kinase, cAMP dependent, catalytic, alpha	protein-coding
mm_153130.1	chr19	34192583	34192620	-	1	NA	5' UTR (NM_029682, exon 1 of 11)	5' UTR (NM_029682, exon 1 of 11)	331	NM_029682	76630	Mm.130952	NM_029682	ENSMUSG00000024776	Stambpl1	1700095N21Rik|8230401J17Rik|ALMalpha|AMSH-FP	STAM binding protein like 1	protein-coding
mm_58670.1	chr7	7277990	7278000	+	1	NA	intron (NR_003555, intron 1 of 6)	CpG	294	NR_003555	76229	Mm.387947	NM_001113468	ENSMUSG00000095730	Vmn2r29	6430701C03Rik	vomeronasal 2, receptor 29	protein-coding
mm_65402.1	chr7	25206528	25206538	-	1	NA	intron (NM_207677, intron 4 of 4)	MIR|SINE|MIR	11192	NR_106015	102466794		NR_106015	ENSMUSG00000098325	Mir7048	Gm27274|mmu-mir-7048	microRNA 7048	ncRNA
mm_54796.1	chr6	41680809	41680818	-	1	NA	promoter-TSS (NM_001007572)	promoter-TSS (NM_001007572)	-90	NM_001007572	194352	Mm.135734	NM_001007572	ENSMUSG00000036899	Trpv5	CAT2|D630033B11|ECAC1	transient receptor potential cation channel, subfamily V, member 5	protein-coding
mm_173199.1	chrX	65784627	65784632	-	1	NA	Intergenic	LTRIS2|LTR|ERV1	736985	NM_027302	70062	Mm.45791	NM_027302	ENSMUSG00000031181	Ctag2	1700030B21Rik	cancer/testis antigen 2	protein-coding
mm_80102.1	chr9	70321386	70321394	+	1	NA	intron (NM_181072, intron 6 of 27)	intron (NM_181072, intron 6 of 27)	84363	NR_049200	100885839		NR_049200	ENSMUSG00000093763	Mir5626	Gm25590|mir-5626|mmu-mir-5626	microRNA 5626	ncRNA
mm_64414.1	chr7	142533547	142533573	+	1	NA	intron (NM_011288, intron 1 of 4)	intron (NM_011288, intron 1 of 4)	443	NM_011288	19935	Mm.12144	NM_011288	ENSMUSG00000037772	Mrpl23	L23mrp|Rpl23|Rpl23l	mitochondrial ribosomal protein L23	protein-coding
mm_15039.1	chr2	152802460	152802463	+	1	NA	intron (NM_001289717, intron 2 of 2)	intron (NM_001289717, intron 2 of 2)	28256	NM_001289716	12048	Mm.238213	NM_009743	ENSMUSG00000007659	Bcl2l1	Bcl(X)L|Bcl-XL|Bcl2l|BclX|bcl-x|bcl2-L-1	BCL2-like 1	protein-coding
mm_8087.1	chr1	135660265	135660277	-	1	NA	Intergenic	Intergenic	-68926	NM_007791	13007	Mm.196484	NM_007791	ENSMUSG00000026421	Csrp1	AA408841|AA959891|AW545626|CRP1|Csrp	cysteine and glycine-rich protein 1	protein-coding
mm_16457.1	chr2	180582751	180582777	+	1	NA	5' UTR (NM_028479, exon 2 of 6)	5' UTR (NM_028479, exon 2 of 6)	1460	NM_028479	73247	Mm.426558	NM_028479	ENSMUSG00000027569	Mrgbp	1600027N09Rik|AW060503|C80444	MRG/MORF4L binding protein	protein-coding
mm_836.1	chr1	51566531	51566551	+	1	NA	Intergenic	Intergenic	-88142	NM_001310549	109019	Mm.196290	NM_028696	ENSMUSG00000026107	Nabp1	4930434H03Rik|4930442A21Rik|4930488J04Rik|4933440J18Rik|5830411E10Rik|AI852561|Nbp1|Obfc2a|Ssb2	nucleic acid binding protein 1	protein-coding
mm_120396.1	chr14	64652560	64652582	+	1	NA	promoter-TSS (NM_001081177)	promoter-TSS (NM_001081177)	40	NM_001081177	16554	Mm.23611	NM_001081177	ENSMUSG00000060012	Kif13b	5330429L19Rik|6030414C01|AI429803|C130021D12Rik|GAKIN	kinesin family member 13B	protein-coding
mm_69744.1	chr7	140955149	140955160	-	1	NA	exon (NM_030694, exon 2 of 2)	exon (NM_030694, exon 2 of 2)	807	NM_030694	80876	Mm.379266	NM_030694	ENSMUSG00000060591	Ifitm2	DSPA2c|Ifitm3l|fragilis3|mil-3	interferon induced transmembrane protein 2	protein-coding
mm_19409.1	chr2	91696017	91696026	-	1	NA	intron (NM_145528, intron 1 of 15)	intron (NM_145528, intron 1 of 15)	14571	NM_145528	51897	Mm.28492	NM_145528	ENSMUSG00000027244	Atg13	1110053A20Rik|D2Ertd391e|Harbi1	autophagy related 13	protein-coding
mm_32053.1	chr4	97772426	97772511	+	1	NA	intron (NM_001122952, intron 1 of 10)	intron (NM_001122952, intron 1 of 10)	-5158	NM_001122953	18027	Mm.31274	NM_010905	ENSMUSG00000028565	Nfia	1110047K16Rik|9430022M17Rik|CTF|NF1-A|NF1A	nuclear factor I/A	protein-coding
mm_128388.1	chr15	43148778	43148780	-	1	NA	intron (NM_172815, intron 2 of 5)	intron (NM_172815, intron 2 of 5)	22039	NM_172815	239405	Mm.193274	NM_172815	ENSMUSG00000051920	Rspo2	2610028F08Rik|AA673245|D430027K22|ftls	R-spondin 2	protein-coding
mm_7003.1	chr1	86442539	86442554	-	1	NA	Intergenic	CpG	16217	NM_027966	71863	Mm.179627	NM_027966	ENSMUSG00000036574	1700019O17Rik	-	RIKEN cDNA 1700019O17 gene	protein-coding
mm_14963.1	chr2	152081375	152081390	+	1	NA	promoter-TSS (NM_001160410)	promoter-TSS (NM_001160410)	-147	NM_001160410	545474	Mm.214317	NM_001160410	ENSMUSG00000060257	Scrt2	AW060659	scratch family zinc finger 2	protein-coding
mm_41682.1	chr5	100077891	100077922	+	1	NA	promoter-TSS (NR_045993)	promoter-TSS (NR_045993)	-56	NR_045993	76003	Mm.447060	NR_045993	ENSMUSG00000086259	Tmem150cos	5830403M04Rik	transmembrane protein 150C, opposite strand	ncRNA
mm_123213.1	chr14	59419070	59419099	-	1	NA	exon (NM_001320721, exon 5 of 13)	exon (NM_001320721, exon 5 of 13)	21796	NM_001320725	107303348		NM_001320725		Setdb2-phf11c	-	Setdb2-Phf11c readthrough	protein-coding
mm_93218.1	chr10	95145399	95145414	-	1	NA	intron (NR_131146, intron 1 of 3)	intron (NR_131146, intron 1 of 3)	419	NR_131146	628062		NR_131146		Gm29684	-	predicted gene, 29684	ncRNA
mm_15089.1	chr2	153241503	153241603	+	1	NA	promoter-TSS (NM_080463)	promoter-TSS (NM_080463)	21	NM_080463	140484	Mm.293761	NM_080463	ENSMUSG00000046020	Pofut1	O-FucT-1|mKIAA0180	protein O-fucosyltransferase 1	protein-coding
mm_28063.1	chr3	84259701	84259728	-	1	NA	promoter-TSS (NM_001271727)	promoter-TSS (NM_001271727)	65	NM_001271727	80890	Mm.44876	NM_030706	ENSMUSG00000027993	Trim2	mKIAA0517|narf	tripartite motif-containing 2	protein-coding
mm_103361.1	chr11	74925659	74925716	-	1	NA	promoter-TSS (NM_001002764)	promoter-TSS (NM_001002764)	111	NM_013761	27364	Mm.131443	NM_013761	ENSMUSG00000001323	Srr	M100034|Rgsc34|Srs	serine racemase	protein-coding
mm_17323.1	chr2	26476171	26476180	-	1	NA	exon (NM_008714, exon 15 of 34)	exon (NM_008714, exon 15 of 34)	-6056	NR_105962	102465602		NR_105962	ENSMUSG00000098548	Mir6996	Gm27531|mmu-mir-6996	microRNA 6996	ncRNA
mm_123231.1	chr14	60086893	60086912	-	1	NA	promoter-TSS (NM_015803)	promoter-TSS (NM_015803)	-68	NM_015803	50769	Mm.319599	NM_015803	ENSMUSG00000021983	Atp8a2	AI415030|Atpc1b|agil|wl	ATPase, aminophospholipid transporter-like, class I, type 8A, member 2	protein-coding
mm_167439.1	chr8	120112935	120112937	+	1	NA	Intergenic	Intergenic	-1216	NM_001163762	234797	Mm.101958	NM_172286	ENSMUSG00000031824	6430548M08Rik	AW049007|Kiaa0513|mKIAA0513	RIKEN cDNA 6430548M08 gene	protein-coding
mm_47949.1	chr5	135465915	135465941	-	1	NA	intron (NM_146001, intron 1 of 30)	intron (NM_146001, intron 1 of 30)	-71382	NM_148932	107939	Mm.28399	NM_148932	ENSMUSG00000053293	Pom121	2610027A18Rik|C80273|mKIAA0618	nuclear pore membrane protein 121	protein-coding
mm_104758.1	chr11	98473804	98473807	-	1	NA	intron (NM_011771, intron 7 of 7)	U2|snRNA|snRNA	26971	NM_010346	14786	Mm.276702	NM_010346	ENSMUSG00000019312	Grb7	mKIAA4028	growth factor receptor bound protein 7	protein-coding
mm_23298.1	chr3	52270199	52270208	+	1	NA	intron (NM_019739, intron 1 of 2)	intron (NM_019739, intron 1 of 2)	1866	NM_019739	56458	Mm.29891	NM_019739	ENSMUSG00000044167	Foxo1	AI876417|Afxh|FKHR|Fkhr1|Foxo1a	forkhead box O1	protein-coding
mm_161312.1	chr14	43015576	43015576	-	1	NA	promoter-TSS (NM_001244671).3	promoter-TSS (NM_001244671).3	0	NM_001244671	100042055	Mm.429109	NM_001244671	ENSMUSG00000095226	Gm10377	ENSMUSG00000072606	predicted gene 10377	protein-coding
mm_133567.1	chr16	91405822	91405844	+	1	NA	promoter-TSS (NM_008349)	promoter-TSS (NM_008349)	-402	NM_008349	16155	Mm.4154	NM_008349	ENSMUSG00000022969	Il10rb	6620401D04Rik|AI528744|CRF2-4|Crfb4|D16H21S58|D21S58h|IL-10R2|Il10r2	interleukin 10 receptor, beta	protein-coding
mm_40695.1	chr5	65791112	65791124	+	1	NA	exon (NM_001024917, exon 6 of 20)	exon (NM_001024917, exon 6 of 20)	27597	NM_001024917	333789	Mm.332398	NM_001024917	ENSMUSG00000037795	N4bp2	B3bp|E430014I16|Gm1791|Gm868	NEDD4 binding protein 2	protein-coding
mm_163781.1	chr13	120172407	120172412	+	1	NA	Intergenic	MT2B1|LTR|ERVL	32163	NM_001039648	639910	Mm.424428	NM_001039648	ENSMUSG00000096323	Gm20767	-	predicted gene, 20767	protein-coding
mm_103135.1	chr11	70237853	70237885	-	1	NA	promoter-TSS (NM_001177601)	promoter-TSS (NM_001177601)	45	NM_001177601	104457	Mm.30016	NM_026757	ENSMUSG00000020831	0610010K14Rik	1110020A23Rik|AL033328|AU045833|Bap18	RIKEN cDNA 0610010K14 gene	protein-coding
mm_97684.1	chr11	80089386	80089417	+	1	NA	promoter-TSS (NM_001029856)	promoter-TSS (NM_001029856)	1	NM_001029856	237877	Mm.89551	NM_001029856	ENSMUSG00000017550	Atad5	C130052G03Rik|FRAG1|Gm17	ATPase family, AAA domain containing 5	protein-coding
mm_138765.1	chr17	37054780	37054821	+	1	NA	exon (NM_019439, exon 8 of 23)	exon (NM_019439, exon 8 of 23)	8834	NM_019439	54393	Mm.32191	NM_019439	ENSMUSG00000024462	Gabbr1	GABAB1|GABAbR1|bM573K1.1	gamma-aminobutyric acid (GABA) B receptor, 1	protein-coding
mm_36729.1	chr4	99120899	99120935	-	1	NA	promoter-TSS (NM_026082)	promoter-TSS (NM_026082)	-2	NM_026082	67299	Mm.260623	NM_026082	ENSMUSG00000028556	Dock7	3110056M06Rik|Gm430	dedicator of cytokinesis 7	protein-coding
mm_24671.1	chr3	94699591	94699593	+	1	NA	exon (NM_019414, exon 6 of 12)	exon (NM_019414, exon 6 of 12)	6019	NM_019414	20342	Mm.225405	NM_019414	ENSMUSG00000068877	Selenbp2	AP56|Lpsb2	selenium binding protein 2	protein-coding
mm_61836.1	chr7	88283899	88283916	+	1	NA	intron (NM_009982, intron 2 of 6)	intron (NM_009982, intron 2 of 6)	5822	NM_001311790	13032	Mm.89295	NM_009982	ENSMUSG00000030560	Ctsc	AI047818|CatC|DPP1|DPPI	cathepsin C	protein-coding
mm_155881.1	chrX	101479290	101479300	+	1	NA	Intergenic	Intergenic	30186	NM_013712	26549	Mm.46232	NM_013712	ENSMUSG00000031312	Itgb1bp2	Chordc3	integrin beta 1 binding protein 2	protein-coding
mm_122819.1	chr14	54641324	54641343	-	1	NA	promoter-TSS (NM_199470)	promoter-TSS (NM_199470)	31	NM_199470	239096	Mm.386871	NM_199470	ENSMUSG00000059674	Cdh24	1700040A22Rik|ENSMUSG00000022188	cadherin-like 24	protein-coding
mm_147437.1	chr18	46522127	46522133	-	1	NA	intron (NM_173423, intron 2 of 2)	intron (NM_173423, intron 2 of 2)	3841	NM_173423	240263	Mm.38249	NM_173423	ENSMUSG00000033319	Fem1c	2610312A07Rik|3632443A22Rik|AI646567	fem-1 homolog c (C.elegans)	protein-coding
mm_27155.1	chr3	33083061	33083069	-	1	NA	promoter-TSS (NM_021483)	promoter-TSS (NM_021483)	-5	NM_001289505	58869	Mm.151332	NM_021483	ENSMUSG00000027674	Pex5l	1700016J08Rik|PXR2|Pex2|TRIP8b|pex5Rp	peroxisomal biogenesis factor 5-like	protein-coding
mm_143394.1	chr17	70679897	70679913	-	1	NA	intron (NM_001347412, intron 8 of 13)	intron (NM_001347412, intron 8 of 13)	118158	NM_001128181	224997	Mm.311840	NM_027712	ENSMUSG00000003279	Dlgap1	4933422O14Rik|9630002F18|AI845682|AI848168|BB075781|D17Bwg0511e|GKAP/SAPAP|GKPA/SAPAP|Gkap|Sapap1|mKIAA4162	discs, large (Drosophila) homolog-associated protein 1	protein-coding
mm_12755.1	chr2	79255418	79255432	+	1	NA	promoter-TSS (NM_010576)	promoter-TSS (NM_010576)	-1	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D|Itga4B	integrin alpha 4	protein-coding
mm_7416.1	chr1	119504598	119504652	-	1	NA	5' UTR (NM_022327, exon 1 of 5)	5' UTR (NM_022327, exon 1 of 5)	157	NM_022327	64143	Mm.27832	NM_022327	ENSMUSG00000004451	Ralb	5730472O18Rik	v-ral simian leukemia viral oncogene B	protein-coding
mm_59003.1	chr7	19181163	19181202	+	1	NA	promoter-TSS (NR_029763)	promoter-TSS (NR_029763)	12	NM_028153	72205	Mm.154121	NM_028153	ENSMUSG00000040811	Eml2	1600029N02Rik|EMAP-2	echinoderm microtubule associated protein like 2	protein-coding
mm_140119.1	chr17	78937211	78937221	+	1	NA	promoter-TSS (NM_028611)	promoter-TSS (NM_028611)	81	NM_028611	73694	Mm.104959	NM_028611	ENSMUSG00000024082	Ndufaf7	2410091C18Rik|AL033374|PRO1853	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex assembly factor 7	protein-coding
mm_107847.1	chr12	69372113	69372172	+	1	NA	promoter-TSS (NM_007481)	promoter-TSS (NM_007481)	-8	NM_007481	11845	Mm.27308	NM_007481	ENSMUSG00000044147	Arf6	AI788669|AW496366	ADP-ribosylation factor 6	protein-coding
mm_142727.1	chr17	48234739	48234751	-	1	NA	intron (NM_001347399, intron 1 of 2)	intron (NM_001347399, intron 1 of 2)	2006	NM_021406	58217	Mm.248352	NM_021406	ENSMUSG00000042265	Trem1	-	triggering receptor expressed on myeloid cells 1	protein-coding
mm_109603.1	chr12	112679591	112679599	+	1	NA	exon (NM_001100460, exon 2 of 2)	exon (NM_001100460, exon 2 of 2)	755	NM_001100460	382639	Mm.11350	NM_001100460	ENSMUSG00000037638	Zbtb42	EG382639|Gm5188|simiRP58	zinc finger and BTB domain containing 42	protein-coding
mm_7754.1	chr1	131097851	131097868	-	1	NA	promoter-TSS (NM_008551)	promoter-TSS (NM_008551)	-16	NM_008551	17164	Mm.221235	NM_008551	ENSMUSG00000016528	Mapkapk2	AA960234|MAPKAP-K2|MK-2|MK2|Rps6kc1	MAP kinase-activated protein kinase 2	protein-coding
mm_166328.1	chr5	112840466	112840469	+	1	NA	intron (NM_028901, intron 15 of 43)	intron (NM_028901, intron 15 of 43)	47175	NR_040676	67360	Mm.59218	NR_040675	ENSMUSG00000098230	1700095B10Rik	-	RIKEN cDNA 1700095B10 gene	ncRNA
mm_74839.1	chr8	23257010	23257031	-	1	NA	promoter-TSS (NM_020585)	promoter-TSS (NM_020585)	60	NM_020585	57437	Mm.196269	NM_020585	ENSMUSG00000015341	Golga7	AB041568|C130038N16Rik|GCP16|GOLGA3AP1|HSPC041|R75586	golgi autoantigen, golgin subfamily a, 7	protein-coding
mm_141892.1	chr17	34861901	34861911	-	1	NA	TTS (NM_013484)	TTS (NM_013484)	608	NM_001142706	14962	Mm.653	NM_008198	ENSMUSG00000090231	Cfb	AI195813|AI255840|B|Bf|C2|Fb|H2-Bf	complement factor B	protein-coding
mm_152377.1	chr19	10231041	10231052	-	1	NA	intron (NM_001033481, intron 1 of 25)	LTR78|LTR|ERV1	9702	NM_001033481	225908	Mm.329716	NM_001033481	ENSMUSG00000036098	Myrf	6030439E18|Gm1804|Gm98|Mrf	myelin regulatory factor	protein-coding
mm_76420.1	chr8	84969763	84969779	-	1	NA	intron (NM_011563, intron 1 of 5)	intron (NM_011563, intron 1 of 5)	149	NM_011563	21672	Mm.347009	NM_011563	ENSMUSG00000005161	Prdx2	AL022839|Band-8|NkefB|PRP|PrxII|TDX1|TPx|TPx-B|TR|TSA|Tdpx1|Torin	peroxiredoxin 2	protein-coding
mm_97729.1	chr11	80391829	80391851	+	1	NA	non-coding (NR_045038, exon 8 of 17)	non-coding (NR_045038, exon 8 of 17)	8561	NM_001130171	22680	Mm.401332	NM_011751	ENSMUSG00000017421	Zfp207	8430401D15Rik|BuGZ|Zep|Znf207	zinc finger protein 207	protein-coding
mm_68728.1	chr7	120202140	120202149	-	1	NA	promoter-TSS (NM_016669)	promoter-TSS (NM_016669)	-156	NM_016669	12971	Mm.9114	NM_016669	ENSMUSG00000030905	Crym	-	crystallin, mu	protein-coding
mm_148582.1	chr19	5038848	5038938	+	1	NA	promoter-TSS (NM_175383)	promoter-TSS (NM_175383)	67	NM_175383	108902	Mm.491160	NM_175383	ENSMUSG00000047379	B4gat1	1500032M01Rik|B3gnt1|B3gnt6|BETA3GNT1|iGAT|iGNT	beta-1,4-glucuronyltransferase 1	protein-coding
mm_14261.1	chr2	128339902	128339914	+	1	NA	intron (NR_028589, intron 1 of 2)	intron (NR_028589, intron 1 of 2)	89443	NR_028591	100043424	Mm.297222	NR_028589		Gm14005	OTTMUSG00000015351	predicted gene 14005	ncRNA
mm_17484.1	chr2	28563374	28563392	-	1	NA	promoter-TSS (NM_009885)	promoter-TSS (NM_009885)	20	NM_009885	12613	Mm.236017	NM_009885	ENSMUSG00000026818	Cel	1810036E18Rik|BAL	carboxyl ester lipase	protein-coding
mm_110145.1	chr12	26448668	26448681	-	1	NA	exon (NM_021384, exon 4 of 6)	exon (NM_021384, exon 4 of 6)	7778	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_115487.1	chr13	3611003	3611013	-	1	NA	promoter-TSS (NM_134063)	promoter-TSS (NM_134063)	100	NM_134063	105203	Mm.221609	NM_134063	ENSMUSG00000033799	Fam208b	AI645998|Pap20|mKIAA2006	family with sequence similarity 208, member B	protein-coding
mm_67145.1	chr7	73464239	73464242	-	1	NA	intron (NM_001081345, intron 27 of 38)	intron (NM_001081345, intron 27 of 38)	77506	NM_001081345	244059	Mm.34539	NM_001081345	ENSMUSG00000078671	Chd2	2810013C04Rik|2810040A01Rik|5630401D06Rik|AI851092|BC029703|CHD-2	chromodomain helicase DNA binding protein 2	protein-coding
mm_111994.1	chr12	110695861	110695876	-	1	NA	intron (NM_010480, intron 1 of 10)	CpG	527	NM_010480	15519	Mm.1843	NM_010480	ENSMUSG00000021270	Hsp90aa1	86kDa|89kDa|AL024080|AL024147|Hsp86-1|Hsp89|Hsp90|Hspca|hsp4	heat shock protein 90, alpha (cytosolic), class A member 1	protein-coding
mm_20505.1	chr2	130488738	130488744	-	1	NA	intron (NM_001163688, intron 1 of 20)	intron (NM_001163688, intron 1 of 20)	38463	NM_001163688	19262	Mm.224246	NM_008980	ENSMUSG00000027303	Ptpra	Ptpa|Ptpalpha|Rptpalpha|Rptra|Rptralpha	protein tyrosine phosphatase, receptor type, A	protein-coding
mm_112321.1	chr12	115194144	115194169	-	1	NA	Intergenic	Intergenic	501638	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
mm_71000.1	chr8	31089607	31089760	+	1	NA	promoter-TSS (NM_025869)	promoter-TSS (NM_025869)	21	NM_025869	66959	Mm.23916	NM_025869	ENSMUSG00000039661	Dusp26	2310043K02Rik|Skrp3	dual specificity phosphatase 26 (putative)	protein-coding
mm_92874.1	chr10	82354162	82354172	-	1	NA	Intergenic	Intergenic	-112892	NM_001105557	237411		NM_172789	ENSMUSG00000062931	Zfp938	B230315N10Rik	zinc finger protein 938	protein-coding
mm_10472.1	chr2	14331457	14331480	+	1	NA	3' UTR (NM_008625, exon 30 of 30)	3' UTR (NM_008625, exon 30 of 30)	-56930	NM_001012305	277468	Mm.44662	NM_001012305	ENSMUSG00000036949	Slc39a12	AW046938|Gm731	solute carrier family 39 (zinc transporter), member 12	protein-coding
mm_82944.1	chr9	35305583	35305595	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	24484	NR_040715	71133	Mm.158577	NR_040715	ENSMUSG00000111746	4933422A05Rik	-	RIKEN cDNA 4933422A05 gene	ncRNA
mm_132958.1	chr16	50044363	50044374	+	1	NA	intron (NR_045935, intron 2 of 3)	MTEa|LTR|ERVL-MaLR	28484	NR_045935	224180	Mm.146439	NM_175010		Gm4827	B130050K08|EG224180	predicted gene 4827	ncRNA
mm_10633.1	chr2	19909997	19910007	+	1	NA	Intergenic	CpG	251940	NM_027715	71198	Mm.83981	NM_027715	ENSMUSG00000043415	Otud1	4933428L19Rik	OTU domain containing 1	protein-coding
mm_141198.1	chr17	27028518	27028528	-	1	NA	promoter-TSS (NM_027544)	promoter-TSS (NM_027544)	103	NM_007523	12018	Mm.2443	NM_007523	ENSMUSG00000057789	Bak1	Bak|N-BAK1|N-Bak	BCL2-antagonist/killer 1	protein-coding
mm_1523.1	chr1	72826575	72826583	+	1	NA	intron (NM_001310659, intron 1 of 3)	intron (NM_001310659, intron 1 of 3)	1192	NM_001310659	16008	Mm.141936	NM_008342	ENSMUSG00000039323	Igfbp2	AI255832|IBP-2|Igfbp-2|mIGFBP-2	insulin-like growth factor binding protein 2	protein-coding
mm_96990.1	chr11	70665291	70665323	+	1	NA	exon (NM_001167669, exon 2 of 7)	exon (NM_001167669, exon 2 of 7)	4109	NM_172561	216873	Mm.432524	NM_172561	ENSMUSG00000018287	Spag7	5730443G10|ACRP|FSA-1|Fsa1l	sperm associated antigen 7	protein-coding
mm_116905.1	chr13	55444875	55444896	-	1	NA	promoter-TSS (NM_001286064)	promoter-TSS (NM_001286064)	-187	NM_001286063	26385	Mm.10193	NM_011938	ENSMUSG00000074886	Grk6	Gprk6	G protein-coupled receptor kinase 6	protein-coding
mm_22752.1	chr3	19971013	19971029	+	1	NA	exon (NM_007752, exon 6 of 19)	exon (NM_007752, exon 6 of 19)	13967	NM_007752	12870	Mm.13787	NM_007752	ENSMUSG00000003617	Cp	D3Ertd555e	ceruloplasmin	protein-coding
mm_151079.1	chr19	47619725	47619737	+	1	NA	exon (NM_001164639, exon 9 of 18)	exon (NM_001164639, exon 9 of 18)	39712	NM_001164639	20874	Mm.281011	NM_009289	ENSMUSG00000025060	Slk	9A2|AV021402|AW411554|Etk4|SMAK|Stk2|mKIAA0204|mSLK	STE20-like kinase	protein-coding
mm_27394.1	chr3	50888442	50888471	-	1	NA	Intergenic	Intergenic	-335991	NM_009834	12457	Mm.86541	NM_009834	ENSMUSG00000023087	Noct	AU043840|Ccr4|Ccrn4l	nocturnin	protein-coding
mm_53515.1	chr6	136398423	136398425	+	1	NA	Intergenic	Intergenic	17145	NM_001201390	100502936	Mm.21182	NM_001201390	ENSMUSG00000045291	E330021D16Rik	C85549	RIKEN cDNA E330021D16 gene	protein-coding
mm_167638.1	chr9	63500726	63500729	+	1	NA	intron (NM_001311098, intron 14 of 21)	intron (NM_001311098, intron 14 of 21)	-101483	NM_027090	69478	Mm.113942	NM_027090	ENSMUSG00000032403	2300009A05Rik	-	RIKEN cDNA 2300009A05 gene	protein-coding
mm_77488.1	chr8	122567772	122567793	-	1	NA	promoter-TSS (NM_026014)	promoter-TSS (NM_026014)	-233	NM_026014	67177	Mm.21873	NM_026014	ENSMUSG00000006585	Cdt1	2610318F11Rik|AW545653|C76791|Ris2	chromatin licensing and DNA replication factor 1	protein-coding
mm_134341.1	chr16	16560119	16560145	-	1	NA	promoter-TSS (NM_139232)	promoter-TSS (NM_139232)	87	NM_139232	224014	Mm.256131	NM_139232	ENSMUSG00000022788	Fgd4	9030023J02Rik|9330209B17Rik|Frabp|ZFYVE6	FYVE, RhoGEF and PH domain containing 4	protein-coding
mm_22114.1	chr2	170134573	170134583	-	1	NA	intron (NM_001159683, intron 1 of 6)	intron (NM_001159683, intron 1 of 6)	-3358	NM_001033299	228913	Mm.22858	NM_001033299	ENSMUSG00000052056	Zfp217	4933431C08Rik|AW987152|Gm562|ZABC1|Znf217	zinc finger protein 217	protein-coding
mm_83609.1	chr9	48605121	48605133	-	1	NA	promoter-TSS (NM_001311062)	promoter-TSS (NM_001311062)	-4	NM_010924	18113	Mm.8362	NM_010924	ENSMUSG00000032271	Nnmt	-	nicotinamide N-methyltransferase	protein-coding
mm_127503.1	chr15	101447760	101447760	+	1	NA	promoter-TSS (NM_025487)	promoter-TSS (NM_025487)	15	NM_025487	66322	Mm.158111	NM_025487	ENSMUSG00000063971	Krt88	1700011A15Rik	keratin 88	protein-coding
mm_133279.1	chr16	77419846	77419849	+	1	NA	intron (NR_015543, intron 2 of 4)	intron (NR_015543, intron 2 of 4)	90519	NR_015543	77994	Mm.394688	NR_015543	ENSMUSG00000090386	Mir99ahg	2810055G20Rik|D730043B02Rik	Mir99a and Mirlet7c-1 host gene (non-protein coding)	ncRNA
mm_168061.1	chr10	100913160	100913161	-	1	NA	Intergenic	L1_Mus3|LINE|L1	320774	NM_001081246	66605	Mm.72646	NM_001081246	ENSMUSG00000056912	1700017N19Rik	-	RIKEN cDNA 1700017N19 gene	protein-coding
mm_145312.1	chr18	53889135	53889147	+	1	NA	intron (NM_152809, intron 1 of 12)	B1_Mus1|SINE|Alu	27028	NM_152809	70425	Mm.368668	NM_152809	ENSMUSG00000073563	Csnk1g3	3300002K07Rik|C330049O21Rik	casein kinase 1, gamma 3	protein-coding
mm_74218.1	chr8	124021156	124021201	+	1	NA	intron (NM_133966, intron 1 of 4)	CpG	131	NM_133966	102162	Mm.291777	NM_133966	ENSMUSG00000038697	Taf5l	1110005N04Rik|AI849020	TATA-box binding protein associated factor 5 like	protein-coding
mm_144563.1	chr18	31760011	31760034	+	1	NA	promoter-TSS (NM_001242430)	promoter-TSS (NM_001242430)	198	NM_153515	225339	Mm.290804	NM_153515	ENSMUSG00000041915	Ammecr1l	5430429D03Rik|AU022236|AU040755|AW111353|E230022H04Rik	AMME chromosomal region gene 1-like	protein-coding
mm_71839.1	chr8	68904617	68904636	+	1	NA	3' UTR (NM_008509, exon 10 of 10)	3' UTR (NM_008509, exon 10 of 10)	24071	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_163482.1	chr12	107970568	107970585	-	1	NA	intron (NM_001079883, intron 2 of 3)	intron (NM_001079883, intron 2 of 3)	32838	NM_001079883	58208	Mm.392694	NM_021399	ENSMUSG00000048251	Bcl11b	9130430L19Rik|AI604821|B630002E05Rik|BCL-11B|Ctip2|Rit1	B cell leukemia/lymphoma 11B	protein-coding
mm_7625.1	chr1	127425186	127425191	-	1	NA	intron (NM_145128, intron 12 of 17)	intron (NM_145128, intron 12 of 17)	220202	NM_145128	107895	Mm.214682	NM_145128	ENSMUSG00000036155	Mgat5	4930471A21Rik|5330407H02Rik|AI480971|GlcNAc-TV	mannoside acetylglucosaminyltransferase 5	protein-coding
mm_146698.1	chr18	12941802	12941866	-	1	NA	promoter-TSS (NM_207530)	promoter-TSS (NM_207530)	7	NM_207530	64291	Mm.259470	NM_020573	ENSMUSG00000044252	Osbpl1a	G430090F17Rik|Gm753|ORP-1|Osbpl1b	oxysterol binding protein-like 1A	protein-coding
mm_104813.1	chr11	98959524	98959527	-	1	NA	promoter-TSS (NM_001176528)	promoter-TSS (NM_001176528)	-946	NM_001176528	19401	Mm.439744	NM_009024	ENSMUSG00000037992	Rara	Nr1b1|RAR|RARalpha1	retinoic acid receptor, alpha	protein-coding
mm_45067.1	chr5	43782064	43782085	-	1	NA	promoter-TSS (NM_178729)	promoter-TSS (NM_178729)	75	NM_001159963	242960	Mm.25794	NM_178729	ENSMUSG00000039753	Fbxl5	Fbl4|Fir4	F-box and leucine-rich repeat protein 5	protein-coding
mm_32267.1	chr4	102605740	102605783	+	1	NA	3' UTR (NM_001177980, exon 10 of 10)	3' UTR (NM_001177980, exon 10 of 10)	15918	NM_001177981	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_45930.1	chr5	89445395	89445432	-	1	NA	exon (NM_008096, exon 3 of 13)	exon (NM_008096, exon 3 of 13)	12485	NM_008096	14473	Mm.196595	NM_008096	ENSMUSG00000035540	Gc	DBP|VDB	group specific component	protein-coding
mm_67.1	chr1	6635998	6636014	+	1	NA	intron (NM_001244693, intron 2 of 22)	intron (NM_001244693, intron 2 of 22)	-94045	NR_045189	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding
mm_142897.1	chr17	51903951	51903961	-	1	NA	intron (NR_045095, intron 1 of 2)	intron (NR_045095, intron 1 of 2)	21229	NR_045095	100504169	Mm.417731	NR_045095		Gm20098	-	predicted gene, 20098	ncRNA
mm_29539.1	chr3	116711850	116711865	-	1	NA	intron (NM_144902, intron 1 of 7)	CpG	423	NM_144902	229782	Mm.190758	NM_144902	ENSMUSG00000027957	Slc35a3	2310050P13Rik	solute carrier family 35 (UDP-N-acetylglucosamine (UDP-GlcNAc) transporter), member 3	protein-coding
mm_141150.1	chr17	26506379	26506395	-	1	NA	exon (NM_013642, exon 4 of 4)	exon (NM_013642, exon 4 of 4)	2085	NM_013642	19252	Mm.239041	NM_013642	ENSMUSG00000024190	Dusp1	3CH134|MKP1|Ptpn16|U19515|erp|mkp-1	dual specificity phosphatase 1	protein-coding
mm_45802.1	chr5	87568967	87568978	-	1	NA	promoter-TSS (NM_016771)	promoter-TSS (NM_016771)	34	NM_016771	53315	Mm.6824	NM_016771	ENSMUSG00000029273	Sult1d1	5033411P13Rik|AI987815|ST1d1|SULT-N|Sultn	sulfotransferase family 1D, member 1	protein-coding
mm_53585.1	chr6	137537929	137537934	+	1	NA	intron (NM_001271595, intron 2 of 20)	intron (NM_001271595, intron 2 of 20)	-18036	NM_001271589	13860	Mm.235346	NM_007945	ENSMUSG00000015766	Eps8	AW261790	epidermal growth factor receptor pathway substrate 8	protein-coding
mm_2644.1	chr1	125434884	125434894	+	1	NA	intron (NM_001205385, intron 2 of 12)	intron (NM_001205385, intron 2 of 12)	838	NM_023735	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding
mm_89615.1	chr10	96044520	96044529	+	1	NA	3' UTR (NM_001001932, exon 29 of 29)	3' UTR (NM_001001932, exon 29 of 29)	103861	NM_001001932	216238	Mm.210035	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding
mm_123648.1	chr14	69102949	69102958	-	1	NA	Intergenic	Intergenic	-68849	NM_010920	18092	Mm.390691	NM_010920	ENSMUSG00000044186	Nkx2-6	AV044928|Nkx-2.6|Nkx2.6|Tix|tinman	NK2 homeobox 6	protein-coding
mm_13995.1	chr2	121934752	121934777	+	1	NA	3' UTR (NM_199038, exon 8 of 8)	3' UTR (NM_199038, exon 8 of 8)	-21237	NM_001290992	329506	Mm.249405	NM_212450	ENSMUSG00000033411	Ctdspl2	D2Ertd485e	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase like 2	protein-coding
mm_33330.1	chr4	129136685	129136704	+	1	NA	promoter-TSS (NM_027402)	promoter-TSS (NM_027402)	-305	NM_027402	384061	Mm.44075	NM_027402	ENSMUSG00000001334	Fndc5	1500001L03Rik|AI836596|C87088|PeP|Pxp	fibronectin type III domain containing 5	protein-coding
mm_158797.1	chrX	167241609	167241637	-	1	NA	3' UTR (NM_001313760, exon 2 of 2)	3' UTR (NM_001313760, exon 2 of 2)	22706	NM_001313761	170744	Mm.196676	NM_133212	ENSMUSG00000040522	Tlr8	-	toll-like receptor 8	protein-coding
mm_143281.1	chr17	65772666	65772676	-	1	NA	promoter-TSS (NM_133685)	promoter-TSS (NM_133685)	81	NM_133685	106572	Mm.29274	NM_133685	ENSMUSG00000056515	Rab31	1700093E07Rik|AI415285|Rab22B	RAB31, member RAS oncogene family	protein-coding
mm_156187.1	chrX	133908475	133908481	+	1	NA	promoter-TSS (NM_026838)	promoter-TSS (NM_026838)	53	NM_001083895	68792	Mm.263553	NM_026838	ENSMUSG00000031253	Srpx2	1110039C07Rik|SRP|SRPUL	sushi-repeat-containing protein, X-linked 2	protein-coding
mm_12902.1	chr2	84809396	84809401	+	1	NA	3' UTR (NM_019949, exon 4 of 4)	3' UTR (NM_019949, exon 4 of 4)	10570	NM_019949	56791	Mm.38261	NM_019949	ENSMUSG00000027078	Ube2l6	2810489I21Rik|RIG-B|UBCH8|Ubce8|Ubcm8	ubiquitin-conjugating enzyme E2L 6	protein-coding
mm_81711.1	chr9	111311805	111311840	+	1	NA	promoter-TSS (NM_001164659)	promoter-TSS (NM_001164659)	83	NM_001164659	320429	Mm.270754	NM_001164659	ENSMUSG00000062296	Trank1	A230061D21Rik|C030048J01Rik|Gm187|Lba1	tetratricopeptide repeat and ankyrin repeat containing 1	protein-coding
mm_85258.1	chr9	99396526	99396536	-	1	NA	intron (NM_008624, intron 2 of 5)	RMER1A|Other|Other	-38001	NM_177775	272636	Mm.490440	NM_177775	ENSMUSG00000037681	Esyt3	D930024E11|D9Ertd280e|Fam62c|mKIAA4186	extended synaptotagmin-like protein 3	protein-coding
mm_25336.1	chr3	106574043	106574069	+	1	NA	3' UTR (NM_026013, exon 9 of 9)	3' UTR (NM_026013, exon 9 of 9)	-26254	NM_133869	99712	Mm.429443	NM_133869	ENSMUSG00000040774	Cept1	9930118K05Rik|mCEPT1	choline/ethanolaminephosphotransferase 1	protein-coding
mm_53554.1	chr6	136873200	136873210	+	1	NA	exon (NM_008597, exon 3 of 4)	exon (NM_008597, exon 3 of 4)	2618	NM_008597	17313	Mm.243085	NM_008597	ENSMUSG00000030218	Mgp	Mglap	matrix Gla protein	protein-coding
mm_133763.1	chr16	94552211	94552224	+	1	NA	Intergenic	Intergenic	-17989	NM_007890	13548	Mm.310973	NM_007890	ENSMUSG00000022897	Dyrk1a	2310043O08Rik|D16Ertd272e|D16Ertd493e|Dyrk|ENSMUSG00000074897|Gm10783|Mnbh|Mp86|mmb	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1a	protein-coding
mm_134520.1	chr16	19236092	19236109	-	1	NA	Intergenic	L1_Mur2|LINE|L1	50641	NM_146451	258443	Mm.377506	NM_146451	ENSMUSG00000050742	Olfr164	MOR279-2	olfactory receptor 164	protein-coding
mm_95053.1	chr11	32385038	32385049	+	1	NA	intron (NM_177364, intron 3 of 12)	intron (NM_177364, intron 3 of 12)	37232	NM_177364	268396	Mm.227616	NM_177364	ENSMUSG00000040711	Sh3pxd2b	G431001E03Rik|TSK4|fad49	SH3 and PX domains 2B	protein-coding
mm_19445.1	chr2	91982799	91982817	-	1	NA	3' UTR (NM_011957, exon 12 of 12)	3' UTR (NM_011957, exon 12 of 12)	-19245	NM_138306	104418	Mm.314923	NM_138306	ENSMUSG00000040479	Dgkz	E130307B02Rik|ENSMUSG00000075035|F730209L11Rik|mDGK[z]	diacylglycerol kinase zeta	protein-coding
mm_22612.1	chr3	14533868	14533889	+	1	NA	promoter-TSS (NM_028915)	promoter-TSS (NM_028915)	90	NM_028915	71710	Mm.257449	NM_028915	ENSMUSG00000027550	Lrrcc1	1200008A14Rik|4932441F23Rik|AI195358|AI447421	leucine rich repeat and coiled-coil domain containing 1	protein-coding
mm_120636.1	chr14	70467682	70467687	+	1	NA	3' UTR (NM_145981, exon 5 of 5)	3' UTR (NM_145981, exon 5 of 5)	10167	NM_145981	105653	Mm.192598	NM_145981	ENSMUSG00000003469	Phyhip	AW049870|C630010D02Rik|Lnap1ip|PAHX-AP#1|PAHX-AP1	phytanoyl-CoA hydroxylase interacting protein	protein-coding
mm_45297.1	chr5	65327642	65327644	-	1	NA	intron (NM_001347358, intron 1 of 24)	intron (NM_001347358, intron 1 of 24)	7996	NM_011258	19687	Mm.148877	NM_011258	ENSMUSG00000029191	Rfc1	140kDa|Alp145|RFC140|Recc1	replication factor C (activator 1) 1	protein-coding
mm_64099.1	chr7	141009646	141009693	+	1	NA	TTS (NM_025378)	TTS (NM_025378)	1075	NM_025378	66141	Mm.141021	NM_025378	ENSMUSG00000025492	Ifitm3	1110004C05Rik|Cd225|Cdw217|DSPA2b|Fgls|IP15|mil-1	interferon induced transmembrane protein 3	protein-coding
mm_163234.1	chr11	103954045	103954046	-	1	NA	promoter-TSS (NM_008740)	promoter-TSS (NM_008740)	11	NM_008740	18195	Mm.260117	NM_008740	ENSMUSG00000034187	Nsf	AI316878|AU020090|AU067812|SKD2	N-ethylmaleimide sensitive fusion protein	protein-coding
mm_140014.1	chr17	73204145	73204216	+	1	NA	intron (NM_001177967, intron 5 of 5)	intron (NM_001177967, intron 5 of 5)	96195	NM_001177967	225010	Mm.329194	NM_001081071	ENSMUSG00000054469	Lclat1	AI181996|Agpat8|Alcat1|Gm91|Lycat	lysocardiolipin acyltransferase 1	protein-coding
mm_48813.1	chr5	148996544	148996571	-	1	NA	Intergenic	Intergenic	-1342	NR_102384	319982	Mm.33303	NR_102383	ENSMUSG00000106951	5930430L01Rik	-	RIKEN cDNA 5930430L01 gene	ncRNA
mm_144372.1	chr18	20556418	20556419	+	1	NA	Intergenic	Intergenic	-1656	NM_007883	13511	Mm.345891	NM_007883	ENSMUSG00000044393	Dsg2	AA408168|D18Ertd293e	desmoglein 2	protein-coding
mm_165703.1	chr3	95653776	95653797	-	1	NA	Intergenic	Intergenic	-4935	NM_008562	17210	Mm.1639	NM_008562	ENSMUSG00000038612	Mcl1	AW556805|Mcl-1	myeloid cell leukemia sequence 1	protein-coding
mm_123428.1	chr14	64440798	64440802	-	1	NA	exon (NM_026322, exon 6 of 11)	exon (NM_026322, exon 6 of 11)	226	NM_001253715	110265	Mm.26713	NM_026322	ENSMUSG00000054733	Msra	2310045J23Rik|6530413P12Rik|MSR-A	methionine sulfoxide reductase A	protein-coding
mm_113209.1	chr13	25074692	25074721	+	1	NA	intron (NM_001195617, intron 2 of 7)	B1_Mus1|SINE|Alu	18702	NM_177577	195208	Mm.284719	NM_177577	ENSMUSG00000035910	Dcdc2a	AW492955|Dcdc2|RU2	doublecortin domain containing 2a	protein-coding
mm_140093.1	chr17	75527461	75527464	+	1	NA	3' UTR (NM_207246, exon 18 of 18)	3' UTR (NM_207246, exon 18 of 18)	24484	NM_133747	72722	Mm.24641	NM_133747	ENSMUSG00000002017	Fam98a	2810405J04Rik|AL024114	family with sequence similarity 98, member A	protein-coding
mm_31214.1	chr4	43972488	43972490	+	1	NA	intron (NM_027450, intron 4 of 4)	intron (NM_027450, intron 4 of 4)	-11015	NM_001002787	442829	Mm.348215	NM_001002787	ENSMUSG00000070999	Ccin	4933417A14Rik	calicin	protein-coding
mm_157412.1	chrX	38442053	38442073	-	1	NA	exon (NM_001017959, exon 2 of 9)	exon (NM_001017959, exon 2 of 9)	14397	NM_010685	16784	Mm.486	NM_010685	ENSMUSG00000016534	Lamp2	CD107b|LGP-B|Lamp II|Lamp-2|Lamp-2a|Lamp-2b|Lamp-2c|Mac3	lysosomal-associated membrane protein 2	protein-coding
mm_121349.1	chr14	116925292	116925362	+	1	NA	promoter-TSS (NM_011821)	promoter-TSS (NM_011821)	30	NM_011821	23888	Mm.440025	NM_011821	ENSMUSG00000058571	Gpc6	-	glypican 6	protein-coding
mm_122860.1	chr14	54894878	54894915	-	1	NA	exon (NM_019402, exon 2 of 7)	exon (NM_019402, exon 2 of 7)	753	NM_019402	54196	Mm.7723	NM_019402	ENSMUSG00000022194	Pabpn1	PAB2|Pabp3|mPABII	poly(A) binding protein, nuclear 1	protein-coding
mm_58942.1	chr7	18245386	18245402	+	1	NA	promoter-TSS (NM_153749)	promoter-TSS (NM_153749)	47	NM_153749	266815	Mm.106769	NM_153749	ENSMUSG00000054005	Mill1	5530400I18Rik	MHC I like leukocyte 1	protein-coding
mm_120007.1	chr14	55650229	55650235	+	1	NA	promoter-TSS (NM_001253889)	promoter-TSS (NM_001253889)	48	NM_001253889	71099	Mm.171300	NM_027673	ENSMUSG00000007591	Tssk4	1700020B19Rik|4933424F08Rik|TSK-4|TSSK-4	testis-specific serine kinase 4	protein-coding
mm_22704.1	chr3	18533513	18533515	+	1	NA	Intergenic	Intergenic	-53037	NR_040544	73959	Mm.60616	NR_040544	ENSMUSG00000102699	4930433B08Rik	-	RIKEN cDNA 4930433B08 gene	ncRNA
mm_9875.1	chr1	185203819	185203838	-	1	NA	promoter-TSS (NM_001163754)	promoter-TSS (NM_001163754)	-340	NM_001163754	98732	Mm.275841	NM_172649	ENSMUSG00000039318	Rab3gap2	1110059F07Rik|2010002H18Rik|5830469C09|AI851069|AW743433|RAB3-GAP150|mKIAA0839	RAB3 GTPase activating protein subunit 2	protein-coding
mm_12589.1	chr2	73561103	73561111	+	1	NA	Intergenic	Intergenic	19231	NM_007389	11435	Mm.4583	NM_007389	ENSMUSG00000027107	Chrna1	AI385656|AI608266|Achr-1|Acra	cholinergic receptor, nicotinic, alpha polypeptide 1 (muscle)	protein-coding
mm_152653.1	chr19	12767755	12767758	-	1	NA	3' UTR (NM_053009, exon 11 of 11)	3' UTR (NM_053009, exon 11 of 11)	-2124	NM_170786	12803	Mm.290924	NM_053007	ENSMUSG00000079415	Cntf	AI429687	ciliary neurotrophic factor	protein-coding
mm_26052.1	chr3	135816841	135816879	+	1	NA	Intergenic	Intergenic	-8419	NM_026228	67547	Mm.30239	NM_026228	ENSMUSG00000053897	Slc39a8	4933419D20Rik|AA986696|BIGM103|ZIP-8|Zip8	solute carrier family 39 (metal ion transporter), member 8	protein-coding
mm_84336.1	chr9	64158048	64158049	-	1	NA	intron (NM_026507, intron 8 of 18)	L1MB8|LINE|L1	14883	NM_026507	68014	Mm.335237	NM_026507	ENSMUSG00000032400	Zwilch	2310031L18Rik	zwilch kinetochore protein	protein-coding
mm_112562.1	chr13	13468390	13468415	+	1	NA	exon (NM_010917, exon 4 of 20)	exon (NM_010917, exon 4 of 20)	30800	NM_010917	18073	Mm.4691	NM_010917	ENSMUSG00000005397	Nid1	A630025O17|Nid|entactin|entactin-1|nidogen-1	nidogen 1	protein-coding
mm_54440.1	chr6	34415454	34415458	-	1	NA	exon (NM_009731, exon 2 of 10)	exon (NM_009731, exon 2 of 10)	3094	NM_009731	11997	Mm.482073	NM_009731	ENSMUSG00000052131	Akr1b7	AR|Avdp|MVDP	aldo-keto reductase family 1, member B7	protein-coding
mm_82094.1	chr9	123056445	123056453	+	1	NA	exon (NM_177911, exon 10 of 14)	exon (NM_177911, exon 10 of 14)	21708	NM_177911	331046	Mm.195309	NM_177911	ENSMUSG00000025787	Tgm4	9530008N10Rik|Eapa1|TGP	transglutaminase 4 (prostate)	protein-coding
mm_120389.1	chr14	64590439	64590452	+	1	NA	promoter-TSS (NR_029813)	promoter-TSS (NR_029813)	-212	NR_029813	387233		NR_029813	ENSMUSG00000065597	Mir124a-1	Mirn124a|Mirn124a-1	microRNA 124a-1	ncRNA
mm_92801.1	chr10	81364847	81364859	-	1	NA	TTS (NM_028657)	TTS (NM_028657)	967	NM_001014836	432479	Mm.440450	NM_001014836	ENSMUSG00000020234	4930404N11Rik	2210409H10Rik|5730551K18Rik|AI854616	RIKEN cDNA 4930404N11 gene	protein-coding
mm_58182.1	chr6	142903358	142903363	-	1	NA	intron (NM_011374, intron 2 of 4)	A-rich|Low_complexity|Low_complexity	61092	NM_011374	20449	Mm.260838	NM_011374	ENSMUSG00000030283	St8sia1	9330109E03Rik|GD3S|Sia-T|Siat8|Siat8a	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 1	protein-coding
mm_10146.1	chr2	4300591	4300599	+	1	NA	intron (NM_172475, intron 1 of 22)	intron (NM_172475, intron 1 of 22)	-100381	NM_001177843	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding
mm_47203.1	chr5	120906876	120906894	-	1	NA	intron (NM_145211, intron 1 of 6)	intron (NM_145211, intron 1 of 6)	640	NM_145211	246730	Mm.14301	NM_145211	ENSMUSG00000052776	Oas1a	L3	2'-5' oligoadenylate synthetase 1A	protein-coding
mm_101634.1	chr11	36432793	36432803	-	1	NA	intron (NM_011856, intron 2 of 28)	intron (NM_011856, intron 2 of 28)	-452709	NM_170779	211652	Mm.31267	NM_170779	ENSMUSG00000018849	Wwc1	AA408228|AU017197|BC037006|Kibra|mKIAA0869	WW, C2 and coiled-coil domain containing 1	protein-coding
mm_95181.1	chr11	42419730	42419785	+	1	NA	promoter-TSS (NM_008070)	promoter-TSS (NM_008070)	0	NM_008070	14401	Mm.338723	NM_008070	ENSMUSG00000007653	Gabrb2	AI834970|C030002O17Rik|C030021G16Rik|Gabrab2|Gabrb-2	gamma-aminobutyric acid (GABA) A receptor, subunit beta 2	protein-coding
mm_98234.1	chr11	88099157	88099181	+	1	NA	promoter-TSS (NM_198013)	promoter-TSS (NM_198013)	23	NM_198013	103841	Mm.374846	NM_198013	ENSMUSG00000018378	Cuedc1	AI841487|C330016O16Rik	CUE domain containing 1	protein-coding
mm_173076.1	chrX	136224904	136224904	-	1	NA	5' UTR (NM_001127169, exon 2 of 3)	5' UTR (NM_001127169, exon 2 of 3)	863	NM_001127169	100040972	Mm.18125	NM_001127169	ENSMUSG00000079428	Tceal7	1110018P05Rik	transcription elongation factor A (SII)-like 7	protein-coding
mm_36392.1	chr4	77525963	77525966	-	1	NA	intron (NM_011211, intron 4 of 39)	intron (NM_011211, intron 4 of 39)	685931	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding
mm_86960.1	chr10	25109936	25109951	+	1	NA	Intergenic	Intergenic	90227	NM_001347460	432442	Mm.485937	NM_018747	ENSMUSG00000039166	Akap7	6430401D08|AI662165|AKAP15|Akap18|BB170514	A kinase (PRKA) anchor protein 7	protein-coding
mm_8022.1	chr1	135105180	135105207	-	1	NA	promoter-TSS (NM_001033409)	promoter-TSS (NM_001033409)	83	NM_001033409	329252	Mm.279594	NM_001033409	ENSMUSG00000042793	Lgr6	A530037C04Rik|D830026M09	leucine-rich repeat-containing G protein-coupled receptor 6	protein-coding
mm_90017.1	chr10	115362552	115362570	+	1	NA	promoter-TSS (NM_133683)	promoter-TSS (NM_133683)	-299	NM_133683	67226	Mm.29647	NM_133683	ENSMUSG00000069520	Tmem19	2810428F02Rik|AW125171	transmembrane protein 19	protein-coding
mm_98383.1	chr11	94139918	94139920	+	1	NA	Intergenic	L1M5|LINE|L1	-71535	NM_009427	22057	Mm.259673	NM_009427	ENSMUSG00000037573	Tob1	Tob|Trob	transducer of ErbB-2.1	protein-coding
mm_54536.1	chr6	36715697	36715715	-	1	NA	TTS (NM_008973)	TTS (NM_008973)	95655	NM_008973	19242	Mm.279690	NM_008973	ENSMUSG00000029838	Ptn	HARP|HB-GAM|HBBN|HBGF-8|HBNF|OSF|Osf-1|Osf1	pleiotrophin	protein-coding
mm_102632.1	chr11	62539200	62539253	-	1	NA	promoter-TSS (NM_028448)	promoter-TSS (NM_028448)	35	NM_028448	73139	Mm.390409	NM_028448	ENSMUSG00000018509	Cenpv	3110013H01Rik|AA671303|Prr6	centromere protein V	protein-coding
mm_63525.1	chr7	127912511	127912528	+	1	NA	promoter-TSS (NM_026370)	promoter-TSS (NM_026370)	2	NM_026370	67773	Mm.425492	NM_026370	ENSMUSG00000030801	Kat8	2010203C02Rik|5830450F21Rik|D7Ertd629e|MOF|Myst1	K(lysine) acetyltransferase 8	protein-coding
mm_1398.1	chr1	67142937	67142950	+	1	NA	exon (NM_001080809, exon 3 of 38)	exon (NM_001080809, exon 3 of 38)	19916	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_107007.1	chr12	11326146	11326179	+	1	NA	3' UTR (NM_012038, exon 4 of 4)	3' UTR (NM_012038, exon 4 of 4)	26275	NR_106136	102465775		NR_106136	ENSMUSG00000098879	Mir7675	Gm27965|mmu-mir-7675	microRNA 7675	ncRNA
mm_82838.1	chr9	31163384	31163478	-	1	NA	intron (NM_001102455, intron 8 of 16)	intron (NM_001102455, intron 8 of 16)	-31632	NM_011176	19143	Mm.243926	NM_011176	ENSMUSG00000031995	St14	Epithin|MT-SP1|Prss14|Tmprss14|mCAP3|matriptase	suppression of tumorigenicity 14 (colon carcinoma)	protein-coding
mm_59980.1	chr7	30465366	30465383	+	1	NA	intron (NM_019459, intron 11 of 29)	intron (NM_019459, intron 11 of 29)	217	NR_004443	445267	Mm.398140	NR_004443	ENSMUSG00000087009	Nphs1os	Nphs1as	nephrosis 1 homolog, nephrin, opposite strand	ncRNA
mm_145236.1	chr18	50181336	50181344	+	1	NA	intron (NM_008292, intron 20 of 23)	intron (NM_008292, intron 20 of 23)	53139	NM_008292	15488	Mm.277857	NM_008292	ENSMUSG00000024507	Hsd17b4	17-beta-HSD|17[b]-HSD|DBP|MFE-2|MFP2|MPF-2|Mfp-2|perMFE-2	hydroxysteroid (17-beta) dehydrogenase 4	protein-coding
mm_135145.1	chr16	35857189	35857220	-	1	NA	exon (NM_001039530, exon 6 of 17)	exon (NM_001039530, exon 6 of 17)	14178	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_39160.1	chr4	155601257	155601292	-	1	NA	promoter-TSS (NM_177186)	promoter-TSS (NM_177186)	-142	NM_177186	320541	Mm.306018	NM_177186	ENSMUSG00000042202	Slc35e2	A530082C11Rik|AI957035	solute carrier family 35, member E2	protein-coding
mm_87372.1	chr10	44268423	44268445	+	1	NA	promoter-TSS (NM_053069)	promoter-TSS (NM_053069)	95	NM_053069	11793	Mm.22264	NM_053069	ENSMUSG00000038160	Atg5	2010107M05Rik|3110067M24Rik|AW319544|Apg5l|Atg5l|C88337|Paddy	autophagy related 5	protein-coding
mm_99560.1	chr11	103649701	103649714	+	1	NA	TTS (NR_131143)	TTS (NR_131143)	198	NM_001033212	104582	Mm.44618	NM_001033212	ENSMUSG00000046215	Rprml	AW049332	reprimo-like	protein-coding
mm_168715.1	chr12	103714139	103714149	-	1	NA	Intergenic	RLTR31D_MM|LTR|ERVK	-18615	NM_026687	68348	Mm.20149	NM_026687	ENSMUSG00000021081	Serpina1f	0610012A11Rik|AI327419|Serpina2|epserin	serine (or cysteine) peptidase inhibitor, clade A, member 1F	protein-coding
mm_114031.1	chr13	52647008	52647018	+	1	NA	3' UTR (NM_011518, exon 14 of 14)	3' UTR (NM_011518, exon 14 of 14)	50131	NM_011518	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_112024.1	chr12	111454142	111454160	-	1	NA	3' UTR (NM_009396, exon 12 of 12)	3' UTR (NM_009396, exon 12 of 12)	11490	NM_009396	21928	Mm.255332	NM_009396	ENSMUSG00000021281	Tnfaip2	B94|Exoc3l3|M-sec|Tnfip2|tnfb94	tumor necrosis factor, alpha-induced protein 2	protein-coding
mm_110166.1	chr12	27334777	27334779	-	1	NA	3' UTR (NM_009234, exon 1 of 1)	3' UTR (NM_009234, exon 1 of 1)	7940	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding
mm_104121.1	chr11	86752516	86752525	-	1	NA	intron (NM_001003908, intron 1 of 31)	(A)n|Simple_repeat|Simple_repeat	4972	NM_001003908	67300	Mm.254588	NM_001003908	ENSMUSG00000047126	Cltc	3110065L21Rik|CHC|R74732	clathrin, heavy polypeptide (Hc)	protein-coding
mm_2851.1	chr1	131672282	131672294	+	1	NA	exon (NM_007799, exon 8 of 10)	exon (NM_007799, exon 8 of 10)	-16407	NM_145509	226421	Mm.44508	NM_145509	ENSMUSG00000052688	Rab7b	5430435G22Rik	RAB7B, member RAS oncogene family	protein-coding
mm_163037.1	chr11	53350911	53350920	+	1	NA	5' UTR (NM_033565, exon 1 of 21)	5' UTR (NM_033565, exon 1 of 21)	148	NM_033565	93736	Mm.395281	NM_033565	ENSMUSG00000049470	Aff4	AF5Q31|Alf4|Laf4l|MCEF	AF4/FMR2 family, member 4	protein-coding
mm_303.1	chr1	23761809	23761830	+	1	NA	promoter-TSS (NM_172124)	promoter-TSS (NM_172124)	-107	NM_172124	280645	Mm.471661	NM_172124	ENSMUSG00000026156	B3gat2	GlcAT-S|Glcats	beta-1,3-glucuronyltransferase 2 (glucuronosyltransferase S)	protein-coding
mm_155936.1	chrX	103630601	103630614	+	1	NA	promoter-TSS (NM_029158)	promoter-TSS (NM_029158)	21	NM_029158	75064	Mm.159414	NM_029158	ENSMUSG00000031330	Zcchc13	4930513O09Rik|Cnbp2	zinc finger, CCHC domain containing 13	protein-coding
mm_118955.1	chr14	27379646	27379661	+	1	NA	exon (NM_027871, exon 4 of 11)	exon (NM_027871, exon 4 of 11)	18264	NM_001289688	71704	Mm.248606	NM_027871	ENSMUSG00000021895	Arhgef3	1200004I24Rik|9830169H03Rik|C76747|Xpln	Rho guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_171397.1	chr4	122474067	122474067	+	1	NA	Intergenic	RLTR10C|LTR|ERVK	-215192	NM_023865	77432	Mm.491436	NM_023865	ENSMUSG00000023263	9530002B09Rik	Aump|Vpp1|Vppl	RIKEN cDNA 9530002B09 gene	protein-coding
mm_72623.1	chr8	84638963	84639017	+	1	NA	intron (NM_001252061, intron 46 of 46)	intron (NM_001252061, intron 46 of 46)	23862	NM_010499	15936	Mm.399	NM_010499	ENSMUSG00000053560	Ier2	AI317238|Ch1|Pip92	immediate early response 2	protein-coding
mm_78909.1	chr9	44920191	44920218	+	1	NA	intron (NM_013795, intron 1 of 2)	intron (NM_013795, intron 1 of 2)	538	NM_013795	27425	Mm.14663	NM_013795	ENSMUSG00000038717	Atp5l	4933437C06Rik	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit G	protein-coding
mm_87963.1	chr10	63386578	63386589	+	1	NA	promoter-TSS (NM_013888)	promoter-TSS (NM_013888)	20	NM_013888	30045	Mm.32550	NM_013888	ENSMUSG00000036764	Dnajc12	Jdp1|mJDP1	DnaJ heat shock protein family (Hsp40) member C12	protein-coding
mm_76464.1	chr8	85365383	85365411	-	1	NA	promoter-TSS (NM_175441)	promoter-TSS (NM_175441)	-73	NM_175441	213435	Mm.32804	NM_175441	ENSMUSG00000031698	Mylk3	D830007F02Rik|MLCK	myosin light chain kinase 3	protein-coding
mm_70797.1	chr8	22757746	22757761	+	1	NA	promoter-TSS (NM_008872)	promoter-TSS (NM_008872)	31	NM_008872	18791	Mm.154660	NM_008872	ENSMUSG00000031538	Plat	AU020998|AW212668|D8Ertd2e|tPA	plasminogen activator, tissue	protein-coding
mm_130694.1	chr15	100682949	100682979	-	1	NA	exon (NM_033612, exon 5 of 8)	exon (NM_033612, exon 5 of 8)	4956	NM_033612	109901	Mm.2131	NM_033612	ENSMUSG00000023031	Cela1	1810009A17Rik|1810062B19Rik|Ela-1|Ela1|PC-TsF	chymotrypsin-like elastase family, member 1	protein-coding
mm_3858.1	chr1	160978608	160978618	+	1	NA	promoter-TSS (NM_080844)	promoter-TSS (NM_080844)	7	NM_080844	11905	Mm.260770	NM_080844	ENSMUSG00000026715	Serpinc1	AI114908|ATIII|At-3|At3	serine (or cysteine) peptidase inhibitor, clade C (antithrombin), member 1	protein-coding
mm_145920.1	chr18	67066628	67066637	+	1	NA	Intergenic	Intergenic	-21666	NM_177137	14680	Mm.440746	NM_010307	ENSMUSG00000024524	Gnal	2610011C15Rik|9630020G10Rik|Galphaolf|Gna10|Golf	guanine nucleotide binding protein, alpha stimulating, olfactory type	protein-coding
mm_22563.1	chr3	9984226	9984242	+	1	NA	Intergenic	Intergenic	-28351	NM_001272097	16592	Mm.741	NM_010634	ENSMUSG00000027533	Fabp5	E-FABP|Fabpe|Klbp|PA-FABP|mal1	fatty acid binding protein 5, epidermal	protein-coding
mm_70571.1	chr8	13159356	13159362	+	1	NA	5' UTR (NM_010684, exon 1 of 9)	5' UTR (NM_010684, exon 1 of 9)	198	NM_010684	16783	Mm.16716	NM_010684	ENSMUSG00000031447	Lamp1	CD107a|LGP-120|LGP-A|Lamp-1|P2B	lysosomal-associated membrane protein 1	protein-coding
mm_103101.1	chr11	69939319	69939325	-	1	NA	exon (NM_016875, exon 4 of 9)	exon (NM_016875, exon 4 of 9)	2994	NM_001347634	53422	Mm.29286	NM_016875	ENSMUSG00000018554	Ybx2	Msy2	Y box protein 2	protein-coding
mm_94704.1	chr11	20231465	20231476	+	1	NA	intron (NM_172260, intron 5 of 6)	intron (NM_172260, intron 5 of 6)	17954	NM_172260	216543	Mm.260314	NM_172260	ENSMUSG00000044066	Cep68	6030463E10Rik|AI481761|BC027174|Kiaa0582	centrosomal protein 68	protein-coding
mm_154033.1	chr19	53464722	53464833	-	1	NA	promoter-TSS (NR_028427)	promoter-TSS (NR_028427)	19	NR_028427	381232	Mm.248624	NR_028427	ENSMUSG00000097636	Mirt1	4833407H14Rik|5430437C04Rik|5830416P10Rik|ENSMUSG00000074788|Gm10758	myocardial infarction associated transcript 1	ncRNA
mm_111746.1	chr12	103907031	103907031	-	1	NA	Intergenic	Intergenic	-2081	NM_009245	20702	Mm.439692	NM_009245	ENSMUSG00000079015	Serpina1c	Pi3|Pi6|Skalp|Spi1-3|Spi1-6|Wap3	serine (or cysteine) peptidase inhibitor, clade A, member 1C	protein-coding
mm_87942.1	chr10	62920631	62920646	+	1	NA	promoter-TSS (NM_175194)	promoter-TSS (NM_175194)	5	NM_175194	73132	Mm.37457	NM_175194	ENSMUSG00000071253	Slc25a16	3110021G18Rik|GDA|GDC|HGT.1|ML7	solute carrier family 25 (mitochondrial carrier, Graves disease autoantigen), member 16	protein-coding
mm_69500.1	chr7	134232044	134232054	-	1	NA	Intergenic	Intergenic	-6952	NM_007400	11489	Mm.439714	NM_007400	ENSMUSG00000054555	Adam12	Mltna	a disintegrin and metallopeptidase domain 12 (meltrin alpha)	protein-coding
mm_11924.1	chr2	52072896	52072906	+	1	NA	promoter-TSS (NM_175238)	promoter-TSS (NM_175238)	64	NM_175238	51869	Mm.254530	NM_175238	ENSMUSG00000036202	Rif1	5730435J01Rik|6530403D07Rik|AU016181|AW549474|D2Ertd145e	replication timing regulatory factor 1	protein-coding
mm_163247.1	chr11	106301166	106301168	+	1	NA	exon (NM_008117, exon 3 of 5)	exon (NM_008117, exon 3 of 5)	729	NM_008117	14599	Mm.343934	NM_008117	ENSMUSG00000020713	Gh	Gh1|Ghb1	growth hormone	protein-coding
mm_44897.1	chr5	35399961	35399969	-	1	NA	Intergenic	CpG	10848	NM_010445	15371	Mm.358606	NM_010445	ENSMUSG00000067438	Hmx1	Nkx5-3	H6 homeobox 1	protein-coding
mm_95201.1	chr11	43445179	43445212	+	1	NA	exon (NM_198936, exon 14 of 16)	exon (NM_198936, exon 14 of 16)	11464	NM_198936	193116	Mm.28200	NM_148673	ENSMUSG00000020409	Slu7	AU018913|D11Ertd730e|D3Bwg0878e	SLU7 splicing factor homolog (S. cerevisiae)	protein-coding
mm_147920.1	chr18	65767087	65767093	-	1	NA	Intergenic	Intergenic	-33488	NM_025468	66286	Mm.27800	NM_025468	ENSMUSG00000024516	Sec11c	1810029G24Rik|Sec11l3	SEC11 homolog C, signal peptidase complex subunit	protein-coding
mm_81313.1	chr9	108393135	108393143	+	1	NA	TTS (NM_011678)	TTS (NM_011678)	305	NM_053216	112418	Mm.78287	NM_053216	ENSMUSG00000032611	1700102P08Rik	AI593206	RIKEN cDNA 1700102P08 gene	protein-coding
mm_92106.1	chr10	63023807	63023824	-	1	NA	promoter-TSS (NM_001079824)	promoter-TSS (NM_001079824)	34	NM_001079824	432467	Mm.274784	NM_001079824	ENSMUSG00000020069	Hnrnph3	AA693301|AI666703|Hnrph3	heterogeneous nuclear ribonucleoprotein H3	protein-coding
mm_95342.1	chr11	48716077	48716081	+	1	NA	Intergenic	Intergenic	-84281	NM_008143	14694	Mm.5305	NM_008143	ENSMUSG00000020372	Rack1	AL033335|GB-like|Gnb2-rs1|Gnb2l1|p205	receptor for activated C kinase 1	protein-coding
mm_12822.1	chr2	80317005	80317024	+	1	NA	intron (NM_024181, intron 1 of 22)	intron (NM_024181, intron 1 of 22)	1548	NM_024181	66861	Mm.21762	NM_024181	ENSMUSG00000027006	Dnajc10	1200006L06Rik|D2Ertd706e|ERdj5|JPDI	DnaJ heat shock protein family (Hsp40) member C10	protein-coding
mm_156710.1	chrX	159627465	159627478	+	1	NA	5' UTR (NM_001135727, exon 1 of 18)	5' UTR (NM_001135727, exon 1 of 18)	199	NM_001135727	58194	Mm.286495	NM_021389	ENSMUSG00000040990	Sh3kbp1	1200007H22Rik|1700125L08Rik|5830464D22Rik|AI447724|Cin85|IN85|Ruk|Seta	SH3-domain kinase binding protein 1	protein-coding
mm_8942.1	chr1	164437978	164437999	-	1	NA	TTS (NM_001293313)	TTS (NM_001293313)	20367	NM_009721	11931	Mm.4550	NM_009721	ENSMUSG00000026576	Atp1b1	Atp4b|Atpb|Atpb-1|NKbeta1	ATPase, Na+/K+ transporting, beta 1 polypeptide	protein-coding
mm_32562.1	chr4	109676569	109676590	+	1	NA	promoter-TSS (NM_007983)	promoter-TSS (NM_007983)	-48	NM_007983	14084	Mm.318259	NM_007983	ENSMUSG00000010517	Faf1	AA408698|Dffrx|Fam	Fas-associated factor 1	protein-coding
mm_79759.1	chr9	62389958	62389960	+	1	NA	Intergenic	Intergenic	48616	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	protein-coding
mm_75042.1	chr8	32763038	32763047	-	1	NA	Intergenic	Lx9|LINE|L1	186984	NM_001177589	100042715	Mm.291093	NM_001177589		Gm3985	-	predicted gene 3985	protein-coding
mm_158372.1	chrX	135036092	135036099	-	1	NA	non-coding (NR_040283, exon 1 of 3)	non-coding (NR_040283, exon 1 of 3)	507	NR_040281	320606	Mm.439072	NR_040281	ENSMUSG00000089759	3632454L22Rik	-	RIKEN cDNA 3632454L22 gene	ncRNA
mm_78780.1	chr9	43804202	43804212	+	1	NA	3' UTR (NM_021424, exon 6 of 6)	3' UTR (NM_021424, exon 6 of 6)	59631	NM_021424	58235	Mm.335096	NM_021424	ENSMUSG00000032012	Nectin1	AI835281|AW549174|Cd111|HIgR|HveC|PRR|PRR1|Pvrl1|nectin-1	nectin cell adhesion molecule 1	protein-coding
mm_40371.1	chr5	52189861	52189871	+	1	NA	promoter-TSS (NR_015537)	promoter-TSS (NR_015537)	680	NR_104311	13204	Mm.993	NM_007839	ENSMUSG00000029169	Dhx15	DBP1|DEAH9|Ddx15|HRH2|mDEAH9	DEAH (Asp-Glu-Ala-His) box polypeptide 15	protein-coding
mm_164736.1	chr17	68406202	68406202	+	1	NA	intron (NM_177278, intron 4 of 20)	intron (NM_177278, intron 4 of 20)	132405	NM_177278	320858	Mm.137356	NM_177278	ENSMUSG00000041565	L3mbtl4	A730037L19Rik|D930040M24Rik	l(3)mbt-like 4 (Drosophila)	protein-coding
mm_108278.1	chr12	78911931	78911933	+	1	NA	Intergenic	Intergenic	-4994	NM_013738	27260	Mm.103380	NM_013738	ENSMUSG00000021118	Plek2	-	pleckstrin 2	protein-coding
mm_129698.1	chr15	81586471	81586496	-	1	NA	5' UTR (NM_177821, exon 1 of 31)	5' UTR (NM_177821, exon 1 of 31)	269	NM_177821	328572	Mm.258397	NM_177821	ENSMUSG00000055024	Ep300	A430090G16|A730011L11|KAT3B|p300|p300 HAT	E1A binding protein p300	protein-coding
mm_14344.1	chr2	129593235	129593258	+	1	NA	promoter-TSS (NM_001291022)	promoter-TSS (NM_001291022)	77	NM_001291022	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_166332.1	chr5	114025025	114025063	+	1	NA	3' UTR (NM_001286397, exon 10 of 10)	3' UTR (NM_001286397, exon 10 of 10)	20236	NM_001286396	13142	Mm.20115	NM_010018	ENSMUSG00000042096	Dao	AI987963|DAAO|DAMOX|Dao-1|Dao1	D-amino acid oxidase	protein-coding
mm_147564.1	chr18	54990125	54990144	-	1	NA	promoter-TSS (NM_175751)	promoter-TSS (NM_175751)	46	NM_175751	269023	Mm.192984	NM_175751	ENSMUSG00000052713	Zfp608	4932417D18Rik|D430007A19Rik|Znf608	zinc finger protein 608	protein-coding
mm_15501.1	chr2	157914661	157914671	+	1	NA	promoter-TSS (NM_198627)	promoter-TSS (NM_198627)	13	NM_198627	277432	Mm.441156	NM_198627	ENSMUSG00000037843	Vstm2l	Gm691	V-set and transmembrane domain containing 2-like	protein-coding
mm_76442.1	chr8	85025232	85025238	-	1	NA	promoter-TSS (NM_019652)	promoter-TSS (NM_019652)	43	NM_019652	56495	Mm.41475	NM_019652	ENSMUSG00000052456	Asna1	1810048H22Rik|ArsA	arsA arsenite transporter, ATP-binding, homolog 1 (bacterial)	protein-coding
mm_132793.1	chr16	45093666	45093681	+	1	NA	promoter-TSS (NM_026439)	promoter-TSS (NM_026439)	-380	NM_026439	67896	Mm.181074	NM_026439	ENSMUSG00000022665	Ccdc80	2610001E17Rik|DRO1|Ssg1|Urb	coiled-coil domain containing 80	protein-coding
mm_71715.1	chr8	61947433	61947444	+	1	NA	intron (NM_001293783, intron 6 of 37)	B3|SINE|B2	19351	NM_001293783	234311	Mm.275233	NM_144928	ENSMUSG00000037921	Ddx60	9830118M07	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	protein-coding
mm_87216.1	chr10	39899305	39899352	+	1	NA	promoter-TSS (NR_033628)	promoter-TSS (NR_033628)	-90	NR_033628	213332	Mm.484359	NR_033628		Mfsd4b4	AA474331	major facilitator superfamily domain containing 4B4	pseudo
mm_52099.1	chr6	97862890	97862934	+	1	NA	intron (NM_001113198, intron 1 of 9)	intron (NM_001113198, intron 1 of 9)	55854	NM_001113198	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_73385.1	chr8	105686232	105686270	+	1	NA	Intergenic	Intergenic	-4655	NM_001033320	234695	Mm.471640	NM_001033320	ENSMUSG00000050357	Carmil2	CG1399-PB|D130029J02Rik|Gm585|Rltpr	capping protein regulator and myosin 1 linker 2	protein-coding
mm_75441.1	chr8	47413834	47413855	-	1	NA	Intergenic	CpG	-61496	NM_175162	71069	Mm.23973	NM_175162	ENSMUSG00000038143	Stox2	4933409N07Rik|AI449080|AI835114|mKIAA1392	storkhead box 2	protein-coding
mm_131603.1	chr16	19067233	19067245	+	1	NA	Intergenic	Intergenic	190489	NM_010435	15260	Mm.15694	NM_010435	ENSMUSG00000022702	Hira	AA138857|D16Ertd95e|Gm15797|N28177|OTTMUSG00000026264|Tuple1	histone cell cycle regulator	protein-coding
mm_4076.1	chr1	166254160	166254170	+	1	NA	promoter-TSS (NM_001164528)	promoter-TSS (NM_001164528)	26	NM_001164528	100039795	Mm.101743	NM_001164528	ENSMUSG00000040612	Ildr2	2810478N18Rik|3110063L10Rik|AI852300|D1Ertd471e|Dbsm1|ENSMUSG00000040612|Ll	immunoglobulin-like domain containing receptor 2	protein-coding
mm_161673.1	chr17	14961104	14961104	-	1	NA	intron (NM_024250, intron 1 of 11)	CpG	156	NM_024250	72057	Mm.440085	NM_024250	ENSMUSG00000023883	Phf10	1810055P05Rik|AV024533	PHD finger protein 10	protein-coding
mm_158779.1	chrX	167207150	167207163	-	1	NA	TTS (NM_021278)	TTS (NM_021278)	2062	NM_021278	19241	Mm.142729	NM_021278	ENSMUSG00000049775	Tmsb4x	Ptmb4|Tb4	thymosin, beta 4, X chromosome	protein-coding
mm_141068.1	chr17	25797033	25797075	-	1	NA	promoter-TSS (NM_133719)	promoter-TSS (NM_133719)	-9	NM_133719	70083	Mm.41925	NM_133719	ENSMUSG00000002274	Metrn	1810034B16Rik|Hyrac	meteorin, glial cell differentiation regulator	protein-coding
mm_32956.1	chr4	119658521	119658543	+	1	NA	intron (NM_008191, intron 1 of 2)	intron (NM_008191, intron 1 of 2)	413	NM_008191	14916	Mm.278	NM_008191	ENSMUSG00000032978	Guca2b	AV066530|Gcap2|Ugn	guanylate cyclase activator 2b (retina)	protein-coding
mm_171497.1	chr4	146224733	146224735	-	1	NA	Intergenic	CpG	-45651	NM_001083918	666532	Mm.392861	NM_001083918	ENSMUSG00000067916	Zfp991	Gm13139|OTTMUSG00000010657	zinc finger protein 991	protein-coding
mm_57267.1	chr6	123287038	123287039	-	1	NA	intron (NM_019948, intron 2 of 5)	intron (NM_019948, intron 2 of 5)	2833	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_2569.1	chr1	118413842	118413845	+	1	NA	intron (NM_001293300, intron 1 of 40)	intron (NM_001293300, intron 1 of 40)	24785	NM_001293301	76707	Mm.138740	NM_029709	ENSMUSG00000064302	Clasp1	1700030C23Rik|5730583A19Rik|B130045P17Rik|CLASP1alpha	CLIP associating protein 1	protein-coding
mm_119.1	chr1	9797987	9798040	+	1	NA	promoter-TSS (NM_133220)	promoter-TSS (NM_133220)	-117	NM_133220	170755	Mm.336410	NM_133220	ENSMUSG00000025915	Sgk3	2510015P22Rik|A330005P07Rik|Cisk|fy|fz	serum/glucocorticoid regulated kinase 3	protein-coding
mm_104435.1	chr11	94951654	94951670	-	1	NA	3' UTR (NM_007742, exon 51 of 51)	3' UTR (NM_007742, exon 51 of 51)	15438	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_42843.1	chr5	122149605	122149608	+	1	NA	Intergenic	RMER10B|LTR|ERVL	-8673	NM_013636	19047	Mm.280784	NM_013636	ENSMUSG00000004455	Ppp1cc	PP-1G|PP1|dis2m1	protein phosphatase 1, catalytic subunit, gamma isoform	protein-coding
mm_166783.1	chr6	143035144	143035188	-	1	NA	intron (NM_001109688, intron 15 of 24)	intron (NM_001109688, intron 15 of 24)	64986	NM_001286578	74741	Mm.130260	NM_029081	ENSMUSG00000030279	C2cd5	5730419I09Rik|C030008B15Rik|CDP138	C2 calcium-dependent domain containing 5	protein-coding
mm_56316.1	chr6	92242742	92242757	-	1	NA	exon (NM_009426, exon 3 of 3)	exon (NM_009426, exon 3 of 3)	1901	NM_009426	22044	Mm.1363	NM_009426	ENSMUSG00000005892	Trh	Pro-TRH|Trf	thyrotropin releasing hormone	protein-coding
mm_25511.1	chr3	110145517	110145520	+	1	NA	Intergenic	Intergenic	-2046	NM_030699	80883	Mm.39262	NM_030699	ENSMUSG00000059857	Ntng1	A930010C08Rik|AI853992|Lmnt1	netrin G1	protein-coding
mm_118778.1	chr14	23432496	23432509	+	1	NA	intron (NM_001253361, intron 19 of 30)	intron (NM_001253361, intron 19 of 30)	-337931	NR_033550	791307	Mm.364384	NR_033550	ENSMUSG00000068680	Gm10248	ENSMUSG00000068680	predicted gene 10248	ncRNA
mm_115435.1	chr13	117273298	117273333	+	1	NA	3' UTR (NM_010330, exon 9 of 9)	3' UTR (NM_010330, exon 9 of 9)	52742	NM_010330	13723	Mm.274926	NM_010330	ENSMUSG00000021728	Emb	AL022799|Gp70	embigin	protein-coding
mm_19564.1	chr2	101621034	101621066	-	1	NA	intron (NM_026592, intron 1 of 6)	intron (NM_026592, intron 1 of 6)	-3698	NM_009020	19374	Mm.4988	NM_009020	ENSMUSG00000032864	Rag2	Rag-2	recombination activating gene 2	protein-coding
mm_171541.1	chr4	146972047	146972054	+	1	NA	Intergenic	Intergenic	-49800	NM_001177767	100043034	Mm.422606	NM_001177767	ENSMUSG00000067919	Rex2	Gm13138|OTTMUSG00000010655	reduced expression 2	protein-coding
mm_91007.1	chr10	14546288	14546298	-	1	NA	Intergenic	Intergenic	-1257	NM_001002268	215798	Mm.440142	NM_001002268	ENSMUSG00000039116	Adgrg6	1190004A11Rik|AI449247|AW045736|DREG|Gm222|Gpr126	adhesion G protein-coupled receptor G6	protein-coding
mm_166666.1	chr6	90570788	90570795	+	1	NA	exon (NM_027406, exon 11 of 23)	exon (NM_027406, exon 11 of 23)	19943	NM_027406	107747	Mm.30035	NM_027406	ENSMUSG00000030088	Aldh1l1	1810048F20Rik|FDH|Fthfd|Neut2	aldehyde dehydrogenase 1 family, member L1	protein-coding
mm_80396.1	chr9	76312453	76312469	+	1	NA	intron (NM_198962, intron 1 of 7)	ORR1B2|LTR|ERVL-MaLR	11117	NM_198962	387285	Mm.335300	NM_198962	ENSMUSG00000032360	Hcrtr2	OX2R|mOX2aR|mOX2bR|mOXR2	hypocretin (orexin) receptor 2	protein-coding
mm_77734.1	chr8	126895238	126895246	-	1	NA	Intergenic	Intergenic	50679	NM_024214	67952	Mm.6932	NM_024214	ENSMUSG00000093904	Tomm20	1810060K07Rik|BB284719|Gm19268|MAS20|MOM19|TOM20|mKIAA0016	translocase of outer mitochondrial membrane 20 homolog (yeast)	protein-coding
mm_152200.1	chr19	7583333	7583336	-	1	NA	intron (NM_139269, intron 4 of 4)	intron (NM_139269, intron 4 of 4)	23842	NM_019516	56072	Mm.298242	NM_019516	ENSMUSG00000024972	Lgals12	AW987437|Grip1	lectin, galactose binding, soluble 12	protein-coding
mm_41341.1	chr5	90498257	90498315	+	1	NA	exon (NM_007423, exon 6 of 15)	exon (NM_007423, exon 6 of 15)	7572	NM_007423	11576	Mm.358570	NM_007423	ENSMUSG00000054932	Afp	-	alpha fetoprotein	protein-coding
mm_128726.1	chr15	64060440	64060478	-	1	NA	promoter-TSS (NM_144846)	promoter-TSS (NM_144846)	-11	NM_144846	223601	Mm.246108	NM_144846	ENSMUSG00000022378	Fam49b	0910001A06Rik|AW122079	family with sequence similarity 49, member B	protein-coding
mm_94428.1	chr11	6291661	6291687	+	1	NA	promoter-TSS (NM_001252282)	promoter-TSS (NM_001252282)	77	NM_001252283	18293	Mm.276348	NM_010956	ENSMUSG00000020456	Ogdh	2210403E04Rik|2210412K19Rik|AA409584|d1401|mKIAA4192	oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)	protein-coding
mm_28508.1	chr3	92573746	92573756	-	1	NA	promoter-TSS (NM_008412)	promoter-TSS (NM_008412)	-16	NM_008412	16447	Mm.207365	NM_008412	ENSMUSG00000049128	Ivl	1110019C06Rik	involucrin	protein-coding
mm_139251.1	chr17	47734340	47734354	+	1	NA	3' UTR (NM_025973, exon 9 of 9)	3' UTR (NM_025973, exon 9 of 9)	-2690	NM_001161722	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_150069.1	chr19	29386528	29386552	+	1	NA	3' UTR (NM_021893, exon 7 of 7)	3' UTR (NM_021893, exon 7 of 7)	19102	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_98008.1	chr11	84179867	84179877	+	1	NA	Intergenic	CpG	-12396	NM_001037932	628813	Mm.390389	NM_001037932	ENSMUSG00000051452	Gm11437	AI463690|OTTMUSG00000000997	predicted gene 11437	protein-coding
mm_77330.1	chr8	119501699	119501726	-	1	NA	promoter-TSS (NM_001009950)	promoter-TSS (NM_001009950)	-14	NM_001009950	234788	Mm.302096	NM_001009950	ENSMUSG00000034224	Slc38a8	Gm587	solute carrier family 38, member 8	protein-coding
mm_50004.1	chr6	41057729	41057737	+	1	NA	Intergenic	Intergenic	-22224	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_141989.1	chr17	35172578	35172599	-	1	NA	5' UTR (NM_019467, exon 3 of 8)	5' UTR (NM_019467, exon 3 of 8)	3413	NM_019467	11629	Mm.10747	NM_019467	ENSMUSG00000024397	Aif1	AI607846|AIF-1|D17H6S50E|G1|Iba1	allograft inflammatory factor 1	protein-coding
mm_151186.1	chr19	53421315	53421328	+	1	NA	Intergenic	Intergenic	-30748	NM_172429	76479	Mm.313687	NM_172429	ENSMUSG00000025024	Smndc1	2410004J23Rik|4933440I19Rik	survival motor neuron domain containing 1	protein-coding
mm_61552.1	chr7	79398666	79398681	+	1	NA	intron (NM_145946, intron 2 of 37)	intron (NM_145946, intron 2 of 37)	6335	NM_145946	208836	Mm.349493	NM_145946	ENSMUSG00000039187	Fanci	-	Fanconi anemia, complementation group I	protein-coding
mm_50379.1	chr6	48685142	48685186	+	1	NA	intron (NM_174990, intron 1 of 2)	intron (NM_174990, intron 1 of 2)	586	NM_174990	107526	Mm.333048	NM_174990	ENSMUSG00000054435	Gimap4	AU019574|E430007K16Rik|Ian-1|Ian1|Imap4	GTPase, IMAP family member 4	protein-coding
mm_155357.1	chrX	69415313	69415339	+	1	NA	intron (NM_008032, intron 1 of 19)	MER77|LTR|ERVL	54995	NM_008032	14266	Mm.466576	NM_008032	ENSMUSG00000031189	Aff2	FMR2P|Fmr2|Ox19|Oxh	AF4/FMR2 family, member 2	protein-coding
mm_88936.1	chr10	81292962	81293005	+	1	NA	promoter-TSS (NM_001146687)	promoter-TSS (NM_001146687)	20	NM_001146687	18717	Mm.24222	NM_008844	ENSMUSG00000034902	Pip5k1c	AI115456|AI835305|Pip5kIgamma	phosphatidylinositol-4-phosphate 5-kinase, type 1 gamma	protein-coding
mm_44588.1	chr5	24925384	24925397	-	1	NA	intron (NM_001310480, intron 2 of 13)	(TG)n|Simple_repeat|Simple_repeat	-16881	NM_001170555	108099	Mm.33649	NM_145401	ENSMUSG00000028944	Prkag2	2410051C13Rik|AAKG|AAKG2|AI854673|H91620p|WPWS	protein kinase, AMP-activated, gamma 2 non-catalytic subunit	protein-coding
mm_33800.1	chr4	134926676	134926690	+	1	NA	intron (NM_023665, intron 3 of 4)	AT_rich|Low_complexity|Low_complexity	3058	NM_023665	27981	Mm.331964	NM_023665	ENSMUSG00000037266	Rsrp1	2700043I21Rik|D4Ucla2|D4Wsu53e	arginine/serine rich protein 1	protein-coding
mm_82220.1	chr9	3022199	3022225	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	16531	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_12555.1	chr2	72444662	72444669	+	1	NA	Intergenic	MTB|LTR|ERVL-MaLR	-31554	NM_025866	66953	Mm.270676	NM_025866	ENSMUSG00000055612	Cdca7	2310021G01Rik|AU044109|JPO1	cell division cycle associated 7	protein-coding
mm_1159.1	chr1	60903423	60903430	+	1	NA	Intergenic	Intergenic	-5599	NM_009843	12477	Mm.390	NM_009843	ENSMUSG00000026011	Ctla4	Cd152|Ctla-4|Ly-56	cytotoxic T-lymphocyte-associated protein 4	protein-coding
mm_100386.1	chr11	119355035	119355089	+	1	NA	promoter-TSS (NM_178743)	promoter-TSS (NM_178743)	448	NM_018822	27029	Mm.103788	NM_018822	ENSMUSG00000005043	Sgsh	4632406A19Rik	N-sulfoglucosamine sulfohydrolase (sulfamidase)	protein-coding
mm_148924.1	chr19	6986019	6986067	+	1	NA	exon (NM_011697, exon 4 of 7)	exon (NM_011697, exon 4 of 7)	1608	NM_001185164	22340	Mm.15607	NM_011697	ENSMUSG00000024962	Vegfb	VEGF-B|Vrf	vascular endothelial growth factor B	protein-coding
mm_42314.1	chr5	114882468	114882474	+	1	NA	intron (NM_026263, intron 11 of 11)	intron (NM_026263, intron 11 of 11)	-14463	NM_011854	23962	Mm.228363	NM_011854	ENSMUSG00000029561	Oasl2	M1204|Mmu-OASL|Oasl	2'-5' oligoadenylate synthetase-like 2	protein-coding
mm_88136.1	chr10	69398924	69398949	+	1	NA	Intergenic	CpG	-46024	NM_007659	12534	Mm.281367	NM_007659	ENSMUSG00000019942	Cdk1	Cdc2|Cdc2a|p34<CDC2>	cyclin-dependent kinase 1	protein-coding
mm_92278.1	chr10	71238275	71238288	-	1	NA	promoter-TSS (NM_009360)	promoter-TSS (NM_009360)	-237	NM_009360	21780	Mm.229292	NM_009360	ENSMUSG00000003923	Tfam	AI661103|Hmgts|mtTFA|tsHMG	transcription factor A, mitochondrial	protein-coding
mm_103348.1	chr11	74770688	74770697	-	1	NA	promoter-TSS (NM_026197)	promoter-TSS (NM_026197)	-171	NM_026197	67493	Mm.45748	NM_026197	ENSMUSG00000010554	Mettl16	2610100D03Rik|2810013M15Rik|A830095F14Rik|AI846133|Mett10d	methyltransferase like 16	protein-coding
mm_157589.1	chrX	53114393	53114412	-	1	NA	promoter-TSS (NM_019538)	promoter-TSS (NM_019538)	3	NM_019538	56096	Mm.274842	NM_019538	ENSMUSG00000061082	Plac1	DXWsu72e|Epcs26|Oosp2l	placental specific protein 1	protein-coding
mm_10164.1	chr2	4401506	4401524	+	1	NA	5' UTR (NM_001177843, exon 1 of 24)	5' UTR (NM_001177843, exon 1 of 24)	539	NM_001177843	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding
mm_5206.1	chr1	13565233	13565274	-	1	NA	3' UTR (NM_028173, exon 11 of 11)	3' UTR (NM_028173, exon 11 of 11)	24657	NM_028173	72265	Mm.28765	NM_028173	ENSMUSG00000025935	Tram1	1810049E02Rik|TRAMP	translocating chain-associating membrane protein 1	protein-coding
mm_82545.1	chr9	20896161	20896183	-	1	NA	exon (NM_016876, exon 6 of 11)	exon (NM_016876, exon 6 of 11)	2418	NM_016876	53356	Mm.427309	NM_016876	ENSMUSG00000070319	Eif3g	44kDa|D0Jmb4|Eif3s4|TU-189B2|eIF3-p44|p44	eukaryotic translation initiation factor 3, subunit G	protein-coding
mm_2515.1	chr1	106251859	106251876	+	1	NA	intron (NM_133821, intron 1 of 16)	B1_Mus1|SINE|Alu	79998	NM_133821	98432	Mm.24115	NM_133821	ENSMUSG00000044340	Phlpp1	AI836256|Phlpp|Plekhe1|SCOP|mKIAA0606	PH domain and leucine rich repeat protein phosphatase 1	protein-coding
mm_72526.1	chr8	83978425	83978461	+	1	NA	intron (NM_001277898, intron 1 of 9)	intron (NM_001277898, intron 1 of 9)	1560	NM_001277898	18747	Mm.19111	NM_008854	ENSMUSG00000005469	Prkaca	PKCD|Pkaca	protein kinase, cAMP dependent, catalytic, alpha	protein-coding
mm_105374.1	chr11	103237876	103237912	-	1	NA	intron (NM_016896, intron 5 of 15)	B2_Mm2|SINE|B2	-19462	NM_177801	328019	Mm.189646	NM_177801	ENSMUSG00000044787	Spata32	4933400C05Rik|VAD1.2	spermatogenesis associated 32	protein-coding
mm_91557.1	chr10	39960244	39960283	-	1	NA	promoter-TSS (NM_001173500)	promoter-TSS (NM_001173500)	-110	NM_001173500	100041085	Mm.332530	NM_001173500	ENSMUSG00000071335	Mfsd4b3	G630090E17Rik|Naglt1c	major facilitator superfamily domain containing 4B3	protein-coding
mm_3541.1	chr1	150395261	150395275	+	1	NA	exon (NM_133780, exon 3 of 52)	exon (NM_133780, exon 3 of 52)	-2213	NM_145511	226499	Mm.222093	NM_145511	ENSMUSG00000006010	BC003331	1810053E15Rik|Odr4|odr-4	cDNA sequence BC003331	protein-coding
mm_91017.1	chr10	17495964	17495985	-	1	NA	Intergenic	Intergenic	-227254	NM_010828	17684	Mm.272321	NM_010828	ENSMUSG00000039910	Cited2	AI835299|ER154-like|Mrg1|Msg2|p35srj	Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 2	protein-coding
mm_34500.1	chr4	148602659	148602660	+	1	NA	intron (NM_001003893, intron 1 of 10)	intron (NM_001003893, intron 1 of 10)	115	NM_001003893	17175	Mm.378962	NM_010767	ENSMUSG00000028979	Masp2	MASP-2|MAp19	mannan-binding lectin serine peptidase 2	protein-coding
mm_131660.1	chr16	20609990	20610009	+	1	NA	intron (NM_145939, intron 1 of 8)	B1_Mur1|SINE|Alu	750	NM_145939	208624	Mm.24950	NM_145939	ENSMUSG00000033809	Alg3	D16Ertd36e|not	asparagine-linked glycosylation 3 (alpha-1,3-mannosyltransferase)	protein-coding
mm_165399.1	chr2	136058105	136058107	+	1	NA	5' UTR (NM_029530, exon 1 of 6)	5' UTR (NM_029530, exon 1 of 6)	179	NM_029530	76161	Mm.41638	NM_029530	ENSMUSG00000027270	Lamp5	3110035N03Rik|6330527O06Rik|BAD-LAMP|LAMP-5	lysosomal-associated membrane protein family, member 5	protein-coding
mm_56253.1	chr6	90764298	90764309	-	1	NA	intron (NM_001134384, intron 1 of 13)	intron (NM_001134384, intron 1 of 13)	45820	NM_001134384	232227	Mm.196943	NM_182784	ENSMUSG00000034312	Iqsec1	AW561907|BC026481|BRAG2|D6Ertd349e|cI-43	IQ motif and Sec7 domain 1	protein-coding
mm_109047.1	chr12	104300704	104300736	+	1	NA	Intergenic	Intergenic	-13850	NM_001101472	238395	Mm.436975	NM_001101472	ENSMUSG00000079013	Serpina3j	AI506554|EG238395|Gm4931	serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3J	protein-coding
mm_39629.1	chr5	24428761	24428772	+	1	NA	intron (NM_009207, intron 2 of 22)	intron (NM_009207, intron 2 of 22)	1245	NM_001253892	20535	Mm.4580	NM_009207	ENSMUSG00000028962	Slc4a2	Ae2|B3RP	solute carrier family 4 (anion exchanger), member 2	protein-coding
mm_91469.1	chr10	34197764	34197768	-	1	NA	intron (NM_172508, intron 1 of 5)	intron (NM_172508, intron 1 of 5)	9785	NM_172508	212898	Mm.34557	NM_172508	ENSMUSG00000039497	Dse	6030499O08|AI480506|B130024B19Rik|DS-epi1|Sart2	dermatan sulfate epimerase	protein-coding
mm_170302.1	chr18	33515003	33515003	+	1	NA	Intergenic	Intergenic	50840	NR_045415	433171	Mm.353332	NR_045415		Gm10549	ENSMUSG00000073610	predicted gene 10549	ncRNA
mm_147226.1	chr18	38203843	38203851	-	1	NA	intron (NM_029357, intron 1 of 2)	intron (NM_029357, intron 1 of 2)	5915	NM_029357	75599	Mm.36560	NM_029357	ENSMUSG00000051375	Pcdh1	2010005A06Rik|AI585920	protocadherin 1	protein-coding
mm_34052.1	chr4	138262190	138262258	+	1	NA	promoter-TSS (NM_001190978)	promoter-TSS (NM_001190978)	-27	NM_001190978	16559	Mm.271936	NM_010623	ENSMUSG00000028758	Kif17	5930435E01Rik|AW492270|Kif17b|mKIAA1405	kinesin family member 17	protein-coding
mm_25598.1	chr3	116903664	116903688	+	1	NA	TTS (NM_001113478)	TTS (NM_001113478)	41996	NM_009146	20321	Mm.66293	NM_009146	ENSMUSG00000033386	Frrs1	AI131732|Sdfr2	ferric-chelate reductase 1	protein-coding
mm_78549.1	chr9	35421626	35421637	+	1	NA	Intergenic	CpG	-30445	NM_021339	57810	Mm.80509	NM_021339	ENSMUSG00000038119	Cdon	CDO|Cd0|Orcam	cell adhesion molecule-related/down-regulated by oncogenes	protein-coding
mm_160318.1	chr7	142658812	142658812	-	1	NA	promoter-TSS (NM_010514)	promoter-TSS (NM_010514)	-8	NM_010514	16002	Mm.3862	NM_010514	ENSMUSG00000048583	Igf2	AL033362|Igf-2|Igf-II|M6pr|Mpr|Peg2	insulin-like growth factor 2	protein-coding
mm_36138.1	chr4	59351723	59351754	-	1	NA	intron (NM_001163288, intron 10 of 16)	intron (NM_001163288, intron 10 of 16)	86895	NM_001163288	634731	Mm.483589	NM_001163288	ENSMUSG00000038578	Susd1	A530080P10|Gm12528|OTTMUSG00000007332	sushi domain containing 1	protein-coding
mm_64893.1	chr7	15946058	15946069	-	1	NA	promoter-TSS (NM_133831)	promoter-TSS (NM_133831)	45	NM_133831	68077	Mm.277634	NM_133831	ENSMUSG00000041560	Gltscr2	5330430H08Rik|9430097C02Rik|AU041936|AW536441|PICT-1|R74911	glioma tumor suppressor candidate region gene 2	protein-coding
mm_16944.1	chr2	15049177	15049198	-	1	NA	5' UTR (NM_001165942, exon 1 of 4)	5' UTR (NM_001165942, exon 1 of 4)	125	NM_001165942	74455	Mm.478923	NM_028950	ENSMUSG00000026707	Nsun6	4933403D21Rik|4933414E04Rik|NOPD1	NOL1/NOP2/Sun domain family member 6	protein-coding
mm_19227.1	chr2	84670651	84670657	-	1	NA	promoter-TSS (NM_001033166)	promoter-TSS (NM_001033166)	54	NM_001033166	72657	Mm.259293	NM_001033166	ENSMUSG00000076437	Selenoh	2700094K13Rik|Selh	selenoprotein H	protein-coding
mm_144163.1	chr18	5772695	5772707	+	1	NA	exon (NM_011546, exon 8 of 8)	exon (NM_011546, exon 8 of 8)	-180264	NR_033552	791318	Mm.84339	NR_033552	ENSMUSG00000063087	Gm10125	ENSMUSG00000063087|Zeb1os	predicted gene 10125	ncRNA
mm_53879.1	chr6	3323382	3323394	-	1	NA	Intergenic	L1_Mur3|LINE|L1	34869	NR_036696	667335	Mm.380219	NR_036696	ENSMUSG00000106779	Gm8579	EG667335	spermatogenesis associated glutamate (E)-rich protein 4a pseudogene	pseudo
mm_45614.1	chr5	75835677	75835697	-	1	NA	Intergenic	Intergenic	142741	NM_010612	16542	Mm.285	NM_010612	ENSMUSG00000062960	Kdr	6130401C07|Flk-1|Flk1|Krd-1|Ly73|VEGFR-2|VEGFR2|sVEGFR-2	kinase insert domain protein receptor	protein-coding
mm_70061.1	chr7	142652194	142652226	-	1	NA	3' UTR (NM_010514, exon 4 of 4)	3' UTR (NM_010514, exon 4 of 4)	2786	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_161518.1	chr15	99249083	99249083	-	1	NA	intron (NM_001164156, intron 3 of 13)	intron (NM_001164156, intron 3 of 13)	-2705	NR_045627	73600	Mm.475134	NR_045627	ENSMUSG00000100599	1700120C14Rik	-	RIKEN cDNA 1700120C14 gene	ncRNA
mm_66305.1	chr7	38271311	38271390	-	1	NA	promoter-TSS (NM_025390)	promoter-TSS (NM_025390)	-2	NM_025390	66161	Mm.22284	NM_025390	ENSMUSG00000030423	Pop4	1110023P21Rik|Rpp29	processing of precursor 4, ribonuclease P/MRP family, (S. cerevisiae)	protein-coding
mm_159181.1	chr2	111449294	111449294	+	1	NA	exon (NM_001011773, exon 1 of 1)	exon (NM_001011773, exon 1 of 1)	152	NM_001011773	257935	Mm.377308	NM_001011773	ENSMUSG00000095586	Olfr1287	MOR248-15	olfactory receptor 1287	protein-coding
mm_154116.1	chr19	57178540	57178541	-	1	NA	intron (NM_001290813, intron 1 of 20)	intron (NM_001290813, intron 1 of 20)	19091	NM_001103177	226251	Mm.217161	NM_178688	ENSMUSG00000025085	Ablim1	2210411C18Rik|2610209L21Rik|4833406P10Rik|9330196J19Rik|AV079770|AW060987|AW215784|Limab1|mKIAA0059	actin-binding LIM protein 1	protein-coding
mm_109546.1	chr12	111698616	111698624	+	1	NA	Intergenic	Intergenic	14333	NM_001324481	70369	Mm.44239	NM_027404	ENSMUSG00000049792	Bag5	1600025G07Rik|4930405J06Rik|Bag-5	BCL2-associated athanogene 5	protein-coding
mm_20347.1	chr2	127729873	127729936	-	1	NA	promoter-TSS (NM_145532)	promoter-TSS (NM_145532)	-7	NM_145532	228576	Mm.133036	NM_145532	ENSMUSG00000027377	Mall	BC012256|BENE	mal, T cell differentiation protein-like	protein-coding
mm_156386.1	chrX	139792592	139792623	+	1	NA	Intergenic	Intergenic	-8201	NM_016675	12738	Mm.117068	NM_016675	ENSMUSG00000047230	Cldn2	AL022813	claudin 2	protein-coding
mm_100285.1	chr11	117809688	117809703	+	1	NA	promoter-TSS (NM_009304)	promoter-TSS (NM_009304)	28	NM_009304	20973	Mm.468228	NM_009304	ENSMUSG00000048277	Syngr2	Clast2|cellugyrin	synaptogyrin 2	protein-coding
mm_51757.1	chr6	87778065	87778082	+	1	NA	promoter-TSS (NM_018762)	promoter-TSS (NM_018762)	-63	NM_018762	54368	Mm.12897	NM_018762	ENSMUSG00000030054	Gp9	Cd42|GPIX	glycoprotein 9 (platelet)	protein-coding
mm_90736.1	chr10	5338884	5338897	-	1	NA	3' UTR (NM_153399, exon 32 of 32)	3' UTR (NM_153399, exon 32 of 32)	-144183	NM_001079686	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_49510.1	chr6	29859375	29859381	+	1	NA	promoter-TSS (NM_001171001)	promoter-TSS (NM_001171001)	-218	NM_001171001	74340	Mm.210899	NM_021414	ENSMUSG00000029772	Ahcyl2	4631427C17Rik|AI227036|Adohcyase3|mKIAA0828	S-adenosylhomocysteine hydrolase-like 2	protein-coding
mm_134433.1	chr16	18073634	18073655	-	1	NA	exon (NM_011172, exon 12 of 14)	exon (NM_011172, exon 12 of 14)	7241	NM_001289813	13353	Mm.27155	NM_010047	ENSMUSG00000003531	Dgcr6	-	DiGeorge syndrome critical region gene 6	protein-coding
mm_144604.1	chr18	32397581	32397595	+	1	NA	intron (NM_001083334, intron 1 of 14)	intron (NM_001083334, intron 1 of 14)	-19304	NR_045403	402767	Mm.385109	NR_045403	ENSMUSG00000097413	A830052D11Rik	-	RIKEN cDNA A830052D11 gene	ncRNA
mm_55862.1	chr6	83456477	83456524	-	1	NA	promoter-TSS (NM_001347313)	promoter-TSS (NM_001347313)	-108	NM_001347313	194388	Mm.211030	NM_183138	ENSMUSG00000034832	Tet3	B430006D22Rik|BC037432|D230004J03Rik	tet methylcytosine dioxygenase 3	protein-coding
mm_163799.1	chr14	18331149	18331170	+	1	NA	intron (NM_009455, intron 1 of 5)	CpG	685	NM_009455	22194	Mm.4429	NM_009455	ENSMUSG00000021774	Ube2e1	UbcM3|Ubce5|ubcM2	ubiquitin-conjugating enzyme E2E 1	protein-coding
mm_3149.1	chr1	135147616	135147626	+	1	NA	intron (NM_026823, intron 1 of 6)	intron (NM_026823, intron 1 of 6)	787	NM_026823	68724	Mm.174998	NM_026823	ENSMUSG00000026426	Arl8a	1110033P22Rik|Arl10b|gie2	ADP-ribosylation factor-like 8A	protein-coding
mm_69372.1	chr7	130847461	130847465	-	1	NA	Intergenic	Intergenic	-18261	NM_001346515	101476	Mm.323554	NM_133942	ENSMUSG00000040268	Plekha1	AA960558|C920009D07Rik|TAPP1	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 1	protein-coding
mm_113056.1	chr13	23695824	23695833	+	1	NA	promoter-TSS (NM_010377)	promoter-TSS (NM_010377)	17	NM_010377	107970	Mm.8048	NM_010377	ENSMUSG00000036211	Hist1h1t	H1.6|H1ft|H1t	histone cluster 1, H1t	protein-coding
mm_53034.1	chr6	124519965	124519979	+	1	NA	intron (NM_023143, intron 9 of 10)	intron (NM_023143, intron 9 of 10)	7351	NM_023143	50909	Mm.333375	NM_023143	ENSMUSG00000055172	C1ra	AI132558|C1r|mC1rA	complement component 1, r subcomponent A	protein-coding
mm_90444.1	chr10	127658352	127658384	+	1	NA	exon (NM_009284, exon 18 of 22)	exon (NM_009284, exon 18 of 22)	8335	NM_001122895	17937	Mm.336898	NM_008668	ENSMUSG00000025402	Nab2	AI451907	Ngfi-A binding protein 2	protein-coding
mm_58464.1	chr7	3366941	3366997	+	1	NA	TTS (NM_133189)	TTS (NM_133189)	-27073	NM_133190	81905	Mm.357990	NM_133190	ENSMUSG00000053395	Cacng8	-	calcium channel, voltage-dependent, gamma subunit 8	protein-coding
mm_117294.1	chr13	66932999	66933009	-	1	NA	promoter-TSS (NM_025547)	promoter-TSS (NM_025547)	68	NM_025547	66410	Mm.347939	NM_025547	ENSMUSG00000021519	Mterf3	2410017I18Rik|Mterfd1	mitochondrial transcription termination factor 3	protein-coding
mm_107838.1	chr12	69296929	69296933	+	1	NA	5' UTR (NM_027117, exon 1 of 13)	5' UTR (NM_027117, exon 1 of 13)	250	NM_027117	69554	Mm.234368	NM_027117	ENSMUSG00000020978	Klhdc2	2310022K15Rik|D12Ertd522e|HCLP-1|LCP	kelch domain containing 2	protein-coding
mm_85408.1	chr9	103365770	103365785	-	1	NA	promoter-TSS (NM_001134427)	promoter-TSS (NM_001134427)	3	NM_175833	321022	Mm.261025	NM_175565	ENSMUSG00000032803	Cdv3	2510010F10Rik|C230084J24Rik|C79446|TPP36	carnitine deficiency-associated gene expressed in ventricle 3	protein-coding
mm_141162.1	chr17	26509495	26509499	-	1	NA	Intergenic	Intergenic	-1025	NM_013642	19252	Mm.239041	NM_013642	ENSMUSG00000024190	Dusp1	3CH134|MKP1|Ptpn16|U19515|erp|mkp-1	dual specificity phosphatase 1	protein-coding
mm_168955.1	chr12	78350956	78350957	+	1	NA	intron (NM_145965, intron 2 of 22)	LSU-rRNA_Hsa|rRNA|rRNA	124301	NM_145965	268566	Mm.341742	NM_145965	ENSMUSG00000047454	Gphn	5730552E08Rik|AI662856|BC027112|C230040D23|GPH|GPHRYN|geph	gephyrin	protein-coding
mm_2926.1	chr1	132190414	132190438	+	1	NA	Intergenic	CpG	-1010	NM_001311104	213409	Mm.426321	NM_001033250	ENSMUSG00000079330	Lemd1	4930540I23Rik|6430514M23Rik|AI428128|LEMP-1	LEM domain containing 1	protein-coding
mm_8074.1	chr1	135585282	135585292	-	1	NA	promoter-TSS (NM_173437)	promoter-TSS (NM_173437)	68	NM_173437	215690	Mm.34977	NM_173437	ENSMUSG00000009418	Nav1	9530089B19|9930003A20Rik|C230080M11Rik|Pomfil3|Unc53h1|mKIAA1151|steerin-1	neuron navigator 1	protein-coding
mm_55204.1	chr6	52208695	52208705	-	1	NA	promoter-TSS (NM_010454)	promoter-TSS (NM_010454)	-76	NM_010454	15403	Mm.222030	NM_010454	ENSMUSG00000043219	Hoxa6	Hox-1.2	homeobox A6	protein-coding
mm_167369.1	chr8	89130944	89130944	+	1	NA	Intergenic	Intergenic	-86782	NM_021390	58198	Mm.214361	NM_021390	ENSMUSG00000031665	Sall1	Msal-3	sal-like 1 (Drosophila)	protein-coding
mm_112066.1	chr12	111981110	111981114	-	1	NA	promoter-TSS (NM_001127685)	promoter-TSS (NM_001127685)	-361	NM_001127685	217874	Mm.134213	NM_001127685	ENSMUSG00000091402	Rd3l	A930011N13	retinal degeneration 3-like	protein-coding
mm_35357.1	chr4	32343747	32343755	-	1	NA	Intergenic	Intergenic	-73684	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_43679.1	chr5	138799668	138799679	+	1	NA	intron (NM_030565, intron 5 of 9)	B4|SINE|B4	-20407	NM_001195128	384244	Mm.485002	NM_001195128	ENSMUSG00000094504	Gm5294	EG384244	predicted gene 5294	protein-coding
mm_129486.1	chr15	78773412	78773422	-	1	NA	promoter-TSS (NM_008595)	promoter-TSS (NM_008595)	28	NM_008595	17305	Mm.149235	NM_008595	ENSMUSG00000018169	Mfng	AW546563	MFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	protein-coding
mm_21592.1	chr2	164237678	164237696	-	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	654	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_108305.1	chr12	79335389	79335434	+	1	NA	intron (NM_009014, intron 7 of 10)	intron (NM_009014, intron 7 of 10)	38060	NM_001252562	19363	Mm.341756	NM_009014	ENSMUSG00000059060	Rad51b	AI553500|R51H2|Rad51l1|mREC2	RAD51 paralog B	protein-coding
mm_66772.1	chr7	46796032	46796085	-	1	NA	promoter-TSS (NM_001167864)	promoter-TSS (NM_001167864)	-36	NM_008186	14884	Mm.22700	NM_008186	ENSMUSG00000006599	Gtf2h1	62kDa|AW743425|AW822074|BTF2 p62|C77871|p62	general transcription factor II H, polypeptide 1	protein-coding
mm_14195.1	chr2	127134009	127134028	+	1	NA	promoter-TSS (NM_144818)	promoter-TSS (NM_144818)	-64	NM_144818	215387	Mm.29786	NM_144818	ENSMUSG00000034906	Ncaph	A730011O11Rik|Brrn1|HCAP-H|mKIAA0074	non-SMC condensin I complex, subunit H	protein-coding
mm_109647.1	chr12	112831019	112831023	+	1	NA	Intergenic	Intergenic	-1632	NM_028023	71963	Mm.313185	NM_028023	ENSMUSG00000047832	Cdca4	2410018C03Rik|HEPP|SEI-3	cell division cycle associated 4	protein-coding
mm_806.1	chr1	45348951	45348961	+	1	NA	3' UTR (NM_009930, exon 51 of 51)	3' UTR (NM_009930, exon 51 of 51)	37418	NM_009930	12825	Mm.249555	NM_009930	ENSMUSG00000026043	Col3a1	AW550625|Col3a-1|Tsk-2|Tsk2	collagen, type III, alpha 1	protein-coding
mm_9163.1	chr1	170966486	170966523	-	1	NA	exon (NM_001077189, exon 4 of 8)	exon (NM_001077189, exon 4 of 8)	9567	NM_001077189	14130	Mm.425062	NM_010187	ENSMUSG00000026656	Fcgr2b	AI528646|CD32|F630109E10Rik|Fc[g]RII|FcgRII|Fcgr2|Fcgr2a|Fcr-2|Fcr-3|Ly-17|Ly-m20|LyM-1|Lym-1|fcRII	Fc receptor, IgG, low affinity IIb	protein-coding
mm_56234.1	chr6	90662171	90662220	-	1	NA	3' UTR (NM_001134384, exon 14 of 14)	3' UTR (NM_001134384, exon 14 of 14)	42949	NM_001037493	71699	Mm.272633	NM_027868	ENSMUSG00000030089	Slc41a3	1010001P06Rik|AI480742|SLC41A1-L2	solute carrier family 41, member 3	protein-coding
mm_159650.1	chr4	146097299	146097299	+	1	NA	promoter-TSS (NM_001037926)	promoter-TSS (NM_001037926)	-13	NM_001037926	626316	Mm.270762	NM_001037926	ENSMUSG00000066009	Zfp987	Gm13051|OTTMUSG00000010104|OTTMUSG00000010173	zinc finger protein 987	protein-coding
mm_123717.1	chr14	70069127	70069129	-	1	NA	Intergenic	Intergenic	-8317	NM_018781	13655	Mm.103737	NM_018781	ENSMUSG00000033730	Egr3	Pilot	early growth response 3	protein-coding
mm_3254.1	chr1	136146653	136146665	+	1	NA	intron (NM_001039472, intron 3 of 34)	intron (NM_001039472, intron 3 of 34)	15258	NM_001039472	16565	Mm.276135	NM_019962	ENSMUSG00000041642	Kif21b	2610511N21Rik|mKIAA0449	kinesin family member 21B	protein-coding
mm_141818.1	chr17	34606908	34606923	-	1	NA	intron (NM_001163379, intron 1 of 6)	intron (NM_001163379, intron 1 of 6)	1054	NM_001163379	55979	Mm.8684	NM_018862	ENSMUSG00000034254	Agpat1	1-AGP|1-AGPAT|AW047140	1-acylglycerol-3-phosphate O-acyltransferase 1 (lysophosphatidic acid acyltransferase, alpha)	protein-coding
mm_61338.1	chr7	68279167	68279181	+	1	NA	intron (NM_001013811, intron 1 of 8)	intron (NM_001013811, intron 1 of 8)	-2580	NR_040340	100504026	Mm.426764	NR_040340	ENSMUSG00000086628	Gm16157	OTTMUSG00000031023	predicted gene 16157	ncRNA
mm_54190.1	chr6	24275419	24275421	-	1	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	-107328	NM_019481	55961	Mm.19299	NM_019481	ENSMUSG00000029700	Slc13a1	AI314066|AI987826|NaSi-1|Nas1	solute carrier family 13 (sodium/sulfate symporters), member 1	protein-coding
mm_88121.1	chr10	69219390	69219405	+	1	NA	intron (NM_001252637, intron 2 of 10)	intron (NM_001252637, intron 2 of 10)	6203	NM_001252638	69288	Mm.26659	NM_001081347	ENSMUSG00000019944	Rhobtb1	1700008H16Rik|3110048G13Rik|AI173445|AI573858|AV350930	Rho-related BTB domain containing 1	protein-coding
mm_46540.1	chr5	105718268	105718274	-	1	NA	intron (NM_178701, intron 1 of 2)	intron (NM_178701, intron 1 of 2)	17461	NM_178701	231549	Mm.23837	NM_178701	ENSMUSG00000046079	Lrrc8d	2810473G09Rik|4930525N13Rik|A930019F03|Lrrc5	leucine rich repeat containing 8D	protein-coding
mm_117219.1	chr13	64128521	64128524	-	1	NA	intron (NM_001001321, intron 1 of 11)	intron (NM_001001321, intron 1 of 11)	808	NM_001001321	70484	Mm.133731	NM_001001321	ENSMUSG00000033114	Slc35d2	5730408I21Rik|SQV7L|UGTrel8|hfrc|mUGTrel8	solute carrier family 35, member D2	protein-coding
mm_47108.1	chr5	118477794	118477806	-	1	NA	Intergenic	Intergenic	-82919	NM_001347445	76199	Mm.206238	NM_172424	ENSMUSG00000018076	Med13l	2210413I17Rik|6330591G05Rik|9030618F05Rik|Thrap2|Trap240L|mKIAA1025	mediator complex subunit 13-like	protein-coding
mm_36964.1	chr4	109200714	109200728	-	1	NA	intron (NM_001346502, intron 1 of 23)	ID4_|SINE|ID	1551	NM_133885	100273	Mm.366315	NM_133885	ENSMUSG00000028559	Osbpl9	2600011I06Rik|AU015843|Orp-9	oxysterol binding protein-like 9	protein-coding
mm_46979.1	chr5	115272486	115272524	-	1	NA	5' UTR (NM_016698, exon 1 of 17)	5' UTR (NM_016698, exon 1 of 17)	390	NM_001302448	50849	Mm.30051	NM_016698	ENSMUSG00000041740	Rnf10	AA675014|RIE2|mKIAA0262	ring finger protein 10	protein-coding
mm_61589.1	chr7	80024892	80024907	+	1	NA	promoter-TSS (NM_001146000)	promoter-TSS (NM_001146000)	85	NM_001146000	209225	Mm.290925	NM_175433	ENSMUSG00000048897	Zfp710	5430400N05Rik|9830165K13|AI324798|Znf710	zinc finger protein 710	protein-coding
mm_154821.1	chrX	16619756	16619758	+	1	NA	promoter-TSS (NM_173740)	promoter-TSS (NM_173740)	59	NM_173740	17161	Mm.21108	NM_173740	ENSMUSG00000025037	Maoa	1110061B18Rik|AA407771	monoamine oxidase A	protein-coding
mm_84876.1	chr9	79718632	79718648	-	1	NA	promoter-TSS (NM_001290308)	promoter-TSS (NM_001290308)	82	NM_001290308	12816	Mm.3819	NM_007730	ENSMUSG00000032332	Col12a1	-	collagen, type XII, alpha 1	protein-coding
mm_125395.1	chr15	41447348	41447353	+	1	NA	promoter-TSS (NM_001130166)	promoter-TSS (NM_001130166)	-132	NM_001130166	170719	Mm.254267	NM_130885	ENSMUSG00000022307	Oxr1	2210416C20Rik|C7|C7B	oxidation resistance 1	protein-coding
mm_134783.1	chr16	23988538	23988544	-	1	NA	promoter-TSS (NM_009744)	promoter-TSS (NM_009744)	71	NM_009744	12053	Mm.347398	NM_009744	ENSMUSG00000022508	Bcl6	Bcl5	B cell leukemia/lymphoma 6	protein-coding
mm_75035.1	chr8	32421140	32421150	-	1	NA	Intergenic	Intergenic	269250	NR_046039	666589	Mm.367675	NR_046039		Gm8179	EG666589	predicted gene 8179	ncRNA
mm_125939.1	chr15	76247978	76247989	+	1	NA	promoter-TSS (NR_105918)	promoter-TSS (NR_105918)	-208	NR_105918	102465575		NR_105918	ENSMUSG00000098625	Mir6953	Gm27738|mmu-mir-6953	microRNA 6953	ncRNA
mm_130676.1	chr15	100675404	100675414	-	1	NA	exon (NM_033612, exon 7 of 8)	exon (NM_033612, exon 7 of 8)	-5909	NM_001270537	668218	Mm.451225	NM_001270537	ENSMUSG00000098112	Bin2	-	bridging integrator 2	protein-coding
mm_49584.1	chr6	30642900	30642912	+	1	NA	exon (NM_025350, exon 8 of 10)	exon (NM_025350, exon 8 of 10)	3688	NM_025350	109697	Mm.25377	NM_025350	ENSMUSG00000054446	Cpa1	0910001L12Rik|Cpa	carboxypeptidase A1, pancreatic	protein-coding
mm_118589.1	chr14	20641026	20641044	+	1	NA	Intergenic	CpG	15505	NM_021508	59011	Mm.439911	NM_021508	ENSMUSG00000068697	Myoz1	2310001N11Rik|AV090278|FATZ|Myoz	myozenin 1	protein-coding
mm_103311.1	chr11	73137279	73137291	-	1	NA	exon (NM_010353, exon 1 of 1)	exon (NM_010353, exon 1 of 1)	1009	NM_010353	14841	Mm.42045	NM_010353	ENSMUSG00000050107	Gsg2	Haspin	germ cell associated 2, haspin	protein-coding
mm_56077.1	chr6	87188232	87188243	-	1	NA	exon (NM_054041, exon 16 of 18)	exon (NM_054041, exon 16 of 18)	83491	NM_001167937	52372	Mm.282851	NM_001167937	ENSMUSG00000090891	D6Ertd527e	AU043841	DNA segment, Chr 6, ERATO Doi 527, expressed	protein-coding
mm_23789.1	chr3	79532011	79532023	+	1	NA	intron (NM_001162999, intron 1 of 16)	intron (NM_001162999, intron 1 of 16)	35662	NM_001162999	329679	Mm.244005	NM_001162999	ENSMUSG00000061175	Fnip2	D630023B12Rik|mKIAA1450	folliculin interacting protein 2	protein-coding
mm_132343.1	chr16	33863623	33863653	+	1	NA	intron (NM_010580, intron 2 of 14)	ID_B1|SINE|B4	33973	NM_001145884	16419	Mm.6424	NM_010580	ENSMUSG00000022817	Itgb5	AA475909|AI874634|ESTM23|[b]-5|[b]5|[b]5A|[b]5B|beta-5|beta5	integrin beta 5	protein-coding
mm_55616.1	chr6	72128347	72128362	-	1	NA	exon (NM_011375, exon 2 of 7)	exon (NM_011375, exon 2 of 7)	-5157	NR_045165	71265	Mm.442035	NR_045163	ENSMUSG00000108709	4933431G14Rik	4930565C19Rik	RIKEN cDNA 4933431G14 gene	ncRNA
mm_155068.1	chrX	42505247	42505258	+	1	NA	promoter-TSS (NM_001313691)	promoter-TSS (NM_001313691)	-70	NM_001313691	20400	Mm.441197	NM_011364	ENSMUSG00000005696	Sh2d1a	Gm686|SAP	SH2 domain containing 1A	protein-coding
mm_38738.1	chr4	145246151	145246177	-	1	NA	intron (NM_011610, intron 1 of 9)	intron (NM_011610, intron 1 of 9)	706	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_41232.1	chr5	88750668	88750671	+	1	NA	intron (NM_026735, intron 4 of 5)	intron (NM_026735, intron 4 of 5)	-14344	NM_007832	13178	Mm.298892	NM_007832	ENSMUSG00000029366	Dck	-	deoxycytidine kinase	protein-coding
mm_113689.1	chr13	42898137	42898182	+	1	NA	intron (NM_001302636, intron 1 of 12)	intron (NM_001302636, intron 1 of 12)	31912	NM_001302636	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding
mm_88156.1	chr10	69574669	69574673	+	1	NA	intron (NM_170730, intron 1 of 17)	intron (NM_170730, intron 1 of 17)	40963	NM_146005	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_28356.1	chr3	89764433	89764443	-	1	NA	5' UTR (NM_009602, exon 1 of 6)	5' UTR (NM_009602, exon 1 of 6)	194	NM_009602	11444	Mm.35088	NM_009602	ENSMUSG00000027950	Chrnb2	Acrb-2|Acrb2|C030030P04Rik|[b]2-nAchR	cholinergic receptor, nicotinic, beta polypeptide 2 (neuronal)	protein-coding
mm_118053.1	chr13	101748543	101748546	-	1	NA	intron (NM_001077495, intron 2 of 15)	intron (NM_001077495, intron 2 of 15)	19673	NM_001077495	18708	Mm.259333	NM_001024955	ENSMUSG00000041417	Pik3r1	PI3K|p50alpha|p55alpha|p85alpha	phosphatidylinositol 3-kinase, regulatory subunit, polypeptide 1 (p85 alpha)	protein-coding
mm_157418.1	chrX	38564123	38564145	-	1	NA	exon (NM_028288, exon 4 of 23)	exon (NM_028288, exon 4 of 23)	12062	NM_028288	72584	Mm.327675	NM_028288	ENSMUSG00000031095	Cul4b	2700050M05Rik|AA409770|CUL-4B|mKIAA0695	cullin 4B	protein-coding
mm_156093.1	chrX	111944397	111944410	+	1	NA	Intergenic	L3|LINE|CR1	-149117	NM_031382	83556	Mm.190608	NM_031382	ENSMUSG00000034555	Tex16	OTTMUSG00000018437	testis expressed gene 16	protein-coding
mm_164027.1	chr14	76610566	76610573	-	1	NA	Intergenic	ORR1G|LTR|ERVL-MaLR	-53680	NR_027699	72661	Mm.320384	NM_001160326	ENSMUSG00000052584	Serp2	2810032E02Rik	stress-associated endoplasmic reticulum protein family member 2	protein-coding
mm_113241.1	chr13	27345662	27345679	+	1	NA	promoter-TSS (NM_010088)	promoter-TSS (NM_010088)	-3	NM_010088	13529	Mm.291450	NM_010088	ENSMUSG00000018259	Prl8a2	D/tPRP|DPRP|Dtprp|Ghd11|mdPRP	prolactin family 8, subfamily a, member 2	protein-coding
mm_138463.1	chr17	35159047	35159097	+	1	NA	exon (NM_020027, exon 12 of 31)	exon (NM_020027, exon 12 of 31)	5805	NM_001199044	53761	Mm.272462	NM_020027	ENSMUSG00000024393	Prrc2a	3110039B05Rik|Bat-2|Bat2|D17H6S51E|G2|Wbp12|mKIAA4178	proline-rich coiled-coil 2A	protein-coding
mm_93226.1	chr10	95267148	95267167	-	1	NA	intron (NM_009950, intron 2 of 2)	intron (NM_009950, intron 2 of 2)	56552	NM_001330138	12905	Mm.473739	NM_009950	ENSMUSG00000045867	Cradd	RAIDD	CASP2 and RIPK1 domain containing adaptor with death domain	protein-coding
mm_118340.1	chr13	114456580	114456589	-	1	NA	intron (NM_001301375, intron 1 of 5)	intron (NM_001301375, intron 1 of 5)	2367	NM_001301373	14313	Mm.4913	NM_008046	ENSMUSG00000021765	Fst	AL033346|FS	follistatin	protein-coding
mm_19819.1	chr2	110791230	110791232	-	1	NA	intron (NM_001128103, intron 5 of 26)	intron (NM_001128103, intron 5 of 26)	69737	NM_172979	269328	Mm.32566	NM_172979	ENSMUSG00000050808	Muc15	4732460E09|D730046L02Rik|MUC-15	mucin 15	protein-coding
mm_118205.1	chr13	109822429	109822440	-	1	NA	intron (NM_011056, intron 7 of 16)	intron (NM_011056, intron 7 of 16)	-81375	NR_035442	100316683		NR_035442	ENSMUSG00000084651	Mir1904	Mirn1904|mmu-mir-1904	microRNA 1904	ncRNA
mm_80563.1	chr9	83664964	83664966	+	1	NA	Intergenic	Intergenic	-26510	NR_046066	100039222	Mm.405596	NR_046066	ENSMUSG00000100155	Gm2109	-	predicted gene 2109	ncRNA
mm_107929.1	chr12	71137171	71137221	+	1	NA	promoter-TSS (NM_001286203)	promoter-TSS (NM_001286203)	348	NM_001163378	76967	Mm.87290	NM_029818	ENSMUSG00000034601	2700049A03Rik	Ta3|Talpid3|mKIAA0586	RIKEN cDNA 2700049A03 gene	protein-coding
mm_144762.1	chr18	35771663	35771671	+	1	NA	5' UTR (NM_019912, exon 1 of 7)	5' UTR (NM_019912, exon 1 of 7)	108	NM_019912	56550	Mm.180052	NM_019912	ENSMUSG00000091896	Ube2d2a	1500034D03Rik|Ubc2e|Ube2d2|ubc4	ubiquitin-conjugating enzyme E2D 2A	protein-coding
mm_93921.1	chr10	127070255	127070302	-	1	NA	promoter-TSS (NR_040660)	promoter-TSS (NR_040660)	-17	NM_025982	67125	Mm.35650	NM_025982	ENSMUSG00000006736	Tspan31	2700085A14Rik|AW742554|Sas	tetraspanin 31	protein-coding
mm_54597.1	chr6	38299223	38299233	-	1	NA	promoter-TSS (NM_172467)	promoter-TSS (NM_172467)	31	NM_172467	209032	Mm.101389	NM_172467	ENSMUSG00000047749	Zc3hav1l	B130055L09Rik|E430016P22Rik	zinc finger CCCH-type, antiviral 1-like	protein-coding
mm_79459.1	chr9	56418416	56418425	+	1	NA	promoter-TSS (NM_025812)	promoter-TSS (NM_025812)	-370	NM_172924	244895	Mm.490331	NM_172924	ENSMUSG00000074305	Peak1	1110049L02Rik|9530046P14|AA690169|BE132841|C230081A13Rik|SGK269|mKIAA2002	pseudopodium-enriched atypical kinase 1	protein-coding
mm_145884.1	chr18	65580378	65580400	+	1	NA	5' UTR (NM_207255, exon 1 of 6)	5' UTR (NM_207255, exon 1 of 6)	159	NM_207255	328977	Mm.286232	NM_207255	ENSMUSG00000042439	Zfp532	C530030I18Rik|Znf532|mKIAA1629	zinc finger protein 532	protein-coding
mm_29070.1	chr3	103809068	103809079	-	1	NA	promoter-TSS (NM_001163552)	promoter-TSS (NM_001163552)	314	NM_133865	140917	Mm.374850	NM_133865	ENSMUSG00000027845	Dclre1b	AI452214|Apollo|SNMIB|mSNM1B	DNA cross-link repair 1B	protein-coding
mm_10810.1	chr2	24349961	24349971	+	1	NA	3' UTR (NM_031167, exon 5 of 5)	3' UTR (NM_031167, exon 5 of 5)	4595	NM_001039701	16181	Mm.882	NM_031167	ENSMUSG00000026981	Il1rn	F630041P17Rik|IL-1ra	interleukin 1 receptor antagonist	protein-coding
mm_27313.1	chr3	50366660	50366671	-	1	NA	3' UTR (NM_011990, exon 12 of 12)	3' UTR (NM_011990, exon 12 of 12)	76948	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_39406.1	chr5	14515003	14515018	+	1	NA	promoter-TSS (NM_011995)	promoter-TSS (NM_011995)	92	NM_001110796	26875	Mm.146275	NM_011995	ENSMUSG00000061601	Pclo	Acz|Pico	piccolo (presynaptic cytomatrix protein)	protein-coding
mm_55958.1	chr6	85451222	85451325	-	1	NA	promoter-TSS (NM_001163427)	promoter-TSS (NM_001163427)	29	NM_001163427	73327	Mm.379221	NM_028505	ENSMUSG00000030008	Pradc1	1700040I03Rik|Pap21	protease-associated domain containing 1	protein-coding
mm_91227.1	chr10	22293333	22293364	-	1	NA	intron (NM_009018, intron 5 of 5)	intron (NM_009018, intron 5 of 5)	-13372	NR_015465	606736	Mm.387042	NR_015465	ENSMUSG00000097352	C920009B18Rik	-	RIKEN cDNA C920009B18 gene	ncRNA
mm_10212.1	chr2	5845018	5845062	+	1	NA	promoter-TSS (NM_133837)	promoter-TSS (NM_133837)	6	NM_016918	53893	Mm.251904	NM_016918	ENSMUSG00000025817	Nudt5	-	nudix (nucleoside diphosphate linked moiety X)-type motif 5	protein-coding
mm_49189.1	chr6	15185608	15185626	+	1	NA	5' UTR (NM_001286607, exon 1 of 17)	5' UTR (NM_001286607, exon 1 of 17)	111	NM_001286607	114142	Mm.332919	NM_053242	ENSMUSG00000029563	Foxp2	2810043D05Rik|AI449000|CAG-16|D0Kist7	forkhead box P2	protein-coding
mm_51619.1	chr6	85298491	85298495	+	1	NA	intron (NM_178639, intron 3 of 13)	HAL1ME|LINE|L1	34929	NM_178639	94282	Mm.121485	NM_178639	ENSMUSG00000033720	Sfxn5	C230001H08Rik	sideroflexin 5	protein-coding
mm_148468.1	chr19	4097338	4097356	+	1	NA	promoter-TSS (NM_026373)	promoter-TSS (NM_026373)	-4	NM_026373	52004	Mm.29609	NM_026373	ENSMUSG00000024856	Cdk2ap2	5830466O21Rik|D19Ertd144e|Doc-1r	CDK2-associated protein 2	protein-coding
mm_142820.1	chr17	51752601	51752605	-	1	NA	intron (NM_009122, intron 9 of 10)	intron (NM_009122, intron 9 of 10)	59451	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_69948.1	chr7	142267795	142267802	-	1	NA	Intergenic	ERVB7_1-LTR_MM|LTR|ERVK	6565	NM_001199309	100043627	Mm.388589	NM_001199309	ENSMUSG00000056885	Gm4559	-	predicted gene 4559	protein-coding
mm_54129.1	chr6	18813884	18813912	-	1	NA	Intergenic	MTC-int|LTR|ERVL-MaLR	-34737	NM_133939	76522	Mm.275158	NM_133939	ENSMUSG00000044155	Lsm8	2010003I05Rik|AW214405|Naa38	LSM8 homolog, U6 small nuclear RNA associated	protein-coding
mm_139921.1	chr17	70986309	70986317	+	1	NA	intron (NM_023402, intron 1 of 3)	intron (NM_023402, intron 1 of 3)	4203	NM_023402	67938	Mm.261329	NM_023402	ENSMUSG00000034868	Myl12b	1500001M02Rik|C77744|Mylc2b|RLC-B	myosin, light chain 12B, regulatory	protein-coding
mm_151817.1	chr19	5503777	5503792	-	1	NA	promoter-TSS (NM_023781)	promoter-TSS (NM_023781)	3	NM_023781	75555	Mm.440432	NM_023781	ENSMUSG00000100937	1700020D05Rik	mage-g2	RIKEN cDNA 1700020D05 gene	protein-coding
mm_170831.1	chr2	176927829	176927841	-	1	NA	promoter-TSS (NM_001305137)	promoter-TSS (NM_001305137)	-22	NM_001305133	102639598	Mm.379980	NM_029813	ENSMUSG00000074527	Gm14296	-	predicted gene 14296	protein-coding
mm_5011.1	chr1	192812177	192812177	+	1	NA	Intergenic	Intergenic	-29528	NR_040468	73455	Mm.414869	NR_040468		1700065J18Rik	-	RIKEN cDNA 1700065J18 gene	ncRNA
mm_106064.1	chr11	116132574	116132584	-	1	NA	intron (NM_024177, intron 7 of 8)	intron (NM_024177, intron 7 of 8)	-1451	NM_178802	338364	Mm.439976	NM_178802	ENSMUSG00000054517	Trim65	4732463G12Rik	tripartite motif-containing 65	protein-coding
mm_122067.1	chr14	30491452	30491458	-	1	NA	promoter-TSS (NM_028981)	promoter-TSS (NM_028981)	-299	NM_028981	12289	Mm.9772	NM_028981	ENSMUSG00000015968	Cacna1d	8430418G19Rik|C79217|Cach3|Cacn4|Cacnl1a2|Cav1.3|Cchl1a|Cchl1a2|D-LTCC	calcium channel, voltage-dependent, L type, alpha 1D subunit	protein-coding
mm_29695.1	chr3	123114347	123114383	-	1	NA	exon (NM_080451, exon 4 of 5)	exon (NM_080451, exon 4 of 5)	-79378	NM_021503	59006	Mm.141157	NM_021503	ENSMUSG00000028116	Myoz2	1110012I24Rik|Fatz-2|Myozl2	myozenin 2	protein-coding
mm_47162.1	chr5	120711614	120711692	-	1	NA	promoter-TSS (NM_008052)	promoter-TSS (NM_008052)	16	NM_008052	14357	Mm.1645	NM_008052	ENSMUSG00000029603	Dtx1	Fxit1|mKIAA4160	deltex 1, E3 ubiquitin ligase	protein-coding
mm_7134.1	chr1	91053038	91053048	-	1	NA	promoter-TSS (NM_008515)	promoter-TSS (NM_008515)	-401	NM_001310732	16978	Mm.45039	NM_008515	ENSMUSG00000026305	Lrrfip1	AU024550|Fliiap1	leucine rich repeat (in FLII) interacting protein 1	protein-coding
mm_138667.1	chr17	35875086	35875110	+	1	NA	3' UTR (NM_001146711, exon 4 of 4)	3' UTR (NM_001146711, exon 4 of 4)	-4680	NM_026987	69192	Mm.390986	NM_026987	ENSMUSG00000024422	Dhx16	2410006N22Rik|DBP2|Ddx16|mKIAA0577	DEAH (Asp-Glu-Ala-His) box polypeptide 16	protein-coding
mm_129522.1	chr15	79163859	79163869	-	1	NA	intron (NM_011437, intron 1 of 3)	CpG-5080	626	NM_011437	20665	Mm.276739	NM_011437	ENSMUSG00000033006	Sox10	Dom|Sox21|gt	SRY (sex determining region Y)-box 10	protein-coding
mm_28760.1	chr3	95882182	95882190	-	1	NA	promoter-TSS (NM_001033302)	promoter-TSS (NM_001033302)	42	NM_001033302	229599	Mm.331218	NM_001033302	ENSMUSG00000038550	Ciart	Chrono|Gm129	circadian associated repressor of transcription	protein-coding
mm_147881.1	chr18	64660957	64660980	-	1	NA	promoter-TSS (NM_001001488)	promoter-TSS (NM_001001488)	32	NM_001001488	54670	Mm.270043	NM_001001488	ENSMUSG00000039529	Atp8b1	AI451886|FIC1|Ic	ATPase, class I, type 8B, member 1	protein-coding
mm_40894.1	chr5	75153523	75153541	+	1	NA	5' UTR (NM_001347719, exon 1 of 16)	5' UTR (NM_001347719, exon 1 of 16)	596	NM_001347719	18595	Mm.221403	NM_011058	ENSMUSG00000029231	Pdgfra	AI115593|CD140a|Pdgfr-2	platelet derived growth factor receptor, alpha polypeptide	protein-coding
mm_54157.1	chr6	23085140	23085148	-	1	NA	intron (NM_013930, intron 18 of 23)	intron (NM_013930, intron 18 of 23)	47842	NM_013930	30956	Mm.18651	NM_013930	ENSMUSG00000029695	Aass	LKR|LKR/SDH|LOR|LOR/SDH|Lorsdh|SDH	aminoadipate-semialdehyde synthase	protein-coding
mm_651.1	chr1	40429197	40429209	+	1	NA	promoter-TSS (NM_001294171)	promoter-TSS (NM_001294171)	-367	NM_001294171	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_41092.1	chr5	87694571	87694577	+	1	NA	exon (NM_001286023, exon 5 of 7)	exon (NM_001286023, exon 5 of 7)	4851	NM_001286020	12991	Mm.268737	NM_009972	ENSMUSG00000063157	Csn2	Csnb	casein beta	protein-coding
mm_118663.1	chr14	21832883	21832918	+	1	NA	exon (NM_011695, exon 3 of 10)	exon (NM_011695, exon 3 of 10)	1339	NM_011695	22334	Mm.262327	NM_011695	ENSMUSG00000021771	Vdac2	Vdac6|mVDAC2|mVDAC6	voltage-dependent anion channel 2	protein-coding
mm_152570.1	chr19	11590000	11590041	-	1	NA	exon (NM_026835, exon 5 of 7)	exon (NM_026835, exon 5 of 7)	14784	NM_026835	68774	Mm.290390	NM_026835	ENSMUSG00000024679	Ms4a6d	1110058E16Rik|AI447446|Ms4a11	membrane-spanning 4-domains, subfamily A, member 6D	protein-coding
mm_25592.1	chr3	116894893	116894897	+	1	NA	intron (NM_009146, intron 9 of 16)	B3|SINE|B2	33215	NM_009146	20321	Mm.66293	NM_009146	ENSMUSG00000033386	Frrs1	AI131732|Sdfr2	ferric-chelate reductase 1	protein-coding
mm_11398.1	chr2	31470289	31470310	+	1	NA	promoter-TSS (NM_007494)	promoter-TSS (NM_007494)	-9	NR_002687	432466	Mm.333323	NR_002687	ENSMUSG00000046687	Gm5424	EG432466	argininosuccinate synthase pseudogene	pseudo
mm_26862.1	chr3	15332266	15332282	-	1	NA	promoter-TSS (NM_001076679)	promoter-TSS (NM_001076679)	28	NM_001076679	751864	Mm.431296	NM_001076679	ENSMUSG00000078783	Gm9733	-	predicted gene 9733	protein-coding
mm_15196.1	chr2	154205479	154205495	+	1	NA	exon (NM_153418, exon 4 of 16)	exon (NM_153418, exon 4 of 16)	5107	NM_153418	228801	Mm.3783	NM_153418	ENSMUSG00000027485	Bpifb1	Lplunc1	BPI fold containing family B, member 1	protein-coding
mm_103423.1	chr11	75594766	75594783	-	1	NA	intron (NM_008850, intron 2 of 11)	intron (NM_008850, intron 2 of 11)	5457	NR_110477	654359	Mm.439961	NR_110477		Gm12338	OTTMUSG00000006216	cytochrome c oxidase, subunit VIIc pseudogene	pseudo
mm_28966.1	chr3	100969680	100969684	-	1	NA	promoter-TSS (NM_001013026)	promoter-TSS (NM_001013026)	-19	NM_001013026	74044	Mm.270961	NM_001013026	ENSMUSG00000033222	Ttf2	4632434F22Rik|8030447N19|AV218430	transcription termination factor, RNA polymerase II	protein-coding
mm_61050.1	chr7	49910084	49910103	+	1	NA	promoter-TSS (NM_001146013)	promoter-TSS (NM_001146013)	-206	NM_001146013	104245	Mm.207053	NM_148931	ENSMUSG00000039728	Slc6a5	Glyt2|prestin	solute carrier family 6 (neurotransmitter transporter, glycine), member 5	protein-coding
mm_109803.1	chr12	3309883	3309895	-	1	NA	promoter-TSS (NM_016676)	promoter-TSS (NM_016676)	80	NM_016676	19325	Mm.378993	NM_016676	ENSMUSG00000020671	Rab10	AW107754	RAB10, member RAS oncogene family	protein-coding
mm_18850.1	chr2	75659776	75659817	-	1	NA	intron (NM_146130, intron 1 of 10)	CpG	506	NR_033513	627828	Mm.459502	NR_033513	ENSMUSG00000092086	Gm6793	EG627828	heterogeneous nuclear ribonucleoprotein A3 pseudogene	pseudo
mm_79571.1	chr9	58134289	58134300	+	1	NA	promoter-TSS (NM_001162479)	promoter-TSS (NM_001162479)	219	NM_001162476	20897	Mm.10801	NM_009291	ENSMUSG00000032327	Stra6	AI891933	stimulated by retinoic acid gene 6	protein-coding
mm_78296.1	chr9	22411516	22411576	+	1	NA	promoter-TSS (NM_026739)	promoter-TSS (NM_026739)	-31	NM_026739	68283	Mm.280669	NM_026739	ENSMUSG00000036411	9530077C05Rik	1110003N12Rik|Kiaa0895|mKIAA0895	RIKEN cDNA 9530077C05 gene	protein-coding
mm_11776.1	chr2	38931976	38932007	+	1	NA	promoter-TSS (NM_172854)	promoter-TSS (NM_172854)	11	NM_172854	241327	Mm.103491	NM_172854	ENSMUSG00000046618	Olfml2a	4932431K08Rik|mFLJ00237	olfactomedin-like 2A	protein-coding
mm_53513.1	chr6	136016764	136016767	+	1	NA	intron (NM_008171, intron 4 of 14)	intron (NM_008171, intron 4 of 14)	156746	NM_008171	14812	Mm.436649	NM_008171	ENSMUSG00000030209	Grin2b	AW490526|GluN2B|NR2B|Nmdar2b	glutamate receptor, ionotropic, NMDA2B (epsilon 2)	protein-coding
mm_96332.1	chr11	65270145	65270161	+	1	NA	promoter-TSS (NM_145136)	promoter-TSS (NM_145136)	-164	NM_146386	214384	Mm.32257	NM_145136	ENSMUSG00000020542	Myocd	BSAC2A|Srfcp	myocardin	protein-coding
mm_5085.1	chr1	4496401	4496420	-	1	NA	5' UTR (NM_001289467, exon 1 of 3)	5' UTR (NM_001289467, exon 1 of 3)	944	NM_001289464	20671	Mm.279103	NM_011441	ENSMUSG00000025902	Sox17	-	SRY (sex determining region Y)-box 17	protein-coding
mm_130430.1	chr15	98162658	98162667	-	1	NA	intron (NM_001170711, intron 1 of 3)	intron (NM_001170711, intron 1 of 3)	2916	NM_001170711	78541	Mm.200766	NM_030121	ENSMUSG00000048175	Asb8	4930539L19Rik|AI788835|C430011H06Rik	ankyrin repeat and SOCS box-containing 8	protein-coding
mm_128757.1	chr15	64923136	64923162	-	1	NA	promoter-TSS (NM_009623)	promoter-TSS (NM_009623)	-853	NM_009623	11514	Mm.1425	NM_009623	ENSMUSG00000022376	Adcy8	AC8|AW060868	adenylate cyclase 8	protein-coding
mm_16973.1	chr2	17731574	17731589	-	1	NA	promoter-TSS (NM_028757)	promoter-TSS (NM_028757)	-513	NM_028757	74103	Mm.120298	NM_028757	ENSMUSG00000053702	Nebl	1200007O21Rik|A630080F05Rik|BB140644|D830029A09Rik|Lnebl	nebulette	protein-coding
mm_118214.1	chr13	110280080	110280094	-	1	NA	5' UTR (NM_023852, exon 1 of 5)	5' UTR (NM_023852, exon 1 of 5)	119	NM_023852	67295	Mm.151600	NM_023852	ENSMUSG00000021700	Rab3c	2700062I01Rik|3110015B08Rik|3110037E15Rik|AI850886	RAB3C, member RAS oncogene family	protein-coding
mm_81710.1	chr9	111311771	111311796	+	1	NA	promoter-TSS (NM_001164659)	promoter-TSS (NM_001164659)	44	NM_001164659	320429	Mm.270754	NM_001164659	ENSMUSG00000062296	Trank1	A230061D21Rik|C030048J01Rik|Gm187|Lba1	tetratricopeptide repeat and ankyrin repeat containing 1	protein-coding
mm_5104.1	chr1	5070306	5070314	-	1	NA	promoter-TSS (NM_001177795)	promoter-TSS (NM_001177795)	-25	NM_001177795	58175	Mm.103771	NM_021374	ENSMUSG00000002459	Rgs20	2900073E09Rik|Rgsz1	regulator of G-protein signaling 20	protein-coding
mm_51718.1	chr6	86850893	86850910	+	1	NA	intron (NM_001040106, intron 1 of 20)	intron (NM_001040106, intron 1 of 20)	1384	NM_001040106	269774	Mm.221038	NM_177762	ENSMUSG00000057230	Aak1	5530400K14Rik|9630042K20|AU067724|AU067726|BC028270|C79663|D6Ertd245e|R75501|mKIAA1048	AP2 associated kinase 1	protein-coding
mm_26754.1	chr3	7954895	7954910	-	1	NA	promoter-TSS (NR_040587)	promoter-TSS (NR_040587)	-15	NR_040587	75476	Mm.491752	NR_040587	ENSMUSG00000100010	1700010I02Rik	-	RIKEN cDNA 1700010I02 gene	ncRNA
mm_38868.1	chr4	149571291	149571324	-	1	NA	Intergenic	Intergenic	-15161	NM_001290989	65945	Mm.38993	NM_023051	ENSMUSG00000039953	Clstn1	1810034E21Rik|Cst-1|Cstn1	calsyntenin 1	protein-coding
mm_62766.1	chr7	112238528	112238538	+	1	NA	intron (NM_001193305, intron 2 of 25)	intron (NM_001193305, intron 2 of 25)	12697	NM_001193305	320878	Mm.52312	NM_177282	ENSMUSG00000038244	Mical2	5330438E18Rik|9530064J02|MICAL-2|mKIAA0750	microtubule associated monooxygenase, calponin and LIM domain containing 2	protein-coding
mm_58207.1	chr6	143925987	143925989	-	1	NA	intron (NM_011444, intron 8 of 14)	intron (NM_011444, intron 8 of 14)	21118	NM_001347506	20678	Mm.1752	NM_011444	ENSMUSG00000041540	Sox5	A730017D01Rik|AI528773	SRY (sex determining region Y)-box 5	protein-coding
mm_115721.1	chr13	16003997	16004001	-	1	NA	Intergenic	Intergenic	-7852	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_59967.1	chr7	30428459	30428461	+	1	NA	3' UTR (NM_172142, exon 11 of 11)	3' UTR (NM_172142, exon 11 of 11)	5156	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_135240.1	chr16	36990273	36990283	-	1	NA	Intergenic	Intergenic	-11142	NM_001037321	207215	Mm.211899	NM_001037321	ENSMUSG00000047746	Fbxo40	9830003A13Rik|mKIAA1195	F-box protein 40	protein-coding
mm_4016.1	chr1	165653880	165653886	+	1	NA	intron (NM_178593, intron 6 of 6)	MLT1C|LTR|ERVL-MaLR	-19342	NM_001083897	68481	Mm.46438	NM_001001880	ENSMUSG00000026566	Mpzl1	1110007A10Rik|PZR	myelin protein zero-like 1	protein-coding
mm_47398.1	chr5	123047000	123047025	-	1	NA	promoter-TSS (NM_029112)	promoter-TSS (NM_029112)	4	NM_001347456	74890	Mm.141383	NM_029112	ENSMUSG00000029477	Morn3	4930438O03Rik	MORN repeat containing 3	protein-coding
mm_46117.1	chr5	92435057	92435065	-	1	NA	exon (NM_183392, exon 1 of 12)	exon (NM_183392, exon 1 of 12)	138	NM_183392	269113	Mm.275289	NM_183392	ENSMUSG00000034826	Nup54	3110079L04Rik|54kDa	nucleoporin 54	protein-coding
mm_8012.1	chr1	134846769	134846779	-	1	NA	intron (NM_001081307, intron 13 of 23)	intron (NM_001081307, intron 13 of 23)	-43053	NR_015606	329251	Mm.188709	NM_001081307	ENSMUSG00000073557	Ppp1r12b	1810037O03Rik|9530009M10Rik|AI132431|Mypt2	protein phosphatase 1, regulatory (inhibitor) subunit 12B	protein-coding
mm_91813.1	chr10	54061704	54061722	-	1	NA	intron (NM_008548, intron 2 of 12)	RLTR20D|LTR|ERVK	14083	NM_008548	17155	Mm.117294	NM_008548	ENSMUSG00000003746	Man1a	Man1a1|PCR1	mannosidase 1, alpha	protein-coding
mm_17087.1	chr2	22988810	22988819	-	1	NA	intron (NM_001331043, intron 2 of 10)	intron (NM_001331043, intron 2 of 10)	51427	NM_001077192	11308	Mm.205647	NM_007380	ENSMUSG00000058835	Abi1	E3B1|NAP1|Ssh3bp1|abi-1	abl-interactor 1	protein-coding
mm_156607.1	chrX	153237813	153237842	+	1	NA	promoter-TSS (NM_173780)	promoter-TSS (NM_173780)	-218	NM_173780	245671	Mm.260751	NM_173780	ENSMUSG00000041649	Klf8	A830097P10Rik|BKLF3|ZNF74	Kruppel-like factor 8	protein-coding
mm_119644.1	chr14	51984527	51984538	+	1	NA	promoter-TSS (NM_001145922)	promoter-TSS (NM_001145922)	-301	NM_001145921	268739	Mm.9239	NM_198249	ENSMUSG00000004562	Arhgef40	E130112L23Rik|Gm669|Solo	Rho guanine nucleotide exchange factor (GEF) 40	protein-coding
mm_96132.1	chr11	60878192	60878196	+	1	NA	intron (NM_001168507, intron 1 of 2)	intron (NM_001168507, intron 1 of 2)	844	NM_173453	216821	Mm.28063	NM_173453	ENSMUSG00000043284	Tmem11	5730466P16Rik|AA409091	transmembrane protein 11	protein-coding
mm_36338.1	chr4	72200740	72200746	-	1	NA	promoter-TSS (NR_027923)	promoter-TSS (NR_027923)	150	NM_011599	21885	Mm.278444	NM_011599	ENSMUSG00000008305	Tle1	C230057C06Rik|Estm14|Grg-1|Grg1|Tle4l	transducin-like enhancer of split 1	protein-coding
mm_65522.1	chr7	25772191	25772223	-	1	NA	intron (NM_001190974, intron 9 of 18)	intron (NM_001190974, intron 9 of 18)	16526	NM_001190974	26362	Mm.4128	NM_009465	ENSMUSG00000002602	Axl	AI323647|Ark|Tyro7|Ufo	AXL receptor tyrosine kinase	protein-coding
mm_68967.1	chr7	126584545	126584609	-	1	NA	promoter-TSS (NM_138310)	promoter-TSS (NM_138310)	-431	NM_138310	171504	Mm.170665	NM_138310	ENSMUSG00000042759	Apobr	Apob-48r|Apob48r	apolipoprotein B receptor	protein-coding
mm_24733.1	chr3	95283127	95283140	+	1	NA	5' UTR (NM_133858, exon 1 of 10)	5' UTR (NM_133858, exon 1 of 10)	198	NM_199475	75007	Mm.279287	NM_133858	ENSMUSG00000038712	Fam63a	1810005H09Rik|4930504E06Rik|AA562754|AA960384|AW561904|cI-40|mKIAA1390|ni	family with sequence similarity 63, member A	protein-coding
mm_58709.1	chr7	12977835	12977900	+	1	NA	promoter-TSS (NM_175558)	promoter-TSS (NM_175558)	19	NM_001168561	269870	Mm.62083	NM_175558	ENSMUSG00000033961	Zfp446	A630035I11Rik|A930031C22|AA120513|AV306632	zinc finger protein 446	protein-coding
mm_78326.1	chr9	25186701	25186711	+	1	NA	Intergenic	Intergenic	-34925	NM_020586	80517	Mm.142843	NM_020586	ENSMUSG00000008429	Herpud2	5031400M07Rik|AB041580	HERPUD family member 2	protein-coding
mm_76396.1	chr8	84844450	84844497	-	1	NA	exon (NM_007591, exon 6 of 9)	exon (NM_007591, exon 6 of 9)	2458	NM_007591	12317	Mm.1971	NM_007591	ENSMUSG00000003814	Calr	CRT|Calregulin	calreticulin	protein-coding
mm_10644.1	chr2	20552102	20552105	+	1	NA	intron (NM_029895, intron 3 of 18)	ID4|SINE|ID	32590	NM_001177631	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding
mm_142225.1	chr17	37480720	37480731	-	1	NA	TTS (NM_008204)	TTS (NM_008204)	2804	NM_008204	14990	Mm.329041	NM_008204	ENSMUSG00000016283	H2-M2	H-2M2|Thy19.4	histocompatibility 2, M region locus 2	protein-coding
mm_148035.1	chr18	70244390	70244395	-	1	NA	5' UTR (NM_029346, exon 1 of 3)	5' UTR (NM_029346, exon 1 of 3)	192	NM_029346	75577	Mm.58214	NM_029346	ENSMUSG00000024512	Dynap	2310002L13Rik	dynactin associated protein	protein-coding
mm_162960.1	chr11	5229796	5229807	-	1	NA	intron (NM_032396, intron 3 of 8)	RSINE1|SINE|B4	-24797	NR_037240	100526548		NR_037240	ENSMUSG00000093169	Mir3079	mmu-mir-3079	microRNA 3079	ncRNA
mm_140240.1	chr17	84126392	84126418	+	1	NA	Intergenic	Intergenic	47745	NR_045458	74473	Mm.399575	NR_045458		4933433H22Rik	-	RIKEN cDNA 4933433H22 gene	ncRNA
mm_164018.1	chr14	74558127	74558128	+	1	NA	Intergenic	Intergenic	-82713	NM_172812	15558	Mm.214351	NM_172812	ENSMUSG00000034997	Htr2a	E030013E04|Htr-2|Htr2	5-hydroxytryptamine (serotonin) receptor 2A	protein-coding
mm_117475.1	chr13	76271907	76271913	-	1	NA	Intergenic	Intergenic	-113051	NM_030174	78771	Mm.316249	NM_030174	ENSMUSG00000021596	Mctp1	2810465F10Rik	multiple C2 domains, transmembrane 1	protein-coding
mm_164878.1	chr18	58210093	58210109	-	1	NA	promoter-TSS (NM_010181)	promoter-TSS (NM_010181)	-175	NM_010181	14119	Mm.20271	NM_010181	ENSMUSG00000024598	Fbn2	BC063774|Fib-2|mKIAA4226|sne|sy	fibrillin 2	protein-coding
mm_98880.1	chr11	97806812	97806815	+	1	NA	intron (NM_010688, intron 1 of 6)	intron (NM_010688, intron 1 of 6)	7141	NM_010688	16796	Mm.271967	NM_010688	ENSMUSG00000038366	Lasp1	AA408629|Def-4|SH3P6|Tg(Col1a1-lacZ)1Ngma	LIM and SH3 protein 1	protein-coding
mm_151097.1	chr19	47854996	47855013	+	1	NA	promoter-TSS (NM_010362)	promoter-TSS (NM_010362)	31	NM_010362	14873	Mm.378931	NM_010362	ENSMUSG00000025068	Gsto1	AA407097|AI194287|AU018802|Gsto-1|Gstx|Spg-r|p28	glutathione S-transferase omega 1	protein-coding
mm_136404.1	chr16	93604784	93604798	-	1	NA	promoter-TSS (NM_145482)	promoter-TSS (NM_145482)	-976	NM_145482	224440	Mm.10628	NM_145482	ENSMUSG00000022948	Setd4	AY037804|C21orf18|ORF21	SET domain containing 4	protein-coding
mm_90163.1	chr10	119240319	119240330	+	1	NA	promoter-TSS (NM_027994)	promoter-TSS (NM_027994)	-269	NM_027994	71902	Mm.203965	NM_027994	ENSMUSG00000020114	Cand1	2310038O07Rik|6330512O03Rik|AI195005|AI846556|D10Ertd516e|Tp120a|mKIAA0829	cullin associated and neddylation disassociated 1	protein-coding
mm_21126.1	chr2	154015966	154015984	-	1	NA	TTS (NM_008953)	TTS (NM_008953)	7699	NM_008953	19194	Mm.29197	NM_008953	ENSMUSG00000042459	Bpifa2	Bpifa2e|Psp	BPI fold containing family A, member 2	protein-coding
mm_14772.1	chr2	145786280	145786307	+	1	NA	intron (NM_028724, intron 1 of 12)	intron (NM_028724, intron 1 of 12)	177	NM_028724	74030	Mm.228799	NM_028724	ENSMUSG00000001768	Rin2	2010003K16Rik|4632403N06Rik|AW821980|RASSF4	Ras and Rab interactor 2	protein-coding
mm_10051.1	chr1	193201395	193201417	-	1	NA	5' UTR (NM_153137, exon 1 of 16)	5' UTR (NM_153137, exon 1 of 16)	140	NM_153137	215243	Mm.261259	NM_153137	ENSMUSG00000037318	Traf3ip3	6030423D04Rik|AI115021|T3jam	TRAF3 interacting protein 3	protein-coding
mm_146286.1	chr18	78062828	78062835	+	1	NA	Intergenic	RLTR13D3A1|LTR|ERVK	-5563	NM_001101038	620235	Mm.35607	NM_001101038	ENSMUSG00000091055	Siglec15	Cd33l3|EG620235|SIGLEC-I	sialic acid binding Ig-like lectin 15	protein-coding
mm_80899.1	chr9	100022306	100022316	+	1	NA	promoter-TSS (NR_040763)	promoter-TSS (NR_040763)	11	NR_040763	108970	Mm.390215	NR_040763	ENSMUSG00000101584	4930519F24Rik	-	RIKEN cDNA 4930519F24 gene	ncRNA
mm_64635.1	chr7	3714269	3714297	-	1	NA	exon (NM_011095, exon 11 of 15)	exon (NM_011095, exon 11 of 15)	6099	NM_011095	18733	Mm.326531	NM_011095	ENSMUSG00000058818	Pirb	Gp91|LIR-3|Lilrb3|PIR-B	paired Ig-like receptor B	protein-coding
mm_510.1	chr1	37246743	37246751	+	1	NA	intron (NM_009918, intron 3 of 5)	ORR1B1|LTR|ERVL-MaLR	27542	NM_009918	12790	Mm.214224	NM_009918	ENSMUSG00000026114	Cnga3	CNG3	cyclic nucleotide gated channel alpha 3	protein-coding
mm_12481.1	chr2	71529799	71529807	+	1	NA	TTS (NR_002854)	TTS (NR_002854)	358	NM_010053	13390	Mm.475101	NM_010053	ENSMUSG00000041911	Dlx1	Dlx|Dlx-1	distal-less homeobox 1	protein-coding
mm_165609.1	chr3	52070001	52070022	-	1	NA	intron (NM_001004176, intron 1 of 4)	intron (NM_001004176, intron 1 of 4)	34995	NM_001004176	433586	Mm.234972	NM_001004176	ENSMUSG00000061143	Maml3	AV234550|BC049812|Mam-2|mKIAA1816	mastermind like 3 (Drosophila)	protein-coding
mm_169325.1	chr14	11561259	11561272	+	1	NA	intron (NM_008981, intron 1 of 29)	intron (NM_008981, intron 1 of 29)	7712	NM_008981	19270	Mm.431266	NM_008981	ENSMUSG00000021745	Ptprg	5430405N12Rik|AW046354|AW549872|RPTPgamma	protein tyrosine phosphatase, receptor type, G	protein-coding
mm_83404.1	chr9	44767793	44767838	-	1	NA	promoter-TSS (NM_145985)	promoter-TSS (NM_145985)	-7	NM_145985	213827	Mm.371682	NM_145985	ENSMUSG00000032096	Arcn1	4632432M07Rik|nur17	archain 1	protein-coding
mm_133596.1	chr16	91465022	91465032	+	1	NA	promoter-TSS (NR_077219)	promoter-TSS (NR_077219)	-77	NR_077219	100503120	Mm.387130	NR_077219	ENSMUSG00000084866	A930006K02Rik	-	RIKEN cDNA A930006K02 gene	ncRNA
mm_130909.1	chr15	102516807	102516855	-	1	NA	5' UTR (NM_001163643, exon 1 of 16)	5' UTR (NM_001163643, exon 1 of 16)	173	NM_001163643	26404	Mm.172897	NM_009582	ENSMUSG00000023050	Map3k12	DLK|MUK|Zpk	mitogen-activated protein kinase kinase kinase 12	protein-coding
mm_50226.1	chr6	42350711	42350754	+	1	NA	intron (NM_001289619, intron 2 of 8)	intron (NM_001289619, intron 2 of 8)	904	NM_001289619	22793	Mm.282303	NM_011777	ENSMUSG00000029860	Zyx	9530098H06Rik|R75157	zyxin	protein-coding
mm_52731.1	chr6	120364463	120364469	+	1	NA	promoter-TSS (NR_045558)	promoter-TSS (NR_045558)	-97	NR_045558	67200	Mm.45767	NM_026028	ENSMUSG00000030177	Ccdc77	2400002C23Rik|2700091N06Rik|AV168274	coiled-coil domain containing 77	protein-coding
mm_83954.1	chr9	56928140	56928161	-	1	NA	5' UTR (NM_175483, exon 1 of 2)	5' UTR (NM_175483, exon 1 of 2)	221	NM_175483	235406	Mm.191459	NM_175483	ENSMUSG00000032733	Snx33	E130307J07Rik|Sh3px3	sorting nexin 33	protein-coding
mm_66952.1	chr7	62209500	62209546	-	1	NA	Intergenic	Intergenic	-124213	NR_049204	100885843		NR_049204	ENSMUSG00000095154	Mir344i	Gm26031|mir-344i|mmu-mir-344i	microRNA 344i	ncRNA
mm_94746.1	chr11	21102504	21102532	+	1	NA	intron (NM_023324, intron 1 of 6)	intron (NM_023324, intron 1 of 6)	11194	NM_023324	67245	Mm.28957	NM_023324	ENSMUSG00000020134	Peli1	2810468L03Rik|A930031K15Rik|AA409794|AI586297|D11Ertd676e	pellino 1	protein-coding
mm_73413.1	chr8	106053082	106053098	+	1	NA	intron (NM_001301176, intron 14 of 14)	intron (NM_001301176, intron 14 of 14)	-6513	NM_010901	18021	Mm.383185	NM_010901	ENSMUSG00000031902	Nfatc3	C80703|D8Ertd281e|NFAT4|NFATx	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 3	protein-coding
mm_45073.1	chr5	43868688	43868699	-	1	NA	promoter-TSS (NM_007646)	promoter-TSS (NM_007646)	-116	NM_007646	12494	Mm.249873	NM_007646	ENSMUSG00000029084	Cd38	ADPRC 1|Cd38-rs1|I-19	CD38 antigen	protein-coding
mm_62087.1	chr7	93079884	93079901	+	1	NA	promoter-TSS (NM_021427)	promoter-TSS (NM_021427)	13	NM_021427	58238	Mm.113787	NM_021427	ENSMUSG00000051515	Fam181b	A830059I20Rik|AB041569	family with sequence similarity 181, member B	protein-coding
mm_103219.1	chr11	70655217	70655235	-	1	NA	promoter-TSS (NM_011072)	promoter-TSS (NM_011072)	-576	NM_011072	18643	Mm.2647	NM_011072	ENSMUSG00000018293	Pfn1	Pfn	profilin 1	protein-coding
mm_130938.1	chr15	103216262	103216285	-	1	NA	promoter-TSS (NM_001110216)	promoter-TSS (NM_001110216)	-921	NM_001110216	12419	Mm.262059	NM_007626	ENSMUSG00000009575	Cbx5	2610029O15Rik|C75991|HP1|Hp1a|Hp1alpha	chromobox 5	protein-coding
mm_12084.1	chr2	60208394	60208421	+	1	NA	Intergenic	MIR|SINE|MIR	-1529	NM_020575	57438	Mm.260635	NM_020575	ENSMUSG00000026977	March7	Axo|Axot|Gtrgeo17	membrane-associated ring finger (C3HC4) 7	protein-coding
mm_123184.1	chr14	57826129	57826180	-	1	NA	promoter-TSS (NM_198605)	promoter-TSS (NM_198605)	9	NM_198605	219114	Mm.30173	NM_198605	ENSMUSG00000021965	Ska3	F630043A04Rik	spindle and kinetochore associated complex subunit 3	protein-coding
mm_68790.1	chr7	123359014	123359018	-	1	NA	intron (NM_001122641, intron 1 of 18)	intron (NM_001122641, intron 1 of 18)	10899	NM_001122643	70497	Mm.403318	NM_144529	ENSMUSG00000030766	Arhgap17	5730403H17Rik|Nadrin|Nadrin2|Rich1|Wbp15	Rho GTPase activating protein 17	protein-coding
mm_8970.1	chr1	165227589	165227597	-	1	NA	exon (NM_145513, exon 3 of 7)	exon (NM_145513, exon 3 of 7)	9365	NM_145513	226591	Mm.21520	NM_145513	ENSMUSG00000040843	Tiprl	1810011K17Rik	TIP41, TOR signalling pathway regulator-like (S. cerevisiae)	protein-coding
mm_15983.1	chr2	166805645	166805653	+	1	NA	promoter-TSS (NM_001085495)	promoter-TSS (NM_001085495)	68	NM_001085495	99371	Mm.297192	NM_001085495	ENSMUSG00000074582	Arfgef2	AI463430|AW493672|BIG2|E230011G24Rik	ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited)	protein-coding
mm_106840.1	chr12	8006868	8006881	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	29197	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_89088.1	chr10	83722949	83722969	+	1	NA	promoter-TSS (NM_001145198)	promoter-TSS (NM_001145198)	94	NM_001145198	69784	Mm.271188	NM_001145198	ENSMUSG00000087651	1500009L16Rik	2700050C19Rik|OCC-1	RIKEN cDNA 1500009L16 gene	protein-coding
mm_140065.1	chr17	74770062	74770071	+	1	NA	intron (NM_152817, intron 9 of 19)	intron (NM_152817, intron 9 of 19)	52316	NM_152817	74196	Mm.209503	NM_152817	ENSMUSG00000024078	Ttc27	2610511O17Rik	tetratricopeptide repeat domain 27	protein-coding
mm_151983.1	chr19	5841328	5841347	-	1	NA	TTS (NR_003513)	TTS (NR_003513)	4141	NR_131212	66961	Mm.281895	NR_003513	ENSMUSG00000092274	Neat1	2310043N10Rik|VINC	nuclear paraspeckle assembly transcript 1 (non-protein coding)	ncRNA
mm_134232.1	chr16	11461631	11461636	-	1	NA	intron (NM_001290148, intron 6 of 13)	intron (NM_001290148, intron 6 of 13)	55985	NM_001290148	74478	Mm.325831	NM_028964	ENSMUSG00000071669	Snx29	4933437K13Rik|ENSMUSG00000079738|Gm11170|Gm1737|Gm930|Rundc2a	sorting nexin 29	protein-coding
mm_83416.1	chr9	44881278	44881323	-	1	NA	promoter-TSS (NM_001081049)	promoter-TSS (NM_001081049)	-26	NM_001081049	214162	Mm.2389	NM_001081049	ENSMUSG00000002028	Kmt2a	6430520K01|ALL-1|All1|Cxxc7|HRX|HTRX1|Mll|Mll1|mKIAA4050	lysine (K)-specific methyltransferase 2A	protein-coding
mm_139436.1	chr17	53628400	53628412	+	1	NA	intron (NM_020005, intron 3 of 17)	intron (NM_020005, intron 3 of 17)	44280	NM_001190846	18519	Mm.255025	NM_020005	ENSMUSG00000000708	Kat2b	A930006P13Rik|AI461839|AW536563|Pcaf|p/CAF	K(lysine) acetyltransferase 2B	protein-coding
mm_28606.1	chr3	94588050	94588079	-	1	NA	Intergenic	Intergenic	-5348	NM_029721	76742	Mm.28160	NM_029721	ENSMUSG00000028136	Snx27	5730552M22Rik|ESTM45|ESTM47|R75405	sorting nexin family member 27	protein-coding
mm_79390.1	chr9	54863681	54863711	+	1	NA	promoter-TSS (NM_022655)	promoter-TSS (NM_022655)	-59	NM_022655	64602	Mm.208991	NM_022655	ENSMUSG00000032293	Ireb2	D9Ertd85e|Irp2	iron responsive element binding protein 2	protein-coding
mm_34945.1	chr4	155892255	155892268	+	1	NA	promoter-TSS (NM_001033490)	promoter-TSS (NM_001033490)	386	NM_207223	140500	Mm.219591	NM_207223	ENSMUSG00000029033	Acap3	Centb5|Kiaa1716-hp|mKIAA1716	ArfGAP with coiled-coil, ankyrin repeat and PH domains 3	protein-coding
mm_167914.1	chrX	96455503	96455505	+	1	NA	promoter-TSS (NM_010417)	promoter-TSS (NM_010417)	68	NM_010417	15203	Mm.277092	NM_010417	ENSMUSG00000031209	Heph	C130006F04Rik|Cpl|mKIAA0698|sla	hephaestin	protein-coding
mm_106894.1	chr12	8012513	8012522	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	34840	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_8671.1	chr1	156674274	156674287	-	1	NA	promoter-TSS (NM_023141)	promoter-TSS (NM_023141)	59	NM_023141	30935	Mm.206737	NM_023141	ENSMUSG00000060519	Tor3a	Adir	torsin family 3, member A	protein-coding
mm_165304.1	chr2	94810614	94810624	+	1	NA	Intergenic	RMER17B|LTR|ERVK	-372433	NM_001305258	11800	Mm.181824	NM_007466	ENSMUSG00000027193	Api5	AAC-11|AI196452|API-5	apoptosis inhibitor 5	protein-coding
mm_131520.1	chr16	17619342	17619387	+	1	NA	promoter-TSS (NM_029945)	promoter-TSS (NM_029945)	10	NM_001164609	77626	Mm.34659	NM_029945	ENSMUSG00000005899	Smpd4	4122402O22Rik|mKIAA1418	sphingomyelin phosphodiesterase 4	protein-coding
mm_6384.1	chr1	72849116	72849124	-	1	NA	exon (NM_008342, exon 2 of 4)	exon (NM_008342, exon 2 of 4)	23733	NM_001310659	16008	Mm.141936	NM_008342	ENSMUSG00000039323	Igfbp2	AI255832|IBP-2|Igfbp-2|mIGFBP-2	insulin-like growth factor binding protein 2	protein-coding
mm_126592.1	chr15	82351771	82351774	+	1	NA	intron (NM_025987, intron 1 of 2)	intron (NM_025987, intron 1 of 2)	2519	NM_025987	67130	Mm.27570	NM_025987	ENSMUSG00000022450	Ndufa6	14kDa|2700038D15Rik|B230217P19Rik	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 6 (B14)	protein-coding
mm_74094.1	chr8	122570231	122570250	+	1	NA	exon (NM_026014, exon 5 of 10)	exon (NM_026014, exon 5 of 10)	2225	NM_026014	67177	Mm.21873	NM_026014	ENSMUSG00000006585	Cdt1	2610318F11Rik|AW545653|C76791|Ris2	chromatin licensing and DNA replication factor 1	protein-coding
mm_96056.1	chr11	59566321	59566343	+	1	NA	3' UTR (NM_145827, exon 10 of 10)	3' UTR (NM_145827, exon 10 of 10)	5406	NM_001011789	257962	Mm.377316	NM_001011789	ENSMUSG00000059610	Olfr222	MOR256-45P	olfactory receptor 222	protein-coding
mm_26909.1	chr3	19644360	19644364	-	1	NA	promoter-TSS (NM_001081281)	promoter-TSS (NM_001081281)	-98	NM_001081281	381485	Mm.35419	NM_001081281	ENSMUSG00000060913	Trim55	D830041C10Rik|Murf2|Rnf29	tripartite motif-containing 55	protein-coding
mm_55856.1	chr6	83452792	83452794	-	1	NA	intron (NM_001347313, intron 2 of 11)	intron (NM_001347313, intron 2 of 11)	3599	NM_001347313	194388	Mm.211030	NM_183138	ENSMUSG00000034832	Tet3	B430006D22Rik|BC037432|D230004J03Rik	tet methylcytosine dioxygenase 3	protein-coding
mm_168837.1	chr12	23158179	23158179	+	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	-147936	NR_015504	69732	Mm.391403	NM_028362	ENSMUSG00000073164	2410018L13Rik	2810480C08Rik	RIKEN cDNA 2410018L13 gene	ncRNA
mm_33757.1	chr4	134343524	134343535	+	1	NA	promoter-TSS (NM_001346578)	promoter-TSS (NM_001346578)	63	NM_001346578	230810	Mm.358876	NM_001039677	ENSMUSG00000028836	Slc30a2	ZnT-2|Znt2	solute carrier family 30 (zinc transporter), member 2	protein-coding
mm_76513.1	chr8	87233405	87233405	-	1	NA	Intergenic	Intergenic	-33555	NR_040697	100038706	Mm.334690	NR_040697	ENSMUSG00000099207	Gm10637	ENSMUSG00000074176	predicted gene 10637	ncRNA
mm_129370.1	chr15	77995091	77995107	-	1	NA	3' UTR (NM_007583, exon 4 of 4)	3' UTR (NM_007583, exon 4 of 4)	-24275	NM_018749	55944	Mm.3955	NM_018749	ENSMUSG00000016554	Eif3d	66/67kDa|AA407891|Eif3s7|eIF3p66	eukaryotic translation initiation factor 3, subunit D	protein-coding
mm_9258.1	chr1	171605252	171605268	-	1	NA	exon (NM_008534, exon 2 of 10)	exon (NM_008534, exon 2 of 10)	2074	NR_102726	17085	Mm.560	NM_008534	ENSMUSG00000004707	Ly9	AI893573|CD229|Lgp100|Ly-9|SLAMF3|T100	lymphocyte antigen 9	protein-coding
mm_18973.1	chr2	76841148	76841160	-	1	NA	exon (NM_011652, exon 150 of 313)	exon (NM_011652, exon 150 of 313)	141393	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_71663.1	chr8	60640380	60640389	+	1	NA	intron (NM_001293769, intron 1 of 1)	intron (NM_001293769, intron 1 of 1)	7559	NM_001293769	71306	Mm.23242	NM_027756	ENSMUSG00000031647	Mfap3l	4933428A15Rik|5430405D20Rik|AI461995|AW125052|NYD-sp9|mKIAA0626	microfibrillar-associated protein 3-like	protein-coding
mm_117453.1	chr13	74808611	74808680	-	1	NA	promoter-TSS (NM_009817)	promoter-TSS (NM_009817)	115	NM_001301153	12380	Mm.29163	NM_009817	ENSMUSG00000021585	Cast	-	calpastatin	protein-coding
mm_15465.1	chr2	157456918	157456946	+	1	NA	intron (NM_009271, intron 3 of 14)	intron (NM_009271, intron 3 of 14)	32639	NM_001025395	20779	Mm.22845	NM_009271	ENSMUSG00000027646	Src	AW259666|pp60c-src	Rous sarcoma oncogene	protein-coding
mm_149396.1	chr19	11388227	11388369	+	1	NA	exon (NM_001310331, exon 5 of 7)	exon (NM_001310331, exon 5 of 7)	12810	NM_001310331	666907		NM_001310331	ENSMUSG00000101389	Ms4a4a	EG666907	membrane-spanning 4-domains, subfamily A, member 4A	protein-coding
mm_88776.1	chr10	80399038	80399049	+	1	NA	intron (NM_001306143, intron 1 of 6)	CpG	488	NM_013595	17192	Mm.7142	NM_013595	ENSMUSG00000035478	Mbd3	AI181826|AU019209	methyl-CpG binding domain protein 3	protein-coding
mm_24468.1	chr3	90654224	90654237	+	1	NA	promoter-TSS (NM_199422)	promoter-TSS (NM_199422)	-72	NM_199422	381493	Mm.291525	NM_199422	ENSMUSG00000063767	S100a7a	AY465109|Gm1020|S100A7L1|S100A7f|S100a15|S100a15a|S100a17l1	S100 calcium binding protein A7A	protein-coding
mm_51164.1	chr6	70726478	70726488	+	1	NA	Intergenic	Intergenic	65692	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_98650.1	chr11	96251639	96251668	+	1	NA	promoter-TSS (NR_037977)	promoter-TSS (NR_037977)	-7	NR_037977	193022	Mm.169508	NR_037977		Gm53	-	predicted gene 53	ncRNA
mm_44797.1	chr5	32746344	32746352	-	1	NA	promoter-TSS (NM_001347332)	promoter-TSS (NM_001347332)	-6	NM_001347332	320951	Mm.273765	NM_177298	ENSMUSG00000023452	Pisd	9030221M09Rik	phosphatidylserine decarboxylase	protein-coding
mm_145391.1	chr18	57142671	57142694	+	1	NA	intron (NM_001001979, intron 1 of 24)	intron (NM_001001979, intron 1 of 24)	9592	NM_001001979	70417	Mm.297863	NM_001001979	ENSMUSG00000024593	Megf10	3000002B06Rik|Gm331	multiple EGF-like-domains 10	protein-coding
mm_49736.1	chr6	34745735	34745749	+	1	NA	exon (NM_145575, exon 3 of 12)	exon (NM_145575, exon 3 of 12)	-34690	NM_001289657	76223	Mm.150047	NM_178630	ENSMUSG00000038836	Agbl3	2900053G10Rik|4930431N21Rik|6530406M24Rik|CCP3	ATP/GTP binding protein-like 3	protein-coding
mm_17201.1	chr2	25469094	25469106	-	1	NA	exon (NM_008963, exon 2 of 7)	exon (NM_008963, exon 2 of 7)	649	NM_008963	19215	Mm.1008	NM_008963	ENSMUSG00000015090	Ptgds	21kDa|L-PGDS|PGD2|PGDS|PGDS2|Ptgs3	prostaglandin D2 synthase (brain)	protein-coding
mm_141211.1	chr17	27133646	27133660	-	1	NA	intron (NM_026063, intron 1 of 3)	CpG	238	NM_026063	67267	Mm.272389	NM_026063	ENSMUSG00000024208	Uqcc2	2900010M23Rik|Cbp6|M19|Mnf1	ubiquinol-cytochrome c reductase complex assembly factor 2	protein-coding
mm_10768.1	chr2	24214771	24214773	+	1	NA	promoter-TSS (NM_019450)	promoter-TSS (NM_019450)	-645	NM_019450	54448	Mm.133095	NM_019450	ENSMUSG00000026984	Il1f6	Fil1|IL-1H1|IL1RP2|Il1f9|Il36a	interleukin 1 family, member 6	protein-coding
mm_156548.1	chrX	151520656	151520681	+	1	NA	promoter-TSS (NM_001113354)	promoter-TSS (NM_001113354)	-4	NM_177201	320595	Mm.17156	NM_177201	ENSMUSG00000041229	Phf8	9830141C09Rik|mKIAA1111	PHD finger protein 8	protein-coding
mm_104471.1	chr11	95309719	95309732	-	1	NA	intron (NM_177619, intron 1 of 12)	CpG	521	NM_001195004	217127	Mm.90213	NM_177619	ENSMUSG00000038909	Kat7	Hbo1|Hboa|Myst2	K(lysine) acetyltransferase 7	protein-coding
mm_4401.1	chr1	172376908	172376933	+	1	NA	exon (NM_026234, exon 1 of 1)	exon (NM_026234, exon 1 of 1)	389	NM_026234	67556	Mm.26612	NM_026234	ENSMUSG00000050229	Pigm	4933437L05Rik|AI644422|AV302080|C920011G20Rik	phosphatidylinositol glycan anchor biosynthesis, class M	protein-coding
mm_11908.1	chr2	51972339	51972384	+	1	NA	intron (NM_019401, intron 1 of 7)	intron (NM_019401, intron 1 of 7)	847	NM_001141949	64685	Mm.7491	NM_019401	ENSMUSG00000026946	Nmi	-	N-myc (and STAT) interactor	protein-coding
mm_25230.1	chr3	103860347	103860359	+	1	NA	promoter-TSS (NM_008979)	promoter-TSS (NM_008979)	76	NM_008979	19260	Mm.395	NM_008979	ENSMUSG00000027843	Ptpn22	70zpep|PEP|Ptpn8	protein tyrosine phosphatase, non-receptor type 22 (lymphoid)	protein-coding
mm_90655.1	chr10	128798943	128798979	+	1	NA	exon (NM_021412, exon 9 of 9)	exon (NM_021412, exon 9 of 9)	5409	NM_178066	73827	Mm.24630	NM_178066	ENSMUSG00000047090	Tmem198b	1110012D08Rik	transmembrane protein 198b	protein-coding
mm_161808.1	chr17	63492752	63492752	-	1	NA	intron (NM_015794, intron 1 of 8)	intron (NM_015794, intron 1 of 8)	7828	NM_015794	50758	Mm.136366	NM_015794	ENSMUSG00000023965	Fbxl17	6330576B01Rik|AI452053|BB073797|C130023C01Rik|Fbx13|Fbxo13	F-box and leucine-rich repeat protein 17	protein-coding
mm_150974.1	chr19	46501686	46501707	+	1	NA	promoter-TSS (NM_053100)	promoter-TSS (NM_053100)	48	NM_053100	93679	Mm.392177	NM_053100	ENSMUSG00000025034	Trim8	AA408830|BB006755|GERP|Rnf27	tripartite motif-containing 8	protein-coding
mm_136443.1	chr16	94856683	94856697	-	1	NA	promoter-TSS (NM_001025590)	promoter-TSS (NM_001025590)	0	NM_001025590	16522	Mm.328720	NM_010606	ENSMUSG00000043301	Kcnj6	BIR1|GIRK2|KATP2|KCNJ7|Kir3.2|weaver|wv	potassium inwardly-rectifying channel, subfamily J, member 6	protein-coding
mm_8821.1	chr1	162246774	162246775	-	1	NA	intron (NM_001038619, intron 13 of 20)	intron (NM_001038619, intron 13 of 20)	23406	NR_029796	387210		NR_029796	ENSMUSG00000065516	Mir214	Mirn214|mir-214|mmu-mir-214	microRNA 214	ncRNA
mm_64431.1	chr7	142577869	142577879	+	1	NA	promoter-TSS (NR_030416)	promoter-TSS (NR_030416)	272	NR_130974	14955	Mm.14802	NR_001592	ENSMUSG00000000031	H19	AI747191	H19, imprinted maternally expressed transcript	ncRNA
mm_11346.1	chr2	30845269	30845304	+	1	NA	promoter-TSS (NM_009116)	promoter-TSS (NM_009116)	-81	NM_009116	20204	Mm.1802	NM_009116	ENSMUSG00000039476	Prrx2	Prx2|S8	paired related homeobox 2	protein-coding
mm_35082.1	chr4	7455077	7455087	-	1	NA	Intergenic	Intergenic	-105606	NR_040645	71510	Mm.410775	NR_040645	ENSMUSG00000086070	8430436N08Rik	-	RIKEN cDNA 8430436N08 gene	ncRNA
mm_33270.1	chr4	127987889	127987910	+	1	NA	promoter-TSS (NM_001281955)	promoter-TSS (NM_001281955)	-145	NM_001281955	329942	Mm.421342	NM_001281955	ENSMUSG00000028804	Csmd2	Gm139	CUB and Sushi multiple domains 2	protein-coding
mm_72572.1	chr8	84130254	84130262	+	1	NA	intron (NM_001013384, intron 7 of 9)	PB1D10|SINE|Alu	4269	NM_001013384	244550	Mm.334654	NM_001013384	ENSMUSG00000012889	Podnl1	5832418A03Rik|Gm506	podocan-like 1	protein-coding
mm_43686.1	chr5	138820964	138820968	+	1	NA	exon (NM_001195128, exon 2 of 3)	exon (NM_001195128, exon 2 of 3)	886	NM_001195128	384244	Mm.485002	NM_001195128	ENSMUSG00000094504	Gm5294	EG384244	predicted gene 5294	protein-coding
mm_74174.1	chr8	123447067	123447081	+	1	NA	intron (NM_001253784, intron 2 of 12)	intron (NM_001253784, intron 2 of 12)	3815	NM_001281803	23854	Mm.275127	NM_054046	ENSMUSG00000001482	Def8	AI449518|D8Ertd713e|DEF-8	differentially expressed in FDCP 8	protein-coding
mm_57238.1	chr6	123283014	123283035	-	1	NA	3' UTR (NM_019948, exon 6 of 6)	3' UTR (NM_019948, exon 6 of 6)	6847	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_35512.1	chr4	41094888	41094927	-	1	NA	intron (NM_016689, intron 2 of 5)	intron (NM_016689, intron 2 of 5)	3276	NM_016689	11828	Mm.34043	NM_016689	ENSMUSG00000028435	Aqp3	AQP-2	aquaporin 3	protein-coding
mm_96949.1	chr11	70562899	70562922	+	1	NA	promoter-TSS (NM_001045964)	promoter-TSS (NM_001045964)	29	NM_016713	50932	Mm.42967	NM_016713	ENSMUSG00000020827	Mink1	B55|MINK|Map4k6|Ysk2	misshapen-like kinase 1 (zebrafish)	protein-coding
mm_81250.1	chr9	107975653	107975660	+	1	NA	promoter-TSS (NM_023738)	promoter-TSS (NM_023738)	89	NM_023738	74153	Mm.277125	NM_023738	ENSMUSG00000032596	Uba7	1300004C08Rik|Ube1l	ubiquitin-like modifier activating enzyme 7	protein-coding
mm_3466.1	chr1	150104405	150104446	+	1	NA	exon (NM_011198, exon 8 of 10)	exon (NM_011198, exon 8 of 10)	4394	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_105640.1	chr11	107012683	107012729	-	1	NA	Intergenic	CpG	-13181	NM_010655	16647	Mm.12508	NM_010655	ENSMUSG00000018362	Kpna2	2410044B12Rik|IPOA1|PTAC58|Rch1	karyopherin (importin) alpha 2	protein-coding
mm_127012.1	chr15	95852179	95852181	+	1	NA	intron (NM_001253813, intron 2 of 20)	L1MB4|LINE|L1	61337	NM_001253813	105722	Mm.38087	NM_175344	ENSMUSG00000064210	Ano6	2900059G15Rik|AA407480|AW554778|F730003B03Rik|Tmem16f	anoctamin 6	protein-coding
mm_75158.1	chr8	36265787	36265799	-	1	NA	Intergenic	Intergenic	-16277	NM_001081150	244421	Mm.324032	NM_001081150	ENSMUSG00000039633	Lonrf1	-	LON peptidase N-terminal domain and ring finger 1	protein-coding
mm_132264.1	chr16	32776331	32776335	+	1	NA	intron (NM_080457, intron 21 of 26)	intron (NM_080457, intron 21 of 26)	21102	NM_146071	224116	Mm.153301	NM_146071	ENSMUSG00000035638	Muc20	BC026367	mucin 20	protein-coding
mm_20078.1	chr2	120609284	120609317	-	1	NA	promoter-TSS (NM_025475)	promoter-TSS (NM_025475)	15	NM_025657	66606	Mm.428639	NM_025657	ENSMUSG00000027286	Lrrc57	2810002D13Rik|AA407405	leucine rich repeat containing 57	protein-coding
mm_28272.1	chr3	88772579	88772601	-	1	NA	promoter-TSS (NM_018804)	promoter-TSS (NM_018804)	9	NM_018804	229521	Mm.379376	NM_018804	ENSMUSG00000068923	Syt11	1500004A13Rik|3632445O20Rik|5430404N14Rik|6530420C11Rik|AI851970	synaptotagmin XI	protein-coding
mm_78242.1	chr9	21632792	21632798	+	1	NA	intron (NM_001174079, intron 1 of 33)	intron (NM_001174079, intron 1 of 33)	16626	NM_001174078	20586	Mm.286593	NM_011417	ENSMUSG00000032187	Smarca4	Brg1|HP1-BP72|SNF2beta|SW1/SNF|b2b508.1Clo|b2b692Clo	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	protein-coding
mm_135589.1	chr16	50591122	50591132	-	1	NA	promoter-TSS (NM_027046)	promoter-TSS (NM_027046)	27	NM_027046	69339	Mm.422869	NM_027046	ENSMUSG00000050685	Ccdc54	1700007N18Rik|AI644412|BB013989|NYD-SP17	coiled-coil domain containing 54	protein-coding
mm_151510.1	chr19	58733420	58733436	+	1	NA	exon (NM_018874, exon 6 of 13)	exon (NM_018874, exon 6 of 13)	4541	NM_018874	18946	Mm.10753	NM_018874	ENSMUSG00000042179	Pnliprp1	Plrp1	pancreatic lipase related protein 1	protein-coding
mm_59744.1	chr7	28818593	28818603	+	1	NA	intron (NM_177301, intron 7 of 12)	intron (NM_177301, intron 7 of 12)	-6740	NM_016772	51798	Mm.291776	NM_016772	ENSMUSG00000053898	Ech1	AA617331	enoyl coenzyme A hydratase 1, peroxisomal	protein-coding
mm_68561.1	chr7	114636300	114636315	-	1	NA	promoter-TSS (NM_001289444)	promoter-TSS (NM_001289444)	50	NM_001289444	12310	Mm.4361	NM_007587	ENSMUSG00000030669	Calca	CA|CGRP-1|CGRP1|Calc|Calc1|Cgrp|Ct|Ctn	calcitonin/calcitonin-related polypeptide, alpha	protein-coding
mm_127979.1	chr15	12419631	12419643	-	1	NA	intron (NM_001081064, intron 5 of 23)	intron (NM_001081064, intron 5 of 23)	98141	NM_025673	66629	Mm.157655	NM_025673	ENSMUSG00000022200	Golph3	4733401N08Rik|5730410D03Rik|AW413496	golgi phosphoprotein 3	protein-coding
mm_146426.1	chr18	84851353	84851376	+	1	NA	promoter-TSS (NM_025797)	promoter-TSS (NM_025797)	-50	NM_025797	109672	Mm.31018	NM_025797	ENSMUSG00000024646	Cyb5a	0610009N12Rik|Cyb5	cytochrome b5 type A (microsomal)	protein-coding
mm_145638.1	chr18	61117061	61117111	+	1	NA	promoter-TSS (NR_105949)	promoter-TSS (NR_105949)	-382	NR_105949	102466212		NR_105949	ENSMUSG00000098389	Mir6983	Gm27496|mmu-mir-6983	microRNA 6983	ncRNA
mm_15587.1	chr2	160364461	160364500	+	1	NA	3' UTR (NM_010658, exon 1 of 1)	3' UTR (NM_010658, exon 1 of 1)	2585	NM_010658	16658	Mm.330745	NM_010658	ENSMUSG00000074622	Mafb	Kreisler|Krml|Krml1|kr	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein B (avian)	protein-coding
mm_103103.1	chr11	69947410	69947432	-	1	NA	intron (NM_009204, intron 1 of 10)	intron (NM_009204, intron 1 of 10)	769	NM_009204	20528	Mm.10661	NM_009204	ENSMUSG00000018566	Slc2a4	Glut-4|Glut4	solute carrier family 2 (facilitated glucose transporter), member 4	protein-coding
mm_141309.1	chr17	28350748	28350820	-	1	NA	promoter-TSS (NM_001204156)	promoter-TSS (NM_001204156)	21	NM_011566	21678	Mm.6655	NM_011566	ENSMUSG00000002249	Tead3	DTEF-1|ETFR-1|TEAD-3|TEF-5|Tcf13r2	TEA domain family member 3	protein-coding
mm_62656.1	chr7	107693285	107693291	+	1	NA	intron (NM_001163557, intron 5 of 25)	intron (NM_001163557, intron 5 of 25)	64744	NM_001205227	320635	Mm.132828	NM_177216	ENSMUSG00000048065	Cyb5r2	D630003K02Rik|b5R.2	cytochrome b5 reductase 2	protein-coding
mm_155223.1	chrX	57066018	57066028	+	1	NA	exon (NM_029371, exon 9 of 9)	exon (NM_029371, exon 9 of 9)	12189	NM_029371	72459	Mm.2152	NM_028242	ENSMUSG00000067873	Htatsf1	1600023H17Rik|2600017A12Rik|2700077B20Rik|TAT-SF1	HIV TAT specific factor 1	protein-coding
mm_53478.1	chr6	134937743	134937746	+	1	NA	intron (NR_037956, intron 1 of 1)	AT_rich|Low_complexity|Low_complexity	8652	NR_037955	381822	Mm.5935	NR_037955	ENSMUSG00000098318	Lockd	1190002F15Rik|AI120476|Droc	lncRNA downstream of Cdkn1b	ncRNA
mm_133506.1	chr16	90738245	90738247	+	1	NA	promoter-TSS (NM_029844)	promoter-TSS (NM_029844)	-78	NM_029844	77037	Mm.22455	NM_029844	ENSMUSG00000039956	Mrap	1110025G12Rik|Falp|ORF61	melanocortin 2 receptor accessory protein	protein-coding
mm_149023.1	chr19	8757140	8757155	+	1	NA	promoter-TSS (NM_001276704)	promoter-TSS (NM_001276704)	30	NM_001276704	53319	Mm.7271	NM_016813	ENSMUSG00000010097	Nxf1	Mex67|Mvb1|Tap	nuclear RNA export factor 1	protein-coding
mm_107040.1	chr12	13594241	13594244	+	1	NA	Intergenic	RMER17B2|LTR|ERVK	33404	NR_136761	102639399	Mm.122052	NR_136761		Gm35725	-	predicted gene, 35725	ncRNA
mm_131098.1	chr16	4964251	4964272	+	1	NA	promoter-TSS (NM_001271586)	promoter-TSS (NM_001271586)	-24	NM_028301	72615	Mm.290628	NM_028301	ENSMUSG00000022515	Anks3	2700067D09Rik|C81345|mKIAA1977	ankyrin repeat and sterile alpha motif domain containing 3	protein-coding
mm_122907.1	chr14	54953864	54953896	-	1	NA	exon (NM_010856, exon 21 of 39)	exon (NM_010856, exon 21 of 39)	-4738	NR_029724	387204		NR_029724	ENSMUSG00000065432	Mir208a	Mirn208|Mirn208a|mir-208|mir-208a|mmu-mir-208	microRNA 208a	ncRNA
mm_151865.1	chr19	5797566	5797631	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	-1617	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_118943.1	chr14	27335793	27335828	+	1	NA	promoter-TSS (NM_001289687)	promoter-TSS (NM_001289687)	-227	NM_001289687	71704	Mm.248606	NM_027871	ENSMUSG00000021895	Arhgef3	1200004I24Rik|9830169H03Rik|C76747|Xpln	Rho guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_160651.1	chr9	111311626	111311626	+	1	NA	promoter-TSS (NM_001164659)	promoter-TSS (NM_001164659)	-113	NM_001164659	320429	Mm.270754	NM_001164659	ENSMUSG00000062296	Trank1	A230061D21Rik|C030048J01Rik|Gm187|Lba1	tetratricopeptide repeat and ankyrin repeat containing 1	protein-coding
mm_17505.1	chr2	28916628	28916635	-	1	NA	promoter-TSS (NM_019446)	promoter-TSS (NM_019446)	-191	NM_001164186	54422	Mm.21390	NM_019446	ENSMUSG00000026805	Barhl1	Dres115|MBH2	BarH-like 1 (Drosophila)	protein-coding
mm_145832.1	chr18	65441777	65441802	+	1	NA	intron (NM_172833, intron 2 of 15)	B2_Mm2|SINE|B2	10792	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_19288.1	chr2	90450806	90450820	-	1	NA	intron (NM_001135657, intron 15 of 25)	intron (NM_001135657, intron 15 of 25)	28361	NM_001135657	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_76227.1	chr8	83573143	83573149	-	1	NA	intron (NM_134118, intron 5 of 12)	intron (NM_134118, intron 5 of 12)	6388	NM_025843	66916	Mm.29683	NM_025843	ENSMUSG00000033938	Ndufb7	1110002H15Rik	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 7	protein-coding
mm_61229.1	chr7	64502091	64502155	+	1	NA	promoter-TSS (NM_001291167)	promoter-TSS (NM_001291167)	-15	NM_001291166	11784	Mm.4657	NM_007461	ENSMUSG00000030519	Apba2	X11-like|X11L|XllL|mXllL	amyloid beta (A4) precursor protein-binding, family A, member 2	protein-coding
mm_32332.1	chr4	104367594	104367624	+	1	NA	promoter-TSS (NM_177259)	promoter-TSS (NM_177259)	71	NM_177259	13131	Mm.289682	NM_010014	ENSMUSG00000028519	Dab1	AI956902|C630028C02Rik|scm|scr|scrambler|yot	disabled 1	protein-coding
mm_131529.1	chr16	17646514	17646530	+	1	NA	promoter-TSS (NM_001166164)	promoter-TSS (NM_001166164)	52	NM_001166164	72315	Mm.297777	NM_001166164	ENSMUSG00000041617	Ccdc74a	2310015A05Rik	coiled-coil domain containing 74A	protein-coding
mm_111155.1	chr12	83424945	83424952	-	1	NA	intron (NM_058212, intron 1 of 8)	intron (NM_058212, intron 1 of 8)	62788	NM_001267626	70127	Mm.151308	NM_058212	ENSMUSG00000021221	Dpf3	2810403B03Rik|6530402L11Rik|BAF45C|C78788|CERD4|cer-d4	D4, zinc and double PHD fingers, family 3	protein-coding
mm_25446.1	chr3	108284090	108284100	+	1	NA	promoter-TSS (NM_019972)	promoter-TSS (NM_019972)	31	NM_019972	20661	Mm.157119	NM_019972	ENSMUSG00000068747	Sort1	2900053A11Rik|AI852375|Ntr3|Ntsr3	sortilin 1	protein-coding
mm_66694.1	chr7	45916773	45916795	-	1	NA	3' UTR (NM_144801, exon 8 of 8)	3' UTR (NM_144801, exon 8 of 8)	4065	NM_001146346	13732	Mm.20829	NM_010129	ENSMUSG00000040212	Emp3	H-4|H4|HNMP-1|MI-35|Ymp	epithelial membrane protein 3	protein-coding
mm_60774.1	chr7	45559212	45559238	+	1	NA	intron (NM_025330, intron 4 of 8)	intron (NM_025330, intron 4 of 8)	4297	NM_025330	66065	Mm.285710	NM_025330	ENSMUSG00000030825	Hsd17b14	0610039E24Rik|Dhrs10|retSDR3	hydroxysteroid (17-beta) dehydrogenase 14	protein-coding
mm_171552.1	chr4	147132017	147132017	+	1	NA	Intergenic	Intergenic	-43849	NM_001039209	195531	Mm.270762	NM_001039209	ENSMUSG00000078496	Zfp982	Gm13152|OTTMUSG00000010671	zinc finger protein 982	protein-coding
mm_60802.1	chr7	45627503	45627532	+	1	NA	promoter-TSS (NM_028544)	promoter-TSS (NM_028544)	-20	NM_028544	69903	Mm.181396	NM_028544	ENSMUSG00000044562	Rasip1	1110025D03Rik|2610025P08Rik|AI853551|Rain	Ras interacting protein 1	protein-coding
mm_133721.1	chr16	93711913	93711921	+	1	NA	promoter-TSS (NM_026700)	promoter-TSS (NM_026700)	10	NM_027293	70028	Mm.23230	NM_026700	ENSMUSG00000022946	Dopey2	0610038M01Rik|2610510B01Rik|AI503246|C21orf5|mKIAA0933	dopey family member 2	protein-coding
mm_94195.1	chr10	130541958	130541967	-	1	NA	Intergenic	Intergenic	-44583	NM_001103366	625131	Mm.469844	NM_001103366	ENSMUSG00000091511	Vmn2r87	EG625131	vomeronasal 2, receptor 87	protein-coding
mm_40069.1	chr5	34278809	34278815	+	1	NA	intron (NM_001015039, intron 1 of 12)	intron (NM_001015039, intron 1 of 12)	9512	NM_001015039	231125	Mm.113388	NM_001015039	ENSMUSG00000037224	Zfyve28	9630058O20Rik|Gm146|mKIAA1643	zinc finger, FYVE domain containing 28	protein-coding
mm_54314.1	chr6	30174101	30174109	-	1	NA	promoter-TSS (NR_126541)	promoter-TSS (NR_126541)	20	NR_126540	101447999		NR_126540		Mirc35hg	-	microRNA cluster 35, host gene	ncRNA
mm_107411.1	chr12	33957818	33957888	+	1	NA	5' UTR (NM_011658, exon 1 of 2)	5' UTR (NM_011658, exon 1 of 2)	182	NM_011658	22160	Mm.3280	NM_011658	ENSMUSG00000035799	Twist1	M-Twist|Pde|Ska10|Ska<m10Jus>|Twist|bHLHa38|pdt	twist basic helix-loop-helix transcription factor 1	protein-coding
mm_58633.1	chr7	5095677	5095705	+	1	NA	exon (NM_001252454, exon 8 of 11)	exon (NM_001252454, exon 8 of 11)	15456	NM_001252454	13854	Mm.3091	NM_010147	ENSMUSG00000035203	Epn1	AA269831|Ibp1	epsin 1	protein-coding
mm_154981.1	chrX	38066539	38066547	+	1	NA	promoter-TSS (NM_001024850)	promoter-TSS (NM_001024850)	68	NM_001024850	434769	Mm.244139	NM_001024850	ENSMUSG00000053909	Rhox10	-	reproductive homeobox 10	protein-coding
mm_124236.1	chr14	101477232	101477240	-	1	NA	intron (NM_001081278, intron 9 of 18)	intron (NM_001081278, intron 9 of 18)	131955	NM_001081278	210789	Mm.320639	NM_173380	ENSMUSG00000033083	Tbc1d4	5930406J04Rik|A930035N22|AV295684|As160	TBC1 domain family, member 4	protein-coding
mm_147879.1	chr18	64660752	64660771	-	1	NA	5' UTR (NM_001001488, exon 1 of 28)	5' UTR (NM_001001488, exon 1 of 28)	239	NM_001001488	54670	Mm.270043	NM_001001488	ENSMUSG00000039529	Atp8b1	AI451886|FIC1|Ic	ATPase, class I, type 8B, member 1	protein-coding
mm_131341.1	chr16	13401101	13401114	+	1	NA	exon (NM_001122667, exon 12 of 17)	exon (NM_001122667, exon 12 of 17)	42686	NM_153588	239719	Mm.270643	NM_153588	ENSMUSG00000009569	Mkl2	ENSMUSG00000075401|Gt4-1|MRTF-B|Mrtfb|mKIAA1243	MKL/myocardin-like 2	protein-coding
mm_159242.1	chr2	150451487	150451487	-	1	NA	promoter-TSS (NM_001310645)	promoter-TSS (NM_001310645)	14	NM_001310645	668923	Mm.393876	NM_001177550	ENSMUSG00000068130	Zfp442	OTTMUSG00000015730|ZIPO-II	zinc finger protein 442	protein-coding
mm_21044.1	chr2	152540095	152540101	-	1	NA	promoter-TSS (NM_001001444)	promoter-TSS (NM_001001444)	-57	NM_001001444	75400	Mm.45560	NM_001001444	ENSMUSG00000044249	Defb29	0610030I09Rik|BD-29|mBD-29	defensin beta 29	protein-coding
mm_46766.1	chr5	112267389	112267401	-	1	NA	exon (NM_001312894, exon 5 of 6)	exon (NM_001312894, exon 5 of 6)	-9296	NM_001326590	22022	Mm.250631	NM_009419	ENSMUSG00000029344	Tpst2	AI448750|D5Ucla3|Tango13b|grm|grt	protein-tyrosine sulfotransferase 2	protein-coding
mm_12031.1	chr2	58567291	58567322	+	1	NA	promoter-TSS (NM_001289660)	promoter-TSS (NM_001289660)	-28	NM_001289660	76654	Mm.200370	NM_029692	ENSMUSG00000026839	Upp2	1700124F02Rik|AI266885|UDRPASE2|UP2|UPASE2	uridine phosphorylase 2	protein-coding
mm_161803.1	chr17	56093608	56093608	+	1	NA	exon (NM_001304785, exon 4 of 16)	exon (NM_001304785, exon 4 of 16)	13977	NM_001304785	15193	Mm.12966	NM_008233	ENSMUSG00000002833	Hdgfrp2	HRP-2	hepatoma-derived growth factor, related protein 2	protein-coding
mm_114615.1	chr13	75849340	75849368	+	1	NA	3' UTR (NM_053108, exon 3 of 3)	3' UTR (NM_053108, exon 3 of 3)	9468	NM_053108	93692	Mm.25844	NM_053108	ENSMUSG00000021591	Glrx	C86710|D13Wsu156e|Glrx1|Grx1|TTase	glutaredoxin	protein-coding
mm_164379.1	chr16	30510698	30510725	+	1	NA	Intergenic	CpG	39867	NM_172614	224090	Mm.241459	NM_172614	ENSMUSG00000022537	Tmem44	1700007N03Rik|9330161C17Rik|B230220N21	transmembrane protein 44	protein-coding
mm_120906.1	chr14	76081693	76081696	+	1	NA	Intergenic	RLTR41|LTR|ERV1	29121	NM_026177	67467	Mm.260767	NM_026177	ENSMUSG00000022008	Gpalpp1	1200011I18Rik|Kiaa1704	GPALPP motifs containing 1	protein-coding
mm_166143.1	chr5	3494922	3494934	+	1	NA	intron (NM_009873, intron 5 of 7)	intron (NM_009873, intron 5 of 7)	-48905	NM_001042501	68152	Mm.240265	NM_026583	ENSMUSG00000058503	Fam133b	2900022K02Rik|5830415L20Rik	family with sequence similarity 133, member B	protein-coding
mm_139364.1	chr17	50643094	50643105	+	1	NA	intron (NM_013880, intron 4 of 5)	intron (NM_013880, intron 4 of 5)	-55582	NM_001297747	12228	Mm.392910	NM_009770	ENSMUSG00000022863	Btg3	ANA|tob5	B cell translocation gene 3	protein-coding
mm_141556.1	chr17	32211290	32211297	-	1	NA	intron (NM_198094, intron 11 of 12)	intron (NM_198094, intron 11 of 12)	-21744	NM_001347341	71932	Mm.176240	NM_001033163	ENSMUSG00000037577	Ephx3	2310063B19Rik|Abhd9	epoxide hydrolase 3	protein-coding
mm_32892.1	chr4	118964221	118964223	+	1	NA	exon (NM_133892, exon 3 of 7)	exon (NM_133892, exon 3 of 7)	2255	NM_133892	100470	Mm.26698	NM_133892	ENSMUSG00000024903	Lao1	AW990848	L-amino acid oxidase 1	protein-coding
mm_45713.1	chr5	84417113	84417119	-	1	NA	5' UTR (NM_007937, exon 1 of 16)	5' UTR (NM_007937, exon 1 of 16)	266	NM_007937	13839	Mm.137991	NM_007937	ENSMUSG00000029245	Epha5	AI854630|AW125296|Cek7|Ehk1|Els1|Hek7|Rek7|bsk	Eph receptor A5	protein-coding
mm_66834.1	chr7	48878059	48878094	-	1	NA	exon (NM_001013368, exon 4 of 13)	exon (NM_001013368, exon 4 of 13)	2965	NM_001013368	108961	Mm.240566	NM_001013368	ENSMUSG00000046179	E2f8	4432406C08Rik|AA410048	E2F transcription factor 8	protein-coding
mm_169047.1	chr13	16490788	16490803	-	1	NA	Intergenic	ERVB7_2B-LTR_MM|LTR|ERVK	478944	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_79258.1	chr9	50752902	50753086	+	1	NA	promoter-TSS (NM_001289784)	promoter-TSS (NM_001289784)	23	NM_009964	12955	Mm.178	NM_009964	ENSMUSG00000032060	Cryab	Crya-2|Crya2|HspB5|P23	crystallin, alpha B	protein-coding
mm_121391.1	chr14	119099474	119099500	+	1	NA	promoter-TSS (NM_001081252)	promoter-TSS (NM_001081252)	-53	NM_001081252	66435	Mm.213406	NM_025561	ENSMUSG00000042104	Uggt2	1810064L21Rik|3110001A05Rik|3110027P15Rik|A230065J02Rik|AW047562|Ugcgl2	UDP-glucose glycoprotein glucosyltransferase 2	protein-coding
mm_68843.1	chr7	126364876	126364880	-	1	NA	intron (NM_010689, intron 8 of 11)	intron (NM_010689, intron 8 of 11)	3167	NR_106025	102466797		NR_106025	ENSMUSG00000099017	Mir7058	Gm27766|mmu-mir-7058	microRNA 7058	ncRNA
mm_92721.1	chr10	80804028	80804071	-	1	NA	exon (NM_013651, exon 9 of 9)	exon (NM_013651, exon 9 of 9)	-1199	NM_007445	11705	Mm.376094	NM_007445	ENSMUSG00000035262	Amh	MIS	anti-Mullerian hormone	protein-coding
mm_121277.1	chr14	103650251	103650257	+	1	NA	promoter-TSS (NM_198014)	promoter-TSS (NM_198014)	11	NM_198014	105439	Mm.27548	NM_198014	ENSMUSG00000055717	Slain1	9630044O09Rik|AA675320|AW742596	SLAIN motif family, member 1	protein-coding
mm_130596.1	chr15	99772396	99772458	-	1	NA	promoter-TSS (NM_028015)	promoter-TSS (NM_028015)	88	NM_028015	71949	Mm.390821	NM_028015	ENSMUSG00000023021	Cers5	2310081H14Rik|AU045339|AW544927|Lass5|Trh4	ceramide synthase 5	protein-coding
mm_15160.1	chr2	154009792	154009801	+	1	NA	exon (NM_008953, exon 3 of 9)	exon (NM_008953, exon 3 of 9)	1520	NM_008953	19194	Mm.29197	NM_008953	ENSMUSG00000042459	Bpifa2	Bpifa2e|Psp	BPI fold containing family A, member 2	protein-coding
mm_15289.1	chr2	155276933	155276955	+	1	NA	intron (NR_046364, intron 1 of 2)	CpG	580	NR_046364	66734	Mm.196239	NM_025735	ENSMUSG00000027602	Map1lc3a	1010001H21Rik|4922501H04Rik|LC3|LC3a	microtubule-associated protein 1 light chain 3 alpha	protein-coding
mm_82717.1	chr9	24723004	24723006	-	1	NA	3' UTR (NM_194263, exon 8 of 8)	3' UTR (NM_194263, exon 8 of 8)	-26712	NM_001166207	320752	Mm.46158	NM_001166207	ENSMUSG00000085576	Dpy19l2	4932443J21Rik|Gm18376	dpy-19-like 2 (C. elegans)	protein-coding
mm_2498.1	chr1	106171651	106171729	+	1	NA	promoter-TSS (NM_133821)	promoter-TSS (NM_133821)	-166	NR_040630	626049	Mm.247410	NR_040630	ENSMUSG00000101583	Gm20753	-	predicted gene, 20753	ncRNA
mm_35508.1	chr4	41093591	41093601	-	1	NA	exon (NM_016689, exon 6 of 6)	exon (NM_016689, exon 6 of 6)	4587	NM_016689	11828	Mm.34043	NM_016689	ENSMUSG00000028435	Aqp3	AQP-2	aquaporin 3	protein-coding
mm_167786.1	chr9	120492653	120492661	+	1	NA	promoter-TSS (NM_026892)	promoter-TSS (NM_026892)	51	NM_026892	68969	Mm.28753	NM_026892	ENSMUSG00000006941	Eif1b	1500010M16Rik|3110001N14Rik|Gc20	eukaryotic translation initiation factor 1B	protein-coding
mm_47221.1	chr5	121191350	121191361	-	1	NA	promoter-TSS (NM_001109992)	promoter-TSS (NM_001109992)	42	NM_001109992	19247	Mm.8681	NM_011202	ENSMUSG00000043733	Ptpn11	2700084A17Rik|AW536184|PTP1D|PTP2C|SAP-2|SH-PTP2|SH-PTP3|SHP-2|Shp2|Syp	protein tyrosine phosphatase, non-receptor type 11	protein-coding
mm_90783.1	chr10	6980500	6980508	-	1	NA	promoter-TSS (NM_001170802)	promoter-TSS (NM_001170802)	-39	NM_001170801	320495	Mm.331674	NM_001033391	ENSMUSG00000064065	Ipcef1	A130090K04Rik	interaction protein for cytohesin exchange factors 1	protein-coding
mm_153892.1	chr19	46969563	46969572	-	1	NA	promoter-TSS (NM_001164365)	promoter-TSS (NM_001164365)	0	NM_001164365	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_155653.1	chrX	85870325	85870335	+	1	NA	promoter-TSS (NM_001163539)	promoter-TSS (NM_001163539)	57	NM_001163539	71398	Mm.185296	NM_001163539	ENSMUSG00000025058	5430427O19Rik	-	RIKEN cDNA 5430427O19 gene	protein-coding
mm_61999.1	chr7	91162660	91162690	+	1	NA	intron (NM_011807, intron 1 of 22)	B4A|SINE|B4	71889	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_73120.1	chr8	94772195	94772210	+	1	NA	promoter-TSS (NM_009142)	promoter-TSS (NM_009142)	22	NM_009142	20312	Mm.103711	NM_009142	ENSMUSG00000031778	Cx3cl1	AB030188|ABCD-3|AI848747|CX3C|Cxc3|D8Bwg0439e|Scyd1	chemokine (C-X3-C motif) ligand 1	protein-coding
mm_75247.1	chr8	39643699	39643721	-	1	NA	intron (NR_035426, intron 4 of 5)	Lx5c|LINE|L1	-1032	NM_001113326	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_135990.1	chr16	75093083	75093096	-	1	NA	Intergenic	Intergenic	492972	NM_001252513	320355	Mm.99517	NM_177142	ENSMUSG00000032948	Lipi	D930038D03Rik|lpd1	lipase, member I	protein-coding
mm_158711.1	chrX	162552574	162552612	-	1	NA	exon (NM_001290633, exon 4 of 18)	exon (NM_001290633, exon 4 of 18)	91065	NM_001290633	194590	Mm.442441	NM_178256	ENSMUSG00000040855	Reps2	POB1	RALBP1 associated Eps domain containing protein 2	protein-coding
mm_91566.1	chr10	40025386	40025402	-	1	NA	promoter-TSS (NM_144821)	promoter-TSS (NM_144821)	-126	NM_144821	215929	Mm.55513	NM_144821	ENSMUSG00000038522	Mfsd4b1	AI317395|AI482555|Naglt1a	major facilitator superfamily domain containing 4B1	protein-coding
mm_35921.1	chr4	53031778	53031791	-	1	NA	3' UTR (NM_013454, exon 50 of 50)	3' UTR (NM_013454, exon 50 of 50)	19904	NM_025623	66536	Mm.38244	NM_025623	ENSMUSG00000015247	Nipsnap3b	2700063N13Rik|Nipsnap3a	nipsnap homolog 3B (C. elegans)	protein-coding
mm_108583.1	chr12	85111162	85111176	+	1	NA	intron (NM_030225, intron 1 of 14)	CpG	336	NM_030225	78920	Mm.296221	NM_030225	ENSMUSG00000004789	Dlst	1600017E01Rik|4632413C10Rik|4930529O08Rik|DLTS	dihydrolipoamide S-succinyltransferase (E2 component of 2-oxo-glutarate complex)	protein-coding
mm_105251.1	chr11	102353278	102353289	-	1	NA	exon (NM_011403, exon 16 of 20)	exon (NM_011403, exon 16 of 20)	11998	NM_011403	20533	Mm.7248	NM_011403	ENSMUSG00000006574	Slc4a1	Ae1|CD233|Empb3|l11Jus51	solute carrier family 4 (anion exchanger), member 1	protein-coding
mm_144490.1	chr18	24205363	24205379	+	1	NA	promoter-TSS (NM_013814)	promoter-TSS (NM_013814)	27	NM_013814	14423	Mm.30249	NM_013814	ENSMUSG00000000420	Galnt1	-	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 1	protein-coding
mm_76524.1	chr8	87472544	87472571	-	1	NA	promoter-TSS (NM_019626)	promoter-TSS (NM_019626)	35	NM_019626	12404	Mm.4880	NM_019626	ENSMUSG00000031654	Cbln1	AI323299	cerebellin 1 precursor protein	protein-coding
mm_154987.1	chrX	38189830	38189842	+	1	NA	promoter-TSS (NM_020256)	promoter-TSS (NM_020256)	43	NM_001079513	56805	Mm.391248	NM_020256	ENSMUSG00000048047	Zbtb33	AW260253|E130014G12Rik|Kaiso|Znf-kaiso	zinc finger and BTB domain containing 33	protein-coding
mm_61402.1	chr7	73391241	73391296	+	1	NA	intron (NM_177740, intron 1 of 3)	intron (NM_177740, intron 1 of 3)	-15494	NR_040324	319783	Mm.349813	NR_040324	ENSMUSG00000097756	A730056A06Rik	C76391	RIKEN cDNA A730056A06 gene	ncRNA
mm_162913.1	chr10	119692425	119692433	+	1	NA	intron (NM_133442, intron 1 of 21)	intron (NM_133442, intron 1 of 21)	69270	NR_045359	75321	Mm.402041	NR_045359	ENSMUSG00000084764	Grip1os2	4930564G21Rik	glutamate receptor interacting protein 1, opposite strand 2	ncRNA
mm_157519.1	chrX	50585488	50585491	-	1	NA	intron (NR_015505, intron 12 of 19)	intron (NR_015505, intron 12 of 19)	48100	NR_131207	102639259	Mm.350898	NR_131207		Gm35612	-	predicted gene, 35612	ncRNA
mm_29746.1	chr3	126972696	126972700	-	1	NA	intron (NM_001327938, intron 27 of 47)	intron (NM_001327938, intron 27 of 47)	25754	NM_178655	109676	Mm.220242	NM_178655	ENSMUSG00000032826	Ank2	100043364|AI835472|AW491075|Ank-2|Gm4392	ankyrin 2, brain	protein-coding
mm_121414.1	chr14	119644035	119644076	+	1	NA	intron (NM_015820, intron 1 of 1)	intron (NM_015820, intron 1 of 1)	-105172	NR_045621	75432	Mm.443277	NR_045621	ENSMUSG00000100274	1700006F04Rik	-	RIKEN cDNA 1700006F04 gene	ncRNA
mm_31649.1	chr4	59633427	59633430	+	1	NA	intron (NM_153158, intron 1 of 2)	B1_Mur2|SINE|Alu	7217	NM_153158	230259	Mm.45688	NM_153158	ENSMUSG00000045071	E130308A19Rik	-	RIKEN cDNA E130308A19 gene	protein-coding
mm_70439.1	chr8	11713275	11713287	+	1	NA	Intergenic	Intergenic	-14824	NM_001113517	54126	Mm.244068	NM_017402	ENSMUSG00000031511	Arhgef7	Cool|PIX|Pak3bp|betaPix|betaPix-b|betaPix-c|cool-1|mKIAA0142|p85Cool1|p85SPR	Rho guanine nucleotide exchange factor (GEF7)	protein-coding
mm_92023.1	chr10	62422419	62422425	-	1	NA	promoter-TSS (NM_145419)	promoter-TSS (NM_145419)	35	NM_145419	216019	Mm.213213	NM_145419	ENSMUSG00000020080	Hkdc1	BC016235	hexokinase domain containing 1	protein-coding
mm_142795.1	chr17	50190288	50190292	-	1	NA	5' UTR (NM_181397, exon 1 of 10)	5' UTR (NM_181397, exon 1 of 10)	207	NM_181397	76438	Mm.41854	NM_181397	ENSMUSG00000039316	Rftn1	2310015N21Rik|AI853526	raftlin lipid raft linker 1	protein-coding
mm_72788.1	chr8	86885143	86885161	+	1	NA	5' UTR (NM_030563, exon 1 of 7)	5' UTR (NM_030563, exon 1 of 7)	106	NM_030563	80750	Mm.25117	NM_030563	ENSMUSG00000031652	N4bp1	AI481586|C81621	NEDD4 binding protein 1	protein-coding
mm_141149.1	chr17	26506249	26506270	-	1	NA	3' UTR (NM_013642, exon 4 of 4)	3' UTR (NM_013642, exon 4 of 4)	2213	NM_013642	19252	Mm.239041	NM_013642	ENSMUSG00000024190	Dusp1	3CH134|MKP1|Ptpn16|U19515|erp|mkp-1	dual specificity phosphatase 1	protein-coding
mm_4843.1	chr1	186967076	186967085	+	1	NA	promoter-TSS (NM_033077)	promoter-TSS (NM_033077)	-336	NM_033077	110957	Mm.108054	NM_033077	ENSMUSG00000039224	D1Pas1	Pl10	DNA segment, Chr 1, Pasteur Institute 1	protein-coding
mm_82369.1	chr9	14614827	14614837	-	1	NA	5' UTR (NM_001081395, exon 1 of 13)	5' UTR (NM_001081395, exon 1 of 13)	168	NM_001081395	75723	Mm.159552	NM_001081395	ENSMUSG00000013076	Amotl1	2310010G08Rik|2310067L22Rik|4932416D09Rik|JEAP|mFLJ00155	angiomotin-like 1	protein-coding
mm_37627.1	chr4	127330800	127330845	-	1	NA	promoter-TSS (NM_001160012)	promoter-TSS (NM_001160012)	14	NM_001160012	14620	Mm.90003	NM_008126	ENSMUSG00000042367	Gjb3	Cnx31|Cx31|D4Wsu144e|Gjb-3	gap junction protein, beta 3	protein-coding
mm_72619.1	chr8	84638520	84638537	+	1	NA	intron (NM_001252059, intron 44 of 45)	intron (NM_001252059, intron 44 of 45)	24324	NM_010499	15936	Mm.399	NM_010499	ENSMUSG00000053560	Ier2	AI317238|Ch1|Pip92	immediate early response 2	protein-coding
mm_17228.1	chr2	25571302	25571321	-	1	NA	promoter-TSS (NM_001081199)	promoter-TSS (NM_001081199)	5	NM_001081199	381352	Mm.289046	NM_001081199	ENSMUSG00000026941	Mamdc4	Gm995	MAM domain containing 4	protein-coding
mm_78681.1	chr9	40784993	40785021	+	1	NA	TTS (NM_133733)	TTS (NM_133733)	-16266	NM_031165	15481	Mm.290774	NM_031165	ENSMUSG00000015656	Hspa8	2410008N15Rik|Hsc70|Hsc71|Hsc73|Hsp73|Hspa10	heat shock protein 8	protein-coding
mm_111908.1	chr12	108792642	108792654	-	1	NA	promoter-TSS (NM_009537)	promoter-TSS (NM_009537)	-663	NM_009537	22632	Mm.3868	NM_009537	ENSMUSG00000021264	Yy1	AW488674|NF-E1	YY1 transcription factor	protein-coding
mm_114036.1	chr13	53001862	53001870	+	1	NA	Intergenic	Intergenic	-20827	NM_017373	18030	Mm.136604	NM_017373	ENSMUSG00000056749	Nfil3	AV225605|E4BP4	nuclear factor, interleukin 3, regulated	protein-coding
mm_120679.1	chr14	70577840	70577891	+	1	NA	promoter-TSS (NM_153136)	promoter-TSS (NM_153136)	18	NM_153136	213484	Mm.34191	NM_153136	ENSMUSG00000045211	Nudt18	BC036718	nudix (nucleoside diphosphate linked moiety X)-type motif 18	protein-coding
mm_60314.1	chr7	44198180	44198183	+	1	NA	promoter-TSS (NM_008693)	promoter-TSS (NM_008693)	-10	NM_008693	18050	Mm.439740	NM_008693	ENSMUSG00000066515	Klk1b3	Ngfg|gamma-NGF|mGk-3	kallikrein 1-related peptidase b3	protein-coding
mm_6855.1	chr1	84262205	84262211	-	1	NA	intron (NM_001003948, intron 1 of 2)	intron (NM_001003948, intron 1 of 2)	22437	NM_001003948	98496	Mm.187470	NM_001003948	ENSMUSG00000045658	Pid1	5033414K04Rik|NYGGF4	phosphotyrosine interaction domain containing 1	protein-coding
mm_60183.1	chr7	43177576	43177609	+	1	NA	promoter-TSS (NM_001034893)	promoter-TSS (NM_001034893)	4	NM_001034893	668620	Mm.388871	NM_001034893	ENSMUSG00000064194	Zfp936	EG435970|EG668620|Gm9272|I1C0022H11Rik	zinc finger protein 936	protein-coding
mm_94800.1	chr11	22990392	22990405	+	1	NA	promoter-TSS (NM_009837)	promoter-TSS (NM_009837)	-195	NM_009837	12464	Mm.296985	NM_009837	ENSMUSG00000007739	Cct4	2610204B21Rik|A45|C78323|Cctd	chaperonin containing Tcp1, subunit 4 (delta)	protein-coding
mm_14246.1	chr2	128063101	128063109	+	1	NA	intron (NM_028765, intron 14 of 17)	intron (NM_028765, intron 14 of 17)	-62933	NM_207681	12125	Mm.141083	NM_009754	ENSMUSG00000027381	Bcl2l11	1500006F24Rik|Bim|Bod|bcl2-L-11	BCL2-like 11 (apoptosis facilitator)	protein-coding
mm_74633.1	chr8	13198143	13198145	-	1	NA	intron (NM_025768, intron 2 of 7)	B1_Mur1|SINE|Alu	2480	NM_025768	66790	Mm.34901	NM_025768	ENSMUSG00000038515	Grtp1	5430401C05Rik|C81211|Tbc1d6	GH regulated TBC protein 1	protein-coding
mm_63906.1	chr7	139213381	139213411	+	1	NA	promoter-TSS (NM_001162540)	promoter-TSS (NM_001162540)	-89	NM_001162540	57740	Mm.65336	NM_021302	ENSMUSG00000015981	Stk32c	PKE|Pkek|YANK3	serine/threonine kinase 32C	protein-coding
mm_127805.1	chr15	4642970	4642972	-	1	NA	Intergenic	Intergenic	-84239	NM_016704	12274	Mm.20247	NM_016704	ENSMUSG00000022181	C6	AW111623	complement component 6	protein-coding
mm_2284.1	chr1	91338652	91338672	+	1	NA	intron (NM_001033292, intron 5 of 8)	intron (NM_001033292, intron 5 of 8)	-12411	NM_027551	70788	Mm.68617	NM_027551	ENSMUSG00000026308	Klhl30	4631423F02Rik	kelch-like 30	protein-coding
mm_119140.1	chr14	31209462	31209486	+	1	NA	intron (NM_009393, intron 1 of 5)	intron (NM_009393, intron 1 of 5)	1162	NM_009393	21924	Mm.439921	NM_009393	ENSMUSG00000091898	Tnnc1	AI874626|TnC|cTnC|cTnI|tncc	troponin C, cardiac/slow skeletal	protein-coding
mm_8331.1	chr1	150015288	150015304	-	1	NA	Intergenic	Intergenic	36906	NR_106112	102465760		NR_106112	ENSMUSG00000098906	Mir7652	Gm27932|mmu-mir-7652	microRNA 7652	ncRNA
mm_112068.1	chr12	111981137	111981151	-	1	NA	promoter-TSS (NM_001127685)	promoter-TSS (NM_001127685)	-393	NM_001127685	217874	Mm.134213	NM_001127685	ENSMUSG00000091402	Rd3l	A930011N13	retinal degeneration 3-like	protein-coding
mm_98458.1	chr11	94947662	94947673	+	1	NA	exon (NM_007742, exon 39 of 51)	exon (NM_007742, exon 39 of 51)	11443	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_64730.1	chr7	4709981	4709996	-	1	NA	intron (NM_177887, intron 4 of 4)	B3|SINE|B2	15094	NM_001142792	330460	Mm.361851	NM_177887	ENSMUSG00000046456	Tmem150b	A630041N19|Tmem224	transmembrane protein 150B	protein-coding
mm_160605.1	chr9	78294017	78294017	+	1	NA	intron (NM_001122660, intron 1 of 6)	MTB|LTR|ERVL-MaLR	4089	NM_001122660	100042314	Mm.482247	NM_001122660	ENSMUSG00000074179	Gm10639	ENSMUSG00000074179	predicted gene 10639	protein-coding
mm_64472.1	chr7	143005771	143005784	+	1	NA	5' UTR (NM_001128082, exon 1 of 6)	5' UTR (NM_001128082, exon 1 of 6)	118	NM_001128081	27027	Mm.28172	NM_020286	ENSMUSG00000000244	Tspan32	AW208513|Art-1|BB235973|D7Wsu37e|Phemx|Tssc6	tetraspanin 32	protein-coding
mm_37282.1	chr4	118968619	118968632	-	1	NA	3' UTR (NM_133892, exon 7 of 7)	3' UTR (NM_133892, exon 7 of 7)	6658	NM_133892	100470	Mm.26698	NM_133892	ENSMUSG00000024903	Lao1	AW990848	L-amino acid oxidase 1	protein-coding
mm_35675.1	chr4	43653543	43653557	-	1	NA	promoter-TSS (NM_001290462)	promoter-TSS (NM_001290462)	44	NM_001290462	433700	Mm.331569	NM_001007463	ENSMUSG00000066196	Spag8	MH-SPAG8|SMP-1	sperm associated antigen 8	protein-coding
mm_164455.1	chr16	55282924	55282958	-	1	NA	5' UTR (NM_178720, exon 2 of 12)	5' UTR (NM_178720, exon 2 of 12)	296	NM_178720	239852	Mm.245045	NM_178720	ENSMUSG00000064310	Zpld1	9430016A21Rik	zona pellucida like domain containing 1	protein-coding
mm_25327.1	chr3	106568056	106568073	+	1	NA	intron (NM_001025582, intron 5 of 6)	Lx7|LINE|L1	-20262	NM_133869	99712	Mm.429443	NM_133869	ENSMUSG00000040774	Cept1	9930118K05Rik|mCEPT1	choline/ethanolaminephosphotransferase 1	protein-coding
mm_108273.1	chr12	78861694	78861749	+	1	NA	promoter-TSS (NM_026114)	promoter-TSS (NM_026114)	-83	NM_023721	73834	Mm.311549	NM_023721	ENSMUSG00000021114	Atp6v1d	1110004P10Rik|Atp6m|VATD|Vma8	ATPase, H+ transporting, lysosomal V1 subunit D	protein-coding
mm_56861.1	chr6	118197751	118197761	-	1	NA	promoter-TSS (NM_009050)	promoter-TSS (NM_009050)	-12	NM_001080780	19713	Mm.57199	NM_009050	ENSMUSG00000030110	Ret	PTC|RET51|RET9|c-Ret	ret proto-oncogene	protein-coding
mm_19836.1	chr2	112368022	112368036	-	1	NA	promoter-TSS (NM_026519)	promoter-TSS (NM_026519)	-2	NM_026519	68032	Mm.220942	NM_026519	ENSMUSG00000027131	Emc4	2610318K02Rik|Tmem85	ER membrane protein complex subunit 4	protein-coding
mm_16467.1	chr2	180710123	180710201	+	1	NA	promoter-TSS (NM_001291432)	promoter-TSS (NM_001291432)	-64	NM_001289652	76425	Mm.41464	NM_029607	ENSMUSG00000027573	Gid8	2310003C23Rik|4833420G11Rik|AI451474|Twa1	GID complex subunit 8	protein-coding
mm_83099.1	chr9	40321330	40321341	-	1	NA	intron (NM_172768, intron 4 of 19)	intron (NM_172768, intron 4 of 19)	-12137	NR_040728	73558	Mm.398307	NR_040728		1700110K17Rik	-	RIKEN cDNA 1700110K17 gene	ncRNA
mm_60927.1	chr7	46847201	46847207	+	1	NA	5' UTR (NM_001136069, exon 1 of 8)	5' UTR (NM_001136069, exon 1 of 8)	122	NM_001136069	16828	Mm.29324	NM_010699	ENSMUSG00000063229	Ldha	Ldh1|Ldhm|l7R2	lactate dehydrogenase A	protein-coding
mm_86335.1	chr9	123113159	123113204	-	1	NA	promoter-TSS (NM_026917)	promoter-TSS (NM_026917)	24	NM_026917	69035	Mm.28300	NM_026917	ENSMUSG00000025786	Zdhhc3	1110020O22Rik|1810006O10Rik|2210017C02Rik|DHHC-3|GODZ|Gramp1|Zfp373	zinc finger, DHHC domain containing 3	protein-coding
mm_68626.1	chr7	118127177	118127229	-	1	NA	exon (NM_019419, exon 2 of 6)	exon (NM_019419, exon 2 of 6)	2422	NM_019419	54208	Mm.29924	NM_019419	ENSMUSG00000030654	Arl6ip1	AIP-6|AL022945|ARMER|AU042858|Aip-1|Arl6ip|C85138|mKIAA0069	ADP-ribosylation factor-like 6 interacting protein 1	protein-coding
mm_121993.1	chr14	26515943	26515961	-	1	NA	intron (NM_001310445, intron 1 of 22)	intron (NM_001310445, intron 1 of 22)	18672	NM_032008	83997	Mm.36769	NM_032008	ENSMUSG00000021870	Slmap	D330001L02Rik|Miranda|Slap|mKIAA1601	sarcolemma associated protein	protein-coding
mm_149491.1	chr19	11818544	11818576	+	1	NA	intron (NM_001025307, intron 1 of 10)	CpG	843	NM_001286543	20908	Mm.272264	NM_011502	ENSMUSG00000041488	Stx3	Syn-3	syntaxin 3	protein-coding
mm_138040.1	chr17	33920399	33920414	+	1	NA	exon (NM_009318, exon 3 of 8)	exon (NM_009318, exon 3 of 8)	928	NM_009318	21356	Mm.154457	NM_009318	ENSMUSG00000024308	Tapbp	D17Wsu91e|TPN	TAP binding protein	protein-coding
mm_86223.1	chr9	120135033	120135042	-	1	NA	Intergenic	B3A|SINE|B2	4603	NR_002902	104433	Mm.453530	NR_002902	ENSMUSG00000064925	Snora62	E2|MBI-13|MBI-136|Rnu108	small nucleolar RNA, H/ACA box 62	snoRNA
mm_70890.1	chr8	25564414	25564437	+	1	NA	exon (NM_010206, exon 8 of 18)	exon (NM_010206, exon 8 of 18)	-8342	NR_110510	102633315	Mm.437828	NR_110510	ENSMUSG00000086134	Gm16159	OTTMUSG00000031030	predicted gene 16159	ncRNA
mm_7861.1	chr1	132542883	132542906	-	1	NA	promoter-TSS (NM_177129)	promoter-TSS (NM_177129)	46	NM_177129	21367	Mm.260861	NM_011531	ENSMUSG00000053024	Cntn2	D130012K04Rik|TAG-1|Tax	contactin 2	protein-coding
mm_82784.1	chr9	28996066	28996096	-	1	NA	3' UTR (NM_172290, exon 8 of 8)	3' UTR (NM_172290, exon 8 of 8)	967048	NM_172290	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding
mm_124970.1	chr15	18818954	18818962	+	1	NA	promoter-TSS (NM_001316758)	promoter-TSS (NM_001316758)	11	NM_001316758	320873	Mm.117794	NM_009865	ENSMUSG00000022321	Cdh10	A830016G23Rik|C030003B10Rik|C030011H18Rik	cadherin 10	protein-coding
mm_35051.1	chr4	6355331	6355337	-	1	NA	Intergenic	Intergenic	-10346	NM_016807	53378	Mm.247473	NM_016807	ENSMUSG00000028249	Sdcbp	MDA-9|Sycl|syntenin-1	syndecan binding protein	protein-coding
mm_44362.1	chr5	17806171	17806206	-	1	NA	intron (NM_007643, intron 8 of 14)	ORR1C1-int|LTR|ERVL-MaLR	29708	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_50059.1	chr6	41178839	41178860	+	1	NA	Intergenic	Intergenic	-123423	NM_011646	22074	Mm.383263	NM_011646	ENSMUSG00000054106	Try4	0910001B19Rik|Td	trypsin 4	protein-coding
mm_92481.1	chr10	78295398	78295418	-	1	NA	intron (NM_053014, intron 2 of 9)	intron (NM_053014, intron 2 of 9)	44799	NR_106119	102465765		NR_106119	ENSMUSG00000098885	Mir7659	Gm27433|mmu-mir-7659	microRNA 7659	ncRNA
mm_141246.1	chr17	27513379	27513383	-	1	NA	Intergenic	CpG	-9848	NM_001291045	268934	Mm.358940	NM_001013385	ENSMUSG00000063239	Grm4	Gprc1d|mGluR4	glutamate receptor, metabotropic 4	protein-coding
mm_113905.1	chr13	49298960	49298961	+	1	NA	intron (NM_015759, intron 1 of 17)	intron (NM_015759, intron 1 of 17)	10248	NM_015759	30938	Mm.291089	NM_015759	ENSMUSG00000037946	Fgd3	5830461L01Rik|ZFYVE5	FYVE, RhoGEF and PH domain containing 3	protein-coding
mm_108077.1	chr12	73945788	73945807	+	1	NA	3' UTR (NM_010431, exon 15 of 15)	3' UTR (NM_010431, exon 15 of 15)	-18733	NM_178392	75627	Mm.25937	NM_178392	ENSMUSG00000021113	Snapc1	2700033G17Rik|AU015787	small nuclear RNA activating complex, polypeptide 1	protein-coding
mm_70245.1	chr8	3360843	3360856	+	1	NA	intron (NM_001033378, intron 1 of 10)	intron (NM_001033378, intron 1 of 10)	7434	NM_001033378	319493	Mm.234565	NM_001033378	ENSMUSG00000074497	A430078G23Rik	-	RIKEN cDNA A430078G23 gene	protein-coding
mm_167441.1	chr8	120116091	120116103	-	1	NA	intron (NM_172286, intron 1 of 12)	intron (NM_172286, intron 1 of 12)	1945	NM_001163761	234797	Mm.101958	NM_172286	ENSMUSG00000031824	6430548M08Rik	AW049007|Kiaa0513|mKIAA0513	RIKEN cDNA 6430548M08 gene	protein-coding
mm_137783.1	chr17	29494628	29494639	+	1	NA	exon (NM_008842, exon 6 of 6)	exon (NM_008842, exon 6 of 6)	3588	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_94819.1	chr11	23255981	23256000	+	1	NA	promoter-TSS (NM_134014)	promoter-TSS (NM_134014)	-51	NM_001035226	103573	Mm.217547	NM_134014	ENSMUSG00000020290	Xpo1	AA420417|Crm1|Exp1	exportin 1	protein-coding
mm_134907.1	chr16	30260096	30260111	-	1	NA	exon (NM_027904, exon 2 of 2)	exon (NM_027904, exon 2 of 2)	7429	NM_027904	71756	Mm.290614	NM_027904	ENSMUSG00000023176	Cpn2	1300018K11Rik	carboxypeptidase N, polypeptide 2	protein-coding
mm_140819.1	chr17	23193217	23193258	-	1	NA	promoter-TSS (NM_009555)	promoter-TSS (NM_009555)	-9	NM_009555	22700	Mm.437934	NM_009555	ENSMUSG00000002617	Zfp40	CTfin12|NTfin12|Zfp-40	zinc finger protein 40	protein-coding
mm_149465.1	chr19	11534142	11534149	+	1	NA	Intergenic	RMER19B2|LTR|ERVK	-2704	NM_025658	66607	Mm.441056	NM_025658	ENSMUSG00000024678	Ms4a4d	2210417J23Rik	membrane-spanning 4-domains, subfamily A, member 4D	protein-coding
mm_109054.1	chr12	104340484	104340488	+	1	NA	intron (NM_011458, intron 1 of 4)	intron (NM_011458, intron 1 of 4)	2000	NM_011458	20714	Mm.291569	NM_011458	ENSMUSG00000058207	Serpina3k	1300001I07Rik|D12Rp54|MMCM2|MMSpi2|RP54|Spi-2|Spi2|contrapsin	serine (or cysteine) peptidase inhibitor, clade A, member 3K	protein-coding
mm_94953.1	chr11	30137260	30137296	+	1	NA	exon (NM_009260, exon 15 of 31)	exon (NM_009260, exon 15 of 31)	60979	NM_009260	20742	Mm.123110	NM_009260	ENSMUSG00000020315	Sptbn1	9930031C03Rik|AL033301|SPTB2|Spnb-2|Spnb2|elf1|elf3|mKIAA4049	spectrin beta, non-erythrocytic 1	protein-coding
mm_36196.1	chr4	62329528	62329560	-	1	NA	intron (NM_001045528, intron 12 of 27)	intron (NM_001045528, intron 12 of 27)	31004	NM_001045528	338355	Mm.357792	NM_001045528	ENSMUSG00000066151	Fkbp15	BB131447|C430014M02Rik|FKBO133|FKBP-133|FKBP-15|FKBP133|mKIAA0674	FK506 binding protein 15	protein-coding
mm_95467.1	chr11	50602100	50602106	+	1	NA	promoter-TSS (NM_175643)	promoter-TSS (NM_175643)	18	NM_175643	216725	Mm.110597	NM_175643	ENSMUSG00000036545	Adamts2	ADAM-TS 2|ADAM-TS2|ADAMTS-2|PC I-NP|PCINP|pNPI	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 2	protein-coding
mm_128001.1	chr15	12813707	12813719	-	1	NA	intron (NM_029998, intron 7 of 8)	B1_Mur1|SINE|Alu	10944	NM_029998	77877	Mm.207311	NM_029998	ENSMUSG00000022195	6030458C11Rik	-	RIKEN cDNA 6030458C11 gene	protein-coding
mm_61074.1	chr7	51621709	51621721	+	1	NA	promoter-TSS (NM_080853)	promoter-TSS (NM_080853)	-115	NM_080853	140919	Mm.256618	NM_080853	ENSMUSG00000030500	Slc17a6	2900073D12Rik|DNPI|VGLUT2	solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 6	protein-coding
mm_58385.1	chr6	149309634	149309650	-	1	NA	5' UTR (NM_001289662, exon 1 of 5)	5' UTR (NM_001289662, exon 1 of 5)	228	NM_001289662	67246	Mm.333515	NM_026054	ENSMUSG00000032712	2810474O19Rik	6720435I21Rik|AA536804|AU020969|GET|Kiaa1551	RIKEN cDNA 2810474O19 gene	protein-coding
mm_86334.1	chr9	123113132	123113156	-	1	NA	promoter-TSS (NM_026917)	promoter-TSS (NM_026917)	61	NM_026917	69035	Mm.28300	NM_026917	ENSMUSG00000025786	Zdhhc3	1110020O22Rik|1810006O10Rik|2210017C02Rik|DHHC-3|GODZ|Gramp1|Zfp373	zinc finger, DHHC domain containing 3	protein-coding
mm_57308.1	chr6	124718838	124718857	-	1	NA	promoter-TSS (NR_029554)	promoter-TSS (NR_029554)	-457	NR_029792	723944		NR_029792	ENSMUSG00000065462	Mir200c	Mirn200c|mir-200c	microRNA 200c	ncRNA
mm_935.1	chr1	55606066	55606069	+	1	NA	intron (NM_001114663, intron 1 of 5)	intron (NM_001114663, intron 1 of 5)	200121	NM_001114663	227120	Mm.194183	NM_001114663	ENSMUSG00000038349	Plcl1	C230017K02Rik|PLC-L|PLC-L1|PLCE|PLCL|PLDL1|PRIP|PRIP-1	phospholipase C-like 1	protein-coding
mm_140731.1	chr17	15527318	15527329	-	1	NA	promoter-TSS (NM_008799)	promoter-TSS (NM_008799)	-22	NM_008799	18567	Mm.323	NM_008799	ENSMUSG00000014771	Pdcd2	AI528543|Pcd2|RP-8	programmed cell death 2	protein-coding
mm_74280.1	chr8	125386293	125386310	+	1	NA	Intergenic	Intergenic	106409	NM_001081337	244668	Mm.271668	NM_001081337	ENSMUSG00000001995	Sipa1l2	BC058408|mKIAA1389	signal-induced proliferation-associated 1 like 2	protein-coding
mm_105431.1	chr11	103953998	103954014	-	1	NA	promoter-TSS (NM_008740)	promoter-TSS (NM_008740)	50	NM_008740	18195	Mm.260117	NM_008740	ENSMUSG00000034187	Nsf	AI316878|AU020090|AU067812|SKD2	N-ethylmaleimide sensitive fusion protein	protein-coding
mm_141518.1	chr17	31681718	31681724	-	1	NA	TTS (NM_001278570)	TTS (NM_001278570)	3790	NM_001278570	12954	Mm.1228	NM_013501	ENSMUSG00000024041	Cryaa	Acry-1|Crya-1|Crya1|DAcry-1|lop18	crystallin, alpha A	protein-coding
mm_154133.1	chr19	57314897	57314930	-	1	NA	Intergenic	CpG	40953	NR_045319	78120	Mm.445892	NR_045319		4930449E18Rik	-	RIKEN cDNA 4930449E18 gene	ncRNA
mm_62167.1	chr7	97254258	97254269	+	1	NA	intron (NM_001162477, intron 2 of 9)	ID4|SINE|ID	71701	NM_001177412	244144	Mm.297541	NM_001177412	ENSMUSG00000035713	Usp35	Gm1088|Gm493	ubiquitin specific peptidase 35	protein-coding
mm_95208.1	chr11	43596079	43596089	+	1	NA	TTS (NM_008375)	TTS (NM_008375)	5478	NM_008375	16204	Mm.142716	NM_008375	ENSMUSG00000020405	Fabp6	GT|I-15P|I-BABP|ILBP|ILBP3|Illbp	fatty acid binding protein 6, ileal (gastrotropin)	protein-coding
mm_82198.1	chr9	124041373	124041382	+	1	NA	Intergenic	Intergenic	19406	NM_009914	12771	Mm.57050	NM_009914	ENSMUSG00000035448	Ccr3	CC-CKR3|CKR3|Cmkbr1l2|Cmkbr3	chemokine (C-C motif) receptor 3	protein-coding
mm_156304.1	chrX	136837978	136837980	+	1	NA	3' UTR (NM_011123, exon 7 of 7)	3' UTR (NM_011123, exon 7 of 7)	15233	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_58586.1	chr7	4943881	4943897	+	1	NA	exon (NM_173008, exon 14 of 14)	exon (NM_173008, exon 14 of 14)	18045	NM_173008	269855	Mm.44190	NM_173008	ENSMUSG00000035279	Ssc5d	A430110N23Rik|S5D-SRCRB	scavenger receptor cysteine rich family, 5 domains	protein-coding
mm_121794.1	chr14	20083064	20083074	-	1	NA	exon (NM_026209, exon 1 of 2)	exon (NM_026209, exon 1 of 2)	103	NM_026209	67509	Mm.292423	NM_026209	ENSMUSG00000045107	Saysd1	1810063B07Rik|4930488P03Rik	SAYSVFN motif domain containing 1	protein-coding
mm_50642.1	chr6	51432679	51432784	+	1	NA	promoter-TSS (NM_010903)	promoter-TSS (NM_010903)	61	NM_010903	18025	Mm.42138	NM_010903	ENSMUSG00000029832	Nfe2l3	Nrf3	nuclear factor, erythroid derived 2, like 3	protein-coding
mm_65482.1	chr7	25615875	25615886	-	1	NA	promoter-TSS (NM_001039243)	promoter-TSS (NM_001039243)	12	NM_001039243	632778	Mm.423112	NM_001039243	ENSMUSG00000074261	Erich4	EG632778|Gm7092|Kseg1	glutamate rich 4	protein-coding
mm_162716.1	chr10	34019391	34019401	-	1	NA	exon (NM_025614, exon 1 of 7)	exon (NM_025614, exon 1 of 7)	220	NM_025614	66521	Mm.28528	NM_025614	ENSMUSG00000019782	Rwdd1	0710001K08Rik|2610002D06Rik|2700069A07Rik|IH1	RWD domain containing 1	protein-coding
mm_15534.1	chr2	158383074	158383082	+	1	NA	3' UTR (NM_175692, exon 5 of 5)	3' UTR (NM_175692, exon 5 of 5)	7440	NM_175692	319317	Mm.294494	NM_175692	ENSMUSG00000044349	Snhg11	A930034L06Rik|AI854265|AL022637|AW319638|E130013N09Rik	small nucleolar RNA host gene 11	protein-coding
mm_112184.1	chr12	113422387	113422414	-	1	NA	Intergenic	Intergenic	-67165	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_56970.1	chr6	120188439	120188463	-	1	NA	intron (NM_016718, intron 1 of 3)	intron (NM_016718, intron 1 of 3)	-5372	NM_001347432	29862	Mm.103668	NM_016718	ENSMUSG00000041377	Ninj2	-	ninjurin 2	protein-coding
mm_30952.1	chr4	33247927	33247999	+	1	NA	exon (NM_001033225, exon 1 of 2)	exon (NM_001033225, exon 1 of 2)	824	NM_001033225	108767	Mm.27769	NM_001033225	ENSMUSG00000040128	Pnrc1	5730463C12Rik|B4-2|PRR2|Prol2	proline-rich nuclear receptor coactivator 1	protein-coding
mm_43030.1	chr5	123930676	123930718	+	1	NA	promoter-TSS (NM_001134767)	promoter-TSS (NM_001134767)	8	NM_001134767	208908	Mm.243679	NM_001134767	ENSMUSG00000061882	Ccdc62	AI661708|Gm150	coiled-coil domain containing 62	protein-coding
mm_78232.1	chr9	21616129	21616147	+	1	NA	promoter-TSS (NM_001174078)	promoter-TSS (NM_001174078)	-31	NM_011417	20586	Mm.286593	NM_011417	ENSMUSG00000032187	Smarca4	Brg1|HP1-BP72|SNF2beta|SW1/SNF|b2b508.1Clo|b2b692Clo	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	protein-coding
mm_155396.1	chrX	72957357	72957369	+	1	NA	exon (NM_010941, exon 8 of 8)	exon (NM_010941, exon 8 of 8)	-29976	NM_009549	22673	Mm.1161	NM_009549	ENSMUSG00000031351	Zfp185	P1|Znf185	zinc finger protein 185	protein-coding
mm_93648.1	chr10	117361178	117361188	-	1	NA	exon (NM_001013391, exon 6 of 10)	exon (NM_001013391, exon 6 of 10)	15790	NM_001013391	432508	Mm.478881	NM_001013391	ENSMUSG00000055531	Cpsf6	4733401N12Rik|AI256641|CFIM|CFIM68|HPBRII-4|HPBRII-7	cleavage and polyadenylation specific factor 6	protein-coding
mm_21892.1	chr2	166155549	166155559	-	1	NA	promoter-TSS (NM_001252578)	promoter-TSS (NM_001252578)	129	NM_001252579	72043	Mm.1011	NM_028072	ENSMUSG00000006800	Sulf2	2010004N24Rik|AU020235|MSulf-2|mKIAA1247	sulfatase 2	protein-coding
mm_19766.1	chr2	105399391	105399421	-	1	NA	promoter-TSS (NM_009037)	promoter-TSS (NM_009037)	-87	NM_009037	19672	Mm.4876	NM_009037	ENSMUSG00000005973	Rcn1	Rcn	reticulocalbin 1	protein-coding
mm_130150.1	chr15	91050226	91050237	-	1	NA	promoter-TSS (NM_001109041)	promoter-TSS (NM_001109041)	-280	NM_001109040	16564	Mm.41379	NM_016705	ENSMUSG00000022629	Kif21a	-	kinesin family member 21A	protein-coding
mm_115743.1	chr13	17893172	17893189	-	1	NA	exon (NM_019491, exon 3 of 5)	exon (NM_019491, exon 3 of 5)	51037	NM_019491	56044	Mm.27348	NM_019491	ENSMUSG00000008859	Rala	3010001O15Rik|AW322615|Ral|Rasl1	v-ral simian leukemia viral oncogene A (ras related)	protein-coding
mm_38545.1	chr4	141599943	141599953	-	1	NA	promoter-TSS (NM_001163256)	promoter-TSS (NM_001163256)	-24	NM_001163256	74202	Mm.490327	NM_133754	ENSMUSG00000006219	Fblim1	2410043F08Rik|Cal|Fblp1|Gt10|migfilin|migfilin(s)	filamin binding LIM protein 1	protein-coding
mm_65799.1	chr7	28948807	28948818	-	1	NA	intron (NM_021895, intron 1 of 20)	intron (NM_021895, intron 1 of 20)	13468	NM_021895	60595	Mm.81144	NM_021895	ENSMUSG00000054808	Actn4	C77391	actinin alpha 4	protein-coding
mm_64729.1	chr7	4684964	4684997	-	1	NA	promoter-TSS (NM_024172)	promoter-TSS (NM_024172)	-17	NM_024172	66245	Mm.6803	NM_024172	ENSMUSG00000063802	Hspbp1	1500019G21Rik	HSPA (heat shock 70kDa) binding protein, cytoplasmic cochaperone 1	protein-coding
mm_92795.1	chr10	81350268	81350290	-	1	NA	5' UTR (NM_010440, exon 1 of 9)	5' UTR (NM_010440, exon 1 of 9)	147	NM_001163165	15353	Mm.38474	NM_010440	ENSMUSG00000020232	Hmg20b	AW610687|BRAF35|Hmgx2|Hmgxb2|Smarce1r	high mobility group 20B	protein-coding
mm_69202.1	chr7	127387160	127387184	-	1	NA	promoter-TSS (NM_030226)	promoter-TSS (NM_030226)	-6	NM_030226	78921	Mm.200950	NM_030226	ENSMUSG00000030823	9130019O22Rik	-	RIKEN cDNA 9130019O22 gene	protein-coding
mm_124176.1	chr14	93841656	93841673	-	1	NA	intron (NM_001346722, intron 2 of 4)	B1_Mus1|SINE|Alu	47224	NM_001271800	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding
mm_9313.1	chr1	171645882	171645894	-	1	NA	intron (NM_001347184, intron 1 of 5)	RSINE1|SINE|B4	3111	NM_001347184	75345	Mm.164642	NM_144539	ENSMUSG00000038179	Slamf7	19A|19A24|4930560D03Rik|CRACC|CS1	SLAM family member 7	protein-coding
mm_103213.1	chr11	70654601	70654616	-	1	NA	promoter-TSS (NM_011072)	promoter-TSS (NM_011072)	42	NM_011072	18643	Mm.2647	NM_011072	ENSMUSG00000018293	Pfn1	Pfn	profilin 1	protein-coding
mm_121808.1	chr14	20348041	20348101	-	1	NA	promoter-TSS (NM_172379)	promoter-TSS (NM_172379)	50	NM_027475	70601	Mm.35105	NM_027475	ENSMUSG00000021810	Ecd	5730461K03Rik|Hsgt1	ecdysoneless homolog (Drosophila)	protein-coding
mm_94947.1	chr11	29719131	29719157	+	1	NA	intron (NM_024226, intron 1 of 6)	intron (NM_024226, intron 1 of 6)	581	NM_024226	68585	Mm.192580	NM_024226	ENSMUSG00000020458	Rtn4	1110020G17Rik|AA407876|AA409940|AA960376|ASY|C130026I10Rik|NOGO|NSP-CL|NgA|Nogo-A|Nogo-B|Nogo-C|mKIAA0886|mKIAA4153	reticulon 4	protein-coding
mm_146594.1	chr18	9437456	9437477	-	1	NA	intron (NM_026484, intron 1 of 9)	intron (NM_026484, intron 1 of 9)	12684	NM_026484	67974	Mm.86523	NM_026484	ENSMUSG00000024286	Ccny	1700025H17Rik|3110050L10Rik|4631402G10Rik|5730405I09Rik	cyclin Y	protein-coding
mm_142774.1	chr17	49821793	49821838	-	1	NA	intron (NM_177052, intron 13 of 22)	RMER19B|LTR|ERVK	206643	NM_177052	319991	Mm.441340	NM_177052	ENSMUSG00000023999	Kif6	D130004B10Rik|D130084M03Rik	kinesin family member 6	protein-coding
mm_118982.1	chr14	28387815	28387827	+	1	NA	intron (NM_001347497, intron 19 of 19)	L1Md_F2|LINE|L1	-117652	NM_009524	22418	Mm.287544	NM_009524	ENSMUSG00000021994	Wnt5a	8030457G12Rik|Wnt-5a	wingless-type MMTV integration site family, member 5A	protein-coding
mm_144643.1	chr18	33181970	33181979	+	1	NA	intron (NM_009793, intron 9 of 10)	intron (NM_009793, intron 9 of 10)	31888	NM_001347624	170459	Mm.127058	NM_133774	ENSMUSG00000024378	Stard4	4632419C16Rik|9030213J02Rik	StAR-related lipid transfer (START) domain containing 4	protein-coding
mm_112230.1	chr12	113482250	113482264	-	1	NA	Intergenic	Intergenic	-7308	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_33160.1	chr4	125948132	125948135	+	1	NA	Intergenic	Intergenic	-25823	NR_015560	72395	Mm.112888	NR_015560	ENSMUSG00000085562	2610028E06Rik	BB043107	RIKEN cDNA 2610028E06 gene	ncRNA
mm_117057.1	chr13	58402450	58402472	-	1	NA	promoter-TSS (NM_025279)	promoter-TSS (NM_025279)	51	NM_001301345	15387	Mm.142872	NM_025279	ENSMUSG00000021546	Hnrnpk	Hnrpk|KBBP|NOVA	heterogeneous nuclear ribonucleoprotein K	protein-coding
mm_104213.1	chr11	88342556	88342572	-	1	NA	3' UTR (NM_054043, exon 14 of 14)	3' UTR (NM_054043, exon 14 of 14)	-10209	NR_039545	100628571		NR_039545	ENSMUSG00000092985	Mir378b	mir-378b|mmu-mir-378b	microRNA 378b	ncRNA
mm_119979.1	chr14	55575535	55575568	+	1	NA	promoter-TSS (NM_026808)	promoter-TSS (NM_026808)	-123	NM_026808	68680	Mm.36758	NM_026808	ENSMUSG00000022215	Fitm1	1110028A07Rik|AV010547|Cg10671|Fit1	fat storage-inducing transmembrane protein 1	protein-coding
mm_78704.1	chr9	41376393	41376406	+	1	NA	promoter-TSS (NR_040725)	promoter-TSS (NR_040725)	-127	NR_040725	73144	Mm.38166	NM_001033153	ENSMUSG00000074415	3110039I08Rik	2610203C20Rik|AI848448|D230004N17Rik|D3Mgi9|Mir100hg	RIKEN cDNA 3110039I08 gene	ncRNA
mm_150364.1	chr19	34649336	34649400	+	1	NA	3' UTR (NM_008331, exon 2 of 2)	3' UTR (NM_008331, exon 2 of 2)	8479	NM_008331	15957	Mm.439751	NM_008331	ENSMUSG00000034459	Ifit1	ISG56|Ifi56|P56	interferon-induced protein with tetratricopeptide repeats 1	protein-coding
mm_137283.1	chr17	24728364	24728381	+	1	NA	exon (NM_001163945, exon 2 of 10)	exon (NM_001163945, exon 2 of 10)	543	NM_001163945	66211	Mm.46198	NM_025425	ENSMUSG00000002500	Rpl3l	1110057H16Rik	ribosomal protein L3-like	protein-coding
mm_6660.1	chr1	80213932	80213949	-	1	NA	promoter-TSS (NM_173425)	promoter-TSS (NM_173425)	4	NM_173425	241128	Mm.145511	NM_173425	ENSMUSG00000043230	Fam124b	A830043J08Rik	family with sequence similarity 124, member B	protein-coding
mm_170792.1	chr2	175175841	175175854	-	1	NA	Intergenic	Intergenic	31070	NM_001164689	626832	Mm.441314	NM_001164689	ENSMUSG00000078887	Gm6710	1600017I02Rik|2310011F05Rik|2900089K14Rik|3100002L24Rik|WF-4	predicted gene 6710	protein-coding
mm_13523.1	chr2	110017807	110017873	+	1	NA	promoter-TSS (NM_026613)	promoter-TSS (NM_026613)	23	NM_026613	68201	Mm.181767	NM_026613	ENSMUSG00000027160	Ccdc34	2810027O19Rik|4930522P10Rik|AI596202	coiled-coil domain containing 34	protein-coding
mm_66022.1	chr7	30605198	30605205	-	1	NA	exon (NM_026815, exon 6 of 8)	exon (NM_026815, exon 6 of 8)	7533	NM_026815	109637	Mm.25471	NM_026815	ENSMUSG00000006313	Upk1a	1110031P12Rik|AU019298|C87192|Tspan21|Upk1	uroplakin 1A	protein-coding
mm_132758.1	chr16	44394806	44394826	+	1	NA	promoter-TSS (NM_001033247)	promoter-TSS (NM_001033247)	17	NM_001033247	212517	Mm.327888	NM_001033247	ENSMUSG00000071550	Cfap44	6330444M21Rik|D16Ertd642e|Gm1750|Wdr52	cilia and flagella associated protein 44	protein-coding
mm_46790.1	chr5	112767293	112767315	-	1	NA	intron (NM_028901, intron 34 of 43)	RLTR20A4|LTR|ERVK	-25988	NR_040675	67360	Mm.59218	NR_040675	ENSMUSG00000098230	1700095B10Rik	-	RIKEN cDNA 1700095B10 gene	ncRNA
mm_62495.1	chr7	101970133	101970185	+	1	NA	intron (NM_133947, intron 1 of 24)	CpG	316	NM_133947	101706	Mm.27259	NM_133947	ENSMUSG00000066306	Numa1	6720401E04Rik|AA764025|AL022610|AU014979|NuMA	nuclear mitotic apparatus protein 1	protein-coding
mm_156271.1	chrX	136833404	136833413	+	1	NA	exon (NM_011123, exon 4 of 7)	exon (NM_011123, exon 4 of 7)	10662	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_44784.1	chr5	32135198	32135220	-	1	NA	Intergenic	CpG	-1263	NM_008037	14284	Mm.24684	NM_008037	ENSMUSG00000029135	Fosl2	Fra-2	fos-like antigen 2	protein-coding
mm_65232.1	chr7	19733159	19733167	-	1	NA	exon (NM_001159724, exon 3 of 6)	exon (NM_001159724, exon 3 of 6)	16410	NM_008990	19294	Mm.4341	NM_008990	ENSMUSG00000062300	Nectin2	AI325026|AI987993|Cd112|MPH|Pvr|Pvrl2|Pvs|nectin-2	nectin cell adhesion molecule 2	protein-coding
mm_93653.1	chr10	117411245	117411265	-	1	NA	Intergenic	RMER17C2|LTR|ERVK	-34282	NM_001310609	432508	Mm.478881	NM_001013391	ENSMUSG00000055531	Cpsf6	4733401N12Rik|AI256641|CFIM|CFIM68|HPBRII-4|HPBRII-7	cleavage and polyadenylation specific factor 6	protein-coding
mm_161399.1	chr14	118923070	118923070	-	1	NA	promoter-TSS (NR_130725)	promoter-TSS (NR_130725)	97	NR_130725	66573	Mm.87456	NM_025943	ENSMUSG00000042156	Dzip1	2510025K24Rik|2810422M04Rik	DAZ interacting protein 1	protein-coding
mm_10595.1	chr2	18677003	18677053	+	1	NA	promoter-TSS (NM_007552)	promoter-TSS (NM_007552)	10	NM_007552	12151	Mm.289584	NM_007552	ENSMUSG00000026739	Bmi1	AW546694|Bmi-1|Pcgf4	Bmi1 polycomb ring finger oncogene	protein-coding
mm_27781.1	chr3	73708369	73708384	-	1	NA	promoter-TSS (NM_009738)	promoter-TSS (NM_009738)	39	NM_009738	12038	Mm.250719	NM_009738	ENSMUSG00000027792	Bche	C730038G20Rik	butyrylcholinesterase	protein-coding
mm_33159.1	chr4	125836911	125836940	+	1	NA	Intergenic	Intergenic	85385	NR_015560	72395	Mm.112888	NR_015560	ENSMUSG00000085562	2610028E06Rik	BB043107	RIKEN cDNA 2610028E06 gene	ncRNA
mm_6062.1	chr1	60566709	60566756	-	1	NA	promoter-TSS (NM_001045513)	promoter-TSS (NM_001045513)	33	NM_001045513	77300	Mm.440325	NM_001045513	ENSMUSG00000026014	Raph1	9430025M21Rik|C730009O10Rik|Lpd	Ras association (RalGDS/AF-6) and pleckstrin homology domains 1	protein-coding
mm_79578.1	chr9	58134911	58134931	+	1	NA	intron (NM_001162479, intron 1 of 18)	intron (NM_001162479, intron 1 of 18)	256	NM_001162479	20897	Mm.10801	NM_009291	ENSMUSG00000032327	Stra6	AI891933	stimulated by retinoic acid gene 6	protein-coding
mm_12123.1	chr2	61626952	61626986	+	1	NA	exon (NM_001164072, exon 3 of 8)	exon (NM_001164072, exon 3 of 8)	33872	NM_001164071	21353	Mm.244393	NM_011529	ENSMUSG00000064289	Tank	C86182|E430026L09Rik|I-TRAF	TRAF family member-associated Nf-kappa B activator	protein-coding
mm_41448.1	chr5	90905388	90905399	+	1	NA	3' UTR (NM_009140, exon 4 of 4)	3' UTR (NM_009140, exon 4 of 4)	1494	NM_009140	20310	Mm.4979	NM_009140	ENSMUSG00000058427	Cxcl2	CINC-2a|GROb|Gro2|MIP-2|MIP-2a|Mgsa-b|Mip2|Scyb|Scyb2	chemokine (C-X-C motif) ligand 2	protein-coding
mm_55473.1	chr6	68807739	68807759	-	1	NA	Intergenic	Intergenic	519425	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_37515.1	chr4	123917227	123917318	-	1	NA	promoter-TSS (NM_017475)	promoter-TSS (NM_017475)	-161	NM_017475	54170	Mm.220922	NM_017475	ENSMUSG00000028646	Rragc	AU041672|Gtr2|RAGC|TIB929|YGR163W	Ras-related GTP binding C	protein-coding
mm_58845.1	chr7	16843022	16843040	+	1	NA	promoter-TSS (NM_178900)	promoter-TSS (NM_178900)	-34	NM_178900	101540	Mm.1881	NM_178900	ENSMUSG00000041187	Prkd2	AI325941|PKD2	protein kinase D2	protein-coding
mm_130420.1	chr15	98093089	98093137	-	1	NA	intron (NM_001163488, intron 1 of 22)	CpG	456	NM_144851	223870	Mm.384023	NM_144851	ENSMUSG00000033075	Senp1	2310046A20Rik|D15Ertd528e|E330036L07Rik|suPr-2	SUMO1/sentrin specific peptidase 1	protein-coding
mm_116446.1	chr13	43154813	43154821	-	1	NA	exon (NM_025935, exon 6 of 8)	exon (NM_025935, exon 6 of 8)	16684	NM_001252639	67046	Mm.269213	NM_025935	ENSMUSG00000021368	Tbc1d7	2610009C09Rik	TBC1 domain family, member 7	protein-coding
mm_142685.1	chr17	47733837	47733862	-	1	NA	exon (NM_025973, exon 8 of 9)	exon (NM_025973, exon 8 of 9)	-3188	NM_001161722	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_80580.1	chr9	84053173	84053173	+	1	NA	intron (NM_001305935, intron 8 of 10)	intron (NM_001305935, intron 8 of 10)	104392	NM_199195	12040	Mm.12819	NM_199195	ENSMUSG00000032263	Bckdhb	BCKDE1B|BCKDH E1-beta	branched chain ketoacid dehydrogenase E1, beta polypeptide	protein-coding
mm_145252.1	chr18	52488374	52488381	+	1	NA	exon (NM_026040, exon 6 of 8)	exon (NM_026040, exon 6 of 8)	22684	NM_026040	67222	Mm.100617	NM_026040	ENSMUSG00000024528	Srfbp1	2810036K01Rik|p49/STRAP	serum response factor binding protein 1	protein-coding
mm_9463.1	chr1	172895049	172895063	-	1	NA	promoter-TSS (NM_011318)	promoter-TSS (NM_011318)	-2	NM_011318	20219	Mm.330510	NM_011318	ENSMUSG00000026542	Apcs	Sap	serum amyloid P-component	protein-coding
mm_52244.1	chr6	105677769	105677794	+	1	NA	promoter-TSS (NM_173004)	promoter-TSS (NM_173004)	36	NM_173004	269784	Mm.321683	NM_173004	ENSMUSG00000064293	Cntn4	9630050B05|Axcam|BIG-2	contactin 4	protein-coding
mm_164960.1	chr19	5799510	5799511	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	3162	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_110217.1	chr12	28623373	28623394	-	1	NA	promoter-TSS (NM_027866)	promoter-TSS (NM_027866)	-53	NM_027866	71693	Mm.30724	NM_027866	ENSMUSG00000036655	Colec11	CL-K1	collectin sub-family member 11	protein-coding
mm_23733.1	chr3	69029447	69029466	+	1	NA	exon (NM_133786, exon 17 of 24)	exon (NM_133786, exon 17 of 24)	15286	NM_025863	66949	Mm.176695	NM_025863	ENSMUSG00000034317	Trim59	2310035M22Rik|2700022F13Rik|Mrf1|TSBF1	tripartite motif-containing 59	protein-coding
mm_84565.1	chr9	68569253	68569257	-	1	NA	Intergenic	Intergenic	-49055	NR_040737	74951	Mm.60678	NR_040737	ENSMUSG00000111303	4930502A04Rik	-	RIKEN cDNA 4930502A04 gene	ncRNA
mm_41925.1	chr5	105651323	105651362	+	1	NA	Intergenic	Intergenic	-48627	NM_001122768	231549	Mm.23837	NM_178701	ENSMUSG00000046079	Lrrc8d	2810473G09Rik|4930525N13Rik|A930019F03|Lrrc5	leucine rich repeat containing 8D	protein-coding
mm_115157.1	chr13	107063672	107063682	+	1	NA	Intergenic	MLT1L|LTR|ERVL-MaLR	41107	NR_015471	100040322	Mm.133867	NR_015471		3830408C21Rik	-	RIKEN cDNA 3830408C21 gene	ncRNA
mm_39125.1	chr4	155043144	155043172	-	1	NA	Intergenic	CpG	-23872	NM_001042407	668173	Mm.133114	NM_001042407	ENSMUSG00000029047	Pex10	AV128229|Gm142	peroxisomal biogenesis factor 10	protein-coding
mm_54197.1	chr6	24653671	24653674	-	1	NA	intron (NM_001167745, intron 1 of 4)	intron (NM_001167745, intron 1 of 4)	11323	NM_001167745	73178	Mm.1574	NM_028459	ENSMUSG00000029684	Wasl	2900021I12Rik|3110031I02Rik|N-WASP	Wiskott-Aldrich syndrome-like (human)	protein-coding
mm_171624.1	chr4	155670546	155670560	+	1	NA	Intergenic	RLTR9D|LTR|ERVK	-1299	NM_001256107	76580	Mm.235738	NM_145124	ENSMUSG00000029060	Mib2	2210008I11Rik|Zzank1|skd	mindbomb E3 ubiquitin protein ligase 2	protein-coding
mm_166963.1	chr7	44480667	44480668	+	1	NA	Intergenic	Intergenic	-3850	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_14016.1	chr2	122150563	122150609	+	1	NA	intron (NM_009735, intron 1 of 3)	intron (NM_009735, intron 1 of 3)	2899	NM_009735	12010	Mm.163	NM_009735	ENSMUSG00000060802	B2m	Ly-m11|beta2-m|beta2m	beta-2 microglobulin	protein-coding
mm_15855.1	chr2	164785958	164785989	+	1	NA	promoter-TSS (NM_133924)	promoter-TSS (NM_133924)	-48	NM_133924	101113	Mm.295647	NM_133924	ENSMUSG00000050373	Snx21	5730407K14Rik|AI481716	sorting nexin family member 21	protein-coding
mm_42409.1	chr5	115053462	115053468	+	1	NA	intron (NM_029012, intron 1 of 10)	intron (NM_029012, intron 1 of 10)	41941	NM_029012	74585	Mm.355894	NM_029012	ENSMUSG00000029550	Sppl3	4833416I09Rik|Psl4|Usmg3	signal peptide peptidase 3	protein-coding
mm_6479.1	chr1	74070209	74070233	-	1	NA	intron (NM_027884, intron 2 of 34)	RMER1A|Other|Other	54226	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_158352.1	chrX	134583115	134583149	-	1	NA	promoter-TSS (NM_013482)	promoter-TSS (NM_013482)	8	NM_013482	12229	Mm.4475	NM_013482	ENSMUSG00000031264	Btk	AI528679|xid	Bruton agammaglobulinemia tyrosine kinase	protein-coding
mm_91134.1	chr10	19609224	19609246	-	1	NA	exon (NM_010511, exon 7 of 7)	exon (NM_010511, exon 7 of 7)	-12793	NM_178258	237310	Mm.331979	NM_178258	ENSMUSG00000039760	Il22ra2	CRF2-10|CRF2-s1|CRF2X|Il-22bp	interleukin 22 receptor, alpha 2	protein-coding
mm_155932.1	chrX	103493565	103493592	+	1	NA	promoter-TSS (NR_015508)	promoter-TSS (NR_015508)	20	NR_015508	70252	Mm.380486	NR_015508	ENSMUSG00000097571	Jpx	2010000I03Rik|2510040I06Rik|Enox	Jpx transcript, Xist activator (non-protein coding)	ncRNA
mm_130215.1	chr15	95654810	95654826	-	1	NA	promoter-TSS (NM_207533)	promoter-TSS (NM_207533)	-47	NM_207533	223843	Mm.152937	NM_207533	ENSMUSG00000045608	Dbx2	9430056A22Rik|9630005K15|AI846217|Gm1229	developing brain homeobox 2	protein-coding
mm_158541.1	chrX	143933214	143933224	-	1	NA	promoter-TSS (NM_010025)	promoter-TSS (NM_010025)	0	NM_010025	13193	Mm.12871	NM_010025	ENSMUSG00000031285	Dcx	Dbct	doublecortin	protein-coding
mm_87516.1	chr10	52690575	52690586	+	1	NA	promoter-TSS (NM_178675)	promoter-TSS (NM_178675)	79	NM_178675	215085	Mm.338690	NM_178675	ENSMUSG00000038602	Slc35f1	Duf6|E130016L02	solute carrier family 35, member F1	protein-coding
mm_44104.1	chr5	149367591	149367607	+	1	NA	Intergenic	Intergenic	-44207	NM_027519	70717	Mm.252139	NM_027519	ENSMUSG00000029659	Medag	6330406I15Rik|Awms3|MEDA-4|Meda4|mAWMS3	mesenteric estrogen dependent adipogenesis	protein-coding
mm_150126.1	chr19	30030420	30030430	+	1	NA	promoter-TSS (NM_144873)	promoter-TSS (NM_144873)	-88	NM_144873	109113	Mm.313364	NM_144873	ENSMUSG00000024817	Uhrf2	2310065A22Rik|AI426270|AW214556|D130071B19Rik|Nirf	ubiquitin-like, containing PHD and RING finger domains 2	protein-coding
mm_52729.1	chr6	120364095	120364163	+	1	NA	promoter-TSS (NM_145997)	promoter-TSS (NM_145997)	30	NM_145997	214899	Mm.404761	NM_145997	ENSMUSG00000030180	Kdm5a	AA409370|C76986|Jarid1a|RBP2|Rbbp2	lysine (K)-specific demethylase 5A	protein-coding
mm_78457.1	chr9	32372471	32372471	+	1	NA	promoter-TSS (NM_019659)	promoter-TSS (NM_019659)	53	NM_019659	56379	Mm.390168	NM_019659	ENSMUSG00000041248	Kcnj1	Kir1.1|ROMK|Romk2	potassium inwardly-rectifying channel, subfamily J, member 1	protein-coding
mm_93973.1	chr10	127311741	127311763	-	1	NA	promoter-TSS (NM_001171582)	promoter-TSS (NM_001171582)	34	NM_001003913	216443	Mm.28173	NM_001003913	ENSMUSG00000040354	Mars	Metrs|Mtrns	methionine-tRNA synthetase	protein-coding
mm_151977.1	chr19	5826960	5826971	-	1	NA	non-coding (NR_131212, exon 1 of 1)	non-coding (NR_131212, exon 1 of 1)	18513	NR_131212	66961	Mm.281895	NR_003513	ENSMUSG00000092274	Neat1	2310043N10Rik|VINC	nuclear paraspeckle assembly transcript 1 (non-protein coding)	ncRNA
mm_83684.1	chr9	50504780	50504821	-	1	NA	promoter-TSS (NR_040714)	promoter-TSS (NR_040714)	5	NR_040714	69631	Mm.414996	NR_040714	ENSMUSG00000101304	Plet1os	2310014F07Rik	placenta expressed transcript 1, opposite strand	ncRNA
mm_49352.1	chr6	21986439	21986457	+	1	NA	5' UTR (NM_001081351, exon 1 of 22)	5' UTR (NM_001081351, exon 1 of 22)	538	NM_001081351	214642	Mm.221404	NM_001081351	ENSMUSG00000062980	Cped1	6720481P07|A430107O13Rik|AI552584	cadherin-like and PC-esterase domain containing 1	protein-coding
mm_55274.1	chr6	54039889	54039892	-	1	NA	promoter-TSS (NM_001163640)	promoter-TSS (NM_001163640)	-42	NM_001163640	69993	Mm.321147	NM_023543	ENSMUSG00000004633	Chn2	1700026N20Rik|4930557O16Rik|ARHGAP3|Bch	chimerin 2	protein-coding
mm_44644.1	chr5	28209819	28209829	-	1	NA	5' UTR (NM_001310511, exon 1 of 3)	5' UTR (NM_001310511, exon 1 of 3)	344	NM_001310511	269637	Mm.68286	NM_175651	ENSMUSG00000044681	Cnpy1	1500012D20Rik|9630008K15Rik|AI853839	canopy FGF signaling regulator 1	protein-coding
mm_60528.1	chr7	44480156	44480168	+	1	NA	Intergenic	Intergenic	-4355	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_56685.1	chr6	113910544	113910552	-	1	NA	intron (NM_001347365, intron 2 of 23)	intron (NM_001347365, intron 2 of 23)	-19009	NM_001036684	11941	Mm.321755	NM_009723	ENSMUSG00000030302	Atp2b2	D6Abb2e|Gena300|PMCA2|Tmy|dfw|jog|wms|wri	ATPase, Ca++ transporting, plasma membrane 2	protein-coding
mm_3255.1	chr1	136162942	136162952	+	1	NA	exon (NM_001039472, exon 25 of 35)	exon (NM_001039472, exon 25 of 35)	31546	NM_001039472	16565	Mm.276135	NM_019962	ENSMUSG00000041642	Kif21b	2610511N21Rik|mKIAA0449	kinesin family member 21B	protein-coding
mm_13015.1	chr2	90965087	90965108	+	1	NA	intron (NM_001244891, intron 2 of 14)	intron (NM_001244891, intron 2 of 14)	24700	NM_017368	13046	Mm.29495	NM_017368	ENSMUSG00000005506	Celf1	1600010O03Rik|AA407467|Brunol2|CUG-BP|CUG-BP1|CUGBP|Cugbp1|D2Wsu101e|HNAB50|NAB50	CUGBP, Elav-like family member 1	protein-coding
mm_134706.1	chr16	22887073	22887098	-	1	NA	non-coding (NR_110508, exon 2 of 4)	non-coding (NR_110508, exon 2 of 4)	-4930	NR_075099	11625	Mm.197554	NM_013465	ENSMUSG00000022868	Ahsg	-	alpha-2-HS-glycoprotein	protein-coding
mm_17796.1	chr2	33131646	33131658	-	1	NA	Intergenic	Intergenic	-44448	NM_178888	99326	Mm.41290	NM_178888	ENSMUSG00000038860	Garnl3	AW120551	GTPase activating RANGAP domain-like 3	protein-coding
mm_44281.1	chr5	7800889	7800890	-	1	NA	Intergenic	Intergenic	-159583	NM_054098	117167	Mm.31403	NM_054098	ENSMUSG00000012428	Steap4	1110021O17Rik|AI481214|Tiarp|Tnfaip9	STEAP family member 4	protein-coding
mm_3380.1	chr1	139454829	139454842	+	1	NA	promoter-TSS (NM_009791)	promoter-TSS (NM_009791)	62	NM_009791	12316	Mm.168523	NM_009791	ENSMUSG00000033952	Aspm	Calmbp1|D330028K02Rik|MCPH5|Sha1	asp (abnormal spindle)-like, microcephaly associated (Drosophila)	protein-coding
mm_30932.1	chr4	32983284	32983308	+	1	NA	5' UTR (NM_027491, exon 1 of 7)	5' UTR (NM_027491, exon 1 of 7)	298	NM_027491	52187	Mm.300814	NM_027491	ENSMUSG00000028278	Rragd	5730543C08Rik|AI467523|C030003H22Rik|D4Ertd174e	Ras-related GTP binding D	protein-coding
mm_111519.1	chr12	99965650	99965675	-	1	NA	5' UTR (NM_001164426, exon 2 of 3)	5' UTR (NM_001164426, exon 2 of 3)	1163	NM_001164427	217826	Mm.312335	NM_146037	ENSMUSG00000045404	Kcnk13	BB085247|F730021E22Rik|Gm1570|Gm1685	potassium channel, subfamily K, member 13	protein-coding
mm_22605.1	chr3	14506447	14506457	+	1	NA	TTS (NM_080852)	TTS (NM_080852)	25753	NM_080852	140918	Mm.215250	NM_080852	ENSMUSG00000039710	Slc7a12	Asc-2|XAT1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 12	protein-coding
mm_36560.1	chr4	87161682	87161692	-	1	NA	intron (NM_172426, intron 2 of 10)	intron (NM_172426, intron 2 of 10)	66276	NM_001110240	76376	Mm.490487	NM_172426	ENSMUSG00000037996	Slc24a2	2810021B17Rik|6330417K15Rik|AI847460|Nckx2	solute carrier family 24 (sodium/potassium/calcium exchanger), member 2	protein-coding
mm_73540.1	chr8	108704075	108704107	+	1	NA	Intergenic	(CCG)n|Simple_repeat|Simple_repeat	-10553	NM_007496	11906	Mm.416972	NM_007496	ENSMUSG00000038872	Zfhx3	A230102L03Rik|Atbf1|Sci|WBP9|mKIAA4228	zinc finger homeobox 3	protein-coding
mm_162747.1	chr10	57788322	57788331	+	1	NA	3' UTR (NM_021272, exon 4 of 4)	3' UTR (NM_021272, exon 4 of 4)	3403	NM_021272	12140	Mm.3644	NM_021272	ENSMUSG00000019874	Fabp7	B-FABP|BFABP|Blbp|MRG	fatty acid binding protein 7, brain	protein-coding
mm_106263.1	chr11	117968184	117968224	-	1	NA	exon (NM_007707, exon 2 of 2)	exon (NM_007707, exon 2 of 2)	1162	NM_007707	12702	Mm.3468	NM_007707	ENSMUSG00000053113	Socs3	Cis3|Cish3|EF-10|Ef10|SSI-3|Ssi3	suppressor of cytokine signaling 3	protein-coding
mm_134169.1	chr16	10796412	10796414	-	1	NA	TTS (NM_013637)	TTS (NM_013637)	410	NM_013637	19118	Mm.42733	NM_013637	ENSMUSG00000022501	Prm1	Prm-1	protamine 1	protein-coding
mm_31958.1	chr4	86874415	86874438	+	1	NA	promoter-TSS (NM_001290543)	promoter-TSS (NM_001290543)	12	NM_139306	230379	Mm.45019	NM_139306	ENSMUSG00000038007	Acer2	2410116I05Rik|Asah3l|CRG-L1|maCER2	alkaline ceramidase 2	protein-coding
mm_28584.1	chr3	94375238	94375241	-	1	NA	intron (NM_011281, intron 2 of 10)	intron (NM_011281, intron 2 of 10)	-2193	NM_001293734	19885	Mm.4372	NM_011281	ENSMUSG00000028150	Rorc	Nr1f3|RORgamma|TOR|Thor	RAR-related orphan receptor gamma	protein-coding
mm_81991.1	chr9	121460253	121460272	+	1	NA	intron (NM_175114, intron 13 of 15)	intron (NM_175114, intron 13 of 15)	35432	NM_001284508	12424	Mm.2619	NM_031161	ENSMUSG00000032532	Cck	-	cholecystokinin	protein-coding
mm_69734.1	chr7	140881858	140881871	-	1	NA	promoter-TSS (NM_001127351)	promoter-TSS (NM_001127351)	5	NM_001127351	64384	Mm.29760	NM_022433	ENSMUSG00000025486	Sirt3	2310003L23Rik|AI848213|Sir2l3	sirtuin 3	protein-coding
mm_87463.1	chr10	51485476	51485507	+	1	NA	intron (NM_001291892, intron 7 of 8)	intron (NM_001291892, intron 7 of 8)	4879	NM_001291892	14727	Mm.439661	NM_008147	ENSMUSG00000062593	Lilr4b	Gp49a|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4B	protein-coding
mm_138504.1	chr17	35233006	35233014	+	1	NA	intron (NM_010909, intron 2 of 3)	intron (NM_010909, intron 2 of 3)	-2000	NM_001347351	66237	Mm.396107	NM_023179	ENSMUSG00000024403	Atp6v1g2	1500002D01Rik|Atp6g2|NG38|VAG2	ATPase, H+ transporting, lysosomal V1 subunit G2	protein-coding
mm_26680.1	chr3	155514444	155514463	+	1	NA	Intergenic	Intergenic	421019	NM_028938	74435	Mm.195711	NM_028938	ENSMUSG00000028182	Lrriq3	4930438B07Rik|4930511J15Rik|4933403H06Rik|BB020367|Lrrc44	leucine-rich repeats and IQ motif containing 3	protein-coding
mm_69582.1	chr7	135704415	135704427	-	1	NA	exon (NM_001081117, exon 9 of 14)	exon (NM_001081117, exon 9 of 14)	11958	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_158104.1	chrX	102042522	102042571	-	1	NA	intron (NM_001163610, intron 1 of 7)	intron (NM_001163610, intron 1 of 7)	28761	NM_001278534	331474	Mm.23297	NM_183318	ENSMUSG00000049191	Rgag4	6430402L03Rik|Mar5|Mart5|mKIAA2001	retrotransposon gag domain containing 4	protein-coding
mm_167203.1	chr7	143548368	143548404	+	1	NA	intron (NM_001285489, intron 1 of 14)	intron (NM_001285489, intron 1 of 14)	442	NM_001285490	17955	Mm.294625	NM_008672	ENSMUSG00000059119	Nap1l4	2810410H14Rik|AI316776|D7Wsu30e|Nap2	nucleosome assembly protein 1-like 4	protein-coding
mm_137827.1	chr17	30651649	30651670	+	1	NA	intron (NM_013811, intron 7 of 92)	ID4|SINE|ID	24723	NM_013811	13417	Mm.426017	NM_013811	ENSMUSG00000033826	Dnah8	ATPase|Dnahc8|Hst6.7b|P1-Loop	dynein, axonemal, heavy chain 8	protein-coding
mm_151539.1	chr19	59081438	59081451	+	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-5375	NM_001114312	71653	Mm.37338	NM_175172	ENSMUSG00000041362	Shtn1	4930506M07Rik|Kiaa1598|Shootin1|mKIAA1598	shootin 1	protein-coding
mm_89784.1	chr10	102079681	102079683	+	1	NA	intron (NM_001205098, intron 3 of 7)	intron (NM_001205098, intron 3 of 7)	-79176	NM_001162368	67569	Mm.25252	NM_026243	ENSMUSG00000019888	Mgat4c	9130411I17Rik|GntIVh	MGAT4 family, member C	protein-coding
mm_24897.1	chr3	96172508	96172530	+	1	NA	promoter-TSS (NM_153053)	promoter-TSS (NM_153053)	13	NM_153053	107701	Mm.219671	NM_153053	ENSMUSG00000068856	Sf3b4	SF3b49|SF3b50|Sap49	splicing factor 3b, subunit 4	protein-coding
mm_82485.1	chr9	18468027	18468043	-	1	NA	exon (NM_028935, exon 5 of 8)	exon (NM_028935, exon 5 of 8)	5524	NM_028935	72230	Mm.289689	NM_028935	ENSMUSG00000074500	Zfp558	1700007A21Rik|4932704I17Rik|Zfp558-ps	zinc finger protein 558	protein-coding
mm_118029.1	chr13	101548076	101548093	-	1	NA	Intergenic	LTR33B|LTR|ERVL	144546	NM_001024955	18708	Mm.259333	NM_001024955	ENSMUSG00000041417	Pik3r1	PI3K|p50alpha|p55alpha|p85alpha	phosphatidylinositol 3-kinase, regulatory subunit, polypeptide 1 (p85 alpha)	protein-coding
mm_50678.1	chr6	51545508	51545529	+	1	NA	intron (NM_028035, intron 1 of 6)	intron (NM_028035, intron 1 of 6)	995	NM_001127348	71982	Mm.294166	NM_028035	ENSMUSG00000038301	Snx10	2410004M09Rik	sorting nexin 10	protein-coding
mm_39805.1	chr5	30623495	30623531	+	1	NA	3' UTR (NM_010608, exon 2 of 2)	3' UTR (NM_010608, exon 2 of 2)	-24423	NR_049199	100885838		NR_049199	ENSMUSG00000093710	Mir5625	Gm23930|mmu-mir-5625	microRNA 5625	ncRNA
mm_47879.1	chr5	134703063	134703067	-	1	NA	3' UTR (NM_007925, exon 37 of 37)	3' UTR (NM_007925, exon 37 of 37)	-14475	NM_010717	16885	Mm.15409	NM_010717	ENSMUSG00000029674	Limk1	KIZ-1|LIMK-1|Limk	LIM-domain containing, protein kinase	protein-coding
mm_96580.1	chr11	69070858	69070880	+	1	NA	promoter-TSS (NM_025838)	promoter-TSS (NM_025838)	60	NM_028336	66910	Mm.33964	NM_025838	ENSMUSG00000020895	Tmem107	1110004B13Rik|2810049P21Rik	transmembrane protein 107	protein-coding
mm_86863.1	chr10	21993537	21993554	+	1	NA	promoter-TSS (NM_001161850)	promoter-TSS (NM_001161850)	-345	NM_001161850	20393	Mm.28405	NM_011361	ENSMUSG00000019970	Sgk1	Sgk	serum/glucocorticoid regulated kinase 1	protein-coding
mm_148451.1	chr19	3986565	3986579	+	1	NA	promoter-TSS (NM_001302481)	promoter-TSS (NM_001302481)	2	NM_001302482	71670	Mm.29735	NM_027857	ENSMUSG00000024866	Acy3	0610006H10Rik|AA3|AAIII|AW107362|Acy-3|HCBP1	aspartoacylase (aminoacylase) 3	protein-coding
mm_162390.1	chr1	75637038	75637038	+	1	NA	Intergenic	Intergenic	90772	NM_009208	20536	Mm.5053	NM_009208	ENSMUSG00000006576	Slc4a3	A930038D23Rik|Ae3	solute carrier family 4 (anion exchanger), member 3	protein-coding
mm_142967.1	chr17	56121966	56121986	-	1	NA	promoter-TSS (NM_029796)	promoter-TSS (NM_029796)	-30	NM_029796	76905	Mm.348025	NM_029796	ENSMUSG00000037095	Lrg1	1300008B03Rik|2310031E04Rik|Lrg|Lrhg	leucine-rich alpha-2-glycoprotein 1	protein-coding
mm_42054.1	chr5	108669327	108669342	+	1	NA	TTS (NM_001310692)	TTS (NM_001310692)	5462	NM_001310692	231583	Mm.440571	NM_174870	ENSMUSG00000046959	Slc26a1	Sat1	solute carrier family 26 (sulfate transporter), member 1	protein-coding
mm_109239.1	chr12	108894280	108894312	+	1	NA	promoter-TSS (NM_177602)	promoter-TSS (NM_177602)	24	NM_177602	212198	Mm.342082	NM_177602	ENSMUSG00000040877	Wdr25	B930090D16Rik	WD repeat domain 25	protein-coding
mm_28575.1	chr3	93445378	93445388	-	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	3053	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_172098.1	chr6	27554244	27554251	+	1	NA	intron (NM_001311072, intron 6 of 9)	L1_Mus1|LINE|L1	382503	NR_030420	735266		NR_030420	ENSMUSG00000076067	Mir592	Mirn592|mir-592|mmu-mir-592	microRNA 592	ncRNA
mm_82336.1	chr9	9269359	9269396	-	1	NA	Intergenic	Intergenic	-30364	NM_027823	71544	Mm.334955	NM_027823	ENSMUSG00000050730	Arhgap42	9030420J04Rik|BE136619	Rho GTPase activating protein 42	protein-coding
mm_130639.1	chr15	100495252	100495267	-	1	NA	promoter-TSS (NM_153407)	promoter-TSS (NM_153407)	-20	NM_153407	207785	Mm.294969	NM_153407	ENSMUSG00000044636	Csrnp2	CSRNP-2|Csnrp2|taip-12	cysteine-serine-rich nuclear protein 2	protein-coding
mm_55766.1	chr6	78466881	78466894	-	1	NA	exon (NM_011260, exon 5 of 6)	exon (NM_011260, exon 5 of 6)	1987	NM_011260	19695	Mm.252385	NM_011260	ENSMUSG00000030017	Reg3g	AI449515|REG-3-gamma|reg III-gamma	regenerating islet-derived 3 gamma	protein-coding
mm_50789.1	chr6	54039647	54039695	+	1	NA	promoter-TSS (NM_001163640)	promoter-TSS (NM_001163640)	-261	NM_001163640	69993	Mm.321147	NM_023543	ENSMUSG00000004633	Chn2	1700026N20Rik|4930557O16Rik|ARHGAP3|Bch	chimerin 2	protein-coding
mm_123777.1	chr14	70323745	70323753	-	1	NA	intron (NM_001135152, intron 2 of 9)	intron (NM_001135152, intron 2 of 9)	24684	NM_001135152	213053	Mm.270647	NM_144808	ENSMUSG00000022094	Slc39a14	FAD-123|ZIP-14|Zip14|fad123	solute carrier family 39 (zinc transporter), member 14	protein-coding
mm_92898.1	chr10	83316734	83316737	-	1	NA	5' UTR (NM_177388, exon 2 of 11)	5' UTR (NM_177388, exon 2 of 11)	21082	NM_177388	338365	Mm.67073	NM_177388	ENSMUSG00000034591	Slc41a2	A230035L05Rik|SLC41A1-L1	solute carrier family 41, member 2	protein-coding
mm_109874.1	chr12	4916689	4916729	-	1	NA	promoter-TSS (NM_001099628)	promoter-TSS (NM_001099628)	-644	NM_001099628	320817	Mm.210966	NM_001099628	ENSMUSG00000052812	Atad2b	1110014E10Rik|BC032887|C79189|D530031C13Rik	ATPase family, AAA domain containing 2B	protein-coding
mm_74616.1	chr8	12779620	12779623	-	1	NA	intron (NR_121603, intron 1 of 29)	intron (NR_121603, intron 1 of 29)	22605	NM_001293667	50770	Mm.257837	NM_015804	ENSMUSG00000031441	Atp11a	4930558F19Rik|AU040868|Atpc1h|Ih	ATPase, class VI, type 11A	protein-coding
mm_131304.1	chr16	11420727	11420744	+	1	NA	exon (NM_028964, exon 11 of 21)	exon (NM_028964, exon 11 of 21)	15087	NM_001290148	74478	Mm.325831	NM_028964	ENSMUSG00000071669	Snx29	4933437K13Rik|ENSMUSG00000079738|Gm11170|Gm1737|Gm930|Rundc2a	sorting nexin 29	protein-coding
mm_43377.1	chr5	135674573	135674592	+	1	NA	Intergenic	Intergenic	-14563	NM_008898	18984	Mm.3863	NM_008898	ENSMUSG00000005514	Por	4933424M13Rik|CPR|CYPOR|P450R	P450 (cytochrome) oxidoreductase	protein-coding
mm_81731.1	chr9	113741440	113741483	+	1	NA	promoter-TSS (NM_001114347)	promoter-TSS (NM_001114347)	-12	NM_001286599	76499	Mm.222272	NM_029633	ENSMUSG00000033392	Clasp2	1500004F14Rik|8030404L10Rik|C77448|CLASP2beta|mKIAA0627	CLIP associating protein 2	protein-coding
mm_131501.1	chr16	17406276	17406289	+	1	NA	promoter-TSS (NM_001001983)	promoter-TSS (NM_001001983)	32	NM_001001983	224020	Mm.5718	NM_001001983	ENSMUSG00000041720	Pi4ka	Pik4ca	phosphatidylinositol 4-kinase, catalytic, alpha polypeptide	protein-coding
mm_866.1	chr1	52150935	52150944	+	1	NA	intron (NM_001205313, intron 19 of 24)	intron (NM_001205313, intron 19 of 24)	31317	NM_001205313	20846	Mm.277406	NM_009283	ENSMUSG00000026104	Stat1	2010005J02Rik|AA408197	signal transducer and activator of transcription 1	protein-coding
mm_19558.1	chr2	98667078	98667109	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	1199436	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_153278.1	chr19	37205941	37205944	-	1	NA	intron (NM_001290827, intron 1 of 10)	intron (NM_001290827, intron 1 of 10)	1529	NM_198300	208922	Mm.391176	NM_198300	ENSMUSG00000039652	Cpeb3	4831444O18Rik|CPE-BP3|mKIAA0940	cytoplasmic polyadenylation element binding protein 3	protein-coding
mm_11621.1	chr2	34772690	34772763	+	1	NA	exon (NM_001163434, exon 3 of 9)	exon (NM_001163434, exon 3 of 9)	636	NM_022310	14828	Mm.330160	NM_022310	ENSMUSG00000026864	Hspa5	AL022860|AU019543|Bip|D2Wsu141e|D2Wsu17e|Grp78|Hsce70|SEZ-7|Sez7|baffled|mBiP	heat shock protein 5	protein-coding
mm_39048.1	chr4	153030456	153030505	-	1	NA	Intergenic	Intergenic	332940	NR_033138	330004	Mm.291863	NM_001033414		Gm833	-	predicted gene 833	ncRNA
mm_30145.1	chr3	142430175	142430188	-	1	NA	Intergenic	Intergenic	-34485	NM_019808	56376	Mm.117709	NM_019808	ENSMUSG00000028273	Pdlim5	1110001A05Rik|AI987914|C87059|Enh|Enh1|Enh2|Enh3|LIM	PDZ and LIM domain 5	protein-coding
mm_2098.1	chr1	87766102	87766119	+	1	NA	exon (NM_029846, exon 4 of 18)	exon (NM_029846, exon 4 of 18)	10099	NM_001205392	77040	Mm.272972	NM_029846	ENSMUSG00000026289	Atg16l1	1500009K01Rik|Apg16l|Atg16l|WDR30	autophagy related 16-like 1 (S. cerevisiae)	protein-coding
mm_12839.1	chr2	82053291	82053311	+	1	NA	promoter-TSS (NM_175513)	promoter-TSS (NM_175513)	-357	NM_175513	241514	Mm.119383	NM_175513	ENSMUSG00000070866	Zfp804a	C630007C17Rik|Znf804a	zinc finger protein 804A	protein-coding
mm_30763.1	chr4	15958560	15958607	+	1	NA	intron (NM_013752, intron 1 of 15)	intron (NM_013752, intron 1 of 15)	616	NM_013752	27354	Mm.20866	NM_013752	ENSMUSG00000028224	Nbn	Nbs1	nibrin	protein-coding
mm_169160.1	chr13	65348625	65348628	-	1	NA	Intergenic	Intergenic	69772	NM_178364	170936	Mm.151546	NM_178364	ENSMUSG00000021514	Zfp369	B930030B22Rik|D230020H11Rik|NRIF2	zinc finger protein 369	protein-coding
mm_17442.1	chr2	28466267	28466359	-	1	NA	promoter-TSS (NM_027040)	promoter-TSS (NM_027040)	11	NM_027040	69327	Mm.46470	NM_027040	ENSMUSG00000026831	1700007K13Rik	Rbest47	RIKEN cDNA 1700007K13 gene	protein-coding
mm_15189.1	chr2	154202621	154202629	+	1	NA	exon (NM_153418, exon 2 of 16)	exon (NM_153418, exon 2 of 16)	2245	NM_153418	228801	Mm.3783	NM_153418	ENSMUSG00000027485	Bpifb1	Lplunc1	BPI fold containing family B, member 1	protein-coding
mm_48155.1	chr5	137152172	137152180	-	1	NA	Intergenic	Intergenic	-35969	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_32127.1	chr4	99037492	99037503	+	1	NA	exon (NM_013913, exon 6 of 7)	exon (NM_013913, exon 6 of 7)	6543	NM_013913	30924	Mm.28341	NM_013913	ENSMUSG00000028553	Angptl3	hypl	angiopoietin-like 3	protein-coding
mm_142079.1	chr17	35702217	35702228	-	1	NA	promoter-TSS (NM_001198831)	promoter-TSS (NM_001198831)	-178	NM_001198831	12305	Mm.5021	NM_007584	ENSMUSG00000003534	Ddr1	6030432F18|AI323681|CD167a|Cak|Nep|PTK3A	discoidin domain receptor family, member 1	protein-coding
mm_38505.1	chr4	141115650	141115669	-	1	NA	non-coding (NR_102344, exon 3 of 3)	non-coding (NR_102344, exon 3 of 3)	24137	NR_102344	213491	Mm.332006	NM_174996	ENSMUSG00000040842	Szrd1	1110022I03|D4Ertd22e	SUZ RNA binding domain containing 1	protein-coding
mm_47930.1	chr5	135064064	135064116	-	1	NA	promoter-TSS (NM_025362)	promoter-TSS (NM_025362)	-116	NM_025362	66114	Mm.178012	NM_025362	ENSMUSG00000061118	Dnajc30	1300007M11Rik|Wbscr18	DnaJ heat shock protein family (Hsp40) member C30	protein-coding
mm_121123.1	chr14	101840603	101840677	+	1	NA	promoter-TSS (NM_001347628)	promoter-TSS (NM_001347628)	17	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_126379.1	chr15	80173206	80173229	+	1	NA	promoter-TSS (NM_010795)	promoter-TSS (NM_010795)	-504	NM_010795	17309	Mm.299693	NM_010795	ENSMUSG00000042428	Mgat3	1110038J12Rik|AI848272|GnT-III	mannoside acetylglucosaminyltransferase 3	protein-coding
mm_104315.1	chr11	93885753	93885773	-	1	NA	promoter-TSS (NM_134012)	promoter-TSS (NM_134012)	3	NM_001013375	217109	Mm.379350	NM_001013375	ENSMUSG00000054079	Utp18	6230425C22Rik|6430513M13|Wdr50	UTP18 small subunit processome component	protein-coding
mm_42249.1	chr5	113945519	113945533	+	1	NA	intron (NM_198109, intron 14 of 14)	intron (NM_198109, intron 14 of 14)	-36820	NM_011779	23790	Mm.260158	NM_011779	ENSMUSG00000004530	Coro1c	AL022675|AW455561|AW548837	coronin, actin binding protein 1C	protein-coding
mm_139875.1	chr17	70747309	70747313	+	1	NA	intron (NM_001347411, intron 9 of 14)	intron (NM_001347411, intron 9 of 14)	99466	NM_001164077	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_149511.1	chr19	11976990	11976995	+	1	NA	intron (NM_001033174, intron 3 of 13)	intron (NM_001033174, intron 3 of 13)	11148	NM_001033174	76303	Mm.291279	NM_001033174	ENSMUSG00000024687	Osbp	1110018F06Rik|AW559088|mKIAA4220	oxysterol binding protein	protein-coding
mm_13357.1	chr2	103424057	103424076	+	1	NA	promoter-TSS (NM_010125)	promoter-TSS (NM_010125)	-2	NM_010125	13711	Mm.20888	NM_010125	ENSMUSG00000027186	Elf5	ESE-2|ESE-5|ESE-5.	E74-like factor 5	protein-coding
mm_112242.1	chr12	113482490	113482507	-	1	NA	Intergenic	Intergenic	-7067	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_148174.1	chr18	78123325	78123338	-	1	NA	promoter-TSS (NM_028122)	promoter-TSS (NM_028122)	95	NM_001171010	108052	Mm.33832	NM_028122	ENSMUSG00000059336	Slc14a1	2610507K20Rik|3021401A05Rik|UT-B|Utb1	solute carrier family 14 (urea transporter), member 1	protein-coding
mm_68571.1	chr7	115725007	115725009	-	1	NA	intron (NM_001025560, intron 4 of 15)	intron (NM_001025560, intron 4 of 15)	76601	NM_001277328	20679	Mm.323365	NM_011445	ENSMUSG00000051910	Sox6	AI987981|SOX-LZ	SRY (sex determining region Y)-box 6	protein-coding
mm_134410.1	chr16	17680613	17680631	-	1	NA	exon (NM_001040683, exon 5 of 17)	exon (NM_001040683, exon 5 of 17)	34152	NM_001166164	72315	Mm.297777	NM_001166164	ENSMUSG00000041617	Ccdc74a	2310015A05Rik	coiled-coil domain containing 74A	protein-coding
mm_103718.1	chr11	79530393	79530402	-	1	NA	5' UTR (NM_010161, exon 1 of 2)	5' UTR (NM_010161, exon 1 of 2)	212	NM_146023	101488212	Mm.439665	NM_146023	ENSMUSG00000070354	Gm21975	Evi2a-evi2b	predicted gene 21975	protein-coding
mm_158190.1	chrX	104670787	104670832	-	1	NA	5' UTR (NM_175358, exon 1 of 12)	5' UTR (NM_175358, exon 1 of 12)	255	NM_175358	108672	Mm.30574	NM_175358	ENSMUSG00000033906	Zdhhc15	6030457O13Rik	zinc finger, DHHC domain containing 15	protein-coding
mm_69707.1	chr7	140102005	140102021	-	1	NA	intron (NM_001286217, intron 1 of 5)	intron (NM_001286217, intron 1 of 5)	428	NM_001286217	69064	Mm.41915	NM_026928	ENSMUSG00000025466	Fuom	Fucu|Le51	fucose mutarotase	protein-coding
mm_67494.1	chr7	80751700	80751737	-	1	NA	intron (NM_016721, intron 13 of 37)	B4A|SINE|B4	51613	NM_016721	29875	Mm.207619	NM_016721	ENSMUSG00000030536	Iqgap1	AA682088|D7Ertd237e|D7Ertd257e|mKIAA0051	IQ motif containing GTPase activating protein 1	protein-coding
mm_20854.1	chr2	148403940	148403942	-	1	NA	TTS (NM_009378)	TTS (NM_009378)	4247	NM_009378	21824	Mm.24096	NM_009378	ENSMUSG00000074743	Thbd	AI385582|CD141|TM	thrombomodulin	protein-coding
mm_113178.1	chr13	24845107	24845120	+	1	NA	promoter-TSS (NM_001081051)	promoter-TSS (NM_001081051)	-18	NM_001081051	210108	Mm.261514	NM_001081051	ENSMUSG00000006711	D130043K22Rik	4930451E12Rik|Kiaa0319	RIKEN cDNA D130043K22 gene	protein-coding
mm_47631.1	chr5	125298687	125298725	-	1	NA	exon (NM_001205082, exon 5 of 12)	exon (NM_001205082, exon 5 of 12)	42388	NM_016741	20778	Mm.282242	NM_016741	ENSMUSG00000037936	Scarb1	AI120173|CD36|Cd36l1|Chohd1|Cla-1|Cla1|D5Ertd460e|Hdlq1|Hlb398|SR-B1|SR-BI|SRBI|Srb1|mSR-BI	scavenger receptor class B, member 1	protein-coding
mm_53462.1	chr6	134897983	134898012	+	1	NA	promoter-TSS (NM_001167694)	promoter-TSS (NM_001167694)	36	NR_029441	72813	Mm.409034	NR_029441	ENSMUSG00000100876	2810454H06Rik	-	RIKEN cDNA 2810454H06 gene	ncRNA
mm_153786.1	chr19	45816008	45816076	-	1	NA	promoter-TSS (NM_030716)	promoter-TSS (NM_030716)	21	NM_145704	80906	Mm.213204	NM_030716	ENSMUSG00000025221	Kcnip2	KChIP2	Kv channel-interacting protein 2	protein-coding
mm_130714.1	chr15	101047381	101047385	-	1	NA	Intergenic	CpG	7016	NM_001214911	668225	Mm.385011	NM_001214911	ENSMUSG00000095440	Fignl2	EG668225	fidgetin-like 2	protein-coding
mm_154086.1	chr19	56746746	56746755	-	1	NA	Intergenic	Intergenic	24378	NM_007419	11554	Mm.46797	NM_007419	ENSMUSG00000035283	Adrb1	Adrb-1|beta-AR	adrenergic receptor, beta 1	protein-coding
mm_33641.1	chr4	132977757	132977765	+	1	NA	intron (NM_010208, intron 1 of 12)	intron (NM_010208, intron 1 of 12)	3666	NM_010208	14191	Mm.271665	NM_010208	ENSMUSG00000028874	Fgr	-	FGR proto-oncogene, Src family tyrosine kinase	protein-coding
mm_112419.1	chr13	4049041	4049043	+	1	NA	Intergenic	Intergenic	-10549	NM_134072	105387	Mm.26838	NM_134072	ENSMUSG00000033715	Akr1c14	9030611N15Rik|AW557061	aldo-keto reductase family 1, member C14	protein-coding
mm_11709.1	chr2	36230487	36230491	+	1	NA	promoter-TSS (NM_008969)	promoter-TSS (NM_008969)	63	NM_008969	19224	Mm.275434	NM_008969	ENSMUSG00000047250	Ptgs1	COX1|Cox-1|Cox-3|PGHS-1|PHS 1|Pghs1	prostaglandin-endoperoxide synthase 1	protein-coding
mm_171522.1	chr4	146610934	146610935	+	1	NA	Intergenic	Intergenic	-64061	NR_045468	67524	Mm.444300	NR_045468	ENSMUSG00000086046	1700095A21Rik	-	RIKEN cDNA 1700095A21 gene	ncRNA
mm_119213.1	chr14	33194002	33194008	+	1	NA	Intergenic	Intergenic	-8939	NM_001146022	545030	Mm.318345	NM_001146022	ENSMUSG00000051506	Wdfy4	Gm18810	WD repeat and FYVE domain containing 4	protein-coding
mm_93672.1	chr10	117710229	117710303	-	1	NA	intron (NM_001288586, intron 1 of 10)	CpG-1528	492	NM_010786	17246	Mm.22670	NM_010786	ENSMUSG00000020184	Mdm2	1700007J15Rik|AA415488|Mdm-2	transformed mouse 3T3 cell double minute 2	protein-coding
mm_80351.1	chr9	75184275	75184285	+	1	NA	exon (NM_010864, exon 26 of 41)	exon (NM_010864, exon 26 of 41)	-47734	NM_001081322	208943	Mm.41339	NM_001081322	ENSMUSG00000033590	Myo5c	9130003O20Rik|BB085560|C330029I24	myosin VC	protein-coding
mm_7083.1	chr1	88462613	88462624	-	1	NA	Intergenic	Intergenic	47448	NM_008132	14659	Mm.5187	NM_008132	ENSMUSG00000062310	Glrp1	GRP-1	glutamine repeat protein 1	protein-coding
mm_154392.1	chrM	13024	13055	+	1	NA	NA	Intergenic	NA	NA								
mm_165586.1	chr3	32426094	32426096	+	1	NA	Intergenic	Intergenic	-10056	NM_008839	18706	Mm.260521	NM_008839	ENSMUSG00000027665	Pik3ca	6330412C24Rik|caPI3K|p110|p110alpha	phosphatidylinositol 3-kinase, catalytic, alpha polypeptide	protein-coding
mm_159706.1	chr5	30155013	30155013	-	1	NA	promoter-TSS (NM_001289798)	promoter-TSS (NM_001289798)	-33	NM_178878	97212	Mm.200497	NM_178878	ENSMUSG00000025745	Hadha	C77020|Mtpa	hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), alpha subunit	protein-coding
mm_167009.1	chr7	55842367	55842373	+	1	NA	intron (NM_011370, intron 1 of 30)	CpG	299	NM_001164661	20430	Mm.37249	NM_011370	ENSMUSG00000030447	Cyfip1	E030028J09Rik|P140SRA-1|P140sra1|Shyc|Sra-1|Sra1|l(7)1Rl|l71Rl|l7Rl1|mKIAA0068|pl-1	cytoplasmic FMR1 interacting protein 1	protein-coding
mm_72079.1	chr8	71570582	71570601	+	1	NA	intron (NM_011977, intron 2 of 13)	CpG	1664	NM_011977	26457	Mm.38165	NM_011977	ENSMUSG00000031808	Slc27a1	FATP1|Fatp	solute carrier family 27 (fatty acid transporter), member 1	protein-coding
mm_101901.1	chr11	49187111	49187124	-	1	NA	promoter-TSS (NM_172793)	promoter-TSS (NM_172793)	-28	NM_172793	237754	Mm.130787	NM_172793	ENSMUSG00000040283	Btnl9	B430208I01|Btn3|D330012D11Rik	butyrophilin-like 9	protein-coding
mm_68774.1	chr7	122046902	122046911	-	1	NA	intron (NM_026140, intron 4 of 8)	intron (NM_026140, intron 4 of 8)	20180	NM_026140	67417	Mm.45171	NM_026140	ENSMUSG00000030871	Ears2	3230401I01Rik|mKIAA1970	glutamyl-tRNA synthetase 2, mitochondrial	protein-coding
mm_51022.1	chr6	65042909	65042911	+	1	NA	promoter-TSS (NM_001253392)	promoter-TSS (NM_001253392)	243	NM_007958	13990	Mm.99113	NM_007958	ENSMUSG00000029920	Smarcad1	AV081750|AW226546|D6Pas1|Etl1|mKIAA1122	SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1	protein-coding
mm_170906.1	chr2	30845645	30845652	+	1	NA	exon (NM_009116, exon 1 of 4)	exon (NM_009116, exon 1 of 4)	281	NM_009116	20204	Mm.1802	NM_009116	ENSMUSG00000039476	Prrx2	Prx2|S8	paired related homeobox 2	protein-coding
mm_161096.1	chr12	98532121	98532121	-	1	NA	intron (NM_029911, intron 1 of 6)	intron (NM_029911, intron 1 of 6)	8277	NR_136759	105245437	Mm.446375	NR_136759		Gm40893	-	predicted gene, 40893	ncRNA
mm_26223.1	chr3	138903002	138903012	+	1	NA	non-coding (NR_121195, exon 8 of 8)	non-coding (NR_121195, exon 8 of 8)	160799	NM_019571	56224	Mm.31927	NM_019571	ENSMUSG00000028152	Tspan5	2810455A09Rik|4930505M03Rik|NET-4|Tm4sf9	tetraspanin 5	protein-coding
mm_59136.1	chr7	24082187	24082198	+	1	NA	5' UTR (NM_172483, exon 1 of 3)	5' UTR (NM_172483, exon 1 of 3)	295	NM_001289637	210135	Mm.32254	NM_172483	ENSMUSG00000057101	Zfp180	2310040I01Rik|AI852378|D130011P11|HHZ168	zinc finger protein 180	protein-coding
mm_85011.1	chr9	87704869	87704879	-	1	NA	3' UTR (NM_023814, exon 8 of 8)	3' UTR (NM_023814, exon 8 of 8)	26386	NM_023814	76365	Mm.158789	NM_023814	ENSMUSG00000032419	Tbx18	2810012F10Rik|2810404D13Rik	T-box18	protein-coding
mm_124345.1	chr14	103844449	103844464	-	1	NA	promoter-TSS (NM_001136061)	promoter-TSS (NM_001136061)	20	NM_001136061	13618	Mm.229532	NM_007904	ENSMUSG00000022122	Ednrb	ET-B|ET-BR|ETR-b|ETb|Sox10m1	endothelin receptor type B	protein-coding
mm_122327.1	chr14	37098212	37098280	-	1	NA	promoter-TSS (NM_130878)	promoter-TSS (NM_130878)	65	NM_130878	170677	Mm.156506	NM_130878	ENSMUSG00000021803	Cdhr1	Pcdh21|Prcad|mKIAA1775	cadherin-related family member 1	protein-coding
mm_87843.1	chr10	60426079	60426080	+	1	NA	intron (NR_045556, intron 20 of 68)	intron (NR_045556, intron 20 of 68)	26353	NM_001164374	100302688	Mm.444135	NM_001164374	ENSMUSG00000090439	Gm17455	-	predicted gene, 17455	protein-coding
mm_126185.1	chr15	78615823	78615837	+	1	NA	intron (NM_028195, intron 9 of 12)	intron (NM_028195, intron 9 of 12)	18783	NM_028195	72318	Mm.32911	NM_028195	ENSMUSG00000018008	Cyth4	2510004M07Rik|5830469K17Rik|AI467541|Pscd4|mFLJ00017	cytohesin 4	protein-coding
mm_151782.1	chr19	5366270	5366280	-	1	NA	promoter-TSS (NM_027236)	promoter-TSS (NM_027236)	88	NM_001038231	23825	Mm.358649	NM_011793	ENSMUSG00000024844	Banf1	Baf|Bcrp1|L2bp1/Baf	barrier to autointegration factor 1	protein-coding
mm_50475.1	chr6	48988003	48988011	+	1	NA	exon (NM_172888, exon 1 of 5)	exon (NM_172888, exon 1 of 5)	1146	NM_172888	243377	Mm.446302	NM_172888	ENSMUSG00000039215	Svs1	9530003A11	seminal vesicle secretory protein 1	protein-coding
mm_70620.1	chr8	13584142	13584149	+	1	NA	intron (NM_009025, intron 14 of 23)	intron (NM_009025, intron 14 of 23)	-21684	NM_001080781	66501	Mm.46136	NM_025601	ENSMUSG00000031452	1700029H14Rik	-	RIKEN cDNA 1700029H14 gene	protein-coding
mm_65766.1	chr7	28741750	28741777	-	1	NA	promoter-TSS (NM_023637)	promoter-TSS (NM_023637)	18	NM_011885	24030	Mm.358650	NM_011885	ENSMUSG00000045948	Mrps12	AI327385|Rpms12|rps12	mitochondrial ribosomal protein S12	protein-coding
mm_161247.1	chr13	100317702	100317702	-	1	NA	promoter-TSS (NM_021545)	promoter-TSS (NM_021545)	-14	NM_021545	53880	Mm.218759	NM_021545		Naip7	Birc1g|Naip-rs4B|Naip6	NLR family, apoptosis inhibitory protein 7	protein-coding
mm_122898.1	chr14	54952281	54952290	-	1	NA	exon (NM_010856, exon 25 of 39)	exon (NM_010856, exon 25 of 39)	-3143	NR_029724	387204		NR_029724	ENSMUSG00000065432	Mir208a	Mirn208|Mirn208a|mir-208|mir-208a|mmu-mir-208	microRNA 208a	ncRNA
mm_96630.1	chr11	69157085	69157110	+	1	NA	promoter-TSS (NM_009659)	promoter-TSS (NM_009659)	25	NM_009659	11686	Mm.340329	NM_009659	ENSMUSG00000032807	Alox12b	12R-LOX|Aloxe2|e-LOX2	arachidonate 12-lipoxygenase, 12R type	protein-coding
mm_28928.1	chr3	98859730	98859749	-	1	NA	promoter-TSS (NM_001304800)	promoter-TSS (NM_001304800)	55	NM_001304800	15492	Mm.140811	NM_008293	ENSMUSG00000027871	Hsd3b1	3-beta-HSD I|D3Ertd383e	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1	protein-coding
mm_28487.1	chr3	92458716	92458730	-	1	NA	promoter-TSS (NM_011478)	promoter-TSS (NM_011478)	-3	NM_011478	20766	Mm.57092	NM_011478	ENSMUSG00000045539	Sprr3	SPR3	small proline-rich protein 3	protein-coding
mm_136381.1	chr16	92825988	92826000	-	1	NA	promoter-TSS (NM_001111021)	promoter-TSS (NM_001111021)	80	NM_001111021	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_132297.1	chr16	33497906	33497927	+	1	NA	3' UTR (NM_011749, exon 9 of 9)	3' UTR (NM_011749, exon 9 of 9)	-20413	NM_134251	171286	Mm.35253	NM_134251	ENSMUSG00000035506	Slc12a8	CCC9|E330020C02Rik	solute carrier family 12 (potassium/chloride transporters), member 8	protein-coding
mm_96095.1	chr11	60417305	60417330	+	1	NA	promoter-TSS (NM_145427)	promoter-TSS (NM_145427)	172	NM_025757	66771	Mm.29950	NM_025757	ENSMUSG00000018415	Gid4	4933439F18Rik	GID complex subunit 4, VID24 homolog	protein-coding
mm_139517.1	chr17	56584974	56585031	+	1	NA	promoter-TSS (NM_001163300)	promoter-TSS (NM_001163300)	20	NM_001163300	224903	Mm.255066	NM_001163300	ENSMUSG00000071054	Safb	3110021E02Rik|5330423C17Rik|AU018122|D18386|E130307D12|HAP|HET|SAF-B1|SAFB1	scaffold attachment factor B	protein-coding
mm_149223.1	chr19	10018266	10018276	+	1	NA	promoter-TSS (NM_144538)	promoter-TSS (NM_144538)	43	NM_144538	74760	Mm.281969	NM_144538	ENSMUSG00000024663	Rab3il1	1200014K04Rik|AI115013|C76746|Rab3ail1	RAB3A interacting protein (rabin3)-like 1	protein-coding
mm_57034.1	chr6	122333329	122333347	-	1	NA	exon (NM_001271579, exon 5 of 15)	exon (NM_001271579, exon 5 of 15)	6319	NM_001042623	13619	Mm.6822	NM_007905	ENSMUSG00000040669	Phc1	AW557034|Edr|Edr1|Mph1|Rae-28|rae28	polyhomeotic-like 1 (Drosophila)	protein-coding
mm_147483.1	chr18	47248254	47248272	-	1	NA	3' UTR (NM_018744, exon 19 of 19)	3' UTR (NM_018744, exon 19 of 19)	120605	NM_018744	20358	Mm.40909	NM_018744	ENSMUSG00000019647	Sema6a	A730020P05Rik|AI851735|Sema6A-1|Semaq|VIa	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A	protein-coding
mm_167269.1	chr8	31975104	31975109	+	1	NA	Intergenic	Intergenic	-56903	NM_178591	211323	Mm.153432	NM_178591	ENSMUSG00000062991	Nrg1	6030402G23Rik|ARIA|D230005F13Rik|GGF|GGFII|HRG|HRGalpha|Hgl|NDF|SMDF	neuregulin 1	protein-coding
mm_139186.1	chr17	47596062	47596071	+	1	NA	intron (NM_001081635, intron 4 of 6)	intron (NM_001081635, intron 4 of 6)	2599	NM_007632	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_168263.1	chr10	90248955	90248955	+	1	NA	intron (NM_001128086, intron 9 of 24)	L1Md_T|LINE|L1	-326772	NM_001177397	77531	Mm.440605	NM_181398	ENSMUSG00000058589	Anks1b	AIDA-1b|C030032C09Rik|E530015N03Rik|ENSMUSG00000078431|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding
mm_39612.1	chr5	24165049	24165055	+	1	NA	promoter-TSS (NM_153092)	promoter-TSS (NM_153092)	89	NM_001346582	231042	Mm.45513	NM_153092	ENSMUSG00000048439	Nupl2	AV116043|CG1|NLP-1|Nlp1	nucleoporin like 2	protein-coding
mm_138103.1	chr17	34092874	34092891	+	1	NA	intron (NR_046183, intron 2 of 4)	intron (NR_046183, intron 2 of 4)	503	NM_008206	15001	Mm.116	NM_008206	ENSMUSG00000024334	H2-Oa	H-2Oa	histocompatibility 2, O region alpha locus	protein-coding
mm_80897.1	chr9	99828660	99828660	+	1	NA	Intergenic	Intergenic	47510	NM_011440	20669	Mm.261595	NM_011440	ENSMUSG00000053747	Sox14	-	SRY (sex determining region Y)-box 14	protein-coding
mm_154017.1	chr19	53283905	53283915	-	1	NA	Intergenic	MLT1H|LTR|ERVL-MaLR	-26596	NM_001008542	17859	Mm.2154	NM_010847	ENSMUSG00000025025	Mxi1	ENSMUSG00000067085|Gm10197|Mad2|bHLHc11	MAX interactor 1, dimerization protein	protein-coding
mm_18634.1	chr2	69380307	69380317	-	1	NA	promoter-TSS (NM_175512)	promoter-TSS (NM_175512)	-150	NM_175512	241452	Mm.211655	NM_175512	ENSMUSG00000027068	Dhrs9	C730025I08Rik|Rdh15	dehydrogenase/reductase (SDR family) member 9	protein-coding
mm_158265.1	chrX	109013491	109013501	-	1	NA	promoter-TSS (NM_016710)	promoter-TSS (NM_016710)	-116	NM_016710	50887	Mm.298443	NM_016710	ENSMUSG00000031245	Hmgn5	GARP45|NBP-45|Nsbp1	high-mobility group nucleosome binding domain 5	protein-coding
mm_157965.1	chrX	90744799	90744834	-	1	NA	Intergenic	Intergenic	-147326	NM_001101450	212952	Mm.477436	NM_001101450	ENSMUSG00000091497	Gm44	-	predicted gene 44	protein-coding
mm_87443.1	chr10	51481658	51481674	+	1	NA	exon (NM_008147, exon 4 of 9)	exon (NM_008147, exon 4 of 9)	1054	NM_001291892	14727	Mm.439661	NM_008147	ENSMUSG00000062593	Lilr4b	Gp49a|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4B	protein-coding
mm_67026.1	chr7	66378040	66378042	-	1	NA	intron (NM_146191, intron 2 of 33)	intron (NM_146191, intron 2 of 33)	3683	NR_106024	102465640		NR_106024	ENSMUSG00000098353	Mir7057	Gm27550|mmu-mir-7057	microRNA 7057	ncRNA
mm_165043.1	chr19	39038097	39038112	+	1	NA	exon (NM_028089, exon 8 of 9)	exon (NM_028089, exon 8 of 9)	-22902	NM_028191	72303	Mm.482578	NM_028191	ENSMUSG00000067231	Cyp2c65	2210009K14Rik	cytochrome P450, family 2, subfamily c, polypeptide 65	protein-coding
mm_147855.1	chr18	63692393	63692416	-	1	NA	promoter-TSS (NM_016792)	promoter-TSS (NM_016792)	-45	NM_016792	53382	Mm.19169	NM_016792	ENSMUSG00000024583	Txnl1	32kDa|TRP32|Txnl	thioredoxin-like 1	protein-coding
mm_83019.1	chr9	36797304	36797425	-	1	NA	promoter-TSS (NM_001199494)	promoter-TSS (NM_001199494)	29	NM_001199494	13663	Mm.4337	NM_007915	ENSMUSG00000062762	Ei24	AA536736|AI115355|PIG8	etoposide induced 2.4 mRNA	protein-coding
mm_122956.1	chr14	54968083	54968096	-	1	NA	promoter-TSS (NR_033497)	promoter-TSS (NR_033497)	-698	NR_033497	791403	Mm.319176	NR_033497	ENSMUSG00000097652	Mhrt	D830015G02Rik|ENSMUSG00000053118|Myheart	myosin heavy chain associated RNA transcript	ncRNA
mm_38485.1	chr4	140750603	140750618	-	1	NA	exon (NM_011061, exon 12 of 16)	exon (NM_011061, exon 12 of 16)	-7967	NM_153106	242726	Mm.271661	NM_153106	ENSMUSG00000040935	Padi6	Pad6|Padi5|ePAD	peptidyl arginine deiminase, type VI	protein-coding
mm_43672.1	chr5	138775402	138775412	+	1	NA	intron (NM_030565, intron 3 of 9)	intron (NM_030565, intron 3 of 9)	20326	NM_030565	80752	Mm.320355	NM_030565	ENSMUSG00000025854	Fam20c	C76981|DMP-4|DMP4|GEF-CK|mKIAA4081	family with sequence similarity 20, member C	protein-coding
mm_134122.1	chr16	10313923	10313936	-	1	NA	promoter-TSS (NM_007929)	promoter-TSS (NM_007929)	39	NM_007929	13731	Mm.246009	NM_007929	ENSMUSG00000022505	Emp2	XMP	epithelial membrane protein 2	protein-coding
mm_151957.1	chr19	5801375	5801386	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	1292	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_10482.1	chr2	14739251	14739290	+	1	NA	intron (NM_023116, intron 2 of 13)	intron (NM_023116, intron 2 of 13)	18628	NR_028497	625342	Mm.484784	NR_028497		Gm13315	OTTMUSG00000011384	lactate dehydrogenase A pseudogene	pseudo
mm_95800.1	chr11	55109373	55109383	+	1	NA	exon (NM_010299, exon 4 of 4)	exon (NM_010299, exon 4 of 4)	11393	NM_010299	14667	Mm.287807	NM_010299	ENSMUSG00000000594	Gm2a	AA408702|AW215435|GM2-AP|SAP-3	GM2 ganglioside activator protein	protein-coding
mm_61700.1	chr7	81213259	81213284	+	1	NA	promoter-TSS (NM_008803)	promoter-TSS (NM_008803)	-533	NM_008803	18584	Mm.371577	NM_008803	ENSMUSG00000025584	Pde8a	AI551852|Pde8	phosphodiesterase 8A	protein-coding
mm_165657.1	chr3	87487393	87487396	+	1	NA	intron (NM_001113238, intron 11 of 11)	intron (NM_001113238, intron 11 of 11)	-38184	NM_001083318	27049	Mm.219460	NM_012051	ENSMUSG00000003382	Etv3	AI414410|METS|Pe1	ets variant 3	protein-coding
mm_162133.1	chrX	73214338	73214338	+	1	NA	promoter-TSS (NM_021365)	promoter-TSS (NM_021365)	5	NM_001293679	27083	Mm.104764	NM_021365	ENSMUSG00000067768	Xlr4b	Xlr4	X-linked lymphocyte-regulated 4B	protein-coding
mm_73495.1	chr8	107150622	107150690	+	1	NA	promoter-TSS (NM_025558)	promoter-TSS (NM_025558)	-5	NM_025558	66427	Mm.20242	NM_025558	ENSMUSG00000031924	Cyb5b	1810044O22Rik|AU015618|Cyb5m	cytochrome b5 type B	protein-coding
mm_64775.1	chr7	4996185	4996195	-	1	NA	promoter-TSS (NM_026741)	promoter-TSS (NM_026741)	-89	NM_026741	68490	Mm.76400	NM_026741	ENSMUSG00000051550	Zfp579	1110003A17Rik|Znf579	zinc finger protein 579	protein-coding
mm_134081.1	chr16	8721713	8721717	-	1	NA	intron (NM_001003918, intron 1 of 30)	intron (NM_001003918, intron 1 of 30)	16627	NM_001003918	252870	Mm.295330	NM_001003918	ENSMUSG00000022710	Usp7	2210010O09Rik|AA409944|AA617399|AU019296|AW548146|C80752|Hausp	ubiquitin specific peptidase 7	protein-coding
mm_90750.1	chr10	5488244	5488255	-	1	NA	promoter-TSS (NM_001347711)	promoter-TSS (NM_001347711)	65	NM_001347711	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_73972.1	chr8	120506013	120506023	+	1	NA	intron (NM_198671, intron 1 of 15)	intron (NM_198671, intron 1 of 15)	17152	NM_198671	382034	Mm.334856	NM_198671	ENSMUSG00000031822	Gse1	2210013I18Rik|mKIAA0182	genetic suppressor element 1, coiled-coil protein	protein-coding
mm_147638.1	chr18	60269583	60269605	-	1	NA	3' UTR (NM_001034859, exon 2 of 2)	3' UTR (NM_001034859, exon 2 of 2)	3673	NM_001034859	225594	Mm.329460	NM_001034859	ENSMUSG00000068606	Gm4841	EG225594|Ifgga3	predicted gene 4841	protein-coding
mm_47387.1	chr5	122994442	122994455	-	1	NA	non-coding (NR_045820, exon 2 of 3)	non-coding (NR_045820, exon 2 of 3)	5094	NR_045820	109202	Mm.30769	NM_175405	ENSMUSG00000056735	A930024E05Rik	-	RIKEN cDNA A930024E05 gene	ncRNA
mm_95919.1	chr11	58221050	58221074	+	1	NA	3' UTR (NM_019440, exon 2 of 2)	3' UTR (NM_019440, exon 2 of 2)	6085	NM_019440	54396	Mm.458517	NM_019440	ENSMUSG00000069874	Irgm2	AI481100|GTPI|Ifggd2|Iigp2	immunity-related GTPase family M member 2	protein-coding
mm_18548.1	chr2	65022741	65022816	-	1	NA	promoter-TSS (NM_016719)	promoter-TSS (NM_016719)	-12	NM_016719	50915	Mm.214554	NM_016719	ENSMUSG00000026888	Grb14	AI505286	growth factor receptor bound protein 14	protein-coding
mm_108323.1	chr12	79766883	79766924	+	1	NA	intron (NM_009014, intron 8 of 10)	intron (NM_009014, intron 8 of 10)	157830	NR_131075	77290	Mm.395042	NR_131073		9430078K24Rik	-	RIKEN cDNA 9430078K24 gene	ncRNA
mm_118181.1	chr13	107022069	107022138	-	1	NA	promoter-TSS (NM_008442)	promoter-TSS (NM_008442)	11	NM_001145779	16563	Mm.355686	NM_008442	ENSMUSG00000021693	Kif2a	C530030B14Rik|Kif2|Kns2|M-kinesin	kinesin family member 2A	protein-coding
mm_154891.1	chrX	20845373	20845380	+	1	NA	Intergenic	B4A|SINE|B4	-3167	NM_009703	11836	Mm.220946	NM_009703	ENSMUSG00000001127	Araf	1200013E08Rik|A-Raf|AW495444|Araf1	Araf proto-oncogene, serine/threonine kinase	protein-coding
mm_52368.1	chr6	113046305	113046369	+	1	NA	promoter-TSS (NM_008188)	promoter-TSS (NM_008188)	10	NM_008188	14911	Mm.781	NM_008188	ENSMUSG00000030264	Thumpd3	AW556087|Gt(ROSA)26asSor|Gtrosa26as	THUMP domain containing 3	protein-coding
mm_141066.1	chr17	25795640	25795664	-	1	NA	intron (NM_133719, intron 2 of 3)	intron (NM_133719, intron 2 of 3)	1393	NM_133719	70083	Mm.41925	NM_133719	ENSMUSG00000002274	Metrn	1810034B16Rik|Hyrac	meteorin, glial cell differentiation regulator	protein-coding
mm_59138.1	chr7	24134149	24134184	+	1	NA	promoter-TSS (NM_019941)	promoter-TSS (NM_019941)	3	NM_019941	56525	Mm.295595	NM_019941	ENSMUSG00000047603	Zfp235	0610030O19Rik|AI428448	zinc finger protein 235	protein-coding
mm_141057.1	chr17	25754049	25754069	-	1	NA	intron (NM_018857, intron 1 of 15)	intron (NM_018857, intron 1 of 15)	268	NM_018857	56047	Mm.17510	NM_018857	ENSMUSG00000063011	Msln	MPF	mesothelin	protein-coding
mm_11678.1	chr2	35461503	35461516	+	1	NA	promoter-TSS (NM_001145821)	promoter-TSS (NM_001145821)	-60	NM_001145821	14594	Mm.281124	NM_010283	ENSMUSG00000035778	Ggta1	AW108479|GALT|Gal|Ggta|Ggta-1|alpha Gal|alpha3GalT	glycoprotein galactosyltransferase alpha 1, 3	protein-coding
mm_118926.1	chr14	27038989	27038993	+	1	NA	promoter-TSS (NM_134437)	promoter-TSS (NM_134437)	-10	NM_134437	171463	Mm.206726	NM_027265	ENSMUSG00000040717	Il17rd	2810004A10Rik|AI428510|Sef|Sef-S	interleukin 17 receptor D	protein-coding
mm_121191.1	chr14	103050302	103050317	+	1	NA	intron (NM_008392, intron 3 of 4)	GA-rich|Low_complexity|Low_complexity	3297	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_14636.1	chr2	136781823	136781827	+	1	NA	3' UTR (NM_001291056, exon 8 of 8)	3' UTR (NM_001291056, exon 8 of 8)	68375	NM_001291056	20614	Mm.45953	NM_011428	ENSMUSG00000027273	Snap25	Bdr|GENA70|SNAP-25|SUP|sp	synaptosomal-associated protein 25	protein-coding
mm_16983.1	chr2	18047816	18047846	-	1	NA	exon (NM_028317, exon 1 of 1)	exon (NM_028317, exon 1 of 1)	618	NM_028317	72668	Mm.102183	NM_028317	ENSMUSG00000054074	Skida1	2810030E01Rik|5730507N06Rik|BB088113	SKI/DACH domain containing 1	protein-coding
mm_88827.1	chr10	80804125	80804150	+	1	NA	exon (NM_013651, exon 9 of 9)	exon (NM_013651, exon 9 of 9)	-1111	NM_007445	11705	Mm.376094	NM_007445	ENSMUSG00000035262	Amh	MIS	anti-Mullerian hormone	protein-coding
mm_85444.1	chr9	104262247	104262267	-	1	NA	intron (NM_001163026, intron 1 of 55)	(A)n|Simple_repeat|Simple_repeat	673	NM_001163026	235567	Mm.217256	NM_001163026	ENSMUSG00000032560	Dnajc13	D030002L11Rik|Gm1124|RME-8|Rme8|mKIAA0678	DnaJ heat shock protein family (Hsp40) member C13	protein-coding
mm_97916.1	chr11	83525985	83525999	+	1	NA	exon (NM_013653, exon 3 of 3)	exon (NM_013653, exon 3 of 3)	-3893	NM_001045543	629303	Mm.390417	NM_001045543	ENSMUSG00000018925	Heatr9	Gm11435|OTTMUSG00000000990	HEAT repeat containing 9	protein-coding
mm_56874.1	chr6	118861461	118861465	-	1	NA	intron (NM_001256002, intron 3 of 47)	intron (NM_001256002, intron 3 of 47)	-18695	NR_046053	74363	Mm.399403	NR_046053		4931430N09Rik	-	RIKEN cDNA 4931430N09 gene	ncRNA
mm_409.1	chr1	34215285	34215298	+	1	NA	intron (NM_001276764, intron 53 of 102)	intron (NM_001276764, intron 53 of 102)	54961	NM_010081	13518	Mm.336625	NM_010081	ENSMUSG00000026131	Dst	2310001O04Rik|A830042E19Rik|AW554249|BP230|BPAG1-n|Bpag|Bpag1|Macf2|ah|athetoid|dt|mKIAA0728|nmf203|nmf339	dystonin	protein-coding
mm_65342.1	chr7	24987515	24987537	-	1	NA	TTS (NR_106014)	TTS (NR_106014)	141	NR_106014	102465634		NR_106014	ENSMUSG00000099258	Mir7047	Gm27270|mmu-mir-7047	microRNA 7047	ncRNA
mm_169740.1	chr15	85034235	85034245	+	1	NA	Intergenic	ERVB7_2B-LTR_MM|LTR|ERVK	-2822	NM_133750	73225	Mm.247535	NM_133750	ENSMUSG00000022434	Fam118a	-	family with sequence similarity 118, member A	protein-coding
mm_168560.1	chr1	168885029	168885046	-	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	394394	NR_105766	102465178		NR_105766	ENSMUSG00000098407	Mir6348	Gm27412|mmu-mir-6348	microRNA 6348	ncRNA
mm_31392.1	chr4	48043856	48043864	+	1	NA	Intergenic	Intergenic	-1445	NM_015743	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_53507.1	chr6	135368964	135368993	+	1	NA	intron (NM_001288627, intron 1 of 4)	B4|SINE|B4	1485	NM_001288627	13730	Mm.182785	NM_010128	ENSMUSG00000030208	Emp1	I-8-09|TMP	epithelial membrane protein 1	protein-coding
mm_152767.1	chr19	20536748	20536763	-	1	NA	non-coding (NR_045778, exon 3 of 3)	non-coding (NR_045778, exon 3 of 3)	15575	NR_045778	320155	Mm.447252	NR_045778		C730002L08Rik	-	RIKEN cDNA C730002L08 gene	ncRNA
mm_52534.1	chr6	115853601	115853615	+	1	NA	promoter-TSS (NM_031177)	promoter-TSS (NM_031177)	80	NM_031177	81896	Mm.333335	NM_031177	ENSMUSG00000030323	Ift122	C86139|Wdr10|sopb	intraflagellar transport 122	protein-coding
mm_42511.1	chr5	115542945	115542956	+	1	NA	intron (NM_133915, intron 1 of 11)	intron (NM_133915, intron 1 of 11)	-16517	NM_007475	11837	Mm.5286	NM_007475	ENSMUSG00000067274	Rplp0	36B4|Arbp|L10E	ribosomal protein, large, P0	protein-coding
mm_31375.1	chr4	47409823	47409826	+	1	NA	intron (NM_001312869, intron 7 of 7)	intron (NM_001312869, intron 7 of 7)	23608	NM_001312869	21812	Mm.197552	NM_009370	ENSMUSG00000007613	Tgfbr1	ALK5|AU017191|Alk-5|ESK2|TGFR-1|TbetaR-I|TbetaRI	transforming growth factor, beta receptor I	protein-coding
mm_134428.1	chr16	17925700	17925713	-	1	NA	3' UTR (NM_153150, exon 9 of 9)	3' UTR (NM_153150, exon 9 of 9)	2513	NM_153150	13358	Mm.229291	NM_153150	ENSMUSG00000003528	Slc25a1	1300019P08Rik|2610100G11Rik|AI194714|Ctp|Dgsj|Slc20a3	solute carrier family 25 (mitochondrial carrier, citrate transporter), member 1	protein-coding
mm_35222.1	chr4	19659649	19659662	-	1	NA	exon (NM_177327, exon 8 of 25)	exon (NM_177327, exon 8 of 25)	49349	NM_177327	107568	Mm.78312	NM_177327	ENSMUSG00000041058	Wwp1	8030445B08Rik|AIP5|SDRP1|Tiul1	WW domain containing E3 ubiquitin protein ligase 1	protein-coding
mm_59404.1	chr7	26835338	26835343	+	1	NA	promoter-TSS (NM_007812)	promoter-TSS (NM_007812)	1	NM_007812	13087	Mm.389848	NM_007812	ENSMUSG00000005547	Cyp2a5	CYPIIA5|Coh|Cyp15a2	cytochrome P450, family 2, subfamily a, polypeptide 5	protein-coding
mm_116979.1	chr13	56288917	56288963	-	1	NA	3' UTR (NM_019568, exon 4 of 4)	3' UTR (NM_019568, exon 4 of 4)	7611	NM_019568	57266	Mm.30211	NM_019568	ENSMUSG00000021508	Cxcl14	1110031L23Rik|1200006I23Rik|AI414372|BMAC|BRAK|KS1|Kec|MIP-2g|MIP2gamma|NJAC|Scyb14|bolekine	chemokine (C-X-C motif) ligand 14	protein-coding
mm_2692.1	chr1	127729431	127729435	+	1	NA	promoter-TSS (NM_001033041)	promoter-TSS (NM_001033041)	20	NM_001033041	266645	Mm.25735	NM_001033041	ENSMUSG00000026348	Acmsd	-	amino carboxymuconate semialdehyde decarboxylase	protein-coding
mm_171188.1	chr3	43250377	43250393	+	1	NA	Intergenic	Intergenic	1507767	NM_027271	73852	Mm.29006	NM_027271	ENSMUSG00000025766	D3Ertd751e	2810009O15Rik|4930415G15Rik	DNA segment, Chr 3, ERATO Doi 751, expressed	protein-coding
mm_79347.1	chr9	53667087	53667130	+	1	NA	exon (NM_001161618, exon 1 of 18)	exon (NM_001161618, exon 1 of 18)	399	NM_001161618	75717	Mm.218910	NM_027807	ENSMUSG00000032030	Cul5	4921514I20Rik|8430423K24Rik|AI852817|C030032G03Rik|C330021I08Rik|VACM-1|VACM1	cullin 5	protein-coding
mm_63018.1	chr7	121032792	121032802	+	1	NA	Intergenic	Intergenic	-1648	NM_021554	59052	Mm.29122	NM_021554	ENSMUSG00000030876	Mettl9	0610012D09Rik|AA517660|Drev|MNCb-5680	methyltransferase like 9	protein-coding
mm_124680.1	chr15	6429686	6429708	+	1	NA	exon (NM_023118, exon 10 of 15)	exon (NM_023118, exon 10 of 15)	-15636	NM_013485	12279	Mm.29095	NM_013485	ENSMUSG00000022149	C9	-	complement component 9	protein-coding
mm_96415.1	chr11	67255627	67255642	+	1	NA	exon (NM_010855, exon 32 of 40)	exon (NM_010855, exon 32 of 40)	17822	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_42350.1	chr5	114911436	114911446	+	1	NA	3' UTR (NM_011854, exon 6 of 6)	3' UTR (NM_011854, exon 6 of 6)	-11799	NM_145209	231655	Mm.95479	NM_145209	ENSMUSG00000041827	Oasl1	7530414C13Rik|oasl9	2'-5' oligoadenylate synthetase-like 1	protein-coding
mm_116685.1	chr13	49287914	49287957	-	1	NA	intron (NM_015759, intron 4 of 17)	B4A|SINE|B4	21273	NM_015759	30938	Mm.291089	NM_015759	ENSMUSG00000037946	Fgd3	5830461L01Rik|ZFYVE5	FYVE, RhoGEF and PH domain containing 3	protein-coding
mm_26004.1	chr3	135281275	135281299	+	1	NA	promoter-TSS (NM_027208)	promoter-TSS (NM_027208)	66	NM_027208	69772	Mm.45121	NM_027208	ENSMUSG00000028167	Bdh2	1810026B04Rik|Dhrs6	3-hydroxybutyrate dehydrogenase, type 2	protein-coding
mm_94708.1	chr11	20316692	20316695	+	1	NA	intron (NM_018861, intron 3 of 7)	intron (NM_018861, intron 3 of 7)	16020	NM_018861	55963	Mm.6379	NM_018861	ENSMUSG00000020142	Slc1a4	ASCT-1|ASCT1|AW045657|SATT	solute carrier family 1 (glutamate/neutral amino acid transporter), member 4	protein-coding
mm_12417.1	chr2	70561987	70562003	+	1	NA	promoter-TSS (NM_008077)	promoter-TSS (NM_008077)	-134	NM_001312900	14415	Mm.272120	NM_008077	ENSMUSG00000070880	Gad1	EP10|Gad-1	glutamate decarboxylase 1	protein-coding
mm_133116.1	chr16	65649413	65649419	+	1	NA	Intergenic	Intergenic	-86719	NM_026879	68942	Mm.432944	NM_026879	ENSMUSG00000004843	Chmp2b	1190006E07Rik	charged multivesicular body protein 2B	protein-coding
mm_1991.1	chr1	87125968	87125977	+	1	NA	exon (NM_007432, exon 5 of 11)	exon (NM_007432, exon 5 of 11)	964	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_146817.1	chr18	20945768	20945775	-	1	NA	intron (NM_026301, intron 1 of 5)	intron (NM_026301, intron 1 of 5)	1146	NM_026301	67664	Mm.45980	NM_026301	ENSMUSG00000033107	Rnf125	4930553F04Rik	ring finger protein 125	protein-coding
mm_68172.1	chr7	103826571	103826579	-	1	NA	TTS (NM_001278161)	TTS (NM_001278161)	1353	NM_001201391	100503605	Mm.288567	NM_001201391	ENSMUSG00000052305	Hbb-bs	Beta-s|Hbbt1|Hbbt2	hemoglobin, beta adult s chain	protein-coding
mm_160303.1	chr7	139213166	139213166	-	1	NA	promoter-TSS (NM_001143755)	promoter-TSS (NM_001143755)	-109	NM_001143755	76612	Mm.17757	NM_027164	ENSMUSG00000015980	Lrrc27	1700071K18Rik|2310044E02Rik	leucine rich repeat containing 27	protein-coding
mm_130234.1	chr15	96460936	96460993	-	1	NA	promoter-TSS (NM_028148)	promoter-TSS (NM_028148)	-121	NM_028148	72193	Mm.324474	NM_028148	ENSMUSG00000033228	Scaf11	1110061H03Rik|2610510E10Rik|AI462454|CASP11|SIP1|SRRP129|Sfrs2ip|Srsf2ip|mKIAA3013	SR-related CTD-associated factor 11	protein-coding
mm_96767.1	chr11	69921780	69921839	+	1	NA	promoter-TSS (NM_001166592)	promoter-TSS (NM_001166592)	149	NM_001166593	276770	Mm.18026	NM_181582	ENSMUSG00000078812	Eif5a	AA410058|D19Wsu54e|Eif4d|Eif5a1|eIF-4D|eIF-5A|eIF-5A-1|eIF-5A1	eukaryotic translation initiation factor 5A	protein-coding
mm_40816.1	chr5	72203379	72203388	+	1	NA	promoter-TSS (NR_003966)	promoter-TSS (NR_003966)	40	NM_153389	231287	Mm.32775	NM_153389	ENSMUSG00000046808	Atp10d	9830145H18Rik|ATPVD|D5Buc24e	ATPase, class V, type 10D	protein-coding
mm_15665.1	chr2	163323376	163323390	+	1	NA	TTS (NM_001098799)	TTS (NM_001098799)	74590	NM_021566	59091	Mm.34459	NM_021566	ENSMUSG00000017817	Jph2	1110002E14Rik|JP-2|Jp2	junctophilin 2	protein-coding
mm_106372.1	chr11	118401827	118401964	-	1	NA	promoter-TSS (NM_011150)	promoter-TSS (NM_011150)	36	NM_011150	19039	Mm.3152	NM_011150	ENSMUSG00000033880	Lgals3bp	90K|CyCAP|MAC-2BP|Ppicap|Tango10b	lectin, galactoside-binding, soluble, 3 binding protein	protein-coding
mm_64776.1	chr7	5013245	5013264	-	1	NA	promoter-TSS (NM_001110330)	promoter-TSS (NM_001110330)	-12	NM_001110330	23877	Mm.38911	NM_011813	ENSMUSG00000061374	Fiz1	AI790204|mFLJ00416	Flt3 interacting zinc finger protein 1	protein-coding
mm_33883.1	chr4	136172946	136172956	+	1	NA	exon (NM_177733, exon 1 of 7)	exon (NM_177733, exon 1 of 7)	677	NM_177733	242705	Mm.307932	NM_177733	ENSMUSG00000018983	E2f2	E2F-2	E2F transcription factor 2	protein-coding
mm_126923.1	chr15	91673051	91673059	+	1	NA	promoter-TSS (NM_025730)	promoter-TSS (NM_025730)	-169	NM_025730	66725	Mm.37558	NM_025730	ENSMUSG00000036273	Lrrk2	4921513O20Rik|9330188B09Rik|AW561911|D630001M17Rik|Gm927|cI-46	leucine-rich repeat kinase 2	protein-coding
mm_98346.1	chr11	93100190	93100201	+	1	NA	5' UTR (NM_028296, exon 1 of 9)	5' UTR (NM_028296, exon 1 of 9)	905	NM_028296	72605	Mm.342160	NM_028296	ENSMUSG00000056158	Car10	2700029L05Rik|BB085816|Ca10	carbonic anhydrase 10	protein-coding
mm_129628.1	chr15	80219375	80219389	-	1	NA	Intergenic	Intergenic	-14698	NM_178719	239555	Mm.307163	NM_178719	ENSMUSG00000022412	Mief1	A230016E22|AI452372|Smcr7l	mitochondrial elongation factor 1	protein-coding
mm_108436.1	chr12	82339697	82339703	+	1	NA	intron (NM_172579, intron 1 of 20)	intron (NM_172579, intron 1 of 20)	28351	NM_172579	217692	Mm.261333	NM_172579	ENSMUSG00000042700	Sipa1l1	4931426N11Rik|AW213287|Spar|mKIAA0440	signal-induced proliferation-associated 1 like 1	protein-coding
mm_38584.1	chr4	141820104	141820113	-	1	NA	intron (NM_007919, intron 5 of 7)	URR1A|DNA|hAT-Charlie	5897	NM_007919	13706	Mm.45316	NM_007919	ENSMUSG00000058579	Cela2a	Ela-2|Ela2|Ela2a	chymotrypsin-like elastase family, member 2A	protein-coding
mm_64778.1	chr7	5014646	5014684	-	1	NA	promoter-TSS (NM_001110329)	promoter-TSS (NM_001110329)	32	NM_001110328	23877	Mm.38911	NM_011813	ENSMUSG00000061374	Fiz1	AI790204|mFLJ00416	Flt3 interacting zinc finger protein 1	protein-coding
mm_98968.1	chr11	98682614	98682624	+	1	NA	promoter-TSS (NM_009439)	promoter-TSS (NM_009439)	65	NM_009439	22123	Mm.12194	NM_009439	ENSMUSG00000017221	Psmd3	AI255837|AntP91a|D11Bwg1349e|Psd3|Tstap91a	proteasome (prosome, macropain) 26S subunit, non-ATPase, 3	protein-coding
mm_76117.1	chr8	80835327	80835331	-	1	NA	intron (NM_021356, intron 1 of 9)	intron (NM_021356, intron 1 of 9)	45150	NM_021356	14388	Mm.277409	NM_021356	ENSMUSG00000031714	Gab1	AA408973|AW107238	growth factor receptor bound protein 2-associated protein 1	protein-coding
mm_41229.1	chr5	88720880	88720925	+	1	NA	promoter-TSS (NM_026735)	promoter-TSS (NM_026735)	31	NM_026735	68473	Mm.35764	NM_026735	ENSMUSG00000006262	Mob1b	1110003E08Rik|AU015450|B230364F10|Mobkl1a	MOB kinase activator 1B	protein-coding
mm_80800.1	chr9	96259009	96259013	+	1	NA	promoter-TSS (NM_001184710)	promoter-TSS (NM_001184710)	-237	NM_001184711	211586	Mm.17977	NM_178667	ENSMUSG00000032411	Tfdp2	1110029I05Rik|A330080J22Rik|DP-3|DP3	transcription factor Dp 2	protein-coding
mm_129474.1	chr15	78710795	78710806	-	1	NA	intron (NM_183141, intron 1 of 1)	(GGGA)n|Simple_repeat|Simple_repeat	7313	NM_183141	207393	Mm.323188	NM_183141	ENSMUSG00000043460	Elfn2	6330514E13|AW048948|BC094219|Lrrc62|Ppp1r29	leucine rich repeat and fibronectin type III, extracellular 2	protein-coding
mm_116998.1	chr13	56703944	56703954	-	1	NA	intron (NM_001164042, intron 1 of 6)	intron (NM_001164042, intron 1 of 6)	281	NM_001164042	17129	Mm.272920	NM_008541	ENSMUSG00000021540	Smad5	1110051M15Rik|AI451355|Dwf-C|Madh5|MusMLP	SMAD family member 5	protein-coding
mm_44271.1	chr5	5694270	5694312	-	1	NA	promoter-TSS (NM_001103156)	promoter-TSS (NM_001103156)	35	NM_001285469	74051	Mm.274956	NM_028734	ENSMUSG00000015653	Steap2	4921538B17Rik|AI930049|AW045895|IPCA-1|IPCA1|PCANAP1|STAMP1|STMP	six transmembrane epithelial antigen of prostate 2	protein-coding
mm_164071.1	chr14	120278953	120278965	-	1	NA	intron (NM_175341, intron 1 of 8)	intron (NM_175341, intron 1 of 8)	3290	NM_175341	105559	Mm.238266	NM_175341	ENSMUSG00000022139	Mbnl2	1110002M11Rik|AI047808|AI837313|AI849185|AL118326|MBLL|R75232|mKIAA4072	muscleblind-like 2	protein-coding
mm_4535.1	chr1	175880776	175880808	+	1	NA	promoter-TSS (NM_012012)	promoter-TSS (NM_012012)	14	NM_012012	26909	Mm.283046	NM_012012	ENSMUSG00000039748	Exo1	5730442G03Rik|Msa	exonuclease 1	protein-coding
mm_48842.1	chr5	149367098	149367102	-	1	NA	Intergenic	Intergenic	-44706	NM_027519	70717	Mm.252139	NM_027519	ENSMUSG00000029659	Medag	6330406I15Rik|Awms3|MEDA-4|Meda4|mAWMS3	mesenteric estrogen dependent adipogenesis	protein-coding
mm_120195.1	chr14	61599571	61599584	+	1	NA	promoter-TSS (NM_023233)	promoter-TSS (NM_023233)	65	NM_023233	66597	Mm.491258	NM_023233	ENSMUSG00000035235	Trim13	3110001L12Rik|CAR|LEU5|RNF77|Rfp2	tripartite motif-containing 13	protein-coding
mm_137012.1	chr17	17831077	17831095	+	1	NA	TTS (NR_029539)	TTS (NR_029539)	111	NM_001162909	75202	Mm.227456	NM_029205	ENSMUSG00000080316	Spaca6	4930546H06Rik|9530079D04Rik|B230206P06Rik|Ncrna00085|SPACA6A|let-7e|mir-125a|mir-99b	sperm acrosome associated 6	protein-coding
mm_90339.1	chr10	127086897	127086906	+	1	NA	intron (NM_001033263, intron 7 of 18)	intron (NM_001033263, intron 7 of 18)	7994	NM_001033263	216439	Mm.336761	NM_001033263	ENSMUSG00000025422	Agap2	AGAP-2|Centg1|PIKE|cnt-g1|mKIAA0167	ArfGAP with GTPase domain, ankyrin repeat and PH domain 2	protein-coding
mm_142480.1	chr17	45686855	45686882	-	1	NA	promoter-TSS (NM_198167)	promoter-TSS (NM_198167)	496	NM_026732	68463	Mm.379158	NM_026732	ENSMUSG00000023939	Mrpl14	1110006I11Rik|AI846816|MRP-L32|Rpml32	mitochondrial ribosomal protein L14	protein-coding
mm_45810.1	chr5	87671029	87671053	-	1	NA	exon (NM_007784, exon 7 of 34)	exon (NM_007784, exon 7 of 34)	4833	NM_001286016	12990	Mm.427467	NM_007784	ENSMUSG00000070702	Csn1s1	AA959832|AW212882|Csna	casein alpha s1	protein-coding
mm_150344.1	chr19	34613027	34613040	+	1	NA	3' UTR (NM_001005858, exon 2 of 2)	3' UTR (NM_001005858, exon 2 of 2)	5076	NM_001005858	667370	Mm.271850	NM_001005858	ENSMUSG00000062488	Ifit3b	I830012O16Rik	interferon-induced protein with tetratricopeptide repeats 3B	protein-coding
mm_108955.1	chr12	102368282	102368321	+	1	NA	intron (NM_177620, intron 5 of 9)	intron (NM_177620, intron 5 of 9)	71512	NM_011175	19141	Mm.17185	NM_011175	ENSMUSG00000021190	Lgmn	AEP|AI746452|AU022324|Prsc1	legumain	protein-coding
mm_162469.1	chr1	132007890	132007903	-	1	NA	5' UTR (NM_007923, exon 1 of 5)	5' UTR (NM_007923, exon 1 of 5)	291	NM_007923	13714	Mm.254233	NM_007923	ENSMUSG00000026436	Elk4	2310011G17Rik|A130026I01Rik|BB162516|SAP-1|Sap1	ELK4, member of ETS oncogene family	protein-coding
mm_33514.1	chr4	130928638	130928656	+	1	NA	exon (NM_010686, exon 4 of 8)	exon (NM_010686, exon 4 of 8)	15313	NM_010686	16792	Mm.271868	NM_010686	ENSMUSG00000028581	Laptm5	E3	lysosomal-associated protein transmembrane 5	protein-coding
mm_39912.1	chr5	31452428	31452452	+	1	NA	promoter-TSS (NM_172993)	promoter-TSS (NM_172993)	4	NM_172993	269639	Mm.259127	NM_172993	ENSMUSG00000062761	Zfp512	2500002M11Rik|AI450173|D230008H22|Znf512	zinc finger protein 512	protein-coding
mm_8586.1	chr1	156000412	156000415	-	1	NA	Intergenic	Intergenic	-27158	NM_001039184	74081	Mm.260247	NM_001039184	ENSMUSG00000033671	Cep350	4933409L06Rik|6430546F08Rik	centrosomal protein 350	protein-coding
mm_87609.1	chr10	57784978	57784990	+	1	NA	promoter-TSS (NM_021272)	promoter-TSS (NM_021272)	61	NM_021272	12140	Mm.3644	NM_021272	ENSMUSG00000019874	Fabp7	B-FABP|BFABP|Blbp|MRG	fatty acid binding protein 7, brain	protein-coding
mm_7106.1	chr1	89563522	89563532	-	1	NA	intron (NM_001037136, intron 1 of 16)	intron (NM_001037136, intron 1 of 16)	108716	NM_001037136	347722	Mm.291135	NM_178119	ENSMUSG00000055013	Agap1	Centg2|Ggap1|R75364|mKIAA1099	ArfGAP with GTPase domain, ankyrin repeat and PH domain 1	protein-coding
mm_135693.1	chr16	52436498	52436515	-	1	NA	intron (NM_009655, intron 1 of 15)	MIRb|SINE|MIR	16575	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_47451.1	chr5	123525436	123525465	-	1	NA	Intergenic	Intergenic	-1286	NM_023232	66593	Mm.46716	NM_023232	ENSMUSG00000029433	Diablo	0610041G12Rik|1700006L01Rik|AU040403|Smac	diablo, IAP-binding mitochondrial protein	protein-coding
mm_158930.1	chr1	64691017	64691017	+	1	NA	promoter-TSS (NM_001097644)	promoter-TSS (NM_001097644)	-328	NM_001097644	227210	Mm.39706	NM_001097644	ENSMUSG00000070871	Ccnyl1	9630037P07Rik|AW554339	cyclin Y-like 1	protein-coding
mm_167886.1	chrX	57053282	57053301	+	1	NA	promoter-TSS (NM_029371)	promoter-TSS (NM_029371)	-279	NM_028242	72459	Mm.2152	NM_028242	ENSMUSG00000067873	Htatsf1	1600023H17Rik|2600017A12Rik|2700077B20Rik|TAT-SF1	HIV TAT specific factor 1	protein-coding
mm_45054.1	chr5	41807196	41807227	-	1	NA	exon (NM_001081422, exon 15 of 27)	exon (NM_001081422, exon 15 of 27)	37104	NM_001310601	665775	Mm.158726	NM_001081422	ENSMUSG00000061755	Bod1l	A230054D04Rik|AI853319|FAM44A|mKIAA1327	biorientation of chromosomes in cell division 1-like	protein-coding
mm_113598.1	chr13	41016276	41016309	+	1	NA	promoter-TSS (NM_025387)	promoter-TSS (NM_025387)	42	NM_025387	66154	Mm.30005	NM_025387	ENSMUSG00000021361	Tmem14c	1110021D01Rik|AU020193|HSPC194	transmembrane protein 14C	protein-coding
mm_148647.1	chr19	5493132	5493169	+	1	NA	intron (NM_007687, intron 2 of 3)	intron (NM_007687, intron 2 of 3)	2695	NM_007687	12631	Mm.329655	NM_007687	ENSMUSG00000056201	Cfl1	AA959946|Cof	cofilin 1, non-muscle	protein-coding
mm_38478.1	chr4	140699800	140699823	-	1	NA	Intergenic	Intergenic	-1662	NM_173867	108911	Mm.253	NM_173867	ENSMUSG00000040945	Rcc2	2610510H01Rik|2610529N02Rik|AA536646|AA675016|Td60|mKIAA1470	regulator of chromosome condensation 2	protein-coding
mm_168070.1	chr10	105238475	105238481	+	1	NA	intron (NM_177368, intron 11 of 11)	LSU-rRNA_Hsa|rRNA|rRNA	336001	NM_177368	278279	Mm.25225	NM_177368	ENSMUSG00000036019	Tmtc2	8430438D04Rik|D330034A10Rik	transmembrane and tetratricopeptide repeat containing 2	protein-coding
mm_10261.1	chr2	9378242	9378261	+	1	NA	Intergenic	Intergenic	188736	NR_038180	73438	Mm.23558	NR_038180	ENSMUSG00000085580	1700061F12Rik	-	RIKEN cDNA 1700061F12 gene	ncRNA
mm_160981.1	chr11	102761546	102761546	+	1	NA	5' UTR (NM_009613, exon 1 of 27)	5' UTR (NM_009613, exon 1 of 27)	111	NM_001110778	11488	Mm.89854	NM_009613	ENSMUSG00000020926	Adam11	AW060611|Mdc	a disintegrin and metallopeptidase domain 11	protein-coding
mm_66582.1	chr7	45366769	45366840	-	1	NA	promoter-TSS (NR_027802)	promoter-TSS (NR_027802)	215	NM_029741	76787	Mm.277235	NM_029741	ENSMUSG00000003863	Ppfia3	2410127E16Rik	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 3	protein-coding
mm_119404.1	chr14	44926819	44926824	+	1	NA	Intergenic	Intergenic	20690	NR_030556	100124437		NR_030556	ENSMUSG00000105372	Mir327	Mirn327|mmu-mir-327	microRNA 327	ncRNA
mm_120201.1	chr14	61648457	61648465	+	1	NA	intron (NR_028264, intron 1 of 6)	CpG	-16351	NR_029733	387174		NR_029733	ENSMUSG00000093007	Mir15a	Mirn15a|mir-15a|mmu-mir-15a	microRNA 15a	ncRNA
mm_37745.1	chr4	129600643	129600653	-	1	NA	promoter-TSS (NM_029748)	promoter-TSS (NM_029748)	0	NM_018799	54709	Mm.250874	NM_018799	ENSMUSG00000028798	Eif3i	36kDa|D4Ertd632e|Eif3s2|Trip1	eukaryotic translation initiation factor 3, subunit I	protein-coding
mm_46489.1	chr5	105132250	105132262	-	1	NA	intron (NM_008620, intron 3 of 10)	L1M2|LINE|L1	7296	NM_008620	17472	Mm.440525	NM_008620	ENSMUSG00000079363	Gbp4	AW228052|Mag-2|Mpa-2|Mpa2	guanylate binding protein 4	protein-coding
mm_8061.1	chr1	135375269	135375277	-	1	NA	promoter-TSS (NM_175259)	promoter-TSS (NM_175259)	-210	NM_175259	77552	Mm.41407	NM_175259	ENSMUSG00000041889	Shisa4	9330132O05Rik|Tmem58|mShisa4	shisa family member 4	protein-coding
mm_150415.1	chr19	37207655	37207693	+	1	NA	promoter-TSS (NM_198300)	promoter-TSS (NM_198300)	129	NM_001164336	69104	Mm.175989	NM_027314	ENSMUSG00000023307	March5	1810015H18Rik|2310008I22Rik|2700055A20Rik|5730499H23Rik|E130202O05Rik|MARCH-V|MITOL|Marchv|Rnf153	membrane-associated ring finger (C3HC4) 5	protein-coding
mm_64646.1	chr7	4028789	4028798	-	1	NA	exon (NM_001113474, exon 3 of 8)	exon (NM_001113474, exon 3 of 8)	34411	NM_001302677	52855	Mm.290880	NM_178611	ENSMUSG00000055541	Lair1	5133400O11Rik|BB115266|D7Bwg0421e|Lair-1	leukocyte-associated Ig-like receptor 1	protein-coding
mm_92691.1	chr10	80665910	80665913	-	1	NA	3' UTR (NM_021462, exon 14 of 14)	3' UTR (NM_021462, exon 14 of 14)	-8840	NM_145361	208198	Mm.60720	NM_145361	ENSMUSG00000003344	Btbd2	2610037C03Rik|4930512K17Rik	BTB (POZ) domain containing 2	protein-coding
mm_104022.1	chr11	85804198	85804218	-	1	NA	intron (NR_077059, intron 2 of 4)	intron (NR_077059, intron 2 of 4)	28180	NR_077059	69909	Mm.440214	NR_077059	ENSMUSG00000087013	2610027K06Rik	-	RIKEN cDNA 2610027K06 gene	ncRNA
mm_115053.1	chr13	100651329	100651397	+	1	NA	promoter-TSS (NM_001015889)	promoter-TSS (NM_001015889)	20	NM_027592	102216272	Mm.301148	NM_027592	ENSMUSG00000078941	Ak6	2810046E22Rik|4921516M08Rik|AK/ATPase	adenylate kinase 6	protein-coding
mm_167615.1	chr9	56161093	56161097	-	1	NA	promoter-TSS (NM_019793)	promoter-TSS (NM_019793)	-25	NM_019793	56434	Mm.28484	NM_019793	ENSMUSG00000032324	Tspan3	1700055K04Rik|TM4-A|Tm4sf8	tetraspanin 3	protein-coding
mm_84385.1	chr9	65422950	65422961	-	1	NA	promoter-TSS (NM_178933)	promoter-TSS (NM_178933)	-182	NM_178933	330962	Mm.335247	NM_178933	ENSMUSG00000053862	Slc51b	Ostb	solute carrier family 51, beta subunit	protein-coding
mm_41745.1	chr5	102824015	102824017	+	1	NA	intron (NM_001286468, intron 1 of 7)	intron (NM_001286468, intron 1 of 7)	-20991	NM_001346585	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding
mm_148889.1	chr19	6877301	6877305	+	1	NA	Intergenic	RLTR19|LTR|ERVK	-19092	NM_001081291	78317	Mm.329596	NM_198008	ENSMUSG00000047810	Ccdc88b	2610041P08Rik|Ccdc88	coiled-coil domain containing 88B	protein-coding
mm_96290.1	chr11	63131503	63131509	+	1	NA	promoter-TSS (NM_008885)	promoter-TSS (NM_008885)	49	NM_001302255	18858	Mm.1237	NM_008885	ENSMUSG00000018217	Pmp22	22kDa|Gas-3|HNPP|Tr|trembler	peripheral myelin protein 22	protein-coding
mm_1915.1	chr1	86021936	86021953	+	1	NA	promoter-TSS (NM_001122732)	promoter-TSS (NM_001122732)	2	NM_027029	70060	Mm.196313	NM_027029	ENSMUSG00000026226	Spata3	1700011N12Rik|1700029H01Rik|4930424D10Rik|Mtsarg1|Tsarg1	spermatogenesis associated 3	protein-coding
mm_167533.1	chr9	21291398	21291408	-	1	NA	promoter-TSS (NM_009878)	promoter-TSS (NM_009878)	-194	NM_009878	12581	Mm.29020	NM_009878	ENSMUSG00000096472	Cdkn2d	INK4d|p19|p19INK4d	cyclin-dependent kinase inhibitor 2D (p19, inhibits CDK4)	protein-coding
mm_116694.1	chr13	49593961	49593965	-	1	NA	intron (NM_025495, intron 5 of 7)	intron (NM_025495, intron 5 of 7)	11216	NM_012050	27047	Mm.390589	NM_012050	ENSMUSG00000048368	Omd	OSAD|SLRR2C	osteomodulin	protein-coding
mm_74563.1	chr8	11007952	11007979	-	1	NA	exon (NM_001081212, exon 1 of 2)	exon (NM_001081212, exon 1 of 2)	115	NR_046017	619321	Mm.403007	NR_046017	ENSMUSG00000096938	9530052E02Rik	-	RIKEN cDNA 9530052E02 gene	ncRNA
mm_91250.1	chr10	22731855	22731872	-	1	NA	promoter-TSS (NM_011603)	promoter-TSS (NM_011603)	-416	NM_011603	237336	Mm.86670	NM_011603	ENSMUSG00000071359	Tbpl1	4732475G08|AW011832|AW491032|D18347|STD|TLF|TRF2|TRP|Tlp	TATA box binding protein-like 1	protein-coding
mm_48870.1	chr5	150583795	150583800	-	1	NA	intron (NM_133898, intron 1 of 4)	B3|SINE|B2	10728	NM_133898	100637	Mm.279932	NM_133898	ENSMUSG00000041132	N4bp2l1	2410024N18Rik|AI428195|B230342M21Rik	NEDD4 binding protein 2-like 1	protein-coding
mm_168971.1	chr1	28580774	28580791	-	1	NA	Intergenic	MurERV4_19-int|LTR|ERVK	199470	NM_001013750	210962	Mm.214178	NM_001013750	ENSMUSG00000048411	Gm597	-	predicted gene 597	protein-coding
mm_7221.1	chr1	93342563	93342572	-	1	NA	5' UTR (NM_080850, exon 1 of 18)	5' UTR (NM_080850, exon 1 of 18)	221	NM_080850	269224	Mm.379454	NM_080850	ENSMUSG00000026274	Pask	mKIAA0135	PAS domain containing serine/threonine kinase	protein-coding
mm_58177.1	chr6	142779069	142779075	-	1	NA	Intergenic	Intergenic	22386	NM_009908	12764	Mm.3820	NM_009908	ENSMUSG00000030282	Cmas	AW208911|CMPNeu5Ac|D6Bwg0250e	cytidine monophospho-N-acetylneuraminic acid synthetase	protein-coding
mm_104789.1	chr11	98707737	98707743	-	1	NA	exon (NM_011869, exon 20 of 26)	exon (NM_011869, exon 20 of 26)	6427	NM_009971	12985	Mm.1238	NM_009971	ENSMUSG00000038067	Csf3	Csfg|G-CSF|MGI-IG	colony stimulating factor 3 (granulocyte)	protein-coding
mm_77982.1	chr9	7871995	7872010	+	1	NA	intron (NM_007464, intron 1 of 8)	B1F2|SINE|Alu	1168	NM_007464	11796	Mm.2026	NM_007464	ENSMUSG00000032000	Birc3	AW107670|Api1|Api2|Birc2|C-IAP2|HIAP2|IAP1|IAP2|MIAP1|MIAP2|MIHB|MIHC|RNF49|cIAP-1|cIAP-2|cIAP1|cIAP2	baculoviral IAP repeat-containing 3	protein-coding
mm_91921.1	chr10	60300011	60300067	-	1	NA	exon (NM_011179, exon 11 of 15)	exon (NM_011179, exon 11 of 15)	15578	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_108067.1	chr12	73941697	73941738	+	1	NA	exon (NM_010431, exon 11 of 15)	exon (NM_010431, exon 11 of 15)	-22813	NM_178392	75627	Mm.25937	NM_178392	ENSMUSG00000021113	Snapc1	2700033G17Rik|AU015787	small nuclear RNA activating complex, polypeptide 1	protein-coding
mm_160654.1	chr9	115016710	115016710	+	1	NA	Intergenic	Intergenic	-50569	NM_148958	74486	Mm.458474	NM_148958	ENSMUSG00000040875	Osbpl10	4933433D06Rik|C820004B04Rik|OPR-10|ORP-10	oxysterol binding protein-like 10	protein-coding
mm_56195.1	chr6	88841829	88841844	-	1	NA	promoter-TSS (NM_030251)	promoter-TSS (NM_030251)	99	NM_030251	80283	Mm.166858	NM_030251	ENSMUSG00000030083	Abtb1	AI847549|BC003234|BPOZ|EF1ABP	ankyrin repeat and BTB (POZ) domain containing 1	protein-coding
mm_90547.1	chr10	128092772	128092819	+	1	NA	promoter-TSS (NM_054078)	promoter-TSS (NM_054078)	12	NM_054078	116848	Mm.252213	NM_054078	ENSMUSG00000040054	Baz2a	AA415431|C030005G16Rik|C78388|Tip5|Walp3|mKIAA0314	bromodomain adjacent to zinc finger domain, 2A	protein-coding
mm_66332.1	chr7	42867218	42867253	-	1	NA	promoter-TSS (NR_046214)	promoter-TSS (NR_046214)	-1	NR_046214	100039706	Mm.260936	NR_046214	ENSMUSG00000092225	Gm2381	-	zinc finger protein 936 pseudogene	pseudo
mm_104422.1	chr11	94832000	94832004	-	1	NA	Intergenic	Intergenic	17591	NM_001205037	432591	Mm.370372	NM_001205037		Gm11544	OTTMUSG00000002042	predicted gene 11544	protein-coding
mm_23746.1	chr3	69344158	69344172	+	1	NA	intron (NM_178726, intron 1 of 3)	intron (NM_178726, intron 1 of 3)	27247	NM_178726	242083	Mm.40577	NM_178726	ENSMUSG00000027784	Ppm1l	3222401G13|5930404J21Rik|AI481720|AW045850|PP2C|PP2Cepsilon|Pp2ce|Ppp2ce|mKIAA4175	protein phosphatase 1 (formerly 2C)-like	protein-coding
mm_76348.1	chr8	84736605	84736619	-	1	NA	intron (NM_001297601, intron 2 of 8)	intron (NM_001297601, intron 2 of 8)	35155	NM_008535	17095	Mm.4925	NM_008535	ENSMUSG00000034041	Lyl1	Lyl-1|bHLHa18	lymphoblastomic leukemia 1	protein-coding
mm_84408.1	chr9	65556045	65556071	-	1	NA	3' UTR (NM_153119, exon 6 of 6)	3' UTR (NM_153119, exon 6 of 6)	24029	NM_153119	102595	Mm.247303	NM_153119	ENSMUSG00000050721	Plekho2	AI840980|Plekhq1	pleckstrin homology domain containing, family O member 2	protein-coding
mm_68267.1	chr7	105595570	105595595	-	1	NA	exon (NM_017371, exon 6 of 10)	exon (NM_017371, exon 6 of 10)	4534	NM_017371	15458	Mm.3485	NM_017371	ENSMUSG00000030895	Hpx	Hpxn|hx	hemopexin	protein-coding
mm_75308.1	chr8	41134229	41134286	-	1	NA	promoter-TSS (NM_001005863)	promoter-TSS (NM_001005863)	-531	NM_001005863	102103	Mm.149438	NM_001005863	ENSMUSG00000045636	Mtus1	AI481402|ATBP135|Atip1|B430010I23Rik|B430305I03Rik|C85752|Cctsg1-440|MD44|MTSG1|mKIAA1288	mitochondrial tumor suppressor 1	protein-coding
mm_168615.1	chr11	77293533	77293546	+	1	NA	intron (NM_177710, intron 1 of 14)	intron (NM_177710, intron 1 of 14)	-54741	NM_001291190	237860	Mm.440381	NM_177710	ENSMUSG00000037926	Ssh2	SSH-2|SSH-2L|mSSH-2L	slingshot homolog 2 (Drosophila)	protein-coding
mm_105507.1	chr11	106193598	106193608	-	1	NA	promoter-TSS (NM_001252449)	promoter-TSS (NM_001252449)	0	NM_001252448	72149	Mm.403722	NM_028126	ENSMUSG00000069631	Strada	2610019A05Rik|6030402H20Rik|AI480680|E130112C09Rik	STE20-related kinase adaptor alpha	protein-coding
mm_137180.1	chr17	23816249	23816269	+	1	NA	exon (NM_175229, exon 10 of 14)	exon (NM_175229, exon 10 of 14)	12850	NM_026305	67673	Mm.153758	NM_026305	ENSMUSG00000055839	Elob	0610040H15Rik|Tceb2	elongin B	protein-coding
mm_24460.1	chr3	90623672	90623689	+	1	NA	Intergenic	Intergenic	10786	NM_011313	20200	Mm.100144	NM_011313	ENSMUSG00000001025	S100a6	2A9|5B10|CALCYCLIN|Cacy|PRA	S100 calcium binding protein A6 (calcyclin)	protein-coding
mm_74942.1	chr8	25840466	25840519	-	1	NA	promoter-TSS (NM_001286207)	promoter-TSS (NM_001286207)	-35	NM_001286207	23808	Mm.27706	NM_011791	ENSMUSG00000031575	Ash2l	-	ash2 (absent, small, or homeotic)-like (Drosophila)	protein-coding
mm_162097.1	chrX	37607620	37607620	-	1	NA	promoter-TSS (NM_001039696)	promoter-TSS (NM_001039696)	66	NM_001039696	636177	Mm.491809	NM_001039696	ENSMUSG00000079630	Rhox4f	Rhox4.6|Rhox4e|Rhox4h	reproductive homeobox 4F	protein-coding
mm_47902.1	chr5	134915495	134915505	-	1	NA	promoter-TSS (NM_020504)	promoter-TSS (NM_020504)	30	NM_020504	57255	Mm.86652	NM_020504	ENSMUSG00000008843	Cldn13	2500004B14Rik	claudin 13	protein-coding
mm_28605.1	chr3	94582760	94582770	-	1	NA	promoter-TSS (NM_029721)	promoter-TSS (NM_029721)	-49	NM_029721	76742	Mm.28160	NM_029721	ENSMUSG00000028136	Snx27	5730552M22Rik|ESTM45|ESTM47|R75405	sorting nexin family member 27	protein-coding
mm_126524.1	chr15	81936912	81936934	+	1	NA	5' UTR (NM_145473, exon 1 of 4)	5' UTR (NM_145473, exon 1 of 4)	164	NM_145473	105859	Mm.22524	NM_145473	ENSMUSG00000042109	Csdc2	AI415250|AI481750|Pippin	cold shock domain containing C2, RNA binding	protein-coding
mm_91707.1	chr10	44099354	44099358	-	1	NA	Intergenic	Intergenic	-71091	NR_001582	70365	Mm.87073	NR_001582	ENSMUSG00000091358	Speer5-ps1	1700007C10Rik|SPEER-5|Speer5-ps	spermatogenesis associated glutamate (E)-rich protein 5, pseudogene 1	pseudo
mm_142717.1	chr17	47924683	47924699	-	1	NA	promoter-TSS (NM_028767)	promoter-TSS (NM_028767)	-59	NM_001110825	74123	Mm.240062	NM_028767	ENSMUSG00000023991	Foxp4	1200010K03Rik|2310007G05Rik|mFKHLA	forkhead box P4	protein-coding
mm_154090.1	chr19	56815801	56815810	-	1	NA	Intergenic	Intergenic	-2122	NM_170757	213993	Mm.469677	NM_170757	ENSMUSG00000035173	Ccdc186	1810028B20Rik|A630007B06Rik|AI159700|Otg1	coiled-coil domain containing 186	protein-coding
mm_101990.1	chr11	50916137	50916179	-	1	NA	promoter-TSS (NM_001044697)	promoter-TSS (NM_001044697)	18	NM_178447	22678	Mm.259230	NM_009550	ENSMUSG00000049321	Zfp2	9930007F06Rik|Fnp-2|Zfp-2|mKR2|mkr-2|mszf87	zinc finger protein 2	protein-coding
mm_81582.1	chr9	110422531	110422535	+	1	NA	3' UTR (NM_008694, exon 4 of 4)	3' UTR (NM_008694, exon 4 of 4)	2725	NM_008694	18054	Mm.236225	NM_008694	ENSMUSG00000032484	Ngp	bectenecin	neutrophilic granule protein	protein-coding
mm_138367.1	chr17	35000966	35000976	+	1	NA	promoter-TSS (NM_011690)	promoter-TSS (NM_011690)	64	NM_011690	22321	Mm.28420	NM_011690	ENSMUSG00000007029	Vars	Bat6|D17H6S56E|G7a|Vars2	valyl-tRNA synthetase	protein-coding
mm_79395.1	chr9	54917253	54917295	+	1	NA	promoter-TSS (NM_177351)	promoter-TSS (NM_177351)	-16	NM_177351	235386	Mm.259334	NM_177351	ENSMUSG00000035878	Hykk	Agphd1|C630028N24Rik	hydroxylysine kinase 1	protein-coding
mm_71081.1	chr8	34623537	34623542	+	1	NA	intron (NR_040706, intron 1 of 4)	Charlie19a|DNA|hAT-Charlie	16777	NR_040706	330734	Mm.149998	NR_040706	ENSMUSG00000109819	B930018H19Rik	B930018H19	RIKEN cDNA B930018H19 gene	ncRNA
mm_75135.1	chr8	35095212	35095215	-	1	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	-129523	NM_175091	21951	Mm.88364	NM_175091	ENSMUSG00000031529	Tnks	4930554K12Rik|AI662855|ARTD5|C86528|D130072O21Rik|TANK1|mTNKS1	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase	protein-coding
mm_42013.1	chr5	108086093	108086099	+	1	NA	intron (NM_001253879, intron 3 of 14)	intron (NM_001253879, intron 3 of 14)	7931	NM_001253878	17765	Mm.257149	NM_013827	ENSMUSG00000029267	Mtf2	9230112N11Rik|AA537621|C76717|M96|Pcl2	metal response element binding transcription factor 2	protein-coding
mm_46754.1	chr5	112228901	112228926	-	1	NA	promoter-TSS (NR_033657)	promoter-TSS (NR_033657)	35	NR_033657	330166	Mm.44854	NR_003718	ENSMUSG00000097767	Miat	3632434I06|A230057G18Rik|Rncr2|gomafu	myocardial infarction associated transcript (non-protein coding)	ncRNA
mm_84777.1	chr9	75683972	75683989	-	1	NA	promoter-TSS (NM_001164790)	promoter-TSS (NM_001164790)	76	NM_001164790	20255	Mm.2386	NM_009130	ENSMUSG00000032181	Scg3	1B1075|AI385542|Chgd|SgIII	secretogranin III	protein-coding
mm_15368.1	chr2	156421117	156421123	+	1	NA	5' UTR (NM_001291121, exon 1 of 22)	5' UTR (NM_001291121, exon 1 of 22)	211	NM_001291123	13821	Mm.20852	NM_013510	ENSMUSG00000027624	Epb41l1	4.1N|Epb4.1l1|NBL1|mKIAA0338	erythrocyte membrane protein band 4.1 like 1	protein-coding
mm_155827.1	chrX	100729981	100729994	+	1	NA	promoter-TSS (NM_001305941)	promoter-TSS (NM_001305941)	140	NM_023608	71584	Mm.283495	NM_023608	ENSMUSG00000019359	Gdpd2	9130017L10Rik|Gde3|Obdpf	glycerophosphodiester phosphodiesterase domain containing 2	protein-coding
mm_159138.1	chr2	84886502	84886502	-	1	NA	intron (NM_199223, intron 1 of 2)	CpG	190	NM_199223	269295	Mm.86447	NM_199223	ENSMUSG00000050896	Rtn4rl2	Ngr2|Ngrh1|Ngrl3	reticulon 4 receptor-like 2	protein-coding
mm_127953.1	chr15	11399553	11399559	-	1	NA	5' UTR (NM_033074, exon 1 of 19)	5' UTR (NM_033074, exon 1 of 19)	102	NM_033074	110960	Mm.286061	NM_033074	ENSMUSG00000022241	Tars	D15Wsu59e|ThrRS	threonyl-tRNA synthetase	protein-coding
mm_45550.1	chr5	73100119	73100121	-	1	NA	intron (NM_028194, intron 21 of 62)	intron (NM_028194, intron 21 of 62)	93216	NM_173403	231290	Mm.491387	NM_173403	ENSMUSG00000029219	Slc10a4	E130304D01	solute carrier family 10 (sodium/bile acid cotransporter family), member 4	protein-coding
mm_66472.1	chr7	44986314	44986352	-	1	NA	promoter-TSS (NR_045266)	promoter-TSS (NR_045266)	87	NM_001252476	15469	Mm.27545	NM_019830	ENSMUSG00000109324	Prmt1	6720434D09Rik|AW214366|Hrmt1l2|Mrmt1	protein arginine N-methyltransferase 1	protein-coding
mm_105819.1	chr11	112711351	112711367	-	1	NA	promoter-TSS (NR_024085)	promoter-TSS (NR_024085)	-3	NR_024085	217294	Mm.297761	NM_146031	ENSMUSG00000041674	BC006965	-	cDNA sequence BC006965	ncRNA
mm_116802.1	chr13	54055651	54055680	-	1	NA	promoter-TSS (NM_001291801)	promoter-TSS (NM_001291801)	-7	NM_010076	13488	Mm.54161	NM_010076	ENSMUSG00000021478	Drd1	C030036C15Rik|Drd-1|Drd1a|Gpcr15	dopamine receptor D1	protein-coding
mm_17841.1	chr2	34371842	34371854	-	1	NA	exon (NM_001290576, exon 1 of 8)	exon (NM_001290576, exon 1 of 8)	197	NM_001290576	18516	Mm.239941	NM_016768	ENSMUSG00000038718	Pbx3	-	pre B cell leukemia homeobox 3	protein-coding
mm_15111.1	chr2	153649443	153649460	+	1	NA	promoter-TSS (NM_010068)	promoter-TSS (NM_010068)	2	NM_001271747	13436	Mm.89772	NM_010068	ENSMUSG00000027478	Dnmt3b	MmuIIIB	DNA methyltransferase 3B	protein-coding
mm_131468.1	chr16	17044204	17044216	+	1	NA	3' UTR (NM_011949, exon 9 of 9)	3' UTR (NM_011949, exon 9 of 9)	-25929	NM_023249	106369	Mm.237941	NM_023249	ENSMUSG00000022773	Ypel1	0610009L05Rik|1700016N17Rik|1700019O22Rik|4921520K19Rik|4930511F14Rik|AV118478|DGL-1|Dgl1|Ppil2|mdgl-1	yippee-like 1 (Drosophila)	protein-coding
mm_130695.1	chr15	100682981	100683000	-	1	NA	exon (NM_033612, exon 5 of 8)	exon (NM_033612, exon 5 of 8)	4930	NM_033612	109901	Mm.2131	NM_033612	ENSMUSG00000023031	Cela1	1810009A17Rik|1810062B19Rik|Ela-1|Ela1|PC-TsF	chymotrypsin-like elastase family, member 1	protein-coding
mm_122720.1	chr14	52279347	52279359	-	1	NA	promoter-TSS (NM_172601)	promoter-TSS (NM_172601)	42	NM_172601	76338	Mm.32870	NM_172601	ENSMUSG00000022159	Rab2b	1500012D09Rik|4930528G15Rik|A230002G14|D530043M21Rik	RAB2B, member RAS oncogene family	protein-coding
mm_150923.1	chr19	46152506	46152514	+	1	NA	promoter-TSS (NM_178930)	promoter-TSS (NM_178930)	-48	NM_178930	107338	Mm.271620	NM_178930	ENSMUSG00000025224	Gbf1	1700083E03Rik|AI035702|AW049900|mKIAA0248	golgi-specific brefeldin A-resistance factor 1	protein-coding
mm_33650.1	chr4	133039544	133039560	+	1	NA	intron (NM_146155, intron 2 of 6)	CpG	28046	NM_146155	230793	Mm.31816	NM_146155	ENSMUSG00000037692	Ahdc1	D030015G18Rik	AT hook, DNA binding motif, containing 1	protein-coding
mm_46936.1	chr5	114773373	114773472	-	1	NA	promoter-TSS (NM_019834)	promoter-TSS (NM_019834)	69	NM_019834	26431	Mm.195632	NM_019834	ENSMUSG00000041890	Git2	1500036H07Rik|5830420E16Rik|6430510B20Rik|9630056M03Rik|B230104M05Rik|CAT2|mKIAA0148	G protein-coupled receptor kinase-interactor 2	protein-coding
mm_158513.1	chrX	143183102	143183104	-	1	NA	Intergenic	Intergenic	83509	NM_001040434	209540	Mm.297608	NM_001040434	ENSMUSG00000085584	Rgag1	Gm385|Mar9|Mart9	retrotransposon gag domain containing 1	protein-coding
mm_24268.1	chr3	89188349	89188366	+	1	NA	exon (NM_001014995, exon 11 of 12)	exon (NM_001014995, exon 11 of 12)	5132	NM_001014995	68521	Mm.274708	NM_001014995	ENSMUSG00000032657	Fam189b	1110013L07Rik	family with sequence similarity 189, member B	protein-coding
mm_160494.1	chr8	129066941	129066941	+	1	NA	promoter-TSS (NM_029292)	promoter-TSS (NM_029292)	-193	NM_029292	75453	Mm.286964	NM_029292	ENSMUSG00000056018	Ccdc7b	1700008F21Rik	coiled-coil domain containing 7B	protein-coding
mm_144993.1	chr18	38296809	38296819	+	1	NA	promoter-TSS (NM_001164621)	promoter-TSS (NM_001164621)	9	NM_001164621	56736	Mm.228903	NM_020012	ENSMUSG00000060450	Rnf14	2310075C09Rik|2610005D23Rik|AA986456|AU041447|D18Ertd188e|D7Bwg0165e|Triad2	ring finger protein 14	protein-coding
mm_14437.1	chr2	130633410	130633423	+	1	NA	3' UTR (NM_001291028, exon 5 of 5)	3' UTR (NM_001291028, exon 5 of 5)	-3378	NM_001255994	140629	Mm.486003	NM_080562	ENSMUSG00000027300	Ubox5	1500010O06Rik|C330018L13Rik|Rnf37|UIP5|Ubce7ip5|Ube7ip5	U box domain containing 5	protein-coding
mm_128569.1	chr15	57660052	57660058	-	1	NA	Intergenic	Intergenic	-34612	NM_199449	387609	Mm.36557	NM_199449	ENSMUSG00000071757	Zhx2	Afr-1|Afr1|Raf|mKIAA0854	zinc fingers and homeoboxes 2	protein-coding
mm_54637.1	chr6	38782267	38782294	-	1	NA	intron (NM_001294144, intron 2 of 14)	intron (NM_001294144, intron 2 of 14)	55031	NM_001136065	15258	Mm.23790	NM_010433	ENSMUSG00000061436	Hipk2	1110014O20Rik|B230339E18Rik|Stank	homeodomain interacting protein kinase 2	protein-coding
mm_120502.1	chr14	66223900	66223910	+	1	NA	intron (NM_001162365, intron 1 of 30)	intron (NM_001162365, intron 1 of 30)	-10353	NM_001162366	19229	Mm.21613	NM_172498	ENSMUSG00000059456	Ptk2b	CADTK|CAKB|CAKbeta|E430023O05Rik|FADK2|FAK2|PYK2|Raftk	PTK2 protein tyrosine kinase 2 beta	protein-coding
mm_96662.1	chr11	69408912	69408944	+	1	NA	intron (NM_001017426, intron 1 of 22)	intron (NM_001017426, intron 1 of 22)	4747	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_5812.1	chr1	52500354	52500449	-	1	NA	promoter-TSS (NM_008667)	promoter-TSS (NM_008667)	47	NM_008667	17936	Mm.25903	NM_008667	ENSMUSG00000002881	Nab1	-	Ngfi-A binding protein 1	protein-coding
mm_121642.1	chr14	8378900	8378923	-	1	NA	promoter-TSS (NM_146050)	promoter-TSS (NM_146050)	-148	NM_146050	18300	Mm.25351	NM_146050	ENSMUSG00000021749	Oit1	2310076N21Rik|AV067083|EF-7|Fam3d	oncoprotein induced transcript 1	protein-coding
mm_126746.1	chr15	85735755	85735808	+	1	NA	promoter-TSS (NM_011144)	promoter-TSS (NM_011144)	5	NM_011144	19013	Mm.212789	NM_011144	ENSMUSG00000022383	Ppara	4933429D07Rik|AW742785|Nr1c1|PPAR-alpha|PPARalpha|Ppar	peroxisome proliferator activated receptor alpha	protein-coding
mm_106285.1	chr11	118202616	118202629	-	1	NA	intron (NM_001112699, intron 1 of 12)	intron (NM_001112699, intron 1 of 12)	10120	NM_001112700	19157	Mm.86413	NM_011180	ENSMUSG00000017132	Cyth1	CLM1|CTH-1|CYTIP|Pscd1	cytohesin 1	protein-coding
mm_117987.1	chr13	100232409	100232411	-	1	NA	intron (NM_010870, intron 5 of 14)	L1_Mur3|LINE|L1	14926	NM_010870	17951	Mm.290476	NM_010870	ENSMUSG00000071203	Naip5	Birc1e|Lgn1|Naip-rs3	NLR family, apoptosis inhibitory protein 5	protein-coding
mm_102990.1	chr11	69685538	69685565	-	1	NA	promoter-TSS (NM_001159505)	promoter-TSS (NM_001159505)	3	NM_001159505	69583	Mm.8983	NM_023517	ENSMUSG00000089669	Tnfsf13	2310026N09Rik|April|Tall2|Tnlg7b|Trdl1	tumor necrosis factor (ligand) superfamily, member 13	protein-coding
mm_43871.1	chr5	143548701	143548756	+	1	NA	promoter-TSS (NM_026050)	promoter-TSS (NM_026050)	22	NM_026050	67238	Mm.383219	NM_026050	ENSMUSG00000083012	Fam220a	1500026F15Rik|2810453I06Rik|AW047776|Acpin1|Sipar	family with sequence similarity 220, member A	protein-coding
mm_11873.1	chr2	49230565	49230565	+	1	NA	intron (NM_029924, intron 6 of 16)	intron (NM_029924, intron 6 of 16)	-15335	NM_001290656	109241	Mm.440436	NM_029924	ENSMUSG00000036792	Mbd5	9430004D19Rik|AA536666|AI426407|C030040A15Rik|Gm1630|OTTMUSG00000012483	methyl-CpG binding domain protein 5	protein-coding
mm_84250.1	chr9	62435772	62435777	-	1	NA	intron (NM_175484, intron 3 of 11)	intron (NM_175484, intron 3 of 11)	94431	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	protein-coding
mm_65163.1	chr7	19675901	19676005	-	1	NA	intron (NM_001309799, intron 1 of 3)	intron (NM_001309799, intron 1 of 3)	1988	NM_001277944	11813	Mm.28394	NM_001277944	ENSMUSG00000002992	Apoc2	apo-CII|apoC-II	apolipoprotein C-II	protein-coding
mm_41610.1	chr5	96793353	96793380	+	1	NA	promoter-TSS (NM_013470)	promoter-TSS (NM_013470)	-19	NM_013470	11745	Mm.7214	NM_013470	ENSMUSG00000029484	Anxa3	Anx3	annexin A3	protein-coding
mm_60167.1	chr7	40898784	40898819	+	1	NA	promoter-TSS (NM_021387)	promoter-TSS (NM_021387)	-477	NR_040329	320210	Mm.126237	NR_040329	ENSMUSG00000100600	A230077H06Rik	-	RIKEN cDNA A230077H06 gene	ncRNA
mm_154709.1	chrX	8277681	8277700	+	1	NA	intron (NM_172479, intron 11 of 15)	intron (NM_172479, intron 11 of 15)	6309	NM_172479	209837	Mm.6055	NM_172479	ENSMUSG00000031170	Slc38a5	C81234|E330031E14|JM24|SN2	solute carrier family 38, member 5	protein-coding
mm_18297.1	chr2	52742170	52742217	-	1	NA	promoter-TSS (NM_019667)	promoter-TSS (NM_019667)	-44	NM_019667	56324	Mm.263639	NM_019667	ENSMUSG00000055371	Stam2	1200004O12Rik|5730456G07Rik|BB145015|Hbp	signal transducing adaptor molecule (SH3 domain and ITAM motif) 2	protein-coding
mm_18758.1	chr2	73440044	73440058	-	1	NA	exon (NM_153138, exon 4 of 8)	exon (NM_153138, exon 4 of 8)	13838	NM_001289722	215280	Mm.223504	NM_153138	ENSMUSG00000075284	Wipf1	AI115543|D2Ertd120e|WIP|Waspip	WAS/WASL interacting protein family, member 1	protein-coding
mm_93476.1	chr10	111799787	111799806	-	1	NA	Intergenic	Intergenic	74580	NR_046029	629206	Mm.391444	NR_046029		Gm20758	-	predicted gene, 20758	ncRNA
mm_161552.1	chr16	10792063	10792063	-	1	NA	promoter-TSS (NM_008933)	promoter-TSS (NM_008933)	42	NM_008933	19119	Mm.325769	NM_008933	ENSMUSG00000038015	Prm2	AI528784|Prm-2	protamine 2	protein-coding
mm_91234.1	chr10	22302760	22302768	-	1	NA	intron (NM_009018, intron 5 of 5)	intron (NM_009018, intron 5 of 5)	-3956	NR_015465	606736	Mm.387042	NR_015465	ENSMUSG00000097352	C920009B18Rik	-	RIKEN cDNA C920009B18 gene	ncRNA
mm_17955.1	chr2	37359236	37359270	-	1	NA	promoter-TSS (NM_026176)	promoter-TSS (NM_026176)	79	NM_026176	67466	Mm.30709	NM_026176	ENSMUSG00000009030	Pdcl	1200011E13Rik|AW108059|PhLP1	phosducin-like	protein-coding
mm_133195.1	chr16	72930934	72930937	+	1	NA	intron (NM_019413, intron 3 of 28)	intron (NM_019413, intron 3 of 28)	267786	NM_019413	19876	Mm.310772	NM_019413	ENSMUSG00000022883	Robo1	AW494633|AW742721|DUTT1|Gm310	roundabout guidance receptor 1	protein-coding
mm_1589.1	chr1	74332597	74332641	+	1	NA	promoter-TSS (NM_019999)	promoter-TSS (NM_019999)	9	NM_019999	56695	Mm.384726	NM_019999	ENSMUSG00000026179	Pnkd	2210013N15Rik|2810403H05Rik|AI854243|Brp17|MNCb-5687|MR-1|Tahccp2	paroxysmal nonkinesiogenic dyskinesia	protein-coding
mm_124123.1	chr14	79662091	79662101	-	1	NA	promoter-TSS (NM_001310655)	promoter-TSS (NM_001310655)	87	NM_001310655	16840	Mm.46561	NM_010701	ENSMUSG00000022025	Cnmd	Bricd3|ChM-I|Chmd|Lect1	chondromodulin	protein-coding
mm_141116.1	chr17	26090113	26090156	-	1	NA	promoter-TSS (NM_011933)	promoter-TSS (NM_011933)	30	NM_011933	26378	Mm.292869	NM_011933	ENSMUSG00000036775	Decr2	-	2-4-dienoyl-Coenzyme A reductase 2, peroxisomal	protein-coding
mm_77247.1	chr8	115705617	115705634	-	1	NA	3' UTR (NM_001025577, exon 1 of 1)	3' UTR (NM_001025577, exon 1 of 1)	1269	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_15460.1	chr2	157444386	157444407	+	1	NA	intron (NM_009271, intron 2 of 14)	B1_Mus1|SINE|Alu	20103	NM_001025395	20779	Mm.22845	NM_009271	ENSMUSG00000027646	Src	AW259666|pp60c-src	Rous sarcoma oncogene	protein-coding
mm_160301.1	chr7	138989433	138989433	+	1	NA	exon (NM_028708, exon 2 of 20)	exon (NM_028708, exon 2 of 20)	48703	NM_028708	74004	Mm.334298	NM_028708		Jakmip3	6330417G02Rik|AI593226|mKIAA4091	janus kinase and microtubule interacting protein 3	protein-coding
mm_167186.1	chr7	142461484	142461514	-	1	NA	intron (NM_001271510, intron 1 of 10)	intron (NM_001271510, intron 1 of 10)	687	NM_001136071	16985	Mm.234003	NM_019391	ENSMUSG00000018819	Lsp1	Lsp-1|WP34|p50|pp52	lymphocyte specific 1	protein-coding
mm_116203.1	chr13	32338566	32338660	-	1	NA	promoter-TSS (NM_146041)	promoter-TSS (NM_146041)	-69	NM_146041	218138	Mm.247143	NM_146041	ENSMUSG00000038372	Gmds	BC031788|C87208	GDP-mannose 4, 6-dehydratase	protein-coding
mm_33899.1	chr4	136270998	136271046	+	1	NA	intron (NM_011542, intron 8 of 10)	intron (NM_011542, intron 8 of 10)	-15047	NM_009557	22704	Mm.1504	NM_009557	ENSMUSG00000051351	Zfp46	AI426962|Mlz-4|Zfp-46|Znf436	zinc finger protein 46	protein-coding
mm_164598.1	chr17	28558234	28558238	-	1	NA	TTS (NR_105935)	TTS (NR_105935)	265	NR_105935	102465585		NR_105935	ENSMUSG00000099152	Mir6969	Gm27305|mmu-mir-6969	microRNA 6969	ncRNA
mm_42597.1	chr5	117413978	117414011	+	1	NA	promoter-TSS (NM_001312914)	promoter-TSS (NM_001312914)	-8	NM_001312914	333050	Mm.437947	NM_001034873	ENSMUSG00000061578	Ksr2	-	kinase suppressor of ras 2	protein-coding
mm_74684.1	chr8	14306980	14306980	-	1	NA	intron (NM_172910, intron 3 of 15)	intron (NM_172910, intron 3 of 15)	211105	NM_172910	244310	Mm.404697	NM_172910	ENSMUSG00000047495	Dlgap2	6430596N04Rik|Dap-2|Dap2|Sapap2	discs, large (Drosophila) homolog-associated protein 2	protein-coding
mm_162640.1	chr1	191507879	191507880	+	1	NA	Intergenic	B1_Mur2|SINE|Alu	67665	NM_001305233	76843	Mm.189102	NM_029766	ENSMUSG00000037474	Dtl	2810047L02Rik|5730564G15Rik|L2dtl|Ramp	denticleless E3 ubiquitin protein ligase	protein-coding
mm_80891.1	chr9	99612469	99612529	+	1	NA	promoter-TSS (NM_001077424)	promoter-TSS (NM_001077424)	-3	NM_001077424	333424	Mm.297753	NM_001077424	ENSMUSG00000037953	A4gnt	AV080780|Alpha4gnt|Gm798	alpha-1,4-N-acetylglucosaminyltransferase	protein-coding
mm_75538.1	chr8	57323034	57323040	-	1	NA	intron (NM_010402, intron 1 of 1)	intron (NM_010402, intron 1 of 1)	2054	NM_010402	15111	Mm.430844	NM_010402	ENSMUSG00000038193	Hand2	AI225906|AI661148|Ehand2|Hed|Th2|Thing2|bHLHa26|dHAND	heart and neural crest derivatives expressed transcript 2	protein-coding
mm_72983.1	chr8	92918325	92918327	+	1	NA	3' UTR (NM_173014, exon 14 of 14)	3' UTR (NM_173014, exon 14 of 14)	16931	NM_027112	69543	Mm.440514	NM_027112	ENSMUSG00000078144	Capns2	2310005G05Rik|30K-2	calpain, small subunit 2	protein-coding
mm_135982.1	chr16	75092534	75092552	-	1	NA	Intergenic	Intergenic	493518	NM_001252513	320355	Mm.99517	NM_177142	ENSMUSG00000032948	Lipi	D930038D03Rik|lpd1	lipase, member I	protein-coding
mm_8181.1	chr1	138080272	138080280	-	1	NA	intron (NM_001111316, intron 23 of 31)	intron (NM_001111316, intron 23 of 31)	94850	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_73197.1	chr8	95551790	95551792	+	1	NA	intron (NM_172914, intron 7 of 8)	intron (NM_172914, intron 7 of 8)	17691	NM_172914	244608	Mm.248902	NM_172914	ENSMUSG00000036598	Ccdc113	4933409I22|BC060957	coiled-coil domain containing 113	protein-coding
mm_99718.1	chr11	106276692	106276702	+	1	NA	promoter-TSS (NM_029467)	promoter-TSS (NM_029467)	25	NM_029467	75870	Mm.159608	NM_029467	ENSMUSG00000020712	Tcam1	4930570F09Rik|AI429105	testicular cell adhesion molecule 1	protein-coding
mm_139086.1	chr17	46772804	46772828	+	1	NA	exon (NM_025966, exon 1 of 1)	exon (NM_025966, exon 1 of 1)	181	NM_025966	67101	Mm.358702	NM_025966	ENSMUSG00000062619	2310039H08Rik	-	RIKEN cDNA 2310039H08 gene	protein-coding
mm_89423.1	chr10	90917752	90917756	+	1	NA	intron (NM_001177396, intron 6 of 11)	intron (NM_001177396, intron 6 of 11)	87911	NM_001347053	77531	Mm.440605	NM_181398	ENSMUSG00000058589	Anks1b	AIDA-1b|C030032C09Rik|E530015N03Rik|ENSMUSG00000078431|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding
mm_104917.1	chr11	99793348	99793354	-	1	NA	promoter-TSS (NM_001099311)	promoter-TSS (NM_001099311)	-59	NM_001099311	670464	Mm.473676	NM_001099311	ENSMUSG00000078261	Gm11596	OTTMUSG00000002547	predicted gene 11596	protein-coding
mm_120273.1	chr14	63124594	63124622	+	1	NA	intron (NM_007798, intron 1 of 9)	B1F|SINE|Alu	2146	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_114651.1	chr13	77438975	77439024	+	1	NA	intron (NM_001145676, intron 19 of 19)	GSAT_MM|Satellite|Satellite	-269691	NM_001163420	68675	Mm.343005	NM_138312	ENSMUSG00000064138	Fam172a	1110033M05Rik|2610318O14Rik|53-E6|9430037D06Rik|AF064782|pEN87	family with sequence similarity 172, member A	protein-coding
mm_19613.1	chr2	102811634	102811645	-	1	NA	3' UTR (NM_009851, exon 19 of 19)	3' UTR (NM_009851, exon 19 of 19)	90026	NM_001177785	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_71673.1	chr8	60842300	60842312	+	1	NA	Intergenic	Intergenic	-48145	NM_028299	72612	Mm.25263	NM_028299	ENSMUSG00000038005	Hpf1	2700029M09Rik|C230006B22Rik|C4orf27	histone PARylation factor 1	protein-coding
mm_88495.1	chr10	77837482	77837483	+	1	NA	TTS (NM_001024709)	TTS (NM_001024709)	1535	NM_001024709	544710	Mm.441890	NM_001024709		Krtap10-10	EG544710	keratin associated protein 10-10	protein-coding
mm_111105.1	chr12	80945339	80945354	-	1	NA	promoter-TSS (NM_001079694)	promoter-TSS (NM_001079694)	53	NR_045057	100504661	Mm.442322	NR_045057		Gm20337	-	predicted gene, 20337	ncRNA
mm_154115.1	chr19	57165817	57165818	-	1	NA	intron (NM_001290813, intron 2 of 20)	intron (NM_001290813, intron 2 of 20)	31814	NM_001103177	226251	Mm.217161	NM_178688	ENSMUSG00000025085	Ablim1	2210411C18Rik|2610209L21Rik|4833406P10Rik|9330196J19Rik|AV079770|AW060987|AW215784|Limab1|mKIAA0059	actin-binding LIM protein 1	protein-coding
mm_105927.1	chr11	115066692	115066711	-	1	NA	Intergenic	L1Md_T|LINE|L1	-4662	NM_172050	217306	Mm.222667	NM_172050	ENSMUSG00000048498	Cd300e	BC034097|CLM2|Cd300le|TREM5	CD300E molecule	protein-coding
mm_54264.1	chr6	28421528	28421542	-	1	NA	5' UTR (NM_028900, exon 1 of 2)	5' UTR (NM_028900, exon 1 of 2)	189	NM_028900	74375	Mm.332950	NM_028900	ENSMUSG00000029708	Gcc1	4932417P04Rik	golgi coiled coil 1	protein-coding
mm_109783.1	chr12	3110067	3110084	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	-125716	NR_015551	74173	Mm.309774	NM_028796	ENSMUSG00000079179	Rab10os	1700012B15Rik|1810036A22Rik	RAB10, member RAS oncogene family, opposite strand	ncRNA
mm_68063.1	chr7	101864161	101864168	-	1	NA	intron (NM_001252552, intron 3 of 6)	intron (NM_001252552, intron 3 of 6)	6624	NM_001252554	14275	Mm.2135	NM_008034	ENSMUSG00000001827	Folr1	FBP1|Folbp-1|Folbp1	folate receptor 1 (adult)	protein-coding
mm_154800.1	chrX	13287239	13287253	+	1	NA	exon (NM_010028, exon 5 of 17)	exon (NM_010028, exon 5 of 17)	6224	NM_010028	13205	Mm.289662	NM_010028	ENSMUSG00000000787	Ddx3x	D1Pas1-rs2|Ddx3|Fin14	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 3, X-linked	protein-coding
mm_129281.1	chr15	77153727	77153750	-	1	NA	promoter-TSS (NM_001110830)	promoter-TSS (NM_001110830)	74	NM_001110830	93686	Mm.202774	NM_053104	ENSMUSG00000033565	Rbfox2	Fbm2|Fxh|Hrnbp2|Rbm9	RNA binding protein, fox-1 homolog (C. elegans) 2	protein-coding
mm_57727.1	chr6	128934306	128934347	-	1	NA	promoter-TSS (NM_027562)	promoter-TSS (NM_027562)	-55	NM_027562	70809	Mm.439891	NM_027562	ENSMUSG00000000248	Clec2g	4632413B12Rik|Clr-c|Clr-d|Clrc|Clrd|Clrx|Ddv10|Ocilrp1	C-type lectin domain family 2, member g	protein-coding
mm_128956.1	chr15	74799505	74799519	-	1	NA	intron (NM_029627, intron 1 of 3)	intron (NM_029627, intron 1 of 3)	456	NM_029627	76486	Mm.273319	NM_029627	ENSMUSG00000044678	Ly6k	2410015A16Rik|3110035B01Rik|mLy-6K	lymphocyte antigen 6 complex, locus K	protein-coding
mm_124391.1	chr14	110755101	110755152	-	1	NA	promoter-TSS (NM_175499)	promoter-TSS (NM_175499)	23	NM_175499	239250	Mm.49728	NM_175499	ENSMUSG00000045871	Slitrk6	4832410J21Rik|Sltk6	SLIT and NTRK-like family, member 6	protein-coding
mm_81324.1	chr9	108490696	108490764	+	1	NA	promoter-TSS (NM_001168373)	promoter-TSS (NM_001168373)	54	NM_027804	71472	Mm.289706	NM_027804	ENSMUSG00000006676	Usp19	8430421I07Rik|AI047774|Zmynd9	ubiquitin specific peptidase 19	protein-coding
mm_122588.1	chr14	50897385	50897397	-	1	NA	Intergenic	Intergenic	-4136	NM_001166651	546611	Mm.390692	NM_001166651	ENSMUSG00000090799	Klhl33	EG546611	kelch-like 33	protein-coding
mm_69630.1	chr7	137410718	137410761	-	1	NA	promoter-TSS (NM_029886)	promoter-TSS (NM_029886)	17	NM_029886	77252	Mm.29184	NM_029886	ENSMUSG00000040139	9430038I01Rik	-	RIKEN cDNA 9430038I01 gene	protein-coding
mm_102774.1	chr11	68386822	68386835	-	1	NA	promoter-TSS (NM_008744)	promoter-TSS (NM_008744)	-2	NM_008744	18208	Mm.39095	NM_008744	ENSMUSG00000020902	Ntn1	AI561871|BC019633|Netrin-1	netrin 1	protein-coding
mm_98446.1	chr11	94943721	94943736	+	1	NA	intron (NM_007742, intron 24 of 50)	intron (NM_007742, intron 24 of 50)	7504	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_18031.1	chr2	38708359	38708403	-	1	NA	exon (NM_139051, exon 4 of 7)	exon (NM_139051, exon 4 of 7)	3853	NM_001316687	26423	Mm.31387	NM_139051	ENSMUSG00000026751	Nr5a1	Ad4BP|ELP|ELP-3|Ftz-F1|Ftzf1|SF-1|SF1|STF-1	nuclear receptor subfamily 5, group A, member 1	protein-coding
mm_38888.1	chr4	149742223	149742223	-	1	NA	Intergenic	A-rich|Low_complexity|Low_complexity	-4155	NM_177672	230917	Mm.266704	NM_177672	ENSMUSG00000044700	Tmem201	AV028368|D4Ertd429e|Net5|Samp1	transmembrane protein 201	protein-coding
mm_75051.1	chr8	32884904	32884915	-	1	NA	Intergenic	CpG	65117	NM_001177589	100042715	Mm.291093	NM_001177589		Gm3985	-	predicted gene 3985	protein-coding
mm_74403.1	chr8	3279626	3279647	-	1	NA	promoter-TSS (NM_001330056)	promoter-TSS (NM_001330056)	-19	NM_001330056	16337	Mm.268003	NM_010568	ENSMUSG00000005534	Insr	4932439J01Rik|CD220|D630014A15Rik|IR|IR-A|IR-B	insulin receptor	protein-coding
mm_143949.1	chr17	86802712	86802717	-	1	NA	intron (NM_010137, intron 2 of 15)	intron (NM_010137, intron 2 of 15)	48850	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_14247.1	chr2	128063122	128063139	+	1	NA	intron (NM_028765, intron 14 of 17)	intron (NM_028765, intron 14 of 17)	-62908	NM_207681	12125	Mm.141083	NM_009754	ENSMUSG00000027381	Bcl2l11	1500006F24Rik|Bim|Bod|bcl2-L-11	BCL2-like 11 (apoptosis facilitator)	protein-coding
mm_152503.1	chr19	11165353	11165356	-	1	NA	promoter-TSS (NM_027074)	promoter-TSS (NM_027074)	-34	NM_027074	69416	Mm.72491	NM_027074	ENSMUSG00000024728	1700025F22Rik	-	RIKEN cDNA 1700025F22 gene	protein-coding
mm_153929.1	chr19	47373664	47373679	-	1	NA	intron (NM_001164717, intron 3 of 13)	intron (NM_001164717, intron 3 of 13)	90740	NM_001164717	14218	Mm.127560	NM_008018	ENSMUSG00000053617	Sh3pxd2a	2310014D11Rik|AA589508|AI256723|AI413738|C230050L11|EG329070|Fish|Gm5098|Sh3md1|TSK5|Tks5	SH3 and PX domains 2A	protein-coding
mm_64599.1	chr7	3206452	3206471	-	1	NA	Intergenic	Intergenic	-12165	NR_029640	100049710		NR_029640	ENSMUSG00000077815	Mir290a	Mir290|Mirn290|mir-290a|mmu-miR-290|mmu-mir-290a	microRNA 290a	ncRNA
mm_87746.1	chr10	60267043	60267059	+	1	NA	Intergenic	Intergenic	-10577	NM_001146123	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_146796.1	chr18	20673685	20673693	-	1	NA	exon (NM_013697, exon 4 of 4)	exon (NM_013697, exon 4 of 4)	8439	NM_013697	22139	Mm.2108	NM_013697	ENSMUSG00000061808	Ttr	AA408768|AI787086|D17860|prealbumin	transthyretin	protein-coding
mm_117920.1	chr13	99433500	99433520	-	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-20684	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_26515.1	chr3	145892016	145892026	+	1	NA	3' UTR (NM_026993, exon 6 of 6)	3' UTR (NM_026993, exon 6 of 6)	-32241	NM_009740	12042	Mm.239141	NM_009740	ENSMUSG00000028191	Bcl10	AI132454|BCL-10|C81403|CARMEN|CIPER|CLAP|ME10|cE10	B cell leukemia/lymphoma 10	protein-coding
mm_58786.1	chr7	16129757	16129845	+	1	NA	promoter-TSS (NM_148946)	promoter-TSS (NM_148946)	-25	NM_001347561	110891	Mm.241147	NM_148946	ENSMUSG00000030376	Slc8a2	Ncx2	solute carrier family 8 (sodium/calcium exchanger), member 2	protein-coding
mm_5681.1	chr1	43163848	43163861	-	1	NA	5' UTR (NM_010212, exon 1 of 6)	5' UTR (NM_010212, exon 1 of 6)	107	NM_010212	14200	Mm.6799	NM_010212	ENSMUSG00000008136	Fhl2	FHL-2|SLIM-3|SLIM3	four and a half LIM domains 2	protein-coding
mm_33972.1	chr4	137621040	137621050	+	1	NA	intron (NM_001347227, intron 11 of 26)	intron (NM_001347227, intron 11 of 26)	26856	NM_130879	170707	Mm.218478	NM_130879	ENSMUSG00000043411	Usp48	2810449C13Rik|AI115503|BC021769|D330022K21Rik|Usp31	ubiquitin specific peptidase 48	protein-coding
mm_81322.1	chr9	108481709	108481733	+	1	NA	intron (NM_008483, intron 7 of 32)	intron (NM_008483, intron 7 of 32)	1859	NM_008483	16779	Mm.27560	NM_008483	ENSMUSG00000052911	Lamb2	AW211941|Lamb-2|Lams|npht	laminin, beta 2	protein-coding
mm_9851.1	chr1	184732532	184732545	-	1	NA	promoter-TSS (NM_008250)	promoter-TSS (NM_008250)	-45	NM_008250	15284	Mm.1347	NM_008250	ENSMUSG00000039377	Hlx	Hlx1	H2.0-like homeobox	protein-coding
mm_37100.1	chr4	116627368	116627397	-	1	NA	exon (NM_016777, exon 2 of 16)	exon (NM_016777, exon 2 of 16)	115	NM_001081475	50927	Mm.257181	NM_016777	ENSMUSG00000028693	Nasp	5033430J04Rik|AI131596|AI317140|D4Ertd767e|Epcs32|Nasp-T	nuclear autoantigenic sperm protein (histone-binding)	protein-coding
mm_171798.1	chr5	121593514	121593524	-	1	NA	5' UTR (NM_001308450, exon 1 of 11)	5' UTR (NM_001308450, exon 1 of 11)	305	NM_009656	11669	Mm.284446	NM_009656	ENSMUSG00000029455	Aldh2	AHD-M1|ALDH-E2|ALDHI|Ahd-5|Ahd5	aldehyde dehydrogenase 2, mitochondrial	protein-coding
mm_65793.1	chr7	28895013	28895034	-	1	NA	intron (NM_021895, intron 19 of 20)	intron (NM_021895, intron 19 of 20)	13367	NM_001110807	60594	Mm.476990	NM_021894	ENSMUSG00000054083	Capn12	CANP 12	calpain 12	protein-coding
mm_36201.1	chr4	62360420	62360433	-	1	NA	promoter-TSS (NM_175090)	promoter-TSS (NM_175090)	122	NM_001045528	338355	Mm.357792	NM_001045528	ENSMUSG00000066151	Fkbp15	BB131447|C430014M02Rik|FKBO133|FKBP-133|FKBP-15|FKBP133|mKIAA0674	FK506 binding protein 15	protein-coding
mm_45175.1	chr5	51547570	51547573	-	1	NA	intron (NR_132764, intron 2 of 12)	intron (NR_132764, intron 2 of 12)	6350	NR_027710	19017	Mm.259072	NM_008904	ENSMUSG00000029167	Ppargc1a	A830037N07Rik|ENSMUSG00000079510|Gm11133|PGC-1|PPARGC-1-alpha|Pgc-1alpha|Pgc1|Pgco1|Ppargc1	peroxisome proliferative activated receptor, gamma, coactivator 1 alpha	protein-coding
mm_17385.1	chr2	27027917	27027995	-	1	NA	promoter-TSS (NM_172659)	promoter-TSS (NM_172659)	42	NM_172659	227659	Mm.41203	NM_172659	ENSMUSG00000036067	Slc2a6	A330096C23|F630103L12Rik|Glut6|Glut9	solute carrier family 2 (facilitated glucose transporter), member 6	protein-coding
mm_122134.1	chr14	31162185	31162214	-	1	NA	exon (NM_138672, exon 7 of 69)	exon (NM_138672, exon 7 of 69)	6442	NM_138672	192187	Mm.220821	NM_138672	ENSMUSG00000042286	Stab1	FEEL-1|FELE-1|MFEEL-1|MS-1|STAB-1|mKIAA0246	stabilin 1	protein-coding
mm_157610.1	chrX	53776296	53776315	-	1	NA	promoter-TSS (NM_001009549)	promoter-TSS (NM_001009549)	89	NM_001009549	333473	Mm.327378	NM_001009549	ENSMUSG00000059334	Zfp36l3	AY661338	zinc finger protein 36, C3H type-like 3	protein-coding
mm_117267.1	chr13	64413380	64413409	-	1	NA	Intergenic	ERVL-B4-int|LTR|ERVL	-19159	NM_053180	105278	Mm.74982	NM_053180	ENSMUSG00000021483	Cdk20	4932702G04Rik|AU019450|AW558027|CDCH|Ccrk|PNQLARE|p42	cyclin-dependent kinase 20	protein-coding
mm_86526.1	chr10	7810357	7810368	+	1	NA	exon (NM_026141, exon 11 of 13)	exon (NM_026141, exon 11 of 13)	17468	NM_026141	67418	Mm.38927	NM_026141	ENSMUSG00000015757	Ppil4	3732410E19Rik|3830425H19Rik|AI788954|AW146233|PPIase	peptidylprolyl isomerase (cyclophilin)-like 4	protein-coding
mm_84101.1	chr9	58278997	58279018	-	1	NA	Intergenic	MLTR25A|LTR|ERVK	25843	NM_026942	69106	Mm.216502	NM_026942	ENSMUSG00000032333	Stoml1	1810015E19Rik|AI847431|SLP1|STORP|UNC24|WPB72	stomatin-like 1	protein-coding
mm_75316.1	chr8	41348629	41348644	-	1	NA	intron (NM_019734, intron 6 of 13)	ORR1C2|LTR|ERVL-MaLR	26061	NM_019734	11886	Mm.22547	NM_019734	ENSMUSG00000031591	Asah1	2310081N20Rik|AC|Asah	N-acylsphingosine amidohydrolase 1	protein-coding
mm_63732.1	chr7	130867535	130867540	+	1	NA	intron (NM_001346515, intron 1 of 12)	intron (NM_001346515, intron 1 of 12)	1627	NM_133942	101476	Mm.323554	NM_133942	ENSMUSG00000040268	Plekha1	AA960558|C920009D07Rik|TAPP1	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 1	protein-coding
mm_100452.1	chr11	119675471	119675482	+	1	NA	intron (NM_028898, intron 3 of 33)	intron (NM_028898, intron 3 of 33)	72571	NM_028898	74370	Mm.209933	NM_028898	ENSMUSG00000025583	Rptor	4932417H02Rik|Rap|Raptor|mKIAA1303	regulatory associated protein of MTOR, complex 1	protein-coding
mm_152480.1	chr19	11047943	11047980	-	1	NA	non-coding (NR_102366, exon 3 of 3)	non-coding (NR_102366, exon 3 of 3)	2605	NR_102366	107350	Mm.6381	NM_001177351	ENSMUSG00000075010	AW112010	-	expressed sequence AW112010	ncRNA
mm_113435.1	chr13	34875564	34875602	+	1	NA	promoter-TSS (NM_013830)	promoter-TSS (NM_013830)	89	NM_013830	19134	Mm.10027	NM_013830	ENSMUSG00000021413	Prpf4b	2610037H07|Prp4|Prp4k|Prpk|cbp143	pre-mRNA processing factor 4B	protein-coding
mm_147103.1	chr18	35655203	35655240	-	1	NA	promoter-TSS (NM_001270646)	promoter-TSS (NM_001270646)	-22	NM_001270646	381148	Mm.297784	NM_001270646	ENSMUSG00000073600	Prob1	Gm1614	proline rich basic protein 1	protein-coding
mm_143376.1	chr17	67842047	67842051	-	1	NA	TTS (NM_172964)	TTS (NM_172964)	108891	NM_001347410	268970	Mm.9935	NM_172964	ENSMUSG00000024043	Arhgap28	AU044757|AW550892|E130310N06	Rho GTPase activating protein 28	protein-coding
mm_34618.1	chr4	150488369	150488444	+	1	NA	intron (NM_001085492, intron 7 of 22)	intron (NM_001085492, intron 7 of 22)	163768	NM_173774	242773	Mm.29280	NM_173774	ENSMUSG00000039838	Slc45a1	C230078B22|Dnb5	solute carrier family 45, member 1	protein-coding
mm_81350.1	chr9	108569886	108569943	+	1	NA	promoter-TSS (NM_026378)	promoter-TSS (NM_026378)	22	NM_026378	67789	Mm.458081	NM_026378	ENSMUSG00000019039	Dalrd3	6330580J24Rik|C77829|mir-425	DALR anticodon binding domain containing 3	protein-coding
mm_135258.1	chr16	37835798	37835821	-	1	NA	3' UTR (NM_008047, exon 11 of 11)	3' UTR (NM_008047, exon 11 of 11)	-32591	NM_177093	320184	Mm.390882	NM_177093	ENSMUSG00000034158	Lrrc58	1810012N18Rik|C330018J07Rik	leucine rich repeat containing 58	protein-coding
mm_14263.1	chr2	128428328	128428351	+	1	NA	intron (NR_028591, intron 1 of 1)	intron (NR_028591, intron 1 of 1)	1012	NR_028591	100043424	Mm.297222	NR_028589		Gm14005	OTTMUSG00000015351	predicted gene 14005	ncRNA
mm_70822.1	chr8	23139036	23139061	+	1	NA	promoter-TSS (NM_001310437)	promoter-TSS (NM_001310437)	18	NM_001310437	11733	Mm.334444	NM_031158	ENSMUSG00000031543	Ank1	Ank-1|nb|pale	ankyrin 1, erythroid	protein-coding
mm_100328.1	chr11	118211978	118211984	+	1	NA	intron (NM_001112699, intron 1 of 12)	intron (NM_001112699, intron 1 of 12)	761	NM_001112700	19157	Mm.86413	NM_011180	ENSMUSG00000017132	Cyth1	CLM1|CTH-1|CYTIP|Pscd1	cytohesin 1	protein-coding
mm_143040.1	chr17	56757517	56757532	-	1	NA	promoter-TSS (NM_008738)	promoter-TSS (NM_008738)	24	NM_008738	18188	Mm.8074	NM_008738	ENSMUSG00000039481	Nrtn	NTN	neurturin	protein-coding
mm_149326.1	chr19	10842818	10842828	+	1	NA	5' UTR (NM_023044, exon 1 of 8)	5' UTR (NM_023044, exon 1 of 8)	279	NM_023044	65221	Mm.27387	NM_023044	ENSMUSG00000024737	Slc15a3	Ci1|cI-1	solute carrier family 15, member 3	protein-coding
mm_28368.1	chr3	89904396	89904410	-	1	NA	intron (NM_001310676, intron 1 of 9)	B3A|SINE|B2	8793	NM_001310676	16194	Mm.2856	NM_010559	ENSMUSG00000027947	Il6ra	CD126|IL-6R|IL-6R-alpha|IL-6RA|Il6r	interleukin 6 receptor, alpha	protein-coding
mm_54038.1	chr6	12749436	12749440	-	1	NA	promoter-TSS (NM_001164805)	promoter-TSS (NM_001164805)	-185	NM_001164805	330267	Mm.11989	NM_001164805	ENSMUSG00000032625	Thsd7a	Gm837	thrombospondin, type I, domain containing 7A	protein-coding
mm_50630.1	chr6	50608421	50608428	+	1	NA	Intergenic	MT2B2|LTR|ERVL	-11834	NM_027564	70821	Mm.157323	NM_027564	ENSMUSG00000029828	4921507P07Rik	TISP74	RIKEN cDNA 4921507P07 gene	protein-coding
mm_171629.1	chr4	18428414	18428424	-	1	NA	Intergenic	L1Md_T|LINE|L1	574961	NM_019724	17389	Mm.187315	NM_019724	ENSMUSG00000028226	Mmp16	MT-MMP 3|MT3-MMP|Mt3mmp	matrix metallopeptidase 16	protein-coding
mm_74974.1	chr8	27140881	27140885	-	1	NA	3' UTR (NM_001080813, exon 6 of 6)	3' UTR (NM_001080813, exon 6 of 6)	-2027	NR_045840	71082	Mm.395259	NR_045840		4933416M07Rik	-	RIKEN cDNA 4933416M07 gene	ncRNA
mm_54378.1	chr6	31207150	31207152	-	1	NA	intron (NR_110469, intron 1 of 3)	intron (NR_110469, intron 1 of 3)	11323	NR_110470	232685	Mm.443019	NM_144555	ENSMUSG00000044471	Lncpint	Lincpint|MNCb-1768|Pint|linc-Pint	long non-protein coding RNA, Trp53 induced transcript	ncRNA
mm_107553.1	chr12	41192888	41192890	+	1	NA	intron (NM_053122, intron 4 of 6)	RMER5|LTR|ERV1	168799	NM_053122	93757	Mm.363813	NM_053122	ENSMUSG00000056899	Immp2l	AI853880|IMP2	IMP2 inner mitochondrial membrane peptidase-like (S. cerevisiae)	protein-coding
mm_55571.1	chr6	71392423	71392435	-	1	NA	3' UTR (NM_024288, exon 9 of 9)	3' UTR (NM_024288, exon 9 of 9)	19002	NM_001081110	12525	Mm.1858	NM_009857	ENSMUSG00000053977	Cd8a	BB154331|Ly-2|Ly-35|Ly-B|Lyt-2	CD8 antigen, alpha chain	protein-coding
mm_148883.1	chr19	6643712	6643713	+	1	NA	Intergenic	Lx8|LINE|L1	-100642	NM_009203	20521	Mm.391146	NM_009203	ENSMUSG00000061742	Slc22a12	AI987855|OAT4L|Rst|Slc22al2|URAT1	solute carrier family 22 (organic anion/cation transporter), member 12	protein-coding
mm_166579.1	chr6	52245925	52245931	+	1	NA	promoter-TSS (NM_010450)	promoter-TSS (NM_010450)	-118	NM_010450	15396	Mm.26954	NM_010450	ENSMUSG00000038210	Hoxa11	Hox-1.9|Hoxa-11	homeobox A11	protein-coding
mm_141701.1	chr17	33997062	33997127	-	1	NA	exon (NM_001001892, exon 5 of 8)	exon (NM_001001892, exon 5 of 8)	3239	NM_001001892	14972	Mm.422886	NM_001001892	ENSMUSG00000061232	H2-K1	H-2K|H-2K(d)|H2-K|K-f	histocompatibility 2, K1, K region	protein-coding
mm_166837.1	chr7	19271771	19271776	-	1	NA	promoter-TSS (NM_001282022)	promoter-TSS (NM_001282022)	81	NM_001282021	22323	Mm.9684	NM_009499	ENSMUSG00000030403	Vasp	-	vasodilator-stimulated phosphoprotein	protein-coding
mm_100400.1	chr11	119393012	119393018	+	1	NA	Intergenic	Intergenic	2543	NR_035453	100316690		NR_035453	ENSMUSG00000088015	Mir1932	mir-1932|mmu-mir-1932	microRNA 1932	ncRNA
mm_23047.1	chr3	34826667	34826671	+	1	NA	Intergenic	Intergenic	54594	NR_110488	102638436	Mm.261793	NR_110488	ENSMUSG00000106519	Gm38509	Peril	predicted gene, 38509	ncRNA
mm_103160.1	chr11	70454557	70454561	-	1	NA	TTS (NM_025397)	TTS (NM_025397)	2628	NM_025397	66172	Mm.46424	NM_025397	ENSMUSG00000018923	Med11	1110030J09Rik|AI465144|AW545069	mediator complex subunit 11	protein-coding
mm_123269.1	chr14	61360396	61360462	-	1	NA	promoter-TSS (NM_026598)	promoter-TSS (NM_026598)	16	NM_026598	68177	Mm.22758	NM_026598	ENSMUSG00000021928	Ebpl	5730442K12Rik|EBRP	emopamil binding protein-like	protein-coding
mm_147675.1	chr18	60649011	60649023	-	1	NA	Intergenic	Intergenic	-14393	NR_045401	328963	Mm.417203	NR_045401		G630071F17Rik	G630071F17	RIKEN cDNA G630071F17 gene	ncRNA
mm_150084.1	chr19	29387617	29387623	+	1	NA	3' UTR (NM_021893, exon 7 of 7)	3' UTR (NM_021893, exon 7 of 7)	20182	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_17281.1	chr2	26122770	26122838	-	1	NA	promoter-TSS (NM_026495)	promoter-TSS (NM_026495)	7	NM_026495	67991	Mm.131074	NM_026495	ENSMUSG00000026932	Nacc2	0610020I02Rik|AI448087|Btbd14a|C030048H19Rik	nucleus accumbens associated 2, BEN and BTB (POZ) domain containing	protein-coding
mm_28504.1	chr3	92532961	92532972	-	1	NA	Intergenic	Intergenic	-32473	NM_173070	229562	Mm.246590	NM_173070	ENSMUSG00000045566	Sprr4	-	small proline-rich protein 4	protein-coding
mm_148715.1	chr19	5812384	5812399	+	1	NA	Intergenic	Intergenic	-9719	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_159993.1	chr6	116208491	116208491	+	1	NA	promoter-TSS (NR_131013)	promoter-TSS (NR_131013)	458	NM_026585	28006	Mm.28524	NM_026585	ENSMUSG00000024104	Washc2	A130095H06|C530005J20Rik|D6Wsu116e|Fam21	WASH complex subunit 2	protein-coding
mm_106595.1	chr11	120730828	120730845	-	1	NA	exon (NM_007621, exon 3 of 8)	exon (NM_007621, exon 3 of 8)	1185	NM_007621	12409	Mm.21454	NM_007621	ENSMUSG00000025150	Cbr2	MLCR	carbonyl reductase 2	protein-coding
mm_118494.1	chr14	13284775	13284793	+	1	NA	promoter-TSS (NM_028052)	promoter-TSS (NM_028052)	4	NM_028052	72003	Mm.317515	NM_028052	ENSMUSG00000056296	Synpr	1500003F20Rik|SPO	synaptoporin	protein-coding
mm_122145.1	chr14	31188766	31188777	-	1	NA	exon (NM_022656, exon 8 of 21)	exon (NM_022656, exon 8 of 21)	18055	NM_022656	64652	Mm.298728	NM_022656	ENSMUSG00000021910	Nisch	1200007D05Rik|3202002H23Rik|AW494485|I-1	nischarin	protein-coding
mm_18926.1	chr2	76745587	76745598	-	1	NA	exon (NM_011652, exon 275 of 313)	exon (NM_011652, exon 275 of 313)	70277	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_42576.1	chr5	117240902	117240923	+	1	NA	intron (NM_001081308, intron 12 of 19)	intron (NM_001081308, intron 12 of 19)	46652	NM_018858	23980	Mm.195898	NM_018858	ENSMUSG00000032959	Pebp1	HCNP|Pbp|Pbp1|Pbpr|Rkip	phosphatidylethanolamine binding protein 1	protein-coding
mm_85417.1	chr9	103480225	103480263	-	1	NA	promoter-TSS (NM_001002896)	promoter-TSS (NM_001002896)	84	NM_001002896	107993	Mm.335403	NM_001002896	ENSMUSG00000032556	Bfsp2	AI448593|CP49	beaded filament structural protein 2, phakinin	protein-coding
mm_169834.1	chr16	25518045	25518060	+	1	NA	Intergenic	ETnERV-int|LTR|ERVK	-165713	NM_001127259	22061	Mm.20894	NM_011641	ENSMUSG00000022510	Trp63	AI462811|Ket|P51/P63|P63|P73l|Tp63|Trp53rp1	transformation related protein 63	protein-coding
mm_3063.1	chr1	134111234	134111248	+	1	NA	promoter-TSS (NM_001284525)	promoter-TSS (NM_001284525)	-1	NM_001284524	71884	Mm.328268	NM_027979	ENSMUSG00000026450	Chit1	2300002L19Rik	chitinase 1 (chitotriosidase)	protein-coding
mm_85664.1	chr9	107675446	107675454	-	1	NA	3' UTR (NM_008140, exon 9 of 9)	3' UTR (NM_008140, exon 9 of 9)	4142	NM_008140	14685	Mm.284853	NM_008140	ENSMUSG00000034837	Gnat1	Gnat-1|Ird1|Ird2|Tralpha|irdc|irdr|transducin	guanine nucleotide binding protein, alpha transducing 1	protein-coding
mm_75699.1	chr8	68212229	68212240	-	1	NA	Intergenic	Intergenic	-64294	NM_028182	72281	Mm.40974	NM_028182	ENSMUSG00000053886	Sh2d4a	2210402M20Rik|SH2A	SH2 domain containing 4A	protein-coding
mm_8713.1	chr1	158969701	158969707	-	1	NA	Intergenic	Intergenic	-12266	NM_001085376	23850	Mm.458621	NM_001085376	ENSMUSG00000073530	Pappa2	PAPP-A2|PLAC3|Pappe	pappalysin 2	protein-coding
mm_67809.1	chr7	98119429	98119437	-	1	NA	promoter-TSS (NM_008663)	promoter-TSS (NM_008663)	60	NM_001256081	17921	Mm.1403	NM_008663	ENSMUSG00000030761	Myo7a	Hdb|Myo7|USH1B|nmf371|polka|sh-1|sh1	myosin VIIA	protein-coding
mm_14815.1	chr2	146200679	146200724	+	1	NA	Intergenic	Intergenic	-21296	NM_016889	53626	Mm.379070	NM_016889	ENSMUSG00000068154	Insm1	IA-1	insulinoma-associated 1	protein-coding
mm_87869.1	chr10	61416280	61416300	+	1	NA	Intergenic	ID_B1|SINE|B4	-1682	NM_013611	18119	Mm.57195	NM_013611	ENSMUSG00000037171	Nodal	Tg.413d	nodal	protein-coding
mm_94390.1	chr11	5525475	5525486	+	1	NA	3' UTR (NM_001271730, exon 6 of 6)	3' UTR (NM_001271730, exon 6 of 6)	4839	NM_001271730	22433	Mm.469937	NM_013842	ENSMUSG00000020484	Xbp1	D11Ertd39e|TREB-5|TREB5|XBP-1	X-box binding protein 1	protein-coding
mm_101249.1	chr11	20741982	20741992	-	1	NA	promoter-TSS (NM_001252503)	promoter-TSS (NM_001252503)	-431	NM_181411	216549	Mm.356580	NM_181411	ENSMUSG00000049659	Aftph	-	aftiphilin	protein-coding
mm_15945.1	chr2	165884823	165884846	+	1	NA	promoter-TSS (NM_001252584)	promoter-TSS (NM_001252584)	4	NM_001252584	228880	Mm.227598	NM_027230	ENSMUSG00000039671	Zmynd8	1110013E22Rik|2010005I16Rik|3632413B07Rik|AI316811|AL024039|Prkcbp1|RACK7	zinc finger, MYND-type containing 8	protein-coding
mm_8427.1	chr1	152536451	152536485	-	1	NA	intron (NM_001346119, intron 11 of 17)	intron (NM_001346119, intron 11 of 17)	88749	NM_016846	19731	Mm.245270	NM_016846	ENSMUSG00000026482	Rgl1	Rgl|mKIAA0959	ral guanine nucleotide dissociation stimulator,-like 1	protein-coding
mm_4163.1	chr1	171029413	171029425	+	1	NA	3' UTR (NM_144559, exon 5 of 5)	3' UTR (NM_144559, exon 5 of 5)	10493	NM_144559	246256	Mm.251254	NM_144559	ENSMUSG00000059089	Fcgr4	4833442P21Rik|CD16-2|FcgRIV|FcgammaRIV|Fcgr3a|Fcrl3	Fc receptor, IgG, low affinity IV	protein-coding
mm_68739.1	chr7	121064190	121064202	-	1	NA	3' UTR (NM_030691, exon 6 of 6)	3' UTR (NM_030691, exon 6 of 6)	10334	NM_030691	80719	Mm.160384	NM_030691	ENSMUSG00000035004	Igsf6	-	immunoglobulin superfamily, member 6	protein-coding
mm_57608.1	chr6	128035029	128035075	-	1	NA	intron (NM_175414, intron 2 of 8)	CpG	108526	NM_175414	109246	Mm.21814	NM_175414	ENSMUSG00000030352	Tspan9	6720474K14Rik|9430079M16Rik|AU018597	tetraspanin 9	protein-coding
mm_50785.1	chr6	53978723	53978730	+	1	NA	promoter-TSS (NM_027749)	promoter-TSS (NM_027749)	35	NR_110484	320178	Mm.320413	NR_110484	ENSMUSG00000108060	4921529L05Rik	-	RIKEN cDNA 4921529L05 gene	ncRNA
mm_126270.1	chr15	79131714	79131749	+	1	NA	intron (NM_177461, intron 13 of 15)	intron (NM_177461, intron 13 of 15)	9520	NM_001310581	27660	Mm.390827	NM_138581	ENSMUSG00000033029	1700088E04Rik	ESTJ0827E04	RIKEN cDNA 1700088E04 gene	protein-coding
mm_103634.1	chr11	78950102	78950110	-	1	NA	exon (NM_010927, exon 20 of 27)	exon (NM_010927, exon 20 of 27)	24815	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_56051.1	chr6	86753885	86753896	-	1	NA	exon (NM_001331120, exon 6 of 13)	exon (NM_001331120, exon 6 of 13)	-20512	NM_011818	23885	Mm.321452	NM_011818	ENSMUSG00000001157	Gmcl1	2810049L19Rik|Btbd13|DIP|Gcl|Gcl-1|glc-1|mglc-1	germ cell-less, spermatogenesis associated 1	protein-coding
mm_88017.1	chr10	67185704	67185723	+	1	NA	promoter-TSS (NM_001242396)	promoter-TSS (NM_001242396)	-37	NM_001242396	108829	Mm.23846	NM_207221	ENSMUSG00000037876	Jmjd1c	5430433L24Rik|D630035I23Rik|Jmjdic|TRIP8	jumonji domain containing 1C	protein-coding
mm_171792.1	chr5	115802199	115802213	-	1	NA	Intergenic	Intergenic	-43450	NM_007708	12704	Mm.8321	NM_007708	ENSMUSG00000029516	Cit	C030025P15Rik|CRIK|CRIK-SK|Cit-k	citron	protein-coding
mm_130314.1	chr15	97167261	97167267	-	1	NA	Intergenic	MLTR31F_MM|LTR|ERVK	-79843	NM_172293	239647	Mm.130036	NM_172293	ENSMUSG00000044250	Pced1b	Fam113b	PC-esterase domain containing 1B	protein-coding
mm_8243.1	chr1	138582314	138582325	-	1	NA	intron (NM_001311148, intron 1 of 7)	LTR16A|LTR|ERVL	37438	NM_021605	59125	Mm.143817	NM_021605	ENSMUSG00000026393	Nek7	2810460C19Rik|AU020186	NIMA (never in mitosis gene a)-related expressed kinase 7	protein-coding
mm_166712.1	chr6	117916812	117916820	-	1	NA	promoter-TSS (NM_001166427)	promoter-TSS (NM_001166427)	-478	NM_001166427	98758	Mm.422979	NM_133834	ENSMUSG00000042079	Hnrnpf	4833420I20Rik|AA407306|Hnrpf	heterogeneous nuclear ribonucleoprotein F	protein-coding
mm_36945.1	chr4	108833609	108833626	-	1	NA	promoter-TSS (NM_027453)	promoter-TSS (NM_027453)	-33	NM_027453	70533	Mm.379178	NM_027453	ENSMUSG00000028568	Btf3l4	4632412E09Rik|5730434I03Rik|AI316863|AU022207|AW552446	basic transcription factor 3-like 4	protein-coding
mm_18491.1	chr2	62606237	62606247	-	1	NA	exon (NM_027835, exon 10 of 16)	exon (NM_027835, exon 10 of 16)	-32221	NM_007986	14089	Mm.41816	NM_007986	ENSMUSG00000000392	Fap	SIMP	fibroblast activation protein	protein-coding
mm_50424.1	chr6	48841477	48841553	+	1	NA	promoter-TSS (NM_001164209)	promoter-TSS (NM_001164209)	32	NM_025326	66058	Mm.27061	NM_025326	ENSMUSG00000023367	Tmem176a	0610011I04Rik|AU040201|AU041743|Keg2	transmembrane protein 176A	protein-coding
mm_16035.1	chr2	167688729	167688765	+	1	NA	promoter-TSS (NM_009883)	promoter-TSS (NM_009883)	-168	NM_009883	12608	Mm.439656	NM_009883	ENSMUSG00000056501	Cebpb	C/EBPbeta|CRP2|IL-6DBP|LAP|LIP|NF-IL6|NF-M|Nfil6	CCAAT/enhancer binding protein (C/EBP), beta	protein-coding
mm_153096.1	chr19	32706872	32706892	-	1	NA	exon (NM_026487, exon 2 of 10)	exon (NM_026487, exon 2 of 10)	5416	NM_026487	67979	Mm.27123	NM_026487	ENSMUSG00000013662	Atad1	4921525H23Rik|AW107648|Thorase	ATPase family, AAA domain containing 1	protein-coding
mm_104414.1	chr11	94653715	94653761	-	1	NA	promoter-TSS (NM_177752)	promoter-TSS (NM_177752)	16	NM_177752	268465	Mm.358937	NM_177752	ENSMUSG00000039055	Eme1	6820428D13	essential meiotic structure-specific endonuclease 1	protein-coding
mm_54486.1	chr6	35307945	35307949	-	1	NA	5' UTR (NM_172892, exon 1 of 16)	5' UTR (NM_172892, exon 1 of 16)	179	NM_172892	243755	Mm.23666	NM_172892	ENSMUSG00000029843	Slc13a4	9630060C05Rik|SUT-1|SUT1	solute carrier family 13 (sodium/sulfate symporters), member 4	protein-coding
mm_170667.1	chr2	116652738	116652739	+	1	NA	Intergenic	IAP1-MM_LTR|LTR|ERVK	-225953	NM_026104	67356	Mm.131623	NM_026104	ENSMUSG00000027355	Tmco5	1700095F04Rik|Tmco5a	transmembrane and coiled-coil domains 5	protein-coding
mm_50523.1	chr6	49044034	49044057	+	1	NA	exon (NM_053110, exon 3 of 11)	exon (NM_053110, exon 3 of 11)	7527	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_89869.1	chr10	108259746	108259764	+	1	NA	intron (NM_027892, intron 14 of 25)	intron (NM_027892, intron 14 of 25)	-72434	NM_054056	114774	Mm.391419	NM_054056	ENSMUSG00000035873	Pawr	2310001G03Rik|PAR4|Par-4	PRKC, apoptosis, WT1, regulator	protein-coding
mm_14862.1	chr2	148798612	148798621	+	1	NA	promoter-TSS (NM_009978)	promoter-TSS (NM_009978)	-223	NM_009978	13012	Mm.20435	NM_009978	ENSMUSG00000027442	Cst8	Cres|Cst-rs1	cystatin 8 (cystatin-related epididymal spermatogenic)	protein-coding
mm_72546.1	chr8	84001456	84001468	+	1	NA	promoter-TSS (NM_183097)	promoter-TSS (NM_183097)	-244	NM_183097	73453	Mm.75101	NM_183097	ENSMUSG00000046408	1700067K01Rik	-	RIKEN cDNA 1700067K01 gene	protein-coding
mm_128795.1	chr15	66812660	66812680	-	1	NA	5' UTR (NM_009192, exon 2 of 9)	5' UTR (NM_009192, exon 2 of 9)	19159	NM_001029841	20491	Mm.7601	NM_009192	ENSMUSG00000022372	Sla	Slap|Slap-1	src-like adaptor	protein-coding
mm_117285.1	chr13	66062936	66062944	-	1	NA	Intergenic	Intergenic	-50513	NM_001177832	628709	Mm.390595	NM_001177832	ENSMUSG00000095909	Gm10324	ENSMUSG00000071302	predicted gene 10324	protein-coding
mm_160580.1	chr9	59707820	59707820	+	1	NA	promoter-TSS (NM_001033498)	promoter-TSS (NM_001033498)	56	NM_001033498	546134	Mm.297580	NM_001033498	ENSMUSG00000074259	Gramd2	BC064463	GRAM domain containing 2	protein-coding
mm_134581.1	chr16	20405632	20405640	-	1	NA	intron (NM_176839, intron 3 of 6)	intron (NM_176839, intron 3 of 6)	20758	NM_013790	27416	Mm.20845	NM_013790	ENSMUSG00000022822	Abcc5	2900011L11Rik|AI132311|Abcc5a|Abcc5b|Mrp5	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	protein-coding
mm_80630.1	chr9	89199320	89199332	+	1	NA	promoter-TSS (NM_007534)	promoter-TSS (NM_007534)	53	NM_007534	12045	Mm.479217	NM_007534	ENSMUSG00000089929	Bcl2a1b	A1-b	B cell leukemia/lymphoma 2 related protein A1b	protein-coding
mm_167805.1	chr9	123928312	123928371	+	1	NA	Intergenic	Intergenic	40351	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_38564.1	chr4	141696044	141696047	-	1	NA	intron (NM_001017966, intron 6 of 9)	B2_Mm2|SINE|B2	-10329	NM_023544	69994	Mm.441022	NM_023544	ENSMUSG00000040715	Rsc1a1	1700027M01Rik|OTTMUSG00000010365|Rs1	regulatory solute carrier protein, family 1, member 1	protein-coding
mm_164257.1	chr15	100063609	100063614	+	1	NA	intron (NM_001159361, intron 1 of 37)	intron (NM_001159361, intron 1 of 37)	24947	NM_001159361	239667	Mm.243658	NM_172819	ENSMUSG00000023026	Dip2b	4932422C22|AI317237|AI854602|mKIAA1463	disco interacting protein 2 homolog B	protein-coding
mm_92279.1	chr10	71285190	71285200	-	1	NA	promoter-TSS (NM_145420)	promoter-TSS (NM_145420)	67	NM_145420	216080	Mm.270530	NM_145420	ENSMUSG00000019927	Ube2d1	UBCH5	ubiquitin-conjugating enzyme E2D 1	protein-coding
mm_94440.1	chr11	6292877	6292898	+	1	NA	intron (NM_001252288, intron 1 of 22)	intron (NM_001252288, intron 1 of 22)	329	NM_001252288	18293	Mm.276348	NM_010956	ENSMUSG00000020456	Ogdh	2210403E04Rik|2210412K19Rik|AA409584|d1401|mKIAA4192	oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)	protein-coding
mm_104881.1	chr11	99521291	99521295	-	1	NA	promoter-TSS (NM_213730)	promoter-TSS (NM_213730)	-35	NM_213730	237934	Mm.484091	NM_213730	ENSMUSG00000064165	Krt39	4732494G06Rik|Ka35	keratin 39	protein-coding
mm_165221.1	chr2	48691504	48691510	-	1	NA	Intergenic	Intergenic	-122602	NM_007396	11480	Mm.314338	NM_007396	ENSMUSG00000052155	Acvr2a	ActrIIa|Acvr2|TactrII	activin receptor IIA	protein-coding
mm_77491.1	chr8	122575432	122575444	-	1	NA	exon (NM_009698, exon 3 of 5)	exon (NM_009698, exon 3 of 5)	1469	NM_009698	11821	Mm.1786	NM_009698	ENSMUSG00000006589	Aprt	C85684	adenine phosphoribosyl transferase	protein-coding
mm_65696.1	chr7	28376971	28376994	-	1	NA	3' UTR (NM_011756, exon 2 of 2)	3' UTR (NM_011756, exon 2 of 2)	2246	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_126222.1	chr15	78926721	78926735	+	1	NA	promoter-TSS (NM_008495)	promoter-TSS (NM_008495)	3	NM_008495	16852	Mm.43831	NM_008495	ENSMUSG00000068220	Lgals1	AA410090|Gal-1|Galbp|L-14.5|L14|Lect14|galectin-1	lectin, galactose binding, soluble 1	protein-coding
mm_154485.1	chrM	4654	4681	-	1	NA	NA	Intergenic	NA	NA								
mm_123538.1	chr14	66815022	66815043	-	1	NA	exon (NM_009955, exon 10 of 14)	exon (NM_009955, exon 10 of 14)	53568	NM_009955	12934	Mm.352648	NM_009955	ENSMUSG00000022048	Dpysl2	AI851130|Crmp2|DRP2|Musunc33|TOAD-64|Ulip2	dihydropyrimidinase-like 2	protein-coding
mm_167572.1	chr9	44268462	44268476	-	1	NA	promoter-TSS (NM_001163743)	promoter-TSS (NM_001163743)	22	NM_178420	270151	Mm.3957	NM_178420	ENSMUSG00000032109	Nlrx1	BC034204|NOD9	NLR family member X1	protein-coding
mm_99175.1	chr11	100859454	100859483	+	1	NA	5' UTR (NM_011488, exon 1 of 20)	5' UTR (NM_011488, exon 1 of 20)	117	NM_011488	20850	Mm.277403	NM_011488	ENSMUSG00000004043	Stat5a	AA959963|STAT5	signal transducer and activator of transcription 5A	protein-coding
mm_148188.1	chr18	78912222	78912223	-	1	NA	intron (NM_053099, intron 3 of 5)	intron (NM_053099, intron 3 of 5)	197169	NM_053099	240427	Mm.312871	NM_053099	ENSMUSG00000024548	Setbp1	C130092E12|Seb|mKIAA0437	SET binding protein 1	protein-coding
mm_31083.1	chr4	41629971	41629977	+	1	NA	intron (NM_175138, intron 14 of 19)	intron (NM_175138, intron 14 of 19)	10328	NM_027147	69638	Mm.372459	NM_027147	ENSMUSG00000028445	Enho	1110065P19Rik|2310040A07Rik	energy homeostasis associated	protein-coding
mm_156163.1	chrX	130006105	130006118	+	1	NA	intron (NM_172493, intron 17 of 26)	intron (NM_172493, intron 17 of 26)	256369	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diaph2	Dia3|Diap2|Drf2|E430022I22Rik	diaphanous related formin 2	protein-coding
mm_120354.1	chr14	63992468	63992479	+	1	NA	promoter-TSS (NM_146246)	promoter-TSS (NM_146246)	42	NM_146246	271209	Mm.300655	NM_146246	ENSMUSG00000046049	Rp1l1	BC031365|BE983540|Dcdc4|Rp1hl1	retinitis pigmentosa 1 homolog like 1	protein-coding
mm_161576.1	chr16	25683763	25683763	+	1	NA	promoter-TSS (NM_001127261)	promoter-TSS (NM_001127261)	-2	NM_001127259	22061	Mm.20894	NM_011641	ENSMUSG00000022510	Trp63	AI462811|Ket|P51/P63|P63|P73l|Tp63|Trp53rp1	transformation related protein 63	protein-coding
mm_133236.1	chr16	77037397	77037414	+	1	NA	exon (NM_013918, exon 3 of 24)	exon (NM_013918, exon 3 of 24)	23336	NM_013918	30940	Mm.40986	NM_013918	ENSMUSG00000022867	Usp25	-	ubiquitin specific peptidase 25	protein-coding
mm_15550.1	chr2	158410168	158410171	+	1	NA	intron (NM_001291137, intron 1 of 30)	CpG	316	NM_001291138	228850	Mm.398185	NM_177227	ENSMUSG00000027652	Ralgapb	AI507211|B230339M05Rik|p170	Ral GTPase activating protein, beta subunit (non-catalytic)	protein-coding
mm_4253.1	chr1	171408211	171408222	+	1	NA	exon (NM_001005508, exon 12 of 12)	exon (NM_001005508, exon 12 of 12)	-3097	NM_001305678	22278	Mm.8	NM_009480	ENSMUSG00000026641	Usf1	bHLHb11	upstream transcription factor 1	protein-coding
mm_133712.1	chr16	93603832	93603847	+	1	NA	promoter-TSS (NM_145482)	promoter-TSS (NM_145482)	-24	NM_145482	224440	Mm.10628	NM_145482	ENSMUSG00000022948	Setd4	AY037804|C21orf18|ORF21	SET domain containing 4	protein-coding
mm_82748.1	chr9	26804486	26804492	-	1	NA	intron (NM_153803, intron 1 of 19)	intron (NM_153803, intron 1 of 19)	1928	NM_153803	244757	Mm.293696	NM_153803	ENSMUSG00000036395	Glb1l2	-	galactosidase, beta 1-like 2	protein-coding
mm_21868.1	chr2	165900923	165900935	-	1	NA	Intergenic	Intergenic	-16091	NM_001252587	228880	Mm.227598	NM_027230	ENSMUSG00000039671	Zmynd8	1110013E22Rik|2010005I16Rik|3632413B07Rik|AI316811|AL024039|Prkcbp1|RACK7	zinc finger, MYND-type containing 8	protein-coding
mm_127.1	chr1	9908655	9908669	+	1	NA	promoter-TSS (NM_177722)	promoter-TSS (NM_177722)	24	NM_177722	240697	Mm.259800	NM_177722	ENSMUSG00000046101	Mcmdc2	6030422M02Rik	minichromosome maintenance domain containing 2	protein-coding
mm_6456.1	chr1	74016655	74016663	-	1	NA	intron (NM_027884, intron 3 of 34)	intron (NM_027884, intron 3 of 34)	107788	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_93733.1	chr10	120112866	120112911	-	1	NA	promoter-TSS (NM_080446)	promoter-TSS (NM_080446)	77	NM_080446	117599	Mm.214703	NM_080446	ENSMUSG00000020228	Helb	AI447783|D10Ertd664e	helicase (DNA) B	protein-coding
mm_118803.1	chr14	25298366	25298367	+	1	NA	Intergenic	MIRb|SINE|MIR	-155125	NR_045718	75862	Mm.109191	NR_045718		4930572O13Rik	-	RIKEN cDNA 4930572O13 gene	ncRNA
mm_46345.1	chr5	102069906	102069940	-	1	NA	promoter-TSS (NM_172882)	promoter-TSS (NM_172882)	-2	NM_172882	72145	Mm.332522	NM_172882	ENSMUSG00000043940	Wdfy3	2610509D04Rik|ALFY|AW319683|B930017C24|BWF1|Bchs|D5Ertd66e|Ggtb3|ZFYVE25|mKIAA0993	WD repeat and FYVE domain containing 3	protein-coding
mm_130491.1	chr15	98803801	98803804	-	1	NA	TTS (NM_001013741)	TTS (NM_001013741)	4123	NM_001013741	13199	Mm.390810	NM_001013741	ENSMUSG00000059213	Ddn	Gm748	dendrin	protein-coding
mm_13036.1	chr2	91070347	91070356	+	1	NA	promoter-TSS (NR_110981)	promoter-TSS (NR_110981)	-36	NM_001290765	68427	Mm.192375	NM_026721	ENSMUSG00000002105	Slc39a13	1100001L14Rik|AA387663|ZIP-13|ZIP13	solute carrier family 39 (metal ion transporter), member 13	protein-coding
mm_173202.1	chrX	69024593	69024598	-	1	NA	Intergenic	L1Md_T|LINE|L1	-131542	NM_001098842	627927	Mm.391264	NM_001098842	ENSMUSG00000056815	Gm6812	EG627927	predicted gene 6812	protein-coding
mm_120209.1	chr14	62332086	62332110	+	1	NA	promoter-TSS (NM_026001)	promoter-TSS (NM_026001)	-7	NM_026001	67153	Mm.26040	NM_026001	ENSMUSG00000021932	Rnaseh2b	1110019N06Rik|2610207P08Rik|Dleu8	ribonuclease H2, subunit B	protein-coding
mm_37945.1	chr4	133159262	133159273	-	1	NA	intron (NM_153423, intron 1 of 8)	intron (NM_153423, intron 1 of 8)	28634	NM_153423	242687	Mm.23566	NM_153423	ENSMUSG00000028868	Wasf2	AW742646|D4Ertd13e|WAVE2	WAS protein family, member 2	protein-coding
mm_118666.1	chr14	21848467	21848487	+	1	NA	5' UTR (NM_176925, exon 1 of 3)	5' UTR (NM_176925, exon 1 of 3)	433	NM_026965	69156	Mm.11827	NM_026965	ENSMUSG00000021773	Comtd1	1810030M08Rik|MT773	catechol-O-methyltransferase domain containing 1	protein-coding
mm_163312.1	chr12	5892049	5892067	+	1	NA	Intergenic	Intergenic	515556	NR_015579	72669	Mm.10434	NM_028318		2810032G03Rik	AI461720	RIKEN cDNA 2810032G03 gene	ncRNA
mm_32126.1	chr4	99037463	99037478	+	1	NA	exon (NM_013913, exon 6 of 7)	exon (NM_013913, exon 6 of 7)	6516	NM_013913	30924	Mm.28341	NM_013913	ENSMUSG00000028553	Angptl3	hypl	angiopoietin-like 3	protein-coding
mm_158526.1	chrX	143861090	143861100	-	1	NA	3' UTR (NM_010025, exon 7 of 7)	3' UTR (NM_010025, exon 7 of 7)	-33683	NM_007603	12338	Mm.30290	NM_007603	ENSMUSG00000067276	Capn6	-	calpain 6	protein-coding
mm_45629.1	chr5	76304732	76304790	-	1	NA	promoter-TSS (NM_001289826)	promoter-TSS (NM_001289826)	31	NM_001289826	12753	Mm.3552	NM_007715	ENSMUSG00000029238	Clock	5330400M04Rik|KAT13D	circadian locomotor output cycles kaput	protein-coding
mm_14971.1	chr2	152093945	152093958	+	1	NA	3' UTR (NM_001160410, exon 2 of 2)	3' UTR (NM_001160410, exon 2 of 2)	-11573	NM_029688	76650	Mm.218639	NM_029688	ENSMUSG00000032802	Srxn1	1700127B04Rik|AI854065|AW488194|Npn3|Srx|Srx1|TX01	sulfiredoxin 1 homolog (S. cerevisiae)	protein-coding
mm_35336.1	chr4	31970542	31970548	-	1	NA	intron (NM_172688, intron 1 of 15)	RMER10B|LTR|ERVL	6438	NM_172688	26409	Mm.258589	NM_009316	ENSMUSG00000028284	Map3k7	B430101B05|C87327|Tak1	mitogen-activated protein kinase kinase kinase 7	protein-coding
mm_75313.1	chr8	41217897	41217927	-	1	NA	Intergenic	RLTR20B3A_MM|LTR|ERVK	-2756	NM_145594	234199	Mm.277955	NM_145594	ENSMUSG00000031594	Fgl1	Mfire1	fibrinogen-like protein 1	protein-coding
mm_116330.1	chr13	38036926	38036947	-	1	NA	promoter-TSS (NM_027724)	promoter-TSS (NM_027724)	1	NM_027724	71213	Mm.314688	NM_027724	ENSMUSG00000044566	Cage1	4933427I01Rik|Ctag3	cancer antigen 1	protein-coding
mm_165901.1	chr4	47284271	47284316	+	1	NA	intron (NM_009928, intron 20 of 39)	intron (NM_009928, intron 20 of 39)	-68929	NM_001312868	21812	Mm.197552	NM_009370	ENSMUSG00000007613	Tgfbr1	ALK5|AU017191|Alk-5|ESK2|TGFR-1|TbetaR-I|TbetaRI	transforming growth factor, beta receptor I	protein-coding
mm_16450.1	chr2	180460989	180460997	+	1	NA	promoter-TSS (NM_148933)	promoter-TSS (NM_148933)	15	NM_148933	108115	Mm.133687	NM_148933	ENSMUSG00000038963	Slco4a1	OATP-E|Slc21a12	solute carrier organic anion transporter family, member 4a1	protein-coding
mm_49947.1	chr6	40038281	40038285	+	1	NA	Intergenic	MIR|SINE|MIR	-71970	NM_001004182	434008	Mm.130209	NM_001004182	ENSMUSG00000057716	Tmem178b	EG434008|Gm5567	transmembrane protein 178B	protein-coding
mm_124272.1	chr14	103014921	103014974	-	1	NA	intron (NR_045657, intron 2 of 2)	RMER1B|Other|Other	18856	NR_045657	71264	Mm.399572	NR_045657		4933432I03Rik	-	RIKEN cDNA 4933432I03 gene	ncRNA
mm_142837.1	chr17	51792386	51792387	-	1	NA	intron (NM_009122, intron 5 of 10)	intron (NM_009122, intron 5 of 10)	19668	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_19173.1	chr2	84345674	84345677	-	1	NA	intron (NM_018782, intron 11 of 15)	intron (NM_018782, intron 11 of 15)	79591	NM_018782	54598	Mm.75467	NM_018782	ENSMUSG00000059588	Calcrl	AV071593|CRLR	calcitonin receptor-like	protein-coding
mm_65135.1	chr7	19562169	19562197	-	1	NA	5' UTR (NM_199149, exon 1 of 13)	5' UTR (NM_199149, exon 1 of 13)	215	NM_199149	232947	Mm.219662	NM_199149	ENSMUSG00000051403	Ppp1r37	Gm158|Lrrc68	protein phosphatase 1, regulatory subunit 37	protein-coding
mm_66821.1	chr7	48558067	48558094	-	1	NA	promoter-TSS (NM_175531)	promoter-TSS (NM_175531)	6	NM_175531	243979	Mm.83689	NM_175531	ENSMUSG00000050425	Mrgprb2	4833406I20Rik|Mgrg14	MAS-related GPR, member B2	protein-coding
mm_159771.1	chr5	100395891	100395891	-	1	NA	exon (NM_026969, exon 8 of 28)	exon (NM_026969, exon 8 of 28)	20343	NM_026969	69162	Mm.18634	NM_026969	ENSMUSG00000035325	Sec31a	1810024J13Rik|ABP125|ABP130|AU042160|HSPC275|Sec31l1	Sec31 homolog A (S. cerevisiae)	protein-coding
mm_90870.1	chr10	8886590	8886612	-	1	NA	promoter-TSS (NM_175155)	promoter-TSS (NM_175155)	-531	NM_175155	70097	Mm.338275	NM_175155	ENSMUSG00000015305	Sash1	1100001C18Rik|2500002E12Rik|A330076K04Rik|mKIAA0790	SAM and SH3 domain containing 1	protein-coding
mm_24624.1	chr3	93547941	93547951	+	1	NA	Intergenic	Intergenic	-7171	NM_009112	20194	Mm.1	NM_009112	ENSMUSG00000041959	S100a10	42C|AA409961|AL024248|CAL12|CLP11|Cal1l|p10|p11	S100 calcium binding protein A10 (calpactin)	protein-coding
mm_66941.1	chr7	61934309	61934324	-	1	NA	Intergenic	Intergenic	5790	NR_030557	100124439		NR_030557	ENSMUSG00000093187	Mir344-2	Mirn344-2|mir-344-2	microRNA 344-2	ncRNA
mm_69545.1	chr7	135695865	135695875	-	1	NA	exon (NM_001081117, exon 12 of 14)	exon (NM_001081117, exon 12 of 14)	20509	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_124050.1	chr14	77861289	77861296	-	1	NA	intron (NM_025384, intron 1 of 5)	RLTR8|LTR|ERVK	13625	NM_025384	66148	Mm.248046	NM_025384	ENSMUSG00000022013	Dnajc15	1110003P16Rik|Dnajd1	DnaJ heat shock protein family (Hsp40) member C15	protein-coding
mm_121871.1	chr14	20794010	20794098	-	1	NA	promoter-TSS (NM_178597)	promoter-TSS (NM_178597)	34	NM_001039138	12325	Mm.235182	NM_178597	ENSMUSG00000021820	Camk2g	Camkg	calcium/calmodulin-dependent protein kinase II gamma	protein-coding
mm_161000.1	chr11	116189634	116189634	-	1	NA	intron (NM_001271898, intron 2 of 13)	intron (NM_001271898, intron 2 of 13)	-9221	NM_027107	69535	Mm.390347	NM_027107	ENSMUSG00000020778	Ten1	2310004N24Rik	TEN1 telomerase capping complex subunit	protein-coding
mm_170821.1	chr2	176636337	176636356	-	1	NA	promoter-TSS (NM_001099349).4	promoter-TSS (NM_001099349).4	-27	NM_001100415	627914	Mm.466613	NM_001100415		Gm14430	OTTMUSG00000016607	predicted gene 14430	protein-coding
mm_114109.1	chr13	54876161	54876185	+	1	NA	Intergenic	Intergenic	-73238	NM_001311128	107448	Mm.23573	NM_153131	ENSMUSG00000025876	Unc5a	Unc5h1|mKIAA1976	unc-5 netrin receptor A	protein-coding
mm_135682.1	chr16	52424352	52424392	-	1	NA	intron (NM_009655, intron 1 of 15)	intron (NM_009655, intron 1 of 15)	28709	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_112992.1	chr13	21722058	21722073	+	1	NA	promoter-TSS (NM_178200)	promoter-TSS (NM_178200)	21	NM_178200	319186	Mm.277425	NM_178200	ENSMUSG00000096807	Hist1h2bm	H2b-291b	histone cluster 1, H2bm	protein-coding
mm_137554.1	chr17	27622257	27622267	+	1	NA	intron (NM_019837, intron 1 of 4)	intron (NM_019837, intron 1 of 4)	702	NM_001291046	56409	Mm.144699	NM_019837	ENSMUSG00000024213	Nudt3	1110011B09Rik|AA960325|Dipp|Dipp1	nudix (nucleotide diphosphate linked moiety X)-type motif 3	protein-coding
mm_21606.1	chr2	164254503	164254513	-	1	NA	3' UTR (NM_173377, exon 3 of 3)	3' UTR (NM_173377, exon 3 of 3)	2135	NM_173377	329557	Mm.118769	NM_173377	ENSMUSG00000050383	Svs3b	9530004A22Rik	seminal vesicle secretory protein 3B	protein-coding
mm_9759.1	chr1	180848925	180848939	-	1	NA	Intergenic	Intergenic	-2219	NM_145943	208768	Mm.272625	NM_145943	ENSMUSG00000038806	Sde2	-	SDE2 telomere maintenance homolog (S. pombe)	protein-coding
mm_42541.1	chr5	115947927	115947947	+	1	NA	exon (NM_007708, exon 21 of 47)	exon (NM_007708, exon 21 of 47)	76491	NM_031869	19079	Mm.458152	NM_031869	ENSMUSG00000029513	Prkab1	1300015D22Rik|AU021155|E430008F22	protein kinase, AMP-activated, beta 1 non-catalytic subunit	protein-coding
mm_132540.1	chr16	37881302	37881326	+	1	NA	exon (NM_177093, exon 4 of 4)	exon (NM_177093, exon 4 of 4)	12914	NM_177093	320184	Mm.390882	NM_177093	ENSMUSG00000034158	Lrrc58	1810012N18Rik|C330018J07Rik	leucine rich repeat containing 58	protein-coding
mm_73049.1	chr8	94355890	94355909	+	1	NA	intron (NM_019415, intron 21 of 24)	intron (NM_019415, intron 21 of 24)	26691	NM_001205311	20497	Mm.25804	NM_019415	ENSMUSG00000031766	Slc12a3	AI035291|NCC|NCCT|TSC	solute carrier family 12, member 3	protein-coding
mm_116846.1	chr13	54749850	54749893	-	1	NA	promoter-TSS (NM_001316710)	promoter-TSS (NM_001316710)	3	NM_001316710	26913	Mm.41812	NM_012014	ENSMUSG00000069227	Gprin1	GRIN1|Z16	G protein-regulated inducer of neurite outgrowth 1	protein-coding
mm_14460.1	chr2	131207079	131207095	+	1	NA	intron (NR_037281, intron 2 of 2)	intron (NR_037281, intron 2 of 2)	-3273	NM_001291032	69596	Mm.2937	NM_027129	ENSMUSG00000068264	Ap5s1	0610038L13Rik|2310035K24Rik|AW060727|sigma5	adaptor-related protein 5 complex, sigma 1 subunit	protein-coding
mm_12085.1	chr2	60209894	60209966	+	1	NA	promoter-TSS (NM_020575)	promoter-TSS (NM_020575)	-6	NM_020575	57438	Mm.260635	NM_020575	ENSMUSG00000026977	March7	Axo|Axot|Gtrgeo17	membrane-associated ring finger (C3HC4) 7	protein-coding
mm_36685.1	chr4	96553566	96553576	-	1	NA	promoter-TSS (NM_010008)	promoter-TSS (NM_010008)	80	NM_010008	13110	Mm.98200	NM_010008	ENSMUSG00000052914	Cyp2j6	-	cytochrome P450, family 2, subfamily j, polypeptide 6	protein-coding
mm_118342.1	chr13	114458834	114458844	-	1	NA	5' UTR (NM_008046, exon 1 of 6)	5' UTR (NM_008046, exon 1 of 6)	112	NM_001301373	14313	Mm.4913	NM_008046	ENSMUSG00000021765	Fst	AL033346|FS	follistatin	protein-coding
mm_126976.1	chr15	93432939	93432947	+	1	NA	intron (NM_175363, intron 3 of 8)	intron (NM_175363, intron 3 of 8)	34479	NM_001285863	223828	Mm.74208	NM_146062	ENSMUSG00000036167	Pphln1	CR|HSPC206|HSPC232	periphilin 1	protein-coding
mm_2290.1	chr1	91413424	91413439	+	1	NA	promoter-TSS (NM_019479)	promoter-TSS (NM_019479)	-209	NM_019479	55927	Mm.280029	NM_019479	ENSMUSG00000067071	Hes6	AI326893|bHLHb41	hairy and enhancer of split 6	protein-coding
mm_89224.1	chr10	87206005	87206009	+	1	NA	intron (NM_029685, intron 4 of 5)	intron (NM_029685, intron 4 of 5)	147961	NM_029685	76640	Mm.78423	NM_029685	ENSMUSG00000047129	1700113H08Rik	-	RIKEN cDNA 1700113H08 gene	protein-coding
mm_81239.1	chr9	107928623	107928663	+	1	NA	exon (NM_026338, exon 1 of 1)	exon (NM_026338, exon 1 of 1)	174	NM_026338	67722	Mm.390222	NM_026338	ENSMUSG00000066368	Actl11	4921517D21Rik	actin-like 11	protein-coding
mm_162174.1	chrX	101654756	101654756	+	1	NA	intron (NM_139144, intron 4 of 21)	intron (NM_139144, intron 4 of 21)	14538	NM_001290535	108155	Mm.487332	NM_139144	ENSMUSG00000034160	Ogt	1110038P24Rik|4831420N21Rik|AI115525|Ogtl	O-linked N-acetylglucosamine (GlcNAc) transferase (UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase)	protein-coding
mm_64203.1	chr7	141470596	141470622	+	1	NA	exon (NM_001111049, exon 8 of 8)	exon (NM_001111049, exon 8 of 8)	1820	NM_001111050	12476	Mm.30246	NM_009842	ENSMUSG00000025510	Cd151	PETA-3|SFA-1|Tspan24	CD151 antigen	protein-coding
mm_163683.1	chr13	93711717	93711722	+	1	NA	intron (NM_028772, intron 10 of 15)	intron (NM_028772, intron 10 of 15)	7456	NR_045086	105364	Mm.443795	NR_045086	ENSMUSG00000087334	AW495222	-	expressed sequence AW495222	ncRNA
mm_107625.1	chr12	51690993	51691039	+	1	NA	promoter-TSS (NM_001329699)	promoter-TSS (NM_001329699)	50	NM_001329698	11782	Mm.386749	NM_021710	ENSMUSG00000020955	Ap4s1	AI314282	adaptor-related protein complex AP-4, sigma 1	protein-coding
mm_85116.1	chr9	95407304	95407333	-	1	NA	promoter-TSS (NM_018763)	promoter-TSS (NM_018763)	-48	NM_018763	54371	Mm.212446	NM_018763	ENSMUSG00000033350	Chst2	AI428561|AW121776|C130041E03Rik|Chts2|GST-2|GlcNAc6ST|Gn6st	carbohydrate sulfotransferase 2	protein-coding
mm_172211.1	chr6	59199707	59199713	+	1	NA	Intergenic	L1Md_Gf|LINE|L1	-9160	NM_001081145	68140	Mm.25843	NM_001081145	ENSMUSG00000049232	Tigd2	3632410O17Rik	tigger transposable element derived 2	protein-coding
mm_15824.1	chr2	164568353	164568405	+	1	NA	3' UTR (NM_026323, exon 5 of 5)	3' UTR (NM_026323, exon 5 of 5)	5077	NM_001177401	629747	Mm.234248	NM_001177401	ENSMUSG00000074596	Spint3	Gm14315|OTTMUSG00000016288	serine peptidase inhibitor, Kunitz type, 3	protein-coding
mm_128343.1	chr15	39325818	39325821	-	1	NA	intron (NM_001256382, intron 2 of 26)	RMER19B|LTR|ERVK	127533	NM_053271	116838	Mm.309296	NM_053271	ENSMUSG00000037386	Rims2	2810036I15Rik|AW048769|RIM2|Rab3ip2|Rim2(+40A)|Rim2(+44A)|Rim2(+4A)|Serg2|Syt3-rs|mKIAA0751	regulating synaptic membrane exocytosis 2	protein-coding
mm_113520.1	chr13	37806157	37806166	+	1	NA	Intergenic	B1_Mur4|SINE|Alu	-19877	NM_026830	68750	Mm.491109	NM_026830	ENSMUSG00000039087	Rreb1	1110037N09Rik|AA414966|B930013M22Rik	ras responsive element binding protein 1	protein-coding
mm_8530.1	chr1	154929185	154929195	-	1	NA	Intergenic	MLT1B|LTR|ERVL-MaLR	170446	NM_010500	15939	Mm.12246	NM_010500	ENSMUSG00000056708	Ier5	-	immediate early response 5	protein-coding
mm_22286.1	chr2	180207784	180207794	-	1	NA	intron (NM_001081171, intron 3 of 78)	intron (NM_001081171, intron 3 of 78)	18070	NM_001081171	16776	Mm.4339	NM_001081171	ENSMUSG00000015647	Lama5	AA408760|AA408762|AI853660|[a]5|laminin-511|mKIAA0533	laminin, alpha 5	protein-coding
mm_104078.1	chr11	86586997	86587012	-	1	NA	intron (NM_029478, intron 10 of 11)	intron (NM_029478, intron 10 of 11)	-2846	NR_029738	387140		NR_029738	ENSMUSG00000065455	Mir21a	Mir21|Mirn21|mmu-mir-21|mmu-mir-21a	microRNA 21a	ncRNA
mm_24401.1	chr3	90359339	90359352	+	1	NA	Intergenic	Intergenic	17691	NM_139304	229542	Mm.270999	NM_139304	ENSMUSG00000042390	Gatad2b	AL118180|C430014D17Rik|P66beta|mKIAA1150	GATA zinc finger domain containing 2B	protein-coding
mm_34477.1	chr4	148375011	148375012	+	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	69740	NM_027873	71707	Mm.292503	NM_027873	ENSMUSG00000047719	Ubiad1	1200002M06Rik|AI426463|AW320947|Tere1	UbiA prenyltransferase domain containing 1	protein-coding
mm_88500.1	chr10	77837829	77837833	+	1	NA	TTS (NM_001024709)	TTS (NM_001024709)	1884	NM_001024709	544710	Mm.441890	NM_001024709		Krtap10-10	EG544710	keratin associated protein 10-10	protein-coding
mm_53339.1	chr6	129238159	129238199	+	1	NA	promoter-TSS (NR_040265)	promoter-TSS (NR_040265)	-134	NR_040265	76432	Mm.261738	NR_040265	ENSMUSG00000097354	2310001H17Rik	AI646108	RIKEN cDNA 2310001H17 gene	ncRNA
mm_129372.1	chr15	78119630	78119652	-	1	NA	promoter-TSS (NM_007583)	promoter-TSS (NM_007583)	-361	NM_007583	12300	Mm.277338	NM_007583	ENSMUSG00000019146	Cacng2	AW060990|B230105C07Rik|B930041E13Rik|stargazer|stargazin|stg|wag|waggler	calcium channel, voltage-dependent, gamma subunit 2	protein-coding
mm_14456.1	chr2	131187078	131187118	+	1	NA	5' UTR (NM_001111075, exon 1 of 15)	5' UTR (NM_001111075, exon 1 of 15)	150	NM_001111075	12531	Mm.38444	NM_023117	ENSMUSG00000027330	Cdc25b	AI604853	cell division cycle 25B	protein-coding
mm_164268.1	chr15	101244176	101244177	+	1	NA	Intergenic	Intergenic	-18990	NR_045328	380977	Mm.399924	NR_045326	ENSMUSG00000097915	A330009N23Rik	-	RIKEN cDNA A330009N23 gene	ncRNA
mm_1471.1	chr1	69951612	69951635	+	1	NA	promoter-TSS (NM_025728)	promoter-TSS (NM_025728)	8	NM_025728	66722	Mm.440554	NM_025728	ENSMUSG00000053153	Spag16	4921511D23Rik|4930524F24Rik|4930585K05Rik|AV261009|Pf20|Wdr29	sperm associated antigen 16	protein-coding
mm_98859.1	chr11	97685795	97685845	+	1	NA	promoter-TSS (NM_001085500)	promoter-TSS (NM_001085500)	-132	NM_001085500	217149	Mm.29659	NM_001085500	ENSMUSG00000078695	Cisd3	Mel-13|Mel13	CDGSH iron sulfur domain 3	protein-coding
mm_52623.1	chr6	117174114	117174126	+	1	NA	3' UTR (NM_021704, exon 3 of 3)	3' UTR (NM_021704, exon 3 of 3)	5585	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_166453.1	chr5	137831409	137831421	-	1	NA	intron (NM_153510, intron 2 of 6)	MLTR14|LTR|ERV1	4863	NM_153510	231805	Mm.379385	NM_153510	ENSMUSG00000046245	Pilra	AV021745|FDF03	paired immunoglobin-like type 2 receptor alpha	protein-coding
mm_29445.1	chr3	110143787	110143842	-	1	NA	promoter-TSS (NM_001163350)	promoter-TSS (NM_001163350)	-342	NM_030699	80883	Mm.39262	NM_030699	ENSMUSG00000059857	Ntng1	A930010C08Rik|AI853992|Lmnt1	netrin G1	protein-coding
mm_99004.1	chr11	98799201	98799215	+	1	NA	exon (NM_028722, exon 2 of 9)	exon (NM_028722, exon 2 of 9)	3439	NM_028722	74026	Mm.258352	NM_028722	ENSMUSG00000052915	Msl1	2810017F12Rik|4121402D02Rik|4930463F05Rik|AA682082|Msl-1	male-specific lethal 1 homolog (Drosophila)	protein-coding
mm_63410.1	chr7	127333782	127333835	+	1	NA	3' UTR (NM_001253873, exon 31 of 31)	3' UTR (NM_001253873, exon 31 of 31)	11506	NM_146202	233890	Mm.23031	NM_146202	ENSMUSG00000047371	Zfp768	BC026432|Znf768	zinc finger protein 768	protein-coding
mm_14009.1	chr2	122118540	122118554	+	1	NA	promoter-TSS (NM_145531)	promoter-TSS (NM_145531)	-161	NM_145531	214585	Mm.222303	NM_145531	ENSMUSG00000033396	Spg11	6030465E24Rik|A330015I11|C530005A01Rik	spastic paraplegia 11	protein-coding
mm_84605.1	chr9	70141357	70141482	-	1	NA	5' UTR (NM_029784, exon 1 of 9)	5' UTR (NM_029784, exon 1 of 9)	138	NM_029784	76886	Mm.44355	NM_029784	ENSMUSG00000032224	Fam81a	6430514L14Rik	family with sequence similarity 81, member A	protein-coding
mm_77387.1	chr8	120116145	120116158	-	1	NA	intron (NM_172286, intron 1 of 12)	intron (NM_172286, intron 1 of 12)	1999	NM_001163761	234797	Mm.101958	NM_172286	ENSMUSG00000031824	6430548M08Rik	AW049007|Kiaa0513|mKIAA0513	RIKEN cDNA 6430548M08 gene	protein-coding
mm_31035.1	chr4	40948536	40948589	+	1	NA	promoter-TSS (NM_001171739)	promoter-TSS (NM_001171739)	9	NM_029814	76959	Mm.212763	NM_029814	ENSMUSG00000028419	Chmp5	2210412K09Rik|AW545668	charged multivesicular body protein 5	protein-coding
mm_26341.1	chr3	142547233	142547250	+	1	NA	3' UTR (NM_001083312, exon 11 of 11)	3' UTR (NM_001083312, exon 11 of 11)	-12811	NM_018734	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_158974.1	chr1	109983679	109983679	+	1	NA	promoter-TSS (NM_172853)	promoter-TSS (NM_172853)	-44	NM_172853	241201	Mm.213407	NM_172853	ENSMUSG00000026312	Cdh7	9330156F07Rik|CDH7L1	cadherin 7, type 2	protein-coding
mm_132903.1	chr16	48872614	48872626	+	1	NA	promoter-TSS (NM_181596)	promoter-TSS (NM_181596)	12	NM_181596	245195	Mm.231288	NM_181596	ENSMUSG00000022651	Retnlg	Fizz3|Relmg|Xcp1	resistin like gamma	protein-coding
mm_70188.1	chr7	143780292	143780302	-	1	NA	3' UTR (NM_175534, exon 2 of 2)	3' UTR (NM_175534, exon 2 of 2)	4203	NM_175534	244238	Mm.183561	NM_175534	ENSMUSG00000048965	Mrgpre	C130069N09Rik|Ebrt3|Mgrf|MrgE	MAS-related GPR, member E	protein-coding
mm_118081.1	chr13	103335822	103335826	-	1	NA	Intergenic	Intergenic	-1332	NM_175171	328329	Mm.202606	NM_175171	ENSMUSG00000034751	Mast4	4930420O11Rik|AI642422|mKIAA0303	microtubule associated serine/threonine kinase family member 4	protein-coding
mm_18096.1	chr2	44986610	44986625	-	1	NA	3' UTR (NM_015753, exon 10 of 10)	3' UTR (NM_015753, exon 10 of 10)	36560	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_109288.1	chr12	109559265	109559291	+	1	NA	non-coding (NR_003633, exon 5 of 5)	non-coding (NR_003633, exon 5 of 5)	-4414	NR_030427	791079		NR_030427	ENSMUSG00000076451	Mir770	Mirn770|mir-770|mmu-mir-770	microRNA 770	ncRNA
mm_11623.1	chr2	34774359	34774390	+	1	NA	exon (NM_001163434, exon 6 of 9)	exon (NM_001163434, exon 6 of 9)	2284	NM_022310	14828	Mm.330160	NM_022310	ENSMUSG00000026864	Hspa5	AL022860|AU019543|Bip|D2Wsu141e|D2Wsu17e|Grp78|Hsce70|SEZ-7|Sez7|baffled|mBiP	heat shock protein 5	protein-coding
mm_151605.1	chr19	3651907	3651930	-	1	NA	intron (NM_008513, intron 3 of 22)	intron (NM_008513, intron 3 of 22)	34646	NM_008513	16973	Mm.274581	NM_008513	ENSMUSG00000024913	Lrp5	BMND1|HBM|LR3|LRP7|OPPG|mKIAA4142	low density lipoprotein receptor-related protein 5	protein-coding
mm_95784.1	chr11	54910019	54910031	+	1	NA	TTS (NM_021327)	TTS (NM_021327)	7171	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_156363.1	chrX	139563203	139563214	+	1	NA	promoter-TSS (NM_001254761)	promoter-TSS (NM_001254761)	-132	NM_001254761	66889	Mm.27764	NM_023270	ENSMUSG00000031438	Rnf128	1300002C13Rik|AI987883|GRAIL|Greul1	ring finger protein 128	protein-coding
mm_4807.1	chr1	185313671	185313674	+	1	NA	promoter-TSS (NR_029908)	promoter-TSS (NR_029908)	91	NR_029908	387211		NR_029908	ENSMUSG00000065562	Mir215	Mirn215|mir-215|mmu-mir-215	microRNA 215	ncRNA
mm_162796.1	chr10	76725942	76725952	-	1	NA	promoter-TSS (NM_009933)	promoter-TSS (NM_009933)	97	NM_009933	12833	Mm.2509	NM_009933	ENSMUSG00000001119	Col6a1	AI747156|Col6a-1	collagen, type VI, alpha 1	protein-coding
mm_145909.1	chr18	65814634	65814655	+	1	NA	intron (NM_025468, intron 3 of 5)	intron (NM_025468, intron 3 of 5)	14066	NM_025468	66286	Mm.27800	NM_025468	ENSMUSG00000024516	Sec11c	1810029G24Rik|Sec11l3	SEC11 homolog C, signal peptidase complex subunit	protein-coding
mm_152904.1	chr19	25672248	25672258	-	1	NA	promoter-TSS (NM_145831)	promoter-TSS (NM_145831)	-14	NR_045347	100503074	Mm.140012	NR_045347	ENSMUSG00000101089	2610016A17Rik	2610317C19Rik	RIKEN cDNA 2610016A17 gene	ncRNA
mm_137929.1	chr17	32536617	32536630	+	1	NA	promoter-TSS (NM_024442)	promoter-TSS (NM_024442)	-6	NM_024442	70101	Mm.30504	NM_024442	ENSMUSG00000048440	Cyp4f16	2310021J05Rik|AI746515	cytochrome P450, family 4, subfamily f, polypeptide 16	protein-coding
mm_12403.1	chr2	70475984	70476004	+	1	NA	intron (NM_022435, intron 1 of 1)	CpG	1071	NM_022435	64406	Mm.423397	NM_022435	ENSMUSG00000075304	Sp5	-	trans-acting transcription factor 5	protein-coding
mm_76660.1	chr8	93270091	93270093	-	1	NA	exon (NM_144930, exon 5 of 14)	exon (NM_144930, exon 5 of 14)	9644	NM_144930	234564	Mm.29110	NM_144930	ENSMUSG00000031725	Ces1f	AU018778|CesML1|TGH-2	carboxylesterase 1F	protein-coding
mm_22990.1	chr3	33807275	33807286	+	1	NA	3' UTR (NM_025978, exon 10 of 10)	3' UTR (NM_025978, exon 10 of 10)	7097	NM_025978	67120	Mm.275710	NM_025978	ENSMUSG00000027677	Ttc14	2700016E08Rik|4930434D01Rik|4931403I22Rik|4933402I15Rik|AI662468|AU014779|AW561908|cI-44|mKIAA1980	tetratricopeptide repeat domain 14	protein-coding
mm_165372.1	chr2	128204293	128204310	+	1	NA	Intergenic	Intergenic	76726	NM_001284410	12125	Mm.141083	NM_009754	ENSMUSG00000027381	Bcl2l11	1500006F24Rik|Bim|Bod|bcl2-L-11	BCL2-like 11 (apoptosis facilitator)	protein-coding
mm_57784.1	chr6	129268295	129268302	-	1	NA	exon (NM_001033122, exon 5 of 5)	exon (NM_001033122, exon 5 of 5)	7071	NM_001033122	12515	Mm.74745	NM_001033122	ENSMUSG00000030156	Cd69	5830438K24Rik|AI452015|AIM|VEA	CD69 antigen	protein-coding
mm_52723.1	chr6	119922209	119922216	+	1	NA	TTS (NM_001166383)	TTS (NM_001166383)	19514	NM_001166381	19365	Mm.149	NM_011236	ENSMUSG00000030166	Rad52	Rad52yh	RAD52 homolog, DNA repair protein	protein-coding
mm_125365.1	chr15	39619681	39619688	+	1	NA	intron (NM_001256382, intron 22 of 26)	intron (NM_001256382, intron 22 of 26)	-39827	NM_001256384	116838	Mm.309296	NM_053271	ENSMUSG00000037386	Rims2	2810036I15Rik|AW048769|RIM2|Rab3ip2|Rim2(+40A)|Rim2(+44A)|Rim2(+4A)|Serg2|Syt3-rs|mKIAA0751	regulating synaptic membrane exocytosis 2	protein-coding
mm_1625.1	chr1	74409199	74409228	+	1	NA	promoter-TSS (NM_009509)	promoter-TSS (NM_009509)	-171	NM_009509	22349	Mm.471601	NM_009509	ENSMUSG00000026175	Vil1	Vil	villin 1	protein-coding
mm_19814.1	chr2	110363093	110363102	-	1	NA	promoter-TSS (NM_026271)	promoter-TSS (NM_026271)	-104	NM_026271	67606	Mm.291809	NM_026271	ENSMUSG00000074971	Fibin	1110018M03Rik	fin bud initiation factor homolog (zebrafish)	protein-coding
mm_160617.1	chr9	89199262	89199262	+	1	NA	promoter-TSS (NM_007534)	promoter-TSS (NM_007534)	-11	NM_007534	12045	Mm.479217	NM_007534	ENSMUSG00000089929	Bcl2a1b	A1-b	B cell leukemia/lymphoma 2 related protein A1b	protein-coding
mm_42317.1	chr5	114896963	114896990	+	1	NA	promoter-TSS (NM_011854)	promoter-TSS (NM_011854)	42	NM_011854	23962	Mm.228363	NM_011854	ENSMUSG00000029561	Oasl2	M1204|Mmu-OASL|Oasl	2'-5' oligoadenylate synthetase-like 2	protein-coding
mm_35284.1	chr4	20866888	20866892	-	1	NA	Intergenic	Intergenic	-88222	NM_172987	269513	Mm.317473	NM_172987	ENSMUSG00000055761	Nkain3	C530048M05|E130310K16Rik	Na+/K+ transporting ATPase interacting 3	protein-coding
mm_43849.1	chr5	143329294	143329322	+	1	NA	promoter-TSS (NM_028379)	promoter-TSS (NM_028379)	0	NR_027874	67672	Mm.30983	NR_027874	ENSMUSG00000089889	0610040B10Rik	-	RIKEN cDNA 0610040B10 gene	ncRNA
mm_49409.1	chr6	28556384	28556385	+	1	NA	intron (NM_019776, intron 10 of 23)	PB1D9|SINE|Alu	76036	NM_019776	56463	Mm.439987	NM_019776	ENSMUSG00000001424	Snd1	AL033314|Tudor-SN	staphylococcal nuclease and tudor domain containing 1	protein-coding
mm_166578.1	chr6	52240639	52240643	-	1	NA	5' UTR (NM_001122950, exon 1 of 2)	5' UTR (NM_001122950, exon 1 of 2)	213	NM_001122950	15395	Mm.5	NM_008263	ENSMUSG00000000938	Hoxa10	Hox-1.8|Hoxa-10	homeobox A10	protein-coding
mm_116016.1	chr13	24800753	24800772	-	1	NA	promoter-TSS (NM_024473)	promoter-TSS (NM_024473)	-895	NM_024473	79555	Mm.266668	NM_024473	ENSMUSG00000019132	BC005537	8030460C05Rik|C78201	cDNA sequence BC005537	protein-coding
mm_149123.1	chr19	8990239	8990261	+	1	NA	intron (NR_104460, intron 1 of 6)	intron (NR_104460, intron 1 of 6)	966	NM_001286518	66395	Mm.203866	NM_009643	ENSMUSG00000069833	Ahnak	DY6	AHNAK nucleoprotein (desmoyokin)	protein-coding
mm_10155.1	chr2	4389595	4389602	+	1	NA	intron (NM_172475, intron 1 of 22)	intron (NM_172475, intron 1 of 22)	-11378	NM_001177843	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding
mm_115724.1	chr13	16027179	16027194	-	1	NA	3' UTR (NM_008380, exon 5 of 5)	3' UTR (NM_008380, exon 5 of 5)	15335	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_91125.1	chr10	19591680	19591692	-	1	NA	promoter-TSS (NM_010511)	promoter-TSS (NM_010511)	-263	NM_010511	15979	Mm.549	NM_010511	ENSMUSG00000020009	Ifngr1	CD119|IFN-gammaR|Ifgr|Ifngr|Nktar	interferon gamma receptor 1	protein-coding
mm_97447.1	chr11	78189080	78189101	+	1	NA	5' UTR (NM_033475, exon 1 of 10)	5' UTR (NM_033475, exon 1 of 10)	342	NM_033475	19376	Mm.275864	NM_033475	ENSMUSG00000002059	Rab34	AI326479|Narr|Rah|Rah1	RAB34, member RAS oncogene family	protein-coding
mm_88455.1	chr10	77559604	77559625	+	1	NA	exon (NM_008404, exon 12 of 16)	exon (NM_008404, exon 12 of 16)	-22153	NM_145925	108705	Mm.28853	NM_145925	ENSMUSG00000009291	Pttg1ip	1810010L20Rik|AI314311|AU018448|C79540	pituitary tumor-transforming 1 interacting protein	protein-coding
mm_95934.1	chr11	58380621	58380637	+	1	NA	promoter-TSS (NM_001330197)	promoter-TSS (NM_001330197)	-17	NM_001330197	70163	Mm.24119	NM_027339	ENSMUSG00000013643	Lypd8	2210415F13Rik	LY6/PLAUR domain containing 8	protein-coding
mm_152301.1	chr19	9085221	9085339	-	1	NA	exon (NM_011681, exon 2 of 3)	exon (NM_011681, exon 2 of 3)	2676	NM_011681	22287	Mm.2258	NM_011681	ENSMUSG00000024653	Scgb1a1	CC10|CC16|CCSP|PCB-BP|UG|UGB|Utg	secretoglobin, family 1A, member 1 (uteroglobin)	protein-coding
mm_83333.1	chr9	44236888	44236907	-	1	NA	Intergenic	Intergenic	-2851	NM_007619	12402	Mm.266871	NM_007619	ENSMUSG00000034342	Cbl	4732447J05Rik|Cbl-2|c-Cbl|cbl	Casitas B-lineage lymphoma	protein-coding
mm_114410.1	chr13	64248650	64248675	+	1	NA	promoter-TSS (NR_045798)	promoter-TSS (NR_045798)	-38	NR_045798	66503	Mm.443331	NR_045798	ENSMUSG00000097101	1810034E14Rik	-	RIKEN cDNA 1810034E14 gene	ncRNA
mm_142252.1	chr17	37569441	37569448	-	1	NA	promoter-TSS (NM_001013575)	promoter-TSS (NM_001013575)	7	NM_001013575	258096	Mm.159619	NM_001013575	ENSMUSG00000051611	Olfr112	4930580F03Rik|MOR218-4	olfactory receptor 112	protein-coding
mm_19454.1	chr2	92024505	92024529	-	1	NA	promoter-TSS (NM_011957)	promoter-TSS (NM_011957)	-347	NM_011957	26427	Mm.10353	NM_011957	ENSMUSG00000027230	Creb3l1	Oasis	cAMP responsive element binding protein 3-like 1	protein-coding
mm_152499.1	chr19	11130806	11130814	-	1	NA	promoter-TSS (NM_027058)	promoter-TSS (NM_027058)	68	NM_027058	69369	Mm.391200	NM_027058	ENSMUSG00000024729	1700017D01Rik	-	RIKEN cDNA 1700017D01 gene	protein-coding
mm_97699.1	chr11	80177313	80177319	+	1	NA	intron (NM_172133, intron 10 of 10)	intron (NM_172133, intron 10 of 10)	-6556	NM_028019	71956	Mm.22985	NM_028019	ENSMUSG00000020707	Rnf135	0610037N03Rik|2410006N06Rik	ring finger protein 135	protein-coding
mm_51310.1	chr6	72313984	72313999	+	1	NA	3' UTR (NM_001282071, exon 11 of 11)	3' UTR (NM_001282071, exon 11 of 11)	9381	NM_147779	20388	Mm.46033	NM_147779	ENSMUSG00000056370	Sftpb	AI562151|SF-B|SP-B|Sftp-3|Sftp3	surfactant associated protein B	protein-coding
mm_2986.1	chr1	133131452	133131473	+	1	NA	5' UTR (NM_133819, exon 1 of 2)	5' UTR (NM_133819, exon 1 of 2)	296	NM_133819	108954	Mm.293628	NM_133819	ENSMUSG00000046062	Ppp1r15b	1810033K10Rik|AI606441|C530022L24Rik|CReP	protein phosphatase 1, regulatory (inhibitor) subunit 15b	protein-coding
mm_67590.1	chr7	83655314	83655432	-	1	NA	exon (NM_010551, exon 13 of 19)	exon (NM_010551, exon 13 of 19)	23356	NM_023377	170460	Mm.357953	NM_023377	ENSMUSG00000046027	Stard5	2310058G22Rik|AI607880|D7Ertd152e	StAR-related lipid transfer (START) domain containing 5	protein-coding
mm_20950.1	chr2	151718663	151718684	-	1	NA	exon (NM_001305244, exon 5 of 5)	exon (NM_001305244, exon 5 of 5)	16665	NM_001160363	108832	Mm.103494	NM_001160363	ENSMUSG00000044364	Tmem74b	5430405G05Rik	transmembrane protein 74B	protein-coding
mm_124320.1	chr14	103346746	103346756	-	1	NA	promoter-TSS (NM_207215)	promoter-TSS (NM_207215)	49	NM_207215	105689	Mm.6478	NM_207215	ENSMUSG00000033004	Mycbp2	AU023734|AW107953|AW546647|C130061D10Rik|Pam|Phr1|R75243	MYC binding protein 2	protein-coding
mm_106119.1	chr11	116359352	116359374	-	1	NA	intron (NM_027258, intron 5 of 18)	(TG)n|Simple_repeat|Simple_repeat	-24009	NM_008240	15223	Mm.378938	NM_008240	ENSMUSG00000034227	Foxj1	FKHL-13|HFH-4|Hfh4	forkhead box J1	protein-coding
mm_74803.1	chr8	22593723	22593733	-	1	NA	promoter-TSS (NM_001198998)	promoter-TSS (NM_001198998)	85	NM_001198998	22335	Mm.227704	NM_011696	ENSMUSG00000008892	Vdac3	-	voltage-dependent anion channel 3	protein-coding
mm_148199.1	chr18	79109839	79109853	-	1	NA	promoter-TSS (NM_053099)	promoter-TSS (NM_053099)	-455	NM_053099	240427	Mm.312871	NM_053099	ENSMUSG00000024548	Setbp1	C130092E12|Seb|mKIAA0437	SET binding protein 1	protein-coding
mm_81631.1	chr9	110857929	110857938	+	1	NA	promoter-TSS (NM_146227)	promoter-TSS (NM_146227)	-34	NM_146227	235631	Mm.102265	NM_146227	ENSMUSG00000048752	Prss50	79H19C|Tsp50	protease, serine 50	protein-coding
mm_97540.1	chr11	78885424	78885428	+	1	NA	Intergenic	RMER16|LTR|ERVK	-35361	NM_010927	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_98961.1	chr11	98626345	98626349	+	1	NA	promoter-TSS (NM_001007461)	promoter-TSS (NM_001007461)	-13	NM_001007461	450219	Mm.371065	NM_001007461	ENSMUSG00000064224	Gsdma3	Bsk|Dfl|Fgn|Gsdm1l|Gsdm3|Rco2|Rim3	gasdermin A3	protein-coding
mm_120824.1	chr14	75151405	75151420	+	1	NA	intron (NM_008879, intron 1 of 16)	intron (NM_008879, intron 1 of 16)	14987	NM_008879	18826	Mm.153911	NM_008879	ENSMUSG00000021998	Lcp1	AW536232|D14Ertd310e|LCP-1|Pls2|pp65	lymphocyte cytosolic protein 1	protein-coding
mm_99968.1	chr11	113687099	113687114	+	1	NA	intron (NM_177777, intron 1 of 4)	RMER10A|LTR|ERVL	2694	NM_177777	276852	Mm.239566	NM_177777	ENSMUSG00000041623	D11Wsu47e	-	DNA segment, Chr 11, Wayne State University 47, expressed	protein-coding
mm_145125.1	chr18	44411239	44411250	+	1	NA	intron (NM_027490, intron 8 of 10)	RSINE1|SINE|B4	30744	NM_027490	70640	Mm.87629	NM_027490	ENSMUSG00000024472	Dcp2	2410015D23Rik|5730537H01Rik|AL118268	decapping mRNA 2	protein-coding
mm_6153.1	chr1	64956808	64956818	-	1	NA	promoter-TSS (NM_001039493)	promoter-TSS (NM_001039493)	11	NM_001039493	241075	Mm.239534	NM_175509	ENSMUSG00000051344	Plekhm3	9430067K14Rik|A230102O09Rik|AI449570|DAPR|Plekhm1l	pleckstrin homology domain containing, family M, member 3	protein-coding
mm_57081.1	chr6	122581952	122581976	-	1	NA	intron (NM_001134391, intron 5 of 7)	intron (NM_001134391, intron 5 of 7)	20480	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_171146.1	chr3	153694366	153694385	-	1	NA	intron (NM_011372, intron 1 of 4)	intron (NM_011372, intron 1 of 4)	30758	NM_011372	20447	Mm.296453	NM_011372	ENSMUSG00000052544	St6galnac3	Siat7c	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 3	protein-coding
mm_168041.1	chrY	90743694	90743715	-	1	NA	Intergenic	CpG	11346	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_132203.1	chr16	32550730	32550755	+	1	NA	Intergenic	PB1D11|SINE|Alu	54461	NM_199309	245308	Mm.76859	NM_199309	ENSMUSG00000052363	Zdhhc19	Gm1744|Gm616	zinc finger, DHHC domain containing 19	protein-coding
mm_92658.1	chr10	80416633	80416645	-	1	NA	intron (NM_001164148, intron 12 of 18)	intron (NM_001164148, intron 12 of 18)	-9818	NM_025650	66594	Mm.379119	NM_025650	ENSMUSG00000020163	Uqcr11	0710008D09Rik|AL022707|Uqcr	ubiquinol-cytochrome c reductase, complex III subunit XI	protein-coding
mm_94220.1	chr11	3202613	3202654	+	1	NA	promoter-TSS (NM_001166549)	promoter-TSS (NM_001166549)	50	NM_023743	74203	Mm.255649	NM_023743	ENSMUSG00000020454	Eif4enif1	2610509L04Rik|A930019J01Rik|AA410001|AU021239|Clast4|D11Ertd166e	eukaryotic translation initiation factor 4E nuclear import factor 1	protein-coding
mm_85098.1	chr9	94533784	94533810	-	1	NA	intron (NM_001033145, intron 1 of 2)	intron (NM_001033145, intron 1 of 2)	4284	NM_001033145	68861	Mm.258746	NM_001033145	ENSMUSG00000045414	1190002N15Rik	GoPro49|HASF	RIKEN cDNA 1190002N15 gene	protein-coding
mm_85997.1	chr9	112217345	112217355	-	1	NA	promoter-TSS (NM_001177623)	promoter-TSS (NM_001177623)	1	NM_001177623	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_30190.1	chr3	144692052	144692060	-	1	NA	exon (NM_019464, exon 8 of 9)	exon (NM_019464, exon 8 of 9)	28279	NM_001282042	54673	Mm.271775	NM_019464	ENSMUSG00000037062	Sh3glb1	AA409932|AI314629|AU015566|Bif-1|mKIAA0491	SH3-domain GRB2-like B1 (endophilin)	protein-coding
mm_50106.1	chr6	41533507	41533518	+	1	NA	Intergenic	Intergenic	11736	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_595.1	chr1	39551923	39551951	+	1	NA	3' UTR (NM_001033135, exon 7 of 7)	3' UTR (NM_001033135, exon 7 of 7)	-3097	NR_028555	100217461		NR_028555	ENSMUSG00000077704	Snord89	MBII-289	small nucleolar RNA, C/D box 89	snoRNA
mm_31146.1	chr4	43384274	43384286	+	1	NA	intron (NM_001037709, intron 1 of 11)	intron (NM_001037709, intron 1 of 11)	2298	NM_001037709	100213	Mm.235730	NM_199057	ENSMUSG00000035969	Rusc2	AI840675|mKIAA0375	RUN and SH3 domain containing 2	protein-coding
mm_164529.1	chr17	6008061	6008069	-	1	NA	exon (NM_001113353, exon 8 of 27)	exon (NM_001113353, exon 8 of 27)	485	NM_001290698	20975	Mm.236068	NM_011523	ENSMUSG00000023805	Synj2	AI481647|SJ2|mKIAA0348	synaptojanin 2	protein-coding
mm_64664.1	chr7	4165027	4165061	-	1	NA	promoter-TSS (NM_021454)	promoter-TSS (NM_021454)	-345	NM_021454	58804	Mm.34268	NM_021454	ENSMUSG00000063838	Cdc42ep5	1700027J19Rik|2010007O02Rik|Borg3|C85526|CEP5	CDC42 effector protein (Rho GTPase binding) 5	protein-coding
mm_164924.1	chr18	77794699	77794719	+	1	NA	5' UTR (NM_013831, exon 1 of 15)	5' UTR (NM_013831, exon 1 of 15)	159	NM_013831	19201	Mm.57174	NM_013831	ENSMUSG00000025429	Pstpip2	MAYP|cmo	proline-serine-threonine phosphatase-interacting protein 2	protein-coding
mm_102653.1	chr11	63463956	63463974	-	1	NA	Intergenic	Intergenic	-77896	NR_105772	102466632		NR_105772	ENSMUSG00000098829	Mir6354	Gm27282|mmu-mir-6354	microRNA 6354	ncRNA
mm_82614.1	chr9	21760299	21760316	-	1	NA	promoter-TSS (NM_026282)	promoter-TSS (NM_026282)	-21	NM_026282	67629	Mm.295642	NM_026282	ENSMUSG00000074476	Spc24	2410030K01Rik|AV109292|Spbc24	SPC24, NDC80 kinetochore complex component, homolog (S. cerevisiae)	protein-coding
mm_110474.1	chr12	51830182	51830221	-	1	NA	promoter-TSS (NM_144788)	promoter-TSS (NM_144788)	-665	NM_144788	207304	Mm.249391	NM_144788	ENSMUSG00000035247	Hectd1	A630086P08Rik|AI844876|b2b327Clo|opm	HECT domain containing 1	protein-coding
mm_66370.1	chr7	43656613	43656621	-	1	NA	exon (NM_031181, exon 5 of 7)	exon (NM_031181, exon 5 of 7)	3544	NM_031181	83382	Mm.157702	NM_031181	ENSMUSG00000030474	Siglece	Cd170|Siglec12|Siglec5|Siglec9|Siglecl1|mSiglec-E	sialic acid binding Ig-like lectin E	protein-coding
mm_162991.1	chr11	24638069	24638072	+	1	NA	Intergenic	MER58A|DNA|hAT-Charlie	92652	NR_033491	100038617	Mm.387376	NR_033491	ENSMUSG00000073103	Gm10466	ENSMUSG00000073103	predicted gene 10466	ncRNA
mm_171319.1	chr3	96240288	96240299	-	1	NA	promoter-TSS (NM_178212)	promoter-TSS (NM_178212)	41	NM_013549	15267	Mm.5220	NM_013549	ENSMUSG00000064220	Hist2h2aa1	AI448581|H2a-614|H2a-615|Hist2	histone cluster 2, H2aa1	protein-coding
mm_124734.1	chr15	6580937	6580950	+	1	NA	exon (NM_001278269, exon 1 of 17)	exon (NM_001278269, exon 1 of 17)	1096	NM_011815	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_92699.1	chr10	80701880	80701899	-	1	NA	promoter-TSS (NM_027829)	promoter-TSS (NM_027829)	-69	NM_172457	208228	Mm.49309	NM_172457	ENSMUSG00000003348	Mob3a	5330417K06Rik|A630029F06|AV218468|Mobkl2a	MOB kinase activator 3A	protein-coding
mm_169375.1	chr14	37000863	37000871	-	1	NA	Intergenic	ERVB7_2B-LTR_MM|LTR|ERVK	-32103	NM_027045	72972	Mm.27621	NM_027045	ENSMUSG00000058690	Ccser2	1700012P13Rik|2900054P12Rik|AI035535|AW108503|Fam190b|Gcap14	coiled-coil serine rich 2	protein-coding
mm_126956.1	chr15	92161536	92161551	+	1	NA	5' UTR (NM_001159647, exon 1 of 24)	5' UTR (NM_001159647, exon 1 of 24)	186	NM_001159647	12805	Mm.4911	NM_007727	ENSMUSG00000055022	Cntn1	AW495098|CNTN|F3cam|usl	contactin 1	protein-coding
mm_29469.1	chr3	115497476	115497477	-	1	NA	Intergenic	Intergenic	217579	NM_007901	13609	Mm.982	NM_007901	ENSMUSG00000045092	S1pr1	AI849002|Edg1|Lpb1|S1p|S1p1	sphingosine-1-phosphate receptor 1	protein-coding
mm_137437.1	chr17	26507495	26507501	+	1	NA	intron (NM_013642, intron 2 of 3)	intron (NM_013642, intron 2 of 3)	974	NM_013642	19252	Mm.239041	NM_013642	ENSMUSG00000024190	Dusp1	3CH134|MKP1|Ptpn16|U19515|erp|mkp-1	dual specificity phosphatase 1	protein-coding
mm_159377.1	chr3	89418585	89418585	+	1	NA	promoter-TSS (NM_011368)	promoter-TSS (NM_011368)	34	NM_011368	20416	Mm.86595	NM_011368	ENSMUSG00000042626	Shc1	Shc|ShcA|p66|p66shc	src homology 2 domain-containing transforming protein C1	protein-coding
mm_64950.1	chr7	16387779	16387788	-	1	NA	5' UTR (NM_019748, exon 1 of 9)	5' UTR (NM_019748, exon 1 of 9)	113	NM_001285892	56459	Mm.258530	NM_019748	ENSMUSG00000052833	Sae1	2400010M20Rik|2610044L12Rik|AL033372|AOS1|AW743391|D7Ertd177e|HSPC140|Sua1|Uble1a	SUMO1 activating enzyme subunit 1	protein-coding
mm_29126.1	chr3	105426563	105426569	-	1	NA	Intergenic	Intergenic	-25764	NM_001039347	56543	Mm.44530	NM_019931	ENSMUSG00000040896	Kcnd3	AW045978|Kncd3|Kv4.3	potassium voltage-gated channel, Shal-related family, member 3	protein-coding
mm_38091.1	chr4	134227391	134227406	-	1	NA	promoter-TSS (NM_177866)	promoter-TSS (NM_177866)	-15	NM_177866	329954	Mm.79072	NM_177866	ENSMUSG00000048003	Catsper4	4933412L05	cation channel, sperm associated 4	protein-coding
mm_165418.1	chr2	148397478	148397480	+	1	NA	TTS (NM_009219)	TTS (NM_009219)	2102	NM_009219	20608	Mm.35324	NM_009219	ENSMUSG00000037014	Sstr4	Smstr4|sst4	somatostatin receptor 4	protein-coding
mm_28039.1	chr3	83841086	83841170	-	1	NA	5' UTR (NM_011905, exon 2 of 3)	5' UTR (NM_011905, exon 2 of 3)	480	NM_011905	24088	Mm.87596	NM_011905	ENSMUSG00000027995	Tlr2	Ly105	toll-like receptor 2	protein-coding
mm_108458.1	chr12	82770728	82770733	+	1	NA	intron (NM_001310478, intron 2 of 17)	intron (NM_001310478, intron 2 of 17)	153231	NM_001282061	50779	Mm.126176	NM_015812	ENSMUSG00000021219	Rgs6	-	regulator of G-protein signaling 6	protein-coding
mm_26057.1	chr3	135826076	135826086	+	1	NA	5' UTR (NM_001135150, exon 1 of 9)	5' UTR (NM_001135150, exon 1 of 9)	291	NM_001135150	67547	Mm.30239	NM_026228	ENSMUSG00000053897	Slc39a8	4933419D20Rik|AA986696|BIGM103|ZIP-8|Zip8	solute carrier family 39 (metal ion transporter), member 8	protein-coding
mm_18010.1	chr2	38287210	38287225	-	1	NA	5' UTR (NM_146122, exon 1 of 22)	5' UTR (NM_146122, exon 1 of 22)	167	NM_146122	227801	Mm.314245	NM_146122	ENSMUSG00000035392	Dennd1a	6030446I19Rik|connecdenn	DENN/MADD domain containing 1A	protein-coding
mm_24066.1	chr3	87915751	87915783	+	1	NA	3' UTR (NM_008231, exon 6 of 6)	3' UTR (NM_008231, exon 6 of 6)	-3777	NM_026591	67707	Mm.393802	NM_026591	ENSMUSG00000019710	Mrpl24	2010005E08Rik|2810470K06Rik|6720473G22Rik|AA407670	mitochondrial ribosomal protein L24	protein-coding
mm_95872.1	chr11	58051307	58051326	+	1	NA	intron (NM_028451, intron 13 of 18)	intron (NM_028451, intron 13 of 18)	42252	NM_028451	73158	Mm.248843	NM_028451	ENSMUSG00000037331	Larp1	1810024J12Rik|3110040D16Rik|Larp|mKIAA0731	La ribonucleoprotein domain family, member 1	protein-coding
mm_119036.1	chr14	30558788	30558805	+	1	NA	exon (NM_009388, exon 2 of 14)	exon (NM_009388, exon 2 of 14)	9665	NM_009388	21881	Mm.290692	NM_009388	ENSMUSG00000021957	Tkt	p68	transketolase	protein-coding
mm_3486.1	chr1	150105700	150105795	+	1	NA	exon (NM_011198, exon 10 of 10)	exon (NM_011198, exon 10 of 10)	5716	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_73967.1	chr8	120488543	120488569	+	1	NA	promoter-TSS (NM_198671)	promoter-TSS (NM_198671)	-310	NM_198671	382034	Mm.334856	NM_198671	ENSMUSG00000031822	Gse1	2210013I18Rik|mKIAA0182	genetic suppressor element 1, coiled-coil protein	protein-coding
mm_106183.1	chr11	116705161	116705175	-	1	NA	Intergenic	RMER21B|LTR|ERV1	-10508	NM_009180	20446	Mm.3947	NM_009180	ENSMUSG00000057286	St6galnac2	II|ST6GalNAc|Siat7|Siat7b	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2	protein-coding
mm_19918.1	chr2	115864325	115864338	-	1	NA	exon (NM_010825, exon 12 of 12)	exon (NM_010825, exon 12 of 12)	200288	NM_001346044	17536	Mm.247566	NM_010825	ENSMUSG00000027210	Meis2	A430109D20Rik|Mrg1|Stra10	Meis homeobox 2	protein-coding
mm_27768.1	chr3	72900048	72900053	-	1	NA	intron (NM_001081137, intron 44 of 46)	RLTR12D|LTR|ERVK	66816	NM_001081137	69983	Mm.261054	NM_001081137	ENSMUSG00000027790	Sis	2010204N08Rik|SI|Si-s	sucrase isomaltase (alpha-glucosidase)	protein-coding
mm_119964.1	chr14	55478816	55478820	+	1	NA	promoter-TSS (NM_030686)	promoter-TSS (NM_030686)	60	NM_030686	28200	Mm.27427	NM_030686	ENSMUSG00000022210	Dhrs4	AI043103|AI790593|CR|D14Ucla2|NDRD|PHCR|PSCD|RRD|mouNRDR	dehydrogenase/reductase (SDR family) member 4	protein-coding
mm_7692.1	chr1	128730044	128730069	-	1	NA	Intergenic	Intergenic	-137757	NM_009911	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding
mm_63025.1	chr7	121035561	121035566	+	1	NA	intron (NM_021554, intron 1 of 4)	intron (NM_021554, intron 1 of 4)	1118	NM_021554	59052	Mm.29122	NM_021554	ENSMUSG00000030876	Mettl9	0610012D09Rik|AA517660|Drev|MNCb-5680	methyltransferase like 9	protein-coding
mm_121068.1	chr14	95881266	95881268	+	1	NA	promoter-TSS (NM_025733)	promoter-TSS (NM_025733)	1	NM_025733	66732	Mm.75060	NM_025733	ENSMUSG00000034689	4921530L21Rik	-	RIKEN cDNA 4921530L21 gene	protein-coding
mm_7676.1	chr1	128589125	128589130	-	1	NA	exon (NM_009911, exon 2 of 2)	exon (NM_009911, exon 2 of 2)	3172	NM_009911	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding
mm_156744.1	chrX	159961763	159961798	+	1	NA	exon (NM_021389, exon 14 of 17)	exon (NM_021389, exon 14 of 17)	19087	NM_001290664	58194	Mm.286495	NM_021389	ENSMUSG00000040990	Sh3kbp1	1200007H22Rik|1700125L08Rik|5830464D22Rik|AI447724|Cin85|IN85|Ruk|Seta	SH3-domain kinase binding protein 1	protein-coding
mm_167000.1	chr7	47050648	47050648	+	1	NA	promoter-TSS (NM_026436)	promoter-TSS (NM_026436)	8	NM_026436	67893	Mm.27338	NM_026436	ENSMUSG00000010307	Tmem86a	1810054O13Rik|AI414959|AW742698	transmembrane protein 86A	protein-coding
mm_169677.1	chr15	66851742	66851743	+	1	NA	Intergenic	MER87|LTR|ERV1	-19913	NM_009192	20491	Mm.7601	NM_009192	ENSMUSG00000022372	Sla	Slap|Slap-1	src-like adaptor	protein-coding
mm_33005.1	chr4	120615817	120615832	+	1	NA	Intergenic	Intergenic	27079	NM_001101603	667063	Mm.90231	NM_001101603	ENSMUSG00000091297	Gm8439	EG667063|Gm1664	predicted gene 8439	protein-coding
mm_85979.1	chr9	112165077	112165081	-	1	NA	intron (NM_001177623, intron 9 of 9)	intron (NM_001177623, intron 9 of 9)	20870	NM_001177618	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_128598.1	chr15	58164827	58164865	-	1	NA	Intergenic	Intergenic	23480	NM_001326599	76773	Mm.26771	NM_029734	ENSMUSG00000022359	Wdyhv1	2410187C16Rik|AU014961|AW550036|Ntaq1	WDYHV motif containing 1	protein-coding
mm_2607.1	chr1	120261403	120261438	+	1	NA	intron (NM_001085409, intron 2 of 5)	intron (NM_001085409, intron 2 of 5)	3860	NM_133186	68428	Mm.181033	NM_133186	ENSMUSG00000026389	Steap3	1010001D01Rik|Tsap6|pHyde	STEAP family member 3	protein-coding
mm_12490.1	chr2	71786899	71786908	+	1	NA	promoter-TSS (NM_008397)	promoter-TSS (NM_008397)	-36	NM_008397	16403	Mm.225096	NM_008397	ENSMUSG00000027111	Itga6	5033401O05Rik|AI115430|Cd49f|VLA-6	integrin alpha 6	protein-coding
mm_36967.1	chr4	109406246	109406262	-	1	NA	promoter-TSS (NM_153392)	promoter-TSS (NM_153392)	3	NR_131195	102635290	Mm.427859	NR_131195		Ttc39aos1	Gm12750|OTTMUSG00000008290|lincRNA-EPS	Ttc39a opposite strand RNA 1	ncRNA
mm_115936.1	chr13	23621938	23621989	-	1	NA	promoter-TSS (NM_178194)	promoter-TSS (NM_178194)	595	NM_015787	50709	Mm.170587	NM_015787	ENSMUSG00000051627	Hist1h1e	H1-4|H1.4|H1e|H1f4|H1s-4|H1var2	histone cluster 1, H1e	protein-coding
mm_86358.1	chr9	123717541	123717574	-	1	NA	promoter-TSS (NM_033322)	promoter-TSS (NM_033322)	0	NM_033322	93730	Mm.378263	NM_033322	ENSMUSG00000025245	Lztfl1	5530402H04Rik|6130400H19Rik|AI414725|AW048545	leucine zipper transcription factor-like 1	protein-coding
mm_128628.1	chr15	59051986	59051999	-	1	NA	intron (NM_001146180, intron 3 of 13)	intron (NM_001146180, intron 3 of 13)	30034	NM_001146180	211401	Mm.215481	NM_144800	ENSMUSG00000022353	Mtss1	2310003N14Rik|BC024131|D130001D01Rik|Mim|mKIAA0429	metastasis suppressor 1	protein-coding
mm_43718.1	chr5	139423173	139423186	+	1	NA	promoter-TSS (NM_029771)	promoter-TSS (NM_029771)	0	NM_029771	76854	Mm.389706	NM_029771	ENSMUSG00000053647	Gper1	6330420K13Rik|CMKRL2|Ceprl|FEG-1|GPCR-Br|Gper|Gpr30	G protein-coupled estrogen receptor 1	protein-coding
mm_150472.1	chr19	38579014	38579028	+	1	NA	intron (NM_019588, intron 1 of 31)	intron (NM_019588, intron 1 of 31)	54824	NM_019588	74055	Mm.34031	NM_019588	ENSMUSG00000024998	Plce1	4933403A21Rik|PLCepsilon|Plce|mKIAA1516	phospholipase C, epsilon 1	protein-coding
mm_75365.1	chr8	45294855	45294863	-	1	NA	promoter-TSS (NM_008455)	promoter-TSS (NM_008455)	-24	NM_008455	16621	Mm.482691	NM_008455	ENSMUSG00000109764	Klkb1	APS|Kal-3|Kal3|Klk3|PSA	kallikrein B, plasma 1	protein-coding
mm_36118.1	chr4	58912038	58912050	-	1	NA	intron (NM_172381, intron 1 of 48)	CpG	681	NM_172381	230249	Mm.234801	NM_172381	ENSMUSG00000050812	AI314180	AW558785|BB181316|mKIAA0368	expressed sequence AI314180	protein-coding
mm_46378.1	chr5	103911197	103911275	-	1	NA	promoter-TSS (NM_178741)	promoter-TSS (NM_178741)	-7	NM_178741	246293	Mm.179871	NM_178741	ENSMUSG00000029312	Klhl8	2310001P09Rik|D5Ertd431e	kelch-like 8	protein-coding
mm_66318.1	chr7	41320502	41320521	-	1	NA	Intergenic	Intergenic	36184	NM_001033782	434172	Mm.247214	NM_001033782	ENSMUSG00000072259	Gm5592	EG434172	predicted gene 5592	protein-coding
mm_38466.1	chr4	140620655	140620684	-	1	NA	intron (NM_001290803, intron 1 of 28)	MIRb|SINE|MIR	28087	NM_001112723	72754	Mm.29329	NM_172415	ENSMUSG00000040964	Arhgef10l	2810441C07Rik	Rho guanine nucleotide exchange factor (GEF) 10-like	protein-coding
mm_40378.1	chr5	52368472	52368517	+	1	NA	exon (NM_011435, exon 2 of 2)	exon (NM_011435, exon 2 of 2)	4690	NM_011435	20657	Mm.2407	NM_011435	ENSMUSG00000072941	Sod3	AI314465|EC-SOD	superoxide dismutase 3, extracellular	protein-coding
mm_116822.1	chr13	54590048	54590089	-	1	NA	promoter-TSS (NM_025933)	promoter-TSS (NM_025933)	6	NM_178605	28126	Mm.439993	NM_178605	ENSMUSG00000025869	Nop16	AA409471|D13Wsu177e	NOP16 nucleolar protein	protein-coding
mm_127485.1	chr15	101286615	101286625	+	1	NA	intron (NM_026566, intron 1 of 2)	intron (NM_026566, intron 1 of 2)	2319	NM_026566	68118	Mm.482360	NM_026566	ENSMUSG00000037204	Atg101	9430023L20Rik|AA407441|AU022967	autophagy related 101	protein-coding
mm_56475.1	chr6	99052850	99052872	-	1	NA	intron (NM_001347345, intron 6 of 19)	intron (NM_001347345, intron 6 of 19)	-24563	NM_001197322	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_49487.1	chr6	29540888	29540891	+	1	NA	TTS (NM_177296)	TTS (NM_177296)	11607	NM_001252382	27056	Mm.6479	NM_012057	ENSMUSG00000029771	Irf5	AW491843|mirf5	interferon regulatory factor 5	protein-coding
mm_160115.1	chr7	26686213	26686213	-	1	NA	intron (NM_001081148, intron 1 of 8)	intron (NM_001081148, intron 1 of 8)	217	NM_001081148	243881	Mm.294678	NM_001081148	ENSMUSG00000040650	Cyp2b23	EG243881	cytochrome P450, family 2, subfamily b, polypeptide 23	protein-coding
mm_121426.1	chr14	120306446	120306461	+	1	NA	intron (NM_175341, intron 1 of 8)	MTD|LTR|ERVL-MaLR	30784	NM_175341	105559	Mm.238266	NM_175341	ENSMUSG00000022139	Mbnl2	1110002M11Rik|AI047808|AI837313|AI849185|AL118326|MBLL|R75232|mKIAA4072	muscleblind-like 2	protein-coding
mm_37730.1	chr4	129572411	129572416	-	1	NA	intron (NM_001162433, intron 1 of 12)	intron (NM_001162433, intron 1 of 12)	1228	NM_001162433	16818	Mm.293753	NM_010693	ENSMUSG00000000409	Lck	Hck-3|Lsk|Lskt|p56<lck>|p56Lck	lymphocyte protein tyrosine kinase	protein-coding
mm_44846.1	chr5	34187671	34187749	-	1	NA	promoter-TSS (NM_010753)	promoter-TSS (NM_010753)	0	NM_010753	17122	Mm.259260	NM_010753	ENSMUSG00000037235	Mxd4	2810410A03Rik|Mad4|bHLHc12	Max dimerization protein 4	protein-coding
mm_62463.1	chr7	101663604	101663613	+	1	NA	promoter-TSS (NM_009191)	promoter-TSS (NM_009191)	-160	NM_009191	20480	Mm.3990	NM_009191	ENSMUSG00000001829	Clpb	AL118244|Skd3	ClpB caseinolytic peptidase B	protein-coding
mm_97020.1	chr11	71750681	71750691	+	1	NA	promoter-TSS (NM_177618)	promoter-TSS (NM_177618)	-17	NM_177618	216881	Mm.48648	NM_177618	ENSMUSG00000020811	Wscd1	mKIAA0523	WSC domain containing 1	protein-coding
mm_85024.1	chr9	88438941	88438947	-	1	NA	promoter-TSS (NM_172926)	promoter-TSS (NM_172926)	7	NM_172926	244962	Mm.439873	NM_172926	ENSMUSG00000032422	Snx14	B830022K16|C330035N22Rik|YR-14	sorting nexin 14	protein-coding
mm_78955.1	chr9	45138883	45138898	+	1	NA	promoter-TSS (NM_001013390)	promoter-TSS (NM_001013390)	-152	NM_001013390	399548	Mm.335112	NM_001013390	ENSMUSG00000046480	Scn4b	Gm1471	sodium channel, type IV, beta	protein-coding
mm_102987.1	chr11	69685276	69685335	-	1	NA	TTS (NM_011614)	TTS (NM_011614)	249	NM_001159505	69583	Mm.8983	NM_023517	ENSMUSG00000089669	Tnfsf13	2310026N09Rik|April|Tall2|Tnlg7b|Trdl1	tumor necrosis factor (ligand) superfamily, member 13	protein-coding
mm_44384.1	chr5	17828865	17828869	-	1	NA	exon (NM_001159558, exon 4 of 16)	exon (NM_001159558, exon 4 of 16)	7029	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_44945.1	chr5	36554042	36554051	-	1	NA	intron (NM_133910, intron 2 of 13)	B3A|SINE|B2	-23423	NM_001113364	100855	Mm.486203	NM_133910	ENSMUSG00000029192	Tbc1d14	2810413P16Rik|AU043625|C86258|D5Ertd110e|mKIAA1322	TBC1 domain family, member 14	protein-coding
mm_91487.1	chr10	37135497	37135538	-	1	NA	3' UTR (NM_008538, exon 2 of 2)	3' UTR (NM_008538, exon 2 of 2)	3409	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_62168.1	chr7	97280309	97280343	+	1	NA	intron (NM_001162477, intron 3 of 9)	ORR1C2|LTR|ERVL-MaLR	45638	NM_001177412	244144	Mm.297541	NM_001177412	ENSMUSG00000035713	Usp35	Gm1088|Gm493	ubiquitin specific peptidase 35	protein-coding
mm_114.1	chr1	9783724	9783735	+	1	NA	Intergenic	Lx6|LINE|L1	-14401	NM_133220	170755	Mm.336410	NM_133220	ENSMUSG00000025915	Sgk3	2510015P22Rik|A330005P07Rik|Cisk|fy|fz	serum/glucocorticoid regulated kinase 3	protein-coding
mm_43886.1	chr5	143902088	143902114	+	1	NA	TTS (NM_146165)	TTS (NM_146165)	-7034	NM_001310772	66729	Mm.439817	NM_025732	ENSMUSG00000029607	Ankrd61	4921520G13Rik	ankyrin repeat domain 61	protein-coding
mm_72175.1	chr8	72318894	72318915	+	1	NA	promoter-TSS (NM_008452)	promoter-TSS (NM_008452)	-158	NM_008452	16598	Mm.26938	NM_008452	ENSMUSG00000055148	Klf2	Lklf	Kruppel-like factor 2 (lung)	protein-coding
mm_9501.1	chr1	173730172	173730204	-	1	NA	exon (NM_001204910, exon 5 of 8)	exon (NM_001204910, exon 5 of 8)	11621	NM_001204910	226691	Mm.440876	NM_001204910	ENSMUSG00000073490	Ifi207	AI607873|Pyhin-A	interferon activated gene 207	protein-coding
mm_42664.1	chr5	119670973	119670983	+	1	NA	promoter-TSS (NM_011535)	promoter-TSS (NM_011535)	116	NM_198052	21386	Mm.219139	NM_011535	ENSMUSG00000018604	Tbx3	D5Ertd189e	T-box 3	protein-coding
mm_85379.1	chr9	103226053	103226069	-	1	NA	exon (NM_133977, exon 4 of 17)	exon (NM_133977, exon 4 of 17)	4225	NM_133977	22041	Mm.37214	NM_133977	ENSMUSG00000032554	Trf	AI266983|Cd176|HP|Tf|Tfn|hpx	transferrin	protein-coding
mm_37646.1	chr4	128618629	128618646	-	1	NA	promoter-TSS (NM_205823)	promoter-TSS (NM_205823)	-18	NM_205823	384059	Mm.331901	NM_205823	ENSMUSG00000062545	Tlr12	Gm1365|Tlr11	toll-like receptor 12	protein-coding
mm_17310.1	chr2	26389268	26389323	-	1	NA	promoter-TSS (NM_001085407)	promoter-TSS (NM_001085407)	21	NM_001085407	68112	Mm.253771	NM_026563	ENSMUSG00000026927	Sdccag3	C330016H24Rik|C630038K21Rik	serologically defined colon cancer antigen 3	protein-coding
mm_86272.1	chr9	121759904	121759920	-	1	NA	promoter-TSS (NM_001166644)	promoter-TSS (NM_001166644)	31	NR_033503	320301	Mm.373883	NR_033503		E530011L22Rik	-	RIKEN cDNA E530011L22 gene	ncRNA
mm_43632.1	chr5	138194278	138194326	+	1	NA	promoter-TSS (NM_177878)	promoter-TSS (NM_177878)	-12	NM_177878	330216	Mm.19719	NM_177878	ENSMUSG00000049285	Mblac1	-	metallo-beta-lactamase domain containing 1	protein-coding
mm_18012.1	chr2	38287317	38287321	-	1	NA	promoter-TSS (NM_146122)	promoter-TSS (NM_146122)	65	NM_146122	227801	Mm.314245	NM_146122	ENSMUSG00000035392	Dennd1a	6030446I19Rik|connecdenn	DENN/MADD domain containing 1A	protein-coding
mm_58913.1	chr7	17672291	17672301	+	1	NA	promoter-TSS (NR_002857)	promoter-TSS (NR_002857)	-17	NR_002857	232919	Mm.153893	NR_002857	ENSMUSG00000108558	Psg-ps1	AV036018|Cea-6|Cea6	pregnancy specific glycoprotein pseudogene 1	pseudo
mm_125997.1	chr15	76441065	76441069	+	1	NA	intron (NM_175457, intron 32 of 43)	intron (NM_175457, intron 32 of 43)	7853	NR_105919	102465576		NR_105919	ENSMUSG00000099260	Mir6954	Gm27770|mmu-mir-6954	microRNA 6954	ncRNA
mm_146083.1	chr18	70930788	70930788	+	1	NA	Intergenic	Intergenic	362496	NM_010773	17191	Mm.322	NM_010773	ENSMUSG00000024513	Mbd2	MBD2a	methyl-CpG binding domain protein 2	protein-coding
mm_9933.1	chr1	189922372	189922393	-	1	NA	promoter-TSS (NM_026796)	promoter-TSS (NM_026796)	-94	NM_026796	226830	Mm.156895	NM_026796	ENSMUSG00000026603	Smyd2	1110020E07Rik|4930402C15|KMT3C|Zmynd14	SET and MYND domain containing 2	protein-coding
mm_87265.1	chr10	41526819	41526854	+	1	NA	exon (NM_016898, exon 5 of 6)	exon (NM_016898, exon 5 of 6)	7336	NM_016898	53599	Mm.269815	NM_016898	ENSMUSG00000019818	Cd164	A115|A24|AA589639|AW540279|MGC-24|MSSP	CD164 antigen	protein-coding
mm_150351.1	chr19	34644336	34644343	+	1	NA	intron (NM_008331, intron 1 of 1)	intron (NM_008331, intron 1 of 1)	3450	NM_008331	15957	Mm.439751	NM_008331	ENSMUSG00000034459	Ifit1	ISG56|Ifi56|P56	interferon-induced protein with tetratricopeptide repeats 1	protein-coding
mm_16620.1	chr2	5671516	5671520	-	1	NA	intron (NM_001290374, intron 1 of 9)	B1_Mur4|SINE|Alu	4528	NM_001290376	227541	Mm.191949	NM_177343	ENSMUSG00000039145	Camk1d	A630059D12Rik|CKLiK|CaMKIdelta|E030025C11Rik|mCKLiK	calcium/calmodulin-dependent protein kinase ID	protein-coding
mm_156003.1	chrX	106703846	106703865	+	1	NA	intron (NM_001033541, intron 3 of 3)	intron (NM_001033541, intron 3 of 3)	-100176	NM_001281859	58861	Mm.287166	NM_021476	ENSMUSG00000052821	Cysltr1	BB147369|CysLT1R|Cyslt1	cysteinyl leukotriene receptor 1	protein-coding
mm_151270.1	chr19	55180800	55180809	+	1	NA	promoter-TSS (NM_009348)	promoter-TSS (NM_009348)	-81	NM_009348	21684	Mm.42139	NM_009348	ENSMUSG00000024979	Tectb	Tctnb	tectorin beta	protein-coding
mm_166518.1	chr6	17749089	17749103	+	1	NA	promoter-TSS (NM_001083315)	promoter-TSS (NM_001083315)	-74	NM_001083315	64213	Mm.12051	NM_022332	ENSMUSG00000029534	St7	9430001H04Rik|Fam4a2|HELG|RAY1|SEN4|TSG7	suppression of tumorigenicity 7	protein-coding
mm_61813.1	chr7	87281483	87281487	+	1	NA	intron (NM_001285833, intron 2 of 19)	Lx3C|LINE|L1	34836	NM_001285833	50490	Mm.31748	NM_015760	ENSMUSG00000030562	Nox4	AI648021	NADPH oxidase 4	protein-coding
mm_127779.1	chr15	3540951	3540954	-	1	NA	intron (NM_001048178, intron 1 of 8)	MTD|LTR|ERVL-MaLR	40890	NM_001286370	14600	Mm.3986	NM_010284	ENSMUSG00000055737	Ghr	GHBP|GHR/BP	growth hormone receptor	protein-coding
mm_89264.1	chr10	87859637	87859647	+	1	NA	intron (NM_001314010, intron 2 of 4)	intron (NM_001314010, intron 2 of 4)	590	NM_010512	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_79779.1	chr9	62851626	62851656	+	1	NA	3' UTR (NM_001033175, exon 7 of 7)	3' UTR (NM_001033175, exon 7 of 7)	-6463	NM_001102468	75600	Mm.440576	NM_138304	ENSMUSG00000032246	Calml4	2010002G05Rik	calmodulin-like 4	protein-coding
mm_169445.1	chr14	57798250	57798256	+	1	NA	promoter-TSS (NM_001142441)	promoter-TSS (NM_001142441)	35	NM_001142441	100041953	Mm.290178	NM_001142441	ENSMUSG00000061104	Sap18b	ENSMUSG00000061104|Gm10094	Sin3-associated polypeptide 18B	protein-coding
mm_55911.1	chr6	83775561	83775569	-	1	NA	intron (NM_009357, intron 1 of 5)	CpG	247	NM_009357	21766	Mm.28371	NM_009357	ENSMUSG00000014748	Tex261	3110001O07Rik|AA409339|AI480706|AL033351|TEG-261	testis expressed gene 261	protein-coding
mm_39271.1	chr5	3657213	3657217	+	1	NA	5' UTR (NM_029154, exon 1 of 11)	5' UTR (NM_029154, exon 1 of 11)	211	NM_029154	75010	Mm.85064	NM_029141	ENSMUSG00000014529	Tmbim7	4930403J02Rik|4930500J03Rik|4930511M11Rik|Lfg5|Lgf5|Tmbim1b	transmembrane BAX inhibitor motif containing 7	protein-coding
mm_162867.1	chr10	93519057	93519058	-	1	NA	Intergenic	Intergenic	20976	NM_027908	71761	Mm.244518	NM_027908	ENSMUSG00000015890	Amdhd1	1300019J08Rik	amidohydrolase domain containing 1	protein-coding
mm_72114.1	chr8	71671816	71671853	+	1	NA	promoter-TSS (NM_001029873)	promoter-TSS (NM_001029873)	-77	NM_001029873	382018	Mm.334606	NM_001029873	ENSMUSG00000034799	Unc13a	2410078G03Rik|Munc13-1	unc-13 homolog A (C. elegans)	protein-coding
mm_125289.1	chr15	36726861	36726872	+	1	NA	Intergenic	RMER17C-int|LTR|ERVK	64066	NM_001253807	22631	Mm.3360	NM_011740	ENSMUSG00000022285	Ywhaz	1110013I11Rik|14-3-3zeta|AI596267|AL022924|AU020854	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide	protein-coding
mm_88140.1	chr10	69399021	69399041	+	1	NA	Intergenic	CpG	-46119	NM_007659	12534	Mm.281367	NM_007659	ENSMUSG00000019942	Cdk1	Cdc2|Cdc2a|p34<CDC2>	cyclin-dependent kinase 1	protein-coding
mm_125925.1	chr15	76243481	76243531	+	1	NA	promoter-TSS (NM_001163575)	promoter-TSS (NM_001163575)	-66	NM_001163575	671535	Mm.373750	NM_001163575	ENSMUSG00000063268	Parp10	-	poly (ADP-ribose) polymerase family, member 10	protein-coding
mm_150541.1	chr19	39309777	39309788	+	1	NA	exon (NM_007815, exon 5 of 9)	exon (NM_007815, exon 5 of 9)	22697	NM_007815	13095	Mm.20764	NM_007815	ENSMUSG00000003053	Cyp2c29	AHOH|AHOHase|AI159681|AI196010|Ah-2|Ahh-1|Cyp2c|P450-2C	cytochrome P450, family 2, subfamily c, polypeptide 29	protein-coding
mm_18026.1	chr2	38623374	38623376	-	1	NA	intron (NM_011187, intron 5 of 7)	intron (NM_011187, intron 5 of 7)	20531	NM_011187	19177	Mm.389251	NM_011187	ENSMUSG00000026750	Psmb7	AU020723|MC14	proteasome (prosome, macropain) subunit, beta type 7	protein-coding
mm_88020.1	chr10	67186021	67186040	+	1	NA	5' UTR (NM_001242396, exon 1 of 25)	5' UTR (NM_001242396, exon 1 of 25)	280	NM_001242396	108829	Mm.23846	NM_207221	ENSMUSG00000037876	Jmjd1c	5430433L24Rik|D630035I23Rik|Jmjdic|TRIP8	jumonji domain containing 1C	protein-coding
mm_168162.1	chr10	45469633	45469648	-	1	NA	intron (NM_001031772, intron 1 of 4)	intron (NM_001031772, intron 1 of 4)	561	NM_001031772	380669	Mm.440328	NM_001031772	ENSMUSG00000063804	Lin28b	2810403D23Rik|D030047M17Rik|Lin-28.2	lin-28 homolog B (C. elegans)	protein-coding
mm_156621.1	chrX	153832309	153832318	+	1	NA	promoter-TSS (NM_001005370)	promoter-TSS (NM_001005370)	20	NM_001005370	278240	Mm.293363	NM_001005370	ENSMUSG00000046550	Spin2c	BC068162|SPIN-2C|Spin2	spindlin family, member 2C	protein-coding
mm_61082.1	chr7	51622170	51622183	+	1	NA	5' UTR (NM_080853, exon 1 of 12)	5' UTR (NM_080853, exon 1 of 12)	346	NM_080853	140919	Mm.256618	NM_080853	ENSMUSG00000030500	Slc17a6	2900073D12Rik|DNPI|VGLUT2	solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 6	protein-coding
mm_112497.1	chr13	7446520	7446539	+	1	NA	Intergenic	Lx|LINE|L1	-756337	NM_001289530	94191	Mm.425794	NM_052977	ENSMUSG00000052551	Adarb2	Adar3|RED2	adenosine deaminase, RNA-specific, B2	protein-coding
mm_47316.1	chr5	122459605	122459620	-	1	NA	exon (NM_009722, exon 16 of 21)	exon (NM_009722, exon 16 of 21)	37168	NM_019805	56317	Mm.37341	NM_019805	ENSMUSG00000029466	Anapc7	APC7|AW545589	anaphase promoting complex subunit 7	protein-coding
mm_22440.1	chr2	181693597	181693629	-	1	NA	5' UTR (NM_001291208, exon 1 of 5)	5' UTR (NM_001291208, exon 1 of 5)	197	NM_001291206	56470	Mm.274366	NM_026446	ENSMUSG00000002458	Rgs19	2610042F04Rik|AI324841|AW547781|GAIP	regulator of G-protein signaling 19	protein-coding
mm_43965.1	chr5	145280528	145280566	+	1	NA	Intergenic	(CGGGG)n|Simple_repeat|Simple_repeat	-2796	NM_001081431	666311	Mm.260773	NM_001081431	ENSMUSG00000070420	Zscan25	EG666311|Zfp498	zinc finger and SCAN domain containing 25	protein-coding
mm_105488.1	chr11	106065901	106065921	-	1	NA	promoter-TSS (NM_027346)	promoter-TSS (NM_027346)	-196	NM_027346	70207	Mm.343857	NM_027346	ENSMUSG00000001983	Taco1	2310066I18Rik|Ccdc44	translational activator of mitochondrially encoded cytochrome c oxidase I	protein-coding
mm_90567.1	chr10	128231582	128231594	+	1	NA	promoter-TSS (NM_001136082)	promoter-TSS (NM_001136082)	-475	NM_001164080	21853	Mm.6458	NM_011589	ENSMUSG00000039994	Timeless	C77407|Debt69|tim	timeless circadian clock 1	protein-coding
mm_35684.1	chr4	43972162	43972172	-	1	NA	intron (NM_027450, intron 4 of 4)	intron (NM_027450, intron 4 of 4)	-11337	NM_001002787	442829	Mm.348215	NM_001002787	ENSMUSG00000070999	Ccin	4933417A14Rik	calicin	protein-coding
mm_84981.1	chr9	85710401	85710407	-	1	NA	exon (NM_001081282, exon 21 of 29)	exon (NM_001081282, exon 21 of 29)	38930	NM_001081282	108837	Mm.22315	NM_175371	ENSMUSG00000035941	Ibtk	5430411K16Rik|AA409502|BTKI|mKIAA1417	inhibitor of Bruton agammaglobulinemia tyrosine kinase	protein-coding
mm_99368.1	chr11	101787729	101787738	+	1	NA	Intergenic	Intergenic	-2423	NM_001316365	18612	Mm.5025	NM_008815	ENSMUSG00000017724	Etv4	AW414408|Pea-3|Pea3	ets variant 4	protein-coding
mm_17200.1	chr2	25469026	25469044	-	1	NA	exon (NM_008963, exon 2 of 7)	exon (NM_008963, exon 2 of 7)	714	NM_008963	19215	Mm.1008	NM_008963	ENSMUSG00000015090	Ptgds	21kDa|L-PGDS|PGD2|PGDS|PGDS2|Ptgs3	prostaglandin D2 synthase (brain)	protein-coding
mm_112833.1	chr13	20824685	20824726	+	1	NA	intron (NM_012054, intron 2 of 20)	L1MB8|LINE|L1	30592	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_144452.1	chr18	23310181	23310202	+	1	NA	5' UTR (NM_001285813, exon 1 of 22)	5' UTR (NM_001285813, exon 1 of 22)	171	NM_001285813	13527	Mm.94371	NM_010087	ENSMUSG00000024302	Dtna	2210407P21Rik|DTN-A|Dtn|Gm19389|a-DB-1|adbn	dystrobrevin alpha	protein-coding
mm_149577.1	chr19	14598523	14598573	+	1	NA	promoter-TSS (NM_011600)	promoter-TSS (NM_011600)	-365	NM_001302947	21888	Mm.103638	NM_011600	ENSMUSG00000024642	Tle4	5730411M05Rik|AA792082|Bce-1|Bce1|ESTM13|ESTM14|Grg4|X83332|X83333|grg-4	transducin-like enhancer of split 4	protein-coding
mm_83071.1	chr9	37613716	37613728	-	1	NA	promoter-TSS (NM_011734)	promoter-TSS (NM_011734)	-1	NM_001324545	20686	Mm.8637	NM_011449	ENSMUSG00000001948	Spa17	Sp17	sperm autoantigenic protein 17	protein-coding
mm_24139.1	chr3	88296644	88296672	+	1	NA	promoter-TSS (NM_009836)	promoter-TSS (NM_009836)	180	NM_029801	76927	Mm.273330	NM_029801	ENSMUSG00000010538	Tsacc	1700021C14Rik|SIP	TSSK6 activating co-chaperone	protein-coding
mm_141449.1	chr17	30005636	30005640	-	1	NA	intron (NM_148926, intron 1 of 4)	intron (NM_148926, intron 1 of 4)	551	NM_148926	21769	Mm.220972	NM_148926	ENSMUSG00000044477	Zfand3	AW539211|TEG-27|Tex27	zinc finger, AN1-type domain 3	protein-coding
mm_100019.1	chr11	114890378	114890386	+	1	NA	exon (NM_170758, exon 1 of 7)	exon (NM_170758, exon 1 of 7)	341	NM_170758	217303	Mm.294439	NM_170758	ENSMUSG00000034652	Cd300a	B230315M08Rik|Clm8|LMIR1|MAIR-I|MAIR-Ia|MMAC8|Pigr4|mcpir1	CD300A molecule	protein-coding
mm_44853.1	chr5	34233014	34233035	-	1	NA	intron (NM_001015039, intron 5 of 12)	intron (NM_001015039, intron 5 of 12)	-45314	NM_010753	17122	Mm.259260	NM_010753	ENSMUSG00000037235	Mxd4	2810410A03Rik|Mad4|bHLHc12	Max dimerization protein 4	protein-coding
mm_61265.1	chr7	66109475	66109505	+	1	NA	promoter-TSS (NM_001081163)	promoter-TSS (NM_001081163)	-25	NM_001081163	269941	Mm.333916	NM_001081163	ENSMUSG00000032640	Chsy1	mKIAA0990	chondroitin sulfate synthase 1	protein-coding
mm_29065.1	chr3	103791574	103791606	-	1	NA	promoter-TSS (NR_125731)	promoter-TSS (NR_125731)	-27	NM_001301304	15257	Mm.20827	NM_010432	ENSMUSG00000008730	Hipk1	1110062K04Rik|Myak	homeodomain interacting protein kinase 1	protein-coding
mm_83965.1	chr9	57148380	57148405	-	1	NA	Intergenic	Intergenic	-1358	NM_028347	72774	Mm.35749	NM_028347	ENSMUSG00000032298	Neil1	2810450N13Rik|Nei1	nei endonuclease VIII-like 1 (E. coli)	protein-coding
mm_129894.1	chr15	83580140	83580147	-	1	NA	exon (NM_183017, exon 11 of 14)	exon (NM_183017, exon 11 of 14)	15014	NM_183017	223723	Mm.46778	NM_183017	ENSMUSG00000016757	Ttll12	BC055368|D430005B17	tubulin tyrosine ligase-like family, member 12	protein-coding
mm_16798.1	chr2	10105170	10105182	-	1	NA	exon (NM_010582, exon 14 of 21)	exon (NM_010582, exon 14 of 21)	24564	NM_025280	16588	Mm.35498	NM_025280	ENSMUSG00000037262	Kin	Kin17	Kin17 DNA and RNA binding protein	protein-coding
mm_123071.1	chr14	55713107	55713110	-	1	NA	promoter-TSS (NM_019984)	promoter-TSS (NM_019984)	-20	NM_019984	21816	Mm.41964	NM_019984	ENSMUSG00000022218	Tgm1	2310004J08Rik|Tgase1	transglutaminase 1, K polypeptide	protein-coding
mm_171438.1	chr4	141060475	141060476	-	1	NA	promoter-TSS (NM_001145958)	promoter-TSS (NM_001145958)	70	NM_001145958	230872	Mm.80685	NM_172122	ENSMUSG00000040860	Crocc	-	ciliary rootlet coiled-coil, rootletin	protein-coding
mm_10187.1	chr2	4882205	4882252	+	1	NA	intron (NM_175400, intron 1 of 8)	CpG	664	NM_175400	109079	Mm.34329	NM_175400	ENSMUSG00000026662	Sephs1	1110046B24Rik|AA589574|AI505014|AW111620|SELD|SPS|SPS1	selenophosphate synthetase 1	protein-coding
mm_92404.1	chr10	76709536	76709581	-	1	NA	3' UTR (NM_009933, exon 35 of 35)	3' UTR (NM_009933, exon 35 of 35)	16486	NM_009933	12833	Mm.2509	NM_009933	ENSMUSG00000001119	Col6a1	AI747156|Col6a-1	collagen, type VI, alpha 1	protein-coding
mm_164928.1	chr18	80791049	80791049	+	1	NA	intron (NM_001201569, intron 13 of 29)	T-rich|Low_complexity|Low_complexity	-77978	NM_001164109	18018	Mm.329560	NM_016791	ENSMUSG00000033016	Nfatc1	2210017P03Rik|AI449492|AV076380|NF-ATc|NFAT2|NFATc|Nfatcb	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 1	protein-coding
mm_111386.1	chr12	87472268	87472332	-	1	NA	promoter-TSS (NM_025507)	promoter-TSS (NM_025507)	-1	NM_025507	66354	Mm.271174	NM_025507	ENSMUSG00000021039	Snw1	2310008B08Rik|AW048543|NCoA-62|SKIP|Skiip	SNW domain containing 1	protein-coding
mm_80377.1	chr9	75408325	75408328	+	1	NA	intron (NM_015806, intron 1 of 5)	intron (NM_015806, intron 1 of 5)	1033	NM_027418	50772	Mm.480076	NM_015806	ENSMUSG00000042688	Mapk6	2610021I23Rik|D130053K17Rik|Erk3|Mapk4|Mapk63|Prkm4|Prkm6	mitogen-activated protein kinase 6	protein-coding
mm_95228.1	chr11	44518960	44519000	+	1	NA	promoter-TSS (NM_001166553)	promoter-TSS (NM_001166553)	16	NM_028862	74315	Mm.156771	NM_028862	ENSMUSG00000019189	Rnf145	3732413I11Rik|TMRF1	ring finger protein 145	protein-coding
mm_1035.1	chr1	58756299	58756313	+	1	NA	3' UTR (NM_207653, exon 10 of 10)	3' UTR (NM_207653, exon 10 of 10)	25754	NM_001293805	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_164419.1	chr16	42955575	42955585	+	1	NA	promoter-TSS (NR_002445)	promoter-TSS (NR_002445)	0	NR_002445	170658	Mm.375824	NR_002445		BC002163	-	NADH dehydrogenase Fe-S protein 5 pseudogene	pseudo
mm_107143.1	chr12	21443277	21443278	+	1	NA	Intergenic	Intergenic	-25841	NM_011739	22630	Mm.289630	NM_011739	ENSMUSG00000076432	Ywhaq	2700028P07Rik|AA409740|AU021156|R74690	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide	protein-coding
mm_12644.1	chr2	74722053	74722074	+	1	NA	promoter-TSS (NM_010469)	promoter-TSS (NM_010469)	85	NM_010469	15436	Mm.482194	NM_010469	ENSMUSG00000101174	Hoxd4	6030436D05Rik|Hox-4.2|Hox-5.1	homeobox D4	protein-coding
mm_86800.1	chr10	20312462	20312492	+	1	NA	promoter-TSS (NM_001025393)	promoter-TSS (NM_001025393)	8	NM_001025393	72567	Mm.294783	NM_153787	ENSMUSG00000037608	Bclaf1	2610102K23Rik|2700025J07Rik|2810454G14Rik|5730534O06Rik|AI450190|AW556225|Btf|mKIAA0164	BCL2-associated transcription factor 1	protein-coding
mm_21014.1	chr2	152396963	152396987	-	1	NA	exon (NM_011438, exon 1 of 1)	exon (NM_011438, exon 1 of 1)	1071	NM_011438	20667	Mm.28424	NM_011438	ENSMUSG00000051817	Sox12	2010205A02Rik	SRY (sex determining region Y)-box 12	protein-coding
mm_170530.1	chr19	34607968	34607968	+	1	NA	promoter-TSS (NM_001005858)	promoter-TSS (NM_001005858)	11	NM_001005858	667370	Mm.271850	NM_001005858	ENSMUSG00000062488	Ifit3b	I830012O16Rik	interferon-induced protein with tetratricopeptide repeats 3B	protein-coding
mm_34452.1	chr4	148039098	148039190	+	1	NA	promoter-TSS (NM_010840)	promoter-TSS (NM_010840)	67	NM_010840	17769	Mm.89959	NM_010840	ENSMUSG00000029009	Mthfr	AI323986	5,10-methylenetetrahydrofolate reductase	protein-coding
mm_61349.1	chr7	68287421	68287438	+	1	NA	intron (NM_001013811, intron 1 of 8)	RMER17C|LTR|ERVK	-10835	NR_040340	100504026	Mm.426764	NR_040340	ENSMUSG00000086628	Gm16157	OTTMUSG00000031023	predicted gene 16157	ncRNA
mm_56824.1	chr6	117173579	117173599	-	1	NA	3' UTR (NM_021704, exon 3 of 3)	3' UTR (NM_021704, exon 3 of 3)	5054	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_29625.1	chr3	121532272	121532341	-	1	NA	promoter-TSS (NM_145394)	promoter-TSS (NM_145394)	38	NM_145394	213603	Mm.33062	NM_145394	ENSMUSG00000039865	Slc44a3	BC010552	solute carrier family 44, member 3	protein-coding
mm_34851.1	chr4	155491354	155491411	+	1	NA	promoter-TSS (NM_008142)	promoter-TSS (NM_008142)	21	NM_001160016	14688	Mm.2344	NM_008142	ENSMUSG00000029064	Gnb1	AA409223|C77571|Gnb-1	guanine nucleotide binding protein (G protein), beta 1	protein-coding
mm_15033.1	chr2	152754143	152754153	+	1	NA	promoter-TSS (NM_053091)	promoter-TSS (NM_053091)	-25	NM_053091	84682	Mm.196668	NM_053091	ENSMUSG00000009876	Cox4i2	Cox4b|CoxIV-2	cytochrome c oxidase subunit IV isoform 2	protein-coding
mm_86678.1	chr10	18251607	18251614	+	1	NA	Intergenic	Intergenic	-16629	NM_144820	215814	Mm.296565	NM_144820	ENSMUSG00000059554	Ccdc28a	1700009P13Rik|AI480677	coiled-coil domain containing 28A	protein-coding
mm_121590.1	chr14	7851536	7851564	-	1	NA	intron (NM_134080, intron 1 of 45)	MLTR14|LTR|ERV1	33593	NM_134080	286940	Mm.489652	NM_134080	ENSMUSG00000025278	Flnb	AL024016|Fln-b	filamin, beta	protein-coding
mm_121336.1	chr14	115043484	115043487	+	1	NA	promoter-TSS (NR_029737)	promoter-TSS (NR_029737)	-186	NR_029785	723905		NR_029785	ENSMUSG00000065508	Mir17	Mirn17|mir-17|mmu-mir-17	microRNA 17	ncRNA
mm_80718.1	chr9	92275815	92275825	+	1	NA	5' UTR (NM_001195084, exon 1 of 8)	5' UTR (NM_001195084, exon 1 of 8)	218	NM_001195084	18828	Mm.10306	NM_008880	ENSMUSG00000032372	Plscr2	-	phospholipid scramblase 2	protein-coding
mm_84081.1	chr9	58202257	58202271	-	1	NA	promoter-TSS (NM_177193)	promoter-TSS (NM_177193)	21	NM_177193	320563	Mm.186499	NM_177193	ENSMUSG00000051243	Islr2	B930052A04Rik|Linx|Mbu-3|mKIAA1465	immunoglobulin superfamily containing leucine-rich repeat 2	protein-coding
mm_77149.1	chr8	111630326	111630344	-	1	NA	promoter-TSS (NM_027570)	promoter-TSS (NM_027570)	-13	NM_027570	52815	Mm.27589	NM_027570	ENSMUSG00000031958	Ldhd	4733401P21Rik|D8Bwg1320e	lactate dehydrogenase D	protein-coding
mm_132733.1	chr16	43697064	43697065	+	1	NA	Intergenic	L1MEd|LINE|L1	-32880	NM_001146325	100043314	Mm.390896	NM_001146325	ENSMUSG00000071552	Tigit	ENSMUSG00000071552|Vstm3	T cell immunoreceptor with Ig and ITIM domains	protein-coding
mm_125796.1	chr15	74835230	74835237	+	1	NA	3' UTR (NM_001033229, exon 9 of 9)	3' UTR (NM_001033229, exon 9 of 9)	6410	NM_001033229	110115	Mm.322606	NM_001033229	ENSMUSG00000075604	Cyp11b1	AA389061|CPN1|Cyp11b|Cyp11b-1|FHI	cytochrome P450, family 11, subfamily b, polypeptide 1	protein-coding
mm_18002.1	chr2	38217016	38217036	-	1	NA	intron (NM_146122, intron 2 of 21)	intron (NM_146122, intron 2 of 21)	70358	NM_146122	227801	Mm.314245	NM_146122	ENSMUSG00000035392	Dennd1a	6030446I19Rik|connecdenn	DENN/MADD domain containing 1A	protein-coding
mm_136145.1	chr16	87491344	87491365	-	1	NA	exon (NM_009840, exon 4 of 15)	exon (NM_009840, exon 4 of 15)	4515	NM_009840	12469	Mm.328673	NM_009840	ENSMUSG00000025613	Cct8	AI132397|Cctq|Tcpq	chaperonin containing Tcp1, subunit 8 (theta)	protein-coding
mm_25022.1	chr3	98045088	98045090	+	1	NA	intron (NM_010928, intron 1 of 33)	intron (NM_010928, intron 1 of 33)	31551	NM_010928	18129	Mm.485843	NM_010928	ENSMUSG00000027878	Notch2	AI853703|N2	notch 2	protein-coding
mm_124369.1	chr14	105897117	105897132	-	1	NA	promoter-TSS (NM_011897)	promoter-TSS (NM_011897)	-305	NM_011897	24064	Mm.89982	NM_011897	ENSMUSG00000022114	Spry2	sprouty2	sprouty homolog 2 (Drosophila)	protein-coding
mm_5338.1	chr1	24099749	24099755	-	1	NA	intron (NM_026604, intron 1 of 20)	CpG	589	NM_026604	68187	Mm.87130	NM_026604	ENSMUSG00000026153	Fam135a	4921533L14Rik|AI256732|AI835491	family with sequence similarity 135, member A	protein-coding
mm_119493.1	chr14	47378361	47378375	+	1	NA	intron (NM_001145953, intron 1 of 5)	intron (NM_001145953, intron 1 of 5)	4508	NM_001145953	16854	Mm.248615	NM_010705	ENSMUSG00000050335	Lgals3	GBP|L-34|Mac-2|gal3	lectin, galactose binding, soluble 3	protein-coding
mm_108176.1	chr12	76406449	76406457	+	1	NA	3' UTR (NM_001002012, exon 2 of 2)	3' UTR (NM_001002012, exon 2 of 2)	2083	NM_008301	15512	Mm.296181	NM_008301	ENSMUSG00000059970	Hspa2	70kDa|HSP70.2|HSP70A2|Hsp70-2	heat shock protein 2	protein-coding
mm_80232.1	chr9	72671248	72671273	+	1	NA	exon (NM_010890, exon 3 of 29)	exon (NM_010890, exon 3 of 29)	8913	NM_010890	17999	Mm.279923	NM_010890	ENSMUSG00000032216	Nedd4	AA959633|AL023035|AU019897|E430025J12Rik|Nedd4-1|Nedd4a|mKIAA0093	neural precursor cell expressed, developmentally down-regulated 4	protein-coding
mm_171152.1	chr3	16077706	16077706	+	1	NA	Intergenic	LTRIS2|LTR|ERV1	-71374	NM_001081687	381484	Mm.217376	NM_001081687	ENSMUSG00000078780	Gm5150	-	predicted gene 5150	protein-coding
mm_13149.1	chr2	92375459	92375561	+	1	NA	5' UTR (NM_145122, exon 1 of 11)	5' UTR (NM_145122, exon 1 of 11)	271	NM_145122	18633	Mm.202782	NM_145122	ENSMUSG00000027222	Pex16	-	peroxisomal biogenesis factor 16	protein-coding
mm_75345.1	chr8	43307051	43307058	-	1	NA	promoter-TSS (NM_009556)	promoter-TSS (NM_009556)	-45	NM_009556	22702	Mm.285848	NM_009556	ENSMUSG00000051176	Zfp42	Rex-1|Rex1|Zfp-42	zinc finger protein 42	protein-coding
mm_146904.1	chr18	31316916	31316926	-	1	NA	exon (NM_009065, exon 1 of 5)	exon (NM_009065, exon 1 of 5)	207	NM_009065	19762	Mm.5163	NM_009065	ENSMUSG00000057455	Rit2	RIBA|Rin|Roc2	Ras-like without CAAX 2	protein-coding
mm_154057.1	chr19	55117002	55117014	-	1	NA	Intergenic	Intergenic	-17561	NM_008149	14732	Mm.210196	NM_008149	ENSMUSG00000024978	Gpam	GPAT|GPAT1	glycerol-3-phosphate acyltransferase, mitochondrial	protein-coding
mm_162758.1	chr10	61383451	61383502	-	1	NA	promoter-TSS (NM_013753)	promoter-TSS (NM_013753)	47	NM_013753	27355	Mm.269699	NM_013753	ENSMUSG00000020092	Pald1	MMPAL|Pald|mKIAA1274	phosphatase domain containing, paladin 1	protein-coding
mm_90164.1	chr10	119255373	119255374	+	1	NA	Intergenic	RLTR13B2|LTR|ERVK	-15318	NM_027994	71902	Mm.203965	NM_027994	ENSMUSG00000020114	Cand1	2310038O07Rik|6330512O03Rik|AI195005|AI846556|D10Ertd516e|Tp120a|mKIAA0829	cullin associated and neddylation disassociated 1	protein-coding
mm_124531.1	chr14	122439248	122439252	-	1	NA	intron (NR_033325, intron 1 of 2)	ID_B1|SINE|B4	11865	NR_033325	328479	Mm.86095	NR_033325	ENSMUSG00000064052	Gm5089	6530402A20|C030005G22Rik|EG328479	predicted gene 5089	ncRNA
mm_44655.1	chr5	28210399	28210405	-	1	NA	promoter-TSS (NM_001310511)	promoter-TSS (NM_001310511)	-234	NM_001310511	269637	Mm.68286	NM_175651	ENSMUSG00000044681	Cnpy1	1500012D20Rik|9630008K15Rik|AI853839	canopy FGF signaling regulator 1	protein-coding
mm_57535.1	chr6	126640061	126640062	-	1	NA	3' UTR (NM_010595, exon 2 of 2)	3' UTR (NM_010595, exon 2 of 2)	5740	NM_010595	16485	Mm.40424	NM_010595	ENSMUSG00000047976	Kcna1	AI840627|Kca1-1|Kv1.1|MBK1|Mk-1|Shak|mceph	potassium voltage-gated channel, shaker-related subfamily, member 1	protein-coding
mm_150625.1	chr19	41329111	41329123	+	1	NA	intron (NM_031376, intron 4 of 16)	intron (NM_031376, intron 4 of 16)	55953	NM_031376	83490	Mm.222266	NM_031376	ENSMUSG00000025017	Pik3ap1	1810044J04Rik|BCAP	phosphoinositide-3-kinase adaptor protein 1	protein-coding
mm_147728.1	chr18	61014102	61014123	-	1	NA	promoter-TSS (NM_201353)	promoter-TSS (NM_201353)	87	NM_201353	240332	Mm.39846	NM_201353	ENSMUSG00000052026	Slc6a7	AW455934|PROT	solute carrier family 6 (neurotransmitter transporter, L-proline), member 7	protein-coding
mm_18352.1	chr2	58160786	58160805	-	1	NA	promoter-TSS (NM_139200)	promoter-TSS (NM_139200)	-673	NM_139200	227929	Mm.273905	NM_139200	ENSMUSG00000026832	Cytip	A130053M09Rik|AI462064|C80816|Cbp|Cybr|Pscdbp	cytohesin 1 interacting protein	protein-coding
mm_112931.1	chr13	20964092	20964102	+	1	NA	intron (NM_012054, intron 12 of 20)	intron (NM_012054, intron 12 of 20)	109202	NM_146535	258528	Mm.377554	NM_146535	ENSMUSG00000042869	Olfr1370	MOR256-14	olfactory receptor 1370	protein-coding
mm_9949.1	chr1	190979161	190979178	-	1	NA	promoter-TSS (NM_144879)	promoter-TSS (NM_144879)	127	NR_027352	226841	Mm.22856	NM_144879	ENSMUSG00000037568	Vash2	B130052G07Rik	vasohibin 2	protein-coding
mm_165158.1	chr2	23247284	23247285	+	1	NA	intron (NM_027635, intron 8 of 10)	ORR1B1|LTR|ERVL-MaLR	39808	NM_027635	70981	Mm.314026	NM_027635	ENSMUSG00000026774	4931423N10Rik	-	RIKEN cDNA 4931423N10 gene	protein-coding
mm_130765.1	chr15	101370157	101370169	-	1	NA	promoter-TSS (NM_028770)	promoter-TSS (NM_028770)	-38	NM_028770	74127	Mm.440055	NM_028770	ENSMUSG00000037185	Krt80	1200016G03Rik|2310041I20Rik|Kb20	keratin 80	protein-coding
mm_20873.1	chr2	148696997	148697007	-	1	NA	3' UTR (NM_019632, exon 11 of 11)	3' UTR (NM_019632, exon 11 of 11)	15882	NM_028986	74533	Mm.136913	NM_028986	ENSMUSG00000027439	Gzf1	8430437G08Rik|Zfp336|mGZF1	GDNF-inducible zinc finger protein 1	protein-coding
mm_71202.1	chr8	40887908	40887919	+	1	NA	intron (NM_007514, intron 1 of 11)	intron (NM_007514, intron 1 of 11)	25546	NM_001044740	11988	Mm.4676	NM_007514	ENSMUSG00000031596	Slc7a2	20.5|AI158848|Atrc2|CAT-2|Cat2|Tea	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	protein-coding
mm_33135.1	chr4	125030073	125030084	+	1	NA	promoter-TSS (NM_145552)	promoter-TSS (NM_145552)	64	NM_145552	230737	Mm.90760	NM_145552	ENSMUSG00000028869	Gnl2	BC003262|HUMAUANTIG|Ngp-1	guanine nucleotide binding protein-like 2 (nucleolar)	protein-coding
mm_149810.1	chr19	23857186	23857190	+	1	NA	intron (NM_177034, intron 1 of 12)	Lx8|LINE|L1	98312	NM_177034	319924	Mm.22879	NM_177034	ENSMUSG00000024897	Apba1	6430513E09Rik|Lin-10|Mint|Mint1|Urop11|X11|X11alpha	amyloid beta (A4) precursor protein binding, family A, member 1	protein-coding
mm_92063.1	chr10	62514374	62514384	-	1	NA	Intergenic	Intergenic	-6624	NM_011157	19073	Mm.338790	NM_011157	ENSMUSG00000020077	Srgn	Prg|Prg1|Sgc	serglycin	protein-coding
mm_27331.1	chr3	50381464	50381467	-	1	NA	intron (NM_011990, intron 8 of 11)	intron (NM_011990, intron 8 of 11)	62148	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_42764.1	chr5	121220192	121220243	+	1	NA	promoter-TSS (NM_181421)	promoter-TSS (NM_181421)	-2	NM_181421	269700	Mm.184589	NM_181421	ENSMUSG00000042744	Gm15800	A130010L24|AU042671|BC019639|EG545802|OTTMUSG00000026283|mKIAA0614	predicted gene 15800	protein-coding
mm_1811.1	chr1	81166878	81166901	+	1	NA	intron (NM_172849, intron 2 of 4)	intron (NM_172849, intron 2 of 4)	89572	NM_172849	241134	Mm.313904	NM_172849	ENSMUSG00000054976	Nyap2	9430031J16Rik|Jr6|Kiaa1486	neuronal tyrosine-phophorylated phosphoinositide 3-kinase adaptor 2	protein-coding
mm_124594.1	chr15	3274890	3274903	+	1	NA	intron (NM_001042613, intron 2 of 4)	intron (NM_001042613, intron 2 of 4)	3919	NM_009155	20363	Mm.392203	NM_009155	ENSMUSG00000064373	Selenop	AU018766|D15Ucla1|Se-P|Sepp1|selp	selenoprotein P	protein-coding
mm_144300.1	chr18	12333949	12333951	+	1	NA	promoter-TSS (NM_010680)	promoter-TSS (NM_010680)	-74	NM_010680	16774	Mm.42012	NM_010680	ENSMUSG00000024421	Lama3	Lama3B|[a]3B	laminin, alpha 3	protein-coding
mm_82377.1	chr9	14615474	14615490	-	1	NA	promoter-TSS (NM_001081395)	promoter-TSS (NM_001081395)	-482	NM_001081395	75723	Mm.159552	NM_001081395	ENSMUSG00000013076	Amotl1	2310010G08Rik|2310067L22Rik|4932416D09Rik|JEAP|mFLJ00155	angiomotin-like 1	protein-coding
mm_44341.1	chr5	17776776	17776798	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	59109	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_161679.1	chr17	15503034	15503034	+	1	NA	5' UTR (NM_013684, exon 2 of 8)	5' UTR (NM_013684, exon 2 of 8)	3146	NM_013684	21374	Mm.244820	NM_013684	ENSMUSG00000014767	Tbp	GTF2D1|Gtf2d|SCA17|TFIID	TATA box binding protein	protein-coding
mm_146420.1	chr18	84720144	84720171	+	1	NA	promoter-TSS (NM_173770)	promoter-TSS (NM_173770)	-85	NM_173770	240479	Mm.472378	NM_173770	ENSMUSG00000047992	Fam69c	B230399E16Rik	family with sequence similarity 69, member C	protein-coding
mm_92860.1	chr10	81565733	81565835	-	1	NA	non-coding (NR_074087, exon 7 of 7)	non-coding (NR_074087, exon 7 of 7)	6340	NM_001276288	14797	Mm.180013	NM_010347	ENSMUSG00000054452	Aes	AL024115|Esp1|Grg|Grg-5|Grg5|Tle5	amino-terminal enhancer of split	protein-coding
mm_8804.1	chr1	161867111	161867115	-	1	NA	intron (NM_172645, intron 1 of 23)	B1_Mur4|SINE|Alu	9548	NM_172645	226551	Mm.170002	NM_172645	ENSMUSG00000040297	Suco	4732491B11|AI848100|AU016931|Opt	SUN domain containing ossification factor	protein-coding
mm_32287.1	chr4	102991914	102991926	+	1	NA	5' UTR (NM_001163768, exon 1 of 4)	5' UTR (NM_001163768, exon 1 of 4)	125	NM_001163768	67344	Mm.111346	NM_026100	ENSMUSG00000028523	Tctex1d1	1700055O19Rik	Tctex1 domain containing 1	protein-coding
mm_152112.1	chr19	6969733	6969743	-	1	NA	promoter-TSS (NM_001290349)	promoter-TSS (NM_001290349)	76	NM_008874	18797	Mm.273204	NM_008874	ENSMUSG00000024960	Plcb3	mKIAA4098	phospholipase C, beta 3	protein-coding
mm_91327.1	chr10	25220848	25220858	-	1	NA	intron (NM_018747, intron 6 of 7)	intron (NM_018747, intron 6 of 7)	-20683	NM_001347460	432442	Mm.485937	NM_018747	ENSMUSG00000039166	Akap7	6430401D08|AI662165|AKAP15|Akap18|BB170514	A kinase (PRKA) anchor protein 7	protein-coding
mm_152039.1	chr19	6121858	6121892	-	1	NA	exon (NM_026912, exon 5 of 8)	exon (NM_026912, exon 5 of 8)	-3289	NM_133678	66406	Mm.303924	NM_133678	ENSMUSG00000024790	Sac3d1	2410004C24Rik|AU015683|shd1	SAC3 domain containing 1	protein-coding
mm_8960.1	chr1	164935523	164935527	-	1	NA	promoter-TSS (NM_008510)	promoter-TSS (NM_008510)	-15	NM_008510	16963	Mm.190	NM_008510	ENSMUSG00000026573	Xcl1	AI661682|ATAC|LTN|Lptn|SCM-1|SCM-1a|Scyc1	chemokine (C motif) ligand 1	protein-coding
mm_119535.1	chr14	47674792	47674811	+	1	NA	exon (NM_001293636, exon 7 of 40)	exon (NM_001293636, exon 7 of 40)	11045	NM_001347522	16709	Mm.3110	NM_008477	ENSMUSG00000021843	Ktn1	-	kinectin 1	protein-coding
mm_117211.1	chr13	64089198	64089208	-	1	NA	promoter-TSS (NM_008291)	promoter-TSS (NM_008291)	-2	NM_008291	15487	Mm.5109	NM_008291	ENSMUSG00000033122	Hsd17b3	-	hydroxysteroid (17-beta) dehydrogenase 3	protein-coding
mm_117373.1	chr13	71963714	71963729	-	1	NA	promoter-TSS (NM_010573)	promoter-TSS (NM_010573)	2	NM_010573	16371	Mm.316056	NM_010573	ENSMUSG00000060969	Irx1	-	Iroquois related homeobox 1 (Drosophila)	protein-coding
mm_57874.1	chr6	130065243	130065260	-	1	NA	exon (NM_001252577, exon 2 of 7)	exon (NM_001252577, exon 2 of 7)	2007	NM_053153	93970	Mm.333431	NM_053153		Klra18	Ly49r	killer cell lectin-like receptor, subfamily A, member 18	protein-coding
mm_65212.1	chr7	19698025	19698031	-	1	NA	intron (NM_001305843, intron 3 of 4)	intron (NM_001305843, intron 3 of 4)	370	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_159382.1	chr3	90249020	90249020	+	1	NA	exon (NM_013901, exon 2 of 4)	exon (NM_013901, exon 2 of 4)	828	NM_013901	30791	Mm.294709	NM_013901	ENSMUSG00000052310	Slc39a1	Zip1|Zirtl	solute carrier family 39 (zinc transporter), member 1	protein-coding
mm_15272.1	chr2	155217813	155217824	+	1	NA	intron (NM_008395, intron 22 of 24)	intron (NM_008395, intron 22 of 24)	-18715	NR_111891	67068	Mm.23693	NM_025947	ENSMUSG00000047459	Dynlrb1	2010012N15Rik|2010320M17Rik|9430076K19Rik|AV124457|DNLC2A|Dncl2a|km23-1	dynein light chain roadblock-type 1	protein-coding
mm_24208.1	chr3	88621460	88621539	+	1	NA	5' UTR (NM_001198913, exon 1 of 22)	5' UTR (NM_001198913, exon 1 of 22)	105	NM_001198912	16800	Mm.239329	NM_008487	ENSMUSG00000028059	Arhgef2	AA408978|GEF|GEF-H1|GEFH1|LFP40|Lbcl1|Lfc|P40|mKIAA0651	rho/rac guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_18253.1	chr2	52235593	52235603	-	1	NA	exon (NM_010889, exon 74 of 157)	exon (NM_010889, exon 74 of 157)	-55404	NR_040620	78049	Mm.243883	NR_040620		4930573O16Rik	-	RIKEN cDNA 4930573O16 gene	ncRNA
mm_153077.1	chr19	32323200	32323234	-	1	NA	intron (NM_144792, intron 2 of 9)	MER99|DNA|hAT?	26099	NM_001168525	208449	Mm.329810	NM_144792	ENSMUSG00000040451	Sgms1	9530058O11Rik|AI841905|C80702|Mob|Sms1|Sor1|Tmem23	sphingomyelin synthase 1	protein-coding
mm_73470.1	chr8	106683053	106683094	+	1	NA	promoter-TSS (NM_173037)	promoter-TSS (NM_173037)	5	NM_173037	272538	Mm.87151	NM_173037	ENSMUSG00000041949	Tango6	AW413431|E330010G16|Tmco7	transport and golgi organization 6	protein-coding
mm_157357.1	chrX	37085185	37085226	-	1	NA	promoter-TSS (NM_026055)	promoter-TSS (NM_026055)	17	NM_026055	67248	Mm.30478	NM_026055	ENSMUSG00000079641	Rpl39	2810465O16Rik	ribosomal protein L39	protein-coding
mm_150109.1	chr19	29537162	29537170	+	1	NA	intron (NM_001081319, intron 2 of 25)	intron (NM_001081319, intron 2 of 25)	14884	NM_001081319	226089	Mm.353838	NM_177641	ENSMUSG00000038658	Ric1	C030046E11Rik|C130057E09Rik|Kiaa1432	RAB6A GEF complex partner 1	protein-coding
mm_159379.1	chr3	90021317	90021317	-	1	NA	exon (NM_001165987, exon 13 of 25)	exon (NM_001165987, exon 13 of 25)	-10107	NR_106129	102465771		NR_106129	ENSMUSG00000098397	Mir7669	Gm27996|mmu-mir-7669	microRNA 7669	ncRNA
mm_37708.1	chr4	129446967	129446971	-	1	NA	Intergenic	RLTR1C|LTR|ERV1	-6151	NM_153541	215627	Mm.428660	NM_153541	ENSMUSG00000048485	Zbtb8b	AV220464|BC023839|BOZF1|Zbtb8	zinc finger and BTB domain containing 8b	protein-coding
mm_51542.1	chr6	83206095	83206104	+	1	NA	Intergenic	Intergenic	20153	NM_001347310	13191	Mm.6919	NM_007835	ENSMUSG00000031865	Dctn1	AL022633|DAP-150|DP-150|Glued|p150|p150-glued|p150<glued>	dynactin 1	protein-coding
mm_34526.1	chr4	149166810	149166843	+	1	NA	promoter-TSS (NM_001081274)	promoter-TSS (NM_001081274)	-119	NM_001081274	110208	Mm.252080	NM_025801	ENSMUSG00000028961	Pgd	0610042A05Rik|AU019875|C78335	phosphogluconate dehydrogenase	protein-coding
mm_111095.1	chr12	80597125	80597139	-	1	NA	exon (NM_001081421, exon 13 of 15)	exon (NM_001081421, exon 13 of 15)	46979	NM_007951	13877	Mm.246551	NM_007951	ENSMUSG00000021131	Erh	Mer|Prei1	enhancer of rudimentary homolog (Drosophila)	protein-coding
mm_169916.1	chr16	57391156	57391158	-	1	NA	intron (NM_001040397, intron 1 of 4)	LSU-rRNA_Hsa|rRNA|rRNA	37880	NM_001040397	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding
mm_29557.1	chr3	116807970	116807976	-	1	NA	intron (NM_001081326, intron 1 of 33)	CpG	193	NM_001081326	77559	Mm.237099	NM_001081326	ENSMUSG00000033400	Agl	1110061O17Rik|9430004C13Rik|9630046L06Rik|AI850929|C77197	amylo-1,6-glucosidase, 4-alpha-glucanotransferase	protein-coding
mm_58496.1	chr7	3704308	3704334	+	1	NA	intron (NM_029767, intron 1 of 4)	CpG	280	NM_029767	76846	Mm.13944	NM_029767	ENSMUSG00000006333	Rps9	3010033P07Rik|AL022771|AL022885	ribosomal protein S9	protein-coding
mm_15325.1	chr2	155751325	155751335	+	1	NA	5' UTR (NM_011171, exon 1 of 4)	5' UTR (NM_011171, exon 1 of 4)	113	NM_011171	19124	Mm.3243	NM_011171	ENSMUSG00000027611	Procr	AI325044|Ccca|Ccd41|Epcr	protein C receptor, endothelial	protein-coding
mm_128805.1	chr15	66948420	66948427	-	1	NA	exon (NM_008681, exon 4 of 16)	exon (NM_008681, exon 4 of 16)	21218	NM_008681	17988	Mm.30837	NM_008681	ENSMUSG00000005125	Ndrg1	CAP43|CMT4D|DRG1|HMSNL|NMSL|Ndr1|Ndrl|PROXY1|RTP|TDD5	N-myc downstream regulated gene 1	protein-coding
mm_142561.1	chr17	46645129	46645159	-	1	NA	promoter-TSS (NM_029091)	promoter-TSS (NM_029091)	0	NM_029091	74764	Mm.279599	NM_029091	ENSMUSG00000003546	Klc4	1200014P03Rik|AA408085|AW146303|Knsl8	kinesin light chain 4	protein-coding
mm_138704.1	chr17	36023820	36023851	+	1	NA	intron (NR_015618, intron 1 of 1)	intron (NR_015618, intron 1 of 1)	-3275	NM_008207	15042	Mm.439654	NM_008207	ENSMUSG00000053835	H2-T24	H-2T24	histocompatibility 2, T region locus 24	protein-coding
mm_167220.1	chr8	11423563	11423564	+	1	NA	exon (NM_009932, exon 23 of 48)	exon (NM_009932, exon 23 of 48)	-54366	NR_126558	102132	Mm.37632	NR_126558	ENSMUSG00000096957	E230013L22Rik	AI645545	RIKEN cDNA E230013L22 gene	ncRNA
mm_100090.1	chr11	115564438	115564490	+	1	NA	promoter-TSS (NM_001002929)	promoter-TSS (NM_001002929)	20	NM_001002929	445007	Mm.4379	NM_001002929	ENSMUSG00000020739	Nup85	Pcnt1|frount	nucleoporin 85	protein-coding
mm_102718.1	chr11	67114909	67114927	-	1	NA	non-coding (NR_038055, exon 4 of 5)	non-coding (NR_038055, exon 4 of 5)	5162	NR_038055	74184	Mm.162554	NR_038055	ENSMUSG00000087410	2310065F04Rik	linc-Myh	RIKEN cDNA 2310065F04 gene	ncRNA
mm_150531.1	chr19	39290832	39290847	+	1	NA	exon (NM_007815, exon 2 of 9)	exon (NM_007815, exon 2 of 9)	3754	NM_007815	13095	Mm.20764	NM_007815	ENSMUSG00000003053	Cyp2c29	AHOH|AHOHase|AI159681|AI196010|Ah-2|Ahh-1|Cyp2c|P450-2C	cytochrome P450, family 2, subfamily c, polypeptide 29	protein-coding
mm_85237.1	chr9	98601643	98601677	-	1	NA	promoter-TSS (NM_025485)	promoter-TSS (NM_025485)	19	NM_025485	64655	Mm.17949	NM_025485	ENSMUSG00000032459	Mrps22	3100002P07Rik|Rpms22	mitochondrial ribosomal protein S22	protein-coding
mm_53614.1	chr6	140041520	140041530	+	1	NA	promoter-TSS (NM_054066)	promoter-TSS (NM_054066)	0	NM_007605	12344	Mm.12817	NM_007605	ENSMUSG00000041791	Capza3	510-4|Cappa3|Gsg3|Tex8|repro32	capping protein (actin filament) muscle Z-line, alpha 3	protein-coding
mm_135306.1	chr16	38712843	38712860	-	1	NA	5' UTR (NM_020260, exon 1 of 12)	5' UTR (NM_020260, exon 1 of 12)	184	NM_020260	12549	Mm.370848	NM_020260	ENSMUSG00000022799	Arhgap31	5830477L08Rik|AU041750|Cdgap|D330026I07Rik	Rho GTPase activating protein 31	protein-coding
mm_150257.1	chr19	34192689	34192723	+	1	NA	intron (NM_029682, intron 1 of 10)	CpG	436	NM_029682	76630	Mm.130952	NM_029682	ENSMUSG00000024776	Stambpl1	1700095N21Rik|8230401J17Rik|ALMalpha|AMSH-FP	STAM binding protein like 1	protein-coding
mm_43337.1	chr5	135041126	135041165	+	1	NA	intron (NR_133683, intron 3 of 9)	intron (NR_133683, intron 3 of 9)	17663	NR_133683	20907	Mm.6225	NM_016801	ENSMUSG00000007207	Stx1a	HPC-1	syntaxin 1A (brain)	protein-coding
mm_47831.1	chr5	134276994	134276999	-	1	NA	intron (NM_001080746, intron 9 of 34)	(A)n|Simple_repeat|Simple_repeat	37764	NM_001080746	14886	Mm.261570	NM_010365	ENSMUSG00000060261	Gtf2i	6030441I21Rik|BAP-135|Diws1t|GtfII-I|Spin|TFII-I|WBSCR6	general transcription factor II I	protein-coding
mm_154918.1	chrX	22461631	22461641	+	1	NA	promoter-TSS (NR_033731)	promoter-TSS (NR_033731)	40	NR_033731	76705	Mm.399727	NM_029707		Ppp1r2-ps7	1700023I07Rik	protein phosphatase 1, regulatory (inhibitor) subunit 2, pseudogene 7	pseudo
mm_75953.1	chr8	71690573	71690574	-	1	NA	TTS (NM_013564)	TTS (NM_013564)	1321	NM_013564	16336	Mm.476857	NM_013564	ENSMUSG00000079019	Insl3	Rlf|Rlnl	insulin-like 3	protein-coding
mm_88512.1	chr10	78019023	78019035	+	1	NA	Intergenic	CpG	-9233	NM_008826	18641	Mm.269649	NM_008826	ENSMUSG00000020277	Pfkl	AA407869|ATP-PFK|PFK-L	phosphofructokinase, liver, B-type	protein-coding
mm_120390.1	chr14	64590462	64590473	+	1	NA	promoter-TSS (NR_029813)	promoter-TSS (NR_029813)	-190	NR_029813	387233		NR_029813	ENSMUSG00000065597	Mir124a-1	Mirn124a|Mirn124a-1	microRNA 124a-1	ncRNA
mm_21703.1	chr2	164573301	164573313	-	1	NA	5' UTR (NM_001177401, exon 1 of 2)	5' UTR (NM_001177401, exon 1 of 2)	149	NM_001177401	629747	Mm.234248	NM_001177401	ENSMUSG00000074596	Spint3	Gm14315|OTTMUSG00000016288	serine peptidase inhibitor, Kunitz type, 3	protein-coding
mm_94388.1	chr11	5525192	5525204	+	1	NA	exon (NM_001271730, exon 6 of 6)	exon (NM_001271730, exon 6 of 6)	4557	NM_001271730	22433	Mm.469937	NM_013842	ENSMUSG00000020484	Xbp1	D11Ertd39e|TREB-5|TREB5|XBP-1	X-box binding protein 1	protein-coding
mm_78003.1	chr9	10080485	10080527	+	1	NA	intron (NM_001033359, intron 3 of 20)	L1VL1|LINE|L1	186075	NR_105745	102466147		NR_105745	ENSMUSG00000098408	Mir6237	Gm27411|mmu-mir-6237	microRNA 6237	ncRNA
mm_84596.1	chr9	70037994	70038018	-	1	NA	promoter-TSS (NM_028087)	promoter-TSS (NM_028087)	82	NM_028087	72077	Mm.195555	NM_028087	ENSMUSG00000032226	Gcnt3	2010013H22Rik|2210021I22Rik|2210401J11Rik	glucosaminyl (N-acetyl) transferase 3, mucin type	protein-coding
mm_41956.1	chr5	105843764	105843764	+	1	NA	Intergenic	MER21C|LTR|ERVL	-32804	NR_030777	54367	Mm.248876	NM_018759	ENSMUSG00000029290	Zfp326	5730470H14Rik|ZAN75|Znf326	zinc finger protein 326	protein-coding
mm_130950.1	chr15	103255260	103255279	-	1	NA	5' UTR (NM_008685, exon 1 of 3)	5' UTR (NM_008685, exon 1 of 3)	170	NM_008685	18022	Mm.457989	NM_008685	ENSMUSG00000058794	Nfe2	NF-E2|NF-E2/P45|p45|p45NFE2|p45nf-e2	nuclear factor, erythroid derived 2	protein-coding
mm_38043.1	chr4	133967236	133967284	-	1	NA	intron (NM_016957, intron 1 of 5)	CpG	731	NM_016957	15331	Mm.319660	NM_016957	ENSMUSG00000003038	Hmgn2	HMG-17|Hmg17	high mobility group nucleosomal binding domain 2	protein-coding
mm_100153.1	chr11	116110328	116110349	+	1	NA	promoter-TSS (NM_001205081)	promoter-TSS (NM_001205081)	-103	NM_172570	217333	Mm.347770	NM_172570	ENSMUSG00000020773	Trim47	2210023F24Rik	tripartite motif-containing 47	protein-coding
mm_120637.1	chr14	70467836	70467845	+	1	NA	3' UTR (NM_145981, exon 5 of 5)	3' UTR (NM_145981, exon 5 of 5)	10323	NM_145981	105653	Mm.192598	NM_145981	ENSMUSG00000003469	Phyhip	AW049870|C630010D02Rik|Lnap1ip|PAHX-AP#1|PAHX-AP1	phytanoyl-CoA hydroxylase interacting protein	protein-coding
mm_77122.1	chr8	111300227	111300241	-	1	NA	promoter-TSS (NM_146218)	promoter-TSS (NM_146218)	-12	NM_146218	234736	Mm.334816	NM_146218	ENSMUSG00000033596	Rfwd3	BC027246	ring finger and WD repeat domain 3	protein-coding
mm_113270.1	chr13	29014407	29014411	+	1	NA	promoter-TSS (NR_045077)	promoter-TSS (NR_045077)	-5	NR_045077	77920	Mm.197051	NR_045073	ENSMUSG00000086363	A330102I10Rik	-	RIKEN cDNA A330102I10 gene	ncRNA
mm_94848.1	chr11	23770273	23770293	+	1	NA	intron (NM_009044, intron 1 of 9)	intron (NM_009044, intron 1 of 9)	687	NM_009044	19696	Mm.4869	NM_009044	ENSMUSG00000020275	Rel	c-Rel	reticuloendotheliosis oncogene	protein-coding
mm_10492.1	chr2	14824126	14824136	+	1	NA	promoter-TSS (NM_001252533)	promoter-TSS (NM_001252533)	39	NM_001252533	12296	Mm.313930	NM_023116	ENSMUSG00000057914	Cacnb2	AW060387|CAB2|Cavbeta2|Cchb2	calcium channel, voltage-dependent, beta 2 subunit	protein-coding
mm_156974.1	chrX	6171828	6171832	-	1	NA	intron (NM_001031664, intron 1 of 1)	(A)n|Simple_repeat|Simple_repeat	1161	NM_001031664	102954	Mm.426101	NM_001031664	ENSMUSG00000073293	Nudt10	AI853080|Dipp3a	nudix (nucleoside diphosphate linked moiety X)-type motif 10	protein-coding
mm_112856.1	chr13	20840959	20840969	+	1	NA	intron (NM_012054, intron 3 of 20)	MLTR14|LTR|ERV1	46851	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_162200.1	chrX	134162050	134162050	-	1	NA	promoter-TSS (NM_183319)	promoter-TSS (NM_183319)	-122	NM_183319	331524	Mm.235055	NM_183319	ENSMUSG00000031258	Xkrx	A630026F04	X-linked Kx blood group related, X-linked	protein-coding
mm_127499.1	chr15	101419613	101419624	+	1	NA	exon (NM_033073, exon 5 of 9)	exon (NM_033073, exon 5 of 9)	7215	NM_033073	110310	Mm.486285	NM_033073	ENSMUSG00000023039	Krt7	D15Wsu77e|K7|Krt2-7	keratin 7	protein-coding
mm_12126.1	chr2	61643747	61643765	+	1	NA	exon (NM_001164072, exon 5 of 8)	exon (NM_001164072, exon 5 of 8)	50659	NM_001164071	21353	Mm.244393	NM_011529	ENSMUSG00000064289	Tank	C86182|E430026L09Rik|I-TRAF	TRAF family member-associated Nf-kappa B activator	protein-coding
mm_123224.1	chr14	59597916	59597961	-	1	NA	promoter-TSS (NM_027986)	promoter-TSS (NM_027986)	21	NM_001168537	71891	Mm.439850	NM_027986	ENSMUSG00000021982	Cdadc1	2310010M10Rik|AI449174|AI463398|BB130816|NYD-SP15	cytidine and dCMP deaminase domain containing 1	protein-coding
mm_143469.1	chr17	71022965	71022978	-	1	NA	exon (NM_001083934, exon 2 of 37)	exon (NM_001083934, exon 2 of 37)	3414	NM_001083934	17929	Mm.4103	NM_010867	ENSMUSG00000024049	Myom1	D430047A17Rik	myomesin 1	protein-coding
mm_151563.1	chr19	60611301	60611312	+	1	NA	Intergenic	Intergenic	-30283	NM_001172096	78832	Mm.259026	NM_030197	ENSMUSG00000033417	Cacul1	2700078E11Rik|2810417M16Rik|9830127L17Rik|AI450346|D130033C15Rik	CDK2 associated, cullin domain 1	protein-coding
mm_115349.1	chr13	112673383	112673416	+	1	NA	intron (NM_178746, intron 2 of 14)	intron (NM_178746, intron 2 of 14)	12633	NM_178746	268706	Mm.40834	NM_175376	ENSMUSG00000047789	Slc38a9	4833412L08Rik|6720411P22Rik|9130023D20Rik|9430067K09Rik|A730092C09	solute carrier family 38, member 9	protein-coding
mm_25020.1	chr3	98013621	98013631	+	1	NA	promoter-TSS (NM_010928)	promoter-TSS (NM_010928)	88	NM_010928	18129	Mm.485843	NM_010928	ENSMUSG00000027878	Notch2	AI853703|N2	notch 2	protein-coding
mm_103860.1	chr11	83298874	83298905	-	1	NA	promoter-TSS (NM_134025)	promoter-TSS (NM_134025)	88	NM_134025	103737	Mm.102205	NM_134025	ENSMUSG00000018733	Pex12	AI451906	peroxisomal biogenesis factor 12	protein-coding
mm_34816.1	chr4	154942965	154942978	+	1	NA	Intergenic	Intergenic	-14894	NM_178931	230979	Mm.215147	NM_178931	ENSMUSG00000042333	Tnfrsf14	Atar|HveA|Hvem|Tnfrs14	tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)	protein-coding
mm_5921.1	chr1	55131039	55131053	-	1	NA	promoter-TSS (NM_025283)	promoter-TSS (NM_025283)	-199	NM_001310585	19070	Mm.291037	NM_025283	ENSMUSG00000025979	Mob4	2610109B12Rik|Mobkl3|Phocn|Prei3	MOB family member 4, phocein	protein-coding
mm_3935.1	chr1	163762177	163762198	+	1	NA	Intergenic	Intergenic	-17396	NM_001305643	16579	Mm.4651	NM_010629	ENSMUSG00000026585	Kifap3	KAP-3|KAP3|SMAP	kinesin-associated protein 3	protein-coding
mm_143245.1	chr17	64309308	64309320	-	1	NA	exon (NM_001025309, exon 4 of 10)	exon (NM_001025309, exon 4 of 10)	22569	NM_144859	224938	Mm.489681	NM_144859	ENSMUSG00000024083	Pja2	AI447901|AL022700|Neurodap1|mKIAA0438	praja 2, RING-H2 motif containing	protein-coding
mm_144999.1	chr18	38339072	38339101	+	1	NA	promoter-TSS (NM_011937)	promoter-TSS (NM_011937)	-93	NM_011937	26384	Mm.22374	NM_011937	ENSMUSG00000052102	Gnpda1	GNPDA|Gnp1|Gnpi|oscillin	glucosamine-6-phosphate deaminase 1	protein-coding
mm_107829.1	chr12	69197201	69197253	+	1	NA	promoter-TSS (NR_033222)	promoter-TSS (NR_033222)	16	NR_033222	414085	Mm.256223	NR_033222	ENSMUSG00000097061	9330151L19Rik	-	RIKEN cDNA 9330151L19 gene	ncRNA
mm_114764.1	chr13	87667351	87667355	+	1	NA	Intergenic	ERVB4_3-I_MM-int|LTR|ERVK	-1154119	NM_010103	13612	Mm.125580	NM_010103	ENSMUSG00000034488	Edil3	Del-1|Del1	EGF-like repeats and discoidin I-like domains 3	protein-coding
mm_113142.1	chr13	24676824	24676838	+	1	NA	intron (NM_001286100, intron 6 of 22)	B4A|SINE|B4	38183	NM_029679	193385	Mm.217319	NM_029679	ENSMUSG00000036006	Fam65b	-	family with sequence similarity 65, member B	protein-coding
mm_58124.1	chr6	140101135	140101149	-	1	NA	Intergenic	Intergenic	59617	NM_007605	12344	Mm.12817	NM_007605	ENSMUSG00000041791	Capza3	510-4|Cappa3|Gsg3|Tex8|repro32	capping protein (actin filament) muscle Z-line, alpha 3	protein-coding
mm_716.1	chr1	42694949	42694982	+	1	NA	promoter-TSS (NR_027826)	promoter-TSS (NR_027826)	-140	NR_027826	66297	Mm.45203	NM_183252	ENSMUSG00000060424	Pantr1	2610017I09Rik|Pou3f3os|linc-Brn1a	POU domain, class 3, transcription factor 3 adjacent noncoding transcript 1	ncRNA
mm_119511.1	chr14	47384717	47384727	+	1	NA	exon (NM_010705, exon 5 of 6)	exon (NM_010705, exon 5 of 6)	10862	NM_001145953	16854	Mm.248615	NM_010705	ENSMUSG00000050335	Lgals3	GBP|L-34|Mac-2|gal3	lectin, galactose binding, soluble 3	protein-coding
mm_111517.1	chr12	99883402	99883428	-	1	NA	promoter-TSS (NM_030172)	promoter-TSS (NM_030172)	27	NM_030172	78767	Mm.235920	NM_030172	ENSMUSG00000021176	Efcab11	2610021K21Rik|2610110A13Rik	EF-hand calcium binding domain 11	protein-coding
mm_57446.1	chr6	124997390	124997416	-	1	NA	intron (NM_175696, intron 1 of 5)	intron (NM_175696, intron 1 of 5)	683	NM_175696	319352	Mm.295327	NM_175696	ENSMUSG00000030329	Pianp	AI255183|AU067746|C530028O21Rik|Panp	PILR alpha associated neural protein	protein-coding
mm_62427.1	chr7	101348062	101348128	+	1	NA	promoter-TSS (NM_001040111)	promoter-TSS (NM_001040111)	26	NM_001040111	69710	Mm.277687	NM_027180	ENSMUSG00000032812	Arap1	2410002L19Rik|Centd2|mKIAA0782	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	protein-coding
mm_98231.1	chr11	88068380	88068385	+	1	NA	5' UTR (NM_016686, exon 1 of 6)	5' UTR (NM_016686, exon 1 of 6)	103	NM_016686	22344	Mm.46628	NM_016686	ENSMUSG00000018377	Vezf1	AI848691|AW046909|db1	vascular endothelial zinc finger 1	protein-coding
mm_100989.1	chr11	7214170	7214179	-	1	NA	promoter-TSS (NM_008343)	promoter-TSS (NM_008343)	-251	NM_008343	16009	Mm.29254	NM_008343	ENSMUSG00000020427	Igfbp3	AI649005|IGFBP-3|IGgfbp3	insulin-like growth factor binding protein 3	protein-coding
mm_143249.1	chr17	64602111	64602156	-	1	NA	intron (NM_008549, intron 1 of 21)	CpG-6542	484	NM_008549	17158	Mm.2433	NM_008549	ENSMUSG00000024085	Man2a1	Mana-2|Mana2|Map-2	mannosidase 2, alpha 1	protein-coding
mm_112523.1	chr13	9242720	9242726	+	1	NA	Intergenic	Intergenic	-33802	NM_001081426	208440	Mm.217326	NM_172459	ENSMUSG00000048264	Dip2c	2900024P20Rik|9630044M06|mKIAA0934	disco interacting protein 2 homolog C	protein-coding
mm_73273.1	chr8	104591465	104591505	+	1	NA	promoter-TSS (NM_001024606)	promoter-TSS (NM_001024606)	17	NM_001024606	382051	Mm.290750	NM_001024606	ENSMUSG00000048371	Pdp2	4833426J09Rik|Gm1705|mKIAA1348	pyruvate dehyrogenase phosphatase catalytic subunit 2	protein-coding
mm_119044.1	chr14	30596642	30596659	+	1	NA	intron (NM_011103, intron 17 of 17)	MER58B|DNA|hAT-Charlie	13660	NM_001310682	18753	Mm.2314	NM_011103	ENSMUSG00000021948	Prkcd	AI385711|D14Ertd420e|PKC[d]|PKCdelta|Pkcd	protein kinase C, delta	protein-coding
mm_116207.1	chr13	32776436	32776446	-	1	NA	intron (NM_001166030, intron 1 of 11)	intron (NM_001166030, intron 1 of 11)	5338	NM_001166030	238564	Mm.60041	NM_001166030	ENSMUSG00000044951	Mylk4	EG238564	myosin light chain kinase family, member 4	protein-coding
mm_109730.1	chr12	116442950	116442976	+	1	NA	exon (NM_133762, exon 24 of 29)	exon (NM_133762, exon 24 of 29)	37561	NM_133762	76044	Mm.491196	NM_133762	ENSMUSG00000042029	Ncapg2	5830426I05Rik|Luzp5|Mtb|mCAP-G2	non-SMC condensin II complex, subunit G2	protein-coding
mm_7361.1	chr1	106711599	106711609	-	1	NA	TTS (NM_177410)	TTS (NM_177410)	2686	NM_009741	12043	Mm.257460	NM_009741	ENSMUSG00000057329	Bcl2	AW986256|Bcl-2|C430015F12Rik|D630044D05Rik|D830018M01Rik	B cell leukemia/lymphoma 2	protein-coding
mm_15139.1	chr2	153974770	153974780	+	1	NA	promoter-TSS (NM_001080811)	promoter-TSS (NM_001080811)	-170	NM_001080811	545477	Mm.379973	NM_001080811	ENSMUSG00000078998	Bpifa6	EG545477|Gm5840|Splunc6	BPI fold containing family A, member 6	protein-coding
mm_21808.1	chr2	165034822	165034859	-	1	NA	promoter-TSS (NM_144892)	promoter-TSS (NM_144892)	-61	NM_144892	228869	Mm.233080	NM_144892	ENSMUSG00000039804	Ncoa5	CIA	nuclear receptor coactivator 5	protein-coding
mm_53716.1	chr6	143402119	143402132	+	1	NA	Intergenic	Intergenic	156237	NR_027803	52285	Mm.354898	NM_001033129		D6Ertd474e	1700001I24Rik|AU023129	DNA segment, Chr 6, ERATO Doi 474, expressed	ncRNA
mm_92266.1	chr10	71156441	71156443	-	1	NA	intron (NM_031397, intron 1 of 20)	intron (NM_031397, intron 1 of 20)	3248	NM_031397	83675	Mm.286834	NM_031397	ENSMUSG00000014329	Bicc1	Bic-C|bpk|jcpk	BicC family RNA binding protein 1	protein-coding
mm_14983.1	chr2	152175088	152175125	+	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	31497	NM_009328	21407	Mm.3881	NM_009328	ENSMUSG00000068079	Tcf15	Meso1|bHLH-EC2	transcription factor 15	protein-coding
mm_62821.1	chr7	113392389	113392389	+	1	NA	Intergenic	Intergenic	-3816	NM_020623	19226	Mm.284168	NM_020623	ENSMUSG00000059077	Pth	Pthp	parathyroid hormone	protein-coding
mm_80490.1	chr9	78395869	78395880	+	1	NA	promoter-TSS (NM_001191044)	promoter-TSS (NM_001191044)	97	NM_001191044	100048658	Mm.158166	NM_001191044	ENSMUSG00000070291	Ddx43	ENSMUSG00000070291|OTTMUSG00000019690	DEAD (Asp-Glu-Ala-Asp) box polypeptide 43	protein-coding
mm_147771.1	chr18	61400464	61400470	-	1	NA	promoter-TSS (NM_133249)	promoter-TSS (NM_133249)	-36	NM_133249	170826	Mm.415302	NM_133249	ENSMUSG00000033871	Ppargc1b	4631412G21Rik|Perc	peroxisome proliferative activated receptor, gamma, coactivator 1 beta	protein-coding
mm_44571.1	chr5	24757844	24757856	-	1	NA	promoter-TSS (NM_153076)	promoter-TSS (NM_153076)	-7	NM_153076	214301	Mm.63484	NM_153076	ENSMUSG00000038135	Crygn	-	crystallin, gamma N	protein-coding
mm_111297.1	chr12	85485792	85485807	-	1	NA	Intergenic	Intergenic	11898	NM_010234	14281	Mm.246513	NM_010234	ENSMUSG00000021250	Fos	D12Rfj1|c-fos|cFos	FBJ osteosarcoma oncogene	protein-coding
mm_39394.1	chr5	14025306	14025327	+	1	NA	promoter-TSS (NM_011348)	promoter-TSS (NM_011348)	40	NM_011348	20349	Mm.134093	NM_011348	ENSMUSG00000063531	Sema3e	6430702L12|AA408817|Semah|mKIAA0331	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	protein-coding
mm_68343.1	chr7	106506485	106506495	-	1	NA	Intergenic	Intergenic	-65417	NR_003967	209380	Mm.461779	NM_001001318		Gm4759	EG209380	GTPase, very large interferon inducible 1 pseudogene	pseudo
mm_147735.1	chr18	61039933	61039958	-	1	NA	Intergenic	Intergenic	-3746	NM_009880	12590	Mm.144448	NM_009880	ENSMUSG00000024619	Cdx1	Cdx|Cdx-1	caudal type homeobox 1	protein-coding
mm_132109.1	chr16	31455106	31455117	+	1	NA	exon (NM_001122683, exon 6 of 7)	exon (NM_001122683, exon 6 of 7)	26358	NM_001122683	71911	Mm.293470	NM_175177	ENSMUSG00000046598	Bdh1	2310032J20Rik|AI327223|Bdh	3-hydroxybutyrate dehydrogenase, type 1	protein-coding
mm_97928.1	chr11	83648129	83648142	+	1	NA	3' UTR (NM_011337, exon 3 of 3)	3' UTR (NM_011337, exon 3 of 3)	1243	NM_011337	20302	Mm.1282	NM_011337	ENSMUSG00000000982	Ccl3	AI323804|G0S19-1|LD78alpha|MIP-1alpha|MIP1-(a)|MIP1-alpha|Mip1a|Scya3	chemokine (C-C motif) ligand 3	protein-coding
mm_91047.1	chr10	18679089	18679091	-	1	NA	intron (NM_001033258, intron 4 of 33)	intron (NM_001033258, intron 4 of 33)	64668	NM_001033258	215821	Mm.40491	NM_001033258	ENSMUSG00000019852	Arfgef3	9630004D11|B930094H20Rik|BIG3|D10Bwg1379e|mKIAA1244	ARFGEF family member 3	protein-coding
mm_149134.1	chr19	9002709	9002732	+	1	NA	exon (NM_009643, exon 5 of 5)	exon (NM_009643, exon 5 of 5)	13436	NM_001286518	66395	Mm.203866	NM_009643	ENSMUSG00000069833	Ahnak	DY6	AHNAK nucleoprotein (desmoyokin)	protein-coding
mm_30229.1	chr3	145651442	145651452	-	1	NA	Intergenic	Intergenic	-1462	NM_010516	16007	Mm.1231	NM_010516	ENSMUSG00000028195	Cyr61	AI325051|CCN1|Igfbp10	cysteine rich protein 61	protein-coding
mm_118938.1	chr14	27238010	27238012	+	1	NA	promoter-TSS (NM_027871)	promoter-TSS (NM_027871)	1	NM_027871	71704	Mm.248606	NM_027871	ENSMUSG00000021895	Arhgef3	1200004I24Rik|9830169H03Rik|C76747|Xpln	Rho guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_92389.1	chr10	76596386	76596402	-	1	NA	exon (NM_146007, exon 28 of 28)	exon (NM_146007, exon 28 of 28)	20746	NM_080845	14317	Mm.36278	NM_080845	ENSMUSG00000001155	Ftcd	-	formiminotransferase cyclodeaminase	protein-coding
mm_16301.1	chr2	174289545	174289582	+	1	NA	intron (NR_002846, intron 1 of 4)	intron (NR_002846, intron 1 of 4)	5243	NM_022000	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_105013.1	chr11	100414778	100414811	-	1	NA	promoter-TSS (NM_010221)	promoter-TSS (NM_010221)	25	NM_176830	66180	Mm.4940	NM_176830	ENSMUSG00000006931	P3h4	1110036O03Rik|AI413214|Leprel4|Sc65	prolyl 3-hydroxylase family member 4 (non-enzymatic)	protein-coding
mm_129209.1	chr15	76522005	76522058	-	1	NA	promoter-TSS (NM_130893)	promoter-TSS (NM_130893)	98	NM_130893	170729	Mm.218747	NM_130893	ENSMUSG00000048385	Scrt1	-	scratch family zinc finger 1	protein-coding
mm_170541.1	chr19	3986506	3986514	+	1	NA	promoter-TSS (NM_001302481)	promoter-TSS (NM_001302481)	-60	NM_001302479	71670	Mm.29735	NM_027857	ENSMUSG00000024866	Acy3	0610006H10Rik|AA3|AAIII|AW107362|Acy-3|HCBP1	aspartoacylase (aminoacylase) 3	protein-coding
mm_30990.1	chr4	35226872	35226875	+	1	NA	promoter-TSS (NM_001081343)	promoter-TSS (NM_001081343)	-993	NM_001081343	73205	Mm.331544	NM_001081343	ENSMUSG00000028300	3110043O21Rik	AI840585	RIKEN cDNA 3110043O21 gene	protein-coding
mm_93149.1	chr10	92938008	92938018	-	1	NA	intron (NM_001347060, intron 42 of 67)	intron (NM_001347060, intron 42 of 67)	143583	NM_001347060	380654	Mm.34980	NM_001347060	ENSMUSG00000020014	Cfap54	4930485B16Rik|Gm872	cilia and flagella associated protein 54	protein-coding
mm_170972.1	chr2	64312590	64312590	+	1	NA	Intergenic	LTR83|LTR|ERVL	-214552	NM_001267847	60344	Mm.130769	NM_021716	ENSMUSG00000075324	Fign	fi|fidget	fidgetin	protein-coding
mm_158964.1	chr1	92934456	92934456	+	1	NA	promoter-TSS (NM_011796)	promoter-TSS (NM_011796)	48	NM_011796	23830	Mm.294315	NM_011796	ENSMUSG00000026270	Capn10	AW049679|Capn8|mKIAA1845	calpain 10	protein-coding
mm_129006.1	chr15	74879384	74879393	-	1	NA	3' UTR (NM_025929, exon 3 of 3)	3' UTR (NM_025929, exon 3 of 3)	2316	NM_025929	67038	Mm.154566	NM_025929	ENSMUSG00000063522	2010109I03Rik	Ly6m	RIKEN cDNA 2010109I03 gene	protein-coding
mm_89079.1	chr10	83344169	83344172	+	1	NA	Intergenic	RMER10A|LTR|ERVL	-6353	NM_177388	338365	Mm.67073	NM_177388	ENSMUSG00000034591	Slc41a2	A230035L05Rik|SLC41A1-L1	solute carrier family 41, member 2	protein-coding
mm_151562.1	chr19	60598524	60598538	+	1	NA	Intergenic	RMER19B|LTR|ERVK	-17508	NM_001172096	78832	Mm.259026	NM_030197	ENSMUSG00000033417	Cacul1	2700078E11Rik|2810417M16Rik|9830127L17Rik|AI450346|D130033C15Rik	CDK2 associated, cullin domain 1	protein-coding
mm_22038.1	chr2	168206876	168206888	-	1	NA	5' UTR (NM_009628, exon 1 of 4)	5' UTR (NM_009628, exon 1 of 4)	230	NM_009628	11538	Mm.201322	NM_009628	ENSMUSG00000051149	Adnp	AA589558|mKIAA0784	activity-dependent neuroprotective protein	protein-coding
mm_73715.1	chr8	111940698	111940708	+	1	NA	promoter-TSS (NM_026693)	promoter-TSS (NM_026693)	0	NM_026693	93739	Mm.371666	NM_026693	ENSMUSG00000031950	Gabarapl2	0610012F20Rik|2900019O08Rik|AI173605|GATE-16|Gef2	gamma-aminobutyric acid (GABA) A receptor-associated protein-like 2	protein-coding
mm_29108.1	chr3	104837287	104837290	-	1	NA	intron (NM_009797, intron 5 of 9)	Lx2|LINE|L1	-18725	NM_001163440	17454	Mm.1597	NM_008619	ENSMUSG00000002227	Mov10	C77703|Mov-10	Moloney leukemia virus 10	protein-coding
mm_51833.1	chr6	89644066	89644074	+	1	NA	promoter-TSS (NM_001178058)	promoter-TSS (NM_001178058)	82	NM_001178058	232223	Mm.229332	NM_153162	ENSMUSG00000000811	Txnrd3	AI196535|TR2|Tgr	thioredoxin reductase 3	protein-coding
mm_16512.1	chr2	181365490	181365500	+	1	NA	promoter-TSS (NM_001165995)	promoter-TSS (NM_001165995)	72	NM_001048148	229007	Mm.87720	NM_144894	ENSMUSG00000027582	Zgpat	1500006I01Rik|BC021513	zinc finger, CCCH-type with G patch domain	protein-coding
mm_156979.1	chrX	7188674	7188712	-	1	NA	promoter-TSS (NM_016691)	promoter-TSS (NM_016691)	21	NM_016691	12728	Mm.486257	NM_016691	ENSMUSG00000004317	Clcn5	5430408K11Rik|ClC-5|Clc4-1|Clc5|Clcn4-1|D930009B12Rik|DXImx42e|Sfc13|T25545	chloride channel, voltage-sensitive 5	protein-coding
mm_57122.1	chr6	122597020	122597034	-	1	NA	intron (NM_001134391, intron 2 of 7)	B1_Mur2|SINE|Alu	5417	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_80418.1	chr9	77838868	77838879	+	1	NA	Intergenic	Intergenic	-78492	NM_134255	68801	Mm.430736	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	ELOVL family member 5, elongation of long chain fatty acids (yeast)	protein-coding
mm_119781.1	chr14	54181485	54181511	+	1	NA	Intergenic	Intergenic	72431	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_120515.1	chr14	66636872	66636901	+	1	NA	intron (NM_001271760, intron 1 of 3)	intron (NM_001271760, intron 1 of 3)	1635	NM_001271760	11549	Mm.57064	NM_013461	ENSMUSG00000045875	Adra1a	Adra1c	adrenergic receptor, alpha 1a	protein-coding
mm_132280.1	chr16	33056500	33056510	+	1	NA	promoter-TSS (NM_021338)	promoter-TSS (NM_021338)	-9	NM_021338	57808	Mm.19355	NM_021338	ENSMUSG00000060636	Rpl35a	2810431L15Rik|Rpl35	ribosomal protein L35A	protein-coding
mm_109431.1	chr12	110628240	110628255	+	1	NA	exon (NM_030238, exon 18 of 77)	exon (NM_030238, exon 18 of 77)	26852	NM_030238	13424	Mm.181430	NM_030238	ENSMUSG00000018707	Dync1h1	9930018I23Rik|AI894280|DHC1|DHC1a|DNCL|Dnchc1|Dnec1|Dnecl|Loa|MAP1C|P22|Swl|mKIAA0325	dynein cytoplasmic 1 heavy chain 1	protein-coding
mm_146218.1	chr18	77038406	77038422	+	1	NA	intron (NM_027721, intron 1 of 13)	MLTR25A|LTR|ERVK	8882	NM_027721	71206	Mm.35803	NM_027721	ENSMUSG00000025420	Katnal2	3110023G01Rik|4933439B08Rik	katanin p60 subunit A-like 2	protein-coding
mm_98777.1	chr11	96789214	96789224	+	1	NA	promoter-TSS (NM_007622)	promoter-TSS (NM_007622)	83	NM_007622	12412	Mm.29055	NM_007622	ENSMUSG00000018666	Cbx1	Cbx|Cbx-rs2|E430007M08Rik|HP1B|Hp1beta|M31|MOD1	chromobox 1	protein-coding
mm_17227.1	chr2	25546962	25546975	-	1	NA	promoter-TSS (NM_001290413)	promoter-TSS (NM_001290413)	-28	NM_009422	22030	Mm.3399	NM_009422	ENSMUSG00000026942	Traf2	AI325259	TNF receptor-associated factor 2	protein-coding
mm_10695.1	chr2	22622494	22622518	+	1	NA	5' UTR (NM_008078, exon 1 of 16)	5' UTR (NM_008078, exon 1 of 16)	179	NM_008078	14417	Mm.4784	NM_008078	ENSMUSG00000026787	Gad2	6330404F12Rik|GAD(65)|GAD65|Gad-2	glutamic acid decarboxylase 2	protein-coding
mm_118223.1	chr13	110541359	110541385	-	1	NA	Intergenic	MIR3|SINE|MIR	146328	NM_152804	20620	Mm.380	NM_152804	ENSMUSG00000021701	Plk2	Snk	polo-like kinase 2	protein-coding
mm_135973.1	chr16	75016166	75016186	-	1	NA	Intergenic	Intergenic	569885	NM_001252513	320355	Mm.99517	NM_177142	ENSMUSG00000032948	Lipi	D930038D03Rik|lpd1	lipase, member I	protein-coding
mm_143897.1	chr17	84682886	84682914	-	1	NA	promoter-TSS (NM_001347418)	promoter-TSS (NM_001347418)	111	NM_031884	27409	Mm.289590	NM_031884	ENSMUSG00000040505	Abcg5	cmp|sterolin-1|trac	ATP-binding cassette, sub-family G (WHITE), member 5	protein-coding
mm_42258.1	chr5	114065440	114065449	+	1	NA	intron (NM_026805, intron 2 of 15)	intron (NM_026805, intron 2 of 15)	25936	NM_026805	68666	Mm.63584	NM_026805	ENSMUSG00000042078	Svop	1110030H18Rik|AI415691|msvop	SV2 related protein	protein-coding
mm_71384.1	chr8	45999283	45999296	+	1	NA	exon (NM_001039562, exon 2 of 5)	exon (NM_001039562, exon 2 of 5)	561	NM_001039562	654824	Mm.334517	NM_001039562	ENSMUSG00000050914	Ankrd37	-	ankyrin repeat domain 37	protein-coding
mm_60015.1	chr7	30763751	30763765	+	1	NA	promoter-TSS (NM_001166174)	promoter-TSS (NM_001166174)	2	NM_001166174	73712	Mm.30138	NM_028618	ENSMUSG00000060962	Dmkn	1110014F24Rik|AW561900|C130074A08|SK30|SK89|cI-36	dermokine	protein-coding
mm_72712.1	chr8	84995941	84995973	+	1	NA	intron (NM_133255, intron 11 of 21)	intron (NM_133255, intron 11 of 21)	5362	NM_001167991	170833	Mm.247775	NM_133255	ENSMUSG00000052566	Hook2	A630054I03Rik	hook microtubule tethering protein 2	protein-coding
mm_158887.1	chr1	11263961	11263961	+	1	NA	promoter-TSS (NM_001033636)	promoter-TSS (NM_001033636)	-2	NM_001033636	109294	Mm.123247	NM_029525	ENSMUSG00000048960	Prex2	6230420N16Rik|AI316880|AI553603|C030045D06Rik|D430013K02|Depdc2|P-Rex2	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	protein-coding
mm_14366.1	chr2	129618455	129618467	+	1	NA	exon (NM_001291022, exon 2 of 5)	exon (NM_001291022, exon 2 of 5)	25292	NM_001291022	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_158467.1	chrX	140956667	140956673	-	1	NA	promoter-TSS (NM_001164177)	promoter-TSS (NM_001164177)	41	NM_016883	53380	Mm.17640	NM_016883	ENSMUSG00000031429	Psmd10	AW554874	proteasome (prosome, macropain) 26S subunit, non-ATPase, 10	protein-coding
mm_84828.1	chr9	78109021	78109067	-	1	NA	promoter-TSS (NM_001081490)	promoter-TSS (NM_001081490)	21	NM_001081490	71538	Mm.28584	NM_023605	ENSMUSG00000001366	Fbxo9	9030401P18Rik|AA986398	f-box protein 9	protein-coding
mm_167493.1	chr9	7699913	7699915	+	1	NA	TTS (NM_010810)	TTS (NM_010810)	-4283	NR_126562	102722	Mm.334941	NR_126562	ENSMUSG00000086381	AV064505	-	expressed sequence AV064505	ncRNA
mm_144306.1	chr18	12504162	12504168	+	1	NA	promoter-TSS (NM_001347461)	promoter-TSS (NM_001347461)	-34	NM_001347461	16774	Mm.42012	NM_010680	ENSMUSG00000024421	Lama3	Lama3B|[a]3B	laminin, alpha 3	protein-coding
mm_43313.1	chr5	134945127	134945130	+	1	NA	TTS (NM_009903)	TTS (NM_009903)	1806	NM_009903	12740	Mm.7339	NM_009903	ENSMUSG00000047501	Cldn4	Cep-r|Cpetr|Cpetr1	claudin 4	protein-coding
mm_63842.1	chr7	135651912	135651920	+	1	NA	promoter-TSS (NM_001316681)	promoter-TSS (NM_001316681)	17	NM_001316681	19267	Mm.945	NM_011212	ENSMUSG00000041836	Ptpre	PTPe|PTPepsilon|RPTPepsilon	protein tyrosine phosphatase, receptor type, E	protein-coding
mm_12033.1	chr2	58754911	58754921	+	1	NA	promoter-TSS (NM_001289659)	promoter-TSS (NM_001289659)	-268	NM_001289659	76654	Mm.200370	NM_029692	ENSMUSG00000026839	Upp2	1700124F02Rik|AI266885|UDRPASE2|UP2|UPASE2	uridine phosphorylase 2	protein-coding
mm_51919.1	chr6	91234291	91234301	+	1	NA	exon (NM_001081437, exon 2 of 17)	exon (NM_001081437, exon 2 of 17)	21532	NM_007992	14115	Mm.249146	NM_007992	ENSMUSG00000064080	Fbln2	5730577E14Rik|FIBL-2	fibulin 2	protein-coding
mm_168778.1	chr12	17549904	17549905	+	1	NA	exon (NM_013614, exon 11 of 12)	exon (NM_013614, exon 11 of 12)	5031	NM_013614	18263	Mm.34102	NM_013614	ENSMUSG00000011179	Odc1	ODC	ornithine decarboxylase, structural 1	protein-coding
mm_23369.1	chr3	55461859	55461863	+	1	NA	5' UTR (NM_001111052, exon 1 of 14)	5' UTR (NM_001111052, exon 1 of 14)	103	NM_001195540	13175	Mm.393242	NM_019978	ENSMUSG00000027797	Dclk1	1700113D08Rik|2810480F11Rik|AI836758|Click-I|Cpg16|Dcamkl1|Dcl|Dclk|mKIAA0369	doublecortin-like kinase 1	protein-coding
mm_130421.1	chr15	98093246	98093260	-	1	NA	intron (NM_001163488, intron 1 of 22)	CpG	316	NM_144851	223870	Mm.384023	NM_144851	ENSMUSG00000033075	Senp1	2310046A20Rik|D15Ertd528e|E330036L07Rik|suPr-2	SUMO1/sentrin specific peptidase 1	protein-coding
mm_121829.1	chr14	20496671	20496686	-	1	NA	5' UTR (NM_029104, exon 1 of 7)	5' UTR (NM_029104, exon 1 of 7)	223	NM_029104	74843	Mm.295241	NM_029104	ENSMUSG00000021815	Mss51	4833444M15Rik|Zmynd17	MSS51 mitochondrial translational activator	protein-coding
mm_144811.1	chr18	36287276	36287286	+	1	NA	exon (NM_008989, exon 2 of 2)	exon (NM_008989, exon 2 of 2)	6119	NM_008989	19290	Mm.231802	NM_008989	ENSMUSG00000043991	Pura	CAGER-1|Pur-alpha|ssCRE-BP	purine rich element binding protein A	protein-coding
mm_163426.1	chr12	82251460	82251474	-	1	NA	intron (NM_001167983, intron 2 of 23)	intron (NM_001167983, intron 2 of 23)	-59882	NM_172579	217692	Mm.261333	NM_172579	ENSMUSG00000042700	Sipa1l1	4931426N11Rik|AW213287|Spar|mKIAA0440	signal-induced proliferation-associated 1 like 1	protein-coding
mm_95297.1	chr11	46056224	46056230	+	1	NA	intron (NM_001291891, intron 1 of 22)	CpG	243	NM_001291891	11492	Mm.89940	NM_009616	ENSMUSG00000011256	Adam19	AL024287|MADDAM|MTLNB|Mltnb	a disintegrin and metallopeptidase domain 19 (meltrin beta)	protein-coding
mm_29585.1	chr3	117360446	117360465	-	1	NA	5' UTR (NM_177664, exon 1 of 7)	5' UTR (NM_177664, exon 1 of 7)	421	NM_177664	229791	Mm.140138	NM_177664	ENSMUSG00000044667	Plppr4	A330086D10|D3Bwg0562e|Lppr4|PRG-1|mKIAA0455	phospholipid phosphatase related 4	protein-coding
mm_34874.1	chr4	155562415	155562425	+	1	NA	promoter-TSS (NM_138671)	promoter-TSS (NM_138671)	28	NM_138671	192185	Mm.28347	NM_138671	ENSMUSG00000029063	Nadk	4432404C02Rik|BC004012	NAD kinase	protein-coding
mm_98063.1	chr11	85832802	85832827	+	1	NA	promoter-TSS (NR_077059)	promoter-TSS (NR_077059)	199	NM_009324	21385	Mm.287052	NM_009324	ENSMUSG00000000093	Tbx2	-	T-box 2	protein-coding
mm_143573.1	chr17	74316086	74316107	-	1	NA	5' UTR (NM_024428, exon 2 of 5)	5' UTR (NM_024428, exon 2 of 5)	115	NM_001146224	66310	Mm.28536	NM_024428	ENSMUSG00000024067	Dpy30	2810410M20Rik|C87842	dpy-30, histone methyltransferase complex regulatory subunit	protein-coding
mm_54105.1	chr6	16898396	16898416	-	1	NA	promoter-TSS (NM_031198)	promoter-TSS (NM_031198)	35	NM_031198	21426	Mm.36217	NM_031198	ENSMUSG00000029553	Tfec	BB107417|Tcfec|bHLHe34	transcription factor EC	protein-coding
mm_90509.1	chr10	128042371	128042382	+	1	NA	exon (NM_001113199, exon 3 of 9)	exon (NM_001113199, exon 3 of 9)	7030	NM_001113199	17938	Mm.3746	NM_013608	ENSMUSG00000061315	Naca	AL022831|AL024382|Gm1878|mKIAA0363|skNAC	nascent polypeptide-associated complex alpha polypeptide	protein-coding
mm_122847.1	chr14	54740125	54740129	-	1	NA	intron (NM_016972, intron 3 of 10)	B1_Mus2|SINE|Alu	-27953	NM_207131	110794	Mm.236223	NM_207131	ENSMUSG00000052435	Cebpe	C/EBPe|CRP1|Gm294	CCAAT/enhancer binding protein (C/EBP), epsilon	protein-coding
mm_14189.1	chr2	127080570	127080580	+	1	NA	5' UTR (NM_026678, exon 2 of 8)	5' UTR (NM_026678, exon 2 of 8)	9918	NM_026678	109778	Mm.22028	NM_026678	ENSMUSG00000001999	Blvra	0610006A11Rik|2500001N03Rik|Blvr	biliverdin reductase A	protein-coding
mm_103786.1	chr11	82807540	82807542	-	1	NA	intron (NM_001164570, intron 7 of 7)	intron (NM_001164570, intron 7 of 7)	21502	NM_026097	67338	Mm.341608	NM_026097	ENSMUSG00000020696	Rffl	1700051E09Rik|4930516L10Rik|BG080975|Carp2	ring finger and FYVE like domain containing protein	protein-coding
mm_83001.1	chr9	36726589	36726607	-	1	NA	promoter-TSS (NM_007691)	promoter-TSS (NM_007691)	60	NM_007691	12649	Mm.16753	NM_007691	ENSMUSG00000032113	Chek1	C85740|Chk1|rad27	checkpoint kinase 1	protein-coding
mm_107863.1	chr12	69907735	69907745	+	1	NA	intron (NM_178628, intron 1 of 14)	intron (NM_178628, intron 1 of 14)	-14577	NM_201519	399510	Mm.291936	NM_201519	ENSMUSG00000034761	Map4k5	4432415E19Rik|GCKR|KHS|MAPKKKK5	mitogen-activated protein kinase kinase kinase kinase 5	protein-coding
mm_91112.1	chr10	19185902	19185911	-	1	NA	intron (NR_038022, intron 1 of 1)	intron (NR_038022, intron 1 of 1)	18668	NR_038022	100504265	Mm.383417	NR_038021		Gm20139	-	predicted gene, 20139	ncRNA
mm_82497.1	chr9	18722073	18722099	-	1	NA	Intergenic	Intergenic	33547	NM_146606	18322	Mm.246530	NM_146606	ENSMUSG00000054141	Olfr24	MOR132-1|MTPCR51	olfactory receptor 24	protein-coding
mm_62682.1	chr7	110003575	110003576	+	1	NA	intron (NR_037959, intron 2 of 2)	intron (NR_037959, intron 2 of 2)	3071	NR_037959	69781	Mm.440728	NR_037959	ENSMUSG00000101585	1600010M07Rik	-	RIKEN cDNA 1600010M07 gene	ncRNA
mm_80840.1	chr9	98003422	98003450	+	1	NA	promoter-TSS (NR_110443)	promoter-TSS (NR_110443)	16	NR_110443	66737	Mm.445908	NR_110443	ENSMUSG00000090255	4921534H16Rik	-	RIKEN cDNA 4921534H16 gene	ncRNA
mm_95254.1	chr11	44621212	44621227	+	1	NA	exon (NM_001290710, exon 3 of 15)	exon (NM_001290710, exon 3 of 15)	3119	NM_001290710	13591	Mm.439662	NM_007897	ENSMUSG00000057098	Ebf1	Ebf|O/E-1|OE-1|Olf-1|Olf1	early B cell factor 1	protein-coding
mm_156319.1	chrX	137049587	137049654	+	1	NA	promoter-TSS (NM_146261)	promoter-TSS (NM_146261)	26	NM_146261	245622	Mm.260106	NM_146261	ENSMUSG00000042595	Fam199x	-	family with sequence similarity 199, X-linked	protein-coding
mm_12718.1	chr2	78051156	78051181	+	1	NA	promoter-TSS (NR_108098)	promoter-TSS (NR_108098)	-9	NR_108098	78158	Mm.78473	NR_108098	ENSMUSG00000085431	4930440I19Rik	-	RIKEN cDNA 4930440I19 gene	ncRNA
mm_47788.1	chr5	132195177	132195188	-	1	NA	intron (NM_177047, intron 2 of 18)	intron (NM_177047, intron 2 of 18)	314913	NR_040704	75369	Mm.389696	NR_040704	ENSMUSG00000105773	4930563F08Rik	-	RIKEN cDNA 4930563F08 gene	ncRNA
mm_6003.1	chr1	58973313	58973325	-	1	NA	promoter-TSS (NM_172656)	promoter-TSS (NM_172656)	163	NM_172406	70827	Mm.222887	NM_172406	ENSMUSG00000026028	Trak2	2900022D04Rik|4733401O11Rik|AI480836|AW046271|Als2cr3|CALS-C|GRIF-1|GRIF1|OIP98|mKIAA0549	trafficking protein, kinesin binding 2	protein-coding
mm_54147.1	chr6	22343456	22343461	-	1	NA	intron (NM_138587, intron 1 of 9)	intron (NM_138587, intron 1 of 9)	12623	NM_138587	27999	Mm.490307	NM_138587	ENSMUSG00000029672	Fam3c	D6Wsu176e|Ilei	family with sequence similarity 3, member C	protein-coding
mm_127412.1	chr15	101256401	101256418	+	1	NA	Intergenic	Intergenic	-10437	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_2464.1	chr1	105357060	105357089	+	1	NA	promoter-TSS (NM_001160368)	promoter-TSS (NM_001160368)	-364	NM_001160368	320311	Mm.389162	NM_178779	ENSMUSG00000047496	Rnf152	A930029B02Rik	ring finger protein 152	protein-coding
mm_100198.1	chr11	116753178	116753188	+	1	NA	intron (NR_003364, intron 1 of 3)	intron (NR_003364, intron 1 of 3)	1016	NR_003364	193217	Mm.100084	NR_003364		BC018473	-	cDNA sequence BC018473	ncRNA
mm_22429.1	chr2	181599244	181599261	-	1	NA	promoter-TSS (NM_172676)	promoter-TSS (NM_172676)	-105	NM_172676	229011	Mm.205422	NM_172676	ENSMUSG00000038605	Samd10	D930033N23Rik|E130318E08	sterile alpha motif domain containing 10	protein-coding
mm_74614.1	chr8	12672100	12672132	-	1	NA	promoter-TSS (NM_198031)	promoter-TSS (NM_198031)	-16	NM_198031	259279	Mm.142095	NM_198031	ENSMUSG00000000759	Tubgcp3	GCP3|Spc98p	tubulin, gamma complex associated protein 3	protein-coding
mm_97432.1	chr11	78100273	78100276	+	1	NA	intron (NM_001346762, intron 1 of 2)	ID_B1|SINE|B4	5601	NM_145430	216971	Mm.119387	NM_145430	ENSMUSG00000037750	Fam222b	9630020I17Rik	family with sequence similarity 222, member B	protein-coding
mm_120110.1	chr14	59440948	59440996	+	1	NA	promoter-TSS (NM_026908)	promoter-TSS (NM_026908)	-9	NM_026908	69008	Mm.179091	NM_026908	ENSMUSG00000021981	Cab39l	1500031K13Rik|2810425O13Rik|4930520C08Rik|AA589432|MO2L	calcium binding protein 39-like	protein-coding
mm_149673.1	chr19	20382041	20382057	+	1	NA	intron (NM_010730, intron 6 of 12)	intron (NM_010730, intron 6 of 12)	8622	NM_010730	16952	Mm.248360	NM_010730	ENSMUSG00000024659	Anxa1	Anx-1|Anx-A1|C430014K04Rik|Lpc-1|Lpc1	annexin A1	protein-coding
mm_88897.1	chr10	81151002	81151013	+	1	NA	3' UTR (NM_010731, exon 3 of 3)	3' UTR (NM_010731, exon 3 of 3)	14736	NM_010731	16969	Mm.20920	NM_010731	ENSMUSG00000035011	Zbtb7a	9030619K07Rik|9130006G12Rik|AI452336|FBI-1|Lrf|Pokemon|Zbtb7	zinc finger and BTB domain containing 7a	protein-coding
mm_60766.1	chr7	45554832	45554836	+	1	NA	promoter-TSS (NM_025330)	promoter-TSS (NM_025330)	-94	NM_025330	66065	Mm.285710	NM_025330	ENSMUSG00000030825	Hsd17b14	0610039E24Rik|Dhrs10|retSDR3	hydroxysteroid (17-beta) dehydrogenase 14	protein-coding
mm_151629.1	chr19	3912734	3912779	-	1	NA	promoter-TSS (NM_001271444)	promoter-TSS (NM_001271444)	18	NM_144870	225887	Mm.44227	NM_144870	ENSMUSG00000059734	Ndufs8	BC021616|CI-23kD|TYKY	NADH dehydrogenase (ubiquinone) Fe-S protein 8	protein-coding
mm_29336.1	chr3	108200416	108200445	-	1	NA	intron (NM_028061, intron 1 of 2)	intron (NM_028061, intron 1 of 2)	404	NM_028061	72023	Mm.246391	NM_028061	ENSMUSG00000048796	Cyb561d1	1600010M23Rik|AI605489|AW457162	cytochrome b-561 domain containing 1	protein-coding
mm_15819.1	chr2	164562708	164562721	+	1	NA	promoter-TSS (NM_026323)	promoter-TSS (NM_026323)	-2	NM_026323	67701	Mm.27289	NM_026323	ENSMUSG00000017723	Wfdc2	1600023A02Rik|HE4|WAP5	WAP four-disulfide core domain 2	protein-coding
mm_22777.1	chr3	20308372	20308378	+	1	NA	Intergenic	Intergenic	-32642	NM_029706	76703	Mm.34692	NM_029706	ENSMUSG00000011463	Cpb1	0910001A18Rik|1810063F02Rik|2210008M23Rik|AI504870	carboxypeptidase B1 (tissue)	protein-coding
mm_170575.1	chr19	53929175	53929176	+	1	NA	TTS (NM_001195338)	TTS (NM_001195338)	-15131	NM_001168505	56392	Mm.228669	NM_019658	ENSMUSG00000024976	Shoc2	AU017287|Sur8|mKIAA0862	soc-2 (suppressor of clear) homolog (C. elegans)	protein-coding
mm_32748.1	chr4	116678777	116678800	+	1	NA	Intergenic	Intergenic	-6811	NM_011034	18477	Mm.30929	NM_011034	ENSMUSG00000028691	Prdx1	MSP23|NkefA|OSF-3|OSF3|PAG|Paga|PrdxI|PrxI|TDX2|TPxA|Tdpx2|prx1	peroxiredoxin 1	protein-coding
mm_104983.1	chr11	100265053	100265059	-	1	NA	intron (NM_212483, intron 4 of 7)	intron (NM_212483, intron 4 of 7)	-4027	NM_010663	16667	Mm.14046	NM_010663	ENSMUSG00000035557	Krt17	K17|Krt1-17	keratin 17	protein-coding
mm_138100.1	chr17	34092356	34092366	+	1	NA	promoter-TSS (NM_008206)	promoter-TSS (NM_008206)	-18	NM_008206	15001	Mm.116	NM_008206	ENSMUSG00000024334	H2-Oa	H-2Oa	histocompatibility 2, O region alpha locus	protein-coding
mm_37544.1	chr4	125124949	125124961	-	1	NA	intron (NM_153159, intron 2 of 5)	intron (NM_153159, intron 2 of 5)	2926	NM_153159	230738	Mm.402	NM_153159	ENSMUSG00000042677	Zc3h12a	BC036563|MCPIP|MCPIP-1|Mcpip1|Reg1	zinc finger CCCH type containing 12A	protein-coding
mm_72702.1	chr8	84978584	84978605	+	1	NA	5' UTR (NM_008416, exon 1 of 1)	5' UTR (NM_008416, exon 1 of 1)	154	NM_008416	16477	Mm.1167	NM_008416	ENSMUSG00000052837	Junb	-	jun B proto-oncogene	protein-coding
mm_69294.1	chr7	128236032	128236036	-	1	NA	3' UTR (NM_177001, exon 1 of 1)	3' UTR (NM_177001, exon 1 of 1)	-1323	NM_146205	233912	Mm.475117	NM_146205	ENSMUSG00000042178	Armc5	AW049683|BC032200	armadillo repeat containing 5	protein-coding
mm_45728.1	chr5	86197848	86197856	-	1	NA	promoter-TSS (NM_001310651)	promoter-TSS (NM_001310651)	49	NM_001310653	14715	Mm.26791	NM_010323	ENSMUSG00000029255	Gnrhr	-	gonadotropin releasing hormone receptor	protein-coding
mm_98842.1	chr11	97574321	97574333	+	1	NA	intron (NM_018873, intron 1 of 19)	intron (NM_018873, intron 1 of 19)	799	NM_018873	56013	Mm.342665	NM_018873	ENSMUSG00000038453	Srcin1	P140|SNIP|mKIAA1684|p140Cap	SRC kinase signaling inhibitor 1	protein-coding
mm_146189.1	chr18	76059465	76059501	+	1	NA	intron (NM_145356, intron 3 of 4)	CpG	38988	NR_045365	73009	Mm.443541	NR_045365		2900057B20Rik	-	RIKEN cDNA 2900057B20 gene	ncRNA
mm_33319.1	chr4	129082741	129082760	+	1	NA	exon (NM_029219, exon 8 of 9)	exon (NM_029219, exon 8 of 9)	-22780	NM_025452	66260	Mm.25295	NM_025452	ENSMUSG00000028786	Tmem54	1810017F10Rik|AI507302	transmembrane protein 54	protein-coding
mm_91509.1	chr10	37137022	37137047	-	1	NA	intron (NM_008538, intron 1 of 1)	CpG	1892	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_51923.1	chr6	91265947	91265959	+	1	NA	intron (NM_007992, intron 12 of 17)	intron (NM_007992, intron 12 of 17)	53189	NM_007992	14115	Mm.249146	NM_007992	ENSMUSG00000064080	Fbln2	5730577E14Rik|FIBL-2	fibulin 2	protein-coding
mm_79126.1	chr9	46913620	46913632	+	1	NA	promoter-TSS (NR_015605)	promoter-TSS (NR_015605)	23	NR_015605	73040	Mm.265384	NR_015605	ENSMUSG00000099696	2900052N01Rik	AU067665	RIKEN cDNA 2900052N01 gene	ncRNA
mm_161264.1	chr14	5050634	5050634	+	1	NA	promoter-TSS (NM_175393)	promoter-TSS (NM_175393)	5	NM_175393	108978	Mm.396152	NM_175393	ENSMUSG00000096197	4930555G01Rik	-	RIKEN cDNA 4930555G01 gene	protein-coding
mm_103055.1	chr11	69818458	69818468	-	1	NA	promoter-TSS (NM_175368)	promoter-TSS (NM_175368)	-23	NM_175368	108803	Mm.73263	NM_175368	ENSMUSG00000044084	4933402P03Rik	-	RIKEN cDNA 4933402P03 gene	protein-coding
mm_45829.1	chr5	87694650	87694655	-	1	NA	exon (NM_001286023, exon 5 of 7)	exon (NM_001286023, exon 5 of 7)	4773	NM_001286020	12991	Mm.268737	NM_009972	ENSMUSG00000063157	Csn2	Csnb	casein beta	protein-coding
mm_11668.1	chr2	35282428	35282442	+	1	NA	promoter-TSS (NM_146120)	promoter-TSS (NM_146120)	55	NM_146120	227753	Mm.443	NM_146120	ENSMUSG00000026879	Gsn	ADF	gelsolin	protein-coding
mm_59866.1	chr7	30184187	30184211	+	1	NA	promoter-TSS (NM_009944)	promoter-TSS (NM_009944)	28	NM_009944	12865	Mm.423030	NM_009944	ENSMUSG00000074218	Cox7a1	COX7A|COX7AH|COX7AM	cytochrome c oxidase subunit VIIa 1	protein-coding
mm_758.1	chr1	43933981	43934076	+	1	NA	promoter-TSS (NM_009418)	promoter-TSS (NM_009418)	34	NM_009418	22019	Mm.401675	NM_009418	ENSMUSG00000041763	Tpp2	TPP-2|TppII	tripeptidyl peptidase II	protein-coding
mm_76848.1	chr8	105323321	105323336	-	1	NA	5' UTR (NM_177449, exon 2 of 5)	5' UTR (NM_177449, exon 2 of 5)	2948	NM_177449	234684	Mm.381717	NM_177449	ENSMUSG00000041679	Lrrc29	A630024J02Rik|FBL9|FBXL9	leucine rich repeat containing 29	protein-coding
mm_55013.1	chr6	48840601	48840614	-	1	NA	promoter-TSS (NM_025326)	promoter-TSS (NM_025326)	381	NM_023056	65963	Mm.28385	NM_023056	ENSMUSG00000029810	Tmem176b	1810009M01Rik|Clast1|Lr8	transmembrane protein 176B	protein-coding
mm_157921.1	chrX	78583851	78583859	-	1	NA	promoter-TSS (NM_001289683)	promoter-TSS (NM_001289683)	42	NM_001289683	546336	Mm.211712	NM_027322	ENSMUSG00000047996	Prrg1	2010007L08Rik	proline rich Gla (G-carboxyglutamic acid) 1	protein-coding
mm_85395.1	chr9	103288291	103288307	-	1	NA	promoter-TSS (NM_027918)	promoter-TSS (NM_027918)	-2	NM_027918	71775	Mm.18802	NM_027918	ENSMUSG00000033688	1300017J02Rik	Ica|mICA	RIKEN cDNA 1300017J02 gene	protein-coding
mm_159116.1	chr2	60284569	60284569	-	1	NA	promoter-TSS (NM_025422)	promoter-TSS (NM_025422)	-85	NM_001290660	66205	Mm.227281	NM_025422	ENSMUSG00000060703	Cd302	1110055L24Rik|AI159627	CD302 antigen	protein-coding
mm_12632.1	chr2	74705087	74705101	+	1	NA	promoter-TSS (NM_001290730)	promoter-TSS (NM_001290730)	-395	NM_001290730	15437	Mm.280673	NM_008276	ENSMUSG00000027102	Hoxd8	4921540P06Rik|AI047735|Hox-4.3|Hox-5.4	homeobox D8	protein-coding
mm_171519.1	chr4	146565178	146565189	-	1	NA	Intergenic	CpG	-18310	NR_045468	67524	Mm.444300	NR_045468	ENSMUSG00000086046	1700095A21Rik	-	RIKEN cDNA 1700095A21 gene	ncRNA
mm_86643.1	chr10	14391096	14391096	+	1	NA	Intergenic	Intergenic	153940	NM_001002268	215798	Mm.440142	NM_001002268	ENSMUSG00000039116	Adgrg6	1190004A11Rik|AI449247|AW045736|DREG|Gm222|Gpr126	adhesion G protein-coupled receptor G6	protein-coding
mm_28956.1	chr3	100489295	100489316	-	1	NA	promoter-TSS (NM_001142952)	promoter-TSS (NM_001142952)	-113	NM_001142952	74645	Mm.226900	NM_001142952	ENSMUSG00000044468	Fam46c	4930431B09Rik|AI449797	family with sequence similarity 46, member C	protein-coding
mm_98068.1	chr11	85886361	85886418	+	1	NA	Intergenic	CpG	-3674	NM_011536	21387	Mm.275336	NM_011536	ENSMUSG00000000094	Tbx4	3930401C23	T-box 4	protein-coding
mm_99601.1	chr11	104550683	104550685	+	1	NA	promoter-TSS (NM_010858)	promoter-TSS (NM_010858)	21	NM_010858	17896	Mm.390355	NM_010858	ENSMUSG00000061086	Myl4	ALC1|AMLC|ELC|ELC1a|GT1|MLC1a|Myla	myosin, light polypeptide 4	protein-coding
mm_55217.1	chr6	52226146	52226162	-	1	NA	exon (NM_001277238, exon 1 of 3)	exon (NM_001277238, exon 1 of 3)	1216	NM_010456	15405	Mm.4694	NM_010456	ENSMUSG00000038227	Hoxa9	D6a9|Hox-1.7	homeobox A9	protein-coding
mm_172571.1	chr8	112015046	112015065	-	1	NA	intron (NM_020584, intron 1 of 2)	intron (NM_020584, intron 1 of 2)	3696	NM_020584	57321	Mm.213064	NM_020584	ENSMUSG00000033430	Terf2ip	Rap1	telomeric repeat binding factor 2, interacting protein	protein-coding
mm_78390.1	chr9	28511023	28511034	+	1	NA	intron (NM_177906, intron 2 of 7)	ID2|SINE|ID	719759	NM_177906	330908	Mm.379474	NM_177906	ENSMUSG00000062257	Opcml	2900075O15Rik|3732419F12|AI844366|B930023M13Rik|C230027C17|Gm181|Obcam	opioid binding protein/cell adhesion molecule-like	protein-coding
mm_134587.1	chr16	20426190	20426233	-	1	NA	intron (NM_176839, intron 1 of 6)	CpG	183	NM_013790	27416	Mm.20845	NM_013790	ENSMUSG00000022822	Abcc5	2900011L11Rik|AI132311|Abcc5a|Abcc5b|Mrp5	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	protein-coding
mm_24532.1	chr3	93278065	93278072	+	1	NA	Intergenic	Intergenic	-41681	NM_133698	68723	Mm.208047	NM_133698	ENSMUSG00000041991	Hrnr	1110033K19Rik|A530063N20Rik|S100a18	hornerin	protein-coding
mm_154922.1	chrX	23693044	23693131	+	1	NA	promoter-TSS (NM_175180)	promoter-TSS (NM_175180)	36	NM_001305675	72404	Mm.423	NM_175180	ENSMUSG00000036769	Wdr44	2610034K17Rik|RAB11BP|RPH11	WD repeat domain 44	protein-coding
mm_134182.1	chr16	10960989	10961002	-	1	NA	exon (NM_019980, exon 4 of 4)	exon (NM_019980, exon 4 of 4)	32126	NM_019980	56722	Mm.294753	NM_019980	ENSMUSG00000022500	Litaf	3222402J11Rik|C85531|N4WBP3|TBX1	LPS-induced TN factor	protein-coding
mm_145316.1	chr18	54422371	54422381	+	1	NA	promoter-TSS (NR_040338)	promoter-TSS (NR_040338)	81	NR_040338	77433	Mm.159919	NR_040338		Redrum	9430076G02Rik	Redrum, erythroid developmental long intergenic non-protein coding transcript	ncRNA
mm_3330.1	chr1	137931853	137931863	+	1	NA	Intergenic	Intergenic	-34597	NR_029795	735252		NR_029795	ENSMUSG00000065565	Mir181a-1	Mirn181a-1|Mirn213|miR-213|mir-181a-1|mmu-mir-213	microRNA 181a-1	ncRNA
mm_159228.1	chr2	131187139	131187139	-	1	NA	5' UTR (NM_001111075, exon 1 of 15)	5' UTR (NM_001111075, exon 1 of 15)	191	NM_001111075	12531	Mm.38444	NM_023117	ENSMUSG00000027330	Cdc25b	AI604853	cell division cycle 25B	protein-coding
mm_84295.1	chr9	63377625	63377766	-	1	NA	5' UTR (NM_011840, exon 1 of 22)	5' UTR (NM_011840, exon 1 of 22)	157	NM_011840	23938	Mm.325746	NM_011840	ENSMUSG00000058444	Map2k5	AI324775|AI428457|MEK5|Mapkk5|Prkmk5	mitogen-activated protein kinase kinase 5	protein-coding
mm_41655.1	chr5	98854409	98854429	+	1	NA	promoter-TSS (NM_001310677)	promoter-TSS (NM_001310677)	4	NM_001310677	110075	Mm.136461	NM_173404	ENSMUSG00000029335	Bmp3	9530029I04Rik	bone morphogenetic protein 3	protein-coding
mm_58602.1	chr7	5051501	5051511	+	1	NA	promoter-TSS (NM_026900)	promoter-TSS (NM_026900)	-26	NM_026900	68992	Mm.41484	NM_026900	ENSMUSG00000055633	Zfp580	1500015O20Rik|AI838225|Znf580	zinc finger protein 580	protein-coding
mm_7212.1	chr1	93101826	93101849	-	1	NA	promoter-TSS (NM_008440)	promoter-TSS (NM_008440)	37	NM_001294149	16560	Mm.276408	NM_008440	ENSMUSG00000014602	Kif1a	ATSV|C630002N23Rik|Gm1626|Kns1	kinesin family member 1A	protein-coding
mm_163029.1	chr11	50543872	50543875	+	1	NA	Intergenic	B3A|SINE|B2	-58212	NM_175643	216725	Mm.110597	NM_175643	ENSMUSG00000036545	Adamts2	ADAM-TS 2|ADAM-TS2|ADAMTS-2|PC I-NP|PCINP|pNPI	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 2	protein-coding
mm_89081.1	chr10	83543942	83544007	+	1	NA	promoter-TSS (NM_001033375)	promoter-TSS (NM_001033375)	33	NM_001033375	319277	Mm.491194	NM_001033375	ENSMUSG00000034560	Washc4	A230046K03Rik|AA589518|Kiaa1033|mKIAA1033	WASH complex subunit 4	protein-coding
mm_38837.1	chr4	149165145	149165163	-	1	NA	exon (NM_001081274, exon 3 of 13)	exon (NM_001081274, exon 3 of 13)	1553	NM_001081274	110208	Mm.252080	NM_025801	ENSMUSG00000028961	Pgd	0610042A05Rik|AU019875|C78335	phosphogluconate dehydrogenase	protein-coding
mm_93013.1	chr10	87492483	87492493	-	1	NA	exon (NM_008553, exon 1 of 2)	exon (NM_008553, exon 1 of 2)	1172	NM_008553	17172	Mm.136217	NM_008553	ENSMUSG00000020052	Ascl1	AI225900|ASH1|Mash1|bHLHa46	achaete-scute family bHLH transcription factor 1	protein-coding
mm_25474.1	chr3	108856132	108856143	+	1	NA	3' UTR (NM_177091, exon 13 of 13)	3' UTR (NM_177091, exon 13 of 13)	-15635	NM_011504	20912	Mm.316894	NM_011504	ENSMUSG00000027882	Stxbp3	Munc-18c|Stxbp3a|Sxtbp3|Unc18-3	syntaxin binding protein 3	protein-coding
mm_96466.1	chr11	67617151	67617167	+	1	NA	intron (NM_001109657, intron 2 of 13)	intron (NM_001109657, intron 2 of 13)	20604	NM_001277079	14457	Mm.40338	NM_008088	ENSMUSG00000033066	Gas7	AW124766|B230343A10Rik|Gas7-cb	growth arrest specific 7	protein-coding
mm_144766.1	chr18	35772119	35772131	+	1	NA	intron (NM_019912, intron 1 of 6)	CpG	566	NM_019912	56550	Mm.180052	NM_019912	ENSMUSG00000091896	Ube2d2a	1500034D03Rik|Ubc2e|Ube2d2|ubc4	ubiquitin-conjugating enzyme E2D 2A	protein-coding
mm_42228.1	chr5	113510840	113510845	+	1	NA	Intergenic	Intergenic	-39578	NM_177292	320916	Mm.102783	NM_177292	ENSMUSG00000063430	Wscd2	4933413A10Rik|C530024P05Rik|Gm450	WSC domain containing 2	protein-coding
mm_92245.1	chr10	70288529	70288548	-	1	NA	Intergenic	RMER17C|LTR|ERVK	43262	NM_025807	66859	Mm.19325	NM_025807	ENSMUSG00000037762	Slc16a9	1200003C15Rik|4930425B13Rik|AI552636	solute carrier family 16 (monocarboxylic acid transporters), member 9	protein-coding
mm_46960.1	chr5	115127518	115127530	-	1	NA	intron (NM_175352, intron 2 of 4)	intron (NM_175352, intron 2 of 4)	7451	NM_175352	106840	Mm.29241	NM_175352	ENSMUSG00000046562	Unc119b	AA407659|AI414892	unc-119 lipid binding chaperone B	protein-coding
mm_75139.1	chr8	35261424	35261463	-	1	NA	Intergenic	Intergenic	-114298	NM_177741	244416	Mm.247126	NM_177741	ENSMUSG00000046794	Ppp1r3b	6430576E21|AW821953|GL|PTG	protein phosphatase 1, regulatory (inhibitor) subunit 3B	protein-coding
mm_62945.1	chr7	119526270	119526300	+	1	NA	promoter-TSS (NM_178758)	promoter-TSS (NM_178758)	20	NM_178758	272428	Mm.185183	NM_178758	ENSMUSG00000030972	Acsm5	C730019D22|C730027J19Rik	acyl-CoA synthetase medium-chain family member 5	protein-coding
mm_103345.1	chr11	74724333	74724393	-	1	NA	promoter-TSS (NR_037610)	promoter-TSS (NR_037610)	21	NM_013625	18472	Mm.397111	NM_013625	ENSMUSG00000020745	Pafah1b1	LIS-1|Lis1|MMS10-U|Mdsh|Ms10u|Pafaha	platelet-activating factor acetylhydrolase, isoform 1b, subunit 1	protein-coding
mm_22937.1	chr3	31228480	31228481	+	1	NA	intron (NM_172861, intron 5 of 7)	intron (NM_172861, intron 5 of 7)	78560	NM_008770	18417	Mm.4425	NM_008770	ENSMUSG00000037625	Cldn11	Claudin-11|Claudin11|Osp|Otm	claudin 11	protein-coding
mm_71716.1	chr8	61947544	61947555	+	1	NA	intron (NM_001293783, intron 6 of 37)	intron (NM_001293783, intron 6 of 37)	19462	NM_001293783	234311	Mm.275233	NM_144928	ENSMUSG00000037921	Ddx60	9830118M07	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	protein-coding
mm_131533.1	chr16	17711624	17711651	+	1	NA	intron (NM_001285886, intron 1 of 16)	intron (NM_001285886, intron 1 of 16)	11263	NM_001285886	94112	Mm.208970	NM_033609	ENSMUSG00000012114	Med15	A230074L19Rik|AW536074|Pcqap|mPcqap	mediator complex subunit 15	protein-coding
mm_91661.1	chr10	42864222	42864240	-	1	NA	intron (NM_172938, intron 1 of 8)	intron (NM_172938, intron 1 of 8)	3719	NM_172938	268297	Mm.98731	NM_172938	ENSMUSG00000044770	Scml4	9330161D17|mFLJ00197	sex comb on midleg-like 4 (Drosophila)	protein-coding
mm_9414.1	chr1	172297990	172298008	-	1	NA	promoter-TSS (NM_178405)	promoter-TSS (NM_178405)	65	NM_178405	98660	Mm.207432	NM_178405	ENSMUSG00000007097	Atp1a2	AW060654|Atpa-3|mKIAA0778	ATPase, Na+/K+ transporting, alpha 2 polypeptide	protein-coding
mm_49755.1	chr6	34753588	34753591	+	1	NA	intron (NM_001347100, intron 6 of 13)	intron (NM_001347100, intron 6 of 13)	-26843	NM_001289657	76223	Mm.150047	NM_178630	ENSMUSG00000038836	Agbl3	2900053G10Rik|4930431N21Rik|6530406M24Rik|CCP3	ATP/GTP binding protein-like 3	protein-coding
mm_60516.1	chr7	44479810	44479877	+	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	-4674	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_87386.1	chr10	45067074	45067088	+	1	NA	promoter-TSS (NM_011156)	promoter-TSS (NM_011156)	-133	NM_011156	19072	Mm.10281	NM_011156	ENSMUSG00000019849	Prep	AI047692|AI450383|D10Wsu136e|PEP|Pop	prolyl endopeptidase	protein-coding
mm_85120.1	chr9	95462602	95462605	-	1	NA	intron (NM_026476, intron 26 of 26)	intron (NM_026476, intron 26 of 26)	49393	NM_026476	67958	Mm.292742	NM_026476	ENSMUSG00000032407	U2surp	2610101N10Rik|AU023006|Sr140	U2 snRNP-associated SURP domain containing	protein-coding
mm_33814.1	chr4	135312962	135312986	+	1	NA	Intergenic	Intergenic	-40214	NM_013885	29876	Mm.257765	NM_013885	ENSMUSG00000037242	Clic4	D0Jmb3|TU-74|mc3s5|mtCLIC	chloride intracellular channel 4 (mitochondrial)	protein-coding
mm_84560.1	chr9	67733767	67733791	-	1	NA	Intergenic	Intergenic	-4202	NR_106101	102465716		NR_106101	ENSMUSG00000098446	Mir7242	Gm27809|mmu-mir-7242	microRNA 7242	ncRNA
mm_71214.1	chr8	40892745	40892758	+	1	NA	intron (NM_007514, intron 1 of 11)	intron (NM_007514, intron 1 of 11)	30384	NM_001044740	11988	Mm.4676	NM_007514	ENSMUSG00000031596	Slc7a2	20.5|AI158848|Atrc2|CAT-2|Cat2|Tea	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	protein-coding
mm_41920.1	chr5	105608375	105608390	+	1	NA	exon (NM_133897, exon 4 of 4)	exon (NM_133897, exon 4 of 4)	88911	NM_133897	100604	Mm.319847	NM_133897	ENSMUSG00000054720	Lrrc8c	AD158|AI326115|E430036I04Rik|fad158	leucine rich repeat containing 8 family, member C	protein-coding
mm_85430.1	chr9	103692760	103692770	-	1	NA	intron (NM_178638, intron 2 of 5)	intron (NM_178638, intron 2 of 5)	69072	NM_178638	81907	Mm.384704	NM_178638	ENSMUSG00000042757	Tmem108	AI462967|B130017P16Rik|R74726	transmembrane protein 108	protein-coding
mm_131086.1	chr16	4835433	4835457	+	1	NA	promoter-TSS (NM_030192)	promoter-TSS (NM_030192)	29	NM_030192	78809	Mm.325551	NM_030192	ENSMUSG00000022518	4930562C15Rik	-	RIKEN cDNA 4930562C15 gene	protein-coding
mm_151788.1	chr19	5388727	5388735	-	1	NA	promoter-TSS (NM_016882)	promoter-TSS (NM_016882)	-28	NM_016882	20227	Mm.34562	NM_016882	ENSMUSG00000039148	Sart1	U5-110K	squamous cell carcinoma antigen recognized by T cells 1	protein-coding
mm_149893.1	chr19	25407078	25407088	+	1	NA	intron (NM_181404, intron 4 of 13)	intron (NM_181404, intron 4 of 13)	-98623	NM_015826	50796	Mm.391208	NM_015826	ENSMUSG00000024837	Dmrt1	-	doublesex and mab-3 related transcription factor 1	protein-coding
mm_45392.1	chr5	66151189	66151197	-	1	NA	promoter-TSS (NM_001291226)	promoter-TSS (NM_001291226)	-215	NM_178446	245945	Mm.36863	NM_139065	ENSMUSG00000070780	Rbm47	9530077J19Rik	RNA binding motif protein 47	protein-coding
mm_8245.1	chr1	138598930	138598932	-	1	NA	intron (NM_001311148, intron 1 of 7)	intron (NM_001311148, intron 1 of 7)	20826	NM_021605	59125	Mm.143817	NM_021605	ENSMUSG00000026393	Nek7	2810460C19Rik|AU020186	NIMA (never in mitosis gene a)-related expressed kinase 7	protein-coding
mm_25801.1	chr3	127789205	127789214	+	1	NA	promoter-TSS (NM_145133)	promoter-TSS (NM_145133)	-704	NM_145133	211550	Mm.31852	NM_145133	ENSMUSG00000046688	Tifa	T2bp	TRAF-interacting protein with forkhead-associated domain	protein-coding
mm_96655.1	chr11	69373755	69373796	+	1	NA	Intergenic	Intergenic	-4349	NM_146019	216848	Mm.178246	NM_146019	ENSMUSG00000018474	Chd3	2600010P09Rik|AF020312|Chd7|Prp7|Prp9-1	chromodomain helicase DNA binding protein 3	protein-coding
mm_94912.1	chr11	29455430	29455451	+	1	NA	exon (NM_176841, exon 11 of 32)	exon (NM_176841, exon 11 of 32)	59593	NM_026465	67939	Mm.251087	NM_026465	ENSMUSG00000032673	Prorsd1	2010316F05Rik|Ncrna00117|Prdxdd1	prolyl-tRNA synthetase domain containing 1	protein-coding
mm_161816.1	chr17	69439347	69439347	+	1	NA	promoter-TSS (NM_001145192)	promoter-TSS (NM_001145192)	21	NM_001145192	320722	Mm.400254	NM_001145192	ENSMUSG00000091636	Akain1	A330050F15Rik	A kinase (PRKA) anchor inhibitor 1	protein-coding
mm_7899.1	chr1	133610254	133610294	-	1	NA	promoter-TSS (NM_009227)	promoter-TSS (NM_009227)	6	NM_009227	20643	Mm.249110	NM_009227	ENSMUSG00000090553	Snrpe	AL022645|C76690|SME	small nuclear ribonucleoprotein E	protein-coding
mm_6051.1	chr1	60097894	60097924	-	1	NA	promoter-TSS (NM_139150)	promoter-TSS (NM_139150)	-2	NM_021312	57750	Mm.281079	NM_021312	ENSMUSG00000026019	Wdr12	4933402C23Rik|Ytm1|Ytm1p	WD repeat domain 12	protein-coding
mm_143161.1	chr17	57224320	57224333	-	1	NA	exon (NM_009778, exon 9 of 41)	exon (NM_009778, exon 9 of 41)	3810	NM_009778	12266	Mm.19131	NM_009778	ENSMUSG00000024164	C3	AI255234|ASP|HSE-MSF|Plp	complement component 3	protein-coding
mm_147384.1	chr18	43737526	43737532	-	1	NA	promoter-TSS (NM_009258)	promoter-TSS (NM_009258)	-292	NM_009258	20730	Mm.272	NM_009258	ENSMUSG00000024503	Spink1	Spink3|p12	serine peptidase inhibitor, Kazal type 1	protein-coding
mm_151648.1	chr19	4059450	4059476	-	1	NA	promoter-TSS (NM_144869)	promoter-TSS (NM_144869)	-169	NM_144869	225884	Mm.440201	NM_144869	ENSMUSG00000058216	Gstp3	-	glutathione S-transferase pi 3	protein-coding
mm_27914.1	chr3	79531718	79531728	-	1	NA	intron (NM_001162999, intron 1 of 16)	intron (NM_001162999, intron 1 of 16)	35956	NM_001162999	329679	Mm.244005	NM_001162999	ENSMUSG00000061175	Fnip2	D630023B12Rik|mKIAA1450	folliculin interacting protein 2	protein-coding
mm_82933.1	chr9	35194544	35194550	-	1	NA	intron (NM_001177845, intron 2 of 6)	intron (NM_001177845, intron 2 of 6)	5358	NM_001177847	117149	Mm.23987	NM_054096	ENSMUSG00000032041	Tirap	AA407980|C130027E04Rik|Mal|Tlr4ap|Wyatt	toll-interleukin 1 receptor (TIR) domain-containing adaptor protein	protein-coding
mm_161509.1	chr15	98379091	98379091	-	1	NA	promoter-TSS (NM_147036)	promoter-TSS (NM_147036)	17	NM_147036	259038	Mm.377802	NM_147036	ENSMUSG00000056184	Olfr283	MOR160-1	olfactory receptor 283	protein-coding
mm_157860.1	chrX	75113643	75113660	-	1	NA	exon (NM_008621, exon 9 of 12)	exon (NM_008621, exon 9 of 12)	17365	NM_008621	17524	Mm.391267	NM_008621	ENSMUSG00000031402	Mpp1	55kDa|C130070C03Rik|p55	membrane protein, palmitoylated	protein-coding
mm_146752.1	chr18	16764806	16764809	-	1	NA	intron (NM_007664, intron 2 of 15)	intron (NM_007664, intron 2 of 15)	44439	NM_007664	12558	Mm.257437	NM_007664	ENSMUSG00000024304	Cdh2	CDHN|N-CAD|Ncad	cadherin 2	protein-coding
mm_14555.1	chr2	133553005	133553017	+	1	NA	5' UTR (NM_007553, exon 1 of 3)	5' UTR (NM_007553, exon 1 of 3)	852	NM_007553	12156	Mm.103205	NM_007553	ENSMUSG00000027358	Bmp2	AI467020|Bmp2a	bone morphogenetic protein 2	protein-coding
mm_89842.1	chr10	106879418	106879429	+	1	NA	intron (NM_001205341, intron 21 of 31)	(CA)n|Simple_repeat|Simple_repeat	244241	NM_001142804	380660	Mm.336072	NM_198636	ENSMUSG00000035948	Acss3	8430416H19Rik|Gm874	acyl-CoA synthetase short-chain family member 3	protein-coding
mm_114681.1	chr13	80886492	80886504	+	1	NA	intron (NM_001042591, intron 1 of 7)	intron (NM_001042591, intron 1 of 7)	3076	NM_001042591	105171	Mm.423137	NM_001042591	ENSMUSG00000074794	Arrdc3	AI450344|mKIAA1376	arrestin domain containing 3	protein-coding
mm_49680.1	chr6	32511119	32511170	+	1	NA	promoter-TSS (NR_040277)	promoter-TSS (NR_040277)	3	NR_040277	319849	Mm.440860	NR_040277	ENSMUSG00000086763	Plxna4os1	B230378P21Rik	plexin A4, opposite strand 1	ncRNA
mm_101083.1	chr11	11769925	11769939	-	1	NA	3' UTR (NM_009578, exon 7 of 7)	3' UTR (NM_009578, exon 7 of 7)	39030	NM_021891	60530	Mm.236114	NM_021891	ENSMUSG00000035455	Fignl1	-	fidgetin-like 1	protein-coding
mm_108185.1	chr12	76547077	76547088	+	1	NA	non-coding (NR_046044, exon 3 of 3)	non-coding (NR_046044, exon 3 of 3)	843	NR_046044	100504549	Mm.440349	NR_046044		AI463170	-	expressed sequence AI463170	ncRNA
mm_125823.1	chr15	74957164	74957178	+	1	NA	intron (NM_001164039, intron 2 of 4)	intron (NM_001164039, intron 2 of 4)	2065	NM_001164040	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_98537.1	chr11	95009937	95009947	+	1	NA	promoter-TSS (NM_146025)	promoter-TSS (NM_146025)	63	NM_146025	217125	Mm.297199	NM_146025	ENSMUSG00000047181	Samd14	AI839049|AI854782|BC034054	sterile alpha motif domain containing 14	protein-coding
mm_44117.1	chr5	149441828	149441840	+	1	NA	intron (NM_001310765, intron 1 of 5)	intron (NM_001310765, intron 1 of 5)	2174	NM_001310765	75860	Mm.159605	NM_029464	ENSMUSG00000029660	Tex26	4930588N13Rik	testis expressed 26	protein-coding
mm_112595.1	chr13	14065986	14065996	+	1	NA	intron (NM_198122, intron 2 of 22)	(T)n|Simple_repeat|Simple_repeat	2207	NM_198122	94246	Mm.439784	NM_194262	ENSMUSG00000039219	Arid4b	BCAA|BRCAA1|RBBP1L1|Rbp1l1|SAP180	AT rich interactive domain 4B (RBP1-like)	protein-coding
mm_26532.1	chr3	146117542	146117544	+	1	NA	Intergenic	Intergenic	-4248	NM_134160	171166	Mm.114683	NM_134160	ENSMUSG00000036853	Mcoln3	6720490O21Rik|TRPML3|Va	mucolipin 3	protein-coding
mm_130323.1	chr15	97596260	97596265	-	1	NA	Intergenic	RMER2|LTR|ERV1	109560	NM_028003	71919	Mm.12255	NM_028003	ENSMUSG00000022466	Rpap3	2310042P20Rik|D15Ertd682e	RNA polymerase II associated protein 3	protein-coding
mm_64181.1	chr7	141459498	141459510	+	1	NA	non-coding (NR_028142, exon 10 of 10)	non-coding (NR_028142, exon 10 of 10)	-1590	NM_001025103	213573	Mm.386851	NM_001025103	ENSMUSG00000048200	Cracr2b	6330520A15Rik|BC026645|Cracr2a|Efcab4|Efcab4a	calcium release activated channel regulator 2B	protein-coding
mm_148348.1	chr18	84676675	84676679	-	1	NA	intron (NM_023149, intron 5 of 11)	PB1D10|SINE|Alu	5382	NM_001289531	66054	Mm.29646	NM_023149	ENSMUSG00000024644	Cndp2	0610010E05Rik|C76600|Cn2|Dip-2|Pep-1|Pep1	CNDP dipeptidase 2 (metallopeptidase M20 family)	protein-coding
mm_159038.1	chr1	180245777	180245777	-	1	NA	intron (NM_001128605, intron 1 of 10)	intron (NM_001128605, intron 1 of 10)	173	NM_011183	19165	Mm.330850	NM_011183	ENSMUSG00000010609	Psen2	ALG-3|Ad4h|Alg3|PS-2|PS2|Psnl2|STM2	presenilin 2	protein-coding
mm_25398.1	chr3	107241790	107241799	+	1	NA	Intergenic	Intergenic	-2087	NM_001044382	246691	Mm.490697	NM_001044382	ENSMUSG00000070368	Prok1	EG-VEGF	prokineticin 1	protein-coding
mm_162229.1	chrX	149784457	149784457	+	1	NA	promoter-TSS (NM_001198987)	promoter-TSS (NM_001198987)	-22	NM_001114400	434866	Mm.491025	NM_001114400	ENSMUSG00000096834	Gm15127	ENSMUSG00000072928|OTTMUSG00000019138	predicted gene 15127	protein-coding
mm_158202.1	chrX	105391727	105391762	-	1	NA	promoter-TSS (NR_015552)	promoter-TSS (NR_015552)	10	NR_015552	100043213	Mm.388967	NR_015552	ENSMUSG00000087620	5330434G04Rik	-	RIKEN cDNA 5330434G04 gene	ncRNA
mm_87504.1	chr10	52319874	52319884	+	1	NA	exon (NM_025705, exon 11 of 11)	exon (NM_025705, exon 11 of 11)	62245	NM_053187	94221	Mm.390258	NM_053187	ENSMUSG00000019861	Gopc	2210402P09Rik|AI844555|CAL|FIG|GOPC1|PIST	golgi associated PDZ and coiled-coil motif containing	protein-coding
mm_170882.1	chr2	20900160	20900162	+	1	NA	intron (NM_001128084, intron 3 of 24)	LSU-rRNA_Hsa|rRNA|rRNA	67560	NM_001081364	71435	Mm.28507	NM_001081364	ENSMUSG00000036591	Arhgap21	5530401C11Rik|AA416458|ARHGAP10	Rho GTPase activating protein 21	protein-coding
mm_76072.1	chr8	78813086	78813118	-	1	NA	intron (NM_030145, intron 1 of 3)	intron (NM_030145, intron 1 of 3)	8050	NM_001191004	78651	Mm.28694	NM_030145	ENSMUSG00000031683	Lsm6	1500031N17Rik|2410088K19Rik|AI747288	LSM6 homolog, U6 small nuclear RNA and mRNA degradation associated	protein-coding
mm_67208.1	chr7	74342135	74342146	-	1	NA	intron (NM_001038643, intron 4 of 10)	B4A|SINE|B4	212640	NM_023908	108116	Mm.425467	NM_023908	ENSMUSG00000025790	Slco3a1	5830414C08Rik|Anr1|MJAM|OATP-D|R75096|Slc21a11	solute carrier organic anion transporter family, member 3a1	protein-coding
mm_35665.1	chr4	43562298	43562308	-	1	NA	promoter-TSS (NM_013497)	promoter-TSS (NM_013497)	280	NM_011602	21894	Mm.208601	NM_011602	ENSMUSG00000028465	Tln1	Tln	talin 1	protein-coding
mm_38171.1	chr4	135218613	135218654	-	1	NA	exon (NM_013885, exon 5 of 6)	exon (NM_013885, exon 5 of 6)	54127	NM_013885	29876	Mm.257765	NM_013885	ENSMUSG00000037242	Clic4	D0Jmb3|TU-74|mc3s5|mtCLIC	chloride intracellular channel 4 (mitochondrial)	protein-coding
mm_80793.1	chr9	96196247	96196280	+	1	NA	promoter-TSS (NM_178667)	promoter-TSS (NM_178667)	-12	NM_178667	211586	Mm.17977	NM_178667	ENSMUSG00000032411	Tfdp2	1110029I05Rik|A330080J22Rik|DP-3|DP3	transcription factor Dp 2	protein-coding
mm_12428.1	chr2	70563630	70563663	+	1	NA	promoter-TSS (NR_040496)	promoter-TSS (NR_040496)	-289	NR_040496	68986	Mm.437697	NR_040496	ENSMUSG00000087264	Gad1os	1500002O10Rik	glutamate decarboxylase 1, opposite strand	ncRNA
mm_82242.1	chr9	4309511	4309517	-	1	NA	promoter-TSS (NM_026962)	promoter-TSS (NM_026962)	-20	NM_001326359	67618	Mm.33970	NM_026276	ENSMUSG00000025894	Aasdhppt	2010309J24Rik|2810407B07Rik|AASD-PPT|CGI-80|LYS2|LYS5	aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase	protein-coding
mm_146226.1	chr18	77065703	77065705	+	1	NA	promoter-TSS (NM_001164168)	promoter-TSS (NM_001164168)	24	NM_001164168	17344	Mm.6370	NM_008602	ENSMUSG00000025423	Pias2	6330408K17Rik|AI462206|ARIP3|AU018068|Dib|Miz1|PIASxalpha|PIASxb|PIASxbeta|SIZ2	protein inhibitor of activated STAT 2	protein-coding
mm_93902.1	chr10	126692526	126692539	-	1	NA	Intergenic	Intergenic	17859	NR_105841	102465224		NR_105841	ENSMUSG00000098756	Mir378d	Gm27650|mmu-mir-378d	microRNA 378d	ncRNA
mm_35972.1	chr4	53158427	53158429	-	1	NA	intron (NM_013454, intron 1 of 49)	intron (NM_013454, intron 1 of 49)	1467	NM_013454	11303	Mm.277376	NM_013454	ENSMUSG00000015243	Abca1	ABC-1|Abc1	ATP-binding cassette, sub-family A (ABC1), member 1	protein-coding
mm_1087.1	chr1	59606744	59606754	+	1	NA	intron (NM_001013771, intron 12 of 19)	intron (NM_001013771, intron 12 of 19)	64085	NM_009460	22218	Mm.362118	NM_009460	ENSMUSG00000026021	Sumo1	GMP1|PIC1|SENTRIN|SMT3|SMT3H3|SMTP3|SUMO-1|Smt3C|Ubl1	small ubiquitin-like modifier 1	protein-coding
mm_116953.1	chr13	56135838	56135848	-	1	NA	promoter-TSS (NM_001159515)	promoter-TSS (NM_001159515)	-293	NM_001159513	26914	Mm.283802	NM_012015	ENSMUSG00000015937	H2afy	H2AF12M|mH2a1|macroH2A1	H2A histone family, member Y	protein-coding
mm_116205.1	chr13	32703490	32703515	-	1	NA	3' UTR (NM_001166030, exon 12 of 12)	3' UTR (NM_001166030, exon 12 of 12)	78277	NM_001166030	238564	Mm.60041	NM_001166030	ENSMUSG00000044951	Mylk4	EG238564	myosin light chain kinase family, member 4	protein-coding
mm_32475.1	chr4	107812255	107812258	+	1	NA	intron (NR_033496, intron 2 of 20)	Lx7|LINE|L1	9997	NM_001080926	16975	Mm.442134	NM_053073	ENSMUSG00000028613	Lrp8	4932703M08Rik|AA921429|AI848122|ApoER2|Lr8b	low density lipoprotein receptor-related protein 8, apolipoprotein e receptor	protein-coding
mm_144828.1	chr18	36348917	36348930	+	1	NA	intron (NM_001081365, intron 1 of 2)	CpG	299	NM_001081365	66060	Mm.272527	NM_001081365	ENSMUSG00000046727	Cystm1	0610010O12Rik	cysteine-rich transmembrane module containing 1	protein-coding
mm_65364.1	chr7	25068883	25068918	-	1	NA	intron (NM_008168, intron 1 of 19)	intron (NM_008168, intron 1 of 19)	3469	NM_008168	14809	Mm.2879	NM_008168	ENSMUSG00000003378	Grik5	GluK5|GluRgamma2|KA2	glutamate receptor, ionotropic, kainate 5 (gamma 2)	protein-coding
mm_118440.1	chr14	8095771	8095817	+	1	NA	Intergenic	Intergenic	-2419	NM_145458	218699	Mm.29515	NM_145458	ENSMUSG00000033885	Pxk	C230080L11Rik|D14Ertd813e|MONaKA	PX domain containing serine/threonine kinase	protein-coding
mm_145317.1	chr18	54427019	54427022	+	1	NA	intron (NR_040338, intron 1 of 2)	intron (NR_040338, intron 1 of 2)	4725	NR_040338	77433	Mm.159919	NR_040338		Redrum	9430076G02Rik	Redrum, erythroid developmental long intergenic non-protein coding transcript	ncRNA
mm_166884.1	chr7	27166541	27166551	-	1	NA	intron (NM_053208, intron 1 of 5)	CpG	256	NM_053208	112406	Mm.29978	NM_053208	ENSMUSG00000058709	Egln2	0610011A13Rik|C85656|Hif-p4h-1|Ier4|Phd1|SM-20	egl-9 family hypoxia-inducible factor 2	protein-coding
mm_87339.1	chr10	43479142	43479194	+	1	NA	promoter-TSS (NM_199028)	promoter-TSS (NM_199028)	28	NM_199028	331623	Mm.490388	NM_199028	ENSMUSG00000038214	Bend3	mKIAA1553	BEN domain containing 3	protein-coding
mm_39434.1	chr5	16553832	16553857	+	1	NA	promoter-TSS (NM_001289461)	promoter-TSS (NM_001289461)	-57	NM_001289461	15234	Mm.267078	NM_010427	ENSMUSG00000028864	Hgf	C230052L06Rik|HGF/SF|NK1|NK2|SF|SF/HGF	hepatocyte growth factor	protein-coding
mm_155062.1	chrX	42502467	42502469	+	1	NA	promoter-TSS (NM_011364)	promoter-TSS (NM_011364)	-97	NM_011364	20400	Mm.441197	NM_011364	ENSMUSG00000005696	Sh2d1a	Gm686|SAP	SH2 domain containing 1A	protein-coding
mm_169666.1	chr15	60614555	60614555	-	1	NA	Intergenic	RLTR10E|LTR|ERVK	-208410	NR_030696	320469	Mm.230853	NM_177166		9930014A18Rik	-	RIKEN cDNA 9930014A18 gene	ncRNA
mm_9155.1	chr1	170958896	170958917	-	1	NA	Intergenic	Intergenic	17165	NM_001077189	14130	Mm.425062	NM_010187	ENSMUSG00000026656	Fcgr2b	AI528646|CD32|F630109E10Rik|Fc[g]RII|FcgRII|Fcgr2|Fcgr2a|Fcr-2|Fcr-3|Ly-17|Ly-m20|LyM-1|Lym-1|fcRII	Fc receptor, IgG, low affinity IIb	protein-coding
mm_135072.1	chr16	34262831	34262841	-	1	NA	intron (NM_001164268, intron 10 of 33)	intron (NM_001164268, intron 10 of 33)	251191	NM_001164268	545156	Mm.82274	NM_177357	ENSMUSG00000061751	Kalrn	2210407G14Rik|AV235988|DUET|E530005C20Rik|Gm539|Hapip|TRAD	kalirin, RhoGEF kinase	protein-coding
mm_18879.1	chr2	76360426	76360439	-	1	NA	promoter-TSS (NM_009989)	promoter-TSS (NM_009989)	21	NM_009989	13067	Mm.4872	NM_009989	ENSMUSG00000056436	Cyct	T-Cc	cytochrome c, testis	protein-coding
mm_62089.1	chr7	93079941	93079955	+	1	NA	promoter-TSS (NM_021427)	promoter-TSS (NM_021427)	69	NM_021427	58238	Mm.113787	NM_021427	ENSMUSG00000051515	Fam181b	A830059I20Rik|AB041569	family with sequence similarity 181, member B	protein-coding
mm_115110.1	chr13	103774668	103774678	+	1	NA	Intergenic	CpG	-10091	NM_172592	218543	Mm.458176	NM_172592	ENSMUSG00000032621	Srek1	8430401B01|AI450757|AI462342|SRrp508|SRrp86|Sfrs12|Srsf12	splicing regulatory glutamine/lysine-rich protein 1	protein-coding
mm_10370.1	chr2	11723316	11723319	+	1	NA	intron (NR_073191, intron 3 of 5)	intron (NR_073191, intron 3 of 5)	17605	NM_001271500	16169	Mm.200196	NM_008358	ENSMUSG00000023206	Il15ra	AA690181|IL-15RA	interleukin 15 receptor, alpha chain	protein-coding
mm_30813.1	chr4	21727729	21727790	+	1	NA	promoter-TSS (NM_016746)	promoter-TSS (NM_016746)	58	NM_001290420	51813	Mm.278584	NM_016746	ENSMUSG00000028252	Ccnc	AI451004|AU020987|CG1C	cyclin C	protein-coding
mm_171948.1	chr5	76233092	76233108	-	1	NA	intron (NM_001305222, intron 17 of 21)	intron (NM_001305222, intron 17 of 21)	49220	NM_011626	21982	Mm.790	NM_011626	ENSMUSG00000029234	Tmem165	AV026557|Tpardl|Tparl|pFT27	transmembrane protein 165	protein-coding
mm_70872.1	chr8	25068489	25068496	+	1	NA	intron (NM_031257, intron 3 of 11)	intron (NM_031257, intron 3 of 11)	-29530	NM_001081187	330723	Mm.334452	NM_001081187	ENSMUSG00000037406	Htra4	B430206E18Rik	HtrA serine peptidase 4	protein-coding
mm_8733.1	chr1	160153572	160153585	-	1	NA	promoter-TSS (NM_177839)	promoter-TSS (NM_177839)	-3	NM_177839	329278	Mm.90140	NM_177839	ENSMUSG00000026725	Tnn	Tnw|tenascin-W	tenascin N	protein-coding
mm_157597.1	chrX	53266298	53266327	-	1	NA	intron (NM_001166583, intron 1 of 8)	intron (NM_001166583, intron 1 of 8)	3493	NM_030167	78755	Mm.28559	NM_030167	ENSMUSG00000036022	Fam122b	4632404H22Rik|AI256344|SPACIA2	family with sequence similarity 122, member B	protein-coding
mm_149598.1	chr19	16318053	16318078	+	1	NA	intron (NM_008139, intron 3 of 6)	intron (NM_008139, intron 3 of 6)	-3061	NR_105832	102465218		NR_105832	ENSMUSG00000098718	Mir496b	Gm28028|mmu-mir-496b	microRNA 496b	ncRNA
mm_9224.1	chr1	171234699	171234729	-	1	NA	promoter-TSS (NM_010185)	promoter-TSS (NM_010185)	-365	NM_010185	14127	Mm.22673	NM_010185	ENSMUSG00000058715	Fcer1g	AI573376|CD23|FcR-gamma|FcR[g]|FcRgamma|Fce1g|FcepsilonRI|Ly-50	Fc receptor, IgE, high affinity I, gamma polypeptide	protein-coding
mm_171181.1	chr3	36571695	36571709	-	1	NA	exon (NM_009828, exon 1 of 8)	exon (NM_009828, exon 1 of 8)	294	NM_009828	12428	Mm.4189	NM_009828	ENSMUSG00000027715	Ccna2	AA408589|Ccn-1|Ccn1|Ccna|CycA2|Cyca	cyclin A2	protein-coding
mm_83074.1	chr9	37657275	37657285	-	1	NA	promoter-TSS (NM_025289)	promoter-TSS (NM_025289)	32	NM_025289	21376	Mm.28689	NM_025289	ENSMUSG00000011114	Tbrg1	AA408552|AA409675|Niam|Tb-5|mFLJ00213	transforming growth factor beta regulated gene 1	protein-coding
mm_116114.1	chr13	28950239	28950249	-	1	NA	TTS (NM_009238)	TTS (NM_009238)	3438	NM_009238	20677	Mm.240627	NM_009238	ENSMUSG00000076431	Sox4	AA682046|Sox-4	SRY (sex determining region Y)-box 4	protein-coding
mm_42400.1	chr5	114968760	114968773	+	1	NA	intron (NM_009327, intron 1 of 9)	intron (NM_009327, intron 1 of 9)	2296	NM_009327	21405	Mm.332607	NM_009327	ENSMUSG00000029556	Hnf1a	AI323641|HNF1|HNF1-alpha|HNF1[a]|Hnf-1|Hnf1alpha|LFB1|Tcf-1|Tcf1	HNF1 homeobox A	protein-coding
mm_109506.1	chr12	111452247	111452262	+	1	NA	intron (NM_009396, intron 11 of 11)	intron (NM_009396, intron 11 of 11)	9593	NM_009396	21928	Mm.255332	NM_009396	ENSMUSG00000021281	Tnfaip2	B94|Exoc3l3|M-sec|Tnfip2|tnfb94	tumor necrosis factor, alpha-induced protein 2	protein-coding
mm_107800.1	chr12	64917992	64918001	+	1	NA	promoter-TSS (NM_001025605)	promoter-TSS (NM_001025605)	85	NM_001025605	217648	Mm.341586	NM_001025605	ENSMUSG00000047227	Gm527	-	predicted gene 527	protein-coding
mm_13025.1	chr2	91042924	91042973	+	1	NA	intron (NM_009023, intron 3 of 7)	intron (NM_009023, intron 3 of 7)	7321	NM_009023	19400	Mm.1272	NM_009023	ENSMUSG00000002104	Rapsn	43kDa|Nraps|Raps|rapsyn	receptor-associated protein of the synapse	protein-coding
mm_42023.1	chr5	108269664	108269677	+	1	NA	exon (NM_026106, exon 1 of 3)	exon (NM_026106, exon 1 of 3)	773	NM_026106	13486	Mm.303534	NM_026106	ENSMUSG00000029265	Dr1	1700121L09Rik|Dr1l|NC2|NC2beta	down-regulator of transcription 1	protein-coding
mm_95762.1	chr11	54907119	54907130	+	1	NA	intron (NM_001329860, intron 1 of 5)	intron (NM_001329860, intron 1 of 5)	4270	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_17704.1	chr2	32384697	32384711	-	1	NA	TTS (NM_008491)	TTS (NM_008491)	-2789	NM_198001	73737	Mm.27608	NM_198001	ENSMUSG00000039195	1110008P14Rik	C79326	RIKEN cDNA 1110008P14 gene	protein-coding
mm_28200.1	chr3	88276902	88276921	-	1	NA	Intergenic	Intergenic	19927	NM_029801	76927	Mm.273330	NM_029801	ENSMUSG00000010538	Tsacc	1700021C14Rik|SIP	TSSK6 activating co-chaperone	protein-coding
mm_37101.1	chr4	116627487	116627503	-	1	NA	promoter-TSS (NM_001284229)	promoter-TSS (NM_001284229)	2	NM_001081475	50927	Mm.257181	NM_016777	ENSMUSG00000028693	Nasp	5033430J04Rik|AI131596|AI317140|D4Ertd767e|Epcs32|Nasp-T	nuclear autoantigenic sperm protein (histone-binding)	protein-coding
mm_76274.1	chr8	84147768	84147786	-	1	NA	promoter-TSS (NM_029045)	promoter-TSS (NM_029045)	-24	NM_145970	212139	Mm.41424	NM_145970	ENSMUSG00000036686	Cc2d1a	BC016188|Freud-1|Tape	coiled-coil and C2 domain containing 1A	protein-coding
mm_157393.1	chrX	38406733	38406767	-	1	NA	intron (NM_001017959, intron 8 of 8)	L1M3|LINE|L1	49710	NM_010685	16784	Mm.486	NM_010685	ENSMUSG00000016534	Lamp2	CD107b|LGP-B|Lamp II|Lamp-2|Lamp-2a|Lamp-2b|Lamp-2c|Mac3	lysosomal-associated membrane protein 2	protein-coding
mm_163586.1	chr13	37895422	37895425	+	1	NA	intron (NR_033615, intron 4 of 9)	intron (NR_033615, intron 4 of 9)	6552	NM_001177869	68750	Mm.491109	NM_026830	ENSMUSG00000039087	Rreb1	1110037N09Rik|AA414966|B930013M22Rik	ras responsive element binding protein 1	protein-coding
mm_47087.1	chr5	117287590	117287623	-	1	NA	promoter-TSS (NM_018858)	promoter-TSS (NM_018858)	-42	NM_018858	23980	Mm.195898	NM_018858	ENSMUSG00000032959	Pebp1	HCNP|Pbp|Pbp1|Pbpr|Rkip	phosphatidylethanolamine binding protein 1	protein-coding
mm_163801.1	chr14	19415708	19415711	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	186878	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_25504.1	chr3	109556940	109556945	+	1	NA	intron (NM_020505, intron 15 of 26)	intron (NM_020505, intron 15 of 26)	-17065	NM_146139	57257	Mm.282257	NM_020505	ENSMUSG00000033721	Vav3	A530094I06Rik|AA986410|Idd18.1	vav 3 oncogene	protein-coding
mm_151359.1	chr19	55910585	55910595	+	1	NA	exon (NM_001142918, exon 6 of 15)	exon (NM_001142918, exon 6 of 15)	15269	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_112161.1	chr12	113330428	113330440	-	1	NA	Intergenic	Intergenic	144531	NM_153776	69195	Mm.313244	NM_153776	ENSMUSG00000049036	Tmem121	2410008J05Rik|Hole	transmembrane protein 121	protein-coding
mm_110409.1	chr12	45086079	45086083	-	1	NA	Intergenic	ORR1A1|LTR|ERVL-MaLR	-11598	NM_144552	217517	Mm.285400	NM_144552	ENSMUSG00000046314	Stxbp6	BC024598|C85317	syntaxin binding protein 6 (amisyn)	protein-coding
mm_89332.1	chr10	87933236	87933296	+	1	NA	3' UTR (NM_010512, exon 5 of 5)	3' UTR (NM_010512, exon 5 of 5)	-33405	NR_000040	22172	Mm.391420	NR_000040		Tyms-ps	-	thymidylate synthase, pseudogene	pseudo
mm_143583.1	chr17	74323897	74323954	-	1	NA	promoter-TSS (NM_024428)	promoter-TSS (NM_024428)	19	NM_024428	66310	Mm.28536	NM_024428	ENSMUSG00000024067	Dpy30	2810410M20Rik|C87842	dpy-30, histone methyltransferase complex regulatory subunit	protein-coding
mm_11071.1	chr2	27677095	27677105	+	1	NA	promoter-TSS (NM_011305)	promoter-TSS (NM_011305)	-101	NM_011305	20181	Mm.24624	NM_011305	ENSMUSG00000015846	Rxra	9530071D11Rik|Nr2b1|RXRalpha1	retinoid X receptor alpha	protein-coding
mm_80811.1	chr9	96478780	96478806	+	1	NA	promoter-TSS (NM_011279)	promoter-TSS (NM_011279)	-118	NM_001311135	19823	Mm.28235	NM_011279	ENSMUSG00000051234	Rnf7	Rbx2|SAG	ring finger protein 7	protein-coding
mm_62380.1	chr7	100786853	100786856	+	1	NA	exon (NM_178764, exon 3 of 9)	exon (NM_178764, exon 3 of 9)	76559	NM_177073	320100	Mm.40336	NM_177073	ENSMUSG00000008318	Relt	E430021K24Rik|Tnfrsf19l	RELT tumor necrosis factor receptor	protein-coding
mm_131456.1	chr16	16870995	16870997	+	1	NA	5' UTR (NM_011624, exon 1 of 18)	5' UTR (NM_011624, exon 1 of 18)	260	NM_011624	21976	Mm.326089	NM_011624	ENSMUSG00000022779	Top3b	-	topoisomerase (DNA) III beta	protein-coding
mm_60853.1	chr7	45833323	45833333	+	1	NA	exon (NM_008172, exon 12 of 12)	exon (NM_008172, exon 12 of 12)	-2539	NM_153419	101612	Mm.274847	NM_153419	ENSMUSG00000053801	Grwd1	A301|AI504353|Grwd|Wdr28	glutamate-rich WD repeat containing 1	protein-coding
mm_53836.1	chr6	148212273	148212315	+	1	NA	promoter-TSS (NM_026168)	promoter-TSS (NM_026168)	6	NR_015615	320737	Mm.137858	NR_015615		4732416N19Rik	-	RIKEN cDNA 4732416N19 gene	ncRNA
mm_141361.1	chr17	28801604	28801621	-	1	NA	intron (NM_001081315, intron 1 of 12)	CpG	486	NM_001081315	268936	Mm.291877	NM_199061	ENSMUSG00000063952	Brpf3	AI413466|AW493400|mKIAA1286	bromodomain and PHD finger containing, 3	protein-coding
mm_43579.1	chr5	137746548	137746617	+	1	NA	intron (NM_029805, intron 1 of 5)	intron (NM_029805, intron 1 of 5)	613	NM_029805	78829	Mm.286399	NM_023910	ENSMUSG00000029723	Tsc22d4	0610009M14Rik|1700023B23Rik|AI415410|Thg-1pit|Tilz2	TSC22 domain family, member 4	protein-coding
mm_162305.1	chr1	36698496	36698496	+	1	NA	TTS (NM_146107)	TTS (NM_146107)	7009	NM_009942	12859	Mm.180182	NM_009942	ENSMUSG00000061518	Cox5b	-	cytochrome c oxidase subunit Vb	protein-coding
mm_23828.1	chr3	81037213	81037225	+	1	NA	5' UTR (NM_019971, exon 1 of 6)	5' UTR (NM_019971, exon 1 of 6)	803	NM_019971	54635	Mm.331089	NM_019971	ENSMUSG00000028019	Pdgfc	1110064L01Rik|AI647969|PDGF-C	platelet-derived growth factor, C polypeptide	protein-coding
mm_135686.1	chr16	52424918	52424940	-	1	NA	intron (NM_009655, intron 1 of 15)	intron (NM_009655, intron 1 of 15)	28152	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_115821.1	chr13	20091198	20091208	-	1	NA	intron (NM_080288, intron 1 of 21)	CpG	696	NM_080288	140580	Mm.342392	NM_080288	ENSMUSG00000041112	Elmo1	6330578D22Rik|C230095H21Rik|CED-12	engulfment and cell motility 1	protein-coding
mm_163748.1	chr13	119755945	119755958	-	1	NA	promoter-TSS (NM_175538)	promoter-TSS (NM_175538)	-69	NM_175538	245269	Mm.403943	NM_175538	ENSMUSG00000095930	Nim1k	E130304F04Rik|Nim1	NIM1 serine/threonine protein kinase	protein-coding
mm_65260.1	chr7	19904706	19904716	-	1	NA	3' UTR (NM_027514, exon 8 of 8)	3' UTR (NM_027514, exon 8 of 8)	16432	NM_027514	52118	Mm.227506	NM_027514	ENSMUSG00000040511	Pvr	3830421F03Rik|CD155|D7Ertd458e|HVED|PVS|Taa1|Tage4|mE4|necl-5	poliovirus receptor	protein-coding
mm_75657.1	chr8	65129614	65129620	-	1	NA	promoter-TSS (NR_033217)	promoter-TSS (NR_033217)	-80	NR_033217	407795	Mm.387876	NR_033217	ENSMUSG00000074300	BC030870	-	cDNA sequence BC030870	ncRNA
mm_117021.1	chr13	58182223	58182246	-	1	NA	intron (NM_026842, intron 7 of 10)	intron (NM_026842, intron 7 of 10)	24585	NM_198004	75731	Mm.293919	NM_198004	ENSMUSG00000050002	Idnk	5133401N09Rik	idnK gluconokinase homolog (E. coli)	protein-coding
mm_13095.1	chr2	91256829	91256877	+	1	NA	promoter-TSS (NM_028733)	promoter-TSS (NM_028733)	40	NM_001289678	80708	Mm.236650	NM_028733	ENSMUSG00000027257	Pacsin3	4921507A02Rik|6330413E15Rik|AW413130	protein kinase C and casein kinase substrate in neurons 3	protein-coding
mm_70998.1	chr8	29719550	29719554	+	1	NA	Intergenic	Intergenic	-499916	NM_001347498	210801	Mm.248433	NM_153135	ENSMUSG00000063626	Unc5d	D930029E11Rik|Unc5h4|mKIAA1777	unc-5 netrin receptor D	protein-coding
mm_17985.1	chr2	37811004	37811007	-	1	NA	intron (NM_146122, intron 20 of 21)	intron (NM_146122, intron 20 of 21)	34756	NM_001163566	241324	Mm.392369	NM_001163566	ENSMUSG00000035403	Crb2	5930402A21|BC043114	crumbs family member 2	protein-coding
mm_148264.1	chr18	80968852	80968855	-	1	NA	3' UTR (NM_178280, exon 4 of 4)	3' UTR (NM_178280, exon 4 of 4)	17725	NM_178280	20689	Mm.215917	NM_178280	ENSMUSG00000024565	Sall3	B130022O04Rik|Msal|Msal-1|Sal|Salt|Spalt	sal-like 3 (Drosophila)	protein-coding
mm_113370.1	chr13	33003159	33003178	+	1	NA	Intergenic	Intergenic	-1373	NM_009256	20723	Mm.245041	NM_009256	ENSMUSG00000045827	Serpinb9	BB283241|CAP-3|CAP3|PI-9|PI9|Spi6|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 9	protein-coding
mm_165816.1	chr3	146221021	146221038	+	1	NA	promoter-TSS (NM_022983)	promoter-TSS (NM_022983)	68	NM_022983	65086	Mm.155520	NM_022983	ENSMUSG00000036832	Lpar3	Edg7|lpA3	lysophosphatidic acid receptor 3	protein-coding
mm_51645.1	chr6	86028693	86028709	+	1	NA	promoter-TSS (NM_001271860)	promoter-TSS (NM_001271860)	20	NM_001271860	11519	Mm.104155	NM_013458	ENSMUSG00000030000	Add2	2900072M03Rik|add97	adducin 2 (beta)	protein-coding
mm_32385.1	chr4	106578260	106578273	+	1	NA	exon (NM_053272, exon 6 of 9)	exon (NM_053272, exon 6 of 9)	17228	NM_053272	74754	Mm.133370	NM_053272	ENSMUSG00000034926	Dhcr24	2310076D10Rik|5830417J06Rik|mKIAA0018	24-dehydrocholesterol reductase	protein-coding
mm_10157.1	chr2	4399246	4399249	+	1	NA	intron (NM_172475, intron 1 of 22)	B4|SINE|B4	-1729	NM_001177843	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding
mm_65830.1	chr7	29179378	29179401	-	1	NA	intron (NM_026545, intron 1 of 6)	intron (NM_026545, intron 1 of 6)	1284	NM_026545	57296	Mm.273152	NM_026545	ENSMUSG00000030591	Psmd8	6720456J22Rik|AA407360|AL033291|AL033322|AL033323|C76433	proteasome (prosome, macropain) 26S subunit, non-ATPase, 8	protein-coding
mm_144013.1	chr17	88599013	88599057	-	1	NA	Intergenic	Intergenic	-27520	NM_029858	77057	Mm.482203	NM_029858	ENSMUSG00000033855	Ston1	4921524J06Rik|C86231|Salf|Sblf	stonin 1	protein-coding
mm_70913.1	chr8	25720055	25720099	+	1	NA	promoter-TSS (NM_001293703)	promoter-TSS (NM_001293703)	29	NR_121643	71910	Mm.385055	NM_028000	ENSMUSG00000031570	Plpp5	1810019D05Rik|2310022A04Rik|AW045471|Ppapdc1|Ppapdc1b	phospholipid phosphatase 5	protein-coding
mm_88046.1	chr10	67539251	67539263	+	1	NA	intron (NM_001347458, intron 2 of 2)	intron (NM_001347458, intron 2 of 2)	1327	NM_001347458	13654	Mm.290421	NM_010118	ENSMUSG00000037868	Egr2	Egr-2|Krox-20|Krox20|NGF1-B|Zfp-25|Zfp-6	early growth response 2	protein-coding
mm_135018.1	chr16	32487668	32487722	-	1	NA	5' UTR (NM_145932, exon 1 of 9)	5' UTR (NM_145932, exon 1 of 9)	184	NM_145932	106407	Mm.476915	NM_145932	ENSMUSG00000035699	Slc51a	AV001382|AW261577|D630035O19Rik|OSTalpha|Osta	solute carrier family 51, alpha subunit	protein-coding
mm_45770.1	chr5	86926522	86926537	-	1	NA	promoter-TSS (NM_152811)	promoter-TSS (NM_152811)	-26	NM_152811	71773	Mm.26741	NM_152811	ENSMUSG00000035836	Ugt2b1	1300012D20Rik	UDP glucuronosyltransferase 2 family, polypeptide B1	protein-coding
mm_23292.1	chr3	52103347	52103373	+	1	NA	intron (NM_001004176, intron 1 of 4)	CpG	1646	NM_001004176	433586	Mm.234972	NM_001004176	ENSMUSG00000061143	Maml3	AV234550|BC049812|Mam-2|mKIAA1816	mastermind like 3 (Drosophila)	protein-coding
mm_21928.1	chr2	166996260	166996283	-	1	NA	promoter-TSS (NM_011490)	promoter-TSS (NM_011490)	28	NM_011490	20853	Mm.73276	NM_011490	ENSMUSG00000039536	Stau1	5830401L18Rik|AW549911|C85792|Stau	staufen (RNA binding protein) homolog 1 (Drosophila)	protein-coding
mm_73352.1	chr8	105438803	105438807	+	1	NA	intron (NM_001033371, intron 2 of 10)	intron (NM_001033371, intron 2 of 10)	11165	NM_001170789	270091	Mm.212709	NM_001033371	ENSMUSG00000054320	Lrrc36	BC036564	leucine rich repeat containing 36	protein-coding
mm_139091.1	chr17	46833738	46833757	+	1	NA	Intergenic	B4|SINE|B4	-2334	NM_001100452	210982	Mm.37642	NM_001100452	ENSMUSG00000036568	Gltscr1l	mKIAA0240	GLTSCR1-like	protein-coding
mm_169380.1	chr14	39763669	39763685	-	1	NA	Intergenic	L1Md_A|LINE|L1	108014	NR_045936	73591	Mm.65499	NR_045936	ENSMUSG00000101261	1700109I08Rik	-	RIKEN cDNA 1700109I08 gene	ncRNA
mm_132952.1	chr16	49913579	49913594	+	1	NA	Intergenic	Intergenic	57932	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_90090.1	chr10	116914359	116914398	+	1	NA	intron (NM_001003950, intron 6 of 9)	intron (NM_001003950, intron 6 of 9)	-17499	NM_001033333	237558	Mm.336386	NM_001033333	ENSMUSG00000034057	Myrfl	Gm239	myelin regulatory factor-like	protein-coding
mm_75527.1	chr8	57310268	57310277	-	1	NA	intron (NR_110474, intron 2 of 4)	intron (NR_110474, intron 2 of 4)	10587	NR_110474	102636514		NR_110474	ENSMUSG00000100510	Uph	-	upperhand	ncRNA
mm_14135.1	chr2	126035782	126035798	+	1	NA	exon (NM_008008, exon 2 of 4)	exon (NM_008008, exon 2 of 4)	1132	NM_008008	14178	Mm.330557	NM_008008	ENSMUSG00000027208	Fgf7	Kgf	fibroblast growth factor 7	protein-coding
mm_123416.1	chr14	64174677	64174690	-	1	NA	intron (NM_001347639, intron 5 of 5)	intron (NM_001347639, intron 5 of 5)	70360	NM_028525	73382	Mm.481055	NM_028525	ENSMUSG00000021966	Prss52	1700049K14Rik|Tesp3	protease, serine 52	protein-coding
mm_87652.1	chr10	58446741	58446743	+	1	NA	promoter-TSS (NM_011240)	promoter-TSS (NM_011240)	-110	NM_011240	19386	Mm.431695	NM_011240	ENSMUSG00000003226	Ranbp2	A430087B05Rik|AI256741|NUP358	RAN binding protein 2	protein-coding
mm_42803.1	chr5	121715128	121715131	+	1	NA	intron (NM_009125, intron 1 of 24)	intron (NM_009125, intron 1 of 24)	3520	NM_009125	20239	Mm.260900	NM_009125	ENSMUSG00000042605	Atxn2	9630045M23Rik|ATX2|AW544490|Sca2	ataxin 2	protein-coding
mm_90966.1	chr10	13388756	13388774	-	1	NA	5' UTR (NM_001195066, exon 1 of 13)	5' UTR (NM_001195066, exon 1 of 13)	205	NM_001195066	215789	Mm.283359	NM_001033257	ENSMUSG00000062866	Phactr2	AV158170|BC012871	phosphatase and actin regulator 2	protein-coding
mm_75314.1	chr8	41239444	41239456	-	1	NA	promoter-TSS (NM_023662)	promoter-TSS (NM_023662)	-309	NM_023662	18536	Mm.117896	NM_023662	ENSMUSG00000031592	Pcm1	2600002H09Rik|9430077F19Rik|C030044G17Rik	pericentriolar material 1	protein-coding
mm_61156.1	chr7	58697322	58697332	+	1	NA	intron (NM_009728, intron 1 of 20)	intron (NM_009728, intron 1 of 20)	39125	NM_009728	11982	Mm.135129	NM_009728	ENSMUSG00000025324	Atp10a	Atp10c|pfatp	ATPase, class V, type 10A	protein-coding
mm_58320.1	chr6	146470718	146470721	-	1	NA	intron (NM_010586, intron 2 of 55)	intron (NM_010586, intron 2 of 55)	31504	NM_010586	16439	Mm.7800	NM_010586	ENSMUSG00000030287	Itpr2	AI649341|InsP3R-2|InsP3R-5|Ip3r2|Itpr5|insP3R2	inositol 1,4,5-triphosphate receptor 2	protein-coding
mm_114706.1	chr13	83524847	83524871	+	1	NA	5' UTR (NM_001347567, exon 1 of 11)	5' UTR (NM_001347567, exon 1 of 11)	116	NM_001347580	17260	Mm.24001	NM_025282	ENSMUSG00000005583	Mef2c	5430401D19Rik|9930028G15Rik|AV011172|Mef2	myocyte enhancer factor 2C	protein-coding
mm_16215.1	chr2	173073240	173073254	+	1	NA	Intergenic	Intergenic	46278	NM_001081387	664799	Mm.389396	NM_001081387	ENSMUSG00000070495	Ctcfl	Boris|OTTMUSG00000016680	CCCTC-binding factor (zinc finger protein)-like	protein-coding
mm_132852.1	chr16	48218530	48218531	+	1	NA	Intergenic	Intergenic	-65205	NM_028610	73693	Mm.35597	NM_028610	ENSMUSG00000058550	Dppa4	2410091M23Rik|C76608|ECAT15-1	developmental pluripotency associated 4	protein-coding
mm_66438.1	chr7	44815910	44815926	-	1	NA	promoter-TSS (NM_030693)	promoter-TSS (NM_030693)	-170	NM_053074	18226	Mm.2565	NM_053074	ENSMUSG00000109511	Nup62	D7Ertd649e|Nupc1|p62	nucleoporin 62	protein-coding
mm_159261.1	chr2	155074456	155074456	-	1	NA	promoter-TSS (NM_016661)	promoter-TSS (NM_016661)	41	NM_016661	269378	Mm.330692	NM_016661	ENSMUSG00000027597	Ahcy	AA987153|AL024110|CuBP|SAHH	S-adenosylhomocysteine hydrolase	protein-coding
mm_67248.1	chr7	75309298	75309309	-	1	NA	promoter-TSS (NM_153579)	promoter-TSS (NM_153579)	-41	NM_153579	64176	Mm.273082	NM_153579	ENSMUSG00000053025	Sv2b	A830038F04Rik|AI850768|mKIAA0735	synaptic vesicle glycoprotein 2 b	protein-coding
mm_20608.1	chr2	131562516	131562535	-	1	NA	promoter-TSS (NM_013460)	promoter-TSS (NM_013460)	-240	NM_013460	11550	Mm.389380	NM_013460	ENSMUSG00000027335	Adra1d	Adra-1|Adra1|Adra1a|Gpcr8|Spr8|[a]1d|alpha1D-AR	adrenergic receptor, alpha 1d	protein-coding
mm_160631.1	chr9	107399980	107399980	+	1	NA	promoter-TSS (NM_001174049)	promoter-TSS (NM_001174049)	100	NM_020263	56808	Mm.273084	NM_020263	ENSMUSG00000010066	Cacna2d2	Cacna2d|a2d2|du|mKIAA0558|td|torpid	calcium channel, voltage-dependent, alpha 2/delta subunit 2	protein-coding
mm_130407.1	chr15	97976799	97976816	-	1	NA	exon (NM_001113515, exon 52 of 53)	exon (NM_001113515, exon 52 of 53)	12578	NM_001252153	380967	Mm.196630	NM_201359	ENSMUSG00000052369	Tmem106c	AI046681|BC046621|D15Ertd405e	transmembrane protein 106C	protein-coding
mm_120005.1	chr14	55650171	55650197	+	1	NA	promoter-TSS (NM_001253889)	promoter-TSS (NM_001253889)	0	NM_001253888	71099	Mm.171300	NM_027673	ENSMUSG00000007591	Tssk4	1700020B19Rik|4933424F08Rik|TSK-4|TSSK-4	testis-specific serine kinase 4	protein-coding
mm_125411.1	chr15	41788767	41788778	+	1	NA	promoter-TSS (NM_001130163)	promoter-TSS (NM_001130163)	-262	NM_001130165	170719	Mm.254267	NM_130885	ENSMUSG00000022307	Oxr1	2210416C20Rik|C7|C7B	oxidation resistance 1	protein-coding
mm_140967.1	chr17	24670676	24670705	-	1	NA	intron (NM_183149, intron 1 of 11)	intron (NM_183149, intron 1 of 11)	938	NM_183149	213753	Mm.219581	NM_183149	ENSMUSG00000041130	Zfp598	BC023040|Ntrap|Znf598	zinc finger protein 598	protein-coding
mm_143005.1	chr17	56425655	56425724	-	1	NA	exon (NM_011218, exon 14 of 33)	exon (NM_011218, exon 14 of 33)	-6780	NR_105943	102465590		NR_105943	ENSMUSG00000098339	Mir6977	Gm27922|mmu-mir-6977	microRNA 6977	ncRNA
mm_25137.1	chr3	102491338	102491344	+	1	NA	intron (NM_001112698, intron 1 of 2)	MER44D|DNA|TcMar-Tigger	21422	NM_013609	18049	Mm.1259	NM_013609	ENSMUSG00000027859	Ngf	Ngfb	nerve growth factor	protein-coding
mm_164910.1	chr18	72443266	72443267	-	1	NA	Intergenic	L1_Mur3|LINE|L1	-92197	NM_007831	13176	Mm.167882	NM_007831	ENSMUSG00000060534	Dcc	C030036D22Rik|Igdcc1	deleted in colorectal carcinoma	protein-coding
mm_146092.1	chr18	73754156	73754167	+	1	NA	intron (NM_053255, intron 1 of 3)	CpG	318	NM_053255	114615	Mm.50642	NM_053255	ENSMUSG00000036941	Elac1	2610018O07Rik|8430417G19Rik	elaC ribonuclease Z 1	protein-coding
mm_58617.1	chr7	5065207	5065211	+	1	NA	intron (NM_133671, intron 1 of 11)	intron (NM_133671, intron 1 of 11)	3066	NM_001205231	22185	Mm.360389	NM_133671	ENSMUSG00000030435	U2af2	65kDa	U2 small nuclear ribonucleoprotein auxiliary factor (U2AF) 2	protein-coding
mm_151149.1	chr19	53140537	53140593	+	1	NA	5' UTR (NM_001164099, exon 1 of 15)	5' UTR (NM_001164099, exon 1 of 15)	122	NM_001164101	27360	Mm.426080	NM_013758	ENSMUSG00000025026	Add3	AI463285|R75380	adducin 3 (gamma)	protein-coding
mm_126482.1	chr15	81586412	81586512	+	1	NA	5' UTR (NM_177821, exon 1 of 31)	5' UTR (NM_177821, exon 1 of 31)	248	NM_177821	328572	Mm.258397	NM_177821	ENSMUSG00000055024	Ep300	A430090G16|A730011L11|KAT3B|p300|p300 HAT	E1A binding protein p300	protein-coding
mm_95517.1	chr11	52098853	52098875	+	1	NA	promoter-TSS (NM_019411)	promoter-TSS (NM_019411)	40	NM_019411	19052	Mm.260288	NM_019411	ENSMUSG00000020349	Ppp2ca	PP2A|R75353	protein phosphatase 2 (formerly 2A), catalytic subunit, alpha isoform	protein-coding
mm_77516.1	chr8	122894601	122894614	-	1	NA	non-coding (NR_037865, exon 10 of 14)	non-coding (NR_037865, exon 10 of 14)	46233	NM_007662	12555	Mm.1976	NM_007662	ENSMUSG00000031962	Cdh15	AI323380|Cdh14|Mcad	cadherin 15	protein-coding
mm_136014.1	chr16	76022267	76022287	-	1	NA	Intergenic	Intergenic	-100336	NR_040575	78215	Mm.243885	NR_040575		4930578N18Rik	-	RIKEN cDNA 4930578N18 gene	ncRNA
mm_53203.1	chr6	125685690	125685699	+	1	NA	intron (NM_011708, intron 50 of 51)	intron (NM_011708, intron 50 of 51)	-4725	NM_153589	243634	Mm.333398	NM_153589	ENSMUSG00000038115	Ano2	BC033409|Tmem16b	anoctamin 2	protein-coding
mm_108849.1	chr12	98276039	98276057	+	1	NA	exon (NM_008152, exon 2 of 2)	exon (NM_008152, exon 2 of 2)	7413	NM_008152	14744	Mm.378924	NM_008152	ENSMUSG00000021886	Gpr65	Dig1|Gpcr25|TDAG8	G-protein coupled receptor 65	protein-coding
mm_24814.1	chr3	95622637	95622668	+	1	NA	Intergenic	Intergenic	-2328	NM_019561	56205	Mm.241365	NM_019561	ENSMUSG00000038619	Ensa	1700020C18Rik|2610007F17Rik|AI451924	endosulfine alpha	protein-coding
mm_139315.1	chr17	48359892	48359926	+	1	NA	promoter-TSS (NM_001289457)	promoter-TSS (NM_001289457)	-7	NM_001289457	71326	Mm.90177	NM_027763	ENSMUSG00000023993	Treml1	5430401J17Rik|TLT-1	triggering receptor expressed on myeloid cells-like 1	protein-coding
mm_13657.1	chr2	114055191	114055209	+	1	NA	non-coding (NR_028422, exon 1 of 3)	non-coding (NR_028422, exon 1 of 3)	804	NR_028422	100303644	Mm.330469	NR_028422	ENSMUSG00000092397	C130080G10Rik	-	RIKEN cDNA C130080G10 gene	ncRNA
mm_39719.1	chr5	28124563	28124573	+	1	NA	Intergenic	Intergenic	-41128	NM_010134	13799	Mm.4298	NM_010134	ENSMUSG00000039095	En2	BB131122|En-2	engrailed 2	protein-coding
mm_75898.1	chr8	71085759	71085763	-	1	NA	Intergenic	Intergenic	-54608	NM_001324526	665858	Mm.411658	NM_001324526		Gm7827	EG665858	predicted gene 7827	protein-coding
mm_96342.1	chr11	66912053	66912071	+	1	NA	promoter-TSS (NM_178656)	promoter-TSS (NM_178656)	71	NM_178656	193003	Mm.440256	NM_178656	ENSMUSG00000048070	Pirt	A530088H08Rik	phosphoinositide-interacting regulator of transient receptor potential channels	protein-coding
mm_108887.1	chr12	99979916	99979927	+	1	NA	intron (NM_146037, intron 2 of 2)	Lx7|LINE|L1	15422	NM_001164427	217826	Mm.312335	NM_146037	ENSMUSG00000045404	Kcnk13	BB085247|F730021E22Rik|Gm1570|Gm1685	potassium channel, subfamily K, member 13	protein-coding
mm_84731.1	chr9	75052259	75052288	-	1	NA	exon (NM_001142655, exon 3 of 4)	exon (NM_001142655, exon 3 of 4)	14541	NM_021548	59046	Mm.247837	NM_021548	ENSMUSG00000007656	Arpp19	19kDa|2700024H10Rik|ARPP-19|AW559096|Arpp12	cAMP-regulated phosphoprotein 19	protein-coding
mm_76263.1	chr8	84012124	84012169	-	1	NA	promoter-TSS (NM_001291292)	promoter-TSS (NM_001291292)	-426	NM_001291292	70134	Mm.41017	NM_001291292	ENSMUSG00000074217	2210011C24Rik	-	RIKEN cDNA 2210011C24 gene	protein-coding
mm_40400.1	chr5	52834185	52834214	+	1	NA	promoter-TSS (NM_024213)	promoter-TSS (NM_024213)	64	NM_024213	52206	Mm.272568	NM_024213	ENSMUSG00000029176	Anapc4	2610306D21Rik|APC4|D5Ertd249e	anaphase promoting complex subunit 4	protein-coding
mm_121086.1	chr14	99294750	99294768	+	1	NA	Intergenic	Intergenic	-3932	NM_009769	12224	Mm.30262	NM_009769	ENSMUSG00000005148	Klf5	4930520J07Rik|Bteb2|CKLF|IKLF	Kruppel-like factor 5	protein-coding
mm_156417.1	chrX	140797303	140797314	+	1	NA	Intergenic	Intergenic	16125	NM_031381	83555	Mm.193025	NM_031381	ENSMUSG00000042386	Tex13b	4933403J23Rik|Tex13	testis expressed 13B	protein-coding
mm_22398.1	chr2	181236230	181236243	-	1	NA	exon (NM_183162, exon 7 of 19)	exon (NM_183162, exon 7 of 19)	5791	NM_183162	229003	Mm.315872	NM_183162	ENSMUSG00000027580	Helz2	PDIP1|Pric285|mKIAA1769|mPDIP1	helicase with zinc finger 2, transcriptional coactivator	protein-coding
mm_126034.1	chr15	76879233	76879246	+	1	NA	promoter-TSS (NM_145916)	promoter-TSS (NM_145916)	-37	NM_145916	223669	Mm.38948	NM_145916	ENSMUSG00000033669	Zfp7	KRAB20|KRAB7|Krox-2|Zfp-7|Zfp65|Zfp80|Zfp86-rs1|mszf73-2	zinc finger protein 7	protein-coding
mm_65684.1	chr7	28350527	28350563	-	1	NA	promoter-TSS (NM_013647)	promoter-TSS (NM_013647)	-144	NM_013647	20055	Mm.702	NM_013647	ENSMUSG00000037563	Rps16	AA420385|AI317031	ribosomal protein S16	protein-coding
mm_172283.1	chr6	91428807	91428808	+	1	NA	Intergenic	Intergenic	12047	NR_045980	75787	Mm.30842	NR_045980	ENSMUSG00000097693	4930471M09Rik	4930427C17Rik	RIKEN cDNA 4930471M09 gene	ncRNA
mm_21209.1	chr2	155652802	155652805	-	1	NA	intron (NM_001163452, intron 8 of 18)	intron (NM_001163452, intron 8 of 18)	29923	NR_030757	735275		NR_030757	ENSMUSG00000076312	Mir499	Mirn499|mir-499|mmu-mir-499	microRNA 499	ncRNA
mm_100631.1	chr11	121708681	121708682	+	1	NA	intron (NM_144797, intron 2 of 3)	intron (NM_144797, intron 2 of 3)	6254	NM_144797	210029	Mm.153566	NM_144797	ENSMUSG00000039208	Metrnl	9430048M07Rik|BC019776	meteorin, glial cell differentiation regulator-like	protein-coding
mm_160236.1	chr7	103840476	103840476	-	1	NA	promoter-TSS (NM_001127686)	promoter-TSS (NM_001127686)	45	NM_001127686	436003	Mm.475617	NM_001127686	ENSMUSG00000078621	Hbb-bh2	EG436003|Gm5736	hemoglobin beta, bh2	protein-coding
mm_32006.1	chr4	94627251	94627260	+	1	NA	exon (NM_001290568, exon 6 of 14)	exon (NM_001290568, exon 6 of 14)	12764	NM_026319	67694	Mm.240619	NM_026319	ENSMUSG00000028576	Ift74	1700029H06Rik|Ccdc2|Cmg1|b2b796Clo	intraflagellar transport 74	protein-coding
mm_46182.1	chr5	97392315	97392328	-	1	NA	promoter-TSS (NM_001033191)	promoter-TSS (NM_001033191)	9	NM_001033191	97243	Mm.11746	NM_001033191	ENSMUSG00000046000	Naa11	Ard1b|Ard2|C80008	N(alpha)-acetyltransferase 11, NatA catalytic subunit	protein-coding
mm_22607.1	chr3	14506659	14506661	+	1	NA	TTS (NM_080852)	TTS (NM_080852)	25961	NM_080852	140918	Mm.215250	NM_080852	ENSMUSG00000039710	Slc7a12	Asc-2|XAT1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 12	protein-coding
mm_121697.1	chr14	14101441	14101459	-	1	NA	intron (NM_139227, intron 11 of 11)	intron (NM_139227, intron 11 of 11)	19454	NM_025550	66413	Mm.27591	NM_025550	ENSMUSG00000021737	Psmd6	2400006A19Rik	proteasome (prosome, macropain) 26S subunit, non-ATPase, 6	protein-coding
mm_169400.1	chr14	48079805	48079816	-	1	NA	Intergenic	Intergenic	-41059	NM_033602	93834	Mm.296457	NM_033602	ENSMUSG00000021846	Peli2	AW047589|BB129927	pellino 2	protein-coding
mm_7668.1	chr1	128588605	128588632	-	1	NA	3' UTR (NM_009911, exon 2 of 2)	3' UTR (NM_009911, exon 2 of 2)	3681	NM_009911	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding
mm_139132.1	chr17	47505212	47505228	+	1	NA	5' UTR (NM_001081636, exon 1 of 7)	5' UTR (NM_001081636, exon 1 of 7)	169	NM_001081635	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_51392.1	chr6	78370878	78370892	+	1	NA	promoter-TSS (NM_011036)	promoter-TSS (NM_011036)	0	NM_011036	18489	Mm.2553	NM_011036	ENSMUSG00000071356	Reg3b	HIP|PAP1|Pap|REG-III	regenerating islet-derived 3 beta	protein-coding
mm_39083.1	chr4	154636120	154636135	-	1	NA	non-coding (NR_045643, exon 1 of 1)	non-coding (NR_045643, exon 1 of 1)	240	NR_045643	320939	Mm.436738	NR_045643		5930403L14Rik	-	RIKEN cDNA 5930403L14 gene	ncRNA
mm_82495.1	chr9	18674789	18674799	-	1	NA	Intergenic	Intergenic	80839	NM_146606	18322	Mm.246530	NM_146606	ENSMUSG00000054141	Olfr24	MOR132-1|MTPCR51	olfactory receptor 24	protein-coding
mm_126066.1	chr15	77084368	77084411	+	1	NA	promoter-TSS (NR_108037)	promoter-TSS (NR_108037)	-9	NR_108037	74303	Mm.444304	NR_108037	ENSMUSG00000097267	1700109K24Rik	4933425G21Rik	RIKEN cDNA 1700109K24 gene	ncRNA
mm_93831.1	chr10	121585923	121585970	-	1	NA	intron (NM_019786, intron 1 of 20)	intron (NM_019786, intron 1 of 20)	848	NM_019786	56480	Mm.34580	NM_019786	ENSMUSG00000020115	Tbk1	1200008B05Rik|AI462036|AW048562	TANK-binding kinase 1	protein-coding
mm_152549.1	chr19	11387742	11387752	-	1	NA	intron (NM_001310331, intron 4 of 6)	RMER19B2|LTR|ERVK	12259	NM_001310331	666907		NM_001310331	ENSMUSG00000101389	Ms4a4a	EG666907	membrane-spanning 4-domains, subfamily A, member 4A	protein-coding
mm_50901.1	chr6	57581309	57581316	+	1	NA	intron (NM_025992, intron 1 of 22)	intron (NM_025992, intron 1 of 22)	320	NM_025992	67138	Mm.297393	NM_025992	ENSMUSG00000029798	Herc6	1700121D12Rik|2510038N07Rik|4930427L17Rik|AI451296|CEB1|Herc5	hect domain and RLD 6	protein-coding
mm_153915.1	chr19	47266122	47266130	-	1	NA	3' UTR (NM_008018, exon 15 of 15)	3' UTR (NM_008018, exon 15 of 15)	7463	NR_105961	102466782		NR_105961	ENSMUSG00000098786	Mir6995	Gm27576|mmu-mir-6995	microRNA 6995	ncRNA
mm_95568.1	chr11	52396415	52396449	+	1	NA	promoter-TSS (NM_153117)	promoter-TSS (NM_153117)	4	NM_153117	213673	Mm.291979	NM_153117	ENSMUSG00000036275	9530068E07Rik	C85061|Kct2	RIKEN cDNA 9530068E07 gene	protein-coding
mm_11488.1	chr2	32450445	32450462	+	1	NA	promoter-TSS (NM_194335)	promoter-TSS (NM_194335)	-4	NM_194335	71254	Mm.102341	NM_194335	ENSMUSG00000039164	Naif1	2310007O20Rik|4933440H19Rik	nuclear apoptosis inducing factor 1	protein-coding
mm_37540.1	chr4	125122461	125122469	-	1	NA	intron (NM_153159, intron 2 of 5)	intron (NM_153159, intron 2 of 5)	5416	NM_153159	230738	Mm.402	NM_153159	ENSMUSG00000042677	Zc3h12a	BC036563|MCPIP|MCPIP-1|Mcpip1|Reg1	zinc finger CCCH type containing 12A	protein-coding
mm_6561.1	chr1	75141730	75141743	-	1	NA	intron (NM_026977, intron 1 of 8)	CpG	632	NM_026977	69171	Mm.28193	NM_026977	ENSMUSG00000033159	Cnppd1	1810031K17Rik|AU043960	cyclin Pas1/PHO80 domain containing 1	protein-coding
mm_154405.1	chrM	14547	14557	+	1	NA	NA	Intergenic	NA	NA								
mm_54028.1	chr6	11907420	11907484	-	1	NA	promoter-TSS (NM_010886)	promoter-TSS (NM_010886)	-6	NM_010886	17992	Mm.415865	NM_010886	ENSMUSG00000029632	Ndufa4	MLRQ	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 4	protein-coding
mm_66046.1	chr7	30671596	30671618	-	1	NA	promoter-TSS (NR_027849)	promoter-TSS (NR_027849)	-2	NR_027848	74927	Mm.87326	NM_183108	ENSMUSG00000049761	Pmis2	1700071L20Rik|4930479M11Rik	Pmis2, sperm specific protein	ncRNA
mm_4544.1	chr1	176997828	176997869	+	1	NA	intron (NM_029756, intron 16 of 17)	intron (NM_029756, intron 16 of 17)	-161715	NR_037996	15365	Mm.441435	NR_037996		Hmga2-ps1	EG666235|Gm7996|Hmgic-ps1|[y]i-c	high mobility group AT-hook 2, pseudogene 1	pseudo
mm_132152.1	chr16	32114672	32114674	+	1	NA	Intergenic	Intergenic	14871	NM_025892	66994	Mm.22990	NM_025892	ENSMUSG00000035790	Cep19	1500031L02Rik|AI428934|AL022620	centrosomal protein 19	protein-coding
mm_161123.1	chr12	110561415	110561415	+	1	NA	exon (NM_001081458, exon 9 of 12)	exon (NM_001081458, exon 9 of 12)	-29959	NR_033340	319786	Mm.129691	NR_033340		B930059L03Rik	-	RIKEN cDNA B930059L03 gene	ncRNA
mm_163802.1	chr14	19415766	19415794	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	186807	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_41302.1	chr5	90466168	90466171	+	1	NA	intron (NM_009654, intron 6 of 14)	intron (NM_009654, intron 6 of 14)	5299	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_133801.1	chr16	95297964	95297985	+	1	NA	non-coding (NR_073406, exon 6 of 6)	non-coding (NR_073406, exon 6 of 6)	40416	NM_001271690	16516	Mm.272239	NM_019664	ENSMUSG00000062609	Kcnj15	4930414N08Rik|AI182284|AI267127|IRKK|Kir4.2	potassium inwardly-rectifying channel, subfamily J, member 15	protein-coding
mm_20277.1	chr2	126876210	126876267	-	1	NA	promoter-TSS (NM_001164325)	promoter-TSS (NM_001164325)	23	NM_001164325	58800	Mm.244705	NM_021450	ENSMUSG00000027365	Trpm7	2310022G15Rik|4833414K03Rik|5033407O22Rik|CHAK|CHAK1|LTrpC-7|Ltpr7|Ltrpc7|TRPPLIK	transient receptor potential cation channel, subfamily M, member 7	protein-coding
mm_110992.1	chr12	77238640	77238663	-	1	NA	promoter-TSS (NR_045554)	promoter-TSS (NR_045554)	-88	NR_045554	53618	Mm.35628	NM_016893	ENSMUSG00000021065	Fut8	-	fucosyltransferase 8	protein-coding
mm_3742.1	chr1	155447468	155447483	+	1	NA	Intergenic	Intergenic	-30031	NM_011273	19775	Mm.266215	NM_011273	ENSMUSG00000026469	Xpr1	Rmc-1|Rmc1|Sxv|Syg1|XR	xenotropic and polytropic retrovirus receptor 1	protein-coding
mm_143316.1	chr17	66187294	66187311	-	1	NA	Intergenic	B1_Mm|SINE|Alu	63782	NM_001003919	320209	Mm.259605	NM_001003919	ENSMUSG00000035842	Ddx11	4732462I11Rik|CHL1|CHLR1|KRG2|essa15a	DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11	protein-coding
mm_52436.1	chr6	113604750	113604768	+	1	NA	promoter-TSS (NM_133937)	promoter-TSS (NM_133937)	-13	NM_133937	101314	Mm.485793	NM_133937	ENSMUSG00000033940	Brk1	6720456B07Rik|AW011779	BRICK1, SCAR/WAVE actin-nucleating complex subunit	protein-coding
mm_106993.1	chr12	11266102	11266178	+	1	NA	promoter-TSS (NM_177331)	promoter-TSS (NM_177331)	254	NM_025695	67241	Mm.173953	NM_025695	ENSMUSG00000020608	Smc6	2810489L22Rik|3830418C19Rik|AA990493|AU018782|AW742439|SMC-6|Smc6l1|mKIAA4103	structural maintenance of chromosomes 6	protein-coding
mm_21767.1	chr2	164844628	164844663	-	1	NA	exon (NM_011125, exon 11 of 16)	exon (NM_011125, exon 11 of 16)	10872	NM_008906	19025	Mm.359633	NM_008906	ENSMUSG00000017760	Ctsa	AU019505|PPCA|Ppgb	cathepsin A	protein-coding
mm_112796.1	chr13	20429060	20429071	+	1	NA	intron (NM_080288, intron 15 of 21)	intron (NM_080288, intron 15 of 21)	-43925	NM_198093	140580	Mm.342392	NM_080288	ENSMUSG00000041112	Elmo1	6330578D22Rik|C230095H21Rik|CED-12	engulfment and cell motility 1	protein-coding
mm_159540.1	chr4	88683845	88683845	-	1	NA	promoter-TSS (NM_010503)	promoter-TSS (NM_010503)	-66	NM_010503	15965	Mm.14091	NM_010503	ENSMUSG00000078354	Ifna2	Ifa2	interferon alpha 2	protein-coding
mm_88736.1	chr10	80261458	80261502	+	1	NA	promoter-TSS (NM_001347119)	promoter-TSS (NM_001347119)	-468	NM_010255	14431	Mm.7329	NM_010255	ENSMUSG00000020150	Gamt	AA571402|Spintz1	guanidinoacetate methyltransferase	protein-coding
mm_101326.1	chr11	22961084	22961087	-	1	NA	intron (NM_144514, intron 1 of 2)	intron (NM_144514, intron 1 of 2)	-10920	NM_011663	22183	Mm.29542	NM_011663	ENSMUSG00000044068	Zrsr1	D11Ncvs75|Irlgs2|SP2|U2af1-rs1|U2afbp-rs	zinc finger (CCCH type), RNA binding motif and serine/arginine rich 1	protein-coding
mm_46262.1	chr5	99728857	99728882	-	1	NA	non-coding (NR_030692, exon 1 of 4)	non-coding (NR_030692, exon 1 of 4)	191	NR_030692	319818	Mm.295233	NR_030692	ENSMUSG00000089809	A930011G23Rik	-	RIKEN cDNA A930011G23 gene	ncRNA
mm_69062.1	chr7	126897514	126897525	-	1	NA	intron (NM_026827, intron 1 of 5)	intron (NM_026827, intron 1 of 5)	759	NM_026827	68742	Mm.248646	NM_026827	ENSMUSG00000060538	Tmem219	1110032O16Rik|2900045G02Rik|IGFBP-3R	transmembrane protein 219	protein-coding
mm_88247.1	chr10	72671354	72671369	+	1	NA	intron (NM_001293683, intron 7 of 7)	intron (NM_001293683, intron 7 of 7)	16515	NM_001293683	52696	Mm.62876	NM_025635	ENSMUSG00000019923	Zwint	2010007E07Rik|2600001N01Rik|D10Ertd749e|Zwint-1	ZW10 interactor	protein-coding
mm_83240.1	chr9	42399741	42399747	-	1	NA	5' UTR (NM_001324548, exon 1 of 24)	5' UTR (NM_001324548, exon 1 of 24)	185	NM_009347	21683	Mm.42209	NM_009347	ENSMUSG00000037705	Tecta	Tctna	tectorin alpha	protein-coding
mm_82526.1	chr9	20645277	20645292	-	1	NA	promoter-TSS (NM_001286529)	promoter-TSS (NM_001286529)	460	NM_001310746	66177	Mm.390165	NM_025401	ENSMUSG00000084786	Ubl5	1110030M22Rik|beacon	ubiquitin-like 5	protein-coding
mm_62486.1	chr7	101896373	101896431	+	1	NA	promoter-TSS (NM_001291349)	promoter-TSS (NM_001291349)	71	NM_001291349	75430	Mm.284491	NM_027532	ENSMUSG00000030649	Anapc15	3200002M19Rik|6330414C15Rik|APC15	anaphase prompoting complex C subunit 15	protein-coding
mm_113506.1	chr13	37581209	37581218	+	1	NA	Intergenic	Intergenic	235868	NM_010745	17084	Mm.2639	NM_010745	ENSMUSG00000021423	Ly86	MD-1|MD1|ly86_tv2	lymphocyte antigen 86	protein-coding
mm_90544.1	chr10	128092168	128092193	+	1	NA	promoter-TSS (NM_054078)	promoter-TSS (NM_054078)	-603	NM_054078	116848	Mm.252213	NM_054078	ENSMUSG00000040054	Baz2a	AA415431|C030005G16Rik|C78388|Tip5|Walp3|mKIAA0314	bromodomain adjacent to zinc finger domain, 2A	protein-coding
mm_82860.1	chr9	31913233	31913244	-	1	NA	promoter-TSS (NM_013800)	promoter-TSS (NM_013800)	47	NM_013800	12023	Mm.261044	NM_013800	ENSMUSG00000032033	Barx2	2310006E12Rik|Barx2b	BarH-like homeobox 2	protein-coding
mm_150758.1	chr19	44203214	44203229	+	1	NA	promoter-TSS (NM_024450)	promoter-TSS (NM_024450)	-67	NM_024450	30049	Mm.480594	NM_024450	ENSMUSG00000025202	Scd3	4930513N16Rik	stearoyl-coenzyme A desaturase 3	protein-coding
mm_30444.1	chr3	153705803	153705819	-	1	NA	intron (NM_011372, intron 1 of 4)	intron (NM_011372, intron 1 of 4)	19322	NM_011372	20447	Mm.296453	NM_011372	ENSMUSG00000052544	St6galnac3	Siat7c	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 3	protein-coding
mm_139011.1	chr17	45570723	45570729	+	1	NA	exon (NM_008302, exon 5 of 11)	exon (NM_008302, exon 5 of 11)	2535	NM_008302	15516	Mm.2180	NM_008302	ENSMUSG00000023944	Hsp90ab1	90kDa|AL022974|C81438|Hsp84|Hsp84-1|Hsp90|Hspcb	heat shock protein 90 alpha (cytosolic), class B member 1	protein-coding
mm_119229.1	chr14	33312770	33312773	+	1	NA	intron (NM_153800, intron 4 of 10)	intron (NM_153800, intron 4 of 10)	95948	NM_153800	239027	Mm.318350	NM_153800	ENSMUSG00000063506	Arhgap22	B230341L19Rik|RHOGAP2|p68RacGAP	Rho GTPase activating protein 22	protein-coding
mm_104445.1	chr11	95012193	95012207	-	1	NA	intron (NM_146025, intron 1 of 9)	intron (NM_146025, intron 1 of 9)	2321	NM_146025	217125	Mm.297199	NM_146025	ENSMUSG00000047181	Samd14	AI839049|AI854782|BC034054	sterile alpha motif domain containing 14	protein-coding
mm_141676.1	chr17	33920344	33920372	-	1	NA	exon (NM_009318, exon 3 of 8)	exon (NM_009318, exon 3 of 8)	880	NM_009318	21356	Mm.154457	NM_009318	ENSMUSG00000024308	Tapbp	D17Wsu91e|TPN	TAP binding protein	protein-coding
mm_108387.1	chr12	80946195	80946215	+	1	NA	promoter-TSS (NR_045057)	promoter-TSS (NR_045057)	706	NM_001347415	20384	Mm.43331	NM_009159	ENSMUSG00000021134	Srsf5	Sfrs5	serine/arginine-rich splicing factor 5	protein-coding
mm_93766.1	chr10	120201414	120201426	-	1	NA	exon (NM_028679, exon 1 of 12)	exon (NM_028679, exon 1 of 12)	117	NM_028679	73914	Mm.146194	NM_028679	ENSMUSG00000020227	Irak3	4833428C18Rik|AI563835|IRAK-M	interleukin-1 receptor-associated kinase 3	protein-coding
mm_164568.1	chr17	20955634	20955637	+	1	NA	intron (NM_016891, intron 3 of 14)	intron (NM_016891, intron 3 of 14)	10181	NM_016891	51792	Mm.294138	NM_016891	ENSMUSG00000007564	Ppp2r1a	6330556D22Rik|PP2A|PR65	protein phosphatase 2, regulatory subunit A, alpha	protein-coding
mm_44711.1	chr5	30933873	30933882	-	1	NA	exon (NM_026770, exon 6 of 6)	exon (NM_026770, exon 6 of 6)	11550	NM_001160149	68567	Mm.45127	NM_026770	ENSMUSG00000029161	Cgref1	1110004G24Rik|AW045201|Cgr11	cell growth regulator with EF hand domain 1	protein-coding
mm_9517.1	chr1	173748282	173748293	-	1	NA	intron (NM_008329, intron 8 of 8)	BGLII_B|LTR|ERVK	-6478	NM_001204910	226691	Mm.440876	NM_001204910	ENSMUSG00000073490	Ifi207	AI607873|Pyhin-A	interferon activated gene 207	protein-coding
mm_102493.1	chr11	60263383	60263393	-	1	NA	intron (NM_153080, intron 4 of 14)	intron (NM_153080, intron 4 of 14)	-42761	NM_001313979	20787	Mm.278701	NM_011480	ENSMUSG00000020538	Srebf1	ADD1|SREBP-1a|SREBP1|SREBP1c|bHLHd1	sterol regulatory element binding transcription factor 1	protein-coding
mm_42155.1	chr5	112156223	112156231	+	1	NA	Intergenic	Intergenic	-50536	NR_045377	75569	Mm.243721	NR_045377	ENSMUSG00000101683	1700028D13Rik	-	RIKEN cDNA 1700028D13 gene	ncRNA
mm_13710.1	chr2	117159858	117159865	+	1	NA	intron (NM_033524, intron 2 of 6)	L1MD2|LINE|L1	-25266	NR_030440	732489		NR_030440	ENSMUSG00000076376	Mir674	Mirn674|mir-674|mmu-mir-674	microRNA 674	ncRNA
mm_120044.1	chr14	56575538	56575546	+	1	NA	promoter-TSS (NM_001145978)	promoter-TSS (NM_001145978)	-77	NM_001145978	328417	Mm.379357	NM_001145978	ENSMUSG00000054509	Parp4	Adprtl1|C030027K23Rik|E230037B21Rik|Gm743|PARPL|PH5P|VAULT3|VPARP|p193	poly (ADP-ribose) polymerase family, member 4	protein-coding
mm_113684.1	chr13	42866272	42866301	+	1	NA	promoter-TSS (NM_001302636)	promoter-TSS (NM_001302636)	39	NM_001302636	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding
mm_78839.1	chr9	44326805	44326896	+	1	NA	promoter-TSS (NM_007875)	promoter-TSS (NM_007875)	5	NM_007875	13478	Mm.18353	NM_007875	ENSMUSG00000032123	Dpagt1	AU021132|Dpagt2|GPT|Gnpta	dolichyl-phosphate (UDP-N-acetylglucosamine) acetylglucosaminephosphotransferase 1 (GlcNAc-1-P transferase)	protein-coding
mm_86647.1	chr10	17476852	17476885	+	1	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	-246360	NM_010828	17684	Mm.272321	NM_010828	ENSMUSG00000039910	Cited2	AI835299|ER154-like|Mrg1|Msg2|p35srj	Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 2	protein-coding
mm_173307.1	chrY	83633756	83633757	+	1	NA	Intergenic	Intergenic	294155	NM_001160131	100040911	Mm.457993	NM_001160131	ENSMUSG00000095650	Gm20854	-	predicted gene, 20854	protein-coding
mm_24846.1	chr3	95673976	95674007	+	1	NA	Intergenic	Intergenic	13926	NM_144899	229595	Mm.490574	NM_144899	ENSMUSG00000015850	Adamtsl4	ADAMTSL-4|Tsrc1	ADAMTS-like 4	protein-coding
mm_49764.1	chr6	34780941	34780988	+	1	NA	5' UTR (NM_001289656, exon 1 of 20)	5' UTR (NM_001289656, exon 1 of 20)	532	NM_001289656	76223	Mm.150047	NM_178630	ENSMUSG00000038836	Agbl3	2900053G10Rik|4930431N21Rik|6530406M24Rik|CCP3	ATP/GTP binding protein-like 3	protein-coding
mm_144100.1	chr18	3447085	3447129	+	1	NA	Intergenic	Intergenic	-60850	NM_026505	68010	Mm.284863	NM_026505	ENSMUSG00000024232	Bambi	2610003H06Rik	BMP and activin membrane-bound inhibitor	protein-coding
mm_147579.1	chr18	56455625	56455629	-	1	NA	intron (NM_026240, intron 1 of 13)	intron (NM_026240, intron 1 of 13)	23495	NM_026240	107022	Mm.24356	NM_026240	ENSMUSG00000001700	Gramd3	9030613F08Rik|9130427A09Rik|AW061306|NS3TP2	GRAM domain containing 3	protein-coding
mm_168821.1	chr12	22274752	22274755	-	1	NA	Intergenic	CpG	-118107	NR_136920	100043416		NM_001004167	ENSMUSG00000093846	Gm4425	EG432637|Gm5433	KRAB-domain protein pseudogene	pseudo
mm_95838.1	chr11	57011799	57011827	+	1	NA	5' UTR (NM_001113325, exon 1 of 16)	5' UTR (NM_001113325, exon 1 of 16)	195	NM_008165	14799	Mm.4920	NM_008165	ENSMUSG00000020524	Gria1	2900051M01Rik|Glr-1|Glr1|GluA1|GluR-A|GluRA|Glur-1|Glur1|HIPA1|gluR-K1	glutamate receptor, ionotropic, AMPA1 (alpha 1)	protein-coding
mm_22783.1	chr3	22076645	22076681	+	1	NA	promoter-TSS (NM_030732)	promoter-TSS (NM_030732)	11	NM_030732	81004	Mm.202966	NM_030732	ENSMUSG00000027630	Tbl1xr1	8030499H02Rik|A630076E03Rik|AW539987|C21|C230089I12Rik|DC42|Ira1|TBLR1	transducin (beta)-like 1X-linked receptor 1	protein-coding
mm_48730.1	chr5	147429812	147429815	-	1	NA	promoter-TSS (NM_028291)	promoter-TSS (NM_028291)	-767	NM_028291	72587	Mm.320469	NM_028291	ENSMUSG00000029647	Pan3	2700050F09Rik|A430027N15Rik|AU014670	PAN3 poly(A) specific ribonuclease subunit	protein-coding
mm_72194.1	chr8	72515268	72515287	+	1	NA	intron (NM_027485, intron 1 of 2)	intron (NM_027485, intron 1 of 2)	-22663	NM_177766	270066	Mm.291461	NM_177766	ENSMUSG00000019731	Slc35e1	6030458H05|AA408278	solute carrier family 35, member E1	protein-coding
mm_115891.1	chr13	22009714	22009724	-	1	NA	promoter-TSS (NM_019429)	promoter-TSS (NM_019429)	22	NM_019429	54373	Mm.32043	NM_019429	ENSMUSG00000006179	Prss16	AI448615|TSSP	protease, serine 16 (thymus)	protein-coding
mm_146543.1	chr18	6039402	6039413	-	1	NA	exon (NM_001039692, exon 11 of 19)	exon (NM_001039692, exon 11 of 19)	96691	NM_029277	75415	Mm.239675	NM_029277	ENSMUSG00000041225	Arhgap12	2810011M08Rik	Rho GTPase activating protein 12	protein-coding
mm_88346.1	chr10	75837514	75837530	+	1	NA	Intergenic	Intergenic	-2641	NM_010361	14872	Mm.24118	NM_010361	ENSMUSG00000033318	Gstt2	AI266894|Yrs|mGSTT2	glutathione S-transferase, theta 2	protein-coding
mm_14049.1	chr2	122313827	122313835	+	1	NA	promoter-TSS (NM_001305262)	promoter-TSS (NM_001305262)	-101	NM_001305262	213696	Mm.247121	NM_145395	ENSMUSG00000027224	Duoxa1	BC019755|Nip|Nip1	dual oxidase maturation factor 1	protein-coding
mm_52041.1	chr6	96375350	96375358	+	1	NA	intron (NM_182808, intron 2 of 4)	intron (NM_182808, intron 2 of 4)	-209149	NR_003643	78482	Mm.391486	NM_030107	ENSMUSG00000072878	1700123L14Rik	-	nucleoporin 50 pseudogene	pseudo
mm_140364.1	chr17	86961483	86961522	+	1	NA	Intergenic	Intergenic	-1609	NM_145491	104215	Mm.826	NM_145491	ENSMUSG00000024143	Rhoq	Arhq|TC10A|Tc10	ras homolog family member Q	protein-coding
mm_32314.1	chr4	103339856	103339864	+	1	NA	intron (NM_025909, intron 7 of 8)	PB1D9|SINE|Alu	26014	NM_025909	67013	Mm.30021	NM_025909	ENSMUSG00000035069	Oma1	2010001O09Rik|MPRP-1|ZMPOMA1	OMA1 zinc metallopeptidase	protein-coding
mm_133049.1	chr16	57570671	57570691	+	1	NA	exon (NM_001040397, exon 5 of 5)	exon (NM_001040397, exon 5 of 5)	21439	NM_001177871	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding
mm_11150.1	chr2	28523986	28523995	+	1	NA	intron (NM_001145834, intron 1 of 17)	intron (NM_001145834, intron 1 of 17)	-9474	NM_001145835	19730	Mm.5236	NM_009058	ENSMUSG00000026821	Ralgds	Gnds|Rgds|mKIAA1308	ral guanine nucleotide dissociation stimulator	protein-coding
mm_92311.1	chr10	75301997	75302005	-	1	NA	intron (NM_153406, intron 13 of 15)	intron (NM_153406, intron 13 of 15)	-14876	NM_009630	11540	Mm.333734	NM_009630	ENSMUSG00000020178	Adora2a	A2AAR|A2aR|AA2AR	adenosine A2a receptor	protein-coding
mm_90537.1	chr10	128090158	128090205	+	1	NA	3' UTR (NM_016774, exon 10 of 10)	3' UTR (NM_016774, exon 10 of 10)	-2602	NM_054078	116848	Mm.252213	NM_054078	ENSMUSG00000040054	Baz2a	AA415431|C030005G16Rik|C78388|Tip5|Walp3|mKIAA0314	bromodomain adjacent to zinc finger domain, 2A	protein-coding
mm_72176.1	chr8	72319054	72319071	+	1	NA	promoter-TSS (NM_008452)	promoter-TSS (NM_008452)	0	NM_008452	16598	Mm.26938	NM_008452	ENSMUSG00000055148	Klf2	Lklf	Kruppel-like factor 2 (lung)	protein-coding
mm_103404.1	chr11	75439552	75439558	-	1	NA	promoter-TSS (NM_008878)	promoter-TSS (NM_008878)	-54	NM_008878	18816	Mm.279733	NM_008878	ENSMUSG00000038224	Serpinf2	AI747498|Pli|Serpimf2	serine (or cysteine) peptidase inhibitor, clade F, member 2	protein-coding
mm_167745.1	chr9	108831825	108831881	+	1	NA	exon (NM_080437, exon 2 of 35)	exon (NM_080437, exon 2 of 35)	5533	NM_080437	107934	Mm.39945	NM_080437	ENSMUSG00000023473	Celsr3	Adgrc3|Fmi1|flamingo|mKIAA0812	cadherin, EGF LAG seven-pass G-type receptor 3	protein-coding
mm_2213.1	chr1	89746997	89747004	+	1	NA	intron (NM_001037136, intron 11 of 16)	intron (NM_001037136, intron 11 of 16)	-63108	NR_015540	74403	Mm.444291	NR_015540		4933400F21Rik	1700091C04Rik|4930565K10Rik	RIKEN cDNA 4933400F21 gene	ncRNA
mm_88744.1	chr10	80284491	80284507	+	1	NA	exon (NM_133188, exon 10 of 12)	exon (NM_133188, exon 10 of 12)	6335	NR_105876	102466207		NR_105876	ENSMUSG00000098672	Mir6911	Gm27822|mmu-mir-6911	microRNA 6911	ncRNA
mm_50767.1	chr6	53619904	53619941	+	1	NA	intron (NM_001327821, intron 7 of 10)	intron (NM_001327821, intron 7 of 10)	46548	NM_172728	231991	Mm.227444	NM_172728	ENSMUSG00000053007	Creb5	9430076C15Rik|CRE-BPa|Crebpa|D430026C09Rik	cAMP responsive element binding protein 5	protein-coding
mm_169569.1	chr15	18314817	18314829	+	1	NA	intron (NR_045711, intron 6 of 11)	L1Md_T|LINE|L1	54804	NR_045711	70886	Mm.399021	NR_045711		4921515E04Rik	-	RIKEN cDNA 4921515E04 gene	ncRNA
mm_114029.1	chr13	52646535	52646547	+	1	NA	3' UTR (NM_011518, exon 14 of 14)	3' UTR (NM_011518, exon 14 of 14)	49659	NM_011518	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_3684.1	chr1	153740536	153740540	+	1	NA	intron (NM_011267, intron 1 of 4)	intron (NM_011267, intron 1 of 4)	185	NM_011267	19734	Mm.181709	NM_011267	ENSMUSG00000026475	Rgs16	Rgs14|Rgsr	regulator of G-protein signaling 16	protein-coding
mm_97920.1	chr11	83574648	83574680	+	1	NA	3' UTR (NM_011338, exon 4 of 4)	3' UTR (NM_011338, exon 4 of 4)	3972	NM_011338	20308	Mm.416125	NM_011338	ENSMUSG00000019122	Ccl9	CCF18|MRP-2|Scya10|Scya9	chemokine (C-C motif) ligand 9	protein-coding
mm_78876.1	chr9	44483184	44483199	+	1	NA	Intergenic	CpG	-15945	NM_030256	80288	Mm.370270	NM_030256	ENSMUSG00000063382	Bcl9l	B9L|BC003321|BCL9-2|DLNB11	B cell CLL/lymphoma 9-like	protein-coding
mm_62838.1	chr7	113766242	113766255	+	1	NA	5' UTR (NM_145584, exon 1 of 16)	5' UTR (NM_145584, exon 1 of 16)	250	NM_145584	233744	Mm.334160	NM_145584	ENSMUSG00000038156	Spon1	AI666765|AW455831|BC020531|D330035F22Rik|FSP	spondin 1, (f-spondin) extracellular matrix protein	protein-coding
mm_163800.1	chr14	18545339	18545368	-	1	NA	Intergenic	Intergenic	-213509	NM_009455	22194	Mm.4429	NM_009455	ENSMUSG00000021774	Ube2e1	UbcM3|Ubce5|ubcM2	ubiquitin-conjugating enzyme E2E 1	protein-coding
mm_51556.1	chr6	83349452	83349496	+	1	NA	promoter-TSS (NM_175277)	promoter-TSS (NM_175277)	-10	NM_175277	78653	Mm.391470	NM_175277	ENSMUSG00000045160	Bola3	1810056O20Rik	bolA-like 3 (E. coli)	protein-coding
mm_161226.1	chr13	74062236	74062236	-	1	NA	promoter-TSS (NM_028959)	promoter-TSS (NM_028959)	49	NM_028959	74470	Mm.73234	NM_028959	ENSMUSG00000021572	Cep72	2610029E11Rik|4933440J22Rik	centrosomal protein 72	protein-coding
mm_126940.1	chr15	91899418	91899422	+	1	NA	exon (NM_207243, exon 27 of 44)	exon (NM_207243, exon 27 of 44)	61092	NM_198927	223809	Mm.486225	NM_198927	ENSMUSG00000047295	Smgc	2310010P21Rik|DXImx49e|Muc19|Muc19/Smgc|Sfc21	submandibular gland protein C	protein-coding
mm_4786.1	chr1	184039543	184039557	+	1	NA	intron (NM_022019, intron 2 of 3)	intron (NM_022019, intron 2 of 3)	5089	NM_022019	63953	Mm.404024	NM_022019	ENSMUSG00000039384	Dusp10	2610306G15Rik|AI158871|MKP-5|MKP5	dual specificity phosphatase 10	protein-coding
mm_81929.1	chr9	120179717	120179727	+	1	NA	Intergenic	L1ME3Cz|LINE|L1	29980	NM_001039364	17433	Mm.486167	NM_008614	ENSMUSG00000032517	Mobp	AI835053|AI839848|MOBP155|MOBP170|MOBP69|MOBP73|MOBP81|R74645	myelin-associated oligodendrocytic basic protein	protein-coding
mm_111261.1	chr12	85140450	85140482	-	1	NA	exon (NM_146244, exon 6 of 11)	exon (NM_146244, exon 6 of 11)	10798	NM_146244	238323	Mm.44829	NM_146244	ENSMUSG00000019235	Rps6kl1	A830084F09Rik|AW046440	ribosomal protein S6 kinase-like 1	protein-coding
mm_132824.1	chr16	45224358	45224364	+	1	NA	promoter-TSS (NM_001037719)	promoter-TSS (NM_001037719)	24	NM_177584	208154	Mm.38199	NM_177584	ENSMUSG00000052013	Btla	A630002H24	B and T lymphocyte associated	protein-coding
mm_27455.1	chr3	52064228	52064232	-	1	NA	intron (NM_001004176, intron 1 of 4)	intron (NM_001004176, intron 1 of 4)	40776	NM_001004176	433586	Mm.234972	NM_001004176	ENSMUSG00000061143	Maml3	AV234550|BC049812|Mam-2|mKIAA1816	mastermind like 3 (Drosophila)	protein-coding
mm_154008.1	chr19	53039232	53039252	-	1	NA	promoter-TSS (NM_133216)	promoter-TSS (NM_133216)	-588	NM_133216	170750	Mm.99776	NM_133216	ENSMUSG00000025027	Xpnpep1	D230045I08Rik|sAMP	X-prolyl aminopeptidase (aminopeptidase P) 1, soluble	protein-coding
mm_31889.1	chr4	82509585	82509592	+	1	NA	intron (NR_137202, intron 1 of 1)	intron (NR_137202, intron 1 of 1)	1599	NR_137202	102635783	Mm.41666	NR_137202		Gm11266	OTTMUSG00000000396	predicted gene 11266	ncRNA
mm_138085.1	chr17	33997024	33997053	+	1	NA	exon (NM_001001892, exon 5 of 8)	exon (NM_001001892, exon 5 of 8)	3295	NM_001001892	14972	Mm.422886	NM_001001892	ENSMUSG00000061232	H2-K1	H-2K|H-2K(d)|H2-K|K-f	histocompatibility 2, K1, K region	protein-coding
mm_149521.1	chr19	12442795	12442808	+	1	NA	Intergenic	RMER1C|Other|Other	14896	NM_019540	56093	Mm.285849	NM_019540	ENSMUSG00000040065	Pfpl	Epcs5|Epcs50	pore forming protein-like	protein-coding
mm_116590.1	chr13	48314607	48314616	-	1	NA	Intergenic	Intergenic	-40727	NR_045162	320315	Mm.185120	NR_045162	ENSMUSG00000097326	A330048O09Rik	-	RIKEN cDNA A330048O09 gene	ncRNA
mm_67170.1	chr7	73556709	73556732	-	1	NA	intron (NR_037569, intron 1 of 4)	intron (NR_037569, intron 1 of 4)	1675	NR_037569	69170	Mm.34539	NR_037569	ENSMUSG00000101970	1810026B05Rik	-	RIKEN cDNA 1810026B05 gene	ncRNA
mm_20530.1	chr2	131025107	131025125	-	1	NA	intron (NM_009730, intron 28 of 28)	intron (NM_009730, intron 28 of 28)	15282	NR_105969	102465606		NR_105969	ENSMUSG00000098686	Mir6973b	Gm27815|mmu-mir-6973b	microRNA 6973b	ncRNA
mm_93780.1	chr10	120476491	120476527	-	1	NA	promoter-TSS (NM_010441)	promoter-TSS (NM_010441)	-40	NM_010441	15364	Mm.157190	NM_010441	ENSMUSG00000056758	Hmga2	9430083A20Rik|HMGI-C|Hmgic|pg|pygmy	high mobility group AT-hook 2	protein-coding
mm_19636.1	chr2	102828577	102828580	-	1	NA	exon (NM_009851, exon 16 of 19)	exon (NM_009851, exon 16 of 19)	73087	NM_001177785	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_66052.1	chr7	30736960	30736963	-	1	NA	exon (NM_001290631, exon 3 of 11)	exon (NM_001290631, exon 3 of 11)	2446	NM_008085	14447	Mm.436562	NM_008085	ENSMUSG00000061099	Gapdhs	Gapd-s|Gapds	glyceraldehyde-3-phosphate dehydrogenase, spermatogenic	protein-coding
mm_38718.1	chr4	145234758	145234766	-	1	NA	intron (NM_011610, intron 1 of 9)	intron (NM_011610, intron 1 of 9)	12108	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_62461.1	chr7	101548080	101548087	+	1	NA	Intergenic	PB1D9|SINE|Alu	7719	NM_007490	11871	Mm.439746	NM_007490	ENSMUSG00000092517	Art2a-ps	ARTC2|Art2a|Ly92a|Rt-6|Rt6|Rt6-1	ADP-ribosyltransferase 2a, pseudogene	protein-coding
mm_93207.1	chr10	94943789	94943859	-	1	NA	exon (NM_018797, exon 1 of 31)	exon (NM_018797, exon 1 of 31)	754	NM_018797	54712	Mm.256712	NM_018797	ENSMUSG00000074785	Plxnc1	2510048K12Rik|AW742158|CD232|Vespr	plexin C1	protein-coding
mm_60983.1	chr7	48990840	48990847	+	1	NA	intron (NM_001111016, intron 2 of 38)	intron (NM_001111016, intron 2 of 38)	31770	NM_001111016	78286	Mm.333881	NM_175272	ENSMUSG00000052512	Nav2	5330421F07Rik|AU067780|BQ960892|HELAD1|POMFIL2|RAINB1|RAINB2|Unc53H2|mKIAA3015	neuron navigator 2	protein-coding
mm_114317.1	chr13	60029705	60029709	+	1	NA	promoter-TSS (NR_046142)	promoter-TSS (NR_046142)	-4	NR_046142	328263	Mm.123405	NR_046142		A530065N20Rik	A530065N20	RIKEN cDNA A530046M15 gene	ncRNA
mm_34183.1	chr4	140700603	140700613	+	1	NA	promoter-TSS (NM_173867)	promoter-TSS (NM_173867)	-865	NM_173867	108911	Mm.253	NM_173867	ENSMUSG00000040945	Rcc2	2610510H01Rik|2610529N02Rik|AA536646|AA675016|Td60|mKIAA1470	regulator of chromosome condensation 2	protein-coding
mm_72839.1	chr8	88293764	88293795	+	1	NA	promoter-TSS (NM_001037724)	promoter-TSS (NM_001037724)	-425	NM_001037724	11513	Mm.288206	NM_007406	ENSMUSG00000031659	Adcy7	AA407758	adenylate cyclase 7	protein-coding
mm_36265.1	chr4	63600751	63600769	-	1	NA	promoter-TSS (NR_028584)	promoter-TSS (NR_028584)	4	NR_028584	670833	Mm.32213	NR_028583	ENSMUSG00000084782	Gm11213	OTTMUSG00000000252	predicted gene 11213	ncRNA
mm_14510.1	chr2	132263323	132263334	+	1	NA	5' UTR (NM_001291040, exon 1 of 4)	5' UTR (NM_001291040, exon 1 of 4)	180	NM_138651	110911	Mm.284503	NM_138651	ENSMUSG00000058793	Cds2	5730450N06Rik|5730460C18Rik|AI854580|D2Wsu127e	CDP-diacylglycerol synthase (phosphatidate cytidylyltransferase) 2	protein-coding
mm_168664.1	chr11	90072156	90072170	+	1	NA	Intergenic	(CAG)n|Simple_repeat|Simple_repeat	41815	NM_026433	67888	Mm.212428	NM_026433	ENSMUSG00000069763	Tmem100	1810057C19Rik|AV011897	transmembrane protein 100	protein-coding
mm_108743.1	chr12	88725001	88725028	+	1	NA	Intergenic	Intergenic	-69490	NM_001198587	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding
mm_28661.1	chr3	95251105	95251118	-	1	NA	promoter-TSS (NM_001168356)	promoter-TSS (NM_001168356)	82	NM_001168356	171388	Mm.331209	NM_134253	ENSMUSG00000028115	Bnipl	1700128A13Rik|BNIP-S|BNIPL1|BNIPL2|PP73|PP753	BCL2/adenovirus E1B 19kD interacting protein like	protein-coding
mm_58958.1	chr7	18884680	18884709	+	1	NA	promoter-TSS (NM_009402)	promoter-TSS (NM_009402)	4	NM_009402	21946	Mm.21855	NM_009402	ENSMUSG00000030413	Pglyrp1	PGRP|PGRP-S|Pglyrp|Tag7|Tasg7|Tnfsf3l	peptidoglycan recognition protein 1	protein-coding
mm_99385.1	chr11	102097207	102097236	+	1	NA	Intergenic	Intergenic	4079	NM_008918	19064	Mm.1269	NM_008918	ENSMUSG00000017316	Ppy	AV061413|IGSPP|PP	pancreatic polypeptide	protein-coding
mm_37306.1	chr4	119294239	119294310	-	1	NA	exon (NM_011732, exon 1 of 8)	exon (NM_011732, exon 1 of 8)	239	NM_011732	22608	Mm.258204	NM_011732	ENSMUSG00000028639	Ybx1	1700102N10Rik|C79409|EF1A|MSY1|Nsep1|YB-1|dbpB|mYB-1a	Y box protein 1	protein-coding
mm_45178.1	chr5	51567144	51567148	-	1	NA	intron (NR_132764, intron 1 of 12)	intron (NR_132764, intron 1 of 12)	579	NR_132764	19017	Mm.259072	NM_008904	ENSMUSG00000029167	Ppargc1a	A830037N07Rik|ENSMUSG00000079510|Gm11133|PGC-1|PPARGC-1-alpha|Pgc-1alpha|Pgc1|Pgco1|Ppargc1	peroxisome proliferative activated receptor, gamma, coactivator 1 alpha	protein-coding
mm_1430.1	chr1	67180103	67180120	+	1	NA	exon (NM_001080809, exon 21 of 38)	exon (NM_001080809, exon 21 of 38)	57084	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_33369.1	chr4	129514758	129514774	+	1	NA	exon (NM_010807, exon 2 of 2)	exon (NM_010807, exon 2 of 2)	1185	NM_010807	17357	Mm.424974	NM_010807	ENSMUSG00000047945	Marcksl1	AL022768|AW215397|AW536807|D4Bc1|F52|MacMARCKS|Macs2|Macs3|Mlp|Mrp	MARCKS-like 1	protein-coding
mm_141480.1	chr17	31198925	31198954	-	1	NA	promoter-TSS (NM_001163776)	promoter-TSS (NM_001163776)	35	NM_001163776	140765	Mm.214638	NM_080727	ENSMUSG00000024034	Tmprss3	-	transmembrane protease, serine 3	protein-coding
mm_23019.1	chr3	34589918	34589954	+	1	NA	intron (NR_015580, intron 2 of 4)	intron (NR_015580, intron 2 of 4)	29555	NR_015580	320478	Mm.444063	NR_015580	ENSMUSG00000105265	Sox2ot	B230215L15Rik	SOX2 overlapping transcript (non-protein coding)	ncRNA
mm_78067.1	chr9	15306222	15306240	+	1	NA	promoter-TSS (NM_001199485)	promoter-TSS (NM_001199485)	17	NM_027261	75316	Mm.354115	NM_026541	ENSMUSG00000031939	Taf1d	2810003M17Rik|4930553M18Rik|5930426I11Rik|Josd3|TAF(I)41|TAFI41	TATA-box binding protein associated factor, RNA polymerase I, D	protein-coding
mm_87398.1	chr10	45336305	45336308	+	1	NA	intron (NM_024285, intron 1 of 7)	intron (NM_024285, intron 1 of 7)	544	NM_024285	23828	Mm.332793	NM_024285	ENSMUSG00000071317	Bves	Pop1|Popdc1|mBVES	blood vessel epicardial substance	protein-coding
mm_85298.1	chr9	100505168	100505171	-	1	NA	intron (NM_010878, intron 2 of 3)	B1_Mur3|SINE|Alu	1687	NM_001324530	17973	Mm.181485	NM_010878	ENSMUSG00000032475	Nck1	6330586M15Rik|D230010O13Rik|Nck|Nck-1	non-catalytic region of tyrosine kinase adaptor protein 1	protein-coding
mm_54005.1	chr6	7694815	7694829	-	1	NA	Intergenic	Intergenic	-1640	NM_012055	27053	Mm.2942	NM_012055	ENSMUSG00000029752	Asns	-	asparagine synthetase	protein-coding
mm_91957.1	chr10	61114153	61114167	-	1	NA	intron (NM_009163, intron 4 of 14)	intron (NM_009163, intron 4 of 14)	24829	NM_025273	13180	Mm.39473	NM_025273	ENSMUSG00000020098	Pcbd1	Dcoh|Pcbd|Pcd|Phs	pterin 4 alpha carbinolamine dehydratase/dimerization cofactor of hepatocyte nuclear factor 1 alpha (TCF1) 1	protein-coding
mm_19725.1	chr2	104493302	104493358	-	1	NA	intron (NM_010434, intron 1 of 15)	CpG	1159	NM_010434	15259	Mm.257925	NM_010434	ENSMUSG00000027177	Hipk3	DYRK6|FIST3|PKY|mir-1902	homeodomain interacting protein kinase 3	protein-coding
mm_29305.1	chr3	107943350	107943360	-	1	NA	intron (NM_008184, intron 1 of 7)	intron (NM_008184, intron 1 of 7)	394	NM_008184	14867	Mm.458154	NM_008184	ENSMUSG00000068762	Gstm6	-	glutathione S-transferase, mu 6	protein-coding
mm_146427.1	chr18	84851379	84851400	+	1	NA	promoter-TSS (NM_025797)	promoter-TSS (NM_025797)	-25	NM_025797	109672	Mm.31018	NM_025797	ENSMUSG00000024646	Cyb5a	0610009N12Rik|Cyb5	cytochrome b5 type A (microsomal)	protein-coding
mm_54808.1	chr6	42040180	42040189	-	1	NA	exon (NM_009299, exon 2 of 4)	exon (NM_009299, exon 2 of 4)	1790	NM_009299	20939	Mm.4119	NM_009299	ENSMUSG00000023289	Sva	-	seminal vesicle antigen	protein-coding
mm_81209.1	chr9	107580648	107580699	+	1	NA	promoter-TSS (NM_178020)	promoter-TSS (NM_178020)	4	NM_019750	56441	Mm.10305	NM_019750	ENSMUSG00000079334	Nat6	AI225910|Fus2	N-acetyltransferase 6	protein-coding
mm_8029.1	chr1	135132544	135132554	-	1	NA	promoter-TSS (NM_177081)	promoter-TSS (NM_177081)	26	NM_007955	13924	Mm.4450	NM_007955		Ptprv	Esp|OST|OST-PTP|mOST-PTP	protein tyrosine phosphatase, receptor type, V	protein-coding
mm_160991.1	chr11	106349148	106349148	-	1	NA	exon (NM_133199, exon 1 of 24)	exon (NM_133199, exon 1 of 24)	242	NM_133199	110880	Mm.432528	NM_133199	ENSMUSG00000001027	Scn4a	Nav1.4|SkM1|mH2	sodium channel, voltage-gated, type IV, alpha	protein-coding
mm_96104.1	chr11	60537963	60537984	+	1	NA	5' UTR (NM_172943, exon 1 of 4)	5' UTR (NM_172943, exon 1 of 4)	290	NM_172943	268420	Mm.262056	NM_172943	ENSMUSG00000042650	Alkbh5	AW050020|AW215868|Abh5|E130207K11|Ofoxd	alkB homolog 5, RNA demethylase	protein-coding
mm_152294.1	chr19	9083668	9083702	-	1	NA	TTS (NM_011681)	TTS (NM_011681)	4271	NM_011681	22287	Mm.2258	NM_011681	ENSMUSG00000024653	Scgb1a1	CC10|CC16|CCSP|PCB-BP|UG|UGB|Utg	secretoglobin, family 1A, member 1 (uteroglobin)	protein-coding
mm_50537.1	chr6	49046040	49046050	+	1	NA	intron (NM_053110, intron 4 of 10)	intron (NM_053110, intron 4 of 10)	9527	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_48341.1	chr5	139150660	139150723	-	1	NA	exon (NM_001081265, exon 1 of 13)	exon (NM_001081265, exon 1 of 13)	468	NM_001081265	433956	Mm.5547	NM_001081265	ENSMUSG00000025857	Dnaaf5	BC053401|C76907|Heatr2	dynein, axonemal assembly factor 5	protein-coding
mm_133119.1	chr16	65815170	65815196	+	1	NA	promoter-TSS (NM_028572)	promoter-TSS (NM_028572)	-450	NM_028572	73569	Mm.25670	NM_028572	ENSMUSG00000091243	Vgll3	1700110N18Rik|4832416J22|C80713|Vgl-3|Vito-2	vestigial like family member 3	protein-coding
mm_131709.1	chr16	20837139	20837148	+	1	NA	Intergenic	RLTR42-int|LTR|ERVK	-102632	NM_009379	21832	Mm.3943	NM_009379	ENSMUSG00000022847	Thpo	Mgdf|Ml|Mpllg|Tpo	thrombopoietin	protein-coding
mm_67194.1	chr7	73996377	73996385	-	1	NA	intron (NM_009181, intron 1 of 5)	intron (NM_009181, intron 1 of 5)	17301	NM_009181	20450	Mm.4954	NM_009181	ENSMUSG00000025789	St8sia2	AI323367|ST8SiaII|STX|Siat8b	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 2	protein-coding
mm_20554.1	chr2	131071380	131071397	-	1	NA	exon (NM_011426, exon 18 of 21)	exon (NM_011426, exon 18 of 21)	-7574	NM_001163529	110751	Mm.108550	NM_033615	ENSMUSG00000027318	Adam33	Adaml	a disintegrin and metallopeptidase domain 33	protein-coding
mm_51471.1	chr6	82960270	82960278	+	1	NA	intron (NM_033079, intron 2 of 9)	intron (NM_033079, intron 2 of 9)	13352	NM_033079	110958	Mm.100652	NM_033079	ENSMUSG00000030041	M1ap	D6Mm5e	meiosis 1 associated protein	protein-coding
mm_38816.1	chr4	148500450	148500466	-	1	NA	promoter-TSS (NM_001039554)	promoter-TSS (NM_001039554)	4	NM_001039554	654812	Mm.388929	NM_001039554	ENSMUSG00000028989	Angptl7	-	angiopoietin-like 7	protein-coding
mm_105537.1	chr11	106301470	106301518	-	1	NA	exon (NM_008117, exon 2 of 5)	exon (NM_008117, exon 2 of 5)	402	NM_008117	14599	Mm.343934	NM_008117	ENSMUSG00000020713	Gh	Gh1|Ghb1	growth hormone	protein-coding
mm_27620.1	chr3	59344052	59344076	-	1	NA	5' UTR (NM_001162884, exon 1 of 7)	5' UTR (NM_001162884, exon 1 of 7)	192	NM_001162884	242050	Mm.228086	NM_001162884	ENSMUSG00000036334	Igsf10	6530405F15Rik|9030224D03|AA409708|AA536958|AI414626|Adlican2|CMF608	immunoglobulin superfamily, member 10	protein-coding
mm_107055.1	chr12	16653605	16653628	+	1	NA	exon (NM_008747, exon 1 of 4)	exon (NM_008747, exon 1 of 4)	146	NM_008747	18217	Mm.281715	NM_008747	ENSMUSG00000020591	Ntsr2	NT2R|NTRL	neurotensin receptor 2	protein-coding
mm_9058.1	chr1	167372418	167372422	-	1	NA	TTS (NM_025569)	TTS (NM_025569)	21377	NM_025569	66447	Mm.218286	NM_025569	ENSMUSG00000026688	Mgst3	2010012L10Rik|2010306B17Rik|2700004G04Rik|AA516734|GST-III	microsomal glutathione S-transferase 3	protein-coding
mm_149976.1	chr19	29081737	29081752	+	1	NA	Intergenic	ERVB7_1-LTR_MM|LTR|ERVK	14443	NR_045687	100503337	Mm.103412	NR_045687		Gm9895	ENSMUSG00000052976	predicted gene 9895	ncRNA
mm_160609.1	chr9	80217617	80217617	+	1	NA	5' UTR (NM_001039546, exon 2 of 33)	5' UTR (NM_001039546, exon 2 of 33)	52583	NM_001039546	17920	Mm.4040	NM_008662	ENSMUSG00000033577	Myo6	BC029719|Tlc|sv	myosin VI	protein-coding
mm_143041.1	chr17	56757544	56757569	-	1	NA	promoter-TSS (NM_008738)	promoter-TSS (NM_008738)	-8	NM_008738	18188	Mm.8074	NM_008738	ENSMUSG00000039481	Nrtn	NTN	neurturin	protein-coding
mm_57407.1	chr6	124865614	124865622	-	1	NA	3' UTR (NM_013488, exon 10 of 10)	3' UTR (NM_013488, exon 10 of 10)	-1701	NM_013533	14788	Mm.2514	NM_013533	ENSMUSG00000038390	Gpr162	A-2|BC031437|Grca	G protein-coupled receptor 162	protein-coding
mm_86673.1	chr10	18077497	18077504	+	1	NA	intron (NM_009048, intron 1 of 19)	intron (NM_009048, intron 1 of 19)	21560	NM_001111065	19707	Mm.4479	NM_009048	ENSMUSG00000019854	Reps1	BB161292	RalBP1 associated Eps domain containing protein	protein-coding
mm_47008.1	chr5	115474574	115474578	-	1	NA	exon (NM_011107, exon 4 of 4)	exon (NM_011107, exon 4 of 4)	8310	NM_011107	18778	Mm.20190	NM_011107	ENSMUSG00000029522	Pla2g1b	Pla2a|sPLA2IB	phospholipase A2, group IB, pancreas	protein-coding
mm_132736.1	chr16	43889866	43889878	+	1	NA	promoter-TSS (NM_029128)	promoter-TSS (NM_029128)	-30	NM_027801	212153	Mm.209835	NM_027801	ENSMUSG00000022701	Ccdc191	2610015P09Rik|8430422M09Rik|AU040712	coiled-coil domain containing 191	protein-coding
mm_37378.1	chr4	120975407	120975432	-	1	NA	exon (NM_133716, exon 6 of 10)	exon (NM_133716, exon 6 of 10)	-2097	NR_105982	102465614		NR_105982	ENSMUSG00000106436	Mir7015	mmu-mir-7015	microRNA 7015	ncRNA
mm_62023.1	chr7	91564672	91564680	+	1	NA	intron (NM_011807, intron 2 of 22)	intron (NM_011807, intron 2 of 22)	473890	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_131920.1	chr16	23317601	23317632	+	1	NA	5' UTR (NM_001252506, exon 2 of 7)	5' UTR (NM_001252506, exon 2 of 7)	27146	NM_001252506	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_86831.1	chr10	21235478	21235488	+	1	NA	Intergenic	Intergenic	-60496	NM_001042593	56422	Mm.25527	NM_019702	ENSMUSG00000019977	Hbs1l	2810035F15Rik|AI326327|eRFS	Hbs1-like (S. cerevisiae)	protein-coding
mm_61135.1	chr7	56050136	56050217	+	1	NA	promoter-TSS (NM_010418)	promoter-TSS (NM_010418)	21	NM_010418	15204	Mm.20929	NM_010418	ENSMUSG00000030451	Herc2	D15F32S1h|D7H15F32S1|D7H15F37S1|jdf2|mKIAA0393|rjs	HECT and RLD domain containing E3 ubiquitin protein ligase 2	protein-coding
mm_108953.1	chr12	102367368	102367390	+	1	NA	intron (NM_177620, intron 5 of 9)	intron (NM_177620, intron 5 of 9)	72434	NM_011175	19141	Mm.17185	NM_011175	ENSMUSG00000021190	Lgmn	AEP|AI746452|AU022324|Prsc1	legumain	protein-coding
mm_30331.1	chr3	151732141	151732141	-	1	NA	3' UTR (NM_133871, exon 8 of 8)	3' UTR (NM_133871, exon 8 of 8)	17818	NM_133871	99899	Mm.30756	NM_133871	ENSMUSG00000028037	Ifi44	A430056A10Rik|AW261460|MTAP44|p44	interferon-induced protein 44	protein-coding
mm_59730.1	chr7	28796010	28796070	+	1	NA	exon (NM_177158, exon 8 of 12)	exon (NM_177158, exon 8 of 12)	7071	NM_177158	320435	Mm.74632	NM_177158	ENSMUSG00000051735	Rinl	5830482F20Rik|9930116N10Rik	Ras and Rab interactor-like	protein-coding
mm_57462.1	chr6	125191499	125191511	-	1	NA	promoter-TSS (NM_025595)	promoter-TSS (NM_025595)	81	NM_146171	68298	Mm.257590	NM_146171	ENSMUSG00000038252	Ncapd2	2810406C15Rik|2810465G24Rik|CAP-D2|CNAP1|mKIAA0159	non-SMC condensin I complex, subunit D2	protein-coding
mm_32605.1	chr4	112006282	112006297	+	1	NA	promoter-TSS (NM_001102662)	promoter-TSS (NM_001102662)	20	NM_001102662	639781	Mm.398873	NM_001102662	ENSMUSG00000089773	Skint1	OTTMUSG00000008542|Skint-1	selection and upkeep of intraepithelial T cells 1	protein-coding
mm_4588.1	chr1	178319329	178319339	+	1	NA	intron (NM_025511, intron 1 of 3)	intron (NM_025511, intron 1 of 3)	181	NM_025511	66359	Mm.489720	NM_025511	ENSMUSG00000026500	Cox20	2310005N03Rik|Fam36a	COX20 Cox2 chaperone	protein-coding
mm_97335.1	chr11	77293996	77293999	+	1	NA	intron (NM_177710, intron 1 of 14)	intron (NM_177710, intron 1 of 14)	-54283	NM_001291190	237860	Mm.440381	NM_177710	ENSMUSG00000037926	Ssh2	SSH-2|SSH-2L|mSSH-2L	slingshot homolog 2 (Drosophila)	protein-coding
mm_120510.1	chr14	66344318	66344368	+	1	NA	promoter-TSS (NM_019675)	promoter-TSS (NM_019675)	47	NM_019675	56471	Mm.35474	NM_019675	ENSMUSG00000022044	Stmn4	Lagl|R75359|RB3	stathmin-like 4	protein-coding
mm_109577.1	chr12	112489462	112489479	+	1	NA	promoter-TSS (NM_177039)	promoter-TSS (NM_177039)	22	NM_177039	319942	Mm.185209	NM_177039	ENSMUSG00000043122	A530016L24Rik	Nrac	RIKEN cDNA A530016L24 gene	protein-coding
mm_163258.1	chr11	111814365	111814368	+	1	NA	Intergenic	Intergenic	748202	NM_008425	16518	Mm.4951	NM_008425	ENSMUSG00000041695	Kcnj2	IRK1|Kcnf1|Kir2.1	potassium inwardly-rectifying channel, subfamily J, member 2	protein-coding
mm_26744.1	chr3	6922586	6922589	-	1	NA	Intergenic	RLTR13D6|LTR|ERVK	-302144	NM_027048	69347	Mm.45822	NM_027048	ENSMUSG00000069118	1700008P02Rik	-	RIKEN cDNA 1700008P02 gene	protein-coding
mm_65006.1	chr7	17056705	17056717	-	1	NA	promoter-TSS (NM_016868)	promoter-TSS (NM_016868)	-32	NM_016868	53417	Mm.135110	NM_016868	ENSMUSG00000004328	Hif3a	Ipas|MOP7|NEPAS|bHLHe17	hypoxia inducible factor 3, alpha subunit	protein-coding
mm_48157.1	chr5	137152406	137152414	-	1	NA	Intergenic	Intergenic	-36203	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_126383.1	chr15	80173516	80173548	+	1	NA	promoter-TSS (NM_010795)	promoter-TSS (NM_010795)	-189	NM_010795	17309	Mm.299693	NM_010795	ENSMUSG00000042428	Mgat3	1110038J12Rik|AI848272|GnT-III	mannoside acetylglucosaminyltransferase 3	protein-coding
mm_169608.1	chr15	37003696	37003697	+	1	NA	exon (NM_026521, exon 2 of 4)	exon (NM_026521, exon 2 of 4)	3706	NM_026521	68036	Mm.371631	NM_026521	ENSMUSG00000062397	Zfp706	3110006P09Rik|AA793007|AW536850|C77232|Znf706	zinc finger protein 706	protein-coding
mm_87878.1	chr10	61648643	61648662	+	1	NA	promoter-TSS (NM_026438)	promoter-TSS (NM_026438)	31	NM_026438	67895	Mm.28897	NM_026438	ENSMUSG00000020089	Ppa1	2010317E03Rik|Pyp	pyrophosphatase (inorganic) 1	protein-coding
mm_76828.1	chr8	104631282	104631295	-	1	NA	promoter-TSS (NM_019662)	promoter-TSS (NM_019662)	33	NM_019662	56437	Mm.29467	NM_019662	ENSMUSG00000031880	Rrad	REM3|Rad	Ras-related associated with diabetes	protein-coding
mm_64177.1	chr7	141458082	141458098	+	1	NA	non-coding (NR_028142, exon 5 of 10)	non-coding (NR_028142, exon 5 of 10)	2902	NM_001163689	66853	Mm.29998	NM_025802	ENSMUSG00000025509	Pnpla2	0610039C21Rik|1110001C14Rik|Atgl|TTS-2.2	patatin-like phospholipase domain containing 2	protein-coding
mm_18853.1	chr2	75676529	75676553	-	1	NA	exon (NM_010902, exon 5 of 5)	exon (NM_010902, exon 5 of 5)	17251	NR_033513	627828	Mm.459502	NR_033513	ENSMUSG00000092086	Gm6793	EG627828	heterogeneous nuclear ribonucleoprotein A3 pseudogene	pseudo
mm_8126.1	chr1	136140379	136140383	-	1	NA	intron (NM_001039472, intron 1 of 34)	CpG	8980	NM_001039472	16565	Mm.276135	NM_019962	ENSMUSG00000041642	Kif21b	2610511N21Rik|mKIAA0449	kinesin family member 21B	protein-coding
mm_159811.1	chr5	119834576	119834576	+	1	NA	promoter-TSS (NM_011537)	promoter-TSS (NM_011537)	-87	NM_011537	21388	Mm.103636	NM_011537	ENSMUSG00000018263	Tbx5	-	T-box 5	protein-coding
mm_161454.1	chr15	75431739	75431739	-	1	NA	promoter-TSS (NR_108041)	promoter-TSS (NR_108041)	90	NR_108041	105892	Mm.38909	NM_001039720	ENSMUSG00000053168	9030619P08Rik	-	lymphocyte antigen 6 complex pseudogene	pseudo
mm_3342.1	chr1	137969660	137969669	+	1	NA	Intergenic	B3A|SINE|B2	3025	NR_029820	723890		NR_029820	ENSMUSG00000065458	Mir181b-1	Mirn181b-1|mir-181b-1	microRNA 181b-1	ncRNA
mm_9305.1	chr1	171639527	171639567	-	1	NA	intron (NM_001347184, intron 2 of 5)	B1_Mur4|SINE|Alu	2353	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_120581.1	chr14	69767471	69767526	+	1	NA	promoter-TSS (NM_020275)	promoter-TSS (NM_020275)	26	NM_020275	21933	Mm.193430	NM_020275	ENSMUSG00000022074	Tnfrsf10b	DR5|KILLER|Ly98|MK|TRAILR2|TRICK2A|TRICK2B|TRICKB	tumor necrosis factor receptor superfamily, member 10b	protein-coding
mm_31621.1	chr4	59189562	59189586	+	1	NA	promoter-TSS (NM_011673)	promoter-TSS (NM_011673)	24	NM_011673	22234	Mm.198803	NM_011673	ENSMUSG00000028381	Ugcg	AU043821|C80537|Epcs21|GlcT-1|Ugcgl	UDP-glucose ceramide glucosyltransferase	protein-coding
mm_131063.1	chr16	4558750	4558763	+	1	NA	intron (NM_031182, intron 1 of 6)	CpG	964	NM_031182	83383	Mm.273210	NM_031182	ENSMUSG00000005718	Tfap4	AI642933|AP-4|D930048N17Rik|Tcfap4|bHLHc41	transcription factor AP4	protein-coding
mm_158430.1	chrX	139871508	139871515	-	1	NA	5' UTR (NM_001193309, exon 1 of 17)	5' UTR (NM_001193309, exon 1 of 17)	143	NM_029413	75746	Mm.23269	NM_029413	ENSMUSG00000031434	Morc4	1600017G11Rik|5630401M14Rik|AA117449|Zcwcc2	microrchidia 4	protein-coding
mm_46851.1	chr5	113650372	113650381	-	1	NA	promoter-TSS (NM_008153)	promoter-TSS (NM_008153)	14	NM_008153	14747	Mm.5196	NM_008153	ENSMUSG00000042190	Cmklr1	ChemR23|DEZ|Gpcr27|mcmklr1	chemokine-like receptor 1	protein-coding
mm_4916.1	chr1	190714078	190714079	+	1	NA	Intergenic	Intergenic	197692	NM_178775	320119	Mm.220912	NM_178775	ENSMUSG00000089872	Rps6kc1	AA682037|B130003F20Rik|C80612|Rpk118	ribosomal protein S6 kinase polypeptide 1	protein-coding
mm_109059.1	chr12	104340855	104340870	+	1	NA	exon (NM_011458, exon 2 of 5)	exon (NM_011458, exon 2 of 5)	2376	NM_011458	20714	Mm.291569	NM_011458	ENSMUSG00000058207	Serpina3k	1300001I07Rik|D12Rp54|MMCM2|MMSpi2|RP54|Spi-2|Spi2|contrapsin	serine (or cysteine) peptidase inhibitor, clade A, member 3K	protein-coding
mm_29706.1	chr3	123385926	123385993	-	1	NA	promoter-TSS (NM_201638)	promoter-TSS (NM_201638)	31	NM_201638	210529	Mm.260039	NM_201638	ENSMUSG00000028114	Mettl14	G430022H21Rik|mKIAA1627	methyltransferase like 14	protein-coding
mm_66335.1	chr7	43310751	43310751	-	1	NA	intron (NM_027264, intron 2 of 4)	intron (NM_027264, intron 2 of 4)	2510	NM_027264	69930	Mm.45367	NM_027264	ENSMUSG00000012640	Zfp715	2610041B18Rik|mszf15	zinc finger protein 715	protein-coding
mm_19144.1	chr2	80499814	80499817	-	1	NA	TTS (NM_001290745)	TTS (NM_001290745)	-52419	NM_011356	20378	Mm.427436	NM_011356	ENSMUSG00000027004	Frzb	Frp|Sfrp3|frezzled|fritz|frzb-1	frizzled-related protein	protein-coding
mm_165980.1	chr4	103119937	103119943	+	1	NA	intron (NM_001039081, intron 1 of 12)	intron (NM_001039081, intron 1 of 12)	550	NM_001039081	71148	Mm.288721	NM_027696	ENSMUSG00000028522	Mier1	4933425I22Rik|5830411K19Rik|er1	MEIR1 treanscription regulator	protein-coding
mm_43007.1	chr5	123641760	123641768	+	1	NA	intron (NM_001347468, intron 7 of 24)	intron (NM_001347468, intron 7 of 24)	42597	NM_019765	56430	Mm.241109	NM_019765	ENSMUSG00000049550	Clip1	1110007I12Rik|4631429H07Rik|AV017631|C81039|CLIP-170|CLIP170|CYLN1|Clip50|Rsn|mKIAA4046|restin	CAP-GLY domain containing linker protein 1	protein-coding
mm_69885.1	chr7	141637077	141637104	-	1	NA	intron (NM_001330001, intron 31 of 33)	intron (NM_001330001, intron 31 of 33)	16389	NR_106030	102466798		NR_106030	ENSMUSG00000098759	Mir7063	Gm27654|mmu-mir-7063	microRNA 7063	ncRNA
mm_127668.1	chr15	102657111	102657118	+	1	NA	Intergenic	Intergenic	13933	NM_026468	67942	Mm.10314	NM_026468	ENSMUSG00000062683	Atp5g2	1810041M08Rik	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit C2 (subunit 9)	protein-coding
mm_36343.1	chr4	73718539	73718542	-	1	NA	intron (NM_001017427, intron 17 of 17)	intron (NM_001017427, intron 17 of 17)	35026	NM_001081644	242502	Mm.331671	NM_001081644	ENSMUSG00000095341	Gm428	-	predicted gene 428	protein-coding
mm_85768.1	chr9	108937190	108937218	-	1	NA	intron (NM_025407, intron 2 of 12)	intron (NM_025407, intron 2 of 12)	556	NM_025407	22273	Mm.335460	NM_025407	ENSMUSG00000025651	Uqcrc1	1110032G10Rik	ubiquinol-cytochrome c reductase core protein 1	protein-coding
mm_117023.1	chr13	58183313	58183326	-	1	NA	exon (NM_152234, exon 7 of 10)	exon (NM_152234, exon 7 of 10)	25670	NM_198004	75731	Mm.293919	NM_198004	ENSMUSG00000050002	Idnk	5133401N09Rik	idnK gluconokinase homolog (E. coli)	protein-coding
mm_113343.1	chr13	31785259	31785270	+	1	NA	Intergenic	Intergenic	-21382	NM_008592	17300	Mm.12949	NM_008592	ENSMUSG00000050295	Foxc1	FREAC3|Fkh1|Mf1|Mf4|ch|fkh-1|frkhda	forkhead box C1	protein-coding
mm_134381.1	chr16	17175956	17175965	-	1	NA	intron (NM_009456, intron 2 of 3)	intron (NM_009456, intron 2 of 3)	25532	NM_009456	22195	Mm.3074	NM_009456	ENSMUSG00000038965	Ube2l3	C79827|UbcM4|Ubce7	ubiquitin-conjugating enzyme E2L 3	protein-coding
mm_27040.1	chr3	26331905	26331917	-	1	NA	promoter-TSS (NM_138666)	promoter-TSS (NM_138666)	-2	NM_138666	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_166890.1	chr7	28131694	28131700	-	1	NA	exon (NM_001164655, exon 3 of 20)	exon (NM_001164655, exon 3 of 20)	2231	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_145336.1	chr18	56432095	56432115	+	1	NA	promoter-TSS (NM_026240)	promoter-TSS (NM_026240)	-27	NM_026240	107022	Mm.24356	NM_026240	ENSMUSG00000001700	Gramd3	9030613F08Rik|9130427A09Rik|AW061306|NS3TP2	GRAM domain containing 3	protein-coding
mm_170943.1	chr2	50296454	50296456	+	1	NA	promoter-TSS (NR_040361)	promoter-TSS (NR_040361)	222	NM_133839	109129	Mm.29214	NM_133839	ENSMUSG00000026766	Mmadhc	2010311D03Rik|AI314967|CblD	methylmalonic aciduria (cobalamin deficiency) cblD type, with homocystinuria	protein-coding
mm_33374.1	chr4	129515591	129515605	+	1	NA	TTS (NM_008228)	TTS (NM_008228)	2017	NM_010807	17357	Mm.424974	NM_010807	ENSMUSG00000047945	Marcksl1	AL022768|AW215397|AW536807|D4Bc1|F52|MacMARCKS|Macs2|Macs3|Mlp|Mrp	MARCKS-like 1	protein-coding
mm_80460.1	chr9	77983572	77983582	+	1	NA	3' UTR (NM_134255, exon 8 of 8)	3' UTR (NM_134255, exon 8 of 8)	66212	NM_134255	68801	Mm.430736	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	ELOVL family member 5, elongation of long chain fatty acids (yeast)	protein-coding
mm_80968.1	chr9	103111992	103112006	+	1	NA	promoter-TSS (NM_173781)	promoter-TSS (NM_173781)	-75	NM_173781	270192	Mm.490252	NM_173781	ENSMUSG00000032549	Rab6b	9630015C03|AI844641|C330006L04Rik|D9Bwg0185e	RAB6B, member RAS oncogene family	protein-coding
mm_147010.1	chr18	34507333	34507348	-	1	NA	promoter-TSS (NM_146084)	promoter-TSS (NM_146084)	-517	NM_146084	225358	Mm.226899	NM_146084	ENSMUSG00000036501	Fam13b	2610024E20Rik|AW060714|AW546153	family with sequence similarity 13, member B	protein-coding
mm_43996.1	chr5	146832990	146832998	+	1	NA	5' UTR (NM_019647, exon 1 of 6)	5' UTR (NM_019647, exon 1 of 6)	104	NM_019647	19933	Mm.316592	NM_019647	ENSMUSG00000041453	Rpl21	8430440E03Rik|L21	ribosomal protein L21	protein-coding
mm_109780.1	chr12	119390633	119390689	+	1	NA	Intergenic	Intergenic	-52749	NM_001163136	238455	Mm.31376	NM_001163136	ENSMUSG00000041886	Macc1	4732474O15Rik|Gm267	metastasis associated in colon cancer 1	protein-coding
mm_170545.1	chr19	40125448	40125457	+	1	NA	Intergenic	RLTR9D|LTR|ERVK	35773	NM_001167875	107141	Mm.474575	NM_134144	ENSMUSG00000054827	Cyp2c50	AI266900	cytochrome P450, family 2, subfamily c, polypeptide 50	protein-coding
mm_127248.1	chr15	99670328	99670396	+	1	NA	promoter-TSS (NM_009597)	promoter-TSS (NM_009597)	-356	NM_009597	11419	Mm.440107	NM_009597	ENSMUSG00000023017	Asic1	AI843610|ASIC|ASIC1a|Accn2|B530003N02Rik|BNaC2	acid-sensing (proton-gated) ion channel 1	protein-coding
mm_54476.1	chr6	34988439	34988455	-	1	NA	Intergenic	Intergenic	-10448	NM_001025573	243753	Mm.440221	NM_001025573	ENSMUSG00000029847	Slc23a4	2010107G12Rik|Gm468	solute carrier family 23 member 4	protein-coding
mm_597.1	chr1	39578892	39578909	+	1	NA	Intergenic	Intergenic	-1553	NM_001033135	67702	Mm.28614	NM_001033135	ENSMUSG00000048234	Rnf149	1600023E10Rik|AV037261|C76763|Gm15832|Greul4|OTTMUSG00000026591	ring finger protein 149	protein-coding
mm_13765.1	chr2	118546744	118546752	+	1	NA	exon (NM_001311140, exon 2 of 4)	exon (NM_001311140, exon 2 of 4)	851	NM_001331221	171543	Mm.210125	NM_138313	ENSMUSG00000040093	Bmf	AW260063|AW411872	BCL2 modifying factor	protein-coding
mm_67059.1	chr7	67373193	67373244	-	1	NA	promoter-TSS (NM_001291196)	promoter-TSS (NM_001291196)	-360	NM_001291195	17258	Mm.132788	NM_001033713	ENSMUSG00000030557	Mef2a	A430079H05Rik	myocyte enhancer factor 2A	protein-coding
mm_171266.1	chr3	86672236	86672246	-	1	NA	intron (NM_001077687, intron 47 of 50)	intron (NM_001077687, intron 47 of 50)	-123958	NM_011839	23937	Mm.389466	NM_011839	ENSMUSG00000057777	Mab21l2	-	mab-21-like 2 (C. elegans)	protein-coding
mm_93751.1	chr10	120170434	120170454	-	1	NA	intron (NM_028679, intron 5 of 11)	intron (NM_028679, intron 5 of 11)	31093	NM_028679	73914	Mm.146194	NM_028679	ENSMUSG00000020227	Irak3	4833428C18Rik|AI563835|IRAK-M	interleukin-1 receptor-associated kinase 3	protein-coding
mm_171800.1	chr5	123628206	123628218	-	1	NA	intron (NM_001291229, intron 9 of 23)	U2|snRNA|snRNA	-55197	NM_029929	77573	Mm.41372	NM_029929	ENSMUSG00000029434	Vps33a	3830421M04Rik|AI503300|AW048546|AW554476|bf	VPS33A CORVET/HOPS core subunit	protein-coding
mm_76922.1	chr8	105933833	105933862	-	1	NA	promoter-TSS (NM_023182)	promoter-TSS (NM_023182)	15	NM_023182	109660	Mm.2745	NM_023182	ENSMUSG00000031896	Ctrl	0910001G08Rik|1810004D15Rik|AV005227|Ctra-1|Ctra1|chymopasin|mFLJ00366	chymotrypsin-like	protein-coding
mm_62974.1	chr7	120102348	120102358	+	1	NA	promoter-TSS (NM_145586)	promoter-TSS (NM_145586)	-73	NM_145586	233806	Mm.257952	NM_145586	ENSMUSG00000030917	Tmem159	8430420C20Rik	transmembrane protein 159	protein-coding
mm_78293.1	chr9	22388903	22388950	+	1	NA	intron (NM_028390, intron 1 of 23)	CpG	280	NM_028390	68743	Mm.282751	NM_028390	ENSMUSG00000036777	Anln	1110037A17Rik|2900037I21Rik|C78101|Scraps	anillin, actin binding protein	protein-coding
mm_90920.1	chr10	12614598	12614617	-	1	NA	intron (NM_011682, intron 50 of 73)	intron (NM_011682, intron 50 of 73)	247128	NM_011682	22288	Mm.331784	NM_011682	ENSMUSG00000019820	Utrn	AA589569|DRP|Dmdl	utrophin	protein-coding
mm_53070.1	chr6	124914905	124914928	+	1	NA	intron (NM_026988, intron 2 of 4)	intron (NM_026988, intron 2 of 4)	3030	NM_026988	69202	Mm.142187	NM_026988	ENSMUSG00000030122	Ptms	2610009E16Rik	parathymosin	protein-coding
mm_56436.1	chr6	97384505	97384510	-	1	NA	intron (NM_001346639, intron 5 of 22)	ORR1F|LTR|ERVL-MaLR	74779	NM_001346639	232288	Mm.27789	NM_145148	ENSMUSG00000030064	Frmd4b	6030440G05Rik|C87375|GOBLIN|GRSP1|R74720	FERM domain containing 4B	protein-coding
mm_13152.1	chr2	92382933	92382941	+	1	NA	promoter-TSS (NM_183112)	promoter-TSS (NM_183112)	19	NM_183112	75641	Mm.330409	NM_183112	ENSMUSG00000044916	1700029I15Rik	1700021K07Rik	RIKEN cDNA 1700029I15 gene	protein-coding
mm_141998.1	chr17	35195717	35195726	-	1	NA	TTS (NR_105939)	TTS (NR_105939)	749	NR_105939	102465588		NR_105939	ENSMUSG00000098291	Mir6973a	Gm27967|mmu-mir-6973a	microRNA 6973a	ncRNA
mm_153665.1	chr19	44395903	44395913	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	11801	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_25729.1	chr3	122834350	122834359	+	1	NA	intron (NM_153422, intron 14 of 20)	intron (NM_153422, intron 14 of 20)	-32374	NR_045168	71647	Mm.449992	NR_045168	ENSMUSG00000106583	4930447N08Rik	-	RIKEN cDNA 4930447N08 gene	ncRNA
mm_23599.1	chr3	65109270	65109287	+	1	NA	promoter-TSS (NM_010597)	promoter-TSS (NM_010597)	-90	NM_010597	16497	Mm.316402	NM_010597	ENSMUSG00000027827	Kcnab1	Akr8a8|Kvbeta1.1|mKv(beta)1	potassium voltage-gated channel, shaker-related subfamily, beta member 1	protein-coding
mm_26284.1	chr3	142505792	142505810	+	1	NA	intron (NM_153564, intron 7 of 10)	intron (NM_153564, intron 7 of 10)	8867	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_42437.1	chr5	115429586	115429613	+	1	NA	promoter-TSS (NM_008629)	promoter-TSS (NM_008629)	-86	NM_008629	17690	Mm.5077	NM_008629	ENSMUSG00000054256	Msi1	Msi1h|Musahi1|m-Msi-1	musashi RNA-binding protein 1	protein-coding
mm_67380.1	chr7	79842209	79842217	-	1	NA	exon (NM_008486, exon 1 of 20)	exon (NM_008486, exon 1 of 20)	139	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_20740.1	chr2	137116756	137116773	-	1	NA	promoter-TSS (NM_013822)	promoter-TSS (NM_013822)	-244	NM_013822	16449	Mm.22398	NM_013822	ENSMUSG00000027276	Jag1	ABE2|Gsfabe2|Htu|Ozz|Ser-1	jagged 1	protein-coding
mm_99402.1	chr11	102192358	102192384	+	1	NA	intron (NM_175935, intron 2 of 5)	intron (NM_175935, intron 2 of 5)	2672	NM_175935	68401	Mm.22385	NM_175935	ENSMUSG00000034793	G6pc3	0710001K01Rik|AU019276|AU045429|AV128920|AW545836|UGRP	glucose 6 phosphatase, catalytic, 3	protein-coding
mm_143852.1	chr17	84156422	84156433	-	1	NA	Intergenic	Intergenic	31520	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_61500.1	chr7	76229770	76229794	+	1	NA	promoter-TSS (NM_001199224)	promoter-TSS (NM_001199224)	-105	NM_001199224	244071	Mm.322829	NM_172902	ENSMUSG00000025754	Agbl1	Ccp4|D430020F16|EG244071|Nna1-l1	ATP/GTP binding protein-like 1	protein-coding
mm_51304.1	chr6	72310625	72310646	+	1	NA	exon (NM_001282071, exon 8 of 11)	exon (NM_001282071, exon 8 of 11)	6025	NM_147779	20388	Mm.46033	NM_147779	ENSMUSG00000056370	Sftpb	AI562151|SF-B|SP-B|Sftp-3|Sftp3	surfactant associated protein B	protein-coding
mm_55212.1	chr6	52224594	52224611	-	1	NA	intron (NM_001277238, intron 2 of 2)	intron (NM_001277238, intron 2 of 2)	2768	NM_010456	15405	Mm.4694	NM_010456	ENSMUSG00000038227	Hoxa9	D6a9|Hox-1.7	homeobox A9	protein-coding
mm_36583.1	chr4	88033290	88033315	-	1	NA	5' UTR (NM_027326, exon 1 of 11)	5' UTR (NM_027326, exon 1 of 11)	105	NM_027326	70122	Mm.288898	NM_027326	ENSMUSG00000028496	Mllt3	2210011H10Rik|2610012I03Rik|3830408D16Rik|Af9|D4Ertd321e	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 3	protein-coding
mm_138586.1	chr17	35506053	35506069	+	1	NA	promoter-TSS (NM_013633)	promoter-TSS (NM_013633)	29	NM_013633	18999	Mm.17031	NM_013633	ENSMUSG00000024406	Pou5f1	NF-A3|Oct-3|Oct-3/4|Oct-4|Oct3|Oct3/4|Oct4|Otf-3|Otf-4|Otf3|Otf3-rs7|Otf3g|Otf4	POU domain, class 5, transcription factor 1	protein-coding
mm_156952.1	chrX	169987512	169987523	+	1	NA	intron (NM_001290512, intron 8 of 9)	CpG	-8600	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_32747.1	chr4	116674987	116675035	+	1	NA	Intergenic	Intergenic	-10588	NM_011034	18477	Mm.30929	NM_011034	ENSMUSG00000028691	Prdx1	MSP23|NkefA|OSF-3|OSF3|PAG|Paga|PrdxI|PrxI|TDX2|TPxA|Tdpx2|prx1	peroxiredoxin 1	protein-coding
mm_8483.1	chr1	153549735	153549745	-	1	NA	promoter-TSS (NM_028749)	promoter-TSS (NM_028749)	-26	NM_028749	74091	Mm.24887	NM_028749	ENSMUSG00000042684	Npl	0610033B02Rik	N-acetylneuraminate pyruvate lyase	protein-coding
mm_121989.1	chr14	26442724	26442734	-	1	NA	intron (NM_001347494, intron 10 of 19)	intron (NM_001347494, intron 10 of 19)	85182	NR_038005	71106	Mm.158564	NR_038005	ENSMUSG00000021874	4933413J09Rik	GCSE	RIKEN cDNA 4933413J09 gene	ncRNA
mm_61370.1	chr7	69917902	69917906	+	1	NA	Intergenic	Intergenic	419918	NR_131145	624549	Mm.116344	NR_131144	ENSMUSG00000109097	Gm29683	-	predicted gene, 29683	ncRNA
mm_110687.1	chr12	67222590	67222600	-	1	NA	promoter-TSS (NM_207010)	promoter-TSS (NM_207010)	-46	NM_207010	320772	Mm.227680	NM_207010	ENSMUSG00000034912	Mdga2	6720489L24Rik|9330209L04Rik|Adp|Mamdc1	MAM domain containing glycosylphosphatidylinositol anchor 2	protein-coding
mm_7799.1	chr1	131525412	131525428	-	1	NA	5' UTR (NM_001081011, exon 2 of 23)	5' UTR (NM_001081011, exon 2 of 23)	1941	NM_001081011	14270	Mm.276259	NM_019520	ENSMUSG00000026425	Srgap2	9930124L22Rik|AI448945|FBP2|Fnbp2|srGAP3	SLIT-ROBO Rho GTPase activating protein 2	protein-coding
mm_29553.1	chr3	116807803	116807866	-	1	NA	intron (NM_001081326, intron 1 of 33)	intron (NM_001081326, intron 1 of 33)	332	NM_001081326	77559	Mm.237099	NM_001081326	ENSMUSG00000033400	Agl	1110061O17Rik|9430004C13Rik|9630046L06Rik|AI850929|C77197	amylo-1,6-glucosidase, 4-alpha-glucanotransferase	protein-coding
mm_126929.1	chr15	91673373	91673383	+	1	NA	exon (NM_025730, exon 1 of 51)	exon (NM_025730, exon 1 of 51)	154	NM_025730	66725	Mm.37558	NM_025730	ENSMUSG00000036273	Lrrk2	4921513O20Rik|9330188B09Rik|AW561911|D630001M17Rik|Gm927|cI-46	leucine-rich repeat kinase 2	protein-coding
mm_125282.1	chr15	36439359	36439366	+	1	NA	Intergenic	Intergenic	57429	NM_175134	68839	Mm.396537	NM_175134	ENSMUSG00000048307	Ankrd46	1110054N06Rik|AI314978|AI987733	ankyrin repeat domain 46	protein-coding
mm_124494.1	chr14	121797640	121797658	-	1	NA	promoter-TSS (NM_134074)	promoter-TSS (NM_134074)	85	NM_134074	105445	Mm.378591	NM_134074	ENSMUSG00000025558	Dock9	AA959601|AW538057|B230309H04Rik|D14Wsu89e|Zizimin1|mKIAA1058	dedicator of cytokinesis 9	protein-coding
mm_100933.1	chr11	6519801	6519828	-	1	NA	intron (NM_178440, intron 1 of 21)	intron (NM_178440, intron 1 of 21)	1144	NM_178440	246177	Mm.239554	NM_178440	ENSMUSG00000020437	Myo1g	E430002D17Rik	myosin IG	protein-coding
mm_136554.1	chr17	3114958	3114982	+	1	NA	promoter-TSS (NM_134123)	promoter-TSS (NM_134123)	-2	NM_134123	106583	Mm.124373	NM_134123	ENSMUSG00000046201	Scaf8	A630086M08Rik|A930036P18Rik|AA408306|AI447644|AI448652|AU015035|Rbm16|mKIAA1116	SR-related CTD-associated factor 8	protein-coding
mm_158096.1	chrX	101639772	101639775	-	1	NA	promoter-TSS (NM_001290535)	promoter-TSS (NM_001290535)	-278	NM_139144	108155	Mm.487332	NM_139144	ENSMUSG00000034160	Ogt	1110038P24Rik|4831420N21Rik|AI115525|Ogtl	O-linked N-acetylglucosamine (GlcNAc) transferase (UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase)	protein-coding
mm_140670.1	chr17	12916792	12916831	-	1	NA	promoter-TSS (NM_026310)	promoter-TSS (NM_026310)	482	NM_013686	21454	Mm.229342	NM_013686	ENSMUSG00000068039	Tcp1	AI528772|CCT|Cct1|Ccta|TRic|Tcp-1|Tp63|c-cpn|p63	t-complex protein 1	protein-coding
mm_117326.1	chr13	67830999	67831011	-	1	NA	promoter-TSS (NR_045194)	promoter-TSS (NR_045194)	-20	NR_045194	320163	Mm.444711	NR_045194	ENSMUSG00000097276	4930525G20Rik	-	RIKEN cDNA 4930525G20 gene	ncRNA
mm_106317.1	chr11	118303086	118303093	-	1	NA	3' UTR (NM_011594, exon 5 of 5)	3' UTR (NM_011594, exon 5 of 5)	-12845	NM_001033528	72344	Mm.232293	NM_001033528	ENSMUSG00000033909	Usp36	2700002L06Rik|mKIAA1453	ubiquitin specific peptidase 36	protein-coding
mm_172605.1	chr8	15519984	15519986	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	462332	NM_008664	17930	Mm.272115	NM_008664	ENSMUSG00000031461	Myom2	AW146149	myomesin 2	protein-coding
mm_93058.1	chr10	88751294	88751297	-	1	NA	intron (NM_175158, intron 57 of 61)	B1F1|SINE|Alu	19881	NM_025859	104303	Mm.291247	NM_025859	ENSMUSG00000060904	Arl1	2310008D22Rik|AU019749	ADP-ribosylation factor-like 1	protein-coding
mm_11871.1	chr2	49132493	49132510	+	1	NA	intron (NM_029924, intron 5 of 16)	L1_Rod|LINE|L1	-113399	NM_001290656	109241	Mm.440436	NM_029924	ENSMUSG00000036792	Mbd5	9430004D19Rik|AA536666|AI426407|C030040A15Rik|Gm1630|OTTMUSG00000012483	methyl-CpG binding domain protein 5	protein-coding
mm_122710.1	chr14	52235285	52235295	-	1	NA	exon (NM_201637, exon 2 of 37)	exon (NM_201637, exon 2 of 37)	2282	NM_201637	67772	Mm.289934	NM_201637	ENSMUSG00000053754	Chd8	5830451P18Rik|AU015341|Duplin|HELSNF1|mKIAA1564	chromodomain helicase DNA binding protein 8	protein-coding
mm_103996.1	chr11	84870129	84870182	-	1	NA	promoter-TSS (NR_131197)	promoter-TSS (NR_131197)	150	NR_131201	102635561	Mm.341797	NR_131197		Ggnbp2os	-	gametogenetin binding protein 2, opposite strand	ncRNA
mm_70092.1	chr7	142656180	142656190	-	1	NA	intron (NM_001315488, intron 1 of 3)	intron (NM_001315488, intron 1 of 3)	-1189	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_103534.1	chr11	77489648	77489654	-	1	NA	promoter-TSS (NM_172945)	promoter-TSS (NM_172945)	27	NM_172945	268445	Mm.39296	NM_172945	ENSMUSG00000037907	Ankrd13b	AW124583|B930093C12Rik	ankyrin repeat domain 13b	protein-coding
mm_140132.1	chr17	79616863	79616873	+	1	NA	intron (NM_201361, intron 1 of 10)	intron (NM_201361, intron 1 of 10)	1968	NM_201361	381110	Mm.209801	NM_201361	ENSMUSG00000036368	Rmdn2	AW061290|Fam82a1|RMD-2|mRMD-2	regulator of microtubule dynamics 2	protein-coding
mm_168118.1	chr10	16943218	16943218	+	1	NA	Intergenic	L1Md_T|LINE|L1	152564	NR_038020	100504235	Mm.84044	NR_038020	ENSMUSG00000101969	Gm20125	-	predicted gene, 20125	ncRNA
mm_38532.1	chr4	141566338	141566344	-	1	NA	Intergenic	Intergenic	20179	NR_030695	320456	Mm.32859	NM_177163		B330016D10Rik	-	RIKEN cDNA B330016D10 gene	ncRNA
mm_9751.1	chr1	180808242	180808246	-	1	NA	intron (NM_008210, intron 3 of 3)	B1_Mus1|SINE|Alu	5361	NM_008210	15078	Mm.138832	NM_008210	ENSMUSG00000060743	H3f3a	H3.3A	H3 histone, family 3A	protein-coding
mm_122641.1	chr14	51255747	51255753	-	1	NA	exon (NM_053113, exon 2 of 2)	exon (NM_053113, exon 2 of 2)	362	NM_053113	93726	Mm.153688	NM_053113	ENSMUSG00000047222	Rnase2a	Ear11	ribonuclease, RNase A family, 2A (liver, eosinophil-derived neurotoxin)	protein-coding
mm_10884.1	chr2	25255666	25255685	+	1	NA	promoter-TSS (NM_001082476)	promoter-TSS (NM_001082476)	236	NM_177344	227615	Mm.213925	NM_177344	ENSMUSG00000078201	Tmem203	C730025P13Rik|Hbebp1	transmembrane protein 203	protein-coding
mm_166204.1	chr5	43672290	43672300	+	1	NA	intron (NM_172274, intron 4 of 39)	intron (NM_172274, intron 4 of 39)	9916	NM_172274	231214	Mm.44434	NM_172274	ENSMUSG00000039765	Cc2d2a	5730509K17Rik|b2b1035Clo	coiled-coil and C2 domain containing 2A	protein-coding
mm_61546.1	chr7	79361133	79361144	+	1	NA	3' UTR (NM_018811, exon 11 of 11)	3' UTR (NM_018811, exon 11 of 11)	25889	NM_020599	19771	Mm.41653	NM_020599	ENSMUSG00000039194	Rlbp1	3110056M11Rik|CRALBP	retinaldehyde binding protein 1	protein-coding
mm_84234.1	chr9	62122627	62122651	-	1	NA	promoter-TSS (NR_039595)	promoter-TSS (NR_039595)	-45	NR_039595	100628602		NR_039595	ENSMUSG00000092696	Mir5133	mir-5133|mmu-mir-5133|mu-mir-5133	microRNA 5133	ncRNA
mm_122768.1	chr14	54384166	54384192	-	1	NA	intron (NM_001253679, intron 3 of 10)	intron (NM_001253679, intron 3 of 10)	23338	NM_026936	69089	Mm.182340	NM_026936	ENSMUSG00000000959	Oxa1l	1810020M02Rik|AI894287	oxidase assembly 1-like	protein-coding
mm_27729.1	chr3	69044651	69044659	-	1	NA	promoter-TSS (NM_025863)	promoter-TSS (NM_025863)	87	NM_025863	66949	Mm.176695	NM_025863	ENSMUSG00000034317	Trim59	2310035M22Rik|2700022F13Rik|Mrf1|TSBF1	tripartite motif-containing 59	protein-coding
mm_114919.1	chr13	95324815	95324874	+	1	NA	promoter-TSS (NM_028106)	promoter-TSS (NM_028106)	19	NM_028106	72114	Mm.3774	NM_028106	ENSMUSG00000041995	Zbed3	0610037K01Rik|2610005H11Rik|AU018975|AU024588	zinc finger, BED type containing 3	protein-coding
mm_59449.1	chr7	27133491	27133516	+	1	NA	3' UTR (NM_007817, exon 10 of 10)	3' UTR (NM_007817, exon 10 of 10)	13548	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_28057.1	chr3	84220836	84220846	-	1	NA	promoter-TSS (NM_030706)	promoter-TSS (NM_030706)	36	NM_030706	80890	Mm.44876	NM_030706	ENSMUSG00000027993	Trim2	mKIAA0517|narf	tripartite motif-containing 2	protein-coding
mm_146813.1	chr18	20831632	20831657	-	1	NA	exon (NM_177038, exon 23 of 29)	exon (NM_177038, exon 23 of 29)	64434	NM_177038	75964	Mm.273769	NM_029491	ENSMUSG00000033382	Trappc8	5033403J15Rik|AI845423|D030074E01Rik|Trs85|mKIAA1012	trafficking protein particle complex 8	protein-coding
mm_173263.1	chrX	94903322	94903339	+	1	NA	Intergenic	Intergenic	-105041	NR_003292	668171	Mm.426134	NR_003292		Zxda	4933406P09Rik|AW413531	zinc finger, X-linked, duplicated A	pseudo
mm_114301.1	chr13	59497209	59497210	+	1	NA	intron (NM_001048008, intron 14 of 17)	intron (NM_001048008, intron 14 of 17)	47242	NM_001284221	67269	Mm.153008	NM_023328	ENSMUSG00000021557	Agtpbp1	1700020N17Rik|2310001G17Rik|2900054O13Rik|4930445M19Rik|5730402G09Rik|CCP1|Nna1|nmf243|pcd	ATP/GTP binding protein 1	protein-coding
mm_12108.1	chr2	61589498	61589509	+	1	NA	intron (NM_011529, intron 1 of 7)	B4|SINE|B4	-3594	NM_001164072	21353	Mm.244393	NM_011529	ENSMUSG00000064289	Tank	C86182|E430026L09Rik|I-TRAF	TRAF family member-associated Nf-kappa B activator	protein-coding
mm_41195.1	chr5	88328090	88328101	+	1	NA	exon (NM_008644, exon 3 of 3)	exon (NM_008644, exon 3 of 3)	10783	NM_008644	17830	Mm.200411	NM_008644	ENSMUSG00000064156	Prol1	Muc10	proline rich, lacrimal 1	protein-coding
mm_80119.1	chr9	70543235	70543247	+	1	NA	intron (NM_026337, intron 1 of 20)	CpG	371	NM_025690	66660	Mm.22379	NM_025690	ENSMUSG00000032212	Sltm	5730455C01Rik|5730555F13Rik|9130215G10Rik|Met	SAFB-like, transcription modulator	protein-coding
mm_150754.1	chr19	43840031	43840039	+	1	NA	non-coding (NR_033472, exon 1 of 1)	non-coding (NR_033472, exon 1 of 1)	1232	NR_033472	100038628	Mm.212585	NR_033472	ENSMUSG00000025194	Gm10768	ENSMUSG00000074828	predicted gene 10768	ncRNA
mm_98571.1	chr11	95440495	95440500	+	1	NA	intron (NM_025287, intron 2 of 10)	intron (NM_025287, intron 2 of 10)	26414	NM_025287	20747	Mm.285454	NM_025287	ENSMUSG00000057522	Spop	AI315626|Pcif1|TEF2	speckle-type POZ protein	protein-coding
mm_99310.1	chr11	101377187	101377192	+	1	NA	3' UTR (NM_008061, exon 5 of 5)	3' UTR (NM_008061, exon 5 of 5)	9473	NM_008061	14377	Mm.18064	NM_008061	ENSMUSG00000078650	G6pc	AW107337|G6Pase|G6pt|Glc-6-Pase	glucose-6-phosphatase, catalytic	protein-coding
mm_110949.1	chr12	76643920	76643922	-	1	NA	intron (NM_013675, intron 2 of 35)	intron (NM_013675, intron 2 of 35)	66626	NM_013675	20741	Mm.32881	NM_013675	ENSMUSG00000021061	Sptb	AI842465|D330027P03Rik|Gm1301|Spnb-1|Spnb1|ja|jaundiced|mKIAA4219	spectrin beta, erythrocytic	protein-coding
mm_42319.1	chr5	114897522	114897599	+	1	NA	5' UTR (NM_011854, exon 1 of 6)	5' UTR (NM_011854, exon 1 of 6)	626	NM_011854	23962	Mm.228363	NM_011854	ENSMUSG00000029561	Oasl2	M1204|Mmu-OASL|Oasl	2'-5' oligoadenylate synthetase-like 2	protein-coding
mm_70115.1	chr7	142699522	142699529	-	1	NA	Intergenic	Intergenic	-19799	NM_001185084	16334	Mm.4946	NM_008387	ENSMUSG00000000215	Ins2	AA986540|Ins-2|InsII|Mody|Mody4	insulin II	protein-coding
mm_166455.1	chr5	137981561	137981569	+	1	NA	promoter-TSS (NM_013478)	promoter-TSS (NM_013478)	44	NM_013478	12007	Mm.30061	NM_013478	ENSMUSG00000037053	Azgp1	Zag	alpha-2-glycoprotein 1, zinc	protein-coding
mm_161963.1	chr19	8405077	8405077	-	1	NA	promoter-TSS (NM_177002)	promoter-TSS (NM_177002)	28	NM_177002	319800	Mm.426083	NM_177002	ENSMUSG00000052562	Slc22a30	AA986766|C730048C13Rik|UST1R	solute carrier family 22, member 30	protein-coding
mm_147210.1	chr18	37945049	37945064	-	1	NA	intron (NM_010411, intron 6 of 14)	intron (NM_010411, intron 6 of 14)	-9580	NM_007858	13367	Mm.195916	NM_007858	ENSMUSG00000024456	Diaph1	D18Wsu154e|Dia1|Diap1|Drf1|p140mDia	diaphanous related formin 1	protein-coding
mm_4009.1	chr1	164960915	164960933	+	1	NA	Intergenic	MIR|SINE|MIR	-25414	NM_008510	16963	Mm.190	NM_008510	ENSMUSG00000026573	Xcl1	AI661682|ATAC|LTN|Lptn|SCM-1|SCM-1a|Scyc1	chemokine (C motif) ligand 1	protein-coding
mm_38499.1	chr4	141067262	141067268	-	1	NA	3' UTR (NM_025383, exon 8 of 8)	3' UTR (NM_025383, exon 8 of 8)	-6720	NM_001145958	230872	Mm.80685	NM_172122	ENSMUSG00000040860	Crocc	-	ciliary rootlet coiled-coil, rootletin	protein-coding
mm_119180.1	chr14	32165875	32165905	+	1	NA	intron (NM_019744, intron 1 of 9)	intron (NM_019744, intron 1 of 9)	101	NM_019744	27057	Mm.371598	NM_019744	ENSMUSG00000056234	Ncoa4	ARA70|Rfg	nuclear receptor coactivator 4	protein-coding
mm_47006.1	chr5	115472056	115472117	-	1	NA	exon (NM_011107, exon 3 of 4)	exon (NM_011107, exon 3 of 4)	5820	NM_011107	18778	Mm.20190	NM_011107	ENSMUSG00000029522	Pla2g1b	Pla2a|sPLA2IB	phospholipase A2, group IB, pancreas	protein-coding
mm_67646.1	chr7	84605766	84605815	-	1	NA	5' UTR (NM_010176, exon 1 of 14)	5' UTR (NM_010176, exon 1 of 14)	152	NM_010176	14085	Mm.3798	NM_010176	ENSMUSG00000030630	Fah	-	fumarylacetoacetate hydrolase	protein-coding
mm_123030.1	chr14	55524267	55524270	-	1	NA	promoter-TSS (NM_008736)	promoter-TSS (NM_008736)	-16	NM_008736	18185	Mm.20422	NM_008736	ENSMUSG00000040632	Nrl	D14H14S46E	neural retina leucine zipper gene	protein-coding
mm_32706.1	chr4	116075567	116075567	+	1	NA	promoter-TSS (NM_025641)	promoter-TSS (NM_025641)	298	NM_153521	230654	Mm.3655	NM_153521	ENSMUSG00000028703	Lrrc41	AA409966|AW555107|D630045E04Rik|D730026A16Rik|MUF1	leucine rich repeat containing 41	protein-coding
mm_138603.1	chr17	35567466	35567490	+	1	NA	promoter-TSS (NM_175148)	promoter-TSS (NM_175148)	-7	NM_175148	69542	Mm.265291	NM_175148	ENSMUSG00000039269	2300002M23Rik	Stg|emprin	RIKEN cDNA 2300002M23 gene	protein-coding
mm_25298.1	chr3	105959411	105959427	+	1	NA	promoter-TSS (NM_027432)	promoter-TSS (NM_027432)	-79	NM_027432	70465	Mm.5110	NM_027432	ENSMUSG00000000561	Wdr77	2610003I18Rik|2610312E17Rik|C79984|p44/MEP50	WD repeat domain 77	protein-coding
mm_34633.1	chr4	150614144	150614162	+	1	NA	exon (NM_001085492, exon 17 of 23)	exon (NM_001085492, exon 17 of 23)	38021	NM_173774	242773	Mm.29280	NM_173774	ENSMUSG00000039838	Slc45a1	C230078B22|Dnb5	solute carrier family 45, member 1	protein-coding
mm_25259.1	chr3	104782322	104782336	+	1	NA	intron (NM_027982, intron 1 of 9)	intron (NM_027982, intron 1 of 9)	1273	NM_027982	71887	Mm.379204	NM_027982	ENSMUSG00000002228	Ppm1j	2310008J22Rik|PP2Czeta|Ppp2cz	protein phosphatase 1J	protein-coding
mm_60055.1	chr7	31150028	31150039	+	1	NA	intron (NM_027898, intron 1 of 18)	intron (NM_027898, intron 1 of 18)	1017	NM_027898	52857	Mm.27366	NM_027898	ENSMUSG00000001248	Gramd1a	1300003M23Rik|AI415002|AW547240|D7Bwg0611e	GRAM domain containing 1A	protein-coding
mm_58247.1	chr6	145048711	145048729	-	1	NA	promoter-TSS (NM_001024468)	promoter-TSS (NM_001024468)	92	NM_001024468	12035	Mm.4606	NM_007532	ENSMUSG00000030268	Bcat1	BCATc|Eca39	branched chain aminotransferase 1, cytosolic	protein-coding
mm_58486.1	chr7	3630046	3630056	+	1	NA	promoter-TSS (NM_001290381)	promoter-TSS (NM_001290381)	66	NM_027328	68988	Mm.246863	NM_027328	ENSMUSG00000008373	Prpf31	1500019O16Rik|2810404O06Rik|AW554706|PRP31|RP11	pre-mRNA processing factor 31	protein-coding
mm_127432.1	chr15	101270152	101270158	+	1	NA	exon (NM_010444, exon 2 of 7)	exon (NM_010444, exon 2 of 7)	3309	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_162511.1	chr1	155054770	155054780	-	1	NA	Intergenic	Intergenic	44861	NM_010500	15939	Mm.12246	NM_010500	ENSMUSG00000056708	Ier5	-	immediate early response 5	protein-coding
mm_53537.1	chr6	136671829	136671876	+	1	NA	Intergenic	Intergenic	-9959	NM_025806	66857	Mm.3311	NM_025806	ENSMUSG00000030214	Plbd1	1100001H23Rik	phospholipase B domain containing 1	protein-coding
mm_116250.1	chr13	33965691	33965711	-	1	NA	intron (NM_001163239, intron 1 of 5)	intron (NM_001163239, intron 1 of 5)	1042	NM_001163241	18105	Mm.264036	NM_020282	ENSMUSG00000046949	Nqo2	NMO2|Nmor2|Ox2	NAD(P)H dehydrogenase, quinone 2	protein-coding
mm_49908.1	chr6	39002686	39002697	+	1	NA	intron (NM_011539, intron 5 of 12)	intron (NM_011539, intron 5 of 12)	64895	NR_040523	69986	Mm.490941	NR_040523	ENSMUSG00000100121	1700025N23Rik	-	RIKEN cDNA 1700025N23 gene	ncRNA
mm_125953.1	chr15	76249077	76249090	+	1	NA	TTS (NR_105918)	TTS (NR_105918)	892	NR_105918	102465575		NR_105918	ENSMUSG00000098625	Mir6953	Gm27738|mmu-mir-6953	microRNA 6953	ncRNA
mm_25471.1	chr3	108744367	108744410	+	1	NA	intron (NM_177859, intron 1 of 11)	intron (NM_177859, intron 1 of 11)	4730	NM_177859	329738	Mm.72322	NM_177859	ENSMUSG00000049565	Aknad1	4921525H12Rik	AKNA domain containing 1	protein-coding
mm_158229.1	chrX	106221146	106221169	-	1	NA	promoter-TSS (NM_001167988)	promoter-TSS (NM_001167988)	1	NM_001167988	407786	Mm.19440	NM_001001176	ENSMUSG00000047242	Taf9b	BC066223|Taf9l	TATA-box binding protein associated factor 9B	protein-coding
mm_76817.1	chr8	104509875	104509894	-	1	NA	promoter-TSS (NM_180958)	promoter-TSS (NM_180958)	3	NM_180958	320022	Mm.249775	NM_180958	ENSMUSG00000052616	Terb1	4930532D21Rik|BB085179|Ccdc79	telomere repeat binding bouquet formation protein 1	protein-coding
mm_119887.1	chr14	54933045	54933056	+	1	NA	exon (NM_080729, exon 2 of 3)	exon (NM_080729, exon 2 of 3)	355	NM_080729	140806	Mm.90154	NM_080729	ENSMUSG00000040770	Il25	IL-17e|Il17e	interleukin 25	protein-coding
mm_102962.1	chr11	69665385	69665395	-	1	NA	intron (NR_110993, intron 1 of 4)	intron (NR_110993, intron 1 of 4)	780	NM_001291058	12514	Mm.15819	NM_009853	ENSMUSG00000018774	Cd68	Lamp4|Scard1|gp110	CD68 antigen	protein-coding
mm_123346.1	chr14	63141758	63141780	-	1	NA	exon (NM_007798, exon 9 of 10)	exon (NM_007798, exon 9 of 10)	19307	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_61554.1	chr7	79499135	79499151	+	1	NA	promoter-TSS (NR_040314)	promoter-TSS (NR_040314)	-883	NR_040311	101694	Mm.41661	NR_040311	ENSMUSG00000097023	Mir9-3hg	AI854517	Mir9-3 host gene	ncRNA
mm_82832.1	chr9	31150091	31150101	-	1	NA	3' UTR (NM_009691, exon 16 of 16)	3' UTR (NM_009691, exon 16 of 16)	-18297	NM_011176	19143	Mm.243926	NM_011176	ENSMUSG00000031995	St14	Epithin|MT-SP1|Prss14|Tmprss14|mCAP3|matriptase	suppression of tumorigenicity 14 (colon carcinoma)	protein-coding
mm_132659.1	chr16	41680967	41680971	+	1	NA	intron (NM_001347236, intron 1 of 6)	intron (NM_001347236, intron 1 of 6)	147627	NM_175548	268890	Mm.310524	NM_175548	ENSMUSG00000061080	Lsamp	5430428I19|AW046674|B130007O04Rik|D930023J12Rik|Lam|Lamp	limbic system-associated membrane protein	protein-coding
mm_47945.1	chr5	135394500	135394558	-	1	NA	promoter-TSS (NM_148932)	promoter-TSS (NM_148932)	17	NM_148932	107939	Mm.28399	NM_148932	ENSMUSG00000053293	Pom121	2610027A18Rik|C80273|mKIAA0618	nuclear pore membrane protein 121	protein-coding
mm_64156.1	chr7	141338964	141339013	+	1	NA	promoter-TSS (NM_001282073)	promoter-TSS (NM_001282073)	-14	NM_133191	98845	Mm.27451	NM_133191	ENSMUSG00000025504	Eps8l2	AI042819|AW545405|Eps8r2	EPS8-like 2	protein-coding
mm_143370.1	chr17	67354992	67355003	-	1	NA	promoter-TSS (NM_008984)	promoter-TSS (NM_008984)	-538	NM_008984	19274	Mm.311809	NM_008984	ENSMUSG00000033278	Ptprm	RPTPmu|mKIAA4044	protein tyrosine phosphatase, receptor type, M	protein-coding
mm_129449.1	chr15	78561225	78561233	-	1	NA	3' UTR (NM_009008, exon 7 of 7)	3' UTR (NM_009008, exon 7 of 7)	11554	NM_009008	19354	Mm.1972	NM_009008	ENSMUSG00000033220	Rac2	AI323801|AI452260	RAS-related C3 botulinum substrate 2	protein-coding
mm_167769.1	chr9	111023550	111023592	+	1	NA	exon (NM_008522, exon 6 of 17)	exon (NM_008522, exon 6 of 17)	4279	NM_008522	17002	Mm.282359	NM_008522	ENSMUSG00000032496	Ltf	Csp82|Lf|MMS10R|Ms10r	lactotransferrin	protein-coding
mm_159880.1	chr6	13224993	13224993	-	1	NA	promoter-TSS (NM_001013757)	promoter-TSS (NM_001013757)	-28	NM_001013757	232585	Mm.389082	NM_001013757	ENSMUSG00000079679	Vwde	Gm467	von Willebrand factor D and EGF domains	protein-coding
mm_147156.1	chr18	36679354	36679380	-	1	NA	promoter-TSS (NM_146085)	promoter-TSS (NM_146085)	-1	NM_146085	225372	Mm.89673	NM_146085	ENSMUSG00000006050	Apbb3	Fe65l2|Rirl2|TR2S	amyloid beta (A4) precursor protein-binding, family B, member 3	protein-coding
mm_45430.1	chr5	67099095	67099103	-	1	NA	promoter-TSS (NM_008888)	promoter-TSS (NM_008888)	27	NM_008888	18935	Mm.62505	NM_008888	ENSMUSG00000012520	Phox2b	Dilp1|NBPhox|Pmx2b|Px2b	paired-like homeobox 2b	protein-coding
mm_87485.1	chr10	51494123	51494145	+	1	NA	exon (NM_013532, exon 6 of 9)	exon (NM_013532, exon 6 of 9)	3236	NM_013532	14728	Mm.34408	NM_013532	ENSMUSG00000062593	Lilrb4a	CD85K|Gp49b|HM18|ILT3|LIR-5|Lilrb4|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4A	protein-coding
mm_18117.1	chr2	44996765	44996790	-	1	NA	exon (NM_015753, exon 8 of 10)	exon (NM_015753, exon 8 of 10)	26400	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_74357.1	chr8	128358568	128358581	+	1	NA	promoter-TSS (NM_008737)	promoter-TSS (NM_008737)	-499	NM_008737	18186	Mm.271745	NM_008737	ENSMUSG00000025810	Nrp1	C530029I03|NP-1|NPN-1|Npn1|Nrp	neuropilin 1	protein-coding
mm_28794.1	chr3	96034246	96034252	-	1	NA	intron (NM_013841, intron 10 of 14)	intron (NM_013841, intron 10 of 14)	24206	NM_013841	22365	Mm.263185	NM_013841	ENSMUSG00000015747	Vps45	AI462172|AW554165|mVps45	vacuolar protein sorting 45	protein-coding
mm_29862.1	chr3	130060839	130060849	-	1	NA	promoter-TSS (NM_207209)	promoter-TSS (NM_207209)	63	NM_207209	99683	Mm.192303	NM_207209	ENSMUSG00000001052	Sec24b	AI605202|SEC24	Sec24 related gene family, member B (S. cerevisiae)	protein-coding
mm_135159.1	chr16	35859069	35859100	-	1	NA	intron (NM_001039530, intron 5 of 16)	B2_Mm2|SINE|B2	12298	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_98738.1	chr11	96365715	96365736	+	1	NA	promoter-TSS (NM_008266)	promoter-TSS (NM_008266)	-33	NM_008266	15407	Mm.890	NM_008266	ENSMUSG00000018973	Hoxb1	Hox-2.9	homeobox B1	protein-coding
mm_96395.1	chr11	67250507	67250526	+	1	NA	exon (NM_010855, exon 21 of 40)	exon (NM_010855, exon 21 of 40)	12704	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_22342.1	chr2	180889683	180889696	-	1	NA	Intergenic	Intergenic	-4351	NR_029538	723951		NR_029538	ENSMUSG00000065454	Mir124a-3	Mirn124a-3|mir-124-3|mir-124a-3	microRNA 124a-3	ncRNA
mm_118658.1	chr14	21797810	21797826	+	1	NA	3' UTR (NM_026283, exon 6 of 6)	3' UTR (NM_026283, exon 6 of 6)	-33743	NM_011695	22334	Mm.262327	NM_011695	ENSMUSG00000021771	Vdac2	Vdac6|mVDAC2|mVDAC6	voltage-dependent anion channel 2	protein-coding
mm_17117.1	chr2	24475560	24475562	-	1	NA	promoter-TSS (NM_011040)	promoter-TSS (NM_011040)	38	NM_011040	18510	Mm.2533	NM_011040	ENSMUSG00000026976	Pax8	Pax-8	paired box 8	protein-coding
mm_4011.1	chr1	165460576	165460642	+	1	NA	promoter-TSS (NM_028759)	promoter-TSS (NM_028759)	-146	NM_028759	74106	Mm.227605	NM_028759	ENSMUSG00000026571	Dcaf6	1200006M05Rik|Iqwd1|PC326	DDB1 and CUL4 associated factor 6	protein-coding
mm_160627.1	chr9	101074813	101074813	+	1	NA	promoter-TSS (NM_001100451)	promoter-TSS (NM_001100451)	51	NM_001100451	77853	Mm.326206	NM_001100451	ENSMUSG00000066415	Msl2	E130103E02Rik|Msl2l1|Rnf184	male-specific lethal 2 homolog (Drosophila)	protein-coding
mm_22445.1	chr2	181697805	181697825	-	1	NA	intron (NM_199023, intron 1 of 3)	intron (NM_199023, intron 1 of 3)	627	NM_199023	277496	Mm.212749	NM_199023	ENSMUSG00000045794	Lkaaear1	4930526D03Rik|Gm692	LKAAEAR motif containing 1 (IKAAEAR murine motif)	protein-coding
mm_42958.1	chr5	123076106	123076132	+	1	NA	promoter-TSS (NM_001039723)	promoter-TSS (NM_001039723)	-156	NM_001039723	330189	Mm.391872	NM_001039723	ENSMUSG00000054434	Tmem120b	-	transmembrane protein 120B	protein-coding
mm_47759.1	chr5	131308095	131308120	-	1	NA	promoter-TSS (NM_145218)	promoter-TSS (NM_145218)	-585	NM_145218	212996	Mm.299204	NM_145218	ENSMUSG00000034040	Wbscr17	AA388321|E330012B09Rik	Williams-Beuren syndrome chromosome region 17 homolog (human)	protein-coding
mm_80970.1	chr9	103112050	103112056	+	1	NA	promoter-TSS (NM_173781)	promoter-TSS (NM_173781)	-21	NM_173781	270192	Mm.490252	NM_173781	ENSMUSG00000032549	Rab6b	9630015C03|AI844641|C330006L04Rik|D9Bwg0185e	RAB6B, member RAS oncogene family	protein-coding
mm_100038.1	chr11	114983829	114983864	+	1	NA	3' UTR (NM_145437, exon 4 of 4)	3' UTR (NM_145437, exon 4 of 4)	6040	NM_145437	217305	Mm.275986	NM_145437	ENSMUSG00000034641	Cd300ld	4732429D16Rik|CLM5|Cd300ld1|LMIR4|MAIR-IV|clm-5	CD300 molecule like family member d	protein-coding
mm_18309.1	chr2	53696866	53696871	-	1	NA	Intergenic	L1_Mur2|LINE|L1	388684	NM_023396	67874	Mm.27086	NM_023396	ENSMUSG00000075334	Rprm	2410012A13Rik|Reprimo	reprimo, TP53 dependent G2 arrest mediator candidate	protein-coding
mm_129946.1	chr15	84960944	84960971	-	1	NA	intron (NM_001033273, intron 1 of 9)	intron (NM_001033273, intron 1 of 9)	-9334	NR_037206	100526461		NR_037206	ENSMUSG00000080441	Mir1249	mir-1249|mmu-mir-1249	microRNA 1249	ncRNA
mm_21262.1	chr2	156722388	156722394	-	1	NA	intron (NM_001042487, intron 1 of 6)	intron (NM_001042487, intron 1 of 6)	1112	NM_001042487	228836	Mm.22094	NM_146128	ENSMUSG00000061689	Dlgap4	AI225853|BC024558|DAP-4|DAP4|SAPAP-4|Sapap4|WBP16	discs, large homolog-associated protein 4 (Drosophila)	protein-coding
mm_55190.1	chr6	52191319	52191342	-	1	NA	exon (NM_008265, exon 1 of 2)	exon (NM_008265, exon 1 of 2)	373	NM_008265	15401	Mm.439647	NM_008265	ENSMUSG00000000942	Hoxa4	AV206827|Hox-1.4	homeobox A4	protein-coding
mm_43580.1	chr5	137746640	137746651	+	1	NA	intron (NM_029805, intron 1 of 5)	intron (NM_029805, intron 1 of 5)	676	NM_029805	78829	Mm.286399	NM_023910	ENSMUSG00000029723	Tsc22d4	0610009M14Rik|1700023B23Rik|AI415410|Thg-1pit|Tilz2	TSC22 domain family, member 4	protein-coding
mm_61828.1	chr7	88221930	88221934	+	1	NA	Intergenic	Lx2|LINE|L1	-56153	NM_009982	13032	Mm.89295	NM_009982	ENSMUSG00000030560	Ctsc	AI047818|CatC|DPP1|DPPI	cathepsin C	protein-coding
mm_115522.1	chr13	5861157	5861173	-	1	NA	promoter-TSS (NM_011803)	promoter-TSS (NM_011803)	-324	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_166668.1	chr6	90905707	90905718	+	1	NA	Intergenic	CpG	-95589	NM_001134384	232227	Mm.196943	NM_182784	ENSMUSG00000034312	Iqsec1	AW561907|BC026481|BRAG2|D6Ertd349e|cI-43	IQ motif and Sec7 domain 1	protein-coding
mm_36056.1	chr4	57339073	57339083	-	1	NA	Intergenic	Intergenic	25214	NR_038179	73349	Mm.393774	NR_038178		1700042G15Rik	-	RIKEN cDNA 1700042G15 gene	ncRNA
mm_112142.1	chr12	113147510	113147521	-	1	NA	Intergenic	Intergenic	-4497	NM_007763	12925	Mm.272368	NM_007763	ENSMUSG00000006360	Crip1	CRHP|CRP1|Crip	cysteine-rich protein 1 (intestinal)	protein-coding
mm_53414.1	chr6	133105241	133105319	+	1	NA	promoter-TSS (NM_001163445)	promoter-TSS (NM_001163445)	41	NR_073368	381820	Mm.291762	NM_001163445	ENSMUSG00000072704	Smim10l1	2700089E24Rik|AI662692	small integral membrane protein 10 like 1	protein-coding
mm_86259.1	chr9	121592031	121592041	-	1	NA	intron (NR_040740, intron 1 of 3)	intron (NR_040740, intron 1 of 3)	5016	NR_040740	75384	Mm.445955	NR_040740	ENSMUSG00000084995	Lyzl4os	4930589B17Rik|4930596M17Rik	lysozyme-like 4, opposite strand	ncRNA
mm_125767.1	chr15	74563384	74563392	+	1	NA	intron (NM_174991, intron 17 of 30)	intron (NM_174991, intron 17 of 30)	47192	NM_174991	107831	Mm.43133	NM_174991	ENSMUSG00000034730	Adgrb1	B830018M07Rik|Bai1|R75078|mKIAA4089	adhesion G protein-coupled receptor B1	protein-coding
mm_43619.1	chr5	138116912	138116986	+	1	NA	promoter-TSS (NM_011757)	promoter-TSS (NM_011757)	44	NM_001044705	22697	Mm.2760	NM_011757	ENSMUSG00000037017	Zscan21	AI326272|CTfin51|RU49|Zfp-38|Zfp38|Zipro1	zinc finger and SCAN domain containing 21	protein-coding
mm_154018.1	chr19	53313254	53313270	-	1	NA	intron (NM_001008542, intron 1 of 5)	CpG	2756	NM_001008542	17859	Mm.2154	NM_010847	ENSMUSG00000025025	Mxi1	ENSMUSG00000067085|Gm10197|Mad2|bHLHc11	MAX interactor 1, dimerization protein	protein-coding
mm_102864.1	chr11	69405269	69405286	-	1	NA	exon (NM_001017426, exon 11 of 23)	exon (NM_001017426, exon 11 of 23)	-7043	NM_025915	67020	Mm.390406	NM_025915	ENSMUSG00000045377	Tmem88	2600017H02Rik	transmembrane protein 88	protein-coding
mm_34987.1	chr4	156027171	156027175	+	1	NA	intron (NM_021985, intron 1 of 3)	intron (NM_021985, intron 1 of 3)	831	NM_021985	21936	Mm.3180	NM_009400	ENSMUSG00000041954	Tnfrsf18	AITR|Gitr	tumor necrosis factor receptor superfamily, member 18	protein-coding
mm_148961.1	chr19	7494034	7494068	+	1	NA	promoter-TSS (NM_001163505)	promoter-TSS (NM_001163505)	11	NM_001163505	109168	Mm.264016	NM_146091	ENSMUSG00000024759	Atl3	4633402C03Rik|5730596K20Rik|AI465397|AW228836	atlastin GTPase 3	protein-coding
mm_106586.1	chr11	120729675	120729696	-	1	NA	3' UTR (NM_007621, exon 8 of 8)	3' UTR (NM_007621, exon 8 of 8)	2336	NM_007621	12409	Mm.21454	NM_007621	ENSMUSG00000025150	Cbr2	MLCR	carbonyl reductase 2	protein-coding
mm_28883.1	chr3	97868067	97868077	-	1	NA	intron (NM_001039376, intron 1 of 46)	CpG	20635	NM_001289702	83679	Mm.129840	NM_031401	ENSMUSG00000038170	Pde4dip	4732458A06Rik|9430063L05Rik|C87016|D130016K21Rik|D3Bwg1078e|Usmg4|mKIAA0454	phosphodiesterase 4D interacting protein (myomegalin)	protein-coding
mm_58123.1	chr6	140041474	140041476	-	1	NA	promoter-TSS (NM_054066)	promoter-TSS (NM_054066)	-50	NM_007605	12344	Mm.12817	NM_007605	ENSMUSG00000041791	Capza3	510-4|Cappa3|Gsg3|Tex8|repro32	capping protein (actin filament) muscle Z-line, alpha 3	protein-coding
mm_42715.1	chr5	120441300	120441307	+	1	NA	3' UTR (NM_008499, exon 5 of 5)	3' UTR (NM_008499, exon 5 of 5)	9417	NM_008499	16873	Mm.5151	NM_008499	ENSMUSG00000029595	Lhx5	Lim2	LIM homeobox protein 5	protein-coding
mm_130325.1	chr15	97680448	97680471	-	1	NA	exon (NM_028003, exon 14 of 17)	exon (NM_028003, exon 14 of 17)	25363	NM_028003	71919	Mm.12255	NM_028003	ENSMUSG00000022466	Rpap3	2310042P20Rik|D15Ertd682e	RNA polymerase II associated protein 3	protein-coding
mm_126988.1	chr15	94544261	94544268	+	1	NA	promoter-TSS (NM_172437)	promoter-TSS (NM_172437)	604	NM_029926	266632	Mm.422858	NM_029926	ENSMUSG00000059883	Irak4	8430405M07Rik|9330209D03Rik|IRAK-4|NY-REN-64	interleukin-1 receptor-associated kinase 4	protein-coding
mm_100805.1	chr11	5063853	5063885	-	1	NA	exon (NM_001190408, exon 2 of 6)	exon (NM_001190408, exon 2 of 6)	1458	NM_144560	78926	Mm.44591	NM_030228	ENSMUSG00000034201	Gas2l1	4930500E24Rik|D0Jmb1|Gar22|TU-71.1	growth arrest-specific 2 like 1	protein-coding
mm_22057.1	chr2	168590292	168590302	-	1	NA	promoter-TSS (NM_001291176)	promoter-TSS (NM_001291176)	68	NM_001291178	18019	Mm.116802	NM_010899	ENSMUSG00000027544	Nfatc2	AI607462|NF-ATc2|NF-ATp|NFAT1|NFAT1-D|Nfatp	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 2	protein-coding
mm_87998.1	chr10	66968774	66968789	+	1	NA	Intergenic	RMER17C|LTR|ERVK	-36294	NR_110511	102634101	Mm.445258	NR_110511		Gm31763	-	predicted gene, 31763	ncRNA
mm_62827.1	chr7	113514086	113514109	+	1	NA	intron (NM_001285831, intron 1 of 12)	L1M4b|LINE|L1	263	NM_027379	67420	Mm.206919	NM_026143	ENSMUSG00000030759	Far1	2600011M19Rik|2900034E22Rik|3732409C05Rik|AI850429|Mlstd2	fatty acyl CoA reductase 1	protein-coding
mm_65540.1	chr7	26188142	26188150	-	1	NA	intron (NM_010000, intron 4 of 8)	intron (NM_010000, intron 4 of 8)	14737	NM_010000	13094	Mm.14413	NM_010000	ENSMUSG00000040660	Cyp2b9	Cyp2b	cytochrome P450, family 2, subfamily b, polypeptide 9	protein-coding
mm_110980.1	chr12	77056956	77056987	-	1	NA	Intergenic	Intergenic	-94723	NM_001146176	17187	Mm.268548	NM_008558	ENSMUSG00000059436	Max	AA960152|AI875693|bHLHd4|bHLHd5|bHLHd6|bHLHd7|bHLHd8	Max protein	protein-coding
mm_153857.1	chr19	46500941	46500945	-	1	NA	promoter-TSS (NM_053100)	promoter-TSS (NM_053100)	-705	NM_053100	93679	Mm.392177	NM_053100	ENSMUSG00000025034	Trim8	AA408830|BB006755|GERP|Rnf27	tripartite motif-containing 8	protein-coding
mm_52783.1	chr6	121256878	121256899	+	1	NA	intron (NM_011909, intron 4 of 10)	L1M2|LINE|L1	10982	NM_011909	24110	Mm.326911	NM_011909	ENSMUSG00000030107	Usp18	1110058H21Rik|AW047653|UBP43|Ubp15	ubiquitin specific peptidase 18	protein-coding
mm_63452.1	chr7	127512404	127512496	+	1	NA	non-coding (NR_024331, exon 1 of 1)	non-coding (NR_024331, exon 1 of 1)	419	NR_024331	629159	Mm.256720	NR_024331	ENSMUSG00000101225	1700008J07Rik	AW048743	RIKEN cDNA 1700008J07 gene	ncRNA
mm_68695.1	chr7	119615713	119615716	-	1	NA	Intergenic	Intergenic	-2114	NM_054094	117147	Mm.427560	NM_054094	ENSMUSG00000033533	Acsm1	Acas3|Bucs1|Macs	acyl-CoA synthetase medium-chain family member 1	protein-coding
mm_124953.1	chr15	12833534	12833591	+	1	NA	intron (NM_001130149, intron 3 of 34)	(CGTG)n|Simple_repeat|Simple_repeat	8747	NM_001130149	14000	Mm.293142	NM_026799	ENSMUSG00000022191	Drosha	1110013A17Rik|AI874853|Etohi2|Rn3|Rnasen	drosha, ribonuclease type III	protein-coding
mm_16388.1	chr2	178494343	178494382	+	1	NA	Intergenic	Intergenic	63847	NM_198656	381409	Mm.330860	NM_198656	ENSMUSG00000039155	Cdh26	Gm1010	cadherin-like 26	protein-coding
mm_30698.1	chr4	11694836	11694842	+	1	NA	Intergenic	Intergenic	-9608	NM_010276	14579	Mm.247486	NM_010276	ENSMUSG00000028214	Gem	AV020497	GTP binding protein (gene overexpressed in skeletal muscle)	protein-coding
mm_160501.1	chr9	15307726	15307726	+	1	NA	intron (NM_029248, intron 1 of 6)	intron (NM_029248, intron 1 of 6)	-1278	NM_001199484	70984	Mm.261842	NM_133732	ENSMUSG00000031938	4931406C07Rik	-	RIKEN cDNA 4931406C07 gene	protein-coding
mm_52727.1	chr6	120112696	120112748	+	1	NA	intron (NM_016718, intron 1 of 3)	intron (NM_016718, intron 1 of 3)	19342	NM_016718	29862	Mm.103668	NM_016718	ENSMUSG00000041377	Ninj2	-	ninjurin 2	protein-coding
mm_9359.1	chr1	172198064	172198079	-	1	NA	3' UTR (NM_001329871, exon 4 of 4)	3' UTR (NM_001329871, exon 4 of 4)	8733	NM_001329871	18611	Mm.544	NM_011063	ENSMUSG00000013698	Pea15a	Mat1|PEA-15|Pea15|Pkcs15	phosphoprotein enriched in astrocytes 15A	protein-coding
mm_19194.1	chr2	84434289	84434300	-	1	NA	exon (NM_011576, exon 8 of 9)	exon (NM_011576, exon 8 of 9)	-9028	NM_018782	54598	Mm.75467	NM_018782	ENSMUSG00000059588	Calcrl	AV071593|CRLR	calcitonin receptor-like	protein-coding
mm_64439.1	chr7	142653640	142653661	+	1	NA	3' UTR (NM_010514, exon 4 of 4)	3' UTR (NM_010514, exon 4 of 4)	1346	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_4739.1	chr1	181853269	181853279	+	1	NA	Intergenic	Intergenic	-10873	NM_133815	98386	Mm.4538	NM_133815	ENSMUSG00000004880	Lbr	AI505894|ic	lamin B receptor	protein-coding
mm_13888.1	chr2	120033430	120033447	+	1	NA	promoter-TSS (NM_145378)	promoter-TSS (NM_145378)	5	NM_145378	211429	Mm.41467	NM_145378	ENSMUSG00000098488	Pla2g4b	A030011C02Rik|Gm1013|cPLA2-beta	phospholipase A2, group IVB (cytosolic)	protein-coding
mm_27388.1	chr3	50628520	50628534	-	1	NA	Intergenic	Intergenic	-184914	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_85971.1	chr9	112157380	112157383	-	1	NA	intron (NM_001177619, intron 10 of 10)	intron (NM_001177619, intron 10 of 10)	28568	NM_001177618	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_8593.1	chr1	156006213	156006231	-	1	NA	3' UTR (NM_144791, exon 7 of 7)	3' UTR (NM_144791, exon 7 of 7)	28595	NM_001160019	208263	Mm.211654	NM_144791	ENSMUSG00000026466	Tor1aip1	LAP1|Lap1B	torsin A interacting protein 1	protein-coding
mm_126655.1	chr15	84192262	84192286	+	1	NA	promoter-TSS (NM_178614)	promoter-TSS (NM_178614)	41	NM_178614	68653	Mm.290725	NM_178614	ENSMUSG00000022437	Samm50	1110030L07Rik	SAMM50 sorting and assembly machinery component	protein-coding
mm_92919.1	chr10	84440506	84440517	-	1	NA	promoter-TSS (NM_001004363)	promoter-TSS (NM_001004363)	-40	NM_001004363	77976	Mm.25874	NM_001004363	ENSMUSG00000020032	Nuak1	AU014801|AW494241|B230104P22Rik|Omphk1	NUAK family, SNF1-like kinase, 1	protein-coding
mm_158123.1	chrX	102505139	102505171	-	1	NA	promoter-TSS (NM_001313742)	promoter-TSS (NM_001313742)	3	NM_001313742	70315	Mm.328128	NM_027382	ENSMUSG00000067567	Hdac8	2610007D20Rik	histone deacetylase 8	protein-coding
mm_87287.1	chr10	42349876	42349876	+	1	NA	intron (NM_145743, intron 8 of 12)	L1M4|LINE|L1	-73134	NM_019740	56484	Mm.338613	NM_019740	ENSMUSG00000048756	Foxo3	1110048B16Rik|2010203A17Rik|C76856|FKHRL1|Fkhr2|Foxo3a	forkhead box O3	protein-coding
mm_59893.1	chr7	30307208	30307230	+	1	NA	3' UTR (NM_001081114, exon 14 of 14)	3' UTR (NM_001081114, exon 14 of 14)	-1534	NM_198027	233065	Mm.276277	NM_198027	ENSMUSG00000042831	Alkbh6	AI839550|Abh6|C130099A02	alkB homolog 6	protein-coding
mm_91789.1	chr10	53349782	53349810	-	1	NA	intron (NM_001204983, intron 2 of 12)	Lx8|LINE|L1	12110	NM_001141927	18821	Mm.34145	NM_023129	ENSMUSG00000038583	Pln	Plb	phospholamban	protein-coding
mm_113232.1	chr13	27243787	27243789	+	1	NA	exon (NM_008865, exon 2 of 5)	exon (NM_008865, exon 2 of 5)	1358	NM_008865	18776	Mm.37203	NM_008865	ENSMUSG00000038891	Prl3b1	Csh2|Ghd8|PL|Pl-2|Pl2|mPL-II|mplII	prolactin family 3, subfamily b, member 1	protein-coding
mm_105149.1	chr11	101462544	101462561	-	1	NA	exon (NM_012037, exon 3 of 6)	exon (NM_012037, exon 3 of 6)	3647	NM_012037	26949	Mm.29210	NM_012037	ENSMUSG00000034993	Vat1	VAT-1	vesicle amine transport 1	protein-coding
mm_78810.1	chr9	44068150	44068165	+	1	NA	intron (NM_198092, intron 1 of 12)	intron (NM_198092, intron 1 of 12)	1136	NM_198092	53376	Mm.272770	NM_016808	ENSMUSG00000032010	Usp2	B930035K21Rik|Ubp41	ubiquitin specific peptidase 2	protein-coding
mm_114412.1	chr13	64276259	64276262	+	1	NA	Intergenic	B1F|SINE|Alu	-1272	NM_172587	218294	Mm.25335	NM_172587	ENSMUSG00000033102	Cdc14b	2810432N10Rik|A530086E13Rik|AA472821|CDC14B3|Cdc14B1	CDC14 cell division cycle 14B	protein-coding
mm_18775.1	chr2	73529546	73529569	-	1	NA	promoter-TSS (NM_153138)	promoter-TSS (NM_153138)	-70	NM_153138	215280	Mm.223504	NM_153138	ENSMUSG00000075284	Wipf1	AI115543|D2Ertd120e|WIP|Waspip	WAS/WASL interacting protein family, member 1	protein-coding
mm_72777.1	chr8	86624065	86624161	+	1	NA	promoter-TSS (NM_025827)	promoter-TSS (NM_025827)	70	NM_025827	66887	Mm.324550	NM_025827	ENSMUSG00000047866	Lonp2	1300002A08Rik|AU015403|Lonp	lon peptidase 2, peroxisomal	protein-coding
mm_55321.1	chr6	55175020	55175036	-	1	NA	promoter-TSS (NM_009349)	promoter-TSS (NM_009349)	-38	NM_009349	21743	Mm.299	NM_009349	ENSMUSG00000003477	Inmt	Temt	indolethylamine N-methyltransferase	protein-coding
mm_72870.1	chr8	88662552	88662578	+	1	NA	intron (NM_145857, intron 3 of 12)	intron (NM_145857, intron 3 of 12)	15218	NM_145857	257632	Mm.222633	NM_145857	ENSMUSG00000055994	Nod2	ACUG|BLAU|CD|Card15|F830032C23Rik|IBD1|Nlrc2	nucleotide-binding oligomerization domain containing 2	protein-coding
mm_130175.1	chr15	93336901	93336915	-	1	NA	promoter-TSS (NM_024189)	promoter-TSS (NM_024189)	27	NR_028315	67057	Mm.4714	NM_024189	ENSMUSG00000022634	Yaf2	2810021M11Rik	YY1 associated factor 2	protein-coding
mm_12957.1	chr2	90373183	90373211	+	1	NA	Intergenic	Intergenic	-27443	NM_146263	258330	Mm.330392	NM_146263	ENSMUSG00000082980	Olfr1274-ps	GA_x5J8B7W2BV0-3116-4045|MOR228-4|MOR228-5|Olfr1274	olfactory receptor 1274, pseudogene	protein-coding
mm_40137.1	chr5	35056851	35056895	+	1	NA	promoter-TSS (NM_172708)	promoter-TSS (NM_172708)	-211	NM_172708	231134	Mm.205483	NM_172708	ENSMUSG00000044716	Dok7	A930013K19Rik|AW049091|Dok-7|EF-12|Oit5	docking protein 7	protein-coding
mm_111435.1	chr12	91849082	91849154	-	1	NA	promoter-TSS (NM_011344)	promoter-TSS (NM_011344)	39	NM_001039089	20338	Mm.250605	NM_011344	ENSMUSG00000020964	Sel1l	AW493766|Sel1h|mKIAA4137	sel-1 suppressor of lin-12-like (C. elegans)	protein-coding
mm_48673.1	chr5	146009702	146009714	-	1	NA	promoter-TSS (NM_019792)	promoter-TSS (NM_019792)	-90	NR_030782	56388	Mm.301900	NM_019792	ENSMUSG00000029630	Cyp3a25	AI327008	cytochrome P450, family 3, subfamily a, polypeptide 25	protein-coding
mm_134608.1	chr16	20717225	20717236	-	1	NA	promoter-TSS (NM_009900)	promoter-TSS (NM_009900)	-594	NM_009900	12724	Mm.177761	NM_009900	ENSMUSG00000022843	Clcn2	AL118368|ClC-2|Clc2|nmf240	chloride channel, voltage-sensitive 2	protein-coding
mm_168208.1	chr10	72309200	72309213	+	1	NA	Intergenic	Intergenic	-328516	NR_003644	108950	Mm.212793	NM_175390	ENSMUSG00000043859	1700049L16Rik	-	hematological and neurological expressed 1-like pseudogene	pseudo
mm_27325.1	chr3	50367732	50367742	-	1	NA	3' UTR (NM_011990, exon 12 of 12)	3' UTR (NM_011990, exon 12 of 12)	75876	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_30570.1	chr4	3792612	3792615	+	1	NA	Intergenic	Intergenic	43042	NM_026147	67427	Mm.21938	NM_026147	ENSMUSG00000028234	Rps20	4632426K06Rik|Dsk4	ribosomal protein S20	protein-coding
mm_169923.1	chr16	57391374	57391381	-	1	NA	intron (NM_001040397, intron 1 of 4)	LSU-rRNA_Hsa|rRNA|rRNA	38100	NM_001040397	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding
mm_23102.1	chr3	37348646	37348716	+	1	NA	promoter-TSS (NM_008006)	promoter-TSS (NM_008006)	28	NM_008006	14173	Mm.473689	NM_008006	ENSMUSG00000037225	Fgf2	Fgf-2|Fgfb|bFGF	fibroblast growth factor 2	protein-coding
mm_50550.1	chr6	49047307	49047323	+	1	NA	exon (NM_053110, exon 5 of 11)	exon (NM_053110, exon 5 of 11)	10797	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_135937.1	chr16	74279416	74279454	-	1	NA	intron (NM_175549, intron 2 of 27)	intron (NM_175549, intron 2 of 27)	62632	NR_030464	751561		NR_030464	ENSMUSG00000104758	Mir691	Mirn691|mir-691|mmu-mir-691	microRNA 691	ncRNA
mm_98867.1	chr11	97799325	97799335	+	1	NA	promoter-TSS (NM_010688)	promoter-TSS (NM_010688)	-342	NM_010688	16796	Mm.271967	NM_010688	ENSMUSG00000038366	Lasp1	AA408629|Def-4|SH3P6|Tg(Col1a1-lacZ)1Ngma	LIM and SH3 protein 1	protein-coding
mm_18924.1	chr2	76743817	76743824	-	1	NA	exon (NM_011652, exon 275 of 313)	exon (NM_011652, exon 275 of 313)	68505	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_38997.1	chr4	151154477	151154483	-	1	NA	intron (NM_001081557, intron 7 of 23)	intron (NM_001081557, intron 7 of 23)	64910	NM_001308446	105704528	Mm.415128	NM_001308446	ENSMUSG00000078491	Gm13090	OTTMUSG00000010356	predicted gene 13090	protein-coding
mm_91010.1	chr10	14747382	14747383	-	1	NA	intron (NR_045824, intron 3 of 5)	intron (NR_045824, intron 3 of 5)	-12907	NM_008703	18101	Mm.487342	NM_008703	ENSMUSG00000019865	Nmbr	BB182387	neuromedin B receptor	protein-coding
mm_74293.1	chr8	125995140	125995185	+	1	NA	promoter-TSS (NM_008430)	promoter-TSS (NM_008430)	60	NM_008430	16525	Mm.10800	NM_008430	ENSMUSG00000033998	Kcnk1	AI788889|TWIK-1	potassium channel, subfamily K, member 1	protein-coding
mm_30731.1	chr4	13790750	13790750	+	1	NA	intron (NM_009822, intron 1 of 10)	intron (NM_009822, intron 1 of 10)	5968	NM_009822	12395	Mm.4909	NM_009822	ENSMUSG00000006586	Runx1t1	Cbfa2t1h|ETO|MTG8	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	protein-coding
mm_44080.1	chr5	149137065	149137078	+	1	NA	intron (NR_015478, intron 1 of 2)	intron (NR_015478, intron 1 of 2)	-7192	NR_137278	105242579	Mm.445929	NR_137278	ENSMUSG00000107388	Gm42788	-	predicted gene 42788	ncRNA
mm_119080.1	chr14	30886412	30886424	+	1	NA	promoter-TSS (NM_001289633)	promoter-TSS (NM_001289633)	-58	NM_001159299	16427	Mm.34819	NM_018746	ENSMUSG00000021922	Itih4	ITI-HC4|Itih-4|PK-120	inter alpha-trypsin inhibitor, heavy chain 4	protein-coding
mm_28903.1	chr3	98339922	98339945	-	1	NA	promoter-TSS (NM_016966)	promoter-TSS (NM_016966)	36	NM_016966	236539	Mm.16898	NM_016966	ENSMUSG00000053398	Phgdh	3-PGDH|3PGDH|4930479N23|A10|PGAD|PGD|PGDH|SERA	3-phosphoglycerate dehydrogenase	protein-coding
mm_50072.1	chr6	41281268	41281304	+	1	NA	Intergenic	Intergenic	-20986	NM_011646	22074	Mm.383263	NM_011646	ENSMUSG00000054106	Try4	0910001B19Rik|Td	trypsin 4	protein-coding
mm_77296.1	chr8	116993440	116993456	-	1	NA	promoter-TSS (NM_026572)	promoter-TSS (NM_026572)	1	NM_026572	68133	Mm.258462	NM_026572	ENSMUSG00000034424	Gcsh	1100001L02Rik|5730591C18Rik	glycine cleavage system protein H (aminomethyl carrier)	protein-coding
mm_117358.1	chr13	70028343	70028356	-	1	NA	promoter-TSS (NR_045965)	promoter-TSS (NR_045965)	-1	NR_045965	74280	Mm.273343	NR_045965	ENSMUSG00000099639	1700084F23Rik	1700003E18Rik|4930589D02Rik	RIKEN cDNA 1700084F23 gene	ncRNA
mm_10993.1	chr2	26319742	26319757	+	1	NA	promoter-TSS (NM_001199147)	promoter-TSS (NM_001199147)	-21	NM_001199147	67839	Mm.266611	NM_153410	ENSMUSG00000026930	Gpsm1	1810037C22Rik|AW107933|Ags3	G-protein signalling modulator 1 (AGS3-like, C. elegans)	protein-coding
mm_107021.1	chr12	12784670	12784680	+	1	NA	Intergenic	Intergenic	-114758	NR_136889	102637952	Mm.421393	NR_136889		Gm34637	-	predicted gene, 34637	ncRNA
mm_127299.1	chr15	100202101	100202107	+	1	NA	intron (NM_001159361, intron 30 of 37)	intron (NM_001159361, intron 30 of 37)	-14068	NR_037311	100499528		NR_037311	ENSMUSG00000092752	Mir3473a	Mir3473|mir-3473a|mmu-mir-3473|mmu-mir-3473a	microRNA 3473a	ncRNA
mm_68373.1	chr7	108924392	108924395	-	1	NA	exon (NM_175532, exon 3 of 3)	exon (NM_175532, exon 3 of 3)	5765	NM_175532	244202	Mm.37991	NM_175532	ENSMUSG00000049709	Nlrp10	6430548I20Rik|Nalp10|Napl10|PAN5|Pynod	NLR family, pyrin domain containing 10	protein-coding
mm_105768.1	chr11	109611418	109611426	-	1	NA	promoter-TSS (NM_145940)	promoter-TSS (NM_145940)	-33	NM_145940	52639	Mm.35817	NM_145940	ENSMUSG00000041895	Wipi1	4930533H01Rik|AW411817|D11Ertd498e	WD repeat domain, phosphoinositide interacting 1	protein-coding
mm_136569.1	chr17	3397221	3397242	+	1	NA	promoter-TSS (NM_011878)	promoter-TSS (NM_011878)	24	NM_011878	24001	Mm.137134	NM_011878	ENSMUSG00000023800	Tiam2	3000002F19Rik|STEF|mKIAA2016	T cell lymphoma invasion and metastasis 2	protein-coding
mm_120712.1	chr14	72584652	72584678	+	1	NA	exon (NM_207636, exon 6 of 26)	exon (NM_207636, exon 6 of 26)	125338	NM_207636	319448	Mm.205421	NM_207636	ENSMUSG00000033487	Fndc3a	1700094E19Rik|D14Ertd453e|F730017H24Rik|Fndc3|sys	fibronectin type III domain containing 3A	protein-coding
mm_22052.1	chr2	168508173	168508221	-	1	NA	intron (NM_001291174, intron 6 of 10)	intron (NM_001291174, intron 6 of 10)	82168	NM_001291178	18019	Mm.116802	NM_010899	ENSMUSG00000027544	Nfatc2	AI607462|NF-ATc2|NF-ATp|NFAT1|NFAT1-D|Nfatp	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 2	protein-coding
mm_37121.1	chr4	116651645	116651665	-	1	NA	promoter-TSS (NM_021473)	promoter-TSS (NM_021473)	19	NM_021473	58810	Mm.30085	NM_021473	ENSMUSG00000028692	Akr1a1	2610201A18Rik|Akr1a4	aldo-keto reductase family 1, member A1 (aldehyde reductase)	protein-coding
mm_119680.1	chr14	53042354	53042360	+	1	NA	Intergenic	Intergenic	-546662	NM_001170918	57269	Mm.88822	NM_020512	ENSMUSG00000059887	Olfr1507	MOR244-1|Mor28|Or28	olfactory receptor 1507	protein-coding
mm_80315.1	chr9	74861876	74861884	+	1	NA	promoter-TSS (NM_008262)	promoter-TSS (NM_008262)	-41	NM_008262	15379	Mm.303355	NM_008262	ENSMUSG00000043013	Onecut1	D9Ertd423e|HNF-6|Hfh12|Hnf6|Hnf6b|OC-1|Oc1	one cut domain, family member 1	protein-coding
mm_59567.1	chr7	28093581	28093606	+	1	NA	exon (NM_001122603, exon 8 of 20)	exon (NM_001122603, exon 8 of 20)	22357	NM_001122603	215384	Mm.292276	NM_175444	ENSMUSG00000047730	Fcgbp	A430096B05Rik	Fc fragment of IgG binding protein	protein-coding
mm_28649.1	chr3	95228594	95228631	-	1	NA	promoter-TSS (NM_019914)	promoter-TSS (NM_019914)	65	NM_019914	56772	Mm.331208	NM_019914	ENSMUSG00000053192	Mllt11	AI839562|Af1q|Zfp692	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 11	protein-coding
mm_157508.1	chrX	49084443	49084450	-	1	NA	intron (NM_001271448, intron 2 of 14)	B4A|SINE|B4	203796	NM_001271449	209224	Mm.327730	NM_145951	ENSMUSG00000031109	Enox2	APK1|Cova1|tNOX	ecto-NOX disulfide-thiol exchanger 2	protein-coding
mm_159345.1	chr3	63296046	63296046	+	1	NA	promoter-TSS (NM_001289463)	promoter-TSS (NM_001289463)	-49	NM_001289463	17380	Mm.296022	NM_008604	ENSMUSG00000027820	Mme	6030454K05Rik|C85356|CALLA|CD10|NEP|SFE	membrane metallo endopeptidase	protein-coding
mm_99125.1	chr11	100206751	100206757	+	1	NA	promoter-TSS (NM_001313957)	promoter-TSS (NM_001313957)	-724	NM_001313957	16664	Mm.439898	NM_016958	ENSMUSG00000045545	Krt14	AI626930|CK-14|K14|Krt-1.14|Krt1-14	keratin 14	protein-coding
mm_62077.1	chr7	92875267	92875284	+	1	NA	promoter-TSS (NM_028243)	promoter-TSS (NM_028243)	22	NM_028243	72461	Mm.389969	NM_028243	ENSMUSG00000061119	Prcp	2510048K03Rik|2610104A14Rik|AI451719|HUMPCP|PCP	prolylcarboxypeptidase (angiotensinase C)	protein-coding
mm_61521.1	chr7	78913927	78913949	+	1	NA	promoter-TSS (NM_001113527)	promoter-TSS (NM_001113527)	173	NM_020583	57444	Mm.322843	NM_020583	ENSMUSG00000039236	Isg20	1600023I01Rik|2010107M23Rik|20kDa|DnaQL|HEM45	interferon-stimulated protein	protein-coding
mm_147851.1	chr18	63692292	63692302	-	1	NA	promoter-TSS (NM_016792)	promoter-TSS (NM_016792)	62	NM_016792	53382	Mm.19169	NM_016792	ENSMUSG00000024583	Txnl1	32kDa|TRP32|Txnl	thioredoxin-like 1	protein-coding
mm_50541.1	chr6	49046178	49046191	+	1	NA	intron (NM_053110, intron 4 of 10)	intron (NM_053110, intron 4 of 10)	9666	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_94587.1	chr11	11719763	11719776	+	1	NA	intron (NM_001301866, intron 3 of 5)	intron (NM_001301866, intron 3 of 5)	29592	NM_001301863	22778	Mm.103545	NM_009578	ENSMUSG00000018654	Ikzf1	5832432G11Rik|Ikaros|LyF-1|Zfpn1a1|Znfn1a1|hlk-1|mKIAA4227	IKAROS family zinc finger 1	protein-coding
mm_139425.1	chr17	53491364	53491393	+	1	NA	intron (NM_025887, intron 2 of 5)	B2_Mm1t|SINE|B2	12144	NM_025887	271457	Mm.329123	NM_025887	ENSMUSG00000017831	Rab5a	2410015H04Rik|AI663973|AU021172|nnyRab5a	RAB5A, member RAS oncogene family	protein-coding
mm_144218.1	chr18	9746673	9746683	+	1	NA	intron (NM_130449, intron 2 of 9)	L1_Mur2|LINE|L1	39030	NM_130449	140792	Mm.218571	NM_130449	ENSMUSG00000036103	Colec12	CL-P1|SRCL|Scara4	collectin sub-family member 12	protein-coding
mm_89483.1	chr10	93641006	93641034	+	1	NA	promoter-TSS (NM_021320)	promoter-TSS (NM_021320)	-29	NM_021320	57764	Mm.483868	NM_021320	ENSMUSG00000020019	Ntn4	-	netrin 4	protein-coding
mm_40139.1	chr5	35098148	35098167	+	1	NA	exon (NM_013587, exon 4 of 8)	exon (NM_013587, exon 4 of 8)	7540	NM_013587	16976	Mm.277661	NM_013587	ENSMUSG00000029103	Lrpap1	AA617339|AI790446|AU042172|C77774|HBP44|RAP	low density lipoprotein receptor-related protein associated protein 1	protein-coding
mm_48531.1	chr5	142903910	142903932	-	1	NA	exon (NM_007393, exon 6 of 6)	exon (NM_007393, exon 6 of 6)	2833	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_171387.1	chr4	12136470	12136480	-	1	NA	Intergenic	MMVL30-int|LTR|ERV1	-3642	NM_028226	72397	Mm.430709	NM_028226	ENSMUSG00000046667	Rbm12b1	3000004N20Rik|Rbm12b|Rbm12ba	RNA binding motif protein 12 B1	protein-coding
mm_73169.1	chr8	95020790	95020819	+	1	NA	intron (NM_173036, intron 1 of 11)	intron (NM_173036, intron 1 of 11)	3112	NM_173036	54672	Mm.27995	NM_173036	ENSMUSG00000060470	Adgrg3	A030001G24Rik|AW214383|Gpr97|Pb1|Pb99	adhesion G protein-coupled receptor G3	protein-coding
mm_75132.1	chr8	34965632	34965714	-	1	NA	promoter-TSS (NM_175091)	promoter-TSS (NM_175091)	17	NM_175091	21951	Mm.88364	NM_175091	ENSMUSG00000031529	Tnks	4930554K12Rik|AI662855|ARTD5|C86528|D130072O21Rik|TANK1|mTNKS1	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase	protein-coding
mm_6103.1	chr1	64030264	64030273	-	1	NA	Intergenic	Intergenic	12233	NR_105864	102466760		NR_105864	ENSMUSG00000098487	Mir6899	Gm27384|mmu-mir-6899	microRNA 6899	ncRNA
mm_111302.1	chr12	85639022	85639046	-	1	NA	3' UTR (NM_001205053, exon 4 of 4)	3' UTR (NM_001205053, exon 4 of 4)	39016	NM_001205053	81703	Mm.103560	NM_030887	ENSMUSG00000034271	Jdp2	Jundm2|Jundp2|TIF	Jun dimerization protein 2	protein-coding
mm_115960.1	chr13	23763503	23763514	-	1	NA	promoter-TSS (NM_030609)	promoter-TSS (NM_030609)	-160	NM_030609	80838	Mm.480242	NM_030609	ENSMUSG00000049539	Hist1h1a	H1.1|H1a|H1f1|H1var3	histone cluster 1, H1a	protein-coding
mm_102487.1	chr11	60222757	60222774	-	1	NA	Intergenic	CpG	-2138	NM_001313979	20787	Mm.278701	NM_011480	ENSMUSG00000020538	Srebf1	ADD1|SREBP-1a|SREBP1|SREBP1c|bHLHd1	sterol regulatory element binding transcription factor 1	protein-coding
mm_9203.1	chr1	171229677	171229685	-	1	NA	3' UTR (NM_010185, exon 5 of 5)	3' UTR (NM_010185, exon 5 of 5)	4627	NM_013474	11807	Mm.389209	NM_013474	ENSMUSG00000005681	Apoa2	Alp-2|Apo-AII|ApoA-II|ApoAII|Apoa-2|Hdl-1	apolipoprotein A-II	protein-coding
mm_73674.1	chr8	111536158	111536186	+	1	NA	promoter-TSS (NM_133206)	promoter-TSS (NM_133206)	-468	NM_001168622	170737	Mm.271578	NM_133206	ENSMUSG00000033545	Znrf1	B830022L21Rik|Rnf42|Zrfp1|nin283	zinc and ring finger 1	protein-coding
mm_117104.1	chr13	60175207	60175224	-	1	NA	3' UTR (NM_008086, exon 1 of 1)	3' UTR (NM_008086, exon 1 of 1)	2320	NM_008086	14451	Mm.22701	NM_008086	ENSMUSG00000052957	Gas1	AW554192|Gas-1	growth arrest specific 1	protein-coding
mm_4591.1	chr1	178336104	178336137	+	1	NA	exon (NM_016805, exon 2 of 14)	exon (NM_016805, exon 2 of 14)	1664	NM_016805	51810	Mm.86589	NM_016805	ENSMUSG00000039630	Hnrnpu	AA408410|AI256620|AL024194|AL024437|AW557595|C86794|Hnrpu|SAFA|Sp120|hnRNP U	heterogeneous nuclear ribonucleoprotein U	protein-coding
mm_13817.1	chr2	119237391	119237420	+	1	NA	promoter-TSS (NM_016907)	promoter-TSS (NM_016907)	45	NM_016907	20732	Mm.104955	NM_016907	ENSMUSG00000027315	Spint1	HAI-1	serine protease inhibitor, Kunitz type 1	protein-coding
mm_62393.1	chr7	101092829	101092859	+	1	NA	Intergenic	Intergenic	-15931	NM_001146010	207278	Mm.263041	NM_199012	ENSMUSG00000030691	Fchsd2	BC034086|R74866|Sh3md3|mKIAA0769	FCH and double SH3 domains 2	protein-coding
mm_88733.1	chr10	80249132	80249154	+	1	NA	promoter-TSS (NM_029272)	promoter-TSS (NM_029272)	-309	NM_029272	75406	Mm.28712	NM_029272	ENSMUSG00000020153	Ndufs7	1010001M04Rik	NADH dehydrogenase (ubiquinone) Fe-S protein 7	protein-coding
mm_49196.1	chr6	15197032	15197042	+	1	NA	exon (NM_001286607, exon 2 of 17)	exon (NM_001286607, exon 2 of 17)	11531	NM_001286607	114142	Mm.332919	NM_053242	ENSMUSG00000029563	Foxp2	2810043D05Rik|AI449000|CAG-16|D0Kist7	forkhead box P2	protein-coding
mm_158236.1	chrX	106485215	106485259	-	1	NA	promoter-TSS (NM_001007580)	promoter-TSS (NM_001007580)	-8	NM_001007580	333564	Mm.298000	NM_001007580	ENSMUSG00000033737	Fndc3c1	Fndc3c|Gm784	fibronectin type III domain containing 3C1	protein-coding
mm_134852.1	chr16	28219831	28219837	-	1	NA	intron (NM_001276419, intron 3 of 4)	Lx7|LINE|L1	226241	NM_183064	14167	Mm.7996	NM_010199	ENSMUSG00000022523	Fgf12	AV114868|B230343J05Rik|FGF-12|FHF-1|Fhf1	fibroblast growth factor 12	protein-coding
mm_101701.1	chr11	40755202	40755288	-	1	NA	promoter-TSS (NM_009831)	promoter-TSS (NM_009831)	41	NM_009831	12450	Mm.2103	NM_009831	ENSMUSG00000020326	Ccng1	AI314029	cyclin G1	protein-coding
mm_22858.1	chr3	28695707	28695741	+	1	NA	Intergenic	Intergenic	-2179	NM_031197	20526	Mm.18443	NM_031197	ENSMUSG00000027690	Slc2a2	AI266973|Glut-2|Glut2	solute carrier family 2 (facilitated glucose transporter), member 2	protein-coding
mm_30693.1	chr4	11573618	11573620	+	1	NA	intron (NM_001039556, intron 3 of 14)	intron (NM_001039556, intron 3 of 14)	-6043	NM_001256142	100503583	Mm.249437	NM_001256142	ENSMUSG00000094595	Fsbp	-	fibrinogen silencer binding protein	protein-coding
mm_112182.1	chr12	113422202	113422229	-	1	NA	Intergenic	Intergenic	-67350	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_88443.1	chr10	77547152	77547187	+	1	NA	exon (NM_008404, exon 5 of 16)	exon (NM_008404, exon 5 of 16)	16821	NM_008404	16414	Mm.1137	NM_008404	ENSMUSG00000000290	Itgb2	2E6|AI528527|Cd18|LAD|LCAMB|Lfa1|MF17	integrin beta 2	protein-coding
mm_163961.1	chr14	54966271	54966302	-	1	NA	intron (NM_001164171, intron 1 of 38)	intron (NM_001164171, intron 1 of 38)	321	NM_001164171	17888	Mm.290003	NM_010856	ENSMUSG00000040752	Myh6	A830009F23Rik|AA517445|Myhc-a|Myhca|alpha-MHC	myosin, heavy polypeptide 6, cardiac muscle, alpha	protein-coding
mm_73546.1	chr8	108812086	108812094	+	1	NA	intron (NM_007496, intron 3 of 9)	intron (NM_007496, intron 3 of 9)	97446	NM_007496	11906	Mm.416972	NM_007496	ENSMUSG00000038872	Zfhx3	A230102L03Rik|Atbf1|Sci|WBP9|mKIAA4228	zinc finger homeobox 3	protein-coding
mm_148183.1	chr18	78206397	78206407	-	1	NA	promoter-TSS (NM_001110274)	promoter-TSS (NM_001110274)	38	NM_001110274	27411	Mm.44158	NM_030683	ENSMUSG00000024552	Slc14a2	UT-A1|UT-A3	solute carrier family 14 (urea transporter), member 2	protein-coding
mm_72688.1	chr8	84969619	84969636	+	1	NA	promoter-TSS (NM_011563)	promoter-TSS (NM_011563)	5	NM_011563	21672	Mm.347009	NM_011563	ENSMUSG00000005161	Prdx2	AL022839|Band-8|NkefB|PRP|PrxII|TDX1|TPx|TPx-B|TR|TSA|Tdpx1|Torin	peroxiredoxin 2	protein-coding
mm_138.1	chr1	10880286	10880291	+	1	NA	Intergenic	RLTR41|LTR|ERV1	-14414	NR_030645	100124448		NR_030645	ENSMUSG00000076948	Mir467e	Mirn467e	microRNA 467e	ncRNA
mm_114328.1	chr13	60636542	60636555	+	1	NA	intron (NM_029653, intron 2 of 25)	B3|SINE|B2	34337	NM_134062	69635	Mm.24103	NM_029653	ENSMUSG00000021559	Dapk1	D13Ucla1|DAP-Kinase	death associated protein kinase 1	protein-coding
mm_66514.1	chr7	45103200	45103228	-	1	NA	5' UTR (NM_010189, exon 2 of 7)	5' UTR (NM_010189, exon 2 of 7)	608	NM_010189	14132	Mm.3303	NM_010189	ENSMUSG00000003420	Fcgrt	FcRn	Fc receptor, IgG, alpha chain transporter	protein-coding
mm_93399.1	chr10	107719894	107719900	-	1	NA	5' UTR (NM_001081432, exon 1 of 45)	5' UTR (NM_001081432, exon 1 of 45)	130	NM_001081432	237523	Mm.391418	NM_001081432	ENSMUSG00000035916	Ptprq	-	protein tyrosine phosphatase, receptor type, Q	protein-coding
mm_24166.1	chr3	88537365	88537377	+	1	NA	promoter-TSS (NR_035434)	promoter-TSS (NR_035434)	-989	NR_035434	100316808		NR_035434	ENSMUSG00000084728	Mir1905	Mirn1905|mmu-mir-1905	microRNA 1905	ncRNA
mm_109668.1	chr12	113050531	113050539	+	1	NA	exon (NM_001291445, exon 5 of 23)	exon (NM_001291445, exon 5 of 23)	-23967	NM_029381	75671	Mm.23377	NM_029381	ENSMUSG00000012211	Tex22	1700028O09Rik|AV210422|Tep22	testis expressed gene 22	protein-coding
mm_122353.1	chr14	38881000	38881016	-	1	NA	intron (NM_001190187, intron 2 of 9)	intron (NM_001190187, intron 2 of 9)	-17294	NR_045713	75170	Mm.372967	NR_045713	ENSMUSG00000093528	Nrg3os	4930529F24Rik	neuregulin 3, opposite strand	ncRNA
mm_148340.1	chr18	84589461	84589486	-	1	NA	promoter-TSS (NM_001033341)	promoter-TSS (NM_001033341)	31	NM_001033341	240476	Mm.329575	NM_001033341	ENSMUSG00000048410	Zfp407	6430585N13Rik|Gm333|Gm334|Gm948|ZNF407	zinc finger protein 407	protein-coding
mm_153441.1	chr19	40994212	40994227	-	1	NA	5' UTR (NM_008528, exon 1 of 17)	5' UTR (NM_008528, exon 1 of 17)	316	NM_008528	17060	Mm.9749	NM_008528	ENSMUSG00000061132	Blnk	BASH|Bca|Ly-57|Ly57|Lyw-57|SLP-65	B cell linker	protein-coding
mm_63951.1	chr7	139894880	139894884	+	1	NA	5' UTR (NM_177261, exon 1 of 31)	5' UTR (NM_177261, exon 1 of 31)	186	NM_177261	76484	Mm.44442	NM_177261	ENSMUSG00000066129	Kndc1	2410012C07Rik|B830014K08Rik|VKIND|very-kind	kinase non-catalytic C-lobe domain (KIND) containing 1	protein-coding
mm_29749.1	chr3	126998521	126998543	-	1	NA	promoter-TSS (NM_178655)	promoter-TSS (NM_178655)	-80	NM_178655	109676	Mm.220242	NM_178655	ENSMUSG00000032826	Ank2	100043364|AI835472|AW491075|Ank-2|Gm4392	ankyrin 2, brain	protein-coding
mm_91699.1	chr10	44004312	44004325	-	1	NA	5' UTR (NM_172393, exon 1 of 20)	5' UTR (NM_172393, exon 1 of 20)	528	NM_172393	11630	Mm.292082	NM_172393	ENSMUSG00000019866	Aim1	AI462491|AI463325	absent in melanoma 1	protein-coding
mm_37941.1	chr4	133070895	133070905	-	1	NA	intron (NM_146155, intron 6 of 6)	MIRb|SINE|MIR	59394	NM_146155	230793	Mm.31816	NM_146155	ENSMUSG00000037692	Ahdc1	D030015G18Rik	AT hook, DNA binding motif, containing 1	protein-coding
mm_68993.1	chr7	126625940	126625970	-	1	NA	promoter-TSS (NM_019738)	promoter-TSS (NM_019738)	-485	NM_019738	56312	Mm.18742	NM_019738	ENSMUSG00000030717	Nupr1	2310032H04Rik|Com1|p8	nuclear protein transcription regulator 1	protein-coding
mm_58700.1	chr7	12927388	12927402	+	1	NA	promoter-TSS (NM_029809)	promoter-TSS (NM_029809)	-21	NM_029809	381845	Mm.439896	NM_029809	ENSMUSG00000033967	Rnf225	2310014L17Rik|AV237412|C77118	ring finger protein 225	protein-coding
mm_3681.1	chr1	153696484	153696502	+	1	NA	3' UTR (NM_026380, exon 7 of 7)	3' UTR (NM_026380, exon 7 of 7)	30820	NM_001347115	67792	Mm.379143	NM_026380	ENSMUSG00000042671	Rgs8	6530413N01Rik	regulator of G-protein signaling 8	protein-coding
mm_80373.1	chr9	75407019	75407028	+	1	NA	intron (NM_015806, intron 1 of 5)	intron (NM_015806, intron 1 of 5)	2336	NM_027418	50772	Mm.480076	NM_015806	ENSMUSG00000042688	Mapk6	2610021I23Rik|D130053K17Rik|Erk3|Mapk4|Mapk63|Prkm4|Prkm6	mitogen-activated protein kinase 6	protein-coding
mm_110183.1	chr12	27337612	27337624	-	1	NA	3' UTR (NM_009234, exon 1 of 1)	3' UTR (NM_009234, exon 1 of 1)	5100	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding
mm_91958.1	chr10	61146324	61146337	-	1	NA	5' UTR (NM_001316673, exon 2 of 15)	5' UTR (NM_001316673, exon 2 of 15)	1354	NM_009163	20397	Mm.412319	NM_009163	ENSMUSG00000020097	Sgpl1	AI428538|D10Xrf456|S1PL|Spl	sphingosine phosphate lyase 1	protein-coding
mm_86892.1	chr10	22301849	22301859	+	1	NA	intron (NM_009018, intron 5 of 5)	ORR1C1|LTR|ERVL-MaLR	-4866	NR_015465	606736	Mm.387042	NR_015465	ENSMUSG00000097352	C920009B18Rik	-	RIKEN cDNA C920009B18 gene	ncRNA
mm_50907.1	chr6	57582595	57582608	+	1	NA	intron (NM_025992, intron 1 of 22)	MER57E1|LTR|ERV1	1609	NM_025992	67138	Mm.297393	NM_025992	ENSMUSG00000029798	Herc6	1700121D12Rik|2510038N07Rik|4930427L17Rik|AI451296|CEB1|Herc5	hect domain and RLD 6	protein-coding
mm_39630.1	chr5	24430719	24430729	+	1	NA	intron (NM_009207, intron 5 of 22)	intron (NM_009207, intron 5 of 22)	3203	NM_001253892	20535	Mm.4580	NM_009207	ENSMUSG00000028962	Slc4a2	Ae2|B3RP	solute carrier family 4 (anion exchanger), member 2	protein-coding
mm_24162.1	chr3	88531905	88531995	+	1	NA	promoter-TSS (NM_001029890)	promoter-TSS (NM_001029890)	-445	NM_001029890	72640	Mm.275154	NM_001029890	ENSMUSG00000074480	Mex3a	2700083E18Rik|Gm411|Rkhd4	mex3 RNA binding family member A	protein-coding
mm_64274.1	chr7	141808525	141808531	+	1	NA	intron (NM_010844, intron 31 of 49)	intron (NM_010844, intron 31 of 49)	19517	NM_010844	17833	Mm.334332	NM_010844	ENSMUSG00000037974	Muc5ac	2210005L13Rik|MGM	mucin 5, subtypes A and C, tracheobronchial/gastric	protein-coding
mm_103488.1	chr11	76509422	76509435	-	1	NA	promoter-TSS (NM_198018)	promoter-TSS (NM_198018)	-9	NM_198018	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_173365.1	chrY	90819896	90819898	+	1	NA	Intergenic	IMPB_01|Satellite|Satellite	19509	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_46320.1	chr5	100680070	100680105	-	1	NA	3' UTR (NM_152803, exon 12 of 12)	3' UTR (NM_152803, exon 12 of 12)	-5831	NM_027978	71883	Mm.260661	NM_027978	ENSMUSG00000029319	Coq2	2310002F18Rik|PHB:PPT	coenzyme Q2 4-hydroxybenzoate polyprenyltransferase	protein-coding
mm_94019.1	chr10	127666599	127666623	-	1	NA	promoter-TSS (NM_008668)	promoter-TSS (NM_008668)	92	NM_001122895	17937	Mm.336898	NM_008668	ENSMUSG00000025402	Nab2	AI451907	Ngfi-A binding protein 2	protein-coding
mm_25687.1	chr3	122245611	122245622	+	1	NA	promoter-TSS (NM_008129)	promoter-TSS (NM_008129)	59	NM_008129	14630	Mm.292676	NM_008129	ENSMUSG00000028124	Gclm	AI649393|Gcmc|Glclr	glutamate-cysteine ligase, modifier subunit	protein-coding
mm_166832.1	chr7	18925969	18926028	+	1	NA	5' UTR (NM_001029877, exon 1 of 4)	5' UTR (NM_001029877, exon 1 of 4)	110	NM_001029877	384569	Mm.262724	NM_001029877	ENSMUSG00000030411	Nova2	Gm1424	neuro-oncological ventral antigen 2	protein-coding
mm_63362.1	chr7	127046907	127046911	+	1	NA	Intergenic	Intergenic	-4489	NM_145588	110033	Mm.286488	NM_145588	ENSMUSG00000030677	Kif22	AU021460|C81217|Kid|Kif22a	kinesin family member 22	protein-coding
mm_5930.1	chr1	55362678	55362687	-	1	NA	promoter-TSS (NM_001113367)	promoter-TSS (NM_001113367)	25	NM_001113367	75388	Mm.483408	NM_029267	ENSMUSG00000025977	Boll	4930554P13Rik|4930597B14Rik	bol, boule-like (Drosophila)	protein-coding
mm_60553.1	chr7	44481084	44481100	+	1	NA	Intergenic	Intergenic	-3425	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_70059.1	chr7	142651622	142651635	-	1	NA	3' UTR (NM_010514, exon 4 of 4)	3' UTR (NM_010514, exon 4 of 4)	3368	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_161482.1	chr15	82620930	82620930	-	1	NA	promoter-TSS (NM_145474)	promoter-TSS (NM_145474)	-23	NM_145474	223706	Mm.436843	NM_145474	ENSMUSG00000094559	Cyp2d34	-	cytochrome P450, family 2, subfamily d, polypeptide 34	protein-coding
mm_118611.1	chr14	20967257	20967275	+	1	NA	intron (NM_009502, intron 1 of 20)	ID_B1|SINE|B4	37833	NM_009502	22330	Mm.279361	NM_009502	ENSMUSG00000021823	Vcl	9430097D22|AA571387|AI462105|AW545629	vinculin	protein-coding
mm_111775.1	chr12	104044432	104044447	-	1	NA	promoter-TSS (NM_026535)	promoter-TSS (NM_026535)	4	NM_026535	68054	Mm.20286	NM_026535	ENSMUSG00000041567	Serpina12	4632419J12Rik	serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 12	protein-coding
mm_130785.1	chr15	101573864	101573870	-	1	NA	promoter-TSS (NM_133357)	promoter-TSS (NM_133357)	37	NM_133357	109052	Mm.106868	NM_133357	ENSMUSG00000022986	Krt75	4732468K03Rik|AA589387|K6hf|Krt2-6hf|Krtcap1	keratin 75	protein-coding
mm_116341.1	chr13	38503547	38503557	-	1	NA	exon (NM_145367, exon 9 of 10)	exon (NM_145367, exon 9 of 10)	24362	NM_001289599	105245	Mm.28622	NM_145367	ENSMUSG00000038991	Txndc5	AL022641|ERp46|PC-TRP	thioredoxin domain containing 5	protein-coding
mm_29076.1	chr3	103868146	103868167	-	1	NA	intron (NR_104070, intron 3 of 22)	intron (NR_104070, intron 3 of 22)	7879	NM_008979	19260	Mm.395	NM_008979	ENSMUSG00000027843	Ptpn22	70zpep|PEP|Ptpn8	protein tyrosine phosphatase, non-receptor type 22 (lymphoid)	protein-coding
mm_145114.1	chr18	44270142	44270146	+	1	NA	promoter-TSS (NM_010935)	promoter-TSS (NM_010935)	17	NM_010935	18169	Mm.57234	NM_010935	ENSMUSG00000038071	Npy6r	-	neuropeptide Y receptor Y6	protein-coding
mm_50729.1	chr6	52368252	52368256	+	1	NA	Intergenic	Intergenic	-53422	NR_038163	70593	Mm.158412	NR_038163	ENSMUSG00000086126	Evx1os	5730457N03Rik|Evx1as	even skipped homeotic gene 1, opposite strand	ncRNA
mm_69120.1	chr7	127026249	127026281	-	1	NA	exon (NM_010772, exon 1 of 5)	exon (NM_010772, exon 1 of 5)	214	NM_010772	17188	Mm.378964	NM_010772	ENSMUSG00000030678	Maz	MAZI|PUR1|Pur-1|SAF-1|SAF-2	MYC-associated zinc finger protein (purine-binding transcription factor)	protein-coding
mm_25271.1	chr3	104864460	104864512	+	1	NA	promoter-TSS (NM_001253703)	promoter-TSS (NM_001253703)	19	NM_009797	12340	Mm.19142	NM_009797	ENSMUSG00000070372	Capza1	CAPZ|CAZ1|Cappa1	capping protein (actin filament) muscle Z-line, alpha 1	protein-coding
mm_149662.1	chr19	18730659	18730689	+	1	NA	Intergenic	(GA)n|Simple_repeat|Simple_repeat	17438	NM_177640	225995	Mm.28101	NM_177640	ENSMUSG00000047044	D030056L22Rik	-	RIKEN cDNA D030056L22 gene	protein-coding
mm_41115.1	chr5	87780104	87780132	+	1	NA	exon (NM_001304767, exon 7 of 13)	exon (NM_001304767, exon 7 of 13)	5668	NM_007785	12993	Mm.4908	NM_007785	ENSMUSG00000061937	Csn1s2a	Csng|PP22	casein alpha s2-like A	protein-coding
mm_17084.1	chr2	22960837	22960856	-	1	NA	exon (NM_001077190, exon 6 of 11)	exon (NM_001077190, exon 6 of 11)	65324	NM_019501	56075	Mm.249752	NM_019501	ENSMUSG00000026784	Pdss1	2610203G20Rik|2700031G06Rik|TPT|TPT 1|Tprt|mDLP1|mSPS1	prenyl (solanesyl) diphosphate synthase, subunit 1	protein-coding
mm_170716.1	chr2	144369010	144369013	+	1	NA	promoter-TSS (NM_001166640)	promoter-TSS (NM_001166640)	-21	NM_001166640	228714	Mm.227925	NM_181417	ENSMUSG00000027425	Csrp2bp	2510008M08Rik|ATAC2|AU023459|D2Ertd473e|D2Wsu131e|E430020F17|Kat14	cysteine and glycine-rich protein 2 binding protein	protein-coding
mm_134041.1	chr16	5132489	5132513	-	1	NA	promoter-TSS (NM_008909)	promoter-TSS (NM_008909)	-20	NM_008909	19041	Mm.266875	NM_008909	ENSMUSG00000039457	Ppl	AW553870	periplakin	protein-coding
mm_43167.1	chr5	127245147	127245153	+	1	NA	intron (NM_175432, intron 1 of 8)	B3|SINE|B2	3324	NM_175432	208213	Mm.444235	NM_175432	ENSMUSG00000034324	Tmem132c	2810482M11Rik|3230401P16|4632425D07Rik	transmembrane protein 132C	protein-coding
mm_19952.1	chr2	117336395	117336405	-	1	NA	intron (NM_011246, intron 2 of 16)	intron (NM_011246, intron 2 of 16)	6477	NM_011246	19419	Mm.42150	NM_011246	ENSMUSG00000027347	Rasgrp1	Rasgrp	RAS guanyl releasing protein 1	protein-coding
mm_77783.1	chr9	3024741	3024777	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	13984	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_128223.1	chr15	36455525	36455542	-	1	NA	Intergenic	Intergenic	41258	NM_175134	68839	Mm.396537	NM_175134	ENSMUSG00000048307	Ankrd46	1110054N06Rik|AI314978|AI987733	ankyrin repeat domain 46	protein-coding
mm_91256.1	chr10	23180172	23180199	-	1	NA	intron (NM_010167, intron 3 of 18)	intron (NM_010167, intron 3 of 18)	169705	NM_001347372	14051	Mm.332128	NM_010167	ENSMUSG00000010461	Eya4	B130023L16Rik	EYA transcriptional coactivator and phosphatase 4	protein-coding
mm_49645.1	chr6	30805658	30805666	+	1	NA	intron (NM_017478, intron 20 of 23)	intron (NM_017478, intron 20 of 23)	64363	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_134251.1	chr16	13672620	13672628	-	1	NA	intron (NM_025976, intron 1 of 7)	intron (NM_025976, intron 1 of 7)	766	NM_025653	67118	Mm.223689	NM_025653	ENSMUSG00000022684	Bfar	3010001A07Rik|3110001I22Rik|AI666707|AW107665|Bar|Rnf47	bifunctional apoptosis regulator	protein-coding
mm_101700.1	chr11	40755177	40755187	-	1	NA	5' UTR (NM_009831, exon 1 of 6)	5' UTR (NM_009831, exon 1 of 6)	104	NM_009831	12450	Mm.2103	NM_009831	ENSMUSG00000020326	Ccng1	AI314029	cyclin G1	protein-coding
mm_164319.1	chr16	3743461	3743475	+	1	NA	promoter-TSS (NM_148924)	promoter-TSS (NM_148924)	-631	NM_148924	74120	Mm.29081	NM_148924	ENSMUSG00000022529	Zfp263	1200014J04Rik|AI326880|AU020888|NT2|mFPM315	zinc finger protein 263	protein-coding
mm_141448.1	chr17	30004621	30004640	-	1	NA	promoter-TSS (NM_148926)	promoter-TSS (NM_148926)	-457	NM_148926	21769	Mm.220972	NM_148926	ENSMUSG00000044477	Zfand3	AW539211|TEG-27|Tex27	zinc finger, AN1-type domain 3	protein-coding
mm_119674.1	chr14	52622574	52622586	+	1	NA	Intergenic	Intergenic	-126885	NM_001170918	57269	Mm.88822	NM_020512	ENSMUSG00000059887	Olfr1507	MOR244-1|Mor28|Or28	olfactory receptor 1507	protein-coding
mm_141172.1	chr17	26570804	26570846	-	1	NA	intron (NM_026170, intron 1 of 9)	intron (NM_026170, intron 1 of 9)	9313	NM_026170	67458	Mm.30496	NM_026170	ENSMUSG00000001576	Ergic1	1200007D18Rik|maa-136	endoplasmic reticulum-golgi intermediate compartment (ERGIC) 1	protein-coding
mm_93781.1	chr10	120476711	120476723	-	1	NA	promoter-TSS (NM_010441)	promoter-TSS (NM_010441)	-248	NM_010441	15364	Mm.157190	NM_010441	ENSMUSG00000056758	Hmga2	9430083A20Rik|HMGI-C|Hmgic|pg|pygmy	high mobility group AT-hook 2	protein-coding
mm_150445.1	chr19	38030242	38030250	+	1	NA	intron (NM_001302140, intron 1 of 53)	intron (NM_001302140, intron 1 of 53)	13331	NM_001099634	226101	Mm.34674	NM_177035	ENSMUSG00000048612	Myof	2310004N10Rik|2310051D19Rik|E030042N20Rik|Fer1l3	myoferlin	protein-coding
mm_47510.1	chr5	124075096	124075115	-	1	NA	intron (NM_019875, intron 9 of 11)	intron (NM_019875, intron 9 of 11)	20693	NM_019875	56325	Mm.254839	NM_019875	ENSMUSG00000029408	Abcb9	TAPL|mKIAA1520	ATP-binding cassette, sub-family B (MDR/TAP), member 9	protein-coding
mm_48354.1	chr5	139345150	139345216	-	1	NA	promoter-TSS (NM_197980)	promoter-TSS (NM_197980)	-17	NM_197980	68033	Mm.261064	NM_197980	ENSMUSG00000045438	Cox19	1810074D02Rik|2810437L13Rik	cytochrome c oxidase assembly protein 19	protein-coding
mm_1279.1	chr1	63446176	63446185	+	1	NA	5' UTR (NM_011780, exon 1 of 26)	5' UTR (NM_011780, exon 1 of 26)	289	NM_011780	23792	Mm.124892	NM_011780	ENSMUSG00000025964	Adam23	AW046396|MDC3	a disintegrin and metallopeptidase domain 23	protein-coding
mm_17262.1	chr2	25983237	25983290	-	1	NA	promoter-TSS (NM_001276361)	promoter-TSS (NM_001276361)	19	NM_001276360	227634	Mm.36834	NM_001115076	ENSMUSG00000026933	Camsap1	9530003A05Rik|C77823|PRO2405	calmodulin regulated spectrin-associated protein 1	protein-coding
mm_55241.1	chr6	52346998	52347004	-	1	NA	Intergenic	Intergenic	-32169	NR_038163	70593	Mm.158412	NR_038163	ENSMUSG00000086126	Evx1os	5730457N03Rik|Evx1as	even skipped homeotic gene 1, opposite strand	ncRNA
mm_8786.1	chr1	161251154	161251186	-	1	NA	promoter-TSS (NM_007453)	promoter-TSS (NM_007453)	40	NR_130150	11758	Mm.186185	NM_007453	ENSMUSG00000026701	Prdx6	1-Cys Prx|1-cysPrx|9430088D19Rik|AA690119|Aop2|Brp-12|CP-3|GPx|Ltw-4|Ltw4|Lvtw-4|NSGPx|ORF06|Prdx5|aiPLA2	peroxiredoxin 6	protein-coding
mm_92490.1	chr10	78298257	78298266	-	1	NA	intron (NM_053014, intron 2 of 9)	intron (NM_053014, intron 2 of 9)	41946	NR_106119	102465765		NR_106119	ENSMUSG00000098885	Mir7659	Gm27433|mmu-mir-7659	microRNA 7659	ncRNA
mm_86734.1	chr10	19087307	19087315	+	1	NA	Intergenic	Intergenic	-54438	NR_038021	100504265	Mm.383417	NR_038021		Gm20139	-	predicted gene, 20139	ncRNA
mm_168548.1	chr1	162893312	162893319	-	1	NA	intron (NM_018881, intron 2 of 8)	intron (NM_018881, intron 2 of 8)	5397	NM_018881	55990	Mm.10929	NM_018881	ENSMUSG00000040170	Fmo2	2310008D08Rik|2310042I22Rik|AW107733	flavin containing monooxygenase 2	protein-coding
mm_103203.1	chr11	70652197	70652207	-	1	NA	TTS (NM_001316728)	TTS (NM_001316728)	2448	NM_011072	18643	Mm.2647	NM_011072	ENSMUSG00000018293	Pfn1	Pfn	profilin 1	protein-coding
mm_134471.1	chr16	18586894	18586898	-	1	NA	promoter-TSS (NM_011532)	promoter-TSS (NM_011532)	73	NM_011532	21380	Mm.295194	NM_011532	ENSMUSG00000009097	Tbx1	-	T-box 1	protein-coding
mm_5775.1	chr1	51477912	51477923	-	1	NA	5' UTR (NM_028696, exon 1 of 6)	5' UTR (NM_028696, exon 1 of 6)	482	NM_028696	109019	Mm.196290	NM_028696	ENSMUSG00000026107	Nabp1	4930434H03Rik|4930442A21Rik|4930488J04Rik|4933440J18Rik|5830411E10Rik|AI852561|Nbp1|Obfc2a|Ssb2	nucleic acid binding protein 1	protein-coding
mm_106419.1	chr11	119228457	119228459	-	1	NA	promoter-TSS (NM_172443)	promoter-TSS (NM_172443)	41	NM_001347625	207592	Mm.205263	NM_172443	ENSMUSG00000039976	Tbc1d16	B930087K01|BC026530|Tcd1d16	TBC1 domain family, member 16	protein-coding
mm_101024.1	chr11	8579205	8579212	-	1	NA	intron (NM_001083587, intron 3 of 30)	intron (NM_001083587, intron 3 of 30)	85327	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_21521.1	chr2	163632201	163632223	-	1	NA	exon (NM_012032, exon 5 of 10)	exon (NM_012032, exon 5 of 10)	-12638	NR_028113	68386	Mm.410649	NR_028113	ENSMUSG00000058812	0610039K10Rik	-	RIKEN cDNA 0610039K10 gene	ncRNA
mm_127404.1	chr15	101232205	101232208	+	1	NA	3' UTR (NM_019518, exon 8 of 8)	3' UTR (NM_019518, exon 8 of 8)	-7020	NR_045328	380977	Mm.399924	NR_045326	ENSMUSG00000097915	A330009N23Rik	-	RIKEN cDNA A330009N23 gene	ncRNA
mm_11805.1	chr2	43900158	43900180	+	1	NA	intron (NM_001301832, intron 7 of 14)	intron (NM_001301832, intron 7 of 14)	151345	NM_001301831	76117	Mm.217350	NM_153820	ENSMUSG00000049744	Arhgap15	5830480G12Rik	Rho GTPase activating protein 15	protein-coding
mm_76762.1	chr8	95735148	95735148	-	1	NA	intron (NM_001205226, intron 36 of 48)	B1_Mus2|SINE|Alu	18066	NR_106041	102465650		NR_106041	ENSMUSG00000106145	Mir7073	mmu-mir-7073	microRNA 7073	ncRNA
mm_114405.1	chr13	64161863	64161910	+	1	NA	promoter-TSS (NM_019986)	promoter-TSS (NM_019986)	20	NM_019986	56541	Mm.40989	NM_019986	ENSMUSG00000021476	Habp4	4933413D03Rik|4933428J01Rik	hyaluronic acid binding protein 4	protein-coding
mm_10718.1	chr2	22804746	22804768	+	1	NA	intron (NM_019456, intron 1 of 13)	intron (NM_019456, intron 1 of 13)	30430	NM_019456	54519	Mm.14255	NM_019456	ENSMUSG00000026786	Apbb1ip	9930118P07Rik|Prp48	amyloid beta (A4) precursor protein-binding, family B, member 1 interacting protein	protein-coding
mm_159711.1	chr5	31297759	31297759	+	1	NA	intron (NM_144909, intron 1 of 18)	intron (NM_144909, intron 1 of 18)	178	NM_144909	231103	Mm.100043	NM_144909	ENSMUSG00000059434	Gckr	GKRP	glucokinase regulatory protein	protein-coding
mm_59517.1	chr7	27592728	27592745	+	1	NA	intron (NM_001110208, intron 1 of 13)	intron (NM_001110208, intron 1 of 13)	1184	NM_001110208	11652	Mm.177194	NM_007434	ENSMUSG00000004056	Akt2	2410016A19Rik|AW554154|PKB|PKBbeta	thymoma viral proto-oncogene 2	protein-coding
mm_47313.1	chr5	122458543	122458551	-	1	NA	intron (NM_001110140, intron 16 of 19)	intron (NM_001110140, intron 16 of 19)	36103	NM_019805	56317	Mm.37341	NM_019805	ENSMUSG00000029466	Anapc7	APC7|AW545589	anaphase promoting complex subunit 7	protein-coding
mm_77199.1	chr8	113528673	113528673	-	1	NA	intron (NR_110476, intron 1 of 2)	intron (NR_110476, intron 1 of 2)	11391	NR_110476	78048	Mm.252797	NR_110476		4930571O06Rik	-	RIKEN cDNA 4930571O06 gene	ncRNA
mm_60871.1	chr7	45942248	45942261	+	1	NA	intron (NM_001033243, intron 7 of 12)	intron (NM_001033243, intron 7 of 12)	13856	NM_001033243	211535	Mm.227539	NM_001033243	ENSMUSG00000040189	Ccdc114	-	coiled-coil domain containing 114	protein-coding
mm_94592.1	chr11	11769554	11769565	+	1	NA	exon (NM_009578, exon 7 of 7)	exon (NM_009578, exon 7 of 7)	39403	NM_021891	60530	Mm.236114	NM_021891	ENSMUSG00000035455	Fignl1	-	fidgetin-like 1	protein-coding
mm_55368.1	chr6	57692008	57692084	-	1	NA	promoter-TSS (NM_025574)	promoter-TSS (NM_025574)	32	NM_025574	66459	Mm.44201	NM_025574	ENSMUSG00000043162	Pyurf	2610022G08Rik|AI847956|Prey	Pigy upstream reading frame	protein-coding
mm_119677.1	chr14	52667357	52667383	+	1	NA	Intergenic	Intergenic	-171675	NM_001170918	57269	Mm.88822	NM_020512	ENSMUSG00000059887	Olfr1507	MOR244-1|Mor28|Or28	olfactory receptor 1507	protein-coding
mm_134777.1	chr16	23977680	23977689	-	1	NA	5' UTR (NM_009744, exon 3 of 10)	5' UTR (NM_009744, exon 3 of 10)	10928	NM_009744	12053	Mm.347398	NM_009744	ENSMUSG00000022508	Bcl6	Bcl5	B cell leukemia/lymphoma 6	protein-coding
mm_144323.1	chr18	12862139	12862156	+	1	NA	5' UTR (NM_001252492, exon 1 of 14)	5' UTR (NM_001252492, exon 1 of 14)	566	NM_001252493	64291	Mm.259470	NM_020573	ENSMUSG00000044252	Osbpl1a	G430090F17Rik|Gm753|ORP-1|Osbpl1b	oxysterol binding protein-like 1A	protein-coding
mm_157722.1	chrX	70344858	70344920	-	1	NA	3' UTR (NM_010498, exon 9 of 9)	3' UTR (NM_010498, exon 9 of 9)	20196	NM_010498	15931	Mm.233083	NM_010498	ENSMUSG00000035847	Ids	AW214631	iduronate 2-sulfatase	protein-coding
mm_108702.1	chr12	86952594	86952614	+	1	NA	intron (NM_001289432, intron 1 of 4)	intron (NM_001289432, intron 1 of 4)	5261	NM_001289432	217732	Mm.22337	NM_173735	ENSMUSG00000034157	Cipc	2310044G17Rik|AI842544|AI853744|Kiaa1737|mKIAA1737	CLOCK interacting protein, circadian	protein-coding
mm_170531.1	chr19	34950333	34950341	+	1	NA	exon (NM_183046, exon 19 of 32)	exon (NM_183046, exon 19 of 32)	27979	NM_183046	240641	Mm.278471	NM_183046	ENSMUSG00000024795	Kif20b	33cex|B130024C23|C330014J10Rik|Mphosph1|magoo	kinesin family member 20B	protein-coding
mm_46042.1	chr5	91972259	91972281	-	1	NA	TTS (NR_028429)	TTS (NR_028429)	-9202	NM_001271797	68098	Mm.159453	NM_026557	ENSMUSG00000029397	Rchy1	ARNIP|CHIMP|Pirh2|Zfp363|Znf363	ring finger and CHY zinc finger domain containing 1	protein-coding
mm_65895.1	chr7	30169682	30169696	-	1	NA	promoter-TSS (NM_001033540)	promoter-TSS (NM_001033540)	38	NM_011980	26465	Mm.446516	NM_011980	ENSMUSG00000037029	Zfp146	OZF|Znf146	zinc finger protein 146	protein-coding
mm_94323.1	chr11	4250630	4250636	+	1	NA	Intergenic	Intergenic	-6935	NM_008501	16878	Mm.4964	NM_008501	ENSMUSG00000034394	Lif	-	leukemia inhibitory factor	protein-coding
mm_120935.1	chr14	76507146	76507164	+	1	NA	3' UTR (NM_207652, exon 3 of 3)	3' UTR (NM_207652, exon 3 of 3)	2645	NM_009366	21807	Mm.153272	NM_009366	ENSMUSG00000022010	Tsc22d1	AA589566|AW105905|Egr5|TSC-22|Tgfb1i4|Tsc|Tsc22	TSC22 domain family, member 1	protein-coding
mm_156962.1	chrX	169989947	169989961	+	1	NA	3' UTR (NM_001290504, exon 10 of 10)	3' UTR (NM_001290504, exon 10 of 10)	-11037	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_97072.1	chr11	72992682	72992694	+	1	NA	3' UTR (NM_001163337, exon 22 of 22)	3' UTR (NM_001163337, exon 22 of 22)	-6457	NM_008771	18436	Mm.25722	NM_008771	ENSMUSG00000020787	P2rx1	AI323649|BB122383|P2x|Pdcd3|RP-2	purinergic receptor P2X, ligand-gated ion channel, 1	protein-coding
mm_102981.1	chr11	69681823	69681856	-	1	NA	TTS (NM_001159503)	TTS (NM_001159503)	131	NM_030702	80886	Mm.284592	NM_030702	ENSMUSG00000005204	Senp3	AA408656|Smt3ip|Smt3ip1	SUMO/sentrin specific peptidase 3	protein-coding
mm_139363.1	chr17	50596490	50596505	+	1	NA	intron (NM_013880, intron 1 of 5)	intron (NM_013880, intron 1 of 5)	86950	NM_013880	224860	Mm.217362	NM_013880	ENSMUSG00000038910	Plcl2	PLC-L2|PRIP-2|Plce2|mKIAA1092	phospholipase C-like 2	protein-coding
mm_2107.1	chr1	87828290	87828292	+	1	NA	intron (NM_009118, intron 9 of 15)	intron (NM_009118, intron 9 of 15)	24611	NM_009118	20215	Mm.1276	NM_009118	ENSMUSG00000056055	Sag	A930001K18Rik|Arr1|Irbp|arrestin	S-antigen, retina and pineal gland (arrestin)	protein-coding
mm_168946.1	chr12	73203272	73203291	-	1	NA	intron (NM_008612, intron 6 of 7)	intron (NM_008612, intron 6 of 7)	79564	NM_008612	17420	Mm.246750	NM_008612	ENSMUSG00000021103	Mnat1	E130115E11Rik|MAT1|P36	menage a trois 1	protein-coding
mm_146642.1	chr18	10782909	10782912	-	1	NA	promoter-TSS (NR_029547)	promoter-TSS (NR_029547)	66	NR_029547	387151		NR_029547	ENSMUSG00000065399	Mir133a-1	Mirn133|Mirn133a-1|mir-133a-1	microRNA 133a-1	ncRNA
mm_170740.1	chr2	154892773	154892774	-	1	NA	5' UTR (NM_026030, exon 1 of 9)	5' UTR (NM_026030, exon 1 of 9)	133	NM_026030	67204	Mm.377134	NM_026030	ENSMUSG00000074656	Eif2s2	2810026E11Rik|38kDa|AA408636|AA571381|AA986487|AW822225|D2Ertd303e|EIF2|EIF2B	eukaryotic translation initiation factor 2, subunit 2 (beta)	protein-coding
mm_51789.1	chr6	88204441	88204449	+	1	NA	intron (NM_008090, intron 4 of 5)	intron (NM_008090, intron 4 of 5)	5781	NM_008090	14461	Mm.491156	NM_008090	ENSMUSG00000015053	Gata2	Gata-2	GATA binding protein 2	protein-coding
mm_135538.1	chr16	49770847	49770863	-	1	NA	Intergenic	MER63A|DNA|hAT-Blackjack	71561	NM_028680	73916	Mm.241276	NM_028680	ENSMUSG00000032965	Ift57	4833420A15Rik|Esrrbl1|Hippi|MHS4R2	intraflagellar transport 57	protein-coding
mm_34915.1	chr4	155718270	155718281	+	1	NA	intron (NM_026899, intron 2 of 4)	B1_Mus2|SINE|Alu	13460	NM_026899	68991	Mm.294770	NM_026899	ENSMUSG00000029038	Ssu72	1190002E22Rik|1500011L16Rik|2610101M12Rik	Ssu72 RNA polymerase II CTD phosphatase homolog (yeast)	protein-coding
mm_167698.1	chr9	88748057	88748060	+	1	NA	Intergenic	Intergenic	-16208	NM_007536	12047	Mm.378888	NM_007536	ENSMUSG00000099974	Bcl2a1d	A1-d	B cell leukemia/lymphoma 2 related protein A1d	protein-coding
mm_139461.1	chr17	55952852	55952862	+	1	NA	5' UTR (NM_015766, exon 1 of 5)	5' UTR (NM_015766, exon 1 of 5)	234	NM_015766	50498	Mm.256798	NM_015766	ENSMUSG00000003206	Ebi3	EBI-3|IL-27	Epstein-Barr virus induced gene 3	protein-coding
mm_17048.1	chr2	20968551	20968613	-	1	NA	promoter-TSS (NM_001081364)	promoter-TSS (NM_001081364)	-292	NR_033225	433408	Mm.386941	NR_033225		Gm13375	OTTMUSG00000011664	predicted gene 13375	ncRNA
mm_40318.1	chr5	43875338	43875347	+	1	NA	intron (NM_007646, intron 1 of 7)	ORR1D1|LTR|ERVL-MaLR	6533	NM_007646	12494	Mm.249873	NM_007646	ENSMUSG00000029084	Cd38	ADPRC 1|Cd38-rs1|I-19	CD38 antigen	protein-coding
mm_83878.1	chr9	55283567	55283580	-	1	NA	promoter-TSS (NM_032002)	promoter-TSS (NM_032002)	52	NM_032002	83961	Mm.443874	NM_032002	ENSMUSG00000032311	Nrg4	AI552600	neuregulin 4	protein-coding
mm_119544.1	chr14	48132866	48132869	+	1	NA	intron (NM_033602, intron 1 of 5)	intron (NM_033602, intron 1 of 5)	11998	NM_033602	93834	Mm.296457	NM_033602	ENSMUSG00000021846	Peli2	AW047589|BB129927	pellino 2	protein-coding
mm_11326.1	chr2	30430043	30430047	+	1	NA	intron (NM_138748, intron 3 of 9)	ID4|SINE|ID	13995	NM_138748	110854	Mm.275393	NM_138748	ENSMUSG00000039515	Ptpa	2610042B21Rik|C77440|N28142|PR53|Ppp2r4	protein phosphatase 2 protein activator	protein-coding
mm_160933.1	chr11	91577396	91577396	-	1	NA	exon (NM_028547, exon 1 of 1)	exon (NM_028547, exon 1 of 1)	159	NM_028547	73470	Mm.67677	NM_028547	ENSMUSG00000046755	Kif2b	1700063D03Rik	kinesin family member 2B	protein-coding
mm_107452.1	chr12	37013578	37013598	+	1	NA	Intergenic	L1M3e|LINE|L1	-94958	NM_008584	17286	Mm.341398	NM_008584	ENSMUSG00000036144	Meox2	AI528662|Gax|Mox-2|Mox2	mesenchyme homeobox 2	protein-coding
mm_83726.1	chr9	50809207	50809211	-	1	NA	intron (NR_045601, intron 12 of 13)	intron (NR_045601, intron 12 of 13)	33984	NR_045601	102580	Mm.160035	NM_133981	ENSMUSG00000032059	Alg9	8230402H15Rik|AI747665|B430313H07Rik|Dibd1	asparagine-linked glycosylation 9 (alpha 1,2 mannosyltransferase)	protein-coding
mm_74751.1	chr8	19064866	19064880	-	1	NA	promoter-TSS (NM_183038)	promoter-TSS (NM_183038)	-63	NM_183038	360214	Mm.271559	NM_183038	ENSMUSG00000061847	Defb39	BD-39	defensin beta 39	protein-coding
mm_125250.1	chr15	35041206	35041207	+	1	NA	intron (NM_019635, intron 6 of 10)	intron (NM_019635, intron 6 of 10)	114600	NM_019635	56274	Mm.262330	NM_019635	ENSMUSG00000022329	Stk3	0610042I06Rik|MST|Mst2|Mst3|Ste20|mess1	serine/threonine kinase 3	protein-coding
mm_150770.1	chr19	44294074	44294099	+	1	NA	5' UTR (NM_009128, exon 1 of 6)	5' UTR (NM_009128, exon 1 of 6)	410	NM_009128	20250	Mm.487021	NM_009128	ENSMUSG00000025203	Scd2	Mir5114|Scd-2|mir-5114|swty	stearoyl-Coenzyme A desaturase 2	protein-coding
mm_43359.1	chr5	135217499	135217509	+	1	NA	exon (NM_011714, exon 7 of 19)	exon (NM_011714, exon 7 of 19)	30181	NM_011714	22385	Mm.40331	NM_011714	ENSMUSG00000002748	Baz1b	C87820|WSTF|Wbscr9	bromodomain adjacent to zinc finger domain, 1B	protein-coding
mm_35783.1	chr4	46451466	46451486	-	1	NA	intron (NM_130889, intron 1 of 6)	CpG	550	NM_130889	67628	Mm.263913	NM_130889	ENSMUSG00000028333	Anp32b	2410015B15Rik|PAL31|PHAPI2a|Ssp29	acidic (leucine-rich) nuclear phosphoprotein 32 family, member B	protein-coding
mm_130887.1	chr15	102279360	102279375	-	1	NA	promoter-TSS (NM_134100)	promoter-TSS (NM_134100)	-89	NM_134100	106073	Mm.287740	NM_134100	ENSMUSG00000045665	Mfsd5	AA409375|AW556797|D15Mgi27	major facilitator superfamily domain containing 5	protein-coding
mm_129355.1	chr15	77928926	77929011	-	1	NA	promoter-TSS (NM_019913)	promoter-TSS (NM_019913)	26	NM_019913	56551	Mm.291917	NM_019913	ENSMUSG00000005354	Txn2	2510006J11Rik|AI788873|Trx2	thioredoxin 2	protein-coding
mm_100193.1	chr11	116752313	116752315	+	1	NA	non-coding (NR_003364, exon 1 of 4)	non-coding (NR_003364, exon 1 of 4)	147	NR_003364	193217	Mm.100084	NR_003364		BC018473	-	cDNA sequence BC018473	ncRNA
mm_30492.1	chr3	156561748	156561775	-	1	NA	promoter-TSS (NM_001039094)	promoter-TSS (NM_001039094)	-15	NR_040400	329782	Mm.183459	NR_040398	ENSMUSG00000085084	4930570G19Rik	C630015G22	RIKEN cDNA 4930570G19 gene	ncRNA
mm_48040.1	chr5	136370986	136370988	-	1	NA	intron (NM_001291239, intron 5 of 22)	intron (NM_001291239, intron 5 of 22)	4816	NR_030500	723975		NR_030500	ENSMUSG00000106479	Mir721	Mirn721|miRY|mir-721|mmu-mir-721	microRNA 721	ncRNA
mm_68324.1	chr7	106503545	106503573	-	1	NA	Intergenic	RMER12B|LTR|ERVK	-62486	NR_003967	209380	Mm.461779	NM_001001318		Gm4759	EG209380	GTPase, very large interferon inducible 1 pseudogene	pseudo
mm_32001.1	chr4	94603522	94603538	+	1	NA	promoter-TSS (NM_172695)	promoter-TSS (NM_172695)	-283	NM_172695	18786	Mm.490101	NM_172695	ENSMUSG00000028577	Plaa	2410007N06|AI536418|AU018445|AW208417|D4Ertd618e|PLA2P|PLAP|Ufd3	phospholipase A2, activating protein	protein-coding
mm_66379.1	chr7	43797508	43797533	-	1	NA	promoter-TSS (NM_008940)	promoter-TSS (NM_008940)	-57	NM_001324398	259277	Mm.458023	NM_008940	ENSMUSG00000064023	Klk8	BSP1|NP|Nrpn|Prss19	kallikrein related-peptidase 8	protein-coding
mm_44539.1	chr5	24540424	24540426	-	1	NA	promoter-TSS (NM_080444)	promoter-TSS (NM_080444)	32	NM_080444	117590	Mm.207071	NM_080444	ENSMUSG00000038204	Asb10	Asb-10|BB137407	ankyrin repeat and SOCS box-containing 10	protein-coding
mm_7667.1	chr1	128588419	128588462	-	1	NA	3' UTR (NM_009911, exon 2 of 2)	3' UTR (NM_009911, exon 2 of 2)	3859	NM_009911	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding
mm_17460.1	chr2	28557732	28557776	-	1	NA	exon (NM_009885, exon 9 of 11)	exon (NM_009885, exon 9 of 11)	5649	NM_009885	12613	Mm.236017	NM_009885	ENSMUSG00000026818	Cel	1810036E18Rik|BAL	carboxyl ester lipase	protein-coding
mm_92018.1	chr10	62362266	62362313	-	1	NA	intron (NM_010438, intron 2 of 21)	intron (NM_010438, intron 2 of 21)	17619	NM_010438	15275	Mm.196605	NM_010438	ENSMUSG00000037012	Hk1	BB404130|Hk-1|Hk1-s|dea|mHk1-s	hexokinase 1	protein-coding
mm_8385.1	chr1	151344319	151344353	-	1	NA	promoter-TSS (NM_001039512)	promoter-TSS (NM_001039512)	-162	NM_001039512	117198	Mm.33764	NM_028582	ENSMUSG00000023150	Ivns1abp	1190004M08Rik|1700126I16Rik|AA960440|HSPC068|ND1|NS-1|NS1-BP|Nd1-L|Nd1-S|mKIAA0850	influenza virus NS1A binding protein	protein-coding
mm_80051.1	chr9	69300532	69300540	+	1	NA	intron (NM_001289916, intron 1 of 9)	intron (NM_001289916, intron 1 of 9)	10695	NM_001289916	19883	Mm.378450	NM_013646	ENSMUSG00000032238	Rora	9530021D13Rik|Nr1f1|ROR1|ROR2|ROR3|nmf267|sg|staggerer|tmgc26	RAR-related orphan receptor alpha	protein-coding
mm_141720.1	chr17	34031685	34031699	-	1	NA	promoter-TSS (NM_001205216)	promoter-TSS (NM_001205216)	-2	NM_008202	14977	Mm.18556	NM_008202	ENSMUSG00000024327	Slc39a7	AA408174|AI117660|AL024048|H-2Ke4|H2-Ke4|Ke-4|Ke4|Ring5|Zip7	solute carrier family 39 (zinc transporter), member 7	protein-coding
mm_121664.1	chr14	12345781	12345789	-	1	NA	promoter-TSS (NM_080433)	promoter-TSS (NM_080433)	80	NM_080433	54713	Mm.34644	NM_080433	ENSMUSG00000021743	Fezf2	AI451466|AI852056|Fez|Fezl|Zfp312	Fez family zinc finger 2	protein-coding
mm_154589.1	chrX	7579667	7579685	+	1	NA	promoter-TSS (NM_054039)	promoter-TSS (NM_054039)	0	NM_001199347	20371	Mm.182291	NM_054039	ENSMUSG00000039521	Foxp3	JM2|scurfin|sf	forkhead box P3	protein-coding
mm_59543.1	chr7	27860567	27860640	+	1	NA	promoter-TSS (NM_001024726)	promoter-TSS (NM_001024726)	18	NM_001024726	545938	Mm.458180	NM_001024726	ENSMUSG00000020420	Zfp607a	4732475C15Rik|Zfp607	zinc finger protein 607A	protein-coding
mm_125744.1	chr15	73723132	73723151	+	1	NA	promoter-TSS (NM_001166390)	promoter-TSS (NM_001166390)	-4	NM_001166390	19245	Mm.390807	NM_008975	ENSMUSG00000059895	Ptp4a3	AV088979|Prl-3|pPtp4a3	protein tyrosine phosphatase 4a3	protein-coding
mm_113636.1	chr13	42052016	42052072	+	1	NA	promoter-TSS (NM_007772)	promoter-TSS (NM_007772)	23	NM_007772	110521	Mm.4808	NM_007772	ENSMUSG00000021366	Hivep1	Cryabp1	human immunodeficiency virus type I enhancer binding protein 1	protein-coding
mm_27418.1	chr3	51516255	51516258	-	1	NA	3' UTR (NM_080793, exon 8 of 8)	3' UTR (NM_080793, exon 8 of 8)	32290	NM_016858	19338	Mm.1664	NM_016858	ENSMUSG00000027739	Rab33b	-	RAB33B, member RAS oncogene family	protein-coding
mm_28437.1	chr3	90489144	90489157	-	1	NA	TTS (NM_026374)	TTS (NM_026374)	1863	NM_133854	20615	Mm.331182	NM_133854	ENSMUSG00000001018	Snapin	25kDa|AA407989|AV026596|Bloc1s7|Snap25bp|Snapap	SNAP-associated protein	protein-coding
mm_111780.1	chr12	104340870	104340909	-	1	NA	exon (NM_011458, exon 2 of 5)	exon (NM_011458, exon 2 of 5)	2403	NM_011458	20714	Mm.291569	NM_011458	ENSMUSG00000058207	Serpina3k	1300001I07Rik|D12Rp54|MMCM2|MMSpi2|RP54|Spi-2|Spi2|contrapsin	serine (or cysteine) peptidase inhibitor, clade A, member 3K	protein-coding
mm_104408.1	chr11	94601797	94601822	-	1	NA	promoter-TSS (NM_153807)	promoter-TSS (NM_153807)	-23	NM_153807	264895	Mm.386885	NM_153807	ENSMUSG00000076435	Acsf2	-	acyl-CoA synthetase family member 2	protein-coding
mm_142793.1	chr17	50182552	50182570	-	1	NA	intron (NM_181397, intron 1 of 9)	intron (NM_181397, intron 1 of 9)	7936	NM_181397	76438	Mm.41854	NM_181397	ENSMUSG00000039316	Rftn1	2310015N21Rik|AI853526	raftlin lipid raft linker 1	protein-coding
mm_103972.1	chr11	84524856	84524870	-	1	NA	promoter-TSS (NR_038057)	promoter-TSS (NR_038057)	671	NM_008498	16869	Mm.4965	NM_008498	ENSMUSG00000018698	Lhx1	Lim1	LIM homeobox protein 1	protein-coding
mm_57414.1	chr6	124888193	124888217	-	1	NA	promoter-TSS (NM_013488)	promoter-TSS (NM_013488)	4	NM_013488	12504	Mm.2209	NM_013488	ENSMUSG00000023274	Cd4	L3T4|Ly-4	CD4 antigen	protein-coding
mm_130222.1	chr15	96204682	96204692	-	1	NA	Intergenic	Intergenic	-6713	NR_040423	70040	Mm.437832	NR_040423		2610037D02Rik	AU024679	RIKEN cDNA 2610037D02 gene	ncRNA
mm_124140.1	chr14	87076158	87076168	-	1	NA	intron (NM_019670, intron 3 of 27)	L1MA6|LINE|L1	64951	NM_019670	56419	Mm.440585	NM_019670	ENSMUSG00000022021	Diaph3	4930417P13Rik|Dia2|Diap3|Drf3|mDia2|mKIAA4117|p134MDia2	diaphanous related formin 3	protein-coding
mm_162551.1	chr1	171229688	171229688	-	1	NA	3' UTR (NM_010185, exon 5 of 5)	3' UTR (NM_010185, exon 5 of 5)	4634	NM_013474	11807	Mm.389209	NM_013474	ENSMUSG00000005681	Apoa2	Alp-2|Apo-AII|ApoA-II|ApoAII|Apoa-2|Hdl-1	apolipoprotein A-II	protein-coding
mm_156281.1	chrX	136837155	136837166	+	1	NA	3' UTR (NM_011123, exon 7 of 7)	3' UTR (NM_011123, exon 7 of 7)	14414	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_88429.1	chr10	77449086	77449090	+	1	NA	Intergenic	Intergenic	30712	NR_027377	100045653	Mm.363175	NR_027377		Gm17769	-	predicted gene, 17769	ncRNA
mm_142475.1	chr17	45686134	45686185	-	1	NA	promoter-TSS (NM_026732)	promoter-TSS (NM_026732)	59	NM_198167	224807	Mm.157904	NM_198167	ENSMUSG00000036026	Tmem63b	BC026370	transmembrane protein 63b	protein-coding
mm_121944.1	chr14	24081999	24082009	-	1	NA	Intergenic	Intergenic	-6873	NR_106069	102465697		NR_106069	ENSMUSG00000105723	Mir7210	mir-7210|mmu-mir-7210	microRNA 7210	ncRNA
mm_115509.1	chr13	4391237	4391249	-	1	NA	Intergenic	Intergenic	-43100	NM_030611	83702	Mm.196666	NM_030611	ENSMUSG00000021210	Akr1c6	3alpha-HSD|Akr1c1|Hsd17b5	aldo-keto reductase family 1, member C6	protein-coding
mm_1348.1	chr1	66321709	66321715	+	1	NA	promoter-TSS (NM_001310634)	promoter-TSS (NM_001310634)	-12	NM_001310634	17756	Mm.256966	NM_008632	ENSMUSG00000015222	Map2	G1-397-34|MAP-2|Mtap-2|Mtap2|repro4	microtubule-associated protein 2	protein-coding
mm_47109.1	chr5	118514031	118514045	-	1	NA	Intergenic	Intergenic	-46681	NM_001347445	76199	Mm.206238	NM_172424	ENSMUSG00000018076	Med13l	2210413I17Rik|6330591G05Rik|9030618F05Rik|Thrap2|Trap240L|mKIAA1025	mediator complex subunit 13-like	protein-coding
mm_94811.1	chr11	23032838	23032849	+	1	NA	Intergenic	ID4|SINE|ID	19456	NM_028672	73873	Mm.252406	NM_028672	ENSMUSG00000049811	Fam161a	4930430E16Rik	family with sequence similarity 161, member A	protein-coding
mm_167727.1	chr9	102819770	102819799	+	1	NA	Intergenic	Intergenic	-15136	NM_013649	20187	Mm.335391	NM_013649	ENSMUSG00000032547	Ryk	AW536699|ERK-3|Vik	receptor-like tyrosine kinase	protein-coding
mm_127428.1	chr15	101269388	101269416	+	1	NA	intron (NM_010444, intron 1 of 6)	intron (NM_010444, intron 1 of 6)	2556	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_60163.1	chr7	40674735	40674744	+	1	NA	promoter-TSS (NR_045504)	promoter-TSS (NR_045504)	2	NR_045504	71029	Mm.399496	NR_045504	ENSMUSG00000102004	4933402C06Rik	-	RIKEN cDNA 4933402C06 gene	ncRNA
mm_85413.1	chr9	103449109	103449117	-	1	NA	intron (NM_001002896, intron 3 of 6)	intron (NM_001002896, intron 3 of 6)	25535	NR_040466	100529079	Mm.437003	NR_040466	ENSMUSG00000086236	5830418P13Rik	-	RIKEN cDNA 5830418P13 gene	ncRNA
mm_101811.1	chr11	46386609	46386622	-	1	NA	intron (NM_010583, intron 1 of 16)	intron (NM_010583, intron 1 of 16)	2900	NM_001281968	16428	Mm.339927	NM_010583	ENSMUSG00000020395	Itk	Emt|Tcsk|Tsk	IL2 inducible T cell kinase	protein-coding
mm_124662.1	chr15	6299798	6299851	+	1	NA	promoter-TSS (NM_001008702)	promoter-TSS (NM_001008702)	35	NM_001008702	13132	Mm.240830	NM_023118	ENSMUSG00000022150	Dab2	5730435J12Rik|AA960054|AI957090|D15Wsu122e|D630005B22Rik|Doc-2|Doc2|p96	disabled 2, mitogen-responsive phosphoprotein	protein-coding
mm_81184.1	chr9	107505885	107505892	+	1	NA	intron (NM_001174047, intron 4 of 38)	intron (NM_001174047, intron 4 of 38)	-28057	NM_019704	56395	Mm.260153	NM_019704	ENSMUSG00000010045	Tmem115	C78915|Pl6|Pp6	transmembrane protein 115	protein-coding
mm_68616.1	chr7	116458957	116458961	-	1	NA	Intergenic	Intergenic	-15501	NM_011083	18704	Mm.3810	NM_011083	ENSMUSG00000030660	Pik3c2a	Cpk-m|PI3KC2	phosphatidylinositol 3-kinase, C2 domain containing, alpha polypeptide	protein-coding
mm_139821.1	chr17	67722280	67722295	+	1	NA	intron (NM_008480, intron 3 of 62)	intron (NM_008480, intron 3 of 62)	25022	NM_008480	16772	Mm.303386	NM_008480	ENSMUSG00000032796	Lama1	AA408497|Lama	laminin, alpha 1	protein-coding
mm_42026.1	chr5	108279428	108279453	+	1	NA	3' UTR (NM_026106, exon 3 of 3)	3' UTR (NM_026106, exon 3 of 3)	10543	NM_026106	13486	Mm.303534	NM_026106	ENSMUSG00000029265	Dr1	1700121L09Rik|Dr1l|NC2|NC2beta	down-regulator of transcription 1	protein-coding
mm_22590.1	chr3	13510012	13510016	+	1	NA	intron (NM_178631, intron 2 of 9)	intron (NM_178631, intron 2 of 9)	38359	NM_001163328	76897	Mm.422625	NM_178631	ENSMUSG00000039717	Ralyl	0710005M24Rik	RALY RNA binding protein-like	protein-coding
mm_67944.1	chr7	100371890	100371988	-	1	NA	promoter-TSS (NM_001017985)	promoter-TSS (NM_001017985)	-43	NM_028292	72590	Mm.177502	NM_028292	ENSMUSG00000030718	Ppme1	1110069N17Rik|2700017M01Rik|PME-1|Pme1	protein phosphatase methylesterase 1	protein-coding
mm_148494.1	chr19	4156101	4156111	+	1	NA	TTS (NM_021485)	TTS (NM_021485)	1460	NM_016933	19265	Mm.271937	NM_016933	ENSMUSG00000045826	Ptprcap	AI605264|CD-45-AP|LPAP|LSM-1	protein tyrosine phosphatase, receptor type, C polypeptide-associated protein	protein-coding
mm_15191.1	chr2	154204695	154204709	+	1	NA	exon (NM_153418, exon 3 of 16)	exon (NM_153418, exon 3 of 16)	4322	NM_153418	228801	Mm.3783	NM_153418	ENSMUSG00000027485	Bpifb1	Lplunc1	BPI fold containing family B, member 1	protein-coding
mm_136575.1	chr17	3482181	3482187	+	1	NA	promoter-TSS (NM_001286758)	promoter-TSS (NM_001286758)	-131	NM_001286758	24001	Mm.137134	NM_011878	ENSMUSG00000023800	Tiam2	3000002F19Rik|STEF|mKIAA2016	T cell lymphoma invasion and metastasis 2	protein-coding
mm_131907.1	chr16	23269578	23269610	+	1	NA	intron (NM_001252505, intron 2 of 7)	intron (NM_001252505, intron 2 of 7)	-20876	NM_001252506	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_136856.1	chr17	12799145	12799162	+	1	NA	intron (NR_027784, intron 2 of 2)	B1F1|SINE|Alu	-29447	NM_010515	16004	Mm.26553	NM_010515	ENSMUSG00000023830	Igf2r	AI661837|CD222|CI-MPR|M6P/IGF2R|Mpr300	insulin-like growth factor 2 receptor	protein-coding
mm_159550.1	chr4	101727875	101727875	+	1	NA	intron (NM_146146, intron 1 of 18)	intron (NM_146146, intron 1 of 18)	10468	NM_010704	16847	Mm.259282	NM_010704	ENSMUSG00000057722	Lepr	LEPROT|Leprb|Modb1|OB-RGRP|Obr|db|diabetes|obese-like|obl	leptin receptor	protein-coding
mm_35096.1	chr4	8822628	8822634	-	1	NA	intron (NM_001277149, intron 8 of 37)	intron (NM_001277149, intron 8 of 37)	132225	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_124607.1	chr15	3279300	3279304	+	1	NA	exon (NM_009155, exon 5 of 5)	exon (NM_009155, exon 5 of 5)	8325	NM_009155	20363	Mm.392203	NM_009155	ENSMUSG00000064373	Selenop	AU018766|D15Ucla1|Se-P|Sepp1|selp	selenoprotein P	protein-coding
mm_6944.1	chr1	85731154	85731159	-	1	NA	intron (NM_177055, intron 1 of 5)	RMER15-int|LTR|ERVL	5450	NM_177055	319997	Mm.116691	NM_177055	ENSMUSG00000052760	A630001G21Rik	-	RIKEN cDNA A630001G21 gene	protein-coding
mm_166951.1	chr7	44210692	44210701	+	1	NA	exon (NM_010915, exon 3 of 5)	exon (NM_010915, exon 3 of 5)	3263	NM_010915	18048	Mm.440886	NM_010915	ENSMUSG00000066513	Klk1b4	Ngfa|alpha-NGF|mGk-4	kallikrein 1-related pepidase b4	protein-coding
mm_161238.1	chr13	95984840	95984840	-	1	NA	intron (NM_029210, intron 8 of 12)	B2_Mm2|SINE|B2	-92918	NM_027711	544963	Mm.38878	NM_027711	ENSMUSG00000021676	Iqgap2	4933417J23Rik|A630053O10|AI788777	IQ motif containing GTPase activating protein 2	protein-coding
mm_58949.1	chr7	18718076	18718092	+	1	NA	promoter-TSS (NM_001004152)	promoter-TSS (NM_001004152)	-6	NM_001004152	243862	Mm.389833	NM_001004152	ENSMUSG00000044903	Psg22	AA408604|cea9	pregnancy-specific glycoprotein 22	protein-coding
mm_84255.1	chr9	62510587	62510605	-	1	NA	intron (NM_175484, intron 1 of 11)	intron (NM_175484, intron 1 of 11)	26448	NM_175484	235431	Mm.335229	NM_175484	ENSMUSG00000041729	Coro2b	CLIPINC|E130012P22Rik	coronin, actin binding protein, 2B	protein-coding
mm_41615.1	chr5	96796083	96796093	+	1	NA	intron (NM_013470, intron 1 of 12)	intron (NM_013470, intron 1 of 12)	2703	NM_013470	11745	Mm.7214	NM_013470	ENSMUSG00000029484	Anxa3	Anx3	annexin A3	protein-coding
mm_113680.1	chr13	42799807	42799817	+	1	NA	intron (NM_001005740, intron 1 of 12)	intron (NM_001005740, intron 1 of 12)	-66435	NM_001302636	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding
mm_21364.1	chr2	157133972	157133974	-	1	NA	intron (NM_018851, intron 1 of 15)	BC1_Mm|scRNA|scRNA	1249	NM_001139520	56045	Mm.248478	NM_018851	ENSMUSG00000027639	Samhd1	E330031J07Rik|Mg11	SAM domain and HD domain, 1	protein-coding
mm_118773.1	chr14	22772793	22772795	+	1	NA	intron (NM_028275, intron 5 of 6)	intron (NM_028275, intron 5 of 6)	-229996	NR_046307	74896	Mm.444661	NR_046307		4930405A10Rik	4930456G20Rik	RIKEN cDNA 4930405A10 gene	ncRNA
mm_114116.1	chr13	55005986	55006015	+	1	NA	TTS (NM_153131)	TTS (NM_153131)	14819	NM_001206390	212032	Mm.267479	NM_001033245	ENSMUSG00000025877	Hk3	HK III|HK-III	hexokinase 3	protein-coding
mm_90033.1	chr10	115431070	115431081	+	1	NA	intron (NM_001033261, intron 32 of 34)	intron (NM_001033261, intron 32 of 34)	46116	NM_001033261	216345	Mm.207621	NM_001033261	ENSMUSG00000034163	Zfc3h1	BC033596|Ccdc131|Psrc2	zinc finger, C3H1-type containing	protein-coding
mm_97021.1	chr11	71750983	71750995	+	1	NA	intron (NM_177618, intron 1 of 8)	CpG	286	NM_177618	216881	Mm.48648	NM_177618	ENSMUSG00000020811	Wscd1	mKIAA0523	WSC domain containing 1	protein-coding
mm_49904.1	chr6	38951861	38951891	+	1	NA	intron (NM_011539, intron 2 of 12)	intron (NM_011539, intron 2 of 12)	32890	NM_011539	21391	Mm.4054	NM_011539	ENSMUSG00000029925	Tbxas1	CYP5|CYP5A1|THAS|TS|TXAS|TXS	thromboxane A synthase 1, platelet	protein-coding
mm_113428.1	chr13	34163040	34163055	+	1	NA	promoter-TSS (NM_001110515)	promoter-TSS (NM_001110515)	83	NM_001110515	69666	Mm.24788	NM_001101430	ENSMUSG00000071451	Psmg4	PAC-4|mPAC4	proteasome (prosome, macropain) assembly chaperone 4	protein-coding
mm_11209.1	chr2	29457367	29457370	+	1	NA	intron (NM_001290490, intron 4 of 5)	RCHARR1|DNA|hAT-Charlie	17926	NR_105753	102465170		NR_105753	ENSMUSG00000098539	Mir133c	Gm27865|mmu-mir-133c	microRNA 133c	ncRNA
mm_12415.1	chr2	70561285	70561307	+	1	NA	promoter-TSS (NM_008077)	promoter-TSS (NM_008077)	-833	NM_001312900	14415	Mm.272120	NM_008077	ENSMUSG00000070880	Gad1	EP10|Gad-1	glutamate decarboxylase 1	protein-coding
mm_10201.1	chr2	4935991	4936026	+	1	NA	exon (NM_010726, exon 7 of 9)	exon (NM_010726, exon 7 of 9)	17012	NM_010726	16922	Mm.391704	NM_010726	ENSMUSG00000026664	Phyh	AI256161|AI265699|Lnap1|PAHX	phytanoyl-CoA hydroxylase	protein-coding
mm_123775.1	chr14	70316591	70316626	-	1	NA	exon (NM_144808, exon 4 of 10)	exon (NM_144808, exon 4 of 10)	-27111	NM_001304992	19057	Mm.439683	NM_008915	ENSMUSG00000022092	Ppp3cc	Calnc|PP2BA gamma	protein phosphatase 3, catalytic subunit, gamma isoform	protein-coding
mm_162629.1	chr1	185969951	185969957	+	1	NA	intron (NR_030555, intron 5 of 6)	intron (NR_030555, intron 5 of 6)	147356	NM_146106	226791	Mm.257116	NM_146106	ENSMUSG00000039246	Lyplal1	BC027340|Q96AVO	lysophospholipase-like 1	protein-coding
mm_49425.1	chr6	29271296	29271311	+	1	NA	Intergenic	Intergenic	-1185	NM_001190461	69573	Mm.45161	NM_023516	ENSMUSG00000043421	Hilpda	2310016C08Rik|AW049004|Hig2	hypoxia inducible lipid droplet associated	protein-coding
mm_57651.1	chr6	128438619	128438636	-	1	NA	promoter-TSS (NM_010219)	promoter-TSS (NM_010219)	4	NM_010219	14228	Mm.12758	NM_010219	ENSMUSG00000030357	Fkbp4	59kDa|AL022792|AW208983|FKBP-4|FKBP-52|FKBP52|FKPB52|p59	FK506 binding protein 4	protein-coding
mm_44370.1	chr5	17814145	17814188	-	1	NA	exon (NM_001159558, exon 7 of 16)	exon (NM_001159558, exon 7 of 16)	21730	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_98757.1	chr11	96545670	96545689	+	1	NA	intron (NM_001033186, intron 4 of 12)	intron (NM_001033186, intron 4 of 12)	81088	NM_001177898	78473	Mm.395840	NM_001033186	ENSMUSG00000057058	Skap1	1700091G21Rik|Scap1|Skap-55	src family associated phosphoprotein 1	protein-coding
mm_101620.1	chr11	35844402	35844420	-	1	NA	intron (NM_170779, intron 19 of 22)	intron (NM_170779, intron 19 of 22)	-9883	NM_025936	104458	Mm.284906	NM_025936	ENSMUSG00000018848	Rars	2610011N19Rik|2610037E21Rik|AL033339|AW985894	arginyl-tRNA synthetase	protein-coding
mm_169986.1	chr17	15041530	15041537	-	1	NA	promoter-TSS (NM_001039552)	promoter-TSS (NM_001039552)	26	NM_001123368	100041586	Mm.440445	NM_001123368	ENSMUSG00000079710	Gm3417	-	predicted gene 3417	protein-coding
mm_115492.1	chr13	3611190	3611210	-	1	NA	promoter-TSS (NM_134063)	promoter-TSS (NM_134063)	-92	NM_134063	105203	Mm.221609	NM_134063	ENSMUSG00000033799	Fam208b	AI645998|Pap20|mKIAA2006	family with sequence similarity 208, member B	protein-coding
mm_98094.1	chr11	86604058	86604066	+	1	NA	intron (NM_029478, intron 9 of 11)	intron (NM_029478, intron 9 of 11)	-19904	NR_029738	387140		NR_029738	ENSMUSG00000065455	Mir21a	Mir21|Mirn21|mmu-mir-21|mmu-mir-21a	microRNA 21a	ncRNA
mm_51175.1	chr6	70726697	70726701	+	1	NA	Intergenic	Intergenic	65476	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_110807.1	chr12	72212562	72212574	-	1	NA	exon (NM_001286448, exon 7 of 7)	exon (NM_001286448, exon 7 of 7)	23178	NR_104446	104001	Mm.221275	NM_153457	ENSMUSG00000021087	Rtn1	Nsp	reticulon 1	protein-coding
mm_59334.1	chr7	25433678	25433688	+	1	NA	intron (NR_015569, intron 4 of 6)	intron (NR_015569, intron 4 of 6)	-20797	NM_153576	232983	Mm.10545	NM_153576	ENSMUSG00000060188	Cxcl17	VCC-1|Vcc1	chemokine (C-X-C motif) ligand 17	protein-coding
mm_109254.1	chr12	109459687	109459739	+	1	NA	exon (NM_010052, exon 5 of 5)	exon (NM_010052, exon 5 of 5)	6258	NM_010052	13386	Mm.157069	NM_010052	ENSMUSG00000040856	Dlk1	AW742678|DLK-1|DlkI|FA1|Ly107|Peg9|SCP1|ZOG|pG2|pref-1	delta-like 1 homolog (Drosophila)	protein-coding
mm_50115.1	chr6	41534316	41534338	+	1	NA	Intergenic	Intergenic	12551	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_157183.1	chrX	10216438	10216482	-	1	NA	promoter-TSS (NM_001177952)	promoter-TSS (NM_001177952)	-7	NM_001177952	19893	Mm.247556	NM_011285	ENSMUSG00000031174	Rpgr	Rp3h	retinitis pigmentosa GTPase regulator	protein-coding
mm_107341.1	chr12	32379746	32379756	+	1	NA	3' UTR (NM_001162903, exon 1 of 1)	3' UTR (NM_001162903, exon 1 of 1)	962	NM_001162903	72123	Mm.341352	NM_028111	ENSMUSG00000090946	Ccdc71l	2010109K11Rik|AV375874	coiled-coil domain containing 71 like	protein-coding
mm_29969.1	chr3	133518773	133518785	-	1	NA	intron (NM_001040400, intron 1 of 10)	intron (NM_001040400, intron 1 of 10)	25611	NM_001346736	214133	Mm.347816	NM_145989	ENSMUSG00000040943	Tet2	Ayu17-449|E130014J05Rik|mKIAA1546	tet methylcytosine dioxygenase 2	protein-coding
mm_43824.1	chr5	142963679	142963689	+	1	NA	intron (NM_007984, intron 1 of 4)	intron (NM_007984, intron 1 of 4)	3329	NM_007984	14086	Mm.289707	NM_007984	ENSMUSG00000029581	Fscn1	AI663989|Fan1|fascin-1	fascin actin-bundling protein 1	protein-coding
mm_114587.1	chr13	75750050	75750061	+	1	NA	exon (NM_138953, exon 4 of 12)	exon (NM_138953, exon 4 of 12)	42571	NM_138953	192657	Mm.21288	NM_138953	ENSMUSG00000001542	Ell2	-	elongation factor RNA polymerase II 2	protein-coding
mm_82389.1	chr9	14675990	14675995	-	1	NA	Intergenic	Intergenic	-60992	NM_001081395	75723	Mm.159552	NM_001081395	ENSMUSG00000013076	Amotl1	2310010G08Rik|2310067L22Rik|4932416D09Rik|JEAP|mFLJ00155	angiomotin-like 1	protein-coding
mm_26359.1	chr3	142549453	142549464	+	1	NA	3' UTR (NM_001083312, exon 11 of 11)	3' UTR (NM_001083312, exon 11 of 11)	-10594	NM_018734	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_30753.1	chr4	14930710	14930720	+	1	NA	promoter-TSS (NM_001243100)	promoter-TSS (NM_001243100)	74	NM_001243100	100038514	Mm.331495	NM_001243100		Gm11837	OTTMUSG00000004551	predicted gene 11837	protein-coding
mm_154515.1	chrM	12658	12678	-	1	NA	NA	Intergenic	NA	NA								
mm_169002.1	chr13	102421596	102421598	+	1	NA	Intergenic	L1Md_T|LINE|L1	-271961	NM_008533	17079	Mm.373974	NM_008533	ENSMUSG00000021624	Cd180	F630107B15|Ly78|RP105	CD180 antigen	protein-coding
mm_105233.1	chr11	102317624	102317642	-	1	NA	promoter-TSS (NM_001044383)	promoter-TSS (NM_001044383)	-346	NM_001044383	21429	Mm.2845	NM_011551	ENSMUSG00000020923	Ubtf	A930005G04Rik|NOR-90|Tcfubf|UBF|UBF-1|UBF1	upstream binding transcription factor, RNA polymerase I	protein-coding
mm_149817.1	chr19	24030819	24030822	+	1	NA	exon (NM_001114174, exon 1 of 11)	exon (NM_001114174, exon 1 of 11)	199	NM_001114174	381217	Mm.426078	NM_001114174	ENSMUSG00000071604	Fam189a2	AI414343|AI666772|Gm967	family with sequence similarity 189, member A2	protein-coding
mm_104676.1	chr11	97687207	97687230	-	1	NA	intron (NM_001085500, intron 2 of 2)	intron (NM_001085500, intron 2 of 2)	1266	NM_001085500	217149	Mm.29659	NM_001085500	ENSMUSG00000078695	Cisd3	Mel-13|Mel13	CDGSH iron sulfur domain 3	protein-coding
mm_30443.1	chr3	153705692	153705703	-	1	NA	intron (NM_011372, intron 1 of 4)	intron (NM_011372, intron 1 of 4)	19436	NM_011372	20447	Mm.296453	NM_011372	ENSMUSG00000052544	St6galnac3	Siat7c	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 3	protein-coding
mm_42993.1	chr5	123344441	123344576	+	1	NA	promoter-TSS (NM_029850)	promoter-TSS (NM_029850)	60	NM_029850	77045	Mm.151960	NM_029850	ENSMUSG00000029438	Bcl7a	4432415N06Rik|AI448316	B cell CLL/lymphoma 7A	protein-coding
mm_151328.1	chr19	55893394	55893398	+	1	NA	intron (NR_138565, intron 4 of 15)	intron (NR_138565, intron 4 of 15)	-1925	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_104211.1	chr11	88340694	88340706	-	1	NA	3' UTR (NM_054043, exon 14 of 14)	3' UTR (NM_054043, exon 14 of 14)	-12073	NR_039545	100628571		NR_039545	ENSMUSG00000092985	Mir378b	mir-378b|mmu-mir-378b	microRNA 378b	ncRNA
mm_100126.1	chr11	115912281	115912303	+	1	NA	5' UTR (NM_001162998, exon 1 of 2)	5' UTR (NM_001162998, exon 1 of 2)	275	NM_001162998	68528	Mm.441893	NM_001162998	ENSMUSG00000075420	Smim6	1110017F19Rik	small integral membrane protein 6	protein-coding
mm_25068.1	chr3	99296503	99296513	+	1	NA	intron (NM_009323, intron 1 of 7)	intron (NM_009323, intron 1 of 7)	42748	NM_009323	21384	Mm.88761	NM_009323	ENSMUSG00000027868	Tbx15	Tbx14|Tbx8|de	T-box 15	protein-coding
mm_77847.1	chr9	5303074	5303100	+	1	NA	exon (NM_009807, exon 5 of 10)	exon (NM_009807, exon 5 of 10)	4570	NM_009807	12362	Mm.1051	NM_009807	ENSMUSG00000025888	Casp1	ICE|Il1bc	caspase 1	protein-coding
mm_90373.1	chr10	127181845	127181855	+	1	NA	TTS (NM_028027)	TTS (NM_028027)	-1205	NM_177615	216441	Mm.248373	NM_177615	ENSMUSG00000040441	Slc26a10	C78409|D630010I07	solute carrier family 26, member 10	protein-coding
mm_118438.1	chr14	8080316	8080385	+	1	NA	promoter-TSS (NM_025938)	promoter-TSS (NM_025938)	37	NM_025938	67053	Mm.210048	NM_025938	ENSMUSG00000023156	Rpp14	2610511E03Rik|AA682089	ribonuclease P 14 subunit	protein-coding
mm_11360.1	chr2	30929130	30929168	+	1	NA	Intergenic	Intergenic	-23852	NM_133673	30934	Mm.249164	NM_133673	ENSMUSG00000026848	Tor1b	2610016F05Rik|DQ1|torsinB	torsin family 1, member B	protein-coding
mm_36571.1	chr4	87881738	87881762	-	1	NA	intron (NM_027326, intron 2 of 10)	intron (NM_027326, intron 2 of 10)	-75427	NM_029931	70122	Mm.288898	NM_027326	ENSMUSG00000028496	Mllt3	2210011H10Rik|2610012I03Rik|3830408D16Rik|Af9|D4Ertd321e	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 3	protein-coding
mm_151146.1	chr19	53140431	53140449	+	1	NA	promoter-TSS (NM_001164099)	promoter-TSS (NM_001164099)	-3	NM_001164099	27360	Mm.426080	NM_013758	ENSMUSG00000025026	Add3	AI463285|R75380	adducin 3 (gamma)	protein-coding
mm_159068.1	chr2	24950396	24950396	+	1	NA	5' UTR (NM_147179, exon 1 of 6)	5' UTR (NM_147179, exon 1 of 6)	238	NM_147179	67187	Mm.296106	NM_026021	ENSMUSG00000026974	Zmynd19	2700064H14Rik|AA536891|AU014915|mizip	zinc finger, MYND domain containing 19	protein-coding
mm_170711.1	chr2	144149167	144149185	+	1	NA	Intergenic	ERVB7_1-LTR_MM|LTR|ERVK	40114	NR_136884	433481	Mm.330630	NR_136884	ENSMUSG00000074758	Gm5535	EG433481	predicted gene 5535	ncRNA
mm_141950.1	chr17	35081234	35081244	-	1	NA	intron (NM_001163192, intron 3 of 5)	intron (NM_001163192, intron 3 of 5)	4297	NM_027366	70274	Mm.250491	NM_027366	ENSMUSG00000013766	Ly6g6e	2310011I02Rik|G6e	lymphocyte antigen 6 complex, locus G6E	protein-coding
mm_144871.1	chr18	36744674	36744737	+	1	NA	promoter-TSS (NM_011879)	promoter-TSS (NM_011879)	49	NM_011879	24010	Mm.30234	NM_011879	ENSMUSG00000024474	Ik	MuRED	IK cytokine	protein-coding
mm_154975.1	chrX	37191221	37191320	+	1	NA	promoter-TSS (NM_019443)	promoter-TSS (NM_019443)	-32	NM_019443	54405	Mm.34869	NM_019443	ENSMUSG00000016427	Ndufa1	1810049F12Rik|MWFE	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 1	protein-coding
mm_99535.1	chr11	103193073	103193084	+	1	NA	exon (NM_001077698, exon 14 of 26)	exon (NM_001077698, exon 14 of 26)	15470	NM_001254724	69441	Mm.380648	NM_027082	ENSMUSG00000020940	1700023F06Rik	-	RIKEN cDNA 1700023F06 gene	protein-coding
mm_164457.1	chr16	55551217	55551219	+	1	NA	Intergenic	L3|LINE|CR1	56487	NR_039578	100628589		NR_039578	ENSMUSG00000093292	Mir5118	mmu-mir-5118|mu-mir-5118	microRNA 5118	ncRNA
mm_94876.1	chr11	24113740	24113752	+	1	NA	intron (NM_016707, intron 2 of 4)	ID4|SINE|ID	33051	NM_001159290	14025	Mm.53687	NM_016707	ENSMUSG00000000861	Bcl11a	2810047E18Rik|BCL-11A|Ctip1|D930021L15Rik|Evi9|Evi9a|Evi9b|Evi9c|mKIAA1809	B cell CLL/lymphoma 11A (zinc finger protein)	protein-coding
mm_136423.1	chr16	93982567	93982573	-	1	NA	intron (NM_019500, intron 1 of 2)	ORR1E|LTR|ERVL-MaLR	26267	NM_019500	56173	Mm.328716	NM_019500	ENSMUSG00000047109	Cldn14	AI851731	claudin 14	protein-coding
mm_71594.1	chr8	54955094	54955117	+	1	NA	5' UTR (NM_153581, exon 1 of 7)	5' UTR (NM_153581, exon 1 of 7)	377	NM_001253756	234267	Mm.241700	NM_153581	ENSMUSG00000031517	Gpm6a	Gpm6|M6A	glycoprotein m6a	protein-coding
mm_126221.1	chr15	78914409	78914475	+	1	NA	exon (NM_020271, exon 1 of 2)	exon (NM_020271, exon 1 of 2)	523	NM_020271	57028	Mm.263169	NM_020271	ENSMUSG00000022436	Pdxp	1600027H05Rik|AB041662|PLPP	pyridoxal (pyridoxine, vitamin B6) phosphatase	protein-coding
mm_152316.1	chr19	9914151	9914168	-	1	NA	Intergenic	Intergenic	-14626	NM_016692	16319	Mm.29755	NM_016692	ENSMUSG00000024660	Incenp	2700067E22Rik|AU019509|C130081E20|C77457	inner centromere protein	protein-coding
mm_146432.1	chr18	84871930	84871934	+	1	NA	intron (NM_025797, intron 2 of 4)	intron (NM_025797, intron 2 of 4)	20518	NM_025797	109672	Mm.31018	NM_025797	ENSMUSG00000024646	Cyb5a	0610009N12Rik|Cyb5	cytochrome b5 type A (microsomal)	protein-coding
mm_13682.1	chr2	116972378	116972399	+	1	NA	Intergenic	Intergenic	72236	NR_040335	320975	Mm.132509	NR_040335	ENSMUSG00000085316	D330050G23Rik	-	RIKEN cDNA D330050G23 gene	ncRNA
mm_73137.1	chr8	94977278	94977288	+	1	NA	5' UTR (NM_001198894, exon 1 of 14)	5' UTR (NM_001198894, exon 1 of 14)	174	NM_001198894	14766	Mm.290834	NM_018882	ENSMUSG00000031785	Adgrg1	Cyt28|Gpr56|TM7LN4|TM7XN1	adhesion G protein-coupled receptor G1	protein-coding
mm_101013.1	chr11	8531734	8531767	-	1	NA	exon (NM_001083587, exon 12 of 31)	exon (NM_001083587, exon 12 of 31)	132785	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_73082.1	chr8	94480585	94480597	+	1	NA	intron (NM_001033207, intron 6 of 48)	B1_Mus1|SINE|Alu	7828	NM_001033207	434341	Mm.334720	NM_001033207	ENSMUSG00000074151	Nlrc5	AI451557|AK220210|NOD27	NLR family, CARD domain containing 5	protein-coding
mm_59473.1	chr7	27448052	27448069	+	1	NA	promoter-TSS (NM_144923)	promoter-TSS (NM_144923)	82	NM_144923	233016	Mm.24021	NM_144923	ENSMUSG00000040466	Blvrb	-	biliverdin reductase B (flavin reductase (NADPH))	protein-coding
mm_115997.1	chr13	24414935	24414947	-	1	NA	promoter-TSS (NM_001284520)	promoter-TSS (NM_001284520)	-181	NM_007717	12763	Mm.8396	NM_007717	ENSMUSG00000016756	Cmah	-	cytidine monophospho-N-acetylneuraminic acid hydroxylase	protein-coding
mm_110663.1	chr12	59219702	59219717	-	1	NA	promoter-TSS (NM_001033156)	promoter-TSS (NM_001033156)	-226	NM_001033156	70611	Mm.311026	NM_001033156	ENSMUSG00000035329	Fbxo33	5730501N20Rik|AI642135	F-box protein 33	protein-coding
mm_10647.1	chr2	20655152	20655158	+	1	NA	intron (NM_029895, intron 3 of 18)	intron (NM_029895, intron 3 of 18)	135642	NM_001177631	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding
mm_31785.1	chr4	63634432	63634439	+	1	NA	Intergenic	Intergenic	-12006	NM_029324	75524	Mm.38543	NM_029324	ENSMUSG00000058935	1700018C11Rik	bM230C2.3	RIKEN cDNA 1700018C11 gene	protein-coding
mm_76663.1	chr8	93337196	93337216	-	1	NA	promoter-TSS (NM_021456)	promoter-TSS (NM_021456)	3	NM_021456	12623	Mm.22720	NM_021456	ENSMUSG00000057074	Ces1g	Ces-1|Ces1|Ses-1	carboxylesterase 1G	protein-coding
mm_51393.1	chr6	78371043	78371050	+	1	NA	intron (NM_011036, intron 1 of 5)	intron (NM_011036, intron 1 of 5)	161	NM_011036	18489	Mm.2553	NM_011036	ENSMUSG00000071356	Reg3b	HIP|PAP1|Pap|REG-III	regenerating islet-derived 3 beta	protein-coding
mm_77027.1	chr8	108884921	108884927	-	1	NA	intron (NM_007496, intron 4 of 9)	intron (NM_007496, intron 4 of 9)	-51936	NR_037295	100526511		NR_037295	ENSMUSG00000093241	Mir3108	mir-3108|mmu-mir-3108	microRNA 3108	ncRNA
mm_50625.1	chr6	50190056	50190059	+	1	NA	intron (NM_019939, intron 10 of 12)	intron (NM_019939, intron 10 of 12)	71712	NM_018769	54722	Mm.248361	NM_018769	ENSMUSG00000029821	Dfna5	2310037D07Rik|4932441K13Rik|Dfna5h|EG14210|Fin15	deafness, autosomal dominant 5 (human)	protein-coding
mm_56149.1	chr6	87838672	87838792	-	1	NA	promoter-TSS (NM_133934)	promoter-TSS (NM_133934)	27	NM_133934	57905	Mm.241546	NM_133934	ENSMUSG00000030056	Isy1	5830446M03Rik|AI181014|AU020769	ISY1 splicing factor homolog	protein-coding
mm_34240.1	chr4	141193663	141193683	+	1	NA	exon (NM_172518, exon 5 of 10)	exon (NM_172518, exon 5 of 10)	-20283	NM_001081174	76166	Mm.271064	NM_001081174	ENSMUSG00000073733	Rsg1	6330545A04Rik|Gm723	REM2 and RAB-like small GTPase 1	protein-coding
mm_22403.1	chr2	181241981	181242018	-	1	NA	promoter-TSS (NM_183162)	promoter-TSS (NM_183162)	28	NM_183162	229003	Mm.315872	NM_183162	ENSMUSG00000027580	Helz2	PDIP1|Pric285|mKIAA1769|mPDIP1	helicase with zinc finger 2, transcriptional coactivator	protein-coding
mm_153950.1	chr19	47669298	47669300	-	1	NA	exon (NM_007732, exon 17 of 53)	exon (NM_007732, exon 17 of 53)	22743	NM_007732	12821	Mm.1225	NM_007732	ENSMUSG00000025064	Col17a1	BP180|Bpag|Bpag2	collagen, type XVII, alpha 1	protein-coding
mm_35906.1	chr4	49681957	49682038	-	1	NA	promoter-TSS (NM_001004025)	promoter-TSS (NM_001004025)	-14	NM_001004025	19059	Mm.46125	NM_001004025	ENSMUSG00000028310	Ppp3r2	CaNB2|CnB2	protein phosphatase 3, regulatory subunit B, alpha isoform (calcineurin B, type II)	protein-coding
mm_9967.1	chr1	191181567	191181577	-	1	NA	intron (NM_007498, intron 1 of 3)	intron (NM_007498, intron 1 of 3)	1761	NM_007498	11910	Mm.2706	NM_007498	ENSMUSG00000026628	Atf3	LRG-21	activating transcription factor 3	protein-coding
mm_24275.1	chr3	89204342	89204382	+	1	NA	exon (NM_001077411, exon 4 of 11)	exon (NM_001077411, exon 4 of 11)	1437	NR_122037	14466	Mm.5031	NM_008094	ENSMUSG00000028048	Gba	GBA1|GC|GCase|GLUC|betaGC	glucosidase, beta, acid	protein-coding
mm_138424.1	chr17	35069691	35069722	+	1	NA	3' UTR (NM_023463, exon 3 of 3)	3' UTR (NM_023463, exon 3 of 3)	2381	NM_023463	68468	Mm.215096	NM_023463	ENSMUSG00000092586	Ly6g6c	1110003M04Rik|AU016360|G6c|NG24	lymphocyte antigen 6 complex, locus G6C	protein-coding
mm_10642.1	chr2	20547962	20547972	+	1	NA	intron (NM_029895, intron 3 of 18)	intron (NM_029895, intron 3 of 18)	28454	NM_001177631	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding
mm_135270.1	chr16	38396049	38396055	-	1	NA	TTS (NM_134102)	TTS (NM_134102)	33862	NM_022318	64082	Mm.390856	NM_022318	ENSMUSG00000022803	Popdc2	AV006127|Pop2	popeye domain containing 2	protein-coding
mm_145003.1	chr18	38418928	38418938	+	1	NA	promoter-TSS (NM_022996)	promoter-TSS (NM_022996)	-42	NM_022996	65113	Mm.102496	NM_022996	ENSMUSG00000024425	Ndfip1	0610010M22Rik|N4wbp5	Nedd4 family interacting protein 1	protein-coding
mm_123426.1	chr14	64439808	64439811	-	1	NA	intron (NM_001253712, intron 1 of 5)	intron (NM_001253712, intron 1 of 5)	1217	NM_001253715	110265	Mm.26713	NM_026322	ENSMUSG00000054733	Msra	2310045J23Rik|6530413P12Rik|MSR-A	methionine sulfoxide reductase A	protein-coding
mm_33204.1	chr4	126321146	126321158	+	1	NA	TTS (NM_011902)	TTS (NM_011902)	551	NM_133883	100206	Mm.11285	NM_133883	ENSMUSG00000042558	Adprhl2	AI836109|Arh3	ADP-ribosylhydrolase like 2	protein-coding
mm_69705.1	chr7	140082490	140082556	-	1	NA	promoter-TSS (NM_026769)	promoter-TSS (NM_026769)	25	NM_001190385	68566	Mm.44241	NM_026769	ENSMUSG00000025468	Caly	0710001P07Rik|1110004A22Rik|Calcyon|Drd1ip	calcyon neuron-specific vesicular protein	protein-coding
mm_49014.1	chr6	4758549	4758581	+	1	NA	3' UTR (NM_130877, exon 2 of 2)	3' UTR (NM_130877, exon 2 of 2)	11259	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_95566.1	chr11	52389140	52389146	+	1	NA	3' UTR (NM_011694, exon 9 of 9)	3' UTR (NM_011694, exon 9 of 9)	-7285	NM_153117	213673	Mm.291979	NM_153117	ENSMUSG00000036275	9530068E07Rik	C85061|Kct2	RIKEN cDNA 9530068E07 gene	protein-coding
mm_75460.1	chr8	47750134	47750140	-	1	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	-36206	NM_172407	70925	Mm.393807	NM_172407	ENSMUSG00000038069	Cdkn2aip	4921511I16Rik|AW208986|CARF	CDKN2A interacting protein	protein-coding
mm_54347.1	chr6	30806614	30806617	-	1	NA	intron (NM_017478, intron 20 of 23)	PB1D10|SINE|Alu	65316	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_15077.1	chr2	153136566	153136568	+	1	NA	intron (NM_001172117, intron 8 of 12)	intron (NM_001172117, intron 8 of 12)	-24734	NM_133847	99237	Mm.330674	NM_133847	ENSMUSG00000068040	Tm9sf4	AA986553|AU045326|B930079E06|mKIAA0255	transmembrane 9 superfamily protein member 4	protein-coding
mm_138142.1	chr17	34200862	34200872	+	1	NA	exon (NM_010724, exon 5 of 6)	exon (NM_010724, exon 5 of 6)	2672	NM_010724	16913	Mm.180191	NM_010724	ENSMUSG00000024338	Psmb8	Lmp-7|Lmp7	proteasome (prosome, macropain) subunit, beta type 8 (large multifunctional peptidase 7)	protein-coding
mm_68868.1	chr7	126429270	126429310	-	1	NA	intron (NM_030566, intron 1 of 12)	CpG	523	NM_030566	70314	Mm.35467	NM_030566	ENSMUSG00000030727	Rabep2	2610011A08Rik|AI462746|Fra	rabaptin, RAB GTPase binding effector protein 2	protein-coding
mm_14232.1	chr2	127587396	127587430	+	1	NA	promoter-TSS (NM_029963)	promoter-TSS (NM_029963)	-13	NM_029963	77721	Mm.274601	NM_029963	ENSMUSG00000027374	Mrps5	1620401I16Rik|AI850294	mitochondrial ribosomal protein S5	protein-coding
mm_79099.1	chr9	46243106	46243115	+	1	NA	exon (NM_007468, exon 3 of 3)	exon (NM_007468, exon 3 of 3)	2266	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_110810.1	chr12	72223400	72223425	-	1	NA	exon (NM_001286448, exon 2 of 7)	exon (NM_001286448, exon 2 of 7)	12334	NR_104446	104001	Mm.221275	NM_153457	ENSMUSG00000021087	Rtn1	Nsp	reticulon 1	protein-coding
mm_151549.1	chr19	59458426	59458450	+	1	NA	promoter-TSS (NM_010132)	promoter-TSS (NM_010132)	197	NR_002863	329078	Mm.80382	NR_002863	ENSMUSG00000087095	Emx2os	-	Emx2 opposite strand/antisense transcript (non-protein coding)	ncRNA
mm_43969.1	chr5	145809785	145809786	+	1	NA	Intergenic	Lx4B|LINE|L1	-3911	NM_177380	337924	Mm.425301	NM_177380	ENSMUSG00000054417	Cyp3a44	-	cytochrome P450, family 3, subfamily a, polypeptide 44	protein-coding
mm_105714.1	chr11	108343918	108343941	-	1	NA	promoter-TSS (NM_011101)	promoter-TSS (NM_011101)	-41	NM_011101	18750	Mm.222178	NM_011101	ENSMUSG00000050965	Prkca	AI875142|Pkca	protein kinase C, alpha	protein-coding
mm_166757.1	chr6	127543153	127543153	+	1	NA	Intergenic	Intergenic	-34822	NM_001033464	381812	Mm.296093	NM_001033464	ENSMUSG00000061414	Cracr2a	Efcab4b|Gm1073|Gm462	calcium release activated channel regulator 2A	protein-coding
mm_146634.1	chr18	10594936	10594947	-	1	NA	exon (NM_001081222, exon 3 of 11)	exon (NM_001081222, exon 3 of 11)	15411	NM_001081222	77805	Mm.210996	NM_144542	ENSMUSG00000024293	Esco1	A930014I12Rik	establishment of sister chromatid cohesion N-acetyltransferase 1	protein-coding
mm_72665.1	chr8	84893380	84893384	+	1	NA	intron (NM_008097, intron 2 of 10)	intron (NM_008097, intron 2 of 10)	539	NM_001044744	270076	Mm.2475	NM_008097	ENSMUSG00000003809	Gcdh	9030411L18|AI266902|D17825|GCD	glutaryl-Coenzyme A dehydrogenase	protein-coding
mm_127417.1	chr15	101260667	101260684	+	1	NA	Intergenic	Intergenic	-6171	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_5056.1	chr1	194977055	194977059	+	1	NA	promoter-TSS (NR_033564)	promoter-TSS (NR_033564)	-98	NR_033564	320400	Mm.417608	NR_033564	ENSMUSG00000097325	Gm16897	C030002c11rik	predicted gene, 16897	ncRNA
mm_88048.1	chr10	67539854	67539878	+	1	NA	exon (NM_010118, exon 2 of 2)	exon (NM_010118, exon 2 of 2)	1936	NM_001347458	13654	Mm.290421	NM_010118	ENSMUSG00000037868	Egr2	Egr-2|Krox-20|Krox20|NGF1-B|Zfp-25|Zfp-6	early growth response 2	protein-coding
mm_136265.1	chr16	91043848	91043856	-	1	NA	intron (NM_026110, intron 1 of 17)	intron (NM_026110, intron 1 of 17)	527	NM_026110	67367	Mm.347	NM_026110	ENSMUSG00000022974	Paxbp1	1810007M14Rik|C21orf66|Gcfc|Gcfc1|Pax3/7bp	PAX3 and PAX7 binding protein 1	protein-coding
mm_75149.1	chr8	36096694	36096699	-	1	NA	intron (NM_172911, intron 1 of 5)	intron (NM_172911, intron 1 of 5)	1868	NM_172911	244418	Mm.244971	NM_172911	ENSMUSG00000050271	Prag1	9830148H23|D8Ertd82e|NACK|Sgk223|mFLJ00269	PEAK1 related kinase activating pseudokinase 1	protein-coding
mm_134766.1	chr16	23520580	23520673	-	1	NA	promoter-TSS (NM_008555)	promoter-TSS (NM_008555)	-36	NM_008555	17174	Mm.1213	NM_008555	ENSMUSG00000022887	Masp1	AW048060|CCPII|Crarf|Masp1/3	mannan-binding lectin serine peptidase 1	protein-coding
mm_123509.1	chr14	66235668	66235680	-	1	NA	intron (NM_001162365, intron 1 of 30)	intron (NM_001162365, intron 1 of 30)	-22122	NM_001162366	19229	Mm.21613	NM_172498	ENSMUSG00000059456	Ptk2b	CADTK|CAKB|CAKbeta|E430023O05Rik|FADK2|FAK2|PYK2|Raftk	PTK2 protein tyrosine kinase 2 beta	protein-coding
mm_160542.1	chr9	44268603	44268603	-	1	NA	promoter-TSS (NM_001163743)	promoter-TSS (NM_001163743)	-4	NM_001163742	270151	Mm.3957	NM_178420	ENSMUSG00000032109	Nlrx1	BC034204|NOD9	NLR family member X1	protein-coding
mm_142281.1	chr17	40221963	40221965	-	1	NA	3' UTR (NM_009639, exon 8 of 8)	3' UTR (NM_009639, exon 8 of 8)	-13355	NM_031190	18663	Mm.717	NM_031190	ENSMUSG00000031233	Pgk2	Pgk-2|Tcp-2	phosphoglycerate kinase 2	protein-coding
mm_152705.1	chr19	17342035	17342053	-	1	NA	intron (NM_010265, intron 1 of 2)	intron (NM_010265, intron 1 of 2)	-2539	NM_001136484	14537	Mm.244825	NM_010265	ENSMUSG00000038843	Gcnt1	5630400D21Rik|B130048E03|C2 GlcNAcT|C2GNT|IGnT	glucosaminyl (N-acetyl) transferase 1, core 2	protein-coding
mm_103041.1	chr11	69761964	69761972	-	1	NA	promoter-TSS (NM_019871)	promoter-TSS (NM_019871)	-124	NM_019871	56293	Mm.6211	NM_019871	ENSMUSG00000018776	Slc35g3	Amac1	solute carrier family 35, member G3	protein-coding
mm_159827.1	chr5	124354654	124354654	-	1	NA	promoter-TSS (NM_013812)	promoter-TSS (NM_013812)	-26	NM_013812	13445	Mm.391838	NM_013812	ENSMUSG00000029394	Cdk2ap1	Apc10|Cdkap1|DORC1|Doc1|ST19|doc-1|p12	CDK2 (cyclin-dependent kinase 2)-associated protein 1	protein-coding
mm_19878.1	chr2	114049314	114049322	-	1	NA	exon (NM_009608, exon 5 of 7)	exon (NM_009608, exon 5 of 7)	3557	NM_009608	11464	Mm.686	NM_009608	ENSMUSG00000068614	Actc1	Actc-1	actin, alpha, cardiac muscle 1	protein-coding
mm_28168.1	chr3	87870114	87870140	-	1	NA	exon (NM_033573, exon 3 of 7)	exon (NM_033573, exon 3 of 7)	15435	NM_033573	94315	Mm.35089	NM_033573	ENSMUSG00000004895	Prcc	-	papillary renal cell carcinoma (translocation-associated)	protein-coding
mm_56912.1	chr6	119330701	119330712	-	1	NA	promoter-TSS (NM_172492)	promoter-TSS (NM_172492)	60	NM_172492	211187	Mm.121498	NM_172492	ENSMUSG00000055003	Lrtm2	A230084J22|AI841794	leucine-rich repeats and transmembrane domains 2	protein-coding
mm_17892.1	chr2	35061422	35061429	-	1	NA	promoter-TSS (NM_010406)	promoter-TSS (NM_010406)	16	NM_010406	15139	Mm.2168	NM_010406	ENSMUSG00000026874	Hc	C5|C5a|He	hemolytic complement	protein-coding
mm_140066.1	chr17	74820743	74820745	+	1	NA	intron (NM_152817, intron 13 of 19)	RSINE1|SINE|B4	102994	NM_152817	74196	Mm.209503	NM_152817	ENSMUSG00000024078	Ttc27	2610511O17Rik	tetratricopeptide repeat domain 27	protein-coding
mm_147883.1	chr18	64661014	64661063	-	1	NA	promoter-TSS (NM_001001488)	promoter-TSS (NM_001001488)	-38	NM_001001488	54670	Mm.270043	NM_001001488	ENSMUSG00000039529	Atp8b1	AI451886|FIC1|Ic	ATPase, class I, type 8B, member 1	protein-coding
mm_12733.1	chr2	78869299	78869321	+	1	NA	5' UTR (NM_009454, exon 1 of 6)	5' UTR (NM_009454, exon 1 of 6)	263	NM_009454	22193	Mm.1485	NM_009454	ENSMUSG00000027011	Ube2e3	Ubce4|ubcM2	ubiquitin-conjugating enzyme E2E 3	protein-coding
mm_114084.1	chr13	54581697	54581702	+	1	NA	TTS (NM_019968)	TTS (NM_019968)	6686	NM_019968	56795	Mm.89484	NM_019968	ENSMUSG00000025870	Arl10	Arl10a|Arm1	ADP-ribosylation factor-like 10	protein-coding
mm_16836.1	chr2	11498444	11498454	-	1	NA	intron (NM_001177758, intron 1 of 14)	intron (NM_001177758, intron 1 of 14)	3641	NM_001177754	170768	Mm.19669	NM_133232	ENSMUSG00000026773	Pfkfb3	E330010H22Rik|iPFK-2|uPFK-2	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	protein-coding
mm_72206.1	chr8	72584708	72584718	+	1	NA	exon (NM_144534, exon 5 of 6)	exon (NM_144534, exon 5 of 6)	12610	NM_144534	74166	Mm.212927	NM_144534	ENSMUSG00000031791	Tmem38a	1110001E17Rik|AI413399|TRIC-A|mg33a	transmembrane protein 38A	protein-coding
mm_74965.1	chr8	26976949	26976986	-	1	NA	promoter-TSS (NM_001110508)	promoter-TSS (NM_001110508)	-369	NM_001101502	353310	Mm.212469	NM_001101502	ENSMUSG00000085795	Zfp703	1110032O19Rik|AI430822|AL022941|Csmn1|End2|Zeppo1|Znf703|Zpo1	zinc finger protein 703	protein-coding
mm_68161.1	chr7	102759490	102759502	-	1	NA	promoter-TSS (NM_001168503)	promoter-TSS (NM_001168503)	-25	NM_001168503	170639	Mm.184372	NM_130866	ENSMUSG00000043366	Olfr78	4633402A21Rik|MOL2.3|MOR18-2|Or51e2|PSGR|RA1c	olfactory receptor 78	protein-coding
mm_153262.1	chr19	36919653	36919659	-	1	NA	promoter-TSS (NM_028263)	promoter-TSS (NM_028263)	-57	NM_028263	72514	Mm.41674	NM_028263	ENSMUSG00000047632	Fgfbp3	2610306H15Rik|Fgf-bp3	fibroblast growth factor binding protein 3	protein-coding
mm_162140.1	chrX	74270965	74270965	+	1	NA	intron (NM_052835, intron 1 of 6)	intron (NM_052835, intron 1 of 6)	149	NM_052835	110954	Mm.100113	NM_052835	ENSMUSG00000008682	Rpl10	D0HXS648|DXHXS648|DXHXS648E|QM|QM16	ribosomal protein L10	protein-coding
mm_44361.1	chr5	17806056	17806075	-	1	NA	intron (NM_007643, intron 8 of 14)	ORR1C1-int|LTR|ERVL-MaLR	29831	NM_001159555	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_151727.1	chr19	4868029	4868035	-	1	NA	exon (NM_013456, exon 10 of 21)	exon (NM_013456, exon 10 of 21)	9877	NM_013456	11474	Mm.5316	NM_013456	ENSMUSG00000006457	Actn3	-	actinin alpha 3	protein-coding
mm_81310.1	chr9	108392821	108392843	+	1	NA	promoter-TSS (NM_053216)	promoter-TSS (NM_053216)	-2	NM_053216	112418	Mm.78287	NM_053216	ENSMUSG00000032611	1700102P08Rik	AI593206	RIKEN cDNA 1700102P08 gene	protein-coding
mm_106790.1	chr12	4780477	4780511	+	1	NA	Intergenic	Intergenic	11199	NM_028376	382562	Mm.251575	NM_028376	ENSMUSG00000020639	Pfn4	2900024P18Rik	profilin family, member 4	protein-coding
mm_82390.1	chr9	14676018	14676028	-	1	NA	Intergenic	Intergenic	-61023	NM_001081395	75723	Mm.159552	NM_001081395	ENSMUSG00000013076	Amotl1	2310010G08Rik|2310067L22Rik|4932416D09Rik|JEAP|mFLJ00155	angiomotin-like 1	protein-coding
mm_34130.1	chr4	139280512	139280533	+	1	NA	exon (NM_001271405, exon 6 of 9)	exon (NM_001271405, exon 6 of 9)	30178	NM_145384	212555	Mm.45131	NM_145384	ENSMUSG00000028744	Pqlc2	BC019216	PQ loop repeat containing 2	protein-coding
mm_106677.1	chr11	121830142	121830150	-	1	NA	promoter-TSS (NM_029049)	promoter-TSS (NM_029049)	-72	NM_029049	74675	Mm.61213	NM_029049	ENSMUSG00000039198	Ptchd3	4930451E13Rik|4933440L20Rik|RNDEu-3	patched domain containing 3	protein-coding
mm_90428.1	chr10	127514952	127514979	+	1	NA	promoter-TSS (NM_001098789)	promoter-TSS (NM_001098789)	26	NM_001098789	407790	Mm.336856	NM_001098789	ENSMUSG00000040280	Ndufa4l2	BC064011	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 4-like 2	protein-coding
mm_148043.1	chr18	70472340	70472408	-	1	NA	promoter-TSS (NM_001289649)	promoter-TSS (NM_001289649)	-80	NM_029019	170461	Mm.83623	NM_029019	ENSMUSG00000079608	Stard6	1700011K09Rik|4833424I06Rik|4933429L05Rik|AI644424	StAR-related lipid transfer (START) domain containing 6	protein-coding
mm_1694.1	chr1	75142719	75142742	+	1	NA	promoter-TSS (NM_026977)	promoter-TSS (NM_026977)	-56	NM_170755	227298	Mm.273062	NM_170755	ENSMUSG00000049339	Fam134a	-	family with sequence similarity 134, member A	protein-coding
mm_65338.1	chr7	24978556	24978563	-	1	NA	exon (NM_001290469, exon 23 of 23)	exon (NM_001290469, exon 23 of 23)	-5831	NM_010261	14470	Mm.22473	NM_010261	ENSMUSG00000003380	Rabac1	2310040I06Rik|Gbpap1|PRA1|prenylin	Rab acceptor 1 (prenylated)	protein-coding
mm_57366.1	chr6	124769506	124769537	-	1	NA	TTS (NM_001302555)	TTS (NM_001302555)	152	NM_001302642	13807	Mm.3913	NM_013509	ENSMUSG00000004267	Eno2	AI837106|D6Ertd375e|Eno-2|NSE	enolase 2, gamma neuronal	protein-coding
mm_158981.1	chr1	126382334	126382334	-	1	NA	intron (NM_001081756, intron 4 of 16)	intron (NM_001081756, intron 4 of 16)	110593	NM_172484	210356	Mm.377234	NM_172484	ENSMUSG00000049690	Nckap5	8430408F21|D130011D22Rik|E030049G20Rik|Erih1|Erih2|Gm1548|Nap5	NCK-associated protein 5	protein-coding
mm_23063.1	chr3	35937543	35937553	+	1	NA	Intergenic	Intergenic	-4582	NM_001205361	114893	Mm.374810	NM_033623	ENSMUSG00000027708	Dcun1d1	Rp42|SCCRO|Tes3|pTes3	DCN1, defective in cullin neddylation 1, domain containing 1 (S. cerevisiae)	protein-coding
mm_12546.1	chr2	72390742	72390755	+	1	NA	TTS (NM_178084)	TTS (NM_178084)	-85471	NM_025866	66953	Mm.270676	NM_025866	ENSMUSG00000055612	Cdca7	2310021G01Rik|AU044109|JPO1	cell division cycle associated 7	protein-coding
mm_133873.1	chr16	96372884	96372905	+	1	NA	exon (NM_028078, exon 3 of 8)	exon (NM_028078, exon 3 of 8)	11130	NM_028078	72058	Mm.119714	NM_028078	ENSMUSG00000000159	Igsf5	2010003D20Rik|JCAM|Jam4	immunoglobulin superfamily, member 5	protein-coding
mm_112603.1	chr13	14176107	14176110	+	1	NA	intron (NM_194262, intron 17 of 23)	intron (NM_194262, intron 17 of 23)	112324	NM_198122	94246	Mm.439784	NM_194262	ENSMUSG00000039219	Arid4b	BCAA|BRCAA1|RBBP1L1|Rbp1l1|SAP180	AT rich interactive domain 4B (RBP1-like)	protein-coding
mm_67434.1	chr7	80384540	80384543	-	1	NA	intron (NM_010194, intron 3 of 18)	intron (NM_010194, intron 3 of 18)	3405	NM_010194	14159	Mm.48757	NM_010194	ENSMUSG00000053158	Fes	AI586313|BB137047|FPS|c-fes	feline sarcoma oncogene	protein-coding
mm_66129.1	chr7	31054816	31054839	-	1	NA	promoter-TSS (NM_194321)	promoter-TSS (NM_194321)	26	NM_052991	56188	Mm.1491	NM_019503	ENSMUSG00000036570	Fxyd1	0610012C17Rik|1110006M24Rik|Plm|Pml	FXYD domain-containing ion transport regulator 1	protein-coding
mm_168539.1	chr1	161932831	161932833	+	1	NA	Intergenic	L1Md_T|LINE|L1	36316	NM_001204905	75368	Mm.108728	NM_001204904	ENSMUSG00000086277	4930558K02Rik	-	RIKEN cDNA 4930558K02 gene	protein-coding
mm_118335.1	chr13	114149749	114149762	-	1	NA	intron (NR_045836, intron 1 of 13)	intron (NR_045836, intron 1 of 13)	1837	NR_045836	319803	Mm.386896	NM_177004		A430090L17Rik	-	RIKEN cDNA A430090L17 gene	ncRNA
mm_92598.1	chr10	80102641	80102651	-	1	NA	promoter-TSS (NM_183426)	promoter-TSS (NM_183426)	56	NM_183426	216161	Mm.262102	NM_183426	ENSMUSG00000035673	Sbno2	BC019206|F730040C21|Sno|Stno	strawberry notch homolog 2 (Drosophila)	protein-coding
mm_146742.1	chr18	15403691	15403701	-	1	NA	promoter-TSS (NM_009700)	promoter-TSS (NM_009700)	62	NM_001317729	11829	Mm.250786	NM_009700	ENSMUSG00000024411	Aqp4	WCH4	aquaporin 4	protein-coding
mm_154964.1	chrX	36983923	36983929	+	1	NA	intron (NM_001177323, intron 1 of 9)	intron (NM_001177323, intron 1 of 9)	5769	NM_001177324	56526	Mm.260036	NM_019942	ENSMUSG00000050379	Sept6	2810035H17Rik|C920001C06Rik|Sep6|mKIAA0128	septin 6	protein-coding
mm_69388.1	chr7	131362688	131362725	-	1	NA	promoter-TSS (NM_026655)	promoter-TSS (NM_026655)	-8	NM_026655	68277	Mm.121122	NM_026655	ENSMUSG00000040177	2310057M21Rik	3110040E10Rik|AI429544	RIKEN cDNA 2310057M21 gene	protein-coding
mm_166033.1	chr4	126808585	126808588	+	1	NA	intron (NM_001035525, intron 3 of 23)	intron (NM_001035525, intron 3 of 23)	54816	NM_001035526	100317	Mm.206206	NM_133886	ENSMUSG00000028830	AU040320	A730047D20Rik|AAVR|Kiaa0319l	expressed sequence AU040320	protein-coding
mm_16874.1	chr2	12301997	12302005	-	1	NA	promoter-TSS (NM_001001309)	promoter-TSS (NM_001001309)	-57	NM_001001309	241226	Mm.329997	NM_001001309	ENSMUSG00000026768	Itga8	AI447669	integrin alpha 8	protein-coding
mm_77562.1	chr8	123427723	123427729	-	1	NA	Intergenic	MuLV-int|LTR|ERV1	-15230	NM_001253784	23854	Mm.275127	NM_054046	ENSMUSG00000001482	Def8	AI449518|D8Ertd713e|DEF-8	differentially expressed in FDCP 8	protein-coding
mm_117375.1	chr13	72263961	72263968	-	1	NA	Intergenic	RMER17B|LTR|ERVK	-300241	NM_010573	16371	Mm.316056	NM_010573	ENSMUSG00000060969	Irx1	-	Iroquois related homeobox 1 (Drosophila)	protein-coding
mm_144745.1	chr18	35598655	35598672	+	1	NA	promoter-TSS (NM_026420)	promoter-TSS (NM_026420)	-4	NM_026420	67869	Mm.126534	NM_026420	ENSMUSG00000037058	Paip2	2310050K10Rik|AU045972	polyadenylate-binding protein-interacting protein 2	protein-coding
mm_168693.1	chr11	97187950	97187951	-	1	NA	promoter-TSS (NM_008379)	promoter-TSS (NM_008379)	-58	NM_008379	16211	Mm.251013	NM_008379	ENSMUSG00000001440	Kpnb1	AA409963|IPOB|Impnb	karyopherin (importin) beta 1	protein-coding
mm_73706.1	chr8	111687115	111687134	+	1	NA	exon (NM_025583, exon 6 of 7)	exon (NM_025583, exon 6 of 7)	2550	NR_106044	102466993		NR_106044	ENSMUSG00000099129	Mir7076	Gm27318|mmu-mir-7076	microRNA 7076	ncRNA
mm_14776.1	chr2	145822186	145822196	+	1	NA	intron (NM_028724, intron 2 of 12)	intron (NM_028724, intron 2 of 12)	36075	NM_028724	74030	Mm.228799	NM_028724	ENSMUSG00000001768	Rin2	2010003K16Rik|4632403N06Rik|AW821980|RASSF4	Ras and Rab interactor 2	protein-coding
mm_108563.1	chr12	84761570	84761615	+	1	NA	intron (NM_023409, intron 2 of 3)	MLTR14|LTR|ERV1	11520	NM_023409	67963	Mm.282556	NM_023409	ENSMUSG00000021242	Npc2	2700012J19Rik|AA408070|AU045843|HE1	Niemann-Pick type C2	protein-coding
mm_103155.1	chr11	70407140	70407143	-	1	NA	intron (NM_029231, intron 1 of 16)	AT_rich|Low_complexity|Low_complexity	2890	NM_029231	75273	Mm.340601	NM_029231	ENSMUSG00000018921	Pelp1	4930563C04Rik|MNAR	proline, glutamic acid and leucine rich protein 1	protein-coding
mm_118201.1	chr13	108044302	108044354	-	1	NA	promoter-TSS (NM_001048250)	promoter-TSS (NM_001048250)	-146	NM_001048250	75616	Mm.491164	NM_001048250	ENSMUSG00000071180	Smim15	2810008M24Rik	small integral membrane protein 15	protein-coding
mm_9572.1	chr1	173979904	173979915	-	1	NA	intron (NM_008327, intron 1 of 6)	Lx9|LINE|L1	2935	NM_008327	26388	Mm.218770	NM_008327	ENSMUSG00000026535	Ifi202b	Ifbip-1|Ifi202|Ifi202a|p202	interferon activated gene 202B	protein-coding
mm_121508.1	chr14	121950095	121950105	+	1	NA	intron (NM_026861, intron 4 of 8)	intron (NM_026861, intron 4 of 8)	15093	NM_183031	321019	Mm.265618	NM_183031	ENSMUSG00000051212	Gpr183	Ebi2	G protein-coupled receptor 183	protein-coding
mm_95952.1	chr11	58390618	58390649	+	1	NA	TTS (NM_001083884)	TTS (NM_001083884)	9987	NM_001330197	70163	Mm.24119	NM_027339	ENSMUSG00000013643	Lypd8	2210415F13Rik	LY6/PLAUR domain containing 8	protein-coding
mm_150201.1	chr19	32758326	32758411	+	1	NA	5' UTR (NM_008960, exon 1 of 9)	5' UTR (NM_008960, exon 1 of 9)	791	NM_008960	19211	Mm.245395	NM_008960	ENSMUSG00000013663	Pten	2310035O07Rik|A130070J02Rik|AI463227|B430203M17Rik|MMAC1|TEP1	phosphatase and tensin homolog	protein-coding
mm_116984.1	chr13	56296351	56296367	-	1	NA	5' UTR (NM_019568, exon 1 of 4)	5' UTR (NM_019568, exon 1 of 4)	192	NM_019568	57266	Mm.30211	NM_019568	ENSMUSG00000021508	Cxcl14	1110031L23Rik|1200006I23Rik|AI414372|BMAC|BRAK|KS1|Kec|MIP-2g|MIP2gamma|NJAC|Scyb14|bolekine	chemokine (C-X-C motif) ligand 14	protein-coding
mm_141191.1	chr17	26956912	26956929	-	1	NA	intron (NM_001281491, intron 7 of 18)	intron (NM_001281491, intron 7 of 18)	-8801	NR_037244	100526534		NR_037244	ENSMUSG00000093118	Mir3083	mir-3083|mmu-mir-3083	microRNA 3083	ncRNA
mm_86022.1	chr9	112235890	112235894	-	1	NA	non-coding (NR_015468, exon 2 of 2)	non-coding (NR_015468, exon 2 of 2)	-1051	NM_001177619	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_113624.1	chr13	41639527	41639566	+	1	NA	3' UTR (NM_001163572, exon 3 of 3)	3' UTR (NM_001163572, exon 3 of 3)	-9897	NM_177808	328231	Mm.227476	NM_177808	ENSMUSG00000054258	Gm5082	A030008J09|EG328231	predicted gene 5082	protein-coding
mm_155124.1	chrX	48872075	48872090	+	1	NA	intron (NM_001085499, intron 8 of 20)	intron (NM_001085499, intron 8 of 20)	5631	NM_001085499	209005	Mm.336054	NM_001085499	ENSMUSG00000079606	Gm595	-	predicted gene 595	protein-coding
mm_118728.1	chr14	22240666	22240674	+	1	NA	intron (NM_028275, intron 2 of 6)	(GGGA)n|Simple_repeat|Simple_repeat	220958	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_98756.1	chr11	96545642	96545649	+	1	NA	intron (NM_001033186, intron 4 of 12)	intron (NM_001033186, intron 4 of 12)	81054	NM_001177898	78473	Mm.395840	NM_001033186	ENSMUSG00000057058	Skap1	1700091G21Rik|Scap1|Skap-55	src family associated phosphoprotein 1	protein-coding
mm_123992.1	chr14	75761191	75761233	-	1	NA	TTS (NM_026232)	TTS (NM_026232)	-6719	NM_177381	338337	Mm.86507	NM_177381	ENSMUSG00000034893	Cog3	E430004N23	component of oligomeric golgi complex 3	protein-coding
mm_56951.1	chr6	119992482	119992496	-	1	NA	exon (NM_001185020, exon 3 of 26)	exon (NM_001185020, exon 3 of 26)	41822	NR_030487	735290		NR_030487	ENSMUSG00000076217	Mir706	Mirn706|mir-706|mmu-mir-706	microRNA 706	ncRNA
mm_7678.1	chr1	128589263	128589270	-	1	NA	exon (NM_009911, exon 2 of 2)	exon (NM_009911, exon 2 of 2)	3033	NM_009911	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding
mm_1744.1	chr1	75479507	75479517	+	1	NA	promoter-TSS (NM_001001566)	promoter-TSS (NM_001001566)	-20	NM_177056	319998	Mm.44401	NM_177056	ENSMUSG00000051703	Tmem198	A230078I05Rik|Tmem198-1|Tmem198a	transmembrane protein 198	protein-coding
mm_42739.1	chr5	120655386	120655389	+	1	NA	intron (NM_013832, intron 5 of 21)	PB1D10|SINE|Alu	6199	NM_001281999	19415	Mm.41209	NM_013832	ENSMUSG00000029602	Rasal1	MRASAL	RAS protein activator like 1 (GAP1 like)	protein-coding
mm_135203.1	chr16	36561602	36561614	-	1	NA	intron (NM_013803, intron 1 of 6)	intron (NM_013803, intron 1 of 6)	526	NM_013803	12374	Mm.103619	NM_013803	ENSMUSG00000051980	Casr	CaR|Gprc2a	calcium-sensing receptor	protein-coding
mm_66142.1	chr7	31126760	31126772	-	1	NA	5' UTR (NM_011322, exon 1 of 6)	5' UTR (NM_011322, exon 1 of 6)	257	NM_011322	20266	Mm.1418	NM_011322	ENSMUSG00000019194	Scn1b	-	sodium channel, voltage-gated, type I, beta	protein-coding
mm_71788.1	chr8	66697467	66697483	+	1	NA	promoter-TSS (NM_010934)	promoter-TSS (NM_010934)	53	NM_010934	18166	Mm.5112	NM_010934	ENSMUSG00000036437	Npy1r	Npyr|Y1-R	neuropeptide Y receptor Y1	protein-coding
mm_888.1	chr1	52845033	52845062	+	1	NA	promoter-TSS (NM_146108)	promoter-TSS (NM_146108)	9	NM_146108	227095	Mm.222063	NM_146108	ENSMUSG00000041426	Hibch	2610509I15Rik|HIBYL-COA-H	3-hydroxyisobutyryl-Coenzyme A hydrolase	protein-coding
mm_117191.1	chr13	63566158	63566182	-	1	NA	promoter-TSS (NM_008957)	promoter-TSS (NM_008957)	-435	NM_008957	19206	Mm.228798	NM_008957	ENSMUSG00000021466	Ptch1	A230106A15Rik|Ptc|Ptc1|Ptch|mes	patched 1	protein-coding
mm_124410.1	chr14	115701709	115701719	-	1	NA	intron (NM_175500, intron 6 of 7)	intron (NM_175500, intron 6 of 7)	-292162	NR_045761	75088	Mm.444706	NR_045761	ENSMUSG00000093551	4930505G20Rik	-	RIKEN cDNA 4930505G20 gene	ncRNA
mm_126181.1	chr15	78608116	78608128	+	1	NA	intron (NM_028195, intron 5 of 12)	intron (NM_028195, intron 5 of 12)	11075	NM_028195	72318	Mm.32911	NM_028195	ENSMUSG00000018008	Cyth4	2510004M07Rik|5830469K17Rik|AI467541|Pscd4|mFLJ00017	cytohesin 4	protein-coding
mm_110329.1	chr12	35047796	35047807	-	1	NA	intron (NM_001014973, intron 1 of 25)	CpG	612	NM_001014973	217463	Mm.213991	NM_001014973	ENSMUSG00000020590	Snx13	Rgs-px1|mKIAA0713	sorting nexin 13	protein-coding
mm_29072.1	chr3	103858289	103858318	-	1	NA	Intergenic	Lx8|LINE|L1	-1492	NR_104070	19260	Mm.395	NM_008979	ENSMUSG00000027843	Ptpn22	70zpep|PEP|Ptpn8	protein tyrosine phosphatase, non-receptor type 22 (lymphoid)	protein-coding
mm_81889.1	chr9	119402157	119402225	+	1	NA	promoter-TSS (NM_007397)	promoter-TSS (NM_007397)	13	NM_007397	11481	Mm.8940	NM_007397	ENSMUSG00000061393	Acvr2b	4930516B21Rik|ActRIIB	activin receptor IIB	protein-coding
mm_40569.1	chr5	63649336	63649350	+	1	NA	5' UTR (NM_177006, exon 1 of 7)	5' UTR (NM_177006, exon 1 of 7)	240	NM_177006	319807	Mm.319487	NM_028470	ENSMUSG00000090061	Nwd2	3110047P20Rik|B830017A01Rik|Hn1-ps2|mKIAA1239	NACHT and WD repeat domain containing 2	protein-coding
mm_7431.1	chr1	119837668	119837673	-	1	NA	promoter-TSS (NM_019933)	promoter-TSS (NM_019933)	-599	NM_019933	19258	Mm.458796	NM_019933	ENSMUSG00000026384	Ptpn4	PTPMEG|Ptn4|TEP|TEP/mPTPMEG|hPTP-MEG	protein tyrosine phosphatase, non-receptor type 4	protein-coding
mm_70931.1	chr8	25814525	25814545	+	1	NA	3' UTR (NM_011485, exon 7 of 7)	3' UTR (NM_011485, exon 7 of 7)	6061	NM_011485	20845	Mm.293314	NM_011485	ENSMUSG00000031574	Star	AV363654|D8Ertd419e|stARD1	steroidogenic acute regulatory protein	protein-coding
mm_63236.1	chr7	126558923	126558982	+	1	NA	exon (NM_146200, exon 9 of 21)	exon (NM_146200, exon 9 of 21)	7414	NM_146200	56347	Mm.22776	NM_146200	ENSMUSG00000030738	Eif3c	110kDa|3230401O13Rik|Eif3s8|NIPIL(A3)|NipilA3|Xs|Xsl	eukaryotic translation initiation factor 3, subunit C	protein-coding
mm_143666.1	chr17	79882348	79882354	-	1	NA	intron (NM_019717, intron 1 of 12)	B2_Mm1t|SINE|B2	13772	NM_178050	56298	Mm.175403	NM_019717	ENSMUSG00000059811	Atl2	2010110I21Rik|AA407293|AV334690|Aip-2|Arl6ip2	atlastin GTPase 2	protein-coding
mm_145938.1	chr18	67308542	67308563	+	1	NA	intron (NM_053261, intron 3 of 7)	intron (NM_053261, intron 3 of 7)	19329	NM_053261	114663	Mm.34079	NM_053261	ENSMUSG00000024525	Impa2	2210415D20Rik|AI326924|AW259601	inositol (myo)-1(or 4)-monophosphatase 2	protein-coding
mm_83872.1	chr9	55026619	55026657	-	1	NA	promoter-TSS (NM_145129)	promoter-TSS (NM_145129)	-79	NM_145129	110834	Mm.63569	NM_145129	ENSMUSG00000032303	Chrna3	(a)3|A730007P14Rik|Acra-3|Acra3	cholinergic receptor, nicotinic, alpha polypeptide 3	protein-coding
mm_125761.1	chr15	73957122	73957158	+	1	NA	Intergenic	Intergenic	-117469	NM_001033365	268816	Mm.440635	NM_001033365	ENSMUSG00000072487	Mroh5	Gm628	maestro heat-like repeat family member 5	protein-coding
mm_121904.1	chr14	21985654	21985657	-	1	NA	exon (NM_145459, exon 3 of 3)	exon (NM_145459, exon 3 of 3)	3946	NM_145459	218820	Mm.292401	NM_145459	ENSMUSG00000039081	Zfp503	AI181838|B830002A16Rik|Nolz-1|Nolz1|Znf503	zinc finger protein 503	protein-coding
mm_1325.1	chr1	65103047	65103065	+	1	NA	exon (NM_007774, exon 2 of 3)	exon (NM_007774, exon 2 of 3)	307	NM_007774	12964	Mm.26904	NM_007774	ENSMUSG00000044429	Cryga	Cryg-4|DGcry-4	crystallin, gamma A	protein-coding
mm_110846.1	chr12	73046856	73046869	-	1	NA	promoter-TSS (NM_009189)	promoter-TSS (NM_009189)	-150	NM_009189	20471	Mm.4645	NM_009189	ENSMUSG00000051367	Six1	BB138287	sine oculis-related homeobox 1	protein-coding
mm_51988.1	chr6	92091513	92091523	+	1	NA	promoter-TSS (NM_011630)	promoter-TSS (NM_011630)	100	NM_011630	22026	Mm.87062	NM_011630	ENSMUSG00000005893	Nr2c2	TAK1|Tr4|mKIAA4145	nuclear receptor subfamily 2, group C, member 2	protein-coding
mm_75206.1	chr8	39605220	39605264	-	1	NA	3' UTR (NM_031195, exon 9 of 9)	3' UTR (NM_031195, exon 9 of 9)	37436	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_98621.1	chr11	95858855	95858880	+	1	NA	promoter-TSS (NR_045187)	promoter-TSS (NR_045187)	50	NR_045187	73906	Mm.399894	NR_045187	ENSMUSG00000086015	4833417C18Rik	-	RIKEN cDNA 4833417C18 gene	ncRNA
mm_45678.1	chr5	77310385	77310432	-	1	NA	promoter-TSS (NM_019836)	promoter-TSS (NM_019836)	-76	NM_153798	231329	Mm.273217	NM_153798	ENSMUSG00000029250	Polr2b	Pol2rb|Rpb140|Rpb2	polymerase (RNA) II (DNA directed) polypeptide B	protein-coding
mm_18069.1	chr2	42256629	42256632	-	1	NA	intron (NM_053011, intron 2 of 90)	intron (NM_053011, intron 2 of 90)	190938	NR_105754	102465171		NR_105754	ENSMUSG00000098660	Mir6336	Gm27584|mmu-mir-6336	microRNA 6336	ncRNA
mm_82396.1	chr9	14740643	14740653	-	1	NA	promoter-TSS (NM_177905)	promoter-TSS (NM_177905)	85	NM_177905	330890	Mm.334969	NM_177905	ENSMUSG00000036912	Piwil4	9230101H05Rik|Miwi2	piwi-like RNA-mediated gene silencing 4	protein-coding
mm_139648.1	chr17	57386671	57386686	+	1	NA	intron (NM_010130, intron 2 of 21)	L1_Mur1|LINE|L1	27992	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_130163.1	chr15	91632515	91632529	-	1	NA	Intergenic	L1MA6|LINE|L1	-40702	NM_025730	66725	Mm.37558	NM_025730	ENSMUSG00000036273	Lrrk2	4921513O20Rik|9330188B09Rik|AW561911|D630001M17Rik|Gm927|cI-46	leucine-rich repeat kinase 2	protein-coding
mm_25031.1	chr3	98149856	98149876	+	1	NA	3' UTR (NM_010928, exon 34 of 34)	3' UTR (NM_010928, exon 34 of 34)	-10768	NM_027665	71078	Mm.50711	NM_027665	ENSMUSG00000043468	Adam30	4933424D07Rik|svph4	a disintegrin and metallopeptidase domain 30	protein-coding
mm_108046.1	chr12	73908056	73908066	+	1	NA	5' UTR (NM_010431, exon 1 of 15)	5' UTR (NM_010431, exon 1 of 15)	194	NM_001313919	15251	Mm.3879	NM_010431	ENSMUSG00000021109	Hif1a	AA959795|HIF-1-alpha|HIF1-alpha|HIF1alpha|MOP1|bHLHe78	hypoxia inducible factor 1, alpha subunit	protein-coding
mm_115824.1	chr13	20885902	20885912	-	1	NA	intron (NM_012054, intron 4 of 20)	RSINE1|SINE|B4	91794	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_2579.1	chr1	118482187	118482194	+	1	NA	intron (NM_001293300, intron 8 of 40)	intron (NM_001293300, intron 8 of 40)	-22925	NR_027901	68204	Mm.443536	NR_027901	ENSMUSG00000107722	2900060B14Rik	-	RIKEN cDNA 2900060B14 gene	ncRNA
mm_6230.1	chr1	66937552	66937561	-	1	NA	intron (NM_021285, intron 1 of 6)	intron (NM_021285, intron 1 of 6)	-2190	NM_001113387	17901	Mm.1000	NM_021285	ENSMUSG00000061816	Myl1	AI325107|MLC1f|MLC3f|Mylf	myosin, light polypeptide 1	protein-coding
mm_9045.1	chr1	167284638	167284650	-	1	NA	intron (NM_030724, intron 1 of 6)	CpG	483	NM_030724	80914	Mm.280895	NM_030724	ENSMUSG00000026558	Uck2	AA407809|AI481316|AU018180|AU020720|TSA903|UK|UMK|Umpk	uridine-cytidine kinase 2	protein-coding
mm_59828.1	chr7	29291370	29291386	+	1	NA	intron (NM_026731, intron 1 of 3)	intron (NM_026731, intron 1 of 3)	2058	NM_026731	68458	Mm.2343	NM_026731	ENSMUSG00000037166	Ppp1r14a	1110001M11Rik|Cpi17	protein phosphatase 1, regulatory (inhibitor) subunit 14A	protein-coding
mm_119351.1	chr14	41111067	41111077	+	1	NA	exon (NM_133653, exon 4 of 10)	exon (NM_133653, exon 4 of 10)	6039	NM_133653	11720	Mm.14064	NM_133653	ENSMUSG00000037798	Mat1a	AI046368|AdoMet|Ams|MAT|MATA1|SAMS|SAMS1	methionine adenosyltransferase I, alpha	protein-coding
mm_45684.1	chr5	77351350	77351364	-	1	NA	intron (NM_001159518, intron 4 of 5)	intron (NM_001159518, intron 4 of 5)	40873	NM_153798	231329	Mm.273217	NM_153798	ENSMUSG00000029250	Polr2b	Pol2rb|Rpb140|Rpb2	polymerase (RNA) II (DNA directed) polypeptide B	protein-coding
mm_8501.1	chr1	153900465	153900492	-	1	NA	TTS (NR_106194)	TTS (NR_106194)	549	NM_008131	14645	Mm.210745	NM_008131	ENSMUSG00000026473	Glul	GS|Glns	glutamate-ammonia ligase (glutamine synthetase)	protein-coding
mm_134427.1	chr16	17921925	17921944	-	1	NA	Intergenic	CpG	6285	NM_153150	13358	Mm.229291	NM_153150	ENSMUSG00000003528	Slc25a1	1300019P08Rik|2610100G11Rik|AI194714|Ctp|Dgsj|Slc20a3	solute carrier family 25 (mitochondrial carrier, citrate transporter), member 1	protein-coding
mm_87582.1	chr10	56504551	56504559	+	1	NA	Intergenic	Intergenic	127255	NM_010288	14609	Mm.378921	NM_010288	ENSMUSG00000050953	Gja1	AU042049|AW546267|Cnx43|Cx43|Cx43alpha1|Gja-1|Npm1|connexin43	gap junction protein, alpha 1	protein-coding
mm_160220.1	chr7	101004130	101004130	-	1	NA	intron (NM_001302346, intron 1 of 2)	L3|LINE|CR1	7868	NM_001302347	18442	Mm.3000	NM_008773	ENSMUSG00000032860	P2ry2	P2U1|P2Y2	purinergic receptor P2Y, G-protein coupled 2	protein-coding
mm_15700.1	chr2	163820833	163820894	+	1	NA	promoter-TSS (NM_016873)	promoter-TSS (NM_016873)	29	NM_016873	22403	Mm.13828	NM_016873	ENSMUSG00000027656	Wisp2	Ccn5|Crgr4|Ctgfl|Rcop1	WNT1 inducible signaling pathway protein 2	protein-coding
mm_57562.1	chr6	127125515	127125532	-	1	NA	TTS (NM_009829)	TTS (NM_009829)	-15971	NM_177003	319801	Mm.101836	NM_177003	ENSMUSG00000038028	Tigar	9630033F20Rik|AA793651|AI595337|C79710|C85509	Trp53 induced glycolysis repulatory phosphatase	protein-coding
mm_99717.1	chr11	106276652	106276688	+	1	NA	promoter-TSS (NM_029467)	promoter-TSS (NM_029467)	-2	NM_029467	75870	Mm.159608	NM_029467	ENSMUSG00000020712	Tcam1	4930570F09Rik|AI429105	testicular cell adhesion molecule 1	protein-coding
mm_126448.1	chr15	80762425	80762457	+	1	NA	intron (NM_144812, intron 3 of 24)	B3|SINE|B2	-36169	NM_177124	213988	Mm.131328	NM_144812	ENSMUSG00000047888	Tnrc6b	2700090M07Rik|A730065C02Rik|AI848765|D230019K20Rik	trinucleotide repeat containing 6b	protein-coding
mm_91470.1	chr10	34207178	34207200	-	1	NA	5' UTR (NM_172508, exon 1 of 6)	5' UTR (NM_172508, exon 1 of 6)	362	NM_172508	212898	Mm.34557	NM_172508	ENSMUSG00000039497	Dse	6030499O08|AI480506|B130024B19Rik|DS-epi1|Sart2	dermatan sulfate epimerase	protein-coding
mm_44874.1	chr5	34634858	34634884	-	1	NA	exon (NM_026660, exon 8 of 13)	exon (NM_026660, exon 8 of 13)	2243	NM_026660	68294	Mm.34564	NM_026660	ENSMUSG00000001082	Mfsd10	0610009O03Rik|Tetran	major facilitator superfamily domain containing 10	protein-coding
mm_77947.1	chr9	7358516	7358526	+	1	NA	3' UTR (NM_008605, exon 10 of 10)	3' UTR (NM_008605, exon 10 of 10)	11147	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_118763.1	chr14	22438668	22438678	+	1	NA	intron (NM_028275, intron 2 of 6)	ID_B1|SINE|B4	104125	NR_046307	74896	Mm.444661	NR_046307		4930405A10Rik	4930456G20Rik	RIKEN cDNA 4930405A10 gene	ncRNA
mm_70339.1	chr8	4524898	4524912	+	1	NA	3' UTR (NM_026058, exon 11 of 11)	3' UTR (NM_026058, exon 11 of 11)	31500	NM_026058	67260	Mm.35511	NM_026058	ENSMUSG00000008206	Cers4	2900019C14Rik|Lass4|Trh1	ceramide synthase 4	protein-coding
mm_57891.1	chr6	131368469	131368499	-	1	NA	exon (NM_011733, exon 7 of 9)	exon (NM_011733, exon 7 of 9)	19966	NM_139117	56449	Mm.458000	NM_011733	ENSMUSG00000030189	Ybx3	Csda|Dpba|MSY3|MSY4|Yb2|dbpA|oxyR	Y box protein 3	protein-coding
mm_19963.1	chr2	117965783	117965801	-	1	NA	intron (NR_126479, intron 8 of 9)	intron (NR_126479, intron 8 of 9)	143864	NR_040631	73938	Mm.399107	NR_040631	ENSMUSG00000086221	4930412B13Rik	-	RIKEN cDNA 4930412B13 gene	ncRNA
mm_25439.1	chr3	108093110	108093120	+	1	NA	promoter-TSS (NM_008141)	promoter-TSS (NM_008141)	49	NM_008141	14686	Mm.439652	NM_008141	ENSMUSG00000009108	Gnat2	AW490837|Gnat-2|Gt-2|Tcalpha	guanine nucleotide binding protein, alpha transducing 2	protein-coding
mm_18524.1	chr2	63123906	63123909	-	1	NA	intron (NM_133207, intron 2 of 15)	Lx9|LINE|L1	60380	NM_133207	170738	Mm.242532	NM_133207	ENSMUSG00000059742	Kcnh7	9330137I11Rik|Kv11.3|erg3	potassium voltage-gated channel, subfamily H (eag-related), member 7	protein-coding
mm_84688.1	chr9	72154323	72154346	-	1	NA	Intergenic	Intergenic	-42515	NM_001253865	21406	Mm.171615	NM_011544	ENSMUSG00000032228	Tcf12	A130037E08Rik|ALF1|HEB|HEBAlt|HTF-4|HTF4|ME1|REB|bHLHb20	transcription factor 12	protein-coding
mm_52697.1	chr6	119215335	119215343	+	1	NA	exon (NM_001033379, exon 7 of 9)	exon (NM_001033379, exon 7 of 9)	-18930	NM_001255999	12288	Mm.41628	NM_009781	ENSMUSG00000051331	Cacna1c	Cav1.2|Cchl1a1|D930026N18Rik|MBC|MELC-CC	calcium channel, voltage-dependent, L type, alpha 1C subunit	protein-coding
mm_128495.1	chr15	51897033	51897042	-	1	NA	Intergenic	L1ME1|LINE|L1	19596	NM_030132	78581	Mm.176347	NM_030132	ENSMUSG00000022313	Utp23	1700010I21Rik|AI662478|BB238373|D530033C11Rik	UTP23 small subunit processome component	protein-coding
mm_145959.1	chr18	67774895	67774915	+	1	NA	promoter-TSS (NM_001039088)	promoter-TSS (NM_001039088)	29	NM_001039088	72124	Mm.307315	NM_028112	ENSMUSG00000079614	Seh1l	2610007A16Rik|AW540070|SEC13L|SEH1A|SEH1B|Seh1	SEH1-like (S. cerevisiae	protein-coding
mm_11809.1	chr2	43932177	43932179	+	1	NA	intron (NM_001301832, intron 7 of 14)	intron (NM_001301832, intron 7 of 14)	133146	NR_040622	320872	Mm.445023	NR_040622	ENSMUSG00000085089	Arhgap15os	A430092G05Rik	Rho GTPase activating protein 15, opposite strand	ncRNA
mm_130902.1	chr15	102405576	102405620	-	1	NA	promoter-TSS (NM_013672)	promoter-TSS (NM_013672)	-718	NM_013672	20683	Mm.4618	NM_013672	ENSMUSG00000001280	Sp1	1110003E12Rik|AA450830|AI845540|Sp1-1	trans-acting transcription factor 1	protein-coding
mm_105612.1	chr11	106786719	106786767	-	1	NA	intron (NM_007840, intron 2 of 12)	intron (NM_007840, intron 2 of 12)	1751	NM_007840	13207	Mm.491096	NM_007840	ENSMUSG00000020719	Ddx5	2600009A06Rik|G17P1|HUMP68|Hlr1|p68	DEAD (Asp-Glu-Ala-Asp) box polypeptide 5	protein-coding
mm_41298.1	chr5	90464846	90464943	+	1	NA	exon (NM_009654, exon 5 of 15)	exon (NM_009654, exon 5 of 15)	4024	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_55925.1	chr6	84106970	84107008	-	1	NA	exon (NM_021469, exon 23 of 55)	exon (NM_021469, exon 23 of 55)	87603	NM_021469	26903	Mm.220982	NM_021469	ENSMUSG00000033788	Dysf	2310004N10Rik|AI604795|D6Pas3	dysferlin	protein-coding
mm_21191.1	chr2	155381681	155381687	-	1	NA	promoter-TSS (NM_178111)	promoter-TSS (NM_178111)	-172	NM_178111	68728	Mm.293605	NM_178111	ENSMUSG00000038375	Trp53inp2	1110029F20Rik|Tp53inp2	transformation related protein 53 inducible nuclear protein 2	protein-coding
mm_80887.1	chr9	99304841	99304882	+	1	NA	Intergenic	Intergenic	53669	NM_177775	272636	Mm.490440	NM_177775	ENSMUSG00000037681	Esyt3	D930024E11|D9Ertd280e|Fam62c|mKIAA4186	extended synaptotagmin-like protein 3	protein-coding
mm_167822.1	chr9	124422716	124422779	-	1	NA	promoter-TSS (NR_027950)	promoter-TSS (NR_027950)	-504	NR_027950	75135	Mm.476814	NR_015516		4930526I15Rik	1600027J15Rik	RIKEN cDNA 4930526I15 gene	ncRNA
mm_78231.1	chr9	21592906	21592963	+	1	NA	promoter-TSS (NM_138303)	promoter-TSS (NM_138303)	-103	NM_001205157	74766	Mm.475712	NM_138303	ENSMUSG00000032182	Yipf2	1300010K09Rik	Yip1 domain family, member 2	protein-coding
mm_93091.1	chr10	89632009	89632019	-	1	NA	Intergenic	Intergenic	-10765	NM_182959	216227	Mm.233921	NM_182959	ENSMUSG00000019935	Slc17a8	BC042593|Vglut3	solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 8	protein-coding
mm_123205.1	chr14	59365421	59365431	-	1	NA	promoter-TSS (NM_199015)	promoter-TSS (NM_199015)	64	NM_199015	219132	Mm.479285	NM_199015	ENSMUSG00000068245	Phf11d	D14Ertd668e|Phf11|Phf11l	PHD finger protein 11D	protein-coding
mm_96820.1	chr11	69994586	69994596	+	1	NA	3' UTR (NM_019749, exon 4 of 4)	3' UTR (NM_019749, exon 4 of 4)	-1175	NM_001291125	78246	Mm.20805	NM_030064	ENSMUSG00000018572	Phf23	JUNE-1	PHD finger protein 23	protein-coding
mm_25188.1	chr3	103386880	103386891	+	1	NA	Intergenic	Intergenic	107592	NM_001079830	94093	Mm.195036	NM_053170	ENSMUSG00000033014	Trim33	8030451N04Rik|AI413936|Ecto|Tif1g	tripartite motif-containing 33	protein-coding
mm_129728.1	chr15	82016204	82016217	-	1	NA	promoter-TSS (NM_010247)	promoter-TSS (NM_010247)	-70	NM_134095	28075	Mm.474453	NM_134095	ENSMUSG00000022472	Desi1	AI427858|AI850401|D15Wsu75e|DeSI-1|Fam152b|Pppde2	desumoylating isopeptidase 1	protein-coding
mm_62444.1	chr7	101383970	101383976	+	1	NA	intron (NM_001040112, intron 1 of 30)	intron (NM_001040112, intron 1 of 30)	-1553	NM_027180	69710	Mm.277687	NM_027180	ENSMUSG00000032812	Arap1	2410002L19Rik|Centd2|mKIAA0782	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	protein-coding
mm_10621.1	chr2	19445633	19445651	+	1	NA	promoter-TSS (NM_018809)	promoter-TSS (NM_018809)	-21	NM_018809	19213	Mm.69647	NM_018809	ENSMUSG00000026735	Ptf1a	PTF1-p48|PTF1p48|bHLHa29	pancreas specific transcription factor, 1a	protein-coding
mm_141338.1	chr17	28515534	28515538	-	1	NA	Intergenic	Intergenic	-15325	NM_026290	67645	Mm.46170	NM_026290	ENSMUSG00000024223	Armc12	4930511I11Rik|AV041658	armadillo repeat containing 12	protein-coding
mm_67020.1	chr7	65894279	65894301	-	1	NA	intron (NM_011048, intron 1 of 21)	MER2|DNA|TcMar-Tigger	32154	NM_011048	18553	Mm.294007	NM_011048	ENSMUSG00000030513	Pcsk6	C86343|Pace4|SPC4	proprotein convertase subtilisin/kexin type 6	protein-coding
mm_147259.1	chr18	38642582	38642583	-	1	NA	Intergenic	ID_B1|SINE|B4	-41314	NM_011898	24066	Mm.42038	NM_011898	ENSMUSG00000024427	Spry4	A030006O18Rik|sprouty4	sprouty homolog 4 (Drosophila)	protein-coding
mm_169402.1	chr14	50466337	50466338	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-6720	NM_207133	258233	Mm.377278	NM_207133	ENSMUSG00000095765	Olfr741	GA_x5J8B7TYL6J-3-280|GA_x5J8B7U07Q4-325-757|GA_x6K02T2PMLR-6197851-6198786|MOR106-10|MOR106-15	olfactory receptor 741	protein-coding
mm_6024.1	chr1	59161560	59161593	-	1	NA	promoter-TSS (NM_145143)	promoter-TSS (NM_145143)	60	NM_145143	227157	Mm.474049	NM_145143	ENSMUSG00000079550	Mpp4	Dlg6	membrane protein, palmitoylated 4 (MAGUK p55 subfamily member 4)	protein-coding
mm_139071.1	chr17	46650551	46650568	+	1	NA	TTS (NM_001316742)	TTS (NM_001316742)	221	NM_025611	66515	Mm.329078	NM_025611	ENSMUSG00000038545	Cul7	2510004L20Rik|AA409809|C230011P08Rik|p185|p193	cullin 7	protein-coding
mm_42631.1	chr5	118437486	118437495	+	1	NA	Intergenic	Intergenic	-123229	NM_001347445	76199	Mm.206238	NM_172424	ENSMUSG00000018076	Med13l	2210413I17Rik|6330591G05Rik|9030618F05Rik|Thrap2|Trap240L|mKIAA1025	mediator complex subunit 13-like	protein-coding
mm_59561.1	chr7	28086334	28086342	+	1	NA	exon (NM_001122603, exon 5 of 20)	exon (NM_001122603, exon 5 of 20)	15102	NM_001122603	215384	Mm.292276	NM_175444	ENSMUSG00000047730	Fcgbp	A430096B05Rik	Fc fragment of IgG binding protein	protein-coding
mm_26679.1	chr3	155093588	155093597	+	1	NA	promoter-TSS (NM_029330)	promoter-TSS (NM_029330)	158	NM_028938	74435	Mm.195711	NM_028938	ENSMUSG00000028182	Lrriq3	4930438B07Rik|4930511J15Rik|4933403H06Rik|BB020367|Lrrc44	leucine-rich repeats and IQ motif containing 3	protein-coding
mm_80271.1	chr9	72970236	72970246	+	1	NA	intron (NM_026314, intron 7 of 8)	intron (NM_026314, intron 7 of 8)	11456	NM_001163725	67685	Mm.31817	NM_026314	ENSMUSG00000089865	Dyx1c1	1700010I24Rik|Dnaaf4|EKN1|b2b811.1Clo|b2b811Clo	dyslexia susceptibility 1 candidate 1	protein-coding
mm_156166.1	chrX	130048899	130048909	+	1	NA	intron (NM_172493, intron 18 of 26)	MER44D|DNA|TcMar-Tigger	299162	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diaph2	Dia3|Diap2|Drf2|E430022I22Rik	diaphanous related formin 2	protein-coding
mm_128648.1	chr15	59604301	59604323	-	1	NA	Intergenic	Intergenic	-44342	NM_144549	211770	Mm.40298	NM_144549	ENSMUSG00000032501	Trib1	A530090O15Rik|TRB-1|Trb1	tribbles pseudokinase 1	protein-coding
mm_122206.1	chr14	31830403	31830440	-	1	NA	promoter-TSS (NM_001024604)	promoter-TSS (NM_001024604)	-6	NM_001024604	105522	Mm.37660	NM_001024604	ENSMUSG00000014496	Ankrd28	AI465466|AI604979|E430019N21Rik|mKIAA0379	ankyrin repeat domain 28	protein-coding
mm_29780.1	chr3	127409015	127409043	-	1	NA	promoter-TSS (NM_001327939)	promoter-TSS (NM_001327939)	29	NM_001327939	109676	Mm.220242	NM_178655	ENSMUSG00000032826	Ank2	100043364|AI835472|AW491075|Ank-2|Gm4392	ankyrin 2, brain	protein-coding
mm_163536.1	chr13	13481004	13481004	+	1	NA	intron (NM_010917, intron 7 of 19)	B1F|SINE|Alu	43402	NM_010917	18073	Mm.4691	NM_010917	ENSMUSG00000005397	Nid1	A630025O17|Nid|entactin|entactin-1|nidogen-1	nidogen 1	protein-coding
mm_103651.1	chr11	78973049	78973075	-	1	NA	exon (NM_010708, exon 3 of 11)	exon (NM_010708, exon 3 of 11)	11862	NM_001159301	16859	Mm.341434	NM_010708	ENSMUSG00000001123	Lgals9	AA407335|AI194909|AI265545|LGALS35|Lgals5|gal-9|galectin-9	lectin, galactose binding, soluble 9	protein-coding
mm_98763.1	chr11	96574897	96574898	+	1	NA	intron (NM_001033186, intron 4 of 12)	intron (NM_001033186, intron 4 of 12)	110306	NM_001177898	78473	Mm.395840	NM_001033186	ENSMUSG00000057058	Skap1	1700091G21Rik|Scap1|Skap-55	src family associated phosphoprotein 1	protein-coding
mm_63909.1	chr7	139214684	139214709	+	1	NA	5' UTR (NM_027164, exon 2 of 11)	5' UTR (NM_027164, exon 2 of 11)	-1389	NM_001162540	57740	Mm.65336	NM_021302	ENSMUSG00000015981	Stk32c	PKE|Pkek|YANK3	serine/threonine kinase 32C	protein-coding
mm_7046.1	chr1	87125747	87125749	-	1	NA	exon (NM_007432, exon 4 of 11)	exon (NM_007432, exon 4 of 11)	740	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_141685.1	chr17	33951080	33951123	-	1	NA	TTS (NM_011296)	TTS (NM_011296)	387	NM_019420	54218	Mm.11132	NM_019420	ENSMUSG00000067370	B3galt4	Gal-T2|Galt2	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 4	protein-coding
mm_74388.1	chr8	128732823	128732846	+	1	NA	3' UTR (NM_010578, exon 16 of 16)	3' UTR (NM_010578, exon 16 of 16)	47180	NM_010578	16412	Mm.263396	NM_010578	ENSMUSG00000025809	Itgb1	4633401G24Rik|AA409975|AA960159|CD29|ENSMUSG00000051907|Fnrb|Gm9863|gpIIa	integrin beta 1 (fibronectin receptor beta)	protein-coding
mm_159591.1	chr4	123684110	123684110	-	1	NA	exon (NM_001199137, exon 1 of 93)	exon (NM_001199137, exon 1 of 93)	250	NM_001199137	11426	Mm.402299	NM_009600	ENSMUSG00000028649	Macf1	ABP620|Acf7|Aclp7|MACF|R74989|mKIAA0465	microtubule-actin crosslinking factor 1	protein-coding
mm_169870.1	chr16	35871409	35871411	-	1	NA	promoter-TSS (NM_001039530)	promoter-TSS (NM_001039530)	-28	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_70427.1	chr8	11497620	11497648	+	1	NA	promoter-TSS (NM_026995)	promoter-TSS (NM_026995)	66	NM_026995	69225	Mm.64911	NM_026995	ENSMUSG00000031505	Naxd	0710008K08Rik|2810407E01Rik|Carkd	NAD(P)HX dehydratase	protein-coding
mm_134534.1	chr16	19673168	19673184	-	1	NA	intron (NM_177356, intron 5 of 5)	intron (NM_177356, intron 5 of 5)	33189	NM_177356	239739	Mm.258059	NM_177356	ENSMUSG00000041247	Lamp3	1200002D17Rik|Cd208|DC-LAMP|DCLAMP|LAMP|TSC403	lysosomal-associated membrane protein 3	protein-coding
mm_2994.1	chr1	133204678	133204709	+	1	NA	Intergenic	Intergenic	-41404	NM_001160268	240753	Mm.253559	NM_182930	ENSMUSG00000041757	Plekha6	9530028L01Rik|AU042621|Pepp3	pleckstrin homology domain containing, family A member 6	protein-coding
mm_142834.1	chr17	51782924	51782949	-	1	NA	exon (NM_001163632, exon 7 of 11)	exon (NM_001163632, exon 7 of 11)	29118	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_20364.1	chr2	128339490	128339491	-	1	NA	intron (NR_028589, intron 1 of 2)	intron (NR_028589, intron 1 of 2)	89861	NR_028591	100043424	Mm.297222	NR_028589		Gm14005	OTTMUSG00000015351	predicted gene 14005	ncRNA
mm_32249.1	chr4	102570395	102570401	+	1	NA	5' UTR (NM_001177980, exon 1 of 10)	5' UTR (NM_001177980, exon 1 of 10)	338	NM_001177980	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_28387.1	chr3	90014428	90014432	-	1	NA	intron (NM_153489, intron 20 of 26)	intron (NM_153489, intron 20 of 26)	-3220	NR_106129	102465771		NR_106129	ENSMUSG00000098397	Mir7669	Gm27996|mmu-mir-7669	microRNA 7669	ncRNA
mm_115987.1	chr13	24329046	24329052	-	1	NA	intron (NM_001111110, intron 1 of 16)	MuLV-int|LTR|ERV1	1645	NM_001111110	12763	Mm.8396	NM_007717	ENSMUSG00000016756	Cmah	-	cytidine monophospho-N-acetylneuraminic acid hydroxylase	protein-coding
mm_93250.1	chr10	95447974	95448006	-	1	NA	Intergenic	Intergenic	30615	NR_045338	70523	Mm.158398	NR_045338	ENSMUSG00000097766	5730420D15Rik	-	RIKEN cDNA 5730420D15 gene	ncRNA
mm_75644.1	chr8	65037140	65037171	-	1	NA	intron (NM_001297554, intron 1 of 3)	intron (NM_001297554, intron 1 of 3)	181	NM_001297554	100038489	Mm.58847	NM_001297554	ENSMUSG00000079042	Apela	ENSMUSG00000074303|Ela|Ende|Gm10664	apelin receptor early endogenous ligand	protein-coding
mm_124055.1	chr14	77875054	77875067	-	1	NA	promoter-TSS (NM_025384)	promoter-TSS (NM_025384)	-143	NM_025384	66148	Mm.248046	NM_025384	ENSMUSG00000022013	Dnajc15	1110003P16Rik|Dnajd1	DnaJ heat shock protein family (Hsp40) member C15	protein-coding
mm_53531.1	chr6	136576333	136576336	+	1	NA	intron (NM_019426, intron 7 of 14)	Lx4A|LINE|L1	57483	NM_019426	54343	Mm.173271	NM_019426	ENSMUSG00000030213	Atf7ip	2610204M12Rik|AM|Mcaf1	activating transcription factor 7 interacting protein	protein-coding
mm_165751.1	chr3	108199917	108199926	+	1	NA	intron (NM_001081320, intron 2 of 2)	intron (NM_001081320, intron 2 of 2)	913	NM_028061	72023	Mm.246391	NM_028061	ENSMUSG00000048796	Cyb561d1	1600010M23Rik|AI605489|AW457162	cytochrome b-561 domain containing 1	protein-coding
mm_155588.1	chrX	81021187	81021187	+	1	NA	Intergenic	Lx6|LINE|L1	-49457	NM_138751	192216	Mm.490421	NM_138751	ENSMUSG00000025666	Tmem47	3010015F07Rik|AI115536|BCMP1|Tm4sf10	transmembrane protein 47	protein-coding
mm_167653.1	chr9	67020652	67020654	+	1	NA	Intergenic	Intergenic	23218	NM_001164252	22003	Mm.121878	NM_024427	ENSMUSG00000032366	Tpm1	AA986836|AI854628|TM2|Tm3|Tmpa|Tpm-1|alpha-TM	tropomyosin 1, alpha	protein-coding
mm_112015.1	chr12	111273030	111273034	-	1	NA	intron (NM_033603, intron 3 of 11)	intron (NM_033603, intron 3 of 11)	1936	NM_033603	93835	Mm.197639	NM_033603	ENSMUSG00000021278	Amn	-	amnionless	protein-coding
mm_64481.1	chr7	143065755	143065763	+	1	NA	intron (NM_133655, intron 3 of 7)	intron (NM_133655, intron 3 of 7)	-3609	NM_020285	56844	Mm.139675	NM_020285	ENSMUSG00000045752	Tssc4	AA241958|ESTM671070	tumor-suppressing subchromosomal transferable fragment 4	protein-coding
mm_117208.1	chr13	64084820	64084829	-	1	NA	intron (NM_008291, intron 2 of 10)	intron (NM_008291, intron 2 of 10)	4377	NM_008291	15487	Mm.5109	NM_008291	ENSMUSG00000033122	Hsd17b3	-	hydroxysteroid (17-beta) dehydrogenase 3	protein-coding
mm_169395.1	chr1	44480451	44480454	+	1	NA	Intergenic	L1Md_T|LINE|L1	-71219	NM_028450	70676	Mm.133132	NM_027506	ENSMUSG00000056870	Gulp1	3110030A04Rik|5730529O06Rik|CED-6|Ced6|GULP|Gulp-2	GULP, engulfment adaptor PTB domain containing 1	protein-coding
mm_135310.1	chr16	38713006	38713016	-	1	NA	promoter-TSS (NM_020260)	promoter-TSS (NM_020260)	24	NM_020260	12549	Mm.370848	NM_020260	ENSMUSG00000022799	Arhgap31	5830477L08Rik|AU041750|Cdgap|D330026I07Rik	Rho GTPase activating protein 31	protein-coding
mm_169079.1	chr13	33373178	33373183	+	1	NA	Intergenic	L1VL4|LINE|L1	49103	NM_183197	20709	Mm.474264	NM_183197	ENSMUSG00000038327	Serpinb9f	BC052216|NK21|NK21L1|Spi13|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 9f	protein-coding
mm_160890.1	chr11	70134041	70134041	+	1	NA	intron (NM_145137, intron 1 of 9)	intron (NM_145137, intron 1 of 9)	3684	NM_145137	216864	Mm.222465	NM_145137	ENSMUSG00000040950	Mgl2	CD301b	macrophage galactose N-acetyl-galactosamine specific lectin 2	protein-coding
mm_86177.1	chr9	119190284	119190290	-	1	NA	intron (NM_001037749, intron 1 of 11)	intron (NM_001037749, intron 1 of 11)	106	NM_001037749	382113	Mm.335525	NM_001037749	ENSMUSG00000070280	Slc22a14	Gm1128	solute carrier family 22 (organic cation transporter), member 14	protein-coding
mm_141416.1	chr17	29430523	29430531	-	1	NA	Intergenic	Intergenic	-60518	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_43537.1	chr5	137350131	137350146	+	1	NA	promoter-TSS (NM_010144)	promoter-TSS (NM_010144)	29	NM_010144	13846	Mm.34533	NM_010144	ENSMUSG00000029710	Ephb4	AI042935|Htk|MDK2|Myk1|Tyro11	Eph receptor B4	protein-coding
mm_86051.1	chr9	114563270	114563283	-	1	NA	5' UTR (NM_001042503, exon 1 of 4)	5' UTR (NM_001042503, exon 1 of 4)	1093	NM_001042503	636931	Mm.17857	NM_001042503	ENSMUSG00000079259	Trim71	2610206G21Rik|AL022943|Gm1127|Lin41|lin-41|mLin41|mlin-41	tripartite motif-containing 71	protein-coding
mm_125461.1	chr15	52712380	52712384	+	1	NA	promoter-TSS (NM_027212)	promoter-TSS (NM_027212)	-63	NM_027212	69790	Mm.195562	NM_027212	ENSMUSG00000038622	Med30	1810038N03Rik|2510044J04Rik|TRAP25|Thrap6	mediator complex subunit 30	protein-coding
mm_92242.1	chr10	70195433	70195458	-	1	NA	Intergenic	MT2B|LTR|ERVL	-9219	NM_001304739	69563	Mm.64672	NM_001304739	ENSMUSG00000019933	Mrln	2310015B20Rik|Mln	myoregulin	protein-coding
mm_152441.1	chr19	10740724	10740746	-	1	NA	promoter-TSS (NR_027805)	promoter-TSS (NR_027805)	-212	NR_027805	403202	Mm.34482	NM_207529	ENSMUSG00000067577	A430093F15Rik	Gm674	RIKEN cDNA A430093F15 gene	ncRNA
mm_43411.1	chr5	135935090	135935120	+	1	NA	promoter-TSS (NM_018871)	promoter-TSS (NM_018871)	-464	NM_018871	22628	Mm.233813	NM_018871	ENSMUSG00000051391	Ywhag	14-3-3gamma|D7Bwg1348e	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, gamma polypeptide	protein-coding
mm_116773.1	chr13	52978160	52978169	-	1	NA	intron (NM_017373, intron 1 of 1)	intron (NM_017373, intron 1 of 1)	2875	NM_017373	18030	Mm.136604	NM_017373	ENSMUSG00000056749	Nfil3	AV225605|E4BP4	nuclear factor, interleukin 3, regulated	protein-coding
mm_14878.1	chr2	148820099	148820111	+	1	NA	promoter-TSS (NM_027024)	promoter-TSS (NM_027024)	6	NM_027024	69294	Mm.46167	NM_027024	ENSMUSG00000036924	Cst13	1700006C19Rik|Cymg1|Mtcg1	cystatin 13	protein-coding
mm_93987.1	chr10	127520777	127520784	-	1	NA	intron (NM_001252316, intron 2 of 11)	intron (NM_001252316, intron 2 of 11)	1664	NM_001252316	108037	Mm.29890	NM_028230	ENSMUSG00000025403	Shmt2	2700043D08Rik|AA408223|AA986903	serine hydroxymethyltransferase 2 (mitochondrial)	protein-coding
mm_120740.1	chr14	73173826	73173836	+	1	NA	exon (NM_001170694, exon 11 of 15)	exon (NM_001170694, exon 11 of 15)	31046	NR_033185	105670	Mm.280068	NM_134083	ENSMUSG00000022106	Rcbtb2	2610028E02Rik|2810420M18Rik|AI448345|AW240694|Chc1l|RC/BTB2	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 2	protein-coding
mm_107263.1	chr12	29002870	29002873	+	1	NA	Intergenic	Intergenic	251043	NM_201357	380752	Mm.273724	NM_201357	ENSMUSG00000036613	Tssc1	D12Ertd604e|Eipr1	tumor suppressing subtransferable candidate 1	protein-coding
mm_72172.1	chr8	72295915	72295918	+	1	NA	Intergenic	Intergenic	-23146	NM_008452	16598	Mm.26938	NM_008452	ENSMUSG00000055148	Klf2	Lklf	Kruppel-like factor 2 (lung)	protein-coding
mm_13364.1	chr2	103454297	103454317	+	1	NA	3' UTR (NM_009804, exon 13 of 13)	3' UTR (NM_009804, exon 13 of 13)	30239	NM_010125	13711	Mm.20888	NM_010125	ENSMUSG00000027186	Elf5	ESE-2|ESE-5|ESE-5.	E74-like factor 5	protein-coding
mm_17529.1	chr2	29621191	29621199	-	1	NA	intron (NM_001039087, intron 1 of 25)	intron (NM_001039087, intron 1 of 25)	1475	NM_001039086	107746	Mm.298274	NM_054050	ENSMUSG00000039844	Rapgef1	4932418O06Rik|C3G|Grf2	Rap guanine nucleotide exchange factor (GEF) 1	protein-coding
mm_69396.1	chr7	132154718	132154745	-	1	NA	promoter-TSS (NM_018867)	promoter-TSS (NM_018867)	10	NM_018867	55987	Mm.471654	NM_018867	ENSMUSG00000030862	Cpxm2	4632435C11Rik|CPX-2|Cpx2	carboxypeptidase X 2 (M14 family)	protein-coding
mm_160348.1	chr8	21065091	21065091	+	1	NA	promoter-TSS (NM_010039)	promoter-TSS (NM_010039)	25	NM_010039	13238	Mm.426634	NM_010039		Defa4	Crp4|Defa28|Defcr4	defensin, alpha, 4	protein-coding
mm_150597.1	chr19	40731064	40731069	+	1	NA	intron (NM_001304721, intron 7 of 9)	Tigger2b|DNA|TcMar-Tigger	71296	NM_009848	12495	Mm.2824	NM_009848	ENSMUSG00000048120	Entpd1	2610206B08Rik|AA408691|Cd39|NTPDase-1	ectonucleoside triphosphate diphosphohydrolase 1	protein-coding
mm_6516.1	chr1	74394922	74394944	-	1	NA	TTS (NR_029743)	TTS (NR_029743)	623	NR_029743	387219		NR_029743	ENSMUSG00000065468	Mir26b	Mirn26b|mir-26b|mmu-mir-26b	microRNA 26b	ncRNA
mm_44039.1	chr5	147513746	147513748	+	1	NA	intron (NM_028291, intron 5 of 18)	MurERV4-int|LTR|ERVK	83167	NM_028291	72587	Mm.320469	NM_028291	ENSMUSG00000029647	Pan3	2700050F09Rik|A430027N15Rik|AU014670	PAN3 poly(A) specific ribonuclease subunit	protein-coding
mm_20586.1	chr2	131159983	131160005	-	1	NA	promoter-TSS (NM_026091)	promoter-TSS (NM_026091)	26	NM_026091	67326	Mm.27711	NM_026091	ENSMUSG00000027327	1700037H04Rik	-	RIKEN cDNA 1700037H04 gene	protein-coding
mm_31935.1	chr4	86575697	86575718	+	1	NA	promoter-TSS (NM_178376)	promoter-TSS (NM_178376)	34	NM_178376	68441	Mm.31178	NM_178376	ENSMUSG00000070934	Rraga	1300010C19Rik|AI255374|FIP-1|RAGA	Ras-related GTP binding A	protein-coding
mm_112650.1	chr13	16018168	16018178	+	1	NA	intron (NM_008380, intron 4 of 4)	intron (NM_008380, intron 4 of 4)	6322	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_99612.1	chr11	104582876	104582899	+	1	NA	intron (NM_010858, intron 4 of 8)	intron (NM_010858, intron 4 of 8)	-20689	NR_130177	100415912	Mm.446786	NR_130177		Gm11665	Gm11664|OTTMUSG00000003182|OTTMUSG00000003183	predicted gene 11665	ncRNA
mm_84077.1	chr9	58201983	58202023	-	1	NA	promoter-TSS (NM_001161540)	promoter-TSS (NM_001161540)	-204	NM_001161540	320563	Mm.186499	NM_177193	ENSMUSG00000051243	Islr2	B930052A04Rik|Linx|Mbu-3|mKIAA1465	immunoglobulin superfamily containing leucine-rich repeat 2	protein-coding
mm_65624.1	chr7	27541734	27541751	-	1	NA	exon (NM_011116, exon 6 of 14)	exon (NM_011116, exon 6 of 14)	11476	NM_011116	18807	Mm.6483	NM_011116	ENSMUSG00000003363	Pld3	Sam-9	phospholipase D family, member 3	protein-coding
mm_98962.1	chr11	98646756	98646772	+	1	NA	promoter-TSS (NM_029727)	promoter-TSS (NM_029727)	5	NM_029727	76758	Mm.159149	NM_029727	ENSMUSG00000017211	Gsdma2	2200001G21Rik|2210006M16Rik|2210009F20Rik|2210411P14Rik|Gsdm2|Gsdml2	gasdermin A2	protein-coding
mm_160048.1	chr6	147091202	147091202	+	1	NA	5' UTR (NM_001081237, exon 1 of 3)	5' UTR (NM_001081237, exon 1 of 3)	127	NM_001081237	232539	Mm.491206	NM_001081237	ENSMUSG00000040102	Klhl42	A330079N23Rik|AI450355|C230080I20Rik|Ctb9|Klhdc5|mKIAA1340	kelch-like 42	protein-coding
mm_120851.1	chr14	75219271	75219288	+	1	NA	intron (NM_008879, intron 14 of 16)	(TTTTC)n|Simple_repeat|Simple_repeat	-23008	NM_019775	56373	Mm.24242	NM_019775	ENSMUSG00000021999	Cpb2	1110032P04Rik|4930405E17Rik|AI255929|CPR|Cpu|TAFI	carboxypeptidase B2 (plasma)	protein-coding
mm_33447.1	chr4	130663354	130663412	+	1	NA	promoter-TSS (NM_001159603)	promoter-TSS (NM_001159603)	24	NM_001159605	80912	Mm.440206	NM_030722	ENSMUSG00000028580	Pum1	AA517475|Pumm|mKIAA0099	pumilio RNA-binding family member 1	protein-coding
mm_129426.1	chr15	78468621	78468646	-	1	NA	promoter-TSS (NM_027902)	promoter-TSS (NM_027902)	1	NM_027902	71753	Mm.34056	NM_027902	ENSMUSG00000016942	Tmprss6	1300008A22Rik	transmembrane serine protease 6	protein-coding
mm_123287.1	chr14	61440026	61440041	-	1	NA	promoter-TSS (NM_008466)	promoter-TSS (NM_008466)	-86	NM_008466	16648	Mm.25548	NM_008466	ENSMUSG00000021929	Kpna3	IPOA4	karyopherin (importin) alpha 3	protein-coding
mm_13007.1	chr2	90905061	90905075	+	1	NA	promoter-TSS (NM_026688)	promoter-TSS (NM_026688)	282	NM_025991	67136	Mm.330394	NM_025991	ENSMUSG00000005505	Kbtbd4	2510026C23Rik	kelch repeat and BTB (POZ) domain containing 4	protein-coding
mm_63060.1	chr7	122067344	122067374	+	1	NA	promoter-TSS (NM_026140)	promoter-TSS (NM_026140)	161	NM_138589	28018	Mm.282122	NM_138589	ENSMUSG00000030870	Ubfd1	AI467302|D7Wsu105e|D7Wsu128e|Ubph	ubiquitin family domain containing 1	protein-coding
mm_88712.1	chr10	80152412	80152448	+	1	NA	intron (NM_001347117, intron 4 of 7)	intron (NM_001347117, intron 4 of 7)	2748	NM_001305799	59090	Mm.143813	NM_021565	ENSMUSG00000035621	Midn	3000003C15Rik	midnolin	protein-coding
mm_43771.1	chr5	141241525	141241542	+	1	NA	promoter-TSS (NM_177879)	promoter-TSS (NM_177879)	-1	NM_177879	330222	Mm.151931	NM_177879	ENSMUSG00000039683	Sdk1	5330440E10|6720466O15Rik	sidekick cell adhesion molecule 1	protein-coding
mm_149275.1	chr19	10605557	10605614	+	1	NA	promoter-TSS (NM_015735)	promoter-TSS (NM_015735)	-40	NM_015735	13194	Mm.289915	NM_015735	ENSMUSG00000024740	Ddb1	127kDa|AA408517|p127-Ddb1	damage specific DNA binding protein 1	protein-coding
mm_49070.1	chr6	5725813	5725858	+	1	NA	5' UTR (NM_010063, exon 1 of 17)	5' UTR (NM_010063, exon 1 of 17)	196	NM_001191026	13426	Mm.20893	NM_010063	ENSMUSG00000029757	Dync1i1	DH IC-1|DHIC-1|DIC|Dncic1|IC74	dynein cytoplasmic 1 intermediate chain 1	protein-coding
mm_112189.1	chr12	113422693	113422714	-	1	NA	Intergenic	Intergenic	-66862	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_47521.1	chr5	124111800	124111854	-	1	NA	promoter-TSS (NM_001347478)	promoter-TSS (NM_001347478)	-473	NM_001347478	66627	Mm.7050	NM_025671	ENSMUSG00000023707	Ogfod2	1300006G11Rik|5730405M13Rik|AU041636|AW552395	2-oxoglutarate and iron-dependent oxygenase domain containing 2	protein-coding
mm_60627.1	chr7	44748603	44748634	+	1	NA	promoter-TSS (NM_178734)	promoter-TSS (NM_178734)	-1	NM_178734	243963	Mm.382935	NM_178734	ENSMUSG00000048012	Zfp473	D030014N22Rik|Znf473|zfp-100	zinc finger protein 473	protein-coding
mm_42857.1	chr5	122210357	122210367	+	1	NA	promoter-TSS (NM_028752)	promoter-TSS (NM_028752)	75	NM_028752	74096	Mm.28804	NM_028752	ENSMUSG00000064267	Hvcn1	0610039P13Rik|AI450555|BTS|HV1|Vsop.|mVSOP	hydrogen voltage-gated channel 1	protein-coding
mm_107943.1	chr12	71889727	71889740	+	1	NA	5' UTR (NM_001286452, exon 1 of 25)	5' UTR (NM_001286452, exon 1 of 25)	190	NM_001286452	208846	Mm.87417	NM_026102	ENSMUSG00000034574	Daam1	-	dishevelled associated activator of morphogenesis 1	protein-coding
mm_21055.1	chr2	152654254	152654259	-	1	NA	Intergenic	Intergenic	-15205	NM_010376	14950	Mm.277327	NM_010376	ENSMUSG00000019188	H13	1200006O09Rik|4930443L17Rik|5031424B04Rik|AV020344|H-13|Hm13|PSL3|Spp	histocompatibility 13	protein-coding
mm_67604.1	chr7	83745797	83745844	-	1	NA	Intergenic	Intergenic	-10330	NM_010551	16170	Mm.10137	NM_010551	ENSMUSG00000001741	Il16	mKIAA4048	interleukin 16	protein-coding
mm_106879.1	chr12	8011546	8011582	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	33887	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_116743.1	chr13	51767564	51767568	-	1	NA	intron (NM_013660, intron 1 of 15)	intron (NM_013660, intron 1 of 15)	26181	NM_001281880	20354	Mm.33903	NM_013660	ENSMUSG00000021451	Sema4d	CD100|Semacl2|Semaj|Semcl2|coll-4	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D	protein-coding
mm_100172.1	chr11	116532442	116532478	+	1	NA	promoter-TSS (NM_001172472)	promoter-TSS (NM_001172472)	16	NM_001172473	20698	Mm.20944	NM_011451	ENSMUSG00000061878	Sphk1	1110006G24Rik|Sk1|Spk1	sphingosine kinase 1	protein-coding
mm_19903.1	chr2	114147098	114147103	-	1	NA	intron (NM_001290788, intron 12 of 33)	L1_Mur3|LINE|L1	3470	NR_105968	102465982		NR_105968	ENSMUSG00000098464	Mir7002	Gm27429|mmu-mir-7002	microRNA 7002	ncRNA
mm_45001.1	chr5	38230672	38230712	-	1	NA	exon (NM_025281, exon 6 of 9)	exon (NM_025281, exon 6 of 9)	10210	NM_025281	17089	Mm.28560	NM_025281	ENSMUSG00000067367	Lyar	MLZ-264	Ly1 antibody reactive clone	protein-coding
mm_40510.1	chr5	57767642	57767661	+	1	NA	intron (NM_001310608, intron 1 of 3)	intron (NM_001310608, intron 1 of 3)	49570	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_157543.1	chrX	51205879	51205900	-	1	NA	5' UTR (NM_134163, exon 1 of 8)	5' UTR (NM_134163, exon 1 of 8)	101	NM_001310515	171170	Mm.295324	NM_134163	ENSMUSG00000036109	Mbnl3	A530038J18Rik|AI661274|CHCR|E430034C16Rik|MBLX|MBLX39|MBXL	muscleblind-like 3 (Drosophila)	protein-coding
mm_63667.1	chr7	129662919	129662921	+	1	NA	Intergenic	B4|SINE|B4	71057	NM_172255	207425	Mm.229323	NM_172255	ENSMUSG00000042055	Wdr11	2900055P10Rik|AW489876|Brwd2|mKIAA1351	WD repeat domain 11	protein-coding
mm_59770.1	chr7	28834069	28834074	+	1	NA	promoter-TSS (NM_010707)	promoter-TSS (NM_010707)	-99	NM_010707	16857	Mm.210336	NM_010707		Lgals6	galectin-6	lectin, galactose binding, soluble 6	protein-coding
mm_53640.1	chr6	140622641	140622659	+	1	NA	promoter-TSS (NM_178803)	promoter-TSS (NM_178803)	-13	NM_178803	11569	Mm.86453	NM_009637	ENSMUSG00000030232	Aebp2	AU023766|B230313N05Rik	AE binding protein 2	protein-coding
mm_95634.1	chr11	53706784	53706814	+	1	NA	intron (NM_009012, intron 1 of 24)	CpG	520	NM_009012	19360	Mm.4888	NM_009012	ENSMUSG00000020380	Rad50	Mrell|Rad50l	RAD50 double strand break repair protein	protein-coding
mm_50701.1	chr6	52102937	52102955	+	1	NA	promoter-TSS (NR_110440)	promoter-TSS (NR_110440)	-3	NR_110440	102635415	Mm.333063	NR_110440	ENSMUSG00000085412	Halr1	Gm15055|Haunt|Linchoxa1|OTTMUSG00000018881|linc-Evx1|linc-Hoxa1|linc1547	Hoxa adjacent long noncoding RNA 1	ncRNA
mm_87057.1	chr10	28837791	28837794	+	1	NA	intron (NM_001305663, intron 5 of 5)	intron (NM_001305663, intron 5 of 5)	85715	NR_033601	114676	Mm.390292	NR_033601		4930519F09Rik	-	pyruvate dehydrogenase E1 alpha 1 pseudogene	pseudo
mm_163042.1	chr11	54568194	54568197	+	1	NA	intron (NM_175258, intron 5 of 27)	intron (NM_175258, intron 5 of 27)	-27951	NM_001252498	192786	Mm.254404	NM_175258	ENSMUSG00000037533	Rapgef6	A530068K01|AI844632|BB085664|C030018K18Rik|PDZ-GEF2|Pdzgef2|RA-GEF-2|Ragef2|mKIAA4052	Rap guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_44698.1	chr5	30461910	30461942	-	1	NA	promoter-TSS (NM_001100395)	promoter-TSS (NM_001100395)	6	NM_001286421	83762	Mm.244502	NM_031875	ENSMUSG00000062372	Otof	-	otoferlin	protein-coding
mm_48009.1	chr5	136165043	136165058	-	1	NA	intron (NM_178751, intron 1 of 2)	intron (NM_178751, intron 1 of 2)	5606	NM_178751	269717	Mm.308396	NM_178751	ENSMUSG00000039747	Orai2	A730041O15Rik|Tmem142b	ORAI calcium release-activated calcium modulator 2	protein-coding
mm_121117.1	chr14	101840362	101840372	+	1	NA	promoter-TSS (NM_001347628)	promoter-TSS (NM_001347628)	-256	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_96034.1	chr11	59556242	59556257	+	1	NA	intron (NM_145827, intron 6 of 9)	intron (NM_145827, intron 6 of 9)	13563	NM_145827	216799	Mm.54174	NM_145827	ENSMUSG00000032691	Nlrp3	AGTAVPRL|AII/AVP|Cias1|FCAS|FCU|MWS|Mmig1|NALP3|Pypaf1	NLR family, pyrin domain containing 3	protein-coding
mm_119740.1	chr14	54122114	54122133	+	1	NA	Intergenic	Intergenic	131806	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_78445.1	chr9	32224247	32224264	+	1	NA	promoter-TSS (NM_177379)	promoter-TSS (NM_177379)	6	NM_177379	330914	Mm.46683	NM_177379	ENSMUSG00000041444	Arhgap32	3426406O18Rik|Gc-gap|Grit|Px-rics|Rics|mKIAA0712|p200Rhogap|p250Gap	Rho GTPase activating protein 32	protein-coding
mm_77514.1	chr8	122894062	122894083	-	1	NA	non-coding (NR_037865, exon 10 of 14)	non-coding (NR_037865, exon 10 of 14)	45698	NM_007662	12555	Mm.1976	NM_007662	ENSMUSG00000031962	Cdh15	AI323380|Cdh14|Mcad	cadherin 15	protein-coding
mm_108006.1	chr12	73584641	73584659	+	1	NA	promoter-TSS (NM_008856)	promoter-TSS (NM_008856)	-146	NM_001313977	18755	Mm.341677	NM_008856	ENSMUSG00000021108	Prkch	Pkch	protein kinase C, eta	protein-coding
mm_119247.1	chr14	33923356	33923364	+	1	NA	promoter-TSS (NM_145741)	promoter-TSS (NM_145741)	-227	NM_145741	14560	Mm.432071	NM_145741	ENSMUSG00000021943	Gdf10	Bmp3b	growth differentiation factor 10	protein-coding
mm_49977.1	chr6	40891351	40891359	+	1	NA	intron (NR_035473, intron 2 of 3)	intron (NR_035473, intron 2 of 3)	-3861	NM_139296	194357	Mm.207087	NM_139296	ENSMUSG00000029885	Moxd2	Dbhl1	monooxygenase, DBH-like 2	protein-coding
mm_103546.1	chr11	77607601	77607635	-	1	NA	5' UTR (NM_144825, exon 1 of 20)	5' UTR (NM_144825, exon 1 of 20)	197	NM_144825	216965	Mm.340436	NM_144825	ENSMUSG00000017291	Taok1	2810468K05Rik|AU020252|D130018F14Rik|Map3k16|Markk|Psk2|mKIAA1361	TAO kinase 1	protein-coding
mm_42976.1	chr5	123167370	123167392	+	1	NA	3' UTR (NM_001040398, exon 17 of 17)	3' UTR (NM_001040398, exon 17 of 17)	15305	NM_008277	15445	Mm.439709	NM_008277	ENSMUSG00000029445	Hpd	Fla|Flp|Hppd|Laf	4-hydroxyphenylpyruvic acid dioxygenase	protein-coding
mm_86036.1	chr9	114026712	114026764	-	1	NA	promoter-TSS (NM_178624)	promoter-TSS (NM_178624)	13	NM_178624	72179	Mm.386808	NM_178624	ENSMUSG00000032507	Fbxl2	2810423A21Rik|Fbl3	F-box and leucine-rich repeat protein 2	protein-coding
mm_128092.1	chr15	27788514	27788525	-	1	NA	intron (NM_001081302, intron 34 of 56)	intron (NM_001081302, intron 34 of 56)	-106977	NM_001242423	223433	Mm.266485	NM_198301	ENSMUSG00000056069	Fam105a	9830126M18	family with sequence similarity 105, member A	protein-coding
mm_146659.1	chr18	11967139	11967156	-	1	NA	Intergenic	Intergenic	-126709	NR_035447	100316686		NR_035447	ENSMUSG00000084565	Mir1901	Mirn1901|mmu-mir-1901	microRNA 1901	ncRNA
mm_40960.1	chr5	76951717	76951795	+	1	NA	promoter-TSS (NM_172146)	promoter-TSS (NM_172146)	-178	NM_172146	231327	Mm.202337	NM_172146	ENSMUSG00000029246	Ppat	5730454C12Rik|AA408689|AA675351|AI507113|C79945	phosphoribosyl pyrophosphate amidotransferase	protein-coding
mm_69878.1	chr7	141636614	141636623	-	1	NA	intron (NM_001330001, intron 31 of 33)	intron (NM_001330001, intron 31 of 33)	15917	NR_106030	102466798		NR_106030	ENSMUSG00000098759	Mir7063	Gm27654|mmu-mir-7063	microRNA 7063	ncRNA
mm_120256.1	chr14	63011766	63011775	+	1	NA	promoter-TSS (NM_001039121)	promoter-TSS (NM_001039121)	-1	NM_001039121	654458	Mm.390737	NM_001039121	ENSMUSG00000075572	Defb43	BD-43|EG654458|mBD-43	defensin beta 43	protein-coding
mm_112217.1	chr12	113428889	113428898	-	1	NA	Intergenic	Intergenic	-60672	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_22303.1	chr2	180381063	180381071	-	1	NA	intron (NR_040745, intron 4 of 6)	intron (NR_040745, intron 4 of 6)	-4537	NR_045331	622283	Mm.447602	NR_045331		Mir1a-1hg	EG622283|Gm6307	Mir1a-1 and Mir133a-2 host gene	ncRNA
mm_154830.1	chrX	18162603	18162657	+	1	NA	promoter-TSS (NM_009483)	promoter-TSS (NM_009483)	55	NM_001310444	22289	Mm.257498	NM_009483	ENSMUSG00000037369	Kdm6a	Utx	lysine (K)-specific demethylase 6A	protein-coding
mm_2594.1	chr1	119523737	119523752	+	1	NA	Intergenic	Intergenic	-2410	NM_146103	226351	Mm.439806	NM_146103	ENSMUSG00000098923	Tmem185b	2500001K11Rik	transmembrane protein 185B	protein-coding
mm_59823.1	chr7	29245740	29245750	+	1	NA	exon (NM_001110201, exon 6 of 8)	exon (NM_001110201, exon 6 of 8)	2722	NM_028179	72275	Mm.441142	NM_028179	ENSMUSG00000030587	2200002D01Rik	2010005J02Rik|H2RSP|IMUP|IMUP-1|IMUP-2	RIKEN cDNA 2200002D01 gene	protein-coding
mm_25032.1	chr3	98160624	98160639	+	1	NA	promoter-TSS (NM_027665)	promoter-TSS (NM_027665)	-3	NM_027665	71078	Mm.50711	NM_027665	ENSMUSG00000043468	Adam30	4933424D07Rik|svph4	a disintegrin and metallopeptidase domain 30	protein-coding
mm_104071.1	chr11	86586444	86586452	-	1	NA	intron (NM_029478, intron 11 of 11)	intron (NM_029478, intron 11 of 11)	-2290	NR_029738	387140		NR_029738	ENSMUSG00000065455	Mir21a	Mir21|Mirn21|mmu-mir-21|mmu-mir-21a	microRNA 21a	ncRNA
mm_104370.1	chr11	94358847	94358856	-	1	NA	exon (NM_029600, exon 23 of 31)	exon (NM_029600, exon 23 of 31)	30850	NM_146024	71452	Mm.141054	NM_027799	ENSMUSG00000020864	Ankrd40	1110011C06Rik|5530600A18Rik|Gcap15	ankyrin repeat domain 40	protein-coding
mm_31022.1	chr4	40728975	40728977	+	1	NA	intron (NM_008298, intron 5 of 8)	intron (NM_008298, intron 5 of 8)	6046	NM_001164672	15502	Mm.27897	NM_008298	ENSMUSG00000028410	Dnaja1	HSJ-2|Hsj2|Nedd7	DnaJ heat shock protein family (Hsp40) member A1	protein-coding
mm_85325.1	chr9	101862444	101862465	-	1	NA	Intergenic	Intergenic	442521	NR_106163	102466241		NR_106163	ENSMUSG00000098521	Mir7243	Gm27363|mmu-mir-7243	microRNA 7243	ncRNA
mm_78611.1	chr9	37545141	37545150	+	1	NA	TTS (NM_020518)	TTS (NM_020518)	5890	NM_020518	57276	Mm.27478	NM_020518	ENSMUSG00000001943	Vsig2	1190004B15Rik|2210413P10Rik|AU040484|CTX|Ctm	V-set and immunoglobulin domain containing 2	protein-coding
mm_17290.1	chr2	26204626	26204636	-	1	NA	intron (NM_010711, intron 1 of 5)	intron (NM_010711, intron 1 of 5)	1944	NM_001039653	16871	Mm.386765	NM_010711	ENSMUSG00000026934	Lhx3	Lim3|P-LIM|mLIM3|mLim-3	LIM homeobox protein 3	protein-coding
mm_50910.1	chr6	57582703	57582718	+	1	NA	intron (NM_025992, intron 1 of 22)	intron (NM_025992, intron 1 of 22)	1718	NM_025992	67138	Mm.297393	NM_025992	ENSMUSG00000029798	Herc6	1700121D12Rik|2510038N07Rik|4930427L17Rik|AI451296|CEB1|Herc5	hect domain and RLD 6	protein-coding
mm_89966.1	chr10	111473221	111473242	+	1	NA	promoter-TSS (NM_015781)	promoter-TSS (NM_015781)	39	NM_015781	53605	Mm.290407	NM_015781	ENSMUSG00000058799	Nap1l1	AA407126|AI256722|D10Ertd68e|NAP-1	nucleosome assembly protein 1-like 1	protein-coding
mm_44861.1	chr5	34288376	34288399	-	1	NA	promoter-TSS (NM_001015039)	promoter-TSS (NM_001015039)	-63	NM_001015039	231125	Mm.113388	NM_001015039	ENSMUSG00000037224	Zfyve28	9630058O20Rik|Gm146|mKIAA1643	zinc finger, FYVE domain containing 28	protein-coding
mm_75917.1	chr8	71463717	71463727	-	1	NA	promoter-TSS (NM_022419)	promoter-TSS (NM_022419)	-65	NM_022419	64296	Mm.276383	NM_022419	ENSMUSG00000007950	Abhd8	0910001L24Rik|AB030191	abhydrolase domain containing 8	protein-coding
mm_144354.1	chr18	15346347	15346365	+	1	NA	Intergenic	RLTR41|LTR|ERV1	56643	NM_001308647	11829	Mm.250786	NM_009700	ENSMUSG00000024411	Aqp4	WCH4	aquaporin 4	protein-coding
mm_62639.1	chr7	107664910	107664927	+	1	NA	intron (NM_001163557, intron 3 of 25)	intron (NM_001163557, intron 3 of 25)	58074	NM_001163557	19024	Mm.2817	NM_008905	ENSMUSG00000036528	Ppfibp2	Cclp1	PTPRF interacting protein, binding protein 2 (liprin beta 2)	protein-coding
mm_139046.1	chr17	46248193	46248201	+	1	NA	promoter-TSS (NM_009085)	promoter-TSS (NM_009085)	117	NM_145353	28064	Mm.248769	NM_145353	ENSMUSG00000071074	Yipf3	C6orf109|D17Wsu94e|KLIP1	Yip1 domain family, member 3	protein-coding
mm_73476.1	chr8	106893617	106893696	+	1	NA	promoter-TSS (NM_011574)	promoter-TSS (NM_011574)	16	NM_011574	21771	Mm.10665	NM_011574	ENSMUSG00000041438	Cirh1a	Cirhin|Naic|Teg-292|Tex292|Utp4	cirrhosis, autosomal recessive 1A (human)	protein-coding
mm_147379.1	chr18	43687696	43687759	-	1	NA	promoter-TSS (NM_001163637)	promoter-TSS (NM_001163637)	46	NM_001163637	76217	Mm.134602	NM_001163637	ENSMUSG00000024502	Jakmip2	6430702L21Rik|AI850334|D930046L20Rik	janus kinase and microtubule interacting protein 2	protein-coding
mm_118748.1	chr14	22330905	22330952	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	211870	NR_046307	74896	Mm.444661	NR_046307		4930405A10Rik	4930456G20Rik	RIKEN cDNA 4930405A10 gene	ncRNA
mm_16599.1	chr2	5001568	5001584	-	1	NA	intron (NM_001305259, intron 8 of 19)	MLT1J|LTR|ERVL-MaLR	10768	NM_001305259	70024	Mm.23828	NM_027290	ENSMUSG00000026669	Mcm10	2410041F14Rik|AU018508|C330019M07Rik|C79164	minichromosome maintenance 10 replication initiation factor	protein-coding
mm_20493.1	chr2	130279376	130279423	-	1	NA	TTS (NM_130884)	TTS (NM_130884)	1373	NR_028528	100217428		NR_028528	ENSMUSG00000065272	Snord57	MBII-434	small nucleolar RNA, C/D box 57	snoRNA
mm_119711.1	chr14	53863058	53863088	+	1	NA	Intergenic	Intergenic	390856	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_128494.1	chr15	51897005	51897028	-	1	NA	Intergenic	L1ME1|LINE|L1	19575	NM_030132	78581	Mm.176347	NM_030132	ENSMUSG00000022313	Utp23	1700010I21Rik|AI662478|BB238373|D530033C11Rik	UTP23 small subunit processome component	protein-coding
mm_7478.1	chr1	120504874	120504878	-	1	NA	5' UTR (NM_010766, exon 1 of 17)	5' UTR (NM_010766, exon 1 of 17)	208	NM_010766	17167	Mm.1856	NM_010766	ENSMUSG00000026390	Marco	AI323439|Ly112|Scara2	macrophage receptor with collagenous structure	protein-coding
mm_149544.1	chr19	12574398	12574402	+	1	NA	intron (NM_001346545, intron 1 of 2)	intron (NM_001346545, intron 1 of 2)	875	NM_026640	107373	Mm.1643	NM_026640	ENSMUSG00000024691	Fam111a	4632417K18Rik|AW413625	family with sequence similarity 111, member A	protein-coding
mm_93112.1	chr10	91121947	91121994	-	1	NA	exon (NM_133668, exon 3 of 8)	exon (NM_133668, exon 3 of 8)	1993	NM_133668	18674	Mm.298	NM_133668	ENSMUSG00000061904	Slc25a3	5730556H19Rik|PTP|Phc	solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 3	protein-coding
mm_12114.1	chr2	61593741	61593749	+	1	NA	intron (NM_001164072, intron 1 of 7)	intron (NM_001164072, intron 1 of 7)	648	NM_001164071	21353	Mm.244393	NM_011529	ENSMUSG00000064289	Tank	C86182|E430026L09Rik|I-TRAF	TRAF family member-associated Nf-kappa B activator	protein-coding
mm_115513.1	chr13	5604178	5604189	-	1	NA	Intergenic	Intergenic	253909	NR_045891	71867	Mm.179181	NR_045891	ENSMUSG00000100625	1700016G22Rik	-	RIKEN cDNA 1700016G22 gene	ncRNA
mm_7227.1	chr1	93342902	93342911	-	1	NA	promoter-TSS (NM_080850)	promoter-TSS (NM_080850)	-118	NM_080850	269224	Mm.379454	NM_080850	ENSMUSG00000026274	Pask	mKIAA0135	PAS domain containing serine/threonine kinase	protein-coding
mm_106207.1	chr11	116851191	116851194	-	1	NA	intron (NM_011358, intron 2 of 2)	intron (NM_011358, intron 2 of 2)	1902	NM_011358	20382	Mm.21841	NM_011358	ENSMUSG00000034120	Srsf2	D11Wsu175e|MRF-1|Pr264|SC35|Sfrs10|Sfrs2	serine/arginine-rich splicing factor 2	protein-coding
mm_95664.1	chr11	53772071	53772087	+	1	NA	intron (NM_001159393, intron 2 of 9)	RSINE1|SINE|B4	1606	NM_001159396	16362	Mm.105218	NM_008390	ENSMUSG00000018899	Irf1	AU020929|Irf-1	interferon regulatory factor 1	protein-coding
mm_117822.1	chr13	98016205	98016215	-	1	NA	intron (NM_012026, intron 9 of 35)	intron (NM_012026, intron 9 of 35)	189955	NM_012026	110596	Mm.252718	NM_012026	ENSMUSG00000021662	Arhgef28	9230110L08Rik|AI323540|D13Bwg1089e|RIP2|Rgnef|RhoGEF|Rhoip2|p190RhoGEF	Rho guanine nucleotide exchange factor (GEF) 28	protein-coding
mm_90842.1	chr10	8725095	8725119	-	1	NA	3' UTR (NM_175155, exon 20 of 20)	3' UTR (NM_175155, exon 20 of 20)	160963	NM_175155	70097	Mm.338275	NM_175155	ENSMUSG00000015305	Sash1	1100001C18Rik|2500002E12Rik|A330076K04Rik|mKIAA0790	SAM and SH3 domain containing 1	protein-coding
mm_118730.1	chr14	22246851	22246864	+	1	NA	intron (NM_028275, intron 2 of 6)	MLT1D|LTR|ERVL-MaLR	227145	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_113881.1	chr13	48969012	48969023	+	1	NA	non-coding (NR_015601, exon 2 of 2)	non-coding (NR_015601, exon 2 of 2)	905	NR_015601	68128	Mm.426304	NR_015601		Fam120aos	C030044B11Rik	family with sequence similarity 120A, opposite strand	ncRNA
mm_37455.1	chr4	123415745	123415755	-	1	NA	intron (NM_001199136, intron 57 of 97)	(A)n|Simple_repeat|Simple_repeat	-3839	NM_001167918	442834	Mm.483803	NM_001167918		D830031N03Rik	Kiaa0754|mKIAA0754	RIKEN cDNA D830031N03 gene	protein-coding
mm_74813.1	chr8	22694062	22694081	-	1	NA	intron (NM_001159774, intron 3 of 21)	intron (NM_001159774, intron 3 of 21)	12512	NM_010546	16150	Mm.277886	NM_010546	ENSMUSG00000031537	Ikbkb	AI132552|IKK-2|IKK-beta|IKK2|IKK[b]|IKKbeta	inhibitor of kappaB kinase beta	protein-coding
mm_22461.1	chr3	3508006	3508021	+	1	NA	promoter-TSS (NM_013920)	promoter-TSS (NM_013920)	-17	NM_013920	30942	Mm.330897	NM_013920	ENSMUSG00000017688	Hnf4g	NR2A2	hepatocyte nuclear factor 4, gamma	protein-coding
mm_143479.1	chr17	71257243	71257259	-	1	NA	intron (NM_145158, intron 4 of 7)	intron (NM_145158, intron 4 of 7)	52597	NM_001164885	64898	Mm.227924	NM_022882	ENSMUSG00000024052	Lpin2	2610511G02Rik|AI481352|AW742896	lipin 2	protein-coding
mm_90085.1	chr10	116914103	116914115	+	1	NA	exon (NM_001003950, exon 7 of 10)	exon (NM_001003950, exon 7 of 10)	-17230	NM_001033333	237558	Mm.336386	NM_001033333	ENSMUSG00000034057	Myrfl	Gm239	myelin regulatory factor-like	protein-coding
mm_58438.1	chr7	3297923	3297933	+	1	NA	3' UTR (NM_016969, exon 3 of 3)	3' UTR (NM_016969, exon 3 of 3)	4900	NM_001093766	50918	Mm.29874	NM_016969	ENSMUSG00000068566	Myadm	D7Wsu62e	myeloid-associated differentiation marker	protein-coding
mm_35693.1	chr4	44126683	44126687	-	1	NA	3' UTR (NM_175201, exon 11 of 11)	3' UTR (NM_175201, exon 11 of 11)	4792	NR_040414	623796	Mm.490409	NR_040414	ENSMUSG00000084274	Gm12504	OTTMUSG00000007209	prothymosin alpha pseudogene	pseudo
mm_54434.1	chr6	34177022	34177041	-	1	NA	promoter-TSS (NM_021435)	promoter-TSS (NM_021435)	23	NM_021435	58246	Mm.245527	NM_021435	ENSMUSG00000018999	Slc35b4	4930474D06Rik|AB041549|AW494345	solute carrier family 35, member B4	protein-coding
mm_75176.1	chr8	36828051	36828064	-	1	NA	intron (NM_001194940, intron 4 of 17)	intron (NM_001194940, intron 4 of 17)	-95003	NM_001194941	50768	Mm.125155	NM_015802	ENSMUSG00000031523	Dlc1	A730069N07Rik|Arhgap7|HP|STARD12|dlc-1	deleted in liver cancer 1	protein-coding
mm_106007.1	chr11	115812137	115812230	-	1	NA	5' UTR (NM_080643, exon 2 of 20)	5' UTR (NM_080643, exon 2 of 20)	1409	NM_080643	140721	Mm.383737	NM_080643	ENSMUSG00000034471	Caskin2	1600028L06Rik|mKIAA1139	CASK-interacting protein 2	protein-coding
mm_153616.1	chr19	43986349	43986359	-	1	NA	5' UTR (NM_030703, exon 1 of 9)	5' UTR (NM_030703, exon 1 of 9)	166	NM_030703	93721	Mm.206774	NM_030703	ENSMUSG00000025196	Cpn1	0610011F20Rik|CPN	carboxypeptidase N, polypeptide 1	protein-coding
mm_87105.1	chr10	33195947	33195957	+	1	NA	exon (NM_029726, exon 8 of 38)	exon (NM_029726, exon 8 of 38)	60405	NR_040657	442820	Mm.490725	NR_040657		D830005E20Rik	-	RIKEN cDNA D830005E20 gene	ncRNA
mm_79683.1	chr9	59942076	59942095	+	1	NA	TTS (NM_013708)	TTS (NM_013708)	7994	NM_013708	23958	Mm.103641	NM_013708	ENSMUSG00000032292	Nr2e3	A930035N01Rik|PNR|RNR|rd7	nuclear receptor subfamily 2, group E, member 3	protein-coding
mm_153745.1	chr19	44750759	44750765	-	1	NA	Intergenic	Intergenic	-6632	NM_011037	18504	Mm.192158	NM_011037	ENSMUSG00000004231	Pax2	Opdc|Pax-2	paired box 2	protein-coding
mm_78900.1	chr9	44673228	44673246	+	1	NA	promoter-TSS (NM_001277851)	promoter-TSS (NM_001277851)	4	NM_021481	58866	Mm.45380	NM_021481	ENSMUSG00000032098	Treh	2210412M19Rik	trehalase (brush-border membrane glycoprotein)	protein-coding
mm_119627.1	chr14	51145388	51145403	+	1	NA	3' UTR (NM_011271, exon 2 of 2)	3' UTR (NM_011271, exon 2 of 2)	1372	NM_011271	19752	Mm.235538	NM_011271	ENSMUSG00000035896	Rnase1	AI574248|Rib-1|Rib1	ribonuclease, RNase A family, 1 (pancreatic)	protein-coding
mm_6989.1	chr1	86357365	86357378	-	1	NA	exon (NM_010880, exon 3 of 14)	exon (NM_010880, exon 3 of 14)	-1044	NR_002851	80828		NR_002851	ENSMUSG00000064823	Snord82	Rnu82|U82|Z25	small nucleolar RNA, C/D box 82	snoRNA
mm_75612.1	chr8	62123187	62123200	-	1	NA	promoter-TSS (NM_001136089)	promoter-TSS (NM_001136089)	0	NM_001136089	26359	Mm.42179	NM_011922	ENSMUSG00000031635	Anxa10	-	annexin A10	protein-coding
mm_72892.1	chr8	90493126	90493131	+	1	NA	Intergenic	Intergenic	-144876	NM_172913	244579	Mm.302755	NM_172913	ENSMUSG00000043668	Tox3	500-9|BC052044|C230068E13|CAGF9|Tnrc9	TOX high mobility group box family member 3	protein-coding
mm_75588.1	chr8	61591131	61591148	-	1	NA	promoter-TSS (NM_001293774)	promoter-TSS (NM_001293774)	30	NM_001293774	72333	Mm.29933	NM_001081390	ENSMUSG00000058056	Palld	2410003B16Rik|6030492A02	palladin, cytoskeletal associated protein	protein-coding
mm_31577.1	chr4	57689512	57689525	+	1	NA	intron (NM_001304544, intron 4 of 8)	intron (NM_001304544, intron 4 of 8)	121270	NM_172868	242481	Mm.331630	NM_172868	ENSMUSG00000090053	Palm2	53-H12|B130066I24|R75368|pEN70	paralemmin 2	protein-coding
mm_69080.1	chr7	127011869	127011877	-	1	NA	intron (NM_080638, intron 1 of 14)	RSINE1|SINE|B4	2721	NM_080638	78388	Mm.228797	NM_080638	ENSMUSG00000030681	Mvp	2310009M24Rik|LRP|VAULT1	major vault protein	protein-coding
mm_153977.1	chr19	47864506	47864516	-	1	NA	3' UTR (NM_010362, exon 6 of 6)	3' UTR (NM_010362, exon 6 of 6)	-1034	NM_030051	68214	Mm.63791	NM_026619	ENSMUSG00000025069	Gsto2	1700020F09Rik|4930425C18Rik|GSTO 2-2	glutathione S-transferase omega 2	protein-coding
mm_37194.1	chr4	117496941	117496957	-	1	NA	5' UTR (NM_025739, exon 1 of 15)	5' UTR (NM_025739, exon 1 of 15)	103	NM_025739	66743	Mm.318331	NM_025739	ENSMUSG00000028677	Rnf220	4732477A13|4931406I20Rik|5730503K05Rik|AV302541	ring finger protein 220	protein-coding
mm_98010.1	chr11	84249399	84249412	+	1	NA	intron (NM_133360, intron 12 of 53)	intron (NM_133360, intron 12 of 53)	53967	NM_133360	107476	Mm.31374	NM_133360	ENSMUSG00000020532	Acaca	A530025K05Rik|Acac|Acc1|Gm738	acetyl-Coenzyme A carboxylase alpha	protein-coding
mm_123675.1	chr14	69476629	69476641	-	1	NA	Intergenic	Intergenic	35914	NM_173420	239167	Mm.259889	NM_173420	ENSMUSG00000047977	Synb	D930020E02Rik|syncytin-B	syncytin b	protein-coding
mm_8235.1	chr1	138175743	138175764	-	1	NA	promoter-TSS (NM_001268286)	promoter-TSS (NM_001268286)	-448	NM_001268286	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_165194.1	chr2	32386072	32386076	-	1	NA	intron (NM_008491, intron 2 of 5)	intron (NM_008491, intron 2 of 5)	1665	NM_008491	16819	Mm.9537	NM_008491	ENSMUSG00000026822	Lcn2	24p3|AW212229|NRL|Sip24	lipocalin 2	protein-coding
mm_59938.1	chr7	30424351	30424366	+	1	NA	5' UTR (NM_172142, exon 3 of 11)	5' UTR (NM_172142, exon 3 of 11)	1054	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_3207.1	chr1	135825041	135825063	+	1	NA	intron (NM_133664, intron 1 of 9)	Charlie5|DNA|hAT-Charlie	6454	NM_133664	16763	Mm.36726	NM_133664	ENSMUSG00000041782	Lad1	-	ladinin	protein-coding
mm_12617.1	chr2	74692052	74692074	+	1	NA	exon (NM_013554, exon 1 of 2)	exon (NM_013554, exon 1 of 2)	172	NM_013554	15430	Mm.24420	NM_013554	ENSMUSG00000050368	Hoxd10	AI385591|AI874987|Hox-4.5|Hox-5.3	homeobox D10	protein-coding
mm_90259.1	chr10	122449387	122449395	+	1	NA	exon (NM_016847, exon 1 of 2)	exon (NM_016847, exon 1 of 2)	892	NM_016847	54140	Mm.4351	NM_016847	ENSMUSG00000020123	Avpr1a	AVPR|Avpr1|V1a|V1aR	arginine vasopressin receptor 1A	protein-coding
mm_131396.1	chr16	14317517	14317533	+	1	NA	promoter-TSS (NM_025345)	promoter-TSS (NM_025345)	-193	NM_025345	66086	Mm.42072	NM_025345	ENSMUSG00000022677	Fopnl	0610037P05Rik	Fgfr1op N-terminal like	protein-coding
mm_88683.1	chr10	80054030	80054043	+	1	NA	promoter-TSS (NM_001037741)	promoter-TSS (NM_001037741)	17	NM_001037741	625249	Mm.332810	NM_008162	ENSMUSG00000075706	Gpx4	GPx-4|GSHPx-4|PHGPx|mtPHGPx|snGPx	glutathione peroxidase 4	protein-coding
mm_2356.1	chr1	92935622	92935622	+	1	NA	intron (NR_015525, intron 1 of 1)	intron (NR_015525, intron 1 of 1)	1214	NM_011796	23830	Mm.294315	NM_011796	ENSMUSG00000026270	Capn10	AW049679|Capn8|mKIAA1845	calpain 10	protein-coding
mm_39834.1	chr5	30853809	30853848	+	1	NA	intron (NM_133350, intron 1 of 6)	intron (NM_133350, intron 1 of 6)	-7979	NM_001310516	100732	Mm.332295	NM_133350	ENSMUSG00000029166	Mapre3	AI790651|EB2|EB3|EBF3|RP3	microtubule-associated protein, RP/EB family, member 3	protein-coding
mm_104437.1	chr11	94972049	94972055	-	1	NA	intron (NM_009161, intron 4 of 10)	intron (NM_009161, intron 4 of 10)	4275	NM_009161	20391	Mm.18709	NM_009161	ENSMUSG00000001508	Sgca	50DAG|Asg	sarcoglycan, alpha (dystrophin-associated glycoprotein)	protein-coding
mm_52980.1	chr6	123262540	123262616	+	1	NA	intron (NM_001163161, intron 1 of 5)	CT-rich|Low_complexity|Low_complexity	471	NM_010819	17474	Mm.441101	NM_010819	ENSMUSG00000030144	Clec4d	Clecsf8|Mpcl|mcl	C-type lectin domain family 4, member d	protein-coding
mm_144505.1	chr18	24606625	24606630	+	1	NA	intron (NM_021448, intron 1 of 21)	intron (NM_021448, intron 1 of 21)	2666	NM_021448	58523	Mm.25298	NM_021448	ENSMUSG00000024271	Elp2	AU023723|Epl2|StIP1|Statip1	elongator acetyltransferase complex subunit 2	protein-coding
mm_131160.1	chr16	6948707	6948724	+	1	NA	intron (NM_021477, intron 5 of 16)	B4A|SINE|B4	-121120	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_43396.1	chr5	135778675	135778689	+	1	NA	promoter-TSS (NM_029659)	promoter-TSS (NM_029659)	33	NM_008617	17448	Mm.297096	NM_008617	ENSMUSG00000019179	Mdh2	MDH|Mdh-2|Mor-1|Mor1	malate dehydrogenase 2, NAD (mitochondrial)	protein-coding
mm_48996.1	chr6	4756619	4756638	+	1	NA	exon (NM_130877, exon 2 of 2)	exon (NM_130877, exon 2 of 2)	9322	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_132011.1	chr16	25862345	25862352	+	1	NA	exon (NM_001127262, exon 3 of 11)	exon (NM_001127262, exon 3 of 11)	60432	NM_001127264	22061	Mm.20894	NM_011641	ENSMUSG00000022510	Trp63	AI462811|Ket|P51/P63|P63|P73l|Tp63|Trp53rp1	transformation related protein 63	protein-coding
mm_110827.1	chr12	72628869	72628887	-	1	NA	Intergenic	Intergenic	35950	NM_025522	66375	Mm.289653	NM_025522	ENSMUSG00000021094	Dhrs7	2310016E22Rik|5730564L20Rik|AW061210|Retdsr4|Retsdr4	dehydrogenase/reductase (SDR family) member 7	protein-coding
mm_1860.1	chr1	84882130	84882175	+	1	NA	intron (NM_025386, intron 2 of 3)	intron (NM_025386, intron 2 of 3)	42311	NM_025386	66153	Mm.381192	NM_025386	ENSMUSG00000073633	Fbxo36	0610008D19Rik|1110020F21Rik|2410002G19Rik|D1Ertd757e	F-box protein 36	protein-coding
mm_99735.1	chr11	106374735	106374747	+	1	NA	promoter-TSS (NM_029345)	promoter-TSS (NM_029345)	-85	NM_029345	75573	Mm.159539	NM_029345	ENSMUSG00000009210	Prr29	2310007L24Rik	proline rich 29	protein-coding
mm_7992.1	chr1	134235421	134235443	-	1	NA	promoter-TSS (NM_001282945)	promoter-TSS (NM_001282945)	25	NM_001291930	11539	Mm.298908	NM_009629	ENSMUSG00000042429	Adora1	A1-AR|A1AR|A1R|AA1R|AI848715|BB176431|Ri	adenosine A1 receptor	protein-coding
mm_67642.1	chr7	84439202	84439210	-	1	NA	Intergenic	Intergenic	-29168	NM_007488	11864	Mm.38594	NM_007488	ENSMUSG00000015709	Arnt2	Hif-2b|bHLHe1|mKIAA0307	aryl hydrocarbon receptor nuclear translocator 2	protein-coding
mm_19198.1	chr2	84469502	84469504	-	1	NA	intron (NM_001177320, intron 2 of 7)	intron (NM_001177320, intron 2 of 7)	4671	NM_011576	21788	Mm.124316	NM_011576	ENSMUSG00000027082	Tfpi	A630013F22Rik|AW552122|EPI|LACI	tissue factor pathway inhibitor	protein-coding
mm_121232.1	chr14	103055821	103055831	+	1	NA	3' UTR (NM_008392, exon 5 of 5)	3' UTR (NM_008392, exon 5 of 5)	8814	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_68923.1	chr7	126471445	126471489	-	1	NA	exon (NM_001289538, exon 4 of 9)	exon (NM_001289538, exon 4 of 9)	1627	NR_110346	20399	Mm.8538	NM_011363	ENSMUSG00000030733	Sh2b1	AI425885|C530001K22Rik|Irip|Psm|SH2-B|SH2-Bb|Sh2bpsm1|mKIAA1299	SH2B adaptor protein 1	protein-coding
mm_111827.1	chr12	107131476	107131487	-	1	NA	Intergenic	Intergenic	-415157	NR_015512	71033	Mm.159404	NR_015512	ENSMUSG00000085820	4933406K04Rik	4930426M03Rik|4930485I22Rik|4933427G14Rik	RIKEN cDNA 4933406K04 gene	ncRNA
mm_21135.1	chr2	154211522	154211534	-	1	NA	exon (NM_153418, exon 8 of 16)	exon (NM_153418, exon 8 of 16)	11148	NM_153418	228801	Mm.3783	NM_153418	ENSMUSG00000027485	Bpifb1	Lplunc1	BPI fold containing family B, member 1	protein-coding
mm_37660.1	chr4	129057958	129057988	-	1	NA	promoter-TSS (NM_029219)	promoter-TSS (NM_029219)	-298	NM_029219	75234	Mm.259672	NM_029219	ENSMUSG00000028793	Rnf19b	4930534K13Rik|4930555L03Rik|Ibrdc3	ring finger protein 19B	protein-coding
mm_44257.1	chr5	5479078	5479107	-	1	NA	promoter-TSS (NM_001200025)	promoter-TSS (NM_001200025)	51	NM_001200025	381716	Mm.276086	NM_001200025	ENSMUSG00000079666	1700015F17Rik	Gm1686	RIKEN cDNA 1700015F17 gene	protein-coding
mm_57480.1	chr6	125236975	125236993	-	1	NA	promoter-TSS (NM_001042564)	promoter-TSS (NM_001042564)	43	NM_001033126	21940	Mm.367714	NM_001033126	ENSMUSG00000030336	Cd27	S152|Tnfrsf7|Tp55	CD27 antigen	protein-coding
mm_58769.1	chr7	15886165	15886173	+	1	NA	intron (NR_038092, intron 2 of 4)	intron (NR_038092, intron 2 of 4)	3552	NR_038092	546024	Mm.259041	NM_001033638	ENSMUSG00000074365	Crxos	AA606869|AY590891|Crxos1|Egam1	cone-rod homeobox, opposite strand	protein-coding
mm_146294.1	chr18	80046855	80046904	+	1	NA	promoter-TSS (NM_053117)	promoter-TSS (NM_053117)	-16	NM_053117	93737	Mm.24678	NM_053117	ENSMUSG00000056214	Pard6g	2410049N21Rik|Par6a	par-6 family cell polarity regulator gamma	protein-coding
mm_126304.1	chr15	79516490	79516506	+	1	NA	promoter-TSS (NM_134090)	promoter-TSS (NM_134090)	90	NM_134090	105785	Mm.298199	NM_134090	ENSMUSG00000010830	Kdelr3	AI173274	KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 3	protein-coding
mm_116240.1	chr13	33905695	33905704	-	1	NA	promoter-TSS (NM_148942)	promoter-TSS (NM_148942)	9	NM_148942	97848	Mm.272188	NM_148942	ENSMUSG00000052180	Serpinb6c	C76171|C76174|SPI3C|SPIC|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 6c	protein-coding
mm_8130.1	chr1	136230383	136230394	-	1	NA	intron (NM_028872, intron 1 of 9)	intron (NM_028872, intron 1 of 9)	3892	NM_028872	67313	Mm.36763	NM_028872	ENSMUSG00000041605	5730559C18Rik	1700034M08Rik|4933426C09Rik|AI586180|D1Mgi54	RIKEN cDNA 5730559C18 gene	protein-coding
mm_16672.1	chr2	6722251	6722261	-	1	NA	promoter-TSS (NM_001310447)	promoter-TSS (NM_001310447)	-594	NM_001310447	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_16002.1	chr2	167358883	167358909	+	1	NA	Intergenic	Intergenic	-9718	NM_019835	56336	Mm.200886	NM_019835	ENSMUSG00000017929	B4galt5	9430078I07Rik|AW049941|AW539721	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 5	protein-coding
mm_37401.1	chr4	121196489	121196492	-	1	NA	intron (NM_001346660, intron 1 of 7)	intron (NM_001346660, intron 1 of 7)	18594	NM_001346660	109263	Mm.215745	NM_001081013	ENSMUSG00000049878	Rlf	9230110M18Rik|AI195322|MommeD8	rearranged L-myc fusion sequence	protein-coding
mm_102165.1	chr11	53818733	53818740	-	1	NA	intron (NR_033332, intron 2 of 3)	intron (NR_033332, intron 2 of 3)	40520	NR_033332	622459	Mm.479656	NR_033332	ENSMUSG00000081769	Gm12216	602-19-115|OTTMUSG00000005650	predicted gene 12216	ncRNA
mm_21866.1	chr2	165899020	165899037	-	1	NA	Intergenic	Intergenic	-14190	NM_001252587	228880	Mm.227598	NM_027230	ENSMUSG00000039671	Zmynd8	1110013E22Rik|2010005I16Rik|3632413B07Rik|AI316811|AL024039|Prkcbp1|RACK7	zinc finger, MYND-type containing 8	protein-coding
mm_158461.1	chrX	140599708	140599713	-	1	NA	intron (NM_001077364, intron 1 of 3)	CpG	812	NM_001077364	14605	Mm.22216	NM_010286	ENSMUSG00000031431	Tsc22d3	DIP|Dsip1|Gilz|TSC-22R|Tilz3	TSC22 domain family, member 3	protein-coding
mm_150905.1	chr19	45749609	45749631	+	1	NA	promoter-TSS (NM_008723)	promoter-TSS (NM_008723)	-57	NM_008723	18150	Mm.1406	NM_008723	ENSMUSG00000056209	Npm3	Nub1	nucleoplasmin 3	protein-coding
mm_2014.1	chr1	87127834	87127836	+	1	NA	TTS (NM_007432)	TTS (NM_007432)	2827	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_79720.1	chr9	61441800	61441833	+	1	NA	Intergenic	Intergenic	69450	NM_001083927	21887	Mm.24255	NM_009389	ENSMUSG00000032280	Tle3	2610103N05Rik|ESG|Grg3a|Grg3b|mKIAA1547	transducin-like enhancer of split 3	protein-coding
mm_84124.1	chr9	58657824	58657878	-	1	NA	intron (NM_028598, intron 4 of 5)	intron (NM_028598, intron 4 of 5)	75611	NM_009145	20320	Mm.15125	NM_009145	ENSMUSG00000032336	Nptn	AW554172|SDR-1|Sdfr1	neuroplastin	protein-coding
mm_8225.1	chr1	138174312	138174339	-	1	NA	intron (NM_001111316, intron 1 of 31)	intron (NM_001111316, intron 1 of 31)	801	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_103004.1	chr11	69695754	69695785	-	1	NA	5' UTR (NM_001159503, exon 1 of 13)	5' UTR (NM_001159503, exon 1 of 13)	329	NM_011614	21944	Mm.8983	NM_011614	ENSMUSG00000097328	Tnfsf12	Apo3l|Dr3l|Dr3lg|Tweak	tumor necrosis factor (ligand) superfamily, member 12	protein-coding
mm_169762.1	chr15	97184942	97184946	-	1	NA	Intergenic	ORR1A0|LTR|ERVL-MaLR	-62163	NM_172293	239647	Mm.130036	NM_172293	ENSMUSG00000044250	Pced1b	Fam113b	PC-esterase domain containing 1B	protein-coding
mm_38067.1	chr4	134093866	134093885	-	1	NA	exon (NM_013706, exon 2 of 2)	exon (NM_013706, exon 2 of 2)	1198	NM_013706	23833	Mm.24130	NM_013706	ENSMUSG00000000682	Cd52	AI463198|B7|B7-Ag|CAMPATH-1|CLS1|MB7	CD52 antigen	protein-coding
mm_81258.1	chr9	107995740	107995790	+	1	NA	Intergenic	Intergenic	-6883	NM_013785	27399	Mm.276155	NM_013785	ENSMUSG00000032594	Ip6k1	1200016D08Rik|AU022776|Ihpk1|InsP6|InsP6k1|Itpk6	inositol hexaphosphate kinase 1	protein-coding
mm_147969.1	chr18	67245449	67245489	-	1	NA	5' UTR (NM_172630, exon 1 of 11)	5' UTR (NM_172630, exon 1 of 11)	361	NM_172630	225651	Mm.235792	NM_172630	ENSMUSG00000062526	Mppe1	A530095G11	metallophosphoesterase 1	protein-coding
mm_169452.1	chr14	60875464	60875467	+	1	NA	intron (NR_040642, intron 18 of 19)	intron (NR_040642, intron 18 of 19)	90899	NR_040642	70478	Mm.274650	NM_027436	ENSMUSG00000021993	Mipep	5730405E07Rik|MIP	mitochondrial intermediate peptidase	protein-coding
mm_5750.1	chr1	46853424	46853442	-	1	NA	promoter-TSS (NM_172653)	promoter-TSS (NM_172653)	76	NM_172653	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|mKIAA1265	solute carrier family 39 (zinc transporter), member 10	protein-coding
mm_37753.1	chr4	129640692	129640725	-	1	NA	promoter-TSS (NM_001005506)	promoter-TSS (NM_001005506)	97	NM_001005506	109658	Mm.268863	NM_001005506	ENSMUSG00000053841	Txlna	2600010N21Rik|AI425952|AW209241|Il14|Txln	taxilin alpha	protein-coding
mm_119793.1	chr14	54194698	54194710	+	1	NA	Intergenic	Intergenic	59225	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_48327.1	chr5	138996058	138996068	-	1	NA	Intergenic	CpG-11694	-1110	NM_008808	18590	Mm.2675	NM_008808	ENSMUSG00000025856	Pdgfa	-	platelet derived growth factor, alpha	protein-coding
mm_4724.1	chr1	181212020	181212047	+	1	NA	promoter-TSS (NM_145514)	promoter-TSS (NM_145514)	-55	NM_145514	226757	Mm.289082	NM_145514	ENSMUSG00000038733	Wdr26	1600024A01Rik|AA693241|AI447817|AU044014|C77982|Gid7	WD repeat domain 26	protein-coding
mm_27199.1	chr3	35666160	35666173	-	1	NA	promoter-TSS (NR_040748)	promoter-TSS (NR_040748)	-3	NR_040748	625963	Mm.251506	NR_040748	ENSMUSG00000105662	Gm6639	-	predicted gene 6639	ncRNA
mm_115702.1	chr13	14521739	14521741	-	1	NA	intron (NM_001081348, intron 1 of 28)	intron (NM_001081348, intron 1 of 28)	1486	NM_001081348	94253	Mm.125298	NM_153130	ENSMUSG00000021301	Hecw1	9330116H24Rik|AV273951|E130207I19Rik|Nedl1	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	protein-coding
mm_5131.1	chr1	9685536	9685539	-	1	NA	intron (NM_008651, intron 6 of 15)	intron (NM_008651, intron 6 of 15)	14672	NM_001290397	17864	Mm.479	NM_008651	ENSMUSG00000025912	Mybl1	A-myb|G1-419-6|repro9	myeloblastosis oncogene-like 1	protein-coding
mm_118145.1	chr13	105054798	105054821	-	1	NA	5' UTR (NM_029879, exon 1 of 6)	5' UTR (NM_029879, exon 1 of 6)	121	NM_029879	52882	Mm.100348	NM_029879	ENSMUSG00000021719	Rgs7bp	A930030I01Rik|AI842293|D13Bwg1146e|R7bp	regulator of G-protein signalling 7 binding protein	protein-coding
mm_90361.1	chr10	127165806	127165822	+	1	NA	promoter-TSS (NM_027739)	promoter-TSS (NM_027739)	-17	NM_027739	14421	Mm.386762	NM_008080	ENSMUSG00000006731	B4galnt1	4933429D13Rik|Gal-NAc-T|GalNAc-T|GalNAcT|Galgt1|Ggm-2|Ggm2	beta-1,4-N-acetyl-galactosaminyl transferase 1	protein-coding
mm_29733.1	chr3	126831432	126831442	-	1	NA	intron (NM_001346636, intron 16 of 20)	intron (NM_001346636, intron 16 of 20)	111949	NM_001034168	109676	Mm.220242	NM_178655	ENSMUSG00000032826	Ank2	100043364|AI835472|AW491075|Ank-2|Gm4392	ankyrin 2, brain	protein-coding
mm_81720.1	chr9	111885291	111885293	+	1	NA	Intergenic	Intergenic	-194944	NM_001324546	20840	Mm.1414	NM_016853	ENSMUSG00000032502	Stac	-	src homology three (SH3) and cysteine rich domain	protein-coding
mm_3617.1	chr1	152399896	152399908	+	1	NA	promoter-TSS (NM_177756)	promoter-TSS (NM_177756)	35	NM_177756	269132	Mm.23782	NM_177756	ENSMUSG00000032649	Colgalt2	AI427652|D730024P12|Glt25d2	collagen beta(1-O)galactosyltransferase 2	protein-coding
mm_28277.1	chr3	88949938	88949989	-	1	NA	5' UTR (NM_022994, exon 1 of 13)	5' UTR (NM_022994, exon 1 of 13)	319	NM_022994	65111	Mm.29028	NM_022994	ENSMUSG00000068921	Dap3	4921514D13Rik|DAP-3|MRP-S29|S29mt	death associated protein 3	protein-coding
mm_78165.1	chr9	21028458	21028476	+	1	NA	promoter-TSS (NM_023892)	promoter-TSS (NM_023892)	-906	NM_023892	78369	Mm.30220	NM_023892	ENSMUSG00000001014	Icam4	1810015M19Rik|Cd242|ICAM-4	intercellular adhesion molecule 4, Landsteiner-Wiener blood group	protein-coding
mm_10777.1	chr2	24321216	24321223	+	1	NA	Intergenic	Intergenic	-15641	NM_031167	16181	Mm.882	NM_031167	ENSMUSG00000026981	Il1rn	F630041P17Rik|IL-1ra	interleukin 1 receptor antagonist	protein-coding
mm_7732.1	chr1	130764073	130764083	-	1	NA	Intergenic	Intergenic	32102	NM_177604	212439	Mm.268547	NM_177604	ENSMUSG00000042510	AA986860	E030025M07|Sarg	expressed sequence AA986860	protein-coding
mm_128632.1	chr15	59081993	59082017	-	1	NA	promoter-TSS (NM_144800)	promoter-TSS (NM_144800)	21	NM_001146180	211401	Mm.215481	NM_144800	ENSMUSG00000022353	Mtss1	2310003N14Rik|BC024131|D130001D01Rik|Mim|mKIAA0429	metastasis suppressor 1	protein-coding
mm_27746.1	chr3	69127099	69127109	-	1	NA	promoter-TSS (NM_008467)	promoter-TSS (NM_008467)	-12	NM_008467	16649	Mm.30601	NM_008467	ENSMUSG00000027782	Kpna4	1110058D08Rik|IPOA3	karyopherin (importin) alpha 4	protein-coding
mm_61149.1	chr7	57792535	57792538	+	1	NA	exon (NM_001038701, exon 6 of 9)	exon (NM_001038701, exon 6 of 9)	201363	NM_008071	14402	Mm.8004	NM_008071	ENSMUSG00000033676	Gabrb3	A230092K12Rik|AW049585|Cp1|Gabrb-3|beta3	gamma-aminobutyric acid (GABA) A receptor, subunit beta 3	protein-coding
mm_5144.1	chr1	9748248	9748272	-	1	NA	non-coding (NR_040462, exon 1 of 4)	non-coding (NR_040462, exon 1 of 4)	122	NM_173443	70675	Mm.274493	NM_173443	ENSMUSG00000045210	Vcpip1	4932442A08|5730421J18Rik|5730538E15Rik|VCIP135|mKIAA1850	valosin containing protein (p97)/p47 complex interacting protein 1	protein-coding
mm_99742.1	chr11	106416906	106416911	+	1	NA	intron (NM_023913, intron 10 of 21)	intron (NM_023913, intron 10 of 21)	-34127	NM_010494	15896	Mm.394	NM_010494	ENSMUSG00000001029	Icam2	CD102|Icam-2|Ly-60	intercellular adhesion molecule 2	protein-coding
mm_89504.1	chr10	94073397	94073415	+	1	NA	intron (NM_053072, intron 2 of 20)	intron (NM_053072, intron 2 of 20)	37405	NM_053072	13998	Mm.269596	NM_053072	ENSMUSG00000020021	Fgd6	AA123052|Etohd4|ZFYVE24	FYVE, RhoGEF and PH domain containing 6	protein-coding
mm_96464.1	chr11	67596628	67596636	+	1	NA	promoter-TSS (NM_001277080)	promoter-TSS (NM_001277080)	77	NM_001277079	14457	Mm.40338	NM_008088	ENSMUSG00000033066	Gas7	AW124766|B230343A10Rik|Gas7-cb	growth arrest specific 7	protein-coding
mm_43462.1	chr5	136691521	136691529	+	1	NA	Intergenic	Intergenic	-1621	NM_001303019	59310	Mm.5178	NM_021611	ENSMUSG00000005474	Myl10	1700027I08Rik|Mylc2pl|PLRLC	myosin, light chain 10, regulatory	protein-coding
mm_106851.1	chr12	8008383	8008392	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	30710	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_11123.1	chr2	28229125	28229136	+	1	NA	exon (NM_001038613, exon 6 of 6)	exon (NM_001038613, exon 6 of 6)	23441	NM_019498	56177	Mm.43278	NM_019498	ENSMUSG00000026833	Olfm1	AMY|AW742568|Noe1|OlfA|Pancortin|Pancortin3	olfactomedin 1	protein-coding
mm_172910.1	chr9	61914463	61914467	-	1	NA	promoter-TSS (NM_018853)	promoter-TSS (NM_018853)	45	NM_018853	56040	Mm.3158	NM_018853	ENSMUSG00000007892	Rplp1	2410042H16Rik|Arpp1|C430017H15Rik	ribosomal protein, large, P1	protein-coding
mm_68442.1	chr7	109986217	109986237	-	1	NA	promoter-TSS (NM_153525)	promoter-TSS (NM_153525)	3	NM_153525	233724	Mm.43212	NM_153525	ENSMUSG00000047554	Tmem41b	1500015G02Rik|1500031M19Rik|AU018901|D7Ertd70e|D7Ertd743e	transmembrane protein 41B	protein-coding
mm_125175.1	chr15	31568818	31568848	+	1	NA	promoter-TSS (NM_181588)	promoter-TSS (NM_181588)	-79	NM_181588	69574	Mm.28108	NM_181588	ENSMUSG00000022235	Cmbl	2310016A09Rik	carboxymethylenebutenolidase-like (Pseudomonas)	protein-coding
mm_121288.1	chr14	105258713	105258758	+	1	NA	promoter-TSS (NM_029561)	promoter-TSS (NM_029561)	62	NM_001190989	76273	Mm.290669	NM_029561	ENSMUSG00000053253	Ndfip2	0710001O20Rik|2810436B12Rik|9130207N19Rik|N4wbp5a|mKIAA1165	Nedd4 family interacting protein 2	protein-coding
mm_113821.1	chr13	46929851	46929873	+	1	NA	promoter-TSS (NM_010617)	promoter-TSS (NM_010617)	-144	NM_010617	16553	Mm.342703	NM_010617	ENSMUSG00000021375	Kif13a	4930505I07Rik|mKIAA4109	kinesin family member 13A	protein-coding
mm_3926.1	chr1	162588207	162588217	+	1	NA	exon (NM_016796, exon 5 of 8)	exon (NM_016796, exon 5 of 8)	17384	NM_001347125	53330	Mm.10699	NM_016796	ENSMUSG00000026696	Vamp4	D1Ertd147e	vesicle-associated membrane protein 4	protein-coding
mm_63289.1	chr7	126797609	126797613	+	1	NA	intron (NM_007438, intron 2 of 8)	intron (NM_007438, intron 2 of 8)	1567	NM_001177307	11674	Mm.275831	NM_007438	ENSMUSG00000030695	Aldoa	Aldo-1|Aldo1	aldolase A, fructose-bisphosphate	protein-coding
mm_131582.1	chr16	18428938	18428970	+	1	NA	intron (NM_013711, intron 1 of 17)	intron (NM_013711, intron 1 of 17)	-2238	NM_001111062	12846	Mm.100940	NM_007744	ENSMUSG00000000326	Comt	Comt1|D16Wsu103e|D330014B15Rik	catechol-O-methyltransferase	protein-coding
mm_109563.1	chr12	111944635	111944646	+	1	NA	promoter-TSS (NR_029464)	promoter-TSS (NR_029464)	-158	NR_029464	77675	Mm.98331	NR_029464		5033406O09Rik	9130204G15Rik	RIKEN cDNA 5033406O09 gene	ncRNA
mm_107776.1	chr12	59158278	59158299	+	1	NA	exon (NM_001165254, exon 9 of 23)	exon (NM_001165254, exon 9 of 23)	26835	NM_001165253	338320	Mm.213215	NM_146034	ENSMUSG00000021000	Mia2	Ctage5|D12Bwg0579e|Mea6|Mgea|Mgea6	melanoma inhibitory activity 2	protein-coding
mm_96998.1	chr11	70715812	70715818	+	1	NA	intron (NM_153103, intron 16 of 22)	B1_Mur1|SINE|Alu	9825	NR_105890	102465557		NR_105890	ENSMUSG00000105932	Mir6925	mmu-mir-6925	microRNA 6925	ncRNA
mm_50176.1	chr6	41570628	41570632	+	1	NA	Intergenic	(GGGA)n|Simple_repeat|Simple_repeat	-34852	NM_001146351	13848	Mm.271976	NM_007680	ENSMUSG00000029869	Ephb6	Cekl|Mep	Eph receptor B6	protein-coding
mm_40588.1	chr5	64160272	64160296	+	1	NA	promoter-TSS (NM_019636)	promoter-TSS (NM_019636)	24	NM_001310611	57915	Mm.286353	NM_019636	ENSMUSG00000029174	Tbc1d1	1110062G02Rik|AI385682|AW555803|Nob1|Nobq1|Tbc1|mKIAA1108	TBC1 domain family, member 1	protein-coding
mm_153346.1	chr19	39463090	39463108	-	1	NA	promoter-TSS (NM_010002)	promoter-TSS (NM_010002)	-24	NM_010002	13097	Mm.42100	NM_010002	ENSMUSG00000032808	Cyp2c38	-	cytochrome P450, family 2, subfamily c, polypeptide 38	protein-coding
mm_131737.1	chr16	22009472	22009543	+	1	NA	promoter-TSS (NM_029457)	promoter-TSS (NM_029457)	23	NR_027488	75826	Mm.297431	NM_029457	ENSMUSG00000022855	Senp2	2310007L05Rik|4930538C18Rik|AI646780|AW554757|Smt3ip2|SuPr-1|mKIAA1331	SUMO/sentrin specific peptidase 2	protein-coding
mm_157159.1	chrX	9464081	9464091	-	1	NA	intron (NM_007807, intron 3 of 12)	B4A|SINE|B4	5238	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_147333.1	chr18	42898937	42898975	-	1	NA	non-coding (NR_073583, exon 1 of 9)	non-coding (NR_073583, exon 1 of 9)	550	NR_073583	72930	Mm.26134	NM_027531	ENSMUSG00000024500	Ppp2r2b	2900026H06Rik|6330404L05Rik|E130009M08Rik|PP2A-PR55B|PR55-BETA|SCA12	protein phosphatase 2, regulatory subunit B, beta	protein-coding
mm_13201.1	chr2	93454664	93454678	+	1	NA	intron (NR_040532, intron 1 of 4)	intron (NR_040532, intron 1 of 4)	1852	NR_040533	100038525	Mm.440596	NR_040532	ENSMUSG00000075025	Gm10804	ENSMUSG00000075025	predicted gene 10804	ncRNA
mm_121583.1	chr14	123987634	123987637	+	1	NA	promoter-TSS (NR_045479)	promoter-TSS (NR_045479)	0	NR_045479	69393	Mm.491348	NR_045479	ENSMUSG00000099994	1700024B18Rik	-	RIKEN cDNA 1700024B18 gene	ncRNA
mm_3074.1	chr1	134276605	134276606	+	1	NA	Intergenic	MIR3|SINE|MIR	-13399	NM_031189	17928	Mm.16528	NM_031189	ENSMUSG00000026459	Myog	MYF4|bHLHc3|myo	myogenin	protein-coding
mm_93160.1	chr10	93177961	93177963	-	1	NA	intron (NM_146239, intron 1 of 16)	MER110A|LTR|ERV1	15177	NR_035452	100316689		NR_035452	ENSMUSG00000089214	Mir1931	mir-1931|mmu-mir-1931	microRNA 1931	ncRNA
mm_17066.1	chr2	22739878	22739890	-	1	NA	Intergenic	(TGAG)n|Simple_repeat|Simple_repeat	-34443	NM_019456	54519	Mm.14255	NM_019456	ENSMUSG00000026786	Apbb1ip	9930118P07Rik|Prp48	amyloid beta (A4) precursor protein-binding, family B, member 1 interacting protein	protein-coding
mm_55774.1	chr6	78468543	78468578	-	1	NA	exon (NM_011260, exon 2 of 6)	exon (NM_011260, exon 2 of 6)	314	NM_011260	19695	Mm.252385	NM_011260	ENSMUSG00000030017	Reg3g	AI449515|REG-3-gamma|reg III-gamma	regenerating islet-derived 3 gamma	protein-coding
mm_28347.1	chr3	89430743	89430752	-	1	NA	promoter-TSS (NM_026869)	promoter-TSS (NM_026869)	7	NM_001293767	68911	Mm.22521	NM_026869	ENSMUSG00000047824	Pygo2	1190004M21Rik	pygopus 2	protein-coding
mm_151656.1	chr19	4125766	4125813	-	1	NA	promoter-TSS (NM_016666)	promoter-TSS (NM_016666)	69	NM_016666	11632	Mm.10433	NM_016666	ENSMUSG00000024847	Aip	AA408703|AW476050|Ara9|D19Bwg1412e|Fkbp16|Xap2	aryl-hydrocarbon receptor-interacting protein	protein-coding
mm_7297.1	chr1	97910746	97910775	-	1	NA	intron (NM_013626, intron 7 of 25)	intron (NM_013626, intron 7 of 25)	137033	NR_037993	78603	Mm.442597	NR_037993	ENSMUSG00000089706	B230216N24Rik	-	RIKEN cDNA B230216N24 gene	ncRNA
mm_149863.1	chr19	25122286	25122291	+	1	NA	intron (NM_028785, intron 16 of 47)	intron (NM_028785, intron 16 of 47)	-114914	NM_181404	107351	Mm.260722	NM_181404	ENSMUSG00000032702	Kank1	A930031B09Rik|AU015049|AW121052|Ankrd15|D330024H06Rik|mKIAA0172	KN motif and ankyrin repeat domains 1	protein-coding
mm_153624.1	chr19	44005477	44005499	-	1	NA	exon (NM_001001446, exon 9 of 9)	exon (NM_001001446, exon 9 of 9)	-18968	NM_030703	93721	Mm.206774	NM_030703	ENSMUSG00000025196	Cpn1	0610011F20Rik|CPN	carboxypeptidase N, polypeptide 1	protein-coding
mm_169063.1	chr13	26492518	26492518	+	1	NA	Intergenic	Intergenic	-180112	NR_045933	73576	Mm.45473	NR_045933		1700092E19Rik	-	RIKEN cDNA 1700092E19 gene	ncRNA
mm_133833.1	chr16	95921336	95921339	+	1	NA	intron (NR_040484, intron 1 of 3)	ORR1B2|LTR|ERVL-MaLR	7740	NR_040484	69776	Mm.120470	NR_040484	ENSMUSG00000086899	1600002D24Rik	-	RIKEN cDNA 1600002D24 gene	ncRNA
mm_90335.1	chr10	127079160	127079170	+	1	NA	5' UTR (NM_001301014, exon 1 of 18)	5' UTR (NM_001301014, exon 1 of 18)	258	NM_001033263	216439	Mm.336761	NM_001033263	ENSMUSG00000025422	Agap2	AGAP-2|Centg1|PIKE|cnt-g1|mKIAA0167	ArfGAP with GTPase domain, ankyrin repeat and PH domain 2	protein-coding
mm_166201.1	chr5	38320232	38320234	+	1	NA	exon (NM_013503, exon 1 of 1)	exon (NM_013503, exon 1 of 1)	724	NM_013503	13492	Mm.167154	NM_013503	ENSMUSG00000039358	Drd5	D5R|Drd-5|Drd1b|Gpcr1	dopamine receptor D5	protein-coding
mm_62302.1	chr7	100176664	100176680	+	1	NA	promoter-TSS (NM_001190869)	promoter-TSS (NM_001190869)	2	NM_001190869	57442	Mm.282386	NM_020574	ENSMUSG00000035165	Kcne3	2210017H05Rik|MiRP2	potassium voltage-gated channel, Isk-related subfamily, gene 3	protein-coding
mm_126226.1	chr15	78930152	78930170	+	1	NA	3' UTR (NM_008495, exon 4 of 4)	3' UTR (NM_008495, exon 4 of 4)	3436	NM_008495	16852	Mm.43831	NM_008495	ENSMUSG00000068220	Lgals1	AA410090|Gal-1|Galbp|L-14.5|L14|Lect14|galectin-1	lectin, galactose binding, soluble 1	protein-coding
mm_124312.1	chr14	103218946	103218958	-	1	NA	intron (NM_207215, intron 33 of 84)	RSINE1|SINE|B4	-119386	NM_001347600	50789	Mm.214746	NM_015822	ENSMUSG00000022124	Fbxl3	AU041772|AW212966|FBK|Fbl3a|Fbxl3a|Ovtm|Play68	F-box and leucine-rich repeat protein 3	protein-coding
mm_113778.1	chr13	45391765	45391779	+	1	NA	intron (NM_153789, intron 2 of 6)	intron (NM_153789, intron 2 of 6)	2030	NM_153789	218203	Mm.212855	NM_153789	ENSMUSG00000038175	Mylip	9430057C20Rik|Mir	myosin regulatory light chain interacting protein	protein-coding
mm_107801.1	chr12	64965757	64965775	+	1	NA	promoter-TSS (NM_177805)	promoter-TSS (NM_177805)	24	NM_177805	328108	Mm.138465	NM_177805	ENSMUSG00000035614	Fam179b	A430041B07Rik|BC062107|C130034K06|mKIAA0423	family with sequence similarity 179, member B	protein-coding
mm_87127.1	chr10	33857711	33857713	+	1	NA	promoter-TSS (NM_020565)	promoter-TSS (NM_020565)	-10	NM_020565	57430	Mm.6590	NM_020565	ENSMUSG00000069668	Sult3a1	ST3A1|Sult-x2|Sultx2	sulfotransferase family 3A, member 1	protein-coding
mm_46228.1	chr5	99037343	99037353	-	1	NA	promoter-TSS (NM_008926)	promoter-TSS (NM_008926)	-269	NM_008926	19092	Mm.263002	NM_008926	ENSMUSG00000029334	Prkg2	AW212535|CGKII|Prkgr2|cGK-II	protein kinase, cGMP-dependent, type II	protein-coding
mm_130558.1	chr15	99248953	99248972	-	1	NA	intron (NM_001164156, intron 3 of 13)	intron (NM_001164156, intron 3 of 13)	-2826	NR_045627	73600	Mm.475134	NR_045627	ENSMUSG00000100599	1700120C14Rik	-	RIKEN cDNA 1700120C14 gene	ncRNA
mm_166044.1	chr4	130549289	130549291	-	1	NA	intron (NM_025998, intron 1 of 6)	intron (NM_025998, intron 1 of 6)	24746	NM_025998	67149	Mm.423029	NM_025998	ENSMUSG00000078532	Nkain1	2610200G18Rik|2810426C15Rik	Na+/K+ transporting ATPase interacting 1	protein-coding
mm_114089.1	chr13	54621781	54621793	+	1	NA	promoter-TSS (NM_178397)	promoter-TSS (NM_178397)	3	NM_178397	76577	Mm.194459	NM_178397	ENSMUSG00000025873	Faf2	2210404D11Rik|AI462440|Ubxd8|mKIAA0887	Fas associated factor family member 2	protein-coding
mm_74604.1	chr8	11715273	11715283	-	1	NA	Intergenic	Intergenic	-12827	NM_001113517	54126	Mm.244068	NM_017402	ENSMUSG00000031511	Arhgef7	Cool|PIX|Pak3bp|betaPix|betaPix-b|betaPix-c|cool-1|mKIAA0142|p85Cool1|p85SPR	Rho guanine nucleotide exchange factor (GEF7)	protein-coding
mm_126564.1	chr15	82170010	82170035	+	1	NA	exon (NM_033218, exon 2 of 19)	exon (NM_033218, exon 2 of 19)	22753	NM_033218	20788	Mm.9002	NM_033218	ENSMUSG00000022463	Srebf2	AI608257|SREBP-2|SREBP2|SREBP2gc|bHLHd2|lop13|nuc	sterol regulatory element binding factor 2	protein-coding
mm_76172.1	chr8	82392399	82392430	-	1	NA	intron (NM_001254747, intron 1 of 7)	Lx7|LINE|L1	10172	NM_001254747	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_53864.1	chr6	149325474	149325502	+	1	NA	exon (NM_001289662, exon 3 of 5)	exon (NM_001289662, exon 3 of 5)	16074	NM_001289662	67246	Mm.333515	NM_026054	ENSMUSG00000032712	2810474O19Rik	6720435I21Rik|AA536804|AU020969|GET|Kiaa1551	RIKEN cDNA 2810474O19 gene	protein-coding
mm_108211.1	chr12	76938660	76938682	+	1	NA	exon (NM_001146176, exon 4 of 4)	exon (NM_001146176, exon 4 of 4)	23577	NM_008558	17187	Mm.268548	NM_008558	ENSMUSG00000059436	Max	AA960152|AI875693|bHLHd4|bHLHd5|bHLHd6|bHLHd7|bHLHd8	Max protein	protein-coding
mm_139394.1	chr17	52304067	52304068	+	1	NA	Intergenic	Intergenic	-298642	NM_001031811	211468	Mm.399068	NM_001031811	ENSMUSG00000035580	Kcnh8	C130090D05Rik|ELK|ELK1|ELK3|Kv12.1	potassium voltage-gated channel, subfamily H (eag-related), member 8	protein-coding
mm_33787.1	chr4	134923590	134923593	+	1	NA	promoter-TSS (NM_023665)	promoter-TSS (NM_023665)	-34	NM_023665	27981	Mm.331964	NM_023665	ENSMUSG00000037266	Rsrp1	2700043I21Rik|D4Ucla2|D4Wsu53e	arginine/serine rich protein 1	protein-coding
mm_41885.1	chr5	105446872	105446896	+	1	NA	intron (NM_001033550, intron 1 of 4)	B2_Mm2|SINE|B2	31109	NM_001033550	433926	Mm.439781	NM_001033550	ENSMUSG00000070639	Lrrc8b	R75581|Ta-lrrp|mKIAA0231	leucine rich repeat containing 8 family, member B	protein-coding
mm_16003.1	chr2	167358918	167358945	+	1	NA	Intergenic	Intergenic	-9753	NM_019835	56336	Mm.200886	NM_019835	ENSMUSG00000017929	B4galt5	9430078I07Rik|AW049941|AW539721	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 5	protein-coding
mm_164159.1	chr15	72814419	72814435	+	1	NA	intron (NM_001164641, intron 17 of 17)	intron (NM_001164641, intron 17 of 17)	-4103	NR_002864	353342	Mm.440245	NR_002864	ENSMUSG00000106847	Peg13	-	paternally expressed 13	ncRNA
mm_34407.1	chr4	145236416	145236454	+	1	NA	intron (NM_011610, intron 1 of 9)	intron (NM_011610, intron 1 of 9)	10435	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_106799.1	chr12	4917347	4917370	+	1	NA	promoter-TSS (NM_001099628)	promoter-TSS (NM_001099628)	5	NM_001099628	320817	Mm.210966	NM_001099628	ENSMUSG00000052812	Atad2b	1110014E10Rik|BC032887|C79189|D530031C13Rik	ATPase family, AAA domain containing 2B	protein-coding
mm_58303.1	chr6	146113222	146113241	-	1	NA	intron (NM_010586, intron 54 of 55)	intron (NM_010586, intron 54 of 55)	179084	NM_010656	16651	Mm.49689	NM_010656	ENSMUSG00000030255	Sspn	Krag	sarcospan	protein-coding
mm_474.1	chr1	36490152	36490154	+	1	NA	intron (NM_033570, intron 1 of 6)	PB1D9|SINE|Alu	18556	NM_033570	94220	Mm.422638	NM_033570	ENSMUSG00000037408	Cnnm4	5430430O18Rik|Acdp4	cyclin M4	protein-coding
mm_86009.1	chr9	112233380	112233412	-	1	NA	promoter-TSS (NM_001177616)	promoter-TSS (NM_001177616)	-881	NR_033432	620760	Mm.259863	NR_015468	ENSMUSG00000087038	2900079G21Rik	C130083B14|Gm6179	RIKEN cDNA 2900079G21 gene	ncRNA
mm_5301.1	chr1	21299987	21300005	-	1	NA	Intergenic	Intergenic	-1684	NR_002858	241041	Mm.290634	NR_002858	ENSMUSG00000025936	Gm4956	EG241041	predicted gene 4956	pseudo
mm_98181.1	chr11	87762049	87762069	+	1	NA	intron (NM_172449, intron 1 of 31)	intron (NM_172449, intron 1 of 31)	1518	NM_172449	207777	Mm.342019	NM_172449	ENSMUSG00000034156	Bzrap1	D230016K05|PRAX-1|Tspoap1|mKIAA0612	benzodiazepine receptor associated protein 1	protein-coding
mm_140654.1	chr17	12725398	12725421	-	1	NA	exon (NM_010515, exon 10 of 48)	exon (NM_010515, exon 10 of 48)	-15902	NR_002853	104103	Mm.26553	NR_002853	ENSMUSG00000078247	Airn	2810051F02Rik|2810434M15Rik|AI256653|AI597500|AW049873|Air|B930018I07Rik|D17Ertd663e|IGF2RAS	antisense Igf2r RNA	ncRNA
mm_168008.1	chrY	6446585	6446585	-	1	NA	Intergenic	Intergenic	721192	NM_001101623	100040160	Mm.482062	NM_001101623	ENSMUSG00000094081	Gm20826	-	predicted gene, 20826	protein-coding
mm_149378.1	chr19	11375597	11375607	+	1	NA	5' UTR (NM_001310331, exon 1 of 7)	5' UTR (NM_001310331, exon 1 of 7)	114	NM_001310331	666907		NM_001310331	ENSMUSG00000101389	Ms4a4a	EG666907	membrane-spanning 4-domains, subfamily A, member 4A	protein-coding
mm_73649.1	chr8	110923029	110923037	+	1	NA	intron (NM_009179, intron 1 of 6)	intron (NM_009179, intron 1 of 6)	3168	NM_009179	20444	Mm.200388	NM_009179	ENSMUSG00000031749	St3gal2	AI429591|AW822065|ST3GalII|Siat5	ST3 beta-galactoside alpha-2,3-sialyltransferase 2	protein-coding
mm_140856.1	chr17	23721999	23722009	-	1	NA	Intergenic	Intergenic	-4332	NM_023058	268930	Mm.182193	NM_023058	ENSMUSG00000023908	Pkmyt1	6230424P17|AW209059|Myt1	protein kinase, membrane associated tyrosine/threonine 1	protein-coding
mm_125897.1	chr15	75909752	75909766	+	1	NA	promoter-TSS (NM_001285431)	promoter-TSS (NM_001285431)	24	NM_178646	105734	Mm.275583	NM_178646	ENSMUSG00000103906	Tigd5	AA409802|AA409995|AI666797	tigger transposable element derived 5	protein-coding
mm_153321.1	chr19	38118347	38118375	-	1	NA	exon (NM_011255, exon 5 of 6)	exon (NM_011255, exon 5 of 6)	6450	NM_011255	19662	Mm.2605	NM_011255	ENSMUSG00000024990	Rbp4	Rbp-4	retinol binding protein 4, plasma	protein-coding
mm_66991.1	chr7	64287555	64287564	-	1	NA	promoter-TSS (NM_172742)	promoter-TSS (NM_172742)	-111	NM_172742	233315	Mm.214959	NM_172742	ENSMUSG00000030522	Mtmr10	BB128963|C79734	myotubularin related protein 10	protein-coding
mm_76803.1	chr8	104293194	104293204	-	1	NA	promoter-TSS (NM_027022)	promoter-TSS (NM_027022)	-18	NM_027022	73381	Mm.272746	NM_027022	ENSMUSG00000074127	Cmtm2a	1700001K04Rik|1700041N15Rik|1700063K20Rik|AI449770|ARR19|C32|CKLF3|CKLF4|CKLF5|Cklf|Cklf1|Cklfsf2-1b|Cklfsf2a|UCK-1	CKLF-like MARVEL transmembrane domain containing 2A	protein-coding
mm_154913.1	chrX	21484608	21484638	+	1	NA	promoter-TSS (NM_007429)	promoter-TSS (NM_007429)	-1	NM_007429	11609	Mm.2679	NM_007429	ENSMUSG00000068122	Agtr2	AI316812|AW107640	angiotensin II receptor, type 2	protein-coding
mm_35663.1	chr4	43562213	43562255	-	1	NA	promoter-TSS (NM_013497)	promoter-TSS (NM_013497)	349	NM_011602	21894	Mm.208601	NM_011602	ENSMUSG00000028465	Tln1	Tln	talin 1	protein-coding
mm_69855.1	chr7	141429559	141429565	-	1	NA	promoter-TSS (NM_021316)	promoter-TSS (NM_021316)	-142	NM_021316	57754	Mm.87027	NM_021316	ENSMUSG00000060240	Cend1	1500001H12Rik|AI415214|BM88	cell cycle exit and neuronal differentiation 1	protein-coding
mm_97239.1	chr11	75661615	75661623	+	1	NA	intron (NM_008659, intron 10 of 31)	intron (NM_008659, intron 10 of 31)	5604	NM_001080775	17913	Mm.234502	NM_008659	ENSMUSG00000017774	Myo1c	C80397|MMIb|MYO1E|NMI|mm1beta|myr2	myosin IC	protein-coding
mm_138387.1	chr17	35050198	35050211	+	1	NA	promoter-TSS (NM_033444)	promoter-TSS (NM_033444)	-39	NM_033444	114584	Mm.29524	NM_033444	ENSMUSG00000007041	Clic1	Clcp|G6	chloride intracellular channel 1	protein-coding
mm_39297.1	chr5	5504817	5504824	+	1	NA	TTS (NM_001193660)	TTS (NM_001193660)	9969	NM_001193660	64945	Mm.40132	NM_022890	ENSMUSG00000046798	Cldn12	-	claudin 12	protein-coding
mm_162446.1	chr1	119523764	119523776	+	1	NA	Intergenic	Intergenic	-2384	NM_146103	226351	Mm.439806	NM_146103	ENSMUSG00000098923	Tmem185b	2500001K11Rik	transmembrane protein 185B	protein-coding
mm_72482.1	chr8	83652652	83652667	+	1	NA	promoter-TSS (NM_018771)	promoter-TSS (NM_018771)	-19	NM_018771	67903	Mm.20945	NM_018771	ENSMUSG00000019433	Gipc1	GIPC|Glut1CIP|Rgs19ip1|Semcap1|TIP-2|TaxIP2	GIPC PDZ domain containing family, member 1	protein-coding
mm_162626.1	chr1	184277118	184277124	-	1	NA	Intergenic	Intergenic	242660	NM_022019	63953	Mm.404024	NM_022019	ENSMUSG00000039384	Dusp10	2610306G15Rik|AI158871|MKP-5|MKP5	dual specificity phosphatase 10	protein-coding
mm_62912.1	chr7	117568474	117568529	+	1	NA	intron (NM_175645, intron 3 of 11)	(CCA)n|Simple_repeat|Simple_repeat	187522	NM_175645	233781	Mm.461427	NM_175645	ENSMUSG00000030657	Xylt1	8030490L12	xylosyltransferase 1	protein-coding
mm_167710.1	chr9	96891497	96891507	-	1	NA	Intergenic	Intergenic	-2028	NM_001289645	235534	Mm.233031	NM_153420	ENSMUSG00000043587	Pxylp1	9430094M07Rik|Acpl2|BB177120|C130099A20Rik	2-phosphoxylose phosphatase 1	protein-coding
mm_95888.1	chr11	58104240	58104280	+	1	NA	intron (NM_026949, intron 1 of 6)	CpG	107	NM_026949	69125	Mm.28910	NM_026949	ENSMUSG00000020515	Cnot8	1500015I04Rik|1810022F04Rik|AA536816|AU015770|AU043059	CCR4-NOT transcription complex, subunit 8	protein-coding
mm_25883.1	chr3	130874026	130874067	+	1	NA	Intergenic	Intergenic	-143648	NM_001005859	68436	Mm.140568	NM_026724	ENSMUSG00000062006	Rpl34	1100001I22Rik	ribosomal protein L34	protein-coding
mm_90623.1	chr10	128458969	128458989	+	1	NA	promoter-TSS (NM_001114096)	promoter-TSS (NM_001114096)	-257	NM_001114096	68094	Mm.417338	NM_198160	ENSMUSG00000025369	Smarcc2	5930405J04Rik	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2	protein-coding
mm_127285.1	chr15	100005146	100005160	+	1	NA	intron (NM_001284523, intron 12 of 15)	intron (NM_001284523, intron 12 of 15)	-31866	NR_028124	70281	Mm.484037	NR_028124	ENSMUSG00000100084	2310068J16Rik	-	RIKEN cDNA 2310068J16 gene	ncRNA
mm_1472.1	chr1	69951642	69951647	+	1	NA	promoter-TSS (NM_025728)	promoter-TSS (NM_025728)	29	NM_025728	66722	Mm.440554	NM_025728	ENSMUSG00000053153	Spag16	4921511D23Rik|4930524F24Rik|4930585K05Rik|AV261009|Pf20|Wdr29	sperm associated antigen 16	protein-coding
mm_171564.1	chr4	147275776	147275794	+	1	NA	intron (NM_001039209, intron 1 of 2)	CpG	99919	NM_001039209	195531	Mm.270762	NM_001039209	ENSMUSG00000078496	Zfp982	Gm13152|OTTMUSG00000010671	zinc finger protein 982	protein-coding
mm_66280.1	chr7	37769745	37769761	-	1	NA	promoter-TSS (NM_172385)	promoter-TSS (NM_172385)	-1	NM_172385	243937	Mm.322505	NM_172385	ENSMUSG00000043456	Zfp536	9630010P11Rik|Znf536|mKIAA0390	zinc finger protein 536	protein-coding
mm_114152.1	chr13	55399686	55399700	+	1	NA	promoter-TSS (NM_011392)	promoter-TSS (NM_011392)	45	NM_011392	20505	Mm.276355	NM_011392	ENSMUSG00000021490	Slc34a1	NaPi-IIa|Npt2|Npt2a|Slc17a2	solute carrier family 34 (sodium phosphate), member 1	protein-coding
mm_46564.1	chr5	107109329	107109333	-	1	NA	3' UTR (NM_011578, exon 17 of 17)	3' UTR (NM_011578, exon 17 of 17)	144770	NM_001271566	12545	Mm.20842	NM_009863	ENSMUSG00000029283	Cdc7	AI597260|Cdc7l1|muCdc7	cell division cycle 7 (S. cerevisiae)	protein-coding
mm_120106.1	chr14	59201275	59201313	+	1	NA	promoter-TSS (NM_027764)	promoter-TSS (NM_027764)	66	NM_027764	71330	Mm.234195	NM_027764	ENSMUSG00000035469	Rcbtb1	5430409I18Rik|AW111883|CLLD7|CLLL7	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 1	protein-coding
mm_1531.1	chr1	72849216	72849234	+	1	NA	exon (NM_008342, exon 2 of 4)	exon (NM_008342, exon 2 of 4)	23838	NM_001310659	16008	Mm.141936	NM_008342	ENSMUSG00000039323	Igfbp2	AI255832|IBP-2|Igfbp-2|mIGFBP-2	insulin-like growth factor binding protein 2	protein-coding
mm_153826.1	chr19	46312370	46312385	-	1	NA	TTS (NM_001177370)	TTS (NM_001177370)	6447	NM_001177370	18034	Mm.102365	NM_019408	ENSMUSG00000025225	Nfkb2	NF-kappaB2|lyt|p49|p49/p100|p50B|p52	nuclear factor of kappa light polypeptide gene enhancer in B cells 2, p49/p100	protein-coding
mm_46583.1	chr5	107597534	107597545	-	1	NA	promoter-TSS (NM_133248)	promoter-TSS (NM_133248)	100	NM_133248	170823	Mm.41417	NM_133248	ENSMUSG00000029276	Glmn	9330160J16Rik|AW227515|Fap48|Fap68	glomulin, FKBP associated protein	protein-coding
mm_56966.1	chr6	120083560	120083582	-	1	NA	Intergenic	Intergenic	-9809	NM_016718	29862	Mm.103668	NM_016718	ENSMUSG00000041377	Ninj2	-	ninjurin 2	protein-coding
mm_108475.1	chr12	83659419	83659425	+	1	NA	intron (NM_027349, intron 6 of 18)	intron (NM_027349, intron 6 of 18)	27188	NM_027349	67039	Mm.46005	NM_027349	ENSMUSG00000010608	Rbm25	2600011C06Rik|2610015J01Rik|A130095G20Rik|AI159652|AL023075|AU043498|RNPC7	RNA binding motif protein 25	protein-coding
mm_96485.1	chr11	67685050	67685064	+	1	NA	3' UTR (NM_001277080, exon 13 of 13)	3' UTR (NM_001277080, exon 13 of 13)	-10269	NM_009038	19674	Mm.439726	NM_009038	ENSMUSG00000020907	Rcvrn	CAR|S-modulin	recoverin	protein-coding
mm_94877.1	chr11	24129067	24129072	+	1	NA	intron (NM_016707, intron 2 of 4)	intron (NM_016707, intron 2 of 4)	48374	NM_001159290	14025	Mm.53687	NM_016707	ENSMUSG00000000861	Bcl11a	2810047E18Rik|BCL-11A|Ctip1|D930021L15Rik|Evi9|Evi9a|Evi9b|Evi9c|mKIAA1809	B cell CLL/lymphoma 11A (zinc finger protein)	protein-coding
mm_122591.1	chr14	50897518	50897529	-	1	NA	Intergenic	Intergenic	-4268	NM_001166651	546611	Mm.390692	NM_001166651	ENSMUSG00000090799	Klhl33	EG546611	kelch-like 33	protein-coding
mm_79791.1	chr9	63737808	63737827	+	1	NA	intron (NM_016769, intron 1 of 8)	MER5B|DNA|hAT-Charlie	20177	NM_016769	17127	Mm.7320	NM_016769	ENSMUSG00000032402	Smad3	AU022421|Madh3	SMAD family member 3	protein-coding
mm_1857.1	chr1	84839608	84839639	+	1	NA	promoter-TSS (NM_025386)	promoter-TSS (NM_025386)	-218	NM_025386	66153	Mm.381192	NM_025386	ENSMUSG00000073633	Fbxo36	0610008D19Rik|1110020F21Rik|2410002G19Rik|D1Ertd757e	F-box protein 36	protein-coding
mm_110800.1	chr12	72212192	72212202	-	1	NA	non-coding (NR_104446, exon 7 of 7)	non-coding (NR_104446, exon 7 of 7)	23549	NR_104446	104001	Mm.221275	NM_153457	ENSMUSG00000021087	Rtn1	Nsp	reticulon 1	protein-coding
mm_76779.1	chr8	96403901	96403905	-	1	NA	Intergenic	Intergenic	142070	NR_039538	100628567		NR_039538	ENSMUSG00000104794	Mir28c	mmu-mir-28c	microRNA 28c	ncRNA
mm_73708.1	chr8	111687202	111687215	+	1	NA	exon (NM_025583, exon 6 of 7)	exon (NM_025583, exon 6 of 7)	2466	NR_106044	102466993		NR_106044	ENSMUSG00000099129	Mir7076	Gm27318|mmu-mir-7076	microRNA 7076	ncRNA
mm_104080.1	chr11	86587040	86587050	-	1	NA	intron (NM_029478, intron 10 of 11)	intron (NM_029478, intron 10 of 11)	-2887	NR_029738	387140		NR_029738	ENSMUSG00000065455	Mir21a	Mir21|Mirn21|mmu-mir-21|mmu-mir-21a	microRNA 21a	ncRNA
mm_66227.1	chr7	35056420	35056428	-	1	NA	5' UTR (NM_009884, exon 1 of 2)	5' UTR (NM_009884, exon 1 of 2)	142	NM_009884	12611	Mm.273090	NM_009884	ENSMUSG00000056216	Cebpg	C/EBP[g]|C/EBPgamma|GPE1-BP|Gpe1bp|Ig/EBP	CCAAT/enhancer binding protein (C/EBP), gamma	protein-coding
mm_19440.1	chr2	91965530	91965560	-	1	NA	Intergenic	CpG	-1982	NM_138306	104418	Mm.314923	NM_138306	ENSMUSG00000040479	Dgkz	E130307B02Rik|ENSMUSG00000075035|F730209L11Rik|mDGK[z]	diacylglycerol kinase zeta	protein-coding
mm_30546.1	chr4	3683959	3683970	+	1	NA	intron (NM_010747, intron 1 of 12)	RLTR20D|LTR|ERVK	5843	NM_010747	17096	Mm.317331	NM_010747	ENSMUSG00000042228	Lyn	AA407514|Hck-2|p53Lyn|p56Lyn	LYN proto-oncogene, Src family tyrosine kinase	protein-coding
mm_2085.1	chr1	87676449	87676467	+	1	NA	intron (NM_010566, intron 6 of 26)	intron (NM_010566, intron 6 of 26)	56146	NM_001110193	16331	Mm.15105	NM_010566	ENSMUSG00000026288	Inpp5d	SHIP|SHIP-1|SHIP1|SIP-145|p150Ship|s-SHIP	inositol polyphosphate-5-phosphatase D	protein-coding
mm_6749.1	chr1	83408160	83408181	-	1	NA	promoter-TSS (NM_172430)	promoter-TSS (NM_172430)	30	NM_172430	77629	Mm.154303	NM_172430	ENSMUSG00000026163	Sphkap	4930544G21Rik|A930009L15Rik|AI852220|SKIP|mKIAA1678	SPHK1 interactor, AKAP domain containing	protein-coding
mm_74976.1	chr8	27141474	27141514	-	1	NA	3' UTR (NM_001080813, exon 6 of 6)	3' UTR (NM_001080813, exon 6 of 6)	-1416	NR_045840	71082	Mm.395259	NR_045840		4933416M07Rik	-	RIKEN cDNA 4933416M07 gene	ncRNA
mm_5590.1	chr1	39555524	39555543	-	1	NA	exon (NM_001033135, exon 6 of 7)	exon (NM_001033135, exon 6 of 7)	-6693	NR_028555	100217461		NR_028555	ENSMUSG00000077704	Snord89	MBII-289	small nucleolar RNA, C/D box 89	snoRNA
mm_103427.1	chr11	75630723	75630763	-	1	NA	promoter-TSS (NM_008916)	promoter-TSS (NM_008916)	-277	NM_008916	19062	Mm.1458	NM_008916	ENSMUSG00000006127	Inpp5k	C62|Pps|SKIP	inositol polyphosphate 5-phosphatase K	protein-coding
mm_69949.1	chr7	142342026	142342030	-	1	NA	intron (NM_177265, intron 3 of 3)	ORR1E|LTR|ERVL-MaLR	30231	NM_177265	320802	Mm.154486	NM_177265	ENSMUSG00000045777	Ifitm10	6330512M04Rik|AI848576|DSPA3	interferon induced transmembrane protein 10	protein-coding
mm_71860.1	chr8	68993357	68993370	+	1	NA	Intergenic	Intergenic	-95373	NM_007509	11966	Mm.249096	NM_007509	ENSMUSG00000006273	Atp6v1b2	AI194269|AI790362|Atp6b2|HO57|R74844	ATPase, H+ transporting, lysosomal V1 subunit B2	protein-coding
mm_137060.1	chr17	17949946	17949980	+	1	NA	Intergenic	L1_Mus4|LINE|L1	-20495	NM_008042	14294	Mm.378918	NM_008042	ENSMUSG00000079700	Fpr3	ALX|Fpr-rs1|Fpr-s1|Fprl1|LXA4-R|Lxa4r	formyl peptide receptor 3	protein-coding
mm_143540.1	chr17	74016901	74016913	-	1	NA	TTS (NM_053188)	TTS (NM_053188)	31009	NM_053188	94224	Mm.38933	NM_053188	ENSMUSG00000038541	Srd5a2	5ART2|S5AR 2	steroid 5 alpha-reductase 2	protein-coding
mm_149255.1	chr19	10426024	10426034	+	1	NA	intron (NM_173067, intron 4 of 9)	intron (NM_173067, intron 4 of 9)	31418	NM_001111140	278795	Mm.490638	NM_001111140	ENSMUSG00000090291	Lrrc10b	Gm705|SerdinR	leucine rich repeat containing 10B	protein-coding
mm_412.1	chr1	34227914	34227924	+	1	NA	exon (NM_134448, exon 57 of 98)	exon (NM_134448, exon 57 of 98)	67589	NM_010081	13518	Mm.336625	NM_010081	ENSMUSG00000026131	Dst	2310001O04Rik|A830042E19Rik|AW554249|BP230|BPAG1-n|Bpag|Bpag1|Macf2|ah|athetoid|dt|mKIAA0728|nmf203|nmf339	dystonin	protein-coding
mm_161261.1	chr13	119488887	119488887	+	1	NA	promoter-TSS (NR_027974)	promoter-TSS (NR_027974)	27	NM_001177666	633640	Mm.46679	NM_001039244	ENSMUSG00000074634	Tmem267	EG633640|Gm7120	transmembrane protein 267	protein-coding
mm_135444.1	chr16	45492932	45492948	-	1	NA	promoter-TSS (NM_001005854)	promoter-TSS (NM_001005854)	29	NM_001005854	208166	Mm.451852	NM_001005854	ENSMUSG00000053182	Gm609	Gm1749|isec1	predicted gene 609	protein-coding
mm_108511.1	chr12	83987908	83987918	+	1	NA	promoter-TSS (NM_134188)	promoter-TSS (NM_134188)	52	NM_134188	171210	Mm.371675	NM_134188	ENSMUSG00000021226	Acot2	AA571646|MTE-I|Mte1	acyl-CoA thioesterase 2	protein-coding
mm_112618.1	chr13	15506748	15506750	+	1	NA	intron (NM_008130, intron 2 of 14)	intron (NM_008130, intron 2 of 14)	43026	NM_008130	14634	Mm.5098	NM_008130	ENSMUSG00000021318	Gli3	AI854843|AU023367|Bph|GLI3-190|GLI3FL|Pdn|Xt|add	GLI-Kruppel family member GLI3	protein-coding
mm_136319.1	chr16	91931624	91931632	-	1	NA	promoter-TSS (NM_138597)	promoter-TSS (NM_138597)	2	NM_138597	28080	Mm.41	NM_138597	ENSMUSG00000022956	Atp5o	ATPO|D12Wsu28e|OSCP	ATP synthase, H+ transporting, mitochondrial F1 complex, O subunit	protein-coding
mm_129852.1	chr15	83172213	83172235	-	1	NA	promoter-TSS (NM_029787)	promoter-TSS (NM_029787)	-16	NM_029787	109754	Mm.22560	NM_029787	ENSMUSG00000018042	Cyb5r3	0610016L08Rik|2500002N19Rik|C85115|Dia-1|Dia1|WU:AL591952.1-001|WU:AL591952.1-002|WU:AL591952.1-003|WU:Cyb5r3	cytochrome b5 reductase 3	protein-coding
mm_94016.1	chr10	127661436	127661458	-	1	NA	TTS (NM_009284)	TTS (NM_009284)	5256	NM_001122895	17937	Mm.336898	NM_008668	ENSMUSG00000025402	Nab2	AI451907	Ngfi-A binding protein 2	protein-coding
mm_15334.1	chr2	155930085	155930107	+	1	NA	non-coding (NR_024487, exon 1 of 10)	non-coding (NR_024487, exon 1 of 10)	214	NM_018888	56046	Mm.158827	NM_018888	ENSMUSG00000005882	Uqcc1	2310079L17Rik|2410003P15Rik|3110038N19Rik|Bfzb|Bfzp|Cbp3|Uqcc	ubiquinol-cytochrome c reductase complex assembly factor 1	protein-coding
mm_15024.1	chr2	152686116	152686130	+	1	NA	TTS (NM_001159553)	TTS (NM_001159553)	-1025	NM_025543	66405	Mm.440291	NM_025543	ENSMUSG00000042814	Mcts2	2400002F11Rik|MCT-2	malignant T cell amplified sequence 2	protein-coding
mm_156636.1	chrX	156881450	156881453	+	1	NA	Intergenic	Lx8|LINE|L1	341968	NR_033598	74941	Mm.484588	NR_033598		4930503H13Rik	-	gem (nuclear organelle) associated protein 8 pseudogene	pseudo
mm_26048.1	chr3	135689140	135689150	+	1	NA	intron (NM_008689, intron 1 of 24)	intron (NM_008689, intron 1 of 24)	2402	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_125191.1	chr15	32675661	32675663	+	1	NA	intron (NM_009154, intron 18 of 22)	Lx9|LINE|L1	-245061	NM_008304	15529	Mm.234266	NM_008304	ENSMUSG00000022261	Sdc2	4833414L08Rik|AA960457|Hspg1|Synd2|syndecan-2	syndecan 2	protein-coding
mm_120513.1	chr14	66635265	66635349	+	1	NA	promoter-TSS (NM_001271761)	promoter-TSS (NM_001271761)	56	NM_001271760	11549	Mm.57064	NM_013461	ENSMUSG00000045875	Adra1a	Adra1c	adrenergic receptor, alpha 1a	protein-coding
mm_116239.1	chr13	33905167	33905214	-	1	NA	intron (NM_148942, intron 1 of 6)	intron (NM_148942, intron 1 of 6)	518	NM_148942	97848	Mm.272188	NM_148942	ENSMUSG00000052180	Serpinb6c	C76171|C76174|SPI3C|SPIC|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 6c	protein-coding
mm_3796.1	chr1	157440621	157440656	+	1	NA	Intergenic	Intergenic	-17944	NM_001033284	226527	Mm.215960	NM_001033284	ENSMUSG00000033488	BC026585	-	cDNA sequence BC026585	protein-coding
mm_63566.1	chr7	128116282	128116289	+	1	NA	exon (NM_008401, exon 27 of 30)	exon (NM_008401, exon 27 of 30)	-13283	NM_021334	16411	Mm.22378	NM_021334	ENSMUSG00000030789	Itgax	AI449405|Cd11c|Cr4|N418	integrin alpha X	protein-coding
mm_171062.1	chr3	109284098	109284105	-	1	NA	Intergenic	MLTR25A|LTR|ERVK	-56582	NM_020505	57257	Mm.282257	NM_020505	ENSMUSG00000033721	Vav3	A530094I06Rik|AA986410|Idd18.1	vav 3 oncogene	protein-coding
mm_157581.1	chrX	52913148	52913156	-	1	NA	intron (NM_001290546, intron 1 of 8)	intron (NM_001290546, intron 1 of 8)	938	NM_001290546	70998	Mm.26870	NM_027642	ENSMUSG00000025626	Phf6	2700007B13Rik|4931428F02Rik|mKIAA1823	PHD finger protein 6	protein-coding
mm_118014.1	chr13	100744589	100744663	-	1	NA	promoter-TSS (NM_025369)	promoter-TSS (NM_025369)	33	NM_001190264	66128	Mm.306173	NM_025369	ENSMUSG00000061474	Mrps36	1110018B13Rik|S36mt	mitochondrial ribosomal protein S36	protein-coding
mm_149168.1	chr19	9075845	9075854	+	1	NA	intron (NR_104460, intron 6 of 6)	intron (NR_104460, intron 6 of 6)	12107	NM_011681	22287	Mm.2258	NM_011681	ENSMUSG00000024653	Scgb1a1	CC10|CC16|CCSP|PCB-BP|UG|UGB|Utg	secretoglobin, family 1A, member 1 (uteroglobin)	protein-coding
mm_57537.1	chr6	126642087	126642098	-	1	NA	exon (NM_010595, exon 2 of 2)	exon (NM_010595, exon 2 of 2)	3709	NM_010595	16485	Mm.40424	NM_010595	ENSMUSG00000047976	Kcna1	AI840627|Kca1-1|Kv1.1|MBK1|Mk-1|Shak|mceph	potassium voltage-gated channel, shaker-related subfamily, member 1	protein-coding
mm_115817.1	chr13	19774203	19774206	-	1	NA	intron (NM_181754, intron 3 of 4)	intron (NM_181754, intron 3 of 4)	-41253	NM_175688	319293	Mm.246657	NM_175688	ENSMUSG00000047462	A530099J19Rik	-	RIKEN cDNA A530099J19 gene	protein-coding
mm_28847.1	chr3	96727454	96727505	-	1	NA	promoter-TSS (NM_026406)	promoter-TSS (NM_026406)	-40	NM_028925	74414	Mm.276043	NM_028925	ENSMUSG00000028099	Polr3c	4933407E01Rik|RPC3|RPC62	polymerase (RNA) III (DNA directed) polypeptide C	protein-coding
mm_7236.1	chr1	93445643	93445660	-	1	NA	promoter-TSS (NM_001301364)	promoter-TSS (NM_001301364)	50	NM_001301364	110611	Mm.30012	NM_133808	ENSMUSG00000034088	Hdlbp	1110005P14Rik|AA960365|AI118566|D1Ertd101e	high density lipoprotein (HDL) binding protein	protein-coding
mm_161748.1	chr17	34264879	34264879	+	1	NA	exon (NM_207105, exon 2 of 6)	exon (NM_207105, exon 2 of 6)	1652	NM_207105	14961	Mm.254067	NM_207105	ENSMUSG00000073421	H2-Ab1	AI845868|Abeta|H-2Ab|H2-Ab|I-Abeta|IAb|Ia-2|Ia2|Rmcs1	histocompatibility 2, class II antigen A, beta 1	protein-coding
mm_3702.1	chr1	153762980	153762985	+	1	NA	3' UTR (NM_011882, exon 9 of 9)	3' UTR (NM_011882, exon 9 of 9)	13556	NM_011882	24014	Mm.259254	NM_011882	ENSMUSG00000066800	Rnasel	E230029I04Rik	ribonuclease L (2', 5'-oligoisoadenylate synthetase-dependent)	protein-coding
mm_148345.1	chr18	84664850	84664896	-	1	NA	Intergenic	Intergenic	-14778	NM_177450	338403	Mm.23278	NM_177450	ENSMUSG00000056162	Cndp1	AI746433|Cn1	carnosine dipeptidase 1 (metallopeptidase M20 family)	protein-coding
mm_27217.1	chr3	35937404	35937451	-	1	NA	Intergenic	Intergenic	-4461	NM_001205361	114893	Mm.374810	NM_033623	ENSMUSG00000027708	Dcun1d1	Rp42|SCCRO|Tes3|pTes3	DCN1, defective in cullin neddylation 1, domain containing 1 (S. cerevisiae)	protein-coding
mm_99314.1	chr11	101425069	101425114	+	1	NA	promoter-TSS (NM_172566)	promoter-TSS (NM_172566)	6	NM_172566	217201	Mm.305941	NM_172566	ENSMUSG00000035007	Rundc1	AW125546|D930024B17	RUN domain containing 1	protein-coding
mm_131228.1	chr16	10192911	10192927	+	1	NA	promoter-TSS (NM_029253)	promoter-TSS (NM_029253)	13	NM_029253	75329	Mm.108729	NM_029253	ENSMUSG00000039200	Atf7ip2	4930558K11Rik|BC018510|Get-1|PSM2	activating transcription factor 7 interacting protein 2	protein-coding
mm_26457.1	chr3	142765217	142765232	+	1	NA	promoter-TSS (NM_145546)	promoter-TSS (NM_145546)	-23	NM_145546	229906	Mm.271756	NM_145546	ENSMUSG00000028271	Gtf2b	-	general transcription factor IIB	protein-coding
mm_132200.1	chr16	32550299	32550309	+	1	NA	Intergenic	Intergenic	54023	NM_199309	245308	Mm.76859	NM_199309	ENSMUSG00000052363	Zdhhc19	Gm1744|Gm616	zinc finger, DHHC domain containing 19	protein-coding
mm_11202.1	chr2	29125340	29125384	+	1	NA	5' UTR (NM_198033, exon 1 of 26)	5' UTR (NM_198033, exon 1 of 26)	370	NM_198033	269254	Mm.41867	NM_198033	ENSMUSG00000043535	Setx	A130090N03|A930037J23Rik|AOA2|AW060766|Als4|SCAR1|Sen1|mKIAA0625	senataxin	protein-coding
mm_118194.1	chr13	107842303	107842310	-	1	NA	intron (NM_145456, intron 2 of 14)	intron (NM_145456, intron 2 of 14)	47758	NM_145456	67263	Mm.490418	NM_145456	ENSMUSG00000032846	Zswim6	2900036G02Rik|mKIAA1577	zinc finger SWIM-type containing 6	protein-coding
mm_117526.1	chr13	81710938	81711008	-	1	NA	promoter-TSS (NM_028372)	promoter-TSS (NM_028372)	40	NM_001081176	67486	Mm.279781	NM_001081176	ENSMUSG00000035834	Polr3g	2310047G20Rik|AV275904|RPC32|RPC7	polymerase (RNA) III (DNA directed) polypeptide G	protein-coding
mm_88312.1	chr10	75517546	75517557	+	1	NA	promoter-TSS (NM_026095)	promoter-TSS (NM_026095)	-170	NM_175133	68778	Mm.29382	NM_175133	ENSMUSG00000033416	Gucd1	1110038D17Rik	guanylyl cyclase domain containing 1	protein-coding
mm_74945.1	chr8	25847682	25847698	-	1	NA	promoter-TSS (NM_001080793)	promoter-TSS (NM_001080793)	4	NM_001080793	23808	Mm.27706	NM_011791	ENSMUSG00000031575	Ash2l	-	ash2 (absent, small, or homeotic)-like (Drosophila)	protein-coding
mm_172709.1	chr8	69563402	69563406	-	1	NA	Intergenic	B3A|SINE|B2	61771	NM_001045553	234362	Mm.458487	NM_172754	ENSMUSG00000060427	Zfp868	AI449175|AW108241|C530032E20|mszf62	zinc finger protein 868	protein-coding
mm_29771.1	chr3	127240773	127240788	-	1	NA	intron (NM_001327938, intron 1 of 47)	intron (NM_001327938, intron 1 of 47)	79475	NR_105029	100862268	Mm.444603	NR_105029	ENSMUSG00000097456	LOC100862268	-	uncharacterized LOC100862268	ncRNA
mm_39317.1	chr5	8065198	8065254	+	1	NA	intron (NM_001080974, intron 7 of 7)	B4|SINE|B4	8684	NM_001080974	109552	Mm.96211	NM_025618	ENSMUSG00000003161	Sri	2210417O06Rik|2900070H08Rik|Sor	sorcin	protein-coding
mm_141775.1	chr17	34287771	34287830	-	1	NA	promoter-TSS (NM_010378)	promoter-TSS (NM_010378)	-29	NM_010378	14960	Mm.235338	NM_010378	ENSMUSG00000036594	H2-Aa	Aalpha|H-2Aa|H2Aa|I-Aalpha|IAalpha|Ia-1|Ia1	histocompatibility 2, class II antigen A, alpha	protein-coding
mm_75503.1	chr8	53601824	53601826	-	1	NA	intron (NM_146208, intron 6 of 9)	intron (NM_146208, intron 6 of 9)	37240	NM_146208	234258	Mm.281749	NM_146208	ENSMUSG00000039396	Neil3	AI449477|BC034753|C85903	nei like 3 (E. coli)	protein-coding
mm_57945.1	chr6	134792711	134792730	-	1	NA	promoter-TSS (NM_130447)	promoter-TSS (NM_130447)	-92	NM_001048054	70686	Mm.491182	NM_130447	ENSMUSG00000030203	Dusp16	3830417M17Rik|AW558566|D6Ertd213e|MKP-7|MKP7|Mkpm	dual specificity phosphatase 16	protein-coding
mm_160679.1	chr10	13966404	13966404	+	1	NA	promoter-TSS (NM_010437)	promoter-TSS (NM_010437)	25	NM_010437	15273	Mm.42157	NM_010437	ENSMUSG00000015501	Hivep2	Gm20114|MIBP1|Schnurri-2|Shn-2	human immunodeficiency virus type I enhancer binding protein 2	protein-coding
mm_32313.1	chr4	103324908	103324953	+	1	NA	intron (NM_025909, intron 3 of 8)	intron (NM_025909, intron 3 of 8)	11084	NM_025909	67013	Mm.30021	NM_025909	ENSMUSG00000035069	Oma1	2010001O09Rik|MPRP-1|ZMPOMA1	OMA1 zinc metallopeptidase	protein-coding
mm_96080.1	chr11	60104972	60105013	+	1	NA	promoter-TSS (NM_009021)	promoter-TSS (NM_009021)	-21	NM_009021	19377	Mm.296366	NM_009021	ENSMUSG00000062115	Rai1	Gt1	retinoic acid induced 1	protein-coding
mm_17854.1	chr2	34771751	34771816	-	1	NA	promoter-TSS (NM_001163434)	promoter-TSS (NM_001163434)	-307	NM_001163434	14828	Mm.330160	NM_022310	ENSMUSG00000026864	Hspa5	AL022860|AU019543|Bip|D2Wsu141e|D2Wsu17e|Grp78|Hsce70|SEZ-7|Sez7|baffled|mBiP	heat shock protein 5	protein-coding
mm_113747.1	chr13	44730882	44730907	+	1	NA	promoter-TSS (NM_001205043)	promoter-TSS (NM_001205043)	120	NM_001205044	16468	Mm.25059	NM_021878	ENSMUSG00000038518	Jarid2	Jmj|jumonji	jumonji, AT rich interactive domain 2	protein-coding
mm_166811.1	chr7	12999077	12999090	+	1	NA	promoter-TSS (NM_009512)	promoter-TSS (NM_009512)	-891	NM_009512	26459	Mm.10984	NM_009512	ENSMUSG00000030382	Slc27a5	FACVL3|FATP5|VLCS-H2|VLCSH2|Vlacsr	solute carrier family 27 (fatty acid transporter), member 5	protein-coding
mm_10686.1	chr2	22622129	22622144	+	1	NA	promoter-TSS (NM_008078)	promoter-TSS (NM_008078)	-191	NM_008078	14417	Mm.4784	NM_008078	ENSMUSG00000026787	Gad2	6330404F12Rik|GAD(65)|GAD65|Gad-2	glutamic acid decarboxylase 2	protein-coding
mm_118725.1	chr14	22222321	22222340	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	202618	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_103259.1	chr11	71019234	71019267	-	1	NA	promoter-TSS (NM_001291148)	promoter-TSS (NM_001291148)	53	NM_001291147	116891	Mm.28131	NM_033562	ENSMUSG00000018442	Derl2	CGI-101|Derlin-2|F-lana|Flana	Der1-like domain family, member 2	protein-coding
mm_27338.1	chr3	50410164	50410167	-	1	NA	intron (NM_011990, intron 6 of 11)	intron (NM_011990, intron 6 of 11)	33448	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_156911.1	chrX	169058801	169058812	+	1	NA	intron (NR_109847, intron 1 of 14)	intron (NR_109847, intron 1 of 14)	22195	NR_109847	11856	Mm.441810	NM_009707	ENSMUSG00000031355	Arhgap6	AI504284|RhoGAPX-1	Rho GTPase activating protein 6	protein-coding
mm_132862.1	chr16	48479561	48479577	+	1	NA	intron (NM_010816, intron 8 of 26)	ORR1D1|LTR|ERVL-MaLR	48332	NM_010816	17450	Mm.250060	NM_010816	ENSMUSG00000022652	Morc1	Morc	microrchidia 1	protein-coding
mm_22479.1	chr3	5219061	5219074	+	1	NA	intron (NM_030708, intron 1 of 10)	C-rich|Low_complexity|Low_complexity	513	NM_030708	80892	Mm.41522	NM_030708	ENSMUSG00000025255	Zfhx4	A930021B15|C130041O22Rik|Zfh-4|Zfh4	zinc finger homeodomain 4	protein-coding
mm_137590.1	chr17	28040815	28040832	+	1	NA	intron (NM_001286040, intron 13 of 24)	intron (NM_001286040, intron 13 of 24)	39761	NM_013687	21463	Mm.29758	NM_013687	ENSMUSG00000062859	Tcp11	D17Ken1|Tcp-11	t-complex protein 11	protein-coding
mm_140425.1	chr17	87986506	87986516	+	1	NA	exon (NM_010830, exon 4 of 10)	exon (NM_010830, exon 4 of 10)	11461	NM_010830	17688	Mm.18210	NM_010830	ENSMUSG00000005370	Msh6	AU044881|AW550279|GTBP|Gtmbp	mutS homolog 6	protein-coding
mm_31540.1	chr4	55477727	55477767	+	1	NA	Intergenic	Intergenic	54728	NM_010637	16600	Mm.4325	NM_010637	ENSMUSG00000003032	Klf4	EZF|Gklf|Zie	Kruppel-like factor 4 (gut)	protein-coding
mm_34574.1	chr4	150066132	150066144	+	1	NA	Intergenic	ID_B1|SINE|B4	-2316	NR_029751	723848		NR_029751	ENSMUSG00000065493	Mir34a	Mirn34a|mir-34a|mmu-mir-34a	microRNA 34a	ncRNA
mm_77881.1	chr9	7277963	7277977	+	1	NA	exon (NM_008607, exon 6 of 10)	exon (NM_008607, exon 6 of 10)	5456	NM_008607	17386	Mm.5022	NM_008607	ENSMUSG00000050578	Mmp13	Clg|MMP-13|Mmp1	matrix metallopeptidase 13	protein-coding
mm_121848.1	chr14	20640933	20640949	-	1	NA	Intergenic	CpG	15599	NM_021508	59011	Mm.439911	NM_021508	ENSMUSG00000068697	Myoz1	2310001N11Rik|AV090278|FATZ|Myoz	myozenin 1	protein-coding
mm_42673.1	chr5	119671829	119671864	+	1	NA	5' UTR (NM_011535, exon 1 of 8)	5' UTR (NM_011535, exon 1 of 8)	613	NM_011535	21386	Mm.219139	NM_011535	ENSMUSG00000018604	Tbx3	D5Ertd189e	T-box 3	protein-coding
mm_22108.1	chr2	170108909	170108917	-	1	NA	3' UTR (NM_001159683, exon 7 of 7)	3' UTR (NM_001159683, exon 7 of 7)	22307	NM_001033299	228913	Mm.22858	NM_001033299	ENSMUSG00000052056	Zfp217	4933431C08Rik|AW987152|Gm562|ZABC1|Znf217	zinc finger protein 217	protein-coding
mm_21155.1	chr2	154558835	154558897	-	1	NA	promoter-TSS (NM_021546)	promoter-TSS (NM_021546)	-13	NM_021546	56846	Mm.143748	NM_021546	ENSMUSG00000027489	Necab3	2900010M17Rik|AI853434|Apba2bp|Nip1|XB51	N-terminal EF-hand calcium binding protein 3	protein-coding
mm_105745.1	chr11	109420635	109420646	-	1	NA	Intergenic	Intergenic	-5306	NM_025275	13929	Mm.211850	NM_025275	ENSMUSG00000020610	Amz2	AA408420|ESTM12|X83328	archaelysin family metallopeptidase 2	protein-coding
mm_48035.1	chr5	136272694	136272699	-	1	NA	3' UTR (NM_009986, exon 24 of 24)	3' UTR (NM_009986, exon 24 of 24)	-27756	NM_018825	23921	Mm.425294	NM_018825	ENSMUSG00000005057	Sh2b2	Aps	SH2B adaptor protein 2	protein-coding
mm_102256.1	chr11	55310090	55310100	-	1	NA	exon (NM_001029988, exon 1 of 23)	exon (NM_001029988, exon 1 of 23)	2162	NM_001029988	245827	Mm.339363	NM_001029988	ENSMUSG00000055333	Fat2	EMI2|Fath2|Gm523|mKIAA0811	FAT atypical cadherin 2	protein-coding
mm_143996.1	chr17	88008886	88008891	-	1	NA	exon (NM_001081034, exon 10 of 23)	exon (NM_001081034, exon 10 of 23)	33838	NM_010830	17688	Mm.18210	NM_010830	ENSMUSG00000005370	Msh6	AU044881|AW550279|GTBP|Gtmbp	mutS homolog 6	protein-coding
mm_104261.1	chr11	88934234	88934237	-	1	NA	intron (NM_029023, intron 9 of 12)	B1_Mus1|SINE|Alu	21207	NM_029023	74617	Mm.34126	NM_029023	ENSMUSG00000000278	Scpep1	2410018F01Rik|4833411K15Rik|AI957256|Risc	serine carboxypeptidase 1	protein-coding
mm_98882.1	chr11	97815640	97815650	+	1	NA	intron (NM_010688, intron 2 of 6)	intron (NM_010688, intron 2 of 6)	15973	NM_010688	16796	Mm.271967	NM_010688	ENSMUSG00000038366	Lasp1	AA408629|Def-4|SH3P6|Tg(Col1a1-lacZ)1Ngma	LIM and SH3 protein 1	protein-coding
mm_80911.1	chr9	100643756	100643764	+	1	NA	5' UTR (NM_009282, exon 1 of 34)	5' UTR (NM_009282, exon 1 of 34)	137	NM_009282	20842	Mm.42135	NM_009282	ENSMUSG00000037286	Stag1	AU045003|SA-1|Scc3	stromal antigen 1	protein-coding
mm_139329.1	chr17	48974055	48974067	+	1	NA	intron (NM_027452, intron 1 of 2)	B3A|SINE|B2	41479	NM_027452	70530	Mm.133607	NM_027452	ENSMUSG00000040490	Lrfn2	5730420O05Rik|SALM1|mKIAA1246	leucine rich repeat and fibronectin type III domain containing 2	protein-coding
mm_141591.1	chr17	32420966	32420986	-	1	NA	promoter-TSS (NM_021319)	promoter-TSS (NM_021319)	-1	NR_073184	57757	Mm.86752	NM_021319	ENSMUSG00000079563	Pglyrp2	C730002N09Rik|PGRP-L|Pglyrpl|tagL	peptidoglycan recognition protein 2	protein-coding
mm_75624.1	chr8	64620492	64620499	-	1	NA	intron (NM_013494, intron 1 of 8)	MLT1B|LTR|ERVL-MaLR	72614	NM_013494	12876	Mm.31395	NM_013494	ENSMUSG00000037852	Cpe	CPH|Cph-1|Cph1|R74677|fat	carboxypeptidase E	protein-coding
mm_116311.1	chr13	37049204	37049220	-	1	NA	promoter-TSS (NM_028784)	promoter-TSS (NM_028784)	1	NM_028784	74145	Mm.235105	NM_028784	ENSMUSG00000039109	F13a1	1200014I03Rik|AI462306|F13a	coagulation factor XIII, A1 subunit	protein-coding
mm_170787.1	chr2	175010210	175010227	+	1	NA	Intergenic	Intergenic	57551	NM_001085546	664987		NM_001085546	ENSMUSG00000078905	Gm14393	OTTMUSG00000016546	predicted gene 14393	protein-coding
mm_93140.1	chr10	92164775	92164791	-	1	NA	intron (NR_028262, intron 1 of 12)	intron (NR_028262, intron 1 of 12)	395	NR_028262	110333	Mm.429764	NR_028262		Rmst	100041799|AI853140|C230053E11Rik|D930049J19Rik|Dmt2|Gm3515|M2|Ncrms	rhabdomyosarcoma 2 associated transcript (non-coding RNA)	ncRNA
mm_7839.1	chr1	132357476	132357502	-	1	NA	3' UTR (NM_178874, exon 5 of 5)	3' UTR (NM_178874, exon 5 of 5)	10459	NM_001311108	68875	Mm.273785	NM_178874	ENSMUSG00000042066	Tmcc2	1110063G11Rik	transmembrane and coiled-coil domains 2	protein-coding
mm_13729.1	chr2	117966067	117966083	+	1	NA	intron (NR_126479, intron 8 of 9)	intron (NR_126479, intron 8 of 9)	144147	NR_040631	73938	Mm.399107	NR_040631	ENSMUSG00000086221	4930412B13Rik	-	RIKEN cDNA 4930412B13 gene	ncRNA
mm_59527.1	chr7	27649898	27649902	+	1	NA	Intergenic	Intergenic	-4024	NM_028417	73032	Mm.44095	NM_028417	ENSMUSG00000007944	Ttc9b	2900074C18Rik	tetratricopeptide repeat domain 9B	protein-coding
mm_13860.1	chr2	119715392	119715428	+	1	NA	intron (NM_030112, intron 6 of 17)	ID_B1|SINE|B4	-26927	NM_146125	228550	Mm.65337	NM_146125	ENSMUSG00000027296	Itpka	-	inositol 1,4,5-trisphosphate 3-kinase A	protein-coding
mm_158280.1	chrX	111536302	111536317	-	1	NA	intron (NM_025949, intron 1 of 24)	intron (NM_025949, intron 1 of 24)	1650	NM_025949	67071	Mm.37617	NM_025949	ENSMUSG00000025665	Rps6ka6	2610524K04Rik|RSK4|S6K-alpha-6	ribosomal protein S6 kinase polypeptide 6	protein-coding
mm_129034.1	chr15	74983416	74983431	-	1	NA	promoter-TSS (NM_020498)	promoter-TSS (NM_020498)	7	NM_020498	57248	Mm.358339	NM_020498	ENSMUSG00000022586	Ly6i	AI789751|Ly-6I|Ly-6M	lymphocyte antigen 6 complex, locus I	protein-coding
mm_4179.1	chr1	171155513	171155529	+	1	NA	promoter-TSS (NM_001315499)	promoter-TSS (NM_001315499)	3	NM_001315500	17528	Mm.9986	NM_008623	ENSMUSG00000056569	Mpz	Mpp|P-zero|P0	myelin protein zero	protein-coding
mm_68897.1	chr7	126449286	126449306	-	1	NA	intron (NM_007504, intron 14 of 22)	(ACTG)n|Simple_repeat|Simple_repeat	13777	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_66211.1	chr7	34313532	34313568	-	1	NA	Intergenic	CpG	-27941	NM_172741	233103	Mm.491097	NM_172741	ENSMUSG00000066571	4931406P16Rik	AA553327|mKIAA0355	RIKEN cDNA 4931406P16 gene	protein-coding
mm_102057.1	chr11	52252887	52252901	-	1	NA	3' UTR (NM_009331, exon 10 of 10)	3' UTR (NM_009331, exon 10 of 10)	20899	NM_011543	21402	Mm.42944	NM_011543	ENSMUSG00000036309	Skp1a	15kDa|2610043E24Rik|2610206H23Rik|EMC19|OCP-II|OCP2|SKP1|Tceb1l|p19A|p19Skp1	S-phase kinase-associated protein 1A	protein-coding
mm_21608.1	chr2	164254672	164254683	-	1	NA	3' UTR (NM_173377, exon 3 of 3)	3' UTR (NM_173377, exon 3 of 3)	1966	NM_173377	329557	Mm.118769	NM_173377	ENSMUSG00000050383	Svs3b	9530004A22Rik	seminal vesicle secretory protein 3B	protein-coding
mm_83671.1	chr9	49765918	49765921	-	1	NA	intron (NM_001081445, intron 1 of 17)	intron (NM_001081445, intron 1 of 17)	33150	NM_001081445	17967	Mm.4974	NM_010875	ENSMUSG00000039542	Ncam1	CD56|E-NCAM|NCAM-1|Ncam	neural cell adhesion molecule 1	protein-coding
mm_12581.1	chr2	73312634	73312665	+	1	NA	promoter-TSS (NM_025854)	promoter-TSS (NM_025854)	-3	NM_029022	74616	Mm.247457	NM_029022	ENSMUSG00000008226	Scrn3	4833415E20Rik|AI427019|AV002033|Ses3	secernin 3	protein-coding
mm_55977.1	chr6	85869083	85869100	-	1	NA	promoter-TSS (NM_053096)	promoter-TSS (NM_053096)	46	NM_053096	93673	Mm.24251	NM_053096	ENSMUSG00000033634	Nat8f2	Cml2	N-acetyltransferase 8 (GCN5-related) family member 2	protein-coding
mm_138616.1	chr17	35823374	35823424	+	1	NA	promoter-TSS (NM_008027)	promoter-TSS (NM_008027)	42	NM_008027	14251	Mm.2931	NM_008027	ENSMUSG00000059714	Flot1	reggie-2	flotillin 1	protein-coding
mm_98233.1	chr11	88098940	88098950	+	1	NA	promoter-TSS (NM_198013)	promoter-TSS (NM_198013)	-201	NM_198013	103841	Mm.374846	NM_198013	ENSMUSG00000018378	Cuedc1	AI841487|C330016O16Rik	CUE domain containing 1	protein-coding
mm_31005.1	chr4	40184933	40184944	+	1	NA	exon (NM_007386, exon 14 of 21)	exon (NM_007386, exon 14 of 21)	41673	NM_007386	11428	Mm.331547	NM_007386	ENSMUSG00000028405	Aco1	Aco-1|Irebp|Irp1	aconitase 1	protein-coding
mm_72625.1	chr8	84653444	84653449	+	1	NA	Intergenic	RLTR41|LTR|ERV1	9406	NM_010499	15936	Mm.399	NM_010499	ENSMUSG00000053560	Ier2	AI317238|Ch1|Pip92	immediate early response 2	protein-coding
mm_133246.1	chr16	77115886	77115899	+	1	NA	3' UTR (NM_013918, exon 24 of 24)	3' UTR (NM_013918, exon 24 of 24)	101823	NM_013918	30940	Mm.40986	NM_013918	ENSMUSG00000022867	Usp25	-	ubiquitin specific peptidase 25	protein-coding
mm_136804.1	chr17	12378630	12378646	+	1	NA	promoter-TSS (NM_008877)	promoter-TSS (NM_008877)	29	NM_008877	18815	Mm.971	NM_008877	ENSMUSG00000059481	Plg	AI649309|Pg	plasminogen	protein-coding
mm_43230.1	chr5	129908599	129908616	+	1	NA	promoter-TSS (NM_026916)	promoter-TSS (NM_026916)	67	NM_026916	69034	Mm.211372	NM_026916	ENSMUSG00000095789	Nupr1l	1810010E01Rik|4930579G22Rik|Nupr2	nuclear protein transcriptional regulator 1 like	protein-coding
mm_91827.1	chr10	56378967	56378972	-	1	NA	intron (NM_010288, intron 1 of 1)	intron (NM_010288, intron 1 of 1)	1669	NM_010288	14609	Mm.378921	NM_010288	ENSMUSG00000050953	Gja1	AU042049|AW546267|Cnx43|Cx43|Cx43alpha1|Gja-1|Npm1|connexin43	gap junction protein, alpha 1	protein-coding
mm_145606.1	chr18	61096672	61096695	+	1	NA	Intergenic	Intergenic	-8889	NM_001037859	12978	Mm.22574	NM_007779	ENSMUSG00000024621	Csf1r	AI323359|CD115|CSF-1R|Csfmr|Fim-2|Fim2|Fms|M-CSF-R|M-CSFR	colony stimulating factor 1 receptor	protein-coding
mm_27130.1	chr3	32365184	32365218	-	1	NA	promoter-TSS (NR_027966)	promoter-TSS (NR_027966)	-288	NR_027966	67576	Mm.435324	NR_027966		4930429B21Rik	-	RIKEN cDNA 4930429B21 gene	ncRNA
mm_145775.1	chr18	65050983	65050998	+	1	NA	intron (NM_031881, intron 1 of 29)	intron (NM_031881, intron 1 of 29)	27463	NM_031881	83814	Mm.98668	NM_031881	ENSMUSG00000024589	Nedd4l	1300012C07Rik|Nedd4-2|Nedd4b	neural precursor cell expressed, developmentally down-regulated gene 4-like	protein-coding
mm_130633.1	chr15	100425051	100425075	-	1	NA	intron (NR_040351, intron 1 of 2)	intron (NR_040351, intron 1 of 2)	1870	NR_040351	432982	Mm.234608	NM_001034883	ENSMUSG00000087444	Gm5475	EG432982	predicted gene 5475	ncRNA
mm_103403.1	chr11	75439490	75439531	-	1	NA	promoter-TSS (NM_008878)	promoter-TSS (NM_008878)	-9	NM_008878	18816	Mm.279733	NM_008878	ENSMUSG00000038224	Serpinf2	AI747498|Pli|Serpimf2	serine (or cysteine) peptidase inhibitor, clade F, member 2	protein-coding
mm_106375.1	chr11	118418957	118419015	-	1	NA	5' UTR (NM_029502, exon 1 of 5)	5' UTR (NM_029502, exon 1 of 5)	132	NM_001025617	76025	Mm.177551	NM_029502	ENSMUSG00000025575	Cant1	5830420C20Rik|Apy1h|D11Bwg0554e|Entpd8|SCAN-1|Shapy	calcium activated nucleotidase 1	protein-coding
mm_161940.1	chr19	3996568	3996568	+	1	NA	exon (NM_001001320, exon 2 of 8)	exon (NM_001001320, exon 2 of 8)	3816	NM_011533	109575	Mm.246555	NM_011533	ENSMUSG00000037477	Tbx10	Dc|Tbx13|Tbx7	T-box 10	protein-coding
mm_75747.1	chr8	69888231	69888237	-	1	NA	promoter-TSS (NM_026818)	promoter-TSS (NM_026818)	-842	NM_026818	68709	Mm.334584	NM_026818	ENSMUSG00000044006	Cilp2	1110031K21Rik|AA407300|CLIP-2	cartilage intermediate layer protein 2	protein-coding
mm_1715.1	chr1	75236766	75236803	+	1	NA	promoter-TSS (NM_001159885)	promoter-TSS (NM_001159885)	82	NM_001159885	56812	Mm.489660	NM_020266	ENSMUSG00000026203	Dnajb2	2700059H22Rik|Dnajb10|Hsj1|mDj8	DnaJ heat shock protein family (Hsp40) member B2	protein-coding
mm_108329.1	chr12	79917548	79917558	+	1	NA	non-coding (NR_131075, exon 3 of 3)	non-coding (NR_131075, exon 3 of 3)	7180	NR_131075	77290	Mm.395042	NR_131073		9430078K24Rik	-	RIKEN cDNA 9430078K24 gene	ncRNA
mm_74990.1	chr8	27168879	27168885	-	1	NA	intron (NM_029423, intron 1 of 4)	intron (NM_029423, intron 1 of 4)	5764	NM_029423	75767	Mm.205335	NM_029423	ENSMUSG00000031488	Rab11fip1	2010200K21Rik|4833414G05Rik|Rcp	RAB11 family interacting protein 1 (class I)	protein-coding
mm_158251.1	chrX	107948433	107948443	-	1	NA	promoter-TSS (NM_001033252)	promoter-TSS (NM_001033252)	-2	NM_001033252	213450	Mm.300779	NM_001033252	ENSMUSG00000073006	Gm732	-	predicted gene 732	protein-coding
mm_154007.1	chr19	53039225	53039227	-	1	NA	promoter-TSS (NM_133216)	promoter-TSS (NM_133216)	-572	NM_133216	170750	Mm.99776	NM_133216	ENSMUSG00000025027	Xpnpep1	D230045I08Rik|sAMP	X-prolyl aminopeptidase (aminopeptidase P) 1, soluble	protein-coding
mm_171904.1	chr5	43913154	43913168	+	1	NA	TTS (NM_007646)	TTS (NM_007646)	44352	NM_007646	12494	Mm.249873	NM_007646	ENSMUSG00000029084	Cd38	ADPRC 1|Cd38-rs1|I-19	CD38 antigen	protein-coding
mm_107046.1	chr12	15815018	15815027	+	1	NA	intron (NM_144551, intron 1 of 2)	CpG	1763	NM_144551	217410	Mm.491136	NM_144551	ENSMUSG00000020601	Trib2	AW319517|TRB-2|TRB2	tribbles pseudokinase 2	protein-coding
mm_2757.1	chr1	129680997	129681007	+	1	NA	intron (NM_172485, intron 7 of 27)	intron (NM_172485, intron 7 of 27)	407698	NM_172485	210417	Mm.380518	NM_172485	ENSMUSG00000042581	Thsd7b	1700074E13Rik|B930082A18|D130067I03Rik	thrombospondin, type I, domain containing 7B	protein-coding
mm_54951.1	chr6	48681731	48681737	-	1	NA	Intergenic	Intergenic	-2844	NM_001243200	107526	Mm.333048	NM_174990	ENSMUSG00000054435	Gimap4	AU019574|E430007K16Rik|Ian-1|Ian1|Imap4	GTPase, IMAP family member 4	protein-coding
mm_164884.1	chr18	60426170	60426180	+	1	NA	Intergenic	Intergenic	50146	NM_001146275	60440	Mm.261140	NM_021792	ENSMUSG00000054072	Iigp1	2900074L10Rik|AI046432|AW111922|Ifgga1|Iigp|Irga6	interferon inducible GTPase 1	protein-coding
mm_16809.1	chr2	11160792	11160807	-	1	NA	Intergenic	Intergenic	-11583	NM_008859	18761	Mm.329993	NM_008859	ENSMUSG00000026778	Prkcq	A130035A12Rik|AW494342|PKC-0|PKC-theta|PKCtheta|Pkcq	protein kinase C, theta	protein-coding
mm_14826.1	chr2	147013923	147013932	+	1	NA	intron (NM_011917, intron 1 of 29)	intron (NM_011917, intron 1 of 29)	867	NM_011917	24128	Mm.3065	NM_011917	ENSMUSG00000027433	Xrn2	-	5'-3' exoribonuclease 2	protein-coding
mm_82596.1	chr9	21287955	21287976	-	1	NA	promoter-TSS (NM_145416)	promoter-TSS (NM_145416)	4	NM_145416	215194	Mm.290690	NM_145416	ENSMUSG00000035047	Kri1	-	KRI1 homolog	protein-coding
mm_145489.1	chr18	60386065	60386075	+	1	NA	intron (NM_001146275, intron 2 of 2)	intron (NM_001146275, intron 2 of 2)	10041	NM_001146275	60440	Mm.261140	NM_021792	ENSMUSG00000054072	Iigp1	2900074L10Rik|AI046432|AW111922|Ifgga1|Iigp|Irga6	interferon inducible GTPase 1	protein-coding
mm_88075.1	chr10	67979593	67979609	+	1	NA	promoter-TSS (NM_001081346)	promoter-TSS (NM_001081346)	3	NM_001081346	170799	Mm.209844	NM_133244	ENSMUSG00000037846	Rtkn2	B130039D23Rik|Mbf|Plekhk1	rhotekin 2	protein-coding
mm_38623.1	chr4	142048570	142048584	-	1	NA	intron (NM_145402, intron 1 of 2)	MLT1J|LTR|ERVL-MaLR	30679	NR_131014	78917	Mm.139995	NR_131014	ENSMUSG00000085761	4930455G09Rik	-	RIKEN cDNA 4930455G09 gene	ncRNA
mm_163607.1	chr13	49215935	49215976	-	1	NA	promoter-TSS (NM_026738)	promoter-TSS (NM_026738)	71	NM_026738	68480	Mm.3336	NM_026738	ENSMUSG00000037960	Card19	1110007C09Rik|AI851695|Bincard	caspase recruitment domain family, member 19	protein-coding
mm_151093.1	chr19	47733653	47733665	+	1	NA	exon (NM_026377, exon 3 of 4)	exon (NM_026377, exon 3 of 4)	1903	NM_026377	67788	Mm.181610	NM_026377	ENSMUSG00000025066	Sfr1	6330577E15Rik|Meir5	SWI5 dependent recombination repair 1	protein-coding
mm_141844.1	chr17	34740261	34740275	-	1	NA	exon (NM_009780, exon 11 of 41)	exon (NM_009780, exon 11 of 41)	3629	NM_009780	12268	Mm.477109	NM_009780	ENSMUSG00000073418	C4b	C4|Ss	complement component 4B (Chido blood group)	protein-coding
mm_54709.1	chr6	39708837	39708840	-	1	NA	intron (NM_139294, intron 1 of 21)	intron (NM_139294, intron 1 of 21)	16625	NM_139294	109880	Mm.245513	NM_139294	ENSMUSG00000002413	Braf	9930012E13Rik|AA120551|AA387315|AA473386|B-raf|Braf-2|Braf2|C230098H17|C87398|D6Ertd631e	Braf transforming gene	protein-coding
mm_39086.1	chr4	154636301	154636357	-	1	NA	promoter-TSS (NR_045643)	promoter-TSS (NR_045643)	38	NR_045643	320939	Mm.436738	NR_045643		5930403L14Rik	-	RIKEN cDNA 5930403L14 gene	ncRNA
mm_15805.1	chr2	164486520	164486655	+	1	NA	promoter-TSS (NM_001048228)	promoter-TSS (NM_001048228)	132	NM_026797	52840	Mm.256927	NM_026797	ENSMUSG00000017734	Dbndd2	1110017A21Rik|2900022J10Rik|AU041050|AW048677|D2Bwg0891e|Nkip|R74724	dysbindin (dystrobrevin binding protein 1) domain containing 2	protein-coding
mm_51621.1	chr6	85431971	85432010	+	1	NA	promoter-TSS (NM_144918)	promoter-TSS (NM_144918)	14	NM_144918	232187	Mm.219946	NM_144918	ENSMUSG00000033706	Smyd5	AW536703|NN8-4AG|Rai15|Rrg1	SET and MYND domain containing 5	protein-coding
mm_26897.1	chr3	19264960	19264974	-	1	NA	promoter-TSS (NM_008802)	promoter-TSS (NM_008802)	41	NM_008802	18583	Mm.355614	NM_008802	ENSMUSG00000069094	Pde7a	AU015378|AW047537	phosphodiesterase 7A	protein-coding
mm_53982.1	chr6	6862829	6862838	-	1	NA	promoter-TSS (NM_010057)	promoter-TSS (NM_010057)	-501	NM_010057	13396	Mm.439763	NM_010057	ENSMUSG00000029754	Dlx6	-	distal-less homeobox 6	protein-coding
mm_137972.1	chr17	33557192	33557205	+	1	NA	intron (NM_053214, intron 1 of 27)	ID_B1|SINE|B4	1491	NM_053214	17916	Mm.42019	NM_053214	ENSMUSG00000024300	Myo1f	C330006B10Rik	myosin IF	protein-coding
mm_73949.1	chr8	120145377	120145421	+	1	NA	exon (NM_001163762, exon 2 of 8)	exon (NM_001163762, exon 2 of 8)	470	NM_001163760	234797	Mm.101958	NM_172286	ENSMUSG00000031824	6430548M08Rik	AW049007|Kiaa0513|mKIAA0513	RIKEN cDNA 6430548M08 gene	protein-coding
mm_169732.1	chr15	82047580	82047581	-	1	NA	promoter-TSS (NM_011482)	promoter-TSS (NM_011482)	18	NM_011482	20826	Mm.299312	NM_011482	ENSMUSG00000063480	Nhp2l1	FA-1|Fta1|Snu13|Ssfa1	NHP2 non-histone chromosome protein 2-like 1 (S. cerevisiae)	protein-coding
mm_4602.1	chr1	178406073	178406105	+	1	NA	5' UTR (NM_026626, exon 1 of 7)	5' UTR (NM_026626, exon 1 of 7)	208	NM_026626	68226	Mm.252132	NM_026626	ENSMUSG00000026495	Efcab2	1700073K01Rik|D830011E08Rik	EF-hand calcium binding domain 2	protein-coding
mm_144944.1	chr18	37768411	37768421	+	1	NA	exon (NM_033595, exon 1 of 4)	exon (NM_033595, exon 1 of 4)	2836	NM_033595	93724	Mm.247203	NM_033595	ENSMUSG00000102428	Pcdhga12	Pcdh13|pc2c	protocadherin gamma subfamily A, 12	protein-coding
mm_96483.1	chr11	67684613	67684635	+	1	NA	3' UTR (NM_001277080, exon 13 of 13)	3' UTR (NM_001277080, exon 13 of 13)	-10702	NM_009038	19674	Mm.439726	NM_009038	ENSMUSG00000020907	Rcvrn	CAR|S-modulin	recoverin	protein-coding
mm_141257.1	chr17	27597177	27597196	-	1	NA	intron (NM_019837, intron 1 of 4)	intron (NM_019837, intron 1 of 4)	25778	NM_001291046	56409	Mm.144699	NM_019837	ENSMUSG00000024213	Nudt3	1110011B09Rik|AA960325|Dipp|Dipp1	nudix (nucleotide diphosphate linked moiety X)-type motif 3	protein-coding
mm_17443.1	chr2	28466398	28466421	-	1	NA	promoter-TSS (NM_027040)	promoter-TSS (NM_027040)	-85	NM_027040	69327	Mm.46470	NM_027040	ENSMUSG00000026831	1700007K13Rik	Rbest47	RIKEN cDNA 1700007K13 gene	protein-coding
mm_45170.1	chr5	51495727	51495741	-	1	NA	non-coding (NR_027710, exon 4 of 13)	non-coding (NR_027710, exon 4 of 13)	58187	NR_027710	19017	Mm.259072	NM_008904	ENSMUSG00000029167	Ppargc1a	A830037N07Rik|ENSMUSG00000079510|Gm11133|PGC-1|PPARGC-1-alpha|Pgc-1alpha|Pgc1|Pgco1|Ppargc1	peroxisome proliferative activated receptor, gamma, coactivator 1 alpha	protein-coding
mm_138567.1	chr17	35379587	35379600	+	1	NA	promoter-TSS (NM_001143689)	promoter-TSS (NM_001143689)	-24	NM_001143689	15015	Mm.464284	NM_001143689	ENSMUSG00000035929	H2-Q4	H-2Q4|H2-Gs10|Qa-4|Qa4|Qat-4|Qb-1|Qb1	histocompatibility 2, Q region locus 4	protein-coding
mm_172951.1	chr9	86695816	86695825	-	1	NA	promoter-TSS (NM_008615)	promoter-TSS (NM_008615)	94	NM_008615	17436	Mm.148155	NM_008615	ENSMUSG00000032418	Me1	D9Ertd267e|Mdh-1|Mod-1|Mod1	malic enzyme 1, NADP(+)-dependent, cytosolic	protein-coding
mm_117350.1	chr13	69738957	69738973	-	1	NA	exon (NM_001145162, exon 1 of 2)	exon (NM_001145162, exon 1 of 2)	932	NM_001145162	76980	Mm.23960	NM_001145162	ENSMUSG00000052981	Ube2ql1	3110006E14Rik	ubiquitin-conjugating enzyme E2Q family-like 1	protein-coding
mm_96150.1	chr11	61142478	61142507	+	1	NA	intron (NM_021349, intron 2 of 3)	intron (NM_021349, intron 2 of 3)	1657	NM_021349	57916	Mm.265915	NM_021349	ENSMUSG00000010142	Tnfrsf13b	1200009E08Rik|Taci	tumor necrosis factor receptor superfamily, member 13b	protein-coding
mm_25197.1	chr3	103774172	103774183	+	1	NA	intron (NM_001301304, intron 2 of 15)	intron (NM_001301304, intron 2 of 15)	17098	NM_001301306	15257	Mm.20827	NM_010432	ENSMUSG00000008730	Hipk1	1110062K04Rik|Myak	homeodomain interacting protein kinase 1	protein-coding
mm_86890.1	chr10	22299628	22299639	+	1	NA	intron (NM_009018, intron 5 of 5)	intron (NM_009018, intron 5 of 5)	-7087	NR_015465	606736	Mm.387042	NR_015465	ENSMUSG00000097352	C920009B18Rik	-	RIKEN cDNA C920009B18 gene	ncRNA
mm_45807.1	chr5	87591583	87591602	-	1	NA	promoter-TSS (NM_023135)	promoter-TSS (NM_023135)	19	NM_023135	20860	Mm.89655	NM_023135	ENSMUSG00000029272	Sult1e1	EST|ST1E1|Ste	sulfotransferase family 1E, member 1	protein-coding
mm_62181.1	chr7	97451433	97451441	+	1	NA	5' UTR (NM_001136235, exon 1 of 3)	5' UTR (NM_001136235, exon 1 of 3)	103	NM_001136235	233529	Mm.334033	NM_001010826	ENSMUSG00000051727	Kctd14	AI449310|D7Ertd760e	potassium channel tetramerisation domain containing 14	protein-coding
mm_130416.1	chr15	98004667	98004682	-	1	NA	promoter-TSS (NM_001113515)	promoter-TSS (NM_001113515)	50	NM_031163	12824	Mm.2423	NM_031163	ENSMUSG00000022483	Col2a1	Col2|Col2a|Col2a-1|Del1|Dmm|Lpk|Rgsc856	collagen, type II, alpha 1	protein-coding
mm_55894.1	chr6	83536524	83536541	-	1	NA	promoter-TSS (NM_009610)	promoter-TSS (NM_009610)	-281	NM_009610	11468	Mm.292865	NM_009610	ENSMUSG00000059430	Actg2	ACTA3|Act-4|Act4|SMGA	actin, gamma 2, smooth muscle, enteric	protein-coding
mm_134693.1	chr16	22561107	22561120	-	1	NA	intron (NM_001346673, intron 16 of 23)	intron (NM_001346673, intron 16 of 23)	-28929	NR_106170	102465887		NR_106170	ENSMUSG00000099071	Mir8095	Gm27566|mmu-mir-8095	microRNA 8095	ncRNA
mm_79932.1	chr9	65676518	65676556	+	1	NA	promoter-TSS (NM_010952)	promoter-TSS (NM_010952)	-11	NM_010952	18247	Mm.116749	NM_010952	ENSMUSG00000040652	Oaz2	AZ-2|AZ2|Oaz2-ps|Sez15	ornithine decarboxylase antizyme 2	protein-coding
mm_151025.1	chr19	46962659	46962699	+	1	NA	promoter-TSS (NM_029810)	promoter-TSS (NM_029810)	-328	NR_028353	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_26517.1	chr3	145893957	145893966	+	1	NA	3' UTR (NM_026993, exon 6 of 6)	3' UTR (NM_026993, exon 6 of 6)	-30301	NM_009740	12042	Mm.239141	NM_009740	ENSMUSG00000028191	Bcl10	AI132454|BCL-10|C81403|CARMEN|CIPER|CLAP|ME10|cE10	B cell leukemia/lymphoma 10	protein-coding
mm_54471.1	chr6	34910526	34910543	-	1	NA	intron (NM_001013366, intron 1 of 14)	MIR3|SINE|MIR	297	NM_001013366	101240	Mm.152120	NM_001013366	ENSMUSG00000058486	Wdr91	9530020G05Rik|AI987683|AU018665	WD repeat domain 91	protein-coding
mm_27105.1	chr3	30647753	30647770	-	1	NA	promoter-TSS (NM_001290510)	promoter-TSS (NM_001290510)	57	NM_027941	71827	Mm.45373	NM_027941	ENSMUSG00000027702	Lrrc34	1700007J06Rik|SPATA34	leucine rich repeat containing 34	protein-coding
mm_23421.1	chr3	58591298	58591316	+	1	NA	3' UTR (NM_001040396, exon 6 of 6)	3' UTR (NM_001040396, exon 6 of 6)	14649	NM_001040396	69227	Mm.270950	NM_001040396	ENSMUSG00000075700	Selenot	2810407C02Rik|5730408P04Rik|Selt	selenoprotein T	protein-coding
mm_24753.1	chr3	95320993	95321014	+	1	NA	exon (NM_001320492, exon 4 of 11)	exon (NM_001320492, exon 4 of 11)	2173	NM_001320492	76893	Mm.181009	NM_029789	ENSMUSG00000015714	Cers2	0610013I17Rik|AI225939|Lass2|TRH3	ceramide synthase 2	protein-coding
mm_46774.1	chr5	112343011	112343050	-	1	NA	promoter-TSS (NM_027323)	promoter-TSS (NM_027323)	10	NM_027323	70118	Mm.172947	NM_027323	ENSMUSG00000029346	Srrd	2810002G02Rik|Srr1	SRR1 domain containing	protein-coding
mm_106434.1	chr11	119408897	119408939	-	1	NA	Intergenic	Intergenic	18446	NR_035453	100316690		NR_035453	ENSMUSG00000088015	Mir1932	mir-1932|mmu-mir-1932	microRNA 1932	ncRNA
mm_21151.1	chr2	154416464	154416466	-	1	NA	Intergenic	ID_B1|SINE|B4	-8381	NM_009228	20648	Mm.1541	NM_009228	ENSMUSG00000027488	Snta1	AW228934|Snt1	syntrophin, acidic 1	protein-coding
mm_172345.1	chr7	11310672	11310684	-	1	NA	Intergenic	Intergenic	-87237	NM_001110316	665902	Mm.425380	NM_001110316	ENSMUSG00000070828	Zscan4f	C330039H09Rik	zinc finger and SCAN domain containing 4F	protein-coding
mm_30332.1	chr3	151732179	151732196	-	1	NA	3' UTR (NM_133871, exon 8 of 8)	3' UTR (NM_133871, exon 8 of 8)	17772	NM_133871	99899	Mm.30756	NM_133871	ENSMUSG00000028037	Ifi44	A430056A10Rik|AW261460|MTAP44|p44	interferon-induced protein 44	protein-coding
mm_2386.1	chr1	93482595	93482600	+	1	NA	intron (NM_001159719, intron 1 of 12)	intron (NM_001159719, intron 1 of 12)	3536	NM_001159719	18000	Mm.428652	NM_010891	ENSMUSG00000026276	Sept2	AW208991|Nedd-5|Nedd5|mKIAA0158	septin 2	protein-coding
mm_19051.1	chr2	77259834	77259848	-	1	NA	intron (NM_175465, intron 1 of 17)	ID4|SINE|ID	20751	NM_175465	228071	Mm.27120	NM_175465	ENSMUSG00000042272	Sestd1	1500031J16Rik|A930010O20|Solo/Trio8	SEC14 and spectrin domains 1	protein-coding
mm_121623.1	chr14	8309735	8309745	-	1	NA	promoter-TSS (NM_183187)	promoter-TSS (NM_183187)	36	NM_183187	268709	Mm.256058	NM_183187	ENSMUSG00000021750	Fam107a	DRR1	family with sequence similarity 107, member A	protein-coding
mm_108918.1	chr12	100779056	100779065	+	1	NA	promoter-TSS (NM_145448)	promoter-TSS (NM_145448)	-63	NM_145448	217830	Mm.218590	NM_145448	ENSMUSG00000021185	9030617O03Rik	-	RIKEN cDNA 9030617O03 gene	protein-coding
mm_170416.1	chr18	68692238	68692238	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-47162	NR_105774	102465183		NR_105774	ENSMUSG00000099300	Mir6356	Gm27461|mmu-mir-6356	microRNA 6356	ncRNA
mm_95707.1	chr11	54450685	54450688	+	1	NA	intron (NM_173753, intron 1 of 17)	intron (NM_173753, intron 1 of 17)	12507	NM_173753	216742	Mm.34087	NM_173753	ENSMUSG00000035992	Fnip1	A730024A03Rik|AI838773|AW557298	folliculin interacting protein 1	protein-coding
mm_27115.1	chr3	30969400	30969425	-	1	NA	promoter-TSS (NM_153421)	promoter-TSS (NM_153421)	3	NM_001165954	241915	Mm.233173	NM_153421	ENSMUSG00000037652	Phc3	E030046K01Rik|Edr3|Hph3	polyhomeotic-like 3 (Drosophila)	protein-coding
mm_166150.1	chr5	6104287	6104287	-	1	NA	Intergenic	LTR16A|LTR|ERVL	-354970	NM_027399	70358	Mm.85429	NM_027399	ENSMUSG00000015652	Steap1	2410007B19Rik|Prss24|Steap	six transmembrane epithelial antigen of the prostate 1	protein-coding
mm_93850.1	chr10	121988061	121988061	-	1	NA	intron (NM_001242411, intron 1 of 21)	intron (NM_001242411, intron 1 of 21)	59254	NM_001242411	117600	Mm.288698	NM_001081037	ENSMUSG00000020121	Srgap1	4930572H05Rik|Arhgap13	SLIT-ROBO Rho GTPase activating protein 1	protein-coding
mm_145240.1	chr18	50395296	50395330	+	1	NA	Intergenic	MLT1K|LTR|ERVL-MaLR	116944	NM_001004061	225497	Mm.329435	NM_001004061	ENSMUSG00000035420	Fam170a	Gm93|Znfd	family with sequence similarity 170, member A	protein-coding
mm_22961.1	chr3	32510691	32510715	+	1	NA	5' UTR (NM_144519, exon 1 of 7)	5' UTR (NM_144519, exon 1 of 7)	111	NM_144519	67778	Mm.285620	NM_144519	ENSMUSG00000027667	Zfp639	6230400O18Rik|ANC-2H01|ZASC1|Znf639	zinc finger protein 639	protein-coding
mm_51808.1	chr6	88733596	88733612	+	1	NA	intron (NM_011844, intron 2 of 7)	intron (NM_011844, intron 2 of 7)	8900	NM_001166251	23945	Mm.272197	NM_011844	ENSMUSG00000033174	Mgll	AA589436|Magl|Mgl	monoglyceride lipase	protein-coding
mm_17535.1	chr2	29772164	29772172	-	1	NA	Intergenic	Intergenic	10640	NM_001177392	433416	Mm.330112	NM_001034887	ENSMUSG00000075425	Gm13547	OTTMUSG00000012686	predicted gene 13547	protein-coding
mm_68791.1	chr7	123369843	123369867	-	1	NA	promoter-TSS (NM_001122643)	promoter-TSS (NM_001122643)	60	NM_001122643	70497	Mm.403318	NM_144529	ENSMUSG00000030766	Arhgap17	5730403H17Rik|Nadrin|Nadrin2|Rich1|Wbp15	Rho GTPase activating protein 17	protein-coding
mm_107051.1	chr12	16532663	16532671	+	1	NA	Intergenic	Intergenic	57103	NM_015763	14245	Mm.153625	NM_015763	ENSMUSG00000020593	Lpin1	4631420P06|Kiaa0188|Lipin1|fld|mKIAA0188	lipin 1	protein-coding
mm_21613.1	chr2	164256639	164256643	-	1	NA	promoter-TSS (NM_173377)	promoter-TSS (NM_173377)	2	NM_173377	329557	Mm.118769	NM_173377	ENSMUSG00000050383	Svs3b	9530004A22Rik	seminal vesicle secretory protein 3B	protein-coding
mm_116530.1	chr13	45832457	45832468	-	1	NA	intron (NM_001199304, intron 3 of 6)	intron (NM_001199304, intron 3 of 6)	132529	NM_001199304	20238	Mm.342683	NM_009124	ENSMUSG00000046876	Atxn1	2900016G23Rik|Atx1|C85907|ENSMUSG00000074917|Gm10786|Sca1	ataxin 1	protein-coding
mm_50241.1	chr6	42351699	42351707	+	1	NA	exon (NM_001289618, exon 4 of 10)	exon (NM_001289618, exon 4 of 10)	1875	NM_001289619	22793	Mm.282303	NM_011777	ENSMUSG00000029860	Zyx	9530098H06Rik|R75157	zyxin	protein-coding
mm_111562.1	chr12	101222026	101222060	-	1	NA	Intergenic	Intergenic	76434	NR_033653	74947	Mm.488905	NR_033653	ENSMUSG00000092054	Kif4-ps	4930463M05Rik|Kif4b	kinesin family member 4, pseudogene	pseudo
mm_158564.1	chrX	150441059	150441069	-	1	NA	promoter-TSS (NM_001164686)	promoter-TSS (NM_001164686)	73	NM_001164684	382245	Mm.277309	NM_001164683	ENSMUSG00000041353	Tmem29	2700081K05Rik|6330540D07Rik|CXorf44-like	transmembrane protein 29	protein-coding
mm_156160.1	chrX	129992952	129992969	+	1	NA	intron (NM_172493, intron 17 of 26)	intron (NM_172493, intron 17 of 26)	243218	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diaph2	Dia3|Diap2|Drf2|E430022I22Rik	diaphanous related formin 2	protein-coding
mm_74507.1	chr8	8618706	8618709	-	1	NA	3' UTR (NM_010111, exon 5 of 5)	3' UTR (NM_010111, exon 5 of 5)	42066	NM_010111	13642	Mm.209813	NM_010111	ENSMUSG00000001300	Efnb2	ELF-2|Epl5|Eplg5|Htk-L|LERK-5|Lerk5|NLERK-1	ephrin B2	protein-coding
mm_5814.1	chr1	52658239	52658262	-	1	NA	3' UTR (NM_133829, exon 7 of 7)	3' UTR (NM_133829, exon 7 of 7)	27545	NM_001142647	227094	Mm.83541	NM_172654	ENSMUSG00000043015	Nemp2	5330401P04Rik|9830163O08|Tmem194b	nuclear envelope integral membrane protein 2	protein-coding
mm_18674.1	chr2	71055517	71055529	-	1	NA	promoter-TSS (NM_001165981)	promoter-TSS (NM_001165981)	83	NM_145524	228019	Mm.490343	NM_145524	ENSMUSG00000041975	Mettl8	BC004636|Tip	methyltransferase like 8	protein-coding
mm_72562.1	chr8	84084095	84084106	+	1	NA	exon (NM_009055, exon 7 of 21)	exon (NM_009055, exon 7 of 21)	-1999	NR_030490	735271		NR_030490	ENSMUSG00000076144	Mir709	Mirn709|mir-709|mmu-mir-709	microRNA 709	ncRNA
mm_122564.1	chr14	50381301	50381311	-	1	NA	Intergenic	Intergenic	-11452	NM_146666	258660	Mm.377623	NM_146666	ENSMUSG00000047716	Olfr736	MOR106-5	olfactory receptor 736	protein-coding
mm_112739.1	chr13	19336561	19336570	+	1	NA	Intergenic	Intergenic	59248	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_59249.1	chr7	24818767	24818773	+	1	NA	promoter-TSS (NR_045096)	promoter-TSS (NR_045096)	-25	NR_045096	545936	Mm.376228	NR_045096	ENSMUSG00000011350	Gm5893	EG545936|Gm477	predicted gene 5893	pseudo
mm_82919.1	chr9	35099047	35099057	-	1	NA	intron (NM_009178, intron 1 of 10)	intron (NM_009178, intron 1 of 10)	-17676	NR_029475	78934	Mm.391688	NR_029475	ENSMUSG00000070315	4930581F22Rik	-	RIKEN cDNA 4930581F22 gene	ncRNA
mm_23124.1	chr3	37654415	37654431	+	1	NA	Intergenic	Intergenic	14476	NM_001305442	24063	Mm.330986	NM_011896	ENSMUSG00000037211	Spry1	sprouty1|spry-1	sprouty homolog 1 (Drosophila)	protein-coding
mm_143917.1	chr17	85615165	85615176	-	1	NA	intron (NR_038084, intron 2 of 3)	CpG	3226	NR_038084	100043902	Mm.150838	NR_015385	ENSMUSG00000093460	Six3os1	D17Mgi26|E130112H22Rik|Rncr1|Six3os	SIX homeobox 3, opposite strand 1	ncRNA
mm_109358.1	chr12	109631926	109631928	+	1	NA	intron (NR_028261, intron 6 of 20)	intron (NR_028261, intron 6 of 20)	-4085	NR_046302	449562		NR_046302	ENSMUSG00000088294	AF357425	MBII-48	snoRNA AF357425	snoRNA
mm_25643.1	chr3	121299331	121299334	+	1	NA	intron (NM_024178, intron 2 of 3)	intron (NM_024178, intron 2 of 3)	7515	NM_024178	66789	Mm.269881	NM_024178	ENSMUSG00000039887	Alg14	5430428G01Rik|AI854024	asparagine-linked glycosylation 14	protein-coding
mm_87320.1	chr10	42860649	42860676	+	1	NA	5' UTR (NM_172938, exon 1 of 9)	5' UTR (NM_172938, exon 1 of 9)	150	NM_172938	268297	Mm.98731	NM_172938	ENSMUSG00000044770	Scml4	9330161D17|mFLJ00197	sex comb on midleg-like 4 (Drosophila)	protein-coding
mm_98352.1	chr11	93568817	93568819	+	1	NA	intron (NM_028296, intron 4 of 8)	intron (NM_028296, intron 4 of 8)	316948	NM_001013375	217109	Mm.379350	NM_001013375	ENSMUSG00000054079	Utp18	6230425C22Rik|6430513M13|Wdr50	UTP18 small subunit processome component	protein-coding
mm_58944.1	chr7	18474837	18474869	+	1	NA	3' UTR (NM_001029893, exon 5 of 5)	3' UTR (NM_001029893, exon 5 of 5)	9296	NM_001029893	574429	Mm.296754	NM_001029893	ENSMUSG00000070799	Psg26	EG574429|cea14	pregnancy-specific glycoprotein 26	protein-coding
mm_153382.1	chr19	40376819	40376823	-	1	NA	exon (NM_178362, exon 7 of 29)	exon (NM_178362, exon 7 of 29)	25489	NM_001034964	20411	Mm.210815	NM_009166	ENSMUSG00000025006	Sorbs1	2310065E01Rik|9530001P15Rik|CAP|SH3P12|Sh3d5|mKIAA1296	sorbin and SH3 domain containing 1	protein-coding
mm_153601.1	chr19	43879773	43879802	-	1	NA	promoter-TSS (NM_001306088)	promoter-TSS (NM_001306088)	-19	NM_001306088	71972	Mm.159024	NM_028029	ENSMUSG00000025195	Dnmbp	2410003L07Rik|2410003M15Rik|TUBA	dynamin binding protein	protein-coding
mm_139019.1	chr17	46109011	46109027	+	1	NA	Intergenic	B1_Mur2|SINE|Alu	-1985	NM_026768	68565	Mm.287443	NM_026768	ENSMUSG00000023967	Mrps18a	1110004O20Rik|C79712	mitochondrial ribosomal protein S18A	protein-coding
mm_78468.1	chr9	32617691	32617711	+	1	NA	Intergenic	Intergenic	-76249	NM_008026	14247	Mm.258908	NM_008026	ENSMUSG00000016087	Fli1	EWSR2|Fli-1|SIC-1|Sic1	Friend leukemia integration 1	protein-coding
mm_104982.1	chr11	100261022	100261036	-	1	NA	promoter-TSS (NM_010663)	promoter-TSS (NM_010663)	0	NM_010663	16667	Mm.14046	NM_010663	ENSMUSG00000035557	Krt17	K17|Krt1-17	keratin 17	protein-coding
mm_11529.1	chr2	32626868	32626879	+	1	NA	intron (NM_001198791, intron 1 of 6)	intron (NM_001198791, intron 1 of 6)	1436	NM_001198791	11636	Mm.29189	NM_021515	ENSMUSG00000026817	Ak1	Ak-1|B430205N08Rik	adenylate kinase 1	protein-coding
mm_71805.1	chr8	68636243	68636246	+	1	NA	intron (NM_172753, intron 2 of 9)	intron (NM_172753, intron 2 of 9)	98902	NM_001252623	234356	Mm.334569	NM_172753	ENSMUSG00000036356	Csgalnact1	4732435N03Rik|CSGalNAcT-1	chondroitin sulfate N-acetylgalactosaminyltransferase 1	protein-coding
mm_65659.1	chr7	28139790	28139803	-	1	NA	exon (NM_001164655, exon 5 of 20)	exon (NM_001164655, exon 5 of 20)	10330	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_125546.1	chr15	58432752	58432761	+	1	NA	intron (NM_145959, intron 13 of 23)	intron (NM_145959, intron 13 of 23)	17288	NM_145959	210998	Mm.3224	NM_145959	ENSMUSG00000037119	Fam91a1	AV220772|BC033609|D15Ertd621e|SKIN|mKIAA0493	family with sequence similarity 91, member A1	protein-coding
mm_29040.1	chr3	102925234	102925247	-	1	NA	exon (NM_011516, exon 9 of 33)	exon (NM_011516, exon 9 of 33)	10860	NM_011516	20957	Mm.243849	NM_011516	ENSMUSG00000027855	Sycp1	SCP1	synaptonemal complex protein 1	protein-coding
mm_164028.1	chr14	76671661	76671665	+	1	NA	Intergenic	Intergenic	-5905	NR_015485	73272	Mm.116804	NR_015485	ENSMUSG00000101009	1700108F19Rik	1700020I02Rik|BB065030	RIKEN cDNA 1700108F19 gene	ncRNA
mm_33050.1	chr4	123081036	123081052	+	1	NA	Intergenic	Intergenic	-24117	NM_007559	12164	Mm.439764	NM_007559	ENSMUSG00000002384	Bmp8b	Op3	bone morphogenetic protein 8b	protein-coding
mm_44944.1	chr5	36553323	36553358	-	1	NA	intron (NM_133910, intron 2 of 13)	intron (NM_133910, intron 2 of 13)	-22717	NM_001113364	100855	Mm.486203	NM_133910	ENSMUSG00000029192	Tbc1d14	2810413P16Rik|AU043625|C86258|D5Ertd110e|mKIAA1322	TBC1 domain family, member 14	protein-coding
mm_37565.1	chr4	126202758	126202762	-	1	NA	promoter-TSS (NM_146153)	promoter-TSS (NM_146153)	-50	NM_146153	230753	Mm.29813	NM_146153	ENSMUSG00000043962	Thrap3	9330151F09Rik|B230333E16Rik|Trap150	thyroid hormone receptor associated protein 3	protein-coding
mm_54177.1	chr6	23804604	23804609	-	1	NA	intron (NM_001252107, intron 1 of 13)	intron (NM_001252107, intron 1 of 13)	34815	NM_001252106	320405	Mm.259632	NM_153163	ENSMUSG00000017978	Cadps2	A230044C21Rik|Caps-2|Caps2|Cpd2	Ca2+-dependent activator protein for secretion 2	protein-coding
mm_13841.1	chr2	119477067	119477102	+	1	NA	intron (NM_026574, intron 1 of 35)	CpG	545	NM_026574	68142	Mm.330496	NM_026574	ENSMUSG00000034154	Ino80	2310079N15Rik|4632409L19Rik|Inoc1	INO80 complex subunit	protein-coding
mm_84242.1	chr9	62343273	62343310	-	1	NA	intron (NM_009672, intron 1 of 6)	CpG	1948	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	protein-coding
mm_41602.1	chr5	96209745	96209763	+	1	NA	promoter-TSS (NM_053158)	promoter-TSS (NM_053158)	-361	NM_001039084	94061	Mm.295499	NM_053158	ENSMUSG00000029486	Mrpl1	2410002L03Rik|5830418D04Rik|AI462572|L1mt	mitochondrial ribosomal protein L1	protein-coding
mm_26172.1	chr3	138286905	138286926	+	1	NA	exon (NM_007409, exon 6 of 9)	exon (NM_007409, exon 6 of 9)	9270	NM_007409	11522	Mm.2409	NM_007409	ENSMUSG00000074207	Adh1	ADH-AA|AI194826|Adh-1|Adh-1-t|Adh-1e|Adh-1t|Adh-3e|Adh1-e|Adh1-t|Adh1tl|Adh3-e	alcohol dehydrogenase 1 (class I)	protein-coding
mm_77405.1	chr8	120537665	120537692	-	1	NA	intron (NM_001145896, intron 1 of 15)	CpG-14578	269	NM_001145896	382034	Mm.334856	NM_198671	ENSMUSG00000031822	Gse1	2210013I18Rik|mKIAA0182	genetic suppressor element 1, coiled-coil protein	protein-coding
mm_133221.1	chr16	76337249	76337259	+	1	NA	intron (NM_173440, intron 2 of 3)	intron (NM_173440, intron 2 of 3)	35795	NM_173440	268903	Mm.74711	NM_173440	ENSMUSG00000048490	Nrip1	6030458L20Rik|8430438I05Rik|9630050P12|AA959574|AW456757|RIP140	nuclear receptor interacting protein 1	protein-coding
mm_135769.1	chr16	56831761	56831771	-	1	NA	intron (NM_019631, intron 1 of 5)	intron (NM_019631, intron 1 of 5)	-35908	NM_172825	239853	Mm.258979	NM_172825	ENSMUSG00000022755	Adgrg7	9130020O16Rik|Gpr128	adhesion G protein-coupled receptor G7	protein-coding
mm_72254.1	chr8	75095836	75095927	+	1	NA	exon (NM_010442, exon 2 of 5)	exon (NM_010442, exon 2 of 5)	2263	NM_010442	15368	Mm.276389	NM_010442	ENSMUSG00000005413	Hmox1	D8Wsu38e|HO-1|HO1|Hemox|Hmox|Hsp32	heme oxygenase 1	protein-coding
mm_61545.1	chr7	79360265	79360276	+	1	NA	3' UTR (NM_018811, exon 11 of 11)	3' UTR (NM_018811, exon 11 of 11)	26757	NM_020599	19771	Mm.41653	NM_020599	ENSMUSG00000039194	Rlbp1	3110056M11Rik|CRALBP	retinaldehyde binding protein 1	protein-coding
mm_120659.1	chr14	70544631	70544665	+	1	NA	promoter-TSS (NM_180588)	promoter-TSS (NM_180588)	-603	NM_180588	72549	Mm.46742	NM_180588	ENSMUSG00000033589	Reep4	2700029E10Rik	receptor accessory protein 4	protein-coding
mm_111735.1	chr12	103863263	103863299	-	1	NA	intron (NM_001252569, intron 1 of 5)	intron (NM_001252569, intron 1 of 5)	338	NM_001252569	20700	Mm.439692	NM_009243	ENSMUSG00000066366	Serpina1a	Aat-2|Aat2|Dom1|PI1|Spi1-1|Spi1-3	serine (or cysteine) peptidase inhibitor, clade A, member 1A	protein-coding
mm_22531.1	chr3	8509478	8509550	+	1	NA	promoter-TSS (NM_025285)	promoter-TSS (NM_025285)	-13	NM_025285	20257	Mm.29580	NM_025285	ENSMUSG00000027500	Stmn2	AI159727|SCG10|Scgn10|Stmb2	stathmin-like 2	protein-coding
mm_158368.1	chrX	135009193	135009225	-	1	NA	promoter-TSS (NM_175446)	promoter-TSS (NM_175446)	0	NM_175446	215693	Mm.336238	NM_175446	ENSMUSG00000052676	Zmat1	A230096A06|AW990744|B930008K04Rik	zinc finger, matrin type 1	protein-coding
mm_119903.1	chr14	54949428	54949456	+	1	NA	promoter-TSS (NR_029724)	promoter-TSS (NR_029724)	-300	NR_029724	387204		NR_029724	ENSMUSG00000065432	Mir208a	Mirn208|Mirn208a|mir-208|mir-208a|mmu-mir-208	microRNA 208a	ncRNA
mm_906.1	chr1	53851593	53851610	+	1	NA	exon (NM_001001883, exon 21 of 29)	exon (NM_001001883, exon 21 of 29)	2177	NR_106149	102465783		NR_106149	ENSMUSG00000098443	Mir7681	Gm27806|mmu-mir-7681	microRNA 7681	ncRNA
mm_112236.1	chr12	113482372	113482378	-	1	NA	Intergenic	Intergenic	-7190	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_168022.1	chrY	90737909	90737920	+	1	NA	Intergenic	IMPB_01|Satellite|Satellite	17136	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_19559.1	chr2	98667148	98667159	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	1199496	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_120667.1	chr14	70552191	70552230	+	1	NA	Intergenic	Intergenic	-1846	NM_021877	15460	Mm.7598	NM_021877	ENSMUSG00000022096	Hr	ALUNC|AU|N|ba|bldy|hr|rh|rh-bmh|rhino	hairless	protein-coding
mm_113565.1	chr13	38216475	38216490	+	1	NA	exon (NM_026382, exon 5 of 9)	exon (NM_026382, exon 5 of 9)	11543	NM_026382	67797	Mm.250783	NM_026382	ENSMUSG00000021431	Snrnp48	1110050F08Rik|6530403A03Rik|C6orf151	small nuclear ribonucleoprotein 48 (U11/U12)	protein-coding
mm_97820.1	chr11	82963568	82963578	+	1	NA	3' UTR (NM_183201, exon 6 of 6)	3' UTR (NM_183201, exon 6 of 6)	-2892	NR_045932	76392	Mm.295205	NR_045932	ENSMUSG00000086327	Slfn5os	1700003F17Rik	schlafen 5, opposite strand	ncRNA
mm_18456.1	chr2	60963265	60963271	-	1	NA	promoter-TSS (NM_020296)	promoter-TSS (NM_020296)	-64	NM_020296	56878	Mm.259667	NM_020296	ENSMUSG00000026970	Rbms1	2600014B10Rik|AI255215|MSSP-1|MSSP-2|MSSP-3|YC1	RNA binding motif, single stranded interacting protein 1	protein-coding
mm_61180.1	chr7	61115093	61115095	+	1	NA	Intergenic	MLTR11B|LTR|ERVK	500233	NR_045727	319752	Mm.294476	NR_045727		B230209E15Rik	-	RIKEN cDNA B230209E15 gene	ncRNA
mm_143499.1	chr17	71486337	71486361	-	1	NA	Intergenic	Intergenic	-11006	NM_028887	74355	Mm.194450	NM_028887	ENSMUSG00000024054	Smchd1	4931400A14Rik|AW554188|MommeD1|mKIAA0650	SMC hinge domain containing 1	protein-coding
mm_96766.1	chr11	69921733	69921762	+	1	NA	promoter-TSS (NM_001166592)	promoter-TSS (NM_001166592)	211	NM_001166593	276770	Mm.18026	NM_181582	ENSMUSG00000078812	Eif5a	AA410058|D19Wsu54e|Eif4d|Eif5a1|eIF-4D|eIF-5A|eIF-5A-1|eIF-5A1	eukaryotic translation initiation factor 5A	protein-coding
mm_20055.1	chr2	120314116	120314136	-	1	NA	promoter-TSS (NM_001024145)	promoter-TSS (NM_001024145)	39	NM_001024145	271844	Mm.24880	NM_001024145	ENSMUSG00000046971	Pla2g4f	4732472I07Rik|Gm647|Pla2zeta	phospholipase A2, group IVF	protein-coding
mm_132354.1	chr16	34649894	34649917	+	1	NA	Intergenic	Intergenic	-1306	NM_030744	76378	Mm.23515	NM_030744	ENSMUSG00000022832	Ropn1	1700008N21Rik|ODF6|RHPNAP1|Rppn|ropporin	ropporin, rhophilin associated protein 1	protein-coding
mm_172801.1	chr9	117371203	117371217	+	1	NA	intron (NM_001172121, intron 1 of 14)	GA-rich|Low_complexity|Low_complexity	-118727	NM_001172126	207181	Mm.326411	NM_178660	ENSMUSG00000039607	Rbms3	6720477E09Rik|8430436O14Rik	RNA binding motif, single stranded interacting protein	protein-coding
mm_65779.1	chr7	28766470	28766510	-	1	NA	promoter-TSS (NM_001122766)	promoter-TSS (NM_001122766)	154	NM_001306222	18036	Mm.220333	NM_010908	ENSMUSG00000030595	Nfkbib	I(Kappa)B(beta)|I-kappa-B-beta|IKB-beta|IKappaBbeta|IkB|IkBb|NF-kappa-BIB|ikB-B	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, beta	protein-coding
mm_8557.1	chr1	155232711	155232729	-	1	NA	Intergenic	Intergenic	74017	NM_021433	58244	Mm.66264	NM_021433	ENSMUSG00000026470	Stx6	2310039E05Rik|2410005I16Rik|AA437559|AI415714|AI845861	syntaxin 6	protein-coding
mm_71176.1	chr8	40675060	40675086	+	1	NA	promoter-TSS (NM_010086)	promoter-TSS (NM_010086)	-4	NM_010086	13526	Mm.67403	NM_010086	ENSMUSG00000046723	Adam24	Dtgn5	a disintegrin and metallopeptidase domain 24 (testase 1)	protein-coding
mm_48515.1	chr5	142822965	142823000	-	1	NA	Intergenic	Intergenic	-5595	NM_001122730	231861	Mm.354649	NM_178242	ENSMUSG00000039477	Tnrc18	BC025631|EG381742|Zfp469	trinucleotide repeat containing 18	protein-coding
mm_26977.1	chr3	25144279	25144330	-	1	NA	Intergenic	CpG	-360298	NM_001326288	635702	Mm.448351	NM_001326288	ENSMUSG00000102758	Naaladl2	2810043G22Rik|EG635702|Gm1021	N-acetylated alpha-linked acidic dipeptidase-like 2	protein-coding
mm_102150.1	chr11	53634699	53634703	-	1	NA	promoter-TSS (NM_008355)	promoter-TSS (NM_008355)	1	NM_008355	16163	Mm.1284	NM_008355	ENSMUSG00000020383	Il13	Il-13	interleukin 13	protein-coding
mm_82095.1	chr9	123056564	123056574	+	1	NA	exon (NM_177911, exon 10 of 14)	exon (NM_177911, exon 10 of 14)	21828	NM_177911	331046	Mm.195309	NM_177911	ENSMUSG00000025787	Tgm4	9530008N10Rik|Eapa1|TGP	transglutaminase 4 (prostate)	protein-coding
mm_103111.1	chr11	69981243	69981264	-	1	NA	promoter-TSS (NM_026017)	promoter-TSS (NM_026017)	-18	NM_018740	54351	Mm.13430	NM_018740	ENSMUSG00000018565	Elp5	Derp6|Rai12	elongator acetyltransferase complex subunit 5	protein-coding
mm_36499.1	chr4	83324255	83324269	-	1	NA	promoter-TSS (NM_027238)	promoter-TSS (NM_027238)	-73	NM_027238	69863	Mm.5540	NM_025782	ENSMUSG00000038172	Ttc39b	1810054D07Rik|9130422G05Rik|AI450603|AV103077|AW215585	tetratricopeptide repeat domain 39B	protein-coding
mm_130441.1	chr15	98482184	98482193	-	1	NA	exon (NM_010679, exon 2 of 4)	exon (NM_010679, exon 2 of 4)	495	NM_010679	16770	Mm.5074	NM_010679	ENSMUSG00000022991	Lalba	AW208827|Lyzg	lactalbumin, alpha	protein-coding
mm_146710.1	chr18	14682757	14682782	-	1	NA	5' UTR (NM_001161371, exon 1 of 9)	5' UTR (NM_001161371, exon 1 of 9)	145	NM_001161369	268996	Mm.31761	NM_009280	ENSMUSG00000037013	Ss18	D130059H17|Ssxt|Syt	SS18, nBAF chromatin remodeling complex subunit	protein-coding
mm_103433.1	chr11	75796049	75796081	-	1	NA	promoter-TSS (NM_007873)	promoter-TSS (NM_007873)	-5	NM_007873	13447	Mm.5137	NM_007873	ENSMUSG00000020848	Doc2b	-	double C2, beta	protein-coding
mm_84459.1	chr9	66580693	66580700	-	1	NA	intron (NM_001302116, intron 1 of 13)	B2_Mm2|SINE|B2	12419	NM_144937	235441	Mm.32465	NM_144937	ENSMUSG00000032376	Usp3	AA409661|BC017156	ubiquitin specific peptidase 3	protein-coding
mm_41819.1	chr5	103846363	103846371	+	1	NA	exon (NM_133919, exon 16 of 20)	exon (NM_133919, exon 16 of 20)	64862	NM_178741	246293	Mm.179871	NM_178741	ENSMUSG00000029312	Klhl8	2310001P09Rik|D5Ertd431e	kelch-like 8	protein-coding
mm_166606.1	chr6	68512418	68512420	+	1	NA	Intergenic	L1MC1|LINE|L1	814755	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_34908.1	chr4	155704790	155704834	+	1	NA	promoter-TSS (NM_026899)	promoter-TSS (NM_026899)	-3	NM_026899	68991	Mm.294770	NM_026899	ENSMUSG00000029038	Ssu72	1190002E22Rik|1500011L16Rik|2610101M12Rik	Ssu72 RNA polymerase II CTD phosphatase homolog (yeast)	protein-coding
mm_53098.1	chr6	125049904	125049947	+	1	NA	promoter-TSS (NM_016845)	promoter-TSS (NM_016845)	-2	NM_001127340	54137	Mm.347910	NM_016845	ENSMUSG00000072770	Acrbp	OY-TES-1|sp32	proacrosin binding protein	protein-coding
mm_2877.1	chr1	131828033	131828049	+	1	NA	promoter-TSS (NM_173865)	promoter-TSS (NM_173865)	29	NM_173865	98396	Mm.389181	NM_173865	ENSMUSG00000013275	Slc41a1	AI573938|B230315F01Rik	solute carrier family 41, member 1	protein-coding
mm_94868.1	chr11	24078230	24078268	+	1	NA	5' UTR (NM_001242934, exon 1 of 4)	5' UTR (NM_001242934, exon 1 of 4)	193	NM_001159289	14025	Mm.53687	NM_016707	ENSMUSG00000000861	Bcl11a	2810047E18Rik|BCL-11A|Ctip1|D930021L15Rik|Evi9|Evi9a|Evi9b|Evi9c|mKIAA1809	B cell CLL/lymphoma 11A (zinc finger protein)	protein-coding
mm_123885.1	chr14	72709887	72709897	-	1	NA	5' UTR (NM_207636, exon 1 of 26)	5' UTR (NM_207636, exon 1 of 26)	111	NM_207636	319448	Mm.205421	NM_207636	ENSMUSG00000033487	Fndc3a	1700094E19Rik|D14Ertd453e|F730017H24Rik|Fndc3|sys	fibronectin type III domain containing 3A	protein-coding
mm_142756.1	chr17	48794855	48794867	-	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-137721	NM_027452	70530	Mm.133607	NM_027452	ENSMUSG00000040490	Lrfn2	5730420O05Rik|SALM1|mKIAA1246	leucine rich repeat and fibronectin type III domain containing 2	protein-coding
mm_130576.1	chr15	99500126	99500148	-	1	NA	3' UTR (NM_028224, exon 12 of 12)	3' UTR (NM_028224, exon 12 of 12)	-25407	NM_029236	75284	Mm.32826	NM_029236	ENSMUSG00000037525	Bcdin3d	4930556P03Rik|AV138748	BCDIN3 domain containing	protein-coding
mm_73826.1	chr8	117459718	117459743	+	1	NA	TTS (NR_106046)	TTS (NR_106046)	465	NR_106046	102465653		NR_106046	ENSMUSG00000098483	Mir7078	Gm27386|mmu-mir-7078	microRNA 7078	ncRNA
mm_137546.1	chr17	27556943	27556963	+	1	NA	5' UTR (NM_001039356, exon 2 of 6)	5' UTR (NM_001039356, exon 2 of 6)	300	NM_001166477	111241	Mm.426212	NM_001166476	ENSMUSG00000078249	Hmga1-rs1	ENSMUSG00000041059|Hmgi-rs1	high mobility group AT-hook I, related sequence 1	protein-coding
mm_103652.1	chr11	78973081	78973093	-	1	NA	exon (NM_010708, exon 3 of 11)	exon (NM_010708, exon 3 of 11)	11837	NM_001159301	16859	Mm.341434	NM_010708	ENSMUSG00000001123	Lgals9	AA407335|AI194909|AI265545|LGALS35|Lgals5|gal-9|galectin-9	lectin, galactose binding, soluble 9	protein-coding
mm_120340.1	chr14	63606044	63606077	+	1	NA	promoter-TSS (NM_173393)	promoter-TSS (NM_173393)	-470	NM_173393	219149	Mm.32071	NM_173393	ENSMUSG00000035067	Xkr6	2700008G24Rik|BC024502|Xrg6	X-linked Kx blood group related 6	protein-coding
mm_162530.1	chr1	164136242	164136250	+	1	NA	intron (NM_011347, intron 8 of 15)	intron (NM_011347, intron 8 of 15)	-15589	NM_007976	14067	Mm.12900	NM_007976	ENSMUSG00000026579	F5	AI173222|Cf-5|Cf5	coagulation factor V	protein-coding
mm_146453.1	chr18	86395003	86395013	+	1	NA	promoter-TSS (NM_144946)	promoter-TSS (NM_144946)	56	NM_144946	246317	Mm.329578	NM_144946	ENSMUSG00000050321	Neto1	AI851453|Btcl1|C130005O10Rik	neuropilin (NRP) and tolloid (TLL)-like 1	protein-coding
mm_131842.1	chr16	22961240	22961247	+	1	NA	exon (NM_053176, exon 7 of 7)	exon (NM_053176, exon 7 of 7)	10171	NM_053176	94175	Mm.358794	NM_053176	ENSMUSG00000022877	Hrg	AI265597|AW413091|D16jh2|D18020|Hprg|Hrgp	histidine-rich glycoprotein	protein-coding
mm_36614.1	chr4	89294507	89294511	-	1	NA	promoter-TSS (NR_132431)	promoter-TSS (NR_132431)	110	NM_009877	12578	Mm.4733	NM_009877	ENSMUSG00000044303	Cdkn2a	ARF-INK4a|Arf|INK4a-ARF|Ink4a/Arf|MTS1|Pctr1|p16|p16(INK4a)|p16INK4a|p19<ARF>|p19ARF	cyclin-dependent kinase inhibitor 2A	protein-coding
mm_121780.1	chr14	19890647	19890657	-	1	NA	intron (NM_001038637, intron 4 of 4)	B4A|SINE|B4	51727	NR_105025	52512	Mm.483998	NR_105025		D14Ertd670e	-	DNA segment, Chr 14, ERATO Doi 670, expressed	ncRNA
mm_161600.1	chr16	36884962	36884962	+	1	NA	promoter-TSS (NM_030035)	promoter-TSS (NM_030035)	-49	NM_030035	224139	Mm.244815	NM_030035	ENSMUSG00000034243	Golgb1	4930428L02Rik|628101|6330407A06Rik|AU042952|C130074L01Rik|F730017E11Rik|Gm6840|mKIAA4151	golgi autoantigen, golgin subfamily b, macrogolgin 1	protein-coding
mm_97881.1	chr11	83226042	83226070	+	1	NA	non-coding (NR_015519, exon 4 of 4)	non-coding (NR_015519, exon 4 of 4)	2480	NR_015519	100043636	Mm.295569	NR_015519	ENSMUSG00000087107	AI662270	AW496474	expressed sequence AI662270	ncRNA
mm_127730.1	chr15	103272894	103272907	+	1	NA	promoter-TSS (NM_019817)	promoter-TSS (NM_019817)	-18	NM_019817	56447	Mm.29473	NM_019817	ENSMUSG00000060992	Copz1	5930435A22Rik|AA407760|D4Ertd360e	coatomer protein complex, subunit zeta 1	protein-coding
mm_172032.1	chr6	124712518	124712528	+	1	NA	promoter-TSS (NM_013536)	promoter-TSS (NM_013536)	234	NM_007531	12034	Mm.36241	NM_007531	ENSMUSG00000004264	Phb2	AU044498|BAP|Bap37|Bcap37|REA	prohibitin 2	protein-coding
mm_101832.1	chr11	47379406	47379414	-	1	NA	promoter-TSS (NM_011891)	promoter-TSS (NM_011891)	-108	NM_011891	24052	Mm.338890	NM_011891	ENSMUSG00000020354	Sgcd	35kDa|delta-SG	sarcoglycan, delta (dystrophin-associated glycoprotein)	protein-coding
mm_69828.1	chr7	141269947	141269957	-	1	NA	exon (NM_028069, exon 13 of 14)	exon (NM_028069, exon 13 of 14)	-3528	NM_001252600	54123	Mm.3233	NM_016850	ENSMUSG00000025498	Irf7	-	interferon regulatory factor 7	protein-coding
mm_83164.1	chr9	40489678	40489686	-	1	NA	Intergenic	Intergenic	-33918	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_99726.1	chr11	106300776	106300779	+	1	NA	exon (NM_008117, exon 4 of 5)	exon (NM_008117, exon 4 of 5)	1119	NM_008117	14599	Mm.343934	NM_008117	ENSMUSG00000020713	Gh	Gh1|Ghb1	growth hormone	protein-coding
mm_34599.1	chr4	150236803	150236809	+	1	NA	promoter-TSS (NM_001025388).2	promoter-TSS (NM_001025388).2	-391	NM_023119	13806	Mm.70666	NM_023119	ENSMUSG00000063524	Eno1	0610008I15|AL022784|Eno-1|MBP-1	enolase 1, alpha non-neuron	protein-coding
mm_48142.1	chr5	137150427	137150441	-	1	NA	Intergenic	Intergenic	-34227	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_94529.1	chr11	9117999	9118017	+	1	NA	promoter-TSS (NM_009477)	promoter-TSS (NM_009477)	0	NM_001159401	22271	Mm.4610	NM_009477	ENSMUSG00000020407	Upp1	AI325217|UPase|UdRPase|Up|Upp	uridine phosphorylase 1	protein-coding
mm_64161.1	chr7	141360237	141360247	+	1	NA	non-coding (NR_033532, exon 2 of 2)	non-coding (NR_033532, exon 2 of 2)	4868	NR_033532	320871	Mm.475463	NM_177280	ENSMUSG00000086844	B230206H07Rik	-	RIKEN cDNA B230206H07 gene	ncRNA
mm_80267.1	chr9	72958813	72958850	+	1	NA	promoter-TSS (NM_001163725)	promoter-TSS (NM_001163725)	46	NM_001163725	67685	Mm.31817	NM_026314	ENSMUSG00000089865	Dyx1c1	1700010I24Rik|Dnaaf4|EKN1|b2b811.1Clo|b2b811Clo	dyslexia susceptibility 1 candidate 1	protein-coding
mm_59585.1	chr7	28129637	28129638	+	1	NA	intron (NM_001164655, intron 1 of 19)	intron (NM_001164655, intron 1 of 19)	171	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_60877.1	chr7	46098826	46098842	+	1	NA	exon (NM_001204411, exon 2 of 2)	exon (NM_001204411, exon 2 of 2)	1403	NM_010602	16514	Mm.333863	NM_010602	ENSMUSG00000096146	Kcnj11	Kir6.2|mBIR	potassium inwardly rectifying channel, subfamily J, member 11	protein-coding
mm_95883.1	chr11	58103971	58104027	+	1	NA	promoter-TSS (NM_026949)	promoter-TSS (NM_026949)	-154	NM_026949	69125	Mm.28910	NM_026949	ENSMUSG00000020515	Cnot8	1500015I04Rik|1810022F04Rik|AA536816|AU015770|AU043059	CCR4-NOT transcription complex, subunit 8	protein-coding
mm_164858.1	chr18	52906403	52906405	+	1	NA	intron (NM_001199154, intron 9 of 10)	intron (NM_001199154, intron 9 of 10)	-3757	NR_035420	100316749		NR_035420	ENSMUSG00000080573	Mir467f	Mirn467f|mmu-mir-467f	microRNA 467f	ncRNA
mm_74737.1	chr8	18741543	18741566	-	1	NA	promoter-TSS (NM_007426)	promoter-TSS (NM_007426)	8	NM_007426	11601	Mm.439874	NM_007426	ENSMUSG00000031465	Angpt2	Agpt2|Ang-2|Ang2	angiopoietin 2	protein-coding
mm_159035.1	chr1	177991483	177991483	+	1	NA	promoter-TSS (NM_001034899)	promoter-TSS (NM_001034899)	48	NM_001034899	545391	Mm.442974	NM_001034899	ENSMUSG00000091476	Gm16432	EG545391|EG666250	predicted gene 16432	protein-coding
mm_172665.1	chr8	43180237	43180237	-	1	NA	Intergenic	B1F|SINE|Alu	-2885	NM_001160412	622117	Mm.390031	NM_001160412	ENSMUSG00000091490	Triml2	EG622117|Tu4	tripartite motif family-like 2	protein-coding
mm_155364.1	chrX	71079940	71079946	+	1	NA	intron (NM_001081354, intron 1 of 6)	Charlie4a|DNA|hAT-Charlie	29687	NM_001081354	333639	Mm.371730	NM_001081354	ENSMUSG00000059401	Mamld1	G630014P10Rik	mastermind-like domain containing 1	protein-coding
mm_84286.1	chr9	62987894	62987898	-	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-7017	NM_019663	56469	Mm.431253	NM_019663	ENSMUSG00000032405	Pias1	2900068C24Rik|Ddxbp1|GBP	protein inhibitor of activated STAT 1	protein-coding
mm_41646.1	chr5	98186174	98186182	+	1	NA	exon (NM_029947, exon 4 of 4)	exon (NM_029947, exon 4 of 4)	5309	NM_029947	77630	Mm.332511	NM_029947	ENSMUSG00000035456	Prdm8	4930565F05Rik|PFM5	PR domain containing 8	protein-coding
mm_78910.1	chr9	44980537	44980558	+	1	NA	promoter-TSS (NM_009850)	promoter-TSS (NM_009850)	-116	NM_009850	12502	Mm.335106	NM_009850	ENSMUSG00000002033	Cd3g	Ctg-3|Ctg3|T3g	CD3 antigen, gamma polypeptide	protein-coding
mm_105062.1	chr11	100716013	100716053	-	1	NA	3' UTR (NM_001305003, exon 6 of 6)	3' UTR (NM_001305003, exon 6 of 6)	2183	NM_029307	75482	Mm.46175	NM_029307	ENSMUSG00000017832	Hspb9	1700007H20Rik	heat shock protein, alpha-crystallin-related, B9	protein-coding
mm_116077.1	chr13	28364316	28364321	-	1	NA	Intergenic	Intergenic	221834	NM_023746	28078	Mm.155058	NM_023746	ENSMUSG00000017064	Prl5a1	1600013P04Rik|D13Wsu14e|Ghd24|PLP-L|Prlpl	prolactin family 5, subfamily a, member 1	protein-coding
mm_140545.1	chr17	6827842	6827882	-	1	NA	Intergenic	CpG	-45082	NM_009510	22350	Mm.277812	NM_009510	ENSMUSG00000052397	Ezr	AW146364|R75297|Vil2|p81	ezrin	protein-coding
mm_25699.1	chr3	122294151	122294160	+	1	NA	promoter-TSS (NR_030439)	promoter-TSS (NR_030439)	-452	NR_030439	791077		NR_030439	ENSMUSG00000076456	Mir760	Mirn760|mir-760|mmu-mir-760	microRNA 760	ncRNA
mm_159738.1	chr5	66098065	66098065	-	1	NA	intron (NM_001127382, intron 2 of 7)	intron (NM_001127382, intron 2 of 7)	114	NM_139065	245945	Mm.36863	NM_139065	ENSMUSG00000070780	Rbm47	9530077J19Rik	RNA binding motif protein 47	protein-coding
mm_30942.1	chr4	33045175	33045188	+	1	NA	exon (NM_019586, exon 7 of 8)	exon (NM_019586, exon 7 of 8)	13756	NM_019586	56228	Mm.259095	NM_019586	ENSMUSG00000028277	Ube2j1	0710008M05Rik|1110030I22Rik|NCUBE-1|Ncube|Ncube1|Ubc6p	ubiquitin-conjugating enzyme E2J 1	protein-coding
mm_32806.1	chr4	117124528	117124551	+	1	NA	non-coding (NR_024078, exon 2 of 7)	non-coding (NR_024078, exon 2 of 7)	1186	NR_024078	78611	Mm.446227	NM_001033187		Btbd19	9530048O09Rik|BB115071	BTB (POZ) domain containing 19	ncRNA
mm_130952.1	chr15	103255391	103255397	-	1	NA	promoter-TSS (NM_008685)	promoter-TSS (NM_008685)	45	NM_008685	18022	Mm.457989	NM_008685	ENSMUSG00000058794	Nfe2	NF-E2|NF-E2/P45|p45|p45NFE2|p45nf-e2	nuclear factor, erythroid derived 2	protein-coding
mm_163663.1	chr13	76803717	76803718	+	1	NA	intron (NM_030174, intron 9 of 20)	intron (NM_030174, intron 9 of 20)	331751	NM_134071	105377	Mm.209730	NM_134071	ENSMUSG00000021597	Slf1	2700017A04Rik|AW545819|Ankrd32|Brctd1|Brctx|C730024G01Rik	SMC5-SMC6 complex localization factor 1	protein-coding
mm_117037.1	chr13	58275648	58275651	-	1	NA	Intergenic	B4|SINE|B4	-1461	NM_019832	56278	Mm.296625	NM_019832	ENSMUSG00000021552	Gkap1	42kDa|4933400B15Rik|D13Ertd340e|Gkap42	G kinase anchoring protein 1	protein-coding
mm_112652.1	chr13	16021674	16021693	+	1	NA	intron (NM_008380, intron 4 of 4)	intron (NM_008380, intron 4 of 4)	9832	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_96426.1	chr11	67257234	67257249	+	1	NA	exon (NM_010855, exon 35 of 40)	exon (NM_010855, exon 35 of 40)	19429	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_60384.1	chr7	44473902	44473936	+	1	NA	Intergenic	IMPB_01|Satellite|Satellite	3572	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_170139.1	chr17	39848338	39848344	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	5344	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_88434.1	chr10	77530560	77530571	+	1	NA	intron (NM_008404, intron 1 of 15)	intron (NM_008404, intron 1 of 15)	217	NM_008404	16414	Mm.1137	NM_008404	ENSMUSG00000000290	Itgb2	2E6|AI528527|Cd18|LAD|LCAMB|Lfa1|MF17	integrin beta 2	protein-coding
mm_81017.1	chr9	104263224	104263243	+	1	NA	promoter-TSS (NM_001163026)	promoter-TSS (NM_001163026)	-303	NM_001163026	235567	Mm.217256	NM_001163026	ENSMUSG00000032560	Dnajc13	D030002L11Rik|Gm1124|RME-8|Rme8|mKIAA0678	DnaJ heat shock protein family (Hsp40) member C13	protein-coding
mm_99116.1	chr11	100141001	100141013	+	1	NA	exon (NM_008471, exon 6 of 6)	exon (NM_008471, exon 6 of 6)	2692	NM_001313963	16669	Mm.439699	NM_008471	ENSMUSG00000020911	Krt19	AI663979|CK-19|EndoC|K19|Krt-1.19|Krt1-19	keratin 19	protein-coding
mm_2566.1	chr1	118389424	118389465	+	1	NA	5' UTR (NM_029709, exon 1 of 37)	5' UTR (NM_029709, exon 1 of 37)	386	NM_001293301	76707	Mm.138740	NM_029709	ENSMUSG00000064302	Clasp1	1700030C23Rik|5730583A19Rik|B130045P17Rik|CLASP1alpha	CLIP associating protein 1	protein-coding
mm_151796.1	chr19	5415790	5415793	-	1	NA	non-coding (NR_015545, exon 3 of 5)	non-coding (NR_015545, exon 3 of 5)	8976	NR_027938	74931	Mm.388511	NR_015545	ENSMUSG00000086938	4930481A15Rik	-	RIKEN cDNA 4930481A15 gene	ncRNA
mm_112666.1	chr13	16027198	16027222	+	1	NA	3' UTR (NM_008380, exon 5 of 5)	3' UTR (NM_008380, exon 5 of 5)	15359	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_83708.1	chr9	50728231	50728251	-	1	NA	promoter-TSS (NM_178118)	promoter-TSS (NM_178118)	-257	NM_178118	330938	Mm.82598	NM_178118	ENSMUSG00000032064	Dixdc1	4930563F16Rik|BC048182|Ccd1|Ccd1Aalpha1L|Ccd1Abeta1L|Ccd1BalphaL|Ccd1BbetaL|Ccd1CL|mKIAA1735	DIX domain containing 1	protein-coding
mm_26939.1	chr3	20265146	20265148	-	1	NA	intron (NM_029706, intron 6 of 10)	intron (NM_029706, intron 6 of 10)	10586	NM_029706	76703	Mm.34692	NM_029706	ENSMUSG00000011463	Cpb1	0910001A18Rik|1810063F02Rik|2210008M23Rik|AI504870	carboxypeptidase B1 (tissue)	protein-coding
mm_110089.1	chr12	25094529	25094530	-	1	NA	3' UTR (NM_010496, exon 3 of 3)	3' UTR (NM_010496, exon 3 of 3)	1563	NM_010496	15902	Mm.34871	NM_010496	ENSMUSG00000020644	Id2	AI255428|C78922|Idb2|bHLHb26	inhibitor of DNA binding 2	protein-coding
mm_3263.1	chr1	136345117	136345120	+	1	NA	intron (NM_001347110, intron 1 of 16)	intron (NM_001347110, intron 1 of 16)	986	NM_001081360	67886	Mm.144143	NM_001081360	ENSMUSG00000041570	Camsap2	1600013L13Rik|4930541M15Rik|Camsap1l1|mKIAA1078	calmodulin regulated spectrin-associated protein family, member 2	protein-coding
mm_162372.1	chr1	67212986	67212987	+	1	NA	intron (NM_001080809, intron 30 of 37)	intron (NM_001080809, intron 30 of 37)	89959	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_140104.1	chr17	78508211	78508217	+	1	NA	5' UTR (NM_001197028, exon 1 of 13)	5' UTR (NM_001197028, exon 1 of 13)	151	NM_028813	74199	Mm.292983	NM_028813	ENSMUSG00000024076	Vit	1700052E02Rik|1700110E08Rik|2810429K11Rik	vitrin	protein-coding
mm_92390.1	chr10	76596451	76596484	-	1	NA	exon (NM_146007, exon 28 of 28)	exon (NM_146007, exon 28 of 28)	20819	NM_080845	14317	Mm.36278	NM_080845	ENSMUSG00000001155	Ftcd	-	formiminotransferase cyclodeaminase	protein-coding
mm_1700.1	chr1	75147299	75147318	+	1	NA	3' UTR (NM_170755, exon 9 of 9)	3' UTR (NM_170755, exon 9 of 9)	4150	NM_001305232	227298	Mm.273062	NM_170755	ENSMUSG00000049339	Fam134a	-	family with sequence similarity 134, member A	protein-coding
mm_144722.1	chr18	35130644	35130646	+	1	NA	intron (NM_009818, intron 1 of 17)	intron (NM_009818, intron 1 of 17)	11733	NM_009818	12385	Mm.18962	NM_009818	ENSMUSG00000037815	Ctnna1	2010010M04Rik|AA517462|AI988031|Catna1	catenin (cadherin associated protein), alpha 1	protein-coding
mm_157940.1	chrX	85775620	85775622	-	1	NA	intron (NM_001331046, intron 1 of 19)	PB1D10|SINE|Alu	1198	NM_001294140	14933	Mm.246682	NM_008194	ENSMUSG00000025059	Gk	D930012N15Rik|Gyk	glycerol kinase	protein-coding
mm_63142.1	chr7	123143748	123143760	+	1	NA	exon (NM_144925, exon 3 of 24)	exon (NM_144925, exon 3 of 24)	19869	NM_144925	233833	Mm.102305	NM_144925	ENSMUSG00000052707	Tnrc6a	2010321I05Rik|3110054G10Rik|AW557223|CAGH26|D130023A07Rik|GW182|Tnrc6	trinucleotide repeat containing 6a	protein-coding
mm_157760.1	chrX	73495173	73495196	-	1	NA	3' UTR (NM_007542, exon 8 of 8)	3' UTR (NM_007542, exon 8 of 8)	-7902	NM_001310537	320707	Mm.210095	NM_177236	ENSMUSG00000031376	Atp2b3	6430519O13Rik|Pmca3	ATPase, Ca++ transporting, plasma membrane 3	protein-coding
mm_887.1	chr1	52684731	52684735	+	1	NA	intron (NM_178081, intron 2 of 5)	intron (NM_178081, intron 2 of 5)	42585	NM_178081	98682	Mm.491173	NM_133829	ENSMUSG00000041439	Mfsd6	2210010L05Rik|9630025I22Rik|AI836200|AW212394|MMR2	major facilitator superfamily domain containing 6	protein-coding
mm_165041.1	chr19	39025843	39025849	+	1	NA	intron (NM_028089, intron 4 of 8)	intron (NM_028089, intron 4 of 8)	18827	NM_028089	72082	Mm.142581	NM_028089	ENSMUSG00000025002	Cyp2c55	2010318C06Rik	cytochrome P450, family 2, subfamily c, polypeptide 55	protein-coding
mm_48431.1	chr5	140621399	140621430	-	1	NA	3' UTR (NM_175274, exon 14 of 14)	3' UTR (NM_175274, exon 14 of 14)	14073	NM_008494	16848	Mm.12834	NM_008494	ENSMUSG00000029570	Lfng	AW061165	LFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	protein-coding
mm_108216.1	chr12	77057235	77057258	+	1	NA	Intergenic	B3|SINE|B2	-94998	NM_001146176	17187	Mm.268548	NM_008558	ENSMUSG00000059436	Max	AA960152|AI875693|bHLHd4|bHLHd5|bHLHd6|bHLHd7|bHLHd8	Max protein	protein-coding
mm_106225.1	chr11	117114982	117114998	-	1	NA	promoter-TSS (NM_001166506)	promoter-TSS (NM_001166506)	-182	NR_029459	74136	Mm.272312	NM_028777	ENSMUSG00000020823	Sec14l1	1200017E04Rik|2810012L19Rik|Naa-35	SEC14-like lipid binding 1	protein-coding
mm_62502.1	chr7	102019153	102019153	+	1	NA	promoter-TSS (NM_010531)	promoter-TSS (NM_010531)	-998	NM_010531	16068	Mm.422756	NM_010531	ENSMUSG00000070427	Il18bp	IL-18BP|Igifbp|MC54L	interleukin 18 binding protein	protein-coding
mm_122951.1	chr14	54967219	54967222	-	1	NA	promoter-TSS (NM_010856)	promoter-TSS (NM_010856)	-613	NM_010856	17888	Mm.290003	NM_010856	ENSMUSG00000040752	Myh6	A830009F23Rik|AA517445|Myhc-a|Myhca|alpha-MHC	myosin, heavy polypeptide 6, cardiac muscle, alpha	protein-coding
mm_86995.1	chr10	26608095	26608095	+	1	NA	Intergenic	B4A|SINE|B4	66556	NR_033633	667572	Mm.482728	NR_033633	ENSMUSG00000098179	Gm8709	EG667572	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_98680.1	chr11	96285594	96285627	+	1	NA	TTS (NM_010461)	TTS (NM_010461)	-1036	NM_010460	15415	Mm.390366	NM_010460	ENSMUSG00000038721	Hoxb7	AI325018|Hox-2.3	homeobox B7	protein-coding
mm_84559.1	chr9	67733756	67733764	-	1	NA	Intergenic	Intergenic	-4183	NR_106101	102465716		NR_106101	ENSMUSG00000098446	Mir7242	Gm27809|mmu-mir-7242	microRNA 7242	ncRNA
mm_170805.1	chr2	175737904	175737923	+	1	NA	promoter-TSS (NM_001099349).2	promoter-TSS (NM_001099349).2	-29	NM_001256480	100043915	Mm.466613	NM_001256480	ENSMUSG00000078897	Gm4724	-	predicted gene 4724	protein-coding
mm_41919.1	chr5	105607348	105607372	+	1	NA	exon (NM_133897, exon 4 of 4)	exon (NM_133897, exon 4 of 4)	87889	NM_133897	100604	Mm.319847	NM_133897	ENSMUSG00000054720	Lrrc8c	AD158|AI326115|E430036I04Rik|fad158	leucine rich repeat containing 8 family, member C	protein-coding
mm_154526.1	chrM	13487	13509	-	1	NA	NA	Intergenic	NA	NA								
mm_121096.1	chr14	99313330	99313375	+	1	NA	TTS (NM_009769)	TTS (NM_009769)	14661	NM_009769	12224	Mm.30262	NM_009769	ENSMUSG00000005148	Klf5	4930520J07Rik|Bteb2|CKLF|IKLF	Kruppel-like factor 5	protein-coding
mm_35671.1	chr4	43578570	43578587	-	1	NA	promoter-TSS (NM_172866)	promoter-TSS (NM_172866)	-157	NM_172866	242406	Mm.259311	NM_172866	ENSMUSG00000028468	Rgp1	1110029E03Rik|AI527196|F730001J03|mKIAA0258	RAB6A GEF compex partner 1	protein-coding
mm_79391.1	chr9	54863721	54863740	+	1	NA	promoter-TSS (NM_022655)	promoter-TSS (NM_022655)	-25	NM_022655	64602	Mm.208991	NM_022655	ENSMUSG00000032293	Ireb2	D9Ertd85e|Irp2	iron responsive element binding protein 2	protein-coding
mm_72501.1	chr8	83740616	83740620	+	1	NA	intron (NM_001163031, intron 1 of 17)	B3|SINE|B2	693	NM_001163029	26364	Mm.334648	NM_011925	ENSMUSG00000002885	Adgre5	AA409984|Cd97|TM7LN1	adhesion G protein-coupled receptor E5	protein-coding
mm_103975.1	chr11	84819451	84819471	-	1	NA	promoter-TSS (NM_145433)	promoter-TSS (NM_145433)	54	NM_145433	217038	Mm.280825	NM_145433	ENSMUSG00000018405	Mrm1	A530065E19Rik|ENSMUSG00000054212	mitochondrial rRNA methyltransferase 1	protein-coding
mm_62064.1	chr7	92561142	92561210	+	1	NA	promoter-TSS (NM_025515)	promoter-TSS (NM_025515)	27	NM_001162918	66365	Mm.21173	NM_025515	ENSMUSG00000030613	Ccdc90b	2310015N07Rik|C86558	coiled-coil domain containing 90B	protein-coding
mm_135695.1	chr16	52442292	52442299	-	1	NA	intron (NM_009655, intron 1 of 15)	intron (NM_009655, intron 1 of 15)	10786	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_59896.1	chr7	30307362	30307378	+	1	NA	3' UTR (NM_001081114, exon 14 of 14)	3' UTR (NM_001081114, exon 14 of 14)	-1383	NM_198027	233065	Mm.276277	NM_198027	ENSMUSG00000042831	Alkbh6	AI839550|Abh6|C130099A02	alkB homolog 6	protein-coding
mm_24110.1	chr3	88142703	88142745	+	1	NA	intron (NM_133665, intron 1 of 10)	CpG	352	NM_001310593	17261	Mm.28184	NM_133665	ENSMUSG00000001419	Mef2d	C80750	myocyte enhancer factor 2D	protein-coding
mm_29436.1	chr3	109768837	109768846	-	1	NA	Intergenic	Intergenic	194834	NM_146139	57257	Mm.282257	NM_020505	ENSMUSG00000033721	Vav3	A530094I06Rik|AA986410|Idd18.1	vav 3 oncogene	protein-coding
mm_134675.1	chr16	22406049	22406060	-	1	NA	intron (NM_023794, intron 7 of 12)	MIRb|SINE|MIR	33516	NM_023794	104156	Mm.155708	NM_023794	ENSMUSG00000013089	Etv5	1110005E01Rik|8430401F14Rik|ERM	ets variant 5	protein-coding
mm_140529.1	chr17	6746814	6746820	-	1	NA	intron (NM_009510, intron 7 of 12)	intron (NM_009510, intron 7 of 12)	35963	NM_009510	22350	Mm.277812	NM_009510	ENSMUSG00000052397	Ezr	AW146364|R75297|Vil2|p81	ezrin	protein-coding
mm_28653.1	chr3	95229482	95229508	-	1	NA	promoter-TSS (NM_019914)	promoter-TSS (NM_019914)	552	NM_001038708	57912	Mm.28189	NM_172395	ENSMUSG00000046722	Cdc42se1	1300002M12Rik|AW558204|Cdcse1|SCIP1|Spec1	CDC42 small effector 1	protein-coding
mm_112509.1	chr13	8885898	8885935	+	1	NA	exon (NM_145360, exon 1 of 5)	exon (NM_145360, exon 1 of 5)	310	NM_145360	319554	Mm.29847	NM_145360	ENSMUSG00000058258	Idi1	4832416K17Rik	isopentenyl-diphosphate delta isomerase	protein-coding
mm_111138.1	chr12	81594965	81595020	-	1	NA	promoter-TSS (NM_027213)	promoter-TSS (NM_027213)	16	NM_001347385	69792	Mm.279993	NM_027213	ENSMUSG00000002679	Med6	1500012F11Rik|AU019660|AV213303	mediator complex subunit 6	protein-coding
mm_88575.1	chr10	79682170	79682230	+	1	NA	promoter-TSS (NM_177613)	promoter-TSS (NM_177613)	5	NM_177613	216150	Mm.21981	NM_177613	ENSMUSG00000020307	Cdc34	AI327276|UBE2R1	cell division cycle 34	protein-coding
mm_43145.1	chr5	125454355	125454416	+	1	NA	exon (NM_029752, exon 3 of 3)	exon (NM_029752, exon 3 of 3)	12817	NM_029752	76809	Mm.290720	NM_029752	ENSMUSG00000037905	Bri3bp	2410150I18Rik|AI841257|AW742481	Bri3 binding protein	protein-coding
mm_121858.1	chr14	20668270	20668324	-	1	NA	promoter-TSS (NM_175132)	promoter-TSS (NM_175132)	57	NM_175132	68760	Mm.35789	NM_175132	ENSMUSG00000039376	Synpo2l	1110054M18Rik|Chap	synaptopodin 2-like	protein-coding
mm_114414.1	chr13	64364164	64364175	+	1	NA	exon (NM_009984, exon 8 of 8)	exon (NM_009984, exon 8 of 8)	6351	NM_009984	13039	Mm.930	NM_009984	ENSMUSG00000021477	Ctsl	1190035F06Rik|CatL|Ctsl1|MEP|fs|nkt	cathepsin L	protein-coding
mm_44732.1	chr5	31093501	31093526	-	1	NA	promoter-TSS (NM_011773)	promoter-TSS (NM_011773)	14	NM_011773	22784	Mm.1396	NM_011773	ENSMUSG00000029151	Slc30a3	Znt3	solute carrier family 30 (zinc transporter), member 3	protein-coding
mm_46379.1	chr5	103967042	103967046	-	1	NA	exon (NM_001163486, exon 5 of 7)	exon (NM_001163486, exon 5 of 7)	10344	NM_198030	243168	Mm.284944	NM_198030	ENSMUSG00000034528	Hsd17b13	AI047820|PAN1B-like|Pan1b	hydroxysteroid (17-beta) dehydrogenase 13	protein-coding
mm_142644.1	chr17	47437366	47437391	-	1	NA	promoter-TSS (NM_029296)	promoter-TSS (NM_029296)	-3	NM_029296	75462	Mm.46129	NM_029296	ENSMUSG00000047150	1700001C19Rik	-	RIKEN cDNA 1700001C19 gene	protein-coding
mm_54812.1	chr6	42324649	42324671	-	1	NA	promoter-TSS (NM_001113327)	promoter-TSS (NM_001113327)	-20	NM_029528	76156	Mm.234314	NM_029528	ENSMUSG00000029861	Fam131b	6330503C03Rik|6530406I18Rik|AV277466	family with sequence similarity 131, member B	protein-coding
mm_18265.1	chr2	52308523	52308547	-	1	NA	exon (NM_010889, exon 15 of 157)	exon (NM_010889, exon 15 of 157)	17533	NR_040620	78049	Mm.243883	NR_040620		4930573O16Rik	-	RIKEN cDNA 4930573O16 gene	ncRNA
mm_143118.1	chr17	57209435	57209503	-	1	NA	exon (NM_009778, exon 32 of 41)	exon (NM_009778, exon 32 of 41)	7759	NR_105944	102465591		NR_105944	ENSMUSG00000099066	Mir6978	Gm27858|mmu-mir-6978	microRNA 6978	ncRNA
mm_148526.1	chr19	4510499	4510508	+	1	NA	promoter-TSS (NM_001162946)	promoter-TSS (NM_001162946)	31	NM_001162946	18563	Mm.1845	NM_008797	ENSMUSG00000024892	Pcx	Pc|Pcb	pyruvate carboxylase	protein-coding
mm_152281.1	chr19	8880833	8880854	-	1	NA	promoter-TSS (NM_001160356)	promoter-TSS (NM_001160356)	90	NM_001160356	107197	Mm.381181	NM_001160356	ENSMUSG00000071654	Uqcc3	AI462493|Cbp4	ubiquinol-cytochrome c reductase complex assembly factor 3	protein-coding
mm_155440.1	chrX	73494816	73494834	+	1	NA	3' UTR (NM_007542, exon 8 of 8)	3' UTR (NM_007542, exon 8 of 8)	-8261	NM_001310537	320707	Mm.210095	NM_177236	ENSMUSG00000031376	Atp2b3	6430519O13Rik|Pmca3	ATPase, Ca++ transporting, plasma membrane 3	protein-coding
mm_19403.1	chr2	91636460	91636462	-	1	NA	promoter-TSS (NM_010168)	promoter-TSS (NM_010168)	-4	NM_010168	14061	Mm.89048	NM_010168	ENSMUSG00000027249	F2	Cf-2|Cf2|FII	coagulation factor II	protein-coding
mm_79523.1	chr9	57589486	57589498	+	1	NA	promoter-TSS (NM_027895)	promoter-TSS (NM_027895)	40	NM_027895	71742	Mm.155877	NM_027895	ENSMUSG00000032308	Ulk3	1200015E14Rik	unc-51-like kinase 3	protein-coding
mm_93947.1	chr10	127242799	127242809	-	1	NA	exon (NM_001039000, exon 11 of 29)	exon (NM_001039000, exon 11 of 29)	20559	NM_008447	16572	Mm.30355	NM_008447	ENSMUSG00000074657	Kif5a	D10Bwg0738e|Khc|Kif5|Kns|mKIAA4086	kinesin family member 5A	protein-coding
mm_32565.1	chr4	109676711	109676740	+	1	NA	promoter-TSS (NM_007983)	promoter-TSS (NM_007983)	98	NM_007983	14084	Mm.318259	NM_007983	ENSMUSG00000010517	Faf1	AA408698|Dffrx|Fam	Fas-associated factor 1	protein-coding
mm_38428.1	chr4	139291750	139291759	-	1	NA	TTS (NM_001271405)	TTS (NM_001271405)	18946	NM_145384	212555	Mm.45131	NM_145384	ENSMUSG00000028744	Pqlc2	BC019216	PQ loop repeat containing 2	protein-coding
mm_141047.1	chr17	25433612	25433621	-	1	NA	5' UTR (NM_021415, exon 1 of 35)	5' UTR (NM_021415, exon 1 of 35)	167	NM_021415	58226	Mm.268378	NM_021415	ENSMUSG00000024112	Cacna1h	Cav3.2|MNCb-1209|alpha13.2	calcium channel, voltage-dependent, T type, alpha 1H subunit	protein-coding
mm_147784.1	chr18	61628155	61628190	-	1	NA	Intergenic	Intergenic	-11481	NR_045420	545261	Mm.426593	NR_045420	ENSMUSG00000098098	Bvht	Braveheart|Gm20748	braveheart long non-coding RNA	ncRNA
mm_170620.1	chr1	96439767	96439767	+	1	NA	Intergenic	Intergenic	222806	NR_040478	75159	Mm.243854	NR_040478	ENSMUSG00000100589	4930533P14Rik	-	RIKEN cDNA 4930533P14 gene	ncRNA
mm_21027.1	chr2	152414740	152414755	-	1	NA	promoter-TSS (NM_177656)	promoter-TSS (NM_177656)	297	NM_175126	67917	Mm.391810	NM_175126	ENSMUSG00000074682	Zcchc3	2810406K24Rik	zinc finger, CCHC domain containing 3	protein-coding
mm_7805.1	chr1	131526557	131526590	-	1	NA	intron (NM_001081011, intron 1 of 22)	CpG	788	NM_001081011	14270	Mm.276259	NM_019520	ENSMUSG00000026425	Srgap2	9930124L22Rik|AI448945|FBP2|Fnbp2|srGAP3	SLIT-ROBO Rho GTPase activating protein 2	protein-coding
mm_172631.1	chr8	20424781	20424793	-	1	NA	promoter-TSS (NR_028428)	promoter-TSS (NR_028428)	27	NR_028428	381598	Mm.359054	NM_001024708	ENSMUSG00000071793	2610005L07Rik	2810038F24Rik|6720476A01Rik	cadherin 11 pseudogene	pseudo
mm_8532.1	chr1	155051300	155051306	-	1	NA	Intergenic	MIRc|SINE|MIR	48333	NM_010500	15939	Mm.12246	NM_010500	ENSMUSG00000056708	Ier5	-	immediate early response 5	protein-coding
mm_168182.1	chr10	59382020	59382024	+	1	NA	Intergenic	IAPLTR1_Mm|LTR|ERVK	-21663	NM_023530	69836	Mm.30268	NM_023530	ENSMUSG00000009646	Pla2g12b	2010002E04Rik|Fksg71|Pla2g13|hlb218	phospholipase A2, group XIIB	protein-coding
mm_46981.1	chr5	115298775	115298793	-	1	NA	exon (NM_019682, exon 3 of 3)	exon (NM_019682, exon 3 of 3)	2206	NM_019682	56455	Mm.256858	NM_019682	ENSMUSG00000009013	Dynll1	Dlc8|Dnclc1|Pin	dynein light chain LC8-type 1	protein-coding
mm_118711.1	chr14	22184486	22184508	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	164785	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_52641.1	chr6	117178696	117178707	+	1	NA	3' UTR (NM_001012477, exon 4 of 4)	3' UTR (NM_001012477, exon 4 of 4)	10166	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_33261.1	chr4	127195232	127195262	+	1	NA	exon (NM_198618, exon 3 of 12)	exon (NM_198618, exon 3 of 12)	22367	NM_001302081	242667	Mm.331885	NM_198618	ENSMUSG00000042388	Dlgap3	BC058433|DAP-3|DAP3|Prpl8|Sapap3	discs, large (Drosophila) homolog-associated protein 3	protein-coding
mm_121985.1	chr14	26439216	26439236	-	1	NA	intron (NM_001310445, intron 14 of 22)	intron (NM_001310445, intron 14 of 22)	81679	NR_038005	71106	Mm.158564	NR_038005	ENSMUSG00000021874	4933413J09Rik	GCSE	RIKEN cDNA 4933413J09 gene	ncRNA
mm_136228.1	chr16	90284272	90284285	-	1	NA	5' UTR (NM_001346799, exon 1 of 20)	5' UTR (NM_001346799, exon 1 of 20)	225	NM_178923	224432	Mm.439811	NM_178923	ENSMUSG00000022983	Scaf4	AA517739|Sfrs15|Sra4|Srsf15	SR-related CTD-associated factor 4	protein-coding
mm_41123.1	chr5	87784555	87784569	+	1	NA	intron (NM_001304769, intron 9 of 12)	intron (NM_001304769, intron 9 of 12)	10112	NM_007785	12993	Mm.4908	NM_007785	ENSMUSG00000061937	Csn1s2a	Csng|PP22	casein alpha s2-like A	protein-coding
mm_3289.1	chr1	136677163	136677214	+	1	NA	Intergenic	Intergenic	-6208	NR_045324	100503460	Mm.30630	NR_045324	ENSMUSG00000097113	Gm19705	-	predicted gene, 19705	ncRNA
mm_97423.1	chr11	78037936	78037955	+	1	NA	promoter-TSS (NM_001284227)	promoter-TSS (NM_001284227)	4	NM_008028	14252	Mm.130227	NM_008028	ENSMUSG00000061981	Flot2	AI573412|Esa|reggie-2	flotillin 2	protein-coding
mm_89916.1	chr10	111178491	111178512	+	1	NA	intron (NM_175489, intron 1 of 23)	intron (NM_175489, intron 1 of 23)	13699	NM_175489	237542	Mm.220204	NM_175489	ENSMUSG00000020189	Osbpl8	AA536976|AA536995|C730029P18Rik|D330025H14Rik|ORP-8	oxysterol binding protein-like 8	protein-coding
mm_80306.1	chr9	74110322	74110340	+	1	NA	promoter-TSS (NM_001033500)	promoter-TSS (NM_001033500)	-3	NM_001033500	546144	Mm.335289	NM_177908	ENSMUSG00000044976	Wdr72	AW558070|D230040E23	WD repeat domain 72	protein-coding
mm_61754.1	chr7	82771317	82771334	+	1	NA	intron (NM_175317, intron 18 of 19)	intron (NM_175317, intron 18 of 19)	-15681	NR_046004	77800	Mm.444811	NR_046004	ENSMUSG00000086690	4933406J10Rik	A930009F24Rik	RIKEN cDNA 4933406J10 gene	ncRNA
mm_2955.1	chr1	132506248	132506259	+	1	NA	promoter-TSS (NM_029025)	promoter-TSS (NM_029025)	23	NM_029025	74626	Mm.34611	NM_029025	ENSMUSG00000048174	Tmem81	4930429O20Rik|AI465369	transmembrane protein 81	protein-coding
mm_106877.1	chr12	8010924	8010932	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	33251	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_48245.1	chr5	137786269	137786300	-	1	NA	5' UTR (NM_144913, exon 1 of 4)	5' UTR (NM_144913, exon 1 of 4)	417	NM_144913	231803	Mm.61193	NM_144913	ENSMUSG00000029726	Mepce	Bcdin3|D5Wsu46e	methylphosphate capping enzyme	protein-coding
mm_30597.1	chr4	6381095	6381103	+	1	NA	exon (NM_016807, exon 4 of 9)	exon (NM_016807, exon 4 of 9)	15419	NM_001098227	53378	Mm.247473	NM_016807	ENSMUSG00000028249	Sdcbp	MDA-9|Sycl|syntenin-1	syndecan binding protein	protein-coding
mm_30902.1	chr4	32353386	32353423	+	1	NA	Intergenic	B4A|SINE|B4	-64031	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_124958.1	chr15	12924065	12924090	+	1	NA	exon (NM_026799, exon 30 of 35)	exon (NM_026799, exon 30 of 35)	99262	NM_001130149	14000	Mm.293142	NM_026799	ENSMUSG00000022191	Drosha	1110013A17Rik|AI874853|Etohi2|Rn3|Rnasen	drosha, ribonuclease type III	protein-coding
mm_151196.1	chr19	53533927	53533942	+	1	NA	exon (NM_001085390, exon 2 of 4)	exon (NM_001085390, exon 2 of 4)	4616	NM_001085390	240672	Mm.482424	NM_001085390	ENSMUSG00000034765	Dusp5	Gm337	dual specificity phosphatase 5	protein-coding
mm_81317.1	chr9	108452494	108452525	+	1	NA	5' UTR (NM_030075, exon 6 of 11)	5' UTR (NM_030075, exon 6 of 11)	-8009	NM_133744	72454	Mm.46488	NM_133744	ENSMUSG00000049305	Ccdc71	2600016J21Rik	coiled-coil domain containing 71	protein-coding
mm_146111.1	chr18	74268180	74268208	+	1	NA	promoter-TSS (NM_013594)	promoter-TSS (NM_013594)	-94	NM_013594	17190	Mm.22522	NM_013594	ENSMUSG00000024561	Mbd1	Cxxc3|PCM1	methyl-CpG binding domain protein 1	protein-coding
mm_75548.1	chr8	57529140	57529148	-	1	NA	intron (NM_001167981, intron 11 of 11)	intron (NM_001167981, intron 11 of 11)	17301	NM_008252	97165	Mm.276881	NM_008252	ENSMUSG00000054717	Hmgb2	C80539|HMG-2|Hmg2	high mobility group box 2	protein-coding
mm_115653.1	chr13	12336548	12336571	-	1	NA	intron (NM_033268, intron 1 of 20)	ID4|SINE|ID	4173	NM_033268	11472	Mm.37638	NM_033268	ENSMUSG00000052374	Actn2	1110008F24Rik	actinin alpha 2	protein-coding
mm_52030.1	chr6	96113107	96113117	+	1	NA	promoter-TSS (NM_182808)	promoter-TSS (NM_182808)	-42	NM_182808	320265	Mm.489890	NM_182808	ENSMUSG00000059187	Fam19a1	C630007B19Rik|FAM19A1 TAFA-1|TAFA1|Tafa-1	family with sequence similarity 19, member A1	protein-coding
mm_128279.1	chr15	36879855	36879884	-	1	NA	Intergenic	L2a|LINE|L2	-82940	NM_001253806	22631	Mm.3360	NM_011740	ENSMUSG00000022285	Ywhaz	1110013I11Rik|14-3-3zeta|AI596267|AL022924|AU020854	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide	protein-coding
mm_171559.1	chr4	147148670	147148678	+	1	NA	Intergenic	Intergenic	-27192	NM_001039209	195531	Mm.270762	NM_001039209	ENSMUSG00000078496	Zfp982	Gm13152|OTTMUSG00000010671	zinc finger protein 982	protein-coding
mm_172055.1	chr6	128931899	128931915	-	1	NA	promoter-TSS (NR_106107)	promoter-TSS (NR_106107)	-62	NR_106107	102465757		NR_106107	ENSMUSG00000098359	Mir7649	mmu-mir-7649	microRNA 7649	ncRNA
mm_23435.1	chr3	59132296	59132318	+	1	NA	promoter-TSS (NM_001287123)	promoter-TSS (NM_001287123)	155	NM_001287120	140795	Mm.439021	NM_133200	ENSMUSG00000036381	P2ry14	A330108O13Rik|Gpr105|P2Y14	purinergic receptor P2Y, G-protein coupled, 14	protein-coding
mm_71350.1	chr8	45628177	45628219	+	1	NA	5' UTR (NM_001310707, exon 1 of 24)	5' UTR (NM_001310707, exon 1 of 24)	447	NM_001310707	234214	Mm.211096	NM_172752	ENSMUSG00000031626	Sorbs2	2010203O03Rik|9430041O17Rik|A530071H08|Argbp2|mKIAA0777|nArgBP2	sorbin and SH3 domain containing 2	protein-coding
mm_67348.1	chr7	79827594	79827604	-	1	NA	exon (NM_008486, exon 15 of 20)	exon (NM_008486, exon 15 of 20)	14753	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_20708.1	chr2	132946084	132946094	-	1	NA	promoter-TSS (NM_198029)	promoter-TSS (NM_198029)	-53	NM_198029	241639	Mm.209784	NM_198029	ENSMUSG00000027356	Fermt1	5830467P10Rik|Kindlin-1	fermitin family member 1	protein-coding
mm_67972.1	chr7	100653952	100653965	-	1	NA	intron (NM_001163185, intron 4 of 6)	intron (NM_001163185, intron 4 of 6)	3007	NM_001163187	27276	Mm.491216	NM_013746	ENSMUSG00000030701	Plekhb1	AI315628|PHR1|Phret1|evt-1	pleckstrin homology domain containing, family B (evectins) member 1	protein-coding
mm_172459.1	chr7	41560842	41560861	-	1	NA	Intergenic	Intergenic	-60961	NM_001033530	101835	Mm.370336	NM_001033530	ENSMUSG00000074166	AW146154	AI451288	expressed sequence AW146154	protein-coding
mm_155228.1	chrX	57179784	57179790	+	1	NA	Intergenic	MIRc|SINE|MIR	-20850	NR_038463	100502842	Mm.164733	NR_038463	ENSMUSG00000085808	Gm14718	OTTMUSG00000017790	predicted gene 14718	ncRNA
mm_51356.1	chr6	72598595	72598609	+	1	NA	promoter-TSS (NM_026159)	promoter-TSS (NM_026159)	-26	NM_026159	67442	Mm.305108	NM_026159	ENSMUSG00000056666	Retsat	0610039N19Rik|C80029|MMT-7|Ppsig	retinol saturase (all trans retinol 13,14 reductase)	protein-coding
mm_146187.1	chr18	75923652	75923658	+	1	NA	intron (NM_145356, intron 2 of 4)	RSINE1|SINE|B4	103477	NM_145356	207259	Mm.159332	NM_145356	ENSMUSG00000044646	Zbtb7c	B230208J24Rik|Kr-pok|Zbtb36	zinc finger and BTB domain containing 7C	protein-coding
mm_100991.1	chr11	8445096	8445102	-	1	NA	intron (NM_001083587, intron 25 of 30)	intron (NM_001083587, intron 25 of 30)	219436	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_61907.1	chr7	90131579	90131627	+	1	NA	intron (NM_001252520, intron 1 of 20)	intron (NM_001252520, intron 1 of 20)	1371	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_150439.1	chr19	37602538	37602541	+	1	NA	intron (NM_175353, intron 17 of 21)	intron (NM_175353, intron 17 of 21)	52121	NM_175353	107371	Mm.24865	NM_175353	ENSMUSG00000053799	Exoc6	4833405E05Rik|AW413330|C430002C19|Sec15|Sec15l1|hbd|msec15	exocyst complex component 6	protein-coding
mm_98931.1	chr11	98355350	98355362	+	1	NA	exon (NM_001313970, exon 5 of 7)	exon (NM_001313970, exon 5 of 7)	2927	NR_045477	69338	Mm.398308	NR_045477	ENSMUSG00000085944	1700003D09Rik	-	RIKEN cDNA 1700003D09 gene	ncRNA
mm_124151.1	chr14	93195796	93195796	-	1	NA	intron (NM_001346722, intron 4 of 4)	intron (NM_001346722, intron 4 of 4)	693092	NM_001271800	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding
mm_103415.1	chr11	75531899	75531909	-	1	NA	promoter-TSS (NM_001199283)	promoter-TSS (NM_001199283)	-208	NM_001199283	215113	Mm.11186	NM_173388	ENSMUSG00000038178	Slc43a2	7630402D21Rik|BC042513|Lat4	solute carrier family 43, member 2	protein-coding
mm_64322.1	chr7	141949853	141949868	+	1	NA	5' UTR (NM_029426, exon 1 of 19)	5' UTR (NM_029426, exon 1 of 19)	109	NM_001009929	75770	Mm.274868	NM_029426	ENSMUSG00000053046	Brsk2	4833424K13Rik|SAD-A|SADA	BR serine/threonine kinase 2	protein-coding
mm_93195.1	chr10	94298586	94298613	-	1	NA	non-coding (NR_033209, exon 1 of 3)	non-coding (NR_033209, exon 1 of 3)	104	NR_033209	215472	Mm.255656	NM_174999	ENSMUSG00000053420	Gm4792	E130012K09|EG215472	predicted gene 4792	ncRNA
mm_162966.1	chr11	9118135	9118141	+	1	NA	promoter-TSS (NM_009477)	promoter-TSS (NM_009477)	35	NM_009477	22271	Mm.4610	NM_009477	ENSMUSG00000020407	Upp1	AI325217|UPase|UdRPase|Up|Upp	uridine phosphorylase 1	protein-coding
mm_164834.1	chr18	38961376	38961378	+	1	NA	intron (NM_001033789, intron 4 of 4)	intron (NM_001033789, intron 4 of 4)	-31768	NM_175164	71302	Mm.329396	NM_175164	ENSMUSG00000036452	Arhgap26	1810044B20Rik|2610010G17Rik|4933432P15Rik|AI853435|mKIAA0621	Rho GTPase activating protein 26	protein-coding
mm_27606.1	chr3	59153647	59153653	-	1	NA	promoter-TSS (NR_045641)	promoter-TSS (NR_045641)	-22	NR_045641	320463	Mm.484506	NR_045641	ENSMUSG00000036381	F630111L10Rik	-	RIKEN cDNA F630111L10 gene	ncRNA
mm_85655.1	chr9	107664199	107664210	-	1	NA	intron (NM_001199218, intron 1 of 15)	intron (NM_001199218, intron 1 of 15)	3195	NM_023805	76257	Mm.296560	NM_023805	ENSMUSG00000010064	Slc38a3	0610012J02Rik|D9Ucla2|Nat1|Slc38-3|Sn1|Snat3|mNAT	solute carrier family 38, member 3	protein-coding
mm_27114.1	chr3	30955220	30955243	-	1	NA	intron (NM_001165955, intron 4 of 13)	intron (NM_001165955, intron 4 of 13)	14184	NM_001165954	241915	Mm.233173	NM_153421	ENSMUSG00000037652	Phc3	E030046K01Rik|Edr3|Hph3	polyhomeotic-like 3 (Drosophila)	protein-coding
mm_77794.1	chr9	3029372	3029395	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	9360	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_73405.1	chr8	105932077	105932133	+	1	NA	TTS (NM_173432)	TTS (NM_173432)	1757	NM_023182	109660	Mm.2745	NM_023182	ENSMUSG00000031896	Ctrl	0910001G08Rik|1810004D15Rik|AV005227|Ctra-1|Ctra1|chymopasin|mFLJ00366	chymotrypsin-like	protein-coding
mm_6405.1	chr1	72863215	72863228	-	1	NA	exon (NM_010518, exon 3 of 4)	exon (NM_010518, exon 3 of 4)	11644	NM_010518	16011	Mm.405761	NM_010518	ENSMUSG00000026185	Igfbp5	AI256729|AW208790|IGFBP-5|IGFBP-5P	insulin-like growth factor binding protein 5	protein-coding
mm_159356.1	chr3	83960685	83960685	-	1	NA	intron (NM_172681, intron 7 of 34)	intron (NM_172681, intron 7 of 34)	79476	NM_172681	229473	Mm.28838	NM_172681	ENSMUSG00000033767	D930015E06Rik	Kiaa0922|mKIAA0922	RIKEN cDNA D930015E06 gene	protein-coding
mm_140815.1	chr17	22867119	22867141	-	1	NA	promoter-TSS (NM_177358)	promoter-TSS (NM_177358)	4	NM_177358	240041	Mm.328828	NM_177358	ENSMUSG00000059142	Zfp945	A630033E08Rik|C730040L01Rik	zinc finger protein 945	protein-coding
mm_167607.1	chr9	54558778	54558815	-	1	NA	intron (NM_019686, intron 1 of 5)	intron (NM_019686, intron 1 of 5)	1283	NM_019686	56506	Mm.42192	NM_019686	ENSMUSG00000037493	Cib2	2810434I23Rik|AI449053	calcium and integrin binding family member 2	protein-coding
mm_123128.1	chr14	56234651	56234655	-	1	NA	promoter-TSS (NM_010371)	promoter-TSS (NM_010371)	4	NM_010371	14940	Mm.14465	NM_010371	ENSMUSG00000079186	Gzmc	AI323531|B10|CCP2|Ctla-5|Ctla5	granzyme C	protein-coding
mm_99806.1	chr11	108062350	108062351	+	1	NA	intron (NM_011101, intron 3 of 16)	intron (NM_011101, intron 3 of 16)	65502	NR_106082	102465705		NR_106082	ENSMUSG00000098989	Mir7223	Gm28009|mmu-mir-7223	microRNA 7223	ncRNA
mm_74085.1	chr8	122550422	122550432	+	1	NA	intron (NM_001037298, intron 1 of 50)	intron (NM_001037298, intron 1 of 50)	902	NM_001037298	234839	Mm.37324	NM_001037298	ENSMUSG00000014444	Piezo1	9630020g22|Fam38a|mKIAA0233	piezo-type mechanosensitive ion channel component 1	protein-coding
mm_7535.1	chr1	124423526	124423530	-	1	NA	Intergenic	MLT1G3|LTR|ERVL-MaLR	-377969	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_59109.1	chr7	19815874	19815898	+	1	NA	intron (NM_033601, intron 2 of 8)	ID2|SINE|ID	6869	NM_033601	12051	Mm.439658	NM_033601	ENSMUSG00000053175	Bcl3	AI528691|Bcl-3	B cell leukemia/lymphoma 3	protein-coding
mm_32250.1	chr4	102570439	102570449	+	1	NA	5' UTR (NM_001177980, exon 1 of 10)	5' UTR (NM_001177980, exon 1 of 10)	384	NM_001177980	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_144179.1	chr18	6765172	6765220	+	1	NA	promoter-TSS (NM_181070)	promoter-TSS (NM_181070)	29	NM_001278447	19330	Mm.132802	NM_181070	ENSMUSG00000073639	Rab18	AA959686	RAB18, member RAS oncogene family	protein-coding
mm_154892.1	chrX	20848560	20848583	+	1	NA	promoter-TSS (NM_009703)	promoter-TSS (NM_009703)	28	NM_001159645	11836	Mm.220946	NM_009703	ENSMUSG00000001127	Araf	1200013E08Rik|A-Raf|AW495444|Araf1	Araf proto-oncogene, serine/threonine kinase	protein-coding
mm_108444.1	chr12	82423031	82423039	+	1	NA	intron (NM_172579, intron 13 of 20)	intron (NM_172579, intron 13 of 20)	111686	NM_172579	217692	Mm.261333	NM_172579	ENSMUSG00000042700	Sipa1l1	4931426N11Rik|AW213287|Spar|mKIAA0440	signal-induced proliferation-associated 1 like 1	protein-coding
mm_159661.1	chr4	150282049	150282049	+	1	NA	5' UTR (NM_001085492, exon 1 of 23)	5' UTR (NM_001085492, exon 1 of 23)	133	NM_001085492	68703	Mm.291274	NM_001085492	ENSMUSG00000039852	Rere	1110033A15Rik|AI414665|ARG|ARP|ATN1L|AW742570|Atr2|DNB1|eye<m03Jus>|eyes3|mKIAA0458	arginine glutamic acid dipeptide (RE) repeats	protein-coding
mm_156409.1	chrX	140506114	140506129	+	1	NA	Intergenic	Intergenic	36547	NR_122039	14605	Mm.22216	NM_010286	ENSMUSG00000031431	Tsc22d3	DIP|Dsip1|Gilz|TSC-22R|Tilz3	TSC22 domain family, member 3	protein-coding
mm_65776.1	chr7	28766276	28766323	-	1	NA	promoter-TSS (NM_001122766)	promoter-TSS (NM_001122766)	345	NM_001306222	18036	Mm.220333	NM_010908	ENSMUSG00000030595	Nfkbib	I(Kappa)B(beta)|I-kappa-B-beta|IKB-beta|IKappaBbeta|IkB|IkBb|NF-kappa-BIB|ikB-B	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, beta	protein-coding
mm_133128.1	chr16	65818654	65818659	+	1	NA	intron (NM_028572, intron 1 of 3)	intron (NM_028572, intron 1 of 3)	3023	NM_028572	73569	Mm.25670	NM_028572	ENSMUSG00000091243	Vgll3	1700110N18Rik|4832416J22|C80713|Vgl-3|Vito-2	vestigial like family member 3	protein-coding
mm_75481.1	chr8	48615643	48615651	-	1	NA	intron (NM_011857, intron 2 of 28)	intron (NM_011857, intron 2 of 28)	59043	NM_001145937	23965	Mm.42191	NM_011857	ENSMUSG00000031561	Tenm3	2610100B16Rik|Odz1|Odz3|Ten-m3|mKIAA1455	teneurin transmembrane protein 3	protein-coding
mm_24334.1	chr3	89662520	89662552	+	1	NA	intron (NM_080466, intron 6 of 7)	intron (NM_080466, intron 6 of 7)	-52486	NM_001038587	56417	Mm.316628	NM_019655	ENSMUSG00000027951	Adar	AV242451|Adar1|Adar1p110|Adar1p150|mZaADAR	adenosine deaminase, RNA-specific	protein-coding
mm_41527.1	chr5	92603077	92603109	+	1	NA	promoter-TSS (NM_175096)	promoter-TSS (NM_175096)	42	NM_175096	52331	Mm.21965	NM_175096	ENSMUSG00000047963	Stbd1	D530019K15Rik|D5Ertd593e	starch binding domain 1	protein-coding
mm_44948.1	chr5	36581816	36581845	-	1	NA	intron (NM_001113362, intron 2 of 14)	CpG	567	NM_133910	100855	Mm.486203	NM_133910	ENSMUSG00000029192	Tbc1d14	2810413P16Rik|AU043625|C86258|D5Ertd110e|mKIAA1322	TBC1 domain family, member 14	protein-coding
mm_128885.1	chr15	73154632	73154643	-	1	NA	intron (NM_153178, intron 1 of 18)	intron (NM_153178, intron 1 of 18)	30310	NM_153178	239528	Mm.23095	NM_153178	ENSMUSG00000036698	Ago2	1110029L17Rik|2310051F07Rik|AI225898|AL022874|AW546247|ENSMUSG00000072493|Eif2c2|Gerp95|Gm10365|mKIAA4215	argonaute RISC catalytic subunit 2	protein-coding
mm_91614.1	chr10	41519110	41519120	-	1	NA	promoter-TSS (NM_016898)	promoter-TSS (NM_016898)	-385	NM_016898	53599	Mm.269815	NM_016898	ENSMUSG00000019818	Cd164	A115|A24|AA589639|AW540279|MGC-24|MSSP	CD164 antigen	protein-coding
mm_74093.1	chr8	122569174	122569195	+	1	NA	exon (NM_026014, exon 2 of 10)	exon (NM_026014, exon 2 of 10)	1169	NM_026014	67177	Mm.21873	NM_026014	ENSMUSG00000006585	Cdt1	2610318F11Rik|AW545653|C76791|Ris2	chromatin licensing and DNA replication factor 1	protein-coding
mm_2589.1	chr1	118852491	118852503	+	1	NA	intron (NM_001081125, intron 8 of 13)	intron (NM_001081125, intron 8 of 13)	-101723	NR_105764	102465176		NR_105764	ENSMUSG00000098273	Mir6346	Gm27829|mmu-mir-6346	microRNA 6346	ncRNA
mm_90248.1	chr10	121510331	121510345	+	1	NA	Intergenic	Intergenic	-34088	NM_138956	192678	Mm.41265	NM_138956	ENSMUSG00000025795	Rassf3	AW212023|AW322379	Ras association (RalGDS/AF-6) domain family member 3	protein-coding
mm_29052.1	chr3	103737939	103737974	-	1	NA	promoter-TSS (NM_133859)	promoter-TSS (NM_133859)	45	NM_133859	99543	Mm.211535	NM_133859	ENSMUSG00000027848	Olfml3	2810002E22Rik|AI115209|AW550633|HNOEL-iso|ONT3|mONT3	olfactomedin-like 3	protein-coding
mm_59587.1	chr7	28131489	28131503	+	1	NA	exon (NM_001164655, exon 3 of 20)	exon (NM_001164655, exon 3 of 20)	2030	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_171712.1	chr4	79327757	79327771	+	1	NA	Intergenic	Intergenic	733717	NR_131142	623726		NR_131142		A430085M09Rik	EG623726	RIKEN cDNA A430085M09 gene	ncRNA
mm_22213.1	chr2	174286159	174286165	-	1	NA	non-coding (NR_002846, exon 2 of 5)	non-coding (NR_002846, exon 2 of 5)	1842	NM_022000	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_118812.1	chr14	25462502	25462509	+	1	NA	intron (NM_001310666, intron 1 of 23)	intron (NM_001310666, intron 1 of 23)	3320	NM_183208	328365	Mm.227484	NM_183208	ENSMUSG00000007817	Zmiz1	BC065120|E330020C23|ENSMUSG00000072684|Gm10397|I920194n01|Rai17|Zimp10	zinc finger, MIZ-type containing 1	protein-coding
mm_10893.1	chr2	25263920	25263931	+	1	NA	exon (NM_175286, exon 1 of 4)	exon (NM_175286, exon 1 of 4)	1327	NM_175286	97031	Mm.308539	NM_175286	ENSMUSG00000048707	Tprn	C430004E15Rik|C87750	taperin	protein-coding
mm_47840.1	chr5	134314486	134314499	-	1	NA	5' UTR (NM_010365, exon 1 of 34)	5' UTR (NM_010365, exon 1 of 34)	268	NM_001080746	14886	Mm.261570	NM_010365	ENSMUSG00000060261	Gtf2i	6030441I21Rik|BAP-135|Diws1t|GtfII-I|Spin|TFII-I|WBSCR6	general transcription factor II I	protein-coding
mm_6608.1	chr1	75479104	75479124	-	1	NA	promoter-TSS (NM_177056)	promoter-TSS (NM_177056)	357	NM_001001565	74241	Mm.260577	NM_001001565	ENSMUSG00000032997	Chpf	1700028N03Rik|AI414328|D1Bwg1363e	chondroitin polymerizing factor	protein-coding
mm_161647.1	chr17	5990149	5990149	+	1	NA	exon (NM_001113353, exon 4 of 27)	exon (NM_001113353, exon 4 of 27)	14563	NM_011523	20975	Mm.236068	NM_011523	ENSMUSG00000023805	Synj2	AI481647|SJ2|mKIAA0348	synaptojanin 2	protein-coding
mm_74216.1	chr8	123979297	123979302	+	1	NA	intron (NM_019552, intron 1 of 12)	intron (NM_019552, intron 1 of 12)	3823	NM_019552	56199	Mm.274243	NM_019552	ENSMUSG00000031974	Abcb10	Abc-me|Abcb12	ATP-binding cassette, sub-family B (MDR/TAP), member 10	protein-coding
mm_113692.1	chr13	43122826	43122830	+	1	NA	promoter-TSS (NM_001005748)	promoter-TSS (NM_001005748)	-11	NM_001005748	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding
mm_103489.1	chr11	76528115	76528119	-	1	NA	intron (NM_198894, intron 1 of 22)	B3|SINE|B2	-18698	NM_198018	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_159339.1	chr3	57692644	57692644	-	1	NA	promoter-TSS (NM_001033349)	promoter-TSS (NM_001033349)	-107	NM_001033349	242037	Mm.291091	NM_001033349	ENSMUSG00000074591	Ankub1	Gm410	ankrin repeat and ubiquitin domain containing 1	protein-coding
mm_130654.1	chr15	100637069	100637082	-	1	NA	promoter-TSS (NM_174992)	promoter-TSS (NM_174992)	-135	NM_001033872	207818	Mm.26282	NM_174992	ENSMUSG00000053559	Smagp	-	small cell adhesion glycoprotein	protein-coding
mm_106047.1	chr11	116080264	116080274	-	1	NA	exon (NM_016852, exon 6 of 8)	exon (NM_016852, exon 6 of 8)	-2308	NM_001009573	70450	Mm.259460	NM_001009573	ENSMUSG00000057948	Unc13d	2610108D09Rik|Jinx|Munc13-4|mFLJ00067	unc-13 homolog D (C. elegans)	protein-coding
mm_151808.1	chr19	5457489	5457494	-	1	NA	promoter-TSS (NM_198616)	promoter-TSS (NM_198616)	72	NM_198616	240514	Mm.329657	NM_198616	ENSMUSG00000095098	Ccdc85b	AI842788|BB115872	coiled-coil domain containing 85B	protein-coding
mm_84881.1	chr9	79718804	79718818	-	1	NA	promoter-TSS (NM_001290308)	promoter-TSS (NM_001290308)	-89	NM_001290308	12816	Mm.3819	NM_007730	ENSMUSG00000032332	Col12a1	-	collagen, type XII, alpha 1	protein-coding
mm_85135.1	chr9	95753923	95753930	-	1	NA	3' UTR (NM_001033210, exon 16 of 16)	3' UTR (NM_001033210, exon 16 of 16)	-3568	NM_011643	22063	Mm.149633	NM_011643	ENSMUSG00000032839	Trpc1	Mtrp1|Trp1|Trrp1	transient receptor potential cation channel, subfamily C, member 1	protein-coding
mm_70445.1	chr8	11728106	11728143	+	1	NA	promoter-TSS (NM_001113517)	promoter-TSS (NM_001113517)	19	NM_001113517	54126	Mm.244068	NM_017402	ENSMUSG00000031511	Arhgef7	Cool|PIX|Pak3bp|betaPix|betaPix-b|betaPix-c|cool-1|mKIAA0142|p85Cool1|p85SPR	Rho guanine nucleotide exchange factor (GEF7)	protein-coding
mm_135207.1	chr16	36610806	36610816	-	1	NA	intron (NM_019388, intron 5 of 7)	intron (NM_019388, intron 5 of 7)	-48677	NM_013803	12374	Mm.103619	NM_013803	ENSMUSG00000051980	Casr	CaR|Gprc2a	calcium-sensing receptor	protein-coding
mm_95377.1	chr11	49092951	49092955	+	1	NA	intron (NM_001271676, intron 2 of 2)	Lx7|LINE|L1	5936	NM_008330	15953	Mm.24769	NM_008330	ENSMUSG00000078920	Ifi47	47kDa|IRG-47|Ifggc1|Igrd|Iigp4|Iipg4|Irgd	interferon gamma inducible protein 47	protein-coding
mm_45103.1	chr5	44782482	44782493	-	1	NA	intron (NM_001347349, intron 1 of 7)	intron (NM_001347349, intron 1 of 7)	17259	NM_001347349	16826	Mm.25785	NM_010698	ENSMUSG00000039706	Ldb2	AI035351|AW146358|CLIM1|CLP-36|Ldb3	LIM domain binding 2	protein-coding
mm_106710.1	chr12	3807018	3807063	+	1	NA	promoter-TSS (NM_001271753)	promoter-TSS (NM_001271753)	60	NM_007872	13435	Mm.5001	NM_007872	ENSMUSG00000020661	Dnmt3a	MmuIIIA	DNA methyltransferase 3A	protein-coding
mm_71115.1	chr8	36094683	36094705	+	1	NA	promoter-TSS (NM_172911)	promoter-TSS (NM_172911)	-134	NM_172911	244418	Mm.244971	NM_172911	ENSMUSG00000050271	Prag1	9830148H23|D8Ertd82e|NACK|Sgk223|mFLJ00269	PEAK1 related kinase activating pseudokinase 1	protein-coding
mm_95940.1	chr11	58382838	58382846	+	1	NA	exon (NM_001083884, exon 4 of 7)	exon (NM_001083884, exon 4 of 7)	2196	NM_001330197	70163	Mm.24119	NM_027339	ENSMUSG00000013643	Lypd8	2210415F13Rik	LY6/PLAUR domain containing 8	protein-coding
mm_73550.1	chr8	108956705	108956715	+	1	NA	exon (NM_007496, exon 10 of 10)	exon (NM_007496, exon 10 of 10)	19850	NR_037295	100526511		NR_037295	ENSMUSG00000093241	Mir3108	mir-3108|mmu-mir-3108	microRNA 3108	ncRNA
mm_22349.1	chr2	180920890	180920923	-	1	NA	promoter-TSS (NM_173761)	promoter-TSS (NM_173761)	30	NM_173761	228994	Mm.30205	NM_173761	ENSMUSG00000038848	Ythdf1	2210410K23Rik|8030473O16	YTH domain family 1	protein-coding
mm_6246.1	chr1	67077829	67077836	-	1	NA	Intergenic	Intergenic	-38960	NM_021295	14768	Mm.20522	NM_021295	ENSMUSG00000026000	Lancl1	AW124738|Gpr69|Gpr69a|p40	LanC (bacterial lantibiotic synthetase component C)-like 1	protein-coding
mm_15163.1	chr2	154010524	154010535	+	1	NA	exon (NM_008953, exon 4 of 9)	exon (NM_008953, exon 4 of 9)	2253	NM_008953	19194	Mm.29197	NM_008953	ENSMUSG00000042459	Bpifa2	Bpifa2e|Psp	BPI fold containing family A, member 2	protein-coding
mm_110126.1	chr12	26444229	26444240	-	1	NA	3' UTR (NM_021384, exon 6 of 6)	3' UTR (NM_021384, exon 6 of 6)	12218	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_151985.1	chr19	5845472	5845485	-	1	NA	promoter-TSS (NR_003513)	promoter-TSS (NR_003513)	0	NR_131212	66961	Mm.281895	NR_003513	ENSMUSG00000092274	Neat1	2310043N10Rik|VINC	nuclear paraspeckle assembly transcript 1 (non-protein coding)	ncRNA
mm_30721.1	chr4	13743353	13743379	+	1	NA	promoter-TSS (NM_001111026)	promoter-TSS (NM_001111026)	64	NM_001111026	12395	Mm.4909	NM_009822	ENSMUSG00000006586	Runx1t1	Cbfa2t1h|ETO|MTG8	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	protein-coding
mm_57133.1	chr6	122604377	122604413	-	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	-1951	NM_001134391	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_116145.1	chr13	29855631	29855676	-	1	NA	promoter-TSS (NM_144536)	promoter-TSS (NM_144536)	20	NR_131896	68916	Mm.212227	NM_144536	ENSMUSG00000006191	Cdkal1	1190005B03Rik|6620401C13Rik	CDK5 regulatory subunit associated protein 1-like 1	protein-coding
mm_125855.1	chr15	74995392	74995397	+	1	NA	exon (NM_001271446, exon 4 of 4)	exon (NM_001271446, exon 4 of 4)	2637	NM_001271417	110454	Mm.425949	NM_010738	ENSMUSG00000075602	Ly6a	Ly-6A.2|Ly-6A/E|Ly-6E.1|Sca-1|Sca1|TAP	lymphocyte antigen 6 complex, locus A	protein-coding
mm_137651.1	chr17	28558340	28558359	+	1	NA	TTS (NR_105935)	TTS (NR_105935)	152	NR_105935	102465585		NR_105935	ENSMUSG00000099152	Mir6969	Gm27305|mmu-mir-6969	microRNA 6969	ncRNA
mm_162019.1	chr19	45659960	45659960	-	1	NA	exon (NM_013907, exon 1 of 9)	exon (NM_013907, exon 1 of 9)	233	NM_013907	30838	Mm.254739	NM_013907	ENSMUSG00000040913	Fbxw4	Dac|Fbw4|SHFM3|SHSF3|dactylin|dactylyn	F-box and WD-40 domain protein 4	protein-coding
mm_159285.1	chr2	169883470	169883470	+	1	NA	intron (NM_080455, intron 1 of 1)	intron (NM_080455, intron 1 of 1)	79717	NR_131974	446211	Mm.266854	NR_131974	ENSMUSG00000103935	AY702102	STDP1	cDNA sequence AY702102	ncRNA
mm_100528.1	chr11	120598621	120598640	+	1	NA	promoter-TSS (NM_011568)	promoter-TSS (NM_011568)	98	NM_001038230	66156	Mm.21645	NM_025389	ENSMUSG00000025135	Anapc11	1110011I19Rik|R75218	anaphase promoting complex subunit 11	protein-coding
mm_109158.1	chr12	108179544	108179582	+	1	NA	promoter-TSS (NM_009832)	promoter-TSS (NM_009832)	-175	NM_009832	12454	Mm.474441	NM_009832	ENSMUSG00000021258	Ccnk	AW123198|AW413594|CPR4|CycK	cyclin K	protein-coding
mm_84616.1	chr9	70484803	70484811	-	1	NA	intron (NM_033604, intron 2 of 14)	intron (NM_033604, intron 2 of 14)	18918	NM_033604	93836	Mm.29783	NM_033604	ENSMUSG00000032217	Rnf111	ARK|Arkadia	ring finger 111	protein-coding
mm_23192.1	chr3	40981485	40981488	+	1	NA	Intergenic	Intergenic	30855	NM_001040399	214048	Mm.46782	NM_027663	ENSMUSG00000025762	Larp1b	1700108L22Rik|4933421B21Rik|AA690246|Larp2	La ribonucleoprotein domain family, member 1B	protein-coding
mm_91839.1	chr10	57522336	57522337	-	1	NA	intron (NM_019760, intron 6 of 8)	L1_Mur2|LINE|L1	10193	NM_019760	56442	Mm.29344	NM_019760	ENSMUSG00000019877	Serinc1	1500011D18Rik|AI315070|AIGP-2|TMS-2|Tde1l|Tde2|Tms2|mKIAA1253	serine incorporator 1	protein-coding
mm_85318.1	chr9	101251471	101251481	-	1	NA	intron (NM_001161362, intron 1 of 13)	CpG	356	NM_001161362	235542	Mm.335386	NM_172144	ENSMUSG00000043154	Ppp2r3a	3222402P14Rik|A730042E07	protein phosphatase 2, regulatory subunit B'', alpha	protein-coding
mm_53868.1	chr6	149329390	149329405	+	1	NA	exon (NM_001289662, exon 3 of 5)	exon (NM_001289662, exon 3 of 5)	19983	NM_001289662	67246	Mm.333515	NM_026054	ENSMUSG00000032712	2810474O19Rik	6720435I21Rik|AA536804|AU020969|GET|Kiaa1551	RIKEN cDNA 2810474O19 gene	protein-coding
mm_130880.1	chr15	102246440	102246510	-	1	NA	promoter-TSS (NM_001042727)	promoter-TSS (NM_001042727)	25	NM_001042727	19411	Mm.1273	NM_011244	ENSMUSG00000001288	Rarg	Nr1b3|RAR-gamma|RARD|RARgamma2	retinoic acid receptor, gamma	protein-coding
mm_94432.1	chr11	6292085	6292111	+	1	NA	promoter-TSS (NM_001252288)	promoter-TSS (NM_001252288)	-460	NM_001252288	18293	Mm.276348	NM_010956	ENSMUSG00000020456	Ogdh	2210403E04Rik|2210412K19Rik|AA409584|d1401|mKIAA4192	oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)	protein-coding
mm_26697.1	chr3	157536547	157536557	+	1	NA	exon (NM_017381, exon 3 of 10)	exon (NM_017381, exon 3 of 10)	2155	NM_017381	53861	Mm.259036	NM_017381	ENSMUSG00000028180	Zranb2	AI227013|Zfp265|Zis|Znf265	zinc finger, RAN-binding domain containing 2	protein-coding
mm_113387.1	chr13	33039899	33039917	+	1	NA	exon (NM_011452, exon 7 of 7)	exon (NM_011452, exon 7 of 7)	12494	NM_011452	20706	Mm.45371	NM_011452	ENSMUSG00000021403	Serpinb9b	1600019A21Rik|R86|SPI-CI|Spi10|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 9b	protein-coding
mm_149430.1	chr19	11469470	11469502	+	1	NA	5' UTR (NM_028595, exon 1 of 7)	5' UTR (NM_028595, exon 1 of 7)	118	NM_028595	73656	Mm.440719	NM_028595	ENSMUSG00000079419	Ms4a6c	2200009H22Rik|2210417N07Rik	membrane-spanning 4-domains, subfamily A, member 6C	protein-coding
mm_124275.1	chr14	103033491	103033504	-	1	NA	intron (NR_045657, intron 1 of 2)	intron (NR_045657, intron 1 of 2)	306	NR_045657	71264	Mm.399572	NR_045657		4933432I03Rik	-	RIKEN cDNA 4933432I03 gene	ncRNA
mm_165975.1	chr4	102368153	102368154	+	1	NA	intron (NM_019840, intron 1 of 14)	intron (NM_019840, intron 1 of 14)	113214	NM_019840	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_166839.1	chr7	19307416	19307426	-	1	NA	exon (NM_008036, exon 2 of 4)	exon (NM_008036, exon 2 of 4)	2624	NM_008036	14282	Mm.248335	NM_008036	ENSMUSG00000003545	Fosb	-	FBJ osteosarcoma oncogene B	protein-coding
mm_26838.1	chr3	14384431	14384448	-	1	NA	Intergenic	Intergenic	21322	NR_033591	622229	Mm.486084	NR_033591		Gm6300	EG622229	solute carrier family 7 (cationic amino acid transporter, y+ system), member pseudogene	pseudo
mm_59627.1	chr7	28155212	28155220	+	1	NA	exon (NM_001164655, exon 14 of 20)	exon (NM_001164655, exon 14 of 20)	-14532	NM_007991	14113	Mm.4595	NM_007991	ENSMUSG00000046865	Fbl	AL022665|FIB|FLRN|RNU3IP1	fibrillarin	protein-coding
mm_11159.1	chr2	28552182	28552193	+	1	NA	exon (NM_009058, exon 18 of 18)	exon (NM_009058, exon 18 of 18)	11216	NM_009885	12613	Mm.236017	NM_009885	ENSMUSG00000026818	Cel	1810036E18Rik|BAL	carboxyl ester lipase	protein-coding
mm_64733.1	chr7	4724372	4724395	-	1	NA	intron (NM_001142792, intron 2 of 5)	intron (NM_001142792, intron 2 of 5)	699	NM_001142792	330460	Mm.361851	NM_177887	ENSMUSG00000046456	Tmem150b	A630041N19|Tmem224	transmembrane protein 150B	protein-coding
mm_150919.1	chr19	46083066	46083076	+	1	NA	exon (NM_001039352, exon 10 of 13)	exon (NM_001039352, exon 10 of 13)	7224	NM_001039351	70769	Mm.402190	NM_053086	ENSMUSG00000015176	Nolc1	NOPP130|NOPP140|P130	nucleolar and coiled-body phosphoprotein 1	protein-coding
mm_63604.1	chr7	128148494	128148510	+	1	NA	exon (NM_021334, exon 27 of 30)	exon (NM_021334, exon 27 of 30)	18934	NM_021334	16411	Mm.22378	NM_021334	ENSMUSG00000030789	Itgax	AI449405|Cd11c|Cr4|N418	integrin alpha X	protein-coding
mm_69458.1	chr7	133123354	133123377	-	1	NA	5' UTR (NM_009980, exon 1 of 11)	5' UTR (NM_009980, exon 1 of 11)	118	NM_009980	13017	Mm.246240	NM_009980	ENSMUSG00000030970	Ctbp2	AA407280|D7Ertd45e|Gtrgeo6|Ribeye	C-terminal binding protein 2	protein-coding
mm_170470.1	chr1	90628246	90628253	-	1	NA	Intergenic	LTRIS2|LTR|ERV1	24824	NM_133805	108679	Mm.119177	NM_133805	ENSMUSG00000034432	Cops8	9430009J09Rik|AA408242|Csn8|Sgn8	COP9 signalosome subunit 8	protein-coding
mm_66662.1	chr7	45717068	45717093	-	1	NA	promoter-TSS (NM_009077)	promoter-TSS (NM_009077)	922	NM_203280	56632	Mm.24222	NM_020011	ENSMUSG00000057342	Sphk2	C76851	sphingosine kinase 2	protein-coding
mm_114433.1	chr13	65241507	65241526	+	1	NA	Intergenic	CpG	-35800	NM_175290	97895	Mm.315815	NM_175290	ENSMUSG00000032999	Nlrp4f	C330026N02Rik|C86045|Nalp-kappa|Nalp4f	NLR family, pyrin domain containing 4F	protein-coding
mm_98789.1	chr11	96929368	96929383	+	1	NA	promoter-TSS (NM_146026)	promoter-TSS (NM_146026)	51	NM_146026	217138	Mm.342551	NM_146026	ENSMUSG00000047040	Prr15l	Atad4|BC022765|E230006A12Rik	proline rich 15-like	protein-coding
mm_165074.1	chr19	45058275	45058287	-	1	NA	Intergenic	Intergenic	10705	NM_001178013	94280	Mm.36169	NM_053197	ENSMUSG00000025212	Sfxn3	-	sideroflexin 3	protein-coding
mm_89122.1	chr10	84838161	84838174	+	1	NA	promoter-TSS (NM_027689)	promoter-TSS (NM_027689)	19	NM_027689	71137	Mm.79070	NM_027689	ENSMUSG00000020037	Rfx4	4933412G19Rik|NYD-sp10	regulatory factor X, 4 (influences HLA class II expression)	protein-coding
mm_142791.1	chr17	50169894	50169925	-	1	NA	intron (NM_181397, intron 1 of 9)	intron (NM_181397, intron 1 of 9)	20588	NM_181397	76438	Mm.41854	NM_181397	ENSMUSG00000039316	Rftn1	2310015N21Rik|AI853526	raftlin lipid raft linker 1	protein-coding
mm_150671.1	chr19	42051772	42051779	+	1	NA	promoter-TSS (NM_025752)	promoter-TSS (NM_025752)	-453	NM_025752	66765	Mm.440412	NM_025752	ENSMUSG00000090369	4933411K16Rik	-	RIKEN cDNA 4933411K16 gene	protein-coding
mm_126070.1	chr15	77370828	77370832	+	1	NA	Intergenic	RMER21B|LTR|ERV1	28280	NM_029419	75761	Mm.232636	NM_029419	ENSMUSG00000010601	Apol7a	9130022K13Rik|Apol3	apolipoprotein L 7a	protein-coding
mm_84315.1	chr9	63738365	63738367	-	1	NA	intron (NM_016769, intron 1 of 8)	intron (NM_016769, intron 1 of 8)	19628	NM_016769	17127	Mm.7320	NM_016769	ENSMUSG00000032402	Smad3	AU022421|Madh3	SMAD family member 3	protein-coding
mm_65833.1	chr7	29180632	29180650	-	1	NA	promoter-TSS (NM_026545)	promoter-TSS (NM_026545)	32	NM_026545	57296	Mm.273152	NM_026545	ENSMUSG00000030591	Psmd8	6720456J22Rik|AA407360|AL033291|AL033322|AL033323|C76433	proteasome (prosome, macropain) 26S subunit, non-ATPase, 8	protein-coding
mm_123581.1	chr14	67008835	67008867	-	1	NA	promoter-TSS (NM_009761)	promoter-TSS (NM_009761)	26	NM_009761	12177	Mm.29820	NM_009761	ENSMUSG00000022051	Bnip3l	C86132|D14Ertd719e|Nip3L|Nix	BCL2/adenovirus E1B interacting protein 3-like	protein-coding
mm_124028.1	chr14	76695026	76695033	-	1	NA	Intergenic	RMER17C|LTR|ERVK	17461	NR_015485	73272	Mm.116804	NR_015485	ENSMUSG00000101009	1700108F19Rik	1700020I02Rik|BB065030	RIKEN cDNA 1700108F19 gene	ncRNA
mm_141667.1	chr17	33824530	33824538	-	1	NA	promoter-TSS (NM_023202)	promoter-TSS (NM_023202)	-36	NM_016844	54127	Mm.352374	NM_016844	ENSMUSG00000067288	Rps28	-	ribosomal protein S28	protein-coding
mm_73985.1	chr8	120628699	120628711	+	1	NA	intron (NM_001308449, intron 1 of 3)	intron (NM_001308449, intron 1 of 3)	5677	NM_197988	68918	Mm.473736	NM_197988	ENSMUSG00000043687	1190005I06Rik	-	RIKEN cDNA 1190005I06 gene	protein-coding
mm_51742.1	chr6	87373358	87373370	+	1	NA	promoter-TSS (NM_025467)	promoter-TSS (NM_025467)	-1	NM_025467	66284	Mm.46446	NM_025467	ENSMUSG00000030049	Gkn2	1810036H07Rik|Bricd1b	gastrokine 2	protein-coding
mm_54199.1	chr6	24664898	24664917	-	1	NA	promoter-TSS (NM_028459)	promoter-TSS (NM_028459)	88	NM_001167745	73178	Mm.1574	NM_028459	ENSMUSG00000029684	Wasl	2900021I12Rik|3110031I02Rik|N-WASP	Wiskott-Aldrich syndrome-like (human)	protein-coding
mm_20317.1	chr2	127314558	127314565	-	1	NA	Intergenic	Intergenic	-21598	NM_010090	13537	Mm.4729	NM_010090	ENSMUSG00000027368	Dusp2	PAC1	dual specificity phosphatase 2	protein-coding
mm_72320.1	chr8	78390977	78390987	+	1	NA	intron (NM_183096, intron 12 of 13)	ORR1E|LTR|ERVL-MaLR	45670	NM_138944	18997	Mm.234261	NM_138944	ENSMUSG00000031688	Pou4f2	Brn-3.2|Brn-3b|Brn3b|Pou4f-rs1|mBrn3-3R	POU domain, class 4, transcription factor 2	protein-coding
mm_109071.1	chr12	104345463	104345471	+	1	NA	3' UTR (NM_011458, exon 5 of 5)	3' UTR (NM_011458, exon 5 of 5)	6981	NM_011458	20714	Mm.291569	NM_011458	ENSMUSG00000058207	Serpina3k	1300001I07Rik|D12Rp54|MMCM2|MMSpi2|RP54|Spi-2|Spi2|contrapsin	serine (or cysteine) peptidase inhibitor, clade A, member 3K	protein-coding
mm_91433.1	chr10	33256370	33256382	-	1	NA	promoter-TSS (NR_040657)	promoter-TSS (NR_040657)	-19	NR_040657	442820	Mm.490725	NR_040657		D830005E20Rik	-	RIKEN cDNA D830005E20 gene	ncRNA
mm_153825.1	chr19	46305580	46305627	-	1	NA	promoter-TSS (NM_001177370)	promoter-TSS (NM_001177370)	-92	NM_019408	18034	Mm.102365	NM_019408	ENSMUSG00000025225	Nfkb2	NF-kappaB2|lyt|p49|p49/p100|p50B|p52	nuclear factor of kappa light polypeptide gene enhancer in B cells 2, p49/p100	protein-coding
mm_151406.1	chr19	56548519	56548543	+	1	NA	promoter-TSS (NM_018831)	promoter-TSS (NM_018831)	270	NM_025811	66866	Mm.46346	NM_025811	ENSMUSG00000025078	Nhlrc2	1200003G01Rik|AI835049|AV002846|AW496455	NHL repeat containing 2	protein-coding
mm_89636.1	chr10	96618764	96618782	+	1	NA	3' UTR (NM_007569, exon 2 of 2)	3' UTR (NM_007569, exon 2 of 2)	1772	NM_007569	12226	Mm.23811	NM_007569	ENSMUSG00000036478	Btg1	AI426953|AW546738	B cell translocation gene 1, anti-proliferative	protein-coding
mm_26412.1	chr3	142608481	142608485	+	1	NA	intron (NM_010259, intron 8 of 10)	intron (NM_010259, intron 8 of 10)	-12180	NM_010260	14469	Mm.24038	NM_010260	ENSMUSG00000028270	Gbp2	-	guanylate binding protein 2	protein-coding
mm_68735.1	chr7	120982261	120982305	-	1	NA	promoter-TSS (NM_007672)	promoter-TSS (NM_007672)	29	NM_007672	12585	Mm.1640	NM_007672	ENSMUSG00000030878	Cdr2	AA617262	cerebellar degeneration-related 2	protein-coding
mm_133547.1	chr16	91269760	91269778	+	1	NA	promoter-TSS (NM_016968)	promoter-TSS (NM_016968)	0	NM_016968	50914	Mm.39300	NM_016968	ENSMUSG00000046160	Olig1	AI836478|AW494459|Bhlhb6|Olg-1|Oligo1|bHLHe21	oligodendrocyte transcription factor 1	protein-coding
mm_122830.1	chr14	54712140	54712153	-	1	NA	promoter-TSS (NM_207131)	promoter-TSS (NM_207131)	28	NM_207131	110794	Mm.236223	NM_207131	ENSMUSG00000052435	Cebpe	C/EBPe|CRP1|Gm294	CCAAT/enhancer binding protein (C/EBP), epsilon	protein-coding
mm_169022.1	chr13	112799218	112799222	+	1	NA	Intergenic	RLTR9D|LTR|ERVK	-1557	NM_008903	19012	Mm.291029	NM_008247	ENSMUSG00000021759	Plpp1	Hic53|Hpic53|LPP-1|LPP1|PAP-2a|PAP2-alpha|PAP2a|Ppap2a|mPAP	phospholipid phosphatase 1	protein-coding
mm_24416.1	chr3	90514985	90514998	+	1	NA	promoter-TSS (NM_011309)	promoter-TSS (NM_011309)	556	NM_009113	20196	Mm.6523	NM_009113	ENSMUSG00000042312	S100a13	-	S100 calcium binding protein A13	protein-coding
mm_42032.1	chr5	108388377	108388387	+	1	NA	promoter-TSS (NM_008806)	promoter-TSS (NM_008806)	9	NM_008806	18587	Mm.1372	NM_008806	ENSMUSG00000029491	Pde6b	Pdeb|r|rd|rd-1|rd1|rd10	phosphodiesterase 6B, cGMP, rod receptor, beta polypeptide	protein-coding
mm_13427.1	chr2	104816871	104816925	+	1	NA	promoter-TSS (NM_001123327)	promoter-TSS (NM_001123327)	-202	NM_001123327	99003	Mm.274314	NM_001123327	ENSMUSG00000074994	Qser1	4732486I23Rik|AI502974	glutamine and serine rich 1	protein-coding
mm_108425.1	chr12	82202946	82202949	+	1	NA	intron (NM_001167983, intron 1 of 23)	B1_Mur4|SINE|Alu	32931	NM_001167983	217692	Mm.261333	NM_172579	ENSMUSG00000042700	Sipa1l1	4931426N11Rik|AW213287|Spar|mKIAA0440	signal-induced proliferation-associated 1 like 1	protein-coding
mm_134970.1	chr16	32010111	32010138	-	1	NA	Intergenic	RMER15|LTR|ERVL	-6837	NM_177103	320213	Mm.152890	NM_023801	ENSMUSG00000022772	Senp5	6230429P13Rik|A730063F07Rik|AI851888|BB189556|SMT3IP3	SUMO/sentrin specific peptidase 5	protein-coding
mm_35245.1	chr4	19877554	19877580	-	1	NA	3' UTR (NM_175406, exon 8 of 8)	3' UTR (NM_175406, exon 8 of 8)	44999	NM_175406	242341	Mm.19298	NM_175406	ENSMUSG00000028238	Atp6v0d2	1620401A02Rik|AI324824|V-ATPase	ATPase, H+ transporting, lysosomal V0 subunit D2	protein-coding
mm_36067.1	chr4	57916442	57916455	-	1	NA	promoter-TSS (NM_178727)	promoter-TSS (NM_178727)	-184	NM_178727	242484	Mm.23214	NM_178727	ENSMUSG00000052117	D630039A03Rik	-	RIKEN cDNA D630039A03 gene	protein-coding
mm_659.1	chr1	40437277	40437292	+	1	NA	intron (NM_001294171, intron 1 of 7)	intron (NM_001294171, intron 1 of 7)	-2345	NM_001025602	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_40367.1	chr5	50543647	50543675	+	1	NA	Intergenic	Intergenic	290899	NR_106197	102465903		NR_106197	ENSMUSG00000099124	Mir8117	Gm27323|mmu-mir-8117	microRNA 8117	ncRNA
mm_119367.1	chr14	41122501	41122511	+	1	NA	exon (NM_133653, exon 10 of 10)	exon (NM_133653, exon 10 of 10)	-9282	NM_023134	20387	Mm.46062	NM_023134	ENSMUSG00000021789	Sftpa1	SP-A|Sftp-1|Sftp1	surfactant associated protein A1	protein-coding
mm_121165.1	chr14	103012894	103012902	+	1	NA	intron (NR_045657, intron 2 of 2)	intron (NR_045657, intron 2 of 2)	20905	NR_045657	71264	Mm.399572	NR_045657		4933432I03Rik	-	RIKEN cDNA 4933432I03 gene	ncRNA
mm_116324.1	chr13	37994053	37994060	-	1	NA	exon (NM_025965, exon 1 of 8)	exon (NM_025965, exon 1 of 8)	134	NM_025965	107513	Mm.426670	NM_025965	ENSMUSG00000021427	Ssr1	2510001K09Rik|6330400D04|AI159733|AI452176|SSR|TRAPA	signal sequence receptor, alpha	protein-coding
mm_124228.1	chr14	101198909	101198919	-	1	NA	exon (NM_029680, exon 3 of 3)	exon (NM_029680, exon 3 of 3)	1155	NM_029680	76627	Mm.31415	NM_029680	ENSMUSG00000042888	Prr30	1700110M21Rik	proline rich 30	protein-coding
mm_111036.1	chr12	79191840	79191861	-	1	NA	promoter-TSS (NM_021557)	promoter-TSS (NM_021557)	-31	NM_021557	17252	Mm.291799	NM_021557	ENSMUSG00000066441	Rdh11	2610319N22Rik|AI428145|AU045252|Arsdr1|C85936|CGI-82|HCBP12|M42C60|Mdt1|Psdr1|SCALD|UBE-1c1|Ube-1c	retinol dehydrogenase 11	protein-coding
mm_19494.1	chr2	93430218	93430229	-	1	NA	exon (NM_007656, exon 5 of 10)	exon (NM_007656, exon 5 of 10)	-8216	NR_105967	102465605		NR_105967	ENSMUSG00000099238	Mir7001	Gm27886|mmu-mir-7001	microRNA 7001	ncRNA
mm_4967.1	chr1	191281424	191281437	+	1	NA	Intergenic	Intergenic	36688	NM_025424	66208	Mm.46444	NM_025424	ENSMUSG00000037499	Nenf	1110060M21Rik|SCIRP10|Spuf	neuron derived neurotrophic factor	protein-coding
mm_154491.1	chrM	6182	6190	-	1	NA	NA	Intergenic	NA	NA								
mm_105321.1	chr11	102889463	102889478	-	1	NA	TTS (NM_001131020)	TTS (NM_001131020)	4301	NM_025766	66784	Mm.483216	NM_025766	ENSMUSG00000075510	Fam187a	4933439F11Rik	family with sequence similarity 187, member A	protein-coding
mm_141315.1	chr17	28361779	28361792	-	1	NA	intron (NM_021478, intron 8 of 14)	ID_B1|SINE|B4	3358	NM_021478	22157	Mm.42102	NM_021478	ENSMUSG00000037446	Tulp1	Tulp1l	tubby like protein 1	protein-coding
mm_78276.1	chr9	22100252	22100265	+	1	NA	intron (NM_009922, intron 1 of 6)	intron (NM_009922, intron 1 of 6)	1005	NM_009922	12797	Mm.4356	NM_009922	ENSMUSG00000001349	Cnn1	CN|CnnI	calponin 1	protein-coding
mm_93247.1	chr10	95417100	95417110	-	1	NA	promoter-TSS (NM_007706)	promoter-TSS (NM_007706)	-248	NM_007706	216233	Mm.474283	NM_007706	ENSMUSG00000020027	Socs2	8030460M17|AI527257|AW108012|CIS2|Cish2|D130043N08Rik|JAB|SOCS-2|SSI-2|hg	suppressor of cytokine signaling 2	protein-coding
mm_98894.1	chr11	97884539	97884549	+	1	NA	promoter-TSS (NM_001081435)	promoter-TSS (NM_001081435)	-390	NM_001081435	72973	Mm.245939	NM_001081435	ENSMUSG00000070336	Fbxo47	2900052P03Rik|Gm1562	F-box protein 47	protein-coding
mm_98123.1	chr11	87216461	87216481	+	1	NA	exon (NM_197987, exon 23 of 24)	exon (NM_197987, exon 23 of 24)	89396	NM_197987	68729	Mm.17436	NM_197987	ENSMUSG00000018548	Trim37	1110032A10Rik|2810004E07Rik|AI848587|AU043018|MUL|TEF3|mKIAA0898	tripartite motif-containing 37	protein-coding
mm_36793.1	chr4	103114317	103114348	-	1	NA	promoter-TSS (NM_027696)	promoter-TSS (NM_027696)	-33	NM_146254	242584	Mm.374877	NM_146254	ENSMUSG00000035126	Wdr78	BC028975	WD repeat domain 78	protein-coding
mm_172252.1	chr6	70144184	70144194	-	1	NA	Intergenic	Intergenic	647986	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_102419.1	chr11	59212667	59212688	-	1	NA	exon (NM_007476, exon 5 of 5)	exon (NM_007476, exon 5 of 5)	4316	NM_024210	67862	Mm.358708	NM_024210	ENSMUSG00000020441	2310033P09Rik	Mmtag2	RIKEN cDNA 2310033P09 gene	protein-coding
mm_60533.1	chr7	44480316	44480330	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-4194	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_77022.1	chr8	108584560	108584576	-	1	NA	non-coding (NR_077224, exon 1 of 2)	non-coding (NR_077224, exon 1 of 2)	109	NR_077224	109215	Mm.65282	NR_077224	ENSMUSG00000110613	Lncbate1	3010033K07Rik|Lnc-BATE1	brown adipose tissue enriched long non-coding RNA 1	ncRNA
mm_18241.1	chr2	52170509	52170519	-	1	NA	exon (NM_010889, exon 134 of 157)	exon (NM_010889, exon 134 of 157)	97677	NM_175238	51869	Mm.254530	NM_175238	ENSMUSG00000036202	Rif1	5730435J01Rik|6530403D07Rik|AU016181|AW549474|D2Ertd145e	replication timing regulatory factor 1	protein-coding
mm_50279.1	chr6	47045023	47045027	+	1	NA	intron (NM_001004357, intron 17 of 23)	CpG	-199371	NM_025771	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding
mm_125004.1	chr15	25363276	25363303	+	1	NA	TTS (NM_027395)	TTS (NM_027395)	50475	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	brain abundant, membrane attached signal protein 1	protein-coding
mm_42425.1	chr5	115327724	115327734	+	1	NA	intron (NR_036616, intron 1 of 4)	CpG	552	NR_036616	108014	Mm.287826	NM_025573	ENSMUSG00000029538	Srsf9	25kDa|2610029M16Rik|SRp30c|Sfrs9	serine/arginine-rich splicing factor 9	protein-coding
mm_102964.1	chr11	69665819	69665825	-	1	NA	exon (NM_001291058, exon 2 of 6)	exon (NM_001291058, exon 2 of 6)	348	NM_001291058	12514	Mm.15819	NM_009853	ENSMUSG00000018774	Cd68	Lamp4|Scard1|gp110	CD68 antigen	protein-coding
mm_15183.1	chr2	154193356	154193358	+	1	NA	intron (NM_001012392, intron 1 of 15)	intron (NM_001012392, intron 1 of 15)	2539	NM_001012392	228801	Mm.3783	NM_153418	ENSMUSG00000027485	Bpifb1	Lplunc1	BPI fold containing family B, member 1	protein-coding
mm_89797.1	chr10	102512217	102512292	+	1	NA	promoter-TSS (NM_146240)	promoter-TSS (NM_146240)	32	NM_146240	237504	Mm.282672	NM_146240	ENSMUSG00000044921	Rassf9	AW322107|Pamci	Ras association (RalGDS/AF-6) domain family (N-terminal) member 9	protein-coding
mm_67446.1	chr7	80389860	80389912	-	1	NA	3' UTR (NM_001081454, exon 16 of 16)	3' UTR (NM_001081454, exon 16 of 16)	-1940	NM_010194	14159	Mm.48757	NM_010194	ENSMUSG00000053158	Fes	AI586313|BB137047|FPS|c-fes	feline sarcoma oncogene	protein-coding
mm_100075.1	chr11	115462465	115462483	+	1	NA	promoter-TSS (NM_001080934)	promoter-TSS (NM_001080934)	1	NM_001080934	217316	Mm.25773	NM_001080934	ENSMUSG00000045775	Slc16a5	A130015N09Rik|MCT 5|MCT 6|MCT5	solute carrier family 16 (monocarboxylic acid transporters), member 5	protein-coding
mm_20806.1	chr2	144330771	144330781	-	1	NA	intron (NM_152947, intron 2 of 3)	CpG	586	NM_152947	107586	Mm.252750	NM_026924	ENSMUSG00000037279	Ovol2	1700108N11Rik|1810007D21Rik|M-OVO|M-OVO-A|M-OVO-B|MOVO|Ovo2|Zfp339|movo2	ovo like zinc finger 2	protein-coding
mm_16312.1	chr2	174298922	174298938	+	1	NA	exon (NM_001077507, exon 1 of 11)	exon (NM_001077507, exon 1 of 11)	1071	NM_001310085	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_84745.1	chr9	75407904	75407907	-	1	NA	intron (NM_015806, intron 1 of 5)	intron (NM_015806, intron 1 of 5)	1454	NM_027418	50772	Mm.480076	NM_015806	ENSMUSG00000042688	Mapk6	2610021I23Rik|D130053K17Rik|Erk3|Mapk4|Mapk63|Prkm4|Prkm6	mitogen-activated protein kinase 6	protein-coding
mm_1798.1	chr1	80225041	80225052	+	1	NA	Intergenic	Intergenic	-11102	NM_173425	241128	Mm.145511	NM_173425	ENSMUSG00000043230	Fam124b	A830043J08Rik	family with sequence similarity 124, member B	protein-coding
mm_33211.1	chr4	126556995	126557020	+	1	NA	promoter-TSS (NM_175554)	promoter-TSS (NM_175554)	27	NM_175554	269582	Mm.243962	NM_175554	ENSMUSG00000042489	Clspn	B130025E01|C85083|E130314M08Rik	claspin	protein-coding
mm_76307.1	chr8	84587623	84587633	-	1	NA	intron (NM_001252059, intron 28 of 45)	ZP3AR|Satellite|Satellite	75224	NM_010499	15936	Mm.399	NM_010499	ENSMUSG00000053560	Ier2	AI317238|Ch1|Pip92	immediate early response 2	protein-coding
mm_140453.1	chr17	88627360	88627434	+	1	NA	intron (NM_029858, intron 1 of 3)	MIRb|SINE|MIR	842	NM_029858	77057	Mm.482203	NM_029858	ENSMUSG00000033855	Ston1	4921524J06Rik|C86231|Salf|Sblf	stonin 1	protein-coding
mm_167484.1	chr8	129252951	129252973	+	1	NA	Intergenic	Intergenic	-10668	NM_001346808	102635552		NM_001346808		Gm32856	-	predicted gene, 32856	protein-coding
mm_77168.1	chr8	111689528	111689549	-	1	NA	TTS (NR_106044)	TTS (NR_106044)	136	NR_106044	102466993		NR_106044	ENSMUSG00000099129	Mir7076	Gm27318|mmu-mir-7076	microRNA 7076	ncRNA
mm_7363.1	chr1	106712389	106712428	-	1	NA	exon (NM_177410, exon 1 of 1)	exon (NM_177410, exon 1 of 1)	1882	NM_009741	12043	Mm.257460	NM_009741	ENSMUSG00000057329	Bcl2	AW986256|Bcl-2|C430015F12Rik|D630044D05Rik|D830018M01Rik	B cell leukemia/lymphoma 2	protein-coding
mm_75870.1	chr8	70764126	70764136	-	1	NA	intron (NM_023065, intron 5 of 7)	intron (NM_023065, intron 5 of 7)	2532	NM_023065	65972	Mm.30241	NM_023065	ENSMUSG00000031838	Ifi30	GILT|IP30	interferon gamma inducible protein 30	protein-coding
mm_7606.1	chr1	126483685	126483739	-	1	NA	intron (NM_001081756, intron 3 of 16)	intron (NM_001081756, intron 3 of 16)	9215	NM_172484	210356	Mm.377234	NM_172484	ENSMUSG00000049690	Nckap5	8430408F21|D130011D22Rik|E030049G20Rik|Erih1|Erih2|Gm1548|Nap5	NCK-associated protein 5	protein-coding
mm_52392.1	chr6	113301577	113301584	+	1	NA	intron (NM_170673, intron 17 of 19)	intron (NM_170673, intron 17 of 19)	-5557	NM_030178	78783	Mm.356059	NM_030178	ENSMUSG00000001632	Brpf1	4833438B11Rik|4930540D11Rik|Brpf2	bromodomain and PHD finger containing, 1	protein-coding
mm_112540.1	chr13	9883299	9883308	+	1	NA	intron (NM_033269, intron 4 of 4)	B4|SINE|B4	-117982	NM_144516	66505	Mm.397307	NM_144516	ENSMUSG00000021156	Zmynd11	2210402G22Rik|BS69	zinc finger, MYND domain containing 11	protein-coding
mm_7746.1	chr1	131058704	131058715	-	1	NA	exon (NM_008551, exon 2 of 10)	exon (NM_008551, exon 2 of 10)	38864	NM_010548	16153	Mm.874	NM_010548	ENSMUSG00000016529	Il10	CSIF|Il-10	interleukin 10	protein-coding
mm_114570.1	chr13	75089370	75089380	+	1	NA	promoter-TSS (NM_013628)	promoter-TSS (NM_013628)	-612	NM_013628	18548	Mm.1333	NM_013628	ENSMUSG00000021587	Pcsk1	Nec-1|Nec1|PC1|PC3|Phpp-1|SPC3	proprotein convertase subtilisin/kexin type 1	protein-coding
mm_12978.1	chr2	90777597	90777623	+	1	NA	exon (NM_018828, exon 15 of 17)	exon (NM_018828, exon 15 of 17)	-5134	NM_178755	271813	Mm.61146	NM_178755	ENSMUSG00000040812	Agbl2	4930524K04|A430081C19Rik|CCP2	ATP/GTP binding protein-like 2	protein-coding
mm_40454.1	chr5	53604037	53604047	+	1	NA	intron (NM_001277116, intron 3 of 12)	intron (NM_001277116, intron 3 of 12)	13556	NM_001080927	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_171871.1	chr5	28593996	28594004	-	1	NA	intron (NR_015562, intron 2 of 6)	L1Md_T|LINE|L1	-126899	NM_009170	20423	Mm.57202	NM_009170	ENSMUSG00000002633	Shh	9530036O11Rik|Dsh|Hhg1|Hx|Hxl3|M100081	sonic hedgehog	protein-coding
mm_51064.1	chr6	65952551	65952553	+	1	NA	promoter-TSS (NM_001161773)	promoter-TSS (NM_001161773)	-19	NM_001161773	67653	Mm.389756	NM_001161773	ENSMUSG00000036463	4930544G11Rik	-	RIKEN cDNA 4930544G11 gene	protein-coding
mm_7228.1	chr1	93343499	93343524	-	1	NA	promoter-TSS (NM_080850)	promoter-TSS (NM_080850)	-134	NM_023200	66385	Mm.88704	NM_023200	ENSMUSG00000026275	Ppp1r7	2310014J01Rik|SDS22	protein phosphatase 1, regulatory (inhibitor) subunit 7	protein-coding
mm_96341.1	chr11	66912005	66912044	+	1	NA	promoter-TSS (NM_178656)	promoter-TSS (NM_178656)	33	NM_178656	193003	Mm.440256	NM_178656	ENSMUSG00000048070	Pirt	A530088H08Rik	phosphoinositide-interacting regulator of transient receptor potential channels	protein-coding
mm_130815.1	chr15	101743100	101743117	-	1	NA	promoter-TSS (NM_019956)	promoter-TSS (NM_019956)	-11	NM_019956	56735	Mm.358677	NM_019956	ENSMUSG00000051879	Krt71	AA589543|Ca|Cal4|Cu|Krt2-6g|mK6irs|mK6irs1	keratin 71	protein-coding
mm_104227.1	chr11	88552590	88552599	-	1	NA	intron (NM_054043, intron 6 of 13)	intron (NM_054043, intron 6 of 13)	-66657	NR_131025	68397	Mm.426889	NR_131025		0610039H22Rik	-	RIKEN cDNA 0610039H22 gene	ncRNA
mm_130632.1	chr15	100424209	100424219	-	1	NA	non-coding (NR_040351, exon 1 of 3)	non-coding (NR_040351, exon 1 of 3)	1021	NR_040351	432982	Mm.234608	NM_001034883	ENSMUSG00000087444	Gm5475	EG432982	predicted gene 5475	ncRNA
mm_104950.1	chr11	100135940	100135954	-	1	NA	promoter-TSS (NM_008469)	promoter-TSS (NM_008469)	2	NM_008469	16665	Mm.440010	NM_008469	ENSMUSG00000054146	Krt15	AI528832|K15|Krt1-15	keratin 15	protein-coding
mm_138187.1	chr17	34268676	34268685	+	1	NA	intron (NM_207105, intron 5 of 5)	intron (NM_207105, intron 5 of 5)	5453	NM_207105	14961	Mm.254067	NM_207105	ENSMUSG00000073421	H2-Ab1	AI845868|Abeta|H-2Ab|H2-Ab|I-Abeta|IAb|Ia-2|Ia2|Rmcs1	histocompatibility 2, class II antigen A, beta 1	protein-coding
mm_118549.1	chr14	17659794	17659802	+	1	NA	Intergenic	Intergenic	-1162	NM_001113417	21834	Mm.32563	NM_009380	ENSMUSG00000021779	Thrb	Nr1a2|T3R[b]|T3Rbeta|Thrb1|Thrb2|c-erbAbeta	thyroid hormone receptor beta	protein-coding
mm_143237.1	chr17	63500301	63500314	-	1	NA	5' UTR (NM_015794, exon 1 of 9)	5' UTR (NM_015794, exon 1 of 9)	273	NM_015794	50758	Mm.136366	NM_015794	ENSMUSG00000023965	Fbxl17	6330576B01Rik|AI452053|BB073797|C130023C01Rik|Fbx13|Fbxo13	F-box and leucine-rich repeat protein 17	protein-coding
mm_143656.1	chr17	79713629	79713662	-	1	NA	exon (NM_009994, exon 2 of 3)	exon (NM_009994, exon 2 of 3)	1396	NM_009994	13078	Mm.214016	NM_009994	ENSMUSG00000024087	Cyp1b1	CP1B|P4501b1	cytochrome P450, family 1, subfamily b, polypeptide 1	protein-coding
mm_56841.1	chr6	117473116	117473131	-	1	NA	Intergenic	Intergenic	278646	NR_045731	72263	Mm.443289	NR_045731	ENSMUSG00000099869	1700030F04Rik	-	RIKEN cDNA 1700030F04 gene	ncRNA
mm_12250.1	chr2	68898876	68898893	+	1	NA	intron (NM_172856, intron 1 of 9)	intron (NM_172856, intron 1 of 9)	37443	NM_001347161	241447	Mm.222222	NM_172856	ENSMUSG00000027035	Cers6	4732462C07Rik|AW544719|Lass6|T1L	ceramide synthase 6	protein-coding
mm_85485.1	chr9	106096777	106096791	-	1	NA	promoter-TSS (NM_026763)	promoter-TSS (NM_026763)	-93	NM_026763	68553	Mm.28854	NM_026763	ENSMUSG00000032572	Col6a4	1110001D15Rik|AI413310|AU023415|Dvwa|EG235580|Vwa6	collagen, type VI, alpha 4	protein-coding
mm_125326.1	chr15	38518744	38518796	+	1	NA	intron (NR_125913, intron 1 of 11)	CpG	496	NM_001301688	54375	Mm.250214	NM_018745	ENSMUSG00000037458	Azin1	1700085L02Rik|AZI|Oazi|Oazin	antizyme inhibitor 1	protein-coding
mm_112535.1	chr13	9684240	9684250	+	1	NA	TTS (NM_001347480)	TTS (NM_001347480)	79565	NM_001347471	66505	Mm.397307	NM_144516	ENSMUSG00000021156	Zmynd11	2210402G22Rik|BS69	zinc finger, MYND domain containing 11	protein-coding
mm_137913.1	chr17	32113847	32113868	+	1	NA	Intergenic	CpG	-22434	NR_027316	435518	Mm.328944	NR_027316	ENSMUSG00000002791	Pdxk-ps	ENSMUSG00000002791|Gm9743	pyridoxal (pyridoxine, vitamin B6) kinase, pseudogene	pseudo
mm_25583.1	chr3	116870434	116870446	+	1	NA	intron (NM_009146, intron 2 of 16)	intron (NM_009146, intron 2 of 16)	8760	NM_009146	20321	Mm.66293	NM_009146	ENSMUSG00000033386	Frrs1	AI131732|Sdfr2	ferric-chelate reductase 1	protein-coding
mm_41455.1	chr5	90905693	90905701	+	1	NA	3' UTR (NM_009140, exon 4 of 4)	3' UTR (NM_009140, exon 4 of 4)	1798	NM_009140	20310	Mm.4979	NM_009140	ENSMUSG00000058427	Cxcl2	CINC-2a|GROb|Gro2|MIP-2|MIP-2a|Mgsa-b|Mip2|Scyb|Scyb2	chemokine (C-X-C motif) ligand 2	protein-coding
mm_47433.1	chr5	123178219	123178228	-	1	NA	exon (NM_008277, exon 8 of 14)	exon (NM_008277, exon 8 of 14)	4463	NM_008277	15445	Mm.439709	NM_008277	ENSMUSG00000029445	Hpd	Fla|Flp|Hppd|Laf	4-hydroxyphenylpyruvic acid dioxygenase	protein-coding
mm_48858.1	chr5	149680179	149680180	-	1	NA	intron (NM_001081204, intron 1 of 14)	intron (NM_001081204, intron 1 of 14)	1922	NM_001081204	381694	Mm.45060	NM_001081204	ENSMUSG00000051950	B3glct	B3galtl|Gm1057	beta-3-glucosyltransferase	protein-coding
mm_163271.1	chr11	115188656	115188680	-	1	NA	intron (NM_001033393, intron 2 of 9)	B3A|SINE|B2	1181	NM_001033393	320534	Mm.260587	NM_001033393	ENSMUSG00000045980	Tmem104	C630005D06Rik|mFLJ00021	transmembrane protein 104	protein-coding
mm_18289.1	chr2	52674743	52674745	-	1	NA	intron (NM_001285426, intron 2 of 13)	intron (NM_001285426, intron 2 of 13)	1115	NM_001285428	12298	Mm.330223	NM_146123	ENSMUSG00000017412	Cacnb4	3110038O15Rik|Cchb4|lh	calcium channel, voltage-dependent, beta 4 subunit	protein-coding
mm_123688.1	chr14	69635177	69635192	-	1	NA	intron (NM_033325, intron 2 of 13)	B1_Mus2|SINE|Alu	25708	NM_033325	94352	Mm.116714	NM_033325	ENSMUSG00000034205	Loxl2	1110004B06Rik|4930526G11Rik|9430067E15Rik	lysyl oxidase-like 2	protein-coding
mm_98670.1	chr11	96282969	96282994	+	1	NA	exon (NM_010461, exon 1 of 2)	exon (NM_010461, exon 1 of 2)	1076	NM_010461	15416	Mm.4822	NM_010461	ENSMUSG00000056648	Hoxb8	Hox-2.4	homeobox B8	protein-coding
mm_14752.1	chr2	144599947	144600039	+	1	NA	promoter-TSS (NM_025314)	promoter-TSS (NM_025314)	40	NM_025314	66044	Mm.28109	NM_025314	ENSMUSG00000027430	Dtd1	0610006H08Rik|DUE-B|Hars2	D-tyrosyl-tRNA deacylase 1	protein-coding
mm_93182.1	chr10	93820812	93820824	-	1	NA	Intergenic	Intergenic	-10737	NM_183199	327799	Mm.491598	NM_183199	ENSMUSG00000020020	Usp44	E430004F17Rik	ubiquitin specific peptidase 44	protein-coding
mm_172512.1	chr7	72654588	72654588	+	1	NA	Intergenic	L1Md_A|LINE|L1	-347993	NM_001024703	244049	Mm.217412	NM_001024703	ENSMUSG00000032776	Mctp2	Gm489	multiple C2 domains, transmembrane 2	protein-coding
mm_129721.1	chr15	81956198	81956241	-	1	NA	exon (NM_001282040, exon 3 of 7)	exon (NM_001282040, exon 3 of 7)	4711	NM_001282040	29858	Mm.18939	NM_013872	ENSMUSG00000022474	Pmm1	C77612	phosphomannomutase 1	protein-coding
mm_63023.1	chr7	121034740	121034765	+	1	NA	5' UTR (NM_021554, exon 1 of 5)	5' UTR (NM_021554, exon 1 of 5)	307	NM_021554	59052	Mm.29122	NM_021554	ENSMUSG00000030876	Mettl9	0610012D09Rik|AA517660|Drev|MNCb-5680	methyltransferase like 9	protein-coding
mm_123960.1	chr14	74876295	74876299	-	1	NA	intron (NM_001252132, intron 1 of 18)	intron (NM_001252132, intron 1 of 18)	71580	NM_001252132	380916	Mm.288868	NM_001033439	ENSMUSG00000068015	Lrch1	4832412D13Rik|AI552548|AW215503|Chdc1|mKIAA1016	leucine-rich repeats and calponin homology (CH) domain containing 1	protein-coding
mm_43983.1	chr5	146292629	146292649	+	1	NA	exon (NM_153599, exon 7 of 13)	exon (NM_153599, exon 7 of 13)	60964	NM_153599	264064	Mm.260576	NM_153599	ENSMUSG00000029635	Cdk8	-	cyclin-dependent kinase 8	protein-coding
mm_122266.1	chr14	34310564	34310585	-	1	NA	promoter-TSS (NM_008133)	promoter-TSS (NM_008133)	-71	NM_029389	75698	Mm.45406	NM_029389	ENSMUSG00000041471	Fam35a	3110001K24Rik	family with sequence similarity 35, member A	protein-coding
mm_28211.1	chr3	88369731	88369735	-	1	NA	promoter-TSS (NM_031368)	promoter-TSS (NM_031368)	98	NM_031368	12095	Mm.482191	NM_031368	ENSMUSG00000074489	Bglap3	AI461847|Bglap-rs1|OC-X|ORG|mOC-X	bone gamma-carboxyglutamate protein 3	protein-coding
mm_65732.1	chr7	28381933	28381943	-	1	NA	Intergenic	Intergenic	-2710	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_101402.1	chr11	26593916	26593943	-	1	NA	promoter-TSS (NM_027260)	promoter-TSS (NM_027260)	-9	NM_001252447	69922	Mm.285351	NM_027260	ENSMUSG00000064090	Vrk2	2810003O05Rik|AI447698	vaccinia related kinase 2	protein-coding
mm_107774.1	chr12	59140453	59140459	+	1	NA	intron (NM_001165253, intron 4 of 22)	intron (NM_001165253, intron 4 of 22)	9003	NM_001165253	338320	Mm.213215	NM_146034	ENSMUSG00000021000	Mia2	Ctage5|D12Bwg0579e|Mea6|Mgea|Mgea6	melanoma inhibitory activity 2	protein-coding
mm_102469.1	chr11	59983500	59983522	-	1	NA	exon (NM_001290013, exon 3 of 7)	exon (NM_001290013, exon 3 of 7)	-18567	NM_009026	19416	Mm.3903	NM_009026	ENSMUSG00000049892	Rasd1	Dexras1	RAS, dexamethasone-induced 1	protein-coding
mm_80097.1	chr9	70275890	70275911	+	1	NA	intron (NM_181072, intron 1 of 27)	intron (NM_181072, intron 1 of 27)	68550	NM_181072	71602	Mm.249311	NM_181072	ENSMUSG00000032220	Myo1e	2310020N23Rik|9130023P14Rik|AA407778|myosin-1e|myr 3	myosin IE	protein-coding
mm_55801.1	chr6	82774449	82774463	-	1	NA	promoter-TSS (NM_013820)	promoter-TSS (NM_013820)	-2	NM_013820	15277	Mm.255848	NM_013820	ENSMUSG00000000628	Hk2	AI642394|HKII	hexokinase 2	protein-coding
mm_153119.1	chr19	33392232	33392242	-	1	NA	promoter-TSS (NM_001146342)	promoter-TSS (NM_001146342)	58	NM_001167818	67795	Mm.204591	NM_001146342	ENSMUSG00000071573	Rnls	6530404N21Rik|AI452315|AW060440|C10orf59	renalase, FAD-dependent amine oxidase	protein-coding
mm_151020.1	chr19	46819496	46819538	+	1	NA	intron (NM_033569, intron 1 of 7)	ORR1B2|LTR|ERVL-MaLR	57908	NM_001102471	94219	Mm.306903	NM_033569	ENSMUSG00000064105	Cnnm2	AU015877|AW048635|Acdp2|Clp2	cyclin M2	protein-coding
mm_37207.1	chr4	117872745	117872792	-	1	NA	promoter-TSS (NM_001034876)	promoter-TSS (NM_001034876)	-298	NM_001034876	381546	Mm.440118	NM_001034876	ENSMUSG00000078588	Ccdc24	Gm1028	coiled-coil domain containing 24	protein-coding
mm_112988.1	chr13	21495219	21495260	+	1	NA	Intergenic	Intergenic	11285	NR_026798	100038371	Mm.133328	NR_026798		Zfp389	ENSMUSG00000075041|OTTMUSG00000018077	zinc finger protein 389	pseudo
mm_103868.1	chr11	83524730	83524734	-	1	NA	Intergenic	B1_Mus1|SINE|Alu	-2633	NM_001045543	629303	Mm.390417	NM_001045543	ENSMUSG00000018925	Heatr9	Gm11435|OTTMUSG00000000990	HEAT repeat containing 9	protein-coding
mm_1177.1	chr1	61638820	61638841	+	1	NA	promoter-TSS (NM_001081050)	promoter-TSS (NM_001081050)	6	NM_001081050	72823	Mm.35153	NM_001081050	ENSMUSG00000052062	Pard3b	1810008K04Rik|2010002N16Rik|2810455B10Rik|Als2cr19|PAR3B|PAR3L|PAR3beta	par-3 family cell polarity regulator beta	protein-coding
mm_40204.1	chr5	37028459	37028491	+	1	NA	Intergenic	CpG	-22382	NM_178394	76071	Mm.85280	NM_178394	ENSMUSG00000063646	Jakmip1	5830437M04Rik|C330021K24Rik|Gababrbp|Marlin-1	janus kinase and microtubule interacting protein 1	protein-coding
mm_163126.1	chr11	77200961	77200963	-	1	NA	Intergenic	Intergenic	-11994	NM_176965	319634	Mm.108786	NM_176965	ENSMUSG00000050944	Efcab5	4930563A03Rik	EF-hand calcium binding domain 5	protein-coding
mm_29405.1	chr3	108907804	108907824	-	1	NA	exon (NM_025845, exon 4 of 6)	exon (NM_025845, exon 4 of 6)	3890	NM_025845	66921	Mm.51049	NM_025845	ENSMUSG00000027881	Prpf38b	1110021E09Rik|AU018955	PRP38 pre-mRNA processing factor 38 (yeast) domain containing B	protein-coding
mm_76271.1	chr8	84104779	84104793	-	1	NA	promoter-TSS (NM_172502)	promoter-TSS (NM_172502)	-24	NM_172502	212123	Mm.260557	NM_172502	ENSMUSG00000037103	Dcaf15	6720484B16	DDB1 and CUL4 associated factor 15	protein-coding
mm_42078.1	chr5	110176554	110176565	+	1	NA	promoter-TSS (NM_008146)	promoter-TSS (NM_008146)	-55	NR_040430	100504007	Mm.441495	NR_040430	ENSMUSG00000086247	Gm15787	OTTMUSG00000026209	predicted gene 15787	ncRNA
mm_106261.1	chr11	117967960	117967967	-	1	NA	exon (NM_007707, exon 2 of 2)	exon (NM_007707, exon 2 of 2)	1403	NM_007707	12702	Mm.3468	NM_007707	ENSMUSG00000053113	Socs3	Cis3|Cish3|EF-10|Ef10|SSI-3|Ssi3	suppressor of cytokine signaling 3	protein-coding
mm_139372.1	chr17	51832758	51832777	+	1	NA	promoter-TSS (NM_009122)	promoter-TSS (NM_009122)	-120	NM_009122	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_21177.1	chr2	154892832	154892883	-	1	NA	promoter-TSS (NM_026030)	promoter-TSS (NM_026030)	49	NM_026030	67204	Mm.377134	NM_026030	ENSMUSG00000074656	Eif2s2	2810026E11Rik|38kDa|AA408636|AA571381|AA986487|AW822225|D2Ertd303e|EIF2|EIF2B	eukaryotic translation initiation factor 2, subunit 2 (beta)	protein-coding
mm_43058.1	chr5	124194895	124194912	+	1	NA	intron (NM_011256, intron 2 of 24)	intron (NM_011256, intron 2 of 24)	-7721	NM_001289472	19679	Mm.44261	NM_011256	ENSMUSG00000029406	Pitpnm2	NIR3|RDGBA2|Rdgb2|mKIAA1457	phosphatidylinositol transfer protein, membrane-associated 2	protein-coding
mm_125104.1	chr15	27770986	27770996	+	1	NA	intron (NM_001081302, intron 36 of 56)	intron (NM_001081302, intron 36 of 56)	-89449	NM_001242423	223433	Mm.266485	NM_198301	ENSMUSG00000056069	Fam105a	9830126M18	family with sequence similarity 105, member A	protein-coding
mm_149304.1	chr19	10732117	10732131	+	1	NA	intron (NM_007650, intron 1 of 10)	(CACCAT)n|Simple_repeat|Simple_repeat	6850	NM_007650	12507	Mm.779	NM_007650	ENSMUSG00000024669	Cd5	Ly-1|Ly-12|Ly-A|Lyt-1	CD5 antigen	protein-coding
mm_13371.1	chr2	103575370	103575373	+	1	NA	intron (NM_178890, intron 1 of 16)	intron (NM_178890, intron 1 of 16)	9061	NM_178890	99382	Mm.35850	NM_178890	ENSMUSG00000032724	Abtb2	AW539457|BPOZ-2	ankyrin repeat and BTB (POZ) domain containing 2	protein-coding
mm_80665.1	chr9	90074082	90074092	+	1	NA	intron (NM_001312649, intron 9 of 10)	intron (NM_001312649, intron 9 of 10)	19820	NM_001312649	13036	Mm.2277	NM_007801	ENSMUSG00000032359	Ctsh	AL022844	cathepsin H	protein-coding
mm_1536.1	chr1	72849627	72849654	+	1	NA	exon (NM_008342, exon 3 of 4)	exon (NM_008342, exon 3 of 4)	24253	NM_001310659	16008	Mm.141936	NM_008342	ENSMUSG00000039323	Igfbp2	AI255832|IBP-2|Igfbp-2|mIGFBP-2	insulin-like growth factor binding protein 2	protein-coding
mm_147717.1	chr18	60812642	60812649	-	1	NA	TTS (NM_010545)	TTS (NM_010545)	569	NR_039567	100628611		NR_039567	ENSMUSG00000093327	Mir5107	mir-5107|mmu-mir-5107|mu-mir-5107	microRNA 5107	ncRNA
mm_58791.1	chr7	16130286	16130333	+	1	NA	5' UTR (NM_148946, exon 1 of 10)	5' UTR (NM_148946, exon 1 of 10)	483	NM_148946	110891	Mm.241147	NM_148946	ENSMUSG00000030376	Slc8a2	Ncx2	solute carrier family 8 (sodium/calcium exchanger), member 2	protein-coding
mm_16123.1	chr2	170133660	170133679	+	1	NA	intron (NM_001159683, intron 1 of 6)	CpG	-2449	NM_001033299	228913	Mm.22858	NM_001033299	ENSMUSG00000052056	Zfp217	4933431C08Rik|AW987152|Gm562|ZABC1|Znf217	zinc finger protein 217	protein-coding
mm_68182.1	chr7	104129787	104129788	-	1	NA	promoter-TSS (NM_027634)	promoter-TSS (NM_027634)	36	NM_027634	70980	Mm.158518	NM_027634	ENSMUSG00000055643	4931431F19Rik	-	RIKEN cDNA 4931431F19 gene	protein-coding
mm_138984.1	chr17	45487408	45487422	+	1	NA	Intergenic	Intergenic	-12477	NM_027649	71020	Mm.44257	NM_027649	ENSMUSG00000023935	Spats1	1700011H05Rik|4933400B06Rik|Daip2|Ddip|Srsp1	spermatogenesis associated, serine-rich 1	protein-coding
mm_32767.1	chr4	116693720	116693745	+	1	NA	exon (NM_011034, exon 5 of 6)	exon (NM_011034, exon 5 of 6)	-7710	NR_040442	100502959	Mm.395400	NR_040442		AV051173	-	expressed sequence AV051173	ncRNA
mm_106399.1	chr11	118868923	118868937	-	1	NA	intron (NM_001285437, intron 1 of 13)	(ATGGTG)n|Simple_repeat|Simple_repeat	40642	NM_001024931	52897	Mm.341103	NM_001024931	ENSMUSG00000025576	Rbfox3	Fox-3|Hrnbp3|NeuN|Neuna60	RNA binding protein, fox-1 homolog (C. elegans) 3	protein-coding
mm_71111.1	chr8	35723662	35723680	+	1	NA	Intergenic	RLTR42|LTR|ERVK	102888	NM_027998	71908	Mm.37817	NM_027998	ENSMUSG00000055976	Cldn23	2310014B08Rik	claudin 23	protein-coding
mm_141155.1	chr17	26506611	26506631	-	1	NA	exon (NM_013642, exon 4 of 4)	exon (NM_013642, exon 4 of 4)	1851	NM_013642	19252	Mm.239041	NM_013642	ENSMUSG00000024190	Dusp1	3CH134|MKP1|Ptpn16|U19515|erp|mkp-1	dual specificity phosphatase 1	protein-coding
mm_135110.1	chr16	35769497	35769534	-	1	NA	promoter-TSS (NM_153550)	promoter-TSS (NM_153550)	-159	NM_153550	224132	Mm.24094	NM_153550	ENSMUSG00000022848	Dirc2	RCC4	disrupted in renal carcinoma 2 (human)	protein-coding
mm_72852.1	chr8	88320819	88320841	+	1	NA	intron (NM_001037723, intron 17 of 27)	RSINE1|SINE|B4	26626	NM_001037724	11513	Mm.288206	NM_007406	ENSMUSG00000031659	Adcy7	AA407758	adenylate cyclase 7	protein-coding
mm_69437.1	chr7	132888641	132888657	-	1	NA	Intergenic	Intergenic	29424	NM_198017	109359	Mm.274824	NM_198017	ENSMUSG00000030965	Fam175b	AA589499|AI853413|Abro1|C430003P19Rik	family with sequence similarity 175, member B	protein-coding
mm_159792.1	chr5	109419783	109419783	+	1	NA	promoter-TSS (NM_001104628)	promoter-TSS (NM_001104628)	-230	NM_001104628	384221	Mm.469879	NM_001104628	ENSMUSG00000091879	Vmn2r17	EG384221	vomeronasal 2, receptor 17	protein-coding
mm_121357.1	chr14	117004577	117004580	+	1	NA	intron (NM_001079844, intron 1 of 9)	intron (NM_001079844, intron 1 of 9)	79281	NM_011821	23888	Mm.440025	NM_011821	ENSMUSG00000058571	Gpc6	-	glypican 6	protein-coding
mm_111524.1	chr12	100203694	100203724	-	1	NA	exon (NM_009790, exon 3 of 6)	exon (NM_009790, exon 3 of 6)	3565	NM_001313934	12313	Mm.285993	NM_009790	ENSMUSG00000001175	Calm1	AI256814|AI327027|AI461935|AL024000|CaM|Calm	calmodulin 1	protein-coding
mm_101238.1	chr11	20694916	20694919	-	1	NA	intron (NM_181411, intron 7 of 8)	intron (NM_181411, intron 7 of 8)	46639	NM_001290545	216549	Mm.356580	NM_181411	ENSMUSG00000049659	Aftph	-	aftiphilin	protein-coding
mm_115016.1	chr13	98355085	98355096	+	1	NA	exon (NM_008242, exon 1 of 1)	exon (NM_008242, exon 1 of 1)	845	NM_008242	15229	Mm.347441	NM_008242	ENSMUSG00000078302	Foxd1	AI385632|BF-2|FREAC4|Hfh10|Hfhbf2	forkhead box D1	protein-coding
mm_140626.1	chr17	12318768	12318803	-	1	NA	promoter-TSS (NR_045290)	promoter-TSS (NR_045290)	-68	NR_045290	224523	Mm.188855	NR_045290	ENSMUSG00000097350	4732491K20Rik	-	RIKEN cDNA 4732491K20 gene	ncRNA
mm_29579.1	chr3	117321497	117321504	-	1	NA	3' UTR (NM_177664, exon 7 of 7)	3' UTR (NM_177664, exon 7 of 7)	39376	NM_177664	229791	Mm.140138	NM_177664	ENSMUSG00000044667	Plppr4	A330086D10|D3Bwg0562e|Lppr4|PRG-1|mKIAA0455	phospholipid phosphatase related 4	protein-coding
mm_75617.1	chr8	64205971	64206011	-	1	NA	promoter-TSS (NM_009390)	promoter-TSS (NM_009390)	2	NM_009390	21892	Mm.418367	NM_009390	ENSMUSG00000053626	Tll1	Tll|Tll-1	tolloid-like	protein-coding
mm_125922.1	chr15	76199551	76199562	+	1	NA	promoter-TSS (NM_201392)	promoter-TSS (NM_201392)	-150	NM_201392	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
mm_47478.1	chr5	123736614	123736638	-	1	NA	exon (NM_001005525, exon 6 of 10)	exon (NM_001005525, exon 6 of 10)	12788	NM_001005525	208606	Mm.276341	NM_025438	ENSMUSG00000029422	Rsrc2	1500011J06Rik	arginine/serine-rich coiled-coil 2	protein-coding
mm_48933.1	chr6	4537846	4537879	+	1	NA	exon (NM_007743, exon 49 of 52)	exon (NM_007743, exon 49 of 52)	32244	NM_007743	12843	Mm.277792	NM_007743	ENSMUSG00000029661	Col1a2	AA960264|AI325291|Col1a-2|Cola-2|Cola2|oim	collagen, type I, alpha 2	protein-coding
mm_47924.1	chr5	135012763	135012808	-	1	NA	TTS (NM_001190437)	TTS (NM_001190437)	372	NR_026688	69812	Mm.18422	NR_026688	ENSMUSG00000085042	Abhd11os	2010001M06Rik|AI462243|Wbscr26|Wnscr26	abhydrolase domain containing 11, opposite strand	ncRNA
mm_145782.1	chr18	65077632	65077639	+	1	NA	intron (NM_001114386, intron 3 of 30)	intron (NM_001114386, intron 3 of 30)	54108	NM_031881	83814	Mm.98668	NM_031881	ENSMUSG00000024589	Nedd4l	1300012C07Rik|Nedd4-2|Nedd4b	neural precursor cell expressed, developmentally down-regulated gene 4-like	protein-coding
mm_2937.1	chr1	132299303	132299312	+	1	NA	exon (NM_144810, exon 1 of 5)	exon (NM_144810, exon 1 of 5)	681	NM_144810	213417	Mm.39723	NM_144810	ENSMUSG00000042115	Klhdc8a	A630065K24Rik	kelch domain containing 8A	protein-coding
mm_40049.1	chr5	33983676	33983709	+	1	NA	intron (NM_001310547, intron 1 of 3)	CpG	259	NM_001310546	381633	Mm.4923	NM_001033458	ENSMUSG00000070858	Gm1673	-	predicted gene 1673	protein-coding
mm_103676.1	chr11	79243315	79243345	-	1	NA	promoter-TSS (NM_001042565)	promoter-TSS (NM_001042565)	-306	NM_001042565	78889	Mm.307022	NM_019653	ENSMUSG00000017677	Wsb1	1110056B13Rik|2700038M07Rik	WD repeat and SOCS box-containing 1	protein-coding
mm_17673.1	chr2	32236366	32236373	-	1	NA	promoter-TSS (NM_145145)	promoter-TSS (NM_145145)	-314	NM_145145	99011	Mm.31192	NM_145145	ENSMUSG00000039254	Pomt1	AI505244	protein-O-mannosyltransferase 1	protein-coding
mm_81360.1	chr9	108689336	108689353	+	1	NA	Intergenic	Intergenic	-2799	NM_008924	19087	Mm.253102	NM_008924	ENSMUSG00000032601	Prkar2a	1110061A24Rik|AI317181|AI836829|RII(alpha)	protein kinase, cAMP dependent regulatory, type II alpha	protein-coding
mm_75920.1	chr8	71485998	71486035	-	1	NA	promoter-TSS (NM_001164679)	promoter-TSS (NM_001164679)	51	NM_001164679	382014	Mm.260360	NM_001164679	ENSMUSG00000034863	Ano8	BC053460|Tmem16h	anoctamin 8	protein-coding
mm_40184.1	chr5	36237718	36237727	+	1	NA	intron (NM_030889, intron 1 of 26)	Lx5c|LINE|L1	33701	NM_175249	76943	Mm.44242	NM_175249	ENSMUSG00000043430	Psapl1	2310020A21Rik	prosaposin-like 1	protein-coding
mm_101882.1	chr11	48928225	48928229	-	1	NA	Intergenic	Intergenic	-1045	NM_001045540	620913	Mm.452174	NM_001045540	ENSMUSG00000048852	Gm12185	Irgb2b1|OTTMUSG00000005523	predicted gene 12185	protein-coding
mm_35354.1	chr4	32280693	32280706	-	1	NA	Intergenic	Intergenic	-136736	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_156416.1	chrX	140664909	140664942	+	1	NA	Intergenic	CpG	-13103	NM_011845	23947	Mm.131097	NM_011845	ENSMUSG00000000266	Mid2	FXY2|Trim1	midline 2	protein-coding
mm_61674.1	chr7	80830812	80830846	+	1	NA	Intergenic	RLTR19-int|LTR|ERVK	-27498	NM_016721	29875	Mm.207619	NM_016721	ENSMUSG00000030536	Iqgap1	AA682088|D7Ertd237e|D7Ertd257e|mKIAA0051	IQ motif containing GTPase activating protein 1	protein-coding
mm_137742.1	chr17	29368990	29369008	+	1	NA	intron (NM_001159538, intron 8 of 15)	intron (NM_001159538, intron 8 of 15)	8085	NM_001159538	26382	Mm.279187	NM_013710	ENSMUSG00000024013	Fgd2	Tcd-2|Tcd2|ZFYVE4|tcs-2|tcs2	FYVE, RhoGEF and PH domain containing 2	protein-coding
mm_87700.1	chr10	59861483	59861503	+	1	NA	intron (NM_001291443, intron 11 of 12)	intron (NM_001291443, intron 11 of 12)	-18098	NM_019965	56709	Mm.103610	NM_019965	ENSMUSG00000020109	Dnajb12	Dj10|mDj10	DnaJ heat shock protein family (Hsp40) member B12	protein-coding
mm_1669.1	chr1	74779415	74779436	+	1	NA	intron (NM_009526, intron 1 of 3)	intron (NM_009526, intron 1 of 3)	7533	NM_009526	22420	Mm.268282	NM_009526	ENSMUSG00000033227	Wnt6	AA409270|Wnt-6	wingless-type MMTV integration site family, member 6	protein-coding
mm_170128.1	chr17	39847142	39847151	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	4149	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_16757.1	chr2	9869405	9869413	-	1	NA	intron (NM_008091, intron 3 of 5)	intron (NM_008091, intron 3 of 5)	9191	NM_008091	14462	Mm.313866	NM_008091	ENSMUSG00000015619	Gata3	Gata-3|jal	GATA binding protein 3	protein-coding
mm_1315.1	chr1	65080229	65080246	+	1	NA	TTS (NM_144761)	TTS (NM_144761)	2053	NM_144761	12965	Mm.440053	NM_144761	ENSMUSG00000073658	Crygb	Cryg-3|DGcry-3|Nop	crystallin, gamma B	protein-coding
mm_29972.1	chr3	133544406	133544412	-	1	NA	promoter-TSS (NM_001346736)	promoter-TSS (NM_001346736)	-19	NM_001040400	214133	Mm.347816	NM_145989	ENSMUSG00000040943	Tet2	Ayu17-449|E130014J05Rik|mKIAA1546	tet methylcytosine dioxygenase 2	protein-coding
mm_167558.1	chr9	37008199	37008200	+	1	NA	intron (NM_001029838, intron 2 of 12)	intron (NM_001029838, intron 2 of 12)	139123	NM_148950	208076	Mm.260335	NM_148950	ENSMUSG00000035934	Pknox2	D230005H23Rik|Prep2	Pbx/knotted 1 homeobox 2	protein-coding
mm_7485.1	chr1	121327652	121327657	-	1	NA	promoter-TSS (NM_001271531)	promoter-TSS (NM_001271531)	24	NM_001271531	72999	Mm.27136	NM_133748	ENSMUSG00000003721	Insig2	2900053I11Rik|C730043J18Rik|Insig-2	insulin induced gene 2	protein-coding
mm_69253.1	chr7	127850985	127851003	-	1	NA	Intergenic	RSINE1|SINE|B4	9186	NM_009294	20909	Mm.24867	NM_009294	ENSMUSG00000030805	Stx4a	Stx4|Syn-4|Syn4	syntaxin 4A (placental)	protein-coding
mm_43993.1	chr5	146795939	146795954	+	1	NA	promoter-TSS (NM_011669)	promoter-TSS (NM_011669)	-990	NM_011669	22217	Mm.167971	NM_011669	ENSMUSG00000029640	Usp12	Ubh1	ubiquitin specific peptidase 12	protein-coding
mm_3700.1	chr1	153762582	153762614	+	1	NA	3' UTR (NM_011882, exon 9 of 9)	3' UTR (NM_011882, exon 9 of 9)	13172	NM_011882	24014	Mm.259254	NM_011882	ENSMUSG00000066800	Rnasel	E230029I04Rik	ribonuclease L (2', 5'-oligoisoadenylate synthetase-dependent)	protein-coding
mm_126159.1	chr15	78428626	78428636	+	1	NA	promoter-TSS (NM_001289671)	promoter-TSS (NM_001289671)	67	NR_110357	72844	Mm.390816	NM_001081367	ENSMUSG00000033287	Kctd17	2900008M13Rik|AA414907|AW742389|N28155	potassium channel tetramerisation domain containing 17	protein-coding
mm_79292.1	chr9	51272887	51272891	+	1	NA	intron (NM_001195681, intron 3 of 4)	intron (NM_001195681, intron 3 of 4)	5665	NM_001195681	100502940	Mm.235705	NM_001195681	ENSMUSG00000079559	Gm684	-	predicted gene 684	protein-coding
mm_59195.1	chr7	24501625	24501637	+	1	NA	exon (NM_153112, exon 7 of 9)	exon (NM_153112, exon 7 of 9)	-5456	NM_001290461	232969	Mm.181332	NM_146183	ENSMUSG00000064264	Zfp428	2410005H09Rik|AV271806|AW047854|Znf428	zinc finger protein 428	protein-coding
mm_120479.1	chr14	65975653	65975659	+	1	NA	exon (NM_013492, exon 5 of 9)	exon (NM_013492, exon 5 of 9)	7173	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_43915.1	chr5	144545884	144545889	+	1	NA	promoter-TSS (NM_016789)	promoter-TSS (NM_016789)	-1	NM_016789	53324	Mm.10099	NM_016789	ENSMUSG00000059991	Nptx2	Narp|np2	neuronal pentraxin 2	protein-coding
mm_76122.1	chr8	80869144	80869152	-	1	NA	intron (NM_021356, intron 1 of 9)	C-rich|Low_complexity|Low_complexity	11331	NM_021356	14388	Mm.277409	NM_021356	ENSMUSG00000031714	Gab1	AA408973|AW107238	growth factor receptor bound protein 2-associated protein 1	protein-coding
mm_47742.1	chr5	130255331	130255339	-	1	NA	promoter-TSS (NM_178897)	promoter-TSS (NM_178897)	195	NM_023248	66711	Mm.280484	NM_023248	ENSMUSG00000025337	Sbds	4733401P19Rik|AI836084|CGI-97|SDS	Shwachman-Bodian-Diamond syndrome homolog (human)	protein-coding
mm_74877.1	chr8	25054872	25054884	-	1	NA	intron (NM_031257, intron 9 of 11)	intron (NM_031257, intron 9 of 11)	-15916	NM_001081187	330723	Mm.334452	NM_001081187	ENSMUSG00000037406	Htra4	B430206E18Rik	HtrA serine peptidase 4	protein-coding
mm_104090.1	chr11	86635512	86635535	-	1	NA	intron (NM_029478, intron 6 of 11)	intron (NM_029478, intron 6 of 11)	-20548	NR_106195	102465902		NR_106195	ENSMUSG00000099324	Mir8115	Gm28012|mmu-mir-8115	microRNA 8115	ncRNA
mm_25563.1	chr3	116563009	116563027	+	1	NA	promoter-TSS (NM_175413)	promoter-TSS (NM_175413)	45	NM_175413	109245	Mm.216027	NM_027321	ENSMUSG00000027961	Lrrc39	2010005E21Rik|9430028I06Rik|Myomasp	leucine rich repeat containing 39	protein-coding
mm_157664.1	chrX	58038650	58038658	-	1	NA	Intergenic	CpG	8026	NM_009575	22773	Mm.255890	NM_009575	ENSMUSG00000067860	Zic3	Bn|Ka	zinc finger protein of the cerebellum 3	protein-coding
mm_97655.1	chr11	79528133	79528137	+	1	NA	5' UTR (NM_001033711, exon 2 of 2)	5' UTR (NM_001033711, exon 2 of 2)	2474	NM_146023	101488212	Mm.439665	NM_146023	ENSMUSG00000070354	Gm21975	Evi2a-evi2b	predicted gene 21975	protein-coding
mm_172630.1	chr8	20424700	20424716	-	1	NA	non-coding (NR_028428, exon 1 of 6)	non-coding (NR_028428, exon 1 of 6)	106	NR_028428	381598	Mm.359054	NM_001024708	ENSMUSG00000071793	2610005L07Rik	2810038F24Rik|6720476A01Rik	cadherin 11 pseudogene	pseudo
mm_30337.1	chr3	151732334	151732340	-	1	NA	3' UTR (NM_133871, exon 8 of 8)	3' UTR (NM_133871, exon 8 of 8)	17622	NM_133871	99899	Mm.30756	NM_133871	ENSMUSG00000028037	Ifi44	A430056A10Rik|AW261460|MTAP44|p44	interferon-induced protein 44	protein-coding
mm_157275.1	chrX	20307283	20307286	-	1	NA	Intergenic	Intergenic	-15520	NM_177353	236727	Mm.132983	NM_177353	ENSMUSG00000037341	Slc9a7	A530087D17Rik|NHE7	solute carrier family 9 (sodium/hydrogen exchanger), member 7	protein-coding
mm_145436.1	chr18	58836722	58836751	+	1	NA	5' UTR (NM_175506, exon 1 of 23)	5' UTR (NM_175506, exon 1 of 23)	373	NM_175506	240322	Mm.71963	NM_175506	ENSMUSG00000053441	Adamts19	4831407I23Rik|AU015154|D230034E10Rik	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 19	protein-coding
mm_163545.1	chr13	18745099	18745112	+	1	NA	intron (NM_172120, intron 3 of 28)	intron (NM_172120, intron 3 of 28)	27813	NM_172120	218035	Mm.27389	NM_172120	ENSMUSG00000041236	Vps41	AI317346|Vam2|mVam2	VPS41 HOPS complex subunit	protein-coding
mm_55238.1	chr6	52260781	52260793	-	1	NA	promoter-TSS (NM_008264)	promoter-TSS (NM_008264)	93	NM_008264	15398	Mm.377086	NM_008264		Hoxa13	Hd|Hox-1.10	homeobox A13	protein-coding
mm_75542.1	chr8	57487591	57487605	-	1	NA	promoter-TSS (NR_126555)	promoter-TSS (NR_126555)	262	NM_021788	60406	Mm.118	NM_021788	ENSMUSG00000031609	Sap30	30kDa	sin3 associated polypeptide	protein-coding
mm_76046.1	chr8	77610598	77610643	-	1	NA	promoter-TSS (NM_145599)	promoter-TSS (NM_145599)	33	NM_145599	234463	Mm.273578	NM_145599	ENSMUSG00000031617	Tmem184c	8430433H16Rik|AI645453|AL033298|BC004056|Tmem34	transmembrane protein 184C	protein-coding
mm_97403.1	chr11	77850723	77850733	+	1	NA	intron (NM_001291214, intron 34 of 38)	intron (NM_001291214, intron 34 of 38)	43144	NM_008952	19193	Mm.8543	NM_008952	ENSMUSG00000017453	Pipox	LPIPOX|Pso	pipecolic acid oxidase	protein-coding
mm_35488.1	chr4	40942858	40942869	-	1	NA	intron (NM_009736, intron 3 of 6)	intron (NM_009736, intron 3 of 6)	5431	NM_009736	12017	Mm.688	NM_009736	ENSMUSG00000028416	Bag1	BAG-1|Rap46	BCL2-associated athanogene 1	protein-coding
mm_106050.1	chr11	116080617	116080628	-	1	NA	exon (NM_016852, exon 5 of 8)	exon (NM_016852, exon 5 of 8)	-2661	NM_001009573	70450	Mm.259460	NM_001009573	ENSMUSG00000057948	Unc13d	2610108D09Rik|Jinx|Munc13-4|mFLJ00067	unc-13 homolog D (C. elegans)	protein-coding
mm_149172.1	chr19	9085184	9085204	+	1	NA	exon (NM_011681, exon 2 of 3)	exon (NM_011681, exon 2 of 3)	2762	NM_011681	22287	Mm.2258	NM_011681	ENSMUSG00000024653	Scgb1a1	CC10|CC16|CCSP|PCB-BP|UG|UGB|Utg	secretoglobin, family 1A, member 1 (uteroglobin)	protein-coding
mm_133495.1	chr16	90386008	90386023	+	1	NA	promoter-TSS (NM_015755)	promoter-TSS (NM_015755)	-382	NM_015755	26559	Mm.125874	NM_015755	ENSMUSG00000053414	Hunk	Bstk1|Mak-v	hormonally upregulated Neu-associated kinase	protein-coding
mm_114755.1	chr13	85126736	85126769	+	1	NA	Intergenic	Intergenic	-62633	NM_001347587	66671	Mm.18474	NM_023243	ENSMUSG00000021548	Ccnh	6330408H09Rik|AI661354|AV102684|AW538719	cyclin H	protein-coding
mm_121600.1	chr14	7994588	7994596	-	1	NA	promoter-TSS (NM_007870)	promoter-TSS (NM_007870)	-410	NM_007870	13421	Mm.272258	NM_007870	ENSMUSG00000025279	Dnase1l3	DNasegamma|Dhp2|Lsd	deoxyribonuclease 1-like 3	protein-coding
mm_16570.1	chr2	3422562	3422573	-	1	NA	promoter-TSS (NM_008579)	promoter-TSS (NM_008579)	81	NM_008579	104362	Mm.2688	NM_008579	ENSMUSG00000026650	Meig1	MLZ-278|Meg1	meiosis expressed gene 1	protein-coding
mm_52363.1	chr6	112696353	112696384	+	1	NA	intron (NM_001167730, intron 1 of 13)	CpG	302	NM_021385	58186	Mm.103812	NM_021385	ENSMUSG00000030254	Rad18	2810024C04Rik|Rad18sc	RAD18 E3 ubiquitin protein ligase	protein-coding
mm_76004.1	chr8	72491687	72491706	-	1	NA	intron (NM_177766, intron 2 of 5)	intron (NM_177766, intron 2 of 5)	918	NM_177766	270066	Mm.291461	NM_177766	ENSMUSG00000019731	Slc35e1	6030458H05|AA408278	solute carrier family 35, member E1	protein-coding
mm_3739.1	chr1	155158705	155158776	+	1	NA	promoter-TSS (NM_021433)	promoter-TSS (NM_021433)	37	NM_021433	58244	Mm.66264	NM_021433	ENSMUSG00000026470	Stx6	2310039E05Rik|2410005I16Rik|AA437559|AI415714|AI845861	syntaxin 6	protein-coding
mm_36744.1	chr4	99972930	99972933	-	1	NA	intron (NM_028132, intron 7 of 10)	intron (NM_028132, intron 7 of 10)	43480	NM_028132	72157	Mm.217764	NM_028132	ENSMUSG00000025791	Pgm2	2610020G18Rik|AA407108|AI098105|Pgm-2|Pgm1	phosphoglucomutase 2	protein-coding
mm_37504.1	chr4	123750237	123750293	-	1	NA	promoter-TSS (NM_023423)	promoter-TSS (NM_023423)	34	NM_023423	68050	Mm.27903	NM_023423	ENSMUSG00000023075	Akirin1	6330407G11Rik	akirin 1	protein-coding
mm_172114.1	chr6	3200997	3200997	+	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	-87522	NR_036696	667335	Mm.380219	NR_036696	ENSMUSG00000106779	Gm8579	EG667335	spermatogenesis associated glutamate (E)-rich protein 4a pseudogene	pseudo
mm_108424.1	chr12	82170314	82170341	+	1	NA	intron (NM_001167983, intron 1 of 23)	CpG	311	NM_001167983	217692	Mm.261333	NM_172579	ENSMUSG00000042700	Sipa1l1	4931426N11Rik|AW213287|Spar|mKIAA0440	signal-induced proliferation-associated 1 like 1	protein-coding
mm_95981.1	chr11	58974661	58974668	+	1	NA	Intergenic	RLTR23|LTR|ERV1	-3429	NM_001290988	94091	Mm.248049	NM_053168	ENSMUSG00000020455	Trim11	-	tripartite motif-containing 11	protein-coding
mm_99829.1	chr11	108921130	108921146	+	1	NA	intron (NM_015732, intron 1 of 10)	CpG	789	NM_015732	12006	Mm.71710	NM_015732	ENSMUSG00000000142	Axin2	Axi1|Axil|Conductin	axin 2	protein-coding
mm_135452.1	chr16	45724472	45724478	-	1	NA	promoter-TSS (NM_019754)	promoter-TSS (NM_019754)	56	NM_019754	56370	Mm.24183	NM_019754	ENSMUSG00000022658	Tagln3	2700038H05Rik|2900005O10Rik|AI426007|Np25	transgelin 3	protein-coding
mm_131693.1	chr16	20693264	20693322	+	1	NA	TTS (NM_145941)	TTS (NM_145941)	-1764	NM_133778	78408	Mm.196512	NM_133778	ENSMUSG00000050821	Fam131a	2900046G09Rik	family with sequence similarity 131, member A	protein-coding
mm_9304.1	chr1	171639248	171639258	-	1	NA	exon (NM_144539, exon 4 of 8)	exon (NM_144539, exon 4 of 8)	2647	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_30688.1	chr4	11485967	11485973	+	1	NA	promoter-TSS (NM_001347055)	promoter-TSS (NM_001347055)	12	NM_001347055	66185	Mm.331487	NM_001081183	ENSMUSG00000040720	1110037F02Rik	4930422M05Rik|Kiaa1429|mKIAA1429	RIKEN cDNA 1110037F02 gene	protein-coding
mm_31396.1	chr4	48045231	48045238	+	1	NA	promoter-TSS (NM_015743)	promoter-TSS (NM_015743)	-71	NM_015743	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_49607.1	chr6	30746272	30746293	+	1	NA	exon (NM_001252293, exon 11 of 12)	exon (NM_001252293, exon 11 of 12)	4983	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_149207.1	chr19	9980708	9980716	+	1	NA	non-coding (NR_073181, exon 1 of 5)	non-coding (NR_073181, exon 1 of 5)	112	NR_073181	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
mm_65739.1	chr7	28401102	28401146	-	1	NA	3' UTR (NM_175021, exon 13 of 13)	3' UTR (NM_175021, exon 13 of 13)	8128	NM_019458	54624	Mm.7916	NM_019458	ENSMUSG00000003437	Paf1	5730511K23Rik|AA675045	Paf1, RNA polymerase II complex component	protein-coding
mm_60914.1	chr7	46796152	46796156	+	1	NA	promoter-TSS (NM_001167864)	promoter-TSS (NM_001167864)	60	NM_008186	14884	Mm.22700	NM_008186	ENSMUSG00000006599	Gtf2h1	62kDa|AW743425|AW822074|BTF2 p62|C77871|p62	general transcription factor II H, polypeptide 1	protein-coding
mm_45788.1	chr5	87424202	87424205	-	1	NA	promoter-TSS (NM_133894)	promoter-TSS (NM_133894)	0	NM_133894	100559	Mm.212589	NM_133894	ENSMUSG00000061906	Ugt2b38	9430041C03Rik|AA986709	UDP glucuronosyltransferase 2 family, polypeptide B38	protein-coding
mm_90126.1	chr10	117693762	117693774	+	1	NA	intron (NM_001288586, intron 8 of 10)	B1_Mur2|SINE|Alu	16990	NM_010786	17246	Mm.22670	NM_010786	ENSMUSG00000020184	Mdm2	1700007J15Rik|AA415488|Mdm-2	transformed mouse 3T3 cell double minute 2	protein-coding
mm_126741.1	chr15	85679462	85679486	+	1	NA	Intergenic	Intergenic	-24299	NR_110483	102800312	Mm.33117	NR_110483		Lncppara	Lincppara|Mirlet7bhg|linc-Ppara	long noncoding RNA near Ppara	ncRNA
mm_134086.1	chr16	8783379	8783402	-	1	NA	Intergenic	RLTR20A3_MM|LTR|ERVK	-45048	NM_001003918	252870	Mm.295330	NM_001003918	ENSMUSG00000022710	Usp7	2210010O09Rik|AA409944|AA617399|AU019296|AW548146|C80752|Hausp	ubiquitin specific peptidase 7	protein-coding
mm_86455.1	chr10	4346808	4346873	+	1	NA	intron (NM_031185, intron 2 of 3)	CpG	41268	NM_001033466	381990	Mm.262466	NM_001033466	ENSMUSG00000075327	Zbtb2	Gm1103	zinc finger and BTB domain containing 2	protein-coding
mm_116483.1	chr13	43923878	43923886	-	1	NA	Intergenic	Intergenic	138770	NM_001289915	12522	Mm.57175	NM_009856	ENSMUSG00000015396	Cd83	-	CD83 antigen	protein-coding
mm_62186.1	chr7	97480995	97481078	+	1	NA	promoter-TSS (NM_027256)	promoter-TSS (NM_027256)	80	NM_027256	101861	Mm.27383	NM_027256	ENSMUSG00000025133	Ints4	2610034N24Rik|AA692684|AW493223	integrator complex subunit 4	protein-coding
mm_124097.1	chr14	79291991	79291998	-	1	NA	intron (NM_025427, intron 2 of 4)	intron (NM_025427, intron 2 of 4)	9641	NM_025427	66214	Mm.29811	NM_025427	ENSMUSG00000022018	Rgcc	1190002H23Rik|Rgc-32|Rgc32	regulator of cell cycle	protein-coding
mm_139464.1	chr17	55954341	55954371	+	1	NA	TTS (NR_108021)	TTS (NR_108021)	1733	NM_015766	50498	Mm.256798	NM_015766	ENSMUSG00000003206	Ebi3	EBI-3|IL-27	Epstein-Barr virus induced gene 3	protein-coding
mm_107426.1	chr12	35534388	35534396	+	1	NA	intron (NM_001314027, intron 1 of 9)	intron (NM_001314027, intron 1 of 9)	597	NM_013464	11622	Mm.341377	NM_013464	ENSMUSG00000019256	Ahr	Ah|Ahh|Ahre|In|bHLHe76	aryl-hydrocarbon receptor	protein-coding
mm_82566.1	chr9	21075281	21075303	-	1	NA	TTS (NR_106050)	TTS (NR_106050)	296	NR_106050	102465656		NR_106050	ENSMUSG00000098907	Mir7082	Gm27933|mmu-mir-7082	microRNA 7082	ncRNA
mm_81904.1	chr9	119983134	119983168	+	1	NA	intron (NM_153287, intron 1 of 4)	CpG	1507	NM_153287	215418	Mm.491094	NM_153287	ENSMUSG00000032515	Csrnp1	4931429D10Rik|Axud1|CSRNP-1|URAX1|taip-3	cysteine-serine-rich nuclear protein 1	protein-coding
mm_48636.1	chr5	145167032	145167077	-	1	NA	promoter-TSS (NM_178576)	promoter-TSS (NM_178576)	50	NM_133735	71799	Mm.277413	NM_133735	ENSMUSG00000029624	Ptcd1	1110069M14Rik	pentatricopeptide repeat domain 1	protein-coding
mm_60476.1	chr7	44478265	44478271	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-6249	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_59324.1	chr7	25306221	25306233	+	1	NA	exon (NM_183311, exon 1 of 15)	exon (NM_183311, exon 1 of 15)	119	NM_183311	330485	Mm.260740	NM_183311	ENSMUSG00000043843	Tmem145	B930076A02Rik	transmembrane protein 145	protein-coding
mm_68830.1	chr7	126200358	126200366	-	1	NA	promoter-TSS (NM_028816)	promoter-TSS (NM_028816)	46	NM_028816	74204	Mm.235663	NM_028816	ENSMUSG00000000131	Xpo6	2610005L19Rik|AL022631|C230091E20Rik|R75304|Ranbp20|mKIAA0370	exportin 6	protein-coding
mm_17138.1	chr2	24975879	24975894	-	1	NA	promoter-TSS (NM_001031808)	promoter-TSS (NM_001031808)	-147	NM_146251	241274	Mm.389243	NM_146251	ENSMUSG00000036833	Pnpla7	BC027342|E430013P11Rik|Nre	patatin-like phospholipase domain containing 7	protein-coding
mm_114810.1	chr13	91484561	91484575	+	1	NA	intron (NM_024272, intron 1 of 16)	intron (NM_024272, intron 1 of 16)	23471	NM_024186	66970	Mm.343095	NM_024186	ENSMUSG00000003992	Ssbp2	1500004K09Rik|2310079I02Rik|9330163K02Rik|A830008M03Rik|AU067692|AW558684|Hspc116|SSDP2	single-stranded DNA binding protein 2	protein-coding
mm_60599.1	chr7	44516942	44516958	+	1	NA	exon (NM_146189, exon 8 of 28)	exon (NM_146189, exon 8 of 28)	7719	NM_146189	233199	Mm.358888	NM_146189	ENSMUSG00000038670	Mybpc2	-	myosin binding protein C, fast-type	protein-coding
mm_92395.1	chr10	76611822	76611843	-	1	NA	exon (NM_146007, exon 7 of 28)	exon (NM_146007, exon 7 of 28)	11572	NM_146007	12834	Mm.1949	NM_146007	ENSMUSG00000020241	Col6a2	Col6a-2	collagen, type VI, alpha 2	protein-coding
mm_52048.1	chr6	97210718	97210728	+	1	NA	promoter-TSS (NM_022992)	promoter-TSS (NM_022992)	-69	NM_022992	65106	Mm.291014	NM_022992	ENSMUSG00000035199	Arl6ip5	5930404D22Rik|AV001879|Aip-5|Gtrap3-18|addiscin	ADP-ribosylation factor-like 6 interacting protein 5	protein-coding
mm_54982.1	chr6	48741435	48741449	-	1	NA	intron (NM_175860, intron 2 of 2)	intron (NM_175860, intron 2 of 2)	2395	NM_008376	16205	Mm.252599	NM_008376	ENSMUSG00000090019	Gimap1	IAP38|Imap38|imap	GTPase, IMAP family member 1	protein-coding
mm_78289.1	chr9	22225703	22225730	+	1	NA	promoter-TSS (NM_001164624)	promoter-TSS (NM_001164624)	4	NM_001164624	235047	Mm.290849	NM_172763	ENSMUSG00000057982	Zfp809	BB114266|C330026E23	zinc finger protein 809	protein-coding
mm_59895.1	chr7	30307317	30307354	+	1	NA	3' UTR (NM_001081114, exon 14 of 14)	3' UTR (NM_001081114, exon 14 of 14)	-1418	NM_198027	233065	Mm.276277	NM_198027	ENSMUSG00000042831	Alkbh6	AI839550|Abh6|C130099A02	alkB homolog 6	protein-coding
mm_169082.1	chr13	3377913	3377918	-	1	NA	Intergenic	B3|SINE|B2	-100388	NR_015522	76937	Mm.487240	NR_015522	ENSMUSG00000097709	2810429I04Rik	AI256682	RIKEN cDNA 2810429I04 gene	ncRNA
mm_113299.1	chr13	30747777	30747805	+	1	NA	Intergenic	Intergenic	-1442	NM_001347508	16364	Mm.4677	NM_013674	ENSMUSG00000021356	Irf4	AI385587|IRF-4|LSIRF|NF-EM5|Spip	interferon regulatory factor 4	protein-coding
mm_117847.1	chr13	98694826	98694847	-	1	NA	promoter-TSS (NM_001025606)	promoter-TSS (NM_001025606)	-5	NM_001025606	380863	Mm.28264	NM_001025606	ENSMUSG00000052485	Tmem171	Gm905	transmembrane protein 171	protein-coding
mm_131371.1	chr16	13830597	13830601	+	1	NA	intron (NR_144374, intron 4 of 7)	intron (NR_144374, intron 4 of 7)	11348	NM_001346111	18203	Mm.380410	NM_010946	ENSMUSG00000022681	Ntan1	PNAA|PNAD	N-terminal Asn amidase	protein-coding
mm_124179.1	chr14	93873438	93873446	-	1	NA	intron (NM_001346722, intron 2 of 4)	intron (NM_001346722, intron 2 of 4)	15446	NM_001271800	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding
mm_153287.1	chr19	37295839	37295845	-	1	NA	intron (NM_031156, intron 13 of 23)	intron (NM_031156, intron 13 of 23)	-31747	NR_040298	77059	Mm.251476	NR_040298		4931408D14Rik	-	RIKEN cDNA 4931408D14 gene	ncRNA
mm_6514.1	chr1	74394660	74394672	-	1	NA	TTS (NR_029743)	TTS (NR_029743)	356	NR_029743	387219		NR_029743	ENSMUSG00000065468	Mir26b	Mirn26b|mir-26b|mmu-mir-26b	microRNA 26b	ncRNA
mm_47413.1	chr5	123136539	123136555	-	1	NA	Intergenic	Intergenic	-3918	NM_175092	23912	Mm.253876	NM_175092	ENSMUSG00000029449	Rhof	AI845056|AV026554|Arhf|Ifld1|Rif	ras homolog family member F (in filopodia)	protein-coding
mm_29942.1	chr3	132883383	132883392	-	1	NA	3' UTR (NM_001287103, exon 12 of 12)	3' UTR (NM_001287103, exon 12 of 12)	-4791	NR_102298	101243624	Mm.306256	NR_102297	ENSMUSG00000106230	Gm29811	-	predicted gene, 29811	ncRNA
mm_73086.1	chr8	94513331	94513341	+	1	NA	intron (NM_001033207, intron 34 of 48)	ID_B1|SINE|B4	8290	NR_106040	102466800		NR_106040	ENSMUSG00000098511	Mir7072	Gm27665|mmu-mir-7072	microRNA 7072	ncRNA
mm_156817.1	chrX	164139351	164139369	+	1	NA	promoter-TSS (NM_001130513)	promoter-TSS (NM_001130513)	18	NM_001130513	70008	Mm.13451	NM_027286	ENSMUSG00000015405	Ace2	2010305L05Rik	angiotensin I converting enzyme (peptidyl-dipeptidase A) 2	protein-coding
mm_160521.1	chr9	35421138	35421138	+	1	NA	Intergenic	CpG	-30938	NM_021339	57810	Mm.80509	NM_021339	ENSMUSG00000038119	Cdon	CDO|Cd0|Orcam	cell adhesion molecule-related/down-regulated by oncogenes	protein-coding
mm_170953.1	chr2	5379211	5379216	-	1	NA	promoter-TSS (NR_030601)	promoter-TSS (NR_030601)	-177	NR_030601	100124465		NR_030601	ENSMUSG00000078031	Mir466d	Mirn466d	microRNA 466d	ncRNA
mm_56289.1	chr6	91491081	91491086	-	1	NA	intron (NM_009531, intron 15 of 15)	intron (NM_009531, intron 15 of 15)	17332	NM_028766	74122	Mm.38801	NM_028766	ENSMUSG00000030095	Tmem43	1200015A22Rik|LUMA	transmembrane protein 43	protein-coding
mm_122316.1	chr14	36919514	36919539	-	1	NA	promoter-TSS (NM_001347503)	promoter-TSS (NM_001347503)	9	NM_001347503	72972	Mm.27621	NM_027045	ENSMUSG00000058690	Ccser2	1700012P13Rik|2900054P12Rik|AI035535|AW108503|Fam190b|Gcap14	coiled-coil serine rich 2	protein-coding
mm_18280.1	chr2	52424827	52424916	-	1	NA	promoter-TSS (NM_182994)	promoter-TSS (NM_182994)	3	NM_182994	75423	Mm.314378	NM_182994	ENSMUSG00000036093	Arl5a	2410015N24Rik|2810410P22Rik|AA408731|AW610751|Arl5|T25534	ADP-ribosylation factor-like 5A	protein-coding
mm_80030.1	chr9	68717737	68717741	+	1	NA	intron (NM_013646, intron 1 of 10)	intron (NM_013646, intron 1 of 10)	-47607	NR_033299	320440	Mm.483129	NM_177159		9530091C08Rik	-	RIKEN cDNA 9530091C08 gene	ncRNA
mm_160028.1	chr6	130382504	130382504	-	1	NA	5' UTR (NM_016659, exon 3 of 9)	5' UTR (NM_016659, exon 3 of 9)	-1696	NM_053152	93969	Mm.333431	NM_053152		Klra22	Ly49v	killer cell lectin-like receptor subfamily A, member 22	protein-coding
mm_167095.1	chr7	109010828	109010835	+	1	NA	promoter-TSS (NM_021885)	promoter-TSS (NM_021885)	-49	NM_021885	22141	Mm.439722	NM_021885	ENSMUSG00000031028	Tub	rd5|tub	tubby candidate gene	protein-coding
mm_144248.1	chr18	10812607	10812621	+	1	NA	TTS (NM_144860)	TTS (NM_144860)	-27062	NR_029781	723959		NR_029781	ENSMUSG00000106348	Mir1a-2	Mir1-2|Mirn1-2|mir-1a-2|mmu-mir-1-2|mmu-mir-1a-2	microRNA 1a-2	ncRNA
mm_120375.1	chr14	64588015	64588058	+	1	NA	promoter-TSS (NR_040709)	promoter-TSS (NR_040709)	-79	NR_040709	268755	Mm.194050	NR_040709	ENSMUSG00000097545	Mir124a-1hg	A930011O12Rik|Rncr3|mir-124-1|mir-3078	Mir124-1 host gene (non-protein coding)	ncRNA
mm_152033.1	chr19	6084942	6084957	-	1	NA	promoter-TSS (NM_024231)	promoter-TSS (NM_024231)	-58	NM_024231	81909	Mm.289471	NM_024231	ENSMUSG00000024792	Zfpl1	1500015B20Rik	zinc finger like protein 1	protein-coding
mm_71261.1	chr8	40917905	40917915	+	1	NA	3' UTR (NM_001044740, exon 12 of 12)	3' UTR (NM_001044740, exon 12 of 12)	-8323	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_67632.1	chr7	84275535	84275584	-	1	NA	intron (NM_007488, intron 11 of 18)	intron (NM_007488, intron 11 of 18)	-123666	NM_133722	70178	Mm.23914	NM_133722	ENSMUSG00000038459	Abhd17c	2210412D01Rik|AL023007|Fam108c|Fam108c1	abhydrolase domain containing 17C	protein-coding
mm_37637.1	chr4	127534674	127534679	-	1	NA	Intergenic	Intergenic	-176512	NM_010291	14622	Mm.26859	NM_010291	ENSMUSG00000042357	Gjb5	Cnx31.1|Cx31.1|Gjb-5	gap junction protein, beta 5	protein-coding
mm_29341.1	chr3	108226574	108226589	-	1	NA	promoter-TSS (NM_008596)	promoter-TSS (NM_008596)	18	NM_008596	17306	Mm.316885	NM_008596	ENSMUSG00000027887	Sypl2	AI552439|Mg29	synaptophysin-like 2	protein-coding
mm_30048.1	chr3	136167165	136167168	-	1	NA	intron (NM_001310749, intron 6 of 15)	intron (NM_001310749, intron 6 of 15)	158900	NM_001310749	242248	Mm.30832	NM_001033350	ENSMUSG00000037922	Bank1	A530094C12Rik|AI451642|AVIEF|BANK	B cell scaffold protein with ankyrin repeats 1	protein-coding
mm_165928.1	chr4	63344491	63344505	+	1	NA	promoter-TSS (NM_008768)	promoter-TSS (NM_008768)	-58	NM_008768	18405	Mm.4777	NM_008768	ENSMUSG00000039196	Orm1	Agp-1|Agp-2|Orm-1	orosomucoid 1	protein-coding
mm_25585.1	chr3	116885828	116885840	+	1	NA	intron (NM_009146, intron 7 of 16)	intron (NM_009146, intron 7 of 16)	24154	NM_009146	20321	Mm.66293	NM_009146	ENSMUSG00000033386	Frrs1	AI131732|Sdfr2	ferric-chelate reductase 1	protein-coding
mm_100131.1	chr11	115974560	115974577	+	1	NA	promoter-TSS (NM_133663)	promoter-TSS (NM_133663)	-157	NM_001005608	192897	Mm.213873	NM_133663	ENSMUSG00000020758	Itgb4	AA407042|C230078O20|CD104	integrin beta 4	protein-coding
mm_122811.1	chr14	54577562	54577577	-	1	NA	promoter-TSS (NM_010590)	promoter-TSS (NM_010590)	92	NM_010590	16475	Mm.100253	NM_010590	ENSMUSG00000022178	Ajuba	Jub	ajuba LIM protein	protein-coding
mm_22003.1	chr2	167753914	167753938	-	1	NA	Intergenic	Intergenic	62749	NR_015500	329562	Mm.123101	NM_177851	ENSMUSG00000006462	A530013C23Rik	-	RIKEN cDNA A530013C23 gene	ncRNA
mm_85497.1	chr9	106136398	106136401	-	1	NA	Intergenic	Intergenic	-17725	NR_029549	387153		NR_029549	ENSMUSG00000065407	Mir135a-1	Mir135a01|Mirn135|Mirn135a-1|mir-135a-1	microRNA 135a-1	ncRNA
mm_5159.1	chr1	10009099	10009160	-	1	NA	promoter-TSS (NM_145692)	promoter-TSS (NM_145692)	7	NR_110971	69312	Mm.386795	NM_027033	ENSMUSG00000025916	Ppp1r42	1700011J18Rik|4930418G15Rik|Lrrc67|TLRR	protein phosphatase 1, regulatory subunit 42	protein-coding
mm_138817.1	chr17	39847315	39847338	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	4329	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_16243.1	chr2	173157990	173158005	+	1	NA	exon (NM_011044, exon 9 of 10)	exon (NM_011044, exon 9 of 10)	4924	NM_011044	18534	Mm.266867	NM_011044	ENSMUSG00000027513	Pck1	AI265463|PEPCK|Pck-1	phosphoenolpyruvate carboxykinase 1, cytosolic	protein-coding
mm_48282.1	chr5	138171249	138171274	-	1	NA	promoter-TSS (NM_021392)	promoter-TSS (NM_021392)	601	NM_008568	17220	Mm.378965	NM_008568	ENSMUSG00000029730	Mcm7	AI747533|Mcmd7|mCDC47	minichromosome maintenance complex component 7	protein-coding
mm_80282.1	chr9	73044803	73044825	+	1	NA	promoter-TSS (NM_023635)	promoter-TSS (NM_023635)	4	NM_001301230	11891	Mm.34867	NM_023635	ENSMUSG00000032202	Rab27a	2210402C08Rik|2410003M20Rik|4933437C11Rik|ash	RAB27A, member RAS oncogene family	protein-coding
mm_152237.1	chr19	8711867	8711892	-	1	NA	exon (NM_008577, exon 3 of 9)	exon (NM_008577, exon 3 of 9)	2018	NM_008577	17254	Mm.4114	NM_008577	ENSMUSG00000010095	Slc3a2	4F2|4F2HC|AI314110|Cd98|Ly-10|Ly-m10|Ly10|Mdu1|Mgp-2hc|NACAE	solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2	protein-coding
mm_43175.1	chr5	127632058	127632075	+	1	NA	promoter-TSS (NM_177005)	promoter-TSS (NM_177005)	-196	NM_177005	319804	Mm.237888	NM_177005	ENSMUSG00000049971	Glt1d1	5730455A04Rik	glycosyltransferase 1 domain containing 1	protein-coding
mm_121408.1	chr14	119321642	119321652	+	1	NA	intron (NM_015820, intron 1 of 1)	intron (NM_015820, intron 1 of 1)	183382	NM_015820	50787	Mm.445777	NM_015820	ENSMUSG00000053465	Hs6st3	6OST3|HS6ST-3	heparan sulfate 6-O-sulfotransferase 3	protein-coding
mm_120948.1	chr14	76722087	76722104	+	1	NA	Intergenic	MER45A|DNA|hAT-Tip100	44527	NR_015485	73272	Mm.116804	NR_015485	ENSMUSG00000101009	1700108F19Rik	1700020I02Rik|BB065030	RIKEN cDNA 1700108F19 gene	ncRNA
mm_109382.1	chr12	109718820	109718822	+	1	NA	promoter-TSS (NR_030446)	promoter-TSS (NR_030446)	67	NR_030446	751522		NR_030446	ENSMUSG00000070105	Mir495	Mirn495|mir-495|mmu-mir-495	microRNA 495	ncRNA
mm_141972.1	chr17	35150566	35150579	-	1	NA	exon (NM_020027, exon 26 of 31)	exon (NM_020027, exon 26 of 31)	14305	NM_001199044	53761	Mm.272462	NM_020027	ENSMUSG00000024393	Prrc2a	3110039B05Rik|Bat-2|Bat2|D17H6S51E|G2|Wbp12|mKIAA4178	proline-rich coiled-coil 2A	protein-coding
mm_51208.1	chr6	71329755	71329775	+	1	NA	exon (NM_009858, exon 3 of 6)	exon (NM_009858, exon 3 of 6)	6953	NM_009858	12526	Mm.333148	NM_009858	ENSMUSG00000053044	Cd8b1	Cd8b|Ly-3|Ly-C|Lyt-3	CD8 antigen, beta chain 1	protein-coding
mm_87725.1	chr10	60106433	60106443	+	1	NA	5' UTR (NM_052994, exon 1 of 11)	5' UTR (NM_052994, exon 1 of 11)	181	NM_052994	94214	Mm.153429	NM_052994	ENSMUSG00000058297	Spock2	AA407235|Gcap26|mKIAA0275	sparc/osteonectin, cwcv and kazal-like domains proteoglycan 2	protein-coding
mm_118581.1	chr14	19811276	19811294	+	1	NA	TTS (NM_026528)	TTS (NM_026528)	12538	NM_026528	68045	Mm.21932	NM_026528	ENSMUSG00000021807	2700060E02Rik	-	RIKEN cDNA 2700060E02 gene	protein-coding
mm_108390.1	chr12	80947475	80947519	+	1	NA	exon (NM_001079694, exon 4 of 8)	exon (NM_001079694, exon 4 of 8)	1998	NM_001347415	20384	Mm.43331	NM_009159	ENSMUSG00000021134	Srsf5	Sfrs5	serine/arginine-rich splicing factor 5	protein-coding
mm_2216.1	chr1	89791265	89791268	+	1	NA	intron (NM_001037136, intron 12 of 16)	PB1D11|SINE|Alu	-107374	NR_015540	74403	Mm.444291	NR_015540		4933400F21Rik	1700091C04Rik|4930565K10Rik	RIKEN cDNA 4933400F21 gene	ncRNA
mm_3810.1	chr1	158362522	158362585	+	1	NA	5' UTR (NM_001205204, exon 1 of 23)	5' UTR (NM_001205204, exon 1 of 23)	249	NM_001205204	11899	Mm.329586	NM_007495	ENSMUSG00000026587	Astn1	Astn|GC14|mKIAA0289	astrotactin 1	protein-coding
mm_158904.1	chr1	36368051	36368051	-	1	NA	intron (NM_001310513, intron 1 of 21)	intron (NM_001310513, intron 1 of 21)	1130	NM_172652	226976	Mm.24734	NM_172652	ENSMUSG00000010453	Kansl3	4632411B12Rik|4932435K23|AI431067|AI647574|C85723|Kiaa1310|mKIAA1310	KAT8 regulatory NSL complex subunit 3	protein-coding
mm_158152.1	chrX	103475577	103475625	-	1	NA	non-coding (NR_001570, exon 1 of 8)	non-coding (NR_001570, exon 1 of 8)	7632	NR_001570	213742	Mm.274770	NR_001463	ENSMUSG00000086503	Xist	A430022B11|AI314753	inactive X specific transcripts	ncRNA
mm_154932.1	chrX	35888723	35888733	+	1	NA	promoter-TSS (NM_001009947)	promoter-TSS (NM_001009947)	-104	NM_001009947	75974	Mm.32873	NM_177745	ENSMUSG00000031093	Dock11	5033414A21Rik|8030476J24|Zizimin2|sph238	dedicator of cytokinesis 11	protein-coding
mm_168356.1	chr1	114182589	114182605	-	1	NA	Intergenic	L1Md_T|LINE|L1	-1502540	NM_001077425	636808	Mm.101576	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding
mm_100176.1	chr11	116533963	116533972	+	1	NA	promoter-TSS (NM_011451)	promoter-TSS (NM_011451)	729	NM_025367	20698	Mm.20944	NM_011451	ENSMUSG00000061878	Sphk1	1110006G24Rik|Sk1|Spk1	sphingosine kinase 1	protein-coding
mm_55072.1	chr6	49110976	49110998	-	1	NA	intron (NM_023670, intron 6 of 14)	intron (NM_023670, intron 6 of 14)	37192	NM_029353	75593	Mm.439947	NM_029353	ENSMUSG00000029815	Malsu1	2410003K15Rik|Matsu1	mitochondrial assembly of ribosomal large subunit 1	protein-coding
mm_133436.1	chr16	87698993	87699034	+	1	NA	promoter-TSS (NM_007520)	promoter-TSS (NM_007520)	59	NM_007520	12013	Mm.26147	NM_007520	ENSMUSG00000025612	Bach1	6230421P05Rik|AI323795	BTB and CNC homology 1, basic leucine zipper transcription factor 1	protein-coding
mm_122398.1	chr14	40994422	40994450	-	1	NA	3' UTR (NM_001316734, exon 6 of 6)	3' UTR (NM_001316734, exon 6 of 6)	12484	NM_001316739	70564	Mm.27227	NM_027464	ENSMUSG00000021792	Fam213a	5730469M10Rik|AU040822|Adrx|Pamm	family with sequence similarity 213, member A	protein-coding
mm_54891.1	chr6	44083349	44083366	-	1	NA	Intergenic	Intergenic	-417079	NM_013861	29807	Mm.320979	NM_013861	ENSMUSG00000029735	Tpk1	-	thiamine pyrophosphokinase	protein-coding
mm_59026.1	chr7	19301236	19301250	+	1	NA	Intergenic	Intergenic	8802	NM_008036	14282	Mm.248335	NM_008036	ENSMUSG00000003545	Fosb	-	FBJ osteosarcoma oncogene B	protein-coding
mm_36974.1	chr4	109476609	109476665	-	1	NA	promoter-TSS (NM_013876)	promoter-TSS (NM_013876)	-132	NM_013876	29864	Mm.392580	NM_013876	ENSMUSG00000028557	Rnf11	-	ring finger protein 11	protein-coding
mm_97638.1	chr11	79051332	79051347	+	1	NA	intron (NM_013571, intron 2 of 17)	intron (NM_013571, intron 2 of 17)	27742	NR_045873	790910	Mm.440410	NR_045873		Gm11201	ENSMUSG00000072637|OTTMUSG00000000169	predicted gene 11201	ncRNA
mm_120048.1	chr14	56647496	56647537	+	1	NA	exon (NM_001145978, exon 32 of 35)	exon (NM_001145978, exon 32 of 35)	-20732	NM_023773	75339	Mm.152466	NM_023773	ENSMUSG00000079184	Mphosph8	1500035L22Rik|4930548G07Rik|AU040635	M-phase phosphoprotein 8	protein-coding
mm_156552.1	chrX	151780629	151780636	+	1	NA	Intergenic	Intergenic	-22650	NM_021523	59026	Mm.27372	NM_021523	ENSMUSG00000025261	Huwe1	5430439H10Rik|AU041296|Arf-bp1|C430014N20Rik|C80292|Gm1718|Ib772|LASU1|Mule|Ureb1	HECT, UBA and WWE domain containing 1	protein-coding
mm_7592.1	chr1	125435695	125435710	-	1	NA	promoter-TSS (NM_023735)	promoter-TSS (NM_023735)	25	NM_023735	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding
mm_99242.1	chr11	101078424	101078435	+	1	NA	promoter-TSS (NM_010475)	promoter-TSS (NM_010475)	18	NM_010475	15485	Mm.188939	NM_010475	ENSMUSG00000019301	Hsd17b1	17HSDB1|17beta-HSD|E2DH|Hsd17ba	hydroxysteroid (17-beta) dehydrogenase 1	protein-coding
mm_78430.1	chr9	31386188	31386235	+	1	NA	promoter-TSS (NM_172766)	promoter-TSS (NM_172766)	19	NM_172766	235134	Mm.238146	NM_172766	ENSMUSG00000042185	Nfrkb	A530090G11Rik	nuclear factor related to kappa B binding protein	protein-coding
mm_66864.1	chr7	56901448	56901448	-	1	NA	intron (NM_008074, intron 5 of 9)	intron (NM_008074, intron 5 of 9)	485423	NM_008074	14407	Mm.434343	NM_008074	ENSMUSG00000055026	Gabrg3	B230362M20Rik|Gabrg-3	gamma-aminobutyric acid (GABA) A receptor, subunit gamma 3	protein-coding
mm_134203.1	chr16	11134602	11134623	-	1	NA	promoter-TSS (NM_029582)	promoter-TSS (NM_029582)	-80	NM_029582	106200	Mm.291015	NM_029582	ENSMUSG00000022498	Txndc11	2810408E11Rik|AI427833|EFP1|Txdc11	thioredoxin domain containing 11	protein-coding
mm_27688.1	chr3	65974731	65974743	-	1	NA	Intergenic	CpG	-16512	NM_019937	56706	Mm.175612	NM_019937	ENSMUSG00000027829	Ccnl1	2610030E23Rik|AU018493|Ccnl|ania-6a	cyclin L1	protein-coding
mm_36210.1	chr4	62468881	62468903	-	1	NA	5' UTR (NM_023597, exon 2 of 11)	5' UTR (NM_023597, exon 2 of 11)	2003	NM_001290522	71354	Mm.155573	NM_023597	ENSMUSG00000028391	Wdr31	5430402I10Rik|spWD	WD repeat domain 31	protein-coding
mm_24014.1	chr3	87435799	87435819	+	1	NA	promoter-TSS (NM_183222)	promoter-TSS (NM_183222)	27	NM_001113238	329693	Mm.331122	NM_183222	ENSMUSG00000048031	Fcrl5	Fcrh3|mBXMH2	Fc receptor-like 5	protein-coding
mm_115278.1	chr13	111715932	111715935	+	1	NA	3' UTR (NM_172593, exon 13 of 13)	3' UTR (NM_172593, exon 13 of 13)	29755	NM_172593	218613	Mm.31012	NM_172593	ENSMUSG00000032727	Mier3	5730509D14|AU015422|D130064H19Rik	MIER family member 3	protein-coding
mm_137141.1	chr17	23617304	23617308	+	1	NA	Intergenic	MLTR11B|LTR|ERVK	16480	NM_001289482	332221	Mm.270315	NM_001033425	ENSMUSG00000023902	Zscan10	BC068284|Zfp206|Zkscan10|Znf206	zinc finger and SCAN domain containing 10	protein-coding
mm_82085.1	chr9	123034732	123034752	+	1	NA	promoter-TSS (NM_177911)	promoter-TSS (NM_177911)	1	NM_177911	331046	Mm.195309	NM_177911	ENSMUSG00000025787	Tgm4	9530008N10Rik|Eapa1|TGP	transglutaminase 4 (prostate)	protein-coding
mm_62385.1	chr7	100839033	100839055	+	1	NA	3' UTR (NM_178764, exon 9 of 9)	3' UTR (NM_178764, exon 9 of 9)	24369	NM_177073	320100	Mm.40336	NM_177073	ENSMUSG00000008318	Relt	E430021K24Rik|Tnfrsf19l	RELT tumor necrosis factor receptor	protein-coding
mm_141706.1	chr17	33999924	33999957	-	1	NA	exon (NM_001001892, exon 2 of 8)	exon (NM_001001892, exon 2 of 8)	393	NM_001001892	14972	Mm.422886	NM_001001892	ENSMUSG00000061232	H2-K1	H-2K|H-2K(d)|H2-K|K-f	histocompatibility 2, K1, K region	protein-coding
mm_124702.1	chr15	6540259	6540270	+	1	NA	Intergenic	Intergenic	-39583	NM_001278269	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_19058.1	chr2	77281059	77281082	-	1	NA	promoter-TSS (NM_175465)	promoter-TSS (NM_175465)	-478	NM_175465	228071	Mm.27120	NM_175465	ENSMUSG00000042272	Sestd1	1500031J16Rik|A930010O20|Solo/Trio8	SEC14 and spectrin domains 1	protein-coding
mm_54916.1	chr6	47799223	47799236	-	1	NA	exon (NM_009787, exon 8 of 10)	exon (NM_009787, exon 8 of 10)	4423	NR_030485	735289		NR_030485	ENSMUSG00000076060	Mir704	Mirn704|mir-704|mmu-mir-704	microRNA 704	ncRNA
mm_59346.1	chr7	25627182	25627196	+	1	NA	promoter-TSS (NM_146184)	promoter-TSS (NM_146184)	-435	NM_001036740	232984	Mm.192369	NM_146184	ENSMUSG00000059479	B3gnt8	B3galt7|B7galt7|BC025206	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 8	protein-coding
mm_119480.1	chr14	47319670	47319730	+	1	NA	3' UTR (NM_178684, exon 4 of 4)	3' UTR (NM_178684, exon 4 of 4)	21386	NM_178684	218975	Mm.212297	NM_178684	ENSMUSG00000021840	Mapk1ip1l	9130202B12|C130032J12Rik	mitogen-activated protein kinase 1 interacting protein 1-like	protein-coding
mm_85601.1	chr9	107554394	107554415	-	1	NA	promoter-TSS (NM_019713)	promoter-TSS (NM_019713)	-179	NM_019713	56289	Mm.12091	NM_019713	ENSMUSG00000010067	Rassf1	123F2|AA536941|AU044980|NORE2A|RDA32|REH3P21|Rassf1A|Rassf1B|Rassf1C	Ras association (RalGDS/AF-6) domain family member 1	protein-coding
mm_118027.1	chr13	101538210	101538234	-	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	-140642	NR_046187	78136	Mm.399065	NR_046187		4922502H24Rik	-	RIKEN cDNA 4922502H24 gene	ncRNA
mm_113335.1	chr13	31625746	31625759	+	1	NA	promoter-TSS (NM_010225)	promoter-TSS (NM_010225)	-64	NM_010225	14238	Mm.125548	NM_010225	ENSMUSG00000038402	Foxf2	FREAC2|Fkh20|LUN	forkhead box F2	protein-coding
mm_130.1	chr1	10039763	10039792	+	1	NA	intron (NM_026493, intron 1 of 29)	CpG	1559	NM_026493	211660	Mm.244046	NM_026493	ENSMUSG00000056763	Cspp1	2310020J12Rik|4930413O22Rik|AA387550|BC055915|Cspp2|Cspp3	centrosome and spindle pole associated protein 1	protein-coding
mm_98262.1	chr11	88950477	88950514	+	1	NA	intron (NM_029023, intron 2 of 12)	intron (NM_029023, intron 2 of 12)	4947	NM_029023	74617	Mm.34126	NM_029023	ENSMUSG00000000278	Scpep1	2410018F01Rik|4833411K15Rik|AI957256|Risc	serine carboxypeptidase 1	protein-coding
mm_54191.1	chr6	24373270	24373278	-	1	NA	Intergenic	Intergenic	141793	NM_172535	214704	Mm.61131	NM_172535	ENSMUSG00000046192	Iqub	4932408B21Rik|Trs4	IQ motif and ubiquitin domain containing	protein-coding
mm_146485.1	chr18	90510232	90510251	+	1	NA	promoter-TSS (NM_198295)	promoter-TSS (NM_198295)	87	NM_198295	67988	Mm.268041	NM_198295	ENSMUSG00000024614	Tmx3	6430411B10Rik|A730024F05Rik|AV259382|Txndc10|mKIAA1830	thioredoxin-related transmembrane protein 3	protein-coding
mm_119359.1	chr14	41115240	41115270	+	1	NA	intron (NM_133653, intron 6 of 9)	intron (NM_133653, intron 6 of 9)	10222	NM_133653	11720	Mm.14064	NM_133653	ENSMUSG00000037798	Mat1a	AI046368|AdoMet|Ams|MAT|MATA1|SAMS|SAMS1	methionine adenosyltransferase I, alpha	protein-coding
mm_105824.1	chr11	113155141	113155157	-	1	NA	intron (NR_015556, intron 1 of 2)	B4A|SINE|B4	46689	NR_015556	72386	Mm.266961	NR_015556	ENSMUSG00000087259	2610035D17Rik	-	RIKEN cDNA 2610035D17 gene	ncRNA
mm_118397.1	chr13	119376265	119376268	-	1	NA	intron (NM_008710, intron 7 of 16)	AT_rich|Low_complexity|Low_complexity	32745	NM_008710	18115	Mm.132584	NM_008710	ENSMUSG00000025453	Nnt	4930423F13Rik|AI323702|BB168308	nicotinamide nucleotide transhydrogenase	protein-coding
mm_113719.1	chr13	43653571	43653571	+	1	NA	intron (NM_183204, intron 1 of 1)	intron (NM_183204, intron 1 of 1)	37774	NM_183204	328234	Mm.40588	NM_183204	ENSMUSG00000044164	Rnf182	C630023L15Rik	ring finger protein 182	protein-coding
mm_155501.1	chrX	73787003	73787017	+	1	NA	promoter-TSS (NM_008323)	promoter-TSS (NM_008323)	-18	NM_001166480	20832	Mm.831	NM_009279	ENSMUSG00000002014	Ssr4	AW743063|C78062|Trap	signal sequence receptor, delta	protein-coding
mm_160739.1	chr10	79970797	79970797	+	1	NA	promoter-TSS (NM_130455)	promoter-TSS (NM_130455)	73	NM_130455	170483	Mm.391566	NM_130455	ENSMUSG00000035745	Grin3b	GluN3B|NR3B	glutamate receptor, ionotropic, NMDA3B	protein-coding
mm_98838.1	chr11	97440180	97440205	+	1	NA	Intergenic	CpG	-9968	NM_021493	58996	Mm.394118	NM_021493	ENSMUSG00000049807	Arhgap23	A330041B18Rik	Rho GTPase activating protein 23	protein-coding
mm_153147.1	chr19	34251073	34251078	-	1	NA	intron (NM_007392, intron 3 of 8)	intron (NM_007392, intron 3 of 8)	4298	NM_007392	11475	Mm.213025	NM_007392	ENSMUSG00000035783	Acta2	0610041G09Rik|Actvs|SMalphaA|a-SMA|alphaSMA	actin, alpha 2, smooth muscle, aorta	protein-coding
mm_27659.1	chr3	65200566	65200566	-	1	NA	intron (NM_001289450, intron 2 of 14)	intron (NM_001289450, intron 2 of 14)	12463	NM_001289450	16497	Mm.316402	NM_010597	ENSMUSG00000027827	Kcnab1	Akr8a8|Kvbeta1.1|mKv(beta)1	potassium voltage-gated channel, shaker-related subfamily, beta member 1	protein-coding
mm_68851.1	chr7	126369424	126369435	-	1	NA	TTS (NM_023712)	TTS (NM_023712)	139	NM_010689	16797	Mm.10280	NM_010689	ENSMUSG00000030742	Lat	p36-38|pp36	linker for activation of T cells	protein-coding
mm_45567.1	chr5	73256523	73256534	-	1	NA	promoter-TSS (NM_028194)	promoter-TSS (NM_028194)	90	NM_028194	72313	Mm.260594	NM_028194	ENSMUSG00000070733	Fryl	2010313D22Rik|2310004H21Rik|2510002A14Rik|9030227G01Rik|mKIAA0826	FRY like transcription coactivator	protein-coding
mm_113378.1	chr13	33013923	33013947	+	1	NA	exon (NM_009256, exon 6 of 7)	exon (NM_009256, exon 6 of 7)	9394	NM_009256	20723	Mm.245041	NM_009256	ENSMUSG00000045827	Serpinb9	BB283241|CAP-3|CAP3|PI-9|PI9|Spi6|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 9	protein-coding
mm_17875.1	chr2	34958130	34958141	-	1	NA	intron (NM_009421, intron 4 of 10)	intron (NM_009421, intron 4 of 10)	3637	NM_009421	22029	Mm.239514	NM_009421	ENSMUSG00000026875	Traf1	4732496E14Rik	TNF receptor-associated factor 1	protein-coding
mm_61647.1	chr7	80400386	80400399	+	1	NA	intron (NM_001081454, intron 1 of 15)	intron (NM_001081454, intron 1 of 15)	2420	NM_011046	18550	Mm.5241	NM_011046	ENSMUSG00000030530	Furin	9130404I01Rik|Fur|PACE|Pcsk3|SPC1	furin (paired basic amino acid cleaving enzyme)	protein-coding
mm_17276.1	chr2	26092019	26092033	-	1	NA	5' UTR (NM_001037098, exon 1 of 6)	5' UTR (NM_001037098, exon 1 of 6)	370	NM_001037098	67991	Mm.131074	NM_026495	ENSMUSG00000026932	Nacc2	0610020I02Rik|AI448087|Btbd14a|C030048H19Rik	nucleus accumbens associated 2, BEN and BTB (POZ) domain containing	protein-coding
mm_64545.1	chr7	144321062	144321089	+	1	NA	intron (NM_001113373, intron 7 of 15)	intron (NM_001113373, intron 7 of 15)	36690	NM_001081370	210274	Mm.483624	NM_001081370	ENSMUSG00000037541	Shank2	ProSAP1|mKIAA1022	SH3/ankyrin domain gene 2	protein-coding
mm_164426.1	chr16	45382691	45382693	-	1	NA	3' UTR (NM_010818, exon 6 of 6)	3' UTR (NM_010818, exon 6 of 6)	26361	NM_010818	17470	Mm.245851	NM_010818	ENSMUSG00000022661	Cd200	Mox2|OX2	CD200 antigen	protein-coding
mm_123973.1	chr14	75131618	75131634	-	1	NA	promoter-TSS (NM_027581)	promoter-TSS (NM_027581)	503	NM_001247984	18826	Mm.153911	NM_008879	ENSMUSG00000021998	Lcp1	AW536232|D14Ertd310e|LCP-1|Pls2|pp65	lymphocyte cytosolic protein 1	protein-coding
mm_124467.1	chr14	121294413	121294421	-	1	NA	intron (NM_145465, intron 7 of 10)	intron (NM_145465, intron 7 of 10)	84813	NM_145465	223255	Mm.390756	NM_145465	ENSMUSG00000063410	Stk24	1810013H02Rik|C76483|MST-3|Mst3|STE20	serine/threonine kinase 24	protein-coding
mm_164046.1	chr14	98110029	98110037	-	1	NA	intron (NM_007826, intron 1 of 11)	intron (NM_007826, intron 1 of 11)	59732	NM_001038610	13134	Mm.320593	NM_007826	ENSMUSG00000055639	Dach1	Dac|Dach	dachshund 1 (Drosophila)	protein-coding
mm_151237.1	chr19	53800853	53800863	+	1	NA	intron (NM_001170847, intron 1 of 13)	intron (NM_001170847, intron 1 of 13)	-91373	NM_011050	18569	Mm.1605	NM_011050	ENSMUSG00000024975	Pdcd4	D19Ucla1|Ma3|Tis	programmed cell death 4	protein-coding
mm_55584.1	chr6	71411587	71411595	-	1	NA	intron (NM_024288, intron 4 of 8)	intron (NM_024288, intron 4 of 8)	29046	NM_024288	68477	Mm.28474	NM_024288	ENSMUSG00000002222	Rmnd5a	1110007A06Rik|AJ237586|AW125795|Gid2|MTA.D02.090	required for meiotic nuclear division 5 homolog A	protein-coding
mm_158753.1	chrX	166440643	166440670	-	1	NA	promoter-TSS (NM_001313722)	promoter-TSS (NM_001313722)	48	NM_177429	237222	Mm.247480	NM_177429	ENSMUSG00000040586	Ofd1	Cxorf5|DXGgc7e|ORF2	oral-facial-digital syndrome 1 gene homolog (human)	protein-coding
mm_75252.1	chr8	40510477	40510480	-	1	NA	intron (NM_001271542, intron 1 of 6)	intron (NM_001271542, intron 1 of 6)	1276	NM_001271543	18983	Mm.272551	NM_011135	ENSMUSG00000031601	Cnot7	AU022737|CAF-1|Caf1|Pop2	CCR4-NOT transcription complex, subunit 7	protein-coding
mm_56070.1	chr6	86793523	86793582	-	1	NA	promoter-TSS (NM_013471)	promoter-TSS (NM_013471)	32	NM_013471	11746	Mm.259702	NM_013471	ENSMUSG00000029994	Anxa4	AI265406|AIV|AW106930|Anx4|Xanx-4	annexin A4	protein-coding
mm_1226.1	chr1	62754826	62754842	+	1	NA	intron (NM_001077405, intron 7 of 15)	intron (NM_001077405, intron 7 of 15)	39898	NR_040601	74992	Mm.401979	NR_040601		4930487H11Rik	-	RIKEN cDNA 4930487H11 gene	ncRNA
mm_132729.1	chr16	43630274	43630285	+	1	NA	Intergenic	Intergenic	-10376	NR_030576	100124467		NR_030576	ENSMUSG00000076372	Mir568	Mirn568|mmu-mir-568	microRNA 568	ncRNA
mm_6554.1	chr1	75137405	75137424	-	1	NA	exon (NM_026977, exon 8 of 9)	exon (NM_026977, exon 8 of 9)	-3524	NM_194333	22626	Mm.68157	NM_194333	ENSMUSG00000026205	Slc23a3	SVCT3|Yspl1	solute carrier family 23 (nucleobase transporters), member 3	protein-coding
mm_89668.1	chr10	97506482	97506512	+	1	NA	exon (NM_007833, exon 4 of 8)	exon (NM_007833, exon 4 of 8)	24166	NM_007833	13179	Mm.56769	NM_007833	ENSMUSG00000019929	Dcn	DC|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding
mm_89829.1	chr10	106141207	106141210	+	1	NA	Intergenic	Intergenic	299729	NM_025602	52713	Mm.339224	NM_025602	ENSMUSG00000019897	Ccdc59	2300004H16Rik|D10Ertd718e	coiled-coil domain containing 59	protein-coding
mm_54273.1	chr6	29028313	29028335	-	1	NA	Intergenic	Intergenic	5705	NR_029567	387237		NR_029567	ENSMUSG00000065469	Mir129-1	Mirn129-1|Mirn129b|miR-129b|mir-129-1	microRNA 129-1	ncRNA
mm_65335.1	chr7	24978444	24978467	-	1	NA	3' UTR (NM_001290469, exon 23 of 23)	3' UTR (NM_001290469, exon 23 of 23)	-5727	NM_010261	14470	Mm.22473	NM_010261	ENSMUSG00000003380	Rabac1	2310040I06Rik|Gbpap1|PRA1|prenylin	Rab acceptor 1 (prenylated)	protein-coding
mm_50075.1	chr6	41339801	41339811	+	1	NA	Intergenic	Intergenic	-14299	NM_001038996	436522	Mm.443385	NM_001038996	ENSMUSG00000071521	Try10	-	trypsin 10	protein-coding
mm_7468.1	chr1	120484832	120484863	-	1	NA	exon (NM_010766, exon 11 of 17)	exon (NM_010766, exon 11 of 17)	20237	NM_010766	17167	Mm.1856	NM_010766	ENSMUSG00000026390	Marco	AI323439|Ly112|Scara2	macrophage receptor with collagenous structure	protein-coding
mm_158508.1	chrX	142852596	142852609	-	1	NA	TTS (NM_019496)	TTS (NM_019496)	113602	NR_030523	723976		NR_030523	ENSMUSG00000076011	Mir652	Mirn652|miRX|mmu-mir-652	microRNA 652	ncRNA
mm_79286.1	chr9	51186118	51186163	+	1	NA	Intergenic	Intergenic	-27550	NM_011136	18985	Mm.897	NM_011136	ENSMUSG00000032053	Pou2af1	BOB.1|Bob-1|Bob1|OBF-1|OBF.1|OCA-B|OCAB	POU domain, class 2, associating factor 1	protein-coding
mm_143575.1	chr17	74316160	74316171	-	1	NA	promoter-TSS (NM_001146224)	promoter-TSS (NM_001146224)	46	NM_001146224	66310	Mm.28536	NM_024428	ENSMUSG00000024067	Dpy30	2810410M20Rik|C87842	dpy-30, histone methyltransferase complex regulatory subunit	protein-coding
mm_58625.1	chr7	5079471	5079497	+	1	NA	promoter-TSS (NM_001252454)	promoter-TSS (NM_001252454)	-751	NM_010147	13854	Mm.3091	NM_010147	ENSMUSG00000035203	Epn1	AA269831|Ibp1	epsin 1	protein-coding
mm_65935.1	chr7	30353347	30353360	-	1	NA	Intergenic	Intergenic	9419	NM_175478	233067	Mm.23157	NM_175478	ENSMUSG00000036957	Lrfn3	A530045B06Rik|SALM4	leucine rich repeat and fibronectin type III domain containing 3	protein-coding
mm_160835.1	chr11	48902149	48902149	-	1	NA	promoter-TSS (NM_001024230)	promoter-TSS (NM_001024230)	3	NM_001024230	432555	Mm.338931	NM_001024230	ENSMUSG00000058163	Gm5431	EG432555|Irgb9b8	predicted gene 5431	protein-coding
mm_53847.1	chr6	149129645	149129659	+	1	NA	Intergenic	Intergenic	-11861	NM_001252096	320204	Mm.274099	NM_177101	ENSMUSG00000039958	Etfbkmt	4833442J19Rik|AI256744|ETFB-KMT|Mettl20	electron transfer flavoprotein beta subunit lysine methyltransferase	protein-coding
mm_2948.1	chr1	132342348	132342362	+	1	NA	Intergenic	Intergenic	25593	NM_001311108	68875	Mm.273785	NM_178874	ENSMUSG00000042066	Tmcc2	1110063G11Rik	transmembrane and coiled-coil domains 2	protein-coding
mm_106046.1	chr11	116079789	116079799	-	1	NA	intron (NM_001347642, intron 5 of 6)	intron (NM_001347642, intron 5 of 6)	-1833	NM_001009573	70450	Mm.259460	NM_001009573	ENSMUSG00000057948	Unc13d	2610108D09Rik|Jinx|Munc13-4|mFLJ00067	unc-13 homolog D (C. elegans)	protein-coding
mm_11507.1	chr2	32567933	32567945	+	1	NA	3' UTR (NM_153560, exon 11 of 11)	3' UTR (NM_153560, exon 11 of 11)	-2919	NM_010073	13481	Mm.22001	NM_010073	ENSMUSG00000026810	Dpm2	AW557993|R75484	dolichol-phosphate (beta-D) mannosyltransferase 2	protein-coding
mm_101174.1	chr11	16990136	16990189	-	1	NA	exon (NM_019549, exon 5 of 10)	exon (NM_019549, exon 5 of 10)	18556	NM_019549	56193	Mm.98232	NM_019549	ENSMUSG00000020120	Plek	2010300B13Rik	pleckstrin	protein-coding
mm_41674.1	chr5	99682414	99682427	+	1	NA	intron (NR_030692, intron 1 of 3)	intron (NR_030692, intron 1 of 3)	46640	NR_030692	319818	Mm.295233	NR_030692	ENSMUSG00000089809	A930011G23Rik	-	RIKEN cDNA A930011G23 gene	ncRNA
mm_4506.1	chr1	174041004	174041028	+	1	NA	promoter-TSS (NM_146717)	promoter-TSS (NM_146717)	-917	NM_146717	258712	Mm.223146	NM_146717	ENSMUSG00000045381	Olfr433	MOR123-1	olfactory receptor 433	protein-coding
mm_78772.1	chr9	43743722	43743758	+	1	NA	promoter-TSS (NM_021424)	promoter-TSS (NM_021424)	-836	NM_021424	58235	Mm.335096	NM_021424	ENSMUSG00000032012	Nectin1	AI835281|AW549174|Cd111|HIgR|HveC|PRR|PRR1|Pvrl1|nectin-1	nectin cell adhesion molecule 1	protein-coding
mm_82767.1	chr9	26923041	26923051	-	1	NA	promoter-TSS (NM_001281475)	promoter-TSS (NM_001281475)	35	NM_001281475	382064	Mm.335028	NM_001177509	ENSMUSG00000079644	Gm1110	-	predicted gene 1110	protein-coding
mm_11035.1	chr2	26934029	26934084	+	1	NA	promoter-TSS (NM_011512)	promoter-TSS (NM_011512)	-13	NM_198628	279029	Mm.330079	NM_198628	ENSMUSG00000049897	Stkld1	Gm711|Sgk071	serine/threonine kinase-like domain containing 1	protein-coding
mm_79536.1	chr9	57825919	57825945	+	1	NA	intron (NM_019689, intron 1 of 7)	intron (NM_019689, intron 1 of 7)	8302	NM_019689	56380	Mm.425588	NM_019689	ENSMUSG00000004661	Arid3b	Bdp|Dri2	AT rich interactive domain 3B (BRIGHT-like)	protein-coding
mm_58281.1	chr6	145862420	145862434	-	1	NA	3' UTR (NM_001271768, exon 5 of 5)	3' UTR (NM_001271768, exon 5 of 5)	2993	NM_001271768	79362	Mm.154529	NM_024469	ENSMUSG00000030256	Bhlhe41	6430520M22Rik|Bhlhb2l|Bhlhb3|DEC2|Sharp1	basic helix-loop-helix family, member e41	protein-coding
mm_57258.1	chr6	123285188	123285206	-	1	NA	intron (NM_019948, intron 5 of 5)	intron (NM_019948, intron 5 of 5)	4674	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_12836.1	chr2	80643981	80643989	+	1	NA	intron (NM_001190179, intron 2 of 8)	MER5A1|DNA|hAT-Charlie	4721	NM_001190179	69482	Mm.29200	NM_027091	ENSMUSG00000026999	Nup35	2310006I24Rik|35kDa|5330402E05Rik|MP44|NO44	nucleoporin 35	protein-coding
mm_95837.1	chr11	57011744	57011782	+	1	NA	5' UTR (NM_001113325, exon 1 of 16)	5' UTR (NM_001113325, exon 1 of 16)	145	NM_008165	14799	Mm.4920	NM_008165	ENSMUSG00000020524	Gria1	2900051M01Rik|Glr-1|Glr1|GluA1|GluR-A|GluRA|Glur-1|Glur1|HIPA1|gluR-K1	glutamate receptor, ionotropic, AMPA1 (alpha 1)	protein-coding
mm_85959.1	chr9	112124825	112124833	-	1	NA	exon (NM_033264, exon 16 of 19)	exon (NM_033264, exon 16 of 19)	-6118	NR_029823	723815		NR_029823	ENSMUSG00000065441	Mir128-2	Mirn128-2|Mirn128b|mir-128-2|mir-128b	microRNA 128-2	ncRNA
mm_121111.1	chr14	101729908	101729958	+	1	NA	promoter-TSS (NM_201529)	promoter-TSS (NM_201529)	5	NM_201529	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_20283.1	chr2	126894103	126894105	-	1	NA	3' UTR (NM_023220, exon 15 of 15)	3' UTR (NM_023220, exon 15 of 15)	8281	NR_106202	102466258		NR_106202	ENSMUSG00000098896	Mir3473g	Gm27751|mmu-mir-3473g	microRNA 3473g	ncRNA
mm_4296.1	chr1	171777177	171777187	+	1	NA	exon (NM_013730, exon 3 of 7)	exon (NM_013730, exon 3 of 7)	10050	NM_013730	27218	Mm.103648	NM_013730	ENSMUSG00000015316	Slamf1	4933415F16|AA177906|CD150|CDw150|ESTM51|IPO-3|Slam	signaling lymphocytic activation molecule family member 1	protein-coding
mm_40401.1	chr5	52974889	52974892	+	1	NA	intron (NR_040413, intron 2 of 2)	B4|SINE|B4	17402	NR_040413	75954	Mm.258937	NR_040413	ENSMUSG00000106352	5033403H07Rik	-	RIKEN cDNA 5033403H07 gene	ncRNA
mm_85383.1	chr9	103226937	103226982	-	1	NA	intron (NM_133977, intron 2 of 16)	intron (NM_133977, intron 2 of 16)	3327	NM_133977	22041	Mm.37214	NM_133977	ENSMUSG00000032554	Trf	AI266983|Cd176|HP|Tf|Tfn|hpx	transferrin	protein-coding
mm_164084.1	chr15	5041804	5041804	+	1	NA	intron (NM_001243837, intron 6 of 17)	intron (NM_001243837, intron 6 of 17)	21969	NM_001243837	109828	Mm.208034	NM_001243837	ENSMUSG00000079105	C7	A530026G17|Gm1238	complement component 7	protein-coding
mm_122115.1	chr14	31001312	31001388	-	1	NA	promoter-TSS (NM_001165930)	promoter-TSS (NM_001165930)	-43	NM_001165930	76485	Mm.8766	NM_029626	ENSMUSG00000021916	Glt8d1	2410004H05Rik|5430414N14Rik|AI450005	glycosyltransferase 8 domain containing 1	protein-coding
mm_116309.1	chr13	36971600	36971602	-	1	NA	intron (NM_001166391, intron 5 of 14)	intron (NM_001166391, intron 5 of 14)	77612	NM_028784	74145	Mm.235105	NM_028784	ENSMUSG00000039109	F13a1	1200014I03Rik|AI462306|F13a	coagulation factor XIII, A1 subunit	protein-coding
mm_124286.1	chr14	103051424	103051437	-	1	NA	exon (NM_008392, exon 4 of 5)	exon (NM_008392, exon 4 of 5)	4418	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_124187.1	chr14	96519068	96519102	-	1	NA	promoter-TSS (NM_053105)	promoter-TSS (NM_053105)	-51	NM_053105	93688	Mm.308735	NM_053105	ENSMUSG00000022076	Klhl1	mKIAA1490	kelch-like 1	protein-coding
mm_117960.1	chr13	99447626	99447644	-	1	NA	intron (NM_008634, intron 2 of 6)	intron (NM_008634, intron 2 of 6)	-34809	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_164669.1	chr17	45487401	45487405	+	1	NA	Intergenic	Intergenic	-12465	NM_027649	71020	Mm.44257	NM_027649	ENSMUSG00000023935	Spats1	1700011H05Rik|4933400B06Rik|Daip2|Ddip|Srsp1	spermatogenesis associated, serine-rich 1	protein-coding
mm_28788.1	chr3	95995811	95995821	-	1	NA	promoter-TSS (NM_023320)	promoter-TSS (NM_023320)	23	NM_023320	67220	Mm.458147	NM_023320	ENSMUSG00000015745	Plekho1	2810052M02Rik|CKIP-1|Ckip1|JZA-20|Jza2	pleckstrin homology domain containing, family O member 1	protein-coding
mm_165830.1	chr3	152120097	152120114	-	1	NA	intron (NM_016867, intron 3 of 5)	intron (NM_016867, intron 3 of 5)	45795	NM_016867	54120	Mm.97	NM_016867	ENSMUSG00000039131	Gipc2	2200002N01Rik|AU021850|Semcap2	GIPC PDZ domain containing family, member 2	protein-coding
mm_61875.1	chr7	89510018	89510028	+	1	NA	exon (NM_029614, exon 2 of 2)	exon (NM_029614, exon 2 of 2)	7563	NM_029614	76453	Mm.250438	NM_029614	ENSMUSG00000039405	Prss23	2310046G15Rik|4930479H08Rik|AI790574|Spuve	protease, serine 23	protein-coding
mm_140643.1	chr17	12675787	12675807	-	1	NA	promoter-TSS (NM_009202)	promoter-TSS (NM_009202)	41	NM_009202	20517	Mm.594	NM_009202	ENSMUSG00000023829	Slc22a1	Lx1|Oct1|Orct|Orct1	solute carrier family 22 (organic cation transporter), member 1	protein-coding
mm_165.1	chr1	12807849	12807887	+	1	NA	exon (NM_001198566, exon 6 of 21)	exon (NM_001198566, exon 6 of 21)	89323	NM_172294	240725	Mm.45563	NM_172294	ENSMUSG00000016918	Sulf1	AI467640|AW121680|mKIAA1077	sulfatase 1	protein-coding
mm_51446.1	chr6	80192567	80192572	+	1	NA	intron (NM_001347261, intron 2 of 2)	Lx4A|LINE|L1	172926	NM_178731	243499	Mm.483425	NM_178731	ENSMUSG00000052581	Lrrtm4	7530419J18Rik|A230052N11	leucine rich repeat transmembrane neuronal 4	protein-coding
mm_56562.1	chr6	101377229	101377244	-	1	NA	exon (NM_018884, exon 1 of 10)	exon (NM_018884, exon 1 of 10)	661	NM_018884	55983	Mm.321654	NM_018884	ENSMUSG00000035357	Pdzrn3	1110020C07Rik|AI429718|AL023082|LNX3|SEMACAP3|Semcap3	PDZ domain containing RING finger 3	protein-coding
mm_17452.1	chr2	28556079	28556086	-	1	NA	exon (NM_009885, exon 11 of 11)	exon (NM_009885, exon 11 of 11)	7321	NM_009885	12613	Mm.236017	NM_009885	ENSMUSG00000026818	Cel	1810036E18Rik|BAL	carboxyl ester lipase	protein-coding
mm_70352.1	chr8	5117325	5117351	+	1	NA	Intergenic	Intergenic	-12051	NM_011388	20494	Mm.3500	NM_011388	ENSMUSG00000023073	Slc10a2	9130221J18Rik|AI605518|ASBT|IBAT|ISBT	solute carrier family 10, member 2	protein-coding
mm_91149.1	chr10	20205893	20205929	-	1	NA	intron (NM_001198635, intron 1 of 17)	intron (NM_001198635, intron 1 of 17)	-2528	NM_001101561	621697	Mm.440587	NM_001101561		Rpl32l	EG621697|Gm6251	ribosomal protein L32-like	protein-coding
mm_10613.1	chr2	19199250	19199263	+	1	NA	5' UTR (NM_001271565, exon 1 of 18)	5' UTR (NM_001271565, exon 1 of 18)	138	NM_001081083	70882	Mm.276696	NM_001081083	ENSMUSG00000037683	Armc3	4921513G22Rik	armadillo repeat containing 3	protein-coding
mm_158983.1	chr1	130800716	130800716	+	1	NA	promoter-TSS (NM_144960)	promoter-TSS (NM_144960)	-186	NM_001170632	64435	Mm.31821	NM_144960	ENSMUSG00000026415	Fcamr	-	Fc receptor, IgA, IgM, high affinity	protein-coding
mm_169278.1	chr1	39367893	39367894	+	1	NA	promoter-TSS (NM_053257)	promoter-TSS (NM_053257)	42	NM_001252218	114641	Mm.379302	NM_053257	ENSMUSG00000073702	Rpl31	Dts	ribosomal protein L31	protein-coding
mm_33092.1	chr4	124695942	124695985	+	1	NA	Intergenic	Intergenic	-2409	NM_026031	67205	Mm.259121	NM_026031	ENSMUSG00000028907	Utp11l	2700082D03Rik|CGI-94|Cgi94|Utp11	UTP11-like, U3 small nucleolar ribonucleoprotein, (yeast)	protein-coding
mm_73531.1	chr8	108638033	108638037	+	1	NA	Intergenic	Intergenic	-53358	NR_077224	109215	Mm.65282	NR_077224	ENSMUSG00000110613	Lncbate1	3010033K07Rik|Lnc-BATE1	brown adipose tissue enriched long non-coding RNA 1	ncRNA
mm_8292.1	chr1	143094609	143094642	-	1	NA	Intergenic	Intergenic	-546072	NM_020025	26878	Mm.285580	NM_020025	ENSMUSG00000033849	B3galt2	-	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 2	protein-coding
mm_71216.1	chr8	40894764	40894766	+	1	NA	intron (NM_007514, intron 1 of 11)	intron (NM_007514, intron 1 of 11)	-31468	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_90536.1	chr10	128088374	128088430	+	1	NA	exon (NM_016774, exon 8 of 10)	exon (NM_016774, exon 8 of 10)	3116	NR_030442	751518		NR_030442	ENSMUSG00000093245	Mir677	Mirn677|mir-677|mmu-mir-677	microRNA 677	ncRNA
mm_3658.1	chr1	153300758	153300773	+	1	NA	intron (NM_010683, intron 1 of 27)	intron (NM_010683, intron 1 of 27)	32021	NM_010683	226519	Mm.1249	NM_010683	ENSMUSG00000026478	Lamc1	Lamb2	laminin, gamma 1	protein-coding
mm_103320.1	chr11	73198987	73199008	-	1	NA	promoter-TSS (NM_031251)	promoter-TSS (NM_031251)	22	NM_031251	83429	Mm.259852	NM_031251	ENSMUSG00000005949	Ctns	AI195360|AW049661	cystinosis, nephropathic	protein-coding
mm_163146.1	chr11	82892130	82892135	+	1	NA	promoter-TSS (NM_030224)	promoter-TSS (NM_030224)	-13	NM_030224	78919	Mm.286733	NM_030224	ENSMUSG00000018844	Fndc8	4930466G16Rik	fibronectin type III domain containing 8	protein-coding
mm_47832.1	chr5	134306583	134306591	-	1	NA	intron (NM_001080746, intron 1 of 34)	ID_B1|SINE|B4	8173	NM_001080746	14886	Mm.261570	NM_010365	ENSMUSG00000060261	Gtf2i	6030441I21Rik|BAP-135|Diws1t|GtfII-I|Spin|TFII-I|WBSCR6	general transcription factor II I	protein-coding
mm_133822.1	chr16	95769930	95769943	+	1	NA	Intergenic	Intergenic	67529	NM_011809	23872	Mm.290207	NM_011809	ENSMUSG00000022895	Ets2	AU022856|Ets-2	E26 avian leukemia oncogene 2, 3' domain	protein-coding
mm_154340.1	chrM	4667	4678	+	1	NA	NA	Intergenic	NA	NA								
mm_62667.1	chr7	108950473	108950485	+	1	NA	Intergenic	CpG	16064	NM_025344	66085	Mm.182962	NM_025344	ENSMUSG00000031029	Eif3f	0610037M02Rik|AA409853|Eif3s5	eukaryotic translation initiation factor 3, subunit F	protein-coding
mm_46819.1	chr5	113138723	113138738	-	1	NA	promoter-TSS (NM_001347397)	promoter-TSS (NM_001347397)	-145	NM_001347397	243219	Mm.160131	NM_172884	ENSMUSG00000051339	2900026A02Rik	8430408O14Rik|A530094D01|AW539426|Gm449|Kiaa1671|mKIAA1671	RIKEN cDNA 2900026A02 gene	protein-coding
mm_73418.1	chr8	106059651	106059695	+	1	NA	promoter-TSS (NM_010901)	promoter-TSS (NM_010901)	70	NM_010901	18021	Mm.383185	NM_010901	ENSMUSG00000031902	Nfatc3	C80703|D8Ertd281e|NFAT4|NFATx	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 3	protein-coding
mm_90003.1	chr10	112271659	112271689	+	1	NA	intron (NM_001025581, intron 1 of 4)	intron (NM_001025581, intron 1 of 4)	551	NM_001025581	268345	Mm.336242	NM_001025581	ENSMUSG00000035681	Kcnc2	AW047325|B230117I07|KShIIIA|Kv3.2	potassium voltage gated channel, Shaw-related subfamily, member 2	protein-coding
mm_133748.1	chr16	94328425	94328439	+	1	NA	promoter-TSS (NM_133229)	promoter-TSS (NM_133229)	10	NM_133229	170765	Mm.42604	NM_133229	ENSMUSG00000022941	Ripply3	Dscr6	ripply transcriptional repressor 3	protein-coding
mm_140301.1	chr17	85621305	85621325	+	1	NA	exon (NM_011381, exon 1 of 2)	exon (NM_011381, exon 1 of 2)	481	NM_011381	20473	Mm.370208	NM_011381	ENSMUSG00000038805	Six3	E130112M24Rik|Six3a|Six3alpha|Six3b|Six3beta	sine oculis-related homeobox 3	protein-coding
mm_153094.1	chr19	32673855	32673866	-	1	NA	3' UTR (NM_026487, exon 10 of 10)	3' UTR (NM_026487, exon 10 of 10)	38438	NM_026487	67979	Mm.27123	NM_026487	ENSMUSG00000013662	Atad1	4921525H23Rik|AW107648|Thorase	ATPase family, AAA domain containing 1	protein-coding
mm_94149.1	chr10	128743962	128743972	-	1	NA	promoter-TSS (NM_016811)	promoter-TSS (NM_016811)	89	NM_016811	13139	Mm.291235	NM_016811	ENSMUSG00000025357	Dgka	80kDa|AW146112|Dagk1	diacylglycerol kinase, alpha	protein-coding
mm_158066.1	chrX	101213445	101213460	-	1	NA	3' UTR (NM_001110310, exon 4 of 4)	3' UTR (NM_001110310, exon 4 of 4)	9111	NM_001110311	55988	Mm.206949	NM_018875	ENSMUSG00000046032	Snx12	2610001F05Rik|AW045757|SDP8	sorting nexin 12	protein-coding
mm_6675.1	chr1	80340681	80340820	-	1	NA	promoter-TSS (NM_016716)	promoter-TSS (NM_016716)	-60	NM_016716	26554	Mm.12665	NM_016716	ENSMUSG00000004364	Cul3	KIAA0617	cullin 3	protein-coding
mm_169245.1	chr13	74768438	74768456	-	1	NA	intron (NM_001301153, intron 3 of 31)	intron (NM_001301153, intron 3 of 31)	2289	NM_001301156	12380	Mm.29163	NM_009817	ENSMUSG00000021585	Cast	-	calpastatin	protein-coding
mm_163693.1	chr13	99434723	99434725	-	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-21898	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_146390.1	chr18	82692956	82692986	+	1	NA	promoter-TSS (NM_177832)	promoter-TSS (NM_177832)	-237	NM_177832	329002	Mm.34438	NM_177832	ENSMUSG00000041258	Zfp236	AI447957|Gm335	zinc finger protein 236	protein-coding
mm_10556.1	chr2	16755318	16755329	+	1	NA	3' UTR (NM_026162, exon 14 of 14)	3' UTR (NM_026162, exon 14 of 14)	258403	NR_040632	75069	Mm.50378	NR_040632		4930515L03Rik	-	RIKEN cDNA 4930515L03 gene	ncRNA
mm_62170.1	chr7	97332312	97332331	+	1	NA	promoter-TSS (NM_001039039)	promoter-TSS (NM_001039039)	-2	NM_001039039	622320	Mm.334029	NM_001039039	ENSMUSG00000044952	Kctd21	EG622320	potassium channel tetramerisation domain containing 21	protein-coding
mm_67186.1	chr7	73940066	73940090	-	1	NA	3' UTR (NM_009181, exon 6 of 6)	3' UTR (NM_009181, exon 6 of 6)	73604	NM_009181	20450	Mm.4954	NM_009181	ENSMUSG00000025789	St8sia2	AI323367|ST8SiaII|STX|Siat8b	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 2	protein-coding
mm_20546.1	chr2	131068612	131068624	-	1	NA	TTS (NM_011426)	TTS (NM_011426)	-4804	NM_001163529	110751	Mm.108550	NM_033615	ENSMUSG00000027318	Adam33	Adaml	a disintegrin and metallopeptidase domain 33	protein-coding
mm_72443.1	chr8	83165420	83165440	+	1	NA	promoter-TSS (NM_001111304)	promoter-TSS (NM_001111304)	78	NM_027758	71310	Mm.24031	NM_027758	ENSMUSG00000031709	Tbc1d9	4933431N12Rik|AI847101|AW490653|C76116	TBC1 domain family, member 9	protein-coding
mm_24735.1	chr3	95283197	95283208	+	1	NA	5' UTR (NM_133858, exon 1 of 10)	5' UTR (NM_133858, exon 1 of 10)	267	NM_199475	75007	Mm.279287	NM_133858	ENSMUSG00000038712	Fam63a	1810005H09Rik|4930504E06Rik|AA562754|AA960384|AW561904|cI-40|mKIAA1390|ni	family with sequence similarity 63, member A	protein-coding
mm_33909.1	chr4	136332454	136332459	+	1	NA	exon (NM_001277123, exon 7 of 10)	exon (NM_001277123, exon 7 of 10)	21514	NM_001277123	74326	Mm.31051	NM_028871	ENSMUSG00000066037	Hnrnpr	2610003J05Rik|2610528B01Rik|Hnrpr	heterogeneous nuclear ribonucleoprotein R	protein-coding
mm_57090.1	chr6	122587252	122587290	-	1	NA	intron (NM_001134391, intron 5 of 7)	B1_Mur3|SINE|Alu	15173	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_9397.1	chr1	172219891	172219901	-	1	NA	promoter-TSS (NM_009813)	promoter-TSS (NM_009813)	-1	NM_009813	12372	Mm.12829	NM_009813	ENSMUSG00000007122	Casq1	CSQ|CSQ-1|CSQ1|sCSQ	calsequestrin 1	protein-coding
mm_105390.1	chr11	103374052	103374063	-	1	NA	exon (NM_183034, exon 8 of 12)	exon (NM_183034, exon 8 of 12)	-10365	NM_001205236	544817	Mm.259113	NM_133715	ENSMUSG00000034255	Arhgap27	2310069I04Rik|5730442P18Rik|Gm21552|Sh3d20	Rho GTPase activating protein 27	protein-coding
mm_71836.1	chr8	68902297	68902318	+	1	NA	exon (NM_008509, exon 9 of 10)	exon (NM_008509, exon 9 of 10)	21752	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_162331.1	chr1	42672790	42672815	+	1	NA	intron (NR_027826, intron 1 of 3)	intron (NR_027826, intron 1 of 3)	22023	NR_027826	66297	Mm.45203	NM_183252	ENSMUSG00000060424	Pantr1	2610017I09Rik|Pou3f3os|linc-Brn1a	POU domain, class 3, transcription factor 3 adjacent noncoding transcript 1	ncRNA
mm_3031.1	chr1	133880918	133880926	+	1	NA	Intergenic	Intergenic	26251	NM_054076	269120	Mm.59985	NM_054076	ENSMUSG00000010311	Optc	-	opticin	protein-coding
mm_5652.1	chr1	40580147	40580152	-	1	NA	promoter-TSS (NM_177084)	promoter-TSS (NM_177084)	-78	NM_177084	110895	Mm.108602	NM_177084	ENSMUSG00000026065	Slc9a4	AW990558|D730009J23Rik|NHE4	solute carrier family 9 (sodium/hydrogen exchanger), member 4	protein-coding
mm_104268.1	chr11	89048399	89048404	-	1	NA	intron (NM_019505, intron 7 of 10)	B1_Mur3|SINE|Alu	12347	NM_019505	56077	Mm.153695	NM_019505	ENSMUSG00000000276	Dgke	C87606|DAGK6|DGK	diacylglycerol kinase, epsilon	protein-coding
mm_133538.1	chr16	91061876	91061879	+	1	NA	intron (NM_028905, intron 1 of 2)	intron (NM_028905, intron 1 of 2)	7268	NM_001163695	74387	Mm.236220	NM_028905	ENSMUSG00000039851	4932438H23Rik	4931406G06Rik|AI550392	RIKEN cDNA 4932438H23 gene	protein-coding
mm_146292.1	chr18	79258223	79258226	+	1	NA	Intergenic	Intergenic	-148833	NM_053099	240427	Mm.312871	NM_053099	ENSMUSG00000024548	Setbp1	C130092E12|Seb|mKIAA0437	SET binding protein 1	protein-coding
mm_120717.1	chr14	72851846	72851861	+	1	NA	Intergenic	Intergenic	-141850	NM_207636	319448	Mm.205421	NM_207636	ENSMUSG00000033487	Fndc3a	1700094E19Rik|D14Ertd453e|F730017H24Rik|Fndc3|sys	fibronectin type III domain containing 3A	protein-coding
mm_114657.1	chr13	78024916	78024924	+	1	NA	promoter-TSS (NM_029315)	promoter-TSS (NM_029315)	18	NM_029315	75507	Mm.443255	NM_029315	ENSMUSG00000093668	Pou5f2	1700013G10Rik|SPRM-1|Sprm1	POU domain class 5, transcription factor 2	protein-coding
mm_154959.1	chrX	36874326	36874336	+	1	NA	promoter-TSS (NM_001313696)	promoter-TSS (NM_001313696)	36	NM_019668	22209	Mm.395649	NM_019668	ENSMUSG00000016308	Ube2a	HHR6A|HR6A|Mhr6a	ubiquitin-conjugating enzyme E2A	protein-coding
mm_14842.1	chr2	147435499	147435510	+	1	NA	Intergenic	Intergenic	70510	NM_008780	18503	Mm.315502	NM_008780	ENSMUSG00000037034	Pax1	Pax-1|hbs|hunchback|un|undulated|wt	paired box 1	protein-coding
mm_90716.1	chr10	4409958	4409992	-	1	NA	intron (NM_025343, intron 10 of 12)	RSINE1|SINE|B4	19191	NR_002891	433224	Mm.153111	NR_002891		Gm5512	EG433224	required for meiotic nuclear division 1 pseudogene	pseudo
mm_9539.1	chr1	173879951	173879969	-	1	NA	5' UTR (NM_001170853, exon 2 of 10)	5' UTR (NM_001170853, exon 2 of 10)	227	NM_001170853	100040462	Mm.463437	NM_001170853	ENSMUSG00000090272	Mndal	Gm2785|Ifi212	myeloid nuclear differentiation antigen like	protein-coding
mm_126096.1	chr15	78044112	78044118	+	1	NA	intron (NM_007583, intron 1 of 3)	intron (NM_007583, intron 1 of 3)	-73291	NM_018749	55944	Mm.3955	NM_018749	ENSMUSG00000016554	Eif3d	66/67kDa|AA407891|Eif3s7|eIF3p66	eukaryotic translation initiation factor 3, subunit D	protein-coding
mm_123850.1	chr14	70766535	70766564	-	1	NA	promoter-TSS (NM_023045)	promoter-TSS (NM_023045)	79	NM_023045	65246	Mm.152987	NM_023045	ENSMUSG00000022100	Xpo7	4930506C02Rik|BB164534|Ranbp16|mKIAA0745	exportin 7	protein-coding
mm_130383.1	chr15	97856808	97856832	-	1	NA	3' UTR (NM_009504, exon 10 of 10)	3' UTR (NM_009504, exon 10 of 10)	-12318	NM_001204278	56233	Mm.384027	NM_019572	ENSMUSG00000022475	Hdac7	5830434K02Rik|HD7|HD7a|Hdac7a|mFLJ00062	histone deacetylase 7	protein-coding
mm_97686.1	chr11	80136353	80136365	+	1	NA	TTS (NM_183275)	TTS (NM_183275)	5794	NM_183275	68550	Mm.18466	NM_183275	ENSMUSG00000046909	Tefm	1110002N22Rik	transcription elongation factor, mitochondrial	protein-coding
mm_95491.1	chr11	51619708	51619714	+	1	NA	promoter-TSS (NM_026631)	promoter-TSS (NM_026631)	-62	NM_026631	52530	Mm.28203	NM_026631	ENSMUSG00000001056	Nhp2	2410130M07Rik|D11Ertd175e|Nola2	NHP2 ribonucleoprotein	protein-coding
mm_157905.1	chrX	78021331	78021343	-	1	NA	Intergenic	Intergenic	70037	NM_008754	18249	Mm.430771	NM_008754	ENSMUSG00000067684	Obp1a	OBP-1a|OBP5	odorant binding protein IA	protein-coding
mm_144501.1	chr18	24474918	24474923	+	1	NA	intron (NM_026529, intron 3 of 4)	intron (NM_026529, intron 3 of 4)	4049	NM_026529	68046	Mm.276574	NM_026529	ENSMUSG00000024273	2700062C07Rik	AI195775|C87515	RIKEN cDNA 2700062C07 gene	protein-coding
mm_153173.1	chr19	34493696	34493706	-	1	NA	3' UTR (NM_021460, exon 10 of 10)	3' UTR (NM_021460, exon 10 of 10)	-18566	NM_009890	12642	Mm.30824	NM_009890	ENSMUSG00000050370	Ch25h	AI462618|m25OH	cholesterol 25-hydroxylase	protein-coding
mm_71357.1	chr8	45658816	45658824	+	1	NA	5' UTR (NM_001205219, exon 2 of 24)	5' UTR (NM_001205219, exon 2 of 24)	-3173	NM_001310708	234214	Mm.211096	NM_172752	ENSMUSG00000031626	Sorbs2	2010203O03Rik|9430041O17Rik|A530071H08|Argbp2|mKIAA0777|nArgBP2	sorbin and SH3 domain containing 2	protein-coding
mm_168982.1	chr12	92883099	92883114	-	1	NA	Intergenic	RLTR3_Mm|LTR|ERVK	561717	NR_126436	75295	Mm.243878	NR_126436		4930559C10Rik	-	RIKEN cDNA 4930559C10 gene	ncRNA
mm_18378.1	chr2	60004736	60004739	-	1	NA	intron (NM_001001182, intron 3 of 35)	intron (NM_001001182, intron 3 of 35)	121003	NM_001001182	407823	Mm.228071	NM_001001182	ENSMUSG00000026987	Baz2b	5830435C13Rik|BC053917|D2Ertd794e	bromodomain adjacent to zinc finger domain, 2B	protein-coding
mm_115248.1	chr13	110396772	110396784	+	1	NA	intron (NM_152804, intron 4 of 13)	intron (NM_152804, intron 4 of 13)	1734	NM_152804	20620	Mm.380	NM_152804	ENSMUSG00000021701	Plk2	Snk	polo-like kinase 2	protein-coding
mm_130126.1	chr15	89841894	89841923	-	1	NA	promoter-TSS (NM_018803)	promoter-TSS (NM_018803)	-48	NM_018803	54526	Mm.261601	NM_018803	ENSMUSG00000063260	Syt10	-	synaptotagmin X	protein-coding
mm_137233.1	chr17	24414914	24414985	+	1	NA	promoter-TSS (NR_033554)	promoter-TSS (NR_033554)	274	NM_001080128	19826	Mm.1951	NM_009070	ENSMUSG00000034681	Rnps1	-	ribonucleic acid binding protein S1	protein-coding
mm_7566.1	chr1	124764391	124764391	-	1	NA	Intergenic	Intergenic	671336	NM_023735	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding
mm_47196.1	chr5	120774124	120774148	-	1	NA	exon (NM_145226, exon 2 of 16)	exon (NM_145226, exon 2 of 16)	3523	NM_145226	246727	Mm.204887	NM_145226	ENSMUSG00000032661	Oas3	Oasl10	2'-5' oligoadenylate synthetase 3	protein-coding
mm_173142.1	chrX	21762509	21762509	-	1	NA	Intergenic	L1Md_T|LINE|L1	47609	NM_020049	56774	Mm.253984	NM_020049	ENSMUSG00000031089	Slc6a14	1110007A17Rik|9030613J17Rik|ATB0plus|CATB0plus	solute carrier family 6 (neurotransmitter transporter), member 14	protein-coding
mm_64821.1	chr7	7299471	7299486	-	1	NA	promoter-TSS (NM_001302387)	promoter-TSS (NM_001302387)	79	NR_126156	12727	Mm.297883	NM_011334	ENSMUSG00000000605	Clcn4	Clc4-2|Clcn4-2	chloride channel, voltage-sensitive 4	protein-coding
mm_65313.1	chr7	24806209	24806212	-	1	NA	Intergenic	Intergenic	-12585	NR_045096	545936	Mm.376228	NR_045096	ENSMUSG00000011350	Gm5893	EG545936|Gm477	predicted gene 5893	pseudo
mm_45244.1	chr5	57616953	57616953	-	1	NA	intron (NR_015588, intron 3 of 4)	intron (NR_015588, intron 3 of 4)	100966	NR_015588	319216	Mm.332387	NR_015588	ENSMUSG00000097216	4932441J04Rik	-	RIKEN cDNA 4932441J04 gene	ncRNA
mm_51047.1	chr6	65627006	65627015	+	1	NA	intron (NM_001001495, intron 7 of 7)	Lx9|LINE|L1	36612	NM_001001495	414084	Mm.117558	NM_001001495	ENSMUSG00000044162	Tnip3	9030611K07Rik|ABIN-3|LIND	TNFAIP3 interacting protein 3	protein-coding
mm_39331.1	chr5	8660606	8660623	+	1	NA	intron (NM_011076, intron 1 of 27)	intron (NM_011076, intron 1 of 27)	522	NM_011076	18671	Mm.207354	NM_011076	ENSMUSG00000040584	Abcb1a	Abcb4|Evi32|Mdr1a|Mdr3|P-gp|Pgp|Pgy-3|Pgy3|mdr-3	ATP-binding cassette, sub-family B (MDR/TAP), member 1A	protein-coding
mm_79980.1	chr9	66918866	66918882	+	1	NA	intron (NM_173413, intron 1 of 7)	intron (NM_173413, intron 1 of 7)	831	NM_173413	235442	Mm.260376	NM_173413	ENSMUSG00000036943	Rab8b	5930437D16|D330025I23Rik	RAB8B, member RAS oncogene family	protein-coding
mm_14705.1	chr2	142699611	142699623	+	1	NA	intron (NM_001081133, intron 22 of 25)	intron (NM_001081133, intron 22 of 25)	201847	NM_001081133	16558	Mm.251934	NM_001081133	ENSMUSG00000038844	Kif16b	8430434E15Rik|AA623607|AI789011|C80253|C80902|mKIAA1590	kinesin family member 16B	protein-coding
mm_64792.1	chr7	6331236	6331290	-	1	NA	promoter-TSS (NM_001033249)	promoter-TSS (NM_001033249)	-829	NM_001033249	213011	Mm.333558	NM_001033249	ENSMUSG00000030443	Zfp583	BC056221|Znf583	zinc finger protein 583	protein-coding
mm_8440.1	chr1	152808311	152808313	-	1	NA	intron (NM_010877, intron 2 of 15)	intron (NM_010877, intron 2 of 15)	8159	NM_010877	17970	Mm.270307	NM_010877	ENSMUSG00000026480	Ncf2	NOXA2|Ncf-2|p67phox	neutrophil cytosolic factor 2	protein-coding
mm_21361.1	chr2	157130042	157130063	-	1	NA	intron (NM_018851, intron 1 of 15)	intron (NM_018851, intron 1 of 15)	5170	NM_001139520	56045	Mm.248478	NM_018851	ENSMUSG00000027639	Samhd1	E330031J07Rik|Mg11	SAM domain and HD domain, 1	protein-coding
mm_46276.1	chr5	100038903	100038919	-	1	NA	exon (NM_016690, exon 1 of 8)	exon (NM_016690, exon 1 of 8)	311	NM_016690	50926	Mm.389579	NM_016690	ENSMUSG00000029328	Hnrnpdl	AA407431|AA959857|D5Ertd650e|D5Wsu145e|Hnrnpdl1|Hnrpdl|JKTBP|hnRNP DL|hnRNP-DL	heterogeneous nuclear ribonucleoprotein D-like	protein-coding
mm_66480.1	chr7	45016081	45016133	-	1	NA	5' UTR (NM_001008422, exon 1 of 11)	5' UTR (NM_001008422, exon 1 of 11)	142	NM_001008422	233208	Mm.28298	NM_001008422	ENSMUSG00000038406	Scaf1	AI480556|SR-A1	SR-related CTD-associated factor 1	protein-coding
mm_151759.1	chr19	5118225	5118322	-	1	NA	non-coding (NR_045528, exon 1 of 16)	non-coding (NR_045528, exon 1 of 16)	135	NR_045528	16594	Mm.271648	NM_008451	ENSMUSG00000024862	Klc2	8030455F02Rik|AW212649|KLC 2|KLC-2	kinesin light chain 2	protein-coding
mm_100335.1	chr11	118333689	118333698	+	1	NA	exon (NM_021440, exon 3 of 3)	exon (NM_021440, exon 3 of 3)	8841	NM_021440	58251	Mm.439815	NM_021440	ENSMUSG00000076433	BC100451	Cep295nl|Ddc8|FS39|Kiaa1731nl	cDNA sequence BC100451	protein-coding
mm_161498.1	chr15	89259143	89259143	+	1	NA	exon (NM_026813, exon 7 of 25)	exon (NM_026813, exon 7 of 25)	46589	NR_105924	102465981		NR_105924	ENSMUSG00000098442	Mir6959	Gm27807|mmu-mir-6959	microRNA 6959	ncRNA
mm_170669.1	chr2	118558120	118558139	+	1	NA	Intergenic	IAPLTR2_Mm|LTR|ERVK	-8443	NM_138313	171543	Mm.210125	NM_138313	ENSMUSG00000040093	Bmf	AW260063|AW411872	BCL2 modifying factor	protein-coding
mm_81484.1	chr9	109969005	109969031	+	1	NA	intron (NM_001205330, intron 1 of 18)	intron (NM_001205330, intron 1 of 18)	37244	NM_008633	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_120944.1	chr14	76687287	76687301	+	1	NA	TTS (NR_015485)	TTS (NR_015485)	9726	NR_015485	73272	Mm.116804	NR_015485	ENSMUSG00000101009	1700108F19Rik	1700020I02Rik|BB065030	RIKEN cDNA 1700108F19 gene	ncRNA
mm_57567.1	chr6	127128821	127128833	-	1	NA	3' UTR (NM_009829, exon 5 of 5)	3' UTR (NM_009829, exon 5 of 5)	-19275	NM_177003	319801	Mm.101836	NM_177003	ENSMUSG00000038028	Tigar	9630033F20Rik|AA793651|AI595337|C79710|C85509	Trp53 induced glycolysis repulatory phosphatase	protein-coding
mm_77170.1	chr8	111689564	111689611	-	1	NA	promoter-TSS (NR_106044)	promoter-TSS (NR_106044)	87	NR_106044	102466993		NR_106044	ENSMUSG00000099129	Mir7076	Gm27318|mmu-mir-7076	microRNA 7076	ncRNA
mm_163951.1	chr14	54253667	54253671	+	1	NA	promoter-TSS (NM_001205181)	promoter-TSS (NM_001205181)	260	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_18644.1	chr2	69533597	69533604	-	1	NA	intron (NM_001081088, intron 8 of 78)	intron (NM_001081088, intron 8 of 78)	52467	NM_001081088	14725	Mm.23847	NM_001081088	ENSMUSG00000027070	Lrp2	AI315343|AW536255|D230004K18Rik|Gp330|Megalin|b2b1625.2Clo	low density lipoprotein receptor-related protein 2	protein-coding
mm_1605.1	chr1	74381743	74381751	+	1	NA	exon (NM_013612, exon 9 of 15)	exon (NM_013612, exon 9 of 15)	6544	NM_013612	18173	Mm.2913	NM_013612	ENSMUSG00000026177	Slc11a1	Bcg|Ity|Ity1|Lsh|Nramp|Nramp1|ity	solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1	protein-coding
mm_140336.1	chr17	86778730	86778757	+	1	NA	intron (NM_010137, intron 1 of 15)	intron (NM_010137, intron 1 of 15)	24879	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_103123.1	chr11	70219046	70219062	-	1	NA	exon (NM_172371, exon 3 of 4)	exon (NM_172371, exon 3 of 4)	1940	NM_172371	69309	Mm.93266	NM_172371	ENSMUSG00000044367	Slc16a13	1700007D07Rik	solute carrier family 16 (monocarboxylic acid transporters), member 13	protein-coding
mm_22002.1	chr2	167753297	167753345	-	1	NA	Intergenic	MER117|DNA|hAT-Charlie	62144	NR_015500	329562	Mm.123101	NM_177851	ENSMUSG00000006462	A530013C23Rik	-	RIKEN cDNA A530013C23 gene	ncRNA
mm_135482.1	chr16	46010213	46010223	-	1	NA	5' UTR (NM_001134480, exon 1 of 4)	5' UTR (NM_001134480, exon 1 of 4)	195	NM_001134480	433022	Mm.380993	NM_001134480	ENSMUSG00000087141	Plcxd2	AW494639|EG433022	phosphatidylinositol-specific phospholipase C, X domain containing 2	protein-coding
mm_31952.1	chr4	86748636	86748645	+	1	NA	promoter-TSS (NM_184088)	promoter-TSS (NM_184088)	85	NM_184088	329877	Mm.273718	NM_184088	ENSMUSG00000038024	Dennd4c	1700065A05Rik|AA420392	DENN/MADD domain containing 4C	protein-coding
mm_32453.1	chr4	107368005	107368038	+	1	NA	5' UTR (NM_028355, exon 1 of 18)	5' UTR (NM_028355, exon 1 of 18)	237	NM_028355	72787	Mm.28478	NM_028355	ENSMUSG00000028614	Ndc1	2810475A17Rik|AI450313|Tmem48|sks	NDC1 transmembrane nucleoporin	protein-coding
mm_118045.1	chr13	101701859	101701873	-	1	NA	exon (NM_001077495, exon 6 of 16)	exon (NM_001077495, exon 6 of 16)	-9236	NM_001024955	18708	Mm.259333	NM_001024955	ENSMUSG00000041417	Pik3r1	PI3K|p50alpha|p55alpha|p85alpha	phosphatidylinositol 3-kinase, regulatory subunit, polypeptide 1 (p85 alpha)	protein-coding
mm_83221.1	chr9	42258614	42258628	-	1	NA	exon (NM_172769, exon 4 of 6)	exon (NM_172769, exon 4 of 6)	5679	NM_172769	235293	Mm.32700	NM_172769	ENSMUSG00000032018	Sc5d	A830037K02|A830073K23Rik|Sc5dl	sterol-C5-desaturase	protein-coding
mm_12476.1	chr2	71528658	71528668	+	1	NA	promoter-TSS (NM_010053)	promoter-TSS (NM_010053)	-782	NM_010053	13390	Mm.475101	NM_010053	ENSMUSG00000041911	Dlx1	Dlx|Dlx-1	distal-less homeobox 1	protein-coding
mm_133795.1	chr16	95278529	95278541	+	1	NA	intron (NM_001271687, intron 3 of 4)	B4A|SINE|B4	20977	NM_001271690	16516	Mm.272239	NM_019664	ENSMUSG00000062609	Kcnj15	4930414N08Rik|AI182284|AI267127|IRKK|Kir4.2	potassium inwardly-rectifying channel, subfamily J, member 15	protein-coding
mm_87359.1	chr10	43746541	43746556	+	1	NA	non-coding (NR_040581, exon 1 of 4)	non-coding (NR_040581, exon 1 of 4)	390	NR_040581	69443	Mm.484042	NR_040581	ENSMUSG00000111422	1700027J07Rik	-	RIKEN cDNA 1700027J07 gene	ncRNA
mm_72539.1	chr8	83997253	83997265	+	1	NA	promoter-TSS (NM_001081415)	promoter-TSS (NM_001081415)	-413	NM_001081415	666704	Mm.298091	NM_001081415	ENSMUSG00000079003	Samd1	AA589507	sterile alpha motif domain containing 1	protein-coding
mm_109024.1	chr12	103763752	103763795	+	1	NA	exon (NM_009246, exon 5 of 5)	exon (NM_009246, exon 5 of 5)	9860	NM_009246	20703	Mm.439695	NM_009246	ENSMUSG00000071177	Serpina1d	AI118301|Dom4|PI4|Spi1-4	serine (or cysteine) peptidase inhibitor, clade A, member 1D	protein-coding
mm_157520.1	chrX	50635248	50635272	-	1	NA	promoter-TSS (NR_015505)	promoter-TSS (NR_015505)	61	NR_015505	103012	Mm.482523	NR_015505	ENSMUSG00000085396	Firre	5830467J12Rik|6720401G13Rik|AW048145	functional intergenic repeating RNA element	ncRNA
mm_167673.1	chr9	75217439	75217452	+	1	NA	intron (NM_010864, intron 39 of 40)	intron (NM_010864, intron 39 of 40)	-14569	NM_001081322	208943	Mm.41339	NM_001081322	ENSMUSG00000033590	Myo5c	9130003O20Rik|BB085560|C330029I24	myosin VC	protein-coding
mm_7963.1	chr1	133930112	133930126	-	1	NA	Intergenic	Intergenic	-8718	NM_054077	116847	Mm.214514	NM_054077	ENSMUSG00000041577	Prelp	7330409J17Rik|SLRR2A	proline arginine-rich end leucine-rich repeat	protein-coding
mm_82511.1	chr9	20498340	20498368	-	1	NA	3' UTR (NM_001135019, exon 9 of 9)	3' UTR (NM_001135019, exon 9 of 9)	-5608	NM_001110309	235028	Mm.297660	NM_146221	ENSMUSG00000059475	Zfp426	2900057C04Rik|KRAB1|Zfo61|Zfp68-rs1|Znf426|mKIAA4237	zinc finger protein 426	protein-coding
mm_72036.1	chr8	70777333	70777364	+	1	NA	promoter-TSS (NM_008841)	promoter-TSS (NM_008841)	486	NR_029440	72093	Mm.271208	NR_029440		2010320M18Rik	-	RIKEN cDNA 2010320M18 gene	ncRNA
mm_78257.1	chr9	21835507	21835516	+	1	NA	promoter-TSS (NM_001080940)	promoter-TSS (NM_001080940)	1	NM_001080940	624219	Mm.440264	NM_001080940	ENSMUSG00000047822	Angptl8	EG624219|Gm6484|Rifl	angiopoietin-like 8	protein-coding
mm_89996.1	chr10	112269779	112269788	+	1	NA	Intergenic	Intergenic	-1340	NM_001025581	268345	Mm.336242	NM_001025581	ENSMUSG00000035681	Kcnc2	AW047325|B230117I07|KShIIIA|Kv3.2	potassium voltage gated channel, Shaw-related subfamily, member 2	protein-coding
mm_86574.1	chr10	12868402	12868432	+	1	NA	Intergenic	Intergenic	-6682	NM_011682	22288	Mm.331784	NM_011682	ENSMUSG00000019820	Utrn	AA589569|DRP|Dmdl	utrophin	protein-coding
mm_139732.1	chr17	57478897	57478914	+	1	NA	exon (NM_010130, exon 20 of 22)	exon (NM_010130, exon 20 of 22)	66409	NM_001104591	224916	Mm.469889	NM_001104591	ENSMUSG00000090655	Vmn2r120	EG224916	vomeronasal 2, receptor 120	protein-coding
mm_37751.1	chr4	129623871	129623925	-	1	NA	promoter-TSS (NM_025455)	promoter-TSS (NM_025455)	10	NM_025455	66264	Mm.383215	NM_025455	ENSMUSG00000028795	Ccdc28b	1110002E08Rik|1810010N17Rik	coiled coil domain containing 28B	protein-coding
mm_148631.1	chr19	5455591	5455612	+	1	NA	3' UTR (NM_010235, exon 4 of 4)	3' UTR (NM_010235, exon 4 of 4)	1962	NM_198616	240514	Mm.329657	NM_198616	ENSMUSG00000095098	Ccdc85b	AI842788|BB115872	coiled-coil domain containing 85B	protein-coding
mm_33527.1	chr4	130932249	130932258	+	1	NA	intron (NM_010686, intron 7 of 7)	RMER1C|Other|Other	-12132	NM_010769	17180	Mm.271796	NM_010769	ENSMUSG00000040533	Matn1	CMP|Crtm|Mat1|matrilin-1	matrilin 1, cartilage matrix protein	protein-coding
mm_92594.1	chr10	80080525	80080531	-	1	NA	intron (NM_183426, intron 4 of 31)	PB1D10|SINE|Alu	22174	NM_183426	216161	Mm.262102	NM_183426	ENSMUSG00000035673	Sbno2	BC019206|F730040C21|Sno|Stno	strawberry notch homolog 2 (Drosophila)	protein-coding
mm_177.1	chr1	13668800	13668812	+	1	NA	promoter-TSS (NM_001011873)	promoter-TSS (NM_001011873)	35	NM_001011873	381246	Mm.311142	NM_001011873	ENSMUSG00000067813	Xkr9	Gm1620|XRG9	X-linked Kx blood group related 9	protein-coding
mm_23316.1	chr3	53260512	53260536	+	1	NA	exon (NM_175386, exon 4 of 4)	exon (NM_175386, exon 4 of 4)	202734	NM_172501	212114	Mm.85744	NM_172501	ENSMUSG00000042997	Nhlrc3	4833441N19|8030451K01Rik|mKIAA4083	NHL repeat containing 3	protein-coding
mm_138757.1	chr17	37050605	37050615	+	1	NA	intron (NM_019439, intron 5 of 22)	intron (NM_019439, intron 5 of 22)	4644	NM_019439	54393	Mm.32191	NM_019439	ENSMUSG00000024462	Gabbr1	GABAB1|GABAbR1|bM573K1.1	gamma-aminobutyric acid (GABA) B receptor, 1	protein-coding
mm_45437.1	chr5	67261069	67261114	-	1	NA	intron (NM_001285452, intron 1 of 6)	CpG	526	NM_030108	67878	Mm.23217	NM_028975	ENSMUSG00000037720	Tmem33	1110006G02Rik|1600019D15Rik|2410089A21Rik|2700052H22Rik|5430406L04Rik|AA388285|AI314185|AI426615|db83	transmembrane protein 33	protein-coding
mm_101441.1	chr11	30159650	30159660	-	1	NA	intron (NM_175836, intron 1 of 34)	intron (NM_175836, intron 1 of 34)	38602	NM_009260	20742	Mm.123110	NM_009260	ENSMUSG00000020315	Sptbn1	9930031C03Rik|AL033301|SPTB2|Spnb-2|Spnb2|elf1|elf3|mKIAA4049	spectrin beta, non-erythrocytic 1	protein-coding
mm_141138.1	chr17	26244204	26244228	-	1	NA	promoter-TSS (NM_001206335)	promoter-TSS (NM_001206335)	26	NM_207217	106581	Mm.28844	NM_207217	ENSMUSG00000024187	Fam234a	Itfg3	family with sequence similarity 234, member A	protein-coding
mm_119556.1	chr14	48670119	48670130	+	1	NA	intron (NR_029384, intron 1 of 4)	intron (NR_029384, intron 1 of 4)	836	NR_029384	606497	Mm.165199	NR_029384	ENSMUSG00000098682	Otx2os1	-	orthodenticle homeobox 2 opposite strand 1	ncRNA
mm_170188.1	chr17	6423039	6423055	-	1	NA	Intergenic	Lx4A|LINE|L1	-7065	NM_009342	21648	Mm.1948	NM_009342	ENSMUSG00000096255	Dynlt1b	AGS2|Dynlt1|Tctex-1|Tctex1	dynein light chain Tctex-type 1B	protein-coding
mm_87624.1	chr10	57805605	57805618	+	1	NA	exon (NM_020561, exon 4 of 8)	exon (NM_020561, exon 4 of 8)	11067	NM_020561	57319	Mm.2379	NM_020561	ENSMUSG00000019872	Smpdl3a	0610010C24Rik|AI529588|ASM3A|ASML3|ASML3A	sphingomyelin phosphodiesterase, acid-like 3A	protein-coding
mm_168465.1	chr11	4815149	4815150	-	1	NA	intron (NM_001252251, intron 4 of 16)	intron (NM_001252251, intron 4 of 16)	17986	NM_001252253	18016	Mm.297109	NM_010898	ENSMUSG00000009073	Nf2	merlin	neurofibromin 2	protein-coding
mm_123041.1	chr14	55588318	55588328	-	1	NA	intron (NM_001029855, intron 7 of 10)	intron (NM_001029855, intron 7 of 10)	2698	NM_011190	19188	Mm.371573	NM_011190	ENSMUSG00000079197	Psme2	AA589371|AI788882|PA28b	proteasome (prosome, macropain) activator subunit 2 (PA28 beta)	protein-coding
mm_164866.1	chr18	56505673	56505677	-	1	NA	Intergenic	Intergenic	-32464	NR_106160	102465790		NR_106160	ENSMUSG00000099196	Mir1258	Gm27371|mmu-mir-1258	microRNA 1258	ncRNA
mm_94981.1	chr11	31796509	31796517	+	1	NA	Intergenic	Intergenic	28034	NR_102310	414116	Mm.150222	NR_102310	ENSMUSG00000085772	D630024D03Rik	-	RIKEN cDNA D630024D03 gene	ncRNA
mm_137130.1	chr17	23599277	23599332	+	1	NA	5' UTR (NM_011747, exon 1 of 6)	5' UTR (NM_011747, exon 1 of 6)	183	NM_011747	22654	Mm.40326	NM_011747	ENSMUSG00000062012	Zfp13	4933429B21|AI835008|Krox-8|Rhit|Zfp-13	zinc finger protein 13	protein-coding
mm_128192.1	chr15	34995290	34995292	-	1	NA	intron (NM_019635, intron 8 of 10)	L1_Mur2|LINE|L1	157242	NM_001271704	16539	Mm.71045	NM_181317	ENSMUSG00000050963	Kcns2	E130006J24Rik|Kv9.2	K+ voltage-gated channel, subfamily S, 2	protein-coding
mm_20349.1	chr2	127755718	127755718	-	1	NA	intron (NM_001291012, intron 15 of 19)	B3|SINE|B2	-25821	NM_145532	228576	Mm.133036	NM_145532	ENSMUSG00000027377	Mall	BC012256|BENE	mal, T cell differentiation protein-like	protein-coding
mm_75471.1	chr8	48009072	48009114	-	1	NA	Intergenic	RCHARR1|DNA|hAT-Charlie	-18542	NM_133791	52357	Mm.235074	NM_133791	ENSMUSG00000031563	Wwc2	5330431C14Rik|AU022508|C85457|D8Ertd594e	WW, C2 and coiled-coil domain containing 2	protein-coding
mm_17335.1	chr2	26592680	26592680	-	1	NA	TTS (NM_001164564)	TTS (NM_001164564)	-1260	NR_106155	102465787		NR_106155	ENSMUSG00000105799	Mir126b	mmu-mir-126b	microRNA 126b	ncRNA
mm_158191.1	chrX	104670956	104670978	-	1	NA	promoter-TSS (NM_175358)	promoter-TSS (NM_175358)	97	NM_175358	108672	Mm.30574	NM_175358	ENSMUSG00000033906	Zdhhc15	6030457O13Rik	zinc finger, DHHC domain containing 15	protein-coding
mm_135202.1	chr16	36561542	36561554	-	1	NA	intron (NM_013803, intron 1 of 6)	intron (NM_013803, intron 1 of 6)	586	NM_013803	12374	Mm.103619	NM_013803	ENSMUSG00000051980	Casr	CaR|Gprc2a	calcium-sensing receptor	protein-coding
mm_140502.1	chr17	4908540	4908571	-	1	NA	Intergenic	CpG	-86519	NM_001085355	239985	Mm.133401	NM_001085355	ENSMUSG00000069729	Arid1b	8030481M12|9330189K18Rik|AI836955|Ardi1b|B230217J03Rik|mKIAA1235	AT rich interactive domain 1B (SWI-like)	protein-coding
mm_63125.1	chr7	122999768	122999781	+	1	NA	exon (NM_011247, exon 17 of 18)	exon (NM_011247, exon 17 of 18)	29210	NM_175023	19647	Mm.4480	NM_011247	ENSMUSG00000030779	Rbbp6	4933422O15Rik|AI316869|BB233631|C030034J04Rik|C77662|P2P-R|PACT	retinoblastoma binding protein 6	protein-coding
mm_44406.1	chr5	17847861	17847870	-	1	NA	intron (NM_001159558, intron 1 of 15)	intron (NM_001159558, intron 1 of 15)	1927	NM_001159557	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_56828.1	chr6	117174276	117174292	-	1	NA	3' UTR (NM_021704, exon 3 of 3)	3' UTR (NM_021704, exon 3 of 3)	5749	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_116713.1	chr13	51568302	51568333	-	1	NA	Intergenic	Intergenic	-1233	NM_009167	20418	Mm.131870	NM_009167	ENSMUSG00000021448	Shc3	N-Shc|Rai|ShcC	src homology 2 domain-containing transforming protein C3	protein-coding
mm_1864.1	chr1	85106090	85106093	+	1	NA	intron (NM_213615, intron 1 of 6)	intron (NM_213615, intron 1 of 6)	3762	NM_213615	381287	Mm.487565	NM_213615	ENSMUSG00000089844	A530032D15Rik	Gm1888	RIKEN cDNA A530032D15Rik gene	protein-coding
mm_41432.1	chr5	90903865	90903880	+	1	NA	promoter-TSS (NM_009140)	promoter-TSS (NM_009140)	-27	NM_009140	20310	Mm.4979	NM_009140	ENSMUSG00000058427	Cxcl2	CINC-2a|GROb|Gro2|MIP-2|MIP-2a|Mgsa-b|Mip2|Scyb|Scyb2	chemokine (C-X-C motif) ligand 2	protein-coding
mm_132617.1	chr16	38742255	38742279	+	1	NA	promoter-TSS (NM_019804)	promoter-TSS (NM_019804)	8	NM_001285793	56375	Mm.182377	NM_019804	ENSMUSG00000022793	B4galt4	9130402O08Rik|B4galt-IV|b4Gal-T4|beta4Gal-T4|beta4GalT-IV	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 4	protein-coding
mm_25463.1	chr3	108591323	108591414	+	1	NA	promoter-TSS (NM_181400)	promoter-TSS (NM_181400)	90	NM_181400	99512	Mm.285968	NM_181400	ENSMUSG00000040389	Wdr47	1810073M12Rik|AA552998|mKIAA0893	WD repeat domain 47	protein-coding
mm_97908.1	chr11	83440398	83440400	+	1	NA	TTS (NM_080453)	TTS (NM_080453)	2705	NM_025492	66330	Mm.44800	NM_025492	ENSMUSG00000035085	1700020L24Rik	-	RIKEN cDNA 1700020L24 gene	protein-coding
mm_73576.1	chr8	109778655	109778678	+	1	NA	promoter-TSS (NM_009677)	promoter-TSS (NM_009677)	83	NM_001301211	11765	Mm.37210	NM_009677	ENSMUSG00000031731	Ap1g1	AA409002|AU041323|AW551707|Adtg|D8Ertd374e	adaptor protein complex AP-1, gamma 1 subunit	protein-coding
mm_14951.1	chr2	151978384	151978400	+	1	NA	intron (NM_146127, intron 1 of 1)	intron (NM_146127, intron 1 of 1)	1827	NM_146127	73847	Mm.272444	NM_028666	ENSMUSG00000027459	Fam110a	1700008J10Rik|5430432M24Rik|AI747080	family with sequence similarity 110, member A	protein-coding
mm_123035.1	chr14	55559964	55559980	-	1	NA	promoter-TSS (NM_001199009)	promoter-TSS (NM_001199009)	-57	NR_037572	28199	Mm.11535	NM_133734	ENSMUSG00000022214	Dcaf11	0710008A13Rik|C76035|D14Ucla1|Dacf11|GLO14|Wdr23	DDB1 and CUL4 associated factor 11	protein-coding
mm_57774.1	chr6	129237968	129237987	-	1	NA	promoter-TSS (NR_040265)	promoter-TSS (NR_040265)	68	NR_040265	76432	Mm.261738	NR_040265	ENSMUSG00000097354	2310001H17Rik	AI646108	RIKEN cDNA 2310001H17 gene	ncRNA
mm_150604.1	chr19	40829092	40829092	+	1	NA	Intergenic	Intergenic	-2187	NM_172839	240665	Mm.309	NM_172839	ENSMUSG00000025010	Ccnj	D430039C20Rik	cyclin J	protein-coding
mm_107199.1	chr12	25320803	25320811	+	1	NA	Intergenic	Intergenic	191633	NR_045844	432641	Mm.112955	NR_045844		Gm17746	-	predicted gene, 17746	ncRNA
mm_86742.1	chr10	19187309	19187341	+	1	NA	intron (NR_038022, intron 1 of 1)	intron (NR_038022, intron 1 of 1)	20087	NR_038022	100504265	Mm.383417	NR_038021		Gm20139	-	predicted gene, 20139	ncRNA
mm_30327.1	chr3	151732031	151732050	-	1	NA	3' UTR (NM_133871, exon 8 of 8)	3' UTR (NM_133871, exon 8 of 8)	17919	NM_133871	99899	Mm.30756	NM_133871	ENSMUSG00000028037	Ifi44	A430056A10Rik|AW261460|MTAP44|p44	interferon-induced protein 44	protein-coding
mm_96571.1	chr11	69045816	69045822	+	1	NA	5' UTR (NM_011496, exon 1 of 8)	5' UTR (NM_011496, exon 1 of 8)	182	NM_011496	20877	Mm.3488	NM_011496	ENSMUSG00000020897	Aurkb	AIM-1|AIRK2|AL022959|Aik2|Aim1|Ark2|AurB|IPL1|STK-1|Stk12|Stk5	aurora kinase B	protein-coding
mm_173247.1	chrX	89488672	89488682	+	1	NA	Intergenic	L1Md_T|LINE|L1	-78988	NM_008821	18630	Mm.3086	NM_008821	ENSMUSG00000035395	Pet2	PC231|PC326|Pex3	plasmacytoma expressed transcript 2	protein-coding
mm_52204.1	chr6	100833607	100833663	+	1	NA	promoter-TSS (NM_182939)	promoter-TSS (NM_182939)	-3	NM_182939	232314	Mm.27223	NM_182939	ENSMUSG00000052144	Ppp4r2	BE691708|C230060M08Rik	protein phosphatase 4, regulatory subunit 2	protein-coding
mm_19486.1	chr2	93203290	93203317	-	1	NA	3' UTR (NM_183180, exon 10 of 10)	3' UTR (NM_183180, exon 10 of 10)	15719	NM_001025246	277414	Mm.41033	NM_001025246	ENSMUSG00000068735	Trp53i11	Tp53i11	transformation related protein 53 inducible protein 11	protein-coding
mm_63221.1	chr7	126293992	126294001	+	1	NA	3' UTR (NM_145587, exon 4 of 4)	3' UTR (NM_145587, exon 4 of 4)	21377	NM_145587	104175	Mm.29660	NM_145587	ENSMUSG00000042978	Sbk1	Sbk	SH3-binding kinase 1	protein-coding
mm_170214.1	chr17	72635653	72635654	-	1	NA	Intergenic	Intergenic	-31346	NM_007439	11682	Mm.311854	NM_007439	ENSMUSG00000055471	Alk	CD246|Tcrz	anaplastic lymphoma kinase	protein-coding
mm_68392.1	chr7	109524182	109524201	-	1	NA	non-coding (NR_037617, exon 20 of 20)	non-coding (NR_037617, exon 20 of 20)	4059	NR_028079	100302499	Mm.482651	NR_028079	ENSMUSG00000065016	Snora3	MBI-28	small nucleolar RNA, H/ACA box 3	snoRNA
mm_63411.1	chr7	127334714	127334748	+	1	NA	3' UTR (NM_001253873, exon 31 of 31)	3' UTR (NM_001253873, exon 31 of 31)	10583	NM_146202	233890	Mm.23031	NM_146202	ENSMUSG00000047371	Zfp768	BC026432|Znf768	zinc finger protein 768	protein-coding
mm_93651.1	chr10	117376956	117376978	-	1	NA	promoter-TSS (NM_001013391)	promoter-TSS (NM_001013391)	6	NM_001013391	432508	Mm.478881	NM_001013391	ENSMUSG00000055531	Cpsf6	4733401N12Rik|AI256641|CFIM|CFIM68|HPBRII-4|HPBRII-7	cleavage and polyadenylation specific factor 6	protein-coding
mm_131803.1	chr16	22899327	22899355	+	1	NA	non-coding (NR_075099, exon 6 of 6)	non-coding (NR_075099, exon 6 of 6)	-4955	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_28882.1	chr3	97824511	97824546	-	1	NA	intron (NM_001039376, intron 3 of 46)	intron (NM_001039376, intron 3 of 46)	-56514	NM_178080	83679	Mm.129840	NM_031401	ENSMUSG00000038170	Pde4dip	4732458A06Rik|9430063L05Rik|C87016|D130016K21Rik|D3Bwg1078e|Usmg4|mKIAA0454	phosphodiesterase 4D interacting protein (myomegalin)	protein-coding
mm_15009.1	chr2	152562978	152562993	+	1	NA	Intergenic	Intergenic	-9759	NM_207276	403172	Mm.84518	NM_207276	ENSMUSG00000056544	Defb21	4930525K10Rik|Gm121	defensin beta 21	protein-coding
mm_81478.1	chr9	109937223	109937238	+	1	NA	intron (NM_001205330, intron 1 of 18)	B1F|SINE|Alu	5456	NM_008633	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_593.1	chr1	39551795	39551813	+	1	NA	3' UTR (NM_001033135, exon 7 of 7)	3' UTR (NM_001033135, exon 7 of 7)	-2964	NR_028555	100217461		NR_028555	ENSMUSG00000077704	Snord89	MBII-289	small nucleolar RNA, C/D box 89	snoRNA
mm_2578.1	chr1	118482042	118482063	+	1	NA	intron (NM_001293300, intron 8 of 40)	intron (NM_001293300, intron 8 of 40)	-22787	NR_027901	68204	Mm.443536	NR_027901	ENSMUSG00000107722	2900060B14Rik	-	RIKEN cDNA 2900060B14 gene	ncRNA
mm_144450.1	chr18	23310048	23310139	+	1	NA	promoter-TSS (NM_001285813)	promoter-TSS (NM_001285813)	73	NM_001285813	13527	Mm.94371	NM_010087	ENSMUSG00000024302	Dtna	2210407P21Rik|DTN-A|Dtn|Gm19389|a-DB-1|adbn	dystrobrevin alpha	protein-coding
mm_39968.1	chr5	32152976	32152986	+	1	NA	exon (NM_008037, exon 4 of 4)	exon (NM_008037, exon 4 of 4)	16509	NM_008037	14284	Mm.24684	NM_008037	ENSMUSG00000029135	Fosl2	Fra-2	fos-like antigen 2	protein-coding
mm_59218.1	chr7	24608315	24608334	+	1	NA	intron (NM_023154, intron 6 of 7)	intron (NM_023154, intron 6 of 7)	-3004	NM_001102613	232970	Mm.333663	NM_001102613	ENSMUSG00000074277	Phldb3	EG232970|ENSMUSG00000061511|Gm10102	pleckstrin homology like domain, family B, member 3	protein-coding
mm_26830.1	chr3	10440009	10440022	-	1	NA	5' UTR (NM_001127191, exon 1 of 7)	5' UTR (NM_001127191, exon 1 of 7)	115	NM_029068	74718	Mm.440548	NM_029068	ENSMUSG00000027534	Snx16	4930522N22Rik|AI117577|AI747675	sorting nexin 16	protein-coding
mm_60002.1	chr7	30698935	30698947	+	1	NA	promoter-TSS (NM_026961)	promoter-TSS (NM_026961)	15	NM_026961	69147	Mm.307035	NM_026961	ENSMUSG00000013083	2200002J24Rik	-	RIKEN cDNA 2200002J24 gene	protein-coding
mm_93256.1	chr10	95548525	95548538	-	1	NA	3' UTR (NM_027722, exon 5 of 5)	3' UTR (NM_027722, exon 5 of 5)	10790	NR_037212	100526463		NR_037212	ENSMUSG00000092867	Mir3058	mir-3058|mmu-mir-3058	microRNA 3058	ncRNA
mm_138277.1	chr17	34605865	34605881	+	1	NA	promoter-TSS (NM_001163379)	promoter-TSS (NM_001163379)	12	NM_001163379	55979	Mm.8684	NM_018862	ENSMUSG00000034254	Agpat1	1-AGP|1-AGPAT|AW047140	1-acylglycerol-3-phosphate O-acyltransferase 1 (lysophosphatidic acid acyltransferase, alpha)	protein-coding
mm_25314.1	chr3	106147556	106147556	+	1	NA	TTS (NM_009892)	TTS (NM_009892)	20008	NM_009892	12655	Mm.387173	NM_009892	ENSMUSG00000040809	Chil3	AI505981|Chi3l3|ECF-L|Ym1	chitinase-like 3	protein-coding
mm_47278.1	chr5	122050134	122050158	-	1	NA	promoter-TSS (NM_001312908)	promoter-TSS (NM_001312908)	-295	NM_001312908	13048	Mm.156172	NM_007804	ENSMUSG00000042589	Cux2	1700051K22Rik|Cutl2|Cux-2|ENSMUSG00000072641	cut-like homeobox 2	protein-coding
mm_131276.1	chr16	11022323	11022332	+	1	NA	Intergenic	Intergenic	13429	NR_040518	100043147	Mm.489001	NR_040518	ENSMUSG00000097056	Gm4262	-	predicted gene 4262	ncRNA
mm_11095.1	chr2	27951366	27951379	+	1	NA	exon (NM_015734, exon 7 of 66)	exon (NM_015734, exon 7 of 66)	64947	NM_015734	12831	Mm.7281	NM_015734	ENSMUSG00000026837	Col5a1	AI413331	collagen, type V, alpha 1	protein-coding
mm_54230.1	chr6	28213822	28213836	-	1	NA	Intergenic	Intergenic	47772	NM_001081678	627049	Mm.84441	NM_001081678	ENSMUSG00000039841	Zfp800	AA407452|Znf800	zinc finger protein 800	protein-coding
mm_34868.1	chr4	155558111	155558115	+	1	NA	3' UTR (NM_008142, exon 12 of 12)	3' UTR (NM_008142, exon 12 of 12)	-4279	NM_138671	192185	Mm.28347	NM_138671	ENSMUSG00000029063	Nadk	4432404C02Rik|BC004012	NAD kinase	protein-coding
mm_8048.1	chr1	135373200	135373210	-	1	NA	exon (NM_175259, exon 3 of 5)	exon (NM_175259, exon 3 of 5)	1858	NM_175259	77552	Mm.41407	NM_175259	ENSMUSG00000041889	Shisa4	9330132O05Rik|Tmem58|mShisa4	shisa family member 4	protein-coding
mm_166433.1	chr5	137187807	137187834	-	1	NA	Intergenic	Intergenic	-71613	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_147125.1	chr18	35889792	35889802	-	1	NA	Intergenic	CpG	59979	NM_133687	67393	Mm.94560	NM_133687	ENSMUSG00000046668	Cxxc5	4930415K17Rik	CXXC finger 5	protein-coding
mm_40659.1	chr5	65155096	65155103	+	1	NA	intron (NM_001347355, intron 5 of 10)	intron (NM_001347355, intron 5 of 10)	23868	NM_175174	71778	Mm.10281	NM_175174	ENSMUSG00000054920	Klhl5	1300013C10Rik	kelch-like 5	protein-coding
mm_19828.1	chr2	111229532	111229542	-	1	NA	promoter-TSS (NM_026248)	promoter-TSS (NM_026248)	63	NM_026248	67575	Mm.84331	NM_026248	ENSMUSG00000027157	4930430A15Rik	-	RIKEN cDNA 4930430A15 gene	protein-coding
mm_145051.1	chr18	40256961	40257018	+	1	NA	promoter-TSS (NR_045177)	promoter-TSS (NR_045177)	27	NR_045177	73001	Mm.428647	NR_045177	ENSMUSG00000071860	2900055J20Rik	-	RIKEN cDNA 2900055J20 gene	ncRNA
mm_25718.1	chr3	122729164	122729182	+	1	NA	promoter-TSS (NM_153422)	promoter-TSS (NM_153422)	15	NM_153422	242202	Mm.134911	NM_153422	ENSMUSG00000053965	Pde5a	Cgbpde|Cn5n|PDE5a2|Pde5|Pde5a1	phosphodiesterase 5A, cGMP-specific	protein-coding
mm_159502.1	chr4	43821256	43821256	-	1	NA	exon (NM_019474, exon 1 of 1)	exon (NM_019474, exon 1 of 1)	177	NM_019474	29846	Mm.377121	NM_019474	ENSMUSG00000110970	Olfr156	MOR262-6|OR37B|Olfr37b|mOR37b	olfactory receptor 156	protein-coding
mm_75698.1	chr8	68212193	68212204	-	1	NA	Intergenic	Intergenic	-64330	NM_028182	72281	Mm.40974	NM_028182	ENSMUSG00000053886	Sh2d4a	2210402M20Rik|SH2A	SH2 domain containing 4A	protein-coding
mm_57884.1	chr6	131348380	131348392	-	1	NA	Intergenic	Intergenic	-34559	NM_172891	243659	Mm.20114	NM_172891	ENSMUSG00000032899	Styk1	9130025L13|AI326477|Nok	serine/threonine/tyrosine kinase 1	protein-coding
mm_102837.1	chr11	69323769	69323832	-	1	NA	promoter-TSS (NM_001024206)	promoter-TSS (NM_001024206)	73	NM_172560	216846	Mm.28774	NM_172560	ENSMUSG00000032782	Cntrob	9830165K03Rik|Lip8|Nip2	centrobin, centrosomal BRCA2 interacting protein	protein-coding
mm_20262.1	chr2	126670676	126670680	-	1	NA	intron (NM_001271470, intron 1 of 8)	intron (NM_001271470, intron 1 of 8)	4914	NM_001271469	14391	Mm.293266	NM_010249	ENSMUSG00000027361	Gabpb1	BABPB2|E4TF1|E4TF1-47|E4TF1-53|E4Tf1B|GABPB|GABPB-1|GABPB-2|GABPB1-1|GABPB1-2|NRF2B1|NRF2B2	GA repeat binding protein, beta 1	protein-coding
mm_69654.1	chr7	139957690	139957694	-	1	NA	promoter-TSS (NR_029589)	promoter-TSS (NR_029589)	68	NR_029589	387198		NR_029589	ENSMUSG00000065502	Mir202	Mirn202|mir-202|mmu-mir-202	microRNA 202	ncRNA
mm_119212.1	chr14	32991431	32991454	+	1	NA	promoter-TSS (NM_001146021)	promoter-TSS (NM_001146021)	60	NM_026253	67580	Mm.46115	NM_026253	ENSMUSG00000041673	Lrrc18	4930442L21Rik|MTLR1	leucine rich repeat containing 18	protein-coding
mm_171169.1	chr3	28557687	28557689	-	1	NA	intron (NM_026910, intron 9 of 32)	intron (NM_026910, intron 9 of 32)	137745	NR_130342	100628591		NR_130342	ENSMUSG00000092990	Mir466q	Mir446q|mmu-mir-466q|mu-mir-446q	microRNA 466q	ncRNA
mm_90894.1	chr10	10344734	10344736	-	1	NA	intron (NM_001127353, intron 34 of 36)	B4A|SINE|B4	127579	NM_001127353	215772	Mm.246573	NM_172547	ENSMUSG00000050994	Adgb	9130014G24Rik	androglobin	protein-coding
mm_163185.1	chr11	94133427	94133469	+	1	NA	Intergenic	Intergenic	-78006	NM_009427	22057	Mm.259673	NM_009427	ENSMUSG00000037573	Tob1	Tob|Trob	transducer of ErbB-2.1	protein-coding
mm_137386.1	chr17	25803393	25803405	+	1	NA	Intergenic	Intergenic	-5686	NM_001164225	214931	Mm.152289	NM_001164225	ENSMUSG00000025738	Fbxl16	BC042620|Scirr1	F-box and leucine-rich repeat protein 16	protein-coding
mm_22475.1	chr3	5218630	5218684	+	1	NA	5' UTR (NM_030708, exon 1 of 11)	5' UTR (NM_030708, exon 1 of 11)	103	NM_030708	80892	Mm.41522	NM_030708	ENSMUSG00000025255	Zfhx4	A930021B15|C130041O22Rik|Zfh-4|Zfh4	zinc finger homeodomain 4	protein-coding
mm_78494.1	chr9	32723387	32723391	+	1	NA	intron (NM_011808, intron 1 of 7)	intron (NM_011808, intron 1 of 7)	27347	NM_001038642	23871	Mm.292415	NM_011808	ENSMUSG00000032035	Ets1	AI196000|AI448617|D230050P06|Ets-1|Tpl1|vs	E26 avian leukemia oncogene 1, 5' domain	protein-coding
mm_35379.1	chr4	33245944	33246009	-	1	NA	3' UTR (NM_001033225, exon 2 of 2)	3' UTR (NM_001033225, exon 2 of 2)	2811	NM_001033225	108767	Mm.27769	NM_001033225	ENSMUSG00000040128	Pnrc1	5730463C12Rik|B4-2|PRR2|Prol2	proline-rich nuclear receptor coactivator 1	protein-coding
mm_44312.1	chr5	9161693	9161762	-	1	NA	promoter-TSS (NM_001110327)	promoter-TSS (NM_001110327)	49	NM_001110327	23857	Mm.22480	NM_011806	ENSMUSG00000042508	Dmtf1	Dimp|Dmp1	cyclin D binding myb-like transcription factor 1	protein-coding
mm_73065.1	chr8	94388194	94388198	+	1	NA	intron (NM_022331, intron 1 of 7)	intron (NM_022331, intron 1 of 7)	1696	NM_022331	64209	Mm.29151	NM_022331	ENSMUSG00000031770	Herpud1	Herp|Mifl|SUP	homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1	protein-coding
mm_156299.1	chrX	136837869	136837884	+	1	NA	3' UTR (NM_011123, exon 7 of 7)	3' UTR (NM_011123, exon 7 of 7)	15130	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_75894.1	chr8	70895884	70895889	-	1	NA	promoter-TSS (NR_002901)	promoter-TSS (NR_002901)	-30	NR_002901	104370		NR_002901		Snora68	MBI-30|Rnu68	small nucleolar RNA, H/ACA box 68	snoRNA
mm_67476.1	chr7	80535069	80535121	-	1	NA	promoter-TSS (NM_007550)	promoter-TSS (NM_007550)	24	NM_001042527	12144	Mm.12932	NM_007550	ENSMUSG00000030528	Blm	-	Bloom syndrome, RecQ helicase-like	protein-coding
mm_20836.1	chr2	147194242	147194249	-	1	NA	intron (NR_030769, intron 1 of 5)	CpG	6821	NR_108091	78068	Mm.261511	NR_108091	ENSMUSG00000053545	6430503K07Rik	-	RIKEN cDNA 6430503K07 gene	ncRNA
mm_22242.1	chr2	174472950	174473019	-	1	NA	promoter-TSS (NM_025531)	promoter-TSS (NM_025531)	-43	NM_025531	66390	Mm.182294	NM_025531	ENSMUSG00000016257	Slmo2	2310042G06Rik|AA407013|Prelid3b	slowmo homolog 2 (Drosophila)	protein-coding
mm_75757.1	chr8	69909373	69909389	-	1	NA	3' UTR (NM_001113346, exon 13 of 13)	3' UTR (NM_001113346, exon 13 of 13)	-6823	NM_023312	67184	Mm.21162	NM_023312	ENSMUSG00000036199	Ndufa13	2700054G14Rik|AU022060|CDA016|CGI-39|GRIM-19|Grim19	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 13	protein-coding
mm_130435.1	chr15	98170502	98170519	-	1	NA	TTS (NM_177716)	TTS (NM_177716)	2704	NM_177716	239650	Mm.54140	NM_177716	ENSMUSG00000029875	Ccdc184	5630400A08|AI836003	coiled-coil domain containing 184	protein-coding
mm_134683.1	chr16	22412896	22412947	-	1	NA	exon (NM_023794, exon 6 of 13)	exon (NM_023794, exon 6 of 13)	26649	NM_023794	104156	Mm.155708	NM_023794	ENSMUSG00000013089	Etv5	1110005E01Rik|8430401F14Rik|ERM	ets variant 5	protein-coding
mm_114819.1	chr13	91678617	91678631	+	1	NA	intron (NM_024272, intron 9 of 16)	intron (NM_024272, intron 9 of 16)	-62897	NM_028790	74156	Mm.275963	NM_028790	ENSMUSG00000021620	Acot12	1300004O04Rik|4930449F15Rik|AV027244|Cach|mCACH-1	acyl-CoA thioesterase 12	protein-coding
mm_140797.1	chr17	21471607	21471609	-	1	NA	Intergenic	RLTR48A|LTR|ERV1	-17380	NM_013843	24132	Mm.42140	NM_013843	ENSMUSG00000057409	Zfp53	D030067O06Rik|KRAZ1|Zfp-53|Zfp118|zfas8	zinc finger protein 53	protein-coding
mm_140401.1	chr17	87639881	87639890	+	1	NA	intron (NM_008532, intron 2 of 9)	intron (NM_008532, intron 2 of 9)	3906	NM_008532	17075	Mm.4259	NM_008532	ENSMUSG00000045394	Epcam	CD326|EGP|EGP-2|Egp314|Ep-CAM|EpCAM1|GA733-2|Ly74|TROP1|Tacsd1|Tacstd1|gp40	epithelial cell adhesion molecule	protein-coding
mm_114415.1	chr13	64365282	64365295	+	1	NA	exon (NM_009984, exon 7 of 8)	exon (NM_009984, exon 7 of 8)	5232	NM_009984	13039	Mm.930	NM_009984	ENSMUSG00000021477	Ctsl	1190035F06Rik|CatL|Ctsl1|MEP|fs|nkt	cathepsin L	protein-coding
mm_143396.1	chr17	70740117	70740119	-	1	NA	intron (NM_001347411, intron 9 of 14)	intron (NM_001347411, intron 9 of 14)	106659	NM_001164077	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_61303.1	chr7	67951858	67951910	+	1	NA	promoter-TSS (NM_010513)	promoter-TSS (NM_010513)	-373	NM_010513	16001	Mm.275742	NM_010513	ENSMUSG00000005533	Igf1r	A330103N21Rik|CD221|D930020L01|IGF-1R|hyft	insulin-like growth factor I receptor	protein-coding
mm_57907.1	chr6	132439742	132439769	-	1	NA	Intergenic	Intergenic	-75620	NM_053251	114600	Mm.428480	NM_053251		Gm4736	EG114600|Mp4|Mp6	predicted gene 4736	protein-coding
mm_152043.1	chr19	6141076	6141122	-	1	NA	promoter-TSS (NM_019722)	promoter-TSS (NM_019722)	38	NM_019722	56327	Mm.21071	NM_019722	ENSMUSG00000024944	Arl2	2610009M23Rik|AI115441|AW553335	ADP-ribosylation factor-like 2	protein-coding
mm_169967.1	chr17	12769792	12769796	+	1	NA	promoter-TSS (NM_010515)	promoter-TSS (NM_010515)	-88	NM_010515	16004	Mm.26553	NM_010515	ENSMUSG00000023830	Igf2r	AI661837|CD222|CI-MPR|M6P/IGF2R|Mpr300	insulin-like growth factor 2 receptor	protein-coding
mm_147506.1	chr18	50181238	50181269	-	1	NA	intron (NM_008292, intron 20 of 23)	B1F|SINE|Alu	53052	NM_008292	15488	Mm.277857	NM_008292	ENSMUSG00000024507	Hsd17b4	17-beta-HSD|17[b]-HSD|DBP|MFE-2|MFP2|MPF-2|Mfp-2|perMFE-2	hydroxysteroid (17-beta) dehydrogenase 4	protein-coding
mm_571.1	chr1	38902867	38902891	+	1	NA	Intergenic	MER21C|LTR|ERVL	-4719	NM_145142	98388	Mm.260054	NM_145142	ENSMUSG00000026080	Chst10	AI507003|AU041319|Hnk-1st|ST	carbohydrate sulfotransferase 10	protein-coding
mm_105812.1	chr11	111066057	111066077	-	1	NA	promoter-TSS (NM_008425)	promoter-TSS (NM_008425)	-97	NM_008425	16518	Mm.4951	NM_008425	ENSMUSG00000041695	Kcnj2	IRK1|Kcnf1|Kir2.1	potassium inwardly-rectifying channel, subfamily J, member 2	protein-coding
mm_129168.1	chr15	76248145	76248173	-	1	NA	promoter-TSS (NR_105918)	promoter-TSS (NR_105918)	-32	NR_105918	102465575		NR_105918	ENSMUSG00000098625	Mir6953	Gm27738|mmu-mir-6953	microRNA 6953	ncRNA
mm_61044.1	chr7	49778335	49778389	+	1	NA	promoter-TSS (NM_133740)	promoter-TSS (NM_133740)	4	NM_133740	71974	Mm.33202	NM_133740	ENSMUSG00000030505	Prmt3	2010005E20Rik|2410018A17Rik|AL033309|Hrmt1l3	protein arginine N-methyltransferase 3	protein-coding
mm_50464.1	chr6	48951870	48951875	+	1	NA	Intergenic	Lx10|LINE|L1	21976	NM_001081273	69761	Mm.333053	NM_001081273	ENSMUSG00000029813	1600015I10Rik	AI429442|Doxl1	RIKEN cDNA 1600015I10 gene	protein-coding
mm_2689.1	chr1	127486725	127486750	+	1	NA	Intergenic	Intergenic	191284	NM_028135	72160	Mm.281287	NM_028135	ENSMUSG00000026347	Tmem163	2610024A01Rik|SV31	transmembrane protein 163	protein-coding
mm_107061.1	chr12	16656305	16656310	+	1	NA	intron (NM_008747, intron 1 of 3)	intron (NM_008747, intron 1 of 3)	2837	NM_008747	18217	Mm.281715	NM_008747	ENSMUSG00000020591	Ntsr2	NT2R|NTRL	neurotensin receptor 2	protein-coding
mm_6251.1	chr1	68910903	68910905	-	1	NA	intron (NM_010154, intron 1 of 26)	intron (NM_010154, intron 1 of 26)	197155	NM_010154	13869	Mm.442420	NM_010154	ENSMUSG00000062209	Erbb4	Her4|c-erbB-4	erb-b2 receptor tyrosine kinase 4	protein-coding
mm_127082.1	chr15	97572278	97572281	+	1	NA	Intergenic	RLTR24B_MM|LTR|ERV1	133543	NM_028003	71919	Mm.12255	NM_028003	ENSMUSG00000022466	Rpap3	2310042P20Rik|D15Ertd682e	RNA polymerase II associated protein 3	protein-coding
mm_274.1	chr1	21240582	21240588	+	1	NA	promoter-TSS (NM_010356)	promoter-TSS (NM_010356)	0	NM_001288617	14859	Mm.394593	NM_010356	ENSMUSG00000025934	Gsta3	Gst2-3	glutathione S-transferase, alpha 3	protein-coding
mm_101131.1	chr11	12428970	12428991	-	1	NA	intron (NM_172496, intron 1 of 14)	intron (NM_172496, intron 1 of 14)	-16840	NM_001282994	12808	Mm.22847	NM_172496	ENSMUSG00000020173	Cobl	-	cordon-bleu WH2 repeat	protein-coding
mm_17907.1	chr2	35315427	35315448	-	1	NA	3' UTR (NM_013515, exon 7 of 7)	3' UTR (NM_013515, exon 7 of 7)	21572	NM_013515	13830	Mm.295284	NM_013515	ENSMUSG00000026880	Stom	Epb7.2	stomatin	protein-coding
mm_29774.1	chr3	127282368	127282384	-	1	NA	intron (NM_001327938, intron 1 of 47)	intron (NM_001327938, intron 1 of 47)	121071	NR_105029	100862268	Mm.444603	NR_105029	ENSMUSG00000097456	LOC100862268	-	uncharacterized LOC100862268	ncRNA
mm_25919.1	chr3	131156450	131156457	+	1	NA	intron (NM_001276403, intron 3 of 11)	intron (NM_001276403, intron 3 of 11)	43662	NM_001276403	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_163891.1	chr14	26970396	26970403	-	1	NA	intron (NM_145221, intron 1 of 21)	CpG	152	NM_145221	72993	Mm.202322	NM_145221	ENSMUSG00000040760	Appl1	2900057D21Rik|7330406P05Rik|AI585782|AW209077|BB022931|C88264|DIP13	adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 1	protein-coding
mm_8760.1	chr1	160577894	160577904	-	1	NA	promoter-TSS (NM_001146330)	promoter-TSS (NM_001146330)	-146	NM_001146330	620246	Mm.478780	NM_001146330		Gpr52	EG620246	G protein-coupled receptor 52	protein-coding
mm_104470.1	chr11	95309683	95309712	-	1	NA	intron (NM_177619, intron 1 of 12)	CpG	549	NM_001195004	217127	Mm.90213	NM_177619	ENSMUSG00000038909	Kat7	Hbo1|Hboa|Myst2	K(lysine) acetyltransferase 7	protein-coding
mm_1044.1	chr1	58795672	58795682	+	1	NA	5' UTR (NM_009812, exon 1 of 9)	5' UTR (NM_009812, exon 1 of 9)	303	NM_009812	12370	Mm.336851	NM_009812	ENSMUSG00000026029	Casp8	CASP-8|FLICE|MACH|Mch5	caspase 8	protein-coding
mm_53952.1	chr6	5298302	5298377	-	1	NA	promoter-TSS (NM_183308)	promoter-TSS (NM_183308)	34	NM_183308	330260	Mm.126984	NM_183308	ENSMUSG00000032667	Pon2	6330405I24Rik|AI481612	paraoxonase 2	protein-coding
mm_2744.1	chr1	128591306	128591316	+	1	NA	intron (NM_009911, intron 1 of 1)	CpG	988	NM_009911	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding
mm_97968.1	chr11	83850833	83850851	+	1	NA	promoter-TSS (NM_001291268)	promoter-TSS (NM_001291268)	-27	NM_001291268	21410	Mm.7226	NM_009330	ENSMUSG00000020679	Hnf1b	HNF-1-beta|HNF-1B|HNF-1Beta|Hnf1beta|LFB3|Tcf-2|Tcf2|vHNF1	HNF1 homeobox B	protein-coding
mm_62445.1	chr7	101383986	101384000	+	1	NA	intron (NM_001040112, intron 1 of 30)	intron (NM_001040112, intron 1 of 30)	-1533	NM_027180	69710	Mm.277687	NM_027180	ENSMUSG00000032812	Arap1	2410002L19Rik|Centd2|mKIAA0782	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	protein-coding
mm_110647.1	chr12	59011878	59011950	-	1	NA	5' UTR (NM_009147, exon 1 of 20)	5' UTR (NM_009147, exon 1 of 20)	103	NM_009147	20334	Mm.491137	NM_009147	ENSMUSG00000020986	Sec23a	Msec23|Sec23r	SEC23 homolog A, COPII coat complex component	protein-coding
mm_8025.1	chr1	135105352	135105362	-	1	NA	promoter-TSS (NM_001033409)	promoter-TSS (NM_001033409)	-81	NM_001033409	329252	Mm.279594	NM_001033409	ENSMUSG00000042793	Lgr6	A530037C04Rik|D830026M09	leucine-rich repeat-containing G protein-coupled receptor 6	protein-coding
mm_159531.1	chr4	65124195	65124195	+	1	NA	promoter-TSS (NM_021362)	promoter-TSS (NM_021362)	21	NM_021362	18491	Mm.317854	NM_021362	ENSMUSG00000028370	Pappa	8430414N03Rik|IGFBP-4ase|PAG1|PAPP-A	pregnancy-associated plasma protein A	protein-coding
mm_136539.1	chr16	97763713	97763780	-	1	NA	promoter-TSS (NM_023663)	promoter-TSS (NM_023663)	9	NM_023663	72388	Mm.35290	NM_023663	ENSMUSG00000005251	Ripk4	2310069J12Rik|AI552420|ANKK2|Ankrd3|DIk|PKK|RIP4	receptor-interacting serine-threonine kinase 4	protein-coding
mm_131227.1	chr16	10170229	10170263	+	1	NA	promoter-TSS (NM_026594)	promoter-TSS (NM_026594)	18	NM_026594	68172	Mm.23690	NM_026594	ENSMUSG00000039209	Rpl39l	4930517K11Rik	ribosomal protein L39-like	protein-coding
mm_113491.1	chr13	37378796	37378828	+	1	NA	intron (NM_010745, intron 3 of 4)	intron (NM_010745, intron 3 of 4)	33467	NM_010745	17084	Mm.2639	NM_010745	ENSMUSG00000021423	Ly86	MD-1|MD1|ly86_tv2	lymphocyte antigen 86	protein-coding
mm_7238.1	chr1	93478786	93478823	-	1	NA	promoter-TSS (NM_010891)	promoter-TSS (NM_010891)	113	NM_133808	110611	Mm.30012	NM_133808	ENSMUSG00000034088	Hdlbp	1110005P14Rik|AA960365|AI118566|D1Ertd101e	high density lipoprotein (HDL) binding protein	protein-coding
mm_9769.1	chr1	180996146	180996155	-	1	NA	exon (NM_010145, exon 4 of 9)	exon (NM_010145, exon 4 of 9)	21419	NM_010145	13849	Mm.9075	NM_010145	ENSMUSG00000038776	Ephx1	EH|Eph-1|Eph1|Epxh1|mEH	epoxide hydrolase 1, microsomal	protein-coding
mm_136067.1	chr16	84735308	84735318	-	1	NA	promoter-TSS (NM_017404)	promoter-TSS (NM_017404)	-11	NM_017404	27393	Mm.103655	NM_017404	ENSMUSG00000022889	Mrpl39	C21orf8|MRP-L5|ORF22|Rpml5	mitochondrial ribosomal protein L39	protein-coding
mm_90030.1	chr10	115430882	115430905	+	1	NA	intron (NM_001033261, intron 32 of 34)	intron (NM_001033261, intron 32 of 34)	45934	NM_001033261	216345	Mm.207621	NM_001033261	ENSMUSG00000034163	Zfc3h1	BC033596|Ccdc131|Psrc2	zinc finger, C3H1-type containing	protein-coding
mm_136243.1	chr16	90934783	90934793	-	1	NA	promoter-TSS (NM_026502)	promoter-TSS (NM_026502)	61	NM_026502	68001	Mm.45374	NM_026502	ENSMUSG00000022972	1110004E09Rik	-	RIKEN cDNA 1110004E09 gene	protein-coding
mm_68228.1	chr7	104441391	104441423	-	1	NA	intron (NM_009099, intron 1 of 7)	Lx6|LINE|L1	23786	NM_009099	20128	Mm.295578	NM_009099	ENSMUSG00000030921	Trim30a	Rpt-1|Rpt1|Trim30	tripartite motif-containing 30A	protein-coding
mm_129403.1	chr15	78285145	78285174	-	1	NA	promoter-TSS (NR_106137).2	promoter-TSS (NR_106137).2	-310	NR_106137	102465776		NR_106137	ENSMUSG00000098996	Mir7676-1	Gm27600|mmu-mir-7676-1	microRNA 7676-1	ncRNA
mm_116795.1	chr13	53472823	53472850	-	1	NA	promoter-TSS (NM_013601)	promoter-TSS (NM_013601)	-56	NM_013601	17702	Mm.1763	NM_013601	ENSMUSG00000021469	Msx2	BB122635|Hox-8|Hox8|Hox8.1	msh homeobox 2	protein-coding
mm_51309.1	chr6	72313791	72313796	+	1	NA	intron (NM_001282071, intron 10 of 10)	MIR3|SINE|MIR	9183	NM_147779	20388	Mm.46033	NM_147779	ENSMUSG00000056370	Sftpb	AI562151|SF-B|SP-B|Sftp-3|Sftp3	surfactant associated protein B	protein-coding
mm_155882.1	chrX	101522274	101522304	+	1	NA	Intergenic	RLTR34D_MM|LTR|ERVK	-10446	NM_001290729	270627	Mm.261750	NM_001081008	ENSMUSG00000031314	Taf1	AU015687|B430306D02Rik|Ccg-1|Ccg1|KAT4|N-TAF1|TAFII250|Taf2a|p250	TATA-box binding protein associated factor 1	protein-coding
mm_132932.1	chr16	49855090	49855100	+	1	NA	promoter-TSS (NM_010581)	promoter-TSS (NM_010581)	-559	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_150522.1	chr19	39037038	39037038	+	1	NA	intron (NM_028089, intron 7 of 8)	intron (NM_028089, intron 7 of 8)	-23968	NM_028191	72303	Mm.482578	NM_028191	ENSMUSG00000067231	Cyp2c65	2210009K14Rik	cytochrome P450, family 2, subfamily c, polypeptide 65	protein-coding
mm_111316.1	chr12	85824846	85824889	-	1	NA	promoter-TSS (NM_001081423)	promoter-TSS (NM_001081423)	-83	NM_001347395	320244	Mm.132172	NM_177114	ENSMUSG00000012609	Ttll5	1700048H13Rik|2310009M18Rik|4930556H18Rik|AI428864|D630041K24Rik|R75373|Stamp|mKIAA0998	tubulin tyrosine ligase-like family, member 5	protein-coding
mm_7513.1	chr1	124025445	124025488	-	1	NA	intron (NM_199021, intron 1 of 25)	(TG)n|Simple_repeat|Simple_repeat	20093	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_70171.1	chr7	143628344	143628361	-	1	NA	promoter-TSS (NM_175649)	promoter-TSS (NM_175649)	-507	NM_175649	244237	Mm.247498	NM_175649	ENSMUSG00000045362	Tnfrsf26	Tnfrh3|Tnfrsf24	tumor necrosis factor receptor superfamily, member 26	protein-coding
mm_112377.1	chr12	119231992	119232000	-	1	NA	intron (NM_177290, intron 1 of 13)	intron (NM_177290, intron 1 of 13)	6280	NM_177290	320910	Mm.217000	NM_177290	ENSMUSG00000025321	Itgb8	4832412O06Rik	integrin beta 8	protein-coding
mm_3042.1	chr1	134040340	134040360	+	1	NA	exon (NM_021355, exon 2 of 3)	exon (NM_021355, exon 2 of 3)	2835	NM_021355	14264	Mm.287146	NM_021355	ENSMUSG00000041559	Fmod	AI131919|AU041740|SLRR2E	fibromodulin	protein-coding
mm_4973.1	chr1	191317874	191317878	+	1	NA	intron (NM_025424, intron 1 of 3)	CpG	242	NM_025424	66208	Mm.46444	NM_025424	ENSMUSG00000037499	Nenf	1110060M21Rik|SCIRP10|Spuf	neuron derived neurotrophic factor	protein-coding
mm_60066.1	chr7	31263615	31263645	+	1	NA	promoter-TSS (NM_001310660)	promoter-TSS (NM_001310660)	-106	NM_001310660	100043827		NM_001310660		Scgb2b1	Abpbg1|Gm4677	secretoglobin, family 2B, member 1	protein-coding
mm_42530.1	chr5	115632037	115632054	+	1	NA	promoter-TSS (NR_027810)	promoter-TSS (NR_027810)	58	NM_198163	77407	Mm.27553	NM_198163	ENSMUSG00000029518	Rab35	9530019H02Rik|AU040256|H-ray|RAB1C|RAY	RAB35, member RAS oncogene family	protein-coding
mm_12116.1	chr2	61595482	61595511	+	1	NA	intron (NM_001164071, intron 2 of 8)	B1_Mur1|SINE|Alu	2399	NM_001164071	21353	Mm.244393	NM_011529	ENSMUSG00000064289	Tank	C86182|E430026L09Rik|I-TRAF	TRAF family member-associated Nf-kappa B activator	protein-coding
mm_101636.1	chr11	36432860	36432875	-	1	NA	intron (NM_011856, intron 2 of 28)	intron (NM_011856, intron 2 of 28)	-452778	NM_170779	211652	Mm.31267	NM_170779	ENSMUSG00000018849	Wwc1	AA408228|AU017197|BC037006|Kibra|mKIAA0869	WW, C2 and coiled-coil domain containing 1	protein-coding
mm_29333.1	chr3	108134689	108134692	-	1	NA	intron (NM_010306, intron 1 of 8)	intron (NM_010306, intron 1 of 8)	11462	NM_010306	14679	Mm.271703	NM_010306	ENSMUSG00000000001	Gnai3	AI158965|AW537698|Galphai3|Gnai-3	guanine nucleotide binding protein (G protein), alpha inhibiting 3	protein-coding
mm_132126.1	chr16	31754699	31754742	+	1	NA	5' UTR (NM_001252436, exon 1 of 23)	5' UTR (NM_001252436, exon 1 of 23)	370	NM_001252436	13383	Mm.382	NM_007862	ENSMUSG00000022770	Dlg1	B130052P05Rik|Dlgh1|E-dlg/SAP97|SAP-97|SAP97|mKIAA4187	discs, large homolog 1 (Drosophila)	protein-coding
mm_114150.1	chr13	55369782	55369813	+	1	NA	promoter-TSS (NM_016758)	promoter-TSS (NM_016758)	65	NM_016758	51791	Mm.1426	NM_016758	ENSMUSG00000052087	Rgs14	RPIP1	regulator of G-protein signaling 14	protein-coding
mm_63264.1	chr7	126759599	126759608	+	1	NA	promoter-TSS (NM_011952)	promoter-TSS (NM_011952)	-23	NM_011952	26417	Mm.8385	NM_011952	ENSMUSG00000063065	Mapk3	Erk-1|Erk1|Ert2|Esrk1|Mnk1|Mtap2k|Prkm3|p44|p44erk1|p44mapk	mitogen-activated protein kinase 3	protein-coding
mm_108244.1	chr12	78226371	78226414	+	1	NA	promoter-TSS (NM_172952)	promoter-TSS (NM_172952)	-263	NM_172952	268566	Mm.341742	NM_145965	ENSMUSG00000047454	Gphn	5730552E08Rik|AI662856|BC027112|C230040D23|GPH|GPHRYN|geph	gephyrin	protein-coding
mm_123497.1	chr14	66199911	66199929	-	1	NA	intron (NM_001162366, intron 1 of 29)	intron (NM_001162366, intron 1 of 29)	13632	NM_001162366	19229	Mm.21613	NM_172498	ENSMUSG00000059456	Ptk2b	CADTK|CAKB|CAKbeta|E430023O05Rik|FADK2|FAK2|PYK2|Raftk	PTK2 protein tyrosine kinase 2 beta	protein-coding
mm_72149.1	chr8	72144591	72144636	+	1	NA	intron (NM_001001491, intron 3 of 7)	intron (NM_001001491, intron 3 of 7)	9321	NM_001001491	326618	Mm.295124	NM_001001491	ENSMUSG00000031799	Tpm4	2610528G24Rik|Tpm4.2|Tpm4.2cy	tropomyosin 4	protein-coding
mm_94792.1	chr11	22860836	22860838	+	1	NA	promoter-TSS (NM_001169114)	promoter-TSS (NM_001169114)	-501	NM_001169114	53625	Mm.395495	NM_016888	ENSMUSG00000051650	B3gnt2	AA408337|AA409404|AW260308|B3Galt6|B3gnt1|BGnT-1|BGnT-2|BGnT1|BGnT2|Beta3gnt	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 2	protein-coding
mm_131934.1	chr16	23612950	23612978	+	1	NA	exon (NM_023386, exon 2 of 2)	exon (NM_023386, exon 2 of 2)	3045	NM_023386	67775	Mm.475107	NM_023386	ENSMUSG00000033355	Rtp4	5830458K16Rik|Ifrg28	receptor transporter protein 4	protein-coding
mm_106774.1	chr12	4601976	4601978	+	1	NA	intron (NM_011365, intron 1 of 38)	B1_Mur4|SINE|Alu	8969	NM_001198968	20403	Mm.341204	NM_011365	ENSMUSG00000020640	Itsn2	AI327390|Ese2|Sh3d1B|Sh3p18|mKIAA1256	intersectin 2	protein-coding
mm_23932.1	chr3	83845004	83845031	+	1	NA	Intergenic	Intergenic	-3409	NM_011905	24088	Mm.87596	NM_011905	ENSMUSG00000027995	Tlr2	Ly105	toll-like receptor 2	protein-coding
mm_169243.1	chr13	74768109	74768112	-	1	NA	intron (NM_001301153, intron 3 of 31)	(CCA)n|Simple_repeat|Simple_repeat	2626	NM_001301156	12380	Mm.29163	NM_009817	ENSMUSG00000021585	Cast	-	calpastatin	protein-coding
mm_5148.1	chr1	9748377	9748451	-	1	NA	promoter-TSS (NM_173443)	promoter-TSS (NM_173443)	-32	NM_173443	70675	Mm.274493	NM_173443	ENSMUSG00000045210	Vcpip1	4932442A08|5730421J18Rik|5730538E15Rik|VCIP135|mKIAA1850	valosin containing protein (p97)/p47 complex interacting protein 1	protein-coding
mm_63913.1	chr7	139224977	139224985	+	1	NA	intron (NM_001143755, intron 6 of 8)	intron (NM_001143755, intron 6 of 8)	-11674	NM_001162540	57740	Mm.65336	NM_021302	ENSMUSG00000015981	Stk32c	PKE|Pkek|YANK3	serine/threonine kinase 32C	protein-coding
mm_61913.1	chr7	90146787	90146804	+	1	NA	intron (NM_001252520, intron 1 of 20)	intron (NM_001252520, intron 1 of 20)	16563	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_52718.1	chr6	119690193	119690200	+	1	NA	intron (NR_104484, intron 16 of 20)	intron (NR_104484, intron 16 of 20)	-145849	NM_009525	22419	Mm.321818	NM_009525	ENSMUSG00000030170	Wnt5b	AW545702|Wnt-5b	wingless-type MMTV integration site family, member 5B	protein-coding
mm_172208.1	chr6	58567812	58567826	-	1	NA	Intergenic	Lx6|LINE|L1	-28853	NM_011920	26357	Mm.333096	NM_011920	ENSMUSG00000029802	Abcg2	ABC15|ABCP|AI428558|BCRP|Bcrp1|MXR|MXR1	ATP-binding cassette, sub-family G (WHITE), member 2	protein-coding
mm_154603.1	chrX	7638675	7638697	+	1	NA	5' UTR (NM_009305, exon 1 of 7)	5' UTR (NM_009305, exon 1 of 7)	106	NM_009305	20977	Mm.223674	NM_009305	ENSMUSG00000031144	Syp	A230093K24Rik|AI848995|Syn|p38	synaptophysin	protein-coding
mm_45046.1	chr5	41707671	41707681	-	1	NA	promoter-TSS (NM_001310592)	promoter-TSS (NM_001310592)	15	NM_001310592	100972	Mm.41555	NM_027295	ENSMUSG00000029128	Rab28	2700023P08Rik|AW496496	RAB28, member RAS oncogene family	protein-coding
mm_77462.1	chr8	122140562	122140585	-	1	NA	Intergenic	Intergenic	-141568	NM_009569	22761	Mm.3105	NM_009569	ENSMUSG00000049577	Zfpm1	FOG|Fog1	zinc finger protein, multitype 1	protein-coding
mm_75207.1	chr8	39605276	39605280	-	1	NA	3' UTR (NM_031195, exon 9 of 9)	3' UTR (NM_031195, exon 9 of 9)	37400	NM_031195	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_3300.1	chr1	136696403	136696414	+	1	NA	intron (NR_037986, intron 1 of 4)	intron (NR_037986, intron 1 of 4)	197	NR_037986	100503474	Mm.428276	NR_037986		Platr22	Gm16880	pluripotency associated transcript 22	ncRNA
mm_49497.1	chr6	29736126	29736149	+	1	NA	exon (NM_176996, exon 1 of 12)	exon (NM_176996, exon 1 of 12)	640	NM_176996	319757	Mm.29279	NM_176996	ENSMUSG00000001761	Smo	E130215L21Rik|Smoh|bnb|smoothened	smoothened, frizzled class receptor	protein-coding
mm_163866.1	chr14	19418970	19419011	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	183597	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_50276.1	chr6	46041062	46041064	+	1	NA	intron (NM_001004357, intron 8 of 23)	intron (NM_001004357, intron 8 of 23)	981002	NM_001004357	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding
mm_140869.1	chr17	23786047	23786083	-	1	NA	promoter-TSS (NM_029798)	promoter-TSS (NM_029798)	12	NM_029798	76917	Mm.269613	NM_029798	ENSMUSG00000023911	Flywch2	2810417J12Rik|3010014L17Rik|AW548203	FLYWCH family member 2	protein-coding
mm_141429.1	chr17	29465484	29465493	-	1	NA	Intergenic	Intergenic	-25557	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_42814.1	chr5	121837284	121837294	+	1	NA	promoter-TSS (NM_001306128)	promoter-TSS (NM_001306128)	-430	NM_008507	16923	Mm.65493	NM_008507	ENSMUSG00000042594	Sh2b3	AI429800|Lnk	SH2B adaptor protein 3	protein-coding
mm_142963.1	chr17	56121011	56121028	-	1	NA	intron (NM_029796, intron 1 of 1)	intron (NM_029796, intron 1 of 1)	927	NM_029796	76905	Mm.348025	NM_029796	ENSMUSG00000037095	Lrg1	1300008B03Rik|2310031E04Rik|Lrg|Lrhg	leucine-rich alpha-2-glycoprotein 1	protein-coding
mm_164332.1	chr16	10284336	10284356	-	1	NA	3' UTR (NM_007929, exon 5 of 5)	3' UTR (NM_007929, exon 5 of 5)	29622	NM_007929	13731	Mm.246009	NM_007929	ENSMUSG00000022505	Emp2	XMP	epithelial membrane protein 2	protein-coding
mm_128948.1	chr15	74752022	74752041	-	1	NA	5' UTR (NM_011838, exon 2 of 4)	5' UTR (NM_011838, exon 2 of 4)	948	NM_011838	23936	Mm.257067	NM_011838	ENSMUSG00000022594	Lynx1	AI838844|SLURP-2	Ly6/neurotoxin 1	protein-coding
mm_139756.1	chr17	64269857	64269872	+	1	NA	Intergenic	Intergenic	62019	NM_144859	224938	Mm.489681	NM_144859	ENSMUSG00000024083	Pja2	AI447901|AL022700|Neurodap1|mKIAA0438	praja 2, RING-H2 motif containing	protein-coding
mm_66458.1	chr7	44885854	44885866	-	1	NA	exon (NM_001331208, exon 4 of 16)	exon (NM_001331208, exon 4 of 16)	6564	NM_001331208	75613	Mm.157778	NM_029365	ENSMUSG00000002968	Med25	2610034E13Rik|2610529E18Rik|ESTM2	mediator complex subunit 25	protein-coding
mm_6465.1	chr1	74030898	74030907	-	1	NA	intron (NM_027884, intron 3 of 34)	L2c|LINE|L2	93545	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_59269.1	chr7	24899186	24899200	+	1	NA	exon (NM_007655, exon 2 of 5)	exon (NM_007655, exon 2 of 5)	1682	NM_007655	12518	Mm.1355	NM_007655	ENSMUSG00000003379	Cd79a	Ig-alpha|Iga|Igalpha|Ly-54|Ly54|mb-1	CD79A antigen (immunoglobulin-associated alpha)	protein-coding
mm_72875.1	chr8	88697039	88697077	+	1	NA	promoter-TSS (NM_001128171)	promoter-TSS (NM_001128171)	30	NM_001128171	74256	Mm.490395	NM_173369	ENSMUSG00000036712	Cyld	2010013M14Rik|2900009M21Rik|C130039D01Rik|CDMT|CYLD1|EAC|mKIAA0849	CYLD lysine 63 deubiquitinase	protein-coding
mm_119716.1	chr14	53881533	53881545	+	1	NA	Intergenic	Intergenic	372390	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_48985.1	chr6	4755599	4755607	+	1	NA	exon (NM_130877, exon 2 of 2)	exon (NM_130877, exon 2 of 2)	8297	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_45597.1	chr5	74879735	74879735	-	1	NA	Intergenic	Intergenic	-69459	NR_045866	619945	Mm.359372	NM_001037908	ENSMUSG00000072874	Gm6116	EG619945	predicted gene 6116	ncRNA
mm_72641.1	chr8	84701772	84701798	+	1	NA	5' UTR (NM_008535, exon 1 of 4)	5' UTR (NM_008535, exon 1 of 4)	328	NM_008535	17095	Mm.4925	NM_008535	ENSMUSG00000034041	Lyl1	Lyl-1|bHLHa18	lymphoblastomic leukemia 1	protein-coding
mm_131515.1	chr16	17509216	17509240	+	1	NA	promoter-TSS (NM_001331226)	promoter-TSS (NM_001331226)	16	NM_001331226	66863	Mm.161726	NM_025808	ENSMUSG00000022761	Lztr1	1200003E21Rik|AI591627|AW550890	leucine-zipper-like transcriptional regulator, 1	protein-coding
mm_99392.1	chr11	102145468	102145470	+	1	NA	promoter-TSS (NM_145829)	promoter-TSS (NM_145829)	-44	NM_145829	217214	Mm.31686	NM_145829	ENSMUSG00000048217	Nags	1700120E20Rik|argA	N-acetylglutamate synthase	protein-coding
mm_156810.1	chrX	163958240	163958312	+	1	NA	exon (NM_009453, exon 1 of 11)	exon (NM_009453, exon 1 of 11)	390	NM_009453	22184	Mm.426178	NM_009453	ENSMUSG00000031370	Zrsr2	35kDa|5031411E02Rik|A230052C13Rik|C77286|U2af1-rs2|URP	zinc finger (CCCH type), RNA binding motif and serine/arginine rich 2	protein-coding
mm_120777.1	chr14	74640898	74640935	+	1	NA	promoter-TSS (NM_172812)	promoter-TSS (NM_172812)	76	NM_172812	15558	Mm.214351	NM_172812	ENSMUSG00000034997	Htr2a	E030013E04|Htr-2|Htr2	5-hydroxytryptamine (serotonin) receptor 2A	protein-coding
mm_94901.1	chr11	29179436	29179443	+	1	NA	intron (NM_134034, intron 2 of 15)	U1|snRNA|snRNA	6532	NM_134034	104570	Mm.276386	NM_134034	ENSMUSG00000020463	Smek2	AW011752|AW557776|Ppp4r3b|mKIAA1387	SMEK homolog 2, suppressor of mek1 (Dictyostelium)	protein-coding
mm_48698.1	chr5	146897092	146897101	-	1	NA	Intergenic	Intergenic	-51561	NM_025652	66596	Mm.196528	NM_025652	ENSMUSG00000016503	Gtf3a	2010015D03Rik|2610111I01Rik|5330403M05Rik	general transcription factor III A	protein-coding
mm_167964.1	chrX	151200010	151200015	+	1	NA	intron (NM_001271678, intron 1 of 21)	ID_B1|SINE|B4	1934	NM_001271678	279561	Mm.441474	NM_001271678	ENSMUSG00000041245	Wnk3	Prkwnk3|Wnk3-ps	WNK lysine deficient protein kinase 3	protein-coding
mm_9599.1	chr1	175492485	175492538	-	1	NA	promoter-TSS (NM_011880)	promoter-TSS (NM_011880)	34	NM_011880	24012	Mm.7956	NM_011880	ENSMUSG00000026527	Rgs7	-	regulator of G protein signaling 7	protein-coding
mm_98965.1	chr11	98664392	98664400	+	1	NA	promoter-TSS (NM_021347)	promoter-TSS (NM_021347)	45	NM_021347	57911	Mm.458085	NM_021347	ENSMUSG00000017204	Gsdma	BB149167|Gsdm|Gsdm1|Gsdma1|H312E	gasdermin A	protein-coding
mm_121550.1	chr14	122475398	122475412	+	1	NA	promoter-TSS (NR_045046)	promoter-TSS (NR_045046)	21	NM_009574	22772	Mm.308936	NM_009574	ENSMUSG00000061524	Zic2	HPE5|Ku	zinc finger protein of the cerebellum 2	protein-coding
mm_171021.1	chr2	83989751	83989768	+	1	NA	Intergenic	CpG	-48533	NM_027964	71861	Mm.116957	NM_027964	ENSMUSG00000034552	Zswim2	1700025P14Rik|4933437F18Rik|MEX	zinc finger SWIM-type containing 2	protein-coding
mm_48332.1	chr5	139024588	139024608	-	1	NA	intron (NM_008923, intron 9 of 10)	intron (NM_008923, intron 9 of 10)	-29645	NM_008808	18590	Mm.2675	NM_008808	ENSMUSG00000025856	Pdgfa	-	platelet derived growth factor, alpha	protein-coding
mm_154962.1	chrX	36883126	36883136	+	1	NA	exon (NM_001313696, exon 6 of 6)	exon (NM_001313696, exon 6 of 6)	8836	NM_019668	22209	Mm.395649	NM_019668	ENSMUSG00000016308	Ube2a	HHR6A|HR6A|Mhr6a	ubiquitin-conjugating enzyme E2A	protein-coding
mm_61978.1	chr7	90887339	90887359	+	1	NA	Intergenic	Intergenic	-203437	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_169799.1	chr16	16820163	16820164	-	1	NA	promoter-TSS (NM_001258458)	promoter-TSS (NM_001258458)	33	NM_001258458	665562	Mm.444358	NM_001258458		Rpl31-ps12	EG665562|Gm7689	ribosomal protein L31, pseudogene 1 2	protein-coding
mm_85147.1	chr9	95857865	95857876	-	1	NA	promoter-TSS (NM_001271569)	promoter-TSS (NM_001271569)	12	NM_001271569	73410	Mm.443314	NM_028533	ENSMUSG00000096655	1700065D16Rik	-	RIKEN cDNA 1700065D16 gene	protein-coding
mm_72128.1	chr8	71780593	71780601	+	1	NA	Intergenic	RLTR4_Mm|LTR|ERV1	-54916	NM_028715	74015	Mm.22025	NM_028715	ENSMUSG00000070000	Fcho1	3322402E17Rik|N28152	FCH domain only 1	protein-coding
mm_86588.1	chr10	13108819	13108822	+	1	NA	intron (NM_009538, intron 2 of 5)	intron (NM_009538, intron 2 of 5)	17975	NR_131912	338438		NR_131912		Hymai	-	hydatidiform mole associated and imprinted transcript	ncRNA
mm_122910.1	chr14	54956528	54956626	-	1	NA	exon (NM_010856, exon 20 of 39)	exon (NM_010856, exon 20 of 39)	-7435	NR_029724	387204		NR_029724	ENSMUSG00000065432	Mir208a	Mirn208|Mirn208a|mir-208|mir-208a|mmu-mir-208	microRNA 208a	ncRNA
mm_71095.1	chr8	34821561	34821582	+	1	NA	Intergenic	Intergenic	13961	NM_176933	319520	Mm.170276	NM_176933	ENSMUSG00000031530	Dusp4	2700078F24Rik|AI844617|BB104621|E130306H24Rik|MKP2	dual specificity phosphatase 4	protein-coding
mm_20305.1	chr2	127143411	127143479	-	1	NA	promoter-TSS (NM_001163528)	promoter-TSS (NM_001163528)	12	NM_001163527	73338	Mm.57559	NM_001163527	ENSMUSG00000074825	Itpripl1	1700041B20Rik	inositol 1,4,5-triphosphate receptor interacting protein-like 1	protein-coding
mm_8097.1	chr1	135848014	135848020	-	1	NA	exon (NM_001130176, exon 7 of 13)	exon (NM_001130176, exon 7 of 13)	7156	NM_001130176	21956	Mm.247470	NM_011619	ENSMUSG00000026414	Tnnt2	Tnt|cTnT	troponin T2, cardiac	protein-coding
mm_63163.1	chr7	123982800	123982863	+	1	NA	promoter-TSS (NM_001252072)	promoter-TSS (NM_001252072)	-350	NM_001252072	628779	Mm.40210	NM_001252072	ENSMUSG00000078591	Hs3st4	EG628779|Gm6915	heparan sulfate (glucosamine) 3-O-sulfotransferase 4	protein-coding
mm_93690.1	chr10	117818577	117818593	-	1	NA	exon (NM_024457, exon 6 of 8)	exon (NM_024457, exon 6 of 8)	-25880	NM_134010	103468	Mm.12568	NM_134010	ENSMUSG00000052798	Nup107	AW541137|C76801	nucleoporin 107	protein-coding
mm_63584.1	chr7	128126793	128126796	+	1	NA	Intergenic	Intergenic	-2774	NM_021334	16411	Mm.22378	NM_021334	ENSMUSG00000030789	Itgax	AI449405|Cd11c|Cr4|N418	integrin alpha X	protein-coding
mm_33345.1	chr4	129312575	129312578	+	1	NA	intron (NM_009030, intron 11 of 11)	B1F1|SINE|Alu	22794	NM_009030	19646	Mm.12145	NM_009030	ENSMUSG00000057236	Rbbp4	RBAP48|mRbAp48	retinoblastoma binding protein 4	protein-coding
mm_172892.1	chr9	56160985	56160994	-	1	NA	promoter-TSS (NM_019793)	promoter-TSS (NM_019793)	81	NM_019793	56434	Mm.28484	NM_019793	ENSMUSG00000032324	Tspan3	1700055K04Rik|TM4-A|Tm4sf8	tetraspanin 3	protein-coding
mm_169737.1	chr15	83536758	83536761	-	1	NA	intron (NM_007546, intron 1 of 4)	RLTR13E|LTR|ERVK	9897	NM_007546	12124	Mm.267006	NM_007546	ENSMUSG00000016758	Bik	Biklk|Blk|Nbk	BCL2-interacting killer	protein-coding
mm_61058.1	chr7	49912056	49912073	+	1	NA	exon (NM_001146013, exon 2 of 16)	exon (NM_001146013, exon 2 of 16)	364	NM_148931	104245	Mm.207053	NM_148931	ENSMUSG00000039728	Slc6a5	Glyt2|prestin	solute carrier family 6 (neurotransmitter transporter, glycine), member 5	protein-coding
mm_115301.1	chr13	112100917	112100944	+	1	NA	Intergenic	Intergenic	-187521	NM_001168403	77318	Mm.159895	NM_029898	ENSMUSG00000049985	Ankrd55	C030011J08Rik	ankyrin repeat domain 55	protein-coding
mm_104083.1	chr11	86602254	86602303	-	1	NA	intron (NM_029478, intron 9 of 11)	intron (NM_029478, intron 9 of 11)	-18120	NR_029738	387140		NR_029738	ENSMUSG00000065455	Mir21a	Mir21|Mirn21|mmu-mir-21|mmu-mir-21a	microRNA 21a	ncRNA
mm_84968.1	chr9	84114481	84114508	-	1	NA	intron (NM_001305935, intron 9 of 10)	intron (NM_001305935, intron 9 of 10)	165713	NM_199195	12040	Mm.12819	NM_199195	ENSMUSG00000032263	Bckdhb	BCKDE1B|BCKDH E1-beta	branched chain ketoacid dehydrogenase E1, beta polypeptide	protein-coding
mm_74100.1	chr8	122709431	122709436	+	1	NA	Intergenic	Intergenic	-10324	NM_009824	12398	Mm.194339	NM_009824	ENSMUSG00000006362	Cbfa2t3	A630044F12Rik|AI465270|AW229127|Cbfa2t3h|ETO-2|Eto2|MTGR2	core-binding factor, runt domain, alpha subunit 2, translocated to, 3 (human)	protein-coding
mm_33341.1	chr4	129287674	129287685	+	1	NA	promoter-TSS (NM_023485)	promoter-TSS (NM_023485)	58	NM_023485	68828	Mm.132243	NM_023485	ENSMUSG00000001333	Sync	1110057H03Rik|SNIP4	syncoilin	protein-coding
mm_83032.1	chr9	37255531	37255553	-	1	NA	5' UTR (NM_001145960, exon 1 of 19)	5' UTR (NM_001145960, exon 1 of 19)	196	NM_020258	56857	Mm.440037	NM_020258	ENSMUSG00000032122	Slc37a2	G3PP|Slc37a1|cI-2|ci2	solute carrier family 37 (glycerol-3-phosphate transporter), member 2	protein-coding
mm_108435.1	chr12	82339464	82339488	+	1	NA	intron (NM_172579, intron 1 of 20)	intron (NM_172579, intron 1 of 20)	28127	NM_172579	217692	Mm.261333	NM_172579	ENSMUSG00000042700	Sipa1l1	4931426N11Rik|AW213287|Spar|mKIAA0440	signal-induced proliferation-associated 1 like 1	protein-coding
mm_141654.1	chr17	33702298	33702302	-	1	NA	intron (NR_045522, intron 3 of 6)	intron (NR_045522, intron 3 of 6)	16377	NM_145486	224703	Mm.311439	NM_145486	ENSMUSG00000079557	March2	9530046H09Rik|MARCH-II	membrane-associated ring finger (C3HC4) 2	protein-coding
mm_92842.1	chr10	81508151	81508189	-	1	NA	intron (NM_010304, intron 5 of 6)	intron (NM_010304, intron 5 of 6)	-8033	NM_010102	13611	Mm.33065	NM_010102	ENSMUSG00000044199	S1pr4	Edg6|Lpc1|S1p4	sphingosine-1-phosphate receptor 4	protein-coding
mm_94680.1	chr11	17953985	17954031	+	1	NA	promoter-TSS (NM_026576)	promoter-TSS (NM_026576)	38	NR_131915	102633673	Mm.396603	NR_131915	ENSMUSG00000086468	Etaa1os	2900053O20Rik|4930542E09Rik	Ewing tumor-associated antigen 1, opposite strand	ncRNA
mm_7309.1	chr1	98047729	98047792	-	1	NA	promoter-TSS (NR_037993)	promoter-TSS (NR_037993)	33	NR_037993	78603	Mm.442597	NR_037993	ENSMUSG00000089706	B230216N24Rik	-	RIKEN cDNA B230216N24 gene	ncRNA
mm_19875.1	chr2	114048246	114048304	-	1	NA	exon (NM_009608, exon 6 of 7)	exon (NM_009608, exon 6 of 7)	4600	NM_009608	11464	Mm.686	NM_009608	ENSMUSG00000068614	Actc1	Actc-1	actin, alpha, cardiac muscle 1	protein-coding
mm_47785.1	chr5	132069310	132069311	-	1	NA	intron (NM_177047, intron 2 of 18)	intron (NM_177047, intron 2 of 18)	189041	NR_040704	75369	Mm.389696	NR_040704	ENSMUSG00000105773	4930563F08Rik	-	RIKEN cDNA 4930563F08 gene	ncRNA
mm_29172.1	chr3	106514082	106514087	-	1	NA	intron (NM_133869, intron 4 of 8)	intron (NM_133869, intron 4 of 8)	28044	NM_028110	72121	Mm.14816	NM_028110	ENSMUSG00000027901	Dennd2d	2010308M01Rik|AI451421	DENN/MADD domain containing 2D	protein-coding
mm_72853.1	chr8	88329658	88329671	+	1	NA	3' UTR (NM_001037724, exon 28 of 28)	3' UTR (NM_001037724, exon 28 of 28)	32527	NM_012047	26992	Mm.5400	NM_012047	ENSMUSG00000031660	Brd7	BP75|CELTIX1|Ptpn13ip	bromodomain containing 7	protein-coding
mm_167056.1	chr7	89538514	89538514	+	1	NA	Intergenic	RMER19B2|LTR|ERVK	-20928	NM_029614	76453	Mm.250438	NM_029614	ENSMUSG00000039405	Prss23	2310046G15Rik|4930479H08Rik|AI790574|Spuve	protease, serine 23	protein-coding
mm_97049.1	chr11	72438652	72438689	+	1	NA	TTS (NM_027819)	TTS (NM_027819)	-2708	NM_016776	18432	Mm.147946	NM_016776	ENSMUSG00000040463	Mybbp1a	AL024407|AU019902|P160|p160MBP|p67MBP	MYB binding protein (P160) 1a	protein-coding
mm_64026.1	chr7	140769092	140769102	+	1	NA	exon (NM_021282, exon 3 of 9)	exon (NM_021282, exon 3 of 9)	5265	NM_021282	13106	Mm.21758	NM_021282	ENSMUSG00000025479	Cyp2e1	Cyp2e	cytochrome P450, family 2, subfamily e, polypeptide 1	protein-coding
mm_3503.1	chr1	150107027	150107037	+	1	NA	3' UTR (NM_011198, exon 10 of 10)	3' UTR (NM_011198, exon 10 of 10)	7001	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_30254.1	chr3	146615627	146615631	-	1	NA	promoter-TSS (NM_019957)	promoter-TSS (NM_019957)	-31	NM_019957	56629	Mm.25853	NM_019957	ENSMUSG00000028185	Dnase2b	AI526873|Dlad|DnaseIIb	deoxyribonuclease II beta	protein-coding
mm_61958.1	chr7	90211714	90211725	+	1	NA	Intergenic	T-rich|Low_complexity|Low_complexity	53713	NM_029256	75338	Mm.487222	NM_029256	ENSMUSG00000030617	Ccdc83	4930549K11Rik|4930554C01Rik|4932423M01Rik	coiled-coil domain containing 83	protein-coding
mm_61202.1	chr7	64001899	64001924	+	1	NA	Intergenic	Intergenic	-62996	NM_021366	50794	Mm.240473	NM_021366	ENSMUSG00000052040	Klf13	0610043C13Rik|9430029L20Rik|Bteb3|FKLF-2|FKLF2|NSLP1|RFLAT-1|RFLAT1	Kruppel-like factor 13	protein-coding
mm_105678.1	chr11	107574523	107574523	-	1	NA	intron (NM_198298, intron 2 of 31)	intron (NM_198298, intron 2 of 31)	26563	NM_198298	78455	Mm.272047	NM_198298	ENSMUSG00000020721	Helz	3110078M01Rik|9430093I07Rik|9630002H22Rik|AI851979|DRHC	helicase with zinc finger domain	protein-coding
mm_34903.1	chr4	155638579	155638591	+	1	NA	exon (NM_007661, exon 7 of 20)	exon (NM_007661, exon 7 of 20)	13716	NM_007661	12537	Mm.267410	NM_007661	ENSMUSG00000029062	Cdk11b	AA989746|CDK11-p110|CDK11-p46|CDK11-p58|Cdc11b|Cdc2l1|Cdc2l2|Cdk11|p58	cyclin-dependent kinase 11B	protein-coding
mm_77908.1	chr9	7349238	7349249	+	1	NA	intron (NM_001320077, intron 3 of 10)	RLTR17B_Mm|LTR|ERVK	1869	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_153186.1	chr19	34500142	34500172	-	1	NA	exon (NM_021460, exon 8 of 10)	exon (NM_021460, exon 8 of 10)	-25022	NM_009890	12642	Mm.30824	NM_009890	ENSMUSG00000050370	Ch25h	AI462618|m25OH	cholesterol 25-hydroxylase	protein-coding
mm_73247.1	chr8	104264469	104264476	+	1	NA	3' UTR (NM_001037841, exon 3 of 3)	3' UTR (NM_001037841, exon 3 of 3)	13611	NM_001286383	75458	Mm.269219	NM_029295	ENSMUSG00000054400	Cklf	1700001C14Rik|1810018M11Rik|A730028G07Rik|C32|CKLF1|CKLF3|CKLF4|CKLF5|Cklf2|Cklf6|HSPC224|UCK-1	chemokine-like factor	protein-coding
mm_51528.1	chr6	83186189	83186201	+	1	NA	5' UTR (NM_001347310, exon 1 of 27)	5' UTR (NM_001347310, exon 1 of 27)	249	NM_001347310	13191	Mm.6919	NM_007835	ENSMUSG00000031865	Dctn1	AL022633|DAP-150|DP-150|Glued|p150|p150-glued|p150<glued>	dynactin 1	protein-coding
mm_56221.1	chr6	89595548	89595645	-	1	NA	promoter-TSS (NM_001167736)	promoter-TSS (NM_001167736)	56	NM_025351	66098	Mm.20313	NM_025351	ENSMUSG00000030086	Chchd6	0710001P09Rik|1700021B03Rik	coiled-coil-helix-coiled-coil-helix domain containing 6	protein-coding
mm_76246.1	chr8	83593360	83593363	-	1	NA	intron (NM_134118, intron 1 of 12)	intron (NM_134118, intron 1 of 12)	1130	NM_027179	106529	Mm.352239	NM_027179	ENSMUSG00000031708	Tecr	2410016D23Rik|A230102P12Rik|AI173355|D17Ertd178e|Gpsn2|SC2	trans-2,3-enoyl-CoA reductase	protein-coding
mm_64626.1	chr7	3677532	3677553	-	1	NA	promoter-TSS (NM_181820)	promoter-TSS (NM_181820)	11	NM_181820	353499	Mm.360398	NM_181820	ENSMUSG00000019734	Tmc4	-	transmembrane channel-like gene family 4	protein-coding
mm_150408.1	chr19	36890792	36890814	+	1	NA	exon (NM_001163635, exon 27 of 27)	exon (NM_001163635, exon 27 of 27)	28796	NM_028263	72514	Mm.41674	NM_028263	ENSMUSG00000047632	Fgfbp3	2610306H15Rik|Fgf-bp3	fibroblast growth factor binding protein 3	protein-coding
mm_119150.1	chr14	31495066	31495095	+	1	NA	promoter-TSS (NM_025907)	promoter-TSS (NM_025907)	1	NM_028932	74427	Mm.491208	NM_028932	ENSMUSG00000021890	Eaf1	4933403C17Rik|AI666536	ELL associated factor 1	protein-coding
mm_108926.1	chr12	100986628	100986632	+	1	NA	intron (NM_026681, intron 3 of 29)	intron (NM_026681, intron 3 of 29)	35138	NR_035421	100316805		NR_035421	ENSMUSG00000080575	Mir1190	Mirn1190|mmu-mir-1190	microRNA 1190	ncRNA
mm_129443.1	chr15	78529643	78529661	-	1	NA	promoter-TSS (NM_001204153)	promoter-TSS (NM_001204153)	-1	NM_028331	72709	Mm.34776	NM_028331	ENSMUSG00000022440	C1qtnf6	2810036M19Rik|CTRP6	C1q and tumor necrosis factor related protein 6	protein-coding
mm_89280.1	chr10	87864330	87864369	+	1	NA	intron (NM_001111274, intron 1 of 4)	intron (NM_001111274, intron 1 of 4)	3238	NM_001111276	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_162069.1	chrX	14211148	14211148	+	1	NA	promoter-TSS (NM_001034100)	promoter-TSS (NM_001034100)	0	NM_001034100	385328	Mm.275681	NM_001034100	ENSMUSG00000078346	H2al1n	EG385328|Gm5382	H2A histone family member L1N	protein-coding
mm_75357.1	chr8	45262013	45262057	-	1	NA	promoter-TSS (NM_028066)	promoter-TSS (NM_028066)	-4	NM_028066	109821	Mm.33326	NM_028066	ENSMUSG00000031645	F11	1600027G01Rik|AI503996|Cf11|FXI|PTA	coagulation factor XI	protein-coding
mm_130702.1	chr15	100687215	100687241	-	1	NA	intron (NM_033612, intron 1 of 7)	intron (NM_033612, intron 1 of 7)	692	NM_033612	109901	Mm.2131	NM_033612	ENSMUSG00000023031	Cela1	1810009A17Rik|1810062B19Rik|Ela-1|Ela1|PC-TsF	chymotrypsin-like elastase family, member 1	protein-coding
mm_137528.1	chr17	27529990	27529994	+	1	NA	Intergenic	Intergenic	-26459	NM_001291045	268934	Mm.358940	NM_001013385	ENSMUSG00000063239	Grm4	Gprc1d|mGluR4	glutamate receptor, metabotropic 4	protein-coding
mm_155315.1	chrX	61785742	61785774	+	1	NA	Intergenic	Intergenic	76142	NM_001018087	434784	Mm.23468	NM_001018087	ENSMUSG00000057615	Ldoc1	Gm366|Mar7|Mart7|Sirh7	leucine zipper, down-regulated in cancer 1	protein-coding
mm_46185.1	chr5	97392372	97392385	-	1	NA	promoter-TSS (NM_001033191)	promoter-TSS (NM_001033191)	-39	NR_045981	75814	Mm.444705	NR_045981		4930467D21Rik	4930448L09Rik|BB013444	RIKEN cDNA 4930467D21 gene	ncRNA
mm_2326.1	chr1	92704997	92705003	+	1	NA	Intergenic	MTA_Mm|LTR|ERVL-MaLR	-56159	NM_153114	260301	Mm.219545	NM_153114	ENSMUSG00000044055	Otos	OTOSP	otospiralin	protein-coding
mm_1067.1	chr1	59150932	59150959	+	1	NA	intron (NM_001164682, intron 5 of 22)	intron (NM_001164682, intron 5 of 22)	10691	NM_145143	227157	Mm.474049	NM_145143	ENSMUSG00000079550	Mpp4	Dlg6	membrane protein, palmitoylated 4 (MAGUK p55 subfamily member 4)	protein-coding
mm_76920.1	chr8	105933561	105933581	-	1	NA	intron (NM_023182, intron 1 of 6)	intron (NM_023182, intron 1 of 6)	291	NM_023182	109660	Mm.2745	NM_023182	ENSMUSG00000031896	Ctrl	0910001G08Rik|1810004D15Rik|AV005227|Ctra-1|Ctra1|chymopasin|mFLJ00366	chymotrypsin-like	protein-coding
mm_57752.1	chr6	129182834	129182844	-	1	NA	intron (NM_053109, intron 1 of 4)	intron (NM_053109, intron 1 of 4)	2224	NM_053109	93694	Mm.197536	NM_053109	ENSMUSG00000030157	Clec2d	Clr-b|Clrb|Ocil	C-type lectin domain family 2, member d	protein-coding
mm_149725.1	chr19	21784803	21784809	+	1	NA	intron (NM_031997, intron 2 of 24)	intron (NM_031997, intron 2 of 24)	6466	NM_031997	83921	Mm.329776	NM_031997	ENSMUSG00000024754	Tmem2	-	transmembrane protein 2	protein-coding
mm_140180.1	chr17	80943982	80944004	+	1	NA	promoter-TSS (NM_026516)	promoter-TSS (NM_026516)	-639	NM_026516	68027	Mm.357108	NM_026516	ENSMUSG00000024245	Tmem178	2810417M05Rik|Tmem178a	transmembrane protein 178	protein-coding
mm_9025.1	chr1	166409748	166409753	-	1	NA	promoter-TSS (NM_001142948)	promoter-TSS (NM_001142948)	78	NM_175170	71592	Mm.192094	NM_175170	ENSMUSG00000040596	Pogk	9130401E23Rik|BASS2|mKIAA1513	pogo transposable element with KRAB domain	protein-coding
mm_55286.1	chr6	54541719	54541722	-	1	NA	intron (NM_027268, intron 2 of 7)	intron (NM_027268, intron 2 of 7)	24662	NM_027268	69938	Mm.41557	NM_027268	ENSMUSG00000019124	Scrn1	2810019K23Rik|6330535A03Rik|AI852905|SES1|mKIAA0193	secernin 1	protein-coding
mm_62601.1	chr7	105736747	105736764	+	1	NA	promoter-TSS (NM_025897)	promoter-TSS (NM_025897)	30	NM_010562	16202	Mm.274846	NM_010562	ENSMUSG00000030890	Ilk	AA511515|ESTM24	integrin linked kinase	protein-coding
mm_87475.1	chr10	51492079	51492095	+	1	NA	exon (NM_013532, exon 4 of 9)	exon (NM_013532, exon 4 of 9)	1189	NM_013532	14728	Mm.34408	NM_013532	ENSMUSG00000062593	Lilrb4a	CD85K|Gp49b|HM18|ILT3|LIR-5|Lilrb4|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4A	protein-coding
mm_63085.1	chr7	122289311	122289347	+	1	NA	5' UTR (NM_008855, exon 1 of 17)	5' UTR (NM_008855, exon 1 of 17)	204	NM_008855	18751	Mm.207496	NM_008855	ENSMUSG00000052889	Prkcb	PKC-B|PKC-Beta|Pkcb|Prkcb1|Prkcb2	protein kinase C, beta	protein-coding
mm_87799.1	chr10	60300136	60300158	+	1	NA	intron (NM_001146120, intron 10 of 13)	intron (NM_001146120, intron 10 of 13)	15686	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_30224.1	chr3	145195817	145195817	-	1	NA	Intergenic	MIR|SINE|MIR	77217	NM_025714	52184	Mm.259105	NM_025714	ENSMUSG00000028256	Odf2l	4733401D09Rik|9630045K08Rik|D3Ertd250e	outer dense fiber of sperm tails 2-like	protein-coding
mm_117030.1	chr13	58274122	58274207	-	1	NA	promoter-TSS (NM_019832)	promoter-TSS (NM_019832)	24	NM_019832	56278	Mm.296625	NM_019832	ENSMUSG00000021552	Gkap1	42kDa|4933400B15Rik|D13Ertd340e|Gkap42	G kinase anchoring protein 1	protein-coding
mm_148006.1	chr18	67775221	67775252	-	1	NA	TTS (NR_045376)	TTS (NR_045376)	360	NM_001039088	72124	Mm.307315	NM_028112	ENSMUSG00000079614	Seh1l	2610007A16Rik|AW540070|SEC13L|SEH1A|SEH1B|Seh1	SEH1-like (S. cerevisiae	protein-coding
mm_28190.1	chr3	88139434	88139467	-	1	NA	Intergenic	Intergenic	-2922	NM_001310587	17261	Mm.28184	NM_133665	ENSMUSG00000001419	Mef2d	C80750	myocyte enhancer factor 2D	protein-coding
mm_109210.1	chr12	108677670	108677674	+	1	NA	intron (NM_001163394, intron 7 of 13)	RLTR21|LTR|ERVK	19052	NR_029771	723909		NR_029771	ENSMUSG00000065436	Mir342	Mirn342|mmu-mir-342	microRNA 342	ncRNA
mm_28972.1	chr3	101012679	101012687	-	1	NA	intron (NM_001167906, intron 5 of 8)	intron (NM_001167906, intron 5 of 8)	16812	NM_001167906	630146	Mm.190915	NM_001099332	ENSMUSG00000086564	Cd101	EWI-101|Gm1016|Gm734|Igsf2	CD101 antigen	protein-coding
mm_155207.1	chrX	56779550	56779565	+	1	NA	promoter-TSS (NM_001077362)	promoter-TSS (NM_001077362)	-126	NM_001077362	14199	Mm.3126	NM_010211	ENSMUSG00000023092	Fhl1	FHL-1|KyoT|RAM14-1|SLIM|SLIM-1	four and a half LIM domains 1	protein-coding
mm_116281.1	chr13	34990839	34990879	-	1	NA	intron (NR_073427, intron 2 of 9)	intron (NR_073427, intron 2 of 9)	3285	NM_011868	23986	Mm.491141	NM_011868	ENSMUSG00000021417	Eci2	Acbd2|Drs1|Hca88|Peci	enoyl-Coenzyme A delta isomerase 2	protein-coding
mm_137166.1	chr17	23808061	23808073	+	1	NA	5' UTR (NM_175229, exon 2 of 14)	5' UTR (NM_175229, exon 2 of 14)	4880	NM_175229	75956	Mm.5222	NM_175229	ENSMUSG00000039218	Srrm2	5033413A03Rik|AA410130|SRm300|mKIAA0324	serine/arginine repetitive matrix 2	protein-coding
mm_68469.1	chr7	110648767	110648784	-	1	NA	Intergenic	Intergenic	21106	NM_009627	11535	Mm.1408	NM_009627	ENSMUSG00000030790	Adm	AM	adrenomedullin	protein-coding
mm_128077.1	chr15	27663637	27663649	-	1	NA	intron (NM_001242423, intron 4 of 7)	intron (NM_001242423, intron 4 of 7)	17899	NM_001242424	223433	Mm.266485	NM_198301	ENSMUSG00000056069	Fam105a	9830126M18	family with sequence similarity 105, member A	protein-coding
mm_99406.1	chr11	102248892	102248937	+	1	NA	promoter-TSS (NM_153544)	promoter-TSS (NM_153544)	32	NM_153544	217216	Mm.247335	NM_153544	ENSMUSG00000034773	BC030867	-	cDNA sequence BC030867	protein-coding
mm_136647.1	chr17	5841395	5841410	+	1	NA	promoter-TSS (NM_025664)	promoter-TSS (NM_025664)	22	NM_025664	66616	Mm.89515	NM_025664	ENSMUSG00000002365	Snx9	2700073N08Rik|SDP1|SH3PX1	sorting nexin 9	protein-coding
mm_113430.1	chr13	34734838	34734862	+	1	NA	Intergenic	Intergenic	-4792	NM_138746	108161	Mm.41991	NM_138746	ENSMUSG00000038246	Fam50b	D0H6S2654E|X5L|XAP-5-like	family with sequence similarity 50, member B	protein-coding
mm_74747.1	chr8	18991047	18991061	-	1	NA	promoter-TSS (NM_181683)	promoter-TSS (NM_181683)	1	NM_181683	353320	Mm.270483	NM_181683	ENSMUSG00000053695	Defb37	BD-37	defensin beta 37	protein-coding
mm_116337.1	chr13	38173845	38173874	-	1	NA	exon (NM_023842, exon 6 of 24)	exon (NM_023842, exon 6 of 24)	22565	NM_023842	109620	Mm.355327	NM_023842	ENSMUSG00000054889	Dsp	2300002E22Rik|5730453H04Rik|AA407887|AA407888|AW109828|DP|rul	desmoplakin	protein-coding
mm_137764.1	chr17	29490607	29490616	+	1	NA	promoter-TSS (NM_008842)	promoter-TSS (NM_008842)	-434	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_32813.1	chr4	117153827	117153838	+	1	NA	TTS (NR_028524)	TTS (NR_028524)	742	NR_028524	100217424		NR_028524	ENSMUSG00000065680	Snord38a	MBII-329	small nucleolar RNA, C/D box 38A	snoRNA
mm_126166.1	chr15	78531088	78531116	+	1	NA	Intergenic	Intergenic	-1451	NM_028331	72709	Mm.34776	NM_028331	ENSMUSG00000022440	C1qtnf6	2810036M19Rik|CTRP6	C1q and tumor necrosis factor related protein 6	protein-coding
mm_24326.1	chr3	89450386	89450404	+	1	NA	3' UTR (NM_146131, exon 11 of 11)	3' UTR (NM_146131, exon 11 of 11)	-4146	NM_001310640	68603	Mm.34242	NM_026784	ENSMUSG00000027952	Pmvk	1110011E12Rik|2900002L22Rik|AV001327|PMK|PMKA|PMKASE	phosphomevalonate kinase	protein-coding
mm_89044.1	chr10	82860248	82860280	+	1	NA	promoter-TSS (NM_001042514)	promoter-TSS (NM_001042514)	-77	NM_001042514	50493	Mm.210155	NM_015762	ENSMUSG00000020250	Txnrd1	TR|TR1|TrxR1	thioredoxin reductase 1	protein-coding
mm_151698.1	chr19	4439389	4439450	-	1	NA	promoter-TSS (NM_001329989)	promoter-TSS (NM_001329989)	24	NM_007485	11854	Mm.27701	NM_007485	ENSMUSG00000041845	Rhod	AI326383|Arhd|Rho|RhoHP1|RhoM	ras homolog family member D	protein-coding
mm_7614.1	chr1	126694097	126694100	-	1	NA	intron (NM_001081756, intron 2 of 16)	intron (NM_001081756, intron 2 of 16)	136534	NM_001081756	210356	Mm.377234	NM_172484	ENSMUSG00000049690	Nckap5	8430408F21|D130011D22Rik|E030049G20Rik|Erih1|Erih2|Gm1548|Nap5	NCK-associated protein 5	protein-coding
mm_20155.1	chr2	121807025	121807045	-	1	NA	promoter-TSS (NM_172673)	promoter-TSS (NM_172673)	22	NM_172673	228564	Mm.121514	NM_172673	ENSMUSG00000027238	Frmd5	1500032A09Rik|5830442F04|A930004K21Rik|R75430	FERM domain containing 5	protein-coding
mm_27253.1	chr3	37125902	37125906	-	1	NA	promoter-TSS (NM_008366)	promoter-TSS (NM_008366)	50	NM_008366	16183	Mm.14190	NM_008366	ENSMUSG00000027720	Il2	Il-2	interleukin 2	protein-coding
mm_27791.1	chr3	75482133	75482166	-	1	NA	Intergenic	Intergenic	74703	NM_019745	56426	Mm.316473	NM_019745	ENSMUSG00000027835	Pdcd10	2410003B13Rik|Ccm3|Tfa15|Tfar15	programmed cell death 10	protein-coding
mm_148878.1	chr19	6498082	6498089	+	1	NA	intron (NM_001205234, intron 17 of 22)	CpG	44985	NM_009203	20521	Mm.391146	NM_009203	ENSMUSG00000061742	Slc22a12	AI987855|OAT4L|Rst|Slc22al2|URAT1	solute carrier family 22 (organic anion/cation transporter), member 12	protein-coding
mm_133887.1	chr16	96569051	96569053	+	1	NA	Intergenic	Intergenic	101446	NM_008791	18546	Mm.5023	NM_008791	ENSMUSG00000090223	Pcp4	P16Rimb19|Pcp-4|Pep19	Purkinje cell protein 4	protein-coding
mm_153062.1	chr19	32196364	32196377	-	1	NA	intron (NM_001168525, intron 5 of 9)	intron (NM_001168525, intron 5 of 9)	14643	NM_001168526	208449	Mm.329810	NM_144792	ENSMUSG00000040451	Sgms1	9530058O11Rik|AI841905|C80702|Mob|Sms1|Sor1|Tmem23	sphingomyelin synthase 1	protein-coding
mm_135809.1	chr16	57391454	57391492	-	1	NA	intron (NM_001040397, intron 1 of 4)	LSU-rRNA_Hsa|rRNA|rRNA	38196	NM_001040397	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding
mm_43203.1	chr5	129096741	129096771	+	1	NA	promoter-TSS (NM_001081342)	promoter-TSS (NM_001081342)	6	NM_001347486	243277	Mm.440501	NM_177734	ENSMUSG00000044017	Adgrd1	E230012M21Rik|Gpr133	adhesion G protein-coupled receptor D1	protein-coding
mm_61420.1	chr7	73618018	73618028	+	1	NA	Intergenic	CpG	-59628	NR_037569	69170	Mm.34539	NR_037569	ENSMUSG00000101970	1810026B05Rik	-	RIKEN cDNA 1810026B05 gene	ncRNA
mm_136979.1	chr17	16557219	16557231	+	1	NA	Intergenic	Intergenic	-506878	NM_001005358	449000	Mm.483718	NM_001005358	ENSMUSG00000096696	Zfp960	-	zinc finger protein 960	protein-coding
mm_137448.1	chr17	26532910	26532930	+	1	NA	Intergenic	Intergenic	-24448	NM_013642	19252	Mm.239041	NM_013642	ENSMUSG00000024190	Dusp1	3CH134|MKP1|Ptpn16|U19515|erp|mkp-1	dual specificity phosphatase 1	protein-coding
mm_152557.1	chr19	11485341	11485354	-	1	NA	Intergenic	Intergenic	-6691	NM_001164202	666926	Mm.486382	NM_001164202	ENSMUSG00000058470	Gm8369	EG666926	predicted gene 8369	protein-coding
mm_60246.1	chr7	43768982	43768991	+	1	NA	promoter-TSS (NM_027097)	promoter-TSS (NM_027097)	-114	NM_027097	69511	Mm.20163	NM_027097	ENSMUSG00000044430	Klk12	2310008B01Rik|AI324852|KLK-L5	kallikrein related-peptidase 12	protein-coding
mm_156545.1	chrX	151344172	151344197	+	1	NA	promoter-TSS (NM_198105)	promoter-TSS (NM_198105)	-39	NM_198105	207375	Mm.391339	NM_198105	ENSMUSG00000025262	Fam120c	D930001I21Rik|ORF34	family with sequence similarity 120, member C	protein-coding
mm_28770.1	chr3	95904699	95904710	-	1	NA	promoter-TSS (NM_011797)	promoter-TSS (NM_011797)	-65	NM_011797	23831	Mm.489647	NM_011797	ENSMUSG00000038526	Car14	AW536446|Ca14	carbonic anhydrase 14	protein-coding
mm_47461.1	chr5	123666702	123666709	-	1	NA	intron (NM_001347468, intron 1 of 24)	intron (NM_001347468, intron 1 of 24)	17656	NM_019765	56430	Mm.241109	NM_019765	ENSMUSG00000049550	Clip1	1110007I12Rik|4631429H07Rik|AV017631|C81039|CLIP-170|CLIP170|CYLN1|Clip50|Rsn|mKIAA4046|restin	CAP-GLY domain containing linker protein 1	protein-coding
mm_122015.1	chr14	27348500	27348519	-	1	NA	intron (NM_001289687, intron 1 of 9)	intron (NM_001289687, intron 1 of 9)	12472	NM_001289687	71704	Mm.248606	NM_027871	ENSMUSG00000021895	Arhgef3	1200004I24Rik|9830169H03Rik|C76747|Xpln	Rho guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_83735.1	chr9	51077031	51077062	-	1	NA	promoter-TSS (NM_001033534)	promoter-TSS (NM_001033534)	48	NM_001033534	244864	Mm.335152	NM_001033534	ENSMUSG00000060594	Layn	E030012M19Rik|Gm511	layilin	protein-coding
mm_118755.1	chr14	22371703	22371714	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	171090	NR_046307	74896	Mm.444661	NR_046307		4930405A10Rik	4930456G20Rik	RIKEN cDNA 4930405A10 gene	ncRNA
mm_130451.1	chr15	98543908	98543924	-	1	NA	exon (NM_009833, exon 9 of 9)	exon (NM_009833, exon 9 of 9)	-9647	NM_001289440	69612	Mm.229107	NM_133714	ENSMUSG00000022992	Kansl2	2310037I24Rik|B930009D17	KAT8 regulatory NSL complex subunit 2	protein-coding
mm_150192.1	chr19	32665848	32665914	+	1	NA	3' UTR (NM_011864, exon 13 of 13)	3' UTR (NM_011864, exon 13 of 13)	45876	NM_011864	23972	Mm.203916	NM_011864	ENSMUSG00000024899	Papss2	1810018P12Rik|AI159688|AtpsU2|Atpsk2|Sk2|bm	3'-phosphoadenosine 5'-phosphosulfate synthase 2	protein-coding
mm_153880.1	chr19	46929223	46929227	-	1	NA	intron (NM_001164365, intron 2 of 17)	intron (NM_001164365, intron 2 of 17)	33126	NM_029810	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_163067.1	chr11	67248578	67248588	+	1	NA	exon (NM_010855, exon 16 of 40)	exon (NM_010855, exon 16 of 40)	10771	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_54256.1	chr6	28262505	28262509	-	1	NA	promoter-TSS (NM_001081678)	promoter-TSS (NM_001081678)	-906	NM_001081678	627049	Mm.84441	NM_001081678	ENSMUSG00000039841	Zfp800	AA407452|Znf800	zinc finger protein 800	protein-coding
mm_136264.1	chr16	91043511	91043521	-	1	NA	intron (NM_026110, intron 1 of 17)	intron (NM_026110, intron 1 of 17)	863	NM_026110	67367	Mm.347	NM_026110	ENSMUSG00000022974	Paxbp1	1810007M14Rik|C21orf66|Gcfc|Gcfc1|Pax3/7bp	PAX3 and PAX7 binding protein 1	protein-coding
mm_129303.1	chr15	77367141	77367150	-	1	NA	Intergenic	Intergenic	31965	NM_029419	75761	Mm.232636	NM_029419	ENSMUSG00000010601	Apol7a	9130022K13Rik|Apol3	apolipoprotein L 7a	protein-coding
mm_130816.1	chr15	101763558	101763566	-	1	NA	promoter-TSS (NR_033444)	promoter-TSS (NR_033444)	-58	NR_033444	406222	Mm.359153	NM_001003669	ENSMUSG00000067596	Krt74	K74|Kb37	keratin 74	pseudo
mm_128230.1	chr15	36598098	36598124	-	1	NA	exon (NM_008774, exon 11 of 15)	exon (NM_008774, exon 11 of 15)	10862	NM_008774	18458	Mm.371570	NM_008774	ENSMUSG00000022283	Pabpc1	PABP|Pabp1|PabpI|Pabpl1|ePAB	poly(A) binding protein, cytoplasmic 1	protein-coding
mm_63459.1	chr7	127561731	127561742	+	1	NA	TTS (NM_001304266)	TTS (NM_001304266)	513	NM_001304267	105180375	Mm.428042	NM_001304267	ENSMUSG00000106715	Tmem265	-	transmembrane protein 265	protein-coding
mm_129917.1	chr15	84185166	84185176	-	1	NA	intron (NM_054088, intron 7 of 7)	intron (NM_054088, intron 7 of 7)	-7062	NM_178614	68653	Mm.290725	NM_178614	ENSMUSG00000022437	Samm50	1110030L07Rik	SAMM50 sorting and assembly machinery component	protein-coding
mm_133875.1	chr16	96386325	96386344	+	1	NA	intron (NM_001177886, intron 4 of 8)	intron (NM_001177886, intron 4 of 8)	24570	NM_028078	72058	Mm.119714	NM_028078	ENSMUSG00000000159	Igsf5	2010003D20Rik|JCAM|Jam4	immunoglobulin superfamily, member 5	protein-coding
mm_45034.1	chr5	39614976	39614993	-	1	NA	exon (NM_010474, exon 2 of 2)	exon (NM_010474, exon 2 of 2)	-11410	NR_045416	75095	Mm.332354	NR_045416	ENSMUSG00000106741	4930513D17Rik	-	RIKEN cDNA 4930513D17 gene	ncRNA
mm_47661.1	chr5	125589031	125589039	-	1	NA	intron (NM_001190352, intron 1 of 8)	intron (NM_001190352, intron 1 of 8)	56617	NM_001190352	208151	Mm.40397	NM_001190352	ENSMUSG00000070498	Tmem132b	AK220418|mKIAA1786	transmembrane protein 132B	protein-coding
mm_171545.1	chr4	147021940	147021944	+	1	NA	promoter-TSS (NM_001177767)	promoter-TSS (NM_001177767)	92	NM_001177767	100043034	Mm.422606	NM_001177767	ENSMUSG00000067919	Rex2	Gm13138|OTTMUSG00000010655	reduced expression 2	protein-coding
mm_160393.1	chr8	58911997	58911997	+	1	NA	promoter-TSS (NM_175032)	promoter-TSS (NM_175032)	242	NM_173411	234290	Mm.39244	NM_173411	ENSMUSG00000049946	BC030500	-	cDNA sequence BC030500	protein-coding
mm_33937.1	chr4	136945616	136945618	+	1	NA	intron (NM_007939, intron 3 of 16)	(CAGC)n|Simple_repeat|Simple_repeat	11199	NM_007939	13842	Mm.1390	NM_007939	ENSMUSG00000028661	Epha8	AW047546|Eek|Hek3|mKIAA1459	Eph receptor A8	protein-coding
mm_113457.1	chr13	35958873	35958886	+	1	NA	Intergenic	ORR1B2|LTR|ERVL-MaLR	-9027	NM_029628	76487	Mm.44745	NM_029628	ENSMUSG00000050423	Ppp1r3g	1600032L17Rik	protein phosphatase 1, regulatory (inhibitor) subunit 3G	protein-coding
mm_156930.1	chrX	169320647	169320657	+	1	NA	promoter-TSS (NM_001331050)	promoter-TSS (NM_001331050)	-280	NM_001331049	15159	Mm.284033	NM_008222	ENSMUSG00000031352	Hccs	-	holocytochrome c synthetase	protein-coding
mm_64809.1	chr7	6707555	6707570	-	1	NA	TTS (NR_023846)	TTS (NR_023846)	802	NR_023846	100169889	Mm.491213	NR_023846		Peg3os	Apeg3|Peg3as	Peg3 opposite strand	ncRNA
mm_83916.1	chr9	56418836	56418846	-	1	NA	promoter-TSS (NM_025812)	promoter-TSS (NM_025812)	-5	NM_025812	66867	Mm.150856	NM_025812	ENSMUSG00000032329	Hmg20a	1200004E06Rik|5730490E10Rik|Hmgxb1|Ibraf	high mobility group 20A	protein-coding
mm_43189.1	chr5	128736087	128736093	+	1	NA	promoter-TSS (NM_021311)	promoter-TSS (NM_021311)	-156	NM_021311	57749	Mm.272720	NM_021311	ENSMUSG00000029423	Piwil1	MIWI	piwi-like RNA-mediated gene silencing 1	protein-coding
mm_93360.1	chr10	103144922	103144930	-	1	NA	intron (NM_001163559, intron 20 of 25)	intron (NM_001163559, intron 20 of 25)	91396	NM_001163559	74978	Mm.483817	NM_029134	ENSMUSG00000019892	Lrriq1	4930503E15Rik|Gm1557	leucine-rich repeats and IQ motif containing 1	protein-coding
mm_48432.1	chr5	140622830	140622851	-	1	NA	3' UTR (NM_175274, exon 14 of 14)	3' UTR (NM_175274, exon 14 of 14)	15499	NM_008494	16848	Mm.12834	NM_008494	ENSMUSG00000029570	Lfng	AW061165	LFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	protein-coding
mm_5136.1	chr1	9721365	9721398	-	1	NA	3' UTR (NM_173443, exon 3 of 3)	3' UTR (NM_173443, exon 3 of 3)	-21172	NM_008651	17864	Mm.479	NM_008651	ENSMUSG00000025912	Mybl1	A-myb|G1-419-6|repro9	myeloblastosis oncogene-like 1	protein-coding
mm_140355.1	chr17	86831416	86831426	+	1	NA	3' UTR (NM_010137, exon 16 of 16)	3' UTR (NM_010137, exon 16 of 16)	77557	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_158865.1	chrY	2519486	2519494	+	1	NA	Intergenic	RLTR6-int|LTR|ERV1	-79609	NM_001113395	100042840	Mm.472681	NM_001113395	ENSMUSG00000095573	H2al2b	ENSMUSG00000069034|Gm16501|H2al2y	H2A histone family member L2B	protein-coding
mm_50757.1	chr6	53448986	53448987	+	1	NA	intron (NM_001327821, intron 5 of 10)	intron (NM_001327821, intron 5 of 10)	-124388	NM_172728	231991	Mm.227444	NM_172728	ENSMUSG00000053007	Creb5	9430076C15Rik|CRE-BPa|Crebpa|D430026C09Rik	cAMP responsive element binding protein 5	protein-coding
mm_110040.1	chr12	17176575	17176587	-	1	NA	5' UTR (NM_201531, exon 1 of 1)	5' UTR (NM_201531, exon 1 of 1)	307	NM_201531	382571	Mm.40173	NM_201531	ENSMUSG00000051726	Kcnf1	Gm1182|Kv5.1	potassium voltage-gated channel, subfamily F, member 1	protein-coding
mm_81058.1	chr9	106148309	106148332	+	1	NA	Intergenic	Intergenic	-5804	NR_029549	387153		NR_029549	ENSMUSG00000065407	Mir135a-1	Mir135a01|Mirn135|Mirn135a-1|mir-135a-1	microRNA 135a-1	ncRNA
mm_55825.1	chr6	83115390	83115397	-	1	NA	promoter-TSS (NM_020619)	promoter-TSS (NM_020619)	-113	NM_020619	57377	Mm.28188	NM_020619	ENSMUSG00000030036	Mogs	1810017N02Rik|AI181835|Gcs1	mannosyl-oligosaccharide glucosidase	protein-coding
mm_108841.1	chr12	97171035	97171043	+	1	NA	Intergenic	Intergenic	1088420	NM_008079	14420	Mm.5120	NM_008079	ENSMUSG00000021003	Galc	2310068B06Rik|A930008M05Rik|AW212969|AW413532|Gacy|twi|twitcher	galactosylceramidase	protein-coding
mm_141968.1	chr17	35121991	35122039	-	1	NA	promoter-TSS (NM_032460)	promoter-TSS (NM_032460)	38	NM_001303446	13001	Mm.378901	NM_009975	ENSMUSG00000024387	Csnk2b	CK II beta	casein kinase 2, beta polypeptide	protein-coding
mm_59271.1	chr7	24901432	24901444	+	1	NA	exon (NM_007655, exon 5 of 5)	exon (NM_007655, exon 5 of 5)	-1548	NM_001130150	16801	Mm.3181	NM_008488	ENSMUSG00000040940	Arhgef1	Lbcl2|Lsc	Rho guanine nucleotide exchange factor (GEF) 1	protein-coding
mm_27216.1	chr3	35933272	35933287	-	1	NA	promoter-TSS (NM_001205362)	promoter-TSS (NM_001205362)	-313	NM_001205361	114893	Mm.374810	NM_033623	ENSMUSG00000027708	Dcun1d1	Rp42|SCCRO|Tes3|pTes3	DCN1, defective in cullin neddylation 1, domain containing 1 (S. cerevisiae)	protein-coding
mm_65210.1	chr7	19697641	19697653	-	1	NA	exon (NM_009696, exon 3 of 4)	exon (NM_009696, exon 3 of 4)	751	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_8211.1	chr1	138136510	138136532	-	1	NA	intron (NM_001111316, intron 1 of 31)	intron (NM_001111316, intron 1 of 31)	38605	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_14417.1	chr2	130450260	130450309	+	1	NA	promoter-TSS (NM_008980)	promoter-TSS (NM_008980)	6	NM_001163688	19262	Mm.224246	NM_008980	ENSMUSG00000027303	Ptpra	Ptpa|Ptpalpha|Rptpalpha|Rptra|Rptralpha	protein tyrosine phosphatase, receptor type, A	protein-coding
mm_120233.1	chr14	62886551	62886580	+	1	NA	intron (NM_175546, intron 2 of 11)	intron (NM_175546, intron 2 of 11)	21023	NR_105860	102465311		NR_105860	ENSMUSG00000098858	Mir6541	Gm27311|mmu-mir-6541	microRNA 6541	ncRNA
mm_34976.1	chr4	156012974	156013021	+	1	NA	promoter-TSS (NM_011659)	promoter-TSS (NM_011659)	-698	NM_011659	22163	Mm.13885	NM_011659	ENSMUSG00000029075	Tnfrsf4	ACT35|CD134|Ly-70|Ox40|TXGP1L|Txgp1	tumor necrosis factor receptor superfamily, member 4	protein-coding
mm_52814.1	chr6	121343932	121343951	+	1	NA	intron (NM_001347433, intron 1 of 14)	intron (NM_001347433, intron 1 of 14)	865	NM_001347433	14411	Mm.274506	NM_133661	ENSMUSG00000030109	Slc6a12	BGT1|GAT-2|GAT2|Gabt2	solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12	protein-coding
mm_97631.1	chr11	78959810	78959876	+	1	NA	3' UTR (NM_010927, exon 27 of 27)	3' UTR (NM_010927, exon 27 of 27)	25081	NM_001159301	16859	Mm.341434	NM_010708	ENSMUSG00000001123	Lgals9	AA407335|AI194909|AI265545|LGALS35|Lgals5|gal-9|galectin-9	lectin, galactose binding, soluble 9	protein-coding
mm_17422.1	chr2	27426993	27427061	-	1	NA	non-coding (NR_133905, exon 1 of 30)	non-coding (NR_133905, exon 1 of 30)	581	NR_133905	22325	Mm.179011	NM_009500	ENSMUSG00000009621	Vav2	2810040F13Rik|AI847175|Vav-2	vav 2 oncogene	protein-coding
mm_107210.1	chr12	26444546	26444569	+	1	NA	3' UTR (NM_021384, exon 6 of 6)	3' UTR (NM_021384, exon 6 of 6)	11895	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_34702.1	chr4	152096699	152096716	+	1	NA	promoter-TSS (NM_001285999)	promoter-TSS (NM_001285999)	-12	NM_001285999	269608	Mm.332102	NM_001004156	ENSMUSG00000039713	Plekhg5	BC023181|Syx	pleckstrin homology domain containing, family G (with RhoGef domain) member 5	protein-coding
mm_149536.1	chr19	12465805	12465815	+	1	NA	TTS (NM_010821)	TTS (NM_010821)	5031	NM_010821	17476	Mm.3999	NM_010821	ENSMUSG00000046805	Mpeg1	MPS1|Mpg-1	macrophage expressed gene 1	protein-coding
mm_161656.1	chr17	6961145	6961145	-	1	NA	promoter-TSS (NM_147155)	promoter-TSS (NM_147155)	11	NM_147155	380608	Mm.371734	NM_147155	ENSMUSG00000052031	Tagap1	2610315E15Rik|AA415005|FKSG15	T cell activation GTPase activating protein 1	protein-coding
mm_112249.1	chr12	113611644	113611648	-	1	NA	Intergenic	Intergenic	67738	NM_174885	238406	Mm.188683	NM_174885	ENSMUSG00000043945	Adam6a	Adam6|tMDCIV	a disintegrin and metallopeptidase domain 6A	protein-coding
mm_16896.1	chr2	13271269	13271348	-	1	NA	5' UTR (NM_009105, exon 1 of 9)	5' UTR (NM_009105, exon 1 of 9)	107	NM_009105	20163	Mm.905	NM_009105	ENSMUSG00000026727	Rsu1	RsuI|rsp-1	Ras suppressor protein 1	protein-coding
mm_117640.1	chr13	92523265	92523276	-	1	NA	exon (NM_173392, exon 3 of 18)	exon (NM_173392, exon 3 of 18)	7540	NM_173392	218441	Mm.259585	NM_173392	ENSMUSG00000021706	Zfyve16	AI035632|B130024H06Rik|B130031L15|mKIAA0305	zinc finger, FYVE domain containing 16	protein-coding
mm_89016.1	chr10	82048151	82048157	+	1	NA	promoter-TSS (NM_001319203)	promoter-TSS (NM_001319203)	27	NM_001024626	408062	Mm.391409	NM_001024626	ENSMUSG00000061371	Zfp873	-	zinc finger protein 873	protein-coding
mm_112299.1	chr12	114683113	114683118	-	1	NA	Intergenic	Intergenic	-169421	NR_106063	102465664		NR_106063	ENSMUSG00000098357	Mir7094-2	Gm27508|mmu-mir-7094-2	microRNA 7094-2	ncRNA
mm_90809.1	chr10	7768540	7768559	-	1	NA	exon (NM_145418, exon 8 of 8)	exon (NM_145418, exon 8 of 8)	12368	NM_145418	215751	Mm.471825	NM_145418	ENSMUSG00000040006	Ginm1	AA589616	glycoprotein integral membrane 1	protein-coding
mm_6390.1	chr1	72852217	72852247	-	1	NA	3' UTR (NM_008342, exon 4 of 4)	3' UTR (NM_008342, exon 4 of 4)	22633	NM_010518	16011	Mm.405761	NM_010518	ENSMUSG00000026185	Igfbp5	AI256729|AW208790|IGFBP-5|IGFBP-5P	insulin-like growth factor binding protein 5	protein-coding
mm_20442.1	chr2	129309139	129309168	-	1	NA	intron (NM_010554, intron 1 of 6)	intron (NM_010554, intron 1 of 6)	819	NM_010554	16175	Mm.15534	NM_010554	ENSMUSG00000027399	Il1a	Il-1a	interleukin 1 alpha	protein-coding
mm_22394.1	chr2	181228022	181228032	-	1	NA	3' UTR (NM_183162, exon 19 of 19)	3' UTR (NM_183162, exon 19 of 19)	8011	NM_199312	332713	Mm.23349	NM_199312	ENSMUSG00000047841	BC051628	1700026M20Rik|Fndc11	cDNA sequence BC051628	protein-coding
mm_7108.1	chr1	89930684	89930708	-	1	NA	exon (NM_010262, exon 1 of 2)	exon (NM_010262, exon 1 of 2)	480	NM_010262	14472	Mm.204730	NM_010262	ENSMUSG00000034486	Gbx2	D130058E05Rik|Gbx-2|MMoxA|Stra7	gastrulation brain homeobox 2	protein-coding
mm_13393.1	chr2	103969772	103969775	+	1	NA	promoter-TSS (NM_008505)	promoter-TSS (NM_008505)	216	NM_001142336	16909	Mm.29266	NM_008505	ENSMUSG00000032698	Lmo2	Rbtn-2|Rbtn2|Rhom-2|Ttg2	LIM domain only 2	protein-coding
mm_23813.1	chr3	79886885	79886895	+	1	NA	exon (NM_133187, exon 1 of 4)	exon (NM_133187, exon 1 of 4)	960	NM_133187	68659	Mm.427274	NM_133187	ENSMUSG00000027955	Fam198b	1110032E23Rik|2210419I08Rik|AV011458|Ened	family with sequence similarity 198, member B	protein-coding
mm_19584.1	chr2	101797659	101797694	-	1	NA	promoter-TSS (NM_001083810)	promoter-TSS (NM_001083810)	31	NM_175181	72446	Mm.24138	NM_175181	ENSMUSG00000032841	Prr5l	2600010E01Rik|4833411O04Rik|Protor-2|Protor2	proline rich 5 like	protein-coding
mm_131866.1	chr16	23157209	23157230	+	1	NA	exon (NM_009605, exon 3 of 3)	exon (NM_009605, exon 3 of 3)	10683	NM_009605	11450	Mm.3969	NM_009605	ENSMUSG00000022878	Adipoq	30kDa|APN|Acdc|Acrp30|Ad|GBP28|adipo|apM1	adiponectin, C1Q and collagen domain containing	protein-coding
mm_11984.1	chr2	55435804	55435816	+	1	NA	promoter-TSS (NM_001304810)	promoter-TSS (NM_001304810)	-160	NM_001304810	16519	Mm.5127	NM_008426	ENSMUSG00000026824	Kcnj3	GIRK-1|GIRK1|Kcnf3|Kir3.1	potassium inwardly-rectifying channel, subfamily J, member 3	protein-coding
mm_38917.1	chr4	150001296	150001304	-	1	NA	intron (NM_173371, intron 1 of 4)	intron (NM_173371, intron 1 of 4)	1936	NM_001291004	100198	Mm.22183	NM_173371	ENSMUSG00000028980	H6pd	AI785303|G6pd1|Gpd-1|Gpd1	hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase)	protein-coding
mm_56010.1	chr6	86516221	86516240	-	1	NA	Intergenic	MIR3|SINE|MIR	9935	NM_011865	23983	Mm.274146	NM_011865	ENSMUSG00000051695	Pcbp1	WBP17|[a]CP-1|alphaCP-1|hnRNP E1	poly(rC) binding protein 1	protein-coding
mm_119771.1	chr14	54174955	54174968	+	1	NA	Intergenic	Intergenic	78968	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_121752.1	chr14	19278191	19278199	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	324392	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_38209.1	chr4	135873858	135873869	-	1	NA	promoter-TSS (NM_026383)	promoter-TSS (NM_026383)	-17	NM_026383	52830	Mm.29159	NM_026383	ENSMUSG00000028675	Pnrc2	0610011E17Rik|D4Bwg0593e	proline-rich nuclear receptor coactivator 2	protein-coding
mm_62496.1	chr7	101970192	101970206	+	1	NA	intron (NM_133947, intron 1 of 24)	CpG	356	NM_133947	101706	Mm.27259	NM_133947	ENSMUSG00000066306	Numa1	6720401E04Rik|AA764025|AL022610|AU014979|NuMA	nuclear mitotic apparatus protein 1	protein-coding
mm_413.1	chr1	34236545	34236570	+	1	NA	intron (NM_001276764, intron 60 of 102)	intron (NM_001276764, intron 60 of 102)	76227	NM_010081	13518	Mm.336625	NM_010081	ENSMUSG00000026131	Dst	2310001O04Rik|A830042E19Rik|AW554249|BP230|BPAG1-n|Bpag|Bpag1|Macf2|ah|athetoid|dt|mKIAA0728|nmf203|nmf339	dystonin	protein-coding
mm_94049.1	chr10	128180041	128180058	-	1	NA	5' UTR (NM_001039080, exon 1 of 14)	5' UTR (NM_001039080, exon 1 of 14)	248	NM_001039080	56516	Mm.42247	NM_019711	ENSMUSG00000040043	Rbms2	2610315E04Rik|Scr3	RNA binding motif, single stranded interacting protein 2	protein-coding
mm_103201.1	chr11	70652099	70652154	-	1	NA	TTS (NM_001316728)	TTS (NM_001316728)	2524	NM_011072	18643	Mm.2647	NM_011072	ENSMUSG00000018293	Pfn1	Pfn	profilin 1	protein-coding
mm_37605.1	chr4	126753350	126753361	-	1	NA	promoter-TSS (NM_001035526)	promoter-TSS (NM_001035526)	74	NM_011986	26562	Mm.206206	NM_011986	ENSMUSG00000028833	Ncdn	AU042419|MMS10-AE|Ms10ae|mKIAA0607|norbin	neurochondrin	protein-coding
mm_161951.1	chr19	5609675	5609675	-	1	NA	promoter-TSS (NR_037603)	promoter-TSS (NR_037603)	32	NR_037603	81601	Mm.228930	NM_178637	ENSMUSG00000024926	Kat5	AI839539|CPLA2|Htatip|Htatip1|PLIP|Tip55|Tip60	K(lysine) acetyltransferase 5	protein-coding
mm_87985.1	chr10	63986370	63986372	+	1	NA	intron (NM_178678, intron 2 of 2)	B1_Mus1|SINE|Alu	103884	NM_178678	216028	Mm.431318	NM_178678	ENSMUSG00000042846	Lrrtm3	9630044H04Rik	leucine rich repeat transmembrane neuronal 3	protein-coding
mm_32679.1	chr4	115784902	115784912	+	1	NA	promoter-TSS (NM_181040)	promoter-TSS (NM_181040)	93	NM_181040	230649	Mm.109600	NM_181040	ENSMUSG00000028710	Atpaf1	6330547J17Rik|AI593252|ATP11|ATP11p	ATP synthase mitochondrial F1 complex assembly factor 1	protein-coding
mm_40151.1	chr5	35389019	35389031	+	1	NA	promoter-TSS (NM_010445)	promoter-TSS (NM_010445)	-92	NM_010445	15371	Mm.358606	NM_010445	ENSMUSG00000067438	Hmx1	Nkx5-3	H6 homeobox 1	protein-coding
mm_46246.1	chr5	99243283	99243284	-	1	NA	intron (NM_145839, intron 1 of 13)	intron (NM_145839, intron 1 of 13)	9644	NM_181318	320292	Mm.259074	NM_145839	ENSMUSG00000089809	Rasgef1b	4732452O09Rik|GPIgamma4|Gpig4	RasGEF domain family, member 1B	protein-coding
mm_164824.1	chr18	36606190	36606196	+	1	NA	intron (NM_175375, intron 10 of 33)	Lx8|LINE|L1	45590	NM_175375	108857	Mm.482287	NM_175375	ENSMUSG00000024483	Ankhd1	1110004O12Rik|4933432B13Rik|9130019P20Rik|A530027J04Rik|A630021B20Rik|AA571404|Mask|mFLJ00246|mKIAA1085	ankyrin repeat and KH domain containing 1	protein-coding
mm_46483.1	chr5	105131975	105131988	-	1	NA	intron (NM_008620, intron 3 of 10)	L1MA6|LINE|L1	7571	NM_008620	17472	Mm.440525	NM_008620	ENSMUSG00000079363	Gbp4	AW228052|Mag-2|Mpa-2|Mpa2	guanylate binding protein 4	protein-coding
mm_41065.1	chr5	87000839	87000884	+	1	NA	promoter-TSS (NM_172881)	promoter-TSS (NM_172881)	1	NM_172881	243085	Mm.312095	NM_172881	ENSMUSG00000035811	Ugt2b35	C730031G17	UDP glucuronosyltransferase 2 family, polypeptide B35	protein-coding
mm_67509.1	chr7	80782911	80782916	-	1	NA	intron (NM_016721, intron 2 of 37)	intron (NM_016721, intron 2 of 37)	20418	NM_016721	29875	Mm.207619	NM_016721	ENSMUSG00000030536	Iqgap1	AA682088|D7Ertd237e|D7Ertd257e|mKIAA0051	IQ motif containing GTPase activating protein 1	protein-coding
mm_18753.1	chr2	73434983	73435014	-	1	NA	exon (NM_153138, exon 6 of 8)	exon (NM_153138, exon 6 of 8)	18891	NM_001289722	215280	Mm.223504	NM_153138	ENSMUSG00000075284	Wipf1	AI115543|D2Ertd120e|WIP|Waspip	WAS/WASL interacting protein family, member 1	protein-coding
mm_59240.1	chr7	24780692	24780726	+	1	NA	intron (NM_007675, intron 2 of 3)	L2a|LINE|L2	3505	NM_007675	26366	Mm.30300	NM_007675	ENSMUSG00000054169	Ceacam10	Bgp3|Cea10	carcinoembryonic antigen-related cell adhesion molecule 10	protein-coding
mm_67834.1	chr7	98361328	98361343	-	1	NA	promoter-TSS (NM_001168539)	promoter-TSS (NM_001168539)	-7	NM_001168539	244152	Mm.25317	NM_001024619	ENSMUSG00000049580	Tsku	9530051K01Rik|E2ig4|Lrrc54|Tsk	tsukushi, small leucine rich proteoglycan	protein-coding
mm_56660.1	chr6	113483171	113483185	-	1	NA	promoter-TSS (NM_133930)	promoter-TSS (NM_133930)	-391	NM_133930	171508	Mm.41593	NM_133930	ENSMUSG00000030284	Creld1	AI843811	cysteine-rich with EGF-like domains 1	protein-coding
mm_85241.1	chr9	98955341	98955348	-	1	NA	promoter-TSS (NR_003248)	promoter-TSS (NR_003248)	-34	NR_003248	768252	Mm.129645	NR_003248	ENSMUSG00000097072	Foxl2os	ENSMUSG00000074122	forkhead box L2, opposite strand	ncRNA
mm_171547.1	chr4	147022248	147022261	+	1	NA	intron (NM_001177767, intron 1 of 4)	intron (NM_001177767, intron 1 of 4)	404	NM_001177767	100043034	Mm.422606	NM_001177767	ENSMUSG00000067919	Rex2	Gm13138|OTTMUSG00000010655	reduced expression 2	protein-coding
mm_8497.1	chr1	153851190	153851198	-	1	NA	promoter-TSS (NM_178243)	promoter-TSS (NM_178243)	1	NM_178243	240817	Mm.439405	NM_178243	ENSMUSG00000045968	Teddm2	5830403L16Rik|AJ554213|Me9|e92	transmembrane epididymal family member 2	protein-coding
mm_158348.1	chrX	134476480	134476495	-	1	NA	promoter-TSS (NM_028958)	promoter-TSS (NM_028958)	3	NM_028958	74469	Mm.103259	NM_028958	ENSMUSG00000009596	Taf7l	4933438I11Rik|Taf2q	TATA-box binding protein associated factor 7 like	protein-coding
mm_126436.1	chr15	80623343	80623354	+	1	NA	promoter-TSS (NM_010815)	promoter-TSS (NM_010815)	-135	NM_010815	17444	Mm.12947	NM_010815	ENSMUSG00000042351	Grap2	GRAP-2|GRB2L|GRBLG|GRID|Gads|GrbX|Grf40|GrpL|Mona|P38	GRB2-related adaptor protein 2	protein-coding
mm_127492.1	chr15	101373327	101373335	+	1	NA	Intergenic	Intergenic	-3206	NM_028770	74127	Mm.440055	NM_028770	ENSMUSG00000037185	Krt80	1200016G03Rik|2310041I20Rik|Kb20	keratin 80	protein-coding
mm_60688.1	chr7	45155866	45155872	+	1	NA	promoter-TSS (NM_001285904)	promoter-TSS (NM_001285904)	-77	NM_001285904	68845	Mm.181689	NM_029406	ENSMUSG00000003423	Pih1d1	1110061L23Rik|4933413A04Rik|Nop17	PIH1 domain containing 1	protein-coding
mm_91782.1	chr10	52381922	52381940	-	1	NA	5' UTR (NM_053187, exon 1 of 8)	5' UTR (NM_053187, exon 1 of 8)	193	NM_053187	94221	Mm.390258	NM_053187	ENSMUSG00000019861	Gopc	2210402P09Rik|AI844555|CAL|FIG|GOPC1|PIST	golgi associated PDZ and coiled-coil motif containing	protein-coding
mm_47641.1	chr5	125341044	125341112	-	1	NA	promoter-TSS (NM_001205082)	promoter-TSS (NM_001205082)	16	NM_016741	20778	Mm.282242	NM_016741	ENSMUSG00000037936	Scarb1	AI120173|CD36|Cd36l1|Chohd1|Cla-1|Cla1|D5Ertd460e|Hdlq1|Hlb398|SR-B1|SR-BI|SRBI|Srb1|mSR-BI	scavenger receptor class B, member 1	protein-coding
mm_129265.1	chr15	76871401	76871453	-	1	NA	promoter-TSS (NM_001007568)	promoter-TSS (NM_001007568)	8	NM_001007568	71591	Mm.38195	NM_001007568	ENSMUSG00000022526	Zfp251	9130001M19Rik|AV339307	zinc finger protein 251	protein-coding
mm_34040.1	chr4	138206342	138206360	+	1	NA	3' UTR (NM_001256198, exon 33 of 33)	3' UTR (NM_001256198, exon 33 of 33)	-10261	NM_001122896	15441	Mm.348429	NM_010470	ENSMUSG00000028759	Hp1bp3	Hp1bp74	heterochromatin protein 1, binding protein 3	protein-coding
mm_136312.1	chr16	91688792	91688802	-	1	NA	promoter-TSS (NM_021720)	promoter-TSS (NM_021720)	-69	NM_021720	60364	Mm.328698	NM_021720	ENSMUSG00000022960	Donson	1110025J21Rik|AI845729|ORF60	downstream neighbor of SON	protein-coding
mm_41427.1	chr5	90892655	90892666	+	1	NA	3' UTR (NM_008176, exon 4 of 4)	3' UTR (NM_008176, exon 4 of 4)	1415	NM_008176	14825	Mm.21013	NM_008176	ENSMUSG00000029380	Cxcl1	Fsp|Gro1|KC|Mgsa|N51|Scyb1|gro	chemokine (C-X-C motif) ligand 1	protein-coding
mm_154233.1	chr19	60534250	60534270	-	1	NA	exon (NM_001172096, exon 6 of 8)	exon (NM_001172096, exon 6 of 8)	46763	NM_001172097	78832	Mm.259026	NM_030197	ENSMUSG00000033417	Cacul1	2700078E11Rik|2810417M16Rik|9830127L17Rik|AI450346|D130033C15Rik	CDK2 associated, cullin domain 1	protein-coding
mm_148167.1	chr18	77796215	77796226	-	1	NA	intron (NM_013831, intron 1 of 14)	MIR|SINE|MIR	1670	NM_013831	19201	Mm.57174	NM_013831	ENSMUSG00000025429	Pstpip2	MAYP|cmo	proline-serine-threonine phosphatase-interacting protein 2	protein-coding
mm_163368.1	chr12	36569912	36569913	+	1	NA	intron (NM_178629, intron 9 of 9)	intron (NM_178629, intron 9 of 9)	154296	NR_037309	100499526		NR_037309	ENSMUSG00000092917	Mir3472	mmu-mir-3472	microRNA 3472	ncRNA
mm_68900.1	chr7	126450302	126450310	-	1	NA	exon (NM_007504, exon 14 of 23)	exon (NM_007504, exon 14 of 23)	12767	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_11179.1	chr2	28840407	28840462	+	1	NA	promoter-TSS (NM_001166033)	promoter-TSS (NM_001166033)	28	NM_001033294	227674	Mm.44179	NM_001033294	ENSMUSG00000026806	Ddx31	5830444G11Rik|Gm997	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 31	protein-coding
mm_3455.1	chr1	150103693	150103702	+	1	NA	exon (NM_011198, exon 6 of 10)	exon (NM_011198, exon 6 of 10)	3666	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_28688.1	chr3	95511857	95511870	-	1	NA	Intergenic	Intergenic	12653	NM_007802	13038	Mm.272085	NM_007802	ENSMUSG00000028111	Ctsk	AI323530|MMS10-Q|Ms10q|catK	cathepsin K	protein-coding
mm_81173.1	chr9	107300094	107300104	+	1	NA	exon (NM_009895, exon 2 of 3)	exon (NM_009895, exon 2 of 3)	3440	NM_009895	12700	Mm.4592	NM_009895	ENSMUSG00000032578	Cish	CIS-1|CIS1|Cis|F17|F23|SOCS	cytokine inducible SH2-containing protein	protein-coding
mm_80999.1	chr9	103425125	103425173	+	1	NA	intron (NM_001002896, intron 6 of 6)	intron (NM_001002896, intron 6 of 6)	1571	NR_040466	100529079	Mm.437003	NR_040466	ENSMUSG00000086236	5830418P13Rik	-	RIKEN cDNA 5830418P13 gene	ncRNA
mm_171811.1	chr5	133468670	133468671	+	1	NA	Intergenic	Intergenic	-631078	NM_030719	80909	Mm.45218	NM_030719	ENSMUSG00000015944	Gatsl2	7530428J21Rik|AW742413|Gats|Gatsl1	GATS protein-like 2	protein-coding
mm_22819.1	chr3	27194695	27194699	+	1	NA	intron (NM_178772, intron 1 of 4)	intron (NM_178772, intron 1 of 4)	11693	NM_178772	320024	Mm.24576	NM_178772	ENSMUSG00000027698	Nceh1	Aadacl1|B230106I24Rik|CPO-BP|Nceh	neutral cholesterol ester hydrolase 1	protein-coding
mm_33852.1	chr4	135862962	135862965	+	1	NA	intron (NM_010178, intron 3 of 5)	intron (NM_010178, intron 3 of 5)	6892	NM_010178	14105	Mm.10229	NM_010178	ENSMUSG00000028676	Srsf10	FUSIP2|Fusip1|NSSR1|NSSR2|Nssr|SRrp40|Sfrs13a|Srsf13a|TASR|TASR1|TASR2	serine/arginine-rich splicing factor 10	protein-coding
mm_5123.1	chr1	9299252	9299306	-	1	NA	5' UTR (NM_001290390, exon 1 of 21)	5' UTR (NM_001290390, exon 1 of 21)	598	NM_001290390	71096	Mm.336395	NM_027671	ENSMUSG00000025909	Sntg1	4933426D16Rik|G1SYN|SYN4	syntrophin, gamma 1	protein-coding
mm_72146.1	chr8	72138630	72138665	+	1	NA	exon (NM_001001491, exon 2 of 8)	exon (NM_001001491, exon 2 of 8)	3355	NM_001001491	326618	Mm.295124	NM_001001491	ENSMUSG00000031799	Tpm4	2610528G24Rik|Tpm4.2|Tpm4.2cy	tropomyosin 4	protein-coding
mm_162788.1	chr10	75351980	75351986	+	1	NA	promoter-TSS (NR_033602)	promoter-TSS (NR_033602)	-72	NR_033602	544707	Mm.349862	NR_033602		Gm5779	EG544707	ribosomal protein, large, P0 pseudogene	pseudo
mm_60764.1	chr7	45549847	45549872	+	1	NA	exon (NM_148927, exon 17 of 20)	exon (NM_148927, exon 17 of 20)	-5069	NM_025330	66065	Mm.285710	NM_025330	ENSMUSG00000030825	Hsd17b14	0610039E24Rik|Dhrs10|retSDR3	hydroxysteroid (17-beta) dehydrogenase 14	protein-coding
mm_124105.1	chr14	79301624	79301641	-	1	NA	promoter-TSS (NM_025427)	promoter-TSS (NM_025427)	3	NM_025427	66214	Mm.29811	NM_025427	ENSMUSG00000022018	Rgcc	1190002H23Rik|Rgc-32|Rgc32	regulator of cell cycle	protein-coding
mm_52423.1	chr6	113471516	113471540	+	1	NA	promoter-TSS (NM_178942)	promoter-TSS (NM_178942)	73	NM_134159	171095	Mm.213397	NM_134159	ENSMUSG00000030281	Il17rc	1110025H02Rik|Gm19850|IL-17RC|IL17-RC|IL17-RL|Il17rl	interleukin 17 receptor C	protein-coding
mm_77972.1	chr9	7837137	7837152	+	1	NA	promoter-TSS (NM_007465)	promoter-TSS (NM_007465)	-87	NM_007465	11797	Mm.335659	NM_007465	ENSMUSG00000057367	Birc2	AW146227|Api1|Api2|Birc3|C-IAP1|C330006D17Rik|HIAP1|HIAP2|IAP1|IAP2|MIAP1|MIAP2|MIHB|MIHC|RNF48|cIAP1|cIAP2|mcIAP1	baculoviral IAP repeat-containing 2	protein-coding
mm_104465.1	chr11	95088851	95088888	-	1	NA	Intergenic	Intergenic	-12058	NM_001306162	16400	Mm.57035	NM_013565	ENSMUSG00000001507	Itga3	AA407068|CD49C|GAPB3	integrin alpha 3	protein-coding
mm_39341.1	chr5	8893607	8893617	+	1	NA	promoter-TSS (NM_008830)	promoter-TSS (NM_008830)	-109	NM_008830	18670	Mm.297825	NM_008830	ENSMUSG00000042476	Abcb4	Mdr2|Pgy-2|Pgy2|mdr-2	ATP-binding cassette, sub-family B (MDR/TAP), member 4	protein-coding
mm_17063.1	chr2	22590215	22590215	-	1	NA	Intergenic	Intergenic	-32112	NM_008078	14417	Mm.4784	NM_008078	ENSMUSG00000026787	Gad2	6330404F12Rik|GAD(65)|GAD65|Gad-2	glutamic acid decarboxylase 2	protein-coding
mm_17826.1	chr2	33887554	33887586	-	1	NA	5' UTR (NM_175184, exon 1 of 10)	5' UTR (NM_175184, exon 1 of 10)	376	NM_175184	72543	Mm.254914	NM_175184	ENSMUSG00000038740	Mvb12b	2610200O14Rik|2610528K11Rik|AI414895|Fam125b	multivesicular body subunit 12B	protein-coding
mm_66274.1	chr7	37479147	37479160	-	1	NA	TTS (NM_172385)	TTS (NM_172385)	290599	NM_172385	243937	Mm.322505	NM_172385	ENSMUSG00000043456	Zfp536	9630010P11Rik|Znf536|mKIAA0390	zinc finger protein 536	protein-coding
mm_126754.1	chr15	85787170	85787177	+	1	NA	exon (NM_011144, exon 4 of 8)	exon (NM_011144, exon 4 of 8)	24524	NM_001164626	72355	Mm.33706	NM_197998	ENSMUSG00000064284	Cdpf1	2210021J22Rik	cysteine rich, DPF motif domain containing 1	protein-coding
mm_21323.1	chr2	157101169	157101175	-	1	NA	intron (NM_018851, intron 15 of 15)	(TG)n|Simple_repeat|Simple_repeat	14117	NM_001177439	383766	Mm.480305	NM_001177439	ENSMUSG00000074628	Tldc2	Gm1332	TBC/LysM associated domain containing 2	protein-coding
mm_104955.1	chr11	100141548	100141593	-	1	NA	exon (NM_008471, exon 4 of 6)	exon (NM_008471, exon 4 of 6)	2129	NM_001313963	16669	Mm.439699	NM_008471	ENSMUSG00000020911	Krt19	AI663979|CK-19|EndoC|K19|Krt-1.19|Krt1-19	keratin 19	protein-coding
mm_162038.1	chr19	56379132	56379132	-	1	NA	exon (NM_198059, exon 10 of 41)	exon (NM_198059, exon 10 of 41)	10906	NM_198059	18175	Mm.386769	NM_008733	ENSMUSG00000049134	Nrap	-	nebulin-related anchoring protein	protein-coding
mm_116559.1	chr13	46727913	46727926	-	1	NA	promoter-TSS (NM_175749)	promoter-TSS (NM_175749)	-70	NM_175749	218210	Mm.255398	NM_175749	ENSMUSG00000021374	Nup153	B130015D15Rik|C88147	nucleoporin 153	protein-coding
mm_495.1	chr1	36903971	36903982	+	1	NA	intron (NM_018872, intron 1 of 40)	intron (NM_018872, intron 1 of 40)	35551	NM_018872	56030	Mm.186943	NM_018872	ENSMUSG00000026116	Tmem131	2610524E03Rik|CC28|D1Bwg0491e|Neg|RW1|YR-23|mKIAA0257	transmembrane protein 131	protein-coding
mm_121204.1	chr14	103052535	103052561	+	1	NA	intron (NM_008392, intron 4 of 4)	Lx8|LINE|L1	5536	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_82866.1	chr9	32344261	32344292	-	1	NA	promoter-TSS (NM_010605)	promoter-TSS (NM_010605)	-39	NM_010605	16521	Mm.69472	NM_010605	ENSMUSG00000032034	Kcnj5	GIRK4|Kir3.4	potassium inwardly-rectifying channel, subfamily J, member 5	protein-coding
mm_52106.1	chr6	97880516	97880519	+	1	NA	intron (NM_001113198, intron 1 of 9)	B4|SINE|B4	-49300	NM_001178049	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_165995.1	chr4	112232331	112232335	+	1	NA	promoter-TSS (NM_177578)	promoter-TSS (NM_177578)	88	NM_177578	195564	Mm.259652	NM_177578	ENSMUSG00000070868	Skint3	A430090E18Rik|Skint-3	selection and upkeep of intraepithelial T cells 3	protein-coding
mm_77312.1	chr8	117673683	117673701	-	1	NA	Intergenic	Intergenic	-2177	NM_028725	74032	Mm.296302	NM_028725	ENSMUSG00000034308	Sdr42e1	4632417N05Rik|AI117603	short chain dehydrogenase/reductase family 42E, member 1	protein-coding
mm_129814.1	chr15	82998989	82999023	-	1	NA	3' UTR (NM_028728, exon 6 of 6)	3' UTR (NM_028728, exon 6 of 6)	24132	NM_028728	74039	Mm.32584	NM_028728	ENSMUSG00000058099	Nfam1	4921501M20Rik|Cnaip	Nfat activating molecule with ITAM motif 1	protein-coding
mm_249.1	chr1	19235327	19235332	+	1	NA	3' UTR (NM_009334, exon 7 of 7)	3' UTR (NM_009334, exon 7 of 7)	23275	NM_001025305	21419	Mm.137021	NM_009334	ENSMUSG00000025927	Tfap2b	AI606113|AP-2(beta)|E130018K07Rik|Tcfap2b	transcription factor AP-2 beta	protein-coding
mm_34347.1	chr4	144523631	144523654	+	1	NA	intron (NM_198662, intron 2 of 3)	intron (NM_198662, intron 2 of 3)	3820	NM_198662	381572	Mm.184290	NM_198662	ENSMUSG00000028593	9430007A20Rik	Aadacl4|Gm1034	RIKEN cDNA 9430007A20 gene	protein-coding
mm_117539.1	chr13	83601876	83601882	-	1	NA	intron (NM_001347569, intron 3 of 10)	intron (NM_001347569, intron 3 of 10)	28272	NM_001347569	17260	Mm.24001	NM_025282	ENSMUSG00000005583	Mef2c	5430401D19Rik|9930028G15Rik|AV011172|Mef2	myocyte enhancer factor 2C	protein-coding
mm_142509.1	chr17	46153518	46153543	-	1	NA	promoter-TSS (NM_025649)	promoter-TSS (NM_025649)	21	NM_025649	66591	Mm.272024	NM_025649	ENSMUSG00000034509	Mad2l1bp	0610009D16Rik|2510031P20Rik|AU018945|AW550977|C76045|CMT2A|CMT2B|Mad2lbp|mKIAA0110	MAD2L1 binding protein	protein-coding
mm_28041.1	chr3	83841576	83841613	-	1	NA	promoter-TSS (NM_011905)	promoter-TSS (NM_011905)	14	NM_011905	24088	Mm.87596	NM_011905	ENSMUSG00000027995	Tlr2	Ly105	toll-like receptor 2	protein-coding
mm_13414.1	chr2	104113355	104113367	+	1	NA	intron (NM_007652, intron 3 of 3)	RMER1B|Other|Other	-9408	NM_026634	68243	Mm.158191	NM_026634	ENSMUSG00000032671	A930018P22Rik	-	RIKEN cDNA A930018P22 gene	protein-coding
mm_64837.1	chr7	12997668	12997671	-	1	NA	exon (NM_009512, exon 1 of 10)	exon (NM_009512, exon 1 of 10)	523	NM_009512	26459	Mm.10984	NM_009512	ENSMUSG00000030382	Slc27a5	FACVL3|FATP5|VLCS-H2|VLCSH2|Vlacsr	solute carrier family 27 (fatty acid transporter), member 5	protein-coding
mm_35376.1	chr4	33172011	33172014	-	1	NA	3' UTR (NM_001034867, exon 7 of 7)	3' UTR (NM_001034867, exon 7 of 7)	17725	NM_001034867	242377	Mm.372465	NM_001034867	ENSMUSG00000054659	Pm20d2	Acy1l2|Gm424	peptidase M20 domain containing 2	protein-coding
mm_121907.1	chr14	21987862	21987882	-	1	NA	5' UTR (NM_145459, exon 2 of 3)	5' UTR (NM_145459, exon 2 of 3)	1729	NM_145459	218820	Mm.292401	NM_145459	ENSMUSG00000039081	Zfp503	AI181838|B830002A16Rik|Nolz-1|Nolz1|Znf503	zinc finger protein 503	protein-coding
mm_147576.1	chr18	56430162	56430167	-	1	NA	Intergenic	Intergenic	-1968	NM_026240	107022	Mm.24356	NM_026240	ENSMUSG00000001700	Gramd3	9030613F08Rik|9130427A09Rik|AW061306|NS3TP2	GRAM domain containing 3	protein-coding
mm_18501.1	chr2	62610581	62610591	-	1	NA	exon (NM_027835, exon 7 of 16)	exon (NM_027835, exon 7 of 16)	35669	NM_027835	71586	Mm.136224	NM_027835	ENSMUSG00000026896	Ifih1	9130009C22Rik|Helicard|Hlcd|MDA5|RLR-2	interferon induced with helicase C domain 1	protein-coding
mm_34796.1	chr4	154619162	154619179	+	1	NA	intron (NM_001177995, intron 1 of 15)	intron (NM_001177995, intron 1 of 15)	17197	NR_045643	320939	Mm.436738	NR_045643		5930403L14Rik	-	RIKEN cDNA 5930403L14 gene	ncRNA
mm_149819.1	chr19	24197563	24197569	+	1	NA	intron (NM_011597, intron 1 of 22)	intron (NM_011597, intron 1 of 22)	-23426	NM_001198985	21873	Mm.104744	NM_011597	ENSMUSG00000024812	Tjp2	ZO-2	tight junction protein 2	protein-coding
mm_167735.1	chr9	106160037	106160067	+	1	NA	Intergenic	CpG	-1914	NM_174846	235582	Mm.335420	NM_174846	ENSMUSG00000020258	Glyctk	6230410P16Rik|C430006L12	glycerate kinase	protein-coding
mm_143896.1	chr17	84682872	84682882	-	1	NA	promoter-TSS (NM_001347418)	promoter-TSS (NM_001347418)	134	NM_031884	27409	Mm.289590	NM_031884	ENSMUSG00000040505	Abcg5	cmp|sterolin-1|trac	ATP-binding cassette, sub-family G (WHITE), member 5	protein-coding
mm_133569.1	chr16	91406175	91406191	+	1	NA	promoter-TSS (NM_008349)	promoter-TSS (NM_008349)	-52	NM_008349	16155	Mm.4154	NM_008349	ENSMUSG00000022969	Il10rb	6620401D04Rik|AI528744|CRF2-4|Crfb4|D16H21S58|D21S58h|IL-10R2|Il10r2	interleukin 10 receptor, beta	protein-coding
mm_116923.1	chr13	55536396	55536434	-	1	NA	intron (NM_134059, intron 1 of 16)	CpG-3910	243	NM_134059	72935	Mm.205045	NM_134059	ENSMUSG00000021494	Ddx41	2900024F02Rik|AA958953|ABS|AI324246	DEAD (Asp-Glu-Ala-Asp) box polypeptide 41	protein-coding
mm_56655.1	chr6	113434758	113434770	-	1	NA	intron (NM_178373, intron 1 of 5)	intron (NM_178373, intron 1 of 5)	991	NM_178373	14311	Mm.10026	NM_178373	ENSMUSG00000030278	Cidec	CIDE-3|Fsp27	cell death-inducing DFFA-like effector c	protein-coding
mm_23083.1	chr3	36862015	36862040	+	1	NA	Intergenic	Intergenic	-1079	NM_172679	229227	Mm.207907	NM_172679	ENSMUSG00000037270	4932438A13Rik	4732443H21|B830039D19Rik|D630029K19Rik|FSA|Kiaa1109|Tweek	RIKEN cDNA 4932438A13 gene	protein-coding
mm_44110.1	chr5	149374401	149374417	+	1	NA	Intergenic	Intergenic	-37397	NM_027519	70717	Mm.252139	NM_027519	ENSMUSG00000029659	Medag	6330406I15Rik|Awms3|MEDA-4|Meda4|mAWMS3	mesenteric estrogen dependent adipogenesis	protein-coding
mm_14921.1	chr2	151127481	151127486	+	1	NA	Intergenic	Intergenic	29238	NM_001097977	433486	Mm.422661	NM_001097977	ENSMUSG00000079006	Gm14151	OTTMUSG00000015806	predicted gene 14151	protein-coding
mm_33122.1	chr4	124798849	124798862	+	1	NA	intron (NR_126474, intron 23 of 24)	B2_Mm2|SINE|B2	-3694	NM_008636	17764	Mm.272397	NM_008636	ENSMUSG00000028890	Mtf1	MTF-1|Thyls	metal response element binding transcription factor 1	protein-coding
mm_1961.1	chr1	86434605	86434656	+	1	NA	Intergenic	CpG	8301	NM_027966	71863	Mm.179627	NM_027966	ENSMUSG00000036574	1700019O17Rik	-	RIKEN cDNA 1700019O17 gene	protein-coding
mm_60411.1	chr7	44476115	44476131	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	5776	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_17518.1	chr2	29252060	29252062	-	1	NA	intron (NR_029460, intron 1 of 1)	CpG	932	NR_029460	76220	Mm.330108	NR_029460	ENSMUSG00000079499	6530402F18Rik	mKIAA1857	RIKEN cDNA 6530402F18 gene	ncRNA
mm_54552.1	chr6	37016994	37016996	-	1	NA	intron (NM_001347104, intron 17 of 32)	intron (NM_001347104, intron 17 of 32)	-205634	NM_008973	19242	Mm.279690	NM_008973	ENSMUSG00000029838	Ptn	HARP|HB-GAM|HBBN|HBGF-8|HBNF|OSF|Osf-1|Osf1	pleiotrophin	protein-coding
mm_156837.1	chrX	164373472	164373484	+	1	NA	promoter-TSS (NM_010216)	promoter-TSS (NM_010216)	-44	NM_001308489	14205	Mm.297978	NM_010216	ENSMUSG00000031380	Vegfd	AI325264|Figf|VEGF-D	vascular endothelial growth factor D	protein-coding
mm_13818.1	chr2	119237454	119237474	+	1	NA	5' UTR (NM_016907, exon 1 of 11)	5' UTR (NM_016907, exon 1 of 11)	104	NM_016907	20732	Mm.104955	NM_016907	ENSMUSG00000027315	Spint1	HAI-1	serine protease inhibitor, Kunitz type 1	protein-coding
mm_117239.1	chr13	64312629	64312654	-	1	NA	promoter-TSS (NM_025370)	promoter-TSS (NM_025370)	69	NM_025370	66129	Mm.491110	NM_025370	ENSMUSG00000021482	Aaed1	1110018J18Rik|AI849003	AhpC/TSA antioxidant enzyme domain containing 1	protein-coding
mm_133226.1	chr16	76403416	76403431	+	1	NA	Intergenic	Intergenic	-30374	NM_173440	268903	Mm.74711	NM_173440	ENSMUSG00000048490	Nrip1	6030458L20Rik|8430438I05Rik|9630050P12|AA959574|AW456757|RIP140	nuclear receptor interacting protein 1	protein-coding
mm_52692.1	chr6	118198402	118198406	+	1	NA	promoter-TSS (NM_009050)	promoter-TSS (NM_009050)	-660	NM_001080780	19713	Mm.57199	NM_009050	ENSMUSG00000030110	Ret	PTC|RET51|RET9|c-Ret	ret proto-oncogene	protein-coding
mm_73170.1	chr8	95020825	95020845	+	1	NA	intron (NM_173036, intron 1 of 11)	intron (NM_173036, intron 1 of 11)	3143	NM_173036	54672	Mm.27995	NM_173036	ENSMUSG00000060470	Adgrg3	A030001G24Rik|AW214383|Gpr97|Pb1|Pb99	adhesion G protein-coupled receptor G3	protein-coding
mm_58045.1	chr6	136827821	136827825	-	1	NA	intron (NM_021714, intron 1 of 11)	CpG	393	NM_021714	60321	Mm.141197	NM_021714	ENSMUSG00000030216	Wbp11	2510026P17Rik|D6Wsu113e|Npwbp|SIPP1	WW domain binding protein 11	protein-coding
mm_85669.1	chr9	107676403	107676413	-	1	NA	intron (NM_008140, intron 6 of 8)	CpG-15374	3184	NM_008140	14685	Mm.284853	NM_008140	ENSMUSG00000034837	Gnat1	Gnat-1|Ird1|Ird2|Tralpha|irdc|irdr|transducin	guanine nucleotide binding protein, alpha transducing 1	protein-coding
mm_155179.1	chrX	53724796	53724815	+	1	NA	promoter-TSS (NM_029142)	promoter-TSS (NM_029142)	-26	NM_029142	75013	Mm.336332	NM_029142	ENSMUSG00000055555	4930502E18Rik	Ct55	RIKEN cDNA 4930502E18 gene	protein-coding
mm_2423.1	chr1	95314107	95314122	+	1	NA	exon (NM_026321, exon 1 of 3)	exon (NM_026321, exon 1 of 3)	486	NM_026321	67698	Mm.272705	NM_026321	ENSMUSG00000051185	Fam174a	2310044D20Rik|Fam174|Naa6|Tmem157	family with sequence similarity 174, member A	protein-coding
mm_172643.1	chr8	26054198	26054208	+	1	NA	intron (NM_207659, intron 15 of 21)	LTRIS2|LTR|ERV1	-28406	NR_110583	76604	Mm.437190	NR_110583	ENSMUSG00000085437	1700047A11Rik	4930554C15Rik	RIKEN cDNA 1700047A11 gene	ncRNA
mm_123954.1	chr14	74733481	74733485	-	1	NA	intron (NM_001285423, intron 1 of 8)	intron (NM_001285423, intron 1 of 8)	1186	NM_016903	13885	Mm.38055	NM_016903	ENSMUSG00000021996	Esd	Es-10|Es10|FGH|sid478	esterase D/formylglutathione hydrolase	protein-coding
mm_58622.1	chr7	5069150	5069185	+	1	NA	intron (NM_133671, intron 5 of 11)	intron (NM_133671, intron 5 of 11)	7024	NM_001205231	22185	Mm.360389	NM_133671	ENSMUSG00000030435	U2af2	65kDa	U2 small nuclear ribonucleoprotein auxiliary factor (U2AF) 2	protein-coding
mm_61915.1	chr7	90147059	90147076	+	1	NA	intron (NM_001252520, intron 1 of 20)	intron (NM_001252520, intron 1 of 20)	16835	NM_001252520	233489	Mm.235175	NM_146194	ENSMUSG00000039361	Picalm	CALM|CLTH|PAP180|fit-1|fit1|mKIAA4114	phosphatidylinositol binding clathrin assembly protein	protein-coding
mm_2237.1	chr1	91049684	91049705	+	1	NA	intron (NM_001111312, intron 1 of 12)	intron (NM_001111312, intron 1 of 12)	-3750	NM_001310732	16978	Mm.45039	NM_008515	ENSMUSG00000026305	Lrrfip1	AU024550|Fliiap1	leucine rich repeat (in FLII) interacting protein 1	protein-coding
mm_102550.1	chr11	61365046	61365050	-	1	NA	intron (NM_026183, intron 6 of 16)	ID4_|SINE|ID	13027	NM_026183	67473	Mm.100741	NM_026183	ENSMUSG00000010122	Slc47a1	1300013J15Rik|AI036982|MATE1|mMATE1	solute carrier family 47, member 1	protein-coding
mm_52759.1	chr6	120794064	120794069	+	1	NA	TTS (NM_001081048)	TTS (NM_001081048)	20298	NM_001081048	71803	Mm.425340	NM_001081048	ENSMUSG00000004902	Slc25a18	1500015I14Rik|AW125787	solute carrier family 25 (mitochondrial carrier), member 18	protein-coding
mm_87262.1	chr10	41519981	41519989	+	1	NA	intron (NM_016898, intron 1 of 5)	intron (NM_016898, intron 1 of 5)	485	NM_016898	53599	Mm.269815	NM_016898	ENSMUSG00000019818	Cd164	A115|A24|AA589639|AW540279|MGC-24|MSSP	CD164 antigen	protein-coding
mm_144979.1	chr18	37955649	37955672	+	1	NA	promoter-TSS (NM_010411)	promoter-TSS (NM_010411)	101	NM_153793	225392	Mm.233516	NM_153793	ENSMUSG00000044024	Rell2	4631403P03Rik|ependolin	RELT-like 2	protein-coding
mm_57627.1	chr6	128300363	128300424	-	1	NA	5' UTR (NM_001080979, exon 1 of 11)	5' UTR (NM_001080979, exon 1 of 11)	420	NM_001080979	21679	Mm.14774	NM_011567	ENSMUSG00000030353	Tead4	ETFR-2|Etfr2|FR-19|Rtef1|TEAD-4|TEF-3|Tcf13r1|Tef3|Tefr|Tefr1|Tefr1a	TEA domain family member 4	protein-coding
mm_163297.1	chr11	120041734	120041744	-	1	NA	promoter-TSS (NM_001198787)	promoter-TSS (NM_001198787)	42	NM_001198787	11302	Mm.6826	NM_007377	ENSMUSG00000025375	Aatk	AATYK|aatyk1|mKIAA0641	apoptosis-associated tyrosine kinase	protein-coding
mm_31575.1	chr4	57645494	57645497	+	1	NA	intron (NM_001304544, intron 2 of 8)	intron (NM_001304544, intron 2 of 8)	77247	NM_172868	242481	Mm.331630	NM_172868	ENSMUSG00000090053	Palm2	53-H12|B130066I24|R75368|pEN70	paralemmin 2	protein-coding
mm_17669.1	chr2	32087450	32087470	-	1	NA	Intergenic	Intergenic	-3755	NM_175511	241303	Mm.250441	NM_175511	ENSMUSG00000050592	Fam78a	A130092J06Rik	family with sequence similarity 78, member A	protein-coding
mm_76374.1	chr8	84815625	84815634	-	1	NA	non-coding (NR_033145, exon 2 of 2)	non-coding (NR_033145, exon 2 of 2)	7194	NM_201227	23863	Mm.304252	NM_201227	ENSMUSG00000053226	Dand5	Cerl-2|Cerr2|Dte|GREM3|coco	DAN domain family member 5, BMP antagonist	protein-coding
mm_32733.1	chr4	116593443	116593490	+	1	NA	3' UTR (NM_029868, exon 12 of 12)	3' UTR (NM_029868, exon 12 of 12)	-3264	NM_001037916	622665	Mm.388905	NM_001037916	ENSMUSG00000034035	Ccdc17	-	coiled-coil domain containing 17	protein-coding
mm_83363.1	chr9	44417984	44418026	-	1	NA	promoter-TSS (NM_201372)	promoter-TSS (NM_201372)	2	NM_201372	382073	Mm.259573	NM_201372	ENSMUSG00000043923	Ccdc84	D630044F24Rik|Gm1114	coiled-coil domain containing 84	protein-coding
mm_58239.1	chr6	145047637	145047660	-	1	NA	intron (NM_007532, intron 1 of 10)	intron (NM_007532, intron 1 of 10)	1164	NM_001024468	12035	Mm.4606	NM_007532	ENSMUSG00000030268	Bcat1	BCATc|Eca39	branched chain aminotransferase 1, cytosolic	protein-coding
mm_23125.1	chr3	37654478	37654505	+	1	NA	Intergenic	Intergenic	14544	NM_001305442	24063	Mm.330986	NM_011896	ENSMUSG00000037211	Spry1	sprouty1|spry-1	sprouty homolog 1 (Drosophila)	protein-coding
mm_127656.1	chr15	102498679	102498689	+	1	NA	3' UTR (NM_001163643, exon 16 of 16)	3' UTR (NM_001163643, exon 16 of 16)	18320	NM_001163643	26404	Mm.172897	NM_009582	ENSMUSG00000023050	Map3k12	DLK|MUK|Zpk	mitogen-activated protein kinase kinase kinase 12	protein-coding
mm_104062.1	chr11	86584684	86584698	-	1	NA	promoter-TSS (NR_029738)	promoter-TSS (NR_029738)	-533	NR_029738	387140		NR_029738	ENSMUSG00000065455	Mir21a	Mir21|Mirn21|mmu-mir-21|mmu-mir-21a	microRNA 21a	ncRNA
mm_76400.1	chr8	84844901	84844968	-	1	NA	exon (NM_007591, exon 4 of 9)	exon (NM_007591, exon 4 of 9)	1997	NM_007591	12317	Mm.1971	NM_007591	ENSMUSG00000003814	Calr	CRT|Calregulin	calreticulin	protein-coding
mm_61573.1	chr7	79770519	79770523	+	1	NA	intron (NM_001037927, intron 10 of 17)	intron (NM_001037927, intron 10 of 17)	23069	NM_008588	17292	Mm.1404	NM_008588	ENSMUSG00000030544	Mesp1	bHLHc5	mesoderm posterior 1	protein-coding
mm_16401.1	chr2	179977442	179977445	+	1	NA	promoter-TSS (NM_001081092)	promoter-TSS (NM_001081092)	590	NR_033782	66730	Mm.31773	NR_033782	ENSMUSG00000085704	4921531C22Rik	-	RIKEN cDNA 4921531C22 gene	ncRNA
mm_53106.1	chr6	125071293	125071305	+	1	NA	promoter-TSS (NM_001163268)	promoter-TSS (NM_001163268)	22	NM_001163268	381810	Mm.333386	NM_001163268	ENSMUSG00000067714	Lpar5	GPR93|Gm1072|Gpr92|LPA5	lysophosphatidic acid receptor 5	protein-coding
mm_289.1	chr1	21368236	21368256	+	1	NA	promoter-TSS (NM_001033904)	promoter-TSS (NM_001033904)	-85	NM_001033904	433278	Mm.26006	NM_001033904	ENSMUSG00000041722	Khdc1c	Khdc1b	KH domain containing 1C	protein-coding
mm_5049.1	chr1	194749483	194749499	+	1	NA	intron (NM_008882, intron 6 of 31)	intron (NM_008882, intron 6 of 31)	129662	NM_008882	18845	Mm.2251	NM_008882	ENSMUSG00000026640	Plxna2	2810428A13Rik|AA589422|AW457381|OCT|PlexA2|Plxn2|mKIAA0463	plexin A2	protein-coding
mm_6273.1	chr1	69667773	69667777	-	1	NA	intron (NM_011770, intron 3 of 7)	intron (NM_011770, intron 3 of 7)	18185	NM_011770	22779	Mm.106343	NM_011770	ENSMUSG00000025997	Ikzf2	A730095J18Rik|Helios|Zfpn1a2|Znfn1a2	IKAROS family zinc finger 2	protein-coding
mm_116575.1	chr13	47105375	47105377	-	1	NA	intron (NM_025900, intron 2 of 10)	intron (NM_025900, intron 2 of 10)	845	NM_025900	110052	Mm.131150	NM_025900	ENSMUSG00000021377	Dek	1810019E15Rik|D13H6S231E	DEK oncogene (DNA binding)	protein-coding
mm_7775.1	chr1	131273476	131273486	-	1	NA	exon (NM_019777, exon 7 of 22)	exon (NM_019777, exon 7 of 22)	6082	NM_019777	56489	Mm.386783	NM_019777	ENSMUSG00000042349	Ikbke	AW558201|IKK-i|IKKepsilon|Ikki	inhibitor of kappaB kinase epsilon	protein-coding
mm_4128.1	chr1	170308803	170308828	+	1	NA	promoter-TSS (NM_001039593)	promoter-TSS (NM_001039593)	-46	NM_001039593	76925	Mm.33631	NM_001039593	ENSMUSG00000042800	1700015E13Rik	-	RIKEN cDNA 1700015E13 gene	protein-coding
mm_136432.1	chr16	94370648	94370694	-	1	NA	promoter-TSS (NM_001159620)	promoter-TSS (NM_001159620)	39	NM_001159616	56176	Mm.474449	NM_019543	ENSMUSG00000022940	Pigp	Dcrc|Dscr5	phosphatidylinositol glycan anchor biosynthesis, class P	protein-coding
mm_16047.1	chr2	167744288	167744312	+	1	NA	Intergenic	Intergenic	53123	NR_015500	329562	Mm.123101	NM_177851	ENSMUSG00000006462	A530013C23Rik	-	RIKEN cDNA A530013C23 gene	ncRNA
mm_167547.1	chr9	29771504	29771504	+	1	NA	intron (NM_172290, intron 1 of 7)	intron (NM_172290, intron 1 of 7)	191625	NM_172290	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding
mm_112071.1	chr12	112511137	112511201	-	1	NA	promoter-TSS (NM_178915)	promoter-TSS (NM_178915)	-9	NM_178915	104885	Mm.37751	NM_178915	ENSMUSG00000054013	Tmem179	AI839735	transmembrane protein 179	protein-coding
mm_29501.1	chr3	116007400	116007411	-	1	NA	promoter-TSS (NM_021388)	promoter-TSS (NM_021388)	1	NM_023214	66500	Mm.34550	NM_023214	ENSMUSG00000054414	Slc30a7	1810059J10Rik|2610034N15Rik|4833428C12Rik|AI467242|ZnT-7|ZnT7|Zntl2	solute carrier family 30 (zinc transporter), member 7	protein-coding
mm_42759.1	chr5	121191485	121191523	+	1	NA	promoter-TSS (NM_001109992)	promoter-TSS (NM_001109992)	-107	NM_011202	19247	Mm.8681	NM_011202	ENSMUSG00000043733	Ptpn11	2700084A17Rik|AW536184|PTP1D|PTP2C|SAP-2|SH-PTP2|SH-PTP3|SHP-2|Shp2|Syp	protein tyrosine phosphatase, non-receptor type 11	protein-coding
mm_101202.1	chr11	19018915	19018941	-	1	NA	promoter-TSS (NM_010789)	promoter-TSS (NM_010789)	41	NM_001193271	17268	Mm.356578	NM_010789	ENSMUSG00000020160	Meis1	C530044H18Rik|Evi8	Meis homeobox 1	protein-coding
mm_38918.1	chr4	150001351	150001360	-	1	NA	intron (NM_173371, intron 1 of 4)	intron (NM_173371, intron 1 of 4)	1881	NM_001291004	100198	Mm.22183	NM_173371	ENSMUSG00000028980	H6pd	AI785303|G6pd1|Gpd-1|Gpd1	hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase)	protein-coding
mm_129367.1	chr15	77991983	77992006	-	1	NA	Intergenic	Intergenic	-21170	NM_018749	55944	Mm.3955	NM_018749	ENSMUSG00000016554	Eif3d	66/67kDa|AA407891|Eif3s7|eIF3p66	eukaryotic translation initiation factor 3, subunit D	protein-coding
mm_33764.1	chr4	134397307	134397326	+	1	NA	promoter-TSS (NM_001285872)	promoter-TSS (NM_001285872)	-155	NM_001285872	100163	Mm.22116	NM_133880	ENSMUSG00000037366	Pafah2	2310074E22Rik|AI507170	platelet-activating factor acetylhydrolase 2	protein-coding
mm_47541.1	chr5	124249911	124249929	-	1	NA	promoter-TSS (NM_011256)	promoter-TSS (NM_011256)	-160	NM_011256	19679	Mm.44261	NM_011256	ENSMUSG00000029406	Pitpnm2	NIR3|RDGBA2|Rdgb2|mKIAA1457	phosphatidylinositol transfer protein, membrane-associated 2	protein-coding
mm_43892.1	chr5	144100354	144100383	+	1	NA	promoter-TSS (NM_001081109)	promoter-TSS (NM_001081109)	-68	NM_001081109	231876	Mm.288726	NM_001081109	ENSMUSG00000038970	Lmtk2	2900041G10Rik|A330101P12Rik|BREK|KPI-2|KPI2|aatyk2|cprk	lemur tyrosine kinase 2	protein-coding
mm_52171.1	chr6	99095774	99095782	+	1	NA	intron (NM_001347345, intron 5 of 19)	intron (NM_001347345, intron 5 of 19)	-67480	NM_001197322	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_40363.1	chr5	48372340	48372362	+	1	NA	promoter-TSS (NM_025755)	promoter-TSS (NM_025755)	-41	NM_025755	66768	Mm.29409	NM_025755	ENSMUSG00000029089	Pacrgl	4933428G09Rik	PARK2 co-regulated-like	protein-coding
mm_4237.1	chr1	171383515	171383520	+	1	NA	intron (NM_001122680, intron 3 of 7)	intron (NM_001122680, intron 3 of 7)	-5443	NM_001005508	226652	Mm.251048	NM_001005508	ENSMUSG00000048865	Arhgap30	6030405P05Rik|Gm102|mFLJ00267	Rho GTPase activating protein 30	protein-coding
mm_8568.1	chr1	155417395	155417435	-	1	NA	promoter-TSS (NM_011273)	promoter-TSS (NM_011273)	29	NM_011273	19775	Mm.266215	NM_011273	ENSMUSG00000026469	Xpr1	Rmc-1|Rmc1|Sxv|Syg1|XR	xenotropic and polytropic retrovirus receptor 1	protein-coding
mm_34576.1	chr4	150087647	150087669	+	1	NA	5' UTR (NM_177366, exon 1 of 4)	5' UTR (NM_177366, exon 1 of 4)	155	NM_177366	269604	Mm.219307	NM_177366	ENSMUSG00000047875	Gpr157	F730108M23Rik	G protein-coupled receptor 157	protein-coding
mm_13156.1	chr2	92541136	92541165	+	1	NA	Intergenic	Intergenic	-51056	NR_106080	102466819		NR_106080	ENSMUSG00000099223	Mir7221	Gm27378|mmu-mir-7221	microRNA 7221	ncRNA
mm_72857.1	chr8	88428779	88428790	+	1	NA	Intergenic	Intergenic	-66593	NM_012047	26992	Mm.5400	NM_012047	ENSMUSG00000031660	Brd7	BP75|CELTIX1|Ptpn13ip	bromodomain containing 7	protein-coding
mm_61849.1	chr7	88297186	88297197	+	1	NA	exon (NM_009982, exon 3 of 7)	exon (NM_009982, exon 3 of 7)	19106	NM_001311790	13032	Mm.89295	NM_009982	ENSMUSG00000030560	Ctsc	AI047818|CatC|DPP1|DPPI	cathepsin C	protein-coding
mm_82833.1	chr9	31150116	31150139	-	1	NA	3' UTR (NM_009691, exon 16 of 16)	3' UTR (NM_009691, exon 16 of 16)	-18328	NM_011176	19143	Mm.243926	NM_011176	ENSMUSG00000031995	St14	Epithin|MT-SP1|Prss14|Tmprss14|mCAP3|matriptase	suppression of tumorigenicity 14 (colon carcinoma)	protein-coding
mm_12230.1	chr2	68565658	68565676	+	1	NA	Intergenic	RMER21B|LTR|ERV1	-16746	NM_177651	227998	Mm.67562	NM_177651	ENSMUSG00000053896	4933409G03Rik	-	RIKEN cDNA 4933409G03 gene	protein-coding
mm_99969.1	chr11	113687129	113687153	+	1	NA	intron (NM_177777, intron 1 of 4)	RMER10A|LTR|ERVL	2729	NM_177777	276852	Mm.239566	NM_177777	ENSMUSG00000041623	D11Wsu47e	-	DNA segment, Chr 11, Wayne State University 47, expressed	protein-coding
mm_110106.1	chr12	26415229	26415242	-	1	NA	promoter-TSS (NR_105856)	promoter-TSS (NR_105856)	27	NM_001081977	108089	Mm.214932	NM_080563	ENSMUSG00000020642	Rnf144a	Rnf144|UIP4|Ubce7ip4	ring finger protein 144A	protein-coding
mm_71449.1	chr8	46521601	46521605	+	1	NA	intron (NM_001302163, intron 11 of 20)	intron (NM_001302163, intron 11 of 20)	-30466	NM_027973	71876	Mm.22108	NM_027973	ENSMUSG00000031629	Cenpu	1700029A22Rik|Mlf1ip	centromere protein U	protein-coding
mm_24797.1	chr3	95547235	95547247	+	1	NA	intron (NM_001267695, intron 6 of 7)	B3|SINE|B2	-12436	NM_026489	67981	Mm.179050	NM_026489	ENSMUSG00000028109	Hormad1	4921522K05Rik|Nohma	HORMA domain containing 1	protein-coding
mm_23990.1	chr3	86263454	86263457	+	1	NA	intron (NM_001077687, intron 2 of 50)	intron (NM_001077687, intron 2 of 50)	38765	NM_001077687	80877	Mm.439825	NM_030695	ENSMUSG00000028080	Lrba	C80285|D3Ertd775e|Lab300|Lba	LPS-responsive beige-like anchor	protein-coding
mm_44533.1	chr5	24451703	24451746	-	1	NA	promoter-TSS (NM_001256431)	promoter-TSS (NM_001256431)	-453	NM_001256431	213990	Mm.250703	NM_139153	ENSMUSG00000023353	Agap3	AGAP-3|AV028425|Centg3|Crag|Crag.|MRIP-1|cnt-g3	ArfGAP with GTPase domain, ankyrin repeat and PH domain 3	protein-coding
mm_143960.1	chr17	87025354	87025403	-	1	NA	promoter-TSS (NM_008838)	promoter-TSS (NM_008838)	23	NM_008838	18701	Mm.219685	NM_008838	ENSMUSG00000024145	Pigf	-	phosphatidylinositol glycan anchor biosynthesis, class F	protein-coding
mm_47227.1	chr5	121374696	121374701	-	1	NA	intron (NM_172275, intron 8 of 11)	intron (NM_172275, intron 8 of 11)	10917	NM_001163470	231712	Mm.20488	NM_172275	ENSMUSG00000042726	Trafd1	1110008K06Rik|Fln29	TRAF type zinc finger domain containing 1	protein-coding
mm_100819.1	chr11	5177226	5177230	-	1	NA	Intergenic	Intergenic	-25006	NM_080595	140703	Mm.840	NM_080595	ENSMUSG00000034164	Emid1	AW122071|CO-5|Emu1	EMI domain containing 1	protein-coding
mm_157698.1	chrX	60446705	60446712	-	1	NA	intron (NM_001039240, intron 2 of 3)	intron (NM_001039240, intron 2 of 3)	9487	NM_001039240	631784	Mm.424878	NM_001039240	ENSMUSG00000079583	Gm7073	-	predicted gene 7073	protein-coding
mm_130141.1	chr15	90898513	90898522	-	1	NA	promoter-TSS (NR_033583)	promoter-TSS (NR_033583)	-41	NR_033583	20738	Mm.431547	NR_033583		Spn-ps	Cd43-ps	sialophorin, pseudogene	pseudo
mm_33676.1	chr4	133226544	133226546	+	1	NA	Intergenic	Intergenic	5736	NM_027152	69655	Mm.285685	NM_027152	ENSMUSG00000028865	Cd164l2	2310047N01Rik	CD164 sialomucin-like 2	protein-coding
mm_38912.1	chr4	149996361	149996383	-	1	NA	exon (NM_173371, exon 2 of 5)	exon (NM_173371, exon 2 of 5)	6864	NM_001291004	100198	Mm.22183	NM_173371	ENSMUSG00000028980	H6pd	AI785303|G6pd1|Gpd-1|Gpd1	hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase)	protein-coding
mm_49087.1	chr6	6867870	6867879	+	1	NA	TTS (NM_010057)	TTS (NM_010057)	1659	NR_015388	320038	Mm.94021	NR_015388		Dlx6os1	A230055N17Rik|Dlx6as1|Evf-1|Evf-2|Evf1|Evf1/2|Evf2|Shhrs|mEvf-1	distal-less homeobox 6, opposite strand 1	ncRNA
mm_6647.1	chr1	79671967	79671993	-	1	NA	promoter-TSS (NM_183027)	promoter-TSS (NM_183027)	-8	NM_183027	252903	Mm.32409	NM_183027	ENSMUSG00000054702	Ap1s3	1190009B22|Jr2|[s]3A	adaptor-related protein complex AP-1, sigma 3	protein-coding
mm_19539.1	chr2	94730693	94730710	-	1	NA	Intergenic	Intergenic	-292515	NM_001305258	11800	Mm.181824	NM_007466	ENSMUSG00000027193	Api5	AAC-11|AI196452|API-5	apoptosis inhibitor 5	protein-coding
mm_67765.1	chr7	92875093	92875133	-	1	NA	promoter-TSS (NM_028243)	promoter-TSS (NM_028243)	-140	NM_028243	72461	Mm.389969	NM_028243	ENSMUSG00000061119	Prcp	2510048K03Rik|2610104A14Rik|AI451719|HUMPCP|PCP	prolylcarboxypeptidase (angiotensinase C)	protein-coding
mm_119320.1	chr14	37054860	37054862	+	1	NA	promoter-TSS (NM_146245)	promoter-TSS (NM_146245)	31	NM_146245	239037	Mm.37907	NM_146245	ENSMUSG00000041044	Lrit1	BC032270|Lrrc21	leucine-rich repeat, immunoglobulin-like and transmembrane domains 1	protein-coding
mm_56598.1	chr6	108664986	108665005	-	1	NA	exon (NM_011498, exon 5 of 5)	exon (NM_011498, exon 5 of 5)	-4061	NR_104577	75394	Mm.395061	NR_040757	ENSMUSG00000087341	0610040F04Rik	-	RIKEN cDNA 0610040F04 gene	ncRNA
mm_107842.1	chr12	69297400	69297446	+	1	NA	intron (NM_027117, intron 1 of 12)	CpG	742	NM_027117	69554	Mm.234368	NM_027117	ENSMUSG00000020978	Klhdc2	2310022K15Rik|D12Ertd522e|HCLP-1|LCP	kelch domain containing 2	protein-coding
mm_62051.1	chr7	92447281	92447285	+	1	NA	3' UTR (NM_001243047, exon 11 of 11)	3' UTR (NM_001243047, exon 11 of 11)	-113866	NM_025515	66365	Mm.21173	NM_025515	ENSMUSG00000030613	Ccdc90b	2310015N07Rik|C86558	coiled-coil domain containing 90B	protein-coding
mm_70185.1	chr7	143775530	143775531	-	1	NA	Intergenic	ORR1A3|LTR|ERVL-MaLR	-8537	NM_203492	381974	Mm.297839	NM_203492	ENSMUSG00000050276	Mrgprg	Gm1098|Mrgg	MAS-related GPR, member G	protein-coding
mm_147970.1	chr18	67245601	67245690	-	1	NA	5' UTR (NM_172630, exon 1 of 11)	5' UTR (NM_172630, exon 1 of 11)	185	NM_172630	225651	Mm.235792	NM_172630	ENSMUSG00000062526	Mppe1	A530095G11	metallophosphoesterase 1	protein-coding
mm_23901.1	chr3	83031824	83031834	+	1	NA	exon (NM_010196, exon 5 of 5)	exon (NM_010196, exon 5 of 5)	5676	NM_001111048	14161	Mm.88793	NM_010196	ENSMUSG00000028001	Fga	ENSMUSG00000059807|Fib	fibrinogen alpha chain	protein-coding
mm_116838.1	chr13	54688100	54688145	-	1	NA	promoter-TSS (NM_001146025)	promoter-TSS (NM_001146025)	78	NM_001146027	105239	Mm.25366	NM_134064	ENSMUSG00000034928	Rnf44	AI854545|mKIAA1100	ring finger protein 44	protein-coding
mm_101384.1	chr11	23846515	23846531	-	1	NA	Intergenic	Intergenic	48747	NM_172555	216578	Mm.470599	NM_172555	ENSMUSG00000020273	Papolg	9630006B20Rik	poly(A) polymerase gamma	protein-coding
mm_24280.1	chr3	89226175	89226196	+	1	NA	TTS (NR_030579)	TTS (NR_030579)	1013	NR_030579	100124470		NR_030579	ENSMUSG00000076255	Mir92b	Mirn92b|mir-92b|mmu-mir-92b	microRNA 92b	ncRNA
mm_113526.1	chr13	37826226	37826250	+	1	NA	promoter-TSS (NM_001177868)	promoter-TSS (NM_001177868)	200	NM_026830	68750	Mm.491109	NM_026830	ENSMUSG00000039087	Rreb1	1110037N09Rik|AA414966|B930013M22Rik	ras responsive element binding protein 1	protein-coding
mm_134201.1	chr16	11134498	11134512	-	1	NA	promoter-TSS (NM_029582)	promoter-TSS (NM_029582)	27	NM_029582	106200	Mm.291015	NM_029582	ENSMUSG00000022498	Txndc11	2810408E11Rik|AI427833|EFP1|Txdc11	thioredoxin domain containing 11	protein-coding
mm_32162.1	chr4	99983986	99984011	+	1	NA	exon (NM_028132, exon 10 of 11)	exon (NM_028132, exon 10 of 11)	54547	NM_028132	72157	Mm.217764	NM_028132	ENSMUSG00000025791	Pgm2	2610020G18Rik|AA407108|AI098105|Pgm-2|Pgm1	phosphoglucomutase 2	protein-coding
mm_143246.1	chr17	64311300	64311328	-	1	NA	exon (NM_001025309, exon 3 of 10)	exon (NM_001025309, exon 3 of 10)	20569	NM_144859	224938	Mm.489681	NM_144859	ENSMUSG00000024083	Pja2	AI447901|AL022700|Neurodap1|mKIAA0438	praja 2, RING-H2 motif containing	protein-coding
mm_23423.1	chr3	58692491	58692536	+	1	NA	promoter-TSS (NM_009174)	promoter-TSS (NM_009174)	-76	NR_045167	71301	Mm.254475	NR_045167	ENSMUSG00000097725	4930593A02Rik	4933440I01Rik	RIKEN cDNA 4930593A02 gene	ncRNA
mm_92136.1	chr10	66698152	66698167	-	1	NA	Intergenic	Intergenic	222225	NR_138560	68488	Mm.338835	NR_138560		1110002J07Rik	-	RIKEN cDNA 1110002J07 gene	ncRNA
mm_166158.1	chr5	15934675	15934679	+	1	NA	promoter-TSS (NM_001110843)	promoter-TSS (NM_001110843)	-14	NM_001110843	12293	Mm.159842	NM_009784	ENSMUSG00000040118	Cacna2d1	Ca(v)alpha2delta1|Cacna2|Cchl2a	calcium channel, voltage-dependent, alpha2/delta subunit 1	protein-coding
mm_7372.1	chr1	106759694	106759725	-	1	NA	promoter-TSS (NM_027534)	promoter-TSS (NM_027534)	33	NM_027534	70750	Mm.458911	NM_027534	ENSMUSG00000009905	Kdsr	6330410P18Rik|9430079B08Rik|Fvt1	3-ketodihydrosphingosine reductase	protein-coding
mm_128014.1	chr15	19366004	19366008	-	1	NA	Intergenic	ERVB4_1B-LTR_MM|LTR|ERVK	545677	NM_009865	320873	Mm.117794	NM_009865	ENSMUSG00000022321	Cdh10	A830016G23Rik|C030003B10Rik|C030011H18Rik	cadherin 10	protein-coding
mm_103172.1	chr11	70459750	70459767	-	1	NA	5' UTR (NM_001029929, exon 1 of 14)	5' UTR (NM_001029929, exon 1 of 14)	136	NM_001029929	574428	Mm.472771	NM_001029929	ENSMUSG00000040829	Zmynd15	-	zinc finger, MYND-type containing 15	protein-coding
mm_119380.1	chr14	41134407	41134413	+	1	NA	exon (NM_023134, exon 6 of 6)	exon (NM_023134, exon 6 of 6)	2622	NM_023134	20387	Mm.46062	NM_023134	ENSMUSG00000021789	Sftpa1	SP-A|Sftp-1|Sftp1	surfactant associated protein A1	protein-coding
mm_137688.1	chr17	28872604	28872608	+	1	NA	intron (NM_001034885, intron 1 of 9)	MTE2b|LTR|ERVL-MaLR	14195	NM_001034885	433091	Mm.328925	NM_001034885	ENSMUSG00000043286	Pnpla1	-	patatin-like phospholipase domain containing 1	protein-coding
mm_16657.1	chr2	6592802	6592831	-	1	NA	intron (NM_001347094, intron 8 of 12)	intron (NM_001347094, intron 8 of 12)	128846	NM_001310447	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_62573.1	chr7	104291837	104291843	+	1	NA	Intergenic	RMER19B2|LTR|ERVK	-3734	NM_001310602	667823	Mm.482375	NM_001310602	ENSMUSG00000060441	Trim5	EG667823|Gm8833	tripartite motif-containing 5	protein-coding
mm_56126.1	chr6	87533220	87533264	-	1	NA	promoter-TSS (NM_001286610)	promoter-TSS (NM_001286610)	17	NM_001037727	232201	Mm.119564	NM_175476	ENSMUSG00000030047	Arhgap25	A130039I20Rik	Rho GTPase activating protein 25	protein-coding
mm_29880.1	chr3	131111767	131111776	-	1	NA	intron (NM_010703, intron 1 of 11)	CpG	-1020	NM_001276403	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_130664.1	chr15	100669497	100669511	-	1	NA	promoter-TSS (NM_001270537)	promoter-TSS (NM_001270537)	-4	NM_001270537	668218	Mm.451225	NM_001270537	ENSMUSG00000098112	Bin2	-	bridging integrator 2	protein-coding
mm_118550.1	chr14	17659808	17659818	+	1	NA	Intergenic	Intergenic	-1147	NM_001113417	21834	Mm.32563	NM_009380	ENSMUSG00000021779	Thrb	Nr1a2|T3R[b]|T3Rbeta|Thrb1|Thrb2|c-erbAbeta	thyroid hormone receptor beta	protein-coding
mm_113728.1	chr13	43948838	43948840	+	1	NA	Intergenic	Intergenic	163727	NM_001289915	12522	Mm.57175	NM_009856	ENSMUSG00000015396	Cd83	-	CD83 antigen	protein-coding
mm_162042.1	chr19	59038285	59038285	-	1	NA	exon (NM_001114312, exon 5 of 17)	exon (NM_001114312, exon 5 of 17)	37784	NM_175172	71653	Mm.37338	NM_175172	ENSMUSG00000041362	Shtn1	4930506M07Rik|Kiaa1598|Shootin1|mKIAA1598	shootin 1	protein-coding
mm_5238.1	chr1	16093287	16093341	-	1	NA	promoter-TSS (NM_001243238)	promoter-TSS (NM_001243238)	11	NM_001305227	75799	Mm.78557	NM_001243238	ENSMUSG00000067795	4930444P10Rik	-	RIKEN cDNA 4930444P10 gene	protein-coding
mm_96933.1	chr11	70519620	70519640	+	1	NA	intron (NM_146020, intron 1 of 2)	intron (NM_146020, intron 1 of 2)	421	NM_146020	216871	Mm.22551	NM_146020	ENSMUSG00000046811	Gltpd2	C730027E14Rik	glycolipid transfer protein domain containing 2	protein-coding
mm_62829.1	chr7	113514165	113514169	+	1	NA	intron (NM_001285831, intron 1 of 12)	L1M4b|LINE|L1	333	NM_027379	67420	Mm.206919	NM_026143	ENSMUSG00000030759	Far1	2600011M19Rik|2900034E22Rik|3732409C05Rik|AI850429|Mlstd2	fatty acyl CoA reductase 1	protein-coding
mm_153793.1	chr19	45998450	45998478	-	1	NA	promoter-TSS (NM_198296)	promoter-TSS (NM_198296)	24	NM_198296	71617	Mm.210949	NM_198296	ENSMUSG00000039901	9130011E15Rik	AI431055|AW050122	RIKEN cDNA 9130011E15 gene	protein-coding
mm_29890.1	chr3	131272010	131272073	-	1	NA	promoter-TSS (NM_008212)	promoter-TSS (NM_008212)	60	NM_008212	15107	Mm.260164	NM_008212	ENSMUSG00000027984	Hadh	AA409008|AU019341|AW742602|HCDH|Hadhsc|Schad	hydroxyacyl-Coenzyme A dehydrogenase	protein-coding
mm_118004.1	chr13	100553168	100553210	-	1	NA	promoter-TSS (NM_008756)	promoter-TSS (NM_008756)	-691	NM_008756	18260	Mm.4807	NM_008756	ENSMUSG00000021638	Ocln	AI503564|Ocl	occludin	protein-coding
mm_1583.1	chr1	74293957	74293983	+	1	NA	exon (NM_027154, exon 3 of 12)	exon (NM_027154, exon 3 of 12)	8936	NM_001039509	56695	Mm.384726	NM_019999	ENSMUSG00000026179	Pnkd	2210013N15Rik|2810403H05Rik|AI854243|Brp17|MNCb-5687|MR-1|Tahccp2	paroxysmal nonkinesiogenic dyskinesia	protein-coding
mm_105040.1	chr11	100584747	100584780	-	1	NA	intron (NM_019795, intron 10 of 13)	intron (NM_019795, intron 10 of 13)	8872	NM_001146318	12799	Mm.15711	NM_009923	ENSMUSG00000006782	Cnp	CNPase|Cnp-1|Cnp1	2',3'-cyclic nucleotide 3' phosphodiesterase	protein-coding
mm_10515.1	chr2	16356626	16356670	+	1	NA	5' UTR (NM_026162, exon 1 of 14)	5' UTR (NM_026162, exon 1 of 14)	344	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding
mm_77497.1	chr8	122596177	122596192	-	1	NA	intron (NM_001193645, intron 8 of 11)	intron (NM_001193645, intron 8 of 11)	15303	NM_001193645	50917	Mm.1786	NM_016722	ENSMUSG00000015027	Galns	mFLJ00319	galactosamine (N-acetyl)-6-sulfate sulfatase	protein-coding
mm_2773.1	chr1	130732095	130732101	+	1	NA	5' UTR (NM_177604, exon 1 of 4)	5' UTR (NM_177604, exon 1 of 4)	122	NM_177604	212439	Mm.268547	NM_177604	ENSMUSG00000042510	AA986860	E030025M07|Sarg	expressed sequence AA986860	protein-coding
mm_38393.1	chr4	138819285	138819296	-	1	NA	promoter-TSS (NM_011110)	promoter-TSS (NM_011110)	-33	NM_011110	18784	Mm.486532	NM_011110	ENSMUSG00000041193	Pla2g5	PLA2|sPLA2	phospholipase A2, group V	protein-coding
mm_169447.1	chr14	58253037	58253049	-	1	NA	Intergenic	L1Md_A|LINE|L1	180357	NM_013518	14180	Mm.8846	NM_013518	ENSMUSG00000021974	Fgf9	Eks	fibroblast growth factor 9	protein-coding
mm_103810.1	chr11	83002221	83002236	-	1	NA	TTS (NM_001167743)	TTS (NM_001167743)	-10398	NM_172796	237886	Mm.270253	NM_172796	ENSMUSG00000069793	Slfn9	9830137M10Rik	schlafen 9	protein-coding
mm_91204.1	chr10	21161371	21161385	-	1	NA	promoter-TSS (NM_001198914)	promoter-TSS (NM_001198914)	-394	NM_010848	17863	Mm.52109	NM_010848	ENSMUSG00000019982	Myb	AI550390|M16449|c-myb	myeloblastosis oncogene	protein-coding
mm_42966.1	chr5	123135834	123135855	+	1	NA	Intergenic	Intergenic	-3215	NM_175092	23912	Mm.253876	NM_175092	ENSMUSG00000029449	Rhof	AI845056|AV026554|Arhf|Ifld1|Rif	ras homolog family member F (in filopodia)	protein-coding
mm_122936.1	chr14	54963149	54963158	-	1	NA	intron (NM_001164171, intron 6 of 38)	intron (NM_001164171, intron 6 of 38)	3454	NM_001164171	17888	Mm.290003	NM_010856	ENSMUSG00000040752	Myh6	A830009F23Rik|AA517445|Myhc-a|Myhca|alpha-MHC	myosin, heavy polypeptide 6, cardiac muscle, alpha	protein-coding
mm_144188.1	chr18	7869160	7869209	+	1	NA	promoter-TSS (NM_001146298)	promoter-TSS (NM_001146298)	-13	NM_001146298	225131	Mm.204524	NM_153085	ENSMUSG00000024283	Wac	1110067P07Rik|A230035H12Rik|AI256735|AI256776|Wwp4	WW domain containing adaptor with coiled-coil	protein-coding
mm_66347.1	chr7	43505927	43505944	-	1	NA	promoter-TSS (NM_028737)	promoter-TSS (NM_028737)	3	NM_028737	74054	Mm.195732	NM_028737	ENSMUSG00000013353	4931406B18Rik	4930538L19Rik	RIKEN cDNA 4931406B18 gene	protein-coding
mm_126767.1	chr15	86004299	86004338	+	1	NA	intron (NM_009886, intron 1 of 34)	intron (NM_009886, intron 1 of 34)	29459	NM_009886	12614	Mm.22680	NM_009886	ENSMUSG00000016028	Celsr1	Adgrc1|Crsh|Scy|crash	cadherin, EGF LAG seven-pass G-type receptor 1	protein-coding
mm_98360.1	chr11	93886230	93886234	+	1	NA	promoter-TSS (NM_134012)	promoter-TSS (NM_134012)	13	NM_134012	103537	Mm.210334	NM_134012	ENSMUSG00000059474	Mbtd1	AA408199|AI194990|hemp	mbt domain containing 1	protein-coding
mm_139079.1	chr17	46680981	46681011	+	1	NA	promoter-TSS (NM_010787)	promoter-TSS (NM_010787)	10	NM_001277309	17256	Mm.329083	NM_010787	ENSMUSG00000002768	Mea1	Mea-1	male enhanced antigen 1	protein-coding
mm_24108.1	chr3	88142537	88142545	+	1	NA	5' UTR (NM_001310593, exon 1 of 11)	5' UTR (NM_001310593, exon 1 of 11)	169	NM_001310593	17261	Mm.28184	NM_133665	ENSMUSG00000001419	Mef2d	C80750	myocyte enhancer factor 2D	protein-coding
mm_142877.1	chr17	51825223	51825233	-	1	NA	intron (NM_001163632, intron 1 of 10)	intron (NM_001163632, intron 1 of 10)	1360	NM_001163631	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_76394.1	chr8	84844411	84844419	-	1	NA	exon (NM_007591, exon 6 of 9)	exon (NM_007591, exon 6 of 9)	2516	NM_007591	12317	Mm.1971	NM_007591	ENSMUSG00000003814	Calr	CRT|Calregulin	calreticulin	protein-coding
mm_133539.1	chr16	91064000	91064026	+	1	NA	intron (NM_028905, intron 1 of 2)	RMER5|LTR|ERV1	5132	NM_001163695	74387	Mm.236220	NM_028905	ENSMUSG00000039851	4932438H23Rik	4931406G06Rik|AI550392	RIKEN cDNA 4932438H23 gene	protein-coding
mm_124332.1	chr14	103843711	103843715	-	1	NA	promoter-TSS (NM_001276296)	promoter-TSS (NM_001276296)	-12	NM_001276296	13618	Mm.229532	NM_007904	ENSMUSG00000022122	Ednrb	ET-B|ET-BR|ETR-b|ETb|Sox10m1	endothelin receptor type B	protein-coding
mm_18913.1	chr2	76736201	76736217	-	1	NA	exon (NM_011652, exon 275 of 313)	exon (NM_011652, exon 275 of 313)	60894	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_144032.1	chr17	90037286	90037300	-	1	NA	exon (NM_001347419, exon 3 of 3)	exon (NM_001347419, exon 3 of 3)	51075	NM_001346962	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_14991.1	chr2	152293832	152293861	+	1	NA	promoter-TSS (NM_024196)	promoter-TSS (NM_024196)	-26	NM_024196	67231	Mm.288733	NM_024196	ENSMUSG00000027465	Tbc1d20	1110028I04Rik|2810442O16Rik|AI414693|bs	TBC1 domain family, member 20	protein-coding
mm_16253.1	chr2	173159201	173159205	+	1	NA	TTS (NM_011044)	TTS (NM_011044)	6130	NM_011044	18534	Mm.266867	NM_011044	ENSMUSG00000027513	Pck1	AI265463|PEPCK|Pck-1	phosphoenolpyruvate carboxykinase 1, cytosolic	protein-coding
mm_106212.1	chr11	116852159	116852192	-	1	NA	exon (NM_011358, exon 2 of 3)	exon (NM_011358, exon 2 of 3)	919	NM_011358	20382	Mm.21841	NM_011358	ENSMUSG00000034120	Srsf2	D11Wsu175e|MRF-1|Pr264|SC35|Sfrs10|Sfrs2	serine/arginine-rich splicing factor 2	protein-coding
mm_60739.1	chr7	45444460	45444473	+	1	NA	intron (NM_030678, intron 8 of 15)	intron (NM_030678, intron 8 of 15)	9627	NM_030678	14936	Mm.275654	NM_030678	ENSMUSG00000003865	Gys1	Gys3|MGS	glycogen synthase 1, muscle	protein-coding
mm_119803.1	chr14	54218975	54218985	+	1	NA	Intergenic	Intergenic	34949	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_158747.1	chrX	164961092	164961098	-	1	NA	intron (NM_029730, intron 5 of 14)	U2|snRNA|snRNA	19280	NM_001290523	76763	Mm.291758	NM_029730	ENSMUSG00000061778	Mospd2	2410013I23Rik	motile sperm domain containing 2	protein-coding
mm_73226.1	chr8	103603773	103603786	+	1	NA	promoter-TSS (NR_045730)	promoter-TSS (NR_045730)	-20	NR_045730	71058	Mm.67707	NR_045730	ENSMUSG00000110336	4933400L20Rik	-	RIKEN cDNA 4933400L20 gene	ncRNA
mm_162901.1	chr10	115556868	115556874	+	1	NA	intron (NM_010195, intron 1 of 17)	intron (NM_010195, intron 1 of 17)	-13115	NM_029982	77798	Mm.446685	NM_029982	ENSMUSG00000092210	A930009A15Rik	-	RIKEN cDNA A930009A15 gene	protein-coding
mm_114218.1	chr13	56426583	56426593	+	1	NA	Intergenic	Intergenic	-11767	NM_177809	328258	Mm.482177	NM_177809	ENSMUSG00000021509	Slc25a48	AU042651|E230025K15	solute carrier family 25, member 48	protein-coding
mm_74045.1	chr8	122015198	122015217	+	1	NA	intron (NM_016812, intron 11 of 13)	intron (NM_016812, intron 11 of 13)	37183	NR_106096	102466915		NR_106096	ENSMUSG00000099140	Mir7237	Gm27482|mmu-mir-7237	microRNA 7237	ncRNA
mm_111429.1	chr12	91745955	91745977	-	1	NA	intron (NM_175367, intron 1 of 6)	intron (NM_175367, intron 1 of 6)	40470	NM_175367	108800	Mm.23125	NM_175367	ENSMUSG00000020961	Ston2	4933401N24Rik|AI425999|AW544599	stonin 2	protein-coding
mm_55090.1	chr6	49245541	49245574	-	1	NA	exon (NM_198102, exon 6 of 8)	exon (NM_198102, exon 6 of 8)	18495	NM_001347209	101214	Mm.196598	NM_198102	ENSMUSG00000029817	Tra2a	1500010G04Rik|AL022798|G430041M01Rik|mAWMS1	transformer 2 alpha homolog (Drosophila)	protein-coding
mm_84092.1	chr9	58239598	58239601	-	1	NA	intron (NM_001311088, intron 2 of 8)	intron (NM_001311088, intron 2 of 8)	10187	NM_178087	18854	Mm.392123	NM_008884	ENSMUSG00000036986	Pml	1200009E24Rik|AI661194|Trim19	promyelocytic leukemia	protein-coding
mm_113277.1	chr13	30003373	30003383	+	1	NA	Intergenic	Intergenic	-17315	NM_010093	13557	Mm.268356	NM_010093	ENSMUSG00000016477	E2f3	E2F3b|E2f3a	E2F transcription factor 3	protein-coding
mm_14385.1	chr2	129636199	129636212	+	1	NA	Intergenic	Lx9|LINE|L1	43036	NM_001291022	19261	Mm.1682	NM_007547	ENSMUSG00000037902	Sirpa	AI835480|Bit|CD172a|P84|Ptpns1|SHP-1|SHPS-1|SIRP	signal-regulatory protein alpha	protein-coding
mm_56440.1	chr6	97459263	97459278	-	1	NA	promoter-TSS (NM_001346639)	promoter-TSS (NM_001346639)	16	NM_001346639	232288	Mm.27789	NM_145148	ENSMUSG00000030064	Frmd4b	6030440G05Rik|C87375|GOBLIN|GRSP1|R74720	FERM domain containing 4B	protein-coding
mm_138289.1	chr17	34627645	34627677	+	1	NA	promoter-TSS (NM_019441)	promoter-TSS (NM_019441)	-226	NM_001302396	54397	Mm.373627	NM_019441	ENSMUSG00000015474	Ppt2	0610007M19Rik|AA672937	palmitoyl-protein thioesterase 2	protein-coding
mm_52581.1	chr6	116650624	116650628	+	1	NA	promoter-TSS (NM_001166580)	promoter-TSS (NM_001166580)	-58	NM_145980	213393	Mm.38231	NM_145980	ENSMUSG00000048489	8430408G22Rik	Depp|Fseg	RIKEN cDNA 8430408G22 gene	protein-coding
mm_96936.1	chr11	70525955	70525975	+	1	NA	intron (NM_008946, intron 2 of 5)	intron (NM_008946, intron 2 of 5)	608	NM_008946	19175	Mm.98	NM_008946	ENSMUSG00000018286	Psmb6	Lmp19|Mpnd	proteasome (prosome, macropain) subunit, beta type 6	protein-coding
mm_44294.1	chr5	8424206	8424238	-	1	NA	intron (NM_001289595, intron 1 of 10)	intron (NM_001289595, intron 1 of 10)	1384	NM_178766	319653	Mm.146262	NM_178766	ENSMUSG00000054099	Slc25a40	B230315F11Rik	solute carrier family 25, member 40	protein-coding
mm_115077.1	chr13	102036208	102036214	+	1	NA	Intergenic	Intergenic	-267994	NM_001077495	18708	Mm.259333	NM_001024955	ENSMUSG00000041417	Pik3r1	PI3K|p50alpha|p55alpha|p85alpha	phosphatidylinositol 3-kinase, regulatory subunit, polypeptide 1 (p85 alpha)	protein-coding
mm_3496.1	chr1	150106766	150106770	+	1	NA	3' UTR (NM_011198, exon 10 of 10)	3' UTR (NM_011198, exon 10 of 10)	6737	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_104229.1	chr11	88622806	88622809	-	1	NA	intron (NR_131025, intron 2 of 2)	intron (NR_131025, intron 2 of 2)	3556	NR_131025	68397	Mm.426889	NR_131025		0610039H22Rik	-	RIKEN cDNA 0610039H22 gene	ncRNA
mm_106778.1	chr12	4634621	4634643	+	1	NA	exon (NM_001198969, exon 12 of 17)	exon (NM_001198969, exon 12 of 17)	41624	NM_001198968	20403	Mm.341204	NM_011365	ENSMUSG00000020640	Itsn2	AI327390|Ese2|Sh3d1B|Sh3p18|mKIAA1256	intersectin 2	protein-coding
mm_97572.1	chr11	78940043	78940061	+	1	NA	exon (NM_010927, exon 10 of 27)	exon (NM_010927, exon 10 of 27)	14761	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_100079.1	chr11	115463799	115463811	+	1	NA	intron (NM_001080934, intron 1 of 3)	intron (NM_001080934, intron 1 of 3)	1332	NM_001080934	217316	Mm.25773	NM_001080934	ENSMUSG00000045775	Slc16a5	A130015N09Rik|MCT 5|MCT 6|MCT5	solute carrier family 16 (monocarboxylic acid transporters), member 5	protein-coding
mm_58624.1	chr7	5079355	5079374	+	1	NA	promoter-TSS (NM_001252454)	promoter-TSS (NM_001252454)	-871	NM_010147	13854	Mm.3091	NM_010147	ENSMUSG00000035203	Epn1	AA269831|Ibp1	epsin 1	protein-coding
mm_76755.1	chr8	95488701	95488707	-	1	NA	5' UTR (NM_009974, exon 1 of 12)	5' UTR (NM_009974, exon 1 of 12)	116	NM_009974	13000	Mm.51136	NM_009974	ENSMUSG00000046707	Csnk2a2	1110035J23Rik|C77789|CK2	casein kinase 2, alpha prime polypeptide	protein-coding
mm_48176.1	chr5	137307522	137307576	-	1	NA	5' UTR (NM_031405, exon 1 of 20)	5' UTR (NM_031405, exon 1 of 20)	125	NM_031405	83701	Mm.387734	NM_031405	ENSMUSG00000037364	Srrt	2810019G02Rik|ASR2A|ASR2B|ASR2C|ASR2D|Ars2|Asr2	serrate RNA effector molecule homolog (Arabidopsis)	protein-coding
mm_142891.1	chr17	51833114	51833138	-	1	NA	promoter-TSS (NM_009122)	promoter-TSS (NM_009122)	164	NM_001163632	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_31483.1	chr4	52450857	52450866	+	1	NA	exon (NM_008017, exon 8 of 25)	exon (NM_008017, exon 8 of 25)	11640	NM_001301412	14211	Mm.2999	NM_008017	ENSMUSG00000028312	Smc2	5730502P04Rik|AI255214|AW545314|CAP-E|CAPE|Fin16|SMC-2|Smc2l1	structural maintenance of chromosomes 2	protein-coding
mm_106718.1	chr12	3834894	3834900	+	1	NA	intron (NM_001271753, intron 1 of 22)	intron (NM_001271753, intron 1 of 22)	27347	NR_045884	100038522	Mm.417270	NR_045884	ENSMUSG00000073242	Dnmt3aos	ENSMUSG00000073242|Gm10485	DNA methyltransferase 3A, opposite strand	ncRNA
mm_41425.1	chr5	90892520	90892614	+	1	NA	3' UTR (NM_008176, exon 4 of 4)	3' UTR (NM_008176, exon 4 of 4)	1322	NM_008176	14825	Mm.21013	NM_008176	ENSMUSG00000029380	Cxcl1	Fsp|Gro1|KC|Mgsa|N51|Scyb1|gro	chemokine (C-X-C motif) ligand 1	protein-coding
mm_89811.1	chr10	103367693	103367747	+	1	NA	promoter-TSS (NM_175328)	promoter-TSS (NM_175328)	-88	NM_001252330	103098	Mm.458408	NM_175328	ENSMUSG00000019894	Slc6a15	AA536730|AI326450|AI326451|v7-3	solute carrier family 6 (neurotransmitter transporter), member 15	protein-coding
mm_86609.1	chr10	13964797	13964814	+	1	NA	Intergenic	CpG	-1574	NM_010437	15273	Mm.42157	NM_010437	ENSMUSG00000015501	Hivep2	Gm20114|MIBP1|Schnurri-2|Shn-2	human immunodeficiency virus type I enhancer binding protein 2	protein-coding
mm_38920.1	chr4	150001402	150001436	-	1	NA	intron (NM_173371, intron 1 of 4)	intron (NM_173371, intron 1 of 4)	1817	NM_001291004	100198	Mm.22183	NM_173371	ENSMUSG00000028980	H6pd	AI785303|G6pd1|Gpd-1|Gpd1	hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase)	protein-coding
mm_2804.1	chr1	130852130	130852138	+	1	NA	3' UTR (NM_011082, exon 11 of 11)	3' UTR (NM_011082, exon 11 of 11)	-13643	NM_026976	69169	Mm.46042	NM_026976	ENSMUSG00000042474	Fcmr	1810037B05Rik|Faim3|FcmuR|Toso	Fc fragment of IgM receptor	protein-coding
mm_167902.1	chrX	75416371	75416416	-	1	NA	promoter-TSS (NM_001166459)	promoter-TSS (NM_001166459)	191	NM_010839	105886298	Mm.16366	NM_010839	ENSMUSG00000090110	Cmc4	Mtcp1nb|p8MTCP1	C-x(9)-C motif containing 4	protein-coding
mm_99584.1	chr11	104289605	104289619	+	1	NA	intron (NM_001038609, intron 3 of 11)	intron (NM_001038609, intron 3 of 11)	58176	NM_001285454	17762	Mm.1287	NM_010838	ENSMUSG00000018411	Mapt	AI413597|AW045860|Mtapt|Tau	microtubule-associated protein tau	protein-coding
mm_150255.1	chr19	34192332	34192344	+	1	NA	promoter-TSS (NM_029682)	promoter-TSS (NM_029682)	68	NM_029682	76630	Mm.130952	NM_029682	ENSMUSG00000024776	Stambpl1	1700095N21Rik|8230401J17Rik|ALMalpha|AMSH-FP	STAM binding protein like 1	protein-coding
mm_77255.1	chr8	115706728	115706759	-	1	NA	exon (NM_001025577, exon 1 of 1)	exon (NM_001025577, exon 1 of 1)	151	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_69518.1	chr7	135528588	135528596	-	1	NA	promoter-TSS (NM_178669)	promoter-TSS (NM_178669)	62	NM_178669	212070	Mm.39721	NM_178669	ENSMUSG00000050866	Clrn3	AI649392|Tmem12	clarin 3	protein-coding
mm_112247.1	chr12	113588722	113588734	-	1	NA	Intergenic	Intergenic	44820	NM_174885	238406	Mm.188683	NM_174885	ENSMUSG00000043945	Adam6a	Adam6|tMDCIV	a disintegrin and metallopeptidase domain 6A	protein-coding
mm_117136.1	chr13	60940184	60940191	-	1	NA	exon (NM_009411, exon 3 of 5)	exon (NM_009411, exon 3 of 5)	1748	NM_009411	21984	Mm.2372	NM_009411	ENSMUSG00000033834	Tpbpa	AV033951|Tb-1|Tb1|Tpbp|b2b1247Clo	trophoblast specific protein alpha	protein-coding
mm_147317.1	chr18	42196681	42196698	-	1	NA	promoter-TSS (NM_027072)	promoter-TSS (NM_027072)	20	NM_027072	69401	Mm.34841	NM_027072	ENSMUSG00000059455	Plac8l1	1700009N18Rik|1700015M15Rik	PLAC8-like 1	protein-coding
mm_169345.1	chr14	16144614	16144620	+	1	NA	Intergenic	RLTR9E|LTR|ERVK	-104697	NM_021504	59007	Mm.258381	NM_021504	ENSMUSG00000021785	Ngly1	1110002C09Rik|PNGase|Png1	N-glycanase 1	protein-coding
mm_134619.1	chr16	21333259	21333293	-	1	NA	promoter-TSS (NR_131983)	promoter-TSS (NR_131983)	80	NR_131983	76222	Mm.86031	NR_131983		Magef1	6430590I03Rik	melanoma antigen family F, 1	pseudo
mm_67754.1	chr7	92666056	92666060	-	1	NA	intron (NM_029078, intron 1 of 15)	intron (NM_029078, intron 1 of 15)	3854	NM_029078	74737	Mm.288645	NM_029078	ENSMUSG00000041328	Pcf11	2500001H09Rik|5730417B17Rik|C77803	PCF11 cleavage and polyadenylation factor subunit	protein-coding
mm_117147.1	chr13	61164198	61164210	-	1	NA	promoter-TSS (NM_020284)	promoter-TSS (NM_020284)	-16	NM_020284	56835	Mm.315715	NM_020284	ENSMUSG00000055679	Ctsr	AI428350	cathepsin R	protein-coding
mm_93068.1	chr10	89257676	89257694	-	1	NA	non-coding (NR_102339, exon 1 of 27)	non-coding (NR_102339, exon 1 of 27)	105	NM_001277188	320091	Mm.236464	NM_178773	ENSMUSG00000035189	Ano4	A330096O15Rik|Gm65|Tmem16d	anoctamin 4	protein-coding
mm_101562.1	chr11	34075078	34075122	-	1	NA	exon (NM_010696, exon 9 of 21)	exon (NM_010696, exon 9 of 21)	27899	NM_010696	16822	Mm.265350	NM_010696	ENSMUSG00000002699	Lcp2	AI323664|BB161688|SLP-76|SLP76|m1Khoe|twm	lymphocyte cytosolic protein 2	protein-coding
mm_108092.1	chr12	74296859	74296861	+	1	NA	promoter-TSS (NM_198866)	promoter-TSS (NM_198866)	-614	NM_198866	386753	Mm.341686	NM_198866	ENSMUSG00000029878	Dbpht2	Spot2	DNA binding protein with his-thr domain	protein-coding
mm_29618.1	chr3	121291599	121291614	-	1	NA	promoter-TSS (NM_024178)	promoter-TSS (NM_024178)	-211	NM_024178	66789	Mm.269881	NM_024178	ENSMUSG00000039887	Alg14	5430428G01Rik|AI854024	asparagine-linked glycosylation 14	protein-coding
mm_128024.1	chr15	24857661	24857691	-	1	NA	Intergenic	A-rich|Low_complexity|Low_complexity	556088	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	brain abundant, membrane attached signal protein 1	protein-coding
mm_37200.1	chr4	117835846	117835847	-	1	NA	intron (NM_008135, intron 1 of 13)	CpG	588	NM_008135	14664	Mm.244549	NM_008135	ENSMUSG00000028542	Slc6a9	Glyt-1|Glyt1	solute carrier family 6 (neurotransmitter transporter, glycine), member 9	protein-coding
mm_146335.1	chr18	82338355	82338357	+	1	NA	Intergenic	Intergenic	68421	NM_008082	14427	Mm.6219	NM_008082	ENSMUSG00000024553	Galr1	Galnr1	galanin receptor 1	protein-coding
mm_89324.1	chr10	87931454	87931464	+	1	NA	3' UTR (NM_010512, exon 5 of 5)	3' UTR (NM_010512, exon 5 of 5)	-35212	NR_000040	22172	Mm.391420	NR_000040		Tyms-ps	-	thymidylate synthase, pseudogene	pseudo
mm_138319.1	chr17	34837083	34837166	+	1	NA	promoter-TSS (NM_019442)	promoter-TSS (NM_019442)	105	NM_001163770	112403	Mm.275309	NM_033613	ENSMUSG00000040482	Dxo	Dom3z|NG6	decapping exoribonuclease	protein-coding
mm_110997.1	chr12	78749590	78749600	-	1	NA	intron (NM_019579, intron 1 of 14)	intron (NM_019579, intron 1 of 14)	648	NM_019579	56217	Mm.425777	NM_019579	ENSMUSG00000021112	Mpp5	3830420B02Rik|AI255216|AI644496|Pals1	membrane protein, palmitoylated 5 (MAGUK p55 subfamily member 5)	protein-coding
mm_150313.1	chr19	34573349	34573360	+	1	NA	exon (NM_008332, exon 3 of 3)	exon (NM_008332, exon 3 of 3)	-10175	NM_010501	15959	Mm.426079	NM_010501	ENSMUSG00000074896	Ifit3	Ifi49|P49	interferon-induced protein with tetratricopeptide repeats 3	protein-coding
mm_106938.1	chr12	8674430	8674450	+	1	NA	promoter-TSS (NM_030723)	promoter-TSS (NM_030723)	181	NM_001160220	80913	Mm.341243	NM_030723	ENSMUSG00000020594	Pum2	5730503J23Rik|Pumm2	pumilio RNA-binding family member 2	protein-coding
mm_155213.1	chrX	56787702	56787715	+	1	NA	intron (NM_001287800, intron 1 of 5)	intron (NM_001287800, intron 1 of 5)	1181	NM_001287800	14199	Mm.3126	NM_010211	ENSMUSG00000023092	Fhl1	FHL-1|KyoT|RAM14-1|SLIM|SLIM-1	four and a half LIM domains 1	protein-coding
mm_100770.1	chr11	4747153	4747188	-	1	NA	promoter-TSS (NM_138948)	promoter-TSS (NM_138948)	-392	NM_138948	192650	Mm.207056	NM_138948	ENSMUSG00000009075	Cabp7	-	calcium binding protein 7	protein-coding
mm_107822.1	chr12	69122975	69122986	+	1	NA	Intergenic	RSINE1|SINE|B4	36206	NM_009093	20090	Mm.379006	NM_009093	ENSMUSG00000034892	Rps29	-	ribosomal protein S29	protein-coding
mm_3791.1	chr1	157412650	157412664	+	1	NA	promoter-TSS (NM_177644)	promoter-TSS (NM_177644)	-62	NM_177644	226525	Mm.235028	NM_177644	ENSMUSG00000070565	Rasal2	6530401P13|A330066M24Rik	RAS protein activator like 2	protein-coding
mm_104644.1	chr11	97537219	97537228	-	1	NA	exon (NM_018873, exon 5 of 20)	exon (NM_018873, exon 5 of 20)	-36883	NM_001289118	100141474	Mm.482426	NM_001289118	ENSMUSG00000047988	4933428G20Rik	-	RIKEN cDNA 4933428G20 gene	protein-coding
mm_131328.1	chr16	13109890	13109954	+	1	NA	5' UTR (NM_015769, exon 1 of 11)	5' UTR (NM_015769, exon 1 of 11)	186	NM_015769	50505	Mm.287837	NM_015769	ENSMUSG00000022545	Ercc4	AI606920|Xpf	excision repair cross-complementing rodent repair deficiency, complementation group 4	protein-coding
mm_8264.1	chr1	139304768	139304774	-	1	NA	intron (NM_133239, intron 5 of 11)	intron (NM_133239, intron 5 of 11)	72305	NM_133239	170788	Mm.95700	NM_133239	ENSMUSG00000063681	Crb1	7530426H14Rik|A930008G09Rik	crumbs family member 1, photoreceptor morphogenesis associated	protein-coding
mm_53834.1	chr6	148109504	148109518	+	1	NA	intron (NM_001347516, intron 1 of 11)	intron (NM_001347516, intron 1 of 11)	62095	NM_178797	330450	Mm.447274	NM_178797	ENSMUSG00000030303	Far2	A230046P18|AW048109|BC055759|Mlstd1	fatty acyl CoA reductase 2	protein-coding
mm_136412.1	chr16	93816389	93816404	-	1	NA	Intergenic	Intergenic	-15725	NM_001045529	338467	Mm.287329	NM_001045529	ENSMUSG00000039456	Morc3	1110051N18Rik|AI452146|BF318192|D16Jhu32e|NXP2|Zcwcc3	microrchidia 3	protein-coding
mm_3323.1	chr1	137920684	137920694	+	1	NA	Intergenic	Intergenic	-45766	NR_029795	735252		NR_029795	ENSMUSG00000065565	Mir181a-1	Mirn181a-1|Mirn213|miR-213|mir-181a-1|mmu-mir-213	microRNA 181a-1	ncRNA
mm_287.1	chr1	21349599	21349619	+	1	NA	promoter-TSS (NM_183322)	promoter-TSS (NM_183322)	-68	NM_183322	368204	Mm.26006	NM_183322	ENSMUSG00000067750	Khdc1a	AU014713|C88118|Ndg1	KH domain containing 1A	protein-coding
mm_103474.1	chr11	76494495	76494547	-	1	NA	promoter-TSS (NM_001346670)	promoter-TSS (NM_001346670)	-26	NM_001346670	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_169519.1	chr14	8800290	8800290	-	1	NA	Intergenic	Intergenic	133900	NR_045968	74859	Mm.84041	NR_045968	ENSMUSG00000097898	4930455B14Rik	1700027C12Rik	RIKEN cDNA 4930455B14 gene	ncRNA
mm_30189.1	chr3	144692015	144692040	-	1	NA	exon (NM_019464, exon 8 of 9)	exon (NM_019464, exon 8 of 9)	28308	NM_001282042	54673	Mm.271775	NM_019464	ENSMUSG00000037062	Sh3glb1	AA409932|AI314629|AU015566|Bif-1|mKIAA0491	SH3-domain GRB2-like B1 (endophilin)	protein-coding
mm_54745.1	chr6	41032399	41032445	-	1	NA	exon (NM_023333, exon 4 of 5)	exon (NM_023333, exon 4 of 5)	3087	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_50628.1	chr6	50394392	50394403	+	1	NA	intron (NM_001347213, intron 2 of 23)	intron (NM_001347213, intron 2 of 23)	-11560	NM_027881	71720	Mm.44153	NM_027881	ENSMUSG00000029822	Osbpl3	1200014M06Rik|6720421I08Rik|A530055M08|ORP-3|ORP3|OSBP3	oxysterol binding protein-like 3	protein-coding
mm_106469.1	chr11	120086791	120086852	-	1	NA	promoter-TSS (NM_009734)	promoter-TSS (NM_009734)	6	NM_009734	12009	Mm.2556	NM_009734	ENSMUSG00000039781	Cep131	AZ1|Azi|Azi1	centrosomal protein 131	protein-coding
mm_70128.1	chr7	143099877	143099877	-	1	NA	Intergenic	Intergenic	-5235	NM_020277	56843	Mm.286668	NM_020277	ENSMUSG00000009246	Trpm5	9430099A16Rik|LTrpC-5|Ltrpc5|Mtr1	transient receptor potential cation channel, subfamily M, member 5	protein-coding
mm_87333.1	chr10	42940455	42940484	+	1	NA	intron (NM_172938, intron 6 of 8)	intron (NM_172938, intron 6 of 8)	79957	NM_172938	268297	Mm.98731	NM_172938	ENSMUSG00000044770	Scml4	9330161D17|mFLJ00197	sex comb on midleg-like 4 (Drosophila)	protein-coding
mm_1968.1	chr1	86503602	86503617	+	1	NA	Intergenic	Intergenic	-23127	NM_008972	19231	Mm.19187	NM_008972	ENSMUSG00000026238	Ptma	Thym	prothymosin alpha	protein-coding
mm_128731.1	chr15	64135804	64135806	-	1	NA	intron (NM_010026, intron 16 of 30)	intron (NM_010026, intron 16 of 30)	-75357	NM_144846	223601	Mm.246108	NM_144846	ENSMUSG00000022378	Fam49b	0910001A06Rik|AW122079	family with sequence similarity 49, member B	protein-coding
mm_63560.1	chr7	128083900	128083913	+	1	NA	intron (NM_001082960, intron 9 of 29)	intron (NM_001082960, intron 9 of 29)	21266	NM_008401	16409	Mm.262106	NM_008401	ENSMUSG00000030786	Itgam	CD11b/CD18|CR3|CR3A|Cd11b|F730045J24Rik|Ly-40|MAC1|Mac-1|Mac-1a	integrin alpha M	protein-coding
mm_146368.1	chr18	82584583	82584599	+	1	NA	3' UTR (NM_010777, exon 7 of 7)	3' UTR (NM_010777, exon 7 of 7)	30083	NM_001025254	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_8303.1	chr1	144002803	144002817	-	1	NA	exon (NM_009061, exon 3 of 5)	exon (NM_009061, exon 3 of 5)	1339	NM_009061	19735	Mm.28262	NM_009061	ENSMUSG00000026360	Rgs2	GOS8	regulator of G-protein signaling 2	protein-coding
mm_139076.1	chr17	46678770	46678793	+	1	NA	intron (NM_001163729, intron 1 of 10)	intron (NM_001163729, intron 1 of 10)	-1672	NM_001277310	17256	Mm.329083	NM_010787	ENSMUSG00000002768	Mea1	Mea-1	male enhanced antigen 1	protein-coding
mm_132970.1	chr16	52031556	52031570	+	1	NA	promoter-TSS (NM_001033238)	promoter-TSS (NM_001033238)	14	NM_001033238	208650	Mm.328206	NM_001033238	ENSMUSG00000022637	Cblb	AI429560|AI851073|Cbl-b	Casitas B-lineage lymphoma b	protein-coding
mm_43020.1	chr5	123907573	123907587	+	1	NA	intron (NM_026603, intron 1 of 7)	intron (NM_026603, intron 1 of 7)	305	NM_026603	68184	Mm.28549	NM_026603	ENSMUSG00000023106	Denr	1500003K04Rik	density-regulated protein	protein-coding
mm_114703.1	chr13	83524548	83524561	+	1	NA	promoter-TSS (NM_001347567)	promoter-TSS (NM_001347567)	-189	NM_001347567	17260	Mm.24001	NM_025282	ENSMUSG00000005583	Mef2c	5430401D19Rik|9930028G15Rik|AV011172|Mef2	myocyte enhancer factor 2C	protein-coding
mm_98800.1	chr11	97030131	97030173	+	1	NA	intron (NM_146027, intron 1 of 7)	intron (NM_146027, intron 1 of 7)	200	NM_146027	217140	Mm.46189	NM_146027	ENSMUSG00000020877	Scrn2	AV001119|D11Moh48|SES2	secernin 2	protein-coding
mm_105709.1	chr11	108295801	108295803	-	1	NA	intron (NM_011101, intron 2 of 16)	intron (NM_011101, intron 2 of 16)	48086	NM_011101	18750	Mm.222178	NM_011101	ENSMUSG00000050965	Prkca	AI875142|Pkca	protein kinase C, alpha	protein-coding
mm_147907.1	chr18	65393955	65393963	-	1	NA	promoter-TSS (NM_001037294)	promoter-TSS (NM_001037294)	-71	NM_001037294	225638	Mm.296528	NM_001037294	ENSMUSG00000032845	Alpk2	Gm549|Hak	alpha-kinase 2	protein-coding
mm_19769.1	chr2	105670302	105670322	-	1	NA	promoter-TSS (NR_002867)	promoter-TSS (NR_002867)	18	NR_002867	402728	Mm.444553	NR_002867	ENSMUSG00000086029	Pax6os1	4831410G09Rik|Pax6os	paired box 6 opposite strand 1	ncRNA
mm_74545.1	chr8	10483959	10483970	-	1	NA	intron (NM_001319151, intron 23 of 34)	MTEa|LTR|ERVL-MaLR	330053	NM_001319151	244281	Mm.422761	NM_001081397	ENSMUSG00000039057	Myo16	BM140241|C230040D10Rik|Gm1105|NYAP3|mKIAA0865	myosin XVI	protein-coding
mm_52603.1	chr6	117173547	117173554	+	1	NA	exon (NM_021704, exon 3 of 3)	exon (NM_021704, exon 3 of 3)	5015	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_78964.1	chr9	45264883	45264895	+	1	NA	intron (NR_136903, intron 3 of 5)	B4|SINE|B4	1818	NR_106054	102466803		NR_106054	ENSMUSG00000098361	Mir7086	Gm27643|mmu-mir-7086	microRNA 7086	ncRNA
mm_62420.1	chr7	101321231	101321320	+	1	NA	promoter-TSS (NM_019990)	promoter-TSS (NM_019990)	-44	NM_019990	56018	Mm.28896	NM_019990	ENSMUSG00000030688	Stard10	AV048538|CGI-52|NY-C0-28|PC-TP2|PCTP2|Pctpl|Sdccag28|SdccagG28|TISP-81	START domain containing 10	protein-coding
mm_119154.1	chr14	31506515	31506516	+	1	NA	intron (NM_028932, intron 5 of 5)	intron (NM_028932, intron 5 of 5)	11436	NM_028932	74427	Mm.491208	NM_028932	ENSMUSG00000021890	Eaf1	4933403C17Rik|AI666536	ELL associated factor 1	protein-coding
mm_91427.1	chr10	33205645	33205665	-	1	NA	intron (NM_029726, intron 9 of 37)	L1VL4|LINE|L1	50702	NR_040657	442820	Mm.490725	NR_040657		D830005E20Rik	-	RIKEN cDNA D830005E20 gene	ncRNA
mm_106124.1	chr11	116412966	116413000	-	1	NA	promoter-TSS (NM_027258)	promoter-TSS (NM_027258)	49	NM_027258	217340	Mm.426344	NM_027258	ENSMUSG00000052949	Rnf157	2610036E23Rik|A130073L17Rik|mKIAA1917	ring finger protein 157	protein-coding
mm_122902.1	chr14	54953073	54953116	-	1	NA	exon (NM_010856, exon 23 of 39)	exon (NM_010856, exon 23 of 39)	-3952	NR_029724	387204		NR_029724	ENSMUSG00000065432	Mir208a	Mirn208|Mirn208a|mir-208|mir-208a|mmu-mir-208	microRNA 208a	ncRNA
mm_61827.1	chr7	88219539	88219547	+	1	NA	Intergenic	Lx2|LINE|L1	-58542	NM_009982	13032	Mm.89295	NM_009982	ENSMUSG00000030560	Ctsc	AI047818|CatC|DPP1|DPPI	cathepsin C	protein-coding
mm_149370.1	chr19	11372564	11372587	+	1	NA	Intergenic	Intergenic	-2913	NM_001310331	666907		NM_001310331	ENSMUSG00000101389	Ms4a4a	EG666907	membrane-spanning 4-domains, subfamily A, member 4A	protein-coding
mm_64855.1	chr7	13035454	13035466	-	1	NA	promoter-TSS (NM_026885)	promoter-TSS (NM_026885)	-683	NM_026885	68953	Mm.295670	NM_026885	ENSMUSG00000033916	Chmp2a	1500016L11Rik	charged multivesicular body protein 2A	protein-coding
mm_65502.1	chr7	25724734	25724835	-	1	NA	exon (NM_144922, exon 13 of 15)	exon (NM_144922, exon 13 of 15)	-5731	NM_028771	52132	Mm.278798	NM_028771	ENSMUSG00000002608	Ccdc97	1200014H14Rik|2810446P04Rik|AA545218|D7Ertd462e	coiled-coil domain containing 97	protein-coding
mm_122652.1	chr14	51910784	51910793	-	1	NA	intron (NM_001145959, intron 2 of 14)	intron (NM_001145959, intron 2 of 14)	2700	NM_001145959	29811	Mm.26722	NM_013864	ENSMUSG00000004558	Ndrg2	AI182517|AU040374|Ndr2|SYLD	N-myc downstream regulated gene 2	protein-coding
mm_99442.1	chr11	102433217	102433237	+	1	NA	exon (NM_008175, exon 3 of 13)	exon (NM_008175, exon 3 of 13)	2905	NM_008175	14824	Mm.1568	NM_008175	ENSMUSG00000034708	Grn	Pgrn|epithelin	granulin	protein-coding
mm_105570.1	chr11	106580595	106580609	-	1	NA	intron (NM_198292, intron 1 of 11)	intron (NM_198292, intron 1 of 11)	32328	NM_198292	21763	Mm.102407	NM_198292	ENSMUSG00000040548	Tex2	4930568E07Rik|AI553404|Def-5|Taz4	testis expressed gene 2	protein-coding
mm_66888.1	chr7	59258738	59258747	-	1	NA	intron (NM_173010, intron 2 of 8)	intron (NM_173010, intron 2 of 8)	29990	NM_011668	22215	Mm.9002	NM_011668	ENSMUSG00000025326	Ube3a	4732496B02|5830462N02Rik|A130086L21Rik|Hpve6a|mKIAA4216	ubiquitin protein ligase E3A	protein-coding
mm_60903.1	chr7	46712183	46712189	+	1	NA	exon (NM_011315, exon 4 of 4)	exon (NM_011315, exon 4 of 4)	-1535	NM_030233	78935	Mm.289866	NM_030233	ENSMUSG00000006763	Saal1	5031425D22Rik|SPACIA1	serum amyloid A-like 1	protein-coding
mm_73023.1	chr8	94137198	94137213	+	1	NA	promoter-TSS (NM_008631)	promoter-TSS (NM_008631)	1	NM_008631	17752	Mm.1536	NM_008631	ENSMUSG00000031757	Mt4	MT-IV	metallothionein 4	protein-coding
mm_5331.1	chr1	23909688	23909706	-	1	NA	promoter-TSS (NM_001290683)	promoter-TSS (NM_001290683)	39	NR_110972	98366	Mm.329963	NM_028534	ENSMUSG00000026155	Smap1	1700056O10Rik|4921514B13Rik|4921525H11Rik|AI462175	small ArfGAP 1	protein-coding
mm_129106.1	chr15	76049214	76049260	-	1	NA	exon (NM_134089, exon 30 of 38)	exon (NM_134089, exon 30 of 38)	15651	NR_105917	102466772		NR_105917	ENSMUSG00000098451	Mir6952	Gm27948|mmu-mir-6952	microRNA 6952	ncRNA
mm_68595.1	chr7	116093120	116093165	-	1	NA	promoter-TSS (NM_019772)	promoter-TSS (NM_019772)	7	NR_029433	69350	Mm.440425	NR_029433	ENSMUSG00000087621	1700003G18Rik	2610312K03Rik	RIKEN cDNA 1700003G18 gene	ncRNA
mm_27430.1	chr3	51559582	51559597	-	1	NA	promoter-TSS (NR_033624)	promoter-TSS (NR_033624)	-168	NR_033624	100039684	Mm.387178	NR_033624		5031434O11Rik	AI481280|Gm2370	RIKEN cDNA 5031434O11 gene	ncRNA
mm_63256.1	chr7	126649378	126649388	+	1	NA	promoter-TSS (NM_029339)	promoter-TSS (NM_029339)	74	NM_029339	75565	Mm.45686	NM_029339	ENSMUSG00000030714	Sgf29	1700023O11Rik|9530025I05Rik|Ccdc101	SAGA complex associated factor 29	protein-coding
mm_86030.1	chr9	113668049	113668070	-	1	NA	intron (NM_011052, intron 12 of 17)	Lx6|LINE|L1	40200	NM_001164678	18571	Mm.29816	NM_011052	ENSMUSG00000032504	Pdcd6ip	AI480591|AW544830|Aip1|Alix|C76364|Eig2|mKIAA1375	programmed cell death 6 interacting protein	protein-coding
mm_161960.1	chr19	7269755	7269755	+	1	NA	intron (NM_001320554, intron 1 of 11)	intron (NM_001320554, intron 1 of 11)	1476	NM_001320554	104383	Mm.283859	NM_054048	ENSMUSG00000024968	Rcor2	1A13|AW122124|CoREST|Rcor|Rcor1	REST corepressor 2	protein-coding
mm_34137.1	chr4	139291310	139291344	+	1	NA	3' UTR (NM_001271405, exon 9 of 9)	3' UTR (NM_001271405, exon 9 of 9)	19373	NM_145384	212555	Mm.45131	NM_145384	ENSMUSG00000028744	Pqlc2	BC019216	PQ loop repeat containing 2	protein-coding
mm_14659.1	chr2	137676210	137676210	+	1	NA	Intergenic	Intergenic	-559690	NM_013822	16449	Mm.22398	NM_013822	ENSMUSG00000027276	Jag1	ABE2|Gsfabe2|Htu|Ozz|Ser-1	jagged 1	protein-coding
mm_48713.1	chr5	147307064	147307139	-	1	NA	5' UTR (NM_007673, exon 1 of 3)	5' UTR (NM_007673, exon 1 of 3)	148	NM_007673	12591	Mm.20358	NM_007673	ENSMUSG00000029646	Cdx2	Cdx-2	caudal type homeobox 2	protein-coding
mm_80533.1	chr9	80281492	80281499	+	1	NA	exon (NM_001039546, exon 21 of 33)	exon (NM_001039546, exon 21 of 33)	116461	NM_001039546	17920	Mm.4040	NM_008662	ENSMUSG00000033577	Myo6	BC029719|Tlc|sv	myosin VI	protein-coding
mm_128098.1	chr15	27856467	27856485	-	1	NA	intron (NM_001081302, intron 11 of 56)	intron (NM_001081302, intron 11 of 56)	169372	NM_001081302	223435	Mm.485422	NM_001081302	ENSMUSG00000022263	Trio	6720464I07Rik|AA408740|Solo	triple functional domain (PTPRF interacting)	protein-coding
mm_36735.1	chr4	99194624	99194629	-	1	NA	intron (NM_175029, intron 1 of 10)	intron (NM_175029, intron 1 of 10)	479	NM_001145967	242557	Mm.241663	NM_175029	ENSMUSG00000028550	Atg4c	Apg4-C|Apg4c|Atg4cl|Autl1	autophagy related 4C, cysteine peptidase	protein-coding
mm_67831.1	chr7	98361249	98361255	-	1	NA	promoter-TSS (NM_001168539)	promoter-TSS (NM_001168539)	36	NM_001168540	244152	Mm.25317	NM_001024619	ENSMUSG00000049580	Tsku	9530051K01Rik|E2ig4|Lrrc54|Tsk	tsukushi, small leucine rich proteoglycan	protein-coding
mm_28352.1	chr3	89667281	89667287	-	1	NA	exon (NM_080466, exon 8 of 8)	exon (NM_080466, exon 8 of 8)	-47738	NM_001038587	56417	Mm.316628	NM_019655	ENSMUSG00000027951	Adar	AV242451|Adar1|Adar1p110|Adar1p150|mZaADAR	adenosine deaminase, RNA-specific	protein-coding
mm_26450.1	chr3	142637629	142637641	+	1	NA	3' UTR (NM_010260, exon 11 of 11)	3' UTR (NM_010260, exon 11 of 11)	-13689	NR_105802	102465200		NR_105802	ENSMUSG00000098871	Mir6381	Gm27963|mmu-mir-6381	microRNA 6381	ncRNA
mm_116455.1	chr13	43271293	43271296	-	1	NA	intron (NM_001033399, intron 1 of 1)	intron (NM_001033399, intron 1 of 1)	32878	NM_001033399	328232	Mm.441399	NM_001033399	ENSMUSG00000051335	Gfod1	9630032O13|AI850995	glucose-fructose oxidoreductase domain containing 1	protein-coding
mm_146824.1	chr18	21300130	21300168	-	1	NA	promoter-TSS (NM_001033445)	promoter-TSS (NM_001033445)	-10	NM_001033445	381126	Mm.312276	NM_001033445	ENSMUSG00000042680	Garem1	C86169|Fam59a|Garem|Gm944|mKIAA4238	GRB2 associated regulator of MAPK1 subtype 1	protein-coding
mm_89843.1	chr10	106879816	106879832	+	1	NA	intron (NM_001205341, intron 21 of 31)	(CA)n|Simple_repeat|Simple_repeat	243840	NM_001142804	380660	Mm.336072	NM_198636	ENSMUSG00000035948	Acss3	8430416H19Rik|Gm874	acyl-CoA synthetase short-chain family member 3	protein-coding
mm_98119.1	chr11	87127109	87127133	+	1	NA	promoter-TSS (NM_197987)	promoter-TSS (NM_197987)	46	NM_197987	68729	Mm.17436	NM_197987	ENSMUSG00000018548	Trim37	1110032A10Rik|2810004E07Rik|AI848587|AU043018|MUL|TEF3|mKIAA0898	tripartite motif-containing 37	protein-coding
mm_70551.1	chr8	13056158	13056175	+	1	NA	3' UTR (NM_007972, exon 9 of 9)	3' UTR (NM_007972, exon 9 of 9)	-4742	NM_025834	66901	Mm.441140	NM_025834	ENSMUSG00000031445	Proz	1300015B06Rik	protein Z, vitamin K-dependent plasma glycoprotein	protein-coding
mm_432.1	chr1	34498370	34498441	+	1	NA	promoter-TSS (NM_009355)	promoter-TSS (NM_009355)	-25	NM_009355	21755	Mm.10725	NM_009355	ENSMUSG00000026125	Prss39	Tesp1	protease, serine 39	protein-coding
mm_148739.1	chr19	5930254	5930296	+	1	NA	Intergenic	Intergenic	-5459	NM_026772	104252	Mm.491103	NM_026772	ENSMUSG00000045664	Cdc42ep2	1110008C05Rik|Borg1|Cep2|D19Bwg1013e	CDC42 effector protein (Rho GTPase binding) 2	protein-coding
mm_87627.1	chr10	58211429	58211439	+	1	NA	Intergenic	Intergenic	21241	NM_001081954	664783	Mm.482575	NM_001081954		Dux	AW822073|Dux4|Duxbl|EG664783	double homeobox	protein-coding
mm_117524.1	chr13	81633175	81633179	-	1	NA	promoter-TSS (NM_054053)	promoter-TSS (NM_054053)	-33	NM_054053	110789	Mm.288694	NM_054053	ENSMUSG00000069170	Adgrv1	Frings|Gpr98|Mass1|Mgr1|VLGR1	adhesion G protein-coupled receptor V1	protein-coding
mm_35548.1	chr4	41507726	41507738	-	1	NA	promoter-TSS (NM_001253780)	promoter-TSS (NM_001253780)	32	NM_028624	73721	Mm.45614	NM_028624	ENSMUSG00000028441	1110017D15Rik	Cbe1|Smrp1	RIKEN cDNA 1110017D15 gene	protein-coding
mm_99223.1	chr11	101039833	101039846	+	1	NA	exon (NM_001243049, exon 13 of 21)	exon (NM_001243049, exon 13 of 21)	9499	NR_105893	102466767		NR_105893	ENSMUSG00000098415	Mir6928	Gm27728|mmu-mir-6928	microRNA 6928	ncRNA
mm_114804.1	chr13	91461106	91461112	+	1	NA	promoter-TSS (NM_024186)	promoter-TSS (NM_024186)	12	NM_024186	66970	Mm.343095	NM_024186	ENSMUSG00000003992	Ssbp2	1500004K09Rik|2310079I02Rik|9330163K02Rik|A830008M03Rik|AU067692|AW558684|Hspc116|SSDP2	single-stranded DNA binding protein 2	protein-coding
mm_108899.1	chr12	100199510	100199514	+	1	NA	promoter-TSS (NM_009790)	promoter-TSS (NM_009790)	77	NM_009790	12313	Mm.285993	NM_009790	ENSMUSG00000001175	Calm1	AI256814|AI327027|AI461935|AL024000|CaM|Calm	calmodulin 1	protein-coding
mm_981.1	chr1	58406839	58406875	+	1	NA	TTS (NM_025824)	TTS (NM_025824)	13721	NM_025824	66882	Mm.21848	NM_025824	ENSMUSG00000051223	Bzw1	1200015E15Rik|mKIAA0005	basic leucine zipper and W2 domains 1	protein-coding
mm_116441.1	chr13	43125712	43125723	-	1	NA	intron (NM_001005740, intron 9 of 12)	intron (NM_001005740, intron 9 of 12)	2878	NM_001005748	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding
mm_105425.1	chr11	103698037	103698045	-	1	NA	promoter-TSS (NM_019650)	promoter-TSS (NM_019650)	317	NR_102396	399609	Mm.351922	NR_102388		C130046K22Rik	-	RIKEN cDNA C130046K22 gene	ncRNA
mm_138486.1	chr17	35199947	35199955	+	1	NA	3' UTR (NM_013693, exon 4 of 4)	3' UTR (NM_013693, exon 4 of 4)	2056	NM_013693	21926	Mm.1293	NM_013693	ENSMUSG00000024401	Tnf	DIF|TNF-a|TNF-alpha|TNFSF2|TNFalpha|Tnfa|Tnfsf1a|Tnlg1f	tumor necrosis factor	protein-coding
mm_78797.1	chr9	44046871	44046884	+	1	NA	exon (NM_009382, exon 3 of 4)	exon (NM_009382, exon 3 of 4)	3493	NM_009382	21838	Mm.3951	NM_009382	ENSMUSG00000032011	Thy1	CD90|T25|Thy-1|Thy-1.2|Thy1.1|Thy1.2	thymus cell antigen 1, theta	protein-coding
mm_96171.1	chr11	61488483	61488515	+	1	NA	TTS (NM_001291037)	TTS (NM_001291037)	3055	NM_029568	76293	Mm.272278	NM_029568	ENSMUSG00000042436	Mfap4	1110007F23Rik	microfibrillar-associated protein 4	protein-coding
mm_34651.1	chr4	150853796	150853812	+	1	NA	intron (NR_040649, intron 1 of 3)	intron (NR_040649, intron 1 of 3)	1145	NR_040649	73348	Mm.396218	NR_040649	ENSMUSG00000078492	1700045H11Rik	-	RIKEN cDNA 1700045H11 gene	ncRNA
mm_112769.1	chr13	19358497	19358504	+	1	NA	intron (NM_024270, intron 8 of 8)	intron (NM_024270, intron 8 of 8)	37313	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_50608.1	chr6	49395560	49395594	+	1	NA	promoter-TSS (NM_029916)	promoter-TSS (NM_029916)	-27	NM_029916	77485	Mm.128054	NM_029916	ENSMUSG00000023403	Stk31	C330007K24Rik	serine threonine kinase 31	protein-coding
mm_71399.1	chr8	46194194	46194205	+	1	NA	3' UTR (NM_025747, exon 4 of 4)	3' UTR (NM_025747, exon 4 of 4)	16810	NM_007450	11739	Mm.16228	NM_007450	ENSMUSG00000031633	Slc25a4	AU019225|Ant1	solute carrier family 25 (mitochondrial carrier, adenine nucleotide translocator), member 4	protein-coding
mm_62819.1	chr7	113368947	113368955	+	1	NA	5' UTR (NM_133700, exon 2 of 11)	5' UTR (NM_133700, exon 2 of 11)	388	NM_133700	68815	Mm.238034	NM_133700	ENSMUSG00000038187	Btbd10	1110056N09Rik|Gmrp1	BTB (POZ) domain containing 10	protein-coding
mm_169537.1	chr14	95419692	95419696	+	1	NA	Intergenic	Intergenic	-461572	NM_025733	66732	Mm.75060	NM_025733	ENSMUSG00000034689	4921530L21Rik	-	RIKEN cDNA 4921530L21 gene	protein-coding
mm_46649.1	chr5	108629672	108629678	-	1	NA	promoter-TSS (NM_001163532)	promoter-TSS (NM_001163532)	102	NM_153569	231580	Mm.276647	NM_153569	ENSMUSG00000062234	Gak	D130045N16Rik	cyclin G associated kinase	protein-coding
mm_51966.1	chr6	91758392	91758402	+	1	NA	3' UTR (NM_009320, exon 15 of 15)	3' UTR (NM_009320, exon 15 of 15)	48996	NM_001159507	243547	Mm.333264	NM_001033353	ENSMUSG00000030098	Grip2	-	glutamate receptor interacting protein 2	protein-coding
mm_168094.1	chr10	12868847	12868848	-	1	NA	Intergenic	Intergenic	-7112	NM_011682	22288	Mm.331784	NM_011682	ENSMUSG00000019820	Utrn	AA589569|DRP|Dmdl	utrophin	protein-coding
mm_109574.1	chr12	112130780	112130785	+	1	NA	promoter-TSS (NR_029590)	promoter-TSS (NR_029590)	-98	NR_029590	387199		NR_029590	ENSMUSG00000065574	Mir203	Mirn203|mir-203|mmu-mir-203	microRNA 203	ncRNA
mm_87929.1	chr10	62602332	62602368	+	1	NA	promoter-TSS (NM_019553)	promoter-TSS (NM_019553)	-52	NM_019553	56200	Mm.413275	NM_019553	ENSMUSG00000020075	Ddx21	AI255159|AL022742|D10Ertd645e|D10Wsu42e	DEAD (Asp-Glu-Ala-Asp) box polypeptide 21	protein-coding
mm_149322.1	chr19	10842532	10842564	+	1	NA	promoter-TSS (NM_023044)	promoter-TSS (NM_023044)	4	NM_023044	65221	Mm.27387	NM_023044	ENSMUSG00000024737	Slc15a3	Ci1|cI-1	solute carrier family 15, member 3	protein-coding
mm_7369.1	chr1	106744374	106744381	-	1	NA	intron (NM_001316750, intron 5 of 8)	ORR1C2|LTR|ERVL-MaLR	15365	NM_027534	70750	Mm.458911	NM_027534	ENSMUSG00000009905	Kdsr	6330410P18Rik|9430079B08Rik|Fvt1	3-ketodihydrosphingosine reductase	protein-coding
mm_96393.1	chr11	67250040	67250051	+	1	NA	exon (NM_010855, exon 19 of 40)	exon (NM_010855, exon 19 of 40)	12233	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_17413.1	chr2	27247211	27247254	-	1	NA	promoter-TSS (NM_138665)	promoter-TSS (NM_138665)	71	NM_138665	192166	Mm.278467	NM_138665	ENSMUSG00000009614	Sardh	-	sarcosine dehydrogenase	protein-coding
mm_84057.1	chr9	58159202	58159239	-	1	NA	promoter-TSS (NM_012043)	promoter-TSS (NM_012043)	1	NM_012043	26968	Mm.367887	NM_012043	ENSMUSG00000037206	Islr	AW553146|Meflin	immunoglobulin superfamily containing leucine-rich repeat	protein-coding
mm_79272.1	chr9	50754282	50754288	+	1	NA	intron (NM_009964, intron 1 of 2)	intron (NM_009964, intron 1 of 2)	1314	NM_009964	12955	Mm.178	NM_009964	ENSMUSG00000032060	Cryab	Crya-2|Crya2|HspB5|P23	crystallin, alpha B	protein-coding
mm_150457.1	chr19	38264588	38264622	+	1	NA	promoter-TSS (NM_020278)	promoter-TSS (NM_020278)	-177	NM_020278	56839	Mm.298251	NM_020278	ENSMUSG00000067242	Lgi1	BB130740	leucine-rich repeat LGI family, member 1	protein-coding
mm_13624.1	chr2	113442335	113442350	+	1	NA	exon (NM_001285459, exon 1 of 17)	exon (NM_001285459, exon 1 of 17)	1278	NM_001285459	14260	Mm.4938	NM_010230	ENSMUSG00000044042	Fmn1	Fmn|formin-1|ld	formin 1	protein-coding
mm_136615.1	chr17	5401008	5401018	+	1	NA	Intergenic	Intergenic	17754	NM_175349	106557	Mm.432764	NM_175349	ENSMUSG00000101959	Ldhal6b	4933402O15Rik|AI326310|LDHL|Ldhal	lactate dehydrogenase A-like 6B	protein-coding
mm_81749.1	chr9	113955972	113955983	+	1	NA	exon (NM_001083319, exon 5 of 17)	exon (NM_001083319, exon 5 of 17)	25043	NM_013699	22221	Mm.28052	NM_013699	ENSMUSG00000009741	Ubp1	Cp2b|LBP-1a|LBP-1b|NF2d9	upstream binding protein 1	protein-coding
mm_156871.1	chrX	164506321	164506344	+	1	NA	intron (NM_027027, intron 1 of 7)	intron (NM_027027, intron 1 of 7)	8429	NM_027027	69299	Mm.79031	NM_027027	ENSMUSG00000031384	Asb9	1700011M07Rik	ankyrin repeat and SOCS box-containing 9	protein-coding
mm_155975.1	chrX	106126719	106126734	+	1	NA	3' UTR (NM_009726, exon 23 of 23)	3' UTR (NM_009726, exon 23 of 23)	-16549	NM_205820	279572	Mm.336203	NM_205820	ENSMUSG00000033777	Tlr13	AI666735|Gm713	toll-like receptor 13	protein-coding
mm_66907.1	chr7	59988668	59988687	-	1	NA	5' UTR (NM_013670, exon 4 of 10)	5' UTR (NM_013670, exon 4 of 10)	-9821	NR_028529	100217429		NR_028529		Snord64	MBII-13	small nucleolar RNA, C/D box 64	snoRNA
mm_38137.1	chr4	134750249	134750261	-	1	NA	intron (NM_145554, intron 5 of 8)	MIRb|SINE|MIR	17749	NM_145554	100017	Mm.27486	NM_145554	ENSMUSG00000037295	Ldlrap1	AA691260|ARH2|Arh|Arh1|FHCB1|FHCB2	low density lipoprotein receptor adaptor protein 1	protein-coding
mm_61422.1	chr7	73618723	73618752	+	1	NA	Intergenic	CpG	-60342	NR_037569	69170	Mm.34539	NR_037569	ENSMUSG00000101970	1810026B05Rik	-	RIKEN cDNA 1810026B05 gene	ncRNA
mm_99506.1	chr11	103043014	103043034	+	1	NA	intron (NM_008707, intron 1 of 11)	intron (NM_008707, intron 1 of 11)	14462	NM_008707	18107	Mm.10265	NM_008707	ENSMUSG00000020936	Nmt1	AW536594	N-myristoyltransferase 1	protein-coding
mm_156559.1	chrX	151803277	151803287	+	1	NA	promoter-TSS (NM_021523)	promoter-TSS (NM_021523)	0	NM_021523	59026	Mm.27372	NM_021523	ENSMUSG00000025261	Huwe1	5430439H10Rik|AU041296|Arf-bp1|C430014N20Rik|C80292|Gm1718|Ib772|LASU1|Mule|Ureb1	HECT, UBA and WWE domain containing 1	protein-coding
mm_173004.1	chrM	1961	1963	+	1	NA	NA	Intergenic	NA	NA								
mm_91901.1	chr10	60189712	60189715	-	1	NA	intron (NM_016803, intron 2 of 3)	intron (NM_016803, intron 2 of 3)	29547	NM_016803	53374	Mm.12866	NM_016803	ENSMUSG00000057337	Chst3	C6ST|C6ST-1|GST-0	carbohydrate (chondroitin 6/keratan) sulfotransferase 3	protein-coding
mm_22861.1	chr3	28721507	28721547	+	1	NA	intron (NM_031197, intron 7 of 10)	intron (NM_031197, intron 7 of 10)	23624	NM_031197	20526	Mm.18443	NM_031197	ENSMUSG00000027690	Slc2a2	AI266973|Glut-2|Glut2	solute carrier family 2 (facilitated glucose transporter), member 2	protein-coding
mm_29254.1	chr3	107219702	107219741	-	1	NA	exon (NM_001111143, exon 2 of 9)	exon (NM_001111143, exon 2 of 9)	2011	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_159560.1	chr4	108383456	108383456	-	1	NA	5' UTR (NM_001099303, exon 1 of 3)	5' UTR (NM_001099303, exon 1 of 3)	199	NM_001099303	545667	Mm.380025	NM_001099303	ENSMUSG00000059816	Fam159a	OTTMUSG00000008243	family with sequence similarity 159, member A	protein-coding
mm_90431.1	chr10	127515778	127515789	+	1	NA	intron (NM_001098789, intron 2 of 3)	intron (NM_001098789, intron 2 of 3)	844	NM_001098789	407790	Mm.336856	NM_001098789	ENSMUSG00000040280	Ndufa4l2	BC064011	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 4-like 2	protein-coding
mm_14946.1	chr2	151911205	151911212	+	1	NA	promoter-TSS (NM_009641)	promoter-TSS (NM_009641)	1	NM_009641	11602	Mm.189536	NM_009641	ENSMUSG00000027460	Angpt4	ANG-3|ANG-4|Agpt4|Ang3	angiopoietin 4	protein-coding
mm_169791.1	chr16	15226761	15226764	+	1	NA	Intergenic	L1Md_F2|LINE|L1	320116	NM_025769	66793	Mm.100270	NM_025769	ENSMUSG00000068617	Efcab1	4930449A16Rik|5430404L10Rik	EF hand calcium binding domain 1	protein-coding
mm_5700.1	chr1	43196755	43196768	-	1	NA	promoter-TSS (NM_001289533)	promoter-TSS (NM_001289533)	0	NM_001289533	14200	Mm.6799	NM_010212	ENSMUSG00000008136	Fhl2	FHL-2|SLIM-3|SLIM3	four and a half LIM domains 2	protein-coding
mm_116335.1	chr13	38037972	38037984	-	1	NA	intron (NM_024242, intron 1 of 16)	intron (NM_024242, intron 1 of 16)	989	NM_024242	71340	Mm.297130	NM_024242	ENSMUSG00000021428	Riok1	3110046C13Rik|5430416A05Rik|Ad034	RIO kinase 1 (yeast)	protein-coding
mm_24579.1	chr3	93444758	93444768	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	2433	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_90621.1	chr10	128415180	128415196	+	1	NA	non-coding (NR_104290, exon 2 of 8)	non-coding (NR_104290, exon 2 of 8)	3572	NM_026259	67588	Mm.294120	NM_026259	ENSMUSG00000025373	Rnf41	2210404G21Rik|4930511A05Rik|4933415P08Rik|D10Ertd722e|FLRF|Nrdp1	ring finger protein 41	protein-coding
mm_8550.1	chr1	155230130	155230143	-	1	NA	Intergenic	Intergenic	71433	NM_021433	58244	Mm.66264	NM_021433	ENSMUSG00000026470	Stx6	2310039E05Rik|2410005I16Rik|AA437559|AI415714|AI845861	syntaxin 6	protein-coding
mm_102627.1	chr11	62538905	62538923	-	1	NA	exon (NM_028448, exon 1 of 5)	exon (NM_028448, exon 1 of 5)	347	NM_028448	73139	Mm.390409	NM_028448	ENSMUSG00000018509	Cenpv	3110013H01Rik|AA671303|Prr6	centromere protein V	protein-coding
mm_144639.1	chr18	33007202	33007214	+	1	NA	intron (NM_009793, intron 1 of 10)	intron (NM_009793, intron 1 of 10)	68167	NM_009793	12326	Mm.222329	NM_009793	ENSMUSG00000038128	Camk4	A430110E23Rik|AI666733|CaMKIV|CaMKIV/Gr|D18Bwg0362e	calcium/calmodulin-dependent protein kinase IV	protein-coding
mm_136656.1	chr17	5975968	5975986	+	1	NA	intron (NM_001113352, intron 2 of 25)	intron (NM_001113352, intron 2 of 25)	391	NM_011523	20975	Mm.236068	NM_011523	ENSMUSG00000023805	Synj2	AI481647|SJ2|mKIAA0348	synaptojanin 2	protein-coding
mm_11782.1	chr2	39008077	39008174	+	1	NA	promoter-TSS (NM_028809)	promoter-TSS (NM_028809)	-14	NM_028809	74192	Mm.38155	NM_028809	ENSMUSG00000026755	Arpc5l	2010015J01Rik|AI852867|ARC16-2|AW555592|AW742746	actin related protein 2/3 complex, subunit 5-like	protein-coding
mm_48087.1	chr5	136987702	136987714	-	1	NA	promoter-TSS (NM_001310748)	promoter-TSS (NM_001310748)	251	NM_027318	70103	Mm.273147	NM_027318	ENSMUSG00000059518	Znhit1	2700001K05Rik|ZNFN4A1	zinc finger, HIT domain containing 1	protein-coding
mm_4933.1	chr1	191097893	191097904	+	1	NA	promoter-TSS (NM_030060)	promoter-TSS (NM_030060)	-516	NM_030060	381319	Mm.6922	NM_030060	ENSMUSG00000026630	Batf3	9130211I03Rik|Snft	basic leucine zipper transcription factor, ATF-like 3	protein-coding
mm_151504.1	chr19	58730467	58730563	+	1	NA	exon (NM_018874, exon 4 of 13)	exon (NM_018874, exon 4 of 13)	1628	NM_018874	18946	Mm.10753	NM_018874	ENSMUSG00000042179	Pnliprp1	Plrp1	pancreatic lipase related protein 1	protein-coding
mm_57204.1	chr6	122850940	122851009	-	1	NA	exon (NM_009779, exon 2 of 2)	exon (NM_009779, exon 2 of 2)	5183	NM_009779	12267	Mm.2408	NM_009779	ENSMUSG00000040552	C3ar1	AZ3B|C3AR|HNFAG09	complement component 3a receptor 1	protein-coding
mm_29475.1	chr3	115711175	115711185	-	1	NA	3' UTR (NM_007901, exon 2 of 2)	3' UTR (NM_007901, exon 2 of 2)	3875	NM_007901	13609	Mm.982	NM_007901	ENSMUSG00000045092	S1pr1	AI849002|Edg1|Lpb1|S1p|S1p1	sphingosine-1-phosphate receptor 1	protein-coding
mm_115252.1	chr13	110397124	110397141	+	1	NA	intron (NM_152804, intron 5 of 13)	intron (NM_152804, intron 5 of 13)	2088	NM_152804	20620	Mm.380	NM_152804	ENSMUSG00000021701	Plk2	Snk	polo-like kinase 2	protein-coding
mm_68751.1	chr7	121065298	121065367	-	1	NA	3' UTR (NM_030691, exon 6 of 6)	3' UTR (NM_030691, exon 6 of 6)	9198	NM_030691	80719	Mm.160384	NM_030691	ENSMUSG00000035004	Igsf6	-	immunoglobulin superfamily, member 6	protein-coding
mm_153511.1	chr19	41370249	41370259	-	1	NA	intron (NM_031376, intron 2 of 16)	MER5A|DNA|hAT-Charlie	14816	NM_031376	83490	Mm.222266	NM_031376	ENSMUSG00000025017	Pik3ap1	1810044J04Rik|BCAP	phosphoinositide-3-kinase adaptor protein 1	protein-coding
mm_126521.1	chr15	81936754	81936839	+	1	NA	promoter-TSS (NM_145473)	promoter-TSS (NM_145473)	37	NM_145473	105859	Mm.22524	NM_145473	ENSMUSG00000042109	Csdc2	AI415250|AI481750|Pippin	cold shock domain containing C2, RNA binding	protein-coding
mm_86872.1	chr10	21995781	21995809	+	1	NA	exon (NM_001161847, exon 4 of 12)	exon (NM_001161847, exon 4 of 12)	1129	NM_011361	20393	Mm.28405	NM_011361	ENSMUSG00000019970	Sgk1	Sgk	serum/glucocorticoid regulated kinase 1	protein-coding
mm_147396.1	chr18	44255841	44255843	-	1	NA	Intergenic	Intergenic	-14285	NM_010935	18169	Mm.57234	NM_010935	ENSMUSG00000038071	Npy6r	-	neuropeptide Y receptor Y6	protein-coding
mm_126360.1	chr15	80042424	80042449	+	1	NA	Intergenic	Intergenic	-27628	NM_011057	18591	Mm.144089	NM_011057	ENSMUSG00000000489	Pdgfb	PDGF-B|Sis	platelet derived growth factor, B polypeptide	protein-coding
mm_160371.1	chr8	34115031	34115031	+	1	NA	promoter-TSS (NM_001126314)	promoter-TSS (NM_001126314)	1	NM_001126314	234155	Mm.324008	NM_001126314	ENSMUSG00000071113	Mboat4	GOAT|Gm171	membrane bound O-acyltransferase domain containing 4	protein-coding
mm_27295.1	chr3	45378250	45378262	-	1	NA	promoter-TSS (NR_045172)	promoter-TSS (NR_045172)	4	NR_045172	72511	Mm.140700	NR_045172	ENSMUSG00000097040	2610316D01Rik	-	RIKEN cDNA 2610316D01 gene	ncRNA
mm_102803.1	chr11	68863879	68863883	-	1	NA	Intergenic	Intergenic	-10750	NM_023668	83431	Mm.31979	NM_023668	ENSMUSG00000018736	Ndel1	2600006O07Rik|MITAP1|NUDEL|mNudel	nudE neurodevelopment protein 1 like 1	protein-coding
mm_155761.1	chrX	96167963	96167973	+	1	NA	3' UTR (NM_010833, exon 13 of 13)	3' UTR (NM_010833, exon 13 of 13)	71923	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_81625.1	chr9	110844498	110844513	+	1	NA	promoter-TSS (NM_183103)	promoter-TSS (NM_183103)	-1	NM_183103	74306	Mm.87419	NM_183103	ENSMUSG00000049719	Prss46	1700112C13Rik|79H19B|Tessp6	protease, serine 46	protein-coding
mm_2190.1	chr1	89070440	89070457	+	1	NA	promoter-TSS (NM_133816)	promoter-TSS (NM_133816)	-14	NM_133816	98402	Mm.170983	NM_133816	ENSMUSG00000036206	Sh3bp4	AI594717|AW227605|BOG25	SH3-domain binding protein 4	protein-coding
mm_143707.1	chr17	80670944	80670953	-	1	NA	intron (NM_001290345, intron 2 of 33)	AT_rich|Low_complexity|Low_complexity	57077	NM_001290345	225028	Mm.311948	NM_001081357	ENSMUSG00000024242	Map4k3	4833416M01Rik|4833416M07Rik|9530052P13Rik|Glk|MAPKKKK3|MEKKK 3|MEKKK3|RAB8IPL1	mitogen-activated protein kinase kinase kinase kinase 3	protein-coding
mm_30531.1	chr4	3231171	3231188	+	1	NA	Intergenic	CpG	-45874	NM_001167535	100312471	Mm.377218	NM_001167535	ENSMUSG00000095982	Vmn1r3	Gm11778|OTTMUSG00000004181	vomeronasal 1 receptor 3	protein-coding
mm_126679.1	chr15	84680975	84681044	+	1	NA	promoter-TSS (NM_146061)	promoter-TSS (NM_146061)	11	NM_146061	109270	Mm.291372	NM_146061	ENSMUSG00000036106	Prr5	AU043908|Arhgap8|C030017C09Rik|C78947|Protor-1|Protor1	proline rich 5 (renal)	protein-coding
mm_88183.1	chr10	69988473	69988476	+	1	NA	intron (NM_146005, intron 36 of 42)	intron (NM_146005, intron 36 of 42)	62942	NM_009670	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_34397.1	chr4	145045888	145045894	+	1	NA	intron (NM_001276502, intron 63 of 68)	intron (NM_001276502, intron 63 of 68)	144775	NM_001276502	230895	Mm.240310	NM_001033190	ENSMUSG00000020220	Vps13d	-	vacuolar protein sorting 13D	protein-coding
mm_156947.1	chrX	169981980	169981990	+	1	NA	exon (NM_001290504, exon 5 of 10)	exon (NM_001290504, exon 5 of 10)	-3068	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_50144.1	chr6	41543496	41543504	+	1	NA	Intergenic	Intergenic	21724	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_32143.1	chr4	99656165	99656176	+	1	NA	promoter-TSS (NM_010425)	promoter-TSS (NM_010425)	-129	NM_010425	15221	Mm.4758	NM_010425	ENSMUSG00000067261	Foxd3	CWH3|Genesis|Hfh2	forkhead box D3	protein-coding
mm_129291.1	chr15	77203576	77203583	-	1	NA	intron (NM_053104, intron 2 of 13)	CT-rich|Low_complexity|Low_complexity	-49767	NM_001286418	93686	Mm.202774	NM_053104	ENSMUSG00000033565	Rbfox2	Fbm2|Fxh|Hrnbp2|Rbm9	RNA binding protein, fox-1 homolog (C. elegans) 2	protein-coding
mm_169173.1	chr13	65699184	65699186	-	1	NA	Intergenic	Intergenic	-414268	NM_001177832	628709	Mm.390595	NM_001177832	ENSMUSG00000095909	Gm10324	ENSMUSG00000071302	predicted gene 10324	protein-coding
mm_54067.1	chr6	14715185	14715189	-	1	NA	3' UTR (NM_080464, exon 4 of 4)	3' UTR (NM_080464, exon 4 of 4)	40087	NM_080464	140491	Mm.209429	NM_080464	ENSMUSG00000042717	Ppp1r3a	GM|RG1|RGL	protein phosphatase 1, regulatory (inhibitor) subunit 3A	protein-coding
mm_95925.1	chr11	58307056	58307104	+	1	NA	promoter-TSS (NM_001040686)	promoter-TSS (NM_001040686)	11	NM_001040686	103836	Mm.41440	NM_182996	ENSMUSG00000037243	Zfp692	AI746306|AI839920|Zfp692-ps|Znf692	zinc finger protein 692	protein-coding
mm_167610.1	chr9	55209030	55209032	+	1	NA	promoter-TSS (NM_028049)	promoter-TSS (NM_028049)	96	NM_028049	71999	Mm.276429	NM_028049	ENSMUSG00000032309	Fbxo22	0610033L19Rik|1600016C16Rik	F-box protein 22	protein-coding
mm_93700.1	chr10	118082948	118082957	-	1	NA	Intergenic	Intergenic	-58835	NM_001162904	17245	Mm.101191	NM_010785	ENSMUSG00000020212	Mdm1	Arrd2|Mdm-1	transformed mouse 3T3 cell double minute 1	protein-coding
mm_89970.1	chr10	111506396	111506419	+	1	NA	exon (NM_009344, exon 1 of 2)	exon (NM_009344, exon 1 of 2)	121	NM_009344	21664	Mm.3117	NM_009344	ENSMUSG00000020205	Phlda1	DT1P1B11|TDAG51|Tdag	pleckstrin homology like domain, family A, member 1	protein-coding
mm_153061.1	chr19	32186534	32186540	-	1	NA	intron (NM_001168525, intron 5 of 9)	intron (NM_001168525, intron 5 of 9)	24476	NM_001168526	208449	Mm.329810	NM_144792	ENSMUSG00000040451	Sgms1	9530058O11Rik|AI841905|C80702|Mob|Sms1|Sor1|Tmem23	sphingomyelin synthase 1	protein-coding
mm_109072.1	chr12	104345476	104345502	+	1	NA	3' UTR (NM_011458, exon 5 of 5)	3' UTR (NM_011458, exon 5 of 5)	7003	NM_011458	20714	Mm.291569	NM_011458	ENSMUSG00000058207	Serpina3k	1300001I07Rik|D12Rp54|MMCM2|MMSpi2|RP54|Spi-2|Spi2|contrapsin	serine (or cysteine) peptidase inhibitor, clade A, member 3K	protein-coding
mm_111133.1	chr12	81532812	81532818	-	1	NA	promoter-TSS (NM_025292)	promoter-TSS (NM_025292)	96	NM_001309847	105940408		NM_001309847	ENSMUSG00000021139	Synj2bp-cox16	ARIP2a	Synj2bp-cox16 readthrough	protein-coding
mm_80896.1	chr9	99632644	99632658	+	1	NA	intron (NM_001311142, intron 1 of 15)	intron (NM_001311142, intron 1 of 15)	3073	NM_001311142	72507	Mm.221455	NM_028258	ENSMUSG00000037784	Dzip1l	2610524A10Rik|AI663976	DAZ interacting protein 1-like	protein-coding
mm_58922.1	chr7	17814070	17814078	+	1	NA	exon (NM_025957, exon 2 of 3)	exon (NM_025957, exon 2 of 3)	1392	NM_025957	67084	Mm.33709	NM_025957	ENSMUSG00000023185	Ceacam14	1600021E03Rik|1600025E09Rik|AV033953	carcinoembryonic antigen-related cell adhesion molecule 14	protein-coding
mm_79738.1	chr9	62345388	62345405	+	1	NA	intron (NM_009672, intron 1 of 6)	intron (NM_009672, intron 1 of 6)	4053	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	protein-coding
mm_126026.1	chr15	76698173	76698221	+	1	NA	intron (NM_182805, intron 5 of 10)	intron (NM_182805, intron 5 of 10)	1471	NM_182805	76282	Mm.30130	NM_182805	ENSMUSG00000022546	Gpt	1300007J06Rik|2310022B03Rik|ALT|ALT1|Gpt-1|Gpt1	glutamic pyruvic transaminase, soluble	protein-coding
mm_107070.1	chr12	16895118	16895132	+	1	NA	5' UTR (NM_009072, exon 1 of 33)	5' UTR (NM_009072, exon 1 of 33)	147	NM_009072	19878	Mm.276024	NM_009072	ENSMUSG00000020580	Rock2	B230113H15Rik|ROKalpha|Rho-kinase|Rock-II|Rock2m|mKIAA0619	Rho-associated coiled-coil containing protein kinase 2	protein-coding
mm_72383.1	chr8	81559003	81559011	+	1	NA	intron (NM_001297591, intron 2 of 24)	RMER19A|LTR|ERVK	216445	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_32018.1	chr4	95052561	95052573	+	1	NA	promoter-TSS (NM_010591)	promoter-TSS (NM_010591)	-345	NM_010591	16476	Mm.275071	NM_010591	ENSMUSG00000052684	Jun	AP-1|Junc|c-jun	jun proto-oncogene	protein-coding
mm_29787.1	chr3	127541425	127541464	-	1	NA	intron (NM_138593, intron 10 of 12)	intron (NM_138593, intron 10 of 12)	-3784	NR_030403	723948		NR_030403	ENSMUSG00000076252	Mir302b	Mirn302b|mir-302b	microRNA 302b	ncRNA
mm_52289.1	chr6	108664740	108664750	+	1	NA	exon (NM_011498, exon 5 of 5)	exon (NM_011498, exon 5 of 5)	-3811	NR_104577	75394	Mm.395061	NR_040757	ENSMUSG00000087341	0610040F04Rik	-	RIKEN cDNA 0610040F04 gene	ncRNA
mm_54898.1	chr6	47454638	47454648	-	1	NA	intron (NM_012042, intron 1 of 21)	CpG	319	NM_012042	26965	Mm.87611	NM_012042	ENSMUSG00000029686	Cul1	-	cullin 1	protein-coding
mm_7975.1	chr1	134063367	134063372	-	1	NA	Intergenic	Intergenic	15786	NM_007570	12227	Mm.392646	NM_007570	ENSMUSG00000020423	Btg2	AA959598|APRO1|Pc3|TIS21	B cell translocation gene 2, anti-proliferative	protein-coding
mm_8578.1	chr1	155812860	155812883	-	1	NA	promoter-TSS (NM_023268)	promoter-TSS (NM_023268)	28	NM_023268	104009	Mm.27035	NM_023268	ENSMUSG00000033684	Qsox1	1300003H02Rik|QSOX|Qscn6|SOx	quiescin Q6 sulfhydryl oxidase 1	protein-coding
mm_37464.1	chr4	123479154	123479195	-	1	NA	intron (NM_001199136, intron 35 of 97)	intron (NM_001199136, intron 35 of 97)	-67263	NM_001167918	442834	Mm.483803	NM_001167918		D830031N03Rik	Kiaa0754|mKIAA0754	RIKEN cDNA D830031N03 gene	protein-coding
mm_118900.1	chr14	26646707	26646715	+	1	NA	exon (NM_007479, exon 2 of 6)	exon (NM_007479, exon 2 of 6)	8514	NM_007479	11843	Mm.297768	NM_007479	ENSMUSG00000021877	Arf4	AA407803	ADP-ribosylation factor 4	protein-coding
mm_14782.1	chr2	145858441	145858463	+	1	NA	exon (NM_028724, exon 8 of 13)	exon (NM_028724, exon 8 of 13)	-44789	NM_026425	67877	Mm.151168	NM_026425	ENSMUSG00000002728	Naa20	1500004D14Rik|2900026I01Rik|AU041458|D2Ertd186e|Nat5	N(alpha)-acetyltransferase 20, NatB catalytic subunit	protein-coding
mm_17807.1	chr2	33439622	33439665	-	1	NA	Intergenic	Intergenic	-8319	NM_001276332	241311	Mm.296512	NM_001085507	ENSMUSG00000068966	Zbtb34	Gm349|mKIAA1993	zinc finger and BTB domain containing 34	protein-coding
mm_75491.1	chr8	50326839	50326842	-	1	NA	Intergenic	Intergenic	-41272	NR_046067	100039954	Mm.400419	NR_046067	ENSMUSG00000110281	Gm2516	-	predicted gene 2516	ncRNA
mm_718.1	chr1	42695730	42695776	+	1	NA	promoter-TSS (NR_027826)	promoter-TSS (NR_027826)	-928	NR_027826	66297	Mm.45203	NM_183252	ENSMUSG00000060424	Pantr1	2610017I09Rik|Pou3f3os|linc-Brn1a	POU domain, class 3, transcription factor 3 adjacent noncoding transcript 1	ncRNA
mm_22989.1	chr3	33800159	33800234	+	1	NA	promoter-TSS (NM_025978)	promoter-TSS (NM_025978)	13	NM_025978	67120	Mm.275710	NM_025978	ENSMUSG00000027677	Ttc14	2700016E08Rik|4930434D01Rik|4931403I22Rik|4933402I15Rik|AI662468|AU014779|AW561908|cI-44|mKIAA1980	tetratricopeptide repeat domain 14	protein-coding
mm_62436.1	chr7	101366573	101366593	+	1	NA	intron (NM_001040111, intron 1 of 33)	intron (NM_001040111, intron 1 of 33)	-11539	NM_001040112	69710	Mm.277687	NM_027180	ENSMUSG00000032812	Arap1	2410002L19Rik|Centd2|mKIAA0782	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	protein-coding
mm_36174.1	chr4	62087289	62087306	-	1	NA	promoter-TSS (NM_001039544)	promoter-TSS (NM_001039544)	15	NM_001039544	17842	Mm.250267	NM_010845	ENSMUSG00000066154	Mup3	MUP15|MUPIII|Mup-3|Mup25	major urinary protein 3	protein-coding
mm_122539.1	chr14	47418195	47418217	-	1	NA	5' UTR (NM_144553, exon 1 of 19)	5' UTR (NM_144553, exon 1 of 19)	201	NM_144553	218977	Mm.240543	NM_144553	ENSMUSG00000037544	Dlgap5	C77459|C86398|Dap-5|Dlg7|Hurp|mKIAA0008	discs, large (Drosophila) homolog-associated protein 5	protein-coding
mm_154073.1	chr19	56390028	56390043	-	1	NA	promoter-TSS (NM_198059)	promoter-TSS (NM_198059)	3	NM_198059	18175	Mm.386769	NM_008733	ENSMUSG00000049134	Nrap	-	nebulin-related anchoring protein	protein-coding
mm_71100.1	chr8	35375769	35375787	+	1	NA	promoter-TSS (NM_177741)	promoter-TSS (NM_177741)	37	NM_177741	244416	Mm.247126	NM_177741	ENSMUSG00000046794	Ppp1r3b	6430576E21|AW821953|GL|PTG	protein phosphatase 1, regulatory (inhibitor) subunit 3B	protein-coding
mm_152450.1	chr19	10829922	10830042	-	1	NA	promoter-TSS (NM_009852)	promoter-TSS (NM_009852)	76	NM_001037801	12511	Mm.290897	NM_009852	ENSMUSG00000024670	Cd6	-	CD6 antigen	protein-coding
mm_94263.1	chr11	3514898	3514928	+	1	NA	5' UTR (NM_053267, exon 1 of 5)	5' UTR (NM_053267, exon 1 of 5)	229	NM_053267	114679	Mm.34046	NM_053267	ENSMUSG00000075702	Selenom	1500040L08Rik|A230103K18|Selm|Sepm	selenoprotein M	protein-coding
mm_162930.1	chr10	123264041	123264068	+	1	NA	promoter-TSS (NM_182807)	promoter-TSS (NM_182807)	-22	NM_182807	268354	Mm.51939	NM_182807	ENSMUSG00000044071	Fam19a2	6330575M02|FAM19A2 TAFA-2|TAFA2|Tafa-2	family with sequence similarity 19, member A2	protein-coding
mm_2265.1	chr1	91180005	91180024	+	1	NA	5' UTR (NM_001168392, exon 1 of 4)	5' UTR (NM_001168392, exon 1 of 4)	192	NM_001168392	51801	Mm.3272	NM_016894	ENSMUSG00000034353	Ramp1	9130218E19Rik	receptor (calcitonin) activity modifying protein 1	protein-coding
mm_97903.1	chr11	83437647	83437651	+	1	NA	promoter-TSS (NM_025492)	promoter-TSS (NM_025492)	-45	NM_025492	66330	Mm.44800	NM_025492	ENSMUSG00000035085	1700020L24Rik	-	RIKEN cDNA 1700020L24 gene	protein-coding
mm_34687.1	chr4	151933686	151933696	+	1	NA	promoter-TSS (NM_172704)	promoter-TSS (NM_172704)	-29	NM_172704	230935	Mm.21353	NM_172704	ENSMUSG00000039768	Dnajc11	E030019A03Rik	DnaJ heat shock protein family (Hsp40) member C11	protein-coding
mm_146952.1	chr18	32559858	32559887	-	1	NA	5' UTR (NM_001048207, exon 1 of 3)	5' UTR (NM_001048207, exon 1 of 3)	162	NM_001347610	71683	Mm.292145	NM_027863	ENSMUSG00000090523	Gypc	0610037F22Rik|Cd236r	glycophorin C	protein-coding
mm_44489.1	chr5	23675790	23675802	-	1	NA	Intergenic	CpG	36871	NR_038090	433855	Mm.205125	NR_015554	ENSMUSG00000105987	AI506816	-	expressed sequence AI506816	ncRNA
mm_21056.1	chr2	152654262	152654266	-	1	NA	Intergenic	Intergenic	-15197	NM_010376	14950	Mm.277327	NM_010376	ENSMUSG00000019188	H13	1200006O09Rik|4930443L17Rik|5031424B04Rik|AV020344|H-13|Hm13|PSL3|Spp	histocompatibility 13	protein-coding
mm_37512.1	chr4	123896617	123896625	-	1	NA	Intergenic	Intergenic	-8392	NM_019660	56309	Mm.446553	NM_019660	ENSMUSG00000028647	Mycbp	5730488M09Rik|AW552132|AW742590|Amy-1	MYC binding protein	protein-coding
mm_136276.1	chr16	91063818	91063844	-	1	NA	intron (NM_028905, intron 1 of 2)	RMER5|LTR|ERV1	5314	NM_001163695	74387	Mm.236220	NM_028905	ENSMUSG00000039851	4932438H23Rik	4931406G06Rik|AI550392	RIKEN cDNA 4932438H23 gene	protein-coding
mm_123491.1	chr14	66110150	66110175	-	1	NA	exon (NM_007940, exon 3 of 19)	exon (NM_007940, exon 3 of 19)	498	NM_001271421	13850	Mm.15295	NM_007940	ENSMUSG00000022040	Ephx2	CEH|Eph2|SEH|sEP	epoxide hydrolase 2, cytoplasmic	protein-coding
mm_122171.1	chr14	31494258	31494265	-	1	NA	promoter-TSS (NM_028932)	promoter-TSS (NM_028932)	716	NM_025907	67011	Mm.291731	NM_025907	ENSMUSG00000021891	Mettl6	1600013P15Rik|AI467521|AU020711	methyltransferase like 6	protein-coding
mm_28417.1	chr3	90433015	90433025	-	1	NA	5' UTR (NM_178876, exon 1 of 31)	5' UTR (NM_178876, exon 1 of 31)	616	NM_145540	229543	Mm.268564	NM_145540	ENSMUSG00000027933	Ints3	C77668	integrator complex subunit 3	protein-coding
mm_65360.1	chr7	25002824	25002837	-	1	NA	intron (NM_001290469, intron 1 of 22)	intron (NM_001290469, intron 1 of 22)	3107	NM_001290469	232975	Mm.44101	NM_144921	ENSMUSG00000040907	Atp1a3	Atpa-2	ATPase, Na+/K+ transporting, alpha 3 polypeptide	protein-coding
mm_136816.1	chr17	12396632	12396640	+	1	NA	exon (NM_008877, exon 9 of 19)	exon (NM_008877, exon 9 of 19)	18027	NM_008877	18815	Mm.971	NM_008877	ENSMUSG00000059481	Plg	AI649309|Pg	plasminogen	protein-coding
mm_21490.1	chr2	163357371	163357379	-	1	NA	intron (NM_021566, intron 2 of 5)	ID_B1|SINE|B4	40598	NM_021566	59091	Mm.34459	NM_021566	ENSMUSG00000017817	Jph2	1110002E14Rik|JP-2|Jp2	junctophilin 2	protein-coding
mm_31409.1	chr4	48047902	48047916	+	1	NA	intron (NM_015743, intron 1 of 7)	intron (NM_015743, intron 1 of 7)	2604	NM_015743	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_147094.1	chr18	35649336	35649344	-	1	NA	promoter-TSS (NM_027222)	promoter-TSS (NM_027222)	27	NM_027222	69816	Mm.27252	NM_027222	ENSMUSG00000024353	Mzb1	2010001M09Rik|AV064572|PACAP|pERp1	marginal zone B and B1 cell-specific protein 1	protein-coding
mm_130646.1	chr15	100615072	100615124	-	1	NA	promoter-TSS (NM_011873)	promoter-TSS (NM_011873)	12	NR_045701	78445	Mm.44383	NR_045701	ENSMUSG00000097093	C330013E15Rik	-	RIKEN cDNA C330013E15 gene	ncRNA
mm_126247.1	chr15	79026992	79027005	+	1	NA	Intergenic	Intergenic	-1214	NM_008197	14958	Mm.24350	NM_008197	ENSMUSG00000096210	H1f0	D130017D06Rik|H1(0)|H1fv	H1 histone family, member 0	protein-coding
mm_168453.1	chr11	41219071	41219079	+	1	NA	Intergenic	LTRIS2|LTR|ERV1	-463789	NM_009831	12450	Mm.2103	NM_009831	ENSMUSG00000020326	Ccng1	AI314029	cyclin G1	protein-coding
mm_69758.1	chr7	140999471	140999502	-	1	NA	Intergenic	Intergenic	11258	NM_025378	66141	Mm.141021	NM_025378	ENSMUSG00000025492	Ifitm3	1110004C05Rik|Cd225|Cdw217|DSPA2b|Fgls|IP15|mil-1	interferon induced transmembrane protein 3	protein-coding
mm_12000.1	chr2	57238415	57238425	+	1	NA	promoter-TSS (NM_010274)	promoter-TSS (NM_010274)	38	NM_010274	14571	Mm.3711	NM_010274	ENSMUSG00000026827	Gpd2	AA408484|AI448216|AU021455|AW494132|GPDH|Gdm1|Gpd-m|Gpdh-m|TISP38	glycerol phosphate dehydrogenase 2, mitochondrial	protein-coding
mm_11530.1	chr2	32628413	32628415	+	1	NA	promoter-TSS (NM_001198792)	promoter-TSS (NM_001198792)	24	NM_001198792	11636	Mm.29189	NM_021515	ENSMUSG00000026817	Ak1	Ak-1|B430205N08Rik	adenylate kinase 1	protein-coding
mm_13460.1	chr2	105674544	105674558	+	1	NA	intron (NM_001244201, intron 1 of 11)	intron (NM_001244201, intron 1 of 11)	-1193	NM_001244200	18508	Mm.3608	NM_013627	ENSMUSG00000027168	Pax6	1500038E17Rik|AEY11|Dey|Gsfaey11|Pax-6|Sey	paired box 6	protein-coding
mm_124255.1	chr14	101892335	101892336	-	1	NA	intron (NM_001347628, intron 8 of 26)	intron (NM_001347628, intron 8 of 26)	51712	NM_001347628	380928	Mm.218981	NM_201529	ENSMUSG00000033060	Lmo7	C78582|FBXO20|Gm914|mKIAA0858	LIM domain only 7	protein-coding
mm_93036.1	chr10	88338669	88338681	-	1	NA	intron (NM_027878, intron 3 of 6)	intron (NM_027878, intron 3 of 6)	18400	NM_027878	71712	Mm.35450	NM_027878	ENSMUSG00000020057	Dram1	1200002N14Rik|Dram	DNA-damage regulated autophagy modulator 1	protein-coding
mm_44263.1	chr5	5559502	5559517	-	1	NA	promoter-TSS (NM_153116)	promoter-TSS (NM_153116)	-8	NM_153116	207704	Mm.323984	NM_153116	ENSMUSG00000040464	Gtpbp10	4930545J22Rik|BC034507	GTP-binding protein 10 (putative)	protein-coding
mm_79818.1	chr9	64340412	64340447	+	1	NA	promoter-TSS (NM_172519)	promoter-TSS (NM_172519)	28	NM_172519	213550	Mm.268341	NM_172519	ENSMUSG00000032396	Dis3l	AV340375	DIS3 like exosome 3'-5' exoribonuclease	protein-coding
mm_31240.1	chr4	44756610	44756682	+	1	NA	promoter-TSS (NM_138590)	promoter-TSS (NM_138590)	87	NM_138590	319885	Mm.331576	NM_138590	ENSMUSG00000035649	Zcchc7	4930572I07Rik|D4Wsu132e	zinc finger, CCHC domain containing 7	protein-coding
mm_9183.1	chr1	171059590	171059595	-	1	NA	promoter-TSS (NM_010188)	promoter-TSS (NM_010188)	-189	NM_010188	14131	Mm.22119	NM_010188	ENSMUSG00000059498	Fcgr3	CD16	Fc receptor, IgG, low affinity III	protein-coding
mm_123446.1	chr14	65149834	65149847	-	1	NA	Intergenic	CpG	-51734	NM_018788	54616	Mm.103748	NM_018788	ENSMUSG00000021978	Extl3	2900009G18Rik|AU040105|Ext1l|mKIAA0519	exostoses (multiple)-like 3	protein-coding
mm_163993.1	chr14	64104339	64104340	+	1	NA	promoter-TSS (NM_028525)	promoter-TSS (NM_028525)	16	NM_028525	73382	Mm.481055	NM_028525	ENSMUSG00000021966	Prss52	1700049K14Rik|Tesp3	protease, serine 52	protein-coding
mm_127991.1	chr15	12550188	12550209	-	1	NA	intron (NM_001081064, intron 1 of 23)	intron (NM_001081064, intron 1 of 23)	42358	NM_001081064	68070	Mm.423205	NM_001081064	ENSMUSG00000022197	Pdzd2	4930537L06Rik|A930022H17Rik|Gm21706|Gm82|Pdzk3|mKIAA0300	PDZ domain containing 2	protein-coding
mm_123464.1	chr14	65833964	65833974	-	1	NA	promoter-TSS (NM_028039)	promoter-TSS (NM_028039)	0	NM_028039	71988	Mm.249280	NM_028039	ENSMUSG00000022034	Esco2	2410004I17Rik|D030072L07Rik	establishment of sister chromatid cohesion N-acetyltransferase 2	protein-coding
mm_45346.1	chr5	65858145	65858161	-	1	NA	Intergenic	Intergenic	-5416	NM_001081105	74734	Mm.20323	NM_001081105	ENSMUSG00000029204	Rhoh	5830400A04Rik|AU019774|Arhh	ras homolog family member H	protein-coding
mm_3043.1	chr1	134040373	134040382	+	1	NA	exon (NM_021355, exon 2 of 3)	exon (NM_021355, exon 2 of 3)	2862	NM_021355	14264	Mm.287146	NM_021355	ENSMUSG00000041559	Fmod	AI131919|AU041740|SLRR2E	fibromodulin	protein-coding
mm_52448.1	chr6	113660710	113660718	+	1	NA	intron (NM_001113553, intron 2 of 11)	ID_B1|SINE|B4	22247	NM_001113553	108960	Mm.152142	NM_172161	ENSMUSG00000060477	Irak2	6330415L08Rik|AI649099|IRAK-2	interleukin-1 receptor-associated kinase 2	protein-coding
mm_51977.1	chr6	91878035	91878089	+	1	NA	promoter-TSS (NM_172730)	promoter-TSS (NM_172730)	9	NM_172730	232236	Mm.234879	NM_172730	ENSMUSG00000034083	Ccdc174	C130022K22Rik	coiled-coil domain containing 174	protein-coding
mm_141484.1	chr17	31208814	31208835	-	1	NA	intron (NM_177823, intron 1 of 13)	intron (NM_177823, intron 1 of 13)	758	NM_177823	328795	Mm.387930	NM_177823	ENSMUSG00000042345	Ubash3a	5830413C03Rik|C330001M22|Sts-2|TULA|TULA-1	ubiquitin associated and SH3 domain containing, A	protein-coding
mm_172083.1	chr6	145932971	145932975	-	1	NA	intron (NM_001310837, intron 1 of 2)	LSU-rRNA_Hsa|rRNA|rRNA	1100	NM_001310837	16651	Mm.49689	NM_010656	ENSMUSG00000030255	Sspn	Krag	sarcospan	protein-coding
mm_100267.1	chr11	117426203	117426212	+	1	NA	Intergenic	Intergenic	-4490	NR_136918	667423	Mm.383716	NR_136918	ENSMUSG00000083705	Gm8624	EG667423	ribosomal protein S23 pseudogene	pseudo
mm_55512.1	chr6	69992994	69993009	-	1	NA	Intergenic	Intergenic	-665827	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_12719.1	chr2	78051221	78051228	+	1	NA	promoter-TSS (NR_108098)	promoter-TSS (NR_108098)	47	NR_108098	78158	Mm.78473	NR_108098	ENSMUSG00000085431	4930440I19Rik	-	RIKEN cDNA 4930440I19 gene	ncRNA
mm_78854.1	chr9	44379504	44379513	+	1	NA	promoter-TSS (NM_021395)	promoter-TSS (NM_021395)	18	NM_021395	12282	Mm.116721	NM_021395	ENSMUSG00000032115	Hyou1	AI415631|CBP-140|Cab140|Grp170|Orp150	hypoxia up-regulated 1	protein-coding
mm_52484.1	chr6	114643095	114643105	+	1	NA	promoter-TSS (NM_028835)	promoter-TSS (NM_028835)	3	NM_001253717	74244	Mm.275332	NM_028835	ENSMUSG00000030314	Atg7	1810013K23Rik|Agp7|Apg7l|Atg7l|Gm21553	autophagy related 7	protein-coding
mm_170052.1	chr17	29007923	29007923	-	1	NA	promoter-TSS (NM_134115)	promoter-TSS (NM_134115)	14	NM_134115	106504	Mm.439986	NM_134115	ENSMUSG00000024006	Stk38	5830476G13Rik|9530097A09Rik|AA617404|Ndr1	serine/threonine kinase 38	protein-coding
mm_84306.1	chr9	63602497	63602505	-	1	NA	promoter-TSS (NM_025857)	promoter-TSS (NM_025857)	-8	NM_001311098	78250	Mm.444612	NM_030068	ENSMUSG00000037801	Iqch	4921504K03Rik	IQ motif containing H	protein-coding
mm_157026.1	chrX	7898951	7898983	-	1	NA	promoter-TSS (NM_001252528)	promoter-TSS (NM_001252528)	33	NM_001252528	54633	Mm.14616	NM_019478	ENSMUSG00000031157	Pqbp1	PQBP-1|Sfc2|npw38	polyglutamine binding protein 1	protein-coding
mm_63115.1	chr7	122671335	122671363	+	1	NA	promoter-TSS (NM_019430)	promoter-TSS (NM_019430)	-395	NM_019430	54376	Mm.444212	NM_019430	ENSMUSG00000066189	Cacng3	-	calcium channel, voltage-dependent, gamma subunit 3	protein-coding
mm_56148.1	chr6	87826518	87826520	-	1	NA	intron (NM_133934, intron 6 of 10)	PB1D10|SINE|Alu	12240	NM_133934	57905	Mm.241546	NM_133934	ENSMUSG00000030056	Isy1	5830446M03Rik|AI181014|AU020769	ISY1 splicing factor homolog	protein-coding
mm_56843.1	chr6	117879513	117879528	-	1	NA	Intergenic	CpG	16443	NM_001001792	22685	Mm.249661	NM_008616	ENSMUSG00000042097	Zfp239	Mok-2|Mok2|Znf239	zinc finger protein 239	protein-coding
mm_157825.1	chrX	74224790	74224820	-	1	NA	exon (NM_001290421, exon 46 of 47)	exon (NM_001290421, exon 46 of 47)	21729	NM_010227	192176	Mm.295533	NM_010227	ENSMUSG00000031328	Flna	ABP-280|Dilp2|F730004A14Rik|Fln1|GENA 379|filamin-1	filamin, alpha	protein-coding
mm_160770.1	chr10	112271088	112271088	+	1	NA	promoter-TSS (NM_001025581)	promoter-TSS (NM_001025581)	-35	NM_001025581	268345	Mm.336242	NM_001025581	ENSMUSG00000035681	Kcnc2	AW047325|B230117I07|KShIIIA|Kv3.2	potassium voltage gated channel, Shaw-related subfamily, member 2	protein-coding
mm_39182.1	chr4	155785050	155785052	-	1	NA	intron (NM_001033394, intron 1 of 1)	intron (NM_001033394, intron 1 of 1)	823	NM_001033394	320587	Mm.384382	NM_001033394	ENSMUSG00000073680	Tmem88b	A230069A22Rik	transmembrane protein 88B	protein-coding
mm_83204.1	chr9	41687838	41687845	-	1	NA	Intergenic	Intergenic	105915	NR_029822	387236		NR_029822	ENSMUSG00000093354	Mir125b-1	Mirn125b|Mirn125b-1|mir-125b-1	microRNA 125b-1	ncRNA
mm_94500.1	chr11	7197651	7197656	+	1	NA	promoter-TSS (NM_008341)	promoter-TSS (NM_008341)	-134	NM_008341	16006	Mm.21300	NM_008341	ENSMUSG00000020429	Igfbp1	-	insulin-like growth factor binding protein 1	protein-coding
mm_5704.1	chr1	43447154	43447164	-	1	NA	intron (NM_010879, intron 1 of 4)	intron (NM_010879, intron 1 of 4)	1408	NM_010879	17974	Mm.389903	NM_010879	ENSMUSG00000066877	Nck2	4833426I10Rik|Grb4|NCKbeta|Nck-2	non-catalytic region of tyrosine kinase adaptor protein 2	protein-coding
mm_87340.1	chr10	43479202	43479249	+	1	NA	promoter-TSS (NM_199028)	promoter-TSS (NM_199028)	85	NM_199028	331623	Mm.490388	NM_199028	ENSMUSG00000038214	Bend3	mKIAA1553	BEN domain containing 3	protein-coding
mm_100682.1	chr11	3497424	3497435	-	1	NA	intron (NM_172439, intron 9 of 12)	intron (NM_172439, intron 9 of 12)	7392	NM_172439	170835	Mm.24313	NM_172439	ENSMUSG00000034570	Inpp5j	Pib5pa|Pipp	inositol polyphosphate 5-phosphatase J	protein-coding
mm_169549.1	chr15	103242378	103242382	+	1	NA	exon (NM_010447, exon 6 of 10)	exon (NM_010447, exon 6 of 10)	1926	NR_002883	434858	Mm.391346	NR_002883		Gm5643	EG434858	heterogeneous nuclear ribonucleoprotein A1 pseudogene	pseudo
mm_138733.1	chr17	36963789	36963797	+	1	NA	intron (NM_029602, intron 1 of 2)	intron (NM_029602, intron 1 of 2)	5201	NM_029602	76416	Mm.26684	NM_029602	ENSMUSG00000036214	Znrd1as	1700022C21Rik|AI746295|Znrd1-as	zinc ribbon domain containing 1, antisense	protein-coding
mm_12570.1	chr2	72995932	72995939	+	1	NA	Intergenic	Intergenic	-15489	NM_001018042	20687	Mm.124328	NM_011450	ENSMUSG00000027109	Sp3	D130027J01Rik	trans-acting transcription factor 3	protein-coding
mm_34126.1	chr4	139261973	139261982	+	1	NA	intron (NM_001037761, intron 3 of 9)	intron (NM_001037761, intron 3 of 9)	48723	NM_145384	212555	Mm.45131	NM_145384	ENSMUSG00000028744	Pqlc2	BC019216	PQ loop repeat containing 2	protein-coding
mm_155664.1	chrX	87921151	87921153	+	1	NA	intron (NM_001160403, intron 1 of 10)	intron (NM_001160403, intron 1 of 10)	194471	NM_001160403	331461	Mm.121680	NM_001160403	ENSMUSG00000052372	Il1rapl1	6330532G10Rik|C030039N24|IL1R8|IL1RAPL|MRX34|OPHN4|TIGIRR-2	interleukin 1 receptor accessory protein-like 1	protein-coding
mm_156074.1	chrX	109161681	109161700	+	1	NA	3' UTR (NM_019989, exon 4 of 4)	3' UTR (NM_019989, exon 4 of 4)	-35066	NM_001037917	622976	Mm.482747	NM_001037917	ENSMUSG00000048621	Gm6377	EG622976	predicted gene 6377	protein-coding
mm_6424.1	chr1	73930717	73930731	-	1	NA	intron (NM_001289895, intron 22 of 32)	intron (NM_001289895, intron 22 of 32)	-66258	NR_045311	109198	Mm.359721	NR_045311	ENSMUSG00000100301	6030407O03Rik	-	RIKEN cDNA 6030407O03 gene	ncRNA
mm_20341.1	chr2	127656210	127656232	-	1	NA	5' UTR (NM_001171187, exon 1 of 3)	5' UTR (NM_001171187, exon 1 of 3)	474	NM_010762	17153	Mm.39040	NM_010762	ENSMUSG00000027375	Mal	Mpv17|Vip17	myelin and lymphocyte protein, T cell differentiation protein	protein-coding
mm_50285.1	chr6	47453875	47453907	+	1	NA	promoter-TSS (NM_012042)	promoter-TSS (NM_012042)	-433	NM_012042	26965	Mm.87611	NM_012042	ENSMUSG00000029686	Cul1	-	cullin 1	protein-coding
mm_165459.1	chr2	158258219	158258219	+	1	NA	promoter-TSS (NM_177850)	promoter-TSS (NM_177850)	-22	NM_177850	329547	Mm.260883	NM_177850	ENSMUSG00000052922	Bpi	9230105K17Rik|Bpifd1	bactericidal permeablility increasing protein	protein-coding
mm_158417.1	chrX	137120129	137120133	-	1	NA	5' UTR (NM_007957, exon 1 of 5)	5' UTR (NM_007957, exon 1 of 5)	195	NM_007957	13984	Mm.8017	NM_007957	ENSMUSG00000023443	Esx1	Spx1	extraembryonic, spermatogenesis, homeobox 1	protein-coding
mm_172981.1	chr9	97228201	97228210	-	1	NA	Intergenic	(CCA)n|Simple_repeat|Simple_repeat	-117164	NM_138756	192287	Mm.228067	NM_138756	ENSMUSG00000032449	Slc25a36	C330005L02Rik	solute carrier family 25, member 36	protein-coding
mm_65234.1	chr7	19749465	19749542	-	1	NA	promoter-TSS (NM_001159724)	promoter-TSS (NM_001159724)	70	NM_008990	19294	Mm.4341	NM_008990	ENSMUSG00000062300	Nectin2	AI325026|AI987993|Cd112|MPH|Pvr|Pvrl2|Pvs|nectin-2	nectin cell adhesion molecule 2	protein-coding
mm_13726.1	chr2	117421675	117421681	+	1	NA	Intergenic	Intergenic	-78801	NM_011246	19419	Mm.42150	NM_011246	ENSMUSG00000027347	Rasgrp1	Rasgrp	RAS guanyl releasing protein 1	protein-coding
mm_157767.1	chrX	73712523	73712543	-	1	NA	exon (NM_012060, exon 3 of 8)	exon (NM_012060, exon 3 of 8)	3671	NM_012060	27061	Mm.17	NM_012060	ENSMUSG00000002015	Bcap31	Bap31	B cell receptor associated protein 31	protein-coding
mm_65841.1	chr7	29247123	29247138	-	1	NA	TTS (NM_028179)	TTS (NM_028179)	1337	NM_028179	72275	Mm.441142	NM_028179	ENSMUSG00000030587	2200002D01Rik	2010005J02Rik|H2RSP|IMUP|IMUP-1|IMUP-2	RIKEN cDNA 2200002D01 gene	protein-coding
mm_53937.1	chr6	4757062	4757084	-	1	NA	exon (NM_130877, exon 2 of 2)	exon (NM_130877, exon 2 of 2)	9767	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_64560.1	chr7	144837862	144837877	+	1	NA	promoter-TSS (NM_008007)	promoter-TSS (NM_008007)	-743	NM_008007	14174	Mm.4947	NM_008007	ENSMUSG00000031074	Fgf3	Fgf-3|Int-2|Int-P	fibroblast growth factor 3	protein-coding
mm_16869.1	chr2	12301051	12301095	-	1	NA	promoter-TSS (NR_040353)	promoter-TSS (NR_040353)	-173	NR_040353	338535	Mm.483275	NR_040353	ENSMUSG00000086843	E030013I19Rik	-	RIKEN cDNA E030013I19 gene	ncRNA
mm_81123.1	chr9	106463381	106463412	+	1	NA	TTS (NM_001159652)	TTS (NM_001159652)	2544	NM_001159652	436090	Mm.482905	NM_001159652	ENSMUSG00000091735	Gpr62	4933402E03Rik	G protein-coupled receptor 62	protein-coding
mm_120041.1	chr14	56449820	56449821	+	1	NA	intron (NM_001033043, intron 11 of 36)	intron (NM_001033043, intron 11 of 36)	47123	NM_001033043	30054	Mm.287783	NM_001033043	ENSMUSG00000000365	Rnf17	MMIP-2|Mmip2|TDRD4	ring finger protein 17	protein-coding
mm_29177.1	chr3	106521793	106521802	-	1	NA	intron (NM_001293694, intron 4 of 8)	intron (NM_001293694, intron 4 of 8)	-26001	NM_001286986	67171	Mm.290488	NM_026013	ENSMUSG00000027900	Dram2	2010305N14Rik|2610318G18Rik|AI647667|Tmem77	DNA-damage regulated autophagy modulator 2	protein-coding
mm_81421.1	chr9	109056278	109056294	+	1	NA	intron (NM_025858, intron 4 of 5)	intron (NM_025858, intron 4 of 5)	1420	NM_026381	66940	Mm.196533	NM_025858	ENSMUSG00000025647	Shisa5	2310008D10Rik|6430628I05Rik|Scotin|mShisa5	shisa family member 5	protein-coding
mm_13129.1	chr2	91764658	91764662	+	1	NA	intron (NM_172669, intron 1 of 17)	intron (NM_172669, intron 1 of 17)	34522	NM_001080754	228361	Mm.436667	NM_172669	ENSMUSG00000040506	Ambra1	2310079H06Rik|A130023A14|AA474864|AV021921|D030051N19Rik|mKIAA1736	autophagy/beclin 1 regulator 1	protein-coding
mm_10610.1	chr2	19012231	19012234	+	1	NA	Intergenic	Intergenic	13913	NR_024323	74629	Mm.117687	NR_024323	ENSMUSG00000026736	4930426L09Rik	-	RIKEN cDNA 4930426L09 gene	ncRNA
mm_138579.1	chr17	35470436	35470441	+	1	NA	exon (NM_010391, exon 2 of 7)	exon (NM_010391, exon 2 of 7)	349	NM_010391	15007	Mm.88795	NM_010391	ENSMUSG00000067235	H2-Q10	H-2Q10|Q10|Qa10	histocompatibility 2, Q region locus 10	protein-coding
mm_160265.1	chr7	110844367	110844367	-	1	NA	promoter-TSS (NM_025999)	promoter-TSS (NM_025999)	14	NM_025999	67150	Mm.96867	NM_025999	ENSMUSG00000030788	Rnf141	2610110L04Rik|AA792898|AU022812|ZFP36|ZNF230	ring finger protein 141	protein-coding
mm_79671.1	chr9	59677072	59677086	+	1	NA	intron (NM_011099, intron 9 of 10)	intron (NM_011099, intron 9 of 10)	20711	NM_001253883	18746	Mm.326167	NM_011099	ENSMUSG00000032294	Pkm	AA414905|AL024370|AL024424|Pk-2|Pk-3|Pk3|Pkm2	pyruvate kinase, muscle	protein-coding
mm_33888.1	chr4	136178274	136178286	+	1	NA	intron (NM_177733, intron 1 of 6)	intron (NM_177733, intron 1 of 6)	-2502	NM_001305399	242705	Mm.307932	NM_177733	ENSMUSG00000018983	E2f2	E2F-2	E2F transcription factor 2	protein-coding
mm_105682.1	chr11	107716457	107716514	-	1	NA	promoter-TSS (NM_007582)	promoter-TSS (NM_007582)	-9	NM_007582	12299	Mm.57093	NM_007582	ENSMUSG00000020722	Cacng1	-	calcium channel, voltage-dependent, gamma subunit 1	protein-coding
mm_171518.1	chr4	146565157	146565159	-	1	NA	Intergenic	CpG	-18285	NR_045468	67524	Mm.444300	NR_045468	ENSMUSG00000086046	1700095A21Rik	-	RIKEN cDNA 1700095A21 gene	ncRNA
mm_135721.1	chr16	55818959	55818960	-	1	NA	intron (NM_001159395, intron 4 of 12)	intron (NM_001159395, intron 4 of 12)	3179	NM_001159394	80859	Mm.247272	NM_030612	ENSMUSG00000035356	Nfkbiz	AA408868|INAP|Mail	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, zeta	protein-coding
mm_24247.1	chr3	89146072	89146075	+	1	NA	TTS (NM_008227)	TTS (NM_008227)	9450	NM_001099779	18770	Mm.383180	NM_013631	ENSMUSG00000041237	Pklr	Pk-1|Pk1|R-PK	pyruvate kinase liver and red blood cell	protein-coding
mm_35491.1	chr4	40948185	40948195	-	1	NA	promoter-TSS (NM_029814)	promoter-TSS (NM_029814)	104	NM_009736	12017	Mm.688	NM_009736	ENSMUSG00000028416	Bag1	BAG-1|Rap46	BCL2-associated athanogene 1	protein-coding
mm_39570.1	chr5	23433084	23433131	+	1	NA	non-coding (NR_040469, exon 1 of 1)	non-coding (NR_040469, exon 1 of 1)	1246	NR_040469	269630	Mm.425231	NR_040469	ENSMUSG00000073147	5031425E22Rik	-	RIKEN cDNA 5031425E22 gene	ncRNA
mm_61387.1	chr7	73105307	73105323	+	1	NA	Intergenic	Intergenic	-3247	NR_046024	625243	Mm.261798	NR_046024	ENSMUSG00000108383	Gm6567	-	predicted gene 6567	ncRNA
mm_34652.1	chr4	150854017	150854050	+	1	NA	intron (NR_040649, intron 1 of 3)	intron (NR_040649, intron 1 of 3)	916	NR_040649	73348	Mm.396218	NR_040649	ENSMUSG00000078492	1700045H11Rik	-	RIKEN cDNA 1700045H11 gene	ncRNA
mm_148399.1	chr19	3787368	3787373	+	1	NA	intron (NM_144871, intron 4 of 11)	Lx2B|LINE|L1	19949	NM_001167885	225888	Mm.278578	NM_144871	ENSMUSG00000045098	Kmt5b	AA117471|C630029K18Rik|Suv4-20h1|Suv420h1	lysine methyltransferase 5B	protein-coding
mm_151254.1	chr19	53929372	53929385	+	1	NA	TTS (NM_001195338)	TTS (NM_001195338)	-14928	NM_001168505	56392	Mm.228669	NM_019658	ENSMUSG00000024976	Shoc2	AU017287|Sur8|mKIAA0862	soc-2 (suppressor of clear) homolog (C. elegans)	protein-coding
mm_157180.1	chrX	9662903	9662942	-	1	NA	promoter-TSS (NM_025975)	promoter-TSS (NM_025975)	61	NM_025975	67117	Mm.29150	NM_025975	ENSMUSG00000031176	Dynlt3	2310075M16Rik|AU042796|Tcte1l	dynein light chain Tctex-type 3	protein-coding
mm_68940.1	chr7	126503268	126503284	-	1	NA	promoter-TSS (NM_183020)	promoter-TSS (NM_183020)	26	NM_183020	233871	Mm.231450	NM_183020	ENSMUSG00000032637	Atxn2l	A2D|A2LG|A2RP|A2lp|Atxnl2	ataxin 2-like	protein-coding
mm_50420.1	chr6	48770983	48771010	+	1	NA	promoter-TSS (NM_031247)	promoter-TSS (NM_031247)	-145	NM_031247	83408	Mm.333050	NM_031247	ENSMUSG00000039264	Gimap3	2010110D23Rik|Gimap5|Ian4	GTPase, IMAP family member 3	protein-coding
mm_168886.1	chr12	46044600	46044600	+	1	NA	Intergenic	L1Md_F2|LINE|L1	774175	NM_021361	664883	Mm.247195	NM_021361	ENSMUSG00000021047	Nova1	9430099M15Rik|G630039L02|Nova-1	neuro-oncological ventral antigen 1	protein-coding
mm_122424.1	chr14	44789936	44789940	-	1	NA	Intergenic	Intergenic	-64951	NM_001162954	666744	Mm.387002	NM_001162954	ENSMUSG00000091923	Gm8267	EG666744	predicted gene 8267	protein-coding
mm_122406.1	chr14	41008224	41008252	-	1	NA	promoter-TSS (NM_001316740)	promoter-TSS (NM_001316740)	28	NM_001316732	70564	Mm.27227	NM_027464	ENSMUSG00000021792	Fam213a	5730469M10Rik|AU040822|Adrx|Pamm	family with sequence similarity 213, member A	protein-coding
mm_93203.1	chr10	94829456	94829483	-	1	NA	intron (NM_018797, intron 20 of 30)	intron (NM_018797, intron 20 of 30)	115109	NM_018797	54712	Mm.256712	NM_018797	ENSMUSG00000074785	Plxnc1	2510048K12Rik|AW742158|CD232|Vespr	plexin C1	protein-coding
mm_146225.1	chr18	77065638	77065685	+	1	NA	promoter-TSS (NM_001164168)	promoter-TSS (NM_001164168)	-19	NM_001164170	17344	Mm.6370	NM_008602	ENSMUSG00000025423	Pias2	6330408K17Rik|AI462206|ARIP3|AU018068|Dib|Miz1|PIASxalpha|PIASxb|PIASxbeta|SIZ2	protein inhibitor of activated STAT 2	protein-coding
mm_109364.1	chr12	109636396	109636432	+	1	NA	TTS (NR_046302)	TTS (NR_046302)	402	NR_046302	449562		NR_046302	ENSMUSG00000088294	AF357425	MBII-48	snoRNA AF357425	snoRNA
mm_9198.1	chr1	171226198	171226221	-	1	NA	exon (NM_013474, exon 4 of 4)	exon (NM_013474, exon 4 of 4)	1155	NM_013474	11807	Mm.389209	NM_013474	ENSMUSG00000005681	Apoa2	Alp-2|Apo-AII|ApoA-II|ApoAII|Apoa-2|Hdl-1	apolipoprotein A-II	protein-coding
mm_113709.1	chr13	43493992	43493994	+	1	NA	Intergenic	L1MB8|LINE|L1	-13020	NM_019930	56705	Mm.148781	NM_019930	ENSMUSG00000038546	Ranbp9	IBAP-1|Ibap1|RanBPM	RAN binding protein 9	protein-coding
mm_28868.1	chr3	97699177	97699206	-	1	NA	exon (NM_001289701, exon 40 of 47)	exon (NM_001289701, exon 40 of 47)	-8629	NR_106084	102466229		NR_106084	ENSMUSG00000098381	Mir7225	Gm27499|mmu-mir-7225	microRNA 7225	ncRNA
mm_44246.1	chr5	5365827	5365827	-	1	NA	intron (NM_011074, intron 2 of 14)	intron (NM_011074, intron 2 of 14)	14424	NM_011074	18647	Mm.389061	NM_011074	ENSMUSG00000028926	Cdk14	Pftk1|mKIAA0834	cyclin-dependent kinase 14	protein-coding
mm_107412.1	chr12	33964337	33964340	+	1	NA	Intergenic	Intergenic	6667	NM_011658	22160	Mm.3280	NM_011658	ENSMUSG00000035799	Twist1	M-Twist|Pde|Ska10|Ska<m10Jus>|Twist|bHLHa38|pdt	twist basic helix-loop-helix transcription factor 1	protein-coding
mm_10388.1	chr2	12924137	12924143	+	1	NA	promoter-TSS (NM_008961)	promoter-TSS (NM_008961)	99	NM_001305437	19212	Mm.229322	NM_008961	ENSMUSG00000026730	Pter	AI790318|Mpr56-1	phosphotriesterase related	protein-coding
mm_92375.1	chr10	76388716	76388718	-	1	NA	promoter-TSS (NR_040580)	promoter-TSS (NR_040580)	-298	NR_040580	67523	Mm.437833	NR_040580	ENSMUSG00000101695	1700094J05Rik	-	RIKEN cDNA 1700094J05 gene	ncRNA
mm_52150.1	chr6	97993290	97993302	+	1	NA	exon (NM_001178049, exon 3 of 10)	exon (NM_001178049, exon 3 of 10)	1513	NM_008601	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_92489.1	chr10	78298193	78298203	-	1	NA	intron (NM_053014, intron 2 of 9)	intron (NM_053014, intron 2 of 9)	42009	NR_106119	102465765		NR_106119	ENSMUSG00000098885	Mir7659	Gm27433|mmu-mir-7659	microRNA 7659	ncRNA
mm_112421.1	chr13	4059588	4059600	+	1	NA	promoter-TSS (NM_134072)	promoter-TSS (NM_134072)	3	NM_134072	105387	Mm.26838	NM_134072	ENSMUSG00000033715	Akr1c14	9030611N15Rik|AW557061	aldo-keto reductase family 1, member C14	protein-coding
mm_84404.1	chr9	65555193	65555203	-	1	NA	3' UTR (NM_153119, exon 6 of 6)	3' UTR (NM_153119, exon 6 of 6)	24889	NM_153119	102595	Mm.247303	NM_153119	ENSMUSG00000050721	Plekho2	AI840980|Plekhq1	pleckstrin homology domain containing, family O member 2	protein-coding
mm_50045.1	chr6	41151645	41151649	+	1	NA	Intergenic	Intergenic	-116138	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_6395.1	chr1	72859800	72859813	-	1	NA	3' UTR (NM_010518, exon 4 of 4)	3' UTR (NM_010518, exon 4 of 4)	15059	NM_010518	16011	Mm.405761	NM_010518	ENSMUSG00000026185	Igfbp5	AI256729|AW208790|IGFBP-5|IGFBP-5P	insulin-like growth factor binding protein 5	protein-coding
mm_82562.1	chr9	21073216	21073239	-	1	NA	TTS (NM_027911)	TTS (NM_027911)	287	NM_001039824	68165	Mm.490294	NM_001039824	ENSMUSG00000079677	Fdx1l	B230118G17Rik|Fdx2	ferredoxin 1-like	protein-coding
mm_12094.1	chr2	60371256	60371259	+	1	NA	intron (NM_013825, intron 2 of 34)	intron (NM_013825, intron 2 of 34)	11974	NM_013825	17076	Mm.2074	NM_013825	ENSMUSG00000026980	Ly75	CD205|DEC-205|DEC205	lymphocyte antigen 75	protein-coding
mm_43928.1	chr5	145083832	145083887	+	1	NA	promoter-TSS (NM_019767)	promoter-TSS (NM_019767)	-10	NM_019767	56443	Mm.371610	NM_019767	ENSMUSG00000029621	Arpc1a	0610010H08Rik|1110030K07Rik|41kDa|AA407347|Sid32|Sid329	actin related protein 2/3 complex, subunit 1A	protein-coding
mm_30350.1	chr3	151749369	151749388	-	1	NA	exon (NM_133871, exon 2 of 8)	exon (NM_133871, exon 2 of 8)	581	NM_133871	99899	Mm.30756	NM_133871	ENSMUSG00000028037	Ifi44	A430056A10Rik|AW261460|MTAP44|p44	interferon-induced protein 44	protein-coding
mm_10436.1	chr2	14174514	14174546	+	1	NA	promoter-TSS (NM_001081310)	promoter-TSS (NM_001081310)	6	NM_001081310	625286	Mm.158781	NM_001081310	ENSMUSG00000061531	Tmem236	2010003H20Rik|Fam23a|Gm613	transmembrane protein 236	protein-coding
mm_124793.1	chr15	8113669	8113679	+	1	NA	exon (NM_133227, exon 3 of 35)	exon (NM_133227, exon 3 of 35)	4361	NM_133227	170762	Mm.295168	NM_133227	ENSMUSG00000022142	Nup155	D930027M19Rik|mKIAA0791	nucleoporin 155	protein-coding
mm_64555.1	chr7	144742058	144742069	+	1	NA	Intergenic	Intergenic	-3471	NM_001242349	101772	Mm.26700	NM_178642	ENSMUSG00000031075	Ano1	Tmem16a	anoctamin 1, calcium activated chloride channel	protein-coding
mm_99235.1	chr11	101063488	101063507	+	1	NA	3' UTR (NM_001243049, exon 21 of 21)	3' UTR (NM_001243049, exon 21 of 21)	-6597	NM_013792	27419	Mm.95452	NM_013792	ENSMUSG00000001751	Naglu	-	alpha-N-acetylglucosaminidase (Sanfilippo disease IIIB)	protein-coding
mm_84142.1	chr9	59353431	59353465	-	1	NA	promoter-TSS (NM_175325)	promoter-TSS (NM_175325)	60	NM_175325	102774	Mm.200714	NM_175325	ENSMUSG00000025235	Bbs4	AW537059|AW742241|D9Ertd464e	Bardet-Biedl syndrome 4 (human)	protein-coding
mm_163347.1	chr12	17364944	17364945	+	1	NA	intron (NM_001008421, intron 9 of 20)	intron (NM_001008421, intron 9 of 20)	9552	NR_037226	100526470		NR_037226	ENSMUSG00000093037	Mir3066	mir-3066|mmu-mir-3066	microRNA 3066	ncRNA
mm_18443.1	chr2	60902763	60902767	-	1	NA	intron (NM_020296, intron 1 of 13)	intron (NM_020296, intron 1 of 13)	-21327	NM_001141931	56878	Mm.259667	NM_020296	ENSMUSG00000026970	Rbms1	2600014B10Rik|AI255215|MSSP-1|MSSP-2|MSSP-3|YC1	RNA binding motif, single stranded interacting protein 1	protein-coding
mm_47616.1	chr5	125141252	125141273	-	1	NA	intron (NM_011424, intron 1 of 46)	intron (NM_011424, intron 1 of 46)	37952	NM_001253905	20602	Mm.278646	NM_011424	ENSMUSG00000029478	Ncor2	N-CoR|SMRT|SMRTe	nuclear receptor co-repressor 2	protein-coding
mm_73214.1	chr8	95825354	95825354	+	1	NA	Intergenic	Intergenic	-17892	NM_001205226	234594	Mm.259220	NM_153164	ENSMUSG00000036550	Cnot1	6030411K04Rik|AA815922|D830048B13	CCR4-NOT transcription complex, subunit 1	protein-coding
mm_18328.1	chr2	57181749	57181762	-	1	NA	promoter-TSS (NR_040356)	promoter-TSS (NR_040356)	-1	NR_040356	767815	Mm.188065	NR_040356	ENSMUSG00000084938	BB557941	-	expressed sequence BB557941	ncRNA
mm_70285.1	chr8	3640714	3640746	+	1	NA	intron (NM_011503, intron 15 of 18)	HAL1b|LINE|L1	9570	NM_011503	20911	Mm.7247	NM_011503	ENSMUSG00000004626	Stxbp2	C79054|Munc-18-2|Munc-18b|Munc18b|Sxtbp2|Sxtp2|Unc18-2|Unc18b|muSec1	syntaxin binding protein 2	protein-coding
mm_18540.1	chr2	64916907	64916913	-	1	NA	exon (NM_016719, exon 12 of 14)	exon (NM_016719, exon 12 of 14)	105856	NM_016719	50915	Mm.214554	NM_016719	ENSMUSG00000026888	Grb14	AI505286	growth factor receptor bound protein 14	protein-coding
mm_24163.1	chr3	88532315	88532396	+	1	NA	promoter-TSS (NM_001029890)	promoter-TSS (NM_001029890)	-40	NM_001029890	72640	Mm.275154	NM_001029890	ENSMUSG00000074480	Mex3a	2700083E18Rik|Gm411|Rkhd4	mex3 RNA binding family member A	protein-coding
mm_74405.1	chr8	3355676	3355686	-	1	NA	intron (NM_001033378, intron 1 of 10)	intron (NM_001033378, intron 1 of 10)	2266	NM_001033378	319493	Mm.234565	NM_001033378	ENSMUSG00000074497	A430078G23Rik	-	RIKEN cDNA A430078G23 gene	protein-coding
mm_132006.1	chr16	25801908	25801928	+	1	NA	promoter-TSS (NM_001127262)	promoter-TSS (NM_001127262)	2	NM_001127264	22061	Mm.20894	NM_011641	ENSMUSG00000022510	Trp63	AI462811|Ket|P51/P63|P63|P73l|Tp63|Trp53rp1	transformation related protein 63	protein-coding
mm_120147.1	chr14	60485172	60485189	+	1	NA	Intergenic	Intergenic	106894	NM_001164705	72125	Mm.275499	NM_028113	ENSMUSG00000021986	Amer2	2600011E07Rik|Fam123a	APC membrane recruitment 2	protein-coding
mm_56125.1	chr6	87533002	87533038	-	1	NA	5' UTR (NM_001286610, exon 1 of 10)	5' UTR (NM_001286610, exon 1 of 10)	239	NM_001037727	232201	Mm.119564	NM_175476	ENSMUSG00000030047	Arhgap25	A130039I20Rik	Rho GTPase activating protein 25	protein-coding
mm_49660.1	chr6	31159494	31159501	+	1	NA	intron (NR_110471, intron 2 of 3)	intron (NR_110471, intron 2 of 3)	58977	NR_110470	232685	Mm.443019	NM_144555	ENSMUSG00000044471	Lncpint	Lincpint|MNCb-1768|Pint|linc-Pint	long non-protein coding RNA, Trp53 induced transcript	ncRNA
mm_145297.1	chr18	53276592	53276595	+	1	NA	intron (NM_029394, intron 1 of 6)	intron (NM_029394, intron 1 of 6)	30931	NM_029394	69226	Mm.32414	NM_029394	ENSMUSG00000024535	Snx24	2810011K15Rik|5730433I16Rik|AI451341	sorting nexing 24	protein-coding
mm_48109.1	chr5	137109105	137109123	-	1	NA	Intergenic	ID_B1|SINE|B4	7093	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_53179.1	chr6	125361945	125361975	+	1	NA	TTS (NM_198604)	TTS (NM_198604)	12237	NM_011609	21937	Mm.1258	NM_011609	ENSMUSG00000030341	Tnfrsf1a	CD120a|FPF|TNF-R|TNF-R-I|TNF-R1|TNF-R55|TNF-alphaR1|TNFAR|TNFR60|TNFRI|TNFRp55|TNFalpha-R1|Tnfr-2|Tnfr1|p55|p55-R	tumor necrosis factor receptor superfamily, member 1a	protein-coding
mm_154614.1	chrX	7652966	7652981	+	1	NA	3' UTR (NM_009305, exon 7 of 7)	3' UTR (NM_009305, exon 7 of 7)	-4406	NM_001290624	54630	Mm.232232	NM_175097	ENSMUSG00000031145	Prickle3	Lmo6|Sfc16	prickle planar cell polarity protein 3	protein-coding
mm_136840.1	chr17	12755435	12755456	+	1	NA	intron (NM_010515, intron 1 of 47)	intron (NM_010515, intron 1 of 47)	14134	NR_027784	104103	Mm.26553	NR_002853	ENSMUSG00000078247	Airn	2810051F02Rik|2810434M15Rik|AI256653|AI597500|AW049873|Air|B930018I07Rik|D17Ertd663e|IGF2RAS	antisense Igf2r RNA	ncRNA
mm_51671.1	chr6	86404258	86404319	+	1	NA	promoter-TSS (NM_011585)	promoter-TSS (NM_011585)	69	NM_001164078	21841	Mm.333219	NM_011585	ENSMUSG00000071337	Tia1	2310050N03Rik|AI256674|TIA-1|mTIA-1	cytotoxic granule-associated RNA binding protein 1	protein-coding
mm_113470.1	chr13	36423379	36423385	+	1	NA	intron (NM_001039189, intron 5 of 5)	Lx7|LINE|L1	305739	NM_001039189	69955	Mm.70690	NM_024274	ENSMUSG00000021420	Fars2	Fars1|pheRS	phenylalanine-tRNA synthetase 2 (mitochondrial)	protein-coding
mm_104048.1	chr11	86357911	86357922	-	1	NA	promoter-TSS (NM_001080931)	promoter-TSS (NM_001080931)	-391	NM_001080931	327987	Mm.341886	NM_001080931	ENSMUSG00000034297	Med13	1110067M05Rik|D030023K18|Thrap1|Trap240	mediator complex subunit 13	protein-coding
mm_32388.1	chr4	106587463	106587482	+	1	NA	3' UTR (NM_053272, exon 9 of 9)	3' UTR (NM_053272, exon 9 of 9)	26434	NM_053272	74754	Mm.133370	NM_053272	ENSMUSG00000034926	Dhcr24	2310076D10Rik|5830417J06Rik|mKIAA0018	24-dehydrocholesterol reductase	protein-coding
mm_78031.1	chr9	13827219	13827226	+	1	NA	promoter-TSS (NM_001310721)	promoter-TSS (NM_001310721)	-115	NM_026665	74360	Mm.157212	NM_026665	ENSMUSG00000031922	Cep57	3110002L15Rik|4921510P06Rik|4931428M20Rik|AI467480|Tsp57|mKIAA0092	centrosomal protein 57	protein-coding
mm_137574.1	chr17	27856521	27856544	+	1	NA	promoter-TSS (NM_001080769)	promoter-TSS (NM_001080769)	25	NM_001080769	224648	Mm.291291	NM_001080769	ENSMUSG00000039512	Uhrf1bp1	1110020K19Rik|AA408674|F830021D11Rik|mKIAA4127	UHRF1 (ICBP90) binding protein 1	protein-coding
mm_100907.1	chr11	6222240	6222283	-	1	NA	exon (NM_207242, exon 9 of 19)	exon (NM_207242, exon 9 of 19)	7984	NM_207242	237636	Mm.212492	NM_207242	ENSMUSG00000020447	Npc1l1	9130221N23Rik|Gm243	NPC1-like 1	protein-coding
mm_146387.1	chr18	82692573	82692586	+	1	NA	intron (NM_177832, intron 1 of 29)	C-rich|Low_complexity|Low_complexity	155	NM_177832	329002	Mm.34438	NM_177832	ENSMUSG00000041258	Zfp236	AI447957|Gm335	zinc finger protein 236	protein-coding
mm_53287.1	chr6	128992938	128992952	+	1	NA	promoter-TSS (NR_015455)	promoter-TSS (NR_015455)	-16	NR_015455	408064	Mm.172429	NR_015455		BC064078	-	cDNA sequence BC064078	ncRNA
mm_119559.1	chr14	48694914	48694924	+	1	NA	intron (NR_029384, intron 2 of 4)	Lx5|LINE|L1	25631	NR_029384	606497	Mm.165199	NR_029384	ENSMUSG00000098682	Otx2os1	-	orthodenticle homeobox 2 opposite strand 1	ncRNA
mm_143627.1	chr17	78882575	78882583	-	1	NA	promoter-TSS (NM_011163)	promoter-TSS (NM_011163)	-7	NM_011163	19106	Mm.378990	NM_011163	ENSMUSG00000024079	Eif2ak2	2310047A08Rik|4732414G15Rik|AI467567|AI747578|Pkr|Prkr|Tik	eukaryotic translation initiation factor 2-alpha kinase 2	protein-coding
mm_55182.1	chr6	52164474	52164490	-	1	NA	exon (NM_010451, exon 1 of 2)	exon (NM_010451, exon 1 of 2)	349	NM_010451	15399	Mm.131	NM_010451	ENSMUSG00000014704	Hoxa2	AI324701|HOX1.11|Hox-1.11	homeobox A2	protein-coding
mm_127597.1	chr15	102399792	102399807	+	1	NA	Intergenic	Intergenic	-6517	NM_013672	20683	Mm.4618	NM_013672	ENSMUSG00000001280	Sp1	1110003E12Rik|AA450830|AI845540|Sp1-1	trans-acting transcription factor 1	protein-coding
mm_130604.1	chr15	99819820	99819835	-	1	NA	exon (NM_001113545, exon 4 of 11)	exon (NM_001113545, exon 4 of 11)	322	NM_023063	65970	Mm.33207	NM_023063	ENSMUSG00000023022	Lima1	Eplin	LIM domain and actin binding 1	protein-coding
mm_131640.1	chr16	20498878	20498919	+	1	NA	promoter-TSS (NM_172265)	promoter-TSS (NM_172265)	81	NM_172265	224045	Mm.233855	NM_172265	ENSMUSG00000003235	Eif2b5	C81315	eukaryotic translation initiation factor 2B, subunit 5 epsilon	protein-coding
mm_172099.1	chr6	29669914	29669918	-	1	NA	Intergenic	RLTR10A|LTR|ERVK	-24298	NM_001301407	232670	Mm.225289	NM_146173	ENSMUSG00000001763	Tspan33	1300010A20Rik|Pen	tetraspanin 33	protein-coding
mm_156189.1	chrX	133908636	133908658	+	1	NA	5' UTR (NM_026838, exon 1 of 12)	5' UTR (NM_026838, exon 1 of 12)	222	NM_001083895	68792	Mm.263553	NM_026838	ENSMUSG00000031253	Srpx2	1110039C07Rik|SRP|SRPUL	sushi-repeat-containing protein, X-linked 2	protein-coding
mm_46350.1	chr5	102846312	102846318	-	1	NA	intron (NM_001346585, intron 1 of 6)	intron (NM_001346585, intron 1 of 6)	1308	NM_001346585	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding
mm_4040.1	chr1	165774575	165774585	+	1	NA	3' UTR (NM_011804, exon 4 of 4)	3' UTR (NM_011804, exon 4 of 4)	10800	NM_011804	433375	Mm.294885	NM_011804	ENSMUSG00000040713	Creg1	AA755314|Creg	cellular repressor of E1A-stimulated genes 1	protein-coding
mm_34785.1	chr4	154170745	154170769	+	1	NA	promoter-TSS (NM_001162977)	promoter-TSS (NM_001162977)	44	NM_001162977	230971	Mm.275216	NM_172273	ENSMUSG00000057751	Megf6	2600001P17Rik|Egfl3	multiple EGF-like-domains 6	protein-coding
mm_128712.1	chr15	63975452	63975455	-	1	NA	intron (NM_144846, intron 1 of 11)	intron (NM_144846, intron 1 of 11)	60992	NR_029414	74460	Mm.390801	NR_029414	ENSMUSG00000100127	Gsdmcl-ps	4933426G20Rik	gasdermin C-like, pseudogene	pseudo
mm_69387.1	chr7	131329528	131329530	-	1	NA	promoter-TSS (NM_027037)	promoter-TSS (NM_027037)	-30	NM_027037	69318	Mm.233840	NM_027037	ENSMUSG00000030858	1700007K09Rik	-	RIKEN cDNA 1700007K09 gene	protein-coding
mm_162059.1	chrX	8976570	8976570	-	1	NA	promoter-TSS (NM_001277184)	promoter-TSS (NM_001277184)	-11	NM_001085525	434727	Mm.291786	NM_001085525	ENSMUSG00000060685	Fthl17c	EG434727|Fthl17L2|Gm14511|OTTMUSG00000016933	ferritin, heavy polypeptide-like 17, member C	protein-coding
mm_173006.1	chrM	219	219	+	1	NA	NA	Intergenic	NA	NA								
mm_153860.1	chr19	46558298	46558333	-	1	NA	exon (NM_019718, exon 2 of 6)	exon (NM_019718, exon 2 of 6)	14770	NM_019718	56350	Mm.22085	NM_019718	ENSMUSG00000025035	Arl3	-	ADP-ribosylation factor-like 3	protein-coding
mm_135706.1	chr16	53246523	53246548	-	1	NA	Intergenic	Intergenic	-430791	NR_040495	73820	Mm.60493	NR_040495		4930404A05Rik	-	RIKEN cDNA 4930404A05 gene	ncRNA
mm_36382.1	chr4	76959113	76959135	-	1	NA	intron (NM_011211, intron 8 of 39)	intron (NM_011211, intron 8 of 39)	1252771	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding
mm_69842.1	chr7	141327739	141327749	-	1	NA	promoter-TSS (NM_001282076)	promoter-TSS (NM_001282076)	-19	NM_001282076	54006	Mm.28392	NM_016874	ENSMUSG00000058886	Deaf1	AU042387|C230009B13Rik|NUDR	deformed epidermal autoregulatory factor 1 (Drosophila)	protein-coding
mm_96502.1	chr11	68435984	68435988	+	1	NA	intron (NM_177320, intron 1 of 18)	intron (NM_177320, intron 1 of 18)	3861	NM_177320	320207	Mm.244960	NM_177320	ENSMUSG00000020901	Pik3r5	AV230647|F730038I15Rik	phosphoinositide-3-kinase, regulatory subunit 5, p101	protein-coding
mm_85904.1	chr9	111056368	111056397	-	1	NA	exon (NM_017466, exon 2 of 2)	exon (NM_017466, exon 2 of 2)	862	NM_001302377	54199	Mm.7336	NM_017466	ENSMUSG00000043953	Ccrl2	1810047I05Rik|Ackr5|CCR11|Cmkbr1l2|E01|L-CCR	chemokine (C-C motif) receptor-like 2	protein-coding
mm_59078.1	chr7	19577804	19577828	+	1	NA	intron (NM_022409, intron 1 of 2)	intron (NM_022409, intron 1 of 2)	529	NM_022409	63872	Mm.23310	NM_022409	ENSMUSG00000011267	Zfp296	2210018A16Rik|Znf296	zinc finger protein 296	protein-coding
mm_112152.1	chr12	113265071	113265082	-	1	NA	Intergenic	Intergenic	79173	NM_153776	69195	Mm.313244	NM_153776	ENSMUSG00000049036	Tmem121	2410008J05Rik|Hole	transmembrane protein 121	protein-coding
mm_48897.1	chr6	3200761	3200769	+	1	NA	Intergenic	B3A|SINE|B2	-87754	NR_036696	667335	Mm.380219	NR_036696	ENSMUSG00000106779	Gm8579	EG667335	spermatogenesis associated glutamate (E)-rich protein 4a pseudogene	pseudo
mm_133406.1	chr16	84835341	84835351	+	1	NA	promoter-TSS (NM_001302216)	promoter-TSS (NM_001302216)	222	NM_008065	14390	Mm.18974	NM_008065	ENSMUSG00000008976	Gabpa	GABPalpha	GA repeat binding protein, alpha	protein-coding
mm_72338.1	chr8	79295019	79295035	+	1	NA	promoter-TSS (NM_133823)	promoter-TSS (NM_133823)	-51	NR_045822	234479	Mm.238026	NR_045822		Gm4890	A630049P17	predicted gene 4890	ncRNA
mm_94852.1	chr11	23894760	23894775	+	1	NA	intron (NM_172555, intron 1 of 21)	CpG	503	NM_172555	216578	Mm.470599	NM_172555	ENSMUSG00000020273	Papolg	9630006B20Rik	poly(A) polymerase gamma	protein-coding
mm_112074.1	chr12	112619937	112619973	-	1	NA	promoter-TSS (NM_007421)	promoter-TSS (NM_007421)	-92	NM_007421	11565	Mm.3440	NM_007421	ENSMUSG00000011148	Adssl1	AI528595|Adss|Adss1	adenylosuccinate synthetase like 1	protein-coding
mm_82147.1	chr9	123774751	123774761	+	1	NA	intron (NM_009913, intron 2 of 2)	intron (NM_009913, intron 2 of 2)	7545	NM_001166625	12769	Mm.440604	NM_009913	ENSMUSG00000029530	Ccr9	A130091K22Rik|Cmkbr10|GPR-9-6	chemokine (C-C motif) receptor 9	protein-coding
mm_24265.1	chr3	89187922	89187965	+	1	NA	intron (NM_001014995, intron 9 of 11)	intron (NM_001014995, intron 9 of 11)	4718	NM_001014995	68521	Mm.274708	NM_001014995	ENSMUSG00000032657	Fam189b	1110013L07Rik	family with sequence similarity 189, member B	protein-coding
mm_122667.1	chr14	51914092	51914102	-	1	NA	promoter-TSS (NM_001145959)	promoter-TSS (NM_001145959)	-609	NM_013864	29811	Mm.26722	NM_013864	ENSMUSG00000004558	Ndrg2	AI182517|AU040374|Ndr2|SYLD	N-myc downstream regulated gene 2	protein-coding
mm_161735.1	chr17	31325569	31325569	+	1	NA	intron (NM_001242427, intron 8 of 19)	intron (NM_001242427, intron 8 of 19)	29345	NM_001242427	224674	Mm.311395	NM_153062	ENSMUSG00000024036	Slc37a1	G3PP	solute carrier family 37 (glycerol-3-phosphate transporter), member 1	protein-coding
mm_1411.1	chr1	67154344	67154368	+	1	NA	intron (NM_001080809, intron 7 of 37)	intron (NM_001080809, intron 7 of 37)	31329	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_133003.1	chr16	55966413	55966430	+	1	NA	5' UTR (NM_024218, exon 1 of 6)	5' UTR (NM_024218, exon 1 of 6)	146	NM_024218	68193	Mm.29221	NM_024218	ENSMUSG00000098274	Rpl24	0610008L05Rik|Bst	ribosomal protein L24	protein-coding
mm_25724.1	chr3	122730048	122730057	+	1	NA	intron (NM_153422, intron 1 of 20)	CpG	894	NM_153422	242202	Mm.134911	NM_153422	ENSMUSG00000053965	Pde5a	Cgbpde|Cn5n|PDE5a2|Pde5|Pde5a1	phosphodiesterase 5A, cGMP-specific	protein-coding
mm_125792.1	chr15	74721698	74721700	+	1	NA	exon (NM_198607, exon 1 of 2)	exon (NM_198607, exon 1 of 2)	465	NM_198607	223626	Mm.268603	NM_198607	ENSMUSG00000056665	Them6	4930572J05Rik	thioesterase superfamily member 6	protein-coding
mm_149689.1	chr19	20919150	20919175	+	1	NA	intron (NM_028953, intron 2 of 20)	intron (NM_028953, intron 2 of 20)	35040	NM_028953	13409	Mm.219585	NM_028953	ENSMUSG00000024749	Tmc1	4933416G09Rik|Beethoven|Bth|CWEA1|dn	transmembrane channel-like gene family 1	protein-coding
mm_28717.1	chr3	95659389	95659400	-	1	NA	exon (NM_008562, exon 1 of 3)	exon (NM_008562, exon 1 of 3)	673	NM_008562	17210	Mm.1639	NM_008562	ENSMUSG00000038612	Mcl1	AW556805|Mcl-1	myeloid cell leukemia sequence 1	protein-coding
mm_79308.1	chr9	52048235	52048245	+	1	NA	5' UTR (NM_009041, exon 1 of 14)	5' UTR (NM_009041, exon 1 of 14)	299	NM_001104617	19684	Mm.245746	NM_009041	ENSMUSG00000032050	Rdx	AA516625	radixin	protein-coding
mm_162177.1	chrX	102251734	102251734	-	1	NA	promoter-TSS (NM_001276474)	promoter-TSS (NM_001276474)	109	NM_007709	12705	Mm.2390	NM_007709	ENSMUSG00000051159	Cited1	AI316840|AU019144|Msg1	Cbp/p300-interacting transactivator with Glu/Asp-rich carboxy-terminal domain 1	protein-coding
mm_83030.1	chr9	37255430	37255442	-	1	NA	5' UTR (NM_001145960, exon 1 of 19)	5' UTR (NM_001145960, exon 1 of 19)	302	NM_020258	56857	Mm.440037	NM_020258	ENSMUSG00000032122	Slc37a2	G3PP|Slc37a1|cI-2|ci2	solute carrier family 37 (glycerol-3-phosphate transporter), member 2	protein-coding
mm_20351.1	chr2	127792468	127792505	-	1	NA	promoter-TSS (NR_015476)	promoter-TSS (NR_015476)	2	NR_015476	67885	Mm.27359	NM_175125	ENSMUSG00000051319	1500011K16Rik	-	RIKEN cDNA 1500011K16 gene	ncRNA
mm_152963.1	chr19	29363760	29363764	-	1	NA	Intergenic	Intergenic	-1891	NM_026362	67759	Mm.275511	NM_026362	ENSMUSG00000016495	Plgrkt	1110007H22Rik|5033414D02Rik|AI852040|Plg-R(KT)|Plg-RKT	plasminogen receptor, C-terminal lysine transmembrane protein	protein-coding
mm_169118.1	chr13	50119320	50119330	+	1	NA	Intergenic	Intergenic	130983	NM_001033438	380882	Mm.425809	NM_001033438	ENSMUSG00000095300	Gm906	-	predicted gene 906	protein-coding
mm_111303.1	chr12	85705613	85705618	-	1	NA	intron (NM_016767, intron 2 of 2)	intron (NM_016767, intron 2 of 2)	18895	NM_016767	53314	Mm.6672	NM_016767	ENSMUSG00000034266	Batf	B-ATF|SFA-2	basic leucine zipper transcription factor, ATF-like	protein-coding
mm_59544.1	chr7	27887333	27887350	+	1	NA	Intergenic	Intergenic	26756	NM_001024726	545938	Mm.458180	NM_001024726	ENSMUSG00000020420	Zfp607a	4732475C15Rik|Zfp607	zinc finger protein 607A	protein-coding
mm_62539.1	chr7	102267796	102267854	+	1	NA	promoter-TSS (NM_009287)	promoter-TSS (NM_009287)	1	NM_009287	20866	Mm.645	NM_009287	ENSMUSG00000030987	Stim1	SIM	stromal interaction molecule 1	protein-coding
mm_157805.1	chrX	73930718	73930728	-	1	NA	exon (NM_001164704, exon 1 of 11)	exon (NM_001164704, exon 1 of 11)	127	NM_023132	19703	Mm.236969	NM_023132	ENSMUSG00000031387	Renbp	Age|Rnbp	renin binding protein	protein-coding
mm_119632.1	chr14	51364246	51364249	+	1	NA	Intergenic	Intergenic	-18758	NR_045736	75377	Mm.402100	NR_045736		4930597G03Rik	-	RIKEN cDNA 4930597G03 gene	ncRNA
mm_118022.1	chr13	100833278	100833312	-	1	NA	5' UTR (NM_022885, exon 1 of 16)	5' UTR (NM_022885, exon 1 of 16)	132	NM_022885	69048	Mm.402215	NM_022885	ENSMUSG00000021629	Slc30a5	1810010K08Rik|AF233321|ZNT5|ZTL1|ZnT-5|Zntl1	solute carrier family 30 (zinc transporter), member 5	protein-coding
mm_42657.1	chr5	119669877	119669916	+	1	NA	promoter-TSS (NM_198052)	promoter-TSS (NM_198052)	-966	NM_198052	21386	Mm.219139	NM_011535	ENSMUSG00000018604	Tbx3	D5Ertd189e	T-box 3	protein-coding
mm_150765.1	chr19	44242255	44242262	+	1	NA	3' UTR (NM_024450, exon 6 of 6)	3' UTR (NM_024450, exon 6 of 6)	38970	NM_024450	30049	Mm.480594	NM_024450	ENSMUSG00000025202	Scd3	4930513N16Rik	stearoyl-coenzyme A desaturase 3	protein-coding
mm_45432.1	chr5	67099153	67099165	-	1	NA	promoter-TSS (NM_008888)	promoter-TSS (NM_008888)	-33	NM_008888	18935	Mm.62505	NM_008888	ENSMUSG00000012520	Phox2b	Dilp1|NBPhox|Pmx2b|Px2b	paired-like homeobox 2b	protein-coding
mm_158311.1	chrX	126833978	126834007	-	1	NA	promoter-TSS (NM_177705)	promoter-TSS (NM_177705)	12	NM_177705	237029	Mm.60998	NM_177705	ENSMUSG00000058670	4932411N23Rik	-	RIKEN cDNA 4932411N23 gene	protein-coding
mm_74271.1	chr8	125012953	125012975	+	1	NA	promoter-TSS (NM_016909)	promoter-TSS (NM_016909)	-33	NM_016909	53424	Mm.5248	NM_016909	ENSMUSG00000056820	Tsnax	R74833|Trax	translin-associated factor X	protein-coding
mm_165192.1	chr2	32384635	32384641	+	1	NA	TTS (NM_008491)	TTS (NM_008491)	-2723	NM_198001	73737	Mm.27608	NM_198001	ENSMUSG00000039195	1110008P14Rik	C79326	RIKEN cDNA 1110008P14 gene	protein-coding
mm_115598.1	chr13	11864517	11864521	-	1	NA	intron (NM_023868, intron 10 of 104)	intron (NM_023868, intron 10 of 104)	242426	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding
mm_152554.1	chr19	11484568	11484590	-	1	NA	Intergenic	Intergenic	-7459	NM_001164202	666926	Mm.486382	NM_001164202	ENSMUSG00000058470	Gm8369	EG666926	predicted gene 8369	protein-coding
mm_15250.1	chr2	154694205	154694226	+	1	NA	3' UTR (NM_029362, exon 5 of 5)	3' UTR (NM_029362, exon 5 of 5)	37189	NM_029362	75608	Mm.262480	NM_029362	ENSMUSG00000038467	Chmp4b	2010012F05Rik|C76846|Snf7-2	charged multivesicular body protein 4B	protein-coding
mm_82805.1	chr9	29939791	29939801	-	1	NA	intron (NM_172290, intron 1 of 7)	intron (NM_172290, intron 1 of 7)	23333	NM_172290	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding
mm_102975.1	chr11	69672308	69672332	-	1	NA	TTS (NM_001163571)	TTS (NM_001163571)	103	NM_144958	13681	Mm.26680	NM_144958	ENSMUSG00000059796	Eif4a1	BM-010|Ddx2a|Eif4	eukaryotic translation initiation factor 4A1	protein-coding
mm_116040.1	chr13	27198797	27198801	-	1	NA	promoter-TSS (NM_001163218)	promoter-TSS (NM_001163218)	-104	NM_001163218	27372	Mm.291456	NM_013766	ENSMUSG00000017922	Prl3c1	Ghd7|PLP-J|Prlpi|Prlpj|decidualin	prolactin family 3, subfamily c, member 1	protein-coding
mm_26446.1	chr3	142635842	142635855	+	1	NA	exon (NM_010260, exon 10 of 11)	exon (NM_010260, exon 10 of 11)	-11902	NR_105802	102465200		NR_105802	ENSMUSG00000098871	Mir6381	Gm27963|mmu-mir-6381	microRNA 6381	ncRNA
mm_36684.1	chr4	96553552	96553562	-	1	NA	promoter-TSS (NM_010008)	promoter-TSS (NM_010008)	94	NM_010008	13110	Mm.98200	NM_010008	ENSMUSG00000052914	Cyp2j6	-	cytochrome P450, family 2, subfamily j, polypeptide 6	protein-coding
mm_116647.1	chr13	49183790	49183800	-	1	NA	Intergenic	Intergenic	-3752	NM_013610	18081	Mm.18503	NM_013610	ENSMUSG00000037966	Ninj1	AU024536	ninjurin 1	protein-coding
mm_115555.1	chr13	8996005	8996052	-	1	NA	promoter-TSS (NM_027000)	promoter-TSS (NM_027000)	-16	NM_027000	69237	Mm.41800	NM_027000	ENSMUSG00000021149	Gtpbp4	2610028C09Rik|Crfg|Gtpbp3|NGB|Nog1	GTP binding protein 4	protein-coding
mm_83841.1	chr9	54424587	54424591	-	1	NA	intron (NM_172771, intron 15 of 43)	RMER4B|LTR|ERVK	77037	NM_172771	235380	Mm.93636	NM_172771	ENSMUSG00000041268	Dmxl2	6330586A12|6430411K14Rik|E130119P06Rik|mKIAA0856	Dmx-like 2	protein-coding
mm_53562.1	chr6	137252278	137252294	+	1	NA	promoter-TSS (NM_011216)	promoter-TSS (NM_011216)	-13	NM_001164401	19277	Mm.186361	NM_011216	ENSMUSG00000030223	Ptpro	D28|GLEPP1|PTPBK|PTPROt|PTPU2|PTPoc|PTPphi|Ptpn15|R-PTP-O	protein tyrosine phosphatase, receptor type, O	protein-coding
mm_76527.1	chr8	87472616	87472633	-	1	NA	promoter-TSS (NM_019626)	promoter-TSS (NM_019626)	-32	NM_019626	12404	Mm.4880	NM_019626	ENSMUSG00000031654	Cbln1	AI323299	cerebellin 1 precursor protein	protein-coding
mm_82246.1	chr9	4765244	4765247	-	1	NA	intron (NM_019691, intron 3 of 16)	intron (NM_019691, intron 3 of 16)	30989	NM_001113180	14802	Mm.209263	NM_019691	ENSMUSG00000025892	Gria4	GluA4|GluR-D|Glur-4|Glur4|Gluralpha4|spkw1	glutamate receptor, ionotropic, AMPA4 (alpha 4)	protein-coding
mm_139069.1	chr17	46646289	46646296	+	1	NA	promoter-TSS (NM_001316742)	promoter-TSS (NM_001316742)	63	NM_025302	27398	Mm.391007	NM_025302	ENSMUSG00000002767	Mrpl2	CGI-22|L2mt|MRP-L14|MRP-L2|Rpml14	mitochondrial ribosomal protein L2	protein-coding
mm_140237.1	chr17	84119870	84119882	+	1	NA	Intergenic	Intergenic	41216	NR_045458	74473	Mm.399575	NR_045458		4933433H22Rik	-	RIKEN cDNA 4933433H22 gene	ncRNA
mm_32292.1	chr4	103114777	103114792	+	1	NA	promoter-TSS (NM_146254)	promoter-TSS (NM_146254)	394	NM_001286222	71148	Mm.288721	NM_027696	ENSMUSG00000028522	Mier1	4933425I22Rik|5830411K19Rik|er1	MEIR1 treanscription regulator	protein-coding
mm_58735.1	chr7	13030328	13030339	+	1	NA	exon (NM_011588, exon 15 of 17)	exon (NM_011588, exon 15 of 17)	4444	NM_026885	68953	Mm.295670	NM_026885	ENSMUSG00000033916	Chmp2a	1500016L11Rik	charged multivesicular body protein 2A	protein-coding
mm_101864.1	chr11	48872280	48872340	-	1	NA	promoter-TSS (NM_008326)	promoter-TSS (NM_008326)	-964	NM_008326	15944	Mm.29938	NM_008326	ENSMUSG00000046879	Irgm1	Ifggd3|Ifi1|Iigp3|Iipg3|Irgm|LRG-47	immunity-related GTPase family M member 1	protein-coding
mm_84693.1	chr9	72393961	72393970	-	1	NA	Intergenic	Intergenic	-44564	NM_008613	17427	Mm.387671	NM_008613	ENSMUSG00000032221	Mns1	AW546487	meiosis-specific nuclear structural protein 1	protein-coding
mm_96991.1	chr11	70670251	70670260	+	1	NA	promoter-TSS (NM_001167669)	promoter-TSS (NM_001167669)	-839	NM_001167669	216873	Mm.432524	NM_172561	ENSMUSG00000018287	Spag7	5730443G10|ACRP|FSA-1|Fsa1l	sperm associated antigen 7	protein-coding
mm_32384.1	chr4	106561075	106561099	+	1	NA	promoter-TSS (NM_053272)	promoter-TSS (NM_053272)	49	NM_053272	74754	Mm.133370	NM_053272	ENSMUSG00000034926	Dhcr24	2310076D10Rik|5830417J06Rik|mKIAA0018	24-dehydrocholesterol reductase	protein-coding
mm_157709.1	chrX	64276915	64276930	-	1	NA	promoter-TSS (NM_178740)	promoter-TSS (NM_178740)	74	NM_178740	245446	Mm.101707	NM_178740	ENSMUSG00000046699	Slitrk4	6430513G13|D930039I09Rik	SLIT and NTRK-like family, member 4	protein-coding
mm_145966.1	chr18	67800102	67800147	+	1	NA	promoter-TSS (NM_027556)	promoter-TSS (NM_027556)	17	NM_027556	70799	Mm.30857	NM_027556	ENSMUSG00000024542	Cep192	4631422C13Rik|D430014P18Rik	centrosomal protein 192	protein-coding
mm_2550.1	chr1	107917255	107917263	+	1	NA	promoter-TSS (NR_102307)	promoter-TSS (NR_102307)	0	NR_102306	319596	Mm.136054	NR_102306	ENSMUSG00000100457	D830032E09Rik	-	RIKEN cDNA D830032E09 gene	ncRNA
mm_30961.1	chr4	33924922	33924990	+	1	NA	5' UTR (NM_007726, exon 1 of 2)	5' UTR (NM_007726, exon 1 of 2)	324	NM_007726	12801	Mm.7992	NM_007726	ENSMUSG00000044288	Cnr1	CB-R|CB1|CB1R	cannabinoid receptor 1 (brain)	protein-coding
mm_11400.1	chr2	31486504	31486515	+	1	NA	exon (NM_007494, exon 6 of 16)	exon (NM_007494, exon 6 of 16)	16201	NR_002687	432466	Mm.333323	NR_002687	ENSMUSG00000046687	Gm5424	EG432466	argininosuccinate synthase pseudogene	pseudo
mm_51246.1	chr6	71707890	71707907	+	1	NA	5' UTR (NM_178608, exon 1 of 7)	5' UTR (NM_178608, exon 1 of 7)	217	NM_178608	52250	Mm.146332	NM_178608	ENSMUSG00000052852	Reep1	D6Ertd253e	receptor accessory protein 1	protein-coding
mm_36641.1	chr4	94327853	94327857	-	1	NA	Intergenic	Intergenic	228941	NM_026368	67770	Mm.35170	NM_026368	ENSMUSG00000028578	Caap1	5830433M19Rik|AI536248|CAAP	caspase activity and apoptosis inhibitor 1	protein-coding
mm_61510.1	chr7	78783344	78783367	+	1	NA	promoter-TSS (NM_023331)	promoter-TSS (NM_023331)	224	NM_026498	67994	Mm.297033	NM_026498	ENSMUSG00000030611	Mrps11	0710005I03Rik|C79873	mitochondrial ribosomal protein S11	protein-coding
mm_15692.1	chr2	163659117	163659131	+	1	NA	intron (NM_001164053, intron 1 of 3)	intron (NM_001164053, intron 1 of 3)	666	NM_001164053	18769	Mm.10091	NM_011106	ENSMUSG00000035268	Pkig	PKIgamma	protein kinase inhibitor, gamma	protein-coding
mm_102082.1	chr11	52280208	52280221	-	1	NA	intron (NM_001313981, intron 3 of 10)	RSINE1|SINE|B4	2381	NM_009331	21414	Mm.31630	NM_009331	ENSMUSG00000000782	Tcf7	AI465550|TCF-1|Tcf1	transcription factor 7, T cell specific	protein-coding
mm_160565.1	chr9	54980847	54980847	+	1	NA	promoter-TSS (NM_176844)	promoter-TSS (NM_176844)	-33	NM_176844	110835	Mm.103778	NM_176844	ENSMUSG00000035594	Chrna5	Acra-5|Acra5	cholinergic receptor, nicotinic, alpha polypeptide 5	protein-coding
mm_61388.1	chr7	73105326	73105344	+	1	NA	Intergenic	Intergenic	-3267	NR_046024	625243	Mm.261798	NR_046024	ENSMUSG00000108383	Gm6567	-	predicted gene 6567	ncRNA
mm_31740.1	chr4	63214135	63214150	+	1	NA	Intergenic	CpG	-1270	NM_025685	373864	Mm.194116	NM_025685	ENSMUSG00000045672	Col27a1	5730512J02Rik|AI449266	collagen, type XXVII, alpha 1	protein-coding
mm_129608.1	chr15	79932585	79932665	-	1	NA	promoter-TSS (NM_144811)	promoter-TSS (NM_144811)	21	NM_144811	52609	Mm.323442	NM_144811	ENSMUSG00000053411	Cbx7	1600014J01Rik|AI851678|D15Ertd417e	chromobox 7	protein-coding
mm_102486.1	chr11	60220551	60220632	-	1	NA	promoter-TSS (NM_011480)	promoter-TSS (NM_011480)	36	NM_011480	20787	Mm.278701	NM_011480	ENSMUSG00000020538	Srebf1	ADD1|SREBP-1a|SREBP1|SREBP1c|bHLHd1	sterol regulatory element binding transcription factor 1	protein-coding
mm_24710.1	chr3	95218001	95218059	+	1	NA	promoter-TSS (NM_172512)	promoter-TSS (NM_172512)	-88	NM_029885	213054	Mm.224820	NM_029885	ENSMUSG00000038766	Gabpb2	1810015F01Rik|5830427M07|9430006E19Rik|A430024B14Rik|AV050852|Gabpb2-1	GA repeat binding protein, beta 2	protein-coding
mm_27444.1	chr3	51875809	51875809	-	1	NA	intron (NM_001004176, intron 1 of 4)	intron (NM_001004176, intron 1 of 4)	214630	NM_001310482	211666	Mm.24679	NM_174995	ENSMUSG00000074604	Mgst2	GST2|MGST-II	microsomal glutathione S-transferase 2	protein-coding
mm_114756.1	chr13	85189380	85189395	+	1	NA	promoter-TSS (NM_001347588)	promoter-TSS (NM_001347588)	2	NM_023243	66671	Mm.18474	NM_023243	ENSMUSG00000021548	Ccnh	6330408H09Rik|AI661354|AV102684|AW538719	cyclin H	protein-coding
mm_128578.1	chr15	57892359	57892483	-	1	NA	promoter-TSS (NM_024207)	promoter-TSS (NM_024207)	-3	NM_024207	67819	Mm.289387	NM_024207	ENSMUSG00000022365	Derl1	1110021N07Rik|AI195141|AW551338|Derlin-1	Der1-like domain family, member 1	protein-coding
mm_122783.1	chr14	54410274	54410283	-	1	NA	promoter-TSS (NM_001253680)	promoter-TSS (NM_001253680)	-806	NM_001253680	20540	Mm.142455	NM_011405	ENSMUSG00000000958	Slc7a7	AI790233|my+lat1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 7	protein-coding
mm_107491.1	chr12	38783456	38783482	+	1	NA	promoter-TSS (NM_001163154)	promoter-TSS (NM_001163154)	-242	NM_001163154	14009	Mm.4866	NM_007960	ENSMUSG00000004151	Etv1	ER81|Etsrp81	ets variant 1	protein-coding
mm_106331.1	chr11	118342524	118342569	-	1	NA	promoter-TSS (NM_021440)	promoter-TSS (NM_021440)	-12	NM_021440	58251	Mm.439815	NM_021440	ENSMUSG00000076433	BC100451	Cep295nl|Ddc8|FS39|Kiaa1731nl	cDNA sequence BC100451	protein-coding
mm_144131.1	chr18	4921543	4921570	+	1	NA	Intergenic	Intergenic	109070	NR_045881	100038439	Mm.387569	NR_045881	ENSMUSG00000097043	Gm10556	ENSMUSG00000073646	predicted gene 10556	ncRNA
mm_149684.1	chr19	20492751	20492785	+	1	NA	promoter-TSS (NR_015502)	promoter-TSS (NR_015502)	53	NR_015502	320092	Mm.482524	NR_015502		E030003E18Rik	1700127G21Rik	RIKEN cDNA E030003E18 gene	ncRNA
mm_63669.1	chr7	129962163	129962173	+	1	NA	promoter-TSS (NR_046077)	promoter-TSS (NR_046077)	3	NR_046077	100043150	Mm.334264	NR_046077	ENSMUSG00000108504	Gm4265	-	predicted gene 4265	ncRNA
mm_157817.1	chrX	74023818	74023839	-	1	NA	promoter-TSS (NM_001177976)	promoter-TSS (NM_001177976)	90	NM_001177975	16179	Mm.38241	NM_008363	ENSMUSG00000031392	Irak1	AA408924|IRAK|IRAK-1|IRAK1-S|IRAK1b|Il1rak|Plpk|mPLK	interleukin-1 receptor-associated kinase 1	protein-coding
mm_37794.1	chr4	130520007	130520023	-	1	NA	Intergenic	Intergenic	54021	NM_025998	67149	Mm.423029	NM_025998	ENSMUSG00000078532	Nkain1	2610200G18Rik|2810426C15Rik	Na+/K+ transporting ATPase interacting 1	protein-coding
mm_1593.1	chr1	74362123	74362156	+	1	NA	promoter-TSS (NM_001033345)	promoter-TSS (NM_001033345)	31	NM_001033345	241112	Mm.310460	NM_001033345	ENSMUSG00000073650	Catip	Gm216	ciliogenesis associated TTC17 interacting protein	protein-coding
mm_26304.1	chr3	142511022	142511030	+	1	NA	intron (NM_153564, intron 10 of 10)	RLTR6-int|LTR|ERV1	14092	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_69335.1	chr7	129420113	129420152	-	1	NA	Intergenic	RLTR11A|LTR|ERVK	163038	NM_001080963	381925	Mm.39184	NM_001080963	ENSMUSG00000070366	Plpp4	C030048B12Rik|Gm1090|Ppapdc1a	phospholipid phosphatase 4	protein-coding
mm_140156.1	chr17	80148250	80148263	+	1	NA	intron (NM_176963, intron 3 of 6)	intron (NM_176963, intron 3 of 6)	20785	NM_176963	319625	Mm.29098	NM_176963	ENSMUSG00000035473	Galm	A530057M15Rik|AU015645|AU020959	galactose mutarotase	protein-coding
mm_136164.1	chr16	88563108	88563118	-	1	NA	promoter-TSS (NM_018778)	promoter-TSS (NM_018778)	70	NM_018778	54420	Mm.25836	NM_018778	ENSMUSG00000050520	Cldn8	AI648025	claudin 8	protein-coding
mm_111619.1	chr12	102405483	102405487	-	1	NA	intron (NM_011175, intron 4 of 13)	(GAAAA)n|Simple_repeat|Simple_repeat	34328	NM_011175	19141	Mm.17185	NM_011175	ENSMUSG00000021190	Lgmn	AEP|AI746452|AU022324|Prsc1	legumain	protein-coding
mm_99296.1	chr11	101337642	101337645	+	1	NA	exon (NM_009675, exon 4 of 4)	exon (NM_009675, exon 4 of 4)	7037	NM_009675	11754	Mm.67281	NM_009675	ENSMUSG00000019326	Aoc3	SSAO|VAP1	amine oxidase, copper containing 3	protein-coding
mm_165622.1	chr3	63299732	63299742	+	1	NA	intron (NM_001289463, intron 1 of 22)	intron (NM_001289463, intron 1 of 22)	3642	NM_001289463	17380	Mm.296022	NM_008604	ENSMUSG00000027820	Mme	6030454K05Rik|C85356|CALLA|CD10|NEP|SFE	membrane metallo endopeptidase	protein-coding
mm_72919.1	chr8	91074086	91074105	+	1	NA	intron (NM_011250, intron 1 of 21)	intron (NM_011250, intron 1 of 21)	4038	NM_001282000	19651	Mm.235580	NM_011250	ENSMUSG00000031666	Rbl2	PRB2|RBR-2|Rb2|p130	retinoblastoma-like 2	protein-coding
mm_101836.1	chr11	48349233	48349234	-	1	NA	Intergenic	Intergenic	-274650	NR_105801	102466638		NR_105801	ENSMUSG00000099011	Mir6380	Gm27356|mmu-mir-6380	microRNA 6380	ncRNA
mm_96078.1	chr11	60074434	60074434	+	1	NA	Intergenic	Intergenic	-27945	NM_001290011	18618	Mm.2731	NM_008819	ENSMUSG00000000301	Pemt	PEAMT|PEMT2|PLMT|Pempt|Pempt2	phosphatidylethanolamine N-methyltransferase	protein-coding
mm_39245.1	chr5	3344195	3344241	+	1	NA	5' UTR (NM_009873, exon 2 of 8)	5' UTR (NM_009873, exon 2 of 8)	325	NM_009873	12571	Mm.31672	NM_009873	ENSMUSG00000040274	Cdk6	AI504062|Crk2	cyclin-dependent kinase 6	protein-coding
mm_78884.1	chr9	44581689	44581708	+	1	NA	Intergenic	Intergenic	-23194	NM_001110826	13209	Mm.267061	NM_007841	ENSMUSG00000032097	Ddx6	1110001P04Rik|E230023J21Rik|HLR2|mRCK/P54|p54|rck	DEAD (Asp-Glu-Ala-Asp) box polypeptide 6	protein-coding
mm_113484.1	chr13	37345416	37345432	+	1	NA	promoter-TSS (NM_010745)	promoter-TSS (NM_010745)	79	NM_010745	17084	Mm.2639	NM_010745	ENSMUSG00000021423	Ly86	MD-1|MD1|ly86_tv2	lymphocyte antigen 86	protein-coding
mm_28885.1	chr3	97868165	97868179	-	1	NA	intron (NM_001039376, intron 1 of 46)	CpG	20535	NM_001289702	83679	Mm.129840	NM_031401	ENSMUSG00000038170	Pde4dip	4732458A06Rik|9430063L05Rik|C87016|D130016K21Rik|D3Bwg1078e|Usmg4|mKIAA0454	phosphodiesterase 4D interacting protein (myomegalin)	protein-coding
mm_31354.1	chr4	47091914	47091969	+	1	NA	promoter-TSS (NM_172693)	promoter-TSS (NM_172693)	-12	NM_172693	230145	Mm.132246	NM_172693	ENSMUSG00000039774	Galnt12	9130206E10|A630062B03Rik	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 12	protein-coding
mm_104980.1	chr11	100258068	100258079	-	1	NA	intron (NM_010663, intron 4 of 7)	intron (NM_010663, intron 4 of 7)	2956	NM_010663	16667	Mm.14046	NM_010663	ENSMUSG00000035557	Krt17	K17|Krt1-17	keratin 17	protein-coding
mm_52523.1	chr6	115601908	115601940	+	1	NA	promoter-TSS (NM_023290)	promoter-TSS (NM_023290)	-14	NM_023290	67027	Mm.101316	NM_023290	ENSMUSG00000000439	Mkrn2	2610002L04Rik|C81377	makorin, ring finger protein, 2	protein-coding
mm_25104.1	chr3	101297482	101297506	+	1	NA	Intergenic	MLT1G1|LTR|ERVL-MaLR	-9555	NM_013486	12481	Mm.22842	NM_013486	ENSMUSG00000027863	Cd2	LFA-2|Ly-37|Ly37	CD2 antigen	protein-coding
mm_112040.1	chr12	111670737	111670745	-	1	NA	intron (NM_021273, intron 5 of 7)	CpG	1597	NM_021273	12709	Mm.16831	NM_021273	ENSMUSG00000001270	Ckb	B-CK|Bck|Ck-3|Ck3|Ckbb	creatine kinase, brain	protein-coding
mm_6997.1	chr1	86359482	86359486	-	1	NA	promoter-TSS (NM_010880)	promoter-TSS (NM_010880)	-29	NM_010880	17975	Mm.154378	NM_010880	ENSMUSG00000026234	Ncl	B530004O11Rik|C23|D0Nds28|D1Nds28|Nucl	nucleolin	protein-coding
mm_1843.1	chr1	82858360	82858409	+	1	NA	exon (NM_010472, exon 2 of 13)	exon (NM_010472, exon 2 of 13)	18924	NM_001347077	15463	Mm.392569	NM_010472	ENSMUSG00000026159	Agfg1	AU045498|C130049H11Rik|C85612|D730048C23Rik|Hrb|RAB|Rip	ArfGAP with FG repeats 1	protein-coding
mm_157332.1	chrX	35881420	35881423	-	1	NA	Intergenic	MLT1G1|LTR|ERVL-MaLR	-7411	NM_001009947	75974	Mm.32873	NM_177745	ENSMUSG00000031093	Dock11	5033414A21Rik|8030476J24|Zizimin2|sph238	dedicator of cytokinesis 11	protein-coding
mm_21408.1	chr2	158117489	158117491	-	1	NA	3' UTR (NM_009373, exon 13 of 13)	3' UTR (NM_009373, exon 13 of 13)	-25693	NR_040609	72340	Mm.443395	NR_040609	ENSMUSG00000100860	2010009K17Rik	-	RIKEN cDNA 2010009K17 gene	ncRNA
mm_68814.1	chr7	125707680	125707718	-	1	NA	promoter-TSS (NM_207239)	promoter-TSS (NM_207239)	-11	NM_207239	233863	Mm.294173	NM_207239	ENSMUSG00000032777	Gtf3c1	-	general transcription factor III C 1	protein-coding
mm_5620.1	chr1	40085824	40085862	-	1	NA	promoter-TSS (NR_037980)	promoter-TSS (NR_037980)	8	NR_037980	100047133	Mm.447052	NR_037980	ENSMUSG00000097899	Gm16894	-	predicted gene, 16894	ncRNA
mm_136328.1	chr16	92358882	92358925	-	1	NA	intron (NM_008424, intron 1 of 1)	intron (NM_008424, intron 1 of 1)	565	NM_008424	16509	Mm.299425	NM_008424	ENSMUSG00000039639	Kcne1	Isk|MinK|nmf190	potassium voltage-gated channel, Isk-related subfamily, member 1	protein-coding
mm_27210.1	chr3	35932513	35932532	-	1	NA	promoter-TSS (NM_001205362)	promoter-TSS (NM_001205362)	-188	NM_001205362	114893	Mm.374810	NM_033623	ENSMUSG00000027708	Dcun1d1	Rp42|SCCRO|Tes3|pTes3	DCN1, defective in cullin neddylation 1, domain containing 1 (S. cerevisiae)	protein-coding
mm_41353.1	chr5	90504895	90504923	+	1	NA	intron (NM_007423, intron 10 of 14)	intron (NM_007423, intron 10 of 14)	-14040	NM_145146	280662	Mm.348786	NM_145146	ENSMUSG00000029369	Afm	Alf|alpha-Alb	afamin	protein-coding
mm_86807.1	chr10	20332102	20332132	+	1	NA	exon (NM_001025393, exon 9 of 12)	exon (NM_001025393, exon 9 of 12)	-15702	NM_027930	71804	Mm.262151	NM_027930	ENSMUSG00000019992	Mtfr2	2610016C23Rik|4933412C16Rik|Dufd1|Fam54a	mitochondrial fission regulator 2	protein-coding
mm_92098.1	chr10	62892801	62892831	-	1	NA	Intergenic	Intergenic	-12802	NM_001253857	52463	Mm.17774	NM_027384	ENSMUSG00000047146	Tet1	2510010B09Rik|AA517754|BB001228|Cxxc6|D10Ertd17e|LCX|mKIAA1676	tet methylcytosine dioxygenase 1	protein-coding
mm_109324.1	chr12	109562305	109562318	+	1	NA	non-coding (NR_003633, exon 5 of 5)	non-coding (NR_003633, exon 5 of 5)	-1381	NR_030427	791079		NR_030427	ENSMUSG00000076451	Mir770	Mirn770|mir-770|mmu-mir-770	microRNA 770	ncRNA
mm_124721.1	chr15	6579982	6579990	+	1	NA	exon (NM_001278269, exon 1 of 17)	exon (NM_001278269, exon 1 of 17)	139	NM_011815	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_96167.1	chr11	61488287	61488305	+	1	NA	TTS (NM_001291037)	TTS (NM_001291037)	2852	NM_029568	76293	Mm.272278	NM_029568	ENSMUSG00000042436	Mfap4	1110007F23Rik	microfibrillar-associated protein 4	protein-coding
mm_19676.1	chr2	103454487	103454491	-	1	NA	3' UTR (NM_009804, exon 13 of 13)	3' UTR (NM_009804, exon 13 of 13)	30421	NM_010125	13711	Mm.20888	NM_010125	ENSMUSG00000027186	Elf5	ESE-2|ESE-5|ESE-5.	E74-like factor 5	protein-coding
mm_151772.1	chr19	5293276	5293289	-	1	NA	exon (NM_030109, exon 4 of 21)	exon (NM_030109, exon 4 of 21)	2173	NM_030109	319322	Mm.196532	NM_030109	ENSMUSG00000024853	Sf3b2	145kDa|2610311M13Rik|2810441F20Rik|B230398H18Rik|SAP145|SF3b1|SF3b145|SF3b150	splicing factor 3b, subunit 2	protein-coding
mm_45314.1	chr5	65435760	65435766	-	1	NA	promoter-TSS (NM_009466)	promoter-TSS (NM_009466)	79	NM_009466	22235	Mm.344831	NM_009466	ENSMUSG00000029201	Ugdh	Udpgdh	UDP-glucose dehydrogenase	protein-coding
mm_62792.1	chr7	112679444	112679466	+	1	NA	5' UTR (NM_001166584, exon 1 of 14)	5' UTR (NM_001166584, exon 1 of 14)	135	NM_009346	21676	Mm.24685	NM_009346	ENSMUSG00000055320	Tead1	2610024B07Rik|B230114H05Rik|Gtrgeo5|TEAD-1|TEF-1|Tcf13|mTEF-1	TEA domain family member 1	protein-coding
mm_56992.1	chr6	120916783	120916807	-	1	NA	promoter-TSS (NM_007544)	promoter-TSS (NM_007544)	25	NM_007544	12122	Mm.235081	NM_007544	ENSMUSG00000004446	Bid	2700049M22Rik|AI875481|AU022477	BH3 interacting domain death agonist	protein-coding
mm_111403.1	chr12	91040584	91040614	-	1	NA	intron (NM_181815, intron 22 of 25)	MIR|SINE|MIR	-5249	NR_045858	71349	Mm.442093	NR_045858		5430427M07Rik	-	RIKEN cDNA 5430427M07 gene	ncRNA
mm_150245.1	chr19	34085543	34085554	+	1	NA	TTS (NM_027340)	TTS (NM_027340)	-15395	NM_023903	78753	Mm.195937	NM_023903	ENSMUSG00000056078	Lipm	4632427C23Rik|AW227514|Lipl3	lipase, family member M	protein-coding
mm_104911.1	chr11	99665956	99665961	-	1	NA	promoter-TSS (NM_026834)	promoter-TSS (NM_026834)	2	NM_026834	68768	Mm.416844	NM_026834	ENSMUSG00000075566	Krtap4-6	1110054P19Rik	keratin associated protein 4-6	protein-coding
mm_160365.1	chr8	22283223	22283223	+	1	NA	promoter-TSS (NM_199257)	promoter-TSS (NM_199257)	-218	NM_199257	234129	Mm.450553	NM_181851	ENSMUSG00000031481	Tpte	Pten2	transmembrane phosphatase with tensin homology	protein-coding
mm_122645.1	chr14	51870766	51870767	-	1	NA	Intergenic	RSINE1|SINE|B4	-14076	NM_001029990	52535	Mm.5750	NM_001029990	ENSMUSG00000004561	Mettl17	2310032K15Rik|D14Ertd209e|Mett11d1	methyltransferase like 17	protein-coding
mm_109876.1	chr12	4918103	4918107	-	1	NA	intron (NM_001099628, intron 1 of 30)	intron (NM_001099628, intron 1 of 30)	752	NM_001099628	320817	Mm.210966	NM_001099628	ENSMUSG00000052812	Atad2b	1110014E10Rik|BC032887|C79189|D530031C13Rik	ATPase family, AAA domain containing 2B	protein-coding
mm_16665.1	chr2	6721651	6721684	-	1	NA	promoter-TSS (NM_001310447)	promoter-TSS (NM_001310447)	-5	NM_001310447	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_19139.1	chr2	80447239	80447245	-	1	NA	5' UTR (NM_011356, exon 1 of 6)	5' UTR (NM_011356, exon 1 of 6)	154	NM_011356	20378	Mm.427436	NM_011356	ENSMUSG00000027004	Frzb	Frp|Sfrp3|frezzled|fritz|frzb-1	frizzled-related protein	protein-coding
mm_81126.1	chr9	106477264	106477274	+	1	NA	promoter-TSS (NM_145619)	promoter-TSS (NM_145619)	-40	NM_145620	27966	Mm.239997	NM_145620	ENSMUSG00000041506	Rrp9	55kDa|D19435|D9Wsu10e|Rnu3ip2|U3-55k	RRP9, small subunit (SSU) processome component, homolog (yeast)	protein-coding
mm_37420.1	chr4	122878398	122878428	-	1	NA	intron (NM_007598, intron 1 of 12)	L3|LINE|CR1	7644	NM_007598	12331	Mm.8687	NM_007598	ENSMUSG00000028656	Cap1	-	CAP, adenylate cyclase-associated protein 1 (yeast)	protein-coding
mm_20469.1	chr2	129370374	129370386	-	1	NA	intron (NM_008361, intron 1 of 6)	intron (NM_008361, intron 1 of 6)	478	NR_015474	329514	Mm.207315	NM_177848	ENSMUSG00000074805	Il1bos	9430083I22|Gm14047|OTTMUSG00000015529	interleukin 1 beta, opposite strand	ncRNA
mm_137566.1	chr17	27825230	27825249	+	1	NA	Intergenic	RMER4B|LTR|ERVK	-4697	NM_001271511	224647	Mm.196577	NM_001033279	ENSMUSG00000056692	D17Wsu92e	AU020189|C030010A15|C80239	DNA segment, Chr 17, Wayne State University 92, expressed	protein-coding
mm_37557.1	chr4	126163308	126163332	-	1	NA	promoter-TSS (NM_001162533)	promoter-TSS (NM_001162533)	21	NM_001162533	66938	Mm.29813	NM_025856	ENSMUSG00000073758	Sh3d21	1700029G01Rik|AU019788	SH3 domain containing 21	protein-coding
mm_170236.1	chr17	87593816	87593833	-	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	-42155	NM_008532	17075	Mm.4259	NM_008532	ENSMUSG00000045394	Epcam	CD326|EGP|EGP-2|Egp314|Ep-CAM|EpCAM1|GA733-2|Ly74|TROP1|Tacsd1|Tacstd1|gp40	epithelial cell adhesion molecule	protein-coding
mm_36952.1	chr4	109108008	109108030	-	1	NA	intron (NM_001346502, intron 4 of 23)	intron (NM_001346502, intron 4 of 23)	10017	NM_173350	100273	Mm.366315	NM_133885	ENSMUSG00000028559	Osbpl9	2600011I06Rik|AU015843|Orp-9	oxysterol binding protein-like 9	protein-coding
mm_72119.1	chr8	71686735	71686774	+	1	NA	intron (NM_010589, intron 21 of 24)	intron (NM_010589, intron 21 of 24)	-2498	NM_013564	16336	Mm.476857	NM_013564	ENSMUSG00000079019	Insl3	Rlf|Rlnl	insulin-like 3	protein-coding
mm_57062.1	chr6	122545314	122545320	-	1	NA	Intergenic	Intergenic	-8492	NM_009645	11628	Mm.391503	NM_009645	ENSMUSG00000040627	Aicda	Aid|Arp2	activation-induced cytidine deaminase	protein-coding
mm_159084.1	chr2	29702124	29702124	+	1	NA	intron (NM_001039087, intron 9 of 25)	intron (NM_001039087, intron 9 of 25)	-59404	NM_001177392	433416	Mm.330112	NM_001034887	ENSMUSG00000075425	Gm13547	OTTMUSG00000012686	predicted gene 13547	protein-coding
mm_92708.1	chr10	80756960	80756973	-	1	NA	intron (NM_199322, intron 1 of 27)	intron (NM_199322, intron 1 of 27)	1760	NM_199322	208266	Mm.152371	NM_199322	ENSMUSG00000061589	Dot1l	A630076O07|AW907654|Dot1|KMT4|mDot1	DOT1-like, histone H3 methyltransferase (S. cerevisiae)	protein-coding
mm_88778.1	chr10	80494856	80494873	+	1	NA	promoter-TSS (NM_139226)	promoter-TSS (NM_139226)	-42	NM_139226	246086	Mm.250572	NM_139226	ENSMUSG00000045518	Onecut3	OC-3|Oc3	one cut domain, family member 3	protein-coding
mm_6285.1	chr1	69686109	69686145	-	1	NA	promoter-TSS (NM_011770)	promoter-TSS (NM_011770)	-167	NM_011770	22779	Mm.106343	NM_011770	ENSMUSG00000025997	Ikzf2	A730095J18Rik|Helios|Zfpn1a2|Znfn1a2	IKAROS family zinc finger 2	protein-coding
mm_74936.1	chr8	25789316	25789324	-	1	NA	intron (NM_026032, intron 1 of 3)	intron (NM_026032, intron 1 of 3)	3729	NM_026032	67207	Mm.30198	NM_026032	ENSMUSG00000037296	Lsm1	2810025O06Rik|CASM	LSM1 homolog, mRNA degradation associated	protein-coding
mm_163594.1	chr13	41473783	41473789	+	1	NA	intron (NM_001111324, intron 1 of 7)	MER68|LTR|ERVL	13574	NM_001111324	18003	Mm.288980	NM_017464	ENSMUSG00000021365	Nedd9	Cas-L|CasL|HEF1|MEF1|Nedd-9|p105	neural precursor cell expressed, developmentally down-regulated gene 9	protein-coding
mm_96064.1	chr11	59662673	59662695	+	1	NA	5' UTR (NM_201245, exon 1 of 23)	5' UTR (NM_201245, exon 1 of 23)	189	NM_012027	26936	Mm.2402	NM_012027	ENSMUSG00000005417	Mprip	9530046C02|AA536749|AI647711|C76423|RIP3|Rhoip3|mKIAA0864|p116Rip	myosin phosphatase Rho interacting protein	protein-coding
mm_67775.1	chr7	97083010	97083058	-	1	NA	intron (NM_001162477, intron 1 of 9)	intron (NM_001162477, intron 1 of 9)	1283	NM_010248	14389	Mm.42033	NM_010248	ENSMUSG00000004508	Gab2	AI463667|D130058I17Rik|p97	growth factor receptor bound protein 2-associated protein 2	protein-coding
mm_94094.1	chr10	128547417	128547448	-	1	NA	TTS (NM_018860)	TTS (NM_018860)	312	NM_134003	103284	Mm.68289	NM_134003	ENSMUSG00000039810	Zc3h10	AI790326	zinc finger CCCH type containing 10	protein-coding
mm_159884.1	chr6	23839434	23839434	-	1	NA	promoter-TSS (NM_153163)	promoter-TSS (NM_153163)	-13	NM_001252105	320405	Mm.259632	NM_153163	ENSMUSG00000017978	Cadps2	A230044C21Rik|Caps-2|Caps2|Cpd2	Ca2+-dependent activator protein for secretion 2	protein-coding
mm_172030.1	chr6	124542327	124542336	-	1	NA	promoter-TSS (NM_144938)	promoter-TSS (NM_144938)	-10	NM_144938	50908	Mm.219527	NM_144938	ENSMUSG00000038521	C1s1	AA959438|AI255193|AI327365|C1s|C1sa	complement component 1, s subcomponent 1	protein-coding
mm_168859.1	chr12	28089315	28089325	-	1	NA	Intergenic	(TC)n|Simple_repeat|Simple_repeat	459017	NM_001177964	68511	Mm.310284	NM_001177964	ENSMUSG00000020633	Dcdc2c	1110015M06Rik	doublecortin domain containing 2C	protein-coding
mm_126878.1	chr15	89429561	89429579	+	1	NA	non-coding (NR_004843, exon 1 of 27)	non-coding (NR_004843, exon 1 of 27)	357	NR_037154	12651	Mm.485045	NM_007692	ENSMUSG00000022617	Chkb	Chetk|Chkl|Ck|Ck/Ek|Ck/Ek-beta|Ckb|Ckekb|Ek	choline kinase beta	protein-coding
mm_57206.1	chr6	122851068	122851085	-	1	NA	exon (NM_009779, exon 2 of 2)	exon (NM_009779, exon 2 of 2)	5081	NM_009779	12267	Mm.2408	NM_009779	ENSMUSG00000040552	C3ar1	AZ3B|C3AR|HNFAG09	complement component 3a receptor 1	protein-coding
mm_148287.1	chr18	82572847	82572880	-	1	NA	exon (NM_010777, exon 5 of 7)	exon (NM_010777, exon 5 of 7)	18355	NM_001025254	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_152001.1	chr19	5911631	5911637	-	1	NA	intron (NM_011262, intron 1 of 10)	intron (NM_011262, intron 1 of 10)	1237	NM_011262	19708	Mm.2651	NM_011262	ENSMUSG00000024826	Dpf2	2210010M07Rik|BAF45D|Req|ubi-d4	D4, zinc and double PHD fingers family 2	protein-coding
mm_13000.1	chr2	90889963	90889994	+	1	NA	exon (NM_026161, exon 2 of 2)	exon (NM_026161, exon 2 of 2)	4192	NM_026161	67445	Mm.258993	NM_026161	ENSMUSG00000040794	C1qtnf4	0710001E10Rik|9430004J15Rik|CTRP4	C1q and tumor necrosis factor related protein 4	protein-coding
mm_1167.1	chr1	60911113	60911122	+	1	NA	intron (NM_001281976, intron 1 of 2)	intron (NM_001281976, intron 1 of 2)	2092	NM_001281976	12477	Mm.390	NM_009843	ENSMUSG00000026011	Ctla4	Cd152|Ctla-4|Ly-56	cytotoxic T-lymphocyte-associated protein 4	protein-coding
mm_60373.1	chr7	44466665	44466674	+	1	NA	exon (NM_026690, exon 4 of 7)	exon (NM_026690, exon 4 of 7)	1234	NM_026690	68352	Mm.88478	NM_026690	ENSMUSG00000038704	Aspdh	0610012D14Rik	aspartate dehydrogenase domain containing	protein-coding
mm_96088.1	chr11	60353077	60353090	+	1	NA	promoter-TSS (NM_001039093)	promoter-TSS (NM_001039093)	-178	NM_001039092	216810	Mm.218875	NM_153080	ENSMUSG00000000538	Tom1l2	2900016I08Rik|A730055F12Rik|AU042072|Srebf1	target of myb1-like 2 (chicken)	protein-coding
mm_138631.1	chr17	35854887	35854892	+	1	NA	exon (NM_001010833, exon 14 of 16)	exon (NM_001010833, exon 14 of 16)	-6429	NM_134122	106582	Mm.390992	NM_134122	ENSMUSG00000059791	Nrm	2610307M02Rik|AI429796	nurim (nuclear envelope membrane protein)	protein-coding
mm_137035.1	chr17	17890610	17890630	+	1	NA	intron (NM_008039, intron 1 of 1)	RMER15|LTR|ERVL	2796	NM_008039	14289	Mm.378918	NM_008039	ENSMUSG00000052270	Fpr2	E330010I07Rik|Fpr-rs2	formyl peptide receptor 2	protein-coding
mm_30690.1	chr4	11535282	11535285	+	1	NA	intron (NM_001081183, intron 18 of 24)	intron (NM_001081183, intron 18 of 24)	-23637	NM_001039556	623474	Mm.491200	NM_177285	ENSMUSG00000078773	Rad54b	E130016E03Rik	RAD54 homolog B (S. cerevisiae)	protein-coding
mm_62381.1	chr7	100806608	100806619	+	1	NA	intron (NM_178764, intron 3 of 8)	MTE2b|LTR|ERVL-MaLR	56800	NM_177073	320100	Mm.40336	NM_177073	ENSMUSG00000008318	Relt	E430021K24Rik|Tnfrsf19l	RELT tumor necrosis factor receptor	protein-coding
mm_22073.1	chr2	168742101	168742142	-	1	NA	promoter-TSS (NM_015731)	promoter-TSS (NM_015731)	15	NM_001289446	11981	Mm.330819	NM_015731	ENSMUSG00000027546	Atp9a	IIa	ATPase, class II, type 9A	protein-coding
mm_93178.1	chr10	93540017	93540027	-	1	NA	promoter-TSS (NM_027908)	promoter-TSS (NM_027908)	11	NM_027908	71761	Mm.244518	NM_027908	ENSMUSG00000015890	Amdhd1	1300019J08Rik	amidohydrolase domain containing 1	protein-coding
mm_45094.1	chr5	44226602	44226633	-	1	NA	promoter-TSS (NM_173764)	promoter-TSS (NM_173764)	-11	NM_173764	231225	Mm.30688	NM_173764	ENSMUSG00000046985	Tapt1	4932414K18Rik	transmembrane anterior posterior transformation 1	protein-coding
mm_67731.1	chr7	90129995	90130045	-	1	NA	promoter-TSS (NM_001252521)	promoter-TSS (NM_001252521)	-84	NR_046007	78329	Mm.389940	NR_046006	ENSMUSG00000097162	2310010J17Rik	-	RIKEN cDNA 2310010J17 gene	ncRNA
mm_5586.1	chr1	39552357	39552367	-	1	NA	3' UTR (NM_001033135, exon 7 of 7)	3' UTR (NM_001033135, exon 7 of 7)	-3522	NR_028555	100217461		NR_028555	ENSMUSG00000077704	Snord89	MBII-289	small nucleolar RNA, C/D box 89	snoRNA
mm_164534.1	chr17	6307994	6307996	+	1	NA	3' UTR (NM_001166629, exon 5 of 5)	3' UTR (NM_001166629, exon 5 of 5)	9479	NM_001166629	100310872	Mm.381893	NM_001166629	ENSMUSG00000092074	Dynlt1a	-	dynein light chain Tctex-type 1A	protein-coding
mm_13044.1	chr2	91096730	91096741	+	1	NA	promoter-TSS (NM_011355)	promoter-TSS (NM_011355)	57	NM_011355	20375	Mm.1302	NM_011355	ENSMUSG00000002111	Spi1	Dis-1|Dis1|PU.1|Sfpi-1|Sfpi1|Spi-1|Tcfpu1|Tfpu.1	spleen focus forming virus (SFFV) proviral integration oncogene	protein-coding
mm_73097.1	chr8	94568321	94568333	+	1	NA	intron (NM_153507, intron 14 of 15)	intron (NM_153507, intron 14 of 15)	33399	NM_028221	102122	Mm.250425	NM_028221	ENSMUSG00000031774	Fam192a	1700001O11Rik|2310065K24Rik|AI596259|Nip30	family with sequence similarity 192, member A	protein-coding
mm_155259.1	chrX	57409148	57409160	+	1	NA	promoter-TSS (NM_001128625)	promoter-TSS (NM_001128625)	5	NM_001128625	245423		NM_001128625	ENSMUSG00000079584	Gm364	-	predicted gene 364	protein-coding
mm_56004.1	chr6	86488088	86488098	-	1	NA	non-coding (NR_040293, exon 1 of 2)	non-coding (NR_040293, exon 1 of 2)	134	NR_040293	381792	Mm.333223	NR_040292	ENSMUSG00000101655	2310040G24Rik	-	RIKEN cDNA 2310040G24 gene	ncRNA
mm_104729.1	chr11	98326452	98326460	-	1	NA	3' UTR (NM_010895, exon 2 of 2)	3' UTR (NM_010895, exon 2 of 2)	3189	NM_010895	18013	Mm.4814	NM_010895	ENSMUSG00000038255	Neurod2	Ndrf|bHLHa1	neurogenic differentiation 2	protein-coding
mm_12535.1	chr2	72285752	72285783	+	1	NA	promoter-TSS (NM_178084)	promoter-TSS (NM_178084)	66	NM_178084	65964	Mm.304143	NM_023057	ENSMUSG00000004085	Map3k20	AV006891|B230120H23Rik|MLTK|MLTKalpha|MLTKbeta|Zak	mitogen-activated protein kinase kinase kinase 20	protein-coding
mm_10285.1	chr2	10153564	10153627	+	1	NA	promoter-TSS (NM_172471)	promoter-TSS (NM_172471)	52	NM_172471	209378	Mm.313876	NM_172471	ENSMUSG00000025780	Itih5	4631408O11Rik|5430408M01Rik|E130106B02	inter-alpha (globulin) inhibitor H5	protein-coding
mm_135722.1	chr16	55819560	55819570	-	1	NA	intron (NM_001159395, intron 3 of 12)	intron (NM_001159395, intron 3 of 12)	2573	NM_001159394	80859	Mm.247272	NM_030612	ENSMUSG00000035356	Nfkbiz	AA408868|INAP|Mail	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, zeta	protein-coding
mm_44768.1	chr5	31698372	31698386	-	1	NA	promoter-TSS (NM_153196)	promoter-TSS (NM_153196)	329	NM_144541	107976	Mm.482126	NM_144541	ENSMUSG00000052139	Bre	6030405P19Rik|AI429776|B830038C02Rik	brain and reproductive organ-expressed protein	protein-coding
mm_149310.1	chr19	10747984	10747999	+	1	NA	intron (NR_027805, intron 1 of 3)	intron (NR_027805, intron 1 of 3)	7044	NR_027805	403202	Mm.34482	NM_207529	ENSMUSG00000067577	A430093F15Rik	Gm674	RIKEN cDNA A430093F15 gene	ncRNA
mm_4468.1	chr1	173419175	173419213	+	1	NA	Intergenic	Intergenic	-1410	NM_001013779	383619	Mm.131453	NM_001013779	ENSMUSG00000037860	Aim2	Gm1313|Ifi210	absent in melanoma 2	protein-coding
mm_45121.1	chr5	45856497	45856507	-	1	NA	promoter-TSS (NM_172153)	promoter-TSS (NM_172153)	50	NM_172153	209707	Mm.71498	NM_172153	ENSMUSG00000015882	Lcorl	Mlr1	ligand dependent nuclear receptor corepressor-like	protein-coding
mm_95154.1	chr11	35769808	35769819	+	1	NA	5' UTR (NM_145962, exon 1 of 7)	5' UTR (NM_145962, exon 1 of 7)	318	NM_145962	211347	Mm.255044	NM_145962	ENSMUSG00000018846	Pank3	-	pantothenate kinase 3	protein-coding
mm_109588.1	chr12	112620031	112620056	+	1	NA	promoter-TSS (NM_007421)	promoter-TSS (NM_007421)	-4	NM_007421	11565	Mm.3440	NM_007421	ENSMUSG00000011148	Adssl1	AI528595|Adss|Adss1	adenylosuccinate synthetase like 1	protein-coding
mm_21519.1	chr2	163632167	163632171	-	1	NA	exon (NM_012032, exon 5 of 10)	exon (NM_012032, exon 5 of 10)	-12681	NR_028113	68386	Mm.410649	NR_028113	ENSMUSG00000058812	0610039K10Rik	-	RIKEN cDNA 0610039K10 gene	ncRNA
mm_162144.1	chrX	74429268	74429268	+	1	NA	promoter-TSS (NM_178590)	promoter-TSS (NM_178590)	-47	NM_001161422	16151	Mm.12967	NM_010547	ENSMUSG00000004221	Ikbkg	1110037D23Rik|AI848108|AI851264|AW124339|IKK[g]|NEMO	inhibitor of kappaB kinase gamma	protein-coding
mm_51999.1	chr6	92816461	92816483	+	1	NA	exon (NM_175314, exon 20 of 30)	exon (NM_175314, exon 20 of 30)	84969	NM_175314	101401	Mm.158235	NM_175314	ENSMUSG00000030022	Adamts9	1810011L16Rik|8430403M15Rik|AW743315|E030027K14Rik	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 9	protein-coding
mm_65798.1	chr7	28925415	28925418	-	1	NA	intron (NM_021895, intron 1 of 20)	intron (NM_021895, intron 1 of 20)	36864	NM_021895	60595	Mm.81144	NM_021895	ENSMUSG00000054808	Actn4	C77391	actinin alpha 4	protein-coding
mm_91667.1	chr10	43174454	43174476	-	1	NA	promoter-TSS (NR_102361)	promoter-TSS (NR_102361)	65	NM_175407	109205	Mm.153750	NM_175407	ENSMUSG00000038248	Sobp	2900009C16Rik|5330439J01Rik|JXC1|jc	sine oculis-binding protein homolog (Drosophila)	protein-coding
mm_43086.1	chr5	124450191	124450203	+	1	NA	intron (NM_001310725, intron 2 of 6)	intron (NM_001310725, intron 2 of 6)	3493	NM_001310727	67956	Mm.137966	NM_030241	ENSMUSG00000049327	Kmt5a	2410195B05Rik|AA617402|AW536475|PR-SET7|PR/SET07|Setd8	lysine methyltransferase 5A	protein-coding
mm_57376.1	chr6	124813046	124813057	-	1	NA	intron (NM_009415, intron 1 of 6)	intron (NM_009415, intron 1 of 6)	1245	NM_009415	21991	Mm.4222	NM_009415	ENSMUSG00000023456	Tpi1	AI255506|Tpi|Tpi-1	triosephosphate isomerase 1	protein-coding
mm_83942.1	chr9	56796873	56796955	-	1	NA	Intergenic	CpG	55049	NM_198673	382075	Mm.335177	NM_198673	ENSMUSG00000045620	Odf3l1	BC049697|Gm1116	outer dense fiber of sperm tails 3-like 1	protein-coding
mm_55480.1	chr6	68930758	68930781	-	1	NA	Intergenic	Intergenic	396405	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_104113.1	chr11	86726335	86726348	-	1	NA	exon (NM_001003908, exon 7 of 32)	exon (NM_001003908, exon 7 of 32)	31151	NM_001003908	67300	Mm.254588	NM_001003908	ENSMUSG00000047126	Cltc	3110065L21Rik|CHC|R74732	clathrin, heavy polypeptide (Hc)	protein-coding
mm_140394.1	chr17	87530919	87530925	+	1	NA	Intergenic	Intergenic	-83987	NM_007589	12314	Mm.329243	NM_007589	ENSMUSG00000036438	Calm2	1500001E21Rik|AL024017	calmodulin 2	protein-coding
mm_152350.1	chr19	9985090	9985097	-	1	NA	TTS (NM_010239)	TTS (NM_010239)	2447	NM_010239	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
mm_119008.1	chr14	29486596	29486597	+	1	NA	intron (NM_009785, intron 3 of 37)	intron (NM_009785, intron 3 of 37)	235268	NM_009785	12294	Mm.386754	NM_009785	ENSMUSG00000021991	Cacna2d3	Cacnad3|alapha2delta3	calcium channel, voltage-dependent, alpha2/delta subunit 3	protein-coding
mm_94509.1	chr11	7210016	7210023	+	1	NA	exon (NM_008343, exon 2 of 5)	exon (NM_008343, exon 2 of 5)	3904	NM_008343	16009	Mm.29254	NM_008343	ENSMUSG00000020427	Igfbp3	AI649005|IGFBP-3|IGgfbp3	insulin-like growth factor binding protein 3	protein-coding
mm_19985.1	chr2	118547019	118547042	-	1	NA	intron (NM_138313, intron 2 of 4)	intron (NM_138313, intron 2 of 4)	569	NM_001331221	171543	Mm.210125	NM_138313	ENSMUSG00000040093	Bmf	AW260063|AW411872	BCL2 modifying factor	protein-coding
mm_136732.1	chr17	8283948	8283971	+	1	NA	exon (NM_018819, exon 1 of 4)	exon (NM_018819, exon 1 of 4)	146	NM_018819	55951	Mm.288510	NM_018819	ENSMUSG00000023861	Mpc1	0610006G08Rik|3830411I18Rik|Brp44l	mitochondrial pyruvate carrier 1	protein-coding
mm_83138.1	chr9	40449936	40449973	-	1	NA	intron (NM_172768, intron 1 of 19)	intron (NM_172768, intron 1 of 19)	5810	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_109290.1	chr12	109559372	109559382	+	1	NA	non-coding (NR_003633, exon 5 of 5)	non-coding (NR_003633, exon 5 of 5)	-4315	NR_030427	791079		NR_030427	ENSMUSG00000076451	Mir770	Mirn770|mir-770|mmu-mir-770	microRNA 770	ncRNA
mm_81829.1	chr9	118059091	118059134	+	1	NA	exon (NM_013727, exon 7 of 8)	exon (NM_013727, exon 7 of 8)	18590	NM_013727	27215	Mm.92705	NM_013727	ENSMUSG00000039285	Azi2	AA410145|AZ2	5-azacytidine induced gene 2	protein-coding
mm_152108.1	chr19	6941429	6941518	-	1	NA	promoter-TSS (NM_001177360)	promoter-TSS (NM_001177360)	34	NM_001177362	107173	Mm.276555	NM_207220	ENSMUSG00000024958	Gpr137	AI428855	G protein-coupled receptor 137	protein-coding
mm_150983.1	chr19	46515323	46515340	+	1	NA	exon (NM_053100, exon 6 of 6)	exon (NM_053100, exon 6 of 6)	13683	NM_053100	93679	Mm.392177	NM_053100	ENSMUSG00000025034	Trim8	AA408830|BB006755|GERP|Rnf27	tripartite motif-containing 8	protein-coding
mm_100694.1	chr11	3529908	3529925	-	1	NA	exon (NM_001284429, exon 11 of 22)	exon (NM_001284429, exon 11 of 22)	9376	NM_013870	29856	Mm.188516	NM_013870	ENSMUSG00000020439	Smtn	smsmo	smoothelin	protein-coding
mm_44085.1	chr5	149184556	149184601	+	1	NA	promoter-TSS (NM_001115151)	promoter-TSS (NM_001115151)	18	NM_001115149	231915	Mm.29402	NM_001013378	ENSMUSG00000041264	Uspl1	E430026A01Rik	ubiquitin specific peptidase like 1	protein-coding
mm_42213.1	chr5	112878044	112878047	+	1	NA	exon (NM_028901, exon 3 of 44)	exon (NM_028901, exon 3 of 44)	18317	NM_028901	74376	Mm.441903	NM_028901	ENSMUSG00000072720	Myo18b	4932408L24Rik|4933411E19Rik|Gm448	myosin XVIIIb	protein-coding
mm_38465.1	chr4	140620627	140620650	-	1	NA	intron (NM_001290803, intron 1 of 28)	MIRb|SINE|MIR	28118	NM_001112723	72754	Mm.29329	NM_172415	ENSMUSG00000040964	Arhgef10l	2810441C07Rik	Rho guanine nucleotide exchange factor (GEF) 10-like	protein-coding
mm_89831.1	chr10	106496867	106496870	+	1	NA	intron (NM_001205341, intron 2 of 31)	intron (NM_001205341, intron 2 of 31)	26558	NM_001205341	327814	Mm.391424	NM_177373	ENSMUSG00000053825	Ppfia2	5330438O12|B230207K17Rik|E130120L08Rik|mKIAA4112	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 2	protein-coding
mm_42661.1	chr5	119670700	119670704	+	1	NA	promoter-TSS (NM_011535)	promoter-TSS (NM_011535)	-160	NM_198052	21386	Mm.219139	NM_011535	ENSMUSG00000018604	Tbx3	D5Ertd189e	T-box 3	protein-coding
mm_59493.1	chr7	27523253	27523269	+	1	NA	promoter-TSS (NM_001033315)	promoter-TSS (NM_001033315)	0	NM_001033315	233020	Mm.429716	NM_001033315	ENSMUSG00000040424	Hipk4	Gm162	homeodomain interacting protein kinase 4	protein-coding
mm_158888.1	chr1	13126978	13126978	-	1	NA	intron (NM_001081209, intron 1 of 7)	A-rich|Low_complexity|Low_complexity	185	NM_001081209	383491	Mm.309380	NM_001081209	ENSMUSG00000042414	Prdm14	-	PR domain containing 14	protein-coding
mm_120853.1	chr14	75224095	75224123	+	1	NA	exon (NM_001247984, exon 14 of 16)	exon (NM_001247984, exon 14 of 16)	-18178	NM_019775	56373	Mm.24242	NM_019775	ENSMUSG00000021999	Cpb2	1110032P04Rik|4930405E17Rik|AI255929|CPR|Cpu|TAFI	carboxypeptidase B2 (plasma)	protein-coding
mm_106878.1	chr12	8011503	8011514	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	33831	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_83245.1	chr9	42399901	42399912	-	1	NA	promoter-TSS (NM_001324548)	promoter-TSS (NM_001324548)	23	NM_009347	21683	Mm.42209	NM_009347	ENSMUSG00000037705	Tecta	Tctna	tectorin alpha	protein-coding
mm_160663.1	chr9	119825459	119825459	-	1	NA	promoter-TSS (NM_011887)	promoter-TSS (NM_011887)	-3	NM_011887	24046	Mm.89981	NM_011887	ENSMUSG00000034115	Scn11a	NSS2|NaN|NaT|NaV1.9|SNS2	sodium channel, voltage-gated, type XI, alpha	protein-coding
mm_8207.1	chr1	138123806	138123840	-	1	NA	intron (NM_001111316, intron 2 of 31)	intron (NM_001111316, intron 2 of 31)	51303	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_40409.1	chr5	53061368	53061378	+	1	NA	exon (NM_011402, exon 6 of 13)	exon (NM_011402, exon 6 of 13)	12020	NM_011402	20531	Mm.284891	NM_011402	ENSMUSG00000029188	Slc34a2	AA536683|D5Ertd227e|NaPi-2b|Npt2b	solute carrier family 34 (sodium phosphate), member 2	protein-coding
mm_109112.1	chr12	105454036	105454047	+	1	NA	5' UTR (NM_001252508, exon 1 of 2)	5' UTR (NM_001252508, exon 1 of 2)	185	NM_001252508	268595	Mm.2388	NM_001252508	ENSMUSG00000094910	D430019H16Rik	AI852661	RIKEN cDNA D430019H16 gene	protein-coding
mm_123183.1	chr14	57746045	57746144	-	1	NA	promoter-TSS (NM_015771)	promoter-TSS (NM_015771)	29	NM_015771	50523	Mm.347899	NM_015771	ENSMUSG00000021959	Lats2	4932411G09Rik|AV277261|AW228608	large tumor suppressor 2	protein-coding
mm_114619.1	chr13	75962464	75962466	+	1	NA	Intergenic	RMER1A|Other|Other	-5274	NM_029343	75571	Mm.443291	NM_029343	ENSMUSG00000021590	Spata9	1700030K01Rik|4930599C08Rik|A930023H06Rik	spermatogenesis associated 9	protein-coding
mm_102001.1	chr11	51263043	51263061	-	1	NA	promoter-TSS (NM_177567)	promoter-TSS (NM_177567)	-62	NM_001304744	12750	Mm.239354	NM_007714	ENSMUSG00000020385	Clk4	AI987988|C85119	CDC like kinase 4	protein-coding
mm_149736.1	chr19	22139029	22139055	+	1	NA	promoter-TSS (NM_001035240)	promoter-TSS (NM_001035240)	-75	NM_001035239	226025	Mm.131943	NM_177341	ENSMUSG00000052387	Trpm3	6330504P12Rik|9330180E14|AU018608|B930001P07Rik|LTRPC3|MLSN2	transient receptor potential cation channel, subfamily M, member 3	protein-coding
mm_92156.1	chr10	67537155	67537158	-	1	NA	promoter-TSS (NM_010118)	promoter-TSS (NM_010118)	-713	NM_010118	13654	Mm.290421	NM_010118	ENSMUSG00000037868	Egr2	Egr-2|Krox-20|Krox20|NGF1-B|Zfp-25|Zfp-6	early growth response 2	protein-coding
mm_54615.1	chr6	38354602	38354604	-	1	NA	promoter-TSS (NM_028421)	promoter-TSS (NM_028421)	0	NM_028864	78781	Mm.25243	NM_028421	ENSMUSG00000029826	Zc3hav1	1200014N16Rik|2900058M19Rik|9130009D18Rik|9830115L13Rik|ARTD13|D6Bwg1452e|ZAP	zinc finger CCCH type, antiviral 1	protein-coding
mm_140092.1	chr17	75520623	75520627	+	1	NA	intron (NM_001166493, intron 13 of 16)	Lx7|LINE|L1	31321	NM_133747	72722	Mm.24641	NM_133747	ENSMUSG00000002017	Fam98a	2810405J04Rik|AL024114	family with sequence similarity 98, member A	protein-coding
mm_117150.1	chr13	61203407	61203418	-	1	NA	promoter-TSS (NM_021445)	promoter-TSS (NM_021445)	-20	NM_021445	58518	Mm.143794	NM_021445	ENSMUSG00000021441	Cts6	1600022N02Rik	cathepsin 6	protein-coding
mm_52381.1	chr6	113133660	113133692	+	1	NA	intron (NM_173005, intron 15 of 20)	intron (NM_173005, intron 15 of 20)	28741	NM_173005	72895	Mm.367159	NM_028385	ENSMUSG00000034269	Setd5	2900045N06Rik|C330007C20|C85544|mKIAA1757	SET domain containing 5	protein-coding
mm_164563.1	chr17	17871142	17871150	+	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	12793	NM_013521	14293	Mm.56951	NM_013521	ENSMUSG00000045551	Fpr1	FPR|LXA4R|fMLF-R	formyl peptide receptor 1	protein-coding
mm_169359.1	chr14	27508441	27508444	-	1	NA	promoter-TSS (NM_177111)	promoter-TSS (NM_177111)	18	NM_177111	320234	Mm.247767	NM_177111	ENSMUSG00000046753	Ccdc66	E230015L20Rik	coiled-coil domain containing 66	protein-coding
mm_65643.1	chr7	27979156	27979181	-	1	NA	promoter-TSS (NM_001081021)	promoter-TSS (NM_001081021)	-11	NM_001081021	338354	Mm.389873	NM_001081021	ENSMUSG00000063047	Zfp780b	B230208L21Rik	zinc finger protein 780B	protein-coding
mm_139327.1	chr17	48931802	48931813	+	1	NA	promoter-TSS (NM_027452)	promoter-TSS (NM_027452)	-775	NM_027452	70530	Mm.133607	NM_027452	ENSMUSG00000040490	Lrfn2	5730420O05Rik|SALM1|mKIAA1246	leucine rich repeat and fibronectin type III domain containing 2	protein-coding
mm_16454.1	chr2	180581200	180581219	+	1	NA	promoter-TSS (NM_028479)	promoter-TSS (NM_028479)	-95	NM_028479	73247	Mm.426558	NM_028479	ENSMUSG00000027569	Mrgbp	1600027N09Rik|AW060503|C80444	MRG/MORF4L binding protein	protein-coding
mm_162799.1	chr10	76798853	76798865	-	1	NA	intron (NM_001347216, intron 5 of 15)	intron (NM_001347216, intron 5 of 15)	-72815	NM_009933	12833	Mm.2509	NM_009933	ENSMUSG00000001119	Col6a1	AI747156|Col6a-1	collagen, type VI, alpha 1	protein-coding
mm_26158.1	chr3	138217815	138217828	+	1	NA	promoter-TSS (NM_009626)	promoter-TSS (NM_009626)	48	NM_009626	11529	Mm.8473	NM_009626	ENSMUSG00000055301	Adh7	AI325182|Adh-3|Adh-3e|Adh-3t|Adh3|Adh3-e|Adh3-t|Adh4|Adt-1	alcohol dehydrogenase 7 (class IV), mu or sigma polypeptide	protein-coding
mm_57646.1	chr6	128437705	128437730	-	1	NA	intron (NM_010219, intron 1 of 9)	CpG	914	NM_010219	14228	Mm.12758	NM_010219	ENSMUSG00000030357	Fkbp4	59kDa|AL022792|AW208983|FKBP-4|FKBP-52|FKBP52|FKPB52|p59	FK506 binding protein 4	protein-coding
mm_88155.1	chr10	69572982	69572997	+	1	NA	intron (NM_170730, intron 1 of 17)	RMER17C|LTR|ERVK	39281	NM_146005	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_78670.1	chr9	40770768	40770792	+	1	NA	intron (NM_133733, intron 2 of 6)	intron (NM_133733, intron 2 of 6)	-30493	NM_031165	15481	Mm.290774	NM_031165	ENSMUSG00000015656	Hspa8	2410008N15Rik|Hsc70|Hsc71|Hsc73|Hsp73|Hspa10	heat shock protein 8	protein-coding
mm_166179.1	chr5	30960234	30960236	-	1	NA	promoter-TSS (NM_001294302)	promoter-TSS (NM_001294302)	92	NM_001294302	50907	Mm.272414	NM_016703	ENSMUSG00000045302	Preb	C85705	prolactin regulatory element binding	protein-coding
mm_67077.1	chr7	68264582	68264596	-	1	NA	promoter-TSS (NM_030101)	promoter-TSS (NM_030101)	-356	NM_030101	78444	Mm.425468	NM_030101	ENSMUSG00000030553	Pgpep1l	C330024D12Rik	pyroglutamyl-peptidase I-like	protein-coding
mm_27680.1	chr3	65958141	65958151	-	1	NA	promoter-TSS (NM_019937)	promoter-TSS (NM_019937)	79	NM_019937	56706	Mm.175612	NM_019937	ENSMUSG00000027829	Ccnl1	2610030E23Rik|AU018493|Ccnl|ania-6a	cyclin L1	protein-coding
mm_91229.1	chr10	22299800	22299815	-	1	NA	intron (NM_009018, intron 5 of 5)	B3|SINE|B2	-6913	NR_015465	606736	Mm.387042	NR_015465	ENSMUSG00000097352	C920009B18Rik	-	RIKEN cDNA C920009B18 gene	ncRNA
mm_66304.1	chr7	38271225	38271245	-	1	NA	5' UTR (NM_025390, exon 1 of 7)	5' UTR (NM_025390, exon 1 of 7)	113	NM_025390	66161	Mm.22284	NM_025390	ENSMUSG00000030423	Pop4	1110023P21Rik|Rpp29	processing of precursor 4, ribonuclease P/MRP family, (S. cerevisiae)	protein-coding
mm_111730.1	chr12	103773600	103773610	-	1	NA	promoter-TSS (NM_009246)	promoter-TSS (NM_009246)	28	NM_009246	20703	Mm.439695	NM_009246	ENSMUSG00000071177	Serpina1d	AI118301|Dom4|PI4|Spi1-4	serine (or cysteine) peptidase inhibitor, clade A, member 1D	protein-coding
mm_103669.1	chr11	79112642	79112648	-	1	NA	intron (NM_013571, intron 1 of 17)	intron (NM_013571, intron 1 of 17)	33709	NM_013571	16706	Mm.4745	NM_013571	ENSMUSG00000018334	Ksr1	AW492498|B-KSR1|D11Bhm183e|D11Bhm184e|Ksr|RSU2|hb	kinase suppressor of ras 1	protein-coding
mm_34360.1	chr4	144892709	144892711	+	1	NA	promoter-TSS (NM_001172424)	promoter-TSS (NM_001172424)	-117	NM_001172424	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding
mm_68732.1	chr7	120751373	120751375	-	1	NA	intron (NM_177697, intron 2 of 33)	intron (NM_177697, intron 2 of 33)	11817	NM_177697	233813	Mm.389939	NM_177697	ENSMUSG00000030889	Vwa3a	E030013G06Rik	von Willebrand factor A domain containing 3A	protein-coding
mm_165203.1	chr2	32978145	32978146	+	1	NA	intron (NM_019488, intron 4 of 9)	RSINE1|SINE|B4	3911	NM_019488	56017	Mm.305754	NM_019488	ENSMUSG00000026791	Slc2a8	D2Ertd44e|GLUT8|GlutX1	solute carrier family 2, (facilitated glucose transporter), member 8	protein-coding
mm_20044.1	chr2	120154487	120154498	-	1	NA	promoter-TSS (NM_133838)	promoter-TSS (NM_133838)	83	NM_133838	98878	Mm.132226	NM_133838	ENSMUSG00000027293	Ehd4	2210022F10Rik|AI197390|AI846352|AV006278|Past2	EH-domain containing 4	protein-coding
mm_162932.1	chr10	123582561	123582563	+	1	NA	intron (NM_182807, intron 2 of 5)	intron (NM_182807, intron 2 of 5)	318486	NM_001252387	268354	Mm.51939	NM_182807	ENSMUSG00000044071	Fam19a2	6330575M02|FAM19A2 TAFA-2|TAFA2|Tafa-2	family with sequence similarity 19, member A2	protein-coding
mm_8119.1	chr1	136040895	136040927	-	1	NA	Intergenic	Intergenic	-9893	NM_001270609	226439	Mm.491831	NM_001270609	ENSMUSG00000097918	Ascl5	Ascl5-ps|Gm197|bHLHa47	achaete-scute family bHLH transcription factor 5	protein-coding
mm_124516.1	chr14	121963417	121963425	-	1	NA	intron (NM_183031, intron 1 of 1)	intron (NM_183031, intron 1 of 1)	1772	NM_183031	321019	Mm.265618	NM_183031	ENSMUSG00000051212	Gpr183	Ebi2	G protein-coupled receptor 183	protein-coding
mm_144187.1	chr18	7869140	7869152	+	1	NA	promoter-TSS (NM_001146298)	promoter-TSS (NM_001146298)	-51	NM_001146298	225131	Mm.204524	NM_153085	ENSMUSG00000024283	Wac	1110067P07Rik|A230035H12Rik|AI256735|AI256776|Wwp4	WW domain containing adaptor with coiled-coil	protein-coding
mm_75265.1	chr8	40634777	40634806	-	1	NA	promoter-TSS (NM_001040699)	promoter-TSS (NM_001040699)	1	NM_001040699	54384	Mm.294871	NM_019433	ENSMUSG00000039431	Mtmr7	-	myotubularin related protein 7	protein-coding
mm_52025.1	chr6	94722173	94722177	+	1	NA	Intergenic	Intergenic	-22030	NM_008377	16206	Mm.245210	NM_008377	ENSMUSG00000030029	Lrig1	D6Bwg0781e|Img|LIG-1	leucine-rich repeats and immunoglobulin-like domains 1	protein-coding
mm_109231.1	chr12	108837046	108837049	+	1	NA	promoter-TSS (NR_029773)	promoter-TSS (NR_029773)	74	NR_029773	723946		NR_029773	ENSMUSG00000065429	Mir345	Mirn345|mir-345|mmu-mir-345	microRNA 345	ncRNA
mm_74151.1	chr8	123373779	123373846	+	1	NA	5' UTR (NM_001037877, exon 1 of 18)	5' UTR (NM_001037877, exon 1 of 18)	101	NM_001286363	66855	Mm.178818	NM_025804	ENSMUSG00000001472	Tcf25	1100001J13Rik|1810041K11Rik|D8Ertd325e|Nulp1|mKIAA1049	transcription factor 25 (basic helix-loop-helix)	protein-coding
mm_116630.1	chr13	48968078	48968082	-	1	NA	promoter-TSS (NR_015601)	promoter-TSS (NR_015601)	-32	NR_015601	68128	Mm.426304	NR_015601		Fam120aos	C030044B11Rik	family with sequence similarity 120A, opposite strand	ncRNA
mm_59820.1	chr7	29238435	29238456	+	1	NA	exon (NM_029887, exon 1 of 8)	exon (NM_029887, exon 1 of 8)	122	NM_029887	77254	Mm.36699	NM_029887	ENSMUSG00000030588	Yif1b	9430029K10Rik|Yip1b	Yip1 interacting factor homolog B (S. cerevisiae)	protein-coding
mm_15840.1	chr2	164715322	164715333	+	1	NA	promoter-TSS (NM_001040055)	promoter-TSS (NM_001040055)	22	NM_001040055	641368	Mm.422380	NM_001040055	ENSMUSG00000074593	Spint5	Gm14316|OTTMUSG00000016293	serine protease inhibitor, Kunitz type 5	protein-coding
mm_34063.1	chr4	138454356	138454377	+	1	NA	promoter-TSS (NM_025451)	promoter-TSS (NM_025451)	-782	NM_025451	66259	Mm.41603	NM_025451	ENSMUSG00000046447	Camk2n1	1810006K23Rik|AI848599|AI891706	calcium/calmodulin-dependent protein kinase II inhibitor 1	protein-coding
mm_133208.1	chr16	74620060	74620069	+	1	NA	Intergenic	Intergenic	-209152	NM_175549	268902	Mm.171736	NM_175549	ENSMUSG00000052516	Robo2	2600013A04Rik|9430089E08Rik|BB097918|D230004I22Rik|mKIAA1568	roundabout guidance receptor 2	protein-coding
mm_158572.1	chrX	150589810	150589821	-	1	NA	promoter-TSS (NM_008824)	promoter-TSS (NM_008824)	-106	NM_008824	18639	Mm.249131	NM_008824	ENSMUSG00000025271	Pfkfb1	PFK/FBPase 1	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1	protein-coding
mm_116992.1	chr13	56503794	56503796	-	1	NA	Intergenic	MT2B2|LTR|ERVL	-18677	NM_001346732	213311	Mm.233904	NM_178674	ENSMUSG00000035509	Fbxl21	D630045D17Rik|FBL3B|FBXL3B|Psttm	F-box and leucine-rich repeat protein 21	protein-coding
mm_168696.1	chr11	97664145	97664160	+	1	NA	intron (NM_139311, intron 1 of 19)	intron (NM_139311, intron 1 of 19)	740	NM_139311	246198	Mm.23685	NM_139311	ENSMUSG00000038437	Mllt6	AI315037|Af17	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 6	protein-coding
mm_125886.1	chr15	75862311	75862370	+	1	NA	promoter-TSS (NM_026960)	promoter-TSS (NM_026960)	1	NM_026960	69146	Mm.27385	NM_026960	ENSMUSG00000022575	Gsdmd	1810036L03Rik|AW558049|DF5L|Dfna5l|Gsdmdc1|M2-4	gasdermin D	protein-coding
mm_135529.1	chr16	49699008	49699022	-	1	NA	promoter-TSS (NM_028680)	promoter-TSS (NM_028680)	-279	NM_028680	73916	Mm.241276	NM_028680	ENSMUSG00000032965	Ift57	4833420A15Rik|Esrrbl1|Hippi|MHS4R2	intraflagellar transport 57	protein-coding
mm_131316.1	chr16	11656145	11656155	+	1	NA	exon (NM_028964, exon 17 of 21)	exon (NM_028964, exon 17 of 21)	-123552	NR_126430	73761	Mm.39183	NR_126430		4833415N18Rik	-	RIKEN cDNA 4833415N18 gene	ncRNA
mm_28980.1	chr3	101110748	101110782	-	1	NA	promoter-TSS (NM_011197)	promoter-TSS (NM_011197)	-599	NM_011197	19221	Mm.24807	NM_011197	ENSMUSG00000027864	Ptgfrn	4833445A08Rik|AU042434|CD9P-1|FPRP|Trim45	prostaglandin F2 receptor negative regulator	protein-coding
mm_82226.1	chr9	3026769	3026788	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	11965	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_161127.1	chr12	111628053	111628053	+	1	NA	intron (NM_022801, intron 10 of 15)	intron (NM_022801, intron 10 of 15)	44285	NM_021273	12709	Mm.16831	NM_021273	ENSMUSG00000001270	Ckb	B-CK|Bck|Ck-3|Ck3|Ckbb	creatine kinase, brain	protein-coding
mm_64247.1	chr7	141704304	141704326	+	1	NA	exon (NM_023566, exon 27 of 46)	exon (NM_023566, exon 27 of 46)	13975	NM_023566	17831	Mm.2041	NM_023566		Muc2	2010015E03Rik|MCM|wnn	mucin 2	protein-coding
mm_25042.1	chr3	98291252	98291264	+	1	NA	exon (NM_008256, exon 2 of 10)	exon (NM_008256, exon 2 of 10)	10827	NM_008256	15360	Mm.289131	NM_008256	ENSMUSG00000027875	Hmgcs2	1300002P16|mHS	3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2	protein-coding
mm_145136.1	chr18	45268877	45268916	+	1	NA	promoter-TSS (NM_001312905)	promoter-TSS (NM_001312905)	36	NM_001312905	140492	Mm.411614	NM_080465	ENSMUSG00000054477	Kcnn2	KCa2.2|SK2|SKCA2|bc|fri	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2	protein-coding
mm_36733.1	chr4	99122469	99122480	-	1	NA	Intergenic	Intergenic	-1559	NM_026082	67299	Mm.260623	NM_026082	ENSMUSG00000028556	Dock7	3110056M06Rik|Gm430	dedicator of cytokinesis 7	protein-coding
mm_76760.1	chr8	95576290	95576333	-	1	NA	promoter-TSS (NM_001310539)	promoter-TSS (NM_001310539)	-704	NM_001310539	70993	Mm.486561	NM_027640	ENSMUSG00000048400	Prss54	4931432M23Rik|Klkbl4	protease, serine 54	protein-coding
mm_104607.1	chr11	97187873	97187926	-	1	NA	promoter-TSS (NM_008379)	promoter-TSS (NM_008379)	-7	NM_008379	16211	Mm.251013	NM_008379	ENSMUSG00000001440	Kpnb1	AA409963|IPOB|Impnb	karyopherin (importin) beta 1	protein-coding
mm_70328.1	chr8	4359735	4359756	+	1	NA	non-coding (NR_033527, exon 6 of 6)	non-coding (NR_033527, exon 6 of 6)	10157	NM_009138	20300	Mm.7275	NM_009138	ENSMUSG00000023235	Ccl25	A130072A22Rik|AI852536|CKb15|Scya25|TECK	chemokine (C-C motif) ligand 25	protein-coding
mm_128456.1	chr15	50778352	50778375	-	1	NA	intron (NM_001310485, intron 5 of 7)	intron (NM_001310485, intron 5 of 7)	110686	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	trichorhinophalangeal syndrome I (human)	protein-coding
mm_13321.1	chr2	102706415	102706430	+	1	NA	promoter-TSS (NM_011393)	promoter-TSS (NM_011393)	-16	NM_011393	20511	Mm.267547	NM_011393	ENSMUSG00000005089	Slc1a2	1700091C19Rik|2900019G14Rik|AI159670|Eaat2|GLT-1|GLT1|MGLT1	solute carrier family 1 (glial high affinity glutamate transporter), member 2	protein-coding
mm_170981.1	chr2	71873218	71873231	+	1	NA	promoter-TSS (NM_172665)	promoter-TSS (NM_172665)	0	NM_172665	228026	Mm.34411	NM_172665	ENSMUSG00000006494	Pdk1	B830012B01|D530020C15Rik	pyruvate dehydrogenase kinase, isoenzyme 1	protein-coding
mm_127449.1	chr15	101270686	101270687	+	1	NA	exon (NM_010444, exon 2 of 7)	exon (NM_010444, exon 2 of 7)	3840	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_95293.1	chr11	45991718	45991759	+	1	NA	exon (NM_173384, exon 4 of 5)	exon (NM_173384, exon 4 of 5)	11428	NM_173384	214105	Mm.66708	NM_173384	ENSMUSG00000040489	Sox30	-	SRY (sex determining region Y)-box 30	protein-coding
mm_3337.1	chr1	137965425	137965442	+	1	NA	Intergenic	Intergenic	-1022	NR_029795	735252		NR_029795	ENSMUSG00000065565	Mir181a-1	Mirn181a-1|Mirn213|miR-213|mir-181a-1|mmu-mir-213	microRNA 181a-1	ncRNA
mm_28869.1	chr3	97702603	97702618	-	1	NA	intron (NM_001039376, intron 36 of 46)	intron (NM_001039376, intron 36 of 46)	-12048	NR_106084	102466229		NR_106084	ENSMUSG00000098381	Mir7225	Gm27499|mmu-mir-7225	microRNA 7225	ncRNA
mm_110766.1	chr12	70231415	70231457	-	1	NA	intron (NR_045174, intron 1 of 4)	LTR16B2|LTR|ERVL	3595	NR_045174	414124	Mm.416164	NR_045174	ENSMUSG00000085298	F730035M05Rik	-	RIKEN cDNA F730035M05 gene	ncRNA
mm_79287.1	chr9	51204853	51204857	+	1	NA	Intergenic	MIRb|SINE|MIR	-8835	NM_011136	18985	Mm.897	NM_011136	ENSMUSG00000032053	Pou2af1	BOB.1|Bob-1|Bob1|OBF-1|OBF.1|OCA-B|OCAB	POU domain, class 2, associating factor 1	protein-coding
mm_4573.1	chr1	177740860	177740897	+	1	NA	intron (NM_027077, intron 2 of 5)	intron (NM_027077, intron 2 of 5)	11064	NM_027077	69428	Mm.84467	NM_027077	ENSMUSG00000015962	1700016C15Rik	-	RIKEN cDNA 1700016C15 gene	protein-coding
mm_1896.1	chr1	85709388	85709403	+	1	NA	3' UTR (NM_013673, exon 20 of 20)	3' UTR (NM_013673, exon 20 of 20)	27211	NM_177055	319997	Mm.116691	NM_177055	ENSMUSG00000052760	A630001G21Rik	-	RIKEN cDNA A630001G21 gene	protein-coding
mm_45696.1	chr5	82124662	82124672	-	1	NA	promoter-TSS (NR_138557)	promoter-TSS (NR_138557)	46	NR_138557	67327	Mm.87058	NR_138557		1700031L13Rik	-	RIKEN cDNA 1700031L13 gene	ncRNA
mm_23233.1	chr3	50443748	50443753	+	1	NA	promoter-TSS (NM_011990)	promoter-TSS (NM_011990)	-137	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_126625.1	chr15	83316581	83316606	+	1	NA	intron (NM_025445, intron 9 of 15)	intron (NM_025445, intron 9 of 15)	33654	NM_025445	66251	Mm.258910	NM_025445	ENSMUSG00000054277	Arfgap3	0610009H19Rik|1810004P07Rik|1810035F16Rik|9130416J18Rik|Arfgap1	ADP-ribosylation factor GTPase activating protein 3	protein-coding
mm_123699.1	chr14	69714808	69714836	-	1	NA	promoter-TSS (NM_001301651)	promoter-TSS (NM_001301651)	-13	NM_001301651	71843	Mm.27738	NM_001146012	ENSMUSG00000034194	R3hcc1	1700020M16Rik|AA407796	R3H domain and coiled-coil containing 1	protein-coding
mm_155968.1	chrX	106085198	106085213	+	1	NA	exon (NM_009726, exon 3 of 23)	exon (NM_009726, exon 3 of 23)	57981	NM_009726	11977	Mm.254297	NM_009726	ENSMUSG00000033792	Atp7a	MNK	ATPase, Cu++ transporting, alpha polypeptide	protein-coding
mm_19710.1	chr2	103819342	103819353	-	1	NA	Intergenic	Intergenic	-8725	NR_040514	78031	Mm.243867	NR_040514	ENSMUSG00000086687	4930547E08Rik	-	RIKEN cDNA 4930547E08 gene	ncRNA
mm_5156.1	chr1	9967806	9967815	-	1	NA	promoter-TSS (NM_001285425)	promoter-TSS (NM_001285425)	-325	NM_001285425	100039596	Mm.412928	NM_001285425	ENSMUSG00000099032	Tcf24	ENSMUSG00000073738|Gm10567|Gm2330	transcription factor 24	protein-coding
mm_148869.1	chr19	6497588	6497666	+	1	NA	intron (NM_001205234, intron 17 of 22)	CpG	45443	NM_009203	20521	Mm.391146	NM_009203	ENSMUSG00000061742	Slc22a12	AI987855|OAT4L|Rst|Slc22al2|URAT1	solute carrier family 22 (organic anion/cation transporter), member 12	protein-coding
mm_4157.1	chr1	171027962	171027972	+	1	NA	intron (NM_144559, intron 4 of 4)	U1|snRNA|snRNA	9041	NM_144559	246256	Mm.251254	NM_144559	ENSMUSG00000059089	Fcgr4	4833442P21Rik|CD16-2|FcgRIV|FcgammaRIV|Fcgr3a|Fcrl3	Fc receptor, IgG, low affinity IV	protein-coding
mm_16775.1	chr2	9884218	9884230	-	1	NA	non-coding (NR_024257, exon 5 of 5)	non-coding (NR_024257, exon 5 of 5)	2978	NR_024257	381347	Mm.441450	NR_024257		4930412O13Rik	ENSMUSG00000075535|Gm10853	RIKEN cDNA 4930412O13 gene	ncRNA
mm_72431.1	chr8	82863811	82863839	+	1	NA	5' UTR (NM_177378, exon 1 of 7)	5' UTR (NM_177378, exon 1 of 7)	469	NM_177378	330812	Mm.491438	NM_177378	ENSMUSG00000047747	Rnf150	A630007N06Rik|C030044C12Rik|Greul5|mKIAA1214	ring finger protein 150	protein-coding
mm_117675.1	chr13	93637798	93637809	-	1	NA	promoter-TSS (NM_016668)	promoter-TSS (NM_016668)	-45	NM_016668	12116	Mm.329582	NM_016668	ENSMUSG00000074768	Bhmt	-	betaine-homocysteine methyltransferase	protein-coding
mm_143529.1	chr17	73902023	73902074	-	1	NA	intron (NM_011723, intron 24 of 35)	intron (NM_011723, intron 24 of 35)	48148	NM_011723	22436	Mm.11223	NM_011723	ENSMUSG00000024066	Xdh	XO|Xor|Xox-1|Xox1	xanthine dehydrogenase	protein-coding
mm_117536.1	chr13	83574999	83575020	-	1	NA	intron (NM_001347577, intron 1 of 10)	intron (NM_001347577, intron 1 of 10)	1402	NM_001347569	17260	Mm.24001	NM_025282	ENSMUSG00000005583	Mef2c	5430401D19Rik|9930028G15Rik|AV011172|Mef2	myocyte enhancer factor 2C	protein-coding
mm_107318.1	chr12	31266313	31266338	+	1	NA	intron (NM_008482, intron 1 of 32)	CpG	1031	NM_008482	16777	Mm.172674	NM_008482	ENSMUSG00000002900	Lamb1	C77966|C80098|C81607|D130003D08Rik|Lamb-1|Lamb1-1	laminin B1	protein-coding
mm_137101.1	chr17	21573840	21573843	+	1	NA	intron (NM_001002008, intron 2 of 5)	intron (NM_001002008, intron 2 of 5)	6795	NM_001002008	381066	Mm.441097	NM_001002008	ENSMUSG00000067931	Zfp948	-	zinc finger protein 948	protein-coding
mm_147099.1	chr18	35654889	35654903	-	1	NA	exon (NM_001270646, exon 1 of 1)	exon (NM_001270646, exon 1 of 1)	303	NM_001270646	381148	Mm.297784	NM_001270646	ENSMUSG00000073600	Prob1	Gm1614	proline rich basic protein 1	protein-coding
mm_40832.1	chr5	72914412	72914476	+	1	NA	promoter-TSS (NM_001113423)	promoter-TSS (NM_001113423)	82	NM_153567	75991	Mm.121285	NM_153567	ENSMUSG00000036087	Slain2	5033405K12Rik|8030444K12Rik|AI596370	SLAIN motif family, member 2	protein-coding
mm_149656.1	chr19	18681243	18681243	+	1	NA	intron (NM_026120, intron 3 of 7)	intron (NM_026120, intron 3 of 7)	10463	NM_026120	67383	Mm.306602	NM_026120	ENSMUSG00000024726	Carnmt1	2410127L17Rik	carnosine N-methyltransferase 1	protein-coding
mm_61122.1	chr7	55768219	55768233	+	1	NA	promoter-TSS (NM_001310740)	promoter-TSS (NM_001310740)	42	NM_178706	233274	Mm.44425	NM_178706	ENSMUSG00000051504	Siglech	6430529G09Rik|Siglec-H	sialic acid binding Ig-like lectin H	protein-coding
mm_83554.1	chr9	46242637	46242655	-	1	NA	exon (NM_007468, exon 3 of 3)	exon (NM_007468, exon 3 of 3)	1802	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_69592.1	chr7	135708239	135708255	-	1	NA	exon (NM_001081117, exon 6 of 14)	exon (NM_001081117, exon 6 of 14)	8132	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_90300.1	chr10	125966215	125966272	+	1	NA	promoter-TSS (NM_177152)	promoter-TSS (NM_177152)	24	NM_177152	320398	Mm.275586	NM_177152	ENSMUSG00000020105	Lrig3	9030421L11Rik|9130004I02Rik|9430095K15Rik|mKIAA3016	leucine-rich repeats and immunoglobulin-like domains 3	protein-coding
mm_36255.1	chr4	63410215	63410231	-	1	NA	Intergenic	Intergenic	-6778	NM_001045514	100182	Mm.387725	NM_001045514	ENSMUSG00000039158	Akna	AI597013	AT-hook transcription factor	protein-coding
mm_24582.1	chr3	93444815	93444831	+	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	2493	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_105453.1	chr11	104503443	104503445	-	1	NA	3' UTR (NM_145436, exon 19 of 19)	3' UTR (NM_145436, exon 19 of 19)	47176	NM_001285990	217232	Mm.89845	NM_145436	ENSMUSG00000020687	Cdc27	AI452358|APC3|BC023187	cell division cycle 27	protein-coding
mm_50812.1	chr6	54326956	54326978	+	1	NA	promoter-TSS (NM_030024)	promoter-TSS (NM_030024)	-45	NM_030024	78004	Mm.41984	NM_030024	ENSMUSG00000045725	Prr15	E130201N16Rik|G90	proline rich 15	protein-coding
mm_62768.1	chr7	112283648	112283652	+	1	NA	intron (NM_001193305, intron 3 of 25)	intron (NM_001193305, intron 3 of 25)	57814	NM_001193305	320878	Mm.52312	NM_177282	ENSMUSG00000038244	Mical2	5330438E18Rik|9530064J02|MICAL-2|mKIAA0750	microtubule associated monooxygenase, calponin and LIM domain containing 2	protein-coding
mm_42955.1	chr5	123041072	123041086	+	1	NA	intron (NM_001347456, intron 2 of 3)	intron (NM_001347456, intron 2 of 3)	5741	NM_029112	74890	Mm.141383	NM_029112	ENSMUSG00000029477	Morn3	4930438O03Rik	MORN repeat containing 3	protein-coding
mm_114994.1	chr13	97579739	97579742	+	1	NA	intron (NR_046157, intron 2 of 2)	intron (NR_046157, intron 2 of 2)	19740	NR_046157	328314	Mm.138047	NR_046157	ENSMUSG00000110235	Gm5086	B230311A21|EG328314	predicted gene 5086	ncRNA
mm_54278.1	chr6	29165014	29165014	-	1	NA	promoter-TSS (NM_133925)	promoter-TSS (NM_133925)	-290	NM_133925	68272	Mm.40802	NM_026650	ENSMUSG00000029701	Rbm28	2810480G15Rik|AI503051	RNA binding motif protein 28	protein-coding
mm_117825.1	chr13	98030074	98030127	-	1	NA	intron (NM_012026, intron 7 of 35)	intron (NM_012026, intron 7 of 35)	176065	NM_012026	110596	Mm.252718	NM_012026	ENSMUSG00000021662	Arhgef28	9230110L08Rik|AI323540|D13Bwg1089e|RIP2|Rgnef|RhoGEF|Rhoip2|p190RhoGEF	Rho guanine nucleotide exchange factor (GEF) 28	protein-coding
mm_19650.1	chr2	102868703	102868712	-	1	NA	intron (NM_001039150, intron 1 of 13)	intron (NM_001039150, intron 1 of 13)	32958	NM_001177785	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_135428.1	chr16	45382744	45382753	-	1	NA	3' UTR (NM_010818, exon 6 of 6)	3' UTR (NM_010818, exon 6 of 6)	26305	NM_010818	17470	Mm.245851	NM_010818	ENSMUSG00000022661	Cd200	Mox2|OX2	CD200 antigen	protein-coding
mm_171332.1	chr3	98580547	98580550	-	1	NA	Intergenic	Intergenic	-16510	NM_008294	15495	Mm.14309	NM_008294	ENSMUSG00000095143	Hsd3b4	-	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 4	protein-coding
mm_73118.1	chr8	94750269	94750285	+	1	NA	3' UTR (NM_009137, exon 3 of 3)	3' UTR (NM_009137, exon 3 of 3)	4593	NM_009137	20299	Mm.12895	NM_009137	ENSMUSG00000031779	Ccl22	ABCD-1|DCBCK|MDC|Scya22	chemokine (C-C motif) ligand 22	protein-coding
mm_172447.1	chr7	3111944	3111967	-	1	NA	Intergenic	Intergenic	-16191	NR_001583	73949	Mm.55687	NR_001583	ENSMUSG00000107956	Speer9-ps1	4930415A14Rik|SPEER-9|Speer9-ps	spermatogenesis associated glutamate (E)-rich protein 9, pseudogene 1	pseudo
mm_147940.1	chr18	66153400	66153407	-	1	NA	intron (NM_178793, intron 2 of 10)	L1_Mur3|LINE|L1	65930	NR_030467	751558		NR_030467	ENSMUSG00000076147	Mir694	Mirn694|mir-694|mmu-mir-694	microRNA 694	ncRNA
mm_9644.1	chr1	177239126	177239127	-	1	NA	intron (NM_011785, intron 1 of 12)	intron (NM_011785, intron 1 of 12)	9641	NM_011785	23797	Mm.235194	NM_011785	ENSMUSG00000019699	Akt3	AI851531|D930002M15Rik|Nmf350	thymoma viral proto-oncogene 3	protein-coding
mm_85193.1	chr9	96720041	96720059	-	1	NA	intron (NM_175537, intron 1 of 2)	CpG	11625	NM_175537	245007	Mm.485954	NM_175537	ENSMUSG00000040433	Zbtb38	A930014K01Rik|CIBZ	zinc finger and BTB domain containing 38	protein-coding
mm_124477.1	chr14	121460429	121460454	-	1	NA	3' UTR (NM_053079, exon 23 of 23)	3' UTR (NM_053079, exon 23 of 23)	44813	NM_053079	56643	Mm.155618	NM_053079	ENSMUSG00000025557	Slc15a1	D630032F02|PECT1|PEPT1	solute carrier family 15 (oligopeptide transporter), member 1	protein-coding
mm_132033.1	chr16	27389912	27389943	+	1	NA	intron (NM_001025615, intron 1 of 9)	intron (NM_001025615, intron 1 of 9)	971	NM_001289436	67501	Mm.258985	NM_026202	ENSMUSG00000038127	Ccdc50	C3orf6	coiled-coil domain containing 50	protein-coding
mm_146747.1	chr18	16274982	16275013	-	1	NA	Intergenic	Intergenic	534249	NM_007664	12558	Mm.257437	NM_007664	ENSMUSG00000024304	Cdh2	CDHN|N-CAD|Ncad	cadherin 2	protein-coding
mm_27902.1	chr3	79481527	79481538	-	1	NA	exon (NM_001162999, exon 13 of 17)	exon (NM_001162999, exon 13 of 17)	86147	NM_001162999	329679	Mm.244005	NM_001162999	ENSMUSG00000061175	Fnip2	D630023B12Rik|mKIAA1450	folliculin interacting protein 2	protein-coding
mm_128352.1	chr15	39943921	39943931	-	1	NA	promoter-TSS (NM_172814)	promoter-TSS (NM_172814)	68	NM_001347036	239393	Mm.39874	NM_172814	ENSMUSG00000022305	Lrp12	AI848829|C820005L12Rik|LRP-12	low density lipoprotein-related protein 12	protein-coding
mm_10701.1	chr2	22773945	22773955	+	1	NA	promoter-TSS (NM_019456)	promoter-TSS (NM_019456)	-377	NM_019456	54519	Mm.14255	NM_019456	ENSMUSG00000026786	Apbb1ip	9930118P07Rik|Prp48	amyloid beta (A4) precursor protein-binding, family B, member 1 interacting protein	protein-coding
mm_90055.1	chr10	116177684	116177700	+	1	NA	5' UTR (NM_001161838, exon 1 of 10)	5' UTR (NM_001161838, exon 1 of 10)	341	NM_001161840	19279	Mm.336316	NM_011217	ENSMUSG00000020151	Ptprr	Gmcp1|PTP-SL|PTPBR7|RPTPRR|mPTP213	protein tyrosine phosphatase, receptor type, R	protein-coding
mm_86700.1	chr10	18525938	18525954	+	1	NA	exon (NM_001163592, exon 6 of 8)	exon (NM_001163592, exon 6 of 8)	20130	NM_019487	56016	Mm.35551	NM_019487	ENSMUSG00000019853	Hebp2	SOUL	heme binding protein 2	protein-coding
mm_21303.1	chr2	157058759	157058771	-	1	NA	intron (NM_001164663, intron 2 of 14)	intron (NM_001164663, intron 2 of 14)	20500	NM_001164663	320706	Mm.79466	NM_001164663	ENSMUSG00000055485	Soga1	9830001H06Rik|AI426038|D430036N24Rik|Soga	suppressor of glucose, autophagy associated 1	protein-coding
mm_55481.1	chr6	68980953	68980956	-	1	NA	Intergenic	RLTR44-int|LTR|ERVK	346220	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_78.1	chr1	6730136	6730151	+	1	NA	promoter-TSS (NR_045189)	promoter-TSS (NR_045189)	92	NR_045188	240690	Mm.234612	NM_173868	ENSMUSG00000033740	St18	AV348974|Myt3|NZF-3|Nzf3|mKIAA0535	suppression of tumorigenicity 18	protein-coding
mm_57590.1	chr6	127769113	127769135	-	1	NA	promoter-TSS (NM_201371)	promoter-TSS (NM_201371)	35	NM_201371	381813	Mm.39750	NM_201371	ENSMUSG00000030350	Prmt8	Hrmt1l3|Hrmt1l4	protein arginine N-methyltransferase 8	protein-coding
mm_118443.1	chr14	8118173	8118187	+	1	NA	intron (NM_178279, intron 1 of 18)	intron (NM_178279, intron 1 of 18)	19967	NM_178279	218699	Mm.29515	NM_145458	ENSMUSG00000033885	Pxk	C230080L11Rik|D14Ertd813e|MONaKA	PX domain containing serine/threonine kinase	protein-coding
mm_57923.1	chr6	134248805	134248815	-	1	NA	intron (NM_001303102, intron 6 of 8)	intron (NM_001303102, intron 6 of 8)	-147519	NM_025778	66813	Mm.474472	NM_025778	ENSMUSG00000030200	Bcl2l14	4930452K23Rik|4933405K19Rik|9030625M01Rik|AI429211|Bclg	BCL2-like 14 (apoptosis facilitator)	protein-coding
mm_7402.1	chr1	119053373	119053423	-	1	NA	5' UTR (NM_001081125, exon 1 of 14)	5' UTR (NM_001081125, exon 1 of 14)	221	NM_001081125	14633	Mm.273292	NM_001081125	ENSMUSG00000048402	Gli2	-	GLI-Kruppel family member GLI2	protein-coding
mm_140298.1	chr17	85621018	85621026	+	1	NA	5' UTR (NM_011381, exon 1 of 2)	5' UTR (NM_011381, exon 1 of 2)	188	NM_011381	20473	Mm.370208	NM_011381	ENSMUSG00000038805	Six3	E130112M24Rik|Six3a|Six3alpha|Six3b|Six3beta	sine oculis-related homeobox 3	protein-coding
mm_113818.1	chr13	46736055	46736057	+	1	NA	Intergenic	Intergenic	-8207	NM_175749	218210	Mm.255398	NM_175749	ENSMUSG00000021374	Nup153	B130015D15Rik|C88147	nucleoporin 153	protein-coding
mm_28948.1	chr3	100162365	100162414	-	1	NA	promoter-TSS (NM_175552)	promoter-TSS (NM_175552)	14	NM_175552	269470	Mm.24591	NM_175552	ENSMUSG00000033285	Wdr3	AW546279|D030020G18Rik	WD repeat domain 3	protein-coding
mm_62618.1	chr7	107209469	107209484	+	1	NA	promoter-TSS (NM_029660)	promoter-TSS (NM_029660)	31	NM_029660	76572	Mm.128134	NM_029660	ENSMUSG00000073894	Rbmxl2	1700012H05Rik|Hnrnpg-t	RNA binding motif protein, X-linked-like 2	protein-coding
mm_51371.1	chr6	72898701	72898712	+	1	NA	intron (NM_019715, intron 1 of 6)	CpG	586	NM_001347231	74287	Mm.29194	NM_019715	ENSMUSG00000055239	Kcmf1	1700094M07Rik|Debt91|Pmcf	potassium channel modulatory factor 1	protein-coding
mm_99123.1	chr11	100204750	100204763	+	1	NA	exon (NM_016958, exon 4 of 8)	exon (NM_016958, exon 4 of 8)	1274	NM_001313957	16664	Mm.439898	NM_016958	ENSMUSG00000045545	Krt14	AI626930|CK-14|K14|Krt-1.14|Krt1-14	keratin 14	protein-coding
mm_139189.1	chr17	47597514	47597524	+	1	NA	exon (NM_007632, exon 3 of 5)	exon (NM_007632, exon 3 of 5)	4052	NM_007632	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_59245.1	chr7	24784582	24784584	+	1	NA	TTS (NM_007675)	TTS (NM_007675)	7379	NM_007675	26366	Mm.30300	NM_007675	ENSMUSG00000054169	Ceacam10	Bgp3|Cea10	carcinoembryonic antigen-related cell adhesion molecule 10	protein-coding
mm_33751.1	chr4	134315095	134315103	+	1	NA	promoter-TSS (NM_001039048)	promoter-TSS (NM_001039048)	-21	NM_001039048	433766	Mm.331961	NM_001039048	ENSMUSG00000028834	Trim63	MuRF1|RF1|Rnf28	tripartite motif-containing 63	protein-coding
mm_145234.1	chr18	50135004	50135048	+	1	NA	intron (NM_008292, intron 2 of 23)	intron (NM_008292, intron 2 of 23)	6825	NM_008292	15488	Mm.277857	NM_008292	ENSMUSG00000024507	Hsd17b4	17-beta-HSD|17[b]-HSD|DBP|MFE-2|MFP2|MPF-2|Mfp-2|perMFE-2	hydroxysteroid (17-beta) dehydrogenase 4	protein-coding
mm_856.1	chr1	52126509	52126565	+	1	NA	exon (NM_001205314, exon 5 of 25)	exon (NM_001205314, exon 5 of 25)	6915	NM_001205313	20846	Mm.277406	NM_009283	ENSMUSG00000026104	Stat1	2010005J02Rik|AA408197	signal transducer and activator of transcription 1	protein-coding
mm_49614.1	chr6	30747444	30747450	+	1	NA	TTS (NM_017478)	TTS (NM_017478)	6148	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_3499.1	chr1	150106960	150106962	+	1	NA	3' UTR (NM_011198, exon 10 of 10)	3' UTR (NM_011198, exon 10 of 10)	6930	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_107835.1	chr12	69295983	69295992	+	1	NA	promoter-TSS (NM_027117)	promoter-TSS (NM_027117)	-694	NM_027117	69554	Mm.234368	NM_027117	ENSMUSG00000020978	Klhdc2	2310022K15Rik|D12Ertd522e|HCLP-1|LCP	kelch domain containing 2	protein-coding
mm_142416.1	chr17	45568012	45568030	-	1	NA	TTS (NM_028662)	TTS (NM_028662)	3869	NM_028662	73836	Mm.289716	NM_028662	ENSMUSG00000037089	Slc35b2	1110003M08Rik|AA407792|AI842275|PAPST1|Slc35b1	solute carrier family 35, member B2	protein-coding
mm_107365.1	chr12	32848667	32848685	+	1	NA	exon (NM_021524, exon 10 of 11)	exon (NM_021524, exon 10 of 11)	24560	NR_045032	100504486	Mm.440246	NR_045032		Gdap10	Gdap-ps	ganglioside-induced differentiation-associated-protein 10	ncRNA
mm_105733.1	chr11	109246961	109246977	-	1	NA	intron (NM_001165934, intron 12 of 16)	intron (NM_001165934, intron 12 of 16)	51212	NM_001165934	19739	Mm.38548	NM_011268	ENSMUSG00000020599	Rgs9	RGS9-1|Rgs9-2	regulator of G-protein signaling 9	protein-coding
mm_5538.1	chr1	38129619	38129679	-	1	NA	promoter-TSS (NM_019570)	promoter-TSS (NM_019570)	13	NM_019570	56210	Mm.389103	NM_019570	ENSMUSG00000026082	Rev1	1110027I23Rik|AU022044|Rev1l	REV1, DNA directed polymerase	protein-coding
mm_94193.1	chr10	130280219	130280242	-	1	NA	promoter-TSS (NM_001329490)	promoter-TSS (NM_001329490)	24	NM_001329490	11923	Mm.10695	NM_007501	ENSMUSG00000048015	Neurod4	AI846749|ATH-3|Atoh3|MATH-3|Math3|bHLHa4	neurogenic differentiation 4	protein-coding
mm_152198.1	chr19	7583231	7583251	-	1	NA	intron (NM_139269, intron 4 of 4)	HAL1|LINE|L1	23935	NM_019516	56072	Mm.298242	NM_019516	ENSMUSG00000024972	Lgals12	AW987437|Grip1	lectin, galactose binding, soluble 12	protein-coding
mm_139437.1	chr17	53769822	53769822	+	1	NA	Intergenic	Intergenic	53313	NR_073205	211496	Mm.251553	NM_177599	ENSMUSG00000062036	4932415M13Rik	-	RIKEN cDNA 4932415M13 gene	ncRNA
mm_14541.1	chr2	132816138	132816145	+	1	NA	promoter-TSS (NM_025676)	promoter-TSS (NM_025676)	0	NM_025676	66634	Mm.157070	NM_025676	ENSMUSG00000027353	Mcm8	5730432L01Rik	minichromosome maintenance 8 homologous recombination repair factor	protein-coding
mm_134740.1	chr16	23029081	23029106	-	1	NA	promoter-TSS (NM_201375)	promoter-TSS (NM_201375)	8	NM_201375	385643	Mm.440414	NM_201375	ENSMUSG00000060459	Kng2	-	kininogen 2	protein-coding
mm_92111.1	chr10	63057473	63057490	-	1	NA	intron (NM_026085, intron 9 of 9)	intron (NM_026085, intron 9 of 9)	-4136	NM_026701	68371	Mm.261389	NM_026701	ENSMUSG00000020072	Pbld1	0610038K03Rik|Mawbp|Pbld	phenazine biosynthesis-like protein domain containing 1	protein-coding
mm_124381.1	chr14	108842032	108842034	-	1	NA	Intergenic	Intergenic	72206	NM_199065	76965	Mm.257268	NM_199065	ENSMUSG00000075478	Slitrk1	3200001I04Rik	SLIT and NTRK-like family, member 1	protein-coding
mm_83048.1	chr9	37544566	37544578	-	1	NA	TTS (NM_022029)	TTS (NM_022029)	5317	NM_020518	57276	Mm.27478	NM_020518	ENSMUSG00000001943	Vsig2	1190004B15Rik|2210413P10Rik|AU040484|CTX|Ctm	V-set and immunoglobulin domain containing 2	protein-coding
mm_16185.1	chr2	172977626	172977632	+	1	NA	Intergenic	Intergenic	-2213	NM_012046	26972	Mm.23495	NM_012046	ENSMUSG00000005883	Spo11	AI449549|Spo11a|Spo11b	SPO11 meiotic protein covalently bound to DSB	protein-coding
mm_73148.1	chr8	94992854	94992874	+	1	NA	intron (NM_018882, intron 1 of 13)	intron (NM_018882, intron 1 of 13)	8465	NM_018882	14766	Mm.290834	NM_018882	ENSMUSG00000031785	Adgrg1	Cyt28|Gpr56|TM7LN4|TM7XN1	adhesion G protein-coupled receptor G1	protein-coding
mm_144136.1	chr18	4993778	4993789	+	1	NA	Intergenic	Intergenic	-52806	NM_153153	225115	Mm.136791	NM_153153	ENSMUSG00000024236	Svil	AU024053|B430302E16Rik	supervillin	protein-coding
mm_51186.1	chr6	70903709	70903715	+	1	NA	intron (NM_010121, intron 16 of 16)	URR1B|DNA|hAT-Charlie	15210	NM_028825	74221	Mm.273326	NM_028825	ENSMUSG00000051896	Tex37	1700011F03Rik	testis expressed 37	protein-coding
mm_87317.1	chr10	42827874	42827885	+	1	NA	exon (NM_153055, exon 20 of 21)	exon (NM_153055, exon 20 of 21)	-32633	NM_172938	268297	Mm.98731	NM_172938	ENSMUSG00000044770	Scml4	9330161D17|mFLJ00197	sex comb on midleg-like 4 (Drosophila)	protein-coding
mm_96007.1	chr11	59541655	59541666	+	1	NA	Intergenic	Intergenic	-1026	NM_145827	216799	Mm.54174	NM_145827	ENSMUSG00000032691	Nlrp3	AGTAVPRL|AII/AVP|Cias1|FCAS|FCU|MWS|Mmig1|NALP3|Pypaf1	NLR family, pyrin domain containing 3	protein-coding
mm_157882.1	chrX	75843129	75843139	-	1	NA	promoter-TSS (NM_001346520)	promoter-TSS (NM_001346520)	-71	NM_001346520	102866	Mm.28777	NM_145629	ENSMUSG00000016382	Pls3	AI115446|AL024105	plastin 3 (T-isoform)	protein-coding
mm_56973.1	chr6	120242697	120242730	-	1	NA	intron (NM_198884, intron 1 of 19)	intron (NM_198884, intron 1 of 19)	48890	NM_001347432	29862	Mm.103668	NM_016718	ENSMUSG00000041377	Ninj2	-	ninjurin 2	protein-coding
mm_85761.1	chr9	108654700	108654736	-	1	NA	Intergenic	Intergenic	-5338	NM_011790	23807	Mm.290447	NM_011790	ENSMUSG00000064145	Arih2	AI843547|ARI2|TRIAD1|UIP48	ariadne RBR E3 ubiquitin protein ligase 2	protein-coding
mm_172634.1	chr8	20567799	20567804	+	1	NA	Intergenic	Intergenic	-47126	NM_001270553	100861668	Mm.491087	NM_001270553	ENSMUSG00000095294	Gm21119	-	predicted gene, 21119	protein-coding
mm_55749.1	chr6	78372210	78372218	-	1	NA	exon (NM_011036, exon 4 of 6)	exon (NM_011036, exon 4 of 6)	1329	NM_011036	18489	Mm.2553	NM_011036	ENSMUSG00000071356	Reg3b	HIP|PAP1|Pap|REG-III	regenerating islet-derived 3 beta	protein-coding
mm_20785.1	chr2	143989673	143989693	-	1	NA	exon (NM_133626, exon 2 of 3)	exon (NM_133626, exon 2 of 3)	21580	NM_133626	81910	Mm.13705	NM_024281	ENSMUSG00000027422	Rrbp1	1700087N07Rik|5730465C04Rik|ES/130|mKIAA1398|mRRp0|mRRp1.8|mRRp10|mRRp15a|mRRp15b|mRRp16.8|mRRp2|mRRp41|mRRp47|mRRp5.4|p180	ribosome binding protein 1	protein-coding
mm_4075.1	chr1	166254096	166254156	+	1	NA	promoter-TSS (NM_001164528)	promoter-TSS (NM_001164528)	-13	NM_001164528	100039795	Mm.101743	NM_001164528	ENSMUSG00000040612	Ildr2	2810478N18Rik|3110063L10Rik|AI852300|D1Ertd471e|Dbsm1|ENSMUSG00000040612|Ll	immunoglobulin-like domain containing receptor 2	protein-coding
mm_105672.1	chr11	107469562	107469584	-	1	NA	intron (NM_145823, intron 1 of 9)	CpG	1147	NM_145823	71795	Mm.397413	NM_145823	ENSMUSG00000040430	Pitpnc1	1110020B03Rik|5830436L09Rik|AI662802|AI851387|C330017I21Rik|Dnr411|RDGBB|RDGBB1|rdgB-beta	phosphatidylinositol transfer protein, cytoplasmic 1	protein-coding
mm_29168.1	chr3	106485929	106485960	-	1	NA	promoter-TSS (NM_028110)	promoter-TSS (NM_028110)	-31	NR_033207	69206	Mm.14816	NM_001033146	ENSMUSG00000091575	2010016I18Rik	-	RIKEN cDNA 2010016I18 gene	ncRNA
mm_11425.1	chr2	31950258	31950281	+	1	NA	promoter-TSS (NM_145144)	promoter-TSS (NM_145144)	-34	NM_145144	108897	Mm.24838	NM_145144	ENSMUSG00000001864	Aif1l	2810003C17Rik|AI043124|C87647|Iba2	allograft inflammatory factor 1-like	protein-coding
mm_80127.1	chr9	70580776	70580787	+	1	NA	intron (NM_026337, intron 12 of 20)	intron (NM_026337, intron 12 of 20)	37911	NM_025690	66660	Mm.22379	NM_025690	ENSMUSG00000032212	Sltm	5730455C01Rik|5730555F13Rik|9130215G10Rik|Met	SAFB-like, transcription modulator	protein-coding
mm_140329.1	chr17	86754101	86754111	+	1	NA	5' UTR (NM_010137, exon 1 of 16)	5' UTR (NM_010137, exon 1 of 16)	242	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_27197.1	chr3	35662289	35662299	-	1	NA	intron (NR_040748, intron 2 of 18)	intron (NR_040748, intron 2 of 18)	3869	NR_040748	625963	Mm.251506	NR_040748	ENSMUSG00000105662	Gm6639	-	predicted gene 6639	ncRNA
mm_33463.1	chr4	130793735	130793768	+	1	NA	intron (NM_011520, intron 1 of 4)	intron (NM_011520, intron 1 of 4)	1214	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_60939.1	chr7	46877910	46877953	+	1	NA	3' UTR (NM_013580, exon 8 of 8)	3' UTR (NM_013580, exon 8 of 8)	16668	NM_013580	16833	Mm.16563	NM_013580	ENSMUSG00000030851	Ldhc	LDH-C4|Ldh-3|Ldh-x|Ldh3|Ldhc4	lactate dehydrogenase C	protein-coding
mm_113643.1	chr13	42301266	42301281	+	1	NA	promoter-TSS (NM_010104)	promoter-TSS (NM_010104)	-203	NM_010104	13614	Mm.14543	NM_010104	ENSMUSG00000021367	Edn1	ET-1|PPET1|preproET	endothelin 1	protein-coding
mm_35816.1	chr4	46991679	46991714	-	1	NA	promoter-TSS (NM_001081141)	promoter-TSS (NM_001081141)	18	NM_001081141	242425	Mm.101909	NM_001081141	ENSMUSG00000039809	Gabbr2	GABABR2|Gb2|Gm425|Gpr51	gamma-aminobutyric acid (GABA) B receptor, 2	protein-coding
mm_166052.1	chr4	131921691	131921694	+	1	NA	promoter-TSS (NM_001201367)	promoter-TSS (NM_001201367)	-79	NM_001201367	623230	Mm.421179	NM_001201367	ENSMUSG00000070720	Tmem200b	EG623230	transmembrane protein 200B	protein-coding
mm_74232.1	chr8	124274683	124274724	+	1	NA	intron (NM_139272, intron 1 of 15)	intron (NM_139272, intron 1 of 15)	43309	NM_139272	108148	Mm.33808	NM_139272	ENSMUSG00000089704	Galnt2	AI480629	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2	protein-coding
mm_56052.1	chr6	86754899	86754911	-	1	NA	exon (NM_001331120, exon 5 of 13)	exon (NM_001331120, exon 5 of 13)	20209	NM_001331120	11746	Mm.259702	NM_013471	ENSMUSG00000029994	Anxa4	AI265406|AIV|AW106930|Anx4|Xanx-4	annexin A4	protein-coding
mm_119681.1	chr14	53078488	53078516	+	1	NA	Intergenic	Intergenic	-582807	NM_001170918	57269	Mm.88822	NM_020512	ENSMUSG00000059887	Olfr1507	MOR244-1|Mor28|Or28	olfactory receptor 1507	protein-coding
mm_116899.1	chr13	55413475	55413480	-	1	NA	exon (NM_011392, exon 13 of 13)	exon (NM_011392, exon 13 of 13)	1755	NM_029303	75477	Mm.432537	NM_029303	ENSMUSG00000044444	Pfn3	1700012P12Rik	profilin 3	protein-coding
mm_7654.1	chr1	128328312	128328326	-	1	NA	promoter-TSS (NM_001081078)	promoter-TSS (NM_001081078)	-1	NM_001081078	226413	Mm.26930	NM_001081078	ENSMUSG00000026354	Lct	Gm100|LAC|LPH|Lphl	lactase	protein-coding
mm_94685.1	chr11	19720214	19720219	+	1	NA	Intergenic	Intergenic	-204226	NM_033523	114716	Mm.266627	NM_033523	ENSMUSG00000045671	Spred2	C79158	sprouty-related, EVH1 domain containing 2	protein-coding
mm_112874.1	chr13	20853876	20853890	+	1	NA	intron (NM_012054, intron 4 of 20)	intron (NM_012054, intron 4 of 20)	59770	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_74192.1	chr8	123738435	123738437	+	1	NA	intron (NR_040702, intron 3 of 3)	(TAGTG)n|Simple_repeat|Simple_repeat	4478	NR_040702	234863	Mm.246601	NR_040702	ENSMUSG00000110599	6030466F02Rik	-	RIKEN cDNA 6030466F02 gene	ncRNA
mm_22058.1	chr2	168590316	168590372	-	1	NA	promoter-TSS (NM_001291176)	promoter-TSS (NM_001291176)	21	NM_001291178	18019	Mm.116802	NM_010899	ENSMUSG00000027544	Nfatc2	AI607462|NF-ATc2|NF-ATp|NFAT1|NFAT1-D|Nfatp	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 2	protein-coding
mm_82734.1	chr9	25251985	25251997	-	1	NA	promoter-TSS (NM_001205367)	promoter-TSS (NM_001205367)	-448	NM_009859	235072	Mm.270259	NM_009859	ENSMUSG00000001833	Sept7	Cdc10|E430034N22	septin 7	protein-coding
mm_161749.1	chr17	34517365	34517365	-	1	NA	promoter-TSS (NM_030747)	promoter-TSS (NM_030747)	-13	NM_030747	624681	Mm.471592	NM_030747	ENSMUSG00000092618	Btnl6	EG624681|Gm6519|NG13	butyrophilin-like 6	protein-coding
mm_94603.1	chr11	14162056	14162066	+	1	NA	intron (NR_131011, intron 1 of 3)	intron (NR_131011, intron 1 of 3)	16980	NR_131011	75280	Mm.108492	NR_131011	ENSMUSG00000085452	4930554G24Rik	-	RIKEN cDNA 4930554G24 gene	ncRNA
mm_171862.1	chr5	22563807	22563807	+	1	NA	Intergenic	Intergenic	13394	NR_102315	320719	Mm.459265	NR_102315	ENSMUSG00000097207	6030443J06Rik	1700030G06Rik	RIKEN cDNA 6030443J06 gene	ncRNA
mm_118179.1	chr13	107021747	107021754	-	1	NA	promoter-TSS (NR_015471)	promoter-TSS (NR_015471)	364	NM_001145779	16563	Mm.355686	NM_008442	ENSMUSG00000021693	Kif2a	C530030B14Rik|Kif2|Kns2|M-kinesin	kinesin family member 2A	protein-coding
mm_85244.1	chr9	99035648	99035676	-	1	NA	promoter-TSS (NM_001080776)	promoter-TSS (NM_001080776)	28	NM_001080776	382097	Mm.293727	NM_001080776	ENSMUSG00000044860	Gm1123	AV052824|CLSP	predicted gene 1123	protein-coding
mm_34298.1	chr4	141664242	141664249	+	1	NA	promoter-TSS (NM_001033150)	promoter-TSS (NM_001033150)	-130	NM_001033150	69582	Mm.33220	NM_001033150	ENSMUSG00000028917	Plekhm2	2310034J19Rik|AI854247|mKIAA0842	pleckstrin homology domain containing, family M (with RUN domain) member 2	protein-coding
mm_167388.1	chr8	94857529	94857558	+	1	NA	promoter-TSS (NM_009090)	promoter-TSS (NM_009090)	93	NM_009090	20021	Mm.292492	NM_009090	ENSMUSG00000031783	Polr2c	33kDa|RPB3|Rpo2-3|mRBP31	polymerase (RNA) II (DNA directed) polypeptide C	protein-coding
mm_69016.1	chr7	126704889	126704906	-	1	NA	promoter-TSS (NM_009898)	promoter-TSS (NM_009898)	-81	NM_009898	12721	Mm.290482	NM_009898	ENSMUSG00000030707	Coro1a	Clabp|Lmb3|TACO|p57	coronin, actin binding protein 1A	protein-coding
mm_171525.1	chr4	146611006	146611010	+	1	NA	Intergenic	Intergenic	-64135	NR_045468	67524	Mm.444300	NR_045468	ENSMUSG00000086046	1700095A21Rik	-	RIKEN cDNA 1700095A21 gene	ncRNA
mm_75194.1	chr8	38661555	38661565	-	1	NA	promoter-TSS (NM_145841)	promoter-TSS (NM_145841)	-52	NM_145841	244431	Mm.210388	NM_145841	ENSMUSG00000039539	Sgcz	C230085N17Rik	sarcoglycan zeta	protein-coding
mm_9066.1	chr1	167689401	167689409	-	1	NA	promoter-TSS (NM_033652)	promoter-TSS (NM_033652)	-153	NM_033652	110648	Mm.330081	NM_033652	ENSMUSG00000026686	Lmx1a	Lmx1.1|dr|dreher|sst	LIM homeobox transcription factor 1 alpha	protein-coding
mm_8349.1	chr1	150203192	150203217	-	1	NA	Intergenic	Intergenic	-38256	NR_110420	102639566	Mm.417208	NR_110420	ENSMUSG00000097754	Ptgs2os2	Gm26687|Linc-cox2|Lincrna-cox2	prostaglandin-endoperoxide synthase 2, opposite strand 2	ncRNA
mm_118945.1	chr14	27337759	27337760	+	1	NA	intron (NM_001289687, intron 1 of 9)	intron (NM_001289687, intron 1 of 9)	1722	NM_001289687	71704	Mm.248606	NM_027871	ENSMUSG00000021895	Arhgef3	1200004I24Rik|9830169H03Rik|C76747|Xpln	Rho guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_155792.1	chrX	98149667	98149714	+	1	NA	5' UTR (NM_013476, exon 1 of 8)	5' UTR (NM_013476, exon 1 of 8)	933	NM_013476	11835	Mm.39005	NM_013476	ENSMUSG00000046532	Ar	AW320017|Tfm	androgen receptor	protein-coding
mm_113471.1	chr13	36475089	36475145	+	1	NA	intron (NM_001039189, intron 5 of 5)	intron (NM_001039189, intron 5 of 5)	259360	NM_153529	68404	Mm.232930	NM_153529	ENSMUSG00000039114	Nrn1	0710008J23Rik|Cpg15|Nrn	neuritin 1	protein-coding
mm_35603.1	chr4	43040280	43040319	-	1	NA	promoter-TSS (NM_001253354)	promoter-TSS (NM_001253354)	2	NM_001253353	230088	Mm.260162	NM_172691	ENSMUSG00000036002	Fam214b	B230312A22Rik	family with sequence similarity 214, member B	protein-coding
mm_99616.1	chr11	104608001	104608012	+	1	NA	promoter-TSS (NM_016780)	promoter-TSS (NM_016780)	6	NM_016780	16416	Mm.87150	NM_016780	ENSMUSG00000020689	Itgb3	CD61|GP3A|INGRB3	integrin beta 3	protein-coding
mm_108673.1	chr12	86678476	86678498	+	1	NA	promoter-TSS (NM_177354)	promoter-TSS (NM_177354)	-213	NM_177354	238328	Mm.216101	NM_177354	ENSMUSG00000021256	Vash1	AI834978|D930046M13Rik|G630009D10Rik	vasohibin 1	protein-coding
mm_138006.1	chr17	33824610	33824644	+	1	NA	promoter-TSS (NM_023202)	promoter-TSS (NM_023202)	-18	NR_103514	66416	Mm.29513	NM_023202	ENSMUSG00000041881	Ndufa7	14.5kDa|2400007M02Rik|CI-B14.5a	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 7 (B14.5a)	protein-coding
mm_54468.1	chr6	34910354	34910381	-	1	NA	intron (NM_001013366, intron 1 of 14)	intron (NM_001013366, intron 1 of 14)	464	NM_001013366	101240	Mm.152120	NM_001013366	ENSMUSG00000058486	Wdr91	9530020G05Rik|AI987683|AU018665	WD repeat domain 91	protein-coding
mm_171535.1	chr4	146909481	146909488	-	1	NA	Intergenic	Intergenic	-112366	NM_001177767	100043034	Mm.422606	NM_001177767	ENSMUSG00000067919	Rex2	Gm13138|OTTMUSG00000010655	reduced expression 2	protein-coding
mm_122636.1	chr14	51146758	51146775	-	1	NA	promoter-TSS (NM_011271)	promoter-TSS (NM_011271)	1	NM_011271	19752	Mm.235538	NM_011271	ENSMUSG00000035896	Rnase1	AI574248|Rib-1|Rib1	ribonuclease, RNase A family, 1 (pancreatic)	protein-coding
mm_44852.1	chr5	34232561	34232587	-	1	NA	intron (NM_001015039, intron 5 of 12)	intron (NM_001015039, intron 5 of 12)	-44864	NM_010753	17122	Mm.259260	NM_010753	ENSMUSG00000037235	Mxd4	2810410A03Rik|Mad4|bHLHc12	Max dimerization protein 4	protein-coding
mm_28500.1	chr3	92484684	92484692	-	1	NA	exon (NM_009264, exon 2 of 2)	exon (NM_009264, exon 2 of 2)	1193	NM_009264	20753	Mm.331191	NM_009264	ENSMUSG00000050359	Sprr1a	AI528815|SPR1a|mSPRR1A	small proline-rich protein 1A	protein-coding
mm_157533.1	chrX	51020044	51020077	-	1	NA	Intergenic	Intergenic	-2042	NM_172413	72065	Mm.43152	NM_172413	ENSMUSG00000050029	Rap2c	2010200P20Rik|AI194294|AL022976	RAP2C, member of RAS oncogene family	protein-coding
mm_56093.1	chr6	87378238	87378275	-	1	NA	exon (NM_025467, exon 5 of 6)	exon (NM_025467, exon 5 of 6)	4891	NM_025467	66284	Mm.46446	NM_025467	ENSMUSG00000030049	Gkn2	1810036H07Rik|Bricd1b	gastrokine 2	protein-coding
mm_13988.1	chr2	121718506	121718509	+	1	NA	intron (NM_172673, intron 1 of 14)	intron (NM_172673, intron 1 of 14)	88550	NM_172673	228564	Mm.121514	NM_172673	ENSMUSG00000027238	Frmd5	1500032A09Rik|5830442F04|A930004K21Rik|R75430	FERM domain containing 5	protein-coding
mm_44249.1	chr5	5380137	5380141	-	1	NA	5' UTR (NM_011074, exon 1 of 15)	5' UTR (NM_011074, exon 1 of 15)	112	NM_011074	18647	Mm.389061	NM_011074	ENSMUSG00000028926	Cdk14	Pftk1|mKIAA0834	cyclin-dependent kinase 14	protein-coding
mm_116633.1	chr13	48968422	48968466	-	1	NA	promoter-TSS (NM_001033268)	promoter-TSS (NM_001033268)	332	NR_015601	68128	Mm.426304	NR_015601		Fam120aos	C030044B11Rik	family with sequence similarity 120A, opposite strand	ncRNA
mm_153299.1	chr19	37955911	37955941	-	1	NA	intron (NM_001302140, intron 22 of 53)	intron (NM_001302140, intron 22 of 53)	87651	NM_001099634	226101	Mm.34674	NM_177035	ENSMUSG00000048612	Myof	2310004N10Rik|2310051D19Rik|E030042N20Rik|Fer1l3	myoferlin	protein-coding
mm_166937.1	chr7	36832767	36832770	+	1	NA	Intergenic	RMER15|LTR|ERVL	134650	NM_172298	243931	Mm.44141	NM_172298	ENSMUSG00000021217	Tshz3	A630038G13Rik|Tsh3|Zfp537|mKIAA1474|teashirt3	teashirt zinc finger family member 3	protein-coding
mm_124466.1	chr14	121288009	121288011	-	1	NA	intron (NM_145465, intron 10 of 10)	intron (NM_145465, intron 10 of 10)	91220	NM_145465	223255	Mm.390756	NM_145465	ENSMUSG00000063410	Stk24	1810013H02Rik|C76483|MST-3|Mst3|STE20	serine/threonine kinase 24	protein-coding
mm_147272.1	chr18	38929402	38929410	-	1	NA	intron (NM_001033789, intron 3 of 4)	intron (NM_001033789, intron 3 of 4)	-10707	NM_010197	14164	Mm.241282	NM_010197	ENSMUSG00000036585	Fgf1	Dffrx|Fam|Fgf-1|Fgfa	fibroblast growth factor 1	protein-coding
mm_8357.1	chr1	150454392	150454428	-	1	NA	exon (NM_021400, exon 7 of 13)	exon (NM_021400, exon 7 of 13)	11755	NM_021400	96875	Mm.174256	NM_021400	ENSMUSG00000006014	Prg4	CACP|DOL54|JCAP|MSF|SZP|lubricin	proteoglycan 4 (megakaryocyte stimulating factor, articular superficial zone protein)	protein-coding
mm_121889.1	chr14	21741481	21741503	-	1	NA	intron (NM_001007268, intron 5 of 7)	intron (NM_001007268, intron 5 of 7)	1387	NM_013849	27389	Mm.390674	NM_013849	ENSMUSG00000021768	Dusp13	DUSP13A|DUSP13B|Gm1203|LMW-DSP6|MDSP|TMDP|TS-DSP6	dual specificity phosphatase 13	protein-coding
mm_37349.1	chr4	119977858	119977863	-	1	NA	intron (NM_010657, intron 1 of 8)	intron (NM_010657, intron 1 of 8)	163182	NM_010657	16656	Mm.302758	NM_010657	ENSMUSG00000028634	Hivep3	2900056N03Rik|A130075N07|AI848000|E030045D18Rik|KBP-1|KBP1|Krc|Rc|Schnurri-3|Shn3|Zas3	human immunodeficiency virus type I enhancer binding protein 3	protein-coding
mm_68420.1	chr7	109723861	109723889	-	1	NA	promoter-TSS (NM_001040700)	promoter-TSS (NM_001040700)	-104	NM_001040700	57355	Mm.358682	NM_020609	ENSMUSG00000031022	BC051019	AA571491|D7H11orf16|ICRFP703B1614Q5.5	cDNA sequence BC051019	protein-coding
mm_59597.1	chr7	28139754	28139758	+	1	NA	exon (NM_001164655, exon 5 of 20)	exon (NM_001164655, exon 5 of 20)	10290	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_13018.1	chr2	90987604	90987612	+	1	NA	intron (NM_001244891, intron 2 of 14)	intron (NM_001244891, intron 2 of 14)	47211	NM_017368	13046	Mm.29495	NM_017368	ENSMUSG00000005506	Celf1	1600010O03Rik|AA407467|Brunol2|CUG-BP|CUG-BP1|CUGBP|Cugbp1|D2Wsu101e|HNAB50|NAB50	CUGBP, Elav-like family member 1	protein-coding
mm_9829.1	chr1	182517617	182517627	-	1	NA	promoter-TSS (NM_009794)	promoter-TSS (NM_009794)	-139	NM_009794	12334	Mm.19306	NM_009794	ENSMUSG00000026509	Capn2	AI326419|Capa-2|Capa2|m-calpain|m-calpin	calpain 2	protein-coding
mm_152965.1	chr19	29367295	29367309	-	1	NA	promoter-TSS (NM_021893)	promoter-TSS (NM_021893)	-136	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_50207.1	chr6	42249353	42249371	+	1	NA	intron (NM_029555, intron 5 of 7)	intron (NM_029555, intron 5 of 7)	3427	NM_029555	76263	Mm.267014	NM_029555	ENSMUSG00000029864	Gstk1	0610025I19Rik|AW260476|DsbA-L	glutathione S-transferase kappa 1	protein-coding
mm_125394.1	chr15	41447302	41447308	+	1	NA	promoter-TSS (NM_001130166)	promoter-TSS (NM_001130166)	-177	NM_001130166	170719	Mm.254267	NM_130885	ENSMUSG00000022307	Oxr1	2210416C20Rik|C7|C7B	oxidation resistance 1	protein-coding
mm_168460.1	chr1	143732811	143732811	+	1	NA	Intergenic	B2_Mm1t|SINE|B2	-6538	NM_001038593	69367	Mm.272727	NM_023505	ENSMUSG00000018196	Glrx2	1700010P22Rik|AI645710|Grx2	glutaredoxin 2 (thioltransferase)	protein-coding
mm_139120.1	chr17	47436648	47436658	+	1	NA	promoter-TSS (NM_145489)	promoter-TSS (NM_145489)	14	NM_145489	224833	Mm.218444	NM_145489	ENSMUSG00000034382	AI661453	-	expressed sequence AI661453	protein-coding
mm_18549.1	chr2	65023189	65023196	-	1	NA	promoter-TSS (NM_016719)	promoter-TSS (NM_016719)	-426	NM_016719	50915	Mm.214554	NM_016719	ENSMUSG00000026888	Grb14	AI505286	growth factor receptor bound protein 14	protein-coding
mm_9416.1	chr1	172326219	172326225	-	1	NA	exon (NM_008429, exon 3 of 4)	exon (NM_008429, exon 3 of 4)	3041	NM_008429	16524	Mm.261168	NM_008429	ENSMUSG00000038026	Kcnj9	1700085N21Rik|Girk3|Kir3.3|mbGIRK3	potassium inwardly-rectifying channel, subfamily J, member 9	protein-coding
mm_18952.1	chr2	76786249	76786260	-	1	NA	exon (NM_011652, exon 222 of 313)	exon (NM_011652, exon 222 of 313)	110939	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_48466.1	chr5	140830364	140830384	-	1	NA	promoter-TSS (NM_010302)	promoter-TSS (NM_010302)	57	NM_010302	14673	Mm.370185	NM_010302	ENSMUSG00000000149	Gna12	AI414047|AI504261|Galpha12	guanine nucleotide binding protein, alpha 12	protein-coding
mm_81506.1	chr9	110034687	110034701	+	1	NA	exon (NM_008633, exon 7 of 19)	exon (NM_008633, exon 7 of 19)	-17327	NM_001311163	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_140252.1	chr17	84188605	84188626	+	1	NA	promoter-TSS (NM_001001806)	promoter-TSS (NM_001001806)	-668	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_50166.1	chr6	41553625	41553632	+	1	NA	Intergenic	L3b|LINE|CR1	31852	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_109814.1	chr12	3427519	3427533	-	1	NA	promoter-TSS (NR_030694)	promoter-TSS (NR_030694)	669	NM_172421	75302	Mm.120475	NM_172421	ENSMUSG00000037486	Asxl2	4930556B16Rik|mKIAA1685	additional sex combs like 2 (Drosophila)	protein-coding
mm_140929.1	chr17	24251383	24251397	-	1	NA	promoter-TSS (NM_007634)	promoter-TSS (NM_007634)	19	NM_007634	12449	Mm.77695	NM_007634	ENSMUSG00000072082	Ccnf	CycF|Fbxo1	cyclin F	protein-coding
mm_146247.1	chr18	77773985	77774006	+	1	NA	5' UTR (NM_007505, exon 1 of 12)	5' UTR (NM_007505, exon 1 of 12)	227	NM_007505	11946	Mm.276137	NM_007505	ENSMUSG00000025428	Atp5a1	AI035633|AL022851|AL023067|Atpm|D18Ertd206e|Mom2	ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1	protein-coding
mm_115297.1	chr13	112000032	112000043	+	1	NA	Intergenic	Intergenic	132101	NR_130345	102636620	Mm.402328	NR_130345	ENSMUSG00000086111	Gm15326	OTTMUSG00000020187	predicted gene 15326	ncRNA
mm_49292.1	chr6	17693906	17693937	+	1	NA	promoter-TSS (NM_001289625)	promoter-TSS (NM_001289625)	-73	NM_001289624	64213	Mm.12051	NM_022332	ENSMUSG00000029534	St7	9430001H04Rik|Fam4a2|HELG|RAY1|SEN4|TSG7	suppression of tumorigenicity 7	protein-coding
mm_53323.1	chr6	129220063	129220071	+	1	NA	Intergenic	RLTR16C_MM|LTR|ERVK	17978	NR_040265	76432	Mm.261738	NR_040265	ENSMUSG00000097354	2310001H17Rik	AI646108	RIKEN cDNA 2310001H17 gene	ncRNA
mm_83736.1	chr9	51077065	51077100	-	1	NA	promoter-TSS (NM_001033534)	promoter-TSS (NM_001033534)	12	NM_001033534	244864	Mm.335152	NM_001033534	ENSMUSG00000060594	Layn	E030012M19Rik|Gm511	layilin	protein-coding
mm_50093.1	chr6	41532950	41532970	+	1	NA	Intergenic	Intergenic	11184	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_75990.1	chr8	72387021	72387055	-	1	NA	exon (NM_007944, exon 9 of 24)	exon (NM_007944, exon 9 of 24)	34436	NM_001122832	13859	Mm.288894	NM_007944	ENSMUSG00000006276	Eps15l1	9830147J04Rik|AI593686|Eps15-rs|Eps15R	epidermal growth factor receptor pathway substrate 15-like 1	protein-coding
mm_7317.1	chr1	99650443	99650444	-	1	NA	Intergenic	Intergenic	-122322	NM_172851	241175	Mm.251301	NM_172851	ENSMUSG00000067028	Cntnap5b	C230078M14Rik|Caspr5-2	contactin associated protein-like 5B	protein-coding
mm_85575.1	chr9	107289503	107289517	-	1	NA	promoter-TSS (NM_001316691)	promoter-TSS (NM_001316691)	-114	NM_001316691	102626	Mm.222612	NM_178907	ENSMUSG00000032577	Mapkapk3	3PK|AI874665|MAPKAP-K3|MAPKAP3|MK-3|MK3|MapkKapk3	mitogen-activated protein kinase-activated protein kinase 3	protein-coding
mm_172646.1	chr8	26587074	26587074	-	1	NA	Intergenic	L1Md_T|LINE|L1	237349	NR_045904	72316	Mm.490534	NR_045904	ENSMUSG00000100335	2310008N11Rik	-	RIKEN cDNA 2310008N11 gene	ncRNA
mm_94639.1	chr11	16912448	16912462	+	1	NA	3' UTR (NM_207655, exon 28 of 28)	3' UTR (NM_207655, exon 28 of 28)	38827	NR_110421	72735	Mm.268598	NR_015469		Eldr	2810442I21Rik|4930500E12Rik|Fabl	Egfr long non-coding downstream RNA	ncRNA
mm_56856.1	chr6	118197319	118197335	-	1	NA	5' UTR (NM_009050, exon 1 of 20)	5' UTR (NM_009050, exon 1 of 20)	417	NM_009050	19713	Mm.57199	NM_009050	ENSMUSG00000030110	Ret	PTC|RET51|RET9|c-Ret	ret proto-oncogene	protein-coding
mm_110768.1	chr12	70263436	70263446	-	1	NA	TTS (NM_001110203)	TTS (NM_001110203)	35600	NR_045174	414124	Mm.416164	NR_045174	ENSMUSG00000085298	F730035M05Rik	-	RIKEN cDNA F730035M05 gene	ncRNA
mm_6270.1	chr1	69548981	69549014	-	1	NA	intron (NM_011770, intron 5 of 7)	intron (NM_011770, intron 5 of 7)	136963	NM_011770	22779	Mm.106343	NM_011770	ENSMUSG00000025997	Ikzf2	A730095J18Rik|Helios|Zfpn1a2|Znfn1a2	IKAROS family zinc finger 2	protein-coding
mm_112581.1	chr13	13709947	13709965	+	1	NA	intron (NM_010748, intron 36 of 52)	MIR|SINE|MIR	-74103	NM_001302997	14706	Mm.215394	NM_010317	ENSMUSG00000021303	Gng4	-	guanine nucleotide binding protein (G protein), gamma 4	protein-coding
mm_165102.1	chr19	55892725	55892729	+	1	NA	intron (NR_138565, intron 4 of 15)	intron (NR_138565, intron 4 of 15)	-2594	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_91693.1	chr10	43997380	43997390	-	1	NA	exon (NM_172393, exon 2 of 20)	exon (NM_172393, exon 2 of 20)	7461	NM_172393	11630	Mm.292082	NM_172393	ENSMUSG00000019866	Aim1	AI462491|AI463325	absent in melanoma 1	protein-coding
mm_106019.1	chr11	116022837	116022850	-	1	NA	3' UTR (NM_008211, exon 4 of 4)	3' UTR (NM_008211, exon 4 of 4)	1661	NM_008211	15081	Mm.18516	NM_008211	ENSMUSG00000016559	H3f3b	9430068D06Rik|H3.3B	H3 histone, family 3B	protein-coding
mm_40673.1	chr5	65536853	65536872	+	1	NA	promoter-TSS (NM_016786)	promoter-TSS (NM_016786)	-383	NM_016786	53323	Mm.319512	NM_016786	ENSMUSG00000029203	Ube2k	AW492011|D5Ertd601e|E2-25k|HIP-2|Hip2|Hypg|Lig	ubiquitin-conjugating enzyme E2K	protein-coding
mm_150356.1	chr19	34649037	34649043	+	1	NA	3' UTR (NM_008331, exon 2 of 2)	3' UTR (NM_008331, exon 2 of 2)	8151	NM_008331	15957	Mm.439751	NM_008331	ENSMUSG00000034459	Ifit1	ISG56|Ifi56|P56	interferon-induced protein with tetratricopeptide repeats 1	protein-coding
mm_156792.1	chrX	162760428	162760488	+	1	NA	promoter-TSS (NM_009031)	promoter-TSS (NM_009031)	86	NM_009031	245688	Mm.270186	NM_009031	ENSMUSG00000031353	Rbbp7	AA409861|AI173248|AU019541|BB114024|mRbAp46	retinoblastoma binding protein 7	protein-coding
mm_101210.1	chr11	20063919	20063931	-	1	NA	3' UTR (NM_146243, exon 9 of 9)	3' UTR (NM_146243, exon 9 of 9)	49026	NM_146243	66713	Mm.259045	NM_146243	ENSMUSG00000020152	Actr2	4921510D23Rik|AA409782|Arp2|D6Ertd746e	ARP2 actin-related protein 2	protein-coding
mm_71741.1	chr8	64445608	64445621	+	1	NA	Intergenic	MTD|LTR|ERVL-MaLR	68827	NR_030491	735270		NR_030491	ENSMUSG00000076042	Mir710	Mirn710|mmu-mir-710	microRNA 710	ncRNA
mm_101356.1	chr11	23740022	23740030	-	1	NA	Intergenic	Intergenic	30944	NM_009044	19696	Mm.4869	NM_009044	ENSMUSG00000020275	Rel	c-Rel	reticuloendotheliosis oncogene	protein-coding
mm_120929.1	chr14	76487720	76487748	+	1	NA	promoter-TSS (NM_001177751)	promoter-TSS (NM_001177751)	-702	NM_001177751	21807	Mm.153272	NM_009366	ENSMUSG00000022010	Tsc22d1	AA589566|AW105905|Egr5|TSC-22|Tgfb1i4|Tsc|Tsc22	TSC22 domain family, member 1	protein-coding
mm_113516.1	chr13	37788072	37788075	+	1	NA	Intergenic	L1MB4|LINE|L1	-37965	NM_026830	68750	Mm.491109	NM_026830	ENSMUSG00000039087	Rreb1	1110037N09Rik|AA414966|B930013M22Rik	ras responsive element binding protein 1	protein-coding
mm_20014.1	chr2	119230392	119230402	-	1	NA	promoter-TSS (NM_028104)	promoter-TSS (NM_028104)	-532	NM_001290796	72112	Mm.46317	NM_028104	ENSMUSG00000027317	Ppp1r14d	2010107K19Rik|GBPI-1|Ppp1r14	protein phosphatase 1, regulatory (inhibitor) subunit 14D	protein-coding
mm_37682.1	chr4	129222717	129222733	-	1	NA	exon (NM_001285867, exon 6 of 7)	exon (NM_001285867, exon 6 of 7)	5186	NM_001285866	97130	Mm.331907	NM_001033189	ENSMUSG00000050390	C77080	Kiaa1522|mKIAA1522	expressed sequence C77080	protein-coding
mm_164931.1	chr18	82692640	82692647	+	1	NA	promoter-TSS (NM_177832)	promoter-TSS (NM_177832)	91	NM_177832	329002	Mm.34438	NM_177832	ENSMUSG00000041258	Zfp236	AI447957|Gm335	zinc finger protein 236	protein-coding
mm_137388.1	chr17	25809091	25809171	+	1	NA	promoter-TSS (NM_001164225)	promoter-TSS (NM_001164225)	46	NM_001164225	214931	Mm.152289	NM_001164225	ENSMUSG00000025738	Fbxl16	BC042620|Scirr1	F-box and leucine-rich repeat protein 16	protein-coding
mm_136238.1	chr16	90810366	90810429	-	1	NA	promoter-TSS (NM_029497)	promoter-TSS (NM_029497)	16	NM_029497	207932	Mm.328688	NM_029497	ENSMUSG00000039929	Urb1	4921511H13Rik|5730405K23Rik|AA670781|AI645590|mKIAA0539	URB1 ribosome biogenesis 1 homolog (S. cerevisiae)	protein-coding
mm_29023.1	chr3	101924525	101924545	-	1	NA	promoter-TSS (NM_001039371)	promoter-TSS (NM_001039371)	-82	NM_001039371	242126	Mm.90204	NM_001039371	ENSMUSG00000033147	Slc22a15	2610034P21Rik|4930477M19|A530052I06Rik|BB219042	solute carrier family 22 (organic anion/cation transporter), member 15	protein-coding
mm_55897.1	chr6	83537121	83537130	-	1	NA	promoter-TSS (NM_009610)	promoter-TSS (NM_009610)	-874	NM_009610	11468	Mm.292865	NM_009610	ENSMUSG00000059430	Actg2	ACTA3|Act-4|Act4|SMGA	actin, gamma 2, smooth muscle, enteric	protein-coding
mm_158084.1	chrX	101266792	101266804	-	1	NA	intron (NM_013563, intron 4 of 7)	intron (NM_013563, intron 4 of 7)	1457	NM_001308535	16186	Mm.2923	NM_013563	ENSMUSG00000031304	Il2rg	CD132|[g]c|gamma(c)|gc|p64	interleukin 2 receptor, gamma chain	protein-coding
mm_5807.1	chr1	52233076	52233097	-	1	NA	5' UTR (NM_001113383, exon 1 of 15)	5' UTR (NM_001113383, exon 1 of 15)	146	NM_001081081	14660	Mm.398608	NM_001081081	ENSMUSG00000026103	Gls	6330442B14|AI314027|B230365M23Rik	glutaminase	protein-coding
mm_133364.1	chr16	84703849	84703869	+	1	NA	Intergenic	Intergenic	-9164	NR_132106	100653389	Mm.261808	NR_132106	ENSMUSG00000097418	Mir155hg	Bic|Gm26667	Mir155 host gene (non-protein coding)	ncRNA
mm_53289.1	chr6	128993072	128993080	+	1	NA	non-coding (NR_015455, exon 1 of 3)	non-coding (NR_015455, exon 1 of 3)	115	NR_015455	408064	Mm.172429	NR_015455		BC064078	-	cDNA sequence BC064078	ncRNA
mm_116084.1	chr13	28537694	28537697	-	1	NA	intron (NR_045053, intron 7 of 8)	L1_Mur3|LINE|L1	173178	NR_105787	102466635		NR_105787	ENSMUSG00000099158	Mir6368	Gm27800|mmu-mir-6368	microRNA 6368	ncRNA
mm_23832.1	chr3	81932636	81932664	+	1	NA	promoter-TSS (NM_177662)	promoter-TSS (NM_177662)	49	NM_177662	229445	Mm.254642	NM_177662	ENSMUSG00000028015	Ctso	A330105D01Rik|AI118514	cathepsin O	protein-coding
mm_70304.1	chr8	4088193	4088211	+	1	NA	Intergenic	Intergenic	17562	NM_026956	69142	Mm.171061	NM_026956	ENSMUSG00000051906	Cd209f	1810029C22Rik|AI647041|SIGNR8	CD209f antigen	protein-coding
mm_14611.1	chr2	136713296	136713313	+	1	NA	promoter-TSS (NM_001291056)	promoter-TSS (NM_001291056)	-146	NM_011428	20614	Mm.45953	NM_011428	ENSMUSG00000027273	Snap25	Bdr|GENA70|SNAP-25|SUP|sp	synaptosomal-associated protein 25	protein-coding
mm_162329.1	chr1	40515496	40515502	+	1	NA	intron (NM_010553, intron 1 of 12)	intron (NM_010553, intron 1 of 12)	137	NM_010553	16174	Mm.20466	NM_010553	ENSMUSG00000026068	Il18rap	AcPL|IL-18R-beta|IL-18RAcP|IL-18Rbeta|IL-1RAcPL	interleukin 18 receptor accessory protein	protein-coding
mm_140273.1	chr17	84738790	84738792	+	1	NA	intron (NM_028233, intron 25 of 37)	RMER20C_Mm|LTR|ERVK	51995	NM_028233	72416	Mm.217027	NM_028233	ENSMUSG00000024120	Lrpprc	3110001K13Rik|C76645|Gp130|Lrp130|Lsfc	leucine-rich PPR-motif containing	protein-coding
mm_146913.1	chr18	31447349	31447376	-	1	NA	promoter-TSS (NM_009308)	promoter-TSS (NM_009308)	53	NM_009308	20983	Mm.233846	NM_009308	ENSMUSG00000024261	Syt4	SytIV	synaptotagmin IV	protein-coding
mm_87259.1	chr10	41519851	41519859	+	1	NA	intron (NM_016898, intron 1 of 5)	CpG	355	NM_016898	53599	Mm.269815	NM_016898	ENSMUSG00000019818	Cd164	A115|A24|AA589639|AW540279|MGC-24|MSSP	CD164 antigen	protein-coding
mm_150129.1	chr19	30030643	30030653	+	1	NA	5' UTR (NM_144873, exon 1 of 16)	5' UTR (NM_144873, exon 1 of 16)	135	NM_144873	109113	Mm.313364	NM_144873	ENSMUSG00000024817	Uhrf2	2310065A22Rik|AI426270|AW214556|D130071B19Rik|Nirf	ubiquitin-like, containing PHD and RING finger domains 2	protein-coding
mm_172649.1	chr8	29194208	29194221	+	1	NA	intron (NM_001347498, intron 1 of 14)	L1Md_T|LINE|L1	25422	NM_001347499	210801	Mm.248433	NM_153135	ENSMUSG00000063626	Unc5d	D930029E11Rik|Unc5h4|mKIAA1777	unc-5 netrin receptor D	protein-coding
mm_11459.1	chr2	32225037	32225046	+	1	NA	intron (NM_172661, intron 27 of 29)	B1_Mm|SINE|Alu	-11642	NM_145145	99011	Mm.31192	NM_145145	ENSMUSG00000039254	Pomt1	AI505244	protein-O-mannosyltransferase 1	protein-coding
mm_132385.1	chr16	34930334	34930350	+	1	NA	intron (NM_139300, intron 17 of 31)	intron (NM_139300, intron 17 of 31)	8987	NR_040536	76649	Mm.420532	NR_040536	ENSMUSG00000100593	1700119H24Rik	-	RIKEN cDNA 1700119H24 gene	ncRNA
mm_20001.1	chr2	119029340	119029347	-	1	NA	promoter-TSS (NM_199310)	promoter-TSS (NM_199310)	50	NM_199310	269336	Mm.292465	NM_199310	ENSMUSG00000039983	Ccdc32	Gm631	coiled-coil domain containing 32	protein-coding
mm_13119.1	chr2	91663982	91664020	+	1	NA	intron (NR_027371, intron 5 of 13)	intron (NR_027371, intron 5 of 13)	10793	NM_146124	228359	Mm.22413	NM_146124	ENSMUSG00000027247	Arhgap1	B230365D05Rik|C76222|Cdc42GAP|p50rhoGAP	Rho GTPase activating protein 1	protein-coding
mm_51566.1	chr6	83575930	83575942	+	1	NA	intron (NR_078345, intron 2 of 7)	intron (NR_078345, intron 2 of 7)	-3432	NM_024239	70527	Mm.32801	NM_024239	ENSMUSG00000006906	Stambp	5330424L14Rik|5730422L11Rik|AW107289|Amsh|mKIAA4198	STAM binding protein	protein-coding
mm_145865.1	chr18	65461109	65461119	+	1	NA	intron (NM_172833, intron 9 of 15)	intron (NM_172833, intron 9 of 15)	30117	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_18415.1	chr2	60700122	60700125	-	1	NA	intron (NM_001159564, intron 1 of 17)	intron (NM_001159564, intron 1 of 17)	22480	NM_001159564	16420	Mm.98193	NM_021359	ENSMUSG00000026971	Itgb6	2210409C20Rik|4831415H04Rik	integrin beta 6	protein-coding
mm_143703.1	chr17	80577744	80577752	-	1	NA	Intergenic	Intergenic	-13914	NM_001033443	381113	Mm.329216	NM_001033443	ENSMUSG00000033966	Cdkl4	AU067824|Gm942	cyclin-dependent kinase-like 4	protein-coding
mm_29955.1	chr3	133092379	133092394	-	1	NA	promoter-TSS (NM_026231)	promoter-TSS (NM_026231)	531	NM_027927	71793	Mm.246726	NM_027927	ENSMUSG00000028016	Ints12	1110020M19Rik|2810027J24Rik|4930529N21Rik|A230056J18Rik|AI666778|Phf22|int12	integrator complex subunit 12	protein-coding
mm_78412.1	chr9	30669451	30669455	+	1	NA	Intergenic	Lx7|LINE|L1	242124	NM_028874	102607	Mm.35084	NM_028874	ENSMUSG00000031993	Snx19	3526401K03Rik|AI195321|AI848208|mKIAA0254	sorting nexin 19	protein-coding
mm_58732.1	chr7	13029874	13029888	+	1	NA	exon (NM_011588, exon 13 of 17)	exon (NM_011588, exon 13 of 17)	4896	NM_026885	68953	Mm.295670	NM_026885	ENSMUSG00000033916	Chmp2a	1500016L11Rik	charged multivesicular body protein 2A	protein-coding
mm_9109.1	chr1	170110830	170110834	-	1	NA	Intergenic	Intergenic	-21888	NM_022563	18214	Mm.229249	NM_022563	ENSMUSG00000026674	Ddr2	AW495251|Ntrkr3|tyro10	discoidin domain receptor family, member 2	protein-coding
mm_29586.1	chr3	117804806	117804809	-	1	NA	intron (NM_029655, intron 7 of 8)	intron (NM_029655, intron 7 of 8)	64129	NM_001190156	76561	Mm.33824	NM_029655	ENSMUSG00000028007	Snx7	2510028H01Rik	sorting nexin 7	protein-coding
mm_59762.1	chr7	28830143	28830156	+	1	NA	intron (NM_016772, intron 5 of 9)	intron (NM_016772, intron 5 of 9)	-3645	NM_010706	16855	Mm.210336	NM_010706	ENSMUSG00000053964	Lgals4	gal-4	lectin, galactose binding, soluble 4	protein-coding
mm_89310.1	chr10	87916477	87916507	+	1	NA	intron (NM_001111274, intron 4 of 4)	(TC)n|Simple_repeat|Simple_repeat	-50179	NR_000040	22172	Mm.391420	NR_000040		Tyms-ps	-	thymidylate synthase, pseudogene	pseudo
mm_103872.1	chr11	83525919	83525993	-	1	NA	3' UTR (NM_013653, exon 3 of 3)	3' UTR (NM_013653, exon 3 of 3)	-3857	NM_001045543	629303	Mm.390417	NM_001045543	ENSMUSG00000018925	Heatr9	Gm11435|OTTMUSG00000000990	HEAT repeat containing 9	protein-coding
mm_34090.1	chr4	138832955	138832969	+	1	NA	non-coding (NR_002926, exon 3 of 5)	non-coding (NR_002926, exon 3 of 5)	1086	NM_001082531	18780	Mm.4675	NM_011108	ENSMUSG00000058908	Pla2g2a	EF|Mom1|Pla2|sPLA2|sPla2-IIA	phospholipase A2, group IIA (platelets, synovial fluid)	protein-coding
mm_64148.1	chr7	141265413	141265428	+	1	NA	exon (NM_001252601, exon 3 of 10)	exon (NM_001252601, exon 3 of 10)	1004	NM_001252601	54123	Mm.3233	NM_016850	ENSMUSG00000025498	Irf7	-	interferon regulatory factor 7	protein-coding
mm_109068.1	chr12	104345345	104345354	+	1	NA	exon (NM_011458, exon 5 of 5)	exon (NM_011458, exon 5 of 5)	6863	NM_011458	20714	Mm.291569	NM_011458	ENSMUSG00000058207	Serpina3k	1300001I07Rik|D12Rp54|MMCM2|MMSpi2|RP54|Spi-2|Spi2|contrapsin	serine (or cysteine) peptidase inhibitor, clade A, member 3K	protein-coding
mm_44731.1	chr5	31093474	31093499	-	1	NA	promoter-TSS (NM_011773)	promoter-TSS (NM_011773)	41	NM_011773	22784	Mm.1396	NM_011773	ENSMUSG00000029151	Slc30a3	Znt3	solute carrier family 30 (zinc transporter), member 3	protein-coding
mm_58159.1	chr6	142472898	142472916	-	1	NA	5' UTR (NM_145572, exon 1 of 17)	5' UTR (NM_145572, exon 1 of 17)	202	NM_145572	232493	Mm.275975	NM_145572	ENSMUSG00000030244	Gys2	BC021322|LGS	glycogen synthase 2	protein-coding
mm_78664.1	chr9	40686003	40686059	+	1	NA	promoter-TSS (NM_133733)	promoter-TSS (NM_133733)	67	NM_133733	71566	Mm.280560	NM_133733	ENSMUSG00000032024	Clmp	9030425E11Rik|ACAM|ASP5|AW557819	CXADR-like membrane protein	protein-coding
mm_119082.1	chr14	30886494	30886510	+	1	NA	promoter-TSS (NM_001289633)	promoter-TSS (NM_001289633)	26	NM_001289632	16427	Mm.34819	NM_018746	ENSMUSG00000021922	Itih4	ITI-HC4|Itih-4|PK-120	inter alpha-trypsin inhibitor, heavy chain 4	protein-coding
mm_105479.1	chr11	105938561	105938567	-	1	NA	intron (NM_007805, intron 1 of 5)	intron (NM_007805, intron 1 of 5)	5583	NM_007805	13056	Mm.149403	NM_007805	ENSMUSG00000019590	Cyb561	-	cytochrome b-561	protein-coding
mm_57678.1	chr6	128496750	128496761	-	1	NA	intron (NM_007376, intron 17 of 35)	intron (NM_007376, intron 17 of 35)	29965	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_137538.1	chr17	27556644	27556652	+	1	NA	promoter-TSS (NM_001166545)	promoter-TSS (NM_001166545)	-5	NM_001166476	111241	Mm.426212	NM_001166476	ENSMUSG00000078249	Hmga1-rs1	ENSMUSG00000041059|Hmgi-rs1	high mobility group AT-hook I, related sequence 1	protein-coding
mm_170101.1	chr17	39843332	39843333	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	335	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_34069.1	chr4	138456809	138456819	+	1	NA	3' UTR (NM_025451, exon 2 of 2)	3' UTR (NM_025451, exon 2 of 2)	1666	NM_025451	66259	Mm.41603	NM_025451	ENSMUSG00000046447	Camk2n1	1810006K23Rik|AI848599|AI891706	calcium/calmodulin-dependent protein kinase II inhibitor 1	protein-coding
mm_6406.1	chr1	72873878	72873917	-	1	NA	exon (NM_010518, exon 1 of 4)	exon (NM_010518, exon 1 of 4)	968	NM_010518	16011	Mm.405761	NM_010518	ENSMUSG00000026185	Igfbp5	AI256729|AW208790|IGFBP-5|IGFBP-5P	insulin-like growth factor binding protein 5	protein-coding
mm_80821.1	chr9	96759619	96759633	+	1	NA	Intergenic	Intergenic	-5936	NR_102295	319707	Mm.392191	NR_102293	ENSMUSG00000101581	C430002N11Rik	-	RIKEN cDNA C430002N11 gene	ncRNA
mm_168731.1	chr12	114094410	114094421	-	1	NA	Intergenic	Intergenic	375051	NR_106062	102465663		NR_106062	ENSMUSG00000105438	Mir7094-1	mmu-mir-7094-1	microRNA 7094-1	ncRNA
mm_106633.1	chr11	120903619	120903626	-	1	NA	exon (NM_027745, exon 5 of 19)	exon (NM_027745, exon 5 of 19)	29250	NM_027745	71276	Mm.275751	NM_027745	ENSMUSG00000048445	Ccdc57	4933434G05Rik	coiled-coil domain containing 57	protein-coding
mm_9213.1	chr1	171231016	171231056	-	1	NA	intron (NM_010185, intron 2 of 4)	intron (NM_010185, intron 2 of 4)	3313	NM_010185	14127	Mm.22673	NM_010185	ENSMUSG00000058715	Fcer1g	AI573376|CD23|FcR-gamma|FcR[g]|FcRgamma|Fce1g|FcepsilonRI|Ly-50	Fc receptor, IgE, high affinity I, gamma polypeptide	protein-coding
mm_9035.1	chr1	167234811	167234831	-	1	NA	exon (NM_030724, exon 4 of 7)	exon (NM_030724, exon 4 of 7)	50306	NM_030724	80914	Mm.280895	NM_030724	ENSMUSG00000026558	Uck2	AA407809|AI481316|AU018180|AU020720|TSA903|UK|UMK|Umpk	uridine-cytidine kinase 2	protein-coding
mm_34931.1	chr4	155839694	155839704	+	1	NA	promoter-TSS (NM_024263)	promoter-TSS (NM_024263)	19	NM_024263	74761	Mm.159028	NM_024263	ENSMUSG00000029070	Mxra8	1200013A08Rik|1700095D18Rik|AI131686|Asp3|Dicam	matrix-remodelling associated 8	protein-coding
mm_13837.1	chr2	119351900	119351913	+	1	NA	intron (NM_026929, intron 1 of 2)	intron (NM_026929, intron 1 of 2)	664	NM_026929	69065	Mm.35083	NM_026929	ENSMUSG00000027313	Chac1	1810008K03Rik	ChaC, cation transport regulator 1	protein-coding
mm_5094.1	chr1	4807661	4807702	-	1	NA	promoter-TSS (NM_008866)	promoter-TSS (NM_008866)	-212	NM_008866	18777	Mm.299955	NM_008866	ENSMUSG00000025903	Lypla1	Pla1a	lysophospholipase 1	protein-coding
mm_93485.1	chr10	111997100	111997112	-	1	NA	5' UTR (NM_028608, exon 1 of 6)	5' UTR (NM_028608, exon 1 of 6)	158	NM_028608	73690	Mm.173790	NM_028608	ENSMUSG00000056888	Glipr1	2410114O14Rik|RTVP-1|RTVP1|mRTVP-1	GLI pathogenesis-related 1 (glioma)	protein-coding
mm_20380.1	chr2	128687401	128687411	-	1	NA	promoter-TSS (NM_008569)	promoter-TSS (NM_008569)	-11	NM_008569	17222	Mm.277408	NM_008569	ENSMUSG00000014355	Anapc1	2610021O03Rik|AI047775|AI853536|AW547281|Apc1|Mcpr|tsg24	anaphase promoting complex subunit 1	protein-coding
mm_50507.1	chr6	49036640	49036658	+	1	NA	5' UTR (NM_053110, exon 1 of 11)	5' UTR (NM_053110, exon 1 of 11)	131	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_8195.1	chr1	138119163	138119183	-	1	NA	intron (NM_001111316, intron 4 of 31)	(CAAAA)n|Simple_repeat|Simple_repeat	55953	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_106527.1	chr11	120572865	120572881	-	1	NA	promoter-TSS (NM_011032)	promoter-TSS (NM_011032)	63	NM_011032	18453	Mm.16660	NM_011032	ENSMUSG00000025130	P4hb	ERp59|PDI|Pdia1|Thbp	prolyl 4-hydroxylase, beta polypeptide	protein-coding
mm_73515.1	chr8	107408585	107408589	+	1	NA	intron (NR_039557, intron 2 of 3).3	PB1D7|SINE|Alu	-5382	NM_008706	18104	Mm.252	NM_008706	ENSMUSG00000003849	Nqo1	AV001255|Dia4|Dtd|Nmo-1|Nmo1|Nmor1|Ox-1|Ox1|Qr1	NAD(P)H dehydrogenase, quinone 1	protein-coding
mm_65457.1	chr7	25464266	25464268	-	1	NA	intron (NM_001039187, intron 5 of 5)	intron (NM_001039187, intron 5 of 5)	13358	NM_001039185	26365	Mm.322502	NM_011926	ENSMUSG00000074272	Ceacam1	Bgp|Bgp1|C-CAM|CD66a|Cc1|Cea-1|Cea-7|Cea1|Cea7|Hv-2|Hv2|MHVR|MHVR1|Mhv-1|bb-1|mCEA1|mmCGM1|mmCGM1a|mmCGM2	carcinoembryonic antigen-related cell adhesion molecule 1	protein-coding
mm_151444.1	chr19	57477596	57477602	+	1	NA	intron (NM_028115, intron 4 of 7)	intron (NM_028115, intron 4 of 7)	24693	NM_028115	72133	Mm.258404	NM_028115	ENSMUSG00000025086	Trub1	2610009I02Rik|9030425C13Rik|AI448235|BB118943|C76870	TruB pseudouridine (psi) synthase family member 1	protein-coding
mm_36396.1	chr4	77784752	77784777	-	1	NA	intron (NM_011211, intron 2 of 39)	Lx|LINE|L1	427131	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding
mm_118652.1	chr14	21750526	21750536	+	1	NA	promoter-TSS (NM_026283)	promoter-TSS (NM_026283)	0	NM_026283	67630	Mm.102765	NM_026283	ENSMUSG00000021770	Samd8	1110053F04Rik|1700010P07Rik|SMSr	sterile alpha motif domain containing 8	protein-coding
mm_109249.1	chr12	109453484	109453497	+	1	NA	promoter-TSS (NM_010052)	promoter-TSS (NM_010052)	35	NM_010052	13386	Mm.157069	NM_010052	ENSMUSG00000040856	Dlk1	AW742678|DLK-1|DlkI|FA1|Ly107|Peg9|SCP1|ZOG|pG2|pref-1	delta-like 1 homolog (Drosophila)	protein-coding
mm_55994.1	chr6	86365541	86365545	-	1	NA	promoter-TSS (NM_025591)	promoter-TSS (NM_025591)	-140	NM_025591	66488	Mm.422972	NM_025591	ENSMUSG00000057497	Fam136a	2010309E21Rik|AW124904|Hyccin	family with sequence similarity 136, member A	protein-coding
mm_73188.1	chr8	95352237	95352251	+	1	NA	promoter-TSS (NM_008609)	promoter-TSS (NM_008609)	-52	NM_008609	17388	Mm.217116	NM_008609	ENSMUSG00000031790	Mmp15	AI503551|MT-MMP 2|MT2-MMP	matrix metallopeptidase 15	protein-coding
mm_93748.1	chr10	120161442	120161452	-	1	NA	intron (NM_028679, intron 8 of 11)	(TCCC)n|Simple_repeat|Simple_repeat	40090	NM_028679	73914	Mm.146194	NM_028679	ENSMUSG00000020227	Irak3	4833428C18Rik|AI563835|IRAK-M	interleukin-1 receptor-associated kinase 3	protein-coding
mm_63673.1	chr7	130524712	130524725	+	1	NA	Intergenic	L1MCa|LINE|L1	-4349	NM_001271343	11907	Mm.216321	NM_013799	ENSMUSG00000030850	Ate1	AI225793|AW547406	arginyltransferase 1	protein-coding
mm_47522.1	chr5	124111863	124111881	-	1	NA	promoter-TSS (NM_001347478)	promoter-TSS (NM_001347478)	-428	NM_001347478	66627	Mm.7050	NM_025671	ENSMUSG00000023707	Ogfod2	1300006G11Rik|5730405M13Rik|AU041636|AW552395	2-oxoglutarate and iron-dependent oxygenase domain containing 2	protein-coding
mm_63905.1	chr7	139213310	139213320	+	1	NA	promoter-TSS (NM_001143755)	promoter-TSS (NM_001143755)	-8	NM_001162540	57740	Mm.65336	NM_021302	ENSMUSG00000015981	Stk32c	PKE|Pkek|YANK3	serine/threonine kinase 32C	protein-coding
mm_24435.1	chr3	90560318	90560332	+	1	NA	Intergenic	Intergenic	19102	NM_026416	67860	Mm.331185	NM_026416	ENSMUSG00000074457	S100a16	2300002L21Rik|AI325039|AI663996|DT1P1A7|S100F	S100 calcium binding protein A16	protein-coding
mm_54137.1	chr6	21852524	21852540	-	1	NA	promoter-TSS (NM_173007)	promoter-TSS (NM_173007)	-17	NM_173007	269831	Mm.21950	NM_173007	ENSMUSG00000029669	Tspan12	9030619E17|AI426782|AI663988|AW111457|Tm4sf12	tetraspanin 12	protein-coding
mm_42743.1	chr5	120735010	120735054	+	1	NA	exon (NM_145227, exon 9 of 11)	exon (NM_145227, exon 9 of 11)	14816	NM_145227	246728	Mm.260926	NM_145227	ENSMUSG00000032690	Oas2	Oasl11	2'-5' oligoadenylate synthetase 2	protein-coding
mm_18941.1	chr2	76760061	76760080	-	1	NA	exon (NM_011652, exon 262 of 313)	exon (NM_011652, exon 262 of 313)	84755	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_127276.1	chr15	99725748	99725767	+	1	NA	TTS (NM_010271)	TTS (NM_010271)	139	NM_183256	66379	Mm.5265	NM_183256	ENSMUSG00000023020	Cox14	2310016M24Rik|AA959804	cytochrome c oxidase assembly protein 14	protein-coding
mm_38840.1	chr4	149166635	149166643	-	1	NA	promoter-TSS (NM_001081274)	promoter-TSS (NM_001081274)	68	NM_001081274	110208	Mm.252080	NM_025801	ENSMUSG00000028961	Pgd	0610042A05Rik|AU019875|C78335	phosphogluconate dehydrogenase	protein-coding
mm_151229.1	chr19	53718025	53718041	+	1	NA	intron (NM_001170847, intron 1 of 13)	intron (NM_001170847, intron 1 of 13)	40727	NM_001170847	73713	Mm.313695	NM_001170847	ENSMUSG00000043639	Rbm20	1110018J23Rik|2010003H22Rik|AI646761	RNA binding motif protein 20	protein-coding
mm_156481.1	chrX	144317992	144318034	+	1	NA	promoter-TSS (NM_026247)	promoter-TSS (NM_026247)	47	NM_026247	67574	Mm.249084	NM_026247	ENSMUSG00000041718	Alg13	2810046O15Rik|4833435D08Rik|Glt28d1|MDS031|OTTMUSG00000018917	asparagine-linked glycosylation 13	protein-coding
mm_56603.1	chr6	109505156	109505191	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	676532	NM_138677	192193	Mm.21596	NM_138677	ENSMUSG00000030104	Edem1	A130059K23Rik|EDEM|mKIAA0212	ER degradation enhancer, mannosidase alpha-like 1	protein-coding
mm_28554.1	chr3	93376377	93376386	-	1	NA	Intergenic	RMER10A|LTR|ERVL	-17318	NM_009100	20129	Mm.1417	NM_009100	ENSMUSG00000041984	Rptn	-	repetin	protein-coding
mm_157493.1	chrX	48453742	48453762	-	1	NA	intron (NM_019680, intron 1 of 8)	CpG	9380	NM_019680	56501	Mm.36808	NM_019680	ENSMUSG00000031103	Elf4	AV314029|BC042423|ENSMUSG00000053512|Gm9907|Mef	E74-like factor 4 (ets domain transcription factor)	protein-coding
mm_167593.1	chr9	47894178	47894208	-	1	NA	Intergenic	Intergenic	-75985	NR_046048	100038460	Mm.447649	NR_046048		Gm10677	ENSMUSG00000074363	predicted gene 10677	ncRNA
mm_138962.1	chr17	44561981	44561996	+	1	NA	intron (NR_073425, intron 5 of 5)	Charlie2a|DNA|hAT-Charlie	174188	NR_073425	12393	Mm.391013	NM_009820	ENSMUSG00000039153	Runx2	AML3|Cbf|Cbfa-1|Cbfa1|LS3|Osf2|PEBP2aA|Pebp2a1|Pebpa2a	runt related transcription factor 2	protein-coding
mm_3857.1	chr1	160978577	160978590	+	1	NA	promoter-TSS (NM_080844)	promoter-TSS (NM_080844)	-23	NM_080844	11905	Mm.260770	NM_080844	ENSMUSG00000026715	Serpinc1	AI114908|ATIII|At-3|At3	serine (or cysteine) peptidase inhibitor, clade C (antithrombin), member 1	protein-coding
mm_89653.1	chr10	97479723	97479750	+	1	NA	5' UTR (NM_001190451, exon 1 of 8)	5' UTR (NM_001190451, exon 1 of 8)	236	NM_001190451	13179	Mm.56769	NM_007833	ENSMUSG00000019929	Dcn	DC|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding
mm_59125.1	chr7	19939873	19939877	+	1	NA	intron (NM_027308, intron 3 of 4)	RLTR26B_MM|LTR|ERVK	10868	NM_027308	70080	Mm.98583	NM_027308	ENSMUSG00000040498	Igsf23	2210010C17Rik	immunoglobulin superfamily, member 23	protein-coding
mm_30341.1	chr3	151736950	151736968	-	1	NA	intron (NM_133871, intron 7 of 7)	intron (NM_133871, intron 7 of 7)	13000	NM_133871	99899	Mm.30756	NM_133871	ENSMUSG00000028037	Ifi44	A430056A10Rik|AW261460|MTAP44|p44	interferon-induced protein 44	protein-coding
mm_45393.1	chr5	66151306	66151308	-	1	NA	promoter-TSS (NM_001291226)	promoter-TSS (NM_001291226)	-329	NM_178446	245945	Mm.36863	NM_139065	ENSMUSG00000070780	Rbm47	9530077J19Rik	RNA binding motif protein 47	protein-coding
mm_69805.1	chr7	141214456	141214476	-	1	NA	promoter-TSS (NM_028050)	promoter-TSS (NM_028050)	-386	NM_028050	72000	Mm.334314	NM_028050	ENSMUSG00000025500	Lmntd2	1600016N20Rik	lamin tail domain containing 2	protein-coding
mm_83747.1	chr9	51160543	51160563	-	1	NA	Intergenic	Intergenic	44552	NM_019493	56057	Mm.431317	NM_019493	ENSMUSG00000032056	Btg4	C86116|PC3B	B cell translocation gene 4	protein-coding
mm_115670.1	chr13	12520378	12520417	-	1	NA	promoter-TSS (NM_133643)	promoter-TSS (NM_133643)	53	NM_133643	171211	Mm.159671	NM_133643	ENSMUSG00000095105	Edaradd	1810032E07Rik|5830469M23Rik|A630043P06|cr	EDAR (ectodysplasin-A receptor)-associated death domain	protein-coding
mm_14665.1	chr2	138278482	138278531	+	1	NA	promoter-TSS (NM_145534)	promoter-TSS (NM_145534)	13	NM_145534	228662	Mm.153405	NM_145534	ENSMUSG00000062098	Btbd3	mKIAA0952	BTB (POZ) domain containing 3	protein-coding
mm_126494.1	chr15	81663915	81663958	+	1	NA	promoter-TSS (NM_145993)	promoter-TSS (NM_145993)	47	NR_110362	214669	Mm.280768	NM_145993	ENSMUSG00000022394	L3mbtl2	4732493N06Rik|M4mbt	l(3)mbt-like 2 (Drosophila)	protein-coding
mm_85555.1	chr9	106691107	106691110	-	1	NA	3' UTR (NM_030730, exon 22 of 22)	3' UTR (NM_030730, exon 22 of 22)	-5156	NM_001286498	21767	Mm.22266	NM_011573	ENSMUSG00000040813	Tex264	TEG-264	testis expressed gene 264	protein-coding
mm_20417.1	chr2	129300881	129300903	-	1	NA	exon (NM_010554, exon 7 of 7)	exon (NM_010554, exon 7 of 7)	3522	NR_040371	100503468	Mm.446943	NR_040371	ENSMUSG00000085498	Gm14023	OTTMUSG00000015408	predicted gene 14023	ncRNA
mm_47524.1	chr5	124152791	124152827	-	1	NA	intron (NM_011256, intron 2 of 24)	MIR3|SINE|MIR	34373	NM_001289472	19679	Mm.44261	NM_011256	ENSMUSG00000029406	Pitpnm2	NIR3|RDGBA2|Rdgb2|mKIAA1457	phosphatidylinositol transfer protein, membrane-associated 2	protein-coding
mm_55002.1	chr6	48835597	48835678	-	1	NA	exon (NM_001164209, exon 6 of 8)	exon (NM_001164209, exon 6 of 8)	5351	NM_023056	65963	Mm.28385	NM_023056	ENSMUSG00000029810	Tmem176b	1810009M01Rik|Clast1|Lr8	transmembrane protein 176B	protein-coding
mm_134097.1	chr16	9921157	9921174	-	1	NA	intron (NM_008170, intron 1 of 11)	intron (NM_008170, intron 1 of 11)	71368	NM_008170	14811	Mm.2953	NM_008170	ENSMUSG00000059003	Grin2a	GluN2A|NMDAR2A|NR2A	glutamate receptor, ionotropic, NMDA2A (epsilon 1)	protein-coding
mm_113611.1	chr13	41468538	41468545	+	1	NA	intron (NM_001111324, intron 1 of 7)	intron (NM_001111324, intron 1 of 7)	18819	NM_001111324	18003	Mm.288980	NM_017464	ENSMUSG00000021365	Nedd9	Cas-L|CasL|HEF1|MEF1|Nedd-9|p105	neural precursor cell expressed, developmentally down-regulated gene 9	protein-coding
mm_45636.1	chr5	76658338	76658361	-	1	NA	Intergenic	CpG	66635	NM_199032	381644	Mm.332452	NM_199032	ENSMUSG00000036403	Cep135	BC062951|Cep4|Gm1044	centrosomal protein 135	protein-coding
mm_163713.1	chr13	109933856	109933872	+	1	NA	intron (NM_011056, intron 8 of 16)	intron (NM_011056, intron 8 of 16)	30055	NR_035442	100316683		NR_035442	ENSMUSG00000084651	Mir1904	Mirn1904|mmu-mir-1904	microRNA 1904	ncRNA
mm_7946.1	chr1	133915019	133915042	-	1	NA	exon (NM_054077, exon 2 of 3)	exon (NM_054077, exon 2 of 3)	6371	NM_054077	116847	Mm.214514	NM_054077	ENSMUSG00000041577	Prelp	7330409J17Rik|SLRR2A	proline arginine-rich end leucine-rich repeat	protein-coding
mm_79317.1	chr9	52088237	52088275	+	1	NA	3' UTR (NM_009041, exon 14 of 14)	3' UTR (NM_009041, exon 14 of 14)	-27367	NR_105750	102465150		NR_105750	ENSMUSG00000099311	Mir6244	Gm27368|mmu-mir-6244	microRNA 6244	ncRNA
mm_10739.1	chr2	23069150	23069169	+	1	NA	promoter-TSS (NM_001102438)	promoter-TSS (NM_001102438)	87	NM_001102438	74159	Mm.181973	NM_028793	ENSMUSG00000026781	Acbd5	1300014E15Rik	acyl-Coenzyme A binding domain containing 5	protein-coding
mm_93540.1	chr10	115384517	115384562	-	1	NA	promoter-TSS (NM_025780)	promoter-TSS (NM_025780)	-104	NM_025780	66816	Mm.32314	NM_025780	ENSMUSG00000020137	Thap2	2900040O07Rik|9030625G08Rik|AI450385|AI649097	THAP domain containing, apoptosis associated protein 2	protein-coding
mm_108264.1	chr12	78691652	78691690	+	1	NA	5' UTR (NM_029069, exon 1 of 9)	5' UTR (NM_029069, exon 1 of 9)	136	NM_029069	70897	Mm.56514	NM_027597	ENSMUSG00000056987	Fam71d	4921509E07Rik|4930516C23Rik|GARI-L2	family with sequence similarity 71, member D	protein-coding
mm_150592.1	chr19	40679320	40679339	+	1	NA	intron (NM_009848, intron 1 of 9)	intron (NM_009848, intron 1 of 9)	19559	NM_009848	12495	Mm.2824	NM_009848	ENSMUSG00000048120	Entpd1	2610206B08Rik|AA408691|Cd39|NTPDase-1	ectonucleoside triphosphate diphosphohydrolase 1	protein-coding
mm_3197.1	chr1	135818662	135818672	+	1	NA	promoter-TSS (NM_133664)	promoter-TSS (NM_133664)	69	NM_133664	16763	Mm.36726	NM_133664	ENSMUSG00000041782	Lad1	-	ladinin	protein-coding
mm_45751.1	chr5	86745788	86745812	-	1	NA	promoter-TSS (NM_172880)	promoter-TSS (NM_172880)	7	NM_172880	243084	Mm.130801	NM_172880	ENSMUSG00000054537	Tmprss11e	A030012E10|AY787860|DESC1|TTSP	transmembrane protease, serine 11e	protein-coding
mm_130992.1	chr15	103429539	103429542	-	1	NA	intron (NM_028797, intron 1 of 8)	intron (NM_028797, intron 1 of 8)	887	NM_028797	74174	Mm.325325	NM_028797	ENSMUSG00000022487	Gtsf1	1700006H03Rik|Cue110	gametocyte specific factor 1	protein-coding
mm_133528.1	chr16	90997103	90997108	+	1	NA	intron (NM_001164483, intron 2 of 31)	L1MC4|LINE|L1	13990	NM_001045515	104015	Mm.187079	NM_001045515	ENSMUSG00000022973	Synj1	A930006D20Rik|AA675315|mKIAA0910	synaptojanin 1	protein-coding
mm_163007.1	chr11	36371952	36371952	+	1	NA	intron (NM_011856, intron 3 of 28)	intron (NM_011856, intron 3 of 28)	-391863	NM_170779	211652	Mm.31267	NM_170779	ENSMUSG00000018849	Wwc1	AA408228|AU017197|BC037006|Kibra|mKIAA0869	WW, C2 and coiled-coil domain containing 1	protein-coding
mm_133209.1	chr16	74804962	74804965	+	1	NA	Intergenic	MLT1B|LTR|ERVL-MaLR	-394051	NM_175549	268902	Mm.171736	NM_175549	ENSMUSG00000052516	Robo2	2600013A04Rik|9430089E08Rik|BB097918|D230004I22Rik|mKIAA1568	roundabout guidance receptor 2	protein-coding
mm_148886.1	chr19	6863676	6863687	+	1	NA	Intergenic	B1_Mur1|SINE|Alu	-5470	NM_001081291	78317	Mm.329596	NM_198008	ENSMUSG00000047810	Ccdc88b	2610041P08Rik|Ccdc88	coiled-coil domain containing 88B	protein-coding
mm_117043.1	chr13	58358782	58358799	-	1	NA	Intergenic	CpG	-3928	NM_175214	75050	Mm.446094	NM_175214	ENSMUSG00000060176	Kif27	4930517I18Rik	kinesin family member 27	protein-coding
mm_149043.1	chr19	8820671	8820681	+	1	NA	exon (NM_001081196, exon 1 of 14)	exon (NM_001081196, exon 1 of 14)	1275	NM_001081196	68693	Mm.476519	NM_001081196	ENSMUSG00000071659	Hnrnpul2	1110031M08Rik|AI465155|Hnrpul2	heterogeneous nuclear ribonucleoprotein U-like 2	protein-coding
mm_10827.1	chr2	24385354	24385358	+	1	NA	promoter-TSS (NM_177611)	promoter-TSS (NM_177611)	-41	NM_177611	215632	Mm.490434	NM_177611	ENSMUSG00000026979	Psd4	BC046518|EFA6B	pleckstrin and Sec7 domain containing 4	protein-coding
mm_134531.1	chr16	19241713	19241736	-	1	NA	Intergenic	Intergenic	45017	NM_146451	258443	Mm.377506	NM_146451	ENSMUSG00000050742	Olfr164	MOR279-2	olfactory receptor 164	protein-coding
mm_16091.1	chr2	168961036	168961048	+	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	-5455	NM_009564	22722	Mm.2095	NM_009564	ENSMUSG00000027551	Zfp64	-	zinc finger protein 64	protein-coding
mm_109361.1	chr12	109636135	109636158	+	1	NA	TTS (NR_046302)	TTS (NR_046302)	134	NR_046302	449562		NR_046302	ENSMUSG00000088294	AF357425	MBII-48	snoRNA AF357425	snoRNA
mm_91135.1	chr10	19609279	19609299	-	1	NA	exon (NM_010511, exon 7 of 7)	exon (NM_010511, exon 7 of 7)	-12739	NM_178258	237310	Mm.331979	NM_178258	ENSMUSG00000039760	Il22ra2	CRF2-10|CRF2-s1|CRF2X|Il-22bp	interleukin 22 receptor, alpha 2	protein-coding
mm_71136.1	chr8	39005962	39005972	+	1	NA	promoter-TSS (NM_030254)	promoter-TSS (NM_030254)	100	NM_030254	80286	Mm.272722	NM_030254	ENSMUSG00000039530	Tusc3	AU022242|BC003311|N33	tumor suppressor candidate 3	protein-coding
mm_68562.1	chr7	114706238	114706241	-	1	NA	Intergenic	Intergenic	-12404	NM_054084	116903	Mm.273838	NM_054084	ENSMUSG00000030666	Calcb	CGRP2|Calc2	calcitonin-related polypeptide, beta	protein-coding
mm_98304.1	chr11	90033056	90033072	+	1	NA	intron (NM_026433, intron 1 of 2)	intron (NM_026433, intron 1 of 2)	2716	NM_026433	67888	Mm.212428	NM_026433	ENSMUSG00000069763	Tmem100	1810057C19Rik|AV011897	transmembrane protein 100	protein-coding
mm_170072.1	chr17	33289543	33289561	+	1	NA	promoter-TSS (NM_001142957)	promoter-TSS (NM_001142957)	8	NM_001142957	100043468	Mm.276296	NM_001142957	ENSMUSG00000096910	Zfp955b	A430003O12Rik|C430039G02Rik|C530035A18Rik|Gm4455|Zfp883b	zinc finger protein 955B	protein-coding
mm_18935.1	chr2	76750584	76750595	-	1	NA	exon (NM_011652, exon 275 of 313)	exon (NM_011652, exon 275 of 313)	75274	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_29240.1	chr3	107215994	107216047	-	1	NA	exon (NM_001111143, exon 5 of 9)	exon (NM_001111143, exon 5 of 9)	5712	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_26477.1	chr3	144597046	144597098	+	1	NA	3' UTR (NM_053102, exon 5 of 5)	3' UTR (NM_053102, exon 5 of 5)	26645	NM_053102	93684	Mm.29812	NM_053102	ENSMUSG00000037072	Selenof	9430015P09Rik|Sep15	selenoprotein F	protein-coding
mm_153520.1	chr19	41743666	41743706	-	1	NA	5' UTR (NM_015748, exon 1 of 37)	5' UTR (NM_015748, exon 1 of 37)	170	NM_015748	20562	Mm.39155	NM_015748	ENSMUSG00000025020	Slit1	Slil1|mKIAA0813	slit homolog 1 (Drosophila)	protein-coding
mm_134430.1	chr16	17927830	17927871	-	1	NA	intron (NM_153150, intron 1 of 8)	CpG-5572	369	NM_153150	13358	Mm.229291	NM_153150	ENSMUSG00000003528	Slc25a1	1300019P08Rik|2610100G11Rik|AI194714|Ctp|Dgsj|Slc20a3	solute carrier family 25 (mitochondrial carrier, citrate transporter), member 1	protein-coding
mm_169547.1	chr15	103242044	103242062	+	1	NA	exon (NM_010447, exon 4 of 10)	exon (NM_010447, exon 4 of 10)	1599	NR_002883	434858	Mm.391346	NR_002883		Gm5643	EG434858	heterogeneous nuclear ribonucleoprotein A1 pseudogene	pseudo
mm_5240.1	chr1	16104386	16104392	-	1	NA	promoter-TSS (NM_011291)	promoter-TSS (NM_011291)	44	NM_011291	19989	Mm.319659	NM_011291	ENSMUSG00000043716	Rpl7	Rpl7a|Surf-3	ribosomal protein L7	protein-coding
mm_167101.1	chr7	110243571	110243574	+	1	NA	intron (NM_009302, intron 2 of 11)	intron (NM_009302, intron 2 of 11)	21869	NM_009302	20947	Mm.334144	NM_009302	ENSMUSG00000031015	Swap70	70kDa|AV235546	SWA-70 protein	protein-coding
mm_156954.1	chrX	169987764	169987775	+	1	NA	intron (NM_001290512, intron 9 of 9)	CpG-16002	-8852	NR_029457	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_45592.1	chr5	74677815	74677873	-	1	NA	promoter-TSS (NM_010727)	promoter-TSS (NM_010727)	28	NM_001159580	16924	Mm.440403	NM_010727	ENSMUSG00000029228	Lnx1	Lnx	ligand of numb-protein X 1	protein-coding
mm_129708.1	chr15	81810858	81810881	-	1	NA	promoter-TSS (NM_017376)	promoter-TSS (NM_017376)	-545	NM_017376	21685	Mm.270278	NM_017376	ENSMUSG00000022389	Tef	2310028D20Rik	thyrotroph embryonic factor	protein-coding
mm_143206.1	chr17	62855904	62855907	-	1	NA	intron (NM_010109, intron 1 of 3)	B1_Mus2|SINE|Alu	25412	NM_207654	13640	Mm.7978	NM_010109	ENSMUSG00000048915	Efna5	AL-1|AV158822|EFL-5|Ephrin-A5|Epl7|LERK-7|RAGS	ephrin A5	protein-coding
mm_39013.1	chr4	152120794	152120801	-	1	NA	TTS (NM_033042)	TTS (NM_033042)	4454	NM_033042	85030	Mm.101198	NM_033042	ENSMUSG00000024793	Tnfrsf25	APO-3|DDR3|DR3|LARD|TR3|TRAMP|Tnfrsf12|WSL-1|WSL-LR|Wsl	tumor necrosis factor receptor superfamily, member 25	protein-coding
mm_107802.1	chr12	64965778	64965788	+	1	NA	promoter-TSS (NM_177805)	promoter-TSS (NM_177805)	41	NM_177805	328108	Mm.138465	NM_177805	ENSMUSG00000035614	Fam179b	A430041B07Rik|BC062107|C130034K06|mKIAA0423	family with sequence similarity 179, member B	protein-coding
mm_147040.1	chr18	34862767	34862814	-	1	NA	exon (NM_007913, exon 2 of 2)	exon (NM_007913, exon 2 of 2)	1583	NM_007913	13653	Mm.181959	NM_007913	ENSMUSG00000038418	Egr1	A530045N19Rik|ETR103|Egr-1|Krox-1|Krox-24|Krox24|NGF1-A|NGFI-A|NGFIA|TIS8|Zenk|Zfp-6|Zif268|egr	early growth response 1	protein-coding
mm_71708.1	chr8	61935072	61935098	+	1	NA	intron (NM_001293783, intron 1 of 37)	intron (NM_001293783, intron 1 of 37)	6998	NM_001293783	234311	Mm.275233	NM_144928	ENSMUSG00000037921	Ddx60	9830118M07	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	protein-coding
mm_2563.1	chr1	118299317	118299328	+	1	NA	3' UTR (NM_011650, exon 6 of 6)	3' UTR (NM_011650, exon 6 of 6)	11810	NM_011650	22099	Mm.426637	NM_011650	ENSMUSG00000026374	Tsn	2610034C24Rik|AU040286|C3PO|TB-RBP	translin	protein-coding
mm_14516.1	chr2	132576055	132576069	+	1	NA	intron (NM_001042672, intron 1 of 18)	intron (NM_001042672, intron 1 of 18)	2186	NM_001291050	74182	Mm.211211	NM_027096	ENSMUSG00000027346	Gpcpd1	2310004G06Rik|2310032D16Rik|AU015213|Gde5|Prei4|mKIAA1434	glycerophosphocholine phosphodiesterase 1	protein-coding
mm_138741.1	chr17	37002511	37002524	+	1	NA	promoter-TSS (NM_001013745)	promoter-TSS (NM_001013745)	-8	NM_001013745	22715	Mm.305561	NM_009559	ENSMUSG00000036036	Zfp57	G19|Zfp-57	zinc finger protein 57	protein-coding
mm_2609.1	chr1	120340606	120340645	+	1	NA	promoter-TSS (NM_207233)	promoter-TSS (NM_207233)	43	NM_207233	226359	Mm.337409	NM_207233	ENSMUSG00000036907	C1ql2	BC040774|CTRP10	complement component 1, q subcomponent-like 2	protein-coding
mm_138307.1	chr17	34644806	34644870	+	1	NA	promoter-TSS (NM_019873)	promoter-TSS (NM_019873)	-45	NM_019873	56299	Mm.10025	NM_019873	ENSMUSG00000033739	Fkbpl	DIR1|NG7|Ppiase-X|Wisp39	FK506 binding protein-like	protein-coding
mm_44794.1	chr5	32742248	32742255	-	1	NA	exon (NM_001347332, exon 3 of 9)	exon (NM_001347332, exon 3 of 9)	4091	NM_001347332	320951	Mm.273765	NM_177298	ENSMUSG00000023452	Pisd	9030221M09Rik	phosphatidylserine decarboxylase	protein-coding
mm_123773.1	chr14	70289417	70289429	-	1	NA	promoter-TSS (NM_001304992)	promoter-TSS (NM_001304992)	74	NM_008915	19057	Mm.439683	NM_008915	ENSMUSG00000022092	Ppp3cc	Calnc|PP2BA gamma	protein phosphatase 3, catalytic subunit, gamma isoform	protein-coding
mm_99978.1	chr11	114217706	114217748	+	1	NA	Intergenic	MER126|DNA|DNA	19469	NR_045930	73536	Mm.54275	NR_045930	ENSMUSG00000078600	1700092K14Rik	-	RIKEN cDNA 1700092K14 gene	ncRNA
mm_100518.1	chr11	120530751	120530764	+	1	NA	promoter-TSS (NM_008101)	promoter-TSS (NM_008101)	30	NM_008101	14527	Mm.22329	NM_008101	ENSMUSG00000025127	Gcgr	GR	glucagon receptor	protein-coding
mm_147670.1	chr18	60624305	60624351	-	1	NA	promoter-TSS (NM_177340)	promoter-TSS (NM_177340)	-23	NM_177340	104027	Mm.252321	NM_177340	ENSMUSG00000043079	Synpo	9030217H17Rik|9130229N11|9330140I15Rik|AW046661	synaptopodin	protein-coding
mm_62920.1	chr7	118592280	118592315	+	1	NA	promoter-TSS (NM_001331201)	promoter-TSS (NM_001331201)	-31	NM_001331201	381914	Mm.291232	NM_001331201	ENSMUSG00000109284	B230311B06Rik	Gm1695	RIKEN cDNA B230311B06 gene	protein-coding
mm_120483.1	chr14	65975804	65975824	+	1	NA	exon (NM_013492, exon 5 of 9)	exon (NM_013492, exon 5 of 9)	7331	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_151897.1	chr19	5799050	5799056	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	-3072	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_21279.1	chr2	156928686	156928702	-	1	NA	3' UTR (NM_180956, exon 17 of 17)	3' UTR (NM_180956, exon 17 of 17)	-41616	NM_029983	77799	Mm.29264	NM_029983	ENSMUSG00000027636	Sla2	A930009E21Rik|AI430952|SLAP-2|SLAP2	Src-like-adaptor 2	protein-coding
mm_95061.1	chr11	32455122	32455140	+	1	NA	promoter-TSS (NM_173784)	promoter-TSS (NM_173784)	-241	NM_173784	327900	Mm.260956	NM_173784	ENSMUSG00000044949	Ubtd2	4930571L24|9630054F20Rik|AI645720	ubiquitin domain containing 2	protein-coding
mm_44936.1	chr5	36398061	36398063	-	1	NA	promoter-TSS (NM_030889)	promoter-TSS (NM_030889)	77	NM_030889	81840	Mm.34113	NM_030889	ENSMUSG00000029093	Sorcs2	N28137|mKIAA1329	sortilin-related VPS10 domain containing receptor 2	protein-coding
mm_127266.1	chr15	99718963	99718965	+	1	NA	intron (NM_010271, intron 2 of 7)	intron (NM_010271, intron 2 of 7)	1371	NM_010271	14555	Mm.252391	NM_010271	ENSMUSG00000023019	Gpd1	AI747587|Gdc-1|Gdc1|mKIAA4010	glycerol-3-phosphate dehydrogenase 1 (soluble)	protein-coding
mm_159152.1	chr2	88768511	88768511	-	1	NA	promoter-TSS (NM_001005227)	promoter-TSS (NM_001005227)	-198	NM_001005227	257887	Mm.377285	NM_001005227	ENSMUSG00000075115	Olfr1200	MOR225-12	olfactory receptor 1200	protein-coding
mm_120422.1	chr14	65380719	65380736	+	1	NA	intron (NM_199029, intron 1 of 9)	intron (NM_199029, intron 1 of 9)	22051	NM_199029	380912	Mm.270087	NM_199029	ENSMUSG00000034522	Zfp395	BC053701|Gm910	zinc finger protein 395	protein-coding
mm_163134.1	chr11	78951187	78951192	+	1	NA	exon (NM_010927, exon 21 of 27)	exon (NM_010927, exon 21 of 27)	25898	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_15701.1	chr2	163890962	163890962	+	1	NA	intron (NM_183023, intron 1 of 5)	intron (NM_183023, intron 1 of 5)	27721	NM_183023	241770	Mm.330760	NM_183023	ENSMUSG00000035226	Rims4	6530406L02|Rim4	regulating synaptic membrane exocytosis 4	protein-coding
mm_162908.1	chr10	117941208	117941232	+	1	NA	intron (NR_045342, intron 3 of 3)	intron (NR_045342, intron 3 of 3)	15761	NR_045342	71067	Mm.410793	NR_045342		4933411E08Rik	-	RIKEN cDNA 4933411E08 gene	ncRNA
mm_110387.1	chr12	40445755	40445798	-	1	NA	promoter-TSS (NM_178845)	promoter-TSS (NM_178845)	14	NM_172575	246196	Mm.26852	NM_172575	ENSMUSG00000055917	Zfp277	2410017E24Rik|NIRF4	zinc finger protein 277	protein-coding
mm_114739.1	chr13	83738875	83738887	+	1	NA	promoter-TSS (NR_029545)	promoter-TSS (NR_029545)	67	NR_029545	723967		NR_029545	ENSMUSG00000065424	Mir9-2	Mirn9-2|mir-9-2|mmu-mir-9-2	microRNA 9-2	ncRNA
mm_66035.1	chr7	30636515	30636529	-	1	NA	promoter-TSS (NM_007959)	promoter-TSS (NM_007959)	-670	NM_007959	14008	Mm.4829	NM_007959	ENSMUSG00000006311	Etv2	Etsrp71	ets variant 2	protein-coding
mm_4945.1	chr1	191190094	191190136	+	1	NA	Intergenic	Intergenic	-6782	NM_007498	11910	Mm.2706	NM_007498	ENSMUSG00000026628	Atf3	LRG-21	activating transcription factor 3	protein-coding
mm_93668.1	chr10	117710074	117710087	-	1	NA	intron (NM_001288586, intron 1 of 10)	CpG-1528	678	NM_010786	17246	Mm.22670	NM_010786	ENSMUSG00000020184	Mdm2	1700007J15Rik|AA415488|Mdm-2	transformed mouse 3T3 cell double minute 2	protein-coding
mm_16618.1	chr2	5657396	5657407	-	1	NA	intron (NM_001290374, intron 1 of 9)	intron (NM_001290374, intron 1 of 9)	18645	NM_001290376	227541	Mm.191949	NM_177343	ENSMUSG00000039145	Camk1d	A630059D12Rik|CKLiK|CaMKIdelta|E030025C11Rik|mCKLiK	calcium/calmodulin-dependent protein kinase ID	protein-coding
mm_73587.1	chr8	109990431	109990447	+	1	NA	promoter-TSS (NM_146214)	promoter-TSS (NM_146214)	3	NM_146214	234724	Mm.28110	NM_146214	ENSMUSG00000001670	Tat	-	tyrosine aminotransferase	protein-coding
mm_114404.1	chr13	64161835	64161859	+	1	NA	promoter-TSS (NM_019986)	promoter-TSS (NM_019986)	-19	NM_019986	56541	Mm.40989	NM_019986	ENSMUSG00000021476	Habp4	4933413D03Rik|4933428J01Rik	hyaluronic acid binding protein 4	protein-coding
mm_146174.1	chr18	75367557	75367561	+	1	NA	5' UTR (NM_001042660, exon 1 of 4)	5' UTR (NM_001042660, exon 1 of 4)	194	NM_001042660	17131	Mm.34407	NM_008543	ENSMUSG00000025880	Smad7	Madh7	SMAD family member 7	protein-coding
mm_149855.1	chr19	25092447	25092457	+	1	NA	intron (NM_028785, intron 9 of 47)	intron (NM_028785, intron 9 of 47)	92923	NM_028785	76088	Mm.102485	NM_028785	ENSMUSG00000052085	Dock8	1200017A24Rik|5830472H07Rik|A130095G14Rik|AI461977	dedicator of cytokinesis 8	protein-coding
mm_134364.1	chr16	17096986	17097002	-	1	NA	intron (NM_001252444, intron 7 of 20)	intron (NM_001252444, intron 7 of 20)	14258	NM_001252445	66053	Mm.253614	NM_144954	ENSMUSG00000022771	Ppil2	0610009L05Rik|1700016N17Rik|4921520K19Rik|4930511F14Rik|AA589416|C130078A06Rik|CYC4	peptidylprolyl isomerase (cyclophilin)-like 2	protein-coding
mm_56168.1	chr6	87994208	87994214	-	1	NA	Intergenic	Intergenic	12528	NR_026990	434064	Mm.371796	NR_026990	ENSMUSG00000084950	Gm5577	EG434064	predicted gene 5577	ncRNA
mm_54215.1	chr6	25689902	25689915	-	1	NA	promoter-TSS (NM_010338)	promoter-TSS (NM_010338)	72	NM_010338	14763	Mm.409670	NM_010338	ENSMUSG00000039904	Gpr37	AI848630|Pael-R	G protein-coupled receptor 37	protein-coding
mm_92484.1	chr10	78297892	78297902	-	1	NA	intron (NM_053014, intron 2 of 9)	intron (NM_053014, intron 2 of 9)	42310	NR_106119	102465765		NR_106119	ENSMUSG00000098885	Mir7659	Gm27433|mmu-mir-7659	microRNA 7659	ncRNA
mm_120189.1	chr14	61598227	61598241	+	1	NA	promoter-TSS (NM_001164220)	promoter-TSS (NM_001164220)	8	NM_001164220	66597	Mm.491258	NM_023233	ENSMUSG00000035235	Trim13	3110001L12Rik|CAR|LEU5|RNF77|Rfp2	tripartite motif-containing 13	protein-coding
mm_96750.1	chr11	69895030	69895034	+	1	NA	intron (NM_153788, intron 1 of 21)	B1F|SINE|Alu	507	NM_153788	216859	Mm.288671	NM_153788	ENSMUSG00000001588	Acap1	Centb1	ArfGAP with coiled-coil, ankyrin repeat and PH domains 1	protein-coding
mm_103539.1	chr11	77506704	77506713	-	1	NA	3' UTR (NM_001004144, exon 20 of 20)	3' UTR (NM_001004144, exon 20 of 20)	6565	NM_001024920	216964	Mm.341211	NM_001024920	ENSMUSG00000044328	Trp53i13	2410019G02Rik|Tp53i13	transformation related protein 53 inducible protein 13	protein-coding
mm_84692.1	chr9	72393883	72393895	-	1	NA	Intergenic	Intergenic	-44640	NM_008613	17427	Mm.387671	NM_008613	ENSMUSG00000032221	Mns1	AW546487	meiosis-specific nuclear structural protein 1	protein-coding
mm_95114.1	chr11	34077267	34077288	+	1	NA	intron (NM_010696, intron 10 of 20)	intron (NM_010696, intron 10 of 20)	30076	NM_010696	16822	Mm.265350	NM_010696	ENSMUSG00000002699	Lcp2	AI323664|BB161688|SLP-76|SLP76|m1Khoe|twm	lymphocyte cytosolic protein 2	protein-coding
mm_48836.1	chr5	149244732	149244742	-	1	NA	Intergenic	Intergenic	-20267	NM_001308462	11690	Mm.19844	NM_009663	ENSMUSG00000060063	Alox5ap	Flap	arachidonate 5-lipoxygenase activating protein	protein-coding
mm_28931.1	chr3	98880674	98880693	-	1	NA	intron (NM_019545, intron 5 of 8)	intron (NM_019545, intron 5 of 8)	12547	NM_019545	56185	Mm.281874	NM_019545	ENSMUSG00000027870	Hao2	AI325478|Hao-2|Hao3|Haox3	hydroxyacid oxidase 2	protein-coding
mm_51114.1	chr6	67724881	67724886	+	1	NA	Intergenic	Intergenic	-159184	NR_003100	75070	Mm.463364	NR_003100		4930515G16Rik	-	myc induced nuclear antigen pseudogene	pseudo
mm_91865.1	chr10	59441870	59441880	-	1	NA	promoter-TSS (NM_010959)	promoter-TSS (NM_010959)	-96	NM_010959	18302	Mm.123013	NM_010959	ENSMUSG00000009654	Oit3	EF-9|LZP	oncoprotein induced transcript 3	protein-coding
mm_99006.1	chr11	98809812	98809864	+	1	NA	promoter-TSS (NM_138660)	promoter-TSS (NM_138660)	30	NM_138660	192160	Mm.40120	NM_138660	ENSMUSG00000078676	Casc3	Btz|Mln51	cancer susceptibility candidate 3	protein-coding
mm_43920.1	chr5	144768159	144768182	+	1	NA	promoter-TSS (NM_001081362)	promoter-TSS (NM_001081362)	-622	NM_001081362	100683	Mm.273570	NM_001081362	ENSMUSG00000045482	Trrap	AI481500	transformation/transcription domain-associated protein	protein-coding
mm_46830.1	chr5	113219634	113219642	-	1	NA	Intergenic	Intergenic	-7271	NM_001033428	333048	Mm.332586	NM_001033428	ENSMUSG00000066964	Tmem211	Gm854	transmembrane protein 211	protein-coding
mm_110431.1	chr12	46819245	46819249	-	1	NA	promoter-TSS (NM_021361)	promoter-TSS (NM_021361)	-472	NM_021361	664883	Mm.247195	NM_021361	ENSMUSG00000021047	Nova1	9430099M15Rik|G630039L02|Nova-1	neuro-oncological ventral antigen 1	protein-coding
mm_5130.1	chr1	9682207	9682208	-	1	NA	intron (NM_008651, intron 7 of 15)	PB1D10|SINE|Alu	18002	NM_001290397	17864	Mm.479	NM_008651	ENSMUSG00000025912	Mybl1	A-myb|G1-419-6|repro9	myeloblastosis oncogene-like 1	protein-coding
mm_26817.1	chr3	10301299	10301310	-	1	NA	promoter-TSS (NM_029310)	promoter-TSS (NM_029310)	-121	NM_029310	75497	Mm.47052	NM_029310	ENSMUSG00000027530	Fabp12	1700008G05Rik	fatty acid binding protein 12	protein-coding
mm_63609.1	chr7	128203398	128203404	+	1	NA	promoter-TSS (NR_045183)	promoter-TSS (NR_045183)	-73	NR_045183	70973	Mm.441564	NR_045183	ENSMUSG00000108354	4931431B13Rik	1700108I23Rik|AA536668	RIKEN cDNA 4931431B13 gene	ncRNA
mm_61760.1	chr7	82771642	82771679	+	1	NA	intron (NM_175317, intron 18 of 19)	intron (NM_175317, intron 18 of 19)	-16016	NR_046004	77800	Mm.444811	NR_046004	ENSMUSG00000086690	4933406J10Rik	A930009F24Rik	RIKEN cDNA 4933406J10 gene	ncRNA
mm_23584.1	chr3	63964832	63964841	+	1	NA	promoter-TSS (NM_001272035)	promoter-TSS (NM_001272035)	-103	NM_015728	11416	Mm.135619	NM_015728	ENSMUSG00000027822	Slc33a1	AI315656|AI788741|Acatn|D630022N01Rik	solute carrier family 33 (acetyl-CoA transporter), member 1	protein-coding
mm_24869.1	chr3	95951059	95951086	+	1	NA	Intergenic	CpG	21815	NM_023210	66471	Mm.218657	NM_023210	ENSMUSG00000015749	Anp32e	2810018A15Rik|AI047746|AI326868|CPD1|LANP-L|LANPL|mLANP-L	acidic (leucine-rich) nuclear phosphoprotein 32 family, member E	protein-coding
mm_156640.1	chrX	157598798	157598801	+	1	NA	promoter-TSS (NM_172307)	promoter-TSS (NM_172307)	-84	NM_172307	270669	Mm.37577	NM_172307	ENSMUSG00000046873	Mbtps2	9630032G22Rik|AI662535	membrane-bound transcription factor peptidase, site 2	protein-coding
mm_63110.1	chr7	122671145	122671158	+	1	NA	promoter-TSS (NM_019430)	promoter-TSS (NM_019430)	-593	NM_019430	54376	Mm.444212	NM_019430	ENSMUSG00000066189	Cacng3	-	calcium channel, voltage-dependent, gamma subunit 3	protein-coding
mm_15017.1	chr2	152626933	152626957	+	1	NA	promoter-TSS (NM_009047)	promoter-TSS (NM_009047)	-63	NM_009047	19700	Mm.8752	NM_009047	ENSMUSG00000000359	Rem1	E030011C07Rik|Ras|Rem	rad and gem related GTP binding protein 1	protein-coding
mm_6148.1	chr1	64928643	64928646	-	1	NA	intron (NM_001039493, intron 2 of 7)	intron (NM_001039493, intron 2 of 7)	28180	NM_001039493	241075	Mm.239534	NM_175509	ENSMUSG00000051344	Plekhm3	9430067K14Rik|A230102O09Rik|AI449570|DAPR|Plekhm1l	pleckstrin homology domain containing, family M, member 3	protein-coding
mm_92742.1	chr10	80954719	80954739	-	1	NA	intron (NM_001038655, intron 2 of 3)	intron (NM_001038655, intron 2 of 3)	24638	NM_008655	17873	Mm.1360	NM_008655	ENSMUSG00000015312	Gadd45b	AI323528|Myd118	growth arrest and DNA-damage-inducible 45 beta	protein-coding
mm_58923.1	chr7	17871760	17871771	+	1	NA	Intergenic	Intergenic	59083	NM_025957	67084	Mm.33709	NM_025957	ENSMUSG00000023185	Ceacam14	1600021E03Rik|1600025E09Rik|AV033953	carcinoembryonic antigen-related cell adhesion molecule 14	protein-coding
mm_110435.1	chr12	47833964	47833975	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	467493	NR_039586	100628593		NR_039586	ENSMUSG00000092981	Mir5125	mmu-mir-5125|mu-mir-5125	microRNA 5125	ncRNA
mm_97158.1	chr11	75468130	75468136	+	1	NA	promoter-TSS (NM_001291156)	promoter-TSS (NM_001291156)	83	NM_027249	380712	Mm.41393	NM_027249	ENSMUSG00000038217	Tlcd2	-	TLC domain containing 2	protein-coding
mm_23165.1	chr3	40745016	40745041	+	1	NA	promoter-TSS (NM_011020)	promoter-TSS (NM_011020)	-585	NM_011020	18415	Mm.39330	NM_011020	ENSMUSG00000025757	Hspa4l	94kDa|AI461691|APG-1|Osp94	heat shock protein 4 like	protein-coding
mm_53168.1	chr6	125342504	125342518	+	1	NA	intron (NM_011324, intron 7 of 11)	intron (NM_011324, intron 7 of 11)	-7212	NM_011609	21937	Mm.1258	NM_011609	ENSMUSG00000030341	Tnfrsf1a	CD120a|FPF|TNF-R|TNF-R-I|TNF-R1|TNF-R55|TNF-alphaR1|TNFAR|TNFR60|TNFRI|TNFRp55|TNFalpha-R1|Tnfr-2|Tnfr1|p55|p55-R	tumor necrosis factor receptor superfamily, member 1a	protein-coding
mm_6896.1	chr1	84696248	84696261	-	1	NA	promoter-TSS (NM_152915)	promoter-TSS (NM_152915)	-33	NM_152915	227325	Mm.292560	NM_152915	ENSMUSG00000036766	Dner	A930026D19Rik|BET|Bret	delta/notch-like EGF repeat containing	protein-coding
mm_160066.1	chr7	5095675	5095675	+	1	NA	exon (NM_001252454, exon 8 of 11)	exon (NM_001252454, exon 8 of 11)	15440	NM_001252454	13854	Mm.3091	NM_010147	ENSMUSG00000035203	Epn1	AA269831|Ibp1	epsin 1	protein-coding
mm_64961.1	chr7	16614671	16614711	-	1	NA	5' UTR (NM_172739, exon 1 of 7)	5' UTR (NM_172739, exon 1 of 7)	302	NM_172739	232906	Mm.28646	NM_172739	ENSMUSG00000058230	Arhgap35	6430596G11Rik|AI841135|Grlf1|mKIAA1722|p190A|p190RhoGAP	Rho GTPase activating protein 35	protein-coding
mm_73251.1	chr8	104322325	104322367	+	1	NA	5' UTR (NM_028524, exon 1 of 4)	5' UTR (NM_028524, exon 1 of 4)	119	NM_028524	75502	Mm.232593	NM_028524	ENSMUSG00000035785	Cmtm2b	1700013O04Rik|Cklfsf22|Cklfsf2b	CKLF-like MARVEL transmembrane domain containing 2B	protein-coding
mm_115356.1	chr13	112800879	112800903	+	1	NA	5' UTR (NM_008903, exon 1 of 6)	5' UTR (NM_008903, exon 1 of 6)	114	NM_008247	19012	Mm.291029	NM_008247	ENSMUSG00000021759	Plpp1	Hic53|Hpic53|LPP-1|LPP1|PAP-2a|PAP2-alpha|PAP2a|Ppap2a|mPAP	phospholipid phosphatase 1	protein-coding
mm_71750.1	chr8	65618030	65618091	+	1	NA	promoter-TSS (NM_001293784)	promoter-TSS (NM_001293784)	20	NM_001166372	72925	Mm.380457	NM_175188	ENSMUSG00000036469	March1	2900024D24Rik|BB085186	membrane-associated ring finger (C3HC4) 1	protein-coding
mm_8337.1	chr1	150101266	150101318	-	1	NA	exon (NM_011198, exon 3 of 10)	exon (NM_011198, exon 3 of 10)	1261	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_49668.1	chr6	31237264	31237283	+	1	NA	intron (NR_040260, intron 1 of 5)	(TC)n|Simple_repeat|Simple_repeat	16922	NR_040261	73652	Mm.441297	NR_040257	ENSMUSG00000087380	2210408F21Rik	-	RIKEN cDNA 2210408F21 gene	ncRNA
mm_136781.1	chr17	10496332	10496342	+	1	NA	intron (NM_027032, intron 4 of 4)	intron (NM_027032, intron 4 of 4)	40121	NR_077238	319750	Mm.383485	NR_077237	ENSMUSG00000089633	A230009B12Rik	-	RIKEN cDNA A230009B12 gene	ncRNA
mm_22102.1	chr2	169405436	169405473	-	1	NA	Intergenic	Intergenic	-228192	NM_080455	228911	Mm.315789	NM_080455	ENSMUSG00000047907	Tshz2	2900073F20Rik|B830045G17|Mtsh2|Sdccag33l|Tsh2|Zfp218|mKIAA4248|teashirt2	teashirt zinc finger family member 2	protein-coding
mm_39172.1	chr4	155704961	155704980	-	1	NA	5' UTR (NM_026899, exon 1 of 5)	5' UTR (NM_026899, exon 1 of 5)	155	NM_026899	68991	Mm.294770	NM_026899	ENSMUSG00000029038	Ssu72	1190002E22Rik|1500011L16Rik|2610101M12Rik	Ssu72 RNA polymerase II CTD phosphatase homolog (yeast)	protein-coding
mm_25613.1	chr3	118430417	118430477	+	1	NA	Intergenic	Intergenic	-3410	NR_029551	387155		NR_029551	ENSMUSG00000065569	Mir137	Mirn137|mir-137|mmu-mir-137	microRNA 137	ncRNA
mm_118583.1	chr14	20294707	20294745	+	1	NA	promoter-TSS (NM_026341)	promoter-TSS (NM_026341)	36	NM_026341	67725	Mm.317636	NM_026341	ENSMUSG00000021809	Nudt13	4933433B15Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 13	protein-coding
mm_137236.1	chr17	24425492	24425526	+	1	NA	3' UTR (NM_001080128, exon 7 of 7)	3' UTR (NM_001080128, exon 7 of 7)	-1174	NM_010023	13177	Mm.291743	NM_010023	ENSMUSG00000024132	Eci1	Dci|eci	enoyl-Coenzyme A delta isomerase 1	protein-coding
mm_142398.1	chr17	45433540	45433561	-	1	NA	promoter-TSS (NR_130961)	promoter-TSS (NR_130961)	157	NM_152810	71702	Mm.28270	NM_152810	ENSMUSG00000023932	Cdc5l	1200002I02Rik|AA408004|PCDC5RP	cell division cycle 5-like (S. pombe)	protein-coding
mm_24994.1	chr3	97159048	97159064	+	1	NA	5' UTR (NM_019800, exon 1 of 10)	5' UTR (NM_019800, exon 1 of 10)	279	NM_019800	66659	Mm.101368	NM_019800	ENSMUSG00000028093	Acp6	5730559A09Rik|ACPL1|AU022842|mPACPL1	acid phosphatase 6, lysophosphatidic	protein-coding
mm_56566.1	chr6	101378003	101378016	-	1	NA	promoter-TSS (NM_018884)	promoter-TSS (NM_018884)	-112	NM_018884	55983	Mm.321654	NM_018884	ENSMUSG00000035357	Pdzrn3	1110020C07Rik|AI429718|AL023082|LNX3|SEMACAP3|Semcap3	PDZ domain containing RING finger 3	protein-coding
mm_132493.1	chr16	36935033	36935050	+	1	NA	promoter-TSS (NM_008225)	promoter-TSS (NM_008225)	58	NM_008225	15163	Mm.4091	NM_008225	ENSMUSG00000022831	Hcls1	AW213261|HS1	hematopoietic cell specific Lyn substrate 1	protein-coding
mm_42060.1	chr5	108704567	108704596	+	1	NA	intron (NM_054071, intron 3 of 6)	intron (NM_054071, intron 3 of 6)	10352	NM_054071	116701	Mm.35691	NM_054071	ENSMUSG00000008090	Fgfrl1	FGFR5|FGFR5beta|FGFR5gamma	fibroblast growth factor receptor-like 1	protein-coding
mm_117835.1	chr13	98637331	98637350	-	1	NA	promoter-TSS (NM_026685)	promoter-TSS (NM_026685)	70	NM_026685	68344	Mm.28766	NM_026685	ENSMUSG00000046082	Tmem174	0610009B10Rik|AA986094	transmembrane protein 174	protein-coding
mm_57953.1	chr6	135138737	135138740	-	1	NA	intron (NM_013546, intron 3 of 3)	intron (NM_013546, intron 3 of 3)	-20455	NM_001205396	93746	Mm.49902	NM_053118	ENSMUSG00000030205	Gprc5d	-	G protein-coupled receptor, family C, group 5, member D	protein-coding
mm_146876.1	chr18	25479512	25479522	-	1	NA	3' UTR (NM_001146294, exon 13 of 13)	3' UTR (NM_001146294, exon 13 of 13)	274466	NM_133195	108013	Mm.266435	NM_133195	ENSMUSG00000024268	Celf4	A230070D14Rik|BRUNOL-4|Brul4|Brunol4|C130060B05Rik	CUGBP, Elav-like family member 4	protein-coding
mm_32183.1	chr4	101002977	101003006	+	1	NA	exon (NM_198037, exon 27 of 27)	exon (NM_198037, exon 27 of 27)	-66047	NM_183024	242570	Mm.185636	NM_183024	ENSMUSG00000035275	Raver2	A430091O22Rik	ribonucleoprotein, PTB-binding 2	protein-coding
mm_20560.1	chr2	131074501	131074518	-	1	NA	exon (NM_011426, exon 14 of 21)	exon (NM_011426, exon 14 of 21)	-10695	NM_001163529	110751	Mm.108550	NM_033615	ENSMUSG00000027318	Adam33	Adaml	a disintegrin and metallopeptidase domain 33	protein-coding
mm_155567.1	chrX	76385332	76385339	+	1	NA	Intergenic	Intergenic	-8015	NM_001033799	619294	Mm.423961	NM_001033799	ENSMUSG00000073085	Cldn34b4	4930428D18Rik	claudin 34B4	protein-coding
mm_8149.1	chr1	136580555	136580562	-	1	NA	Intergenic	Intergenic	-44343	NM_177643	226442	Mm.62521	NM_177643	ENSMUSG00000041483	Zfp281	Znf281	zinc finger protein 281	protein-coding
mm_25374.1	chr3	107211339	107211374	+	1	NA	TTS (NM_001111143)	TTS (NM_001111143)	10376	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_48136.1	chr5	137150244	137150257	-	1	NA	Intergenic	(TGG)n|Simple_repeat|Simple_repeat	-34043	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_90328.1	chr10	127078923	127078946	+	1	NA	promoter-TSS (NM_001301014)	promoter-TSS (NM_001301014)	27	NM_001033263	216439	Mm.336761	NM_001033263	ENSMUSG00000025422	Agap2	AGAP-2|Centg1|PIKE|cnt-g1|mKIAA0167	ArfGAP with GTPase domain, ankyrin repeat and PH domain 2	protein-coding
mm_46842.1	chr5	113347651	113347657	-	1	NA	Intergenic	Intergenic	-9640	NM_001012726	503692	Mm.348794	NM_001012726	ENSMUSG00000053873	Aym1	-	activator of yeast meiotic promoters 1	protein-coding
mm_165987.1	chr4	108101512	108101516	+	1	NA	intron (NM_011327, intron 5 of 15)	RSINE1|SINE|B4	14157	NR_105823	102465213		NR_105823	ENSMUSG00000098980	Mir6397	Gm28004|mmu-mir-6397	microRNA 6397	ncRNA
mm_56384.1	chr6	94654618	94654622	-	1	NA	intron (NM_008377, intron 3 of 18)	intron (NM_008377, intron 3 of 18)	45525	NM_008377	16206	Mm.245210	NM_008377	ENSMUSG00000030029	Lrig1	D6Bwg0781e|Img|LIG-1	leucine-rich repeats and immunoglobulin-like domains 1	protein-coding
mm_26246.1	chr3	141527700	141527702	+	1	NA	intron (NM_001293561, intron 1 of 16)	intron (NM_001293561, intron 1 of 16)	62137	NM_001293561	22253	Mm.24430	NM_009472	ENSMUSG00000059921	Unc5c	B130051O18Rik|Unc5h3|rcm	unc-5 netrin receptor C	protein-coding
mm_12576.1	chr2	73271948	73271959	+	1	NA	promoter-TSS (NM_001005343)	promoter-TSS (NM_001005343)	27	NM_001005343	381373	Mm.330293	NM_001005343	ENSMUSG00000068859	Sp9	-	trans-acting transcription factor 9	protein-coding
mm_7802.1	chr1	131525592	131525618	-	1	NA	intron (NM_001081011, intron 1 of 22)	intron (NM_001081011, intron 1 of 22)	1756	NM_001081011	14270	Mm.276259	NM_019520	ENSMUSG00000026425	Srgap2	9930124L22Rik|AI448945|FBP2|Fnbp2|srGAP3	SLIT-ROBO Rho GTPase activating protein 2	protein-coding
mm_148321.1	chr18	83828094	83828114	-	1	NA	Intergenic	Intergenic	258458	NM_001081300	110796	Mm.102136	NM_001081300	ENSMUSG00000046982	Tshz1	5730407I04Rik|D18Bwg1409e|Mtsh1|NY-CO-33|Sdccag33|Tsh1|mKIAA4206|teashirt1	teashirt zinc finger family member 1	protein-coding
mm_30223.1	chr3	145099025	145099075	-	1	NA	promoter-TSS (NM_178697)	promoter-TSS (NM_178697)	56	NM_178697	229933	Mm.331420	NM_178697	ENSMUSG00000036960	Clca2	4732440A06|AI586120|Clca5	chloride channel accessory 2	protein-coding
mm_91189.1	chr10	21127708	21127708	-	1	NA	intron (NM_010848, intron 14 of 14)	intron (NM_010848, intron 14 of 14)	33276	NM_001198914	17863	Mm.52109	NM_010848	ENSMUSG00000019982	Myb	AI550390|M16449|c-myb	myeloblastosis oncogene	protein-coding
mm_38455.1	chr4	140581501	140581529	-	1	NA	intron (NM_001290803, intron 9 of 28)	intron (NM_001290803, intron 9 of 28)	67241	NM_001112723	72754	Mm.29329	NM_172415	ENSMUSG00000040964	Arhgef10l	2810441C07Rik	Rho guanine nucleotide exchange factor (GEF) 10-like	protein-coding
mm_66754.1	chr7	46712698	46712737	-	1	NA	exon (NM_011315, exon 3 of 4)	exon (NM_011315, exon 3 of 4)	-2066	NM_030233	78935	Mm.289866	NM_030233	ENSMUSG00000006763	Saal1	5031425D22Rik|SPACIA1	serum amyloid A-like 1	protein-coding
mm_172475.1	chr7	45333814	45333814	-	1	NA	promoter-TSS (NM_175130)	promoter-TSS (NM_175130)	-34	NM_175130	68667	Mm.439890	NM_175130	ENSMUSG00000038260	Trpm4	1110030C19Rik|AW047689|LTRPC4|LTrpC-4|TRPM4B	transient receptor potential cation channel, subfamily M, member 4	protein-coding
mm_111067.1	chr12	80115481	80115494	-	1	NA	Intergenic	Intergenic	-2474	NM_007564	12192	Mm.235132	NM_007564	ENSMUSG00000021127	Zfp36l1	AW742437|AW743212|Berg36|Brf1|D530020L18Rik|ERF1|TIS11b|cMG1	zinc finger protein 36, C3H type-like 1	protein-coding
mm_170565.1	chr19	46962336	46962337	-	1	NA	promoter-TSS (NM_029810)	promoter-TSS (NM_029810)	15	NM_029810	76952	Mm.40965	NM_029810	ENSMUSG00000025041	Nt5c2	2010002I23Rik|CnII|ENSMUSG00000025039|Gm9751|Gmp|Nt5b|Pnt5|cN-II	5'-nucleotidase, cytosolic II	protein-coding
mm_141759.1	chr17	34264995	34265015	-	1	NA	exon (NM_207105, exon 2 of 6)	exon (NM_207105, exon 2 of 6)	1778	NM_207105	14961	Mm.254067	NM_207105	ENSMUSG00000073421	H2-Ab1	AI845868|Abeta|H-2Ab|H2-Ab|I-Abeta|IAb|Ia-2|Ia2|Rmcs1	histocompatibility 2, class II antigen A, beta 1	protein-coding
mm_39395.1	chr5	14025339	14025373	+	1	NA	promoter-TSS (NM_011348)	promoter-TSS (NM_011348)	80	NM_011348	20349	Mm.134093	NM_011348	ENSMUSG00000063531	Sema3e	6430702L12|AA408817|Semah|mKIAA0331	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	protein-coding
mm_61507.1	chr7	78719369	78719379	+	1	NA	Intergenic	Tigger15a|DNA|TcMar-Tigger	-1154	NR_015542	414121	Mm.482537	NR_015542	ENSMUSG00000059146	E430016F16Rik	-	RIKEN cDNA E430016F16 gene	ncRNA
mm_110866.1	chr12	73546422	73546449	-	1	NA	promoter-TSS (NM_178715)	promoter-TSS (NM_178715)	-40	NM_178715	238257	Mm.251196	NM_178715	ENSMUSG00000034435	Tmem30b	9130011B11Rik	transmembrane protein 30B	protein-coding
mm_126401.1	chr15	80235496	80235517	+	1	NA	intron (NM_178719, intron 1 of 5)	MIRc|SINE|MIR	1426	NM_178719	239555	Mm.307163	NM_178719	ENSMUSG00000022412	Mief1	A230016E22|AI452372|Smcr7l	mitochondrial elongation factor 1	protein-coding
mm_21972.1	chr2	167339387	167339392	-	1	NA	intron (NM_019835, intron 1 of 8)	intron (NM_019835, intron 1 of 8)	9789	NM_019835	56336	Mm.200886	NM_019835	ENSMUSG00000017929	B4galt5	9430078I07Rik|AW049941|AW539721	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 5	protein-coding
mm_53413.1	chr6	133105200	133105208	+	1	NA	promoter-TSS (NM_001163445)	promoter-TSS (NM_001163445)	-35	NM_001271583	381820	Mm.291762	NM_001163445	ENSMUSG00000072704	Smim10l1	2700089E24Rik|AI662692	small integral membrane protein 10 like 1	protein-coding
mm_160101.1	chr7	18821484	18821484	-	1	NA	5' UTR (NM_007677, exon 1 of 5)	5' UTR (NM_007677, exon 1 of 5)	107	NM_007677	26437	Mm.302844	NM_007677	ENSMUSG00000004540	Psg17	Cea-2|Cea2|mmCGM5	pregnancy specific glycoprotein 17	protein-coding
mm_107480.1	chr12	37880880	37880899	+	1	NA	5' UTR (NM_178681, exon 1 of 25)	5' UTR (NM_178681, exon 1 of 25)	184	NM_178681	217480	Mm.126525	NM_178681	ENSMUSG00000036095	Dgkb	6430574F24|90kda|C630029D13Rik|DAGK2|DGK|DGK-beta|mKIAA0718	diacylglycerol kinase, beta	protein-coding
mm_72760.1	chr8	85492701	85492709	+	1	NA	promoter-TSS (NM_173866)	promoter-TSS (NM_173866)	88	NM_173866	108682	Mm.200423	NM_173866	ENSMUSG00000031700	Gpt2	4631422C05Rik|ALT2|AU014768|AU041193|C87201	glutamic pyruvate transaminase (alanine aminotransferase) 2	protein-coding
mm_113084.1	chr13	23839599	23839620	+	1	NA	5' UTR (NM_001164743, exon 1 of 12)	5' UTR (NM_001164743, exon 1 of 12)	175	NM_134069	105355	Mm.27038	NM_134069	ENSMUSG00000036083	Slc17a3	AW261723|Npt4	solute carrier family 17 (sodium phosphate), member 3	protein-coding
mm_108783.1	chr12	90239264	90239267	+	1	NA	intron (NM_001252074, intron 5 of 6)	intron (NM_001252074, intron 5 of 6)	426782	NM_001252074	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding
mm_59342.1	chr7	25476386	25476402	+	1	NA	exon (NM_001039186, exon 2 of 8)	exon (NM_001039186, exon 2 of 8)	1231	NM_001039185	26365	Mm.322502	NM_011926	ENSMUSG00000074272	Ceacam1	Bgp|Bgp1|C-CAM|CD66a|Cc1|Cea-1|Cea-7|Cea1|Cea7|Hv-2|Hv2|MHVR|MHVR1|Mhv-1|bb-1|mCEA1|mmCGM1|mmCGM1a|mmCGM2	carcinoembryonic antigen-related cell adhesion molecule 1	protein-coding
mm_110605.1	chr12	56536609	56536621	-	1	NA	5' UTR (NM_009385, exon 1 of 3)	5' UTR (NM_009385, exon 1 of 3)	293	NM_009385	21869	Mm.89972	NM_009385	ENSMUSG00000001496	Nkx2-1	AV026640|Nkx2.1|T/EBP|Titf1|Ttf-1	NK2 homeobox 1	protein-coding
mm_140289.1	chr17	85465490	85465522	+	1	NA	Intergenic	Intergenic	152890	NR_038084	100043902	Mm.150838	NR_015385	ENSMUSG00000093460	Six3os1	D17Mgi26|E130112H22Rik|Rncr1|Six3os	SIX homeobox 3, opposite strand 1	ncRNA
mm_129005.1	chr15	74878387	74878387	-	1	NA	TTS (NM_025929)	TTS (NM_025929)	3317	NM_025929	67038	Mm.154566	NM_025929	ENSMUSG00000063522	2010109I03Rik	Ly6m	RIKEN cDNA 2010109I03 gene	protein-coding
mm_121876.1	chr14	21050719	21050722	-	1	NA	intron (NM_018829, intron 1 of 8)	intron (NM_018829, intron 1 of 8)	1722	NM_018829	55946	Mm.376269	NM_018829	ENSMUSG00000021824	Ap3m1	1200013D09Rik|C78982|R75378	adaptor-related protein complex 3, mu 1 subunit	protein-coding
mm_152909.1	chr19	27257416	27257418	-	1	NA	Intergenic	Intergenic	40397	NM_001161420	22359	Mm.4141	NM_013703	ENSMUSG00000024924	Vldlr	AA408956|AI451093|AW047288	very low density lipoprotein receptor	protein-coding
mm_158863.1	chrY	2174799	2174799	+	1	NA	Intergenic	Intergenic	-4390	NM_009571	22768	Mm.411381	NM_009571	ENSMUSG00000000103	Zfy2	Zfy-2	zinc finger protein 2, Y-linked	protein-coding
mm_42781.1	chr5	121399826	121399869	+	1	NA	intron (NM_172722, intron 1 of 23)	RSINE1|SINE|B4	1865	NM_172722	231713	Mm.33919	NM_172722	ENSMUSG00000042719	Naa25	4833422K13Rik|A630046C11|AI450868|C330023M02Rik|Mdm20	N(alpha)-acetyltransferase 25, NatB auxiliary subunit	protein-coding
mm_66647.1	chr7	45666339	45666347	-	1	NA	promoter-TSS (NM_001271993)	promoter-TSS (NM_001271993)	51	NM_018876	14344	Mm.290046	NM_018876	ENSMUSG00000055978	Fut2	-	fucosyltransferase 2	protein-coding
mm_12463.1	chr2	71356649	71356652	+	1	NA	intron (NM_172436, intron 2 of 17)	intron (NM_172436, intron 2 of 17)	10904	NM_172436	78830	Mm.30928	NM_172436	ENSMUSG00000027010	Slc25a12	2610002D09Rik|AI839531|B230107K20Rik|BB129864	solute carrier family 25 (mitochondrial carrier, Aralar), member 12	protein-coding
mm_104020.1	chr11	85769128	85769138	-	1	NA	intron (NR_046194, intron 1 of 2)	B1F1|SINE|Alu	6547	NR_046194	78420	Mm.488197	NR_046194	ENSMUSG00000085514	Bcas3os2	9530048J24Rik	breast carcinoma amplified sequence 3 opposite strand 2	ncRNA
mm_55297.1	chr6	54760229	54760237	-	1	NA	Intergenic	Intergenic	-56683	NM_199143	387524	Mm.286149	NM_199143	ENSMUSG00000058446	Znrf2	1190002C14Rik|AU044205|D6Ertd365e	zinc and ring finger 2	protein-coding
mm_23730.1	chr3	69027679	69027685	+	1	NA	exon (NM_133786, exon 14 of 24)	exon (NM_133786, exon 14 of 24)	17060	NM_025863	66949	Mm.176695	NM_025863	ENSMUSG00000034317	Trim59	2310035M22Rik|2700022F13Rik|Mrf1|TSBF1	tripartite motif-containing 59	protein-coding
mm_61340.1	chr7	68279204	68279209	+	1	NA	intron (NM_001013811, intron 1 of 8)	intron (NM_001013811, intron 1 of 8)	-2612	NR_040340	100504026	Mm.426764	NR_040340	ENSMUSG00000086628	Gm16157	OTTMUSG00000031023	predicted gene 16157	ncRNA
mm_151555.1	chr19	59459106	59459138	+	1	NA	promoter-TSS (NR_002863)	promoter-TSS (NR_002863)	432	NM_010132	13797	Mm.245394	NM_010132	ENSMUSG00000043969	Emx2	Pdo	empty spiracles homeobox 2	protein-coding
mm_78993.1	chr9	45403197	45403210	+	1	NA	promoter-TSS (NM_052823)	promoter-TSS (NM_052823)	65	NM_052823	11936	Mm.22742	NM_007503	ENSMUSG00000059412	Fxyd2	Atp1g1	FXYD domain-containing ion transport regulator 2	protein-coding
mm_39806.1	chr5	30623838	30623844	+	1	NA	3' UTR (NM_010608, exon 2 of 2)	3' UTR (NM_010608, exon 2 of 2)	-24095	NR_049199	100885838		NR_049199	ENSMUSG00000093710	Mir5625	Gm23930|mmu-mir-5625	microRNA 5625	ncRNA
mm_168519.1	chr11	58199647	58199647	+	1	NA	promoter-TSS (NM_018738)	promoter-TSS (NM_018738)	91	NM_018738	16145	Mm.33902	NM_018738	ENSMUSG00000078853	Igtp	AW558444|Irgm3	interferon gamma induced GTPase	protein-coding
mm_31658.1	chr4	59884638	59884642	+	1	NA	intron (NM_172468, intron 4 of 8)	intron (NM_172468, intron 4 of 8)	30416	NM_021053	30936	Mm.284433	NM_021053	ENSMUSG00000028386	Slc46a2	5430429N04Rik|Ly110|TSO-1C12|Tscot	solute carrier family 46, member 2	protein-coding
mm_100187.1	chr11	116678255	116678255	+	1	NA	intron (NM_009180, intron 8 of 8)	intron (NM_009180, intron 8 of 8)	3658	NR_028570	100216538		NR_028570	ENSMUSG00000065094	Snord1a	snR38	small nucleolar RNA, C/D box 1A	snoRNA
mm_119563.1	chr14	48878879	48878891	+	1	NA	promoter-TSS (NR_033783)	promoter-TSS (NR_033783)	12	NR_033783	66770	Mm.136954	NR_033783		4933429O19Rik	1700031B11Rik	RIKEN cDNA 4933429O19 gene	ncRNA
mm_43582.1	chr5	137746886	137746917	+	1	NA	5' UTR (NM_023910, exon 2 of 5)	5' UTR (NM_023910, exon 2 of 5)	932	NM_029805	78829	Mm.286399	NM_023910	ENSMUSG00000029723	Tsc22d4	0610009M14Rik|1700023B23Rik|AI415410|Thg-1pit|Tilz2	TSC22 domain family, member 4	protein-coding
mm_27663.1	chr3	65302756	65302765	-	1	NA	promoter-TSS (NR_126080)	promoter-TSS (NR_126080)	-75	NR_126080	102637797	Mm.446731	NR_126080	ENSMUSG00000104093	A330015K06Rik	-	RIKEN cDNA A330015K06 gene	ncRNA
mm_38775.1	chr4	148038553	148038567	-	1	NA	promoter-TSS (NM_010840)	promoter-TSS (NM_010840)	253	NM_011929	26372	Mm.89987	NM_011929	ENSMUSG00000029016	Clcn6	AI850629|Clc6	chloride channel, voltage-sensitive 6	protein-coding
mm_112758.1	chr13	19345957	19345967	+	1	NA	Intergenic	Intergenic	49851	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_54846.1	chr6	42587178	42587183	-	1	NA	TTS (NM_203396)	TTS (NM_203396)	10192	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_81259.1	chr9	107997988	107997999	+	1	NA	Intergenic	Intergenic	-4655	NM_013785	27399	Mm.276155	NM_013785	ENSMUSG00000032594	Ip6k1	1200016D08Rik|AU022776|Ihpk1|InsP6|InsP6k1|Itpk6	inositol hexaphosphate kinase 1	protein-coding
mm_164517.1	chr16	96434581	96434585	-	1	NA	intron (NM_008405, intron 6 of 15)	intron (NM_008405, intron 6 of 15)	9031	NM_008405	16415	Mm.12872	NM_008405	ENSMUSG00000000157	Itgb2l	5033406G21Rik|pactolus	integrin beta 2-like	protein-coding
mm_25425.1	chr3	107877106	107877123	+	1	NA	promoter-TSS (NM_133867)	promoter-TSS (NM_133867)	-116	NM_133867	99662	Mm.108491	NM_133867	ENSMUSG00000040600	Eps8l3	AI504489|Eps8r3	EPS8-like 3	protein-coding
mm_89673.1	chr10	97507754	97507769	+	1	NA	exon (NM_007833, exon 5 of 8)	exon (NM_007833, exon 5 of 8)	25430	NM_007833	13179	Mm.56769	NM_007833	ENSMUSG00000019929	Dcn	DC|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding
mm_72120.1	chr8	71686789	71686808	+	1	NA	intron (NM_010589, intron 21 of 24)	intron (NM_010589, intron 21 of 24)	-2454	NM_013564	16336	Mm.476857	NM_013564	ENSMUSG00000079019	Insl3	Rlf|Rlnl	insulin-like 3	protein-coding
mm_135088.1	chr16	34542163	34542166	-	1	NA	Intergenic	Intergenic	-28137	NM_177357	545156	Mm.82274	NM_177357	ENSMUSG00000061751	Kalrn	2210407G14Rik|AV235988|DUET|E530005C20Rik|Gm539|Hapip|TRAD	kalirin, RhoGEF kinase	protein-coding
mm_76676.1	chr8	93813497	93813574	-	1	NA	promoter-TSS (NR_026888)	promoter-TSS (NR_026888)	20	NR_026888	75809	Mm.443272	NM_029449		4930488L21Rik	4930452J22Rik	RIKEN cDNA 4930488L21 gene	ncRNA
mm_156104.1	chrX	113724325	113724349	+	1	NA	exon (NM_001142570, exon 5 of 12)	exon (NM_001142570, exon 5 of 12)	426081	NM_001142570	93837	Mm.79760	NM_033605	ENSMUSG00000025592	Dach2	9430028N04Rik	dachshund 2 (Drosophila)	protein-coding
mm_156866.1	chrX	164438040	164438052	+	1	NA	5' UTR (NM_026853, exon 2 of 8)	5' UTR (NM_026853, exon 2 of 8)	1052	NM_001313737	68854	Mm.33225	NM_026853	ENSMUSG00000031382	Asb11	1110067L12Rik|1600009D24Rik	ankyrin repeat and SOCS box-containing 11	protein-coding
mm_16264.1	chr2	173522623	173522635	+	1	NA	promoter-TSS (NM_028158)	promoter-TSS (NM_028158)	37	NM_028158	72221	Mm.46132	NM_028158	ENSMUSG00000027518	1700021F07Rik	-	RIKEN cDNA 1700021F07 gene	protein-coding
mm_58155.1	chr6	142387036	142387092	-	1	NA	promoter-TSS (NM_001204907)	promoter-TSS (NM_001204907)	23	NM_001204906	19691	Mm.27407	NM_023042	ENSMUSG00000030243	Recql	RecQ1	RecQ protein-like	protein-coding
mm_172248.1	chr6	69417477	69417481	-	1	NA	Intergenic	Intergenic	-90305	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_93472.1	chr10	111171380	111171382	-	1	NA	intron (NM_175489, intron 1 of 23)	intron (NM_175489, intron 1 of 23)	6579	NM_175489	237542	Mm.220204	NM_175489	ENSMUSG00000020189	Osbpl8	AA536976|AA536995|C730029P18Rik|D330025H14Rik|ORP-8	oxysterol binding protein-like 8	protein-coding
mm_111511.1	chr12	99610279	99610303	-	1	NA	intron (NR_136760, intron 2 of 3)	intron (NR_136760, intron 2 of 3)	17683	NR_045288	73457	Mm.383439	NR_045288	ENSMUSG00000100211	1700064M15Rik	-	RIKEN cDNA 1700064M15 gene	ncRNA
mm_45277.1	chr5	64865455	64865504	-	1	NA	Intergenic	Intergenic	61956	NM_008453	16599	Mm.392759	NM_008453	ENSMUSG00000029178	Klf3	9930027G08Rik|AL024007|Bklf|Tef-2	Kruppel-like factor 3 (basic)	protein-coding
mm_162234.1	chrX	152240068	152240068	+	1	NA	exon (NM_013668, exon 4 of 26)	exon (NM_013668, exon 4 of 26)	6841	NM_013668	20591	Mm.142655	NM_013668	ENSMUSG00000025332	Kdm5c	D930009K15Rik|Jarid1c|Smcx|mKIAA0234	lysine (K)-specific demethylase 5C	protein-coding
mm_33530.1	chr4	130932350	130932356	+	1	NA	intron (NM_010686, intron 7 of 7)	RMER1C|Other|Other	-12032	NM_010769	17180	Mm.271796	NM_010769	ENSMUSG00000040533	Matn1	CMP|Crtm|Mat1|matrilin-1	matrilin 1, cartilage matrix protein	protein-coding
mm_168516.1	chr11	57449086	57449110	+	1	NA	Intergenic	Intergenic	69546	NM_001168667	67726	Mm.25632	NM_026342	ENSMUSG00000020523	Fam114a2	1810073G14Rik|9030624B09Rik	family with sequence similarity 114, member A2	protein-coding
mm_96137.1	chr11	60931999	60932038	+	1	NA	promoter-TSS (NR_027800)	promoter-TSS (NR_027800)	-39	NM_008928	26397	Mm.18494	NM_008928	ENSMUSG00000018932	Map2k3	AW212142|MEK3|MKK3|Prkmk3|mMKK3b	mitogen-activated protein kinase kinase 3	protein-coding
mm_98897.1	chr11	97995051	97995058	+	1	NA	intron (NM_207231, intron 2 of 5)	intron (NM_207231, intron 2 of 5)	1119	NM_207231	217151	Mm.277896	NM_207231	ENSMUSG00000038352	Arl5c	Arl12|BC065791	ADP-ribosylation factor-like 5C	protein-coding
mm_116740.1	chr13	51763385	51763398	-	1	NA	intron (NM_013660, intron 1 of 15)	intron (NM_013660, intron 1 of 15)	30356	NM_001281880	20354	Mm.33903	NM_013660	ENSMUSG00000021451	Sema4d	CD100|Semacl2|Semaj|Semcl2|coll-4	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D	protein-coding
mm_35308.1	chr4	25242826	25242830	-	1	NA	promoter-TSS (NM_021318)	promoter-TSS (NM_021318)	48	NM_021318	57756	Mm.87325	NM_021318	ENSMUSG00000028259	Fhl5	1700027G07Rik|Act	four and a half LIM domains 5	protein-coding
mm_124806.1	chr15	8832322	8832333	+	1	NA	Intergenic	Intergenic	-121520	NM_148938	20512	Mm.204834	NM_148938	ENSMUSG00000005360	Slc1a3	AI504299|B430115D02Rik|Eaat1|GLAST|GLAST-1|GLU-T|GluT-1|Gmt1|MGluT1	solute carrier family 1 (glial high affinity glutamate transporter), member 3	protein-coding
mm_141417.1	chr17	29430544	29430551	-	1	NA	Intergenic	Intergenic	-60498	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_21067.1	chr2	152806076	152806100	-	1	NA	intron (NM_001289717, intron 2 of 2)	L2a|LINE|L2	24629	NM_001289716	12048	Mm.238213	NM_009743	ENSMUSG00000007659	Bcl2l1	Bcl(X)L|Bcl-XL|Bcl2l|BclX|bcl-x|bcl2-L-1	BCL2-like 1	protein-coding
mm_164328.1	chr16	7070017	7070023	+	1	NA	exon (NM_183188, exon 1 of 13)	exon (NM_183188, exon 1 of 13)	185	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_115281.1	chr13	111807761	111807778	+	1	NA	intron (NM_011945, intron 1 of 19)	intron (NM_011945, intron 1 of 19)	1214	NM_011945	26401	Mm.15918	NM_011945	ENSMUSG00000021754	Map3k1	MAPKKK1|MEKK1|Mekk	mitogen-activated protein kinase kinase kinase 1	protein-coding
mm_138191.1	chr17	34269203	34269239	+	1	NA	3' UTR (NM_207105, exon 6 of 6)	3' UTR (NM_207105, exon 6 of 6)	5994	NM_207105	14961	Mm.254067	NM_207105	ENSMUSG00000073421	H2-Ab1	AI845868|Abeta|H-2Ab|H2-Ab|I-Abeta|IAb|Ia-2|Ia2|Rmcs1	histocompatibility 2, class II antigen A, beta 1	protein-coding
mm_80006.1	chr9	67759424	67759428	+	1	NA	promoter-TSS (NM_001081314)	promoter-TSS (NM_001081314)	-11	NM_001081314	75697	Mm.105353	NM_001081314	ENSMUSG00000091956	C2cd4b	3300001A09Rik|Fam148b	C2 calcium-dependent domain containing 4B	protein-coding
mm_31680.1	chr4	62295159	62295169	+	1	NA	intron (NM_001290518, intron 2 of 3)	B1F|SINE|Alu	3617	NM_001290518	20530	Mm.292539	NM_025286	ENSMUSG00000066152	Slc31a2	AI604396|CTR2	solute carrier family 31, member 2	protein-coding
mm_27824.1	chr3	79082516	79082517	-	1	NA	intron (NM_001310536, intron 17 of 23)	intron (NM_001310536, intron 17 of 23)	62371	NM_001310536	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_110702.1	chr12	69297235	69297245	-	1	NA	intron (NM_027117, intron 1 of 12)	CpG	559	NM_027117	69554	Mm.234368	NM_027117	ENSMUSG00000020978	Klhdc2	2310022K15Rik|D12Ertd522e|HCLP-1|LCP	kelch domain containing 2	protein-coding
mm_4894.1	chr1	189728249	189728259	+	1	NA	promoter-TSS (NM_008976)	promoter-TSS (NM_008976)	-14	NM_008976	19250	Mm.4498	NM_008976	ENSMUSG00000026604	Ptpn14	C130080N23Rik|OTTMUSG00000022087|PTP36	protein tyrosine phosphatase, non-receptor type 14	protein-coding
mm_144863.1	chr18	36725769	36725787	+	1	NA	exon (NM_009841, exon 2 of 2)	exon (NM_009841, exon 2 of 2)	1037	NM_009841	12475	Mm.3460	NM_009841	ENSMUSG00000051439	Cd14	-	CD14 antigen	protein-coding
mm_139330.1	chr17	49004188	49004190	+	1	NA	intron (NM_027452, intron 1 of 2)	MTD|LTR|ERVL-MaLR	71607	NM_027452	70530	Mm.133607	NM_027452	ENSMUSG00000040490	Lrfn2	5730420O05Rik|SALM1|mKIAA1246	leucine rich repeat and fibronectin type III domain containing 2	protein-coding
mm_104924.1	chr11	99858761	99858763	-	1	NA	3' UTR (NM_001205030, exon 1 of 1)	3' UTR (NM_001205030, exon 1 of 1)	845	NM_001205030	432600	Mm.60039	NM_001205030	ENSMUSG00000069717	Gm11568	OTTMUSG00000002207	predicted gene 11568	protein-coding
mm_105217.1	chr11	102185203	102185238	-	1	NA	promoter-TSS (NM_172947)	promoter-TSS (NM_172947)	36	NM_172947	268490	Mm.259079	NM_172947	ENSMUSG00000020922	Lsm12	1110032E16Rik|1110059P07|2600001B17Rik	LSM12 homolog	protein-coding
mm_45059.1	chr5	41828838	41828850	-	1	NA	exon (NM_001081422, exon 6 of 27)	exon (NM_001081422, exon 6 of 27)	15471	NM_001310601	665775	Mm.158726	NM_001081422	ENSMUSG00000061755	Bod1l	A230054D04Rik|AI853319|FAM44A|mKIAA1327	biorientation of chromosomes in cell division 1-like	protein-coding
mm_63368.1	chr7	127091368	127091423	+	1	NA	promoter-TSS (NM_178901)	promoter-TSS (NM_178901)	-41	NM_178901	101602	Mm.490357	NM_178901	ENSMUSG00000045165	AI467606	-	expressed sequence AI467606	protein-coding
mm_17711.1	chr2	32385775	32385830	-	1	NA	exon (NM_008491, exon 4 of 6)	exon (NM_008491, exon 4 of 6)	1937	NM_008491	16819	Mm.9537	NM_008491	ENSMUSG00000026822	Lcn2	24p3|AW212229|NRL|Sip24	lipocalin 2	protein-coding
mm_81381.1	chr9	108926605	108926624	+	1	NA	Intergenic	Intergenic	-10034	NM_025407	22273	Mm.335460	NM_025407	ENSMUSG00000025651	Uqcrc1	1110032G10Rik	ubiquinol-cytochrome c reductase core protein 1	protein-coding
mm_125563.1	chr15	58933775	58933836	+	1	NA	promoter-TSS (NM_023172)	promoter-TSS (NM_023172)	-5	NM_023172	66218	Mm.322294	NM_023172	ENSMUSG00000022354	Ndufb9	1190008J14Rik	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 9	protein-coding
mm_120734.1	chr14	73165122	73165126	+	1	NA	intron (NR_033185, intron 8 of 15)	MTC|LTR|ERVL-MaLR	22339	NR_033185	105670	Mm.280068	NM_134083	ENSMUSG00000022106	Rcbtb2	2610028E02Rik|2810420M18Rik|AI448345|AW240694|Chc1l|RC/BTB2	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 2	protein-coding
mm_119625.1	chr14	51129119	51129139	+	1	NA	promoter-TSS (NM_030098)	promoter-TSS (NM_030098)	61	NM_030098	78416	Mm.103835	NM_030098	ENSMUSG00000021880	Rnase6	9530043P15Rik|BB119466	ribonuclease, RNase A family, 6	protein-coding
mm_115369.1	chr13	113032198	113032201	+	1	NA	Intergenic	Intergenic	-3180	NM_001281487	238896		NM_001281487	ENSMUSG00000078926	Cdc20b	EG238896|EG622422	cell division cycle 20B	protein-coding
mm_6084.1	chr1	63095997	63096000	-	1	NA	intron (NM_001081436, intron 2 of 11)	intron (NM_001081436, intron 2 of 11)	18269	NM_001081436	227195	Mm.74718	NM_001081436	ENSMUSG00000040865	Ino80d	7330405I11|A430093A21Rik|BC010584|OTTMUSG00000002594	INO80 complex subunit D	protein-coding
mm_69615.1	chr7	137304396	137304399	-	1	NA	intron (NM_001113415, intron 6 of 15)	intron (NM_001113415, intron 6 of 15)	10048	NM_001113415	13593	Mm.258708	NM_010096	ENSMUSG00000010476	Ebf3	3110018A08Rik|O/E-2|mKIAA4201	early B cell factor 3	protein-coding
mm_36626.1	chr4	91376332	91376355	-	1	NA	5' UTR (NM_001177883, exon 1 of 7)	5' UTR (NM_001177883, exon 1 of 7)	148	NM_001347149	15569	Mm.318042	NM_010486	ENSMUSG00000008489	Elavl2	Hub|mel-N1	ELAV (embryonic lethal, abnormal vision, Drosophila)-like 2 (Hu antigen B)	protein-coding
mm_66792.1	chr7	47132311	47132388	-	1	NA	5' UTR (NM_001163565, exon 1 of 14)	5' UTR (NM_001163565, exon 1 of 14)	249	NM_001163565	19259	Mm.4654	NM_013643	ENSMUSG00000030854	Ptpn5	Step	protein tyrosine phosphatase, non-receptor type 5	protein-coding
mm_125375.1	chr15	40162617	40162629	+	1	NA	Intergenic	RLTR17|LTR|ERVK	28258	NM_001256056	328531	Mm.60703	NM_001256056	ENSMUSG00000094112	9330182O14Rik	-	RIKEN cDNA 9330182O14 gene	protein-coding
mm_63983.1	chr7	140036386	140036452	+	1	NA	promoter-TSS (NM_001286011)	promoter-TSS (NM_001286011)	28	NM_027201	69752	Mm.200818	NM_027201	ENSMUSG00000025470	Zfp511	2410004P19Rik|C86579|Znf511	zinc finger protein 511	protein-coding
mm_165014.1	chr19	28995181	28995195	+	1	NA	exon (NM_025950, exon 2 of 7)	exon (NM_025950, exon 2 of 7)	4836	NM_025950	67072	Mm.78875	NM_025950	ENSMUSG00000024780	Cdc37l1	2700033A15Rik|BB159850|Cdc37l|Harc	cell division cycle 37-like 1	protein-coding
mm_13751.1	chr2	118125863	118125874	+	1	NA	3' UTR (NM_011580, exon 22 of 22)	3' UTR (NM_011580, exon 22 of 22)	13992	NM_001313914	21825	Mm.4159	NM_011580	ENSMUSG00000040152	Thbs1	TSP-1|TSP1|Thbs-1|tbsp1	thrombospondin 1	protein-coding
mm_40926.1	chr5	76140712	76140725	+	1	NA	intron (NM_020611, intron 1 of 5)	intron (NM_020611, intron 1 of 5)	445	NM_020611	57357	Mm.289446	NM_020611	ENSMUSG00000029233	Srd5a3	1110025P14Rik|A430076C09|AV364670|AW987574|D730040M03Rik|H5ar|S5AR 3|Srd5a2l	steroid 5 alpha-reductase 3	protein-coding
mm_52819.1	chr6	121356402	121356416	+	1	NA	intron (NM_001347433, intron 6 of 14)	intron (NM_001347433, intron 6 of 14)	9712	NM_133661	14411	Mm.274506	NM_133661	ENSMUSG00000030109	Slc6a12	BGT1|GAT-2|GAT2|Gabt2	solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12	protein-coding
mm_47449.1	chr5	123524125	123524167	-	1	NA	promoter-TSS (NM_023232)	promoter-TSS (NM_023232)	18	NM_023232	66593	Mm.46716	NM_023232	ENSMUSG00000029433	Diablo	0610041G12Rik|1700006L01Rik|AU040403|Smac	diablo, IAP-binding mitochondrial protein	protein-coding
mm_66512.1	chr7	45103085	45103098	-	1	NA	5' UTR (NM_010189, exon 2 of 7)	5' UTR (NM_010189, exon 2 of 7)	731	NM_010189	14132	Mm.3303	NM_010189	ENSMUSG00000003420	Fcgrt	FcRn	Fc receptor, IgG, alpha chain transporter	protein-coding
mm_155733.1	chrX	96166039	96166054	+	1	NA	exon (NM_010833, exon 12 of 13)	exon (NM_010833, exon 12 of 13)	70001	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_132744.1	chr16	44139822	44139900	+	1	NA	promoter-TSS (NM_007508)	promoter-TSS (NM_007508)	52	NM_028108	72117	Mm.278726	NM_028108	ENSMUSG00000022698	Naa50	2600005K24Rik|2810441M03Rik|AW112078|Mak3|Mak3p|Nat13|Nat5|San	N(alpha)-acetyltransferase 50, NatE catalytic subunit	protein-coding
mm_162270.1	chr1	10233048	10233056	+	1	NA	promoter-TSS (NM_001102430)	promoter-TSS (NM_001102430)	-382	NM_001102430	211673	Mm.229141	NM_001102430	ENSMUSG00000067851	Arfgef1	ARFGEP1|BIG1|D130059B05Rik|D730028O18Rik|P200	ADP-ribosylation factor guanine nucleotide-exchange factor 1(brefeldin A-inhibited)	protein-coding
mm_149788.1	chr19	23140980	23141004	+	1	NA	promoter-TSS (NM_010638)	promoter-TSS (NM_010638)	-234	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_33681.1	chr4	133369703	133369709	+	1	NA	promoter-TSS (NM_016981)	promoter-TSS (NM_016981)	-66	NM_016981	20544	Mm.4312	NM_016981	ENSMUSG00000028854	Slc9a1	AW554487|Apnh|Mir5122|Nhe1|mir-5122|swe	solute carrier family 9 (sodium/hydrogen exchanger), member 1	protein-coding
mm_166989.1	chr7	45922841	45922874	-	1	NA	Intergenic	Intergenic	-1431	NM_010129	13732	Mm.20829	NM_010129	ENSMUSG00000040212	Emp3	H-4|H4|HNMP-1|MI-35|Ymp	epithelial membrane protein 3	protein-coding
mm_25096.1	chr3	101081733	101081737	+	1	NA	intron (NM_011197, intron 1 of 8)	MLT1C|LTR|ERVL-MaLR	28431	NM_011197	19221	Mm.24807	NM_011197	ENSMUSG00000027864	Ptgfrn	4833445A08Rik|AU042434|CD9P-1|FPRP|Trim45	prostaglandin F2 receptor negative regulator	protein-coding
mm_19726.1	chr2	104493364	104493384	-	1	NA	intron (NM_010434, intron 1 of 15)	CpG	1115	NM_010434	15259	Mm.257925	NM_010434	ENSMUSG00000027177	Hipk3	DYRK6|FIST3|PKY|mir-1902	homeodomain interacting protein kinase 3	protein-coding
mm_39863.1	chr5	30969771	30969787	+	1	NA	intron (NM_053085, intron 1 of 2)	intron (NM_053085, intron 1 of 2)	1102	NM_053085	69852	Mm.57874	NM_053085	ENSMUSG00000006642	Tcf23	2010002O16Rik|Out|bHLHa24	transcription factor 23	protein-coding
mm_133063.1	chr16	58498709	58498719	+	1	NA	intron (NM_018784, intron 2 of 10)	intron (NM_018784, intron 2 of 10)	24598	NM_018784	54613	Mm.212742	NM_018784	ENSMUSG00000022747	St3gal6	1700023B24Rik|AI930218|AW552396|Siat10|St3galVI	ST3 beta-galactoside alpha-2,3-sialyltransferase 6	protein-coding
mm_104693.1	chr11	97855536	97855562	-	1	NA	intron (NM_001081435, intron 9 of 10)	intron (NM_001081435, intron 9 of 10)	14769	NM_001080935	68127	Mm.110270	NM_001080935	ENSMUSG00000050538	B230217C12Rik	AI840637	RIKEN cDNA B230217C12 gene	protein-coding
mm_47114.1	chr5	119583720	119583730	-	1	NA	Intergenic	Intergenic	-3367	NR_045702	100993	Mm.381453	NR_045702	ENSMUSG00000087516	AW549542	-	expressed sequence AW549542	ncRNA
mm_73558.1	chr8	109075209	109075224	+	1	NA	promoter-TSS (NR_126329)	promoter-TSS (NR_126329)	-6	NR_126329	628686	Mm.203332	NR_126329	ENSMUSG00000097393	D030068K23Rik	-	RIKEN cDNA D030068K23 gene	ncRNA
mm_8667.1	chr1	156666819	156666830	-	1	NA	intron (NM_023141, intron 3 of 5)	intron (NM_023141, intron 3 of 5)	7515	NM_023141	30935	Mm.206737	NM_023141	ENSMUSG00000060519	Tor3a	Adir	torsin family 3, member A	protein-coding
mm_21689.1	chr2	164443297	164443341	-	1	NA	promoter-TSS (NM_011521)	promoter-TSS (NM_011521)	-131	NM_011521	20971	Mm.3815	NM_011521	ENSMUSG00000017009	Sdc4	AA959608|AW108331|S4|Synd4|ryudocan|syndecan-4	syndecan 4	protein-coding
mm_155397.1	chrX	72957829	72957836	+	1	NA	3' UTR (NM_010941, exon 8 of 8)	3' UTR (NM_010941, exon 8 of 8)	-29507	NM_009549	22673	Mm.1161	NM_009549	ENSMUSG00000031351	Zfp185	P1|Znf185	zinc finger protein 185	protein-coding
mm_84301.1	chr9	63399065	63399140	-	1	NA	exon (NM_027090, exon 1 of 2)	exon (NM_027090, exon 1 of 2)	142	NM_027090	69478	Mm.113942	NM_027090	ENSMUSG00000032403	2300009A05Rik	-	RIKEN cDNA 2300009A05 gene	protein-coding
mm_123817.1	chr14	70536085	70536128	-	1	NA	intron (NM_145219, intron 7 of 7)	intron (NM_145219, intron 7 of 7)	5285	NM_145219	213469	Mm.41708	NM_145219	ENSMUSG00000033595	Lgi3	AI841179|AW049851	leucine-rich repeat LGI family, member 3	protein-coding
mm_68423.1	chr7	109752211	109752290	-	1	NA	promoter-TSS (NM_020050)	promoter-TSS (NM_020050)	13	NM_020050	56786	Mm.240668	NM_020050	ENSMUSG00000031021	Tmem9b	2310004K06Rik|AW539847|D7H11orf15|ICRFP703B1614Q5.3	TMEM9 domain family, member B	protein-coding
mm_137656.1	chr17	28575782	28575803	+	1	NA	promoter-TSS (NM_026571)	promoter-TSS (NM_026571)	73	NM_026571	328789	Mm.284760	NM_026571	ENSMUSG00000062252	Lhfpl5	9330179O15Rik|Tmhs|hscy	lipoma HMGIC fusion partner-like 5	protein-coding
mm_68884.1	chr7	126447953	126447966	-	1	NA	exon (NM_007504, exon 17 of 23)	exon (NM_007504, exon 17 of 23)	15114	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_55088.1	chr6	49217959	49217983	-	1	NA	Intergenic	CpG	-3017	NM_023670	140488	Mm.281018	NM_023670	ENSMUSG00000029814	Igf2bp3	2610101N11Rik|AA522010|AL022933|AU045931|IMP-3|IMP3|Koc13|Neilsen|mimp3	insulin-like growth factor 2 mRNA binding protein 3	protein-coding
mm_156195.1	chrX	134187493	134187503	+	1	NA	promoter-TSS (NM_028947)	promoter-TSS (NM_028947)	-3	NM_028947	74448	Mm.159203	NM_028947	ENSMUSG00000052549	Arl13a	4933422M21Rik|Arl13	ADP-ribosylation factor-like 13A	protein-coding
mm_10592.1	chr2	18672494	18672504	+	1	NA	promoter-TSS (NM_147778)	promoter-TSS (NM_147778)	37	NM_147778	12238	Mm.249586	NM_147778	ENSMUSG00000051154	Commd3	AW550818|Bup|D2Ertd542e	COMM domain containing 3	protein-coding
mm_91296.1	chr10	24915681	24915687	-	1	NA	exon (NM_007482, exon 8 of 8)	exon (NM_007482, exon 8 of 8)	5020	NR_105870	102465545		NR_105870	ENSMUSG00000099181	Mir6905	Gm27879|mmu-mir-6905	microRNA 6905	ncRNA
mm_63570.1	chr7	128117397	128117439	+	1	NA	3' UTR (NM_008401, exon 30 of 30)	3' UTR (NM_008401, exon 30 of 30)	-12150	NM_021334	16411	Mm.22378	NM_021334	ENSMUSG00000030789	Itgax	AI449405|Cd11c|Cr4|N418	integrin alpha X	protein-coding
mm_98554.1	chr11	95119821	95119833	+	1	NA	promoter-TSS (NM_010055)	promoter-TSS (NM_010055)	-290	NM_010055	13393	Mm.5194	NM_010055	ENSMUSG00000001510	Dlx3	AV237891|Dlx-3	distal-less homeobox 3	protein-coding
mm_80544.1	chr9	81632337	81632361	+	1	NA	promoter-TSS (NR_040397)	promoter-TSS (NR_040397)	-9	NR_040397	319405	Mm.246494	NR_040393	ENSMUSG00000097466	D430036J16Rik	-	RIKEN cDNA D430036J16 gene	ncRNA
mm_29179.1	chr3	106528143	106528190	-	1	NA	intron (NM_001293694, intron 4 of 8)	intron (NM_001293694, intron 4 of 8)	-19632	NM_001286986	67171	Mm.290488	NM_026013	ENSMUSG00000027900	Dram2	2010305N14Rik|2610318G18Rik|AI647667|Tmem77	DNA-damage regulated autophagy modulator 2	protein-coding
mm_132016.1	chr16	25948308	25948310	+	1	NA	Intergenic	Intergenic	146393	NM_001127264	22061	Mm.20894	NM_011641	ENSMUSG00000022510	Trp63	AI462811|Ket|P51/P63|P63|P73l|Tp63|Trp53rp1	transformation related protein 63	protein-coding
mm_62903.1	chr7	116665734	116665736	+	1	NA	Intergenic	Intergenic	161366	NM_001130479	53322	Mm.9901	NM_016773	ENSMUSG00000030659	Nucb2	AI607786|Calnuc|Nefa|Nesfatin-1	nucleobindin 2	protein-coding
mm_144398.1	chr18	20741157	20741181	+	1	NA	intron (NM_019737, intron 1 of 8)	intron (NM_019737, intron 1 of 8)	5235	NM_019737	56386	Mm.393827	NM_019737	ENSMUSG00000056124	B4galt6	AA536803|AU022389	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 6	protein-coding
mm_79663.1	chr9	59657616	59657631	+	1	NA	intron (NM_001253883, intron 1 of 10)	intron (NM_001253883, intron 1 of 10)	1255	NM_001253883	18746	Mm.326167	NM_011099	ENSMUSG00000032294	Pkm	AA414905|AL024370|AL024424|Pk-2|Pk-3|Pk3|Pkm2	pyruvate kinase, muscle	protein-coding
mm_155867.1	chrX	101384297	101384311	+	1	NA	exon (NM_008124, exon 2 of 2)	exon (NM_008124, exon 2 of 2)	572	NM_001302497	14618	Mm.21198	NM_008124	ENSMUSG00000047797	Gjb1	Cnx32|Cx32|connexin-32	gap junction protein, beta 1	protein-coding
mm_24487.1	chr3	92194327	92194328	+	1	NA	Intergenic	Intergenic	-21508	NM_001164787	100303744	Mm.429851	NM_001164787	ENSMUSG00000068893	Sprr2a2	-	small proline-rich protein 2A2	protein-coding
mm_15821.1	chr2	164563415	164563430	+	1	NA	exon (NM_026323, exon 2 of 5)	exon (NM_026323, exon 2 of 5)	706	NM_026323	67701	Mm.27289	NM_026323	ENSMUSG00000017723	Wfdc2	1600023A02Rik|HE4|WAP5	WAP four-disulfide core domain 2	protein-coding
mm_110229.1	chr12	28886414	28886415	-	1	NA	Intergenic	Intergenic	134586	NM_201357	380752	Mm.273724	NM_201357	ENSMUSG00000036613	Tssc1	D12Ertd604e|Eipr1	tumor suppressing subtransferable candidate 1	protein-coding
mm_16469.1	chr2	180710221	180710274	+	1	NA	promoter-TSS (NM_001291432)	promoter-TSS (NM_001291432)	21	NM_001289652	76425	Mm.41464	NM_029607	ENSMUSG00000027573	Gid8	2310003C23Rik|4833420G11Rik|AI451474|Twa1	GID complex subunit 8	protein-coding
mm_157013.1	chrX	7671401	7671412	-	1	NA	promoter-TSS (NM_019755)	promoter-TSS (NM_019755)	-16	NM_019755	18824	Mm.18565	NM_019755	ENSMUSG00000031146	Plp2	mIMA4	proteolipid protein 2	protein-coding
mm_100488.1	chr11	120361507	120361543	+	1	NA	promoter-TSS (NM_172802)	promoter-TSS (NM_172802)	-9	NM_172802	238021	Mm.481403	NM_172802	ENSMUSG00000025380	Fscn2	A930022G03|Ahl8|C630046B20Rik	fascin actin-bundling protein 2	protein-coding
mm_81274.1	chr9	108110971	108110989	+	1	NA	exon (NM_007567, exon 5 of 12)	exon (NM_007567, exon 5 of 12)	-16500	NM_146226	235606	Mm.219639	NM_146226	ENSMUSG00000032590	Apeh	-	acylpeptide hydrolase	protein-coding
mm_8334.1	chr1	150099572	150099610	-	1	NA	promoter-TSS (NM_011198)	promoter-TSS (NM_011198)	283	NR_015466	320019	Mm.353072	NR_015466	ENSMUSG00000097028	Ptgs2os	7530420F21Rik	prostaglandin-endoperoxide synthase 2, opposite strand	ncRNA
mm_141548.1	chr17	32036315	32036330	-	1	NA	5' UTR (NM_028244, exon 1 of 16)	5' UTR (NM_028244, exon 1 of 16)	160	NM_028244	72462	Mm.102761	NM_028244	ENSMUSG00000058392	Rrp1b	2600005C20Rik|D030064A17|Kiaa0179|mKIAA0179	ribosomal RNA processing 1 homolog B (S. cerevisiae)	protein-coding
mm_153803.1	chr19	46044980	46044988	-	1	NA	5' UTR (NM_001113408, exon 1 of 11)	5' UTR (NM_001113408, exon 1 of 11)	227	NM_001113408	16825	Mm.327442	NM_010697	ENSMUSG00000025223	Ldb1	CLIM2|NLI	LIM domain binding 1	protein-coding
mm_150052.1	chr19	29380552	29380564	+	1	NA	exon (NM_021893, exon 4 of 7)	exon (NM_021893, exon 4 of 7)	13120	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_7283.1	chr1	97661951	97662013	-	1	NA	promoter-TSS (NM_133825)	promoter-TSS (NM_133825)	36	NM_133825	52392	Mm.12309	NM_133825	ENSMUSG00000044768	D1Ertd622e	AI987691|AW047450	DNA segment, Chr 1, ERATO Doi 622, expressed	protein-coding
mm_170232.1	chr17	8384686	8384700	-	1	NA	intron (NR_045795, intron 2 of 2)	intron (NR_045795, intron 2 of 2)	4775	NR_045795	100504601	Mm.365131	NR_045795	ENSMUSG00000097796	Gm16702	AU016609	predicted gene, 16702	ncRNA
mm_65038.1	chr7	18561929	18561961	-	1	NA	exon (NM_001037168, exon 3 of 5)	exon (NM_001037168, exon 3 of 5)	5360	NM_001037168	545925	Mm.440302	NM_001037168	ENSMUSG00000070797	Psg27	EG545925|cea15	pregnancy-specific glycoprotein 27	protein-coding
mm_13137.1	chr2	92058710	92058729	+	1	NA	Intergenic	CpG	-34549	NM_011957	26427	Mm.10353	NM_011957	ENSMUSG00000027230	Creb3l1	Oasis	cAMP responsive element binding protein 3-like 1	protein-coding
mm_132061.1	chr16	29845958	29845966	+	1	NA	Intergenic	B3|SINE|B2	133162	NR_037689	328657	Mm.425982	NM_001033403		Gm1968	-	predicted gene 1968	ncRNA
mm_86407.1	chr9	123986772	123986776	-	1	NA	Intergenic	Intergenic	-8366	NM_007718	12770	Mm.423532	NM_007718	ENSMUSG00000064039	Ccr1l1	Cmkbr1l1	chemokine (C-C motif) receptor 1-like 1	protein-coding
mm_48031.1	chr5	136246560	136246570	-	1	NA	Intergenic	Intergenic	-1625	NM_018825	23921	Mm.425294	NM_018825	ENSMUSG00000005057	Sh2b2	Aps	SH2B adaptor protein 2	protein-coding
mm_151400.1	chr19	56461655	56461668	+	1	NA	promoter-TSS (NM_001164263)	promoter-TSS (NM_001164263)	24	NM_172641	226245	Mm.156742	NM_172641	ENSMUSG00000035818	Plekhs1	9930023K05Rik	pleckstrin homology domain containing, family S member 1	protein-coding
mm_158327.1	chrX	133961628	133961649	-	1	NA	intron (NM_001290719, intron 3 of 12)	intron (NM_001290719, intron 3 of 12)	20174	NM_001290718	27359	Mm.38674	NM_013757	ENSMUSG00000031255	Sytl4	Gph|Slp4	synaptotagmin-like 4	protein-coding
mm_111363.1	chr12	87147485	87147495	-	1	NA	promoter-TSS (NM_001252556)	promoter-TSS (NM_001252556)	-217	NM_001252556	14874	Mm.29652	NM_010363	ENSMUSG00000021033	Gstz1	MAAI	glutathione transferase zeta 1 (maleylacetoacetate isomerase)	protein-coding
mm_112658.1	chr13	16026901	16026911	+	1	NA	exon (NM_008380, exon 5 of 5)	exon (NM_008380, exon 5 of 5)	15055	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_88055.1	chr10	67547866	67547885	+	1	NA	3' UTR (NM_001005419, exon 1 of 1)	3' UTR (NM_001005419, exon 1 of 1)	1080	NM_001005419	211488	Mm.297250	NM_001005419	ENSMUSG00000057134	Ado	Gm237	2-aminoethanethiol (cysteamine) dioxygenase	protein-coding
mm_147484.1	chr18	47248335	47248345	-	1	NA	3' UTR (NM_018744, exon 19 of 19)	3' UTR (NM_018744, exon 19 of 19)	120528	NM_018744	20358	Mm.40909	NM_018744	ENSMUSG00000019647	Sema6a	A730020P05Rik|AI851735|Sema6A-1|Semaq|VIa	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A	protein-coding
mm_49862.1	chr6	38551504	38551536	+	1	NA	5' UTR (NM_001170849, exon 1 of 8)	5' UTR (NM_001170849, exon 1 of 8)	186	NM_001170848	192196	Mm.276133	NM_138680	ENSMUSG00000029823	Luc7l2	4930471C18Rik|AA522013|AU015269|CGI59|Cgi74	LUC7-like 2 (S. cerevisiae)	protein-coding
mm_83200.1	chr9	41157756	41157796	-	1	NA	promoter-TSS (NM_176860)	promoter-TSS (NM_176860)	-282	NM_176860	72828	Mm.133615	NM_176860	ENSMUSG00000032020	Ubash3b	2810457I06Rik|BB125008|TULA-2|p70	ubiquitin associated and SH3 domain containing, B	protein-coding
mm_159427.1	chr3	108739564	108739564	+	1	NA	promoter-TSS (NM_177859)	promoter-TSS (NM_177859)	-94	NM_177859	329738	Mm.72322	NM_177859	ENSMUSG00000049565	Aknad1	4921525H12Rik	AKNA domain containing 1	protein-coding
mm_141804.1	chr17	34535992	34536001	-	1	NA	Intergenic	Intergenic	-18644	NM_030747	624681	Mm.471592	NM_030747	ENSMUSG00000092618	Btnl6	EG624681|Gm6519|NG13	butyrophilin-like 6	protein-coding
mm_105721.1	chr11	109011706	109011732	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	91370	NM_015732	12006	Mm.71710	NM_015732	ENSMUSG00000000142	Axin2	Axi1|Axil|Conductin	axin 2	protein-coding
mm_92281.1	chr10	71285235	71285245	-	1	NA	promoter-TSS (NM_145420)	promoter-TSS (NM_145420)	22	NM_145420	216080	Mm.270530	NM_145420	ENSMUSG00000019927	Ube2d1	UBCH5	ubiquitin-conjugating enzyme E2D 1	protein-coding
mm_74498.1	chr8	7002767	7002788	-	1	NA	Intergenic	Intergenic	1657996	NM_010111	13642	Mm.209813	NM_010111	ENSMUSG00000001300	Efnb2	ELF-2|Epl5|Eplg5|Htk-L|LERK-5|Lerk5|NLERK-1	ephrin B2	protein-coding
mm_47043.1	chr5	116024379	116024438	-	1	NA	promoter-TSS (NM_031869)	promoter-TSS (NM_031869)	20	NM_031869	19079	Mm.458152	NM_031869	ENSMUSG00000029513	Prkab1	1300015D22Rik|AU021155|E430008F22	protein kinase, AMP-activated, beta 1 non-catalytic subunit	protein-coding
mm_111521.1	chr12	100179011	100179011	-	1	NA	Intergenic	Intergenic	-8957	NR_045282	100038378	Mm.387075	NR_045282	ENSMUSG00000072884	Gm10433	ENSMUSG00000072884	predicted gene 10433	ncRNA
mm_108378.1	chr12	80859111	80859111	+	1	NA	intron (NM_001242419, intron 3 of 6)	intron (NM_001242419, intron 3 of 6)	65336	NR_033786	67340	Mm.386790	NR_033786	ENSMUSG00000101912	1700052I22Rik	-	RIKEN cDNA 1700052I22 gene	ncRNA
mm_113408.1	chr13	33964765	33964771	+	1	NA	5' UTR (NM_001163241, exon 1 of 7)	5' UTR (NM_001163241, exon 1 of 7)	109	NM_001163241	18105	Mm.264036	NM_020282	ENSMUSG00000046949	Nqo2	NMO2|Nmor2|Ox2	NAD(P)H dehydrogenase, quinone 2	protein-coding
mm_24244.1	chr3	89136574	89136593	+	1	NA	promoter-TSS (NM_001099779)	promoter-TSS (NM_001099779)	-40	NM_001099779	18770	Mm.383180	NM_013631	ENSMUSG00000041237	Pklr	Pk-1|Pk1|R-PK	pyruvate kinase liver and red blood cell	protein-coding
mm_168932.1	chr12	66396271	66396272	+	1	NA	Intergenic	RLTR9C|LTR|ERVK	-111870	NM_001162933	238217	Mm.188575	NM_001162933	ENSMUSG00000060499	Rpl10l	EG238217	ribosomal protein L10-like	protein-coding
mm_17705.1	chr2	32384750	32384901	-	1	NA	3' UTR (NM_008491, exon 6 of 6)	3' UTR (NM_008491, exon 6 of 6)	-2910	NM_198001	73737	Mm.27608	NM_198001	ENSMUSG00000039195	1110008P14Rik	C79326	RIKEN cDNA 1110008P14 gene	protein-coding
mm_89456.1	chr10	93161092	93161147	+	1	NA	5' UTR (NM_146239, exon 1 of 17)	5' UTR (NM_146239, exon 1 of 17)	243	NM_146239	237459	Mm.217404	NM_146239	ENSMUSG00000020015	Cdk17	6430598J10Rik|Pctk2	cyclin-dependent kinase 17	protein-coding
mm_152930.1	chr19	28283884	28283914	-	1	NA	intron (NM_001305671, intron 7 of 9)	intron (NM_001305671, intron 7 of 9)	-272733	NM_011265	19726	Mm.313321	NM_011265	ENSMUSG00000040929	Rfx3	C230093O12Rik|MRFX3	regulatory factor X, 3 (influences HLA class II expression)	protein-coding
mm_8542.1	chr1	155098733	155098746	-	1	NA	exon (NM_010500, exon 1 of 1)	exon (NM_010500, exon 1 of 1)	897	NM_010500	15939	Mm.12246	NM_010500	ENSMUSG00000056708	Ier5	-	immediate early response 5	protein-coding
mm_50808.1	chr6	54314068	54314075	+	1	NA	intron (NR_033635, intron 4 of 13)	PB1D7|SINE|Alu	-12941	NM_030024	78004	Mm.41984	NM_030024	ENSMUSG00000045725	Prr15	E130201N16Rik|G90	proline rich 15	protein-coding
mm_42303.1	chr5	114772896	114772897	+	1	NA	TTS (NR_027872)	TTS (NR_027872)	595	NM_019834	26431	Mm.195632	NM_019834	ENSMUSG00000041890	Git2	1500036H07Rik|5830420E16Rik|6430510B20Rik|9630056M03Rik|B230104M05Rik|CAT2|mKIAA0148	G protein-coupled receptor kinase-interactor 2	protein-coding
mm_18523.1	chr2	63113124	63113133	-	1	NA	intron (NM_133207, intron 2 of 15)	(A)n|Simple_repeat|Simple_repeat	71159	NM_133207	170738	Mm.242532	NM_133207	ENSMUSG00000059742	Kcnh7	9330137I11Rik|Kv11.3|erg3	potassium voltage-gated channel, subfamily H (eag-related), member 7	protein-coding
mm_20092.1	chr2	120850608	120850618	-	1	NA	promoter-TSS (NM_001024856)	promoter-TSS (NM_001024856)	-29	NM_080788	140810	Mm.275698	NM_080788	ENSMUSG00000090100	Ttbk2	2610507N02Rik|AI326283|B930008N24Rik|TTK|Ttbk|Ttbk1|mKIAA0847	tau tubulin kinase 2	protein-coding
mm_5222.1	chr1	14304543	14304550	-	1	NA	intron (NM_001310459, intron 1 of 17)	intron (NM_001310459, intron 1 of 17)	5653	NM_001310459	14048	Mm.250185	NM_010164	ENSMUSG00000025932	Eya1	bor	EYA transcriptional coactivator and phosphatase 1	protein-coding
mm_16661.1	chr2	6720825	6720840	-	1	NA	intron (NM_001347094, intron 2 of 12)	intron (NM_001347094, intron 2 of 12)	830	NM_001310447	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_96665.1	chr11	69409695	69409720	+	1	NA	intron (NM_001017426, intron 1 of 22)	intron (NM_001017426, intron 1 of 22)	3968	NM_001017426	216850	Mm.261201	NM_001017426	ENSMUSG00000018476	Kdm6b	1700064E03Rik|BC038313|Jmjd3|mKIAA0346	KDM1 lysine (K)-specific demethylase 6B	protein-coding
mm_77317.1	chr8	117801904	117801949	-	1	NA	promoter-TSS (NM_026758)	promoter-TSS (NM_026758)	3	NM_026758	68533	Mm.181836	NM_026758	ENSMUSG00000031843	Mphosph6	1110001M01Rik|AA536809|C86426	M phase phosphoprotein 6	protein-coding
mm_141077.1	chr17	25861351	25861361	-	1	NA	exon (NM_001163766, exon 1 of 41)	exon (NM_001163766, exon 1 of 41)	159	NM_001163766	106618	Mm.35470	NM_134124	ENSMUSG00000073434	Wdr90	3230401M21Rik|AI551153|mKIAA1924	WD repeat domain 90	protein-coding
mm_143365.1	chr17	67354473	67354485	-	1	NA	promoter-TSS (NM_008984)	promoter-TSS (NM_008984)	-20	NM_008984	19274	Mm.311809	NM_008984	ENSMUSG00000033278	Ptprm	RPTPmu|mKIAA4044	protein tyrosine phosphatase, receptor type, M	protein-coding
mm_169665.1	chr15	60614554	60614554	-	1	NA	Intergenic	RLTR10E|LTR|ERVK	-208411	NR_030696	320469	Mm.230853	NM_177166		9930014A18Rik	-	RIKEN cDNA 9930014A18 gene	ncRNA
mm_15130.1	chr2	153900375	153900378	+	1	NA	promoter-TSS (NM_199303)	promoter-TSS (NM_199303)	-12	NM_199303	228796	Mm.137570	NM_199303	ENSMUSG00000068009	Bpifb6	Bpil3|Gm119|Lplunc6	BPI fold containing family B, member 6	protein-coding
mm_71006.1	chr8	31111897	31111907	+	1	NA	promoter-TSS (NM_175136)	promoter-TSS (NM_175136)	56	NM_175136	68867	Mm.29532	NM_175136	ENSMUSG00000039328	Rnf122	1110063C11Rik	ring finger protein 122	protein-coding
mm_55382.1	chr6	58907121	58907131	-	1	NA	promoter-TSS (NM_021432)	promoter-TSS (NM_021432)	0	NM_021432	58243	Mm.389747	NM_021432	ENSMUSG00000055430	Nap1l5	1110020M21Rik	nucleosome assembly protein 1-like 5	protein-coding
mm_104060.1	chr11	86584425	86584433	-	1	NA	promoter-TSS (NR_029738)	promoter-TSS (NR_029738)	-271	NR_029738	387140		NR_029738	ENSMUSG00000065455	Mir21a	Mir21|Mirn21|mmu-mir-21|mmu-mir-21a	microRNA 21a	ncRNA
mm_57249.1	chr6	123283401	123283411	-	1	NA	3' UTR (NM_019948, exon 6 of 6)	3' UTR (NM_019948, exon 6 of 6)	6465	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_74423.1	chr8	3659025	3659046	-	1	NA	TTS (NM_022984)	TTS (NM_022984)	3265	NM_022984	57264	Mm.1181	NM_022984	ENSMUSG00000012705	Retn	ADSF|Fizz3|Rstn|Xcp4	resistin	protein-coding
mm_50381.1	chr6	48685941	48685976	+	1	NA	intron (NM_174990, intron 1 of 2)	intron (NM_174990, intron 1 of 2)	1380	NM_174990	107526	Mm.333048	NM_174990	ENSMUSG00000054435	Gimap4	AU019574|E430007K16Rik|Ian-1|Ian1|Imap4	GTPase, IMAP family member 4	protein-coding
mm_114046.1	chr13	54107204	54107205	+	1	NA	3' UTR (NM_027324, exon 11 of 11)	3' UTR (NM_027324, exon 11 of 11)	35359	NM_027324	14057	Mm.134191	NM_027324	ENSMUSG00000021474	Sfxn1	2810002O05Rik|A930015P12Rik|f	sideroflexin 1	protein-coding
mm_36426.1	chr4	82291094	82291114	-	1	NA	3' UTR (NM_001113209, exon 12 of 12)	3' UTR (NM_001113209, exon 12 of 12)	214675	NM_001286127	18028	Mm.317947	NM_008687	ENSMUSG00000008575	Nfib	6720429L07Rik|CTF|E030026I10Rik|NF-I/B|NF1-B|NFI-B	nuclear factor I/B	protein-coding
mm_25108.1	chr3	101377075	101377158	+	1	NA	promoter-TSS (NM_207205)	promoter-TSS (NM_207205)	-9	NM_207205	78908	Mm.257997	NM_207205	ENSMUSG00000042035	Igsf3	1700016K10Rik|2810035F16Rik|4833439O17Rik|mKIAA0466	immunoglobulin superfamily, member 3	protein-coding
mm_142799.1	chr17	50239100	50239106	-	1	NA	promoter-TSS (NR_131975)	promoter-TSS (NR_131975)	-105	NR_131975	446210	Mm.378184	NM_001004437	ENSMUSG00000067103	AY702103	STDP2	cDNA sequence AY702103	ncRNA
mm_123948.1	chr14	73384333	73384357	-	1	NA	intron (NM_008410, intron 1 of 5)	intron (NM_008410, intron 1 of 5)	926	NM_008410	16432	Mm.4266	NM_008410	ENSMUSG00000022108	Itm2b	AI256040|Bri|Bri2|Bricd2b|D14Sel6|E25BMM|imBRI2	integral membrane protein 2B	protein-coding
mm_121274.1	chr14	103513379	103513429	+	1	NA	promoter-TSS (NM_022886)	promoter-TSS (NM_022886)	63	NM_022886	64929	Mm.244003	NM_022886	ENSMUSG00000022123	Scel	9230114I02Rik	sciellin	protein-coding
mm_112612.1	chr13	15463247	15463303	+	1	NA	promoter-TSS (NM_008130)	promoter-TSS (NM_008130)	-448	NM_008130	14634	Mm.5098	NM_008130	ENSMUSG00000021318	Gli3	AI854843|AU023367|Bph|GLI3-190|GLI3FL|Pdn|Xt|add	GLI-Kruppel family member GLI3	protein-coding
mm_112917.1	chr13	20923168	20923178	+	1	NA	intron (NM_012054, intron 11 of 20)	Lx8b|LINE|L1	129060	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_8789.1	chr1	161704660	161704679	-	1	NA	Intergenic	Intergenic	83826	NM_001205243	14103	Mm.3355	NM_010177	ENSMUSG00000000817	Fasl	APT1LG1|CD178|CD95-L|CD95L|Fas-L|Faslg|Tnfsf6|Tnlg1a|gld	Fas ligand (TNF superfamily, member 6)	protein-coding
mm_160179.1	chr7	45813843	45813843	-	1	NA	intron (NM_011181, intron 1 of 11)	CpG	473	NM_011181	19158	Mm.272130	NM_011181	ENSMUSG00000003269	Cyth2	ARNO|CLM2|Pscd2	cytohesin 2	protein-coding
mm_77251.1	chr8	115705903	115705979	-	1	NA	exon (NM_001025577, exon 1 of 1)	exon (NM_001025577, exon 1 of 1)	953	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_152943.1	chr19	28929224	28929237	-	1	NA	intron (NM_198651, intron 10 of 12)	intron (NM_198651, intron 10 of 12)	-34690	NM_028922	74411	Mm.441887	NM_028922	ENSMUSG00000040105	Plpp6	4932443D16Rik|Ppapdc2	phospholipid phosphatase 6	protein-coding
mm_38279.1	chr4	136890057	136890063	-	1	NA	exon (NM_007574, exon 3 of 3)	exon (NM_007574, exon 3 of 3)	2854	NM_007574	12262	Mm.439732	NM_007574	ENSMUSG00000036896	C1qc	AI385742|C1qg|Ciqc	complement component 1, q subcomponent, C chain	protein-coding
mm_113997.1	chr13	52583389	52583400	+	1	NA	promoter-TSS (NM_001198977)	promoter-TSS (NM_001198977)	-43	NM_001198977	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_1152.1	chr1	60807933	60807948	+	1	NA	Intergenic	ORR1B1|LTR|ERVL-MaLR	61552	NM_007642	12487	Mm.255003	NM_007642	ENSMUSG00000026012	Cd28	-	CD28 antigen	protein-coding
mm_146912.1	chr18	31447328	31447328	-	1	NA	promoter-TSS (NM_009308)	promoter-TSS (NM_009308)	87	NM_009308	20983	Mm.233846	NM_009308	ENSMUSG00000024261	Syt4	SytIV	synaptotagmin IV	protein-coding
mm_22573.1	chr3	10342789	10342837	+	1	NA	intron (NM_025512, intron 6 of 7)	RLTR20D|LTR|ERVK	-7157	NM_001010834	241877	Mm.442146	NM_001010834	ENSMUSG00000058921	Slc10a5	Gm405|mP5	solute carrier family 10 (sodium/bile acid cotransporter family), member 5	protein-coding
mm_96587.1	chr11	69089769	69089812	+	1	NA	exon (NM_009497, exon 3 of 5)	exon (NM_009497, exon 3 of 5)	1262	NM_009497	22318	Mm.28643	NM_009497	ENSMUSG00000020894	Vamp2	Syb-2|Syb2|sybII	vesicle-associated membrane protein 2	protein-coding
mm_119413.1	chr14	45155740	45155746	+	1	NA	intron (NM_001310534, intron 14 of 20)	MT2A|LTR|ERVL	63682	NM_172597	70561	Mm.28129	NM_172597	ENSMUSG00000021830	Txndc16	5730420B22Rik|C77647	thioredoxin domain containing 16	protein-coding
mm_47691.1	chr5	129670075	129670100	-	1	NA	promoter-TSS (NM_172462)	promoter-TSS (NM_172462)	1	NM_172462	22648	Mm.135067	NM_172462	ENSMUSG00000051034	Zfp11	6720465D24|Krox-6|Zfp-11	zinc finger protein 11	protein-coding
mm_126902.1	chr15	89553311	89553314	+	1	NA	intron (NM_021423, intron 21 of 21)	intron (NM_021423, intron 21 of 21)	-15014	NM_013455	11434	Mm.57	NM_013455	ENSMUSG00000022622	Acr	-	acrosin prepropeptide	protein-coding
mm_163775.1	chr13	120018494	120018499	+	1	NA	Intergenic	B1_Mur2|SINE|Alu	33708	NM_001302966	100861753	Mm.165042	NM_001302966	ENSMUSG00000095609	Gm21188	-	predicted gene, 21188	protein-coding
mm_109836.1	chr12	4233905	4233925	-	1	NA	promoter-TSS (NM_001204912)	promoter-TSS (NM_001204912)	-112	NM_001204912	69709	Mm.250552	NM_001204912	ENSMUSG00000096199	Ptrhd1	2410017P09Rik	peptidyl-tRNA hydrolase domain containing 1	protein-coding
mm_75300.1	chr8	41083065	41083088	-	1	NA	exon (NM_001286413, exon 2 of 14)	exon (NM_001286413, exon 2 of 14)	-28280	NM_001005864	102103	Mm.149438	NM_001005863	ENSMUSG00000045636	Mtus1	AI481402|ATBP135|Atip1|B430010I23Rik|B430305I03Rik|C85752|Cctsg1-440|MD44|MTSG1|mKIAA1288	mitochondrial tumor suppressor 1	protein-coding
mm_155925.1	chrX	103356575	103356602	+	1	NA	exon (NM_009767, exon 1 of 6)	exon (NM_009767, exon 1 of 6)	112	NM_009767	12212	Mm.42223	NM_009767	ENSMUSG00000031327	Chic1	Brx|ENSMUSG00000073019|Gm10454	cysteine-rich hydrophobic domain 1	protein-coding
mm_3359.1	chr1	138174448	138174458	+	1	NA	intron (NM_001111316, intron 1 of 31)	intron (NM_001111316, intron 1 of 31)	673	NM_001111316	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_82778.1	chr9	27155390	27155416	-	1	NA	promoter-TSS (NM_023277)	promoter-TSS (NM_023277)	18	NM_023277	83964	Mm.28770	NM_023277	ENSMUSG00000031990	Jam3	1110002N23Rik|JAM-3|JAM-C|Jcam3	junction adhesion molecule 3	protein-coding
mm_55986.1	chr6	85961598	85961598	-	1	NA	promoter-TSS (NM_028099)	promoter-TSS (NM_028099)	69	NM_028099	72102	Mm.24007	NM_028099	ENSMUSG00000030002	Dusp11	2010300F21Rik|AI481497	dual specificity phosphatase 11 (RNA/RNP complex 1-interacting)	protein-coding
mm_126903.1	chr15	89568323	89568325	+	1	NA	promoter-TSS (NM_013455)	promoter-TSS (NM_013455)	-2	NM_013455	11434	Mm.57	NM_013455	ENSMUSG00000022622	Acr	-	acrosin prepropeptide	protein-coding
mm_17113.1	chr2	24423000	24423010	-	1	NA	exon (NM_011040, exon 11 of 12)	exon (NM_011040, exon 11 of 12)	37608	NM_177611	215632	Mm.490434	NM_177611	ENSMUSG00000026979	Psd4	BC046518|EFA6B	pleckstrin and Sec7 domain containing 4	protein-coding
mm_119119.1	chr14	31093501	31093504	+	1	NA	intron (NM_001081251, intron 25 of 32)	Lx3C|LINE|L1	35428	NM_001308466	66487	Mm.379116	NM_001308091	ENSMUSG00000058351	Smim4	2010107H07Rik|Gm41122	small integral membrane protein 4	protein-coding
mm_57806.1	chr6	129421146	129421149	-	1	NA	exon (NM_001205364, exon 5 of 6)	exon (NM_001205364, exon 5 of 6)	12285	NM_172732	232414	Mm.391518	NM_172732	ENSMUSG00000046080	Clec9a	9830005G06Rik|DNGR-1	C-type lectin domain family 9, member a	protein-coding
mm_108616.1	chr12	85524690	85524713	+	1	NA	Intergenic	Intergenic	50800	NM_010234	14281	Mm.246513	NM_010234	ENSMUSG00000021250	Fos	D12Rfj1|c-fos|cFos	FBJ osteosarcoma oncogene	protein-coding
mm_11151.1	chr2	28527789	28527804	+	1	NA	intron (NM_001145834, intron 1 of 17)	intron (NM_001145834, intron 1 of 17)	-5668	NM_001145835	19730	Mm.5236	NM_009058	ENSMUSG00000026821	Ralgds	Gnds|Rgds|mKIAA1308	ral guanine nucleotide dissociation stimulator	protein-coding
mm_18246.1	chr2	52194434	52194445	-	1	NA	exon (NM_010889, exon 114 of 157)	exon (NM_010889, exon 114 of 157)	-96563	NR_040620	78049	Mm.243883	NR_040620		4930573O16Rik	-	RIKEN cDNA 4930573O16 gene	ncRNA
mm_92145.1	chr10	67037971	67037974	-	1	NA	intron (NR_110511, intron 4 of 6)	PB1D9|SINE|Alu	32897	NR_110511	102634101	Mm.445258	NR_110511		Gm31763	-	predicted gene, 31763	ncRNA
mm_73498.1	chr8	107183100	107183103	+	1	NA	intron (NM_025558, intron 4 of 4)	PB1D9|SINE|Alu	32440	NM_025558	66427	Mm.20242	NM_025558	ENSMUSG00000031924	Cyb5b	1810044O22Rik|AU015618|Cyb5m	cytochrome b5 type B	protein-coding
mm_173097.1	chrX	152043507	152043527	-	1	NA	intron (NM_019710, intron 16 of 24)	intron (NM_019710, intron 16 of 24)	27089	NM_019710	24061	Mm.482095	NM_019710	ENSMUSG00000041133	Smc1a	5830426I24Rik|SMC-1A|Sb1.8|Smc1|Smc1alpha|Smc1l1|Smcb|mKIAA0178	structural maintenance of chromosomes 1A	protein-coding
mm_28998.1	chr3	101576363	101576376	-	1	NA	3' UTR (NM_144900, exon 23 of 23)	3' UTR (NM_144900, exon 23 of 23)	28338	NM_144900	11928	Mm.193670	NM_144900	ENSMUSG00000033161	Atp1a1	Atpa-1|BC010319	ATPase, Na+/K+ transporting, alpha 1 polypeptide	protein-coding
mm_86794.1	chr10	20229763	20229764	+	1	NA	intron (NM_001198635, intron 1 of 17)	intron (NM_001198635, intron 1 of 17)	21324	NM_001101561	621697	Mm.440587	NM_001101561		Rpl32l	EG621697|Gm6251	ribosomal protein L32-like	protein-coding
mm_103731.1	chr11	79962349	79962373	-	1	NA	promoter-TSS (NM_144826)	promoter-TSS (NM_144826)	26	NM_144826	216987	Mm.274961	NM_144826	ENSMUSG00000035575	Utp6	4732497O03Rik|HCA66	UTP6 small subunit processome component	protein-coding
mm_96848.1	chr11	70038563	70038587	+	1	NA	intron (NM_001109752, intron 8 of 19)	intron (NM_001109752, intron 8 of 19)	-15549	NM_001291131	11889	Mm.6559	NM_009714	ENSMUSG00000020884	Asgr1	ASGPR1|Asgr|Asgr-1|HL-1	asialoglycoprotein receptor 1	protein-coding
mm_137843.1	chr17	31057687	31057699	+	1	NA	promoter-TSS (NM_009593)	promoter-TSS (NM_009593)	-1	NM_009593	11307	Mm.15691	NM_009593	ENSMUSG00000024030	Abcg1	AW413978|Abc8|White	ATP-binding cassette, sub-family G (WHITE), member 1	protein-coding
mm_102443.1	chr11	59544125	59544160	-	1	NA	intron (NM_145827, intron 2 of 9)	intron (NM_145827, intron 2 of 9)	1456	NM_145827	216799	Mm.54174	NM_145827	ENSMUSG00000032691	Nlrp3	AGTAVPRL|AII/AVP|Cias1|FCAS|FCU|MWS|Mmig1|NALP3|Pypaf1	NLR family, pyrin domain containing 3	protein-coding
mm_64621.1	chr7	3665445	3665488	-	1	NA	TTS (NM_181820)	TTS (NM_181820)	374	NM_027203	69757	Mm.389782	NM_027203	ENSMUSG00000078813	Leng1	1500001K17Rik	leukocyte receptor cluster (LRC) member 1	protein-coding
mm_79325.1	chr9	53301507	53301521	+	1	NA	promoter-TSS (NM_176846)	promoter-TSS (NM_176846)	-156	NM_176846	320051	Mm.277540	NM_176846	ENSMUSG00000034584	Exph5	AC079869.22gm5|B130009M24Rik|E030050P12|Kiaa0624|Slac2b|slac2-b	exophilin 5	protein-coding
mm_157944.1	chrX	85776645	85776658	-	1	NA	5' UTR (NM_212444, exon 1 of 20)	5' UTR (NM_212444, exon 1 of 20)	168	NM_001294140	14933	Mm.246682	NM_008194	ENSMUSG00000025059	Gk	D930012N15Rik|Gyk	glycerol kinase	protein-coding
mm_95961.1	chr11	58867231	58867275	+	1	NA	promoter-TSS (NM_172403)	promoter-TSS (NM_172403)	13	NM_172403	69944	Mm.32118	NM_172403	ENSMUSG00000020491	2810021J22Rik	AI449137	RIKEN cDNA 2810021J22 gene	protein-coding
mm_62202.1	chr7	97790794	97790800	+	1	NA	Intergenic	Intergenic	-52142	NM_011035	18479	Mm.260227	NM_011035	ENSMUSG00000030774	Pak1	AW045634|PAK-1|Paka	p21 protein (Cdc42/Rac)-activated kinase 1	protein-coding
mm_8807.1	chr1	161876657	161876682	-	1	NA	promoter-TSS (NM_172645)	promoter-TSS (NM_172645)	-8	NM_172645	226551	Mm.170002	NM_172645	ENSMUSG00000040297	Suco	4732491B11|AI848100|AU016931|Opt	SUN domain containing ossification factor	protein-coding
mm_3591.1	chr1	151363061	151363064	+	1	NA	intron (NM_054102, intron 14 of 14)	AT_rich|Low_complexity|Low_complexity	18564	NM_001039511	117198	Mm.33764	NM_028582	ENSMUSG00000023150	Ivns1abp	1190004M08Rik|1700126I16Rik|AA960440|HSPC068|ND1|NS-1|NS1-BP|Nd1-L|Nd1-S|mKIAA0850	influenza virus NS1A binding protein	protein-coding
mm_111737.1	chr12	103865673	103865685	-	1	NA	Intergenic	Intergenic	-2060	NM_009243	20700	Mm.439692	NM_009243	ENSMUSG00000066366	Serpina1a	Aat-2|Aat2|Dom1|PI1|Spi1-1|Spi1-3	serine (or cysteine) peptidase inhibitor, clade A, member 1A	protein-coding
mm_31533.1	chr4	55351324	55351334	+	1	NA	intron (NM_009011, intron 1 of 9)	intron (NM_009011, intron 1 of 9)	1287	NM_009011	19359	Mm.196846	NM_009011	ENSMUSG00000028426	Rad23b	0610007D13Rik|AV001138|HR23B|mHR23B|p58	RAD23 homolog B, nucleotide excision repair protein	protein-coding
mm_43039.1	chr5	124006468	124006490	+	1	NA	exon (NM_177876, exon 4 of 4)	exon (NM_177876, exon 4 of 4)	9627	NR_105999	102465625		NR_105999	ENSMUSG00000098454	Mir7032	Gm27309|mmu-mir-7032	microRNA 7032	ncRNA
mm_69661.1	chr7	139979509	139979520	-	1	NA	promoter-TSS (NM_001033465)	promoter-TSS (NM_001033465)	-759	NM_001347613	381933	Mm.440431	NM_001033465	ENSMUSG00000073795	6430531B16Rik	Gm1093	RIKEN cDNA 6430531B16 gene	protein-coding
mm_94242.1	chr11	3293277	3293288	+	1	NA	exon (NM_001253691, exon 2 of 5)	exon (NM_001253691, exon 2 of 5)	2825	NM_019574	56218	Mm.275563	NM_019574	ENSMUSG00000020453	Patz1	8430401L15Rik|AI447519|Mazr|Patz|Zfp278	POZ (BTB) and AT hook containing zinc finger 1	protein-coding
mm_60565.1	chr7	44481405	44481414	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-3108	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_133443.1	chr16	87729738	87729759	+	1	NA	exon (NM_007520, exon 5 of 5)	exon (NM_007520, exon 5 of 5)	30794	NM_007520	12013	Mm.26147	NM_007520	ENSMUSG00000025612	Bach1	6230421P05Rik|AI323795	BTB and CNC homology 1, basic leucine zipper transcription factor 1	protein-coding
mm_124324.1	chr14	103815868	103815872	-	1	NA	3' UTR (NM_001136061, exon 8 of 8)	3' UTR (NM_001136061, exon 8 of 8)	27831	NM_007904	13618	Mm.229532	NM_007904	ENSMUSG00000022122	Ednrb	ET-B|ET-BR|ETR-b|ETb|Sox10m1	endothelin receptor type B	protein-coding
mm_147157.1	chr18	36679424	36679438	-	1	NA	promoter-TSS (NM_146085)	promoter-TSS (NM_146085)	-65	NM_146085	225372	Mm.89673	NM_146085	ENSMUSG00000006050	Apbb3	Fe65l2|Rirl2|TR2S	amyloid beta (A4) precursor protein-binding, family B, member 3	protein-coding
mm_68592.1	chr7	116038735	116038750	-	1	NA	promoter-TSS (NM_001025559)	promoter-TSS (NM_001025559)	2	NM_001025559	20679	Mm.323365	NM_011445	ENSMUSG00000051910	Sox6	AI987981|SOX-LZ	SRY (sex determining region Y)-box 6	protein-coding
mm_56579.1	chr6	106771639	106771649	-	1	NA	intron (NM_001242360, intron 2 of 5)	intron (NM_001242360, intron 2 of 5)	2506	NM_001242358	70047	Mm.196332	NM_027296	ENSMUSG00000013736	Trnt1	2410043H24Rik|2610044E04Rik|9830143O18Rik|AA408384|C76540|CGI-47|mt-Trat	tRNA nucleotidyl transferase, CCA-adding, 1	protein-coding
mm_51993.1	chr6	92103659	92103662	+	1	NA	intron (NM_001347342, intron 1 of 14)	intron (NM_001347342, intron 1 of 14)	11227	NM_001347342	22026	Mm.87062	NM_011630	ENSMUSG00000005893	Nr2c2	TAK1|Tr4|mKIAA4145	nuclear receptor subfamily 2, group C, member 2	protein-coding
mm_18377.1	chr2	59979678	59979681	-	1	NA	intron (NM_001001182, intron 4 of 35)	B1_Mur4|SINE|Alu	-97073	NM_028118	72137	Mm.288734	NM_028118	ENSMUSG00000026988	Wdsub1	1700048E19Rik|2610014F08Rik	WD repeat, SAM and U-box domain containing 1	protein-coding
mm_52714.1	chr6	119481521	119481541	+	1	NA	3' UTR (NM_133940, exon 1 of 1)	3' UTR (NM_133940, exon 1 of 1)	1863	NM_133940	101358	Mm.125477	NM_133940	ENSMUSG00000030019	Fbxl14	AW322056|Fbx14l	F-box and leucine-rich repeat protein 14	protein-coding
mm_151998.1	chr19	5898205	5898216	-	1	NA	3' UTR (NM_001291078, exon 12 of 12)	3' UTR (NM_001291078, exon 12 of 12)	-4103	NM_198634	332359	Mm.329642	NM_198634	ENSMUSG00000044390	Tigd3	-	tigger transposable element derived 3	protein-coding
mm_101100.1	chr11	11931635	11931645	-	1	NA	3' UTR (NM_010345, exon 17 of 17)	3' UTR (NM_010345, exon 17 of 17)	-33496	NM_001190448	13195	Mm.12906	NM_016672	ENSMUSG00000020182	Ddc	Aadc	dopa decarboxylase	protein-coding
mm_27050.1	chr3	27209836	27209839	-	1	NA	intron (NM_178772, intron 1 of 4)	intron (NM_178772, intron 1 of 4)	26833	NM_178772	320024	Mm.24576	NM_178772	ENSMUSG00000027698	Nceh1	Aadacl1|B230106I24Rik|CPO-BP|Nceh	neutral cholesterol ester hydrolase 1	protein-coding
mm_92382.1	chr10	76442735	76442756	-	1	NA	5' UTR (NM_001282992, exon 1 of 42)	5' UTR (NM_001282992, exon 1 of 42)	167	NM_008787	18541	Mm.251794	NM_008787	ENSMUSG00000001151	Pcnt	AW476095|C86676|KEN|Pcnt2|kendrin|m239Asp|m275Asp	pericentrin (kendrin)	protein-coding
mm_84380.1	chr9	65422777	65422777	-	1	NA	promoter-TSS (NM_178933)	promoter-TSS (NM_178933)	-4	NM_178933	330962	Mm.335247	NM_178933	ENSMUSG00000053862	Slc51b	Ostb	solute carrier family 51, beta subunit	protein-coding
mm_41740.1	chr5	102727611	102727652	+	1	NA	intron (NM_146161, intron 2 of 8)	intron (NM_146161, intron 2 of 8)	-41179	NM_001286468	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding
mm_104675.1	chr11	97664804	97664832	-	1	NA	intron (NM_139311, intron 1 of 19)	intron (NM_139311, intron 1 of 19)	1406	NM_139311	246198	Mm.23685	NM_139311	ENSMUSG00000038437	Mllt6	AI315037|Af17	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 6	protein-coding
mm_128147.1	chr15	31601717	31601783	-	1	NA	promoter-TSS (NM_007637)	promoter-TSS (NM_007637)	54	NM_007637	12465	Mm.282158	NM_007637	ENSMUSG00000022234	Cct5	CCT-epsilon|Ccte|TCP-1-epsilon|TCPE|mKIAA0098	chaperonin containing Tcp1, subunit 5 (epsilon)	protein-coding
mm_96440.1	chr11	67321779	67321783	+	1	NA	Intergenic	Intergenic	-5322	NM_001081250	544791	Mm.461064	NM_001081250	ENSMUSG00000060180	Myh13	MyHC-eo	myosin, heavy polypeptide 13, skeletal muscle	protein-coding
mm_163130.1	chr11	78401384	78401384	+	1	NA	intron (NM_022411, intron 6 of 11)	intron (NM_022411, intron 6 of 11)	6899	NR_003282	790911	Mm.457257	NR_003282	ENSMUSG00000085747	Slc13a2os	Gm11194|OTTMUSG00000000132	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 2, opposite strand	ncRNA
mm_81837.1	chr9	118478852	118478866	+	1	NA	exon (NM_010136, exon 1 of 6)	exon (NM_010136, exon 1 of 6)	670	NM_010136	13813	Mm.200692	NM_010136	ENSMUSG00000032446	Eomes	C77258|TBR-2|Tbr2	eomesodermin	protein-coding
mm_157007.1	chrX	7595211	7595219	-	1	NA	TTS (NM_054039)	TTS (NM_054039)	10205	NM_138603	54638	Mm.288192	NM_138603	ENSMUSG00000031143	Ccdc22	AI481216|DXImx40e|Ppp1r3f|Sfc22	coiled-coil domain containing 22	protein-coding
mm_112267.1	chr12	114128017	114128045	-	1	NA	Intergenic	Intergenic	341435	NR_106062	102465663		NR_106062	ENSMUSG00000105438	Mir7094-1	mmu-mir-7094-1	microRNA 7094-1	ncRNA
mm_27055.1	chr3	27439077	27439084	-	1	NA	intron (NM_173182, intron 23 of 25)	intron (NM_173182, intron 23 of 25)	67729	NM_177330	208188	Mm.194721	NM_177330	ENSMUSG00000051136	Ghsr	C530020I22Rik|Ghsr1a	growth hormone secretagogue receptor	protein-coding
mm_943.1	chr1	56972034	56972044	+	1	NA	promoter-TSS (NM_139146)	promoter-TSS (NM_139146)	570	NR_024325	329160	Mm.419039	NR_024325	ENSMUSG00000087022	9130024F11Rik	B530002L08|EG329160	RIKEN cDNA 9130024F11 gene	ncRNA
mm_42913.1	chr5	122650406	122650412	+	1	NA	promoter-TSS (NM_001284402)	promoter-TSS (NM_001284402)	-15	NM_001284402	18439	Mm.42026	NM_011027	ENSMUSG00000029468	P2rx7	AI467586|P2X(7)|P2X7R	purinergic receptor P2X, ligand-gated ion channel, 7	protein-coding
mm_164895.1	chr18	65222987	65222993	+	1	NA	intron (NR_105742, intron 4 of 6)	intron (NR_105742, intron 4 of 6)	-25871	NR_029600	387231		NR_029600	ENSMUSG00000065402	Mir122	Mir122a|Mirn122a|mir-122|mmu-mir-122	microRNA 122	ncRNA
mm_166502.1	chr6	4538656	4538668	+	1	NA	exon (NM_007743, exon 50 of 52)	exon (NM_007743, exon 50 of 52)	33044	NM_007743	12843	Mm.277792	NM_007743	ENSMUSG00000029661	Col1a2	AA960264|AI325291|Col1a-2|Cola-2|Cola2|oim	collagen, type I, alpha 2	protein-coding
mm_167193.1	chr7	142577912	142577926	+	1	NA	promoter-TSS (NR_030416)	promoter-TSS (NR_030416)	227	NR_130974	14955	Mm.14802	NR_001592	ENSMUSG00000000031	H19	AI747191	H19, imprinted maternally expressed transcript	ncRNA
mm_81102.1	chr9	106429550	106429602	+	1	NA	5' UTR (NM_001324533, exon 1 of 4)	5' UTR (NM_001324533, exon 1 of 4)	165	NM_009082	19944	Mm.288696	NM_009082	ENSMUSG00000048758	Rpl29	Rpl43	ribosomal protein L29	protein-coding
mm_23563.1	chr3	63266816	63266819	+	1	NA	Intergenic	Intergenic	-28618	NM_001289462	17380	Mm.296022	NM_008604	ENSMUSG00000027820	Mme	6030454K05Rik|C85356|CALLA|CD10|NEP|SFE	membrane metallo endopeptidase	protein-coding
mm_150757.1	chr19	44107522	44107588	+	1	NA	promoter-TSS (NM_007700)	promoter-TSS (NM_007700)	-78	NM_001162410	12675	Mm.3996	NM_007700	ENSMUSG00000025199	Chuk	AI256658|Chuk1|Fbx24|Fbxo24|IKBKA|IKK1|Ikka|NFKBIKA	conserved helix-loop-helix ubiquitous kinase	protein-coding
mm_2889.1	chr1	131867487	131867528	+	1	NA	intron (NM_144875, intron 1 of 5)	intron (NM_144875, intron 1 of 5)	230	NM_144875	226422	Mm.34027	NM_144875	ENSMUSG00000026433	Rab29	Rab7l1	RAB29, member RAS oncogene family	protein-coding
mm_40530.1	chr5	57920241	57920255	+	1	NA	intron (NM_001122758, intron 2 of 2)	B1_Mur2|SINE|Alu	202167	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_101795.1	chr11	46196052	46196067	-	1	NA	3' UTR (NM_001252459, exon 31 of 31)	3' UTR (NM_001252459, exon 31 of 31)	25972	NR_106098	102465715		NR_106098	ENSMUSG00000099331	Mir7239	Gm27504|mmu-mir-7239	microRNA 7239	ncRNA
mm_7706.1	chr1	130449150	130449175	-	1	NA	intron (NM_010016, intron 7 of 9)	intron (NM_010016, intron 7 of 9)	13582	NM_010016	13136	Mm.101591	NM_010016	ENSMUSG00000026399	Cd55	Daf|Daf-GPI|Daf1|GPI-DAF	CD55 molecule, decay accelerating factor for complement	protein-coding
mm_146109.1	chr18	74230185	74230189	+	1	NA	Intergenic	MERV1_LTR|LTR|ERV1	13975	NM_028868	74322	Mm.17537	NM_028868	ENSMUSG00000024560	Cxxc1	2410002I16Rik|5830420C16Rik|AI426635|Cfp1|Cgbp|PHF18	CXXC finger 1 (PHD domain)	protein-coding
mm_65419.1	chr7	25250872	25250881	-	1	NA	promoter-TSS (NM_010155)	promoter-TSS (NM_010155)	-118	NM_010155	13875	Mm.8068	NM_010155	ENSMUSG00000040857	Erf	-	Ets2 repressor factor	protein-coding
mm_137828.1	chr17	30651680	30651701	+	1	NA	intron (NM_013811, intron 7 of 92)	ID4|SINE|ID	24754	NM_013811	13417	Mm.426017	NM_013811	ENSMUSG00000033826	Dnah8	ATPase|Dnahc8|Hst6.7b|P1-Loop	dynein, axonemal, heavy chain 8	protein-coding
mm_64003.1	chr7	140173300	140173313	+	1	NA	Intergenic	Intergenic	-2798	NM_146518	258511	Mm.334306	NM_146518	ENSMUSG00000051051	Olfr523	MOR104-4	olfactory receptor 523	protein-coding
mm_22288.1	chr2	180225909	180225919	-	1	NA	promoter-TSS (NM_001081171)	promoter-TSS (NM_001081171)	-55	NM_001081171	16776	Mm.4339	NM_001081171	ENSMUSG00000015647	Lama5	AA408760|AA408762|AI853660|[a]5|laminin-511|mKIAA0533	laminin, alpha 5	protein-coding
mm_122274.1	chr14	34378572	34378582	-	1	NA	intron (NM_153127, intron 1 of 6)	intron (NM_153127, intron 1 of 6)	3073	NM_153127	105450	Mm.272673	NM_153127	ENSMUSG00000041445	Mmrn2	AA986839|ENDOGLYX1|Emilin3|EndoGlyx-1	multimerin 2	protein-coding
mm_19648.1	chr2	102865536	102865538	-	1	NA	intron (NM_001039150, intron 1 of 13)	intron (NM_001039150, intron 1 of 13)	36128	NM_001177785	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_165274.1	chr2	76747145	76747156	-	1	NA	exon (NM_011652, exon 275 of 313)	exon (NM_011652, exon 275 of 313)	71835	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_148132.1	chr18	75697613	75697626	-	1	NA	promoter-TSS (NM_201354)	promoter-TSS (NM_201354)	77	NM_201354	269037	Mm.36745	NM_201354	ENSMUSG00000052928	Ctif	Gm672	CBP80/20-dependent translation initiation factor	protein-coding
mm_108301.1	chr12	79297346	79297377	+	1	NA	promoter-TSS (NM_009014)	promoter-TSS (NM_009014)	10	NM_001252562	19363	Mm.341756	NM_009014	ENSMUSG00000059060	Rad51b	AI553500|R51H2|Rad51l1|mREC2	RAD51 paralog B	protein-coding
mm_117563.1	chr13	85284076	85284102	-	1	NA	intron (NM_145452, intron 1 of 24)	intron (NM_145452, intron 1 of 24)	5397	NM_145452	218397	Mm.259653	NM_145452	ENSMUSG00000021549	Rasa1	Gap|RasGAP|Rasa	RAS p21 protein activator 1	protein-coding
mm_28553.1	chr3	93279809	93279822	-	1	NA	Intergenic	Intergenic	-39934	NM_133698	68723	Mm.208047	NM_133698	ENSMUSG00000041991	Hrnr	1110033K19Rik|A530063N20Rik|S100a18	hornerin	protein-coding
mm_169206.1	chr13	66441234	66441245	+	1	NA	promoter-TSS (NM_001290196)	promoter-TSS (NM_001290196)	-121	NM_001290196	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
mm_111250.1	chr12	84876484	84876497	-	1	NA	promoter-TSS (NM_013589)	promoter-TSS (NM_013589)	5	NM_013589	16997	Mm.3900	NM_013589	ENSMUSG00000002020	Ltbp2	AW208642	latent transforming growth factor beta binding protein 2	protein-coding
mm_159197.1	chr2	119547476	119547476	-	1	NA	promoter-TSS (NM_019769)	promoter-TSS (NM_019769)	151	NM_172857	241624	Mm.212773	NM_172857	ENSMUSG00000048647	Exd1	4932702D22Rik|Exdl1|mExd1	exonuclease 3'-5' domain containing 1	protein-coding
mm_9230.1	chr1	171251665	171251675	-	1	NA	intron (NM_172845, intron 1 of 8)	intron (NM_172845, intron 1 of 8)	1541	NM_172845	240913	Mm.491147	NM_172845	ENSMUSG00000006403	Adamts4	ADAM-TS4|ADAMTS-2|ADMP-1	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 4	protein-coding
mm_90053.1	chr10	116177218	116177243	+	1	NA	promoter-TSS (NM_001161839)	promoter-TSS (NM_001161839)	-28	NM_001161839	19279	Mm.336316	NM_011217	ENSMUSG00000020151	Ptprr	Gmcp1|PTP-SL|PTPBR7|RPTPRR|mPTP213	protein tyrosine phosphatase, receptor type, R	protein-coding
mm_151867.1	chr19	5797740	5797760	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	-1769	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_36518.1	chr4	84532256	84532256	-	1	NA	intron (NM_172870, intron 2 of 5)	intron (NM_172870, intron 2 of 5)	142830	NM_172870	242509	Mm.190774	NM_172870	ENSMUSG00000028487	Bnc2	5031434M05Rik|8430420F16Rik	basonuclin 2	protein-coding
mm_89800.1	chr10	102512447	102512458	+	1	NA	5' UTR (NM_146240, exon 1 of 2)	5' UTR (NM_146240, exon 1 of 2)	230	NM_146240	237504	Mm.282672	NM_146240	ENSMUSG00000044921	Rassf9	AW322107|Pamci	Ras association (RalGDS/AF-6) domain family (N-terminal) member 9	protein-coding
mm_89928.1	chr10	111232421	111232456	+	1	NA	intron (NM_175489, intron 3 of 23)	RMER17C2|LTR|ERVK	-66241	NM_027914	71769	Mm.45256	NM_027914	ENSMUSG00000035759	Bbs10	1300007O09Rik|AI452285	Bardet-Biedl syndrome 10 (human)	protein-coding
mm_50472.1	chr6	48987888	48987896	+	1	NA	exon (NM_172888, exon 1 of 5)	exon (NM_172888, exon 1 of 5)	1031	NM_172888	243377	Mm.446302	NM_172888	ENSMUSG00000039215	Svs1	9530003A11	seminal vesicle secretory protein 1	protein-coding
mm_84177.1	chr9	59949719	59949731	-	1	NA	intron (NM_013708, intron 1 of 7)	intron (NM_013708, intron 1 of 7)	354	NM_013708	23958	Mm.103641	NM_013708	ENSMUSG00000032292	Nr2e3	A930035N01Rik|PNR|RNR|rd7	nuclear receptor subfamily 2, group E, member 3	protein-coding
mm_106916.1	chr12	8216671	8216684	+	1	NA	intron (NM_001167767, intron 1 of 5)	intron (NM_001167767, intron 1 of 5)	8550	NM_001167767	68832	Mm.25608	NM_172401	ENSMUSG00000037669	Ldah	1110057K04Rik|mLDAH	lipid droplet associated hydrolase	protein-coding
mm_133335.1	chr16	78707272	78707274	+	1	NA	Intergenic	Intergenic	-130585	NM_025967	67102	Mm.37332	NM_025967	ENSMUSG00000022864	D16Ertd472e	1700010I10Rik|2310009O17Rik|E330003K22Rik|Eurl	DNA segment, Chr 16, ERATO Doi 472, expressed	protein-coding
mm_35123.1	chr4	11147718	11147730	-	1	NA	Intergenic	Intergenic	-8717	NM_001199105	60599	Mm.393018	NM_021897	ENSMUSG00000028211	Trp53inp1	2700057G22Rik|SIP|SIP18|SIP27|Stinp|Teap	transformation related protein 53 inducible nuclear protein 1	protein-coding
mm_74617.1	chr8	12831910	12831927	-	1	NA	promoter-TSS (NR_045775)	promoter-TSS (NR_045775)	1	NR_045775	100504249	Mm.441494	NR_045775	ENSMUSG00000084780	Gm15350	OTTMUSG00000020611	predicted gene 15350	ncRNA
mm_28699.1	chr3	95543122	95543165	-	1	NA	exon (NM_021281, exon 4 of 8)	exon (NM_021281, exon 4 of 8)	16357	NM_001267695	13040	Mm.3619	NM_021281	ENSMUSG00000038642	Ctss	Cats	cathepsin S	protein-coding
mm_5522.1	chr1	37864802	37864813	-	1	NA	intron (NM_001290720, intron 1 of 17)	CpG	275	NM_207228	211484	Mm.332756	NM_207228	ENSMUSG00000060771	Tsga10	4933432N21Rik|AI843383|Gm217|Mtsga10	testis specific 10	protein-coding
mm_138782.1	chr17	37270521	37270536	+	1	NA	exon (NM_013819, exon 2 of 8)	exon (NM_013819, exon 2 of 8)	294	NM_013819	14991	Mm.14437	NM_013819	ENSMUSG00000016206	H2-M3	H-2M3|Hmt|M3a|MuprM3|MuprM301|MuprM302|R4B2	histocompatibility 2, M region locus 3	protein-coding
mm_124463.1	chr14	121159654	121159684	-	1	NA	intron (NM_134082, intron 2 of 26)	intron (NM_134082, intron 2 of 26)	124095	NM_134082	223254	Mm.223980	NM_134082	ENSMUSG00000025555	Farp1	AW228844|BC030329|Cdep	FERM, RhoGEF (Arhgef) and pleckstrin domain protein 1 (chondrocyte-derived)	protein-coding
mm_40283.1	chr5	43233244	43233259	+	1	NA	promoter-TSS (NM_001177379)	promoter-TSS (NM_001177379)	-212	NM_175937	231207	Mm.7233	NM_175937	ENSMUSG00000039782	Cpeb2	A630055H10Rik|Cpe-bp2	cytoplasmic polyadenylation element binding protein 2	protein-coding
mm_113622.1	chr13	41636646	41636693	+	1	NA	3' UTR (NM_001163572, exon 3 of 3)	3' UTR (NM_001163572, exon 3 of 3)	-12774	NM_177808	328231	Mm.227476	NM_177808	ENSMUSG00000054258	Gm5082	A030008J09|EG328231	predicted gene 5082	protein-coding
mm_157495.1	chrX	48454223	48454243	-	1	NA	intron (NM_019680, intron 1 of 8)	CpG	8899	NM_019680	56501	Mm.36808	NM_019680	ENSMUSG00000031103	Elf4	AV314029|BC042423|ENSMUSG00000053512|Gm9907|Mef	E74-like factor 4 (ets domain transcription factor)	protein-coding
mm_59156.1	chr7	24370341	24370347	+	1	NA	promoter-TSS (NM_001163510)	promoter-TSS (NM_001163510)	81	NM_008433	16534	Mm.9911	NM_008433	ENSMUSG00000054342	Kcnn4	IK1|IKCA1|KCA4|KCa3.1|SK4|SKCas|mIKCa1	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4	protein-coding
mm_168917.1	chr12	58156465	58156465	+	1	NA	Intergenic	L1Md_A|LINE|L1	-55339	NM_009216	20605	Mm.278336	NM_009216	ENSMUSG00000035431	Sstr1	SRIF-2|SS-1-R|SS1-R|SS1R|Smstr-1|Smstr1|sst1	somatostatin receptor 1	protein-coding
mm_46920.1	chr5	114658415	114658424	-	1	NA	promoter-TSS (NM_022017)	promoter-TSS (NM_022017)	2	NM_022017	63873	Mm.266450	NM_022017	ENSMUSG00000014158	Trpv4	0610033B08Rik|OTRPC4|Trp12|VR-OAC|VRL-2|VROAC	transient receptor potential cation channel, subfamily V, member 4	protein-coding
mm_58109.1	chr6	138422514	138422522	-	1	NA	promoter-TSS (NR_126073)	promoter-TSS (NR_126073)	-587	NR_126073	319702	Mm.403785	NR_126072	ENSMUSG00000089957	A830011K09Rik	-	RIKEN cDNA A830011K09 gene	ncRNA
mm_82076.1	chr9	122981543	122981557	+	1	NA	intron (NM_010620, intron 10 of 34)	intron (NM_010620, intron 10 of 34)	30469	NM_010620	209737	Mm.278920	NM_010620	ENSMUSG00000036768	Kif15	3110023M17Rik|3930402I10Rik|D330038N01|HKLP2|Knsl7|b2b1117.1Clo|b2b1117.1aClo	kinesin family member 15	protein-coding
mm_9546.1	chr1	173913029	173913042	-	1	NA	promoter-TSS (NM_001301745)	promoter-TSS (NM_001301745)	11	NM_001301745	381308	Mm.490248	NM_001033450	ENSMUSG00000026536	Ifi211	A730048F03|Ifi205b|Mnda|ifi-205-B	interferon activated gene 211	protein-coding
mm_125578.1	chr15	59461997	59462023	+	1	NA	intron (NM_026746, intron 4 of 6)	Lx3_Mus|LINE|L1	87812	NM_001164604	68501	Mm.27762	NM_026746	ENSMUSG00000059586	Nsmce2	1110014D18Rik|AI661537	NSE2/MMS21 homolog, SMC5-SMC6 complex SUMO ligase	protein-coding
mm_101602.1	chr11	34783123	34783135	-	1	NA	intron (NM_033374, intron 1 of 51)	intron (NM_033374, intron 1 of 51)	776	NM_033374	94176	Mm.380679	NM_033374	ENSMUSG00000020143	Dock2	AI662014|AW122239|CED-5|Hch|MBC	dedicator of cyto-kinesis 2	protein-coding
mm_12519.1	chr2	72137169	72137182	+	1	NA	intron (NM_001204166, intron 1 of 27)	intron (NM_001204166, intron 1 of 27)	82558	NM_001204166	56508	Mm.196153	NM_019688	ENSMUSG00000049044	Rapgef4	1300003D15Rik|5730402K07Rik|6330581N18Rik|EPAC 2|Epac-2|Epac2|mKIAA4040	Rap guanine nucleotide exchange factor (GEF) 4	protein-coding
mm_7074.1	chr1	88205751	88205770	-	1	NA	promoter-TSS (NM_008299)	promoter-TSS (NM_008299)	-12	NM_008299	15504	Mm.439983	NM_008299	ENSMUSG00000081984	Dnajb3	Hsj3|MSJ-1|Msj1	DnaJ heat shock protein family (Hsp40) member B3	protein-coding
mm_71661.1	chr8	60632819	60632836	+	1	NA	promoter-TSS (NM_027756)	promoter-TSS (NM_027756)	2	NM_001293769	71306	Mm.23242	NM_027756	ENSMUSG00000031647	Mfap3l	4933428A15Rik|5430405D20Rik|AI461995|AW125052|NYD-sp9|mKIAA0626	microfibrillar-associated protein 3-like	protein-coding
mm_13957.1	chr2	121358592	121358713	+	1	NA	promoter-TSS (NM_009897)	promoter-TSS (NM_009897)	11	NM_009897	12716	Mm.252145	NM_009897	ENSMUSG00000000308	Ckmt1	Mt-CK|ScCKmit|UbCKmit|mi-CK	creatine kinase, mitochondrial 1, ubiquitous	protein-coding
mm_30982.1	chr4	34893752	34893759	+	1	NA	promoter-TSS (NM_009889)	promoter-TSS (NM_009889)	-24	NM_009889	12640	Mm.1361	NM_009889	ENSMUSG00000028298	Cga	CG-alpha|FSHA|GPHA1|GPHalpha|HCG|LHA|Tsha|aGSU|alpha-GSU|alphaGSU|alphaSU	glycoprotein hormones, alpha subunit	protein-coding
mm_86094.1	chr9	115186039	115186071	-	1	NA	intron (NM_148958, intron 4 of 9)	intron (NM_148958, intron 4 of 9)	96015	NR_029430	111186	Mm.484753	NR_029430		Stmn1-rs1	Lag-rs1|Lap18-rs1	stathmin 1, related sequence 1	pseudo
mm_43454.1	chr5	136199024	136199060	+	1	NA	promoter-TSS (NM_025774)	promoter-TSS (NM_025774)	-88	NM_025774	66801	Mm.425295	NM_025774	ENSMUSG00000039737	Prkrip1	8430424D23Rik|C114	Prkr interacting protein 1 (IL11 inducible)	protein-coding
mm_91697.1	chr10	44003814	44003818	-	1	NA	exon (NM_172393, exon 1 of 20)	exon (NM_172393, exon 1 of 20)	1030	NM_172393	11630	Mm.292082	NM_172393	ENSMUSG00000019866	Aim1	AI462491|AI463325	absent in melanoma 1	protein-coding
mm_1124.1	chr1	60117230	60117240	+	1	NA	intron (NR_104344, intron 2 of 11)	intron (NR_104344, intron 2 of 11)	9152	NR_104344	241066	Mm.276441	NM_139150	ENSMUSG00000026017	Carf	Als2cr8|ECBRC-FC1|ECBRC-FC2	calcium response factor	protein-coding
mm_112790.1	chr13	20185404	20185410	+	1	NA	5' UTR (NM_080288, exon 2 of 22)	5' UTR (NM_080288, exon 2 of 22)	94900	NM_080288	140580	Mm.342392	NM_080288	ENSMUSG00000041112	Elmo1	6330578D22Rik|C230095H21Rik|CED-12	engulfment and cell motility 1	protein-coding
mm_8541.1	chr1	155097987	155098002	-	1	NA	3' UTR (NM_010500, exon 1 of 1)	3' UTR (NM_010500, exon 1 of 1)	1642	NM_010500	15939	Mm.12246	NM_010500	ENSMUSG00000056708	Ier5	-	immediate early response 5	protein-coding
mm_58223.1	chr6	144209634	144209647	-	1	NA	promoter-TSS (NM_011444)	promoter-TSS (NM_011444)	-72	NM_001243163	20678	Mm.1752	NM_011444	ENSMUSG00000041540	Sox5	A730017D01Rik|AI528773	SRY (sex determining region Y)-box 5	protein-coding
mm_24694.1	chr3	95032785	95032791	+	1	NA	TTS (NM_008951)	TTS (NM_008951)	9826	NM_001282017	19185	Mm.2261	NM_008951	ENSMUSG00000005625	Psmd4	Af1|Mcb1|angiocidin	proteasome (prosome, macropain) 26S subunit, non-ATPase, 4	protein-coding
mm_83162.1	chr9	40465819	40465825	-	1	NA	Intergenic	Intergenic	-10058	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_85532.1	chr9	106476591	106476675	-	1	NA	promoter-TSS (NM_145620)	promoter-TSS (NM_145620)	316	NM_001311150	235587	Mm.273659	NM_145619	ENSMUSG00000023249	Parp3	A930002C11Rik|AW990611|Adprt3|Adprtl3|PARP-3|pADPRT-3	poly (ADP-ribose) polymerase family, member 3	protein-coding
mm_104502.1	chr11	95914885	95914901	-	1	NA	promoter-TSS (NM_008081)	promoter-TSS (NM_008081)	-22	NM_008081	14422	Mm.340702	NM_008081	ENSMUSG00000013418	B4galnt2	AI593864|Dlb-1|Dlb1|Galg2|Galgt2|Ggm3|Igf2bp1	beta-1,4-N-acetyl-galactosaminyl transferase 2	protein-coding
mm_79587.1	chr9	58273107	58273123	+	1	NA	Intergenic	Intergenic	19951	NM_026942	69106	Mm.216502	NM_026942	ENSMUSG00000032333	Stoml1	1810015E19Rik|AI847431|SLP1|STORP|UNC24|WPB72	stomatin-like 1	protein-coding
mm_160054.1	chr7	3739889	3739889	-	1	NA	intron (NM_001289428, intron 12 of 12)	intron (NM_001289428, intron 12 of 12)	-19507	NM_011095	18733	Mm.326531	NM_011095	ENSMUSG00000058818	Pirb	Gp91|LIR-3|Lilrb3|PIR-B	paired Ig-like receptor B	protein-coding
mm_35192.1	chr4	16013869	16013884	-	1	NA	promoter-TSS (NM_145950)	promoter-TSS (NM_145950)	1	NM_145950	209212	Mm.46455	NM_145950	ENSMUSG00000041153	Osgin2	BC010311|C230027H09Rik	oxidative stress induced growth inhibitor family member 2	protein-coding
mm_130699.1	chr15	100685163	100685243	-	1	NA	exon (NM_033612, exon 3 of 8)	exon (NM_033612, exon 3 of 8)	2717	NM_033612	109901	Mm.2131	NM_033612	ENSMUSG00000023031	Cela1	1810009A17Rik|1810062B19Rik|Ela-1|Ela1|PC-TsF	chymotrypsin-like elastase family, member 1	protein-coding
mm_47807.1	chr5	133598398	133598404	-	1	NA	Intergenic	ORR1C2|LTR|ERVL-MaLR	-501347	NM_030719	80909	Mm.45218	NM_030719	ENSMUSG00000015944	Gatsl2	7530428J21Rik|AW742413|Gats|Gatsl1	GATS protein-like 2	protein-coding
mm_117296.1	chr13	66933081	66933092	-	1	NA	promoter-TSS (NM_025547)	promoter-TSS (NM_025547)	-14	NM_025547	66410	Mm.347939	NM_025547	ENSMUSG00000021519	Mterf3	2410017I18Rik|Mterfd1	mitochondrial transcription termination factor 3	protein-coding
mm_121106.1	chr14	101198996	101199038	+	1	NA	exon (NM_029680, exon 3 of 3)	exon (NM_029680, exon 3 of 3)	1052	NM_029680	76627	Mm.31415	NM_029680	ENSMUSG00000042888	Prr30	1700110M21Rik	proline rich 30	protein-coding
mm_45194.1	chr5	52190485	52190524	-	1	NA	promoter-TSS (NM_001042620)	promoter-TSS (NM_001042620)	42	NR_104311	13204	Mm.993	NM_007839	ENSMUSG00000029169	Dhx15	DBP1|DEAH9|Ddx15|HRH2|mDEAH9	DEAH (Asp-Glu-Ala-His) box polypeptide 15	protein-coding
mm_147230.1	chr18	38209768	38209786	-	1	NA	promoter-TSS (NM_029357)	promoter-TSS (NM_029357)	-15	NM_029357	75599	Mm.36560	NM_029357	ENSMUSG00000051375	Pcdh1	2010005A06Rik|AI585920	protocadherin 1	protein-coding
mm_21088.1	chr2	153109019	153109022	-	1	NA	intron (NM_001172117, intron 1 of 12)	intron (NM_001172117, intron 1 of 12)	552	NM_010407	15162	Mm.715	NM_010407	ENSMUSG00000003283	Hck	AI849071|Bmk	hemopoietic cell kinase	protein-coding
mm_159749.1	chr5	76840817	76840817	+	1	NA	exon (NM_001163793, exon 2 of 9)	exon (NM_001163793, exon 2 of 9)	218	NM_001163793	320827	Mm.101504	NM_001163793	ENSMUSG00000036377	C530008M17Rik	2810489J07Rik|4930529A19Rik|4931405B09Rik|Kiaa1211|mKIAA1211	RIKEN cDNA C530008M17 gene	protein-coding
mm_165369.1	chr2	127336037	127336046	+	1	NA	promoter-TSS (NM_010090)	promoter-TSS (NM_010090)	-118	NM_010090	13537	Mm.4729	NM_010090	ENSMUSG00000027368	Dusp2	PAC1	dual specificity phosphatase 2	protein-coding
mm_134773.1	chr16	23890806	23890861	-	1	NA	promoter-TSS (NM_009215)	promoter-TSS (NM_009215)	11	NM_009215	20604	Mm.2453	NM_009215	ENSMUSG00000004366	Sst	SOM|SRIF|SS|Smst	somatostatin	protein-coding
mm_2718.1	chr1	128151807	128151834	+	1	NA	5' UTR (NM_181750, exon 2 of 27)	5' UTR (NM_181750, exon 2 of 27)	48514	NM_181750	226412	Mm.221041	NM_181750	ENSMUSG00000056211	R3hdm1	R3hdm	R3H domain containing 1	protein-coding
mm_70131.1	chr7	143238197	143238209	-	1	NA	non-coding (NR_001461, exon 1 of 1)	non-coding (NR_001461, exon 1 of 1)	58344	NR_001461	63830	Mm.356096	NR_001461	ENSMUSG00000101609	Kcnq1ot1	Kvlqt1-as|Lit1|Tssc8	KCNQ1 overlapping transcript 1	ncRNA
mm_51006.1	chr6	64729119	64729132	+	1	NA	promoter-TSS (NM_007500)	promoter-TSS (NM_007500)	-21	NM_007500	11921	Mm.57229	NM_007500	ENSMUSG00000073043	Atoh1	Hath1|MATH-1|Math1|bHLHa14	atonal bHLH transcription factor 1	protein-coding
mm_33638.1	chr4	132974158	132974162	+	1	NA	promoter-TSS (NM_010208)	promoter-TSS (NM_010208)	65	NM_010208	14191	Mm.271665	NM_010208	ENSMUSG00000028874	Fgr	-	FGR proto-oncogene, Src family tyrosine kinase	protein-coding
mm_32233.1	chr4	102254934	102254943	+	1	NA	promoter-TSS (NM_019840)	promoter-TSS (NM_019840)	-1	NM_019840	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_95733.1	chr11	54626565	54626586	+	1	NA	intron (NM_175258, intron 10 of 27)	intron (NM_175258, intron 10 of 27)	30429	NM_001252497	192786	Mm.254404	NM_175258	ENSMUSG00000037533	Rapgef6	A530068K01|AI844632|BB085664|C030018K18Rik|PDZ-GEF2|Pdzgef2|RA-GEF-2|Ragef2|mKIAA4052	Rap guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_13404.1	chr2	103980967	103980985	+	1	NA	exon (NM_001142337, exon 4 of 4)	exon (NM_001142337, exon 4 of 4)	10689	NM_001142335	16909	Mm.29266	NM_008505	ENSMUSG00000032698	Lmo2	Rbtn-2|Rbtn2|Rhom-2|Ttg2	LIM domain only 2	protein-coding
mm_72479.1	chr8	83608537	83608544	+	1	NA	promoter-TSS (NM_001308227)	promoter-TSS (NM_001308227)	-8	NM_001308227	81489	Mm.282092	NM_018808	ENSMUSG00000005483	Dnajb1	0610007I11Rik|DjB1|HSPF1|Hdj1|Hsp40	DnaJ heat shock protein family (Hsp40) member B1	protein-coding
mm_2947.1	chr1	132342338	132342344	+	1	NA	Intergenic	Intergenic	25607	NM_001311108	68875	Mm.273785	NM_178874	ENSMUSG00000042066	Tmcc2	1110063G11Rik	transmembrane and coiled-coil domains 2	protein-coding
mm_22581.1	chr3	10760336	10760380	+	1	NA	Intergenic	RLTR13D6|LTR|ERVK	-320228	NM_001127191	74718	Mm.440548	NM_029068	ENSMUSG00000027534	Snx16	4930522N22Rik|AI117577|AI747675	sorting nexin 16	protein-coding
mm_131636.1	chr16	20421254	20421261	+	1	NA	intron (NM_176839, intron 2 of 6)	MTC|LTR|ERVL-MaLR	5137	NM_013790	27416	Mm.20845	NM_013790	ENSMUSG00000022822	Abcc5	2900011L11Rik|AI132311|Abcc5a|Abcc5b|Mrp5	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	protein-coding
mm_129429.1	chr15	78493608	78493617	-	1	NA	intron (NM_008368, intron 1 of 9)	intron (NM_008368, intron 1 of 9)	1454	NM_008368	16185	Mm.35287	NM_008368	ENSMUSG00000068227	Il2rb	CD122|IL-15Rbeta|IL15Rbeta|Il-2/15Rbeta|Il-2Rbeta|p70	interleukin 2 receptor, beta chain	protein-coding
mm_30979.1	chr4	34886643	34886654	+	1	NA	Intergenic	Intergenic	-3700	NM_013889	30046	Mm.38193	NM_013889	ENSMUSG00000039967	Zfp292	5730450D02Rik|5830493J20Rik|9430062L07Rik|AI449016|Krox-10|Zfp-15|Zfp15|Zn-15|Zn-16|mKIAA0530	zinc finger protein 292	protein-coding
mm_72672.1	chr8	84908738	84908767	+	1	NA	5' UTR (NM_010062, exon 1 of 6)	5' UTR (NM_010062, exon 1 of 6)	128	NM_010062	13423	Mm.350831	NM_010062	ENSMUSG00000003812	Dnase2a	Dnase2	deoxyribonuclease II alpha	protein-coding
mm_89020.1	chr10	82128025	82128046	+	1	NA	promoter-TSS (NM_001163064)	promoter-TSS (NM_001163064)	22	NM_001163064	216177	Mm.482395	NM_001163064	ENSMUSG00000078435	AU041133	-	expressed sequence AU041133	protein-coding
mm_158605.1	chrX	152327431	152327491	-	1	NA	promoter-TSS (NR_040269)	promoter-TSS (NR_040269)	32	NR_040269	72997	Mm.254833	NR_040269		Kantr	2810454L23Rik|2900056M20Rik|Spasm	Kdm5c adjacent non-coding transcript	ncRNA
mm_69725.1	chr7	140770179	140770196	-	1	NA	exon (NM_021282, exon 5 of 9)	exon (NM_021282, exon 5 of 9)	6355	NM_021282	13106	Mm.21758	NM_021282	ENSMUSG00000025479	Cyp2e1	Cyp2e	cytochrome P450, family 2, subfamily e, polypeptide 1	protein-coding
mm_33453.1	chr4	130709697	130709703	+	1	NA	intron (NM_001159606, intron 3 of 17)	intron (NM_001159606, intron 3 of 17)	-39938	NR_028565	100217460		NR_028565	ENSMUSG00000065196	Snord85	MBII-251|Z50	small nucleolar RNA, C/D box 85	snoRNA
mm_70060.1	chr7	142652032	142652042	-	1	NA	3' UTR (NM_010514, exon 4 of 4)	3' UTR (NM_010514, exon 4 of 4)	2959	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_58737.1	chr7	13030476	13030493	+	1	NA	exon (NM_011588, exon 16 of 17)	exon (NM_011588, exon 16 of 17)	4293	NM_026885	68953	Mm.295670	NM_026885	ENSMUSG00000033916	Chmp2a	1500016L11Rik	charged multivesicular body protein 2A	protein-coding
mm_75928.1	chr8	71507743	71507766	-	1	NA	exon (NM_032398, exon 3 of 6)	exon (NM_032398, exon 3 of 6)	4015	NM_032398	84094	Mm.260768	NM_032398	ENSMUSG00000034845	Plvap	MECA32|Pv1	plasmalemma vesicle associated protein	protein-coding
mm_102406.1	chr11	59163760	59163788	-	1	NA	promoter-TSS (NM_001270791)	promoter-TSS (NM_001270791)	-29	NM_173785	216792	Mm.266175	NM_173785	ENSMUSG00000049287	Iba57	4930543L23Rik|A230051G13Rik|C1orf69	IBA57 homolog, iron-sulfur cluster assembly	protein-coding
mm_98706.1	chr11	96304123	96304139	+	1	NA	exon (NM_008268, exon 1 of 2)	exon (NM_008268, exon 1 of 2)	619	NM_008268	15413	Mm.207	NM_008268	ENSMUSG00000038700	Hoxb5	AI385717|Hox-2.1	homeobox B5	protein-coding
mm_16254.1	chr2	173215706	173215749	+	1	NA	exon (NM_021394, exon 3 of 8)	exon (NM_021394, exon 3 of 8)	3195	NM_021394	58203	Mm.116687	NM_021394	ENSMUSG00000027514	Zbp1	2010010H03Rik|Dai|Dlm1|mZaDLM	Z-DNA binding protein 1	protein-coding
mm_36973.1	chr4	109476598	109476608	-	1	NA	promoter-TSS (NM_013876)	promoter-TSS (NM_013876)	-98	NM_013876	29864	Mm.392580	NM_013876	ENSMUSG00000028557	Rnf11	-	ring finger protein 11	protein-coding
mm_59022.1	chr7	19282580	19282609	+	1	NA	promoter-TSS (NM_013648)	promoter-TSS (NM_013648)	-30	NM_013648	20167	Mm.24142	NM_013648	ENSMUSG00000030401	Rtn2	MMS10-P|Ms10p|NSPLI|Nspl1	reticulon 2 (Z-band associated protein)	protein-coding
mm_89663.1	chr10	97483454	97483475	+	1	NA	exon (NM_007833, exon 2 of 8)	exon (NM_007833, exon 2 of 8)	1133	NM_007833	13179	Mm.56769	NM_007833	ENSMUSG00000019929	Dcn	DC|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding
mm_145471.1	chr18	60301205	60301215	+	1	NA	3' UTR (NM_001101475, exon 2 of 2)	3' UTR (NM_001101475, exon 2 of 2)	7830	NM_001101475	240328	Mm.329461	NM_001101475	ENSMUSG00000090942	F830016B08Rik	Ifgga4	RIKEN cDNA F830016B08 gene	protein-coding
mm_150825.1	chr19	44562842	44562879	+	1	NA	promoter-TSS (NM_176958)	promoter-TSS (NM_176958)	6	NM_176958	319594	Mm.145278	NM_176958	ENSMUSG00000036450	Hif1an	2310046M24Rik|A830014H24Rik|FIH|FIH1	hypoxia-inducible factor 1, alpha subunit inhibitor	protein-coding
mm_134899.1	chr16	30039303	30039313	-	1	NA	non-coding (NR_045878, exon 1 of 4)	non-coding (NR_045878, exon 1 of 4)	171	NR_045878	71528	Mm.297640	NR_045878		9030404E10Rik	-	RIKEN cDNA 9030404E10 gene	ncRNA
mm_119071.1	chr14	30870636	30870646	+	1	NA	intron (NM_028839, intron 4 of 7)	intron (NM_028839, intron 4 of 7)	-8616	NM_181390	66175	Mm.220895	NM_181390	ENSMUSG00000042485	Mustn1	1110028G01Rik|Mustang	musculoskeletal, embryonic nuclear protein 1	protein-coding
mm_171759.1	chr5	105110271	105110291	-	1	NA	promoter-TSS (NM_172777)	promoter-TSS (NM_172777)	11	NM_172777	236573	Mm.425261	NM_172777	ENSMUSG00000029298	Gbp9	-	guanylate-binding protein 9	protein-coding
mm_81416.1	chr9	109055030	109055040	+	1	NA	intron (NM_026381, intron 1 of 3)	intron (NM_026381, intron 1 of 3)	169	NM_026381	66940	Mm.196533	NM_025858	ENSMUSG00000025647	Shisa5	2310008D10Rik|6430628I05Rik|Scotin|mShisa5	shisa family member 5	protein-coding
mm_50040.1	chr6	41141298	41141307	+	1	NA	Intergenic	Intergenic	-105793	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_168712.1	chr11	99932698	99932706	+	1	NA	Intergenic	CpG	-3589	NM_001025244	432602	Mm.246878	NM_001025244	ENSMUSG00000051481	Krtap31-2	OTTMUSG00000002177	keratin associated protein 31-2	protein-coding
mm_10434.1	chr2	14130843	14130853	+	1	NA	intron (NM_011484, intron 7 of 13)	intron (NM_011484, intron 7 of 13)	-43676	NM_001081310	625286	Mm.158781	NM_001081310	ENSMUSG00000061531	Tmem236	2010003H20Rik|Fam23a|Gm613	transmembrane protein 236	protein-coding
mm_62538.1	chr7	102267295	102267349	+	1	NA	promoter-TSS (NM_009287)	promoter-TSS (NM_009287)	-502	NM_009287	20866	Mm.645	NM_009287	ENSMUSG00000030987	Stim1	SIM	stromal interaction molecule 1	protein-coding
mm_61539.1	chr7	79290566	79290570	+	1	NA	intron (NM_018811, intron 1 of 10)	intron (NM_018811, intron 1 of 10)	17302	NM_018811	54608	Mm.365490	NM_018811	ENSMUSG00000039202	Abhd2	2210009N18Rik|LABH2|Labh-2	abhydrolase domain containing 2	protein-coding
mm_34592.1	chr4	150196095	150196095	+	1	NA	exon (NM_009802, exon 4 of 8)	exon (NM_009802, exon 4 of 8)	5040	NM_009802	12353	Mm.232523	NM_009802	ENSMUSG00000028972	Car6	Ca6|DOC1	carbonic anhydrase 6	protein-coding
mm_4301.1	chr1	171839695	171839699	+	1	NA	promoter-TSS (NM_013489)	promoter-TSS (NM_013489)	0	NM_001252472	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_158879.1	chr1	4858323	4858323	+	1	NA	promoter-TSS (NM_001159751)	promoter-TSS (NM_001159751)	-5	NM_001159751	21399	Mm.207263	NM_011541	ENSMUSG00000033813	Tcea1	S-II	transcription elongation factor A (SII) 1	protein-coding
mm_39550.1	chr5	21785254	21785301	+	1	NA	promoter-TSS (NM_009584)	promoter-TSS (NM_009584)	-6	NM_011188	19181	Mm.2462	NM_011188	ENSMUSG00000028932	Psmc2	-	proteasome (prosome, macropain) 26S subunit, ATPase 2	protein-coding
mm_71525.1	chr8	46852693	46852703	+	1	NA	Intergenic	LTR67B|LTR|ERVL	112953	NM_008391	16363	Mm.1149	NM_008391	ENSMUSG00000031627	Irf2	9830146E22Rik|AI646973|Irf-2	interferon regulatory factor 2	protein-coding
mm_125149.1	chr15	30646704	30646716	+	1	NA	intron (NM_008729, intron 6 of 22)	CpG	-392416	NR_045186	73784	Mm.66947	NR_045186		4930430F21Rik	-	RIKEN cDNA 4930430F21 gene	ncRNA
mm_6495.1	chr1	74267980	74267990	-	1	NA	3' UTR (NM_029711, exon 10 of 10)	3' UTR (NM_029711, exon 10 of 10)	-10615	NM_174985	227289	Mm.246587	NM_174985	ENSMUSG00000064272	Gpbar1	BG37|GPCR|GPR131|M-BAR|TGR5	G protein-coupled bile acid receptor 1	protein-coding
mm_18637.1	chr2	69405820	69405846	-	1	NA	Intergenic	Intergenic	25371	NM_175512	241452	Mm.211655	NM_175512	ENSMUSG00000027068	Dhrs9	C730025I08Rik|Rdh15	dehydrogenase/reductase (SDR family) member 9	protein-coding
mm_31294.1	chr4	45972376	45972386	+	1	NA	promoter-TSS (NM_146142)	promoter-TSS (NM_146142)	84	NM_146142	100121	Mm.275413	NM_146142	ENSMUSG00000035517	Tdrd7	5730495N10Rik|AI447470|PCTAIRE2BP	tudor domain containing 7	protein-coding
mm_59044.1	chr7	19345637	19345651	+	1	NA	exon (NM_007948, exon 2 of 10)	exon (NM_007948, exon 2 of 10)	573	NM_007948	13870	Mm.280913	NM_007948	ENSMUSG00000003549	Ercc1	Ercc-1	excision repair cross-complementing rodent repair deficiency, complementation group 1	protein-coding
mm_104446.1	chr11	95026700	95026714	-	1	NA	TTS (NM_146025)	TTS (NM_146025)	14664	NM_133667	18604	Mm.29768	NM_133667	ENSMUSG00000038967	Pdk2	-	pyruvate dehydrogenase kinase, isoenzyme 2	protein-coding
mm_130600.1	chr15	99780373	99780378	-	1	NA	exon (NM_001113545, exon 11 of 11)	exon (NM_001113545, exon 11 of 11)	-7860	NM_028015	71949	Mm.390821	NM_028015	ENSMUSG00000023021	Cers5	2310081H14Rik|AU045339|AW544927|Lass5|Trh4	ceramide synthase 5	protein-coding
mm_23681.1	chr3	68618106	68618117	+	1	NA	intron (NM_001113419, intron 8 of 10)	intron (NM_001113419, intron 8 of 10)	45743	NM_013928	30953	Mm.331064	NM_013928	ENSMUSG00000027777	Schip1	Nf2ip|Schip-1	schwannomin interacting protein 1	protein-coding
mm_159067.1	chr2	24277009	24277009	+	1	NA	promoter-TSS (NM_019451)	promoter-TSS (NM_019451)	55	NM_001146087	54450	Mm.29261	NM_019451	ENSMUSG00000026983	Il1f5	AI413231|Fil1delta|IL-36Ra|IL36RN|Il-1h3|Il1hy1	interleukin 1 family, member 5 (delta)	protein-coding
mm_118464.1	chr14	11553462	11553484	+	1	NA	promoter-TSS (NM_008981)	promoter-TSS (NM_008981)	-80	NM_008981	19270	Mm.431266	NM_008981	ENSMUSG00000021745	Ptprg	5430405N12Rik|AW046354|AW549872|RPTPgamma	protein tyrosine phosphatase, receptor type, G	protein-coding
mm_36863.1	chr4	107057454	107057495	-	1	NA	exon (NM_025500, exon 6 of 7)	exon (NM_025500, exon 6 of 7)	9392	NM_025500	56280	Mm.29517	NM_025500	ENSMUSG00000028622	Mrpl37	2300004O14Rik|AI132596|MRP-L2|Rpml2	mitochondrial ribosomal protein L37	protein-coding
mm_56555.1	chr6	101150342	101150352	-	1	NA	3' UTR (NM_018884, exon 10 of 10)	3' UTR (NM_018884, exon 10 of 10)	227550	NM_018884	55983	Mm.321654	NM_018884	ENSMUSG00000035357	Pdzrn3	1110020C07Rik|AI429718|AL023082|LNX3|SEMACAP3|Semcap3	PDZ domain containing RING finger 3	protein-coding
mm_36502.1	chr4	83462175	83462183	-	1	NA	3' UTR (NM_001290527, exon 11 of 11)	3' UTR (NM_001290527, exon 11 of 11)	24269	NM_001290527	101739	Mm.105331	NM_133948	ENSMUSG00000028484	Psip1	AA408851|AU015605|Dfs70|Ledgfa|Ledgfb|Psip2	PC4 and SFRS1 interacting protein 1	protein-coding
mm_98071.1	chr11	86201333	86201399	+	1	NA	promoter-TSS (NM_178309)	promoter-TSS (NM_178309)	6	NR_130958	74038	Mm.171304	NR_130958	ENSMUSG00000085208	Brip1os	4632419I22Rik	BRCA1 interacting protein C-terminal helicase 1, opposite strand	ncRNA
mm_75525.1	chr8	57305423	57305427	-	1	NA	intron (NR_110474, intron 3 of 4)	intron (NR_110474, intron 3 of 4)	15434	NR_110474	102636514		NR_110474	ENSMUSG00000100510	Uph	-	upperhand	ncRNA
mm_123057.1	chr14	55660240	55660259	-	1	NA	intron (NM_023397, intron 1 of 5)	intron (NM_023397, intron 1 of 5)	259	NM_023397	67881	Mm.24601	NM_023397	ENSMUSG00000002329	Mdp1	1810034K20Rik|AI035604	magnesium-dependent phosphatase 1	protein-coding
mm_146732.1	chr18	15331798	15331825	-	1	NA	Intergenic	Intergenic	71188	NM_001308647	11829	Mm.250786	NM_009700	ENSMUSG00000024411	Aqp4	WCH4	aquaporin 4	protein-coding
mm_35364.1	chr4	32425185	32425195	-	1	NA	intron (NM_001109661, intron 1 of 4)	intron (NM_001109661, intron 1 of 4)	7755	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_109528.1	chr12	111538332	111538375	+	1	NA	intron (NM_173363, intron 1 of 11)	CpG	252	NM_173363	217869	Mm.271222	NM_173363	ENSMUSG00000021282	Eif5	2810011H21Rik|D12Ertd549e	eukaryotic translation initiation factor 5	protein-coding
mm_27334.1	chr3	50398570	50398612	-	1	NA	intron (NM_011990, intron 6 of 11)	MTD|LTR|ERVL-MaLR	45022	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_21636.1	chr2	164278423	164278430	-	1	NA	promoter-TSS (NM_009300)	promoter-TSS (NM_009300)	-119	NM_009300	20941	Mm.1286	NM_009300	ENSMUSG00000016998	Svs4	SVS-IV|Svp-2|Svp-4|Svp2|Svp4	seminal vesicle secretory protein 4	protein-coding
mm_49285.1	chr6	17662014	17662023	+	1	NA	intron (NM_007604, intron 7 of 9)	intron (NM_007604, intron 7 of 9)	24920	NM_007604	12343	Mm.392504	NM_007604	ENSMUSG00000015733	Capza2	1110053K06Rik|AW208808|Cappa2	capping protein (actin filament) muscle Z-line, alpha 2	protein-coding
mm_133389.1	chr16	84774164	84774174	+	1	NA	promoter-TSS (NM_023844)	promoter-TSS (NM_023844)	46	NM_023844	67374	Mm.41758	NM_023844	ENSMUSG00000053062	Jam2	1110002N23Rik|2410030G21Rik|2410167M24Rik|JAM-2|JAM-B|Jcam2|VE-JAM	junction adhesion molecule 2	protein-coding
mm_72800.1	chr8	87460515	87460521	+	1	NA	Intergenic	Intergenic	12074	NM_019626	12404	Mm.4880	NM_019626	ENSMUSG00000031654	Cbln1	AI323299	cerebellin 1 precursor protein	protein-coding
mm_101488.1	chr11	31370120	31370128	-	1	NA	promoter-TSS (NM_011491)	promoter-TSS (NM_011491)	-63	NM_011491	20856	Mm.32506	NM_011491	ENSMUSG00000020303	Stc2	AW125853|Stc2l|mustc2	stanniocalcin 2	protein-coding
mm_164814.1	chr18	33321884	33321887	+	1	NA	Intergenic	Intergenic	-108023	NM_133774	170459	Mm.127058	NM_133774	ENSMUSG00000024378	Stard4	4632419C16Rik|9030213J02Rik	StAR-related lipid transfer (START) domain containing 4	protein-coding
mm_153484.1	chr19	41302457	41302484	-	1	NA	exon (NM_031376, exon 10 of 17)	exon (NM_031376, exon 10 of 17)	-38466	NM_133352	107358	Mm.246440	NM_133352	ENSMUSG00000025016	Tm9sf3	1810073M23Rik|2810031D16Rik|AI115521|AI413748|AW146116|AW549777|Smbp|mKIAA4036	transmembrane 9 superfamily member 3	protein-coding
mm_68421.1	chr7	109731709	109731715	-	1	NA	promoter-TSS (NM_020051)	promoter-TSS (NM_020051)	20	NM_020051	56787	Mm.29275	NM_020051	ENSMUSG00000035951	Ascl3	Sgn1|bHLHa42	achaete-scute family bHLH transcription factor 3	protein-coding
mm_143046.1	chr17	56874401	56874414	-	1	NA	promoter-TSS (NM_001039114)	promoter-TSS (NM_001039114)	40	NM_001039114	328845	Mm.179421	NM_001039114	ENSMUSG00000024207	Acsbg2	Bgr	acyl-CoA synthetase bubblegum family member 2	protein-coding
mm_56246.1	chr6	90736757	90736777	-	1	NA	intron (NM_001134384, intron 1 of 13)	CpG	-20238	NM_001134383	232227	Mm.196943	NM_182784	ENSMUSG00000034312	Iqsec1	AW561907|BC026481|BRAG2|D6Ertd349e|cI-43	IQ motif and Sec7 domain 1	protein-coding
mm_117230.1	chr13	64248624	64248648	-	1	NA	promoter-TSS (NR_045798)	promoter-TSS (NR_045798)	-64	NR_045798	66503	Mm.443331	NR_045798	ENSMUSG00000097101	1810034E14Rik	-	RIKEN cDNA 1810034E14 gene	ncRNA
mm_71847.1	chr8	68905812	68905829	+	1	NA	3' UTR (NM_008509, exon 10 of 10)	3' UTR (NM_008509, exon 10 of 10)	25265	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_15286.1	chr2	155276718	155276772	+	1	NA	intron (NR_046364, intron 1 of 2)	CpG	381	NR_046364	66734	Mm.196239	NM_025735	ENSMUSG00000027602	Map1lc3a	1010001H21Rik|4922501H04Rik|LC3|LC3a	microtubule-associated protein 1 light chain 3 alpha	protein-coding
mm_128590.1	chr15	58119308	58119321	-	1	NA	intron (NM_027435, intron 8 of 27)	intron (NM_027435, intron 8 of 27)	15768	NM_027435	70472	Mm.221758	NM_027435	ENSMUSG00000022360	Atad2	2610509G12Rik	ATPase family, AAA domain containing 2	protein-coding
mm_96113.1	chr11	60699719	60699750	+	1	NA	promoter-TSS (NM_001159405)	promoter-TSS (NM_001159405)	44	NM_008502	16897	Mm.285453	NM_008502	ENSMUSG00000020536	Llgl1	AI325176|Lgl1|Llglh|Mgl1	lethal giant larvae homolog 1 (Drosophila)	protein-coding
mm_47119.1	chr5	119671379	119671398	-	1	NA	5' UTR (NM_011535, exon 1 of 8)	5' UTR (NM_011535, exon 1 of 8)	155	NM_011535	21386	Mm.219139	NM_011535	ENSMUSG00000018604	Tbx3	D5Ertd189e	T-box 3	protein-coding
mm_8011.1	chr1	134803781	134803863	-	1	NA	promoter-TSS (NR_015606)	promoter-TSS (NR_015606)	-101	NR_015606	329251	Mm.188709	NM_001081307	ENSMUSG00000073557	Ppp1r12b	1810037O03Rik|9530009M10Rik|AI132431|Mypt2	protein phosphatase 1, regulatory (inhibitor) subunit 12B	protein-coding
mm_144675.1	chr18	34625043	34625053	+	1	NA	promoter-TSS (NM_001166406)	promoter-TSS (NM_001166406)	15	NM_001166406	19348	Mm.258846	NM_009004	ENSMUSG00000003779	Kif20a	AA415432|Rab6kifl	kinesin family member 20A	protein-coding
mm_23719.1	chr3	69005928	69005946	+	1	NA	intron (NM_133786, intron 1 of 23)	CpG	965	NM_133786	70099	Mm.206841	NM_133786	ENSMUSG00000034349	Smc4	2500002A22Rik|C79747|SMC-4|Smc4l1	structural maintenance of chromosomes 4	protein-coding
mm_25958.1	chr3	132629815	132629831	+	1	NA	promoter-TSS (NM_001270430)	promoter-TSS (NM_001270430)	-368	NM_001270430	433653		NM_001270430	ENSMUSG00000091721	Gimd1	EG433653|Gm5549	GIMAP family P-loop NTPase domain containing 1	protein-coding
mm_124543.1	chr14	122465455	122465486	-	1	NA	5' UTR (NM_022987, exon 1 of 2)	5' UTR (NM_022987, exon 1 of 2)	188	NM_022987	65100	Mm.390761	NM_022987	ENSMUSG00000041703	Zic5	1700049L20Rik|Opr	zinc finger protein of the cerebellum 5	protein-coding
mm_67778.1	chr7	97211240	97211281	-	1	NA	intron (NM_001162477, intron 1 of 9)	intron (NM_001162477, intron 1 of 9)	114704	NM_001177412	244144	Mm.297541	NM_001177412	ENSMUSG00000035713	Usp35	Gm1088|Gm493	ubiquitin specific peptidase 35	protein-coding
mm_36906.1	chr4	107923520	107923615	-	1	NA	promoter-TSS (NM_009949)	promoter-TSS (NM_009949)	22	NM_009949	12896	Mm.307620	NM_009949	ENSMUSG00000028607	Cpt2	AI323697|CPTII	carnitine palmitoyltransferase 2	protein-coding
mm_115155.1	chr13	106947105	106947164	+	1	NA	promoter-TSS (NM_025447)	promoter-TSS (NM_025447)	5	NM_025447	66254	Mm.9563	NM_025447	ENSMUSG00000021692	Dimt1	1500031M22Rik|AV111347|Dimt1l	DIM1 dimethyladenosine transferase 1-like (S. cerevisiae)	protein-coding
mm_43389.1	chr5	135733549	135733563	+	1	NA	exon (NM_008898, exon 11 of 16)	exon (NM_008898, exon 11 of 16)	2333	NR_106001	102466791		NR_106001	ENSMUSG00000099197	Mir7034	Gm27372|mmu-mir-7034	microRNA 7034	ncRNA
mm_170901.1	chr2	30069569	30069569	+	1	NA	exon (NM_001204875, exon 5 of 8)	exon (NM_001204875, exon 5 of 8)	3095	NM_001204875	56086	Mm.326055	NM_023871	ENSMUSG00000054766	Set	2610030F17Rik|5730420M11Rik|AA407739|I-2PP2A|StF-IT-1|TAF-I	SET nuclear oncogene	protein-coding
mm_53293.1	chr6	129036594	129036607	+	1	NA	Intergenic	RMER19A|LTR|ERVK	-9301	NR_024262	232408	Mm.259262	NM_153094	ENSMUSG00000030154	Klrb1f	A630024B12Rik|Nkr-p1f|Nkrp1-f|Nkrp1f	killer cell lectin-like receptor subfamily B member 1F	protein-coding
mm_54865.1	chr6	42597629	42597649	-	1	NA	promoter-TSS (NM_203396)	promoter-TSS (NM_203396)	-267	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_72905.1	chr8	90900121	90900123	+	1	NA	intron (NM_177224, intron 2 of 39)	intron (NM_177224, intron 2 of 39)	-32127	NM_001310530	109151	Mm.100615	NM_177224	ENSMUSG00000056608	Chd9	1810014J18Rik|9030205D12Rik|A330063D19Rik|AD013|PRIC320|mKIAA0308	chromodomain helicase DNA binding protein 9	protein-coding
mm_3727.1	chr1	155059687	155059710	+	1	NA	Intergenic	Intergenic	39938	NM_010500	15939	Mm.12246	NM_010500	ENSMUSG00000056708	Ier5	-	immediate early response 5	protein-coding
mm_141230.1	chr17	27426468	27426478	-	1	NA	3' UTR (NM_001291045, exon 10 of 10)	3' UTR (NM_001291045, exon 10 of 10)	68376	NR_106077	102466228		NR_106077	ENSMUSG00000106215	Mir7218	mmu-mir-7218	microRNA 7218	ncRNA
mm_136024.1	chr16	76359721	76359723	-	1	NA	intron (NM_173440, intron 1 of 3)	intron (NM_173440, intron 1 of 3)	13327	NM_173440	268903	Mm.74711	NM_173440	ENSMUSG00000048490	Nrip1	6030458L20Rik|8430438I05Rik|9630050P12|AA959574|AW456757|RIP140	nuclear receptor interacting protein 1	protein-coding
mm_101540.1	chr11	33527372	33527380	-	1	NA	Intergenic	Intergenic	-13630	NM_023146	66011	Mm.383775	NM_023146	ENSMUSG00000040594	Ranbp17	-	RAN binding protein 17	protein-coding
mm_142141.1	chr17	35979238	35979308	-	1	NA	promoter-TSS (NM_001282012)	promoter-TSS (NM_001282012)	194	NM_145487	75210	Mm.40036	NM_145487	ENSMUSG00000038500	Prr3	4930540G07Rik|Cat56	proline-rich polypeptide 3	protein-coding
mm_102291.1	chr11	55409961	55410008	-	1	NA	exon (NM_009242, exon 2 of 10)	exon (NM_009242, exon 2 of 10)	10096	NM_009242	20692	Mm.291442	NM_009242	ENSMUSG00000018593	Sparc	BM-40|ON	secreted acidic cysteine rich glycoprotein	protein-coding
mm_106609.1	chr11	120796370	120796405	-	1	NA	promoter-TSS (NM_026824)	promoter-TSS (NM_026824)	8	NM_026824	68730	Mm.180622	NM_026824	ENSMUSG00000025155	Dus1l	1110032N12Rik	dihydrouridine synthase 1-like (S. cerevisiae)	protein-coding
mm_156061.1	chrX	109160268	109160283	+	1	NA	3' UTR (NM_019989, exon 4 of 4)	3' UTR (NM_019989, exon 4 of 4)	-36481	NM_001037917	622976	Mm.482747	NM_001037917	ENSMUSG00000048621	Gm6377	EG622976	predicted gene 6377	protein-coding
mm_127380.1	chr15	100870896	100870909	+	1	NA	intron (NM_001077499, intron 1 of 26)	intron (NM_001077499, intron 1 of 26)	257	NM_001077499	20273	Mm.385012	NM_011323	ENSMUSG00000023033	Scn8a	AI853486|C630029C19Rik|NaCh6|Nav1.6|dmu|med|mnd-2|mnd2|nmf2|nmf335|nmf58|nur14|seal	sodium channel, voltage-gated, type VIII, alpha	protein-coding
mm_18682.1	chr2	71367538	71367561	-	1	NA	promoter-TSS (NM_172436)	promoter-TSS (NM_172436)	5	NM_172436	78830	Mm.30928	NM_172436	ENSMUSG00000027010	Slc25a12	2610002D09Rik|AI839531|B230107K20Rik|BB129864	solute carrier family 25 (mitochondrial carrier, Aralar), member 12	protein-coding
mm_85488.1	chr9	106112483	106112486	-	1	NA	Intergenic	B1_Mur2|SINE|Alu	-15793	NM_026763	68553	Mm.28854	NM_026763	ENSMUSG00000032572	Col6a4	1110001D15Rik|AI413310|AU023415|Dvwa|EG235580|Vwa6	collagen, type VI, alpha 4	protein-coding
mm_77077.1	chr8	110444382	110444397	-	1	NA	intron (NM_172916, intron 19 of 86)	ORR1G|LTR|ERVL-MaLR	57967	NR_105058	100861869	Mm.84499	NR_105058		Gm21283	-	predicted gene, 21283	ncRNA
mm_68259.1	chr7	105591837	105591863	-	1	NA	exon (NM_017371, exon 10 of 10)	exon (NM_017371, exon 10 of 10)	8266	NM_017371	15458	Mm.3485	NM_017371	ENSMUSG00000030895	Hpx	Hpxn|hx	hemopexin	protein-coding
mm_111919.1	chr12	108875571	108875580	-	1	NA	intron (NM_011710, intron 5 of 10)	intron (NM_011710, intron 5 of 10)	17623	NM_001164488	22375	Mm.38433	NM_011710	ENSMUSG00000021266	Wars	TrpRS|WRS	tryptophanyl-tRNA synthetase	protein-coding
mm_111889.1	chr12	108275319	108275329	-	1	NA	promoter-TSS (NM_001159910)	promoter-TSS (NM_001159910)	93	NM_001159910	668158	Mm.482792	NM_001159910	ENSMUSG00000084883	Ccdc85c	EG668158|Gm265|Gm9010	coiled-coil domain containing 85C	protein-coding
mm_16114.1	chr2	169708272	169708275	+	1	NA	intron (NM_080455, intron 1 of 1)	intron (NM_080455, intron 1 of 1)	74627	NM_080455	228911	Mm.315789	NM_080455	ENSMUSG00000047907	Tshz2	2900073F20Rik|B830045G17|Mtsh2|Sdccag33l|Tsh2|Zfp218|mKIAA4248|teashirt2	teashirt zinc finger family member 2	protein-coding
mm_118337.1	chr13	114337123	114337126	-	1	NA	intron (NM_010887, intron 2 of 4)	intron (NM_010887, intron 2 of 4)	50970	NM_010887	17993	Mm.253142	NM_010887	ENSMUSG00000021764	Ndufs4	6720411N02Rik|C1-18k	NADH dehydrogenase (ubiquinone) Fe-S protein 4	protein-coding
mm_4132.1	chr1	170630910	170630911	+	1	NA	Intergenic	Intergenic	-13622	NM_177068	320078	Mm.287131	NM_177068	ENSMUSG00000038463	Olfml2b	1110018N05Rik|4832415H08Rik|AI467542	olfactomedin-like 2B	protein-coding
mm_7276.1	chr1	97128293	97128313	-	1	NA	promoter-TSS (NM_028942)	promoter-TSS (NM_028942)	0	NM_028942	74441	Mm.60362	NM_028942	ENSMUSG00000026331	Slco6c1	4933404A18Rik|C79179	solute carrier organic anion transporter family, member 6c1	protein-coding
mm_161506.1	chr15	98195451	98195451	-	1	NA	promoter-TSS (NM_001011733)	promoter-TSS (NM_001011733)	91	NM_001011733	545140	Mm.432690	NM_001011733	ENSMUSG00000075427	Olfr288	C85333|GA_x5J8B7W76D0-7609197-7608973|MOR286-3P	olfactory receptor 288	protein-coding
mm_33074.1	chr4	123858343	123858353	+	1	NA	Intergenic	B3A|SINE|B2	-46665	NM_019660	56309	Mm.446553	NM_019660	ENSMUSG00000028647	Mycbp	5730488M09Rik|AW552132|AW742590|Amy-1	MYC binding protein	protein-coding
mm_44835.1	chr5	34157258	34157261	-	1	NA	intron (NM_146159, intron 4 of 4)	PB1D11|SINE|Alu	12165	NM_146159	231123	Mm.319286	NM_146159	ENSMUSG00000079555	Haus3	D4S43h|D5H4S43|D5H4S43E	HAUS augmin-like complex, subunit 3	protein-coding
mm_108708.1	chr12	87026287	87026297	+	1	NA	promoter-TSS (NM_172583)	promoter-TSS (NM_172583)	-272	NM_172583	217733	Mm.110032	NM_172583	ENSMUSG00000034145	Tmem63c	4932420N09|9330187M14Rik	transmembrane protein 63c	protein-coding
mm_46152.1	chr5	96077146	96077161	-	1	NA	3' UTR (NM_178854, exon 12 of 12)	3' UTR (NM_178854, exon 12 of 12)	84394	NM_001285511	231464	Mm.28374	NM_144910	ENSMUSG00000034724	Cnot6l	4932442K20Rik	CCR4-NOT transcription complex, subunit 6-like	protein-coding
mm_52040.1	chr6	96357085	96357106	+	1	NA	intron (NM_182808, intron 2 of 4)	Lx10|LINE|L1	-190890	NR_003643	78482	Mm.391486	NM_030107	ENSMUSG00000072878	1700123L14Rik	-	nucleoporin 50 pseudogene	pseudo
mm_51644.1	chr6	86019244	86019253	+	1	NA	intron (NM_012013, intron 2 of 2)	intron (NM_012013, intron 2 of 2)	2057	NM_012013	26910	Mm.8024	NM_012013	ENSMUSG00000030001	Figla	FIGalpha|bHLHc8	folliculogenesis specific basic helix-loop-helix	protein-coding
mm_153411.1	chr19	40588339	40588371	-	1	NA	5' UTR (NM_153554, exon 1 of 19)	5' UTR (NM_153554, exon 1 of 19)	108	NM_019698	56454	Mm.233117	NM_019698	ENSMUSG00000025007	Aldh18a1	2810433K04Rik|AI429789|Pycs	aldehyde dehydrogenase 18 family, member A1	protein-coding
mm_128347.1	chr15	39784848	39784875	-	1	NA	intron (NM_022722, intron 8 of 9)	intron (NM_022722, intron 8 of 9)	-12184	NR_045788	100503072	Mm.446661	NR_045788	ENSMUSG00000087695	Gm16291	OTTMUSG00000033244	predicted gene 16291	ncRNA
mm_65728.1	chr7	28381069	28381087	-	1	NA	Intergenic	Intergenic	-1850	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_24504.1	chr3	92483953	92483957	+	1	NA	TTS (NM_009264)	TTS (NM_009264)	1926	NM_009264	20753	Mm.331191	NM_009264	ENSMUSG00000050359	Sprr1a	AI528815|SPR1a|mSPRR1A	small proline-rich protein 1A	protein-coding
mm_63281.1	chr7	126766431	126766452	+	1	NA	promoter-TSS (NM_024228)	promoter-TSS (NM_024228)	27	NM_024228	68616	Mm.246881	NM_024228	ENSMUSG00000030703	Gdpd3	1110015E22Rik	glycerophosphodiester phosphodiesterase domain containing 3	protein-coding
mm_47351.1	chr5	122647554	122647578	-	1	NA	intron (NM_001038845, intron 1 of 12)	intron (NM_001038845, intron 1 of 12)	-2858	NM_001284402	18439	Mm.42026	NM_011027	ENSMUSG00000029468	P2rx7	AI467586|P2X(7)|P2X7R	purinergic receptor P2X, ligand-gated ion channel, 7	protein-coding
mm_132675.1	chr16	42908602	42908621	+	1	NA	intron (NM_001285805, intron 1 of 10)	intron (NM_001285805, intron 1 of 10)	966	NM_001285805	56490	Mm.136238	NM_019778	ENSMUSG00000022708	Zbtb20	1300017A20Rik|7330412A13Rik|A930017C21Rik|D16Wsu73e|DPZF|HOF|ODA-8S|Oda8|Zfp288	zinc finger and BTB domain containing 20	protein-coding
mm_168646.1	chr11	85240513	85240516	+	1	NA	Intergenic	RLTR11A2|LTR|ERVK	5348	NR_028329	654810	Mm.209580	NR_028329	ENSMUSG00000085628	Appbp2os	D630032N06Rik	amyloid beta precursor protein (cytoplasmic tail) binding protein 2, opposite strand	ncRNA
mm_18748.1	chr2	73351941	73351963	-	1	NA	intron (NM_001276444, intron 12 of 15)	intron (NM_001276444, intron 12 of 15)	34528	NM_001276443	68526	Mm.451014	NM_001080707	ENSMUSG00000041762	Gpr155	1110017O10Rik|DEPDC3|F730029F15Rik|PGR22	G protein-coupled receptor 155	protein-coding
mm_122454.1	chr14	45318531	45318546	-	1	NA	promoter-TSS (NM_015774)	promoter-TSS (NM_015774)	34	NM_015774	50527	Mm.387108	NM_015774	ENSMUSG00000021831	Ero1l	ERO1-L|Ero1a	ERO1-like (S. cerevisiae)	protein-coding
mm_111736.1	chr12	103863596	103863630	-	1	NA	promoter-TSS (NM_009243)	promoter-TSS (NM_009243)	6	NM_001252569	20700	Mm.439692	NM_009243	ENSMUSG00000066366	Serpina1a	Aat-2|Aat2|Dom1|PI1|Spi1-1|Spi1-3	serine (or cysteine) peptidase inhibitor, clade A, member 1A	protein-coding
mm_165621.1	chr3	62396423	62396426	+	1	NA	intron (NM_001081295, intron 5 of 13)	intron (NM_001081295, intron 5 of 13)	57647	NM_001081295	622434	Mm.153974	NM_001081295	ENSMUSG00000036885	Arhgef26	4631416L12Rik|8430436L14Rik|AI303572|AW491953|SGEF	Rho guanine nucleotide exchange factor (GEF) 26	protein-coding
mm_79907.1	chr9	65435767	65435793	+	1	NA	promoter-TSS (NM_027134)	promoter-TSS (NM_027134)	-2	NM_027134	69606	Mm.287956	NM_027134	ENSMUSG00000059183	Mtfmt	2310020P08Rik	mitochondrial methionyl-tRNA formyltransferase	protein-coding
mm_127868.1	chr15	8430749	8430761	-	1	NA	intron (NM_201232, intron 1 of 45)	RLTR20D|LTR|ERVK	13708	NM_027707	71175	Mm.240329	NM_027707	ENSMUSG00000022141	Nipbl	Idn3	Nipped-B homolog (Drosophila)	protein-coding
mm_167911.1	chrX	92837469	92837474	+	1	NA	Intergenic	B3|SINE|B2	-237899	NM_173783	215641	Mm.327999	NM_173783	ENSMUSG00000067649	Mageb18	B430216B18Rik	melanoma antigen family B, 18	protein-coding
mm_83211.1	chr9	42033913	42033928	-	1	NA	intron (NM_011436, intron 18 of 47)	intron (NM_011436, intron 18 of 47)	90369	NM_011436	20660	Mm.121920	NM_011436	ENSMUSG00000049313	Sorl1	2900010L19Rik|AI596264|AW261561|LR11|SorLA|gp250|mSorLA	sortilin-related receptor, LDLR class A repeats-containing	protein-coding
mm_103402.1	chr11	75439476	75439486	-	1	NA	promoter-TSS (NM_008878)	promoter-TSS (NM_008878)	20	NM_008878	18816	Mm.279733	NM_008878	ENSMUSG00000038224	Serpinf2	AI747498|Pli|Serpimf2	serine (or cysteine) peptidase inhibitor, clade F, member 2	protein-coding
mm_39786.1	chr5	30232689	30232695	+	1	NA	non-coding (NR_137634, exon 1 of 9)	non-coding (NR_137634, exon 1 of 9)	111	NR_137634	28042	Mm.168854	NM_027652	ENSMUSG00000075703	Selenoi	4933402G07Rik|AI448296|AI452230|C79563|D5Wsu178e|Ept1|SELI|mKIAA1724	selenoprotein I	protein-coding
mm_69144.1	chr7	127052650	127052663	-	1	NA	promoter-TSS (NM_026918)	promoter-TSS (NM_026918)	-679	NM_026918	69036	Mm.21835	NM_026918	ENSMUSG00000049350	Zg16	1810010M01Rik|AI593689|ZG16p	zymogen granule protein 16	protein-coding
mm_100736.1	chr11	4095314	4095318	-	1	NA	5' UTR (NM_026443, exon 1 of 4)	5' UTR (NM_026443, exon 1 of 4)	115	NM_026443	67900	Mm.41719	NM_026443	ENSMUSG00000004748	Mtfp1	1700020C11Rik|2610507A21Rik|AV005788|Mtp18	mitochondrial fission process 1	protein-coding
mm_141681.1	chr17	33931072	33931096	-	1	NA	intron (NM_009059, intron 2 of 17)	intron (NM_009059, intron 2 of 17)	1190	NM_009059	19732	Mm.43777	NM_009059	ENSMUSG00000041354	Rgl2	KE1.5|Rab2l|Rgt2|Rlf	ral guanine nucleotide dissociation stimulator-like 2	protein-coding
mm_20161.1	chr2	122150911	122150922	-	1	NA	exon (NM_009735, exon 2 of 4)	exon (NM_009735, exon 2 of 4)	3229	NM_009735	12010	Mm.163	NM_009735	ENSMUSG00000060802	B2m	Ly-m11|beta2-m|beta2m	beta-2 microglobulin	protein-coding
mm_84964.1	chr9	83806188	83806194	-	1	NA	5' UTR (NM_148941, exon 1 of 6)	5' UTR (NM_148941, exon 1 of 6)	114	NM_148941	83603	Mm.83949	NM_148941	ENSMUSG00000032262	Elovl4	-	elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 4	protein-coding
mm_5414.1	chr1	33864664	33864679	-	1	NA	exon (NM_001310484, exon 3 of 6)	exon (NM_001310484, exon 3 of 6)	-25757	NM_001161816	433287	Mm.383632	NM_001161816		Gm15455	AA692849|OTTMUSG00000022109	predicted gene 15455	protein-coding
mm_99640.1	chr11	105292112	105292153	+	1	NA	promoter-TSS (NM_008626)	promoter-TSS (NM_008626)	-514	NM_008626	17534	Mm.235616	NM_008626	ENSMUSG00000020695	Mrc2	Endo180|mKIAA0709|uPARAP	mannose receptor, C type 2	protein-coding
mm_149898.1	chr19	25505776	25505780	+	1	NA	promoter-TSS (NM_015826)	promoter-TSS (NM_015826)	72	NM_015826	50796	Mm.391208	NM_015826	ENSMUSG00000024837	Dmrt1	-	doublesex and mab-3 related transcription factor 1	protein-coding
mm_15482.1	chr2	157561874	157561896	+	1	NA	3' UTR (NM_010923, exon 3 of 3)	3' UTR (NM_010923, exon 3 of 3)	1807	NM_180960	18111	Mm.34330	NM_010923	ENSMUSG00000067786	Nnat	5730414I02Rik|AW107673|Peg5	neuronatin	protein-coding
mm_112534.1	chr13	9601687	9601687	+	1	NA	intron (NM_001081426, intron 18 of 36)	MTC|LTR|ERVL-MaLR	162123	NM_001347471	66505	Mm.397307	NM_144516	ENSMUSG00000021156	Zmynd11	2210402G22Rik|BS69	zinc finger, MYND domain containing 11	protein-coding
mm_78400.1	chr9	28920976	28920989	+	1	NA	3' UTR (NM_177906, exon 8 of 8)	3' UTR (NM_177906, exon 8 of 8)	1042147	NM_172290	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding
mm_157169.1	chrX	9469251	9469281	-	1	NA	promoter-TSS (NM_007807)	promoter-TSS (NM_007807)	58	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_112263.1	chr12	114048737	114048746	-	1	NA	Intergenic	Intergenic	420725	NR_106062	102465663		NR_106062	ENSMUSG00000105438	Mir7094-1	mmu-mir-7094-1	microRNA 7094-1	ncRNA
mm_89216.1	chr10	86779020	86779044	+	1	NA	promoter-TSS (NM_175331)	promoter-TSS (NM_175331)	27	NM_175331	103466	Mm.200446	NM_175331	ENSMUSG00000054027	Nt5dc3	AU040402|AW540062|C630002B14Rik|TU12B1-TY	5'-nucleotidase domain containing 3	protein-coding
mm_85378.1	chr9	103225981	103226046	-	1	NA	exon (NM_133977, exon 4 of 17)	exon (NM_133977, exon 4 of 17)	4273	NM_133977	22041	Mm.37214	NM_133977	ENSMUSG00000032554	Trf	AI266983|Cd176|HP|Tf|Tfn|hpx	transferrin	protein-coding
mm_57360.1	chr6	124761336	124761347	-	1	NA	exon (NM_013509, exon 12 of 12)	exon (NM_013509, exon 12 of 12)	-4854	NM_007881	13498	Mm.333380	NM_007881	ENSMUSG00000004263	Atn1	Atr1|Drpla|atrophin-1	atrophin 1	protein-coding
mm_9837.1	chr1	184034149	184034186	-	1	NA	promoter-TSS (NM_028516)	promoter-TSS (NM_028516)	-169	NM_028516	73363	Mm.50115	NM_028516	ENSMUSG00000044854	1700056E22Rik	-	RIKEN cDNA 1700056E22 gene	protein-coding
mm_120680.1	chr14	70619128	70619159	+	1	NA	promoter-TSS (NM_001252666)	promoter-TSS (NM_001252666)	-574	NM_001252666	13829	Mm.210863	NM_013514	ENSMUSG00000022099	Dmtn	AI325486|Epb4.9|Epb49|dematin	dematin actin binding protein	protein-coding
mm_45535.1	chr5	72763713	72763734	-	1	NA	exon (NM_001113460, exon 15 of 19)	exon (NM_001113460, exon 15 of 19)	-10946	NM_001122754	22165	Mm.3264	NM_013698	ENSMUSG00000054892	Txk	A130089B16Rik|Btkl|PTK-RL-18|PTK4|Rlk	TXK tyrosine kinase	protein-coding
mm_70265.1	chr8	3587446	3587487	+	1	NA	promoter-TSS (NM_027171)	promoter-TSS (NM_027171)	16	NM_001347111	69697	Mm.390010	NM_027171	ENSMUSG00000044433	Camsap3	2310057J16Rik|Kiaa1543|Nezha	calmodulin regulated spectrin-associated protein family, member 3	protein-coding
mm_92347.1	chr10	75860215	75860221	-	1	NA	promoter-TSS (NM_010798)	promoter-TSS (NM_010798)	32	NM_010798	17319	Mm.2326	NM_010798	ENSMUSG00000033307	Mif	GIF|Glif	macrophage migration inhibitory factor	protein-coding
mm_153136.1	chr19	34244992	34245039	-	1	NA	exon (NM_007392, exon 7 of 9)	exon (NM_007392, exon 7 of 9)	10358	NM_007392	11475	Mm.213025	NM_007392	ENSMUSG00000035783	Acta2	0610041G09Rik|Actvs|SMalphaA|a-SMA|alphaSMA	actin, alpha 2, smooth muscle, aorta	protein-coding
mm_101360.1	chr11	23740954	23740984	-	1	NA	TTS (NM_009044)	TTS (NM_009044)	30001	NM_009044	19696	Mm.4869	NM_009044	ENSMUSG00000020275	Rel	c-Rel	reticuloendotheliosis oncogene	protein-coding
mm_57372.1	chr6	124805718	124805745	-	1	NA	Intergenic	CpG	-2930	NM_001306051	14794	Mm.261906	NM_013539	ENSMUSG00000038451	Spsb2	AI461677|C9|Grcc9|SSB2	splA/ryanodine receptor domain and SOCS box containing 2	protein-coding
mm_40506.1	chr5	57731680	57731688	+	1	NA	intron (NM_001310608, intron 1 of 3)	B1_Mur4|SINE|Alu	13603	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_134015.1	chr16	4879811	4879836	-	1	NA	promoter-TSS (NM_145359)	promoter-TSS (NM_145359)	28	NM_145359	207740	Mm.268895	NM_145359	ENSMUSG00000039568	Ubald1	1500031H01Rik|BC013706|Fam100a	UBA-like domain containing 1	protein-coding
mm_64438.1	chr7	142653590	142653618	+	1	NA	3' UTR (NM_010514, exon 4 of 4)	3' UTR (NM_010514, exon 4 of 4)	1392	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_149580.1	chr19	15599201	15599220	+	1	NA	Intergenic	Intergenic	325412	NM_001205339	107272	Mm.289936	NM_177420	ENSMUSG00000024640	Psat1	D8Ertd814e|EPIP|PSA|Psat	phosphoserine aminotransferase 1	protein-coding
mm_142049.1	chr17	35534244	35534256	-	1	NA	exon (NM_020576, exon 2 of 2)	exon (NM_020576, exon 2 of 2)	1049	NM_020576	57390	Mm.34201	NM_020576	ENSMUSG00000024409	Psors1c2	AI448740|Pcg|SPR1	psoriasis susceptibility 1 candidate 2 (human)	protein-coding
mm_14153.1	chr2	126568402	126568408	+	1	NA	intron (NM_011978, intron 4 of 9)	intron (NM_011978, intron 4 of 9)	15381	NM_011978	26458	Mm.290044	NM_011978	ENSMUSG00000027359	Slc27a2	ACSVL1|FATP2|VLCS|Vlac|Vlacs	solute carrier family 27 (fatty acid transporter), member 2	protein-coding
mm_23367.1	chr3	55324389	55324391	+	1	NA	intron (NM_019978, intron 3 of 16)	intron (NM_019978, intron 3 of 16)	81864	NM_001195538	13175	Mm.393242	NM_019978	ENSMUSG00000027797	Dclk1	1700113D08Rik|2810480F11Rik|AI836758|Click-I|Cpg16|Dcamkl1|Dcl|Dclk|mKIAA0369	doublecortin-like kinase 1	protein-coding
mm_160556.1	chr9	49340421	49340421	+	1	NA	promoter-TSS (NM_010077)	promoter-TSS (NM_010077)	-241	NM_010077	13489	Mm.41970	NM_010077	ENSMUSG00000032259	Drd2	D2R|Drd-2	dopamine receptor D2	protein-coding
mm_119486.1	chr14	47374177	47374189	+	1	NA	intron (NM_001145953, intron 1 of 5)	CpG	323	NM_001145953	16854	Mm.248615	NM_010705	ENSMUSG00000050335	Lgals3	GBP|L-34|Mac-2|gal3	lectin, galactose binding, soluble 3	protein-coding
mm_37360.1	chr4	120746910	120746969	-	1	NA	exon (NM_001081142, exon 1 of 14)	exon (NM_001081142, exon 1 of 14)	237	NM_001081142	60613	Mm.249977	NM_001081142	ENSMUSG00000028631	Kcnq4	-	potassium voltage-gated channel, subfamily Q, member 4	protein-coding
mm_166.1	chr1	12990413	12990426	+	1	NA	exon (NM_172841, exon 1 of 9)	exon (NM_172841, exon 1 of 9)	716	NM_172841	240726	Mm.24481	NM_172841	ENSMUSG00000025938	Slco5a1	4732454B15|A630033C23Rik|AA407151	solute carrier organic anion transporter family, member 5A1	protein-coding
mm_8093.1	chr1	135840907	135840920	-	1	NA	promoter-TSS (NM_001130176)	promoter-TSS (NM_001130176)	52	NM_001130176	21956	Mm.247470	NM_011619	ENSMUSG00000026414	Tnnt2	Tnt|cTnT	troponin T2, cardiac	protein-coding
mm_134319.1	chr16	15966656	15966670	-	1	NA	exon (NM_146068, exon 10 of 20)	exon (NM_146068, exon 10 of 20)	79377	NM_007679	12609	Mm.347407	NM_007679	ENSMUSG00000071637	Cebpd	c/EBPdelta	CCAAT/enhancer binding protein (C/EBP), delta	protein-coding
mm_13991.1	chr2	121866421	121866432	+	1	NA	promoter-TSS (NM_199038)	promoter-TSS (NM_199038)	-544	NM_199038	319996	Mm.292109	NM_177054	ENSMUSG00000060227	Casc4	D130060C09Rik|VGFG2573	cancer susceptibility candidate 4	protein-coding
mm_135700.1	chr16	52452990	52453013	-	1	NA	promoter-TSS (NM_001331110)	promoter-TSS (NM_001331110)	80	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_67487.1	chr7	80720899	80720909	-	1	NA	exon (NM_016721, exon 36 of 38)	exon (NM_016721, exon 36 of 38)	-32027	NM_173863	70461	Mm.392175	NM_173863	ENSMUSG00000030527	Crtc3	2610312F20Rik|6332415K15Rik|AI429792|BC011210|TORC3	CREB regulated transcription coactivator 3	protein-coding
mm_20847.1	chr2	148046213	148046241	-	1	NA	promoter-TSS (NM_001291067)	promoter-TSS (NM_001291067)	-279	NM_001291065	15376	Mm.938	NM_010446	ENSMUSG00000037025	Foxa2	HNF3-beta|HNF3beta|Hnf-3b|Hnf3b|Tcf-3b|Tcf3b	forkhead box A2	protein-coding
mm_85229.1	chr9	97370001	97370021	-	1	NA	promoter-TSS (NM_030219)	promoter-TSS (NM_030219)	-53	NM_030219	78911	Mm.108347	NM_030219	ENSMUSG00000032451	Trim42	4930486B16Rik	tripartite motif-containing 42	protein-coding
mm_115493.1	chr13	3767167	3767181	-	1	NA	Intergenic	Intergenic	37144	NM_027416	70405	Mm.20079	NM_027416	ENSMUSG00000063130	Calml3	2310068O22Rik|AI326174	calmodulin-like 3	protein-coding
mm_92669.1	chr10	80520272	80520286	-	1	NA	exon (NM_026094, exon 28 of 28)	exon (NM_026094, exon 28 of 28)	18845	NM_026094	67331	Mm.52511	NM_026094	ENSMUSG00000003341	Atp8b3	1700042F02Rik|1700056N23Rik|ATPIK|SAPLT	ATPase, class I, type 8B, member 3	protein-coding
mm_6789.1	chr1	84140999	84141012	-	1	NA	intron (NM_001003948, intron 2 of 2)	L1_Mur3|LINE|L1	77956	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_95169.1	chr11	40733728	40733762	+	1	NA	promoter-TSS (NM_013552)	promoter-TSS (NM_013552)	84	NM_001290697	52653	Mm.276504	NM_026023	ENSMUSG00000020328	Nudcd2	-	NudC domain containing 2	protein-coding
mm_108741.1	chr12	88724935	88724962	+	1	NA	Intergenic	Intergenic	-69556	NM_001198587	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding
mm_138867.1	chr17	43036349	43036382	+	1	NA	intron (NM_178589, intron 1 of 5)	intron (NM_178589, intron 1 of 5)	19810	NM_178589	94185	Mm.200792	NM_178589	ENSMUSG00000023915	Tnfrsf21	AA959878|DR6|R74815|TR7	tumor necrosis factor receptor superfamily, member 21	protein-coding
mm_168122.1	chr10	20146296	20146300	+	1	NA	Intergenic	B1_Mus2|SINE|Alu	-2622	NM_008635	17761	Mm.20928	NM_008635	ENSMUSG00000019996	Map7	E-MAP-115|MAP-7|Mtap7|R75000|mshi|mste|ste	microtubule-associated protein 7	protein-coding
mm_120798.1	chr14	74737247	74737250	+	1	NA	intron (NM_001285423, intron 2 of 8)	intron (NM_001285423, intron 2 of 8)	4951	NM_016903	13885	Mm.38055	NM_016903	ENSMUSG00000021996	Esd	Es-10|Es10|FGH|sid478	esterase D/formylglutathione hydrolase	protein-coding
mm_42382.1	chr5	114933631	114933641	+	1	NA	intron (NM_145209, intron 5 of 6)	intron (NM_145209, intron 5 of 6)	-8566	NM_028211	72357	Mm.292672	NM_028211	ENSMUSG00000029559	2210016L21Rik	-	RIKEN cDNA 2210016L21 gene	protein-coding
mm_27263.1	chr3	38484780	38484791	-	1	NA	promoter-TSS (NM_001167883)	promoter-TSS (NM_001167883)	31	NM_001167883	99696	Mm.290937	NM_001033198	ENSMUSG00000044864	Ankrd50	AI662170|E430012K20Rik|mKIAA1223|mKIAA3019	ankyrin repeat domain 50	protein-coding
mm_89384.1	chr10	89686366	89686421	+	1	NA	promoter-TSS (NM_001310704)	promoter-TSS (NM_001310704)	30	NR_130956	69002	Mm.293947	NR_130956	ENSMUSG00000097383	1500026H17Rik	-	RIKEN cDNA 1500026H17 gene	ncRNA
mm_146381.1	chr18	82585190	82585223	+	1	NA	3' UTR (NM_010777, exon 7 of 7)	3' UTR (NM_010777, exon 7 of 7)	30698	NM_001025254	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_84154.1	chr9	59486611	59486621	-	1	NA	promoter-TSS (NM_019927)	promoter-TSS (NM_019927)	-242	NM_019927	23806	Mm.305925	NM_019927	ENSMUSG00000025234	Arih1	AU021774|Ari|Ari1|Hari|Hhari|Ubch7bp|Uip77	ariadne RBR E3 ubiquitin protein ligase 1	protein-coding
mm_93912.1	chr10	127060164	127060206	-	1	NA	promoter-TSS (NM_001033262)	promoter-TSS (NM_001033262)	-1	NM_001033262	216438	Mm.37892	NM_001033262	ENSMUSG00000040502	March9	AI608492|BC019560	membrane-associated ring finger (C3HC4) 9	protein-coding
mm_169372.1	chr14	34355468	34355468	-	1	NA	promoter-TSS (NM_183278)	promoter-TSS (NM_183278)	-75	NM_183278	69134	Mm.27156	NM_183278	ENSMUSG00000043681	Fam25c	2200001I15Rik|Fam25	family with sequence similarity 25, member C	protein-coding
mm_85030.1	chr9	88475353	88475356	-	1	NA	intron (NM_001311113, intron 5 of 10)	intron (NM_001311113, intron 5 of 10)	7043	NM_019666	56403	Mm.260545	NM_019666	ENSMUSG00000032423	Syncrip	2610109K23Rik|4632417O19Rik|GRY-RBP|Nsap1|Nsap1l|hnRNP Q|pp68	synaptotagmin binding, cytoplasmic RNA interacting protein	protein-coding
mm_87699.1	chr10	59861464	59861470	+	1	NA	intron (NM_001291443, intron 11 of 12)	intron (NM_001291443, intron 11 of 12)	-18124	NM_019965	56709	Mm.103610	NM_019965	ENSMUSG00000020109	Dnajb12	Dj10|mDj10	DnaJ heat shock protein family (Hsp40) member B12	protein-coding
mm_172127.1	chr6	3201453	3201456	+	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	-87065	NR_036696	667335	Mm.380219	NR_036696	ENSMUSG00000106779	Gm8579	EG667335	spermatogenesis associated glutamate (E)-rich protein 4a pseudogene	pseudo
mm_20985.1	chr2	151980194	151980223	-	1	NA	promoter-TSS (NM_146127)	promoter-TSS (NM_146127)	11	NM_146127	73847	Mm.272444	NM_028666	ENSMUSG00000027459	Fam110a	1700008J10Rik|5430432M24Rik|AI747080	family with sequence similarity 110, member A	protein-coding
mm_18129.1	chr2	45004671	45004694	-	1	NA	intron (NM_001289521, intron 3 of 8)	intron (NM_001289521, intron 3 of 8)	18495	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_147964.1	chr18	67134166	67134189	-	1	NA	intron (NM_010307, intron 1 of 11)	intron (NM_010307, intron 1 of 11)	617	NM_010307	14680	Mm.440746	NM_010307	ENSMUSG00000024524	Gnal	2610011C15Rik|9630020G10Rik|Galphaolf|Gna10|Golf	guanine nucleotide binding protein, alpha stimulating, olfactory type	protein-coding
mm_53878.1	chr6	3183003	3183021	-	1	NA	Intergenic	Intergenic	-105507	NR_036696	667335	Mm.380219	NR_036696	ENSMUSG00000106779	Gm8579	EG667335	spermatogenesis associated glutamate (E)-rich protein 4a pseudogene	pseudo
mm_62617.1	chr7	107209440	107209451	+	1	NA	promoter-TSS (NM_029660)	promoter-TSS (NM_029660)	0	NM_029660	76572	Mm.128134	NM_029660	ENSMUSG00000073894	Rbmxl2	1700012H05Rik|Hnrnpg-t	RNA binding motif protein, X-linked-like 2	protein-coding
mm_135653.1	chr16	52400394	52400406	-	1	NA	intron (NM_009655, intron 1 of 15)	intron (NM_009655, intron 1 of 15)	52681	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_170724.1	chr2	150485084	150485095	-	1	NA	promoter-TSS (NM_001034900)	promoter-TSS (NM_001034900)	-26	NM_001034900	545471	Mm.451002	NM_001034900	ENSMUSG00000074731	Zfp345	OTTMUSG00000015743	zinc finger protein 345	protein-coding
mm_2913.1	chr1	132008325	132008357	+	1	NA	intron (NM_007923, intron 1 of 4)	CpG	736	NM_007923	13714	Mm.254233	NM_007923	ENSMUSG00000026436	Elk4	2310011G17Rik|A130026I01Rik|BB162516|SAP-1|Sap1	ELK4, member of ETS oncogene family	protein-coding
mm_129515.1	chr15	79062764	79062770	-	1	NA	promoter-TSS (NM_144849)	promoter-TSS (NM_144849)	92	NM_144849	223690	Mm.24262	NM_144849	ENSMUSG00000033055	Ankrd54	C730048E16Rik|EST1068184|EST475269|Liar	ankyrin repeat domain 54	protein-coding
mm_112297.1	chr12	114612694	114612729	-	1	NA	Intergenic	Intergenic	-99017	NR_106063	102465664		NR_106063	ENSMUSG00000098357	Mir7094-2	Gm27508|mmu-mir-7094-2	microRNA 7094-2	ncRNA
mm_149837.1	chr19	24997422	24997425	+	1	NA	Intergenic	Intergenic	-2106	NM_028785	76088	Mm.102485	NM_028785	ENSMUSG00000052085	Dock8	1200017A24Rik|5830472H07Rik|A130095G14Rik|AI461977	dedicator of cytokinesis 8	protein-coding
mm_142568.1	chr17	46675138	46675185	-	1	NA	promoter-TSS (NM_144857)	promoter-TSS (NM_144857)	-906	NM_144857	224823	Mm.45101	NM_144857	ENSMUSG00000023971	Rrp36	-	ribosomal RNA processing 36 homolog (S. cerevisiae)	protein-coding
mm_108127.1	chr12	75983889	75983898	+	1	NA	intron (NM_001005510, intron 53 of 115)	intron (NM_001005510, intron 53 of 115)	74790	NR_039560	100628610		NR_039560	ENSMUSG00000092922	Mir5101	mmu-mir-5101|mu-mir-5101	microRNA 5101	ncRNA
mm_109381.1	chr12	109709607	109709610	+	1	NA	promoter-TSS (NR_029916)	promoter-TSS (NR_029916)	548	NR_029880	723858		NR_029880	ENSMUSG00000065498	Mir379	Mirn379|mir-379|mmu-mir-379	microRNA 379	ncRNA
mm_59704.1	chr7	28693033	28693043	+	1	NA	promoter-TSS (NM_001163702)	promoter-TSS (NM_001163702)	-106	NM_001163702	233040	Mm.116116	NM_207238	ENSMUSG00000037463	Fbxo27	E130008B10Rik|FBG5|Gm161	F-box protein 27	protein-coding
mm_39151.1	chr4	155398060	155398080	-	1	NA	promoter-TSS (NM_008072)	promoter-TSS (NM_008072)	-1	NM_008072	14403	Mm.388925	NM_008072	ENSMUSG00000029054	Gabrd	AI853201	gamma-aminobutyric acid (GABA) A receptor, subunit delta	protein-coding
mm_110640.1	chr12	58268604	58268633	-	1	NA	exon (NM_025809, exon 1 of 1)	exon (NM_025809, exon 1 of 1)	640	NM_025809	66864	Mm.280563	NM_025809	ENSMUSG00000045930	Clec14a	1200003C23Rik|AI642649	C-type lectin domain family 14, member a	protein-coding
mm_99520.1	chr11	103133364	103133376	+	1	NA	promoter-TSS (NM_027658)	promoter-TSS (NM_027658)	11	NM_027658	71059	Mm.273871	NM_027658	ENSMUSG00000043372	Hexim2	4933402L21Rik	hexamethylene bis-acetamide inducible 2	protein-coding
mm_173081.1	chrX	142297988	142298006	+	1	NA	non-coding (NR_002883, exon 1 of 1)	non-coding (NR_002883, exon 1 of 1)	492	NR_002883	434858	Mm.391346	NR_002883		Gm5643	EG434858	heterogeneous nuclear ribonucleoprotein A1 pseudogene	pseudo
mm_1496.1	chr1	71913516	71913521	+	1	NA	Intergenic	Intergenic	25406	NR_027659	667931	Mm.214128	NR_027658	ENSMUSG00000099707	Gm8883	EG667931|Gm554	predicted gene 8883	ncRNA
mm_11125.1	chr2	28229474	28229490	+	1	NA	exon (NM_001038613, exon 6 of 6)	exon (NM_001038613, exon 6 of 6)	23793	NM_019498	56177	Mm.43278	NM_019498	ENSMUSG00000026833	Olfm1	AMY|AW742568|Noe1|OlfA|Pancortin|Pancortin3	olfactomedin 1	protein-coding
mm_18773.1	chr2	73486466	73486477	-	1	NA	promoter-TSS (NM_001289723)	promoter-TSS (NM_001289723)	-718	NM_001289723	215280	Mm.223504	NM_153138	ENSMUSG00000075284	Wipf1	AI115543|D2Ertd120e|WIP|Waspip	WAS/WASL interacting protein family, member 1	protein-coding
mm_79615.1	chr9	58640738	58640759	+	1	NA	exon (NM_009145, exon 4 of 8)	exon (NM_009145, exon 4 of 8)	58508	NM_009145	20320	Mm.15125	NM_009145	ENSMUSG00000032336	Nptn	AW554172|SDR-1|Sdfr1	neuroplastin	protein-coding
mm_111448.1	chr12	98259417	98259446	-	1	NA	promoter-TSS (NM_008079)	promoter-TSS (NM_008079)	28	NM_008079	14420	Mm.5120	NM_008079	ENSMUSG00000021003	Galc	2310068B06Rik|A930008M05Rik|AW212969|AW413532|Gacy|twi|twitcher	galactosylceramidase	protein-coding
mm_59653.1	chr7	28179488	28179535	+	1	NA	promoter-TSS (NM_001271370)	promoter-TSS (NM_001271370)	28	NM_010092	13549	Mm.57249	NM_010092	ENSMUSG00000002409	Dyrk1b	Mirk	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1b	protein-coding
mm_48243.1	chr5	137786181	137786193	-	1	NA	5' UTR (NM_144913, exon 1 of 4)	5' UTR (NM_144913, exon 1 of 4)	514	NM_144913	231803	Mm.61193	NM_144913	ENSMUSG00000029726	Mepce	Bcdin3|D5Wsu46e	methylphosphate capping enzyme	protein-coding
mm_161753.1	chr17	35074333	35074333	-	1	NA	intron (NM_033478, intron 1 of 2)	intron (NM_033478, intron 1 of 2)	131	NM_033478	114654	Mm.246697	NM_033478	ENSMUSG00000073413	Ly6g6d	A930024F17Rik|G6d|G6f|MEGT1|NG25|NG32	lymphocyte antigen 6 complex, locus G6D	protein-coding
mm_42845.1	chr5	122168126	122168136	+	1	NA	intron (NM_013636, intron 1 of 6)	intron (NM_013636, intron 1 of 6)	9852	NM_013636	19047	Mm.280784	NM_013636	ENSMUSG00000004455	Ppp1cc	PP-1G|PP1|dis2m1	protein phosphatase 1, catalytic subunit, gamma isoform	protein-coding
mm_80687.1	chr9	91377961	91377985	+	1	NA	intron (NM_009576, intron 2 of 4)	intron (NM_009576, intron 2 of 4)	9001	NM_009576	22774	Mm.8062	NM_009576	ENSMUSG00000036972	Zic4	-	zinc finger protein of the cerebellum 4	protein-coding
mm_70215.1	chr7	144932510	144932520	-	1	NA	promoter-TSS (NR_039539)	promoter-TSS (NR_039539)	-380	NR_039539	100628615		NR_039539	ENSMUSG00000092633	Mir3962	mmu-mir-3962|mu-mir-3962	microRNA 3962	ncRNA
mm_121449.1	chr14	120430869	120430887	+	1	NA	3' UTR (NM_207515, exon 8 of 8)	3' UTR (NM_207515, exon 8 of 8)	-47583	NM_029519	76108	Mm.261448	NM_029519	ENSMUSG00000051615	Rap2a	5830461H18Rik	RAS related protein 2a	protein-coding
mm_105285.1	chr11	102436804	102436807	-	1	NA	TTS (NM_008175)	TTS (NM_008175)	6483	NM_008175	14824	Mm.1568	NM_008175	ENSMUSG00000034708	Grn	Pgrn|epithelin	granulin	protein-coding
mm_14851.1	chr2	148499987	148499990	+	1	NA	Intergenic	Intergenic	-56453	NM_010740	17064	Mm.681	NM_010740	ENSMUSG00000027435	Cd93	6030404G09Rik|AA145088|AA4.1|AW555904|C1qr1|C1qrp|Ly68	CD93 antigen	protein-coding
mm_161131.1	chr12	113074450	113074450	+	1	NA	promoter-TSS (NM_029381)	promoter-TSS (NM_029381)	-52	NM_029381	75671	Mm.23377	NM_029381	ENSMUSG00000012211	Tex22	1700028O09Rik|AV210422|Tep22	testis expressed gene 22	protein-coding
mm_85085.1	chr9	91365779	91365815	-	1	NA	promoter-TSS (NM_009573)	promoter-TSS (NM_009573)	2	NM_009573	22771	Mm.335350	NM_009573	ENSMUSG00000032368	Zic1	ZIC|ZNF201	zinc finger protein of the cerebellum 1	protein-coding
mm_5634.1	chr1	40437086	40437094	-	1	NA	intron (NM_001294171, intron 1 of 7)	intron (NM_001294171, intron 1 of 7)	-2539	NM_001025602	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_131033.1	chr16	3744193	3744206	+	1	NA	promoter-TSS (NM_148924)	promoter-TSS (NM_148924)	100	NM_148924	74120	Mm.29081	NM_148924	ENSMUSG00000022529	Zfp263	1200014J04Rik|AI326880|AU020888|NT2|mFPM315	zinc finger protein 263	protein-coding
mm_157608.1	chrX	53757837	53757849	-	1	NA	promoter-TSS (NM_001200013)	promoter-TSS (NM_001200013)	-12	NM_001200013	75514	Mm.116929	NM_001200013	ENSMUSG00000054727	1700013H16Rik	Slx2|Xlr6	RIKEN cDNA 1700013H16 gene	protein-coding
mm_100535.1	chr11	120629585	120629603	+	1	NA	exon (NM_010756, exon 3 of 3)	exon (NM_010756, exon 3 of 3)	3953	NM_010756	17134	Mm.268010	NM_010756	ENSMUSG00000051510	Mafg	AA545192|C630022N07Rik	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein G (avian)	protein-coding
mm_136019.1	chr16	76318610	76318618	-	1	NA	intron (NM_173440, intron 3 of 3)	intron (NM_173440, intron 3 of 3)	54435	NM_173440	268903	Mm.74711	NM_173440	ENSMUSG00000048490	Nrip1	6030458L20Rik|8430438I05Rik|9630050P12|AA959574|AW456757|RIP140	nuclear receptor interacting protein 1	protein-coding
mm_127694.1	chr15	102990516	102990530	+	1	NA	promoter-TSS (NM_010466)	promoter-TSS (NM_010466)	-16	NM_010466	15426	Mm.6167	NM_010466	ENSMUSG00000001657	Hoxc8	D130011F21Rik|Hox-3.1	homeobox C8	protein-coding
mm_148104.1	chr18	74065351	74065360	-	1	NA	promoter-TSS (NM_172632)	promoter-TSS (NM_172632)	-406	NM_172632	225724	Mm.254517	NM_172632	ENSMUSG00000024558	Mapk4	A330097D03Rik|Erk3|Prkm4|p63Mapk	mitogen-activated protein kinase 4	protein-coding
mm_163689.1	chr13	96924763	96924765	+	1	NA	promoter-TSS (NM_001166065)	promoter-TSS (NM_001166065)	75	NM_001166065	218476	Mm.483490	NM_001166065	ENSMUSG00000091387	Gcnt4	C2gnt3|Gm279|Gm73	glucosaminyl (N-acetyl) transferase 4, core 2 (beta-1,6-N-acetylglucosaminyltransferase)	protein-coding
mm_105529.1	chr11	106300823	106300842	-	1	NA	exon (NM_008117, exon 4 of 5)	exon (NM_008117, exon 4 of 5)	1064	NM_008117	14599	Mm.343934	NM_008117	ENSMUSG00000020713	Gh	Gh1|Ghb1	growth hormone	protein-coding
mm_90059.1	chr10	116275492	116275504	+	1	NA	TTS (NM_001161837)	TTS (NM_001161837)	-25876	NM_029928	19263	Mm.37213	NM_029928	ENSMUSG00000020154	Ptprb	3230402H02Rik|C130094E24|Ptpz|Rptpb|VE-PTP|Veptp	protein tyrosine phosphatase, receptor type, B	protein-coding
mm_137418.1	chr17	26131314	26131327	+	1	NA	Intergenic	Intergenic	-7366	NM_009733	12005	Mm.23684	NM_009733	ENSMUSG00000024182	Axin1	AI316800|Axin|Fu|Kb|Ki|fused|kinky|knobbly	axin 1	protein-coding
mm_129538.1	chr15	79348186	79348207	-	1	NA	promoter-TSS (NM_001304832)	promoter-TSS (NM_001304832)	135	NM_001304831	17133	Mm.86646	NM_010755	ENSMUSG00000042622	Maff	-	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein F (avian)	protein-coding
mm_3553.1	chr1	150421686	150421707	+	1	NA	exon (NM_133780, exon 23 of 52)	exon (NM_133780, exon 23 of 52)	-28641	NM_145511	226499	Mm.222093	NM_145511	ENSMUSG00000006010	BC003331	1810053E15Rik|Odr4|odr-4	cDNA sequence BC003331	protein-coding
mm_151243.1	chr19	53891259	53891264	+	1	NA	promoter-TSS (NM_011050)	promoter-TSS (NM_011050)	-970	NM_011050	18569	Mm.1605	NM_011050	ENSMUSG00000024975	Pdcd4	D19Ucla1|Ma3|Tis	programmed cell death 4	protein-coding
mm_104192.1	chr11	87828310	87828324	-	1	NA	Intergenic	Intergenic	-2203	NM_080420	76113	Mm.41236	NM_080420	ENSMUSG00000009356	Lpo	5830499B15Rik	lactoperoxidase	protein-coding
mm_161162.1	chr13	27780804	27780804	-	1	NA	promoter-TSS (NM_026206)	promoter-TSS (NM_026206)	0	NM_026206	67505	Mm.49048	NM_026206	ENSMUSG00000060738	Prl7c1	1600017N11Rik|Ghd20|PLP-O|Prlpo|Prplo	prolactin family 7, subfamily c, member 1	protein-coding
mm_17597.1	chr2	30801699	30801742	-	1	NA	promoter-TSS (NM_198000)	promoter-TSS (NM_198000)	17	NM_198000	73598	Mm.34166	NM_198000	ENSMUSG00000044320	1700001O22Rik	1700113K14Rik|4930549G18Rik	RIKEN cDNA 1700001O22 gene	protein-coding
mm_73457.1	chr8	106555998	106556001	+	1	NA	3' UTR (NM_007665, exon 16 of 16)	3' UTR (NM_007665, exon 16 of 16)	-31144	NR_045470	68692	Mm.416843	NR_045470	ENSMUSG00000099139	1110028F18Rik	-	RIKEN cDNA 1110028F18 gene	ncRNA
mm_83698.1	chr9	50659465	50659477	-	1	NA	5' UTR (NM_145614, exon 1 of 14)	5' UTR (NM_145614, exon 1 of 14)	309	NM_145614	235339	Mm.285076	NM_145614	ENSMUSG00000000168	Dlat	6332404G05Rik|DLTA|PDC-E2	dihydrolipoamide S-acetyltransferase (E2 component of pyruvate dehydrogenase complex)	protein-coding
mm_66196.1	chr7	34229416	34229436	-	1	NA	intron (NM_008155, intron 1 of 17)	intron (NM_008155, intron 1 of 17)	910	NM_008155	14751	Mm.589	NM_008155	ENSMUSG00000036427	Gpi1	Amf|Gpi|Gpi-1|Gpi-1r|Gpi-1s|Gpi-1t|Gpi1-r|Gpi1-s|Gpi1-t|Gpi1s|MF|NK|NK/GPI|Nlk|Org|Pgi|Phi	glucose phosphate isomerase 1	protein-coding
mm_64862.1	chr7	13037963	13037969	-	1	NA	promoter-TSS (NM_145578)	promoter-TSS (NM_145578)	12	NM_145578	22192	Mm.196580	NM_145578	ENSMUSG00000005575	Ube2m	2510040H03Rik|UBC12|Ubc-rs2	ubiquitin-conjugating enzyme E2M	protein-coding
mm_146173.1	chr18	75367377	75367401	+	1	NA	promoter-TSS (NM_001042660)	promoter-TSS (NM_001042660)	24	NM_001042660	17131	Mm.34407	NM_008543	ENSMUSG00000025880	Smad7	Madh7	SMAD family member 7	protein-coding
mm_89449.1	chr10	93143838	93143851	+	1	NA	Intergenic	Intergenic	-17032	NM_146239	237459	Mm.217404	NM_146239	ENSMUSG00000020015	Cdk17	6430598J10Rik|Pctk2	cyclin-dependent kinase 17	protein-coding
mm_168568.1	chr11	69670638	69670644	-	1	NA	exon (NM_144958, exon 3 of 11)	exon (NM_144958, exon 3 of 11)	1782	NM_144958	13681	Mm.26680	NM_144958	ENSMUSG00000059796	Eif4a1	BM-010|Ddx2a|Eif4	eukaryotic translation initiation factor 4A1	protein-coding
mm_55280.1	chr6	54337237	54337242	-	1	NA	intron (NR_033635, intron 3 of 13)	RLTR31_Mur|LTR|ERVK	10227	NM_030024	78004	Mm.41984	NM_030024	ENSMUSG00000045725	Prr15	E130201N16Rik|G90	proline rich 15	protein-coding
mm_90768.1	chr10	5805395	5805408	-	1	NA	promoter-TSS (NM_025995)	promoter-TSS (NM_025995)	64	NM_025995	67141	Mm.197520	NM_025995	ENSMUSG00000019773	Fbxo5	2510044I10Rik|C85305|Emi1|Fbxo31	F-box protein 5	protein-coding
mm_43949.1	chr5	145140366	145140414	+	1	NA	promoter-TSS (NM_001033313)	promoter-TSS (NM_001033313)	14	NM_001008705	231889	Mm.277413	NM_001008705	ENSMUSG00000038722	Bud31	C77604|EDG-2|EDG2|G10	BUD31 homolog	protein-coding
mm_67443.1	chr7	80387936	80387953	-	1	NA	promoter-TSS (NM_010194)	promoter-TSS (NM_010194)	2	NM_010194	14159	Mm.48757	NM_010194	ENSMUSG00000053158	Fes	AI586313|BB137047|FPS|c-fes	feline sarcoma oncogene	protein-coding
mm_20803.1	chr2	144270781	144270800	-	1	NA	promoter-TSS (NM_024225)	promoter-TSS (NM_024225)	112	NM_001199188	69178	Mm.273379	NM_024225	ENSMUSG00000027423	Snx5	0910001N05Rik|1810032P22Rik|AU019504|D2Ertd52e	sorting nexin 5	protein-coding
mm_75959.1	chr8	71717209	71717217	-	1	NA	exon (NM_028715, exon 6 of 28)	exon (NM_028715, exon 6 of 28)	8468	NR_131256	74015	Mm.22025	NM_028715	ENSMUSG00000070000	Fcho1	3322402E17Rik|N28152	FCH domain only 1	protein-coding
mm_129204.1	chr15	76512200	76512211	-	1	NA	promoter-TSS (NM_010046)	promoter-TSS (NM_010046)	-387	NM_010046	13350	Mm.22633	NM_010046	ENSMUSG00000022555	Dgat1	ARAT|C75990|D15Ertd23e|Dgat	diacylglycerol O-acyltransferase 1	protein-coding
mm_47554.1	chr5	124373266	124373269	-	1	NA	3' UTR (NM_001081203, exon 32 of 32)	3' UTR (NM_001081203, exon 32 of 32)	-18639	NM_013812	13445	Mm.391838	NM_013812	ENSMUSG00000029394	Cdk2ap1	Apc10|Cdkap1|DORC1|Doc1|ST19|doc-1|p12	CDK2 (cyclin-dependent kinase 2)-associated protein 1	protein-coding
mm_117758.1	chr13	96081279	96081302	-	1	NA	intron (NM_029210, intron 2 of 12)	intron (NM_029210, intron 2 of 12)	51287	NM_029210	75209	Mm.40436	NM_029210	ENSMUSG00000051111	Sv2c	4930527L09Rik|AI841971	synaptic vesicle glycoprotein 2c	protein-coding
mm_138777.1	chr17	37246932	37246946	+	1	NA	Intergenic	Intergenic	-14571	NM_146512	258505	Mm.353371	NM_146512	ENSMUSG00000058802	Olfr97	MOR156-2	olfactory receptor 97	protein-coding
mm_6440.1	chr1	73998425	73998446	-	1	NA	intron (NM_027884, intron 6 of 34)	intron (NM_027884, intron 6 of 34)	126012	NM_027884	21961	Mm.309975	NM_027884	ENSMUSG00000055322	Tns1	1110018I21Rik|1200014E20Rik|AI648117|E030018G17Rik|E030037J05Rik|Tns	tensin 1	protein-coding
mm_102131.1	chr11	53430469	53430480	-	1	NA	intron (NM_001326614, intron 2 of 2)	CpG	357	NM_025352	22272	Mm.251621	NM_025352	ENSMUSG00000044894	Uqcrq	1100001F06Rik|1500040F11Rik|5830407L17Rik|9.5kDa|AA959903|QP-C|Qpc|Uqcrb|c1502	ubiquinol-cytochrome c reductase, complex III subunit VII	protein-coding
mm_141579.1	chr17	32364431	32364488	-	1	NA	intron (NR_033525, intron 4 of 10)	intron (NR_033525, intron 4 of 10)	-13882	NM_017476	54194	Mm.281005	NM_017476	ENSMUSG00000002625	Akap8l	HAP95|Nakap95	A kinase (PRKA) anchor protein 8-like	protein-coding
mm_121969.1	chr14	25587444	25587476	-	1	NA	non-coding (NR_033492, exon 1 of 1)	non-coding (NR_033492, exon 1 of 1)	656	NR_033492	77592	Mm.444871	NM_175264		4931406H21Rik	-	RIKEN cDNA 4931406H21 gene	ncRNA
mm_93849.1	chr10	121826330	121826332	-	1	NA	intron (NM_001081037, intron 12 of 21)	intron (NM_001081037, intron 12 of 21)	86394	NM_173022	270802	Mm.209172	NM_173022	ENSMUSG00000053684	BC048403	E030027L10	cDNA sequence BC048403	protein-coding
mm_137671.1	chr17	28769383	28769385	+	1	NA	promoter-TSS (NM_011950)	promoter-TSS (NM_011950)	67	NM_011950	26415	Mm.27970	NM_011950	ENSMUSG00000004864	Mapk13	SAPK4|Serk4	mitogen-activated protein kinase 13	protein-coding
mm_78028.1	chr9	13766825	13766841	+	1	NA	intron (NR_024025, intron 1 of 15)	intron (NR_024025, intron 1 of 15)	17652	NR_024025	77116	Mm.210405	NM_023858	ENSMUSG00000031918	Mtmr2	6030445P13Rik	myotubularin related protein 2	protein-coding
mm_104008.1	chr11	85094123	85094126	-	1	NA	intron (NM_001029934, intron 2 of 33)	intron (NM_001029934, intron 2 of 33)	45831	NM_001029934	237898	Mm.178524	NM_001029934	ENSMUSG00000000804	Usp32	2900074J03Rik|6430526O11Rik|AW045245	ubiquitin specific peptidase 32	protein-coding
mm_91199.1	chr10	21160812	21160820	-	1	NA	5' UTR (NM_001198914, exon 1 of 16)	5' UTR (NM_001198914, exon 1 of 16)	168	NM_001198914	17863	Mm.52109	NM_010848	ENSMUSG00000019982	Myb	AI550390|M16449|c-myb	myeloblastosis oncogene	protein-coding
mm_46967.1	chr5	115156928	115156932	-	1	NA	intron (NM_175403, intron 1 of 4)	intron (NM_175403, intron 1 of 4)	1246	NM_175403	109154	Mm.153963	NM_175403	ENSMUSG00000048578	Mlec	2410014A08Rik|AI850530|ESTM19|X83352|mKIAA0152	malectin	protein-coding
mm_133395.1	chr16	84774362	84774423	+	1	NA	5' UTR (NM_023844, exon 1 of 10)	5' UTR (NM_023844, exon 1 of 10)	269	NM_023844	67374	Mm.41758	NM_023844	ENSMUSG00000053062	Jam2	1110002N23Rik|2410030G21Rik|2410167M24Rik|JAM-2|JAM-B|Jcam2|VE-JAM	junction adhesion molecule 2	protein-coding
mm_168994.1	chr12	99645611	99645629	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-17646	NR_045288	73457	Mm.383439	NR_045288	ENSMUSG00000100211	1700064M15Rik	-	RIKEN cDNA 1700064M15 gene	ncRNA
mm_25416.1	chr3	107461147	107461148	+	1	NA	Intergenic	Intergenic	-2249	NM_145922	99738	Mm.101976	NM_145922	ENSMUSG00000027895	Kcnc4	AI850292|KSHIIIC|Kcr2-4|Kv3.4	potassium voltage gated channel, Shaw-related subfamily, member 4	protein-coding
mm_15615.1	chr2	160880699	160880726	+	1	NA	promoter-TSS (NM_022883)	promoter-TSS (NM_022883)	42	NM_022883	64899	Mm.292111	NM_022883	ENSMUSG00000027412	Lpin3	9130206L11Rik|AA438110|AV236139|mKIAA4023	lipin 3	protein-coding
mm_91185.1	chr10	21083561	21083573	-	1	NA	Intergenic	Intergenic	42747	NM_001177776	52906	Mm.253280	NM_026203	ENSMUSG00000019986	Ahi1	1700015F03Rik|Ahi-1|D10Bwg0629e	Abelson helper integration site 1	protein-coding
mm_86484.1	chr10	4959587	4959591	+	1	NA	intron (NM_001302531, intron 6 of 8)	intron (NM_001302531, intron 6 of 8)	109474	NM_022027	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_39635.1	chr5	24473609	24473614	+	1	NA	intron (NM_139153, intron 1 of 17)	intron (NM_139153, intron 1 of 17)	21434	NM_139153	213990	Mm.250703	NM_139153	ENSMUSG00000023353	Agap3	AGAP-3|AV028425|Centg3|Crag|Crag.|MRIP-1|cnt-g3	ArfGAP with GTPase domain, ankyrin repeat and PH domain 3	protein-coding
mm_95117.1	chr11	34078124	34078135	+	1	NA	intron (NM_010696, intron 10 of 20)	intron (NM_010696, intron 10 of 20)	30928	NM_010696	16822	Mm.265350	NM_010696	ENSMUSG00000002699	Lcp2	AI323664|BB161688|SLP-76|SLP76|m1Khoe|twm	lymphocyte cytosolic protein 2	protein-coding
mm_143453.1	chr17	70974195	70974227	-	1	NA	3' UTR (NM_023402, exon 4 of 4)	3' UTR (NM_023402, exon 4 of 4)	16305	NM_023402	67938	Mm.261329	NM_023402	ENSMUSG00000034868	Myl12b	1500001M02Rik|C77744|Mylc2b|RLC-B	myosin, light chain 12B, regulatory	protein-coding
mm_101556.1	chr11	33843694	33843713	-	1	NA	promoter-TSS (NM_001290690)	promoter-TSS (NM_001290690)	-118	NM_001290690	70357	Mm.252514	NM_027398	ENSMUSG00000053519	Kcnip1	KCHIP1|Kchip1.2	Kv channel-interacting protein 1	protein-coding
mm_90899.1	chr10	10558132	10558190	-	1	NA	promoter-TSS (NM_026405)	promoter-TSS (NM_026405)	46	NM_026405	67844	Mm.31486	NM_026405	ENSMUSG00000019832	Rab32	2810011A17Rik|AU022057	RAB32, member RAS oncogene family	protein-coding
mm_53503.1	chr6	135362947	135362961	+	1	NA	promoter-TSS (NM_001288628)	promoter-TSS (NM_001288628)	23	NM_001288628	13730	Mm.182785	NM_010128	ENSMUSG00000030208	Emp1	I-8-09|TMP	epithelial membrane protein 1	protein-coding
mm_45554.1	chr5	73168410	73168420	-	1	NA	intron (NM_028194, intron 3 of 62)	intron (NM_028194, intron 3 of 62)	88203	NM_028194	72313	Mm.260594	NM_028194	ENSMUSG00000070733	Fryl	2010313D22Rik|2310004H21Rik|2510002A14Rik|9030227G01Rik|mKIAA0826	FRY like transcription coactivator	protein-coding
mm_69890.1	chr7	141637247	141637251	-	1	NA	intron (NM_001330001, intron 31 of 33)	intron (NM_001330001, intron 31 of 33)	16548	NR_106030	102466798		NR_106030	ENSMUSG00000098759	Mir7063	Gm27654|mmu-mir-7063	microRNA 7063	ncRNA
mm_9114.1	chr1	170174885	170174899	-	1	NA	promoter-TSS (NM_133806)	promoter-TSS (NM_133806)	72	NM_001305046	107652	Mm.27969	NM_133806	ENSMUSG00000026670	Uap1	AA420407|AA437972|AGX-1|AGX-2|AGX1|AgX|ESTM38|SPAG2	UDP-N-acetylglucosamine pyrophosphorylase 1	protein-coding
mm_42080.1	chr5	110176641	110176678	+	1	NA	promoter-TSS (NM_008146)	promoter-TSS (NM_008146)	-42	NM_001347389	269682	Mm.9392	NM_008146	ENSMUSG00000029502	Golga3	5330413L04|5430416E01Rik|AI449376|AW490576|G1-499-14|Mea-2|Mea2|repro27	golgi autoantigen, golgin subfamily a, 3	protein-coding
mm_144039.1	chr17	90178569	90178573	-	1	NA	intron (NM_001346959, intron 3 of 6)	intron (NM_001346959, intron 3 of 6)	-90203	NM_001347419	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_123856.1	chr14	70994487	70994497	-	1	NA	Intergenic	Intergenic	104385	NM_001302094	14586	Mm.32619	NM_008115	ENSMUSG00000022103	Gfra2	-	glial cell line derived neurotrophic factor family receptor alpha 2	protein-coding
mm_129970.1	chr15	85790194	85790203	-	1	NA	intron (NM_001113418, intron 5 of 7)	(TAGA)n|Simple_repeat|Simple_repeat	21499	NM_001164626	72355	Mm.33706	NM_197998	ENSMUSG00000064284	Cdpf1	2210021J22Rik	cysteine rich, DPF motif domain containing 1	protein-coding
mm_81333.1	chr9	108517160	108517170	+	1	NA	promoter-TSS (NM_175143)	promoter-TSS (NM_175143)	78	NM_175143	69232	Mm.335449	NM_175143	ENSMUSG00000006673	Qrich1	2610028H07Rik	glutamine-rich 1	protein-coding
mm_33661.1	chr4	133132861	133132867	+	1	NA	intron (NM_153423, intron 1 of 8)	B3A|SINE|B2	2231	NM_153423	242687	Mm.23566	NM_153423	ENSMUSG00000028868	Wasf2	AW742646|D4Ertd13e|WAVE2	WAS protein family, member 2	protein-coding
mm_97944.1	chr11	83663481	83663500	+	1	NA	exon (NM_013652, exon 2 of 3)	exon (NM_013652, exon 2 of 3)	906	NM_013652	20303	Mm.244263	NM_013652	ENSMUSG00000018930	Ccl4	AT744.1|Act-2|MIP-1B|Mip1b|Scya4	chemokine (C-C motif) ligand 4	protein-coding
mm_160051.1	chr7	3336700	3336700	+	1	NA	exon (NM_133189, exon 1 of 5)	exon (NM_133189, exon 1 of 5)	115	NM_133189	81904	Mm.214994	NM_133189	ENSMUSG00000069806	Cacng7	-	calcium channel, voltage-dependent, gamma subunit 7	protein-coding
mm_48841.1	chr5	149367079	149367085	-	1	NA	Intergenic	Intergenic	-44724	NM_027519	70717	Mm.252139	NM_027519	ENSMUSG00000029659	Medag	6330406I15Rik|Awms3|MEDA-4|Meda4|mAWMS3	mesenteric estrogen dependent adipogenesis	protein-coding
mm_87711.1	chr10	60003384	60003392	+	1	NA	promoter-TSS (NM_001199187)	promoter-TSS (NM_001199187)	61	NM_001199187	69090	Mm.155839	NM_026937	ENSMUSG00000044475	Ascc1	1810015P09Rik|AI550520|ASC1p50|CGI-18	activating signal cointegrator 1 complex subunit 1	protein-coding
mm_140877.1	chr17	23828770	23828815	-	1	NA	intron (NM_026305, intron 2 of 3)	CpG	317	NM_026305	67673	Mm.153758	NM_026305	ENSMUSG00000055839	Elob	0610040H15Rik|Tceb2	elongin B	protein-coding
mm_59768.1	chr7	28834039	28834049	+	1	NA	promoter-TSS (NM_010707)	promoter-TSS (NM_010707)	-126	NM_010707	16857	Mm.210336	NM_010707		Lgals6	galectin-6	lectin, galactose binding, soluble 6	protein-coding
mm_111425.1	chr12	91635914	91635917	-	1	NA	3' UTR (NM_175367, exon 7 of 7)	3' UTR (NM_175367, exon 7 of 7)	-45428	NM_175335	83602	Mm.275728	NM_031391	ENSMUSG00000020962	Gtf2a1	6330549H03Rik|AA536742|AA959775|AW060250|TfIIAa/b|Tfiia1	general transcription factor II A, 1	protein-coding
mm_16304.1	chr2	174289679	174289687	+	1	NA	intron (NR_002846, intron 1 of 4)	(CA)n|Simple_repeat|Simple_repeat	5363	NM_022000	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_147667.1	chr18	60621992	60622005	-	1	NA	intron (NM_177340, intron 1 of 2)	intron (NM_177340, intron 1 of 2)	2307	NM_177340	104027	Mm.252321	NM_177340	ENSMUSG00000043079	Synpo	9030217H17Rik|9130229N11|9330140I15Rik|AW046661	synaptopodin	protein-coding
mm_133191.1	chr16	72669509	72669512	+	1	NA	intron (NM_019413, intron 1 of 28)	intron (NM_019413, intron 1 of 28)	6361	NM_019413	19876	Mm.310772	NM_019413	ENSMUSG00000022883	Robo1	AW494633|AW742721|DUTT1|Gm310	roundabout guidance receptor 1	protein-coding
mm_26328.1	chr3	142543884	142543884	+	1	NA	intron (NM_145545, intron 7 of 10)	intron (NM_145545, intron 7 of 10)	13548	NM_145545	229900	Mm.45740	NM_145545	ENSMUSG00000040253	Gbp7	9830147J24Rik	guanylate binding protein 7	protein-coding
mm_32316.1	chr4	103563324	103563331	+	1	NA	Intergenic	Intergenic	180827	NR_040673	622167	Mm.244115	NR_040673	ENSMUSG00000086136	Gm12718	OTTMUSG00000008109	predicted gene 12718	ncRNA
mm_121184.1	chr14	103049346	103049366	+	1	NA	exon (NM_008392, exon 2 of 5)	exon (NM_008392, exon 2 of 5)	2344	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_153765.1	chr19	45591915	45591935	-	1	NA	intron (NM_013907, intron 5 of 8)	intron (NM_013907, intron 5 of 8)	31310	NM_172639	226162	Mm.21978	NM_172639	ENSMUSG00000041035	Dpcd	5330431N19Rik|Ndac	deleted in primary ciliary dyskinesia	protein-coding
mm_136571.1	chr17	3453230	3453244	+	1	NA	intron (NM_001122998, intron 12 of 26)	intron (NM_001122998, intron 12 of 26)	-29078	NM_001286758	24001	Mm.137134	NM_011878	ENSMUSG00000023800	Tiam2	3000002F19Rik|STEF|mKIAA2016	T cell lymphoma invasion and metastasis 2	protein-coding
mm_144047.1	chr17	90445095	90445103	-	1	NA	intron (NM_001346957, intron 14 of 18)	intron (NM_001346957, intron 14 of 18)	10781	NM_001346958	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_99359.1	chr11	101627944	101627972	+	1	NA	promoter-TSS (NM_025654)	promoter-TSS (NM_025654)	9	NM_025654	66599	Mm.41449	NM_025654	ENSMUSG00000010362	Rdm1	2410008M22Rik|AW212028|Rad52b	RAD52 motif 1	protein-coding
mm_38342.1	chr4	137766475	137766501	-	1	NA	promoter-TSS (NM_001287172)	promoter-TSS (NM_001287172)	-13	NM_001287172	11647	Mm.288186	NM_007431	ENSMUSG00000028766	Alpl	ALP|APTNAP|Akp-2|Akp2|TNAP|TNSALP	alkaline phosphatase, liver/bone/kidney	protein-coding
mm_11622.1	chr2	34774181	34774216	+	1	NA	exon (NM_001163434, exon 6 of 9)	exon (NM_001163434, exon 6 of 9)	2108	NM_022310	14828	Mm.330160	NM_022310	ENSMUSG00000026864	Hspa5	AL022860|AU019543|Bip|D2Wsu141e|D2Wsu17e|Grp78|Hsce70|SEZ-7|Sez7|baffled|mBiP	heat shock protein 5	protein-coding
mm_19602.1	chr2	102401158	102401210	-	1	NA	promoter-TSS (NM_020267)	promoter-TSS (NM_020267)	-284	NM_020267	80985	Mm.315002	NM_020267	ENSMUSG00000027189	Trim44	Dipb|Mc7	tripartite motif-containing 44	protein-coding
mm_19604.1	chr2	102451798	102451815	-	1	NA	promoter-TSS (NM_010218)	promoter-TSS (NM_010218)	-14	NM_010218	14221	Mm.29730	NM_010218	ENSMUSG00000075012	Fjx1	-	four jointed box 1 (Drosophila)	protein-coding
mm_85910.1	chr9	111057191	111057233	-	1	NA	promoter-TSS (NM_017466)	promoter-TSS (NM_017466)	32	NM_001302377	54199	Mm.7336	NM_017466	ENSMUSG00000043953	Ccrl2	1810047I05Rik|Ackr5|CCR11|Cmkbr1l2|E01|L-CCR	chemokine (C-C motif) receptor-like 2	protein-coding
mm_82008.1	chr9	121710390	121710422	+	1	NA	promoter-TSS (NM_026794)	promoter-TSS (NM_026794)	17	NM_026794	26901	Mm.24848	NM_026794	ENSMUSG00000032526	Ss18l2	1110020I04Rik|AI463209|Deb1	SS18, nBAF chromatin remodeling complex subunit like 2	protein-coding
mm_53539.1	chr6	136808223	136808228	+	1	NA	promoter-TSS (NM_177688)	promoter-TSS (NM_177688)	-23	NM_177688	232440	Mm.154564	NM_177688	ENSMUSG00000060032	H2afj	E130307C13	H2A histone family, member J	protein-coding
mm_3447.1	chr1	150102861	150102871	+	1	NA	intron (NM_011198, intron 5 of 9)	intron (NM_011198, intron 5 of 9)	2835	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_27920.1	chr3	79532061	79532087	-	1	NA	intron (NM_001162999, intron 1 of 16)	intron (NM_001162999, intron 1 of 16)	35605	NM_001162999	329679	Mm.244005	NM_001162999	ENSMUSG00000061175	Fnip2	D630023B12Rik|mKIAA1450	folliculin interacting protein 2	protein-coding
mm_62576.1	chr7	104332133	104332135	+	1	NA	intron (NM_001243916, intron 3 of 6)	T-rich|Low_complexity|Low_complexity	2663	NM_001243916	434218	Mm.485757	NM_001243916	ENSMUSG00000090215	Trim34b	Gm15134|OTTMUSG00000019188|Trim34-2	tripartite motif-containing 34B	protein-coding
mm_173110.1	chrX	158600806	158600806	+	1	NA	Intergenic	Intergenic	-557609	NM_177751	245684	Mm.197074	NM_177751	ENSMUSG00000025658	Cnksr2	Cnk2|Ksr2	connector enhancer of kinase suppressor of Ras 2	protein-coding
mm_142990.1	chr17	56290477	56290482	-	1	NA	promoter-TSS (NM_025836)	promoter-TSS (NM_025836)	32	NM_025836	66905	Mm.311696	NM_025836	ENSMUSG00000024197	Plin3	1300012C15Rik|M6prbp1|Tip47	perilipin 3	protein-coding
mm_127968.1	chr15	12010802	12010811	-	1	NA	Intergenic	Intergenic	-14799	NM_011294	20024	Mm.41746	NM_011294	ENSMUSG00000022205	Sub1	AI842364|P15|P9|Pc4|Rpo2tc1	SUB1 homolog (S. cerevisiae)	protein-coding
mm_85062.1	chr9	90250530	90250563	-	1	NA	intron (NM_194334, intron 1 of 12)	Lx8|LINE|L1	20223	NM_194334	67016	Mm.335347	NM_194334	ENSMUSG00000037410	Tbc1d2b	1810061M12Rik|AI480956|AV021536|AV023399|AW491493|mKIAA1055	TBC1 domain family, member 2B	protein-coding
mm_167371.1	chr8	89580207	89580209	+	1	NA	Intergenic	Intergenic	-536046	NM_021390	58198	Mm.214361	NM_021390	ENSMUSG00000031665	Sall1	Msal-3	sal-like 1 (Drosophila)	protein-coding
mm_31164.1	chr4	43443103	43443130	+	1	NA	5' UTR (NM_011571, exon 1 of 10)	5' UTR (NM_011571, exon 1 of 10)	839	NM_011571	21754	Mm.485441	NM_011571	ENSMUSG00000028458	Tesk1	AI326901	testis specific protein kinase 1	protein-coding
mm_78505.1	chr9	32747927	32747943	+	1	NA	intron (NM_011808, intron 6 of 7)	intron (NM_011808, intron 6 of 7)	51893	NM_001038642	23871	Mm.292415	NM_011808	ENSMUSG00000032035	Ets1	AI196000|AI448617|D230050P06|Ets-1|Tpl1|vs	E26 avian leukemia oncogene 1, 5' domain	protein-coding
mm_147034.1	chr18	34751503	34751541	-	1	NA	promoter-TSS (NM_009860)	promoter-TSS (NM_009860)	11	NM_009860	12532	Mm.286602	NM_009860	ENSMUSG00000044201	Cdc25c	Cdc25	cell division cycle 25C	protein-coding
mm_156691.1	chrX	159459134	159459165	+	1	NA	promoter-TSS (NM_001313752)	promoter-TSS (NM_001313752)	24	NM_001313753	78283	Mm.160079	NM_001081124	ENSMUSG00000041020	Map7d2	1600028E09Rik|2900002G04Rik|5330432J06Rik|C030036K04Rik|Mtap7d2	MAP7 domain containing 2	protein-coding
mm_86317.1	chr9	122903103	122903162	-	1	NA	Intergenic	Intergenic	14661	NM_001177505	382118	Mm.86999	NM_001177505	ENSMUSG00000063488	Zkscan7	BC042569|Zfp167	zinc finger with KRAB and SCAN domains 7	protein-coding
mm_21114.1	chr2	153492474	153492510	-	1	NA	intron (NM_001134300, intron 1 of 10)	CpG	37479	NM_001134300	329540	Mm.50600	NM_001001986	ENSMUSG00000061411	Nol4l	4931410H15|8430427H17Rik|AI429157|Gm1636	nucleolar protein 4-like	protein-coding
mm_123155.1	chr14	57132030	57132045	-	1	NA	intron (NM_001010937, intron 1 of 2)	intron (NM_001010937, intron 1 of 2)	1574	NM_001271663	14623	Mm.25652	NM_008128	ENSMUSG00000040055	Gjb6	AA958971|Cx30|D14Bwg0506e	gap junction protein, beta 6	protein-coding
mm_104410.1	chr11	94601863	94601873	-	1	NA	promoter-TSS (NM_153807)	promoter-TSS (NM_153807)	-82	NM_153807	264895	Mm.386885	NM_153807	ENSMUSG00000076435	Acsf2	-	acyl-CoA synthetase family member 2	protein-coding
mm_91979.1	chr10	61680248	61680258	-	1	NA	promoter-TSS (NM_009120)	promoter-TSS (NM_009120)	37	NR_126477	75539		NR_126477		1700022H01Rik	-	RIKEN cDNA 1700022H01 gene	ncRNA
mm_10331.1	chr2	11522077	11522095	+	1	NA	intron (NM_001177758, intron 1 of 14)	intron (NM_001177758, intron 1 of 14)	-19996	NM_001177757	170768	Mm.19669	NM_133232	ENSMUSG00000026773	Pfkfb3	E330010H22Rik|iPFK-2|uPFK-2	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	protein-coding
mm_103514.1	chr11	76734727	76734752	-	1	NA	intron (NM_016810, intron 7 of 8)	intron (NM_016810, intron 7 of 8)	28816	NM_016810	53334	Mm.20931	NM_016810	ENSMUSG00000010392	Gosr1	AI414660|AI426320|BB145494|GOS-28|GOSRI|GS28	golgi SNAP receptor complex member 1	protein-coding
mm_24637.1	chr3	94372812	94372872	+	1	NA	promoter-TSS (NM_011281)	promoter-TSS (NM_011281)	48	NM_011281	19885	Mm.4372	NM_011281	ENSMUSG00000028150	Rorc	Nr1f3|RORgamma|TOR|Thor	RAR-related orphan receptor gamma	protein-coding
mm_27397.1	chr3	51211560	51211571	-	1	NA	Intergenic	Intergenic	-12882	NM_009834	12457	Mm.86541	NM_009834	ENSMUSG00000023087	Noct	AU043840|Ccr4|Ccrn4l	nocturnin	protein-coding
mm_65760.1	chr7	28630898	28630920	-	1	NA	5' UTR (NM_175319, exon 1 of 13)	5' UTR (NM_175319, exon 1 of 13)	106	NM_175319	101744	Mm.26022	NM_175319	ENSMUSG00000037469	Acp7	AU017076|C330005M16Rik|Papl	acid phosphatase 7, tartrate resistant	protein-coding
mm_84532.1	chr9	67155220	67155231	-	1	NA	intron (NR_045748, intron 1 of 2)	intron (NR_045748, intron 1 of 2)	21664	NR_045748	100502636	Mm.412607	NR_045748	ENSMUSG00000111556	Gm19299	-	predicted gene, 19299	ncRNA
mm_86060.1	chr9	114640053	114640113	-	1	NA	5' UTR (NM_153585, exon 1 of 20)	5' UTR (NM_153585, exon 1 of 20)	117	NM_153585	78893	Mm.283708	NM_153585	ENSMUSG00000056167	Cnot10	2600001P13Rik	CCR4-NOT transcription complex, subunit 10	protein-coding
mm_43420.1	chr5	136038772	136038803	+	1	NA	5' UTR (NM_175309, exon 1 of 6)	5' UTR (NM_175309, exon 1 of 6)	291	NM_175309	100647	Mm.3089	NM_175309	ENSMUSG00000042985	Upk3b	AI447729|AI957187|P35|PMS2L14|UpIIIb	uroplakin 3B	protein-coding
mm_114781.1	chr13	88823592	88823595	+	1	NA	intron (NM_010103, intron 1 of 9)	intron (NM_010103, intron 1 of 9)	2121	NM_001037987	13612	Mm.125580	NM_010103	ENSMUSG00000034488	Edil3	Del-1|Del1	EGF-like repeats and discoidin I-like domains 3	protein-coding
mm_94010.1	chr10	127621108	127621166	-	1	NA	promoter-TSS (NM_008512)	promoter-TSS (NM_008512)	11	NM_008512	16971	Mm.271854	NM_008512	ENSMUSG00000040249	Lrp1	A2mr|AI316852|CD91|Lrp|b2b1554Clo	low density lipoprotein receptor-related protein 1	protein-coding
mm_138662.1	chr17	35869668	35869716	+	1	NA	intron (NM_175242, intron 1 of 2)	intron (NM_175242, intron 1 of 2)	3077	NM_175242	76448	Mm.359982	NM_175242	ENSMUSG00000034595	Ppp1r18	2310014H01Rik|AA407849|AI450394	protein phosphatase 1, regulatory subunit 18	protein-coding
mm_122655.1	chr14	51911335	51911353	-	1	NA	intron (NM_013864, intron 2 of 15)	intron (NM_013864, intron 2 of 15)	2144	NM_001145959	29811	Mm.26722	NM_013864	ENSMUSG00000004558	Ndrg2	AI182517|AU040374|Ndr2|SYLD	N-myc downstream regulated gene 2	protein-coding
mm_95989.1	chr11	59002958	59002969	+	1	NA	intron (NM_001171512, intron 89 of 103)	intron (NM_001171512, intron 89 of 103)	24870	NM_053168	94091	Mm.248049	NM_053168	ENSMUSG00000020455	Trim11	-	tripartite motif-containing 11	protein-coding
mm_38824.1	chr4	148952880	148952917	-	1	NA	3' UTR (NM_001159344, exon 21 of 21)	3' UTR (NM_001159344, exon 21 of 21)	146914	NM_019781	56273	Mm.184172	NM_019781	ENSMUSG00000028975	Pex14	Pex14p|R75137	peroxisomal biogenesis factor 14	protein-coding
mm_72378.1	chr8	81353167	81353168	+	1	NA	intron (NM_001024617, intron 1 of 24)	intron (NM_001024617, intron 1 of 24)	10605	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_10367.1	chr2	11712039	11712043	+	1	NA	intron (NM_001271499, intron 1 of 6)	intron (NM_001271499, intron 1 of 6)	6329	NM_001271500	16169	Mm.200196	NM_008358	ENSMUSG00000023206	Il15ra	AA690181|IL-15RA	interleukin 15 receptor, alpha chain	protein-coding
mm_113377.1	chr13	33004621	33004640	+	1	NA	promoter-TSS (NM_009256)	promoter-TSS (NM_009256)	89	NM_009256	20723	Mm.245041	NM_009256	ENSMUSG00000045827	Serpinb9	BB283241|CAP-3|CAP3|PI-9|PI9|Spi6|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 9	protein-coding
mm_23122.1	chr3	37644133	37644144	+	1	NA	3' UTR (NM_011896, exon 3 of 3)	3' UTR (NM_011896, exon 3 of 3)	4191	NM_001305442	24063	Mm.330986	NM_011896	ENSMUSG00000037211	Spry1	sprouty1|spry-1	sprouty homolog 1 (Drosophila)	protein-coding
mm_25707.1	chr3	122510879	122510882	+	1	NA	intron (NM_013867, intron 5 of 11)	intron (NM_013867, intron 5 of 11)	30801	NR_106117	102465764		NR_106117	ENSMUSG00000104773	Mir7657	mmu-mir-7657	microRNA 7657	ncRNA
mm_23500.1	chr3	60528065	60528134	+	1	NA	intron (NM_001253710, intron 1 of 7)	intron (NM_001253710, intron 1 of 7)	26920	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_111281.1	chr12	85350626	85350630	-	1	NA	intron (NM_026775, intron 3 of 4)	intron (NM_026775, intron 3 of 4)	-11266	NM_145138	217718	Mm.29071	NM_145138	ENSMUSG00000034290	Nek9	C130021H08Rik	NIMA (never in mitosis gene a)-related expressed kinase 9	protein-coding
mm_53454.1	chr6	134696020	134696022	+	1	NA	intron (NM_026371, intron 3 of 3)	intron (NM_026371, intron 3 of 3)	55081	NM_026371	67774	Mm.41892	NM_026371	ENSMUSG00000042992	Borcs5	5830457J20Rik|AW124643|Loh12cr1	BLOC-1 related complex subunit 5	protein-coding
mm_113176.1	chr13	24831662	24831687	+	1	NA	promoter-TSS (NM_019551)	promoter-TSS (NM_019551)	15	NM_019551	56196	Mm.427162	NM_019551	ENSMUSG00000035958	Tdp2	D13Ertd656e|Ttrap	tyrosyl-DNA phosphodiesterase 2	protein-coding
mm_128819.1	chr15	67128853	67128874	-	1	NA	intron (NM_009177, intron 2 of 8)	intron (NM_009177, intron 2 of 8)	48019	NM_009177	20442	Mm.248334	NM_009177	ENSMUSG00000013846	St3gal1	5330418N22Rik|AI467004|ST3GalI|Siat4|Siat4a|St3gal-1	ST3 beta-galactoside alpha-2,3-sialyltransferase 1	protein-coding
mm_172885.1	chr9	52610803	52610804	+	1	NA	Intergenic	Intergenic	68634	NM_178906	330941	Mm.335160	NM_177907	ENSMUSG00000078307	AI593442	E130102D23	expressed sequence AI593442	protein-coding
mm_11168.1	chr2	28558021	28558053	+	1	NA	exon (NM_009885, exon 8 of 11)	exon (NM_009885, exon 8 of 11)	5366	NM_009885	12613	Mm.236017	NM_009885	ENSMUSG00000026818	Cel	1810036E18Rik|BAL	carboxyl ester lipase	protein-coding
mm_72802.1	chr8	87472784	87472794	+	1	NA	promoter-TSS (NM_019626)	promoter-TSS (NM_019626)	-23	NR_033430	100040294	Mm.213632	NR_033430	ENSMUSG00000097248	Gm2694	C230036H16Rik|linc1582	predicted gene 2694	ncRNA
mm_84594.1	chr9	70036819	70036841	-	1	NA	5' UTR (NM_028087, exon 2 of 3)	5' UTR (NM_028087, exon 2 of 3)	1258	NM_028087	72077	Mm.195555	NM_028087	ENSMUSG00000032226	Gcnt3	2010013H22Rik|2210021I22Rik|2210401J11Rik	glucosaminyl (N-acetyl) transferase 3, mucin type	protein-coding
mm_167234.1	chr8	14596620	14596638	-	1	NA	intron (NM_172910, intron 4 of 15)	intron (NM_172910, intron 4 of 15)	-291907	NM_012000	26889	Mm.254027	NM_012000	ENSMUSG00000026317	Cln8	mnd	ceroid-lipofuscinosis, neuronal 8	protein-coding
mm_32344.1	chr4	104774008	104774015	+	1	NA	intron (NM_001316671, intron 1 of 10)	intron (NM_001316671, intron 1 of 10)	7694	NM_001316671	110382	Mm.87072	NM_133882	ENSMUSG00000029656	C8b	4930439B20Rik|AI595927	complement component 8, beta polypeptide	protein-coding
mm_41954.1	chr5	105793616	105793652	+	1	NA	intron (NM_001122768, intron 2 of 2)	intron (NM_001122768, intron 2 of 2)	-82934	NR_030777	54367	Mm.248876	NM_018759	ENSMUSG00000029290	Zfp326	5730470H14Rik|ZAN75|Znf326	zinc finger protein 326	protein-coding
mm_158215.1	chrX	105876027	105876040	-	1	NA	exon (NM_009530, exon 9 of 35)	exon (NM_009530, exon 9 of 35)	53339	NM_009530	22589	Mm.10141	NM_009530	ENSMUSG00000031229	Atrx	4833408C14Rik|AI447451|ATR2|DXHXS6677E|HP1-BP38|Hp1bp2|Hp1bp38|MRXS3|RAD54L|Rad54|XH2|Xnp|ZNF-HX	alpha thalassemia/mental retardation syndrome X-linked	protein-coding
mm_140380.1	chr17	87107622	87107684	+	1	NA	promoter-TSS (NM_019654)	promoter-TSS (NM_019654)	-26	NM_019654	56468	Mm.126885	NM_019654	ENSMUSG00000037104	Socs5	1810018L08Rik|Cish5|mKIAA0671	suppressor of cytokine signaling 5	protein-coding
mm_119603.1	chr14	51091090	51091160	+	1	NA	promoter-TSS (NM_001161731)	promoter-TSS (NM_001161731)	48	NM_021472	58809	Mm.202665	NM_021472	ENSMUSG00000021876	Rnase4	C730049F20Rik|Rab1	ribonuclease, RNase A family 4	protein-coding
mm_54579.1	chr6	38124466	38124473	-	1	NA	5' UTR (NM_080467, exon 1 of 21)	5' UTR (NM_080467, exon 1 of 21)	117	NM_080467	140494	Mm.462308	NM_080467	ENSMUSG00000038600	Atp6v0a4	Atp6n1b|a4	ATPase, H+ transporting, lysosomal V0 subunit A4	protein-coding
mm_5479.1	chr1	36699910	36699933	-	1	NA	3' UTR (NM_146107, exon 11 of 11)	3' UTR (NM_146107, exon 11 of 11)	8434	NM_009942	12859	Mm.180182	NM_009942	ENSMUSG00000061518	Cox5b	-	cytochrome c oxidase subunit Vb	protein-coding
mm_168488.1	chr1	149513215	149513215	-	1	NA	Intergenic	IAPLTR1_Mm|LTR|ERVK	409224	NM_001305632	18783	Mm.4186	NM_008869	ENSMUSG00000056220	Pla2g4a	Pla2g4|cPLA2|cPLA2-alpha|cPLA2alpha	phospholipase A2, group IVA (cytosolic, calcium-dependent)	protein-coding
mm_75847.1	chr8	70638869	70638879	-	1	NA	Intergenic	Intergenic	-6418	NM_001330687	23886	Mm.31325	NM_011819	ENSMUSG00000038508	Gdf15	MIC-1|NAG-1|SBF	growth differentiation factor 15	protein-coding
mm_98883.1	chr11	97815654	97815667	+	1	NA	intron (NM_010688, intron 2 of 6)	intron (NM_010688, intron 2 of 6)	15988	NM_010688	16796	Mm.271967	NM_010688	ENSMUSG00000038366	Lasp1	AA408629|Def-4|SH3P6|Tg(Col1a1-lacZ)1Ngma	LIM and SH3 protein 1	protein-coding
mm_37501.1	chr4	123718182	123718195	-	1	NA	promoter-TSS (NR_002445).2	promoter-TSS (NR_002445).2	-2	NM_001030274	595136	Mm.42805	NM_001030274	ENSMUSG00000028648	Ndufs5	AI256693	NADH dehydrogenase (ubiquinone) Fe-S protein 5	protein-coding
mm_148205.1	chr18	79110407	79110451	-	1	NA	Intergenic	Intergenic	-1038	NM_053099	240427	Mm.312871	NM_053099	ENSMUSG00000024548	Setbp1	C130092E12|Seb|mKIAA0437	SET binding protein 1	protein-coding
mm_140053.1	chr17	74549584	74549598	+	1	NA	intron (NM_007566, intron 3 of 72)	B3|SINE|B2	21296	NM_007566	12211	Mm.442564	NM_007566	ENSMUSG00000024073	Birc6	A430032G04Rik|A430040A19Rik|AA501170|Bruce|D630005A10Rik|mKIAA1289	baculoviral IAP repeat-containing 6	protein-coding
mm_66935.1	chr7	61595839	61595839	-	1	NA	intron (NR_045727, intron 2 of 4)	intron (NR_045727, intron 2 of 4)	19488	NR_045727	319752	Mm.294476	NR_045727		B230209E15Rik	-	RIKEN cDNA B230209E15 gene	ncRNA
mm_173223.1	chrX	75104359	75104360	+	1	NA	exon (NM_001030307, exon 10 of 15)	exon (NM_001030307, exon 10 of 15)	8505	NM_001030307	245474	Mm.291062	NM_001030307	ENSMUSG00000031403	Dkc1	BC068171	dyskeratosis congenita 1, dyskerin	protein-coding
mm_163182.1	chr11	91577587	91577590	-	1	NA	promoter-TSS (NM_028547)	promoter-TSS (NM_028547)	-33	NM_028547	73470	Mm.67677	NM_028547	ENSMUSG00000046755	Kif2b	1700063D03Rik	kinesin family member 2B	protein-coding
mm_24915.1	chr3	96263720	96263729	+	1	NA	promoter-TSS (NM_033596)	promoter-TSS (NM_033596)	-407	NM_033596	97122	Mm.227295	NM_033596	ENSMUSG00000091405	Hist2h4	H4|X04652	histone cluster 2, H4	protein-coding
mm_146770.1	chr18	20002340	20002361	-	1	NA	promoter-TSS (NM_001291809)	promoter-TSS (NM_001291809)	-253	NM_001291809	13507	Mm.89935	NM_007882	ENSMUSG00000059898	Dsc3	5430426I24Rik	desmocollin 3	protein-coding
mm_147132.1	chr18	36197316	36197329	-	1	NA	promoter-TSS (NM_001167891)	promoter-TSS (NM_001167891)	-162	NM_001167891	100042150	Mm.380390	NM_001167891	ENSMUSG00000060275	Nrg2	Don1|NTAK	neuregulin 2	protein-coding
mm_120254.1	chr14	63011730	63011740	+	1	NA	promoter-TSS (NM_001039121)	promoter-TSS (NM_001039121)	-36	NM_001039121	654458	Mm.390737	NM_001039121	ENSMUSG00000075572	Defb43	BD-43|EG654458|mBD-43	defensin beta 43	protein-coding
mm_3632.1	chr1	152807878	152807898	+	1	NA	5' UTR (NM_010877, exon 2 of 16)	5' UTR (NM_010877, exon 2 of 16)	7735	NM_010877	17970	Mm.270307	NM_010877	ENSMUSG00000026480	Ncf2	NOXA2|Ncf-2|p67phox	neutrophil cytosolic factor 2	protein-coding
mm_52320.1	chr6	108836360	108836370	+	1	NA	intron (NM_138677, intron 1 of 11)	intron (NM_138677, intron 1 of 11)	7724	NM_138677	192193	Mm.21596	NM_138677	ENSMUSG00000030104	Edem1	A130059K23Rik|EDEM|mKIAA0212	ER degradation enhancer, mannosidase alpha-like 1	protein-coding
mm_130168.1	chr15	93270602	93270608	-	1	NA	intron (NM_001346785, intron 1 of 7)	MLTR11B|LTR|ERVK	4479	NM_001033275	223827	Mm.22819	NM_001033275	ENSMUSG00000036197	Gxylt1	Glt8d3|Gm1228|Gm87	glucoside xylosyltransferase 1	protein-coding
mm_99128.1	chr11	100319844	100319850	+	1	NA	promoter-TSS (NM_011508)	promoter-TSS (NM_011508)	-102	NM_011508	20918	Mm.13886	NM_011508	ENSMUSG00000035530	Eif1	Sui1-rs1	eukaryotic translation initiation factor 1	protein-coding
mm_70425.1	chr8	11477922	11477953	+	1	NA	promoter-TSS (NR_126558)	promoter-TSS (NR_126558)	8	NR_126558	102132	Mm.37632	NR_126558	ENSMUSG00000096957	E230013L22Rik	AI645545	RIKEN cDNA E230013L22 gene	ncRNA
mm_85405.1	chr9	103365624	103365694	-	1	NA	promoter-TSS (NM_001134427)	promoter-TSS (NM_001134427)	121	NM_175833	321022	Mm.261025	NM_175565	ENSMUSG00000032803	Cdv3	2510010F10Rik|C230084J24Rik|C79446|TPP36	carnitine deficiency-associated gene expressed in ventricle 3	protein-coding
mm_64849.1	chr7	13034020	13034036	-	1	NA	5' UTR (NM_026885, exon 2 of 6)	5' UTR (NM_026885, exon 2 of 6)	749	NM_026885	68953	Mm.295670	NM_026885	ENSMUSG00000033916	Chmp2a	1500016L11Rik	charged multivesicular body protein 2A	protein-coding
mm_10704.1	chr2	22774052	22774072	+	1	NA	promoter-TSS (NM_019456)	promoter-TSS (NM_019456)	-265	NM_019456	54519	Mm.14255	NM_019456	ENSMUSG00000026786	Apbb1ip	9930118P07Rik|Prp48	amyloid beta (A4) precursor protein-binding, family B, member 1 interacting protein	protein-coding
mm_149606.1	chr19	16383616	16383630	+	1	NA	3' UTR (NM_008139, exon 7 of 7)	3' UTR (NM_008139, exon 7 of 7)	-52044	NM_008137	14675	Mm.313181	NM_008137	ENSMUSG00000024697	Gna14	AU023208	guanine nucleotide binding protein, alpha 14	protein-coding
mm_166224.1	chr5	65019172	65019178	-	1	NA	intron (NM_026667, intron 7 of 13)	intron (NM_026667, intron 7 of 13)	48857	NR_030577	100124451		NR_030577	ENSMUSG00000077042	Mir574	Mirn574|mir-574|mmu-mir-574	microRNA 574	ncRNA
mm_66489.1	chr7	45052866	45052914	-	1	NA	promoter-TSS (NM_175022)	promoter-TSS (NM_175022)	-9	NM_175022	233210	Mm.219137	NM_175022	ENSMUSG00000046574	Prr12	6720469B10|BC058674	proline rich 12	protein-coding
mm_44963.1	chr5	36713258	36713295	-	1	NA	Intergenic	Intergenic	-17255	NM_001081232	320661	Mm.26480	NM_177221	ENSMUSG00000029190	D5Ertd579e	9030221A05Rik|A930018H20Rik|Kiaa0232	DNA segment, Chr 5, ERATO Doi 579, expressed	protein-coding
mm_76032.1	chr8	77289957	77289978	-	1	NA	intron (NM_030113, intron 19 of 22)	intron (NM_030113, intron 19 of 22)	-227089	NR_028125	70345	Mm.411813	NR_028125	ENSMUSG00000097882	0610038B21Rik	-	RIKEN cDNA 0610038B21 gene	ncRNA
mm_143998.1	chr17	88051738	88051741	-	1	NA	intron (NM_001081034, intron 1 of 22)	B1_Mm|SINE|Alu	13546	NM_001081034	225055	Mm.386857	NM_001081034	ENSMUSG00000005371	Fbxo11	C80048|Jf	F-box protein 11	protein-coding
mm_164548.1	chr17	12550084	12550086	+	1	NA	Intergenic	RLTR10D|LTR|ERVK	-34104	NM_013667	20518	Mm.17322	NM_013667	ENSMUSG00000040966	Slc22a2	Oct2|Orct2	solute carrier family 22 (organic cation transporter), member 2	protein-coding
mm_50892.1	chr6	56832164	56832175	+	1	NA	5' UTR (NM_012056, exon 1 of 10)	5' UTR (NM_012056, exon 1 of 10)	110	NM_012056	27055	Mm.20943	NM_012056	ENSMUSG00000029781	Fkbp9	1810014L23|AW549641|FKBP-63|FKBP-9|FKBP60|FKBP63|FKBP65RS	FK506 binding protein 9	protein-coding
mm_169571.1	chr15	19864044	19864060	-	1	NA	Intergenic	BGLII|LTR|ERVK	802698	NM_022816	64833	Mm.352763	NM_022816	ENSMUSG00000047565	Acot10	Acate3|MT-ACT48|p48	acyl-CoA thioesterase 10	protein-coding
mm_36093.1	chr4	58499391	58499395	-	1	NA	promoter-TSS (NM_001290486)	promoter-TSS (NM_001290486)	10	NM_001290486	14745	Mm.4772	NM_010336	ENSMUSG00000038668	Lpar1	AI326300|Edg2|Gpcr26|Kdt2|lpA1|vzg-1	lysophosphatidic acid receptor 1	protein-coding
mm_88151.1	chr10	69534103	69534156	+	1	NA	5' UTR (NM_170688, exon 1 of 43)	5' UTR (NM_170688, exon 1 of 43)	421	NM_146005	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_66704.1	chr7	45921112	45921127	-	1	NA	promoter-TSS (NM_001146346)	promoter-TSS (NM_001146346)	-270	NM_001146346	13732	Mm.20829	NM_010129	ENSMUSG00000040212	Emp3	H-4|H4|HNMP-1|MI-35|Ymp	epithelial membrane protein 3	protein-coding
mm_121586.1	chr14	6889921	6889959	-	1	NA	Intergenic	CpG	-132883	NM_001309401	100041151	Mm.396155	NM_001309401	ENSMUSG00000091754	Gm3636	100042043	predicted gene 3636	protein-coding
mm_123676.1	chr14	69484105	69484113	-	1	NA	Intergenic	Intergenic	28440	NM_173420	239167	Mm.259889	NM_173420	ENSMUSG00000047977	Synb	D930020E02Rik|syncytin-B	syncytin b	protein-coding
mm_135391.1	chr16	44332926	44333004	-	1	NA	promoter-TSS (NM_001159419)	promoter-TSS (NM_001159419)	-127	NM_001159419	320007	Mm.242144	NM_198034	ENSMUSG00000022696	Sidt1	AW045928|B830021E24Rik	SID1 transmembrane family, member 1	protein-coding
mm_157191.1	chrX	12058753	12058766	-	1	NA	exon (NM_029510, exon 4 of 15)	exon (NM_029510, exon 4 of 15)	21794	NM_175045	71458	Mm.196328	NM_029510	ENSMUSG00000040363	Bcor	2900008C10Rik|5830466J11Rik|8430401K06Rik|BcorR|D930024N20Rik|mKIAA1575	BCL6 interacting corepressor	protein-coding
mm_121293.1	chr14	105258850	105258890	+	1	NA	exon (NM_029561, exon 1 of 8)	exon (NM_029561, exon 1 of 8)	197	NM_001190989	76273	Mm.290669	NM_029561	ENSMUSG00000053253	Ndfip2	0710001O20Rik|2810436B12Rik|9130207N19Rik|N4wbp5a|mKIAA1165	Nedd4 family interacting protein 2	protein-coding
mm_59845.1	chr7	29768569	29768642	+	1	NA	promoter-TSS (NM_023750)	promoter-TSS (NM_023750)	53	NM_023750	74352	Mm.251083	NM_023750	ENSMUSG00000046185	Zfp84	2210410P13Rik|4633401C23Rik|AI415447|BB081605|C86188|KRAB18|Zfp69	zinc finger protein 84	protein-coding
mm_123589.1	chr14	67072695	67072699	-	1	NA	promoter-TSS (NM_028032)	promoter-TSS (NM_028032)	-226	NM_001205188	71978	Mm.273997	NM_028032	ENSMUSG00000022052	Ppp2r2a	2410004D02Rik|mKIAA1541	protein phosphatase 2, regulatory subunit B, alpha	protein-coding
mm_12900.1	chr2	84809307	84809323	+	1	NA	3' UTR (NM_019949, exon 4 of 4)	3' UTR (NM_019949, exon 4 of 4)	10487	NM_019949	56791	Mm.38261	NM_019949	ENSMUSG00000027078	Ube2l6	2810489I21Rik|RIG-B|UBCH8|Ubce8|Ubcm8	ubiquitin-conjugating enzyme E2L 6	protein-coding
mm_157.1	chr1	12692490	12692539	+	1	NA	promoter-TSS (NM_001198566)	promoter-TSS (NM_001198566)	84	NM_001198566	240725	Mm.45563	NM_172294	ENSMUSG00000016918	Sulf1	AI467640|AW121680|mKIAA1077	sulfatase 1	protein-coding
mm_45958.1	chr5	90464047	90464099	-	1	NA	exon (NM_009654, exon 4 of 15)	exon (NM_009654, exon 4 of 15)	3203	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_34003.1	chr4	137920873	137920887	+	1	NA	intron (NM_199307, intron 3 of 19)	intron (NM_199307, intron 3 of 19)	58643	NM_199307	230857	Mm.401062	NM_199307	ENSMUSG00000057530	Ece1	AW322500|ECE-1|ECE-1a|ECE-1b|ECE-1d	endothelin converting enzyme 1	protein-coding
mm_105829.1	chr11	113197487	113197490	-	1	NA	intron (NR_015556, intron 1 of 2)	intron (NR_015556, intron 1 of 2)	4350	NR_015556	72386	Mm.266961	NR_015556	ENSMUSG00000087259	2610035D17Rik	-	RIKEN cDNA 2610035D17 gene	ncRNA
mm_99970.1	chr11	113687764	113687767	+	1	NA	intron (NM_177777, intron 1 of 4)	intron (NM_177777, intron 1 of 4)	3353	NM_177777	276852	Mm.239566	NM_177777	ENSMUSG00000041623	D11Wsu47e	-	DNA segment, Chr 11, Wayne State University 47, expressed	protein-coding
mm_165035.1	chr19	36118237	36118246	+	1	NA	exon (NM_013468, exon 3 of 9)	exon (NM_013468, exon 3 of 9)	1603	NM_013468	107765	Mm.10279	NM_013468	ENSMUSG00000024803	Ankrd1	Alrp|CARP|Crap|MARP1	ankyrin repeat domain 1 (cardiac muscle)	protein-coding
mm_171192.1	chr3	44857516	44857531	+	1	NA	Intergenic	L1Md_T|LINE|L1	520737	NR_045172	72511	Mm.140700	NR_045172	ENSMUSG00000097040	2610316D01Rik	-	RIKEN cDNA 2610316D01 gene	ncRNA
mm_77867.1	chr9	5335409	5335424	+	1	NA	intron (NM_007609, intron 7 of 8)	intron (NM_007609, intron 7 of 8)	-10060	NM_009808	12364	Mm.42163	NM_009808	ENSMUSG00000025887	Casp12	-	caspase 12	protein-coding
mm_140396.1	chr17	87635975	87635990	+	1	NA	promoter-TSS (NM_008532)	promoter-TSS (NM_008532)	3	NM_008532	17075	Mm.4259	NM_008532	ENSMUSG00000045394	Epcam	CD326|EGP|EGP-2|Egp314|Ep-CAM|EpCAM1|GA733-2|Ly74|TROP1|Tacsd1|Tacstd1|gp40	epithelial cell adhesion molecule	protein-coding
mm_68778.1	chr7	122132864	122132943	-	1	NA	promoter-TSS (NM_001081238)	promoter-TSS (NM_001081238)	43	NM_001289844	233826	Mm.38348	NM_172744	ENSMUSG00000044702	Palb2	BC066140	partner and localizer of BRCA2	protein-coding
mm_141395.1	chr17	29238071	29238083	-	1	NA	promoter-TSS (NM_153166)	promoter-TSS (NM_153166)	-287	NM_153166	240058	Mm.39905	NM_153166	ENSMUSG00000024008	Cpne5	A830083G22Rik	copine V	protein-coding
mm_163047.1	chr11	57513857	57513857	-	1	NA	intron (NM_001168667, intron 2 of 13)	intron (NM_001168667, intron 2 of 13)	4787	NM_001168667	67726	Mm.25632	NM_026342	ENSMUSG00000020523	Fam114a2	1810073G14Rik|9030624B09Rik	family with sequence similarity 114, member A2	protein-coding
mm_38475.1	chr4	140665892	140665913	-	1	NA	promoter-TSS (NM_001112722)	promoter-TSS (NM_001112722)	3	NM_001112722	72754	Mm.29329	NM_172415	ENSMUSG00000040964	Arhgef10l	2810441C07Rik	Rho guanine nucleotide exchange factor (GEF) 10-like	protein-coding
mm_99582.1	chr11	104231575	104231577	+	1	NA	5' UTR (NM_010838, exon 1 of 10)	5' UTR (NM_010838, exon 1 of 10)	140	NM_001285454	17762	Mm.1287	NM_010838	ENSMUSG00000018411	Mapt	AI413597|AW045860|Mtapt|Tau	microtubule-associated protein tau	protein-coding
mm_166981.1	chr7	45434433	45434451	-	1	NA	promoter-TSS (NM_030678)	promoter-TSS (NM_030678)	22	NM_011304	20174	Mm.34410	NM_011304	ENSMUSG00000003868	Ruvbl2	mp47|p47	RuvB-like protein 2	protein-coding
mm_132375.1	chr16	34900232	34900248	+	1	NA	intron (NM_139300, intron 11 of 31)	intron (NM_139300, intron 11 of 31)	39089	NR_040536	76649	Mm.420532	NR_040536	ENSMUSG00000100593	1700119H24Rik	-	RIKEN cDNA 1700119H24 gene	ncRNA
mm_56331.1	chr6	92578500	92578503	-	1	NA	intron (NM_001081146, intron 2 of 8)	intron (NM_001081146, intron 2 of 8)	-11135	NM_001134461	243548	Mm.248820	NM_001081146	ENSMUSG00000030020	Prickle2	6230400G14Rik|6720451F06Rik|mpk2	prickle planar cell polarity protein 2	protein-coding
mm_17002.1	chr2	18392737	18392838	-	1	NA	promoter-TSS (NM_001190817)	promoter-TSS (NM_001190817)	43	NM_001190817	13418	Mm.246674	NM_007869	ENSMUSG00000026740	Dnajc1	4733401K02Rik|AA960110|D230036H06Rik|Dnajl1|ERdj1|ERj1p|MTJ1	DnaJ heat shock protein family (Hsp40) member C1	protein-coding
mm_82452.1	chr9	15494174	15494190	-	1	NA	Intergenic	CpG	-11313	NM_133214	170748	Mm.86572	NM_133214	ENSMUSG00000058173	Smco4	Fn5	single-pass membrane protein with coiled-coil domains 4	protein-coding
mm_65724.1	chr7	28380950	28380954	-	1	NA	Intergenic	Intergenic	-1724	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_138679.1	chr17	35916880	35916910	+	1	NA	promoter-TSS (NM_025878)	promoter-TSS (NM_025878)	-301	NM_001163818	52040	Mm.29385	NM_175934	ENSMUSG00000039220	Ppp1r10	2610025H06Rik|Cat53|D17Ertd808e|Fb19|Pnuts	protein phosphatase 1, regulatory subunit 10	protein-coding
mm_77674.1	chr8	124945738	124945741	-	1	NA	intron (NM_053207, intron 1 of 4)	B1_Mur2|SINE|Alu	3515	NM_053207	112405	Mm.140619	NM_053207	ENSMUSG00000031987	Egln1	AI503754|C1orf12|HIF-PH2|HPH-2|Hif-p4h-2|ORF13|Phd2|SM-20	egl-9 family hypoxia-inducible factor 1	protein-coding
mm_109005.1	chr12	103314979	103314989	+	1	NA	promoter-TSS (NM_001195726)	promoter-TSS (NM_001195726)	25	NM_001195726	100504156	Mm.425749	NM_001195726	ENSMUSG00000096753	Fam181a	EG544888	family with sequence similarity 181, member A	protein-coding
mm_142813.1	chr17	51737848	51737858	-	1	NA	3' UTR (NM_001163632, exon 11 of 11)	3' UTR (NM_001163632, exon 11 of 11)	74201	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_23266.1	chr3	51484185	51484260	+	1	NA	5' UTR (NM_016858, exon 1 of 2)	5' UTR (NM_016858, exon 1 of 2)	256	NM_016858	19338	Mm.1664	NM_016858	ENSMUSG00000027739	Rab33b	-	RAB33B, member RAS oncogene family	protein-coding
mm_115026.1	chr13	99184686	99184726	+	1	NA	promoter-TSS (NM_001004149)	promoter-TSS (NM_001004149)	-117	NM_001004149	238803	Mm.343207	NM_001004149	ENSMUSG00000050919	Zfp366	DC-SCRIPT|Znf366	zinc finger protein 366	protein-coding
mm_4706.1	chr1	180904279	180904343	+	1	NA	promoter-TSS (NM_133705)	promoter-TSS (NM_133705)	37	NM_133705	69051	Mm.274180	NM_133705	ENSMUSG00000026520	Pycr2	1810018M05Rik|P5cr2	pyrroline-5-carboxylate reductase family, member 2	protein-coding
mm_168798.1	chr12	20071578	20071588	+	1	NA	Intergenic	CpG	744196	NR_015521	69513	Mm.273972	NR_015521	ENSMUSG00000099759	1700030C10Rik	-	RIKEN cDNA 1700030C10 gene	ncRNA
mm_23908.1	chr3	83042421	83042444	+	1	NA	exon (NM_181849, exon 8 of 8)	exon (NM_181849, exon 8 of 8)	7431	NM_181849	110135	Mm.30063	NM_181849	ENSMUSG00000033831	Fgb	2510049G14Rik	fibrinogen beta chain	protein-coding
mm_61014.1	chr7	49372195	49372216	+	1	NA	intron (NM_175272, intron 2 of 37)	intron (NM_175272, intron 2 of 37)	126016	NM_175272	78286	Mm.333881	NM_175272	ENSMUSG00000052512	Nav2	5330421F07Rik|AU067780|BQ960892|HELAD1|POMFIL2|RAINB1|RAINB2|Unc53H2|mKIAA3015	neuron navigator 2	protein-coding
mm_12129.1	chr2	61649964	61649995	+	1	NA	exon (NM_001164072, exon 7 of 8)	exon (NM_001164072, exon 7 of 8)	56882	NM_001164071	21353	Mm.244393	NM_011529	ENSMUSG00000064289	Tank	C86182|E430026L09Rik|I-TRAF	TRAF family member-associated Nf-kappa B activator	protein-coding
mm_95564.1	chr11	52361070	52361126	+	1	NA	5' UTR (NM_011694, exon 1 of 9)	5' UTR (NM_011694, exon 1 of 9)	236	NM_011694	22333	Mm.3555	NM_011694	ENSMUSG00000020402	Vdac1	AL033343|Vdac5|mVDAC1|mVDAC5	voltage-dependent anion channel 1	protein-coding
mm_49856.1	chr6	38441955	38441958	+	1	NA	intron (NM_177185, intron 2 of 16)	intron (NM_177185, intron 2 of 16)	8031	NM_177185	320538	Mm.302831	NM_177185	ENSMUSG00000038538	Ubn2	2900060J04Rik|6030408G03Rik|BC060116|D130059P03Rik|mKIAA2030	ubinuclein 2	protein-coding
mm_79956.1	chr9	66126799	66126832	+	1	NA	5' UTR (NM_026635, exon 1 of 5)	5' UTR (NM_026635, exon 1 of 5)	204	NM_026635	68250	Mm.27107	NM_026635	ENSMUSG00000032381	Fam96a	5730536A07Rik	family with sequence similarity 96, member A	protein-coding
mm_22706.1	chr3	19187303	19187316	+	1	NA	promoter-TSS (NM_001253391)	promoter-TSS (NM_001253391)	-20	NM_001253390	67472	Mm.45125	NM_026182	ENSMUSG00000027601	Mtfr1	1300002C08Rik|1700080D04Rik|2810026O10Rik|4930579E05Rik|Chppr|Fam54a2	mitochondrial fission regulator 1	protein-coding
mm_7645.1	chr1	128281017	128281020	-	1	NA	Intergenic	Intergenic	36837	NM_026390	67812	Mm.293321	NM_026390	ENSMUSG00000026353	Ubxn4	1300013G12Rik|Ubxd2|mKIAA0242	UBX domain protein 4	protein-coding
mm_127973.1	chr15	12137924	12137937	-	1	NA	exon (NM_011767, exon 4 of 20)	exon (NM_011767, exon 4 of 20)	20079	NM_011767	22763	Mm.273496	NM_011767	ENSMUSG00000022201	Zfr	C920030H05Rik	zinc finger RNA binding protein	protein-coding
mm_6669.1	chr1	80340385	80340395	-	1	NA	5' UTR (NM_016716, exon 1 of 16)	5' UTR (NM_016716, exon 1 of 16)	300	NM_001313728	26554	Mm.12665	NM_016716	ENSMUSG00000004364	Cul3	KIAA0617	cullin 3	protein-coding
mm_21485.1	chr2	163087771	163087779	-	1	NA	5' UTR (NM_026630, exon 2 of 2)	5' UTR (NM_026630, exon 2 of 2)	1826	NM_026630	68236	Mm.33648	NM_026630	ENSMUSG00000070708	Gtsf1l	2410116G06Rik	gametocyte specific factor 1-like	protein-coding
mm_82189.1	chr9	123938267	123938276	+	1	NA	Intergenic	Intergenic	30421	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_123294.1	chr14	61556882	61556890	-	1	NA	promoter-TSS (NM_001310603)	promoter-TSS (NM_001310603)	0	NM_025697	66674	Mm.282706	NM_025697	ENSMUSG00000021930	Spryd7	6330409N04Rik|Clld6	SPRY domain containing 7	protein-coding
mm_171867.1	chr5	24581872	24581893	-	1	NA	Intergenic	Intergenic	-4415	NM_001190443	27407	Mm.21629	NM_013853	ENSMUSG00000028953	Abcf2	0710005O05Rik|Drr3|E430001O06	ATP-binding cassette, sub-family F (GCN20), member 2	protein-coding
mm_31251.1	chr4	44981479	44981485	+	1	NA	promoter-TSS (NM_001312880)	promoter-TSS (NM_001312880)	88	NM_001312880	76238	Mm.196574	NM_080289	ENSMUSG00000035637	Grhpr	1110059D05Rik|6430629L09Rik|Glxr	glyoxylate reductase/hydroxypyruvate reductase	protein-coding
mm_115793.1	chr13	19338782	19338795	-	1	NA	Intergenic	L1M2|LINE|L1	57025	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_73553.1	chr8	108958872	108958890	+	1	NA	3' UTR (NM_007496, exon 10 of 10)	3' UTR (NM_007496, exon 10 of 10)	22021	NR_037295	100526511		NR_037295	ENSMUSG00000093241	Mir3108	mir-3108|mmu-mir-3108	microRNA 3108	ncRNA
mm_142343.1	chr17	43592427	43592445	-	1	NA	promoter-TSS (NR_045445)	promoter-TSS (NR_045445)	-927	NR_045444	73504	Mm.9277	NR_045444	ENSMUSG00000090307	1700071M16Rik	-	RIKEN cDNA 1700071M16 gene	ncRNA
mm_70369.1	chr8	9977712	9977725	+	1	NA	promoter-TSS (NM_026868)	promoter-TSS (NM_026868)	1	NM_026868	68904	Mm.142570	NM_026868	ENSMUSG00000040396	Abhd13	1110065L07Rik|AI463703|AI788994	abhydrolase domain containing 13	protein-coding
mm_26243.1	chr3	141465593	141465611	+	1	NA	promoter-TSS (NM_009472)	promoter-TSS (NM_009472)	38	NM_001293561	22253	Mm.24430	NM_009472	ENSMUSG00000059921	Unc5c	B130051O18Rik|Unc5h3|rcm	unc-5 netrin receptor C	protein-coding
mm_108989.1	chr12	102758013	102758024	+	1	NA	promoter-TSS (NM_001142939)	promoter-TSS (NM_001142939)	43	NM_025666	66622	Mm.34261	NM_025666	ENSMUSG00000041712	Ubr7	5730410I19Rik|AA589405|AW557761	ubiquitin protein ligase E3 component n-recognin 7 (putative)	protein-coding
mm_167465.1	chr8	124614560	124614581	+	1	NA	exon (NM_023709, exon 17 of 20)	exon (NM_023709, exon 17 of 20)	38459	NM_023709	73647	Mm.6209	NM_023709	ENSMUSG00000031981	Capn9	2200003B16Rik|GC36|nCL-4|nCL4	calpain 9	protein-coding
mm_38254.1	chr4	136738171	136738174	-	1	NA	intron (NM_001290753, intron 3 of 15)	intron (NM_001290753, intron 3 of 15)	97840	NM_001290753	13844	Mm.250981	NM_010142	ENSMUSG00000028664	Ephb2	Cek5|Drt|ETECK|Erk|Hek5|Nuk|Prkm5|Qek5|Sek3|Tyro5	Eph receptor B2	protein-coding
mm_11253.1	chr2	29893055	29893073	+	1	NA	exon (NM_001113213, exon 3 of 21)	exon (NM_001113213, exon 3 of 21)	3001	NM_013615	18286	Mm.330116	NM_013615	ENSMUSG00000026790	Odf2	AI848335|MMTEST29	outer dense fiber of sperm tails 2	protein-coding
mm_31429.1	chr4	48085523	48085533	+	1	NA	3' UTR (NM_015743, exon 8 of 8)	3' UTR (NM_015743, exon 8 of 8)	34282	NM_001307989	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_121849.1	chr14	20640955	20640986	-	1	NA	Intergenic	CpG	15570	NM_021508	59011	Mm.439911	NM_021508	ENSMUSG00000068697	Myoz1	2310001N11Rik|AV090278|FATZ|Myoz	myozenin 1	protein-coding
mm_93320.1	chr10	99132287	99132303	-	1	NA	intron (NM_027740, intron 4 of 11)	intron (NM_027740, intron 4 of 11)	24160	NM_015737	14426	Mm.314	NM_015737	ENSMUSG00000090035	Galnt4	AV011803	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 4	protein-coding
mm_101135.1	chr11	12464851	12464879	-	1	NA	promoter-TSS (NM_001282993)	promoter-TSS (NM_001282993)	95	NM_172496	12808	Mm.22847	NM_172496	ENSMUSG00000020173	Cobl	-	cordon-bleu WH2 repeat	protein-coding
mm_122095.1	chr14	30716924	30716955	-	1	NA	intron (NM_001166532, intron 1 of 20)	intron (NM_001166532, intron 1 of 20)	1324	NM_001166532	54650	Mm.294662	NM_019460	ENSMUSG00000006527	Sfmbt1	4930442N21Rik|9330180L21Rik|AA536974|Sfmbt|Smr	Scm-like with four mbt domains 1	protein-coding
mm_76424.1	chr8	84977994	84978000	-	1	NA	exon (NM_008416, exon 1 of 1)	exon (NM_008416, exon 1 of 1)	751	NM_008416	16477	Mm.1167	NM_008416	ENSMUSG00000052837	Junb	-	jun B proto-oncogene	protein-coding
mm_103575.1	chr11	78073746	78073754	-	1	NA	promoter-TSS (NR_105850)	promoter-TSS (NR_105850)	-509	NR_105850	102466649		NR_105850	ENSMUSG00000104813	Mir451b	mmu-mir-451b	microRNA 451b	ncRNA
mm_53500.1	chr6	135362663	135362696	+	1	NA	promoter-TSS (NM_001288628)	promoter-TSS (NM_001288628)	-252	NM_010128	13730	Mm.182785	NM_010128	ENSMUSG00000030208	Emp1	I-8-09|TMP	epithelial membrane protein 1	protein-coding
mm_133323.1	chr16	78222603	78222634	+	1	NA	Intergenic	Intergenic	32836	NR_045698	100503619	Mm.387531	NR_045698	ENSMUSG00000109841	E330011O21Rik	-	RIKEN cDNA E330011O21 gene	ncRNA
mm_170666.1	chr2	11637144	11637155	-	1	NA	Intergenic	Intergenic	-5643	NM_008367	16184	Mm.915	NM_008367	ENSMUSG00000026770	Il2ra	CD25|Il2r|Ly-43	interleukin 2 receptor, alpha chain	protein-coding
mm_6510.1	chr1	74305608	74305621	-	1	NA	intron (NM_001039509, intron 2 of 9)	ORR1A3|LTR|ERVL-MaLR	-1278	NM_027154	69660	Mm.261182	NM_027154	ENSMUSG00000006301	Tmbim1	2310061B02Rik|AA960455|AU024746|C78899|RECS1|Tmbib1|mKIAA4161	transmembrane BAX inhibitor motif containing 1	protein-coding
mm_10745.1	chr2	23155510	23155530	+	1	NA	promoter-TSS (NM_013771)	promoter-TSS (NM_013771)	504	NM_025979	67121	Mm.253721	NM_025979	ENSMUSG00000026779	Mastl	2700091H24Rik|C88295|GW|GWL|MAST-L|THC2	microtubule associated serine/threonine kinase-like	protein-coding
mm_157700.1	chrX	60891703	60891719	-	1	NA	3' UTR (NM_009237, exon 1 of 1)	3' UTR (NM_009237, exon 1 of 1)	1719	NM_009237	20675	Mm.35784	NM_009237	ENSMUSG00000045179	Sox3	Sox-3	SRY (sex determining region Y)-box 3	protein-coding
mm_91361.1	chr10	28986210	28986259	-	1	NA	promoter-TSS (NM_026336)	promoter-TSS (NM_026336)	72	NM_026336	67719	Mm.440480	NM_026336	ENSMUSG00000015519	2310057J18Rik	2210414P04Rik|Leg1	RIKEN cDNA 2310057J18 gene	protein-coding
mm_83305.1	chr9	44034057	44034070	-	1	NA	Intergenic	Intergenic	-9321	NM_009382	21838	Mm.3951	NM_009382	ENSMUSG00000032011	Thy1	CD90|T25|Thy-1|Thy-1.2|Thy1.1|Thy1.2	thymus cell antigen 1, theta	protein-coding
mm_7001.1	chr1	86438046	86438057	-	1	NA	Intergenic	Intergenic	11722	NM_027966	71863	Mm.179627	NM_027966	ENSMUSG00000036574	1700019O17Rik	-	RIKEN cDNA 1700019O17 gene	protein-coding
mm_138999.1	chr17	45556260	45556270	+	1	NA	exon (NM_008690, exon 1 of 6)	exon (NM_008690, exon 1 of 6)	565	NM_001304956	18037	Mm.57043	NM_008690	ENSMUSG00000023947	Nfkbie	I-kappa-B-epsilon|IKBE|IkB-E|NF-kappa-BIE|ikB-epsilon	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, epsilon	protein-coding
mm_39200.1	chr4	156026207	156026225	-	1	NA	promoter-TSS (NM_009400)	promoter-TSS (NM_009400)	-126	NM_009400	21936	Mm.3180	NM_009400	ENSMUSG00000041954	Tnfrsf18	AITR|Gitr	tumor necrosis factor receptor superfamily, member 18	protein-coding
mm_172809.1	chr9	12368048	12368048	-	1	NA	Intergenic	L1Md_A|LINE|L1	737807	NR_040755	78219	Mm.414868	NR_040755	ENSMUSG00000111830	4930568E12Rik	-	RIKEN cDNA 4930568E12 gene	ncRNA
mm_122612.1	chr14	51057675	51057689	-	1	NA	promoter-TSS (NM_001011875)	promoter-TSS (NM_001011875)	-440	NM_001011875	497106	Mm.379740	NM_001011875	ENSMUSG00000068407	Rnase12	Rai1	ribonuclease, RNase A family, 12 (non-active)	protein-coding
mm_126853.1	chr15	89211523	89211606	+	1	NA	promoter-TSS (NM_026813)	promoter-TSS (NM_026813)	5	NM_027805	71474	Mm.184055	NM_026813	ENSMUSG00000036561	Ppp6r2	1110033O10Rik|8430411H09Rik|B230107H12Rik|Pp6r2|Saps2	protein phosphatase 6, regulatory subunit 2	protein-coding
mm_143510.1	chr17	72604634	72604645	-	1	NA	promoter-TSS (NM_007439)	promoter-TSS (NM_007439)	-332	NM_007439	11682	Mm.311854	NM_007439	ENSMUSG00000055471	Alk	CD246|Tcrz	anaplastic lymphoma kinase	protein-coding
mm_95658.1	chr11	53770807	53770823	+	1	NA	intron (NM_001159396, intron 1 of 9)	intron (NM_001159396, intron 1 of 9)	342	NM_001159396	16362	Mm.105218	NM_008390	ENSMUSG00000018899	Irf1	AU020929|Irf-1	interferon regulatory factor 1	protein-coding
mm_35002.1	chr4	156215893	156215903	+	1	NA	promoter-TSS (NM_172417)	promoter-TSS (NM_172417)	-29	NM_172417	74183	Mm.431343	NM_172417	ENSMUSG00000078486	Perm1	2310042D19Rik	PPARGC1 and ESRR induced regulator, muscle 1	protein-coding
mm_43469.1	chr5	136693658	136693662	+	1	NA	promoter-TSS (NM_001303021)	promoter-TSS (NM_001303021)	-16	NM_001303021	59310	Mm.5178	NM_021611	ENSMUSG00000005474	Myl10	1700027I08Rik|Mylc2pl|PLRLC	myosin, light chain 10, regulatory	protein-coding
mm_119984.1	chr14	55578162	55578180	+	1	NA	promoter-TSS (NM_011189)	promoter-TSS (NM_011189)	-323	NM_011189	19186	Mm.830	NM_011189	ENSMUSG00000022216	Psme1	AW413925|PA28a	proteasome (prosome, macropain) activator subunit 1 (PA28 alpha)	protein-coding
mm_143610.1	chr17	78736511	78736524	-	1	NA	promoter-TSS (NM_011500)	promoter-TSS (NM_011500)	43	NM_011500	268980	Mm.311915	NM_011500	ENSMUSG00000024077	Strn	AU022939|D130055P19	striatin, calmodulin binding protein	protein-coding
mm_121832.1	chr14	20496781	20496787	-	1	NA	5' UTR (NM_029104, exon 1 of 7)	5' UTR (NM_029104, exon 1 of 7)	117	NM_029104	74843	Mm.295241	NM_029104	ENSMUSG00000021815	Mss51	4833444M15Rik|Zmynd17	MSS51 mitochondrial translational activator	protein-coding
mm_27516.1	chr3	56183709	56183757	-	1	NA	promoter-TSS (NM_030595)	promoter-TSS (NM_030595)	-32	NM_030595	26422	Mm.384353	NM_030595	ENSMUSG00000027799	Nbea	Lyst2|mKIAA1544	neurobeachin	protein-coding
mm_95390.1	chr11	49250098	49250115	+	1	NA	promoter-TSS (NM_001110150)	promoter-TSS (NM_001110150)	-446	NM_001110150	17308	Mm.196933	NM_010794	ENSMUSG00000020346	Mgat1	Mgat-1	mannoside acetylglucosaminyltransferase 1	protein-coding
mm_83978.1	chr9	57262762	57262797	-	1	NA	promoter-TSS (NM_028820)	promoter-TSS (NM_028820)	-180	NM_028820	74211	Mm.428905	NM_028820	ENSMUSG00000032300	1700017B05Rik	AA682102|D9Ertd278e	RIKEN cDNA 1700017B05 gene	protein-coding
mm_149469.1	chr19	11601826	11601865	+	1	NA	exon (NM_026835, exon 3 of 7)	exon (NM_026835, exon 3 of 7)	2959	NM_026835	68774	Mm.290390	NM_026835	ENSMUSG00000024679	Ms4a6d	1110058E16Rik|AI447446|Ms4a11	membrane-spanning 4-domains, subfamily A, member 6D	protein-coding
mm_38472.1	chr4	140661297	140661306	-	1	NA	intron (NM_001290803, intron 1 of 28)	intron (NM_001290803, intron 1 of 28)	4586	NM_001290803	72754	Mm.29329	NM_172415	ENSMUSG00000040964	Arhgef10l	2810441C07Rik	Rho guanine nucleotide exchange factor (GEF) 10-like	protein-coding
mm_52305.1	chr6	108828509	108828517	+	1	NA	promoter-TSS (NM_138677)	promoter-TSS (NM_138677)	-128	NM_138677	192193	Mm.21596	NM_138677	ENSMUSG00000030104	Edem1	A130059K23Rik|EDEM|mKIAA0212	ER degradation enhancer, mannosidase alpha-like 1	protein-coding
mm_136473.1	chr16	95750384	95750398	-	1	NA	Intergenic	Intergenic	47984	NM_011809	23872	Mm.290207	NM_011809	ENSMUSG00000022895	Ets2	AU022856|Ets-2	E26 avian leukemia oncogene 2, 3' domain	protein-coding
mm_115018.1	chr13	98356236	98356238	+	1	NA	3' UTR (NM_008242, exon 1 of 1)	3' UTR (NM_008242, exon 1 of 1)	1992	NM_008242	15229	Mm.347441	NM_008242	ENSMUSG00000078302	Foxd1	AI385632|BF-2|FREAC4|Hfh10|Hfhbf2	forkhead box D1	protein-coding
mm_84056.1	chr9	58159154	58159179	-	1	NA	promoter-TSS (NM_012043)	promoter-TSS (NM_012043)	55	NM_012043	26968	Mm.367887	NM_012043	ENSMUSG00000037206	Islr	AW553146|Meflin	immunoglobulin superfamily containing leucine-rich repeat	protein-coding
mm_153189.1	chr19	34509054	34509107	-	1	NA	exon (NM_021460, exon 5 of 10)	exon (NM_021460, exon 5 of 10)	18394	NM_001111100	16889	Mm.157545	NM_021460	ENSMUSG00000024781	Lipa	AA960673|Lal|Lip-1|Lip1	lysosomal acid lipase A	protein-coding
mm_10591.1	chr2	18672418	18672482	+	1	NA	promoter-TSS (NM_147778)	promoter-TSS (NM_147778)	-12	NM_147778	12238	Mm.249586	NM_147778	ENSMUSG00000051154	Commd3	AW550818|Bup|D2Ertd542e	COMM domain containing 3	protein-coding
mm_85650.1	chr9	107657872	107657886	-	1	NA	exon (NM_001199218, exon 6 of 16)	exon (NM_001199218, exon 6 of 16)	9520	NM_023805	76257	Mm.296560	NM_023805	ENSMUSG00000010064	Slc38a3	0610012J02Rik|D9Ucla2|Nat1|Slc38-3|Sn1|Snat3|mNAT	solute carrier family 38, member 3	protein-coding
mm_125564.1	chr15	58936422	58936432	+	1	NA	exon (NM_023172, exon 2 of 4)	exon (NM_023172, exon 2 of 4)	2617	NM_023172	66218	Mm.322294	NM_023172	ENSMUSG00000022354	Ndufb9	1190008J14Rik	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 9	protein-coding
mm_103585.1	chr11	78183552	78183574	-	1	NA	promoter-TSS (NR_037683)	promoter-TSS (NR_037683)	21	NM_207523	268449	Mm.22723	NM_207523	ENSMUSG00000058546	Rpl23a	BC029892|MDA20	ribosomal protein L23A	protein-coding
mm_82023.1	chr9	121777685	121777701	+	1	NA	promoter-TSS (NM_028202)	promoter-TSS (NM_028202)	86	NM_028202	72330	Mm.45734	NM_028202	ENSMUSG00000074001	Klhl40	2310024D23Rik|Kbtbd5	kelch-like 40	protein-coding
mm_37067.1	chr4	116123619	116123695	-	1	NA	promoter-TSS (NM_001122958)	promoter-TSS (NM_001122958)	32	NM_009015	19366	Mm.3655	NM_009015	ENSMUSG00000028702	Rad54l	RAD54	RAD54 like (S. cerevisiae)	protein-coding
mm_60202.1	chr7	43427665	43427679	+	1	NA	Intergenic	Intergenic	-2429	NM_177693	233187	Mm.267027	NM_177693	ENSMUSG00000004613	Lim2	19kDa|4833403J20|MP19|To3	lens intrinsic membrane protein 2	protein-coding
mm_16525.1	chr2	181520583	181520593	+	1	NA	non-coding (NR_073369, exon 1 of 6)	non-coding (NR_073369, exon 1 of 6)	103	NM_001271584	13002	Mm.140761	NM_016775	ENSMUSG00000000826	Dnajc5	2610314I24Rik|AU018536|Csp	DnaJ heat shock protein family (Hsp40) member C5	protein-coding
mm_70773.1	chr8	22186065	22186076	+	1	NA	promoter-TSS (NM_001004140)	promoter-TSS (NM_001004140)	-251	NM_001004140	80986	Mm.22448	NM_001004140	ENSMUSG00000037725	Ckap2	AI461656|AW228814|LB1	cytoskeleton associated protein 2	protein-coding
mm_29642.1	chr3	121838109	121838116	-	1	NA	Intergenic	RMER1C|Other|Other	-22897	NM_008991	19299	Mm.399042	NM_008991	ENSMUSG00000028127	Abcd3	AI313901|AU018866|AW146054|PMP68|PMP70|Pxmp1	ATP-binding cassette, sub-family D (ALD), member 3	protein-coding
mm_66571.1	chr7	45322841	45322870	-	1	NA	intron (NM_175130, intron 6 of 24)	B4|SINE|B4	-2103	NR_110499	100040970	Mm.289810	NR_110499	ENSMUSG00000046721	Rpl14-ps1	ENSMUSG00000046721|Gm9811	ribosomal protein L14, pseudogene 1	pseudo
mm_42017.1	chr5	108268898	108268924	+	1	NA	promoter-TSS (NM_026106)	promoter-TSS (NM_026106)	14	NM_026106	13486	Mm.303534	NM_026106	ENSMUSG00000029265	Dr1	1700121L09Rik|Dr1l|NC2|NC2beta	down-regulator of transcription 1	protein-coding
mm_63717.1	chr7	130774133	130774185	+	1	NA	promoter-TSS (NM_001081038)	promoter-TSS (NM_001081038)	90	NM_001081038	330660	Mm.271550	NM_001081038	ENSMUSG00000040298	Btbd16	E330040A16Rik	BTB (POZ) domain containing 16	protein-coding
mm_110676.1	chr12	66284395	66284412	-	1	NA	promoter-TSS (NM_001162933)	promoter-TSS (NM_001162933)	-2	NM_001162933	238217	Mm.188575	NM_001162933	ENSMUSG00000060499	Rpl10l	EG238217	ribosomal protein L10-like	protein-coding
mm_6387.1	chr1	72849244	72849266	-	1	NA	exon (NM_008342, exon 2 of 4)	exon (NM_008342, exon 2 of 4)	23868	NM_001310659	16008	Mm.141936	NM_008342	ENSMUSG00000039323	Igfbp2	AI255832|IBP-2|Igfbp-2|mIGFBP-2	insulin-like growth factor binding protein 2	protein-coding
mm_108052.1	chr12	73913110	73913120	+	1	NA	intron (NM_010431, intron 1 of 14)	intron (NM_010431, intron 1 of 14)	5248	NM_001313919	15251	Mm.3879	NM_010431	ENSMUSG00000021109	Hif1a	AA959795|HIF-1-alpha|HIF1-alpha|HIF1alpha|MOP1|bHLHe78	hypoxia inducible factor 1, alpha subunit	protein-coding
mm_77464.1	chr8	122424980	122424998	-	1	NA	exon (NM_007806, exon 6 of 6)	exon (NM_007806, exon 6 of 6)	2904	NM_145834	234836	Mm.222808	NM_145834	ENSMUSG00000046108	Il17c	IL-17C	interleukin 17C	protein-coding
mm_161894.1	chr18	42394433	42394433	+	1	NA	promoter-TSS (NM_138945)	promoter-TSS (NM_138945)	-164	NM_138945	18998	Mm.488204	NM_138945	ENSMUSG00000024497	Pou4f3	Brn3.1|Brn3c|ddl|dreidel	POU domain, class 4, transcription factor 3	protein-coding
mm_60395.1	chr7	44475268	44475268	+	1	NA	Intergenic	Intergenic	4921	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_120558.1	chr14	68120324	68120407	+	1	NA	exon (NM_008691, exon 3 of 3)	exon (NM_008691, exon 3 of 3)	-3387	NR_045897	100043072	Mm.242832	NR_045897		A230070E04Rik	Gm4210	RIKEN cDNA A230070E04 gene	ncRNA
mm_32229.1	chr4	102224891	102224895	+	1	NA	Intergenic	Intergenic	-29849	NM_001177983	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_166186.1	chr5	32492282	32492296	+	1	NA	3' UTR (NM_172707, exon 8 of 8)	3' UTR (NM_172707, exon 8 of 8)	33319	NM_172707	19046	Mm.241931	NM_172707	ENSMUSG00000014956	Ppp1cb	1200010B19	protein phosphatase 1, catalytic subunit, beta isoform	protein-coding
mm_86246.1	chr9	121314127	121314140	-	1	NA	Intergenic	Intergenic	-36961	NM_177589	209012	Mm.371804	NM_177589	ENSMUSG00000040936	Ulk4	4932415A06Rik|A730098P15	unc-51-like kinase 4	protein-coding
mm_43606.1	chr5	137887995	137888013	+	1	NA	Intergenic	Intergenic	-16246	NM_001024932	545812	Mm.332769	NM_001024932	ENSMUSG00000066682	Pilrb2	EG545812	paired immunoglobin-like type 2 receptor beta 2	protein-coding
mm_5887.1	chr1	54155321	54155325	-	1	NA	intron (NM_001001883, intron 1 of 28)	intron (NM_001001883, intron 1 of 28)	39711	NM_001001883	329152	Mm.132150	NM_172655	ENSMUSG00000042807	Hecw2	A730039N16Rik|D030049F17Rik|Gm971|Nedl2|mKIAA1301	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2	protein-coding
mm_161572.1	chr16	22161524	22161524	-	1	NA	intron (NM_183029, intron 1 of 15)	CpG	1775	NM_183029	319765	Mm.489442	NM_183029	ENSMUSG00000033581	Igf2bp2	C330012H03Rik|IMP-2|Imp2|Neilsen	insulin-like growth factor 2 mRNA binding protein 2	protein-coding
mm_61867.1	chr7	89404357	89404367	+	1	NA	promoter-TSS (NM_008055)	promoter-TSS (NM_008055)	-4	NM_008055	14366	Mm.86755	NM_008055	ENSMUSG00000049791	Fzd4	Fz4	frizzled class receptor 4	protein-coding
mm_167531.1	chr9	21291250	21291263	-	1	NA	promoter-TSS (NM_009878)	promoter-TSS (NM_009878)	-47	NM_009878	12581	Mm.29020	NM_009878	ENSMUSG00000096472	Cdkn2d	INK4d|p19|p19INK4d	cyclin-dependent kinase inhibitor 2D (p19, inhibits CDK4)	protein-coding
mm_2668.1	chr1	127205198	127205294	+	1	NA	5' UTR (NM_145128, exon 1 of 18)	5' UTR (NM_145128, exon 1 of 18)	260	NM_145128	107895	Mm.214682	NM_145128	ENSMUSG00000036155	Mgat5	4930471A21Rik|5330407H02Rik|AI480971|GlcNAc-TV	mannoside acetylglucosaminyltransferase 5	protein-coding
mm_37421.1	chr4	122885748	122885753	-	1	NA	intron (NM_007598, intron 1 of 12)	intron (NM_007598, intron 1 of 12)	307	NM_007598	12331	Mm.8687	NM_007598	ENSMUSG00000028656	Cap1	-	CAP, adenylate cyclase-associated protein 1 (yeast)	protein-coding
mm_45491.1	chr5	71657914	71657953	-	1	NA	5' UTR (NM_010251, exon 1 of 9)	5' UTR (NM_010251, exon 1 of 9)	375	NM_010251	14397	Mm.248731	NM_010251	ENSMUSG00000029211	Gabra4	Gabra-4	gamma-aminobutyric acid (GABA) A receptor, subunit alpha 4	protein-coding
mm_49875.1	chr6	38585811	38585819	+	1	NA	intron (NM_001331223, intron 7 of 12)	B2_Mm1t|SINE|B2	30092	NM_001331223	192196	Mm.276133	NM_138680	ENSMUSG00000029823	Luc7l2	4930471C18Rik|AA522013|AU015269|CGI59|Cgi74	LUC7-like 2 (S. cerevisiae)	protein-coding
mm_6063.1	chr1	60566811	60566836	-	1	NA	promoter-TSS (NM_001045513)	promoter-TSS (NM_001045513)	-58	NM_001045513	77300	Mm.440325	NM_001045513	ENSMUSG00000026014	Raph1	9430025M21Rik|C730009O10Rik|Lpd	Ras association (RalGDS/AF-6) and pleckstrin homology domains 1	protein-coding
mm_157276.1	chrX	20581335	20581371	-	1	NA	Intergenic	Intergenic	31535	NM_009060	19733	Mm.2118	NM_009060	ENSMUSG00000023070	Rgn	AI265316|GNL|SMP30	regucalcin	protein-coding
mm_78284.1	chr9	22156839	22156881	+	1	NA	promoter-TSS (NM_001082532)	promoter-TSS (NM_001082532)	14	NM_001082532	66268	Mm.28924	NM_025457	ENSMUSG00000010607	Pigyl	1810008A14Rik|PIG-Y|Pigy	phosphatidylinositol glycan anchor biosynthesis, class Y-like	protein-coding
mm_140686.1	chr17	13345801	13345802	-	1	NA	Intergenic	Intergenic	-8771	NM_001167578	100041352	Mm.490251	NM_001167578	ENSMUSG00000052469	Tcp10c	D17Leh66C|D17Leh66ca|Gm9880|T66C-a|Tcp-10c	t-complex protein 10c	protein-coding
mm_59901.1	chr7	30308773	30308818	+	1	NA	promoter-TSS (NM_198027)	promoter-TSS (NM_198027)	42	NM_198027	233065	Mm.276277	NM_198027	ENSMUSG00000042831	Alkbh6	AI839550|Abh6|C130099A02	alkB homolog 6	protein-coding
mm_73191.1	chr8	95370117	95370128	+	1	NA	intron (NM_008609, intron 6 of 9)	intron (NM_008609, intron 6 of 9)	17826	NM_008609	17388	Mm.217116	NM_008609	ENSMUSG00000031790	Mmp15	AI503551|MT-MMP 2|MT2-MMP	matrix metallopeptidase 15	protein-coding
mm_164043.1	chr14	92875420	92875420	+	1	NA	Intergenic	Intergenic	1013468	NM_001271800	211712	Mm.37126	NM_001081377	ENSMUSG00000055421	Pcdh9	-	protocadherin 9	protein-coding
mm_44452.1	chr5	21773818	21773831	-	1	NA	exon (NM_009584, exon 6 of 17)	exon (NM_009584, exon 6 of 17)	11341	NM_009584	22791	Mm.266312	NM_009584	ENSMUSG00000029014	Dnajc2	AU020218|MIDA1|Zrf1|Zrf2	DnaJ heat shock protein family (Hsp40) member C2	protein-coding
mm_59661.1	chr7	28267810	28267932	+	1	NA	promoter-TSS (NM_198425)	promoter-TSS (NM_198425)	-10	NM_198425	386655	Mm.258201	NM_198425	ENSMUSG00000046058	Eid2	Cri2|EID-2	EP300 interacting inhibitor of differentiation 2	protein-coding
mm_31349.1	chr4	46650272	46650317	+	1	NA	promoter-TSS (NM_198664)	promoter-TSS (NM_198664)	-95	NM_198664	381605	Mm.331595	NM_198664	ENSMUSG00000039813	Tbc1d2	A630005A06Rik|BC022630|Gm1037|PARIS-1|PARIS1	TBC1 domain family, member 2	protein-coding
mm_53786.1	chr6	146585682	146585720	+	1	NA	exon (NM_026218, exon 2 of 7)	exon (NM_026218, exon 2 of 7)	7790	NM_026218	67529	Mm.333499	NM_026218	ENSMUSG00000040242	Fgfr1op2	1500031J01Rik	FGFR1 oncogene partner 2	protein-coding
mm_106121.1	chr11	116359461	116359478	-	1	NA	intron (NM_027258, intron 5 of 18)	intron (NM_027258, intron 5 of 18)	-24115	NM_008240	15223	Mm.378938	NM_008240	ENSMUSG00000034227	Foxj1	FKHL-13|HFH-4|Hfh4	forkhead box J1	protein-coding
mm_171316.1	chr3	95929257	95929257	+	1	NA	promoter-TSS (NM_001253757)	promoter-TSS (NM_001253757)	0	NM_001253758	66471	Mm.218657	NM_023210	ENSMUSG00000015749	Anp32e	2810018A15Rik|AI047746|AI326868|CPD1|LANP-L|LANPL|mLANP-L	acidic (leucine-rich) nuclear phosphoprotein 32 family, member E	protein-coding
mm_38248.1	chr4	136602777	136602798	-	1	NA	promoter-TSS (NM_133872)	promoter-TSS (NM_133872)	-64	NM_001347221	99982	Mm.28540	NM_133872	ENSMUSG00000036940	Kdm1a	1810043O07Rik|AA408884|Aof2|D4Ertd478e|Kdm1|Lsd1|mKIAA0601	lysine (K)-specific demethylase 1A	protein-coding
mm_109554.1	chr12	111737681	111737683	+	1	NA	intron (NM_001163388, intron 4 of 5)	B1_Mur3|SINE|Alu	-21167	NM_008450	16593	Mm.278357	NM_008450	ENSMUSG00000021288	Klc1	AI874768|Kns2	kinesin light chain 1	protein-coding
mm_97495.1	chr11	78343531	78343541	+	1	NA	promoter-TSS (NM_011676)	promoter-TSS (NM_011676)	41	NM_011676	22248	Mm.284811	NM_011676	ENSMUSG00000002058	Unc119	D11Bhm52|HRG4|MRG4|Rg4|Rtg4|Unc119h	unc-119 lipid binding chaperone	protein-coding
mm_145182.1	chr18	48045355	48045355	+	1	NA	promoter-TSS (NM_001025388)	promoter-TSS (NM_001025388)	20	NM_001025388	433182	Mm.70666	NM_001025388	ENSMUSG00000059040	Eno1b	EG433182|Eno1|Gm5506	enolase 1B, retrotransposed	protein-coding
mm_25286.1	chr3	105704689	105704697	+	1	NA	promoter-TSS (NM_001163356)	promoter-TSS (NM_001163356)	94	NM_175398	109050	Mm.212591	NM_175398	ENSMUSG00000048458	Fam212b	6530418L21Rik|inka2	family with sequence similarity 212, member B	protein-coding
mm_92583.1	chr10	80031461	80031470	-	1	NA	TTS (NM_027521)	TTS (NM_027521)	8194	NM_025554	66420	Mm.18579	NM_025554	ENSMUSG00000004667	Polr2e	2410021N14Rik|25kDa|AW208866|RPB5|XAP4	polymerase (RNA) II (DNA directed) polypeptide E	protein-coding
mm_56617.1	chr6	112693594	112693604	-	1	NA	intron (NM_001167730, intron 1 of 13)	intron (NM_001167730, intron 1 of 13)	3071	NM_021385	58186	Mm.103812	NM_021385	ENSMUSG00000030254	Rad18	2810024C04Rik|Rad18sc	RAD18 E3 ubiquitin protein ligase	protein-coding
mm_103228.1	chr11	70670040	70670079	-	1	NA	promoter-TSS (NM_001167669)	promoter-TSS (NM_001167669)	-643	NM_001167669	216873	Mm.432524	NM_172561	ENSMUSG00000018287	Spag7	5730443G10|ACRP|FSA-1|Fsa1l	sperm associated antigen 7	protein-coding
mm_78024.1	chr9	13765930	13765944	+	1	NA	intron (NR_024025, intron 1 of 15)	intron (NR_024025, intron 1 of 15)	16756	NR_024025	77116	Mm.210405	NM_023858	ENSMUSG00000031918	Mtmr2	6030445P13Rik	myotubularin related protein 2	protein-coding
mm_36769.1	chr4	102569097	102569103	-	1	NA	promoter-TSS (NM_001177980)	promoter-TSS (NM_001177980)	-960	NM_001177980	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_18869.1	chr2	75938408	75938453	-	1	NA	promoter-TSS (NM_028235)	promoter-TSS (NM_028235)	32	NM_028235	72421	Mm.275109	NM_028235	ENSMUSG00000075273	Ttc30b	2510042P03Rik|Tcc30b	tetratricopeptide repeat domain 30B	protein-coding
mm_48004.1	chr5	136161382	136161392	-	1	NA	intron (NM_178751, intron 2 of 2)	intron (NM_178751, intron 2 of 2)	9269	NM_178751	269717	Mm.308396	NM_178751	ENSMUSG00000039747	Orai2	A730041O15Rik|Tmem142b	ORAI calcium release-activated calcium modulator 2	protein-coding
mm_24318.1	chr3	89430396	89430500	+	1	NA	promoter-TSS (NM_026869)	promoter-TSS (NM_026869)	234	NM_001293763	68911	Mm.22521	NM_026869	ENSMUSG00000047824	Pygo2	1190004M21Rik	pygopus 2	protein-coding
mm_54188.1	chr6	24168084	24168097	-	1	NA	promoter-TSS (NM_019481)	promoter-TSS (NM_019481)	2	NM_019481	55961	Mm.19299	NM_019481	ENSMUSG00000029700	Slc13a1	AI314066|AI987826|NaSi-1|Nas1	solute carrier family 13 (sodium/sulfate symporters), member 1	protein-coding
mm_91151.1	chr10	20365498	20365499	-	1	NA	Intergenic	Intergenic	17679	NM_027930	71804	Mm.262151	NM_027930	ENSMUSG00000019992	Mtfr2	2610016C23Rik|4933412C16Rik|Dufd1|Fam54a	mitochondrial fission regulator 2	protein-coding
mm_108692.1	chr12	86895319	86895339	+	1	NA	Intergenic	Intergenic	-10515	NM_145836	238330	Mm.248358	NM_145836	ENSMUSG00000034168	Irf2bpl	6430527G18Rik|Eap1	interferon regulatory factor 2 binding protein-like	protein-coding
mm_134503.1	chr16	19063239	19063249	-	1	NA	Intergenic	Intergenic	186494	NM_010435	15260	Mm.15694	NM_010435	ENSMUSG00000022702	Hira	AA138857|D16Ertd95e|Gm15797|N28177|OTTMUSG00000026264|Tuple1	histone cell cycle regulator	protein-coding
mm_42265.1	chr5	114131185	114131220	+	1	NA	promoter-TSS (NM_011677)	promoter-TSS (NM_011677)	46	NM_011677	22256	Mm.1393	NM_011677	ENSMUSG00000029591	Ung	UNG1|UNG2	uracil DNA glycosylase	protein-coding
mm_153649.1	chr19	44294955	44294972	-	1	NA	exon (NM_009128, exon 2 of 6)	exon (NM_009128, exon 2 of 6)	1287	NM_009128	20250	Mm.487021	NM_009128	ENSMUSG00000025203	Scd2	Mir5114|Scd-2|mir-5114|swty	stearoyl-Coenzyme A desaturase 2	protein-coding
mm_3634.1	chr1	152807919	152807934	+	1	NA	5' UTR (NM_010877, exon 2 of 16)	5' UTR (NM_010877, exon 2 of 16)	7773	NM_010877	17970	Mm.270307	NM_010877	ENSMUSG00000026480	Ncf2	NOXA2|Ncf-2|p67phox	neutrophil cytosolic factor 2	protein-coding
mm_633.1	chr1	40356254	40356273	+	1	NA	intron (NM_133193, intron 8 of 10)	intron (NM_133193, intron 8 of 10)	31636	NM_133193	107527	Mm.155583	NM_133193	ENSMUSG00000070942	Il1rl2	AI481289|AW551444|IL-1Rrp2	interleukin 1 receptor-like 2	protein-coding
mm_113644.1	chr13	42301425	42301435	+	1	NA	promoter-TSS (NM_010104)	promoter-TSS (NM_010104)	-46	NM_010104	13614	Mm.14543	NM_010104	ENSMUSG00000021367	Edn1	ET-1|PPET1|preproET	endothelin 1	protein-coding
mm_159816.1	chr5	120907485	120907485	-	1	NA	promoter-TSS (NM_145211)	promoter-TSS (NM_145211)	40	NM_145211	246730	Mm.14301	NM_145211	ENSMUSG00000052776	Oas1a	L3	2'-5' oligoadenylate synthetase 1A	protein-coding
mm_130095.1	chr15	89425327	89425357	-	1	NA	non-coding (NR_004843, exon 11 of 27)	non-coding (NR_004843, exon 11 of 27)	520	NM_009948	12895	Mm.227738	NM_009948	ENSMUSG00000078937	Cpt1b	Cpt1|Cpt1-m|Cpti|Cpti-m|M-cpti	carnitine palmitoyltransferase 1b, muscle	protein-coding
mm_61566.1	chr7	79691880	79691887	+	1	NA	exon (NM_029835, exon 19 of 22)	exon (NM_029835, exon 19 of 22)	22303	NM_010626	16576	Mm.101633	NM_010626	ENSMUSG00000050382	Kif7	-	kinesin family member 7	protein-coding
mm_129800.1	chr15	82899780	82899823	-	1	NA	intron (NR_045068, intron 1 of 3)	CpG	721	NR_045068	100504637	Mm.440928	NR_045068	ENSMUSG00000100199	Gm20324	-	predicted gene, 20324	ncRNA
mm_52738.1	chr6	120441082	120441092	+	1	NA	3' UTR (NM_145997, exon 28 of 28)	3' UTR (NM_145997, exon 28 of 28)	-22110	NM_008359	16172	Mm.4481	NM_008359	ENSMUSG00000002897	Il17ra	AW538159|Cdw217|Il17r|VDw217	interleukin 17 receptor A	protein-coding
mm_49543.1	chr6	30359473	30359475	+	1	NA	Intergenic	Intergenic	31536	NM_172735	232679	Mm.29780	NM_172735	ENSMUSG00000039130	Zc3hc1	1110054L24Rik|AU018540|AU019789|HSPC216|Nipa	zinc finger, C3HC type 1	protein-coding
mm_154639.1	chrX	7764311	7764321	+	1	NA	intron (NM_001271491, intron 1 of 8)	intron (NM_001271491, intron 1 of 8)	275	NM_001271491	209446	Mm.249142	NM_172472	ENSMUSG00000000134	Tfe3	F830016E06Rik|Tcfe3|Tfe-3|bHLHe33	transcription factor E3	protein-coding
mm_7171.1	chr1	92127891	92127903	-	1	NA	intron (NM_207225, intron 2 of 26)	intron (NM_207225, intron 2 of 26)	52444	NM_207225	208727	Mm.318567	NM_207225	ENSMUSG00000026313	Hdac4	4932408F19Rik|HD4	histone deacetylase 4	protein-coding
mm_84193.1	chr9	60522018	60522058	-	1	NA	Intergenic	CpG	-11003	NM_001040426	207596	Mm.28791	NM_172444	ENSMUSG00000032289	Thsd4	ADAMTSL-6|ADAMTSL6|AI585901|Adamtsl4|B230114P05Rik	thrombospondin, type I, domain containing 4	protein-coding
mm_167479.1	chr8	129067155	129067163	+	1	NA	promoter-TSS (NM_029292)	promoter-TSS (NM_029292)	25	NM_001168369	75453	Mm.286964	NM_029292	ENSMUSG00000056018	Ccdc7b	1700008F21Rik	coiled-coil domain containing 7B	protein-coding
mm_133435.1	chr16	87698962	87698984	+	1	NA	promoter-TSS (NM_007520)	promoter-TSS (NM_007520)	19	NM_007520	12013	Mm.26147	NM_007520	ENSMUSG00000025612	Bach1	6230421P05Rik|AI323795	BTB and CNC homology 1, basic leucine zipper transcription factor 1	protein-coding
mm_90873.1	chr10	9027226	9027255	-	1	NA	Intergenic	Intergenic	-141170	NM_175155	70097	Mm.338275	NM_175155	ENSMUSG00000015305	Sash1	1100001C18Rik|2500002E12Rik|A330076K04Rik|mKIAA0790	SAM and SH3 domain containing 1	protein-coding
mm_166251.1	chr5	81020129	81020145	+	1	NA	promoter-TSS (NM_001347367)	promoter-TSS (NM_001347367)	-434	NM_001347367	319387	Mm.273631	NM_198702	ENSMUSG00000037605	Adgrl3	5430402I23Rik|CIRL-3|D130075K09Rik|Gm1379|LEC3|Lphn3|mKIAA0768	adhesion G protein-coupled receptor L3	protein-coding
mm_123036.1	chr14	55559984	55560008	-	1	NA	promoter-TSS (NM_001199009)	promoter-TSS (NM_001199009)	-33	NR_037572	28199	Mm.11535	NM_133734	ENSMUSG00000022214	Dcaf11	0710008A13Rik|C76035|D14Ucla1|Dacf11|GLO14|Wdr23	DDB1 and CUL4 associated factor 11	protein-coding
mm_135106.1	chr16	35652267	35652270	-	1	NA	intron (NM_013661, intron 11 of 21)	intron (NM_013661, intron 11 of 21)	110906	NM_013661	20357	Mm.42015	NM_013661	ENSMUSG00000052133	Sema5b	AI893641|SemG|Semag|mKIAA1445	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B	protein-coding
mm_119353.1	chr14	41114256	41114260	+	1	NA	exon (NM_133653, exon 5 of 10)	exon (NM_133653, exon 5 of 10)	9225	NM_133653	11720	Mm.14064	NM_133653	ENSMUSG00000037798	Mat1a	AI046368|AdoMet|Ams|MAT|MATA1|SAMS|SAMS1	methionine adenosyltransferase I, alpha	protein-coding
mm_154178.1	chr19	58744074	58744086	-	1	NA	TTS (NM_018874)	TTS (NM_018874)	15193	NM_018874	18946	Mm.10753	NM_018874	ENSMUSG00000042179	Pnliprp1	Plrp1	pancreatic lipase related protein 1	protein-coding
mm_126841.1	chr15	89059786	89059804	+	1	NA	promoter-TSS (NM_001002005)	promoter-TSS (NM_001002005)	69	NM_001002005	406218	Mm.483059	NM_001002005	ENSMUSG00000058441	Panx2	-	pannexin 2	protein-coding
mm_69194.1	chr7	127335122	127335139	-	1	NA	TTS (NM_001253873)	TTS (NM_001253873)	10184	NM_146202	233890	Mm.23031	NM_146202	ENSMUSG00000047371	Zfp768	BC026432|Znf768	zinc finger protein 768	protein-coding
mm_90115.1	chr10	117277717	117277766	+	1	NA	3' UTR (NM_017372, exon 4 of 4)	3' UTR (NM_017372, exon 4 of 4)	4531	NM_017372	17105	Mm.45436	NM_017372	ENSMUSG00000069516	Lyz2	AI326280|Lys|Lysm|Lyzf2|Lyzs|Lzm|Lzm-s1|Lzp	lysozyme 2	protein-coding
mm_19465.1	chr2	92401238	92401352	-	1	NA	promoter-TSS (NM_011162)	promoter-TSS (NM_011162)	-32	NM_011162	19099	Mm.2720	NM_011162	ENSMUSG00000027223	Mapk8ip1	IB1|JIP-1|Jip1|Prkm8ip|Skip|mjip-2a	mitogen-activated protein kinase 8 interacting protein 1	protein-coding
mm_162399.1	chr1	84242530	84242531	+	1	NA	intron (NM_001003948, intron 1 of 2)	intron (NM_001003948, intron 1 of 2)	-23569	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_26733.1	chr3	5576112	5576162	-	1	NA	5' UTR (NM_008994, exon 1 of 6)	5' UTR (NM_008994, exon 1 of 6)	111	NM_001163301	19302	Mm.132336	NM_008994	ENSMUSG00000040374	Pex2	D3Ertd138e|PAF-1|PMP35|Pxmp3	peroxisomal biogenesis factor 2	protein-coding
mm_62093.1	chr7	94042757	94042772	+	1	NA	Intergenic	Intergenic	962885	NM_021427	58238	Mm.113787	NM_021427	ENSMUSG00000051515	Fam181b	A830059I20Rik|AB041569	family with sequence similarity 181, member B	protein-coding
mm_128778.1	chr15	66792858	66792858	-	1	NA	intron (NM_009192, intron 4 of 8)	RSINE1|SINE|B4	38971	NM_001029841	20491	Mm.7601	NM_009192	ENSMUSG00000022372	Sla	Slap|Slap-1	src-like adaptor	protein-coding
mm_172934.1	chr9	78175615	78175633	-	1	NA	promoter-TSS (NR_040401)	promoter-TSS (NR_040401)	-290	NR_040401	320295	Mm.131285	NR_040401	ENSMUSG00000097574	C920006O11Rik	-	RIKEN cDNA C920006O11 gene	ncRNA
mm_40126.1	chr5	34999047	34999069	+	1	NA	promoter-TSS (NM_001163512)	promoter-TSS (NM_001163512)	-20	NM_001163512	71729	Mm.196208	NM_173402	ENSMUSG00000029101	Rgs12	1200016K18Rik|4632412M04Rik|AI481290|E130309H11	regulator of G-protein signaling 12	protein-coding
mm_85170.1	chr9	96478597	96478622	-	1	NA	promoter-TSS (NM_011279)	promoter-TSS (NM_011279)	66	NM_011279	19823	Mm.28235	NM_011279	ENSMUSG00000051234	Rnf7	Rbx2|SAG	ring finger protein 7	protein-coding
mm_99013.1	chr11	98863611	98863646	+	1	NA	promoter-TSS (NM_197940)	promoter-TSS (NM_197940)	30	NM_197940	68524	Mm.28661	NM_197940	ENSMUSG00000038013	Wipf2	1110014J05Rik|5730509C05Rik|AA407487|Gm1176|Wich|Wire	WAS/WASL interacting protein family, member 2	protein-coding
mm_136839.1	chr17	12754814	12754827	+	1	NA	intron (NM_010515, intron 1 of 47)	intron (NM_010515, intron 1 of 47)	13509	NR_027784	104103	Mm.26553	NR_002853	ENSMUSG00000078247	Airn	2810051F02Rik|2810434M15Rik|AI256653|AI597500|AW049873|Air|B930018I07Rik|D17Ertd663e|IGF2RAS	antisense Igf2r RNA	ncRNA
mm_164904.1	chr18	68007499	68007509	+	1	NA	intron (NM_172631, intron 1 of 5)	intron (NM_172631, intron 1 of 5)	74247	NM_172631	52662	Mm.440183	NM_172631	ENSMUSG00000024544	Ldlrad4	8230401C20Rik|A430083H02|A430108L08Rik|C18orf1|D18Ertd653e|D330030L18Rik	low density lipoprotein receptor class A domain containing 4	protein-coding
mm_19213.1	chr2	84635717	84635742	-	1	NA	intron (NM_007615, intron 1 of 19)	intron (NM_007615, intron 1 of 19)	14781	NM_001085453	12388	Mm.35738	NM_007615	ENSMUSG00000034101	Ctnnd1	AA409437|AU019353|Catns|Ctnnd|P120|mKIAA0384	catenin (cadherin associated protein), delta 1	protein-coding
mm_13522.1	chr2	110013498	110013500	+	1	NA	3' UTR (NM_172671, exon 18 of 18)	3' UTR (NM_172671, exon 18 of 18)	-4318	NM_026613	68201	Mm.181767	NM_026613	ENSMUSG00000027160	Ccdc34	2810027O19Rik|4930522P10Rik|AI596202	coiled-coil domain containing 34	protein-coding
mm_144040.1	chr17	90292590	90292591	-	1	NA	intron (NM_001346959, intron 2 of 6)	intron (NM_001346959, intron 2 of 6)	163290	NM_001346958	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_53695.1	chr6	142756681	142756700	+	1	NA	promoter-TSS (NM_009908)	promoter-TSS (NM_009908)	4	NM_009908	12764	Mm.3820	NM_009908	ENSMUSG00000030282	Cmas	AW208911|CMPNeu5Ac|D6Bwg0250e	cytidine monophospho-N-acetylneuraminic acid synthetase	protein-coding
mm_163391.1	chr12	62066053	62066055	+	1	NA	Intergenic	Intergenic	542887	NM_001310586	238205	Mm.28802	NM_178714	ENSMUSG00000035653	Lrfn5	AI427653|AI604817|C130061B21|mKIAA4208	leucine rich repeat and fibronectin type III domain containing 5	protein-coding
mm_22043.1	chr2	168230070	168230113	-	1	NA	promoter-TSS (NM_001160330)	promoter-TSS (NM_001160330)	288	NM_010072	13480	Mm.422657	NM_010072	ENSMUSG00000078919	Dpm1	AI118379|AI194292	dolichol-phosphate (beta-D) mannosyltransferase 1	protein-coding
mm_171131.1	chr3	147225415	147225430	-	1	NA	Intergenic	L1Md_T|LINE|L1	373055	NM_001302958	70892	Mm.187793	NM_027594	ENSMUSG00000036745	Ttll7	1110049N09Rik|4921517B04Rik|C630030B20|mTTLL7	tubulin tyrosine ligase-like family, member 7	protein-coding
mm_33162.1	chr4	126017907	126017914	+	1	NA	Intergenic	Intergenic	-6749	NR_045561	12986	Mm.271701	NM_007782	ENSMUSG00000028859	Csf3r	Cd114|Csfgr|G-CSF-R|G-CSFR	colony stimulating factor 3 receptor (granulocyte)	protein-coding
mm_23986.1	chr3	86143069	86143094	+	1	NA	promoter-TSS (NM_016959)	promoter-TSS (NM_016959)	-413	NM_016959	20091	Mm.391785	NM_016959	ENSMUSG00000028081	Rps3a1	Rps3a	ribosomal protein S3A1	protein-coding
mm_88347.1	chr10	75837535	75837553	+	1	NA	Intergenic	Intergenic	-2663	NM_010361	14872	Mm.24118	NM_010361	ENSMUSG00000033318	Gstt2	AI266894|Yrs|mGSTT2	glutathione S-transferase, theta 2	protein-coding
mm_7452.1	chr1	120265313	120265321	-	1	NA	promoter-TSS (NM_133186)	promoter-TSS (NM_133186)	-37	NM_133186	68428	Mm.181033	NM_133186	ENSMUSG00000026389	Steap3	1010001D01Rik|Tsap6|pHyde	STEAP family member 3	protein-coding
mm_48115.1	chr5	137116414	137116462	-	1	NA	promoter-TSS (NM_201373)	promoter-TSS (NM_201373)	-231	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_1684.1	chr1	74856624	74856626	+	1	NA	3' UTR (NM_009872, exon 1 of 1)	3' UTR (NM_009872, exon 1 of 1)	1596	NM_009872	12570	Mm.153833	NM_009872	ENSMUSG00000090071	Cdk5r2	B230310J22Rik|p39	cyclin-dependent kinase 5, regulatory subunit 2 (p39)	protein-coding
mm_51179.1	chr6	70726794	70726802	+	1	NA	Intergenic	Intergenic	65377	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_18747.1	chr2	73312704	73312724	-	1	NA	promoter-TSS (NM_025854)	promoter-TSS (NM_025854)	62	NM_029022	74616	Mm.247457	NM_029022	ENSMUSG00000008226	Scrn3	4833415E20Rik|AI427019|AV002033|Ses3	secernin 3	protein-coding
mm_30457.1	chr3	153929631	153929639	-	1	NA	intron (NM_007382, intron 9 of 11)	intron (NM_007382, intron 9 of 11)	15008	NM_007382	11364	Mm.10530	NM_007382	ENSMUSG00000062908	Acadm	AU018656|MCAD	acyl-Coenzyme A dehydrogenase, medium chain	protein-coding
mm_51209.1	chr6	71334109	71334121	+	1	NA	exon (NM_009858, exon 5 of 6)	exon (NM_009858, exon 5 of 6)	11303	NM_009858	12526	Mm.333148	NM_009858	ENSMUSG00000053044	Cd8b1	Cd8b|Ly-3|Ly-C|Lyt-3	CD8 antigen, beta chain 1	protein-coding
mm_48420.1	chr5	140386157	140386161	-	1	NA	intron (NM_172277, intron 1 of 10)	B2_Mm2|SINE|B2	3149	NM_172277	231834	Mm.27098	NM_172277	ENSMUSG00000029560	Snx8	B130023O14Rik	sorting nexin 8	protein-coding
mm_4820.1	chr1	185431962	185431979	+	1	NA	non-coding (NR_038006, exon 2 of 2)	non-coding (NR_038006, exon 2 of 2)	9849	NR_038006	319562	Mm.184335	NM_176943	ENSMUSG00000051295	9630028B13Rik	-	RIKEN cDNA 9630028B13 gene	ncRNA
mm_12062.1	chr2	59384121	59384128	+	1	NA	intron (NR_040510, intron 2 of 2)	RMER17C|LTR|ERVK	2558	NR_040510	76676	Mm.110038	NR_040510	ENSMUSG00000087455	5330411J11Rik	-	RIKEN cDNA 5330411J11 gene	ncRNA
mm_76216.1	chr8	83458407	83458417	-	1	NA	promoter-TSS (NM_001039137)	promoter-TSS (NM_001039137)	-16	NM_001039137	56367	Mm.246911	NM_019708	ENSMUSG00000063253	Scoc	0610011C06Rik|2810002J11Rik|AA415030|SCOCO	short coiled-coil protein	protein-coding
mm_68336.1	chr7	106504993	106505004	-	1	NA	Intergenic	Intergenic	-63925	NR_003967	209380	Mm.461779	NM_001001318		Gm4759	EG209380	GTPase, very large interferon inducible 1 pseudogene	pseudo
mm_128941.1	chr15	74734293	74734299	-	1	NA	promoter-TSS (NM_026671)	promoter-TSS (NM_026671)	17	NM_026671	68311	Mm.306880	NM_026671	ENSMUSG00000022595	Lypd2	0610005K03Rik|Lypdc2|VLL	Ly6/Plaur domain containing 2	protein-coding
mm_6842.1	chr1	84234110	84234118	-	1	NA	intron (NM_001003948, intron 1 of 2)	MTEb|LTR|ERVL-MaLR	-15153	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_23708.1	chr3	68869308	68869322	+	1	NA	promoter-TSS (NM_001167996)	promoter-TSS (NM_001167996)	-271	NM_001167996	68725	Mm.45741	NM_001167996	ENSMUSG00000046999	1110032F04Rik	AI115547	RIKEN cDNA 1110032F04 gene	protein-coding
mm_152415.1	chr19	10668998	10669006	-	1	NA	TTS (NM_021453)	TTS (NM_021453)	9069	NM_021453	58803	Mm.34037	NM_021453	ENSMUSG00000024738	Pga5	1110035E17Rik|Pepf	pepsinogen 5, group I	protein-coding
mm_44451.1	chr5	21768466	21768496	-	1	NA	exon (NM_009584, exon 9 of 17)	exon (NM_009584, exon 9 of 17)	16684	NM_009584	22791	Mm.266312	NM_009584	ENSMUSG00000029014	Dnajc2	AU020218|MIDA1|Zrf1|Zrf2	DnaJ heat shock protein family (Hsp40) member C2	protein-coding
mm_157896.1	chrX	77795922	77795985	-	1	NA	promoter-TSS (NM_016979)	promoter-TSS (NM_016979)	7	NM_016979	19108	Mm.290338	NM_016979	ENSMUSG00000035725	Prkx	PKX1|Pkare	protein kinase, X-linked	protein-coding
mm_9834.1	chr1	184033768	184033781	-	1	NA	promoter-TSS (NM_022019)	promoter-TSS (NM_022019)	224	NM_028516	73363	Mm.50115	NM_028516	ENSMUSG00000044854	1700056E22Rik	-	RIKEN cDNA 1700056E22 gene	protein-coding
mm_99098.1	chr11	99936290	99936293	+	1	NA	promoter-TSS (NM_001025244)	promoter-TSS (NM_001025244)	0	NM_001025244	432602	Mm.246878	NM_001025244	ENSMUSG00000051481	Krtap31-2	OTTMUSG00000002177	keratin associated protein 31-2	protein-coding
mm_134361.1	chr16	16863939	16863955	-	1	NA	promoter-TSS (NM_001190325)	promoter-TSS (NM_001190325)	38	NM_001190325	16136	Mm.184441	NM_001190325	ENSMUSG00000075370	Igll1	BB139905|Igl-5|Igll|Lambda5	immunoglobulin lambda-like polypeptide 1	protein-coding
mm_6146.1	chr1	64928077	64928096	-	1	NA	intron (NM_001039493, intron 2 of 7)	intron (NM_001039493, intron 2 of 7)	28738	NM_001039493	241075	Mm.239534	NM_175509	ENSMUSG00000051344	Plekhm3	9430067K14Rik|A230102O09Rik|AI449570|DAPR|Plekhm1l	pleckstrin homology domain containing, family M, member 3	protein-coding
mm_102414.1	chr11	59202142	59202154	-	1	NA	promoter-TSS (NM_026035)	promoter-TSS (NM_026035)	283	NR_037964	72203	Mm.339566	NR_037964		2610507I01Rik	5033414D05Rik	RIKEN cDNA 2610507I01 gene	ncRNA
mm_170986.1	chr2	73867952	73867959	+	1	NA	intron (NM_001284374, intron 3 of 11)	LSU-rRNA_Hsa|rRNA|rRNA	24684	NM_001284371	11909	Mm.209903	NM_009715	ENSMUSG00000027104	Atf2	Atf-2|CRE-BP|Creb2|D130078H02Rik|D18875|Tg(Gzma-Klra1)7Wum|mXBP	activating transcription factor 2	protein-coding
mm_60138.1	chr7	38090537	38090571	+	1	NA	Intergenic	Intergenic	16936	NM_007633	12447	Mm.16110	NM_007633	ENSMUSG00000002068	Ccne1	AW538188|CycE1	cyclin E1	protein-coding
mm_149625.1	chr19	17125619	17125670	+	1	NA	exon (NM_181348, exon 9 of 20)	exon (NM_181348, exon 9 of 20)	169526	NM_181348	353211	Mm.257354	NM_181348	ENSMUSG00000039126	Prune2	6330414G02Rik|A230083H22Rik|A330102H22Rik|Bmcc1|mKIAA0367	prune homolog 2	protein-coding
mm_39084.1	chr4	154636205	154636215	-	1	NA	non-coding (NR_045643, exon 1 of 1)	non-coding (NR_045643, exon 1 of 1)	157	NR_045643	320939	Mm.436738	NR_045643		5930403L14Rik	-	RIKEN cDNA 5930403L14 gene	ncRNA
mm_110117.1	chr12	26443923	26443931	-	1	NA	3' UTR (NM_021384, exon 6 of 6)	3' UTR (NM_021384, exon 6 of 6)	12525	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_88014.1	chr10	67177800	67177807	+	1	NA	intron (NM_207221, intron 2 of 25)	intron (NM_207221, intron 2 of 25)	-7947	NM_001242396	108829	Mm.23846	NM_207221	ENSMUSG00000037876	Jmjd1c	5430433L24Rik|D630035I23Rik|Jmjdic|TRIP8	jumonji domain containing 1C	protein-coding
mm_34746.1	chr4	152297206	152297220	+	1	NA	promoter-TSS (NM_133788)	promoter-TSS (NM_133788)	-1	NR_037908	57295	Mm.277464	NM_133788	ENSMUSG00000039662	Icmt	1700008E11Rik|C80758|Gm13095|HSTE14|OTTMUSG00000010406|PPMT|STE14|pcCMT	isoprenylcysteine carboxyl methyltransferase	protein-coding
mm_82449.1	chr9	15357664	15357674	-	1	NA	exon (NM_176976, exon 1 of 27)	exon (NM_176976, exon 1 of 27)	119	NM_176976	319675	Mm.218317	NM_176976	ENSMUSG00000046111	Cep295	5830418K08Rik|5832426L23Rik|Gm1131|Kiaa1731	centrosomal protein 295	protein-coding
mm_97827.1	chr11	83041257	83041288	+	1	NA	promoter-TSS (NR_073524)	promoter-TSS (NR_073524)	-739	NR_073524	237887	Mm.341645	NM_181542	ENSMUSG00000072621	Slfn10-ps	Slfn10|mFLJ00257	schlafen 10, pseudogene	pseudo
mm_20439.1	chr2	129307911	129307938	-	1	NA	TTS (NR_040371)	TTS (NR_040371)	2048	NM_010554	16175	Mm.15534	NM_010554	ENSMUSG00000027399	Il1a	Il-1a	interleukin 1 alpha	protein-coding
mm_4948.1	chr1	191194304	191194321	+	1	NA	Intergenic	Intergenic	-10979	NM_007498	11910	Mm.2706	NM_007498	ENSMUSG00000026628	Atf3	LRG-21	activating transcription factor 3	protein-coding
mm_166162.1	chr5	17302744	17302745	+	1	NA	Intergenic	Intergenic	-173378	NM_027609	70935	Mm.332225	NM_027609	ENSMUSG00000058643	Speer4f1	4922502J04Rik|SPEER-4F|Speer4f	spermatogenesis associated glutamate (E)-rich protein 4F1	protein-coding
mm_129401.1	chr15	78284341	78284351	-	1	NA	TTS (NR_106137).2	TTS (NR_106137).2	503	NR_106138	102466845		NR_106138	ENSMUSG00000099059	Mir7676-2	Gm27790|mmu-mir-7676-2	microRNA 7676-2	ncRNA
mm_96529.1	chr11	68534206	68534238	+	1	NA	exon (NM_001081566, exon 12 of 20)	exon (NM_001081566, exon 12 of 20)	-21964	NM_146004	215723	Mm.131205	NM_146004	ENSMUSG00000048329	Mfsd6l	-	major facilitator superfamily domain containing 6-like	protein-coding
mm_133148.1	chr16	70314058	70314071	+	1	NA	5' UTR (NM_028803, exon 1 of 16)	5' UTR (NM_028803, exon 1 of 16)	115	NM_028803	74185	Mm.396102	NM_028803	ENSMUSG00000022707	Gbe1	2310045H19Rik|2810426P10Rik|D16Ertd536e	glucan (1,4-alpha-), branching enzyme 1	protein-coding
mm_34068.1	chr4	138456712	138456721	+	1	NA	intron (NM_025451, intron 1 of 1)	intron (NM_025451, intron 1 of 1)	1568	NM_025451	66259	Mm.41603	NM_025451	ENSMUSG00000046447	Camk2n1	1810006K23Rik|AI848599|AI891706	calcium/calmodulin-dependent protein kinase II inhibitor 1	protein-coding
mm_23415.1	chr3	58526009	58526010	+	1	NA	promoter-TSS (NM_030685)	promoter-TSS (NM_030685)	-125	NM_030685	28146	Mm.29702	NM_030685	ENSMUSG00000027808	Serp1	D3Ucla1|Ramp4	stress-associated endoplasmic reticulum protein 1	protein-coding
mm_64805.1	chr7	6696424	6696456	-	1	NA	promoter-TSS (NM_011769)	promoter-TSS (NM_011769)	-8	NM_011769	22776	Mm.89976	NM_011769	ENSMUSG00000002266	Zim1	-	zinc finger, imprinted 1	protein-coding
mm_55374.1	chr6	57839916	57839922	-	1	NA	Intergenic	Intergenic	4538	NM_134183	171201	Mm.377179	NM_134183	ENSMUSG00000058588	Vmn1r21	V1rc28	vomeronasal 1 receptor 21	protein-coding
mm_13391.1	chr2	103969651	103969655	+	1	NA	promoter-TSS (NM_008505)	promoter-TSS (NM_008505)	96	NM_001142336	16909	Mm.29266	NM_008505	ENSMUSG00000032698	Lmo2	Rbtn-2|Rbtn2|Rhom-2|Ttg2	LIM domain only 2	protein-coding
mm_23851.1	chr3	83008515	83008532	+	1	NA	exon (NM_133862, exon 3 of 10)	exon (NM_133862, exon 3 of 10)	799	NM_001317105	99571	Mm.16422	NM_133862	ENSMUSG00000033860	Fgg	3010002H13Rik|AI256424	fibrinogen gamma chain	protein-coding
mm_110904.1	chr12	75735730	75735736	-	1	NA	promoter-TSS (NM_030750)	promoter-TSS (NM_030750)	-4	NM_030750	81535	Mm.280199	NM_030750	ENSMUSG00000021054	Sgpp1	AI463453|SPP|SPP1|Spph1	sphingosine-1-phosphate phosphatase 1	protein-coding
mm_122150.1	chr14	31251020	31251020	-	1	NA	promoter-TSS (NM_027088)	promoter-TSS (NM_027088)	198	NM_027949	71838	Mm.5348	NM_027949	ENSMUSG00000021902	Phf7	1700006H01Rik|1700010P14Rik|AI427892|AW555949	PHD finger protein 7	protein-coding
mm_136458.1	chr16	95259611	95259622	-	1	NA	intron (NM_001271687, intron 3 of 4)	intron (NM_001271687, intron 3 of 4)	2058	NM_001271690	16516	Mm.272239	NM_019664	ENSMUSG00000062609	Kcnj15	4930414N08Rik|AI182284|AI267127|IRKK|Kir4.2	potassium inwardly-rectifying channel, subfamily J, member 15	protein-coding
mm_6029.1	chr1	59377360	59377371	-	1	NA	Intergenic	Intergenic	-104782	NM_008057	14369	Mm.297906	NM_008057	ENSMUSG00000041075	Fzd7	Fz7	frizzled class receptor 7	protein-coding
mm_167029.1	chr7	68282952	68282958	+	1	NA	intron (NM_001013811, intron 1 of 8)	intron (NM_001013811, intron 1 of 8)	-6361	NR_040340	100504026	Mm.426764	NR_040340	ENSMUSG00000086628	Gm16157	OTTMUSG00000031023	predicted gene 16157	ncRNA
mm_149701.1	chr19	21377296	21377305	+	1	NA	Intergenic	Intergenic	95361	NM_010266	14544	Mm.45054	NM_010266	ENSMUSG00000058624	Gda	AU015411|AW047581|GAH	guanine deaminase	protein-coding
mm_52674.1	chr6	117907796	117907832	+	1	NA	promoter-TSS (NM_001166429)	promoter-TSS (NM_001166429)	10	NM_001166429	98758	Mm.422979	NM_133834	ENSMUSG00000042079	Hnrnpf	4833420I20Rik|AA407306|Hnrpf	heterogeneous nuclear ribonucleoprotein F	protein-coding
mm_44119.1	chr5	149441854	149441880	+	1	NA	intron (NM_001310765, intron 1 of 5)	intron (NM_001310765, intron 1 of 5)	2207	NM_001310765	75860	Mm.159605	NM_029464	ENSMUSG00000029660	Tex26	4930588N13Rik	testis expressed 26	protein-coding
mm_23657.1	chr3	67892190	67892226	+	1	NA	promoter-TSS (NM_177585)	promoter-TSS (NM_177585)	-12	NM_001113419	100505386	Mm.331064	NM_001113419	ENSMUSG00000102422	Gm21949	Iqcj-schip1|Schip-1-iqcj|Schip1	predicted gene, 21949	protein-coding
mm_35869.1	chr4	49521037	49521089	-	1	NA	promoter-TSS (NM_001289901)	promoter-TSS (NM_001289901)	20	NM_178603	28028	Mm.30052	NM_178603	ENSMUSG00000044018	Mrpl50	AA408971|AI317351|D4Wsu125e	mitochondrial ribosomal protein L50	protein-coding
mm_8508.1	chr1	154395153	154395158	-	1	NA	3' UTR (NM_009782, exon 47 of 47)	3' UTR (NM_009782, exon 47 of 47)	-138249	NR_040629	78112	Mm.401935	NR_040629	ENSMUSG00000099933	4930452N14Rik	-	RIKEN cDNA 4930452N14 gene	ncRNA
mm_113712.1	chr13	43531699	43531705	+	1	NA	Intergenic	Intergenic	28489	NM_001081059	76137	Mm.426290	NM_001081059	ENSMUSG00000021371	Mcur1	6230416A05Rik|AU015498|AV136929|AW554392|C88263|Ccdc90a	mitochondrial calcium uniporter regulator 1	protein-coding
mm_168255.1	chr10	86705406	86705413	-	1	NA	promoter-TSS (NM_011631)	promoter-TSS (NM_011631)	35	NM_011631	22027	Mm.87773	NM_011631	ENSMUSG00000020048	Hsp90b1	ERp99|GRP94|TA-3|Targ2|Tra-1|Tra1|endoplasmin|gp96	heat shock protein 90, beta (Grp94), member 1	protein-coding
mm_121604.1	chr14	8172959	8172977	-	1	NA	promoter-TSS (NM_024221)	promoter-TSS (NM_024221)	24	NM_024221	68263	Mm.301527	NM_024221	ENSMUSG00000021748	Pdhb	2610103L06Rik|AL024199|C81408	pyruvate dehydrogenase (lipoamide) beta	protein-coding
mm_58463.1	chr7	3366878	3366891	+	1	NA	TTS (NM_133189)	TTS (NM_133189)	-27158	NM_133190	81905	Mm.357990	NM_133190	ENSMUSG00000053395	Cacng8	-	calcium channel, voltage-dependent, gamma subunit 8	protein-coding
mm_81629.1	chr9	110849508	110849529	+	1	NA	intron (NM_183103, intron 1 of 4)	intron (NM_183103, intron 1 of 4)	5012	NM_183103	74306	Mm.87419	NM_183103	ENSMUSG00000049719	Prss46	1700112C13Rik|79H19B|Tessp6	protease, serine 46	protein-coding
mm_65769.1	chr7	28759958	28759988	-	1	NA	exon (NM_010908, exon 5 of 7)	exon (NM_010908, exon 5 of 7)	3799	NM_001195091	100504112	Mm.379654	NM_001195091	ENSMUSG00000096257	Ccer2	EG624918|Gm6537	coiled-coil glutamate-rich protein 2	protein-coding
mm_132514.1	chr16	37539884	37539918	+	1	NA	promoter-TSS (NM_001042499)	promoter-TSS (NM_001042499)	7	NM_001042499	67657	Mm.28158	NM_026297	ENSMUSG00000022827	Rabl3	4930553C05Rik|AA958834	RAB, member RAS oncogene family-like 3	protein-coding
mm_18896.1	chr2	76713483	76713504	-	1	NA	exon (NM_011652, exon 307 of 313)	exon (NM_011652, exon 307 of 313)	38178	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_125770.1	chr15	74563739	74563825	+	1	NA	intron (NM_174991, intron 17 of 30)	GC_rich|Low_complexity|Low_complexity	47586	NM_174991	107831	Mm.43133	NM_174991	ENSMUSG00000034730	Adgrb1	B830018M07Rik|Bai1|R75078|mKIAA4089	adhesion G protein-coupled receptor B1	protein-coding
mm_113850.1	chr13	47207441	47207468	+	1	NA	exon (NM_146042, exon 2 of 8)	exon (NM_146042, exon 2 of 8)	13451	NM_001170643	218215	Mm.287609	NM_146042	ENSMUSG00000038068	Rnf144b	BC025007|E130105P19Rik|Ibrdc2|Pir2	ring finger protein 144B	protein-coding
mm_131806.1	chr16	22917933	22917935	+	1	NA	promoter-TSS (NM_001083905)	promoter-TSS (NM_001083905)	-448	NM_001083905	59083	Mm.28461	NM_021564	ENSMUSG00000022871	Fetub	2310011O17Rik|AI255764|D17980|Gugu	fetuin beta	protein-coding
mm_10190.1	chr2	4918892	4918905	+	1	NA	promoter-TSS (NM_010726)	promoter-TSS (NM_010726)	-98	NM_010726	16922	Mm.391704	NM_010726	ENSMUSG00000026664	Phyh	AI256161|AI265699|Lnap1|PAHX	phytanoyl-CoA hydroxylase	protein-coding
mm_63161.1	chr7	123462351	123462368	+	1	NA	promoter-TSS (NM_007474)	promoter-TSS (NM_007474)	65	NM_001109045	11833	Mm.273175	NM_007474	ENSMUSG00000030762	Aqp8	AI255744|AQP-8	aquaporin 8	protein-coding
mm_79436.1	chr9	56057498	56057537	+	1	NA	exon (NM_011992, exon 6 of 7)	exon (NM_011992, exon 6 of 7)	15672	NM_011992	26611	Mm.1782	NM_011992	ENSMUSG00000032320	Rcn2	AA408742|Tcbp49	reticulocalbin 2	protein-coding
mm_124990.1	chr15	21592834	21592835	+	1	NA	Intergenic	Intergenic	481382	NM_001008420	215654	Mm.300909	NM_001008420	ENSMUSG00000040452	Cdh12	Cdhb	cadherin 12	protein-coding
mm_46281.1	chr5	100147091	100147099	-	1	NA	intron (NM_182841, intron 1 of 7)	L1M2|LINE|L1	12713	NM_182841	231503	Mm.99790	NM_182841	ENSMUSG00000050640	Tmem150c	-	transmembrane protein 150C	protein-coding
mm_47713.1	chr5	130000402	130000417	-	1	NA	exon (NM_010368, exon 3 of 12)	exon (NM_010368, exon 3 of 12)	2419	NM_010368	110006	Mm.3317	NM_010368	ENSMUSG00000025534	Gusb	AI747421|Gur|Gus|Gus-r|Gus-s|Gus-t|Gus-u|Gut|asd|g	glucuronidase, beta	protein-coding
mm_84554.1	chr9	67703671	67703673	-	1	NA	Intergenic	Intergenic	24108	NR_106100	102466824		NR_106100	ENSMUSG00000098937	Mir7241	Gm27918|mmu-mir-7241	microRNA 7241	ncRNA
mm_41914.1	chr5	105591641	105591651	+	1	NA	intron (NM_133897, intron 3 of 3)	(CATA)n|Simple_repeat|Simple_repeat	72175	NM_133897	100604	Mm.319847	NM_133897	ENSMUSG00000054720	Lrrc8c	AD158|AI326115|E430036I04Rik|fad158	leucine rich repeat containing 8 family, member C	protein-coding
mm_130246.1	chr15	96640620	96640623	-	1	NA	intron (NM_001166458, intron 1 of 15)	intron (NM_001166458, intron 1 of 15)	1341	NM_134086	105727	Mm.103568	NM_134086	ENSMUSG00000023169	Slc38a1	AA408026|AA409865|AL022800|AU015942|NAT2	solute carrier family 38, member 1	protein-coding
mm_85692.1	chr9	108079280	108079341	-	1	NA	promoter-TSS (NM_032543)	promoter-TSS (NM_032543)	-9	NM_001311152	84585	Mm.379272	NM_032543	ENSMUSG00000041528	Rnf123	BC003945|Kpc1	ring finger protein 123	protein-coding
mm_50184.1	chr6	41641719	41641733	+	1	NA	Intergenic	Intergenic	-5321	NM_022413	64177	Mm.296889	NM_022413	ENSMUSG00000029868	Trpv6	CAT|CaT1|Cac|Ecac2|Otrpc3	transient receptor potential cation channel, subfamily V, member 6	protein-coding
mm_38759.1	chr4	147868632	147868695	-	1	NA	promoter-TSS (NM_010244)	promoter-TSS (NM_010244)	56	NM_001025365	28010	Mm.250504	NM_133873	ENSMUSG00000029022	Miip	AA553001|AI853621|D4Wsu114e|IIP45	migration and invasion inhibitory protein	protein-coding
mm_111074.1	chr12	80139269	80139270	-	1	NA	Intergenic	Intergenic	-6425	NR_033514	69548	Mm.269712	NR_033514	ENSMUSG00000097729	2310015A10Rik	5330419I17Rik	RIKEN cDNA 2310015A10 gene	ncRNA
mm_168143.1	chr10	3254744	3254773	-	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	13013	NM_001204916	670558	Mm.398582	NM_001204916	ENSMUSG00000091618	H60c	4632413I24Rik|Gm9491	histocompatibility 60c	protein-coding
mm_111977.1	chr12	110087937	110087980	-	1	NA	Intergenic	Tigger7|DNA|TcMar-Tigger	70115	NR_045466	67280	Mm.390495	NR_045466		3110009F21Rik	-	RIKEN cDNA 3110009F21 gene	ncRNA
mm_168789.1	chr12	19187132	19187138	-	1	NA	Intergenic	RLTR1B|LTR|ERV1	672625	NM_001201330	236366	Mm.352227	NM_001033157	ENSMUSG00000073197	5730507C01Rik	-	RIKEN cDNA 5730507C01 gene	protein-coding
mm_84978.1	chr9	85328454	85328481	-	1	NA	Intergenic	Intergenic	-1317	NM_001160379	212943	Mm.74610	NM_001160378	ENSMUSG00000032265	Fam46a	BAP014|D930050G01Rik	family with sequence similarity 46, member A	protein-coding
mm_171463.1	chr4	145674504	145674506	+	1	NA	intron (NM_001103158, intron 2 of 4)	intron (NM_001103158, intron 2 of 4)	3808	NM_001103158	100041379	Mm.276881	NM_001103158	ENSMUSG00000058186	Zfp980	Gm13242|OTTMUSG00000011070	zinc finger protein 980	protein-coding
mm_107352.1	chr12	32820769	32820810	+	1	NA	intron (NM_021524, intron 1 of 10)	CpG	454	NM_021524	59027	Mm.202727	NM_021524	ENSMUSG00000020572	Nampt	1110035O14Rik|AI314458|AI480535|NAmPRTase|Pbef|Pbef1|Visfatin	nicotinamide phosphoribosyltransferase	protein-coding
mm_165877.1	chr4	41135731	41135741	+	1	NA	promoter-TSS (NM_026275)	promoter-TSS (NM_026275)	-285	NM_026275	67615	Mm.389540	NM_026275	ENSMUSG00000036241	Ube2r2	1200003M11Rik|Cdc34b|Ubc3b	ubiquitin-conjugating enzyme E2R 2	protein-coding
mm_92215.1	chr10	68239709	68239746	-	1	NA	intron (NM_023598, intron 3 of 9)	intron (NM_023598, intron 3 of 9)	38999	NM_023598	71371	Mm.440357	NM_023598	ENSMUSG00000019947	Arid5b	4930580B11|5430435G07Rik|AI467247|Desrt|Mrf2|Mrf2alpha|Mrf2beta	AT rich interactive domain 5B (MRF1-like)	protein-coding
mm_39264.1	chr5	3571665	3571671	+	1	NA	promoter-TSS (NM_029843)	promoter-TSS (NM_029843)	-48	NM_029843	77036	Mm.389069	NM_029843	ENSMUSG00000008307	1700109H08Rik	-	RIKEN cDNA 1700109H08 gene	protein-coding
mm_76205.1	chr8	83332417	83332494	-	1	NA	promoter-TSS (NM_178736)	promoter-TSS (NM_178736)	31	NM_001170691	244548	Mm.38762	NM_178736	ENSMUSG00000035151	Elmod2	9830169G11Rik	ELMO/CED-12 domain containing 2	protein-coding
mm_131960.1	chr16	24525144	24525148	+	1	NA	intron (NM_001145952, intron 2 of 11)	intron (NM_001145952, intron 2 of 11)	-4168	NR_038091	624582	Mm.439775	NR_038091		Morf4l1-ps1	A730098P11Rik	mortality factor 4 like 1, pseudogene 1	pseudo
mm_158819.1	chrX	167333058	167333065	-	1	NA	Intergenic	Intergenic	-2490	NM_001290756	170743	Mm.23979	NM_133211	ENSMUSG00000044583	Tlr7	-	toll-like receptor 7	protein-coding
mm_153943.1	chr19	47507895	47507912	-	1	NA	intron (NM_175360, intron 8 of 9)	intron (NM_175360, intron 8 of 9)	-5079	NR_045322	100503104	Mm.442735	NR_045322	ENSMUSG00000097990	Gm19557	-	predicted gene, 19557	ncRNA
mm_21131.1	chr2	154206436	154206457	-	1	NA	exon (NM_153418, exon 5 of 16)	exon (NM_153418, exon 5 of 16)	6066	NM_153418	228801	Mm.3783	NM_153418	ENSMUSG00000027485	Bpifb1	Lplunc1	BPI fold containing family B, member 1	protein-coding
mm_2373.1	chr1	93300275	93300283	+	1	NA	TTS (NM_001310756)	TTS (NM_001310756)	5600	NM_178051	69821	Mm.52809	NM_178051	ENSMUSG00000026273	Mterf4	1810059A23Rik|4933412H03Rik|Mterfd2	mitochondrial transcription termination factor 4	protein-coding
mm_25283.1	chr3	105639883	105639886	+	1	NA	intron (NM_001039347, intron 2 of 6)	L1MA4A|LINE|L1	47687	NM_017397	53975	Mm.272826	NM_017397	ENSMUSG00000027905	Ddx20	GEMIN3|dp103	DEAD (Asp-Glu-Ala-Asp) box polypeptide 20	protein-coding
mm_35570.1	chr4	41640366	41640376	-	1	NA	promoter-TSS (NM_027147)	promoter-TSS (NM_027147)	-69	NM_027147	69638	Mm.372459	NM_027147	ENSMUSG00000028445	Enho	1110065P19Rik|2310040A07Rik	energy homeostasis associated	protein-coding
mm_81247.1	chr9	107975611	107975621	+	1	NA	promoter-TSS (NM_023738)	promoter-TSS (NM_023738)	49	NM_023738	74153	Mm.277125	NM_023738	ENSMUSG00000032596	Uba7	1300004C08Rik|Ube1l	ubiquitin-like modifier activating enzyme 7	protein-coding
mm_91524.1	chr10	37138864	37138937	-	1	NA	promoter-TSS (NM_008538)	promoter-TSS (NM_008538)	26	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_37184.1	chr4	117288526	117288572	-	1	NA	intron (NM_025739, intron 6 of 14)	intron (NM_025739, intron 6 of 14)	906	NM_001310730	66743	Mm.318331	NM_025739	ENSMUSG00000028677	Rnf220	4732477A13|4931406I20Rik|5730503K05Rik|AV302541	ring finger protein 220	protein-coding
mm_144517.1	chr18	24746579	24746591	+	1	NA	intron (NM_175276, intron 1 of 26)	B3|SINE|B2	37962	NM_001289655	225288	Mm.329322	NM_175276	ENSMUSG00000034295	Fhod3	A930009H06Rik|FHOS2|mKIAA1695	formin homology 2 domain containing 3	protein-coding
mm_80629.1	chr9	89199298	89199310	+	1	NA	promoter-TSS (NM_007534)	promoter-TSS (NM_007534)	31	NM_007534	12045	Mm.479217	NM_007534	ENSMUSG00000089929	Bcl2a1b	A1-b	B cell leukemia/lymphoma 2 related protein A1b	protein-coding
mm_73458.1	chr8	106603361	106603374	+	1	NA	promoter-TSS (NM_009864)	promoter-TSS (NM_009864)	17	NM_009864	12550	Mm.35605	NM_009864	ENSMUSG00000000303	Cdh1	AA960649|ARC-1|E-cad|Ecad|L-CAM|UVO|Um	cadherin 1	protein-coding
mm_93249.1	chr10	95447962	95447970	-	1	NA	Intergenic	Intergenic	30591	NR_045338	70523	Mm.158398	NR_045338	ENSMUSG00000097766	5730420D15Rik	-	RIKEN cDNA 5730420D15 gene	ncRNA
mm_144844.1	chr18	36571704	36571707	+	1	NA	intron (NM_175375, intron 1 of 33)	intron (NM_175375, intron 1 of 33)	11102	NM_175375	108857	Mm.482287	NM_175375	ENSMUSG00000024483	Ankhd1	1110004O12Rik|4933432B13Rik|9130019P20Rik|A530027J04Rik|A630021B20Rik|AA571404|Mask|mFLJ00246|mKIAA1085	ankyrin repeat and KH domain containing 1	protein-coding
mm_150176.1	chr19	32595753	32595780	+	1	NA	promoter-TSS (NM_001201470)	promoter-TSS (NM_001201470)	51	NM_001201470	23972	Mm.203916	NM_011864	ENSMUSG00000024899	Papss2	1810018P12Rik|AI159688|AtpsU2|Atpsk2|Sk2|bm	3'-phosphoadenosine 5'-phosphosulfate synthase 2	protein-coding
mm_113911.1	chr13	49493596	49493606	+	1	NA	intron (NM_025495, intron 5 of 7)	intron (NM_025495, intron 5 of 7)	-11209	NM_001012324	407800	Mm.386931	NM_001012324	ENSMUSG00000043631	Ecm2	9030618O22Rik|BC065151|tenonectin	extracellular matrix protein 2, female organ and adipocyte specific	protein-coding
mm_94612.1	chr11	16526108	16526113	+	1	NA	Intergenic	RLTR41|LTR|ERV1	-17626	NM_001109971	20335	Mm.325350	NM_011343	ENSMUSG00000078974	Sec61g	-	SEC61, gamma subunit	protein-coding
mm_56038.1	chr6	86669137	86669164	-	1	NA	promoter-TSS (NM_010751)	promoter-TSS (NM_010751)	9	NM_010751	17119	Mm.279580	NM_010751	ENSMUSG00000001156	Mxd1	AW122478|Mad|Mad1	MAX dimerization protein 1	protein-coding
mm_76553.1	chr8	88361912	88361925	-	1	NA	exon (NM_012047, exon 1 of 17)	exon (NM_012047, exon 1 of 17)	273	NM_012047	26992	Mm.5400	NM_012047	ENSMUSG00000031660	Brd7	BP75|CELTIX1|Ptpn13ip	bromodomain containing 7	protein-coding
mm_85169.1	chr9	96438162	96438226	-	1	NA	Intergenic	Intergenic	40481	NM_011279	19823	Mm.28235	NM_011279	ENSMUSG00000051234	Rnf7	Rbx2|SAG	ring finger protein 7	protein-coding
mm_38167.1	chr4	135217030	135217045	-	1	NA	3' UTR (NM_013885, exon 6 of 6)	3' UTR (NM_013885, exon 6 of 6)	55723	NM_013885	29876	Mm.257765	NM_013885	ENSMUSG00000037242	Clic4	D0Jmb3|TU-74|mc3s5|mtCLIC	chloride intracellular channel 4 (mitochondrial)	protein-coding
mm_151664.1	chr19	4156580	4156618	-	1	NA	TTS (NM_021485)	TTS (NM_021485)	1953	NM_016933	19265	Mm.271937	NM_016933	ENSMUSG00000045826	Ptprcap	AI605264|CD-45-AP|LPAP|LSM-1	protein tyrosine phosphatase, receptor type, C polypeptide-associated protein	protein-coding
mm_17278.1	chr2	26092150	26092157	-	1	NA	5' UTR (NM_001037098, exon 1 of 6)	5' UTR (NM_001037098, exon 1 of 6)	243	NM_001037098	67991	Mm.131074	NM_026495	ENSMUSG00000026932	Nacc2	0610020I02Rik|AI448087|Btbd14a|C030048H19Rik	nucleus accumbens associated 2, BEN and BTB (POZ) domain containing	protein-coding
mm_155400.1	chrX	72997262	72997268	+	1	NA	intron (NM_009549, intron 2 of 18)	intron (NM_009549, intron 2 of 18)	5186	NR_035517	100316779		NR_035517	ENSMUSG00000089357	Mir2137	mmu-mir-2137	microRNA 2137	ncRNA
mm_81869.1	chr9	119052771	119052795	+	1	NA	promoter-TSS (NM_011700)	promoter-TSS (NM_011700)	5	NM_001164567	22351	Mm.83817	NM_011700	ENSMUSG00000038775	Vill	Villp	villin-like	protein-coding
mm_113841.1	chr13	47193943	47194010	+	1	NA	promoter-TSS (NM_001170643)	promoter-TSS (NM_001170643)	-27	NM_001170643	218215	Mm.287609	NM_146042	ENSMUSG00000038068	Rnf144b	BC025007|E130105P19Rik|Ibrdc2|Pir2	ring finger protein 144B	protein-coding
mm_26619.1	chr3	152396363	152396394	+	1	NA	promoter-TSS (NM_001287139)	promoter-TSS (NM_001287139)	-306	NM_001287139	108946	Mm.379292	NM_198416	ENSMUSG00000039068	Zzz3	3110065C23Rik|6430567E01Rik|AA408566|AI481057|AW556059|R75514	zinc finger, ZZ domain containing 3	protein-coding
mm_125669.1	chr15	65865664	65865698	+	1	NA	intron (NM_133766, intron 19 of 22)	intron (NM_133766, intron 19 of 22)	46573	NM_001347038	18256	Mm.41776	NM_010953	ENSMUSG00000015001	Oc90	Ocn-95|PLA2L|Pla2ll|oc95	otoconin 90	protein-coding
mm_49623.1	chr6	30803822	30803836	+	1	NA	intron (NM_017478, intron 20 of 23)	B1_Mur4|SINE|Alu	62530	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_22889.1	chr3	30647994	30648007	+	1	NA	promoter-TSS (NM_027941)	promoter-TSS (NM_027941)	114	NM_001290510	68307	Mm.389425	NM_026668	ENSMUSG00000027703	Lrriq4	4930558O21Rik	leucine-rich repeats and IQ motif containing 4	protein-coding
mm_144697.1	chr18	34862525	34862570	+	1	NA	exon (NM_007913, exon 2 of 2)	exon (NM_007913, exon 2 of 2)	1340	NM_007913	13653	Mm.181959	NM_007913	ENSMUSG00000038418	Egr1	A530045N19Rik|ETR103|Egr-1|Krox-1|Krox-24|Krox24|NGF1-A|NGFI-A|NGFIA|TIS8|Zenk|Zfp-6|Zif268|egr	early growth response 1	protein-coding
mm_12325.1	chr2	69393103	69393175	+	1	NA	exon (NM_175512, exon 2 of 5)	exon (NM_175512, exon 2 of 5)	12677	NM_175512	241452	Mm.211655	NM_175512	ENSMUSG00000027068	Dhrs9	C730025I08Rik|Rdh15	dehydrogenase/reductase (SDR family) member 9	protein-coding
mm_82864.1	chr9	31936894	31936905	-	1	NA	Intergenic	Intergenic	-23614	NM_013800	12023	Mm.261044	NM_013800	ENSMUSG00000032033	Barx2	2310006E12Rik|Barx2b	BarH-like homeobox 2	protein-coding
mm_161566.1	chr16	18622444	18622444	-	1	NA	promoter-TSS (NM_010327)	promoter-TSS (NM_010327)	-41	NM_010327	14724	Mm.475622	NM_010327	ENSMUSG00000050761	Gp1bb	-	glycoprotein Ib, beta polypeptide	protein-coding
mm_159029.1	chr1	174391194	174391194	+	1	NA	exon (NM_146714, exon 1 of 1)	exon (NM_146714, exon 1 of 1)	148	NM_146714	258709	Mm.377646	NM_146714	ENSMUSG00000059503	Olfr248	MOR267-7|Olfr248-ps1|Olfr415	olfactory receptor 248	protein-coding
mm_47574.1	chr5	124530984	124531040	-	1	NA	5' UTR (NM_021430, exon 1 of 7)	5' UTR (NM_021430, exon 1 of 7)	379	NM_021430	75695	Mm.41180	NM_021430	ENSMUSG00000029392	Rilpl1	2900002H16Rik|6330559I19Rik|GOSPEL	Rab interacting lysosomal protein-like 1	protein-coding
mm_31170.1	chr4	43453826	43453838	+	1	NA	intron (NM_007654, intron 2 of 8)	intron (NM_007654, intron 2 of 8)	794	NM_001110320	12517	Mm.188157	NM_007654	ENSMUSG00000028459	Cd72	CD72c|Ly-19|Ly-32|Ly-m19|Lyb-2	CD72 antigen	protein-coding
mm_116945.1	chr13	56135406	56135416	-	1	NA	5' UTR (NM_001159515, exon 1 of 9)	5' UTR (NM_001159515, exon 1 of 9)	139	NM_012015	26914	Mm.283802	NM_012015	ENSMUSG00000015937	H2afy	H2AF12M|mH2a1|macroH2A1	H2A histone family, member Y	protein-coding
mm_65093.1	chr7	19270444	19270447	-	1	NA	intron (NR_104069, intron 1 of 10)	intron (NR_104069, intron 1 of 10)	1409	NM_001282021	22323	Mm.9684	NM_009499	ENSMUSG00000030403	Vasp	-	vasodilator-stimulated phosphoprotein	protein-coding
mm_64478.1	chr7	143053555	143053569	+	1	NA	non-coding (NR_015529, exon 1 of 4)	non-coding (NR_015529, exon 1 of 4)	124	NR_110355	97423	Mm.5250	NM_133790	ENSMUSG00000059277	R74862	-	expressed sequence R74862	ncRNA
mm_124360.1	chr14	105177254	105177261	-	1	NA	promoter-TSS (NM_134077)	promoter-TSS (NM_134077)	70	NM_134077	74213	Mm.474531	NM_134077	ENSMUSG00000022119	Rbm26	1700009P03Rik|AI447318|C230097K14Rik|C86225|MLZ-393|Pro1777|Se70-2	RNA binding motif protein 26	protein-coding
mm_20992.1	chr2	152332200	152332213	-	1	NA	5' UTR (NM_001083921, exon 1 of 12)	5' UTR (NM_001083921, exon 1 of 12)	219	NM_001083921	24105	Mm.182145	NM_019705	ENSMUSG00000027466	Rbck1	AL033326|HOIL-1|HOIL-1L|UIP28|Ubce7ip3	RanBP-type and C3HC4-type zinc finger containing 1	protein-coding
mm_30272.1	chr3	146812872	146812920	-	1	NA	promoter-TSS (NM_011100)	promoter-TSS (NM_011100)	50	NM_011100	18749	Mm.16766	NM_011100	ENSMUSG00000005034	Prkacb	CbPKA|Pkacb	protein kinase, cAMP dependent, catalytic, beta	protein-coding
mm_84196.1	chr9	60598931	60598942	-	1	NA	intron (NM_001311095, intron 13 of 15)	B4A|SINE|B4	-53054	NR_040463	100504561	Mm.410770	NR_040463	ENSMUSG00000111761	9230112J17Rik	-	RIKEN cDNA 9230112J17 gene	ncRNA
mm_117580.1	chr13	88821775	88821795	-	1	NA	5' UTR (NM_001037987, exon 1 of 11)	5' UTR (NM_001037987, exon 1 of 11)	313	NM_001037987	13612	Mm.125580	NM_010103	ENSMUSG00000034488	Edil3	Del-1|Del1	EGF-like repeats and discoidin I-like domains 3	protein-coding
mm_162060.1	chrX	8986758	8986758	-	1	NA	promoter-TSS (NM_001099326)	promoter-TSS (NM_001099326)	-86	NM_001099326	100042782	Mm.388703	NM_001099326	ENSMUSG00000078206	Fthl17d	Fthl17L3|Gm14458|OTTMUSG00000016694	ferritin, heavy polypeptide-like 17, member D	protein-coding
mm_71013.1	chr8	31187318	31187357	+	1	NA	promoter-TSS (NM_001286425)	promoter-TSS (NM_001286425)	6	NM_001286425	171167	Mm.334477	NM_134161	ENSMUSG00000046152	Fut10	fuc-TX|fut10A	fucosyltransferase 10	protein-coding
mm_70674.1	chr8	14911705	14911742	+	1	NA	promoter-TSS (NM_001037736)	promoter-TSS (NM_001037736)	60	NM_001037736	234094	Mm.240298	NM_172751	ENSMUSG00000071176	Arhgef10	6430549H08Rik|mKIAA0294	Rho guanine nucleotide exchange factor (GEF) 10	protein-coding
mm_121641.1	chr14	8378891	8378897	-	1	NA	promoter-TSS (NM_146050)	promoter-TSS (NM_146050)	-131	NM_146050	18300	Mm.25351	NM_146050	ENSMUSG00000021749	Oit1	2310076N21Rik|AV067083|EF-7|Fam3d	oncoprotein induced transcript 1	protein-coding
mm_60225.1	chr7	43579695	43579764	+	1	NA	5' UTR (NM_172482, exon 1 of 4)	5' UTR (NM_172482, exon 1 of 4)	143	NM_172482	210105	Mm.234422	NM_172482	ENSMUSG00000030469	Zfp719	8030458J18|9430094P17Rik|C630016O21Rik|mszf6	zinc finger protein 719	protein-coding
mm_102961.1	chr11	69665358	69665365	-	1	NA	non-coding (NR_110993, exon 2 of 5)	non-coding (NR_110993, exon 2 of 5)	809	NM_001291058	12514	Mm.15819	NM_009853	ENSMUSG00000018774	Cd68	Lamp4|Scard1|gp110	CD68 antigen	protein-coding
mm_44592.1	chr5	24995749	24995759	-	1	NA	promoter-TSS (NM_001310480)	promoter-TSS (NM_001310480)	-1	NM_001310480	108099	Mm.33649	NM_145401	ENSMUSG00000028944	Prkag2	2410051C13Rik|AAKG|AAKG2|AI854673|H91620p|WPWS	protein kinase, AMP-activated, gamma 2 non-catalytic subunit	protein-coding
mm_98186.1	chr11	87793471	87793483	+	1	NA	promoter-TSS (NM_010824)	promoter-TSS (NM_010824)	-307	NM_010824	17523	Mm.4668	NM_010824	ENSMUSG00000009350	Mpo	mKIAA4033	myeloperoxidase	protein-coding
mm_7377.1	chr1	107052332	107052345	-	1	NA	promoter-TSS (NM_009126)	promoter-TSS (NM_009126)	-35	NM_009126	20248	Mm.482944	NM_009126	ENSMUSG00000044594	Serpinb3a	1110001H02Rik|1110013A16Rik|Scca2|Serpinb4|Sqn5	serine (or cysteine) peptidase inhibitor, clade B (ovalbumin), member 3A	protein-coding
mm_23623.1	chr3	65958308	65958335	+	1	NA	promoter-TSS (NM_019937)	promoter-TSS (NM_019937)	-96	NM_019937	56706	Mm.175612	NM_019937	ENSMUSG00000027829	Ccnl1	2610030E23Rik|AU018493|Ccnl|ania-6a	cyclin L1	protein-coding
mm_37903.1	chr4	132732515	132732558	-	1	NA	promoter-TSS (NM_201368)	promoter-TSS (NM_201368)	10	NM_201368	381560	Mm.44558	NM_201368	ENSMUSG00000037752	Xkr8	4931440N07Rik|AI597014|Gm1031|XRG8|mXkr8	X-linked Kx blood group related 8	protein-coding
mm_11698.1	chr2	35978844	35978861	+	1	NA	intron (NM_029774, intron 1 of 9)	MIR3|SINE|MIR	772	NM_029774	74410	Mm.21591	NM_028921	ENSMUSG00000026885	Ttll11	4932702F08Rik|4933424A20Rik|AU043211|D2Ertd624e	tubulin tyrosine ligase-like family, member 11	protein-coding
mm_155340.1	chrX	68495397	68495420	+	1	NA	Intergenic	Intergenic	182991	NR_033481	100038638	Mm.368431	NR_033481	ENSMUSG00000096946	Fmr1os	Asfmr1|ENSMUSG00000073146|Gm10474	fragile X mental retardation syndrome 1, opposite strand	ncRNA
mm_33476.1	chr4	130818728	130818743	+	1	NA	exon (NM_011520, exon 3 of 5)	exon (NM_011520, exon 3 of 5)	26198	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_161604.1	chr16	43762056	43762056	+	1	NA	promoter-TSS (NM_007877)	promoter-TSS (NM_007877)	-165	NM_007877	13490	Mm.439735	NM_007877	ENSMUSG00000022705	Drd3	D3R	dopamine receptor D3	protein-coding
mm_97488.1	chr11	78325934	78325943	+	1	NA	exon (NM_009657, exon 7 of 8)	exon (NM_009657, exon 7 of 8)	1740	NM_009657	11676	Mm.7729	NM_009657	ENSMUSG00000017390	Aldoc	AI847350|AU040929|Aldo3|Scrg2	aldolase C, fructose-bisphosphate	protein-coding
mm_62441.1	chr7	101378184	101378210	+	1	NA	promoter-TSS (NM_001040112)	promoter-TSS (NM_001040112)	75	NM_001040112	69710	Mm.277687	NM_027180	ENSMUSG00000032812	Arap1	2410002L19Rik|Centd2|mKIAA0782	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	protein-coding
mm_76167.1	chr8	82380302	82380321	-	1	NA	intron (NM_001254747, intron 1 of 7)	intron (NM_001254747, intron 1 of 7)	22275	NM_001254747	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_67818.1	chr7	98178140	98178232	-	1	NA	promoter-TSS (NM_007602)	promoter-TSS (NM_007602)	88	NM_007602	12337	Mm.326847	NM_007602	ENSMUSG00000035547	Capn5	nCL-3	calpain 5	protein-coding
mm_24438.1	chr3	90589708	90589717	+	1	NA	promoter-TSS (NM_001195760)	promoter-TSS (NM_001195760)	-535	NM_001195760	628324	Mm.33816	NM_001195760	ENSMUSG00000094018	S100a2	CaN19|EG628324|S100L	S100 calcium binding protein A2	protein-coding
mm_64704.1	chr7	4547525	4547535	-	1	NA	promoter-TSS (NM_016908)	promoter-TSS (NM_016908)	-963	NM_016908	53420	Mm.358663	NM_016908	ENSMUSG00000004961	Syt5	SytV	synaptotagmin V	protein-coding
mm_104373.1	chr11	94365420	94365426	-	1	NA	intron (NM_029600, intron 11 of 30)	intron (NM_029600, intron 11 of 30)	27553	NM_029600	76408	Mm.23942	NM_029600	ENSMUSG00000020865	Abcc3	1700019L09Rik|ABC31|MLP2|MOAT-D|MRP3	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	protein-coding
mm_112774.1	chr13	19623334	19623340	+	1	NA	5' UTR (NM_016687, exon 1 of 6)	5' UTR (NM_016687, exon 1 of 6)	162	NM_016687	20379	Mm.42095	NM_016687	ENSMUSG00000021319	Sfrp4	-	secreted frizzled-related protein 4	protein-coding
mm_98157.1	chr11	87617254	87617258	+	1	NA	promoter-TSS (NM_001045527)	promoter-TSS (NM_001045527)	92	NM_001045527	327992	Mm.390371	NM_001045527	ENSMUSG00000070345	Hsf5	Gm739|MLZ-220	heat shock transcription factor family member 5	protein-coding
mm_33459.1	chr4	130792481	130792508	+	1	NA	promoter-TSS (NM_011520)	promoter-TSS (NM_011520)	-43	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_76895.1	chr8	105758571	105758657	-	1	NA	promoter-TSS (NM_027469)	promoter-TSS (NM_027469)	-7	NM_027469	70575	Mm.40954	NM_027469	ENSMUSG00000013150	Gfod2	5730466C23Rik	glucose-fructose oxidoreductase domain containing 2	protein-coding
mm_49097.1	chr6	7844807	7844859	+	1	NA	promoter-TSS (NM_052993)	promoter-TSS (NM_052993)	-391	NM_052993	94192	Mm.102752	NM_052993	ENSMUSG00000042460	C1galt1	2210410E06Rik|AV284120|T-synthase	core 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase, 1	protein-coding
mm_61455.1	chr7	75586387	75586412	+	1	NA	intron (NM_029332, intron 5 of 36)	intron (NM_029332, intron 5 of 36)	130865	NM_029332	75547	Mm.216107	NM_029332	ENSMUSG00000066406	Akap13	1700026G02Rik|5730522G15Rik|5830460E08Rik|AKAP-13|AKAP-Lbc|BRX|Ht31|LBC|PROTO-LB|PROTO-LBC	A kinase (PRKA) anchor protein 13	protein-coding
mm_134658.1	chr16	22076106	22076126	-	1	NA	exon (NM_183029, exon 10 of 16)	exon (NM_183029, exon 10 of 16)	66632	NR_027488	75826	Mm.297431	NM_029457	ENSMUSG00000022855	Senp2	2310007L05Rik|4930538C18Rik|AI646780|AW554757|Smt3ip2|SuPr-1|mKIAA1331	SUMO/sentrin specific peptidase 2	protein-coding
mm_3974.1	chr1	164193442	164193465	+	1	NA	exon (NM_007976, exon 13 of 25)	exon (NM_007976, exon 13 of 25)	-41236	NR_037987	100503816	Mm.398579	NR_037987	ENSMUSG00000086593	Gm16548	-	predicted gene 16548	ncRNA
mm_26325.1	chr3	142533481	142533483	+	1	NA	intron (NM_001083312, intron 1 of 10)	L1_Mur2|LINE|L1	3146	NM_145545	229900	Mm.45740	NM_145545	ENSMUSG00000040253	Gbp7	9830147J24Rik	guanylate binding protein 7	protein-coding
mm_93273.1	chr10	95825152	95825155	-	1	NA	Intergenic	Intergenic	-115510	NM_001001932	216238	Mm.210035	NM_001001932	ENSMUSG00000036499	Eea1	A430109M19Rik|B230358H09Rik|ZFYVE2	early endosome antigen 1	protein-coding
mm_36259.1	chr4	63418702	63418711	-	1	NA	intron (NM_001008791, intron 9 of 12)	intron (NM_001008791, intron 9 of 12)	-15261	NM_001045514	100182	Mm.387725	NM_001045514	ENSMUSG00000039158	Akna	AI597013	AT-hook transcription factor	protein-coding
mm_102754.1	chr11	67298497	67298533	-	1	NA	exon (NM_177369, exon 27 of 40)	exon (NM_177369, exon 27 of 40)	21391	NM_177369	17885	Mm.340163	NM_177369	ENSMUSG00000055775	Myh8	4832426G23Rik|AI327267|MHCp|MyHC-pn|Myhs-p|Myhsp	myosin, heavy polypeptide 8, skeletal muscle, perinatal	protein-coding
mm_76796.1	chr8	102786632	102786651	-	1	NA	Intergenic	Intergenic	-1530	NM_009866	12552	Mm.1571	NM_009866	ENSMUSG00000031673	Cdh11	Cad11|OSF-4	cadherin 11	protein-coding
mm_172025.1	chr6	122770253	122770263	-	1	NA	Intergenic	Intergenic	-27513	NM_011401	20527	Mm.395108	NM_011401	ENSMUSG00000003153	Slc2a3	AA408729|AL023014|AL024341|AU040424|C78366|Glut-3|Glut3	solute carrier family 2 (facilitated glucose transporter), member 3	protein-coding
mm_51357.1	chr6	72606392	72606394	+	1	NA	exon (NM_026159, exon 8 of 11)	exon (NM_026159, exon 8 of 11)	7765	NM_026159	67442	Mm.305108	NM_026159	ENSMUSG00000056666	Retsat	0610039N19Rik|C80029|MMT-7|Ppsig	retinol saturase (all trans retinol 13,14 reductase)	protein-coding
mm_163733.1	chr13	119680039	119680059	+	1	NA	promoter-TSS (NR_138420)	promoter-TSS (NR_138420)	7	NR_138420	73480	Mm.71100	NR_045296	ENSMUSG00000099872	1700074H08Rik	CH25-211A23.1	RIKEN cDNA 1700074H08 gene	ncRNA
mm_90082.1	chr10	116581590	116581607	+	1	NA	promoter-TSS (NM_028082)	promoter-TSS (NM_028082)	-87	NM_001037846	72068	Mm.351553	NM_028082	ENSMUSG00000020166	Cnot2	2600016M12Rik|2810470K03Rik|AA537049|AA959607|AW557563|C79650	CCR4-NOT transcription complex, subunit 2	protein-coding
mm_13450.1	chr2	105372974	105373010	+	1	NA	intron (NM_001159638, intron 2 of 2)	intron (NM_001159638, intron 2 of 2)	26327	NM_009037	19672	Mm.4876	NM_009037	ENSMUSG00000005973	Rcn1	Rcn	reticulocalbin 1	protein-coding
mm_19854.1	chr2	113828745	113828774	-	1	NA	intron (NM_009162, intron 1 of 5)	intron (NM_009162, intron 1 of 5)	332	NM_009162	20394	Mm.4836	NM_009162	ENSMUSG00000023236	Scg5	7B2|AI325031|Sgne-1|Sgne1	secretogranin V	protein-coding
mm_49666.1	chr6	31220433	31220464	+	1	NA	promoter-TSS (NR_040262)	promoter-TSS (NR_040262)	97	NR_040261	73652	Mm.441297	NR_040257	ENSMUSG00000087380	2210408F21Rik	-	RIKEN cDNA 2210408F21 gene	ncRNA
mm_112271.1	chr12	114196925	114196937	-	1	NA	Intergenic	Intergenic	272535	NR_106062	102465663		NR_106062	ENSMUSG00000105438	Mir7094-1	mmu-mir-7094-1	microRNA 7094-1	ncRNA
mm_54987.1	chr6	48747536	48747547	-	1	NA	intron (NM_175035, intron 1 of 2)	intron (NM_175035, intron 1 of 2)	1344	NM_175035	317757	Mm.455917	NM_175035	ENSMUSG00000043505	Gimap5	D630024P16|E230026N22Rik	GTPase, IMAP family member 5	protein-coding
mm_37896.1	chr4	132608298	132608313	-	1	NA	Intergenic	ID_B1|SINE|B4	-30741	NM_210071	14050	Mm.227733	NM_010166	ENSMUSG00000028886	Eya3	AI844637	EYA transcriptional coactivator and phosphatase 3	protein-coding
mm_154739.1	chrX	10254420	10254420	+	1	NA	intron (NM_008769, intron 1 of 9)	intron (NM_008769, intron 1 of 9)	2115	NM_008769	18416	Mm.2611	NM_008769	ENSMUSG00000031173	Otc	AI265390|Sf|spf	ornithine transcarbamylase	protein-coding
mm_143417.1	chr17	70840911	70840956	-	1	NA	Intergenic	Intergenic	5844	NM_001164077	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_128504.1	chr15	53068561	53068582	-	1	NA	3' UTR (NM_010162, exon 11 of 11)	3' UTR (NM_010162, exon 11 of 11)	277612	NM_010162	14042	Mm.309395	NM_010162	ENSMUSG00000061731	Ext1	AA409028	exostoses (multiple) 1	protein-coding
mm_119968.1	chr14	55510594	55510631	+	1	NA	promoter-TSS (NM_009947)	promoter-TSS (NM_009947)	164	NM_001136057	12891	Mm.5249	NM_009947	ENSMUSG00000022212	Cpne6	AU067659|BB076446	copine VI	protein-coding
mm_38368.1	chr4	138367953	138367965	-	1	NA	promoter-TSS (NM_028176)	promoter-TSS (NM_028176)	-4	NM_028176	72269	Mm.46182	NM_028176	ENSMUSG00000028755	Cda	2210401N16Rik	cytidine deaminase	protein-coding
mm_56380.1	chr6	94283742	94283791	-	1	NA	5' UTR (NM_010367, exon 1 of 22)	5' UTR (NM_010367, exon 1 of 22)	151	NM_001286786	14924	Mm.217216	NM_010367	ENSMUSG00000045095	Magi1	AIP3|BAP1|Baiap1|Gukmi1|MAGI1c|Magi-1|TNRC19|WWP3|mKIAA4129	membrane associated guanylate kinase, WW and PDZ domain containing 1	protein-coding
mm_48972.1	chr6	4754132	4754145	+	1	NA	5' UTR (NM_130877, exon 2 of 2)	5' UTR (NM_130877, exon 2 of 2)	6832	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_155972.1	chrX	106125515	106125526	+	1	NA	3' UTR (NM_009726, exon 23 of 23)	3' UTR (NM_009726, exon 23 of 23)	-17755	NM_205820	279572	Mm.336203	NM_205820	ENSMUSG00000033777	Tlr13	AI666735|Gm713	toll-like receptor 13	protein-coding
mm_72000.1	chr8	70659966	70659980	+	1	NA	promoter-TSS (NM_023217)	promoter-TSS (NM_023217)	-235	NM_023217	66522	Mm.154906	NM_023217	ENSMUSG00000056204	Pgpep1	2810003H13Rik|Gm19458|PAP-I|PGP|PGP-I|PGPI|Pcp	pyroglutamyl-peptidase I	protein-coding
mm_85033.1	chr9	88480280	88480288	-	1	NA	intron (NM_001311113, intron 1 of 10)	intron (NM_001311113, intron 1 of 10)	2113	NM_019666	56403	Mm.260545	NM_019666	ENSMUSG00000032423	Syncrip	2610109K23Rik|4632417O19Rik|GRY-RBP|Nsap1|Nsap1l|hnRNP Q|pp68	synaptotagmin binding, cytoplasmic RNA interacting protein	protein-coding
mm_21752.1	chr2	164833439	164833480	-	1	NA	promoter-TSS (NM_008906)	promoter-TSS (NM_008906)	137	NM_001082974	415115	Mm.474586	NM_001082974	ENSMUSG00000039873	Neurl2	Neur2|Ozz|Ozz-E3	neuralized E3 ubiquitin protein ligase 2	protein-coding
mm_116872.1	chr13	55019131	55019140	-	1	NA	intron (NM_001206392, intron 1 of 17)	intron (NM_001206392, intron 1 of 17)	1684	NM_001206390	212032	Mm.267479	NM_001033245	ENSMUSG00000025877	Hk3	HK III|HK-III	hexokinase 3	protein-coding
mm_110410.1	chr12	45099455	45099463	-	1	NA	Intergenic	Intergenic	-24976	NM_144552	217517	Mm.285400	NM_144552	ENSMUSG00000046314	Stxbp6	BC024598|C85317	syntaxin binding protein 6 (amisyn)	protein-coding
mm_122011.1	chr14	27237939	27237949	-	1	NA	promoter-TSS (NM_027871)	promoter-TSS (NM_027871)	-66	NM_027871	71704	Mm.248606	NM_027871	ENSMUSG00000021895	Arhgef3	1200004I24Rik|9830169H03Rik|C76747|Xpln	Rho guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_47934.1	chr5	135132463	135132467	-	1	NA	exon (NM_021455, exon 9 of 17)	exon (NM_021455, exon 9 of 17)	-17246	NM_013763	27368	Mm.36746	NM_013763	ENSMUSG00000005374	Tbl2	C76179|WS-bTRP	transducin (beta)-like 2	protein-coding
mm_86449.1	chr10	4314613	4314624	+	1	NA	intron (NM_031185, intron 2 of 3)	intron (NM_031185, intron 2 of 3)	48289	NM_031185	83397	Mm.27481	NM_031185	ENSMUSG00000038587	Akap12	AI317366|SSeCKS|Srcs5|Tsga12	A kinase (PRKA) anchor protein (gravin) 12	protein-coding
mm_169125.1	chr13	54190043	54190049	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-2083	NM_001010973	15466	Mm.57243	NM_008286	ENSMUSG00000034987	Hrh2	-	histamine receptor H2	protein-coding
mm_137468.1	chr17	26676388	26676388	+	1	NA	promoter-TSS (NM_025272)	promoter-TSS (NM_025272)	-8	NM_025272	11974	Mm.22602	NM_025272	ENSMUSG00000015575	Atp6v0e	Atp6k|Atp6v0e1|M9.2	ATPase, H+ transporting, lysosomal V0 subunit E	protein-coding
mm_125587.1	chr15	59618685	59618715	+	1	NA	Intergenic	MTEb|LTR|ERVL-MaLR	-29954	NM_144549	211770	Mm.40298	NM_144549	ENSMUSG00000032501	Trib1	A530090O15Rik|TRB-1|Trb1	tribbles pseudokinase 1	protein-coding
mm_8068.1	chr1	135470763	135470780	-	1	NA	exon (NM_173437, exon 6 of 29)	exon (NM_173437, exon 6 of 29)	-16088	NR_049188	100885827		NR_049188	ENSMUSG00000093515	Mir1231	Gm23720|mir-1231|mmu-mir-1231	microRNA 1231	ncRNA
mm_68848.1	chr7	126368569	126368588	-	1	NA	promoter-TSS (NR_106025)	promoter-TSS (NR_106025)	-533	NR_106025	102466797		NR_106025	ENSMUSG00000099017	Mir7058	Gm27766|mmu-mir-7058	microRNA 7058	ncRNA
mm_98112.1	chr11	87109222	87109239	+	1	NA	promoter-TSS (NM_175563)	promoter-TSS (NM_175563)	-31	NM_025377	66140	Mm.45008	NM_025377	ENSMUSG00000020492	Ska2	1110001A07Rik|C78640|Fam33a	spindle and kinetochore associated complex subunit 2	protein-coding
mm_165205.1	chr2	34774021	34774048	+	1	NA	exon (NM_001163434, exon 6 of 9)	exon (NM_001163434, exon 6 of 9)	1944	NM_022310	14828	Mm.330160	NM_022310	ENSMUSG00000026864	Hspa5	AL022860|AU019543|Bip|D2Wsu141e|D2Wsu17e|Grp78|Hsce70|SEZ-7|Sez7|baffled|mBiP	heat shock protein 5	protein-coding
mm_33255.1	chr4	127168656	127168682	+	1	NA	promoter-TSS (NM_198618)	promoter-TSS (NM_198618)	-535	NM_198618	242667	Mm.331885	NM_198618	ENSMUSG00000042388	Dlgap3	BC058433|DAP-3|DAP3|Prpl8|Sapap3	discs, large (Drosophila) homolog-associated protein 3	protein-coding
mm_163235.1	chr11	103964044	103964054	-	1	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	-2676	NM_001304574	11841	Mm.5061	NM_007477	ENSMUSG00000062421	Arf2	-	ADP-ribosylation factor 2	protein-coding
mm_117494.1	chr13	78198772	78198788	-	1	NA	promoter-TSS (NM_010151)	promoter-TSS (NM_010151)	93	NM_010151	13865	Mm.439653	NM_010151	ENSMUSG00000069171	Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR-3|EAR3|Erbal3|SVP44|Tcfcoup1	nuclear receptor subfamily 2, group F, member 1	protein-coding
mm_11412.1	chr2	31572776	31572841	+	1	NA	5' UTR (NM_001290548, exon 1 of 19)	5' UTR (NM_001290548, exon 1 of 19)	157	NM_001290548	320267	Mm.207261	NM_001033389	ENSMUSG00000026843	Fubp3	A330051M14Rik|AV006371|FBP3|Marta2	far upstream element (FUSE) binding protein 3	protein-coding
mm_94042.1	chr10	128176440	128176465	-	1	NA	5' UTR (NM_019711, exon 1 of 13)	5' UTR (NM_019711, exon 1 of 13)	116	NM_019711	56516	Mm.42247	NM_019711	ENSMUSG00000040043	Rbms2	2610315E04Rik|Scr3	RNA binding motif, single stranded interacting protein 2	protein-coding
mm_107987.1	chr12	73123695	73123705	+	1	NA	promoter-TSS (NM_008612)	promoter-TSS (NM_008612)	-17	NM_008612	17420	Mm.246750	NM_008612	ENSMUSG00000021103	Mnat1	E130115E11Rik|MAT1|P36	menage a trois 1	protein-coding
mm_118497.1	chr14	13453972	13454005	+	1	NA	promoter-TSS (NM_001163032)	promoter-TSS (NM_001163032)	30	NM_001163032	72003	Mm.317515	NM_028052	ENSMUSG00000056296	Synpr	1500003F20Rik|SPO	synaptoporin	protein-coding
mm_172210.1	chr6	59199642	59199643	+	1	NA	Intergenic	Intergenic	-9228	NM_001081145	68140	Mm.25843	NM_001081145	ENSMUSG00000049232	Tigd2	3632410O17Rik	tigger transposable element derived 2	protein-coding
mm_68686.1	chr7	119459267	119459280	-	1	NA	promoter-TSS (NM_025989)	promoter-TSS (NM_025989)	-1	NM_025989	67133	Mm.46403	NM_025989	ENSMUSG00000030954	Gp2	2310037I18Rik|AV060639	glycoprotein 2 (zymogen granule membrane)	protein-coding
mm_149714.1	chr19	21653429	21653445	+	1	NA	promoter-TSS (NM_025423)	promoter-TSS (NM_025423)	128	NM_146096	226016	Mm.28796	NM_146096	ENSMUSG00000047368	Abhd17b	5730446C15Rik|Cgi67|Fam108b|Fam108b1	abhydrolase domain containing 17B	protein-coding
mm_24645.1	chr3	94385680	94385682	+	1	NA	intron (NR_121656, intron 1 of 9)	tRNA-Ala-GCY_|tRNA|tRNA	8249	NR_121656	19885	Mm.4372	NM_011281	ENSMUSG00000028150	Rorc	Nr1f3|RORgamma|TOR|Thor	RAR-related orphan receptor gamma	protein-coding
mm_144382.1	chr18	20666541	20666551	+	1	NA	exon (NM_013697, exon 2 of 4)	exon (NM_013697, exon 2 of 4)	1296	NM_013697	22139	Mm.2108	NM_013697	ENSMUSG00000061808	Ttr	AA408768|AI787086|D17860|prealbumin	transthyretin	protein-coding
mm_74778.1	chr8	21970423	21970467	-	1	NA	promoter-TSS (NM_026459)	promoter-TSS (NM_026459)	-151	NM_026459	67929	Mm.60688	NM_026459	ENSMUSG00000017049	Ccdc70	1700112P19Rik	coiled-coil domain containing 70	protein-coding
mm_155999.1	chrX	106187138	106187179	+	1	NA	promoter-TSS (NM_008828)	promoter-TSS (NM_008828)	58	NM_008828	18655	Mm.316355	NM_008828	ENSMUSG00000062070	Pgk1	Pgk-1	phosphoglycerate kinase 1	protein-coding
mm_39692.1	chr5	26904897	26904914	+	1	NA	5' UTR (NM_001198886, exon 1 of 26)	5' UTR (NM_001198886, exon 1 of 26)	127	NM_001198886	13483	Mm.42078	NM_010075	ENSMUSG00000061576	Dpp6	B930011P16Rik|D5Buc3|D5Buc4|D5Buc5|DPP VI|Dpp-6|Gm1377|In(5)6H-p|Peplb|Rw	dipeptidylpeptidase 6	protein-coding
mm_158213.1	chrX	105875501	105875517	-	1	NA	exon (NM_009530, exon 9 of 35)	exon (NM_009530, exon 9 of 35)	53863	NM_009530	22589	Mm.10141	NM_009530	ENSMUSG00000031229	Atrx	4833408C14Rik|AI447451|ATR2|DXHXS6677E|HP1-BP38|Hp1bp2|Hp1bp38|MRXS3|RAD54L|Rad54|XH2|Xnp|ZNF-HX	alpha thalassemia/mental retardation syndrome X-linked	protein-coding
mm_153432.1	chr19	40954024	40954033	-	1	NA	intron (NM_008528, intron 6 of 16)	intron (NM_008528, intron 6 of 16)	40507	NM_008528	17060	Mm.9749	NM_008528	ENSMUSG00000061132	Blnk	BASH|Bca|Ly-57|Ly57|Lyw-57|SLP-65	B cell linker	protein-coding
mm_36802.1	chr4	103173410	103173417	-	1	NA	3' UTR (NM_177732, exon 10 of 10)	3' UTR (NM_177732, exon 10 of 10)	41471	NM_177732	242585	Mm.281800	NM_177732	ENSMUSG00000028521	Slc35d1	AI834976|C330011J09|UGTREL7|mKIAA0260	solute carrier family 35 (UDP-glucuronic acid/UDP-N-acetylgalactosamine dual transporter), member D1	protein-coding
mm_103591.1	chr11	78245943	78245977	-	1	NA	promoter-TSS (NM_009297)	promoter-TSS (NM_009297)	214	NM_009143	20316	Mm.20755	NM_009143	ENSMUSG00000002064	Sdf2	AI853825	stromal cell derived factor 2	protein-coding
mm_139302.1	chr17	48346499	48346526	+	1	NA	5' UTR (NM_031254, exon 1 of 5)	5' UTR (NM_031254, exon 1 of 5)	111	NM_001272078	83433	Mm.261623	NM_031254	ENSMUSG00000023992	Trem2	TREM-2|Trem2a|Trem2b|Trem2c	triggering receptor expressed on myeloid cells 2	protein-coding
mm_70212.1	chr7	144930000	144930021	-	1	NA	TTS (NM_007631)	TTS (NM_007631)	2125	NR_039539	100628615		NR_039539	ENSMUSG00000092633	Mir3962	mmu-mir-3962|mu-mir-3962	microRNA 3962	ncRNA
mm_94386.1	chr11	5520971	5520989	+	1	NA	5' UTR (NM_001271730, exon 1 of 6)	5' UTR (NM_001271730, exon 1 of 6)	339	NM_001271730	22433	Mm.469937	NM_013842	ENSMUSG00000020484	Xbp1	D11Ertd39e|TREB-5|TREB5|XBP-1	X-box binding protein 1	protein-coding
mm_127393.1	chr15	101128526	101128536	+	1	NA	promoter-TSS (NM_001277259)	promoter-TSS (NM_001277259)	9	NM_001277257	11482	Mm.279542	NM_009612	ENSMUSG00000000530	Acvrl1	AI115505|AI427544|Acvrlk1|Alk1	activin A receptor, type II-like 1	protein-coding
mm_116273.1	chr13	34653084	34653114	-	1	NA	promoter-TSS (NM_025831)	promoter-TSS (NM_025831)	176	NR_105041	101056149	Mm.421309	NR_105041	ENSMUSG00000086786	Gm15908	OTTMUSG00000027716	predicted gene 15908	ncRNA
mm_89217.1	chr10	86779047	86779068	+	1	NA	promoter-TSS (NM_175331)	promoter-TSS (NM_175331)	52	NM_175331	103466	Mm.200446	NM_175331	ENSMUSG00000054027	Nt5dc3	AU040402|AW540062|C630002B14Rik|TU12B1-TY	5'-nucleotidase domain containing 3	protein-coding
mm_128365.1	chr15	41869704	41869727	-	1	NA	promoter-TSS (NM_175456)	promoter-TSS (NM_175456)	5	NM_175456	223513	Mm.148913	NM_175456	ENSMUSG00000042895	Abra	C130068O12Rik|STARS	actin-binding Rho activating protein	protein-coding
mm_121515.1	chr14	122012008	122012018	+	1	NA	intron (NM_026861, intron 8 of 8)	intron (NM_026861, intron 8 of 8)	-22661	NM_001037744	223262	Mm.297637	NM_001037744	ENSMUSG00000071229	Timm8a2	-	translocase of inner mitochondrial membrane 8A2	protein-coding
mm_128838.1	chr15	68363140	68363160	-	1	NA	Intergenic	Intergenic	-21861	NR_029718	387228		NR_029718	ENSMUSG00000065437	Mir30d	Mirn30d|mir-30d|mmu-mir-30d	microRNA 30d	ncRNA
mm_5904.1	chr1	54926294	54926304	-	1	NA	promoter-TSS (NM_001081433)	promoter-TSS (NM_001081433)	88	NM_001081433	329154	Mm.397910	NM_001081433	ENSMUSG00000052331	Ankrd44	4930444A19Rik|A130096K20|E130014H08Rik|PP6-ARS-B	ankyrin repeat domain 44	protein-coding
mm_156939.1	chrX	169916154	169916156	+	1	NA	intron (NM_001290506, intron 1 of 9)	intron (NM_001290506, intron 1 of 9)	36536	NM_001290505	17318	Mm.34441	NM_010797	ENSMUSG00000035299	Mid1	61B3-R|DXHXS1141|Fxy|Trim18	midline 1	protein-coding
mm_126549.1	chr15	82059138	82059140	+	1	NA	promoter-TSS (NM_001166475)	promoter-TSS (NM_001166475)	-12	NM_001166475	328573	Mm.399189	NM_001166475	ENSMUSG00000075524	4930407I10Rik	Gm747	RIKEN cDNA 4930407I10 gene	protein-coding
mm_68034.1	chr7	101301700	101301711	-	1	NA	intron (NM_001111111, intron 1 of 17)	intron (NM_001111111, intron 1 of 17)	383	NM_001111111	73683	Mm.275744	NM_001111111	ENSMUSG00000047767	Atg16l2	2410118P20Rik	autophagy related 16-like 2 (S. cerevisiae)	protein-coding
mm_136665.1	chr17	6106522	6106563	+	1	NA	promoter-TSS (NM_001103181)	promoter-TSS (NM_001103181)	-288	NM_001103181	68842	Mm.449307	NM_054040	ENSMUSG00000034377	Tulp4	1110057P05Rik|2210038L17Rik|Tusp	tubby like protein 4	protein-coding
mm_19957.1	chr2	117342901	117342909	-	1	NA	promoter-TSS (NM_011246)	promoter-TSS (NM_011246)	-28	NM_011246	19419	Mm.42150	NM_011246	ENSMUSG00000027347	Rasgrp1	Rasgrp	RAS guanyl releasing protein 1	protein-coding
mm_83848.1	chr9	54501648	54501683	-	1	NA	promoter-TSS (NM_172771)	promoter-TSS (NM_172771)	-39	NM_172771	235380	Mm.93636	NM_172771	ENSMUSG00000041268	Dmxl2	6330586A12|6430411K14Rik|E130119P06Rik|mKIAA0856	Dmx-like 2	protein-coding
mm_71939.1	chr8	70329908	70329929	+	1	NA	5' UTR (NM_001163282, exon 7 of 8)	5' UTR (NM_001163282, exon 7 of 8)	153	NM_008107	14559	Mm.258280	NM_008107	ENSMUSG00000087408	Gdf1	AI385651|Gdf-1	growth differentiation factor 1	protein-coding
mm_72883.1	chr8	89012618	89012655	+	1	NA	Intergenic	Intergenic	-12099	NR_106190	102465899		NR_106190	ENSMUSG00000099078	Mir8110	Gm27571|mmu-mir-8110	microRNA 8110	ncRNA
mm_119103.1	chr14	30951432	30951450	+	1	NA	promoter-TSS (NM_001308328)	promoter-TSS (NM_001308328)	64	NM_011849	23955	Mm.251494	NM_011849	ENSMUSG00000021918	Nek4	Stk2	NIMA (never in mitosis gene a)-related expressed kinase 4	protein-coding
mm_85195.1	chr9	96731362	96731372	-	1	NA	TTS (NR_015511)	TTS (NR_015511)	308	NM_175537	245007	Mm.485954	NM_175537	ENSMUSG00000040433	Zbtb38	A930014K01Rik|CIBZ	zinc finger and BTB domain containing 38	protein-coding
mm_84988.1	chr9	86571094	86571116	-	1	NA	promoter-TSS (NM_001145969)	promoter-TSS (NM_001145969)	737	NM_001163746	109785	Mm.390201	NM_028352	ENSMUSG00000056131	Pgm3	2810473H05Rik|Agm1|BB187688|C77933|PAGM|Pgm-3	phosphoglucomutase 3	protein-coding
mm_110932.1	chr12	76370348	76370353	-	1	NA	promoter-TSS (NM_001172104)	promoter-TSS (NM_001172104)	84	NM_178744	268564	Mm.77065	NM_178744	ENSMUSG00000033454	Zbtb1	9430077A12|AI256369|Bsg2|C430003J21Rik	zinc finger and BTB domain containing 1	protein-coding
mm_39528.1	chr5	21278375	21278378	+	1	NA	intron (NM_175437, intron 24 of 30)	B4A|SINE|B4	92109	NM_175437	212167	Mm.121705	NM_175437	ENSMUSG00000039934	Gsap	A530088I07Rik|Pion	gamma-secretase activating protein	protein-coding
mm_130999.1	chr15	103448474	103448492	-	1	NA	promoter-TSS (NM_177631)	promoter-TSS (NM_177631)	-24	NM_177631	223927	Mm.243718	NM_177631	ENSMUSG00000053508	BC048502	-	cDNA sequence BC048502	protein-coding
mm_151802.1	chr19	5424823	5424845	-	1	NA	promoter-TSS (NM_001256515)	promoter-TSS (NM_001256515)	145	NM_024176	66556	Mm.275446	NM_024176	ENSMUSG00000024914	Drap1	2310074H19Rik|NC2-alpha	Dr1 associated protein 1 (negative cofactor 2 alpha)	protein-coding
mm_76225.1	chr8	83573064	83573070	-	1	NA	exon (NM_027179, exon 5 of 12)	exon (NM_027179, exon 5 of 12)	6309	NM_025843	66916	Mm.29683	NM_025843	ENSMUSG00000033938	Ndufb7	1110002H15Rik	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 7	protein-coding
mm_152796.1	chr19	21630735	21630741	-	1	NA	intron (NM_025423, intron 1 of 3)	intron (NM_025423, intron 1 of 3)	22053	NM_025423	66206	Mm.272430	NM_025423	ENSMUSG00000035171	1110059E24Rik	-	RIKEN cDNA 1110059E24 gene	protein-coding
mm_46853.1	chr5	113650570	113650580	-	1	NA	promoter-TSS (NM_008153)	promoter-TSS (NM_008153)	-185	NM_008153	14747	Mm.5196	NM_008153	ENSMUSG00000042190	Cmklr1	ChemR23|DEZ|Gpcr27|mcmklr1	chemokine-like receptor 1	protein-coding
mm_76323.1	chr8	84705127	84705138	-	1	NA	TTS (NM_008535)	TTS (NM_008535)	3675	NM_008535	17095	Mm.4925	NM_008535	ENSMUSG00000034041	Lyl1	Lyl-1|bHLHa18	lymphoblastomic leukemia 1	protein-coding
mm_8269.1	chr1	139436890	139436909	-	1	NA	intron (NM_172643, intron 5 of 10)	intron (NM_172643, intron 5 of 10)	14516	NM_172643	226470	Mm.119711	NM_172643	ENSMUSG00000033964	Zbtb41	8430415N23Rik|9430031N01|9830132G07Rik|AI316857	zinc finger and BTB domain containing 41	protein-coding
mm_95084.1	chr11	33203731	33203741	+	1	NA	promoter-TSS (NM_019916)	promoter-TSS (NM_019916)	-148	NM_019916	27140	Mm.25362	NM_019916	ENSMUSG00000040610	Tlx3	Hox11l2|Rnx|Tlx1l2	T cell leukemia, homeobox 3	protein-coding
mm_55201.1	chr6	52204416	52204463	-	1	NA	5' UTR (NM_010453, exon 1 of 2)	5' UTR (NM_010453, exon 1 of 2)	148	NM_010453	15402	Mm.173	NM_010453	ENSMUSG00000038253	Hoxa5	Hox-1.3	homeobox A5	protein-coding
mm_18359.1	chr2	58567022	58567032	-	1	NA	promoter-TSS (NM_001289660)	promoter-TSS (NM_001289660)	-199	NM_001110204	11477	Mm.689	NM_007394	ENSMUSG00000026836	Acvr1	ALK2|ActR-I|ActRIA|Acvr|Acvrlk2|Alk-2|Alk8|D330013D15Rik|SKR1|Tsk7L	activin A receptor, type 1	protein-coding
mm_93546.1	chr10	116113875	116113880	-	1	NA	promoter-TSS (NM_001161855)	promoter-TSS (NM_001161855)	40	NM_001161855	619332	Mm.391427	NM_001033821	ENSMUSG00000074734	4933416C03Rik	-	RIKEN cDNA 4933416C03 gene	protein-coding
mm_82494.1	chr9	18674759	18674771	-	1	NA	Intergenic	Intergenic	80868	NM_146606	18322	Mm.246530	NM_146606	ENSMUSG00000054141	Olfr24	MOR132-1|MTPCR51	olfactory receptor 24	protein-coding
mm_94383.1	chr11	5505965	5505982	+	1	NA	Intergenic	Intergenic	-14668	NM_013842	22433	Mm.469937	NM_013842	ENSMUSG00000020484	Xbp1	D11Ertd39e|TREB-5|TREB5|XBP-1	X-box binding protein 1	protein-coding
mm_76785.1	chr8	99446751	99446754	-	1	NA	intron (NR_132435, intron 1 of 4)	RMER19B|LTR|ERVK	30078	NR_132435	234624	Mm.124595	NM_175479	ENSMUSG00000052479	A330008L17Rik	-	RIKEN cDNA A330008L17 gene	ncRNA
mm_47251.1	chr5	121593553	121593603	-	1	NA	5' UTR (NM_001308450, exon 1 of 11)	5' UTR (NM_001308450, exon 1 of 11)	246	NM_009656	11669	Mm.284446	NM_009656	ENSMUSG00000029455	Aldh2	AHD-M1|ALDH-E2|ALDHI|Ahd-5|Ahd5	aldehyde dehydrogenase 2, mitochondrial	protein-coding
mm_69130.1	chr7	127026797	127026827	-	1	NA	promoter-TSS (NM_010772)	promoter-TSS (NM_010772)	-333	NM_010772	17188	Mm.378964	NM_010772	ENSMUSG00000030678	Maz	MAZI|PUR1|Pur-1|SAF-1|SAF-2	MYC-associated zinc finger protein (purine-binding transcription factor)	protein-coding
mm_2780.1	chr1	130826763	130826769	+	1	NA	promoter-TSS (NM_011082)	promoter-TSS (NM_011082)	82	NM_011082	18703	Mm.276414	NM_011082	ENSMUSG00000026417	Pigr	-	polymeric immunoglobulin receptor	protein-coding
mm_167125.1	chr7	123543492	123543495	+	1	NA	Intergenic	Intergenic	-43044	NM_001081329	210162	Mm.135397	NM_175435	ENSMUSG00000030757	Zkscan2	9430065N20Rik|AW493225|Zfp694	zinc finger with KRAB and SCAN domains 2	protein-coding
mm_41418.1	chr5	90876316	90876331	+	1	NA	Intergenic	Intergenic	-14922	NM_008176	14825	Mm.21013	NM_008176	ENSMUSG00000029380	Cxcl1	Fsp|Gro1|KC|Mgsa|N51|Scyb1|gro	chemokine (C-X-C motif) ligand 1	protein-coding
mm_75404.1	chr8	46209240	46209258	-	1	NA	exon (NM_007450, exon 2 of 4)	exon (NM_007450, exon 2 of 4)	1760	NM_007450	11739	Mm.16228	NM_007450	ENSMUSG00000031633	Slc25a4	AU019225|Ant1	solute carrier family 25 (mitochondrial carrier, adenine nucleotide translocator), member 4	protein-coding
mm_142086.1	chr17	35779103	35779123	-	1	NA	intron (NR_045459, intron 2 of 2)	intron (NR_045459, intron 2 of 2)	6663	NR_045459	74601	Mm.410840	NR_045459	ENSMUSG00000092171	4833427F10Rik	-	RIKEN cDNA 4833427F10 gene	ncRNA
mm_148358.1	chr18	84951478	84951536	-	1	NA	promoter-TSS (NM_025969)	promoter-TSS (NM_025969)	17	NM_025969	67105	Mm.250617	NM_025969	ENSMUSG00000024645	Timm21	1700034H14Rik|2700002I20Rik	tranlocase of inner mitochondrial membrane 21	protein-coding
mm_32765.1	chr4	116691817	116691899	+	1	NA	exon (NM_011034, exon 3 of 6)	exon (NM_011034, exon 3 of 6)	-5836	NR_040442	100502959	Mm.395400	NR_040442		AV051173	-	expressed sequence AV051173	ncRNA
mm_76932.1	chr8	105938047	105938134	-	1	NA	5' UTR (NM_013640, exon 1 of 8)	5' UTR (NM_013640, exon 1 of 8)	302	NM_013640	19171	Mm.787	NM_013640	ENSMUSG00000031897	Psmb10	Mecl-1|Mecl1	proteasome (prosome, macropain) subunit, beta type 10	protein-coding
mm_142671.1	chr17	47730122	47730127	-	1	NA	exon (NM_025973, exon 4 of 9)	exon (NM_025973, exon 4 of 9)	3282	NM_025973	109820	Mm.22957	NM_025973	ENSMUSG00000023987	Pgc	2210410L06Rik|Upg-1|Upg1	progastricsin (pepsinogen C)	protein-coding
mm_69320.1	chr7	128461550	128461560	-	1	NA	promoter-TSS (NM_009383)	promoter-TSS (NM_009383)	-42	NM_009383	21843	Mm.242072	NM_009383	ENSMUSG00000030846	Tial1	5330433G13Rik|AL033329|TIAR|mTIAR	Tia1 cytotoxic granule-associated RNA binding protein-like 1	protein-coding
mm_27065.1	chr3	27711256	27711338	-	1	NA	promoter-TSS (NM_173182)	promoter-TSS (NM_173182)	-858	NM_173182	72007	Mm.38832	NM_173182	ENSMUSG00000039286	Fndc3b	1600019O04Rik|AW550168|Fad104|mKIAA4164	fibronectin type III domain containing 3B	protein-coding
mm_18079.1	chr2	43738676	43738680	-	1	NA	Intergenic	Intergenic	-10146	NM_001301832	76117	Mm.217350	NM_153820	ENSMUSG00000049744	Arhgap15	5830480G12Rik	Rho GTPase activating protein 15	protein-coding
mm_168362.1	chr11	16025966	16025967	-	1	NA	Intergenic	L1Md_Gf|LINE|L1	-231758	NM_001290539	211739	Mm.284015	NM_145967	ENSMUSG00000048834	Vstm2a	Vstm2	V-set and transmembrane domain containing 2A	protein-coding
mm_137477.1	chr17	26850667	26850687	+	1	NA	Intergenic	CpG	-9112	NM_008700	18091	Mm.41974	NM_008700	ENSMUSG00000015579	Nkx2-5	Csx|Nkx-2.5|Nkx2.5|tinman	NK2 homeobox 5	protein-coding
mm_154468.1	chrM	3698	3709	-	1	NA	NA	Intergenic	NA	NA								
mm_53783.1	chr6	146577607	146577623	+	1	NA	promoter-TSS (NM_026218)	promoter-TSS (NM_026218)	220	NM_138757	71177	Mm.271774	NM_138757	ENSMUSG00000040250	Asun	4933424B01Rik|Spata30	asunder, spermatogenesis regulator	protein-coding
mm_169947.1	chr16	71276434	71276435	+	1	NA	Intergenic	L1Md_T|LINE|L1	26530	NR_040576	78221	Mm.399298	NR_040576		4930567J20Rik	-	RIKEN cDNA 4930567J20 gene	ncRNA
mm_87820.1	chr10	60346648	60346655	+	1	NA	promoter-TSS (NM_001159572)	promoter-TSS (NM_001159572)	-200	NM_001159572	74048	Mm.273584	NM_028732	ENSMUSG00000020101	Vsir	4632428N05Rik|Dies1|PD-1H|VISTA	V-set immunoregulatory receptor	protein-coding
mm_127352.1	chr15	100619828	100619840	+	1	NA	3' UTR (NM_011873, exon 4 of 4)	3' UTR (NM_011873, exon 4 of 4)	4172	NM_011873	23994	Mm.486175	NM_011873	ENSMUSG00000000346	Dazap2	AI314727|Brbp|Gcap28|Prtb|gt6-12|mKIAA0058	DAZ associated protein 2	protein-coding
mm_35731.1	chr4	45011947	45011974	-	1	NA	5' UTR (NM_001163284, exon 1 of 2)	5' UTR (NM_001163284, exon 1 of 2)	452	NM_001163284	230119	Mm.44222	NM_173399	ENSMUSG00000049657	Zbtb5	5930421I10|9430083K24Rik|AI646847|mKIAA0354	zinc finger and BTB domain containing 5	protein-coding
mm_72058.1	chr8	71371826	71371832	+	1	NA	exon (NM_001293800, exon 1 of 3)	exon (NM_001293800, exon 1 of 3)	531	NM_001293800	77090	Mm.440170	NM_029865	ENSMUSG00000002396	Ocel1	9430098E02Rik|AI326022|AI593544	occludin/ELL domain containing 1	protein-coding
mm_77684.1	chr8	125851128	125851136	-	1	NA	intron (NM_175561, intron 13 of 33)	intron (NM_175561, intron 13 of 33)	47185	NM_175561	270109	Mm.145535	NM_175561	ENSMUSG00000060212	Pcnx2	A830048P05|AU067631|E330039K12Rik|Pcnxl2|mKIAA0435	pecanex homolog 2	protein-coding
mm_5474.1	chr1	36593316	36593338	-	1	NA	promoter-TSS (NM_027957)	promoter-TSS (NM_027957)	5	NM_027957	381337	Mm.17413	NM_027957	ENSMUSG00000046337	Fam178b	1700024G10Rik|Gm990	family with sequence similarity 178, member B	protein-coding
mm_30885.1	chr4	32249386	32249420	+	1	NA	Intergenic	Intergenic	-168032	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_102405.1	chr11	59163697	59163726	-	1	NA	promoter-TSS (NM_001270791)	promoter-TSS (NM_001270791)	34	NM_001270791	216792	Mm.266175	NM_173785	ENSMUSG00000049287	Iba57	4930543L23Rik|A230051G13Rik|C1orf69	IBA57 homolog, iron-sulfur cluster assembly	protein-coding
mm_97115.1	chr11	74770882	74770907	+	1	NA	promoter-TSS (NM_026197)	promoter-TSS (NM_026197)	31	NM_026197	67493	Mm.45748	NM_026197	ENSMUSG00000010554	Mettl16	2610100D03Rik|2810013M15Rik|A830095F14Rik|AI846133|Mett10d	methyltransferase like 16	protein-coding
mm_101198.1	chr11	19016694	19016704	-	1	NA	intron (NM_001193271, intron 1 of 12)	intron (NM_001193271, intron 1 of 12)	2270	NM_001193271	17268	Mm.356578	NM_010789	ENSMUSG00000020160	Meis1	C530044H18Rik|Evi8	Meis homeobox 1	protein-coding
mm_47210.1	chr5	121009050	121009051	-	1	NA	promoter-TSS (NM_001302345)	promoter-TSS (NM_001302345)	488	NM_011286	19894	Mm.181166	NM_011286	ENSMUSG00000029608	Rph3a	2900002P20Rik|AU022689|AW108370	rabphilin 3A	protein-coding
mm_8794.1	chr1	161788465	161788471	-	1	NA	promoter-TSS (NM_001205243)	promoter-TSS (NM_001205243)	27	NM_001205243	14103	Mm.3355	NM_010177	ENSMUSG00000000817	Fasl	APT1LG1|CD178|CD95-L|CD95L|Fas-L|Faslg|Tnfsf6|Tnlg1a|gld	Fas ligand (TNF superfamily, member 6)	protein-coding
mm_29385.1	chr3	108858603	108858636	-	1	NA	intron (NM_001165965, intron 10 of 11)	intron (NM_001165965, intron 10 of 11)	-18117	NM_011504	20912	Mm.316894	NM_011504	ENSMUSG00000027882	Stxbp3	Munc-18c|Stxbp3a|Sxtbp3|Unc18-3	syntaxin binding protein 3	protein-coding
mm_9044.1	chr1	167283906	167283916	-	1	NA	intron (NM_030724, intron 1 of 6)	CpG	1216	NM_030724	80914	Mm.280895	NM_030724	ENSMUSG00000026558	Uck2	AA407809|AI481316|AU018180|AU020720|TSA903|UK|UMK|Umpk	uridine-cytidine kinase 2	protein-coding
mm_86493.1	chr10	5593824	5593855	+	1	NA	5' UTR (NM_026793, exon 1 of 2)	5' UTR (NM_026793, exon 1 of 2)	111	NM_026793	68632	Mm.338242	NM_026793	ENSMUSG00000046916	Myct1	1110020B04Rik|AI225941|AI642973|Mtmc1	myc target 1	protein-coding
mm_59700.1	chr7	28692817	28692834	+	1	NA	promoter-TSS (NM_001163702)	promoter-TSS (NM_001163702)	-24	NM_207238	233040	Mm.116116	NM_207238	ENSMUSG00000037463	Fbxo27	E130008B10Rik|FBG5|Gm161	F-box protein 27	protein-coding
mm_41191.1	chr5	88327925	88327931	+	1	NA	exon (NM_008644, exon 3 of 3)	exon (NM_008644, exon 3 of 3)	10616	NM_008644	17830	Mm.200411	NM_008644	ENSMUSG00000064156	Prol1	Muc10	proline rich, lacrimal 1	protein-coding
mm_45916.1	chr5	89439609	89439646	-	1	NA	exon (NM_008096, exon 7 of 13)	exon (NM_008096, exon 7 of 13)	18271	NM_008096	14473	Mm.196595	NM_008096	ENSMUSG00000035540	Gc	DBP|VDB	group specific component	protein-coding
mm_121809.1	chr14	20378841	20378886	-	1	NA	exon (NM_172379, exon 10 of 12)	exon (NM_172379, exon 10 of 12)	10047	NM_134081	108671	Mm.2871	NM_134081	ENSMUSG00000021811	Dnajc9	5330419I01Rik|AU020082	DnaJ heat shock protein family (Hsp40) member C9	protein-coding
mm_78291.1	chr9	22239806	22239819	+	1	NA	TTS (NM_001164624)	TTS (NM_001164624)	14100	NM_001164624	235047	Mm.290849	NM_172763	ENSMUSG00000057982	Zfp809	BB114266|C330026E23	zinc finger protein 809	protein-coding
mm_4861.1	chr1	187662120	187662131	+	1	NA	intron (NM_001243792, intron 1 of 7)	intron (NM_001243792, intron 1 of 7)	53119	NM_001243792	26381	Mm.89989	NM_011935	ENSMUSG00000026610	Esrrg	ERR3|Errg|NR3B3|mKIAA0832	estrogen-related receptor gamma	protein-coding
mm_88887.1	chr10	81136332	81136382	+	1	NA	promoter-TSS (NM_010731)	promoter-TSS (NM_010731)	86	NM_010731	16969	Mm.20920	NM_010731	ENSMUSG00000035011	Zbtb7a	9030619K07Rik|9130006G12Rik|AI452336|FBI-1|Lrf|Pokemon|Zbtb7	zinc finger and BTB domain containing 7a	protein-coding
mm_173331.1	chrY	90784853	90784865	+	1	NA	promoter-TSS (NR_137282)	promoter-TSS (NR_137282)	-583	NR_137282	170942	Mm.76062	NM_133362	ENSMUSG00000096768	Erdr1	edr	erythroid differentiation regulator 1	protein-coding
mm_126492.1	chr15	81627301	81627318	+	1	NA	exon (NM_177821, exon 14 of 31)	exon (NM_177821, exon 14 of 31)	-36580	NM_001289712	214669	Mm.280768	NM_145993	ENSMUSG00000022394	L3mbtl2	4732493N06Rik|M4mbt	l(3)mbt-like 2 (Drosophila)	protein-coding
mm_117404.1	chr13	73847604	73847619	-	1	NA	promoter-TSS (NM_028186)	promoter-TSS (NM_028186)	20	NM_028186	72293	Mm.45506	NM_028186	ENSMUSG00000021567	Nkd2	2210403L10Rik|AW212591|mNkd2	naked cuticle 2 homolog (Drosophila)	protein-coding
mm_162047.1	chrX	4291222	4291222	-	1	NA	promoter-TSS (NM_001085553)	promoter-TSS (NM_001085553)	23	NM_001085553	668963	Mm.457966	NM_001085553	ENSMUSG00000094596	Btbd35f20	ENSMUSG00000078215|Gm10921|OTTMUSG00000016420	BTB domain containing 35, family member 20	protein-coding
mm_31822.1	chr4	66844480	66844488	+	1	NA	3' UTR (NM_021297, exon 3 of 3)	3' UTR (NM_021297, exon 3 of 3)	16933	NM_021297	21898	Mm.38049	NM_021297	ENSMUSG00000039005	Tlr4	Lps|Ly87|Ran/M1|Rasl2-8	toll-like receptor 4	protein-coding
mm_44456.1	chr5	22344671	22344681	-	1	NA	promoter-TSS (NM_011261)	promoter-TSS (NM_011261)	29	NM_011261	19699	Mm.425236	NM_011261	ENSMUSG00000042453	Reln	reeler|rl	reelin	protein-coding
mm_77731.1	chr8	126872667	126872715	-	1	NA	Intergenic	MLT1G|LTR|ERVL-MaLR	73230	NM_024214	67952	Mm.6932	NM_024214	ENSMUSG00000093904	Tomm20	1810060K07Rik|BB284719|Gm19268|MAS20|MOM19|TOM20|mKIAA0016	translocase of outer mitochondrial membrane 20 homolog (yeast)	protein-coding
mm_149649.1	chr19	18631928	18631963	+	1	NA	promoter-TSS (NM_017375)	promoter-TSS (NM_017375)	-71	NM_145497	225994	Mm.211595	NM_145497	ENSMUSG00000037847	Nmrk1	AA408380|D630020N23Rik|Nrk1	nicotinamide riboside kinase 1	protein-coding
mm_64676.1	chr7	4501637	4501711	-	1	NA	promoter-TSS (NM_029834)	promoter-TSS (NM_029834)	6	NM_029834	232807	Mm.360391	NM_029834	ENSMUSG00000019254	Ppp1r12c	2410197A17Rik|AI839747|B430101M08|Mbs85	protein phosphatase 1, regulatory (inhibitor) subunit 12C	protein-coding
mm_101059.1	chr11	9039586	9039601	-	1	NA	promoter-TSS (NM_001290519)	promoter-TSS (NM_001290519)	-2	NM_001290519	194974	Mm.79210	NM_177576	ENSMUSG00000040985	Sun3	Sunc1	Sad1 and UNC84 domain containing 3	protein-coding
mm_15143.1	chr2	153974863	153974874	+	1	NA	promoter-TSS (NM_001080811)	promoter-TSS (NM_001080811)	-77	NM_001080811	545477	Mm.379973	NM_001080811	ENSMUSG00000078998	Bpifa6	EG545477|Gm5840|Splunc6	BPI fold containing family A, member 6	protein-coding
mm_111449.1	chr12	98269718	98269728	-	1	NA	intron (NM_008152, intron 1 of 1)	MIRb|SINE|MIR	1088	NM_008152	14744	Mm.378924	NM_008152	ENSMUSG00000021886	Gpr65	Dig1|Gpcr25|TDAG8	G-protein coupled receptor 65	protein-coding
mm_50369.1	chr6	48676161	48676190	+	1	NA	promoter-TSS (NM_174960)	promoter-TSS (NM_174960)	40	NM_174960	317758	Mm.116971	NM_174960	ENSMUSG00000051124	Gimap9	A630002K24|BB145400	GTPase, IMAP family member 9	protein-coding
mm_50066.1	chr6	41216051	41216069	+	1	NA	Intergenic	Intergenic	-86212	NM_011646	22074	Mm.383263	NM_011646	ENSMUSG00000054106	Try4	0910001B19Rik|Td	trypsin 4	protein-coding
mm_155183.1	chrX	56136548	56136583	+	1	NA	promoter-TSS (NM_027510)	promoter-TSS (NM_027510)	-7	NM_027510	70691	Mm.335676	NM_027510	ENSMUSG00000031125	3830403N18Rik	Xlrl	RIKEN cDNA 3830403N18 gene	protein-coding
mm_61864.1	chr7	88430327	88430364	+	1	NA	promoter-TSS (NM_028238)	promoter-TSS (NM_028238)	72	NM_028238	72433	Mm.276669	NM_028238	ENSMUSG00000030559	Rab38	2310011F14Rik|AU043391|cht	RAB38, member RAS oncogene family	protein-coding
mm_14440.1	chr2	130906462	130906500	+	1	NA	promoter-TSS (NR_015523)	promoter-TSS (NR_015523)	-14	NM_009730	11990	Mm.119936	NM_009730	ENSMUSG00000027312	Atrn	AW558010|Mgca|mg	attractin	protein-coding
mm_118927.1	chr14	27038996	27039008	+	1	NA	promoter-TSS (NM_134437)	promoter-TSS (NM_134437)	1	NM_134437	171463	Mm.206726	NM_027265	ENSMUSG00000040717	Il17rd	2810004A10Rik|AI428510|Sef|Sef-S	interleukin 17 receptor D	protein-coding
mm_64789.1	chr7	6168592	6168602	-	1	NA	Intergenic	RLTR25A|LTR|ERVK	-3916	NM_028316	72667	Mm.274089	NM_028316	ENSMUSG00000044876	Zfp444	2810031J10Rik|6230401O10Rik|mFLJ00134	zinc finger protein 444	protein-coding
mm_151322.1	chr19	55892930	55892934	+	1	NA	intron (NR_138565, intron 4 of 15)	intron (NR_138565, intron 4 of 15)	-2389	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_74090.1	chr8	122564919	122564956	+	1	NA	Intergenic	Intergenic	-3078	NM_026014	67177	Mm.21873	NM_026014	ENSMUSG00000006585	Cdt1	2610318F11Rik|AW545653|C76791|Ris2	chromatin licensing and DNA replication factor 1	protein-coding
mm_135976.1	chr16	75047768	75047781	-	1	NA	Intergenic	Lx2|LINE|L1	538287	NM_001252513	320355	Mm.99517	NM_177142	ENSMUSG00000032948	Lipi	D930038D03Rik|lpd1	lipase, member I	protein-coding
mm_120453.1	chr14	65969715	65969738	+	1	NA	intron (NM_013492, intron 1 of 8)	intron (NM_013492, intron 1 of 8)	1243	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_109820.1	chr12	3856053	3856070	-	1	NA	intron (NM_007872, intron 3 of 22)	intron (NM_007872, intron 3 of 22)	6183	NR_045884	100038522	Mm.417270	NR_045884	ENSMUSG00000073242	Dnmt3aos	ENSMUSG00000073242|Gm10485	DNA methyltransferase 3A, opposite strand	ncRNA
mm_121666.1	chr14	12345848	12345872	-	1	NA	promoter-TSS (NM_080433)	promoter-TSS (NM_080433)	5	NM_080433	54713	Mm.34644	NM_080433	ENSMUSG00000021743	Fezf2	AI451466|AI852056|Fez|Fezl|Zfp312	Fez family zinc finger 2	protein-coding
mm_74068.1	chr8	122431691	122431705	+	1	NA	intron (NM_001301284, intron 1 of 4)	intron (NM_001301284, intron 1 of 4)	1242	NM_001301284	13057	Mm.271671	NM_007806	ENSMUSG00000006519	Cyba	b558|nmf333|p22-phox|p22phox	cytochrome b-245, alpha polypeptide	protein-coding
mm_152063.1	chr19	6532111	6532151	-	1	NA	exon (NM_020253, exon 23 of 23)	exon (NM_020253, exon 23 of 23)	10939	NM_009203	20521	Mm.391146	NM_009203	ENSMUSG00000061742	Slc22a12	AI987855|OAT4L|Rst|Slc22al2|URAT1	solute carrier family 22 (organic anion/cation transporter), member 12	protein-coding
mm_154624.1	chrX	7728500	7728510	+	1	NA	promoter-TSS (NM_138602)	promoter-TSS (NM_138602)	-66	NM_138602	54637	Mm.28850	NM_138602	ENSMUSG00000031149	Praf2	AA986329|C78013|DXImx39e|JM4|Sfc20	PRA1 domain family 2	protein-coding
mm_167474.1	chr8	127844601	127844602	+	1	NA	Intergenic	Intergenic	433624	NR_105822	102465212		NR_105822	ENSMUSG00000099326	Mir21c	Gm28013|mmu-mir-21c	microRNA 21c	ncRNA
mm_151635.1	chr19	3931793	3931835	-	1	NA	Intergenic	Intergenic	-2098	NM_026316	67689	Mm.109341	NM_026316	ENSMUSG00000024885	Aldh3b1	1700001N19Rik|ALDH4|ALDH7	aldehyde dehydrogenase 3 family, member B1	protein-coding
mm_61430.1	chr7	73740422	73740430	+	1	NA	5' UTR (NM_001162532, exon 1 of 3)	5' UTR (NM_001162532, exon 1 of 3)	119	NM_001162532	100038347	Mm.425464	NM_001162532	ENSMUSG00000078670	Fam174b	-	family with sequence similarity 174, member B	protein-coding
mm_170843.1	chr2	177398360	177398360	-	1	NA	Intergenic	Intergenic	-66382	NM_001177568	628308	Mm.460436	NM_001177568	ENSMUSG00000078866	Zfp970	Gm14420|OTTMUSG00000016588	zinc finger protein 970	protein-coding
mm_91424.1	chr10	32889972	32889996	-	1	NA	promoter-TSS (NM_001025286)	promoter-TSS (NM_001025286)	-69	NM_001025286	432450	Mm.49665	NM_001013411	ENSMUSG00000069670	Nkain2	6330571D19Rik|AW455467|Tcba1	Na+/K+ transporting ATPase interacting 2	protein-coding
mm_11291.1	chr2	30080433	30080473	+	1	NA	intron (NM_153805, intron 3 of 21)	intron (NM_153805, intron 3 of 21)	1687	NM_153805	263803	Mm.233843	NM_153805	ENSMUSG00000026785	Pkn3	AW209115|BC034126	protein kinase N3	protein-coding
mm_98983.1	chr11	98741847	98741857	+	1	NA	promoter-TSS (NM_001313983)	promoter-TSS (NM_001313983)	67	NM_001313983	21833	Mm.265917	NM_178060	ENSMUSG00000058756	Thra	6430529J03Rik|AW259572|Erba|Nr1a1|Rvr|T3R[a]|T3Ralpha|Thra1|Thra2|c-erbA-1|c-erbA-alpha|c-erbAalpha	thyroid hormone receptor alpha	protein-coding
mm_85968.1	chr9	112156088	112156133	-	1	NA	intron (NM_001177619, intron 10 of 10)	intron (NM_001177619, intron 10 of 10)	29839	NM_001177618	74100	Mm.297444	NM_028755	ENSMUSG00000032503	Arpp21	0710001E13Rik|AI853636|ARPP-21|D9Bwg1012e|R3hdm3|Tarpp	cyclic AMP-regulated phosphoprotein, 21	protein-coding
mm_116451.1	chr13	43171462	43171488	-	1	NA	promoter-TSS (NM_025935)	promoter-TSS (NM_025935)	26	NM_001252639	67046	Mm.269213	NM_025935	ENSMUSG00000021368	Tbc1d7	2610009C09Rik	TBC1 domain family, member 7	protein-coding
mm_11446.1	chr2	32063331	32063345	+	1	NA	Intergenic	Intergenic	12392	NR_106135	102466844		NR_106135	ENSMUSG00000099075	Mir7674	Gm27563|mmu-mir-7674	microRNA 7674	ncRNA
mm_29195.1	chr3	106760802	106760812	-	1	NA	exon (NM_007651, exon 8 of 8)	exon (NM_007651, exon 8 of 8)	29342	NM_007651	12508	Mm.316861	NM_007651	ENSMUSG00000040747	Cd53	AI323659|Ox-44|Tspan25	CD53 antigen	protein-coding
mm_25575.1	chr3	116859558	116859568	+	1	NA	promoter-TSS (NM_001113478)	promoter-TSS (NM_001113478)	-4	NM_001113478	20321	Mm.66293	NM_009146	ENSMUSG00000033386	Frrs1	AI131732|Sdfr2	ferric-chelate reductase 1	protein-coding
mm_81932.1	chr9	120179931	120179941	+	1	NA	Intergenic	L1ME3Cz|LINE|L1	30194	NM_001039364	17433	Mm.486167	NM_008614	ENSMUSG00000032517	Mobp	AI835053|AI839848|MOBP155|MOBP170|MOBP69|MOBP73|MOBP81|R74645	myelin-associated oligodendrocytic basic protein	protein-coding
mm_139529.1	chr17	56673274	56673287	+	1	NA	promoter-TSS (NM_027933)	promoter-TSS (NM_027933)	55	NM_027933	71810	Mm.29608	NM_027933	ENSMUSG00000002372	Ranbp3	2610024N24Rik|AA408221	RAN binding protein 3	protein-coding
mm_172728.1	chr8	7542220	7542220	+	1	NA	Intergenic	Intergenic	1118553	NM_010111	13642	Mm.209813	NM_010111	ENSMUSG00000001300	Efnb2	ELF-2|Epl5|Eplg5|Htk-L|LERK-5|Lerk5|NLERK-1	ephrin B2	protein-coding
mm_107139.1	chr12	21374253	21374257	+	1	NA	promoter-TSS (NM_009615)	promoter-TSS (NM_009615)	-623	NM_009615	11491	Mm.27681	NM_009615	ENSMUSG00000052593	Adam17	CD156b|Tace	a disintegrin and metallopeptidase domain 17	protein-coding
mm_75188.1	chr8	38111171	38111173	-	1	NA	intron (NM_145841, intron 1 of 7)	intron (NM_145841, intron 1 of 7)	141030	NR_029884	723860		NR_029884	ENSMUSG00000065457	Mir383	Mirn383|mir-383|mmu-mir-383	microRNA 383	ncRNA
mm_90519.1	chr10	128058975	128059025	+	1	NA	promoter-TSS (NM_019766)	promoter-TSS (NM_019766)	18	NM_019766	56351	Mm.305816	NM_019766	ENSMUSG00000071072	Ptges3	5730442A20Rik|Ptges|Tebp|cPGES|p23|sid3177	prostaglandin E synthase 3 (cytosolic)	protein-coding
mm_56274.1	chr6	91110354	91110356	-	1	NA	intron (NM_018815, intron 1 of 39)	intron (NM_018815, intron 1 of 39)	6471	NM_018815	54563	Mm.28162	NM_018815	ENSMUSG00000030091	Nup210	9830001L10|AI836801|Pom210|gp190|gp210	nucleoporin 210	protein-coding
mm_133496.1	chr16	90386026	90386052	+	1	NA	promoter-TSS (NM_015755)	promoter-TSS (NM_015755)	-358	NM_015755	26559	Mm.125874	NM_015755	ENSMUSG00000053414	Hunk	Bstk1|Mak-v	hormonally upregulated Neu-associated kinase	protein-coding
mm_106858.1	chr12	8009241	8009259	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	31573	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_152275.1	chr19	8819758	8819790	-	1	NA	promoter-TSS (NM_027412)	promoter-TSS (NM_027412)	373	NM_001081196	68693	Mm.476519	NM_001081196	ENSMUSG00000071659	Hnrnpul2	1110031M08Rik|AI465155|Hnrpul2	heterogeneous nuclear ribonucleoprotein U-like 2	protein-coding
mm_20248.1	chr2	126499777	126499794	-	1	NA	Intergenic	Intergenic	-8232	NM_001080944	241633	Mm.222235	NM_001080944	ENSMUSG00000060131	Atp8b4	A530043E15|Im	ATPase, class I, type 8B, member 4	protein-coding
mm_171990.1	chr5	96374393	96374396	+	1	NA	5' UTR (NM_175473, exon 1 of 74)	5' UTR (NM_175473, exon 1 of 74)	439	NM_175473	231470	Mm.291120	NM_175473	ENSMUSG00000034687	Fras1	E130113P14Rik|bl|mKIAA1500	Fraser extracellular matrix complex subunit 1	protein-coding
mm_85232.1	chr9	98033112	98033122	-	1	NA	promoter-TSS (NM_022319)	promoter-TSS (NM_022319)	50	NM_022319	64085	Mm.440903	NM_022319	ENSMUSG00000032452	Clstn2	2900042C18Rik|AI448973|CSTN2|Cs2|Cst-2|mKIAA4134	calsyntenin 2	protein-coding
mm_80607.1	chr9	86743642	86743654	+	1	NA	promoter-TSS (NM_178738)	promoter-TSS (NM_178738)	15	NM_178738	244954	Mm.257629	NM_178738	ENSMUSG00000033491	Prss35	6030424L22Rik|P3D9	protease, serine 35	protein-coding
mm_113147.1	chr13	24729642	24729645	+	1	NA	intron (NM_001286100, intron 22 of 22)	BC1_Mm|scRNA|scRNA	32294	NM_020567	57441	Mm.12239	NM_020567	ENSMUSG00000006715	Gmnn	AW546347|Gem	geminin	protein-coding
mm_92881.1	chr10	82690574	82690591	-	1	NA	promoter-TSS (NM_029102)	promoter-TSS (NM_029102)	68	NM_029102	74782	Mm.191281	NM_029102	ENSMUSG00000020251	Glt8d2	1110021D20Rik	glycosyltransferase 8 domain containing 2	protein-coding
mm_28503.1	chr3	92501762	92501765	-	1	NA	Intergenic	Intergenic	-1270	NM_173070	229562	Mm.246590	NM_173070	ENSMUSG00000045566	Sprr4	-	small proline-rich protein 4	protein-coding
mm_54364.1	chr6	31126338	31126341	-	1	NA	intron (NR_110471, intron 3 of 3)	intron (NR_110471, intron 3 of 3)	-63246	NR_029532	387223		NR_029532	ENSMUSG00000065604	Mir29b-1	Mirn29b|Mirn29b-1|mir-29b-1	microRNA 29b-1	ncRNA
mm_129421.1	chr15	78405825	78405917	-	1	NA	promoter-TSS (NM_009437)	promoter-TSS (NM_009437)	-12	NM_009437	22117	Mm.15312	NM_009437	ENSMUSG00000044986	Tst	Rhodanese	thiosulfate sulfurtransferase, mitochondrial	protein-coding
mm_118715.1	chr14	22195866	22195881	+	1	NA	intron (NM_028275, intron 2 of 6)	intron (NM_028275, intron 2 of 6)	176161	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_161373.1	chr14	67233513	67233513	+	1	NA	5' UTR (NM_001276387, exon 1 of 17)	5' UTR (NM_001276387, exon 1 of 17)	221	NM_001276387	13592	Mm.319947	NM_010095	ENSMUSG00000022053	Ebf2	D14Ggc1e|EBF-2|Mmot1|O/E-3|OE-3	early B cell factor 2	protein-coding
mm_119659.1	chr14	52136557	52136581	+	1	NA	intron (NM_023879, intron 10 of 24)	intron (NM_023879, intron 10 of 24)	25666	NM_023879	77945	Mm.21662	NM_023879	ENSMUSG00000057132	Rpgrip1	0610005A07Rik|4930401L23Rik|4930505G06Rik|A930002K18Rik|AA415034|nmf247	retinitis pigmentosa GTPase regulator interacting protein 1	protein-coding
mm_165697.1	chr3	93505016	93505023	+	1	NA	Intergenic	Looper|DNA|PiggyBac	-15477	NM_016740	20195	Mm.280038	NM_016740	ENSMUSG00000027907	S100a11	EMAPI|Emap1|S100a14|S100c|cal	S100 calcium binding protein A11	protein-coding
mm_17607.1	chr2	30919656	30919676	-	1	NA	Intergenic	L1MEd|LINE|L1	-16369	NM_022415	64292	Mm.28768	NM_022415	ENSMUSG00000050737	Ptges	2410099E23Rik|D2Ertd369e|Pges|mPGES|mPGES-1	prostaglandin E synthase	protein-coding
mm_82853.1	chr9	31280152	31280184	-	1	NA	Intergenic	Intergenic	8767	NM_001101597	638580	Mm.373655	NM_001101597		Gm7244	EG638580	predicted gene 7244	protein-coding
mm_149789.1	chr19	23141020	23141033	+	1	NA	promoter-TSS (NM_010638)	promoter-TSS (NM_010638)	-200	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_9034.1	chr1	167226357	167226376	-	1	NA	3' UTR (NM_030724, exon 7 of 7)	3' UTR (NM_030724, exon 7 of 7)	58761	NM_030724	80914	Mm.280895	NM_030724	ENSMUSG00000026558	Uck2	AA407809|AI481316|AU018180|AU020720|TSA903|UK|UMK|Umpk	uridine-cytidine kinase 2	protein-coding
mm_101591.1	chr11	34682075	34682097	-	1	NA	intron (NM_033374, intron 22 of 51)	RLTR44-int|LTR|ERVK	101819	NM_033374	94176	Mm.380679	NM_033374	ENSMUSG00000020143	Dock2	AI662014|AW122239|CED-5|Hch|MBC	dedicator of cyto-kinesis 2	protein-coding
mm_30552.1	chr4	3694045	3694056	+	1	NA	intron (NM_010747, intron 1 of 12)	PB1D10|SINE|Alu	15929	NM_010747	17096	Mm.317331	NM_010747	ENSMUSG00000042228	Lyn	AA407514|Hck-2|p53Lyn|p56Lyn	LYN proto-oncogene, Src family tyrosine kinase	protein-coding
mm_126154.1	chr15	78409761	78409776	+	1	NA	intron (NM_138670, intron 1 of 2)	intron (NM_138670, intron 1 of 2)	2664	NM_138670	246221	Mm.294215	NM_138670	ENSMUSG00000071711	Mpst	Mst	mercaptopyruvate sulfurtransferase	protein-coding
mm_20593.1	chr2	131174765	131174779	-	1	NA	promoter-TSS (NM_027641)	promoter-TSS (NM_027641)	38	NM_027641	70997	Mm.252722	NM_027641	ENSMUSG00000027329	Spef1	4931426K16Rik|Clamp	sperm flagellar 1	protein-coding
mm_99621.1	chr11	104637350	104637365	+	1	NA	intron (NM_016780, intron 5 of 14)	intron (NM_016780, intron 5 of 14)	29357	NM_016780	16416	Mm.87150	NM_016780	ENSMUSG00000020689	Itgb3	CD61|GP3A|INGRB3	integrin beta 3	protein-coding
mm_157906.1	chrX	78091339	78091344	-	1	NA	promoter-TSS (NM_008754)	promoter-TSS (NM_008754)	33	NM_008754	18249	Mm.430771	NM_008754	ENSMUSG00000067684	Obp1a	OBP-1a|OBP5	odorant binding protein IA	protein-coding
mm_76059.1	chr8	77724427	77724483	-	1	NA	promoter-TSS (NM_010332)	promoter-TSS (NM_010332)	-3	NM_010332	13617	Mm.283168	NM_010332	ENSMUSG00000031616	Ednra	ET-AR|ETa|Gpcr10	endothelin receptor type A	protein-coding
mm_166342.1	chr5	114897640	114897643	+	1	NA	5' UTR (NM_011854, exon 1 of 6)	5' UTR (NM_011854, exon 1 of 6)	707	NM_011854	23962	Mm.228363	NM_011854	ENSMUSG00000029561	Oasl2	M1204|Mmu-OASL|Oasl	2'-5' oligoadenylate synthetase-like 2	protein-coding
mm_153813.1	chr19	46045491	46045521	-	1	NA	promoter-TSS (NM_001113408)	promoter-TSS (NM_001113408)	-295	NM_001113408	16825	Mm.327442	NM_010697	ENSMUSG00000025223	Ldb1	CLIM2|NLI	LIM domain binding 1	protein-coding
mm_61026.1	chr7	49522645	49522666	+	1	NA	intron (NM_175272, intron 11 of 37)	intron (NM_175272, intron 11 of 37)	114180	NM_001005232	13172	Mm.307176	NM_001005232	ENSMUSG00000030507	Dbx1	AI426026|Dbx	developing brain homeobox 1	protein-coding
mm_18160.1	chr2	45098750	45098773	-	1	NA	intron (NM_001289521, intron 1 of 8)	intron (NM_001289521, intron 1 of 8)	11516	NM_001289521	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_35389.1	chr4	33290108	33290119	-	1	NA	Intergenic	Intergenic	-20198	NM_011884	24018	Mm.240024	NM_011884	ENSMUSG00000028274	Rngtt	AU020997|HCE|MCE1	RNA guanylyltransferase and 5'-phosphatase	protein-coding
mm_31104.1	chr4	41773699	41773708	+	1	NA	intron (NM_001347065, intron 2 of 5)	CpG-9830	398	NM_001164045	20301	Mm.335946	NM_011336	ENSMUSG00000073888	Ccl27a	ALP|AW558992|CTACK|CTAK|Ccl27|ESkine|ILC|PESKY|Scya27|Scya27a	chemokine (C-C motif) ligand 27A	protein-coding
mm_48626.1	chr5	145132941	145132969	-	1	NA	exon (NM_001033313, exon 4 of 6)	exon (NM_001033313, exon 4 of 6)	7134	NM_001033313	231887	Mm.188851	NM_001033313	ENSMUSG00000029623	Pdap1	HASPP28|PAP|PAP1	PDGFA associated protein 1	protein-coding
mm_81534.1	chr9	110117494	110117519	+	1	NA	5' UTR (NM_001252682, exon 1 of 23)	5' UTR (NM_001252682, exon 1 of 23)	110	NM_001252682	72831	Mm.276305	NM_133347	ENSMUSG00000032480	Dhx30	2810477H02Rik|C130058C04Rik|Ddx30|HELG|Ret-CoR	DEAH (Asp-Glu-Ala-His) box polypeptide 30	protein-coding
mm_84793.1	chr9	77128820	77128823	-	1	NA	intron (NM_027150, intron 7 of 7)	intron (NM_027150, intron 7 of 7)	-83040	NM_012033	26944	Mm.23199	NM_012033	ENSMUSG00000032357	Tinag	AI452335|TIN-ag	tubulointerstitial nephritis antigen	protein-coding
mm_132167.1	chr16	32277480	32277524	+	1	NA	promoter-TSS (NM_027355)	promoter-TSS (NM_027355)	41	NM_027355	70238	Mm.228263	NM_027355	ENSMUSG00000014074	Rnf168	3110001H15Rik	ring finger protein 168	protein-coding
mm_44955.1	chr5	36696057	36696068	-	1	NA	promoter-TSS (NM_001081232)	promoter-TSS (NM_001081232)	-41	NM_001081232	320661	Mm.26480	NM_177221	ENSMUSG00000029190	D5Ertd579e	9030221A05Rik|A930018H20Rik|Kiaa0232	DNA segment, Chr 5, ERATO Doi 579, expressed	protein-coding
mm_150177.1	chr19	32595783	32595799	+	1	NA	promoter-TSS (NM_001201470)	promoter-TSS (NM_001201470)	76	NM_001201470	23972	Mm.203916	NM_011864	ENSMUSG00000024899	Papss2	1810018P12Rik|AI159688|AtpsU2|Atpsk2|Sk2|bm	3'-phosphoadenosine 5'-phosphosulfate synthase 2	protein-coding
mm_34365.1	chr4	144892892	144892907	+	1	NA	promoter-TSS (NM_001172424)	promoter-TSS (NM_001172424)	72	NM_001172424	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding
mm_147942.1	chr18	66211977	66211981	-	1	NA	intron (NM_178793, intron 2 of 10)	intron (NM_178793, intron 2 of 10)	7354	NR_030467	751558		NR_030467	ENSMUSG00000076147	Mir694	Mirn694|mir-694|mmu-mir-694	microRNA 694	ncRNA
mm_20870.1	chr2	148443531	148443542	-	1	NA	promoter-TSS (NM_010740)	promoter-TSS (NM_010740)	-1	NM_010740	17064	Mm.681	NM_010740	ENSMUSG00000027435	Cd93	6030404G09Rik|AA145088|AA4.1|AW555904|C1qr1|C1qrp|Ly68	CD93 antigen	protein-coding
mm_154576.1	chrX	7566536	7566576	+	1	NA	intron (NM_138605, intron 1 of 3)	intron (NM_138605, intron 1 of 3)	-7044	NR_029473	78185	Mm.160055	NR_029473	ENSMUSG00000039545	Ppp1r3fos	4930524L23Rik	protein phosphatase 1, regulatory subunit 3F, opposite strand	ncRNA
mm_105978.1	chr11	115590660	115590675	-	1	NA	intron (NM_001252067, intron 7 of 15)	intron (NM_001252067, intron 7 of 15)	13249	NM_001252067	260302	Mm.119479	NM_173048	ENSMUSG00000020740	Gga3	C230037M19Rik|mKIAA0154	golgi associated, gamma adaptin ear containing, ARF binding protein 3	protein-coding
mm_137467.1	chr17	26663198	26663212	+	1	NA	Intergenic	Intergenic	-13191	NM_025272	11974	Mm.22602	NM_025272	ENSMUSG00000015575	Atp6v0e	Atp6k|Atp6v0e1|M9.2	ATPase, H+ transporting, lysosomal V0 subunit E	protein-coding
mm_154462.1	chrM	3241	3282	-	1	NA	NA	Intergenic	NA	NA								
mm_29302.1	chr3	107931747	107931762	-	1	NA	promoter-TSS (NM_026672)	promoter-TSS (NM_026672)	-9	NM_026672	68312	Mm.458189	NM_026672	ENSMUSG00000004035	Gstm7	0610005A07Rik|AI894236|Cd203c	glutathione S-transferase, mu 7	protein-coding
mm_15209.1	chr2	154214022	154214054	+	1	NA	exon (NM_153418, exon 11 of 16)	exon (NM_153418, exon 11 of 16)	-9704	NM_144890	228802	Mm.167411	NM_144890	ENSMUSG00000038572	Bpifb5	Lplunc5	BPI fold containing family B, member 5	protein-coding
mm_150655.1	chr19	41933465	41933540	+	1	NA	promoter-TSS (NM_001320233)	promoter-TSS (NM_001320233)	30	NM_023740	74168	Mm.20387	NM_023740	ENSMUSG00000025157	Zdhhc16	1500015N03Rik|Aph2	zinc finger, DHHC domain containing 16	protein-coding
mm_75578.1	chr8	61381419	61381420	-	1	NA	intron (NM_021506, intron 10 of 11)	intron (NM_021506, intron 10 of 11)	-92547	NR_045475	69279	Mm.417857	NR_045475	ENSMUSG00000099419	1700001D01Rik	-	RIKEN cDNA 1700001D01 gene	ncRNA
mm_126232.1	chr15	78947948	78947960	+	1	NA	5' UTR (NM_001039155, exon 1 of 8)	5' UTR (NM_001039155, exon 1 of 8)	230	NM_001039155	110253	Mm.123714	NM_138579	ENSMUSG00000033088	Triobp	AI428493|EST478828|Tara|mKIAA1662	TRIO and F-actin binding protein	protein-coding
mm_147896.1	chr18	65307740	65307770	-	1	NA	exon (NM_001037294, exon 5 of 13)	exon (NM_001037294, exon 5 of 13)	58894	NR_029600	387231		NR_029600	ENSMUSG00000065402	Mir122	Mir122a|Mirn122a|mir-122|mmu-mir-122	microRNA 122	ncRNA
mm_114803.1	chr13	91318821	91318822	+	1	NA	Intergenic	Intergenic	69264	NR_045161	320297	Mm.375866	NR_045161	ENSMUSG00000097182	A830009L08Rik	-	RIKEN cDNA A830009L08 gene	ncRNA
mm_168958.1	chr12	7859707	7859724	+	1	NA	Intergenic	Intergenic	-117962	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_37772.1	chr4	129819865	129819878	-	1	NA	promoter-TSS (NM_001164745)	promoter-TSS (NM_001164745)	-608	NM_008974	19244	Mm.193688	NM_008974	ENSMUSG00000028788	Ptp4a2	Prl-2	protein tyrosine phosphatase 4a2	protein-coding
mm_63170.1	chr7	125182531	125182549	+	1	NA	Intergenic	Intergenic	167246	NR_045804	71208	Mm.159465	NM_172408	ENSMUSG00000045928	4933440M02Rik	-	RIKEN cDNA 4933440M02 gene	ncRNA
mm_149448.1	chr19	11485909	11485941	+	1	NA	Intergenic	RMER19B2|LTR|ERVK	-6113	NM_001164202	666926	Mm.486382	NM_001164202	ENSMUSG00000058470	Gm8369	EG666926	predicted gene 8369	protein-coding
mm_99650.1	chr11	105589829	105589835	+	1	NA	promoter-TSS (NM_181071)	promoter-TSS (NM_181071)	-154	NM_181071	77097	Mm.22501	NM_175492	ENSMUSG00000053580	Tanc2	3526402J09Rik|5730590C14Rik	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2	protein-coding
mm_66100.1	chr7	31037882	31037890	-	1	NA	exon (NM_001111073, exon 4 of 8)	exon (NM_001111073, exon 4 of 8)	2431	NR_106017	102465635		NR_106017	ENSMUSG00000098783	Mir7050	Gm27578|mmu-mir-7050	microRNA 7050	ncRNA
mm_69088.1	chr7	127017252	127017262	-	1	NA	promoter-TSS (NM_030240)	promoter-TSS (NM_030240)	95	NM_030240	67278	Mm.345385	NM_030240	ENSMUSG00000030680	Pagr1a	2900092E17Rik|C77040|PA1|PAGR1	PAXIP1 associated glutamate rich protein 1A	protein-coding
mm_129994.1	chr15	86185661	86185671	-	1	NA	5' UTR (NM_145475, exon 1 of 13)	5' UTR (NM_145475, exon 1 of 13)	475	NM_145475	223753	Mm.222685	NM_145475	ENSMUSG00000035891	Cerk	AI848610|D330016D08Rik|mKIAA1646	ceramide kinase	protein-coding
mm_22513.1	chr3	7618732	7618744	+	1	NA	Intergenic	Intergenic	-4978	NM_001313888	16196	Mm.3825	NM_008371	ENSMUSG00000040329	Il7	A630026I06Rik|Il-7|hlb368	interleukin 7	protein-coding
mm_83241.1	chr9	42399756	42399764	-	1	NA	5' UTR (NM_001324548, exon 1 of 24)	5' UTR (NM_001324548, exon 1 of 24)	169	NM_009347	21683	Mm.42209	NM_009347	ENSMUSG00000037705	Tecta	Tctna	tectorin alpha	protein-coding
mm_146745.1	chr18	15822585	15822586	-	1	NA	Intergenic	HERVL40-int|LTR|ERVL	-104539	NM_199055	71367	Mm.329304	NM_199055	ENSMUSG00000047161	Chst9	5430438D01Rik	carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 9	protein-coding
mm_144025.1	chr17	90036721	90036741	-	1	NA	3' UTR (NM_001347419, exon 3 of 3)	3' UTR (NM_001347419, exon 3 of 3)	51637	NM_001346962	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_146050.1	chr18	69593584	69593607	+	1	NA	intron (NM_013685, intron 8 of 19)	intron (NM_013685, intron 8 of 19)	247874	NM_001083967	21413	Mm.4269	NM_013685	ENSMUSG00000053477	Tcf4	5730422P05Rik|ASP-I2|E2-2|E2.2|ITF-2|ITF-2b|ITF2|ME2|MITF-2A|MITF-2B|SEF-2|SEF2|SEF2-1|TFE|Tcf-4|bHLHb19	transcription factor 4	protein-coding
mm_46135.1	chr5	92675430	92675446	-	1	NA	promoter-TSS (NM_177230)	promoter-TSS (NM_177230)	-311	NM_177230	320696	Mm.209991	NM_177230	ENSMUSG00000050050	Ccdc158	4932413O14Rik	coiled-coil domain containing 158	protein-coding
mm_58189.1	chr6	142989734	142989754	-	1	NA	Intergenic	Intergenic	-25292	NM_011374	20449	Mm.260838	NM_011374	ENSMUSG00000030283	St8sia1	9330109E03Rik|GD3S|Sia-T|Siat8|Siat8a	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 1	protein-coding
mm_137830.1	chr17	30684822	30684826	+	1	NA	intron (NM_013811, intron 20 of 92)	B4A|SINE|B4	57888	NM_013811	13417	Mm.426017	NM_013811	ENSMUSG00000033826	Dnah8	ATPase|Dnahc8|Hst6.7b|P1-Loop	dynein, axonemal, heavy chain 8	protein-coding
mm_77407.1	chr8	120538648	120538666	-	1	NA	promoter-TSS (NR_106159)	promoter-TSS (NR_106159)	-39	NR_106159	102466849		NR_106159	ENSMUSG00000098280	Mir7687	Gm27573|mmu-mir-7687	microRNA 7687	ncRNA
mm_14236.1	chr2	127691847	127691878	+	1	NA	Intergenic	Intergenic	-35167	NM_001171187	17153	Mm.39040	NM_010762	ENSMUSG00000027375	Mal	Mpv17|Vip17	myelin and lymphocyte protein, T cell differentiation protein	protein-coding
mm_104815.1	chr11	98968746	98968757	-	1	NA	intron (NM_001176528, intron 3 of 7)	intron (NM_001176528, intron 3 of 7)	8280	NM_001176528	19401	Mm.439744	NM_009024	ENSMUSG00000037992	Rara	Nr1b1|RAR|RARalpha1	retinoic acid receptor, alpha	protein-coding
mm_169968.1	chr17	13006840	13006845	+	1	NA	promoter-TSS (NM_013671)	promoter-TSS (NM_013671)	-997	NM_013671	20656	Mm.290876	NM_013671	ENSMUSG00000006818	Sod2	MnSOD|Sod-2	superoxide dismutase 2, mitochondrial	protein-coding
mm_41069.1	chr5	87667227	87667237	+	1	NA	intron (NM_001286015, intron 1 of 32)	intron (NM_001286015, intron 1 of 32)	1024	NM_001286016	12990	Mm.427467	NM_007784	ENSMUSG00000070702	Csn1s1	AA959832|AW212882|Csna	casein alpha s1	protein-coding
mm_154277.1	chr19	60790585	60790602	-	1	NA	promoter-TSS (NM_010123)	promoter-TSS (NM_010123)	100	NM_010123	13669	Mm.2238	NM_010123	ENSMUSG00000024991	Eif3a	A830012B05Rik|Csma|Eif3|Eif3s10|mKIAA0139	eukaryotic translation initiation factor 3, subunit A	protein-coding
mm_47258.1	chr5	121673988	121673989	-	1	NA	intron (NM_001289544, intron 5 of 11)	PB1D10|SINE|Alu	13119	NM_001289544	72399	Mm.153372	NM_028227	ENSMUSG00000029458	Brap	3010002G07Rik|BRAP2|IMP	BRCA1 associated protein	protein-coding
mm_55064.1	chr6	49050440	49050479	-	1	NA	exon (NM_053110, exon 7 of 11)	exon (NM_053110, exon 7 of 11)	13941	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_47688.1	chr5	129116609	129116622	-	1	NA	intron (NM_001347486, intron 4 of 24)	Lx8|LINE|L1	19865	NM_001347486	243277	Mm.440501	NM_177734	ENSMUSG00000044017	Adgrd1	E230012M21Rik|Gpr133	adhesion G protein-coupled receptor D1	protein-coding
mm_23662.1	chr3	68489576	68489579	+	1	NA	intron (NM_001282045, intron 1 of 7)	intron (NM_001282045, intron 1 of 7)	-4604	NM_001282044	30953	Mm.331064	NM_013928	ENSMUSG00000027777	Schip1	Nf2ip|Schip-1	schwannomin interacting protein 1	protein-coding
mm_5307.1	chr1	22315849	22315867	-	1	NA	intron (NM_001012623, intron 10 of 14)	intron (NM_001012623, intron 10 of 14)	116985	NM_053270	116837	Mm.60061	NM_053270	ENSMUSG00000041670	Rims1	C030033M19Rik|RIM1|RIM1a|RIM1alpha|Rab3ip1|Rim|Serg1|mKIAA0340	regulating synaptic membrane exocytosis 1	protein-coding
mm_122362.1	chr14	39242492	39242496	-	1	NA	intron (NM_001190187, intron 1 of 9)	Lx2|LINE|L1	-229935	NR_131973	432842	Mm.352566	NR_131973		LOC432842	-	uncharacterized LOC432842	ncRNA
mm_50267.1	chr6	45060101	45060109	+	1	NA	promoter-TSS (NM_001004357)	promoter-TSS (NM_001004357)	44	NM_001004357	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding
mm_158126.1	chrX	102644166	102644177	-	1	NA	promoter-TSS (NM_008832)	promoter-TSS (NM_008832)	75	NM_008832	18679	Mm.212889	NM_008832	ENSMUSG00000034055	Phka1	5330411D17|9830108K24Rik|Phka	phosphorylase kinase alpha 1	protein-coding
mm_110418.1	chr12	46816924	46816961	-	1	NA	exon (NM_021361, exon 2 of 5)	exon (NM_021361, exon 2 of 5)	1833	NM_021361	664883	Mm.247195	NM_021361	ENSMUSG00000021047	Nova1	9430099M15Rik|G630039L02|Nova-1	neuro-oncological ventral antigen 1	protein-coding
mm_89342.1	chr10	87935954	87935994	+	1	NA	3' UTR (NM_010512, exon 5 of 5)	3' UTR (NM_010512, exon 5 of 5)	-30697	NR_000040	22172	Mm.391420	NR_000040		Tyms-ps	-	thymidylate synthase, pseudogene	pseudo
mm_85128.1	chr9	95558954	95558983	-	1	NA	promoter-TSS (NM_198414)	promoter-TSS (NM_198414)	-849	NM_198414	75552	Mm.151485	NM_198414	ENSMUSG00000064225	Paqr9	1700020G04Rik	progestin and adipoQ receptor family member IX	protein-coding
mm_46634.1	chr5	108519699	108519710	-	1	NA	3' UTR (NM_007756, exon 4 of 4)	3' UTR (NM_007756, exon 4 of 4)	30323	NM_007756	12889	Mm.5195	NM_007756	ENSMUSG00000033615	Cplx1	921-S	complexin 1	protein-coding
mm_163813.1	chr14	19416353	19416410	-	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	186206	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_103819.1	chr11	83003727	83003737	-	1	NA	exon (NM_181545, exon 6 of 6)	exon (NM_181545, exon 6 of 6)	-11902	NM_172796	237886	Mm.270253	NM_172796	ENSMUSG00000069793	Slfn9	9830137M10Rik	schlafen 9	protein-coding
mm_51634.1	chr6	85889310	85889311	+	1	NA	Intergenic	Intergenic	13223	NM_001145895	75541	Mm.24454	NM_029331	ENSMUSG00000068299	Nat8f4	1700019G17Rik	N-acetyltransferase 8 (GCN5-related) family member 4	protein-coding
mm_5837.1	chr1	52948012	52948018	-	1	NA	intron (NM_144953, intron 1 of 1)	B4A|SINE|B4	4825	NM_144953	67080	Mm.236287	NM_144953	ENSMUSG00000043629	1700019D03Rik	2410136C24Rik|AA410151|smAKAP	RIKEN cDNA 1700019D03 gene	protein-coding
mm_106958.1	chr12	8921688	8921704	+	1	NA	5' UTR (NM_008640, exon 1 of 7)	5' UTR (NM_008640, exon 1 of 7)	389	NM_008640	17775	Mm.30071	NM_008640	ENSMUSG00000020585	Laptm4a	AA286466|LAPTM4|MTP|Mtrp|mKIAA0108	lysosomal-associated protein transmembrane 4A	protein-coding
mm_16380.1	chr2	178327512	178327534	+	1	NA	intron (NM_001177790, intron 8 of 12)	intron (NM_001177790, intron 8 of 12)	80135	NM_177191	320558	Mm.70781	NM_177191	ENSMUSG00000060445	Sycp2	3830402K23Rik|4930518F03Rik	synaptonemal complex protein 2	protein-coding
mm_15088.1	chr2	153241453	153241466	+	1	NA	promoter-TSS (NM_080463)	promoter-TSS (NM_080463)	-73	NM_080463	140484	Mm.293761	NM_080463	ENSMUSG00000046020	Pofut1	O-FucT-1|mKIAA0180	protein O-fucosyltransferase 1	protein-coding
mm_27045.1	chr3	27191931	27191944	-	1	NA	intron (NM_178772, intron 1 of 4)	intron (NM_178772, intron 1 of 4)	8933	NM_178772	320024	Mm.24576	NM_178772	ENSMUSG00000027698	Nceh1	Aadacl1|B230106I24Rik|CPO-BP|Nceh	neutral cholesterol ester hydrolase 1	protein-coding
mm_97523.1	chr11	78501715	78501730	+	1	NA	exon (NM_011707, exon 7 of 8)	exon (NM_011707, exon 7 of 8)	-1791	NM_008759	18292	Mm.134360	NM_008759	ENSMUSG00000001103	Sebox	OG9|Og9x	SEBOX homeobox	protein-coding
mm_17037.1	chr2	20671059	20671088	-	1	NA	intron (NM_029895, intron 4 of 18)	intron (NM_029895, intron 4 of 18)	151560	NM_001177631	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding
mm_138668.1	chr17	35879771	35879824	+	1	NA	promoter-TSS (NM_026987)	promoter-TSS (NM_026987)	19	NM_026987	69192	Mm.390986	NM_026987	ENSMUSG00000024422	Dhx16	2410006N22Rik|DBP2|Ddx16|mKIAA0577	DEAH (Asp-Glu-Ala-His) box polypeptide 16	protein-coding
mm_89570.1	chr10	95514871	95514888	+	1	NA	promoter-TSS (NM_080560)	promoter-TSS (NM_080560)	-283	NM_080560	93765	Mm.371667	NM_080560	ENSMUSG00000074781	Ube2n	1500026J17Rik|AL022654|BB101821|UBC13	ubiquitin-conjugating enzyme E2N	protein-coding
mm_157568.1	chrX	52543192	52543195	-	1	NA	intron (NM_016697, intron 2 of 7)	intron (NM_016697, intron 2 of 7)	-32650	NR_045367	100504594	Mm.447008	NR_045367	ENSMUSG00000055110	A630012P03Rik	-	RIKEN cDNA A630012P03 gene	ncRNA
mm_83941.1	chr9	56796271	56796319	-	1	NA	Intergenic	CpG	55668	NM_198673	382075	Mm.335177	NM_198673	ENSMUSG00000045620	Odf3l1	BC049697|Gm1116	outer dense fiber of sperm tails 3-like 1	protein-coding
mm_102168.1	chr11	53891613	53891623	-	1	NA	promoter-TSS (NM_011396)	promoter-TSS (NM_011396)	85	NM_011396	20520	Mm.42253	NM_011396	ENSMUSG00000018900	Slc22a5	Lstpl|Octn2|jvs	solute carrier family 22 (organic cation transporter), member 5	protein-coding
mm_156016.1	chrX	107089643	107089656	+	1	NA	5' UTR (NM_172435, exon 2 of 3)	5' UTR (NM_172435, exon 2 of 3)	314	NM_172435	78826	Mm.74639	NM_172435	ENSMUSG00000050921	P2ry10	5830408N17Rik|Lypsr2|P2Y10	purinergic receptor P2Y, G-protein coupled 10	protein-coding
mm_83782.1	chr9	52164517	52164524	-	1	NA	intron (NM_001162921, intron 1 of 5)	RSINE1|SINE|B4	3591	NM_001162921	244871	Mm.295686	NM_001162921	ENSMUSG00000035164	Zc3h12c	A230108E06|C230027N18Rik|mKIAA1726	zinc finger CCCH type containing 12C	protein-coding
mm_97933.1	chr11	83648529	83648531	+	1	NA	intron (NM_011337, intron 2 of 2)	intron (NM_011337, intron 2 of 2)	848	NM_011337	20302	Mm.1282	NM_011337	ENSMUSG00000000982	Ccl3	AI323804|G0S19-1|LD78alpha|MIP-1alpha|MIP1-(a)|MIP1-alpha|Mip1a|Scya3	chemokine (C-C motif) ligand 3	protein-coding
mm_137570.1	chr17	27840157	27840177	+	1	NA	promoter-TSS (NM_011432)	promoter-TSS (NM_011432)	80	NM_011432	20630	Mm.103949	NM_011432	ENSMUSG00000024217	Snrpc	Snrp1c|U1-C|U1C	U1 small nuclear ribonucleoprotein C	protein-coding
mm_163462.1	chr12	100569860	100569860	+	1	NA	intron (NM_153587, intron 14 of 17)	B1_Mus1|SINE|Alu	-49038	NM_001033213	104718	Mm.295441	NM_001033213	ENSMUSG00000033530	Ttc7b	AA408451|Ttc7l1	tetratricopeptide repeat domain 7B	protein-coding
mm_23308.1	chr3	53041518	53041579	+	1	NA	promoter-TSS (NM_175386)	promoter-TSS (NM_175386)	1	NM_175386	108927	Mm.118617	NM_175386	ENSMUSG00000048332	Lhfp	2810489O06Rik|AI194968	lipoma HMGIC fusion partner	protein-coding
mm_90147.1	chr10	118141561	118141565	+	1	NA	promoter-TSS (NM_010785)	promoter-TSS (NM_010785)	-224	NM_001162904	17245	Mm.101191	NM_010785	ENSMUSG00000020212	Mdm1	Arrd2|Mdm-1	transformed mouse 3T3 cell double minute 1	protein-coding
mm_4327.1	chr1	171852093	171852105	+	1	NA	exon (NM_013489, exon 3 of 9)	exon (NM_013489, exon 3 of 9)	12402	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_69179.1	chr7	127218838	127218856	-	1	NA	promoter-TSS (NM_017461)	promoter-TSS (NM_017461)	-402	NM_017461	54204	Mm.18	NM_017461	ENSMUSG00000000486	Sept1	Diff6|Pnutl3	septin 1	protein-coding
mm_108469.1	chr12	83641501	83641505	+	1	NA	intron (NM_027349, intron 1 of 18)	intron (NM_027349, intron 1 of 18)	9269	NM_027349	67039	Mm.46005	NM_027349	ENSMUSG00000010608	Rbm25	2600011C06Rik|2610015J01Rik|A130095G20Rik|AI159652|AL023075|AU043498|RNPC7	RNA binding motif protein 25	protein-coding
mm_139075.1	chr17	46655516	46655520	+	1	NA	exon (NM_025611, exon 8 of 26)	exon (NM_025611, exon 8 of 26)	5180	NM_025611	66515	Mm.329078	NM_025611	ENSMUSG00000038545	Cul7	2510004L20Rik|AA409809|C230011P08Rik|p185|p193	cullin 7	protein-coding
mm_55163.1	chr6	51873677	51873692	-	1	NA	intron (NM_018773, intron 11 of 12)	intron (NM_018773, intron 11 of 12)	138865	NM_018773	54353	Mm.221479	NM_018773	ENSMUSG00000059182	Skap2	2610021A10Rik|AA960083|BB137539|RA70|SKAP-HOM|Saps|Scap2|mSKAP55R	src family associated phosphoprotein 2	protein-coding
mm_56259.1	chr6	90810080	90810094	-	1	NA	promoter-TSS (NM_001134384)	promoter-TSS (NM_001134384)	36	NM_001134384	232227	Mm.196943	NM_182784	ENSMUSG00000034312	Iqsec1	AW561907|BC026481|BRAG2|D6Ertd349e|cI-43	IQ motif and Sec7 domain 1	protein-coding
mm_141209.1	chr17	27133593	27133603	-	1	NA	intron (NM_026063, intron 1 of 3)	CpG	293	NM_026063	67267	Mm.272389	NM_026063	ENSMUSG00000024208	Uqcc2	2900010M23Rik|Cbp6|M19|Mnf1	ubiquinol-cytochrome c reductase complex assembly factor 2	protein-coding
mm_142292.1	chr17	40792676	40792681	-	1	NA	intron (NM_001204071, intron 2 of 9)	intron (NM_001204071, intron 2 of 9)	1468	NM_001204071	22024	Mm.1296	NM_009420	ENSMUSG00000023930	Crisp2	CRISP-2|GAPDL5|Tpx-1|Tpx1	cysteine-rich secretory protein 2	protein-coding
mm_64292.1	chr7	141858347	141858390	+	1	NA	exon (NM_028801, exon 31 of 49)	exon (NM_028801, exon 31 of 49)	19296	NM_028801	74180	Mm.200752	NM_028801	ENSMUSG00000066108	Muc5b	2300002I04Rik|A130042M24|AV085033|MUC5|MUC9|mucin 5b	mucin 5, subtype B, tracheobronchial	protein-coding
mm_22371.1	chr2	181150970	181150996	-	1	NA	exon (NM_007906, exon 5 of 8)	exon (NM_007906, exon 5 of 8)	6032	NM_007906	13628	Mm.2645	NM_007906	ENSMUSG00000016349	Eef1a2	Eef1a|S1|wasted|wst	eukaryotic translation elongation factor 1 alpha 2	protein-coding
mm_11438.1	chr2	32017488	32017503	+	1	NA	intron (NM_172268, intron 22 of 35)	intron (NM_172268, intron 22 of 35)	-33451	NR_106135	102466844		NR_106135	ENSMUSG00000099075	Mir7674	Gm27563|mmu-mir-7674	microRNA 7674	ncRNA
mm_164804.1	chr18	25194957	25194998	+	1	NA	intron (NM_001033532, intron 4 of 10)	RLTR10D|LTR|ERVK	25957	NM_001033532	225289	Mm.391081	NM_001033532	ENSMUSG00000033632	AW554918	4921538P22|AI461742|Kiaa1328|mKIAA1328	expressed sequence AW554918	protein-coding
mm_1784.1	chr1	78537963	78537972	+	1	NA	exon (NM_026713, exon 7 of 7)	exon (NM_026713, exon 7 of 7)	26907	NM_026713	68393	Mm.41325	NM_026713	ENSMUSG00000012187	Mogat1	0610030A14Rik|1110064N14Rik|Dgat2l|Dgat2l1|MGAT1|WI1-2612I11.1|mDC2	monoacylglycerol O-acyltransferase 1	protein-coding
mm_55627.1	chr6	72314042	72314077	-	1	NA	3' UTR (NM_001282071, exon 11 of 11)	3' UTR (NM_001282071, exon 11 of 11)	9449	NM_147779	20388	Mm.46033	NM_147779	ENSMUSG00000056370	Sftpb	AI562151|SF-B|SP-B|Sftp-3|Sftp3	surfactant associated protein B	protein-coding
mm_48446.1	chr5	140649019	140649052	-	1	NA	promoter-TSS (NM_175274)	promoter-TSS (NM_175274)	-4	NM_175274	78339	Mm.28947	NM_175274	ENSMUSG00000036565	Ttyh3	2900029G13Rik|AI414930|TTY3|mTTY3	tweety family member 3	protein-coding
mm_69256.1	chr7	127875634	127875673	-	1	NA	intron (NM_146259, intron 1 of 2)	CpG	1170	NM_146259	244219	Mm.207872	NM_146259	ENSMUSG00000049728	Zfp668	BC030314|E130018B19Rik|Znf668	zinc finger protein 668	protein-coding
mm_125217.1	chr15	34083012	34083020	+	1	NA	5' UTR (NM_026002, exon 1 of 12)	5' UTR (NM_026002, exon 1 of 12)	297	NM_026002	67154	Mm.130883	NM_026002	ENSMUSG00000022255	Mtdh	2610103J23Rik|3D3|3D3/Lyric|AEG-1|AV353288|D8Bwg1112e|Lyric	metadherin	protein-coding
mm_4587.1	chr1	178319270	178319289	+	1	NA	intron (NM_025511, intron 1 of 3)	CpG	126	NM_025511	66359	Mm.489720	NM_025511	ENSMUSG00000026500	Cox20	2310005N03Rik|Fam36a	COX20 Cox2 chaperone	protein-coding
mm_106421.1	chr11	119252290	119252319	-	1	NA	intron (NM_175430, intron 13 of 18)	intron (NM_175430, intron 13 of 18)	-15659	NM_001159324	14387	Mm.4793	NM_008064	ENSMUSG00000025579	Gaa	E430018M07Rik	glucosidase, alpha, acid	protein-coding
mm_38179.1	chr4	135272707	135272717	-	1	NA	promoter-TSS (NM_013885)	promoter-TSS (NM_013885)	48	NM_013885	29876	Mm.257765	NM_013885	ENSMUSG00000037242	Clic4	D0Jmb3|TU-74|mc3s5|mtCLIC	chloride intracellular channel 4 (mitochondrial)	protein-coding
mm_43474.1	chr5	136695192	136695203	+	1	NA	intron (NM_001085387, intron 1 of 4)	intron (NM_001085387, intron 1 of 4)	1020	NM_001085387	59310	Mm.5178	NM_021611	ENSMUSG00000005474	Myl10	1700027I08Rik|Mylc2pl|PLRLC	myosin, light chain 10, regulatory	protein-coding
mm_57956.1	chr6	135168163	135168210	-	1	NA	promoter-TSS (NM_013546)	promoter-TSS (NM_013546)	29	NM_013546	15199	Mm.378937	NM_013546	ENSMUSG00000042770	Hebp1	Hebp|p22HBP	heme binding protein 1	protein-coding
mm_133015.1	chr16	56204285	56204289	+	1	NA	promoter-TSS (NM_174876)	promoter-TSS (NM_174876)	-26	NM_174876	224224	Mm.151998	NM_174876	ENSMUSG00000035270	Impg2	IPM200|PG10.2|Rsbp|Spacrcan	interphotoreceptor matrix proteoglycan 2	protein-coding
mm_91385.1	chr10	30629649	30629653	-	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	-11285	NM_025798	66847	Mm.46218	NM_025798	ENSMUSG00000019791	Hint3	0610010I17Rik|AV009015|HINT-3|HINT-4|HINT4	histidine triad nucleotide binding protein 3	protein-coding
mm_90176.1	chr10	119692034	119692048	+	1	NA	intron (NM_133442, intron 1 of 21)	intron (NM_133442, intron 1 of 21)	69658	NR_045359	75321	Mm.402041	NR_045359	ENSMUSG00000084764	Grip1os2	4930564G21Rik	glutamate receptor interacting protein 1, opposite strand 2	ncRNA
mm_140206.1	chr17	83775523	83775539	+	1	NA	intron (NM_001171053, intron 8 of 13)	intron (NM_001171053, intron 8 of 13)	69368	NM_001171052	116871	Mm.277668	NM_054082	ENSMUSG00000055817	Mta3	1110002J22Rik|mKIAA1266	metastasis associated 3	protein-coding
mm_134595.1	chr16	20589985	20590042	-	1	NA	intron (NM_001144953, intron 1 of 22)	intron (NM_001144953, intron 1 of 22)	431	NM_001144953	328643	Mm.40539	NM_182636	ENSMUSG00000046613	Vwa5b2	BB182430|EG328644|Gm1738|Gm931	von Willebrand factor A domain containing 5B2	protein-coding
mm_114548.1	chr13	73956572	73956572	+	1	NA	intron (NM_001308041, intron 14 of 15)	intron (NM_001308041, intron 14 of 15)	-7290	NM_027704	71164	Mm.66995	NM_027704	ENSMUSG00000069189	Zdhhc11	4933421L13Rik|DHHC-11|Zdhhc20	zinc finger, DHHC domain containing 11	protein-coding
mm_90512.1	chr10	128042834	128042847	+	1	NA	exon (NM_001113199, exon 3 of 9)	exon (NM_001113199, exon 3 of 9)	7494	NM_001113199	17938	Mm.3746	NM_013608	ENSMUSG00000061315	Naca	AL022831|AL024382|Gm1878|mKIAA0363|skNAC	nascent polypeptide-associated complex alpha polypeptide	protein-coding
mm_151393.1	chr19	56425757	56425771	+	1	NA	intron (NM_007611, intron 2 of 6)	intron (NM_007611, intron 2 of 6)	28635	NM_007611	12369	Mm.35687	NM_007611	ENSMUSG00000025076	Casp7	AI314680|CMH-1|ICE-IAP3|Mch3|caspase-7|mCASP-7	caspase 7	protein-coding
mm_119460.1	chr14	47068994	47069032	+	1	NA	promoter-TSS (NM_001310544)	promoter-TSS (NM_001310544)	36	NM_001310544	74480	Mm.214454	NM_028966	ENSMUSG00000021838	Samd4	1700024G08Rik|1700111L17Rik|4933436G17Rik|Samd4a|Smaug|Smaug1|sunk	sterile alpha motif domain containing 4	protein-coding
mm_104688.1	chr11	97766509	97766574	-	1	NA	promoter-TSS (NM_026186)	promoter-TSS (NM_026186)	72	NM_026186	67480	Mm.33206	NM_026186	ENSMUSG00000018541	Cwc25	1300013D05Rik|AA473636|Ccdc49|R75228	CWC25 spliceosome-associated protein	protein-coding
mm_161032.1	chr12	16740194	16740194	-	1	NA	5' UTR (NM_015764, exon 4 of 35)	5' UTR (NM_015764, exon 4 of 35)	17045	NM_001252071	268527	Mm.428062	NM_015764	ENSMUSG00000036523	Greb1	5730583K22Rik|9130004E13|AF180470|AU023194|mKIAA0575	gene regulated by estrogen in breast cancer protein	protein-coding
mm_1846.1	chr1	82925382	82925390	+	1	NA	Intergenic	Intergenic	85926	NM_001347077	15463	Mm.392569	NM_010472	ENSMUSG00000026159	Agfg1	AU045498|C130049H11Rik|C85612|D730048C23Rik|Hrb|RAB|Rip	ArfGAP with FG repeats 1	protein-coding
mm_42921.1	chr5	122720342	122720353	+	1	NA	intron (NM_001310720, intron 5 of 10)	B1F|SINE|Alu	12803	NM_001310718	18438	Mm.290884	NM_011026	ENSMUSG00000029470	P2rx4	AI504491|AW555605|D5Ertd444e|P2X4	purinergic receptor P2X, ligand-gated ion channel 4	protein-coding
mm_27149.1	chr3	33079253	33079258	-	1	NA	intron (NR_040595, intron 3 of 7)	intron (NR_040595, intron 3 of 7)	3805	NM_021483	58869	Mm.151332	NM_021483	ENSMUSG00000027674	Pex5l	1700016J08Rik|PXR2|Pex2|TRIP8b|pex5Rp	peroxisomal biogenesis factor 5-like	protein-coding
mm_153316.1	chr19	38043761	38043801	-	1	NA	promoter-TSS (NM_001099634)	promoter-TSS (NM_001099634)	-204	NM_001302140	226101	Mm.34674	NM_177035	ENSMUSG00000048612	Myof	2310004N10Rik|2310051D19Rik|E030042N20Rik|Fer1l3	myoferlin	protein-coding
mm_107235.1	chr12	26478255	26478277	+	1	NA	3' UTR (NM_020557, exon 5 of 5)	3' UTR (NM_020557, exon 5 of 5)	9051	NM_020557	22169	Mm.271839	NM_020557	ENSMUSG00000020638	Cmpk2	1200004E04Rik|TDKI|Tyki	cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial	protein-coding
mm_152253.1	chr19	8723357	8723378	-	1	NA	promoter-TSS (NR_002896)	promoter-TSS (NR_002896)	2	NM_001161413	17254	Mm.4114	NM_008577	ENSMUSG00000010095	Slc3a2	4F2|4F2HC|AI314110|Cd98|Ly-10|Ly-m10|Ly10|Mdu1|Mgp-2hc|NACAE	solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2	protein-coding
mm_172485.1	chr7	51862379	51862380	+	1	NA	promoter-TSS (NM_001115087)	promoter-TSS (NM_001115087)	-112	NM_001115087	100040608	Mm.322643	NM_001115087	ENSMUSG00000092118	Fancf	A730016A17	Fanconi anemia, complementation group F	protein-coding
mm_83274.1	chr9	43071152	43071160	-	1	NA	intron (NM_027144, intron 1 of 40)	intron (NM_027144, intron 1 of 40)	34562	NM_027144	69632	Mm.275266	NM_027144	ENSMUSG00000059495	Arhgef12	2310014B11Rik|AU019857|Larg|mKIAA0382	Rho guanine nucleotide exchange factor (GEF) 12	protein-coding
mm_171947.1	chr5	7622593	7622597	-	1	NA	Intergenic	Intergenic	-278217	NM_001163223	207618	Mm.478808	NM_001163223	ENSMUSG00000092094	Zfp804b	Gm441	zinc finger protein 804B	protein-coding
mm_108308.1	chr12	79482002	79482004	+	1	NA	intron (NM_009014, intron 7 of 10)	intron (NM_009014, intron 7 of 10)	184652	NM_001252562	19363	Mm.341756	NM_009014	ENSMUSG00000059060	Rad51b	AI553500|R51H2|Rad51l1|mREC2	RAD51 paralog B	protein-coding
mm_84861.1	chr9	78585114	78585124	-	1	NA	intron (NM_001276452, intron 1 of 10)	RLTR18B|LTR|ERVK	2926	NM_172773	235504	Mm.46932	NM_172773	ENSMUSG00000049624	Slc17a5	4631416G20Rik|4732491M05|AST|ISSD|NSD|SD|SIALIN|SIASD|SLD	solute carrier family 17 (anion/sugar transporter), member 5	protein-coding
mm_89527.1	chr10	94467909	94467933	+	1	NA	Intergenic	Intergenic	-46936	NM_172051	319880	Mm.23047	NM_172051	ENSMUSG00000020023	Tmcc3	AW488095|C630016B22Rik|C88213|Tmcc1	transmembrane and coiled coil domains 3	protein-coding
mm_72872.1	chr8	88680941	88680943	+	1	NA	intron (NM_145857, intron 9 of 12)	intron (NM_145857, intron 9 of 12)	-16086	NM_001128170	74256	Mm.490395	NM_173369	ENSMUSG00000036712	Cyld	2010013M14Rik|2900009M21Rik|C130039D01Rik|CDMT|CYLD1|EAC|mKIAA0849	CYLD lysine 63 deubiquitinase	protein-coding
mm_96006.1	chr11	59541602	59541615	+	1	NA	Intergenic	Intergenic	-1078	NM_145827	216799	Mm.54174	NM_145827	ENSMUSG00000032691	Nlrp3	AGTAVPRL|AII/AVP|Cias1|FCAS|FCU|MWS|Mmig1|NALP3|Pypaf1	NLR family, pyrin domain containing 3	protein-coding
mm_32870.1	chr4	118437478	118437504	+	1	NA	promoter-TSS (NM_023223)	promoter-TSS (NM_023223)	-148	NM_023223	107995	Mm.261764	NM_023223	ENSMUSG00000006398	Cdc20	2310042N09Rik|C87100|p55CDC	cell division cycle 20	protein-coding
mm_67361.1	chr7	79838683	79838692	-	1	NA	exon (NM_008486, exon 7 of 20)	exon (NM_008486, exon 7 of 20)	3665	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_20721.1	chr2	136387692	136387698	-	1	NA	5' UTR (NM_172858, exon 1 of 10)	5' UTR (NM_172858, exon 1 of 10)	272	NM_172858	241656	Mm.131572	NM_172858	ENSMUSG00000039913	Pak7	2900083L08Rik|6430627N20|Pak5	p21 protein (Cdc42/Rac)-activated kinase 7	protein-coding
mm_113290.1	chr13	30331829	30331861	+	1	NA	Intergenic	Intergenic	-4511	NM_177322	11607	Mm.35062	NM_177322	ENSMUSG00000049115	Agtr1a	1810074K20Rik|AG2S|AI551199|AT1|AT1a|AT2R1|AT2R1A|Agtr-1a|Agtr1|Angtr-1a	angiotensin II receptor, type 1a	protein-coding
mm_17217.1	chr2	25493895	25493904	-	1	NA	promoter-TSS (NM_029958)	promoter-TSS (NM_029958)	12	NM_029958	77701	Mm.99123	NM_029958	ENSMUSG00000026943	Lcn12	9230102M18Rik	lipocalin 12	protein-coding
mm_120772.1	chr14	73552828	73552838	+	1	NA	promoter-TSS (NM_011506)	promoter-TSS (NM_011506)	47	NM_011506	20916	Mm.38951	NM_011506	ENSMUSG00000022110	Sucla2	4930547K18Rik|A-SCS	succinate-Coenzyme A ligase, ADP-forming, beta subunit	protein-coding
mm_76771.1	chr8	95818265	95818281	-	1	NA	intron (NR_015574, intron 3 of 3)	intron (NR_015574, intron 3 of 3)	-10811	NM_001205226	234594	Mm.259220	NM_153164	ENSMUSG00000036550	Cnot1	6030411K04Rik|AA815922|D830048B13	CCR4-NOT transcription complex, subunit 1	protein-coding
mm_56194.1	chr6	88837443	88837451	-	1	NA	intron (NM_030251, intron 10 of 11)	intron (NM_030251, intron 10 of 11)	4488	NM_030251	80283	Mm.166858	NM_030251	ENSMUSG00000030083	Abtb1	AI847549|BC003234|BPOZ|EF1ABP	ankyrin repeat and BTB (POZ) domain containing 1	protein-coding
mm_151550.1	chr19	59458650	59458662	+	1	NA	promoter-TSS (NM_010132)	promoter-TSS (NM_010132)	-21	NR_002863	329078	Mm.80382	NR_002863	ENSMUSG00000087095	Emx2os	-	Emx2 opposite strand/antisense transcript (non-protein coding)	ncRNA
mm_157536.1	chrX	51130166	51130198	-	1	NA	exon (NM_134163, exon 5 of 8)	exon (NM_134163, exon 5 of 8)	75808	NM_001310515	171170	Mm.295324	NM_134163	ENSMUSG00000036109	Mbnl3	A530038J18Rik|AI661274|CHCR|E430034C16Rik|MBLX|MBLX39|MBXL	muscleblind-like 3 (Drosophila)	protein-coding
mm_64183.1	chr7	141459611	141459626	+	1	NA	non-coding (NR_028142, exon 10 of 10)	non-coding (NR_028142, exon 10 of 10)	-1476	NM_001025103	213573	Mm.386851	NM_001025103	ENSMUSG00000048200	Cracr2b	6330520A15Rik|BC026645|Cracr2a|Efcab4|Efcab4a	calcium release activated channel regulator 2B	protein-coding
mm_131522.1	chr16	17619471	17619479	+	1	NA	intron (NM_001164609, intron 1 of 19)	CpG	121	NM_001164609	77626	Mm.34659	NM_029945	ENSMUSG00000005899	Smpd4	4122402O22Rik|mKIAA1418	sphingomyelin phosphodiesterase 4	protein-coding
mm_43174.1	chr5	127615811	127615822	+	1	NA	intron (NM_133895, intron 1 of 7)	intron (NM_133895, intron 1 of 7)	1576	NM_133895	100561	Mm.28506	NM_133895	ENSMUSG00000029416	Slc15a4	AA987064|AW742963|C130069N12Rik|PHT1|PTR4	solute carrier family 15, member 4	protein-coding
mm_37079.1	chr4	116371660	116371663	-	1	NA	intron (NM_008641, intron 4 of 28)	AT_rich|Low_complexity|Low_complexity	92520	NM_001042743	17776	Mm.9287	NM_008641	ENSMUSG00000003810	Mast2	MAST205|Mtssk	microtubule associated serine/threonine kinase 2	protein-coding
mm_147030.1	chr18	34720246	34720262	-	1	NA	5' UTR (NM_010280, exon 1 of 8)	5' UTR (NM_010280, exon 1 of 8)	133	NM_010280	14587	Mm.16520	NM_010280	ENSMUSG00000024366	Gfra3	GFRalpha3|Y15110	glial cell line derived neurotrophic factor family receptor alpha 3	protein-coding
mm_135359.1	chr16	43973914	43973922	-	1	NA	exon (NM_001007460, exon 2 of 4)	exon (NM_001007460, exon 2 of 4)	5132	NM_001007460	332175	Mm.327852	NM_001007460	ENSMUSG00000036304	Zdhhc23	Gm1751|Gm779|nidd	zinc finger, DHHC domain containing 23	protein-coding
mm_147375.1	chr18	43634789	43634792	-	1	NA	intron (NM_001163637, intron 1 of 21)	ORR1C2|LTR|ERVL-MaLR	52983	NM_001163637	76217	Mm.134602	NM_001163637	ENSMUSG00000024502	Jakmip2	6430702L21Rik|AI850334|D930046L20Rik	janus kinase and microtubule interacting protein 2	protein-coding
mm_97141.1	chr11	75214104	75214127	+	1	NA	intron (NM_177708, intron 1 of 1)	intron (NM_177708, intron 1 of 1)	20122	NM_177708	237847	Mm.82661	NM_177708	ENSMUSG00000045287	Rtn4rl1	Ngr3|Ngrh2|Ngrl2	reticulon 4 receptor-like 1	protein-coding
mm_74006.1	chr8	121084353	121084368	+	1	NA	promoter-TSS (NM_010426)	promoter-TSS (NM_010426)	-26	NM_010426	15227	Mm.33897	NM_010426	ENSMUSG00000042812	Foxf1	AI450827|FREAC1|Foxf1a|Freac-1|HFH-8|Hfh8	forkhead box F1	protein-coding
mm_46068.1	chr5	92309949	92310000	-	1	NA	promoter-TSS (NM_172713)	promoter-TSS (NM_172713)	50	NM_172713	231452	Mm.86564	NM_172713	ENSMUSG00000029415	Sdad1	4931421J16|AA591032|AW538460	SDA1 domain containing 1	protein-coding
mm_100850.1	chr11	5803684	5803689	-	1	NA	exon (NM_018870, exon 1 of 3)	exon (NM_018870, exon 1 of 3)	110	NM_018870	56012	Mm.219627	NM_018870	ENSMUSG00000020475	Pgam2	-	phosphoglycerate mutase 2	protein-coding
mm_145654.1	chr18	61129700	61129718	+	1	NA	exon (NM_001037859, exon 20 of 22)	exon (NM_001037859, exon 20 of 22)	12241	NR_105949	102466212		NR_105949	ENSMUSG00000098389	Mir6983	Gm27496|mmu-mir-6983	microRNA 6983	ncRNA
mm_60458.1	chr7	44477654	44477674	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-6853	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_102495.1	chr11	60352870	60352896	-	1	NA	promoter-TSS (NM_001039093)	promoter-TSS (NM_001039093)	22	NM_153080	216810	Mm.218875	NM_153080	ENSMUSG00000000538	Tom1l2	2900016I08Rik|A730055F12Rik|AU042072|Srebf1	target of myb1-like 2 (chicken)	protein-coding
mm_138774.1	chr17	37195251	37195273	+	1	NA	exon (NM_023137, exon 2 of 2)	exon (NM_023137, exon 2 of 2)	1370	NM_023137	24108	Mm.140210	NM_023137	ENSMUSG00000035186	Ubd	FAT10	ubiquitin D	protein-coding
mm_145824.1	chr18	65436125	65436138	+	1	NA	intron (NM_172833, intron 1 of 15)	B3A|SINE|B2	5134	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_39466.1	chr5	19227056	19227066	+	1	NA	promoter-TSS (NR_102342)	promoter-TSS (NR_102342)	15	NM_001170746	50791	Mm.332231	NM_015823	ENSMUSG00000040003	Magi2	AIP-1|Acvri1|Acvrinp1|Acvrip1|Magi-2|S-SCAM|mKIAA0705	membrane associated guanylate kinase, WW and PDZ domain containing 2	protein-coding
mm_41799.1	chr5	103753736	103753758	+	1	NA	promoter-TSS (NM_133919)	promoter-TSS (NM_133919)	-415	NM_133919	17355	Mm.6949	NM_133919	ENSMUSG00000029313	Aff1	9630032B01Rik|AW319193|Af4|Mllt2h|Rob	AF4/FMR2 family, member 1	protein-coding
mm_142855.1	chr17	51812310	51812326	-	1	NA	promoter-TSS (NM_001163630)	promoter-TSS (NM_001163630)	-264	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_40531.1	chr5	57920307	57920327	+	1	NA	intron (NM_001122758, intron 2 of 2)	intron (NM_001122758, intron 2 of 2)	202236	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_29334.1	chr3	108146081	108146150	-	1	NA	promoter-TSS (NM_010306)	promoter-TSS (NM_010306)	37	NM_010306	14679	Mm.271703	NM_010306	ENSMUSG00000000001	Gnai3	AI158965|AW537698|Galphai3|Gnai-3	guanine nucleotide binding protein (G protein), alpha inhibiting 3	protein-coding
mm_34378.1	chr4	144895565	144895596	+	1	NA	intron (NM_011303, intron 1 of 5)	intron (NM_011303, intron 1 of 5)	2443	NM_011303	20148	Mm.14063	NM_011303	ENSMUSG00000066026	Dhrs3	Rsdr1|retSDR1	dehydrogenase/reductase (SDR family) member 3	protein-coding
mm_75601.1	chr8	61760068	61760103	-	1	NA	promoter-TSS (NM_001293773)	promoter-TSS (NM_001293773)	13	NM_001293773	72333	Mm.29933	NM_001081390	ENSMUSG00000058056	Palld	2410003B16Rik|6030492A02	palladin, cytoskeletal associated protein	protein-coding
mm_104534.1	chr11	96308874	96308891	-	1	NA	Intergenic	Intergenic	-1972	NR_131758	75395	Mm.440014	NR_131758	ENSMUSG00000085645	Hoxb5os	0610040B09Rik|AV302770|Hoxb5/6as	homeobox B5 and homeobox B6, opposite strand	ncRNA
mm_143070.1	chr17	57022422	57022436	-	1	NA	3' UTR (NM_010613, exon 18 of 18)	3' UTR (NM_010613, exon 18 of 18)	9078	NM_010613	16549	Mm.34296	NM_010613	ENSMUSG00000007670	Khsrp	6330409F21Rik|Fbp2|Fubp2|Ksrp	KH-type splicing regulatory protein	protein-coding
mm_148235.1	chr18	80469665	80469719	-	1	NA	promoter-TSS (NM_026295)	promoter-TSS (NM_026295)	-25	NM_026295	67655	Mm.312893	NM_026295	ENSMUSG00000033323	Ctdp1	4930563P03Rik|AW553592	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) phosphatase, subunit 1	protein-coding
mm_22310.1	chr2	180429785	180429828	-	1	NA	Intergenic	B4A|SINE|B4	-31172	NM_148933	108115	Mm.133687	NM_148933	ENSMUSG00000038963	Slco4a1	OATP-E|Slc21a12	solute carrier organic anion transporter family, member 4a1	protein-coding
mm_47803.1	chr5	132543137	132543159	-	1	NA	promoter-TSS (NM_177047)	promoter-TSS (NM_177047)	-805	NM_177047	319974	Mm.409595	NM_177047	ENSMUSG00000029673	Auts2	2700063G02Rik|A730011F23Rik|D830032G16Rik	autism susceptibility candidate 2	protein-coding
mm_62342.1	chr7	100498118	100498142	+	1	NA	exon (NM_011671, exon 5 of 8)	exon (NM_011671, exon 5 of 8)	4772	NM_011671	22228	Mm.171378	NM_011671	ENSMUSG00000033685	Ucp2	Slc25a8	uncoupling protein 2 (mitochondrial, proton carrier)	protein-coding
mm_21395.1	chr2	157566701	157566723	-	1	NA	promoter-TSS (NM_016916)	promoter-TSS (NM_016916)	-351	NM_016916	53619	Mm.480461	NM_016916	ENSMUSG00000067787	Blcap	AI462828|Bc10	bladder cancer associated protein	protein-coding
mm_130513.1	chr15	98862905	98862918	-	1	NA	exon (NM_001033276, exon 11 of 55)	exon (NM_001033276, exon 11 of 55)	8294	NM_001033276	381022	Mm.264889	NM_001033276	ENSMUSG00000048154	Kmt2d	ALR|BC032281|BC058659|C430014K11Rik|KMT2B|Mll2|Mll4	lysine (K)-specific methyltransferase 2D	protein-coding
mm_171138.1	chr3	150073590	150073592	-	1	NA	Intergenic	Intergenic	798854	NR_040591	381482	Mm.393866	NR_040591		Gm1653	-	predicted gene 1653	ncRNA
mm_65706.1	chr7	28378050	28378058	-	1	NA	exon (NM_011756, exon 2 of 2)	exon (NM_011756, exon 2 of 2)	1174	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_78229.1	chr9	21589229	21589244	+	1	NA	non-coding (NR_038062, exon 9 of 9)	non-coding (NR_038062, exon 9 of 9)	-3486	NM_178619	69773	Mm.39704	NM_178619	ENSMUSG00000048429	Timm29	1810026J23Rik	translocase of inner mitochondrial membrane 29	protein-coding
mm_61609.1	chr7	80038332	80038342	+	1	NA	intron (NM_175433, intron 1 of 4)	(T)n|Simple_repeat|Simple_repeat	12109	NM_175433	209225	Mm.290925	NM_175433	ENSMUSG00000048897	Zfp710	5430400N05Rik|9830165K13|AI324798|Znf710	zinc finger protein 710	protein-coding
mm_12882.1	chr2	84727675	84727680	+	1	NA	promoter-TSS (NM_133840)	promoter-TSS (NM_133840)	-409	NM_133840	98985	Mm.21583	NM_133840	ENSMUSG00000027079	Clp1	AI462438|Heab	CLP1, cleavage and polyadenylation factor I subunit	protein-coding
mm_52297.1	chr6	108783208	108783245	+	1	NA	5' UTR (NM_026011, exon 1 of 7)	5' UTR (NM_026011, exon 1 of 7)	167	NM_026011	67166	Mm.271178	NM_026011	ENSMUSG00000030105	Arl8b	2610313E07Rik|3100002J04Rik|Arl10c|gie1	ADP-ribosylation factor-like 8B	protein-coding
mm_122182.1	chr14	31577319	31577334	-	1	NA	promoter-TSS (NM_009937)	promoter-TSS (NM_009937)	57	NM_009937	382864	Mm.239821	NM_009937	ENSMUSG00000057606	Colq	A130034K24Rik	collagen-like tail subunit (single strand of homotrimer) of asymmetric acetylcholinesterase	protein-coding
mm_134159.1	chr16	10791585	10791587	-	1	NA	promoter-TSS (NM_013638)	promoter-TSS (NM_013638)	519	NM_008933	19119	Mm.325769	NM_008933	ENSMUSG00000038015	Prm2	AI528784|Prm-2	protamine 2	protein-coding
mm_111418.1	chr12	91573570	91573572	-	1	NA	intron (NM_175335, intron 3 of 8)	intron (NM_175335, intron 3 of 8)	16078	NM_031391	83602	Mm.275728	NM_031391	ENSMUSG00000020962	Gtf2a1	6330549H03Rik|AA536742|AA959775|AW060250|TfIIAa/b|Tfiia1	general transcription factor II A, 1	protein-coding
mm_79811.1	chr9	64178276	64178356	+	1	NA	promoter-TSS (NM_183316)	promoter-TSS (NM_183316)	-981	NM_183316	330959	Mm.24082	NM_183316	ENSMUSG00000032398	Snapc5	2010103A03Rik	small nuclear RNA activating complex, polypeptide 5	protein-coding
mm_148194.1	chr18	79061055	79061059	-	1	NA	intron (NM_053099, intron 2 of 5)	ORR1A3|LTR|ERVL-MaLR	48334	NM_053099	240427	Mm.312871	NM_053099	ENSMUSG00000024548	Setbp1	C130092E12|Seb|mKIAA0437	SET binding protein 1	protein-coding
mm_29452.1	chr3	113195107	113195112	-	1	NA	Intergenic	LTRIS_Mm|LTR|ERV1	-38382	NM_001190403	545562	Mm.462977	NM_001190403		Amy2b	Amy-X|Amy2-2|OTTMUSG00000022462|mAmy2-1	amylase 2b	protein-coding
mm_7639.1	chr1	127976474	127976484	-	1	NA	exon (NM_001285945, exon 13 of 21)	exon (NM_001285945, exon 13 of 21)	107706	NM_178690	226407	Mm.489713	NM_178690	ENSMUSG00000036104	Rab3gap1	1700003B17Rik|4732493F09Rik|AL117896|Rab3gap|p130	RAB3 GTPase activating protein subunit 1	protein-coding
mm_97490.1	chr11	78328426	78328472	+	1	NA	promoter-TSS (NM_201406)	promoter-TSS (NM_201406)	27	NM_201406	276846	Mm.295908	NM_201406	ENSMUSG00000041958	Pigs	BC058979|Gm393|Gm689	phosphatidylinositol glycan anchor biosynthesis, class S	protein-coding
mm_86939.1	chr10	24595435	24595445	+	1	NA	promoter-TSS (NM_010217)	promoter-TSS (NM_010217)	-2	NM_010217	14219	Mm.390287	NM_010217	ENSMUSG00000019997	Ctgf	Ccn2|Fisp12|Hcs24|fisp-12	connective tissue growth factor	protein-coding
mm_106311.1	chr11	118302391	118302404	-	1	NA	3' UTR (NM_011594, exon 5 of 5)	3' UTR (NM_011594, exon 5 of 5)	-12153	NM_001033528	72344	Mm.232293	NM_001033528	ENSMUSG00000033909	Usp36	2700002L06Rik|mKIAA1453	ubiquitin specific peptidase 36	protein-coding
mm_162316.1	chr1	37998295	37998297	+	1	NA	exon (NM_198303, exon 1 of 24)	exon (NM_198303, exon 1 of 24)	286	NM_198303	226982	Mm.260943	NM_198303	ENSMUSG00000026083	Eif5b	A030003E17Rik|BC018347|IF2	eukaryotic translation initiation factor 5B	protein-coding
mm_17499.1	chr2	28699729	28699739	-	1	NA	promoter-TSS (NM_027283)	promoter-TSS (NM_027283)	-83	NM_027283	69987	Mm.239376	NM_027283	ENSMUSG00000026809	Spaca9	1700026L06Rik|MAST	sperm acrosome associated 9	protein-coding
mm_64744.1	chr7	4771280	4771328	-	1	NA	promoter-TSS (NM_172895)	promoter-TSS (NM_172895)	-34	NM_172895	243822	Mm.333542	NM_172895	ENSMUSG00000092518	Fam71e2	4930401F20Rik	family with sequence similarity 71, member E2	protein-coding
mm_168072.1	chr10	109099561	109099564	+	1	NA	Intergenic	RLTR10A|LTR|ERVK	-88587	NM_001252341	20979	Mm.289702	NM_009306	ENSMUSG00000035864	Syt1	AW124717|G630098F17Rik|SytI	synaptotagmin I	protein-coding
mm_91284.1	chr10	24785001	24785045	-	1	NA	intron (NM_134005, intron 19 of 24)	intron (NM_134005, intron 19 of 24)	51172	NM_134005	209558	Mm.338425	NM_134005	ENSMUSG00000019989	Enpp3	AI876438|CD203c	ectonucleotide pyrophosphatase/phosphodiesterase 3	protein-coding
mm_31888.1	chr4	82508007	82508019	+	1	NA	promoter-TSS (NR_137202)	promoter-TSS (NR_137202)	24	NR_137202	102635783	Mm.41666	NR_137202		Gm11266	OTTMUSG00000000396	predicted gene 11266	ncRNA
mm_64314.1	chr7	141864874	141864883	+	1	NA	exon (NM_028801, exon 31 of 49)	exon (NM_028801, exon 31 of 49)	25806	NM_028801	74180	Mm.200752	NM_028801	ENSMUSG00000066108	Muc5b	2300002I04Rik|A130042M24|AV085033|MUC5|MUC9|mucin 5b	mucin 5, subtype B, tracheobronchial	protein-coding
mm_54856.1	chr6	42593524	42593534	-	1	NA	exon (NM_203396, exon 2 of 7)	exon (NM_203396, exon 2 of 7)	3843	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_53583.1	chr6	137459292	137459315	+	1	NA	intron (NM_001164402, intron 14 of 15)	intron (NM_001164402, intron 14 of 15)	48582	NM_001164403	19277	Mm.186361	NM_011216	ENSMUSG00000030223	Ptpro	D28|GLEPP1|PTPBK|PTPROt|PTPU2|PTPoc|PTPphi|Ptpn15|R-PTP-O	protein tyrosine phosphatase, receptor type, O	protein-coding
mm_32412.1	chr4	107009701	107009726	+	1	NA	exon (NM_198438, exon 5 of 17)	exon (NM_198438, exon 5 of 17)	57153	NM_025500	56280	Mm.29517	NM_025500	ENSMUSG00000028622	Mrpl37	2300004O14Rik|AI132596|MRP-L2|Rpml2	mitochondrial ribosomal protein L37	protein-coding
mm_13774.1	chr2	118709868	118709884	+	1	NA	intron (NM_001290790, intron 29 of 30)	intron (NM_001290790, intron 29 of 30)	-5913	NM_001081971	383787	Mm.35758	NM_001081971	ENSMUSG00000078137	Ankrd63	Gm1337	ankyrin repeat domain 63	protein-coding
mm_159417.1	chr3	105960255	105960255	-	1	NA	promoter-TSS (NM_009725)	promoter-TSS (NM_009725)	-7	NM_009725	11950	Mm.251152	NM_009725	ENSMUSG00000000563	Atp5f1	C76477	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit B1	protein-coding
mm_146854.1	chr18	24121811	24121881	-	1	NA	promoter-TSS (NM_172625)	promoter-TSS (NM_172625)	-27	NM_172625	225280	Mm.258973	NM_172625	ENSMUSG00000047989	Ino80c	D030070L09Rik	INO80 complex subunit C	protein-coding
mm_7449.1	chr1	120258869	120258885	-	1	NA	intron (NM_001085409, intron 2 of 5)	intron (NM_001085409, intron 2 of 5)	6403	NM_133186	68428	Mm.181033	NM_133186	ENSMUSG00000026389	Steap3	1010001D01Rik|Tsap6|pHyde	STEAP family member 3	protein-coding
mm_93336.1	chr10	99759451	99759469	-	1	NA	5' UTR (NM_027945, exon 1 of 1)	5' UTR (NM_027945, exon 1 of 1)	198	NM_027945	71832	Mm.483162	NM_027945	ENSMUSG00000046934	Csl	1700007H16Rik	citrate synthase like	protein-coding
mm_107229.1	chr12	26478012	26478021	+	1	NA	exon (NM_020557, exon 5 of 5)	exon (NM_020557, exon 5 of 5)	8801	NM_020557	22169	Mm.271839	NM_020557	ENSMUSG00000020638	Cmpk2	1200004E04Rik|TDKI|Tyki	cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial	protein-coding
mm_126786.1	chr15	86214462	86214472	+	1	NA	promoter-TSS (NM_145476)	promoter-TSS (NM_145476)	8	NM_145476	223754	Mm.28904	NM_145476	ENSMUSG00000051864	Tbc1d22a	BC023106|D15Ertd781e	TBC1 domain family, member 22a	protein-coding
mm_166409.1	chr5	137149260	137149268	-	1	NA	Intergenic	Intergenic	-33057	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_144115.1	chr18	4375584	4375623	+	1	NA	promoter-TSS (NM_026157)	promoter-TSS (NM_026157)	11	NM_026157	67440	Mm.49826	NM_026157	ENSMUSG00000024234	Mtpap	0610027A18Rik|AW551379|Papd1	mitochondrial poly(A) polymerase	protein-coding
mm_162346.1	chr1	52934562	52934563	+	1	NA	intron (NM_144953, intron 1 of 1)	L1MC1|LINE|L1	18278	NM_144953	67080	Mm.236287	NM_144953	ENSMUSG00000043629	1700019D03Rik	2410136C24Rik|AA410151|smAKAP	RIKEN cDNA 1700019D03 gene	protein-coding
mm_71359.1	chr8	45658904	45658914	+	1	NA	5' UTR (NM_001205219, exon 2 of 24)	5' UTR (NM_001205219, exon 2 of 24)	-3084	NM_001310708	234214	Mm.211096	NM_172752	ENSMUSG00000031626	Sorbs2	2010203O03Rik|9430041O17Rik|A530071H08|Argbp2|mKIAA0777|nArgBP2	sorbin and SH3 domain containing 2	protein-coding
mm_96900.1	chr11	70451956	70451974	+	1	NA	promoter-TSS (NM_025397)	promoter-TSS (NM_025397)	34	NM_025397	66172	Mm.46424	NM_025397	ENSMUSG00000018923	Med11	1110030J09Rik|AI465144|AW545069	mediator complex subunit 11	protein-coding
mm_23969.1	chr3	84978130	84978133	+	1	NA	3' UTR (NM_080428, exon 11 of 11)	3' UTR (NM_080428, exon 11 of 11)	25920	NM_080428	50754	Mm.196475	NM_080428	ENSMUSG00000028086	Fbxw7	1110001A17Rik|AGO|Cdc4|Fbw7|Fbwd6|Fbx30|Fbxo30|Fbxw6|SEL-10	F-box and WD-40 domain protein 7	protein-coding
mm_41049.1	chr5	86110244	86110249	+	1	NA	TTS (NM_172712)	TTS (NM_172712)	38500	NM_001310639	56792	Mm.131237	NM_019992	ENSMUSG00000029254	Stap1	AI586015|Brdg1|STAP-1	signal transducing adaptor family member 1	protein-coding
mm_86561.1	chr10	11281361	11281383	+	1	NA	promoter-TSS (NM_027968)	promoter-TSS (NM_027968)	42	NM_027968	71865	Mm.276229	NM_027968	ENSMUSG00000047648	Fbxo30	1700026A16Rik|MUSA1	F-box protein 30	protein-coding
mm_151927.1	chr19	5800139	5800149	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	2528	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_48652.1	chr5	145868582	145868598	-	1	NA	exon (NM_007818, exon 7 of 13)	exon (NM_007818, exon 7 of 13)	11264	NM_007818	13112	Mm.332844	NM_007818	ENSMUSG00000056035	Cyp3a11	AI256190|Cyp3a|IIIAm1|Pcn	cytochrome P450, family 3, subfamily a, polypeptide 11	protein-coding
mm_62322.1	chr7	100372093	100372101	+	1	NA	promoter-TSS (NM_001017985)	promoter-TSS (NM_001017985)	-136	NM_001017985	277939	Mm.276374	NM_001017985	ENSMUSG00000047248	C2cd3	AU020772	C2 calcium-dependent domain containing 3	protein-coding
mm_2154.1	chr1	88186603	88186619	+	1	NA	intron (NM_201643, intron 1 of 4)	intron (NM_201643, intron 1 of 4)	-14000	NM_013701	22236	Mm.300095	NM_013701	ENSMUSG00000090171	Ugt1a2	UDPGT 1-2|Ugt1	UDP glucuronosyltransferase 1 family, polypeptide A2	protein-coding
mm_68694.1	chr7	119601114	119601118	-	1	NA	TTS (NM_146197)	TTS (NM_146197)	-16712	NM_054094	117147	Mm.427560	NM_054094	ENSMUSG00000033533	Acsm1	Acas3|Bucs1|Macs	acyl-CoA synthetase medium-chain family member 1	protein-coding
mm_24372.1	chr3	90220784	90220830	+	1	NA	promoter-TSS (NM_026677)	promoter-TSS (NM_026677)	23	NM_026677	68328	Mm.29355	NM_026677	ENSMUSG00000027935	Rab13	0610007N03Rik|B230212B15Rik	RAB13, member RAS oncogene family	protein-coding
mm_35666.1	chr4	43562313	43562323	-	1	NA	promoter-TSS (NM_013497)	promoter-TSS (NM_013497)	265	NM_011602	21894	Mm.208601	NM_011602	ENSMUSG00000028465	Tln1	Tln	talin 1	protein-coding
mm_50533.1	chr6	49045670	49045680	+	1	NA	intron (NM_053110, intron 4 of 10)	intron (NM_053110, intron 4 of 10)	9157	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_42589.1	chr5	117357211	117357223	+	1	NA	promoter-TSS (NM_021539)	promoter-TSS (NM_021539)	-88	NM_021539	59043	Mm.28489	NM_021539	ENSMUSG00000029364	Wsb2	AA673511|Swip2|WSB-2	WD repeat and SOCS box-containing 2	protein-coding
mm_20018.1	chr2	119324957	119324980	-	1	NA	promoter-TSS (NM_019454)	promoter-TSS (NM_019454)	-816	NM_019454	54485	Mm.143719	NM_019454	ENSMUSG00000027314	Dll4	Delta4	delta-like 4 (Drosophila)	protein-coding
mm_120869.1	chr14	75230166	75230180	+	1	NA	3' UTR (NM_001247984, exon 16 of 16)	3' UTR (NM_001247984, exon 16 of 16)	-12114	NM_019775	56373	Mm.24242	NM_019775	ENSMUSG00000021999	Cpb2	1110032P04Rik|4930405E17Rik|AI255929|CPR|Cpu|TAFI	carboxypeptidase B2 (plasma)	protein-coding
mm_95599.1	chr11	53350877	53350890	+	1	NA	5' UTR (NM_033565, exon 1 of 21)	5' UTR (NM_033565, exon 1 of 21)	116	NM_033565	93736	Mm.395281	NM_033565	ENSMUSG00000049470	Aff4	AF5Q31|Alf4|Laf4l|MCEF	AF4/FMR2 family, member 4	protein-coding
mm_58034.1	chr6	136722699	136722741	-	1	NA	intron (NM_145067, intron 15 of 25)	intron (NM_145067, intron 15 of 25)	59022	NM_145067	14917	Mm.222729	NM_145067	ENSMUSG00000042638	Gucy2c	AI893437|GC-C|Gcc	guanylate cyclase 2c	protein-coding
mm_114165.1	chr13	55445302	55445374	+	1	NA	promoter-TSS (NM_001286064)	promoter-TSS (NM_001286064)	7	NM_001112711	26385	Mm.10193	NM_011938	ENSMUSG00000074886	Grk6	Gprk6	G protein-coupled receptor kinase 6	protein-coding
mm_17922.1	chr2	35442155	35442180	-	1	NA	intron (NM_001308300, intron 1 of 6)	intron (NM_001308300, intron 1 of 6)	19282	NM_001308299	14594	Mm.281124	NM_010283	ENSMUSG00000035778	Ggta1	AW108479|GALT|Gal|Ggta|Ggta-1|alpha Gal|alpha3GalT	glycoprotein galactosyltransferase alpha 1, 3	protein-coding
mm_113248.1	chr13	27559290	27559292	+	1	NA	exon (NM_023332, exon 5 of 6)	exon (NM_023332, exon 5 of 6)	5315	NM_001316721	67310	Mm.46091	NM_023332	ENSMUSG00000006490	Prl8a9	1600019F10Rik|Ghd15|PLP-C2|PLP-Cbeta|Prlpc2	prolactin family8, subfamily a, member 9	protein-coding
mm_45725.1	chr5	86065579	86065587	-	1	NA	promoter-TSS (NM_001345902)	promoter-TSS (NM_001345902)	0	NM_001345902	12617	Mm.4649	NM_007683	ENSMUSG00000029253	Cenpc1	CENP-C|Cenpc	centromere protein C1	protein-coding
mm_52252.1	chr6	106793478	106793502	+	1	NA	intron (NM_175357, intron 4 of 10)	intron (NM_175357, intron 4 of 10)	6597	NM_021449	58799	Mm.290085	NM_021449	ENSMUSG00000005362	Crbn	2610203G15Rik|2900045O07Rik|AF229032|AW108261|piL	cereblon	protein-coding
mm_97499.1	chr11	78360731	78360777	+	1	NA	intron (NM_001277290, intron 8 of 8)	intron (NM_001277290, intron 8 of 8)	14044	NM_001313987	22248	Mm.284811	NM_011676	ENSMUSG00000002058	Unc119	D11Bhm52|HRG4|MRG4|Rg4|Rtg4|Unc119h	unc-119 lipid binding chaperone	protein-coding
mm_53865.1	chr6	149326035	149326040	+	1	NA	exon (NM_001289662, exon 3 of 5)	exon (NM_001289662, exon 3 of 5)	16623	NM_001289662	67246	Mm.333515	NM_026054	ENSMUSG00000032712	2810474O19Rik	6720435I21Rik|AA536804|AU020969|GET|Kiaa1551	RIKEN cDNA 2810474O19 gene	protein-coding
mm_121026.1	chr14	79702891	79702904	+	1	NA	promoter-TSS (NR_045060)	promoter-TSS (NR_045060)	-23	NR_045060	73989	Mm.107775	NR_045060		4930452G13Rik	-	RIKEN cDNA 4930452G13 gene	ncRNA
mm_71323.1	chr8	44938138	44938214	+	1	NA	Intergenic	CpG	-12032	NM_001081286	14107	Mm.27365	NM_001081286	ENSMUSG00000070047	Fat1	2310038E12Rik|AU023433|Fath|mFat1	FAT atypical cadherin 1	protein-coding
mm_87342.1	chr10	43479345	43479354	+	1	NA	5' UTR (NM_199028, exon 1 of 4)	5' UTR (NM_199028, exon 1 of 4)	209	NM_199028	331623	Mm.490388	NM_199028	ENSMUSG00000038214	Bend3	mKIAA1553	BEN domain containing 3	protein-coding
mm_61079.1	chr7	51622034	51622049	+	1	NA	5' UTR (NM_080853, exon 1 of 12)	5' UTR (NM_080853, exon 1 of 12)	211	NM_080853	140919	Mm.256618	NM_080853	ENSMUSG00000030500	Slc17a6	2900073D12Rik|DNPI|VGLUT2	solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 6	protein-coding
mm_4541.1	chr1	176874400	176874410	+	1	NA	intron (NM_029756, intron 10 of 17)	intron (NM_029756, intron 10 of 17)	-38272	NR_037996	15365	Mm.441435	NR_037996		Hmga2-ps1	EG666235|Gm7996|Hmgic-ps1|[y]i-c	high mobility group AT-hook 2, pseudogene 1	pseudo
mm_107571.1	chr12	44328883	44328954	+	1	NA	promoter-TSS (NM_176930)	promoter-TSS (NM_176930)	33	NM_001146031	319504	Mm.208439	NM_176930	ENSMUSG00000020598	Nrcam	Bravo|C030017F07Rik|C130076O07Rik|mKIAA0343	neuronal cell adhesion molecule	protein-coding
mm_53201.1	chr6	125584416	125584431	+	1	NA	intron (NM_011708, intron 6 of 51)	intron (NM_011708, intron 6 of 51)	31475	NM_011708	22371	Mm.22339	NM_011708	ENSMUSG00000001930	Vwf	6820430P06Rik|AI551257|B130011O06Rik|C630030D09|F8VWF|VWD	Von Willebrand factor	protein-coding
mm_54610.1	chr6	38350642	38350647	-	1	NA	intron (NM_001347122, intron 1 of 12)	B2_Mm1a|SINE|B2	3959	NM_028864	78781	Mm.25243	NM_028421	ENSMUSG00000029826	Zc3hav1	1200014N16Rik|2900058M19Rik|9130009D18Rik|9830115L13Rik|ARTD13|D6Bwg1452e|ZAP	zinc finger CCCH type, antiviral 1	protein-coding
mm_84712.1	chr9	73039698	73039725	-	1	NA	promoter-TSS (NM_018889)	promoter-TSS (NM_018889)	-7	NM_001308425	66364	Mm.392089	NM_001308425		2310009A05Rik	5031420N21Rik	RIKEN cDNA 2310009A05 gene	protein-coding
mm_168858.1	chr12	27423720	27423738	-	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	-81011	NM_009234	20666	Mm.41702	NM_009234	ENSMUSG00000063632	Sox11	1110038H03Rik|6230403H02Rik|AI836553|end1	SRY (sex determining region Y)-box 11	protein-coding
mm_92792.1	chr10	81346703	81346770	-	1	NA	intron (NM_001163165, intron 8 of 9)	CpG-1359	-3470	NM_148951	209047	Mm.218755	NM_148951	ENSMUSG00000034872	Gipc3	Ahl5|Rgs19ip3	GIPC PDZ domain containing family, member 3	protein-coding
mm_107422.1	chr12	35047253	35047263	+	1	NA	promoter-TSS (NM_001014973)	promoter-TSS (NM_001014973)	69	NM_001014973	217463	Mm.213991	NM_001014973	ENSMUSG00000020590	Snx13	Rgs-px1|mKIAA0713	sorting nexin 13	protein-coding
mm_87161.1	chr10	36974537	36974556	+	1	NA	promoter-TSS (NM_008229)	promoter-TSS (NM_008229)	2	NM_008229	15182	Mm.19806	NM_008229	ENSMUSG00000019777	Hdac2	D10Wsu179e|YAF1|Yy1bp|mRPD3	histone deacetylase 2	protein-coding
mm_140218.1	chr17	83846630	83846644	+	1	NA	exon (NM_025325, exon 1 of 10)	exon (NM_025325, exon 1 of 10)	153	NM_025325	107766	Mm.30100	NM_025325	ENSMUSG00000000673	Haao	0610007K21Rik|0610012J07Rik|3-HAO|3-HAOxase|3HAO	3-hydroxyanthranilate 3,4-dioxygenase	protein-coding
mm_64072.1	chr7	140906050	140906091	+	1	NA	promoter-TSS (NR_015583)	promoter-TSS (NR_015583)	6	NR_015583	212965	Mm.387212	NR_015583	ENSMUSG00000109628	BC024386	BC039766	cDNA sequence BC023486	ncRNA
mm_37655.1	chr4	128806488	128806513	-	1	NA	promoter-TSS (NM_001081098)	promoter-TSS (NM_001081098)	-388	NM_001081098	230761	Mm.22616	NM_001081098	ENSMUSG00000028799	Zfp362	-	zinc finger protein 362	protein-coding
mm_4779.1	chr1	182965473	182965476	+	1	NA	intron (NM_016928, intron 1 of 3)	ID_B1|SINE|B4	10686	NM_016928	53791	Mm.116894	NM_016928	ENSMUSG00000079164	Tlr5	-	toll-like receptor 5	protein-coding
mm_139402.1	chr17	52348717	52348731	+	1	NA	Intergenic	Intergenic	-253985	NM_001031811	211468	Mm.399068	NM_001031811	ENSMUSG00000035580	Kcnh8	C130090D05Rik|ELK|ELK1|ELK3|Kv12.1	potassium voltage-gated channel, subfamily H (eag-related), member 8	protein-coding
mm_96392.1	chr11	67250005	67250013	+	1	NA	exon (NM_010855, exon 19 of 40)	exon (NM_010855, exon 19 of 40)	12197	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_109764.1	chr12	118239564	118239566	+	1	NA	intron (NM_001166385, intron 5 of 5)	RMER16_Mm|LTR|ERVK	-40522	NM_010060	13411	Mm.390540	NM_010060	ENSMUSG00000018581	Dnah11	Dnahc11|b2b1203Clo|b2b1279Clo|b2b1289Clo|b2b1727Clo|b2b598Clo|iv|lrd	dynein, axonemal, heavy chain 11	protein-coding
mm_171302.1	chr3	93729725	93729732	-	1	NA	Intergenic	MT2B1|LTR|ERVL	-53445	NM_148949	207213	Mm.425165	NM_148949	ENSMUSG00000094084	Tdpoz1	2cpoz56|Mapp2|Spopl1	TD and POZ domain containing 1	protein-coding
mm_65741.1	chr7	28436275	28436340	-	1	NA	promoter-TSS (NM_175021)	promoter-TSS (NM_175021)	-116	NM_175021	233033	Mm.54120	NM_175021	ENSMUSG00000109336	Samd4b	BC042901	sterile alpha motif domain containing 4B	protein-coding
mm_50390.1	chr6	48706534	48706549	+	1	NA	intron (NM_153175, intron 1 of 2)	intron (NM_153175, intron 1 of 2)	1703	NM_153175	231931	Mm.321047	NM_153175	ENSMUSG00000047867	Gimap6	4833419H03Rik|Ian6|mFLJ00102	GTPase, IMAP family member 6	protein-coding
mm_73493.1	chr8	107095936	107095949	+	1	NA	TTS (NR_106043)	TTS (NR_106043)	164	NR_106043	102465652		NR_106043	ENSMUSG00000098671	Mir7075	Gm27821|mmu-mir-7075	microRNA 7075	ncRNA
mm_89888.1	chr10	108716564	108716569	+	1	NA	intron (NM_001252341, intron 4 of 11)	intron (NM_001252341, intron 4 of 11)	-16406	NM_203660	368203	Mm.452758	NM_203660		Gm5136	C6.1AL|EG368203	predicted gene 5136	protein-coding
mm_14778.1	chr2	145822551	145822612	+	1	NA	intron (NM_028724, intron 3 of 12)	intron (NM_028724, intron 3 of 12)	36465	NM_028724	74030	Mm.228799	NM_028724	ENSMUSG00000001768	Rin2	2010003K16Rik|4632403N06Rik|AW821980|RASSF4	Ras and Rab interactor 2	protein-coding
mm_47606.1	chr5	125081285	125081328	-	1	NA	intron (NM_011424, intron 12 of 46)	intron (NM_011424, intron 12 of 46)	77831	NM_028443	73121	Mm.296138	NM_028443	ENSMUSG00000037962	Rflna	3110032G18Rik|Fam101a|cfm|cfm2	refilin A	protein-coding
mm_123633.1	chr14	68533732	68533757	-	1	NA	promoter-TSS (NM_007402)	promoter-TSS (NM_007402)	-55	NM_007402	11500	Mm.261495	NM_007402	ENSMUSG00000022056	Adam7	ADAM 7|EAP1|EAPI	a disintegrin and metallopeptidase domain 7	protein-coding
mm_6369.1	chr1	72255683	72255694	-	1	NA	Intergenic	Intergenic	28626	NM_023523	111175	Mm.281738	NM_023523	ENSMUSG00000026189	Pecr	2400003B18Rik|TERP	peroxisomal trans-2-enoyl-CoA reductase	protein-coding
mm_97664.1	chr11	79660533	79660561	+	1	NA	intron (NM_175543, intron 3 of 14)	CpG	14539	NR_045898	72218	Mm.443271	NR_045898	ENSMUSG00000086569	Rab11fip4os2	1700020F10Rik|4930542H20Rik|Rab11fib4os2	RAB11 family interacting protein 4 (class II), opposite strand 2	ncRNA
mm_5.1	chr1	4771095	4771122	+	1	NA	Intergenic	Intergenic	14618	NR_033530	27395	Mm.182927	NM_025300	ENSMUSG00000033845	Mrpl15	HSPC145|MRP-L7|Rpml7	mitochondrial ribosomal protein L15	protein-coding
mm_165349.1	chr2	119826369	119826383	-	1	NA	Intergenic	RMER6C|LTR|ERVK	26862	NM_019392	22174	Mm.2901	NM_019392	ENSMUSG00000027298	Tyro3	AI323366|Brt|Dtk|Etk-2|Rse|Sky|TK19-2|Tif|etk2/tyro3|tk19-1	TYRO3 protein tyrosine kinase 3	protein-coding
mm_146411.1	chr18	84088219	84088243	+	1	NA	promoter-TSS (NM_146090)	promoter-TSS (NM_146090)	73	NM_146090	225791	Mm.147052	NM_146090	ENSMUSG00000049090	Zadh2	C530046K17Rik|PTGR-3|Pthr3	zinc binding alcohol dehydrogenase, domain containing 2	protein-coding
mm_66959.1	chr7	62423398	62423406	-	1	NA	Intergenic	Intergenic	-3263	NM_011746	22652	Mm.146	NM_011746	ENSMUSG00000070527	Mkrn3	D7H15S9-1|Zfp127	makorin, ring finger protein, 3	protein-coding
mm_137568.1	chr17	27840058	27840119	+	1	NA	promoter-TSS (NM_011432)	promoter-TSS (NM_011432)	1	NM_011432	20630	Mm.103949	NM_011432	ENSMUSG00000024217	Snrpc	Snrp1c|U1-C|U1C	U1 small nuclear ribonucleoprotein C	protein-coding
mm_112809.1	chr13	20794188	20794204	+	1	NA	promoter-TSS (NM_001281854)	promoter-TSS (NM_001281854)	83	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_52921.1	chr6	122874527	122874573	+	1	NA	promoter-TSS (NM_026267)	promoter-TSS (NM_026267)	-7	NM_026267	67602	Mm.288114	NM_026267	ENSMUSG00000030327	Necap1	1200016B17Rik|AI747569|mFLJ00061	NECAP endocytosis associated 1	protein-coding
mm_158985.1	chr1	132191385	132191385	+	1	NA	promoter-TSS (NM_001033250)	promoter-TSS (NM_001033250)	-51	NM_001311104	213409	Mm.426321	NM_001033250	ENSMUSG00000079330	Lemd1	4930540I23Rik|6430514M23Rik|AI428128|LEMP-1	LEM domain containing 1	protein-coding
mm_60341.1	chr7	44351754	44351766	+	1	NA	exon (NM_001034115, exon 24 of 25)	exon (NM_001034115, exon 24 of 25)	23270	NM_027049	69349	Mm.358922	NM_027049	ENSMUSG00000008028	1700008O03Rik	-	RIKEN cDNA 1700008O03 gene	protein-coding
mm_126898.1	chr15	89523708	89523743	+	1	NA	intron (NM_021423, intron 10 of 21)	intron (NM_021423, intron 10 of 21)	23868	NM_021423	58234	Mm.146855	NM_021423	ENSMUSG00000022623	Shank3	AI841104|SHANK3c-3|SHANK3c-4|Shank3b	SH3/ankyrin domain gene 3	protein-coding
mm_76875.1	chr8	105565958	105565982	-	1	NA	promoter-TSS (NM_013477)	promoter-TSS (NM_013477)	70	NM_013477	11972	Mm.17708	NM_013477	ENSMUSG00000013160	Atp6v0d1	AI267038|Ac39|Atp6d|P39|VATX|Vma6	ATPase, H+ transporting, lysosomal V0 subunit D1	protein-coding
mm_78301.1	chr9	22475774	22475786	+	1	NA	promoter-TSS (NM_181316)	promoter-TSS (NM_181316)	65	NM_178415	319845	Mm.176725	NM_178415	ENSMUSG00000035919	Bbs9	E130103I17Rik	Bardet-Biedl syndrome 9 (human)	protein-coding
mm_41875.1	chr5	104609391	104609436	+	1	NA	Intergenic	Intergenic	37741	NM_001346671	69623	Mm.69919	NM_027142		Zfp33b	2310012P17Rik	zinc finger protein 33B	protein-coding
mm_102941.1	chr11	69602811	69602832	-	1	NA	exon (NM_013415, exon 4 of 7)	exon (NM_013415, exon 4 of 7)	3139	NM_013415	11932	Mm.235204	NM_013415	ENSMUSG00000041329	Atp1b2	Amog|Atpb-2	ATPase, Na+/K+ transporting, beta 2 polypeptide	protein-coding
mm_115484.1	chr13	3610266	3610270	-	1	NA	intron (NM_134063, intron 1 of 19)	intron (NM_134063, intron 1 of 19)	840	NM_134063	105203	Mm.221609	NM_134063	ENSMUSG00000033799	Fam208b	AI645998|Pap20|mKIAA2006	family with sequence similarity 208, member B	protein-coding
mm_37115.1	chr4	116651390	116651409	-	1	NA	5' UTR (NM_021473, exon 1 of 9)	5' UTR (NM_021473, exon 1 of 9)	275	NM_021473	58810	Mm.30085	NM_021473	ENSMUSG00000028692	Akr1a1	2610201A18Rik|Akr1a4	aldo-keto reductase family 1, member A1 (aldehyde reductase)	protein-coding
mm_67634.1	chr7	84372448	84372463	-	1	NA	intron (NM_007488, intron 1 of 18)	intron (NM_007488, intron 1 of 18)	37583	NM_007488	11864	Mm.38594	NM_007488	ENSMUSG00000015709	Arnt2	Hif-2b|bHLHe1|mKIAA0307	aryl hydrocarbon receptor nuclear translocator 2	protein-coding
mm_57635.1	chr6	128355827	128355856	-	1	NA	promoter-TSS (NM_011657)	promoter-TSS (NM_011657)	10	NM_011657	22158	Mm.291783	NM_011657	ENSMUSG00000001521	Tulp3	2310022L06Rik|AI316887	tubby-like protein 3	protein-coding
mm_121241.1	chr14	103056270	103056276	+	1	NA	3' UTR (NM_008392, exon 5 of 5)	3' UTR (NM_008392, exon 5 of 5)	9261	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_21957.1	chr2	167188830	167188836	-	1	NA	promoter-TSS (NM_008420)	promoter-TSS (NM_008420)	-15	NM_008420	16500	Mm.205341	NM_008420	ENSMUSG00000050556	Kcnb1	Kcr1-1|Kv2.1|Shab	potassium voltage gated channel, Shab-related subfamily, member 1	protein-coding
mm_63476.1	chr7	127712710	127712745	+	1	NA	promoter-TSS (NM_001301282)	promoter-TSS (NM_001301282)	-9	NM_007795	13019	Mm.389954	NM_007795	ENSMUSG00000042340	Ctf1	CT-1	cardiotrophin 1	protein-coding
mm_98578.1	chr11	95712985	95713030	+	1	NA	promoter-TSS (NR_045780)	promoter-TSS (NR_045780)	-253	NR_045780	432396	Mm.426849	NR_045780	ENSMUSG00000086191	Zfp652os	1110035M17Rik	zinc finger protein 652, opposite strand	ncRNA
mm_70591.1	chr8	13174583	13174606	+	1	NA	3' UTR (NM_010684, exon 9 of 9)	3' UTR (NM_010684, exon 9 of 9)	14504	NR_035494	100316713		NR_035494	ENSMUSG00000088054	Mir1968	mir-1968|mmu-mir-1968	microRNA 1968	ncRNA
mm_150466.1	chr19	38396021	38396022	+	1	NA	promoter-TSS (NM_175507)	promoter-TSS (NM_175507)	41	NM_175507	240660	Mm.262085	NM_175507	ENSMUSG00000044026	Slc35g1	AA590464|D330039I19Rik|Tmem20	solute carrier family 35, member G1	protein-coding
mm_161776.1	chr17	37671897	37671897	+	1	NA	promoter-TSS (NM_213721)	promoter-TSS (NM_213721)	-128	NM_213721	404308	Mm.484787	NM_213721	ENSMUSG00000080990	Olfr118	MOR263-13	olfactory receptor 118	protein-coding
mm_154809.1	chrX	13623573	13623575	+	1	NA	intron (NM_009806, intron 6 of 24)	intron (NM_009806, intron 6 of 24)	-9195	NM_011823	23890	Mm.487326	NM_011823	ENSMUSG00000040229	Gpr34	Lypsr1	G protein-coupled receptor 34	protein-coding
mm_117828.1	chr13	98262947	98263020	-	1	NA	promoter-TSS (NM_178918)	promoter-TSS (NM_178918)	9	NM_178918	105372	Mm.28221	NM_178918	ENSMUSG00000041747	Utp15	AW544865	UTP15 small subunit processome component	protein-coding
mm_50116.1	chr6	41534805	41534827	+	1	NA	Intergenic	Intergenic	13040	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_111339.1	chr12	86884467	86884475	-	1	NA	5' UTR (NM_145836, exon 1 of 1)	5' UTR (NM_145836, exon 1 of 1)	343	NM_145836	238330	Mm.248358	NM_145836	ENSMUSG00000034168	Irf2bpl	6430527G18Rik|Eap1	interferon regulatory factor 2 binding protein-like	protein-coding
mm_166505.1	chr6	4747443	4747452	+	1	NA	promoter-TSS (NM_001130188)	promoter-TSS (NM_001130188)	141	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_87300.1	chr10	42534905	42534927	+	1	NA	3' UTR (NM_017472, exon 4 of 4)	3' UTR (NM_017472, exon 4 of 4)	32862	NM_017472	54198	Mm.277870	NM_017472	ENSMUSG00000019804	Snx3	SDP3	sorting nexin 3	protein-coding
mm_67481.1	chr7	80712192	80712195	-	1	NA	3' UTR (NM_016721, exon 38 of 38)	3' UTR (NM_016721, exon 38 of 38)	-23316	NM_173863	70461	Mm.392175	NM_173863	ENSMUSG00000030527	Crtc3	2610312F20Rik|6332415K15Rik|AI429792|BC011210|TORC3	CREB regulated transcription coactivator 3	protein-coding
mm_20841.1	chr2	148009274	148009297	-	1	NA	Intergenic	B3|SINE|B2	36179	NM_001291067	15376	Mm.938	NM_010446	ENSMUSG00000037025	Foxa2	HNF3-beta|HNF3beta|Hnf-3b|Hnf3b|Tcf-3b|Tcf3b	forkhead box A2	protein-coding
mm_85463.1	chr9	105495131	105495146	-	1	NA	promoter-TSS (NM_175025)	promoter-TSS (NM_175025)	-5	NM_001253836	235574	Mm.326247	NM_175025	ENSMUSG00000032570	Atp2c1	1700121J11Rik|ATP2C1A|AW061228|BCPM|D930003G21Rik|HHD|SPCA|pmr1	ATPase, Ca++-sequestering	protein-coding
mm_118819.1	chr14	25529812	25529822	+	1	NA	intron (NM_001310666, intron 2 of 23)	intron (NM_001310666, intron 2 of 23)	-4622	NR_037236	100526533		NR_037236	ENSMUSG00000093081	Mir3075	mir-3075|mmu-mir-3075	microRNA 3075	ncRNA
mm_170907.1	chr2	31141832	31141833	-	1	NA	5' UTR (NM_019406, exon 1 of 9)	5' UTR (NM_019406, exon 1 of 9)	176	NM_001177649	14269	Mm.52297	NM_019406	ENSMUSG00000075415	Fnbp1	1110057E06Rik|2210010H06Rik|FBP1|Fbp17	formin binding protein 1	protein-coding
mm_25148.1	chr3	102748181	102748184	+	1	NA	intron (NM_001243132, intron 1 of 7)	intron (NM_001243132, intron 1 of 7)	-12765	NR_040588	78491	Mm.243766	NR_040588	ENSMUSG00000086745	Tspan2os	2410057H14Rik	tetraspanin 2, opposite strand	ncRNA
mm_6421.1	chr1	73905384	73905398	-	1	NA	Intergenic	Intergenic	-40925	NR_045311	109198	Mm.359721	NR_045311	ENSMUSG00000100301	6030407O03Rik	-	RIKEN cDNA 6030407O03 gene	ncRNA
mm_77894.1	chr9	7348204	7348237	+	1	NA	intron (NM_001320077, intron 2 of 10)	ID4|SINE|ID	846	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_6258.1	chr1	69108040	69108064	-	1	NA	promoter-TSS (NM_010154)	promoter-TSS (NM_010154)	7	NM_010154	13869	Mm.442420	NM_010154	ENSMUSG00000062209	Erbb4	Her4|c-erbB-4	erb-b2 receptor tyrosine kinase 4	protein-coding
mm_139424.1	chr17	53479528	53479538	+	1	NA	5' UTR (NM_025887, exon 1 of 6)	5' UTR (NM_025887, exon 1 of 6)	299	NM_025887	271457	Mm.329123	NM_025887	ENSMUSG00000017831	Rab5a	2410015H04Rik|AI663973|AU021172|nnyRab5a	RAB5A, member RAS oncogene family	protein-coding
mm_39929.1	chr5	31613950	31613979	+	1	NA	promoter-TSS (NM_025796)	promoter-TSS (NM_025796)	13	NM_025796	66845	Mm.120763	NM_025796	ENSMUSG00000106918	Mrpl33	0610009M10Rik|L33mt|MRP-L33	mitochondrial ribosomal protein L33	protein-coding
mm_66258.1	chr7	35647391	35647415	-	1	NA	promoter-TSS (NM_019746)	promoter-TSS (NM_019746)	79	NM_019746	56330	Mm.371609	NM_019746	ENSMUSG00000030417	Pdcd5	2200003D22Rik|AA408513|Tfar19	programmed cell death 5	protein-coding
mm_58348.1	chr6	147263964	147263977	-	1	NA	promoter-TSS (NM_008970)	promoter-TSS (NM_008970)	43	NM_008970	19227	Mm.28440	NM_008970	ENSMUSG00000048776	Pthlh	PLP|PTH-like|Pthrp	parathyroid hormone-like peptide	protein-coding
mm_1633.1	chr1	74506112	74506120	+	1	NA	promoter-TSS (NM_001310662)	promoter-TSS (NM_001310662)	56	NM_021383	58184	Mm.291708	NM_021383	ENSMUSG00000026174	Cnot9	2610007F23Rik|AI593551|Fl10|Rqcd1	CCR4-NOT transcription complex, subunit 9	protein-coding
mm_82764.1	chr9	26917189	26917191	-	1	NA	intron (NM_001281475, intron 3 of 20)	L1MCa|LINE|L1	5891	NM_001281475	382064	Mm.335028	NM_001177509	ENSMUSG00000079644	Gm1110	-	predicted gene 1110	protein-coding
mm_3845.1	chr1	160053857	160053870	+	1	NA	intron (NM_001162896, intron 1 of 2)	intron (NM_001162896, intron 1 of 2)	9483	NM_001162896	67647	Mm.171518	NM_001024470	ENSMUSG00000090394	4930523C07Rik	-	RIKEN cDNA 4930523C07 gene	protein-coding
mm_100568.1	chr11	120730869	120730877	+	1	NA	exon (NM_007621, exon 3 of 8)	exon (NM_007621, exon 3 of 8)	1148	NM_007621	12409	Mm.21454	NM_007621	ENSMUSG00000025150	Cbr2	MLCR	carbonyl reductase 2	protein-coding
mm_103690.1	chr11	79503985	79504056	-	1	NA	promoter-TSS (NM_019409)	promoter-TSS (NM_019409)	62	NM_019409	18377	Mm.93335	NM_019409	ENSMUSG00000049612	Omg	-	oligodendrocyte myelin glycoprotein	protein-coding
mm_45777.1	chr5	87092549	87092563	-	1	NA	promoter-TSS (NM_001029867)	promoter-TSS (NM_001029867)	-1	NM_001029867	231396	Mm.439851	NM_001029867	ENSMUSG00000070704	Ugt2b36	-	UDP glucuronosyltransferase 2 family, polypeptide B36	protein-coding
mm_10558.1	chr2	16776655	16776657	+	1	NA	Intergenic	L2|LINE|L2	237070	NR_040632	75069	Mm.50378	NR_040632		4930515L03Rik	-	RIKEN cDNA 4930515L03 gene	ncRNA
mm_78213.1	chr9	21505029	21505039	+	1	NA	intron (NM_007871, intron 18 of 19)	intron (NM_007871, intron 18 of 19)	4860	NM_001324510	17083	Mm.196618	NM_010744	ENSMUSG00000032180	Tmed1	Il1rl1l|Ly84l|St2l	transmembrane p24 trafficking protein 1	protein-coding
mm_67086.1	chr7	68283812	68283821	-	1	NA	intron (NM_001013811, intron 1 of 8)	intron (NM_001013811, intron 1 of 8)	-7222	NR_040340	100504026	Mm.426764	NR_040340	ENSMUSG00000086628	Gm16157	OTTMUSG00000031023	predicted gene 16157	ncRNA
mm_110593.1	chr12	56533601	56533611	-	1	NA	exon (NM_009385, exon 3 of 3)	exon (NM_009385, exon 3 of 3)	3302	NM_009385	21869	Mm.89972	NM_009385	ENSMUSG00000001496	Nkx2-1	AV026640|Nkx2.1|T/EBP|Titf1|Ttf-1	NK2 homeobox 1	protein-coding
mm_56527.1	chr6	99521729	99521744	-	1	NA	promoter-TSS (NM_001347345)	promoter-TSS (NM_001347345)	-743	NM_001347345	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_103789.1	chr11	82845871	82845900	-	1	NA	5' UTR (NM_001164569, exon 2 of 8)	5' UTR (NM_001164569, exon 2 of 8)	-16842	NM_026097	67338	Mm.341608	NM_026097	ENSMUSG00000020696	Rffl	1700051E09Rik|4930516L10Rik|BG080975|Carp2	ring finger and FYVE like domain containing protein	protein-coding
mm_2675.1	chr1	127228661	127228670	+	1	NA	intron (NM_145128, intron 1 of 17)	intron (NM_145128, intron 1 of 17)	23679	NM_145128	107895	Mm.214682	NM_145128	ENSMUSG00000036155	Mgat5	4930471A21Rik|5330407H02Rik|AI480971|GlcNAc-TV	mannoside acetylglucosaminyltransferase 5	protein-coding
mm_158443.1	chrX	140537755	140537791	-	1	NA	Intergenic	Intergenic	4895	NR_122039	14605	Mm.22216	NM_010286	ENSMUSG00000031431	Tsc22d3	DIP|Dsip1|Gilz|TSC-22R|Tilz3	TSC22 domain family, member 3	protein-coding
mm_150952.1	chr19	46328704	46328768	+	1	NA	exon (NM_133694, exon 2 of 4)	exon (NM_133694, exon 2 of 4)	552	NM_133694	68431	Mm.19973	NM_133694	ENSMUSG00000025226	Fbxl15	0710008C12Rik|Fbxo37	F-box and leucine-rich repeat protein 15	protein-coding
mm_137800.1	chr17	29769348	29769357	+	1	NA	Intergenic	MLT1I|LTR|ERVL-MaLR	-52335	NM_001163741	68597	Mm.390979	NM_026782	ENSMUSG00000024018	Ccdc167	1110021J02Rik	coiled-coil domain containing 167	protein-coding
mm_164101.1	chr15	20931347	20931347	+	1	NA	Intergenic	MLT1-int|LTR|ERVL-MaLR	-180105	NM_001008420	215654	Mm.300909	NM_001008420	ENSMUSG00000040452	Cdh12	Cdhb	cadherin 12	protein-coding
mm_36936.1	chr4	108579175	108579188	-	1	NA	promoter-TSS (NM_011015)	promoter-TSS (NM_011015)	155	NM_172697	230596	Mm.157534	NM_172697	ENSMUSG00000063800	Prpf38a	2410002M20Rik	PRP38 pre-mRNA processing factor 38 (yeast) domain containing A	protein-coding
mm_53117.1	chr6	125096809	125096840	+	1	NA	promoter-TSS (NR_106012)	promoter-TSS (NR_106012)	-200	NR_106012	102466272		NR_106012	ENSMUSG00000098762	Mir7045	Gm27758|mmu-mir-7045	microRNA 7045	ncRNA
mm_21475.1	chr2	161109195	161109199	-	1	NA	promoter-TSS (NM_173368)	promoter-TSS (NM_173368)	-111	NR_126509	71389	Mm.122738	NM_173368	ENSMUSG00000057133	Chd6	5430439G14Rik|6330406J24Rik|CHD-6	chromodomain helicase DNA binding protein 6	protein-coding
mm_128930.1	chr15	74636338	74636346	-	1	NA	promoter-TSS (NM_001177437)	promoter-TSS (NM_001177437)	-24	NM_001177437	69439	Mm.263708	NM_001177437	ENSMUSG00000022603	Mroh4	1700016M24Rik	maestro heat-like repeat family member 4	protein-coding
mm_170806.1	chr2	175801048	175801057	-	1	NA	promoter-TSS (NM_001199308).2	promoter-TSS (NM_001199308).2	-14	NM_001033123	13999		NM_001033123	ENSMUSG00000078889	Gm14288	OTTMUSG00000016199	predicted gene 14288	protein-coding
mm_42491.1	chr5	115474519	115474575	+	1	NA	exon (NM_011107, exon 4 of 4)	exon (NM_011107, exon 4 of 4)	8281	NM_011107	18778	Mm.20190	NM_011107	ENSMUSG00000029522	Pla2g1b	Pla2a|sPLA2IB	phospholipase A2, group IB, pancreas	protein-coding
mm_112400.1	chr13	3478227	3478269	+	1	NA	promoter-TSS (NR_015522)	promoter-TSS (NR_015522)	-55	NR_015522	76937	Mm.487240	NR_015522	ENSMUSG00000097709	2810429I04Rik	AI256682	RIKEN cDNA 2810429I04 gene	ncRNA
mm_139133.1	chr17	47508288	47508306	+	1	NA	intron (NM_001081635, intron 1 of 6)	intron (NM_001081635, intron 1 of 6)	3246	NM_001081635	12445	Mm.27291	NM_007632	ENSMUSG00000034165	Ccnd3	9230106B05Rik|AA682053|AL024085|AW146355|C78795	cyclin D3	protein-coding
mm_14918.1	chr2	150927287	150927293	+	1	NA	intron (NM_027014, intron 5 of 6)	intron (NM_027014, intron 5 of 6)	17696	NM_001163476	69270	Mm.271603	NM_027014	ENSMUSG00000027454	Gins1	2810418N01Rik|Gins4|PSF1|mKIAA0186	GINS complex subunit 1 (Psf1 homolog)	protein-coding
mm_146541.1	chr18	5593910	5593917	-	1	NA	intron (NM_011546, intron 1 of 7)	intron (NM_011546, intron 1 of 7)	-1476	NR_033552	791318	Mm.84339	NR_033552	ENSMUSG00000063087	Gm10125	ENSMUSG00000063087|Zeb1os	predicted gene 10125	ncRNA
mm_151353.1	chr19	55898278	55898289	+	1	NA	intron (NM_001142924, intron 1 of 11)	intron (NM_001142924, intron 1 of 11)	2962	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_136347.1	chr16	92646782	92646785	-	1	NA	intron (NM_001111023, intron 3 of 5)	intron (NM_001111023, intron 3 of 5)	50546	NM_001111023	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_85683.1	chr9	107872784	107872811	-	1	NA	promoter-TSS (NM_029169)	promoter-TSS (NM_029169)	22	NM_011251	19654	Mm.139926	NM_011251	ENSMUSG00000032582	Rbm6	4930506F14Rik|Def-3|NY-LU-12|g16|mKIAA4015	RNA binding motif protein 6	protein-coding
mm_17835.1	chr2	34311150	34311155	-	1	NA	intron (NM_016768, intron 2 of 8)	intron (NM_016768, intron 2 of 8)	60893	NM_001290576	18516	Mm.239941	NM_016768	ENSMUSG00000038718	Pbx3	-	pre B cell leukemia homeobox 3	protein-coding
mm_109896.1	chr12	7681639	7681641	-	1	NA	Intergenic	Intergenic	-296037	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_144241.1	chr18	10725578	10725607	+	1	NA	promoter-TSS (NM_144860)	promoter-TSS (NM_144860)	-33	NM_144860	225164	Mm.21500	NM_144860	ENSMUSG00000024294	Mib1	DIP-1|E430019M12Rik|Mib|mKIAA1323	mindbomb E3 ubiquitin protein ligase 1	protein-coding
mm_86759.1	chr10	19622015	19622035	+	1	NA	promoter-TSS (NM_178258)	promoter-TSS (NM_178258)	-3	NM_178258	237310	Mm.331979	NM_178258	ENSMUSG00000039760	Il22ra2	CRF2-10|CRF2-s1|CRF2X|Il-22bp	interleukin 22 receptor, alpha 2	protein-coding
mm_55847.1	chr6	83362343	83362344	-	1	NA	TTS (NM_183138)	TTS (NM_183138)	12859	NM_175277	78653	Mm.391470	NM_175277	ENSMUSG00000045160	Bola3	1810056O20Rik	bolA-like 3 (E. coli)	protein-coding
mm_95413.1	chr11	50025310	50025374	+	1	NA	promoter-TSS (NM_021540)	promoter-TSS (NM_021540)	11	NM_001290750	59044	Mm.359004	NM_021540	ENSMUSG00000020376	Rnf130	2510042A13Rik|G1RZFP|G1rp|GOLIATH|GP	ring finger protein 130	protein-coding
mm_170038.1	chr17	23599094	23599115	-	1	NA	intron (NM_011747, intron 1 of 5)	intron (NM_011747, intron 1 of 5)	383	NM_011747	22654	Mm.40326	NM_011747	ENSMUSG00000062012	Zfp13	4933429B21|AI835008|Krox-8|Rhit|Zfp-13	zinc finger protein 13	protein-coding
mm_83059.1	chr9	37545286	37545292	-	1	NA	3' UTR (NM_022029, exon 4 of 4)	3' UTR (NM_022029, exon 4 of 4)	6034	NM_020518	57276	Mm.27478	NM_020518	ENSMUSG00000001943	Vsig2	1190004B15Rik|2210413P10Rik|AU040484|CTX|Ctm	V-set and immunoglobulin domain containing 2	protein-coding
mm_72327.1	chr8	78993257	78993258	+	1	NA	Intergenic	L1MD1|LINE|L1	-35180	NM_001294279	622675	Mm.48724	NM_178267	ENSMUSG00000071064	Zfp827	2810449M09Rik|D630040G17Rik|Znf827	zinc finger protein 827	protein-coding
mm_106439.1	chr11	119676956	119676963	-	1	NA	intron (NM_028898, intron 3 of 33)	intron (NM_028898, intron 3 of 33)	74054	NM_028898	74370	Mm.209933	NM_028898	ENSMUSG00000025583	Rptor	4932417H02Rik|Rap|Raptor|mKIAA1303	regulatory associated protein of MTOR, complex 1	protein-coding
mm_118700.1	chr14	22158727	22158763	+	1	NA	intron (NM_028275, intron 2 of 6)	B4A|SINE|B4	139033	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_76521.1	chr8	87472162	87472196	-	1	NA	promoter-TSS (NR_125722)	promoter-TSS (NR_125722)	413	NM_019626	12404	Mm.4880	NM_019626	ENSMUSG00000031654	Cbln1	AI323299	cerebellin 1 precursor protein	protein-coding
mm_160112.1	chr7	26061591	26061591	+	1	NA	promoter-TSS (NM_007813)	promoter-TSS (NM_007813)	96	NM_007813	13089	Mm.482696	NM_007813	ENSMUSG00000040583	Cyp2b13	-	cytochrome P450, family 2, subfamily b, polypeptide 13	protein-coding
mm_90207.1	chr10	120616908	120616911	+	1	NA	Intergenic	Intergenic	-140440	NM_010441	15364	Mm.157190	NM_010441	ENSMUSG00000056758	Hmga2	9430083A20Rik|HMGI-C|Hmgic|pg|pygmy	high mobility group AT-hook 2	protein-coding
mm_61995.1	chr7	91138298	91138310	+	1	NA	intron (NM_011807, intron 1 of 22)	(T)n|Simple_repeat|Simple_repeat	47518	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_144177.1	chr18	6765087	6765098	+	1	NA	promoter-TSS (NM_181070)	promoter-TSS (NM_181070)	-75	NM_181070	19330	Mm.132802	NM_181070	ENSMUSG00000073639	Rab18	AA959686	RAB18, member RAS oncogene family	protein-coding
mm_165951.1	chr4	84675694	84675730	-	1	NA	promoter-TSS (NM_172870)	promoter-TSS (NM_172870)	-626	NM_172870	242509	Mm.190774	NM_172870	ENSMUSG00000028487	Bnc2	5031434M05Rik|8430420F16Rik	basonuclin 2	protein-coding
mm_36881.1	chr4	107179317	107179326	-	1	NA	promoter-TSS (NM_025617)	promoter-TSS (NM_025617)	691	NM_029565	56374	Mm.291192	NM_029565	ENSMUSG00000028618	Tmem59	1110001M20Rik|3110046P06Rik|AI256529|D4Ertd20e|MTDCF1|ORF18	transmembrane protein 59	protein-coding
mm_27826.1	chr3	79091922	79091932	-	1	NA	exon (NM_001099624, exon 11 of 24)	exon (NM_001099624, exon 11 of 24)	52960	NM_001310536	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_73408.1	chr8	105989742	105989757	+	1	NA	intron (NM_001301205, intron 2 of 9)	intron (NM_001301205, intron 2 of 9)	2024	NM_001301204	319446	Mm.248357	NM_176913	ENSMUSG00000053687	Dpep2	F630103D06Rik|MBD-2	dipeptidase 2	protein-coding
mm_24100.1	chr3	88081998	88082051	+	1	NA	promoter-TSS (NM_001033484)	promoter-TSS (NM_001033484)	-27	NM_001033484	404710	Mm.331133	NM_001033484	ENSMUSG00000028068	Iqgap3	AI593484|D030034H08	IQ motif containing GTPase activating protein 3	protein-coding
mm_27709.1	chr3	67515488	67515502	-	1	NA	promoter-TSS (NM_001164763)	promoter-TSS (NM_001164763)	28	NM_001164763	109222	Mm.38002	NM_001164763	ENSMUSG00000049404	Rarres1	5430417P09Rik|AI662122	retinoic acid receptor responder (tazarotene induced) 1	protein-coding
mm_157922.1	chrX	78583883	78583901	-	1	NA	promoter-TSS (NM_001289683)	promoter-TSS (NM_001289683)	5	NM_001289683	546336	Mm.211712	NM_027322	ENSMUSG00000047996	Prrg1	2010007L08Rik	proline rich Gla (G-carboxyglutamic acid) 1	protein-coding
mm_81155.1	chr9	107289961	107289978	+	1	NA	promoter-TSS (NM_178907)	promoter-TSS (NM_178907)	-92	NM_178907	102626	Mm.222612	NM_178907	ENSMUSG00000032577	Mapkapk3	3PK|AI874665|MAPKAP-K3|MAPKAP3|MK-3|MK3|MapkKapk3	mitogen-activated protein kinase-activated protein kinase 3	protein-coding
mm_142985.1	chr17	56287864	56287866	-	1	NA	5' UTR (NM_025836, exon 2 of 8)	5' UTR (NM_025836, exon 2 of 8)	2646	NM_025836	66905	Mm.311696	NM_025836	ENSMUSG00000024197	Plin3	1300012C15Rik|M6prbp1|Tip47	perilipin 3	protein-coding
mm_61530.1	chr7	78920175	78920198	+	1	NA	3' UTR (NM_020583, exon 4 of 4)	3' UTR (NM_020583, exon 4 of 4)	5951	NM_001113527	57444	Mm.322843	NM_020583	ENSMUSG00000039236	Isg20	1600023I01Rik|2010107M23Rik|20kDa|DnaQL|HEM45	interferon-stimulated protein	protein-coding
mm_100269.1	chr11	117654212	117654258	+	1	NA	promoter-TSS (NM_198022)	promoter-TSS (NM_198022)	-54	NM_198022	217351	Mm.40272	NM_198022	ENSMUSG00000025571	Tnrc6c	9930033H14Rik|mKIAA1582	trinucleotide repeat containing 6C	protein-coding
mm_41027.1	chr5	81800736	81800740	+	1	NA	Intergenic	Intergenic	323975	NR_138557	67327	Mm.87058	NR_138557		1700031L13Rik	-	RIKEN cDNA 1700031L13 gene	ncRNA
mm_104317.1	chr11	93886503	93886512	-	1	NA	promoter-TSS (NM_001013375)	promoter-TSS (NM_001013375)	288	NM_134012	103537	Mm.210334	NM_134012	ENSMUSG00000059474	Mbtd1	AA408199|AI194990|hemp	mbt domain containing 1	protein-coding
mm_82463.1	chr9	15710202	15710212	-	1	NA	intron (NM_172289, intron 1 of 10)	(TCTG)n|Simple_repeat|Simple_repeat	438	NM_172289	234967	Mm.138815	NM_172289	ENSMUSG00000043885	Slc36a4	6330573I15Rik|PAT4	solute carrier family 36 (proton/amino acid symporter), member 4	protein-coding
mm_124715.1	chr15	6579693	6579703	+	1	NA	promoter-TSS (NM_001278269)	promoter-TSS (NM_001278269)	-149	NM_001278269	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_88763.1	chr10	80334730	80334746	+	1	NA	exon (NM_139292, exon 5 of 6)	exon (NM_139292, exon 5 of 6)	4593	NM_139292	70335	Mm.28147	NM_139292	ENSMUSG00000035504	Reep6	0610011M24Rik|Dp1l1	receptor accessory protein 6	protein-coding
mm_61244.1	chr7	65803031	65803048	+	1	NA	Intergenic	Intergenic	-1013	NR_045301	100503969	Mm.383527	NR_045301		1810008I18Rik	-	RIKEN cDNA 1810008I18 gene	ncRNA
mm_6764.1	chr1	84105680	84105692	-	1	NA	intron (NM_001003948, intron 2 of 2)	ORR1F|LTR|ERVL-MaLR	113275	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_38459.1	chr4	140581810	140581820	-	1	NA	intron (NM_001290803, intron 9 of 28)	intron (NM_001290803, intron 9 of 28)	66941	NM_001112723	72754	Mm.29329	NM_172415	ENSMUSG00000040964	Arhgef10l	2810441C07Rik	Rho guanine nucleotide exchange factor (GEF) 10-like	protein-coding
mm_98997.1	chr11	98795470	98795483	+	1	NA	promoter-TSS (NM_028722)	promoter-TSS (NM_028722)	-293	NM_028722	74026	Mm.258352	NM_028722	ENSMUSG00000052915	Msl1	2810017F12Rik|4121402D02Rik|4930463F05Rik|AA682082|Msl-1	male-specific lethal 1 homolog (Drosophila)	protein-coding
mm_156165.1	chrX	130048841	130048854	+	1	NA	intron (NM_172493, intron 18 of 26)	MER44D|DNA|TcMar-Tigger	299105	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diaph2	Dia3|Diap2|Drf2|E430022I22Rik	diaphanous related formin 2	protein-coding
mm_117505.1	chr13	78200380	78200397	-	1	NA	intron (NR_045195, intron 1 of 2)	intron (NR_045195, intron 1 of 2)	-1515	NM_010151	13865	Mm.439653	NM_010151	ENSMUSG00000069171	Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR-3|EAR3|Erbal3|SVP44|Tcfcoup1	nuclear receptor subfamily 2, group F, member 1	protein-coding
mm_166153.1	chr5	10709028	10709029	+	1	NA	Intergenic	B3|SINE|B2	-156001	NR_003596	623849	Mm.335888	NR_003596	ENSMUSG00000091422	Gm6455	EG623849	predicted gene 6455	pseudo
mm_117645.1	chr13	92610925	92610950	-	1	NA	promoter-TSS (NM_172588)	promoter-TSS (NM_172588)	-201	NM_172588	218442	Mm.297970	NM_172588	ENSMUSG00000021703	Serinc5	A130038L21Rik|AIGP3|C86123|TPO1	serine incorporator 5	protein-coding
mm_141535.1	chr17	31855761	31855774	-	1	NA	promoter-TSS (NM_010831)	promoter-TSS (NM_010831)	25	NM_010831	17691	Mm.290941	NM_010831	ENSMUSG00000024042	Sik1	Msk|Sik|Snf1lk	salt inducible kinase 1	protein-coding
mm_150899.1	chr19	45545357	45545367	+	1	NA	Intergenic	Intergenic	15202	NM_001330506	56626	Mm.46509	NM_020032	ENSMUSG00000025218	Poll	1110003P06Rik|AV007317	polymerase (DNA directed), lambda	protein-coding
mm_127924.1	chr15	10229311	10229326	-	1	NA	intron (NM_001253781, intron 1 of 9)	Lx9|LINE|L1	5412	NM_001253781	19116	Mm.10516	NM_011169	ENSMUSG00000005268	Prlr	AI987712|Pr-1|Pr-3|Prlr-rs1	prolactin receptor	protein-coding
mm_23410.1	chr3	58502181	58502185	+	1	NA	Intergenic	Intergenic	-23638	NM_001005509	229317	Mm.21617	NM_001005509	ENSMUSG00000027810	Eif2a	D030048D22|D3Ertd194e	eukaryotic translation initiation factor 2A	protein-coding
mm_147198.1	chr18	37864512	37864517	-	1	NA	intron (NM_007858, intron 16 of 26)	RMER17C2|LTR|ERVK	-9854	NR_105945	102465592		NR_105945	ENSMUSG00000098706	Mir6979	Gm27524|mmu-mir-6979	microRNA 6979	ncRNA
mm_129775.1	chr15	82792571	82792580	-	1	NA	exon (NM_029562, exon 4 of 9)	exon (NM_029562, exon 4 of 9)	1670	NM_029562	76279	Mm.439931	NM_029562	ENSMUSG00000022445	Cyp2d26	1300006E06Rik	cytochrome P450, family 2, subfamily d, polypeptide 26	protein-coding
mm_124247.1	chr14	101609128	101609173	-	1	NA	promoter-TSS (NM_001081278)	promoter-TSS (NM_001081278)	41	NM_001081278	210789	Mm.320639	NM_173380	ENSMUSG00000033083	Tbc1d4	5930406J04Rik|A930035N22|AV295684|As160	TBC1 domain family, member 4	protein-coding
mm_155977.1	chrX	106126830	106126848	+	1	NA	3' UTR (NM_009726, exon 23 of 23)	3' UTR (NM_009726, exon 23 of 23)	-16436	NM_205820	279572	Mm.336203	NM_205820	ENSMUSG00000033777	Tlr13	AI666735|Gm713	toll-like receptor 13	protein-coding
mm_1532.1	chr1	72849246	72849269	+	1	NA	exon (NM_008342, exon 2 of 4)	exon (NM_008342, exon 2 of 4)	23870	NM_001310659	16008	Mm.141936	NM_008342	ENSMUSG00000039323	Igfbp2	AI255832|IBP-2|Igfbp-2|mIGFBP-2	insulin-like growth factor binding protein 2	protein-coding
mm_12662.1	chr2	75634615	75634618	+	1	NA	Intergenic	MMERGLN_LTR|LTR|ERV1	-24643	NM_146130	229279	Mm.316306	NM_053263	ENSMUSG00000059005	Hnrnpa3	2410013L13Rik|2610209F03Rik|2610510D13Rik|Hnrpa3	heterogeneous nuclear ribonucleoprotein A3	protein-coding
mm_33688.1	chr4	133415423	133415440	+	1	NA	exon (NM_016981, exon 3 of 12)	exon (NM_016981, exon 3 of 12)	45655	NR_039582	100628620		NR_039582	ENSMUSG00000092745	Mir5122	mmu-mir-5122|mu-mir-5122	microRNA 5122	ncRNA
mm_22180.1	chr2	173216962	173216987	-	1	NA	exon (NM_021394, exon 2 of 8)	exon (NM_021394, exon 2 of 8)	1948	NM_021394	58203	Mm.116687	NM_021394	ENSMUSG00000027514	Zbp1	2010010H03Rik|Dai|Dlm1|mZaDLM	Z-DNA binding protein 1	protein-coding
mm_52669.1	chr6	117907026	117907029	+	1	NA	promoter-TSS (NM_001166429)	intron (NM_133834, intron 1 of 3)	245	NM_133834	98758	Mm.422979	NM_133834	ENSMUSG00000042079	Hnrnpf	4833420I20Rik|AA407306|Hnrpf	heterogeneous nuclear ribonucleoprotein F	protein-coding
mm_130750.1	chr15	101266534	101266564	-	1	NA	promoter-TSS (NM_010444)	promoter-TSS (NM_010444)	-297	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_169200.1	chr13	66291490	66291501	+	1	NA	Intergenic	Intergenic	149623	NM_183119	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
mm_150748.1	chr19	43788106	43788116	+	1	NA	intron (NM_013806, intron 2 of 31)	intron (NM_013806, intron 2 of 31)	5803	NM_013806	12780	Mm.39054	NM_013806	ENSMUSG00000025194	Abcc2	AI173996|Abc30|Cmoat|Mrp2|cMRP	ATP-binding cassette, sub-family C (CFTR/MRP), member 2	protein-coding
mm_2664.1	chr1	126573935	126573939	+	1	NA	intron (NM_001081756, intron 2 of 16)	intron (NM_001081756, intron 2 of 16)	-81010	NM_172484	210356	Mm.377234	NM_172484	ENSMUSG00000049690	Nckap5	8430408F21|D130011D22Rik|E030049G20Rik|Erih1|Erih2|Gm1548|Nap5	NCK-associated protein 5	protein-coding
mm_98418.1	chr11	94629742	94629834	+	1	NA	promoter-TSS (NM_133807)	promoter-TSS (NM_133807)	-36	NM_133807	98238	Mm.172720	NM_133807	ENSMUSG00000020869	Lrrc59	AA959742|C78668	leucine rich repeat containing 59	protein-coding
mm_54029.1	chr6	11998348	11998351	-	1	NA	intron (NM_029404, intron 14 of 16)	ORR1D1-int|LTR|ERVL-MaLR	72468	NM_001168382	75725	Mm.212411	NM_029404	ENSMUSG00000029629	Phf14	1110001C23Rik|4932409F11Rik|5730446A07Rik|AA623952|AV297001|mKIAA0783	PHD finger protein 14	protein-coding
mm_169442.1	chr14	56811443	56811444	-	1	NA	promoter-TSS (NM_001253753)	promoter-TSS (NM_001253753)	21	NM_001253753	219105	Mm.473172	NM_144842	ENSMUSG00000040123	Zmym5	9830124H08Rik	zinc finger, MYM-type 5	protein-coding
mm_148181.1	chr18	78205890	78205917	-	1	NA	intron (NM_030683, intron 5 of 11)	intron (NM_030683, intron 5 of 11)	537	NM_001110274	27411	Mm.44158	NM_030683	ENSMUSG00000024552	Slc14a2	UT-A1|UT-A3	solute carrier family 14 (urea transporter), member 2	protein-coding
mm_82350.1	chr9	13827009	13827028	-	1	NA	promoter-TSS (NM_001310721)	promoter-TSS (NM_001310721)	35	NR_037622	74360	Mm.157212	NM_026665	ENSMUSG00000031922	Cep57	3110002L15Rik|4921510P06Rik|4931428M20Rik|AI467480|Tsp57|mKIAA0092	centrosomal protein 57	protein-coding
mm_51302.1	chr6	72309867	72309881	+	1	NA	exon (NM_001282071, exon 7 of 11)	exon (NM_001282071, exon 7 of 11)	5264	NM_147779	20388	Mm.46033	NM_147779	ENSMUSG00000056370	Sftpb	AI562151|SF-B|SP-B|Sftp-3|Sftp3	surfactant associated protein B	protein-coding
mm_1977.1	chr1	86526824	86526859	+	1	NA	5' UTR (NM_008972, exon 1 of 5)	5' UTR (NM_008972, exon 1 of 5)	105	NM_008972	19231	Mm.19187	NM_008972	ENSMUSG00000026238	Ptma	Thym	prothymosin alpha	protein-coding
mm_34466.1	chr4	148140796	148140811	+	1	NA	exon (NM_027985, exon 1 of 8)	exon (NM_027985, exon 1 of 8)	313	NM_027985	71890	Mm.9648	NM_027985	ENSMUSG00000029003	Mad2l2	2310033C13Rik|G1-453-4|MAD2B|REV7|repro22	MAD2 mitotic arrest deficient-like 2	protein-coding
mm_57140.1	chr6	122609984	122610007	-	1	NA	promoter-TSS (NM_008108)	promoter-TSS (NM_008108)	92	NM_008108	14562	Mm.299742	NM_008108	ENSMUSG00000030117	Gdf3	C78318|Gdf-3|Vgr-2|Vgr2|ecat9	growth differentiation factor 3	protein-coding
mm_39065.1	chr4	154042661	154042714	-	1	NA	promoter-TSS (NM_001033455)	promoter-TSS (NM_001033455)	-10	NM_001033455	381580	Mm.51001	NM_001033455	ENSMUSG00000039492	Ccdc27	Gm1035	coiled-coil domain containing 27	protein-coding
mm_163136.1	chr11	79076633	79076636	-	1	NA	intron (NM_013571, intron 1 of 17)	intron (NM_013571, intron 1 of 17)	53037	NR_045873	790910	Mm.440410	NR_045873		Gm11201	ENSMUSG00000072637|OTTMUSG00000000169	predicted gene 11201	ncRNA
mm_76812.1	chr8	104442903	104442920	-	1	NA	5' UTR (NM_001013380, exon 1 of 13)	5' UTR (NM_001013380, exon 1 of 13)	136	NM_001013380	234663	Mm.289583	NM_001013380	ENSMUSG00000035770	Dync1li2	AA409702|C920003I06|Dncli2|Dnclic2|LIC2	dynein, cytoplasmic 1 light intermediate chain 2	protein-coding
mm_126286.1	chr15	79229450	79229460	+	1	NA	promoter-TSS (NM_001045558)	promoter-TSS (NM_001045558)	73	NM_001045558	18693	Mm.259464	NM_008837	ENSMUSG00000068206	Pick1	Prkcabp	protein interacting with C kinase 1	protein-coding
mm_92441.1	chr10	77418231	77418276	-	1	NA	promoter-TSS (NR_004429)	promoter-TSS (NR_004429)	20	NM_130895	110532	Mm.276815	NM_130895	ENSMUSG00000020262	Adarb1	1700057H01Rik|AW124433|AW558573|Adar2|BB220382|D10Bwg0447e|Red1	adenosine deaminase, RNA-specific, B1	protein-coding
mm_89837.1	chr10	106675814	106675814	+	1	NA	intron (NM_001205341, intron 3 of 31)	Lx3_Mus|LINE|L1	-73334	NR_131026	75833	Mm.159596	NR_131026		4930532I03Rik	-	RIKEN cDNA 4930532I03 gene	ncRNA
mm_133317.1	chr16	77653709	77653714	+	1	NA	Intergenic	Intergenic	7438	NR_029540	723952		NR_029540	ENSMUSG00000065472	Mir125b-2	Mirn125b-2|mir-125b-2	microRNA 125b-2	ncRNA
mm_169411.1	chr14	52075414	52075417	-	1	NA	exon (NM_001170982, exon 7 of 8)	exon (NM_001170982, exon 7 of 8)	6100	NR_028552	100217457		NR_028552	ENSMUSG00000064871	Snord58b	MBII-199	small nucleolar RNA, C/D box 58B	snoRNA
mm_103273.1	chr11	72037552	72037558	-	1	NA	promoter-TSS (NM_053245)	promoter-TSS (NM_053245)	-46	NM_053245	114230	Mm.95707	NM_053245	ENSMUSG00000040554	Aipl1	A930007I01Rik	aryl hydrocarbon receptor-interacting protein-like 1	protein-coding
mm_154097.1	chr19	57008178	57008184	-	1	NA	5' UTR (NM_001177797, exon 1 of 19)	5' UTR (NM_001177797, exon 1 of 19)	394	NM_146102	226250	Mm.226284	NM_146102	ENSMUSG00000025083	Afap1l2	AU041783|C86904|mKIAA1914	actin filament associated protein 1-like 2	protein-coding
mm_114655.1	chr13	78024879	78024887	+	1	NA	promoter-TSS (NM_029315)	promoter-TSS (NM_029315)	-19	NM_029315	75507	Mm.443255	NM_029315	ENSMUSG00000093668	Pou5f2	1700013G10Rik|SPRM-1|Sprm1	POU domain class 5, transcription factor 2	protein-coding
mm_97662.1	chr11	79653133	79653145	+	1	NA	intron (NM_175543, intron 3 of 14)	intron (NM_175543, intron 3 of 14)	21947	NR_045898	72218	Mm.443271	NR_045898	ENSMUSG00000086569	Rab11fip4os2	1700020F10Rik|4930542H20Rik|Rab11fib4os2	RAB11 family interacting protein 4 (class II), opposite strand 2	ncRNA
mm_39662.1	chr5	25181460	25181463	+	1	NA	promoter-TSS (NM_026449)	promoter-TSS (NM_026449)	-19	NM_026449	67909	Mm.141471	NM_026449	ENSMUSG00000028938	Galntl5	1700021B12Rik|Galnt15	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 5	protein-coding
mm_99803.1	chr11	107993984	107993992	+	1	NA	intron (NM_011101, intron 8 of 16)	intron (NM_011101, intron 8 of 16)	-2860	NR_106082	102465705		NR_106082	ENSMUSG00000098989	Mir7223	Gm28009|mmu-mir-7223	microRNA 7223	ncRNA
mm_72117.1	chr8	71676502	71676580	+	1	NA	5' UTR (NM_001190830, exon 1 of 24)	5' UTR (NM_001190830, exon 1 of 24)	158	NM_010589	16453	Mm.249645	NM_010589	ENSMUSG00000031805	Jak3	fae|wil	Janus kinase 3	protein-coding
mm_131186.1	chr16	7217716	7217724	+	1	NA	intron (NM_183188, intron 1 of 12)	intron (NM_183188, intron 1 of 12)	147885	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_101378.1	chr11	23771200	23771210	-	1	NA	promoter-TSS (NM_009044)	promoter-TSS (NM_009044)	-235	NM_009044	19696	Mm.4869	NM_009044	ENSMUSG00000020275	Rel	c-Rel	reticuloendotheliosis oncogene	protein-coding
mm_46828.1	chr5	113219539	113219549	-	1	NA	Intergenic	Intergenic	-7365	NM_001033428	333048	Mm.332586	NM_001033428	ENSMUSG00000066964	Tmem211	Gm854	transmembrane protein 211	protein-coding
mm_5861.1	chr1	53774004	53774014	-	1	NA	intron (NM_133810, intron 2 of 7)	intron (NM_133810, intron 2 of 7)	11206	NM_133810	98267	Mm.25559	NM_133810	ENSMUSG00000026094	Stk17b	3110009A03Rik|AI120141|Drak2	serine/threonine kinase 17b (apoptosis-inducing)	protein-coding
mm_155954.1	chrX	105106358	105106364	+	1	NA	intron (NM_001281871, intron 5 of 5)	intron (NM_001281871, intron 5 of 5)	-14017	NM_053201	107528	Mm.24341	NM_053201	ENSMUSG00000031227	Magee1	AI847422|DAMAGE|mMage-e1	melanoma antigen, family E, 1	protein-coding
mm_3853.1	chr1	160906476	160906500	+	1	NA	promoter-TSS (NM_001024952)	promoter-TSS (NM_001024952)	77	NM_001024952	381305	Mm.329667	NM_001024952	ENSMUSG00000040423	Rc3h1	5730557L09Rik|Gm551|N28103|mKIAA2025	RING CCCH (C3H) domains 1	protein-coding
mm_100803.1	chr11	5061781	5061804	-	1	NA	exon (NM_001190408, exon 6 of 6)	exon (NM_001190408, exon 6 of 6)	3535	NM_144560	78926	Mm.44591	NM_030228	ENSMUSG00000034201	Gas2l1	4930500E24Rik|D0Jmb1|Gar22|TU-71.1	growth arrest-specific 2 like 1	protein-coding
mm_109621.1	chr12	112765034	112765050	+	1	NA	exon (NM_178911, exon 6 of 11)	exon (NM_178911, exon 6 of 11)	4387	NM_178911	104759	Mm.203915	NM_178911	ENSMUSG00000052160	Pld4	AI132321|thss	phospholipase D family, member 4	protein-coding
mm_166066.1	chr4	134507597	134507620	+	1	NA	exon (NM_001285846, exon 4 of 4)	exon (NM_001285846, exon 4 of 4)	-3391	NM_001081099	69885	Mm.141592	NM_001081099	ENSMUSG00000078521	Aunip	2610002D18Rik|Clhc1	aurora kinase A and ninein interacting protein	protein-coding
mm_48386.1	chr5	139812996	139813006	-	1	NA	exon (NM_001161548, exon 2 of 9)	exon (NM_001161548, exon 2 of 9)	242	NM_144914	231832	Mm.482655	NM_144914	ENSMUSG00000036687	Tmem184a	Sdmg1	transmembrane protein 184a	protein-coding
mm_37559.1	chr4	126169000	126169004	-	1	NA	intron (NM_146153, intron 8 of 10)	B3|SINE|B2	-5661	NM_001162533	66938	Mm.29813	NM_025856	ENSMUSG00000073758	Sh3d21	1700029G01Rik|AU019788	SH3 domain containing 21	protein-coding
mm_122952.1	chr14	54967953	54967975	-	1	NA	promoter-TSS (NR_033497)	promoter-TSS (NR_033497)	-823	NR_033497	791403	Mm.319176	NR_033497	ENSMUSG00000097652	Mhrt	D830015G02Rik|ENSMUSG00000053118|Myheart	myosin heavy chain associated RNA transcript	ncRNA
mm_19395.1	chr2	91629266	91629276	-	1	NA	exon (NM_010168, exon 10 of 14)	exon (NM_010168, exon 10 of 14)	7186	NM_010168	14061	Mm.89048	NM_010168	ENSMUSG00000027249	F2	Cf-2|Cf2|FII	coagulation factor II	protein-coding
mm_22679.1	chr3	16183178	16183206	+	1	NA	promoter-TSS (NM_001145919)	promoter-TSS (NM_001145919)	9	NM_001145919	229096	Mm.23834	NM_172677	ENSMUSG00000047213	Ythdf3	9130022A11Rik	YTH domain family 3	protein-coding
mm_61681.1	chr7	80994015	80994016	+	1	NA	intron (NM_178707, intron 1 of 9)	CpG	331	NM_178707	233410	Mm.29525	NM_178707	ENSMUSG00000005621	Zfp592	8430405N24|A730014M16Rik|Znf592|mKIAA0211	zinc finger protein 592	protein-coding
mm_115350.1	chr13	112673427	112673433	+	1	NA	intron (NM_178746, intron 2 of 14)	intron (NM_178746, intron 2 of 14)	12664	NM_178746	268706	Mm.40834	NM_175376	ENSMUSG00000047789	Slc38a9	4833412L08Rik|6720411P22Rik|9130023D20Rik|9430067K09Rik|A730092C09	solute carrier family 38, member 9	protein-coding
mm_89369.1	chr10	88731353	88731400	+	1	NA	promoter-TSS (NM_025859)	promoter-TSS (NM_025859)	-38	NM_025859	104303	Mm.291247	NM_025859	ENSMUSG00000060904	Arl1	2310008D22Rik|AU019749	ADP-ribosylation factor-like 1	protein-coding
mm_100921.1	chr11	6415650	6415691	-	1	NA	promoter-TSS (NM_008907)	promoter-TSS (NM_008907)	-200	NM_008907	268373	Mm.5246	NM_008907	ENSMUSG00000071866	Ppia	2700098C05|Cphn|CyP-18|CypA	peptidylprolyl isomerase A	protein-coding
mm_154012.1	chr19	53143148	53143177	-	1	NA	promoter-TSS (NM_013758)	promoter-TSS (NM_013758)	406	NM_001164100	27360	Mm.426080	NM_013758	ENSMUSG00000025026	Add3	AI463285|R75380	adducin 3 (gamma)	protein-coding
mm_107063.1	chr12	16657970	16657978	+	1	NA	intron (NM_008747, intron 2 of 3)	intron (NM_008747, intron 2 of 3)	4504	NM_008747	18217	Mm.281715	NM_008747	ENSMUSG00000020591	Ntsr2	NT2R|NTRL	neurotensin receptor 2	protein-coding
mm_68418.1	chr7	109703583	109703621	-	1	NA	promoter-TSS (NM_020616)	promoter-TSS (NM_020616)	-135	NM_020616	57373	Mm.334138	NM_020616	ENSMUSG00000031023	Akip1	BCA3|C11orf17|D7H11orf17|D930014E17Rik|ICRFP703B1614Q5.6|ORF27	A kinase (PRKA) interacting protein 1	protein-coding
mm_40294.1	chr5	43515514	43515534	+	1	NA	promoter-TSS (NM_001135172)	promoter-TSS (NM_001135172)	-45	NM_001135172	109323	Mm.275553	NM_175425	ENSMUSG00000061535	C1qtnf7	5530401N20Rik|8430425G24Rik|Ctrp7	C1q and tumor necrosis factor related protein 7	protein-coding
mm_145960.1	chr18	67774920	67774934	+	1	NA	promoter-TSS (NM_001039088)	promoter-TSS (NM_001039088)	51	NM_001039088	72124	Mm.307315	NM_028112	ENSMUSG00000079614	Seh1l	2610007A16Rik|AW540070|SEC13L|SEH1A|SEH1B|Seh1	SEH1-like (S. cerevisiae	protein-coding
mm_79402.1	chr9	54956847	54956851	+	1	NA	exon (NM_011966, exon 8 of 9)	exon (NM_011966, exon 8 of 9)	-5895	NM_145229	246735	Mm.473773	NM_145229	ENSMUSG00000044820	AY074887	Mcpr1	cDNA sequence AY074887	protein-coding
mm_11480.1	chr2	32385475	32385486	+	1	NA	exon (NM_008491, exon 5 of 6)	exon (NM_008491, exon 5 of 6)	2259	NM_008491	16819	Mm.9537	NM_008491	ENSMUSG00000026822	Lcn2	24p3|AW212229|NRL|Sip24	lipocalin 2	protein-coding
mm_107154.1	chr12	24572277	24572308	+	1	NA	promoter-TSS (NM_001161406)	promoter-TSS (NM_001161406)	5	NM_001161406	195733	Mm.263068	NM_145890	ENSMUSG00000020656	Grhl1	LBP-32|MGR|Tcfcp2l2	grainyhead-like 1 (Drosophila)	protein-coding
mm_157483.1	chrX	48208542	48208556	-	1	NA	5' UTR (NM_172465, exon 1 of 10)	5' UTR (NM_172465, exon 1 of 10)	153	NM_172465	208884	Mm.207367	NM_172465	ENSMUSG00000036985	Zdhhc9	6430508G22|9530098M12Rik	zinc finger, DHHC domain containing 9	protein-coding
mm_88464.1	chr10	77564752	77564773	+	1	NA	exon (NM_008404, exon 15 of 16)	exon (NM_008404, exon 15 of 16)	-17005	NM_145925	108705	Mm.28853	NM_145925	ENSMUSG00000009291	Pttg1ip	1810010L20Rik|AI314311|AU018448|C79540	pituitary tumor-transforming 1 interacting protein	protein-coding
mm_28037.1	chr3	83789974	83789992	-	1	NA	Intergenic	CpG	23662	NM_009144	20319	Mm.19155	NM_009144	ENSMUSG00000027996	Sfrp2	AI851596|Sdf5	secreted frizzled-related protein 2	protein-coding
mm_76606.1	chr8	90817032	90817045	-	1	NA	Intergenic	Intergenic	-11797	NM_177224	109151	Mm.100615	NM_177224	ENSMUSG00000056608	Chd9	1810014J18Rik|9030205D12Rik|A330063D19Rik|AD013|PRIC320|mKIAA0308	chromodomain helicase DNA binding protein 9	protein-coding
mm_2109.1	chr1	87835531	87835535	+	1	NA	intron (NM_009118, intron 12 of 15)	intron (NM_009118, intron 12 of 15)	-17754	NM_177646	227333	Mm.277217	NM_177646	ENSMUSG00000070738	Dgkd	AI841987|D330025K09|DGKdelta|dgkd-2	diacylglycerol kinase, delta	protein-coding
mm_143210.1	chr17	62881253	62881353	-	1	NA	promoter-TSS (NM_207654)	promoter-TSS (NM_207654)	14	NM_207654	13640	Mm.7978	NM_010109	ENSMUSG00000048915	Efna5	AL-1|AV158822|EFL-5|Ephrin-A5|Epl7|LERK-7|RAGS	ephrin A5	protein-coding
mm_26999.1	chr3	25835299	25835302	-	1	NA	intron (NM_001163387, intron 3 of 5)	intron (NM_001163387, intron 3 of 5)	318007	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_2846.1	chr1	131638486	131638496	+	1	NA	5' UTR (NM_007799, exon 1 of 10)	5' UTR (NM_007799, exon 1 of 10)	177	NM_007799	13034	Mm.230249	NM_007799	ENSMUSG00000004552	Ctse	A430072O03Rik|C920004C08Rik|CE|CatE	cathepsin E	protein-coding
mm_101537.1	chr11	33513723	33513733	-	1	NA	promoter-TSS (NR_110973)	promoter-TSS (NR_110973)	18	NR_110973	66011	Mm.383775	NM_023146	ENSMUSG00000040594	Ranbp17	-	RAN binding protein 17	protein-coding
mm_67200.1	chr7	74284374	74284387	-	1	NA	exon (NM_023908, exon 10 of 10)	exon (NM_023908, exon 10 of 10)	270400	NM_023908	108116	Mm.425467	NM_023908	ENSMUSG00000025790	Slco3a1	5830414C08Rik|Anr1|MJAM|OATP-D|R75096|Slc21a11	solute carrier organic anion transporter family, member 3a1	protein-coding
mm_1267.1	chr1	63200582	63200592	+	1	NA	5' UTR (NM_001285937, exon 1 of 6)	5' UTR (NM_001285937, exon 1 of 6)	229	NM_001285936	73884	Mm.86986	NM_028673	ENSMUSG00000027520	Zdbf2	4930431J08Rik|9330107J05Rik	zinc finger, DBF-type containing 2	protein-coding
mm_59925.1	chr7	30423267	30423293	+	1	NA	promoter-TSS (NM_172142)	promoter-TSS (NM_172142)	-24	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_108124.1	chr12	75960385	75960398	+	1	NA	intron (NM_001005510, intron 45 of 115)	intron (NM_001005510, intron 45 of 115)	51288	NR_039560	100628610		NR_039560	ENSMUSG00000092922	Mir5101	mmu-mir-5101|mu-mir-5101	microRNA 5101	ncRNA
mm_82380.1	chr9	14634292	14634324	-	1	NA	Intergenic	Intergenic	-19308	NM_001081395	75723	Mm.159552	NM_001081395	ENSMUSG00000013076	Amotl1	2310010G08Rik|2310067L22Rik|4932416D09Rik|JEAP|mFLJ00155	angiomotin-like 1	protein-coding
mm_92918.1	chr10	84398656	84398667	-	1	NA	intron (NM_001004363, intron 2 of 6)	MTD|LTR|ERVL-MaLR	41810	NM_001004363	77976	Mm.25874	NM_001004363	ENSMUSG00000020032	Nuak1	AU014801|AW494241|B230104P22Rik|Omphk1	NUAK family, SNF1-like kinase, 1	protein-coding
mm_169744.1	chr15	86195143	86195145	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-9003	NM_145475	223753	Mm.222685	NM_145475	ENSMUSG00000035891	Cerk	AI848610|D330016D08Rik|mKIAA1646	ceramide kinase	protein-coding
mm_98300.1	chr11	90030691	90030708	+	1	NA	5' UTR (NM_026433, exon 1 of 3)	5' UTR (NM_026433, exon 1 of 3)	351	NM_026433	67888	Mm.212428	NM_026433	ENSMUSG00000069763	Tmem100	1810057C19Rik|AV011897	transmembrane protein 100	protein-coding
mm_29507.1	chr3	116252770	116252805	-	1	NA	intron (NM_022427, intron 1 of 1)	intron (NM_022427, intron 1 of 1)	697	NM_022427	64378	Mm.40025	NM_022427	ENSMUSG00000068696	Gpr88	AW061286|Strg	G-protein coupled receptor 88	protein-coding
mm_158244.1	chrX	106840531	106840554	-	1	NA	5' UTR (NM_199468, exon 1 of 2)	5' UTR (NM_199468, exon 1 of 2)	101	NM_199468	213436	Mm.85581	NM_199468	ENSMUSG00000047686	Zcchc5	D430021I08Rik|Gm375|Mar3|Mart3|ZHC5	zinc finger, CCHC domain containing 5	protein-coding
mm_121312.1	chr14	106194337	106194345	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	88143	NR_073203	212085	Mm.78128	NM_198601	ENSMUSG00000022113	Trim52	4921513B05Rik	tripartite motif-containing 52	protein-coding
mm_44411.1	chr5	17849784	17849794	-	1	NA	promoter-TSS (NM_001159557)	promoter-TSS (NM_001159557)	3	NM_001159557	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_24481.1	chr3	92012429	92012462	+	1	NA	Intergenic	Intergenic	-2138	NM_207247	242100	Mm.297406	NM_207247	ENSMUSG00000042244	Pglyrp3	Gm420	peptidoglycan recognition protein 3	protein-coding
mm_130025.1	chr15	88891456	88891478	-	1	NA	Intergenic	Intergenic	29273	NM_145478	223775	Mm.400129	NM_145478	ENSMUSG00000035828	Pim3	BC026639|Kid1	proviral integration site 3	protein-coding
mm_81395.1	chr9	108989929	108989958	+	1	NA	Intergenic	Intergenic	-1959	NM_173019	270198	Mm.132391	NM_173019	ENSMUSG00000025648	Pfkfb4	C230090D14	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4	protein-coding
mm_56845.1	chr6	117906495	117906502	-	1	NA	promoter-TSS (NM_001166431)	promoter-TSS (NM_001166431)	-284	NM_001166431	98758	Mm.422979	NM_133834	ENSMUSG00000042079	Hnrnpf	4833420I20Rik|AA407306|Hnrpf	heterogeneous nuclear ribonucleoprotein F	protein-coding
mm_18580.1	chr2	66125131	66125143	-	1	NA	promoter-TSS (NM_015736)	promoter-TSS (NM_015736)	-344	NM_015736	14425	Mm.439760	NM_015736	ENSMUSG00000026994	Galnt3	-	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 3	protein-coding
mm_116861.1	chr13	54766501	54766503	-	1	NA	promoter-TSS (NM_033610)	promoter-TSS (NM_033610)	-62	NM_033610	104069	Mm.200843	NM_033610	ENSMUSG00000034891	Sncb	AI838531|betaSYN	synuclein, beta	protein-coding
mm_88060.1	chr10	67572061	67572076	+	1	NA	Intergenic	MLT1L|LTR|ERVL-MaLR	-23113	NM_001005419	211488	Mm.297250	NM_001005419	ENSMUSG00000057134	Ado	Gm237	2-aminoethanethiol (cysteamine) dioxygenase	protein-coding
mm_134981.1	chr16	32079271	32079368	-	1	NA	promoter-TSS (NM_177326)	promoter-TSS (NM_177326)	23	NM_177326	224105	Mm.234204	NM_177326	ENSMUSG00000022781	Pak2	5330420P17Rik|A130002K10Rik|AI836325|D16Ertd269e|PAK-2|mKIAA4182	p21 protein (Cdc42/Rac)-activated kinase 2	protein-coding
mm_169701.1	chr15	75086826	75086834	+	1	NA	Intergenic	Intergenic	25119	NM_001099217	100041546	Mm.482110	NM_001099217	ENSMUSG00000022584	Ly6c2	Ly-6C.2|Ly-6C2	lymphocyte antigen 6 complex, locus C2	protein-coding
mm_150240.1	chr19	34085175	34085181	+	1	NA	TTS (NM_027340)	TTS (NM_027340)	-15765	NM_023903	78753	Mm.195937	NM_023903	ENSMUSG00000056078	Lipm	4632427C23Rik|AW227514|Lipl3	lipase, family member M	protein-coding
mm_83008.1	chr9	36760285	36760288	-	1	NA	intron (NM_008408, intron 3 of 17)	ID_B1|SINE|B4	7292	NM_008408	16430	Mm.2863	NM_008408	ENSMUSG00000032116	Stt3a	AA408947|BB081708|Itm1	STT3, subunit of the oligosaccharyltransferase complex, homolog A (S. cerevisiae)	protein-coding
mm_159057.1	chr1	193168053	193168053	+	1	NA	intron (NM_016851, intron 6 of 7)	intron (NM_016851, intron 6 of 7)	-5416	NM_001160360	319266	Mm.482460	NM_181048	ENSMUSG00000079144	A130010J15Rik	-	RIKEN cDNA A130010J15 gene	protein-coding
mm_3643.1	chr1	152902845	152902873	+	1	NA	promoter-TSS (NM_001160256)	promoter-TSS (NM_001160256)	-213	NM_001005507	226517	Mm.270775	NM_001005507	ENSMUSG00000042772	Smg7	9430023P16Rik|mKIAA0250	Smg-7 homolog, nonsense mediated mRNA decay factor (C. elegans)	protein-coding
mm_57443.1	chr6	124965404	124965458	-	1	NA	promoter-TSS (NM_001164089)	promoter-TSS (NM_001164089)	-34	NM_012003	26894	Mm.244536	NM_012003	ENSMUSG00000030127	Cops7a	D6Ertd35e	COP9 signalosome subunit 7A	protein-coding
mm_14934.1	chr2	151542693	151542695	+	1	NA	non-coding (NR_126058, exon 1 of 4)	non-coding (NR_126058, exon 1 of 4)	211	NM_001302078	14225	Mm.278458	NM_008019	ENSMUSG00000032966	Fkbp1a	FKBP12|Fkbp|Fkbp1	FK506 binding protein 1a	protein-coding
mm_168841.1	chr12	23427173	23427185	-	1	NA	Intergenic	CpG	-416936	NR_015504	69732	Mm.391403	NM_028362	ENSMUSG00000073164	2410018L13Rik	2810480C08Rik	RIKEN cDNA 2410018L13 gene	ncRNA
mm_86279.1	chr9	121839461	121839465	-	1	NA	promoter-TSS (NM_028384)	promoter-TSS (NM_028384)	-2	NM_028384	100502861	Mm.335550	NM_028384	ENSMUSG00000079235	Ccdc13	2900041A11Rik|Gm188	coiled-coil domain containing 13	protein-coding
mm_43639.1	chr5	138229868	138229881	+	1	NA	5' UTR (NM_001013773, exon 2 of 6)	5' UTR (NM_001013773, exon 2 of 6)	3970	NM_001013773	381680	Mm.156846	NM_001013773	ENSMUSG00000047592	Nxpe5	-	neurexophilin and PC-esterase domain family, member 5	protein-coding
mm_90781.1	chr10	6980390	6980398	-	1	NA	promoter-TSS (NM_001170802)	promoter-TSS (NM_001170802)	71	NM_001170800	320495	Mm.331674	NM_001033391	ENSMUSG00000064065	Ipcef1	A130090K04Rik	interaction protein for cytohesin exchange factors 1	protein-coding
mm_133966.1	chr16	4213952	4213995	-	1	NA	promoter-TSS (NM_001025432)	promoter-TSS (NM_001025432)	-569	NM_001025432	12914	Mm.132238	NM_001025432	ENSMUSG00000022521	Crebbp	AW558298|CBP|CBP/p300|KAT3A|p300/CBP	CREB binding protein	protein-coding
mm_103848.1	chr11	83079867	83079871	-	1	NA	Intergenic	RLTR8|LTR|ERVK	14757	NM_011408	20556	Mm.278689	NM_011408	ENSMUSG00000072620	Slfn2	Shlf2	schlafen 2	protein-coding
mm_169769.1	chr15	99874668	99874680	-	1	NA	intron (NM_001113545, intron 1 of 10)	intron (NM_001113545, intron 1 of 10)	782	NM_001113545	65970	Mm.33207	NM_023063	ENSMUSG00000023022	Lima1	Eplin	LIM domain and actin binding 1	protein-coding
mm_156118.1	chrX	114904996	114905025	+	1	NA	promoter-TSS (NM_001276396)	promoter-TSS (NM_001276396)	-2	NM_001276396	237009	Mm.302216	NM_207241	ENSMUSG00000050435	Ube2dnl1	Ube2dnl	ubiquitin-conjugating enzyme E2D N-terminal like 1	protein-coding
mm_99313.1	chr11	101377307	101377314	+	1	NA	3' UTR (NM_008061, exon 5 of 5)	3' UTR (NM_008061, exon 5 of 5)	9594	NM_008061	14377	Mm.18064	NM_008061	ENSMUSG00000078650	G6pc	AW107337|G6Pase|G6pt|Glc-6-Pase	glucose-6-phosphatase, catalytic	protein-coding
mm_114037.1	chr13	53184503	53184513	+	1	NA	intron (NM_013846, intron 1 of 8)	intron (NM_013846, intron 1 of 8)	101601	NM_013846	26564	Mm.342774	NM_013846	ENSMUSG00000021464	Ror2	Ntrkr2|mRor2	receptor tyrosine kinase-like orphan receptor 2	protein-coding
mm_140665.1	chr17	12909913	12909954	-	1	NA	promoter-TSS (NM_001034866)	promoter-TSS (NM_001034866)	67	NM_001034866	240023	Mm.242315	NM_001034866	ENSMUSG00000073460	Pnldc1	Gm313	poly(A)-specific ribonuclease (PARN)-like domain containing 1	protein-coding
mm_133878.1	chr16	96467710	96467725	+	1	NA	5' UTR (NM_008791, exon 1 of 3)	5' UTR (NM_008791, exon 1 of 3)	111	NM_008791	18546	Mm.5023	NM_008791	ENSMUSG00000090223	Pcp4	P16Rimb19|Pcp-4|Pep19	Purkinje cell protein 4	protein-coding
mm_138871.1	chr17	43087763	43087773	+	1	NA	exon (NM_178589, exon 6 of 6)	exon (NM_178589, exon 6 of 6)	70523	NR_045155	545207	Mm.329050	NR_045153		E130008D07Rik	-	RIKEN cDNA E130008D07 gene	ncRNA
mm_68112.1	chr7	102072410	102072417	-	1	NA	intron (NM_001286689, intron 3 of 10)	B1F|SINE|Alu	1194	NM_011644	102443351	Mm.292904	NM_011644	ENSMUSG00000070425	Xntrpc	Xndr-trpc2	Xndc1-transient receptor potential cation channel, subfamily C, member 2 readthrough	protein-coding
mm_21663.1	chr2	164425256	164425266	-	1	NA	3' UTR (NM_011521, exon 5 of 5)	3' UTR (NM_011521, exon 5 of 5)	17927	NM_011521	20971	Mm.3815	NM_011521	ENSMUSG00000017009	Sdc4	AA959608|AW108331|S4|Synd4|ryudocan|syndecan-4	syndecan 4	protein-coding
mm_77934.1	chr9	7354803	7354823	+	1	NA	exon (NM_008605, exon 7 of 10)	exon (NM_008605, exon 7 of 10)	7439	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_172115.1	chr6	3201004	3201010	+	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	-87512	NR_036696	667335	Mm.380219	NR_036696	ENSMUSG00000106779	Gm8579	EG667335	spermatogenesis associated glutamate (E)-rich protein 4a pseudogene	pseudo
mm_133754.1	chr16	94426185	94426197	+	1	NA	exon (NM_009441, exon 24 of 46)	exon (NM_009441, exon 24 of 46)	-55176	NM_001159617	56176	Mm.474449	NM_019543	ENSMUSG00000022940	Pigp	Dcrc|Dscr5	phosphatidylinositol glycan anchor biosynthesis, class P	protein-coding
mm_155765.1	chrX	96168424	96168453	+	1	NA	3' UTR (NM_010833, exon 13 of 13)	3' UTR (NM_010833, exon 13 of 13)	-71488	NR_030718	100038363	Mm.30815	NR_030718	ENSMUSG00000078122	F630028O10Rik	ENSMUSG00000065522|Gm14924|OTTMUSG00000018496|mir-223	RIKEN cDNA F630028O10 gene	ncRNA
mm_32120.1	chr4	99031287	99031303	+	1	NA	exon (NM_013913, exon 1 of 7)	exon (NM_013913, exon 1 of 7)	341	NM_013913	30924	Mm.28341	NM_013913	ENSMUSG00000028553	Angptl3	hypl	angiopoietin-like 3	protein-coding
mm_163218.1	chr11	101376303	101376331	+	1	NA	exon (NM_008061, exon 5 of 5)	exon (NM_008061, exon 5 of 5)	8601	NM_008061	14377	Mm.18064	NM_008061	ENSMUSG00000078650	G6pc	AW107337|G6Pase|G6pt|Glc-6-Pase	glucose-6-phosphatase, catalytic	protein-coding
mm_54868.1	chr6	42597713	42597720	-	1	NA	promoter-TSS (NM_203396)	promoter-TSS (NM_203396)	-344	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_34774.1	chr4	153975116	153975136	+	1	NA	promoter-TSS (NM_177673)	promoter-TSS (NM_177673)	-45	NM_007859	13368	Mm.388918	NM_007859	ENSMUSG00000029027	Dffb	40kDa|5730477D02Rik|CAD|CPAN|DFF40|Didff	DNA fragmentation factor, beta subunit	protein-coding
mm_123901.1	chr14	73180787	73180797	-	1	NA	intron (NR_033185, intron 15 of 15)	intron (NR_033185, intron 15 of 15)	26059	NR_030459	751541		NR_030459	ENSMUSG00000076121	Mir687	Mirn687|mir-687|mmu-mir-687	microRNA 687	ncRNA
mm_137695.1	chr17	28970883	28970890	+	1	NA	TTS (NM_134115)	TTS (NM_134115)	17670	NM_025888	66989	Mm.435	NM_025888	ENSMUSG00000005936	Kctd20	2410004N11Rik|AI451943|AW541186|D17Ertd562e	potassium channel tetramerisation domain containing 20	protein-coding
mm_31346.1	chr4	46576801	46576803	+	1	NA	intron (NM_001164804, intron 1 of 11)	MMTV-int|LTR|ERVK	-10362	NM_178893	107684	Mm.416311	NM_178893	ENSMUSG00000028337	Coro2a	9030208C03Rik|AI563590|IR10	coronin, actin binding protein 2A	protein-coding
mm_96357.1	chr11	67052642	67052708	+	1	NA	promoter-TSS (NM_025510)	promoter-TSS (NM_025510)	5	NM_001040026	52892	Mm.129731	NM_001040026	ENSMUSG00000069844	Sco1	2610001C07Rik|D11Bwg1310e	SCO1 cytochrome c oxidase assembly protein	protein-coding
mm_69222.1	chr7	127588266	127588278	-	1	NA	promoter-TSS (NM_172281)	promoter-TSS (NM_172281)	323	NM_001033040	233899	Mm.25220	NM_001033040	ENSMUSG00000057176	Ccdc189	Gm166	coiled-coil domain containing 189	protein-coding
mm_28049.1	chr3	84040277	84040290	-	1	NA	promoter-TSS (NM_172681)	promoter-TSS (NM_172681)	-122	NM_172681	229473	Mm.28838	NM_172681	ENSMUSG00000033767	D930015E06Rik	Kiaa0922|mKIAA0922	RIKEN cDNA D930015E06 gene	protein-coding
mm_46438.1	chr5	105021897	105021909	-	1	NA	intron (NM_029509, intron 5 of 9)	intron (NM_029509, intron 5 of 9)	31658	NM_029509	76074	Mm.458519	NM_029509	ENSMUSG00000034438	Gbp8	5830443L24Rik|mGBP8	guanylate-binding protein 8	protein-coding
mm_63288.1	chr7	126797446	126797469	+	1	NA	exon (NM_001177307, exon 4 of 10)	exon (NM_001177307, exon 4 of 10)	1721	NM_001177307	11674	Mm.275831	NM_007438	ENSMUSG00000030695	Aldoa	Aldo-1|Aldo1	aldolase A, fructose-bisphosphate	protein-coding
mm_151591.1	chr19	3388644	3388650	-	1	NA	promoter-TSS (NM_001286558)	promoter-TSS (NM_001286558)	-210	NM_001039658	17771	Mm.209941	NM_010841	ENSMUSG00000024905	Mtl5	tesmin	metallothionein-like 5, testis-specific (tesmin)	protein-coding
mm_90580.1	chr10	128268625	128268639	+	1	NA	5' UTR (NM_133997, exon 1 of 2)	5' UTR (NM_133997, exon 1 of 2)	635	NM_133997	103161	Mm.26513	NM_133997	ENSMUSG00000047631	Apof	AI255964	apolipoprotein F	protein-coding
mm_152712.1	chr19	17372916	17372926	-	1	NA	promoter-TSS (NM_010265)	promoter-TSS (NM_010265)	-77	NM_010265	14537	Mm.244825	NM_010265	ENSMUSG00000038843	Gcnt1	5630400D21Rik|B130048E03|C2 GlcNAcT|C2GNT|IGnT	glucosaminyl (N-acetyl) transferase 1, core 2	protein-coding
mm_106832.1	chr12	8004907	8004918	+	1	NA	exon (NM_009693, exon 25 of 29)	exon (NM_009693, exon 25 of 29)	27235	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_18421.1	chr2	60750594	60750613	-	1	NA	Intergenic	Intergenic	-28000	NM_001159564	16420	Mm.98193	NM_021359	ENSMUSG00000026971	Itgb6	2210409C20Rik|4831415H04Rik	integrin beta 6	protein-coding
mm_85173.1	chr9	96479528	96479536	-	1	NA	promoter-TSS (NM_011279)	promoter-TSS (NM_011279)	-857	NM_001311135	19823	Mm.28235	NM_011279	ENSMUSG00000051234	Rnf7	Rbx2|SAG	ring finger protein 7	protein-coding
mm_154650.1	chrX	7822891	7822901	+	1	NA	promoter-TSS (NM_008423)	promoter-TSS (NM_008423)	-863	NM_008423	16506	Mm.335968	NM_008423	ENSMUSG00000009731	Kcnd1	1110037K09Rik|Kca2-1|Kv4.1|Shal|Shal1|mShal1	potassium voltage-gated channel, Shal-related family, member 1	protein-coding
mm_10896.1	chr2	25265558	25265558	+	1	NA	intron (NM_175286, intron 1 of 3)	intron (NM_175286, intron 1 of 3)	2960	NM_175286	97031	Mm.308539	NM_175286	ENSMUSG00000048707	Tprn	C430004E15Rik|C87750	taperin	protein-coding
mm_82738.1	chr9	25541426	25541434	-	1	NA	intron (NM_026189, intron 2 of 7)	RLTR53_Mm|LTR|ERVK	59833	NM_026189	67484	Mm.112977	NM_026189	ENSMUSG00000036611	Eepd1	2310005P05Rik|AI481005	endonuclease/exonuclease/phosphatase family domain containing 1	protein-coding
mm_95459.1	chr11	50378011	50378046	+	1	NA	intron (NM_001347487, intron 1 of 12)	CpG	309	NM_001347487	59013	Mm.21740	NM_021510	ENSMUSG00000007850	Hnrnph1	AI642080|E430005G16Rik|Hnrnph|Hnrph1	heterogeneous nuclear ribonucleoprotein H1	protein-coding
mm_51476.1	chr6	83008918	83008931	+	1	NA	intron (NM_033079, intron 7 of 9)	intron (NM_033079, intron 7 of 9)	24547	NM_010070	13448	Mm.156	NM_010070	ENSMUSG00000068335	Dok1	AW557123|p62DOK	docking protein 1	protein-coding
mm_141595.1	chr17	32424158	32424162	-	1	NA	promoter-TSS (NM_001271478)	promoter-TSS (NM_001271478)	7	NM_001271476	57757	Mm.86752	NM_021319	ENSMUSG00000079563	Pglyrp2	C730002N09Rik|PGRP-L|Pglyrpl|tagL	peptidoglycan recognition protein 2	protein-coding
mm_23314.1	chr3	53231727	53231736	+	1	NA	exon (NM_175386, exon 3 of 4)	exon (NM_175386, exon 3 of 4)	190184	NM_175386	108927	Mm.118617	NM_175386	ENSMUSG00000048332	Lhfp	2810489O06Rik|AI194968	lipoma HMGIC fusion partner	protein-coding
mm_92595.1	chr10	80098544	80098546	-	1	NA	intron (NM_183426, intron 1 of 31)	intron (NM_183426, intron 1 of 31)	4157	NM_183426	216161	Mm.262102	NM_183426	ENSMUSG00000035673	Sbno2	BC019206|F730040C21|Sno|Stno	strawberry notch homolog 2 (Drosophila)	protein-coding
mm_161979.1	chr19	16873826	16873826	-	1	NA	promoter-TSS (NM_008023)	promoter-TSS (NM_008023)	4	NM_008023	14240	Mm.7971	NM_008023	ENSMUSG00000056829	Foxb2	Fkh4	forkhead box B2	protein-coding
mm_125168.1	chr15	31332023	31332031	+	1	NA	intron (NM_027496, intron 1 of 3)	MLT1A0|LTR|ERVL-MaLR	35732	NM_001164441	67434	Mm.102470	NM_026153	ENSMUSG00000022237	Ankrd33b	0610012A05Rik|3021401C12Rik|5730557B15Rik	ankyrin repeat domain 33B	protein-coding
mm_104519.1	chr11	96065273	96065307	-	1	NA	promoter-TSS (NM_172300)	promoter-TSS (NM_172300)	74	NM_172300	268470	Mm.38802	NM_172300	ENSMUSG00000014349	Ube2z	AW049199|C030047H17Rik|D11Moh35	ubiquitin-conjugating enzyme E2Z	protein-coding
mm_63335.1	chr7	126950812	126950829	+	1	NA	5' UTR (NM_001252566, exon 1 of 17)	5' UTR (NM_001252566, exon 1 of 17)	285	NM_001252566	233878	Mm.283926	NM_144926	ENSMUSG00000030683	Sez6l2	AI835913|AW121566|BSRP-A|Psk1	seizure related 6 homolog like 2	protein-coding
mm_29178.1	chr3	106525455	106525503	-	1	NA	intron (NM_001293694, intron 4 of 8)	MTD|LTR|ERVL-MaLR	-22319	NM_001286986	67171	Mm.290488	NM_026013	ENSMUSG00000027900	Dram2	2010305N14Rik|2610318G18Rik|AI647667|Tmem77	DNA-damage regulated autophagy modulator 2	protein-coding
mm_1776.1	chr1	78310392	78310400	+	1	NA	promoter-TSS (NM_001004173)	promoter-TSS (NM_001004173)	50	NM_001004173	433323	Mm.276248	NM_001004173	ENSMUSG00000032908	Sgpp2	SPPase2|Spp2	sphingosine-1-phosphate phosphotase 2	protein-coding
mm_76061.1	chr8	77724913	77724923	-	1	NA	promoter-TSS (NM_010332)	promoter-TSS (NM_010332)	-466	NM_010332	13617	Mm.283168	NM_010332	ENSMUSG00000031616	Ednra	ET-AR|ETa|Gpcr10	endothelin receptor type A	protein-coding
mm_2451.1	chr1	101155764	101155782	+	1	NA	promoter-TSS (NR_037989)	promoter-TSS (NR_037989)	5	NR_037989	100504525	Mm.87065	NR_037989	ENSMUSG00000100684	Gm20268	-	predicted gene, 20268	ncRNA
mm_17047.1	chr2	20943426	20943442	-	1	NA	intron (NM_001128084, intron 1 of 24)	intron (NM_001128084, intron 1 of 24)	24287	NM_001081364	71435	Mm.28507	NM_001081364	ENSMUSG00000036591	Arhgap21	5530401C11Rik|AA416458|ARHGAP10	Rho GTPase activating protein 21	protein-coding
mm_168076.1	chr10	112699268	112699269	+	1	NA	Intergenic	L1Md_Gf|LINE|L1	-27658	NR_040579	69355	Mm.84337	NR_040579	ENSMUSG00000100314	1700010J16Rik	-	RIKEN cDNA 1700010J16 gene	ncRNA
mm_88360.1	chr10	75936325	75936333	+	1	NA	exon (NM_175329, exon 2 of 4)	exon (NM_175329, exon 2 of 4)	756	NM_175329	103172	Mm.333849	NM_175329	ENSMUSG00000049422	Chchd10	1620401E04Rik|AI267078|Ndg2	coiled-coil-helix-coiled-coil-helix domain containing 10	protein-coding
mm_131908.1	chr16	23269618	23269634	+	1	NA	intron (NM_001252505, intron 2 of 7)	intron (NM_001252505, intron 2 of 7)	-20844	NM_001252506	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_78551.1	chr9	35423392	35423407	+	1	NA	Intergenic	Intergenic	-28677	NM_021339	57810	Mm.80509	NM_021339	ENSMUSG00000038119	Cdon	CDO|Cd0|Orcam	cell adhesion molecule-related/down-regulated by oncogenes	protein-coding
mm_119663.1	chr14	52279133	52279188	+	1	NA	promoter-TSS (NM_023434)	promoter-TSS (NM_023434)	14	NM_023434	268741	Mm.246237	NM_023434	ENSMUSG00000016831	Tox4	5730589K01Rik|A630040M18|AA410149|LCP1	TOX high mobility group box family member 4	protein-coding
mm_151279.1	chr19	55253901	55253950	+	1	NA	5' UTR (NM_027976, exon 1 of 22)	5' UTR (NM_027976, exon 1 of 22)	556	NM_027976	433256	Mm.292056	NM_027976	ENSMUSG00000024981	Acsl5	1700030F05Rik|ACS2|ACS5|Facl5	acyl-CoA synthetase long-chain family member 5	protein-coding
mm_48910.1	chr6	3993995	3994000	+	1	NA	promoter-TSS (NM_010314)	promoter-TSS (NM_010314)	-15	NM_010314	14699	Mm.95398	NM_010314	ENSMUSG00000029663	Gngt1	G(y)1|Gng1	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1	protein-coding
mm_126391.1	chr15	80191846	80191878	+	1	NA	intron (NM_010795, intron 1 of 1)	intron (NM_010795, intron 1 of 1)	18141	NM_010795	17309	Mm.299693	NM_010795	ENSMUSG00000042428	Mgat3	1110038J12Rik|AI848272|GnT-III	mannoside acetylglucosaminyltransferase 3	protein-coding
mm_149925.1	chr19	26623942	26623960	+	1	NA	exon (NM_011416, exon 3 of 33)	exon (NM_011416, exon 3 of 33)	18791	NM_011416	67155	Mm.342988	NM_011416	ENSMUSG00000024921	Smarca2	2610209L14Rik|SNF2alpha|Snf2l2|brahma|brm	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	protein-coding
mm_18196.1	chr2	45117350	45117375	-	1	NA	Intergenic	Intergenic	-4083	NM_015753	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_109791.1	chr12	3253316	3253328	-	1	NA	exon (NM_016676, exon 4 of 6)	exon (NM_016676, exon 4 of 6)	17531	NR_015551	74173	Mm.309774	NM_028796	ENSMUSG00000079179	Rab10os	1700012B15Rik|1810036A22Rik	RAB10, member RAS oncogene family, opposite strand	ncRNA
mm_28793.1	chr3	96016864	96016873	-	1	NA	intron (NM_013841, intron 14 of 14)	intron (NM_013841, intron 14 of 14)	-21029	NM_023320	67220	Mm.458147	NM_023320	ENSMUSG00000015745	Plekho1	2810052M02Rik|CKIP-1|Ckip1|JZA-20|Jza2	pleckstrin homology domain containing, family O member 1	protein-coding
mm_157116.1	chrX	9439949	9439993	-	1	NA	exon (NM_007807, exon 12 of 13)	exon (NM_007807, exon 12 of 13)	29353	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_153174.1	chr19	34493830	34493848	-	1	NA	3' UTR (NM_021460, exon 10 of 10)	3' UTR (NM_021460, exon 10 of 10)	-18704	NM_009890	12642	Mm.30824	NM_009890	ENSMUSG00000050370	Ch25h	AI462618|m25OH	cholesterol 25-hydroxylase	protein-coding
mm_76814.1	chr8	104442972	104442976	-	1	NA	promoter-TSS (NM_001013380)	promoter-TSS (NM_001013380)	73	NM_001013380	234663	Mm.289583	NM_001013380	ENSMUSG00000035770	Dync1li2	AA409702|C920003I06|Dncli2|Dnclic2|LIC2	dynein, cytoplasmic 1 light intermediate chain 2	protein-coding
mm_106123.1	chr11	116359990	116360003	-	1	NA	intron (NM_027258, intron 4 of 18)	intron (NM_027258, intron 4 of 18)	-24642	NM_008240	15223	Mm.378938	NM_008240	ENSMUSG00000034227	Foxj1	FKHL-13|HFH-4|Hfh4	forkhead box J1	protein-coding
mm_72865.1	chr8	88647337	88647391	+	1	NA	promoter-TSS (NM_145857)	promoter-TSS (NM_145857)	17	NM_145857	257632	Mm.222633	NM_145857	ENSMUSG00000055994	Nod2	ACUG|BLAU|CD|Card15|F830032C23Rik|IBD1|Nlrc2	nucleotide-binding oligomerization domain containing 2	protein-coding
mm_67273.1	chr7	75791079	75791082	-	1	NA	Intergenic	RLTR9A3|LTR|ERVK	-57258	NM_001122780	207952	Mm.206223	NM_029652	ENSMUSG00000055652	Klhl25	2810402K13Rik|BC027373|Enc-1	kelch-like 25	protein-coding
mm_20633.1	chr2	132002679	132002684	-	1	NA	intron (NM_175445, intron 7 of 10)	PB1|SINE|Alu	27307	NM_175445	215653	Mm.204737	NM_175445	ENSMUSG00000027339	Rassf2	3830431H01Rik|9030412M04Rik|AI852669|AW495050	Ras association (RalGDS/AF-6) domain family member 2	protein-coding
mm_165974.1	chr4	102255066	102255068	+	1	NA	5' UTR (NM_001177983, exon 1 of 6)	5' UTR (NM_001177983, exon 1 of 6)	128	NM_019840	18578	Mm.20181	NM_019840	ENSMUSG00000028525	Pde4b	Dpde4|R74983|dunce	phosphodiesterase 4B, cAMP specific	protein-coding
mm_3448.1	chr1	150102881	150102887	+	1	NA	intron (NM_011198, intron 5 of 9)	intron (NM_011198, intron 5 of 9)	2853	NM_011198	19225	Mm.292547	NM_011198	ENSMUSG00000032487	Ptgs2	COX2|Cox-2|PES-2|PGHS-2|PHS II|PHS-2|Pghs2|TIS10|gripghs	prostaglandin-endoperoxide synthase 2	protein-coding
mm_28209.1	chr3	88336166	88336198	-	1	NA	promoter-TSS (NM_178246)	promoter-TSS (NM_178246)	-78	NM_178246	229512	Mm.439830	NM_173188	ENSMUSG00000001415	Smg5	BC024683|mKIAA1089	Smg-5 homolog, nonsense mediated mRNA decay factor (C. elegans)	protein-coding
mm_80436.1	chr9	77924425	77924435	+	1	NA	intron (NM_134255, intron 1 of 7)	intron (NM_134255, intron 1 of 7)	7065	NM_134255	68801	Mm.430736	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	ELOVL family member 5, elongation of long chain fatty acids (yeast)	protein-coding
mm_24022.1	chr3	87527300	87527306	+	1	NA	exon (NM_012051, exon 2 of 5)	exon (NM_012051, exon 2 of 5)	1725	NM_012051	27049	Mm.219460	NM_012051	ENSMUSG00000003382	Etv3	AI414410|METS|Pe1	ets variant 3	protein-coding
mm_89293.1	chr10	87907966	87907977	+	1	NA	intron (NM_001314010, intron 3 of 4)	intron (NM_001314010, intron 3 of 4)	46860	NM_001111276	16000	Mm.268521	NM_010512	ENSMUSG00000020053	Igf1	C730016P09Rik|Igf-1|Igf-I	insulin-like growth factor 1	protein-coding
mm_21640.1	chr2	164333377	164333386	-	1	NA	exon (NM_009301, exon 2 of 3)	exon (NM_009301, exon 2 of 3)	616	NM_009301	20944	Mm.140154	NM_009301	ENSMUSG00000017004	Svs5	BB115186|Semg1|Svp-1|Svp1|Svp5	seminal vesicle secretory protein 5	protein-coding
mm_40621.1	chr5	64803615	64803627	+	1	NA	promoter-TSS (NM_008453)	promoter-TSS (NM_008453)	98	NM_008453	16599	Mm.392759	NM_008453	ENSMUSG00000029178	Klf3	9930027G08Rik|AL024007|Bklf|Tef-2	Kruppel-like factor 3 (basic)	protein-coding
mm_41156.1	chr5	87929869	87929872	+	1	NA	exon (NM_007786, exon 4 of 5)	exon (NM_007786, exon 4 of 5)	4237	NM_007786	12994	Mm.296303	NM_007786	ENSMUSG00000001622	Csn3	AW208918|CSN10|Csnk	casein kappa	protein-coding
mm_82971.1	chr9	35790102	35790106	-	1	NA	promoter-TSS (NM_026593)	promoter-TSS (NM_026593)	8	NM_026593	68171	Mm.99495	NM_026593	ENSMUSG00000032108	D730048I06Rik	Pate-C|Pate6|mANLP2	RIKEN cDNA D730048I06 gene	protein-coding
mm_117813.1	chr13	97760633	97760633	-	1	NA	Intergenic	Intergenic	200633	NR_046157	328314	Mm.138047	NR_046157	ENSMUSG00000110235	Gm5086	B230311A21|EG328314	predicted gene 5086	ncRNA
mm_77176.1	chr8	111690856	111690864	-	1	NA	intron (NM_025583, intron 1 of 6)	intron (NM_025583, intron 1 of 6)	150	NM_025583	66473	Mm.34374	NM_025583	ENSMUSG00000031957	Ctrb1	2200008D09Rik|AI504462|Ctrb|Prt-2	chymotrypsinogen B1	protein-coding
mm_132517.1	chr16	37580229	37580258	+	1	NA	promoter-TSS (NR_027778)	promoter-TSS (NR_027778)	90	NM_013547	15233	Mm.157442	NM_013547	ENSMUSG00000022821	Hgd	Hgo|aku	homogentisate 1, 2-dioxygenase	protein-coding
mm_96609.1	chr11	69096571	69096574	+	1	NA	Intergenic	Intergenic	-2384	NM_011065	18626	Mm.7373	NM_011065	ENSMUSG00000020893	Per1	Hftm|Per|m-rigui|mPer1	period circadian clock 1	protein-coding
mm_50159.1	chr6	41547381	41547385	+	1	NA	Intergenic	Intergenic	25607	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_32740.1	chr4	116612019	116612037	+	1	NA	exon (NM_016777, exon 6 of 16)	exon (NM_016777, exon 6 of 16)	-14398	NR_029450	654318	Mm.255685	NR_029450	ENSMUSG00000085408	C530005A16Rik	D930044c15rik	RIKEN cDNA C530005A16 gene	ncRNA
mm_65009.1	chr7	17060925	17060936	-	1	NA	intron (NM_001162950, intron 1 of 14)	intron (NM_001162950, intron 1 of 14)	1497	NM_001162950	53417	Mm.135110	NM_016868	ENSMUSG00000004328	Hif3a	Ipas|MOP7|NEPAS|bHLHe17	hypoxia inducible factor 3, alpha subunit	protein-coding
mm_67929.1	chr7	99917403	99917431	-	1	NA	exon (NM_001164258, exon 19 of 19)	exon (NM_001164258, exon 19 of 19)	58199	NM_001164258	446101	Mm.440757	NM_001164258	ENSMUSG00000035211	Xrra1	AI449753	X-ray radiation resistance associated 1	protein-coding
mm_97510.1	chr11	78499088	78499123	+	1	NA	promoter-TSS (NM_011707)	promoter-TSS (NM_011707)	-15	NM_011707	22370	Mm.3667	NM_011707	ENSMUSG00000017344	Vtn	AI256434|Vn	vitronectin	protein-coding
mm_35422.1	chr4	35158250	35158260	-	1	NA	promoter-TSS (NM_178061)	promoter-TSS (NM_178061)	-771	NM_178061	214944	Mm.32968	NM_178061	ENSMUSG00000073910	Mob3b	8430436F23Rik|A430018A01Rik|Mobkl2b	MOB kinase activator 3B	protein-coding
mm_31810.1	chr4	66827546	66827617	+	1	NA	promoter-TSS (NM_021297)	promoter-TSS (NM_021297)	30	NM_021297	21898	Mm.38049	NM_021297	ENSMUSG00000039005	Tlr4	Lps|Ly87|Ran/M1|Rasl2-8	toll-like receptor 4	protein-coding
mm_117735.1	chr13	95659341	95659347	-	1	NA	intron (NM_027711, intron 27 of 35)	intron (NM_027711, intron 27 of 35)	-37576	NM_010170	14064	Mm.440952	NM_010170	ENSMUSG00000021675	F2rl2	F730031A08|PAR3	coagulation factor II (thrombin) receptor-like 2	protein-coding
mm_66978.1	chr7	63937240	63937245	-	1	NA	intron (NM_021366, intron 1 of 1)	intron (NM_021366, intron 1 of 1)	1673	NM_021366	50794	Mm.240473	NM_021366	ENSMUSG00000052040	Klf13	0610043C13Rik|9430029L20Rik|Bteb3|FKLF-2|FKLF2|NSLP1|RFLAT-1|RFLAT1	Kruppel-like factor 13	protein-coding
mm_133998.1	chr16	4769674	4769691	-	1	NA	exon (NM_025670, exon 4 of 6)	exon (NM_025670, exon 4 of 6)	20253	NM_025670	66626	Mm.157648	NM_025670	ENSMUSG00000004071	Cdip1	2700048O17Rik|5730403B10Rik|AU018521|AW742692|CDIP	cell death inducing Trp53 target 1	protein-coding
mm_99044.1	chr11	98964903	98964913	+	1	NA	intron (NM_001176528, intron 1 of 7)	intron (NM_001176528, intron 1 of 7)	4437	NM_001176528	19401	Mm.439744	NM_009024	ENSMUSG00000037992	Rara	Nr1b1|RAR|RARalpha1	retinoic acid receptor, alpha	protein-coding
mm_158419.1	chrX	137950496	137950500	-	1	NA	intron (NM_030688, intron 2 of 10)	intron (NM_030688, intron 2 of 10)	259082	NM_026469	67944	Mm.443280	NM_026469	ENSMUSG00000071686	Tex13a	1700025D03Rik	testis expressed 13A	protein-coding
mm_171684.1	chr4	58206711	58206711	-	1	NA	promoter-TSS (NM_022814)	promoter-TSS (NM_022814)	-115	NM_022814	64817	Mm.261024	NM_022814	ENSMUSG00000028369	Svep1	1110021D17Rik|4833413O10Rik|AA387071|D430029O09Rik|Polydom	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	protein-coding
mm_14163.1	chr2	126606661	126606670	+	1	NA	intron (NM_008230, intron 3 of 11)	intron (NM_008230, intron 3 of 11)	12013	NM_008230	15186	Mm.18603	NM_008230	ENSMUSG00000027360	Hdc	AW108189|Hdc-a|Hdc-c|Hdc-e|Hdc-s	histidine decarboxylase	protein-coding
mm_104385.1	chr11	94474359	94474385	-	1	NA	promoter-TSS (NM_001177890)	promoter-TSS (NM_001177890)	-174	NM_001112813	12291	Mm.29585	NM_009783	ENSMUSG00000020866	Cacna1g	Cav3.1d|[a]1G|a1G|alpha-1G|mKIAA1123	calcium channel, voltage-dependent, T type, alpha 1G subunit	protein-coding
mm_138154.1	chr17	34214903	34214908	+	1	NA	intron (NM_011530, intron 10 of 11)	B4|SINE|B4	10426	NM_011530	21355	Mm.14814	NM_011530	ENSMUSG00000024339	Tap2	ABC18|AI462429|APT2|Abcb3|Ham-2|Ham2|MTP2|PSF2|RING11|Tap-2|Y1|jas	transporter 2, ATP-binding cassette, sub-family B (MDR/TAP)	protein-coding
mm_51508.1	chr6	83137041	83137059	+	1	NA	promoter-TSS (NM_133641)	promoter-TSS (NM_133641)	-34	NM_133641	20166	Mm.4139	NM_009106	ENSMUSG00000034930	Rtkn	-	rhotekin	protein-coding
mm_51504.1	chr6	83121706	83121730	+	1	NA	promoter-TSS (NM_001083922)	promoter-TSS (NM_001083922)	-257	NM_001083922	22377	Mm.1109	NM_016757	ENSMUSG00000030035	Wbp1	AI255152	WW domain binding protein 1	protein-coding
mm_162917.1	chr10	120227880	120227886	+	1	NA	intron (NM_025431, intron 1 of 2)	intron (NM_025431, intron 1 of 2)	823	NM_025431	66225	Mm.291755	NM_025431	ENSMUSG00000020224	Llph	1190005P17Rik	LLP homolog, long-term synaptic facilitation (Aplysia)	protein-coding
mm_74031.1	chr8	121792479	121792488	+	1	NA	Intergenic	Intergenic	37086	NM_145605	234825	Mm.209329	NM_145605	ENSMUSG00000040263	Klhdc4	AA408426|AV352552|BC012312|G430025P05Rik	kelch domain containing 4	protein-coding
mm_164750.1	chr17	75455657	75455663	+	1	NA	intron (NM_001166493, intron 1 of 16)	intron (NM_001166493, intron 1 of 16)	-9878	NM_207246	240168	Mm.329203	NM_207246	ENSMUSG00000071042	Rasgrp3	BC066069|Gm327	RAS, guanyl releasing protein 3	protein-coding
mm_12435.1	chr2	70661557	70661692	+	1	NA	non-coding (NR_027343, exon 1 of 11)	non-coding (NR_027343, exon 1 of 11)	115	NM_027352	70231	Mm.271950	NM_027352	ENSMUSG00000014959	Gorasp2	0610011A07Rik|2410043M02Rik|5730520M13Rik|9430094F20Rik|AW552058|ENSMUSG00000075299|GOLPH2|GRASP55|GRS2|p59	golgi reassembly stacking protein 2	protein-coding
mm_139254.1	chr17	47734439	47734441	+	1	NA	TTS (NM_025973)	TTS (NM_025973)	-2597	NM_001161722	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_170082.1	chr17	34966074	34966079	+	1	NA	Intergenic	Intergenic	6080	NM_010479	193740	Mm.6388	NM_010479	ENSMUSG00000091971	Hspa1a	Hsp70-3|Hsp70.3|Hsp72|hsp68|hsp70A1	heat shock protein 1A	protein-coding
mm_165978.1	chr4	102976125	102976154	+	1	NA	intron (NR_040444, intron 3 of 3)	intron (NR_040444, intron 3 of 3)	-10240	NM_001163767	67344	Mm.111346	NM_026100	ENSMUSG00000028523	Tctex1d1	1700055O19Rik	Tctex1 domain containing 1	protein-coding
mm_76190.1	chr8	82402789	82402840	-	1	NA	promoter-TSS (NM_001254747)	promoter-TSS (NM_001254747)	-228	NM_008357	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_14885.1	chr2	148871718	148871732	+	1	NA	TTS (NM_009976)	TTS (NM_009976)	3787	NM_009976	13010	Mm.4263	NM_009976	ENSMUSG00000027447	Cst3	CysC	cystatin C	protein-coding
mm_24677.1	chr3	94837612	94837627	+	1	NA	promoter-TSS (NM_172683)	promoter-TSS (NM_172683)	52	NM_172683	229584	Mm.274787	NM_172683	ENSMUSG00000038902	Pogz	9530006B08Rik	pogo transposable element with ZNF domain	protein-coding
mm_82641.1	chr9	22002600	22002640	-	1	NA	promoter-TSS (NM_029939)	promoter-TSS (NM_029939)	14	NM_001163787	77609	Mm.159953	NM_029939	ENSMUSG00000039632	Ccdc151	AI644415|C330001K17Rik|b2b1885Clo	coiled-coil domain containing 151	protein-coding
mm_165542.1	chr2	181546416	181546427	+	1	NA	exon (NM_001271585, exon 3 of 6)	exon (NM_001271585, exon 3 of 6)	25936	NM_001271584	13002	Mm.140761	NM_016775	ENSMUSG00000000826	Dnajc5	2610314I24Rik|AU018536|Csp	DnaJ heat shock protein family (Hsp40) member C5	protein-coding
mm_148660.1	chr19	5568003	5568062	+	1	NA	promoter-TSS (NM_001033448)	promoter-TSS (NM_001033448)	-42	NM_001033448	381201	Mm.441906	NM_001033448	ENSMUSG00000049562	Ap5b1	Gm962	adaptor-related protein complex 5, beta 1 subunit	protein-coding
mm_123052.1	chr14	55635603	55635718	-	1	NA	promoter-TSS (NM_024267)	promoter-TSS (NM_024267)	18	NM_024267	75751	Mm.27546	NM_024267	ENSMUSG00000002319	Ipo4	8430408O15Rik|AA409693|Imp4a|RanBP4	importin 4	protein-coding
mm_30101.1	chr3	138489373	138489411	-	1	NA	promoter-TSS (NM_175224)	promoter-TSS (NM_175224)	-10	NM_175224	75624	Mm.26833	NM_175224	ENSMUSG00000005813	Metap1	1700029C17Rik|AW047992|mKIAA0094	methionyl aminopeptidase 1	protein-coding
mm_18248.1	chr2	52205686	52205696	-	1	NA	exon (NM_010889, exon 101 of 157)	exon (NM_010889, exon 101 of 157)	-85311	NR_040620	78049	Mm.243883	NR_040620		4930573O16Rik	-	RIKEN cDNA 4930573O16 gene	ncRNA
mm_125691.1	chr15	66812361	66812378	+	1	NA	intron (NM_001029841, intron 1 of 7)	intron (NM_001029841, intron 1 of 7)	19460	NM_001029841	20491	Mm.7601	NM_009192	ENSMUSG00000022372	Sla	Slap|Slap-1	src-like adaptor	protein-coding
mm_51048.1	chr6	65627145	65627157	+	1	NA	intron (NM_001001495, intron 7 of 7)	intron (NM_001001495, intron 7 of 7)	36753	NM_001001495	414084	Mm.117558	NM_001001495	ENSMUSG00000044162	Tnip3	9030611K07Rik|ABIN-3|LIND	TNFAIP3 interacting protein 3	protein-coding
mm_123376.1	chr14	63245501	63245544	-	1	NA	promoter-TSS (NM_008092)	promoter-TSS (NM_008092)	-251	NM_001310610	14463	Mm.247669	NM_008092	ENSMUSG00000021944	Gata4	Gata-4	GATA binding protein 4	protein-coding
mm_168275.1	chr1	102897643	102897647	-	1	NA	Intergenic	L1Md_Gf|LINE|L1	1741877	NR_037989	100504525	Mm.87065	NR_037989	ENSMUSG00000100684	Gm20268	-	predicted gene, 20268	ncRNA
mm_108801.1	chr12	91668785	91668794	+	1	NA	intron (NM_175367, intron 4 of 6)	intron (NM_175367, intron 4 of 6)	-78302	NM_175335	83602	Mm.275728	NM_031391	ENSMUSG00000020962	Gtf2a1	6330549H03Rik|AA536742|AA959775|AW060250|TfIIAa/b|Tfiia1	general transcription factor II A, 1	protein-coding
mm_117936.1	chr13	99434548	99434556	-	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-21726	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_4455.1	chr1	172699080	172699094	+	1	NA	3' UTR (NM_007768, exon 2 of 2)	3' UTR (NM_007768, exon 2 of 2)	1031	NM_007768	12944	Mm.28767	NM_007768	ENSMUSG00000037942	Crp	AI255847	C-reactive protein, pentraxin-related	protein-coding
mm_137393.1	chr17	25820380	25820393	+	1	NA	3' UTR (NM_001164225, exon 6 of 6)	3' UTR (NM_001164225, exon 6 of 6)	-3241	NM_173741	268933	Mm.95512	NM_173741	ENSMUSG00000025737	Wdr24	BC037651	WD repeat domain 24	protein-coding
mm_99095.1	chr11	99914730	99914733	+	1	NA	promoter-TSS (NM_001126323)	promoter-TSS (NM_001126323)	-20	NM_001126323	670550	Mm.379775	NM_001126323	ENSMUSG00000078256	Gm11565	OTTMUSG00000002203	predicted gene 11565	protein-coding
mm_33001.1	chr4	120517641	120517659	+	1	NA	intron (NM_001159630, intron 13 of 17)	intron (NM_001159630, intron 13 of 17)	-14581	NM_177570	194219	Mm.29788	NM_177570	ENSMUSG00000047518	Slfnl1	4933406A14Rik	schlafen like 1	protein-coding
mm_108299.1	chr12	79296438	79296450	+	1	NA	promoter-TSS (NM_009014)	promoter-TSS (NM_009014)	-162	NM_001008550	211978	Mm.297919	NM_001008550	ENSMUSG00000066440	Zfyve26	4930465A13|9330197E15Rik|A630028O16Rik|Gm893|mKIAA0321	zinc finger, FYVE domain containing 26	protein-coding
mm_23736.1	chr3	69045119	69045136	+	1	NA	promoter-TSS (NM_025863)	promoter-TSS (NM_025863)	-385	NM_025863	66949	Mm.176695	NM_025863	ENSMUSG00000034317	Trim59	2310035M22Rik|2700022F13Rik|Mrf1|TSBF1	tripartite motif-containing 59	protein-coding
mm_46487.1	chr5	105132142	105132159	-	1	NA	intron (NM_008620, intron 3 of 10)	intron (NM_008620, intron 3 of 10)	7402	NM_008620	17472	Mm.440525	NM_008620	ENSMUSG00000079363	Gbp4	AW228052|Mag-2|Mpa-2|Mpa2	guanylate binding protein 4	protein-coding
mm_67660.1	chr7	86775577	86775587	-	1	NA	intron (NM_016770, intron 1 of 18)	intron (NM_016770, intron 1 of 18)	282	NM_016770	53320	Mm.269137	NM_016770	ENSMUSG00000001773	Folh1	GCP2|mopsm	folate hydrolase 1	protein-coding
mm_24219.1	chr3	88647731	88647744	+	1	NA	3' UTR (NM_001198913, exon 22 of 22)	3' UTR (NM_001198913, exon 22 of 22)	5405	NM_181817	242093	Mm.269130	NM_181817	ENSMUSG00000049741	Rxfp4	GPCR142|Gpr100|Rln3r2|SALPR	relaxin family peptide receptor 4	protein-coding
mm_60089.1	chr7	34659971	34660004	+	1	NA	Intergenic	Intergenic	-7146	NM_146188	233107	Mm.486198	NM_146188	ENSMUSG00000030499	Kctd15	BC031749	potassium channel tetramerisation domain containing 15	protein-coding
mm_72125.1	chr8	71690484	71690537	+	1	NA	TTS (NM_013564)	TTS (NM_013564)	1258	NM_013564	16336	Mm.476857	NM_013564	ENSMUSG00000079019	Insl3	Rlf|Rlnl	insulin-like 3	protein-coding
mm_116297.1	chr13	36577979	36578000	-	1	NA	Intergenic	Intergenic	156488	NM_153529	68404	Mm.232930	NM_153529	ENSMUSG00000039114	Nrn1	0710008J23Rik|Cpg15|Nrn	neuritin 1	protein-coding
mm_136509.1	chr16	97170708	97170759	-	1	NA	promoter-TSS (NM_031174)	promoter-TSS (NM_031174)	2	NM_031174	13508	Mm.102437	NM_031174	ENSMUSG00000050272	Dscam	4932410A21Rik	Down syndrome cell adhesion molecule	protein-coding
mm_154042.1	chr19	53944166	53944226	-	1	NA	promoter-TSS (NM_019658)	promoter-TSS (NM_019658)	-110	NM_001168505	56392	Mm.228669	NM_019658	ENSMUSG00000024976	Shoc2	AU017287|Sur8|mKIAA0862	soc-2 (suppressor of clear) homolog (C. elegans)	protein-coding
mm_138951.1	chr17	44134795	44134811	+	1	NA	Intergenic	Intergenic	-28995	NM_199016	224794	Mm.255971	NM_199016	ENSMUSG00000023961	Enpp4	4933413N07Rik|AA986363|AI195364|E-NPP 4|Gm90|mKIAA0879	ectonucleotide pyrophosphatase/phosphodiesterase 4	protein-coding
mm_152199.1	chr19	7583266	7583273	-	1	NA	intron (NM_139269, intron 4 of 4)	HAL1|LINE|L1	23907	NM_019516	56072	Mm.298242	NM_019516	ENSMUSG00000024972	Lgals12	AW987437|Grip1	lectin, galactose binding, soluble 12	protein-coding
mm_152882.1	chr19	24555805	24555815	-	1	NA	promoter-TSS (NM_008846)	promoter-TSS (NM_008846)	17	NM_008846	18719	Mm.217214	NM_008846	ENSMUSG00000024867	Pip5k1b	PI4P5K-I[b]|PIP5K1-beta|PIP5KIbeta|Pipk5b|STM7	phosphatidylinositol-4-phosphate 5-kinase, type 1 beta	protein-coding
mm_16969.1	chr2	17731036	17731087	-	1	NA	promoter-TSS (NM_028757)	promoter-TSS (NM_028757)	7	NM_028757	74103	Mm.120298	NM_028757	ENSMUSG00000053702	Nebl	1200007O21Rik|A630080F05Rik|BB140644|D830029A09Rik|Lnebl	nebulette	protein-coding
mm_120159.1	chr14	60709492	60709519	+	1	NA	exon (NM_001033272, exon 4 of 13)	exon (NM_001033272, exon 4 of 13)	-23399	NM_001310594	219140	Mm.149776	NM_001033272	ENSMUSG00000021990	Spata13	C79050|ESTM11|X83327|mFLJ00298	spermatogenesis associated 13	protein-coding
mm_19939.1	chr2	116066035	116066063	-	1	NA	promoter-TSS (NM_010825)	promoter-TSS (NM_010825)	-991	NM_010825	17536	Mm.247566	NM_010825	ENSMUSG00000027210	Meis2	A430109D20Rik|Mrg1|Stra10	Meis homeobox 2	protein-coding
mm_92759.1	chr10	81060135	81060204	-	1	NA	promoter-TSS (NM_024499)	promoter-TSS (NM_024499)	-15	NM_024499	52551	Mm.30068	NM_024499	ENSMUSG00000004937	Sgta	5330427H01Rik|AI194281|D10Ertd190e|Sgt|Stg	small glutamine-rich tetratricopeptide repeat (TPR)-containing, alpha	protein-coding
mm_167115.1	chr7	118210623	118210631	-	1	NA	intron (NM_001031814, intron 4 of 62)	intron (NM_001031814, intron 4 of 62)	33010	NM_001031814	233789	Mm.309053	NM_177180	ENSMUSG00000030655	Smg1	2610207I05Rik|5430435M13Rik|C130002K18Rik|mKIAA0421	SMG1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)	protein-coding
mm_149527.1	chr19	12460810	12460825	+	1	NA	promoter-TSS (NM_010821)	promoter-TSS (NM_010821)	38	NM_010821	17476	Mm.3999	NM_010821	ENSMUSG00000046805	Mpeg1	MPS1|Mpg-1	macrophage expressed gene 1	protein-coding
mm_89582.1	chr10	95746067	95746092	+	1	NA	Intergenic	Intergenic	-181912	NM_027722	71207	Mm.24397	NM_027722	ENSMUSG00000020029	Nudt4	4933436C10Rik|DIPP2|DIPP2alpha|DIPP2beta|HDCMB47P	nudix (nucleoside diphosphate linked moiety X)-type motif 4	protein-coding
mm_12222.1	chr2	67654166	67654169	+	1	NA	Intergenic	MLTR11A|LTR|ERVK	-21290	NR_106083	102465706		NR_106083	ENSMUSG00000098299	Mir7224	Gm27971|mmu-mir-7224	microRNA 7224	ncRNA
mm_36405.1	chr4	77905019	77905031	-	1	NA	intron (NM_011211, intron 2 of 39)	intron (NM_011211, intron 2 of 39)	306870	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding
mm_60450.1	chr7	44477392	44477398	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	7048	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_52032.1	chr6	96113147	96113170	+	1	NA	promoter-TSS (NM_182808)	promoter-TSS (NM_182808)	4	NM_182808	320265	Mm.489890	NM_182808	ENSMUSG00000059187	Fam19a1	C630007B19Rik|FAM19A1 TAFA-1|TAFA1|Tafa-1	family with sequence similarity 19, member A1	protein-coding
mm_73866.1	chr8	118549705	118549705	+	1	NA	intron (NM_019707, intron 2 of 13)	intron (NM_019707, intron 2 of 13)	266094	NM_019707	12554	Mm.334841	NM_019707	ENSMUSG00000031841	Cdh13	4932416G01Rik|Cdht|Tcad	cadherin 13	protein-coding
mm_37981.1	chr4	133601893	133601904	-	1	NA	5' UTR (NM_018754, exon 1 of 1)	5' UTR (NM_018754, exon 1 of 1)	270	NM_018754	55948	Mm.44482	NM_018754	ENSMUSG00000047281	Sfn	Er|Mme1|Ywhas	stratifin	protein-coding
mm_135147.1	chr16	35857481	35857520	-	1	NA	exon (NM_001039530, exon 6 of 17)	exon (NM_001039530, exon 6 of 17)	13882	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_73152.1	chr8	94994394	94994433	+	1	NA	intron (NM_018882, intron 1 of 13)	intron (NM_018882, intron 1 of 13)	10014	NM_018882	14766	Mm.290834	NM_018882	ENSMUSG00000031785	Adgrg1	Cyt28|Gpr56|TM7LN4|TM7XN1	adhesion G protein-coupled receptor G1	protein-coding
mm_44402.1	chr5	17836067	17836077	-	1	NA	promoter-TSS (NM_001159555)	promoter-TSS (NM_001159555)	-176	NM_007643	12491	Mm.18628	NM_007643	ENSMUSG00000002944	Cd36	FAT|GPIV|Scarb3	CD36 antigen	protein-coding
mm_69150.1	chr7	127122029	127122056	-	1	NA	promoter-TSS (NM_133686)	promoter-TSS (NM_133686)	-13	NM_133686	67375	Mm.26928	NM_133686	ENSMUSG00000030674	Qprt	2410027J01Rik|AI647766|QPRTase	quinolinate phosphoribosyltransferase	protein-coding
mm_94114.1	chr10	128626533	128626537	-	1	NA	promoter-TSS (NM_013765)	promoter-TSS (NM_013765)	-29	NM_013765	27370	Mm.32118	NM_013765	ENSMUSG00000025362	Rps26	-	ribosomal protein S26	protein-coding
mm_86491.1	chr10	5593765	5593809	+	1	NA	promoter-TSS (NM_026793)	promoter-TSS (NM_026793)	59	NM_026793	68632	Mm.338242	NM_026793	ENSMUSG00000046916	Myct1	1110020B04Rik|AI225941|AI642973|Mtmc1	myc target 1	protein-coding
mm_140033.1	chr17	74338857	74338902	+	1	NA	promoter-TSS (NM_001162870)	promoter-TSS (NM_001162870)	-108	NM_001162870	50850	Mm.19804	NM_016962	ENSMUSG00000024068	Spast	Spg4|mKIAA1083	spastin	protein-coding
mm_113381.1	chr13	33016185	33016232	+	1	NA	3' UTR (NM_009256, exon 7 of 7)	3' UTR (NM_009256, exon 7 of 7)	-11206	NM_011452	20706	Mm.45371	NM_011452	ENSMUSG00000021403	Serpinb9b	1600019A21Rik|R86|SPI-CI|Spi10|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 9b	protein-coding
mm_68375.1	chr7	108930169	108930183	-	1	NA	promoter-TSS (NM_175532)	promoter-TSS (NM_175532)	-18	NM_175532	244202	Mm.37991	NM_175532	ENSMUSG00000049709	Nlrp10	6430548I20Rik|Nalp10|Napl10|PAN5|Pynod	NLR family, pyrin domain containing 10	protein-coding
mm_11761.1	chr2	38517358	38517385	+	1	NA	intron (NM_001159631, intron 1 of 9)	L1MB5|LINE|L1	5495	NM_001159631	59126	Mm.143818	NM_021606	ENSMUSG00000026749	Nek6	1300007C09Rik	NIMA (never in mitosis gene a)-related expressed kinase 6	protein-coding
mm_164314.1	chr15	103898432	103898456	-	1	NA	exon (NM_009268, exon 2 of 5)	exon (NM_009268, exon 2 of 5)	856	NM_009268	20771	Mm.30276	NM_009268		Mucl1	Spt-2|Spt2	mucin-like 1	protein-coding
mm_137481.1	chr17	26933044	26933060	+	1	NA	promoter-TSS (NM_009343)	promoter-TSS (NM_009343)	-75	NM_001302397	21652	Mm.258953	NM_009343	ENSMUSG00000024193	Phf1	AW557215|D17Ertd455e|Pcl1|Phf2|Tctex3	PHD finger protein 1	protein-coding
mm_10909.1	chr2	25366590	25366604	+	1	NA	promoter-TSS (NM_001033293)	promoter-TSS (NM_001033293)	-971	NM_001033293	227620	Mm.33797	NM_001033293	ENSMUSG00000026956	Uap1l1	5730445F03Rik	UDP-N-acteylglucosamine pyrophosphorylase 1-like 1	protein-coding
mm_85294.1	chr9	100466885	100466893	-	1	NA	intron (NM_001033543, intron 4 of 6)	intron (NM_001033543, intron 4 of 6)	19584	NM_001033543	213208	Mm.242896	NM_001033543	ENSMUSG00000044244	Il20rb	AV228068|Fndc6|Gm186|Il20R2	interleukin 20 receptor beta	protein-coding
mm_9269.1	chr1	171633165	171633180	-	1	NA	3' UTR (NM_144539, exon 8 of 8)	3' UTR (NM_144539, exon 8 of 8)	8728	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_130022.1	chr15	88819444	88819455	-	1	NA	promoter-TSS (NM_001142357)	promoter-TSS (NM_001142357)	-131	NM_145477	223774	Mm.41512	NM_145477	ENSMUSG00000035845	Alg12	ECM39	asparagine-linked glycosylation 12 (alpha-1,6-mannosyltransferase)	protein-coding
mm_130925.1	chr15	102977464	102977478	-	1	NA	intron (NM_008272, intron 1 of 2)	intron (NM_008272, intron 1 of 2)	439	NM_008272	15427	Mm.4765	NM_008272	ENSMUSG00000036139	Hoxc9	Hox-3.2	homeobox C9	protein-coding
mm_24903.1	chr3	96195397	96195406	+	1	NA	TTS (NM_022030)	TTS (NM_022030)	2185	NM_026975	69168	Mm.104531	NM_026975	ENSMUSG00000015943	Bola1	1810037G04Rik	bolA-like 1 (E. coli)	protein-coding
mm_91071.1	chr10	19008704	19008707	-	1	NA	intron (NM_001166402, intron 1 of 7)	intron (NM_001166402, intron 1 of 7)	3258	NM_001166402	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_36786.1	chr4	103026650	103026667	-	1	NA	promoter-TSS (NM_011831)	promoter-TSS (NM_011831)	70	NM_011831	23919	Mm.100163	NM_011831	ENSMUSG00000066090	Insl5	RIF2	insulin-like 5	protein-coding
mm_96977.1	chr11	70652926	70652946	+	1	NA	exon (NM_011072, exon 2 of 3)	exon (NM_011072, exon 2 of 3)	1714	NM_011072	18643	Mm.2647	NM_011072	ENSMUSG00000018293	Pfn1	Pfn	profilin 1	protein-coding
mm_34765.1	chr4	152488306	152488332	+	1	NA	intron (NM_153424, intron 2 of 29)	intron (NM_153424, intron 2 of 29)	10177	NM_153424	260305	Mm.302496	NM_153424	ENSMUSG00000039577	Nphp4	4930564O18Rik|nmf192	nephronophthisis 4 (juvenile) homolog (human)	protein-coding
mm_28527.1	chr3	92621207	92621220	-	1	NA	5' UTR (NM_001166172, exon 2 of 3)	5' UTR (NM_001166172, exon 2 of 3)	447	NM_001166172	78382	Mm.235474	NM_001166172	ENSMUSG00000086848	Lce6a	2210420J11Rik	late cornified envelope 6A	protein-coding
mm_86716.1	chr10	19009600	19009614	+	1	NA	intron (NM_001166402, intron 1 of 7)	intron (NM_001166402, intron 1 of 7)	2356	NM_001166402	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_142748.1	chr17	48445908	48445908	-	1	NA	Intergenic	Intergenic	5593	NM_027292	70026	Mm.22613	NM_027292	ENSMUSG00000023995	Tspo2	2510027D20Rik|Bzrpl1	translocator protein 2	protein-coding
mm_107483.1	chr12	38123872	38123877	+	1	NA	intron (NM_178681, intron 6 of 24)	intron (NM_178681, intron 6 of 24)	243169	NM_178681	217480	Mm.126525	NM_178681	ENSMUSG00000036095	Dgkb	6430574F24|90kda|C630029D13Rik|DAGK2|DGK|DGK-beta|mKIAA0718	diacylglycerol kinase, beta	protein-coding
mm_1891.1	chr1	85685088	85685104	+	1	NA	intron (NM_001313712, intron 11 of 16)	intron (NM_001313712, intron 11 of 16)	35108	NM_001313714	20684	Mm.290906	NM_013673	ENSMUSG00000026222	Sp100	A430075G10Rik	nuclear antigen Sp100	protein-coding
mm_153003.1	chr19	30115350	30115365	-	1	NA	intron (NM_138595, intron 18 of 24)	intron (NM_138595, intron 18 of 24)	60084	NM_138595	104174	Mm.274852	NM_138595	ENSMUSG00000024827	Gldc	D030049L12Rik|D19Wsu57e	glycine decarboxylase	protein-coding
mm_104908.1	chr11	99658979	99658984	-	1	NA	promoter-TSS (NM_001126320)	promoter-TSS (NM_001126320)	-22	NM_001126320	100040248	Mm.340791	NM_001126320	ENSMUSG00000069718	Gm11563	2310045F10Rik|OTTMUSG00000002200	predicted gene 11563	protein-coding
mm_96422.1	chr11	67256243	67256251	+	1	NA	exon (NM_010855, exon 34 of 40)	exon (NM_010855, exon 34 of 40)	18435	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_135917.1	chr16	67618788	67618791	-	1	NA	intron (NM_178721, intron 1 of 9)	intron (NM_178721, intron 1 of 9)	2119	NM_001347247	239857	Mm.394300	NM_178721	ENSMUSG00000064115	Cadm2	2900078E11Rik|9330131D06|A830029E02Rik|Igdf4d|Igsf4d|NECL3|SynCAM 2|SynCAM2	cell adhesion molecule 2	protein-coding
mm_17277.1	chr2	26092049	26092059	-	1	NA	5' UTR (NM_001037098, exon 1 of 6)	5' UTR (NM_001037098, exon 1 of 6)	342	NM_001037098	67991	Mm.131074	NM_026495	ENSMUSG00000026932	Nacc2	0610020I02Rik|AI448087|Btbd14a|C030048H19Rik	nucleus accumbens associated 2, BEN and BTB (POZ) domain containing	protein-coding
mm_105364.1	chr11	103193525	103193540	-	1	NA	exon (NM_001077698, exon 15 of 26)	exon (NM_001077698, exon 15 of 26)	15016	NM_001254724	69441	Mm.380648	NM_027082	ENSMUSG00000020940	1700023F06Rik	-	RIKEN cDNA 1700023F06 gene	protein-coding
mm_137456.1	chr17	26561480	26561505	+	1	NA	promoter-TSS (NM_026170)	promoter-TSS (NM_026170)	-20	NM_026170	67458	Mm.30496	NM_026170	ENSMUSG00000001576	Ergic1	1200007D18Rik|maa-136	endoplasmic reticulum-golgi intermediate compartment (ERGIC) 1	protein-coding
mm_92298.1	chr10	73326988	73326996	-	1	NA	Intergenic	RLTR17|LTR|ERVK	-240287	NR_040646	327768	Mm.417745	NR_040646		A330049N07Rik	-	RIKEN cDNA A330049N07 gene	ncRNA
mm_15560.1	chr2	158502709	158502720	+	1	NA	5' UTR (NM_145635, exon 1 of 3)	5' UTR (NM_145635, exon 1 of 3)	102	NM_145635	246747	Mm.28800	NM_145635	ENSMUSG00000044405	Adig	SMAF-1|Smaf1	adipogenin	protein-coding
mm_88019.1	chr10	67185942	67185955	+	1	NA	5' UTR (NM_001242396, exon 1 of 25)	5' UTR (NM_001242396, exon 1 of 25)	198	NM_001242396	108829	Mm.23846	NM_207221	ENSMUSG00000037876	Jmjd1c	5430433L24Rik|D630035I23Rik|Jmjdic|TRIP8	jumonji domain containing 1C	protein-coding
mm_138316.1	chr17	34681405	34681416	+	1	NA	intron (NM_031176, intron 5 of 32)	intron (NM_031176, intron 5 of 32)	10875	NM_031176	81877	Mm.290527	NM_031176	ENSMUSG00000033327	Tnxb	Tn-mhc|Tnx	tenascin XB	protein-coding
mm_49240.1	chr6	17306416	17306430	+	1	NA	promoter-TSS (NM_007616)	promoter-TSS (NM_007616)	88	NM_007616	12389	Mm.28278	NM_007616	ENSMUSG00000007655	Cav1	Cav|Cav-1	caveolin 1, caveolae protein	protein-coding
mm_156170.1	chrX	130186716	130186729	+	1	NA	intron (NM_172493, intron 23 of 26)	intron (NM_172493, intron 23 of 26)	436980	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diaph2	Dia3|Diap2|Drf2|E430022I22Rik	diaphanous related formin 2	protein-coding
mm_78180.1	chr9	21196723	21196771	+	1	NA	promoter-TSS (NM_019798)	promoter-TSS (NM_019798)	42	NM_019798	18577	Mm.191749	NM_019798	ENSMUSG00000032177	Pde4a	D9Ertd60e|Dpde2	phosphodiesterase 4A, cAMP specific	protein-coding
mm_172198.1	chr6	51466699	51466708	-	1	NA	exon (NM_182650, exon 4 of 10)	exon (NM_182650, exon 4 of 10)	3191	NM_182650	53379	Mm.155896	NM_016806	ENSMUSG00000004980	Hnrnpa2b1	9130414A06Rik|Hnrpa2|Hnrpa2b1|hnrnp-A	heterogeneous nuclear ribonucleoprotein A2/B1	protein-coding
mm_172960.1	chr9	88482231	88482232	-	1	NA	5' UTR (NM_001284328, exon 1 of 12)	5' UTR (NM_001284328, exon 1 of 12)	166	NM_019666	56403	Mm.260545	NM_019666	ENSMUSG00000032423	Syncrip	2610109K23Rik|4632417O19Rik|GRY-RBP|Nsap1|Nsap1l|hnRNP Q|pp68	synaptotagmin binding, cytoplasmic RNA interacting protein	protein-coding
mm_109575.1	chr12	112146188	112146222	+	1	NA	promoter-TSS (NM_001097621)	promoter-TSS (NM_001097621)	-3	NM_001097621	668303	Mm.313104	NM_001097621	ENSMUSG00000021294	Kif26a	mKIAA1236	kinesin family member 26A	protein-coding
mm_74446.1	chr8	4105759	4105767	-	1	NA	promoter-TSS (NM_026956)	promoter-TSS (NM_026956)	1	NM_026956	69142	Mm.171061	NM_026956	ENSMUSG00000051906	Cd209f	1810029C22Rik|AI647041|SIGNR8	CD209f antigen	protein-coding
mm_115802.1	chr13	19357344	19357399	-	1	NA	TTS (NM_024270)	TTS (NM_024270)	38442	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_139202.1	chr17	47672669	47672680	+	1	NA	exon (NM_198421, exon 3 of 7)	exon (NM_198421, exon 3 of 7)	-14936	NR_045945	100415787	Mm.392206	NR_045945	ENSMUSG00000084880	Tomm6os	Gm14872|OTTMUSG00000018355|Prickle4os	translocase of outer mitochondrial membrane 6, opposite strand	ncRNA
mm_3167.1	chr1	135631750	135631773	+	1	NA	Intergenic	Intergenic	-46406	NM_173437	215690	Mm.34977	NM_173437	ENSMUSG00000009418	Nav1	9530089B19|9930003A20Rik|C230080M11Rik|Pomfil3|Unc53h1|mKIAA1151|steerin-1	neuron navigator 1	protein-coding
mm_105210.1	chr11	102162647	102162650	-	1	NA	TTS (NM_172947)	TTS (NM_172947)	-6241	NM_029649	76547	Mm.46529	NM_029649	ENSMUSG00000020921	Tmem101	2610511E22Rik	transmembrane protein 101	protein-coding
mm_24167.1	chr3	88553755	88553806	+	1	NA	promoter-TSS (NM_033526)	promoter-TSS (NM_033526)	64	NM_033526	94232	Mm.303059	NM_033526	ENSMUSG00000008604	Ubqln4	A1Up|A1u|AI663987|CIP75|UBIN	ubiquilin 4	protein-coding
mm_26188.1	chr3	138415485	138415510	+	1	NA	promoter-TSS (NM_011996)	promoter-TSS (NM_011996)	0	NM_011996	26876	Mm.158750	NM_011996	ENSMUSG00000037797	Adh4	Adh2	alcohol dehydrogenase 4 (class II), pi polypeptide	protein-coding
mm_84799.1	chr9	77230464	77230476	-	1	NA	intron (NM_027150, intron 2 of 7)	intron (NM_027150, intron 2 of 7)	117400	NM_027150	69642	Mm.35008	NM_027150	ENSMUSG00000032355	Mlip	2310046A06Rik|AI931782|CIP	muscular LMNA-interacting protein	protein-coding
mm_118233.1	chr13	111489970	111489978	-	1	NA	promoter-TSS (NM_028487)	promoter-TSS (NM_028487)	67	NM_028487	73274	Mm.57286	NM_028487	ENSMUSG00000032745	Gpbp1	1700034P14Rik|AU019836|D230035M11Rik|Gpbp|mGPBP	GC-rich promoter binding protein 1	protein-coding
mm_36524.1	chr4	84675397	84675411	-	1	NA	promoter-TSS (NM_172870)	promoter-TSS (NM_172870)	-318	NM_172870	242509	Mm.190774	NM_172870	ENSMUSG00000028487	Bnc2	5031434M05Rik|8430420F16Rik	basonuclin 2	protein-coding
mm_121522.1	chr14	122107066	122107070	+	1	NA	promoter-TSS (NM_080556)	promoter-TSS (NM_080556)	-14	NM_080556	68059	Mm.275191	NM_080556	ENSMUSG00000025544	Tm9sf2	1500001N15Rik|AA536814|D14Ertd64e|P76	transmembrane 9 superfamily member 2	protein-coding
mm_134013.1	chr16	4879043	4879053	-	1	NA	intron (NM_145359, intron 1 of 2)	intron (NM_145359, intron 1 of 2)	803	NM_145359	207740	Mm.268895	NM_145359	ENSMUSG00000039568	Ubald1	1500031H01Rik|BC013706|Fam100a	UBA-like domain containing 1	protein-coding
mm_169055.1	chr13	22707423	22707425	+	1	NA	Intergenic	Intergenic	19198	NM_001166709	432735	Mm.480282	NM_001166709		Vmn1r207-ps	Gm11312|OTTMUSG00000000511|Vmn1r207	vomeronasal 1 receptor 207, pseudogene	protein-coding
mm_168854.1	chr12	24252472	24252473	-	1	NA	Intergenic	CpG	-155203	NM_001256489	66808	Mm.379124	NM_001256489	ENSMUSG00000073158	9030624G23Rik	-	RIKEN cDNA 9030624G23 gene	protein-coding
mm_10266.1	chr2	9869618	9869622	+	1	NA	intron (NM_008091, intron 3 of 5)	intron (NM_008091, intron 3 of 5)	8980	NM_008091	14462	Mm.313866	NM_008091	ENSMUSG00000015619	Gata3	Gata-3|jal	GATA binding protein 3	protein-coding
mm_68448.1	chr7	110059678	110059734	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-1996	NM_009281	20841	Mm.10815	NM_009281	ENSMUSG00000061079	Zfp143	AA959806|AU015869|D7Ertd805e|KRAB14|SBF|Staf|Zfp79|Zfp80-rs1|Znf143|pHZ-1	zinc finger protein 143	protein-coding
mm_96927.1	chr11	70510838	70510849	+	1	NA	exon (NM_029360, exon 5 of 5)	exon (NM_029360, exon 5 of 5)	3773	NM_001013607	327956	Mm.244514	NM_001013607	ENSMUSG00000020830	Vmo1	Gm741	vitelline membrane outer layer 1 homolog (chicken)	protein-coding
mm_107102.1	chr12	17732212	17732253	+	1	NA	intron (NM_016677, intron 1 of 3)	intron (NM_016677, intron 1 of 3)	41418	NM_016677	53602	Mm.313619	NM_016677	ENSMUSG00000071379	Hpcal1	NVP-3|Nvp3|VILIP3|Vnsl3|Vsnl3	hippocalcin-like 1	protein-coding
mm_92205.1	chr10	68137205	68137208	-	1	NA	intron (NM_023598, intron 4 of 9)	intron (NM_023598, intron 4 of 9)	141520	NM_023598	71371	Mm.440357	NM_023598	ENSMUSG00000019947	Arid5b	4930580B11|5430435G07Rik|AI467247|Desrt|Mrf2|Mrf2alpha|Mrf2beta	AT rich interactive domain 5B (MRF1-like)	protein-coding
mm_79574.1	chr9	58134719	58134735	+	1	NA	promoter-TSS (NM_001162479)	promoter-TSS (NM_001162479)	62	NM_001162479	20897	Mm.10801	NM_009291	ENSMUSG00000032327	Stra6	AI891933	stimulated by retinoic acid gene 6	protein-coding
mm_24373.1	chr3	90220857	90220867	+	1	NA	promoter-TSS (NM_026677)	promoter-TSS (NM_026677)	78	NM_026677	68328	Mm.29355	NM_026677	ENSMUSG00000027935	Rab13	0610007N03Rik|B230212B15Rik	RAB13, member RAS oncogene family	protein-coding
mm_37374.1	chr4	120968902	120968920	-	1	NA	3' UTR (NM_133716, exon 10 of 10)	3' UTR (NM_133716, exon 10 of 10)	4411	NR_105982	102465614		NR_105982	ENSMUSG00000106436	Mir7015	mmu-mir-7015	microRNA 7015	ncRNA
mm_99286.1	chr11	101322055	101322095	+	1	NA	3' UTR (NM_011192, exon 11 of 11)	3' UTR (NM_011192, exon 11 of 11)	-2988	NM_178932	237940	Mm.302277	NM_178932	ENSMUSG00000078651	Aoc2	RAO	amine oxidase, copper containing 2 (retina-specific)	protein-coding
mm_144582.1	chr18	31931454	31931460	+	1	NA	promoter-TSS (NM_144862)	promoter-TSS (NM_144862)	-50	NM_144862	225341	Mm.24551	NM_144862	ENSMUSG00000024395	Lims2	PINCH2	LIM and senescent cell antigen like domains 2	protein-coding
mm_10882.1	chr2	25243239	25243249	+	1	NA	5' UTR (NM_176834, exon 1 of 1)	5' UTR (NM_176834, exon 1 of 1)	315	NM_176834	68846	Mm.24777	NM_176834	ENSMUSG00000044628	Rnf208	1110061N23Rik	ring finger protein 208	protein-coding
mm_96532.1	chr11	68586987	68587030	+	1	NA	promoter-TSS (NM_177779)	promoter-TSS (NM_177779)	-29	NM_177779	276920	Mm.123046	NM_177779	ENSMUSG00000045915	Ccdc42	A530001H01Rik	coiled-coil domain containing 42	protein-coding
mm_72261.1	chr8	75097131	75097141	+	1	NA	exon (NM_010442, exon 3 of 5)	exon (NM_010442, exon 3 of 5)	3518	NM_010442	15368	Mm.276389	NM_010442	ENSMUSG00000005413	Hmox1	D8Wsu38e|HO-1|HO1|Hemox|Hmox|Hsp32	heme oxygenase 1	protein-coding
mm_30914.1	chr4	32615478	32615487	+	1	NA	promoter-TSS (NM_011997)	promoter-TSS (NM_011997)	12	NM_011997	26885	Mm.22279	NM_011997	ENSMUSG00000028282	Casp8ap2	D4Ertd659e|FLASH	caspase 8 associated protein 2	protein-coding
mm_53777.1	chr6	146219841	146219851	+	1	NA	intron (NM_010586, intron 44 of 55)	intron (NM_010586, intron 44 of 55)	282377	NM_010586	16439	Mm.7800	NM_010586	ENSMUSG00000030287	Itpr2	AI649341|InsP3R-2|InsP3R-5|Ip3r2|Itpr5|insP3R2	inositol 1,4,5-triphosphate receptor 2	protein-coding
mm_89999.1	chr10	112270035	112270067	+	1	NA	Intergenic	Intergenic	-1072	NM_001025581	268345	Mm.336242	NM_001025581	ENSMUSG00000035681	Kcnc2	AW047325|B230117I07|KShIIIA|Kv3.2	potassium voltage gated channel, Shaw-related subfamily, member 2	protein-coding
mm_98806.1	chr11	97050812	97050856	+	1	NA	promoter-TSS (NM_001081434)	promoter-TSS (NM_001081434)	14	NM_001081434	71240	Mm.190450	NM_001081434	ENSMUSG00000038534	Osbpl7	4933437E18Rik	oxysterol binding protein-like 7	protein-coding
mm_31122.1	chr4	42957459	42957466	+	1	NA	exon (NM_019874, exon 3 of 3)	exon (NM_019874, exon 3 of 3)	4368	NM_019874	56323	Mm.20437	NM_019874	ENSMUSG00000036052	Dnajb5	1110058L06Rik|AI462558|Hsc40|Hsp40-3	DnaJ heat shock protein family (Hsp40) member B5	protein-coding
mm_156789.1	chrX	162638088	162638093	+	1	NA	intron (NR_038088, intron 4 of 5)	Lx9|LINE|L1	5568	NM_001290633	194590	Mm.442441	NM_178256	ENSMUSG00000040855	Reps2	POB1	RALBP1 associated Eps domain containing protein 2	protein-coding
mm_116783.1	chr13	53286053	53286129	-	1	NA	promoter-TSS (NM_013846)	promoter-TSS (NM_013846)	18	NM_013846	26564	Mm.342774	NM_013846	ENSMUSG00000021464	Ror2	Ntrkr2|mRor2	receptor tyrosine kinase-like orphan receptor 2	protein-coding
mm_87734.1	chr10	60133619	60133647	+	1	NA	3' UTR (NM_052994, exon 11 of 11)	3' UTR (NM_052994, exon 11 of 11)	6857	NR_105871	102465546		NR_105871	ENSMUSG00000105468	Mir6906	mmu-mir-6906	microRNA 6906	ncRNA
mm_647.1	chr1	40425578	40425590	+	1	NA	Intergenic	RMER12B|LTR|ERVK	-3986	NM_001294171	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_139367.1	chr17	51435537	51435543	+	1	NA	intron (NR_046166, intron 2 of 4)	ORR1B1|LTR|ERVL-MaLR	12729	NR_046166	328837	Mm.236143	NR_046166		C330011F03Rik	C330011F03	RIKEN cDNA C330011F03 gene	ncRNA
mm_5632.1	chr1	40427331	40427359	-	1	NA	Intergenic	Intergenic	-2225	NM_001294171	17082	Mm.289824	NM_010743	ENSMUSG00000026069	Il1rl1	DER4|Fit-1|Ly84|ST2L|St2|St2-rs1|T1|T1/ST2	interleukin 1 receptor-like 1	protein-coding
mm_149619.1	chr19	16919639	16919653	+	1	NA	Intergenic	Intergenic	-36472	NM_181348	353211	Mm.257354	NM_181348	ENSMUSG00000039126	Prune2	6330414G02Rik|A230083H22Rik|A330102H22Rik|Bmcc1|mKIAA0367	prune homolog 2	protein-coding
mm_55030.1	chr6	48948882	48948888	-	1	NA	Intergenic	L1_Mur3|LINE|L1	18989	NM_001081273	69761	Mm.333053	NM_001081273	ENSMUSG00000029813	1600015I10Rik	AI429442|Doxl1	RIKEN cDNA 1600015I10 gene	protein-coding
mm_6297.1	chr1	71068968	71068975	-	1	NA	intron (NM_007525, intron 4 of 10)	intron (NM_007525, intron 4 of 10)	34001	NM_007525	12021	Mm.10764	NM_007525	ENSMUSG00000026196	Bard1	ENSMUSG00000060893|ENSMUSG00000073653	BRCA1 associated RING domain 1	protein-coding
mm_117612.1	chr13	91388080	91388090	-	1	NA	promoter-TSS (NR_045161)	promoter-TSS (NR_045161)	0	NR_045161	320297	Mm.375866	NR_045161	ENSMUSG00000097182	A830009L08Rik	-	RIKEN cDNA A830009L08 gene	ncRNA
mm_68775.1	chr7	122046915	122046933	-	1	NA	intron (NM_026140, intron 4 of 8)	intron (NM_026140, intron 4 of 8)	20162	NM_026140	67417	Mm.45171	NM_026140	ENSMUSG00000030871	Ears2	3230401I01Rik|mKIAA1970	glutamyl-tRNA synthetase 2, mitochondrial	protein-coding
mm_19306.1	chr2	90505910	90505913	-	1	NA	intron (NM_008982, intron 1 of 23)	intron (NM_008982, intron 1 of 23)	-26737	NM_001135657	19271	Mm.330393	NM_008982	ENSMUSG00000025314	Ptprj	AI450271|BET|Byp|CD148|DEP-1|PTPbeta2|Ptpb2|RPTPJ|Scc-1|Scc1	protein tyrosine phosphatase, receptor type, J	protein-coding
mm_39326.1	chr5	8606565	8606568	+	1	NA	intron (NM_001347311, intron 1 of 10)	intron (NM_001347311, intron 1 of 10)	16386	NM_001347311	242819	Mm.332192	NM_198620	ENSMUSG00000040570	Rundc3b	Gm440	RUN domain containing 3B	protein-coding
mm_73851.1	chr8	117702057	117702061	+	1	NA	exon (NM_008290, exon 1 of 5)	exon (NM_008290, exon 1 of 5)	113	NM_008290	15486	Mm.276466	NM_008290	ENSMUSG00000031844	Hsd17b2	AI194836|AI194967|AI255511	hydroxysteroid (17-beta) dehydrogenase 2	protein-coding
mm_130848.1	chr15	101938664	101938696	-	1	NA	intron (NM_146063, intron 1 of 8)	B3|SINE|B2	1644	NM_146063	223917	Mm.162744	NM_146063	ENSMUSG00000061397	Krt79	BC031593	keratin 79	protein-coding
mm_25083.1	chr3	100439347	100439387	+	1	NA	Intergenic	Intergenic	12962	NR_040543	73806	Mm.396549	NR_040543	ENSMUSG00000086923	4930406D18Rik	-	RIKEN cDNA 4930406D18 gene	ncRNA
mm_110356.1	chr12	40037369	40037382	-	1	NA	promoter-TSS (NM_007487)	promoter-TSS (NM_007487)	1	NM_007487	11861	Mm.12723	NM_007487	ENSMUSG00000047446	Arl4a	AI467555|Arl4	ADP-ribosylation factor-like 4A	protein-coding
mm_88529.1	chr10	78352523	78352536	+	1	NA	promoter-TSS (NM_053014)	promoter-TSS (NM_053014)	-829	NM_053014	28169	Mm.141230	NM_053014	ENSMUSG00000001211	Agpat3	AW061257|AW493985|D10Jhu12e|lpaat3	1-acylglycerol-3-phosphate O-acyltransferase 3	protein-coding
mm_145352.1	chr18	56505822	56505827	+	1	NA	Intergenic	Intergenic	-32315	NR_106160	102465790		NR_106160	ENSMUSG00000099196	Mir1258	Gm27371|mmu-mir-1258	microRNA 1258	ncRNA
mm_114121.1	chr13	55190418	55190440	+	1	NA	Intergenic	CpG	-19353	NM_008739	18193	Mm.12964	NM_008739	ENSMUSG00000021488	Nsd1	AI528500|KMT3B	nuclear receptor-binding SET-domain protein 1	protein-coding
mm_75274.1	chr8	40887100	40887104	-	1	NA	intron (NM_007514, intron 1 of 11)	intron (NM_007514, intron 1 of 11)	24735	NM_001044740	11988	Mm.4676	NM_007514	ENSMUSG00000031596	Slc7a2	20.5|AI158848|Atrc2|CAT-2|Cat2|Tea	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	protein-coding
mm_27030.1	chr3	26153897	26153899	-	1	NA	promoter-TSS (NM_001163387)	promoter-TSS (NM_001163387)	-591	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_91863.1	chr10	59441839	59441839	-	1	NA	promoter-TSS (NM_010959)	promoter-TSS (NM_010959)	-60	NM_010959	18302	Mm.123013	NM_010959	ENSMUSG00000009654	Oit3	EF-9|LZP	oncoprotein induced transcript 3	protein-coding
mm_143058.1	chr17	57005450	57005469	-	1	NA	exon (NM_133801, exon 6 of 13)	exon (NM_133801, exon 6 of 13)	-5354	NM_008954	19197	Mm.86487	NM_008954	ENSMUSG00000002664	Pspn	PSP	persephin	protein-coding
mm_113797.1	chr13	46418469	46418510	+	1	NA	5' UTR (NM_001081425, exon 1 of 4)	5' UTR (NM_001081425, exon 1 of 4)	189	NM_001081425	666794	Mm.38269	NM_001081425	ENSMUSG00000038132	Rbm24	6330546B05Rik|AI606861	RNA binding motif protein 24	protein-coding
mm_157868.1	chrX	75379796	75379823	-	1	NA	5' UTR (NM_001161373, exon 1 of 25)	5' UTR (NM_001161373, exon 1 of 25)	232	NM_007977	14069	Mm.1805	NM_007977	ENSMUSG00000031196	F8	Cf-8|Cf8|FVIII	coagulation factor VIII	protein-coding
mm_53696.1	chr6	142756711	142756756	+	1	NA	promoter-TSS (NM_009908)	promoter-TSS (NM_009908)	47	NM_009908	12764	Mm.3820	NM_009908	ENSMUSG00000030282	Cmas	AW208911|CMPNeu5Ac|D6Bwg0250e	cytidine monophospho-N-acetylneuraminic acid synthetase	protein-coding
mm_4985.1	chr1	191718071	191718090	+	1	NA	promoter-TSS (NM_001134829)	promoter-TSS (NM_001134829)	56	NM_172266	226856	Mm.277958	NM_172266	ENSMUSG00000026623	Lpgat1	AI649174|AW112037|BC013667	lysophosphatidylglycerol acyltransferase 1	protein-coding
mm_167649.1	chr9	65541917	65541934	+	1	NA	Intergenic	Intergenic	38162	NM_153119	102595	Mm.247303	NM_153119	ENSMUSG00000050721	Plekho2	AI840980|Plekhq1	pleckstrin homology domain containing, family O member 2	protein-coding
mm_44473.1	chr5	23432751	23432779	-	1	NA	non-coding (NR_040469, exon 1 of 1)	non-coding (NR_040469, exon 1 of 1)	1588	NR_040469	269630	Mm.425231	NR_040469	ENSMUSG00000073147	5031425E22Rik	-	RIKEN cDNA 5031425E22 gene	ncRNA
mm_115994.1	chr13	24391656	24391657	-	1	NA	intron (NM_001284519, intron 2 of 17)	B1F1|SINE|Alu	-23466	NM_007717	12763	Mm.8396	NM_007717	ENSMUSG00000016756	Cmah	-	cytidine monophospho-N-acetylneuraminic acid hydroxylase	protein-coding
mm_96264.1	chr11	62648783	62648790	+	1	NA	promoter-TSS (NM_198861)	promoter-TSS (NM_198861)	122	NM_175002	216829	Mm.295306	NM_175002	ENSMUSG00000048497	Mmgt2	AI852046	membrane magnesium transporter 2	protein-coding
mm_13560.1	chr2	112265735	112265760	+	1	NA	promoter-TSS (NM_133649)	promoter-TSS (NM_133649)	-567	NM_133649	107723	Mm.491155	NM_133648	ENSMUSG00000027130	Slc12a6	9530023I19Rik|KCC3|gaxp	solute carrier family 12, member 6	protein-coding
mm_167461.1	chr8	123443342	123443355	+	1	NA	promoter-TSS (NM_001281803)	promoter-TSS (NM_001281803)	89	NM_001281803	23854	Mm.275127	NM_054046	ENSMUSG00000001482	Def8	AI449518|D8Ertd713e|DEF-8	differentially expressed in FDCP 8	protein-coding
mm_111530.1	chr12	100520779	100520853	-	1	NA	promoter-TSS (NM_001033213)	promoter-TSS (NM_001033213)	6	NM_001033213	104718	Mm.295441	NM_001033213	ENSMUSG00000033530	Ttc7b	AA408451|Ttc7l1	tetratricopeptide repeat domain 7B	protein-coding
mm_4703.1	chr1	180851114	180851130	+	1	NA	promoter-TSS (NM_145943)	promoter-TSS (NM_145943)	-29	NM_145943	208768	Mm.272625	NM_145943	ENSMUSG00000038806	Sde2	-	SDE2 telomere maintenance homolog (S. pombe)	protein-coding
mm_73042.1	chr8	94267106	94267151	+	1	NA	intron (NM_172410, intron 4 of 22)	intron (NM_172410, intron 4 of 22)	52527	NM_172410	71805	Mm.458170	NM_172410	ENSMUSG00000032939	Nup93	2410008G02Rik	nucleoporin 93	protein-coding
mm_61524.1	chr7	78914217	78914294	+	1	NA	promoter-TSS (NM_001113527)	promoter-TSS (NM_001113527)	20	NM_001113527	57444	Mm.322843	NM_020583	ENSMUSG00000039236	Isg20	1600023I01Rik|2010107M23Rik|20kDa|DnaQL|HEM45	interferon-stimulated protein	protein-coding
mm_103600.1	chr11	78400819	78400829	-	1	NA	exon (NM_022411, exon 7 of 12)	exon (NM_022411, exon 7 of 12)	6339	NR_003282	790911	Mm.457257	NR_003282	ENSMUSG00000085747	Slc13a2os	Gm11194|OTTMUSG00000000132	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 2, opposite strand	ncRNA
mm_53495.1	chr6	135242163	135242184	+	1	NA	exon (NM_010352, exon 4 of 7)	exon (NM_010352, exon 4 of 7)	5711	NM_001080552	14840	Mm.272306	NM_010352	ENSMUSG00000030206	Gsg1	-	germ cell associated 1	protein-coding
mm_50352.1	chr6	48593890	48593890	+	1	NA	promoter-TSS (NM_001079905)	promoter-TSS (NM_001079905)	7	NM_001079904	58887	Mm.219183	NM_175099	ENSMUSG00000052751	Repin1	AI425994|Ap4|E430037F08Rik|Zfp-464|Zfp464	replication initiator 1	protein-coding
mm_124019.1	chr14	76520810	76520820	-	1	NA	promoter-TSS (NR_045660)	promoter-TSS (NR_045660)	40	NR_045660	75789	Mm.159571	NR_045660	ENSMUSG00000097172	4930444M15Rik	-	RIKEN cDNA 4930444M15 gene	ncRNA
mm_139245.1	chr17	47734179	47734201	+	1	NA	exon (NM_025973, exon 9 of 9)	exon (NM_025973, exon 9 of 9)	-2847	NM_001161722	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_54589.1	chr6	38147422	38147440	-	1	NA	intron (NM_194061, intron 14 of 19)	intron (NM_194061, intron 14 of 19)	-22845	NM_080467	140494	Mm.462308	NM_080467	ENSMUSG00000038600	Atp6v0a4	Atp6n1b|a4	ATPase, H+ transporting, lysosomal V0 subunit A4	protein-coding
mm_26776.1	chr3	9003832	9003856	-	1	NA	intron (NM_001025263, intron 1 of 6)	intron (NM_001025263, intron 1 of 6)	671	NM_009412	21985	Mm.371590	NM_009412	ENSMUSG00000027506	Tpd52	AI043038|mD52	tumor protein D52	protein-coding
mm_85493.1	chr9	106136050	106136068	-	1	NA	Intergenic	Intergenic	-18065	NR_029549	387153		NR_029549	ENSMUSG00000065407	Mir135a-1	Mir135a01|Mirn135|Mirn135a-1|mir-135a-1	microRNA 135a-1	ncRNA
mm_52642.1	chr6	117178713	117178725	+	1	NA	3' UTR (NM_001012477, exon 4 of 4)	3' UTR (NM_001012477, exon 4 of 4)	10184	NM_021704	20315	Mm.303231	NM_013655	ENSMUSG00000061353	Cxcl12	Pbsf|Scyb12|Sdf1|Tlsf|Tpar1	chemokine (C-X-C motif) ligand 12	protein-coding
mm_59771.1	chr7	28834088	28834115	+	1	NA	promoter-TSS (NM_010707)	promoter-TSS (NM_010707)	-69	NM_010707	16857	Mm.210336	NM_010707		Lgals6	galectin-6	lectin, galactose binding, soluble 6	protein-coding
mm_126560.1	chr15	82167020	82167054	+	1	NA	intron (NM_033218, intron 1 of 18)	intron (NM_033218, intron 1 of 18)	19768	NM_033218	20788	Mm.9002	NM_033218	ENSMUSG00000022463	Srebf2	AI608257|SREBP-2|SREBP2|SREBP2gc|bHLHd2|lop13|nuc	sterol regulatory element binding factor 2	protein-coding
mm_54822.1	chr6	42353317	42353328	-	1	NA	intron (NM_001289619, intron 4 of 8)	intron (NM_001289619, intron 4 of 8)	3494	NM_001289619	22793	Mm.282303	NM_011777	ENSMUSG00000029860	Zyx	9530098H06Rik|R75157	zyxin	protein-coding
mm_17248.1	chr2	25627934	25627952	-	1	NA	promoter-TSS (NM_007995)	promoter-TSS (NM_007995)	31	NM_007995	14133	Mm.10510	NM_007995	ENSMUSG00000026938	Fcna	Fcn1	ficolin A	protein-coding
mm_63918.1	chr7	139248478	139248532	+	1	NA	promoter-TSS (NM_001098636)	promoter-TSS (NM_001098636)	23	NM_001098636	101631	Mm.334300	NM_001033206	ENSMUSG00000060260	Pwwp2b	AI594893|D7Ertd517e|D930023J19Rik|Pwwp2	PWWP domain containing 2B	protein-coding
mm_860.1	chr1	52137387	52137402	+	1	NA	exon (NM_001205314, exon 9 of 25)	exon (NM_001205314, exon 9 of 25)	17772	NM_001205313	20846	Mm.277406	NM_009283	ENSMUSG00000026104	Stat1	2010005J02Rik|AA408197	signal transducer and activator of transcription 1	protein-coding
mm_57505.1	chr6	125460631	125460641	-	1	NA	3' UTR (NM_007657, exon 8 of 8)	3' UTR (NM_007657, exon 8 of 8)	34119	NM_007657	12527	Mm.210676	NM_007657	ENSMUSG00000030342	Cd9	Tspan29	CD9 antigen	protein-coding
mm_117626.1	chr13	91896568	91896578	-	1	NA	intron (NM_009027, intron 7 of 14)	RMER20B|LTR|ERVK	-19688	NM_198415	76722	Mm.316438	NM_198415	ENSMUSG00000021622	Ckmt2	2300008A19Rik|ScCKmit	creatine kinase, mitochondrial 2	protein-coding
mm_113230.1	chr13	27242423	27242437	+	1	NA	promoter-TSS (NM_008865)	promoter-TSS (NM_008865)	0	NM_008865	18776	Mm.37203	NM_008865	ENSMUSG00000038891	Prl3b1	Csh2|Ghd8|PL|Pl-2|Pl2|mPL-II|mplII	prolactin family 3, subfamily b, member 1	protein-coding
mm_52687.1	chr6	118066357	118066410	+	1	NA	promoter-TSS (NM_027526)	promoter-TSS (NM_027526)	-2	NM_027526	70727	Mm.87660	NM_027526	ENSMUSG00000030134	Rasgef1a	6330404M18Rik|AI835194	RasGEF domain family, member 1A	protein-coding
mm_20591.1	chr2	131164144	131164152	-	1	NA	intron (NR_037281, intron 2 of 2)	MLT2F|LTR|ERVL	-4067	NM_001311138	67326	Mm.27711	NM_026091	ENSMUSG00000027327	1700037H04Rik	-	RIKEN cDNA 1700037H04 gene	protein-coding
mm_70167.1	chr7	143608450	143608461	-	1	NA	3' UTR (NM_175649, exon 8 of 8)	3' UTR (NM_175649, exon 8 of 8)	-8365	NM_013742	27267	Mm.125659	NM_013742	ENSMUSG00000010755	Cars	CA3	cysteinyl-tRNA synthetase	protein-coding
mm_14916.1	chr2	150786807	150786817	+	1	NA	promoter-TSS (NM_153781)	promoter-TSS (NM_153781)	16	NM_153781	110078	Mm.222584	NM_153781	ENSMUSG00000033059	Pygb	-	brain glycogen phosphorylase	protein-coding
mm_166507.1	chr6	5511138	5511144	+	1	NA	Intergenic	Intergenic	-14863	NM_013743	27273	Mm.235547	NM_013743	ENSMUSG00000019577	Pdk4	AV005916	pyruvate dehydrogenase kinase, isoenzyme 4	protein-coding
mm_62718.1	chr7	110772783	110772793	+	1	NA	5' UTR (NM_009667, exon 1 of 15)	5' UTR (NM_009667, exon 1 of 15)	184	NM_009667	11717	Mm.3238	NM_009667	ENSMUSG00000005686	Ampd3	-	adenosine monophosphate deaminase 3	protein-coding
mm_140398.1	chr17	87636683	87636698	+	1	NA	5' UTR (NM_008532, exon 2 of 10)	5' UTR (NM_008532, exon 2 of 10)	711	NM_008532	17075	Mm.4259	NM_008532	ENSMUSG00000045394	Epcam	CD326|EGP|EGP-2|Egp314|Ep-CAM|EpCAM1|GA733-2|Ly74|TROP1|Tacsd1|Tacstd1|gp40	epithelial cell adhesion molecule	protein-coding
mm_161161.1	chr13	27199052	27199052	+	1	NA	intron (NM_001163218, intron 1 of 4)	RMER17A2|LTR|ERVK	149	NM_001163218	27372	Mm.291456	NM_013766	ENSMUSG00000017922	Prl3c1	Ghd7|PLP-J|Prlpi|Prlpj|decidualin	prolactin family 3, subfamily c, member 1	protein-coding
mm_66401.1	chr7	44359844	44359855	-	1	NA	TTS (NM_027049)	TTS (NM_027049)	15181	NM_027049	69349	Mm.358922	NM_027049	ENSMUSG00000008028	1700008O03Rik	-	RIKEN cDNA 1700008O03 gene	protein-coding
mm_142944.1	chr17	56074599	56074610	-	1	NA	intron (NM_024432, intron 1 of 10)	CpG	385	NM_024432	66530	Mm.28000	NM_024432	ENSMUSG00000019578	Ubxn6	1200008L11Rik|2210415J11Rik|AU040909|Ubxd1|Ubxdc2	UBX domain protein 6	protein-coding
mm_151123.1	chr19	47865778	47865808	+	1	NA	promoter-TSS (NM_026619)	promoter-TSS (NM_026619)	-1	NM_026619	68214	Mm.63791	NM_026619	ENSMUSG00000025069	Gsto2	1700020F09Rik|4930425C18Rik|GSTO 2-2	glutathione S-transferase omega 2	protein-coding
mm_115394.1	chr13	113736005	113736028	+	1	NA	Intergenic	Intergenic	-58492	NM_172595	218639	Mm.79837	NM_172595	ENSMUSG00000042348	Arl15	A430036I03|Arfrp2|C230032K13Rik	ADP-ribosylation factor-like 15	protein-coding
mm_33454.1	chr4	130727641	130727644	+	1	NA	intron (NM_030722, intron 5 of 21)	intron (NM_030722, intron 5 of 21)	-21996	NR_028565	100217460		NR_028565	ENSMUSG00000065196	Snord85	MBII-251|Z50	small nucleolar RNA, C/D box 85	snoRNA
mm_37930.1	chr4	132884517	132884523	-	1	NA	promoter-TSS (NM_133887)	promoter-TSS (NM_133887)	-62	NM_133887	100226	Mm.28237	NM_133887	ENSMUSG00000028879	Stx12	AI850350|AU041521|Stx13	syntaxin 12	protein-coding
mm_60379.1	chr7	44473532	44473549	+	1	NA	Intergenic	Intergenic	3193	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_130497.1	chr15	98807996	98808002	-	1	NA	promoter-TSS (NM_001013741)	promoter-TSS (NM_001013741)	-74	NM_001013741	13199	Mm.390810	NM_001013741	ENSMUSG00000059213	Ddn	Gm748	dendrin	protein-coding
mm_14900.1	chr2	149899682	149899684	+	1	NA	exon (NM_001085521, exon 2 of 4)	exon (NM_001085521, exon 2 of 4)	68900	NM_001085521	433485	Mm.330649	NM_001085521	ENSMUSG00000074736	Syndig1	AW123113|DSPC2|Gm14134|H2C20orf39|OTTMUSG00000015750|Tmem90b	synapse differentiation inducing 1	protein-coding
mm_16544.1	chr2	181693671	181693701	+	1	NA	5' UTR (NM_001291208, exon 1 of 5)	5' UTR (NM_001291208, exon 1 of 5)	124	NM_001291206	56470	Mm.274366	NM_026446	ENSMUSG00000002458	Rgs19	2610042F04Rik|AI324841|AW547781|GAIP	regulator of G-protein signaling 19	protein-coding
mm_117535.1	chr13	83572148	83572154	-	1	NA	intron (NM_001347566, intron 1 of 10)	intron (NM_001347566, intron 1 of 10)	-1456	NM_001347577	17260	Mm.24001	NM_025282	ENSMUSG00000005583	Mef2c	5430401D19Rik|9930028G15Rik|AV011172|Mef2	myocyte enhancer factor 2C	protein-coding
mm_17399.1	chr2	27189471	27189505	-	1	NA	3' UTR (NM_138665, exon 21 of 21)	3' UTR (NM_138665, exon 21 of 21)	23981	NM_138942	13166	Mm.167781	NM_138942	ENSMUSG00000000889	Dbh	-	dopamine beta hydroxylase	protein-coding
mm_16395.1	chr2	179442408	179442421	+	1	NA	promoter-TSS (NM_009867)	promoter-TSS (NM_009867)	-17	NM_001316723	12561	Mm.184711	NM_009867	ENSMUSG00000000305	Cdh4	AW120700|R-CAD|R-Cadh|Rcad	cadherin 4	protein-coding
mm_74624.1	chr8	13105432	13105484	-	1	NA	promoter-TSS (NM_178708)	promoter-TSS (NM_178708)	-115	NM_178708	234069	Mm.103427	NM_178708	ENSMUSG00000038542	Pcid2	A730042J05Rik	PCI domain containing 2	protein-coding
mm_69563.1	chr7	135700484	135700494	-	1	NA	exon (NM_001081117, exon 12 of 14)	exon (NM_001081117, exon 12 of 14)	15890	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_46426.1	chr5	104310114	104310136	-	1	NA	exon (NM_008318, exon 7 of 7)	exon (NM_008318, exon 7 of 7)	10838	NM_008318	15891	Mm.4987	NM_008318	ENSMUSG00000029306	Ibsp	BSP|BSP II|BSPII|Bsp2	integrin binding sialoprotein	protein-coding
mm_47818.1	chr5	134229582	134229599	-	1	NA	promoter-TSS (NM_001286037)	promoter-TSS (NM_001286037)	35	NM_001286037	17969	Mm.425296	NM_010876	ENSMUSG00000015950	Ncf1	NCF-47K|NOXO2|Ncf-1|p47-phox|p47<phox>|p47phox	neutrophil cytosolic factor 1	protein-coding
mm_78825.1	chr9	44107227	44107235	+	1	NA	promoter-TSS (NM_001040631)	promoter-TSS (NM_001040631)	-14	NM_001040631	235312	Mm.227110	NM_145613	ENSMUSG00000079592	C1qtnf5	Ctrp5	C1q and tumor necrosis factor related protein 5	protein-coding
mm_134096.1	chr16	9919799	9919810	-	1	NA	intron (NM_008170, intron 1 of 11)	ID_B1|SINE|B4	72729	NM_008170	14811	Mm.2953	NM_008170	ENSMUSG00000059003	Grin2a	GluN2A|NMDAR2A|NR2A	glutamate receptor, ionotropic, NMDA2A (epsilon 1)	protein-coding
mm_106395.1	chr11	118797731	118797746	-	1	NA	intron (NM_001039168, intron 2 of 14)	intron (NM_001039168, intron 2 of 14)	-36697	NM_001285438	52897	Mm.341103	NM_001024931	ENSMUSG00000025576	Rbfox3	Fox-3|Hrnbp3|NeuN|Neuna60	RNA binding protein, fox-1 homolog (C. elegans) 3	protein-coding
mm_172060.1	chr6	132528121	132528122	-	1	NA	Intergenic	ERVB7_1-LTR_MM|LTR|ERVK	-41721	NM_011174	19131	Mm.425348	NM_011174	ENSMUSG00000059934	Prh1	MP2|Prp	proline rich protein HaeIII subfamily 1	protein-coding
mm_24757.1	chr3	95443459	95443463	+	1	NA	intron (NM_009709, intron 1 of 20)	AT_rich|Low_complexity|Low_complexity	9071	NM_001037737	11863	Mm.250265	NM_009709	ENSMUSG00000015522	Arnt	D3Ertd557e|Drnt|ESTM42|Hif1b|W08714|bHLHe2|mKIAA4051	aryl hydrocarbon receptor nuclear translocator	protein-coding
mm_130781.1	chr15	101532820	101532824	-	1	NA	promoter-TSS (NM_008474)	promoter-TSS (NM_008474)	-2	NM_008474	16680	Mm.25292	NM_008474	ENSMUSG00000044294	Krt84	AV235125|HRb-1|Krt2-16|Krt2-3	keratin 84	protein-coding
mm_7897.1	chr1	133493429	133493441	-	1	NA	Intergenic	Intergenic	-69223	NM_011439	20668	Mm.8575	NM_011439	ENSMUSG00000070643	Sox13	AA407916|AW259412|AW540933|Sox-13	SRY (sex determining region Y)-box 13	protein-coding
mm_134795.1	chr16	24193628	24193650	-	1	NA	Intergenic	Intergenic	-199711	NM_178665	210126	Mm.209385	NM_178665	ENSMUSG00000033306	Lpp	9430020K16Rik|AA959454|AU024130|B130055L10Rik|C79715|D630048H16	LIM domain containing preferred translocation partner in lipoma	protein-coding
mm_8826.1	chr1	162478005	162478022	-	1	NA	promoter-TSS (NM_172646)	promoter-TSS (NM_172646)	17	NM_001038619	103967	Mm.441620	NM_172646	ENSMUSG00000040265	Dnm3	9630020E24Rik|AW061159|B230343F03Rik|C530045C17|mKIAA0820	dynamin 3	protein-coding
mm_1408.1	chr1	67153508	67153512	+	1	NA	intron (NM_001080809, intron 7 of 37)	intron (NM_001080809, intron 7 of 37)	30483	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_129459.1	chr15	78572710	78572750	-	1	NA	promoter-TSS (NM_009008)	promoter-TSS (NM_009008)	53	NM_009008	19354	Mm.1972	NM_009008	ENSMUSG00000033220	Rac2	AI323801|AI452260	RAS-related C3 botulinum substrate 2	protein-coding
mm_70302.1	chr8	4087560	4087570	+	1	NA	Intergenic	CpG	18199	NM_026956	69142	Mm.171061	NM_026956	ENSMUSG00000051906	Cd209f	1810029C22Rik|AI647041|SIGNR8	CD209f antigen	protein-coding
mm_134084.1	chr16	8738900	8738952	-	1	NA	promoter-TSS (NM_001003918)	promoter-TSS (NM_001003918)	-584	NM_001003918	252870	Mm.295330	NM_001003918	ENSMUSG00000022710	Usp7	2210010O09Rik|AA409944|AA617399|AU019296|AW548146|C80752|Hausp	ubiquitin specific peptidase 7	protein-coding
mm_111952.1	chr12	109539766	109539769	-	1	NA	Intergenic	Intergenic	-1229	NR_027652	17263	Mm.289645	NM_144513	ENSMUSG00000021268	Meg3	2900016C05Rik|3110050O07Rik|6330408G06Rik|AI425946|AW108224|D12Bwg1266e|Gtl2|R74756|R75394	maternally expressed 3	ncRNA
mm_126793.1	chr15	86334473	86334486	+	1	NA	intron (NM_145476, intron 8 of 12)	intron (NM_145476, intron 8 of 12)	120020	NM_145476	223754	Mm.28904	NM_145476	ENSMUSG00000051864	Tbc1d22a	BC023106|D15Ertd781e	TBC1 domain family, member 22a	protein-coding
mm_122598.1	chr14	50939078	50939091	-	1	NA	Intergenic	RLTR12B|LTR|ERVK	-5219	NM_013632	18950	Mm.17932	NM_013632	ENSMUSG00000021871	Pnp	AL024301|AU015798|Np|Np-1|Np-2|Pnp1	purine-nucleoside phosphorylase	protein-coding
mm_116064.1	chr13	27564599	27564609	-	1	NA	promoter-TSS (NM_023332)	promoter-TSS (NM_023332)	2	NM_001316721	67310	Mm.46091	NM_023332	ENSMUSG00000006490	Prl8a9	1600019F10Rik|Ghd15|PLP-C2|PLP-Cbeta|Prlpc2	prolactin family8, subfamily a, member 9	protein-coding
mm_54432.1	chr6	34176919	34176932	-	1	NA	5' UTR (NM_021435, exon 1 of 10)	5' UTR (NM_021435, exon 1 of 10)	129	NM_021435	58246	Mm.245527	NM_021435	ENSMUSG00000018999	Slc35b4	4930474D06Rik|AB041549|AW494345	solute carrier family 35, member B4	protein-coding
mm_161642.1	chr16	96192316	96192316	-	1	NA	promoter-TSS (NM_001001492)	promoter-TSS (NM_001001492)	-59	NM_001001492	385668	Mm.24626	NM_001001492	ENSMUSG00000045275	Lca5l	4921526F01Rik|Lcca5l	Leber congenital amaurosis 5-like	protein-coding
mm_117318.1	chr13	67637777	67637801	-	1	NA	promoter-TSS (NM_183146)	promoter-TSS (NM_183146)	-36	NM_183146	212281	Mm.342918	NM_183146	ENSMUSG00000021510	Zfp729a	A530054K11Rik|Rslcan3	zinc finger protein 729a	protein-coding
mm_17425.1	chr2	27456990	27457005	-	1	NA	exon (NM_001113574, exon 7 of 13)	exon (NM_001113574, exon 7 of 13)	-6367	NR_106102	102466836		NR_106102	ENSMUSG00000098812	Mir7578	Gm27789|mmu-mir-7578	microRNA 7578	ncRNA
mm_148529.1	chr19	4517782	4517811	+	1	NA	intron (NM_001162946, intron 2 of 20)	intron (NM_001162946, intron 2 of 20)	7324	NM_001162946	18563	Mm.1845	NM_008797	ENSMUSG00000024892	Pcx	Pc|Pcb	pyruvate carboxylase	protein-coding
mm_28893.1	chr3	97888828	97888845	-	1	NA	promoter-TSS (NM_001289701)	promoter-TSS (NM_001289701)	-129	NM_001289701	83679	Mm.129840	NM_031401	ENSMUSG00000038170	Pde4dip	4732458A06Rik|9430063L05Rik|C87016|D130016K21Rik|D3Bwg1078e|Usmg4|mKIAA0454	phosphodiesterase 4D interacting protein (myomegalin)	protein-coding
mm_21402.1	chr2	157794261	157794267	-	1	NA	intron (NM_025680, intron 4 of 15)	intron (NM_025680, intron 4 of 15)	56863	NM_025680	66642	Mm.45193	NM_025680	ENSMUSG00000027649	Ctnnbl1	5730471K09Rik|NAP|NYD-SP19|P14L	catenin, beta like 1	protein-coding
mm_172313.1	chr7	105953977	105953979	-	1	NA	promoter-TSS (NM_001243039)	promoter-TSS (NM_001243039)	-8	NM_029000	74558	Mm.458429	NM_029000	ENSMUSG00000045868	Gvin1	9130002C22Rik|9830104F22Rik|Iigs1|VLIG|VLIG-1	GTPase, very large interferon inducible 1	protein-coding
mm_13399.1	chr2	103970272	103970307	+	1	NA	promoter-TSS (NM_008505)	promoter-TSS (NM_008505)	2	NM_001142335	16909	Mm.29266	NM_008505	ENSMUSG00000032698	Lmo2	Rbtn-2|Rbtn2|Rhom-2|Ttg2	LIM domain only 2	protein-coding
mm_38654.1	chr4	143299466	143299482	-	1	NA	promoter-TSS (NM_010329)	promoter-TSS (NM_010329)	90	NM_010329	14726	Mm.2976	NM_010329	ENSMUSG00000028583	Pdpn	Gp38|OTS-8|RANDAM-2|T1-alpha|T1a|T1alpha	podoplanin	protein-coding
mm_58962.1	chr7	18950461	18950472	+	1	NA	exon (NM_001029877, exon 3 of 4)	exon (NM_001029877, exon 3 of 4)	24578	NM_001029877	384569	Mm.262724	NM_001029877	ENSMUSG00000030411	Nova2	Gm1424	neuro-oncological ventral antigen 2	protein-coding
mm_156780.1	chrX	161717026	161717039	+	1	NA	promoter-TSS (NM_198409)	promoter-TSS (NM_198409)	-4	NM_001103367	24004	Mm.328503	NM_198409	ENSMUSG00000043518	Rai2	3f8	retinoic acid induced 2	protein-coding
mm_172084.1	chr6	145933002	145933002	-	1	NA	intron (NM_001310837, intron 1 of 2)	LSU-rRNA_Hsa|rRNA|rRNA	1129	NM_001310837	16651	Mm.49689	NM_010656	ENSMUSG00000030255	Sspn	Krag	sarcospan	protein-coding
mm_71400.1	chr8	46207545	46207599	+	1	NA	exon (NM_007450, exon 4 of 4)	exon (NM_007450, exon 4 of 4)	3437	NM_007450	11739	Mm.16228	NM_007450	ENSMUSG00000031633	Slc25a4	AU019225|Ant1	solute carrier family 25 (mitochondrial carrier, adenine nucleotide translocator), member 4	protein-coding
mm_53262.1	chr6	127913852	127913866	+	1	NA	intron (NM_026743, intron 2 of 7)	intron (NM_026743, intron 2 of 7)	26237	NM_026743	68498	Mm.174368	NM_026743	ENSMUSG00000030351	Tspan11	1110014F12Rik|AU067806	tetraspanin 11	protein-coding
mm_93938.1	chr10	127188829	127188837	-	1	NA	intron (NM_001166413, intron 2 of 15)	CpG	990	NM_001166413	52666	Mm.272230	NM_028027	ENSMUSG00000019467	Arhgef25	2410008H17Rik|D10Ertd610e|GEFT	Rho guanine nucleotide exchange factor (GEF) 25	protein-coding
mm_13433.1	chr2	105126280	105126298	+	1	NA	promoter-TSS (NM_144783)	promoter-TSS (NM_144783)	221	NR_015462	329480	Mm.246679	NR_015462	ENSMUSG00000074987	Wt1os	6030498F17|AI314831|Wt1-as	Wilms tumor 1 homolog, opposite strand	ncRNA
mm_89948.1	chr10	111284380	111284401	+	1	NA	exon (NM_001003717, exon 17 of 23)	exon (NM_001003717, exon 17 of 23)	-14289	NM_027914	71769	Mm.45256	NM_027914	ENSMUSG00000035759	Bbs10	1300007O09Rik|AI452285	Bardet-Biedl syndrome 10 (human)	protein-coding
mm_49971.1	chr6	40769031	40769071	+	1	NA	TTS (NM_001171003)	TTS (NM_001171003)	118443	NM_139296	194357	Mm.207087	NM_139296	ENSMUSG00000029885	Moxd2	Dbhl1	monooxygenase, DBH-like 2	protein-coding
mm_45940.1	chr5	90243851	90243861	-	1	NA	exon (NM_030886, exon 29 of 34)	exon (NM_030886, exon 29 of 34)	-19860	NM_001163456	231430	Mm.319697	NM_001033310	ENSMUSG00000035505	Cox18	BC038311	cytochrome c oxidase assembly protein 18	protein-coding
mm_170588.1	chr19	5799926	5799926	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	2746	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_63545.1	chr7	128063727	128063740	+	1	NA	intron (NM_001082960, intron 1 of 29)	MER58D|DNA|hAT-Charlie	1093	NM_008401	16409	Mm.262106	NM_008401	ENSMUSG00000030786	Itgam	CD11b/CD18|CR3|CR3A|Cd11b|F730045J24Rik|Ly-40|MAC1|Mac-1|Mac-1a	integrin alpha M	protein-coding
mm_49833.1	chr6	37870929	37870956	+	1	NA	5' UTR (NM_145076, exon 1 of 19)	5' UTR (NM_145076, exon 1 of 19)	131	NM_145076	21848	Mm.41063	NM_145076	ENSMUSG00000029833	Trim24	A130082H20Rik|AI447469|D430004I05Rik|TIF1|TIF1-alpha|TIF1alpha|Tif1a	tripartite motif-containing 24	protein-coding
mm_39001.1	chr4	151861699	151861761	-	1	NA	promoter-TSS (NM_001195565)	promoter-TSS (NM_001195565)	38	NM_001081557	100072	Mm.318846	NM_001081557	ENSMUSG00000014592	Camta1	1810059M14Rik|2310058O09Rik|AI316882|AW987475|mKIAA0833	calmodulin binding transcription activator 1	protein-coding
mm_101767.1	chr11	43836244	43836311	-	1	NA	5' UTR (NM_001284381, exon 4 of 5)	5' UTR (NM_001284381, exon 4 of 5)	212	NM_007416	11548	Mm.39086	NM_007416	ENSMUSG00000050541	Adra1b	[a]1b	adrenergic receptor, alpha 1b	protein-coding
mm_6022.1	chr1	59120080	59120135	-	1	NA	promoter-TSS (NM_001037812)	promoter-TSS (NM_001037812)	-11	NM_001033449	381259	Mm.261275	NM_001033449	ENSMUSG00000038079	Tmem237	AI853305|Als2cr4|Gm972	transmembrane protein 237	protein-coding
mm_143177.1	chr17	57247332	57247343	-	1	NA	5' UTR (NM_001308074, exon 1 of 17)	5' UTR (NM_001308074, exon 1 of 17)	133	NM_001308074	78308	Mm.28468	NM_030084	ENSMUSG00000005823	Gpr108	1810015L19Rik|AA589464|C79132|Lustr2	G protein-coupled receptor 108	protein-coding
mm_13865.1	chr2	119798479	119798489	+	1	NA	5' UTR (NM_001290800, exon 2 of 20)	5' UTR (NM_001290800, exon 2 of 20)	744	NM_001290800	22174	Mm.2901	NM_019392	ENSMUSG00000027298	Tyro3	AI323366|Brt|Dtk|Etk-2|Rse|Sky|TK19-2|Tif|etk2/tyro3|tk19-1	TYRO3 protein tyrosine kinase 3	protein-coding
mm_34100.1	chr4	138972886	138972920	+	1	NA	promoter-TSS (NM_029857)	promoter-TSS (NM_029857)	-2	NM_029857	77056	Mm.122336	NM_029857	ENSMUSG00000041143	Tmco4	4632413C14Rik|AI430825	transmembrane and coiled-coil domains 4	protein-coding
mm_153279.1	chr19	37207437	37207498	-	1	NA	promoter-TSS (NM_027314)	promoter-TSS (NM_027314)	4	NM_198300	208922	Mm.391176	NM_198300	ENSMUSG00000039652	Cpeb3	4831444O18Rik|CPE-BP3|mKIAA0940	cytoplasmic polyadenylation element binding protein 3	protein-coding
mm_154833.1	chrX	18163057	18163061	+	1	NA	exon (NM_009483, exon 1 of 29)	exon (NM_009483, exon 1 of 29)	484	NM_001310444	22289	Mm.257498	NM_009483	ENSMUSG00000037369	Kdm6a	Utx	lysine (K)-specific demethylase 6A	protein-coding
mm_139923.1	chr17	71019284	71019296	+	1	NA	promoter-TSS (NM_001083934)	promoter-TSS (NM_001083934)	-267	NM_010867	17929	Mm.4103	NM_010867	ENSMUSG00000024049	Myom1	D430047A17Rik	myomesin 1	protein-coding
mm_121837.1	chr14	20546463	20546481	-	1	NA	5' UTR (NM_008914, exon 1 of 14)	5' UTR (NM_008914, exon 1 of 14)	101	NM_001310426	19056	Mm.274432	NM_008914	ENSMUSG00000021816	Ppp3cb	1110063J16Rik|Calnb|CnAbeta|Cnab	protein phosphatase 3, catalytic subunit, beta isoform	protein-coding
mm_71643.1	chr8	57589669	57589672	+	1	NA	intron (NM_001167981, intron 1 of 11)	intron (NM_001167981, intron 1 of 11)	-62083	NR_040698	100502619	Mm.393851	NR_040698		AW046200	-	expressed sequence AW046200	ncRNA
mm_56203.1	chr6	88898665	88898713	-	1	NA	promoter-TSS (NM_008564)	promoter-TSS (NM_008564)	91	NM_008564	17216	Mm.16711	NM_008564	ENSMUSG00000002870	Mcm2	AA959861|AW476101|BM28|CDCL1|Mcmd2|mKIAA0030	minichromosome maintenance complex component 2	protein-coding
mm_117172.1	chr13	62888381	62888393	-	1	NA	promoter-TSS (NM_019395)	promoter-TSS (NM_019395)	-105	NM_019395	14121	Mm.423078	NM_019395	ENSMUSG00000069805	Fbp1	Fbp-2|Fbp2|Fbp3	fructose bisphosphatase 1	protein-coding
mm_111734.1	chr12	103855867	103855904	-	1	NA	exon (NM_009243, exon 3 of 5)	exon (NM_009243, exon 3 of 5)	7734	NM_001252569	20700	Mm.439692	NM_009243	ENSMUSG00000066366	Serpina1a	Aat-2|Aat2|Dom1|PI1|Spi1-1|Spi1-3	serine (or cysteine) peptidase inhibitor, clade A, member 1A	protein-coding
mm_57436.1	chr6	124917757	124917762	-	1	NA	5' UTR (NM_026988, exon 1 of 5)	5' UTR (NM_026988, exon 1 of 5)	187	NM_026988	69202	Mm.142187	NM_026988	ENSMUSG00000030122	Ptms	2610009E16Rik	parathymosin	protein-coding
mm_51857.1	chr6	90465288	90465301	+	1	NA	intron (NM_023184, intron 1 of 2)	intron (NM_023184, intron 1 of 2)	2668	NM_023184	66277	Mm.38343	NM_023184	ENSMUSG00000030087	Klf15	1810013I09Rik|AV048136|AW494632|CKLF|KKLF	Kruppel-like factor 15	protein-coding
mm_125163.1	chr15	31268263	31268266	+	1	NA	intron (NM_146057, intron 2 of 3)	intron (NM_146057, intron 2 of 3)	43879	NM_146057	223453	Mm.222867	NM_146057	ENSMUSG00000039168	Dap	4921531N22Rik|AI789753|AU040360	death-associated protein	protein-coding
mm_54189.1	chr6	24212313	24212345	-	1	NA	Intergenic	MLT1D|LTR|ERVL-MaLR	-44237	NM_019481	55961	Mm.19299	NM_019481	ENSMUSG00000029700	Slc13a1	AI314066|AI987826|NaSi-1|Nas1	solute carrier family 13 (sodium/sulfate symporters), member 1	protein-coding
mm_102633.1	chr11	62539258	62539264	-	1	NA	promoter-TSS (NM_028448)	promoter-TSS (NM_028448)	0	NM_028448	73139	Mm.390409	NM_028448	ENSMUSG00000018509	Cenpv	3110013H01Rik|AA671303|Prr6	centromere protein V	protein-coding
mm_160211.1	chr7	97919731	97919731	+	1	NA	promoter-TSS (NM_177696)	promoter-TSS (NM_177696)	-227	NM_177696	233537	Mm.375772	NM_177696	ENSMUSG00000035582	Gdpd4	4921513O04	glycerophosphodiester phosphodiesterase domain containing 4	protein-coding
mm_106192.1	chr11	116816214	116816247	-	1	NA	exon (NM_026280, exon 2 of 4)	exon (NM_026280, exon 2 of 4)	11816	NM_026280	67622	Mm.64962	NM_026280	ENSMUSG00000020814	Mxra7	1810057P16Rik|E130302J09Rik	matrix-remodelling associated 7	protein-coding
mm_162055.1	chrX	7823833	7823833	+	1	NA	promoter-TSS (NM_008423)	promoter-TSS (NM_008423)	74	NM_008423	16506	Mm.335968	NM_008423	ENSMUSG00000009731	Kcnd1	1110037K09Rik|Kca2-1|Kv4.1|Shal|Shal1|mShal1	potassium voltage-gated channel, Shal-related family, member 1	protein-coding
mm_3550.1	chr1	150414491	150414510	+	1	NA	exon (NM_133780, exon 17 of 52)	exon (NM_133780, exon 17 of 52)	-21445	NM_145511	226499	Mm.222093	NM_145511	ENSMUSG00000006010	BC003331	1810053E15Rik|Odr4|odr-4	cDNA sequence BC003331	protein-coding
mm_87673.1	chr10	58827220	58827223	+	1	NA	intron (NM_172788, intron 1 of 9)	intron (NM_172788, intron 1 of 9)	13862	NM_172788	237353	Mm.333078	NM_172788	ENSMUSG00000037990	Sh3rf3	4831416G18Rik|Igfbp5-ip|Sh3md4|Sh3rf31	SH3 domain containing ring finger 3	protein-coding
mm_34748.1	chr4	152297261	152297273	+	1	NA	promoter-TSS (NM_133788)	promoter-TSS (NM_133788)	53	NM_133788	57295	Mm.277464	NM_133788	ENSMUSG00000039662	Icmt	1700008E11Rik|C80758|Gm13095|HSTE14|OTTMUSG00000010406|PPMT|STE14|pcCMT	isoprenylcysteine carboxyl methyltransferase	protein-coding
mm_9940.1	chr1	190170672	190170744	-	1	NA	promoter-TSS (NM_008937)	promoter-TSS (NM_008937)	-28	NM_008937	19130	Mm.132579	NM_008937	ENSMUSG00000010175	Prox1	A230003G05Rik	prospero homeobox 1	protein-coding
mm_28246.1	chr3	88503188	88503323	-	1	NA	promoter-TSS (NM_001111102)	promoter-TSS (NM_001111102)	97	NM_001111102	16905	Mm.243014	NM_019390	ENSMUSG00000028063	Lmna	Dhe	lamin A	protein-coding
mm_147602.1	chr18	56846349	56846352	-	1	NA	intron (NM_177115, intron 1 of 4)	intron (NM_177115, intron 1 of 4)	79198	NM_177115	320253	Mm.312623	NM_177115	ENSMUSG00000032656	March3	6330411I15Rik|A530081L18Rik|AI843639|MARCH-III	membrane-associated ring finger (C3HC4) 3	protein-coding
mm_160166.1	chr7	44748306	44748306	-	1	NA	promoter-TSS (NM_133945)	promoter-TSS (NM_133945)	43	NM_001289836	243963	Mm.382935	NM_178734	ENSMUSG00000048012	Zfp473	D030014N22Rik|Znf473|zfp-100	zinc finger protein 473	protein-coding
mm_86311.1	chr9	122843995	122844001	-	1	NA	Intergenic	Intergenic	22008	NM_173364	235682	Mm.326477	NM_173364	ENSMUSG00000047036	Zfp445	AW610627|ZNF168|Znf445|mszf29|mszf50	zinc finger protein 445	protein-coding
mm_71351.1	chr8	45658274	45658298	+	1	NA	intron (NM_001310707, intron 1 of 23)	intron (NM_001310707, intron 1 of 23)	-3707	NM_001310708	234214	Mm.211096	NM_172752	ENSMUSG00000031626	Sorbs2	2010203O03Rik|9430041O17Rik|A530071H08|Argbp2|mKIAA0777|nArgBP2	sorbin and SH3 domain containing 2	protein-coding
mm_168795.1	chr12	19490270	19490289	+	1	NA	Intergenic	CpG	975769	NM_001201330	236366	Mm.352227	NM_001033157	ENSMUSG00000073197	5730507C01Rik	-	RIKEN cDNA 5730507C01 gene	protein-coding
mm_32366.1	chr4	105258538	105258559	+	1	NA	Intergenic	Intergenic	101201	NM_080555	67916	Mm.348326	NM_080555	ENSMUSG00000028517	Plpp3	1110003O22Rik|2610002D05Rik|AV025606|D4Bwg0538e|D4Bwg1535e|Lpp3|Ppab2b|Ppap2b	phospholipid phosphatase 3	protein-coding
mm_88419.1	chr10	77196396	77196401	+	1	NA	Intergenic	RMER17C|LTR|ERVK	-29868	NM_009929	12822	Mm.4352	NM_009929	ENSMUSG00000001435	Col18a1	-	collagen, type XVIII, alpha 1	protein-coding
mm_1747.1	chr1	75505590	75505628	+	1	NA	exon (NM_178884, exon 1 of 20)	exon (NM_178884, exon 1 of 20)	843	NM_178884	98733	Mm.236454	NM_178884	ENSMUSG00000026211	Obsl1	AW822216	obscurin-like 1	protein-coding
mm_157558.1	chrX	52053157	52053167	-	1	NA	3' UTR (NM_008150, exon 9 of 9)	3' UTR (NM_008150, exon 9 of 9)	-80390	NM_028851	74279	Mm.159154	NM_028851	ENSMUSG00000031118	1700080O16Rik	-	RIKEN cDNA 1700080O16 gene	protein-coding
mm_148168.1	chr18	78049448	78049457	-	1	NA	intron (NM_001101038, intron 1 of 5)	intron (NM_001101038, intron 1 of 5)	7816	NM_001101038	620235	Mm.35607	NM_001101038	ENSMUSG00000091055	Siglec15	Cd33l3|EG620235|SIGLEC-I	sialic acid binding Ig-like lectin 15	protein-coding
mm_7894.1	chr1	133422698	133422714	-	1	NA	intron (NM_011439, intron 1 of 13)	intron (NM_011439, intron 1 of 13)	1506	NM_011439	20668	Mm.8575	NM_011439	ENSMUSG00000070643	Sox13	AA407916|AW259412|AW540933|Sox-13	SRY (sex determining region Y)-box 13	protein-coding
mm_71627.1	chr8	57436486	57436490	+	1	NA	Intergenic	Intergenic	-19435	NM_009136	20284	Mm.12886	NM_009136	ENSMUSG00000031610	Scrg1	AW124307	scrapie responsive gene 1	protein-coding
mm_157125.1	chrX	9446113	9446124	-	1	NA	intron (NM_007807, intron 9 of 12)	ID4_|SINE|ID	23206	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_44665.1	chr5	29365093	29365100	-	1	NA	intron (NM_020295, intron 1 of 16)	L1MA9|LINE|L1	13294	NM_020295	56873	Mm.41572	NM_020295	ENSMUSG00000010721	Lmbr1	1110048D14Rik|AU017641	limb region 1	protein-coding
mm_125245.1	chr15	34495303	34495347	+	1	NA	promoter-TSS (NM_008287)	promoter-TSS (NM_008287)	14	NM_152894	67724	Mm.248779	NM_026340	ENSMUSG00000022325	Pop1	4932434G09Rik	processing of precursor 1, ribonuclease P/MRP family, (S. cerevisiae)	protein-coding
mm_87990.1	chr10	64608428	64608432	+	1	NA	intron (NM_177612, intron 12 of 17)	intron (NM_177612, intron 12 of 17)	-518175	NM_178678	216028	Mm.431318	NM_178678	ENSMUSG00000042846	Lrrtm3	9630044H04Rik	leucine rich repeat transmembrane neuronal 3	protein-coding
mm_154323.1	chrM	2346	2356	+	1	NA	NA	Intergenic	NA	NA								
mm_21326.1	chr2	157101278	157101290	-	1	NA	intron (NM_018851, intron 15 of 15)	intron (NM_018851, intron 15 of 15)	14229	NM_001177439	383766	Mm.480305	NM_001177439	ENSMUSG00000074628	Tldc2	Gm1332	TBC/LysM associated domain containing 2	protein-coding
mm_27578.1	chr3	58822390	58822393	-	1	NA	Intergenic	Intergenic	62821	NM_153386	229320	Mm.131502	NM_153384	ENSMUSG00000043850	Clrn1	A130002D11Rik|USH3|Ush3a|clarin-1	clarin 1	protein-coding
mm_104205.1	chr11	88026734	88026737	-	1	NA	Intergenic	B1_Mur2|SINE|Alu	-20638	NM_001078167	110809	Mm.391719	NM_173374	ENSMUSG00000018379	Srsf1	1110054N12Rik|5730507C05Rik|6330415C05Rik|AI482334|AW491331|Asf|Sf2|Sfrs1	serine/arginine-rich splicing factor 1	protein-coding
mm_112822.1	chr13	20801613	20801620	+	1	NA	intron (NM_012054, intron 1 of 20)	L1M4a1|LINE|L1	7503	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_27571.1	chr3	58687111	58687114	-	1	NA	intron (NM_009174, intron 1 of 1)	intron (NM_009174, intron 1 of 1)	5276	NM_009174	20439	Mm.2847	NM_009174	ENSMUSG00000036432	Siah2	AA415433|Sinh2	seven in absentia 2	protein-coding
mm_95889.1	chr11	58117727	58117750	+	1	NA	3' UTR (NM_026949, exon 7 of 7)	3' UTR (NM_026949, exon 7 of 7)	13585	NM_026949	69125	Mm.28910	NM_026949	ENSMUSG00000020515	Cnot8	1500015I04Rik|1810022F04Rik|AA536816|AU015770|AU043059	CCR4-NOT transcription complex, subunit 8	protein-coding
mm_4096.1	chr1	167349977	167350065	+	1	NA	promoter-TSS (NM_019993)	promoter-TSS (NM_019993)	30	NM_019993	56752	Mm.292539	NM_019993	ENSMUSG00000026687	Aldh9a1	AA139417|Abaldh|ESTM40|TMABA-DH|Tmabadh	aldehyde dehydrogenase 9, subfamily A1	protein-coding
mm_97374.1	chr11	77687252	77687274	+	1	NA	intron (NM_001024205, intron 1 of 3)	CpG	1124	NM_001024205	68564	Mm.428996	NM_001024205	ENSMUSG00000037857	Nufip2	1110001M19Rik|9530056D24Rik|AI256692|AI461731|PIG1|mKIAA1321	nuclear fragile X mental retardation protein interacting protein 2	protein-coding
mm_157216.1	chrX	12994646	12994654	-	1	NA	Intergenic	Intergenic	-47365	NR_038158	70489	Mm.383563	NR_038158	ENSMUSG00000087424	5730405O15Rik	-	RIKEN cDNA 5730405O15 gene	ncRNA
mm_123804.1	chr14	70520969	70520989	-	1	NA	promoter-TSS (NM_009755)	promoter-TSS (NM_009755)	-719	NR_033241	12153	Mm.27757	NM_009755	ENSMUSG00000022098	Bmp1	Pcp|Tld	bone morphogenetic protein 1	protein-coding
mm_149534.1	chr19	12464938	12464950	+	1	NA	3' UTR (NM_010821, exon 2 of 2)	3' UTR (NM_010821, exon 2 of 2)	4165	NM_010821	17476	Mm.3999	NM_010821	ENSMUSG00000046805	Mpeg1	MPS1|Mpg-1	macrophage expressed gene 1	protein-coding
mm_119516.1	chr14	47421875	47421880	+	1	NA	Intergenic	RMER17C|LTR|ERVK	-3470	NM_144553	218977	Mm.240543	NM_144553	ENSMUSG00000037544	Dlgap5	C77459|C86398|Dap-5|Dlg7|Hurp|mKIAA0008	discs, large (Drosophila) homolog-associated protein 5	protein-coding
mm_1261.1	chr1	63177052	63177054	+	1	NA	promoter-TSS (NM_001160039)	promoter-TSS (NM_001160039)	222	NM_018796	55949	Mm.2718	NM_018796	ENSMUSG00000025967	Eef1b2	2810017J07Rik|Eef1b	eukaryotic translation elongation factor 1 beta 2	protein-coding
mm_80795.1	chr9	96258698	96258711	+	1	NA	promoter-TSS (NM_001184710)	promoter-TSS (NM_001184710)	-1	NM_001184709	211586	Mm.17977	NM_178667	ENSMUSG00000032411	Tfdp2	1110029I05Rik|A330080J22Rik|DP-3|DP3	transcription factor Dp 2	protein-coding
mm_68115.1	chr7	102099933	102099943	-	1	NA	non-coding (NR_111935, exon 1 of 6)	non-coding (NR_111935, exon 1 of 6)	291	NR_111935	11875	Mm.2816	NM_007491	ENSMUSG00000070424	Art5	ARTC5|Yac-2	ADP-ribosyltransferase 5	protein-coding
mm_4675.1	chr1	180421033	180421042	+	1	NA	intron (NM_001081175, intron 6 of 7)	intron (NM_001081175, intron 6 of 7)	62467	NM_001081227	381310	Mm.44791	NM_001081227	ENSMUSG00000053963	Stum	6330403A02Rik|ENSMUSG00000056615|Gm10001|R75555	mechanosensory transduction mediator	protein-coding
mm_145682.1	chr18	61628348	61628367	+	1	NA	Intergenic	Intergenic	-11296	NR_045420	545261	Mm.426593	NR_045420	ENSMUSG00000098098	Bvht	Braveheart|Gm20748	braveheart long non-coding RNA	ncRNA
mm_163209.1	chr11	99610247	99610253	-	1	NA	promoter-TSS (NM_001099346)	promoter-TSS (NM_001099346)	-61	NM_001099346	100041488	Mm.465212	NM_001099346	ENSMUSG00000058725	Gm11937	-	predicted gene 11937	protein-coding
mm_64282.1	chr7	141819130	141819138	+	1	NA	TTS (NM_010844)	TTS (NM_010844)	-19938	NM_028801	74180	Mm.200752	NM_028801	ENSMUSG00000066108	Muc5b	2300002I04Rik|A130042M24|AV085033|MUC5|MUC9|mucin 5b	mucin 5, subtype B, tracheobronchial	protein-coding
mm_128781.1	chr15	66801606	66801620	-	1	NA	intron (NM_001029841, intron 1 of 7)	intron (NM_001029841, intron 1 of 7)	30216	NM_001029841	20491	Mm.7601	NM_009192	ENSMUSG00000022372	Sla	Slap|Slap-1	src-like adaptor	protein-coding
mm_119185.1	chr14	32318171	32318181	+	1	NA	Intergenic	Intergenic	-3843	NM_001081130	239017	Mm.318302	NM_001081130	ENSMUSG00000021913	Ogdhl	-	oxoglutarate dehydrogenase-like	protein-coding
mm_57885.1	chr6	131353535	131353555	-	1	NA	Intergenic	Intergenic	34905	NM_139117	56449	Mm.458000	NM_011733	ENSMUSG00000030189	Ybx3	Csda|Dpba|MSY3|MSY4|Yb2|dbpA|oxyR	Y box protein 3	protein-coding
mm_30585.1	chr4	5644134	5644211	+	1	NA	promoter-TSS (NM_173426)	promoter-TSS (NM_173426)	-7	NM_173426	242297	Mm.331470	NM_173426	ENSMUSG00000049119	Fam110b	1700012H17Rik|5031405P22|AW049855	family with sequence similarity 110, member B	protein-coding
mm_143748.1	chr17	81561954	81561959	-	1	NA	intron (NR_104580, intron 2 of 8)	intron (NR_104580, intron 2 of 8)	176431	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_82266.1	chr9	7177001	7177063	-	1	NA	promoter-TSS (NM_029851)	promoter-TSS (NM_029851)	14	NM_029851	110350	Mm.237596	NM_029851	ENSMUSG00000047193	Dync2h1	4432416O06Rik|AI448217|D030010H02Rik|D330044F14Rik|DHC1b|DHC2|Dnchc2|b2b414Clo|mKIAA1997	dynein cytoplasmic 2 heavy chain 1	protein-coding
mm_158465.1	chrX	140822556	140822575	-	1	NA	Intergenic	Intergenic	-9132	NM_031381	83555	Mm.193025	NM_031381	ENSMUSG00000042386	Tex13b	4933403J23Rik|Tex13	testis expressed 13B	protein-coding
mm_98769.1	chr11	96658763	96658773	+	1	NA	intron (NM_001033186, intron 4 of 12)	intron (NM_001033186, intron 4 of 12)	118787	NM_028965	74479	Mm.270781	NM_028965	ENSMUSG00000020876	Snx11	4933439F10Rik|A930041K09Rik|AI117694	sorting nexin 11	protein-coding
mm_31683.1	chr4	62298077	62298087	+	1	NA	3' UTR (NM_025286, exon 4 of 4)	3' UTR (NM_025286, exon 4 of 4)	6535	NM_001290518	20530	Mm.292539	NM_025286	ENSMUSG00000066152	Slc31a2	AI604396|CTR2	solute carrier family 31, member 2	protein-coding
mm_73933.1	chr8	119992501	119992526	+	1	NA	promoter-TSS (NM_001310635)	promoter-TSS (NM_001310635)	75	NM_001310635	78892	Mm.264680	NM_030209	ENSMUSG00000031825	Crispld2	1810049K24Rik|Lcrisp2|Lgl1|coffeecrisp	cysteine-rich secretory protein LCCL domain containing 2	protein-coding
mm_121206.1	chr14	103053407	103053422	+	1	NA	intron (NM_008392, intron 4 of 4)	Lx8|LINE|L1	6402	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_168471.1	chr11	48752618	48752631	-	1	NA	Intergenic	Intergenic	-47736	NM_008143	14694	Mm.5305	NM_008143	ENSMUSG00000020372	Rack1	AL033335|GB-like|Gnb2-rs1|Gnb2l1|p205	receptor for activated C kinase 1	protein-coding
mm_29717.1	chr3	124425990	124425996	-	1	NA	promoter-TSS (NM_027939)	promoter-TSS (NM_027939)	35	NM_027939	71824	Mm.331353	NM_027939	ENSMUSG00000027973	1700006A11Rik	-	RIKEN cDNA 1700006A11 gene	protein-coding
mm_165931.1	chr4	65408016	65408024	+	1	NA	intron (NM_019514, intron 19 of 21)	Lx5|LINE|L1	-196966	NM_053084	69807	Mm.22786	NM_053084	ENSMUSG00000051675	Trim32	1810045E12Rik|3f3|BBS11|Zfp117	tripartite motif-containing 32	protein-coding
mm_119925.1	chr14	54968752	54968775	+	1	NA	promoter-TSS (NR_033497)	promoter-TSS (NR_033497)	-24	NR_033497	791403	Mm.319176	NR_033497	ENSMUSG00000097652	Mhrt	D830015G02Rik|ENSMUSG00000053118|Myheart	myosin heavy chain associated RNA transcript	ncRNA
mm_46723.1	chr5	110762459	110762461	-	1	NA	intron (NM_173066, intron 1 of 50)	intron (NM_173066, intron 1 of 50)	8257	NM_029337	75560	Mm.270487	NM_029337	ENSMUSG00000029505	Ep400	1700020J09Rik|AU023439|mDomino|mKIAA1498|p400	E1A binding protein p400	protein-coding
mm_87810.1	chr10	60301806	60301828	+	1	NA	TTS (NM_001252635)	TTS (NM_001252635)	17356	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_35280.1	chr4	20778697	20778707	-	1	NA	promoter-TSS (NM_172987)	promoter-TSS (NM_172987)	-34	NM_172987	269513	Mm.317473	NM_172987	ENSMUSG00000055761	Nkain3	C530048M05|E130310K16Rik	Na+/K+ transporting ATPase interacting 3	protein-coding
mm_74316.1	chr8	126736826	126736863	+	1	NA	Intergenic	Intergenic	-143408	NM_001164598	270110	Mm.334918	NM_001164598	ENSMUSG00000051495	Irf2bp2	E130305N23Rik|IRF-2BP2	interferon regulatory factor 2 binding protein 2	protein-coding
mm_135527.1	chr16	49255780	49255786	-	1	NA	Intergenic	Intergenic	198297	NM_001166210	667772	Mm.301387	NM_001166210	ENSMUSG00000092009	Myh15	EG667772	myosin, heavy chain 15	protein-coding
mm_164614.1	chr17	31161479	31161484	-	1	NA	TTS (NM_009362)	TTS (NM_009362)	3572	NM_009362	21784	Mm.2854	NM_009362	ENSMUSG00000024032	Tff1	Bcei|PS2	trefoil factor 1	protein-coding
mm_73121.1	chr8	94779823	94779834	+	1	NA	exon (NM_009142, exon 3 of 3)	exon (NM_009142, exon 3 of 3)	7648	NM_009142	20312	Mm.103711	NM_009142	ENSMUSG00000031778	Cx3cl1	AB030188|ABCD-3|AI848747|CX3C|Cxc3|D8Bwg0439e|Scyd1	chemokine (C-X3-C motif) ligand 1	protein-coding
mm_53677.1	chr6	141881107	141881129	+	1	NA	Intergenic	Intergenic	-24947	NM_030687	28250	Mm.255586	NM_030687	ENSMUSG00000030237	Slco1a4	AI785519|Oatp1a4|Oatp2|Slc21a5	solute carrier organic anion transporter family, member 1a4	protein-coding
mm_72473.1	chr8	83576040	83576050	+	1	NA	intron (NM_134118, intron 1 of 12)	intron (NM_134118, intron 1 of 12)	9287	NM_025843	66916	Mm.29683	NM_025843	ENSMUSG00000033938	Ndufb7	1110002H15Rik	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 7	protein-coding
mm_58368.1	chr6	148896175	148896188	-	1	NA	promoter-TSS (NM_181541)	promoter-TSS (NM_181541)	56	NM_001301351	232560	Mm.150568	NM_181541	ENSMUSG00000030309	Caprin2	C1qdc1|Eeg1|rng140	caprin family member 2	protein-coding
mm_19837.1	chr2	112454901	112454933	-	1	NA	promoter-TSS (NM_133749)	promoter-TSS (NM_133749)	-108	NM_133749	73024	Mm.268027	NM_133749	ENSMUSG00000055943	Emc7	2900064A13Rik|AI451465|ORF3|c11orf3	ER membrane protein complex subunit 7	protein-coding
mm_36991.1	chr4	110234381	110234387	-	1	NA	intron (NM_001347178, intron 2 of 6)	intron (NM_001347178, intron 2 of 6)	52450	NM_010488	15572	Mm.3970	NM_010488	ENSMUSG00000028546	Elavl4	Elav|Hud|PNEM	ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4 (Hu antigen D)	protein-coding
mm_91688.1	chr10	43980281	43980313	-	1	NA	intron (NM_172393, intron 6 of 19)	intron (NM_172393, intron 6 of 19)	24549	NM_172393	11630	Mm.292082	NM_172393	ENSMUSG00000019866	Aim1	AI462491|AI463325	absent in melanoma 1	protein-coding
mm_109755.1	chr12	117763512	117763526	+	1	NA	Intergenic	Intergenic	-80342	NM_146040	217946	Mm.281149	NM_146040	ENSMUSG00000021175	Cdca7l	BC006933|JPO2	cell division cycle associated 7 like	protein-coding
mm_13605.1	chr2	113285732	113285749	+	1	NA	promoter-TSS (NM_029232)	promoter-TSS (NM_029232)	8	NM_029232	75275	Mm.159484	NM_029232	ENSMUSG00000041255	Tmco5b	4930563P21Rik	transmembrane and coiled-coil domains 5B	protein-coding
mm_111441.1	chr12	96047145	96047161	-	1	NA	promoter-TSS (NR_103800)	promoter-TSS (NR_103800)	69	NR_103800	69423	Mm.46121	NM_027076		1700019M22Rik	-	NFX-like protein	pseudo
mm_130335.1	chr15	97731160	97731168	-	1	NA	intron (NM_001168693, intron 1 of 9)	intron (NM_001168693, intron 1 of 9)	241	NM_001168693	19011	Mm.1001	NM_008902	ENSMUSG00000022468	Endou	Pp11r|Tcl-30	endonuclease, polyU-specific	protein-coding
mm_91868.1	chr10	59469464	59469475	-	1	NA	intron (NM_001033259, intron 2 of 7)	L1MEf|LINE|L1	-27690	NM_010959	18302	Mm.123013	NM_010959	ENSMUSG00000009654	Oit3	EF-9|LZP	oncoprotein induced transcript 3	protein-coding
mm_155538.1	chrX	74304173	74304191	+	1	NA	promoter-TSS (NM_010273)	promoter-TSS (NM_010273)	-830	NM_010273	14567	Mm.205830	NM_010273	ENSMUSG00000015291	Gdi1	GDIA|GDIalpha	guanosine diphosphate (GDP) dissociation inhibitor 1	protein-coding
mm_128908.1	chr15	73487269	73487278	-	1	NA	Intergenic	Intergenic	-25287	NM_001081066	105841	Mm.322557	NM_001081066	ENSMUSG00000036661	Dennd3	AI447457|E030003N15Rik	DENN/MADD domain containing 3	protein-coding
mm_79315.1	chr9	52069697	52069709	+	1	NA	exon (NM_009041, exon 9 of 14)	exon (NM_009041, exon 9 of 14)	-20998	NR_023357	629557	Mm.422775	NR_023357		Gm6981	EG629557	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_171668.1	chr4	46584462	46584472	+	1	NA	intron (NM_001164804, intron 1 of 11)	RLTR3_Mm|LTR|ERVK	17462	NM_001164804	107684	Mm.416311	NM_178893	ENSMUSG00000028337	Coro2a	9030208C03Rik|AI563590|IR10	coronin, actin binding protein 2A	protein-coding
mm_70568.1	chr8	13159142	13159168	+	1	NA	promoter-TSS (NM_010684)	promoter-TSS (NM_010684)	-6	NM_001317353	16783	Mm.16716	NM_010684	ENSMUSG00000031447	Lamp1	CD107a|LGP-120|LGP-A|Lamp-1|P2B	lysosomal-associated membrane protein 1	protein-coding
mm_24530.1	chr3	93277640	93277652	+	1	NA	Intergenic	Intergenic	-42103	NM_133698	68723	Mm.208047	NM_133698	ENSMUSG00000041991	Hrnr	1110033K19Rik|A530063N20Rik|S100a18	hornerin	protein-coding
mm_151999.1	chr19	5902665	5902694	-	1	NA	exon (NM_001291078, exon 8 of 12)	exon (NM_001291078, exon 8 of 12)	-8572	NM_198634	332359	Mm.329642	NM_198634	ENSMUSG00000044390	Tigd3	-	tigger transposable element derived 3	protein-coding
mm_54082.1	chr6	15728192	15728205	-	1	NA	intron (NM_175088, intron 2 of 4)	intron (NM_175088, intron 2 of 4)	7537	NM_175088	16543	Mm.1314	NM_175088	ENSMUSG00000041390	Mdfic	Kdt1|Mdfid	MyoD family inhibitor domain containing	protein-coding
mm_126487.1	chr15	81616813	81616826	+	1	NA	exon (NM_177821, exon 8 of 31)	exon (NM_177821, exon 8 of 31)	30605	NM_177821	328572	Mm.258397	NM_177821	ENSMUSG00000055024	Ep300	A430090G16|A730011L11|KAT3B|p300|p300 HAT	E1A binding protein p300	protein-coding
mm_82265.1	chr9	7176971	7176997	-	1	NA	promoter-TSS (NM_029851)	promoter-TSS (NM_029851)	62	NM_029851	110350	Mm.237596	NM_029851	ENSMUSG00000047193	Dync2h1	4432416O06Rik|AI448217|D030010H02Rik|D330044F14Rik|DHC1b|DHC2|Dnchc2|b2b414Clo|mKIAA1997	dynein cytoplasmic 2 heavy chain 1	protein-coding
mm_49670.1	chr6	31314112	31314139	+	1	NA	intron (NR_040261, intron 3 of 4)	intron (NR_040261, intron 3 of 4)	84648	NR_040300	100503869	Mm.370532	NR_040300	ENSMUSG00000086212	Mkln1os	Gm13845|OTTMUSG00000014733	muskelin 1, intracellular mediator containing kelch motifs, opposite strand	ncRNA
mm_160309.1	chr7	141063644	141063644	+	1	NA	intron (NM_177897, intron 1 of 19)	intron (NM_177897, intron 1 of 19)	2370	NM_177897	330671	Mm.133741	NM_177897	ENSMUSG00000055629	B4galnt4	BC038881|Gm1095|beta4GalNAcT4	beta-1,4-N-acetyl-galactosaminyl transferase 4	protein-coding
mm_135689.1	chr16	52427803	52427841	-	1	NA	intron (NM_009655, intron 1 of 15)	intron (NM_009655, intron 1 of 15)	25259	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_125320.1	chr15	38299509	38299514	+	1	NA	intron (NM_001289471, intron 1 of 4)	CpG	1200	NM_013692	21847	Mm.4292	NM_013692	ENSMUSG00000037465	Klf10	AI115143|EGR[a]|Egral|Gdnfif|TIEG-1|Tieg|Tieg1|mGIF	Kruppel-like factor 10	protein-coding
mm_54561.1	chr6	37407701	37407704	-	1	NA	intron (NM_178661, intron 1 of 11)	intron (NM_178661, intron 1 of 11)	34446	NM_178661	208647	Mm.169929	NM_178661	ENSMUSG00000038648	Creb3l2	BBF2H7|C530025K05Rik|SCIRR69	cAMP responsive element binding protein 3-like 2	protein-coding
mm_144777.1	chr18	35829829	35829839	+	1	NA	promoter-TSS (NM_133687)	promoter-TSS (NM_133687)	16	NM_133687	67393	Mm.94560	NM_133687	ENSMUSG00000046668	Cxxc5	4930415K17Rik	CXXC finger 5	protein-coding
mm_126581.1	chr15	82292787	82292812	+	1	NA	3' UTR (NM_011889, exon 10 of 10)	3' UTR (NM_011889, exon 10 of 10)	-6185	NM_029066	74716	Mm.159315	NM_029066	ENSMUSG00000022455	Wbp2nl	4930521I23Rik|PAWP	WBP2 N-terminal like	protein-coding
mm_88233.1	chr10	71181356	71181398	+	1	NA	intron (NR_038040, intron 1 of 7)	intron (NR_038040, intron 1 of 7)	663	NR_038040	319572	Mm.211663	NR_038040		C730027H18Rik	-	RIKEN cDNA C730027H18 gene	ncRNA
mm_152284.1	chr19	8921844	8921851	-	1	NA	exon (NM_024256, exon 2 of 5)	exon (NM_024256, exon 2 of 5)	1454	NM_024256	72727	Mm.259	NM_024256	ENSMUSG00000071649	B3gat3	2810405M13Rik	beta-1,3-glucuronyltransferase 3 (glucuronosyltransferase I)	protein-coding
mm_160543.1	chr9	44287539	44287539	-	1	NA	intron (NM_138955, intron 1 of 14)	intron (NM_138955, intron 1 of 14)	705	NM_138955	192663	Mm.101876	NM_138955	ENSMUSG00000032131	Abcg4	6430517O04Rik	ATP-binding cassette, sub-family G (WHITE), member 4	protein-coding
mm_143052.1	chr17	56982105	56982118	-	1	NA	promoter-TSS (NM_175731)	promoter-TSS (NM_175731)	15	NM_175731	171168	Mm.218784	NM_175731	ENSMUSG00000045019	Acer1	2310024P18Rik|AI662009|Alkcdase1|Asah3|Cer1	alkaline ceramidase 1	protein-coding
mm_47341.1	chr5	122502284	122502294	-	1	NA	promoter-TSS (NM_009722)	promoter-TSS (NM_009722)	-64	NR_027838	11938	Mm.227583	NM_009722	ENSMUSG00000029467	Atp2a2	9530097L16Rik|D5Wsu150e|SERCA2|SERCA2B|Serca2a|mKIAA4195	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	protein-coding
mm_27129.1	chr3	32365145	32365155	-	1	NA	promoter-TSS (NR_027966)	promoter-TSS (NR_027966)	-339	NR_027966	67576	Mm.435324	NR_027966		4930429B21Rik	-	RIKEN cDNA 4930429B21 gene	ncRNA
mm_38335.1	chr4	137598563	137598569	-	1	NA	intron (NM_001347227, intron 1 of 26)	RLTR41|LTR|ERV1	4377	NM_130879	170707	Mm.218478	NM_130879	ENSMUSG00000043411	Usp48	2810449C13Rik|AI115503|BC021769|D330022K21Rik|Usp31	ubiquitin specific peptidase 48	protein-coding
mm_127111.1	chr15	97908409	97908436	+	1	NA	promoter-TSS (NM_009504)	promoter-TSS (NM_009504)	-126	NM_009504	22337	Mm.245084	NM_009504	ENSMUSG00000022479	Vdr	Nr1i1	vitamin D receptor	protein-coding
mm_34956.1	chr4	155993231	155993296	+	1	NA	promoter-TSS (NM_080445)	promoter-TSS (NM_080445)	-74	NM_001302468	20318	Mm.293517	NM_011341	ENSMUSG00000029076	Sdf4	Cab45	stromal cell derived factor 4	protein-coding
mm_26333.1	chr3	142546433	142546443	+	1	NA	exon (NM_001083312, exon 11 of 11)	exon (NM_001083312, exon 11 of 11)	-13614	NM_018734	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_141423.1	chr17	29437013	29437070	-	1	NA	Intergenic	Intergenic	-54004	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_77768.1	chr9	3005126	3005137	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	33612	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_45324.1	chr5	65486090	65486096	-	1	NA	intron (NM_133697, intron 1 of 4)	intron (NM_133697, intron 1 of 4)	6742	NM_133697	68552	Mm.10709	NM_133697	ENSMUSG00000037822	Smim14	1110003E01Rik|1700127H04Rik|5430439C17Rik|MAd4	small integral membrane protein 14	protein-coding
mm_17317.1	chr2	26445176	26445226	-	1	NA	promoter-TSS (NM_153125)	promoter-TSS (NM_153125)	15	NM_153125	227648	Mm.206371	NM_153125	ENSMUSG00000026924	Sec16a	AU024582|C230052J16Rik	SEC16 homolog A, endoplasmic reticulum export factor	protein-coding
mm_104887.1	chr11	99559506	99559512	-	1	NA	Intergenic	Intergenic	-2656	NM_025720	66708	Mm.46389	NM_025720	ENSMUSG00000069721	Krtap3-2	2310020D06Rik|4733401L16Rik|KAP3.2|KRTAP3.2	keratin associated protein 3-2	protein-coding
mm_138484.1	chr17	35195866	35195897	+	1	NA	TTS (NR_105939)	TTS (NR_105939)	909	NR_105939	102465588		NR_105939	ENSMUSG00000098291	Mir6973a	Gm27967|mmu-mir-6973a	microRNA 6973a	ncRNA
mm_27023.1	chr3	26059433	26059437	-	1	NA	intron (NM_138666, intron 3 of 7)	intron (NM_138666, intron 3 of 7)	93872	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_105699.1	chr11	108241029	108241048	-	1	NA	intron (NM_011101, intron 2 of 16)	intron (NM_011101, intron 2 of 16)	102850	NM_011101	18750	Mm.222178	NM_011101	ENSMUSG00000050965	Prkca	AI875142|Pkca	protein kinase C, alpha	protein-coding
mm_77659.1	chr8	124651745	124651781	-	1	NA	intron (NM_175149, intron 1 of 3)	intron (NM_175149, intron 1 of 3)	11606	NM_175149	69551	Mm.261920	NM_175149	ENSMUSG00000031983	2310022B05Rik	-	RIKEN cDNA 2310022B05 gene	protein-coding
mm_87045.1	chr10	28791668	28791678	+	1	NA	intron (NM_001305663, intron 5 of 5)	L1_Mur1|LINE|L1	123313	NM_178666	210757	Mm.123021	NM_178666	ENSMUSG00000049109	Themis	E430004N04Rik|Gasp|Spot|Tsepa|thylex	thymocyte selection associated	protein-coding
mm_115527.1	chr13	5864353	5864362	-	1	NA	intron (NM_011803, intron 1 of 3)	intron (NM_011803, intron 1 of 3)	2868	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_165091.1	chr19	53185741	53185750	+	1	NA	intron (NM_013758, intron 1 of 15)	intron (NM_013758, intron 1 of 15)	41748	NM_013758	27360	Mm.426080	NM_013758	ENSMUSG00000025026	Add3	AI463285|R75380	adducin 3 (gamma)	protein-coding
mm_82358.1	chr9	14499346	14499370	-	1	NA	intron (NM_173433, intron 1 of 1)	intron (NM_173433, intron 1 of 1)	1124	NM_173433	244694	Mm.240457	NM_173433	ENSMUSG00000053914	Kdm4d	4932416A15|Jmjd2d	lysine (K)-specific demethylase 4D	protein-coding
mm_165060.1	chr19	42147467	42147471	+	1	NA	promoter-TSS (NM_183195)	promoter-TSS (NM_183195)	80	NM_183195	277010	Mm.206250	NM_183195	ENSMUSG00000044345	Marveld1	AI504298|Mrvldc1	MARVEL (membrane-associating) domain containing 1	protein-coding
mm_53627.1	chr6	140491117	140491127	+	1	NA	intron (NM_144920, intron 3 of 30)	intron (NM_144920, intron 3 of 30)	67023	NM_144920	109135	Mm.247670	NM_144920	ENSMUSG00000030231	Plekha5	2810431N21Rik|AI428202|AK129423|AMH-Cre|Ayu21-9|Gt(pU21)9Imeg|Pepp2|Tg(AMH-cre)1Flor	pleckstrin homology domain containing, family A member 5	protein-coding
mm_150973.1	chr19	46501665	46501675	+	1	NA	promoter-TSS (NM_053100)	promoter-TSS (NM_053100)	22	NM_053100	93679	Mm.392177	NM_053100	ENSMUSG00000025034	Trim8	AA408830|BB006755|GERP|Rnf27	tripartite motif-containing 8	protein-coding
mm_147927.1	chr18	65939099	65939103	-	1	NA	promoter-TSS (NM_013833)	promoter-TSS (NM_013833)	-12	NM_013833	19434	Mm.431047	NM_013833	ENSMUSG00000024518	Rax	7530406A22Rik|E130303K03Rik|Rx|ey-1|ey1	retina and anterior neural fold homeobox	protein-coding
mm_58688.1	chr7	12835951	12835954	+	1	NA	intron (NM_022981, intron 2 of 7)	intron (NM_022981, intron 2 of 7)	1142	NM_022981	65020	Mm.292297	NM_022981	ENSMUSG00000058638	Zfp110	2900024E01Rik|N28112|NRIF|Nrif1	zinc finger protein 110	protein-coding
mm_125202.1	chr15	32985578	32985609	+	1	NA	intron (NM_008304, intron 1 of 4)	RMER17A2|LTR|ERVK	64870	NM_008304	15529	Mm.234266	NM_008304	ENSMUSG00000022261	Sdc2	4833414L08Rik|AA960457|Hspg1|Synd2|syndecan-2	syndecan 2	protein-coding
mm_167318.1	chr8	66386421	66386432	+	1	NA	exon (NM_001166375, exon 1 of 4)	exon (NM_001166375, exon 1 of 4)	125	NM_001166375	72925	Mm.380457	NM_175188	ENSMUSG00000036469	March1	2900024D24Rik|BB085186	membrane-associated ring finger (C3HC4) 1	protein-coding
mm_24025.1	chr3	87535651	87535663	+	1	NA	exon (NM_012051, exon 5 of 5)	exon (NM_012051, exon 5 of 5)	10079	NM_012051	27049	Mm.219460	NM_012051	ENSMUSG00000003382	Etv3	AI414410|METS|Pe1	ets variant 3	protein-coding
mm_100485.1	chr11	120253045	120253063	+	1	NA	intron (NM_001347621, intron 2 of 27)	intron (NM_001347621, intron 2 of 27)	20107	NM_198423	268515	Mm.309498	NM_198423	ENSMUSG00000039741	Bahcc1	B930044J06|BC060615	BAH domain and coiled-coil containing 1	protein-coding
mm_95484.1	chr11	51289969	51290011	+	1	NA	promoter-TSS (NM_153393)	promoter-TSS (NM_153393)	70	NM_153393	237759	Mm.154093	NM_153393	ENSMUSG00000063564	Col23a1	2810458L13Rik|AI429655	collagen, type XXIII, alpha 1	protein-coding
mm_5450.1	chr1	36244246	36244320	-	1	NA	promoter-TSS (NM_198899)	promoter-TSS (NM_198899)	19	NM_198899	320011	Mm.261022	NM_198899	ENSMUSG00000037470	Uggt1	0910001L17Rik|A930007H10Rik|AA589501|AI414429|AI448372|C820010P03Rik|GT|UGT1|Ugcgl1	UDP-glucose glycoprotein glucosyltransferase 1	protein-coding
mm_71270.1	chr8	40919269	40919279	+	1	NA	3' UTR (NM_001044740, exon 12 of 12)	3' UTR (NM_001044740, exon 12 of 12)	-6959	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_138220.1	chr17	34315903	34315925	+	1	NA	3' UTR (NM_010382, exon 6 of 6)	3' UTR (NM_010382, exon 6 of 6)	-9761	NM_001033978	381091	Mm.139204	NM_001033978	ENSMUSG00000067341	H2-Eb2	A130038H09Rik|H-2Eb2|Ia-5|Ia5|Iebeta2	histocompatibility 2, class II antigen E beta2	protein-coding
mm_33970.1	chr4	137611951	137611951	+	1	NA	intron (NM_001347227, intron 8 of 26)	intron (NM_001347227, intron 8 of 26)	17762	NM_130879	170707	Mm.218478	NM_130879	ENSMUSG00000043411	Usp48	2810449C13Rik|AI115503|BC021769|D330022K21Rik|Usp31	ubiquitin specific peptidase 48	protein-coding
mm_55390.1	chr6	59426280	59426345	-	1	NA	promoter-TSS (NM_183183)	promoter-TSS (NM_183183)	-22	NM_183183	243385	Mm.138080	NM_183183	ENSMUSG00000045441	Gprin3	C030038J10Rik|C730021L23	GPRIN family member 3	protein-coding
mm_114593.1	chr13	75763800	75763818	+	1	NA	exon (NM_138953, exon 8 of 12)	exon (NM_138953, exon 8 of 12)	56325	NM_138953	192657	Mm.21288	NM_138953	ENSMUSG00000001542	Ell2	-	elongation factor RNA polymerase II 2	protein-coding
mm_93325.1	chr10	99241926	99241934	-	1	NA	Intergenic	Intergenic	-21301	NM_026268	67603	Mm.1791	NM_026268	ENSMUSG00000019960	Dusp6	1300019I03Rik|MKP-3|MKP3|PYST1	dual specificity phosphatase 6	protein-coding
mm_150266.1	chr19	34217447	34217451	+	1	NA	intron (NM_029682, intron 1 of 10)	intron (NM_029682, intron 1 of 10)	25179	NM_029682	76630	Mm.130952	NM_029682	ENSMUSG00000024776	Stambpl1	1700095N21Rik|8230401J17Rik|ALMalpha|AMSH-FP	STAM binding protein like 1	protein-coding
mm_8731.1	chr1	160133699	160133708	-	1	NA	intron (NM_177839, intron 6 of 21)	intron (NM_177839, intron 6 of 21)	19872	NM_177839	329278	Mm.90140	NM_177839	ENSMUSG00000026725	Tnn	Tnw|tenascin-W	tenascin N	protein-coding
mm_62268.1	chr7	99535440	99535498	+	1	NA	promoter-TSS (NM_178220)	promoter-TSS (NM_178220)	-17	NM_178220	109689	Mm.260193	NM_177231	ENSMUSG00000018909	Arrb1	1200006I17Rik|AW208571|G430100A01Rik	arrestin, beta 1	protein-coding
mm_118321.1	chr13	113600740	113600750	-	1	NA	intron (NM_130796, intron 1 of 1)	B4A|SINE|B4	17819	NM_130796	170625	Mm.33721	NM_130796	ENSMUSG00000042364	Snx18	Snag1	sorting nexin 18	protein-coding
mm_13980.1	chr2	121457438	121457491	+	1	NA	promoter-TSS (NM_001025371)	promoter-TSS (NM_001025371)	376	NM_026318	67693	Mm.330525	NM_026318	ENSMUSG00000027245	Hypk	2310003F16Rik|HSPC136	huntingtin interacting protein K	protein-coding
mm_22061.1	chr2	168601753	168601773	-	1	NA	promoter-TSS (NM_001291173)	promoter-TSS (NM_001291173)	-106	NM_001291173	18019	Mm.116802	NM_010899	ENSMUSG00000027544	Nfatc2	AI607462|NF-ATc2|NF-ATp|NFAT1|NFAT1-D|Nfatp	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 2	protein-coding
mm_97554.1	chr11	78929836	78929845	+	1	NA	exon (NM_010927, exon 4 of 27)	exon (NM_010927, exon 4 of 27)	4549	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_77799.1	chr9	3031885	3031894	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	6854	NR_039546	100628572		NR_039546	ENSMUSG00000106183	Mir101c	mir-101c|mmu-mir-101c	microRNA 101c	ncRNA
mm_46002.1	chr5	90694566	90694569	-	1	NA	Intergenic	Intergenic	-54040	NM_001310656	73246	Mm.30172	NM_028478	ENSMUSG00000029370	Rassf6	1600016B17Rik	Ras association (RalGDS/AF-6) domain family member 6	protein-coding
mm_60804.1	chr7	45628968	45628980	+	1	NA	exon (NM_028544, exon 3 of 12)	exon (NM_028544, exon 3 of 12)	1437	NM_028544	69903	Mm.181396	NM_028544	ENSMUSG00000044562	Rasip1	1110025D03Rik|2610025P08Rik|AI853551|Rain	Ras interacting protein 1	protein-coding
mm_118887.1	chr14	26579536	26579612	+	1	NA	promoter-TSS (NM_145969)	promoter-TSS (NM_145969)	24	NM_145969	211922	Mm.260512	NM_145969	ENSMUSG00000040818	Dennd6a	Fam116a	DENN/MADD domain containing 6A	protein-coding
mm_162513.1	chr1	155096728	155096748	-	1	NA	3' UTR (NM_010500, exon 1 of 1)	3' UTR (NM_010500, exon 1 of 1)	2898	NM_010500	15939	Mm.12246	NM_010500	ENSMUSG00000056708	Ier5	-	immediate early response 5	protein-coding
mm_118020.1	chr13	100833184	100833200	-	1	NA	5' UTR (NM_022885, exon 1 of 16)	5' UTR (NM_022885, exon 1 of 16)	235	NM_022885	69048	Mm.402215	NM_022885	ENSMUSG00000021629	Slc30a5	1810010K08Rik|AF233321|ZNT5|ZTL1|ZnT-5|Zntl1	solute carrier family 30 (zinc transporter), member 5	protein-coding
mm_53926.1	chr6	4717136	4717166	-	1	NA	intron (NM_011360, intron 3 of 10)	intron (NM_011360, intron 3 of 10)	30053	NM_001130188	20392	Mm.8739	NM_011360	ENSMUSG00000004631	Sgce	e-SG	sarcoglycan, epsilon	protein-coding
mm_51182.1	chr6	70824696	70824744	+	1	NA	Intergenic	Intergenic	-19795	NM_010121	13666	Mm.247167	NM_010121	ENSMUSG00000031668	Eif2ak3	Pek|Perk	eukaryotic translation initiation factor 2 alpha kinase 3	protein-coding
mm_51110.1	chr6	67555580	67555595	+	1	NA	Intergenic	Intergenic	10112	NR_003100	75070	Mm.463364	NR_003100		4930515G16Rik	-	myc induced nuclear antigen pseudogene	pseudo
mm_89619.1	chr10	96181665	96181682	+	1	NA	Intergenic	L2c|LINE|L2	-44534	NR_110448	74881	Mm.410819	NR_110448		4930459C07Rik	-	RIKEN cDNA 4930459C07 gene	ncRNA
mm_68241.1	chr7	105399966	105399982	-	1	NA	promoter-TSS (NM_199009)	promoter-TSS (NM_199009)	80	NM_001242364	74349	Mm.30254	NM_199009	ENSMUSG00000044465	Fam160a2	4632419K20Rik|6530415H11Rik|FHIP	family with sequence similarity 160, member A2	protein-coding
mm_17134.1	chr2	24974992	24975071	-	1	NA	promoter-TSS (NM_001031808)	promoter-TSS (NM_001031808)	67	NM_001031808	107733	Mm.23010	NM_001031808	ENSMUSG00000036850	Mrpl41	MRP-L27|Rpml27	mitochondrial ribosomal protein L41	protein-coding
mm_113619.1	chr13	41605868	41605902	+	1	NA	promoter-TSS (NM_001163572)	promoter-TSS (NM_001163572)	-331	NM_001163572	621976	Mm.259830	NM_001163572	ENSMUSG00000087370	Tmem170b	EG621976	transmembrane protein 170B	protein-coding
mm_134419.1	chr16	17838174	17838218	-	1	NA	promoter-TSS (NM_030558)	promoter-TSS (NM_030558)	-10	NM_030558	80733	Mm.390864	NM_030558	ENSMUSG00000090236	Car15	AI315043|Ca15|Cals2	carbonic anhydrase 15	protein-coding
mm_128033.1	chr15	25363810	25363831	-	1	NA	3' UTR (NM_027395, exon 2 of 2)	3' UTR (NM_027395, exon 2 of 2)	49944	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	brain abundant, membrane attached signal protein 1	protein-coding
mm_169939.1	chr16	62716949	62716970	+	1	NA	Intergenic	Intergenic	69757	NM_178925	106338	Mm.26321	NM_178925	ENSMUSG00000050312	Nsun3	6720484A09Rik|AU022521	NOL1/NOP2/Sun domain family member 3	protein-coding
mm_47993.1	chr5	135962276	135962328	-	1	NA	intron (NM_001160366, intron 9 of 10)	intron (NM_001160366, intron 9 of 10)	12174	NM_001160366	109267	Mm.332750	NM_001160366	ENSMUSG00000029699	Ssc4d	C330016E03Rik|S4D-SRCRB|SRCRB-S4D|Srcrb4d	scavenger receptor cysteine rich family, 4 domains	protein-coding
mm_5854.1	chr1	53342218	53342242	-	1	NA	Intergenic	Intergenic	10522	NM_001290984	70396	Mm.285783	NM_133728	ENSMUSG00000026095	Asnsd1	2210409M21Rik	asparagine synthetase domain containing 1	protein-coding
mm_106215.1	chr11	116852429	116852456	-	1	NA	intron (NM_011358, intron 1 of 2)	CpG	652	NM_011358	20382	Mm.21841	NM_011358	ENSMUSG00000034120	Srsf2	D11Wsu175e|MRF-1|Pr264|SC35|Sfrs10|Sfrs2	serine/arginine-rich splicing factor 2	protein-coding
mm_129428.1	chr15	78481677	78481714	-	1	NA	exon (NM_008368, exon 10 of 10)	exon (NM_008368, exon 10 of 10)	-13061	NM_027902	71753	Mm.34056	NM_027902	ENSMUSG00000016942	Tmprss6	1300008A22Rik	transmembrane serine protease 6	protein-coding
mm_159254.1	chr2	152604217	152604217	+	1	NA	promoter-TSS (NM_001037247)	promoter-TSS (NM_001037247)	-110	NM_001037247	266620	Mm.330669	NM_001037247	ENSMUSG00000044863	Defb36	BD-36|Defb123|mBD-36	defensin beta 36	protein-coding
mm_77365.1	chr8	119810089	119810136	-	1	NA	3' UTR (NM_028071, exon 4 of 4)	3' UTR (NM_028071, exon 4 of 4)	30467	NM_028071	72042	Mm.393405	NM_028071	ENSMUSG00000031827	Cotl1	1810074P22Rik|2010004C08Rik|Clp	coactosin-like 1 (Dictyostelium)	protein-coding
mm_84994.1	chr9	86695772	86695789	-	1	NA	5' UTR (NM_008615, exon 1 of 14)	5' UTR (NM_008615, exon 1 of 14)	134	NM_008615	17436	Mm.148155	NM_008615	ENSMUSG00000032418	Me1	D9Ertd267e|Mdh-1|Mod-1|Mod1	malic enzyme 1, NADP(+)-dependent, cytosolic	protein-coding
mm_53344.1	chr6	129284704	129284711	+	1	NA	Intergenic	Intergenic	-9338	NM_001033122	12515	Mm.74745	NM_001033122	ENSMUSG00000030156	Cd69	5830438K24Rik|AI452015|AIM|VEA	CD69 antigen	protein-coding
mm_3324.1	chr1	137920888	137920900	+	1	NA	Intergenic	Intergenic	-45561	NR_029795	735252		NR_029795	ENSMUSG00000065565	Mir181a-1	Mirn181a-1|Mirn213|miR-213|mir-181a-1|mmu-mir-213	microRNA 181a-1	ncRNA
mm_71554.1	chr8	48347539	48347540	+	1	NA	intron (NM_011857, intron 6 of 28)	intron (NM_011857, intron 6 of 28)	237526	NM_001161515	320685	Mm.121549	NM_178788	ENSMUSG00000031562	Dctd	6030466N05Rik	dCMP deaminase	protein-coding
mm_124081.1	chr14	78650538	78650548	-	1	NA	intron (NM_001081336, intron 3 of 28)	intron (NM_001081336, intron 3 of 28)	-6092	NR_104044	380921	Mm.89591	NM_001081336	ENSMUSG00000034731	Dgkh	5930402B05Rik|D130015C16|DGK	diacylglycerol kinase, eta	protein-coding
mm_30649.1	chr4	8840366	8840391	+	1	NA	intron (NM_001277149, intron 17 of 37)	intron (NM_001277149, intron 17 of 37)	149972	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_11288.1	chr2	30066800	30066821	+	1	NA	5' UTR (NM_001204875, exon 1 of 8)	5' UTR (NM_001204875, exon 1 of 8)	336	NM_001204875	56086	Mm.326055	NM_023871	ENSMUSG00000054766	Set	2610030F17Rik|5730420M11Rik|AA407739|I-2PP2A|StF-IT-1|TAF-I	SET nuclear oncogene	protein-coding
mm_31703.1	chr4	62559826	62559838	+	1	NA	promoter-TSS (NM_019492)	promoter-TSS (NM_019492)	-15	NM_019492	50780	Mm.286753	NM_019492	ENSMUSG00000059810	Rgs3	4930506N09Rik|C2PA-RGS3|C2pa|PDZ-RGS3|RGS3S	regulator of G-protein signaling 3	protein-coding
mm_147194.1	chr18	37644186	37644209	-	1	NA	promoter-TSS (NM_175770)	promoter-TSS (NM_175770)	7	NM_175770	24074	Mm.236009	NM_175770	ENSMUSG00000051316	Taf7	55kDa|AI607308|BB007175|TAFII55|Taf2f	TATA-box binding protein associated factor 7	protein-coding
mm_53693.1	chr6	142751592	142751603	+	1	NA	Intergenic	RLTR41A2|LTR|ERV1	-5089	NM_009908	12764	Mm.3820	NM_009908	ENSMUSG00000030282	Cmas	AW208911|CMPNeu5Ac|D6Bwg0250e	cytidine monophospho-N-acetylneuraminic acid synthetase	protein-coding
mm_88480.1	chr10	77616420	77616469	+	1	NA	non-coding (NR_125904, exon 5 of 5)	non-coding (NR_125904, exon 5 of 5)	2735	NR_125903	20610	Mm.24433	NM_019929	ENSMUSG00000020265	Sumo3	2810014B19Rik|D10Ertd345e|SMT3A|SUMO-3|Smt3h1	small ubiquitin-like modifier 3	protein-coding
mm_20225.1	chr2	125782775	125782802	-	1	NA	promoter-TSS (NM_177608)	promoter-TSS (NM_177608)	82	NM_177608	70354	Mm.138091	NM_133725	ENSMUSG00000035093	Secisbp2l	3110001I20Rik|AI504340|C630011I23	SECIS binding protein 2-like	protein-coding
mm_114611.1	chr13	75845097	75845100	+	1	NA	intron (NM_053108, intron 1 of 2)	intron (NM_053108, intron 1 of 2)	5212	NM_053108	93692	Mm.25844	NM_053108	ENSMUSG00000021591	Glrx	C86710|D13Wsu156e|Glrx1|Grx1|TTase	glutaredoxin	protein-coding
mm_2660.1	chr1	125677288	125677302	+	1	NA	5' UTR (NM_027677, exon 1 of 2)	5' UTR (NM_027677, exon 1 of 2)	299	NM_027677	71111	Mm.32727	NM_027677	ENSMUSG00000026343	Gpr39	4933415E13Rik	G protein-coupled receptor 39	protein-coding
mm_130239.1	chr15	96576438	96576453	-	1	NA	3' UTR (NM_001166456, exon 16 of 16)	3' UTR (NM_001166456, exon 16 of 16)	65517	NM_134086	105727	Mm.103568	NM_134086	ENSMUSG00000023169	Slc38a1	AA408026|AA409865|AL022800|AU015942|NAT2	solute carrier family 38, member 1	protein-coding
mm_157690.1	chrX	60403832	60403834	-	1	NA	5' UTR (NM_001001798, exon 1 of 29)	5' UTR (NM_001001798, exon 1 of 29)	148	NM_001001798	320940	Mm.490394	NM_001001798	ENSMUSG00000062949	Atp11c	A330005H02Rik|AI315324|Ig	ATPase, class VI, type 11C	protein-coding
mm_81800.1	chr9	116145442	116145468	+	1	NA	intron (NM_029575, intron 1 of 6)	intron (NM_029575, intron 1 of 6)	29908	NM_029575	21813	Mm.172346	NM_009371	ENSMUSG00000032440	Tgfbr2	1110020H15Rik|AU042018|DNIIR|RIIDN|TBR-II|TbetaR-II|TbetaRII	transforming growth factor, beta receptor II	protein-coding
mm_78749.1	chr9	42142120	42142134	+	1	NA	Intergenic	Intergenic	-17838	NM_011436	20660	Mm.121920	NM_011436	ENSMUSG00000049313	Sorl1	2900010L19Rik|AI596264|AW261561|LR11|SorLA|gp250|mSorLA	sortilin-related receptor, LDLR class A repeats-containing	protein-coding
mm_101656.1	chr11	36677682	36677690	-	1	NA	intron (NM_011856, intron 2 of 28)	intron (NM_011856, intron 2 of 28)	266555	NM_001290702	23964	Mm.439889	NM_011856	ENSMUSG00000049336	Tenm2	Odz2|Odz3|Ten-2|Ten-m2	teneurin transmembrane protein 2	protein-coding
mm_116867.1	chr13	55018098	55018108	-	1	NA	intron (NM_001206392, intron 1 of 17)	intron (NM_001206392, intron 1 of 17)	2716	NM_001206390	212032	Mm.267479	NM_001033245	ENSMUSG00000025877	Hk3	HK III|HK-III	hexokinase 3	protein-coding
mm_110455.1	chr12	51691708	51691712	-	1	NA	5' UTR (NM_001172098, exon 1 of 16)	5' UTR (NM_001172098, exon 1 of 16)	204	NM_001172098	94186	Mm.65979	NM_052973	ENSMUSG00000020954	Strn3	Gs2na|SG2NA	striatin, calmodulin binding protein 3	protein-coding
mm_109312.1	chr12	109560960	109560988	+	1	NA	non-coding (NR_003633, exon 5 of 5)	non-coding (NR_003633, exon 5 of 5)	-2718	NR_030427	791079		NR_030427	ENSMUSG00000076451	Mir770	Mirn770|mir-770|mmu-mir-770	microRNA 770	ncRNA
mm_136344.1	chr16	92603299	92603311	-	1	NA	3' UTR (NM_001111021, exon 8 of 8)	3' UTR (NM_001111021, exon 8 of 8)	94024	NM_001111023	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_77651.1	chr8	124564181	124564193	-	1	NA	exon (NM_007428, exon 2 of 5)	exon (NM_007428, exon 2 of 5)	5520	NM_007428	11606	Mm.301626	NM_007428	ENSMUSG00000031980	Agt	AI265500|AngI|AngII|Aogen|Serpina8	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	protein-coding
mm_139023.1	chr17	46124288	46124313	+	1	NA	intron (NM_026768, intron 3 of 5)	intron (NM_026768, intron 3 of 5)	13296	NM_026768	68565	Mm.287443	NM_026768	ENSMUSG00000023967	Mrps18a	1110004O20Rik|C79712	mitochondrial ribosomal protein S18A	protein-coding
mm_27029.1	chr3	26153642	26153657	-	1	NA	promoter-TSS (NM_001163387)	promoter-TSS (NM_001163387)	-342	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_156709.1	chrX	159627433	159627441	+	1	NA	5' UTR (NM_001135727, exon 1 of 18)	5' UTR (NM_001135727, exon 1 of 18)	165	NM_001135727	58194	Mm.286495	NM_021389	ENSMUSG00000040990	Sh3kbp1	1200007H22Rik|1700125L08Rik|5830464D22Rik|AI447724|Cin85|IN85|Ruk|Seta	SH3-domain kinase binding protein 1	protein-coding
mm_154085.1	chr19	56746733	56746742	-	1	NA	Intergenic	Intergenic	24365	NM_007419	11554	Mm.46797	NM_007419	ENSMUSG00000035283	Adrb1	Adrb-1|beta-AR	adrenergic receptor, beta 1	protein-coding
mm_66906.1	chr7	59984793	59984796	-	1	NA	intron (NM_033174, intron 8 of 9)	B1_Mur4|SINE|Alu	-5938	NR_028529	100217429		NR_028529		Snord64	MBII-13	small nucleolar RNA, C/D box 64	snoRNA
mm_125720.1	chr15	73090393	73090441	+	1	NA	promoter-TSS (NM_053068)	promoter-TSS (NM_053068)	5	NM_053068	93696	Mm.23095	NM_053068	ENSMUSG00000068391	Chrac1	2410152E03Rik|2810406L04Rik|YCL1	chromatin accessibility complex 1	protein-coding
mm_134931.1	chr16	31081355	31081359	-	1	NA	promoter-TSS (NM_198626)	promoter-TSS (NM_198626)	75	NM_198626	268880	Mm.286693	NM_198626	ENSMUSG00000047434	Xxylt1	AI480653	xyloside xylosyltransferase 1	protein-coding
mm_20000.1	chr2	118834158	118834196	-	1	NA	3' UTR (NM_026412, exon 9 of 9)	3' UTR (NM_026412, exon 9 of 9)	20174	NM_026412	51944	Mm.252695	NM_026412	ENSMUSG00000027331	Knstrn	1700025D04Rik|C15orf23|D2Ertd750e|SKAP|Traf4af1	kinetochore-localized astrin/SPAG5 binding	protein-coding
mm_130936.1	chr15	103215119	103215136	-	1	NA	intron (NM_001110216, intron 1 of 5)	intron (NM_001110216, intron 1 of 5)	225	NM_007626	12419	Mm.262059	NM_007626	ENSMUSG00000009575	Cbx5	2610029O15Rik|C75991|HP1|Hp1a|Hp1alpha	chromobox 5	protein-coding
mm_49134.1	chr6	8948916	8948929	+	1	NA	Intergenic	CpG	-1097	NM_008751	18231	Mm.46954	NM_008751	ENSMUSG00000046178	Nxph1	C130005L03Rik	neurexophilin 1	protein-coding
mm_134657.1	chr16	22069258	22069260	-	1	NA	intron (NM_183029, intron 11 of 15)	intron (NM_183029, intron 11 of 15)	59775	NR_027488	75826	Mm.297431	NM_029457	ENSMUSG00000022855	Senp2	2310007L05Rik|4930538C18Rik|AI646780|AW554757|Smt3ip2|SuPr-1|mKIAA1331	SUMO/sentrin specific peptidase 2	protein-coding
mm_154219.1	chr19	59350705	59350722	-	1	NA	Intergenic	Intergenic	-4933	NM_001033222	107368	Mm.27250	NM_001033222	ENSMUSG00000074746	Pdzd8	A630041P07Rik|AV329468|AW228944|Pdzk8	PDZ domain containing 8	protein-coding
mm_138734.1	chr17	36963823	36963837	+	1	NA	intron (NM_029602, intron 1 of 2)	intron (NM_029602, intron 1 of 2)	5238	NM_029602	76416	Mm.26684	NM_029602	ENSMUSG00000036214	Znrd1as	1700022C21Rik|AI746295|Znrd1-as	zinc ribbon domain containing 1, antisense	protein-coding
mm_91332.1	chr10	25298278	25298313	-	1	NA	intron (NM_018747, intron 1 of 7)	intron (NM_018747, intron 1 of 7)	868	NM_018747	432442	Mm.485937	NM_018747	ENSMUSG00000039166	Akap7	6430401D08|AI662165|AKAP15|Akap18|BB170514	A kinase (PRKA) anchor protein 7	protein-coding
mm_151697.1	chr19	4439370	4439386	-	1	NA	promoter-TSS (NM_001329989)	promoter-TSS (NM_001329989)	55	NR_045990	319314	Mm.393810	NR_045989	ENSMUSG00000087132	A930001C03Rik	-	RIKEN cDNA A930001C03 gene	ncRNA
mm_152197.1	chr19	7483242	7483279	-	1	NA	promoter-TSS (NM_053076)	promoter-TSS (NM_053076)	31	NM_001271486	20168	Mm.246990	NM_053076	ENSMUSG00000024758	Rtn3	RTN3-A1	reticulon 3	protein-coding
mm_124593.1	chr15	3274872	3274885	+	1	NA	intron (NM_001042613, intron 2 of 4)	intron (NM_001042613, intron 2 of 4)	3901	NM_009155	20363	Mm.392203	NM_009155	ENSMUSG00000064373	Selenop	AU018766|D15Ucla1|Se-P|Sepp1|selp	selenoprotein P	protein-coding
mm_24957.1	chr3	96670299	96670346	+	1	NA	5' UTR (NM_001081139, exon 1 of 13)	5' UTR (NM_001081139, exon 1 of 13)	191	NM_001081139	213121	Mm.39732	NM_001081139	ENSMUSG00000038354	Ankrd35	4732436F15Rik	ankyrin repeat domain 35	protein-coding
mm_122105.1	chr14	30920742	30920751	-	1	NA	exon (NM_008407, exon 6 of 21)	exon (NM_008407, exon 6 of 21)	2841	NM_008407	16426	Mm.4517	NM_008407	ENSMUSG00000006522	Itih3	AW108094|ITI-HC3|Intin3|Itih-3	inter-alpha trypsin inhibitor, heavy chain 3	protein-coding
mm_89713.1	chr10	98781250	98781254	+	1	NA	Intergenic	Intergenic	-133900	NM_026482	67972	Mm.166944	NM_026482	ENSMUSG00000019943	Atp2b1	2810442I22Rik|E130111D10Rik|Pmca1	ATPase, Ca++ transporting, plasma membrane 1	protein-coding
mm_159422.1	chr3	108186306	108186306	+	1	NA	promoter-TSS (NM_001287093)	promoter-TSS (NM_001287093)	17	NM_001287093	229715	Mm.275752	NM_146137	ENSMUSG00000050947	Amigo1	Amigo|ali2	adhesion molecule with Ig like domain 1	protein-coding
mm_105741.1	chr11	109362535	109362604	-	1	NA	promoter-TSS (NM_010303)	promoter-TSS (NM_010303)	-225	NM_010303	14674	Mm.193925	NM_010303	ENSMUSG00000020611	Gna13	AU024132|AU043124|Galpha13	guanine nucleotide binding protein, alpha 13	protein-coding
mm_33266.1	chr4	127262314	127262318	+	1	NA	Intergenic	Intergenic	18532	NM_030252	80284	Mm.139607	NM_030252	ENSMUSG00000042380	Smim12	BC003266	small integral membrane protein 12	protein-coding
mm_137687.1	chr17	28858566	28858573	+	1	NA	5' UTR (NM_001034885, exon 1 of 10)	5' UTR (NM_001034885, exon 1 of 10)	158	NM_001034885	433091	Mm.328925	NM_001034885	ENSMUSG00000043286	Pnpla1	-	patatin-like phospholipase domain containing 1	protein-coding
mm_87283.1	chr10	42184373	42184373	+	1	NA	Intergenic	Intergenic	92369	NM_019740	56484	Mm.338613	NM_019740	ENSMUSG00000048756	Foxo3	1110048B16Rik|2010203A17Rik|C76856|FKHRL1|Fkhr2|Foxo3a	forkhead box O3	protein-coding
mm_105849.1	chr11	113710013	113710023	-	1	NA	promoter-TSS (NM_001164532)	promoter-TSS (NM_001164532)	-1	NM_029794	52670	Mm.229207	NM_026682	ENSMUSG00000018727	Cpsf4l	0610010C04Rik|1500000C01Rik|D11Ertd636e	cleavage and polyadenylation specific factor 4-like	protein-coding
mm_102019.1	chr11	51637965	51637984	-	1	NA	Intergenic	Intergenic	-2078	NM_025346	66089	Mm.288183	NM_025346	ENSMUSG00000001054	Rmnd5b	0610039K22Rik|Gid2	required for meiotic nuclear division 5 homolog B	protein-coding
mm_154636.1	chrX	7763952	7763965	+	1	NA	promoter-TSS (NM_001271491)	promoter-TSS (NM_001271491)	15	NM_001105197	209446	Mm.249142	NM_172472	ENSMUSG00000000134	Tfe3	F830016E06Rik|Tcfe3|Tfe-3|bHLHe33	transcription factor E3	protein-coding
mm_79420.1	chr9	55326938	55326958	+	1	NA	promoter-TSS (NM_172923)	promoter-TSS (NM_172923)	-1	NM_172923	244886	Mm.24361	NM_172923	ENSMUSG00000032313	Tmem266	9630029F15|AI118078|HVRP1	transmembrane protein 266	protein-coding
mm_6555.1	chr1	75139397	75139400	-	1	NA	exon (NM_026977, exon 6 of 9)	exon (NM_026977, exon 6 of 9)	2970	NM_026977	69171	Mm.28193	NM_026977	ENSMUSG00000033159	Cnppd1	1810031K17Rik|AU043960	cyclin Pas1/PHO80 domain containing 1	protein-coding
mm_102470.1	chr11	60021219	60021231	-	1	NA	intron (NM_001290011, intron 2 of 6)	MT2A|LTR|ERVL	15780	NM_008819	18618	Mm.2731	NM_008819	ENSMUSG00000000301	Pemt	PEAMT|PEMT2|PLMT|Pempt|Pempt2	phosphatidylethanolamine N-methyltransferase	protein-coding
mm_11115.1	chr2	28193296	28193304	+	1	NA	5' UTR (NM_001038613, exon 1 of 6)	5' UTR (NM_001038613, exon 1 of 6)	207	NM_001038614	56177	Mm.43278	NM_019498	ENSMUSG00000026833	Olfm1	AMY|AW742568|Noe1|OlfA|Pancortin|Pancortin3	olfactomedin 1	protein-coding
mm_71506.1	chr8	46834139	46834155	+	1	NA	intron (NM_008391, intron 6 of 8)	intron (NM_008391, intron 6 of 8)	94402	NM_008391	16363	Mm.1149	NM_008391	ENSMUSG00000031627	Irf2	9830146E22Rik|AI646973|Irf-2	interferon regulatory factor 2	protein-coding
mm_26056.1	chr3	135825789	135825800	+	1	NA	promoter-TSS (NM_001135150)	promoter-TSS (NM_001135150)	4	NM_001135150	67547	Mm.30239	NM_026228	ENSMUSG00000053897	Slc39a8	4933419D20Rik|AA986696|BIGM103|ZIP-8|Zip8	solute carrier family 39 (metal ion transporter), member 8	protein-coding
mm_74770.1	chr8	21232271	21232278	-	1	NA	Intergenic	Intergenic	-17488	NM_001177487	100041787	Mm.437206	NM_001177487	ENSMUSG00000074441	Gm15292	ENSMUSG00000074441|OTTMUSG00000019784	predicted gene 15292	protein-coding
mm_94743.1	chr11	21095815	21095822	+	1	NA	intron (NM_023324, intron 1 of 6)	L1MC5|LINE|L1	4494	NM_023324	67245	Mm.28957	NM_023324	ENSMUSG00000020134	Peli1	2810468L03Rik|A930031K15Rik|AA409794|AI586297|D11Ertd676e	pellino 1	protein-coding
mm_65882.1	chr7	29726992	29727007	-	1	NA	promoter-TSS (NM_029714)	promoter-TSS (NM_029714)	16	NM_029714	76718	Mm.69030	NM_029714	ENSMUSG00000049123	Catsperg2	1700067C01Rik|CATSPERG	catsper channel auxiliary subunit gamma 2	protein-coding
mm_87678.1	chr10	59221879	59221929	+	1	NA	promoter-TSS (NM_001024910)	promoter-TSS (NM_001024910)	-18	NM_172939	268301	Mm.3036	NM_172939	ENSMUSG00000098188	Sowahc	4921515A04Rik|9430099J10Rik|Ankrd57|C820004L04Rik	sosondowah ankyrin repeat domain family member C	protein-coding
mm_126215.1	chr15	78908426	78908470	+	1	NA	exon (NM_009164, exon 16 of 18)	exon (NM_009164, exon 16 of 18)	-5471	NM_020271	57028	Mm.263169	NM_020271	ENSMUSG00000022436	Pdxp	1600027H05Rik|AB041662|PLPP	pyridoxal (pyridoxine, vitamin B6) phosphatase	protein-coding
mm_67084.1	chr7	68278719	68278740	-	1	NA	intron (NM_001013811, intron 1 of 8)	MIR3|SINE|MIR	-2135	NR_040340	100504026	Mm.426764	NR_040340	ENSMUSG00000086628	Gm16157	OTTMUSG00000031023	predicted gene 16157	ncRNA
mm_13756.1	chr2	118126722	118126740	+	1	NA	3' UTR (NM_011580, exon 22 of 22)	3' UTR (NM_011580, exon 22 of 22)	14855	NM_001313914	21825	Mm.4159	NM_011580	ENSMUSG00000040152	Thbs1	TSP-1|TSP1|Thbs-1|tbsp1	thrombospondin 1	protein-coding
mm_54517.1	chr6	35520969	35520975	-	1	NA	intron (NM_008098, intron 3 of 3)	B1_Mm|SINE|Alu	18916	NM_008098	14489	Mm.182746	NM_008098	ENSMUSG00000029840	Mtpn	5033418D15Rik|Gcdp|V1	myotrophin	protein-coding
mm_35149.1	chr4	11965700	11965752	-	1	NA	promoter-TSS (NM_001098231)	promoter-TSS (NM_001098231)	-13	NM_001098231	381511	Mm.331489	NM_001033453	ENSMUSG00000049225	Pdp1	Gm1024|Ppm2c	pyruvate dehyrogenase phosphatase catalytic subunit 1	protein-coding
mm_66659.1	chr7	45715181	45715212	-	1	NA	promoter-TSS (NM_020011)	promoter-TSS (NM_020011)	11	NM_020011	56632	Mm.24222	NM_020011	ENSMUSG00000057342	Sphk2	C76851	sphingosine kinase 2	protein-coding
mm_133408.1	chr16	84852611	84852619	+	1	NA	exon (NM_008065, exon 6 of 10)	exon (NM_008065, exon 6 of 10)	-16990	NM_001302213	11957	Mm.353	NM_016755	ENSMUSG00000022890	Atp5j	CF6	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit F	protein-coding
mm_66799.1	chr7	47133396	47133413	-	1	NA	promoter-TSS (NM_001163565)	promoter-TSS (NM_001163565)	280	NM_013643	19259	Mm.4654	NM_013643	ENSMUSG00000030854	Ptpn5	Step	protein tyrosine phosphatase, non-receptor type 5	protein-coding
mm_5546.1	chr1	38627416	38627467	-	1	NA	promoter-TSS (NM_001290814)	promoter-TSS (NM_001290814)	-197	NM_001290814	16764	Mm.336679	NM_010678	ENSMUSG00000037138	Aff3	3222402O04Rik|A730046J16|LAF-4|Laf4	AF4/FMR2 family, member 3	protein-coding
mm_2490.1	chr1	105990777	105990813	+	1	NA	exon (NM_001122675, exon 1 of 13)	exon (NM_001122675, exon 1 of 13)	389	NM_001122675	227449	Mm.210188	NM_001122675	ENSMUSG00000038866	Zcchc2	9930114B20Rik|AW212015	zinc finger, CCHC domain containing 2	protein-coding
mm_4505.1	chr1	173735211	173735218	+	1	NA	exon (NM_001204910, exon 3 of 8)	exon (NM_001204910, exon 3 of 8)	6595	NM_001204910	226691	Mm.440876	NM_001204910	ENSMUSG00000073490	Ifi207	AI607873|Pyhin-A	interferon activated gene 207	protein-coding
mm_27790.1	chr3	75270074	75270085	-	1	NA	promoter-TSS (NM_026460)	promoter-TSS (NM_026460)	-1	NM_026460	67931	Mm.259446	NM_026460	ENSMUSG00000034139	Serpini2	Spi14	serine (or cysteine) peptidase inhibitor, clade I, member 2	protein-coding
mm_96883.1	chr11	70432573	70432590	+	1	NA	promoter-TSS (NM_001271358)	promoter-TSS (NM_001271358)	1	NM_001271358	216869	Mm.203747	NM_145429	ENSMUSG00000060216	Arrb2	AI326910|AW122872	arrestin, beta 2	protein-coding
mm_74097.1	chr8	122589695	122589696	+	1	NA	intron (NM_001193645, intron 9 of 11)	MTC|LTR|ERVL-MaLR	-12788	NM_009698	11821	Mm.1786	NM_009698	ENSMUSG00000006589	Aprt	C85684	adenine phosphoribosyl transferase	protein-coding
mm_109843.1	chr12	4592512	4592524	-	1	NA	promoter-TSS (NM_001198969)	promoter-TSS (NM_001198969)	-490	NM_001198969	20403	Mm.341204	NM_011365	ENSMUSG00000020640	Itsn2	AI327390|Ese2|Sh3d1B|Sh3p18|mKIAA1256	intersectin 2	protein-coding
mm_101684.1	chr11	40694839	40694849	-	1	NA	5' UTR (NM_001199274, exon 1 of 7)	5' UTR (NM_001199274, exon 1 of 7)	359	NM_001199274	108645	Mm.293771	NM_134017	ENSMUSG00000042032	Mat2b	1110064C04Rik|2410018D16Rik|AI182287|AU022853|MAT-II|MATIIbeta|TGR	methionine adenosyltransferase II, beta	protein-coding
mm_76208.1	chr8	83442443	83442467	-	1	NA	5' UTR (NM_019708, exon 1 of 4)	5' UTR (NM_019708, exon 1 of 4)	207	NM_001285992	56367	Mm.246911	NM_019708	ENSMUSG00000063253	Scoc	0610011C06Rik|2810002J11Rik|AA415030|SCOCO	short coiled-coil protein	protein-coding
mm_21345.1	chr2	157111685	157111700	-	1	NA	intron (NM_018851, intron 9 of 15)	B2_Mm2|SINE|B2	23530	NM_001139520	56045	Mm.248478	NM_018851	ENSMUSG00000027639	Samhd1	E330031J07Rik|Mg11	SAM domain and HD domain, 1	protein-coding
mm_35495.1	chr4	41045382	41045448	-	1	NA	5' UTR (NM_007473, exon 3 of 8)	5' UTR (NM_007473, exon 3 of 8)	2721	NM_007473	11832	Mm.8728	NM_007473	ENSMUSG00000028427	Aqp7	AQP7L|AQPap	aquaporin 7	protein-coding
mm_59794.1	chr7	29000824	29000837	+	1	NA	intron (NM_008279, intron 26 of 31)	intron (NM_008279, intron 26 of 31)	17976	NM_008279	26411	Mm.148278	NM_008279	ENSMUSG00000037337	Map4k1	Hpk1|mHPK1	mitogen-activated protein kinase kinase kinase kinase 1	protein-coding
mm_114806.1	chr13	91461127	91461143	+	1	NA	promoter-TSS (NM_024186)	promoter-TSS (NM_024186)	38	NM_024186	66970	Mm.343095	NM_024186	ENSMUSG00000003992	Ssbp2	1500004K09Rik|2310079I02Rik|9330163K02Rik|A830008M03Rik|AU067692|AW558684|Hspc116|SSDP2	single-stranded DNA binding protein 2	protein-coding
mm_86587.1	chr10	13090826	13090843	+	1	NA	promoter-TSS (NR_131912)	promoter-TSS (NR_131912)	-11	NR_131912	338438		NR_131912		Hymai	-	hydatidiform mole associated and imprinted transcript	ncRNA
mm_74970.1	chr8	27043035	27043047	-	1	NA	intron (NM_001039077, intron 1 of 4)	CpG	486	NM_054057	114863	Mm.277501	NM_054057	ENSMUSG00000031485	Prosc	1700024N20Rik|2200002F22Rik	proline synthetase co-transcribed	protein-coding
mm_114457.1	chr13	67173157	67173204	+	1	NA	promoter-TSS (NM_001013769)	promoter-TSS (NM_001013769)	-2	NM_001013769	380855	Mm.284988	NM_001013769	ENSMUSG00000058900	Rsl1	rslcan-9	regulator of sex limited protein 1	protein-coding
mm_68549.1	chr7	114276043	114276102	-	1	NA	promoter-TSS (NM_011965)	promoter-TSS (NM_011965)	44	NM_011965	26440	Mm.121265	NM_011965	ENSMUSG00000030751	Psma1	C2|HC2|Pros-30|alpha-type	proteasome (prosome, macropain) subunit, alpha type 1	protein-coding
mm_127696.1	chr15	102990577	102990590	+	1	NA	promoter-TSS (NM_010466)	promoter-TSS (NM_010466)	44	NM_010466	15426	Mm.6167	NM_010466	ENSMUSG00000001657	Hoxc8	D130011F21Rik|Hox-3.1	homeobox C8	protein-coding
mm_76189.1	chr8	82402746	82402785	-	1	NA	promoter-TSS (NM_001254747)	promoter-TSS (NM_001254747)	-179	NM_008357	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_144223.1	chr18	9877166	9877180	+	1	NA	3' UTR (NM_130449, exon 10 of 10)	3' UTR (NM_130449, exon 10 of 10)	-81007	NM_153552	225160	Mm.219648	NM_153552	ENSMUSG00000024287	Thoc1	3110002N20Rik|AW107452|NMP-84	THO complex 1	protein-coding
mm_12279.1	chr2	69004839	69004849	+	1	NA	intron (NM_172856, intron 4 of 9)	intron (NM_172856, intron 4 of 9)	-130956	NM_181547	329416	Mm.90047	NM_181547	ENSMUSG00000034738	Nostrin	Daip2|mDaIP2	nitric oxide synthase trafficker	protein-coding
mm_124677.1	chr15	6428678	6428688	+	1	NA	intron (NM_001008702, intron 9 of 13)	intron (NM_001008702, intron 9 of 13)	-16650	NM_013485	12279	Mm.29095	NM_013485	ENSMUSG00000022149	C9	-	complement component 9	protein-coding
mm_76084.1	chr8	79399418	79399435	-	1	NA	promoter-TSS (NM_008539)	promoter-TSS (NM_008539)	42	NM_008539	17125	Mm.223717	NM_008539	ENSMUSG00000031681	Smad1	AI528653|Madh1|Madr1|Mlp1|MusMLP	SMAD family member 1	protein-coding
mm_78950.1	chr9	45138748	45138758	+	1	NA	promoter-TSS (NM_001013390)	promoter-TSS (NM_001013390)	-289	NM_001013390	399548	Mm.335112	NM_001013390	ENSMUSG00000046480	Scn4b	Gm1471	sodium channel, type IV, beta	protein-coding
mm_131927.1	chr16	23520335	23520363	+	1	NA	intron (NM_008555, intron 1 of 15)	intron (NM_008555, intron 1 of 15)	241	NM_008555	17174	Mm.1213	NM_008555	ENSMUSG00000022887	Masp1	AW048060|CCPII|Crarf|Masp1/3	mannan-binding lectin serine peptidase 1	protein-coding
mm_48287.1	chr5	138172384	138172418	-	1	NA	promoter-TSS (NM_008568)	promoter-TSS (NM_008568)	380	NM_021392	11781	Mm.113205	NM_021392	ENSMUSG00000019518	Ap4m1	4930443L05Rik|Ap4m4	adaptor-related protein complex AP-4, mu 1	protein-coding
mm_13237.1	chr2	98662442	98662462	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	1194795	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
mm_52073.1	chr6	97827235	97827242	+	1	NA	intron (NM_001113198, intron 1 of 9)	intron (NM_001113198, intron 1 of 9)	20180	NM_001113198	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_6671.1	chr1	80340533	80340543	-	1	NA	5' UTR (NM_016716, exon 1 of 16)	5' UTR (NM_016716, exon 1 of 16)	152	NM_001313728	26554	Mm.12665	NM_016716	ENSMUSG00000004364	Cul3	KIAA0617	cullin 3	protein-coding
mm_64703.1	chr7	4547510	4547520	-	1	NA	promoter-TSS (NM_016908)	promoter-TSS (NM_016908)	-948	NM_016908	53420	Mm.358663	NM_016908	ENSMUSG00000004961	Syt5	SytV	synaptotagmin V	protein-coding
mm_42043.1	chr5	108461223	108461241	+	1	NA	promoter-TSS (NM_172716)	promoter-TSS (NM_172716)	-100	NM_172716	69587	Mm.261218	NM_172716	ENSMUSG00000033623	Pcgf3	2310035N15Rik|AI662857|D630042K08Rik|DONG1|E430039C14|RNF3A|Rnf3	polycomb group ring finger 3	protein-coding
mm_68460.1	chr7	110166353	110166363	-	1	NA	Intergenic	Intergenic	44299	NM_009516	22390	Mm.287173	NM_009516	ENSMUSG00000031016	Wee1	Wee1A	WEE 1 homolog 1 (S. pombe)	protein-coding
mm_24392.1	chr3	90265956	90265967	+	1	NA	promoter-TSS (NM_201407)	promoter-TSS (NM_201407)	-553	NM_201407	229541	Mm.30571	NM_201407	ENSMUSG00000042404	Dennd4b	-	DENN/MADD domain containing 4B	protein-coding
mm_148377.1	chr19	3205633	3205641	+	1	NA	Intergenic	Intergenic	-7934	NR_045304	70011	Mm.393871	NR_045304	ENSMUSG00000100969	1700030N03Rik	1700087C08Rik	RIKEN cDNA 1700030N03 gene	ncRNA
mm_57052.1	chr6	122455882	122455885	-	1	NA	3' UTR (NM_027664, exon 6 of 6)	3' UTR (NM_027664, exon 6 of 6)	30422	NM_027664	108653	Mm.277939	NM_027664	ENSMUSG00000040649	Rimklb	4931417E21Rik|4933426K21Rik|AA097693|AI325948|AU015629|Naags	ribosomal modification protein rimK-like family member B	protein-coding
mm_169857.1	chr16	3345899	3345899	+	1	NA	Intergenic	Intergenic	-246499	NM_146860	258859	Mm.377723	NM_146860	ENSMUSG00000051003	Olfr161	MOR131-1|OR912-47M6	olfactory receptor 161	protein-coding
mm_75060.1	chr8	33664469	33664469	-	1	NA	intron (NM_010344, intron 1 of 12)	RLTR6_Mm|LTR|ERV1	11231	NM_010344	14782	Mm.283573	NM_010344	ENSMUSG00000031584	Gsr	AI325518|D8Ertd238e|Gr-1|Gr1	glutathione reductase	protein-coding
mm_141949.1	chr17	35081193	35081203	-	1	NA	exon (NM_001163192, exon 4 of 6)	exon (NM_001163192, exon 4 of 6)	4256	NM_027366	70274	Mm.250491	NM_027366	ENSMUSG00000013766	Ly6g6e	2310011I02Rik|G6e	lymphocyte antigen 6 complex, locus G6E	protein-coding
mm_13285.1	chr2	101644393	101644435	+	1	NA	exon (NM_009019, exon 2 of 2)	exon (NM_009019, exon 2 of 2)	5118	NM_009019	19373	Mm.828	NM_009019	ENSMUSG00000061311	Rag1	Rag-1	recombination activating gene 1	protein-coding
mm_62288.1	chr7	99906444	99906450	+	1	NA	intron (NM_001164258, intron 11 of 18)	intron (NM_001164258, intron 11 of 18)	47229	NM_001164258	446101	Mm.440757	NM_001164258	ENSMUSG00000035211	Xrra1	AI449753	X-ray radiation resistance associated 1	protein-coding
mm_162601.1	chr1	183154933	183154942	-	1	NA	intron (NM_001278219, intron 2 of 8)	intron (NM_001278219, intron 2 of 8)	-7380	NM_001278220	68897	Mm.327216	NM_026866	ENSMUSG00000030768	Disp1	1190008H24Rik|DispA	dispatched RND transporter family member 1	protein-coding
mm_124790.1	chr15	8109368	8109374	+	1	NA	promoter-TSS (NM_133227)	promoter-TSS (NM_133227)	58	NM_133227	170762	Mm.295168	NM_133227	ENSMUSG00000022142	Nup155	D930027M19Rik|mKIAA0791	nucleoporin 155	protein-coding
mm_168251.1	chr10	82955329	82955329	-	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	-30168	NM_021439	58250	Mm.360747	NM_021439	ENSMUSG00000034612	Chst11	1110020P09Rik|C4ST|C4ST-1|C4ST1|C4s	carbohydrate sulfotransferase 11	protein-coding
mm_134020.1	chr16	4880285	4880302	-	1	NA	promoter-TSS (NM_145359)	promoter-TSS (NM_145359)	-442	NM_145359	207740	Mm.268895	NM_145359	ENSMUSG00000039568	Ubald1	1500031H01Rik|BC013706|Fam100a	UBA-like domain containing 1	protein-coding
mm_121182.1	chr14	103049283	103049299	+	1	NA	exon (NM_008392, exon 2 of 5)	exon (NM_008392, exon 2 of 5)	2279	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_74455.1	chr8	4214369	4214380	-	1	NA	exon (NM_207203, exon 6 of 7)	exon (NM_207203, exon 6 of 7)	2938	NM_207203	73072	Mm.477379	NM_207203	ENSMUSG00000064125	Prr36	-	proline rich 36	protein-coding
mm_33839.1	chr4	135752178	135752182	+	1	NA	3' UTR (NM_178257, exon 7 of 7)	3' UTR (NM_178257, exon 7 of 7)	-7535	NM_001085509	242702	Mm.318639	NM_001085509	ENSMUSG00000037139	Myom3	8430427K15Rik|Gm434	myomesin family, member 3	protein-coding
mm_79212.1	chr9	49055575	49055629	+	1	NA	promoter-TSS (NM_012039)	promoter-TSS (NM_012039)	21	NM_012039	26951	Mm.24791	NM_012039	ENSMUSG00000032264	Zw10	6330566F14Rik|MmZw10	zw10 kinetochore protein	protein-coding
mm_92839.1	chr10	81499651	81499670	-	1	NA	5' UTR (NM_010102, exon 1 of 1)	5' UTR (NM_010102, exon 1 of 1)	477	NM_010102	13611	Mm.33065	NM_010102	ENSMUSG00000044199	S1pr4	Edg6|Lpc1|S1p4	sphingosine-1-phosphate receptor 4	protein-coding
mm_91781.1	chr10	52343660	52343674	-	1	NA	intron (NM_001199272, intron 8 of 8)	intron (NM_001199272, intron 8 of 8)	38457	NM_053187	94221	Mm.390258	NM_053187	ENSMUSG00000019861	Gopc	2210402P09Rik|AI844555|CAL|FIG|GOPC1|PIST	golgi associated PDZ and coiled-coil motif containing	protein-coding
mm_163165.1	chr11	86593308	86593316	+	1	NA	intron (NM_029478, intron 10 of 11)	intron (NM_029478, intron 10 of 11)	-9154	NR_029738	387140		NR_029738	ENSMUSG00000065455	Mir21a	Mir21|Mirn21|mmu-mir-21|mmu-mir-21a	microRNA 21a	ncRNA
mm_23894.1	chr3	83031616	83031628	+	1	NA	exon (NM_010196, exon 5 of 5)	exon (NM_010196, exon 5 of 5)	5469	NM_001111048	14161	Mm.88793	NM_010196	ENSMUSG00000028001	Fga	ENSMUSG00000059807|Fib	fibrinogen alpha chain	protein-coding
mm_115907.1	chr13	23430946	23430979	-	1	NA	promoter-TSS (NR_015492)	promoter-TSS (NR_015492)	55	NR_015492	320842	Mm.487476	NR_015492	ENSMUSG00000085024	C230035I16Rik	-	RIKEN cDNA C230035I16 gene	ncRNA
mm_37929.1	chr4	132884407	132884501	-	1	NA	promoter-TSS (NM_133887)	promoter-TSS (NM_133887)	4	NM_133887	100226	Mm.28237	NM_133887	ENSMUSG00000028879	Stx12	AI850350|AU041521|Stx13	syntaxin 12	protein-coding
mm_23475.1	chr3	60480954	60480965	+	1	NA	intron (NM_001253713, intron 2 of 9)	intron (NM_001253713, intron 2 of 9)	8129	NM_001253713	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_55020.1	chr6	48841073	48841095	-	1	NA	promoter-TSS (NM_001164209)	promoter-TSS (NM_001164209)	53	NM_001286652	65963	Mm.28385	NM_023056	ENSMUSG00000029810	Tmem176b	1810009M01Rik|Clast1|Lr8	transmembrane protein 176B	protein-coding
mm_1936.1	chr1	86128251	86128271	+	1	NA	exon (NM_027357, exon 20 of 25)	exon (NM_027357, exon 20 of 25)	-16291	NM_008311	15559	Mm.439747	NM_008311	ENSMUSG00000026228	Htr2b	5-HT2B|AJ012488|AV377389	5-hydroxytryptamine (serotonin) receptor 2B	protein-coding
mm_65962.1	chr7	30435233	30435273	-	1	NA	3' UTR (NM_007467, exon 17 of 17)	3' UTR (NM_007467, exon 17 of 17)	10329	NM_007467	11803	Mm.2381	NM_007467	ENSMUSG00000006651	Aplp1	-	amyloid beta (A4) precursor-like protein 1	protein-coding
mm_46703.1	chr5	110230861	110230919	-	1	NA	promoter-TSS (NM_001253814)	promoter-TSS (NM_001253814)	-114	NM_001253814	71782	Mm.288442	NM_027922	ENSMUSG00000029501	Ankle2	1110001J12Rik|AI661024|D5Ertd585e	ankyrin repeat and LEM domain containing 2	protein-coding
mm_107816.1	chr12	65225724	65225744	+	1	NA	5' UTR (NM_027614, exon 1 of 2)	5' UTR (NM_027614, exon 1 of 2)	217	NM_027614	70948	Mm.219475	NM_027614	ENSMUSG00000035560	Wdr20rt	4921538B03Rik|4930427E19Rik|Wdr20|Wdr20b	WD repeat domain 20, retrogene	protein-coding
mm_17020.1	chr2	18998131	18998202	-	1	NA	promoter-TSS (NR_024323)	promoter-TSS (NR_024323)	-45	NM_008845	18718	Mm.313977	NM_008845	ENSMUSG00000026737	Pip4k2a	AW742916|Pip5k2a	phosphatidylinositol-5-phosphate 4-kinase, type II, alpha	protein-coding
mm_155601.1	chrX	82948862	82948915	+	1	NA	promoter-TSS (NM_007868)	promoter-TSS (NM_007868)	18	NM_007868	13405	Mm.275608	NM_007868	ENSMUSG00000045103	Dmd	DXSmh7|DXSmh9|Dp427|Dp71|dys|mdx|pke	dystrophin, muscular dystrophy	protein-coding
mm_104639.1	chr11	97523942	97523946	-	1	NA	intron (NM_018873, intron 16 of 19)	intron (NM_018873, intron 16 of 19)	-23604	NM_001289118	100141474	Mm.482426	NM_001289118	ENSMUSG00000047988	4933428G20Rik	-	RIKEN cDNA 4933428G20 gene	protein-coding
mm_7375.1	chr1	106796610	106796669	-	1	NA	promoter-TSS (NM_009190)	promoter-TSS (NM_009190)	86	NM_009190	20479	Mm.18705	NM_009190	ENSMUSG00000009907	Vps4b	8030489C12Rik|Skd1	vacuolar protein sorting 4B	protein-coding
mm_36642.1	chr4	94329429	94329432	-	1	NA	Intergenic	Intergenic	227366	NM_026368	67770	Mm.35170	NM_026368	ENSMUSG00000028578	Caap1	5830433M19Rik|AI536248|CAAP	caspase activity and apoptosis inhibitor 1	protein-coding
mm_42254.1	chr5	114003834	114003886	+	1	NA	promoter-TSS (NM_001286397)	promoter-TSS (NM_001286397)	-24	NM_001286397	13142	Mm.20115	NM_010018	ENSMUSG00000042096	Dao	AI987963|DAAO|DAMOX|Dao-1|Dao1	D-amino acid oxidase	protein-coding
mm_40896.1	chr5	75155438	75155480	+	1	NA	promoter-TSS (NM_001083316)	promoter-TSS (NM_001083316)	-707	NM_001083316	18595	Mm.221403	NM_011058	ENSMUSG00000029231	Pdgfra	AI115593|CD140a|Pdgfr-2	platelet derived growth factor receptor, alpha polypeptide	protein-coding
mm_167678.1	chr9	78333306	78333307	+	1	NA	intron (NM_008182, intron 5 of 6)	intron (NM_008182, intron 5 of 6)	5276	NM_205822	382088	Mm.360477	NM_205822	ENSMUSG00000038750	Omt2b	AU018149|C86230|Mosg|OM2b	oocyte maturation, beta	protein-coding
mm_72234.1	chr8	74873292	74873303	+	1	NA	5' UTR (NM_027837, exon 1 of 4)	5' UTR (NM_027837, exon 1 of 4)	123	NM_001294278	71597	Mm.158735	NM_027837	ENSMUSG00000031621	Isx	9130012O13Rik|Pix-1	intestine specific homeobox	protein-coding
mm_167077.1	chr7	100706738	100706762	+	1	NA	promoter-TSS (NM_178764)	promoter-TSS (NM_178764)	48	NM_178764	319604	Mm.260362	NM_178764	ENSMUSG00000029461	Fam168a	2610030B18Rik|B930006L02Rik|mKIAA0280	family with sequence similarity 168, member A	protein-coding
mm_2424.1	chr1	95314125	95314143	+	1	NA	exon (NM_026321, exon 1 of 3)	exon (NM_026321, exon 1 of 3)	506	NM_026321	67698	Mm.272705	NM_026321	ENSMUSG00000051185	Fam174a	2310044D20Rik|Fam174|Naa6|Tmem157	family with sequence similarity 174, member A	protein-coding
mm_142783.1	chr17	50156173	50156205	-	1	NA	intron (NM_181397, intron 2 of 9)	B1_Mus2|SINE|Alu	34308	NM_181397	76438	Mm.41854	NM_181397	ENSMUSG00000039316	Rftn1	2310015N21Rik|AI853526	raftlin lipid raft linker 1	protein-coding
mm_137790.1	chr17	29614948	29614958	+	1	NA	non-coding (NR_132314, exon 1 of 28)	non-coding (NR_132314, exon 1 of 28)	164	NM_021419	58230	Mm.305994	NM_021419	ENSMUSG00000090083	Rnf8	3830404E21Rik|AIP37|laXp180	ring finger protein 8	protein-coding
mm_90721.1	chr10	4568211	4568215	-	1	NA	Intergenic	Lx5c|LINE|L1	-43776	NM_001302532	13982	Mm.9213	NM_007956	ENSMUSG00000019768	Esr1	ER|ER-alpha|ERa|ERalpha|ESR|Estr|Estra|Nr3a1	estrogen receptor 1 (alpha)	protein-coding
mm_90360.1	chr10	127165788	127165804	+	1	NA	promoter-TSS (NM_027739)	promoter-TSS (NM_027739)	-35	NM_027739	14421	Mm.386762	NM_008080	ENSMUSG00000006731	B4galnt1	4933429D13Rik|Gal-NAc-T|GalNAc-T|GalNAcT|Galgt1|Ggm-2|Ggm2	beta-1,4-N-acetyl-galactosaminyl transferase 1	protein-coding
mm_103932.1	chr11	83648619	83648643	-	1	NA	exon (NM_011337, exon 2 of 3)	exon (NM_011337, exon 2 of 3)	747	NM_011337	20302	Mm.1282	NM_011337	ENSMUSG00000000982	Ccl3	AI323804|G0S19-1|LD78alpha|MIP-1alpha|MIP1-(a)|MIP1-alpha|Mip1a|Scya3	chemokine (C-C motif) ligand 3	protein-coding
mm_82113.1	chr9	123366922	123366953	+	1	NA	promoter-TSS (NM_153168)	promoter-TSS (NM_153168)	-3	NM_153168	102436	Mm.276076	NM_153168	ENSMUSG00000035202	Lars2	AI035546|Kiaa0028|LEURS	leucyl-tRNA synthetase, mitochondrial	protein-coding
mm_166778.1	chr6	137735163	137735167	+	1	NA	promoter-TSS (NM_011499)	promoter-TSS (NM_011499)	83	NM_011499	20901	Mm.22584	NM_011499	ENSMUSG00000030224	Strap	AW557906|C78091|C79202|Unrip	serine/threonine kinase receptor associated protein	protein-coding
mm_93096.1	chr10	89686251	89686306	-	1	NA	promoter-TSS (NM_001310704)	promoter-TSS (NM_001310704)	7	NM_198021	213326	Mm.27651	NM_198021	ENSMUSG00000069539	Scyl2	AU015688|AW536445|BC030932|CVAK104|D10Ertd802e	SCY1-like 2 (S. cerevisiae)	protein-coding
mm_53715.1	chr6	143285989	143285999	+	1	NA	intron (NR_027803, intron 3 of 3)	intron (NR_027803, intron 3 of 3)	40106	NR_027803	52285	Mm.354898	NM_001033129		D6Ertd474e	1700001I24Rik|AU023129	DNA segment, Chr 6, ERATO Doi 474, expressed	ncRNA
mm_120823.1	chr14	75139627	75139640	+	1	NA	intron (NM_008879, intron 1 of 16)	intron (NM_008879, intron 1 of 16)	3208	NM_008879	18826	Mm.153911	NM_008879	ENSMUSG00000021998	Lcp1	AW536232|D14Ertd310e|LCP-1|Pls2|pp65	lymphocyte cytosolic protein 1	protein-coding
mm_165326.1	chr2	110600465	110600470	+	1	NA	intron (NM_001177624, intron 1 of 14)	Lx|LINE|L1	3168	NM_001177624	241612	Mm.277148	NM_001003915	ENSMUSG00000041644	Slc5a12	AI315119|D630015G19|SMCT2	solute carrier family 5 (sodium/glucose cotransporter), member 12	protein-coding
mm_163988.1	chr14	61805171	61805171	+	1	NA	Intergenic	B4|SINE|B4	-122798	NR_028264	668253	Mm.32886	NR_028264	ENSMUSG00000097589	Dleu2	1810047A16Rik|4932411A06Rik|7730401J12Rik|AI197277|AI788824|Alt1|Gm9069|Leu2	deleted in lymphocytic leukemia, 2	ncRNA
mm_141838.1	chr17	34659484	34659485	-	1	NA	Intergenic	Intergenic	-11051	NM_031176	81877	Mm.290527	NM_031176	ENSMUSG00000033327	Tnxb	Tn-mhc|Tnx	tenascin XB	protein-coding
mm_85351.1	chr9	103211834	103211853	-	1	NA	exon (NM_133977, exon 15 of 17)	exon (NM_133977, exon 15 of 17)	-9778	NM_009275	20818	Mm.273053	NM_009275	ENSMUSG00000032553	Srprb	AA409543	signal recognition particle receptor, B subunit	protein-coding
mm_112781.1	chr13	20090645	20090655	+	1	NA	5' UTR (NM_080288, exon 1 of 22)	5' UTR (NM_080288, exon 1 of 22)	143	NM_080288	140580	Mm.342392	NM_080288	ENSMUSG00000041112	Elmo1	6330578D22Rik|C230095H21Rik|CED-12	engulfment and cell motility 1	protein-coding
mm_117636.1	chr13	92354944	92355025	-	1	NA	promoter-TSS (NM_010829)	promoter-TSS (NM_010829)	19	NM_001311120	17686	Mm.343101	NM_010829	ENSMUSG00000014850	Msh3	D13Em1|Rep-3|Rep3	mutS homolog 3	protein-coding
mm_159715.1	chr5	33658103	33658103	+	1	NA	promoter-TSS (NM_026698)	promoter-TSS (NM_026698)	-25	NM_001310541	21335	Mm.379024	NM_011524	ENSMUSG00000037313	Tacc3	Aint|C86661|Eric1	transforming, acidic coiled-coil containing protein 3	protein-coding
mm_128243.1	chr15	36608795	36608802	-	1	NA	5' UTR (NM_008774, exon 1 of 15)	5' UTR (NM_008774, exon 1 of 15)	175	NM_008774	18458	Mm.371570	NM_008774	ENSMUSG00000022283	Pabpc1	PABP|Pabp1|PabpI|Pabpl1|ePAB	poly(A) binding protein, cytoplasmic 1	protein-coding
mm_99145.1	chr11	100441948	100441954	+	1	NA	promoter-TSS (NM_001102650)	promoter-TSS (NM_001102650)	27	NM_025727	66720	Mm.34168	NM_025727	ENSMUSG00000001558	Klhl10	4921517C11Rik	kelch-like 10	protein-coding
mm_44440.1	chr5	21424693	21424703	-	1	NA	promoter-TSS (NM_177869)	promoter-TSS (NM_177869)	-21	NM_029195	75172	Mm.426695	NM_029195	ENSMUSG00000064280	Ccdc146	4930528G09Rik|mKIAA1505	coiled-coil domain containing 146	protein-coding
mm_96884.1	chr11	70432602	70432624	+	1	NA	promoter-TSS (NM_001271358)	promoter-TSS (NM_001271358)	33	NM_001271358	216869	Mm.203747	NM_145429	ENSMUSG00000060216	Arrb2	AI326910|AW122872	arrestin, beta 2	protein-coding
mm_110545.1	chr12	55391497	55391505	-	1	NA	intron (NM_001310583, intron 1 of 6)	RMER19B|LTR|ERVK	7279	NM_001310583	26443	Mm.30210	NM_011968	ENSMUSG00000021024	Psma6	IOTA	proteasome (prosome, macropain) subunit, alpha type 6	protein-coding
mm_47434.1	chr5	123178262	123178272	-	1	NA	exon (NM_008277, exon 8 of 14)	exon (NM_008277, exon 8 of 14)	4419	NM_008277	15445	Mm.439709	NM_008277	ENSMUSG00000029445	Hpd	Fla|Flp|Hppd|Laf	4-hydroxyphenylpyruvic acid dioxygenase	protein-coding
mm_139781.1	chr17	65783349	65783403	+	1	NA	promoter-TSS (NM_001114131)	promoter-TSS (NM_001114131)	21	NR_104465	70351	Mm.48686	NM_146081	ENSMUSG00000061950	Ppp4r1	3110001J10Rik|Pp4r1	protein phosphatase 4, regulatory subunit 1	protein-coding
mm_20388.1	chr2	128968226	128968241	-	1	NA	intron (NM_178404, intron 1 of 11)	intron (NM_178404, intron 1 of 11)	831	NM_178404	78751	Mm.26377	NM_178404	ENSMUSG00000042851	Zc3h6	4631426G04Rik|4833425H18Rik|AU024389|AW060453|Zc3hdc6|mKIAA2035	zinc finger CCCH type containing 6	protein-coding
mm_158338.1	chrX	134111807	134111814	-	1	NA	promoter-TSS (NM_172203)	promoter-TSS (NM_172203)	44	NM_172203	237038	Mm.67938	NM_172203	ENSMUSG00000031257	Nox1	GP91-2|MOX1|NOH-1|NOH1|NOX1a|NOX1alpha|Nox-1	NADPH oxidase 1	protein-coding
mm_130232.1	chr15	96460839	96460856	-	1	NA	promoter-TSS (NM_028148)	promoter-TSS (NM_028148)	-4	NM_028148	72193	Mm.324474	NM_028148	ENSMUSG00000033228	Scaf11	1110061H03Rik|2610510E10Rik|AI462454|CASP11|SIP1|SRRP129|Sfrs2ip|Srsf2ip|mKIAA3013	SR-related CTD-associated factor 11	protein-coding
mm_7336.1	chr1	105356935	105356963	-	1	NA	promoter-TSS (NM_001160368)	promoter-TSS (NM_001160368)	-239	NM_001160368	320311	Mm.389162	NM_178779	ENSMUSG00000047496	Rnf152	A930029B02Rik	ring finger protein 152	protein-coding
mm_106473.1	chr11	120139408	120139422	-	1	NA	intron (NM_024249, intron 4 of 16)	intron (NM_024249, intron 4 of 16)	11936	NM_001164799	72055	Mm.253403	NM_024249	ENSMUSG00000061306	Slc38a10	1810073N04Rik	solute carrier family 38, member 10	protein-coding
mm_130843.1	chr15	101918569	101918578	-	1	NA	TTS (NM_008475)	TTS (NM_008475)	6162	NM_008475	16682	Mm.46425	NM_008475	ENSMUSG00000059668	Krt4	AW108092|K4|Krt-2.4|Krt2-4	keratin 4	protein-coding
mm_37400.1	chr4	121115344	121115344	-	1	NA	Intergenic	Intergenic	-6118	NM_001081312	69469	Mm.481120	NM_001081312	ENSMUSG00000078577	Tmco2	1700028F16Rik	transmembrane and coiled-coil domains 2	protein-coding
mm_8561.1	chr1	155279357	155279370	-	1	NA	3' UTR (NM_011273, exon 15 of 15)	3' UTR (NM_011273, exon 15 of 15)	120660	NM_021433	58244	Mm.66264	NM_021433	ENSMUSG00000026470	Stx6	2310039E05Rik|2410005I16Rik|AA437559|AI415714|AI845861	syntaxin 6	protein-coding
mm_97073.1	chr11	72997014	72997014	+	1	NA	Intergenic	B4A|SINE|B4	-2131	NM_008771	18436	Mm.25722	NM_008771	ENSMUSG00000020787	P2rx1	AI323649|BB122383|P2x|Pdcd3|RP-2	purinergic receptor P2X, ligand-gated ion channel, 1	protein-coding
mm_117868.1	chr13	98874855	98874858	-	1	NA	intron (NM_001048267, intron 6 of 23)	intron (NM_001048267, intron 6 of 23)	16186	NM_001048267	238799	Mm.173286	NM_178716	ENSMUSG00000009470	Tnpo1	AU021749|D13Ertd688e|IPO2|Kpnb2|MIP|MIP1|TRN	transportin 1	protein-coding
mm_138195.1	chr17	34287972	34287983	+	1	NA	promoter-TSS (NM_010378)	promoter-TSS (NM_010378)	-206	NM_010378	14960	Mm.235338	NM_010378	ENSMUSG00000036594	H2-Aa	Aalpha|H-2Aa|H2Aa|I-Aalpha|IAalpha|Ia-1|Ia1	histocompatibility 2, class II antigen A, alpha	protein-coding
mm_52227.1	chr6	103511896	103511910	+	1	NA	intron (NM_007697, intron 1 of 26)	intron (NM_007697, intron 1 of 26)	1027	NM_007697	12661	Mm.251288	NM_007697	ENSMUSG00000030077	Chl1	A530023M13Rik|AI465420|CALL|LICAM2	cell adhesion molecule L1-like	protein-coding
mm_171900.1	chr5	4192372	4192382	+	1	NA	promoter-TSS (NM_001042670)	promoter-TSS (NM_001042670)	10	NM_001042670	208595	Mm.129815	NM_001042670	ENSMUSG00000053178	Mterf1b	ENSMUSG00000053178|Gm9897	mitochondrial transcription termination factor 1b	protein-coding
mm_27270.1	chr3	39937417	39937422	-	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	585493	NR_040445	100040882	Mm.272869	NR_040445	ENSMUSG00000037884	1700017G19Rik	-	RIKEN cDNA 1700017G19 gene	ncRNA
mm_110733.1	chr12	69790256	69790273	-	1	NA	promoter-TSS (NR_033573)	promoter-TSS (NR_033573)	-80	NR_033573	74724	Mm.399254	NR_033573		4930512B01Rik	4930472D12Rik	RIKEN cDNA 4930512B01 gene	ncRNA
mm_158359.1	chrX	134600977	134600990	-	1	NA	promoter-TSS (NM_001313716)	promoter-TSS (NM_001313716)	22	NM_013463	11605	Mm.1114	NM_013463	ENSMUSG00000031266	Gla	Ags	galactosidase, alpha	protein-coding
mm_58121.1	chr6	139501922	139501933	-	1	NA	promoter-TSS (NM_001128090)	promoter-TSS (NM_001128090)	-18	NM_001128090	632971	Mm.475610	NM_001128090	ENSMUSG00000092164	Rergl	EG632971	RERG/RAS-like	protein-coding
mm_16455.1	chr2	180581221	180581243	+	1	NA	promoter-TSS (NM_028479)	promoter-TSS (NM_028479)	-72	NM_028479	73247	Mm.426558	NM_028479	ENSMUSG00000027569	Mrgbp	1600027N09Rik|AW060503|C80444	MRG/MORF4L binding protein	protein-coding
mm_119422.1	chr14	45341276	45341310	+	1	NA	exon (NM_025959, exon 10 of 14)	exon (NM_025959, exon 10 of 14)	-9893	NM_019637	56291	Mm.202561	NM_019637	ENSMUSG00000053205	Styx	0610039A20Rik|hStyxb	serine/threonine/tyrosine interaction protein	protein-coding
mm_165332.1	chr2	114047563	114047569	-	1	NA	exon (NM_009608, exon 7 of 7)	exon (NM_009608, exon 7 of 7)	5309	NM_009608	11464	Mm.686	NM_009608	ENSMUSG00000068614	Actc1	Actc-1	actin, alpha, cardiac muscle 1	protein-coding
mm_53209.1	chr6	125690669	125690679	+	1	NA	5' UTR (NM_153589, exon 1 of 26)	5' UTR (NM_153589, exon 1 of 26)	255	NM_153589	243634	Mm.333398	NM_153589	ENSMUSG00000038115	Ano2	BC033409|Tmem16b	anoctamin 2	protein-coding
mm_38782.1	chr4	148079376	148079396	-	1	NA	3' UTR (NM_001301281, exon 5 of 5)	3' UTR (NM_001301281, exon 5 of 5)	8678	NM_009642	11610	Mm.46247	NM_009642	ENSMUSG00000029007	Agtrap	3300002E14Rik|AT1R|Atrap|D4Wsu124e	angiotensin II, type I receptor-associated protein	protein-coding
mm_42073.1	chr5	110110069	110110114	+	1	NA	promoter-TSS (NM_001163996)	promoter-TSS (NM_001163996)	-1	NM_001163996	675812	Mm.442122	NM_001163996	ENSMUSG00000023284	Zfp605	A830023I12Rik	zinc finger protein 605	protein-coding
mm_156822.1	chrX	164140655	164140659	+	1	NA	5' UTR (NM_027286, exon 1 of 18)	5' UTR (NM_027286, exon 1 of 18)	177	NM_027286	70008	Mm.13451	NM_027286	ENSMUSG00000015405	Ace2	2010305L05Rik	angiotensin I converting enzyme (peptidyl-dipeptidase A) 2	protein-coding
mm_886.1	chr1	52655528	52655532	+	1	NA	TTS (NM_133829)	TTS (NM_133829)	24825	NM_001142647	227094	Mm.83541	NM_172654	ENSMUSG00000043015	Nemp2	5330401P04Rik|9830163O08|Tmem194b	nuclear envelope integral membrane protein 2	protein-coding
mm_148379.1	chr19	3205910	3205915	+	1	NA	Intergenic	Intergenic	-8209	NR_045304	70011	Mm.393871	NR_045304	ENSMUSG00000100969	1700030N03Rik	1700087C08Rik	RIKEN cDNA 1700030N03 gene	ncRNA
mm_132607.1	chr16	38562903	38562913	+	1	NA	promoter-TSS (NM_026407)	promoter-TSS (NM_026407)	94	NM_026407	67846	Mm.310476	NM_026407	ENSMUSG00000002845	Tmem39a	2610033C09Rik	transmembrane protein 39a	protein-coding
mm_148650.1	chr19	5493651	5493667	+	1	NA	3' UTR (NM_007687, exon 4 of 4)	3' UTR (NM_007687, exon 4 of 4)	3204	NM_007687	12631	Mm.329655	NM_007687	ENSMUSG00000056201	Cfl1	AA959946|Cof	cofilin 1, non-muscle	protein-coding
mm_154134.1	chr19	57314990	57315000	-	1	NA	Intergenic	CpG	41035	NR_045319	78120	Mm.445892	NR_045319		4930449E18Rik	-	RIKEN cDNA 4930449E18 gene	ncRNA
mm_77948.1	chr9	7445838	7445855	+	1	NA	promoter-TSS (NM_010809)	promoter-TSS (NM_010809)	24	NM_010809	17392	Mm.4993	NM_010809	ENSMUSG00000043613	Mmp3	EMS-2|MMP-3|SL-1|SLN-1|SLN1|STR-1|Stmy1|Str1	matrix metallopeptidase 3	protein-coding
mm_30506.1	chr3	158024006	158024024	-	1	NA	intron (NM_001093752, intron 3 of 12)	intron (NM_001093752, intron 3 of 12)	7739	NM_001093753	69207	Mm.223946	NM_026989	ENSMUSG00000055436	Srsf11	0610009J05Rik|2610019N13Rik|BF642805|Sfrs11	serine/arginine-rich splicing factor 11	protein-coding
mm_19770.1	chr2	105673979	105673981	-	1	NA	intron (NM_001244201, intron 1 of 11)	intron (NM_001244201, intron 1 of 11)	-1764	NM_001244200	18508	Mm.3608	NM_013627	ENSMUSG00000027168	Pax6	1500038E17Rik|AEY11|Dey|Gsfaey11|Pax-6|Sey	paired box 6	protein-coding
mm_87758.1	chr10	60279804	60279807	+	1	NA	intron (NM_001146120, intron 1 of 13)	B1F|SINE|Alu	2177	NM_001146121	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_139811.1	chr17	66480494	66480543	+	1	NA	Intergenic	Intergenic	-30768	NM_001114098	68617	Mm.33421	NM_172963	ENSMUSG00000052105	Mtcl1	1110012J17Rik|Ccdc165|D130071O13|Kiaa0802|Soga2|mKIAA0802|t8219b25	microtubule crosslinking factor 1	protein-coding
mm_105020.1	chr11	100441796	100441813	-	1	NA	promoter-TSS (NM_001102650)	promoter-TSS (NM_001102650)	-120	NM_025727	66720	Mm.34168	NM_025727	ENSMUSG00000001558	Klhl10	4921517C11Rik	kelch-like 10	protein-coding
mm_112994.1	chr13	21750748	21750753	+	1	NA	promoter-TSS (NM_178211)	promoter-TSS (NM_178211)	-197	NM_178211	319160	Mm.255646	NM_178211	ENSMUSG00000064288	Hist1h4k	-	histone cluster 1, H4k	protein-coding
mm_25611.1	chr3	118430042	118430074	+	1	NA	Intergenic	Intergenic	-3799	NR_029551	387155		NR_029551	ENSMUSG00000065569	Mir137	Mirn137|mir-137|mmu-mir-137	microRNA 137	ncRNA
mm_35670.1	chr4	43578532	43578561	-	1	NA	promoter-TSS (NM_172866)	promoter-TSS (NM_172866)	-189	NM_172866	242406	Mm.259311	NM_172866	ENSMUSG00000028468	Rgp1	1110029E03Rik|AI527196|F730001J03|mKIAA0258	RAB6A GEF compex partner 1	protein-coding
mm_128053.1	chr15	25830518	25830529	-	1	NA	Intergenic	Intergenic	-12775	NM_001034851	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_157236.1	chrX	17319317	17319334	-	1	NA	promoter-TSS (NM_028916)	promoter-TSS (NM_028916)	43	NM_028916	74405	Mm.248531	NM_028916	ENSMUSG00000025038	Efhc2	4933407D04Rik|mRib72-2	EF-hand domain (C-terminal) containing 2	protein-coding
mm_133418.1	chr16	86044974	86044984	+	1	NA	Intergenic	Intergenic	-143854	NM_011782	23794	Mm.112933	NM_011782	ENSMUSG00000022894	Adamts5	9530092O11Rik|ADAM-TS5|ADAMTS1|ADAMTS11|ADMP-2|AI481094|ASMP-2	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)	protein-coding
mm_51676.1	chr6	86438667	86438713	+	1	NA	promoter-TSS (NM_001243742)	promoter-TSS (NM_001243742)	44	NM_001243741	232196	Mm.404040	NM_146170	ENSMUSG00000046679	C87436	-	expressed sequence C87436	protein-coding
mm_114714.1	chr13	83575626	83575634	+	1	NA	5' UTR (NM_025282, exon 3 of 11)	5' UTR (NM_025282, exon 3 of 11)	2023	NM_001347569	17260	Mm.24001	NM_025282	ENSMUSG00000005583	Mef2c	5430401D19Rik|9930028G15Rik|AV011172|Mef2	myocyte enhancer factor 2C	protein-coding
mm_69128.1	chr7	127026628	127026638	-	1	NA	promoter-TSS (NM_010772)	promoter-TSS (NM_010772)	-154	NM_010772	17188	Mm.378964	NM_010772	ENSMUSG00000030678	Maz	MAZI|PUR1|Pur-1|SAF-1|SAF-2	MYC-associated zinc finger protein (purine-binding transcription factor)	protein-coding
mm_57452.1	chr6	125165318	125165334	-	1	NA	intron (NM_001289726, intron 1 of 6)	CpG-12474	447	NM_008084	14433	Mm.304088	NM_008084	ENSMUSG00000057666	Gapdh	Gapd	glyceraldehyde-3-phosphate dehydrogenase	protein-coding
mm_103030.1	chr11	69735357	69735367	-	1	NA	exon (NM_001291068, exon 29 of 29)	exon (NM_001291068, exon 29 of 29)	23271	NM_001291068	20020	Mm.16533	NM_009089	ENSMUSG00000005198	Polr2a	220kDa|Rpb1|Rpo2-1	polymerase (RNA) II (DNA directed) polypeptide A	protein-coding
mm_72515.1	chr8	83941573	83941595	+	1	NA	3' UTR (NM_181039, exon 23 of 23)	3' UTR (NM_181039, exon 23 of 23)	-14110	NM_024184	66929	Mm.29680	NM_024184	ENSMUSG00000005470	Asf1b	1700003K02Rik|AA409591	anti-silencing function 1B histone chaperone	protein-coding
mm_149623.1	chr19	16956111	16956124	+	1	NA	promoter-TSS (NM_181348)	promoter-TSS (NM_181348)	-1	NM_181348	353211	Mm.257354	NM_181348	ENSMUSG00000039126	Prune2	6330414G02Rik|A230083H22Rik|A330102H22Rik|Bmcc1|mKIAA0367	prune homolog 2	protein-coding
mm_53019.1	chr6	124065806	124065808	+	1	NA	Intergenic	RLTR9A3B|LTR|ERVK	41049	NM_019917	56552	Mm.23795	NM_019917	ENSMUSG00000096630	Vmn2r26	V2R1|V2r1b	vomeronasal 2, receptor 26	protein-coding
mm_66159.1	chr7	31151642	31151674	-	1	NA	promoter-TSS (NM_027898)	promoter-TSS (NM_027898)	-608	NM_027898	52857	Mm.27366	NM_027898	ENSMUSG00000001248	Gramd1a	1300003M23Rik|AI415002|AW547240|D7Bwg0611e	GRAM domain containing 1A	protein-coding
mm_134871.1	chr16	28714543	28714546	-	1	NA	intron (NM_010199, intron 2 of 5)	intron (NM_010199, intron 2 of 5)	38699	NM_010199	14167	Mm.7996	NM_010199	ENSMUSG00000022523	Fgf12	AV114868|B230343J05Rik|FGF-12|FHF-1|Fhf1	fibroblast growth factor 12	protein-coding
mm_122746.1	chr14	54151400	54151410	-	1	NA	Intergenic	Intergenic	102524	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_149510.1	chr19	11970300	11970311	+	1	NA	intron (NM_001033174, intron 1 of 13)	L1ME1|LINE|L1	4461	NM_001033174	76303	Mm.291279	NM_001033174	ENSMUSG00000024687	Osbp	1110018F06Rik|AW559088|mKIAA4220	oxysterol binding protein	protein-coding
mm_115963.1	chr13	23892665	23892709	-	1	NA	intron (NR_121611, intron 12 of 12)	intron (NR_121611, intron 12 of 12)	22320	NM_177016	319848	Mm.97959	NM_177016	ENSMUSG00000021336	Slc17a4	9130214H05Rik	solute carrier family 17 (sodium phosphate), member 4	protein-coding
mm_143200.1	chr17	62770898	62770903	-	1	NA	intron (NM_010109, intron 1 of 3)	intron (NM_010109, intron 1 of 3)	110417	NM_207654	13640	Mm.7978	NM_010109	ENSMUSG00000048915	Efna5	AL-1|AV158822|EFL-5|Ephrin-A5|Epl7|LERK-7|RAGS	ephrin A5	protein-coding
mm_168421.1	chr11	33160906	33160914	-	1	NA	exon (NM_001252261, exon 4 of 10)	exon (NM_001252261, exon 4 of 10)	2296	NM_001252261	18148	Mm.485384	NM_008722	ENSMUSG00000057113	Npm1	B23|NO38|Npm	nucleophosmin 1	protein-coding
mm_57149.1	chr6	122728380	122728410	-	1	NA	3' UTR (NM_011401, exon 10 of 10)	3' UTR (NM_011401, exon 10 of 10)	14350	NM_011401	20527	Mm.395108	NM_011401	ENSMUSG00000003153	Slc2a3	AA408729|AL023014|AL024341|AU040424|C78366|Glut-3|Glut3	solute carrier family 2 (facilitated glucose transporter), member 3	protein-coding
mm_14783.1	chr2	145860035	145860057	+	1	NA	exon (NM_028724, exon 9 of 13)	exon (NM_028724, exon 9 of 13)	-43195	NM_026425	67877	Mm.151168	NM_026425	ENSMUSG00000002728	Naa20	1500004D14Rik|2900026I01Rik|AU041458|D2Ertd186e|Nat5	N(alpha)-acetyltransferase 20, NatB catalytic subunit	protein-coding
mm_132794.1	chr16	45093747	45093760	+	1	NA	promoter-TSS (NM_026439)	promoter-TSS (NM_026439)	-300	NM_026439	67896	Mm.181074	NM_026439	ENSMUSG00000022665	Ccdc80	2610001E17Rik|DRO1|Ssg1|Urb	coiled-coil domain containing 80	protein-coding
mm_64976.1	chr7	16874366	16874396	-	1	NA	promoter-TSS (NM_001081655)	promoter-TSS (NM_001081655)	-936	NM_001081655	629378	Mm.491123	NM_001081655	ENSMUSG00000078794	Dact3	EG666671|naa-3	dishevelled-binding antagonist of beta-catenin 3	protein-coding
mm_16398.1	chr2	179976821	179976841	+	1	NA	promoter-TSS (NM_001081092)	promoter-TSS (NM_001081092)	-22	NR_033782	66730	Mm.31773	NR_033782	ENSMUSG00000085704	4921531C22Rik	-	RIKEN cDNA 4921531C22 gene	ncRNA
mm_120407.1	chr14	65172310	65172330	+	1	NA	Intergenic	Intergenic	-74214	NM_018788	54616	Mm.103748	NM_018788	ENSMUSG00000021978	Extl3	2900009G18Rik|AU040105|Ext1l|mKIAA0519	exostoses (multiple)-like 3	protein-coding
mm_115767.1	chr13	19304989	19304993	-	1	NA	Intergenic	Intergenic	90822	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_28159.1	chr3	87768968	87768975	-	1	NA	promoter-TSS (NM_001289601)	promoter-TSS (NM_001289601)	-18	NM_001032414	73182	Mm.158962	NM_028460	ENSMUSG00000028073	Pear1	3110045G13Rik|Jedi-1|Megf12	platelet endothelial aggregation receptor 1	protein-coding
mm_78917.1	chr9	45002276	45002293	+	1	NA	exon (NM_007648, exon 5 of 8)	exon (NM_007648, exon 5 of 8)	7306	NM_007648	12501	Mm.210361	NM_007648	ENSMUSG00000032093	Cd3e	AI504783|CD3|CD3epsilon|T3e	CD3 antigen, epsilon polypeptide	protein-coding
mm_102172.1	chr11	53979950	53979968	-	1	NA	promoter-TSS (NM_019723)	promoter-TSS (NM_019723)	68	NM_019723	56517	Mm.154284	NM_019723	ENSMUSG00000063652	Slc22a21	Octn3|Slc22a9	solute carrier family 22 (organic cation transporter), member 21	protein-coding
mm_17181.1	chr2	25365613	25365635	-	1	NA	promoter-TSS (NM_001033293)	promoter-TSS (NM_001033293)	2	NM_001033293	227620	Mm.33797	NM_001033293	ENSMUSG00000026956	Uap1l1	5730445F03Rik	UDP-N-acteylglucosamine pyrophosphorylase 1-like 1	protein-coding
mm_20004.1	chr2	119029393	119029395	-	1	NA	promoter-TSS (NM_199310)	promoter-TSS (NM_199310)	-1	NM_199310	269336	Mm.292465	NM_199310	ENSMUSG00000039983	Ccdc32	Gm631	coiled-coil domain containing 32	protein-coding
mm_171783.1	chr5	110118581	110118583	-	1	NA	intron (NM_001163996, intron 2 of 4)	intron (NM_001163996, intron 2 of 4)	8490	NM_001163996	675812	Mm.442122	NM_001163996	ENSMUSG00000023284	Zfp605	A830023I12Rik	zinc finger protein 605	protein-coding
mm_122231.1	chr14	33185116	33185131	-	1	NA	promoter-TSS (NM_001146022)	promoter-TSS (NM_001146022)	-57	NM_001146022	545030	Mm.318345	NM_001146022	ENSMUSG00000051506	Wdfy4	Gm18810	WD repeat and FYVE domain containing 4	protein-coding
mm_36186.1	chr4	62228488	62228495	-	1	NA	Intergenic	Intergenic	-19945	NM_001290350	22696	Mm.5011	NM_009554	ENSMUSG00000028389	Zfp37	Tzn|Zfp-37	zinc finger protein 37	protein-coding
mm_119270.1	chr14	34086009	34086026	+	1	NA	promoter-TSS (NM_001281845)	promoter-TSS (NM_001281845)	38	NM_013473	11752	Mm.3267	NM_013473	ENSMUSG00000021950	Anxa8	AI466995|Anx8	annexin A8	protein-coding
mm_133050.1	chr16	57572052	57572076	+	1	NA	exon (NM_001040397, exon 5 of 5)	exon (NM_001040397, exon 5 of 5)	22822	NM_001177871	78749	Mm.328360	NM_001040397	ENSMUSG00000043336	Filip1l	4631422O05Rik|Doc1	filamin A interacting protein 1-like	protein-coding
mm_135728.1	chr16	55828454	55828460	-	1	NA	intron (NM_030612, intron 2 of 13)	intron (NM_030612, intron 2 of 13)	-6319	NM_001159394	80859	Mm.247272	NM_030612	ENSMUSG00000035356	Nfkbiz	AA408868|INAP|Mail	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, zeta	protein-coding
mm_32727.1	chr4	116557592	116557617	+	1	NA	promoter-TSS (NM_029868)	promoter-TSS (NM_029868)	-123	NM_029868	77110	Mm.41715	NM_029868	ENSMUSG00000034042	Gpbp1l1	5330440M15Rik|BC002292	GC-rich promoter binding protein 1-like 1	protein-coding
mm_115946.1	chr13	23710846	23710892	-	1	NA	promoter-TSS (NM_001347493)	promoter-TSS (NM_001347493)	-15	NM_010424	15216	Mm.2681	NM_010424	ENSMUSG00000006611	Hfe	MR2	hemochromatosis	protein-coding
mm_98131.1	chr11	87447888	87447891	+	1	NA	intron (NM_001199293, intron 2 of 30)	B1_Mur2|SINE|Alu	20298	NM_001199293	83560	Mm.440758	NM_031386	ENSMUSG00000010342	Tex14	C85585	testis expressed gene 14	protein-coding
mm_88302.1	chr10	75317077	75317124	+	1	NA	promoter-TSS (NM_001331095)	promoter-TSS (NM_001331095)	223	NM_009630	11540	Mm.333734	NM_009630	ENSMUSG00000020178	Adora2a	A2AAR|A2aR|AA2AR	adenosine A2a receptor	protein-coding
mm_82299.1	chr9	7850631	7850657	-	1	NA	intron (NM_007464, intron 7 of 8)	intron (NM_007464, intron 7 of 8)	-13587	NM_007465	11797	Mm.335659	NM_007465	ENSMUSG00000057367	Birc2	AW146227|Api1|Api2|Birc3|C-IAP1|C330006D17Rik|HIAP1|HIAP2|IAP1|IAP2|MIAP1|MIAP2|MIHB|MIHC|RNF48|cIAP1|cIAP2|mcIAP1	baculoviral IAP repeat-containing 2	protein-coding
mm_9221.1	chr1	171234486	171234501	-	1	NA	promoter-TSS (NM_010185)	promoter-TSS (NM_010185)	-144	NM_010185	14127	Mm.22673	NM_010185	ENSMUSG00000058715	Fcer1g	AI573376|CD23|FcR-gamma|FcR[g]|FcRgamma|Fce1g|FcepsilonRI|Ly-50	Fc receptor, IgE, high affinity I, gamma polypeptide	protein-coding
mm_113849.1	chr13	47201662	47201673	+	1	NA	intron (NM_001170643, intron 1 of 7)	intron (NM_001170643, intron 1 of 7)	7664	NM_001170643	218215	Mm.287609	NM_146042	ENSMUSG00000038068	Rnf144b	BC025007|E130105P19Rik|Ibrdc2|Pir2	ring finger protein 144B	protein-coding
mm_109763.1	chr12	117917837	117917846	+	1	NA	intron (NM_010060, intron 70 of 81)	B3A|SINE|B2	73980	NM_146040	217946	Mm.281149	NM_146040	ENSMUSG00000021175	Cdca7l	BC006933|JPO2	cell division cycle associated 7 like	protein-coding
mm_25694.1	chr3	122262658	122262697	+	1	NA	exon (NM_008129, exon 5 of 7)	exon (NM_008129, exon 5 of 7)	-11737	NM_153806	99480	Mm.398647	NM_153806	ENSMUSG00000039756	Dnttip2	4930588M11Rik|AA408582|AU014960|HSU15552	deoxynucleotidyltransferase, terminal, interacting protein 2	protein-coding
mm_64131.1	chr7	141172601	141172644	+	1	NA	intron (NM_001172100, intron 1 of 9)	CpG	229	NM_001172100	107702	Mm.197493	NM_145135	ENSMUSG00000038650	Rnh1	AW546468|C80305|RNH	ribonuclease/angiogenin inhibitor 1	protein-coding
mm_19664.1	chr2	103283603	103283620	-	1	NA	exon (NM_007914, exon 2 of 9)	exon (NM_007914, exon 2 of 9)	19585	NM_007914	13661	Mm.10724	NM_007914	ENSMUSG00000012350	Ehf	9030625L19Rik|AU019492	ets homologous factor	protein-coding
mm_63772.1	chr7	131371196	131371206	+	1	NA	promoter-TSS (NM_001039534)	promoter-TSS (NM_001039534)	55	NM_001039534	214580	Mm.272948	NM_177609	ENSMUSG00000063179	Pstk	5430423O14Rik|5730458D16Rik|Gm1099|R75284	phosphoseryl-tRNA kinase	protein-coding
mm_170897.1	chr2	29965658	29965659	+	1	NA	promoter-TSS (NM_001177668)	promoter-TSS (NM_001177668)	98	NM_001309460	20740	Mm.204969	NM_001076554	ENSMUSG00000057738	Sptan1	2610027H02Rik|Spna-2|Spna2	spectrin alpha, non-erythrocytic 1	protein-coding
mm_85812.1	chr9	110388085	110388102	-	1	NA	exon (NM_001081043, exon 20 of 25)	exon (NM_001081043, exon 20 of 25)	20117	NM_001081043	104831	Mm.335477	NM_001081043	ENSMUSG00000036057	Ptpn23	AI462446|PTP-TD14	protein tyrosine phosphatase, non-receptor type 23	protein-coding
mm_15521.1	chr2	158375704	158375721	+	1	NA	promoter-TSS (NM_175692)	promoter-TSS (NM_175692)	74	NM_175692	319317	Mm.294494	NM_175692	ENSMUSG00000044349	Snhg11	A930034L06Rik|AI854265|AL022637|AW319638|E130013N09Rik	small nucleolar RNA host gene 11	protein-coding
mm_31969.1	chr4	88094661	88094672	+	1	NA	promoter-TSS (NM_001081184)	promoter-TSS (NM_001081184)	36	NM_001081184	230393	Mm.287210	NM_001081184	ENSMUSG00000038368	Focad	-	focadhesin	protein-coding
mm_6055.1	chr1	60098189	60098199	-	1	NA	promoter-TSS (NM_139150)	promoter-TSS (NM_139150)	-53	NM_001285463	241066	Mm.276441	NM_139150	ENSMUSG00000026017	Carf	Als2cr8|ECBRC-FC1|ECBRC-FC2	calcium response factor	protein-coding
mm_105225.1	chr11	102296257	102296316	-	1	NA	intron (NM_001098837, intron 1 of 12)	CpG	343	NM_001098836	217218	Mm.390381	NM_001098836	ENSMUSG00000059995	Atxn7l3	E030022H21Rik	ataxin 7-like 3	protein-coding
mm_164550.1	chr17	13590954	13590980	+	1	NA	Intergenic	Intergenic	-36873	NR_045437	72578	Mm.46549	NR_045436	ENSMUSG00000038347	2700054A10Rik	-	RIKEN cDNA 2700054A10 gene	ncRNA
mm_77663.1	chr8	124663412	124663432	-	1	NA	promoter-TSS (NM_175149)	promoter-TSS (NM_175149)	-53	NM_175149	69551	Mm.261920	NM_175149	ENSMUSG00000031983	2310022B05Rik	-	RIKEN cDNA 2310022B05 gene	protein-coding
mm_122050.1	chr14	30125092	30125140	-	1	NA	intron (NM_001302637, intron 12 of 48)	intron (NM_001302637, intron 12 of 48)	102483	NM_175343	218865	Mm.259916	NM_172264	ENSMUSG00000015970	Chdh	AU041472|D630034H06Rik	choline dehydrogenase	protein-coding
mm_11377.1	chr2	31152319	31152360	+	1	NA	promoter-TSS (NM_178760)	promoter-TSS (NM_178760)	23	NM_178760	277463	Mm.236074	NM_178760	ENSMUSG00000000194	Gpr107	9930033D15Rik|AI790205|C530034M11|mKIAA1624	G protein-coupled receptor 107	protein-coding
mm_58872.1	chr7	16983066	16983150	+	1	NA	Intergenic	Intergenic	-11480	NM_001101535	434130	Mm.459162	NM_001101535	ENSMUSG00000041117	Ccdc8	ENSMUSG00000041117	coiled-coil domain containing 8	protein-coding
mm_170899.1	chr2	30062243	30062254	+	1	NA	exon (NM_023871, exon 1 of 8)	exon (NM_023871, exon 1 of 8)	252	NM_023871	56086	Mm.326055	NM_023871	ENSMUSG00000054766	Set	2610030F17Rik|5730420M11Rik|AA407739|I-2PP2A|StF-IT-1|TAF-I	SET nuclear oncogene	protein-coding
mm_62166.1	chr7	97245380	97245389	+	1	NA	intron (NM_001162477, intron 2 of 9)	intron (NM_001162477, intron 2 of 9)	80580	NM_001177412	244144	Mm.297541	NM_001177412	ENSMUSG00000035713	Usp35	Gm1088|Gm493	ubiquitin specific peptidase 35	protein-coding
mm_11746.1	chr2	38351681	38351690	+	1	NA	5' UTR (NM_010710, exon 1 of 5)	5' UTR (NM_010710, exon 1 of 5)	377	NM_010710	16870	Mm.142856	NM_010710	ENSMUSG00000000247	Lhx2	LH2A|Lh-2|Lim2|ap|apterous	LIM homeobox protein 2	protein-coding
mm_83085.1	chr9	40239898	40239921	-	1	NA	Intergenic	RMER16A3|LTR|ERVK	-29307	NM_001083917	235281	Mm.290083	NM_153522	ENSMUSG00000049281	Scn3b	1110001K16Rik|4833414B02Rik|Scnb3	sodium channel, voltage-gated, type III, beta	protein-coding
mm_102549.1	chr11	61342822	61342868	-	1	NA	promoter-TSS (NM_001033542)	promoter-TSS (NM_001033542)	15	NM_001033542	380701	Mm.340166	NM_001033542	ENSMUSG00000069855	Slc47a2	4933429E10Rik	solute carrier family 47, member 2	protein-coding
mm_88221.1	chr10	70364843	70364872	+	1	NA	Intergenic	MIR|SINE|MIR	-75811	NM_001143777	71721	Mm.477813	NM_024244	ENSMUSG00000043259	Fam13c	1200015N20Rik|C030038O19Rik|mKIAA1796	family with sequence similarity 13, member C	protein-coding
mm_7181.1	chr1	92645725	92645731	-	1	NA	5' UTR (NM_153114, exon 2 of 5)	5' UTR (NM_153114, exon 2 of 5)	3113	NM_153114	260301	Mm.219545	NM_153114	ENSMUSG00000044055	Otos	OTOSP	otospiralin	protein-coding
mm_35294.1	chr4	22486562	22486572	-	1	NA	3' UTR (NM_008899, exon 1 of 1)	3' UTR (NM_008899, exon 1 of 1)	1799	NM_008899	18992	Mm.129387	NM_008899	ENSMUSG00000095139	Pou3f2	9430075J19Rik|A230098E07Rik|Brn-2|Brn2|OTF-7|Otf7|oct-7	POU domain, class 3, transcription factor 2	protein-coding
mm_102938.1	chr11	69601231	69601250	-	1	NA	3' UTR (NM_013415, exon 7 of 7)	3' UTR (NM_013415, exon 7 of 7)	4720	NM_013415	11932	Mm.235204	NM_013415	ENSMUSG00000041329	Atp1b2	Amog|Atpb-2	ATPase, Na+/K+ transporting, beta 2 polypeptide	protein-coding
mm_137530.1	chr17	27555520	27555528	+	1	NA	Intergenic	CpG	-1050	NM_001166536	15361	Mm.4438	NM_016660	ENSMUSG00000046711	Hmga1	AL023995|Hmga1a|Hmga1b|Hmgi|Hmgiy|Hmgy	high mobility group AT-hook 1	protein-coding
mm_144277.1	chr18	11657832	11657876	+	1	NA	intron (NR_045526, intron 1 of 17)	CpG	505	NM_001081223	225182	Mm.154275	NM_175458	ENSMUSG00000041238	Rbbp8	9930104E21Rik|CtIP|RBBP-8|RIM|SAE2	retinoblastoma binding protein 8	protein-coding
mm_148165.1	chr18	77767753	77767804	-	1	NA	promoter-TSS (NM_146089)	promoter-TSS (NM_146089)	2	NM_146089	225745	Mm.39293	NM_146089	ENSMUSG00000041840	Haus1	BC024400|Ccdc5|HEI-C	HAUS augmin-like complex, subunit 1	protein-coding
mm_29009.1	chr3	101604581	101604629	-	1	NA	5' UTR (NM_144900, exon 1 of 23)	5' UTR (NM_144900, exon 1 of 23)	102	NM_144900	11928	Mm.193670	NM_144900	ENSMUSG00000033161	Atp1a1	Atpa-1|BC010319	ATPase, Na+/K+ transporting, alpha 1 polypeptide	protein-coding
mm_92492.1	chr10	78307370	78307393	-	1	NA	intron (NM_053014, intron 2 of 9)	intron (NM_053014, intron 2 of 9)	32826	NR_106119	102465765		NR_106119	ENSMUSG00000098885	Mir7659	Gm27433|mmu-mir-7659	microRNA 7659	ncRNA
mm_93003.1	chr10	86885842	86885852	-	1	NA	intron (NM_138673, intron 42 of 68)	intron (NM_138673, intron 42 of 68)	106842	NM_175331	103466	Mm.200446	NM_175331	ENSMUSG00000054027	Nt5dc3	AU040402|AW540062|C630002B14Rik|TU12B1-TY	5'-nucleotidase domain containing 3	protein-coding
mm_122692.1	chr14	52020699	52020737	-	1	NA	promoter-TSS (NM_027248)	promoter-TSS (NM_027248)	15	NM_001253696	69890	Mm.475652	NM_027248	ENSMUSG00000049295	Zfp219	2010302A17Rik	zinc finger protein 219	protein-coding
mm_130656.1	chr15	100637110	100637155	-	1	NA	promoter-TSS (NM_174992)	promoter-TSS (NM_174992)	-192	NM_001033872	207818	Mm.26282	NM_174992	ENSMUSG00000053559	Smagp	-	small cell adhesion glycoprotein	protein-coding
mm_120058.1	chr14	56777642	56777701	+	1	NA	intron (NM_025682, intron 1 of 8)	CpG	645	NM_025682	66645	Mm.20129	NM_025682	ENSMUSG00000021938	Pspc1	5730470C09Rik|AI327109|AI449052|PSP1	paraspeckle protein 1	protein-coding
mm_101709.1	chr11	42000783	42000801	-	1	NA	promoter-TSS (NM_008073)	promoter-TSS (NM_008073)	-78	NM_008073	14406	Mm.5309	NM_008073	ENSMUSG00000020436	Gabrg2	GABAA-R|Gabrg-2|gamma2	gamma-aminobutyric acid (GABA) A receptor, subunit gamma 2	protein-coding
mm_61372.1	chr7	70360525	70360540	+	1	NA	promoter-TSS (NM_009697)	promoter-TSS (NM_009697)	61	NM_009697	11819	Mm.158143	NM_009697	ENSMUSG00000030551	Nr2f2	2700033K02Rik|9430015G03Rik|ARP-1|Aporp1|COUP-TF2|COUP-TFII|COUPTFB|EAR3|SVP40|Tcfcoup2	nuclear receptor subfamily 2, group F, member 2	protein-coding
mm_141011.1	chr17	25015690	25015703	-	1	NA	promoter-TSS (NM_020608)	promoter-TSS (NM_020608)	-390	NM_134126	106633	Mm.32802	NM_134126	ENSMUSG00000024169	Ift140	AI661311|Tce5|Wdtc2|mKIAA0590	intraflagellar transport 140	protein-coding
mm_28823.1	chr3	96290186	96290195	-	1	NA	intron (NM_010186, intron 3 of 5)	intron (NM_010186, intron 3 of 5)	3779	NM_010186	14129	Mm.150	NM_010186	ENSMUSG00000015947	Fcgr1	AI323638|AV092959|CD64|FcgammaRI|IGGHAFC	Fc receptor, IgG, high affinity I	protein-coding
mm_19166.1	chr2	84332088	84332104	-	1	NA	3' UTR (NM_018782, exon 16 of 16)	3' UTR (NM_018782, exon 16 of 16)	93170	NM_018782	54598	Mm.75467	NM_018782	ENSMUSG00000059588	Calcrl	AV071593|CRLR	calcitonin receptor-like	protein-coding
mm_90810.1	chr10	7780867	7780923	-	1	NA	promoter-TSS (NM_145418)	promoter-TSS (NM_145418)	22	NM_145418	215751	Mm.471825	NM_145418	ENSMUSG00000040006	Ginm1	AA589616	glycoprotein integral membrane 1	protein-coding
mm_137506.1	chr17	27029370	27029415	+	1	NA	promoter-TSS (NM_007523)	promoter-TSS (NM_007523)	133	NM_027544	70772	Mm.440437	NM_027544	ENSMUSG00000048731	Ggnbp1	0610031G08Rik|mdf	gametogenetin binding protein 1	protein-coding
mm_151603.1	chr19	3575703	3575705	-	1	NA	promoter-TSS (NM_028999)	promoter-TSS (NM_028999)	45	NM_001164159	52036	Mm.284686	NM_028999	ENSMUSG00000024908	Ppp6r3	4930528G08Rik|9130026N02Rik|D19Bwg1430e|D19Ertd703e|Pp6r3|Ppcs3|Pptcs3|Sapl|Saps3|mKIAA1558	protein phosphatase 6, regulatory subunit 3	protein-coding
mm_167658.1	chr9	70942827	70942841	+	1	NA	intron (NM_001324472, intron 1 of 9)	intron (NM_001324472, intron 1 of 9)	-8026	NM_008280	15450	Mm.390187	NM_008280	ENSMUSG00000032207	Lipc	AI256194|HL|Hpl	lipase, hepatic	protein-coding
mm_77350.1	chr8	119575128	119575138	-	1	NA	promoter-TSS (NM_026648)	promoter-TSS (NM_026648)	67	NM_175185	72552	Mm.36756	NM_175185	ENSMUSG00000034189	Hsdl1	2700067E09Rik	hydroxysteroid dehydrogenase like 1	protein-coding
mm_38591.1	chr4	141822264	141822266	-	1	NA	exon (NM_007919, exon 3 of 8)	exon (NM_007919, exon 3 of 8)	3740	NM_007919	13706	Mm.45316	NM_007919	ENSMUSG00000058579	Cela2a	Ela-2|Ela2|Ela2a	chymotrypsin-like elastase family, member 2A	protein-coding
mm_149411.1	chr19	11411858	11411903	+	1	NA	intron (NM_029499, intron 1 of 6)	intron (NM_029499, intron 1 of 6)	4219	NM_029499	64380	Mm.440715	NM_029499	ENSMUSG00000024675	Ms4a4c	5830413L19Rik|AI449185|Ms4a9	membrane-spanning 4-domains, subfamily A, member 4C	protein-coding
mm_50745.1	chr6	52737078	52737111	+	1	NA	exon (NM_025816, exon 7 of 18)	exon (NM_025816, exon 7 of 18)	23365	NM_025816	52440	Mm.389757	NM_025816	ENSMUSG00000004535	Tax1bp1	1200003J11Rik|1700069J21Rik|AA930106|D6Ertd404e|D6Ertd772e|T6bp|TXBP151	Tax1 (human T cell leukemia virus type I) binding protein 1	protein-coding
mm_103281.1	chr11	72207414	72207488	-	1	NA	promoter-TSS (NM_026559)	promoter-TSS (NM_026559)	-103	NM_026559	52700	Mm.27670	NM_026559	ENSMUSG00000020803	Txndc17	4831443O22Rik|D11Ertd672e|TRP14|Txnl5	thioredoxin domain containing 17	protein-coding
mm_13552.1	chr2	112242036	112242053	+	1	NA	exon (NM_207206, exon 3 of 14)	exon (NM_207206, exon 3 of 14)	2203	NM_207206	99010	Mm.33438	NM_207206	ENSMUSG00000027134	Lpcat4	AI505034|Agpat7|Aytl3|LPEAT2	lysophosphatidylcholine acyltransferase 4	protein-coding
mm_120604.1	chr14	70100084	70100144	+	1	NA	promoter-TSS (NM_021328)	promoter-TSS (NM_021328)	-31	NM_021328	57784	Mm.24186	NM_021328	ENSMUSG00000022089	Bin3	1700015F07Rik	bridging integrator 3	protein-coding
mm_116201.1	chr13	32338501	32338542	-	1	NA	promoter-TSS (NM_146041)	promoter-TSS (NM_146041)	23	NM_146041	218138	Mm.247143	NM_146041	ENSMUSG00000038372	Gmds	BC031788|C87208	GDP-mannose 4, 6-dehydratase	protein-coding
mm_170881.1	chr2	20900131	20900144	+	1	NA	intron (NM_001128084, intron 3 of 24)	LSU-rRNA_Hsa|rRNA|rRNA	67584	NM_001081364	71435	Mm.28507	NM_001081364	ENSMUSG00000036591	Arhgap21	5530401C11Rik|AA416458|ARHGAP10	Rho GTPase activating protein 21	protein-coding
mm_84498.1	chr9	66915494	66915508	-	1	NA	intron (NM_173413, intron 1 of 7)	intron (NM_173413, intron 1 of 7)	4204	NM_173413	235442	Mm.260376	NM_173413	ENSMUSG00000036943	Rab8b	5930437D16|D330025I23Rik	RAB8B, member RAS oncogene family	protein-coding
mm_76517.1	chr8	87470452	87470461	-	1	NA	intron (NM_019626, intron 2 of 2)	CpG	2136	NM_019626	12404	Mm.4880	NM_019626	ENSMUSG00000031654	Cbln1	AI323299	cerebellin 1 precursor protein	protein-coding
mm_41858.1	chr5	104440495	104440527	+	1	NA	exon (NM_001204203, exon 7 of 7)	exon (NM_001204203, exon 7 of 7)	4319	NM_001204233	20750	Mm.288474	NM_009263	ENSMUSG00000029304	Spp1	2AR|Apl-1|BNSP|BSPI|Bsp|ETA-1|Eta|OP|Opn|Opnl|Ric|Spp-1	secreted phosphoprotein 1	protein-coding
mm_123153.1	chr14	57104694	57104709	-	1	NA	promoter-TSS (NM_008125)	promoter-TSS (NM_008125)	1	NM_008125	14619	Mm.390683	NM_008125	ENSMUSG00000046352	Gjb2	AI325222|Cnx26|Cx26|Gjb-2	gap junction protein, beta 2	protein-coding
mm_71435.1	chr8	46506142	46506151	+	1	NA	intron (NM_001302163, intron 3 of 20)	intron (NM_001302163, intron 3 of 20)	15180	NM_001302163	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_112069.1	chr12	112405725	112405733	-	1	NA	Intergenic	Intergenic	17469	NR_036459	100504733	Mm.255309	NM_176956		A730018C14Rik	-	RIKEN cDNA A730018C14 gene	ncRNA
mm_6673.1	chr1	80340618	80340648	-	1	NA	promoter-TSS (NM_016716)	promoter-TSS (NM_016716)	57	NM_001313728	26554	Mm.12665	NM_016716	ENSMUSG00000004364	Cul3	KIAA0617	cullin 3	protein-coding
mm_85839.1	chr9	110532809	110532826	-	1	NA	intron (NM_001081340, intron 1 of 20)	CpG	220	NM_001081340	235626	Mm.288949	NM_001081340	ENSMUSG00000044791	Setd2	4921524K10Rik|BC031601|KMT3A	SET domain containing 2	protein-coding
mm_11882.1	chr2	49619253	49619272	+	1	NA	promoter-TSS (NM_008449)	promoter-TSS (NM_008449)	-52	NM_008449	16574	Mm.256342	NM_008449	ENSMUSG00000026764	Kif5c	KINN|Khc|NKHC|NKHC2	kinesin family member 5C	protein-coding
mm_85722.1	chr9	108305964	108305997	-	1	NA	promoter-TSS (NM_016802)	promoter-TSS (NM_016802)	179	NM_133986	102791	Mm.24670	NM_133986	ENSMUSG00000039461	Tcta	9130410M22Rik|AW553637|C85065|Tctal	T cell leukemia translocation altered gene	protein-coding
mm_170358.1	chr18	52529583	52529583	-	1	NA	5' UTR (NM_010728, exon 1 of 7)	5' UTR (NM_010728, exon 1 of 7)	138	NM_001286181	16948	Mm.172	NM_010728	ENSMUSG00000024529	Lox	AI893619|TSC-160|rrg	lysyl oxidase	protein-coding
mm_96938.1	chr11	70528915	70528930	+	1	NA	Intergenic	MT2A|LTR|ERVL	3565	NM_008946	19175	Mm.98	NM_008946	ENSMUSG00000018286	Psmb6	Lmp19|Mpnd	proteasome (prosome, macropain) subunit, beta type 6	protein-coding
mm_91060.1	chr10	18941597	18941601	-	1	NA	Intergenic	RLTR14_RN|LTR|ERV1	70364	NM_001166402	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_77625.1	chr8	123960192	123960211	-	1	NA	intron (NM_019552, intron 9 of 12)	intron (NM_019552, intron 9 of 12)	-10936	NM_172288	234865	Mm.267812	NM_172288	ENSMUSG00000039509	Nup133	mermaid	nucleoporin 133	protein-coding
mm_95890.1	chr11	58171649	58171688	+	1	NA	promoter-TSS (NM_175001)	promoter-TSS (NM_175001)	14	NM_175001	216767	Mm.259907	NM_175001	ENSMUSG00000020514	Mrpl22	E030011D16Rik|HSPC158|MRP-L25|Rpml25	mitochondrial ribosomal protein L22	protein-coding
mm_29089.1	chr3	104637558	104637561	-	1	NA	Intergenic	B1_Mur1|SINE|Alu	-1105	NM_009196	20501	Mm.9086	NM_009196	ENSMUSG00000032902	Slc16a1	AL022710|Mct1	solute carrier family 16 (monocarboxylic acid transporters), member 1	protein-coding
mm_5327.1	chr1	23383150	23383225	-	1	NA	promoter-TSS (NM_001081079)	promoter-TSS (NM_001081079)	-12	NM_001081079	70155	Mm.28013	NM_001081079	ENSMUSG00000026158	Ogfrl1	2210417C17Rik	opioid growth factor receptor-like 1	protein-coding
mm_96592.1	chr11	69090831	69090841	+	1	NA	3' UTR (NM_009497, exon 5 of 5)	3' UTR (NM_009497, exon 5 of 5)	2308	NM_009497	22318	Mm.28643	NM_009497	ENSMUSG00000020894	Vamp2	Syb-2|Syb2|sybII	vesicle-associated membrane protein 2	protein-coding
mm_9566.1	chr1	173979434	173979450	-	1	NA	intron (NM_008327, intron 1 of 6)	L1_Mur3|LINE|L1	3402	NM_008327	26388	Mm.218770	NM_008327	ENSMUSG00000026535	Ifi202b	Ifbip-1|Ifi202|Ifi202a|p202	interferon activated gene 202B	protein-coding
mm_135535.1	chr16	49770791	49770803	-	1	NA	Intergenic	Intergenic	71503	NM_028680	73916	Mm.241276	NM_028680	ENSMUSG00000032965	Ift57	4833420A15Rik|Esrrbl1|Hippi|MHS4R2	intraflagellar transport 57	protein-coding
mm_54363.1	chr6	31115088	31115104	-	1	NA	intron (NR_110471, intron 3 of 3)	intron (NR_110471, intron 3 of 3)	-52003	NR_029532	387223		NR_029532	ENSMUSG00000065604	Mir29b-1	Mirn29b|Mirn29b-1|mir-29b-1	microRNA 29b-1	ncRNA
mm_57847.1	chr6	129468896	129468909	-	1	NA	exon (NM_020008, exon 3 of 6)	exon (NM_020008, exon 3 of 6)	3877	NM_001309637	56644	Mm.239516	NM_020008	ENSMUSG00000079293	Clec7a	BGR|Clecsf12|beta-GR	C-type lectin domain family 7, member a	protein-coding
mm_94559.1	chr11	11641102	11641108	+	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	-13267	NM_001305143	102631730	Mm.159430	NM_001305143	ENSMUSG00000062511	4930512M02Rik	-	RIKEN cDNA 4930512M02 gene	protein-coding
mm_26553.1	chr3	146405009	146405030	+	1	NA	intron (NM_001253769, intron 1 of 13)	CpG	377	NM_138744	99167	Mm.200783	NM_138744	ENSMUSG00000036825	Ssx2ip	AU014939|AU042321|Adip	synovial sarcoma, X 2 interacting protein	protein-coding
mm_1069.1	chr1	59237469	59237493	+	1	NA	promoter-TSS (NM_001159948)	promoter-TSS (NM_001159948)	-250	NM_146109	74018	Mm.272078	NM_028717	ENSMUSG00000026024	Als2	3222402C23Rik|9430073A21Rik|Als2cr6|Alsin|mKIAA1563	amyotrophic lateral sclerosis 2 (juvenile)	protein-coding
mm_844.1	chr1	51987124	51987132	+	1	NA	promoter-TSS (NM_001308266)	promoter-TSS (NM_001308266)	-20	NM_001308266	20849	Mm.1550	NM_011487	ENSMUSG00000062939	Stat4	-	signal transducer and activator of transcription 4	protein-coding
mm_5399.1	chr1	33669796	33669806	-	1	NA	promoter-TSS (NR_033199)	promoter-TSS (NR_033199)	-7	NM_008922	19076	Mm.27705	NM_008922	ENSMUSG00000026134	Prim2	AI323589	DNA primase, p58 subunit	protein-coding
mm_6767.1	chr1	84115010	84115017	-	1	NA	intron (NM_001003948, intron 2 of 2)	MLT2B2|LTR|ERVL	103948	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_96603.1	chr11	69091174	69091178	+	1	NA	3' UTR (NM_009497, exon 5 of 5)	3' UTR (NM_009497, exon 5 of 5)	2648	NM_009497	22318	Mm.28643	NM_009497	ENSMUSG00000020894	Vamp2	Syb-2|Syb2|sybII	vesicle-associated membrane protein 2	protein-coding
mm_120204.1	chr14	61681978	61681986	+	1	NA	intron (NR_028264, intron 1 of 6)	CpG	391	NR_028264	668253	Mm.32886	NR_028264	ENSMUSG00000097589	Dleu2	1810047A16Rik|4932411A06Rik|7730401J12Rik|AI197277|AI788824|Alt1|Gm9069|Leu2	deleted in lymphocytic leukemia, 2	ncRNA
mm_64444.1	chr7	142653849	142653875	+	1	NA	exon (NM_010514, exon 4 of 4)	exon (NM_010514, exon 4 of 4)	1134	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_146537.1	chr18	5592432	5592469	-	1	NA	promoter-TSS (NR_033552)	promoter-TSS (NR_033552)	-13	NR_033552	791318	Mm.84339	NR_033552	ENSMUSG00000063087	Gm10125	ENSMUSG00000063087|Zeb1os	predicted gene 10125	ncRNA
mm_155886.1	chrX	101533520	101533536	+	1	NA	exon (NM_001290729, exon 2 of 39)	exon (NM_001290729, exon 2 of 39)	793	NM_001290729	270627	Mm.261750	NM_001081008	ENSMUSG00000031314	Taf1	AU015687|B430306D02Rik|Ccg-1|Ccg1|KAT4|N-TAF1|TAFII250|Taf2a|p250	TATA-box binding protein associated factor 1	protein-coding
mm_43907.1	chr5	144255806	144255823	+	1	NA	exon (NM_001163709, exon 2 of 3)	exon (NM_001163709, exon 2 of 3)	589	NM_018772	55950	Mm.38011	NM_018772	ENSMUSG00000047843	Bri3	I3	brain protein I3	protein-coding
mm_22262.1	chr2	178369373	178369382	-	1	NA	exon (NM_177191, exon 24 of 44)	exon (NM_177191, exon 24 of 44)	38281	NM_177191	320558	Mm.70781	NM_177191	ENSMUSG00000060445	Sycp2	3830402K23Rik|4930518F03Rik	synaptonemal complex protein 2	protein-coding
mm_40309.1	chr5	43842118	43842138	+	1	NA	3' UTR (NM_009763, exon 9 of 9)	3' UTR (NM_009763, exon 9 of 9)	23235	NM_009763	12182	Mm.246332	NM_009763	ENSMUSG00000029082	Bst1	114/A10|A530073F09|BP-3|Bp3|Bsta1|CD157|Ly65	bone marrow stromal cell antigen 1	protein-coding
mm_168174.1	chr10	56031081	56031084	+	1	NA	intron (NM_001033385, intron 31 of 32)	intron (NM_001033385, intron 31 of 32)	-75835	NM_001163833	73390	Mm.181475	NM_133751	ENSMUSG00000047669	Msl3l2	1700060H10Rik	male-specific lethal 3-like 2 (Drosophila)	protein-coding
mm_159219.1	chr2	127522107	127522107	-	1	NA	promoter-TSS (NR_110989)	promoter-TSS (NR_110989)	-13	NR_110989	56461	Mm.315292	NM_019789	ENSMUSG00000079056	Kcnip3	4933407H12Rik|AI413860|Csen|DREAM|KChIP3|R74849	Kv channel interacting protein 3, calsenilin	protein-coding
mm_69043.1	chr7	126800526	126800530	-	1	NA	promoter-TSS (NM_001177308)	promoter-TSS (NM_001177308)	-81	NM_001177308	11674	Mm.275831	NM_007438	ENSMUSG00000030695	Aldoa	Aldo-1|Aldo1	aldolase A, fructose-bisphosphate	protein-coding
mm_36573.1	chr4	87983283	87983306	-	1	NA	intron (NM_027326, intron 2 of 10)	intron (NM_027326, intron 2 of 10)	50113	NM_027326	70122	Mm.288898	NM_027326	ENSMUSG00000028496	Mllt3	2210011H10Rik|2610012I03Rik|3830408D16Rik|Af9|D4Ertd321e	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 3	protein-coding
mm_146831.1	chr18	21652363	21652373	-	1	NA	promoter-TSS (NM_001081403)	promoter-TSS (NM_001081403)	0	NM_001081403	225266	Mm.436836	NM_001081403	ENSMUSG00000042514	Klhl14	6330403N15Rik|AI785250|printor	kelch-like 14	protein-coding
mm_39130.1	chr4	155086249	155086265	-	1	NA	promoter-TSS (NM_001081100)	promoter-TSS (NM_001081100)	40	NM_026395	67830	Mm.241604	NM_026395	ENSMUSG00000029048	Rer1	1110060F11Rik|5830454N22Rik|AU043380	retention in endoplasmic reticulum sorting receptor 1	protein-coding
mm_32548.1	chr4	109385999	109386011	+	1	NA	3' UTR (NM_007943, exon 25 of 25)	3' UTR (NM_007943, exon 25 of 25)	20252	NR_131195	102635290	Mm.427859	NR_131195		Ttc39aos1	Gm12750|OTTMUSG00000008290|lincRNA-EPS	Ttc39a opposite strand RNA 1	ncRNA
mm_138056.1	chr17	33926658	33926676	+	1	NA	exon (NM_009318, exon 7 of 8)	exon (NM_009318, exon 7 of 8)	-3227	NM_009059	19732	Mm.43777	NM_009059	ENSMUSG00000041354	Rgl2	KE1.5|Rab2l|Rgt2|Rlf	ral guanine nucleotide dissociation stimulator-like 2	protein-coding
mm_25345.1	chr3	106722226	106722258	+	1	NA	intron (NM_028081, intron 1 of 2)	CpG	560	NM_001286685	321000	Mm.259638	NM_028081	ENSMUSG00000056260	Lrif1	2010012G17Rik|4933421E11Rik|AI450568	ligand dependent nuclear receptor interacting factor 1	protein-coding
mm_82293.1	chr9	7836800	7836810	-	1	NA	promoter-TSS (NM_001291503)	promoter-TSS (NM_001291503)	1	NM_001291503	11797	Mm.335659	NM_007465	ENSMUSG00000057367	Birc2	AW146227|Api1|Api2|Birc3|C-IAP1|C330006D17Rik|HIAP1|HIAP2|IAP1|IAP2|MIAP1|MIAP2|MIHB|MIHC|RNF48|cIAP1|cIAP2|mcIAP1	baculoviral IAP repeat-containing 2	protein-coding
mm_127934.1	chr15	10485957	10485967	-	1	NA	promoter-TSS (NM_011232)	promoter-TSS (NM_011232)	-25	NM_026396	67832	Mm.28057	NM_026396	ENSMUSG00000022247	Brix1	1110064N10Rik|Bxdc2|C76935	BRX1, biogenesis of ribosomes	protein-coding
mm_99449.1	chr11	102434127	102434134	+	1	NA	intron (NM_008175, intron 5 of 12)	intron (NM_008175, intron 5 of 12)	3808	NM_008175	14824	Mm.1568	NM_008175	ENSMUSG00000034708	Grn	Pgrn|epithelin	granulin	protein-coding
mm_130112.1	chr15	89476343	89476370	-	1	NA	5' UTR (NM_009713, exon 2 of 9)	5' UTR (NM_009713, exon 2 of 9)	104	NR_077233	100532730	Mm.461541	NR_077233		C230037L18Rik	-	RIKEN cDNA C230037L18 gene	ncRNA
mm_109097.1	chr12	104992584	104992594	+	1	NA	intron (NM_172500, intron 1 of 16)	intron (NM_172500, intron 1 of 16)	6088	NM_001042699	212073	Mm.212688	NM_172500	ENSMUSG00000054150	Syne3	nesprin-3	spectrin repeat containing, nuclear envelope family member 3	protein-coding
mm_49043.1	chr6	4760229	4760238	+	1	NA	3' UTR (NM_130877, exon 2 of 2)	3' UTR (NM_130877, exon 2 of 2)	12927	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_1513.1	chr1	72583246	72583282	+	1	NA	promoter-TSS (NM_018817)	promoter-TSS (NM_018817)	13	NM_018817	54380	Mm.274232	NM_018817	ENSMUSG00000039354	Smarcal1	6030401P21Rik|AI851716|Mharp	SWI/SNF related matrix associated, actin dependent regulator of chromatin, subfamily a-like 1	protein-coding
mm_32841.1	chr4	117835388	117835428	+	1	NA	5' UTR (NM_008135, exon 1 of 14)	5' UTR (NM_008135, exon 1 of 14)	150	NM_008135	14664	Mm.244549	NM_008135	ENSMUSG00000028542	Slc6a9	Glyt-1|Glyt1	solute carrier family 6 (neurotransmitter transporter, glycine), member 9	protein-coding
mm_61685.1	chr7	81005006	81005014	+	1	NA	intron (NM_178707, intron 1 of 9)	intron (NM_178707, intron 1 of 9)	11326	NM_178707	233410	Mm.29525	NM_178707	ENSMUSG00000005621	Zfp592	8430405N24|A730014M16Rik|Znf592|mKIAA0211	zinc finger protein 592	protein-coding
mm_116678.1	chr13	49242902	49242923	-	1	NA	intron (NM_028340, intron 1 of 4)	intron (NM_028340, intron 1 of 4)	5251	NM_025491	66329	Mm.34308	NM_025491	ENSMUSG00000021384	Susd3	1700017I11Rik|2810440J20Rik	sushi domain containing 3	protein-coding
mm_163372.1	chr12	41013304	41013313	+	1	NA	Intergenic	L1MC5a|LINE|L1	-10782	NM_053122	93757	Mm.363813	NM_053122	ENSMUSG00000056899	Immp2l	AI853880|IMP2	IMP2 inner mitochondrial membrane peptidase-like (S. cerevisiae)	protein-coding
mm_58996.1	chr7	19176417	19176440	+	1	NA	promoter-TSS (NM_001347582)	promoter-TSS (NM_001347582)	7	NM_001347582	72205	Mm.154121	NM_028153	ENSMUSG00000040811	Eml2	1600029N02Rik|EMAP-2	echinoderm microtubule associated protein like 2	protein-coding
mm_19530.1	chr2	94264746	94264764	-	1	NA	Intergenic	G-rich|Low_complexity|Low_complexity	-3356	NR_030431	735259		NR_030431	ENSMUSG00000076335	Mir670	Mirn670|mir-670|mmu-mir-670	microRNA 670	ncRNA
mm_171094.1	chr3	12855820	12855820	+	1	NA	Intergenic	Intergenic	-615835	NM_178631	76897	Mm.422625	NM_178631	ENSMUSG00000039717	Ralyl	0710005M24Rik	RALY RNA binding protein-like	protein-coding
mm_25554.1	chr3	116008326	116008372	+	1	NA	promoter-TSS (NM_001163514)	promoter-TSS (NM_001163514)	52	NM_001163514	58193	Mm.41739	NM_021388	ENSMUSG00000027963	Extl2	3000001D04Rik|AW146439	exostoses (multiple)-like 2	protein-coding
mm_102126.1	chr11	53423124	53423135	-	1	NA	promoter-TSS (NM_153069)	promoter-TSS (NM_153069)	7	NM_153069	259301	Mm.24283	NM_153069	ENSMUSG00000036216	Leap2	leap-2	liver-expressed antimicrobial peptide 2	protein-coding
mm_45860.1	chr5	87843408	87843410	-	1	NA	exon (NM_001163551, exon 5 of 6)	exon (NM_001163551, exon 5 of 6)	-6950	NR_003652	654494	Mm.475331	NM_001039193	ENSMUSG00000067156	Gm7337	EG654494	DAZ interacting protein 1 pseudogene	pseudo
mm_136332.1	chr16	92400068	92400083	-	1	NA	promoter-TSS (NM_019466)	promoter-TSS (NM_019466)	3	NM_019466	54720	Mm.265744	NM_019466	ENSMUSG00000022951	Rcan1	Adapt78|CALP1L|CSP1|DSC1|Dscr1|MCIP1|RCN1	regulator of calcineurin 1	protein-coding
mm_97044.1	chr11	72361912	72361926	+	1	NA	promoter-TSS (NM_011569)	promoter-TSS (NM_011569)	-37	NM_011569	21689	Mm.42257	NM_011569	ENSMUSG00000020799	Tekt1	MT14	tektin 1	protein-coding
mm_49308.1	chr6	18169792	18169812	+	1	NA	promoter-TSS (NM_021050)	promoter-TSS (NM_021050)	-885	NM_021050	12638	Mm.15621	NM_021050	ENSMUSG00000041301	Cftr	AW495489|Abcc7	cystic fibrosis transmembrane conductance regulator	protein-coding
mm_112594.1	chr13	14063777	14063822	+	1	NA	promoter-TSS (NM_001331176)	promoter-TSS (NM_001331176)	15	NM_198122	94246	Mm.439784	NM_194262	ENSMUSG00000039219	Arid4b	BCAA|BRCAA1|RBBP1L1|Rbp1l1|SAP180	AT rich interactive domain 4B (RBP1-like)	protein-coding
mm_90486.1	chr10	127902042	127902056	+	1	NA	intron (NM_027301, intron 1 of 3)	intron (NM_027301, intron 1 of 3)	3514	NM_027301	70061	Mm.158320	NM_027301	ENSMUSG00000040127	Sdr9c7	1810054F20Rik|Rdh20|Rdhs|SDR-O|Sdro	4short chain dehydrogenase/reductase family 9C, member 7	protein-coding
mm_84116.1	chr9	58462820	58462826	-	1	NA	intron (NR_040736, intron 1 of 2)	intron (NR_040736, intron 1 of 2)	7650	NR_040736	74879	Mm.416924	NR_040736	ENSMUSG00000097651	4930461G14Rik	-	RIKEN cDNA 4930461G14 gene	ncRNA
mm_155978.1	chrX	106126851	106126871	+	1	NA	3' UTR (NM_009726, exon 23 of 23)	3' UTR (NM_009726, exon 23 of 23)	-16414	NM_205820	279572	Mm.336203	NM_205820	ENSMUSG00000033777	Tlr13	AI666735|Gm713	toll-like receptor 13	protein-coding
mm_43021.1	chr5	123907597	123907607	+	1	NA	intron (NM_026603, intron 1 of 7)	intron (NM_026603, intron 1 of 7)	327	NM_026603	68184	Mm.28549	NM_026603	ENSMUSG00000023106	Denr	1500003K04Rik	density-regulated protein	protein-coding
mm_77579.1	chr8	123655324	123655324	-	1	NA	intron (NM_133955, intron 1 of 2)	intron (NM_133955, intron 1 of 2)	1395	NM_133955	69581	Mm.168257	NM_133955	ENSMUSG00000039960	Rhou	2310026M05Rik|AI182090|Arhu|CDC42L1|G28K|WRCH-1|WRCH1|mG28K	ras homolog family member U	protein-coding
mm_56750.1	chr6	115994886	115994888	-	1	NA	5' UTR (NM_026376, exon 1 of 36)	5' UTR (NM_026376, exon 1 of 36)	118	NM_026376	67784	Mm.3085	NM_026376	ENSMUSG00000030123	Plxnd1	6230425C21Rik|b2b1863Clo|b2b553Clo	plexin D1	protein-coding
mm_26930.1	chr3	20262445	20262530	-	1	NA	exon (NM_029706, exon 9 of 11)	exon (NM_029706, exon 9 of 11)	13246	NM_029706	76703	Mm.34692	NM_029706	ENSMUSG00000011463	Cpb1	0910001A18Rik|1810063F02Rik|2210008M23Rik|AI504870	carboxypeptidase B1 (tissue)	protein-coding
mm_130463.1	chr15	98609315	98609344	-	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	-1696	NM_007405	11512	Mm.157091	NM_007405	ENSMUSG00000022994	Adcy6	AC6|mKIAA0422	adenylate cyclase 6	protein-coding
mm_125298.1	chr15	37090357	37090370	+	1	NA	Intergenic	Intergenic	-82961	NM_026521	68036	Mm.371631	NM_026521	ENSMUSG00000062397	Zfp706	3110006P09Rik|AA793007|AW536850|C77232|Znf706	zinc finger protein 706	protein-coding
mm_40131.1	chr5	35042288	35042334	+	1	NA	exon (NM_019447, exon 2 of 14)	exon (NM_019447, exon 2 of 14)	802	NM_019447	54426	Mm.27369	NM_019447	ENSMUSG00000029102	Hgfac	HGFA	hepatocyte growth factor activator	protein-coding
mm_48100.1	chr5	137066961	137066971	-	1	NA	exon (NM_008871, exon 5 of 9)	exon (NM_008871, exon 5 of 9)	5306	NM_008871	18787	Mm.250422	NM_008871	ENSMUSG00000037411	Serpine1	PAI-1|PAI1|Planh1	serine (or cysteine) peptidase inhibitor, clade E, member 1	protein-coding
mm_10843.1	chr2	24975309	24975320	+	1	NA	promoter-TSS (NM_001031808)	promoter-TSS (NM_001031808)	-216	NM_001031808	107733	Mm.23010	NM_001031808	ENSMUSG00000036850	Mrpl41	MRP-L27|Rpml27	mitochondrial ribosomal protein L41	protein-coding
mm_34399.1	chr4	145209972	145209980	+	1	NA	Intergenic	Intergenic	-14971	NM_001276465	230895	Mm.240310	NM_001033190	ENSMUSG00000020220	Vps13d	-	vacuolar protein sorting 13D	protein-coding
mm_153817.1	chr19	46186828	46186833	-	1	NA	intron (NM_178930, intron 3 of 39)	intron (NM_178930, intron 3 of 39)	34272	NM_178930	107338	Mm.271620	NM_178930	ENSMUSG00000025224	Gbf1	1700083E03Rik|AI035702|AW049900|mKIAA0248	golgi-specific brefeldin A-resistance factor 1	protein-coding
mm_36579.1	chr4	88032770	88032802	-	1	NA	intron (NM_027326, intron 1 of 10)	CpG	621	NM_027326	70122	Mm.288898	NM_027326	ENSMUSG00000028496	Mllt3	2210011H10Rik|2610012I03Rik|3830408D16Rik|Af9|D4Ertd321e	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 3	protein-coding
mm_131054.1	chr16	4068895	4068921	+	1	NA	exon (NM_026508, exon 2 of 18)	exon (NM_026508, exon 2 of 18)	8902	NM_026508	68015	Mm.123366	NM_026508	ENSMUSG00000005981	Trap1	2410002K23Rik|HSP75	TNF receptor-associated protein 1	protein-coding
mm_157093.1	chrX	9437202	9437213	-	1	NA	3' UTR (NM_007807, exon 13 of 13)	3' UTR (NM_007807, exon 13 of 13)	32117	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_46900.1	chr5	114128172	114128219	-	1	NA	promoter-TSS (NM_175016)	promoter-TSS (NM_175016)	-19	NM_175016	231642	Mm.332593	NM_175016	ENSMUSG00000044339	Alkbh2	9530023G02|AU016977|Abh2|mABH2	alkB homolog 2, alpha-ketoglutarate-dependent dioxygenase	protein-coding
mm_105940.1	chr11	115187828	115187836	-	1	NA	promoter-TSS (NM_025400)	promoter-TSS (NM_025400)	345	NM_001033393	320534	Mm.260587	NM_001033393	ENSMUSG00000045980	Tmem104	C630005D06Rik|mFLJ00021	transmembrane protein 104	protein-coding
mm_140318.1	chr17	86360322	86360335	+	1	NA	intron (NM_011104, intron 2 of 14)	intron (NM_011104, intron 2 of 14)	-73150	NR_045435	72104	Mm.443401	NR_045435	ENSMUSG00000100738	2010106C02Rik	-	RIKEN cDNA 2010106C02 gene	ncRNA
mm_51404.1	chr6	78373227	78373236	+	1	NA	exon (NM_011036, exon 6 of 6)	exon (NM_011036, exon 6 of 6)	2346	NM_011036	18489	Mm.2553	NM_011036	ENSMUSG00000071356	Reg3b	HIP|PAP1|Pap|REG-III	regenerating islet-derived 3 beta	protein-coding
mm_65398.1	chr7	25179774	25179786	-	1	NA	Intergenic	CpG	24711	NR_045848	434147	Mm.59171	NM_001033781	ENSMUSG00000074274	D930028M14Rik	EG434147	RIKEN cDNA D930028M14 gene	ncRNA
mm_123401.1	chr14	63500164	63500190	-	1	NA	exon (NM_021480, exon 2 of 9)	exon (NM_021480, exon 2 of 9)	8915	NM_021480	58865	Mm.354229	NM_021480	ENSMUSG00000021953	Tdh	-	L-threonine dehydrogenase	protein-coding
mm_149348.1	chr19	10859888	10859898	+	1	NA	intron (NM_133804, intron 9 of 10)	intron (NM_133804, intron 9 of 10)	9886	NM_133804	98170	Mm.490254	NM_133804	ENSMUSG00000024736	Tmem132a	6720481D13Rik|Hspa5bp1|Orai1|R74613	transmembrane protein 132A	protein-coding
mm_153781.1	chr19	45783513	45783558	-	1	NA	promoter-TSS (NM_023799)	promoter-TSS (NM_023799)	-244	NM_023799	76055	Mm.122725	NM_023799	ENSMUSG00000025220	Mgea5	2810009A20Rik|4833427O07Rik|5830447M11Rik|AA408215|Hy5|Ncoat|OGA|mKIAA0679	meningioma expressed antigen 5 (hyaluronidase)	protein-coding
mm_96519.1	chr11	68496451	68496457	+	1	NA	3' UTR (NM_177320, exon 19 of 19)	3' UTR (NM_177320, exon 19 of 19)	-6565	NM_001004435	104709	Mm.234573	NM_001004435	ENSMUSG00000046207	Pik3r6	BB220380|p84|p84 PIKAP|p87(PIKAP)|p87PIKAP	phosphoinositide-3-kinase, regulatory subunit 6	protein-coding
mm_149259.1	chr19	10525316	10525326	+	1	NA	promoter-TSS (NM_025333)	promoter-TSS (NM_025333)	77	NM_172302	269061	Mm.490260	NM_172302	ENSMUSG00000034820	Cpsf7	5730453I16Rik|AL022757|C330017N18Rik	cleavage and polyadenylation specific factor 7	protein-coding
mm_48046.1	chr5	136458508	136458520	-	1	NA	intron (NM_001291239, intron 2 of 22)	intron (NM_001291239, intron 2 of 22)	-82711	NR_030500	723975		NR_030500	ENSMUSG00000106479	Mir721	Mirn721|miRY|mir-721|mmu-mir-721	microRNA 721	ncRNA
mm_75329.1	chr8	43180254	43180258	-	1	NA	Intergenic	B1F|SINE|Alu	-2866	NM_001160412	622117	Mm.390031	NM_001160412	ENSMUSG00000091490	Triml2	EG622117|Tu4	tripartite motif family-like 2	protein-coding
mm_19640.1	chr2	102835780	102835808	-	1	NA	intron (NM_001177786, intron 5 of 11)	intron (NM_001177786, intron 5 of 11)	65871	NM_001177785	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_95058.1	chr11	32405628	32405631	+	1	NA	intron (NM_177364, intron 7 of 12)	intron (NM_177364, intron 7 of 12)	-49743	NM_173784	327900	Mm.260956	NM_173784	ENSMUSG00000044949	Ubtd2	4930571L24|9630054F20Rik|AI645720	ubiquitin domain containing 2	protein-coding
mm_143093.1	chr17	57080659	57080662	-	1	NA	3' UTR (NM_009451, exon 4 of 4)	3' UTR (NM_009451, exon 4 of 4)	-2150	NM_153551	70785	Mm.284447	NM_153551	ENSMUSG00000002668	Dennd1c	4432409M07Rik	DENN/MADD domain containing 1C	protein-coding
mm_103154.1	chr11	70394412	70394428	-	1	NA	exon (NM_029231, exon 16 of 17)	exon (NM_029231, exon 16 of 17)	15611	NM_029231	75273	Mm.340601	NM_029231	ENSMUSG00000018921	Pelp1	4930563C04Rik|MNAR	proline, glutamic acid and leucine rich protein 1	protein-coding
mm_116892.1	chr13	55362588	55362630	-	1	NA	5' UTR (NM_025828, exon 1 of 8)	5' UTR (NM_025828, exon 1 of 8)	174	NM_025828	66890	Mm.38868	NM_025828	ENSMUSG00000021484	Lman2	1110003H06Rik|1300009F09Rik|AA408240|AL023023|AU040819|GP36B|VIP36	lectin, mannose-binding 2	protein-coding
mm_10688.1	chr2	22622249	22622260	+	1	NA	promoter-TSS (NM_008078)	promoter-TSS (NM_008078)	-73	NM_008078	14417	Mm.4784	NM_008078	ENSMUSG00000026787	Gad2	6330404F12Rik|GAD(65)|GAD65|Gad-2	glutamic acid decarboxylase 2	protein-coding
mm_24774.1	chr3	95530182	95530200	+	1	NA	intron (NM_001267695, intron 2 of 7)	intron (NM_001267695, intron 2 of 7)	3405	NM_001267695	13040	Mm.3619	NM_021281	ENSMUSG00000038642	Ctss	Cats	cathepsin S	protein-coding
mm_71073.1	chr8	34154700	34154730	+	1	NA	exon (NM_026432, exon 1 of 6)	exon (NM_026432, exon 1 of 6)	152	NM_026432	67887	Mm.290353	NM_026432	ENSMUSG00000031532	Saraf	1810045K07Rik|Tmem66	store-operated calcium entry-associated regulatory factor	protein-coding
mm_130187.1	chr15	93595878	93595909	-	1	NA	promoter-TSS (NM_001033217)	promoter-TSS (NM_001033217)	-2	NM_001033217	106042	Mm.150314	NM_001033217	ENSMUSG00000036158	Prickle1	1110058P22Rik|AW215793|Prickle|b2b019Clo|mpk1	prickle planar cell polarity protein 1	protein-coding
mm_84360.1	chr9	64737635	64737645	-	1	NA	5' UTR (NM_017382, exon 1 of 5)	5' UTR (NM_017382, exon 1 of 5)	116	NM_017382	53869	Mm.1387	NM_017382	ENSMUSG00000004771	Rab11a	-	RAB11A, member RAS oncogene family	protein-coding
mm_12275.1	chr2	68999948	68999961	+	1	NA	intron (NM_172856, intron 3 of 9)	intron (NM_172856, intron 3 of 9)	-135846	NM_181547	329416	Mm.90047	NM_181547	ENSMUSG00000034738	Nostrin	Daip2|mDaIP2	nitric oxide synthase trafficker	protein-coding
mm_41720.1	chr5	102207198	102207224	+	1	NA	Intergenic	Intergenic	-137290	NM_172882	72145	Mm.332522	NM_172882	ENSMUSG00000043940	Wdfy3	2610509D04Rik|ALFY|AW319683|B930017C24|BWF1|Bchs|D5Ertd66e|Ggtb3|ZFYVE25|mKIAA0993	WD repeat and FYVE domain containing 3	protein-coding
mm_84703.1	chr9	72663305	72663326	-	1	NA	intron (NM_010890, intron 1 of 28)	intron (NM_010890, intron 1 of 28)	968	NM_010890	17999	Mm.279923	NM_010890	ENSMUSG00000032216	Nedd4	AA959633|AL023035|AU019897|E430025J12Rik|Nedd4-1|Nedd4a|mKIAA0093	neural precursor cell expressed, developmentally down-regulated 4	protein-coding
mm_3911.1	chr1	161968954	161968971	+	1	NA	promoter-TSS (NM_026078)	promoter-TSS (NM_026078)	186	NM_001204905	75368	Mm.108728	NM_001204904	ENSMUSG00000086277	4930558K02Rik	-	RIKEN cDNA 4930558K02 gene	protein-coding
mm_1861.1	chr1	84939322	84939343	+	1	NA	Intergenic	Intergenic	-4249	NM_027921	71781	Mm.158754	NM_027921	ENSMUSG00000026220	Slc16a14	1110004H10Rik	solute carrier family 16 (monocarboxylic acid transporters), member 14	protein-coding
mm_89714.1	chr10	98798912	98798922	+	1	NA	Intergenic	Intergenic	-116235	NM_026482	67972	Mm.166944	NM_026482	ENSMUSG00000019943	Atp2b1	2810442I22Rik|E130111D10Rik|Pmca1	ATPase, Ca++ transporting, plasma membrane 1	protein-coding
mm_37844.1	chr4	132148918	132148931	-	1	NA	Intergenic	Intergenic	-4438	NM_013622	18386	Mm.5243	NM_013622	ENSMUSG00000050511	Oprd1	DOR|DOR-1|Nbor|mDOR	opioid receptor, delta 1	protein-coding
mm_2005.1	chr1	87127331	87127338	+	1	NA	exon (NM_007432, exon 10 of 11)	exon (NM_007432, exon 10 of 11)	2326	NM_007432	11648	Mm.377076	NM_007432	ENSMUSG00000036500	Akp3	Akp-3|IAP|dIAP	alkaline phosphatase 3, intestine, not Mn requiring	protein-coding
mm_97899.1	chr11	83409656	83409718	+	1	NA	promoter-TSS (NM_001013386)	promoter-TSS (NM_001013386)	-385	NM_001013386	276952	Mm.66275	NM_001013386	ENSMUSG00000020684	Rasl10b	B230331P10Rik|Gm729|VTS58635	RAS-like, family 10, member B	protein-coding
mm_63220.1	chr7	126293818	126293831	+	1	NA	3' UTR (NM_145587, exon 4 of 4)	3' UTR (NM_145587, exon 4 of 4)	21205	NM_145587	104175	Mm.29660	NM_145587	ENSMUSG00000042978	Sbk1	Sbk	SH3-binding kinase 1	protein-coding
mm_150613.1	chr19	40908666	40908673	+	1	NA	intron (NM_028319, intron 3 of 4)	intron (NM_028319, intron 3 of 4)	13964	NM_028319	72672	Mm.313523	NM_028319	ENSMUSG00000049164	Zfp518a	2810401C22Rik|6330417C12Rik|AI426493|Zfp518|Znf518|Znf518a|mKIAA0335	zinc finger protein 518A	protein-coding
mm_100012.1	chr11	114878014	114878038	+	1	NA	Intergenic	RLTR15|LTR|ERVK	-12015	NM_001347654	217303	Mm.294439	NM_170758	ENSMUSG00000034652	Cd300a	B230315M08Rik|Clm8|LMIR1|MAIR-I|MAIR-Ia|MMAC8|Pigr4|mcpir1	CD300A molecule	protein-coding
mm_155304.1	chrX	61185879	61185889	+	1	NA	promoter-TSS (NM_001166658)	promoter-TSS (NM_001166658)	-326	NM_001166658	631990	Mm.401324	NM_001166658	ENSMUSG00000090546	Cdr1	100039759|Cdr|Cdr34|EG631990|Gm2409|Gm7077	cerebellar degeneration related antigen 1	protein-coding
mm_19642.1	chr2	102835892	102835911	-	1	NA	intron (NM_001177786, intron 5 of 11)	intron (NM_001177786, intron 5 of 11)	65764	NM_001177785	12505	Mm.423621	NM_009851	ENSMUSG00000005087	Cd44	AU023126|AW121933|AW146109|HERMES|Ly-24|Pgp-1	CD44 antigen	protein-coding
mm_42230.1	chr5	113539048	113539053	+	1	NA	Intergenic	Intergenic	-11370	NM_177292	320916	Mm.102783	NM_177292	ENSMUSG00000063430	Wscd2	4933413A10Rik|C530024P05Rik|Gm450	WSC domain containing 2	protein-coding
mm_45493.1	chr5	71658092	71658115	-	1	NA	5' UTR (NM_010251, exon 1 of 9)	5' UTR (NM_010251, exon 1 of 9)	205	NM_010251	14397	Mm.248731	NM_010251	ENSMUSG00000029211	Gabra4	Gabra-4	gamma-aminobutyric acid (GABA) A receptor, subunit alpha 4	protein-coding
mm_21065.1	chr2	152792576	152792585	-	1	NA	intron (NM_001289717, intron 2 of 2)	intron (NM_001289717, intron 2 of 2)	38137	NM_001289716	12048	Mm.238213	NM_009743	ENSMUSG00000007659	Bcl2l1	Bcl(X)L|Bcl-XL|Bcl2l|BclX|bcl-x|bcl2-L-1	BCL2-like 1	protein-coding
mm_47686.1	chr5	129008495	129008537	-	1	NA	promoter-TSS (NM_007941)	promoter-TSS (NM_007941)	56	NM_001286034	13852	Mm.260716	NM_007941	ENSMUSG00000029428	Stx2	AW538950|Epim|G1-536-1|Syn-2|repro34	syntaxin 2	protein-coding
mm_159281.1	chr2	165877583	165877583	-	1	NA	5' UTR (NM_001291158, exon 1 of 24)	5' UTR (NM_001291158, exon 1 of 24)	854	NM_001291158	228880	Mm.227598	NM_027230	ENSMUSG00000039671	Zmynd8	1110013E22Rik|2010005I16Rik|3632413B07Rik|AI316811|AL024039|Prkcbp1|RACK7	zinc finger, MYND-type containing 8	protein-coding
mm_48286.1	chr5	138172359	138172365	-	1	NA	promoter-TSS (NM_008568)	promoter-TSS (NM_008568)	341	NM_021392	11781	Mm.113205	NM_021392	ENSMUSG00000019518	Ap4m1	4930443L05Rik|Ap4m4	adaptor-related protein complex AP-4, mu 1	protein-coding
mm_157070.1	chrX	8193388	8193397	-	1	NA	TTS (NM_145907)	TTS (NM_145907)	120	NM_007898	13595	Mm.27183	NM_007898	ENSMUSG00000031168	Ebp	AI255399|Pabp|SI|Td|mSI	phenylalkylamine Ca2+ antagonist (emopamil) binding protein	protein-coding
mm_12866.1	chr2	83812649	83812701	+	1	NA	promoter-TSS (NM_175514)	promoter-TSS (NM_175514)	-53	NM_175514	241520	Mm.330351	NM_175514	ENSMUSG00000048388	Fam171b	D430039N05Rik	family with sequence similarity 171, member B	protein-coding
mm_127780.1	chr15	3542351	3542361	-	1	NA	intron (NM_001048178, intron 1 of 8)	Tigger7|DNA|TcMar-Tigger	39486	NM_001286370	14600	Mm.3986	NM_010284	ENSMUSG00000055737	Ghr	GHBP|GHR/BP	growth hormone receptor	protein-coding
mm_25750.1	chr3	123267446	123267500	+	1	NA	promoter-TSS (NM_027135)	promoter-TSS (NM_027135)	-23	NM_027135	69608	Mm.29293	NM_027135	ENSMUSG00000039234	Sec24d	2310020L09Rik|Gm1349	Sec24 related gene family, member D (S. cerevisiae)	protein-coding
mm_99653.1	chr11	105634541	105634546	+	1	NA	intron (NM_181071, intron 2 of 25)	intron (NM_181071, intron 2 of 25)	44557	NM_181071	77097	Mm.22501	NM_175492	ENSMUSG00000053580	Tanc2	3526402J09Rik|5730590C14Rik	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2	protein-coding
mm_24789.1	chr3	95545355	95545365	+	1	NA	exon (NM_021281, exon 5 of 8)	exon (NM_021281, exon 5 of 8)	-14317	NM_026489	67981	Mm.179050	NM_026489	ENSMUSG00000028109	Hormad1	4921522K05Rik|Nohma	HORMA domain containing 1	protein-coding
mm_53316.1	chr6	129186045	129186049	+	1	NA	3' UTR (NM_053109, exon 5 of 5)	3' UTR (NM_053109, exon 5 of 5)	5432	NM_053109	93694	Mm.197536	NM_053109	ENSMUSG00000030157	Clec2d	Clr-b|Clrb|Ocil	C-type lectin domain family 2, member d	protein-coding
mm_123106.1	chr14	55882871	55882902	-	1	NA	3' UTR (NM_019820, exon 3 of 3)	3' UTR (NM_019820, exon 3 of 3)	1370	NM_019820	56410	Mm.97163	NM_019820	ENSMUSG00000040380	Cbln3	-	cerebellin 3 precursor protein	protein-coding
mm_152094.1	chr19	6909565	6909596	-	1	NA	promoter-TSS (NM_026306)	promoter-TSS (NM_026306)	65	NM_012021	54683	Mm.279782	NM_012021	ENSMUSG00000024953	Prdx5	AOEB166|AOPP|Pmp20|Prdx6|PrxV	peroxiredoxin 5	protein-coding
mm_124066.1	chr14	78536763	78536851	-	1	NA	promoter-TSS (NM_001164503)	promoter-TSS (NM_001164503)	53	NM_001164503	219181	Mm.89413	NM_001164503	ENSMUSG00000022016	Akap11	6330501D17Rik|AKAP220|Gm80|PRKA11|mKIAA0629	A kinase (PRKA) anchor protein 11	protein-coding
mm_117029.1	chr13	58274097	58274115	-	1	NA	promoter-TSS (NM_019832)	promoter-TSS (NM_019832)	82	NM_019832	56278	Mm.296625	NM_019832	ENSMUSG00000021552	Gkap1	42kDa|4933400B15Rik|D13Ertd340e|Gkap42	G kinase anchoring protein 1	protein-coding
mm_95158.1	chr11	35889112	35889118	+	1	NA	intron (NM_170779, intron 7 of 22)	intron (NM_170779, intron 7 of 22)	-54587	NM_025936	104458	Mm.284906	NM_025936	ENSMUSG00000018848	Rars	2610011N19Rik|2610037E21Rik|AL033339|AW985894	arginyl-tRNA synthetase	protein-coding
mm_147399.1	chr18	44555871	44555920	-	1	NA	intron (NM_001085373, intron 3 of 18)	L2b|LINE|L2	-105770	NR_026853	626275	Mm.427116	NR_026853	ENSMUSG00000097610	A930012L18Rik	-	RIKEN cDNA A930012L18 gene	ncRNA
mm_142755.1	chr17	48738731	48738758	-	1	NA	Intergenic	MIRb|SINE|MIR	-193838	NM_027452	70530	Mm.133607	NM_027452	ENSMUSG00000040490	Lrfn2	5730420O05Rik|SALM1|mKIAA1246	leucine rich repeat and fibronectin type III domain containing 2	protein-coding
mm_144411.1	chr18	20961481	20961511	+	1	NA	intron (NM_026301, intron 1 of 5)	CpG	16871	NM_026301	67664	Mm.45980	NM_026301	ENSMUSG00000033107	Rnf125	4930553F04Rik	ring finger protein 125	protein-coding
mm_128735.1	chr15	64285289	64285296	-	1	NA	intron (NM_010026, intron 3 of 30)	intron (NM_010026, intron 3 of 30)	27381	NM_001276462	13196	Mm.277236	NM_010026	ENSMUSG00000022377	Asap1	AV239055|DEF-1|Ddef1|PAP|mKIAA1249|s19	ArfGAP with SH3 domain, ankyrin repeat and PH domain1	protein-coding
mm_50955.1	chr6	58831881	58831898	+	1	NA	Intergenic	L1M4b|LINE|L1	-1811	NM_028705	73998	Mm.191892	NM_028705	ENSMUSG00000029804	Herc3	5730409F18Rik|AI646603|mKIAA0032	hect domain and RLD 3	protein-coding
mm_118508.1	chr14	14012628	14012693	+	1	NA	5' UTR (NM_139227, exon 1 of 12)	5' UTR (NM_139227, exon 1 of 12)	169	NM_139227	246103	Mm.133625	NM_139227	ENSMUSG00000021738	Atxn7	A430107N12Rik|AI627028|Sca7|ataxin-7	ataxin 7	protein-coding
mm_97569.1	chr11	78937889	78937898	+	1	NA	exon (NM_010927, exon 9 of 27)	exon (NM_010927, exon 9 of 27)	12602	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_57302.1	chr6	124636877	124636878	-	1	NA	promoter-TSS (NM_173864)	promoter-TSS (NM_173864)	-792	NM_173864	317677	Mm.483270	NM_173864	ENSMUSG00000079343	C1s2	C1sb|EG317677|Gm5077	complement component 1, s subcomponent 2	protein-coding
mm_9323.1	chr1	171770939	171770946	-	1	NA	intron (NM_013730, intron 1 of 6)	intron (NM_013730, intron 1 of 6)	3810	NM_013730	27218	Mm.103648	NM_013730	ENSMUSG00000015316	Slamf1	4933415F16|AA177906|CD150|CDw150|ESTM51|IPO-3|Slam	signaling lymphocytic activation molecule family member 1	protein-coding
mm_112756.1	chr13	19343443	19343459	+	1	NA	Intergenic	Intergenic	52362	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_74549.1	chr8	10741002	10741027	-	1	NA	Intergenic	Intergenic	141440	NR_040705	320014	Mm.403203	NR_040705	ENSMUSG00000109473	B930025P03Rik	-	RIKEN cDNA B930025P03 gene	ncRNA
mm_59030.1	chr7	19304308	19304311	+	1	NA	3' UTR (NM_008036, exon 4 of 4)	3' UTR (NM_008036, exon 4 of 4)	5736	NM_008036	14282	Mm.248335	NM_008036	ENSMUSG00000003545	Fosb	-	FBJ osteosarcoma oncogene B	protein-coding
mm_61045.1	chr7	49778422	49778432	+	1	NA	promoter-TSS (NM_133740)	promoter-TSS (NM_133740)	69	NM_133740	71974	Mm.33202	NM_133740	ENSMUSG00000030505	Prmt3	2010005E20Rik|2410018A17Rik|AL033309|Hrmt1l3	protein arginine N-methyltransferase 3	protein-coding
mm_136988.1	chr17	17374265	17374278	+	1	NA	promoter-TSS (NM_025934)	promoter-TSS (NM_025934)	-61	NM_025934	67045	Mm.35117	NM_025934	ENSMUSG00000023852	Riok2	2010110K24Rik|2410085M17Rik	RIO kinase 2 (yeast)	protein-coding
mm_54127.1	chr6	18514779	18514789	-	1	NA	promoter-TSS (NM_080285)	promoter-TSS (NM_080285)	41	NM_080285	30785	Mm.224189	NM_080285	ENSMUSG00000000416	Cttnbp2	3010022N24Rik|4732477G22Rik|6430526E05|9130022E09Rik|AU040881|Cortbp2|ORF4|mKIAA1758	cortactin binding protein 2	protein-coding
mm_162062.1	chrX	9063021	9063021	+	1	NA	promoter-TSS (NM_001038697)	promoter-TSS (NM_001038697)	-69	NM_001038697	434729	Mm.386954	NM_001038697	ENSMUSG00000072249	Fthl17f	EG434729|Fthl17L5|Gm5635	ferritin, heavy polypeptide-like 17, member F	protein-coding
mm_97140.1	chr11	75206828	75206832	+	1	NA	intron (NM_177708, intron 1 of 1)	intron (NM_177708, intron 1 of 1)	12837	NM_177708	237847	Mm.82661	NM_177708	ENSMUSG00000045287	Rtn4rl1	Ngr3|Ngrh2|Ngrl2	reticulon 4 receptor-like 1	protein-coding
mm_115397.1	chr13	113794620	113794630	+	1	NA	5' UTR (NM_172595, exon 1 of 5)	5' UTR (NM_172595, exon 1 of 5)	117	NM_172595	218639	Mm.79837	NM_172595	ENSMUSG00000042348	Arl15	A430036I03|Arfrp2|C230032K13Rik	ADP-ribosylation factor-like 15	protein-coding
mm_58330.1	chr6	146577757	146577799	-	1	NA	promoter-TSS (NM_026218)	promoter-TSS (NM_026218)	57	NM_138757	71177	Mm.271774	NM_138757	ENSMUSG00000040250	Asun	4933424B01Rik|Spata30	asunder, spermatogenesis regulator	protein-coding
mm_4276.1	chr1	171580532	171580533	+	1	NA	intron (NM_018729, intron 6 of 8)	intron (NM_018729, intron 6 of 8)	21339	NM_018729	18106	Mm.2299	NM_018729	ENSMUSG00000004709	Cd244	2B4|C9.1|F730046O15Rik|Ly90|NAIL|NKR2B4|Nmrk|SLAMF4	CD244 natural killer cell receptor 2B4	protein-coding
mm_107454.1	chr12	37108555	37108607	+	1	NA	promoter-TSS (NM_008584)	promoter-TSS (NM_008584)	35	NM_008584	17286	Mm.341398	NM_008584	ENSMUSG00000036144	Meox2	AI528662|Gax|Mox-2|Mox2	mesenchyme homeobox 2	protein-coding
mm_34149.1	chr4	139363593	139363622	+	1	NA	intron (NM_001039200, intron 12 of 22)	intron (NM_001039200, intron 12 of 22)	11020	NM_146157	230866	Mm.394288	NM_146157	ENSMUSG00000078517	Emc1	2700016F22Rik	ER membrane protein complex subunit 1	protein-coding
mm_157895.1	chrX	77511808	77511821	-	1	NA	intron (NM_020601, intron 1 of 15)	intron (NM_020601, intron 1 of 15)	587	NM_020601	21372	Mm.258476	NM_020601	ENSMUSG00000025246	Tbl1x	5330429M20|Tbl1	transducin (beta)-like 1 X-linked	protein-coding
mm_113170.1	chr13	24813507	24813522	+	1	NA	TTS (NM_024473)	TTS (NM_024473)	11857	NM_024473	79555	Mm.266668	NM_024473	ENSMUSG00000019132	BC005537	8030460C05Rik|C78201	cDNA sequence BC005537	protein-coding
mm_4021.1	chr1	165722999	165723048	+	1	NA	Intergenic	Intergenic	-14929	NM_001038846	226594	Mm.265552	NM_178593	ENSMUSG00000040723	Rcsd1	A430105K13Rik|BC025872|CapZIP	RCSD domain containing 1	protein-coding
mm_31100.1	chr4	41760462	41760490	+	1	NA	promoter-TSS (NM_001172054)	promoter-TSS (NM_001172054)	33	NM_001172054	16157	Mm.193451	NM_010549	ENSMUSG00000073889	Il11ra1	AI314697|GP130|Il-11ra|Il11ra|Il11ra2|NR1	interleukin 11 receptor, alpha chain 1	protein-coding
mm_55117.1	chr6	50394101	50394124	-	1	NA	intron (NM_001347213, intron 2 of 23)	intron (NM_001347213, intron 2 of 23)	-11275	NM_027881	71720	Mm.44153	NM_027881	ENSMUSG00000029822	Osbpl3	1200014M06Rik|6720421I08Rik|A530055M08|ORP-3|ORP3|OSBP3	oxysterol binding protein-like 3	protein-coding
mm_74921.1	chr8	25589451	25589460	-	1	NA	intron (NM_173012, intron 4 of 10)	intron (NM_173012, intron 4 of 10)	8032	NM_173012	270035	Mm.268349	NM_173012	ENSMUSG00000037363	Letm2	6030453H13|D030041N04Rik	leucine zipper-EF-hand containing transmembrane protein 2	protein-coding
mm_56797.1	chr6	116655474	116655496	-	1	NA	intron (NM_178045, intron 3 of 10)	intron (NM_178045, intron 3 of 10)	4801	NM_001166580	213393	Mm.38231	NM_145980	ENSMUSG00000048489	8430408G22Rik	Depp|Fseg	RIKEN cDNA 8430408G22 gene	protein-coding
mm_84654.1	chr9	71631087	71631100	-	1	NA	intron (NM_001304362, intron 16 of 18)	intron (NM_001304362, intron 16 of 18)	-38733	NM_001033208	102371	Mm.27585	NM_001033208	ENSMUSG00000041361	Myzap	AA407270|AV006038|Gcom1|Gm640|Grinl1a7|Myozap	myocardial zonula adherens protein	protein-coding
mm_57892.1	chr6	131368509	131368524	-	1	NA	exon (NM_011733, exon 7 of 9)	exon (NM_011733, exon 7 of 9)	19934	NM_139117	56449	Mm.458000	NM_011733	ENSMUSG00000030189	Ybx3	Csda|Dpba|MSY3|MSY4|Yb2|dbpA|oxyR	Y box protein 3	protein-coding
mm_159028.1	chr1	173982861	173982861	-	1	NA	promoter-TSS (NM_011940)	promoter-TSS (NM_011940)	-17	NM_011940	26388	Mm.218770	NM_008327	ENSMUSG00000026535	Ifi202b	Ifbip-1|Ifi202|Ifi202a|p202	interferon activated gene 202B	protein-coding
mm_105500.1	chr11	106160488	106160499	-	1	NA	promoter-TSS (NM_172397)	promoter-TSS (NM_172397)	-351	NM_172397	67803	Mm.21687	NM_172397	ENSMUSG00000040699	Limd2	0610025L06Rik|AI413966	LIM domain containing 2	protein-coding
mm_77308.1	chr8	117671502	117671523	-	1	NA	promoter-TSS (NM_028725)	promoter-TSS (NM_028725)	3	NM_028725	74032	Mm.296302	NM_028725	ENSMUSG00000034308	Sdr42e1	4632417N05Rik|AI117603	short chain dehydrogenase/reductase family 42E, member 1	protein-coding
mm_39923.1	chr5	31569375	31569387	+	1	NA	TTS (NR_102275)	TTS (NR_102275)	2016	NR_102275	100740	Mm.23370	NR_102275		AI839979	-	expressed sequence AI839979	ncRNA
mm_53086.1	chr6	124997063	124997082	+	1	NA	intron (NM_175696, intron 1 of 5)	intron (NM_175696, intron 1 of 5)	352	NM_175696	319352	Mm.295327	NM_175696	ENSMUSG00000030329	Pianp	AI255183|AU067746|C530028O21Rik|Panp	PILR alpha associated neural protein	protein-coding
mm_102028.1	chr11	51688504	51688514	-	1	NA	intron (NM_025319, intron 1 of 1)	intron (NM_025319, intron 1 of 1)	125	NM_025319	66050	Mm.35693	NM_025319	ENSMUSG00000007777	0610009B22Rik	-	RIKEN cDNA 0610009B22 gene	protein-coding
mm_153142.1	chr19	34248045	34248048	-	1	NA	intron (NM_007392, intron 4 of 8)	intron (NM_007392, intron 4 of 8)	7327	NM_007392	11475	Mm.213025	NM_007392	ENSMUSG00000035783	Acta2	0610041G09Rik|Actvs|SMalphaA|a-SMA|alphaSMA	actin, alpha 2, smooth muscle, aorta	protein-coding
mm_106682.1	chr12	3235490	3235522	+	1	NA	promoter-TSS (NR_015551)	promoter-TSS (NR_015551)	-285	NR_015551	74173	Mm.309774	NM_028796	ENSMUSG00000079179	Rab10os	1700012B15Rik|1810036A22Rik	RAB10, member RAS oncogene family, opposite strand	ncRNA
mm_152670.1	chr19	14598006	14598016	-	1	NA	promoter-TSS (NM_001302951)	promoter-TSS (NM_001302951)	172	NM_001302950	21888	Mm.103638	NM_011600	ENSMUSG00000024642	Tle4	5730411M05Rik|AA792082|Bce-1|Bce1|ESTM13|ESTM14|Grg4|X83332|X83333|grg-4	transducin-like enhancer of split 4	protein-coding
mm_52912.1	chr6	122826617	122826656	+	1	NA	intron (NM_021899, intron 1 of 10)	intron (NM_021899, intron 1 of 10)	-4741	NR_106090	102465710		NR_106090	ENSMUSG00000106580	Mir7231	mmu-mir-7231	microRNA 7231	ncRNA
mm_94389.1	chr11	5525256	5525275	+	1	NA	3' UTR (NM_001271730, exon 6 of 6)	3' UTR (NM_001271730, exon 6 of 6)	4624	NM_001271730	22433	Mm.469937	NM_013842	ENSMUSG00000020484	Xbp1	D11Ertd39e|TREB-5|TREB5|XBP-1	X-box binding protein 1	protein-coding
mm_128043.1	chr15	25390627	25390640	-	1	NA	intron (NM_027395, intron 1 of 1)	intron (NM_027395, intron 1 of 1)	23131	NM_027395	70350	Mm.29586	NM_027395	ENSMUSG00000045763	Basp1	2610024P12Rik|CAP-23|CAP23|Ckap3|NAP-22|NAP22	brain abundant, membrane attached signal protein 1	protein-coding
mm_105641.1	chr11	107015677	107015680	-	1	NA	Intergenic	Intergenic	-12545	NM_001163473	69066	Mm.40679	NM_001163473	ENSMUSG00000078607	1810010H24Rik	OTTMUSG00000003581	RIKEN cDNA 1810010H24 gene	protein-coding
mm_171554.1	chr4	147132067	147132071	+	1	NA	Intergenic	Intergenic	-43797	NM_001039209	195531	Mm.270762	NM_001039209	ENSMUSG00000078496	Zfp982	Gm13152|OTTMUSG00000010671	zinc finger protein 982	protein-coding
mm_66838.1	chr7	48881033	48881050	-	1	NA	promoter-TSS (NM_001013368)	promoter-TSS (NM_001013368)	0	NM_001013368	108961	Mm.240566	NM_001013368	ENSMUSG00000046179	E2f8	4432406C08Rik|AA410048	E2F transcription factor 8	protein-coding
mm_66691.1	chr7	45896657	45896674	-	1	NA	promoter-TSS (NM_144801)	promoter-TSS (NM_144801)	46	NM_001291064	58867	Mm.214217	NM_021482	ENSMUSG00000040231	Syngr4	1700016O14Rik	synaptogyrin 4	protein-coding
mm_11079.1	chr2	27710275	27710281	+	1	NA	promoter-TSS (NM_001290482)	promoter-TSS (NM_001290482)	-305	NM_001290482	20181	Mm.24624	NM_011305	ENSMUSG00000015846	Rxra	9530071D11Rik|Nr2b1|RXRalpha1	retinoid X receptor alpha	protein-coding
mm_138053.1	chr17	33926418	33926429	+	1	NA	intron (NM_001025313, intron 5 of 7)	intron (NM_001025313, intron 5 of 7)	-3471	NM_009059	19732	Mm.43777	NM_009059	ENSMUSG00000041354	Rgl2	KE1.5|Rab2l|Rgt2|Rlf	ral guanine nucleotide dissociation stimulator-like 2	protein-coding
mm_39888.1	chr5	31116703	31116713	+	1	NA	promoter-TSS (NM_021447)	promoter-TSS (NM_021447)	96	NM_021447	58522	Mm.143796	NM_021447	ENSMUSG00000062077	Trim54	4930486E09Rik|4930566I02Rik|MURF|MURF-3|MuRF3|Rnf30	tripartite motif-containing 54	protein-coding
mm_7188.1	chr1	92902870	92902875	-	1	NA	promoter-TSS (NM_172850)	promoter-TSS (NM_172850)	34	NM_172850	241158	Mm.108280	NM_172850	ENSMUSG00000034212	Ankmy1	4930483I10Rik|ZMYND13	ankyrin repeat and MYND domain containing 1	protein-coding
mm_160683.1	chr10	18056127	18056127	+	1	NA	intron (NM_009048, intron 1 of 19)	CpG	187	NM_001111065	19707	Mm.4479	NM_009048	ENSMUSG00000019854	Reps1	BB161292	RalBP1 associated Eps domain containing protein	protein-coding
mm_156761.1	chrX	160502713	160502731	+	1	NA	5' UTR (NM_001177878, exon 1 of 33)	5' UTR (NM_001177878, exon 1 of 33)	288	NM_001177878	110094	Mm.350712	NM_172783	ENSMUSG00000031295	Phka2	6330505C01Rik|D330034O08|Phk	phosphorylase kinase alpha 2	protein-coding
mm_158214.1	chrX	105875622	105875634	-	1	NA	exon (NM_009530, exon 9 of 35)	exon (NM_009530, exon 9 of 35)	53744	NM_009530	22589	Mm.10141	NM_009530	ENSMUSG00000031229	Atrx	4833408C14Rik|AI447451|ATR2|DXHXS6677E|HP1-BP38|Hp1bp2|Hp1bp38|MRXS3|RAD54L|Rad54|XH2|Xnp|ZNF-HX	alpha thalassemia/mental retardation syndrome X-linked	protein-coding
mm_8107.1	chr1	135851377	135851390	-	1	NA	exon (NM_001130176, exon 11 of 13)	exon (NM_001130176, exon 11 of 13)	10522	NM_001130176	21956	Mm.247470	NM_011619	ENSMUSG00000026414	Tnnt2	Tnt|cTnT	troponin T2, cardiac	protein-coding
mm_158550.1	chrX	145505176	145505212	-	1	NA	Intergenic	Intergenic	-17555	NM_153319	27494	Mm.100068	NM_153319	ENSMUSG00000041688	Amot	CAG-2|D0Kist1|Sii6	angiomotin	protein-coding
mm_38429.1	chr4	139310647	139310664	-	1	NA	promoter-TSS (NM_025337)	promoter-TSS (NM_025337)	45	NM_145384	212555	Mm.45131	NM_145384	ENSMUSG00000028744	Pqlc2	BC019216	PQ loop repeat containing 2	protein-coding
mm_123993.1	chr14	75761381	75761407	-	1	NA	TTS (NM_026232)	TTS (NM_026232)	-6901	NM_177381	338337	Mm.86507	NM_177381	ENSMUSG00000034893	Cog3	E430004N23	component of oligomeric golgi complex 3	protein-coding
mm_170454.1	chr18	85698270	85698272	-	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-696681	NM_144946	246317	Mm.329578	NM_144946	ENSMUSG00000050321	Neto1	AI851453|Btcl1|C130005O10Rik	neuropilin (NRP) and tolloid (TLL)-like 1	protein-coding
mm_116200.1	chr13	32214101	32214127	-	1	NA	intron (NM_146041, intron 4 of 10)	intron (NM_146041, intron 4 of 10)	124430	NM_146041	218138	Mm.247143	NM_146041	ENSMUSG00000038372	Gmds	BC031788|C87208	GDP-mannose 4, 6-dehydratase	protein-coding
mm_93053.1	chr10	88583753	88583763	-	1	NA	intron (NM_175418, intron 2 of 28)	PB1D10|SINE|Alu	21394	NM_001252372	109272	Mm.147208	NM_175418	ENSMUSG00000020061	Mybpc1	8030451F13Rik	myosin binding protein C, slow-type	protein-coding
mm_96932.1	chr11	70519184	70519203	+	1	NA	promoter-TSS (NM_146020)	promoter-TSS (NM_146020)	-16	NM_146020	216871	Mm.22551	NM_146020	ENSMUSG00000046811	Gltpd2	C730027E14Rik	glycolipid transfer protein domain containing 2	protein-coding
mm_79874.1	chr9	65185753	65185767	+	1	NA	3' UTR (NM_008988, exon 14 of 14)	3' UTR (NM_008988, exon 14 of 14)	-28930	NM_177460	214424	Mm.31129	NM_177460	ENSMUSG00000032392	Parp16	ARTD15|BC055447|C79952|PARP-16	poly (ADP-ribose) polymerase family, member 16	protein-coding
mm_55781.1	chr6	81965666	81965679	-	1	NA	intron (NM_026490, intron 1 of 4)	CpG	277	NM_026490	56284	Mm.276293	NM_026490	ENSMUSG00000030045	Mrpl19	9030416F12Rik|9130412E02Rik|D6Ertd157e|MRP-L15|RLX1|Rpml15	mitochondrial ribosomal protein L19	protein-coding
mm_80289.1	chr9	73065862	73065885	+	1	NA	intron (NM_001301232, intron 1 of 5)	intron (NM_001301232, intron 1 of 5)	1725	NM_001301232	11891	Mm.34867	NM_023635	ENSMUSG00000032202	Rab27a	2210402C08Rik|2410003M20Rik|4933437C11Rik|ash	RAB27A, member RAS oncogene family	protein-coding
mm_124829.1	chr15	9140528	9140577	+	1	NA	promoter-TSS (NM_013787)	promoter-TSS (NM_013787)	-18	NM_177178	320506	Mm.259886	NM_177178	ENSMUSG00000039704	Lmbrd2	9930036E21Rik	LMBR1 domain containing 2	protein-coding
mm_68714.1	chr7	119895698	119895752	-	1	NA	promoter-TSS (NM_001285961)	promoter-TSS (NM_001285961)	20	NM_001163703	233805	Mm.31539	NM_173408	ENSMUSG00000048787	Dcun1d3	1700020A13Rik|BC030335	DCN1, defective in cullin neddylation 1, domain containing 3 (S. cerevisiae)	protein-coding
mm_159378.1	chr3	89454603	89454603	+	1	NA	promoter-TSS (NM_001310640)	promoter-TSS (NM_001310640)	62	NM_001310640	68603	Mm.34242	NM_026784	ENSMUSG00000027952	Pmvk	1110011E12Rik|2900002L22Rik|AV001327|PMK|PMKA|PMKASE	phosphomevalonate kinase	protein-coding
mm_80137.1	chr9	70710040	70710040	+	1	NA	intron (NM_007399, intron 2 of 15)	intron (NM_007399, intron 2 of 15)	31058	NM_007399	11487	Mm.3037	NM_007399	ENSMUSG00000054693	Adam10	1700031C13Rik|MADM|kuz|kuzbanian	a disintegrin and metallopeptidase domain 10	protein-coding
mm_101592.1	chr11	34682115	34682172	-	1	NA	intron (NM_033374, intron 22 of 51)	RLTR44-int|LTR|ERVK	101762	NM_033374	94176	Mm.380679	NM_033374	ENSMUSG00000020143	Dock2	AI662014|AW122239|CED-5|Hch|MBC	dedicator of cyto-kinesis 2	protein-coding
mm_92563.1	chr10	79874212	79874223	-	1	NA	non-coding (NR_033210, exon 1 of 6)	non-coding (NR_033210, exon 1 of 6)	417	NM_181681	216152	Mm.29678	NM_181681	ENSMUSG00000035835	Plppr3	Lppr3|Prg2	phospholipid phosphatase related 3	protein-coding
mm_94395.1	chr11	5569680	5569690	+	1	NA	promoter-TSS (NM_023816)	promoter-TSS (NM_023816)	1	NM_023816	76389	Mm.67300	NM_023816	ENSMUSG00000020481	Ankrd36	1700008J08Rik|1700012M14Rik|Ankrd48	ankyrin repeat domain 36	protein-coding
mm_51525.1	chr6	83179702	83179702	+	1	NA	5' UTR (NM_007835, exon 1 of 32)	5' UTR (NM_007835, exon 1 of 32)	113	NM_007835	13191	Mm.6919	NM_007835	ENSMUSG00000031865	Dctn1	AL022633|DAP-150|DP-150|Glued|p150|p150-glued|p150<glued>	dynactin 1	protein-coding
mm_147245.1	chr18	38375548	38375557	-	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	-36559	NM_011937	26384	Mm.22374	NM_011937	ENSMUSG00000052102	Gnpda1	GNPDA|Gnp1|Gnpi|oscillin	glucosamine-6-phosphate deaminase 1	protein-coding
mm_145186.1	chr18	49755734	49755751	+	1	NA	promoter-TSS (NM_001170960)	promoter-TSS (NM_001170960)	-141	NM_001170960	68857	Mm.96010	NM_026854	ENSMUSG00000024505	Dtwd2	1190002H09Rik|8030470C17Rik|AI414673|BB115449	DTW domain containing 2	protein-coding
mm_76074.1	chr8	78813211	78813275	-	1	NA	intron (NM_030145, intron 1 of 3)	intron (NM_030145, intron 1 of 3)	7909	NM_001191004	78651	Mm.28694	NM_030145	ENSMUSG00000031683	Lsm6	1500031N17Rik|2410088K19Rik|AI747288	LSM6 homolog, U6 small nuclear RNA and mRNA degradation associated	protein-coding
mm_125686.1	chr15	66801667	66801670	+	1	NA	intron (NM_001029841, intron 1 of 7)	intron (NM_001029841, intron 1 of 7)	30161	NM_001029841	20491	Mm.7601	NM_009192	ENSMUSG00000022372	Sla	Slap|Slap-1	src-like adaptor	protein-coding
mm_85119.1	chr9	95460096	95460099	-	1	NA	3' UTR (NM_001114977, exon 28 of 28)	3' UTR (NM_001114977, exon 28 of 28)	51899	NM_026476	67958	Mm.292742	NM_026476	ENSMUSG00000032407	U2surp	2610101N10Rik|AU023006|Sr140	U2 snRNP-associated SURP domain containing	protein-coding
mm_127533.1	chr15	102102927	102102975	+	1	NA	promoter-TSS (NM_153533)	promoter-TSS (NM_153533)	-37	NM_153533	209039	Mm.29389	NM_153533	ENSMUSG00000037003	Tns2	C1-ten|Tenc1|nep|nph	tensin 2	protein-coding
mm_97969.1	chr11	83850864	83850881	+	1	NA	promoter-TSS (NM_001291268)	promoter-TSS (NM_001291268)	3	NM_009330	21410	Mm.7226	NM_009330	ENSMUSG00000020679	Hnf1b	HNF-1-beta|HNF-1B|HNF-1Beta|Hnf1beta|LFB3|Tcf-2|Tcf2|vHNF1	HNF1 homeobox B	protein-coding
mm_7477.1	chr1	120504821	120504833	-	1	NA	5' UTR (NM_010766, exon 1 of 17)	5' UTR (NM_010766, exon 1 of 17)	257	NM_010766	17167	Mm.1856	NM_010766	ENSMUSG00000026390	Marco	AI323439|Ly112|Scara2	macrophage receptor with collagenous structure	protein-coding
mm_89132.1	chr10	85115987	85115994	+	1	NA	3' UTR (NM_001013028, exon 3 of 3)	3' UTR (NM_001013028, exon 3 of 3)	12037	NM_028832	74238	Mm.255401	NM_028832	ENSMUSG00000049038	Mterf2	1700007D05Rik|Mterfd3	mitochondrial transcription termination factor 2	protein-coding
mm_134856.1	chr16	28422460	28422462	-	1	NA	intron (NM_010199, intron 2 of 5)	intron (NM_010199, intron 2 of 5)	23614	NM_183064	14167	Mm.7996	NM_010199	ENSMUSG00000022523	Fgf12	AV114868|B230343J05Rik|FGF-12|FHF-1|Fhf1	fibroblast growth factor 12	protein-coding
mm_52516.1	chr6	115421999	115422004	+	1	NA	promoter-TSS (NM_011146)	promoter-TSS (NM_011146)	-65	NM_011146	19016	Mm.3020	NM_011146	ENSMUSG00000000440	Pparg	Nr1c3|PPAR-gamma|PPAR-gamma2|PPARgamma|PPARgamma2	peroxisome proliferator activated receptor gamma	protein-coding
mm_152083.1	chr19	6870738	6870761	-	1	NA	Intergenic	RMER4A|LTR|ERVK	-12538	NM_001081291	78317	Mm.329596	NM_198008	ENSMUSG00000047810	Ccdc88b	2610041P08Rik|Ccdc88	coiled-coil domain containing 88B	protein-coding
mm_65699.1	chr7	28377175	28377219	-	1	NA	3' UTR (NM_011756, exon 2 of 2)	3' UTR (NM_011756, exon 2 of 2)	2031	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_59049.1	chr7	19368503	19368553	+	1	NA	intron (NM_001010836, intron 1 of 12)	intron (NM_001010836, intron 1 of 12)	7312	NM_001010836	333654	Mm.333640	NM_001010836	ENSMUSG00000040734	Ppp1r13l	AV260376|IASPP|Nkip1|wa3	protein phosphatase 1, regulatory (inhibitor) subunit 13 like	protein-coding
mm_109162.1	chr12	108189142	108189147	+	1	NA	exon (NM_009832, exon 5 of 12)	exon (NM_009832, exon 5 of 12)	9406	NM_009832	12454	Mm.474441	NM_009832	ENSMUSG00000021258	Ccnk	AW123198|AW413594|CPR4|CycK	cyclin K	protein-coding
mm_170247.1	chr1	79380832	79380834	+	1	NA	Intergenic	Intergenic	59257	NM_009129	20254	Mm.5038	NM_009129	ENSMUSG00000050711	Scg2	Chgc|SgII	secretogranin II	protein-coding
mm_38707.1	chr4	145215555	145215569	-	1	NA	3' UTR (NM_011610, exon 10 of 10)	3' UTR (NM_011610, exon 10 of 10)	-20557	NM_001276465	230895	Mm.240310	NM_001033190	ENSMUSG00000020220	Vps13d	-	vacuolar protein sorting 13D	protein-coding
mm_138144.1	chr17	34204478	34204500	+	1	NA	promoter-TSS (NM_011530)	promoter-TSS (NM_011530)	10	NM_011530	21355	Mm.14814	NM_011530	ENSMUSG00000024339	Tap2	ABC18|AI462429|APT2|Abcb3|Ham-2|Ham2|MTP2|PSF2|RING11|Tap-2|Y1|jas	transporter 2, ATP-binding cassette, sub-family B (MDR/TAP)	protein-coding
mm_64070.1	chr7	140890843	140890850	+	1	NA	intron (NM_011875, intron 9 of 12)	intron (NM_011875, intron 9 of 12)	8452	NM_011875	23997	Mm.29760	NM_011875	ENSMUSG00000025487	Psmd13	S11	proteasome (prosome, macropain) 26S subunit, non-ATPase, 13	protein-coding
mm_126964.1	chr15	92597105	92597121	+	1	NA	promoter-TSS (NM_001164594)	promoter-TSS (NM_001164594)	4	NM_001164594	239618	Mm.309826	NM_001164593	ENSMUSG00000036218	Pdzrn4	1110017D07Rik|LNX4|SAMCAP3L|mKIAA3027	PDZ domain containing RING finger 4	protein-coding
mm_61505.1	chr7	78578558	78578586	+	1	NA	promoter-TSS (NM_182809)	promoter-TSS (NM_182809)	-734	NM_182809	18213	Mm.33496	NM_008746	ENSMUSG00000059146	Ntrk3	AW125844|Ntrk3_tv3|TrkC	neurotrophic tyrosine kinase, receptor, type 3	protein-coding
mm_160036.1	chr6	132738215	132738215	-	1	NA	promoter-TSS (NM_207020)	promoter-TSS (NM_207020)	-229	NM_207020	353325	Mm.377892	NM_207020	ENSMUSG00000071149	Tas2r115	T2R15|Tas2r15|mGR15|mt2r49	taste receptor, type 2, member 115	protein-coding
mm_13463.1	chr2	105675616	105675623	+	1	NA	promoter-TSS (NM_013627)	promoter-TSS (NM_013627)	-125	NM_001244200	18508	Mm.3608	NM_013627	ENSMUSG00000027168	Pax6	1500038E17Rik|AEY11|Dey|Gsfaey11|Pax-6|Sey	paired box 6	protein-coding
mm_145778.1	chr18	65072268	65072279	+	1	NA	intron (NM_031881, intron 1 of 29)	intron (NM_031881, intron 1 of 29)	48746	NM_031881	83814	Mm.98668	NM_031881	ENSMUSG00000024589	Nedd4l	1300012C07Rik|Nedd4-2|Nedd4b	neural precursor cell expressed, developmentally down-regulated gene 4-like	protein-coding
mm_83127.1	chr9	40425679	40425682	-	1	NA	intron (NM_172768, intron 1 of 19)	PB1D10|SINE|Alu	30084	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_132274.1	chr16	32916291	32916295	+	1	NA	intron (NM_001310674, intron 1 of 21)	intron (NM_001310674, intron 1 of 21)	2193	NM_001310672	70144	Mm.491178	NM_001081255	ENSMUSG00000022801	Lrch3	2210409B11Rik|AW215594|Gm1742	leucine-rich repeats and calponin homology (CH) domain containing 3	protein-coding
mm_95651.1	chr11	53724586	53724599	+	1	NA	3' UTR (NM_010558, exon 4 of 4)	3' UTR (NM_010558, exon 4 of 4)	3798	NM_010558	16191	Mm.4461	NM_010558	ENSMUSG00000036117	Il5	Il-5	interleukin 5	protein-coding
mm_98246.1	chr11	88204016	88204039	+	1	NA	promoter-TSS (NM_024174)	promoter-TSS (NM_024174)	-361	NM_024174	64656	Mm.168680	NM_024174	ENSMUSG00000023723	Mrps23	D11Bwg1153e|MRP-S23|Rpms23|S23mt	mitochondrial ribosomal protein S23	protein-coding
mm_112470.1	chr13	5868440	5868464	+	1	NA	3' UTR (NM_011803, exon 4 of 4)	3' UTR (NM_011803, exon 4 of 4)	6963	NM_011803	23849	Mm.275036	NM_011803	ENSMUSG00000000078	Klf6	AI448727|BCD1|C86813|CPBP|Copeb|FM2|FM6|Ierepo1|Ierepo3|R75280|Zf9	Kruppel-like factor 6	protein-coding
mm_160418.1	chr8	83976750	83976750	+	1	NA	promoter-TSS (NM_001277898)	promoter-TSS (NM_001277898)	-133	NM_001277898	18747	Mm.19111	NM_008854	ENSMUSG00000005469	Prkaca	PKCD|Pkaca	protein kinase, cAMP dependent, catalytic, alpha	protein-coding
mm_35786.1	chr4	46469947	46469992	-	1	NA	exon (NM_130889, exon 5 of 7)	exon (NM_130889, exon 5 of 7)	19043	NM_130889	67628	Mm.263913	NM_130889	ENSMUSG00000028333	Anp32b	2410015B15Rik|PAL31|PHAPI2a|Ssp29	acidic (leucine-rich) nuclear phosphoprotein 32 family, member B	protein-coding
mm_72078.1	chr8	71569658	71569689	+	1	NA	intron (NM_011977, intron 2 of 13)	CpG	746	NM_011977	26457	Mm.38165	NM_011977	ENSMUSG00000031808	Slc27a1	FATP1|Fatp	solute carrier family 27 (fatty acid transporter), member 1	protein-coding
mm_162043.1	chr19	59169881	59169881	-	1	NA	exon (NM_009501, exon 1 of 3)	exon (NM_009501, exon 1 of 3)	148	NM_009501	22326	Mm.23801	NM_009501	ENSMUSG00000006270	Vax1	-	ventral anterior homeobox 1	protein-coding
mm_146845.1	chr18	23867570	23867571	-	1	NA	intron (NM_153058, intron 4 of 6)	MLT1E1A|LTR|ERVL-MaLR	63600	NM_153058	212307	Mm.132237	NM_153058	ENSMUSG00000024277	Mapre2	AI314113|C820009F03Rik|D18Abb1e|EB1|EB2|RP1	microtubule-associated protein, RP/EB family, member 2	protein-coding
mm_156985.1	chrX	7319261	7319288	-	1	NA	promoter-TSS (NM_001243762)	promoter-TSS (NM_001243762)	84	NM_001243762	12728	Mm.486257	NM_016691	ENSMUSG00000004317	Clcn5	5430408K11Rik|ClC-5|Clc4-1|Clc5|Clcn4-1|D930009B12Rik|DXImx42e|Sfc13|T25545	chloride channel, voltage-sensitive 5	protein-coding
mm_76002.1	chr8	72487111	72487133	-	1	NA	intron (NM_177766, intron 4 of 5)	intron (NM_177766, intron 4 of 5)	5492	NM_177766	270066	Mm.291461	NM_177766	ENSMUSG00000019731	Slc35e1	6030458H05|AA408278	solute carrier family 35, member E1	protein-coding
mm_44046.1	chr5	147860603	147860613	+	1	NA	promoter-TSS (NM_025624)	promoter-TSS (NM_025624)	-20	NM_025624	66537	Mm.332855	NM_025624	ENSMUSG00000029649	Pomp	2510048O06Rik|Ump1	proteasome maturation protein	protein-coding
mm_127130.1	chr15	98160658	98160689	+	1	NA	intron (NM_001170711, intron 1 of 3)	intron (NM_001170711, intron 1 of 3)	4905	NM_001170711	78541	Mm.200766	NM_030121	ENSMUSG00000048175	Asb8	4930539L19Rik|AI788835|C430011H06Rik	ankyrin repeat and SOCS box-containing 8	protein-coding
mm_72232.1	chr8	74873197	74873228	+	1	NA	promoter-TSS (NM_027837)	promoter-TSS (NM_027837)	38	NM_001294278	71597	Mm.158735	NM_027837	ENSMUSG00000031621	Isx	9130012O13Rik|Pix-1	intestine specific homeobox	protein-coding
mm_123348.1	chr14	63141863	63141870	-	1	NA	intron (NM_007798, intron 9 of 9)	intron (NM_007798, intron 9 of 9)	19404	NM_007798	13030	Mm.236553	NM_007798	ENSMUSG00000021939	Ctsb	CB	cathepsin B	protein-coding
mm_32285.1	chr4	102991289	102991295	+	1	NA	promoter-TSS (NM_001163768)	promoter-TSS (NM_001163768)	-503	NM_001163768	67344	Mm.111346	NM_026100	ENSMUSG00000028523	Tctex1d1	1700055O19Rik	Tctex1 domain containing 1	protein-coding
mm_30354.1	chr3	151762496	151762521	-	1	NA	intron (NM_031367, intron 1 of 4)	intron (NM_031367, intron 1 of 4)	383	NM_031367	15061	Mm.219544	NM_031367	ENSMUSG00000039146	Ifi44l	H-28|H28|H28-1|NS1178	interferon-induced protein 44 like	protein-coding
mm_60537.1	chr7	44480404	44480414	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-4108	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_105594.1	chr11	106736500	106736506	-	1	NA	Intergenic	Intergenic	-14723	NM_001271375	380732	Mm.343952	NM_001033435	ENSMUSG00000040528	Milr1	Allergin-1|Gm885|Mca32	mast cell immunoglobulin like receptor 1	protein-coding
mm_169217.1	chr13	66706431	66706449	+	1	NA	Intergenic	Intergenic	198910	NM_026219	67530	Mm.379136	NM_026219	ENSMUSG00000021520	Uqcrb	2210415M14Rik|QP-C|QPC|UQBC|UQBP|UQPC	ubiquinol-cytochrome c reductase binding protein	protein-coding
mm_17035.1	chr2	20669289	20669295	-	1	NA	intron (NM_029895, intron 4 of 18)	RLTR41C|LTR|ERV1	149779	NM_001177631	208618	Mm.237935	NM_029895	ENSMUSG00000036617	Etl4	6620402G01Rik|9430077C05Rik|BC026657|E330027G05Rik|Etl-4|Skt	enhancer trap locus 4	protein-coding
mm_158463.1	chrX	140642260	140642261	-	1	NA	Intergenic	7SK|RNA|RNA	-35768	NM_011845	23947	Mm.131097	NM_011845	ENSMUSG00000000266	Mid2	FXY2|Trim1	midline 2	protein-coding
mm_128656.1	chr15	59794955	59794959	-	1	NA	promoter-TSS (NR_045076)	promoter-TSS (NR_045076)	2	NR_045076	100503021	Mm.402924	NR_045076		Gm19510	-	predicted gene, 19510	ncRNA
mm_160961.1	chr11	99285248	99285248	-	1	NA	promoter-TSS (NM_029393)	promoter-TSS (NM_029393)	-10	NM_029393	75706	Mm.46378	NM_029393	ENSMUSG00000020913	Krt24	2310058N18Rik|2310075C18Rik	keratin 24	protein-coding
mm_11752.1	chr2	38472195	38472208	+	1	NA	Intergenic	Intergenic	-39496	NM_021606	59126	Mm.143818	NM_021606	ENSMUSG00000026749	Nek6	1300007C09Rik	NIMA (never in mitosis gene a)-related expressed kinase 6	protein-coding
mm_109102.1	chr12	105020114	105020143	+	1	NA	Intergenic	Intergenic	-10319	NM_172500	212073	Mm.212688	NM_172500	ENSMUSG00000054150	Syne3	nesprin-3	spectrin repeat containing, nuclear envelope family member 3	protein-coding
mm_87037.1	chr10	28668649	28668652	+	1	NA	non-coding (NR_131208, exon 1 of 4)	non-coding (NR_131208, exon 1 of 4)	290	NM_178666	210757	Mm.123021	NM_178666	ENSMUSG00000049109	Themis	E430004N04Rik|Gasp|Spot|Tsepa|thylex	thymocyte selection associated	protein-coding
mm_122689.1	chr14	52020662	52020666	-	1	NA	promoter-TSS (NM_001253694)	promoter-TSS (NM_001253694)	69	NM_001253696	69890	Mm.475652	NM_027248	ENSMUSG00000049295	Zfp219	2010302A17Rik	zinc finger protein 219	protein-coding
mm_118142.1	chr13	105054440	105054562	-	1	NA	5' UTR (NM_029879, exon 1 of 6)	5' UTR (NM_029879, exon 1 of 6)	429	NM_029879	52882	Mm.100348	NM_029879	ENSMUSG00000021719	Rgs7bp	A930030I01Rik|AI842293|D13Bwg1146e|R7bp	regulator of G-protein signalling 7 binding protein	protein-coding
mm_86796.1	chr10	20267220	20267229	+	1	NA	exon (NM_008635, exon 10 of 18)	exon (NM_008635, exon 10 of 18)	30464	NR_105840	102466647		NR_105840	ENSMUSG00000098887	Mir6413	Gm27432|mmu-mir-6413	microRNA 6413	ncRNA
mm_3975.1	chr1	164220014	164220017	+	1	NA	3' UTR (NM_007976, exon 25 of 25)	3' UTR (NM_007976, exon 25 of 25)	-29031	NM_054087	116914	Mm.35444	NM_054087	ENSMUSG00000040918	Slc19a2	AV276020|AW322295|DDA1|THTR1|TRMA	solute carrier family 19 (thiamine transporter), member 2	protein-coding
mm_95684.1	chr11	54261756	54261763	+	1	NA	Intergenic	ORR1A1|LTR|ERVL-MaLR	5520	NM_010556	16187	Mm.983	NM_010556	ENSMUSG00000018914	Il3	BPA|Csfmu|HCGF|Il-3|MCGF|PSF	interleukin 3	protein-coding
mm_160557.1	chr9	49426953	49426953	-	1	NA	promoter-TSS (NM_172922)	promoter-TSS (NM_172922)	68	NM_172922	244859	Mm.119994	NM_172922	ENSMUSG00000032257	Ankk1	9930020N01Rik	ankyrin repeat and kinase domain containing 1	protein-coding
mm_31648.1	chr4	59626190	59626253	+	1	NA	promoter-TSS (NM_001015681)	promoter-TSS (NM_001015681)	10	NM_153158	230259	Mm.45688	NM_153158	ENSMUSG00000045071	E130308A19Rik	-	RIKEN cDNA E130308A19 gene	protein-coding
mm_48325.1	chr5	138995625	138995640	-	1	NA	promoter-TSS (NM_008808)	promoter-TSS (NM_008808)	-679	NM_008808	18590	Mm.2675	NM_008808	ENSMUSG00000025856	Pdgfa	-	platelet derived growth factor, alpha	protein-coding
mm_77821.1	chr9	3372523	3372525	+	1	NA	intron (NM_026303, intron 10 of 11)	B1_Mus2|SINE|Alu	-31561	NM_027545	244672	Mm.245482	NM_027545	ENSMUSG00000025898	Cwf19l2	3230401L03Rik|9030209E10	CWF19-like 2, cell cycle control (S. pombe)	protein-coding
mm_139519.1	chr17	56609886	56609916	+	1	NA	promoter-TSS (NM_153152)	promoter-TSS (NM_153152)	-130	NM_153152	224904	Mm.34002	NM_153152	ENSMUSG00000049760	2410015M20Rik	Mic13|QIL1|sr104	RIKEN cDNA 2410015M20 gene	protein-coding
mm_115161.1	chr13	107469816	107469828	+	1	NA	promoter-TSS (NR_045084)	promoter-TSS (NR_045084)	0	NR_045083	105120	Mm.417700	NR_045083		AI197445	-	expressed sequence AI197445	ncRNA
mm_75688.1	chr8	68205743	68205748	-	1	NA	Intergenic	Intergenic	-70783	NM_028182	72281	Mm.40974	NM_028182	ENSMUSG00000053886	Sh2d4a	2210402M20Rik|SH2A	SH2 domain containing 4A	protein-coding
mm_115043.1	chr13	99641984	99641992	+	1	NA	Intergenic	Intergenic	-125386	NM_008634	17755	Mm.4173	NM_008634	ENSMUSG00000052727	Map1b	A230055D22|AI843217|LC1|MAP5|Mtap-5|Mtap1b|Mtap5	microtubule-associated protein 1B	protein-coding
mm_109230.1	chr12	108836386	108836396	+	1	NA	promoter-TSS (NM_181328)	promoter-TSS (NM_181328)	-515	NM_181328	214663	Mm.266264	NM_181328	ENSMUSG00000021265	Slc25a29	C030003J19Rik|CACL|mCACL	solute carrier family 25 (mitochondrial carrier, palmitoylcarnitine transporter), member 29	protein-coding
mm_137941.1	chr17	32685640	32685643	+	1	NA	promoter-TSS (NM_134127)	promoter-TSS (NM_134127)	10	NM_001346538	106648	Mm.26539	NM_134127	ENSMUSG00000073424	Cyp4f15	AI787289|Cyp4f-15	cytochrome P450, family 4, subfamily f, polypeptide 15	protein-coding
mm_68620.1	chr7	117486497	117486522	-	1	NA	intron (NM_175645, intron 2 of 11)	intron (NM_175645, intron 2 of 11)	105530	NM_175645	233781	Mm.461427	NM_175645	ENSMUSG00000030657	Xylt1	8030490L12	xylosyltransferase 1	protein-coding
mm_147118.1	chr18	35740107	35740128	-	1	NA	intron (NM_028261, intron 1 of 7)	intron (NM_028261, intron 1 of 7)	437	NM_001289592	72512	Mm.45995	NM_028261	ENSMUSG00000024349	Tmem173	2610307O08Rik|ERIS|MPYS|Mita|STING	transmembrane protein 173	protein-coding
mm_148528.1	chr19	4510537	4510552	+	1	NA	promoter-TSS (NM_001162946)	promoter-TSS (NM_001162946)	72	NM_001162946	18563	Mm.1845	NM_008797	ENSMUSG00000024892	Pcx	Pc|Pcb	pyruvate carboxylase	protein-coding
mm_41797.1	chr5	103753707	103753718	+	1	NA	promoter-TSS (NM_133919)	promoter-TSS (NM_133919)	-450	NM_133919	17355	Mm.6949	NM_133919	ENSMUSG00000029313	Aff1	9630032B01Rik|AW319193|Af4|Mllt2h|Rob	AF4/FMR2 family, member 1	protein-coding
mm_130093.1	chr15	89424766	89424780	-	1	NA	non-coding (NR_004843, exon 12 of 27)	non-coding (NR_004843, exon 12 of 27)	1089	NM_009948	12895	Mm.227738	NM_009948	ENSMUSG00000078937	Cpt1b	Cpt1|Cpt1-m|Cpti|Cpti-m|M-cpti	carnitine palmitoyltransferase 1b, muscle	protein-coding
mm_36577.1	chr4	88031701	88031732	-	1	NA	intron (NM_027326, intron 1 of 10)	CpG	1691	NM_027326	70122	Mm.288898	NM_027326	ENSMUSG00000028496	Mllt3	2210011H10Rik|2610012I03Rik|3830408D16Rik|Af9|D4Ertd321e	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 3	protein-coding
mm_137004.1	chr17	17624710	17624726	+	1	NA	promoter-TSS (NM_172827)	promoter-TSS (NM_172827)	-229	NM_172827	240028	Mm.328807	NM_172827	ENSMUSG00000023845	Lnpep	2010309L07Rik|4732490P18Rik|CAP|IRAP|PLAP|gp160|vp165	leucyl/cystinyl aminopeptidase	protein-coding
mm_145396.1	chr18	57142783	57142796	+	1	NA	intron (NM_001001979, intron 1 of 24)	intron (NM_001001979, intron 1 of 24)	9699	NM_001001979	70417	Mm.297863	NM_001001979	ENSMUSG00000024593	Megf10	3000002B06Rik|Gm331	multiple EGF-like-domains 10	protein-coding
mm_2583.1	chr1	118627987	118628014	+	1	NA	promoter-TSS (NM_023755)	promoter-TSS (NM_023755)	55	NM_023755	81879	Mm.24621	NM_023755	ENSMUSG00000026380	Tfcp2l1	1810030F05Rik|4932442M07Rik|AA575098|Cp2l1|Crtr-1|D930018N21Rik|LBP-9|Tcfcp2l1	transcription factor CP2-like 1	protein-coding
mm_60665.1	chr7	45016588	45016608	+	1	NA	promoter-TSS (NM_001008422)	promoter-TSS (NM_001008422)	-349	NM_001008422	233208	Mm.28298	NM_001008422	ENSMUSG00000038406	Scaf1	AI480556|SR-A1	SR-related CTD-associated factor 1	protein-coding
mm_88157.1	chr10	69630792	69630795	+	1	NA	intron (NM_170730, intron 1 of 17)	T-rich|Low_complexity|Low_complexity	97085	NM_146005	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_91210.1	chr10	21342025	21342036	-	1	NA	promoter-TSS (NR_045352)	promoter-TSS (NR_045352)	25	NR_045352	73990	Mm.399240	NR_045352		4930455C13Rik	-	RIKEN cDNA 4930455C13 gene	ncRNA
mm_32503.1	chr4	108460820	108460842	+	1	NA	intron (NM_175472, intron 2 of 30)	CpG	1405	NM_175472	230594	Mm.25181	NM_175472	ENSMUSG00000034610	Zcchc11	6030404K05Rik|9230115F04Rik|PPAPD3|mKIAA0191	zinc finger, CCHC domain containing 11	protein-coding
mm_6978.1	chr1	86353811	86353859	-	1	NA	exon (NM_010880, exon 8 of 14)	exon (NM_010880, exon 8 of 14)	-1708	NR_106184	102465895		NR_106184	ENSMUSG00000104627	Gm24148	Mir3535|mir-3535|mmu-mir-3535	predicted gene, 24148	ncRNA
mm_106039.1	chr11	116079234	116079244	-	1	NA	3' UTR (NM_016852, exon 8 of 8)	3' UTR (NM_016852, exon 8 of 8)	-1278	NM_001009573	70450	Mm.259460	NM_001009573	ENSMUSG00000057948	Unc13d	2610108D09Rik|Jinx|Munc13-4|mFLJ00067	unc-13 homolog D (C. elegans)	protein-coding
mm_121684.1	chr14	13597108	13597110	-	1	NA	intron (NM_001163032, intron 3 of 4)	intron (NM_001163032, intron 3 of 4)	-73767	NM_177624	218739	Mm.39919	NM_177624	ENSMUSG00000044772	Sntn	A430083B19Rik	sentan, cilia apical structure protein	protein-coding
mm_112767.1	chr13	19358043	19358053	+	1	NA	3' UTR (NM_024270, exon 9 of 9)	3' UTR (NM_024270, exon 9 of 9)	37765	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_80664.1	chr9	90073924	90073934	+	1	NA	intron (NM_001312649, intron 9 of 10)	intron (NM_001312649, intron 9 of 10)	19662	NM_001312649	13036	Mm.2277	NM_007801	ENSMUSG00000032359	Ctsh	AL022844	cathepsin H	protein-coding
mm_74822.1	chr8	23095502	23095519	-	1	NA	intron (NR_102385, intron 11 of 45)	GSAT_MM|Satellite|Satellite	37251	NR_102385	11733	Mm.334444	NM_031158	ENSMUSG00000031543	Ank1	Ank-1|nb|pale	ankyrin 1, erythroid	protein-coding
mm_61358.1	chr7	68433094	68433109	+	1	NA	Intergenic	Intergenic	15677	NR_046208	71244	Mm.410787	NR_046208	ENSMUSG00000108924	4933436H12Rik	-	RIKEN cDNA 4933436H12 gene	ncRNA
mm_38060.1	chr4	134018748	134018754	-	1	NA	promoter-TSS (NM_145833)	promoter-TSS (NM_145833)	65	NM_145833	83557	Mm.302567	NM_145833	ENSMUSG00000050966	Lin28a	AL024421|ENSMUSG00000070700|Gm10299|Lin-28|Lin28|Tex17|lin-28A	lin-28 homolog A (C. elegans)	protein-coding
mm_14762.1	chr2	145167847	145167900	+	1	NA	Intergenic	CpG	-74738	NM_053195	94249	Mm.217171	NM_053195	ENSMUSG00000063873	Slc24a3	NCKX3	solute carrier family 24 (sodium/potassium/calcium exchanger), member 3	protein-coding
mm_27593.1	chr3	59130751	59130764	-	1	NA	promoter-TSS (NM_001287124)	promoter-TSS (NM_001287124)	5	NM_001008497	140795	Mm.439021	NM_133200	ENSMUSG00000036381	P2ry14	A330108O13Rik|Gpr105|P2Y14	purinergic receptor P2Y, G-protein coupled, 14	protein-coding
mm_11931.1	chr2	52326998	52327011	+	1	NA	exon (NM_010889, exon 6 of 157)	exon (NM_010889, exon 6 of 157)	11794	NM_010889	17996	Mm.389247	NM_010889	ENSMUSG00000026950	Neb	AI595938	nebulin	protein-coding
mm_7387.1	chr1	110977353	110977365	-	1	NA	promoter-TSS (NM_001081386)	promoter-TSS (NM_001081386)	13	NM_001081386	227485	Mm.322070	NM_001081386	ENSMUSG00000047216	Cdh19	-	cadherin 19, type 2	protein-coding
mm_128544.1	chr15	55072140	55072161	-	1	NA	promoter-TSS (NM_001081288)	promoter-TSS (NM_001081288)	2	NM_001081288	319944	Mm.380957	NM_001081288	ENSMUSG00000037343	Taf2	150kDa|4732460C16Rik|AI425886|CIF150|TAF2B|TAFII-150|TAFII150	TATA-box binding protein associated factor 2	protein-coding
mm_136052.1	chr16	78576683	78576696	-	1	NA	promoter-TSS (NM_001252440)	promoter-TSS (NM_001252440)	-1	NM_025967	67102	Mm.37332	NM_025967	ENSMUSG00000022864	D16Ertd472e	1700010I10Rik|2310009O17Rik|E330003K22Rik|Eurl	DNA segment, Chr 16, ERATO Doi 472, expressed	protein-coding
mm_108907.1	chr12	100206093	100206109	+	1	NA	exon (NM_009790, exon 5 of 6)	exon (NM_009790, exon 5 of 6)	5957	NM_001313934	12313	Mm.285993	NM_009790	ENSMUSG00000001175	Calm1	AI256814|AI327027|AI461935|AL024000|CaM|Calm	calmodulin 1	protein-coding
mm_132931.1	chr16	49854538	49854544	+	1	NA	Intergenic	RMER15|LTR|ERVL	-1113	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_58169.1	chr6	142701957	142701968	-	1	NA	intron (NM_001310143, intron 1 of 38)	intron (NM_001310143, intron 1 of 38)	312	NM_021041	20928	Mm.35670	NM_011511	ENSMUSG00000030249	Abcc9	AI414027|AI449286|SUR2A|SUR2B|Sur2	ATP-binding cassette, sub-family C (CFTR/MRP), member 9	protein-coding
mm_121605.1	chr14	8172987	8173003	-	1	NA	promoter-TSS (NM_024221)	promoter-TSS (NM_024221)	-3	NM_024221	68263	Mm.301527	NM_024221	ENSMUSG00000021748	Pdhb	2610103L06Rik|AL024199|C81408	pyruvate dehydrogenase (lipoamide) beta	protein-coding
mm_4987.1	chr1	191718379	191718394	+	1	NA	promoter-TSS (NM_001134829)	promoter-TSS (NM_001134829)	-9	NM_001134829	226856	Mm.277958	NM_172266	ENSMUSG00000026623	Lpgat1	AI649174|AW112037|BC013667	lysophosphatidylglycerol acyltransferase 1	protein-coding
mm_47372.1	chr5	122952686	122952689	-	1	NA	intron (NM_001003953, intron 6 of 22)	intron (NM_001003953, intron 6 of 22)	36412	NM_001003953	30841	Mm.86406	NM_013910	ENSMUSG00000029475	Kdm2b	Cxxc2|Fbl10|Fbxl10|Jhdm1b|PCCX2	lysine (K)-specific demethylase 2B	protein-coding
mm_90066.1	chr10	116310022	116310025	+	1	NA	intron (NM_029928, intron 2 of 31)	intron (NM_029928, intron 2 of 31)	8649	NM_029928	19263	Mm.37213	NM_029928	ENSMUSG00000020154	Ptprb	3230402H02Rik|C130094E24|Ptpz|Rptpb|VE-PTP|Veptp	protein tyrosine phosphatase, receptor type, B	protein-coding
mm_37810.1	chr4	130929500	130929532	-	1	NA	exon (NM_010686, exon 5 of 8)	exon (NM_010686, exon 5 of 8)	-14869	NM_010769	17180	Mm.271796	NM_010769	ENSMUSG00000040533	Matn1	CMP|Crtm|Mat1|matrilin-1	matrilin 1, cartilage matrix protein	protein-coding
mm_3360.1	chr1	138175629	138175637	+	1	NA	promoter-TSS (NM_001268286)	promoter-TSS (NM_001268286)	-328	NM_001268286	19264	Mm.391573	NM_011210	ENSMUSG00000026395	Ptprc	B220|CD45R|Cd45|L-CA|Ly-5|Lyt-4|T200|loc	protein tyrosine phosphatase, receptor type, C	protein-coding
mm_6183.1	chr1	65109825	65109832	-	1	NA	intron (NM_175293, intron 6 of 7)	intron (NM_175293, intron 6 of 7)	-6465	NM_007774	12964	Mm.26904	NM_007774	ENSMUSG00000044429	Cryga	Cryg-4|DGcry-4	crystallin, gamma A	protein-coding
mm_14448.1	chr2	131103448	131103458	+	1	NA	Intergenic	Intergenic	-16688	NM_011426	20612	Mm.1374	NM_011426	ENSMUSG00000027322	Siglec1	Cd169|Siglec-1|Sn	sialic acid binding Ig-like lectin 1, sialoadhesin	protein-coding
mm_156686.1	chrX	159372306	159372316	+	1	NA	5' UTR (NM_025437, exon 1 of 7)	5' UTR (NM_025437, exon 1 of 7)	116	NM_025437	66235	Mm.294623	NM_025437	ENSMUSG00000067194	Eif1ax	1500010B24Rik|AI426898|Eif1ay	eukaryotic translation initiation factor 1A, X-linked	protein-coding
mm_99793.1	chr11	107470900	107470905	+	1	NA	promoter-TSS (NM_145823)	promoter-TSS (NM_145823)	-182	NM_145823	71795	Mm.397413	NM_145823	ENSMUSG00000040430	Pitpnc1	1110020B03Rik|5830436L09Rik|AI662802|AI851387|C330017I21Rik|Dnr411|RDGBB|RDGBB1|rdgB-beta	phosphatidylinositol transfer protein, cytoplasmic 1	protein-coding
mm_75589.1	chr8	61591182	61591205	-	1	NA	promoter-TSS (NM_001293774)	promoter-TSS (NM_001293774)	-24	NM_001293774	72333	Mm.29933	NM_001081390	ENSMUSG00000058056	Palld	2410003B16Rik|6030492A02	palladin, cytoskeletal associated protein	protein-coding
mm_54732.1	chr6	40929713	40929716	-	1	NA	intron (NM_028550, intron 2 of 6)	intron (NM_028550, intron 2 of 6)	10843	NM_028550	73481	Mm.333010	NM_028550	ENSMUSG00000029883	1700074P13Rik	AV047902|Tryx5	RIKEN cDNA 1700074P13 gene	protein-coding
mm_140002.1	chr17	73037089	73037125	+	1	NA	Intergenic	Intergenic	-70878	NM_001177968	225010	Mm.329194	NM_001081071	ENSMUSG00000054469	Lclat1	AI181996|Agpat8|Alcat1|Gm91|Lycat	lysocardiolipin acyltransferase 1	protein-coding
mm_12773.1	chr2	79326828	79326841	+	1	NA	3' UTR (NM_010576, exon 28 of 28)	3' UTR (NM_010576, exon 28 of 28)	71408	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D|Itga4B	integrin alpha 4	protein-coding
mm_74075.1	chr8	122443663	122443721	+	1	NA	promoter-TSS (NM_138656)	promoter-TSS (NM_138656)	36	NR_045696	100689703	Mm.271989	NR_045696		9330133O14Rik	-	RIKEN cDNA 9330133O14 gene	ncRNA
mm_22194.1	chr2	173276527	173276544	-	1	NA	promoter-TSS (NM_022995)	promoter-TSS (NM_022995)	-2	NM_022995	65112	Mm.73682	NM_022995	ENSMUSG00000038400	Pmepa1	2210418I02Rik|AW455466|Erg1.2|N4wbp4|Stag1|Tmepai	prostate transmembrane protein, androgen induced 1	protein-coding
mm_167528.1	chr9	21288723	21288728	+	1	NA	promoter-TSS (NM_145416)	promoter-TSS (NM_145416)	-756	NM_145416	215194	Mm.290690	NM_145416	ENSMUSG00000035047	Kri1	-	KRI1 homolog	protein-coding
mm_161325.1	chr14	49960946	49960946	-	1	NA	exon (NM_146492, exon 1 of 1)	exon (NM_146492, exon 1 of 1)	150	NM_146492	258485	Mm.271405	NM_146492	ENSMUSG00000096254	Olfr724	MOR247-2	olfactory receptor 724	protein-coding
mm_165649.1	chr3	83031699	83031701	+	1	NA	exon (NM_010196, exon 5 of 5)	exon (NM_010196, exon 5 of 5)	5547	NM_001111048	14161	Mm.88793	NM_010196	ENSMUSG00000028001	Fga	ENSMUSG00000059807|Fib	fibrinogen alpha chain	protein-coding
mm_33770.1	chr4	134468335	134468406	+	1	NA	promoter-TSS (NM_019641)	promoter-TSS (NM_019641)	50	NM_019641	16765	Mm.378957	NM_019641	ENSMUSG00000028832	Stmn1	19k|Lag|Lap18|Op18|P18|P19|Pig|Pp17|Pp18|Pp19|Pr22|Smn	stathmin 1	protein-coding
mm_56615.1	chr6	112620792	112620800	-	1	NA	3' UTR (NM_021385, exon 12 of 12)	3' UTR (NM_021385, exon 12 of 12)	75874	NM_021385	58186	Mm.103812	NM_021385	ENSMUSG00000030254	Rad18	2810024C04Rik|Rad18sc	RAD18 E3 ubiquitin protein ligase	protein-coding
mm_159664.1	chr4	152130898	152130898	-	1	NA	exon (NM_207687, exon 10 of 16)	exon (NM_207687, exon 10 of 16)	-1973	NM_019585	56226	Mm.264215	NM_019585	ENSMUSG00000028943	Espn	je	espin	protein-coding
mm_20569.1	chr2	131083852	131083865	-	1	NA	exon (NM_011426, exon 4 of 21)	exon (NM_011426, exon 4 of 21)	2907	NM_011426	20612	Mm.1374	NM_011426	ENSMUSG00000027322	Siglec1	Cd169|Siglec-1|Sn	sialic acid binding Ig-like lectin 1, sialoadhesin	protein-coding
mm_61217.1	chr7	64287729	64287749	+	1	NA	promoter-TSS (NM_172742)	promoter-TSS (NM_172742)	69	NM_172742	233315	Mm.214959	NM_172742	ENSMUSG00000030522	Mtmr10	BB128963|C79734	myotubularin related protein 10	protein-coding
mm_90725.1	chr10	5185550	5185578	-	1	NA	intron (NM_001347732, intron 93 of 145)	intron (NM_001347732, intron 93 of 145)	9143	NM_001079686	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
mm_167395.1	chr8	95306557	95306576	-	1	NA	promoter-TSS (NM_145601)	promoter-TSS (NM_145601)	19	NM_145601	333329	Mm.484049	NM_145601	ENSMUSG00000031789	Cngb1	Cngb1b|Garp2|Gm1959	cyclic nucleotide gated channel beta 1	protein-coding
mm_19570.1	chr2	101640103	101640123	-	1	NA	3' UTR (NM_009019, exon 2 of 2)	3' UTR (NM_009019, exon 2 of 2)	9419	NM_009019	19373	Mm.828	NM_009019	ENSMUSG00000061311	Rag1	Rag-1	recombination activating gene 1	protein-coding
mm_80049.1	chr9	69289910	69289937	+	1	NA	promoter-TSS (NM_001289916)	promoter-TSS (NM_001289916)	82	NM_001289916	19883	Mm.378450	NM_013646	ENSMUSG00000032238	Rora	9530021D13Rik|Nr1f1|ROR1|ROR2|ROR3|nmf267|sg|staggerer|tmgc26	RAR-related orphan receptor alpha	protein-coding
mm_70646.1	chr8	14247153	14247170	+	1	NA	intron (NM_172910, intron 2 of 15)	ORR1E|LTR|ERVL-MaLR	151286	NM_172910	244310	Mm.404697	NM_172910	ENSMUSG00000047495	Dlgap2	6430596N04Rik|Dap-2|Dap2|Sapap2	discs, large (Drosophila) homolog-associated protein 2	protein-coding
mm_93359.1	chr10	103046303	103046305	-	1	NA	Intergenic	Intergenic	-17527	NM_172553	216285	Mm.19287	NM_172553	ENSMUSG00000036602	Alx1	AI314867|C130005I02|Cart1	ALX homeobox 1	protein-coding
mm_70552.1	chr8	13060576	13060587	+	1	NA	promoter-TSS (NM_025834)	promoter-TSS (NM_025834)	-327	NM_025834	66901	Mm.441140	NM_025834	ENSMUSG00000031445	Proz	1300015B06Rik	protein Z, vitamin K-dependent plasma glycoprotein	protein-coding
mm_116925.1	chr13	55568073	55568077	-	1	NA	intron (NM_145382, intron 1 of 10)	(A)n|Simple_repeat|Simple_repeat	3045	NM_145382	212483	Mm.35661	NM_145382	ENSMUSG00000021495	Fam193b	IRIZIO|Kiaa1931	family with sequence similarity 193, member B	protein-coding
mm_169844.1	chr16	3120594	3120595	-	1	NA	Intergenic	Intergenic	-471804	NM_146860	258859	Mm.377723	NM_146860	ENSMUSG00000051003	Olfr161	MOR131-1|OR912-47M6	olfactory receptor 161	protein-coding
mm_116880.1	chr13	55073797	55073811	-	1	NA	intron (NM_001293660, intron 4 of 12)	ID_B1|SINE|B4	26491	NM_011307	20184	Mm.259301	NM_011307	ENSMUSG00000025878	Uimc1	9430016E08Rik|D330018D10Rik|D630032M02Rik|RIP110|Rxrip110	ubiquitin interaction motif containing 1	protein-coding
mm_30560.1	chr4	3779337	3779352	+	1	NA	intron (NM_010747, intron 10 of 12)	(CA)n|Simple_repeat|Simple_repeat	56311	NM_026147	67427	Mm.21938	NM_026147	ENSMUSG00000028234	Rps20	4632426K06Rik|Dsk4	ribosomal protein S20	protein-coding
mm_75296.1	chr8	41054859	41054869	-	1	NA	promoter-TSS (NM_001005864)	promoter-TSS (NM_001005864)	-68	NM_001005864	102103	Mm.149438	NM_001005863	ENSMUSG00000045636	Mtus1	AI481402|ATBP135|Atip1|B430010I23Rik|B430305I03Rik|C85752|Cctsg1-440|MD44|MTSG1|mKIAA1288	mitochondrial tumor suppressor 1	protein-coding
mm_89096.1	chr10	84516711	84516715	+	1	NA	Intergenic	Intergenic	17175	NM_175451	216197	Mm.334999	NM_175451	ENSMUSG00000046841	Ckap4	5630400A09Rik|CLIMP-63|P63	cytoskeleton-associated protein 4	protein-coding
mm_96270.1	chr11	62820431	62820447	+	1	NA	5' UTR (NM_053169, exon 1 of 6)	5' UTR (NM_053169, exon 1 of 6)	186	NM_053169	94092	Mm.117087	NM_053169	ENSMUSG00000047821	Trim16	9130006M08Rik|AI482483|EBBP	tripartite motif-containing 16	protein-coding
mm_4944.1	chr1	191186689	191186701	+	1	NA	Intergenic	Intergenic	-3362	NM_007498	11910	Mm.2706	NM_007498	ENSMUSG00000026628	Atf3	LRG-21	activating transcription factor 3	protein-coding
mm_9121.1	chr1	170215381	170215420	-	1	NA	promoter-TSS (NM_010633)	promoter-TSS (NM_010633)	-7	NM_010633	16589	Mm.209150	NM_010633	ENSMUSG00000026667	Uhmk1	4732477C12Rik|4930500M09Rik|AA673513|AI449218|AU021979|C820018A03Rik|KIS|Kist|OTTMUSG00000021542|P-CIP2	U2AF homology motif (UHM) kinase 1	protein-coding
mm_104037.1	chr11	86286476	86286482	-	1	NA	exon (NM_001080931, exon 20 of 30)	exon (NM_001080931, exon 20 of 30)	-28911	NM_027421	70422	Mm.171304	NM_027421	ENSMUSG00000018068	Ints2	2810417D08Rik|AA408260|AI987735|mKIAA1287	integrator complex subunit 2	protein-coding
mm_95122.1	chr11	34083506	34083520	+	1	NA	intron (NM_010696, intron 17 of 20)	intron (NM_010696, intron 17 of 20)	36312	NM_010696	16822	Mm.265350	NM_010696	ENSMUSG00000002699	Lcp2	AI323664|BB161688|SLP-76|SLP76|m1Khoe|twm	lymphocyte cytosolic protein 2	protein-coding
mm_64863.1	chr7	13038202	13038307	-	1	NA	promoter-TSS (NM_145578)	promoter-TSS (NM_145578)	21	NM_001168469	22192	Mm.196580	NM_145578	ENSMUSG00000005575	Ube2m	2510040H03Rik|UBC12|Ubc-rs2	ubiquitin-conjugating enzyme E2M	protein-coding
mm_102366.1	chr11	58390165	58390178	-	1	NA	exon (NM_001083884, exon 7 of 7)	exon (NM_001083884, exon 7 of 7)	9525	NM_001330197	70163	Mm.24119	NM_027339	ENSMUSG00000013643	Lypd8	2210415F13Rik	LY6/PLAUR domain containing 8	protein-coding
mm_50374.1	chr6	48681988	48681996	+	1	NA	Intergenic	Intergenic	-2586	NM_001243200	107526	Mm.333048	NM_174990	ENSMUSG00000054435	Gimap4	AU019574|E430007K16Rik|Ian-1|Ian1|Imap4	GTPase, IMAP family member 4	protein-coding
mm_5067.1	chr1	195018596	195018600	+	1	NA	intron (NR_015566, intron 1 of 7)	intron (NR_015566, intron 1 of 7)	1199	NR_015566	320977	Mm.99905	NR_015566	ENSMUSG00000096929	A330023F24Rik	C030002C11Rik	RIKEN cDNA A330023F24 gene	ncRNA
mm_130712.1	chr15	100755298	100755301	-	1	NA	Intergenic	Intergenic	-6448	NM_021530	59033	Mm.209856	NM_021530	ENSMUSG00000023032	Slc4a8	AW493845|C230026C11|NDCBE|kNBC-3	solute carrier family 4 (anion exchanger), member 8	protein-coding
mm_169729.1	chr15	8109359	8109359	+	1	NA	promoter-TSS (NM_133227)	promoter-TSS (NM_133227)	46	NM_133227	170762	Mm.295168	NM_133227	ENSMUSG00000022142	Nup155	D930027M19Rik|mKIAA0791	nucleoporin 155	protein-coding
mm_126186.1	chr15	78615840	78615850	+	1	NA	intron (NM_028195, intron 9 of 12)	intron (NM_028195, intron 9 of 12)	18798	NM_028195	72318	Mm.32911	NM_028195	ENSMUSG00000018008	Cyth4	2510004M07Rik|5830469K17Rik|AI467541|Pscd4|mFLJ00017	cytohesin 4	protein-coding
mm_53387.1	chr6	129533252	129533268	+	1	NA	promoter-TSS (NR_045270)	promoter-TSS (NR_045270)	24	NR_045270	100504641	Mm.398286	NR_045270	ENSMUSG00000097675	1700101I11Rik	-	RIKEN cDNA 1700101I11 gene	ncRNA
mm_158817.1	chrX	167330482	167330503	-	1	NA	promoter-TSS (NM_001290758)	promoter-TSS (NM_001290758)	79	NM_001290757	170743	Mm.23979	NM_133211	ENSMUSG00000044583	Tlr7	-	toll-like receptor 7	protein-coding
mm_138062.1	chr17	33929961	33929998	+	1	NA	promoter-TSS (NM_009059)	promoter-TSS (NM_009059)	85	NM_009059	19732	Mm.43777	NM_009059	ENSMUSG00000041354	Rgl2	KE1.5|Rab2l|Rgt2|Rlf	ral guanine nucleotide dissociation stimulator-like 2	protein-coding
mm_166405.1	chr5	136460320	136460324	+	1	NA	intron (NM_001291239, intron 2 of 22)	B3A|SINE|B2	-84519	NR_030500	723975		NR_030500	ENSMUSG00000106479	Mir721	Mirn721|miRY|mir-721|mmu-mir-721	microRNA 721	ncRNA
mm_121608.1	chr14	8258801	8258813	-	1	NA	promoter-TSS (NM_001161667)	promoter-TSS (NM_001161667)	32	NM_001161667	93732	Mm.28700	NM_053115	ENSMUSG00000021751	Acox2	THCCox	acyl-Coenzyme A oxidase 2, branched chain	protein-coding
mm_26844.1	chr3	14766571	14766597	-	1	NA	exon (NM_001083957, exon 7 of 7)	exon (NM_001083957, exon 7 of 7)	11876	NM_001083957	12346	Mm.273195	NM_009799	ENSMUSG00000027556	Car1	AW555628|Ca1|Car-1	carbonic anhydrase 1	protein-coding
mm_28104.1	chr3	86548269	86548290	-	1	NA	promoter-TSS (NM_011839)	promoter-TSS (NM_011839)	4	NM_011839	23937	Mm.389466	NM_011839	ENSMUSG00000057777	Mab21l2	-	mab-21-like 2 (C. elegans)	protein-coding
mm_31437.1	chr4	48540153	48540167	+	1	NA	promoter-TSS (NM_028137)	promoter-TSS (NM_028137)	79	NM_001145924	66665	Mm.140749	NM_028137	ENSMUSG00000039693	Msantd3	2410046L14Rik|2810429P03Rik|5730528L13Rik|Mysantd3	Myb/SANT-like DNA-binding domain containing 3	protein-coding
mm_31907.1	chr4	84698305	84698326	+	1	NA	Intergenic	Intergenic	-23229	NM_172870	242509	Mm.190774	NM_172870	ENSMUSG00000028487	Bnc2	5031434M05Rik|8430420F16Rik	basonuclin 2	protein-coding
mm_114798.1	chr13	90089678	90089688	+	1	NA	promoter-TSS (NM_025335)	promoter-TSS (NM_025335)	16	NM_025335	66074	Mm.241387	NM_025335	ENSMUSG00000012422	Tmem167	0610041E09Rik|5730424F14Rik|AU041184|AW537806|ENSMUSG00000060669|Gm10085|Tmem167a	transmembrane protein 167	protein-coding
mm_9598.1	chr1	175479540	175479545	-	1	NA	intron (NM_001347195, intron 2 of 17)	intron (NM_001347195, intron 2 of 17)	13003	NM_011880	24012	Mm.7956	NM_011880	ENSMUSG00000026527	Rgs7	-	regulator of G protein signaling 7	protein-coding
mm_17140.1	chr2	25095081	25095092	-	1	NA	5' UTR (NM_001163626, exon 1 of 12)	5' UTR (NM_001163626, exon 1 of 12)	119	NM_001163626	241275	Mm.218774	NM_172204	ENSMUSG00000036805	Noxa1	NY-CO-31|SDCCAG31	NADPH oxidase activator 1	protein-coding
mm_173230.1	chrX	7950876	7950883	-	1	NA	Intergenic	Intergenic	-2990	NM_010413	15185	Mm.29854	NM_010413	ENSMUSG00000031161	Hdac6	Hd6|Hdac5|Sfc6|mHDA2	histone deacetylase 6	protein-coding
mm_107082.1	chr12	17266610	17266618	+	1	NA	promoter-TSS (NM_027959)	promoter-TSS (NM_027959)	19	NM_027959	71853	Mm.222825	NM_027959	ENSMUSG00000020571	Pdia6	1700015E05Rik|AL023058|C77895|CaBP5|P5|Txndc7	protein disulfide isomerase associated 6	protein-coding
mm_54920.1	chr6	47807215	47807225	-	1	NA	intron (NM_009787, intron 2 of 9)	intron (NM_009787, intron 2 of 9)	-3568	NR_030485	735289		NR_030485	ENSMUSG00000076060	Mir704	Mirn704|mir-704|mmu-mir-704	microRNA 704	ncRNA
mm_35596.1	chr4	43025793	43025832	-	1	NA	promoter-TSS (NM_020035)	promoter-TSS (NM_020035)	2	NM_001305386	56703	Mm.143738	NM_020035	ENSMUSG00000028454	Pigo	PIG-O	phosphatidylinositol glycan anchor biosynthesis, class O	protein-coding
mm_163364.1	chr12	32995732	32995783	+	1	NA	Intergenic	Intergenic	41571	NM_198710	19027	Mm.246304	NM_013635	ENSMUSG00000020570	Sypl	AI314763|AI604763|D12Ertd446e|PanI|Pphn|Sypl1	synaptophysin-like protein	protein-coding
mm_135278.1	chr16	38443923	38443929	-	1	NA	Intergenic	ID_B1|SINE|B4	8763	NM_007414	11544	Mm.20047	NM_007414	ENSMUSG00000002844	Adprh	Arh1	ADP-ribosylarginine hydrolase	protein-coding
mm_89137.1	chr10	85540165	85540202	+	1	NA	intron (NM_028709, intron 1 of 16)	intron (NM_028709, intron 1 of 16)	-58228	NM_001017525	74007	Mm.36544	NM_028709	ENSMUSG00000020042	Btbd11	6330404E16Rik	BTB (POZ) domain containing 11	protein-coding
mm_18057.1	chr2	39226344	39226354	-	1	NA	promoter-TSS (NM_024209)	promoter-TSS (NM_024209)	-11	NM_024209	67857	Mm.389242	NM_024209	ENSMUSG00000026753	Ppp6c	2310003C10Rik	protein phosphatase 6, catalytic subunit	protein-coding
mm_28624.1	chr3	95106908	95106922	-	1	NA	promoter-TSS (NM_008847)	promoter-TSS (NM_008847)	15	NM_001293707	18720	Mm.296409	NM_008847	ENSMUSG00000028126	Pip5k1a	PI4P5K-I[a]|PIP5K1-alpha|PIP5KIalpha|Pipk5a	phosphatidylinositol-4-phosphate 5-kinase, type 1 alpha	protein-coding
mm_134128.1	chr16	10395477	10395483	-	1	NA	promoter-TSS (NM_001099275)	promoter-TSS (NM_001099275)	-15	NM_001291001	70426	Mm.142181	NM_001099275	ENSMUSG00000039179	Tekt5	3300001K11Rik	tektin 5	protein-coding
mm_121305.1	chr14	105897485	105897496	+	1	NA	promoter-TSS (NM_011897)	promoter-TSS (NM_011897)	-671	NM_011897	24064	Mm.89982	NM_011897	ENSMUSG00000022114	Spry2	sprouty2	sprouty homolog 2 (Drosophila)	protein-coding
mm_121745.1	chr14	18868955	18868970	-	1	NA	intron (NM_144839, intron 3 of 5)	L1M4|LINE|L1	24665	NM_144839	218793	Mm.23551	NM_144839	ENSMUSG00000058317	Ube2e2	BC016265	ubiquitin-conjugating enzyme E2E 2	protein-coding
mm_124638.1	chr15	4375575	4375623	+	1	NA	5' UTR (NM_177355, exon 1 of 3)	5' UTR (NM_177355, exon 1 of 3)	108	NM_177355	239318	Mm.308996	NM_177355	ENSMUSG00000049148	Plcxd3	B130016O10Rik	phosphatidylinositol-specific phospholipase C, X domain containing 3	protein-coding
mm_165189.1	chr2	29903309	29903319	+	1	NA	intron (NM_013615, intron 6 of 16)	intron (NM_013615, intron 6 of 16)	13251	NM_013615	18286	Mm.330116	NM_013615	ENSMUSG00000026790	Odf2	AI848335|MMTEST29	outer dense fiber of sperm tails 2	protein-coding
mm_160271.1	chr7	118442435	118442435	-	1	NA	exon (NM_138649, exon 3 of 8)	exon (NM_138649, exon 3 of 8)	1117	NM_138649	110058	Mm.156558	NM_138649	ENSMUSG00000058420	Syt17	Bk	synaptotagmin XVII	protein-coding
mm_14831.1	chr2	147361960	147361966	+	1	NA	intron (NR_040330, intron 1 of 1)	intron (NR_040330, intron 1 of 1)	830	NR_040330	99041	Mm.373081	NR_040330		AI646519	Aspax1|OTTMUSG00000015701	expressed sequence AI646519	ncRNA
mm_156112.1	chrX	114474510	114474522	+	1	NA	exon (NM_001290478, exon 1 of 11)	exon (NM_001290478, exon 1 of 11)	183	NM_001290477	237010	Mm.132583	NM_172781	ENSMUSG00000025597	Klhl4	B130014A11|C130018J01Rik	kelch-like 4	protein-coding
mm_57416.1	chr6	124911624	124911628	-	1	NA	promoter-TSS (NM_008479)	promoter-TSS (NM_008479)	79	NM_008479	16768	Mm.4528	NM_008479	ENSMUSG00000030124	Lag3	CD223|LAG-3|Ly66	lymphocyte-activation gene 3	protein-coding
mm_125432.1	chr15	44457424	44457434	+	1	NA	promoter-TSS (NM_138674)	promoter-TSS (NM_138674)	-124	NM_138674	192190	Mm.211494	NM_138674	ENSMUSG00000038725	Pkhd1l1	AB055648|PKHDL1	polycystic kidney and hepatic disease 1-like 1	protein-coding
mm_79750.1	chr9	62373160	62373182	+	1	NA	intron (NM_009672, intron 3 of 6)	intron (NM_009672, intron 3 of 6)	31828	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	protein-coding
mm_96479.1	chr11	67682526	67682535	+	1	NA	intron (NM_001109657, intron 12 of 13)	intron (NM_001109657, intron 12 of 13)	-12796	NM_009038	19674	Mm.439726	NM_009038	ENSMUSG00000020907	Rcvrn	CAR|S-modulin	recoverin	protein-coding
mm_54507.1	chr6	35511116	35511148	-	1	NA	3' UTR (NM_008098, exon 4 of 4)	3' UTR (NM_008098, exon 4 of 4)	28756	NM_008098	14489	Mm.182746	NM_008098	ENSMUSG00000029840	Mtpn	5033418D15Rik|Gcdp|V1	myotrophin	protein-coding
mm_144635.1	chr18	32958565	32958577	+	1	NA	intron (NM_009793, intron 1 of 10)	intron (NM_009793, intron 1 of 10)	19530	NM_009793	12326	Mm.222329	NM_009793	ENSMUSG00000038128	Camk4	A430110E23Rik|AI666733|CaMKIV|CaMKIV/Gr|D18Bwg0362e	calcium/calmodulin-dependent protein kinase IV	protein-coding
mm_13188.1	chr2	93187773	93187783	+	1	NA	intron (NM_001025246, intron 1 of 7)	CpG	194	NM_001025246	277414	Mm.41033	NM_001025246	ENSMUSG00000068735	Trp53i11	Tp53i11	transformation related protein 53 inducible protein 11	protein-coding
mm_20599.1	chr2	131352814	131352832	-	1	NA	promoter-TSS (NM_178607)	promoter-TSS (NM_178607)	69	NM_178607	51902	Mm.477523	NM_178607	ENSMUSG00000048911	Rnf24	2810473M14Rik|4930505A13Rik|AI317164|C86507|D2Ertd504e	ring finger protein 24	protein-coding
mm_134543.1	chr16	19873100	19873102	-	1	NA	Intergenic	RodERV21-int|LTR|ERV1	11173	NR_027896	68162	Mm.35159	NR_015488		A930003A15Rik	AI853191	RIKEN cDNA A930003A15 gene	ncRNA
mm_26320.1	chr3	142521731	142521743	+	1	NA	3' UTR (NM_153564, exon 11 of 11)	3' UTR (NM_153564, exon 11 of 11)	-8599	NM_001083312	229900	Mm.45740	NM_145545	ENSMUSG00000040253	Gbp7	9830147J24Rik	guanylate binding protein 7	protein-coding
mm_81508.1	chr9	110034776	110034791	+	1	NA	exon (NM_008633, exon 7 of 19)	exon (NM_008633, exon 7 of 19)	-17238	NM_001311163	17758	Mm.217318	NM_008633	ENSMUSG00000032479	Map4	AA407148|MAP-4|Mtap-4|Mtap4	microtubule-associated protein 4	protein-coding
mm_29963.1	chr3	133464265	133464268	-	1	NA	3' UTR (NM_001346736, exon 12 of 12)	3' UTR (NM_001346736, exon 12 of 12)	80124	NM_001346736	214133	Mm.347816	NM_145989	ENSMUSG00000040943	Tet2	Ayu17-449|E130014J05Rik|mKIAA1546	tet methylcytosine dioxygenase 2	protein-coding
mm_154882.1	chrX	20698744	20698778	+	1	NA	3' UTR (NM_011049, exon 16 of 16)	3' UTR (NM_011049, exon 16 of 16)	-5148	NM_145628	236733	Mm.34489	NM_145628	ENSMUSG00000031066	Usp11	6230415D12Rik|mKIAA4085	ubiquitin specific peptidase 11	protein-coding
mm_120463.1	chr14	65971050	65971074	+	1	NA	intron (NM_013492, intron 1 of 8)	intron (NM_013492, intron 1 of 8)	2579	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_821.1	chr1	46852917	46852931	+	1	NA	intron (NM_172653, intron 1 of 9)	CpG	585	NM_172653	227059	Mm.233889	NM_172653	ENSMUSG00000025986	Slc39a10	2900042E17Rik|5430433I10|mKIAA1265	solute carrier family 39 (zinc transporter), member 10	protein-coding
mm_34869.1	chr4	155558258	155558279	+	1	NA	3' UTR (NM_008142, exon 12 of 12)	3' UTR (NM_008142, exon 12 of 12)	-4124	NM_138671	192185	Mm.28347	NM_138671	ENSMUSG00000029063	Nadk	4432404C02Rik|BC004012	NAD kinase	protein-coding
mm_91190.1	chr10	21143052	21143062	-	1	NA	exon (NM_001198914, exon 11 of 16)	exon (NM_001198914, exon 11 of 16)	17927	NM_001198914	17863	Mm.52109	NM_010848	ENSMUSG00000019982	Myb	AI550390|M16449|c-myb	myeloblastosis oncogene	protein-coding
mm_154074.1	chr19	56420499	56420503	-	1	NA	intron (NM_007611, intron 2 of 6)	RLTR11B|LTR|ERVK	23372	NM_007611	12369	Mm.35687	NM_007611	ENSMUSG00000025076	Casp7	AI314680|CMH-1|ICE-IAP3|Mch3|caspase-7|mCASP-7	caspase 7	protein-coding
mm_36248.1	chr4	63403270	63403274	-	1	NA	5' UTR (NM_001045514, exon 1 of 22)	5' UTR (NM_001045514, exon 1 of 22)	173	NM_001045514	100182	Mm.387725	NM_001045514	ENSMUSG00000039158	Akna	AI597013	AT-hook transcription factor	protein-coding
mm_109719.1	chr12	116077721	116077839	+	1	NA	promoter-TSS (NM_009511)	promoter-TSS (NM_009511)	54	NM_009511	22355	Mm.395245	NM_009511	ENSMUSG00000011171	Vipr2	VPAC2|VPAC2R|Vip2	vasoactive intestinal peptide receptor 2	protein-coding
mm_149539.1	chr19	12501179	12501198	+	1	NA	exon (NM_172442, exon 1 of 9)	exon (NM_172442, exon 1 of 9)	808	NM_172442	207521	Mm.247695	NM_172442	ENSMUSG00000039982	Dtx4	AI449438|BC044798|D930042H13|RNF155	deltex 4, E3 ubiquitin ligase	protein-coding
mm_150362.1	chr19	34649219	34649238	+	1	NA	3' UTR (NM_008331, exon 2 of 2)	3' UTR (NM_008331, exon 2 of 2)	8339	NM_008331	15957	Mm.439751	NM_008331	ENSMUSG00000034459	Ifit1	ISG56|Ifi56|P56	interferon-induced protein with tetratricopeptide repeats 1	protein-coding
mm_161198.1	chr13	55402979	55402979	+	1	NA	exon (NM_011392, exon 7 of 13)	exon (NM_011392, exon 7 of 13)	3331	NM_011392	20505	Mm.276355	NM_011392	ENSMUSG00000021490	Slc34a1	NaPi-IIa|Npt2|Npt2a|Slc17a2	solute carrier family 34 (sodium phosphate), member 1	protein-coding
mm_124747.1	chr15	6619679	6619708	+	1	NA	exon (NM_001278269, exon 2 of 17)	exon (NM_001278269, exon 2 of 17)	39846	NM_011815	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_10306.1	chr2	11172055	11172072	+	1	NA	promoter-TSS (NM_008859)	promoter-TSS (NM_008859)	-319	NM_008859	18761	Mm.329993	NM_008859	ENSMUSG00000026778	Prkcq	A130035A12Rik|AW494342|PKC-0|PKC-theta|PKCtheta|Pkcq	protein kinase C, theta	protein-coding
mm_1981.1	chr1	86703789	86703843	+	1	NA	promoter-TSS (NM_001172157)	promoter-TSS (NM_001172157)	12	NM_001172157	208718	Mm.389152	NM_153530	ENSMUSG00000053333	Dis3l2	4930429A22Rik|8030493P09Rik	DIS3 like 3'-5' exoribonuclease 2	protein-coding
mm_158955.1	chr1	88227001	88227001	+	1	NA	promoter-TSS (NM_001281466)	promoter-TSS (NM_001281466)	-19	NM_001281466	100040766	Mm.386915	NM_001177364	ENSMUSG00000079429	Mroh2a	ENSMUSG00000044873|Heatr7b1|OTTMUSG00000020804	maestro heat-like repeat family member 2A	protein-coding
mm_34892.1	chr4	155624500	155624514	+	1	NA	promoter-TSS (NM_007661)	promoter-TSS (NM_007661)	248	NR_040441	100502734	Mm.306018	NR_040441	ENSMUSG00000086682	Gm16023	OTTMUSG00000029160	predicted gene 16023	ncRNA
mm_53491.1	chr6	135198011	135198023	+	1	NA	promoter-TSS (NM_028982)	promoter-TSS (NM_028982)	30	NM_028982	74525	Mm.34182	NM_028982	ENSMUSG00000030207	Fam234b	8430419L09Rik|Kiaa1467|mKIAA1467	family with sequence similarity 234, member B	protein-coding
mm_32346.1	chr4	104799199	104799219	+	1	NA	intron (NM_001316671, intron 8 of 10)	intron (NM_001316671, intron 8 of 10)	32892	NM_001316671	110382	Mm.87072	NM_133882	ENSMUSG00000029656	C8b	4930439B20Rik|AI595927	complement component 8, beta polypeptide	protein-coding
mm_157111.1	chrX	9438218	9438218	-	1	NA	exon (NM_007807, exon 13 of 13)	exon (NM_007807, exon 13 of 13)	31106	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_129846.1	chr15	83162265	83162305	-	1	NA	exon (NM_029787, exon 3 of 9)	exon (NM_029787, exon 3 of 9)	9923	NM_029787	109754	Mm.22560	NM_029787	ENSMUSG00000018042	Cyb5r3	0610016L08Rik|2500002N19Rik|C85115|Dia-1|Dia1|WU:AL591952.1-001|WU:AL591952.1-002|WU:AL591952.1-003|WU:Cyb5r3	cytochrome b5 reductase 3	protein-coding
mm_104946.1	chr11	100121559	100121572	-	1	NA	promoter-TSS (NM_010662)	promoter-TSS (NM_010662)	1	NM_010662	16663	Mm.4646	NM_010662	ENSMUSG00000044041	Krt13	CK13|K13|Krt-1.13|Krt1-13	keratin 13	protein-coding
mm_18904.1	chr2	76718990	76719001	-	1	NA	exon (NM_011652, exon 299 of 313)	exon (NM_011652, exon 299 of 313)	43680	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_1569.1	chr1	74238293	74238320	+	1	NA	intron (NM_029711, intron 1 of 9)	intron (NM_029711, intron 1 of 9)	1756	NM_029711	76709	Mm.337038	NM_029711	ENSMUSG00000006304	Arpc2	2210023N03Rik|34kDa|p34-Arc	actin related protein 2/3 complex, subunit 2	protein-coding
mm_120459.1	chr14	65970611	65970621	+	1	NA	intron (NM_013492, intron 1 of 8)	intron (NM_013492, intron 1 of 8)	2133	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_125032.1	chr15	25754822	25754838	+	1	NA	intron (NM_019472, intron 19 of 40)	intron (NM_019472, intron 19 of 40)	-88468	NM_001034851	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_524.1	chr1	37614440	37614449	+	1	NA	intron (NM_028096, intron 8 of 9)	intron (NM_028096, intron 8 of 9)	-73428	NM_173870	269181	Mm.25861	NM_173870	ENSMUSG00000026110	Mgat4a	9530018I07Rik|GnT-IVa|glcNAc-T-IVa	mannoside acetylglucosaminyltransferase 4, isoenzyme A	protein-coding
mm_142172.1	chr17	36231569	36231586	-	1	NA	Intergenic	CpG	26269	NM_026308	67676	Mm.27131	NM_026308	ENSMUSG00000024446	Rpp21	0610037N01Rik	ribonuclease P 21 subunit	protein-coding
mm_86820.1	chr10	20952583	20952593	+	1	NA	promoter-TSS (NM_026203)	promoter-TSS (NM_026203)	41	NM_026203	52906	Mm.253280	NM_026203	ENSMUSG00000019986	Ahi1	1700015F03Rik|Ahi-1|D10Bwg0629e	Abelson helper integration site 1	protein-coding
mm_63164.1	chr7	123993257	123993271	+	1	NA	intron (NM_001252072, intron 1 of 1)	B4A|SINE|B4	10083	NM_001252072	628779	Mm.40210	NM_001252072	ENSMUSG00000078591	Hs3st4	EG628779|Gm6915	heparan sulfate (glucosamine) 3-O-sulfotransferase 4	protein-coding
mm_61984.1	chr7	90972428	90972442	+	1	NA	Intergenic	Intergenic	-118351	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_27262.1	chr3	37724322	37724338	-	1	NA	promoter-TSS (NM_198657)	promoter-TSS (NM_198657)	30	NM_198657	381438	Mm.490549	NM_198657	ENSMUSG00000058174	Gm5148	EG381438	predicted gene 5148	protein-coding
mm_155191.1	chrX	56454837	56454849	+	1	NA	promoter-TSS (NM_172779)	promoter-TSS (NM_172779)	4	NM_172779	236790	Mm.474772	NM_172779	ENSMUSG00000035967	Ints6l	4930535D10Rik|6330505F04Rik|D130066O12|Ddx26b	integrator complex subunit 6 like	protein-coding
mm_92166.1	chr10	67549078	67549094	-	1	NA	promoter-TSS (NM_001005419)	promoter-TSS (NM_001005419)	-131	NM_001005419	211488	Mm.297250	NM_001005419	ENSMUSG00000057134	Ado	Gm237	2-aminoethanethiol (cysteamine) dioxygenase	protein-coding
mm_97498.1	chr11	78348171	78348200	+	1	NA	exon (NM_011676, exon 4 of 5)	exon (NM_011676, exon 4 of 5)	1475	NM_001313987	22248	Mm.284811	NM_011676	ENSMUSG00000002058	Unc119	D11Bhm52|HRG4|MRG4|Rg4|Rtg4|Unc119h	unc-119 lipid binding chaperone	protein-coding
mm_98504.1	chr11	94952094	94952098	+	1	NA	3' UTR (NM_007742, exon 51 of 51)	3' UTR (NM_007742, exon 51 of 51)	-15497	NM_018792	54388	Mm.30482	NM_018792	ENSMUSG00000038994	Hils1	H1.9|TISP64	histone H1-like protein in spermatids 1	protein-coding
mm_154643.1	chrX	7774770	7774781	+	1	NA	3' UTR (NM_001271491, exon 9 of 9)	3' UTR (NM_001271491, exon 9 of 9)	10734	NM_001271491	209446	Mm.249142	NM_172472	ENSMUSG00000000134	Tfe3	F830016E06Rik|Tcfe3|Tfe-3|bHLHe33	transcription factor E3	protein-coding
mm_81205.1	chr9	107569157	107569184	+	1	NA	promoter-TSS (NM_010489)	promoter-TSS (NM_010489)	7	NM_010489	15587	Mm.4834	NM_010489	ENSMUSG00000010047	Hyal2	AI256841|AU020858|AW555733	hyaluronoglucosaminidase 2	protein-coding
mm_86725.1	chr10	19062742	19062756	+	1	NA	Intergenic	Intergenic	-47339	NM_009397	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_2057.1	chr1	87470291	87470291	+	1	NA	promoter-TSS (NM_028473)	promoter-TSS (NM_028473)	27	NM_028473	73234	Mm.7310	NM_028473	ENSMUSG00000026258	3110079O15Rik	Snorc	RIKEN cDNA 3110079O15 gene	protein-coding
mm_17509.1	chr2	29100888	29100924	-	1	NA	Intergenic	MLTR25A|LTR|ERVK	-24086	NM_198033	269254	Mm.41867	NM_198033	ENSMUSG00000043535	Setx	A130090N03|A930037J23Rik|AOA2|AW060766|Als4|SCAR1|Sen1|mKIAA0625	senataxin	protein-coding
mm_161100.1	chr12	100112334	100112334	+	1	NA	promoter-TSS (NM_008947)	promoter-TSS (NM_008947)	3	NM_008947	19179	Mm.157105	NM_008947	ENSMUSG00000021178	Psmc1	AI325227|P26s4|Rpt2/S4|S4|rpt2	protease (prosome, macropain) 26S subunit, ATPase 1	protein-coding
mm_169784.1	chr16	11272224	11272228	-	1	NA	Intergenic	B1_Mus1|SINE|Alu	-17781	NR_035466	100316833		NR_035466	ENSMUSG00000088544	Mir1945	mir-1945|mmu-mir-1945	microRNA 1945	ncRNA
mm_105310.1	chr11	102819664	102819685	-	1	NA	promoter-TSS (NM_001159382)	promoter-TSS (NM_001159382)	12	NM_001159383	14615	Mm.390369	NM_008122	ENSMUSG00000034520	Gjc1	C130009G16Rik|Cnx45|Cx45|Gja-7|Gja7	gap junction protein, gamma 1	protein-coding
mm_73403.1	chr8	105893543	105893576	+	1	NA	promoter-TSS (NM_175024)	promoter-TSS (NM_175024)	-8	NM_001301174	234700	Mm.133990	NM_175024	ENSMUSG00000044287	Nrn1l	Cpg15-2|G630049C14Rik	neuritin 1-like	protein-coding
mm_82543.1	chr9	20879743	20879749	-	1	NA	promoter-TSS (NM_145154)	promoter-TSS (NM_145154)	-36	NM_145154	70726	Mm.34019	NM_145154	ENSMUSG00000038742	Angptl6	6330404E11Rik|AGF|ARP3|Arp5	angiopoietin-like 6	protein-coding
mm_154307.1	chr19	61226651	61226700	-	1	NA	intron (NM_009970, intron 4 of 11)	CpG-7695	1743	NM_009970	12982	Mm.287228	NM_009970	ENSMUSG00000059326	Csf2ra	CD116|Csfgmra|GM-CSF-Ra|GM-CSFR	colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)	protein-coding
mm_50157.1	chr6	41547298	41547308	+	1	NA	Intergenic	Intergenic	25527	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_66629.1	chr7	45510352	45510360	-	1	NA	promoter-TSS (NM_008749)	promoter-TSS (NM_008749)	52	NM_008749	18220	Mm.258923	NM_008749	ENSMUSG00000030824	Nucb1	B230337F23Rik|C77483|Calnuc|MTEST82|Nucb	nucleobindin 1	protein-coding
mm_114428.1	chr13	64687633	64687636	+	1	NA	Intergenic	Intergenic	-189842	NM_001195435	68880	Mm.390594	NM_001195435	ENSMUSG00000096537	1190003K10Rik	-	RIKEN cDNA 1190003K10 gene	protein-coding
mm_45743.1	chr5	86518678	86518690	-	1	NA	promoter-TSS (NM_177162)	promoter-TSS (NM_177162)	-84	NM_177162	320454	Mm.184522	NM_177162	ENSMUSG00000079451	Tmprss11g	9930032O22Rik|Desc4	transmembrane protease, serine 11g	protein-coding
mm_92902.1	chr10	83337423	83337447	-	1	NA	intron (NM_177388, intron 1 of 10)	CpG	382	NM_177388	338365	Mm.67073	NM_177388	ENSMUSG00000034591	Slc41a2	A230035L05Rik|SLC41A1-L1	solute carrier family 41, member 2	protein-coding
mm_99102.1	chr11	100052282	100052292	+	1	NA	Intergenic	Intergenic	-1736	NM_010659	16660	Mm.439673	NM_010659	ENSMUSG00000048981	Krt31	Ha1|Kha1|Krt1-1|MKHA-1	keratin 31	protein-coding
mm_103061.1	chr11	69837288	69837297	-	1	NA	Intergenic	CpG	-1233	NM_026982	69186	Mm.248772	NM_026982	ENSMUSG00000070394	Tmem256	1810027O10Rik|3110009M16Rik	transmembrane protein 256	protein-coding
mm_36014.1	chr4	56874610	56874626	-	1	NA	Intergenic	MurERV4-int|LTR|ERVK	-9407	NM_018761	54366	Mm.218891	NM_018761	ENSMUSG00000038816	Ctnnal1	ACRP|AI616177|AW545119|C86009|Catnal1	catenin (cadherin associated protein), alpha-like 1	protein-coding
mm_14822.1	chr2	146951366	146951371	+	1	NA	intron (NM_001033298, intron 10 of 13)	intron (NM_001033298, intron 10 of 13)	-61692	NM_011917	24128	Mm.3065	NM_011917	ENSMUSG00000027433	Xrn2	-	5'-3' exoribonuclease 2	protein-coding
mm_30062.1	chr3	137878109	137878120	-	1	NA	intron (NM_001033155, intron 1 of 7)	HAL1M8|LINE|L1	10439	NM_001033155	70604	Mm.256488	NM_001033155	ENSMUSG00000074212	Dnajb14	5730496F10Rik	DnaJ heat shock protein family (Hsp40) member B14	protein-coding
mm_79834.1	chr9	64803699	64803731	+	1	NA	Intergenic	RMER15|LTR|ERVL	-7296	NM_001162917	102442	Mm.222473	NM_176935	ENSMUSG00000053641	Dennd4a	AI115600|AI851943|F730015K02Rik	DENN/MADD domain containing 4A	protein-coding
mm_93420.1	chr10	108700110	108700143	-	1	NA	promoter-TSS (NM_203660)	promoter-TSS (NM_203660)	34	NM_203660	368203	Mm.452758	NM_203660		Gm5136	C6.1AL|EG368203	predicted gene 5136	protein-coding
mm_79423.1	chr9	55430266	55430277	+	1	NA	intron (NM_172923, intron 8 of 10)	intron (NM_172923, intron 8 of 10)	81972	NM_145615	110842	Mm.290853	NM_145615	ENSMUSG00000032314	Etfa	2010200I21Rik|D9Ertd394e	electron transferring flavoprotein, alpha polypeptide	protein-coding
mm_98909.1	chr11	98185311	98185330	+	1	NA	intron (NM_001080118, intron 2 of 16)	intron (NM_001080118, intron 2 of 16)	7586	NM_013634	19014	Mm.12926	NM_013634	ENSMUSG00000018160	Med1	AI480703|CRSP210|DRIP205|PBP|Pparbp|TRAP220|l11Jus15	mediator complex subunit 1	protein-coding
mm_129297.1	chr15	77306613	77306651	-	1	NA	5' UTR (NM_175387, exon 1 of 13)	5' UTR (NM_175387, exon 1 of 13)	421	NM_001110827	93686	Mm.202774	NM_053104	ENSMUSG00000033565	Rbfox2	Fbm2|Fxh|Hrnbp2|Rbm9	RNA binding protein, fox-1 homolog (C. elegans) 2	protein-coding
mm_48993.1	chr6	4756466	4756475	+	1	NA	exon (NM_130877, exon 2 of 2)	exon (NM_130877, exon 2 of 2)	9164	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_28593.1	chr3	94436575	94436592	-	1	NA	promoter-TSS (NM_016901)	promoter-TSS (NM_016901)	68	NM_016901	53814	Mm.440422	NM_016901	ENSMUSG00000028141	Oaz3	AZ3|Az-3|Oaz-t	ornithine decarboxylase antizyme 3	protein-coding
mm_100055.1	chr11	115187482	115187562	+	1	NA	promoter-TSS (NM_025400)	promoter-TSS (NM_025400)	35	NM_001033393	320534	Mm.260587	NM_001033393	ENSMUSG00000045980	Tmem104	C630005D06Rik|mFLJ00021	transmembrane protein 104	protein-coding
mm_8342.1	chr1	150164983	150164991	-	1	NA	promoter-TSS (NR_110420)	promoter-TSS (NR_110420)	-39	NR_110420	102639566	Mm.417208	NR_110420	ENSMUSG00000097754	Ptgs2os2	Gm26687|Linc-cox2|Lincrna-cox2	prostaglandin-endoperoxide synthase 2, opposite strand 2	ncRNA
mm_31142.1	chr4	43383418	43383428	+	1	NA	intron (NM_001037709, intron 1 of 11)	intron (NM_001037709, intron 1 of 11)	1441	NM_001037709	100213	Mm.235730	NM_199057	ENSMUSG00000035969	Rusc2	AI840675|mKIAA0375	RUN and SH3 domain containing 2	protein-coding
mm_131758.1	chr16	22878960	22878992	+	1	NA	3' UTR (NM_026400, exon 11 of 11)	3' UTR (NM_026400, exon 11 of 11)	-13039	NR_075099	11625	Mm.197554	NM_013465	ENSMUSG00000022868	Ahsg	-	alpha-2-HS-glycoprotein	protein-coding
mm_5569.1	chr1	38898085	38898177	-	1	NA	promoter-TSS (NM_145142)	promoter-TSS (NM_145142)	29	NM_145142	98388	Mm.260054	NM_145142	ENSMUSG00000026080	Chst10	AI507003|AU041319|Hnk-1st|ST	carbohydrate sulfotransferase 10	protein-coding
mm_64823.1	chr7	10495323	10495401	-	1	NA	promoter-TSS (NM_009577)	promoter-TSS (NM_009577)	19	NM_009577	22775	Mm.49441	NM_009577	ENSMUSG00000030393	Zik1	-	zinc finger protein interacting with K protein 1	protein-coding
mm_57277.1	chr6	123290598	123290609	-	1	NA	promoter-TSS (NM_019948)	promoter-TSS (NM_019948)	-732	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_126167.1	chr15	78558837	78558841	+	1	NA	TTS (NM_009008)	TTS (NM_009008)	13944	NM_009008	19354	Mm.1972	NM_009008	ENSMUSG00000033220	Rac2	AI323801|AI452260	RAS-related C3 botulinum substrate 2	protein-coding
mm_42125.1	chr5	110906398	110906406	+	1	NA	intron (NM_001267622, intron 2 of 22)	Lx8|LINE|L1	26599	NM_001267622	209683	Mm.295660	NM_024477	ENSMUSG00000033209	Ttc28	2310015L07Rik|6030435N04|AI428795|AI851761|BC002262|TPRBK	tetratricopeptide repeat domain 28	protein-coding
mm_88640.1	chr10	79927376	79927384	+	1	NA	promoter-TSS (NM_001288625)	promoter-TSS (NM_001288625)	39	NM_001288625	13496	Mm.301282	NM_007880	ENSMUSG00000019564	Arid3a	Bright|Dri1|Dril1	AT rich interactive domain 3A (BRIGHT-like)	protein-coding
mm_23817.1	chr3	79936438	79936446	+	1	NA	intron (NM_133187, intron 2 of 3)	intron (NM_133187, intron 2 of 3)	50512	NM_133187	68659	Mm.427274	NM_133187	ENSMUSG00000027955	Fam198b	1110032E23Rik|2210419I08Rik|AV011458|Ened	family with sequence similarity 198, member B	protein-coding
mm_37129.1	chr4	116685974	116686011	-	1	NA	promoter-TSS (NR_040442)	promoter-TSS (NR_040442)	30	NR_040442	100502959	Mm.395400	NR_040442		AV051173	-	expressed sequence AV051173	ncRNA
mm_166983.1	chr7	45666289	45666291	-	1	NA	5' UTR (NM_001271993, exon 1 of 3)	5' UTR (NM_001271993, exon 1 of 3)	104	NM_018876	14344	Mm.290046	NM_018876	ENSMUSG00000055978	Fut2	-	fucosyltransferase 2	protein-coding
mm_74752.1	chr8	19064886	19064907	-	1	NA	promoter-TSS (NM_183038)	promoter-TSS (NM_183038)	-86	NM_183038	360214	Mm.271559	NM_183038	ENSMUSG00000061847	Defb39	BD-39	defensin beta 39	protein-coding
mm_126914.1	chr15	91037496	91037501	+	1	NA	intron (NM_001109040, intron 1 of 36)	ORR1A0|LTR|ERVL-MaLR	12453	NM_001109041	16564	Mm.41379	NM_016705	ENSMUSG00000022629	Kif21a	-	kinesin family member 21A	protein-coding
mm_47281.1	chr5	122102726	122102765	-	1	NA	exon (NM_010861, exon 3 of 7)	exon (NM_010861, exon 3 of 7)	1765	NM_010861	17906	Mm.1529	NM_010861	ENSMUSG00000013936	Myl2	MLC-2|MLC-2s/v|MLC-2v|Mlc2v|Mylpc	myosin, light polypeptide 2, regulatory, cardiac, slow	protein-coding
mm_30249.1	chr3	146596494	146596516	-	1	NA	promoter-TSS (NM_009474)	promoter-TSS (NM_009474)	-644	NM_009474	22262	Mm.10865	NM_009474	ENSMUSG00000028186	Uox	AI663847	urate oxidase	protein-coding
mm_20139.1	chr2	121413781	121413814	-	1	NA	promoter-TSS (NM_007952)	promoter-TSS (NM_007952)	-5	NM_153075	212670	Mm.384318	NM_153075	ENSMUSG00000033486	Catsper2	-	cation channel, sperm associated 2	protein-coding
mm_132772.1	chr16	44766168	44766180	+	1	NA	intron (NM_021325, intron 1 of 6)	intron (NM_021325, intron 1 of 6)	438	NM_021325	57781	Mm.416152	NM_021325	ENSMUSG00000022667	Cd200r1	CD200R|Mox2r|OX2R	CD200 receptor 1	protein-coding
mm_89533.1	chr10	94514826	94514922	+	1	NA	promoter-TSS (NM_172051)	promoter-TSS (NM_172051)	17	NM_172051	319880	Mm.23047	NM_172051	ENSMUSG00000020023	Tmcc3	AW488095|C630016B22Rik|C88213|Tmcc1	transmembrane and coiled coil domains 3	protein-coding
mm_59670.1	chr7	28377997	28378053	+	1	NA	exon (NM_011756, exon 2 of 2)	exon (NM_011756, exon 2 of 2)	1203	NM_011756	22695	Mm.389856	NM_011756	ENSMUSG00000044786	Zfp36	Gos24|Nup475|TIS11D|TISII|Tis11|Ttp|Zfp-36	zinc finger protein 36	protein-coding
mm_53364.1	chr6	129377461	129377465	+	1	NA	intron (NM_001204223, intron 6 of 6)	intron (NM_001204223, intron 6 of 6)	8040	NM_027709	71183	Mm.79402	NM_027709	ENSMUSG00000030158	Clec12b	4933425B16Rik	C-type lectin domain family 12, member B	protein-coding
mm_71402.1	chr8	46419702	46419707	+	1	NA	Intergenic	Intergenic	-51333	NM_007981	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_154312.1	chrM	67	79	+	1	NA	NA	Intergenic	NA	NA								
mm_170581.1	chr19	5726299	5726300	-	1	NA	promoter-TSS (NM_001114597)	promoter-TSS (NM_001114597)	18	NM_001114595	114601	Mm.210447	NM_053252	ENSMUSG00000024937	Ehbp1l1	G430002G23Rik	EH domain binding protein 1-like 1	protein-coding
mm_169734.1	chr15	8281040	8281044	-	1	NA	Intergenic	RLTR1C|LTR|ERV1	111936	NM_001162906	73692	Mm.164436	NM_001162906	ENSMUSG00000039801	2410089E03Rik	4732468D17Rik|Hug|Jbts17|b2b012Clo	RIKEN cDNA 2410089E03 gene	protein-coding
mm_22366.1	chr2	181109756	181109759	-	1	NA	exon (NM_010611, exon 6 of 17)	exon (NM_010611, exon 6 of 17)	25532	NM_001006668	16536	Mm.40615	NM_010611	ENSMUSG00000016346	Kcnq2	HNSPC|KQT2|Nmf134	potassium voltage-gated channel, subfamily Q, member 2	protein-coding
mm_80111.1	chr9	70512225	70512244	+	1	NA	Intergenic	Intergenic	-8509	NM_033604	93836	Mm.29783	NM_033604	ENSMUSG00000032217	Rnf111	ARK|Arkadia	ring finger 111	protein-coding
mm_52444.1	chr6	113650602	113650603	+	1	NA	intron (NM_001113553, intron 2 of 11)	ID4|SINE|ID	12135	NM_001113553	108960	Mm.152142	NM_172161	ENSMUSG00000060477	Irak2	6330415L08Rik|AI649099|IRAK-2	interleukin-1 receptor-associated kinase 2	protein-coding
mm_123630.1	chr14	68498019	68498050	-	1	NA	3' UTR (NM_007402, exon 23 of 23)	3' UTR (NM_007402, exon 23 of 23)	35655	NM_007402	11500	Mm.261495	NM_007402	ENSMUSG00000022056	Adam7	ADAM 7|EAP1|EAPI	a disintegrin and metallopeptidase domain 7	protein-coding
mm_71491.1	chr8	46750377	46750398	+	1	NA	intron (NM_008391, intron 1 of 8)	intron (NM_008391, intron 1 of 8)	10642	NM_008391	16363	Mm.1149	NM_008391	ENSMUSG00000031627	Irf2	9830146E22Rik|AI646973|Irf-2	interferon regulatory factor 2	protein-coding
mm_99325.1	chr11	101448404	101448487	+	1	NA	promoter-TSS (NM_027320)	promoter-TSS (NM_027320)	33	NM_027320	70110	Mm.45558	NM_027320	ENSMUSG00000010358	Ifi35	2010008K16Rik|AW986054|IFP35|ifi-35	interferon-induced protein 35	protein-coding
mm_161627.1	chr16	77014113	77014113	+	1	NA	promoter-TSS (NM_013918)	promoter-TSS (NM_013918)	44	NM_013918	30940	Mm.40986	NM_013918	ENSMUSG00000022867	Usp25	-	ubiquitin specific peptidase 25	protein-coding
mm_5749.1	chr1	46425428	46425437	-	1	NA	promoter-TSS (NM_001310335)	promoter-TSS (NM_001310335)	-86	NM_001310335	100101919	Mm.383402	NM_001310335	ENSMUSG00000101337	Dnah7c	Dnahc7c	dynein, axonemal, heavy chain 7C	protein-coding
mm_14108.1	chr2	125674055	125674074	+	1	NA	3' UTR (NM_025613, exon 1 of 1)	3' UTR (NM_025613, exon 1 of 1)	964	NM_025613	58521	Mm.425101	NM_025613	ENSMUSG00000091337	Eid1	2610002K20Rik|Cri1|EID-1|ORF12|PNAS-22|PTD014	EP300 interacting inhibitor of differentiation 1	protein-coding
mm_166045.1	chr4	130663675	130663701	+	1	NA	intron (NM_001159606, intron 1 of 17)	CpG	329	NM_001159605	80912	Mm.440206	NM_030722	ENSMUSG00000028580	Pum1	AA517475|Pumm|mKIAA0099	pumilio RNA-binding family member 1	protein-coding
mm_149369.1	chr19	11372542	11372556	+	1	NA	Intergenic	Intergenic	-2939	NM_001310331	666907		NM_001310331	ENSMUSG00000101389	Ms4a4a	EG666907	membrane-spanning 4-domains, subfamily A, member 4A	protein-coding
mm_167091.1	chr7	105752011	105752027	-	1	NA	TTS (NM_001162943)	TTS (NM_001162943)	216	NM_009906	12751	Mm.20837	NM_009906	ENSMUSG00000030894	Tpp1	Cln2|LPIC|TPP-1|TPP-I	tripeptidyl peptidase I	protein-coding
mm_3688.1	chr1	153749707	153749746	+	1	NA	intron (NM_011882, intron 1 of 8)	intron (NM_011882, intron 1 of 8)	300	NM_011882	24014	Mm.259254	NM_011882	ENSMUSG00000066800	Rnasel	E230029I04Rik	ribonuclease L (2', 5'-oligoisoadenylate synthetase-dependent)	protein-coding
mm_157436.1	chrX	38635038	38635042	-	1	NA	5' UTR (NM_021550, exon 1 of 2)	5' UTR (NM_021550, exon 1 of 2)	103	NM_021550	59048	Mm.441410	NM_021550	ENSMUSG00000048970	C1galt1c1	1500002I11Rik|AB030184|C1GalT2|C81205|Cosmc	C1GALT1-specific chaperone 1	protein-coding
mm_43479.1	chr5	136697820	136697828	+	1	NA	intron (NM_001303019, intron 4 of 6)	ZP3AR|Satellite|Satellite	3647	NM_001085387	59310	Mm.5178	NM_021611	ENSMUSG00000005474	Myl10	1700027I08Rik|Mylc2pl|PLRLC	myosin, light chain 10, regulatory	protein-coding
mm_155344.1	chrX	68678610	68678620	+	1	NA	promoter-TSS (NM_008031)	promoter-TSS (NM_008031)	74	NM_001290424	14265	Mm.3451	NM_008031	ENSMUSG00000000838	Fmr1	FMRP|Fmr-1	fragile X mental retardation syndrome 1	protein-coding
mm_53319.1	chr6	129187401	129187412	+	1	NA	TTS (NM_053109)	TTS (NM_053109)	6791	NM_053109	93694	Mm.197536	NM_053109	ENSMUSG00000030157	Clec2d	Clr-b|Clrb|Ocil	C-type lectin domain family 2, member d	protein-coding
mm_137142.1	chr17	23620764	23620785	+	1	NA	Intergenic	Intergenic	19948	NM_001289482	332221	Mm.270315	NM_001033425	ENSMUSG00000023902	Zscan10	BC068284|Zfp206|Zkscan10|Znf206	zinc finger and SCAN domain containing 10	protein-coding
mm_82604.1	chr9	21367424	21367442	-	1	NA	promoter-TSS (NM_001042707)	promoter-TSS (NM_001042707)	-438	NM_001042708	16201	Mm.440026	NM_010561	ENSMUSG00000032178	Ilf3	MBII-26|MPHOSPH4|NF90|NFAR	interleukin enhancer binding factor 3	protein-coding
mm_74762.1	chr8	20297519	20297549	-	1	NA	promoter-TSS (NR_030708)	promoter-TSS (NR_030708)	-102	NR_030708	547150	Mm.359054	NR_030708	ENSMUSG00000071796	6820431F20Rik	-	cadherin 11 pseudogene	pseudo
mm_9337.1	chr1	172004529	172004535	-	1	NA	3' UTR (NM_033509, exon 8 of 8)	3' UTR (NM_033509, exon 8 of 8)	22763	NM_033509	93840	Mm.36148	NM_033509	ENSMUSG00000026556	Vangl2	C530001F03Rik|Lootl|Lp|Lpp1|Ltap|Vang1l2|loop-tail|ska17|ska<m17Jus>|stbm|strabismus	vang-like 2 (van gogh, Drosophila)	protein-coding
mm_125330.1	chr15	38661915	38661981	+	1	NA	promoter-TSS (NM_025494)	promoter-TSS (NM_025494)	44	NM_025494	66335	Mm.276618	NM_025494	ENSMUSG00000022295	Atp6v1c1	1700025B18Rik|U13839	ATPase, H+ transporting, lysosomal V1 subunit C1	protein-coding
mm_76410.1	chr8	84893737	84893806	-	1	NA	5' UTR (NM_001044744, exon 1 of 12)	5' UTR (NM_001044744, exon 1 of 12)	150	NM_001044744	270076	Mm.2475	NM_008097	ENSMUSG00000003809	Gcdh	9030411L18|AI266902|D17825|GCD	glutaryl-Coenzyme A dehydrogenase	protein-coding
mm_53192.1	chr6	125494420	125494454	+	1	NA	intron (NM_007657, intron 1 of 7)	CpG	318	NM_007657	12527	Mm.210676	NM_007657	ENSMUSG00000030342	Cd9	Tspan29	CD9 antigen	protein-coding
mm_3922.1	chr1	162570668	162570672	+	1	NA	promoter-TSS (NM_016796)	promoter-TSS (NM_016796)	-158	NM_016796	53330	Mm.10699	NM_016796	ENSMUSG00000026696	Vamp4	D1Ertd147e	vesicle-associated membrane protein 4	protein-coding
mm_104920.1	chr11	99840346	99840368	-	1	NA	Intergenic	Intergenic	-2291	NM_001195383	100502865	Mm.476649	NM_001195383	ENSMUSG00000078257	2300003K06Rik	-	RIKEN cDNA 2300003K06 gene	protein-coding
mm_88867.1	chr10	80940265	80940269	+	1	NA	Intergenic	ID_B1|SINE|B4	10176	NM_008655	17873	Mm.1360	NM_008655	ENSMUSG00000015312	Gadd45b	AI323528|Myd118	growth arrest and DNA-damage-inducible 45 beta	protein-coding
mm_116931.1	chr13	55784503	55784510	-	1	NA	promoter-TSS (NM_001252487)	promoter-TSS (NM_001252487)	-73	NM_029772	76856	Mm.159795	NM_029772	ENSMUSG00000021499	Catsper3	4921522D01Rik|CACRC	cation channel, sperm associated 3	protein-coding
mm_2318.1	chr1	92049094	92049104	+	1	NA	intron (NM_207225, intron 3 of 26)	intron (NM_207225, intron 3 of 26)	131242	NM_207225	208727	Mm.318567	NM_207225	ENSMUSG00000026313	Hdac4	4932408F19Rik|HD4	histone deacetylase 4	protein-coding
mm_116061.1	chr13	27513207	27513225	-	1	NA	promoter-TSS (NM_023741)	promoter-TSS (NM_023741)	1	NM_001311125	74188	Mm.46090	NM_023741	ENSMUSG00000021346	Prl8a8	1600032B14Rik|Ghd14|PLP-Cgamma|Prlpc3	prolactin family 8, subfamily a, member 81	protein-coding
mm_542.1	chr1	38017866	38017877	+	1	NA	exon (NM_198303, exon 2 of 24)	exon (NM_198303, exon 2 of 24)	19861	NM_198303	226982	Mm.260943	NM_198303	ENSMUSG00000026083	Eif5b	A030003E17Rik|BC018347|IF2	eukaryotic translation initiation factor 5B	protein-coding
mm_47110.1	chr5	119080851	119080862	-	1	NA	Intergenic	Intergenic	-27380	NR_040693	73477	Mm.410863	NR_040693	ENSMUSG00000100573	1700081H04Rik	-	RIKEN cDNA 1700081H04 gene	ncRNA
mm_129712.1	chr15	81858533	81858541	-	1	NA	promoter-TSS (NM_020507)	promoter-TSS (NM_020507)	-211	NM_020507	57259	Mm.323595	NM_020507	ENSMUSG00000048546	Tob2	2900090N22Rik|4930545K18Rik|AV071822|mKIAA1663	transducer of ERBB2, 2	protein-coding
mm_40749.1	chr5	66745857	66745896	+	1	NA	promoter-TSS (NM_001001980)	promoter-TSS (NM_001001980)	36	NM_001001980	77569	Mm.374778	NM_001001980	ENSMUSG00000037736	Limch1	3732412D22Rik|mKIAA1102	LIM and calponin homology domains 1	protein-coding
mm_19759.1	chr2	105126557	105126570	-	1	NA	promoter-TSS (NM_144783)	promoter-TSS (NM_144783)	34	NM_144783	22431	Mm.389339	NM_144783	ENSMUSG00000016458	Wt1	D630046I19Rik|Wt-1	Wilms tumor 1 homolog	protein-coding
mm_36309.1	chr4	69758448	69758454	-	1	NA	Intergenic	Intergenic	651984	NM_001313762	214444	Mm.370777	NM_145990	ENSMUSG00000039298	Cdk5rap2	2900018K03Rik|an|mKIAA1633	CDK5 regulatory subunit associated protein 2	protein-coding
mm_1650.1	chr1	74661699	74661713	+	1	NA	promoter-TSS (NM_001014974)	promoter-TSS (NM_001014974)	-48	NM_001014974	67534	Mm.260714	NM_001014974	ENSMUSG00000033257	Ttll4	4632407P03Rik|AI451681|mKIAA0173	tubulin tyrosine ligase-like family, member 4	protein-coding
mm_65252.1	chr7	19871332	19871345	-	1	NA	Intergenic	Intergenic	-10039	NM_001033419	330483	Mm.260192	NM_001033419	ENSMUSG00000014686	Ceacam16	Gm769	carcinoembryonic antigen-related cell adhesion molecule 16	protein-coding
mm_154923.1	chrX	23693485	23693494	+	1	NA	exon (NM_175180, exon 1 of 20)	exon (NM_175180, exon 1 of 20)	438	NM_001305675	72404	Mm.423	NM_175180	ENSMUSG00000036769	Wdr44	2610034K17Rik|RAB11BP|RPH11	WD repeat domain 44	protein-coding
mm_28158.1	chr3	87768933	87768960	-	1	NA	promoter-TSS (NM_001289601)	promoter-TSS (NM_001289601)	7	NM_001032413	73182	Mm.158962	NM_028460	ENSMUSG00000028073	Pear1	3110045G13Rik|Jedi-1|Megf12	platelet endothelial aggregation receptor 1	protein-coding
mm_125143.1	chr15	30634694	30634709	+	1	NA	exon (NM_008729, exon 6 of 23)	exon (NM_008729, exon 6 of 23)	-404425	NR_045186	73784	Mm.66947	NR_045186		4930430F21Rik	-	RIKEN cDNA 4930430F21 gene	ncRNA
mm_145561.1	chr18	60812368	60812378	+	1	NA	TTS (NR_039567)	TTS (NR_039567)	297	NR_039567	100628611		NR_039567	ENSMUSG00000093327	Mir5107	mir-5107|mmu-mir-5107|mu-mir-5107	microRNA 5107	ncRNA
mm_51890.1	chr6	90604973	90604986	+	1	NA	promoter-TSS (NM_027868)	promoter-TSS (NM_027868)	99	NM_027868	71699	Mm.272633	NM_027868	ENSMUSG00000030089	Slc41a3	1010001P06Rik|AI480742|SLC41A1-L2	solute carrier family 41, member 3	protein-coding
mm_35269.1	chr4	19900990	19901000	-	1	NA	intron (NM_175406, intron 2 of 7)	MIR|SINE|MIR	21571	NM_175406	242341	Mm.19298	NM_175406	ENSMUSG00000028238	Atp6v0d2	1620401A02Rik|AI324824|V-ATPase	ATPase, H+ transporting, lysosomal V0 subunit D2	protein-coding
mm_98868.1	chr11	97799391	97799401	+	1	NA	promoter-TSS (NM_010688)	promoter-TSS (NM_010688)	-276	NM_010688	16796	Mm.271967	NM_010688	ENSMUSG00000038366	Lasp1	AA408629|Def-4|SH3P6|Tg(Col1a1-lacZ)1Ngma	LIM and SH3 protein 1	protein-coding
mm_46849.1	chr5	113639202	113639205	-	1	NA	intron (NM_008153, intron 1 of 2)	intron (NM_008153, intron 1 of 2)	11187	NM_008153	14747	Mm.5196	NM_008153	ENSMUSG00000042190	Cmklr1	ChemR23|DEZ|Gpcr27|mcmklr1	chemokine-like receptor 1	protein-coding
mm_140326.1	chr17	86753837	86753847	+	1	NA	promoter-TSS (NM_010137)	promoter-TSS (NM_010137)	-22	NM_010137	13819	Mm.1415	NM_010137	ENSMUSG00000024140	Epas1	HIF-2alpha|HIF2A|HLF|HRF|MOP2|bHLHe73	endothelial PAS domain protein 1	protein-coding
mm_66091.1	chr7	30973400	30973435	-	1	NA	promoter-TSS (NM_017405)	promoter-TSS (NM_017405)	52	NM_001164185	54135	Mm.4067	NM_017405	ENSMUSG00000001247	Lsr	ILDR3|Lisch7	lipolysis stimulated lipoprotein receptor	protein-coding
mm_110432.1	chr12	46819354	46819371	-	1	NA	promoter-TSS (NM_021361)	promoter-TSS (NM_021361)	-587	NM_021361	664883	Mm.247195	NM_021361	ENSMUSG00000021047	Nova1	9430099M15Rik|G630039L02|Nova-1	neuro-oncological ventral antigen 1	protein-coding
mm_46821.1	chr5	113163289	113163308	-	1	NA	promoter-TSS (NM_172884)	promoter-TSS (NM_172884)	15	NM_172884	243219	Mm.160131	NM_172884	ENSMUSG00000051339	2900026A02Rik	8430408O14Rik|A530094D01|AW539426|Gm449|Kiaa1671|mKIAA1671	RIKEN cDNA 2900026A02 gene	protein-coding
mm_24930.1	chr3	96559585	96559597	+	1	NA	exon (NM_023719, exon 5 of 8)	exon (NM_023719, exon 5 of 8)	1634	NM_023719	56338	Mm.410189	NM_023719	ENSMUSG00000038393	Txnip	1200008J08Rik|AA682105|Hyplip1|THIF|Tbp-2|VDUP1	thioredoxin interacting protein	protein-coding
mm_75996.1	chr8	72443773	72443784	-	1	NA	promoter-TSS (NM_028500)	promoter-TSS (NM_028500)	0	NM_028500	73316	Mm.196315	NM_028500	ENSMUSG00000019732	Calr3	1700031L01Rik|6330586I20Rik|Crt2|cspn	calreticulin 3	protein-coding
mm_36799.1	chr4	103171787	103171791	-	1	NA	TTS (NM_177732)	TTS (NM_177732)	43095	NM_177732	242585	Mm.281800	NM_177732	ENSMUSG00000028521	Slc35d1	AI834976|C330011J09|UGTREL7|mKIAA0260	solute carrier family 35 (UDP-glucuronic acid/UDP-N-acetylgalactosamine dual transporter), member D1	protein-coding
mm_16658.1	chr2	6627935	6627939	-	1	NA	intron (NM_001347094, intron 3 of 12)	MTB|LTR|ERVL-MaLR	93725	NM_001310447	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_16995.1	chr2	18316943	18316976	-	1	NA	exon (NM_001190817, exon 2 of 13)	exon (NM_001190817, exon 2 of 13)	75871	NM_001190817	13418	Mm.246674	NM_007869	ENSMUSG00000026740	Dnajc1	4733401K02Rik|AA960110|D230036H06Rik|Dnajl1|ERdj1|ERj1p|MTJ1	DnaJ heat shock protein family (Hsp40) member C1	protein-coding
mm_171530.1	chr4	146627782	146627790	+	1	NA	Intergenic	Intergenic	-80913	NR_045468	67524	Mm.444300	NR_045468	ENSMUSG00000086046	1700095A21Rik	-	RIKEN cDNA 1700095A21 gene	ncRNA
mm_58261.1	chr6	145250387	145250397	-	1	NA	promoter-TSS (NM_021284)	promoter-TSS (NM_021284)	-160	NR_045598	100039495	Mm.121014	NR_045598	ENSMUSG00000086013	Gm15706	OTTMUSG00000025463	predicted gene 15706	ncRNA
mm_94648.1	chr11	16951441	16951468	+	1	NA	promoter-TSS (NM_176982)	promoter-TSS (NM_176982)	44	NM_176982	319701	Mm.120672	NM_176982	ENSMUSG00000044966	Fbxo48	A630050E13Rik	F-box protein 48	protein-coding
mm_102814.1	chr11	68957446	68957485	-	1	NA	promoter-TSS (NM_177566)	promoter-TSS (NM_177566)	-607	NM_177566	442801	Mm.376147	NM_177566	ENSMUSG00000052921	Arhgef15	D130071N09|D530030K12Rik|E5	Rho guanine nucleotide exchange factor (GEF) 15	protein-coding
mm_158165.1	chrX	103483244	103483252	-	1	NA	promoter-TSS (NR_001570)	promoter-TSS (NR_001570)	-15	NR_001463	213742	Mm.274770	NR_001463	ENSMUSG00000086503	Xist	A430022B11|AI314753	inactive X specific transcripts	ncRNA
mm_21284.1	chr2	156970281	156970293	-	1	NA	intron (NM_013865, intron 1 of 15)	MLT1F2|LTR|ERVL-MaLR	21824	NM_013865	29812	Mm.279256	NM_013865	ENSMUSG00000027634	Ndrg3	4833415O14Rik|AI747193|Ndr3	N-myc downstream regulated gene 3	protein-coding
mm_60618.1	chr7	44596044	44596055	+	1	NA	exon (NM_001290682, exon 2 of 5)	exon (NM_001290682, exon 2 of 5)	5163	NM_001290682	16504	Mm.40312	NM_008422	ENSMUSG00000062785	Kcnc3	KShIIID|Kcr2-3|Kv3.3	potassium voltage gated channel, Shaw-related subfamily, member 3	protein-coding
mm_143742.1	chr17	81512910	81512923	-	1	NA	intron (NR_104580, intron 2 of 8)	intron (NR_104580, intron 2 of 8)	225471	NM_001286684	20541	Mm.265834	NM_011406	ENSMUSG00000054640	Slc8a1	AI852629|AV344025|D930008O12Rik|Ncx1	solute carrier family 8 (sodium/calcium exchanger), member 1	protein-coding
mm_11387.1	chr2	31314304	31314376	+	1	NA	Intergenic	CpG	68417	NM_019681	14299	Mm.249318	NM_019681	ENSMUSG00000062661	Ncs1	9430075O15Rik|A730032G13Rik|AI836659|Freq|Mfreq|NCS-1	neuronal calcium sensor 1	protein-coding
mm_154222.1	chr19	59458495	59458577	-	1	NA	promoter-TSS (NM_010132)	promoter-TSS (NM_010132)	99	NR_002863	329078	Mm.80382	NR_002863	ENSMUSG00000087095	Emx2os	-	Emx2 opposite strand/antisense transcript (non-protein coding)	ncRNA
mm_159391.1	chr3	92621657	92621657	-	1	NA	promoter-TSS (NM_001166172)	promoter-TSS (NM_001166172)	3	NM_001166172	78382	Mm.235474	NM_001166172	ENSMUSG00000086848	Lce6a	2210420J11Rik	late cornified envelope 6A	protein-coding
mm_130210.1	chr15	95528703	95528777	-	1	NA	promoter-TSS (NM_001289653)	promoter-TSS (NM_001289653)	-488	NM_001289653	54003	Mm.3959	NM_016743	ENSMUSG00000022454	Nell2	A330108N19Rik|R75516|mel91	NEL-like 2	protein-coding
mm_34334.1	chr4	143349809	143349834	+	1	NA	promoter-TSS (NM_001162983)	promoter-TSS (NM_001162983)	71	NM_001162983	242735	Mm.94020	NM_001162983	ENSMUSG00000028584	Lrrc38	A230053A07Rik	leucine rich repeat containing 38	protein-coding
mm_101209.1	chr11	20063675	20063699	-	1	NA	3' UTR (NM_146243, exon 9 of 9)	3' UTR (NM_146243, exon 9 of 9)	49264	NM_146243	66713	Mm.259045	NM_146243	ENSMUSG00000020152	Actr2	4921510D23Rik|AA409782|Arp2|D6Ertd746e	ARP2 actin-related protein 2	protein-coding
mm_24394.1	chr3	90266508	90266566	+	1	NA	promoter-TSS (NM_201407)	promoter-TSS (NM_201407)	23	NM_201407	229541	Mm.30571	NM_201407	ENSMUSG00000042404	Dennd4b	-	DENN/MADD domain containing 4B	protein-coding
mm_140753.1	chr17	17374208	17374242	-	1	NA	promoter-TSS (NM_025934)	promoter-TSS (NM_025934)	-107	NM_025934	67045	Mm.35117	NM_025934	ENSMUSG00000023852	Riok2	2010110K24Rik|2410085M17Rik	RIO kinase 2 (yeast)	protein-coding
mm_151538.1	chr19	59075032	59075097	+	1	NA	intron (NM_175172, intron 1 of 14)	intron (NM_175172, intron 1 of 14)	1005	NM_175172	71653	Mm.37338	NM_175172	ENSMUSG00000041362	Shtn1	4930506M07Rik|Kiaa1598|Shootin1|mKIAA1598	shootin 1	protein-coding
mm_31224.1	chr4	44019931	44019946	+	1	NA	exon (NM_001080385, exon 3 of 7)	exon (NM_001080385, exon 3 of 7)	7288	NM_001290470	12757	Mm.298875	NM_016760	ENSMUSG00000028478	Clta	AV026556|Lca	clathrin, light polypeptide (Lca)	protein-coding
mm_86964.1	chr10	25295458	25295462	+	1	NA	intron (NM_018747, intron 1 of 7)	intron (NM_018747, intron 1 of 7)	3703	NM_018747	432442	Mm.485937	NM_018747	ENSMUSG00000039166	Akap7	6430401D08|AI662165|AKAP15|Akap18|BB170514	A kinase (PRKA) anchor protein 7	protein-coding
mm_72303.1	chr8	76901544	76901556	+	1	NA	promoter-TSS (NM_001083906)	promoter-TSS (NM_001083906)	-958	NM_001083906	110784	Mm.324393	NM_001083906	ENSMUSG00000031618	Nr3c2	MR|Mlr	nuclear receptor subfamily 3, group C, member 2	protein-coding
mm_172330.1	chr7	108026867	108026877	+	1	NA	Intergenic	L1Md_T|LINE|L1	5469	NM_146734	258729	Mm.223162	NM_146734	ENSMUSG00000094426	Olfr478	MOR204-13	olfactory receptor 478	protein-coding
mm_81010.1	chr9	104035511	104035533	+	1	NA	intron (NM_028721, intron 19 of 26)	intron (NM_028721, intron 19 of 26)	27599	NM_025692	66663	Mm.224935	NM_025692	ENSMUSG00000032557	Uba5	5730525G14Rik|AW240750|Ube1dc1	ubiquitin-like modifier activating enzyme 5	protein-coding
mm_135796.1	chr16	57199031	57199059	-	1	NA	intron (NM_026254, intron 5 of 17)	intron (NM_026254, intron 5 of 17)	-31713	NM_023175	52633	Mm.383203	NM_023175	ENSMUSG00000022751	Nit2	1190017B19Rik|D16Ertd502e	nitrilase family, member 2	protein-coding
mm_52995.1	chr6	123267185	123267218	+	1	NA	intron (NM_001163161, intron 3 of 5)	intron (NM_001163161, intron 3 of 5)	5094	NM_010819	17474	Mm.441101	NM_010819	ENSMUSG00000030144	Clec4d	Clecsf8|Mpcl|mcl	C-type lectin domain family 4, member d	protein-coding
mm_75954.1	chr8	71693823	71693857	-	1	NA	exon (NM_028189, exon 2 of 3)	exon (NM_028189, exon 2 of 3)	4588	NM_013564	16336	Mm.476857	NM_013564	ENSMUSG00000079019	Insl3	Rlf|Rlnl	insulin-like 3	protein-coding
mm_44672.1	chr5	29735884	29735893	-	1	NA	promoter-TSS (NM_001037941)	promoter-TSS (NM_001037941)	-10	NM_001037940	23950	Mm.290110	NM_011847	ENSMUSG00000029131	Dnajb6	Mrj|mDj4	DnaJ heat shock protein family (Hsp40) member B6	protein-coding
mm_46017.1	chr5	90903189	90903197	-	1	NA	promoter-TSS (NM_009140)	promoter-TSS (NM_009140)	-706	NM_009140	20310	Mm.4979	NM_009140	ENSMUSG00000058427	Cxcl2	CINC-2a|GROb|Gro2|MIP-2|MIP-2a|Mgsa-b|Mip2|Scyb|Scyb2	chemokine (C-X-C motif) ligand 2	protein-coding
mm_131045.1	chr16	3908950	3909031	+	1	NA	promoter-TSS (NM_029738)	promoter-TSS (NM_029738)	-19	NM_029738	76779	Mm.458921	NM_029738	ENSMUSG00000014232	Cluap1	2310030D15Rik|2610111M03Rik	clusterin associated protein 1	protein-coding
mm_77424.1	chr8	121083167	121083191	-	1	NA	promoter-TSS (NR_045471)	promoter-TSS (NR_045471)	-69	NR_130109	68790	Mm.246916	NR_045471	ENSMUSG00000097336	Fendrr	1110050K14Rik|LL66|linc-Foxf1a|lincFoxf1	Foxf1 adjacent non-coding developmental regulatory RNA	ncRNA
mm_129755.1	chr15	82354313	82354323	-	1	NA	promoter-TSS (NM_025987)	promoter-TSS (NM_025987)	-27	NM_025987	67130	Mm.27570	NM_025987	ENSMUSG00000022450	Ndufa6	14kDa|2700038D15Rik|B230217P19Rik	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 6 (B14)	protein-coding
mm_136536.1	chr16	97734808	97734839	-	1	NA	Intergenic	Intergenic	28932	NM_023663	72388	Mm.35290	NM_023663	ENSMUSG00000005251	Ripk4	2310069J12Rik|AI552420|ANKK2|Ankrd3|DIk|PKK|RIP4	receptor-interacting serine-threonine kinase 4	protein-coding
mm_7714.1	chr1	130629599	130629607	-	1	NA	promoter-TSS (NM_009581)	promoter-TSS (NM_009581)	3	NM_009581	22789	Mm.4644	NM_009581	ENSMUSG00000042554	Zp3r	AV264399|SP56	zona pellucida 3 receptor	protein-coding
mm_119035.1	chr14	30558712	30558728	+	1	NA	intron (NM_009388, intron 1 of 13)	intron (NM_009388, intron 1 of 13)	9589	NM_009388	21881	Mm.290692	NM_009388	ENSMUSG00000021957	Tkt	p68	transketolase	protein-coding
mm_173257.1	chrX	94827708	94827710	+	1	NA	Intergenic	IAP1-MM_LTR|LTR|ERVK	-29420	NR_003292	668171	Mm.426134	NR_003292		Zxda	4933406P09Rik|AW413531	zinc finger, X-linked, duplicated A	pseudo
mm_84983.1	chr9	85749287	85749303	-	1	NA	promoter-TSS (NM_001081282)	promoter-TSS (NM_001081282)	39	NM_001081282	108837	Mm.22315	NM_175371	ENSMUSG00000035941	Ibtk	5430411K16Rik|AA409502|BTKI|mKIAA1417	inhibitor of Bruton agammaglobulinemia tyrosine kinase	protein-coding
mm_51040.1	chr6	65601166	65601208	+	1	NA	intron (NM_001001495, intron 5 of 7)	intron (NM_001001495, intron 5 of 7)	10789	NM_001001495	414084	Mm.117558	NM_001001495	ENSMUSG00000044162	Tnip3	9030611K07Rik|ABIN-3|LIND	TNFAIP3 interacting protein 3	protein-coding
mm_14436.1	chr2	130629343	130629345	+	1	NA	intron (NM_198176, intron 1 of 2)	intron (NM_198176, intron 1 of 2)	683	NM_198176	380601	Mm.27090	NM_198176	ENSMUSG00000079043	Fastkd5	C78212|mKIAA1792	FAST kinase domains 5	protein-coding
mm_14736.1	chr2	144331487	144331560	+	1	NA	promoter-TSS (NM_152947)	promoter-TSS (NM_152947)	-161	NM_152947	107586	Mm.252750	NM_026924	ENSMUSG00000037279	Ovol2	1700108N11Rik|1810007D21Rik|M-OVO|M-OVO-A|M-OVO-B|MOVO|Ovo2|Zfp339|movo2	ovo like zinc finger 2	protein-coding
mm_146856.1	chr18	24178891	24178907	-	1	NA	Intergenic	ORR1E|LTR|ERVL-MaLR	-26445	NM_013814	14423	Mm.30249	NM_013814	ENSMUSG00000000420	Galnt1	-	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 1	protein-coding
mm_45627.1	chr5	76304475	76304507	-	1	NA	promoter-TSS (NM_007715)	promoter-TSS (NM_007715)	57	NM_007715	12753	Mm.3552	NM_007715	ENSMUSG00000029238	Clock	5330400M04Rik|KAT13D	circadian locomotor output cycles kaput	protein-coding
mm_148272.1	chr18	81927421	81927431	-	1	NA	Intergenic	Intergenic	64654	NR_039589	100628596		NR_039589	ENSMUSG00000093036	Mir5127	mmu-mir-5127|mu-mir-5127	microRNA 5127	ncRNA
mm_24029.1	chr3	87536057	87536073	+	1	NA	exon (NM_012051, exon 5 of 5)	exon (NM_012051, exon 5 of 5)	10487	NM_012051	27049	Mm.219460	NM_012051	ENSMUSG00000003382	Etv3	AI414410|METS|Pe1	ets variant 3	protein-coding
mm_24626.1	chr3	93555127	93555152	+	1	NA	promoter-TSS (NM_009112)	promoter-TSS (NM_009112)	22	NM_009112	20194	Mm.1	NM_009112	ENSMUSG00000041959	S100a10	42C|AA409961|AL024248|CAL12|CLP11|Cal1l|p10|p11	S100 calcium binding protein A10 (calpactin)	protein-coding
mm_65774.1	chr7	28764612	28764617	-	1	NA	intron (NM_001306222, intron 1 of 5)	RLTR31C_MM|LTR|ERVK	2030	NM_001306222	18036	Mm.220333	NM_010908	ENSMUSG00000030595	Nfkbib	I(Kappa)B(beta)|I-kappa-B-beta|IKB-beta|IKappaBbeta|IkB|IkBb|NF-kappa-BIB|ikB-B	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, beta	protein-coding
mm_29266.1	chr3	107333954	107333973	-	1	NA	promoter-TSS (NM_001045807)	promoter-TSS (NM_001045807)	-674	NM_001045807	229700	Mm.27966	NM_001045807	ENSMUSG00000048109	Rbm15	C230088J01Rik|mKIAA1438	RNA binding motif protein 15	protein-coding
mm_82897.1	chr9	32701188	32701192	-	1	NA	intron (NM_011808, intron 1 of 7)	intron (NM_011808, intron 1 of 7)	5148	NM_001038642	23871	Mm.292415	NM_011808	ENSMUSG00000032035	Ets1	AI196000|AI448617|D230050P06|Ets-1|Tpl1|vs	E26 avian leukemia oncogene 1, 5' domain	protein-coding
mm_77246.1	chr8	115705462	115705514	-	1	NA	3' UTR (NM_001025577, exon 1 of 1)	3' UTR (NM_001025577, exon 1 of 1)	1406	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_117165.1	chr13	62858365	62858411	-	1	NA	promoter-TSS (NM_007994)	promoter-TSS (NM_007994)	-18	NM_007994	14120	Mm.391871	NM_007994	ENSMUSG00000021456	Fbp2	Fbp-1|Fbp1|Rae-30	fructose bisphosphatase 2	protein-coding
mm_106326.1	chr11	118317454	118317467	-	1	NA	exon (NM_011594, exon 3 of 5)	exon (NM_011594, exon 3 of 5)	25074	NM_021440	58251	Mm.439815	NM_021440	ENSMUSG00000076433	BC100451	Cep295nl|Ddc8|FS39|Kiaa1731nl	cDNA sequence BC100451	protein-coding
mm_147733.1	chr18	61036190	61036210	-	1	NA	promoter-TSS (NM_009880)	promoter-TSS (NM_009880)	-1	NM_009880	12590	Mm.144448	NM_009880	ENSMUSG00000024619	Cdx1	Cdx|Cdx-1	caudal type homeobox 1	protein-coding
mm_56784.1	chr6	116637323	116637338	-	1	NA	3' UTR (NM_178045, exon 11 of 11)	3' UTR (NM_178045, exon 11 of 11)	-8331	NM_026057	67255	Mm.18810	NM_026057	ENSMUSG00000059878	Zfp422	2900028O21Rik|AU041373|KOX15|Krox-25-2|Krox-26|Krox25|Krox26|Znf22	zinc finger protein 422	protein-coding
mm_69770.1	chr7	141016777	141016783	-	1	NA	exon (NM_001033632, exon 1 of 2)	exon (NM_001033632, exon 1 of 2)	112	NM_001033632	213002	Mm.276440	NM_001033632	ENSMUSG00000059108	Ifitm6	A330075D07|Dspa2f|Fgls5|fragilis5	interferon induced transmembrane protein 6	protein-coding
mm_67195.1	chr7	74013636	74013667	-	1	NA	promoter-TSS (NM_009181)	promoter-TSS (NM_009181)	31	NM_009181	20450	Mm.4954	NM_009181	ENSMUSG00000025789	St8sia2	AI323367|ST8SiaII|STX|Siat8b	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 2	protein-coding
mm_20555.1	chr2	131072624	131072632	-	1	NA	exon (NM_011426, exon 17 of 21)	exon (NM_011426, exon 17 of 21)	-8814	NM_001163529	110751	Mm.108550	NM_033615	ENSMUSG00000027318	Adam33	Adaml	a disintegrin and metallopeptidase domain 33	protein-coding
mm_136054.1	chr16	78577024	78577035	-	1	NA	promoter-TSS (NM_001252440)	promoter-TSS (NM_001252440)	-341	NM_025967	67102	Mm.37332	NM_025967	ENSMUSG00000022864	D16Ertd472e	1700010I10Rik|2310009O17Rik|E330003K22Rik|Eurl	DNA segment, Chr 16, ERATO Doi 472, expressed	protein-coding
mm_128253.1	chr15	36770996	36771010	-	1	NA	3' UTR (NM_001253807, exon 5 of 5)	3' UTR (NM_001253807, exon 5 of 5)	19929	NM_001253807	22631	Mm.3360	NM_011740	ENSMUSG00000022285	Ywhaz	1110013I11Rik|14-3-3zeta|AI596267|AL022924|AU020854	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide	protein-coding
mm_67099.1	chr7	69909549	69909554	-	1	NA	Intergenic	Intergenic	413457	NR_045940	73796	Mm.410832	NR_045940	ENSMUSG00000108885	4930402F11Rik	-	RIKEN cDNA 4930402F11 gene	ncRNA
mm_91177.1	chr10	20725119	20725123	-	1	NA	promoter-TSS (NM_013875)	promoter-TSS (NM_013875)	-43	NM_013875	29863	Mm.425617	NM_013875	ENSMUSG00000019990	Pde7b	-	phosphodiesterase 7B	protein-coding
mm_97302.1	chr11	76601280	76601283	+	1	NA	Intergenic	CpG	-23542	NM_198894	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_74251.1	chr8	124831804	124831814	+	1	NA	3' UTR (NM_198632, exon 10 of 10)	3' UTR (NM_198632, exon 10 of 10)	31220	NM_025615	66523	Mm.436864	NM_025615	ENSMUSG00000031984	2810004N23Rik	3110004G14Rik|Ayu21-55|Gt(pU21)55Imeg|GtAyu21-55	RIKEN cDNA 2810004N23 gene	protein-coding
mm_39512.1	chr5	21256107	21256115	+	1	NA	intron (NM_175437, intron 18 of 30)	intron (NM_175437, intron 18 of 30)	69844	NM_175437	212167	Mm.121705	NM_175437	ENSMUSG00000039934	Gsap	A530088I07Rik|Pion	gamma-secretase activating protein	protein-coding
mm_116320.1	chr13	37769932	37769935	-	1	NA	Intergenic	MTC|LTR|ERVL-MaLR	-56105	NM_026830	68750	Mm.491109	NM_026830	ENSMUSG00000039087	Rreb1	1110037N09Rik|AA414966|B930013M22Rik	ras responsive element binding protein 1	protein-coding
mm_162504.1	chr1	148841701	148841701	+	1	NA	Intergenic	Intergenic	1080738	NM_001305632	18783	Mm.4186	NM_008869	ENSMUSG00000056220	Pla2g4a	Pla2g4|cPLA2|cPLA2-alpha|cPLA2alpha	phospholipase A2, group IVA (cytosolic, calcium-dependent)	protein-coding
mm_124705.1	chr15	6540347	6540353	+	1	NA	Intergenic	Intergenic	-39497	NM_001278269	23880	Mm.170905	NM_011815	ENSMUSG00000022148	Fyb	ADAP|B630013F22Rik|FYB-120/130|Slap130|p120/130|p120/p130	FYN binding protein	protein-coding
mm_106899.1	chr12	8012686	8012696	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	35014	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_168869.1	chr12	35909051	35909054	-	1	NA	Intergenic	Intergenic	-16569	NM_207531	403205	Mm.190508	NM_207531	ENSMUSG00000036231	Agr3	BCMP11|E030025L21Rik|Gm888	anterior gradient 3	protein-coding
mm_106151.1	chr11	116605028	116605045	-	1	NA	exon (NM_172572, exon 6 of 19)	exon (NM_172572, exon 6 of 19)	11349	NM_009591	11298	Mm.42233	NM_009591	ENSMUSG00000020804	Aanat	AA-NAT|Nat-2|Nat4|Snat	arylalkylamine N-acetyltransferase	protein-coding
mm_14537.1	chr2	132785976	132785988	+	1	NA	intron (NM_007694, intron 1 of 4)	intron (NM_007694, intron 1 of 4)	4704	NM_007694	12653	Mm.255241	NM_007694	ENSMUSG00000027350	Chgb	Scg-1	chromogranin B	protein-coding
mm_98741.1	chr11	96365863	96365899	+	1	NA	exon (NM_008266, exon 1 of 2)	exon (NM_008266, exon 1 of 2)	123	NM_008266	15407	Mm.890	NM_008266	ENSMUSG00000018973	Hoxb1	Hox-2.9	homeobox B1	protein-coding
mm_55344.1	chr6	56704674	56704712	-	1	NA	promoter-TSS (NM_025520)	promoter-TSS (NM_025520)	6	NM_025520	66373	Mm.25642	NM_025520	ENSMUSG00000091625	Lsm5	2010208O10Rik|2310034K10Rik	LSM5 homolog, U6 small nuclear RNA and mRNA degradation associated	protein-coding
mm_1800.1	chr1	80445889	80445895	+	1	NA	promoter-TSS (NR_040460)	promoter-TSS (NR_040460)	-40	NR_040460	72208	Mm.396181	NR_040460	ENSMUSG00000101483	1700016L21Rik	Jr3	RIKEN cDNA 1700016L21 gene	ncRNA
mm_43308.1	chr5	134722027	134722052	+	1	NA	exon (NM_007925, exon 15 of 37)	exon (NM_007925, exon 15 of 37)	25284	NM_007925	13717	Mm.275320	NM_007925	ENSMUSG00000029675	Eln	AI385707|AI480567|E030024M20Rik	elastin	protein-coding
mm_93816.1	chr10	121435739	121435774	-	1	NA	intron (NM_138956, intron 1 of 4)	intron (NM_138956, intron 1 of 4)	40494	NM_138956	192678	Mm.41265	NM_138956	ENSMUSG00000025795	Rassf3	AW212023|AW322379	Ras association (RalGDS/AF-6) domain family member 3	protein-coding
mm_96369.1	chr11	67219698	67219708	+	1	NA	exon (NM_030679, exon 32 of 40)	exon (NM_030679, exon 32 of 40)	-18109	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_142451.1	chr17	45592863	45592896	-	1	NA	promoter-TSS (NM_022880)	promoter-TSS (NM_022880)	-486	NM_022880	63959	Mm.29744	NM_022880	ENSMUSG00000023942	Slc29a1	1200014D21Rik|AA407560|ENT1	solute carrier family 29 (nucleoside transporters), member 1	protein-coding
mm_41192.1	chr5	88327939	88328011	+	1	NA	exon (NM_008644, exon 3 of 3)	exon (NM_008644, exon 3 of 3)	10663	NM_008644	17830	Mm.200411	NM_008644	ENSMUSG00000064156	Prol1	Muc10	proline rich, lacrimal 1	protein-coding
mm_93264.1	chr10	95630379	95630380	-	1	NA	Intergenic	RMER17B2|LTR|ERVK	-66212	NM_027722	71207	Mm.24397	NM_027722	ENSMUSG00000020029	Nudt4	4933436C10Rik|DIPP2|DIPP2alpha|DIPP2beta|HDCMB47P	nudix (nucleoside diphosphate linked moiety X)-type motif 4	protein-coding
mm_30516.1	chr3	158528924	158528938	-	1	NA	intron (NM_001081358, intron 1 of 27)	intron (NM_001081358, intron 1 of 27)	33290	NM_001291453	242274	Mm.132162	NM_001081358	ENSMUSG00000028176	Lrrc7	AK122498|densin|mKIAA1365	leucine rich repeat containing 7	protein-coding
mm_131375.1	chr16	13923988	13923992	+	1	NA	intron (NM_001289562, intron 1 of 3)	B3|SINE|B2	-16639	NM_001289563	93734	Mm.76554	NM_033564	ENSMUSG00000022679	Mpv17l	M-LP	Mpv17 transgene, kidney disease mutant-like	protein-coding
mm_117268.1	chr13	64421658	64421674	-	1	NA	Intergenic	Intergenic	-10887	NM_053180	105278	Mm.74982	NM_053180	ENSMUSG00000021483	Cdk20	4932702G04Rik|AU019450|AW558027|CDCH|Ccrk|PNQLARE|p42	cyclin-dependent kinase 20	protein-coding
mm_15374.1	chr2	156475508	156475561	+	1	NA	promoter-TSS (NM_001006664)	promoter-TSS (NM_001006664)	0	NM_001006664	13821	Mm.20852	NM_013510	ENSMUSG00000027624	Epb41l1	4.1N|Epb4.1l1|NBL1|mKIAA0338	erythrocyte membrane protein band 4.1 like 1	protein-coding
mm_106826.1	chr12	7988750	7988769	+	1	NA	exon (NM_009693, exon 10 of 29)	exon (NM_009693, exon 10 of 29)	11082	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_85224.1	chr9	97076895	97076897	-	1	NA	TTS (NM_138756)	TTS (NM_138756)	34145	NM_138756	192287	Mm.228067	NM_138756	ENSMUSG00000032449	Slc25a36	C330005L02Rik	solute carrier family 25, member 36	protein-coding
mm_98261.1	chr11	88905926	88905938	+	1	NA	promoter-TSS (NR_045955)	promoter-TSS (NR_045955)	4	NR_045955	73921	Mm.439148	NR_045955	ENSMUSG00000087338	Scpep1os	4930405P13Rik	serine carboxypeptidase 1, opposite strand	ncRNA
mm_90641.1	chr10	128637394	128637420	+	1	NA	intron (NM_011772, intron 5 of 7)	intron (NM_011772, intron 5 of 7)	8586	NM_011772	22781	Mm.358648	NM_011772	ENSMUSG00000002578	Ikzf4	A630026H08Rik|Eos|Zfpn1a4|Znfn1a4	IKAROS family zinc finger 4	protein-coding
mm_60842.1	chr7	45783687	45783732	+	1	NA	promoter-TSS (NR_110987)	promoter-TSS (NR_110987)	-238	NM_001005511	381983	Mm.44928	NM_001005511	ENSMUSG00000062044	Lmtk3	BC059845|aatyk3	lemur tyrosine kinase 3	protein-coding
mm_7373.1	chr1	106759728	106759748	-	1	NA	promoter-TSS (NM_027534)	promoter-TSS (NM_027534)	4	NM_027534	70750	Mm.458911	NM_027534	ENSMUSG00000009905	Kdsr	6330410P18Rik|9430079B08Rik|Fvt1	3-ketodihydrosphingosine reductase	protein-coding
mm_36115.1	chr4	58907557	58907561	-	1	NA	intron (NM_172381, intron 1 of 48)	intron (NM_172381, intron 1 of 48)	5166	NM_172381	230249	Mm.234801	NM_172381	ENSMUSG00000050812	AI314180	AW558785|BB181316|mKIAA0368	expressed sequence AI314180	protein-coding
mm_159689.1	chr5	17962537	17962537	+	1	NA	promoter-TSS (NM_001081143)	promoter-TSS (NM_001081143)	-33	NM_001081143	242851	Mm.332230	NM_001081143	ENSMUSG00000028777	Gnat3	Ggust|Gtn	guanine nucleotide binding protein, alpha transducing 3	protein-coding
mm_104918.1	chr11	99815662	99815664	-	1	NA	promoter-TSS (NM_001100614)	promoter-TSS (NM_001100614)	3	NM_001100614	670496	Mm.466614	NM_001100614	ENSMUSG00000078258	Gm11564	OTTMUSG00000002201	predicted gene 11564	protein-coding
mm_82000.1	chr9	121675189	121675229	+	1	NA	Intergenic	ORR1D2|LTR|ERVL-MaLR	29820	NM_001164562	215474	Mm.31421	NM_178677	ENSMUSG00000061536	Sec22c	4932412K21|5930407I15Rik|C530046H07|Sec22l3	SEC22 homolog C, vesicle trafficking protein	protein-coding
mm_28778.1	chr3	95989295	95989306	-	1	NA	exon (NM_023320, exon 6 of 6)	exon (NM_023320, exon 6 of 6)	3790	NR_045872	668224	Mm.357766	NR_045872		Gm9054	EG668224	predicted gene 9054	ncRNA
mm_135037.1	chr16	32869959	32869962	-	1	NA	Intergenic	Intergenic	-1594	NM_172615	100502698	Mm.327319	NM_172615	ENSMUSG00000035629	Rubcn	1700021K19Rik|5330403K09|Kiaa0226|Rubicon|mKIAA0226	RUN domain and cysteine-rich domain containing, Beclin 1-interacting protein	protein-coding
mm_121721.1	chr14	16575158	16575170	-	1	NA	5' UTR (NM_011243, exon 1 of 8)	5' UTR (NM_011243, exon 1 of 8)	312	NM_011243	218772	Mm.259318	NM_011243	ENSMUSG00000017491	Rarb	A830025K23|Hap|Nr1b2	retinoic acid receptor, beta	protein-coding
mm_110486.1	chr12	51971251	51971284	-	1	NA	promoter-TSS (NM_177171)	promoter-TSS (NM_177171)	54	NM_177171	320487	Mm.131941	NM_177171	ENSMUSG00000035181	Heatr5a	C230081H03Rik|D930036F22Rik|mKIAA1316	HEAT repeat containing 5A	protein-coding
mm_47991.1	chr5	135957581	135957590	-	1	NA	Intergenic	Intergenic	16891	NM_001160366	109267	Mm.332750	NM_001160366	ENSMUSG00000029699	Ssc4d	C330016E03Rik|S4D-SRCRB|SRCRB-S4D|Srcrb4d	scavenger receptor cysteine rich family, 4 domains	protein-coding
mm_59363.1	chr7	25687542	25687569	+	1	NA	TTS (NM_172148)	TTS (NM_172148)	553	NM_011577	21803	Mm.248380	NM_011577	ENSMUSG00000002603	Tgfb1	TGF-beta1|TGFbeta1|Tgfb|Tgfb-1	transforming growth factor, beta 1	protein-coding
mm_127348.1	chr15	100616903	100616925	+	1	NA	exon (NM_011873, exon 2 of 4)	exon (NM_011873, exon 2 of 4)	1252	NM_011873	23994	Mm.486175	NM_011873	ENSMUSG00000000346	Dazap2	AI314727|Brbp|Gcap28|Prtb|gt6-12|mKIAA0058	DAZ associated protein 2	protein-coding
mm_102282.1	chr11	55398575	55398679	-	1	NA	exon (NM_009242, exon 8 of 10)	exon (NM_009242, exon 8 of 10)	21453	NM_009242	20692	Mm.291442	NM_009242	ENSMUSG00000018593	Sparc	BM-40|ON	secreted acidic cysteine rich glycoprotein	protein-coding
mm_32073.1	chr4	97930434	97930437	+	1	NA	intron (NM_010905, intron 2 of 10)	intron (NM_010905, intron 2 of 10)	152809	NM_010905	18027	Mm.31274	NM_010905	ENSMUSG00000028565	Nfia	1110047K16Rik|9430022M17Rik|CTF|NF1-A|NF1A	nuclear factor I/A	protein-coding
mm_48632.1	chr5	145139992	145140002	-	1	NA	promoter-TSS (NM_001033313)	promoter-TSS (NM_001033313)	92	NM_001033313	231887	Mm.188851	NM_001033313	ENSMUSG00000029623	Pdap1	HASPP28|PAP|PAP1	PDGFA associated protein 1	protein-coding
mm_31867.1	chr4	80003470	80003499	+	1	NA	Intergenic	Intergenic	-830729	NM_031202	22178	Mm.30438	NM_031202	ENSMUSG00000005994	Tyrp1	Oca3|TRP-1|TRP1|Tyrp|b|brown|isa	tyrosinase-related protein 1	protein-coding
mm_28213.1	chr3	88378741	88378753	-	1	NA	promoter-TSS (NM_001032298)	promoter-TSS (NM_001032298)	-46	NM_001032298	12097	Mm.425160	NM_001032298	ENSMUSG00000074486	Bglap2	BGP2|Bglap1|Bgp|Og2|mOC-B	bone gamma-carboxyglutamate protein 2	protein-coding
mm_114824.1	chr13	91807781	91807793	+	1	NA	promoter-TSS (NM_145453)	promoter-TSS (NM_145453)	-91	NM_145453	69085	Mm.52356	NM_145453	ENSMUSG00000021621	Zcchc9	1810019C21Rik	zinc finger, CCHC domain containing 9	protein-coding
mm_133087.1	chr16	62814839	62814859	+	1	NA	5' UTR (NM_026588, exon 1 of 2)	5' UTR (NM_026588, exon 1 of 2)	173	NM_026588	68159	Mm.386793	NM_026588	ENSMUSG00000047854	Stx19	A030009B12Rik	syntaxin 19	protein-coding
mm_100747.1	chr11	4160219	4160231	-	1	NA	promoter-TSS (NM_177616)	promoter-TSS (NM_177616)	68	NM_177616	216516	Mm.386854	NM_177616	ENSMUSG00000051427	Ccdc157	4930562D19Rik|mKIAA1656	coiled-coil domain containing 157	protein-coding
mm_135988.1	chr16	75092921	75092931	-	1	NA	Intergenic	Intergenic	493135	NM_001252513	320355	Mm.99517	NM_177142	ENSMUSG00000032948	Lipi	D930038D03Rik|lpd1	lipase, member I	protein-coding
mm_116091.1	chr13	28757618	28757642	-	1	NA	intron (NR_045053, intron 3 of 8)	intron (NR_045053, intron 3 of 8)	-46757	NR_105787	102466635		NR_105787	ENSMUSG00000099158	Mir6368	Gm27800|mmu-mir-6368	microRNA 6368	ncRNA
mm_31868.1	chr4	80003991	80003992	+	1	NA	Intergenic	Intergenic	-830222	NM_031202	22178	Mm.30438	NM_031202	ENSMUSG00000005994	Tyrp1	Oca3|TRP-1|TRP1|Tyrp|b|brown|isa	tyrosinase-related protein 1	protein-coding
mm_56140.1	chr6	87745274	87745300	-	1	NA	intron (NM_001159697, intron 2 of 7)	intron (NM_001159697, intron 2 of 7)	14418	NM_001159697	58229	Mm.333229	NM_021418	ENSMUSG00000068263	Efcc1	Ccdc48	EF hand and coiled-coil domain containing 1	protein-coding
mm_127605.1	chr15	102407145	102407147	+	1	NA	intron (NM_013672, intron 1 of 5)	B1_Mur2|SINE|Alu	830	NM_013672	20683	Mm.4618	NM_013672	ENSMUSG00000001280	Sp1	1110003E12Rik|AA450830|AI845540|Sp1-1	trans-acting transcription factor 1	protein-coding
mm_158204.1	chrX	105845926	105845943	-	1	NA	exon (NM_009530, exon 18 of 35)	exon (NM_009530, exon 18 of 35)	81457	NM_030614	80903	Mm.154768	NM_030614	ENSMUSG00000031230	Fgf16	-	fibroblast growth factor 16	protein-coding
mm_98993.1	chr11	98766315	98766347	+	1	NA	intron (NM_001313983, intron 9 of 9)	intron (NM_001313983, intron 9 of 9)	9046	NM_145434	217166	Mm.390397	NM_145434	ENSMUSG00000020889	Nr1d1	A530070C09Rik|R75201	nuclear receptor subfamily 1, group D, member 1	protein-coding
mm_149919.1	chr19	26607232	26607256	+	1	NA	intron (NM_011416, intron 1 of 32)	CpG	2084	NM_011416	67155	Mm.342988	NM_011416	ENSMUSG00000024921	Smarca2	2610209L14Rik|SNF2alpha|Snf2l2|brahma|brm	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	protein-coding
mm_12158.1	chr2	62046624	62046634	+	1	NA	5' UTR (NM_001242379, exon 1 of 25)	5' UTR (NM_001242379, exon 1 of 25)	114	NM_033552	94229	Mm.314497	NM_033552	ENSMUSG00000026904	Slc4a10	NCBE|mKIAA4136	solute carrier family 4, sodium bicarbonate cotransporter-like, member 10	protein-coding
mm_149316.1	chr19	10784582	10784599	+	1	NA	intron (NR_027805, intron 2 of 3)	intron (NR_027805, intron 2 of 3)	43643	NR_027805	403202	Mm.34482	NM_207529	ENSMUSG00000067577	A430093F15Rik	Gm674	RIKEN cDNA A430093F15 gene	ncRNA
mm_84262.1	chr9	62537037	62537061	-	1	NA	promoter-TSS (NM_175484)	promoter-TSS (NM_175484)	-5	NM_175484	235431	Mm.335229	NM_175484	ENSMUSG00000041729	Coro2b	CLIPINC|E130012P22Rik	coronin, actin binding protein, 2B	protein-coding
mm_41622.1	chr5	96849499	96849510	+	1	NA	Intergenic	Intergenic	56119	NM_013470	11745	Mm.7214	NM_013470	ENSMUSG00000029484	Anxa3	Anx3	annexin A3	protein-coding
mm_23511.1	chr3	60530320	60530325	+	1	NA	intron (NM_001310514, intron 2 of 8)	intron (NM_001310514, intron 2 of 8)	29143	NM_001253708	56758	Mm.255723	NM_020007	ENSMUSG00000027763	Mbnl1	Mbnl|mKIAA0428	muscleblind-like 1 (Drosophila)	protein-coding
mm_172563.1	chr8	109340881	109340897	-	1	NA	promoter-TSS (NR_002928)	promoter-TSS (NR_002928)	19	NR_002928	384864	Mm.390083	NR_002928		Gm1943	-	WD repeat domain 70 pseudogene	pseudo
mm_110736.1	chr12	69790606	69790631	-	1	NA	promoter-TSS (NM_183294)	promoter-TSS (NM_183294)	89	NM_183294	71091	Mm.132325	NM_183294	ENSMUSG00000020990	Cdkl1	4933411O17Rik	cyclin-dependent kinase-like 1 (CDC2-related kinase)	protein-coding
mm_85329.1	chr9	102354597	102354607	-	1	NA	promoter-TSS (NM_173447)	promoter-TSS (NM_173447)	91	NM_001168296	270190	Mm.22897	NM_173447	ENSMUSG00000032537	Ephb1	9330129L11|AW488255|C130099E04Rik|Cek6|ENSMUSG00000074119|Elk|Elkh|Hek6|Net	Eph receptor B1	protein-coding
mm_53477.1	chr6	134936871	134936874	+	1	NA	intron (NR_037956, intron 1 of 1)	intron (NR_037956, intron 1 of 1)	7780	NR_037955	381822	Mm.5935	NR_037955	ENSMUSG00000098318	Lockd	1190002F15Rik|AI120476|Droc	lncRNA downstream of Cdkn1b	ncRNA
mm_105468.1	chr11	105455278	105455288	-	1	NA	intron (NM_172568, intron 1 of 11)	intron (NM_172568, intron 1 of 11)	1452	NM_172568	632687	Mm.121570	NM_172568	ENSMUSG00000078627	March10	4933417C16Rik|AV039223|OTTMUSG00000002847|Rnf190	membrane-associated ring finger (C3HC4) 10	protein-coding
mm_65296.1	chr7	24512445	24512483	-	1	NA	intron (NR_110958, intron 2 of 2)	intron (NR_110958, intron 2 of 2)	5377	NR_110958	232969	Mm.181332	NM_146183	ENSMUSG00000064264	Zfp428	2410005H09Rik|AV271806|AW047854|Znf428	zinc finger protein 428	protein-coding
mm_9924.1	chr1	189688075	189688098	-	1	NA	promoter-TSS (NM_001081363)	promoter-TSS (NM_001081363)	0	NM_001081363	108000	Mm.129746	NM_001081363	ENSMUSG00000026605	Cenpf	6530404A22Rik|AI325968|CENF|Lek1|PRO1779|mitosin	centromere protein F	protein-coding
mm_141736.1	chr17	34120994	34121039	-	1	NA	intron (NM_001204973, intron 1 of 12)	CpG-6274	731	NM_010238	14312	Mm.3444	NM_010238	ENSMUSG00000024335	Brd2	AW228947|D17H6S113E|Frg-1|Fsrg-1|Fsrg1|Nat|Ring3|Rnf3|mKIAA4005	bromodomain containing 2	protein-coding
mm_169168.1	chr13	65557933	65557952	+	1	NA	Intergenic	Intergenic	279088	NM_178364	170936	Mm.151546	NM_178364	ENSMUSG00000021514	Zfp369	B930030B22Rik|D230020H11Rik|NRIF2	zinc finger protein 369	protein-coding
mm_14479.1	chr2	131508968	131508979	+	1	NA	intron (NM_001177836, intron 1 of 7)	intron (NM_001177836, intron 1 of 7)	17111	NM_001177838	228608	Mm.136586	NM_145533	ENSMUSG00000027333	Smox	B130066H01Rik|PAO|PAOh1|SMO	spermine oxidase	protein-coding
mm_24092.1	chr3	87977210	87977213	+	1	NA	exon (NM_016701, exon 4 of 4)	exon (NM_016701, exon 4 of 4)	6118	NM_016701	18008	Mm.331129	NM_016701	ENSMUSG00000004891	Nes	AA166324|C78523|ESTM46	nestin	protein-coding
mm_48213.1	chr5	137610465	137610489	-	1	NA	exon (NM_008788, exon 2 of 9)	exon (NM_008788, exon 2 of 9)	927	NM_008788	18542	Mm.262345	NM_008788	ENSMUSG00000029718	Pcolce	Astt-2|Astt2|P14|PCPE-1	procollagen C-endopeptidase enhancer protein	protein-coding
mm_129133.1	chr15	76196607	76196624	-	1	NA	promoter-TSS (NM_201394)	promoter-TSS (NM_201394)	-905	NM_201394	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
mm_113970.1	chr13	51645737	51645747	+	1	NA	intron (NM_025415, intron 1 of 2)	CpG	510	NM_025415	66197	Mm.222228	NM_025415	ENSMUSG00000062248	Cks2	1110038L14Rik|CKSHS2	CDC28 protein kinase regulatory subunit 2	protein-coding
mm_14485.1	chr2	131843123	131843138	+	1	NA	intron (NR_029381, intron 1 of 2)	ORR1D1|LTR|ERVL-MaLR	4526	NR_029381	414081	Mm.246905	NR_029381	ENSMUSG00000086822	5330413P13Rik	-	RIKEN cDNA 5330413P13 gene	ncRNA
mm_79284.1	chr9	51062175	51062191	+	1	NA	exon (NM_001033534, exon 6 of 8)	exon (NM_001033534, exon 6 of 8)	14911	NM_001033534	244864	Mm.335152	NM_001033534	ENSMUSG00000060594	Layn	E030012M19Rik|Gm511	layilin	protein-coding
mm_130651.1	chr15	100636834	100636848	-	1	NA	promoter-TSS (NM_174992)	promoter-TSS (NM_174992)	99	NR_104338	207818	Mm.26282	NM_174992	ENSMUSG00000053559	Smagp	-	small cell adhesion glycoprotein	protein-coding
mm_161277.1	chr14	15436318	15436318	-	1	NA	intron (NM_146052, intron 1 of 1)	intron (NM_146052, intron 1 of 1)	2669	NM_146052	218763	Mm.138039	NM_146052	ENSMUSG00000045201	Lrrc3b	BC019794|LRP15	leucine rich repeat containing 3B	protein-coding
mm_46296.1	chr5	100429453	100429465	-	1	NA	promoter-TSS (NR_034038)	promoter-TSS (NR_034038)	76	NR_034038	100503199	Mm.392282	NR_034038	ENSMUSG00000097772	5430416N02Rik	100041797|Adapt33|Gm3514	RIKEN cDNA 5430416N02 gene	ncRNA
mm_120884.1	chr14	75330958	75330978	+	1	NA	exon (NM_026083, exon 14 of 19)	exon (NM_026083, exon 14 of 19)	46595	NM_026083	67302	Mm.74704	NM_026083	ENSMUSG00000022000	Zc3h13	2600010B19Rik|3110050K21Rik|4930570G11Rik|C87618	zinc finger CCCH type containing 13	protein-coding
mm_15548.1	chr2	158409908	158409918	+	1	NA	promoter-TSS (NM_001291138)	promoter-TSS (NM_001291138)	60	NM_001291138	228850	Mm.398185	NM_177227	ENSMUSG00000027652	Ralgapb	AI507211|B230339M05Rik|p170	Ral GTPase activating protein, beta subunit (non-catalytic)	protein-coding
mm_162701.1	chr10	21161342	21161348	-	1	NA	promoter-TSS (NM_001198914)	promoter-TSS (NM_001198914)	-361	NM_010848	17863	Mm.52109	NM_010848	ENSMUSG00000019982	Myb	AI550390|M16449|c-myb	myeloblastosis oncogene	protein-coding
mm_119023.1	chr14	30009163	30009174	+	1	NA	promoter-TSS (NM_019583)	promoter-TSS (NM_019583)	168	NM_001136240	218865	Mm.259916	NM_172264	ENSMUSG00000015970	Chdh	AU041472|D630034H06Rik	choline dehydrogenase	protein-coding
mm_109661.1	chr12	113014560	113014568	+	1	NA	promoter-TSS (NM_001291445)	promoter-TSS (NM_001291445)	56	NM_001291444	217893	Mm.35754	NM_198165	ENSMUSG00000021143	Pacs2	6720425G15Rik|AW208651|AW489976|E230011J22|Pacs1l|mKIAA0602	phosphofurin acidic cluster sorting protein 2	protein-coding
mm_103512.1	chr11	76623512	76623557	-	1	NA	Intergenic	CpG	-45795	NM_198894	109934	Mm.258939	NM_198018	ENSMUSG00000017631	Abr	-	active BCR-related gene	protein-coding
mm_108291.1	chr12	79149945	79149984	+	1	NA	exon (NM_009705, exon 4 of 8)	exon (NM_009705, exon 4 of 8)	19176	NM_009705	11847	Mm.3506	NM_009705	ENSMUSG00000021125	Arg2	AII|AU022422	arginase type II	protein-coding
mm_4530.1	chr1	175637880	175637895	+	1	NA	exon (NM_133809, exon 3 of 15)	exon (NM_133809, exon 3 of 15)	5694	NM_133809	98256	Mm.27217	NM_133809	ENSMUSG00000039783	Kmo	AI046660	kynurenine 3-monooxygenase (kynurenine 3-hydroxylase)	protein-coding
mm_138379.1	chr17	35024137	35024145	+	1	NA	intron (NM_001347347, intron 13 of 16)	intron (NM_001347347, intron 13 of 16)	3875	NR_028258	78376	Mm.390966	NM_023893	ENSMUSG00000036185	Sapcd1	2810436B06Rik|G7d|Ng23	suppressor APC domain containing 1	protein-coding
mm_15217.1	chr2	154307203	154307208	+	1	NA	promoter-TSS (NM_001025574)	promoter-TSS (NM_001025574)	-39	NM_001025574	433492	Mm.330682	NM_001025574	ENSMUSG00000067996	Bpifb9b	5430413K10Rik|AI413838|OTTMUSG00000015915	BPI fold containing family B, member 9B	protein-coding
mm_87584.1	chr10	56599428	56599438	+	1	NA	Intergenic	Intergenic	222133	NM_010288	14609	Mm.378921	NM_010288	ENSMUSG00000050953	Gja1	AU042049|AW546267|Cnx43|Cx43|Cx43alpha1|Gja-1|Npm1|connexin43	gap junction protein, alpha 1	protein-coding
mm_829.1	chr1	51289246	51289279	+	1	NA	5' UTR (NM_138741, exon 1 of 2)	5' UTR (NM_138741, exon 1 of 2)	136	NM_138741	20324	Mm.398690	NM_138741	ENSMUSG00000045954	Sdpr	-	serum deprivation response	protein-coding
mm_149165.1	chr19	9018626	9018640	+	1	NA	TTS (NR_105786)	TTS (NR_105786)	729	NR_105786	102465190		NR_105786	ENSMUSG00000099308	Mir6367	Gm27467|mmu-mir-6367	microRNA 6367	ncRNA
mm_143208.1	chr17	62870145	62870146	-	1	NA	intron (NM_010109, intron 1 of 3)	intron (NM_010109, intron 1 of 3)	11172	NM_207654	13640	Mm.7978	NM_010109	ENSMUSG00000048915	Efna5	AL-1|AV158822|EFL-5|Ephrin-A5|Epl7|LERK-7|RAGS	ephrin A5	protein-coding
mm_7788.1	chr1	131472622	131472629	-	1	NA	intron (NM_001081011, intron 2 of 22)	intron (NM_001081011, intron 2 of 22)	54736	NM_001081011	14270	Mm.276259	NM_019520	ENSMUSG00000026425	Srgap2	9930124L22Rik|AI448945|FBP2|Fnbp2|srGAP3	SLIT-ROBO Rho GTPase activating protein 2	protein-coding
mm_167037.1	chr7	78783299	78783302	+	1	NA	promoter-TSS (NM_023331)	promoter-TSS (NM_023331)	169	NM_026498	67994	Mm.297033	NM_026498	ENSMUSG00000030611	Mrps11	0710005I03Rik|C79873	mitochondrial ribosomal protein S11	protein-coding
mm_132974.1	chr16	52033932	52033937	+	1	NA	intron (NM_001033238, intron 2 of 17)	intron (NM_001033238, intron 2 of 17)	2385	NM_001033238	208650	Mm.328206	NM_001033238	ENSMUSG00000022637	Cblb	AI429560|AI851073|Cbl-b	Casitas B-lineage lymphoma b	protein-coding
mm_71583.1	chr8	54779523	54779583	+	1	NA	5' UTR (NM_001253754, exon 1 of 7)	5' UTR (NM_001253754, exon 1 of 7)	119	NM_001253754	234267	Mm.241700	NM_153581	ENSMUSG00000031517	Gpm6a	Gpm6|M6A	glycoprotein m6a	protein-coding
mm_172499.1	chr7	66542183	66542183	-	1	NA	Intergenic	Intergenic	-114706	NM_053080	56847	Mm.140988	NM_053080	ENSMUSG00000015134	Aldh1a3	ALDH6|RALDH3|V1	aldehyde dehydrogenase family 1, subfamily A3	protein-coding
mm_111612.1	chr12	102401594	102401604	-	1	NA	intron (NM_011175, intron 8 of 13)	B3A|SINE|B2	38214	NM_011175	19141	Mm.17185	NM_011175	ENSMUSG00000021190	Lgmn	AEP|AI746452|AU022324|Prsc1	legumain	protein-coding
mm_103338.1	chr11	74676614	74676616	-	1	NA	non-coding (NR_037610, exon 11 of 11)	non-coding (NR_037610, exon 11 of 11)	27120	NM_001081158	74148	Mm.214574	NM_001081158	ENSMUSG00000020741	Cluh	1300001I01Rik|Kiaa0664|mKIAA0664	clustered mitochondria (cluA/CLU1) homolog	protein-coding
mm_115829.1	chr13	21286810	21286810	-	1	NA	3' UTR (NM_010343, exon 5 of 5)	3' UTR (NM_010343, exon 5 of 5)	5876	NM_010343	14780	Mm.1332	NM_010343	ENSMUSG00000004344	Gpx5	AV379049|Arep	glutathione peroxidase 5	protein-coding
mm_13701.1	chr2	117128195	117128228	+	1	NA	intron (NM_033524, intron 1 of 6)	B1_Mus2|SINE|Alu	7140	NM_033524	114715	Mm.245890	NM_033524	ENSMUSG00000027351	Spred1	5730461F13Rik|AL024345|AW047647	sprouty protein with EVH-1 domain 1, related sequence	protein-coding
mm_25824.1	chr3	127930986	127930990	+	1	NA	intron (NR_040552, intron 3 of 4)	intron (NR_040552, intron 3 of 4)	14817	NR_040552	329753	Mm.119720	NR_040552	ENSMUSG00000104763	9830132P13Rik	9830132P13	RIKEN cDNA 9830132P13 gene	ncRNA
mm_92835.1	chr10	81496314	81496324	-	1	NA	promoter-TSS (NM_134009)	promoter-TSS (NM_134009)	44	NM_134009	103425	Mm.302791	NM_134009	ENSMUSG00000020238	Ncln	3100002P13Rik|AW120537	nicalin	protein-coding
mm_72348.1	chr8	79639764	79639780	+	1	NA	promoter-TSS (NM_001256033)	promoter-TSS (NM_001256033)	96	NM_001081164	73945	Mm.34348	NM_001081164	ENSMUSG00000036990	Otud4	4930431L18Rik|AI449692|D8Ertd69e|mKIAA1046	OTU domain containing 4	protein-coding
mm_4959.1	chr1	191267005	191267016	+	1	NA	Intergenic	Intergenic	51108	NM_025424	66208	Mm.46444	NM_025424	ENSMUSG00000037499	Nenf	1110060M21Rik|SCIRP10|Spuf	neuron derived neurotrophic factor	protein-coding
mm_169130.1	chr13	58399959	58399964	-	1	NA	exon (NM_025279, exon 3 of 16)	exon (NM_025279, exon 3 of 16)	2208	NM_001301343	15387	Mm.142872	NM_025279	ENSMUSG00000021546	Hnrnpk	Hnrpk|KBBP|NOVA	heterogeneous nuclear ribonucleoprotein K	protein-coding
mm_106755.1	chr12	4133511	4133518	+	1	NA	promoter-TSS (NM_138305)	promoter-TSS (NM_138305)	117	NM_001159536	104111	Mm.489807	NM_138305	ENSMUSG00000020654	Adcy3	AC3|mKIAA0511	adenylate cyclase 3	protein-coding
mm_158242.1	chrX	106603678	106603702	-	1	NA	promoter-TSS (NM_001281859)	promoter-TSS (NM_001281859)	-11	NM_001281859	58861	Mm.287166	NM_021476	ENSMUSG00000052821	Cysltr1	BB147369|CysLT1R|Cyslt1	cysteinyl leukotriene receptor 1	protein-coding
mm_140247.1	chr17	84181975	84182001	+	1	NA	Intergenic	Intergenic	5959	NM_001001806	12193	Mm.259321	NM_001001806	ENSMUSG00000045817	Zfp36l2	Brf2|ERF2|Tis11d	zinc finger protein 36, C3H type-like 2	protein-coding
mm_65633.1	chr7	27553139	27553249	-	1	NA	promoter-TSS (NM_011116)	promoter-TSS (NM_011116)	24	NM_011116	18807	Mm.6483	NM_011116	ENSMUSG00000003363	Pld3	Sam-9	phospholipase D family, member 3	protein-coding
mm_134572.1	chr16	20372148	20372195	-	1	NA	exon (NM_013790, exon 17 of 30)	exon (NM_013790, exon 17 of 30)	-46767	NM_183158	224044	Mm.276400	NM_183158	ENSMUSG00000022818	Cyp2ab1	EG224044|F730023N20	cytochrome P450, family 2, subfamily ab, polypeptide 1	protein-coding
mm_145646.1	chr18	61124217	61124281	+	1	NA	exon (NM_001037859, exon 12 of 22)	exon (NM_001037859, exon 12 of 22)	6781	NR_105949	102466212		NR_105949	ENSMUSG00000098389	Mir6983	Gm27496|mmu-mir-6983	microRNA 6983	ncRNA
mm_170241.1	chr17	89942554	89942569	+	1	NA	Intergenic	IAPLTR1_Mm|LTR|ERVK	145807	NM_001346962	18189	Mm.478418	NM_020252	ENSMUSG00000024109	Nrxn1	1700062G21Rik|9330127H16Rik|A230068P09Rik|mKIAA0578	neurexin I	protein-coding
mm_152343.1	chr19	9984220	9984237	-	1	NA	TTS (NM_011913)	TTS (NM_011913)	1582	NM_010239	14319	Mm.1776	NM_010239	ENSMUSG00000024661	Fth1	FHC|Fth|HFt|MFH	ferritin heavy polypeptide 1	protein-coding
mm_35917.1	chr4	53031543	53031553	-	1	NA	3' UTR (NM_013454, exon 50 of 50)	3' UTR (NM_013454, exon 50 of 50)	19668	NM_025623	66536	Mm.38244	NM_025623	ENSMUSG00000015247	Nipsnap3b	2700063N13Rik|Nipsnap3a	nipsnap homolog 3B (C. elegans)	protein-coding
mm_98717.1	chr11	96318756	96318775	+	1	NA	5' UTR (NM_010459, exon 1 of 2)	5' UTR (NM_010459, exon 1 of 2)	498	NM_010459	15412	Mm.3546	NM_010459	ENSMUSG00000038692	Hoxb4	Hox-2.6	homeobox B4	protein-coding
mm_158312.1	chrX	126915291	126915297	-	1	NA	Intergenic	Intergenic	-81290	NM_177705	237029	Mm.60998	NM_177705	ENSMUSG00000058670	4932411N23Rik	-	RIKEN cDNA 4932411N23 gene	protein-coding
mm_57979.1	chr6	135729862	135729880	-	1	NA	TTS (NM_008171)	TTS (NM_008171)	70958	NR_126088	75024	Mm.399147	NR_126088	ENSMUSG00000107396	4930425L21Rik	4930473P14Rik	RIKEN cDNA 4930425L21 gene	ncRNA
mm_105078.1	chr11	100821023	100821026	-	1	NA	intron (NM_001113563, intron 1 of 18)	PB1D10|SINE|Alu	1546	NM_011489	20851	Mm.34064	NM_011489	ENSMUSG00000020919	Stat5b	-	signal transducer and activator of transcription 5B	protein-coding
mm_12332.1	chr2	69646867	69646875	+	1	NA	promoter-TSS (NM_028284)	promoter-TSS (NM_028284)	-384	NM_028284	72569	Mm.252136	NM_028284	ENSMUSG00000063145	Bbs5	1700049I01Rik|2700023J09Rik	Bardet-Biedl syndrome 5 (human)	protein-coding
mm_90133.1	chr10	117719339	117719342	+	1	NA	Intergenic	MLTR14|LTR|ERV1	-8582	NM_001288586	17246	Mm.22670	NM_010786	ENSMUSG00000020184	Mdm2	1700007J15Rik|AA415488|Mdm-2	transformed mouse 3T3 cell double minute 2	protein-coding
mm_173315.1	chrY	90735648	90735660	+	1	NA	Intergenic	IMPB_01|Satellite|Satellite	19396	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_6718.1	chr1	82478092	82478096	-	1	NA	intron (NM_007735, intron 37 of 47)	intron (NM_007735, intron 37 of 47)	108755	NM_007735	12829	Mm.40253	NM_007735	ENSMUSG00000067158	Col4a4	E130010M05Rik|[a]4(IV)	collagen, type IV, alpha 4	protein-coding
mm_2054.1	chr1	87440465	87440477	+	1	NA	exon (NM_001110212, exon 24 of 29)	exon (NM_001110212, exon 24 of 29)	-29793	NM_028473	73234	Mm.7310	NM_028473	ENSMUSG00000026258	3110079O15Rik	Snorc	RIKEN cDNA 3110079O15 gene	protein-coding
mm_17896.1	chr2	35100653	35100665	-	1	NA	promoter-TSS (NM_178885)	promoter-TSS (NM_178885)	26	NM_001243102	98870	Mm.415380	NM_178885	ENSMUSG00000035875	AI182371	AI046667	expressed sequence AI182371	protein-coding
mm_173069.1	chrX	135866678	135866681	+	1	NA	Intergenic	RLTR1B|LTR|ERV1	-19172	NM_001098222	70237	Mm.440847	NM_198161	ENSMUSG00000072964	Bhlhb9	2700087I09Rik	basic helix-loop-helix domain containing, class B9	protein-coding
mm_30480.1	chr3	154847427	154847438	-	1	NA	intron (NM_177066, intron 21 of 24)	intron (NM_177066, intron 21 of 24)	136299	NM_175176	209601	Mm.331454	NM_175176	ENSMUSG00000078161	Erich3	1700013E18Rik|4922501L14Rik|5031409G23Rik|AI596448|Gm133	glutamate rich 3	protein-coding
mm_172829.1	chr9	19601524	19601524	-	1	NA	Intergenic	L1Md_T|LINE|L1	17013	NM_146524	258517	Mm.377548	NM_146524	ENSMUSG00000043087	Olfr855	MOR148-1	olfactory receptor 855	protein-coding
mm_161769.1	chr17	36672217	36672217	-	1	NA	promoter-TSS (NM_177636)	promoter-TSS (NM_177636)	-20	NM_177636	224756	Mm.246583	NM_177636	ENSMUSG00000037334	H2-M1	H-2M1|H2-Qa-Mb1|Mb1	histocompatibility 2, M region locus 1	protein-coding
mm_15803.1	chr2	164461232	164461284	+	1	NA	intron (NM_025575, intron 1 of 3)	CpG	287	NM_025575	66460	Mm.44218	NM_025575	ENSMUSG00000045503	Sys1	2610042O14Rik|AI266964|C87389	SYS1 Golgi-localized integral membrane protein homolog (S. cerevisiae)	protein-coding
mm_141413.1	chr17	29423890	29423893	-	1	NA	Intergenic	B1_Mus1|SINE|Alu	62977	NM_001159538	26382	Mm.279187	NM_013710	ENSMUSG00000024013	Fgd2	Tcd-2|Tcd2|ZFYVE4|tcs-2|tcs2	FYVE, RhoGEF and PH domain containing 2	protein-coding
mm_70963.1	chr8	27022074	27022079	+	1	NA	Intergenic	Intergenic	-1723	NM_153592	244373	Mm.277699	NM_153592	ENSMUSG00000031483	Erlin2	BC036333|C87251|Spfh2	ER lipid raft associated 2	protein-coding
mm_49115.1	chr6	8509784	8509794	+	1	NA	promoter-TSS (NR_040452)	promoter-TSS (NR_040452)	189	NM_133236	170772	Mm.210787	NM_133236	ENSMUSG00000029638	Glcci1	2310047L21Rik|A130036A18Rik|Fam117c|Gig18|Tssn1	glucocorticoid induced transcript 1	protein-coding
mm_116411.1	chr13	41486697	41486705	-	1	NA	intron (NM_001111324, intron 1 of 7)	intron (NM_001111324, intron 1 of 7)	659	NM_001111324	18003	Mm.288980	NM_017464	ENSMUSG00000021365	Nedd9	Cas-L|CasL|HEF1|MEF1|Nedd-9|p105	neural precursor cell expressed, developmentally down-regulated gene 9	protein-coding
mm_1974.1	chr1	86525491	86525525	+	1	NA	Intergenic	CpG	-1228	NM_008972	19231	Mm.19187	NM_008972	ENSMUSG00000026238	Ptma	Thym	prothymosin alpha	protein-coding
mm_152873.1	chr19	24477619	24477627	-	1	NA	promoter-TSS (NM_026520)	promoter-TSS (NM_026520)	-149	NM_026520	68034	Mm.440181	NM_026520	ENSMUSG00000074922	Fam122a	2410124L17Rik|2900009I07Rik|ENSMUSG00000051082|Gm9849	family with sequence similarity 122, member A	protein-coding
mm_139889.1	chr17	70846511	70846512	+	1	NA	5' UTR (NM_001164077, exon 1 of 2)	5' UTR (NM_001164077, exon 1 of 2)	266	NM_001164077	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_87618.1	chr10	57794572	57794664	+	1	NA	promoter-TSS (NM_020561)	promoter-TSS (NM_020561)	74	NM_020561	57319	Mm.2379	NM_020561	ENSMUSG00000019872	Smpdl3a	0610010C24Rik|AI529588|ASM3A|ASML3|ASML3A	sphingomyelin phosphodiesterase, acid-like 3A	protein-coding
mm_24171.1	chr3	88570599	88570637	+	1	NA	TTS (NM_033526)	TTS (NM_033526)	-9053	NM_025448	66256	Mm.7091	NM_025448	ENSMUSG00000041355	Ssr2	1500032E05Rik|AI315033|AU020133|TLAP|TRAPB|TRAPbeta	signal sequence receptor, beta	protein-coding
mm_67804.1	chr7	98111463	98111476	-	1	NA	intron (NM_001256081, intron 2 of 48)	CpG	-2221	NM_001256083	17921	Mm.1403	NM_008663	ENSMUSG00000030761	Myo7a	Hdb|Myo7|USH1B|nmf371|polka|sh-1|sh1	myosin VIIA	protein-coding
mm_153703.1	chr19	44397765	44397771	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	9941	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_44202.1	chr5	3657165	3657177	-	1	NA	5' UTR (NM_029154, exon 1 of 11)	5' UTR (NM_029154, exon 1 of 11)	167	NM_029154	75010	Mm.85064	NM_029141	ENSMUSG00000014529	Tmbim7	4930403J02Rik|4930500J03Rik|4930511M11Rik|Lfg5|Lgf5|Tmbim1b	transmembrane BAX inhibitor motif containing 7	protein-coding
mm_160009.1	chr6	124931478	124931478	+	1	NA	promoter-TSS (NM_001170341)	promoter-TSS (NM_001170341)	90	NM_001170341	30853	Mm.29737	NM_145385	ENSMUSG00000030120	Mlf2	AI256856|AU018944|C77284	myeloid leukemia factor 2	protein-coding
mm_21450.1	chr2	160650106	160650110	-	1	NA	intron (NM_009408, intron 2 of 20)	intron (NM_009408, intron 2 of 20)	4211	NM_009408	21969	Mm.217233	NM_009408	ENSMUSG00000070544	Top1	AI467334|D130064I21Rik|Top-1	topoisomerase (DNA) I	protein-coding
mm_163324.1	chr12	8008697	8008712	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	31027	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_151540.1	chr19	59081611	59081646	+	1	NA	Intergenic	Intergenic	-5559	NM_001114312	71653	Mm.37338	NM_175172	ENSMUSG00000041362	Shtn1	4930506M07Rik|Kiaa1598|Shootin1|mKIAA1598	shootin 1	protein-coding
mm_80256.1	chr9	72807194	72807220	+	1	NA	promoter-TSS (NM_175485)	promoter-TSS (NM_175485)	-67	NM_175485	235472	Mm.31696	NM_175485	ENSMUSG00000036030	Prtg	A230098A12Rik|Igdcc5	protogenin	protein-coding
mm_69163.1	chr7	127208573	127208643	-	1	NA	promoter-TSS (NM_144522)	promoter-TSS (NM_144522)	-140	NM_144522	68449	Mm.41420	NM_144522	ENSMUSG00000042492	Tbc1d10b	1110003P22Rik|C87963	TBC1 domain family, member 10b	protein-coding
mm_35518.1	chr4	41191243	41191255	-	1	NA	3' UTR (NM_026275, exon 5 of 5)	3' UTR (NM_026275, exon 5 of 5)	55228	NM_026275	67615	Mm.389540	NM_026275	ENSMUSG00000036241	Ube2r2	1200003M11Rik|Cdc34b|Ubc3b	ubiquitin-conjugating enzyme E2R 2	protein-coding
mm_67782.1	chr7	97413418	97413435	-	1	NA	3' UTR (NM_009381, exon 2 of 2)	3' UTR (NM_009381, exon 2 of 2)	4124	NM_009381	21835	Mm.28585	NM_009381	ENSMUSG00000035686	Thrsp	S14|SPOT14	thyroid hormone responsive	protein-coding
mm_98023.1	chr11	85111078	85111089	+	1	NA	intron (NM_001029934, intron 1 of 33)	intron (NM_001029934, intron 1 of 33)	28872	NM_001029934	237898	Mm.178524	NM_001029934	ENSMUSG00000000804	Usp32	2900074J03Rik|6430526O11Rik|AW045245	ubiquitin specific peptidase 32	protein-coding
mm_28509.1	chr3	92573868	92573871	-	1	NA	promoter-TSS (NM_008412)	promoter-TSS (NM_008412)	-134	NM_008412	16447	Mm.207365	NM_008412	ENSMUSG00000049128	Ivl	1110019C06Rik	involucrin	protein-coding
mm_15213.1	chr2	154217168	154217209	+	1	NA	exon (NM_153418, exon 14 of 16)	exon (NM_153418, exon 14 of 16)	-6554	NM_144890	228802	Mm.167411	NM_144890	ENSMUSG00000038572	Bpifb5	Lplunc5	BPI fold containing family B, member 5	protein-coding
mm_155826.1	chrX	100729918	100729963	+	1	NA	promoter-TSS (NM_023608)	promoter-TSS (NM_023608)	93	NM_023608	71584	Mm.283495	NM_023608	ENSMUSG00000019359	Gdpd2	9130017L10Rik|Gde3|Obdpf	glycerophosphodiester phosphodiesterase domain containing 2	protein-coding
mm_91955.1	chr10	61100562	61100577	-	1	NA	3' UTR (NM_001316673, exon 15 of 15)	3' UTR (NM_001316673, exon 15 of 15)	11238	NM_025273	13180	Mm.39473	NM_025273	ENSMUSG00000020098	Pcbd1	Dcoh|Pcbd|Pcd|Phs	pterin 4 alpha carbinolamine dehydratase/dimerization cofactor of hepatocyte nuclear factor 1 alpha (TCF1) 1	protein-coding
mm_81199.1	chr9	107554818	107554831	+	1	NA	exon (NM_019713, exon 1 of 5)	exon (NM_019713, exon 1 of 5)	241	NM_019713	56289	Mm.12091	NM_019713	ENSMUSG00000010067	Rassf1	123F2|AA536941|AU044980|NORE2A|RDA32|REH3P21|Rassf1A|Rassf1B|Rassf1C	Ras association (RalGDS/AF-6) domain family member 1	protein-coding
mm_95127.1	chr11	34136960	34136965	+	1	NA	Intergenic	Intergenic	71127	NM_023907	14233	Mm.32926	NM_023907	ENSMUSG00000047861	Foxi1	5830401E05Rik|FREAC6|Fkh10|HFH-3|Hfh3	forkhead box I1	protein-coding
mm_42014.1	chr5	108132804	108132884	+	1	NA	promoter-TSS (NM_028481)	promoter-TSS (NM_028481)	-70	NM_028481	73254	Mm.441231	NM_028481	ENSMUSG00000056531	Ccdc18	1700021E15Rik|4932411G06Rik|NY-SAR-41	coiled-coil domain containing 18	protein-coding
mm_56199.1	chr6	88874759	88874784	-	1	NA	promoter-TSS (NM_176973)	promoter-TSS (NM_176973)	273	NM_001347327	319655	Mm.302613	NM_176973	ENSMUSG00000033152	Podxl2	D130074J02Rik|PODLX2	podocalyxin-like 2	protein-coding
mm_87968.1	chr10	63430062	63430085	+	1	NA	promoter-TSS (NM_177612)	promoter-TSS (NM_177612)	-25	NM_177612	216033	Mm.444692	NM_177612	ENSMUSG00000060843	Ctnna3	4930429L08Rik|4933408A16|Catna3|Vr22	catenin (cadherin associated protein), alpha 3	protein-coding
mm_140586.1	chr17	10216239	10216263	-	1	NA	exon (NM_001159517, exon 6 of 8)	exon (NM_001159517, exon 6 of 8)	103110	NM_021881	19317	Mm.130694	NM_021881	ENSMUSG00000062078	Qk	1110003F05Rik|1500005P18|QkI|l(17)-1Wis|l17Wis1	quaking	protein-coding
mm_49311.1	chr6	18170743	18170756	+	1	NA	promoter-TSS (NM_021050)	promoter-TSS (NM_021050)	62	NM_021050	12638	Mm.15621	NM_021050	ENSMUSG00000041301	Cftr	AW495489|Abcc7	cystic fibrosis transmembrane conductance regulator	protein-coding
mm_153438.1	chr19	40994134	40994144	-	1	NA	5' UTR (NM_008528, exon 1 of 17)	5' UTR (NM_008528, exon 1 of 17)	396	NM_008528	17060	Mm.9749	NM_008528	ENSMUSG00000061132	Blnk	BASH|Bca|Ly-57|Ly57|Lyw-57|SLP-65	B cell linker	protein-coding
mm_79408.1	chr9	55149454	55149469	+	1	NA	promoter-TSS (NM_180600)	promoter-TSS (NM_180600)	92	NM_001346657	109161	Mm.207894	NM_180600	ENSMUSG00000032307	Ube2q2	3010021M21Rik	ubiquitin-conjugating enzyme E2Q family member 2	protein-coding
mm_41119.1	chr5	87781808	87781812	+	1	NA	exon (NM_001304768, exon 8 of 13)	exon (NM_001304768, exon 8 of 13)	7360	NM_007785	12993	Mm.4908	NM_007785	ENSMUSG00000061937	Csn1s2a	Csng|PP22	casein alpha s2-like A	protein-coding
mm_81893.1	chr9	119441554	119441559	+	1	NA	3' UTR (NM_007397, exon 10 of 10)	3' UTR (NM_007397, exon 10 of 10)	-3367	NM_001172136	208194	Mm.101578	NM_172456	ENSMUSG00000042787	Exog	AW557704|ENGL-B|ENGL-a|Endogl1|Endogl2|Engl|Engla|Englb	endo/exonuclease (5'-3'), endonuclease G-like	protein-coding
mm_64370.1	chr7	142442350	142442354	+	1	NA	promoter-TSS (NM_009405)	promoter-TSS (NM_009405)	-116	NM_009405	21953	Mm.39469	NM_009405	ENSMUSG00000031097	Tnni2	-	troponin I, skeletal, fast 2	protein-coding
mm_161117.1	chr12	105202173	105202173	+	1	NA	promoter-TSS (NM_013774)	promoter-TSS (NM_013774)	-249	NM_013774	27380	Mm.103652	NM_013774	ENSMUSG00000079007	Tcl1b4	AA675342	T cell leukemia/lymphoma 1B, 4	protein-coding
mm_77864.1	chr9	5327223	5327238	+	1	NA	exon (NM_007609, exon 6 of 9)	exon (NM_007609, exon 6 of 9)	-18246	NM_009808	12364	Mm.42163	NM_009808	ENSMUSG00000025887	Casp12	-	caspase 12	protein-coding
mm_113888.1	chr13	49188509	49188558	+	1	NA	intron (NM_013610, intron 1 of 3)	intron (NM_013610, intron 1 of 3)	986	NM_013610	18081	Mm.18503	NM_013610	ENSMUSG00000037966	Ninj1	AU024536	ninjurin 1	protein-coding
mm_1332.1	chr1	65247410	65247433	+	1	NA	intron (NM_011086, intron 20 of 41)	intron (NM_011086, intron 20 of 41)	60736	NM_001310624	18711	Mm.38370	NM_011086	ENSMUSG00000025949	Pikfyve	5230400C17Rik|Pip5k|Pip5k3|Pipk5k3|PipkIII|p235	phosphoinositide kinase, FYVE finger containing	protein-coding
mm_116214.1	chr13	32783995	32784007	-	1	NA	Intergenic	Intergenic	-2222	NM_001166030	238564	Mm.60041	NM_001166030	ENSMUSG00000044951	Mylk4	EG238564	myosin light chain kinase family, member 4	protein-coding
mm_139596.1	chr17	57248075	57248085	+	1	NA	promoter-TSS (NM_030084)	promoter-TSS (NM_030084)	-391	NM_030084	78308	Mm.28468	NM_030084	ENSMUSG00000005823	Gpr108	1810015L19Rik|AA589464|C79132|Lustr2	G protein-coupled receptor 108	protein-coding
mm_66805.1	chr7	47252828	47252832	-	1	NA	promoter-TSS (NM_001288801)	promoter-TSS (NM_001288801)	18	NM_001288801	668725	Mm.436563	NM_001177566	ENSMUSG00000074111	Mrgpra9	EG668725|MrgA9	MAS-related GPR, member A9	protein-coding
mm_70915.1	chr8	25720260	25720304	+	1	NA	TTS (NM_001081269)	TTS (NM_001081269)	234	NR_121643	71910	Mm.385055	NM_028000	ENSMUSG00000031570	Plpp5	1810019D05Rik|2310022A04Rik|AW045471|Ppapdc1|Ppapdc1b	phospholipid phosphatase 5	protein-coding
mm_91386.1	chr10	30647065	30647077	-	1	NA	3' UTR (NM_001111267, exon 6 of 6)	3' UTR (NM_001111267, exon 6 of 6)	8796	NM_001111267	211329	Mm.297903	NM_172495	ENSMUSG00000039697	Ncoa7	9030406N13Rik	nuclear receptor coactivator 7	protein-coding
mm_50989.1	chr6	63256053	63256069	+	1	NA	promoter-TSS (NM_008167)	promoter-TSS (NM_008167)	-796	NM_008167	14804	Mm.439651	NM_008167	ENSMUSG00000071424	Grid2	B230104L07Rik|GluD2|GluRdelta2|Lc|Lc<J>|MMS10-AC|Ms10ac|cpr|ho|nmf408|tpr	glutamate receptor, ionotropic, delta 2	protein-coding
mm_6830.1	chr1	84205824	84205851	-	1	NA	intron (NM_001003948, intron 1 of 2)	RLTR9E|LTR|ERVK	13124	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_141164.1	chr17	26514761	26514765	-	1	NA	Intergenic	Intergenic	-6291	NM_013642	19252	Mm.239041	NM_013642	ENSMUSG00000024190	Dusp1	3CH134|MKP1|Ptpn16|U19515|erp|mkp-1	dual specificity phosphatase 1	protein-coding
mm_47586.1	chr5	124861873	124861931	-	1	NA	promoter-TSS (NM_001081750)	promoter-TSS (NM_001081750)	319	NM_144819	215707	Mm.389693	NM_144819	ENSMUSG00000037979	Ccdc92	AW050178|D5Bwg0834e	coiled-coil domain containing 92	protein-coding
mm_777.1	chr1	44551712	44551714	+	1	NA	promoter-TSS (NM_028450)	promoter-TSS (NM_028450)	42	NM_028450	70676	Mm.133132	NM_027506	ENSMUSG00000056870	Gulp1	3110030A04Rik|5730529O06Rik|CED-6|Ced6|GULP|Gulp-2	GULP, engulfment adaptor PTB domain containing 1	protein-coding
mm_54391.1	chr6	31220238	31220248	-	1	NA	promoter-TSS (NR_040262)	promoter-TSS (NR_040262)	-108	NR_040258	73652	Mm.441297	NR_040257	ENSMUSG00000087380	2210408F21Rik	-	RIKEN cDNA 2210408F21 gene	ncRNA
mm_5022.1	chr1	193156664	193156678	+	1	NA	intron (NM_016851, intron 1 of 7)	intron (NM_016851, intron 1 of 7)	3559	NM_016851	54139	Mm.273695	NM_016851	ENSMUSG00000026638	Irf6	AI876454|E230028I05Rik|mirf6	interferon regulatory factor 6	protein-coding
mm_88458.1	chr10	77560290	77560314	+	1	NA	exon (NM_008404, exon 13 of 16)	exon (NM_008404, exon 13 of 16)	-21465	NM_145925	108705	Mm.28853	NM_145925	ENSMUSG00000009291	Pttg1ip	1810010L20Rik|AI314311|AU018448|C79540	pituitary tumor-transforming 1 interacting protein	protein-coding
mm_30411.1	chr3	152264959	152264989	-	1	NA	intron (NM_199465, intron 1 of 12)	intron (NM_199465, intron 1 of 12)	1346	NM_199465	68810	Mm.200188	NM_199465	ENSMUSG00000039103	Nexn	1110046H09Rik|AA553326|NELIN	nexilin	protein-coding
mm_33680.1	chr4	133251524	133251548	+	1	NA	intron (NM_016693, intron 24 of 28)	CpG	10718	NM_016693	53608	Mm.36640	NM_016693	ENSMUSG00000028862	Map3k6	Ask2|MAPKKK6|MEKK6	mitogen-activated protein kinase kinase kinase 6	protein-coding
mm_84820.1	chr9	77544878	77544914	-	1	NA	promoter-TSS (NM_001146048)	promoter-TSS (NM_001146048)	-44	NM_001146048	214345	Mm.28534	NM_172528	ENSMUSG00000032352	Lrrc1	A430093J20Rik|AU016091|D030059I21|mKIAA4018	leucine rich repeat containing 1	protein-coding
mm_63934.1	chr7	139552939	139552954	+	1	NA	intron (NM_183144, intron 9 of 15)	Lx7|LINE|L1	29851	NM_183248	14912	Mm.28308	NM_183248	ENSMUSG00000041309	Nkx6-2	Gtx|Nkx6.2	NK6 homeobox 2	protein-coding
mm_142447.1	chr17	45592486	45592497	-	1	NA	promoter-TSS (NM_022880)	promoter-TSS (NM_022880)	-98	NM_022880	63959	Mm.29744	NM_022880	ENSMUSG00000023942	Slc29a1	1200014D21Rik|AA407560|ENT1	solute carrier family 29 (nucleoside transporters), member 1	protein-coding
mm_26200.1	chr3	138526563	138526582	+	1	NA	promoter-TSS (NM_001313980)	promoter-TSS (NM_001313980)	151	NR_035481	100316706		NR_035481	ENSMUSG00000088373	Mir1956	mir-1956|mmu-mir-1956	microRNA 1956	ncRNA
mm_20066.1	chr2	120404059	120404092	-	1	NA	promoter-TSS (NM_173734)	promoter-TSS (NM_173734)	41	NM_173734	211499	Mm.260712	NM_173734	ENSMUSG00000033808	Tmem87a	A930025J12Rik	transmembrane protein 87A	protein-coding
mm_24371.1	chr3	90220748	90220773	+	1	NA	promoter-TSS (NM_026677)	promoter-TSS (NM_026677)	-24	NM_026677	68328	Mm.29355	NM_026677	ENSMUSG00000027935	Rab13	0610007N03Rik|B230212B15Rik	RAB13, member RAS oncogene family	protein-coding
mm_54702.1	chr6	39558157	39558169	-	1	NA	promoter-TSS (NM_172477)	promoter-TSS (NM_172477)	-329	NM_172477	209773	Mm.440021	NM_172477	ENSMUSG00000038456	Dennd2a	B930096L08Rik|C130031G22|mKIAA1277	DENN/MADD domain containing 2A	protein-coding
mm_144262.1	chr18	11052609	11052635	+	1	NA	promoter-TSS (NR_105023)	promoter-TSS (NR_105023)	-55	NR_105023	68434	Mm.57626	NR_105022	ENSMUSG00000097222	1010001N08Rik	Gata6as	RIKEN cDNA 1010001N08 gene	ncRNA
mm_149280.1	chr19	10607793	10607813	+	1	NA	exon (NM_015735, exon 3 of 27)	exon (NM_015735, exon 3 of 27)	2178	NM_015735	13194	Mm.289915	NM_015735	ENSMUSG00000024740	Ddb1	127kDa|AA408517|p127-Ddb1	damage specific DNA binding protein 1	protein-coding
mm_130877.1	chr15	102246256	102246273	-	1	NA	5' UTR (NM_001042727, exon 1 of 8)	5' UTR (NM_001042727, exon 1 of 8)	236	NM_001042727	19411	Mm.1273	NM_011244	ENSMUSG00000001288	Rarg	Nr1b3|RAR-gamma|RARD|RARgamma2	retinoic acid receptor, gamma	protein-coding
mm_30299.1	chr3	149077152	149077160	-	1	NA	Intergenic	Intergenic	-122521	NM_001081298	99633	Mm.9776	NM_001081298	ENSMUSG00000028184	Adgrl2	AI450192|CIRL-2|Gm619|Lec1|Lphh1|Lphn2|mKIAA0786	adhesion G protein-coupled receptor L2	protein-coding
mm_53638.1	chr6	140621116	140621146	+	1	NA	Intergenic	LTR88b|LTR|Gypsy?	-1532	NM_178803	11569	Mm.86453	NM_009637	ENSMUSG00000030232	Aebp2	AU023766|B230313N05Rik	AE binding protein 2	protein-coding
mm_143536.1	chr17	73950355	73950379	-	1	NA	promoter-TSS (NM_011723)	promoter-TSS (NM_011723)	-171	NM_011723	22436	Mm.11223	NM_011723	ENSMUSG00000024066	Xdh	XO|Xor|Xox-1|Xox1	xanthine dehydrogenase	protein-coding
mm_20239.1	chr2	126321561	126321570	-	1	NA	3' UTR (NM_001080944, exon 28 of 28)	3' UTR (NM_001080944, exon 28 of 28)	169424	NM_026981	69185	Mm.29019	NM_026981	ENSMUSG00000023330	Dtwd1	1810033A06Rik	DTW domain containing 1	protein-coding
mm_141717.1	chr17	34031557	34031634	-	1	NA	promoter-TSS (NM_001205216)	promoter-TSS (NM_001205216)	95	NM_001077709	14977	Mm.18556	NM_008202	ENSMUSG00000024327	Slc39a7	AA408174|AI117660|AL024048|H-2Ke4|H2-Ke4|Ke-4|Ke4|Ring5|Zip7	solute carrier family 39 (zinc transporter), member 7	protein-coding
mm_59409.1	chr7	27119949	27119966	+	1	NA	promoter-TSS (NM_007817)	promoter-TSS (NM_007817)	2	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_63387.1	chr7	127223794	127223808	+	1	NA	Intergenic	ORR1D1|LTR|ERVL-MaLR	-5356	NM_017461	54204	Mm.18	NM_017461	ENSMUSG00000000486	Sept1	Diff6|Pnutl3	septin 1	protein-coding
mm_109720.1	chr12	116140943	116140955	+	1	NA	intron (NM_009511, intron 10 of 12)	MTC|LTR|ERVL-MaLR	63223	NM_009511	22355	Mm.395245	NM_009511	ENSMUSG00000011171	Vipr2	VPAC2|VPAC2R|Vip2	vasoactive intestinal peptide receptor 2	protein-coding
mm_73742.1	chr8	114205575	114205585	+	1	NA	promoter-TSS (NM_173016)	promoter-TSS (NM_173016)	-60	NM_173016	270097	Mm.334825	NM_173016	ENSMUSG00000046844	Vat1l	9430073I07|AI427515|mKIAA1576	vesicle amine transport protein 1 like	protein-coding
mm_43353.1	chr5	135169018	135169023	+	1	NA	intron (NM_009745, intron 1 of 5)	intron (NM_009745, intron 1 of 5)	648	NM_009745	12054	Mm.405834	NM_009745	ENSMUSG00000029681	Bcl7b	-	B cell CLL/lymphoma 7B	protein-coding
mm_84063.1	chr9	58200448	58200468	-	1	NA	5' UTR (NM_001161538, exon 3 of 4)	5' UTR (NM_001161538, exon 3 of 4)	1257	NM_001161535	320563	Mm.186499	NM_177193	ENSMUSG00000051243	Islr2	B930052A04Rik|Linx|Mbu-3|mKIAA1465	immunoglobulin superfamily containing leucine-rich repeat 2	protein-coding
mm_73887.1	chr8	119348125	119348189	+	1	NA	3' UTR (NM_024219, exon 4 of 4)	3' UTR (NM_024219, exon 4 of 4)	3619	NM_024219	68196	Mm.358714	NM_024219	ENSMUSG00000031839	Hsbp1	0610007A03Rik|AA408769|Hsp25	heat shock factor binding protein 1	protein-coding
mm_168466.1	chr1	148302025	148302028	-	1	NA	Intergenic	L1Md_T|LINE|L1	1620413	NM_001305632	18783	Mm.4186	NM_008869	ENSMUSG00000056220	Pla2g4a	Pla2g4|cPLA2|cPLA2-alpha|cPLA2alpha	phospholipase A2, group IVA (cytosolic, calcium-dependent)	protein-coding
mm_94187.1	chr10	128960672	128960695	-	1	NA	exon (NM_027853, exon 1 of 2)	exon (NM_027853, exon 1 of 2)	305	NM_027853	71664	Mm.337232	NM_027853	ENSMUSG00000025347	Mettl7b	0610006F02Rik|AI266817	methyltransferase like 7B	protein-coding
mm_46445.1	chr5	105103841	105103842	-	1	NA	exon (NM_172777, exon 3 of 11)	exon (NM_172777, exon 3 of 11)	6451	NM_172777	236573	Mm.425261	NM_172777	ENSMUSG00000029298	Gbp9	-	guanylate-binding protein 9	protein-coding
mm_61657.1	chr7	80507778	80507781	+	1	NA	intron (NM_001042527, intron 4 of 21)	CpG	27219	NM_007550	12144	Mm.12932	NM_007550	ENSMUSG00000030528	Blm	-	Bloom syndrome, RecQ helicase-like	protein-coding
mm_167426.1	chr8	115194892	115194892	+	1	NA	intron (NM_019573, intron 8 of 8)	intron (NM_019573, intron 8 of 8)	512002	NM_001025577	17132	Mm.275549	NM_001025577	ENSMUSG00000055435	Maf	2810401A20Rik|A230108G15Rik|AW047063|c-maf	avian musculoaponeurotic fibrosarcoma oncogene homolog	protein-coding
mm_4980.1	chr1	191611796	191611818	+	1	NA	intron (NM_001306204, intron 10 of 17)	intron (NM_001306204, intron 10 of 17)	36171	NM_001306204	77065	Mm.338175	NM_178632	ENSMUSG00000037461	Ints7	5930412E23Rik|int7	integrator complex subunit 7	protein-coding
mm_11043.1	chr2	27079372	27079385	+	1	NA	promoter-TSS (NM_029981)	promoter-TSS (NM_029981)	-3	NM_029981	77794	Mm.330088	NM_029981	ENSMUSG00000036040	Adamtsl2	A930008K15Rik|tcp-1	ADAMTS-like 2	protein-coding
mm_33186.1	chr4	126139346	126139362	+	1	NA	3' UTR (NM_028800, exon 11 of 11)	3' UTR (NM_028800, exon 11 of 11)	-8649	NM_172145	230752	Mm.41569	NM_172145	ENSMUSG00000050212	Eva1b	2610027C15Rik|Fam176b	eva-1 homolog B (C. elegans)	protein-coding
mm_110838.1	chr12	72917873	72917942	-	1	NA	promoter-TSS (NM_029444)	promoter-TSS (NM_029444)	-142	NM_029444	75801	Mm.242892	NM_029444	ENSMUSG00000021098	4930447C04Rik	4921504I02Rik|A930035O15Rik|Six6OS|Six6as|Six6os1	RIKEN cDNA 4930447C04 gene	protein-coding
mm_96317.1	chr11	63989708	63989729	+	1	NA	intron (NM_178379, intron 5 of 6)	intron (NM_178379, intron 5 of 6)	25492	NR_131111	78883	Mm.410764	NR_131111	ENSMUSG00000086359	9630013K17Rik	-	RIKEN cDNA 9630013K17 gene	ncRNA
mm_488.1	chr1	36767415	36767425	+	1	NA	intron (NM_001289765, intron 1 of 12)	intron (NM_001289765, intron 1 of 12)	486	NM_001289765	22637	Mm.8038	NM_009539	ENSMUSG00000026117	Zap70	Srk|ZAP-70|mrtle|mur	zeta-chain (TCR) associated protein kinase	protein-coding
mm_152445.1	chr19	10784257	10784272	-	1	NA	intron (NR_027805, intron 2 of 3)	intron (NR_027805, intron 2 of 3)	43317	NR_027805	403202	Mm.34482	NM_207529	ENSMUSG00000067577	A430093F15Rik	Gm674	RIKEN cDNA A430093F15 gene	ncRNA
mm_133586.1	chr16	91420975	91421013	+	1	NA	intron (NM_008349, intron 5 of 6)	(TCCA)n|Simple_repeat|Simple_repeat	14759	NM_008349	16155	Mm.4154	NM_008349	ENSMUSG00000022969	Il10rb	6620401D04Rik|AI528744|CRF2-4|Crfb4|D16H21S58|D21S58h|IL-10R2|Il10r2	interleukin 10 receptor, beta	protein-coding
mm_20172.1	chr2	122313715	122313736	-	1	NA	promoter-TSS (NM_001305262)	promoter-TSS (NM_001305262)	5	NM_001305262	213696	Mm.247121	NM_145395	ENSMUSG00000027224	Duoxa1	BC019755|Nip|Nip1	dual oxidase maturation factor 1	protein-coding
mm_53773.1	chr6	146113334	146113380	+	1	NA	intron (NM_010586, intron 54 of 55)	intron (NM_010586, intron 54 of 55)	179210	NM_010656	16651	Mm.49689	NM_010656	ENSMUSG00000030255	Sspn	Krag	sarcospan	protein-coding
mm_42840.1	chr5	122106783	122106809	+	1	NA	TTS (NM_010861)	TTS (NM_010861)	5816	NM_010861	17906	Mm.1529	NM_010861	ENSMUSG00000013936	Myl2	MLC-2|MLC-2s/v|MLC-2v|Mlc2v|Mylpc	myosin, light polypeptide 2, regulatory, cardiac, slow	protein-coding
mm_118387.1	chr13	117272078	117272098	-	1	NA	exon (NM_010330, exon 8 of 9)	exon (NM_010330, exon 8 of 9)	51515	NM_010330	13723	Mm.274926	NM_010330	ENSMUSG00000021728	Emb	AL022799|Gp70	embigin	protein-coding
mm_148836.1	chr19	6363672	6363704	+	1	NA	promoter-TSS (NR_122118)	promoter-TSS (NR_122118)	-2	NM_011750	22668	Mm.256422	NM_011750	ENSMUSG00000024949	Sf1	BBP|MZFM|WBP4|Zfp162	splicing factor 1	protein-coding
mm_152886.1	chr19	24678620	24678642	-	1	NA	3' UTR (NM_183160, exon 2 of 2)	3' UTR (NM_183160, exon 2 of 2)	4623	NM_183160	226040	Mm.391170	NM_183160	ENSMUSG00000048572	Tmem252	E030010A14Rik	transmembrane protein 252	protein-coding
mm_11661.1	chr2	35132195	35132247	+	1	NA	promoter-TSS (NM_001290635)	promoter-TSS (NM_001290635)	-13	NM_001290635	26920	Mm.231332	NM_012018	ENSMUSG00000057110	Cntrl	6720467O09Rik|AA968343|Cep1|Cep110|IB3/5|Ma2a8|b2b1468.1Clo|b2b1468Clo	centriolin	protein-coding
mm_79964.1	chr9	66350560	66350566	+	1	NA	5' UTR (NM_145617, exon 1 of 78)	5' UTR (NM_145617, exon 1 of 78)	113	NM_145617	235439	Mm.244179	NM_145617	ENSMUSG00000038664	Herc1	2810449H11Rik|B230218H07|D130015N03Rik|tbl	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	protein-coding
mm_59024.1	chr7	19291071	19291124	+	1	NA	promoter-TSS (NM_001025364)	promoter-TSS (NM_001025364)	28	NM_001025364	20167	Mm.24142	NM_013648	ENSMUSG00000030401	Rtn2	MMS10-P|Ms10p|NSPLI|Nspl1	reticulon 2 (Z-band associated protein)	protein-coding
mm_124022.1	chr14	76556663	76556716	-	1	NA	promoter-TSS (NM_001160326)	promoter-TSS (NM_001160326)	-2	NM_001160326	72661	Mm.320384	NM_001160326	ENSMUSG00000052584	Serp2	2810032E02Rik	stress-associated endoplasmic reticulum protein family member 2	protein-coding
mm_87252.1	chr10	41490437	41490483	+	1	NA	promoter-TSS (NM_009213)	promoter-TSS (NM_009213)	21	NM_028430	73075	Mm.359762	NM_028430	ENSMUSG00000078451	Ppil6	2900084F20Rik	peptidylprolyl isomerase (cyclophilin)-like 6	protein-coding
mm_64874.1	chr7	14436441	14436457	-	1	NA	intron (NM_175250, intron 1 of 6)	Lx2B2|LINE|L1	2102	NM_001199306	76971	Mm.290727	NM_175250	ENSMUSG00000030378	Sult2a8	2810007J24Rik	sulfotransferase family 2A, dehydroepiandrosterone (DHEA)-preferring, member 8	protein-coding
mm_71774.1	chr8	66469248	66469265	+	1	NA	3' UTR (NM_001293784, exon 9 of 9)	3' UTR (NM_001293784, exon 9 of 9)	17251	NM_025465	66282	Mm.294985	NM_025465	ENSMUSG00000025591	Tma16	1810029B16Rik	translation machinery associated 16	protein-coding
mm_75248.1	chr8	39928127	39928135	-	1	NA	intron (NR_035426, intron 3 of 5)	intron (NR_035426, intron 3 of 5)	-285453	NM_001113326	20288	Mm.239291	NM_031195	ENSMUSG00000025044	Msr1	MRS-A|MSR|MSR-A|SR-AI|SR-AII|Scara1|Scvr	macrophage scavenger receptor 1	protein-coding
mm_54305.1	chr6	29554833	29554867	-	1	NA	exon (NM_177296, exon 20 of 23)	exon (NM_177296, exon 20 of 23)	25568	NM_001252382	27056	Mm.6479	NM_012057	ENSMUSG00000029771	Irf5	AW491843|mirf5	interferon regulatory factor 5	protein-coding
mm_46931.1	chr5	114733287	114733314	-	1	NA	exon (NM_019834, exon 17 of 19)	exon (NM_019834, exon 17 of 19)	13785	NR_105995	102465622		NR_105995	ENSMUSG00000098656	Mir7028	Gm27674|mmu-mir-7028	microRNA 7028	ncRNA
mm_130166.1	chr15	93085413	93085419	-	1	NA	Intergenic	Intergenic	189668	NM_001033275	223827	Mm.22819	NM_001033275	ENSMUSG00000036197	Gxylt1	Glt8d3|Gm1228|Gm87	glucoside xylosyltransferase 1	protein-coding
mm_112908.1	chr13	20903050	20903060	+	1	NA	intron (NM_012054, intron 5 of 20)	intron (NM_012054, intron 5 of 20)	108942	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_103261.1	chr11	71032901	71032913	-	1	NA	3' UTR (NM_134022, exon 1 of 2)	3' UTR (NM_134022, exon 1 of 2)	710	NM_134022	103712	Mm.27768	NM_134022		6330403K07Rik	AI415455|AV161034|UGS148	RIKEN cDNA 6330403K07 gene	protein-coding
mm_23683.1	chr3	68626054	68626058	+	1	NA	3' UTR (NM_001282045, exon 8 of 8)	3' UTR (NM_001282045, exon 8 of 8)	53688	NM_013928	30953	Mm.331064	NM_013928	ENSMUSG00000027777	Schip1	Nf2ip|Schip-1	schwannomin interacting protein 1	protein-coding
mm_25449.1	chr3	108364883	108364911	+	1	NA	promoter-TSS (NM_026831)	promoter-TSS (NM_026831)	-14	NM_026831	68753	Mm.75201	NM_026831	ENSMUSG00000068745	Mybphl	1110037P11Rik	myosin binding protein H-like	protein-coding
mm_120008.1	chr14	55671152	55671152	+	1	NA	intron (NM_008683, intron 1 of 3)	intron (NM_008683, intron 1 of 3)	754	NM_008683	18002	Mm.296566	NM_008683	ENSMUSG00000010376	Nedd8	Rub1	neural precursor cell expressed, developmentally down-regulated gene 8	protein-coding
mm_2229.1	chr1	90915116	90915135	+	1	NA	promoter-TSS (NM_053015)	promoter-TSS (NM_053015)	25	NM_053015	171531	Mm.105208	NM_053015	ENSMUSG00000026303	Mlph	2210418F23Rik|5031433I09Rik|AW228792|D1Wsu84e|Slac-2a|l(1)-3Rk|l1Rk3|ln	melanophilin	protein-coding
mm_166309.1	chr5	106445297	106445298	-	1	NA	Intergenic	(TAGA)n|Simple_repeat|Simple_repeat	12869	NM_001005477	104382	Mm.271593	NM_001005477	ENSMUSG00000034384	Barhl2	E130309B19Rik|MBH1	BarH-like 2 (Drosophila)	protein-coding
mm_36944.1	chr4	108833545	108833597	-	1	NA	promoter-TSS (NM_027453)	promoter-TSS (NM_027453)	13	NM_027453	70533	Mm.379178	NM_027453	ENSMUSG00000028568	Btf3l4	4632412E09Rik|5730434I03Rik|AI316863|AU022207|AW552446	basic transcription factor 3-like 4	protein-coding
mm_162354.1	chr1	56869109	56869113	-	1	NA	intron (NM_139146, intron 7 of 10)	(A)n|Simple_repeat|Simple_repeat	102223	NM_139146	212712	Mm.145599	NM_139146	ENSMUSG00000038331	Satb2	mKIAA1034	special AT-rich sequence binding protein 2	protein-coding
mm_32648.1	chr4	115059555	115059561	+	1	NA	5' UTR (NM_011527, exon 2 of 5)	5' UTR (NM_011527, exon 2 of 5)	1747	NM_001287388	21349	Mm.239869	NM_011527	ENSMUSG00000028717	Tal1	Hpt|SCL/tal-1|Scl|bHLHa17|tal-1	T cell acute lymphocytic leukemia 1	protein-coding
mm_86859.1	chr10	21886623	21886645	+	1	NA	intron (NM_001161845, intron 1 of 13)	intron (NM_001161845, intron 1 of 13)	4450	NM_001161845	20393	Mm.28405	NM_011361	ENSMUSG00000019970	Sgk1	Sgk	serum/glucocorticoid regulated kinase 1	protein-coding
mm_671.1	chr1	40465642	40465698	+	1	NA	promoter-TSS (NM_001161843)	promoter-TSS (NM_001161843)	49	NM_001161843	16182	Mm.253664	NM_008365	ENSMUSG00000026070	Il18r1	Il18ralpha|Il1rrp	interleukin 18 receptor 1	protein-coding
mm_11741.1	chr2	38339259	38339278	+	1	NA	promoter-TSS (NM_001290646)	promoter-TSS (NM_001290646)	-13	NM_001290646	16870	Mm.142856	NM_010710	ENSMUSG00000000247	Lhx2	LH2A|Lh-2|Lim2|ap|apterous	LIM homeobox protein 2	protein-coding
mm_106985.1	chr12	9585014	9585040	+	1	NA	Intergenic	Intergenic	10585	NM_011859	23967	Mm.45055	NM_011859	ENSMUSG00000048387	Osr1	Odd1|Osr	odd-skipped related 1 (Drosophila)	protein-coding
mm_62949.1	chr7	119596036	119596045	+	1	NA	3' UTR (NM_146197, exon 14 of 14)	3' UTR (NM_146197, exon 14 of 14)	-21788	NM_054094	117147	Mm.427560	NM_054094	ENSMUSG00000033533	Acsm1	Acas3|Bucs1|Macs	acyl-CoA synthetase medium-chain family member 1	protein-coding
mm_20345.1	chr2	127705747	127705753	-	1	NA	3' UTR (NM_145532, exon 4 of 4)	3' UTR (NM_145532, exon 4 of 4)	24147	NM_145532	228576	Mm.133036	NM_145532	ENSMUSG00000027377	Mall	BC012256|BENE	mal, T cell differentiation protein-like	protein-coding
mm_44132.1	chr5	149832399	149832402	+	1	NA	Intergenic	B1_Mur1|SINE|Alu	-15347	NR_045758	70969	Mm.78499	NR_045758	ENSMUSG00000107214	4930500F04Rik	4931407C17Rik	RIKEN cDNA 4930500F04 gene	ncRNA
mm_69841.1	chr7	141327701	141327737	-	1	NA	promoter-TSS (NM_001282076)	promoter-TSS (NM_001282076)	6	NM_016874	54006	Mm.28392	NM_016874	ENSMUSG00000058886	Deaf1	AU042387|C230009B13Rik|NUDR	deformed epidermal autoregulatory factor 1 (Drosophila)	protein-coding
mm_165852.1	chr4	11105396	11105397	+	1	NA	Intergenic	Intergenic	-28701	NR_030455	735261		NR_030455	ENSMUSG00000105333	Mir684-2	Mirn684-2	microRNA 684-2	ncRNA
mm_64456.1	chr7	142660455	142660459	+	1	NA	non-coding (NR_002855, exon 1 of 4)	non-coding (NR_002855, exon 1 of 4)	777	NR_002855	111975	Mm.440180	NR_002855	ENSMUSG00000086266	Igf2os	Igf2as|Peg8	insulin-like growth factor 2, opposite strand	ncRNA
mm_8988.1	chr1	165700992	165701004	-	1	NA	intron (NM_178593, intron 1 of 6)	intron (NM_178593, intron 1 of 6)	7096	NM_178593	226594	Mm.265552	NM_178593	ENSMUSG00000040723	Rcsd1	A430105K13Rik|BC025872|CapZIP	RCSD domain containing 1	protein-coding
mm_1975.1	chr1	86526689	86526722	+	1	NA	promoter-TSS (NM_008972)	promoter-TSS (NM_008972)	-31	NM_008972	19231	Mm.19187	NM_008972	ENSMUSG00000026238	Ptma	Thym	prothymosin alpha	protein-coding
mm_120551.1	chr14	67745266	67745269	+	1	NA	promoter-TSS (NM_008145)	promoter-TSS (NM_008145)	86	NR_133010	14714	Mm.358309	NM_008145	ENSMUSG00000015812	Gnrh1	Gnrh|Gnrh2|LHRH|Lhrh1|Lnrh|hpg	gonadotropin releasing hormone 1	protein-coding
mm_119028.1	chr14	30024948	30024954	+	1	NA	intron (NM_175343, intron 1 of 7)	L1MB4|LINE|L1	2318	NM_175343	218865	Mm.259916	NM_172264	ENSMUSG00000015970	Chdh	AU041472|D630034H06Rik	choline dehydrogenase	protein-coding
mm_165086.1	chr19	47508956	47508964	+	1	NA	intron (NM_175360, intron 8 of 9)	intron (NM_175360, intron 8 of 9)	-4022	NR_045322	100503104	Mm.442735	NR_045322	ENSMUSG00000097990	Gm19557	-	predicted gene, 19557	ncRNA
mm_56933.1	chr6	119714062	119714081	-	1	NA	intron (NM_053204, intron 15 of 20)	intron (NM_053204, intron 15 of 20)	134079	NM_053204	111173	Mm.288860	NM_053204	ENSMUSG00000030172	Erc1	4930404L01Rik|5033405M01Rik|9630025C19Rik|B430107L16Rik|CAST2|ELKS|Elks1|RAB6IP2A|RAB6IP2B|Rab6ip2|mKIAA1081	ELKS/RAB6-interacting/CAST family member 1	protein-coding
mm_156907.1	chrX	169048388	169048412	+	1	NA	intron (NR_109847, intron 1 of 14)	URR1B|DNA|hAT-Charlie	11789	NR_109847	11856	Mm.441810	NM_009707	ENSMUSG00000031355	Arhgap6	AI504284|RhoGAPX-1	Rho GTPase activating protein 6	protein-coding
mm_107461.1	chr12	37241730	37241758	+	1	NA	5' UTR (NM_178767, exon 1 of 13)	5' UTR (NM_178767, exon 1 of 13)	105	NM_178767	319660	Mm.485540	NM_178767	ENSMUSG00000050103	Agmo	A530016O06Rik|AI790538|Tmem195	alkylglycerol monooxygenase	protein-coding
mm_168802.1	chr12	20415636	20415643	+	1	NA	Intergenic	CpG	400140	NR_015521	69513	Mm.273972	NR_015521	ENSMUSG00000099759	1700030C10Rik	-	RIKEN cDNA 1700030C10 gene	ncRNA
mm_113895.1	chr13	49195685	49195699	+	1	NA	3' UTR (NM_013610, exon 4 of 4)	3' UTR (NM_013610, exon 4 of 4)	8145	NM_013610	18081	Mm.18503	NM_013610	ENSMUSG00000037966	Ninj1	AU024536	ninjurin 1	protein-coding
mm_88593.1	chr10	79761025	79761035	+	1	NA	exon (NM_144528, exon 7 of 9)	exon (NM_144528, exon 7 of 9)	5911	NM_023304	67112	Mm.154211	NM_023304	ENSMUSG00000020327	Fgf22	2210414E06Rik|FGF-22	fibroblast growth factor 22	protein-coding
mm_91640.1	chr10	42276646	42276656	-	1	NA	promoter-TSS (NM_019740)	promoter-TSS (NM_019740)	91	NM_019740	56484	Mm.338613	NM_019740	ENSMUSG00000048756	Foxo3	1110048B16Rik|2010203A17Rik|C76856|FKHRL1|Fkhr2|Foxo3a	forkhead box O3	protein-coding
mm_104164.1	chr11	87358908	87358944	-	1	NA	promoter-TSS (NM_177167)	promoter-TSS (NM_177167)	68	NM_177167	320472	Mm.341988	NM_177167	ENSMUSG00000046442	Ppm1e	AW049266|B930008A12Rik|POPX1|PP2CH|mKIAA1072	protein phosphatase 1E (PP2C domain containing)	protein-coding
mm_105671.1	chr11	107466220	107466223	-	1	NA	intron (NM_145823, intron 1 of 9)	B4|SINE|B4	4499	NM_145823	71795	Mm.397413	NM_145823	ENSMUSG00000040430	Pitpnc1	1110020B03Rik|5830436L09Rik|AI662802|AI851387|C330017I21Rik|Dnr411|RDGBB|RDGBB1|rdgB-beta	phosphatidylinositol transfer protein, cytoplasmic 1	protein-coding
mm_88080.1	chr10	68042152	68042164	+	1	NA	3' UTR (NM_001081346, exon 13 of 13)	3' UTR (NM_001081346, exon 13 of 13)	62560	NM_001081346	170799	Mm.209844	NM_133244	ENSMUSG00000037846	Rtkn2	B130039D23Rik|Mbf|Plekhk1	rhotekin 2	protein-coding
mm_80670.1	chr9	90163167	90163173	+	1	NA	5' UTR (NM_001326351, exon 1 of 24)	5' UTR (NM_001326351, exon 1 of 24)	192	NM_001311115	108153	Mm.102141	NM_001003911	ENSMUSG00000032363	Adamts7	ADAM-TS7|ADAMTS7B	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 7	protein-coding
mm_92891.1	chr10	82859054	82859131	-	1	NA	promoter-TSS (NM_015762)	promoter-TSS (NM_015762)	-114	NM_001042513	50493	Mm.210155	NM_015762	ENSMUSG00000020250	Txnrd1	TR|TR1|TrxR1	thioredoxin reductase 1	protein-coding
mm_151761.1	chr19	5118373	5118390	-	1	NA	promoter-TSS (NM_008451)	promoter-TSS (NM_008451)	27	NR_045528	16594	Mm.271648	NM_008451	ENSMUSG00000024862	Klc2	8030455F02Rik|AW212649|KLC 2|KLC-2	kinesin light chain 2	protein-coding
mm_146597.1	chr18	9450051	9450061	-	1	NA	promoter-TSS (NM_026484)	promoter-TSS (NM_026484)	94	NM_026484	67974	Mm.86523	NM_026484	ENSMUSG00000024286	Ccny	1700025H17Rik|3110050L10Rik|4631402G10Rik|5730405I09Rik	cyclin Y	protein-coding
mm_165717.1	chr3	101110297	101110336	-	1	NA	promoter-TSS (NM_011197)	promoter-TSS (NM_011197)	-150	NM_011197	19221	Mm.24807	NM_011197	ENSMUSG00000027864	Ptgfrn	4833445A08Rik|AU042434|CD9P-1|FPRP|Trim45	prostaglandin F2 receptor negative regulator	protein-coding
mm_14650.1	chr2	136911232	136911243	+	1	NA	intron (NM_001038641, intron 2 of 7)	MER58A|DNA|hAT-Charlie	11886	NM_001038641	74243	Mm.330612	NM_028201	ENSMUSG00000027281	Slx4ip	2210009G21Rik|2410004I22Rik|C85661|Slxip	SLX4 interacting protein	protein-coding
mm_91918.1	chr10	60299490	60299513	-	1	NA	exon (NM_011179, exon 10 of 15)	exon (NM_011179, exon 10 of 15)	15040	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_102430.1	chr11	59490075	59490075	-	1	NA	intron (NM_001291014, intron 9 of 9)	intron (NM_001291014, intron 9 of 9)	-15578	NR_135273	74476	Mm.440257	NR_015585	ENSMUSG00000072893	4933439C10Rik	2610028M21Rik	RIKEN cDNA 4933439C10 gene	ncRNA
mm_169943.1	chr16	69208657	69208673	+	1	NA	Intergenic	Intergenic	591716	NR_130991	78110	Mm.211406	NR_130991	ENSMUSG00000107073	4930428D20Rik	-	RIKEN cDNA 4930428D20 gene	ncRNA
mm_64041.1	chr7	140773626	140773645	+	1	NA	exon (NM_021282, exon 8 of 9)	exon (NM_021282, exon 8 of 9)	9803	NM_021282	13106	Mm.21758	NM_021282	ENSMUSG00000025479	Cyp2e1	Cyp2e	cytochrome P450, family 2, subfamily e, polypeptide 1	protein-coding
mm_9992.1	chr1	191378109	191378113	-	1	NA	intron (NM_144880, intron 1 of 12)	MT2A|LTR|ERVL	18930	NM_144880	226849	Mm.205569	NM_144880	ENSMUSG00000026626	Ppp2r5a	PR61alpha	protein phosphatase 2, regulatory subunit B', alpha	protein-coding
mm_72270.1	chr8	75099908	75099949	+	1	NA	exon (NM_010442, exon 5 of 5)	exon (NM_010442, exon 5 of 5)	6310	NM_010442	15368	Mm.276389	NM_010442	ENSMUSG00000005413	Hmox1	D8Wsu38e|HO-1|HO1|Hemox|Hmox|Hsp32	heme oxygenase 1	protein-coding
mm_61531.1	chr7	78920215	78920234	+	1	NA	3' UTR (NM_020583, exon 4 of 4)	3' UTR (NM_020583, exon 4 of 4)	5989	NM_001113527	57444	Mm.322843	NM_020583	ENSMUSG00000039236	Isg20	1600023I01Rik|2010107M23Rik|20kDa|DnaQL|HEM45	interferon-stimulated protein	protein-coding
mm_90349.1	chr10	127163539	127163548	+	1	NA	Intergenic	B3A|SINE|B2	-1613	NR_045166	14421	Mm.386762	NM_008080	ENSMUSG00000006731	B4galnt1	4933429D13Rik|Gal-NAc-T|GalNAc-T|GalNAcT|Galgt1|Ggm-2|Ggm2	beta-1,4-N-acetyl-galactosaminyl transferase 1	protein-coding
mm_139607.1	chr17	57303967	57303977	+	1	NA	intron (NM_001163816, intron 15 of 25)	intron (NM_001163816, intron 15 of 25)	24872	NM_001163815	22324	Mm.248172	NM_011691	ENSMUSG00000034116	Vav1	Vav|vav-T	vav 1 oncogene	protein-coding
mm_30802.1	chr4	20008509	20008517	+	1	NA	exon (NM_015767, exon 1 of 5)	exon (NM_015767, exon 1 of 5)	184	NM_015767	50500	Mm.24375	NM_015767	ENSMUSG00000073988	Ttpa	alpha-TTP	tocopherol (alpha) transfer protein	protein-coding
mm_44594.1	chr5	24995860	24995866	-	1	NA	promoter-TSS (NM_001310480)	promoter-TSS (NM_001310480)	-110	NM_001310480	108099	Mm.33649	NM_145401	ENSMUSG00000028944	Prkag2	2410051C13Rik|AAKG|AAKG2|AI854673|H91620p|WPWS	protein kinase, AMP-activated, gamma 2 non-catalytic subunit	protein-coding
mm_76886.1	chr8	105637317	105637333	-	1	NA	intron (NM_181322, intron 1 of 11)	CpG	787	NM_181322	13018	Mm.269474	NM_181322	ENSMUSG00000005698	Ctcf	AW108038	CCCTC-binding factor	protein-coding
mm_116668.1	chr13	49205508	49205519	-	1	NA	intron (NM_026738, intron 2 of 5)	intron (NM_026738, intron 2 of 5)	10513	NM_026738	68480	Mm.3336	NM_026738	ENSMUSG00000037960	Card19	1110007C09Rik|AI851695|Bincard	caspase recruitment domain family, member 19	protein-coding
mm_67057.1	chr7	67372863	67372871	-	1	NA	promoter-TSS (NM_001291196)	promoter-TSS (NM_001291196)	-9	NM_001291195	17258	Mm.132788	NM_001033713	ENSMUSG00000030557	Mef2a	A430079H05Rik	myocyte enhancer factor 2A	protein-coding
mm_129840.1	chr15	83154523	83154547	-	1	NA	3' UTR (NM_029787, exon 9 of 9)	3' UTR (NM_029787, exon 9 of 9)	4890	NR_004432	104307	Mm.471434	NR_004432	ENSMUSG00000065176	Rnu12	-	RNA U12, small nuclear	snRNA
mm_127692.1	chr15	102988291	102988291	+	1	NA	Intergenic	Intergenic	-2248	NM_010466	15426	Mm.6167	NM_010466	ENSMUSG00000001657	Hoxc8	D130011F21Rik|Hox-3.1	homeobox C8	protein-coding
mm_16513.1	chr2	181365519	181365532	+	1	NA	promoter-TSS (NM_001165995)	promoter-TSS (NM_001165995)	102	NM_001048148	229007	Mm.87720	NM_144894	ENSMUSG00000027582	Zgpat	1500006I01Rik|BC021513	zinc finger, CCCH-type with G patch domain	protein-coding
mm_159600.1	chr4	127970715	127970715	-	1	NA	exon (NM_001134733, exon 1 of 7)	exon (NM_001134733, exon 1 of 7)	126	NM_001134733	635169	Mm.346755	NM_001134733	ENSMUSG00000028813	CK137956	-	cDNA sequence CK137956	protein-coding
mm_72384.1	chr8	81559034	81559050	+	1	NA	intron (NM_001297591, intron 2 of 24)	RMER19A|LTR|ERVK	216480	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_11416.1	chr2	31670715	31670741	+	1	NA	promoter-TSS (NM_144886)	promoter-TSS (NM_144886)	13	NM_144886	227715	Mm.150972	NM_144886	ENSMUSG00000039356	Exosc2	Rrp4	exosome component 2	protein-coding
mm_2696.1	chr1	127774242	127774272	+	1	NA	promoter-TSS (NM_028399)	promoter-TSS (NM_028399)	93	NM_028399	72949	Mm.268672	NM_028399	ENSMUSG00000026349	Ccnt2	2900041I18Rik|C81304|CycT2|CycT2a|CycT2b	cyclin T2	protein-coding
mm_127297.1	chr15	100198640	100198654	+	1	NA	intron (NM_001159361, intron 28 of 37)	intron (NM_001159361, intron 28 of 37)	-10611	NR_037311	100499528		NR_037311	ENSMUSG00000092752	Mir3473a	Mir3473|mir-3473a|mmu-mir-3473|mmu-mir-3473a	microRNA 3473a	ncRNA
mm_115073.1	chr13	101664149	101664153	+	1	NA	Intergenic	Intergenic	28479	NM_001024955	18708	Mm.259333	NM_001024955	ENSMUSG00000041417	Pik3r1	PI3K|p50alpha|p55alpha|p85alpha	phosphatidylinositol 3-kinase, regulatory subunit, polypeptide 1 (p85 alpha)	protein-coding
mm_171622.1	chr4	154655624	154655639	-	1	NA	Intergenic	RLTR16B_MM|LTR|ERVK	12236	NM_028513	73353	Mm.30958	NM_028513	ENSMUSG00000051276	Actrt2	1700052K15Rik|Arp-T2|Arpm2	actin-related protein T2	protein-coding
mm_7291.1	chr1	97770069	97770099	-	1	NA	promoter-TSS (NM_001310773)	promoter-TSS (NM_001310773)	8	NM_173760	227399	Mm.220817	NM_173760	ENSMUSG00000040648	Ppip5k2	AW555814|Cfap160|D330021B20|Hisppd1|Vip2|mKIAA0433	diphosphoinositol pentakisphosphate kinase 2	protein-coding
mm_149956.1	chr19	28835125	28835142	+	1	NA	promoter-TSS (NM_009199)	promoter-TSS (NM_009199)	-33	NM_009199	20510	Mm.246670	NM_009199	ENSMUSG00000024935	Slc1a1	D130048G10Rik|EAAC1|EAAC2|EAAT3|MEAAC1	solute carrier family 1 (neuronal/epithelial high affinity glutamate transporter, system Xag), member 1	protein-coding
mm_38264.1	chr4	136880518	136880529	-	1	NA	exon (NM_009777, exon 3 of 3)	exon (NM_009777, exon 3 of 3)	5654	NM_009777	12260	Mm.2570	NM_009777	ENSMUSG00000036905	C1qb	-	complement component 1, q subcomponent, beta polypeptide	protein-coding
mm_40344.1	chr5	45512322	45512337	+	1	NA	3' UTR (NM_024434, exon 13 of 13)	3' UTR (NM_024434, exon 13 of 13)	-7900	NM_025895	66999	Mm.283045	NM_025895	ENSMUSG00000015804	Med28	1500003D12Rik|AI451633|AU045690|Eg1|FKSG20|magicin	mediator complex subunit 28	protein-coding
mm_36521.1	chr4	84548394	84548403	-	1	NA	intron (NM_172870, intron 2 of 5)	C-rich|Low_complexity|Low_complexity	126688	NM_172870	242509	Mm.190774	NM_172870	ENSMUSG00000028487	Bnc2	5031434M05Rik|8430420F16Rik	basonuclin 2	protein-coding
mm_25281.1	chr3	105526052	105526061	+	1	NA	intron (NM_001039347, intron 2 of 6)	L1MEc|LINE|L1	67240	NM_019931	56543	Mm.44530	NM_019931	ENSMUSG00000040896	Kcnd3	AW045978|Kncd3|Kv4.3	potassium voltage-gated channel, Shal-related family, member 3	protein-coding
mm_20336.1	chr2	127541413	127541454	-	1	NA	promoter-TSS (NM_178047)	promoter-TSS (NM_178047)	-16	NM_138750	192212	Mm.34171	NM_138750	ENSMUSG00000027376	Prom2	AI507243|Prom-rp	prominin 2	protein-coding
mm_7300.1	chr1	97977035	97977058	-	1	NA	5' UTR (NM_013626, exon 2 of 26)	5' UTR (NM_013626, exon 2 of 26)	70747	NR_037993	78603	Mm.442597	NR_037993	ENSMUSG00000089706	B230216N24Rik	-	RIKEN cDNA B230216N24 gene	ncRNA
mm_3118.1	chr1	134646552	134646561	+	1	NA	promoter-TSS (NM_009307)	promoter-TSS (NM_009307)	-125	NM_009307	20980	Mm.5102	NM_009307	ENSMUSG00000026452	Syt2	IP4BP|R74640|mKIAA4194	synaptotagmin II	protein-coding
mm_142531.1	chr17	46440117	46440125	-	1	NA	Intergenic	Intergenic	-1644	NM_144856	108114	Mm.387538	NM_144856	ENSMUSG00000067144	Slc22a7	NLT|OAT2	solute carrier family 22 (organic anion transporter), member 7	protein-coding
mm_86086.1	chr9	114844729	114844734	-	1	NA	promoter-TSS (NM_027294)	promoter-TSS (NM_027294)	-579	NM_027294	70031	Mm.150064	NM_027294	ENSMUSG00000041012	Cmtm8	2700018N07Rik|AA408515|Cklfsf8	CKLF-like MARVEL transmembrane domain containing 8	protein-coding
mm_43446.1	chr5	136110574	136110597	+	1	NA	intron (NM_001039103, intron 18 of 19)	PB1D9|SINE|Alu	5063	NR_106002	102465626		NR_106002	ENSMUSG00000099003	Mir7035	Gm27661|mmu-mir-7035	microRNA 7035	ncRNA
mm_158929.1	chr1	63114234	63114234	-	1	NA	promoter-TSS (NM_001114609)	promoter-TSS (NM_001114609)	33	NM_001081436	227195	Mm.74718	NM_001081436	ENSMUSG00000040865	Ino80d	7330405I11|A430093A21Rik|BC010584|OTTMUSG00000002594	INO80 complex subunit D	protein-coding
mm_4392.1	chr1	172341327	172341349	+	1	NA	5' UTR (NM_001039484, exon 1 of 2)	5' UTR (NM_001039484, exon 1 of 2)	128	NM_001039484	16513	Mm.254563	NM_020269	ENSMUSG00000044708	Kcnj10	BIR10|BIRK-1|Kir1.2|Kir4.1	potassium inwardly-rectifying channel, subfamily J, member 10	protein-coding
mm_101480.1	chr11	30986265	30986296	-	1	NA	promoter-TSS (NM_026527)	promoter-TSS (NM_026527)	85	NM_026527	68044	Mm.32656	NM_026527	ENSMUSG00000020309	Chac2	-	ChaC, cation transport regulator 2	protein-coding
mm_146533.1	chr18	5334768	5334835	-	1	NA	promoter-TSS (NM_178722)	promoter-TSS (NM_178722)	-362	NM_178722	240186	Mm.118257	NM_178722	ENSMUSG00000050945	Zfp438	9430031G09|9430091M14Rik|B830013J05Rik	zinc finger protein 438	protein-coding
mm_59803.1	chr7	29134972	29134992	+	1	NA	promoter-TSS (NM_001174155)	promoter-TSS (NM_001174155)	49	NR_045676	233046	Mm.465324	NM_145149	ENSMUSG00000030589	Rasgrp4	-	RAS guanyl releasing protein 4	protein-coding
mm_23722.1	chr3	69009521	69009607	+	1	NA	promoter-TSS (NR_029735)	promoter-TSS (NR_029735)	-208	NR_029529	387175		NR_029529	ENSMUSG00000065580	Mir15b	Mirn15b|mir-15b|mmu-mir-15b	microRNA 15b	ncRNA
mm_126561.1	chr15	82169905	82169935	+	1	NA	exon (NM_033218, exon 2 of 19)	exon (NM_033218, exon 2 of 19)	22651	NM_033218	20788	Mm.9002	NM_033218	ENSMUSG00000022463	Srebf2	AI608257|SREBP-2|SREBP2|SREBP2gc|bHLHd2|lop13|nuc	sterol regulatory element binding factor 2	protein-coding
mm_31865.1	chr4	80003165	80003172	+	1	NA	Intergenic	Intergenic	-831045	NM_031202	22178	Mm.30438	NM_031202	ENSMUSG00000005994	Tyrp1	Oca3|TRP-1|TRP1|Tyrp|b|brown|isa	tyrosinase-related protein 1	protein-coding
mm_77118.1	chr8	111258136	111258141	-	1	NA	intron (NM_009149, intron 1 of 25)	intron (NM_009149, intron 1 of 25)	1064	NM_009149	20340	Mm.276271	NM_009149	ENSMUSG00000003316	Glg1	AI593353|AW537898|CFR|CFR-1|ESL-1|MG-160|MG160|Selel	golgi apparatus protein 1	protein-coding
mm_40431.1	chr5	53588961	53588965	+	1	NA	intron (NM_001080928, intron 1 of 10)	intron (NM_001080928, intron 1 of 10)	-1383	NM_009035	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_145185.1	chr18	49523287	49523293	+	1	NA	promoter-TSS (NR_033785)	promoter-TSS (NR_033785)	1	NR_033785	67321	Mm.245802	NR_033785	ENSMUSG00000100297	1700044K03Rik	-	RIKEN cDNA 1700044K03 gene	ncRNA
mm_81985.1	chr9	121382860	121382893	+	1	NA	intron (NM_175114, intron 1 of 15)	intron (NM_175114, intron 1 of 15)	15918	NM_175114	67095	Mm.491112	NM_175114	ENSMUSG00000032536	Trak1	2310001H13Rik|AI413908|AI467545|hyrt|mKIAA1042	trafficking protein, kinesin binding 1	protein-coding
mm_137221.1	chr17	24172016	24172044	+	1	NA	Intergenic	Intergenic	-2601	NM_009729	11984	Mm.30155	NM_009729	ENSMUSG00000024121	Atp6v0c	Atp6c|Atp6c2|Atp6l|Atpl|Atpl-rs1|PL16|VATL|Vma3	ATPase, H+ transporting, lysosomal V0 subunit C	protein-coding
mm_62983.1	chr7	120203959	120203968	+	1	NA	promoter-TSS (NM_026458)	promoter-TSS (NM_026458)	-1	NM_026458	67928	Mm.158178	NM_026458	ENSMUSG00000062017	Abca14	1700110B15Rik|4930539G24Rik	ATP-binding cassette, sub-family A (ABC1), member 14	protein-coding
mm_139590.1	chr17	57224068	57224110	+	1	NA	exon (NM_009778, exon 10 of 41)	exon (NM_009778, exon 10 of 41)	4047	NM_009778	12266	Mm.19131	NM_009778	ENSMUSG00000024164	C3	AI255234|ASP|HSE-MSF|Plp	complement component 3	protein-coding
mm_26555.1	chr3	146450519	146450536	+	1	NA	promoter-TSS (NM_001293672)	promoter-TSS (NM_001293672)	60	NM_001293672	74245	Mm.45396	NM_028836	ENSMUSG00000028189	Ctbs	2210401K11Rik|CTB	chitobiase, di-N-acetyl-	protein-coding
mm_103525.1	chr11	77046243	77046254	-	1	NA	exon (NM_001012309, exon 7 of 7)	exon (NM_001012309, exon 7 of 7)	31924	NR_030756	751519		NR_030756	ENSMUSG00000065518	Mir423	Mirn423|mir-423|mmu-mir-423	microRNA 423	ncRNA
mm_72076.1	chr8	71568867	71568931	+	1	NA	promoter-TSS (NM_011977)	promoter-TSS (NM_011977)	-28	NM_011977	26457	Mm.38165	NM_011977	ENSMUSG00000031808	Slc27a1	FATP1|Fatp	solute carrier family 27 (fatty acid transporter), member 1	protein-coding
mm_160061.1	chr7	4922310	4922310	+	1	NA	promoter-TSS (NM_201355)	promoter-TSS (NM_201355)	59	NM_201355	269854	Mm.42652	NM_201355	ENSMUSG00000035285	Nat14	BC047219	N-acetyltransferase 14	protein-coding
mm_8350.1	chr1	150218836	150218842	-	1	NA	Intergenic	Intergenic	-53891	NR_110420	102639566	Mm.417208	NR_110420	ENSMUSG00000097754	Ptgs2os2	Gm26687|Linc-cox2|Lincrna-cox2	prostaglandin-endoperoxide synthase 2, opposite strand 2	ncRNA
mm_119531.1	chr14	47650387	47650389	+	1	NA	intron (NM_001347528, intron 1 of 37)	intron (NM_001347528, intron 1 of 37)	1077	NM_001347524	16709	Mm.3110	NM_008477	ENSMUSG00000021843	Ktn1	-	kinectin 1	protein-coding
mm_5282.1	chr1	20617993	20618089	-	1	NA	promoter-TSS (NM_153179)	promoter-TSS (NM_153179)	16	NM_153179	241035	Mm.249253	NM_153179	ENSMUSG00000043760	Pkhd1	AI118496|AI182499|FPC|Tigm1	polycystic kidney and hepatic disease 1	protein-coding
mm_102694.1	chr11	65788248	65788260	-	1	NA	5' UTR (NM_001316367, exon 1 of 12)	5' UTR (NM_001316367, exon 1 of 12)	105	NM_009157	26398	Mm.412922	NM_009157	ENSMUSG00000033352	Map2k4	JNKK1|MEK4|MKK4|PRKMK4|Sek1|Serk1	mitogen-activated protein kinase kinase 4	protein-coding
mm_153628.1	chr19	44013846	44013854	-	1	NA	intron (NM_001001446, intron 5 of 8)	intron (NM_001001446, intron 5 of 8)	15397	NM_001001446	226143	Mm.329866	NM_001001446	ENSMUSG00000025197	Cyp2c44	AW107714|BC034834|b2b386Clo	cytochrome P450, family 2, subfamily c, polypeptide 44	protein-coding
mm_136846.1	chr17	12775218	12775228	+	1	NA	intron (NR_027773, intron 1 of 2)	intron (NR_027773, intron 1 of 2)	-5517	NM_010515	16004	Mm.26553	NM_010515	ENSMUSG00000023830	Igf2r	AI661837|CD222|CI-MPR|M6P/IGF2R|Mpr300	insulin-like growth factor 2 receptor	protein-coding
mm_25189.1	chr3	103386984	103387004	+	1	NA	Intergenic	Intergenic	107701	NM_001079830	94093	Mm.195036	NM_053170	ENSMUSG00000033014	Trim33	8030451N04Rik|AI413936|Ecto|Tif1g	tripartite motif-containing 33	protein-coding
mm_106807.1	chr12	5808265	5808304	+	1	NA	Intergenic	Intergenic	431782	NR_015579	72669	Mm.10434	NM_028318		2810032G03Rik	AI461720	RIKEN cDNA 2810032G03 gene	ncRNA
mm_104680.1	chr11	97699635	97699698	-	1	NA	promoter-TSS (NM_001163308)	promoter-TSS (NM_001163308)	-18	NM_001163308	22658	Mm.2418	NM_009545	ENSMUSG00000018537	Pcgf2	Mel18|Rnf110|Zfp144|mel-18	polycomb group ring finger 2	protein-coding
mm_140837.1	chr17	23670864	23670873	-	1	NA	exon (NM_001008425, exon 2 of 13)	exon (NM_001008425, exon 2 of 13)	-2740	NM_181821	353502	Mm.359030	NM_181821	ENSMUSG00000023904	Hcfc1r1	HPIP	host cell factor C1 regulator 1 (XPO1-dependent)	protein-coding
mm_142184.1	chr17	36867104	36867110	-	1	NA	promoter-TSS (NM_001024134)	promoter-TSS (NM_001024134)	80	NM_001024134	69097	Mm.307027	NM_001024134	ENSMUSG00000050747	Trim15	1810012B10Rik	tripartite motif-containing 15	protein-coding
mm_92677.1	chr10	80567908	80567908	-	1	NA	3' UTR (NM_078477, exon 2 of 2)	3' UTR (NM_078477, exon 2 of 2)	-6348	NM_025852	66932	Mm.1116	NM_025852	ENSMUSG00000047417	Rexo1	1700021P10Rik|2610511M11Rik|AW050347|EloA-BP1|Rex1|Tceb3bp1	REX1, RNA exonuclease 1	protein-coding
mm_86758.1	chr10	19621993	19622004	+	1	NA	promoter-TSS (NM_178258)	promoter-TSS (NM_178258)	-30	NM_178258	237310	Mm.331979	NM_178258	ENSMUSG00000039760	Il22ra2	CRF2-10|CRF2-s1|CRF2X|Il-22bp	interleukin 22 receptor, alpha 2	protein-coding
mm_94519.1	chr11	8773624	8773635	+	1	NA	Intergenic	Intergenic	-109094	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_138394.1	chr17	35051458	35051509	+	1	NA	intron (NM_033444, intron 1 of 5)	intron (NM_033444, intron 1 of 5)	1240	NM_033444	114584	Mm.29524	NM_033444	ENSMUSG00000007041	Clic1	Clcp|G6	chloride intracellular channel 1	protein-coding
mm_139248.1	chr17	47734258	47734298	+	1	NA	exon (NM_025973, exon 9 of 9)	exon (NM_025973, exon 9 of 9)	-2759	NM_001161722	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_26449.1	chr3	142637493	142637517	+	1	NA	3' UTR (NM_010260, exon 11 of 11)	3' UTR (NM_010260, exon 11 of 11)	-13559	NR_105802	102465200		NR_105802	ENSMUSG00000098871	Mir6381	Gm27963|mmu-mir-6381	microRNA 6381	ncRNA
mm_87542.1	chr10	53596887	53596898	+	1	NA	promoter-TSS (NM_025541)	promoter-TSS (NM_025541)	-69	NM_025541	66403	Mm.272989	NM_025541	ENSMUSG00000019857	Asf1a	2310079C17Rik|C79052	anti-silencing function 1A histone chaperone	protein-coding
mm_54369.1	chr6	31131697	31131711	-	1	NA	intron (NR_110471, intron 3 of 3)	intron (NR_110471, intron 3 of 3)	-68611	NR_029532	387223		NR_029532	ENSMUSG00000065604	Mir29b-1	Mirn29b|Mirn29b-1|mir-29b-1	microRNA 29b-1	ncRNA
mm_172878.1	chr9	44920687	44920687	-	1	NA	promoter-TSS (NM_013795)	promoter-TSS (NM_013795)	55	NM_013795	27425	Mm.14663	NM_013795	ENSMUSG00000038717	Atp5l	4933437C06Rik	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit G	protein-coding
mm_56041.1	chr6	86704723	86704768	-	1	NA	intron (NM_011818, intron 10 of 13)	intron (NM_011818, intron 10 of 13)	-20254	NM_025665	66618	Mm.182650	NM_025665	ENSMUSG00000001158	Snrnp27	2610209M04Rik|AI449063|AU022368|Ry1	small nuclear ribonucleoprotein 27 (U4/U6.U5)	protein-coding
mm_91575.1	chr10	40128962	40129005	-	1	NA	intron (NM_001114332, intron 1 of 5)	RSINE1|SINE|B4	13271	NM_028247	72472	Mm.186778	NM_028247	ENSMUSG00000019838	Slc16a10	2610103N14Rik|9830169E08|Mct10|PRO0813|TAT1	solute carrier family 16 (monocarboxylic acid transporters), member 10	protein-coding
mm_18623.1	chr2	68565376	68565387	-	1	NA	Intergenic	RMER21B|LTR|ERV1	-17032	NM_177651	227998	Mm.67562	NM_177651	ENSMUSG00000053896	4933409G03Rik	-	RIKEN cDNA 4933409G03 gene	protein-coding
mm_154531.1	chrM	13726	13748	-	1	NA	NA	Intergenic	NA	NA								
mm_63493.1	chr7	127769945	127769971	+	1	NA	5' UTR (NM_198424, exon 1 of 2)	5' UTR (NM_198424, exon 1 of 2)	143	NM_198424	269999	Mm.36852	NM_198424	ENSMUSG00000043964	Orai3	9930124N15|BC061259|Tmem142c	ORAI calcium release-activated calcium modulator 3	protein-coding
mm_20218.1	chr2	125760383	125760403	-	1	NA	exon (NM_177608, exon 8 of 18)	exon (NM_177608, exon 8 of 18)	22477	NM_177608	70354	Mm.138091	NM_133725	ENSMUSG00000035093	Secisbp2l	3110001I20Rik|AI504340|C630011I23	SECIS binding protein 2-like	protein-coding
mm_20375.1	chr2	128429386	128429399	-	1	NA	promoter-TSS (NR_028591)	promoter-TSS (NR_028591)	-41	NR_028590	100043424	Mm.297222	NR_028589		Gm14005	OTTMUSG00000015351	predicted gene 14005	ncRNA
mm_118645.1	chr14	21536715	21536723	+	1	NA	intron (NM_017479, intron 2 of 16)	intron (NM_017479, intron 2 of 16)	36934	NM_017479	54169	Mm.248967	NM_017479	ENSMUSG00000021767	Kat6b	AI507552|B130044K16Rik|MYST-4|Morf|Myst4|mKIAA0383|qkf|querkopf	K(lysine) acetyltransferase 6B	protein-coding
mm_106243.1	chr11	117782156	117782167	-	1	NA	promoter-TSS (NM_181856)	promoter-TSS (NM_181856)	-136	NM_001195090	217356	Mm.116675	NM_181856	ENSMUSG00000050106	Tmc8	EVIN2|Ever2|mFLJ00400	transmembrane channel-like gene family 8	protein-coding
mm_22850.1	chr3	28263232	28263333	+	1	NA	promoter-TSS (NM_001163009)	promoter-TSS (NM_001163009)	68	NM_001163009	665113	Mm.126193	NM_026910	ENSMUSG00000027692	Tnik	1500031A17Rik|4831440I19Rik|AI451411|C530008O15Rik|C630040K21Rik	TRAF2 and NCK interacting kinase	protein-coding
mm_9705.1	chr1	179403883	179403886	-	1	NA	intron (NM_027188, intron 5 of 11)	B1_Mur3|SINE|Alu	114119	NM_027188	69726	Mm.222338	NM_027188	ENSMUSG00000055067	Smyd3	2410008A19Rik|Zmynd1	SET and MYND domain containing 3	protein-coding
mm_94005.1	chr10	127607119	127607164	-	1	NA	intron (NM_008512, intron 4 of 88)	intron (NM_008512, intron 4 of 88)	14007	NM_008512	16971	Mm.271854	NM_008512	ENSMUSG00000040249	Lrp1	A2mr|AI316852|CD91|Lrp|b2b1554Clo	low density lipoprotein receptor-related protein 1	protein-coding
mm_52066.1	chr6	97536592	97536593	+	1	NA	intron (NM_145148, intron 1 of 23)	L1M5|LINE|L1	-48772	NM_001346637	232288	Mm.27789	NM_145148	ENSMUSG00000030064	Frmd4b	6030440G05Rik|C87375|GOBLIN|GRSP1|R74720	FERM domain containing 4B	protein-coding
mm_132439.1	chr16	35938513	35938526	+	1	NA	promoter-TSS (NM_030253)	promoter-TSS (NM_030253)	49	NM_030253	80285	Mm.49074	NM_030253	ENSMUSG00000022906	Parp9	ARTD9|AW214463|BC003281|Bagl|Bal|PARP-9	poly (ADP-ribose) polymerase family, member 9	protein-coding
mm_35817.1	chr4	46991762	46991782	-	1	NA	promoter-TSS (NM_001081141)	promoter-TSS (NM_001081141)	-58	NM_001081141	242425	Mm.101909	NM_001081141	ENSMUSG00000039809	Gabbr2	GABABR2|Gb2|Gm425|Gpr51	gamma-aminobutyric acid (GABA) B receptor, 2	protein-coding
mm_18588.1	chr2	66440896	66440905	-	1	NA	promoter-TSS (NR_033495)	promoter-TSS (NR_033495)	20	NR_033495	100038743	Mm.330264	NR_033495		Gm13629	OTTMUSG00000013098	predicted gene 13629	ncRNA
mm_24376.1	chr3	90231589	90231663	+	1	NA	promoter-TSS (NM_206924)	promoter-TSS (NM_206924)	29	NM_206924	23922	Mm.13912	NM_206924	ENSMUSG00000027937	Jtb	Gm622	jumping translocation breakpoint	protein-coding
mm_92558.1	chr10	79807069	79807099	-	1	NA	exon (NM_001161747, exon 3 of 8)	exon (NM_001161747, exon 3 of 8)	13512	NM_001161747	18483	Mm.34650	NM_023128	ENSMUSG00000035863	Palm	-	paralemmin	protein-coding
mm_117330.1	chr13	68961609	68961612	-	1	NA	intron (NM_153534, intron 2 of 24)	intron (NM_153534, intron 2 of 24)	37931	NM_153534	210044	Mm.390617	NM_153534	ENSMUSG00000021536	Adcy2	mKIAA1060	adenylate cyclase 2	protein-coding
mm_145101.1	chr18	44071391	44071402	+	1	NA	promoter-TSS (NM_001013797)	promoter-TSS (NM_001013797)	3	NM_001013797	433180	Mm.57302	NM_001013797	ENSMUSG00000055095	Spink6	EG433180	serine peptidase inhibitor, Kazal type 6	protein-coding
mm_116332.1	chr13	38037166	38037184	-	1	NA	promoter-TSS (NM_027724)	promoter-TSS (NM_027724)	186	NM_024242	71340	Mm.297130	NM_024242	ENSMUSG00000021428	Riok1	3110046C13Rik|5430416A05Rik|Ad034	RIO kinase 1 (yeast)	protein-coding
mm_104225.1	chr11	88551164	88551176	-	1	NA	intron (NM_054043, intron 6 of 13)	intron (NM_054043, intron 6 of 13)	-68081	NR_131025	68397	Mm.426889	NR_131025		0610039H22Rik	-	RIKEN cDNA 0610039H22 gene	ncRNA
mm_114869.1	chr13	94057758	94057838	+	1	NA	promoter-TSS (NM_172589)	promoter-TSS (NM_172589)	2	NM_172589	218454	Mm.316553	NM_172589	ENSMUSG00000045312	Lhfpl2	6030465B15|AI447312|AW050335|mKIAA0206|vgim	lipoma HMGIC fusion partner-like 2	protein-coding
mm_16218.1	chr2	173082801	173082810	+	1	NA	Intergenic	Intergenic	36720	NM_001081387	664799	Mm.389396	NM_001081387	ENSMUSG00000070495	Ctcfl	Boris|OTTMUSG00000016680	CCCTC-binding factor (zinc finger protein)-like	protein-coding
mm_68140.1	chr7	102239930	102239993	-	1	NA	exon (NM_019566, exon 2 of 2)	exon (NM_019566, exon 2 of 2)	10157	NM_019566	56212	Mm.259795	NM_019566	ENSMUSG00000073982	Rhog	2810426G09Rik|Arhg|Sid10750	ras homolog family member G	protein-coding
mm_156113.1	chrX	114474570	114474593	+	1	NA	exon (NM_001290478, exon 1 of 11)	exon (NM_001290478, exon 1 of 11)	248	NM_001290477	237010	Mm.132583	NM_172781	ENSMUSG00000025597	Klhl4	B130014A11|C130018J01Rik	kelch-like 4	protein-coding
mm_35203.1	chr4	19520240	19520252	-	1	NA	3' UTR (NM_027769, exon 16 of 16)	3' UTR (NM_027769, exon 16 of 16)	49858	NM_027769	70568	Mm.38390	NM_027769	ENSMUSG00000028228	Cpne3	5430428M23Rik|5730450C07Rik|C85108|CPN3	copine III	protein-coding
mm_45142.1	chr5	49131028	49131072	-	1	NA	intron (NM_001199244, intron 1 of 7)	RMER17D|LTR|ERVK	154609	NM_001199244	80334	Mm.160172	NM_030265	ENSMUSG00000029088	Kcnip4	AV032399|Calp|Calp250|KChIP4|KChIP4a	Kv channel interacting protein 4	protein-coding
mm_96083.1	chr11	60105080	60105097	+	1	NA	promoter-TSS (NM_009021)	promoter-TSS (NM_009021)	75	NM_009021	19377	Mm.296366	NM_009021	ENSMUSG00000062115	Rai1	Gt1	retinoic acid induced 1	protein-coding
mm_17260.1	chr2	25983131	25983154	-	1	NA	5' UTR (NM_001276361, exon 1 of 18)	5' UTR (NM_001276361, exon 1 of 18)	140	NM_001276360	227634	Mm.36834	NM_001115076	ENSMUSG00000026933	Camsap1	9530003A05Rik|C77823|PRO2405	calmodulin regulated spectrin-associated protein 1	protein-coding
mm_66986.1	chr7	63939711	63939724	-	1	NA	promoter-TSS (NM_021366)	promoter-TSS (NM_021366)	-802	NM_021366	50794	Mm.240473	NM_021366	ENSMUSG00000052040	Klf13	0610043C13Rik|9430029L20Rik|Bteb3|FKLF-2|FKLF2|NSLP1|RFLAT-1|RFLAT1	Kruppel-like factor 13	protein-coding
mm_119165.1	chr14	32029605	32029657	+	1	NA	exon (NM_030166, exon 1 of 10)	exon (NM_030166, exon 1 of 10)	528	NM_030166	78754	Mm.40681	NM_030166	ENSMUSG00000021903	Galnt15	4631401E18Rik|Galntl2|mpp-GalNAc-T15	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 15	protein-coding
mm_124894.1	chr15	10346734	10346756	+	1	NA	TTS (NM_001253782)	TTS (NM_001253782)	-11788	NM_001310736	268782	Mm.482244	NM_001031851	ENSMUSG00000089678	Agxt2	AI303810|AI663818	alanine-glyoxylate aminotransferase 2	protein-coding
mm_87851.1	chr10	61089328	61089345	+	1	NA	promoter-TSS (NM_025273)	promoter-TSS (NM_025273)	5	NM_025273	13180	Mm.39473	NM_025273	ENSMUSG00000020098	Pcbd1	Dcoh|Pcbd|Pcd|Phs	pterin 4 alpha carbinolamine dehydratase/dimerization cofactor of hepatocyte nuclear factor 1 alpha (TCF1) 1	protein-coding
mm_154656.1	chrX	7841992	7842008	+	1	NA	promoter-TSS (NM_001290537)	promoter-TSS (NM_001290537)	-82	NM_001290537	54644	Mm.142827	NM_138604	ENSMUSG00000031154	Otud5	AA407879|AI553596|BB114028|DUBA|DXImx46e|Sfc7	OTU domain containing 5	protein-coding
mm_100396.1	chr11	119390668	119390683	+	1	NA	TTS (NR_035453)	TTS (NR_035453)	203	NR_035453	100316690		NR_035453	ENSMUSG00000088015	Mir1932	mir-1932|mmu-mir-1932	microRNA 1932	ncRNA
mm_136016.1	chr16	76093983	76093996	-	1	NA	Intergenic	Intergenic	-28624	NR_040575	78215	Mm.243885	NR_040575		4930578N18Rik	-	RIKEN cDNA 4930578N18 gene	ncRNA
mm_121056.1	chr14	87416125	87416142	+	1	NA	promoter-TSS (NM_001253755)	promoter-TSS (NM_001253755)	-450	NM_172605	219249	Mm.35168	NM_172605	ENSMUSG00000022019	Tdrd3	4732418C03Rik|6720468N18	tudor domain containing 3	protein-coding
mm_7664.1	chr1	128417353	128417384	-	1	NA	promoter-TSS (NM_145507)	promoter-TSS (NM_145507)	48	NM_177445	226414	Mm.28693	NM_145507	ENSMUSG00000026356	Dars	5730439G15Rik	aspartyl-tRNA synthetase	protein-coding
mm_33885.1	chr4	136177937	136177957	+	1	NA	intron (NM_177733, intron 1 of 6)	intron (NM_177733, intron 1 of 6)	-2835	NM_001305399	242705	Mm.307932	NM_177733	ENSMUSG00000018983	E2f2	E2F-2	E2F transcription factor 2	protein-coding
mm_92547.1	chr10	79746554	79746586	-	1	NA	promoter-TSS (NM_172551)	promoter-TSS (NM_172551)	11	NM_172551	216151	Mm.39001	NM_172551	ENSMUSG00000020329	Polrmt	1110018N15Rik|4932416K13	polymerase (RNA) mitochondrial (DNA directed)	protein-coding
mm_123043.1	chr14	55590811	55590849	-	1	NA	promoter-TSS (NM_194346)	promoter-TSS (NM_194346)	191	NM_011190	19188	Mm.371573	NM_011190	ENSMUSG00000079197	Psme2	AA589371|AI788882|PA28b	proteasome (prosome, macropain) activator subunit 2 (PA28 beta)	protein-coding
mm_46469.1	chr5	105123155	105123158	-	1	NA	intron (NM_008620, intron 5 of 10)	intron (NM_008620, intron 5 of 10)	-12864	NM_172777	236573	Mm.425261	NM_172777	ENSMUSG00000029298	Gbp9	-	guanylate-binding protein 9	protein-coding
mm_60424.1	chr7	44476551	44476575	+	1	NA	Intergenic	L1MEd|LINE|L1	6216	NR_106019	102465637		NR_106019	ENSMUSG00000098661	Mir7052	Gm27583|mmu-mir-7052	microRNA 7052	ncRNA
mm_139675.1	chr17	57412513	57412525	+	1	NA	intron (NM_010130, intron 9 of 21)	CT-rich|Low_complexity|Low_complexity	53833	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_459.1	chr1	36307728	36307735	+	1	NA	promoter-TSS (NM_001290727)	promoter-TSS (NM_001290727)	-2	NM_001290727	214855	Mm.34316	NM_145996	ENSMUSG00000037447	Arid5a	D430024K22Rik|Mrf1	AT rich interactive domain 5A (MRF1-like)	protein-coding
mm_54052.1	chr6	13839181	13839210	-	1	NA	intron (NM_145066, intron 1 of 3)	(A)n|Simple_repeat|Simple_repeat	747	NM_001330666	64450	Mm.167625	NM_145066	ENSMUSG00000048216	Gpr85	2900026B03Rik	G protein-coupled receptor 85	protein-coding
mm_17863.1	chr2	34826161	34826181	-	1	NA	promoter-TSS (NM_013890)	promoter-TSS (NM_013890)	64	NM_001164770	30050	Mm.4465	NM_013890	ENSMUSG00000035949	Fbxw2	2700071L08Rik|FBW2|Fwd2|MD6	F-box and WD-40 domain protein 2	protein-coding
mm_119960.1	chr14	55371454	55371455	+	1	NA	Intergenic	Intergenic	-107304	NM_001037938	28200	Mm.27427	NM_030686	ENSMUSG00000022210	Dhrs4	AI043103|AI790593|CR|D14Ucla2|NDRD|PHCR|PSCD|RRD|mouNRDR	dehydrogenase/reductase (SDR family) member 4	protein-coding
mm_89431.1	chr10	91083082	91083103	+	1	NA	promoter-TSS (NM_026166)	promoter-TSS (NM_026166)	53	NM_026166	67454	Mm.252843	NM_026166	ENSMUSG00000019975	Ikbip	1200009F10Rik|1700023M03Rik|D18354|Ikip	IKBKB interacting protein	protein-coding
mm_107186.1	chr12	25096438	25096449	+	1	NA	promoter-TSS (NM_010496)	promoter-TSS (NM_010496)	-351	NM_010496	15902	Mm.34871	NM_010496	ENSMUSG00000020644	Id2	AI255428|C78922|Idb2|bHLHb26	inhibitor of DNA binding 2	protein-coding
mm_39448.1	chr5	17574471	17574486	+	1	NA	promoter-TSS (NM_013657)	promoter-TSS (NM_013657)	-338	NM_013657	20348	Mm.5071	NM_013657	ENSMUSG00000028780	Sema3c	1110036B02Rik|SemE|Semae	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	protein-coding
mm_76265.1	chr8	84034422	84034424	-	1	NA	intron (NM_016671, intron 8 of 13)	intron (NM_016671, intron 8 of 13)	8152	NM_016671	50931	Mm.38386	NM_016671	ENSMUSG00000005465	Il27ra	CRL1|IL-27R|Tccr|WSX-1|Wsx1|zcytor1	interleukin 27 receptor, alpha	protein-coding
mm_93619.1	chr10	117277665	117277689	-	1	NA	3' UTR (NM_017372, exon 4 of 4)	3' UTR (NM_017372, exon 4 of 4)	4595	NM_017372	17105	Mm.45436	NM_017372	ENSMUSG00000069516	Lyz2	AI326280|Lys|Lysm|Lyzf2|Lyzs|Lzm|Lzm-s1|Lzp	lysozyme 2	protein-coding
mm_151003.1	chr19	46654611	46654636	+	1	NA	exon (NM_001177813, exon 4 of 4)	exon (NM_001177813, exon 4 of 4)	18377	NM_007809	13074	Mm.1262	NM_007809	ENSMUSG00000003555	Cyp17a1	Cyp17|p450c17	cytochrome P450, family 17, subfamily a, polypeptide 1	protein-coding
mm_145518.1	chr18	60500259	60500280	+	1	NA	intron (NM_134133, intron 1 of 1)	intron (NM_134133, intron 1 of 1)	1714	NM_134133	106878	Mm.273197	NM_134133	ENSMUSG00000038059	Smim3	2010002N04Rik|AI195350|AW561905|Nid67|cI-41	small integral membrane protein 3	protein-coding
mm_86480.1	chr10	4711675	4711685	+	1	NA	intron (NM_001302531, intron 1 of 8)	intron (NM_001302531, intron 1 of 8)	1522	NM_001302533	13982	Mm.9213	NM_007956	ENSMUSG00000019768	Esr1	ER|ER-alpha|ERa|ERalpha|ESR|Estr|Estra|Nr3a1	estrogen receptor 1 (alpha)	protein-coding
mm_117096.1	chr13	59822813	59822833	-	1	NA	intron (NM_153538, intron 1 of 27)	CpG	324	NM_153538	214290	Mm.233082	NM_153538	ENSMUSG00000035248	Zcchc6	6030448M23Rik|AA420405	zinc finger, CCHC domain containing 6	protein-coding
mm_30083.1	chr3	138131333	138131355	-	1	NA	promoter-TSS (NM_008642)	promoter-TSS (NM_008642)	33	NM_008642	17777	Mm.2941	NM_008642	ENSMUSG00000028158	Mttp	1810043K16Rik|MTP	microsomal triglyceride transfer protein	protein-coding
mm_41012.1	chr5	81021584	81021589	+	1	NA	promoter-TSS (NM_198702)	promoter-TSS (NM_198702)	-7	NM_198702	319387	Mm.273631	NM_198702	ENSMUSG00000037605	Adgrl3	5430402I23Rik|CIRL-3|D130075K09Rik|Gm1379|LEC3|Lphn3|mKIAA0768	adhesion G protein-coupled receptor L3	protein-coding
mm_46543.1	chr5	105800373	105800407	-	1	NA	intron (NM_001122768, intron 2 of 2)	intron (NM_001122768, intron 2 of 2)	-76178	NR_030777	54367	Mm.248876	NM_018759	ENSMUSG00000029290	Zfp326	5730470H14Rik|ZAN75|Znf326	zinc finger protein 326	protein-coding
mm_40268.1	chr5	38546455	38546460	+	1	NA	intron (NM_011715, intron 4 of 14)	intron (NM_011715, intron 4 of 14)	15138	NM_011715	22388	Mm.2654	NM_011715	ENSMUSG00000005103	Wdr1	Aip1|D5Wsu185e|rede	WD repeat domain 1	protein-coding
mm_6656.1	chr1	79923503	79923508	-	1	NA	Intergenic	Intergenic	-64840	NM_009255	20720	Mm.3093	NM_009255	ENSMUSG00000026249	Serpine2	B230326M24Rik|PAI-1|PI-7|PI7|PN-1|Spi4	serine (or cysteine) peptidase inhibitor, clade E, member 2	protein-coding
mm_88012.1	chr10	67132369	67132372	+	1	NA	intron (NM_207221, intron 1 of 25)	B1_Mur2|SINE|Alu	5112	NM_207221	108829	Mm.23846	NM_207221	ENSMUSG00000037876	Jmjd1c	5430433L24Rik|D630035I23Rik|Jmjdic|TRIP8	jumonji domain containing 1C	protein-coding
mm_101597.1	chr11	34718951	34718985	-	1	NA	exon (NM_033374, exon 8 of 52)	exon (NM_033374, exon 8 of 52)	64937	NM_033374	94176	Mm.380679	NM_033374	ENSMUSG00000020143	Dock2	AI662014|AW122239|CED-5|Hch|MBC	dedicator of cyto-kinesis 2	protein-coding
mm_18251.1	chr2	52212767	52212776	-	1	NA	exon (NM_010889, exon 89 of 157)	exon (NM_010889, exon 89 of 157)	-78231	NR_040620	78049	Mm.243883	NR_040620		4930573O16Rik	-	RIKEN cDNA 4930573O16 gene	ncRNA
mm_155282.1	chrX	61181121	61181128	+	1	NA	Intergenic	Intergenic	4434	NM_001166658	631990	Mm.401324	NM_001166658	ENSMUSG00000090546	Cdr1	100039759|Cdr|Cdr34|EG631990|Gm2409|Gm7077	cerebellar degeneration related antigen 1	protein-coding
mm_6291.1	chr1	69768736	69768744	-	1	NA	Intergenic	Intergenic	-58230	NM_029160	66722	Mm.440554	NM_025728	ENSMUSG00000053153	Spag16	4921511D23Rik|4930524F24Rik|4930585K05Rik|AV261009|Pf20|Wdr29	sperm associated antigen 16	protein-coding
mm_102643.1	chr11	62731866	62731910	-	1	NA	Intergenic	CpG	-2795	NM_133208	170740	Mm.339982	NM_133208	ENSMUSG00000005267	Zfp287	B230333C16Rik|SKAT-2|Skat2|Znf287|mszf16|mszf74	zinc finger protein 287	protein-coding
mm_71133.1	chr8	36993552	36993611	+	1	NA	promoter-TSS (NM_001039220)	promoter-TSS (NM_001039220)	6	NM_001039220	621080	Mm.373292	NM_001039220	ENSMUSG00000074384	AI429214	-	expressed sequence AI429214	protein-coding
mm_114395.1	chr13	63278907	63278919	+	1	NA	intron (NR_110520, intron 2 of 5)	intron (NR_110520, intron 2 of 5)	18234	NR_045794	100504114	Mm.437070	NR_045794	ENSMUSG00000097242	Gm16907	-	predicted gene, 16907	ncRNA
mm_92979.1	chr10	86693451	86693461	-	1	NA	exon (NM_011631, exon 14 of 18)	exon (NM_011631, exon 14 of 18)	7929	NR_015572	66263	Mm.392261	NR_015572		1810014B01Rik	-	RIKEN cDNA 1810014B01 gene	pseudo
mm_11870.1	chr2	48989025	48989026	+	1	NA	intron (NM_029924, intron 1 of 16)	intron (NM_029924, intron 1 of 16)	39517	NM_029924	109241	Mm.440436	NM_029924	ENSMUSG00000036792	Mbd5	9430004D19Rik|AA536666|AI426407|C030040A15Rik|Gm1630|OTTMUSG00000012483	methyl-CpG binding domain protein 5	protein-coding
mm_42049.1	chr5	108620222	108620225	+	1	NA	intron (NM_153569, intron 4 of 27)	Tigger7|DNA|TcMar-Tigger	9554	NM_153569	231580	Mm.276647	NM_153569	ENSMUSG00000062234	Gak	D130045N16Rik	cyclin G associated kinase	protein-coding
mm_91349.1	chr10	27525965	27525969	-	1	NA	intron (NM_008481, intron 1 of 63)	intron (NM_008481, intron 1 of 63)	90975	NM_008481	16773	Mm.256087	NM_008481	ENSMUSG00000019899	Lama2	5830440B04|dy|mKIAA4087|mer|merosin	laminin, alpha 2	protein-coding
mm_61328.1	chr7	68250798	68250803	+	1	NA	intron (NM_030101, intron 1 of 3)	RMER19B2|LTR|ERVK	13433	NM_030101	78444	Mm.425468	NM_030101	ENSMUSG00000030553	Pgpep1l	C330024D12Rik	pyroglutamyl-peptidase I-like	protein-coding
mm_107475.1	chr12	37880572	37880648	+	1	NA	promoter-TSS (NM_178681)	promoter-TSS (NM_178681)	-95	NM_178681	217480	Mm.126525	NM_178681	ENSMUSG00000036095	Dgkb	6430574F24|90kda|C630029D13Rik|DAGK2|DGK|DGK-beta|mKIAA0718	diacylglycerol kinase, beta	protein-coding
mm_42278.1	chr5	114155454	114155467	+	1	NA	Intergenic	Intergenic	-10058	NM_133904	100705	Mm.81793	NM_133904	ENSMUSG00000042010	Acacb	AI597064|AW743042|Acc2|Accb	acetyl-Coenzyme A carboxylase beta	protein-coding
mm_53150.1	chr6	125265514	125265530	+	1	NA	promoter-TSS (NR_015527)	promoter-TSS (NR_015527)	-3	NR_015527	73870	Mm.440681	NR_015527	ENSMUSG00000108129	4930417O13Rik	-	RIKEN cDNA 4930417O13 gene	ncRNA
mm_128847.1	chr15	71727816	71727848	-	1	NA	promoter-TSS (NM_177819)	promoter-TSS (NM_177819)	6	NM_177819	70363	Mm.126450	NM_177819	ENSMUSG00000036800	Fam135b	1700010C24Rik|A830008O07Rik	family with sequence similarity 135, member B	protein-coding
mm_80994.1	chr9	103423073	103423085	+	1	NA	promoter-TSS (NR_040466)	promoter-TSS (NR_040466)	-499	NR_040466	100529079	Mm.437003	NR_040466	ENSMUSG00000086236	5830418P13Rik	-	RIKEN cDNA 5830418P13 gene	ncRNA
mm_90587.1	chr10	128270507	128270541	+	1	NA	promoter-TSS (NM_019963)	promoter-TSS (NM_019963)	-52	NM_019963	20847	Mm.293120	NM_019963	ENSMUSG00000040033	Stat2	1600010G07Rik|AW496480	signal transducer and activator of transcription 2	protein-coding
mm_72143.1	chr8	72135303	72135314	+	1	NA	promoter-TSS (NM_001001491)	promoter-TSS (NM_001001491)	16	NM_001001491	326618	Mm.295124	NM_001001491	ENSMUSG00000031799	Tpm4	2610528G24Rik|Tpm4.2|Tpm4.2cy	tropomyosin 4	protein-coding
mm_25725.1	chr3	122730114	122730119	+	1	NA	intron (NM_153422, intron 1 of 20)	CpG	958	NM_153422	242202	Mm.134911	NM_153422	ENSMUSG00000053965	Pde5a	Cgbpde|Cn5n|PDE5a2|Pde5|Pde5a1	phosphodiesterase 5A, cGMP-specific	protein-coding
mm_53636.1	chr6	140621047	140621055	+	1	NA	Intergenic	LTR88b|LTR|Gypsy?	-1612	NM_178803	11569	Mm.86453	NM_009637	ENSMUSG00000030232	Aebp2	AU023766|B230313N05Rik	AE binding protein 2	protein-coding
mm_82646.1	chr9	22017701	22017734	-	1	NA	3' UTR (NM_010487, exon 7 of 7)	3' UTR (NM_010487, exon 7 of 7)	14729	NM_008925	19089	Mm.214593	NM_008925	ENSMUSG00000003402	Prkcsh	80K-H|PKCSH	protein kinase C substrate 80K-H	protein-coding
mm_416.1	chr1	34236684	34236694	+	1	NA	intron (NM_001276764, intron 60 of 102)	intron (NM_001276764, intron 60 of 102)	76359	NM_010081	13518	Mm.336625	NM_010081	ENSMUSG00000026131	Dst	2310001O04Rik|A830042E19Rik|AW554249|BP230|BPAG1-n|Bpag|Bpag1|Macf2|ah|athetoid|dt|mKIAA0728|nmf203|nmf339	dystonin	protein-coding
mm_96100.1	chr11	60468412	60468426	+	1	NA	promoter-TSS (NM_010862)	promoter-TSS (NM_010862)	-920	NM_010862	17910	Mm.89960	NM_010862	ENSMUSG00000042678	Myo15	Myo15a|sh-2|sh2	myosin XV	protein-coding
mm_164527.1	chr17	5799488	5799499	+	1	NA	promoter-TSS (NR_045079)	promoter-TSS (NR_045079)	3	NR_045080	78512	Mm.23696	NR_045079	ENSMUSG00000096965	3300005D01Rik	-	RIKEN cDNA 3300005D01 gene	ncRNA
mm_92949.1	chr10	85127978	85128035	-	1	NA	promoter-TSS (NM_028832)	promoter-TSS (NM_028832)	21	NM_028832	74238	Mm.255401	NM_028832	ENSMUSG00000049038	Mterf2	1700007D05Rik|Mterfd3	mitochondrial transcription termination factor 2	protein-coding
mm_62037.1	chr7	92180679	92180734	+	1	NA	intron (NM_011807, intron 13 of 22)	intron (NM_011807, intron 13 of 22)	-54264	NM_001243047	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_133783.1	chr16	95241019	95241024	+	1	NA	Intergenic	Intergenic	-16537	NM_001271693	16516	Mm.272239	NM_019664	ENSMUSG00000062609	Kcnj15	4930414N08Rik|AI182284|AI267127|IRKK|Kir4.2	potassium inwardly-rectifying channel, subfamily J, member 15	protein-coding
mm_99799.1	chr11	107547926	107547959	+	1	NA	promoter-TSS (NM_198298)	promoter-TSS (NM_198298)	-18	NM_198298	78455	Mm.272047	NM_198298	ENSMUSG00000020721	Helz	3110078M01Rik|9430093I07Rik|9630002H22Rik|AI851979|DRHC	helicase with zinc finger domain	protein-coding
mm_62310.1	chr7	100227639	100227706	+	1	NA	promoter-TSS (NM_027629)	promoter-TSS (NM_027629)	65	NM_027629	70974	Mm.440524	NM_027629	ENSMUSG00000030729	Pgm2l1	4931406N15Rik|AI553438|BM32A	phosphoglucomutase 2-like 1	protein-coding
mm_27839.1	chr3	79147502	79147504	-	1	NA	Intergenic	Intergenic	-1628	NM_001099624	76089	Mm.31220	NM_001099624	ENSMUSG00000062232	Rapgef2	5830453M24Rik|CNRasGEF|Pdzgef1|RA-GEF-1|mKIAA0313|nRapGEP	Rap guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_1213.1	chr1	62726951	62726968	+	1	NA	intron (NM_001077405, intron 2 of 15)	(CA)n|Simple_repeat|Simple_repeat	23642	NM_001077405	18187	Mm.266341	NM_010939	ENSMUSG00000025969	Nrp2	1110048P06Rik|Np-2|Np2|Npn-2|Npn2	neuropilin 2	protein-coding
mm_75430.1	chr8	47288285	47288295	-	1	NA	5' UTR (NM_001286376, exon 1 of 5)	5' UTR (NM_001286376, exon 1 of 5)	1112	NM_001286376	71069	Mm.23973	NM_175162	ENSMUSG00000038143	Stox2	4933409N07Rik|AI449080|AI835114|mKIAA1392	storkhead box 2	protein-coding
mm_164680.1	chr17	47010436	47010458	-	1	NA	promoter-TSS (NM_001177374)	promoter-TSS (NM_001177374)	85	NM_146078	224826	Mm.28234	NM_146078	ENSMUSG00000023977	Ubr2	9930021A08Rik|AI462103|AW540746|E130209G04Rik|ENSMUSG00000043296|mKIAA0349	ubiquitin protein ligase E3 component n-recognin 2	protein-coding
mm_168933.1	chr12	67510718	67510732	+	1	NA	Intergenic	Intergenic	-288176	NM_207010	320772	Mm.227680	NM_207010	ENSMUSG00000034912	Mdga2	6720489L24Rik|9330209L04Rik|Adp|Mamdc1	MAM domain containing glycosylphosphatidylinositol anchor 2	protein-coding
mm_135854.1	chr16	59600145	59600148	-	1	NA	Intergenic	Intergenic	-36799	NR_040564	75145	Mm.399348	NR_040564		4930547E14Rik	-	RIKEN cDNA 4930547E14 gene	ncRNA
mm_87809.1	chr10	60301773	60301783	+	1	NA	TTS (NM_001252635)	TTS (NM_001252635)	17317	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_31277.1	chr4	45799060	45799149	+	1	NA	promoter-TSS (NM_028270)	promoter-TSS (NM_028270)	82	NM_028270	72535	Mm.331583	NM_028270	ENSMUSG00000035561	Aldh1b1	2700007F14Rik	aldehyde dehydrogenase 1 family, member B1	protein-coding
mm_146986.1	chr18	34006541	34006582	-	1	NA	intron (NM_013512, intron 1 of 23)	CpG-6813	645	NM_013512	13824	Mm.3465	NM_013512	ENSMUSG00000024376	Epb41l4a	Epb4.1l4|Epb4.1l4a|NBL4	erythrocyte membrane protein band 4.1 like 4a	protein-coding
mm_141396.1	chr17	29238090	29238166	-	1	NA	promoter-TSS (NM_153166)	promoter-TSS (NM_153166)	-338	NM_153166	240058	Mm.39905	NM_153166	ENSMUSG00000024008	Cpne5	A830083G22Rik	copine V	protein-coding
mm_94723.1	chr11	20647150	20647156	+	1	NA	intron (NM_001038625, intron 1 of 1)	intron (NM_001038625, intron 1 of 1)	15176	NM_001038625	58172	Mm.339676	NM_021372	ENSMUSG00000049800	Sertad2	AB041541|AU021878|Kiaa0127|MNCb-1504|SEI-2|Sei2|TRIP-Br2|mKIAA0127	SERTA domain containing 2	protein-coding
mm_86739.1	chr10	19185158	19185173	+	1	NA	intron (NR_038022, intron 1 of 1)	intron (NR_038022, intron 1 of 1)	17927	NR_038022	100504265	Mm.383417	NR_038021		Gm20139	-	predicted gene, 20139	ncRNA
mm_41786.1	chr5	103722992	103723007	+	1	NA	Intergenic	Intergenic	-31163	NM_133919	17355	Mm.6949	NM_133919	ENSMUSG00000029313	Aff1	9630032B01Rik|AW319193|Af4|Mllt2h|Rob	AF4/FMR2 family, member 1	protein-coding
mm_68087.1	chr7	101896204	101896275	-	1	NA	promoter-TSS (NM_001291349)	promoter-TSS (NM_001291349)	-92	NM_001291348	75430	Mm.284491	NM_027532	ENSMUSG00000030649	Anapc15	3200002M19Rik|6330414C15Rik|APC15	anaphase prompoting complex C subunit 15	protein-coding
mm_4692.1	chr1	180727274	180727286	+	1	NA	intron (NM_133225, intron 1 of 7)	intron (NM_133225, intron 1 of 7)	1237	NM_133225	170760	Mm.272981	NM_133225	ENSMUSG00000026499	Acbd3	60kDa|8430407O11Rik|D1Ertd10e|GCP60|GOLPH1|Gocap1|Pap7	acyl-Coenzyme A binding domain containing 3	protein-coding
mm_169116.1	chr13	4982803	4982814	-	1	NA	Intergenic	L1Md_T|LINE|L1	-373644	NM_018859	56043	Mm.251908	NM_018859	ENSMUSG00000045410	Akr1e1	1810061I10Rik|Akr1e2	aldo-keto reductase family 1, member E1	protein-coding
mm_10424.1	chr2	13582463	13582542	+	1	NA	exon (NM_011701, exon 9 of 9)	exon (NM_011701, exon 9 of 9)	8191	NM_011701	22352	Mm.268000	NM_011701	ENSMUSG00000026728	Vim	-	vimentin	protein-coding
mm_79249.1	chr9	50603893	50603903	+	1	NA	promoter-TSS (NM_013897)	promoter-TSS (NM_013897)	-3	NM_013897	30057	Mm.335149	NM_013897	ENSMUSG00000039016	Timm8b	Tim8b	translocase of inner mitochondrial membrane 8B	protein-coding
mm_164189.1	chr15	77942123	77942126	-	1	NA	3' UTR (NM_001017983, exon 9 of 9)	3' UTR (NM_001017983, exon 9 of 9)	-13130	NM_019913	56551	Mm.291917	NM_019913	ENSMUSG00000005354	Txn2	2510006J11Rik|AI788873|Trx2	thioredoxin 2	protein-coding
mm_46368.1	chr5	103629237	103629269	-	1	NA	5' UTR (NM_029415, exon 1 of 6)	5' UTR (NM_029415, exon 1 of 6)	150	NM_029415	75750	Mm.7446	NM_029415	ENSMUSG00000029321	Slc10a6	8430417G17Rik|C78479|Soat	solute carrier family 10 (sodium/bile acid cotransporter family), member 6	protein-coding
mm_142338.1	chr17	43569972	43569983	-	1	NA	intron (NM_013737, intron 1 of 11)	intron (NM_013737, intron 1 of 11)	1526	NM_013737	27226	Mm.9277	NM_013737	ENSMUSG00000023913	Pla2g7	PAF-AH|R75400	phospholipase A2, group VII (platelet-activating factor acetylhydrolase, plasma)	protein-coding
mm_150562.1	chr19	39510845	39510855	+	1	NA	promoter-TSS (NM_010003)	promoter-TSS (NM_010003)	28	NM_010003	13098	Mm.42101	NM_010003	ENSMUSG00000025003	Cyp2c39	CYPIIC39	cytochrome P450, family 2, subfamily c, polypeptide 39	protein-coding
mm_109398.1	chr12	109947196	109947212	+	1	NA	Intergenic	Intergenic	199326	NR_037233	100499517		NR_037233	ENSMUSG00000093351	Mir3072	mir-3072|mmu-mir-3072	microRNA 3072	ncRNA
mm_113373.1	chr13	33004159	33004161	+	1	NA	promoter-TSS (NM_009256)	promoter-TSS (NM_009256)	-381	NM_009256	20723	Mm.245041	NM_009256	ENSMUSG00000045827	Serpinb9	BB283241|CAP-3|CAP3|PI-9|PI9|Spi6|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 9	protein-coding
mm_61816.1	chr7	87304289	87304305	+	1	NA	intron (NM_015760, intron 4 of 17)	intron (NM_015760, intron 4 of 17)	57648	NM_001285833	50490	Mm.31748	NM_015760	ENSMUSG00000030562	Nox4	AI648021	NADPH oxidase 4	protein-coding
mm_24746.1	chr3	95318783	95318793	+	1	NA	promoter-TSS (NM_001320492)	promoter-TSS (NM_001320492)	-42	NM_001320492	76893	Mm.181009	NM_029789	ENSMUSG00000015714	Cers2	0610013I17Rik|AI225939|Lass2|TRH3	ceramide synthase 2	protein-coding
mm_96303.1	chr11	63158344	63158368	+	1	NA	exon (NM_008885, exon 5 of 5)	exon (NM_008885, exon 5 of 5)	25553	NM_001302260	18858	Mm.1237	NM_008885	ENSMUSG00000018217	Pmp22	22kDa|Gas-3|HNPP|Tr|trembler	peripheral myelin protein 22	protein-coding
mm_17971.1	chr2	37592728	37592731	-	1	NA	intron (NM_009261, intron 14 of 16)	intron (NM_009261, intron 14 of 16)	54556	NM_009261	20744	Mm.237095	NM_009261	ENSMUSG00000026915	Strbp	6430510M02Rik|AI852513|C230082I21Rik|C86322|Spnr	spermatid perinuclear RNA binding protein	protein-coding
mm_94303.1	chr11	4160509	4160518	+	1	NA	promoter-TSS (NM_177616)	promoter-TSS (NM_177616)	159	NM_026175	67465	Mm.156914	NM_026175	ENSMUSG00000002129	Sf3a1	1200014H24Rik|5930416L09Rik|AI159724	splicing factor 3a, subunit 1	protein-coding
mm_10958.1	chr2	25682726	25682746	+	1	NA	promoter-TSS (NM_178036)	promoter-TSS (NM_178036)	10	NM_178036	332578	Mm.246797	NM_178036	ENSMUSG00000047356	Lcn10	9230112J07Rik	lipocalin 10	protein-coding
mm_98584.1	chr11	95748583	95748602	+	1	NA	promoter-TSS (NM_201609)	promoter-TSS (NM_201609)	-475	NM_201609	268469	Mm.389038	NM_201609	ENSMUSG00000075595	Zfp652	9530033F24Rik|ZNF652	zinc finger protein 652	protein-coding
mm_166468.1	chr5	142742191	142742195	-	1	NA	intron (NM_001122730, intron 17 of 27)	intron (NM_001122730, intron 17 of 27)	40092	NM_146257	243328	Mm.125942	NM_146257	ENSMUSG00000050822	Slc29a4	ENT4|mPMAT	solute carrier family 29 (nucleoside transporters), member 4	protein-coding
mm_54166.1	chr6	23132921	23132956	-	1	NA	promoter-TSS (NM_013930)	promoter-TSS (NM_013930)	48	NM_013930	30956	Mm.18651	NM_013930	ENSMUSG00000029695	Aass	LKR|LKR/SDH|LOR|LOR/SDH|Lorsdh|SDH	aminoadipate-semialdehyde synthase	protein-coding
mm_124908.1	chr15	10992370	10992370	+	1	NA	intron (NM_008537, intron 4 of 4)	L1M4|LINE|L1	-8351	NM_053077	22293	Mm.138278	NM_053077	ENSMUSG00000022243	Slc45a2	Aim-1|Aim1|Dbr|Matp|Oca4|blanc-sale|bls|uw	solute carrier family 45, member 2	protein-coding
mm_116881.1	chr13	55100217	55100242	-	1	NA	promoter-TSS (NM_001293660)	promoter-TSS (NM_001293660)	66	NM_011307	20184	Mm.259301	NM_011307	ENSMUSG00000025878	Uimc1	9430016E08Rik|D330018D10Rik|D630032M02Rik|RIP110|Rxrip110	ubiquitin interaction motif containing 1	protein-coding
mm_46324.1	chr5	100798568	100798610	-	1	NA	promoter-TSS (NM_026826)	promoter-TSS (NM_026826)	11	NM_001081107	191578	Mm.21469	NM_180984	ENSMUSG00000035266	Helq	AU021725|D430018E21Rik|Hel308	helicase, POLQ-like	protein-coding
mm_68635.1	chr7	118243526	118243536	-	1	NA	promoter-TSS (NR_027879)	promoter-TSS (NR_027879)	106	NM_001031814	233789	Mm.309053	NM_177180	ENSMUSG00000030655	Smg1	2610207I05Rik|5430435M13Rik|C130002K18Rik|mKIAA0421	SMG1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)	protein-coding
mm_87117.1	chr10	33256580	33256611	+	1	NA	promoter-TSS (NR_040657)	promoter-TSS (NR_040657)	-238	NR_040657	442820	Mm.490725	NR_040657		D830005E20Rik	-	RIKEN cDNA D830005E20 gene	ncRNA
mm_35184.1	chr4	15958347	15958357	-	1	NA	intron (NM_013752, intron 1 of 15)	CpG	385	NM_013752	27354	Mm.20866	NM_013752	ENSMUSG00000028224	Nbn	Nbs1	nibrin	protein-coding
mm_131102.1	chr16	5007307	5007341	+	1	NA	promoter-TSS (NM_001253803)	promoter-TSS (NM_001253803)	8	NR_045596	432995	Mm.271618	NM_001253796	ENSMUSG00000096215	Smim22	EG432995|Gm5480	small integral membrane protein 22	protein-coding
mm_102203.1	chr11	54764182	54764207	-	1	NA	intron (NM_178626, intron 1 of 5)	intron (NM_178626, intron 1 of 5)	23509	NM_178626	72729	Mm.29476	NM_178626	ENSMUSG00000052298	Cdc42se2	2810404F18Rik|AA408783|AA536669|SPEC2	CDC42 small effector 2	protein-coding
mm_30882.1	chr4	32247758	32247764	+	1	NA	Intergenic	Intergenic	-169674	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_89474.1	chr10	93516967	93516971	+	1	NA	TTS (NM_010401)	TTS (NM_010401)	23064	NM_027908	71761	Mm.244518	NM_027908	ENSMUSG00000015890	Amdhd1	1300019J08Rik	amidohydrolase domain containing 1	protein-coding
mm_92511.1	chr10	78427616	78427623	-	1	NA	TTS (NM_007793)	TTS (NM_007793)	1949	NM_007793	13014	Mm.6095	NM_007793	ENSMUSG00000005054	Cstb	AA960480|Stfb	cystatin B	protein-coding
mm_70880.1	chr8	25200459	25200463	+	1	NA	intron (NM_177089, intron 1 of 12)	intron (NM_177089, intron 1 of 12)	1081	NM_199323	320165	Mm.308452	NM_177089	ENSMUSG00000065954	Tacc1	4833447E04Rik|AA960202|B230378H13Rik	transforming, acidic coiled-coil containing protein 1	protein-coding
mm_98049.1	chr11	85739907	85739917	+	1	NA	intron (NM_138681, intron 24 of 25)	intron (NM_138681, intron 24 of 25)	-20168	NR_045875	71489	Mm.442482	NR_045875	ENSMUSG00000086199	Bcas3os1	8430403D17Rik	breast carcinoma amplified sequence 3, opposite strand 1	ncRNA
mm_24657.1	chr3	94478323	94478343	+	1	NA	promoter-TSS (NM_001289613)	promoter-TSS (NM_001289613)	38	NM_001289620	78784	Mm.44292	NM_172434	ENSMUSG00000028137	Celf3	4930415M08Rik|BRUNOL1|CAGH4|ERDA4|Tnrc4	CUGBP, Elav-like family member 3	protein-coding
mm_32289.1	chr4	103114403	103114445	+	1	NA	promoter-TSS (NM_027696)	promoter-TSS (NM_027696)	34	NM_001286222	71148	Mm.288721	NM_027696	ENSMUSG00000028522	Mier1	4933425I22Rik|5830411K19Rik|er1	MEIR1 treanscription regulator	protein-coding
mm_45983.1	chr5	90476515	90476523	-	1	NA	TTS (NM_009654)	TTS (NM_009654)	-14195	NM_007423	11576	Mm.358570	NM_007423	ENSMUSG00000054932	Afp	-	alpha fetoprotein	protein-coding
mm_145636.1	chr18	61112750	61112771	+	1	NA	exon (NM_001037859, exon 6 of 22)	exon (NM_001037859, exon 6 of 22)	-4708	NR_105949	102466212		NR_105949	ENSMUSG00000098389	Mir6983	Gm27496|mmu-mir-6983	microRNA 6983	ncRNA
mm_128842.1	chr15	69234992	69234999	-	1	NA	Intergenic	Intergenic	-35538	NR_130983	75076		NR_130983		4930504C09Rik	-	RIKEN cDNA 4930504C09 gene	ncRNA
mm_16627.1	chr2	5682033	5682037	-	1	NA	intron (NM_001290374, intron 1 of 9)	MER21C|LTR|ERVL	-5989	NM_001290376	227541	Mm.191949	NM_177343	ENSMUSG00000039145	Camk1d	A630059D12Rik|CKLiK|CaMKIdelta|E030025C11Rik|mCKLiK	calcium/calmodulin-dependent protein kinase ID	protein-coding
mm_31874.1	chr4	80834331	80834355	+	1	NA	5' UTR (NM_031202, exon 1 of 8)	5' UTR (NM_031202, exon 1 of 8)	130	NM_001282015	22178	Mm.30438	NM_031202	ENSMUSG00000005994	Tyrp1	Oca3|TRP-1|TRP1|Tyrp|b|brown|isa	tyrosinase-related protein 1	protein-coding
mm_66124.1	chr7	31053557	31053567	-	1	NA	intron (NM_052991, intron 3 of 7)	GA-rich|Low_complexity|Low_complexity	1291	NM_052991	56188	Mm.1491	NM_019503	ENSMUSG00000036570	Fxyd1	0610012C17Rik|1110006M24Rik|Plm|Pml	FXYD domain-containing ion transport regulator 1	protein-coding
mm_29623.1	chr3	121532205	121532215	-	1	NA	5' UTR (NM_145394, exon 1 of 15)	5' UTR (NM_145394, exon 1 of 15)	134	NM_145394	213603	Mm.33062	NM_145394	ENSMUSG00000039865	Slc44a3	BC010552	solute carrier family 44, member 3	protein-coding
mm_70431.1	chr8	11556062	11556099	+	1	NA	promoter-TSS (NM_001302457)	promoter-TSS (NM_001302457)	15	NM_001302460	26356	Mm.25709	NM_011919	ENSMUSG00000045969	Ing1	2610028J21Rik|AA407184|AI875420|mING1h|p33Ing1|p37Ing1b	inhibitor of growth family, member 1	protein-coding
mm_41380.1	chr5	90723507	90723519	+	1	NA	Intergenic	Intergenic	-35785	NM_009141	20311	Mm.4660	NM_009141	ENSMUSG00000029371	Cxcl5	AMCF-II|Cxcl6|ENA-78|GCP-2|LIX|Scyb5|Scyb6	chemokine (C-X-C motif) ligand 5	protein-coding
mm_92067.1	chr10	62527439	62527459	-	1	NA	Intergenic	Intergenic	-19694	NM_011157	19073	Mm.338790	NM_011157	ENSMUSG00000020077	Srgn	Prg|Prg1|Sgc	serglycin	protein-coding
mm_4523.1	chr1	175632065	175632094	+	1	NA	promoter-TSS (NM_133809)	promoter-TSS (NM_133809)	-114	NM_133809	98256	Mm.27217	NM_133809	ENSMUSG00000039783	Kmo	AI046660	kynurenine 3-monooxygenase (kynurenine 3-hydroxylase)	protein-coding
mm_60629.1	chr7	44748907	44748928	+	1	NA	promoter-TSS (NM_178734)	promoter-TSS (NM_178734)	288	NM_133945	101568	Mm.28816	NM_133945	ENSMUSG00000002205	Vrk3	AI428238	vaccinia related kinase 3	protein-coding
mm_17438.1	chr2	27596360	27596381	-	1	NA	Intergenic	Intergenic	-80831	NM_011305	20181	Mm.24624	NM_011305	ENSMUSG00000015846	Rxra	9530071D11Rik|Nr2b1|RXRalpha1	retinoid X receptor alpha	protein-coding
mm_132209.1	chr16	32608974	32608990	+	1	NA	promoter-TSS (NM_011638)	promoter-TSS (NM_011638)	86	NM_011638	22042	Mm.28683	NM_011638	ENSMUSG00000022797	Tfrc	2610028K12Rik|CD71|E430033M20Rik|Mtvr1|TFR|TFR1|TR|Trfr|p90	transferrin receptor	protein-coding
mm_125622.1	chr15	61988165	61988173	+	1	NA	exon (NM_001177354, exon 2 of 3)	exon (NM_001177354, exon 2 of 3)	2828	NM_001177352	17869	Mm.2444	NM_010849	ENSMUSG00000022346	Myc	AU016757|Myc2|Niard|Nird|bHLHe39	myelocytomatosis oncogene	protein-coding
mm_34108.1	chr4	139192967	139192994	+	1	NA	promoter-TSS (NM_009798)	promoter-TSS (NM_009798)	81	NM_001037761	12345	Mm.2945	NM_009798	ENSMUSG00000028745	Capzb	1700120C01Rik|AI325129|CPB1|CPB2|CPbeat2|CPbeta1|CPbeta2|Cappb1	capping protein (actin filament) muscle Z-line, beta	protein-coding
mm_25200.1	chr3	103787491	103787497	+	1	NA	intron (NM_001301304, intron 1 of 15)	intron (NM_001301304, intron 1 of 15)	3781	NM_001301306	15257	Mm.20827	NM_010432	ENSMUSG00000008730	Hipk1	1110062K04Rik|Myak	homeodomain interacting protein kinase 1	protein-coding
mm_25786.1	chr3	126780398	126780407	+	1	NA	exon (NM_001293663, exon 7 of 20)	exon (NM_001293663, exon 7 of 20)	162984	NM_001034168	109676	Mm.220242	NM_178655	ENSMUSG00000032826	Ank2	100043364|AI835472|AW491075|Ank-2|Gm4392	ankyrin 2, brain	protein-coding
mm_141761.1	chr17	34269225	34269263	-	1	NA	3' UTR (NM_207105, exon 6 of 6)	3' UTR (NM_207105, exon 6 of 6)	6017	NM_207105	14961	Mm.254067	NM_207105	ENSMUSG00000073421	H2-Ab1	AI845868|Abeta|H-2Ab|H2-Ab|I-Abeta|IAb|Ia-2|Ia2|Rmcs1	histocompatibility 2, class II antigen A, beta 1	protein-coding
mm_83028.1	chr9	37255382	37255392	-	1	NA	5' UTR (NM_001145960, exon 1 of 19)	5' UTR (NM_001145960, exon 1 of 19)	351	NM_020258	56857	Mm.440037	NM_020258	ENSMUSG00000032122	Slc37a2	G3PP|Slc37a1|cI-2|ci2	solute carrier family 37 (glycerol-3-phosphate transporter), member 2	protein-coding
mm_54848.1	chr6	42589868	42589871	-	1	NA	exon (NM_203396, exon 6 of 7)	exon (NM_203396, exon 6 of 7)	7503	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_155982.1	chrX	106127110	106127120	+	1	NA	3' UTR (NM_009726, exon 23 of 23)	3' UTR (NM_009726, exon 23 of 23)	-16160	NM_205820	279572	Mm.336203	NM_205820	ENSMUSG00000033777	Tlr13	AI666735|Gm713	toll-like receptor 13	protein-coding
mm_34016.1	chr4	137994772	137994817	+	1	NA	intron (NM_172703, intron 2 of 34)	intron (NM_172703, intron 2 of 34)	1338	NM_172703	230861	Mm.268903	NM_172703	ENSMUSG00000028760	Eif4g3	1500002J22Rik|4930523M17Rik|G1-419-52|eIF4GII|repro8	eukaryotic translation initiation factor 4 gamma, 3	protein-coding
mm_57991.1	chr6	136172313	136172323	-	1	NA	intron (NM_008171, intron 2 of 14)	intron (NM_008171, intron 2 of 14)	1193	NM_008171	14812	Mm.436649	NM_008171	ENSMUSG00000030209	Grin2b	AW490526|GluN2B|NR2B|Nmdar2b	glutamate receptor, ionotropic, NMDA2B (epsilon 2)	protein-coding
mm_16355.1	chr2	174427493	174427497	+	1	NA	TTS (NM_022325)	TTS (NM_022325)	11544	NM_022325	64138	Mm.156919	NM_022325	ENSMUSG00000016256	Ctsz	AI787083|AU019819|CTSX|D2Wsu143e	cathepsin Z	protein-coding
mm_24176.1	chr3	88575894	88575934	+	1	NA	Intergenic	RLTR11A2|LTR|ERVK	-3757	NM_025448	66256	Mm.7091	NM_025448	ENSMUSG00000041355	Ssr2	1500032E05Rik|AI315033|AU020133|TLAP|TRAPB|TRAPbeta	signal sequence receptor, beta	protein-coding
mm_148830.1	chr19	6341747	6341793	+	1	NA	TTS (NM_001168489)	TTS (NM_001168489)	610	NR_117093	26412	Mm.25860	NM_009006	ENSMUSG00000024948	Map4k2	AI385662|BL44|GCK|Rab8ip	mitogen-activated protein kinase kinase kinase kinase 2	protein-coding
mm_45877.1	chr5	88328158	88328172	-	1	NA	exon (NM_008644, exon 3 of 3)	exon (NM_008644, exon 3 of 3)	10853	NM_008644	17830	Mm.200411	NM_008644	ENSMUSG00000064156	Prol1	Muc10	proline rich, lacrimal 1	protein-coding
mm_9488.1	chr1	173729315	173729321	-	1	NA	exon (NM_001204910, exon 5 of 8)	exon (NM_001204910, exon 5 of 8)	12491	NM_001204910	226691	Mm.440876	NM_001204910	ENSMUSG00000073490	Ifi207	AI607873|Pyhin-A	interferon activated gene 207	protein-coding
mm_34323.1	chr4	141844301	141844310	+	1	NA	promoter-TSS (NR_040641)	promoter-TSS (NR_040641)	-16	NR_040641	69139	Mm.491056	NR_040641	ENSMUSG00000086818	Ctrcos	1810035I16Rik	chymotrypsin C (caldecrin), opposite strand	ncRNA
mm_125904.1	chr15	75982039	75982061	+	1	NA	exon (NM_001163518, exon 1 of 1)	exon (NM_001163518, exon 1 of 1)	235	NM_001163518	223648	Mm.17610	NM_146059	ENSMUSG00000098176	Ccdc166	2410075B13Rik	coiled-coil domain containing 166	protein-coding
mm_122962.1	chr14	54970733	54970765	-	1	NA	TTS (NM_080728)	TTS (NM_080728)	1962	NR_033497	791403	Mm.319176	NR_033497	ENSMUSG00000097652	Mhrt	D830015G02Rik|ENSMUSG00000053118|Myheart	myosin heavy chain associated RNA transcript	ncRNA
mm_7933.1	chr1	133912322	133912343	-	1	NA	3' UTR (NM_054077, exon 3 of 3)	3' UTR (NM_054077, exon 3 of 3)	-4333	NM_001160420	269120	Mm.59985	NM_054076	ENSMUSG00000010311	Optc	-	opticin	protein-coding
mm_116460.1	chr13	43304300	43304309	-	1	NA	promoter-TSS (NM_001033399)	promoter-TSS (NM_001033399)	-132	NM_001033399	328232	Mm.441399	NM_001033399	ENSMUSG00000051335	Gfod1	9630032O13|AI850995	glucose-fructose oxidoreductase domain containing 1	protein-coding
mm_5278.1	chr1	20511704	20511706	-	1	NA	intron (NM_153179, intron 33 of 66)	intron (NM_153179, intron 33 of 66)	106352	NM_153179	241035	Mm.249253	NM_153179	ENSMUSG00000043760	Pkhd1	AI118496|AI182499|FPC|Tigm1	polycystic kidney and hepatic disease 1	protein-coding
mm_147055.1	chr18	34940882	34940894	-	1	NA	exon (NM_010481, exon 12 of 17)	exon (NM_010481, exon 12 of 17)	-8885	NM_144866	225363	Mm.329353	NM_144866	ENSMUSG00000024360	Etf1	AI463371|D6Ertd109e|ERF|ERF1|SUP45L1|TB3-1	eukaryotic translation termination factor 1	protein-coding
mm_150011.1	chr19	29334398	29334407	+	1	NA	exon (NM_011272, exon 1 of 2)	exon (NM_011272, exon 1 of 2)	268	NM_011272	19773	Mm.5033	NM_011272	ENSMUSG00000039097	Rln1	Rln|rlx	relaxin 1	protein-coding
mm_144954.1	chr18	37812871	37812897	+	1	NA	intron (NM_033581, intron 1 of 3)	RLTR20A4|LTR|ERVK	-2195	NM_033582	93707	Mm.247203	NM_033582	ENSMUSG00000023036	Pcdhgc4	-	protocadherin gamma subfamily C, 4	protein-coding
mm_36905.1	chr4	107923509	107923517	-	1	NA	promoter-TSS (NM_009949)	promoter-TSS (NM_009949)	76	NM_009949	12896	Mm.307620	NM_009949	ENSMUSG00000028607	Cpt2	AI323697|CPTII	carnitine palmitoyltransferase 2	protein-coding
mm_170585.1	chr19	5798951	5798952	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	-2970	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_46094.1	chr5	92347227	92347237	-	1	NA	3' UTR (NM_021274, exon 4 of 4)	3' UTR (NM_021274, exon 4 of 4)	1657	NM_021274	15945	Mm.877	NM_021274	ENSMUSG00000034855	Cxcl10	C7|CRG-2|INP10|IP-10|IP10|Ifi10|Scyb10|gIP-10|mob-1	chemokine (C-X-C motif) ligand 10	protein-coding
mm_73177.1	chr8	95056684	95056696	+	1	NA	exon (NM_001042715, exon 3 of 18)	exon (NM_001042715, exon 3 of 18)	1587	NM_001042715	330830	Mm.277112	NM_001042715	ENSMUSG00000031786	Drc7	Ccdc135|Gm770|SRG-L|SRG-S	dynein regulatory complex subunit 7	protein-coding
mm_161313.1	chr14	43347811	43347811	-	1	NA	promoter-TSS (NM_027940)	promoter-TSS (NM_027940)	0	NM_027940	71826	Mm.335855	NM_027940	ENSMUSG00000095384	1700001F09Rik	Gm10377	RIKEN cDNA 1700001F09 gene	protein-coding
mm_107274.1	chr12	29533478	29533492	+	1	NA	intron (NM_001093778, intron 1 of 24)	intron (NM_001093778, intron 1 of 24)	-1420	NM_001093776	17933	Mm.253067	NM_008666	ENSMUSG00000061911	Myt1l	2900046C06Rik|2900093J19Rik|C630034G21Rik|Nztf1|Pmng1|Png-1|mKIAA1106	myelin transcription factor 1-like	protein-coding
mm_68888.1	chr7	126448036	126448041	-	1	NA	exon (NM_007504, exon 17 of 23)	exon (NM_007504, exon 17 of 23)	15035	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_79631.1	chr9	59486746	59486767	+	1	NA	promoter-TSS (NM_019927)	promoter-TSS (NM_019927)	-382	NM_019927	23806	Mm.305925	NM_019927	ENSMUSG00000025234	Arih1	AU021774|Ari|Ari1|Hari|Hhari|Ubch7bp|Uip77	ariadne RBR E3 ubiquitin protein ligase 1	protein-coding
mm_163187.1	chr11	94677358	94677379	-	1	NA	exon (NM_145828, exon 1 of 11)	exon (NM_145828, exon 1 of 11)	125	NM_145828	217119	Mm.100638	NM_145828	ENSMUSG00000020868	Xylt2	E030002B02Rik|XT-II|XT2|xylT-II	xylosyltransferase II	protein-coding
mm_122736.1	chr14	53863318	53863320	-	1	NA	Intergenic	Intergenic	390610	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_1474.1	chr1	70568955	70568956	+	1	NA	intron (NM_029160, intron 16 of 16)	intron (NM_029160, intron 16 of 16)	-156760	NM_177164	320460	Mm.360649	NM_177164	ENSMUSG00000045648	Vwc2l	A830006F12Rik|Brl	von Willebrand factor C domain-containing protein 2-like	protein-coding
mm_13868.1	chr2	119799726	119799760	+	1	NA	5' UTR (NM_019392, exon 1 of 19)	5' UTR (NM_019392, exon 1 of 19)	229	NM_019392	22174	Mm.2901	NM_019392	ENSMUSG00000027298	Tyro3	AI323366|Brt|Dtk|Etk-2|Rse|Sky|TK19-2|Tif|etk2/tyro3|tk19-1	TYRO3 protein tyrosine kinase 3	protein-coding
mm_25654.1	chr3	121531592	121531600	+	1	NA	intron (NM_145394, intron 2 of 14)	intron (NM_145394, intron 2 of 14)	748	NM_145394	213603	Mm.33062	NM_145394	ENSMUSG00000039865	Slc44a3	BC010552	solute carrier family 44, member 3	protein-coding
mm_78315.1	chr9	23401012	23401013	+	1	NA	intron (NM_028472, intron 12 of 14)	intron (NM_028472, intron 12 of 14)	177936	NM_028472	73230	Mm.335020	NM_028472	ENSMUSG00000031963	Bmper	3110056H04Rik|CV-2|Crim3|Cv2	BMP-binding endothelial regulator	protein-coding
mm_117439.1	chr13	74734196	74734207	-	1	NA	promoter-TSS (NM_001301181)	promoter-TSS (NM_001301181)	60	NM_001301158	12380	Mm.29163	NM_009817	ENSMUSG00000021585	Cast	-	calpastatin	protein-coding
mm_19447.1	chr2	91982911	91982924	-	1	NA	3' UTR (NM_011957, exon 12 of 12)	3' UTR (NM_011957, exon 12 of 12)	-19354	NM_138306	104418	Mm.314923	NM_138306	ENSMUSG00000040479	Dgkz	E130307B02Rik|ENSMUSG00000075035|F730209L11Rik|mDGK[z]	diacylglycerol kinase zeta	protein-coding
mm_148716.1	chr19	5815362	5815383	+	1	NA	Intergenic	YREP_Mm|Unknown|Unknown	-12700	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_69197.1	chr7	127345583	127345609	-	1	NA	promoter-TSS (NM_146202)	promoter-TSS (NM_146202)	-282	NM_146202	233890	Mm.23031	NM_146202	ENSMUSG00000047371	Zfp768	BC026432|Znf768	zinc finger protein 768	protein-coding
mm_158943.1	chr1	81077018	81077018	+	1	NA	promoter-TSS (NM_172849)	promoter-TSS (NM_172849)	-299	NM_172849	241134	Mm.313904	NM_172849	ENSMUSG00000054976	Nyap2	9430031J16Rik|Jr6|Kiaa1486	neuronal tyrosine-phophorylated phosphoinositide 3-kinase adaptor 2	protein-coding
mm_40545.1	chr5	58035388	58035391	+	1	NA	intron (NM_001310608, intron 3 of 3)	intron (NM_001310608, intron 3 of 3)	317308	NM_018764	54216	Mm.332387	NM_018764	ENSMUSG00000029108	Pcdh7	-	protocadherin 7	protein-coding
mm_134796.1	chr16	24199894	24199926	-	1	NA	Intergenic	Intergenic	-193440	NM_178665	210126	Mm.209385	NM_178665	ENSMUSG00000033306	Lpp	9430020K16Rik|AA959454|AU024130|B130055L10Rik|C79715|D630048H16	LIM domain containing preferred translocation partner in lipoma	protein-coding
mm_137397.1	chr17	25828792	25828826	+	1	NA	promoter-TSS (NM_028101)	promoter-TSS (NM_028101)	-234	NM_028101	72106	Mm.277599	NM_028101	ENSMUSG00000025736	Jmjd8	2610003J06Rik	jumonji domain containing 8	protein-coding
mm_166616.1	chr6	71396107	71396116	-	1	NA	intron (NM_024288, intron 7 of 8)	intron (NM_024288, intron 7 of 8)	22684	NM_001081110	12525	Mm.1858	NM_009857	ENSMUSG00000053977	Cd8a	BB154331|Ly-2|Ly-35|Ly-B|Lyt-2	CD8 antigen, alpha chain	protein-coding
mm_115804.1	chr13	19358138	19358148	-	1	NA	intron (NM_024270, intron 8 of 8)	intron (NM_024270, intron 8 of 8)	37670	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_69754.1	chr7	140956297	140956315	-	1	NA	promoter-TSS (NM_030694)	promoter-TSS (NM_030694)	-345	NM_030694	80876	Mm.379266	NM_030694	ENSMUSG00000060591	Ifitm2	DSPA2c|Ifitm3l|fragilis3|mil-3	interferon induced transmembrane protein 2	protein-coding
mm_30579.1	chr4	5153048	5153053	+	1	NA	Intergenic	L1Md_F2|LINE|L1	-359744	NM_177730	242291	Mm.218889	NM_177730	ENSMUSG00000066324	Impad1	1110001C20Rik|AA408880|AI451589|AL022796|B230207P20|Jaws|gPAPP	inositol monophosphatase domain containing 1	protein-coding
mm_74540.1	chr8	9976267	9976286	-	1	NA	promoter-TSS (NM_176953)	promoter-TSS (NM_176953)	47	NM_176953	319583	Mm.80584	NM_176953	ENSMUSG00000049717	Lig4	5830471N16Rik|tiny	ligase IV, DNA, ATP-dependent	protein-coding
mm_2529.1	chr1	106934481	106934494	+	1	NA	promoter-TSS (NM_027971)	promoter-TSS (NM_027971)	38	NM_027971	71869	Mm.321740	NM_027971	ENSMUSG00000059956	Serpinb12	2300003F07Rik|4833409F13Rik	serine (or cysteine) peptidase inhibitor, clade B (ovalbumin), member 12	protein-coding
mm_113512.1	chr13	37778439	37778468	+	1	NA	Intergenic	CpG	-47585	NM_026830	68750	Mm.491109	NM_026830	ENSMUSG00000039087	Rreb1	1110037N09Rik|AA414966|B930013M22Rik	ras responsive element binding protein 1	protein-coding
mm_75047.1	chr8	32820269	32820296	-	1	NA	Intergenic	Intergenic	129744	NM_001177589	100042715	Mm.291093	NM_001177589		Gm3985	-	predicted gene 3985	protein-coding
mm_142316.1	chr17	42876679	42876692	-	1	NA	promoter-TSS (NM_009847)	promoter-TSS (NM_009847)	-261	NM_009847	12488	Mm.218637	NM_009847	ENSMUSG00000061665	Cd2ap	AL024079|C78928|METS-1|Mets1	CD2-associated protein	protein-coding
mm_62423.1	chr7	101324403	101324405	+	1	NA	intron (NM_019990, intron 2 of 6)	MIRc|SINE|MIR	3085	NM_019990	56018	Mm.28896	NM_019990	ENSMUSG00000030688	Stard10	AV048538|CGI-52|NY-C0-28|PC-TP2|PCTP2|Pctpl|Sdccag28|SdccagG28|TISP-81	START domain containing 10	protein-coding
mm_51161.1	chr6	70723875	70723900	+	1	NA	Intergenic	Intergenic	68288	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_35194.1	chr4	16145742	16145753	-	1	NA	intron (NR_138102, intron 4 of 11)	RMER17C2|LTR|ERVK	17896	NM_138952	192656	Mm.112765	NM_138952	ENSMUSG00000041135	Ripk2	2210420D18Rik|CARD3|CARDIAK|CCK|D4Bwg0615e|RICK|RIP2	receptor (TNFRSF)-interacting serine-threonine kinase 2	protein-coding
mm_120171.1	chr14	60784681	60784694	+	1	NA	non-coding (NR_040642, exon 1 of 20)	non-coding (NR_040642, exon 1 of 20)	121	NR_040642	70478	Mm.274650	NM_027436	ENSMUSG00000021993	Mipep	5730405E07Rik|MIP	mitochondrial intermediate peptidase	protein-coding
mm_5311.1	chr1	22509376	22509397	-	1	NA	intron (NM_001012623, intron 8 of 14).2	intron (NM_001012623, intron 8 of 14).2	-76543	NM_183018	116837	Mm.60061	NM_053270	ENSMUSG00000041670	Rims1	C030033M19Rik|RIM1|RIM1a|RIM1alpha|Rab3ip1|Rim|Serg1|mKIAA0340	regulating synaptic membrane exocytosis 1	protein-coding
mm_42285.1	chr5	114323347	114323358	+	1	NA	exon (NM_001164573, exon 5 of 31)	exon (NM_001164573, exon 5 of 31)	8411	NM_001164573	231646	Mm.238285	NM_146163	ENSMUSG00000066952	Myo1h	4631401O15Rik	myosin 1H	protein-coding
mm_77818.1	chr9	3335136	3335161	+	1	NA	promoter-TSS (NM_026303)	promoter-TSS (NM_026303)	-83	NM_026303	67667	Mm.116968	NM_026303	ENSMUSG00000025899	Alkbh8	4930562C03Rik|8030431D03Rik|9430088N01Rik|Abh8	alkB homolog 8, tRNA methyltransferase	protein-coding
mm_14556.1	chr2	133856949	133856952	+	1	NA	Intergenic	Intergenic	292242	NR_037273	100526500		NR_037273	ENSMUSG00000093338	Mir3090	mmu-mir-3090	microRNA 3090	ncRNA
mm_118499.1	chr14	13454131	13454145	+	1	NA	5' UTR (NM_001163032, exon 1 of 5)	5' UTR (NM_001163032, exon 1 of 5)	180	NM_001163032	72003	Mm.317515	NM_028052	ENSMUSG00000056296	Synpr	1500003F20Rik|SPO	synaptoporin	protein-coding
mm_157909.1	chrX	78465209	78465213	-	1	NA	intron (NM_027322, intron 3 of 3)	Lx8b|LINE|L1	95568	NM_001177966	74910	Mm.159364	NM_001177966	ENSMUSG00000035651	4930480E11Rik	-	RIKEN cDNA 4930480E11 gene	protein-coding
mm_12005.1	chr2	57267360	57267363	+	1	NA	intron (NM_010274, intron 1 of 16)	intron (NM_010274, intron 1 of 16)	28979	NM_010274	14571	Mm.3711	NM_010274	ENSMUSG00000026827	Gpd2	AA408484|AI448216|AU021455|AW494132|GPDH|Gdm1|Gpd-m|Gpdh-m|TISP38	glycerol phosphate dehydrogenase 2, mitochondrial	protein-coding
mm_5978.1	chr1	57970105	57970118	-	1	NA	promoter-TSS (NM_001159864)	promoter-TSS (NM_001159864)	-27	NM_001159865	51960	Mm.339711	NM_030211	ENSMUSG00000054770	Kctd18	4932411A20Rik|6530404F10Rik	potassium channel tetramerisation domain containing 18	protein-coding
mm_143165.1	chr17	57225264	57225321	-	1	NA	exon (NM_009778, exon 5 of 41)	exon (NM_009778, exon 5 of 41)	2844	NM_009778	12266	Mm.19131	NM_009778	ENSMUSG00000024164	C3	AI255234|ASP|HSE-MSF|Plp	complement component 3	protein-coding
mm_126925.1	chr15	91673083	91673105	+	1	NA	promoter-TSS (NM_025730)	promoter-TSS (NM_025730)	-130	NM_025730	66725	Mm.37558	NM_025730	ENSMUSG00000036273	Lrrk2	4921513O20Rik|9330188B09Rik|AW561911|D630001M17Rik|Gm927|cI-46	leucine-rich repeat kinase 2	protein-coding
mm_130066.1	chr15	89196444	89196454	-	1	NA	promoter-TSS (NM_027081)	promoter-TSS (NM_027081)	25	NM_027081	69440	Mm.482128	NM_027081	ENSMUSG00000015377	Dennd6b	1700027J05Rik|AI414881|Fam116b	DENN/MADD domain containing 6B	protein-coding
mm_27683.1	chr3	65958237	65958252	-	1	NA	promoter-TSS (NM_019937)	promoter-TSS (NM_019937)	-19	NM_019937	56706	Mm.175612	NM_019937	ENSMUSG00000027829	Ccnl1	2610030E23Rik|AU018493|Ccnl|ania-6a	cyclin L1	protein-coding
mm_88445.1	chr10	77547822	77547829	+	1	NA	intron (NM_008404, intron 5 of 15)	B2_Mm2|SINE|B2	17477	NM_008404	16414	Mm.1137	NM_008404	ENSMUSG00000000290	Itgb2	2E6|AI528527|Cd18|LAD|LCAMB|Lfa1|MF17	integrin beta 2	protein-coding
mm_15731.1	chr2	164236926	164236958	+	1	NA	exon (NM_017390, exon 2 of 3)	exon (NM_017390, exon 2 of 3)	1399	NM_017390	53878	Mm.99395	NM_017390	ENSMUSG00000040132	Svs2	BB115391|Semg1|SvsII	seminal vesicle secretory protein 2	protein-coding
mm_18585.1	chr2	66409932	66409948	-	1	NA	intron (NM_018733, intron 1 of 26)	intron (NM_018733, intron 1 of 26)	30897	NM_018733	20265	Mm.439704	NM_018733	ENSMUSG00000064329	Scn1a	B230332M13|Nav1.1	sodium channel, voltage-gated, type I, alpha	protein-coding
mm_148639.1	chr19	5474912	5474938	+	1	NA	5' UTR (NM_001164352, exon 1 of 10)	5' UTR (NM_001164352, exon 1 of 10)	190	NM_001164352	58859	Mm.276367	NM_021474	ENSMUSG00000024909	Efemp2	0610011K11Rik|Fbln4|MBP1	epidermal growth factor-containing fibulin-like extracellular matrix protein 2	protein-coding
mm_69036.1	chr7	126798787	126798804	-	1	NA	intron (NM_001177307, intron 1 of 9)	intron (NM_001177307, intron 1 of 9)	383	NM_001177307	11674	Mm.275831	NM_007438	ENSMUSG00000030695	Aldoa	Aldo-1|Aldo1	aldolase A, fructose-bisphosphate	protein-coding
mm_80321.1	chr9	74953075	74953091	+	1	NA	promoter-TSS (NM_001113283)	promoter-TSS (NM_001113283)	30	NM_001113283	235493	Mm.208955	NM_153584	ENSMUSG00000034858	Fam214a	6330415I01Rik|AI553555|C130047D21Rik|Kiaa1370|mKIAA1370	family with sequence similarity 214, member A	protein-coding
mm_135905.1	chr16	67197538	67197542	-	1	NA	intron (NM_178721, intron 1 of 9)	intron (NM_178721, intron 1 of 9)	423368	NM_001347247	239857	Mm.394300	NM_178721	ENSMUSG00000064115	Cadm2	2900078E11Rik|9330131D06|A830029E02Rik|Igdf4d|Igsf4d|NECL3|SynCAM 2|SynCAM2	cell adhesion molecule 2	protein-coding
mm_120810.1	chr14	75016049	75016074	+	1	NA	promoter-TSS (NM_198642)	promoter-TSS (NM_198642)	34	NM_198642	271221	Mm.320280	NM_198642	ENSMUSG00000034959	Rubcnl	5031414D18Rik|Gm744|Gm911|Kiaa0226l	RUN and cysteine rich domain containing beclin 1 interacting protein like	protein-coding
mm_28331.1	chr3	89382930	89382937	-	1	NA	intron (NM_009565, intron 1 of 2)	intron (NM_009565, intron 1 of 2)	-8931	NR_040403	545539	Mm.393389	NR_040403	ENSMUSG00000074466	Gm15417	ENSMUSG00000074466|OTTMUSG00000021274	predicted gene 15417	ncRNA
mm_42444.1	chr5	115430581	115430629	+	1	NA	intron (NM_008629, intron 2 of 14)	CpG-11404	920	NM_008629	17690	Mm.5077	NM_008629	ENSMUSG00000054256	Msi1	Msi1h|Musahi1|m-Msi-1	musashi RNA-binding protein 1	protein-coding
mm_76168.1	chr8	82389946	82389990	-	1	NA	intron (NM_001254747, intron 1 of 7)	PB1D10|SINE|Alu	12618	NM_001254747	16168	Mm.4392	NM_008357	ENSMUSG00000031712	Il15	AI503618|IL-15	interleukin 15	protein-coding
mm_126313.1	chr15	79671074	79671133	+	1	NA	intron (NM_172609, intron 1 of 3)	CpG	235	NM_172609	223696	Mm.246435	NM_172609	ENSMUSG00000022427	Tomm22	2310047D01|Tom22	translocase of outer mitochondrial membrane 22 homolog (yeast)	protein-coding
mm_101566.1	chr11	34207563	34207572	-	1	NA	exon (NM_023907, exon 1 of 2)	exon (NM_023907, exon 1 of 2)	522	NM_023907	14233	Mm.32926	NM_023907	ENSMUSG00000047861	Foxi1	5830401E05Rik|FREAC6|Fkh10|HFH-3|Hfh3	forkhead box I1	protein-coding
mm_115264.1	chr13	110633760	110633761	+	1	NA	Intergenic	Intergenic	238716	NM_152804	20620	Mm.380	NM_152804	ENSMUSG00000021701	Plk2	Snk	polo-like kinase 2	protein-coding
mm_79519.1	chr9	57541476	57541479	+	1	NA	3' UTR (NM_001166364, exon 5 of 5)	3' UTR (NM_001166364, exon 5 of 5)	3949	NM_001166364	78323	Mm.25814	NM_175273	ENSMUSG00000032305	Fam219b	2310046O06Rik|AI594866	family with sequence similarity 219, member B	protein-coding
mm_21903.1	chr2	166194316	166194346	-	1	NA	Intergenic	MLTR73|LTR|ERV1	-38648	NM_028072	72043	Mm.1011	NM_028072	ENSMUSG00000006800	Sulf2	2010004N24Rik|AU020235|MSulf-2|mKIAA1247	sulfatase 2	protein-coding
mm_132070.1	chr16	30065309	30065312	+	1	NA	promoter-TSS (NM_008235)	promoter-TSS (NM_008235)	-47	NM_008235	15205	Mm.390859	NM_008235	ENSMUSG00000022528	Hes1	Hry|bHLHb39	hairy and enhancer of split 1 (Drosophila)	protein-coding
mm_38714.1	chr4	145225883	145225888	-	1	NA	intron (NM_011610, intron 3 of 9)	B1F1|SINE|Alu	20985	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_33772.1	chr4	134493622	134493623	+	1	NA	Intergenic	Intergenic	-3139	NM_001285845	71904	Mm.142343	NM_027995	ENSMUSG00000037348	Paqr7	2310021M12Rik|AV001994|BB007237|Mpra|PGLP|mPR	progestin and adipoQ receptor family member VII	protein-coding
mm_49963.1	chr6	40656410	40656420	+	1	NA	exon (NM_001171003, exon 7 of 48)	exon (NM_001171003, exon 7 of 48)	27584	NM_001171003	232714	Mm.33401	NM_001171003	ENSMUSG00000068587	Mgam	6030407P20Rik|MGA	maltase-glucoamylase	protein-coding
mm_91764.1	chr10	51496022	51496060	-	1	NA	exon (NM_013532, exon 8 of 9)	exon (NM_013532, exon 8 of 9)	5143	NM_013532	14728	Mm.34408	NM_013532	ENSMUSG00000062593	Lilrb4a	CD85K|Gp49b|HM18|ILT3|LIR-5|Lilrb4|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4A	protein-coding
mm_172548.1	chr8	101107470	101107475	+	1	NA	Intergenic	L1Md_F3|LINE|L1	1677639	NM_009866	12552	Mm.1571	NM_009866	ENSMUSG00000031673	Cdh11	Cad11|OSF-4	cadherin 11	protein-coding
mm_47347.1	chr5	122560769	122560777	-	1	NA	intron (NM_009879, intron 14 of 18)	intron (NM_009879, intron 14 of 18)	53745	NM_009879	12589	Mm.10125	NM_009879	ENSMUSG00000029469	Ift81	AW060663|Cdv-1|Cdv-1r|Cdv1	intraflagellar transport 81	protein-coding
mm_18268.1	chr2	52326975	52326981	-	1	NA	exon (NM_010889, exon 6 of 157)	exon (NM_010889, exon 6 of 157)	11820	NM_010889	17996	Mm.389247	NM_010889	ENSMUSG00000026950	Neb	AI595938	nebulin	protein-coding
mm_15131.1	chr2	153918392	153918396	+	1	NA	intron (NM_194357, intron 1 of 15)	intron (NM_194357, intron 1 of 15)	164	NM_194357	378700	Mm.55392	NM_194357	ENSMUSG00000068008	Bpifb3	Lplunc3|Rya3	BPI fold containing family B, member 3	protein-coding
mm_65191.1	chr7	19696649	19696674	-	1	NA	exon (NM_009696, exon 4 of 4)	exon (NM_009696, exon 4 of 4)	1737	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_170744.1	chr2	154892829	154892830	-	1	NA	promoter-TSS (NM_026030)	promoter-TSS (NM_026030)	77	NM_026030	67204	Mm.377134	NM_026030	ENSMUSG00000074656	Eif2s2	2810026E11Rik|38kDa|AA408636|AA571381|AA986487|AW822225|D2Ertd303e|EIF2|EIF2B	eukaryotic translation initiation factor 2, subunit 2 (beta)	protein-coding
mm_68805.1	chr7	125491507	125491520	-	1	NA	promoter-TSS (NM_026330)	promoter-TSS (NM_026330)	29	NM_026330	67711	Mm.4467	NM_026330	ENSMUSG00000030750	Nsmce1	2510027N19Rik	NSE1 homolog, SMC5-SMC6 complex component	protein-coding
mm_142216.1	chr17	37057157	37057175	-	1	NA	intron (NM_019439, intron 11 of 22)	intron (NM_019439, intron 11 of 22)	11200	NM_019439	54393	Mm.32191	NM_019439	ENSMUSG00000024462	Gabbr1	GABAB1|GABAbR1|bM573K1.1	gamma-aminobutyric acid (GABA) B receptor, 1	protein-coding
mm_111246.1	chr12	84876162	84876175	-	1	NA	non-coding (NR_028577, exon 1 of 1)	non-coding (NR_028577, exon 1 of 1)	327	NM_013589	16997	Mm.3900	NM_013589	ENSMUSG00000002020	Ltbp2	AW208642	latent transforming growth factor beta binding protein 2	protein-coding
mm_8102.1	chr1	135849379	135849424	-	1	NA	exon (NM_001130176, exon 9 of 13)	exon (NM_001130176, exon 9 of 13)	8540	NM_001130176	21956	Mm.247470	NM_011619	ENSMUSG00000026414	Tnnt2	Tnt|cTnT	troponin T2, cardiac	protein-coding
mm_157365.1	chrX	37191161	37191196	-	1	NA	promoter-TSS (NM_019443)	promoter-TSS (NM_019443)	-44	NM_153503	69942	Mm.307182	NM_153503	ENSMUSG00000036537	Rnf113a1	2810428C21Rik|Rnf113a	ring finger protein 113A1	protein-coding
mm_172410.1	chr7	18872805	18872808	+	1	NA	Intergenic	Intergenic	-11884	NM_009402	21946	Mm.21855	NM_009402	ENSMUSG00000030413	Pglyrp1	PGRP|PGRP-S|Pglyrp|Tag7|Tasg7|Tnfsf3l	peptidoglycan recognition protein 1	protein-coding
mm_104389.1	chr11	94485332	94485356	-	1	NA	promoter-TSS (NM_144827)	promoter-TSS (NM_144827)	-34	NM_144827	217116	Mm.156123	NM_144827	ENSMUSG00000020867	Spata20	Tisp78	spermatogenesis associated 20	protein-coding
mm_16642.1	chr2	6130036	6130055	-	1	NA	5' UTR (NM_001159657, exon 1 of 4)	5' UTR (NM_001159657, exon 1 of 4)	140	NM_144883	227545	Mm.133542	NM_144883	ENSMUSG00000045319	Proser2	5430407P10Rik|AU067770	proline and serine rich 2	protein-coding
mm_75913.1	chr8	71405891	71405904	-	1	NA	promoter-TSS (NM_172756)	promoter-TSS (NM_172756)	-115	NM_001310502	234396	Mm.216549	NM_172756	ENSMUSG00000046295	Ankle1	8430438L13Rik|Ankrd41|C430003I23|Lem3	ankyrin repeat and LEM domain containing 1	protein-coding
mm_63455.1	chr7	127525135	127525138	+	1	NA	intron (NM_001304266, intron 6 of 33)	intron (NM_001304266, intron 6 of 33)	-2761	NR_034045	100217442	Mm.451113	NR_034045	ENSMUSG00000065259	Snora30	MBI-26	small nucleolar RNA, H/ACA box 30	snoRNA
mm_60950.1	chr7	47050611	47050621	+	1	NA	promoter-TSS (NM_026436)	promoter-TSS (NM_026436)	-24	NM_026436	67893	Mm.27338	NM_026436	ENSMUSG00000010307	Tmem86a	1810054O13Rik|AI414959|AW742698	transmembrane protein 86A	protein-coding
mm_69234.1	chr7	127708681	127708706	-	1	NA	promoter-TSS (NM_009746)	promoter-TSS (NM_009746)	73	NM_009746	12055	Mm.89667	NM_009746	ENSMUSG00000030814	Bcl7c	C230096E12Rik	B cell CLL/lymphoma 7C	protein-coding
mm_96540.1	chr11	68692091	68692095	+	1	NA	5' UTR (NM_175260, exon 1 of 41)	5' UTR (NM_175260, exon 1 of 41)	178	NM_175260	77579	Mm.218233	NM_175260	ENSMUSG00000020900	Myh10	5730504C04Rik|9330167F11Rik|Fltn|Myhn-2|Myhn2|NMHC II-B|NMHC-B|NMHCII-B|NMMHC II-b|NMMHC-B|NMMHC-IIB|SMemb|mKIAA3005	myosin, heavy polypeptide 10, non-muscle	protein-coding
mm_84552.1	chr9	67633933	67633944	-	1	NA	Intergenic	CpG	-74235	NM_001081242	70549	Mm.33645	NM_027458	ENSMUSG00000052698	Tln2	5730421P04Rik|AI507121|AI787438|AL118320|mKIAA0320	talin 2	protein-coding
mm_41912.1	chr5	105591349	105591375	+	1	NA	intron (NM_133897, intron 3 of 3)	intron (NM_133897, intron 3 of 3)	71891	NM_133897	100604	Mm.319847	NM_133897	ENSMUSG00000054720	Lrrc8c	AD158|AI326115|E430036I04Rik|fad158	leucine rich repeat containing 8 family, member C	protein-coding
mm_33532.1	chr4	130932375	130932391	+	1	NA	intron (NM_010686, intron 7 of 7)	RMER1C|Other|Other	-12002	NM_010769	17180	Mm.271796	NM_010769	ENSMUSG00000040533	Matn1	CMP|Crtm|Mat1|matrilin-1	matrilin 1, cartilage matrix protein	protein-coding
mm_48820.1	chr5	149051303	149051313	-	1	NA	5' UTR (NM_001313894, exon 1 of 5)	5' UTR (NM_001313894, exon 1 of 5)	308	NM_001313894	15289	Mm.207047	NM_010439	ENSMUSG00000066551	Hmgb1	HMG-1|Hmg1|SBP-1|p30	high mobility group box 1	protein-coding
mm_49270.1	chr6	17516228	17516232	+	1	NA	intron (NM_008591, intron 4 of 21)	intron (NM_008591, intron 4 of 21)	52273	NM_008591	17295	Mm.86844	NM_008591	ENSMUSG00000009376	Met	AI838057|HGF|HGFR|Par4|c-Met	met proto-oncogene	protein-coding
mm_143588.1	chr17	74459097	74459127	-	1	NA	promoter-TSS (NM_001033367)	promoter-TSS (NM_001033367)	-4	NM_001033367	268973	Mm.311884	NM_001033367	ENSMUSG00000039193	Nlrc4	9530011P19Rik|CLAN|CLAN1|CLANA|CLANB|CLANC|CLAND|Card12|IPAF	NLR family, CARD domain containing 4	protein-coding
mm_7702.1	chr1	130423023	130423065	-	1	NA	promoter-TSS (NM_007827)	promoter-TSS (NM_007827)	-1	NM_001317361	13137	Mm.436759	NM_007827	ENSMUSG00000026401	Cd55b	AI323748|Daf|Daf-TM|Daf2|TM-DAF	CD55 molecule, decay accelerating factor for complement B	protein-coding
mm_36768.1	chr4	101551198	101551202	-	1	NA	intron (NM_001164583, intron 1 of 18)	intron (NM_001164583, intron 1 of 18)	606	NM_001164583	72685	Mm.76494	NM_198412	ENSMUSG00000028528	Dnajc6	2810027M23Rik|mKIAA0473	DnaJ heat shock protein family (Hsp40) member C6	protein-coding
mm_155512.1	chrX	74177226	74177236	+	1	NA	promoter-TSS (NM_031379)	promoter-TSS (NM_031379)	-28	NM_031379	83553	Mm.25057	NM_031379	ENSMUSG00000031397	Tktl1	C79967	transketolase-like 1	protein-coding
mm_21049.1	chr2	152596437	152596454	-	1	NA	promoter-TSS (NM_001037752)	promoter-TSS (NM_001037752)	40	NM_001037752	433490	Mm.23779	NM_001037752	ENSMUSG00000062124	Defb45	Defb27|OTTMUSG00000015859	defensin beta 45	protein-coding
mm_1400.1	chr1	67144820	67144835	+	1	NA	intron (NM_001080809, intron 4 of 37)	intron (NM_001080809, intron 4 of 37)	21800	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_151412.1	chr19	56669283	56669287	+	1	NA	Intergenic	Intergenic	-53087	NM_007419	11554	Mm.46797	NM_007419	ENSMUSG00000035283	Adrb1	Adrb-1|beta-AR	adrenergic receptor, beta 1	protein-coding
mm_32649.1	chr4	115062842	115062861	+	1	NA	intron (NM_001287388, intron 2 of 4)	intron (NM_001287388, intron 2 of 4)	5040	NM_001287388	21349	Mm.239869	NM_011527	ENSMUSG00000028717	Tal1	Hpt|SCL/tal-1|Scl|bHLHa17|tal-1	T cell acute lymphocytic leukemia 1	protein-coding
mm_60360.1	chr7	44428844	44428867	+	1	NA	Intergenic	CpG	-13632	NM_198250	272381	Mm.44173	NM_198250	ENSMUSG00000047085	Lrrc4b	A830007M12|Lrig4	leucine rich repeat containing 4B	protein-coding
mm_58567.1	chr7	4792925	4793026	+	1	NA	promoter-TSS (NM_009081)	promoter-TSS (NM_009081)	10	NM_009081	19943	Mm.379002	NM_009081	ENSMUSG00000030432	Rpl28	D7Wsu21e	ribosomal protein L28	protein-coding
mm_160875.1	chr11	68955013	68955013	-	1	NA	exon (NM_177566, exon 2 of 16)	exon (NM_177566, exon 2 of 16)	1845	NM_177566	442801	Mm.376147	NM_177566	ENSMUSG00000052921	Arhgef15	D130071N09|D530030K12Rik|E5	Rho guanine nucleotide exchange factor (GEF) 15	protein-coding
mm_121201.1	chr14	103051900	103051921	+	1	NA	intron (NM_008392, intron 4 of 4)	B3A|SINE|B2	4898	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_59094.1	chr7	19696781	19696790	+	1	NA	exon (NM_009696, exon 4 of 4)	exon (NM_009696, exon 4 of 4)	1613	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_161489.1	chr15	85580546	85580546	-	1	NA	promoter-TSS (NR_040433)	promoter-TSS (NR_040433)	183	NM_001163633	22422	Mm.306946	NM_009528	ENSMUSG00000022382	Wnt7b	Wnt-7b	wingless-type MMTV integration site family, member 7B	protein-coding
mm_89762.1	chr10	100038129	100038136	+	1	NA	intron (NM_001347156, intron 1 of 8)	(T)n|Simple_repeat|Simple_repeat	22311	NM_013598	17311	Mm.45124	NM_013598	ENSMUSG00000019966	Kitl	Clo|Con|Gb|Kitlg|Mgf|SCF|SF|SLF|Sl|blz|contrasted	kit ligand	protein-coding
mm_50983.1	chr6	62167228	62167233	+	1	NA	intron (NM_001164316, intron 10 of 10)	intron (NM_001164316, intron 10 of 10)	-986420	NR_040287	100504262	Mm.438066	NR_040287		A730020E08Rik	-	RIKEN cDNA A730020E08 gene	ncRNA
mm_68558.1	chr7	114479913	114479925	-	1	NA	intron (NM_011055, intron 1 of 15)	intron (NM_011055, intron 1 of 15)	64665	NM_011055	18576	Mm.430730	NM_011055	ENSMUSG00000030671	Pde3b	9830102A01Rik|AI847709	phosphodiesterase 3B, cGMP-inhibited	protein-coding
mm_122808.1	chr14	54577481	54577498	-	1	NA	5' UTR (NM_010590, exon 1 of 8)	5' UTR (NM_010590, exon 1 of 8)	172	NM_010590	16475	Mm.100253	NM_010590	ENSMUSG00000022178	Ajuba	Jub	ajuba LIM protein	protein-coding
mm_94954.1	chr11	30139278	30139301	+	1	NA	exon (NM_009260, exon 13 of 31)	exon (NM_009260, exon 13 of 31)	58968	NM_009260	20742	Mm.123110	NM_009260	ENSMUSG00000020315	Sptbn1	9930031C03Rik|AL033301|SPTB2|Spnb-2|Spnb2|elf1|elf3|mKIAA4049	spectrin beta, non-erythrocytic 1	protein-coding
mm_40891.1	chr5	75152160	75152186	+	1	NA	promoter-TSS (NM_011058)	promoter-TSS (NM_011058)	-78	NR_144636	18595	Mm.221403	NM_011058	ENSMUSG00000029231	Pdgfra	AI115593|CD140a|Pdgfr-2	platelet derived growth factor receptor, alpha polypeptide	protein-coding
mm_125069.1	chr15	25941109	25941129	+	1	NA	5' UTR (NM_001277315, exon 1 of 7)	5' UTR (NM_001277315, exon 1 of 7)	293	NM_025459	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_88016.1	chr10	67185681	67185697	+	1	NA	promoter-TSS (NM_001242396)	promoter-TSS (NM_001242396)	-61	NM_001242396	108829	Mm.23846	NM_207221	ENSMUSG00000037876	Jmjd1c	5430433L24Rik|D630035I23Rik|Jmjdic|TRIP8	jumonji domain containing 1C	protein-coding
mm_32826.1	chr4	117560473	117560476	+	1	NA	intron (NM_001285899, intron 2 of 8)	intron (NM_001285899, intron 2 of 8)	10109	NM_080469	140546	Mm.235891	NM_080469	ENSMUSG00000033423	Eri3	PINT1|Prnpip1	exoribonuclease 3	protein-coding
mm_74055.1	chr8	122307241	122307268	+	1	NA	intron (NM_009569, intron 2 of 9)	intron (NM_009569, intron 2 of 9)	25113	NM_009569	22761	Mm.3105	NM_009569	ENSMUSG00000049577	Zfpm1	FOG|Fog1	zinc finger protein, multitype 1	protein-coding
mm_88650.1	chr10	79988590	79988683	+	1	NA	promoter-TSS (NM_007725)	promoter-TSS (NM_007725)	36	NM_007725	12798	Mm.157770	NM_007725	ENSMUSG00000004665	Cnn2	AA408047|AI324678|Calpo2	calponin 2	protein-coding
mm_153687.1	chr19	44396820	44396842	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	10878	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_21626.1	chr2	164277188	164277194	-	1	NA	exon (NM_009300, exon 2 of 3)	exon (NM_009300, exon 2 of 3)	1116	NM_009300	20941	Mm.1286	NM_009300	ENSMUSG00000016998	Svs4	SVS-IV|Svp-2|Svp-4|Svp2|Svp4	seminal vesicle secretory protein 4	protein-coding
mm_63936.1	chr7	139586341	139586341	+	1	NA	Intergenic	Intergenic	-3544	NR_027857	14912	Mm.28308	NM_183248	ENSMUSG00000041309	Nkx6-2	Gtx|Nkx6.2	NK6 homeobox 2	protein-coding
mm_4758.1	chr1	182341727	182341735	+	1	NA	promoter-TSS (NM_175127)	promoter-TSS (NM_175127)	-125	NM_175127	67948	Mm.30737	NM_175127	ENSMUSG00000047539	Fbxo28	4833428J17Rik|5730505P19Rik|D1Ertd578e|Fbx28|mKIAA0483	F-box protein 28	protein-coding
mm_150349.1	chr19	34644217	34644227	+	1	NA	intron (NM_008331, intron 1 of 1)	intron (NM_008331, intron 1 of 1)	3333	NM_008331	15957	Mm.439751	NM_008331	ENSMUSG00000034459	Ifit1	ISG56|Ifi56|P56	interferon-induced protein with tetratricopeptide repeats 1	protein-coding
mm_9565.1	chr1	173977327	173977341	-	1	NA	exon (NM_011940, exon 2 of 7)	exon (NM_011940, exon 2 of 7)	5510	NM_008327	26388	Mm.218770	NM_008327	ENSMUSG00000026535	Ifi202b	Ifbip-1|Ifi202|Ifi202a|p202	interferon activated gene 202B	protein-coding
mm_148724.1	chr19	5846900	5846910	+	1	NA	Intergenic	Intergenic	-1425	NR_003513	66961	Mm.281895	NR_003513	ENSMUSG00000092274	Neat1	2310043N10Rik|VINC	nuclear paraspeckle assembly transcript 1 (non-protein coding)	ncRNA
mm_171993.1	chr5	98797701	98797701	-	1	NA	intron (NM_001024614, intron 5 of 5)	LTR37-int|LTR|ERV1	-56714	NM_173404	110075	Mm.136461	NM_173404	ENSMUSG00000029335	Bmp3	9530029I04Rik	bone morphogenetic protein 3	protein-coding
mm_127006.1	chr15	95800696	95800707	+	1	NA	intron (NM_175344, intron 1 of 19)	Lx8|LINE|L1	9858	NM_001253813	105722	Mm.38087	NM_175344	ENSMUSG00000064210	Ano6	2900059G15Rik|AA407480|AW554778|F730003B03Rik|Tmem16f	anoctamin 6	protein-coding
mm_78389.1	chr9	28459983	28459987	+	1	NA	intron (NM_177906, intron 2 of 7)	intron (NM_177906, intron 2 of 7)	668716	NM_177906	330908	Mm.379474	NM_177906	ENSMUSG00000062257	Opcml	2900075O15Rik|3732419F12|AI844366|B930023M13Rik|C230027C17|Gm181|Obcam	opioid binding protein/cell adhesion molecule-like	protein-coding
mm_128360.1	chr15	40014680	40014687	-	1	NA	Intergenic	Intergenic	52034	NR_045719	105976	Mm.394885	NR_045719		AU022793	-	expressed sequence AU022793	ncRNA
mm_111208.1	chr12	84392852	84392874	-	1	NA	intron (NM_001026214, intron 5 of 15)	intron (NM_001026214, intron 5 of 15)	8071	NM_001286058	12499	Mm.10211	NM_007647	ENSMUSG00000021236	Entpd5	AI196558|AI987697|Cd39l4|ER-UDPase|NTPDase-5|NTPDase5|Pcph|mNTPase	ectonucleoside triphosphate diphosphohydrolase 5	protein-coding
mm_111084.1	chr12	80260336	80260352	-	1	NA	promoter-TSS (NM_134156)	promoter-TSS (NM_134156)	27	NM_134156	109711	Mm.253564	NM_134156	ENSMUSG00000015143	Actn1	3110023F10Rik|Actn1a	actinin, alpha 1	protein-coding
mm_19948.1	chr2	117298927	117298970	-	1	NA	intron (NM_011246, intron 5 of 16)	intron (NM_011246, intron 5 of 16)	43929	NM_011246	19419	Mm.42150	NM_011246	ENSMUSG00000027347	Rasgrp1	Rasgrp	RAS guanyl releasing protein 1	protein-coding
mm_160846.1	chr11	50953616	50953616	-	1	NA	promoter-TSS (NM_008936)	promoter-TSS (NM_008936)	16	NM_008936	19127	Mm.1386	NM_008936	ENSMUSG00000044542	Prop1	Prop-1|df	paired like homeodomain factor 1	protein-coding
mm_137782.1	chr17	29494501	29494523	+	1	NA	intron (NM_008842, intron 5 of 5)	intron (NM_008842, intron 5 of 5)	3467	NM_008842	18712	Mm.405293	NM_008842	ENSMUSG00000024014	Pim1	Pim-1	proviral integration site 1	protein-coding
mm_150435.1	chr19	37547374	37547394	+	1	NA	Intergenic	Intergenic	-3034	NM_175353	107371	Mm.24865	NM_175353	ENSMUSG00000053799	Exoc6	4833405E05Rik|AW413330|C430002C19|Sec15|Sec15l1|hbd|msec15	exocyst complex component 6	protein-coding
mm_54604.1	chr6	38311687	38311697	-	1	NA	exon (NM_028421, exon 11 of 12)	exon (NM_028421, exon 11 of 12)	-12433	NM_172467	209032	Mm.101389	NM_172467	ENSMUSG00000047749	Zc3hav1l	B130055L09Rik|E430016P22Rik	zinc finger CCCH-type, antiviral 1-like	protein-coding
mm_74493.1	chr8	5085930	5085963	-	1	NA	3' UTR (NM_011388, exon 6 of 6)	3' UTR (NM_011388, exon 6 of 6)	19341	NM_011388	20494	Mm.3500	NM_011388	ENSMUSG00000023073	Slc10a2	9130221J18Rik|AI605518|ASBT|IBAT|ISBT	solute carrier family 10, member 2	protein-coding
mm_42504.1	chr5	115492366	115492381	+	1	NA	Intergenic	Intergenic	-7889	NM_133760	75387	Mm.332616	NM_133760	ENSMUSG00000029524	Sirt4	4930596O17Rik	sirtuin 4	protein-coding
mm_43569.1	chr5	137638483	137638507	+	1	NA	exon (NM_146164, exon 13 of 18)	exon (NM_146164, exon 13 of 18)	-2978	NM_001081962	751865	Mm.200763	NM_001081962	ENSMUSG00000079165	Sap25	-	sin3 associated polypeptide	protein-coding
mm_33200.1	chr4	126286793	126286803	+	1	NA	promoter-TSS (NM_199473)	promoter-TSS (NM_199473)	4	NM_199473	329941	Mm.296327	NM_199473	ENSMUSG00000056174	Col8a2	AI429819	collagen, type VIII, alpha 2	protein-coding
mm_124643.1	chr15	4727266	4727282	+	1	NA	promoter-TSS (NM_016704)	promoter-TSS (NM_016704)	64	NM_016704	12274	Mm.20247	NM_016704	ENSMUSG00000022181	C6	AW111623	complement component 6	protein-coding
mm_164036.1	chr14	82845512	82845513	+	1	NA	Intergenic	RMER6C|LTR|ERVK	-1598051	NM_001013753	219228	Mm.153643	NM_001013753	ENSMUSG00000035566	Pcdh17	C030033F14Rik|Gm78	protocadherin 17	protein-coding
mm_51480.1	chr6	83032806	83032820	+	1	NA	exon (NM_001291799, exon 2 of 5)	exon (NM_001291799, exon 2 of 5)	658	NM_010070	13448	Mm.156	NM_010070	ENSMUSG00000068335	Dok1	AW557123|p62DOK	docking protein 1	protein-coding
mm_45812.1	chr5	87674077	87674095	-	1	NA	exon (NM_007784, exon 11 of 34)	exon (NM_007784, exon 11 of 34)	7878	NM_001286016	12990	Mm.427467	NM_007784	ENSMUSG00000070702	Csn1s1	AA959832|AW212882|Csna	casein alpha s1	protein-coding
mm_38709.1	chr4	145215767	145215779	-	1	NA	3' UTR (NM_011610, exon 10 of 10)	3' UTR (NM_011610, exon 10 of 10)	-20768	NM_001276465	230895	Mm.240310	NM_001033190	ENSMUSG00000020220	Vps13d	-	vacuolar protein sorting 13D	protein-coding
mm_16387.1	chr2	178455467	178455473	+	1	NA	intron (NM_001291189, intron 3 of 13)	intron (NM_001291189, intron 3 of 13)	24955	NM_198656	381409	Mm.330860	NM_198656	ENSMUSG00000039155	Cdh26	Gm1010	cadherin-like 26	protein-coding
mm_126918.1	chr15	91641912	91641918	+	1	NA	Intergenic	Intergenic	-31309	NM_025730	66725	Mm.37558	NM_025730	ENSMUSG00000036273	Lrrk2	4921513O20Rik|9330188B09Rik|AW561911|D630001M17Rik|Gm927|cI-46	leucine-rich repeat kinase 2	protein-coding
mm_109545.1	chr12	111678147	111678160	+	1	NA	promoter-TSS (NM_001099793)	promoter-TSS (NM_001099793)	48	NM_177374	328162	Mm.425747	NM_177374	ENSMUSG00000060950	Trmt61a	6720458F09Rik|AI606093|Gcd14|Trm61	tRNA methyltransferase 61A	protein-coding
mm_5090.1	chr1	4497396	4497409	-	1	NA	promoter-TSS (NM_001289467)	promoter-TSS (NM_001289467)	-48	NM_001289465	20671	Mm.279103	NM_011441	ENSMUSG00000025902	Sox17	-	SRY (sex determining region Y)-box 17	protein-coding
mm_102573.1	chr11	61579638	61579707	-	1	NA	promoter-TSS (NM_010148)	promoter-TSS (NM_010148)	15	NM_010148	13855	Mm.139695	NM_010148	ENSMUSG00000001036	Epn2	9530051D10Rik|AA536924|Ibp2	epsin 2	protein-coding
mm_29002.1	chr3	101592436	101592447	-	1	NA	exon (NM_144900, exon 4 of 23)	exon (NM_144900, exon 4 of 23)	12266	NM_144900	11928	Mm.193670	NM_144900	ENSMUSG00000033161	Atp1a1	Atpa-1|BC010319	ATPase, Na+/K+ transporting, alpha 1 polypeptide	protein-coding
mm_66118.1	chr7	31051412	31051422	-	1	NA	promoter-TSS (NM_022007)	promoter-TSS (NM_022007)	37	NM_022007	57780	Mm.41770	NM_022007	ENSMUSG00000036578	Fxyd7	1110035I01Rik	FXYD domain-containing ion transport regulator 7	protein-coding
mm_144656.1	chr18	34247657	34247683	+	1	NA	intron (NM_007462, intron 1 of 15)	intron (NM_007462, intron 1 of 15)	-25898	NR_040534	633395	Mm.414290	NR_040534	ENSMUSG00000073607	Gm10548	ENSMUSG00000073607	ribosomal protein L29 pseudogene	pseudo
mm_158759.1	chrX	166483896	166483904	-	1	NA	Intergenic	Intergenic	-4033	NM_019773	56382	Mm.25306	NM_019773	ENSMUSG00000079316	Rab9	2410064E05Rik|AI195561|Rab9a|Sid6061p	RAB9, member RAS oncogene family	protein-coding
mm_61452.1	chr7	75586280	75586304	+	1	NA	exon (NM_029332, exon 5 of 37)	exon (NM_029332, exon 5 of 37)	130758	NM_029332	75547	Mm.216107	NM_029332	ENSMUSG00000066406	Akap13	1700026G02Rik|5730522G15Rik|5830460E08Rik|AKAP-13|AKAP-Lbc|BRX|Ht31|LBC|PROTO-LB|PROTO-LBC	A kinase (PRKA) anchor protein 13	protein-coding
mm_48043.1	chr5	136432193	136432208	-	1	NA	intron (NM_001291239, intron 2 of 22)	intron (NM_001291239, intron 2 of 22)	-56397	NR_030500	723975		NR_030500	ENSMUSG00000106479	Mir721	Mirn721|miRY|mir-721|mmu-mir-721	microRNA 721	ncRNA
mm_100953.1	chr11	6624231	6624263	-	1	NA	5' UTR (NM_134011, exon 3 of 12)	5' UTR (NM_134011, exon 3 of 12)	1820	NM_001130457	21379	Mm.247761	NM_134011	ENSMUSG00000000384	Tbrg4	2310042P22Rik|AA120735|AA408001|AI527316|Cpr2|R74877|Tb-12|mKIAA0948	transforming growth factor beta regulated gene 4	protein-coding
mm_96787.1	chr11	69965597	69965621	+	1	NA	5' UTR (NM_016887, exon 1 of 4)	5' UTR (NM_016887, exon 1 of 4)	188	NM_016887	53624	Mm.281896	NM_016887	ENSMUSG00000018569	Cldn7	-	claudin 7	protein-coding
mm_38809.1	chr4	148287928	148287954	-	1	NA	promoter-TSS (NM_001083342)	promoter-TSS (NM_001083342)	24	NM_001083342	242748	Mm.33873	NM_001083342	ENSMUSG00000041544	Ptchd2	Disp3|G630052C06Rik|RNDEu-2	patched domain containing 2	protein-coding
mm_112577.1	chr13	13638280	13638296	+	1	NA	exon (NM_010748, exon 6 of 53)	exon (NM_010748, exon 6 of 53)	47879	NM_010748	17101	Mm.342337	NM_010748	ENSMUSG00000019726	Lyst	D13Sfk13|beige|bg	lysosomal trafficking regulator	protein-coding
mm_137897.1	chr17	31681607	31681615	+	1	NA	3' UTR (NM_001278570, exon 3 of 3)	3' UTR (NM_001278570, exon 3 of 3)	3680	NM_001278570	12954	Mm.1228	NM_013501	ENSMUSG00000024041	Cryaa	Acry-1|Crya-1|Crya1|DAcry-1|lop18	crystallin, alpha A	protein-coding
mm_16251.1	chr2	173158871	173158888	+	1	NA	3' UTR (NM_011044, exon 10 of 10)	3' UTR (NM_011044, exon 10 of 10)	5806	NM_011044	18534	Mm.266867	NM_011044	ENSMUSG00000027513	Pck1	AI265463|PEPCK|Pck-1	phosphoenolpyruvate carboxykinase 1, cytosolic	protein-coding
mm_118409.1	chr14	3208436	3208479	+	1	NA	promoter-TSS (NM_001320366)	promoter-TSS (NM_001320366)	-36	NM_001320366	320333	Mm.350858	NM_177135	ENSMUSG00000096039	D830030K20Rik	-	RIKEN cDNA D830030K20 gene	protein-coding
mm_46663.1	chr5	108678458	108678489	-	1	NA	intron (NM_008325, intron 3 of 14)	intron (NM_008325, intron 3 of 14)	-3108	NM_174870	231583	Mm.440571	NM_174870	ENSMUSG00000046959	Slc26a1	Sat1	solute carrier family 26 (sulfate transporter), member 1	protein-coding
mm_69259.1	chr7	127876811	127876854	-	1	NA	promoter-TSS (NM_146259)	promoter-TSS (NM_146259)	-9	NM_146259	244219	Mm.207872	NM_146259	ENSMUSG00000049728	Zfp668	BC030314|E130018B19Rik|Znf668	zinc finger protein 668	protein-coding
mm_69168.1	chr7	127215015	127215033	-	1	NA	TTS (NM_016754)	TTS (NM_016754)	3416	NM_016754	17907	Mm.14526	NM_016754	ENSMUSG00000030672	Mylpf	2410014J02Rik|MLC-2|Mlc2	myosin light chain, phosphorylatable, fast skeletal muscle	protein-coding
mm_14841.1	chr2	147375529	147375529	+	1	NA	TTS (NM_008780)	TTS (NM_008780)	10535	NM_008780	18503	Mm.315502	NM_008780	ENSMUSG00000037034	Pax1	Pax-1|hbs|hunchback|un|undulated|wt	paired box 1	protein-coding
mm_33526.1	chr4	130932233	130932239	+	1	NA	intron (NM_010686, intron 7 of 7)	RMER1C|Other|Other	-12149	NM_010769	17180	Mm.271796	NM_010769	ENSMUSG00000040533	Matn1	CMP|Crtm|Mat1|matrilin-1	matrilin 1, cartilage matrix protein	protein-coding
mm_138140.1	chr17	34198605	34198620	+	1	NA	intron (NM_010724, intron 1 of 5)	intron (NM_010724, intron 1 of 5)	417	NM_010724	16913	Mm.180191	NM_010724	ENSMUSG00000024338	Psmb8	Lmp-7|Lmp7	proteasome (prosome, macropain) subunit, beta type 8 (large multifunctional peptidase 7)	protein-coding
mm_6679.1	chr1	80549850	80549853	-	1	NA	intron (NM_175291, intron 29 of 55)	intron (NM_175291, intron 29 of 55)	103919	NR_040460	72208	Mm.396181	NR_040460	ENSMUSG00000101483	1700016L21Rik	Jr3	RIKEN cDNA 1700016L21 gene	ncRNA
mm_152927.1	chr19	28011595	28011634	-	1	NA	promoter-TSS (NM_011265)	promoter-TSS (NM_011265)	-448	NM_011265	19726	Mm.313321	NM_011265	ENSMUSG00000040929	Rfx3	C230093O12Rik|MRFX3	regulatory factor X, 3 (influences HLA class II expression)	protein-coding
mm_71499.1	chr8	46795163	46795188	+	1	NA	intron (NM_008391, intron 2 of 8)	(T)n|Simple_repeat|Simple_repeat	55430	NM_008391	16363	Mm.1149	NM_008391	ENSMUSG00000031627	Irf2	9830146E22Rik|AI646973|Irf-2	interferon regulatory factor 2	protein-coding
mm_126947.1	chr15	92054156	92054157	+	1	NA	intron (NM_001159648, intron 1 of 23)	MTD|LTR|ERVL-MaLR	2991	NM_001159648	12805	Mm.4911	NM_007727	ENSMUSG00000055022	Cntn1	AW495098|CNTN|F3cam|usl	contactin 1	protein-coding
mm_104832.1	chr11	99145077	99145096	-	1	NA	exon (NM_007719, exon 3 of 3)	exon (NM_007719, exon 3 of 3)	9991	NM_001301713	12775	Mm.2932	NM_007719	ENSMUSG00000037944	Ccr7	CC-CKR-7|CCR-7|CD197|Cdw197|Cmkbr7|EBI1|Ebi1h	chemokine (C-C motif) receptor 7	protein-coding
mm_113495.1	chr13	37418536	37418548	+	1	NA	exon (NM_010745, exon 5 of 5)	exon (NM_010745, exon 5 of 5)	73197	NM_010745	17084	Mm.2639	NM_010745	ENSMUSG00000021423	Ly86	MD-1|MD1|ly86_tv2	lymphocyte antigen 86	protein-coding
mm_61374.1	chr7	70365261	70365263	+	1	NA	promoter-TSS (NR_045850)	promoter-TSS (NR_045850)	-121	NR_045850	434198	Mm.389911	NR_045850	ENSMUSG00000100005	B130024G19Rik	-	RIKEN cDNA B130024G19 gene	ncRNA
mm_111366.1	chr12	87200201	87200284	-	1	NA	promoter-TSS (NM_001290288)	promoter-TSS (NM_001290288)	-13	NM_001033475	382620	Mm.374912	NM_001033475	ENSMUSG00000034111	Tmed8	6430595O10Rik|AI447224|Gm1184|Mem1	transmembrane p24 trafficking protein 8	protein-coding
mm_19108.1	chr2	79455022	79455031	-	1	NA	exon (NM_010894, exon 2 of 2)	exon (NM_010894, exon 2 of 2)	1610	NM_010894	18012	Mm.4636	NM_010894	ENSMUSG00000034701	Neurod1	BETA2|BHF-1|Nd1|Neurod|bHLHa3	neurogenic differentiation 1	protein-coding
mm_150857.1	chr19	45014996	45015006	+	1	NA	promoter-TSS (NM_001130525)	promoter-TSS (NM_001130525)	-175	NM_145503	226154	Mm.28204	NM_145503	ENSMUSG00000035342	Lzts2	BC014695|LAPSER1|mKIAA1813	leucine zipper, putative tumor suppressor 2	protein-coding
mm_85254.1	chr9	99304724	99304741	-	1	NA	Intergenic	Intergenic	53798	NM_177775	272636	Mm.490440	NM_177775	ENSMUSG00000037681	Esyt3	D930024E11|D9Ertd280e|Fam62c|mKIAA4186	extended synaptotagmin-like protein 3	protein-coding
mm_73520.1	chr8	107502563	107502597	+	1	NA	intron (NM_025830, intron 6 of 23)	intron (NM_025830, intron 6 of 23)	-48664	NR_029553	387158		NR_029553	ENSMUSG00000065439	Mir140	Mirn140|mir-140|mmu-mir-140	microRNA 140	ncRNA
mm_119600.1	chr14	51009017	51009027	+	1	NA	intron (NM_029145, intron 1 of 1)	intron (NM_029145, intron 1 of 1)	1093	NM_029145	75019	Mm.318775	NM_029145	ENSMUSG00000021872	Rnase10	4930474F22Rik|Rah1	ribonuclease, RNase A family, 10 (non-active)	protein-coding
mm_9784.1	chr1	181212008	181212012	-	1	NA	promoter-TSS (NM_145514)	promoter-TSS (NM_145514)	-32	NM_145514	226757	Mm.289082	NM_145514	ENSMUSG00000038733	Wdr26	1600024A01Rik|AA693241|AI447817|AU044014|C77982|Gid7	WD repeat domain 26	protein-coding
mm_18212.1	chr2	48949265	48949275	-	1	NA	promoter-TSS (NM_001177313)	promoter-TSS (NM_001177313)	-3	NM_011958	26428	Mm.291059	NM_011958	ENSMUSG00000026761	Orc4	Orc4P|Orc4l|mMmORC4	origin recognition complex, subunit 4	protein-coding
mm_53738.1	chr6	145121942	145121953	+	1	NA	5' UTR (NM_008511, exon 1 of 19)	5' UTR (NM_008511, exon 1 of 19)	208	NM_008511	16970	Mm.843	NM_008511	ENSMUSG00000030263	Lrmp	D6Int3|D6Int4|D6Int5|D6Int7|D6Int8|Jaw1	lymphoid-restricted membrane protein	protein-coding
mm_110548.1	chr12	55489648	55489666	-	1	NA	3' UTR (NM_010907, exon 6 of 6)	3' UTR (NM_010907, exon 6 of 6)	2990	NM_010907	18035	Mm.170515	NM_010907	ENSMUSG00000021025	Nfkbia	AI462015|Nfkbi	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, alpha	protein-coding
mm_23588.1	chr3	64022787	64022788	+	1	NA	Intergenic	ORR1D2-int|LTR|ERVL-MaLR	46644	NM_001033300	229363	Mm.331051	NM_001033300	ENSMUSG00000027823	Gmps	670032|AA591640|AI047208|Gm9479	guanine monophosphate synthetase	protein-coding
mm_7220.1	chr1	93307269	93307277	-	1	NA	Intergenic	Intergenic	-1394	NM_001310756	69821	Mm.52809	NM_178051	ENSMUSG00000026273	Mterf4	1810059A23Rik|4933412H03Rik|Mterfd2	mitochondrial transcription termination factor 4	protein-coding
mm_42937.1	chr5	122989266	122989281	+	1	NA	promoter-TSS (NM_001003953)	promoter-TSS (NM_001003953)	-81	NR_045820	109202	Mm.30769	NM_175405	ENSMUSG00000056735	A930024E05Rik	-	RIKEN cDNA A930024E05 gene	ncRNA
mm_146414.1	chr18	84293189	84293205	+	1	NA	intron (NM_001033341, intron 8 of 8)	intron (NM_001033341, intron 8 of 8)	205039	NM_146090	225791	Mm.147052	NM_146090	ENSMUSG00000049090	Zadh2	C530046K17Rik|PTGR-3|Pthr3	zinc binding alcohol dehydrogenase, domain containing 2	protein-coding
mm_116876.1	chr13	55021473	55021485	-	1	NA	promoter-TSS (NM_001206391)	promoter-TSS (NM_001206391)	-94	NM_001033245	212032	Mm.267479	NM_001033245	ENSMUSG00000025877	Hk3	HK III|HK-III	hexokinase 3	protein-coding
mm_41461.1	chr5	90931090	90931112	+	1	NA	promoter-TSS (NM_026788)	promoter-TSS (NM_026788)	-95	NM_026788	665563	Mm.153030	NM_026788	ENSMUSG00000029376	Mthfd2l	1110019K23Rik|C630010D07Rik	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2-like	protein-coding
mm_162003.1	chr19	40402286	40402286	-	1	NA	promoter-TSS (NM_001034964)	promoter-TSS (NM_001034964)	24	NM_001034964	20411	Mm.210815	NM_009166	ENSMUSG00000025006	Sorbs1	2310065E01Rik|9530001P15Rik|CAP|SH3P12|Sh3d5|mKIAA1296	sorbin and SH3 domain containing 1	protein-coding
mm_86630.1	chr10	13983110	13983130	+	1	NA	intron (NM_010437, intron 1 of 8)	intron (NM_010437, intron 1 of 8)	16741	NM_010437	15273	Mm.42157	NM_010437	ENSMUSG00000015501	Hivep2	Gm20114|MIBP1|Schnurri-2|Shn-2	human immunodeficiency virus type I enhancer binding protein 2	protein-coding
mm_118378.1	chr13	117025348	117025364	-	1	NA	intron (NM_001081009, intron 1 of 26)	CpG-4196	160	NM_001081009	52552	Mm.274466	NM_027272	ENSMUSG00000021725	Parp8	2810430O08Rik|ARTD16|D13Ertd275e	poly (ADP-ribose) polymerase family, member 8	protein-coding
mm_89759.1	chr10	100015818	100015833	+	1	NA	promoter-TSS (NM_013598)	promoter-TSS (NM_013598)	4	NM_013598	17311	Mm.45124	NM_013598	ENSMUSG00000019966	Kitl	Clo|Con|Gb|Kitlg|Mgf|SCF|SF|SLF|Sl|blz|contrasted	kit ligand	protein-coding
mm_1096.1	chr1	59707000	59707038	+	1	NA	exon (NM_018868, exon 12 of 15)	exon (NM_018868, exon 12 of 15)	2211	NR_028521	100217421		NR_028521		Snord11	MBII-95	small nucleolar RNA, C/D box 11	snoRNA
mm_110009.1	chr12	16577229	16577241	-	1	NA	exon (NM_015763, exon 4 of 21)	exon (NM_015763, exon 4 of 21)	12535	NM_015763	14245	Mm.153625	NM_015763	ENSMUSG00000020593	Lpin1	4631420P06|Kiaa0188|Lipin1|fld|mKIAA0188	lipin 1	protein-coding
mm_62615.1	chr7	107209378	107209383	+	1	NA	promoter-TSS (NM_029660)	promoter-TSS (NM_029660)	-65	NM_029660	76572	Mm.128134	NM_029660	ENSMUSG00000073894	Rbmxl2	1700012H05Rik|Hnrnpg-t	RNA binding motif protein, X-linked-like 2	protein-coding
mm_3104.1	chr1	134481192	134481195	+	1	NA	intron (NM_001311136, intron 6 of 11)	B1_Mus2|SINE|Alu	-13467	NM_145510	98710	Mm.198119	NM_145510	ENSMUSG00000042229	Rabif	AI842864|AW549708|E130318E12Rik|MSS4|RASGFR3	RAB interacting factor	protein-coding
mm_159289.1	chr2	173119382	173119382	-	1	NA	5' UTR (NM_001081387, exon 1 of 11)	5' UTR (NM_001081387, exon 1 of 11)	143	NM_001081387	664799	Mm.389396	NM_001081387	ENSMUSG00000070495	Ctcfl	Boris|OTTMUSG00000016680	CCCTC-binding factor (zinc finger protein)-like	protein-coding
mm_43106.1	chr5	124497101	124497140	+	1	NA	intron (NM_021430, intron 6 of 6)	intron (NM_021430, intron 6 of 6)	13965	NM_029532	76167	Mm.156035	NM_029532	ENSMUSG00000029402	Snrnp35	6330548G22Rik	small nuclear ribonucleoprotein 35 (U11/U12)	protein-coding
mm_17944.1	chr2	36105400	36105434	-	1	NA	promoter-TSS (NM_008500)	promoter-TSS (NM_008500)	-9	NM_008500	16874	Mm.12881	NM_008500	ENSMUSG00000026890	Lhx6	Lhx6.1	LIM homeobox protein 6	protein-coding
mm_24908.1	chr3	96219878	96219900	+	1	NA	promoter-TSS (NM_178213)	promoter-TSS (NM_178213)	-27	NM_178213	621893		NM_178213	ENSMUSG00000063689	Hist2h2ab	EG621893|H2a-613a	histone cluster 2, H2ab	protein-coding
mm_39990.1	chr5	32491868	32491910	+	1	NA	3' UTR (NM_172707, exon 8 of 8)	3' UTR (NM_172707, exon 8 of 8)	32919	NM_172707	19046	Mm.241931	NM_172707	ENSMUSG00000014956	Ppp1cb	1200010B19	protein phosphatase 1, catalytic subunit, beta isoform	protein-coding
mm_81358.1	chr9	108662100	108662219	+	1	NA	promoter-TSS (NM_020520)	promoter-TSS (NM_020520)	61	NM_020520	57279	Mm.29666	NM_020520	ENSMUSG00000032602	Slc25a20	1110007P09Rik|C78826|Cact|mCAC	solute carrier family 25 (mitochondrial carnitine/acylcarnitine translocase), member 20	protein-coding
mm_54473.1	chr6	34910603	34910629	-	1	NA	intron (NM_001013366, intron 1 of 14)	CpG	215	NM_001013366	101240	Mm.152120	NM_001013366	ENSMUSG00000058486	Wdr91	9530020G05Rik|AI987683|AU018665	WD repeat domain 91	protein-coding
mm_14680.1	chr2	139677702	139677720	+	1	NA	promoter-TSS (NM_001276489)	promoter-TSS (NM_001276489)	-467	NM_001276489	319909	Mm.41113	NM_001126490	ENSMUSG00000074766	Ism1	5430433G21Rik|Ism	isthmin 1, angiogenesis inhibitor	protein-coding
mm_136189.1	chr16	89047899	89047902	-	1	NA	promoter-TSS (NM_130856)	promoter-TSS (NM_130856)	-1	NM_130856	68484	Mm.46209	NM_130856	ENSMUSG00000062400	Krtap6-5	1110002D05Rik|Krtap16-8	keratin associated protein 6-5	protein-coding
mm_134230.1	chr16	11442593	11442600	-	1	NA	intron (NM_001290148, intron 4 of 13)	ORR1B1|LTR|ERVL-MaLR	36948	NM_001290148	74478	Mm.325831	NM_028964	ENSMUSG00000071669	Snx29	4933437K13Rik|ENSMUSG00000079738|Gm11170|Gm1737|Gm930|Rundc2a	sorting nexin 29	protein-coding
mm_113701.1	chr13	43137873	43137884	+	1	NA	3' UTR (NM_001302636, exon 13 of 13)	3' UTR (NM_001302636, exon 13 of 13)	15039	NM_001005748	218194	Mm.160124	NM_198419	ENSMUSG00000054728	Phactr1	9630030F18Rik|Rpel1	phosphatase and actin regulator 1	protein-coding
mm_97557.1	chr11	78931649	78931657	+	1	NA	exon (NM_010927, exon 5 of 27)	exon (NM_010927, exon 5 of 27)	6362	NM_001313922	18126	Mm.2893	NM_010927	ENSMUSG00000020826	Nos2	MAC-NOS|NOS-II|Nos-2|Nos2a|i-NOS|iNOS	nitric oxide synthase 2, inducible	protein-coding
mm_106711.1	chr12	3807077	3807086	+	1	NA	promoter-TSS (NM_001271753)	promoter-TSS (NM_001271753)	-79	NM_001271753	13435	Mm.5001	NM_007872	ENSMUSG00000020661	Dnmt3a	MmuIIIA	DNA methyltransferase 3A	protein-coding
mm_131428.1	chr16	15345535	15345535	+	1	NA	Intergenic	ORR1D2|LTR|ERVL-MaLR	248983	NM_001159351	70620	Mm.235407	NM_023585	ENSMUSG00000022674	Ube2v2	1110021H13Rik|4632410D19Rik|5730524P06Rik|6820402M05|AI848315|C81524|MMS2	ubiquitin-conjugating enzyme E2 variant 2	protein-coding
mm_93024.1	chr10	87930806	87930841	-	1	NA	3' UTR (NM_010512, exon 5 of 5)	3' UTR (NM_010512, exon 5 of 5)	-35848	NR_000040	22172	Mm.391420	NR_000040		Tyms-ps	-	thymidylate synthase, pseudogene	pseudo
mm_91220.1	chr10	22048514	22048514	-	1	NA	Intergenic	Intergenic	19565	NM_053264	114671	Mm.288194	NM_053264	ENSMUSG00000069712	4930444G20Rik	-	RIKEN cDNA 4930444G20 gene	protein-coding
mm_172760.1	chr8	88806521	88806528	+	1	NA	Intergenic	Intergenic	109496	NM_001128171	74256	Mm.490395	NM_173369	ENSMUSG00000036712	Cyld	2010013M14Rik|2900009M21Rik|C130039D01Rik|CDMT|CYLD1|EAC|mKIAA0849	CYLD lysine 63 deubiquitinase	protein-coding
mm_59970.1	chr7	30442209	30442235	+	1	NA	exon (NM_007467, exon 6 of 17)	exon (NM_007467, exon 6 of 17)	3360	NM_007467	11803	Mm.2381	NM_007467	ENSMUSG00000006651	Aplp1	-	amyloid beta (A4) precursor-like protein 1	protein-coding
mm_144324.1	chr18	12866601	12866610	+	1	NA	intron (NM_207530, intron 15 of 27)	RLTR17|LTR|ERVK	-3225	NM_001252490	64291	Mm.259470	NM_020573	ENSMUSG00000044252	Osbpl1a	G430090F17Rik|Gm753|ORP-1|Osbpl1b	oxysterol binding protein-like 1A	protein-coding
mm_14502.1	chr2	132151938	132151951	+	1	NA	Intergenic	L2a|LINE|L2	-6836	NM_018824	54338	Mm.103581	NM_018824	ENSMUSG00000027340	Slc23a2	AI844736|NBTL1|SVCT2|Slc23a1|YSPL2|YSPL3|mKIAA0238	solute carrier family 23 (nucleobase transporters), member 2	protein-coding
mm_79611.1	chr9	58618764	58618777	+	1	NA	intron (NM_001293673, intron 1 of 7)	intron (NM_001293673, intron 1 of 7)	36530	NM_009145	20320	Mm.15125	NM_009145	ENSMUSG00000032336	Nptn	AW554172|SDR-1|Sdfr1	neuroplastin	protein-coding
mm_70729.1	chr8	18846252	18846328	+	1	NA	promoter-TSS (NM_026792)	promoter-TSS (NM_026792)	11	NM_026792	52123	Mm.24117	NM_026792	ENSMUSG00000031467	Agpat5	1110013A05Rik|D8Ertd319e	1-acylglycerol-3-phosphate O-acyltransferase 5 (lysophosphatidic acid acyltransferase, epsilon)	protein-coding
mm_123879.1	chr14	72683745	72683779	-	1	NA	5' UTR (NM_207636, exon 2 of 26)	5' UTR (NM_207636, exon 2 of 26)	26241	NM_207636	319448	Mm.205421	NM_207636	ENSMUSG00000033487	Fndc3a	1700094E19Rik|D14Ertd453e|F730017H24Rik|Fndc3|sys	fibronectin type III domain containing 3A	protein-coding
mm_61378.1	chr7	70606791	70606801	+	1	NA	Intergenic	Intergenic	-240050	NM_183261	11819	Mm.158143	NM_009697	ENSMUSG00000030551	Nr2f2	2700033K02Rik|9430015G03Rik|ARP-1|Aporp1|COUP-TF2|COUP-TFII|COUPTFB|EAR3|SVP40|Tcfcoup2	nuclear receptor subfamily 2, group F, member 2	protein-coding
mm_37635.1	chr4	127408819	127408820	-	1	NA	Intergenic	Intergenic	-50655	NM_010291	14622	Mm.26859	NM_010291	ENSMUSG00000042357	Gjb5	Cnx31.1|Cx31.1|Gjb-5	gap junction protein, beta 5	protein-coding
mm_133301.1	chr16	77594063	77594076	+	1	NA	Intergenic	Intergenic	-4867	NR_029535	387229		NR_029535	ENSMUSG00000065530	Mir99a	Mirn99a|mir-99a|mmu-mir-99a	microRNA 99a	ncRNA
mm_50881.1	chr6	55681289	55681305	+	1	NA	promoter-TSS (NM_009717)	promoter-TSS (NM_009717)	-34	NM_009717	11922	Mm.5106	NM_009717	ENSMUSG00000037984	Neurod6	Atoh2|Math-2|Math2|Nex|Nex1m|bHLHa2	neurogenic differentiation 6	protein-coding
mm_136731.1	chr17	8283771	8283829	+	1	NA	promoter-TSS (NM_018819)	promoter-TSS (NM_018819)	-13	NM_018819	55951	Mm.288510	NM_018819	ENSMUSG00000023861	Mpc1	0610006G08Rik|3830411I18Rik|Brp44l	mitochondrial pyruvate carrier 1	protein-coding
mm_65033.1	chr7	18556738	18556751	-	1	NA	3' UTR (NM_001037168, exon 5 of 5)	3' UTR (NM_001037168, exon 5 of 5)	10561	NM_001037168	545925	Mm.440302	NM_001037168	ENSMUSG00000070797	Psg27	EG545925|cea15	pregnancy-specific glycoprotein 27	protein-coding
mm_1336.1	chr1	66062744	66062747	+	1	NA	Intergenic	Intergenic	-112584	NM_008632	17756	Mm.256966	NM_008632	ENSMUSG00000015222	Map2	G1-397-34|MAP-2|Mtap-2|Mtap2|repro4	microtubule-associated protein 2	protein-coding
mm_55462.1	chr6	67535195	67535226	-	1	NA	exon (NM_020047, exon 1 of 1)	exon (NM_020047, exon 1 of 1)	612	NM_020047	56753	Mm.439913	NM_020047	ENSMUSG00000051397	Tacstd2	C80403|EGP-1|GA733-1|Ly97|TROP2	tumor-associated calcium signal transducer 2	protein-coding
mm_134564.1	chr16	20338673	20338684	-	1	NA	intron (NM_013790, intron 27 of 29)	RSINE1|SINE|B4	-13274	NM_183158	224044	Mm.276400	NM_183158	ENSMUSG00000022818	Cyp2ab1	EG224044|F730023N20	cytochrome P450, family 2, subfamily ab, polypeptide 1	protein-coding
mm_19025.1	chr2	76967093	76967105	-	1	NA	exon (NM_011652, exon 10 of 313)	exon (NM_011652, exon 10 of 313)	15448	NM_028004	22138	Mm.373672	NM_011652	ENSMUSG00000051747	Ttn	1100001C23Rik|2310036G12Rik|2310057K23Rik|2310074I15Rik|AF006999|AV006427|D330041I19Rik|D830007G01Rik|L56|mdm|shru	titin	protein-coding
mm_173286.1	chrY	1732804	1732804	+	1	NA	Intergenic	IAPLTR4|LTR|ERVK	-273022	NM_148943	107868	Mm.347376	NM_148943	ENSMUSG00000069044	Usp9y	Dffry|Fafl2	ubiquitin specific peptidase 9, Y chromosome	protein-coding
mm_46004.1	chr5	90696103	90696116	-	1	NA	Intergenic	Intergenic	-55582	NM_001310656	73246	Mm.30172	NM_028478	ENSMUSG00000029370	Rassf6	1600016B17Rik	Ras association (RalGDS/AF-6) domain family member 6	protein-coding
mm_23598.1	chr3	65109044	65109089	+	1	NA	promoter-TSS (NM_010597)	promoter-TSS (NM_010597)	-302	NM_010597	16497	Mm.316402	NM_010597	ENSMUSG00000027827	Kcnab1	Akr8a8|Kvbeta1.1|mKv(beta)1	potassium voltage-gated channel, shaker-related subfamily, beta member 1	protein-coding
mm_167247.1	chr8	23058582	23058597	+	1	NA	non-coding (NR_102386, exon 1 of 45)	non-coding (NR_102386, exon 1 of 45)	330	NR_102385	11733	Mm.334444	NM_031158	ENSMUSG00000031543	Ank1	Ank-1|nb|pale	ankyrin 1, erythroid	protein-coding
mm_87849.1	chr10	60933088	60933099	+	1	NA	intron (NR_033616, intron 1 of 2)	intron (NR_033616, intron 1 of 2)	5039	NR_033616	73616	Mm.159038	NR_033616	ENSMUSG00000037247	Pldi	1700125F08Rik|Poldi	polymorphic derived intron containing	ncRNA
mm_69057.1	chr7	126884961	126884977	-	1	NA	promoter-TSS (NM_001163775)	promoter-TSS (NM_001163775)	-2	NM_001163774	381921	Mm.259634	NM_001163774	ENSMUSG00000059981	Taok2	1110033K02Rik|B230344N16|MAP3K17|PSK|PSK1|TAO1|TAO2|mKIAA0881	TAO kinase 2	protein-coding
mm_73721.1	chr8	112018704	112018722	+	1	NA	3' UTR (NM_020584, exon 3 of 3)	3' UTR (NM_020584, exon 3 of 3)	7354	NM_020584	57321	Mm.213064	NM_020584	ENSMUSG00000033430	Terf2ip	Rap1	telomeric repeat binding factor 2, interacting protein	protein-coding
mm_159630.1	chr4	137593793	137593793	+	1	NA	promoter-TSS (NM_130879)	promoter-TSS (NM_130879)	-396	NM_001347227	170707	Mm.218478	NM_130879	ENSMUSG00000043411	Usp48	2810449C13Rik|AI115503|BC021769|D330022K21Rik|Usp31	ubiquitin specific peptidase 48	protein-coding
mm_165019.1	chr19	31910375	31910380	-	1	NA	intron (NM_001081074, intron 3 of 11)	intron (NM_001081074, intron 3 of 11)	41616	NM_001081074	69865	Mm.87538	NM_001081074	ENSMUSG00000052595	A1cf	1810073H04Rik|ACF64|ACF65|ASP|Acf|MCM|MerCreMer|Tg(Myh6-cre/Esr1*)1Jmk|mer	APOBEC1 complementation factor	protein-coding
mm_158412.1	chrX	136993028	136993058	-	1	NA	promoter-TSS (NM_025893)	promoter-TSS (NM_025893)	-11	NM_001114179	67062	Mm.276518	NM_001082412	ENSMUSG00000044348	Slc25a53	2310046F18Rik|2810402A17Rik|AI448995|AI841128|Mcart6	solute carrier family 25, member 53	protein-coding
mm_52855.1	chr6	121871311	121871321	+	1	NA	exon (NM_008645, exon 17 of 36)	exon (NM_008645, exon 17 of 36)	32775	NM_008645	17836	Mm.1311	NM_008645	ENSMUSG00000059908	Mug1	-	murinoglobulin 1	protein-coding
mm_6678.1	chr1	80544244	80544263	-	1	NA	intron (NM_175291, intron 31 of 55)	RLTR21|LTR|ERVK	98321	NR_040460	72208	Mm.396181	NR_040460	ENSMUSG00000101483	1700016L21Rik	Jr3	RIKEN cDNA 1700016L21 gene	ncRNA
mm_76670.1	chr8	93500773	93500778	-	1	NA	intron (NM_001003951, intron 11 of 12)	RMER17C|LTR|ERVK	34932	NM_001003951	67935	Mm.65457	NM_001003951	ENSMUSG00000058019	Ces5a	1700081L16Rik|1700122C07Rik|BB081581|Ces7|Gm503|cauxin	carboxylesterase 5A	protein-coding
mm_12817.1	chr2	80316757	80316768	+	1	NA	intron (NM_024181, intron 1 of 22)	intron (NM_024181, intron 1 of 22)	1296	NM_024181	66861	Mm.21762	NM_024181	ENSMUSG00000027006	Dnajc10	1200006L06Rik|D2Ertd706e|ERdj5|JPDI	DnaJ heat shock protein family (Hsp40) member C10	protein-coding
mm_47920.1	chr5	135001366	135001376	-	1	NA	promoter-TSS (NR_026907)	promoter-TSS (NR_026907)	-21	NR_026907	71304	Mm.482317	NR_026907	ENSMUSG00000054909	Wbscr25	4933433J03Rik|4933439O14Rik	Williams Beuren syndrome chromosome region 25 (human)	ncRNA
mm_141438.1	chr17	29579430	29579451	-	1	NA	non-coding (NR_045447, exon 4 of 4)	non-coding (NR_045447, exon 4 of 4)	16865	NR_045447	74092	Mm.396264	NR_045447	ENSMUSG00000089900	Tbc1d22bos	0610038L08Rik	TBC1 domain family, member 22B, opposite strand	ncRNA
mm_81903.1	chr9	119983125	119983131	+	1	NA	intron (NM_153287, intron 1 of 4)	CpG	1530	NM_153287	215418	Mm.491094	NM_153287	ENSMUSG00000032515	Csrnp1	4931429D10Rik|Axud1|CSRNP-1|URAX1|taip-3	cysteine-serine-rich nuclear protein 1	protein-coding
mm_15793.1	chr2	164425968	164426011	+	1	NA	3' UTR (NM_011521, exon 5 of 5)	3' UTR (NM_011521, exon 5 of 5)	17199	NM_011521	20971	Mm.3815	NM_011521	ENSMUSG00000017009	Sdc4	AA959608|AW108331|S4|Synd4|ryudocan|syndecan-4	syndecan 4	protein-coding
mm_121817.1	chr14	20452177	20452183	-	1	NA	promoter-TSS (NM_001163638)	promoter-TSS (NM_001163638)	45	NM_001163638	76670	Mm.159759	NM_029698	ENSMUSG00000039543	Cfap70	Ttc18	cilia and flagella associated protein 70	protein-coding
mm_114289.1	chr13	58806635	58806655	+	1	NA	promoter-TSS (NM_008745)	promoter-TSS (NM_008745)	76	NM_008745	18212	Mm.130054	NM_008745	ENSMUSG00000055254	Ntrk2	GP145-TrkB/GP95-TrkB|Tkrb|trk-B|trkB	neurotrophic tyrosine kinase, receptor, type 2	protein-coding
mm_260.1	chr1	20836827	20836848	+	1	NA	Intergenic	Intergenic	-16624	NM_008563	17215	Mm.4502	NM_008563	ENSMUSG00000041859	Mcm3	AL033361|C80350|Mcmd|P1|p1.m	minichromosome maintenance complex component 3	protein-coding
mm_74500.1	chr8	7580231	7580241	-	1	NA	Intergenic	L1MB1|LINE|L1	1080537	NM_010111	13642	Mm.209813	NM_010111	ENSMUSG00000001300	Efnb2	ELF-2|Epl5|Eplg5|Htk-L|LERK-5|Lerk5|NLERK-1	ephrin B2	protein-coding
mm_7580.1	chr1	125393767	125393777	-	1	NA	3' UTR (NM_023735, exon 12 of 12)	3' UTR (NM_023735, exon 12 of 12)	41955	NM_023735	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding
mm_75340.1	chr8	43306724	43306744	-	1	NA	intron (NM_009556, intron 1 of 3)	intron (NM_009556, intron 1 of 3)	275	NM_009556	22702	Mm.285848	NM_009556	ENSMUSG00000051176	Zfp42	Rex-1|Rex1|Zfp-42	zinc finger protein 42	protein-coding
mm_37066.1	chr4	116122793	116122796	-	1	NA	intron (NM_009015, intron 2 of 17)	intron (NM_009015, intron 2 of 17)	895	NM_009015	19366	Mm.3655	NM_009015	ENSMUSG00000028702	Rad54l	RAD54	RAD54 like (S. cerevisiae)	protein-coding
mm_124679.1	chr15	6429466	6429481	+	1	NA	exon (NM_023118, exon 10 of 15)	exon (NM_023118, exon 10 of 15)	-15860	NM_013485	12279	Mm.29095	NM_013485	ENSMUSG00000022149	C9	-	complement component 9	protein-coding
mm_82715.1	chr9	24695558	24695558	-	1	NA	intron (NM_001166207, intron 1 of 21)	intron (NM_001166207, intron 1 of 21)	735	NM_001166207	320752	Mm.46158	NM_001166207	ENSMUSG00000085576	Dpy19l2	4932443J21Rik|Gm18376	dpy-19-like 2 (C. elegans)	protein-coding
mm_38353.1	chr4	137785507	137785516	-	1	NA	intron (NM_007431, intron 1 of 11)	intron (NM_007431, intron 1 of 11)	10873	NM_007431	11647	Mm.288186	NM_007431	ENSMUSG00000028766	Alpl	ALP|APTNAP|Akp-2|Akp2|TNAP|TNSALP	alkaline phosphatase, liver/bone/kidney	protein-coding
mm_25615.1	chr3	118431494	118431519	+	1	NA	Intergenic	Intergenic	-2351	NR_029551	387155		NR_029551	ENSMUSG00000065569	Mir137	Mirn137|mir-137|mmu-mir-137	microRNA 137	ncRNA
mm_136902.1	chr17	13015247	13015261	+	1	NA	3' UTR (NM_013671, exon 5 of 5)	3' UTR (NM_013671, exon 5 of 5)	7415	NM_013671	20656	Mm.290876	NM_013671	ENSMUSG00000006818	Sod2	MnSOD|Sod-2	superoxide dismutase 2, mitochondrial	protein-coding
mm_143909.1	chr17	85090205	85090275	-	1	NA	promoter-TSS (NM_001163624)	promoter-TSS (NM_001163624)	27	NM_145984	213760	Mm.259035	NM_145984	ENSMUSG00000024127	Prepl	2810457N15Rik|9530014L06Rik|D030028O16Rik|mKIAA0436	prolyl endopeptidase-like	protein-coding
mm_169751.1	chr15	89659643	89659655	+	1	NA	Intergenic	L1Md_A|LINE|L1	-67726	NM_026817	68708	Mm.23258	NM_026817	ENSMUSG00000022621	Rabl2	1110031N17Rik|AW549303|Rabl2a	RAB, member RAS oncogene family-like 2	protein-coding
mm_106967.1	chr12	8936008	8936039	+	1	NA	exon (NM_008640, exon 5 of 7)	exon (NM_008640, exon 5 of 7)	-11906	NM_010770	17182	Mm.42226	NM_010770	ENSMUSG00000020583	Matn3	AV009181	matrilin 3	protein-coding
mm_114444.1	chr13	66563899	66563916	+	1	NA	Intergenic	Intergenic	-122789	NM_001290196	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
mm_94737.1	chr11	21091298	21091339	+	1	NA	promoter-TSS (NM_023324)	promoter-TSS (NM_023324)	-6	NM_023324	67245	Mm.28957	NM_023324	ENSMUSG00000020134	Peli1	2810468L03Rik|A930031K15Rik|AA409794|AI586297|D11Ertd676e	pellino 1	protein-coding
mm_50141.1	chr6	41543340	41543351	+	1	NA	Intergenic	Intergenic	21569	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_84830.1	chr9	78205997	78206029	-	1	NA	exon (NM_010357, exon 5 of 7)	exon (NM_010357, exon 5 of 7)	14047	NM_010357	14860	Mm.2662	NM_010357	ENSMUSG00000032348	Gsta4	GST5.7|mGsta4	glutathione S-transferase, alpha 4	protein-coding
mm_112839.1	chr13	20827665	20827700	+	1	NA	intron (NM_012054, intron 2 of 20)	RLTR25B|LTR|ERVK	33569	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_155719.1	chrX	96112194	96112210	+	1	NA	intron (NM_010833, intron 1 of 12)	ID_B1|SINE|B4	16157	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_18179.1	chr2	45110337	45110376	-	1	NA	promoter-TSS (NM_001289521)	promoter-TSS (NM_001289521)	-79	NM_001289521	24136	Mm.440702	NM_015753	ENSMUSG00000026872	Zeb2	9130203F04Rik|D130016B08Rik|SIP1|Zfhx1b|Zfx1b|Zfxh1b	zinc finger E-box binding homeobox 2	protein-coding
mm_162330.1	chr1	41743570	41743588	+	1	NA	Intergenic	Intergenic	-562327	NR_040475	74897	Mm.243822	NR_040475	ENSMUSG00000104072	4930448I06Rik	-	RIKEN cDNA 4930448I06 gene	ncRNA
mm_145277.1	chr18	53109363	53109365	+	1	NA	Intergenic	Lx8|LINE|L1	-67001	NM_026386	67804	Mm.252171	NM_026386	ENSMUSG00000034484	Snx2	0610030A03Rik	sorting nexin 2	protein-coding
mm_127927.1	chr15	10454808	10454841	-	1	NA	exon (NM_030046, exon 7 of 12)	exon (NM_030046, exon 7 of 12)	15692	NM_030046	78244	Mm.297862	NM_030046	ENSMUSG00000044224	Dnajc21	4930461P20Rik|9930116P15Rik	DnaJ heat shock protein family (Hsp40) member C21	protein-coding
mm_145667.1	chr18	61256795	61256800	+	1	NA	intron (NM_146086, intron 10 of 21)	MIRb|SINE|MIR	36298	NM_146086	225600	Mm.391106	NM_146086	ENSMUSG00000024575	Pde6a	Pdea|nmf282	phosphodiesterase 6A, cGMP-specific, rod, alpha	protein-coding
mm_11212.1	chr2	29625061	29625072	+	1	NA	intron (NM_001039087, intron 1 of 25)	intron (NM_001039087, intron 1 of 25)	5346	NM_001039086	107746	Mm.298274	NM_054050	ENSMUSG00000039844	Rapgef1	4932418O06Rik|C3G|Grf2	Rap guanine nucleotide exchange factor (GEF) 1	protein-coding
mm_37832.1	chr4	132029971	132029975	-	1	NA	intron (NM_183428, intron 1 of 20)	PB1D9|SINE|Alu	19105	NM_001128606	269587	Mm.30038	NM_183428	ENSMUSG00000028906	Epb41	4.1R|AI415518|D4Ertd442e|Elp-1|Elp1|Epb4.1|mKIAA4056	erythrocyte membrane protein band 4.1	protein-coding
mm_52507.1	chr6	115361013	115361047	+	1	NA	promoter-TSS (NM_001127330)	promoter-TSS (NM_001127330)	79	NM_001127330	19016	Mm.3020	NM_011146	ENSMUSG00000000440	Pparg	Nr1c3|PPAR-gamma|PPAR-gamma2|PPARgamma|PPARgamma2	peroxisome proliferator activated receptor gamma	protein-coding
mm_7262.1	chr1	94052558	94052573	-	1	NA	promoter-TSS (NM_008798)	promoter-TSS (NM_008798)	-12	NM_008798	18566	Mm.5024	NM_008798	ENSMUSG00000026285	Pdcd1	Ly101|PD-1|Pdc1	programmed cell death 1	protein-coding
mm_97670.1	chr11	79673932	79673944	+	1	NA	intron (NR_045898, intron 2 of 2)	intron (NR_045898, intron 2 of 2)	1148	NR_045898	72218	Mm.443271	NR_045898	ENSMUSG00000086569	Rab11fip4os2	1700020F10Rik|4930542H20Rik|Rab11fib4os2	RAB11 family interacting protein 4 (class II), opposite strand 2	ncRNA
mm_103657.1	chr11	78977733	78977739	-	1	NA	intron (NM_001159301, intron 1 of 9)	intron (NM_001159301, intron 1 of 9)	7188	NM_001159301	16859	Mm.341434	NM_010708	ENSMUSG00000001123	Lgals9	AA407335|AI194909|AI265545|LGALS35|Lgals5|gal-9|galectin-9	lectin, galactose binding, soluble 9	protein-coding
mm_63047.1	chr7	121734496	121734508	+	1	NA	promoter-TSS (NM_011326)	promoter-TSS (NM_011326)	23	NM_011326	20278	Mm.35247	NM_011326	ENSMUSG00000000216	Scnn1g	SCNEG	sodium channel, nonvoltage-gated 1 gamma	protein-coding
mm_62082.1	chr7	92933148	92933161	+	1	NA	exon (NM_028243, exon 9 of 9)	exon (NM_028243, exon 9 of 9)	57901	NM_028243	72461	Mm.389969	NM_028243	ENSMUSG00000061119	Prcp	2510048K03Rik|2610104A14Rik|AI451719|HUMPCP|PCP	prolylcarboxypeptidase (angiotensinase C)	protein-coding
mm_146261.1	chr18	77820356	77820381	+	1	NA	intron (NM_013831, intron 1 of 14)	PB1D10|SINE|Alu	25818	NM_013831	19201	Mm.57174	NM_013831	ENSMUSG00000025429	Pstpip2	MAYP|cmo	proline-serine-threonine phosphatase-interacting protein 2	protein-coding
mm_134764.1	chr16	23496259	23496261	-	1	NA	intron (NM_008555, intron 2 of 15)	intron (NM_008555, intron 2 of 15)	24330	NM_008555	17174	Mm.1213	NM_008555	ENSMUSG00000022887	Masp1	AW048060|CCPII|Crarf|Masp1/3	mannan-binding lectin serine peptidase 1	protein-coding
mm_66781.1	chr7	46958476	46958480	-	1	NA	promoter-TSS (NM_001040695)	promoter-TSS (NM_001040695)	40	NM_001040695	54122	Mm.1999	NM_016855	ENSMUSG00000043262	Uevld	8430408E05Rik|Attp	UEV and lactate/malate dehyrogenase domains	protein-coding
mm_18906.1	chr2	76720707	76720718	-	1	NA	exon (NM_011652, exon 296 of 313)	exon (NM_011652, exon 296 of 313)	45397	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_76873.1	chr8	105565907	105565914	-	1	NA	TTS (NM_001271806)	TTS (NM_001271806)	130	NM_013477	11972	Mm.17708	NM_013477	ENSMUSG00000013160	Atp6v0d1	AI267038|Ac39|Atp6d|P39|VATX|Vma6	ATPase, H+ transporting, lysosomal V0 subunit D1	protein-coding
mm_169521.1	chr14	8800321	8800330	-	1	NA	Intergenic	Intergenic	133935	NR_045968	74859	Mm.84041	NR_045968	ENSMUSG00000097898	4930455B14Rik	1700027C12Rik	RIKEN cDNA 4930455B14 gene	ncRNA
mm_91590.1	chr10	40258113	40258132	-	1	NA	promoter-TSS (NM_026113)	promoter-TSS (NM_026113)	-457	NM_026113	67371	Mm.64104	NM_026113	ENSMUSG00000019837	Gtf3c6	2410016F19Rik|AU019813	general transcription factor IIIC, polypeptide 6, alpha	protein-coding
mm_158452.1	chrX	140543178	140543195	-	1	NA	promoter-TSS (NM_010286)	promoter-TSS (NM_010286)	1	NM_010286	14605	Mm.22216	NM_010286	ENSMUSG00000031431	Tsc22d3	DIP|Dsip1|Gilz|TSC-22R|Tilz3	TSC22 domain family, member 3	protein-coding
mm_153170.1	chr19	34493487	34493515	-	1	NA	3' UTR (NM_021460, exon 10 of 10)	3' UTR (NM_021460, exon 10 of 10)	-18366	NM_009890	12642	Mm.30824	NM_009890	ENSMUSG00000050370	Ch25h	AI462618|m25OH	cholesterol 25-hydroxylase	protein-coding
mm_26365.1	chr3	142560155	142560166	+	1	NA	promoter-TSS (NM_001289493)	promoter-TSS (NM_001289493)	108	NM_001289492	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_127653.1	chr15	102493490	102493501	+	1	NA	intron (NM_001103165, intron 14 of 14)	intron (NM_001103165, intron 14 of 14)	22863	NM_001174073	18521	Mm.236513	NM_011042	ENSMUSG00000056851	Pcbp2	AW412548|Hnrpx|alphaCP-2	poly(rC) binding protein 2	protein-coding
mm_130722.1	chr15	101078490	101078513	-	1	NA	Intergenic	CpG	-24102	NM_001214911	668225	Mm.385011	NM_001214911	ENSMUSG00000095440	Fignl2	EG668225	fidgetin-like 2	protein-coding
mm_129703.1	chr15	81726222	81726226	-	1	NA	intron (NM_001146174, intron 1 of 15)	intron (NM_001146174, intron 1 of 15)	3695	NM_011241	19387	Mm.270975	NM_011241	ENSMUSG00000022391	Rangap1	C79654|Fug1|mKIAA1835	RAN GTPase activating protein 1	protein-coding
mm_120447.1	chr14	65968562	65968567	+	1	NA	promoter-TSS (NM_013492)	promoter-TSS (NM_013492)	81	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_80984.1	chr9	103220981	103220991	+	1	NA	exon (NM_133977, exon 9 of 17)	exon (NM_133977, exon 9 of 17)	9300	NM_133977	22041	Mm.37214	NM_133977	ENSMUSG00000032554	Trf	AI266983|Cd176|HP|Tf|Tfn|hpx	transferrin	protein-coding
mm_8404.1	chr1	151517975	151517982	-	1	NA	Intergenic	RMER17B2|LTR|ERVK	-17155	NM_011277	19821	Mm.474038	NM_011277	ENSMUSG00000026484	Rnf2	AI326319|AI450156|AU019207|Ring1B|dinG	ring finger protein 2	protein-coding
mm_30590.1	chr4	6191094	6191122	+	1	NA	promoter-TSS (NM_026534)	promoter-TSS (NM_026534)	3	NM_026534	68053	Mm.404043	NM_026534	ENSMUSG00000028243	Ubxn2b	3110003A22Rik|6430407D20Rik|AI451665|p37	UBX domain protein 2B	protein-coding
mm_71784.1	chr8	66697252	66697262	+	1	NA	promoter-TSS (NM_010934)	promoter-TSS (NM_010934)	-165	NM_010934	18166	Mm.5112	NM_010934	ENSMUSG00000036437	Npy1r	Npyr|Y1-R	neuropeptide Y receptor Y1	protein-coding
mm_60250.1	chr7	43774653	43774664	+	1	NA	promoter-TSS (NM_001177373)	promoter-TSS (NM_001177373)	41	NM_001177373	56538	Mm.154276	NM_019974	ENSMUSG00000067616	Klk11	2310015I08Rik|Prss20|TLSP	kallikrein related-peptidase 11	protein-coding
mm_81552.1	chr9	110333341	110333389	+	1	NA	promoter-TSS (NM_001001144)	promoter-TSS (NM_001001144)	9	NM_001001144	235623	Mm.288741	NM_001001144	ENSMUSG00000032485	Scap	9530044G19|mKIAA0199	SREBF chaperone	protein-coding
mm_79843.1	chr9	64811452	64811476	+	1	NA	5' UTR (NM_001162917, exon 2 of 35)	5' UTR (NM_001162917, exon 2 of 35)	453	NM_001162917	102442	Mm.222473	NM_176935	ENSMUSG00000053641	Dennd4a	AI115600|AI851943|F730015K02Rik	DENN/MADD domain containing 4A	protein-coding
mm_119604.1	chr14	51091172	51091192	+	1	NA	5' UTR (NM_001161731, exon 1 of 2)	5' UTR (NM_001161731, exon 1 of 2)	105	NM_021472	58809	Mm.202665	NM_021472	ENSMUSG00000021876	Rnase4	C730049F20Rik|Rab1	ribonuclease, RNase A family 4	protein-coding
mm_25825.1	chr3	127950304	127950304	+	1	NA	intron (NR_040552, intron 4 of 4)	MER5A|DNA|hAT-Charlie	34133	NR_040552	329753	Mm.119720	NR_040552	ENSMUSG00000104763	9830132P13Rik	9830132P13	RIKEN cDNA 9830132P13 gene	ncRNA
mm_156142.1	chrX	129749831	129749842	+	1	NA	promoter-TSS (NM_172493)	promoter-TSS (NM_172493)	94	NM_172493	54004	Mm.10763	NM_017398	ENSMUSG00000034480	Diaph2	Dia3|Diap2|Drf2|E430022I22Rik	diaphanous related formin 2	protein-coding
mm_106220.1	chr11	117040316	117040325	-	1	NA	Intergenic	LTR53|LTR|ERVL	-36463	NR_027059	76972	Mm.309167	NR_027059	ENSMUSG00000086859	Snhg20	2810008D09Rik	small nucleolar RNA host gene 20	ncRNA
mm_167392.1	chr8	94985607	94985609	+	1	NA	intron (NM_018882, intron 1 of 13)	intron (NM_018882, intron 1 of 13)	1209	NM_018882	14766	Mm.290834	NM_018882	ENSMUSG00000031785	Adgrg1	Cyt28|Gpr56|TM7LN4|TM7XN1	adhesion G protein-coupled receptor G1	protein-coding
mm_43827.1	chr5	142970570	142970592	+	1	NA	exon (NM_007984, exon 4 of 5)	exon (NM_007984, exon 4 of 5)	10226	NM_007984	14086	Mm.289707	NM_007984	ENSMUSG00000029581	Fscn1	AI663989|Fan1|fascin-1	fascin actin-bundling protein 1	protein-coding
mm_75408.1	chr8	46426342	46426382	-	1	NA	Intergenic	Intergenic	-44675	NM_007981	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_33867.1	chr4	135948417	135948427	+	1	NA	intron (NM_008254, intron 1 of 8)	L2c|LINE|L2	1969	NM_008254	15356	Mm.482102	NM_008254	ENSMUSG00000028672	Hmgcl	AW476067|HL	3-hydroxy-3-methylglutaryl-Coenzyme A lyase	protein-coding
mm_125409.1	chr15	41751655	41751683	+	1	NA	intron (NM_001130166, intron 3 of 16)	intron (NM_001130166, intron 3 of 16)	-37365	NM_001130165	170719	Mm.254267	NM_130885	ENSMUSG00000022307	Oxr1	2210416C20Rik|C7|C7B	oxidation resistance 1	protein-coding
mm_73033.1	chr8	94180094	94180203	+	1	NA	exon (NM_013602, exon 3 of 3)	exon (NM_013602, exon 3 of 3)	1059	NM_013602	17748	Mm.192991	NM_013602	ENSMUSG00000031765	Mt1	MT-I|Mt-1	metallothionein 1	protein-coding
mm_45002.1	chr5	38230717	38230761	-	1	NA	exon (NM_025281, exon 6 of 9)	exon (NM_025281, exon 6 of 9)	10257	NM_025281	17089	Mm.28560	NM_025281	ENSMUSG00000067367	Lyar	MLZ-264	Ly1 antibody reactive clone	protein-coding
mm_73781.1	chr8	116979085	116979109	+	1	NA	promoter-TSS (NM_027103)	promoter-TSS (NM_027103)	-154	NM_027103	69528	Mm.272846	NM_027103	ENSMUSG00000031847	1700030J22Rik	-	RIKEN cDNA 1700030J22 gene	protein-coding
mm_35313.1	chr4	25614973	25614984	-	1	NA	3' UTR (NM_010243, exon 3 of 3)	3' UTR (NM_010243, exon 3 of 3)	185025	NM_010243	14348	Mm.39101	NM_010243	ENSMUSG00000055373	Fut9	AI746471|AU067636|mFUT9|mFuc-TIX	fucosyltransferase 9	protein-coding
mm_29055.1	chr3	103749432	103749446	-	1	NA	non-coding (NR_125731, exon 14 of 16)	non-coding (NR_125731, exon 14 of 16)	-11438	NM_133859	99543	Mm.211535	NM_133859	ENSMUSG00000027848	Olfml3	2810002E22Rik|AI115209|AW550633|HNOEL-iso|ONT3|mONT3	olfactomedin-like 3	protein-coding
mm_40103.1	chr5	34660295	34660302	+	1	NA	promoter-TSS (NM_019497)	promoter-TSS (NM_019497)	-81	NM_001080743	14772	Mm.117076	NM_019497	ENSMUSG00000052783	Grk4	A830025H08Rik|GRK|Gprk2l|Gprk4	G protein-coupled receptor kinase 4	protein-coding
mm_76522.1	chr8	87472201	87472261	-	1	NA	promoter-TSS (NR_125722)	promoter-TSS (NR_125722)	361	NM_019626	12404	Mm.4880	NM_019626	ENSMUSG00000031654	Cbln1	AI323299	cerebellin 1 precursor protein	protein-coding
mm_118439.1	chr14	8080387	8080399	+	1	NA	promoter-TSS (NM_025938)	promoter-TSS (NM_025938)	80	NM_025938	67053	Mm.210048	NM_025938	ENSMUSG00000023156	Rpp14	2610511E03Rik|AA682089	ribonuclease P 14 subunit	protein-coding
mm_104899.1	chr11	99614846	99614847	-	1	NA	promoter-TSS (NM_027800)	promoter-TSS (NM_027800)	0	NM_027800	71453	Mm.51510	NM_027800	ENSMUSG00000060756	Krtap2-4	5530401P19Rik|KAP2.4|KRTAP2.4	keratin associated protein 2-4	protein-coding
mm_98512.1	chr11	94952371	94952384	+	1	NA	3' UTR (NM_007742, exon 51 of 51)	3' UTR (NM_007742, exon 51 of 51)	-15216	NM_018792	54388	Mm.30482	NM_018792	ENSMUSG00000038994	Hils1	H1.9|TISP64	histone H1-like protein in spermatids 1	protein-coding
mm_35306.1	chr4	24851080	24851112	-	1	NA	promoter-TSS (NM_001163020)	promoter-TSS (NM_001163020)	-10	NM_001033531	212390	Mm.412074	NM_001033531	ENSMUSG00000040387	Klhl32	6430524H05Rik|D4Ertd389e|Gm1356|mKIAA1900	kelch-like 32	protein-coding
mm_167061.1	chr7	94141625	94141626	+	1	NA	Intergenic	Lx3A|LINE|L1	1061746	NM_021427	58238	Mm.113787	NM_021427	ENSMUSG00000051515	Fam181b	A830059I20Rik|AB041569	family with sequence similarity 181, member B	protein-coding
mm_51666.1	chr6	86365641	86365658	+	1	NA	promoter-TSS (NM_025591)	promoter-TSS (NM_025591)	-34	NM_025591	66488	Mm.422972	NM_025591	ENSMUSG00000057497	Fam136a	2010309E21Rik|AW124904|Hyccin	family with sequence similarity 136, member A	protein-coding
mm_131043.1	chr16	3889705	3889714	+	1	NA	intron (NM_001290689, intron 1 of 5)	AT_rich|Low_complexity|Low_complexity	5090	NM_001290689	74763	Mm.28403	NM_029090	ENSMUSG00000005982	Naa60	1200013P24Rik|AI315146|Nat15	N(alpha)-acetyltransferase 60, NatF catalytic subunit	protein-coding
mm_125991.1	chr15	76354450	76354468	+	1	NA	TTS (NM_026859)	TTS (NM_026859)	3165	NM_026859	68877	Mm.289680	NM_026859	ENSMUSG00000022553	Maf1	1110068E11Rik|AU042856	MAF1 homolog, negative regulator of RNA polymerase III	protein-coding
mm_168874.1	chr12	38527376	38527379	+	1	NA	intron (NM_178681, intron 22 of 24)	intron (NM_178681, intron 22 of 24)	87144	NR_045943	73867	Mm.78933	NR_045943		4930428E07Rik	-	RIKEN cDNA 4930428E07 gene	ncRNA
mm_166889.1	chr7	28131593	28131599	-	1	NA	exon (NM_001164655, exon 3 of 20)	exon (NM_001164655, exon 3 of 20)	2130	NM_001164655	319482	Mm.483194	NM_176924	ENSMUSG00000078776	9530053A07Rik	FCGBP	RIKEN cDNA 9530053A07 gene	protein-coding
mm_72674.1	chr8	84911103	84911118	+	1	NA	TTS (NM_019945)	TTS (NM_019945)	-2225	NR_103491	100503676	Mm.437155	NR_103491	ENSMUSG00000003812	Gm38426	-	predicted gene, 38426	ncRNA
mm_123126.1	chr14	56180779	56180781	-	1	NA	Intergenic	Intergenic	-6181	NM_153052	245839	Mm.207063	NM_153052	ENSMUSG00000015443	Gzmn	GrN	granzyme N	protein-coding
mm_79133.1	chr9	47554356	47554359	+	1	NA	intron (NM_001025600, intron 1 of 8)	intron (NM_001025600, intron 1 of 8)	24005	NM_018770	54725	Mm.234832	NM_018770	ENSMUSG00000032076	Cadm1	2900073G06Rik|3100001I08Rik|AI987920|Bl2|Igsf4|Igsf4a|Necl2|RA175|RA175A|RA175B|RA175C|RA175N|ST17|SgIGSF|SynCam|Tslc1	cell adhesion molecule 1	protein-coding
mm_128554.1	chr15	55906590	55906620	-	1	NA	5' UTR (NM_016667, exon 1 of 7)	5' UTR (NM_016667, exon 1 of 7)	344	NM_016667	20649	Mm.309425	NM_016667	ENSMUSG00000060429	Sntb1	-	syntrophin, basic 1	protein-coding
mm_115838.1	chr13	21287230	21287235	-	1	NA	3' UTR (NM_010343, exon 5 of 5)	3' UTR (NM_010343, exon 5 of 5)	5454	NM_010343	14780	Mm.1332	NM_010343	ENSMUSG00000004344	Gpx5	AV379049|Arep	glutathione peroxidase 5	protein-coding
mm_80612.1	chr9	88327036	88327045	+	1	NA	promoter-TSS (NM_011851)	promoter-TSS (NM_011851)	-569	NM_011851	23959	Mm.244235	NM_011851	ENSMUSG00000032420	Nt5e	2210401F01Rik|5'-NT|AI447961|CD73|NT|Nt5|eNT	5' nucleotidase, ecto	protein-coding
mm_120383.1	chr14	64589803	64589848	+	1	NA	promoter-TSS (NR_029813)	promoter-TSS (NR_029813)	-832	NR_029813	387233		NR_029813	ENSMUSG00000065597	Mir124a-1	Mirn124a|Mirn124a-1	microRNA 124a-1	ncRNA
mm_140549.1	chr17	6993252	6993265	-	1	NA	intron (NM_026611, intron 6 of 8)	(CTG)n|Simple_repeat|Simple_repeat	14398	NM_026611	68195	Mm.181237	NM_026611	ENSMUSG00000094724	Rnaset2b	0610007O07Rik|4833423A10Rik|4930532K22Rik|C79750|RNASE6PL|Rnaset2	ribonuclease T2B	protein-coding
mm_95156.1	chr11	35784073	35784075	+	1	NA	intron (NM_145962, intron 6 of 6)	B4|SINE|B4	1678	NR_029754	723824		NR_029754	ENSMUSG00000065553	Mir103-1	Mirn103-1|mir-103-1	microRNA 103-1	ncRNA
mm_96216.1	chr11	62458415	62458469	+	1	NA	promoter-TSS (NM_001039536)	promoter-TSS (NM_001039536)	-18	NM_001039536	327942	Mm.390358	NM_199026	ENSMUSG00000014245	Pigl	Gm737	phosphatidylinositol glycan anchor biosynthesis, class L	protein-coding
mm_67700.1	chr7	89527065	89527082	-	1	NA	Intergenic	Intergenic	-9487	NM_029614	76453	Mm.250438	NM_029614	ENSMUSG00000039405	Prss23	2310046G15Rik|4930479H08Rik|AI790574|Spuve	protease, serine 23	protein-coding
mm_133884.1	chr16	96525500	96525563	+	1	NA	3' UTR (NM_008791, exon 3 of 3)	3' UTR (NM_008791, exon 3 of 3)	57925	NM_008791	18546	Mm.5023	NM_008791	ENSMUSG00000090223	Pcp4	P16Rimb19|Pcp-4|Pep19	Purkinje cell protein 4	protein-coding
mm_151401.1	chr19	56477725	56477731	+	1	NA	intron (NM_172641, intron 8 of 12)	intron (NM_172641, intron 8 of 12)	16091	NM_172641	226245	Mm.156742	NM_172641	ENSMUSG00000035818	Plekhs1	9930023K05Rik	pleckstrin homology domain containing, family S member 1	protein-coding
mm_83183.1	chr9	40984489	40984500	-	1	NA	intron (NM_001281954, intron 5 of 9)	intron (NM_001281954, intron 5 of 9)	20134	NM_001281954	54698	Mm.42791	NM_019465	ENSMUSG00000032021	Crtam	-	cytotoxic and regulatory T cell molecule	protein-coding
mm_168102.1	chr10	130594771	130594772	+	1	NA	Intergenic	(TTAGGG)n|Simple_repeat|Simple_repeat	-97392	NM_001103366	625131	Mm.469844	NM_001103366	ENSMUSG00000091511	Vmn2r87	EG625131	vomeronasal 2, receptor 87	protein-coding
mm_3875.1	chr1	160998083	160998087	+	1	NA	intron (NM_080844, intron 6 of 7)	PB1D7|SINE|Alu	19479	NM_080844	11905	Mm.260770	NM_080844	ENSMUSG00000026715	Serpinc1	AI114908|ATIII|At-3|At3	serine (or cysteine) peptidase inhibitor, clade C (antithrombin), member 1	protein-coding
mm_28430.1	chr3	90465611	90465620	-	1	NA	5' UTR (NM_008727, exon 1 of 22)	5' UTR (NM_008727, exon 1 of 22)	251	NM_008727	18160	Mm.4627	NM_008727	ENSMUSG00000027931	Npr1	AI893888|GC-A|NPR-A|NPRA|Pndr	natriuretic peptide receptor 1	protein-coding
mm_8320.1	chr1	144775445	144775451	-	1	NA	promoter-TSS (NM_022881)	promoter-TSS (NM_022881)	-27	NM_022881	64214	Mm.253927	NM_022881	ENSMUSG00000026357	Rgs18	-	regulator of G-protein signaling 18	protein-coding
mm_172808.1	chr9	123461818	123461819	+	1	NA	3' UTR (NM_153168, exon 21 of 21)	3' UTR (NM_153168, exon 21 of 21)	-16883	NM_013860	29806	Mm.10987	NM_013860	ENSMUSG00000025239	Limd1	AW822033|D9Ertd192e	LIM domains containing 1	protein-coding
mm_23154.1	chr3	40531392	40531432	+	1	NA	Intergenic	Intergenic	-8500	NR_040445	100040882	Mm.272869	NR_040445	ENSMUSG00000037884	1700017G19Rik	-	RIKEN cDNA 1700017G19 gene	ncRNA
mm_114868.1	chr13	94057664	94057686	+	1	NA	promoter-TSS (NM_172589)	promoter-TSS (NM_172589)	-121	NM_172589	218454	Mm.316553	NM_172589	ENSMUSG00000045312	Lhfpl2	6030465B15|AI447312|AW050335|mKIAA0206|vgim	lipoma HMGIC fusion partner-like 2	protein-coding
mm_140719.1	chr17	15375970	15375983	-	1	NA	promoter-TSS (NM_007865)	promoter-TSS (NM_007865)	-153	NM_007865	13388	Mm.4875	NM_007865	ENSMUSG00000014773	Dll1	Delta1	delta-like 1 (Drosophila)	protein-coding
mm_128211.1	chr15	36140500	36140510	-	1	NA	promoter-TSS (NM_001195748)	promoter-TSS (NM_001195748)	-105	NM_001195748	626596	Mm.321798	NM_001195748	ENSMUSG00000037627	Rgs22	-	regulator of G-protein signalling 22	protein-coding
mm_46430.1	chr5	104440616	104440642	-	1	NA	3' UTR (NM_001204203, exon 7 of 7)	3' UTR (NM_001204203, exon 7 of 7)	4437	NM_001204233	20750	Mm.288474	NM_009263	ENSMUSG00000029304	Spp1	2AR|Apl-1|BNSP|BSPI|Bsp|ETA-1|Eta|OP|Opn|Opnl|Ric|Spp-1	secreted phosphoprotein 1	protein-coding
mm_79565.1	chr9	58131889	58131902	+	1	NA	intron (NM_009291, intron 1 of 18)	intron (NM_009291, intron 1 of 18)	-2180	NM_001162476	20897	Mm.10801	NM_009291	ENSMUSG00000032327	Stra6	AI891933	stimulated by retinoic acid gene 6	protein-coding
mm_72364.1	chr8	80811601	80811602	+	1	NA	intron (NM_021356, intron 1 of 9)	intron (NM_021356, intron 1 of 9)	68878	NM_021356	14388	Mm.277409	NM_021356	ENSMUSG00000031714	Gab1	AA408973|AW107238	growth factor receptor bound protein 2-associated protein 1	protein-coding
mm_16022.1	chr2	167504142	167504150	+	1	NA	intron (NM_030743, intron 3 of 7)	CpG-8879	-11272	NM_170756	263876	Mm.34342	NM_170756	ENSMUSG00000047030	Spata2	AI504642|mKIAA0757	spermatogenesis associated 2	protein-coding
mm_58862.1	chr7	16908056	16908088	+	1	NA	intron (NM_008967, intron 1 of 1)	intron (NM_008967, intron 1 of 1)	1582	NM_008967	19222	Mm.287572	NM_008967	ENSMUSG00000043017	Ptgir	IP|PGI2	prostaglandin I receptor (IP)	protein-coding
mm_79739.1	chr9	62345424	62345442	+	1	NA	intron (NM_009672, intron 1 of 6)	intron (NM_009672, intron 1 of 6)	4090	NM_009672	11737	Mm.269088	NM_009672	ENSMUSG00000032249	Anp32a	Anp32|I1PP2A|LANP|PHAP1|W91701|pp32	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	protein-coding
mm_126317.1	chr15	79687997	79688013	+	1	NA	promoter-TSS (NM_028792)	promoter-TSS (NM_028792)	-133	NM_028792	74158	Mm.323393	NM_028792	ENSMUSG00000022426	Josd1	1300006C06Rik|mKIAA0063	Josephin domain containing 1	protein-coding
mm_99419.1	chr11	102316849	102316859	+	1	NA	intron (NM_001302955, intron 1 of 19)	CpG	433	NM_001044383	21429	Mm.2845	NM_011551	ENSMUSG00000020923	Ubtf	A930005G04Rik|NOR-90|Tcfubf|UBF|UBF-1|UBF1	upstream binding transcription factor, RNA polymerase I	protein-coding
mm_43067.1	chr5	124444469	124444471	+	1	NA	intron (NM_001310725, intron 1 of 6)	B1_Mus1|SINE|Alu	-1029	NM_001310723	67956	Mm.137966	NM_030241	ENSMUSG00000049327	Kmt5a	2410195B05Rik|AA617402|AW536475|PR-SET7|PR/SET07|Setd8	lysine methyltransferase 5A	protein-coding
mm_114001.1	chr13	52585234	52585269	+	1	NA	intron (NM_001198977, intron 1 of 13)	LTR65|LTR|ERV1	1814	NM_001198977	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_140312.1	chr17	86167819	86167825	+	1	NA	promoter-TSS (NM_011104)	promoter-TSS (NM_011104)	37	NM_011104	18754	Mm.24614	NM_011104	ENSMUSG00000045038	Prkce	5830406C15Rik|PKC[e]|PKCepsilon|Pkce|R75156	protein kinase C, epsilon	protein-coding
mm_73606.1	chr8	109999351	109999364	+	1	NA	3' UTR (NM_146214, exon 12 of 12)	3' UTR (NM_146214, exon 12 of 12)	8921	NM_146214	234724	Mm.28110	NM_146214	ENSMUSG00000001670	Tat	-	tyrosine aminotransferase	protein-coding
mm_167908.1	chrX	83779842	83779848	+	1	NA	intron (NM_007868, intron 19 of 78)	Lx3A|LINE|L1	-291921	NM_021898	100502723	Mm.383210	NM_021898	ENSMUSG00000035522	Tsga8	Halap-X|Halapx	testis specific gene A8	protein-coding
mm_111513.1	chr12	99627946	99627961	-	1	NA	promoter-TSS (NR_045288)	promoter-TSS (NR_045288)	21	NR_045288	73457	Mm.383439	NR_045288	ENSMUSG00000100211	1700064M15Rik	-	RIKEN cDNA 1700064M15 gene	ncRNA
mm_36437.1	chr4	82295878	82295882	-	1	NA	3' UTR (NM_001113209, exon 12 of 12)	3' UTR (NM_001113209, exon 12 of 12)	209899	NM_001286127	18028	Mm.317947	NM_008687	ENSMUSG00000008575	Nfib	6720429L07Rik|CTF|E030026I10Rik|NF-I/B|NF1-B|NFI-B	nuclear factor I/B	protein-coding
mm_102420.1	chr11	59227880	59227930	-	1	NA	5' UTR (NM_001130408, exon 1 of 5)	5' UTR (NM_001130408, exon 1 of 5)	257	NM_001130408	11840	Mm.371546	NM_007476	ENSMUSG00000048076	Arf1	-	ADP-ribosylation factor 1	protein-coding
mm_109451.1	chr12	111040834	111040839	+	1	NA	intron (NM_198023, intron 2 of 11)	intron (NM_198023, intron 2 of 11)	1038	NM_198023	217864	Mm.23808	NM_198023	ENSMUSG00000037896	Rcor1	5730409O11|6720480E22Rik|AU042633|D12Wsu95e|Rocr1|mKIAA0071	REST corepressor 1	protein-coding
mm_117202.1	chr13	64066142	64066146	-	1	NA	intron (NM_008291, intron 6 of 10)	B4A|SINE|B4	23057	NM_008291	15487	Mm.5109	NM_008291	ENSMUSG00000033122	Hsd17b3	-	hydroxysteroid (17-beta) dehydrogenase 3	protein-coding
mm_14105.1	chr2	125673078	125673133	+	1	NA	promoter-TSS (NM_025613)	promoter-TSS (NM_025613)	5	NM_025613	58521	Mm.425101	NM_025613	ENSMUSG00000091337	Eid1	2610002K20Rik|Cri1|EID-1|ORF12|PNAS-22|PTD014	EP300 interacting inhibitor of differentiation 1	protein-coding
mm_24010.1	chr3	87376461	87376465	+	1	NA	promoter-TSS (NM_178165)	promoter-TSS (NM_178165)	76	NM_001136236	229499	Mm.255203	NM_153090	ENSMUSG00000059994	Fcrl1	A230020G22Rik|Bxmas1|Bxmh1|Bxmh1b|Fcrh1|Fcrh1l|Fcrh1s|Ifgp1	Fc receptor-like 1	protein-coding
mm_166271.1	chr5	90472123	90472125	-	1	NA	exon (NM_009654, exon 11 of 15)	exon (NM_009654, exon 11 of 15)	11254	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_63751.1	chr7	131044295	131044298	+	1	NA	intron (NM_001347632, intron 5 of 47)	intron (NM_001347632, intron 5 of 47)	12220	NM_007769	12945	Mm.4138	NM_007769	ENSMUSG00000047517	Dmbt1	CRP|CRP-[a]|CRP-[b]|Crpd|DBMT1|gp300|p80	deleted in malignant brain tumors 1	protein-coding
mm_145206.1	chr18	50019740	50019748	+	1	NA	intron (NM_001177759, intron 1 of 1)	MER20|DNA|hAT-Charlie	-33538	NM_134131	106869	Mm.27740	NM_134131	ENSMUSG00000062210	Tnfaip8	AA987150|E130304C20Rik|ENSMUSG00000073567|Gg2-1|Gm10539|Nded|Ssc-2|Tipe	tumor necrosis factor, alpha-induced protein 8	protein-coding
mm_35589.1	chr4	42949517	42949527	-	1	NA	Intergenic	Intergenic	-3572	NM_019874	56323	Mm.20437	NM_019874	ENSMUSG00000036052	Dnajb5	1110058L06Rik|AI462558|Hsc40|Hsp40-3	DnaJ heat shock protein family (Hsp40) member B5	protein-coding
mm_339.1	chr1	30718726	30718735	+	1	NA	Intergenic	Intergenic	144526	NM_001081080	213109	Mm.194486	NM_025871	ENSMUSG00000048874	Phf3	2310061N19Rik|mKIAA0244	PHD finger protein 3	protein-coding
mm_116057.1	chr13	27509615	27509619	-	1	NA	exon (NM_023741, exon 4 of 6)	exon (NM_023741, exon 4 of 6)	3596	NM_023741	74188	Mm.46090	NM_023741	ENSMUSG00000021346	Prl8a8	1600032B14Rik|Ghd14|PLP-Cgamma|Prlpc3	prolactin family 8, subfamily a, member 81	protein-coding
mm_171709.1	chr4	76729058	76729062	+	1	NA	intron (NM_011211, intron 9 of 39)	L1Md_T|LINE|L1	-1450774	NM_025849	66928	Mm.24332	NM_025849	ENSMUSG00000028398	Tmem261	1700027K24Rik|3110001D03Rik	transmembrane protein 261	protein-coding
mm_143935.1	chr17	86167450	86167493	-	1	NA	promoter-TSS (NM_011104)	promoter-TSS (NM_011104)	-314	NM_011104	18754	Mm.24614	NM_011104	ENSMUSG00000045038	Prkce	5830406C15Rik|PKC[e]|PKCepsilon|Pkce|R75156	protein kinase C, epsilon	protein-coding
mm_117491.1	chr13	78196478	78196486	-	1	NA	promoter-TSS (NM_001347539)	promoter-TSS (NM_001347539)	-33	NM_001347539	13865	Mm.439653	NM_010151	ENSMUSG00000069171	Nr2f1	COUP-TF1|COUP-TFI|COUPTFA|EAR-3|EAR3|Erbal3|SVP44|Tcfcoup1	nuclear receptor subfamily 2, group F, member 1	protein-coding
mm_45630.1	chr5	76304957	76304993	-	1	NA	promoter-TSS (NM_001289826)	promoter-TSS (NM_001289826)	-183	NM_001289826	12753	Mm.3552	NM_007715	ENSMUSG00000029238	Clock	5330400M04Rik|KAT13D	circadian locomotor output cycles kaput	protein-coding
mm_158807.1	chrX	167264294	167264304	-	1	NA	promoter-TSS (NM_001313760)	promoter-TSS (NM_001313760)	30	NM_001313761	170744	Mm.196676	NM_133212	ENSMUSG00000040522	Tlr8	-	toll-like receptor 8	protein-coding
mm_87208.1	chr10	39732195	39732203	+	1	NA	promoter-TSS (NM_011264)	promoter-TSS (NM_011264)	39	NM_011264	19714	Mm.439723	NM_011264	ENSMUSG00000019841	Rev3l	Rev|Rev3|Sez4	REV3 like, DNA directed polymerase zeta catalytic subunit	protein-coding
mm_978.1	chr1	58393502	58393522	+	1	NA	intron (NM_025824, intron 1 of 11)	CpG	376	NM_025824	66882	Mm.21848	NM_025824	ENSMUSG00000051223	Bzw1	1200015E15Rik|mKIAA0005	basic leucine zipper and W2 domains 1	protein-coding
mm_59703.1	chr7	28693013	28693021	+	1	NA	promoter-TSS (NM_001163702)	promoter-TSS (NM_001163702)	-127	NM_001163702	233040	Mm.116116	NM_207238	ENSMUSG00000037463	Fbxo27	E130008B10Rik|FBG5|Gm161	F-box protein 27	protein-coding
mm_120799.1	chr14	74744210	74744219	+	1	NA	intron (NM_001285423, intron 6 of 8)	(T)n|Simple_repeat|Simple_repeat	11917	NM_016903	13885	Mm.38055	NM_016903	ENSMUSG00000021996	Esd	Es-10|Es10|FGH|sid478	esterase D/formylglutathione hydrolase	protein-coding
mm_87562.1	chr10	56115323	56115384	+	1	NA	exon (NM_001163833, exon 2 of 2)	exon (NM_001163833, exon 2 of 2)	8436	NM_001163833	73390	Mm.181475	NM_133751	ENSMUSG00000047669	Msl3l2	1700060H10Rik	male-specific lethal 3-like 2 (Drosophila)	protein-coding
mm_71619.1	chr8	57323327	57323335	+	1	NA	intron (NM_010402, intron 1 of 1)	intron (NM_010402, intron 1 of 1)	2348	NM_010402	15111	Mm.430844	NM_010402	ENSMUSG00000038193	Hand2	AI225906|AI661148|Ehand2|Hed|Th2|Thing2|bHLHa26|dHAND	heart and neural crest derivatives expressed transcript 2	protein-coding
mm_93210.1	chr10	94944536	94944546	-	1	NA	promoter-TSS (NM_018797)	promoter-TSS (NM_018797)	37	NM_018797	54712	Mm.256712	NM_018797	ENSMUSG00000074785	Plxnc1	2510048K12Rik|AW742158|CD232|Vespr	plexin C1	protein-coding
mm_134524.1	chr16	19236819	19236829	-	1	NA	Intergenic	RMER17B|LTR|ERVK	49917	NM_146451	258443	Mm.377506	NM_146451	ENSMUSG00000050742	Olfr164	MOR279-2	olfactory receptor 164	protein-coding
mm_130074.1	chr15	89356452	89356458	-	1	NA	promoter-TSS (NM_178919)	promoter-TSS (NM_178919)	736	NM_001271601	52683	Mm.143167	NM_001115132	ENSMUSG00000008690	Ncaph2	-	non-SMC condensin II complex, subunit H2	protein-coding
mm_128593.1	chr15	58125682	58125685	-	1	NA	intron (NM_027435, intron 6 of 27)	B2_Mm2|SINE|B2	9399	NM_027435	70472	Mm.221758	NM_027435	ENSMUSG00000022360	Atad2	2610509G12Rik	ATPase family, AAA domain containing 2	protein-coding
mm_16140.1	chr2	170731928	170731951	+	1	NA	5' UTR (NM_029761, exon 1 of 8)	5' UTR (NM_029761, exon 1 of 8)	132	NM_001163686	76829	Mm.41633	NM_029761	ENSMUSG00000027560	Dok5	2700055C10Rik	docking protein 5	protein-coding
mm_66373.1	chr7	43656660	43656668	-	1	NA	intron (NM_031181, intron 4 of 6)	intron (NM_031181, intron 4 of 6)	3497	NM_031181	83382	Mm.157702	NM_031181	ENSMUSG00000030474	Siglece	Cd170|Siglec12|Siglec5|Siglec9|Siglecl1|mSiglec-E	sialic acid binding Ig-like lectin E	protein-coding
mm_120060.1	chr14	56850675	56850676	+	1	NA	Intergenic	A-rich|Low_complexity|Low_complexity	-37120	NM_029498	76007	Mm.31417	NM_029498	ENSMUSG00000021945	Zmym2	5830413P05Rik|FIM|MYM|RAMP|SCLL|Zfp198|Znf198	zinc finger, MYM-type 2	protein-coding
mm_53167.1	chr6	125337795	125337813	+	1	NA	exon (NM_011324, exon 4 of 12)	exon (NM_011324, exon 4 of 12)	-11919	NM_011609	21937	Mm.1258	NM_011609	ENSMUSG00000030341	Tnfrsf1a	CD120a|FPF|TNF-R|TNF-R-I|TNF-R1|TNF-R55|TNF-alphaR1|TNFAR|TNFR60|TNFRI|TNFRp55|TNFalpha-R1|Tnfr-2|Tnfr1|p55|p55-R	tumor necrosis factor receptor superfamily, member 1a	protein-coding
mm_36305.1	chr4	68954415	68954423	-	1	NA	promoter-TSS (NM_019967)	promoter-TSS (NM_019967)	-22	NM_019967	56710	Mm.248788	NM_019967	ENSMUSG00000028351	Brinp1	BRINP|Dbc1|Dbccr1|Fam5a	bone morphogenic protein/retinoic acid inducible neural specific 1	protein-coding
mm_33072.1	chr4	123787844	123787855	+	1	NA	promoter-TSS (NM_183163)	promoter-TSS (NM_183163)	-26	NM_183163	230726	Mm.37334	NM_183163	ENSMUSG00000043333	Rhbdl2	9130416B15|RRP2	rhomboid, veinlet-like 2 (Drosophila)	protein-coding
mm_59818.1	chr7	29238305	29238315	+	1	NA	promoter-TSS (NM_001110201)	promoter-TSS (NM_001110201)	-13	NM_001110201	77254	Mm.36699	NM_029887	ENSMUSG00000030588	Yif1b	9430029K10Rik|Yip1b	Yip1 interacting factor homolog B (S. cerevisiae)	protein-coding
mm_147029.1	chr18	34703857	34703863	-	1	NA	intron (NM_010280, intron 3 of 7)	MLTR25A|LTR|ERVK	16527	NM_010280	14587	Mm.16520	NM_010280	ENSMUSG00000024366	Gfra3	GFRalpha3|Y15110	glial cell line derived neurotrophic factor family receptor alpha 3	protein-coding
mm_84775.1	chr9	75683848	75683855	-	1	NA	5' UTR (NM_001164790, exon 1 of 12)	5' UTR (NM_001164790, exon 1 of 12)	205	NM_001164790	20255	Mm.2386	NM_009130	ENSMUSG00000032181	Scg3	1B1075|AI385542|Chgd|SgIII	secretogranin III	protein-coding
mm_163847.1	chr14	19418171	19418205	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	184399	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_170445.1	chr18	83044292	83044306	-	1	NA	Intergenic	RLTRETN_Mm|LTR|ERVK	-123739	NR_033307	75853	Mm.420737	NR_033307		4930592I03Rik	-	RIKEN cDNA 4930592I03 gene	ncRNA
mm_46080.1	chr5	92326816	92326830	-	1	NA	exon (NM_008599, exon 2 of 4)	exon (NM_008599, exon 2 of 4)	1256	NM_008599	17329	Mm.766	NM_008599	ENSMUSG00000029417	Cxcl9	BB139920|CMK|Mig|MuMIG|Scyb9|crg-10	chemokine (C-X-C motif) ligand 9	protein-coding
mm_81365.1	chr9	108783791	108783844	+	1	NA	Intergenic	CpG	-12177	NM_029634	76500	Mm.276336	NM_029634	ENSMUSG00000032599	Ip6k2	1500005N04Rik|AW050208|Ihpk2	inositol hexaphosphate kinase 2	protein-coding
mm_4897.1	chr1	189775020	189775061	+	1	NA	intron (NM_008976, intron 1 of 18)	intron (NM_008976, intron 1 of 18)	46772	NM_008976	19250	Mm.4498	NM_008976	ENSMUSG00000026604	Ptpn14	C130080N23Rik|OTTMUSG00000022087|PTP36	protein tyrosine phosphatase, non-receptor type 14	protein-coding
mm_18702.1	chr2	71750084	71750095	-	1	NA	intron (NR_039557, intron 2 of 3).2	intron (NR_039557, intron 2 of 3).2	30672	NR_037979	381371	Mm.330284	NM_201366	ENSMUSG00000064263	Platr26	Gm1631	pluripotency associated transcript 26	ncRNA
mm_59199.1	chr7	24507100	24507110	+	1	NA	promoter-TSS (NM_001290461)	promoter-TSS (NM_001290461)	18	NR_110958	232969	Mm.181332	NM_146183	ENSMUSG00000064264	Zfp428	2410005H09Rik|AV271806|AW047854|Znf428	zinc finger protein 428	protein-coding
mm_138490.1	chr17	35200372	35200392	+	1	NA	exon (NM_013693, exon 4 of 4)	exon (NM_013693, exon 4 of 4)	1625	NM_013693	21926	Mm.1293	NM_013693	ENSMUSG00000024401	Tnf	DIF|TNF-a|TNF-alpha|TNFSF2|TNFalpha|Tnfa|Tnfsf1a|Tnlg1f	tumor necrosis factor	protein-coding
mm_169873.1	chr16	36875222	36875222	+	1	NA	promoter-TSS (NM_134111)	promoter-TSS (NM_134111)	-396	NM_134111	106389	Mm.432078	NM_134111	ENSMUSG00000022838	Eaf2	AW048865|FESTA-L|FESTA-S|Festa|Traits|U19	ELL associated factor 2	protein-coding
mm_8664.1	chr1	156654517	156654535	-	1	NA	3' UTR (NM_023141, exon 6 of 6)	3' UTR (NM_023141, exon 6 of 6)	19813	NM_023141	30935	Mm.206737	NM_023141	ENSMUSG00000060519	Tor3a	Adir	torsin family 3, member A	protein-coding
mm_39186.1	chr4	155841029	155841055	-	1	NA	exon (NM_024263, exon 3 of 10)	exon (NM_024263, exon 3 of 10)	1362	NM_024263	74761	Mm.159028	NM_024263	ENSMUSG00000029070	Mxra8	1200013A08Rik|1700095D18Rik|AI131686|Asp3|Dicam	matrix-remodelling associated 8	protein-coding
mm_116855.1	chr13	54762714	54762729	-	1	NA	exon (NM_033610, exon 4 of 6)	exon (NM_033610, exon 4 of 6)	3719	NM_033610	104069	Mm.200843	NM_033610	ENSMUSG00000034891	Sncb	AI838531|betaSYN	synuclein, beta	protein-coding
mm_155337.1	chrX	66656912	66656916	+	1	NA	3' UTR (NM_001161431, exon 3 of 3)	3' UTR (NM_001161431, exon 3 of 3)	3755	NM_198863	245450	Mm.336081	NM_198863	ENSMUSG00000036790	Slitrk2	A930040J07	SLIT and NTRK-like family, member 2	protein-coding
mm_34418.1	chr4	145274148	145274162	+	1	NA	intron (NM_009401, intron 12 of 12)	intron (NM_009401, intron 12 of 12)	-27285	NM_011610	21938	Mm.235328	NM_011610	ENSMUSG00000028599	Tnfrsf1b	CD120b|TNF-R-II|TNF-R2|TNF-R75|TNF-alphaR2|TNFBR|TNFR80|TNFRII|TNFalpha-R2|Tnfr-1|Tnfr2|p75	tumor necrosis factor receptor superfamily, member 1b	protein-coding
mm_41409.1	chr5	90787450	90787489	+	1	NA	3' UTR (NM_203320, exon 4 of 4)	3' UTR (NM_203320, exon 4 of 4)	1368	NM_203320	330122	Mm.244289	NM_203320	ENSMUSG00000029379	Cxcl3	Dcip1|Gm1960	chemokine (C-X-C motif) ligand 3	protein-coding
mm_86762.1	chr10	19933599	19933613	+	1	NA	promoter-TSS (NM_008580)	promoter-TSS (NM_008580)	-920	NM_008580	26408	Mm.6595	NM_008580	ENSMUSG00000071369	Map3k5	7420452D20Rik|ASK|ASK1|MAPKKK5|Mekk5	mitogen-activated protein kinase kinase kinase 5	protein-coding
mm_140737.1	chr17	15706145	15706163	-	1	NA	intron (NM_007690, intron 1 of 35)	intron (NM_007690, intron 1 of 35)	1187	NM_007690	12648	Mm.8137	NM_007690	ENSMUSG00000023852	Chd1	4930525N21Rik|AI851787|AW555109	chromodomain helicase DNA binding protein 1	protein-coding
mm_85550.1	chr9	106685742	106685752	-	1	NA	promoter-TSS (NM_011573)	promoter-TSS (NM_011573)	69	NM_011573	21767	Mm.22266	NM_011573	ENSMUSG00000040813	Tex264	TEG-264	testis expressed gene 264	protein-coding
mm_7801.1	chr1	131525558	131525585	-	1	NA	5' UTR (NM_001081011, exon 2 of 23)	5' UTR (NM_001081011, exon 2 of 23)	1790	NM_001081011	14270	Mm.276259	NM_019520	ENSMUSG00000026425	Srgap2	9930124L22Rik|AI448945|FBP2|Fnbp2|srGAP3	SLIT-ROBO Rho GTPase activating protein 2	protein-coding
mm_44787.1	chr5	32146910	32146937	-	1	NA	exon (NM_008037, exon 2 of 4)	exon (NM_008037, exon 2 of 4)	10451	NM_008037	14284	Mm.24684	NM_008037	ENSMUSG00000029135	Fosl2	Fra-2	fos-like antigen 2	protein-coding
mm_27559.1	chr3	58525868	58525872	-	1	NA	promoter-TSS (NM_030685)	promoter-TSS (NM_030685)	14	NM_030685	28146	Mm.29702	NM_030685	ENSMUSG00000027808	Serp1	D3Ucla1|Ramp4	stress-associated endoplasmic reticulum protein 1	protein-coding
mm_125809.1	chr15	74931180	74931192	+	1	NA	Intergenic	RMER17C|LTR|ERVK	-23865	NM_001164039	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_164667.1	chr17	44709985	44710023	-	1	NA	intron (NR_073392, intron 4 of 7)	intron (NR_073392, intron 4 of 7)	26172	NR_073425	12393	Mm.391013	NM_009820	ENSMUSG00000039153	Runx2	AML3|Cbf|Cbfa-1|Cbfa1|LS3|Osf2|PEBP2aA|Pebp2a1|Pebpa2a	runt related transcription factor 2	protein-coding
mm_83824.1	chr9	53975098	53975115	-	1	NA	5' UTR (NM_177769, exon 1 of 11)	5' UTR (NM_177769, exon 1 of 11)	195	NM_177769	270162	Mm.259791	NM_177769	ENSMUSG00000041986	Elmod1	4831417L10|AI428506|AI834991	ELMO/CED-12 domain containing 1	protein-coding
mm_120020.1	chr14	55761409	55761436	+	1	NA	promoter-TSS (NM_020490)	promoter-TSS (NM_020490)	-6	NM_020490	57260	Mm.159670	NM_020490	ENSMUSG00000040432	Ltb4r2	5830462O07Rik|BLT2|LTB4-R 2|LTB4-R-2|LTB4-R2	leukotriene B4 receptor 2	protein-coding
mm_161865.1	chr18	34006349	34006349	-	1	NA	5' UTR (NM_013512, exon 2 of 24)	5' UTR (NM_013512, exon 2 of 24)	857	NM_013512	13824	Mm.3465	NM_013512	ENSMUSG00000024376	Epb41l4a	Epb4.1l4|Epb4.1l4a|NBL4	erythrocyte membrane protein band 4.1 like 4a	protein-coding
mm_162023.1	chr19	46148340	46148340	-	1	NA	promoter-TSS (NM_008852)	promoter-TSS (NM_008852)	-15	NM_008852	18742	Mm.6255	NM_008852	ENSMUSG00000025229	Pitx3	Ptx3|ak	paired-like homeodomain transcription factor 3	protein-coding
mm_15847.1	chr2	164771687	164771697	+	1	NA	intron (NM_026785, intron 3 of 5)	intron (NM_026785, intron 3 of 5)	1763	NM_026785	68612	Mm.89830	NM_026785	ENSMUSG00000001403	Ube2c	1110015A16Rik|D2Ertd695e	ubiquitin-conjugating enzyme E2C	protein-coding
mm_37643.1	chr4	128618317	128618327	-	1	NA	exon (NM_205823, exon 1 of 1)	exon (NM_205823, exon 1 of 1)	297	NM_205823	384059	Mm.331901	NM_205823	ENSMUSG00000062545	Tlr12	Gm1365|Tlr11	toll-like receptor 12	protein-coding
mm_152221.1	chr19	8479031	8479034	-	1	NA	Intergenic	Intergenic	-73927	NM_177002	319800	Mm.426083	NM_177002	ENSMUSG00000052562	Slc22a30	AA986766|C730048C13Rik|UST1R	solute carrier family 22, member 30	protein-coding
mm_171901.1	chr5	4192395	4192398	+	1	NA	promoter-TSS (NM_001042670)	promoter-TSS (NM_001042670)	29	NM_001042670	208595	Mm.129815	NM_001042670	ENSMUSG00000053178	Mterf1b	ENSMUSG00000053178|Gm9897	mitochondrial transcription termination factor 1b	protein-coding
mm_127229.1	chr15	99404410	99404434	+	1	NA	exon (NM_026669, exon 4 of 10)	exon (NM_026669, exon 4 of 10)	11203	NM_001171035	110213	Mm.16769	NM_026669	ENSMUSG00000023010	Tmbim6	5031406P05Rik|Bi1|Tegt	transmembrane BAX inhibitor motif containing 6	protein-coding
mm_82403.1	chr9	14771005	14771044	-	1	NA	promoter-TSS (NM_029306)	promoter-TSS (NM_029306)	6	NM_029306	69325	Mm.440453	NM_029306	ENSMUSG00000031927	1700012B09Rik	1700007P19Rik	RIKEN cDNA 1700012B09 gene	protein-coding
mm_76056.1	chr8	77724287	77724308	-	1	NA	5' UTR (NM_010332, exon 1 of 8)	5' UTR (NM_010332, exon 1 of 8)	155	NM_010332	13617	Mm.283168	NM_010332	ENSMUSG00000031616	Ednra	ET-AR|ETa|Gpcr10	endothelin receptor type A	protein-coding
mm_95372.1	chr11	49087062	49087072	+	1	NA	promoter-TSS (NM_008330)	promoter-TSS (NM_008330)	50	NM_008330	15953	Mm.24769	NM_008330	ENSMUSG00000078920	Ifi47	47kDa|IRG-47|Ifggc1|Igrd|Iigp4|Iipg4|Irgd	interferon gamma inducible protein 47	protein-coding
mm_106054.1	chr11	116110212	116110259	-	1	NA	promoter-TSS (NM_001205081)	promoter-TSS (NM_001205081)	0	NM_001205081	217333	Mm.347770	NM_172570	ENSMUSG00000020773	Trim47	2210023F24Rik	tripartite motif-containing 47	protein-coding
mm_65152.1	chr7	19622382	19622397	-	1	NA	intron (NM_009046, intron 2 of 10)	(CACCC)n|Simple_repeat|Simple_repeat	7049	NM_001290457	19698	Mm.1741	NM_009046	ENSMUSG00000002983	Relb	shep	avian reticuloendotheliosis viral (v-rel) oncogene related B	protein-coding
mm_18958.1	chr2	76791284	76791294	-	1	NA	exon (NM_011652, exon 211 of 313)	exon (NM_011652, exon 211 of 313)	115974	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_22419.1	chr2	181581131	181581169	-	1	NA	TTS (NM_001164597)	TTS (NM_001164597)	823	NM_026765	68556	Mm.232400	NM_026765	ENSMUSG00000089917	Uckl1	1110007H10Rik|Urkl1	uridine-cytidine kinase 1-like 1	protein-coding
mm_2925.1	chr1	132143395	132143405	+	1	NA	Intergenic	Intergenic	-3715	NM_008795	18557	Mm.28130	NM_008795	ENSMUSG00000026437	Cdk18	AA682070|Ctk18|Pctk3	cyclin-dependent kinase 18	protein-coding
mm_44980.1	chr5	36830648	36830657	-	1	NA	promoter-TSS (NM_008550)	promoter-TSS (NM_008550)	-3	NM_008550	17160	Mm.761	NM_008550	ENSMUSG00000029119	Man2b2	mKIAA0935	mannosidase 2, alpha B2	protein-coding
mm_67073.1	chr7	68157578	68157605	-	1	NA	intron (NM_010513, intron 2 of 20)	intron (NM_010513, intron 2 of 20)	106642	NM_030101	78444	Mm.425468	NM_030101	ENSMUSG00000030553	Pgpep1l	C330024D12Rik	pyroglutamyl-peptidase I-like	protein-coding
mm_13745.1	chr2	118120248	118120260	+	1	NA	exon (NM_011580, exon 14 of 22)	exon (NM_011580, exon 14 of 22)	8378	NM_001313914	21825	Mm.4159	NM_011580	ENSMUSG00000040152	Thbs1	TSP-1|TSP1|Thbs-1|tbsp1	thrombospondin 1	protein-coding
mm_113396.1	chr13	33084096	33084104	+	1	NA	promoter-TSS (NM_173052)	promoter-TSS (NM_173052)	-3	NM_173052	282663	Mm.314490	NM_173052	ENSMUSG00000051029	Serpinb1b	6330533H24Rik|EIB|Serpin1b1|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 1b	protein-coding
mm_7795.1	chr1	131525141	131525162	-	1	NA	5' UTR (NM_001081011, exon 2 of 23)	5' UTR (NM_001081011, exon 2 of 23)	2210	NM_001081011	14270	Mm.276259	NM_019520	ENSMUSG00000026425	Srgap2	9930124L22Rik|AI448945|FBP2|Fnbp2|srGAP3	SLIT-ROBO Rho GTPase activating protein 2	protein-coding
mm_127480.1	chr15	101274189	101274199	+	1	NA	exon (NM_010444, exon 7 of 7)	exon (NM_010444, exon 7 of 7)	7348	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
mm_148136.1	chr18	76015649	76015659	-	1	NA	intron (NM_145356, intron 3 of 4)	intron (NM_145356, intron 3 of 4)	82817	NR_045365	73009	Mm.443541	NR_045365		2900057B20Rik	-	RIKEN cDNA 2900057B20 gene	ncRNA
mm_77002.1	chr8	107393130	107393162	-	1	NA	intron (NM_008706, intron 1 of 5)	intron (NM_008706, intron 1 of 5)	10059	NM_008706	18104	Mm.252	NM_008706	ENSMUSG00000003849	Nqo1	AV001255|Dia4|Dtd|Nmo-1|Nmo1|Nmor1|Ox-1|Ox1|Qr1	NAD(P)H dehydrogenase, quinone 1	protein-coding
mm_23386.1	chr3	56575661	56575673	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	-391966	NM_030595	26422	Mm.384353	NM_030595	ENSMUSG00000027799	Nbea	Lyst2|mKIAA1544	neurobeachin	protein-coding
mm_11957.1	chr2	53054543	53054569	+	1	NA	exon (NM_172409, exon 6 of 27)	exon (NM_172409, exon 6 of 27)	136631	NM_018785	56194	Mm.257474	NM_018785	ENSMUSG00000061136	Prpf40a	2810012K09Rik|FBP-11|FBP11|Fnbp11|Fnbp3	pre-mRNA processing factor 40A	protein-coding
mm_72412.1	chr8	81825126	81825162	+	1	NA	intron (NM_001024617, intron 7 of 24)	intron (NM_001024617, intron 7 of 24)	482582	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_129736.1	chr15	82147512	82147523	-	1	NA	intron (NM_033218, intron 1 of 18)	CpG	248	NM_033218	20788	Mm.9002	NM_033218	ENSMUSG00000022463	Srebf2	AI608257|SREBP-2|SREBP2|SREBP2gc|bHLHd2|lop13|nuc	sterol regulatory element binding factor 2	protein-coding
mm_49416.1	chr6	28888475	28888505	+	1	NA	3' UTR (NM_019776, exon 24 of 24)	3' UTR (NM_019776, exon 24 of 24)	-56743	NM_138682	192198	Mm.443660	NM_138682	ENSMUSG00000049939	Lrrc4	MBAG1|NGL-2|NGL2|NLG-2|Nag14	leucine rich repeat containing 4	protein-coding
mm_83347.1	chr9	44320362	44320380	-	1	NA	promoter-TSS (NM_027909)	promoter-TSS (NM_027909)	-89	NM_027909	71764	Mm.491174	NM_027909	ENSMUSG00000032120	C2cd2l	1300006O23Rik|Tmem24	C2 calcium-dependent domain containing 2-like	protein-coding
mm_12073.1	chr2	59656513	59656516	+	1	NA	intron (NM_198294, intron 2 of 26)	intron (NM_198294, intron 2 of 26)	9745	NM_001290659	66860	Mm.27917	NM_198294	ENSMUSG00000035168	Tanc1	1200003E16Rik|Tanc|mKIAA1728	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	protein-coding
mm_79885.1	chr9	65294158	65294169	+	1	NA	promoter-TSS (NM_011802)	promoter-TSS (NM_011802)	-97	NM_001044389	270166	Mm.30088	NM_011802	ENSMUSG00000015357	Clpx	AU014732|E330029I21	caseinolytic mitochondrial matrix peptidase chaperone subunit	protein-coding
mm_101992.1	chr11	50943714	50943756	-	1	NA	Intergenic	Intergenic	9897	NM_008936	19127	Mm.1386	NM_008936	ENSMUSG00000044542	Prop1	Prop-1|df	paired like homeodomain factor 1	protein-coding
mm_127236.1	chr15	99408700	99408714	+	1	NA	3' UTR (NM_026669, exon 10 of 10)	3' UTR (NM_026669, exon 10 of 10)	15488	NM_001171035	110213	Mm.16769	NM_026669	ENSMUSG00000023010	Tmbim6	5031406P05Rik|Bi1|Tegt	transmembrane BAX inhibitor motif containing 6	protein-coding
mm_40394.1	chr5	52807135	52807140	+	1	NA	intron (NM_001308144, intron 7 of 12)	AT_rich|Low_complexity|Low_complexity	24082	NM_030185	78796	Mm.266886	NM_030185	ENSMUSG00000029179	Zcchc4	4930449I23Rik	zinc finger, CCHC domain containing 4	protein-coding
mm_11034.1	chr2	26916788	26916835	+	1	NA	promoter-TSS (NM_013677)	promoter-TSS (NM_013677)	-281	NM_013677	20930	Mm.347512	NM_013677	ENSMUSG00000015790	Surf1	0610010F23Rik|Surf-1	surfeit gene 1	protein-coding
mm_83249.1	chr9	42400060	42400074	-	1	NA	promoter-TSS (NM_001324548)	promoter-TSS (NM_001324548)	-138	NM_001324548	21683	Mm.42209	NM_009347	ENSMUSG00000037705	Tecta	Tctna	tectorin alpha	protein-coding
mm_67406.1	chr7	80056183	80056196	-	1	NA	intron (NM_175433, intron 1 of 4)	intron (NM_175433, intron 1 of 4)	19068	NR_045695	100859962	Mm.392575	NR_045695	ENSMUSG00000108714	Gm21057	-	predicted gene, 21057	ncRNA
mm_121007.1	chr14	79521958	79521974	+	1	NA	intron (NM_001286411, intron 1 of 8)	intron (NM_001286411, intron 1 of 8)	6292	NM_001286411	13709	Mm.20938	NM_007920	ENSMUSG00000036461	Elf1	Elf-1|Sts1|mElf-1|p70	E74-like factor 1	protein-coding
mm_120336.1	chr14	63451458	63451469	+	1	NA	intron (NM_177628, intron 2 of 3)	intron (NM_177628, intron 2 of 3)	15069	NM_177628	219148	Mm.37882	NM_177628	ENSMUSG00000035095	Fam167a	A030013D21	family with sequence similarity 167, member A	protein-coding
mm_146440.1	chr18	84934654	84934665	+	1	NA	promoter-TSS (NM_015798)	promoter-TSS (NM_015798)	-366	NM_015798	50764	Mm.28369	NM_015798	ENSMUSG00000034391	Fbxo15	AU019763|Fbx15|ecat3	F-box protein 15	protein-coding
mm_113283.1	chr13	30136620	30136630	+	1	NA	5' UTR (NM_153546, exon 1 of 13)	5' UTR (NM_153546, exon 1 of 13)	135	NM_153546	218121	Mm.89682	NM_153546	ENSMUSG00000038732	Mboat1	9130215M02Rik|BC023845|LPEAT1|Moact1|Oact1	membrane bound O-acyltransferase domain containing 1	protein-coding
mm_97718.1	chr11	80209067	80209164	+	1	NA	promoter-TSS (NM_001163354)	promoter-TSS (NM_001163354)	60	NM_021536	59040	Mm.489674	NM_021536	ENSMUSG00000017686	Rhot1	2210403N23Rik|AA415293|AF244542|AI834919|Arht1|C430039G08Rik|Miro1	ras homolog family member T1	protein-coding
mm_167635.1	chr9	63148916	63148934	-	1	NA	promoter-TSS (NM_001163758)	promoter-TSS (NM_001163758)	36	NM_001163758	207667	Mm.36349	NM_172446	ENSMUSG00000022245	Skor1	AV273001|C230094B15Rik|Corl1|Lbxcor1	SKI family transcriptional corepressor 1	protein-coding
mm_57737.1	chr6	128974977	128975014	-	1	NA	promoter-TSS (NR_045009)	promoter-TSS (NR_045009)	34	NR_045009	100504591	Mm.441029	NR_045009		Gm15987	OTTMUSG00000028624	predicted gene 15987	ncRNA
mm_113525.1	chr13	37826057	37826081	+	1	NA	promoter-TSS (NM_001177868)	promoter-TSS (NM_001177868)	31	NM_026830	68750	Mm.491109	NM_026830	ENSMUSG00000039087	Rreb1	1110037N09Rik|AA414966|B930013M22Rik	ras responsive element binding protein 1	protein-coding
mm_32614.1	chr4	114163421	114163434	+	1	NA	promoter-TSS (NM_177669)	promoter-TSS (NM_177669)	43	NM_001166027	230623	Mm.124482	NM_177669	ENSMUSG00000057977	Skint11	A630098G03Rik|Gm569	selection and upkeep of intraepithelial T cells 11	protein-coding
mm_8714.1	chr1	158969744	158969749	-	1	NA	Intergenic	Intergenic	-12308	NM_001085376	23850	Mm.458621	NM_001085376	ENSMUSG00000073530	Pappa2	PAPP-A2|PLAC3|Pappe	pappalysin 2	protein-coding
mm_17930.1	chr2	35462794	35462832	-	1	NA	Intergenic	Intergenic	-1364	NM_001145821	14594	Mm.281124	NM_010283	ENSMUSG00000035778	Ggta1	AW108479|GALT|Gal|Ggta|Ggta-1|alpha Gal|alpha3GalT	glycoprotein galactosyltransferase alpha 1, 3	protein-coding
mm_56132.1	chr6	87672191	87672202	-	1	NA	promoter-TSS (NM_001170489)	promoter-TSS (NM_001170489)	-28	NM_001170489	72103	Mm.31770	NM_024251	ENSMUSG00000030051	Aplf	2010301N04Rik|AI452191	aprataxin and PNKP like factor	protein-coding
mm_81048.1	chr9	105491896	105491902	+	1	NA	intron (NM_001253831, intron 1 of 26)	intron (NM_001253831, intron 1 of 26)	3234	NM_175025	235574	Mm.326247	NM_175025	ENSMUSG00000032570	Atp2c1	1700121J11Rik|ATP2C1A|AW061228|BCPM|D930003G21Rik|HHD|SPCA|pmr1	ATPase, Ca++-sequestering	protein-coding
mm_92285.1	chr10	71343208	71343215	-	1	NA	intron (NM_134007, intron 1 of 2)	intron (NM_134007, intron 1 of 2)	1638	NM_134007	52637	Mm.254114	NM_134007	ENSMUSG00000037710	Cisd1	AU043990|AW743335|D10Ertd214e|Zcd1|mitoNEET	CDGSH iron sulfur domain 1	protein-coding
mm_14979.1	chr2	152109370	152109381	+	1	NA	3' UTR (NM_029688, exon 2 of 2)	3' UTR (NM_029688, exon 2 of 2)	3851	NM_029688	76650	Mm.218639	NM_029688	ENSMUSG00000032802	Srxn1	1700127B04Rik|AI854065|AW488194|Npn3|Srx|Srx1|TX01	sulfiredoxin 1 homolog (S. cerevisiae)	protein-coding
mm_167790.1	chr9	123510486	123510516	+	1	NA	intron (NM_013860, intron 2 of 7)	intron (NM_013860, intron 2 of 7)	-19381	NM_030692	83493	Mm.273671	NM_030692	ENSMUSG00000025240	Sacm1l	SAC1|Sac1p|mKIAA0851	SAC1 suppressor of actin mutations 1-like (yeast)	protein-coding
mm_172977.1	chr9	95292060	95292062	+	1	NA	Intergenic	L1Md_T|LINE|L1	115209	NM_018763	54371	Mm.212446	NM_018763	ENSMUSG00000033350	Chst2	AI428561|AW121776|C130041E03Rik|Chts2|GST-2|GlcNAc6ST|Gn6st	carbohydrate sulfotransferase 2	protein-coding
mm_26911.1	chr3	20035270	20035283	-	1	NA	promoter-TSS (NM_001146323)	promoter-TSS (NM_001146323)	34	NM_001146323	12807	Mm.291533	NM_080634	ENSMUSG00000027615	Hps3	coa	Hermansky-Pudlak syndrome 3	protein-coding
mm_154592.1	chrX	7580486	7580491	+	1	NA	promoter-TSS (NM_001199348)	promoter-TSS (NM_001199348)	5	NM_001199348	20371	Mm.182291	NM_054039	ENSMUSG00000039521	Foxp3	JM2|scurfin|sf	forkhead box P3	protein-coding
mm_58120.1	chr6	139501908	139501918	-	1	NA	promoter-TSS (NM_001128090)	promoter-TSS (NM_001128090)	-4	NM_001128090	632971	Mm.475610	NM_001128090	ENSMUSG00000092164	Rergl	EG632971	RERG/RAS-like	protein-coding
mm_62200.1	chr7	97788786	97788834	+	1	NA	Intergenic	CpG	-50563	NM_175105	66333	Mm.29756	NM_175105	ENSMUSG00000042797	Aqp11	1700015P13Rik|AI648923|sjds	aquaporin 11	protein-coding
mm_44506.1	chr5	24030298	24030319	-	1	NA	promoter-TSS (NM_001310471)	promoter-TSS (NM_001310471)	4	NM_001310471	84652	Mm.304976	NM_053090	ENSMUSG00000028995	Fam126a	AB030242|Drctnnb1a	family with sequence similarity 126, member A	protein-coding
mm_101052.1	chr11	8664068	8664114	-	1	NA	intron (NM_001083587, intron 1 of 30)	intron (NM_001083587, intron 1 of 30)	444	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_103857.1	chr11	83286723	83286729	-	1	NA	promoter-TSS (NM_001166028)	promoter-TSS (NM_001166028)	0	NM_001166028	237890	Mm.297670	NM_001166028	ENSMUSG00000082101	Slfn14	Gm20|Slfn14-ps	schlafen 14	protein-coding
mm_152643.1	chr19	12527544	12527558	-	1	NA	Intergenic	L1MC3|LINE|L1	-25555	NM_172442	207521	Mm.247695	NM_172442	ENSMUSG00000039982	Dtx4	AI449438|BC044798|D930042H13|RNF155	deltex 4, E3 ubiquitin ligase	protein-coding
mm_161638.1	chr16	94008857	94008857	-	1	NA	promoter-TSS (NM_019500)	promoter-TSS (NM_019500)	-20	NM_019500	56173	Mm.328716	NM_019500	ENSMUSG00000047109	Cldn14	AI851731	claudin 14	protein-coding
mm_81666.1	chr9	111024383	111024392	+	1	NA	exon (NM_008522, exon 7 of 17)	exon (NM_008522, exon 7 of 17)	5095	NM_008522	17002	Mm.282359	NM_008522	ENSMUSG00000032496	Ltf	Csp82|Lf|MMS10R|Ms10r	lactotransferrin	protein-coding
mm_4846.1	chr1	186967668	186967690	+	1	NA	5' UTR (NM_033077, exon 1 of 1)	5' UTR (NM_033077, exon 1 of 1)	263	NM_033077	110957	Mm.108054	NM_033077	ENSMUSG00000039224	D1Pas1	Pl10	DNA segment, Chr 1, Pasteur Institute 1	protein-coding
mm_26165.1	chr3	138280406	138280434	+	1	NA	exon (NM_007409, exon 3 of 9)	exon (NM_007409, exon 3 of 9)	2775	NM_007409	11522	Mm.2409	NM_007409	ENSMUSG00000074207	Adh1	ADH-AA|AI194826|Adh-1|Adh-1-t|Adh-1e|Adh-1t|Adh-3e|Adh1-e|Adh1-t|Adh1tl|Adh3-e	alcohol dehydrogenase 1 (class I)	protein-coding
mm_39463.1	chr5	18014427	18014439	+	1	NA	intron (NM_001081143, intron 5 of 7)	intron (NM_001081143, intron 5 of 7)	51863	NM_001081143	242851	Mm.332230	NM_001081143	ENSMUSG00000028777	Gnat3	Ggust|Gtn	guanine nucleotide binding protein, alpha transducing 3	protein-coding
mm_77102.1	chr8	111030916	111030918	-	1	NA	intron (NM_001190786, intron 1 of 11)	intron (NM_001190786, intron 1 of 11)	834	NM_001190786	234733	Mm.482176	NM_172284	ENSMUSG00000033658	Ddx19b	2810457M08Rik|4921519L13Rik|AW260119	DEAD (Asp-Glu-Ala-Asp) box polypeptide 19b	protein-coding
mm_72822.1	chr8	88199230	88199232	+	1	NA	promoter-TSS (NM_001164497)	promoter-TSS (NM_001164497)	18	NM_001164498	214627	Mm.491211	NM_001164497	ENSMUSG00000036779	Papd5	5730445M16Rik|5830428A09	PAP associated domain containing 5	protein-coding
mm_162668.1	chr10	7063166	7063169	-	1	NA	Intergenic	Intergenic	-39982	NM_001033391	320495	Mm.331674	NM_001033391	ENSMUSG00000064065	Ipcef1	A130090K04Rik	interaction protein for cytohesin exchange factors 1	protein-coding
mm_82974.1	chr9	35844180	35844197	-	1	NA	promoter-TSS (NM_029863)	promoter-TSS (NM_029863)	-38	NM_029863	77080	Mm.159846	NM_029863	ENSMUSG00000047980	9230110F15Rik	Pate-A|Pate5|mANLP3	RIKEN cDNA 9230110F15 gene	protein-coding
mm_22501.1	chr3	7366703	7366713	+	1	NA	5' UTR (NM_008862, exon 1 of 3)	5' UTR (NM_008862, exon 1 of 3)	104	NM_008862	18767	Mm.3193	NM_008862	ENSMUSG00000027499	Pkia	AI415001|PKIalpha	protein kinase inhibitor, alpha	protein-coding
mm_54719.1	chr6	40431579	40431581	-	1	NA	intron (NM_175528, intron 1 of 7)	intron (NM_175528, intron 1 of 7)	4553	NM_175528	243780	Mm.333006	NM_175528	ENSMUSG00000037172	E330009J07Rik	AI841796|Lchn|mKIAA1147	RIKEN cDNA E330009J07 gene	protein-coding
mm_78558.1	chr9	35672665	35672675	+	1	NA	3' UTR (NM_001033421, exon 4 of 4)	3' UTR (NM_001033421, exon 4 of 4)	3031	NM_001033421	330921	Mm.479701	NM_001033421	ENSMUSG00000074452	Pate2	Gm846|Pate-M|mANLP1	prostate and testis expressed 2	protein-coding
mm_4328.1	chr1	171854171	171854181	+	1	NA	3' UTR (NM_001252472, exon 3 of 3)	3' UTR (NM_001252472, exon 3 of 3)	14479	NM_013489	12523	Mm.259115	NM_013489	ENSMUSG00000038147	Cd84	A130013D22Rik|CDw84|SLAMF5	CD84 antigen	protein-coding
mm_107753.1	chr12	59070215	59070227	+	1	NA	exon (NM_008891, exon 7 of 9)	exon (NM_008891, exon 7 of 9)	3302	NM_008891	18949	Mm.22347	NM_008891	ENSMUSG00000020994	Pnn	AU045199|D12Ertd512e	pinin	protein-coding
mm_58969.1	chr7	18992426	18992428	+	1	NA	exon (NM_145579, exon 2 of 3)	exon (NM_145579, exon 2 of 3)	1182	NM_145579	232934	Mm.440069	NM_145579	ENSMUSG00000048481	Mypop	Myodysa|P42pop	Myb-related transcription factor, partner of profilin	protein-coding
mm_98604.1	chr11	95837265	95837285	+	1	NA	intron (NM_001163464, intron 1 of 7)	intron (NM_001163464, intron 1 of 7)	-5020	NM_023121	14710	Mm.46299	NM_023121	ENSMUSG00000038811	Gngt2	AV096488	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 2	protein-coding
mm_153759.1	chr19	45451212	45451237	-	1	NA	intron (NM_001286465, intron 2 of 14)	intron (NM_001286465, intron 2 of 14)	87490	NM_001037758	12234	Mm.119717	NM_009771	ENSMUSG00000025217	Btrc	Beta-Trcp1|E3RS-IkappaB|E3RSIkappaB|FWD1|Fbw1a|HOS|Slimb|b-TrCP|beta-TrCP	beta-transducin repeat containing protein	protein-coding
mm_81810.1	chr9	117859980	117859983	+	1	NA	Intergenic	Intergenic	-180541	NM_001286508	27215	Mm.92705	NM_013727	ENSMUSG00000039285	Azi2	AA410145|AZ2	5-azacytidine induced gene 2	protein-coding
mm_109515.1	chr12	111454305	111454326	+	1	NA	3' UTR (NM_009396, exon 12 of 12)	3' UTR (NM_009396, exon 12 of 12)	11654	NM_009396	21928	Mm.255332	NM_009396	ENSMUSG00000021281	Tnfaip2	B94|Exoc3l3|M-sec|Tnfip2|tnfb94	tumor necrosis factor, alpha-induced protein 2	protein-coding
mm_114955.1	chr13	97065605	97065611	+	1	NA	Intergenic	RLTR41|LTR|ERV1	-1679	NM_001146045	320557	Mm.458280	NM_001100458	ENSMUSG00000041817	Fam169a	B230112C05Rik|SLAP75	family with sequence similarity 169, member A	protein-coding
mm_73294.1	chr8	104962439	104962487	+	1	NA	intron (NM_197999, intron 1 of 11)	intron (NM_197999, intron 1 of 11)	745	NM_197999	72361	Mm.26580	NM_197999	ENSMUSG00000031877	Ces2g	2210023G05Rik|Ces2l	carboxylesterase 2G	protein-coding
mm_132761.1	chr16	44578213	44578215	+	1	NA	Intergenic	Intergenic	-19344	NM_172506	117606	Mm.41561	NM_172506	ENSMUSG00000022687	Boc	4732455C11|mFLJ00376	biregional cell adhesion molecule-related/down-regulated by oncogenes (Cdon) binding protein	protein-coding
mm_141321.1	chr17	28438033	28438047	-	1	NA	exon (NM_010220, exon 3 of 11)	exon (NM_010220, exon 3 of 11)	48109	NM_010220	14229	Mm.276405	NM_010220	ENSMUSG00000024222	Fkbp5	D17Ertd592e|Dit1|FKBP-5|FKBP51	FK506 binding protein 5	protein-coding
mm_30625.1	chr4	8735932	8735942	+	1	NA	intron (NM_001277149, intron 1 of 37)	intron (NM_001277149, intron 1 of 37)	45531	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_108778.1	chr12	89813302	89813304	+	1	NA	5' UTR (NM_001252074, exon 1 of 7)	5' UTR (NM_001252074, exon 1 of 7)	820	NM_001252074	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding
mm_99570.1	chr11	103961817	103961848	+	1	NA	Intergenic	Intergenic	-4893	NM_001304574	11841	Mm.5061	NM_007477	ENSMUSG00000062421	Arf2	-	ADP-ribosylation factor 2	protein-coding
mm_9792.1	chr1	181834554	181834569	-	1	NA	intron (NM_133815, intron 3 of 13)	B2_Mm1a|SINE|B2	7840	NM_133815	98386	Mm.4538	NM_133815	ENSMUSG00000004880	Lbr	AI505894|ic	lamin B receptor	protein-coding
mm_28548.1	chr3	93019058	93019060	-	1	NA	promoter-TSS (NM_025420)	promoter-TSS (NM_025420)	1	NM_025420	66203	Mm.292457	NM_025420	ENSMUSG00000027912	Lce1m	1110059L13Rik|AI131654|Lce5a|Sprrl10	late cornified envelope 1M	protein-coding
mm_66190.1	chr7	34207941	34207944	-	1	NA	intron (NM_008155, intron 10 of 17)	intron (NM_008155, intron 10 of 17)	-11295	NM_026549	68079	Mm.38173	NM_026549	ENSMUSG00000002635	Pdcd2l	6030457N17Rik	programmed cell death 2-like	protein-coding
mm_159508.1	chr4	49845085	49845085	-	1	NA	5' UTR (NM_001276355, exon 1 of 9)	5' UTR (NM_001276355, exon 1 of 9)	684	NM_001033351	242443	Mm.440095	NM_001033351	ENSMUSG00000039579	Grin3a	6430537F04|A830097C19Rik|NMDAR-L|NR3A|mKIAA1973	glutamate receptor ionotropic, NMDA3A	protein-coding
mm_85261.1	chr9	99411825	99411870	-	1	NA	intron (NM_008624, intron 1 of 5)	intron (NM_008624, intron 1 of 5)	24865	NM_008624	17532	Mm.2045	NM_008624	ENSMUSG00000032470	Mras	2900078C09Rik|AI326250	muscle and microspikes RAS	protein-coding
mm_81153.1	chr9	107288949	107288967	+	1	NA	intron (NM_001316691, intron 1 of 7)	intron (NM_001316691, intron 1 of 7)	438	NM_001316691	102626	Mm.222612	NM_178907	ENSMUSG00000032577	Mapkapk3	3PK|AI874665|MAPKAP-K3|MAPKAP3|MK-3|MK3|MapkKapk3	mitogen-activated protein kinase-activated protein kinase 3	protein-coding
mm_4622.1	chr1	179174450	179174478	+	1	NA	intron (NM_027188, intron 5 of 11)	intron (NM_027188, intron 5 of 11)	343539	NM_027188	69726	Mm.222338	NM_027188	ENSMUSG00000055067	Smyd3	2410008A19Rik|Zmynd1	SET and MYND domain containing 3	protein-coding
mm_77349.1	chr8	119574974	119574984	-	1	NA	promoter-TSS (NM_026648)	promoter-TSS (NM_026648)	221	NM_175185	72552	Mm.36756	NM_175185	ENSMUSG00000034189	Hsdl1	2700067E09Rik	hydroxysteroid dehydrogenase like 1	protein-coding
mm_55457.1	chr6	67376148	67376171	-	1	NA	promoter-TSS (NM_008354)	promoter-TSS (NM_008354)	-22	NM_008354	16162	Mm.188337	NM_008354	ENSMUSG00000018341	Il12rb2	A930027I18Rik|IL-12RB2|Ifnm	interleukin 12 receptor, beta 2	protein-coding
mm_162778.1	chr10	69551295	69551305	+	1	NA	intron (NM_170730, intron 1 of 17)	(CA)n|Simple_repeat|Simple_repeat	17592	NM_146005	11735	Mm.235960	NM_009670	ENSMUSG00000069601	Ank3	2900054D09Rik|AI314020|Ank-3|AnkG|Ankyrin-3|Ankyrin-G	ankyrin 3, epithelial	protein-coding
mm_128952.1	chr15	74763705	74763748	-	1	NA	promoter-TSS (NM_010742)	promoter-TSS (NM_010742)	-159	NM_010742	17068	Mm.878	NM_010742	ENSMUSG00000034634	Ly6d	Ly-61|Ly61|Thb	lymphocyte antigen 6 complex, locus D	protein-coding
mm_129867.1	chr15	83367298	83367314	-	1	NA	promoter-TSS (NR_027980)	promoter-TSS (NR_027980)	-9	NR_027980	69291	Mm.66794	NM_001033147		1700001L05Rik	-	RIKEN cDNA 1700001L05 gene	ncRNA
mm_120034.1	chr14	56017966	56017970	+	1	NA	promoter-TSS (NM_008570)	promoter-TSS (NM_008570)	4	NM_008570	17224	Mm.201549	NM_008570	ENSMUSG00000022227	Mcpt1	AV080368|Mcp-1	mast cell protease 1	protein-coding
mm_155325.1	chrX	64173546	64173558	+	1	NA	promoter-TSS (NM_027512)	promoter-TSS (NM_027512)	4	NM_027512	70696	Mm.54544	NM_027512	ENSMUSG00000031179	3830417A13Rik	-	RIKEN cDNA 3830417A13 gene	protein-coding
mm_157800.1	chrX	73921931	73921941	-	1	NA	promoter-TSS (NM_019870)	promoter-TSS (NM_019870)	8	NM_001310538	56292	Mm.246654	NM_019870	ENSMUSG00000031388	Naa10	2310039H09Rik|Ard1|Ard1a|Te2	N(alpha)-acetyltransferase 10, NatA catalytic subunit	protein-coding
mm_61287.1	chr7	67645430	67645461	+	1	NA	promoter-TSS (NR_028144)	promoter-TSS (NR_028144)	-209	NR_028143	67867	Mm.31247	NM_027413	ENSMUSG00000030556	Lrrc28	1300004K21Rik|2210012C09Rik|2310058O11Rik	leucine rich repeat containing 28	protein-coding
mm_135691.1	chr16	52434496	52434507	-	1	NA	intron (NM_009655, intron 1 of 15)	Lx2B|LINE|L1	18580	NM_009655	11658	Mm.288282	NM_009655	ENSMUSG00000022636	Alcam	AI853494|BEN|CD166|DM-GRASP|MuSC|SC1	activated leukocyte cell adhesion molecule	protein-coding
mm_92337.1	chr10	75822490	75822511	-	1	NA	promoter-TSS (NM_029472)	promoter-TSS (NM_029472)	43	NM_029472	75886	Mm.268996	NM_029472	ENSMUSG00000009093	Gstt4	4930583C14Rik|AI507011	glutathione S-transferase, theta 4	protein-coding
mm_40726.1	chr5	65975979	65975989	+	1	NA	intron (NM_001081104, intron 4 of 4)	B4A|SINE|B4	8860	NM_001081104	231252	Mm.140015	NM_001081104	ENSMUSG00000029205	Chrna9	2410015I05Rik|Acra9|EG666827|Gm8311	cholinergic receptor, nicotinic, alpha polypeptide 9	protein-coding
mm_81278.1	chr9	108296692	108296702	+	1	NA	promoter-TSS (NM_001013814)	promoter-TSS (NM_001013814)	-225	NM_001013814	434437	Mm.390225	NM_001013814	ENSMUSG00000032607	Amt	EG434437	aminomethyltransferase	protein-coding
mm_3098.1	chr1	134428116	134428155	+	1	NA	exon (NM_001306069, exon 6 of 8)	exon (NM_001306069, exon 6 of 8)	12471	NM_001306069	72674	Mm.259976	NM_028320	ENSMUSG00000026457	Adipor1	2810031L11Rik|ACDCR1|CGI-45|Paqr1	adiponectin receptor 1	protein-coding
mm_146230.1	chr18	77117616	77117624	+	1	NA	intron (NM_008602, intron 3 of 13)	intron (NM_008602, intron 3 of 13)	51940	NM_001164168	17344	Mm.6370	NM_008602	ENSMUSG00000025423	Pias2	6330408K17Rik|AI462206|ARIP3|AU018068|Dib|Miz1|PIASxalpha|PIASxb|PIASxbeta|SIZ2	protein inhibitor of activated STAT 2	protein-coding
mm_79102.1	chr9	46243376	46243385	+	1	NA	TTS (NM_007468)	TTS (NM_007468)	2536	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_96629.1	chr11	69157064	69157081	+	1	NA	promoter-TSS (NM_009659)	promoter-TSS (NM_009659)	0	NM_009659	11686	Mm.340329	NM_009659	ENSMUSG00000032807	Alox12b	12R-LOX|Aloxe2|e-LOX2	arachidonate 12-lipoxygenase, 12R type	protein-coding
mm_23741.1	chr3	69316858	69316869	+	1	NA	promoter-TSS (NM_178726)	promoter-TSS (NM_178726)	-55	NM_178726	242083	Mm.40577	NM_178726	ENSMUSG00000027784	Ppm1l	3222401G13|5930404J21Rik|AI481720|AW045850|PP2C|PP2Cepsilon|Pp2ce|Ppp2ce|mKIAA4175	protein phosphatase 1 (formerly 2C)-like	protein-coding
mm_9689.1	chr1	178336398	178336408	-	1	NA	intron (NM_016805, intron 1 of 13)	intron (NM_016805, intron 1 of 13)	1381	NM_016805	51810	Mm.86589	NM_016805	ENSMUSG00000039630	Hnrnpu	AA408410|AI256620|AL024194|AL024437|AW557595|C86794|Hnrpu|SAFA|Sp120|hnRNP U	heterogeneous nuclear ribonucleoprotein U	protein-coding
mm_41160.1	chr5	87929923	87929948	+	1	NA	exon (NM_007786, exon 4 of 5)	exon (NM_007786, exon 4 of 5)	4302	NM_007786	12994	Mm.296303	NM_007786	ENSMUSG00000001622	Csn3	AW208918|CSN10|Csnk	casein kappa	protein-coding
mm_124271.1	chr14	103007855	103007861	-	1	NA	intron (NR_045657, intron 2 of 2)	Lx10|LINE|L1	-25221	NM_177715	239217	Mm.246466	NM_177715	ENSMUSG00000098557	Kctd12	AU046135|AW538430|Pfet1|Pfetin	potassium channel tetramerisation domain containing 12	protein-coding
mm_154996.1	chrX	38600627	38600691	+	1	NA	promoter-TSS (NM_026902)	promoter-TSS (NM_026902)	1	NM_026902	68995	Mm.262453	NM_026902	ENSMUSG00000000355	Mcts1	1500019M23Rik|MCT-1	malignant T cell amplified sequence 1	protein-coding
mm_155260.1	chrX	57766862	57766875	+	1	NA	Intergenic	Intergenic	-263111	NM_001033360	245424	Mm.336070	NM_001033360	ENSMUSG00000036357	Gpr101	GPCR6|Gm365	G protein-coupled receptor 101	protein-coding
mm_24744.1	chr3	95315241	95315273	+	1	NA	promoter-TSS (NM_029789)	promoter-TSS (NM_029789)	67	NM_029789	76893	Mm.181009	NM_029789	ENSMUSG00000015714	Cers2	0610013I17Rik|AI225939|Lass2|TRH3	ceramide synthase 2	protein-coding
mm_53003.1	chr6	123270392	123270404	+	1	NA	intron (NM_001163161, intron 5 of 5)	intron (NM_001163161, intron 5 of 5)	8291	NM_010819	17474	Mm.441101	NM_010819	ENSMUSG00000030144	Clec4d	Clecsf8|Mpcl|mcl	C-type lectin domain family 4, member d	protein-coding
mm_117857.1	chr13	98815222	98815257	-	1	NA	5' UTR (NM_172591, exon 1 of 26)	5' UTR (NM_172591, exon 1 of 26)	210	NM_172591	218503	Mm.23928	NM_172591	ENSMUSG00000041685	Fcho2	5832424M12Rik|AA387320	FCH domain only 2	protein-coding
mm_92900.1	chr10	83326716	83326757	-	1	NA	intron (NM_177388, intron 1 of 10)	intron (NM_177388, intron 1 of 10)	11081	NM_177388	338365	Mm.67073	NM_177388	ENSMUSG00000034591	Slc41a2	A230035L05Rik|SLC41A1-L1	solute carrier family 41, member 2	protein-coding
mm_91542.1	chr10	39618578	39618595	-	1	NA	intron (NM_134000, intron 1 of 8)	intron (NM_134000, intron 1 of 8)	5652	NM_134000	103213	Mm.436686	NM_134000	ENSMUSG00000019842	Traf3ip2	AI429613|Act1|CIKS	TRAF3 interacting protein 2	protein-coding
mm_157120.1	chrX	9444583	9444644	-	1	NA	exon (NM_007807, exon 10 of 13)	exon (NM_007807, exon 10 of 13)	24711	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_104432.1	chr11	94951543	94951577	-	1	NA	exon (NM_007742, exon 51 of 51)	exon (NM_007742, exon 51 of 51)	15336	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_13720.1	chr2	117249767	117249773	+	1	NA	promoter-TSS (NM_026620)	promoter-TSS (NM_026620)	31	NM_026620	68215	Mm.219389	NM_026620	ENSMUSG00000027349	Fam98b	2610510H03Rik	family with sequence similarity 98, member B	protein-coding
mm_154.1	chr1	12692359	12692365	+	1	NA	promoter-TSS (NM_001198566)	promoter-TSS (NM_001198566)	-68	NM_001198565	240725	Mm.45563	NM_172294	ENSMUSG00000016918	Sulf1	AI467640|AW121680|mKIAA1077	sulfatase 1	protein-coding
mm_138749.1	chr17	37045811	37045819	+	1	NA	promoter-TSS (NM_019439)	promoter-TSS (NM_019439)	-151	NM_019439	54393	Mm.32191	NM_019439	ENSMUSG00000024462	Gabbr1	GABAB1|GABAbR1|bM573K1.1	gamma-aminobutyric acid (GABA) B receptor, 1	protein-coding
mm_125549.1	chr15	58528326	58528337	+	1	NA	Intergenic	Intergenic	112863	NM_145959	210998	Mm.3224	NM_145959	ENSMUSG00000037119	Fam91a1	AV220772|BC033609|D15Ertd621e|SKIN|mKIAA0493	family with sequence similarity 91, member A1	protein-coding
mm_144250.1	chr18	10816075	10816083	+	1	NA	Intergenic	Intergenic	-30527	NR_029781	723959		NR_029781	ENSMUSG00000106348	Mir1a-2	Mir1-2|Mirn1-2|mir-1a-2|mmu-mir-1-2|mmu-mir-1a-2	microRNA 1a-2	ncRNA
mm_66008.1	chr7	30563236	30563256	-	1	NA	promoter-TSS (NM_025498)	promoter-TSS (NM_025498)	-62	NM_025498	66340	Mm.86557	NM_025498	ENSMUSG00000036835	Psenen	1700023M09Rik|Pen-2	presenilin enhancer gamma secretase subunit	protein-coding
mm_77661.1	chr8	124663369	124663383	-	1	NA	promoter-TSS (NM_175149)	promoter-TSS (NM_175149)	-7	NM_175149	69551	Mm.261920	NM_175149	ENSMUSG00000031983	2310022B05Rik	-	RIKEN cDNA 2310022B05 gene	protein-coding
mm_86798.1	chr10	20267269	20267310	+	1	NA	exon (NM_008635, exon 10 of 18)	exon (NM_008635, exon 10 of 18)	30399	NR_105840	102466647		NR_105840	ENSMUSG00000098887	Mir6413	Gm27432|mmu-mir-6413	microRNA 6413	ncRNA
mm_80625.1	chr9	88957012	88957022	+	1	NA	promoter-TSS (NM_009742)	promoter-TSS (NM_009742)	97	NM_009742	12044	Mm.425593	NM_009742	ENSMUSG00000102037	Bcl2a1a	A1|BB218357|Bcl2a1|Bfl-1|Hbpa1	B cell leukemia/lymphoma 2 related protein A1a	protein-coding
mm_66663.1	chr7	45717342	45717353	-	1	NA	promoter-TSS (NM_009077)	promoter-TSS (NM_009077)	655	NM_203280	56632	Mm.24222	NM_020011	ENSMUSG00000057342	Sphk2	C76851	sphingosine kinase 2	protein-coding
mm_30985.1	chr4	34893795	34893816	+	1	NA	promoter-TSS (NM_009889)	promoter-TSS (NM_009889)	26	NM_009889	12640	Mm.1361	NM_009889	ENSMUSG00000028298	Cga	CG-alpha|FSHA|GPHA1|GPHalpha|HCG|LHA|Tsha|aGSU|alpha-GSU|alphaGSU|alphaSU	glycoprotein hormones, alpha subunit	protein-coding
mm_131831.1	chr16	22957495	22957516	+	1	NA	exon (NM_053176, exon 5 of 7)	exon (NM_053176, exon 5 of 7)	6433	NM_053176	94175	Mm.358794	NM_053176	ENSMUSG00000022877	Hrg	AI265597|AW413091|D16jh2|D18020|Hprg|Hrgp	histidine-rich glycoprotein	protein-coding
mm_130145.1	chr15	90943618	90943641	-	1	NA	intron (NM_001109040, intron 31 of 36)	B3A|SINE|B2	-45153	NR_033583	20738	Mm.431547	NR_033583		Spn-ps	Cd43-ps	sialophorin, pseudogene	pseudo
mm_46690.1	chr5	110083176	110083186	-	1	NA	Intergenic	RLTR30E_MM|LTR|ERV1	-16788	NM_207279	403178	Mm.297057	NM_207279	ENSMUSG00000064247	Plcxd1	A330045H12Rik|Gm576	phosphatidylinositol-specific phospholipase C, X domain containing 1	protein-coding
mm_55635.1	chr6	72333275	72333287	-	1	NA	intron (NM_138592, intron 6 of 12)	intron (NM_138592, intron 6 of 12)	11894	NM_138592	28035	Mm.281900	NM_138592	ENSMUSG00000056305	Usp39	AA408960|AI894154|CGI-21|D6Wsu157e|SAD1	ubiquitin specific peptidase 39	protein-coding
mm_104715.1	chr11	98053279	98053291	-	1	NA	5' UTR (NM_146028, exon 1 of 11)	5' UTR (NM_146028, exon 1 of 11)	177	NM_146028	217154	Mm.181008	NM_146028	ENSMUSG00000017400	Stac2	24b2|24b2/STAC2|AW240854	SH3 and cysteine rich domain 2	protein-coding
mm_170296.1	chr18	31447172	31447182	-	1	NA	5' UTR (NM_009308, exon 1 of 4)	5' UTR (NM_009308, exon 1 of 4)	238	NM_009308	20983	Mm.233846	NM_009308	ENSMUSG00000024261	Syt4	SytIV	synaptotagmin IV	protein-coding
mm_5304.1	chr1	21962335	21962392	-	1	NA	promoter-TSS (NM_023872)	promoter-TSS (NM_023872)	287	NM_001310477	226922	Mm.336519	NM_023872	ENSMUSG00000028033	Kcnq5	7730402H11|9230107O05Rik|AA589396|D1Mgi1	potassium voltage-gated channel, subfamily Q, member 5	protein-coding
mm_142995.1	chr17	56301163	56301202	-	1	NA	promoter-TSS (NM_029799)	promoter-TSS (NM_029799)	-896	NM_029799	76920	Mm.329132	NM_029799	ENSMUSG00000073380	Arrdc5	1700013E09Rik	arrestin domain containing 5	protein-coding
mm_90654.1	chr10	128790904	128790968	+	1	NA	promoter-TSS (NM_021412)	promoter-TSS (NM_021412)	-19	NM_021412	58223	Mm.131266	NM_021412	ENSMUSG00000025355	Mmp19	-	matrix metallopeptidase 19	protein-coding
mm_124378.1	chr14	106486516	106486528	-	1	NA	promoter-TSS (NR_045938)	promoter-TSS (NR_045938)	-2	NR_045938	73631	Mm.48862	NR_045938	ENSMUSG00000099794	1700128A07Rik	-	RIKEN cDNA 1700128A07 gene	ncRNA
mm_31425.1	chr4	48083680	48083683	+	1	NA	3' UTR (NM_015743, exon 8 of 8)	3' UTR (NM_015743, exon 8 of 8)	32435	NM_001307989	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_115851.1	chr13	21288742	21288751	-	1	NA	exon (NM_010343, exon 4 of 5)	exon (NM_010343, exon 4 of 5)	3940	NM_010343	14780	Mm.1332	NM_010343	ENSMUSG00000004344	Gpx5	AV379049|Arep	glutathione peroxidase 5	protein-coding
mm_132092.1	chr16	31234356	31234367	+	1	NA	intron (NR_035427, intron 1 of 2)	intron (NR_035427, intron 1 of 2)	-33123	NM_030138	78618	Mm.274646	NM_030138	ENSMUSG00000049076	Acap2	4832442G16|9530039J15Rik|CNT-B2|Centb2|mKIAA0041	ArfGAP with coiled-coil, ankyrin repeat and PH domains 2	protein-coding
mm_92348.1	chr10	75860255	75860289	-	1	NA	promoter-TSS (NM_010798)	promoter-TSS (NM_010798)	-22	NM_010798	17319	Mm.2326	NM_010798	ENSMUSG00000033307	Mif	GIF|Glif	macrophage migration inhibitory factor	protein-coding
mm_157237.1	chrX	17319366	17319400	-	1	NA	promoter-TSS (NM_028916)	promoter-TSS (NM_028916)	-15	NM_028916	74405	Mm.248531	NM_028916	ENSMUSG00000025038	Efhc2	4933407D04Rik|mRib72-2	EF-hand domain (C-terminal) containing 2	protein-coding
mm_23742.1	chr3	69316874	69316937	+	1	NA	promoter-TSS (NM_178726)	promoter-TSS (NM_178726)	-13	NM_178726	242083	Mm.40577	NM_178726	ENSMUSG00000027784	Ppm1l	3222401G13|5930404J21Rik|AI481720|AW045850|PP2C|PP2Cepsilon|Pp2ce|Ppp2ce|mKIAA4175	protein phosphatase 1 (formerly 2C)-like	protein-coding
mm_109237.1	chr12	108893632	108893655	+	1	NA	promoter-TSS (NM_177602)	promoter-TSS (NM_177602)	-432	NM_011710	22375	Mm.38433	NM_011710	ENSMUSG00000021266	Wars	TrpRS|WRS	tryptophanyl-tRNA synthetase	protein-coding
mm_29830.1	chr3	129754950	129754955	-	1	NA	exon (NM_010113, exon 1 of 24)	exon (NM_010113, exon 1 of 24)	370	NM_010113	13645	Mm.252481	NM_010113	ENSMUSG00000028017	Egf	AI790464	epidermal growth factor	protein-coding
mm_167875.1	chrX	37753937	37753937	+	1	NA	promoter-TSS (NM_008818)	promoter-TSS (NM_008818)	-671	NM_008818	18617	Mm.423066	NM_008818	ENSMUSG00000095180	Rhox5	AA409564|Pem	reproductive homeobox 5	protein-coding
mm_85393.1	chr9	103288226	103288256	-	1	NA	promoter-TSS (NM_027918)	promoter-TSS (NM_027918)	56	NM_027918	71775	Mm.18802	NM_027918	ENSMUSG00000033688	1300017J02Rik	Ica|mICA	RIKEN cDNA 1300017J02 gene	protein-coding
mm_75006.1	chr8	27240290	27240292	-	1	NA	Intergenic	ORR1B2|LTR|ERVL-MaLR	-10703	NM_013462	11556	Mm.278475	NM_013462	ENSMUSG00000031489	Adrb3	Adrb-3	adrenergic receptor, beta 3	protein-coding
mm_149563.1	chr19	12795869	12795897	+	1	NA	non-coding (NR_024093, exon 1 of 13)	non-coding (NR_024093, exon 1 of 13)	240	NR_024093	664779	Mm.290924	NM_001039718	ENSMUSG00000024695	Gm44505	Zfp91-Cntf|Zfp91Cntf	predicted readthrough transcript (NMD candidate), 44505	ncRNA
mm_23757.1	chr3	70007648	70007656	+	1	NA	promoter-TSS (NM_001018031)	promoter-TSS (NM_001018031)	39	NM_001018031	229389	Mm.331071	NM_001018031	ENSMUSG00000027788	Otol1	Gm414	otolin 1	protein-coding
mm_169234.1	chr1	36957444	36957446	-	1	NA	Intergenic	L1Md_T|LINE|L1	-17918	NM_018872	56030	Mm.186943	NM_018872	ENSMUSG00000026116	Tmem131	2610524E03Rik|CC28|D1Bwg0491e|Neg|RW1|YR-23|mKIAA0257	transmembrane protein 131	protein-coding
mm_1833.1	chr1	82785938	82785939	+	1	NA	Intergenic	Intergenic	-17482	NM_025453	66261	Mm.46325	NM_025453	ENSMUSG00000026149	Tm4sf20	1810018L02Rik	transmembrane 4 L six family member 20	protein-coding
mm_72449.1	chr8	83165657	83165677	+	1	NA	5' UTR (NM_001111304, exon 1 of 21)	5' UTR (NM_001111304, exon 1 of 21)	315	NM_027758	71310	Mm.24031	NM_027758	ENSMUSG00000031709	Tbc1d9	4933431N12Rik|AI847101|AW490653|C76116	TBC1 domain family, member 9	protein-coding
mm_29595.1	chr3	119749983	119749986	-	1	NA	intron (NM_001310711, intron 5 of 13)	intron (NM_001310711, intron 5 of 13)	33404	NM_001310711	56195	Mm.29966	NM_019550	ENSMUSG00000028134	Ptbp2	Ptb2|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding
mm_162149.1	chrX	75163728	75163728	-	1	NA	promoter-TSS (NM_001033786)	promoter-TSS (NM_001033786)	23	NM_001033786	434800	Mm.460747	NM_001033786	ENSMUSG00000073094	Smim9	4930428E23Rik	small integral membrane protein 9	protein-coding
mm_31362.1	chr4	47259702	47259717	+	1	NA	intron (NM_009928, intron 8 of 39)	intron (NM_009928, intron 8 of 39)	51697	NM_009928	12819	Mm.233547	NM_009928	ENSMUSG00000028339	Col15a1	-	collagen, type XV, alpha 1	protein-coding
mm_64081.1	chr7	140942910	140942918	+	1	NA	intron (NM_145387, intron 2 of 13)	intron (NM_145387, intron 2 of 13)	1333	NM_145387	212974	Mm.260139	NM_145387	ENSMUSG00000062031	Pgghg	5730511L01Rik|Athl1|BC023151	protein glucosylgalactosylhydroxylysine glucosidase	protein-coding
mm_135309.1	chr16	38712948	38712978	-	1	NA	promoter-TSS (NM_020260)	promoter-TSS (NM_020260)	72	NM_020260	12549	Mm.370848	NM_020260	ENSMUSG00000022799	Arhgap31	5830477L08Rik|AU041750|Cdgap|D330026I07Rik	Rho GTPase activating protein 31	protein-coding
mm_143223.1	chr17	63304133	63304145	-	1	NA	intron (NM_015794, intron 6 of 8)	RMER19B|LTR|ERVK	8834	NR_130176	414079	Mm.444282	NR_130176	ENSMUSG00000090565	4930405O22Rik	-	RIKEN cDNA 4930405O22 gene	ncRNA
mm_25574.1	chr3	116845146	116845163	+	1	NA	Intergenic	Intergenic	-14413	NM_001113478	20321	Mm.66293	NM_009146	ENSMUSG00000033386	Frrs1	AI131732|Sdfr2	ferric-chelate reductase 1	protein-coding
mm_5647.1	chr1	40516476	40516482	-	1	NA	5' UTR (NM_010553, exon 3 of 13)	5' UTR (NM_010553, exon 3 of 13)	1117	NM_010553	16174	Mm.20466	NM_010553	ENSMUSG00000026068	Il18rap	AcPL|IL-18R-beta|IL-18RAcP|IL-18Rbeta|IL-1RAcPL	interleukin 18 receptor accessory protein	protein-coding
mm_61335.1	chr7	68276109	68276134	+	1	NA	intron (NR_040340, intron 1 of 3)	intron (NR_040340, intron 1 of 3)	473	NR_040340	100504026	Mm.426764	NR_040340	ENSMUSG00000086628	Gm16157	OTTMUSG00000031023	predicted gene 16157	ncRNA
mm_104871.1	chr11	99416970	99416987	-	1	NA	intron (NM_010661, intron 6 of 7)	intron (NM_010661, intron 6 of 7)	5281	NM_010661	268482	Mm.436651	NM_010661	ENSMUSG00000020912	Krt12	AI835216|K12|Krt-12|Krt1-12	keratin 12	protein-coding
mm_87422.1	chr10	50729912	50729939	+	1	NA	exon (NM_198007, exon 26 of 42)	exon (NM_198007, exon 26 of 42)	137256	NM_198007	77987	Mm.222497	NM_198007	ENSMUSG00000038774	Ascc3	ASC1p200|B630009I04Rik|BC023451|D430001L07Rik|D630041L21|Helic1|RNAH	activating signal cointegrator 1 complex subunit 3	protein-coding
mm_146605.1	chr18	9619424	9619434	-	1	NA	promoter-TSS (NM_007593)	promoter-TSS (NM_007593)	40	NM_007593	26369	Mm.195831	NM_007593	ENSMUSG00000050996	Cetn1	caltractin	centrin 1	protein-coding
mm_150110.1	chr19	29584051	29584077	+	1	NA	intron (NM_001081319, intron 12 of 25)	intron (NM_001081319, intron 12 of 25)	61782	NM_001081319	226089	Mm.353838	NM_177641	ENSMUSG00000038658	Ric1	C030046E11Rik|C130057E09Rik|Kiaa1432	RAB6A GEF complex partner 1	protein-coding
mm_15115.1	chr2	153670841	153670882	+	1	NA	exon (NM_001271746, exon 10 of 21)	exon (NM_001271746, exon 10 of 21)	21412	NM_001271747	13436	Mm.89772	NM_010068	ENSMUSG00000027478	Dnmt3b	MmuIIIB	DNA methyltransferase 3B	protein-coding
mm_143341.1	chr17	66519667	66519727	-	1	NA	promoter-TSS (NM_024448)	promoter-TSS (NM_024448)	-27	NM_024448	19328	Mm.248313	NM_024448	ENSMUSG00000023460	Rab12	2900054P15Rik|AW555448|C77700	RAB12, member RAS oncogene family	protein-coding
mm_170746.1	chr2	155531051	155531051	-	1	NA	intron (NM_019811, intron 2 of 17)	B1_Mus2|SINE|Alu	13008	NM_019811	60525	Mm.255026	NM_019811	ENSMUSG00000027605	Acss2	1110017C11Rik|ACAS|Acas1|Acas2|AceCS1|Acs1	acyl-CoA synthetase short-chain family member 2	protein-coding
mm_98661.1	chr11	96271918	96271933	+	1	NA	exon (NM_008270, exon 1 of 2)	exon (NM_008270, exon 1 of 2)	595	NM_008270	15417	Mm.258271	NM_008270	ENSMUSG00000020875	Hoxb9	Hox-2.5	homeobox B9	protein-coding
mm_39577.1	chr5	23434503	23434513	+	1	NA	promoter-TSS (NM_026984)	promoter-TSS (NM_026984)	79	NM_026984	69188	Mm.205190	NM_026984	ENSMUSG00000029004	Kmt2e	1810033J14Rik|9530077A04Rik|D230038D11Rik|Mll5|NKp44L	lysine (K)-specific methyltransferase 2E	protein-coding
mm_12654.1	chr2	75138847	75138859	+	1	NA	Intergenic	Intergenic	305326	NR_040635	77269	Mm.389278	NR_040635		9430019J16Rik	-	RIKEN cDNA 9430019J16 gene	ncRNA
mm_68255.1	chr7	105581502	105581569	-	1	NA	promoter-TSS (NM_001253886)	promoter-TSS (NM_001253886)	-44	NM_001253886	11785	Mm.38469	NM_009685	ENSMUSG00000037032	Apbb1	Fe65|Rir	amyloid beta (A4) precursor protein-binding, family B, member 1	protein-coding
mm_120788.1	chr14	74732414	74732424	+	1	NA	5' UTR (NM_001285423, exon 1 of 9)	5' UTR (NM_001285423, exon 1 of 9)	122	NM_016903	13885	Mm.38055	NM_016903	ENSMUSG00000021996	Esd	Es-10|Es10|FGH|sid478	esterase D/formylglutathione hydrolase	protein-coding
mm_87370.1	chr10	44268329	44268379	+	1	NA	promoter-TSS (NM_053069)	promoter-TSS (NM_053069)	15	NM_053069	11793	Mm.22264	NM_053069	ENSMUSG00000038160	Atg5	2010107M05Rik|3110067M24Rik|AW319544|Apg5l|Atg5l|C88337|Paddy	autophagy related 5	protein-coding
mm_117929.1	chr13	99434302	99434313	-	1	NA	exon (NM_008634, exon 5 of 7)	exon (NM_008634, exon 5 of 7)	-21481	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_160174.1	chr7	45394765	45394765	-	1	NA	non-coding (NR_126539, exon 2 of 10)	non-coding (NR_126539, exon 2 of 10)	977	NM_009224	20637	Mm.216386	NM_009224	ENSMUSG00000063511	Snrnp70	2700022N21Rik|3200002N22Rik|AI325098|R74807|Rnu1p70|Rnulp70|Snrp70|Srnp70|U1-70|U1-70K	small nuclear ribonucleoprotein 70 (U1)	protein-coding
mm_18624.1	chr2	68565395	68565398	-	1	NA	Intergenic	RMER21B|LTR|ERV1	-17017	NM_177651	227998	Mm.67562	NM_177651	ENSMUSG00000053896	4933409G03Rik	-	RIKEN cDNA 4933409G03 gene	protein-coding
mm_27356.1	chr3	50417887	50417899	-	1	NA	intron (NM_011990, intron 6 of 11)	intron (NM_011990, intron 6 of 11)	25720	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_89678.1	chr10	97517548	97517570	+	1	NA	exon (NM_007833, exon 8 of 8)	exon (NM_007833, exon 8 of 8)	35228	NM_007833	13179	Mm.56769	NM_007833	ENSMUSG00000019929	Dcn	DC|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding
mm_10410.1	chr2	13579030	13579053	+	1	NA	intron (NM_011701, intron 4 of 8)	intron (NM_011701, intron 4 of 8)	4730	NM_011701	22352	Mm.268000	NM_011701	ENSMUSG00000026728	Vim	-	vimentin	protein-coding
mm_140482.1	chr17	3114763	3114828	-	1	NA	promoter-TSS (NM_134123)	promoter-TSS (NM_134123)	-177	NM_134123	106583	Mm.124373	NM_134123	ENSMUSG00000046201	Scaf8	A630086M08Rik|A930036P18Rik|AA408306|AI447644|AI448652|AU015035|Rbm16|mKIAA1116	SR-related CTD-associated factor 8	protein-coding
mm_45455.1	chr5	67766715	67766718	-	1	NA	intron (NM_001284345, intron 11 of 36)	intron (NM_001284345, intron 11 of 36)	80715	NM_009727	11980	Mm.153230	NM_009727	ENSMUSG00000037685	Atp8a1	AI481521|AI853962|APLT|AW743152|AW822227|Atp3a2|B230107D19Rik|ClassI	ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1	protein-coding
mm_167701.1	chr9	90242997	90243001	-	1	NA	intron (NM_194334, intron 2 of 12)	intron (NM_194334, intron 2 of 12)	27770	NM_194334	67016	Mm.335347	NM_194334	ENSMUSG00000037410	Tbc1d2b	1810061M12Rik|AI480956|AV021536|AV023399|AW491493|mKIAA1055	TBC1 domain family, member 2B	protein-coding
mm_51939.1	chr6	91701650	91701662	+	1	NA	intron (NM_009320, intron 2 of 14)	intron (NM_009320, intron 2 of 14)	17589	NM_009320	21366	Mm.395650	NM_009320	ENSMUSG00000030096	Slc6a6	AA589629|C80501|Taut	solute carrier family 6 (neurotransmitter transporter, taurine), member 6	protein-coding
mm_55522.1	chr6	70429969	70429981	-	1	NA	Intergenic	Intergenic	362200	NM_009075	19895	Mm.17905	NM_009075	ENSMUSG00000053604	Rpia	RPI	ribose 5-phosphate isomerase A	protein-coding
mm_137261.1	chr17	24639962	24640005	+	1	NA	3' UTR (NM_023055, exon 7 of 7)	3' UTR (NM_023055, exon 7 of 7)	4974	NM_023449	65962	Mm.21587	NM_023055	ENSMUSG00000002504	Slc9a3r2	0610011L07Rik|1200011K07Rik|2010007A20Rik|E3karp|NHERF-2|Nherf2|Octs2|Sip-1|Sip1|Sryip1|Tka-1	solute carrier family 9 (sodium/hydrogen exchanger), member 3 regulator 2	protein-coding
mm_24058.1	chr3	87915082	87915095	+	1	NA	3' UTR (NM_008231, exon 6 of 6)	3' UTR (NM_008231, exon 6 of 6)	-4456	NM_026591	67707	Mm.393802	NM_026591	ENSMUSG00000019710	Mrpl24	2010005E08Rik|2810470K06Rik|6720473G22Rik|AA407670	mitochondrial ribosomal protein L24	protein-coding
mm_108788.1	chr12	90738848	90738870	+	1	NA	5' UTR (NM_010050, exon 1 of 2)	5' UTR (NM_010050, exon 1 of 2)	178	NM_010050	13371	Mm.21389	NM_010050	ENSMUSG00000007682	Dio2	5DII|AI324267|DIOII	deiodinase, iodothyronine, type II	protein-coding
mm_52964.1	chr6	123124515	123124529	+	1	NA	intron (NM_011999, intron 1 of 5)	B1F2|SINE|Alu	1206	NM_001170333	26888	Mm.47384	NM_011999	ENSMUSG00000030148	Clec4a2	Clec4a|Clecsf6|DCIR|Dcir1	C-type lectin domain family 4, member a2	protein-coding
mm_91619.1	chr10	41685971	41685981	-	1	NA	Intergenic	Intergenic	-79381	NM_001303469	75973	Mm.228517	NM_029493	ENSMUSG00000075225	Ccdc162	5033413D22Rik|Ccdc162p|Gm29096|Gm61|Gm6976	coiled-coil domain containing 162	protein-coding
mm_78677.1	chr9	40782405	40782427	+	1	NA	exon (NM_133733, exon 7 of 7)	exon (NM_133733, exon 7 of 7)	-18857	NM_031165	15481	Mm.290774	NM_031165	ENSMUSG00000015656	Hspa8	2410008N15Rik|Hsc70|Hsc71|Hsc73|Hsp73|Hspa10	heat shock protein 8	protein-coding
mm_77356.1	chr8	119635468	119635478	-	1	NA	5' UTR (NM_025734, exon 1 of 3)	5' UTR (NM_025734, exon 1 of 3)	207	NM_025734	66733	Mm.358699	NM_025734	ENSMUSG00000045246	Kcng4	4921535I01Rik|AW049024|KV6.3|KV6.4	potassium voltage-gated channel, subfamily G, member 4	protein-coding
mm_38966.1	chr4	150902092	150902098	-	1	NA	intron (NM_020569, intron 5 of 6)	intron (NM_020569, intron 5 of 6)	7826	NM_020569	57320	Mm.277349	NM_020569	ENSMUSG00000028964	Park7	DJ-1|Dj1	Parkinson disease (autosomal recessive, early onset) 7	protein-coding
mm_95367.1	chr11	49086673	49086677	+	1	NA	promoter-TSS (NM_008330)	promoter-TSS (NM_008330)	-342	NM_001271676	15953	Mm.24769	NM_008330	ENSMUSG00000078920	Ifi47	47kDa|IRG-47|Ifggc1|Igrd|Iigp4|Iipg4|Irgd	interferon gamma inducible protein 47	protein-coding
mm_16371.1	chr2	178023275	178023291	+	1	NA	promoter-TSS (NM_001177399)	promoter-TSS (NM_001177399)	-1	NM_001177400	626848	Mm.422604	NM_001177399	ENSMUSG00000074519	Zfp971	Etohi1	zinc finger protein 971	protein-coding
mm_55811.1	chr6	83033201	83033211	-	1	NA	intron (NM_010070, intron 1 of 4)	CpG-12178	265	NM_010070	13448	Mm.156	NM_010070	ENSMUSG00000068335	Dok1	AW557123|p62DOK	docking protein 1	protein-coding
mm_21807.1	chr2	165034771	165034820	-	1	NA	promoter-TSS (NM_144892)	promoter-TSS (NM_144892)	-16	NM_144892	228869	Mm.233080	NM_144892	ENSMUSG00000039804	Ncoa5	CIA	nuclear receptor coactivator 5	protein-coding
mm_51312.1	chr6	72314283	72314312	+	1	NA	TTS (NM_001282071)	TTS (NM_001282071)	9687	NM_147779	20388	Mm.46033	NM_147779	ENSMUSG00000056370	Sftpb	AI562151|SF-B|SP-B|Sftp-3|Sftp3	surfactant associated protein B	protein-coding
mm_43257.1	chr5	130222392	130222403	+	1	NA	promoter-TSS (NM_027854)	promoter-TSS (NM_027854)	62	NM_027854	71667	Mm.258508	NM_027854	ENSMUSG00000053094	Tmem248	0610007L01Rik|A930023A16Rik|AW557951|G430067H08Rik	transmembrane protein 248	protein-coding
mm_16182.1	chr2	172938780	172938808	+	1	NA	intron (NM_007557, intron 1 of 6)	intron (NM_007557, intron 1 of 6)	1527	NM_007557	12162	Mm.595	NM_007557	ENSMUSG00000008999	Bmp7	OP1	bone morphogenetic protein 7	protein-coding
mm_4873.1	chr1	187810394	187810396	+	1	NA	intron (NM_001243792, intron 2 of 7)	intron (NM_001243792, intron 2 of 7)	-187432	NM_011935	26381	Mm.89989	NM_011935	ENSMUSG00000026610	Esrrg	ERR3|Errg|NR3B3|mKIAA0832	estrogen-related receptor gamma	protein-coding
mm_15756.1	chr2	164276059	164276070	+	1	NA	3' UTR (NM_009300, exon 3 of 3)	3' UTR (NM_009300, exon 3 of 3)	2243	NM_009300	20941	Mm.1286	NM_009300	ENSMUSG00000016998	Svs4	SVS-IV|Svp-2|Svp-4|Svp2|Svp4	seminal vesicle secretory protein 4	protein-coding
mm_68323.1	chr7	106503516	106503526	-	1	NA	Intergenic	RMER12B|LTR|ERVK	-62448	NR_003967	209380	Mm.461779	NM_001001318		Gm4759	EG209380	GTPase, very large interferon inducible 1 pseudogene	pseudo
mm_161288.1	chr14	26182289	26182289	-	1	NA	promoter-TSS (NM_001270503).3	promoter-TSS (NM_001270503).3	-16	NM_207229	211623	Mm.439926	NM_207229	ENSMUSG00000095304	Plac9a	Plac9	placenta specific 9a	protein-coding
mm_166978.1	chr7	45175194	45175203	+	1	NA	3' UTR (NM_182993, exon 12 of 12)	3' UTR (NM_182993, exon 12 of 12)	1895	NR_106022	102465638		NR_106022	ENSMUSG00000106470	Mir7055	mmu-mir-7055	microRNA 7055	ncRNA
mm_94204.1	chr11	3104245	3104287	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	-19755	NR_003517	236604	Mm.247625	NM_001004146		Pisd-ps1	-	phosphatidylserine decarboxylase, pseudogene 1	pseudo
mm_139955.1	chr17	71311011	71311057	+	1	NA	promoter-TSS (NM_145158)	promoter-TSS (NM_145158)	-69	NM_145158	246707	Mm.23462	NM_145158	ENSMUSG00000024053	Emilin2	FOAP-10	elastin microfibril interfacer 2	protein-coding
mm_12776.1	chr2	79328664	79328674	+	1	NA	3' UTR (NM_010576, exon 28 of 28)	3' UTR (NM_010576, exon 28 of 28)	73243	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D|Itga4B	integrin alpha 4	protein-coding
mm_168579.1	chr1	171711071	171711087	+	1	NA	Intergenic	Intergenic	29024	NM_007649	12506	Mm.1738	NM_007649	ENSMUSG00000015355	Cd48	AI449234|AW610730|BCM1|BLAST|BLAST-1|BLAST1|Bcm-1|MEM-102|SLAMF2|Sgp-60	CD48 antigen	protein-coding
mm_101981.1	chr11	50422003	50422062	-	1	NA	intron (NM_172557, intron 1 of 17)	intron (NM_172557, intron 1 of 17)	9079	NM_172557	216724	Mm.390400	NM_172557	ENSMUSG00000020375	Rufy1	3000002E04Rik|Rabip4|ZFYVE12	RUN and FYVE domain containing 1	protein-coding
mm_140785.1	chr17	17910245	17910273	-	1	NA	Intergenic	CpG	22435	NM_008039	14289	Mm.378918	NM_008039	ENSMUSG00000052270	Fpr2	E330010I07Rik|Fpr-rs2	formyl peptide receptor 2	protein-coding
mm_170368.1	chr1	85327346	85327347	-	1	NA	Intergenic	Intergenic	-56780	NM_001037909	620078	Mm.386456	NM_175219	ENSMUSG00000052477	C130026I21Rik	4930565N07Rik|OTTMUSG00000029174	RIKEN cDNA C130026I21 gene	protein-coding
mm_24193.1	chr3	88607536	88607543	+	1	NA	Intergenic	Intergenic	-8668	NM_001198911	16800	Mm.239329	NM_008487	ENSMUSG00000028059	Arhgef2	AA408978|GEF|GEF-H1|GEFH1|LFP40|Lbcl1|Lfc|P40|mKIAA0651	rho/rac guanine nucleotide exchange factor (GEF) 2	protein-coding
mm_156381.1	chrX	139672191	139672205	+	1	NA	3' UTR (NM_023270, exon 7 of 7)	3' UTR (NM_023270, exon 7 of 7)	-12798	NM_001081499	245638	Mm.275869	NM_001081499	ENSMUSG00000042473	Tbc1d8b	4921505D17Rik|9030605E16Rik	TBC1 domain family, member 8B	protein-coding
mm_118951.1	chr14	27379492	27379494	+	1	NA	intron (NM_001289686, intron 5 of 12)	intron (NM_001289686, intron 5 of 12)	18104	NM_001289688	71704	Mm.248606	NM_027871	ENSMUSG00000021895	Arhgef3	1200004I24Rik|9830169H03Rik|C76747|Xpln	Rho guanine nucleotide exchange factor (GEF) 3	protein-coding
mm_74748.1	chr8	19026544	19026557	-	1	NA	promoter-TSS (NM_183036)	promoter-TSS (NM_183036)	-21	NM_183036	360212	Mm.271558	NM_183036	ENSMUSG00000053790	Defb38	BD-38	defensin beta 38	protein-coding
mm_93254.1	chr10	95514743	95514769	-	1	NA	promoter-TSS (NM_080560)	promoter-TSS (NM_080560)	-406	NM_080560	93765	Mm.371667	NM_080560	ENSMUSG00000074781	Ube2n	1500026J17Rik|AL022654|BB101821|UBC13	ubiquitin-conjugating enzyme E2N	protein-coding
mm_143718.1	chr17	81065057	81065099	-	1	NA	promoter-TSS (NM_028138)	promoter-TSS (NM_028138)	7	NM_028138	72167	Mm.273257	NM_028138	ENSMUSG00000024246	Thumpd2	2810025A12Rik	THUMP domain containing 2	protein-coding
mm_165087.1	chr19	48063564	48063566	+	1	NA	Intergenic	Intergenic	125853	NM_001163267	381229	Mm.300553	NM_001163267	ENSMUSG00000046585	Cfap58	Ccdc147|Gm969	cilia and flagella associated protein 58	protein-coding
mm_157799.1	chrX	73921918	73921922	-	1	NA	promoter-TSS (NM_019870)	promoter-TSS (NM_019870)	24	NM_001310538	56292	Mm.246654	NM_019870	ENSMUSG00000031388	Naa10	2310039H09Rik|Ard1|Ard1a|Te2	N(alpha)-acetyltransferase 10, NatA catalytic subunit	protein-coding
mm_87170.1	chr10	37239044	37239046	+	1	NA	Intergenic	Intergenic	-100119	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_13204.1	chr2	93462026	93462045	+	1	NA	promoter-TSS (NM_001271461)	promoter-TSS (NM_001271461)	-184	NM_001271461	12521	Mm.4261	NM_007656	ENSMUSG00000027215	Cd82	AA682076|AL023070|C33|IA4|Kai1|Tspan27	CD82 antigen	protein-coding
mm_110639.1	chr12	57546878	57546923	-	1	NA	promoter-TSS (NM_008259)	promoter-TSS (NM_008259)	-779	NM_008259	15375	Mm.4578	NM_008259	ENSMUSG00000035451	Foxa1	Hnf-3a|Hnf3a|Tcf-3a|Tcf3a	forkhead box A1	protein-coding
mm_169507.1	chr1	4802838	4802853	+	1	NA	Intergenic	RLTR9D|LTR|ERVK	-5048	NM_008866	18777	Mm.299955	NM_008866	ENSMUSG00000025903	Lypla1	Pla1a	lysophospholipase 1	protein-coding
mm_118422.1	chr14	7858611	7858656	+	1	NA	intron (NM_134080, intron 1 of 45)	intron (NM_134080, intron 1 of 45)	40676	NM_134080	286940	Mm.489652	NM_134080	ENSMUSG00000025278	Flnb	AL024016|Fln-b	filamin, beta	protein-coding
mm_111106.1	chr12	80956032	80956057	-	1	NA	exon (NM_001177561, exon 4 of 5)	exon (NM_001177561, exon 4 of 5)	10545	NM_001347415	20384	Mm.43331	NM_009159	ENSMUSG00000021134	Srsf5	Sfrs5	serine/arginine-rich splicing factor 5	protein-coding
mm_142578.1	chr17	46680871	46680933	-	1	NA	promoter-TSS (NM_010787)	promoter-TSS (NM_010787)	28	NM_001163729	71765	Mm.254784	NM_027910	ENSMUSG00000063576	Klhdc3	1300011D16Rik|Peas	kelch domain containing 3	protein-coding
mm_117024.1	chr13	58192141	58192145	-	1	NA	exon (NM_152234, exon 5 of 10)	exon (NM_152234, exon 5 of 10)	23510	NM_152234	56085	Mm.182053	NM_026842	ENSMUSG00000005312	Ubqln1	1110046H03Rik|1810030E05Rik|AU019746|C77538|D13Ertd372e|Da41|Dsk2|Plic-1|Plic1|Xdrp1	ubiquilin 1	protein-coding
mm_88909.1	chr10	81179635	81179648	+	1	NA	TTS (NR_028549)	TTS (NR_028549)	680	NR_028549	100217454		NR_028549	ENSMUSG00000064441	Snord37	MBII-376	small nucleolar RNA, C/D box 37	snoRNA
mm_9197.1	chr1	171226167	171226181	-	1	NA	exon (NM_013474, exon 4 of 4)	exon (NM_013474, exon 4 of 4)	1120	NM_013474	11807	Mm.389209	NM_013474	ENSMUSG00000005681	Apoa2	Alp-2|Apo-AII|ApoA-II|ApoAII|Apoa-2|Hdl-1	apolipoprotein A-II	protein-coding
mm_121355.1	chr14	116925773	116925789	+	1	NA	5' UTR (NM_011821, exon 1 of 9)	5' UTR (NM_011821, exon 1 of 9)	484	NM_011821	23888	Mm.440025	NM_011821	ENSMUSG00000058571	Gpc6	-	glypican 6	protein-coding
mm_105868.1	chr11	114237139	114237153	-	1	NA	Intergenic	MTE2a|LTR|ERVL-MaLR	38888	NR_045930	73536	Mm.54275	NR_045930	ENSMUSG00000078600	1700092K14Rik	-	RIKEN cDNA 1700092K14 gene	ncRNA
mm_58144.1	chr6	142161084	142161099	-	1	NA	5' UTR (NM_023718, exon 2 of 15)	5' UTR (NM_023718, exon 2 of 15)	25058	NM_023718	28254	Mm.38953	NM_023718	ENSMUSG00000079262	Slco1a6	4930422F19Rik|AI790453|Oatp-5|Oatp5|Slc21a13	solute carrier organic anion transporter family, member 1a6	protein-coding
mm_113273.1	chr13	29653664	29653682	+	1	NA	intron (NR_131896, intron 8 of 16)	MTC|LTR|ERVL-MaLR	202000	NR_131896	68916	Mm.212227	NM_144536	ENSMUSG00000006191	Cdkal1	1190005B03Rik|6620401C13Rik	CDK5 regulatory subunit associated protein 1-like 1	protein-coding
mm_66528.1	chr7	45136070	45136081	-	1	NA	non-coding (NR_102725, exon 2 of 8)	non-coding (NR_102725, exon 2 of 8)	357	NM_013520	14256	Mm.1658	NM_013520	ENSMUSG00000110206	Flt3l	Flt3lg|Ly72L	FMS-like tyrosine kinase 3 ligand	protein-coding
mm_31639.1	chr4	59581523	59581532	+	1	NA	promoter-TSS (NM_024255)	promoter-TSS (NM_024255)	-36	NM_001301367	72479	Mm.272905	NM_024255	ENSMUSG00000028383	Hsdl2	2610207I16Rik	hydroxysteroid dehydrogenase like 2	protein-coding
mm_49178.1	chr6	15105865	15105869	+	1	NA	intron (NM_053242, intron 3 of 18)	intron (NM_053242, intron 3 of 18)	-79639	NM_212435	114142	Mm.332919	NM_053242	ENSMUSG00000029563	Foxp2	2810043D05Rik|AI449000|CAG-16|D0Kist7	forkhead box P2	protein-coding
mm_28531.1	chr3	92656926	92656927	-	1	NA	promoter-TSS (NM_026822)	promoter-TSS (NM_026822)	0	NM_026822	68720	Mm.291769	NM_026822	ENSMUSG00000027923	Lce1b	1110029C13Rik|Sprrl5	late cornified envelope 1B	protein-coding
mm_109223.1	chr12	108793101	108793132	+	1	NA	promoter-TSS (NM_009537)	promoter-TSS (NM_009537)	-195	NM_009537	22632	Mm.3868	NM_009537	ENSMUSG00000021264	Yy1	AW488674|NF-E1	YY1 transcription factor	protein-coding
mm_28216.1	chr3	88410068	88410094	-	1	NA	TTS (NM_001281795)	TTS (NM_001281795)	316	NM_001310605	67037	Mm.36715	NM_025928	ENSMUSG00000028066	Pmf1	2600009M07Rik|AL033286|AW060657	polyamine-modulated factor 1	protein-coding
mm_167941.1	chrX	118427216	118427231	+	1	NA	promoter-TSS (NM_153109)	promoter-TSS (NM_153109)	-4	NM_001142750	100039551	Mm.272850	NM_001142750	ENSMUSG00000100194	Tgif2lx2	-	TGFB-induced factor homeobox 2-like, X-linked 2	protein-coding
mm_52358.1	chr6	112489040	112489050	+	1	NA	exon (NM_001081147, exon 1 of 2)	exon (NM_001081147, exon 1 of 2)	763	NM_001081147	18430	Mm.333310	NM_001081147	ENSMUSG00000049112	Oxtr	OTR	oxytocin receptor	protein-coding
mm_108626.1	chr12	85599389	85599407	+	1	NA	promoter-TSS (NM_001205053)	promoter-TSS (NM_001205053)	-18	NM_030887	81703	Mm.103560	NM_030887	ENSMUSG00000034271	Jdp2	Jundm2|Jundp2|TIF	Jun dimerization protein 2	protein-coding
mm_117308.1	chr13	67451592	67451638	-	1	NA	promoter-TSS (NM_177712)	promoter-TSS (NM_177712)	9	NM_177712	238692	Mm.486478	NM_177712	ENSMUSG00000069206	Zfp874a	C330011K17Rik|Rslcan15|Zfp874	zinc finger protein 874a	protein-coding
mm_159678.1	chr4	156223617	156223617	-	1	NA	exon (NM_001008233, exon 10 of 16)	exon (NM_001008233, exon 10 of 16)	4925	NM_001008233	231002	Mm.423124	NM_001008233	ENSMUSG00000078485	Plekhn1	BC025458	pleckstrin homology domain containing, family N member 1	protein-coding
mm_157219.1	chrX	13072549	13072567	-	1	NA	intron (NM_009481, intron 1 of 44)	CpG	1060	NM_009481	22284	Mm.242646	NM_009481	ENSMUSG00000031010	Usp9x	5730589N07Rik|AA407302|AA407699|AL022658|AL022749|Dffrx|FAF-X|Fafl	ubiquitin specific peptidase 9, X chromosome	protein-coding
mm_130586.1	chr15	99628672	99628691	-	1	NA	exon (NM_001253809, exon 10 of 17)	exon (NM_001253809, exon 10 of 17)	22975	NM_001253808	26934	Mm.273804	NM_012025	ENSMUSG00000023015	Racgap1	AI227039|AI327394|Band25|GTPase|MgcRacGAP|gtl11|mKIAA1478	Rac GTPase-activating protein 1	protein-coding
mm_136664.1	chr17	6106465	6106482	+	1	NA	promoter-TSS (NM_001103181)	promoter-TSS (NM_001103181)	-357	NM_001103181	68842	Mm.449307	NM_054040	ENSMUSG00000034377	Tulp4	1110057P05Rik|2210038L17Rik|Tusp	tubby like protein 4	protein-coding
mm_95317.1	chr11	46436943	46437017	+	1	NA	promoter-TSS (NM_025426)	promoter-TSS (NM_025426)	19	NM_025426	66213	Mm.24159	NM_025426	ENSMUSG00000020397	Med7	1110063B05Rik|Crsp33|Crsp9	mediator complex subunit 7	protein-coding
mm_129149.1	chr15	76209057	76209126	-	1	NA	promoter-TSS (NM_201388)	promoter-TSS (NM_201388)	74	NM_201386	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
mm_51098.1	chr6	67271258	67271278	+	1	NA	exon (NM_025814, exon 2 of 8)	exon (NM_025814, exon 2 of 8)	4289	NM_025814	66870	Mm.240490	NM_025814	ENSMUSG00000036371	Serbp1	1200009K13Rik|9330147J08Rik|AL022786|Pairbp1	serpine1 mRNA binding protein 1	protein-coding
mm_139667.1	chr17	57411287	57411311	+	1	NA	intron (NM_010130, intron 9 of 21)	ID_B1|SINE|B4	52613	NM_010130	13733	Mm.2254	NM_010130	ENSMUSG00000004730	Adgre1	DD7A5-7|EGF-TM7|Emr1|F4/80|Gpf480|Ly71|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding
mm_23098.1	chr3	37231485	37231495	+	1	NA	intron (NM_021782, intron 2 of 4)	intron (NM_021782, intron 2 of 4)	1146	NM_001291041	60505	Mm.157689	NM_021782	ENSMUSG00000027718	Il21	IL-21	interleukin 21	protein-coding
mm_35238.1	chr4	19877212	19877221	-	1	NA	3' UTR (NM_175406, exon 8 of 8)	3' UTR (NM_175406, exon 8 of 8)	45350	NM_175406	242341	Mm.19298	NM_175406	ENSMUSG00000028238	Atp6v0d2	1620401A02Rik|AI324824|V-ATPase	ATPase, H+ transporting, lysosomal V0 subunit D2	protein-coding
mm_107852.1	chr12	69375574	69375577	+	1	NA	3' UTR (NM_007481, exon 2 of 2)	3' UTR (NM_007481, exon 2 of 2)	3425	NM_007481	11845	Mm.27308	NM_007481	ENSMUSG00000044147	Arf6	AI788669|AW496366	ADP-ribosylation factor 6	protein-coding
mm_50503.1	chr6	49036528	49036540	+	1	NA	promoter-TSS (NM_053110)	promoter-TSS (NM_053110)	16	NM_053110	93695	Mm.302602	NM_053110	ENSMUSG00000029816	Gpnmb	DC-HIL|Dchil|ipd	glycoprotein (transmembrane) nmb	protein-coding
mm_157998.1	chrX	94541985	94542031	-	1	NA	promoter-TSS (NM_019791)	promoter-TSS (NM_019791)	66	NM_019791	94275	Mm.27578	NM_019791	ENSMUSG00000025151	Maged1	2810433C11Rik|5430405L04Rik|DXBwg1492e|Dlixin|Dlxin-1|Dlxin1|MAGE-D1|NRAGE|mFLJ00163	melanoma antigen, family D, 1	protein-coding
mm_52043.1	chr6	96399644	96399664	+	1	NA	intron (NM_182808, intron 2 of 4)	intron (NM_182808, intron 2 of 4)	-233449	NR_003643	78482	Mm.391486	NM_030107	ENSMUSG00000072878	1700123L14Rik	-	nucleoporin 50 pseudogene	pseudo
mm_68646.1	chr7	118488254	118488288	-	1	NA	3' UTR (NM_001033380, exon 1 of 1)	3' UTR (NM_001033380, exon 1 of 1)	3704	NM_001033380	319622	Mm.323386	NM_001033380	ENSMUSG00000095115	Itpripl2	C130081G24|E030018N11Rik	inositol 1,4,5-triphosphate receptor interacting protein-like 2	protein-coding
mm_104061.1	chr11	86584510	86584560	-	1	NA	promoter-TSS (NR_029738)	promoter-TSS (NR_029738)	-377	NR_029738	387140		NR_029738	ENSMUSG00000065455	Mir21a	Mir21|Mirn21|mmu-mir-21|mmu-mir-21a	microRNA 21a	ncRNA
mm_156060.1	chrX	109160121	109160180	+	1	NA	exon (NM_019989, exon 4 of 4)	exon (NM_019989, exon 4 of 4)	-36606	NM_001037917	622976	Mm.482747	NM_001037917	ENSMUSG00000048621	Gm6377	EG622976	predicted gene 6377	protein-coding
mm_111662.1	chr12	103336087	103336111	-	1	NA	intron (NM_023049, intron 3 of 9)	intron (NM_023049, intron 3 of 9)	19902	NM_023049	65256	Mm.27159	NM_023049	ENSMUSG00000021200	Asb2	1110008E15Rik	ankyrin repeat and SOCS box-containing 2	protein-coding
mm_54825.1	chr6	42373255	42373274	-	1	NA	promoter-TSS (NM_023580)	promoter-TSS (NM_023580)	4	NM_023580	13835	Mm.133330	NM_023580	ENSMUSG00000029859	Epha1	5730453L17Rik|AL033318|Eph|Esk	Eph receptor A1	protein-coding
mm_40107.1	chr5	34761735	34761780	+	1	NA	promoter-TSS (NM_010414)	promoter-TSS (NM_010414)	17	NM_010414	15194	Mm.209071	NM_010414	ENSMUSG00000029104	Htt	AI256365|C430023I11Rik|Hd|Hdh|IT15	huntingtin	protein-coding
mm_111447.1	chr12	98259340	98259360	-	1	NA	5' UTR (NM_008079, exon 1 of 17)	5' UTR (NM_008079, exon 1 of 17)	109	NM_008079	14420	Mm.5120	NM_008079	ENSMUSG00000021003	Galc	2310068B06Rik|A930008M05Rik|AW212969|AW413532|Gacy|twi|twitcher	galactosylceramidase	protein-coding
mm_107358.1	chr12	32831998	32832014	+	1	NA	intron (NM_021524, intron 2 of 10)	RCHARR1|DNA|hAT-Charlie	7890	NR_045032	100504486	Mm.440246	NR_045032		Gdap10	Gdap-ps	ganglioside-induced differentiation-associated-protein 10	ncRNA
mm_155489.1	chrX	73716754	73716779	+	1	NA	promoter-TSS (NM_012060)	promoter-TSS (NM_012060)	169	NM_007435	11666	Mm.365	NM_007435	ENSMUSG00000031378	Abcd1	ALDP|Ald|Aldgh	ATP-binding cassette, sub-family D (ALD), member 1	protein-coding
mm_98362.1	chr11	93898622	93898624	+	1	NA	intron (NM_001346525, intron 3 of 17)	B2_Mm2|SINE|B2	12404	NM_134012	103537	Mm.210334	NM_134012	ENSMUSG00000059474	Mbtd1	AA408199|AI194990|hemp	mbt domain containing 1	protein-coding
mm_87642.1	chr10	58371611	58371627	+	1	NA	exon (NM_201242, exon 1 of 10)	exon (NM_201242, exon 1 of 10)	165	NM_201242	110829	Mm.57734	NM_026148	ENSMUSG00000019920	Lims1	2310016J22Rik|4921524A02Rik|AI507642|AU021743|AW551584|C430041B13Rik|Lims1l|PINCH|PINCH1	LIM and senescent cell antigen-like domains 1	protein-coding
mm_156642.1	chrX	157698986	157699013	+	1	NA	promoter-TSS (NM_001252591)	promoter-TSS (NM_001252591)	26	NR_103722	66106	Mm.140340	NM_025357	ENSMUSG00000041476	Smpx	1010001C09Rik|Csl	small muscle protein, X-linked	protein-coding
mm_156231.1	chrX	135839172	135839175	+	1	NA	5' UTR (NM_001163017, exon 1 of 7)	5' UTR (NM_001163017, exon 1 of 7)	139	NM_001163017	245607	Mm.489763	NM_001163015	ENSMUSG00000072966	Gprasp2	5330440H13Rik|GASP-2|GASP2|Prpl5	G protein-coupled receptor associated sorting protein 2	protein-coding
mm_20762.1	chr2	140955958	140955986	-	1	NA	intron (NM_001013802, intron 4 of 18)	intron (NM_001013802, intron 4 of 18)	-284496	NM_178382	71436	Mm.426781	NM_178382	ENSMUSG00000051379	Flrt3	5530600M07Rik|C430047I10Rik|mKIAA1469	fibronectin leucine rich transmembrane protein 3	protein-coding
mm_154395.1	chrM	13372	13384	+	1	NA	NA	Intergenic	NA	NA								
mm_92185.1	chr10	68095927	68095959	-	1	NA	3' UTR (NM_023598, exon 10 of 10)	3' UTR (NM_023598, exon 10 of 10)	116345	NM_001081346	170799	Mm.209844	NM_133244	ENSMUSG00000037846	Rtkn2	B130039D23Rik|Mbf|Plekhk1	rhotekin 2	protein-coding
mm_36602.1	chr4	88917282	88917288	-	1	NA	intron (NR_132735, intron 2 of 2)	intron (NR_132735, intron 2 of 2)	-6623	NR_029747	723895		NR_029747	ENSMUSG00000065408	Mir31	Mirn31|miR-31|mmu-mir-31	microRNA 31	ncRNA
mm_148642.1	chr19	5480273	5480320	+	1	NA	exon (NM_021474, exon 9 of 11)	exon (NM_021474, exon 9 of 11)	5561	NM_001164352	58859	Mm.276367	NM_021474	ENSMUSG00000024909	Efemp2	0610011K11Rik|Fbln4|MBP1	epidermal growth factor-containing fibulin-like extracellular matrix protein 2	protein-coding
mm_86264.1	chr9	121704997	121705041	-	1	NA	promoter-TSS (NM_178677)	promoter-TSS (NM_178677)	10	NM_001164562	215474	Mm.31421	NM_178677	ENSMUSG00000061536	Sec22c	4932412K21|5930407I15Rik|C530046H07|Sec22l3	SEC22 homolog C, vesicle trafficking protein	protein-coding
mm_43624.1	chr5	138171338	138171402	+	1	NA	promoter-TSS (NM_021392)	promoter-TSS (NM_021392)	492	NM_008568	17220	Mm.378965	NM_008568	ENSMUSG00000029730	Mcm7	AI747533|Mcmd7|mCDC47	minichromosome maintenance complex component 7	protein-coding
mm_164286.1	chr15	103245587	103245593	+	1	NA	TTS (NM_010447)	TTS (NM_010447)	5136	NR_002883	434858	Mm.391346	NR_002883		Gm5643	EG434858	heterogeneous nuclear ribonucleoprotein A1 pseudogene	pseudo
mm_65938.1	chr7	30394309	30394310	-	1	NA	Intergenic	Intergenic	-19479	NM_011662	22177	Mm.46301	NM_011662	ENSMUSG00000030579	Tyrobp	DAP12|KARAP|Ly83	TYRO protein tyrosine kinase binding protein	protein-coding
mm_73293.1	chr8	104961788	104961798	+	1	NA	promoter-TSS (NM_197999)	promoter-TSS (NM_197999)	75	NM_197999	72361	Mm.26580	NM_197999	ENSMUSG00000031877	Ces2g	2210023G05Rik|Ces2l	carboxylesterase 2G	protein-coding
mm_29014.1	chr3	101836147	101836177	-	1	NA	promoter-TSS (NM_172295)	promoter-TSS (NM_172295)	61	NM_172295	242125	Mm.32900	NM_172295	ENSMUSG00000044313	Mab21l3	-	mab-21-like 3 (C. elegans)	protein-coding
mm_85168.1	chr9	96394977	96394995	-	1	NA	Intergenic	Intergenic	-30687	NM_007502	11933	Mm.424	NM_007502	ENSMUSG00000032412	Atp1b3	AA409958|AI664000|AW212096	ATPase, Na+/K+ transporting, beta 3 polypeptide	protein-coding
mm_166679.1	chr6	98382936	98382942	+	1	NA	Intergenic	Intergenic	-40185	NM_001128092	330390	Mm.484161	NM_001128092	ENSMUSG00000090667	Gm765	-	predicted gene 765	protein-coding
mm_150249.1	chr19	34101006	34101016	+	1	NA	promoter-TSS (NM_023903)	promoter-TSS (NM_023903)	68	NM_023903	78753	Mm.195937	NM_023903	ENSMUSG00000056078	Lipm	4632427C23Rik|AW227514|Lipl3	lipase, family member M	protein-coding
mm_172425.1	chr7	28259180	28259193	-	1	NA	Intergenic	Intergenic	-8695	NM_198425	386655	Mm.258201	NM_198425	ENSMUSG00000046058	Eid2	Cri2|EID-2	EP300 interacting inhibitor of differentiation 2	protein-coding
mm_61249.1	chr7	65804025	65804038	+	1	NA	promoter-TSS (NR_045301)	promoter-TSS (NR_045301)	-21	NR_045301	100503969	Mm.383527	NR_045301		1810008I18Rik	-	RIKEN cDNA 1810008I18 gene	ncRNA
mm_47186.1	chr5	120753993	120754026	-	1	NA	3' UTR (NM_145226, exon 16 of 16)	3' UTR (NM_145226, exon 16 of 16)	-4161	NM_001347448	246728	Mm.260926	NM_145227	ENSMUSG00000032690	Oas2	Oasl11	2'-5' oligoadenylate synthetase 2	protein-coding
mm_111502.1	chr12	99420509	99420512	-	1	NA	intron (NM_183186, intron 1 of 5)	intron (NM_183186, intron 1 of 5)	29564	NM_183186	71375	Mm.341972	NM_183186	ENSMUSG00000033713	Foxn3	5430426H20Rik|AA589593|AW556347|Ches1|Ches1l|HTLFL1	forkhead box N3	protein-coding
mm_159335.1	chr3	41563746	41563746	+	1	NA	promoter-TSS (NM_001130185)	promoter-TSS (NM_001130185)	-5	NM_001130185	269424	Mm.286285	NM_172303	ENSMUSG00000025764	Jade1	AU041499|D530048A03Rik|Phf17|mKIAA1807	jade family PHD finger 1	protein-coding
mm_82701.1	chr9	22468230	22468246	-	1	NA	5' UTR (NM_018739, exon 1 of 6)	5' UTR (NM_018739, exon 1 of 6)	118	NM_018739	55934	Mm.38235	NM_018739	ENSMUSG00000032239	Rp9	PAP-1|Rp9h	retinitis pigmentosa 9 (human)	protein-coding
mm_111664.1	chr12	103336294	103336304	-	1	NA	intron (NM_023049, intron 3 of 9)	intron (NM_023049, intron 3 of 9)	19702	NM_023049	65256	Mm.27159	NM_023049	ENSMUSG00000021200	Asb2	1110008E15Rik	ankyrin repeat and SOCS box-containing 2	protein-coding
mm_105747.1	chr11	109452868	109452885	-	1	NA	non-coding (NR_040680, exon 2 of 2)	non-coding (NR_040680, exon 2 of 2)	12798	NR_040680	100503496	Mm.265874	NR_040680		LOC100503496	-	uncharacterized LOC100503496	ncRNA
mm_159134.1	chr2	76338443	76338443	-	1	NA	exon (NM_001081033, exon 1 of 20)	exon (NM_001081033, exon 1 of 20)	210	NM_001081033	241489	Mm.246613	NM_001081033	ENSMUSG00000075270	Pde11a	6330414F14Rik|A630086N24Rik|Gm350|PDE11A1	phosphodiesterase 11A	protein-coding
mm_81661.1	chr9	111009122	111009129	+	1	NA	Intergenic	Intergenic	-10167	NM_008522	17002	Mm.282359	NM_008522	ENSMUSG00000032496	Ltf	Csp82|Lf|MMS10R|Ms10r	lactotransferrin	protein-coding
mm_114757.1	chr13	85189404	85189425	+	1	NA	promoter-TSS (NM_001347588)	promoter-TSS (NM_001347588)	29	NM_023243	66671	Mm.18474	NM_023243	ENSMUSG00000021548	Ccnh	6330408H09Rik|AI661354|AV102684|AW538719	cyclin H	protein-coding
mm_4295.1	chr1	171775365	171775372	+	1	NA	intron (NM_013730, intron 2 of 6)	intron (NM_013730, intron 2 of 6)	8236	NM_013730	27218	Mm.103648	NM_013730	ENSMUSG00000015316	Slamf1	4933415F16|AA177906|CD150|CDw150|ESTM51|IPO-3|Slam	signaling lymphocytic activation molecule family member 1	protein-coding
mm_125857.1	chr15	75070804	75070814	+	1	NA	Intergenic	Intergenic	-21972	NM_001252056	17067	Mm.1583	NM_010741	ENSMUSG00000079018	Ly6c1	AA682074|AA959465|Ly-6C|Ly-6C1|Ly6c	lymphocyte antigen 6 complex, locus C1	protein-coding
mm_17869.1	chr2	34940038	34940072	-	1	NA	Intergenic	Intergenic	21717	NM_009421	22029	Mm.239514	NM_009421	ENSMUSG00000026875	Traf1	4732496E14Rik	TNF receptor-associated factor 1	protein-coding
mm_30654.1	chr4	8913008	8913018	+	1	NA	Intergenic	Intergenic	222607	NM_001277149	320790	Mm.138792	NM_001033395	ENSMUSG00000041235	Chd7	A730019I05Rik|Cycn|Cyn|Dz|Edy|Flo|GENA 47|GENA 60|Gena 52|Lda|Mt|Obt|Todo|WBE1|Whi|metis	chromodomain helicase DNA binding protein 7	protein-coding
mm_21725.1	chr2	164674073	164674080	-	1	NA	promoter-TSS (NM_001161806)	promoter-TSS (NM_001161806)	11	NM_001161806	629761	Mm.389336	NM_001161806	ENSMUSG00000078940	Wfdc11	-	WAP four-disulfide core domain 11	protein-coding
mm_146880.1	chr18	25679511	25679534	-	1	NA	intron (NM_001146292, intron 1 of 12)	intron (NM_001146292, intron 1 of 12)	74461	NM_133195	108013	Mm.266435	NM_133195	ENSMUSG00000024268	Celf4	A230070D14Rik|BRUNOL-4|Brul4|Brunol4|C130060B05Rik	CUGBP, Elav-like family member 4	protein-coding
mm_122490.1	chr14	46516436	46516470	-	1	NA	Intergenic	MER5A|DNA|hAT-Charlie	59398	NR_046459	100873094	Mm.318596	NR_046459		Rubie	-	RNA upstream of Bmp4 expressed in inner ear	ncRNA
mm_64541.1	chr7	144264079	144264091	+	1	NA	intron (NM_001113373, intron 5 of 15)	MIRc|SINE|MIR	-20300	NM_001081370	210274	Mm.483624	NM_001081370	ENSMUSG00000037541	Shank2	ProSAP1|mKIAA1022	SH3/ankyrin domain gene 2	protein-coding
mm_144982.1	chr18	38190794	38190804	+	1	NA	Intergenic	Intergenic	18963	NM_029357	75599	Mm.36560	NM_029357	ENSMUSG00000051375	Pcdh1	2010005A06Rik|AI585920	protocadherin 1	protein-coding
mm_38841.1	chr4	149166655	149166677	-	1	NA	promoter-TSS (NM_001081274)	promoter-TSS (NM_001081274)	41	NM_001081274	110208	Mm.252080	NM_025801	ENSMUSG00000028961	Pgd	0610042A05Rik|AU019875|C78335	phosphogluconate dehydrogenase	protein-coding
mm_85217.1	chr9	96966588	96966613	-	1	NA	intron (NM_145134, intron 2 of 2)	intron (NM_145134, intron 2 of 2)	51755	NM_145134	211949	Mm.491271	NM_145134	ENSMUSG00000046997	Spsb4	D030068E18Rik|SSB-4|Ssb4	splA/ryanodine receptor domain and SOCS box containing 4	protein-coding
mm_5475.1	chr1	36643978	36644008	-	1	NA	intron (NM_001126046, intron 4 of 14)	MTD|LTR|ERVL-MaLR	39190	NM_001126046	381337	Mm.17413	NM_027957	ENSMUSG00000046337	Fam178b	1700024G10Rik|Gm990	family with sequence similarity 178, member B	protein-coding
mm_7454.1	chr1	120270254	120270293	-	1	NA	intron (NM_001085409, intron 1 of 5)	intron (NM_001085409, intron 1 of 5)	809	NM_001085409	68428	Mm.181033	NM_133186	ENSMUSG00000026389	Steap3	1010001D01Rik|Tsap6|pHyde	STEAP family member 3	protein-coding
mm_154144.1	chr19	58412165	58412167	-	1	NA	intron (NR_104342, intron 4 of 11)	intron (NR_104342, intron 4 of 11)	43232	NM_001285457	14585	Mm.88367	NM_010279	ENSMUSG00000025089	Gfra1	AU042498	glial cell line derived neurotrophic factor family receptor alpha 1	protein-coding
mm_169355.1	chr14	25571418	25571426	+	1	NA	intron (NM_001310666, intron 3 of 23)	ORR1A1|LTR|ERVL-MaLR	-15382	NR_033492	77592	Mm.444871	NM_175264		4931406H21Rik	-	RIKEN cDNA 4931406H21 gene	ncRNA
mm_76319.1	chr8	84687605	84687619	-	1	NA	intron (NM_025788, intron 1 of 5)	CpG	250	NM_025788	66830	Mm.289698	NM_025788	ENSMUSG00000001910	Nacc1	2010001H03Rik|4930511N13Rik|Btbd14b|Nac1	nucleus accumbens associated 1, BEN and BTB (POZ) domain containing	protein-coding
mm_131862.1	chr16	23107755	23107761	+	1	NA	non-coding (NR_110335, exon 1 of 12)	non-coding (NR_110335, exon 1 of 12)	290	NR_110335	13682	Mm.260084	NM_013506	ENSMUSG00000022884	Eif4a2	4833432N07Rik|BM-010|Ddx2b|Eif4|eIF-4A-II|eIF4A-II	eukaryotic translation initiation factor 4A2	protein-coding
mm_85637.1	chr9	107655052	107655070	-	1	NA	exon (NM_001199218, exon 14 of 16)	exon (NM_001199218, exon 14 of 16)	12338	NM_023805	76257	Mm.296560	NM_023805	ENSMUSG00000010064	Slc38a3	0610012J02Rik|D9Ucla2|Nat1|Slc38-3|Sn1|Snat3|mNAT	solute carrier family 38, member 3	protein-coding
mm_23837.1	chr3	82358134	82358165	+	1	NA	promoter-TSS (NM_001081230)	promoter-TSS (NM_001081230)	77	NM_001081230	213582	Mm.271269	NM_001081230	ENSMUSG00000033900	Map9	5033421J10Rik|5330427D05Rik|ASAP|Mtap9	microtubule-associated protein 9	protein-coding
mm_166337.1	chr5	114707917	114707928	+	1	NA	5' UTR (NM_029992, exon 1 of 13)	5' UTR (NM_029992, exon 1 of 13)	143	NM_029992	77832	Mm.239698	NM_029992	ENSMUSG00000002486	Tchp	A930031F18Rik|AV279199	trichoplein, keratin filament binding	protein-coding
mm_104176.1	chr11	87748845	87748860	-	1	NA	Intergenic	Intergenic	-8012	NR_029555	387160		NR_029555	ENSMUSG00000105196	Mir142	Mirn142|miR-142|mir-142a|mmu-mir-142|mmu-mir-142a	microRNA 142	ncRNA
mm_59658.1	chr7	28180273	28180289	+	1	NA	promoter-TSS (NM_001271370)	promoter-TSS (NM_001271370)	-35	NM_001271370	13549	Mm.57249	NM_010092	ENSMUSG00000002409	Dyrk1b	Mirk	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1b	protein-coding
mm_60536.1	chr7	44480390	44480400	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-4122	NR_131001	71368	Mm.66246	NR_131001	ENSMUSG00000108322	5430431A17Rik	-	RIKEN cDNA 5430431A17 gene	ncRNA
mm_64337.1	chr7	142376582	142376614	+	1	NA	exon (NM_009983, exon 9 of 9)	exon (NM_009983, exon 9 of 9)	-2852	NM_001347541	320802	Mm.154486	NM_177265	ENSMUSG00000045777	Ifitm10	6330512M04Rik|AI848576|DSPA3	interferon induced transmembrane protein 10	protein-coding
mm_120982.1	chr14	78849156	78849166	+	1	NA	promoter-TSS (NM_027906)	promoter-TSS (NM_027906)	-17	NM_027906	219189	Mm.159651	NM_027906	ENSMUSG00000058997	Vwa8	1300010F03Rik|4932416F07Rik|AI957255|Kiaa0564|mKIAA0564	von Willebrand factor A domain containing 8	protein-coding
mm_131108.1	chr16	5050200	5050210	+	1	NA	promoter-TSS (NM_028720)	promoter-TSS (NM_028720)	137	NM_026666	170644	Mm.66356	NM_026666	ENSMUSG00000039473	Ubn1	1110029L11Rik|2610108L02Rik|AA673476|AW124741	ubinuclein 1	protein-coding
mm_103912.1	chr11	83588276	83588293	-	1	NA	3' UTR (NM_009139, exon 4 of 4)	3' UTR (NM_009139, exon 4 of 4)	4803	NM_009139	20305	Mm.137	NM_009139	ENSMUSG00000018927	Ccl6	MRP-1|Scya6|c10	chemokine (C-C motif) ligand 6	protein-coding
mm_75914.1	chr8	71463557	71463572	-	1	NA	promoter-TSS (NM_022419)	promoter-TSS (NM_022419)	93	NM_022419	64296	Mm.276383	NM_022419	ENSMUSG00000007950	Abhd8	0910001L24Rik|AB030191	abhydrolase domain containing 8	protein-coding
mm_48146.1	chr5	137150783	137150817	-	1	NA	Intergenic	Intergenic	-34593	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_140738.1	chr17	15807081	15807094	-	1	NA	3' UTR (NM_178615, exon 3 of 3)	3' UTR (NM_178615, exon 3 of 3)	19499	NM_178615	68799	Mm.293466	NM_178615	ENSMUSG00000048027	Rgmb	1110059F19Rik|DRAGON	repulsive guidance molecule family member B	protein-coding
mm_66206.1	chr7	34292088	34292091	-	1	NA	Intergenic	PB1D9|SINE|Alu	-6480	NM_172741	233103	Mm.491097	NM_172741	ENSMUSG00000066571	4931406P16Rik	AA553327|mKIAA0355	RIKEN cDNA 4931406P16 gene	protein-coding
mm_58426.1	chr7	3296958	3296990	+	1	NA	exon (NM_016969, exon 3 of 3)	exon (NM_016969, exon 3 of 3)	3946	NM_001093766	50918	Mm.29874	NM_016969	ENSMUSG00000068566	Myadm	D7Wsu62e	myeloid-associated differentiation marker	protein-coding
mm_145828.1	chr18	65438565	65438586	+	1	NA	intron (NM_172833, intron 2 of 15)	intron (NM_172833, intron 2 of 15)	7578	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_35230.1	chr4	19708540	19708542	-	1	NA	intron (NR_074089, intron 1 of 23)	intron (NR_074089, intron 1 of 23)	463	NM_177327	107568	Mm.78312	NM_177327	ENSMUSG00000041058	Wwp1	8030445B08Rik|AIP5|SDRP1|Tiul1	WW domain containing E3 ubiquitin protein ligase 1	protein-coding
mm_9145.1	chr1	170885453	170885467	-	1	NA	promoter-TSS (NM_023173)	promoter-TSS (NM_023173)	80	NM_023173	80915	Mm.34365	NM_023173	ENSMUSG00000026659	Dusp12	1190004O14Rik|AA027408|AW049275|ENSMUSG00000045460|ESTM36|LMW-DSP4|T-DSP4|VH1|mVH1	dual specificity phosphatase 12	protein-coding
mm_62750.1	chr7	111156225	111156233	+	1	NA	Intergenic	Intergenic	-33554	NR_015573	75479	Mm.381620	NR_015573	ENSMUSG00000110424	1700012D14Rik	-	RIKEN cDNA 1700012D14 gene	ncRNA
mm_87261.1	chr10	41519949	41519961	+	1	NA	intron (NM_016898, intron 1 of 5)	CpG	455	NM_016898	53599	Mm.269815	NM_016898	ENSMUSG00000019818	Cd164	A115|A24|AA589639|AW540279|MGC-24|MSSP	CD164 antigen	protein-coding
mm_100572.1	chr11	120763085	120763106	+	1	NA	Intergenic	Intergenic	21109	NM_009053	19719	Mm.871	NM_009053	ENSMUSG00000025158	Rfng	-	RFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	protein-coding
mm_33264.1	chr4	127214746	127214777	+	1	NA	exon (NM_198618, exon 7 of 12)	exon (NM_198618, exon 7 of 12)	-29023	NM_030252	80284	Mm.139607	NM_030252	ENSMUSG00000042380	Smim12	BC003266	small integral membrane protein 12	protein-coding
mm_63086.1	chr7	122291316	122291323	+	1	NA	intron (NM_001316672, intron 2 of 16)	intron (NM_001316672, intron 2 of 16)	2194	NM_008855	18751	Mm.207496	NM_008855	ENSMUSG00000052889	Prkcb	PKC-B|PKC-Beta|Pkcb|Prkcb1|Prkcb2	protein kinase C, beta	protein-coding
mm_64054.1	chr7	140847755	140847760	+	1	NA	promoter-TSS (NM_027019)	promoter-TSS (NM_027019)	-159	NM_027019	69287	Mm.56404	NM_027019	ENSMUSG00000025482	Odf3	1700011O04Rik|SHIPPO1	outer dense fiber of sperm tails 3	protein-coding
mm_25376.1	chr3	107211422	107211434	+	1	NA	exon (NM_001111143, exon 9 of 9)	exon (NM_001111143, exon 9 of 9)	10304	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_171141.1	chr3	151624313	151624313	+	1	NA	Intergenic	L1Md_A|LINE|L1	125646	NM_133871	99899	Mm.30756	NM_133871	ENSMUSG00000028037	Ifi44	A430056A10Rik|AW261460|MTAP44|p44	interferon-induced protein 44	protein-coding
mm_155724.1	chrX	96152889	96152892	+	1	NA	intron (NM_010833, intron 4 of 12)	intron (NM_010833, intron 4 of 12)	56845	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_80759.1	chr9	95559080	95559096	+	1	NA	promoter-TSS (NM_198414)	promoter-TSS (NM_198414)	-729	NM_198414	75552	Mm.151485	NM_198414	ENSMUSG00000064225	Paqr9	1700020G04Rik	progestin and adipoQ receptor family member IX	protein-coding
mm_159384.1	chr3	90613121	90613121	+	1	NA	5' UTR (NM_011313, exon 1 of 3)	5' UTR (NM_011313, exon 1 of 3)	227	NM_011313	20200	Mm.100144	NM_011313	ENSMUSG00000001025	S100a6	2A9|5B10|CALCYCLIN|Cacy|PRA	S100 calcium binding protein A6 (calcyclin)	protein-coding
mm_29113.1	chr3	104865089	104865117	-	1	NA	promoter-TSS (NM_009797)	promoter-TSS (NM_009797)	597	NM_153091	229681	Mm.206379	NM_153091	ENSMUSG00000045576	St7l	St7r	suppression of tumorigenicity 7-like	protein-coding
mm_155985.1	chrX	106135245	106135254	+	1	NA	Intergenic	MLT2F|LTR|ERVL	-8026	NM_205820	279572	Mm.336203	NM_205820	ENSMUSG00000033777	Tlr13	AI666735|Gm713	toll-like receptor 13	protein-coding
mm_173030.1	chrX	105856529	105856535	-	1	NA	exon (NM_009530, exon 11 of 35)	exon (NM_009530, exon 11 of 35)	72840	NM_009530	22589	Mm.10141	NM_009530	ENSMUSG00000031229	Atrx	4833408C14Rik|AI447451|ATR2|DXHXS6677E|HP1-BP38|Hp1bp2|Hp1bp38|MRXS3|RAD54L|Rad54|XH2|Xnp|ZNF-HX	alpha thalassemia/mental retardation syndrome X-linked	protein-coding
mm_66427.1	chr7	44625833	44625838	-	1	NA	intron (NM_001271538, intron 26 of 40)	ORR1E|LTR|ERVL-MaLR	34949	NM_001290682	16504	Mm.40312	NM_008422	ENSMUSG00000062785	Kcnc3	KShIIID|Kcr2-3|Kv3.3	potassium voltage gated channel, Shaw-related subfamily, member 3	protein-coding
mm_85775.1	chr9	109052690	109052714	-	1	NA	intron (NM_025858, intron 3 of 5)	intron (NM_025858, intron 3 of 5)	-2164	NM_026381	66940	Mm.196533	NM_025858	ENSMUSG00000025647	Shisa5	2310008D10Rik|6430628I05Rik|Scotin|mShisa5	shisa family member 5	protein-coding
mm_81085.1	chr9	106281013	106281042	+	1	NA	promoter-TSS (NM_027354)	promoter-TSS (NM_027354)	-34	NM_027354	70235	Mm.23054	NM_027354	ENSMUSG00000023345	Poc1a	2510040D07Rik|Wdr51a|cha	POC1 centriolar protein A	protein-coding
mm_157101.1	chrX	9437626	9437635	-	1	NA	3' UTR (NM_007807, exon 13 of 13)	3' UTR (NM_007807, exon 13 of 13)	31694	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_74715.1	chr8	17343625	17343627	-	1	NA	intron (NM_053171, intron 1 of 69)	intron (NM_053171, intron 1 of 69)	191759	NM_053171	94109	Mm.436988	NM_053171	ENSMUSG00000060924	Csmd1	B930082H09|mKIAA1890	CUB and Sushi multiple domains 1	protein-coding
mm_128535.1	chr15	54890766	54890769	-	1	NA	intron (NM_001136077, intron 8 of 25)	intron (NM_001136077, intron 8 of 25)	29379	NM_015744	18606	Mm.250256	NM_015744	ENSMUSG00000022425	Enpp2	ATX|E-NPP 2|Npps2|PD-Ialpha|Pdnp2|lysoPLD	ectonucleotide pyrophosphatase/phosphodiesterase 2	protein-coding
mm_84526.1	chr9	67044951	67044954	-	1	NA	intron (NM_001164249, intron 2 of 8)	intron (NM_001164249, intron 2 of 8)	-1081	NM_001164253	22003	Mm.121878	NM_024427	ENSMUSG00000032366	Tpm1	AA986836|AI854628|TM2|Tm3|Tmpa|Tpm-1|alpha-TM	tropomyosin 1, alpha	protein-coding
mm_173209.1	chrX	72579062	72579062	-	1	NA	intron (NM_008067, intron 1 of 9)	L1Md_T|LINE|L1	11032	NR_035528	100316827		NR_035528	ENSMUSG00000076455	Mir767	mmu-mir-767	microRNA 767	ncRNA
mm_77107.1	chr8	111081671	111081679	-	1	NA	promoter-TSS (NM_181549)	promoter-TSS (NM_181549)	33	NM_181549	353287	Mm.135495	NM_181549	ENSMUSG00000033633	Clec18a	Mrcl	C-type lectin domain family 18, member A	protein-coding
mm_150400.1	chr19	36554720	36554731	+	1	NA	promoter-TSS (NM_001163471)	promoter-TSS (NM_001163471)	86	NM_172637	226098	Mm.61107	NM_172637	ENSMUSG00000041180	Hectd2	4921524L07|A630025O09Rik|AW212605	HECT domain containing 2	protein-coding
mm_172625.1	chr8	20297437	20297460	-	1	NA	promoter-TSS (NR_030708)	promoter-TSS (NR_030708)	-16	NR_030708	547150	Mm.359054	NR_030708	ENSMUSG00000071796	6820431F20Rik	-	cadherin 11 pseudogene	pseudo
mm_140729.1	chr17	15527268	15527278	-	1	NA	promoter-TSS (NM_008799)	promoter-TSS (NM_008799)	28	NM_008799	18567	Mm.323	NM_008799	ENSMUSG00000014771	Pdcd2	AI528543|Pcd2|RP-8	programmed cell death 2	protein-coding
mm_120444.1	chr14	65968512	65968524	+	1	NA	promoter-TSS (NM_013492)	promoter-TSS (NM_013492)	35	NM_013492	12759	Mm.200608	NM_013492	ENSMUSG00000022037	Clu	AI893575|ApoJ|Cli|D14Ucla3|SP-40|Sgp-2|Sgp2|Sugp-2	clusterin	protein-coding
mm_31614.1	chr4	59033206	59033217	+	1	NA	Intergenic	Intergenic	-1945	NM_025277	14700	Mm.41780	NM_025277	ENSMUSG00000038607	Gng10	AV006524	guanine nucleotide binding protein (G protein), gamma 10	protein-coding
mm_163349.1	chr12	17786310	17786345	+	1	NA	exon (NM_016677, exon 2 of 4)	exon (NM_016677, exon 2 of 4)	95513	NM_016677	53602	Mm.313619	NM_016677	ENSMUSG00000071379	Hpcal1	NVP-3|Nvp3|VILIP3|Vnsl3|Vsnl3	hippocalcin-like 1	protein-coding
mm_6628.1	chr1	78196833	78196845	-	1	NA	5' UTR (NM_008781, exon 1 of 8)	5' UTR (NM_008781, exon 1 of 8)	297	NM_008781	18505	Mm.1371	NM_008781	ENSMUSG00000004872	Pax3	Pax-3|Sp|Splchl2|splotch	paired box 3	protein-coding
mm_35307.1	chr4	25242257	25242271	-	1	NA	intron (NM_021318, intron 1 of 5)	intron (NM_021318, intron 1 of 5)	612	NM_021318	57756	Mm.87325	NM_021318	ENSMUSG00000028259	Fhl5	1700027G07Rik|Act	four and a half LIM domains 5	protein-coding
mm_83690.1	chr9	50561283	50561301	-	1	NA	promoter-TSS (NM_025687)	promoter-TSS (NM_025687)	-24	NM_025687	66654	Mm.442255	NM_025687	ENSMUSG00000032065	Tex12	5730518K06Rik	testis expressed gene 12	protein-coding
mm_71735.1	chr8	62014425	62014436	+	1	NA	intron (NM_001293783, intron 30 of 37)	intron (NM_001293783, intron 30 of 37)	86343	NM_001293783	234311	Mm.275233	NM_144928	ENSMUSG00000037921	Ddx60	9830118M07	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	protein-coding
mm_156222.1	chrX	135263308	135263316	+	1	NA	Intergenic	Intergenic	-39004	NM_031390	83565	Mm.108239	NM_031390	ENSMUSG00000067360	Pramel3	-	preferentially expressed antigen in melanoma-like 3	protein-coding
mm_63902.1	chr7	139212975	139212993	+	1	NA	promoter-TSS (NM_027164)	promoter-TSS (NM_027164)	-4	NM_027164	76612	Mm.17757	NM_027164	ENSMUSG00000015980	Lrrc27	1700071K18Rik|2310044E02Rik	leucine rich repeat containing 27	protein-coding
mm_83323.1	chr9	44196117	44196120	-	1	NA	intron (NM_007619, intron 2 of 15)	ID_B1|SINE|B4	37928	NM_007619	12402	Mm.266871	NM_007619	ENSMUSG00000034342	Cbl	4732447J05Rik|Cbl-2|c-Cbl|cbl	Casitas B-lineage lymphoma	protein-coding
mm_148884.1	chr19	6645147	6645151	+	1	NA	Intergenic	RLTR31C_MM|LTR|ERVK	-102079	NM_009203	20521	Mm.391146	NM_009203	ENSMUSG00000061742	Slc22a12	AI987855|OAT4L|Rst|Slc22al2|URAT1	solute carrier family 22 (organic anion/cation transporter), member 12	protein-coding
mm_162371.1	chr1	67206831	67206834	+	1	NA	intron (NM_001080809, intron 28 of 37)	intron (NM_001080809, intron 28 of 37)	83805	NM_001080809	227231	Mm.343942	NM_001080809	ENSMUSG00000025991	Cps1	4732433M03Rik|CPS|D1Ucla3	carbamoyl-phosphate synthetase 1	protein-coding
mm_141442.1	chr17	29716970	29717028	-	1	NA	promoter-TSS (NM_026782)	promoter-TSS (NM_026782)	18	NM_026782	68597	Mm.390979	NM_026782	ENSMUSG00000024018	Ccdc167	1110021J02Rik	coiled-coil domain containing 167	protein-coding
mm_121518.1	chr14	122058339	122058366	+	1	NA	Intergenic	Intergenic	23678	NM_001037744	223262	Mm.297637	NM_001037744	ENSMUSG00000071229	Timm8a2	-	translocase of inner mitochondrial membrane 8A2	protein-coding
mm_161324.1	chr14	48665048	48665048	-	1	NA	promoter-TSS (NM_001286483)	promoter-TSS (NM_001286483)	61	NM_001286483	18424	Mm.134516	NM_144841	ENSMUSG00000021848	Otx2	E130306E05Rik	orthodenticle homeobox 2	protein-coding
mm_165648.1	chr3	83008507	83008514	+	1	NA	exon (NM_133862, exon 3 of 10)	exon (NM_133862, exon 3 of 10)	786	NM_001317105	99571	Mm.16422	NM_133862	ENSMUSG00000033860	Fgg	3010002H13Rik|AI256424	fibrinogen gamma chain	protein-coding
mm_40071.1	chr5	34288684	34288694	+	1	NA	promoter-TSS (NM_001015039)	promoter-TSS (NM_001015039)	-365	NM_001015039	231125	Mm.113388	NM_001015039	ENSMUSG00000037224	Zfyve28	9630058O20Rik|Gm146|mKIAA1643	zinc finger, FYVE domain containing 28	protein-coding
mm_54860.1	chr6	42597377	42597384	-	1	NA	promoter-TSS (NM_203396)	promoter-TSS (NM_203396)	-8	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_9943.1	chr1	190617473	190617473	-	1	NA	Intergenic	RMER19B|LTR|ERVK	294297	NM_178775	320119	Mm.220912	NM_178775	ENSMUSG00000089872	Rps6kc1	AA682037|B130003F20Rik|C80612|Rpk118	ribosomal protein S6 kinase polypeptide 1	protein-coding
mm_6698.1	chr1	80758517	80758532	-	1	NA	promoter-TSS (NM_175291)	promoter-TSS (NM_175291)	29	NM_175291	210293	Mm.133473	NM_175291	ENSMUSG00000038608	Dock10	9330153B10Rik|A630054M16Rik|Jr4|Jr5|R75174|ZIZ3|Zizimin3|mKIAA0694	dedicator of cytokinesis 10	protein-coding
mm_164020.1	chr14	75174944	75174952	+	1	NA	intron (NM_008879, intron 1 of 16)	intron (NM_008879, intron 1 of 16)	38523	NM_008879	18826	Mm.153911	NM_008879	ENSMUSG00000021998	Lcp1	AW536232|D14Ertd310e|LCP-1|Pls2|pp65	lymphocyte cytosolic protein 1	protein-coding
mm_58646.1	chr7	6258583	6258609	+	1	NA	intron (NM_001177417, intron 2 of 10)	intron (NM_001177417, intron 2 of 10)	2674	NM_001177417	627821	Mm.99441	NM_001177416	ENSMUSG00000053367	Gm6792	EG627821	predicted gene 6792	protein-coding
mm_148289.1	chr18	82584218	82584230	-	1	NA	3' UTR (NM_010777, exon 7 of 7)	3' UTR (NM_010777, exon 7 of 7)	29716	NM_001025254	17196	Mm.252063	NM_010777	ENSMUSG00000041607	Mbp	C76307|Hmbpr|R75289|golli-mbp|jve|mld|shi	myelin basic protein	protein-coding
mm_80501.1	chr9	78615453	78615474	+	1	NA	promoter-TSS (NM_153098)	promoter-TSS (NM_153098)	-83	NM_153098	235505	Mm.32955	NM_153098	ENSMUSG00000046186	Cd109	9930012E15Rik|AI480638|GARP	CD109 antigen	protein-coding
mm_75321.1	chr8	41417043	41417135	-	1	NA	promoter-TSS (NM_013522)	promoter-TSS (NM_013522)	29	NM_013522	14300	Mm.217312	NM_013522	ENSMUSG00000031590	Frg1	-	FSHD region gene 1	protein-coding
mm_8267.1	chr1	139377048	139377078	-	1	NA	promoter-TSS (NM_133239)	promoter-TSS (NM_133239)	13	NM_133239	170788	Mm.95700	NM_133239	ENSMUSG00000063681	Crb1	7530426H14Rik|A930008G09Rik	crumbs family member 1, photoreceptor morphogenesis associated	protein-coding
mm_84511.1	chr9	67032529	67032550	-	1	NA	exon (NM_001164251, exon 6 of 10)	exon (NM_001164251, exon 6 of 10)	11332	NM_001164252	22003	Mm.121878	NM_024427	ENSMUSG00000032366	Tpm1	AA986836|AI854628|TM2|Tm3|Tmpa|Tpm-1|alpha-TM	tropomyosin 1, alpha	protein-coding
mm_70524.1	chr8	12951232	12951246	+	1	NA	intron (NM_001159486, intron 1 of 29)	intron (NM_001159486, intron 1 of 29)	1821	NM_001159485	17207	Mm.334413	NM_178076	ENSMUSG00000031442	Mcf2l	C130040G20Rik|Dbs|Ost|mKIAA0362	mcf.2 transforming sequence-like	protein-coding
mm_23643.1	chr3	67374117	67374154	+	1	NA	promoter-TSS (NM_010801)	promoter-TSS (NM_010801)	38	NM_001039543	17349	Mm.10414	NM_010801	ENSMUSG00000048416	Mlf1	HLS7	myeloid leukemia factor 1	protein-coding
mm_68066.1	chr7	101867392	101867420	-	1	NA	intron (NM_001252552, intron 3 of 6)	B1_Mur3|SINE|Alu	3382	NM_001252554	14275	Mm.2135	NM_008034	ENSMUSG00000001827	Folr1	FBP1|Folbp-1|Folbp1	folate receptor 1 (adult)	protein-coding
mm_84030.1	chr9	57764843	57764856	-	1	NA	intron (NM_007713, intron 1 of 12)	CpG	1011	NM_007713	102414	Mm.25720	NM_007713	ENSMUSG00000032316	Clk3	AI256811	CDC-like kinase 3	protein-coding
mm_104558.1	chr11	96824174	96824198	-	1	NA	promoter-TSS (NM_001130451)	promoter-TSS (NM_001130451)	-59	NM_001130451	18023	Mm.6743	NM_008686	ENSMUSG00000038615	Nfe2l1	AA408798|AW212678|LCR-F1|Lcrf1|NRF1|TCF-11|TCF11	nuclear factor, erythroid derived 2,-like 1	protein-coding
mm_55549.1	chr6	71201707	71201714	-	1	NA	exon (NM_017399, exon 2 of 4)	exon (NM_017399, exon 2 of 4)	1822	NM_017399	14080	Mm.22126	NM_017399	ENSMUSG00000054422	Fabp1	Fabpl|L-FABP	fatty acid binding protein 1, liver	protein-coding
mm_161848.1	chr18	11657819	11657819	+	1	NA	intron (NR_045526, intron 1 of 17)	CpG	470	NM_001081223	225182	Mm.154275	NM_175458	ENSMUSG00000041238	Rbbp8	9930104E21Rik|CtIP|RBBP-8|RIM|SAE2	retinoblastoma binding protein 8	protein-coding
mm_36395.1	chr4	77775329	77775333	-	1	NA	intron (NM_011211, intron 2 of 39)	intron (NM_011211, intron 2 of 39)	436564	NM_011211	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding
mm_117672.1	chr13	93637632	93637649	-	1	NA	5' UTR (NM_016668, exon 1 of 8)	5' UTR (NM_016668, exon 1 of 8)	118	NM_016668	12116	Mm.329582	NM_016668	ENSMUSG00000074768	Bhmt	-	betaine-homocysteine methyltransferase	protein-coding
mm_98985.1	chr11	98742128	98742147	+	1	NA	intron (NM_178060, intron 1 of 8)	CpG	352	NM_001313983	21833	Mm.265917	NM_178060	ENSMUSG00000058756	Thra	6430529J03Rik|AW259572|Erba|Nr1a1|Rvr|T3R[a]|T3Ralpha|Thra1|Thra2|c-erbA-1|c-erbA-alpha|c-erbAalpha	thyroid hormone receptor alpha	protein-coding
mm_100325.1	chr11	118146074	118146091	+	1	NA	Intergenic	Intergenic	-16863	NM_001167746	69926	Mm.473893	NM_001167746	ENSMUSG00000033987	Dnah17	2810003K23Rik|Dnahc17|Dnahcl1|Gm1178|mKIAA3028	dynein, axonemal, heavy chain 17	protein-coding
mm_106901.1	chr12	8013043	8013049	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	35369	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_103129.1	chr11	70229756	70229761	-	1	NA	promoter-TSS (NM_007528)	promoter-TSS (NM_007528)	40	NM_007528	12029	Mm.12930	NM_007528	ENSMUSG00000000317	Bcl6b	Bazf	B cell CLL/lymphoma 6, member B	protein-coding
mm_140320.1	chr17	86428799	86428829	+	1	NA	intron (NM_011104, intron 2 of 14)	intron (NM_011104, intron 2 of 14)	-141636	NR_045435	72104	Mm.443401	NR_045435	ENSMUSG00000100738	2010106C02Rik	-	RIKEN cDNA 2010106C02 gene	ncRNA
mm_72662.1	chr8	84872159	84872168	+	1	NA	promoter-TSS (NR_031759)	promoter-TSS (NR_031759)	52	NM_001168246	71846	Mm.229128	NM_027954	ENSMUSG00000003824	Syce2	1700013H19Rik|AA407907|Cesc1	synaptonemal complex central element protein 2	protein-coding
mm_155541.1	chrX	74305240	74305278	+	1	NA	TTS (NM_018794)	TTS (NM_018794)	247	NM_010273	14567	Mm.205830	NM_010273	ENSMUSG00000015291	Gdi1	GDIA|GDIalpha	guanosine diphosphate (GDP) dissociation inhibitor 1	protein-coding
mm_95823.1	chr11	55395802	55395864	+	1	NA	exon (NM_009242, exon 9 of 10)	exon (NM_009242, exon 9 of 10)	24247	NM_009242	20692	Mm.291442	NM_009242	ENSMUSG00000018593	Sparc	BM-40|ON	secreted acidic cysteine rich glycoprotein	protein-coding
mm_24102.1	chr3	88138892	88138904	+	1	NA	Intergenic	Intergenic	-3474	NM_001310587	17261	Mm.28184	NM_133665	ENSMUSG00000001419	Mef2d	C80750	myocyte enhancer factor 2D	protein-coding
mm_107970.1	chr12	72765256	72765257	+	1	NA	intron (NM_008910, intron 1 of 5)	B3|SINE|B2	4045	NM_008910	19042	Mm.261045	NM_008910	ENSMUSG00000021096	Ppm1a	2310003C21Rik|2900017D14Rik|AI427932|AU017636|MMPa-2|MPPa-1	protein phosphatase 1A, magnesium dependent, alpha isoform	protein-coding
mm_38885.1	chr4	149715775	149715778	-	1	NA	3' UTR (NM_001284270, exon 11 of 11)	3' UTR (NM_001284270, exon 11 of 11)	-14147	NM_001029837	18707	Mm.229108	NM_008840	ENSMUSG00000039936	Pik3cd	2410099E07Rik|2610208K16Rik|AW545373|p110delta	phosphatidylinositol 3-kinase catalytic delta polypeptide	protein-coding
mm_119537.1	chr14	47786335	47786338	+	1	NA	Intergenic	Intergenic	-112528	NR_045959	73961	Mm.390702	NR_045959		4930447J18Rik	4930425M13Rik	RIKEN cDNA 4930447J18 gene	ncRNA
mm_27177.1	chr3	34081257	34081347	-	1	NA	promoter-TSS (NM_026332)	promoter-TSS (NM_026332)	52	NM_001286972	67713	Mm.274266	NM_026332	ENSMUSG00000027679	Dnajc19	1810055D05Rik|AA959924|Tim14	DnaJ heat shock protein family (Hsp40) member C19	protein-coding
mm_39077.1	chr4	154316316	154316318	-	1	NA	3' UTR (NM_027504, exon 17 of 17)	3' UTR (NM_027504, exon 17 of 17)	-16422	NM_001112744	230972	Mm.38481	NM_001112744	ENSMUSG00000029032	Arhgef16	-	Rho guanine nucleotide exchange factor (GEF) 16	protein-coding
mm_98556.1	chr11	95124988	95124992	+	1	NA	3' UTR (NM_010055, exon 3 of 3)	3' UTR (NM_010055, exon 3 of 3)	4873	NM_010055	13393	Mm.5194	NM_010055	ENSMUSG00000001510	Dlx3	AV237891|Dlx-3	distal-less homeobox 3	protein-coding
mm_142415.1	chr17	45567986	45568009	-	1	NA	TTS (NM_028662)	TTS (NM_028662)	3845	NM_028662	73836	Mm.289716	NM_028662	ENSMUSG00000037089	Slc35b2	1110003M08Rik|AA407792|AI842275|PAPST1|Slc35b1	solute carrier family 35, member B2	protein-coding
mm_146330.1	chr18	81117888	81117897	+	1	NA	Intergenic	Intergenic	-131314	NM_178280	20689	Mm.215917	NM_178280	ENSMUSG00000024565	Sall3	B130022O04Rik|Msal|Msal-1|Sal|Salt|Spalt	sal-like 3 (Drosophila)	protein-coding
mm_103580.1	chr11	78166772	78166807	-	1	NA	intron (NM_080849, intron 14 of 14)	intron (NM_080849, intron 14 of 14)	-1239	NM_009423	22032	Mm.390418	NM_009423	ENSMUSG00000017386	Traf4	A530032M13Rik|CART1|msp2	TNF receptor associated factor 4	protein-coding
mm_39189.1	chr4	155869829	155869832	-	1	NA	promoter-TSS (NM_024472)	promoter-TSS (NM_024472)	263	NM_028020	71957	Mm.475640	NM_028020	ENSMUSG00000029034	Cpsf3l	2410006F12Rik|AU044035	cleavage and polyadenylation specific factor 3-like	protein-coding
mm_76120.1	chr8	80859827	80859829	-	1	NA	intron (NM_021356, intron 1 of 9)	intron (NM_021356, intron 1 of 9)	20651	NM_021356	14388	Mm.277409	NM_021356	ENSMUSG00000031714	Gab1	AA408973|AW107238	growth factor receptor bound protein 2-associated protein 1	protein-coding
mm_88297.1	chr10	75316872	75316882	+	1	NA	promoter-TSS (NM_009630)	promoter-TSS (NM_009630)	0	NM_009630	11540	Mm.333734	NM_009630	ENSMUSG00000020178	Adora2a	A2AAR|A2aR|AA2AR	adenosine A2a receptor	protein-coding
mm_58233.1	chr6	145030394	145030398	-	1	NA	intron (NM_007532, intron 5 of 10)	PB1D9|SINE|Alu	18416	NM_001024468	12035	Mm.4606	NM_007532	ENSMUSG00000030268	Bcat1	BCATc|Eca39	branched chain aminotransferase 1, cytosolic	protein-coding
mm_125624.1	chr15	61988245	61988251	+	1	NA	exon (NM_001177354, exon 2 of 3)	exon (NM_001177354, exon 2 of 3)	2907	NM_001177352	17869	Mm.2444	NM_010849	ENSMUSG00000022346	Myc	AU016757|Myc2|Niard|Nird|bHLHe39	myelocytomatosis oncogene	protein-coding
mm_119476.1	chr14	47319442	47319454	+	1	NA	3' UTR (NM_178684, exon 4 of 4)	3' UTR (NM_178684, exon 4 of 4)	21134	NM_178684	218975	Mm.212297	NM_178684	ENSMUSG00000021840	Mapk1ip1l	9130202B12|C130032J12Rik	mitogen-activated protein kinase 1 interacting protein 1-like	protein-coding
mm_149757.1	chr19	22750671	22750672	+	1	NA	promoter-TSS (NR_029591)	promoter-TSS (NR_029591)	66	NR_029591	387200		NR_029591	ENSMUSG00000065507	Mir204	Mirn204|mir-204|mmu-mir-204	microRNA 204	ncRNA
mm_911.1	chr1	54681761	54681770	+	1	NA	intron (NM_001081433, intron 16 of 27)	intron (NM_001081433, intron 16 of 27)	-124081	NM_001163314	241062	Mm.103539	NM_175508	ENSMUSG00000073678	Pgap1	5033403E17Rik|9030223K07Rik|A530084K22|D230012E17Rik|oto	post-GPI attachment to proteins 1	protein-coding
mm_42267.1	chr5	114143434	114143441	+	1	NA	Intergenic	Intergenic	12281	NM_011677	22256	Mm.1393	NM_011677	ENSMUSG00000029591	Ung	UNG1|UNG2	uracil DNA glycosylase	protein-coding
mm_102805.1	chr11	68871849	68871857	-	1	NA	Intergenic	Intergenic	-16700	NM_177060	320040	Mm.305696	NM_177060	ENSMUSG00000046490	Rnf222	9930039A11Rik	ring finger protein 222	protein-coding
mm_115308.1	chr13	112288791	112288806	+	1	NA	5' UTR (NM_029898, exon 1 of 11)	5' UTR (NM_029898, exon 1 of 11)	280	NM_001168404	77318	Mm.159895	NM_029898	ENSMUSG00000049985	Ankrd55	C030011J08Rik	ankyrin repeat domain 55	protein-coding
mm_114308.1	chr13	59726699	59726729	+	1	NA	exon (NM_177711, exon 4 of 4)	exon (NM_177711, exon 4 of 4)	5038	NM_177711	238663	Mm.444776	NM_177711	ENSMUSG00000043986	Spata31d1d	4932411G14Rik|Fam75d1d	spermatogenesis associated 31 subfamily D, member 1D	protein-coding
mm_117484.1	chr13	77438931	77438935	-	1	NA	intron (NM_001145676, intron 19 of 19)	GSAT_MM|Satellite|Satellite	-269757	NM_001163420	68675	Mm.343005	NM_138312	ENSMUSG00000064138	Fam172a	1110033M05Rik|2610318O14Rik|53-E6|9430037D06Rik|AF064782|pEN87	family with sequence similarity 172, member A	protein-coding
mm_140942.1	chr17	24477592	24477604	-	1	NA	intron (NM_001252463, intron 4 of 8)	intron (NM_001252463, intron 4 of 8)	1480	NM_001252464	56716	Mm.289516	NM_019988	ENSMUSG00000024142	Mlst8	0610033N12Rik|AA409454|AI505104|AI851821|Gbl	MTOR associated protein, LST8 homolog (S. cerevisiae)	protein-coding
mm_150288.1	chr19	34492710	34492755	+	1	NA	3' UTR (NM_021460, exon 10 of 10)	3' UTR (NM_021460, exon 10 of 10)	-17597	NM_009890	12642	Mm.30824	NM_009890	ENSMUSG00000050370	Ch25h	AI462618|m25OH	cholesterol 25-hydroxylase	protein-coding
mm_15198.1	chr2	154206449	154206458	+	1	NA	exon (NM_153418, exon 5 of 16)	exon (NM_153418, exon 5 of 16)	6073	NM_153418	228801	Mm.3783	NM_153418	ENSMUSG00000027485	Bpifb1	Lplunc1	BPI fold containing family B, member 1	protein-coding
mm_124966.1	chr15	17103606	17103621	+	1	NA	Intergenic	Intergenic	325512	NM_009869	12565	Mm.439758	NM_009869	ENSMUSG00000025370	Cdh9	-	cadherin 9	protein-coding
mm_91483.1	chr10	34882407	34882410	-	1	NA	Intergenic	L1_Mus2|LINE|L1	399008	NM_010237	14302	Mm.332432	NM_010237	ENSMUSG00000019779	Frk	BSK|BSK/IYK|C85044|GTK|RAK	fyn-related kinase	protein-coding
mm_134515.1	chr16	19200309	19200318	-	1	NA	Intergenic	Intergenic	86428	NM_146451	258443	Mm.377506	NM_146451	ENSMUSG00000050742	Olfr164	MOR279-2	olfactory receptor 164	protein-coding
mm_156194.1	chrX	134059316	134059366	+	1	NA	5' UTR (NM_133196, exon 1 of 14)	5' UTR (NM_133196, exon 1 of 14)	165	NM_133196	108062	Mm.67938	NM_133196	ENSMUSG00000031256	Cstf2	C630034J23Rik|Cstf64|mir-3112	cleavage stimulation factor, 3' pre-RNA subunit 2	protein-coding
mm_111232.1	chr12	84762536	84762541	-	1	NA	intron (NM_023409, intron 2 of 3)	intron (NM_023409, intron 2 of 3)	10574	NM_023409	67963	Mm.282556	NM_023409	ENSMUSG00000021242	Npc2	2700012J19Rik|AA408070|AU045843|HE1	Niemann-Pick type C2	protein-coding
mm_44962.1	chr5	36713111	36713142	-	1	NA	Intergenic	Intergenic	-17105	NM_001081232	320661	Mm.26480	NM_177221	ENSMUSG00000029190	D5Ertd579e	9030221A05Rik|A930018H20Rik|Kiaa0232	DNA segment, Chr 5, ERATO Doi 579, expressed	protein-coding
mm_85874.1	chr9	110946089	110946112	-	1	NA	promoter-TSS (NM_011562)	promoter-TSS (NM_011562)	58	NM_011562	21667	Mm.5090	NM_011562	ENSMUSG00000032494	Tdgf1	CR1|cripto	teratocarcinoma-derived growth factor 1	protein-coding
mm_163351.1	chr12	21287511	21287514	+	1	NA	intron (NM_018813, intron 1 of 17)	intron (NM_018813, intron 1 of 17)	1215	NM_018813	54451	Mm.356778	NM_018813	ENSMUSG00000054309	Cpsf3	-	cleavage and polyadenylation specificity factor 3	protein-coding
mm_24091.1	chr3	87976221	87976246	+	1	NA	exon (NM_016701, exon 4 of 4)	exon (NM_016701, exon 4 of 4)	5140	NM_016701	18008	Mm.331129	NM_016701	ENSMUSG00000004891	Nes	AA166324|C78523|ESTM46	nestin	protein-coding
mm_166377.1	chr5	128757304	128757309	+	1	NA	TTS (NM_001081388)	TTS (NM_001081388)	21060	NM_021311	57749	Mm.272720	NM_021311	ENSMUSG00000029423	Piwil1	MIWI	piwi-like RNA-mediated gene silencing 1	protein-coding
mm_117788.1	chr13	97035283	97035295	-	1	NA	promoter-TSS (NM_001284205)	promoter-TSS (NM_001284205)	-35	NR_104276	66479	Mm.390629	NM_025585	ENSMUSG00000052075	1700029F12Rik	-	RIKEN cDNA 1700029F12 gene	protein-coding
mm_9701.1	chr1	178989351	178989360	-	1	NA	intron (NM_027188, intron 10 of 11)	intron (NM_027188, intron 10 of 11)	460230	NM_001161665	269152	Mm.129727	NM_177724	ENSMUSG00000026494	Kif26b	4832420M10|BC056349|D230039L06Rik	kinesin family member 26B	protein-coding
mm_26538.1	chr3	146123361	146123368	+	1	NA	intron (NM_134160, intron 1 of 11)	intron (NM_134160, intron 1 of 11)	1573	NM_134160	171166	Mm.114683	NM_134160	ENSMUSG00000036853	Mcoln3	6720490O21Rik|TRPML3|Va	mucolipin 3	protein-coding
mm_124590.1	chr15	3274679	3274691	+	1	NA	exon (NM_009155, exon 2 of 5)	exon (NM_009155, exon 2 of 5)	3708	NM_009155	20363	Mm.392203	NM_009155	ENSMUSG00000064373	Selenop	AU018766|D15Ucla1|Se-P|Sepp1|selp	selenoprotein P	protein-coding
mm_99382.1	chr11	102043147	102043182	+	1	NA	exon (NM_001160713, exon 2 of 7)	exon (NM_001160713, exon 2 of 7)	1653	NM_001160713	52685	Mm.266885	NM_027987	ENSMUSG00000017309	Cd300lg	2310016B05Rik|Clm9|D11Ertd736e	CD300 molecule like family member G	protein-coding
mm_164045.1	chr14	94919536	94919536	+	1	NA	Intergenic	Intergenic	-961730	NM_025733	66732	Mm.75060	NM_025733	ENSMUSG00000034689	4921530L21Rik	-	RIKEN cDNA 4921530L21 gene	protein-coding
mm_57073.1	chr6	122578264	122578274	-	1	NA	3' UTR (NM_031159, exon 8 of 8)	3' UTR (NM_031159, exon 8 of 8)	24175	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_100621.1	chr11	121601694	121601710	+	1	NA	intron (NM_029878, intron 29 of 38)	intron (NM_029878, intron 29 of 38)	71449	NM_178664	210004	Mm.386847	NM_178664	ENSMUSG00000046605	B3gntl1	6030413G23Rik	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase-like 1	protein-coding
mm_143696.1	chr17	80480415	80480434	-	1	NA	promoter-TSS (NM_009231)	promoter-TSS (NM_009231)	29	NM_009231	20662	Mm.60975	NM_009231	ENSMUSG00000024241	Sos1	4430401P03Rik|9630010N06|AI449023	son of sevenless homolog 1 (Drosophila)	protein-coding
mm_12725.1	chr2	78709502	78709508	+	1	NA	Intergenic	Intergenic	-159542	NM_009454	22193	Mm.1485	NM_009454	ENSMUSG00000027011	Ube2e3	Ubce4|ubcM2	ubiquitin-conjugating enzyme E2E 3	protein-coding
mm_127494.1	chr15	101373646	101373679	+	1	NA	Intergenic	Intergenic	-3537	NM_028770	74127	Mm.440055	NM_028770	ENSMUSG00000037185	Krt80	1200016G03Rik|2310041I20Rik|Kb20	keratin 80	protein-coding
mm_4044.1	chr1	165774757	165774767	+	1	NA	3' UTR (NM_011804, exon 4 of 4)	3' UTR (NM_011804, exon 4 of 4)	10982	NM_011804	433375	Mm.294885	NM_011804	ENSMUSG00000040713	Creg1	AA755314|Creg	cellular repressor of E1A-stimulated genes 1	protein-coding
mm_155251.1	chrX	57223782	57223788	+	1	NA	3' UTR (NM_011616, exon 5 of 5)	3' UTR (NM_011616, exon 5 of 5)	11642	NM_011616	21947	Mm.4861	NM_011616	ENSMUSG00000031132	Cd40lg	CD154|CD40-L|Cd40l|HIGM1|IGM|IMD3|Ly-62|Ly62|T-BAM|TRAP|Tnfsf5|Tnlg8b|gp39	CD40 ligand	protein-coding
mm_35678.1	chr4	43661964	43662005	-	1	NA	intron (NM_175517, intron 3 of 6)	intron (NM_175517, intron 3 of 6)	-5539	NM_026871	68917	Mm.25285	NM_026871	ENSMUSG00000028470	Hint2	1190005L05Rik	histidine triad nucleotide binding protein 2	protein-coding
mm_30118.1	chr3	140964433	140964476	-	1	NA	Intergenic	Lx9|LINE|L1	247901	NM_008811	18598	Mm.4223	NM_008811	ENSMUSG00000047674	Pdha2	Pdhal	pyruvate dehydrogenase E1 alpha 2	protein-coding
mm_68972.1	chr7	126584864	126584889	-	1	NA	promoter-TSS (NM_138310)	promoter-TSS (NM_138310)	-132	NM_138310	171504	Mm.170665	NM_138310	ENSMUSG00000042759	Apobr	Apob-48r|Apob48r	apolipoprotein B receptor	protein-coding
mm_130921.1	chr15	102707339	102707415	-	1	NA	exon (NM_026192, exon 15 of 15)	exon (NM_026192, exon 15 of 15)	14801	NM_026192	67488	Mm.71682	NM_026192	ENSMUSG00000023055	Calcoco1	1810009B06Rik|Cocoa|Gcap11|mKIAA1536	calcium binding and coiled coil domain 1	protein-coding
mm_129318.1	chr15	77761768	77761783	-	1	NA	3' UTR (NM_022410, exon 41 of 41)	3' UTR (NM_022410, exon 41 of 41)	-6546	NM_001081970	239552	Mm.125650	NM_001081970	ENSMUSG00000056656	Apol8	9830006J20Rik|APOL-II|Apol2	apolipoprotein L 8	protein-coding
mm_115333.1	chr13	112480035	112480061	+	1	NA	exon (NM_010560, exon 4 of 17)	exon (NM_010560, exon 4 of 17)	15978	NM_010560	16195	Mm.4364	NM_010560	ENSMUSG00000021756	Il6st	5133400A03Rik|AA389424|BB405851|CD130|D13Ertd699e|gp130	interleukin 6 signal transducer	protein-coding
mm_113460.1	chr13	35967861	35967888	+	1	NA	promoter-TSS (NM_029628)	promoter-TSS (NM_029628)	-32	NM_029628	76487	Mm.44745	NM_029628	ENSMUSG00000050423	Ppp1r3g	1600032L17Rik	protein phosphatase 1, regulatory (inhibitor) subunit 3G	protein-coding
mm_79602.1	chr9	58489036	58489039	+	1	NA	5' UTR (NM_176921, exon 1 of 3)	5' UTR (NM_176921, exon 1 of 3)	434	NM_176921	319477	Mm.153674	NM_176921	ENSMUSG00000066607	6030419C18Rik	-	RIKEN cDNA 6030419C18 gene	protein-coding
mm_28112.1	chr3	86551132	86551140	-	1	NA	intron (NM_001077687, intron 40 of 50)	intron (NM_001077687, intron 40 of 50)	-2853	NM_011839	23937	Mm.389466	NM_011839	ENSMUSG00000057777	Mab21l2	-	mab-21-like 2 (C. elegans)	protein-coding
mm_114318.1	chr13	60248565	60248567	+	1	NA	Intergenic	Intergenic	43095	NR_036449	100503759	Mm.38101	NM_177810		Gm5084	A030007L22|EG328264	predicted gene 5084	ncRNA
mm_153785.1	chr19	45812381	45812389	-	1	NA	promoter-TSS (NM_001276358)	promoter-TSS (NM_001276358)	-94	NM_001276358	80906	Mm.213204	NM_030716	ENSMUSG00000025221	Kcnip2	KChIP2	Kv channel-interacting protein 2	protein-coding
mm_68903.1	chr7	126453396	126453426	-	1	NA	exon (NM_007504, exon 10 of 23)	exon (NM_007504, exon 10 of 23)	9662	NM_007504	11937	Mm.35134	NM_007504	ENSMUSG00000030730	Atp2a1	SERCA1	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	protein-coding
mm_890.1	chr1	52845100	52845110	+	1	NA	promoter-TSS (NM_146108)	promoter-TSS (NM_146108)	67	NM_146108	227095	Mm.222063	NM_146108	ENSMUSG00000041426	Hibch	2610509I15Rik|HIBYL-COA-H	3-hydroxyisobutyryl-Coenzyme A hydrolase	protein-coding
mm_26269.1	chr3	142503104	142503113	+	1	NA	exon (NM_153564, exon 4 of 11)	exon (NM_153564, exon 4 of 11)	6174	NM_153564	229898	Mm.459245	NM_153564	ENSMUSG00000105504	Gbp5	5330409J06Rik|Gbp5a	guanylate binding protein 5	protein-coding
mm_154056.1	chr19	55114632	55114651	-	1	NA	Intergenic	MIRb|SINE|MIR	-15194	NM_008149	14732	Mm.210196	NM_008149	ENSMUSG00000024978	Gpam	GPAT|GPAT1	glycerol-3-phosphate acyltransferase, mitochondrial	protein-coding
mm_86997.1	chr10	26772489	26772515	+	1	NA	promoter-TSS (NM_176837)	promoter-TSS (NM_176837)	-10	NM_176837	73910	Mm.356496	NM_176837	ENSMUSG00000039031	Arhgap18	4833419J07Rik|AI314906|AI843501	Rho GTPase activating protein 18	protein-coding
mm_23661.1	chr3	68468163	68468209	+	1	NA	promoter-TSS (NM_001282045)	promoter-TSS (NM_001282045)	3	NM_001282045	30953	Mm.331064	NM_013928	ENSMUSG00000027777	Schip1	Nf2ip|Schip-1	schwannomin interacting protein 1	protein-coding
mm_127079.1	chr15	97424600	97424606	+	1	NA	Intergenic	Intergenic	-177316	NM_001164602	105827	Mm.24005	NM_178114	ENSMUSG00000048218	Amigo2	AI415330|AMIGO-2|AW208913|Ali1	adhesion molecule with Ig like domain 2	protein-coding
mm_49802.1	chr6	35997081	35997091	+	1	NA	Intergenic	MT2A|LTR|ERVL	-390998	NM_203491	243764	Mm.448632	NM_203491	ENSMUSG00000045613	Chrm2	AChR-M2|Chrm-2|M2	cholinergic receptor, muscarinic 2, cardiac	protein-coding
mm_115068.1	chr13	101455737	101455739	+	1	NA	Intergenic	Intergenic	-58158	NR_046187	78136	Mm.399065	NR_046187		4922502H24Rik	-	RIKEN cDNA 4922502H24 gene	ncRNA
mm_97411.1	chr11	77953854	77953863	+	1	NA	exon (NM_021286, exon 2 of 17)	exon (NM_021286, exon 2 of 17)	23019	NM_021286	20370	Mm.229330	NM_021286	ENSMUSG00000000632	Sez6	BSRP-C|D11Bhm177e|sez-6	seizure related gene 6	protein-coding
mm_76070.1	chr8	78810222	78810235	-	1	NA	intron (NM_001191004, intron 3 of 4)	intron (NM_001191004, intron 3 of 4)	10924	NM_001191004	78651	Mm.28694	NM_030145	ENSMUSG00000031683	Lsm6	1500031N17Rik|2410088K19Rik|AI747288	LSM6 homolog, U6 small nuclear RNA and mRNA degradation associated	protein-coding
mm_7845.1	chr1	132360672	132360683	-	1	NA	exon (NM_178874, exon 3 of 5)	exon (NM_178874, exon 3 of 5)	7271	NM_001311108	68875	Mm.273785	NM_178874	ENSMUSG00000042066	Tmcc2	1110063G11Rik	transmembrane and coiled-coil domains 2	protein-coding
mm_4763.1	chr1	182452725	182452745	+	1	NA	exon (NM_173378, exon 14 of 18)	exon (NM_173378, exon 14 of 18)	43568	NM_173378	209456	Mm.287450	NM_173378	ENSMUSG00000026510	Trp53bp2	53BP2|AI746547|ASPP2|PPP1R13A|Tp53bp2|X98550	transformation related protein 53 binding protein 2	protein-coding
mm_125067.1	chr15	25941055	25941068	+	1	NA	5' UTR (NM_001277315, exon 1 of 7)	5' UTR (NM_001277315, exon 1 of 7)	235	NM_025459	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_6688.1	chr1	80665309	80665355	-	1	NA	promoter-TSS (NM_001285927)	promoter-TSS (NM_001285927)	20	NM_001285927	210293	Mm.133473	NM_175291	ENSMUSG00000038608	Dock10	9330153B10Rik|A630054M16Rik|Jr4|Jr5|R75174|ZIZ3|Zizimin3|mKIAA0694	dedicator of cytokinesis 10	protein-coding
mm_102781.1	chr11	68387169	68387194	-	1	NA	promoter-TSS (NM_008744)	promoter-TSS (NM_008744)	-355	NM_008744	18208	Mm.39095	NM_008744	ENSMUSG00000020902	Ntn1	AI561871|BC019633|Netrin-1	netrin 1	protein-coding
mm_28927.1	chr3	98859712	98859721	-	1	NA	promoter-TSS (NM_001304800)	promoter-TSS (NM_001304800)	78	NM_001304800	15492	Mm.140811	NM_008293	ENSMUSG00000027871	Hsd3b1	3-beta-HSD I|D3Ertd383e	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1	protein-coding
mm_139299.1	chr17	48346407	48346417	+	1	NA	promoter-TSS (NM_031254)	promoter-TSS (NM_031254)	11	NM_001272078	83433	Mm.261623	NM_031254	ENSMUSG00000023992	Trem2	TREM-2|Trem2a|Trem2b|Trem2c	triggering receptor expressed on myeloid cells 2	protein-coding
mm_65813.1	chr7	29042309	29042320	-	1	NA	intron (NM_009109, intron 84 of 105)	B4A|SINE|B4	41380	NR_035489	100316710		NR_035489	ENSMUSG00000089219	Mir1963	mir-1963|mmu-mir-1963	microRNA 1963	ncRNA
mm_149344.1	chr19	10850480	10850488	+	1	NA	intron (NM_023044, intron 2 of 7)	(CA)n|Simple_repeat|Simple_repeat	7940	NM_023044	65221	Mm.27387	NM_023044	ENSMUSG00000024737	Slc15a3	Ci1|cI-1	solute carrier family 15, member 3	protein-coding
mm_16479.1	chr2	180836196	180836198	+	1	NA	Intergenic	Intergenic	-57843	NR_029538	723951		NR_029538	ENSMUSG00000065454	Mir124a-3	Mirn124a-3|mir-124-3|mir-124a-3	microRNA 124a-3	ncRNA
mm_135405.1	chr16	44746254	44746273	-	1	NA	promoter-TSS (NM_025332)	promoter-TSS (NM_025332)	100	NM_001159329	66067	Mm.34520	NM_025332	ENSMUSG00000022668	Gtpbp8	0610037H22Rik	GTP-binding protein 8 (putative)	protein-coding
mm_96852.1	chr11	70048411	70048413	+	1	NA	Intergenic	B1_Mus1|SINE|Alu	-5712	NM_001291131	11889	Mm.6559	NM_009714	ENSMUSG00000020884	Asgr1	ASGPR1|Asgr|Asgr-1|HL-1	asialoglycoprotein receptor 1	protein-coding
mm_171967.1	chr5	87370527	87370538	-	1	NA	Intergenic	Intergenic	-33337	NM_028094	72094	Mm.482739	NM_028094	ENSMUSG00000035780	Ugt2a3	2010321J07Rik	UDP glucuronosyltransferase 2 family, polypeptide A3	protein-coding
mm_131815.1	chr16	22920318	22920328	+	1	NA	5' UTR (NM_021564, exon 1 of 8)	5' UTR (NM_021564, exon 1 of 8)	101	NM_001083904	59083	Mm.28461	NM_021564	ENSMUSG00000022871	Fetub	2310011O17Rik|AI255764|D17980|Gugu	fetuin beta	protein-coding
mm_66578.1	chr7	45336479	45336511	-	1	NA	exon (NM_010473, exon 1 of 6)	exon (NM_010473, exon 1 of 6)	1226	NM_010473	15464	Mm.39968	NM_010473	ENSMUSG00000038239	Hrc	-	histidine rich calcium binding protein	protein-coding
mm_165472.1	chr2	164289589	164289593	+	1	NA	exon (NM_021363, exon 2 of 3)	exon (NM_021363, exon 2 of 3)	323	NM_021363	64335	Mm.389393	NM_021363	ENSMUSG00000017003	Svs3a	9530026M05Rik|BB121242|Semg2|Svp-3|Svp3|Svs3	seminal vesicle secretory protein 3A	protein-coding
mm_7959.1	chr1	133930026	133930038	-	1	NA	Intergenic	Intergenic	-8631	NM_054077	116847	Mm.214514	NM_054077	ENSMUSG00000041577	Prelp	7330409J17Rik|SLRR2A	proline arginine-rich end leucine-rich repeat	protein-coding
mm_97622.1	chr11	78957472	78957484	+	1	NA	exon (NM_010927, exon 26 of 27)	exon (NM_010927, exon 26 of 27)	27446	NM_001159301	16859	Mm.341434	NM_010708	ENSMUSG00000001123	Lgals9	AA407335|AI194909|AI265545|LGALS35|Lgals5|gal-9|galectin-9	lectin, galactose binding, soluble 9	protein-coding
mm_173148.1	chrX	24008415	24008438	+	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	115663	NM_001034864	236749	Mm.296422	NM_001034864	ENSMUSG00000068113	Gm4907	EG236749	predicted gene 4907	protein-coding
mm_40315.1	chr5	43868803	43868866	+	1	NA	promoter-TSS (NM_007646)	promoter-TSS (NM_007646)	25	NM_007646	12494	Mm.249873	NM_007646	ENSMUSG00000029084	Cd38	ADPRC 1|Cd38-rs1|I-19	CD38 antigen	protein-coding
mm_90767.1	chr10	5805354	5805364	-	1	NA	5' UTR (NM_025995, exon 1 of 5)	5' UTR (NM_025995, exon 1 of 5)	106	NM_025995	67141	Mm.197520	NM_025995	ENSMUSG00000019773	Fbxo5	2510044I10Rik|C85305|Emi1|Fbxo31	F-box protein 5	protein-coding
mm_17977.1	chr2	37689157	37689159	-	1	NA	Intergenic	Intergenic	-41873	NM_009261	20744	Mm.237095	NM_009261	ENSMUSG00000026915	Strbp	6430510M02Rik|AI852513|C230082I21Rik|C86322|Spnr	spermatid perinuclear RNA binding protein	protein-coding
mm_109107.1	chr12	105337181	105337191	+	1	NA	intron (NR_125773, intron 1 of 3)	CpG	193	NR_125773	69952	Mm.158311	NR_045047	ENSMUSG00000097929	Tunar	2810011L19Rik|Tuna	Tcl1 upstream neural differentiation associated RNA	ncRNA
mm_159809.1	chr5	118560523	118560523	+	1	NA	promoter-TSS (NM_172424)	promoter-TSS (NM_172424)	-196	NM_001347445	76199	Mm.206238	NM_172424	ENSMUSG00000018076	Med13l	2210413I17Rik|6330591G05Rik|9030618F05Rik|Thrap2|Trap240L|mKIAA1025	mediator complex subunit 13-like	protein-coding
mm_107523.1	chr12	40465213	40465226	+	1	NA	intron (NM_172803, intron 1 of 52)	(TCCC)n|Simple_repeat|Simple_repeat	19166	NM_172803	238130	Mm.341423	NM_172803	ENSMUSG00000035954	Dock4	5330406C03|6330411N01Rik|AF263288|C030023J22|mKIAA0716	dedicator of cytokinesis 4	protein-coding
mm_9171.1	chr1	170976568	170976608	-	1	NA	promoter-TSS (NM_001077189)	promoter-TSS (NM_001077189)	-517	NM_010187	14130	Mm.425062	NM_010187	ENSMUSG00000026656	Fcgr2b	AI528646|CD32|F630109E10Rik|Fc[g]RII|FcgRII|Fcgr2|Fcgr2a|Fcr-2|Fcr-3|Ly-17|Ly-m20|LyM-1|Lym-1|fcRII	Fc receptor, IgG, low affinity IIb	protein-coding
mm_45216.1	chr5	53009053	53009075	-	1	NA	Intergenic	ID_B1|SINE|B4	-16772	NR_040413	75954	Mm.258937	NR_040413	ENSMUSG00000106352	5033403H07Rik	-	RIKEN cDNA 5033403H07 gene	ncRNA
mm_99772.1	chr11	107025854	107025892	+	1	NA	Intergenic	Intergenic	-2350	NM_001163473	69066	Mm.40679	NM_001163473	ENSMUSG00000078607	1810010H24Rik	OTTMUSG00000003581	RIKEN cDNA 1810010H24 gene	protein-coding
mm_7126.1	chr1	90969384	90969402	-	1	NA	5' UTR (NM_008998, exon 1 of 6)	5' UTR (NM_008998, exon 1 of 6)	227	NM_008998	19329	Mm.279780	NM_008998	ENSMUSG00000026304	Rab17	AW413472	RAB17, member RAS oncogene family	protein-coding
mm_158220.1	chrX	105929398	105929408	-	1	NA	promoter-TSS (NM_009530)	promoter-TSS (NM_009530)	-31	NM_009530	22589	Mm.10141	NM_009530	ENSMUSG00000031229	Atrx	4833408C14Rik|AI447451|ATR2|DXHXS6677E|HP1-BP38|Hp1bp2|Hp1bp38|MRXS3|RAD54L|Rad54|XH2|Xnp|ZNF-HX	alpha thalassemia/mental retardation syndrome X-linked	protein-coding
mm_121098.1	chr14	99314726	99314729	+	1	NA	Intergenic	Intergenic	16036	NM_009769	12224	Mm.30262	NM_009769	ENSMUSG00000005148	Klf5	4930520J07Rik|Bteb2|CKLF|IKLF	Kruppel-like factor 5	protein-coding
mm_158094.1	chrX	101420349	101420364	-	1	NA	promoter-TSS (NM_019831)	promoter-TSS (NM_019831)	-134	NM_019831	56364	Mm.23458	NM_019831	ENSMUSG00000031310	Zmym3	9030216B10Rik|AW122925|DXS6673El|Zfp261	zinc finger, MYM-type 3	protein-coding
mm_97795.1	chr11	82933485	82933488	+	1	NA	intron (NM_178680, intron 13 of 19)	intron (NM_178680, intron 13 of 19)	-18616	NM_183201	327978	Mm.42147	NM_183201	ENSMUSG00000054404	Slfn5	AI956840	schlafen 5	protein-coding
mm_19259.1	chr2	84775421	84775438	-	1	NA	promoter-TSS (NM_009776)	promoter-TSS (NM_009776)	0	NM_009776	12258	Mm.38888	NM_009776	ENSMUSG00000023224	Serping1	C1INH|C1nh	serine (or cysteine) peptidase inhibitor, clade G, member 1	protein-coding
mm_27303.1	chr3	49743892	49743893	-	1	NA	3' UTR (NM_130448, exon 4 of 4)	3' UTR (NM_130448, exon 4 of 4)	13424	NM_130448	73173	Mm.87246	NM_130448	ENSMUSG00000037892	Pcdh18	3110038E07Rik|BB095589|PCDH68L	protocadherin 18	protein-coding
mm_163004.1	chr11	35834375	35834382	-	1	NA	intron (NM_025936, intron 1 of 14)	CpG	150	NM_025936	104458	Mm.284906	NM_025936	ENSMUSG00000018848	Rars	2610011N19Rik|2610037E21Rik|AL033339|AW985894	arginyl-tRNA synthetase	protein-coding
mm_94433.1	chr11	6292121	6292203	+	1	NA	promoter-TSS (NM_001252288)	promoter-TSS (NM_001252288)	-396	NM_001252288	18293	Mm.276348	NM_010956	ENSMUSG00000020456	Ogdh	2210403E04Rik|2210412K19Rik|AA409584|d1401|mKIAA4192	oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)	protein-coding
mm_38506.1	chr4	141135224	141135263	-	1	NA	intron (NM_001025608, intron 1 of 3)	intron (NM_001025608, intron 1 of 3)	4553	NR_102344	213491	Mm.332006	NM_174996	ENSMUSG00000040842	Szrd1	1110022I03|D4Ertd22e	SUZ RNA binding domain containing 1	protein-coding
mm_13512.1	chr2	109899969	109899972	+	1	NA	3' UTR (NM_011699, exon 5 of 5)	3' UTR (NM_011699, exon 5 of 5)	9092	NM_011699	22343	Mm.235300	NM_011699	ENSMUSG00000027162	Lin7c	9130007B12Rik|AI303698|AU019331|AW125731|D2Ertd520e|LIN-7-C|LIN-7C|MALS-3|Veli3	lin-7 homolog C (C. elegans)	protein-coding
mm_73142.1	chr8	94982174	94982177	+	1	NA	intron (NM_001198894, intron 1 of 13)	intron (NM_001198894, intron 1 of 13)	-2224	NM_018882	14766	Mm.290834	NM_018882	ENSMUSG00000031785	Adgrg1	Cyt28|Gpr56|TM7LN4|TM7XN1	adhesion G protein-coupled receptor G1	protein-coding
mm_81852.1	chr9	118703349	118703359	+	1	NA	intron (NM_133721, intron 15 of 27)	intron (NM_133721, intron 15 of 27)	-8338	NM_001113514	104099	Mm.335520	NM_133721	ENSMUSG00000039115	Itga9	(alpha)9|2610002H11Rik|6720458D17Rik|AI461869|D130073C02|D9Ertd428e	integrin alpha 9	protein-coding
mm_38109.1	chr4	134534967	134534973	-	1	NA	intron (NM_029759, intron 1 of 6)	CpG	298	NM_001256112	76824	Mm.30153	NM_029759	ENSMUSG00000046671	Mtfr1l	2410166I05Rik|AI480750|Fam54b	mitochondrial fission regulator 1-like	protein-coding
mm_95502.1	chr11	51884266	51884284	+	1	NA	Intergenic	Intergenic	-26794	NM_199299	76901	Mm.259996	NM_199299	ENSMUSG00000020387	Jade2	1200017K05Rik|AI480685|Phf15|mKIAA0239	jade family PHD finger 2	protein-coding
mm_39856.1	chr5	30921826	30921866	+	1	NA	TTS (NM_133918)	TTS (NM_133918)	287	NM_001310524	16548	Mm.22451	NM_008439	ENSMUSG00000029162	Khk	-	ketohexokinase	protein-coding
mm_85506.1	chr9	106235486	106235504	-	1	NA	exon (NM_020559, exon 10 of 11)	exon (NM_020559, exon 10 of 11)	12235	NM_001291835	11655	Mm.290578	NM_020559	ENSMUSG00000032786	Alas1	ALAS|ALAS-N|Alas-1|Alas-h	aminolevulinic acid synthase 1	protein-coding
mm_107724.1	chr12	57227876	57227882	+	1	NA	Intergenic	Lx5b|LINE|L1	-2533	NM_001037746	328099	Mm.268180	NM_001037746	ENSMUSG00000079104	Prps1l3	AU021838|AW536152|Gm5081	phosphoribosyl pyrophosphate synthetase 1-like 3	protein-coding
mm_138446.1	chr17	35135197	35135243	+	1	NA	promoter-TSS (NM_001252469)	promoter-TSS (NM_001252469)	42	NM_057171	224727	Mm.203962	NM_057171	ENSMUSG00000024392	Bag6	2410045D21Rik|AA408914|BAG-6|Bat3|D17H6S52E|G3|Scythe	BCL2-associated athanogene 6	protein-coding
mm_16192.1	chr2	172977876	172977901	+	1	NA	Intergenic	Intergenic	-1954	NM_012046	26972	Mm.23495	NM_012046	ENSMUSG00000005883	Spo11	AI449549|Spo11a|Spo11b	SPO11 meiotic protein covalently bound to DSB	protein-coding
mm_85945.1	chr9	112104963	112104966	-	1	NA	intron (NM_001177618, intron 17 of 18)	intron (NM_001177618, intron 17 of 18)	13747	NR_029823	723815		NR_029823	ENSMUSG00000065441	Mir128-2	Mirn128-2|Mirn128b|mir-128-2|mir-128b	microRNA 128-2	ncRNA
mm_34110.1	chr4	139193280	139193286	+	1	NA	promoter-TSS (NM_001271405)	promoter-TSS (NM_001271405)	384	NM_001037761	12345	Mm.2945	NM_009798	ENSMUSG00000028745	Capzb	1700120C01Rik|AI325129|CPB1|CPB2|CPbeat2|CPbeta1|CPbeta2|Cappb1	capping protein (actin filament) muscle Z-line, beta	protein-coding
mm_105148.1	chr11	101462433	101462472	-	1	NA	exon (NM_012037, exon 3 of 6)	exon (NM_012037, exon 3 of 6)	3747	NM_012037	26949	Mm.29210	NM_012037	ENSMUSG00000034993	Vat1	VAT-1	vesicle amine transport 1	protein-coding
mm_98420.1	chr11	94641311	94641328	+	1	NA	exon (NM_133807, exon 6 of 7)	exon (NM_133807, exon 6 of 7)	11495	NM_133807	98238	Mm.172720	NM_133807	ENSMUSG00000020869	Lrrc59	AA959742|C78668	leucine rich repeat containing 59	protein-coding
mm_7683.1	chr1	128589434	128589445	-	1	NA	exon (NM_009911, exon 2 of 2)	exon (NM_009911, exon 2 of 2)	2860	NM_009911	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding
mm_21869.1	chr2	165949806	165949818	-	1	NA	Intergenic	MamRep4096|DNA|hAT?	-42825	NM_008679	17979	Mm.469663	NM_008679	ENSMUSG00000027678	Ncoa3	2010305B15Rik|AW321064|Actr|Aib1|KAT13B|Rac3|Src3|Tram-1|Tram1|bHLHe42|p/Cip|pCip	nuclear receptor coactivator 3	protein-coding
mm_59339.1	chr7	25471879	25471891	+	1	NA	exon (NM_001039186, exon 5 of 8)	exon (NM_001039186, exon 5 of 8)	5740	NM_001039185	26365	Mm.322502	NM_011926	ENSMUSG00000074272	Ceacam1	Bgp|Bgp1|C-CAM|CD66a|Cc1|Cea-1|Cea-7|Cea1|Cea7|Hv-2|Hv2|MHVR|MHVR1|Mhv-1|bb-1|mCEA1|mmCGM1|mmCGM1a|mmCGM2	carcinoembryonic antigen-related cell adhesion molecule 1	protein-coding
mm_2323.1	chr1	92058971	92058977	+	1	NA	intron (NM_207225, intron 2 of 26)	L1M5|LINE|L1	121367	NM_207225	208727	Mm.318567	NM_207225	ENSMUSG00000026313	Hdac4	4932408F19Rik|HD4	histone deacetylase 4	protein-coding
mm_168494.1	chr11	51455679	51455685	-	1	NA	intron (NM_153393, intron 2 of 28)	(CCCTAA)n|Simple_repeat|Simple_repeat	-129075	NM_028398	72947	Mm.256875	NM_028398	ENSMUSG00000020359	Phykpl	2900006B13Rik|Agxt2l2	5-phosphohydroxy-L-lysine phospholyase	protein-coding
mm_31678.1	chr4	62286442	62286516	+	1	NA	promoter-TSS (NM_025286)	promoter-TSS (NM_025286)	50	NM_025286	20530	Mm.292539	NM_025286	ENSMUSG00000066152	Slc31a2	AI604396|CTR2	solute carrier family 31, member 2	protein-coding
mm_44915.1	chr5	35722465	35722485	-	1	NA	intron (NM_194344, intron 2 of 17)	L1M5|LINE|L1	6801	NM_194344	231147	Mm.290429	NM_194344	ENSMUSG00000036553	Sh3tc1	4631428G15|BC024909	SH3 domain and tetratricopeptide repeats 1	protein-coding
mm_75025.1	chr8	31918776	31918801	-	1	NA	promoter-TSS (NM_178591)	promoter-TSS (NM_178591)	-585	NM_178591	211323	Mm.153432	NM_178591	ENSMUSG00000062991	Nrg1	6030402G23Rik|ARIA|D230005F13Rik|GGF|GGFII|HRG|HRGalpha|Hgl|NDF|SMDF	neuregulin 1	protein-coding
mm_152383.1	chr19	10304855	10304865	-	1	NA	promoter-TSS (NM_198114)	promoter-TSS (NM_198114)	17	NM_198114	269060	Mm.329718	NM_198114	ENSMUSG00000035735	Dagla	Nsddr	diacylglycerol lipase, alpha	protein-coding
mm_91154.1	chr10	20505571	20505586	-	1	NA	intron (NM_013875, intron 2 of 12)	intron (NM_013875, intron 2 of 12)	42750	NM_001347366	29863	Mm.425617	NM_013875	ENSMUSG00000019990	Pde7b	-	phosphodiesterase 7B	protein-coding
mm_167361.1	chr8	84846243	84846265	+	1	NA	exon (NM_007591, exon 2 of 9)	exon (NM_007591, exon 2 of 9)	677	NM_007591	12317	Mm.1971	NM_007591	ENSMUSG00000003814	Calr	CRT|Calregulin	calreticulin	protein-coding
mm_133365.1	chr16	84705567	84705580	+	1	NA	Intergenic	Intergenic	-7450	NR_132106	100653389	Mm.261808	NR_132106	ENSMUSG00000097418	Mir155hg	Bic|Gm26667	Mir155 host gene (non-protein coding)	ncRNA
mm_53582.1	chr6	137425358	137425370	+	1	NA	intron (NM_001164402, intron 6 of 15)	(CA)n|Simple_repeat|Simple_repeat	14643	NM_001164403	19277	Mm.186361	NM_011216	ENSMUSG00000030223	Ptpro	D28|GLEPP1|PTPBK|PTPROt|PTPU2|PTPoc|PTPphi|Ptpn15|R-PTP-O	protein tyrosine phosphatase, receptor type, O	protein-coding
mm_159572.1	chr4	115411643	115411643	+	1	NA	promoter-TSS (NM_172306)	promoter-TSS (NM_172306)	19	NM_172306	13118	Mm.448292	NM_172306	ENSMUSG00000078597	Cyp4a12b	BC060945|Cyp4a12	cytochrome P450, family 4, subfamily a, polypeptide 12B	protein-coding
mm_127333.1	chr15	100461198	100461208	+	1	NA	Intergenic	Lx8|LINE|L1	-7831	NM_134093	68614	Mm.275272	NM_134093	ENSMUSG00000037353	Letmd1	1110019O13Rik|AI593524|BB130465|BB235638|HCCR-2|HCCR1|MCC-32|Mccr	LETM1 domain containing 1	protein-coding
mm_167797.1	chr9	123927356	123927380	-	1	NA	Intergenic	Intergenic	41324	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_33127.1	chr4	124839958	124839961	+	1	NA	intron (NM_008636, intron 9 of 10)	B1_Mur3|SINE|Alu	10605	NM_001347196	68920	Mm.272397	NM_001142727	ENSMUSG00000078570	1110065P20Rik	C530005M16Rik	RIKEN cDNA 1110065P20 gene	protein-coding
mm_41785.1	chr5	103722954	103722971	+	1	NA	Intergenic	Intergenic	-31200	NM_133919	17355	Mm.6949	NM_133919	ENSMUSG00000029313	Aff1	9630032B01Rik|AW319193|Af4|Mllt2h|Rob	AF4/FMR2 family, member 1	protein-coding
mm_71126.1	chr8	36458111	36458159	+	1	NA	Intergenic	CpG	-31056	NM_176952	319582	Mm.180924	NM_176952	ENSMUSG00000039620	6430573F11Rik	Kiaa1456|TRM9L	RIKEN cDNA 6430573F11 gene	protein-coding
mm_92847.1	chr10	81524080	81524098	-	1	NA	5' UTR (NM_010304, exon 1 of 7)	5' UTR (NM_010304, exon 1 of 7)	136	NM_010304	14676	Mm.1546	NM_010304	ENSMUSG00000034792	Gna15	G[a]15|Galpha15	guanine nucleotide binding protein, alpha 15	protein-coding
mm_90833.1	chr10	8451823	8451826	-	1	NA	intron (NM_177387, intron 1 of 7)	intron (NM_177387, intron 1 of 7)	67001	NM_177387	338362	Mm.41163	NM_177387	ENSMUSG00000047712	Ust	D930010O20Rik|UA2OST	uronyl-2-sulfotransferase	protein-coding
mm_169747.1	chr1	58646624	58646625	+	1	NA	Intergenic	Intergenic	-6017	NR_045007	100504501	Mm.440933	NR_045007	ENSMUSG00000102059	Gm20257	-	caspase 8 pseudogene	pseudo
mm_101879.1	chr11	48902152	48902201	-	1	NA	promoter-TSS (NM_001024230)	promoter-TSS (NM_001024230)	-24	NM_001024230	432555	Mm.338931	NM_001024230	ENSMUSG00000058163	Gm5431	EG432555|Irgb9b8	predicted gene 5431	protein-coding
mm_166630.1	chr6	78466899	78466899	-	1	NA	intron (NM_011260, intron 4 of 5)	intron (NM_011260, intron 4 of 5)	1975	NM_011260	19695	Mm.252385	NM_011260	ENSMUSG00000030017	Reg3g	AI449515|REG-3-gamma|reg III-gamma	regenerating islet-derived 3 gamma	protein-coding
mm_170354.1	chr1	85111805	85111811	+	1	NA	Intergenic	Intergenic	-1955	NM_213615	381287	Mm.487565	NM_213615	ENSMUSG00000089844	A530032D15Rik	Gm1888	RIKEN cDNA A530032D15Rik gene	protein-coding
mm_14418.1	chr2	130450311	130450326	+	1	NA	promoter-TSS (NM_008980)	promoter-TSS (NM_008980)	40	NM_001163688	19262	Mm.224246	NM_008980	ENSMUSG00000027303	Ptpra	Ptpa|Ptpalpha|Rptpalpha|Rptra|Rptralpha	protein tyrosine phosphatase, receptor type, A	protein-coding
mm_95501.1	chr11	51884140	51884147	+	1	NA	Intergenic	B1F|SINE|Alu	-26662	NM_199299	76901	Mm.259996	NM_199299	ENSMUSG00000020387	Jade2	1200017K05Rik|AI480685|Phf15|mKIAA0239	jade family PHD finger 2	protein-coding
mm_35209.1	chr4	19608777	19608807	-	1	NA	non-coding (NR_074090, exon 25 of 25)	non-coding (NR_074090, exon 25 of 25)	33726	NM_025476	66302	Mm.440686	NM_025476	ENSMUSG00000028229	Rmdn1	Fam82b|RMD-1	regulator of microtubule dynamics 1	protein-coding
mm_55071.1	chr6	49056778	49056781	-	1	NA	3' UTR (NM_053110, exon 11 of 11)	3' UTR (NM_053110, exon 11 of 11)	-17016	NM_029353	75593	Mm.439947	NM_029353	ENSMUSG00000029815	Malsu1	2410003K15Rik|Matsu1	mitochondrial assembly of ribosomal large subunit 1	protein-coding
mm_40416.1	chr5	53267131	53267189	+	1	NA	promoter-TSS (NM_001145433)	promoter-TSS (NM_001145433)	54	NM_001145433	66278	Mm.27900	NM_001145433	ENSMUSG00000061461	Smim20	1110067B18Rik|1810013D10Rik|N28078	small integral membrane protein 20	protein-coding
mm_136127.1	chr16	85901119	85901133	-	1	NA	promoter-TSS (NM_011782)	promoter-TSS (NM_011782)	-1	NM_011782	23794	Mm.112933	NM_011782	ENSMUSG00000022894	Adamts5	9530092O11Rik|ADAM-TS5|ADAMTS1|ADAMTS11|ADMP-2|AI481094|ASMP-2	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)	protein-coding
mm_78697.1	chr9	41164333	41164343	+	1	NA	Intergenic	Intergenic	-6844	NM_176860	72828	Mm.133615	NM_176860	ENSMUSG00000032020	Ubash3b	2810457I06Rik|BB125008|TULA-2|p70	ubiquitin associated and SH3 domain containing, B	protein-coding
mm_128687.1	chr15	60921281	60921288	-	1	NA	promoter-TSS (NM_001081067)	promoter-TSS (NM_001081067)	-14	NM_001081067	117586	Mm.291499	NM_001081067	ENSMUSG00000022347	A1bg	C44	alpha-1-B glycoprotein	protein-coding
mm_7367.1	chr1	106714218	106714330	-	1	NA	promoter-TSS (NM_177410)	promoter-TSS (NM_177410)	16	NM_009741	12043	Mm.257460	NM_009741	ENSMUSG00000057329	Bcl2	AW986256|Bcl-2|C430015F12Rik|D630044D05Rik|D830018M01Rik	B cell leukemia/lymphoma 2	protein-coding
mm_35295.1	chr4	22486603	22486613	-	1	NA	3' UTR (NM_008899, exon 1 of 1)	3' UTR (NM_008899, exon 1 of 1)	1758	NM_008899	18992	Mm.129387	NM_008899	ENSMUSG00000095139	Pou3f2	9430075J19Rik|A230098E07Rik|Brn-2|Brn2|OTF-7|Otf7|oct-7	POU domain, class 3, transcription factor 2	protein-coding
mm_100013.1	chr11	114881004	114881052	+	1	NA	Intergenic	B1_Mur2|SINE|Alu	-9013	NM_001347654	217303	Mm.294439	NM_170758	ENSMUSG00000034652	Cd300a	B230315M08Rik|Clm8|LMIR1|MAIR-I|MAIR-Ia|MMAC8|Pigr4|mcpir1	CD300A molecule	protein-coding
mm_115962.1	chr13	23764198	23764220	-	1	NA	exon (NM_030609, exon 1 of 1)	exon (NM_030609, exon 1 of 1)	541	NM_030609	80838	Mm.480242	NM_030609	ENSMUSG00000049539	Hist1h1a	H1.1|H1a|H1f1|H1var3	histone cluster 1, H1a	protein-coding
mm_92650.1	chr10	80399390	80399428	-	1	NA	5' UTR (NM_013595, exon 1 of 7)	5' UTR (NM_013595, exon 1 of 7)	122	NM_013595	17192	Mm.7142	NM_013595	ENSMUSG00000035478	Mbd3	AI181826|AU019209	methyl-CpG binding domain protein 3	protein-coding
mm_89045.1	chr10	82860284	82860299	+	1	NA	promoter-TSS (NM_001042514)	promoter-TSS (NM_001042514)	-50	NM_001042514	50493	Mm.210155	NM_015762	ENSMUSG00000020250	Txnrd1	TR|TR1|TrxR1	thioredoxin reductase 1	protein-coding
mm_33571.1	chr4	132274386	132274433	+	1	NA	promoter-TSS (NM_025579)	promoter-TSS (NM_025579)	34	NM_025579	66464	Mm.331926	NM_025579	ENSMUSG00000028899	Taf12	20kDa|2810422D08Rik|AW557038|Taf2J	TATA-box binding protein associated factor 12	protein-coding
mm_112067.1	chr12	111981119	111981129	-	1	NA	promoter-TSS (NM_001127685)	promoter-TSS (NM_001127685)	-373	NM_001127685	217874	Mm.134213	NM_001127685	ENSMUSG00000091402	Rd3l	A930011N13	retinal degeneration 3-like	protein-coding
mm_130801.1	chr15	101707550	101707563	-	1	NA	exon (NM_027011, exon 9 of 9)	exon (NM_027011, exon 9 of 9)	5335	NM_027011	110308	Mm.451847	NM_027011	ENSMUSG00000061527	Krt5	3300001P10Rik|AW146334|CK5|K5|Krt2-5|Tfip8	keratin 5	protein-coding
mm_156362.1	chrX	139524830	139524851	+	1	NA	intron (NM_001346522, intron 10 of 13)	RMER20B|LTR|ERVK	-38500	NM_001254761	66889	Mm.27764	NM_023270	ENSMUSG00000031438	Rnf128	1300002C13Rik|AI987883|GRAIL|Greul1	ring finger protein 128	protein-coding
mm_7226.1	chr1	93342869	93342889	-	1	NA	promoter-TSS (NM_080850)	promoter-TSS (NM_080850)	-91	NM_080850	269224	Mm.379454	NM_080850	ENSMUSG00000026274	Pask	mKIAA0135	PAS domain containing serine/threonine kinase	protein-coding
mm_27026.1	chr3	26116323	26116323	-	1	NA	intron (NM_138666, intron 3 of 7)	intron (NM_138666, intron 3 of 7)	36984	NM_001163387	192167	Mm.316080	NM_138666	ENSMUSG00000063887	Nlgn1	6330415N05Rik|BB179718|NL1|Nlg1|mKIAA1070	neuroligin 1	protein-coding
mm_39106.1	chr4	154924412	154924414	-	1	NA	intron (NM_178931, intron 5 of 7)	intron (NM_178931, intron 5 of 7)	3664	NM_178931	230979	Mm.215147	NM_178931	ENSMUSG00000042333	Tnfrsf14	Atar|HveA|Hvem|Tnfrs14	tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)	protein-coding
mm_17849.1	chr2	34725440	34725448	-	1	NA	exon (NM_025709, exon 6 of 27)	exon (NM_025709, exon 6 of 27)	29788	NM_025709	66691	Mm.156452	NM_025709	ENSMUSG00000026867	Gapvd1	2010005B09Rik|4432404J10Rik|AW108497|Gapex-5|RAP6|RME-6|mKIAA1521	GTPase activating protein and VPS9 domains 1	protein-coding
mm_1945.1	chr1	86306778	86306802	+	1	NA	3' UTR (NM_145222, exon 2 of 2)	3' UTR (NM_145222, exon 2 of 2)	3569	NM_145222	227327	Mm.86467	NM_145222	ENSMUSG00000079445	B3gnt7	C330001H22Rik|beta-3GnT7	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 7	protein-coding
mm_95694.1	chr11	54327027	54327033	+	1	NA	intron (NM_001033597, intron 6 of 20)	intron (NM_001033597, intron 6 of 20)	12127	NM_001033599	216739	Mm.267478	NM_144823	ENSMUSG00000020333	Acsl6	A330035H04Rik|AW050338|Facl6|LACS|Lacsl|mKIAA0837	acyl-CoA synthetase long-chain family member 6	protein-coding
mm_37259.1	chr4	118437267	118437275	-	1	NA	promoter-TSS (NM_023223)	promoter-TSS (NM_023223)	72	NM_023223	107995	Mm.261764	NM_023223	ENSMUSG00000006398	Cdc20	2310042N09Rik|C87100|p55CDC	cell division cycle 20	protein-coding
mm_115037.1	chr13	99415154	99415157	+	1	NA	3' UTR (NM_173757, exon 11 of 11)	3' UTR (NM_173757, exon 11 of 11)	-2329	NR_015515	320893	Mm.470842	NR_015515		6430562O15Rik	-	RIKEN cDNA 6430562O15 gene	ncRNA
mm_109295.1	chr12	109559750	109559763	+	1	NA	non-coding (NR_003633, exon 5 of 5)	non-coding (NR_003633, exon 5 of 5)	-3936	NR_030427	791079		NR_030427	ENSMUSG00000076451	Mir770	Mirn770|mir-770|mmu-mir-770	microRNA 770	ncRNA
mm_29244.1	chr3	107218139	107218146	-	1	NA	exon (NM_001111143, exon 4 of 9)	exon (NM_001111143, exon 4 of 9)	3590	NM_001111143	229697	Mm.297051	NM_001111143	ENSMUSG00000046213	Cym	Gm131	chymosin	protein-coding
mm_168510.1	chr1	156523971	156523973	+	1	NA	Intergenic	Intergenic	-34815	NM_009595	11352	Mm.329515	NM_009595	ENSMUSG00000026596	Abl2	AA536808|Abll|Arg	v-abl Abelson murine leukemia viral oncogene 2 (arg, Abelson-related gene)	protein-coding
mm_44036.1	chr5	147488126	147488145	+	1	NA	exon (NM_028291, exon 5 of 19)	exon (NM_028291, exon 5 of 19)	57555	NM_028291	72587	Mm.320469	NM_028291	ENSMUSG00000029647	Pan3	2700050F09Rik|A430027N15Rik|AU014670	PAN3 poly(A) specific ribonuclease subunit	protein-coding
mm_121289.1	chr14	105258765	105258781	+	1	NA	promoter-TSS (NM_029561)	promoter-TSS (NM_029561)	100	NM_001190989	76273	Mm.290669	NM_029561	ENSMUSG00000053253	Ndfip2	0710001O20Rik|2810436B12Rik|9130207N19Rik|N4wbp5a|mKIAA1165	Nedd4 family interacting protein 2	protein-coding
mm_3262.1	chr1	136279980	136279983	+	1	NA	intron (NM_001347110, intron 11 of 16)	intron (NM_001347110, intron 11 of 16)	-19108	NM_001101516	383563	Mm.40367	NM_001101516	ENSMUSG00000052759	Gpr25	Gm1300	G protein-coupled receptor 25	protein-coding
mm_107230.1	chr12	26478098	26478111	+	1	NA	exon (NM_020557, exon 5 of 5)	exon (NM_020557, exon 5 of 5)	8889	NM_020557	22169	Mm.271839	NM_020557	ENSMUSG00000020638	Cmpk2	1200004E04Rik|TDKI|Tyki	cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial	protein-coding
mm_140769.1	chr17	17625268	17625293	-	1	NA	promoter-TSS (NM_172827)	promoter-TSS (NM_172827)	-791	NM_172827	240028	Mm.328807	NM_172827	ENSMUSG00000023845	Lnpep	2010309L07Rik|4732490P18Rik|CAP|IRAP|PLAP|gp160|vp165	leucyl/cystinyl aminopeptidase	protein-coding
mm_13327.1	chr2	102783822	102783842	+	1	NA	3' UTR (NM_001077514, exon 11 of 11)	3' UTR (NM_001077514, exon 11 of 11)	77394	NM_001077515	20511	Mm.267547	NM_011393	ENSMUSG00000005089	Slc1a2	1700091C19Rik|2900019G14Rik|AI159670|Eaat2|GLT-1|GLT1|MGLT1	solute carrier family 1 (glial high affinity glutamate transporter), member 2	protein-coding
mm_55972.1	chr6	85832240	85832263	-	1	NA	promoter-TSS (NM_023455)	promoter-TSS (NM_023455)	-361	NM_023455	68396	Mm.154782	NM_023455	ENSMUSG00000030004	Nat8	0610037O16Rik|CCNAT|Cml4	N-acetyltransferase 8 (GCN5-related)	protein-coding
mm_116486.1	chr13	44455306	44455324	-	1	NA	intron (NR_045489, intron 2 of 3)	intron (NR_045489, intron 2 of 3)	15588	NR_045489	69491	Mm.392410	NR_045489	ENSMUSG00000098144	1700029N11Rik	-	RIKEN cDNA 1700029N11 gene	ncRNA
mm_4649.1	chr1	180331619	180331622	+	1	NA	intron (NM_001081175, intron 1 of 7)	CpG	-1071	NR_003623	277333	Mm.389223	NM_199472		Gm5069	EG277333	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_22881.1	chr3	29541894	29541895	+	1	NA	intron (NM_001167748, intron 5 of 12)	intron (NM_001167748, intron 5 of 12)	-94850	NR_105796	102466637		NR_105796	ENSMUSG00000098315	Mir21b	Gm27951|mmu-mir-21b	microRNA 21b	ncRNA
mm_97472.1	chr11	78315061	78315076	+	1	NA	exon (NM_017407, exon 12 of 24)	exon (NM_017407, exon 12 of 24)	-8005	NM_001303423	11676	Mm.7729	NM_009657	ENSMUSG00000017390	Aldoc	AI847350|AU040929|Aldo3|Scrg2	aldolase C, fructose-bisphosphate	protein-coding
mm_37989.1	chr4	133632121	133632137	-	1	NA	intron (NM_001017968, intron 1 of 7)	MIRb|SINE|MIR	1300	NM_001017968	503610	Mm.331948	NM_001017968	ENSMUSG00000037553	Zdhhc18	-	zinc finger, DHHC domain containing 18	protein-coding
mm_433.1	chr1	34535627	34535657	+	1	NA	promoter-TSS (NM_007685)	promoter-TSS (NM_007685)	-6	NM_007685	12627	Mm.2531	NM_007685	ENSMUSG00000026124	Cfc1	AV265756|b2b970Clo|cryptic	cripto, FRL-1, cryptic family 1	protein-coding
mm_66872.1	chr7	57509380	57509395	-	1	NA	intron (NM_176942, intron 1 of 9)	CpG	622	NM_176942	110886	Mm.273114	NM_176942	ENSMUSG00000055078	Gabra5	A230018I05Rik	gamma-aminobutyric acid (GABA) A receptor, subunit alpha 5	protein-coding
mm_58333.1	chr6	146634454	146634493	-	1	NA	5' UTR (NM_026281, exon 1 of 12)	5' UTR (NM_026281, exon 1 of 12)	119	NM_026281	67623	Mm.278037	NM_026281	ENSMUSG00000040234	Tm7sf3	2010003B14Rik|NARP1	transmembrane 7 superfamily member 3	protein-coding
mm_23270.1	chr3	51559974	51559976	+	1	NA	intron (NR_033624, intron 1 of 4)	CpG	218	NR_033624	100039684	Mm.387178	NR_033624		5031434O11Rik	AI481280|Gm2370	RIKEN cDNA 5031434O11 gene	ncRNA
mm_117436.1	chr13	74725409	74725419	-	1	NA	exon (NM_009817, exon 20 of 31)	exon (NM_009817, exon 20 of 31)	8847	NM_001301158	12380	Mm.29163	NM_009817	ENSMUSG00000021585	Cast	-	calpastatin	protein-coding
mm_48522.1	chr5	142903322	142903333	-	1	NA	3' UTR (NM_007393, exon 6 of 6)	3' UTR (NM_007393, exon 6 of 6)	3427	NM_007393	11461	Mm.328431	NM_007393	ENSMUSG00000029580	Actb	Actx|E430023M04Rik|beta-actin	actin, beta	protein-coding
mm_118284.1	chr13	112762707	112762710	-	1	NA	Intergenic	L1ME4a|LINE|L1	-38069	NM_008903	19012	Mm.291029	NM_008247	ENSMUSG00000021759	Plpp1	Hic53|Hpic53|LPP-1|LPP1|PAP-2a|PAP2-alpha|PAP2a|Ppap2a|mPAP	phospholipid phosphatase 1	protein-coding
mm_150468.1	chr19	38458540	38458585	+	1	NA	Intergenic	Intergenic	62582	NM_175507	240660	Mm.262085	NM_175507	ENSMUSG00000044026	Slc35g1	AA590464|D330039I19Rik|Tmem20	solute carrier family 35, member G1	protein-coding
mm_39810.1	chr5	30647936	30647998	+	1	NA	promoter-TSS (NM_175675)	promoter-TSS (NM_175675)	28	NM_175675	74919	Mm.247985	NM_175675	ENSMUSG00000029175	Slc35f6	4930471M23Rik|5730478O19Rik|ANT2BP|P40|Tango9	solute carrier family 35, member F6	protein-coding
mm_80154.1	chr9	70932673	70932678	+	1	NA	intron (NM_001324473, intron 1 of 8)	MER97a|DNA|hAT-Tip100	2133	NM_008280	15450	Mm.390187	NM_008280	ENSMUSG00000032207	Lipc	AI256194|HL|Hpl	lipase, hepatic	protein-coding
mm_134921.1	chr16	30388769	30388802	-	1	NA	promoter-TSS (NM_001128094)	promoter-TSS (NM_001128094)	-255	NM_001128096	224088	Mm.8924	NM_001128094	ENSMUSG00000022533	Atp13a3	AU022875|Gm1745|Gm541|Gm542	ATPase type 13A3	protein-coding
mm_55720.1	chr6	73469467	73469473	-	1	NA	exon (NM_025737, exon 1 of 1)	exon (NM_025737, exon 1 of 1)	197	NM_025737	66740	Mm.440760	NM_025737	ENSMUSG00000056197	4931417E11Rik	-	RIKEN cDNA 4931417E11 gene	protein-coding
mm_114285.1	chr13	58402686	58402705	+	1	NA	promoter-TSS (NM_025279)	promoter-TSS (NM_025279)	98	NM_001168248	74386	Mm.85289	NM_028904	ENSMUSG00000035367	Rmi1	4932432N11Rik|C79893	RecQ mediated genome instability 1	protein-coding
mm_106273.1	chr11	117988100	117988131	-	1	NA	intron (NM_133757, intron 1 of 9)	intron (NM_133757, intron 1 of 9)	1258	NM_133757	74451	Mm.28864	NM_133757	ENSMUSG00000017715	Pgs1	2610019F11Rik|4933424M23Rik|SAF	phosphatidylglycerophosphate synthase 1	protein-coding
mm_39254.1	chr5	3521582	3521601	+	1	NA	3' UTR (NM_009873, exon 8 of 8)	3' UTR (NM_009873, exon 8 of 8)	-22242	NM_001042501	68152	Mm.240265	NM_026583	ENSMUSG00000058503	Fam133b	2900022K02Rik|5830415L20Rik	family with sequence similarity 133, member B	protein-coding
mm_106841.1	chr12	8006959	8006967	+	1	NA	exon (NM_009693, exon 26 of 29)	exon (NM_009693, exon 26 of 29)	29286	NM_009693	238055	Mm.221239	NM_009693	ENSMUSG00000020609	Apob	AI315052|Apo B-100|apob-100|apob-48	apolipoprotein B	protein-coding
mm_151340.1	chr19	55895398	55895414	+	1	NA	promoter-TSS (NM_001142924)	promoter-TSS (NM_001142924)	85	NM_001142924	21416	Mm.139815	NM_009333	ENSMUSG00000024985	Tcf7l2	TCF4B|TCF4E|Tcf-4|Tcf4	transcription factor 7 like 2, T cell specific, HMG box	protein-coding
mm_37333.1	chr4	119656636	119656648	-	1	NA	TTS (NM_008191)	TTS (NM_008191)	2303	NM_008191	14916	Mm.278	NM_008191	ENSMUSG00000032978	Guca2b	AV066530|Gcap2|Ugn	guanylate cyclase activator 2b (retina)	protein-coding
mm_6970.1	chr1	86301355	86301366	-	1	NA	Intergenic	Intergenic	-1861	NM_145222	227327	Mm.86467	NM_145222	ENSMUSG00000079445	B3gnt7	C330001H22Rik|beta-3GnT7	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 7	protein-coding
mm_110867.1	chr12	73583907	73583923	-	1	NA	promoter-TSS (NM_008856)	promoter-TSS (NM_008856)	-881	NM_001313977	18755	Mm.341677	NM_008856	ENSMUSG00000021108	Prkch	Pkch	protein kinase C, eta	protein-coding
mm_70817.1	chr8	23119433	23119436	+	1	NA	intron (NR_102385, intron 34 of 45)	intron (NR_102385, intron 34 of 45)	-19596	NM_001310436	11733	Mm.334444	NM_031158	ENSMUSG00000031543	Ank1	Ank-1|nb|pale	ankyrin 1, erythroid	protein-coding
mm_163727.1	chr13	119598006	119598039	-	1	NA	intron (NM_001039244, intron 2 of 2)	intron (NM_001039244, intron 2 of 2)	-25797	NM_020279	56838	Mm.143745	NM_020279	ENSMUSG00000074715	Ccl28	CCK1|MEC|Scya28	chemokine (C-C motif) ligand 28	protein-coding
mm_146316.1	chr18	80470159	80470171	+	1	NA	promoter-TSS (NM_026295)	promoter-TSS (NM_026295)	-498	NM_026295	67655	Mm.312893	NM_026295	ENSMUSG00000033323	Ctdp1	4930563P03Rik|AW553592	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) phosphatase, subunit 1	protein-coding
mm_33857.1	chr4	135895385	135895396	+	1	NA	5' UTR (NM_009924, exon 1 of 2)	5' UTR (NM_009924, exon 1 of 2)	201	NM_009924	12802	Mm.297251	NM_009924	ENSMUSG00000062585	Cnr2	CB-2|CB2|CB2-R	cannabinoid receptor 2 (macrophage)	protein-coding
mm_97385.1	chr11	77763270	77763339	+	1	NA	Intergenic	CpG	-13931	NM_001291213	360013	Mm.341248	NM_011586	ENSMUSG00000000631	Myo18a	MAJN|MyoPDZ|MysPDZ|SP-R210	myosin XVIIIA	protein-coding
mm_161152.1	chr13	23622509	23622509	-	1	NA	promoter-TSS (NM_015787)	promoter-TSS (NM_015787)	49	NM_015787	50709	Mm.170587	NM_015787	ENSMUSG00000051627	Hist1h1e	H1-4|H1.4|H1e|H1f4|H1s-4|H1var2	histone cluster 1, H1e	protein-coding
mm_2271.1	chr1	91250194	91250216	+	1	NA	promoter-TSS (NM_026454)	promoter-TSS (NM_026454)	-114	NM_026454	67921	Mm.337238	NM_026454	ENSMUSG00000034343	Ube2f	2510010F15Rik|AI851109	ubiquitin-conjugating enzyme E2F (putative)	protein-coding
mm_22505.1	chr3	7442763	7442776	+	1	NA	3' UTR (NM_008862, exon 3 of 3)	3' UTR (NM_008862, exon 3 of 3)	-60657	NM_173181	67306	Mm.332366	NM_173181	ENSMUSG00000043542	Zc2hc1a	3110050N22Rik|AI790358|AU023959|Fam164a	zinc finger, C2HC-type containing 1A	protein-coding
mm_139585.1	chr17	57223194	57223210	+	1	NA	exon (NM_009778, exon 12 of 41)	exon (NM_009778, exon 12 of 41)	4934	NM_009778	12266	Mm.19131	NM_009778	ENSMUSG00000024164	C3	AI255234|ASP|HSE-MSF|Plp	complement component 3	protein-coding
mm_16986.1	chr2	18048788	18048822	-	1	NA	promoter-TSS (NM_028317)	promoter-TSS (NM_028317)	-356	NM_028317	72668	Mm.102183	NM_028317	ENSMUSG00000054074	Skida1	2810030E01Rik|5730507N06Rik|BB088113	SKI/DACH domain containing 1	protein-coding
mm_27046.1	chr3	27191975	27191986	-	1	NA	intron (NM_178772, intron 1 of 4)	intron (NM_178772, intron 1 of 4)	8976	NM_178772	320024	Mm.24576	NM_178772	ENSMUSG00000027698	Nceh1	Aadacl1|B230106I24Rik|CPO-BP|Nceh	neutral cholesterol ester hydrolase 1	protein-coding
mm_87932.1	chr10	62651688	62651706	+	1	NA	promoter-TSS (NM_053183)	promoter-TSS (NM_053183)	-499	NM_053183	94213	Mm.114116	NM_053183	ENSMUSG00000020076	Ddx50	4933429B04Rik|8430408E17Rik|GU2|RH-II	DEAD (Asp-Glu-Ala-Asp) box polypeptide 50	protein-coding
mm_167728.1	chr9	103217440	103217471	+	1	NA	exon (NM_133977, exon 12 of 17)	exon (NM_133977, exon 12 of 17)	12831	NM_133977	22041	Mm.37214	NM_133977	ENSMUSG00000032554	Trf	AI266983|Cd176|HP|Tf|Tfn|hpx	transferrin	protein-coding
mm_134786.1	chr16	23988626	23988641	-	1	NA	promoter-TSS (NM_009744)	promoter-TSS (NM_009744)	-21	NM_009744	12053	Mm.347398	NM_009744	ENSMUSG00000022508	Bcl6	Bcl5	B cell leukemia/lymphoma 6	protein-coding
mm_171099.1	chr3	132677119	132677120	-	1	NA	exon (NM_007926, exon 2 of 7)	exon (NM_007926, exon 2 of 7)	6760	NM_007926	13722	Mm.235137	NM_007926	ENSMUSG00000028029	Aimp1	9830137A06Rik|AIMP1/p43|EMAPII|Emap2|Scye1|p43	aminoacyl tRNA synthetase complex-interacting multifunctional protein 1	protein-coding
mm_5211.1	chr1	13589718	13589904	-	1	NA	promoter-TSS (NM_028173)	promoter-TSS (NM_028173)	99	NM_028173	72265	Mm.28765	NM_028173	ENSMUSG00000025935	Tram1	1810049E02Rik|TRAMP	translocating chain-associating membrane protein 1	protein-coding
mm_137626.1	chr17	28328550	28328570	+	1	NA	promoter-TSS (NM_011287)	promoter-TSS (NM_011287)	89	NM_011287	19896	Mm.336955	NM_011287	ENSMUSG00000037805	Rpl10a	CsA-19|Nedd6	ribosomal protein L10A	protein-coding
mm_19181.1	chr2	84390797	84390809	-	1	NA	intron (NM_018782, intron 2 of 15)	intron (NM_018782, intron 2 of 15)	34463	NM_018782	54598	Mm.75467	NM_018782	ENSMUSG00000059588	Calcrl	AV071593|CRLR	calcitonin receptor-like	protein-coding
mm_21104.1	chr2	153241498	153241500	-	1	NA	promoter-TSS (NM_080463)	promoter-TSS (NM_080463)	-33	NM_080463	140484	Mm.293761	NM_080463	ENSMUSG00000046020	Pofut1	O-FucT-1|mKIAA0180	protein O-fucosyltransferase 1	protein-coding
mm_72223.1	chr8	72725601	72725621	+	1	NA	exon (NM_009188, exon 3 of 19)	exon (NM_009188, exon 3 of 19)	2341	NM_009188	20467	Mm.2137	NM_009188	ENSMUSG00000031622	Sin3b	2810430C10Rik	transcriptional regulator, SIN3B (yeast)	protein-coding
mm_124193.1	chr14	98110056	98110065	-	1	NA	intron (NM_007826, intron 1 of 11)	intron (NM_007826, intron 1 of 11)	59705	NM_001038610	13134	Mm.320593	NM_007826	ENSMUSG00000055639	Dach1	Dac|Dach	dachshund 1 (Drosophila)	protein-coding
mm_148764.1	chr19	6061504	6061527	+	1	NA	exon (NM_013859, exon 1 of 1)	exon (NM_013859, exon 1 of 1)	308	NM_013859	29805	Mm.2310	NM_013859	ENSMUSG00000075227	Znhit2	C11orf5|Fon|ORF6|Znhit2-ps	zinc finger, HIT domain containing 2	protein-coding
mm_5198.1	chr1	13374028	13374069	-	1	NA	promoter-TSS (NM_008678)	promoter-TSS (NM_008678)	35	NM_008678	17978	Mm.2537	NM_008678	ENSMUSG00000005886	Ncoa2	D1Ertd433e|GRIP-1|Grip1|KAT13C|NCoA-2|SRC-2|TIF2|bHLHe75	nuclear receptor coactivator 2	protein-coding
mm_69242.1	chr7	127806960	127806992	-	1	NA	3' UTR (NM_024414, exon 10 of 10)	3' UTR (NM_024414, exon 10 of 10)	6367	NM_001040684	101502	Mm.157103	NM_133943	ENSMUSG00000042289	Hsd3b7	AI195443|BB098564	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 7	protein-coding
mm_158402.1	chrX	136837445	136837453	-	1	NA	3' UTR (NM_011123, exon 7 of 7)	3' UTR (NM_011123, exon 7 of 7)	14703	NM_001290562	18823	Mm.1268	NM_011123	ENSMUSG00000031425	Plp1	DM20|Plp|jimpy|jp|msd|rsh	proteolipid protein (myelin) 1	protein-coding
mm_103015.1	chr11	69734852	69734860	-	1	NA	exon (NM_001291068, exon 29 of 29)	exon (NM_001291068, exon 29 of 29)	23777	NM_001291068	20020	Mm.16533	NM_009089	ENSMUSG00000005198	Polr2a	220kDa|Rpb1|Rpo2-1	polymerase (RNA) II (DNA directed) polypeptide A	protein-coding
mm_44895.1	chr5	35105692	35105720	-	1	NA	promoter-TSS (NM_013587)	promoter-TSS (NM_013587)	-9	NM_013587	16976	Mm.277661	NM_013587	ENSMUSG00000029103	Lrpap1	AA617339|AI790446|AU042172|C77774|HBP44|RAP	low density lipoprotein receptor-related protein associated protein 1	protein-coding
mm_148408.1	chr19	3907260	3907273	+	1	NA	promoter-TSS (NM_001136091)	promoter-TSS (NM_001136091)	-133	NM_001136091	27060	Mm.271689	NM_016921	ENSMUSG00000001750	Tcirg1	ATP6N1C|ATP6a3|Atp6i|OC-116|OPTB1|Stv1|TIRC7|Vph1|oc	T cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 protein A3	protein-coding
mm_162054.1	chrX	7766546	7766546	+	1	NA	intron (NM_001271489, intron 2 of 9)	intron (NM_001271489, intron 2 of 9)	2505	NM_001271491	209446	Mm.249142	NM_172472	ENSMUSG00000000134	Tfe3	F830016E06Rik|Tcfe3|Tfe-3|bHLHe33	transcription factor E3	protein-coding
mm_7689.1	chr1	128614871	128614881	-	1	NA	Intergenic	Intergenic	-22577	NM_009911	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding
mm_165082.1	chr19	46654922	46654959	-	1	NA	3' UTR (NM_001177813, exon 4 of 4)	3' UTR (NM_001177813, exon 4 of 4)	18060	NM_007809	13074	Mm.1262	NM_007809	ENSMUSG00000003555	Cyp17a1	Cyp17|p450c17	cytochrome P450, family 17, subfamily a, polypeptide 1	protein-coding
mm_122159.1	chr14	31374739	31374761	-	1	NA	3' UTR (NM_001347585, exon 8 of 8)	3' UTR (NM_001347585, exon 8 of 8)	38026	NM_009796	12339	Mm.201535	NM_009796	ENSMUSG00000021893	Capn7	AU022319|PalBH	calpain 7	protein-coding
mm_116083.1	chr13	28523167	28523169	-	1	NA	intron (NR_045053, intron 7 of 8)	intron (NR_045053, intron 7 of 8)	187705	NR_105787	102466635		NR_105787	ENSMUSG00000099158	Mir6368	Gm27800|mmu-mir-6368	microRNA 6368	ncRNA
mm_4193.1	chr1	171225271	171225332	+	1	NA	non-coding (NR_131173, exon 2 of 3)	non-coding (NR_131173, exon 2 of 3)	247	NM_013474	11807	Mm.389209	NM_013474	ENSMUSG00000005681	Apoa2	Alp-2|Apo-AII|ApoA-II|ApoAII|Apoa-2|Hdl-1	apolipoprotein A-II	protein-coding
mm_8457.1	chr1	153186072	153186092	-	1	NA	5' UTR (NM_008485, exon 2 of 24)	5' UTR (NM_008485, exon 2 of 24)	365	NM_008485	16782	Mm.329272	NM_008485	ENSMUSG00000026479	Lamc2	AA589349	laminin, gamma 2	protein-coding
mm_50697.1	chr6	51598918	51598930	+	1	NA	Intergenic	B3A|SINE|B2	54401	NM_001127348	71982	Mm.294166	NM_028035	ENSMUSG00000038301	Snx10	2410004M09Rik	sorting nexin 10	protein-coding
mm_45610.1	chr5	75828479	75828491	-	1	NA	Intergenic	L2a|LINE|L2	149943	NM_010612	16542	Mm.285	NM_010612	ENSMUSG00000062960	Kdr	6130401C07|Flk-1|Flk1|Krd-1|Ly73|VEGFR-2|VEGFR2|sVEGFR-2	kinase insert domain protein receptor	protein-coding
mm_65646.1	chr7	28055164	28055168	-	1	NA	Intergenic	Intergenic	-5074	NM_011874	23996	Mm.29582	NM_011874	ENSMUSG00000030603	Psmc4	CIP21|MIP224	proteasome (prosome, macropain) 26S subunit, ATPase, 4	protein-coding
mm_160670.1	chr9	123178278	123178278	-	1	NA	intron (NM_133974, intron 6 of 8)	ORR1F|LTR|ERVL-MaLR	27332	NM_011606	21922	Mm.34588	NM_011606	ENSMUSG00000025784	Clec3b	Tna	C-type lectin domain family 3, member b	protein-coding
mm_93790.1	chr10	120686245	120686253	-	1	NA	Intergenic	Intergenic	-79483	NR_038000	70874	Mm.427286	NR_038000	ENSMUSG00000044544	4921513I03Rik	-	RIKEN cDNA 4921513I03 gene	ncRNA
mm_105963.1	chr11	115463646	115463661	-	1	NA	intron (NM_001080934, intron 1 of 3)	intron (NM_001080934, intron 1 of 3)	1180	NM_001080934	217316	Mm.25773	NM_001080934	ENSMUSG00000045775	Slc16a5	A130015N09Rik|MCT 5|MCT 6|MCT5	solute carrier family 16 (monocarboxylic acid transporters), member 5	protein-coding
mm_116606.1	chr13	48819681	48819694	-	1	NA	intron (NM_011078, intron 9 of 21)	intron (NM_011078, intron 9 of 21)	51198	NM_011078	18676	Mm.486213	NM_011078	ENSMUSG00000038025	Phf2	GRC5	PHD finger protein 2	protein-coding
mm_72840.1	chr8	88294223	88294236	+	1	NA	promoter-TSS (NM_001037724)	promoter-TSS (NM_001037724)	25	NM_001037724	11513	Mm.288206	NM_007406	ENSMUSG00000031659	Adcy7	AA407758	adenylate cyclase 7	protein-coding
mm_153690.1	chr19	44397045	44397055	-	1	NA	3' UTR (NM_009127, exon 6 of 6)	3' UTR (NM_009127, exon 6 of 6)	10659	NM_009127	20249	Mm.267377	NM_009127	ENSMUSG00000037071	Scd1	AA589638|AI265570|Scd|Scd-1|ab	stearoyl-Coenzyme A desaturase 1	protein-coding
mm_98088.1	chr11	86587282	86587291	+	1	NA	intron (NM_029478, intron 10 of 11)	intron (NM_029478, intron 10 of 11)	-3128	NR_029738	387140		NR_029738	ENSMUSG00000065455	Mir21a	Mir21|Mirn21|mmu-mir-21|mmu-mir-21a	microRNA 21a	ncRNA
mm_28574.1	chr3	93445353	93445362	-	1	NA	exon (NM_001163098, exon 2 of 2)	exon (NM_001163098, exon 2 of 2)	3027	NM_001163098	99681	Mm.316671	NM_001163098	ENSMUSG00000052415	Tchh	AHF|AI597080|Thh	trichohyalin	protein-coding
mm_13475.1	chr2	105689579	105689587	+	1	NA	intron (NM_001310146, intron 4 of 9)	intron (NM_001310146, intron 4 of 9)	7120	NM_001310145	18508	Mm.3608	NM_013627	ENSMUSG00000027168	Pax6	1500038E17Rik|AEY11|Dey|Gsfaey11|Pax-6|Sey	paired box 6	protein-coding
mm_131470.1	chr16	17045106	17045143	+	1	NA	3' UTR (NM_011949, exon 9 of 9)	3' UTR (NM_011949, exon 9 of 9)	-25015	NM_023249	106369	Mm.237941	NM_023249	ENSMUSG00000022773	Ypel1	0610009L05Rik|1700016N17Rik|1700019O22Rik|4921520K19Rik|4930511F14Rik|AV118478|DGL-1|Dgl1|Ppil2|mdgl-1	yippee-like 1 (Drosophila)	protein-coding
mm_112103.1	chr12	112785484	112785495	-	1	NA	Intergenic	Intergenic	-23486	NM_145450	217887	Mm.186678	NM_145450	ENSMUSG00000037594	BC022687	AW050009|C130001I08Rik|Flj20080	cDNA sequence BC022687	protein-coding
mm_141479.1	chr17	31165046	31165053	-	1	NA	promoter-TSS (NM_009362)	promoter-TSS (NM_009362)	4	NM_009362	21784	Mm.2854	NM_009362	ENSMUSG00000024032	Tff1	Bcei|PS2	trefoil factor 1	protein-coding
mm_77888.1	chr9	7344358	7344406	+	1	NA	promoter-TSS (NM_001320077)	promoter-TSS (NM_001320077)	-15	NM_001320077	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_108249.1	chr12	78226670	78226680	+	1	NA	promoter-TSS (NM_172952)	promoter-TSS (NM_172952)	20	NM_145965	268566	Mm.341742	NM_145965	ENSMUSG00000047454	Gphn	5730552E08Rik|AI662856|BC027112|C230040D23|GPH|GPHRYN|geph	gephyrin	protein-coding
mm_42135.1	chr5	111235353	111235374	+	1	NA	intron (NM_001267622, intron 11 of 22)	intron (NM_001267622, intron 11 of 22)	-95334	NM_001301644	56305	Mm.200516	NM_019640	ENSMUSG00000050017	Pitpnb	PI-TP-beta	phosphatidylinositol transfer protein, beta	protein-coding
mm_129154.1	chr15	76232080	76232096	-	1	NA	promoter-TSS (NM_001163542)	promoter-TSS (NM_001163542)	-710	NM_011117	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
mm_35505.1	chr4	41093424	41093440	-	1	NA	3' UTR (NM_016689, exon 6 of 6)	3' UTR (NM_016689, exon 6 of 6)	4751	NM_016689	11828	Mm.34043	NM_016689	ENSMUSG00000028435	Aqp3	AQP-2	aquaporin 3	protein-coding
mm_15430.1	chr2	157134485	157134487	+	1	NA	intron (NM_018851, intron 1 of 15)	intron (NM_018851, intron 1 of 15)	736	NM_001139520	56045	Mm.248478	NM_018851	ENSMUSG00000027639	Samhd1	E330031J07Rik|Mg11	SAM domain and HD domain, 1	protein-coding
mm_57207.1	chr6	122851091	122851101	-	1	NA	exon (NM_009779, exon 2 of 2)	exon (NM_009779, exon 2 of 2)	5061	NM_009779	12267	Mm.2408	NM_009779	ENSMUSG00000040552	C3ar1	AZ3B|C3AR|HNFAG09	complement component 3a receptor 1	protein-coding
mm_66856.1	chr7	52015711	52015723	-	1	NA	promoter-TSS (NM_001195601)	promoter-TSS (NM_001195601)	-1	NM_001195601	100503036	Mm.279725	NM_001195601	ENSMUSG00000094445	1700015G11Rik	Ccdc179	RIKEN cDNA 1700015G11 gene	protein-coding
mm_124351.1	chr14	104467985	104468041	-	1	NA	promoter-TSS (NM_011143)	promoter-TSS (NM_011143)	-14	NM_011143	18996	Mm.246550	NM_011143	ENSMUSG00000048349	Pou4f1	Brn-3|Brn-3.0|Brn3|Brn3.0|Brn3a|E130119J07Rik	POU domain, class 4, transcription factor 1	protein-coding
mm_71828.1	chr8	68896691	68896701	+	1	NA	exon (NM_008509, exon 6 of 10)	exon (NM_008509, exon 6 of 10)	16141	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_126983.1	chr15	93804672	93804675	+	1	NA	Intergenic	L1MC3|LINE|L1	122438	NR_045737	77248	Mm.410768	NR_045737		9430014N10Rik	-	RIKEN cDNA 9430014N10 gene	ncRNA
mm_155791.1	chrX	98148720	98148782	+	1	NA	promoter-TSS (NM_013476)	promoter-TSS (NM_013476)	-6	NM_013476	11835	Mm.39005	NM_013476	ENSMUSG00000046532	Ar	AW320017|Tfm	androgen receptor	protein-coding
mm_9453.1	chr1	172632792	172632809	-	1	NA	exon (NM_026725, exon 1 of 2)	exon (NM_026725, exon 1 of 2)	174	NM_026725	68440	Mm.33024	NM_026725	ENSMUSG00000026544	Dusp23	1300005N15Rik|LDP-3	dual specificity phosphatase 23	protein-coding
mm_161668.1	chr17	13061085	13061085	+	1	NA	promoter-TSS (NM_009341)	promoter-TSS (NM_009341)	-26	NM_009341	21462	Mm.264651	NM_009341	ENSMUSG00000055602	Tcp10b	D17Leh66B|D17Leh66ba|T66B-a|Tcp-10b|Tcp-10bt	t-complex protein 10b	protein-coding
mm_23618.1	chr3	65666261	65666293	+	1	NA	promoter-TSS (NM_001037923)	promoter-TSS (NM_001037923)	49	NM_001166659	624866	Mm.296317	NM_001037923	ENSMUSG00000074579	Lekr1	EG546798|EG624866|Gm6534	leucine, glutamate and lysine rich 1	protein-coding
mm_92020.1	chr10	62379920	62379930	-	1	NA	promoter-TSS (NM_010438)	promoter-TSS (NM_010438)	-17	NM_010438	15275	Mm.196605	NM_010438	ENSMUSG00000037012	Hk1	BB404130|Hk-1|Hk1-s|dea|mHk1-s	hexokinase 1	protein-coding
mm_108026.1	chr12	73713912	73713916	+	1	NA	intron (NM_001313977, intron 10 of 14)	intron (NM_001313977, intron 10 of 14)	129118	NM_008856	18755	Mm.341677	NM_008856	ENSMUSG00000021108	Prkch	Pkch	protein kinase C, eta	protein-coding
mm_136911.1	chr17	13016955	13016985	+	1	NA	3' UTR (NM_013671, exon 5 of 5)	3' UTR (NM_013671, exon 5 of 5)	9131	NM_013671	20656	Mm.290876	NM_013671	ENSMUSG00000006818	Sod2	MnSOD|Sod-2	superoxide dismutase 2, mitochondrial	protein-coding
mm_145760.1	chr18	64888904	64888921	+	1	NA	intron (NM_001114386, intron 1 of 30)	intron (NM_001114386, intron 1 of 30)	1156	NM_001114386	83814	Mm.98668	NM_031881	ENSMUSG00000024589	Nedd4l	1300012C07Rik|Nedd4-2|Nedd4b	neural precursor cell expressed, developmentally down-regulated gene 4-like	protein-coding
mm_74018.1	chr8	121544395	121544425	+	1	NA	promoter-TSS (NR_045903)	promoter-TSS (NR_045903)	22	NR_045903	72259	Mm.396206	NR_045903	ENSMUSG00000097424	1700030M09Rik	-	RIKEN cDNA 1700030M09 gene	ncRNA
mm_37445.1	chr4	123350066	123350069	-	1	NA	3' UTR (NM_001199137, exon 93 of 93)	3' UTR (NM_001199137, exon 93 of 93)	-6815	NM_007558	12163	Mm.439749	NM_007558	ENSMUSG00000032726	Bmp8a	Bmp7r1|OP-2|OP2	bone morphogenetic protein 8a	protein-coding
mm_129794.1	chr15	82852725	82852737	-	1	NA	exon (NM_013836, exon 2 of 5)	exon (NM_013836, exon 2 of 5)	45730	NR_027799	21378	Mm.417272	NR_027799		Tbrg3	TB-11	transforming growth factor beta regulated gene 3	ncRNA
mm_122355.1	chr14	38998774	38998777	-	1	NA	intron (NM_001190187, intron 2 of 9)	intron (NM_001190187, intron 2 of 9)	100473	NR_045713	75170	Mm.372967	NR_045713	ENSMUSG00000093528	Nrg3os	4930529F24Rik	neuregulin 3, opposite strand	ncRNA
mm_96968.1	chr11	70647876	70647904	+	1	NA	promoter-TSS (NM_024211)	promoter-TSS (NM_024211)	603	NM_027445	70510	Mm.261818	NM_027445	ENSMUSG00000040746	Rnf167	0610010G05Rik|5730408C10Rik|AU019305|AV328608	ring finger protein 167	protein-coding
mm_95048.1	chr11	32296492	32296492	+	1	NA	promoter-TSS (NM_008218).2	promoter-TSS (NM_008218).2	0	NM_001083955	110257	Mm.196110	NM_001083955	ENSMUSG00000069917	Hba-a2	-	hemoglobin alpha, adult chain 2	protein-coding
mm_104330.1	chr11	93995186	93995196	-	1	NA	promoter-TSS (NM_001199204)	promoter-TSS (NM_001199204)	-900	NM_001199203	70834	Mm.260737	NM_027569	ENSMUSG00000020859	Spag9	3110018C07Rik|4733401I23Rik|4831406C20Rik|AW552012|JLP|JSAP2|JSAP2a|Jip4|Mapk8ip4|syd1	sperm associated antigen 9	protein-coding
mm_140137.1	chr17	79653377	79653390	+	1	NA	intron (NM_201361, intron 4 of 10)	MTD|LTR|ERVL-MaLR	38483	NM_201361	381110	Mm.209801	NM_201361	ENSMUSG00000036368	Rmdn2	AW061290|Fam82a1|RMD-2|mRMD-2	regulator of microtubule dynamics 2	protein-coding
mm_13308.1	chr2	102658678	102658695	+	1	NA	promoter-TSS (NM_001077514)	promoter-TSS (NM_001077514)	3	NM_001077514	20511	Mm.267547	NM_011393	ENSMUSG00000005089	Slc1a2	1700091C19Rik|2900019G14Rik|AI159670|Eaat2|GLT-1|GLT1|MGLT1	solute carrier family 1 (glial high affinity glutamate transporter), member 2	protein-coding
mm_82697.1	chr9	22389114	22389196	-	1	NA	promoter-TSS (NM_028390)	promoter-TSS (NM_028390)	51	NM_028390	68743	Mm.282751	NM_028390	ENSMUSG00000036777	Anln	1110037A17Rik|2900037I21Rik|C78101|Scraps	anillin, actin binding protein	protein-coding
mm_56492.1	chr6	99203128	99203131	-	1	NA	intron (NM_001347345, intron 4 of 19)	intron (NM_001347345, intron 4 of 19)	63386	NM_001197321	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_51762.1	chr6	87851172	87851243	+	1	NA	promoter-TSS (NM_013493)	promoter-TSS (NM_013493)	-101	NM_001347325	12785	Mm.290251	NM_013493	ENSMUSG00000030057	Cnbp	AA408710|Cnbp1|Znf9	cellular nucleic acid binding protein	protein-coding
mm_3189.1	chr1	135799963	135799969	+	1	NA	intron (NM_001112702, intron 1 of 8)	intron (NM_001112702, intron 1 of 8)	455	NM_001112702	21952	Mm.44379	NM_021467	ENSMUSG00000026418	Tnni1	2700018B22Rik|AI747285|ssTnI	troponin I, skeletal, slow 1	protein-coding
mm_108065.1	chr12	73940545	73940574	+	1	NA	exon (NM_010431, exon 10 of 15)	exon (NM_010431, exon 10 of 15)	-23971	NM_178392	75627	Mm.25937	NM_178392	ENSMUSG00000021113	Snapc1	2700033G17Rik|AU015787	small nuclear RNA activating complex, polypeptide 1	protein-coding
mm_95654.1	chr11	53752969	53752973	+	1	NA	Intergenic	RMER19A|LTR|ERVK	10683	NR_106131	102465772		NR_106131	ENSMUSG00000099153	Mir7671	Gm27802|mmu-mir-7671	microRNA 7671	ncRNA
mm_102238.1	chr11	54971953	54971954	-	1	NA	Intergenic	Intergenic	-9013	NM_001271455	57783	Mm.259671	NM_021327	ENSMUSG00000020400	Tnip1	ABIN|ABIN-1|ABIN1|AU018810|Naf1|Nef|VAN	TNFAIP3 interacting protein 1	protein-coding
mm_165844.1	chr4	3786213	3786215	+	1	NA	intron (NM_010747, intron 12 of 12)	intron (NM_010747, intron 12 of 12)	49441	NM_026147	67427	Mm.21938	NM_026147	ENSMUSG00000028234	Rps20	4632426K06Rik|Dsk4	ribosomal protein S20	protein-coding
mm_125858.1	chr15	75155308	75155329	+	1	NA	promoter-TSS (NM_001310438)	promoter-TSS (NM_001310438)	57	NM_001310438	546644		NM_008531	ENSMUSG00000022582	Ly6g	Gr-1|Gr1|Ly-6G	lymphocyte antigen 6 complex, locus G	protein-coding
mm_88442.1	chr10	77546140	77546157	+	1	NA	exon (NM_008404, exon 4 of 16)	exon (NM_008404, exon 4 of 16)	15800	NM_008404	16414	Mm.1137	NM_008404	ENSMUSG00000000290	Itgb2	2E6|AI528527|Cd18|LAD|LCAMB|Lfa1|MF17	integrin beta 2	protein-coding
mm_140544.1	chr17	6827800	6827835	-	1	NA	Intergenic	CpG	-45037	NM_009510	22350	Mm.277812	NM_009510	ENSMUSG00000052397	Ezr	AW146364|R75297|Vil2|p81	ezrin	protein-coding
mm_110580.1	chr12	56521389	56521397	-	1	NA	intron (NR_045082, intron 1 of 6)	intron (NR_045082, intron 1 of 6)	8027	NR_045082	104798	Mm.310950	NR_045082		E030019B13Rik	AI413669	RIKEN cDNA E030019B13 gene	ncRNA
mm_103434.1	chr11	75847697	75847702	-	1	NA	intron (NR_136932, intron 4 of 4)	intron (NR_136932, intron 4 of 4)	-51639	NM_007873	13447	Mm.5137	NM_007873	ENSMUSG00000020848	Doc2b	-	double C2, beta	protein-coding
mm_108047.1	chr12	73908161	73908170	+	1	NA	5' UTR (NM_010431, exon 1 of 15)	5' UTR (NM_010431, exon 1 of 15)	298	NM_001313919	15251	Mm.3879	NM_010431	ENSMUSG00000021109	Hif1a	AA959795|HIF-1-alpha|HIF1-alpha|HIF1alpha|MOP1|bHLHe78	hypoxia inducible factor 1, alpha subunit	protein-coding
mm_66437.1	chr7	44815665	44815682	-	1	NA	promoter-TSS (NM_030693)	promoter-TSS (NM_030693)	-15	NM_030693	107503	Mm.389890	NM_030693	ENSMUSG00000038539	Atf5	AFTA|Atf7|Atfx|ODA-10	activating transcription factor 5	protein-coding
mm_161824.1	chr17	74323869	74323869	-	1	NA	promoter-TSS (NM_024428)	promoter-TSS (NM_024428)	75	NM_024428	66310	Mm.28536	NM_024428	ENSMUSG00000024067	Dpy30	2810410M20Rik|C87842	dpy-30, histone methyltransferase complex regulatory subunit	protein-coding
mm_66954.1	chr7	62416174	62416193	-	1	NA	Intergenic	Intergenic	3956	NM_011746	22652	Mm.146	NM_011746	ENSMUSG00000070527	Mkrn3	D7H15S9-1|Zfp127	makorin, ring finger protein, 3	protein-coding
mm_21392.1	chr2	157561980	157562014	-	1	NA	3' UTR (NM_010923, exon 3 of 3)	3' UTR (NM_010923, exon 3 of 3)	1919	NM_180960	18111	Mm.34330	NM_010923	ENSMUSG00000067786	Nnat	5730414I02Rik|AW107673|Peg5	neuronatin	protein-coding
mm_115953.1	chr13	23752196	23752210	-	1	NA	promoter-TSS (NM_178203)	promoter-TSS (NM_178203)	-177	NM_178203	319150		NM_178203	ENSMUSG00000069267	Hist1h3b	H3-53	histone cluster 1, H3b	protein-coding
mm_141691.1	chr17	33975032	33975055	-	1	NA	non-coding (NR_004446, exon 6 of 6)	non-coding (NR_004446, exon 6 of 6)	3748	NR_004446	630499	Mm.440940	NM_001081015		H2-K2	EG630499|Gm7035|H-2K1|H-2K1K|H-2K2|H2-K1	histocompatibility 2, K region locus 2	pseudo
mm_28266.1	chr3	88745057	88745068	-	1	NA	3' UTR (NM_018804, exon 4 of 4)	3' UTR (NM_018804, exon 4 of 4)	27537	NM_018804	229521	Mm.379376	NM_018804	ENSMUSG00000068923	Syt11	1500004A13Rik|3632445O20Rik|5430404N14Rik|6530420C11Rik|AI851970	synaptotagmin XI	protein-coding
mm_113989.1	chr13	52582813	52582819	+	1	NA	promoter-TSS (NM_001198977)	promoter-TSS (NM_001198977)	-621	NM_001198977	20963	Mm.375031	NM_011518	ENSMUSG00000021457	Syk	Sykb	spleen tyrosine kinase	protein-coding
mm_140927.1	chr17	24223988	24223995	-	1	NA	exon (NM_007634, exon 17 of 17)	exon (NM_007634, exon 17 of 17)	-3222	NM_028056	72016	Mm.23881	NM_028056	ENSMUSG00000024118	1600002H07Rik	-	RIKEN cDNA 1600002H07 gene	protein-coding
mm_7574.1	chr1	124846024	124846026	-	1	NA	Intergenic	Intergenic	589702	NM_023735	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding
mm_149811.1	chr19	23893486	23893502	+	1	NA	exon (NM_177034, exon 2 of 13)	exon (NM_177034, exon 2 of 13)	134618	NM_177034	319924	Mm.22879	NM_177034	ENSMUSG00000024897	Apba1	6430513E09Rik|Lin-10|Mint|Mint1|Urop11|X11|X11alpha	amyloid beta (A4) precursor protein binding, family A, member 1	protein-coding
mm_30908.1	chr4	32424754	32424774	+	1	NA	intron (NM_001109661, intron 1 of 4)	intron (NM_001109661, intron 1 of 4)	7329	NM_001109661	12014	Mm.491223	NM_007521	ENSMUSG00000040270	Bach2	E030004N02Rik	BTB and CNC homology, basic leucine zipper transcription factor 2	protein-coding
mm_58833.1	chr7	16793531	16793541	+	1	NA	intron (NM_009201, intron 5 of 8)	intron (NM_009201, intron 5 of 8)	12190	NM_009201	20514	Mm.1056	NM_009201	ENSMUSG00000001918	Slc1a5	AAAT|ASCT2|ATBO|M7V1|M7VS1|R16|RDRC|Slc1a7	solute carrier family 1 (neutral amino acid transporter), member 5	protein-coding
mm_53140.1	chr6	125221826	125221841	+	1	NA	3' UTR (NM_001080557, exon 4 of 4)	3' UTR (NM_001080557, exon 4 of 4)	6252	NM_001080557	22317	Mm.32321	NM_009496	ENSMUSG00000030337	Vamp1	Syb-1|Syb1|VAMP-1|lew	vesicle-associated membrane protein 1	protein-coding
mm_158644.1	chrX	155338461	155338471	-	1	NA	promoter-TSS (NM_016764)	promoter-TSS (NM_016764)	-6	NM_001313711	53381	Mm.247542	NM_016764	ENSMUSG00000025289	Prdx4	AOE372|Prx-iv|Prx4|TRANK	peroxiredoxin 4	protein-coding
mm_161115.1	chr12	105147277	105147277	+	1	NA	intron (NM_013775, intron 1 of 3)	intron (NM_013775, intron 1 of 3)	244	NM_013775	27381	Mm.103653	NM_013775	ENSMUSG00000060863	Tcl1b2	-	T cell leukemia/lymphoma 1B, 2	protein-coding
mm_138176.1	chr17	34264936	34264958	+	1	NA	exon (NM_207105, exon 2 of 6)	exon (NM_207105, exon 2 of 6)	1720	NM_207105	14961	Mm.254067	NM_207105	ENSMUSG00000073421	H2-Ab1	AI845868|Abeta|H-2Ab|H2-Ab|I-Abeta|IAb|Ia-2|Ia2|Rmcs1	histocompatibility 2, class II antigen A, beta 1	protein-coding
mm_171173.1	chr3	32773122	32773128	+	1	NA	Intergenic	IAPLTR2b|LTR|ERVK	36062	NM_025316	66046	Mm.28058	NM_025316	ENSMUSG00000027673	Ndufb5	0610007D05Rik|AU015782|CI-SGDH|SGDH	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 5	protein-coding
mm_34523.1	chr4	149104202	149104231	+	1	NA	promoter-TSS (NM_001025296)	promoter-TSS (NM_001025296)	74	NM_001025296	13347	Mm.41433	NM_010044	ENSMUSG00000028974	Dffa	A330085O09Rik|DFF35|Dff45|ICAD|ICAD-L|ICAD-S	DNA fragmentation factor, alpha subunit	protein-coding
mm_22302.1	chr2	180334936	180334955	-	1	NA	promoter-TSS (NM_008093)	promoter-TSS (NM_008093)	-266	NM_008093	14464	Mm.388880	NM_008093	ENSMUSG00000015627	Gata5	-	GATA binding protein 5	protein-coding
mm_110424.1	chr12	46818750	46818788	-	1	NA	promoter-TSS (NM_021361)	promoter-TSS (NM_021361)	6	NM_021361	664883	Mm.247195	NM_021361	ENSMUSG00000021047	Nova1	9430099M15Rik|G630039L02|Nova-1	neuro-oncological ventral antigen 1	protein-coding
mm_31184.1	chr4	43519409	43519474	+	1	NA	exon (NM_009416, exon 4 of 9)	exon (NM_009416, exon 4 of 9)	4113	NM_009416	22004	Mm.646	NM_009416	ENSMUSG00000028464	Tpm2	Tpm-2|Trop-2	tropomyosin 2, beta	protein-coding
mm_75653.1	chr8	65129466	65129482	-	1	NA	promoter-TSS (NR_033217)	promoter-TSS (NR_033217)	63	NR_033217	407795	Mm.387876	NR_033217	ENSMUSG00000074300	BC030870	-	cDNA sequence BC030870	ncRNA
mm_146069.1	chr18	70472622	70472635	+	1	NA	promoter-TSS (NM_001289649)	promoter-TSS (NM_001289649)	0	NM_001289649	170461	Mm.83623	NM_029019	ENSMUSG00000079608	Stard6	1700011K09Rik|4833424I06Rik|4933429L05Rik|AI644424	StAR-related lipid transfer (START) domain containing 6	protein-coding
mm_120802.1	chr14	74797687	74797693	+	1	NA	intron (NM_001252132, intron 13 of 18)	intron (NM_001252132, intron 13 of 18)	65393	NM_016903	13885	Mm.38055	NM_016903	ENSMUSG00000021996	Esd	Es-10|Es10|FGH|sid478	esterase D/formylglutathione hydrolase	protein-coding
mm_138127.1	chr17	34187042	34187052	+	1	NA	promoter-TSS (NM_001161730)	promoter-TSS (NM_001161730)	283	NM_013585	16912	Mm.390983	NM_013585	ENSMUSG00000096727	Psmb9	Lmp-2|Lmp2	proteasome (prosome, macropain) subunit, beta type 9 (large multifunctional peptidase 2)	protein-coding
mm_44957.1	chr5	36696625	36696686	-	1	NA	promoter-TSS (NM_001081232)	promoter-TSS (NM_001081232)	-634	NM_001081232	320661	Mm.26480	NM_177221	ENSMUSG00000029190	D5Ertd579e	9030221A05Rik|A930018H20Rik|Kiaa0232	DNA segment, Chr 5, ERATO Doi 579, expressed	protein-coding
mm_47355.1	chr5	122771404	122771406	-	1	NA	intron (NM_145358, intron 1 of 15)	intron (NM_145358, intron 1 of 15)	8005	NM_001199676	207565	Mm.289237	NM_145358	ENSMUSG00000029471	Camkk2	6330570N16Rik|AW061083|mKIAA0787	calcium/calmodulin-dependent protein kinase kinase 2, beta	protein-coding
mm_152562.1	chr19	11586737	11586751	-	1	NA	3' UTR (NM_026835, exon 7 of 7)	3' UTR (NM_026835, exon 7 of 7)	18060	NM_026835	68774	Mm.290390	NM_026835	ENSMUSG00000024679	Ms4a6d	1110058E16Rik|AI447446|Ms4a11	membrane-spanning 4-domains, subfamily A, member 6D	protein-coding
mm_125650.1	chr15	62741061	62741070	+	1	NA	Intergenic	Intergenic	-521614	NR_003523	67552	Mm.484027	NM_026230		H2afy3	4933432H23Rik	H2A histone family, member Y3	pseudo
mm_41142.1	chr5	87887525	87887531	+	1	NA	exon (NM_027128, exon 4 of 10)	exon (NM_027128, exon 4 of 10)	1833	NM_027128	69592	Mm.389652	NM_027128	ENSMUSG00000009580	Odam	2310011G06Rik|APIN	odontogenic, ameloblast asssociated	protein-coding
mm_146167.1	chr18	75245852	75245855	+	1	NA	intron (NM_027727, intron 16 of 16)	intron (NM_027727, intron 16 of 16)	51464	NR_045394	100503117	Mm.250517	NR_045393	ENSMUSG00000102047	2010010A06Rik	5033420E22Rik	RIKEN cDNA 2010010A06 gene	ncRNA
mm_37252.1	chr4	118291306	118291325	-	1	NA	promoter-TSS (NM_011213)	promoter-TSS (NM_011213)	82	NM_011213	19268	Mm.29855	NM_011213	ENSMUSG00000033295	Ptprf	AA591035|LAR|LARS|RPTP-LAR	protein tyrosine phosphatase, receptor type, F	protein-coding
mm_96584.1	chr11	69088516	69088553	+	1	NA	promoter-TSS (NM_009497)	promoter-TSS (NM_009497)	6	NM_009497	22318	Mm.28643	NM_009497	ENSMUSG00000020894	Vamp2	Syb-2|Syb2|sybII	vesicle-associated membrane protein 2	protein-coding
mm_74099.1	chr8	122613902	122613920	+	1	NA	intron (NM_021502, intron 2 of 4)	intron (NM_021502, intron 2 of 4)	2285	NM_021502	59005	Mm.38746	NM_021502	ENSMUSG00000015013	Trappc2l	1810017G16Rik|AB030200|Hspc176|Tca17	trafficking protein particle complex 2-like	protein-coding
mm_128997.1	chr15	74841756	74841764	-	1	NA	promoter-TSS (NM_001033229)	promoter-TSS (NM_001033229)	-117	NM_001033229	110115	Mm.322606	NM_001033229	ENSMUSG00000075604	Cyp11b1	AA389061|CPN1|Cyp11b|Cyp11b-1|FHI	cytochrome P450, family 11, subfamily b, polypeptide 1	protein-coding
mm_117419.1	chr13	74337432	74337436	-	1	NA	exon (NM_023281, exon 6 of 15)	exon (NM_023281, exon 6 of 15)	12806	NM_023281	66945	Mm.158231	NM_023281	ENSMUSG00000021577	Sdha	1500032O14Rik|2310034D06Rik|4921513A11|C81073|FP|SDH2|SDHF	succinate dehydrogenase complex, subunit A, flavoprotein (Fp)	protein-coding
mm_24964.1	chr3	96699303	96699304	+	1	NA	intron (NM_018812, intron 1 of 14)	intron (NM_018812, intron 1 of 14)	2227	NM_018812	229615	Mm.1635	NM_018812	ENSMUSG00000028101	Pias3	Pias3l	protein inhibitor of activated STAT 3	protein-coding
mm_22116.1	chr2	170142674	170142678	-	1	NA	promoter-TSS (NM_001159683)	promoter-TSS (NM_001159683)	-1	NM_001159683	228913	Mm.22858	NM_001033299	ENSMUSG00000052056	Zfp217	4933431C08Rik|AW987152|Gm562|ZABC1|Znf217	zinc finger protein 217	protein-coding
mm_45187.1	chr5	52115772	52115791	-	1	NA	Intergenic	CpG	20236	NR_105845	102466648		NR_105845	ENSMUSG00000098726	Mir6417	Gm27334|mmu-mir-6417	microRNA 6417	ncRNA
mm_19373.1	chr2	91183978	91184023	-	1	NA	promoter-TSS (NM_145527)	promoter-TSS (NM_145527)	-953	NM_145527	228355	Mm.36410	NM_145527	ENSMUSG00000040687	Madd	9630059K23Rik|IG20	MAP-kinase activating death domain	protein-coding
mm_15053.1	chr2	152905008	152905010	+	1	NA	Intergenic	Intergenic	-6343	NM_001081044	228785	Mm.250604	NM_001081044	ENSMUSG00000027470	Mylk2	9830004H17Rik|BB138278	myosin, light polypeptide kinase 2, skeletal muscle	protein-coding
mm_65179.1	chr7	19696293	19696329	-	1	NA	TTS (NM_009696)	TTS (NM_009696)	2087	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_159958.1	chr6	87981526	87981526	-	1	NA	promoter-TSS (NR_026990)	promoter-TSS (NR_026990)	-44	NM_198622	243529	Mm.33796	NM_198622	ENSMUSG00000044927	H1fx	Gm461|H1.10|H1X	H1 histone family, member X	protein-coding
mm_171534.1	chr4	146806138	146806150	-	1	NA	Intergenic	RLTR27|LTR|ERVK	-215706	NM_001177767	100043034	Mm.422606	NM_001177767	ENSMUSG00000067919	Rex2	Gm13138|OTTMUSG00000010655	reduced expression 2	protein-coding
mm_57137.1	chr6	122609854	122609868	-	1	NA	exon (NM_008108, exon 1 of 2)	exon (NM_008108, exon 1 of 2)	226	NM_008108	14562	Mm.299742	NM_008108	ENSMUSG00000030117	Gdf3	C78318|Gdf-3|Vgr-2|Vgr2|ecat9	growth differentiation factor 3	protein-coding
mm_46639.1	chr5	108532414	108532417	-	1	NA	intron (NM_007756, intron 2 of 3)	intron (NM_007756, intron 2 of 3)	17612	NM_007756	12889	Mm.5195	NM_007756	ENSMUSG00000033615	Cplx1	921-S	complexin 1	protein-coding
mm_118771.1	chr14	22722408	22722417	+	1	NA	intron (NM_028275, intron 5 of 6)	intron (NM_028275, intron 5 of 6)	-179614	NR_046307	74896	Mm.444661	NR_046307		4930405A10Rik	4930456G20Rik	RIKEN cDNA 4930405A10 gene	ncRNA
mm_155919.1	chrX	102050838	102050853	+	1	NA	intron (NM_001163610, intron 1 of 7)	intron (NM_001163610, intron 1 of 7)	20462	NM_001278534	331474	Mm.23297	NM_183318	ENSMUSG00000049191	Rgag4	6430402L03Rik|Mar5|Mart5|mKIAA2001	retrotransposon gag domain containing 4	protein-coding
mm_55556.1	chr6	71271482	71271512	-	1	NA	promoter-TSS (NM_145568)	promoter-TSS (NM_145568)	-174	NR_106192	102465900		NR_106192	ENSMUSG00000098623	Mir8112	Gm27739|mmu-mir-8112	microRNA 8112	ncRNA
mm_17761.1	chr2	32784425	32784446	-	1	NA	promoter-TSS (NM_025619)	promoter-TSS (NM_025619)	-30	NM_025619	227736	Mm.441499	NM_025619	ENSMUSG00000038987	Cfap157	1700019L03Rik	cilia and flagella associated protein 157	protein-coding
mm_106631.1	chr11	120882930	120882936	-	1	NA	intron (NM_027745, intron 12 of 18)	intron (NM_027745, intron 12 of 18)	49939	NM_027745	71276	Mm.275751	NM_027745	ENSMUSG00000048445	Ccdc57	4933434G05Rik	coiled-coil domain containing 57	protein-coding
mm_114838.1	chr13	92575778	92575789	+	1	NA	exon (NM_030237, exon 1 of 1)	exon (NM_030237, exon 1 of 1)	449	NM_030237	79401	Mm.23520	NM_030237	ENSMUSG00000046957	Spz1	1700027M20Rik|AI429130	spermatogenic leucine zipper 1	protein-coding
mm_15135.1	chr2	153943946	153943952	+	1	NA	intron (NM_001034875, intron 3 of 15)	intron (NM_001034875, intron 3 of 15)	3087	NM_001034875	381399	Mm.315572	NM_001034875	ENSMUSG00000074665	Bpifb4	Gm1006|Lplunc4	BPI fold containing family B, member 4	protein-coding
mm_167583.1	chr9	45945787	45945803	-	1	NA	intron (NM_172257, intron 12 of 25)	intron (NM_172257, intron 12 of 25)	-6205	NR_106055	102465659		NR_106055	ENSMUSG00000098327	Mir7087	Gm27273|mmu-mir-7087	microRNA 7087	ncRNA
mm_31538.1	chr4	55464599	55464616	+	1	NA	Intergenic	L1MB3|LINE|L1	-45765	NR_040674	100415914	Mm.261765	NR_040674	ENSMUSG00000087070	Gm12505	OTTMUSG00000007226	predicted gene 12505	ncRNA
mm_39695.1	chr5	27057840	27057847	+	1	NA	intron (NM_207282, intron 1 of 25)	T-rich|Low_complexity|Low_complexity	8644	NM_207282	13483	Mm.42078	NM_010075	ENSMUSG00000061576	Dpp6	B930011P16Rik|D5Buc3|D5Buc4|D5Buc5|DPP VI|Dpp-6|Gm1377|In(5)6H-p|Peplb|Rw	dipeptidylpeptidase 6	protein-coding
mm_152104.1	chr19	6925331	6925366	-	1	NA	promoter-TSS (NM_001039494)	promoter-TSS (NM_001039494)	32	NM_001039494	67077	Mm.251306	NM_001039494	ENSMUSG00000050623	Tex40	1700019N12Rik|A430107B04Rik|MLZ-622	testis expressed 40	protein-coding
mm_92696.1	chr10	80676291	80676295	-	1	NA	promoter-TSS (NM_021462)	promoter-TSS (NM_021462)	0	NM_021462	17347	Mm.42126	NM_021462	ENSMUSG00000020190	Mknk2	2010016G11Rik|Gprk7|Mnk2	MAP kinase-interacting serine/threonine kinase 2	protein-coding
mm_82554.1	chr9	20976722	20976748	-	1	NA	promoter-TSS (NM_010333)	promoter-TSS (NM_010333)	58	NM_010333	14739	Mm.46493	NM_010333	ENSMUSG00000043895	S1pr2	1100001A16Rik|Edg5|Gpcr13|H218|LPb2|S1P2	sphingosine-1-phosphate receptor 2	protein-coding
mm_93057.1	chr10	88685030	88685034	-	1	NA	Intergenic	Intergenic	-2009	NM_011461	20728	Mm.21642	NM_011461	ENSMUSG00000004359	Spic	AU019198|C76795|Prf|Spi-C	Spi-C transcription factor (Spi-1/PU.1 related)	protein-coding
mm_27317.1	chr3	50366876	50366888	-	1	NA	3' UTR (NM_011990, exon 12 of 12)	3' UTR (NM_011990, exon 12 of 12)	76731	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_53403.1	chr6	131380908	131380919	+	1	NA	exon (NM_011733, exon 4 of 9)	exon (NM_011733, exon 4 of 9)	7537	NM_139117	56449	Mm.458000	NM_011733	ENSMUSG00000030189	Ybx3	Csda|Dpba|MSY3|MSY4|Yb2|dbpA|oxyR	Y box protein 3	protein-coding
mm_168223.1	chr10	79435464	79435469	+	1	NA	Intergenic	L1Md_F2|LINE|L1	-33492	NM_001104537	625029	Mm.469865	NM_001104537	ENSMUSG00000091381	Vmn2r83	EG625029	vomeronasal 2, receptor 83	protein-coding
mm_120814.1	chr14	75131274	75131278	+	1	NA	promoter-TSS (NM_027581)	promoter-TSS (NM_027581)	153	NM_001247984	18826	Mm.153911	NM_008879	ENSMUSG00000021998	Lcp1	AW536232|D14Ertd310e|LCP-1|Pls2|pp65	lymphocyte cytosolic protein 1	protein-coding
mm_71436.1	chr8	46507094	46507095	+	1	NA	intron (NM_001302163, intron 3 of 20)	intron (NM_001302163, intron 3 of 20)	16128	NM_001302163	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_148641.1	chr19	5480086	5480098	+	1	NA	exon (NM_021474, exon 8 of 11)	exon (NM_021474, exon 8 of 11)	5357	NM_001164352	58859	Mm.276367	NM_021474	ENSMUSG00000024909	Efemp2	0610011K11Rik|Fbln4|MBP1	epidermal growth factor-containing fibulin-like extracellular matrix protein 2	protein-coding
mm_35777.1	chr4	46404126	46404140	-	1	NA	promoter-TSS (NM_053149)	promoter-TSS (NM_053149)	50	NM_053149	93966	Mm.25793	NM_053149	ENSMUSG00000028332	Hemgn	4921524M03Rik|AI317176|EDAG|Hgn|mNDR	hemogen	protein-coding
mm_148455.1	chr19	4003291	4003333	+	1	NA	promoter-TSS (NM_021791)	promoter-TSS (NM_021791)	-73	NM_021791	60425	Mm.266972	NM_021791	ENSMUSG00000024871	Doc2g	D830013O18Rik	double C2, gamma	protein-coding
mm_154504.1	chrM	11946	11973	-	1	NA	NA	Intergenic	NA	NA								
mm_125656.1	chr15	63611448	63611471	+	1	NA	Intergenic	Intergenic	-131851	NR_045279	432958	Mm.255105	NR_045279		Gm20740	-	predicted gene, 20740	ncRNA
mm_158647.1	chrX	155340769	155340773	-	1	NA	Intergenic	Intergenic	-2311	NM_001313711	53381	Mm.247542	NM_016764	ENSMUSG00000025289	Prdx4	AOE372|Prx-iv|Prx4|TRANK	peroxiredoxin 4	protein-coding
mm_124306.1	chr14	103098992	103099045	-	1	NA	promoter-TSS (NM_001347601)	promoter-TSS (NM_001347601)	-14	NM_001347601	50789	Mm.214746	NM_015822	ENSMUSG00000022124	Fbxl3	AU041772|AW212966|FBK|Fbl3a|Fbxl3a|Ovtm|Play68	F-box and leucine-rich repeat protein 3	protein-coding
mm_105287.1	chr11	102447598	102447610	-	1	NA	promoter-TSS (NM_199200)	promoter-TSS (NM_199200)	59	NM_199200	217219	Mm.259924	NM_199200	ENSMUSG00000034685	Fam171a2	-	family with sequence similarity 171, member A2	protein-coding
mm_82642.1	chr9	22015257	22015284	-	1	NA	3' UTR (NM_010487, exon 7 of 7)	3' UTR (NM_010487, exon 7 of 7)	12282	NM_008925	19089	Mm.214593	NM_008925	ENSMUSG00000003402	Prkcsh	80K-H|PKCSH	protein kinase C substrate 80K-H	protein-coding
mm_148456.1	chr19	4003335	4003366	+	1	NA	promoter-TSS (NM_021791)	promoter-TSS (NM_021791)	-35	NM_021791	60425	Mm.266972	NM_021791	ENSMUSG00000024871	Doc2g	D830013O18Rik	double C2, gamma	protein-coding
mm_105917.1	chr11	115001588	115001638	-	1	NA	5' UTR (NM_134158, exon 1 of 4)	5' UTR (NM_134158, exon 1 of 4)	267	NM_134158	140497	Mm.2699	NM_134158	ENSMUSG00000044811	Cd300c2	CLM4|Cd300c|Cd300d|DIgR1|Igsf7|Lmir2|MAIR-II	CD300C molecule 2	protein-coding
mm_154218.1	chr19	59345747	59345853	-	1	NA	promoter-TSS (NM_001033222)	promoter-TSS (NM_001033222)	-20	NM_001033222	107368	Mm.27250	NM_001033222	ENSMUSG00000074746	Pdzd8	A630041P07Rik|AV329468|AW228944|Pdzk8	PDZ domain containing 8	protein-coding
mm_42809.1	chr5	121797713	121797725	+	1	NA	intron (NM_009125, intron 17 of 24)	intron (NM_009125, intron 17 of 24)	21554	NR_105998	102465624		NR_105998	ENSMUSG00000099063	Mir7031	Gm27859|mmu-mir-7031	microRNA 7031	ncRNA
mm_72070.1	chr8	71523521	71523527	+	1	NA	Intergenic	Intergenic	-11755	NM_032398	84094	Mm.260768	NM_032398	ENSMUSG00000034845	Plvap	MECA32|Pv1	plasmalemma vesicle associated protein	protein-coding
mm_172339.1	chr7	110501128	110501134	-	1	NA	intron (NM_177324, intron 2 of 40)	B2_Mm2|SINE|B2	113789	NM_177324	319934	Mm.102970	NM_177324	ENSMUSG00000038371	Sbf2	4833411B01Rik|AA414977|AI317167|B430219L04Rik|Mtmr13|mMTMH1	SET binding factor 2	protein-coding
mm_41155.1	chr5	87929854	87929865	+	1	NA	exon (NM_007786, exon 4 of 5)	exon (NM_007786, exon 4 of 5)	4226	NM_007786	12994	Mm.296303	NM_007786	ENSMUSG00000001622	Csn3	AW208918|CSN10|Csnk	casein kappa	protein-coding
mm_58323.1	chr6	146502040	146502060	-	1	NA	5' UTR (NM_019923, exon 1 of 57)	5' UTR (NM_019923, exon 1 of 57)	173	NM_010586	16439	Mm.7800	NM_010586	ENSMUSG00000030287	Itpr2	AI649341|InsP3R-2|InsP3R-5|Ip3r2|Itpr5|insP3R2	inositol 1,4,5-triphosphate receptor 2	protein-coding
mm_43367.1	chr5	135404929	135404936	+	1	NA	Intergenic	Intergenic	-10386	NM_148932	107939	Mm.28399	NM_148932	ENSMUSG00000053293	Pom121	2610027A18Rik|C80273|mKIAA0618	nuclear pore membrane protein 121	protein-coding
mm_164501.1	chr16	91633821	91633867	+	1	NA	intron (NM_010256, intron 11 of 21)	intron (NM_010256, intron 11 of 21)	13128	NM_010256	14450	Mm.4505	NM_010256	ENSMUSG00000022962	Gart	Gaps|Prgs	phosphoribosylglycinamide formyltransferase	protein-coding
mm_10071.1	chr1	194651829	194651860	-	1	NA	intron (NM_008882, intron 3 of 31)	intron (NM_008882, intron 3 of 31)	32015	NM_008882	18845	Mm.2251	NM_008882	ENSMUSG00000026640	Plxna2	2810428A13Rik|AA589422|AW457381|OCT|PlexA2|Plxn2|mKIAA0463	plexin A2	protein-coding
mm_141763.1	chr17	34269364	34269388	-	1	NA	TTS (NM_207105)	TTS (NM_207105)	6149	NM_207105	14961	Mm.254067	NM_207105	ENSMUSG00000073421	H2-Ab1	AI845868|Abeta|H-2Ab|H2-Ab|I-Abeta|IAb|Ia-2|Ia2|Rmcs1	histocompatibility 2, class II antigen A, beta 1	protein-coding
mm_133700.1	chr16	92946833	92946839	+	1	NA	Intergenic	Intergenic	-120762	NM_001111022	12394	Mm.4081	NM_009821	ENSMUSG00000022952	Runx1	AML1|CBF-alpha-2|Cbfa2|Pebp2a2|Pebpa2b	runt related transcription factor 1	protein-coding
mm_168074.1	chr10	111492910	111492924	+	1	NA	exon (NM_015781, exon 9 of 16)	exon (NM_015781, exon 9 of 16)	-7871	NR_033603	382421	Mm.245643	NR_033603		Gm5176	EG382421	high mobility group box 2 pseudogene	pseudo
mm_70466.1	chr8	11952590	11952624	+	1	NA	Intergenic	Intergenic	112086	NM_029326	75528	Mm.440342	NM_029326	ENSMUSG00000031512	Tex29	1700018L24Rik	testis expressed 29	protein-coding
mm_166391.1	chr5	134915386	134915406	-	1	NA	5' UTR (NM_020504, exon 1 of 2)	5' UTR (NM_020504, exon 1 of 2)	134	NM_020504	57255	Mm.86652	NM_020504	ENSMUSG00000008843	Cldn13	2500004B14Rik	claudin 13	protein-coding
mm_121490.1	chr14	121248730	121248733	+	1	NA	intron (NM_134082, intron 13 of 26)	intron (NM_134082, intron 13 of 26)	130499	NM_145465	223255	Mm.390756	NM_145465	ENSMUSG00000063410	Stk24	1810013H02Rik|C76483|MST-3|Mst3|STE20	serine/threonine kinase 24	protein-coding
mm_103409.1	chr11	75451110	75451127	-	1	NA	exon (NM_138950, exon 1 of 10)	exon (NM_138950, exon 1 of 10)	3599	NM_138950	192652	Mm.340378	NM_138950	ENSMUSG00000045374	Wdr81	BC054822|Gm883|mFLJ00182|nur5	WD repeat domain 81	protein-coding
mm_44667.1	chr5	29378320	29378335	-	1	NA	promoter-TSS (NM_020295)	promoter-TSS (NM_020295)	63	NM_020295	56873	Mm.41572	NM_020295	ENSMUSG00000010721	Lmbr1	1110048D14Rik|AU017641	limb region 1	protein-coding
mm_147110.1	chr18	35708389	35708406	-	1	NA	Intergenic	Intergenic	-5253	NM_029669	76594	Mm.108596	NM_029669	ENSMUSG00000024350	Dnajc18	2700075B01Rik|AU041129	DnaJ heat shock protein family (Hsp40) member C18	protein-coding
mm_34625.1	chr4	150569250	150569278	+	1	NA	intron (NM_001085492, intron 11 of 22)	CpG	82910	NM_173774	242773	Mm.29280	NM_173774	ENSMUSG00000039838	Slc45a1	C230078B22|Dnb5	solute carrier family 45, member 1	protein-coding
mm_40573.1	chr5	63815728	63815733	+	1	NA	intron (NM_029554, intron 1 of 3)	intron (NM_029554, intron 1 of 3)	3235	NM_029554	76261	Mm.38143	NM_029554	ENSMUSG00000060512	0610040J01Rik	AI662686	RIKEN cDNA 0610040J01 gene	protein-coding
mm_15510.1	chr2	158258226	158258232	+	1	NA	promoter-TSS (NM_177850)	promoter-TSS (NM_177850)	-12	NM_177850	329547	Mm.260883	NM_177850	ENSMUSG00000052922	Bpi	9230105K17Rik|Bpifd1	bactericidal permeablility increasing protein	protein-coding
mm_49135.1	chr6	8948952	8948963	+	1	NA	Intergenic	CpG	-1062	NM_008751	18231	Mm.46954	NM_008751	ENSMUSG00000046178	Nxph1	C130005L03Rik	neurexophilin 1	protein-coding
mm_113780.1	chr13	45403488	45403490	+	1	NA	intron (NM_153789, intron 2 of 6)	intron (NM_153789, intron 2 of 6)	13747	NM_153789	218203	Mm.212855	NM_153789	ENSMUSG00000038175	Mylip	9430057C20Rik|Mir	myosin regulatory light chain interacting protein	protein-coding
mm_151687.1	chr19	4306216	4306369	-	1	NA	promoter-TSS (NM_130863)	promoter-TSS (NM_130863)	-70	NM_001290818	110355	Mm.254144	NM_130863	ENSMUSG00000024858	Grk2	Adrbk-1|Adrbk1|Bark-1|beta ARK|betaARK1	G protein-coupled receptor kinase 2	protein-coding
mm_118554.1	chr14	17727397	17727401	+	1	NA	intron (NM_001113417, intron 1 of 9)	intron (NM_001113417, intron 1 of 9)	66439	NM_001113417	21834	Mm.32563	NM_009380	ENSMUSG00000021779	Thrb	Nr1a2|T3R[b]|T3Rbeta|Thrb1|Thrb2|c-erbAbeta	thyroid hormone receptor beta	protein-coding
mm_145795.1	chr18	65247117	65247127	+	1	NA	intron (NR_105742, intron 4 of 6)	intron (NR_105742, intron 4 of 6)	-1739	NR_029600	387231		NR_029600	ENSMUSG00000065402	Mir122	Mir122a|Mirn122a|mir-122|mmu-mir-122	microRNA 122	ncRNA
mm_55112.1	chr6	50384473	50384494	-	1	NA	intron (NM_001347213, intron 2 of 23)	ORR1E|LTR|ERVL-MaLR	-1646	NM_027881	71720	Mm.44153	NM_027881	ENSMUSG00000029822	Osbpl3	1200014M06Rik|6720421I08Rik|A530055M08|ORP-3|ORP3|OSBP3	oxysterol binding protein-like 3	protein-coding
mm_11074.1	chr2	27677235	27677295	+	1	NA	promoter-TSS (NM_011305)	promoter-TSS (NM_011305)	64	NM_011305	20181	Mm.24624	NM_011305	ENSMUSG00000015846	Rxra	9530071D11Rik|Nr2b1|RXRalpha1	retinoid X receptor alpha	protein-coding
mm_42942.1	chr5	122989745	122989762	+	1	NA	promoter-TSS (NM_001003953)	promoter-TSS (NM_001003953)	399	NR_045820	109202	Mm.30769	NM_175405	ENSMUSG00000056735	A930024E05Rik	-	RIKEN cDNA A930024E05 gene	ncRNA
mm_30046.1	chr3	135840255	135840288	-	1	NA	promoter-TSS (NR_040540)	promoter-TSS (NR_040540)	-2	NR_040540	71038	Mm.410798	NR_040540	ENSMUSG00000106306	4933401H06Rik	-	RIKEN cDNA 4933401H06 gene	ncRNA
mm_31296.1	chr4	45972674	45972697	+	1	NA	intron (NM_146142, intron 1 of 16)	CpG	388	NM_146142	100121	Mm.275413	NM_146142	ENSMUSG00000035517	Tdrd7	5730495N10Rik|AI447470|PCTAIRE2BP	tudor domain containing 7	protein-coding
mm_4711.1	chr1	180942435	180942445	+	1	NA	promoter-TSS (NM_144794)	promoter-TSS (NM_144794)	-78	NM_144794	208795	Mm.185518	NM_144794	ENSMUSG00000026519	Tmem63a	BC014795|Tmem64a	transmembrane protein 63a	protein-coding
mm_62437.1	chr7	101373200	101373231	+	1	NA	exon (NM_001040111, exon 3 of 34)	exon (NM_001040111, exon 3 of 34)	-4907	NM_001040112	69710	Mm.277687	NM_027180	ENSMUSG00000032812	Arap1	2410002L19Rik|Centd2|mKIAA0782	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	protein-coding
mm_122132.1	chr14	31160627	31160639	-	1	NA	intron (NM_138672, intron 11 of 68)	intron (NM_138672, intron 11 of 68)	8008	NM_138672	192187	Mm.220821	NM_138672	ENSMUSG00000042286	Stab1	FEEL-1|FELE-1|MFEEL-1|MS-1|STAB-1|mKIAA0246	stabilin 1	protein-coding
mm_151874.1	chr19	5798358	5798364	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	-2380	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_72500.1	chr8	83740565	83740574	+	1	NA	intron (NM_001163031, intron 1 of 17)	intron (NM_001163031, intron 1 of 17)	742	NM_001163029	26364	Mm.334648	NM_011925	ENSMUSG00000002885	Adgre5	AA409984|Cd97|TM7LN1	adhesion G protein-coupled receptor E5	protein-coding
mm_134092.1	chr16	9570988	9570994	-	1	NA	Intergenic	(A)n|Simple_repeat|Simple_repeat	421542	NM_008170	14811	Mm.2953	NM_008170	ENSMUSG00000059003	Grin2a	GluN2A|NMDAR2A|NR2A	glutamate receptor, ionotropic, NMDA2A (epsilon 1)	protein-coding
mm_9726.1	chr1	180195942	180195946	-	1	NA	promoter-TSS (NM_023341)	promoter-TSS (NM_023341)	76	NM_023341	67426	Mm.38330	NM_023341	ENSMUSG00000026489	Coq8a	4632432J16Rik|AI462003|Adck3|Cabc1|mKIAA0451	coenzyme Q8A	protein-coding
mm_73542.1	chr8	108714959	108715057	+	1	NA	5' UTR (NM_007496, exon 1 of 10)	5' UTR (NM_007496, exon 1 of 10)	364	NM_007496	11906	Mm.416972	NM_007496	ENSMUSG00000038872	Zfhx3	A230102L03Rik|Atbf1|Sci|WBP9|mKIAA4228	zinc finger homeobox 3	protein-coding
mm_66017.1	chr7	30598900	30598912	-	1	NA	Intergenic	Intergenic	-5964	NM_021397	58206	Mm.116789	NM_021397	ENSMUSG00000006310	Zbtb32	4930524C15Rik|FAXF|FAZF|PLZP|Rog|Tzfp	zinc finger and BTB domain containing 32	protein-coding
mm_140689.1	chr17	13741551	13741558	-	1	NA	intron (NM_022311, intron 1 of 2)	intron (NM_022311, intron 1 of 2)	-18987	NM_010806	17356	Mm.59167	NM_010806	ENSMUSG00000068036	Afdn	5033403D15Rik|AF6|Af-6|Afadin|Gm314|I-afadin|Mllt4|S-afadin	afadin, adherens junction formation factor	protein-coding
mm_140402.1	chr17	87640311	87640323	+	1	NA	exon (NM_008532, exon 4 of 10)	exon (NM_008532, exon 4 of 10)	4338	NM_008532	17075	Mm.4259	NM_008532	ENSMUSG00000045394	Epcam	CD326|EGP|EGP-2|Egp314|Ep-CAM|EpCAM1|GA733-2|Ly74|TROP1|Tacsd1|Tacstd1|gp40	epithelial cell adhesion molecule	protein-coding
mm_25686.1	chr3	122245582	122245608	+	1	NA	promoter-TSS (NM_008129)	promoter-TSS (NM_008129)	38	NM_008129	14630	Mm.292676	NM_008129	ENSMUSG00000028124	Gclm	AI649393|Gcmc|Glclr	glutamate-cysteine ligase, modifier subunit	protein-coding
mm_137322.1	chr17	24896536	24896549	+	1	NA	promoter-TSS (NM_019730)	promoter-TSS (NM_019730)	42	NM_019730	79059	Mm.430765	NM_019730	ENSMUSG00000073435	Nme3	1810009F08Rik|AI413736|DR-nm23|Ndk3|Nm23-DR|Nm23-M3	NME/NM23 nucleoside diphosphate kinase 3	protein-coding
mm_13956.1	chr2	121357769	121357782	+	1	NA	promoter-TSS (NM_009897)	promoter-TSS (NM_009897)	-866	NM_009897	12716	Mm.252145	NM_009897	ENSMUSG00000000308	Ckmt1	Mt-CK|ScCKmit|UbCKmit|mi-CK	creatine kinase, mitochondrial 1, ubiquitous	protein-coding
mm_58111.1	chr6	138422865	138422894	-	1	NA	promoter-TSS (NR_126073)	promoter-TSS (NR_126073)	-226	NR_126073	319702	Mm.403785	NR_126072	ENSMUSG00000089957	A830011K09Rik	-	RIKEN cDNA A830011K09 gene	ncRNA
mm_111705.1	chr12	103694675	103694680	-	1	NA	promoter-TSS (NM_001164742)	promoter-TSS (NM_001164742)	12	NM_001164742	68348	Mm.20149	NM_026687	ENSMUSG00000021081	Serpina1f	0610012A11Rik|AI327419|Serpina2|epserin	serine (or cysteine) peptidase inhibitor, clade A, member 1F	protein-coding
mm_64682.1	chr7	4510065	4510075	-	1	NA	intron (NM_011618, intron 7 of 13)	intron (NM_011618, intron 7 of 13)	5905	NM_001277903	21955	Mm.358643	NM_011618	ENSMUSG00000064179	Tnnt1	AW146156|Tnt|sTnT|ssTnT	troponin T1, skeletal, slow	protein-coding
mm_62689.1	chr7	110046350	110046354	+	1	NA	promoter-TSS (NR_033336)	promoter-TSS (NR_033336)	-12	NR_033336	100379145	Mm.484711	NR_033336	ENSMUSG00000064451	Snora23	MBI-1	small nucleolar RNA, H/ACA box 23	snoRNA
mm_12562.1	chr2	72597546	72597548	+	1	NA	Intergenic	Intergenic	-105963	NR_040503	74541	Mm.410774	NR_040503	ENSMUSG00000085252	8430437L04Rik	-	RIKEN cDNA 8430437L04 gene	ncRNA
mm_7096.1	chr1	88701688	88701705	-	1	NA	5' UTR (NM_177305, exon 1 of 1)	5' UTR (NM_177305, exon 1 of 1)	495	NM_177305	320982	Mm.27968	NM_177305	ENSMUSG00000049866	Arl4c	A630084M22Rik|Arl7|LAK	ADP-ribosylation factor-like 4C	protein-coding
mm_164792.1	chr18	15194753	15194765	+	1	NA	Intergenic	MT2A|LTR|ERVL	-43313	NM_134112	106931	Mm.329299	NM_134112	ENSMUSG00000036225	Kctd1	4933402K10Rik|AI661543|AW553000	potassium channel tetramerisation domain containing 1	protein-coding
mm_115781.1	chr13	19311482	19311498	-	1	NA	Intergenic	Intergenic	84323	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_10320.1	chr2	11218494	11218504	+	1	NA	intron (NM_008859, intron 1 of 17)	intron (NM_008859, intron 1 of 17)	46117	NM_008859	18761	Mm.329993	NM_008859	ENSMUSG00000026778	Prkcq	A130035A12Rik|AW494342|PKC-0|PKC-theta|PKCtheta|Pkcq	protein kinase C, theta	protein-coding
mm_135759.1	chr16	56116251	56116265	-	1	NA	intron (NM_001003972, intron 5 of 6)	RLTR17|LTR|ERVK	40778	NM_001304503	66315	Mm.255784	NM_025483	ENSMUSG00000052917	Senp7	2410152H17Rik|2810413I22Rik|2900036C23Rik|6030449K19Rik|AI790676	SUMO1/sentrin specific peptidase 7	protein-coding
mm_158479.1	chrX	142196918	142196924	-	1	NA	promoter-TSS (NM_001007576)	promoter-TSS (NM_001007576)	15	NM_001007576	245650	Mm.208511	NM_001007576	ENSMUSG00000042282	Gucy2f	A930002I06|GC-F|GC2	guanylate cyclase 2f	protein-coding
mm_163246.1	chr11	106159880	106159890	-	1	NA	intron (NM_172397, intron 1 of 4)	CpG	257	NM_172397	67803	Mm.21687	NM_172397	ENSMUSG00000040699	Limd2	0610025L06Rik|AI413966	LIM domain containing 2	protein-coding
mm_73357.1	chr8	105518885	105518917	+	1	NA	exon (NM_008289, exon 1 of 5)	exon (NM_008289, exon 1 of 5)	155	NM_008289	15484	Mm.5079	NM_008289	ENSMUSG00000031891	Hsd11b2	11HSD2	hydroxysteroid 11-beta dehydrogenase 2	protein-coding
mm_18013.1	chr2	38287348	38287394	-	1	NA	promoter-TSS (NM_146122)	promoter-TSS (NM_146122)	13	NM_146122	227801	Mm.314245	NM_146122	ENSMUSG00000035392	Dennd1a	6030446I19Rik|connecdenn	DENN/MADD domain containing 1A	protein-coding
mm_142096.1	chr17	35834741	35834844	-	1	NA	3' UTR (NM_011655, exon 4 of 4)	3' UTR (NM_011655, exon 4 of 4)	3509	NM_011655	22154	Mm.273538	NM_011655	ENSMUSG00000001525	Tubb5	AA408537|AI596182|B130022C14Rik|M(beta)5	tubulin, beta 5 class I	protein-coding
mm_105239.1	chr11	102319094	102319105	-	1	NA	promoter-TSS (NM_001302954)	promoter-TSS (NM_001302954)	-3	NM_011551	21429	Mm.2845	NM_011551	ENSMUSG00000020923	Ubtf	A930005G04Rik|NOR-90|Tcfubf|UBF|UBF-1|UBF1	upstream binding transcription factor, RNA polymerase I	protein-coding
mm_159202.1	chr2	120977569	120977569	+	1	NA	intron (NM_175285, intron 1 of 13)	CpG	507	NM_175285	96957	Mm.315212	NM_175285	ENSMUSG00000054484	Tmem62	B830009D23Rik|C77355	transmembrane protein 62	protein-coding
mm_56675.1	chr6	113717674	113717713	-	1	NA	promoter-TSS (NR_138135)	promoter-TSS (NR_138135)	-1	NR_138135	58991	Mm.379095	NM_021488	ENSMUSG00000064177	Ghrl	2210006E23Rik|Ghr|MTLRP|MTLRPAP|m46	ghrelin	protein-coding
mm_117521.1	chr13	81545269	81545273	-	1	NA	intron (NM_054053, intron 21 of 89)	PB1D10|SINE|Alu	87873	NM_054053	110789	Mm.288694	NM_054053	ENSMUSG00000069170	Adgrv1	Frings|Gpr98|Mass1|Mgr1|VLGR1	adhesion G protein-coupled receptor V1	protein-coding
mm_57989.1	chr6	136172157	136172176	-	1	NA	intron (NM_008171, intron 2 of 14)	intron (NM_008171, intron 2 of 14)	1345	NM_008171	14812	Mm.436649	NM_008171	ENSMUSG00000030209	Grin2b	AW490526|GluN2B|NR2B|Nmdar2b	glutamate receptor, ionotropic, NMDA2B (epsilon 2)	protein-coding
mm_64202.1	chr7	141470373	141470392	+	1	NA	exon (NM_001111049, exon 7 of 8)	exon (NM_001111049, exon 7 of 8)	1593	NM_001111050	12476	Mm.30246	NM_009842	ENSMUSG00000025510	Cd151	PETA-3|SFA-1|Tspan24	CD151 antigen	protein-coding
mm_89676.1	chr10	97517495	97517506	+	1	NA	exon (NM_007833, exon 8 of 8)	exon (NM_007833, exon 8 of 8)	35169	NM_007833	13179	Mm.56769	NM_007833	ENSMUSG00000019929	Dcn	DC|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding
mm_39194.1	chr4	155992605	155992674	-	1	NA	promoter-TSS (NM_011341)	promoter-TSS (NM_011341)	39	NM_080445	117592	Mm.440185	NM_080445	ENSMUSG00000050796	B3galt6	BB129894|GalTII	UDP-Gal:betaGal beta 1,3-galactosyltransferase, polypeptide 6	protein-coding
mm_63090.1	chr7	122337596	122337607	+	1	NA	intron (NM_001316672, intron 2 of 16)	intron (NM_001316672, intron 2 of 16)	48476	NM_008855	18751	Mm.207496	NM_008855	ENSMUSG00000052889	Prkcb	PKC-B|PKC-Beta|Pkcb|Prkcb1|Prkcb2	protein kinase C, beta	protein-coding
mm_111291.1	chr12	85468664	85468668	-	1	NA	Intergenic	Intergenic	-5235	NM_010234	14281	Mm.246513	NM_010234	ENSMUSG00000021250	Fos	D12Rfj1|c-fos|cFos	FBJ osteosarcoma oncogene	protein-coding
mm_139556.1	chr17	56875510	56875518	+	1	NA	promoter-TSS (NM_030141)	promoter-TSS (NM_030141)	-119	NM_030141	78625	Mm.160106	NM_030141	ENSMUSG00000024209	1700061G19Rik	1700026H02|AI507598	RIKEN cDNA 1700061G19 gene	protein-coding
mm_164206.1	chr15	82181154	82181156	+	1	NA	intron (NM_033218, intron 9 of 18)	intron (NM_033218, intron 9 of 18)	-16967	NR_029804	723897		NR_029804	ENSMUSG00000065465	Mir33	Mirn33|mir-33|mmu-mir-33	microRNA 33	ncRNA
mm_87767.1	chr10	60293382	60293393	+	1	NA	exon (NM_011179, exon 4 of 15)	exon (NM_011179, exon 4 of 15)	8926	NM_001146124	19156	Mm.29978	NM_011179	ENSMUSG00000004207	Psap	AI037048|SGP-1	prosaposin	protein-coding
mm_102309.1	chr11	55608598	55608613	-	1	NA	promoter-TSS (NM_020492)	promoter-TSS (NM_020492)	-407	NM_020492	14654	Mm.89320	NM_020492	ENSMUSG00000000263	Glra1	nmf11|oscillator|ot|spasmodic|spd	glycine receptor, alpha 1 subunit	protein-coding
mm_4281.1	chr1	171634758	171634769	+	1	NA	3' UTR (NM_144539, exon 8 of 8)	3' UTR (NM_144539, exon 8 of 8)	7137	NR_106151	102465784		NR_106151	ENSMUSG00000098316	Mir7683	Gm27950|mmu-mir-7683	microRNA 7683	ncRNA
mm_56496.1	chr6	99234307	99234310	-	1	NA	intron (NM_001347345, intron 4 of 19)	intron (NM_001347345, intron 4 of 19)	32207	NM_001197321	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_25779.1	chr3	126597239	126597254	+	1	NA	5' UTR (NM_001293663, exon 1 of 20)	5' UTR (NM_001293663, exon 1 of 20)	295	NM_023813	108058	Mm.255822	NM_023813	ENSMUSG00000053819	Camk2d	2810011D23Rik|8030469K03Rik|CaMK II|[d]-CaMKII	calcium/calmodulin-dependent protein kinase II, delta	protein-coding
mm_55636.1	chr6	72333355	72333368	-	1	NA	intron (NM_138592, intron 6 of 12)	intron (NM_138592, intron 6 of 12)	11814	NM_138592	28035	Mm.281900	NM_138592	ENSMUSG00000056305	Usp39	AA408960|AI894154|CGI-21|D6Wsu157e|SAD1	ubiquitin specific peptidase 39	protein-coding
mm_51339.1	chr6	72414354	72414388	+	1	NA	promoter-TSS (NM_019802)	promoter-TSS (NM_019802)	63	NM_019802	56316	Mm.19937	NM_019802	ENSMUSG00000053460	Ggcx	-	gamma-glutamyl carboxylase	protein-coding
mm_121025.1	chr14	79619737	79619770	+	1	NA	exon (NM_026474, exon 11 of 13)	exon (NM_026474, exon 11 of 13)	32062	NM_026474	67955	Mm.18972	NM_026474	ENSMUSG00000022024	Sugt1	2410174K12Rik|SGT1	SGT1, suppressor of G2 allele of SKP1 (S. cerevisiae)	protein-coding
mm_167576.1	chr9	44567786	44567786	-	1	NA	Intergenic	Intergenic	-37106	NM_001110826	13209	Mm.267061	NM_007841	ENSMUSG00000032097	Ddx6	1110001P04Rik|E230023J21Rik|HLR2|mRCK/P54|p54|rck	DEAD (Asp-Glu-Ala-Asp) box polypeptide 6	protein-coding
mm_87119.1	chr10	33256943	33256968	+	1	NA	promoter-TSS (NR_040657)	promoter-TSS (NR_040657)	-598	NR_040657	442820	Mm.490725	NR_040657		D830005E20Rik	-	RIKEN cDNA D830005E20 gene	ncRNA
mm_58986.1	chr7	19083843	19083894	+	1	NA	promoter-TSS (NM_001190490)	promoter-TSS (NM_001190490)	19	NM_001190491	13400	Mm.6529	NM_032418	ENSMUSG00000030409	Dmpk	DM|DMK|Dm15|MDPK|MT-PK	dystrophia myotonica-protein kinase	protein-coding
mm_37691.1	chr4	129239213	129239228	-	1	NA	promoter-TSS (NM_001285865)	promoter-TSS (NM_001285865)	-2	NM_001285865	97130	Mm.331907	NM_001033189	ENSMUSG00000050390	C77080	Kiaa1522|mKIAA1522	expressed sequence C77080	protein-coding
mm_172895.1	chr9	56223767	56223769	-	1	NA	intron (NM_172924, intron 6 of 6)	LSU-rRNA_Hsa|rRNA|rRNA	-62698	NM_019793	56434	Mm.28484	NM_019793	ENSMUSG00000032324	Tspan3	1700055K04Rik|TM4-A|Tm4sf8	tetraspanin 3	protein-coding
mm_75394.1	chr8	45999897	45999904	-	1	NA	promoter-TSS (NM_001039562)	promoter-TSS (NM_001039562)	-50	NM_001039562	654824	Mm.334517	NM_001039562	ENSMUSG00000050914	Ankrd37	-	ankyrin repeat domain 37	protein-coding
mm_30812.1	chr4	21727696	21727716	+	1	NA	promoter-TSS (NM_016746)	promoter-TSS (NM_016746)	5	NM_001290420	51813	Mm.278584	NM_016746	ENSMUSG00000028252	Ccnc	AI451004|AU020987|CG1C	cyclin C	protein-coding
mm_72300.1	chr8	76899246	76899279	+	1	NA	intron (NR_028579, intron 1 of 1)	intron (NR_028579, intron 1 of 1)	911	NR_028579	100039211	Mm.367571	NR_028579	ENSMUSG00000074235	Gm10649	ENSMUSG00000074235	predicted gene 10649	ncRNA
mm_118813.1	chr14	25465608	25465621	+	1	NA	intron (NM_001310666, intron 1 of 23)	intron (NM_001310666, intron 1 of 23)	6429	NM_183208	328365	Mm.227484	NM_183208	ENSMUSG00000007817	Zmiz1	BC065120|E330020C23|ENSMUSG00000072684|Gm10397|I920194n01|Rai17|Zimp10	zinc finger, MIZ-type containing 1	protein-coding
mm_20689.1	chr2	132792610	132792622	-	1	NA	exon (NM_007694, exon 4 of 5)	exon (NM_007694, exon 4 of 5)	11338	NM_007694	12653	Mm.255241	NM_007694	ENSMUSG00000027350	Chgb	Scg-1	chromogranin B	protein-coding
mm_53410.1	chr6	132572020	132572062	+	1	NA	exon (NM_011174, exon 2 of 2)	exon (NM_011174, exon 2 of 2)	2199	NM_011174	19131	Mm.425348	NM_011174	ENSMUSG00000059934	Prh1	MP2|Prp	proline rich protein HaeIII subfamily 1	protein-coding
mm_53079.1	chr6	124935780	124935800	+	1	NA	3' UTR (NM_001170341, exon 9 of 9)	3' UTR (NM_001170341, exon 9 of 9)	4402	NM_001170341	30853	Mm.29737	NM_145385	ENSMUSG00000030120	Mlf2	AI256856|AU018944|C77284	myeloid leukemia factor 2	protein-coding
mm_56591.1	chr6	108471650	108471664	-	1	NA	intron (NM_010585, intron 45 of 61)	MTEb|LTR|ERVL-MaLR	-18086	NR_106121	102465766		NR_106121	ENSMUSG00000105697	Mir7661	mmu-mir-7661	microRNA 7661	ncRNA
mm_85739.1	chr9	108566895	108566905	-	1	NA	exon (NM_023247, exon 1 of 5)	exon (NM_023247, exon 1 of 5)	442	NM_023247	66706	Mm.29471	NM_023247	ENSMUSG00000070283	Ndufaf3	4733401H18Rik	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, assembly factor 3	protein-coding
mm_68665.1	chr7	118855975	118855981	-	1	NA	promoter-TSS (NM_001168218)	promoter-TSS (NM_001168218)	20	NM_001168218	66356	Mm.482278	NM_023197	ENSMUSG00000030980	Knop1	2310008H09Rik|Tsg118	lysine rich nucleolar protein 1	protein-coding
mm_142029.1	chr17	35235216	35235260	-	1	NA	5' UTR (NM_001347351, exon 1 of 4)	5' UTR (NM_001347351, exon 1 of 4)	228	NM_001347351	66237	Mm.396107	NM_023179	ENSMUSG00000024403	Atp6v1g2	1500002D01Rik|Atp6g2|NG38|VAG2	ATPase, H+ transporting, lysosomal V1 subunit G2	protein-coding
mm_116628.1	chr13	48968005	48968029	-	1	NA	promoter-TSS (NR_015601)	promoter-TSS (NR_015601)	-95	NR_015601	68128	Mm.426304	NR_015601		Fam120aos	C030044B11Rik	family with sequence similarity 120A, opposite strand	ncRNA
mm_111657.1	chr12	102878456	102878477	-	1	NA	promoter-TSS (NM_172806)	promoter-TSS (NM_172806)	-60	NM_172806	238386	Mm.63456	NM_172806	ENSMUSG00000041702	Btbd7	5730507E09Rik|8030448M07|E130118E17Rik|FUP1|mKIAA1525	BTB (POZ) domain containing 7	protein-coding
mm_17952.1	chr2	37350845	37350861	-	1	NA	3' UTR (NM_026176, exon 4 of 4)	3' UTR (NM_026176, exon 4 of 4)	8479	NM_026176	67466	Mm.30709	NM_026176	ENSMUSG00000009030	Pdcl	1200011E13Rik|AW108059|PhLP1	phosducin-like	protein-coding
mm_66806.1	chr7	47252851	47252861	-	1	NA	promoter-TSS (NM_001288801)	promoter-TSS (NM_001288801)	-8	NM_001288801	668725	Mm.436563	NM_001177566	ENSMUSG00000074111	Mrgpra9	EG668725|MrgA9	MAS-related GPR, member A9	protein-coding
mm_40022.1	chr5	33336271	33336281	+	1	NA	intron (NM_021500, intron 1 of 8)	intron (NM_021500, intron 1 of 8)	704	NM_021500	59003	Mm.138617	NM_021500	ENSMUSG00000079562	Maea	1110030D19Rik|EMP|Gid9	macrophage erythroblast attacher	protein-coding
mm_14970.1	chr2	152093728	152093734	+	1	NA	exon (NM_001160410, exon 2 of 2)	exon (NM_001160410, exon 2 of 2)	-11793	NM_029688	76650	Mm.218639	NM_029688	ENSMUSG00000032802	Srxn1	1700127B04Rik|AI854065|AW488194|Npn3|Srx|Srx1|TX01	sulfiredoxin 1 homolog (S. cerevisiae)	protein-coding
mm_85480.1	chr9	106040773	106040812	-	1	NA	intron (NM_026763, intron 18 of 37)	ID4_|SINE|ID	55899	NM_026763	68553	Mm.28854	NM_026763	ENSMUSG00000032572	Col6a4	1110001D15Rik|AI413310|AU023415|Dvwa|EG235580|Vwa6	collagen, type VI, alpha 4	protein-coding
mm_107286.1	chr12	29811569	29811583	+	1	NA	exon (NM_001093776, exon 9 of 25)	exon (NM_001093776, exon 9 of 25)	-125131	NR_046080	328075	Mm.447832	NR_046080		C630031E19Rik	C630031E19	RIKEN cDNA C630031E19 gene	ncRNA
mm_83693.1	chr9	50593074	50593079	-	1	NA	Intergenic	Intergenic	10773	NM_025848	66925	Mm.10406	NM_025848	ENSMUSG00000000171	Sdhd	3110001M13Rik|AVLL5809|C78570|PRO19626	succinate dehydrogenase complex, subunit D, integral membrane protein	protein-coding
mm_2367.1	chr1	93168599	93168619	+	1	NA	5' UTR (NM_001310428, exon 1 of 32)	5' UTR (NM_001310428, exon 1 of 32)	186	NM_001310428	381284	Mm.193346	NM_001310428	ENSMUSG00000084989	Crocc2	E030010N08Rik|Gm976	ciliary rootlet coiled-coil, rootletin family member 2	protein-coding
mm_154850.1	chrX	20547739	20547742	+	1	NA	Intergenic	Intergenic	-2078	NM_009060	19733	Mm.2118	NM_009060	ENSMUSG00000023070	Rgn	AI265316|GNL|SMP30	regucalcin	protein-coding
mm_123332.1	chr14	63049892	63049901	-	1	NA	Intergenic	Intergenic	2905	NM_001034910	619548	Mm.387101	NM_001034910	ENSMUSG00000054763	Defb42	BD-42|Defb44|mBD-42	defensin beta 42	protein-coding
mm_108596.1	chr12	85389422	85389435	+	1	NA	Intergenic	L2b|LINE|L2	-14711	NM_026775	68581	Mm.379159	NM_026775	ENSMUSG00000021248	Tmed10	1110014C03Rik|Tmp21|p23|p24delta1	transmembrane p24 trafficking protein 10	protein-coding
mm_79140.1	chr9	47645078	47645097	+	1	NA	intron (NM_001025600, intron 1 of 8)	intron (NM_001025600, intron 1 of 8)	114735	NM_018770	54725	Mm.234832	NM_018770	ENSMUSG00000032076	Cadm1	2900073G06Rik|3100001I08Rik|AI987920|Bl2|Igsf4|Igsf4a|Necl2|RA175|RA175A|RA175B|RA175C|RA175N|ST17|SgIGSF|SynCam|Tslc1	cell adhesion molecule 1	protein-coding
mm_37576.1	chr4	126256227	126256370	-	1	NA	promoter-TSS (NM_144941)	promoter-TSS (NM_144941)	21	NM_144941	245877	Mm.266716	NM_144941	ENSMUSG00000028849	Map7d1	AV028413|BC019977|Mtap7d1|Parcc1|Rprc1|mKIAA1187	MAP7 domain containing 1	protein-coding
mm_121435.1	chr14	120413327	120413367	+	1	NA	intron (NM_175341, intron 8 of 8)	intron (NM_175341, intron 8 of 8)	-65114	NM_029519	76108	Mm.261448	NM_029519	ENSMUSG00000051615	Rap2a	5830461H18Rik	RAS related protein 2a	protein-coding
mm_80552.1	chr9	83008595	83008624	+	1	NA	Intergenic	RMER15|LTR|ERVL	-33120	NM_001081216	83946	Mm.221688	NM_031879	ENSMUSG00000032253	Phip	2810004D21Rik|4632404O06Rik|Ndrp|Wdr11	pleckstrin homology domain interacting protein	protein-coding
mm_119245.1	chr14	33923316	33923329	+	1	NA	promoter-TSS (NM_145741)	promoter-TSS (NM_145741)	-265	NM_145741	14560	Mm.432071	NM_145741	ENSMUSG00000021943	Gdf10	Bmp3b	growth differentiation factor 10	protein-coding
mm_26635.1	chr3	152979754	152979778	+	1	NA	intron (NM_012028, intron 2 of 4)	intron (NM_012028, intron 2 of 4)	2441	NM_012028	26938	Mm.40915	NM_012028	ENSMUSG00000039037	St6galnac5	AI851940|Siat7e	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 5	protein-coding
mm_98610.1	chr11	95842669	95842704	+	1	NA	promoter-TSS (NM_001284397)	promoter-TSS (NM_001284397)	18	NM_001038664	14710	Mm.46299	NM_023121	ENSMUSG00000038811	Gngt2	AV096488	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 2	protein-coding
mm_149663.1	chr19	18731430	18731440	+	1	NA	Intergenic	Intergenic	18199	NM_177640	225995	Mm.28101	NM_177640	ENSMUSG00000047044	D030056L22Rik	-	RIKEN cDNA D030056L22 gene	protein-coding
mm_151415.1	chr19	56722111	56722128	+	1	NA	promoter-TSS (NM_007419)	promoter-TSS (NM_007419)	-253	NM_007419	11554	Mm.46797	NM_007419	ENSMUSG00000035283	Adrb1	Adrb-1|beta-AR	adrenergic receptor, beta 1	protein-coding
mm_165236.1	chr2	60284341	60284345	-	1	NA	5' UTR (NM_025422, exon 1 of 5)	5' UTR (NM_025422, exon 1 of 5)	141	NM_025422	66205	Mm.227281	NM_025422	ENSMUSG00000060703	Cd302	1110055L24Rik|AI159627	CD302 antigen	protein-coding
mm_78278.1	chr9	22101076	22101133	+	1	NA	intron (NM_009922, intron 1 of 6)	intron (NM_009922, intron 1 of 6)	1851	NM_009922	12797	Mm.4356	NM_009922	ENSMUSG00000001349	Cnn1	CN|CnnI	calponin 1	protein-coding
mm_138323.1	chr17	34850374	34850422	+	1	NA	promoter-TSS (NM_021337)	promoter-TSS (NM_021337)	7	NM_001045864	27632	Mm.653	NM_138580	ENSMUSG00000024369	Nelfe	D17H6S45|NELF-E|RD|Rdbp	negative elongation factor complex member E, Rdbp	protein-coding
mm_123245.1	chr14	60251474	60251484	-	1	NA	promoter-TSS (NM_170591)	promoter-TSS (NM_170591)	-101	NM_170591	71844	Mm.258051	NM_170591	ENSMUSG00000063895	Nupl1	1700017F11Rik|Nup58|mKIAA0410	nucleoporin like 1	protein-coding
mm_115186.1	chr13	108450018	108450020	+	1	NA	Intergenic	Intergenic	133682	NM_178683	218581	Mm.32318	NM_178683	ENSMUSG00000021697	Depdc1b	9830132O03|AW260467|XTP1	DEP domain containing 1B	protein-coding
mm_95665.1	chr11	53772108	53772127	+	1	NA	intron (NM_001159393, intron 2 of 9)	RSINE1|SINE|B4	1644	NM_001159396	16362	Mm.105218	NM_008390	ENSMUSG00000018899	Irf1	AU020929|Irf-1	interferon regulatory factor 1	protein-coding
mm_125285.1	chr15	36726321	36726325	+	1	NA	Intergenic	Intergenic	64609	NM_001253807	22631	Mm.3360	NM_011740	ENSMUSG00000022285	Ywhaz	1110013I11Rik|14-3-3zeta|AI596267|AL022924|AU020854	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide	protein-coding
mm_170264.1	chr18	16994563	16994570	-	1	NA	Intergenic	L1Md_T|LINE|L1	-40942	NR_130158	75433	Mm.60907	NR_130158	ENSMUSG00000087170	1700001G01Rik	-	RIKEN cDNA 1700001G01 gene	ncRNA
mm_173066.1	chrX	134541620	134541620	-	1	NA	promoter-TSS (NM_013898).2	promoter-TSS (NM_013898).2	50	NM_013898	30058	Mm.214504	NM_013898	ENSMUSG00000048007	Timm8a1	DXHXS1274E|Ddp1|Fci-12|Tim8a|Timm8a	translocase of inner mitochondrial membrane 8A1	protein-coding
mm_82806.1	chr9	29963036	29963046	-	1	NA	promoter-TSS (NM_172290)	promoter-TSS (NM_172290)	88	NM_172290	235106	Mm.283138	NM_172290	ENSMUSG00000059974	Ntm	6230410L23Rik|B230210G24Rik|Hnt|Igdcc2|R75390	neurotrimin	protein-coding
mm_32986.1	chr4	120137673	120137683	+	1	NA	Intergenic	Intergenic	-23528	NM_007902	13615	Mm.284855	NM_007902	ENSMUSG00000028635	Edn2	ET-2|PPET2|VIC	endothelin 2	protein-coding
mm_5028.1	chr1	193274602	193274612	+	1	NA	Intergenic	Intergenic	-1419	NM_008059	14373	Mm.439721	NM_008059	ENSMUSG00000009633	G0s2	AI255151|AV006465	G0/G1 switch gene 2	protein-coding
mm_74421.1	chr8	3625579	3625580	-	1	NA	promoter-TSS (NM_001129804)	promoter-TSS (NM_001129804)	-34	NM_001129803	18545	Mm.440882	NM_008790	ENSMUSG00000004630	Pcp2	L7|Pcp-2	Purkinje cell protein 2 (L7)	protein-coding
mm_65593.1	chr7	27329882	27329885	-	1	NA	intron (NM_001310678, intron 2 of 22)	intron (NM_001310678, intron 2 of 22)	3765	NM_001113549	108075	Mm.272251	NM_175641	ENSMUSG00000040488	Ltbp4	2310046A13Rik	latent transforming growth factor beta binding protein 4	protein-coding
mm_100745.1	chr11	4123415	4123424	-	1	NA	Intergenic	Intergenic	-4690	NM_144520	67815	Mm.253922	NM_144520	ENSMUSG00000003585	Sec14l2	1300013M05Rik|Spf|TAP	SEC14-like lipid binding 2	protein-coding
mm_147254.1	chr18	38631561	38631580	-	1	NA	Intergenic	Intergenic	-30302	NM_011898	24066	Mm.42038	NM_011898	ENSMUSG00000024427	Spry4	A030006O18Rik|sprouty4	sprouty homolog 4 (Drosophila)	protein-coding
mm_118441.1	chr14	8098197	8098296	+	1	NA	promoter-TSS (NM_145458)	promoter-TSS (NM_145458)	33	NM_178279	218699	Mm.29515	NM_145458	ENSMUSG00000033885	Pxk	C230080L11Rik|D14Ertd813e|MONaKA	PX domain containing serine/threonine kinase	protein-coding
mm_138528.1	chr17	35242869	35242880	+	1	NA	promoter-TSS (NM_001252457)	promoter-TSS (NM_001252457)	57	NM_001252457	53817	Mm.439827	NM_019693	ENSMUSG00000019432	Ddx39b	0610030D10Rik|AI428441|Bat-1|Bat1|Bat1a|D17H6S81E|D17H6S81E-1|D6S81Eh	DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B	protein-coding
mm_142111.1	chr17	35836206	35836281	-	1	NA	exon (NM_011655, exon 3 of 4)	exon (NM_011655, exon 3 of 4)	2058	NM_011655	22154	Mm.273538	NM_011655	ENSMUSG00000001525	Tubb5	AA408537|AI596182|B130022C14Rik|M(beta)5	tubulin, beta 5 class I	protein-coding
mm_50924.1	chr6	57608916	57608936	+	1	NA	intron (NM_025992, intron 8 of 22)	intron (NM_025992, intron 8 of 22)	27934	NM_025992	67138	Mm.297393	NM_025992	ENSMUSG00000029798	Herc6	1700121D12Rik|2510038N07Rik|4930427L17Rik|AI451296|CEB1|Herc5	hect domain and RLD 6	protein-coding
mm_136675.1	chr17	6158764	6158767	+	1	NA	intron (NM_054040, intron 1 of 13)	ID_B1|SINE|B4	20617	NM_054040	68842	Mm.449307	NM_054040	ENSMUSG00000034377	Tulp4	1110057P05Rik|2210038L17Rik|Tusp	tubby like protein 4	protein-coding
mm_148081.1	chr18	73179333	73179334	-	1	NA	Intergenic	L1_Mur3|LINE|L1	-393372	NM_001039214	240396	Mm.24131	NM_001039214	ENSMUSG00000037253	Mex3c	A130001D14Rik|BC035207|BM-013|Rkhd2	mex3 RNA binding family member C	protein-coding
mm_90829.1	chr10	7956275	7956290	-	1	NA	promoter-TSS (NM_138667)	promoter-TSS (NM_138667)	-159	NM_138667	68652	Mm.193041	NM_138667	ENSMUSG00000015755	Tab2	1110030N06Rik|A530078N03Rik|Map3k7ip2|mKIAA0733	TGF-beta activated kinase 1/MAP3K7 binding protein 2	protein-coding
mm_166483.1	chr5	146385236	146385236	+	1	NA	5' UTR (NM_145155, exon 1 of 10)	5' UTR (NM_145155, exon 1 of 10)	230	NM_145155	245880	Mm.472750	NM_145155	ENSMUSG00000029636	Wasf3	Scar3|Wave3	WAS protein family, member 3	protein-coding
mm_132598.1	chr16	38483172	38483185	+	1	NA	intron (NM_009855, intron 4 of 4)	intron (NM_009855, intron 4 of 4)	24245	NM_009855	12519	Mm.89474	NM_009855	ENSMUSG00000075122	Cd80	B71|Cd28l|Ly-53|Ly53|MIC17|TSA1	CD80 antigen	protein-coding
mm_6630.1	chr1	78311977	78311979	-	1	NA	intron (NM_001004173, intron 1 of 4)	intron (NM_001004173, intron 1 of 4)	1632	NM_001004173	433323	Mm.276248	NM_001004173	ENSMUSG00000032908	Sgpp2	SPPase2|Spp2	sphingosine-1-phosphate phosphotase 2	protein-coding
mm_95533.1	chr11	52253662	52253698	+	1	NA	3' UTR (NM_009331, exon 10 of 10)	3' UTR (NM_009331, exon 10 of 10)	21685	NM_011543	21402	Mm.42944	NM_011543	ENSMUSG00000036309	Skp1a	15kDa|2610043E24Rik|2610206H23Rik|EMC19|OCP-II|OCP2|SKP1|Tceb1l|p19A|p19Skp1	S-phase kinase-associated protein 1A	protein-coding
mm_129781.1	chr15	82794237	82794260	-	1	NA	promoter-TSS (NM_029562)	promoter-TSS (NM_029562)	-3	NM_029562	76279	Mm.439931	NM_029562	ENSMUSG00000022445	Cyp2d26	1300006E06Rik	cytochrome P450, family 2, subfamily d, polypeptide 26	protein-coding
mm_65443.1	chr7	25390129	25390131	-	1	NA	promoter-TSS (NM_001039507)	promoter-TSS (NM_001039507)	-18	NM_001039507	16890	Mm.158548	NM_010719	ENSMUSG00000003123	Lipe	4933403G17Rik|HSL	lipase, hormone sensitive	protein-coding
mm_87661.1	chr10	58485990	58486003	+	1	NA	intron (NM_011240, intron 24 of 28)	intron (NM_011240, intron 24 of 28)	-11941	NM_001162956	76138	Mm.211744	NM_001162956	ENSMUSG00000038010	Ccdc138	6230424H07Rik|BC042726	coiled-coil domain containing 138	protein-coding
mm_65768.1	chr7	28759945	28759956	-	1	NA	TTS (NM_001195091)	TTS (NM_001195091)	3776	NM_001195091	100504112	Mm.379654	NM_001195091	ENSMUSG00000096257	Ccer2	EG624918|Gm6537	coiled-coil glutamate-rich protein 2	protein-coding
mm_148222.1	chr18	80312980	80312984	-	1	NA	intron (NM_001190373, intron 3 of 3)	intron (NM_001190373, intron 3 of 3)	51272	NM_001190373	240444	Mm.279568	NM_001190373	ENSMUSG00000059852	Kcng2	AA591524	potassium voltage-gated channel, subfamily G, member 2	protein-coding
mm_28436.1	chr3	90466363	90466404	-	1	NA	promoter-TSS (NM_008727)	promoter-TSS (NM_008727)	-517	NM_008727	18160	Mm.4627	NM_008727	ENSMUSG00000027931	Npr1	AI893888|GC-A|NPR-A|NPRA|Pndr	natriuretic peptide receptor 1	protein-coding
mm_165345.1	chr2	118677229	118677283	+	1	NA	promoter-TSS (NM_001145854)	promoter-TSS (NM_001145854)	10	NM_001145854	214230	Mm.241857	NM_001033254	ENSMUSG00000074923	Pak6	4732456M09	p21 protein (Cdc42/Rac)-activated kinase 6	protein-coding
mm_3895.1	chr1	161417811	161417853	+	1	NA	3' UTR (NM_009452, exon 3 of 3)	3' UTR (NM_009452, exon 3 of 3)	22394	NM_009452	22164	Mm.4994	NM_009452	ENSMUSG00000026700	Tnfsf4	Ath-1|Ath1|CD134L|OX-40L|Ox40l|TXGP1|Tnlg2b|Txgp1l|gp34	tumor necrosis factor (ligand) superfamily, member 4	protein-coding
mm_140409.1	chr17	87646271	87646292	+	1	NA	exon (NM_008532, exon 8 of 10)	exon (NM_008532, exon 8 of 10)	10302	NM_008532	17075	Mm.4259	NM_008532	ENSMUSG00000045394	Epcam	CD326|EGP|EGP-2|Egp314|Ep-CAM|EpCAM1|GA733-2|Ly74|TROP1|Tacsd1|Tacstd1|gp40	epithelial cell adhesion molecule	protein-coding
mm_118545.1	chr14	17659228	17659238	+	1	NA	Intergenic	Intergenic	-1727	NM_001113417	21834	Mm.32563	NM_009380	ENSMUSG00000021779	Thrb	Nr1a2|T3R[b]|T3Rbeta|Thrb1|Thrb2|c-erbAbeta	thyroid hormone receptor beta	protein-coding
mm_116554.1	chr13	46727590	46727616	-	1	NA	5' UTR (NM_175749, exon 1 of 22)	5' UTR (NM_175749, exon 1 of 22)	246	NM_175749	218210	Mm.255398	NM_175749	ENSMUSG00000021374	Nup153	B130015D15Rik|C88147	nucleoporin 153	protein-coding
mm_144642.1	chr18	33067409	33067447	+	1	NA	intron (NM_009793, intron 1 of 10)	intron (NM_009793, intron 1 of 10)	128387	NM_009793	12326	Mm.222329	NM_009793	ENSMUSG00000038128	Camk4	A430110E23Rik|AI666733|CaMKIV|CaMKIV/Gr|D18Bwg0362e	calcium/calmodulin-dependent protein kinase IV	protein-coding
mm_166792.1	chr6	145615988	145615994	+	1	NA	promoter-TSS (NM_009449)	promoter-TSS (NM_009449)	28	NM_009449	22147	Mm.270295	NM_009449	ENSMUSG00000067338	Tuba3b	M[a]7|Tuba7	tubulin, alpha 3B	protein-coding
mm_99226.1	chr11	101048437	101048455	+	1	NA	exon (NM_001243049, exon 17 of 21)	exon (NM_001243049, exon 17 of 21)	18106	NR_105893	102466767		NR_105893	ENSMUSG00000098415	Mir6928	Gm27728|mmu-mir-6928	microRNA 6928	ncRNA
mm_21536.1	chr2	163690765	163690767	-	1	NA	intron (NM_001039390, intron 2 of 4)	intron (NM_001039390, intron 2 of 4)	-3271	NM_011106	18769	Mm.10091	NM_011106	ENSMUSG00000035268	Pkig	PKIgamma	protein kinase inhibitor, gamma	protein-coding
mm_53295.1	chr6	129036708	129036722	+	1	NA	Intergenic	RMER19A|LTR|ERVK	-9186	NR_024262	232408	Mm.259262	NM_153094	ENSMUSG00000030154	Klrb1f	A630024B12Rik|Nkr-p1f|Nkrp1-f|Nkrp1f	killer cell lectin-like receptor subfamily B member 1F	protein-coding
mm_134976.1	chr16	32073792	32073808	-	1	NA	intron (NM_177326, intron 1 of 14)	RSINE1|SINE|B4	5542	NM_177326	224105	Mm.234204	NM_177326	ENSMUSG00000022781	Pak2	5330420P17Rik|A130002K10Rik|AI836325|D16Ertd269e|PAK-2|mKIAA4182	p21 protein (Cdc42/Rac)-activated kinase 2	protein-coding
mm_137413.1	chr17	26113811	26113815	+	1	NA	intron (NM_021793, intron 1 of 12)	CpG	497	NM_021793	60455	Mm.304656	NM_021793	ENSMUSG00000024180	Tmem8	AW490096|M83|Tmem8a	transmembrane protein 8 (five membrane-spanning domains)	protein-coding
mm_32529.1	chr4	108879131	108879141	+	1	NA	promoter-TSS (NM_023537)	promoter-TSS (NM_023537)	66	NM_023537	69908	Mm.41580	NM_023537	ENSMUSG00000003411	Rab3b	2610528C18Rik	RAB3B, member RAS oncogene family	protein-coding
mm_71462.1	chr8	46530980	46530992	+	1	NA	exon (NM_007981, exon 17 of 21)	exon (NM_007981, exon 17 of 21)	-21083	NM_027973	71876	Mm.22108	NM_027973	ENSMUSG00000031629	Cenpu	1700029A22Rik|Mlf1ip	centromere protein U	protein-coding
mm_145816.1	chr18	65430985	65431011	+	1	NA	promoter-TSS (NM_172833)	promoter-TSS (NM_172833)	1	NM_172833	240354	Mm.132613	NM_172833	ENSMUSG00000032688	Malt1	A630046N12|D430033E09Rik|Pcasp1	MALT1 paracaspase	protein-coding
mm_25371.1	chr3	107102581	107102601	+	1	NA	intron (NM_008417, intron 1 of 2)	intron (NM_008417, intron 1 of 2)	1024	NM_008417	16490	Mm.39285	NM_008417	ENSMUSG00000040724	Kcna2	Akr6a4|ENSMUSG00000074335|Gm10672|Kca1-2|Kv1.2|Mk-2	potassium voltage-gated channel, shaker-related subfamily, member 2	protein-coding
mm_162863.1	chr10	93261493	93261504	+	1	NA	intron (NM_001282967, intron 2 of 3)	intron (NM_001282967, intron 2 of 3)	49661	NM_001322268	13713	Mm.4454	NM_013508	ENSMUSG00000008398	Elk3	D430049E23Rik|Erp|Etrp|Net|Sap-2	ELK3, member of ETS oncogene family	protein-coding
mm_140399.1	chr17	87636711	87636737	+	1	NA	5' UTR (NM_008532, exon 2 of 10)	5' UTR (NM_008532, exon 2 of 10)	745	NM_008532	17075	Mm.4259	NM_008532	ENSMUSG00000045394	Epcam	CD326|EGP|EGP-2|Egp314|Ep-CAM|EpCAM1|GA733-2|Ly74|TROP1|Tacsd1|Tacstd1|gp40	epithelial cell adhesion molecule	protein-coding
mm_144204.1	chr18	9490008	9490010	+	1	NA	Intergenic	Intergenic	-39859	NM_026484	67974	Mm.86523	NM_026484	ENSMUSG00000024286	Ccny	1700025H17Rik|3110050L10Rik|4631402G10Rik|5730405I09Rik	cyclin Y	protein-coding
mm_127921.1	chr15	9580647	9580655	-	1	NA	intron (NM_001305042, intron 36 of 36)	intron (NM_001305042, intron 36 of 36)	-50775	NM_008372	16197	Mm.389	NM_008372	ENSMUSG00000003882	Il7r	CD127|IL-7Ralpha	interleukin 7 receptor	protein-coding
mm_23539.1	chr3	61363757	61363760	+	1	NA	promoter-TSS (NM_028712)	promoter-TSS (NM_028712)	-749	NM_028712	74012	Mm.422674	NM_028712	ENSMUSG00000036894	Rap2b	4021402C18Rik|AA408554	RAP2B, member of RAS oncogene family	protein-coding
mm_9797.1	chr1	181843035	181843050	-	1	NA	promoter-TSS (NM_133815)	promoter-TSS (NM_133815)	-641	NM_133815	98386	Mm.4538	NM_133815	ENSMUSG00000004880	Lbr	AI505894|ic	lamin B receptor	protein-coding
mm_17264.1	chr2	26013729	26013753	-	1	NA	intron (NM_133835, intron 3 of 9)	intron (NM_133835, intron 3 of 9)	8019	NM_133835	98766	Mm.247824	NM_133835	ENSMUSG00000036352	Ubac1	1110033G07Rik|AA407978|GBDR1|Gdbr1|Kpc2|Ubadc1	ubiquitin associated domain containing 1	protein-coding
mm_106655.1	chr11	121196353	121196355	-	1	NA	intron (NM_025402, intron 6 of 8)	intron (NM_025402, intron 6 of 8)	-8079	NM_001001333	238023	Mm.275130	NM_001001333	ENSMUSG00000039307	Hexdc	BC069960	hexosaminidase (glycosyl hydrolase family 20, catalytic domain) containing	protein-coding
mm_114750.1	chr13	84285228	84285232	+	1	NA	intron (NR_029419, intron 8 of 11)	intron (NR_029419, intron 8 of 11)	62934	NM_175187	72745	Mm.295063	NM_175187	ENSMUSG00000035762	Tmem161b	2810446P07Rik|AI843389	transmembrane protein 161B	protein-coding
mm_23888.1	chr3	83031319	83031345	+	1	NA	exon (NM_010196, exon 5 of 5)	exon (NM_010196, exon 5 of 5)	5179	NM_001111048	14161	Mm.88793	NM_010196	ENSMUSG00000028001	Fga	ENSMUSG00000059807|Fib	fibrinogen alpha chain	protein-coding
mm_72407.1	chr8	81775678	81775690	+	1	NA	intron (NM_001024617, intron 7 of 24)	L1ME2|LINE|L1	433122	NM_001297593	234515	Mm.324468	NM_001024617	ENSMUSG00000037940	Inpp4b	E130107I17Rik	inositol polyphosphate-4-phosphatase, type II	protein-coding
mm_41062.1	chr5	86903813	86903821	+	1	NA	intron (NM_153598, intron 2 of 5)	intron (NM_153598, intron 2 of 5)	3120	NM_153598	100727	Mm.281844	NM_153598	ENSMUSG00000029260	Ugt2b34	AI788959	UDP glucuronosyltransferase 2 family, polypeptide B34	protein-coding
mm_60044.1	chr7	31059548	31059635	+	1	NA	promoter-TSS (NM_144556)	promoter-TSS (NM_144556)	-344	NM_144556	243914	Mm.389870	NM_144556	ENSMUSG00000036560	Lgi4	Lgil3|clp	leucine-rich repeat LGI family, member 4	protein-coding
mm_97649.1	chr11	79412678	79412681	+	1	NA	intron (NM_010897, intron 10 of 57)	intron (NM_010897, intron 10 of 57)	71352	NR_045305	104522	Mm.436987	NR_045305	ENSMUSG00000091523	AU040972	AU040954	expressed sequence AU040972	ncRNA
mm_115495.1	chr13	3804215	3804239	-	1	NA	promoter-TSS (NM_027416)	promoter-TSS (NM_027416)	91	NM_027416	70405	Mm.20079	NM_027416	ENSMUSG00000063130	Calml3	2310068O22Rik|AI326174	calmodulin-like 3	protein-coding
mm_131192.1	chr16	7278190	7278225	+	1	NA	intron (NM_021477, intron 7 of 16)	intron (NM_021477, intron 7 of 16)	208372	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_45837.1	chr5	87694975	87695011	-	1	NA	exon (NM_001286023, exon 5 of 7)	exon (NM_001286023, exon 5 of 7)	4432	NM_001286020	12991	Mm.268737	NM_009972	ENSMUSG00000063157	Csn2	Csnb	casein beta	protein-coding
mm_70122.1	chr7	143008698	143008713	-	1	NA	intron (NM_001128081, intron 2 of 6)	intron (NM_001128081, intron 2 of 6)	3046	NM_001128081	27027	Mm.28172	NM_020286	ENSMUSG00000000244	Tspan32	AW208513|Art-1|BB235973|D7Wsu37e|Phemx|Tssc6	tetraspanin 32	protein-coding
mm_159447.1	chr3	134240067	134240067	+	1	NA	TTS (NR_035435)	TTS (NR_035435)	516	NR_035435	100316832		NR_035435	ENSMUSG00000084564	Mir1895	Mirn1895|mmu-mir-1895	microRNA 1895	ncRNA
mm_112868.1	chr13	20849995	20850041	+	1	NA	intron (NM_012054, intron 3 of 20)	B1_Mus1|SINE|Alu	55905	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_19526.1	chr2	94178912	94178926	-	1	NA	Intergenic	Intergenic	-21010	NM_019657	56348	Mm.22505	NM_019657	ENSMUSG00000027195	Hsd17b12	2610510O05Rik|AI172963|KIK-I|Kik1	hydroxysteroid (17-beta) dehydrogenase 12	protein-coding
mm_48622.1	chr5	144965897	144965909	-	1	NA	promoter-TSS (NM_029438)	promoter-TSS (NM_029438)	-73	NM_029438	75788	Mm.27735	NM_029438	ENSMUSG00000038780	Smurf1	4930431E10Rik|mKIAA1625	SMAD specific E3 ubiquitin protein ligase 1	protein-coding
mm_124632.1	chr15	4026697	4026763	+	1	NA	non-coding (NR_028266, exon 1 of 2)	non-coding (NR_028266, exon 1 of 2)	302	NM_024188	67041	Mm.13445	NM_024188	ENSMUSG00000022186	Oxct1	2610008O03Rik|Oxct|Oxct2a|Scot-s	3-oxoacid CoA transferase 1	protein-coding
mm_156212.1	chrX	134685162	134685179	+	1	NA	non-coding (NR_045454, exon 3 of 3)	non-coding (NR_045454, exon 3 of 3)	1292	NR_045454	77983	Mm.153204	NR_045454	ENSMUSG00000087024	B230119M05Rik	-	RIKEN cDNA B230119M05 gene	ncRNA
mm_145156.1	chr18	46525153	46525192	+	1	NA	intron (NM_173423, intron 1 of 2)	CpG	799	NM_173423	240263	Mm.38249	NM_173423	ENSMUSG00000033319	Fem1c	2610312A07Rik|3632443A22Rik|AI646567	fem-1 homolog c (C.elegans)	protein-coding
mm_111481.1	chr12	98737502	98737515	-	1	NA	promoter-TSS (NM_001146199)	promoter-TSS (NM_001146199)	-103	NM_001146199	24000	Mm.4420	NM_011877	ENSMUSG00000021009	Ptpn21	PTPD1|PTPRL10	protein tyrosine phosphatase, non-receptor type 21	protein-coding
mm_167614.1	chr9	56160180	56160183	+	1	NA	intron (NM_019793, intron 1 of 6)	intron (NM_019793, intron 1 of 6)	889	NM_019793	56434	Mm.28484	NM_019793	ENSMUSG00000032324	Tspan3	1700055K04Rik|TM4-A|Tm4sf8	tetraspanin 3	protein-coding
mm_158320.1	chrX	133689008	133689016	-	1	NA	promoter-TSS (NM_001105246)	promoter-TSS (NM_001105246)	-19	NM_001105246	279653	Mm.39738	NM_001105245	ENSMUSG00000051323	Pcdh19	B530002L05Rik|Gm717|mKIAA1313	protocadherin 19	protein-coding
mm_80175.1	chr9	72274902	72274913	+	1	NA	promoter-TSS (NM_146224)	promoter-TSS (NM_146224)	19	NM_001311105	235469	Mm.242791	NM_146224	ENSMUSG00000038535	Zfp280d	A930005F02Rik|BC027163|Suhw4|ZNF634|Znf280d	zinc finger protein 280D	protein-coding
mm_75080.1	chr8	33914201	33914239	-	1	NA	intron (NM_001042674, intron 1 of 7)	RMER10B|LTR|ERVL	15643	NM_019733	19663	Mm.323997	NM_019733	ENSMUSG00000031586	Rbpms	2010300K22Rik|2700019M19Rik|AU017537|RBP-MS|hermes	RNA binding protein gene with multiple splicing	protein-coding
mm_112831.1	chr13	20818869	20818877	+	1	NA	intron (NM_012054, intron 2 of 20)	L1MC5|LINE|L1	24760	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_42706.1	chr5	120145800	120145803	+	1	NA	intron (NM_028762, intron 21 of 23)	intron (NM_028762, intron 21 of 23)	-6538	NR_045793	100503427	Mm.446834	NR_045793	ENSMUSG00000097368	Gm10390	ENSMUSG00000072671	predicted gene 10390	ncRNA
mm_112853.1	chr13	20836214	20836240	+	1	NA	intron (NM_012054, intron 2 of 20)	intron (NM_012054, intron 2 of 20)	42114	NM_012054	27052	Mm.314046	NM_012054	ENSMUSG00000021322	Aoah	4930433E13Rik	acyloxyacyl hydrolase	protein-coding
mm_112770.1	chr13	19382612	19382617	+	1	NA	intron (NM_001347485, intron 1 of 7)	ORR1A4|LTR|ERVL-MaLR	13199	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_131390.1	chr16	14215746	14215770	+	1	NA	exon (NM_013607, exon 25 of 42)	exon (NM_013607, exon 25 of 42)	52483	NM_001114085	67203	Mm.24105	NM_023317	ENSMUSG00000022678	Nde1	2810027M15Rik|AU042936|AW822251|Nude|mNudE	nudE neurodevelopment protein 1	protein-coding
mm_145669.1	chr18	61399170	61399195	+	1	NA	intron (NM_133249, intron 1 of 11)	CpG	1249	NM_133249	170826	Mm.415302	NM_133249	ENSMUSG00000033871	Ppargc1b	4631412G21Rik|Perc	peroxisome proliferative activated receptor, gamma, coactivator 1 beta	protein-coding
mm_109961.1	chr12	12492844	12492881	-	1	NA	Intergenic	MLT1F-int|LTR|ERVL-MaLR	-100387	NR_045829	70858	Mm.410838	NR_045829		4921511I17Rik	-	RIKEN cDNA 4921511I17 gene	ncRNA
mm_30943.1	chr4	33056340	33056340	+	1	NA	Intergenic	Intergenic	-6772	NM_008076	14409	Mm.6227	NM_008076	ENSMUSG00000023267	Gabrr2	-	gamma-aminobutyric acid (GABA) C receptor, subunit rho 2	protein-coding
mm_25510.1	chr3	109684571	109684576	+	1	NA	3' UTR (NM_020505, exon 27 of 27)	3' UTR (NM_020505, exon 27 of 27)	110566	NM_146139	57257	Mm.282257	NM_020505	ENSMUSG00000033721	Vav3	A530094I06Rik|AA986410|Idd18.1	vav 3 oncogene	protein-coding
mm_170507.1	chr19	24876018	24876035	-	1	NA	Intergenic	Intergenic	-14184	NM_175013	226041	Mm.105222	NM_175013	ENSMUSG00000041731	Pgm5	4833423B07|9530034F03Rik|D830025G17|aciculin	phosphoglucomutase 5	protein-coding
mm_6312.1	chr1	71593139	71593159	-	1	NA	exon (NM_001276413, exon 40 of 44)	exon (NM_001276413, exon 40 of 44)	35993	NM_026195	108147	Mm.38010	NM_026195	ENSMUSG00000026192	Atic	2610509C24Rik|AA536954|AW212393	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	protein-coding
mm_167756.1	chr9	110422392	110422400	-	1	NA	exon (NM_008694, exon 4 of 4)	exon (NM_008694, exon 4 of 4)	2588	NM_008694	18054	Mm.236225	NM_008694	ENSMUSG00000032484	Ngp	bectenecin	neutrophilic granule protein	protein-coding
mm_105566.1	chr11	106572183	106572200	-	1	NA	intron (NM_198292, intron 1 of 11)	intron (NM_198292, intron 1 of 11)	40739	NM_198292	21763	Mm.102407	NM_198292	ENSMUSG00000040548	Tex2	4930568E07Rik|AI553404|Def-5|Taz4	testis expressed gene 2	protein-coding
mm_44631.1	chr5	27745576	27745581	-	1	NA	intron (NM_018878, intron 17 of 20)	RLTR40|LTR|ERVK	45972	NM_018878	55982	Mm.277190	NM_018878	ENSMUSG00000002221	Paxip1	D5Ertd149e|PTIP	PAX interacting (with transcription-activation domain) protein 1	protein-coding
mm_154717.1	chrX	9199965	9200000	+	1	NA	promoter-TSS (NM_173414)	promoter-TSS (NM_173414)	9	NM_173414	236285	Mm.245119	NM_173414	ENSMUSG00000047344	Lancl3	6030463G20Rik	LanC lantibiotic synthetase component C-like 3 (bacterial)	protein-coding
mm_89046.1	chr10	82860302	82860343	+	1	NA	promoter-TSS (NM_001042514)	promoter-TSS (NM_001042514)	-19	NM_001042514	50493	Mm.210155	NM_015762	ENSMUSG00000020250	Txnrd1	TR|TR1|TrxR1	thioredoxin reductase 1	protein-coding
mm_32476.1	chr4	107830950	107830957	+	1	NA	intron (NR_033496, intron 2 of 20)	intron (NR_033496, intron 2 of 20)	28694	NM_001080926	16975	Mm.442134	NM_053073	ENSMUSG00000028613	Lrp8	4932703M08Rik|AA921429|AI848122|ApoER2|Lr8b	low density lipoprotein receptor-related protein 8, apolipoprotein e receptor	protein-coding
mm_160529.1	chr9	37992592	37992592	+	1	NA	promoter-TSS (NM_146418)	promoter-TSS (NM_146418)	100	NM_146418	258413	Mm.335066	NM_146418	ENSMUSG00000060583	Olfr881	MOR162-7	olfactory receptor 881	protein-coding
mm_98492.1	chr11	94951578	94951600	+	1	NA	exon (NM_007742, exon 51 of 51)	exon (NM_007742, exon 51 of 51)	15365	NM_007742	12842	Mm.277735	NM_007742	ENSMUSG00000001506	Col1a1	Col1a-1|Cola-1|Cola1|Mov-13|Mov13	collagen, type I, alpha 1	protein-coding
mm_143962.1	chr17	87050649	87050675	-	1	NA	Intergenic	Intergenic	25101	NM_019936	56724	Mm.109329	NM_019936	ENSMUSG00000024146	Cript	1200020A08Rik|AA589469	cysteine-rich PDZ-binding protein	protein-coding
mm_160922.1	chr11	84880145	84880145	-	1	NA	promoter-TSS (NM_027388)	promoter-TSS (NM_027388)	50	NM_027388	70325	Mm.390414	NM_027388	ENSMUSG00000045140	Pigw	2610044A17Rik|Gwt1	phosphatidylinositol glycan anchor biosynthesis, class W	protein-coding
mm_148637.1	chr19	5474797	5474822	+	1	NA	promoter-TSS (NM_001164352)	promoter-TSS (NM_001164352)	74	NM_001164352	58859	Mm.276367	NM_021474	ENSMUSG00000024909	Efemp2	0610011K11Rik|Fbln4|MBP1	epidermal growth factor-containing fibulin-like extracellular matrix protein 2	protein-coding
mm_78066.1	chr9	15306213	15306219	+	1	NA	promoter-TSS (NM_001199485)	promoter-TSS (NM_001199485)	2	NM_027261	75316	Mm.354115	NM_026541	ENSMUSG00000031939	Taf1d	2810003M17Rik|4930553M18Rik|5930426I11Rik|Josd3|TAF(I)41|TAFI41	TATA-box binding protein associated factor, RNA polymerase I, D	protein-coding
mm_138104.1	chr17	34092906	34092916	+	1	NA	intron (NR_046183, intron 2 of 4)	intron (NR_046183, intron 2 of 4)	532	NM_008206	15001	Mm.116	NM_008206	ENSMUSG00000024334	H2-Oa	H-2Oa	histocompatibility 2, O region alpha locus	protein-coding
mm_106274.1	chr11	117989860	117989868	-	1	NA	intron (NM_133757, intron 1 of 9)	intron (NM_133757, intron 1 of 9)	3007	NM_133757	74451	Mm.28864	NM_133757	ENSMUSG00000017715	Pgs1	2610019F11Rik|4933424M23Rik|SAF	phosphatidylglycerophosphate synthase 1	protein-coding
mm_84933.1	chr9	82908714	82908755	-	1	NA	exon (NM_001081216, exon 19 of 40)	exon (NM_001081216, exon 19 of 40)	66755	NM_001081216	83946	Mm.221688	NM_031879	ENSMUSG00000032253	Phip	2810004D21Rik|4632404O06Rik|Ndrp|Wdr11	pleckstrin homology domain interacting protein	protein-coding
mm_122297.1	chr14	34588682	34588690	-	1	NA	promoter-TSS (NM_001039071)	promoter-TSS (NM_001039071)	-5	NM_001039073	24131	Mm.29733	NM_011918	ENSMUSG00000021798	Ldb3	AW742271|PDLIM6|ZASP	LIM domain binding 3	protein-coding
mm_40390.1	chr5	52742611	52742624	+	1	NA	intron (NM_025951, intron 1 of 9)	(T)n|Simple_repeat|Simple_repeat	1043	NM_025951	67073	Mm.248647	NM_025951	ENSMUSG00000029186	Pi4k2b	2610042N09Rik|4933409G22Rik	phosphatidylinositol 4-kinase type 2 beta	protein-coding
mm_37124.1	chr4	116666770	116666784	-	1	NA	Intergenic	Intergenic	-15103	NM_021473	58810	Mm.30085	NM_021473	ENSMUSG00000028692	Akr1a1	2610201A18Rik|Akr1a4	aldo-keto reductase family 1, member A1 (aldehyde reductase)	protein-coding
mm_39242.1	chr5	3341478	3341485	+	1	NA	Intergenic	CpG	-2412	NM_009873	12571	Mm.31672	NM_009873	ENSMUSG00000040274	Cdk6	AI504062|Crk2	cyclin-dependent kinase 6	protein-coding
mm_15170.1	chr2	154014914	154014922	+	1	NA	intron (NM_008953, intron 7 of 8)	intron (NM_008953, intron 7 of 8)	6642	NM_008953	19194	Mm.29197	NM_008953	ENSMUSG00000042459	Bpifa2	Bpifa2e|Psp	BPI fold containing family A, member 2	protein-coding
mm_159109.1	chr2	42653451	42653451	-	1	NA	5' UTR (NM_053011, exon 1 of 91)	5' UTR (NM_053011, exon 1 of 91)	147	NM_053011	94217	Mm.441398	NM_053011	ENSMUSG00000049252	Lrp1b	9630004P12Rik|LRP-DIT	low density lipoprotein-related protein 1B (deleted in tumors)	protein-coding
mm_51139.1	chr6	69516340	69516341	+	1	NA	Intergenic	7SLRNA|srpRNA|srpRNA	-189166	NR_004434	19783		NR_004434	ENSMUSG00000106222	Rprl1	Rmrp2|Rpr|Rprh2	ribonuclease P RNA-like 1	ncRNA
mm_51994.1	chr6	92136850	92136853	+	1	NA	intron (NM_001347342, intron 2 of 14)	PB1D7|SINE|Alu	44418	NM_001347342	22026	Mm.87062	NM_011630	ENSMUSG00000005893	Nr2c2	TAK1|Tr4|mKIAA4145	nuclear receptor subfamily 2, group C, member 2	protein-coding
mm_70459.1	chr8	11840502	11840508	+	1	NA	promoter-TSS (NM_029326)	promoter-TSS (NM_029326)	-16	NM_029326	75528	Mm.440342	NM_029326	ENSMUSG00000031512	Tex29	1700018L24Rik	testis expressed 29	protein-coding
mm_129862.1	chr15	83355914	83355916	-	1	NA	non-coding (NR_027980, exon 4 of 4)	non-coding (NR_027980, exon 4 of 4)	-5668	NM_025445	66251	Mm.258910	NM_025445	ENSMUSG00000054277	Arfgap3	0610009H19Rik|1810004P07Rik|1810035F16Rik|9130416J18Rik|Arfgap1	ADP-ribosylation factor GTPase activating protein 3	protein-coding
mm_143062.1	chr17	57011272	57011326	-	1	NA	promoter-TSS (NM_133801)	promoter-TSS (NM_133801)	-11	NM_133801	98053	Mm.24632	NM_133801	ENSMUSG00000002658	Gtf2f1	2810405L04Rik|C76800|RAP74	general transcription factor IIF, polypeptide 1	protein-coding
mm_78510.1	chr9	32906558	32906568	+	1	NA	non-coding (NR_131058, exon 4 of 4)	non-coding (NR_131058, exon 4 of 4)	22403	NR_131058	330917	Mm.488283	NR_131058		Gm27162	A430016B06	predicted gene 27162	ncRNA
mm_139463.1	chr17	55954319	55954338	+	1	NA	TTS (NR_108021)	TTS (NR_108021)	1705	NM_015766	50498	Mm.256798	NM_015766	ENSMUSG00000003206	Ebi3	EBI-3|IL-27	Epstein-Barr virus induced gene 3	protein-coding
mm_40290.1	chr5	43233929	43233951	+	1	NA	exon (NM_001177379, exon 1 of 11)	exon (NM_001177379, exon 1 of 11)	477	NM_001177379	231207	Mm.7233	NM_175937	ENSMUSG00000039782	Cpeb2	A630055H10Rik|Cpe-bp2	cytoplasmic polyadenylation element binding protein 2	protein-coding
mm_135389.1	chr16	44332704	44332714	-	1	NA	5' UTR (NM_001159419, exon 1 of 26)	5' UTR (NM_001159419, exon 1 of 26)	129	NM_198034	320007	Mm.242144	NM_198034	ENSMUSG00000022696	Sidt1	AW045928|B830021E24Rik	SID1 transmembrane family, member 1	protein-coding
mm_19594.1	chr2	102186323	102186394	-	1	NA	5' UTR (NM_178886, exon 1 of 6)	5' UTR (NM_178886, exon 1 of 6)	102	NM_178886	241576	Mm.489740	NM_178886	ENSMUSG00000048058	Ldlrad3	6430500P08|AI194318|Lrad3	low density lipoprotein receptor class A domain containing 3	protein-coding
mm_109448.1	chr12	110991600	110991601	+	1	NA	Intergenic	Intergenic	-2798	NR_036598	77878	Mm.293198	NR_036598		6030440G07Rik	-	RIKEN cDNA 6030440G07 gene	ncRNA
mm_133315.1	chr16	77646339	77646342	+	1	NA	promoter-TSS (NR_029540)	promoter-TSS (NR_029540)	67	NR_029540	723952		NR_029540	ENSMUSG00000065472	Mir125b-2	Mirn125b-2|mir-125b-2	microRNA 125b-2	ncRNA
mm_78739.1	chr9	41588375	41588382	+	1	NA	intron (NR_015483, intron 1 of 1)	intron (NR_015483, intron 1 of 1)	6452	NR_029822	387236		NR_029822	ENSMUSG00000093354	Mir125b-1	Mirn125b|Mirn125b-1|mir-125b-1	microRNA 125b-1	ncRNA
mm_107967.1	chr12	72761130	72761140	+	1	NA	promoter-TSS (NM_008910)	promoter-TSS (NM_008910)	-76	NM_008910	19042	Mm.261045	NM_008910	ENSMUSG00000021096	Ppm1a	2310003C21Rik|2900017D14Rik|AI427932|AU017636|MMPa-2|MPPa-1	protein phosphatase 1A, magnesium dependent, alpha isoform	protein-coding
mm_5519.1	chr1	37712758	37712766	-	1	NA	intron (NM_028096, intron 1 of 9)	MT2C_Mm|LTR|ERVL	7049	NM_028096	72097	Mm.142607	NM_028096	ENSMUSG00000026090	2010300C02Rik	-	RIKEN cDNA 2010300C02 gene	protein-coding
mm_168652.1	chr11	87443232	87443252	+	1	NA	intron (NM_001199293, intron 2 of 30)	U3|snRNA|snRNA	15651	NM_001199293	83560	Mm.440758	NM_031386	ENSMUSG00000010342	Tex14	C85585	testis expressed gene 14	protein-coding
mm_134634.1	chr16	21694571	21694601	-	1	NA	promoter-TSS (NM_001001881)	promoter-TSS (NM_001001881)	79	NM_001001881	72190	Mm.131606	NM_001001881	ENSMUSG00000043391	2510009E07Rik	AI194952	RIKEN cDNA 2510009E07 gene	protein-coding
mm_79450.1	chr9	56114667	56114677	+	1	NA	intron (NM_011193, intron 2 of 14)	intron (NM_011193, intron 2 of 14)	24696	NM_011193	19200	Mm.2534	NM_011193	ENSMUSG00000032322	Pstpip1	CD2BP1|def-2	proline-serine-threonine phosphatase-interacting protein 1	protein-coding
mm_132966.1	chr16	50783392	50783423	+	1	NA	promoter-TSS (NR_131006)	promoter-TSS (NR_131006)	-2	NR_131006	78639	Mm.160109	NR_131005	ENSMUSG00000092276	1700116B05Rik	-	RIKEN cDNA 1700116B05 gene	ncRNA
mm_148746.1	chr19	6047022	6047041	+	1	NA	promoter-TSS (NM_001164709)	promoter-TSS (NM_001164709)	-114	NM_001164709	74126	Mm.149870	NM_028769	ENSMUSG00000024807	Syvn1	1200010C09Rik|AW211966|C85322|D530017H19Rik|Hrd1	synovial apoptosis inhibitor 1, synoviolin	protein-coding
mm_41397.1	chr5	90772538	90772551	+	1	NA	5' UTR (NM_019932, exon 1 of 3)	5' UTR (NM_019932, exon 1 of 3)	109	NM_019932	56744	Mm.332490	NM_019932	ENSMUSG00000029373	Pf4	Cxcl4|Scyb4	platelet factor 4	protein-coding
mm_7331.1	chr1	105157897	105157905	-	1	NA	Intergenic	LTR72_RN|LTR|ERV1	198809	NM_178779	320311	Mm.389162	NM_178779	ENSMUSG00000047496	Rnf152	A930029B02Rik	ring finger protein 152	protein-coding
mm_131886.1	chr16	23225475	23225496	+	1	NA	promoter-TSS (NM_001252505)	promoter-TSS (NM_001252505)	-536	NM_001252505	20440	Mm.149029	NM_145933	ENSMUSG00000022885	St6gal1	AW742324|Siat1|St6Gal-I|St6gal|St6galI	beta galactoside alpha 2,6 sialyltransferase 1	protein-coding
mm_48776.1	chr5	148551649	148551681	-	1	NA	intron (NM_011908, intron 1 of 4)	intron (NM_011908, intron 1 of 4)	1123	NM_011908	24109	Mm.21846	NM_011908	ENSMUSG00000001687	Ubl3	AW108023|HCG	ubiquitin-like 3	protein-coding
mm_110898.1	chr12	75631328	75631360	-	1	NA	non-coding (NR_038063, exon 1 of 1)	non-coding (NR_038063, exon 1 of 1)	405	NR_038063	665931	Mm.341719	NR_038063		Rplp2-ps1	Gm7852	ribosomal protein, large P2, pseudogene 1	pseudo
mm_130760.1	chr15	101349448	101349452	-	1	NA	TTS (NM_028770)	TTS (NM_028770)	-19902	NR_035462	100316694		NR_035462	ENSMUSG00000088459	Mir1941	mmu-mir-1941	microRNA 1941	ncRNA
mm_77081.1	chr8	110503073	110503080	-	1	NA	promoter-TSS (NR_105058)	promoter-TSS (NR_105058)	-720	NR_105058	100861869	Mm.84499	NR_105058		Gm21283	-	predicted gene, 21283	ncRNA
mm_154286.1	chr19	60864433	60864450	-	1	NA	3' UTR (NM_007452, exon 7 of 7)	3' UTR (NM_007452, exon 7 of 7)	-3011	NM_053198	94281	Mm.48179	NM_053198	ENSMUSG00000063698	Sfxn4	-	sideroflexin 4	protein-coding
mm_48217.1	chr5	137611373	137611428	-	1	NA	promoter-TSS (NM_008788)	promoter-TSS (NM_008788)	4	NM_008788	18542	Mm.262345	NM_008788	ENSMUSG00000029718	Pcolce	Astt-2|Astt2|P14|PCPE-1	procollagen C-endopeptidase enhancer protein	protein-coding
mm_105643.1	chr11	107081300	107081317	-	1	NA	exon (NM_176850, exon 6 of 28)	exon (NM_176850, exon 6 of 28)	50614	NM_176850	207165	Mm.343986	NM_176850	ENSMUSG00000040481	Bptf	9430093H17Rik|Falz	bromodomain PHD finger transcription factor	protein-coding
mm_150545.1	chr19	39315540	39315547	+	1	NA	intron (NM_007815, intron 5 of 8)	intron (NM_007815, intron 5 of 8)	28458	NM_007815	13095	Mm.20764	NM_007815	ENSMUSG00000003053	Cyp2c29	AHOH|AHOHase|AI159681|AI196010|Ah-2|Ahh-1|Cyp2c|P450-2C	cytochrome P450, family 2, subfamily c, polypeptide 29	protein-coding
mm_155893.1	chrX	101652503	101652515	+	1	NA	intron (NM_139144, intron 4 of 21)	intron (NM_139144, intron 4 of 21)	12291	NM_001290535	108155	Mm.487332	NM_139144	ENSMUSG00000034160	Ogt	1110038P24Rik|4831420N21Rik|AI115525|Ogtl	O-linked N-acetylglucosamine (GlcNAc) transferase (UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase)	protein-coding
mm_118286.1	chr13	112874125	112874133	-	1	NA	intron (NM_028151, intron 24 of 26)	(A)n|Simple_repeat|Simple_repeat	53251	NM_028151	72198	Mm.291029	NM_028151	ENSMUSG00000016018	Skiv2l2	2610528A15Rik|mKIAA0052	superkiller viralicidic activity 2-like 2 (S. cerevisiae)	protein-coding
mm_132763.1	chr16	44724336	44724340	+	1	NA	promoter-TSS (NM_145972)	promoter-TSS (NM_145972)	37	NM_145972	212547	Mm.310573	NM_145972	ENSMUSG00000036208	Nepro	-	nucleolus and neural progenitor protein	protein-coding
mm_49244.1	chr6	17307633	17307651	+	1	NA	promoter-TSS (NM_001243064)	promoter-TSS (NM_001243064)	2	NM_001243064	12389	Mm.28278	NM_007616	ENSMUSG00000007655	Cav1	Cav|Cav-1	caveolin 1, caveolae protein	protein-coding
mm_144143.1	chr18	4994711	4994717	+	1	NA	Intergenic	Intergenic	-51875	NM_153153	225115	Mm.136791	NM_153153	ENSMUSG00000024236	Svil	AU024053|B430302E16Rik	supervillin	protein-coding
mm_83742.1	chr9	51102063	51102085	-	1	NA	promoter-TSS (NM_177702)	promoter-TSS (NM_177702)	4	NM_177702	235345	Mm.72828	NM_177702	ENSMUSG00000032057	4833427G06Rik	-	RIKEN cDNA 4833427G06 gene	protein-coding
mm_150146.1	chr19	31881955	31881973	+	1	NA	intron (NM_001081074, intron 1 of 11)	intron (NM_001081074, intron 1 of 11)	13203	NM_001081074	69865	Mm.87538	NM_001081074	ENSMUSG00000052595	A1cf	1810073H04Rik|ACF64|ACF65|ASP|Acf|MCM|MerCreMer|Tg(Myh6-cre/Esr1*)1Jmk|mer	APOBEC1 complementation factor	protein-coding
mm_24891.1	chr3	96161957	96161977	+	1	NA	promoter-TSS (NM_181409)	promoter-TSS (NM_181409)	-3	NM_181409	194126	Mm.268536	NM_181409	ENSMUSG00000045934	Mtmr11	AI035306|BC051083|Cra	myotubularin related protein 11	protein-coding
mm_29033.1	chr3	102167632	102167659	-	1	NA	intron (NM_177545, intron 4 of 7)	intron (NM_177545, intron 4 of 7)	37048	NM_177545	229658	Mm.118004	NM_177545	ENSMUSG00000027860	Vangl1	Kitenin|Lpp2|Stb2|Stbm	vang-like 1 (van gogh, Drosophila)	protein-coding
mm_110860.1	chr12	73444869	73444884	-	1	NA	Intergenic	Intergenic	-35313	NR_046013	380765	Mm.490476	NR_046013		D830013O20Rik	Gm891	RIKEN cDNA D830013O20 gene	ncRNA
mm_6941.1	chr1	85727187	85727199	-	1	NA	intron (NM_177055, intron 1 of 5)	intron (NM_177055, intron 1 of 5)	9413	NM_177055	319997	Mm.116691	NM_177055	ENSMUSG00000052760	A630001G21Rik	-	RIKEN cDNA A630001G21 gene	protein-coding
mm_121988.1	chr14	26442693	26442701	-	1	NA	intron (NM_001347494, intron 10 of 19)	intron (NM_001347494, intron 10 of 19)	85150	NR_038005	71106	Mm.158564	NR_038005	ENSMUSG00000021874	4933413J09Rik	GCSE	RIKEN cDNA 4933413J09 gene	ncRNA
mm_125760.1	chr15	73920015	73920018	+	1	NA	Intergenic	Intergenic	-80345	NM_001033365	268816	Mm.440635	NM_001033365	ENSMUSG00000072487	Mroh5	Gm628	maestro heat-like repeat family member 5	protein-coding
mm_140222.1	chr17	83917932	83917949	+	1	NA	Intergenic	Intergenic	-71150	NM_025325	107766	Mm.30100	NM_025325	ENSMUSG00000000673	Haao	0610007K21Rik|0610012J07Rik|3-HAO|3-HAOxase|3HAO	3-hydroxyanthranilate 3,4-dioxygenase	protein-coding
mm_25070.1	chr3	99316489	99316503	+	1	NA	intron (NM_009323, intron 5 of 7)	Lx5c|LINE|L1	62736	NM_009323	21384	Mm.88761	NM_009323	ENSMUSG00000027868	Tbx15	Tbx14|Tbx8|de	T-box 15	protein-coding
mm_141168.1	chr17	26532666	26532676	-	1	NA	Intergenic	Intergenic	-24199	NM_013642	19252	Mm.239041	NM_013642	ENSMUSG00000024190	Dusp1	3CH134|MKP1|Ptpn16|U19515|erp|mkp-1	dual specificity phosphatase 1	protein-coding
mm_146726.1	chr18	15064448	15064476	-	1	NA	promoter-TSS (NM_001142731)	promoter-TSS (NM_001142731)	-880	NM_001142731	106931	Mm.329299	NM_134112	ENSMUSG00000036225	Kctd1	4933402K10Rik|AI661543|AW553000	potassium channel tetramerisation domain containing 1	protein-coding
mm_151189.1	chr19	53424413	53424417	+	1	NA	Intergenic	Arthur1|DNA|hAT-Tip100	-33842	NM_172429	76479	Mm.313687	NM_172429	ENSMUSG00000025024	Smndc1	2410004J23Rik|4933440I19Rik	survival motor neuron domain containing 1	protein-coding
mm_129719.1	chr15	81936696	81936716	-	1	NA	promoter-TSS (NM_145473)	promoter-TSS (NM_145473)	-53	NM_145473	105859	Mm.22524	NM_145473	ENSMUSG00000042109	Csdc2	AI415250|AI481750|Pippin	cold shock domain containing C2, RNA binding	protein-coding
mm_171000.1	chr2	75663571	75663587	+	1	NA	exon (NM_198090, exon 8 of 11)	exon (NM_198090, exon 8 of 11)	4289	NR_033513	627828	Mm.459502	NR_033513	ENSMUSG00000092086	Gm6793	EG627828	heterogeneous nuclear ribonucleoprotein A3 pseudogene	pseudo
mm_17634.1	chr2	31100986	31100995	-	1	NA	intron (NM_001038700, intron 2 of 14)	intron (NM_001038700, intron 2 of 14)	-4490	NM_001177650	14269	Mm.52297	NM_019406	ENSMUSG00000075415	Fnbp1	1110057E06Rik|2210010H06Rik|FBP1|Fbp17	formin binding protein 1	protein-coding
mm_46231.1	chr5	99215643	99215662	-	1	NA	Intergenic	Intergenic	37275	NM_181318	320292	Mm.259074	NM_145839	ENSMUSG00000089809	Rasgef1b	4732452O09Rik|GPIgamma4|Gpig4	RasGEF domain family, member 1B	protein-coding
mm_129215.1	chr15	76522600	76522608	-	1	NA	promoter-TSS (NM_130893)	promoter-TSS (NM_130893)	-475	NM_130893	170729	Mm.218747	NM_130893	ENSMUSG00000048385	Scrt1	-	scratch family zinc finger 1	protein-coding
mm_57685.1	chr6	128512335	128512346	-	1	NA	exon (NM_007376, exon 12 of 36)	exon (NM_007376, exon 12 of 36)	14380	NM_007376	11287	Mm.260144	NM_007376	ENSMUSG00000030359	Pzp	A1m|A2m|AI893533|MAM	pregnancy zone protein	protein-coding
mm_112667.1	chr13	16027327	16027369	+	1	NA	3' UTR (NM_008380, exon 5 of 5)	3' UTR (NM_008380, exon 5 of 5)	15497	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_104372.1	chr11	94360149	94360150	-	1	NA	intron (NM_029600, intron 19 of 30)	(CAAAA)n|Simple_repeat|Simple_repeat	32148	NM_146024	71452	Mm.141054	NM_027799	ENSMUSG00000020864	Ankrd40	1110011C06Rik|5530600A18Rik|Gcap15	ankyrin repeat domain 40	protein-coding
mm_21772.1	chr2	164844765	164844775	-	1	NA	intron (NM_011125, intron 10 of 15)	intron (NM_011125, intron 10 of 15)	10997	NM_008906	19025	Mm.359633	NM_008906	ENSMUSG00000017760	Ctsa	AU019505|PPCA|Ppgb	cathepsin A	protein-coding
mm_39580.1	chr5	23446703	23446708	+	1	NA	intron (NM_026984, intron 1 of 25)	intron (NM_026984, intron 1 of 25)	12276	NM_026984	69188	Mm.205190	NM_026984	ENSMUSG00000029004	Kmt2e	1810033J14Rik|9530077A04Rik|D230038D11Rik|Mll5|NKp44L	lysine (K)-specific methyltransferase 2E	protein-coding
mm_3682.1	chr1	153723845	153723874	+	1	NA	non-coding (NR_046171, exon 3 of 3)	non-coding (NR_046171, exon 3 of 3)	13970	NR_046171	329271	Mm.384841	NR_046171	ENSMUSG00000100334	C230024C17Rik	C230024C17	RIKEN cDNA C230024C17 gene	ncRNA
mm_114466.1	chr13	67744221	67744225	+	1	NA	intron (NR_027969, intron 1 of 2)	intron (NR_027969, intron 1 of 2)	10911	NM_001001130	22746	Mm.288396	NM_001001130	ENSMUSG00000058331	Zfp85	KRAB19|Rslcan2|Zfp71|Zfp85-rs1	zinc finger protein 85	protein-coding
mm_45119.1	chr5	45823429	45823432	-	1	NA	intron (NM_001163073, intron 1 of 6)	Lx8|LINE|L1	33122	NM_172153	209707	Mm.71498	NM_172153	ENSMUSG00000015882	Lcorl	Mlr1	ligand dependent nuclear receptor corepressor-like	protein-coding
mm_15994.1	chr2	167061292	167061302	+	1	NA	intron (NM_001033196, intron 1 of 13)	intron (NM_001033196, intron 1 of 13)	-1637	NR_138563	68949	Mm.391959	NM_001081005		Zfas1	1500012F01Rik|Zfos1	zinc finger, NFX1-type containing 1, antisense RNA 1	ncRNA
mm_28952.1	chr3	100483636	100483637	-	1	NA	intron (NM_001142952, intron 1 of 1)	intron (NM_001142952, intron 1 of 1)	5556	NM_001142952	74645	Mm.226900	NM_001142952	ENSMUSG00000044468	Fam46c	4930431B09Rik|AI449797	family with sequence similarity 46, member C	protein-coding
mm_161311.1	chr14	40948191	40948191	-	1	NA	promoter-TSS (NM_001316748)	promoter-TSS (NM_001316748)	18	NM_001316748	52588	Mm.28876	NM_145928	ENSMUSG00000037824	Tspan14	AA958793|D14Ertd226e|Tm4sf14|tspan-14	tetraspanin 14	protein-coding
mm_146116.1	chr18	74283138	74283153	+	1	NA	promoter-TSS (NM_028948)	promoter-TSS (NM_028948)	45	NM_028948	74453	Mm.182293	NM_028948	ENSMUSG00000035394	Cfap53	4933415I03Rik|Ccdc11	cilia and flagella associated protein 53	protein-coding
mm_59079.1	chr7	19628979	19628998	+	1	NA	intron (NM_001290457, intron 1 of 10)	CpG	450	NM_001290457	19698	Mm.1741	NM_009046	ENSMUSG00000002983	Relb	shep	avian reticuloendotheliosis viral (v-rel) oncogene related B	protein-coding
mm_135799.1	chr16	57231351	57231359	-	1	NA	exon (NM_026254, exon 1 of 18)	exon (NM_026254, exon 1 of 18)	111	NM_026254	67581	Mm.257819	NM_026254	ENSMUSG00000022749	Tbc1d23	4930451A13Rik|AU015720|AU043671|AU043778|D030022P07Rik|W51689	TBC1 domain family, member 23	protein-coding
mm_146875.1	chr18	25479305	25479315	-	1	NA	3' UTR (NM_001146294, exon 13 of 13)	3' UTR (NM_001146294, exon 13 of 13)	274673	NM_133195	108013	Mm.266435	NM_133195	ENSMUSG00000024268	Celf4	A230070D14Rik|BRUNOL-4|Brul4|Brunol4|C130060B05Rik	CUGBP, Elav-like family member 4	protein-coding
mm_111603.1	chr12	102368160	102368162	-	1	NA	intron (NM_177620, intron 5 of 9)	intron (NM_177620, intron 5 of 9)	71652	NM_011175	19141	Mm.17185	NM_011175	ENSMUSG00000021190	Lgmn	AEP|AI746452|AU022324|Prsc1	legumain	protein-coding
mm_131165.1	chr16	7009026	7009034	+	1	NA	intron (NM_021477, intron 5 of 16)	RSINE1|SINE|B4	-60805	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_125736.1	chr15	73512560	73512607	+	1	NA	promoter-TSS (NM_001081066)	promoter-TSS (NM_001081066)	23	NM_001081066	105841	Mm.322557	NM_001081066	ENSMUSG00000036661	Dennd3	AI447457|E030003N15Rik	DENN/MADD domain containing 3	protein-coding
mm_100234.1	chr11	117228743	117228748	+	1	NA	intron (NM_001113486, intron 2 of 11)	intron (NM_001113486, intron 2 of 11)	29084	NM_001113486	53860	Mm.38450	NM_017380	ENSMUSG00000059248	Sept9	MSF1|Msf|PNUTL4|Sint1	septin 9	protein-coding
mm_28963.1	chr3	100685875	100685892	-	1	NA	promoter-TSS (NM_010763)	promoter-TSS (NM_010763)	-410	NM_010763	17156	Mm.271617	NM_010763	ENSMUSG00000008763	Man1a2	AI428775|AI528764|AI854422|Man1b|PCR2	mannosidase, alpha, class 1A, member 2	protein-coding
mm_169771.1	chr15	99905372	99905372	-	1	NA	Intergenic	B1F|SINE|Alu	26286	NM_028180	72277	Mm.272766	NM_028180	ENSMUSG00000045350	1700030F18Rik	FAM186A	RIKEN cDNA 1700030F18 gene	protein-coding
mm_83605.1	chr9	48605008	48605018	-	1	NA	5' UTR (NM_001311062, exon 1 of 4)	5' UTR (NM_001311062, exon 1 of 4)	110	NM_001311062	18113	Mm.8362	NM_010924	ENSMUSG00000032271	Nnmt	-	nicotinamide N-methyltransferase	protein-coding
mm_105336.1	chr11	102994311	102994328	-	1	NA	3' UTR (NM_026551, exon 5 of 5)	3' UTR (NM_026551, exon 5 of 5)	5602	NR_105896	102466988		NR_105896	ENSMUSG00000098613	Mir6931	Gm27303|mmu-mir-6931	microRNA 6931	ncRNA
mm_107983.1	chr12	73039337	73039345	+	1	NA	Intergenic	Intergenic	7371	NM_009189	20471	Mm.4645	NM_009189	ENSMUSG00000051367	Six1	BB138287	sine oculis-related homeobox 1	protein-coding
mm_9220.1	chr1	171234334	171234344	-	1	NA	promoter-TSS (NM_010185)	promoter-TSS (NM_010185)	10	NM_010185	14127	Mm.22673	NM_010185	ENSMUSG00000058715	Fcer1g	AI573376|CD23|FcR-gamma|FcR[g]|FcRgamma|Fce1g|FcepsilonRI|Ly-50	Fc receptor, IgE, high affinity I, gamma polypeptide	protein-coding
mm_23909.1	chr3	83042463	83042479	+	1	NA	exon (NM_181849, exon 8 of 8)	exon (NM_181849, exon 8 of 8)	7392	NM_181849	110135	Mm.30063	NM_181849	ENSMUSG00000033831	Fgb	2510049G14Rik	fibrinogen beta chain	protein-coding
mm_76631.1	chr8	91801949	91801970	-	1	NA	promoter-TSS (NM_001253822)	promoter-TSS (NM_001253822)	-305	NM_008393	16373	Mm.238044	NM_008393	ENSMUSG00000031734	Irx3	AI894186	Iroquois related homeobox 3	protein-coding
mm_7285.1	chr1	97721283	97721288	-	1	NA	intron (NM_173760, intron 24 of 27)	intron (NM_173760, intron 24 of 27)	48807	NM_173760	227399	Mm.220817	NM_173760	ENSMUSG00000040648	Ppip5k2	AW555814|Cfap160|D330021B20|Hisppd1|Vip2|mKIAA0433	diphosphoinositol pentakisphosphate kinase 2	protein-coding
mm_44427.1	chr5	20945483	20945530	-	1	NA	intron (NM_001080977, intron 1 of 7)	MLT1B|LTR|ERVL-MaLR	-5483	NR_030699	320770	Mm.491217	NR_030699	ENSMUSG00000101013	A630072M18Rik	Aptr	RIKEN cDNA A630072M18 gene	ncRNA
mm_100315.1	chr11	117987290	117987311	+	1	NA	intron (NM_133757, intron 1 of 9)	CpG	443	NM_133757	74451	Mm.28864	NM_133757	ENSMUSG00000017715	Pgs1	2610019F11Rik|4933424M23Rik|SAF	phosphatidylglycerophosphate synthase 1	protein-coding
mm_166070.1	chr4	135612368	135612369	-	1	NA	Intergenic	Intergenic	-14287	NR_015613	73937	Mm.292326	NM_028688	ENSMUSG00000086788	1700029M20Rik	4930406E24Rik	RIKEN cDNA 1700029M20 gene	ncRNA
mm_136457.1	chr16	94997739	94997753	-	1	NA	promoter-TSS (NM_010606)	promoter-TSS (NM_010606)	-50	NM_010606	16522	Mm.328720	NM_010606	ENSMUSG00000043301	Kcnj6	BIR1|GIRK2|KATP2|KCNJ7|Kir3.2|weaver|wv	potassium inwardly-rectifying channel, subfamily J, member 6	protein-coding
mm_100554.1	chr11	120722210	120722220	+	1	NA	intron (NM_133223, intron 1 of 5)	intron (NM_133223, intron 1 of 5)	747	NM_133223	170758	Mm.34008	NM_133223	ENSMUSG00000018012	Rac3	Rac1B	RAS-related C3 botulinum substrate 3	protein-coding
mm_31829.1	chr4	70378143	70378159	+	1	NA	intron (NM_145990, intron 4 of 36)	GSAT_MM|Satellite|Satellite	32284	NM_001313762	214444	Mm.370777	NM_145990	ENSMUSG00000039298	Cdk5rap2	2900018K03Rik|an|mKIAA1633	CDK5 regulatory subunit associated protein 2	protein-coding
mm_70598.1	chr8	13292690	13292727	+	1	NA	intron (NM_172282, intron 2 of 12)	intron (NM_172282, intron 2 of 12)	-4582	NM_001042650	102323	Mm.368890	NM_001024504	ENSMUSG00000038506	Dcun1d2	AW495713|mFLJ10704	DCN1, defective in cullin neddylation 1, domain containing 2 (S. cerevisiae)	protein-coding
mm_134530.1	chr16	19241696	19241710	-	1	NA	Intergenic	Intergenic	45038	NM_146451	258443	Mm.377506	NM_146451	ENSMUSG00000050742	Olfr164	MOR279-2	olfactory receptor 164	protein-coding
mm_74278.1	chr8	125327881	125327885	+	1	NA	Intergenic	LTR16A|LTR|ERVL	164827	NM_001081337	244668	Mm.271668	NM_001081337	ENSMUSG00000001995	Sipa1l2	BC058408|mKIAA1389	signal-induced proliferation-associated 1 like 2	protein-coding
mm_109544.1	chr12	111678095	111678140	+	1	NA	promoter-TSS (NM_001099793)	promoter-TSS (NM_001099793)	12	NM_177374	328162	Mm.425747	NM_177374	ENSMUSG00000060950	Trmt61a	6720458F09Rik|AI606093|Gcd14|Trm61	tRNA methyltransferase 61A	protein-coding
mm_148655.1	chr19	5494630	5494633	+	1	NA	TTS (NM_007687)	TTS (NM_007687)	4176	NM_007687	12631	Mm.329655	NM_007687	ENSMUSG00000056201	Cfl1	AA959946|Cof	cofilin 1, non-muscle	protein-coding
mm_41554.1	chr5	92962069	92962093	+	1	NA	intron (NM_001077595, intron 8 of 9)	intron (NM_001077595, intron 8 of 9)	64088	NM_001077596	27428	Mm.46014	NM_015756	ENSMUSG00000029381	Shroom3	AL022960|D5Ertd287e|Shrm|Shrm3	shroom family member 3	protein-coding
mm_168991.1	chr12	99645268	99645274	+	1	NA	Intergenic	LSU-rRNA_Hsa|rRNA|rRNA	-17297	NR_045288	73457	Mm.383439	NR_045288	ENSMUSG00000100211	1700064M15Rik	-	RIKEN cDNA 1700064M15 gene	ncRNA
mm_61785.1	chr7	83756511	83756531	+	1	NA	Intergenic	Intergenic	-21031	NM_010551	16170	Mm.10137	NM_010551	ENSMUSG00000001741	Il16	mKIAA4048	interleukin 16	protein-coding
mm_58265.1	chr6	145340092	145340108	-	1	NA	Intergenic	Intergenic	-47525	NR_003625	381827	Mm.179075	NM_001001987		1700073E17Rik	-	ribosomal protein L7 pseudogene	pseudo
mm_118754.1	chr14	22369320	22369321	+	1	NA	intron (NM_028275, intron 2 of 6)	Charlie5|DNA|hAT-Charlie	173478	NR_046307	74896	Mm.444661	NR_046307		4930405A10Rik	4930456G20Rik	RIKEN cDNA 4930405A10 gene	ncRNA
mm_140470.1	chr17	93199508	93199518	+	1	NA	5' UTR (NM_009625, exon 1 of 5)	5' UTR (NM_009625, exon 1 of 5)	345	NM_009625	11516	Mm.3407	NM_009625	ENSMUSG00000024256	Adcyap1	PACAP	adenylate cyclase activating polypeptide 1	protein-coding
mm_95632.1	chr11	53632041	53632056	+	1	NA	3' UTR (NM_008355, exon 4 of 4)	3' UTR (NM_008355, exon 4 of 4)	2654	NM_008355	16163	Mm.1284	NM_008355	ENSMUSG00000020383	Il13	Il-13	interleukin 13	protein-coding
mm_162417.1	chr1	88956276	88956278	+	1	NA	Intergenic	B4A|SINE|B4	-59836	NR_040471	73475	Mm.491040	NR_040471	ENSMUSG00000099378	1700067G17Rik	-	RIKEN cDNA 1700067G17 gene	ncRNA
mm_167953.1	chrX	140664332	140664342	+	1	NA	Intergenic	Intergenic	-13691	NM_011845	23947	Mm.131097	NM_011845	ENSMUSG00000000266	Mid2	FXY2|Trim1	midline 2	protein-coding
mm_112590.1	chr13	13825451	13825463	+	1	NA	3' UTR (NM_010317, exon 4 of 4)	3' UTR (NM_010317, exon 4 of 4)	41150	NM_010317	14706	Mm.215394	NM_010317	ENSMUSG00000021303	Gng4	-	guanine nucleotide binding protein (G protein), gamma 4	protein-coding
mm_46606.1	chr5	107869154	107869175	-	1	NA	intron (NM_007964, intron 1 of 17)	CpG	5943	NM_007964	14020	Mm.35796	NM_007964	ENSMUSG00000011831	Evi5	NB4S	ecotropic viral integration site 5	protein-coding
mm_54876.1	chr6	42645080	42645097	-	1	NA	promoter-TSS (NM_146174)	promoter-TSS (NM_146174)	-47	NM_146174	232748	Mm.279659	NM_146174	ENSMUSG00000029851	Tcaf2	Fam115c	TRPM8 channel-associated factor 2	protein-coding
mm_163626.1	chr13	56630879	56630898	+	1	NA	intron (NM_009369, intron 9 of 16)	intron (NM_009369, intron 9 of 16)	21285	NM_009369	21810	Mm.14455	NM_009369	ENSMUSG00000035493	Tgfbi	68kDa|AI181842|AI747162|Beta-ig|big-h3	transforming growth factor, beta induced	protein-coding
mm_1725.1	chr1	75367643	75367689	+	1	NA	TTS (NR_037976)	TTS (NR_037976)	7349	NR_037976	100503248	Mm.403916	NR_037976	ENSMUSG00000085653	Gm15179	OTTMUSG00000019417	predicted gene 15179	ncRNA
mm_25923.1	chr3	131171703	131171726	+	1	NA	intron (NM_001276403, intron 3 of 11)	intron (NM_001276403, intron 3 of 11)	58923	NM_001276403	16842	Mm.255219	NM_010703	ENSMUSG00000027985	Lef1	3000002B05|AI451430|Lef-1	lymphoid enhancer binding factor 1	protein-coding
mm_66530.1	chr7	45136103	45136122	-	1	NA	intron (NR_102725, intron 1 of 7)	intron (NR_102725, intron 1 of 7)	320	NM_013520	14256	Mm.1658	NM_013520	ENSMUSG00000110206	Flt3l	Flt3lg|Ly72L	FMS-like tyrosine kinase 3 ligand	protein-coding
mm_122611.1	chr14	51057640	51057667	-	1	NA	promoter-TSS (NM_001011875)	promoter-TSS (NM_001011875)	-411	NM_001011875	497106	Mm.379740	NM_001011875	ENSMUSG00000068407	Rnase12	Rai1	ribonuclease, RNase A family, 12 (non-active)	protein-coding
mm_165142.1	chr2	15375577	15375577	+	1	NA	Intergenic	Intergenic	-150902	NM_001310455	102635496		NM_001310455	ENSMUSG00000075520	Malrd1	-	MAM and LDL receptor class A domain containing 1	protein-coding
mm_7657.1	chr1	128359611	128359698	-	1	NA	promoter-TSS (NM_008567)	promoter-TSS (NM_008567)	51	NM_008567	17219	Mm.4933	NM_008567	ENSMUSG00000026355	Mcm6	ASP-l1|D1Wsu22e|Mcmd6	minichromosome maintenance complex component 6	protein-coding
mm_5128.1	chr1	9636889	9636901	-	1	NA	Intergenic	Intergenic	-5803	NR_015470	72481	Mm.279818	NR_015470	ENSMUSG00000079671	2610203C22Rik	2310007M24Rik	RIKEN cDNA 2610203C22 gene	ncRNA
mm_80549.1	chr9	82829968	82830076	+	1	NA	5' UTR (NM_001168240, exon 1 of 3)	5' UTR (NM_001168240, exon 1 of 3)	216	NM_022986	65099	Mm.41415	NM_022986	ENSMUSG00000032251	Irak1bp1	4921528N06Rik|AI851240|Aabp3|Aip70|Simpl	interleukin-1 receptor-associated kinase 1 binding protein 1	protein-coding
mm_84508.1	chr9	67026824	67026827	-	1	NA	intron (NM_001164255, intron 8 of 8)	intron (NM_001164255, intron 8 of 8)	17046	NM_001164252	22003	Mm.121878	NM_024427	ENSMUSG00000032366	Tpm1	AA986836|AI854628|TM2|Tm3|Tmpa|Tpm-1|alpha-TM	tropomyosin 1, alpha	protein-coding
mm_4656.1	chr1	180346032	180346045	+	1	NA	intron (NM_001081175, intron 2 of 7)	intron (NM_001081175, intron 2 of 7)	-15489	NR_003623	277333	Mm.389223	NM_199472		Gm5069	EG277333	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
mm_6116.1	chr1	64121316	64121324	-	1	NA	promoter-TSS (NM_033563)	promoter-TSS (NM_033563)	69	NM_033563	93691	Mm.29466	NM_033563	ENSMUSG00000025959	Klf7	9830124P08Rik	Kruppel-like factor 7 (ubiquitous)	protein-coding
mm_163845.1	chr14	19418086	19418107	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	184491	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_25884.1	chr3	130874072	130874096	+	1	NA	Intergenic	Intergenic	-143686	NM_001005859	68436	Mm.140568	NM_026724	ENSMUSG00000062006	Rpl34	1100001I22Rik	ribosomal protein L34	protein-coding
mm_7504.1	chr1	121567896	121567905	-	1	NA	promoter-TSS (NM_025860)	promoter-TSS (NM_025860)	80	NM_025860	66942	Mm.44219	NM_025860	ENSMUSG00000001674	Ddx18	2310005B10Rik	DEAD (Asp-Glu-Ala-Asp) box polypeptide 18	protein-coding
mm_18234.1	chr2	51972991	51973022	-	1	NA	5' UTR (NM_001141948, exon 1 of 8)	5' UTR (NM_001141948, exon 1 of 8)	202	NM_001141949	64685	Mm.7491	NM_019401	ENSMUSG00000026946	Nmi	-	N-myc (and STAT) interactor	protein-coding
mm_79387.1	chr9	54772954	54772968	+	1	NA	3' UTR (NM_001284507, exon 3 of 3)	3' UTR (NM_001284507, exon 3 of 3)	8213	NM_013496	12903	Mm.34797	NM_013496	ENSMUSG00000032291	Crabp1	AI326249|CRABP-I|Crabp-1|CrabpI|Rbp-5	cellular retinoic acid binding protein I	protein-coding
mm_169992.1	chr17	15576162	15576163	-	1	NA	Intergenic	Intergenic	-12839	NM_144809	213389	Mm.215162	NM_144809	ENSMUSG00000051977	Prdm9	BC012016|Dsbc1|G1-419-29|Meisetz|PRDM9-B|Rcr1|repro7	PR domain containing 9	protein-coding
mm_155231.1	chrX	57200511	57200519	+	1	NA	promoter-TSS (NR_038463)	promoter-TSS (NR_038463)	-122	NR_038463	100502842	Mm.164733	NR_038463	ENSMUSG00000085808	Gm14718	OTTMUSG00000017790	predicted gene 14718	ncRNA
mm_59946.1	chr7	30425551	30425572	+	1	NA	exon (NM_172142, exon 5 of 11)	exon (NM_172142, exon 5 of 11)	2257	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_129498.1	chr15	78851146	78851157	-	1	NA	TTS (NM_027219)	TTS (NM_027219)	4378	NM_025622	107753	Mm.390793	NM_025622	ENSMUSG00000043501	Lgals2	2200008F12Rik|AI324147	lectin, galactose-binding, soluble 2	protein-coding
mm_165660.1	chr3	87906128	87906145	+	1	NA	promoter-TSS (NM_008231)	promoter-TSS (NM_008231)	-185	NM_008231	15191	Mm.292208	NM_008231	ENSMUSG00000004897	Hdgf	AI118077|D3Ertd299e	hepatoma-derived growth factor	protein-coding
mm_104833.1	chr11	99152257	99152262	-	1	NA	intron (NM_007719, intron 1 of 2)	intron (NM_007719, intron 1 of 2)	2818	NM_001301713	12775	Mm.2932	NM_007719	ENSMUSG00000037944	Ccr7	CC-CKR-7|CCR-7|CD197|Cdw197|Cmkbr7|EBI1|Ebi1h	chemokine (C-C motif) receptor 7	protein-coding
mm_92366.1	chr10	75940634	75940683	-	1	NA	promoter-TSS (NM_001277132)	promoter-TSS (NM_001277132)	14	NM_001277132	333670	Mm.291320	NM_001037714	ENSMUSG00000050157	Gm867	Gm736	predicted gene 867	protein-coding
mm_40109.1	chr5	34801361	34801383	+	1	NA	intron (NM_010414, intron 6 of 66)	(T)n|Simple_repeat|Simple_repeat	39632	NM_010414	15194	Mm.209071	NM_010414	ENSMUSG00000029104	Htt	AI256365|C430023I11Rik|Hd|Hdh|IT15	huntingtin	protein-coding
mm_159725.1	chr5	38277223	38277223	+	1	NA	promoter-TSS (NM_172709)	promoter-TSS (NM_172709)	-181	NM_172709	21906	Mm.204765	NM_172709	ENSMUSG00000051596	Otop1	A530025J20Rik|Otp1|tlt	otopetrin 1	protein-coding
mm_87088.1	chr10	31313448	31313452	+	1	NA	promoter-TSS (NM_027168)	promoter-TSS (NM_027168)	45	NM_027168	69692	Mm.245537	NM_027168	ENSMUSG00000000295	Hddc2	2310057G13Rik	HD domain containing 2	protein-coding
mm_104722.1	chr11	98179975	98180019	-	1	NA	intron (NM_001080118, intron 5 of 16)	intron (NM_001080118, intron 5 of 16)	12909	NM_013634	19014	Mm.12926	NM_013634	ENSMUSG00000018160	Med1	AI480703|CRSP210|DRIP205|PBP|Pparbp|TRAP220|l11Jus15	mediator complex subunit 1	protein-coding
mm_159714.1	chr5	32611334	32611334	+	1	NA	5' UTR (NM_009535, exon 1 of 12)	5' UTR (NM_009535, exon 1 of 12)	163	NM_009535	22612	Mm.4558	NM_009535	ENSMUSG00000014932	Yes1	Yes|p61-Yes	YES proto-oncogene 1, Src family tyrosine kinase	protein-coding
mm_5738.1	chr1	45343489	45343504	-	1	NA	exon (NM_009930, exon 43 of 51)	exon (NM_009930, exon 43 of 51)	31958	NM_009930	12825	Mm.249555	NM_009930	ENSMUSG00000026043	Col3a1	AW550625|Col3a-1|Tsk-2|Tsk2	collagen, type III, alpha 1	protein-coding
mm_54971.1	chr6	48738884	48738899	-	1	NA	promoter-TSS (NM_008376)	promoter-TSS (NM_008376)	-156	NM_175860	16205	Mm.252599	NM_008376	ENSMUSG00000090019	Gimap1	IAP38|Imap38|imap	GTPase, IMAP family member 1	protein-coding
mm_77133.1	chr8	111348071	111348081	-	1	NA	exon (NM_178086, exon 6 of 7)	exon (NM_178086, exon 6 of 7)	-9871	NM_029005	74568	Mm.207971	NM_029005	ENSMUSG00000012519	Mlkl	9130019I15Rik	mixed lineage kinase domain-like	protein-coding
mm_86169.1	chr9	119089318	119089321	-	1	NA	intron (NR_121571, intron 1 of 14)	L1MEg|LINE|L1	-1058	NM_001293648	18799	Mm.23963	NM_019676	ENSMUSG00000010660	Plcd1	AW212592|C79986	phospholipase C, delta 1	protein-coding
mm_167743.1	chr9	108392794	108392812	+	1	NA	promoter-TSS (NM_053216)	promoter-TSS (NM_053216)	-31	NM_053216	112418	Mm.78287	NM_053216	ENSMUSG00000032611	1700102P08Rik	AI593206	RIKEN cDNA 1700102P08 gene	protein-coding
mm_43529.1	chr5	137289955	137289967	+	1	NA	intron (NM_009599, intron 1 of 4)	intron (NM_009599, intron 1 of 4)	1707	NM_001290010	11423	Mm.255464	NM_009599	ENSMUSG00000023328	Ache	-	acetylcholinesterase	protein-coding
mm_113476.1	chr13	36730097	36730111	+	1	NA	intron (NM_153529, intron 2 of 2)	intron (NM_153529, intron 2 of 2)	4373	NM_153529	68404	Mm.232930	NM_153529	ENSMUSG00000039114	Nrn1	0710008J23Rik|Cpg15|Nrn	neuritin 1	protein-coding
mm_171012.1	chr2	83557372	83557376	+	1	NA	Intergenic	L1Md_T|LINE|L1	-87204	NM_026934	69082	Mm.27804	NM_026934	ENSMUSG00000027091	Zc3h15	1700006A17Rik|1810012H02Rik|2610312B22Rik|FM22|Ierepo4	zinc finger CCCH-type containing 15	protein-coding
mm_33818.1	chr4	135357726	135357734	+	1	NA	Intergenic	B1_Mur4|SINE|Alu	-4516	NM_001130477	51796	Mm.1963	NM_016799	ENSMUSG00000028809	Srrm1	AA407769|POP101|Srm160	serine/arginine repetitive matrix 1	protein-coding
mm_154971.1	chrX	37172442	37172449	+	1	NA	Intergenic	RMER19B|LTR|ERVK	-3603	NM_001033785	434756	Mm.471848	NM_001033785	ENSMUSG00000036551	Akap14	-	A kinase (PRKA) anchor protein 14	protein-coding
mm_101158.1	chr11	16972832	16972854	-	1	NA	3' UTR (NM_019549, exon 10 of 10)	3' UTR (NM_019549, exon 10 of 10)	21433	NM_176982	319701	Mm.120672	NM_176982	ENSMUSG00000044966	Fbxo48	A630050E13Rik	F-box protein 48	protein-coding
mm_130893.1	chr15	102366360	102366368	-	1	NA	promoter-TSS (NM_130458)	promoter-TSS (NM_130458)	-93	NM_130458	170574	Mm.263284	NM_130458	ENSMUSG00000060284	Sp7	6430578P22Rik|C22|Osx	Sp7 transcription factor 7	protein-coding
mm_157609.1	chrX	53775478	53775488	-	1	NA	exon (NM_001009549, exon 1 of 2)	exon (NM_001009549, exon 1 of 2)	911	NM_001009549	333473	Mm.327378	NM_001009549	ENSMUSG00000059334	Zfp36l3	AY661338	zinc finger protein 36, C3H type-like 3	protein-coding
mm_117611.1	chr13	91370943	91370974	-	1	NA	non-coding (NR_045161, exon 3 of 3)	non-coding (NR_045161, exon 3 of 3)	17127	NR_045161	320297	Mm.375866	NR_045161	ENSMUSG00000097182	A830009L08Rik	-	RIKEN cDNA A830009L08 gene	ncRNA
mm_39969.1	chr5	32156437	32156447	+	1	NA	3' UTR (NM_008037, exon 4 of 4)	3' UTR (NM_008037, exon 4 of 4)	19970	NM_008037	14284	Mm.24684	NM_008037	ENSMUSG00000029135	Fosl2	Fra-2	fos-like antigen 2	protein-coding
mm_116993.1	chr13	56548419	56548468	-	1	NA	promoter-TSS (NM_010702)	promoter-TSS (NM_010702)	95	NM_010702	16841	Mm.16973	NM_010702	ENSMUSG00000021539	Lect2	-	leukocyte cell-derived chemotaxin 2	protein-coding
mm_127510.1	chr15	101690464	101690482	+	1	NA	exon (NM_008476, exon 9 of 9)	exon (NM_008476, exon 9 of 9)	3832	NM_008476	16687	Mm.302399	NM_008476	ENSMUSG00000058354	Krt6a	2310016L08Rik|Krt2-6a|Krt2-6c|MK6a|mK6[a]	keratin 6A	protein-coding
mm_17744.1	chr2	32713221	32713251	-	1	NA	promoter-TSS (NM_130860)	promoter-TSS (NM_130860)	-264	NR_039536	100628606		NR_039536	ENSMUSG00000105841	Mir3960	mmu-mir-3960	microRNA 3960	ncRNA
mm_147585.1	chr18	56505591	56505599	-	1	NA	Intergenic	B3|SINE|B2	-32544	NR_106160	102465790		NR_106160	ENSMUSG00000099196	Mir1258	Gm27371|mmu-mir-1258	microRNA 1258	ncRNA
mm_39092.1	chr4	154667864	154667868	-	1	NA	promoter-TSS (NM_028513)	promoter-TSS (NM_028513)	1	NM_028513	73353	Mm.30958	NM_028513	ENSMUSG00000051276	Actrt2	1700052K15Rik|Arp-T2|Arpm2	actin-related protein T2	protein-coding
mm_131840.1	chr16	22961045	22961072	+	1	NA	exon (NM_053176, exon 7 of 7)	exon (NM_053176, exon 7 of 7)	9986	NM_053176	94175	Mm.358794	NM_053176	ENSMUSG00000022877	Hrg	AI265597|AW413091|D16jh2|D18020|Hprg|Hrgp	histidine-rich glycoprotein	protein-coding
mm_113653.1	chr13	42307257	42307267	+	1	NA	3' UTR (NM_010104, exon 5 of 5)	3' UTR (NM_010104, exon 5 of 5)	5786	NM_010104	13614	Mm.14543	NM_010104	ENSMUSG00000021367	Edn1	ET-1|PPET1|preproET	endothelin 1	protein-coding
mm_172119.1	chr6	3201157	3201166	+	1	NA	Intergenic	SSU-rRNA_Hsa|rRNA|rRNA	-87358	NR_036696	667335	Mm.380219	NR_036696	ENSMUSG00000106779	Gm8579	EG667335	spermatogenesis associated glutamate (E)-rich protein 4a pseudogene	pseudo
mm_101957.1	chr11	50298219	50298248	-	1	NA	exon (NM_001110500, exon 12 of 15)	exon (NM_001110500, exon 12 of 15)	-5897	NM_175334	103806	Mm.51116	NM_175334	ENSMUSG00000050567	Maml1	AI644666|AW743257|D930008C07Rik|Mam-1|Mam1|mKIAA0200	mastermind like 1 (Drosophila)	protein-coding
mm_912.1	chr1	54926156	54926191	+	1	NA	5' UTR (NM_001081433, exon 1 of 28)	5' UTR (NM_001081433, exon 1 of 28)	214	NM_001081433	329154	Mm.397910	NM_001081433	ENSMUSG00000052331	Ankrd44	4930444A19Rik|A130096K20|E130014H08Rik|PP6-ARS-B	ankyrin repeat domain 44	protein-coding
mm_6853.1	chr1	84257523	84257530	-	1	NA	intron (NM_001003948, intron 1 of 2)	intron (NM_001003948, intron 1 of 2)	27119	NM_001003948	98496	Mm.187470	NM_001003948	ENSMUSG00000045658	Pid1	5033414K04Rik|NYGGF4	phosphotyrosine interaction domain containing 1	protein-coding
mm_12801.1	chr2	79786561	79786569	+	1	NA	intron (NR_110979, intron 4 of 4)	Lx5b|LINE|L1	78785	NM_001290743	75276	Mm.257373	NM_172420	ENSMUSG00000034683	Ppp1r1c	4930565M23Rik|4930579P15Rik	protein phosphatase 1, regulatory (inhibitor) subunit 1C	protein-coding
mm_44188.1	chr5	151406501	151406511	+	1	NA	promoter-TSS (NR_131166)	promoter-TSS (NR_131166)	2	NR_131166	100042166	Mm.443286	NR_131166	ENSMUSG00000097321	Gm3704	-	predicted gene 3704	ncRNA
mm_58797.1	chr7	16175359	16175438	+	1	NA	promoter-TSS (NM_008627)	promoter-TSS (NM_008627)	3	NR_102730	17537	Mm.360516	NM_008627	ENSMUSG00000041420	Meis3	AI573393|Mrg2	Meis homeobox 3	protein-coding
mm_145255.1	chr18	52528796	52528814	+	1	NA	exon (NM_010728, exon 1 of 7)	exon (NM_010728, exon 1 of 7)	916	NM_001286181	16948	Mm.172	NM_010728	ENSMUSG00000024529	Lox	AI893619|TSC-160|rrg	lysyl oxidase	protein-coding
mm_167087.1	chr7	103706435	103706442	+	1	NA	Intergenic	RLTR10D|LTR|ERVK	-10158	NM_001025386	436002	Mm.389933	NM_001025386	ENSMUSG00000094822	Olfr243	MOR22-4|Olfr243-ps1|Olfr627|Olfr627-ps1	olfactory receptor 243	protein-coding
mm_11958.1	chr2	53103726	53103738	+	1	NA	exon (NM_172409, exon 12 of 27)	exon (NM_172409, exon 12 of 27)	87455	NM_018785	56194	Mm.257474	NM_018785	ENSMUSG00000061136	Prpf40a	2810012K09Rik|FBP-11|FBP11|Fnbp11|Fnbp3	pre-mRNA processing factor 40A	protein-coding
mm_159123.1	chr2	70562274	70562274	+	1	NA	5' UTR (NM_008077, exon 1 of 17)	5' UTR (NM_008077, exon 1 of 17)	145	NM_008077	14415	Mm.272120	NM_008077	ENSMUSG00000070880	Gad1	EP10|Gad-1	glutamate decarboxylase 1	protein-coding
mm_123701.1	chr14	69724770	69724774	-	1	NA	intron (NM_134078, intron 2 of 9)	B1F|SINE|Alu	7798	NM_134078	105513	Mm.159637	NM_134078	ENSMUSG00000034190	Chmp7	4930596K11Rik|6330407G04Rik|AI450338|AW550775	charged multivesicular body protein 7	protein-coding
mm_78051.1	chr9	14784639	14784658	+	1	NA	promoter-TSS (NM_018736)	promoter-TSS (NM_018736)	-6	NM_001310728	17535	Mm.149071	NM_018736	ENSMUSG00000031928	Mre11a	Mre11|Mre11b	MRE11A homolog A, double strand break repair nuclease	protein-coding
mm_70712.1	chr8	15060283	15060301	+	1	NA	intron (NM_008664, intron 1 of 36)	intron (NM_008664, intron 1 of 36)	2639	NM_008664	17930	Mm.272115	NM_008664	ENSMUSG00000031461	Myom2	AW146149	myomesin 2	protein-coding
mm_29144.1	chr3	105932591	105932622	-	1	NA	promoter-TSS (NM_001033780)	promoter-TSS (NM_001033780)	58	NM_001033780	433638	Mm.239081	NM_001033780	ENSMUSG00000074342	I830077J02Rik	-	RIKEN cDNA I830077J02 gene	protein-coding
mm_35645.1	chr4	43523456	43523471	-	1	NA	promoter-TSS (NM_009416)	promoter-TSS (NM_009416)	91	NM_009416	22004	Mm.646	NM_009416	ENSMUSG00000028464	Tpm2	Tpm-2|Trop-2	tropomyosin 2, beta	protein-coding
mm_156338.1	chrX	139009927	139009929	+	1	NA	TTS (NM_013724)	TTS (NM_013724)	75308	NM_177920	331535	Mm.211704	NM_177920	ENSMUSG00000031271	Serpina7	C730040N12Rik|Tbg	serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 7	protein-coding
mm_22056.1	chr2	168571424	168571449	-	1	NA	exon (NM_010899, exon 2 of 10)	exon (NM_010899, exon 2 of 10)	18929	NM_001291178	18019	Mm.116802	NM_010899	ENSMUSG00000027544	Nfatc2	AI607462|NF-ATc2|NF-ATp|NFAT1|NFAT1-D|Nfatp	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 2	protein-coding
mm_45102.1	chr5	44776679	44776681	-	1	NA	intron (NM_001347349, intron 1 of 7)	intron (NM_001347349, intron 1 of 7)	23066	NM_001347349	16826	Mm.25785	NM_010698	ENSMUSG00000039706	Ldb2	AI035351|AW146358|CLIM1|CLP-36|Ldb3	LIM domain binding 2	protein-coding
mm_62417.1	chr7	101320627	101320637	+	1	NA	promoter-TSS (NM_019990)	promoter-TSS (NM_019990)	-687	NM_019990	56018	Mm.28896	NM_019990	ENSMUSG00000030688	Stard10	AV048538|CGI-52|NY-C0-28|PC-TP2|PCTP2|Pctpl|Sdccag28|SdccagG28|TISP-81	START domain containing 10	protein-coding
mm_22291.1	chr2	180236611	180236620	-	1	NA	Intergenic	Intergenic	-10756	NM_001081171	16776	Mm.4339	NM_001081171	ENSMUSG00000015647	Lama5	AA408760|AA408762|AI853660|[a]5|laminin-511|mKIAA0533	laminin, alpha 5	protein-coding
mm_155358.1	chrX	70184660	70184661	+	1	NA	Intergenic	Intergenic	-41072	NR_033213	74305	Mm.410860	NR_033213	ENSMUSG00000100511	1700111N16Rik	-	RIKEN cDNA 1700111N16 gene	ncRNA
mm_93366.1	chr10	104127360	104127361	-	1	NA	Intergenic	Lx|LINE|L1	-15627	NM_001270898	100861880	Mm.441727	NM_001270898	ENSMUSG00000091779	Gm21293	-	predicted gene, 21293	protein-coding
mm_131807.1	chr16	22918258	22918267	+	1	NA	promoter-TSS (NM_001083905)	promoter-TSS (NM_001083905)	-120	NM_001083905	59083	Mm.28461	NM_021564	ENSMUSG00000022871	Fetub	2310011O17Rik|AI255764|D17980|Gugu	fetuin beta	protein-coding
mm_170814.1	chr2	176226569	176226576	+	1	NA	promoter-TSS (NM_001305136)	promoter-TSS (NM_001305136)	7	NR_130970	102639598	Mm.379980	NM_029813	ENSMUSG00000074527	Gm14296	-	predicted gene 14296	protein-coding
mm_106921.1	chr12	8313456	8313462	+	1	NA	promoter-TSS (NM_021429)	promoter-TSS (NM_021429)	26	NM_021429	58240	Mm.309954	NM_021429	ENSMUSG00000020605	Hs1bp3	-	HCLS1 binding protein 3	protein-coding
mm_166624.1	chr6	72970480	72970482	+	1	NA	Intergenic	MLT1G3|LTR|ERVL-MaLR	-11733	NM_001190327	19240	Mm.3532	NM_025284	ENSMUSG00000079523	Tmsb10	Ptmb10|Tb10	thymosin, beta 10	protein-coding
mm_104003.1	chr11	84916235	84916260	-	1	NA	intron (NM_001005223, intron 1 of 4)	CpG	109	NM_001005223	448850	Mm.379733	NM_001005223	ENSMUSG00000020526	Znhit3	Myohd1|Trip3	zinc finger, HIT type 3	protein-coding
mm_116088.1	chr13	28652703	28652706	-	1	NA	intron (NR_045053, intron 5 of 8)	intron (NR_045053, intron 5 of 8)	58169	NR_105787	102466635		NR_105787	ENSMUSG00000099158	Mir6368	Gm27800|mmu-mir-6368	microRNA 6368	ncRNA
mm_140972.1	chr17	24696122	24696136	-	1	NA	promoter-TSS (NM_027988)	promoter-TSS (NM_027988)	27	NM_023040	11692	Mm.28124	NM_023040	ENSMUSG00000040888	Gfer	Alr|ERV1	growth factor, erv1 (S. cerevisiae)-like (augmenter of liver regeneration)	protein-coding
mm_57550.1	chr6	126740628	126740681	-	1	NA	promoter-TSS (NM_013568)	promoter-TSS (NM_013568)	20	NM_013568	16494	Mm.62535	NM_013568	ENSMUSG00000038077	Kcna6	Kv1.6|MK1.6	potassium voltage-gated channel, shaker-related, subfamily, member 6	protein-coding
mm_12850.1	chr2	83644582	83644592	+	1	NA	promoter-TSS (NM_026934)	promoter-TSS (NM_026934)	9	NM_026934	69082	Mm.27804	NM_026934	ENSMUSG00000027091	Zc3h15	1700006A17Rik|1810012H02Rik|2610312B22Rik|FM22|Ierepo4	zinc finger CCCH-type containing 15	protein-coding
mm_65452.1	chr7	25412858	25412885	-	1	NA	promoter-TSS (NM_153576)	promoter-TSS (NM_153576)	15	NM_153576	232983	Mm.10545	NM_153576	ENSMUSG00000060188	Cxcl17	VCC-1|Vcc1	chemokine (C-X-C motif) ligand 17	protein-coding
mm_145273.1	chr18	52800227	52800235	+	1	NA	intron (NM_001199154, intron 1 of 10)	intron (NM_001199154, intron 1 of 10)	32087	NM_001199154	67847	Mm.292168	NM_026408	ENSMUSG00000024534	Sncaip	2810407O15Rik|4933427B05Rik|BB104594|SYPH1	synuclein, alpha interacting protein (synphilin)	protein-coding
mm_57621.1	chr6	128215250	128215257	-	1	NA	Intergenic	Intergenic	-31450	NR_077223	330427	Mm.426356	NR_077223	ENSMUSG00000107879	9330102E08Rik	-	RIKEN cDNA 9330102E08 gene	ncRNA
mm_132838.1	chr16	45610442	45610450	+	1	NA	promoter-TSS (NM_008099)	promoter-TSS (NM_008099)	6	NM_001159297	14525	Mm.4799	NM_008099	ENSMUSG00000022659	Gcsam	Gcet|Gcet2|M17|M17-L	germinal center associated, signaling and motility	protein-coding
mm_170842.1	chr2	177324367	177324368	-	1	NA	Intergenic	Intergenic	-140375	NM_001177568	628308	Mm.460436	NM_001177568	ENSMUSG00000078866	Zfp970	Gm14420|OTTMUSG00000016588	zinc finger protein 970	protein-coding
mm_44692.1	chr5	30232345	30232349	-	1	NA	promoter-TSS (NM_027652)	promoter-TSS (NM_027652)	-234	NM_027652	28042	Mm.168854	NM_027652	ENSMUSG00000075703	Selenoi	4933402G07Rik|AI448296|AI452230|C79563|D5Wsu178e|Ept1|SELI|mKIAA1724	selenoprotein I	protein-coding
mm_84332.1	chr9	64022044	64022066	-	1	NA	promoter-TSS (NM_008542)	promoter-TSS (NM_008542)	4	NM_008542	17130	Mm.325757	NM_008542	ENSMUSG00000036867	Smad6	Madh6|b2b390Clo	SMAD family member 6	protein-coding
mm_132383.1	chr16	34926189	34926194	+	1	NA	intron (NM_139300, intron 16 of 31)	intron (NM_139300, intron 16 of 31)	13138	NR_040536	76649	Mm.420532	NR_040536	ENSMUSG00000100593	1700119H24Rik	-	RIKEN cDNA 1700119H24 gene	ncRNA
mm_110250.1	chr12	31559984	31559984	-	1	NA	promoter-TSS (NM_011867)	promoter-TSS (NM_011867)	-15	NM_011867	23985	Mm.100187	NM_011867	ENSMUSG00000020651	Slc26a4	Pds|pendrin	solute carrier family 26, member 4	protein-coding
mm_27318.1	chr3	50366915	50366927	-	1	NA	3' UTR (NM_011990, exon 12 of 12)	3' UTR (NM_011990, exon 12 of 12)	76692	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_13047.1	chr2	91096822	91096866	+	1	NA	5' UTR (NM_011355, exon 1 of 5)	5' UTR (NM_011355, exon 1 of 5)	166	NM_011355	20375	Mm.1302	NM_011355	ENSMUSG00000002111	Spi1	Dis-1|Dis1|PU.1|Sfpi-1|Sfpi1|Spi-1|Tcfpu1|Tfpu.1	spleen focus forming virus (SFFV) proviral integration oncogene	protein-coding
mm_986.1	chr1	58505136	58505162	+	1	NA	promoter-TSS (NM_001271526)	promoter-TSS (NM_001271526)	-40	NM_008765	18393	Mm.3411	NM_008765	ENSMUSG00000026037	Orc2	AU041563|Orc2l	origin recognition complex, subunit 2	protein-coding
mm_112206.1	chr12	113426961	113426971	-	1	NA	Intergenic	Intergenic	-62599	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_96389.1	chr11	67249258	67249266	+	1	NA	exon (NM_010855, exon 17 of 40)	exon (NM_010855, exon 17 of 40)	11450	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_106335.1	chr11	118393045	118393064	-	1	NA	exon (NM_011150, exon 6 of 6)	exon (NM_011150, exon 6 of 6)	8877	NM_011150	19039	Mm.3152	NM_011150	ENSMUSG00000033880	Lgals3bp	90K|CyCAP|MAC-2BP|Ppicap|Tango10b	lectin, galactoside-binding, soluble, 3 binding protein	protein-coding
mm_71676.1	chr8	60864535	60864544	+	1	NA	Intergenic	B2_Mm2|SINE|B2	-25912	NM_028299	72612	Mm.25263	NM_028299	ENSMUSG00000038005	Hpf1	2700029M09Rik|C230006B22Rik|C4orf27	histone PARylation factor 1	protein-coding
mm_103133.1	chr11	70237639	70237651	-	1	NA	TTS (NM_173742)	TTS (NM_173742)	269	NM_001177601	104457	Mm.30016	NM_026757	ENSMUSG00000020831	0610010K14Rik	1110020A23Rik|AL033328|AU045833|Bap18	RIKEN cDNA 0610010K14 gene	protein-coding
mm_145761.1	chr18	64888961	64889035	+	1	NA	intron (NM_001114386, intron 1 of 30)	intron (NM_001114386, intron 1 of 30)	1242	NM_001114386	83814	Mm.98668	NM_031881	ENSMUSG00000024589	Nedd4l	1300012C07Rik|Nedd4-2|Nedd4b	neural precursor cell expressed, developmentally down-regulated gene 4-like	protein-coding
mm_62991.1	chr7	120553040	120553058	+	1	NA	Intergenic	Intergenic	-44576	NR_024324	78552	Mm.289190	NR_024324	ENSMUSG00000044141	E130201H02Rik	-	Y box protein 1 pseudogene	pseudo
mm_71678.1	chr8	60890388	60890401	+	1	NA	promoter-TSS (NM_028299)	promoter-TSS (NM_028299)	-57	NM_028299	72612	Mm.25263	NM_028299	ENSMUSG00000038005	Hpf1	2700029M09Rik|C230006B22Rik|C4orf27	histone PARylation factor 1	protein-coding
mm_15304.1	chr2	155386936	155386952	+	1	NA	3' UTR (NM_178111, exon 4 of 4)	3' UTR (NM_178111, exon 4 of 4)	5088	NM_178111	68728	Mm.293605	NM_178111	ENSMUSG00000038375	Trp53inp2	1110029F20Rik|Tp53inp2	transformation related protein 53 inducible nuclear protein 2	protein-coding
mm_93560.1	chr10	116473876	116473929	-	1	NA	promoter-TSS (NM_021452)	promoter-TSS (NM_021452)	-379	NM_021452	58802	Mm.440652	NM_021452	ENSMUSG00000054934	Kcnmb4	1700058G18Rik|2900045G12Rik	potassium large conductance calcium-activated channel, subfamily M, beta member 4	protein-coding
mm_7153.1	chr1	91413164	91413234	-	1	NA	promoter-TSS (NM_019479)	promoter-TSS (NM_019479)	23	NM_019479	55927	Mm.280029	NM_019479	ENSMUSG00000067071	Hes6	AI326893|bHLHb41	hairy and enhancer of split 6	protein-coding
mm_43101.1	chr5	124483129	124483158	+	1	NA	promoter-TSS (NM_029532)	promoter-TSS (NM_029532)	-12	NM_029532	76167	Mm.156035	NM_029532	ENSMUSG00000029402	Snrnp35	6330548G22Rik	small nuclear ribonucleoprotein 35 (U11/U12)	protein-coding
mm_154495.1	chrM	11261	11281	-	1	NA	NA	Intergenic	NA	NA								
mm_75266.1	chr8	40653680	40653724	-	1	NA	Intergenic	Intergenic	-18910	NM_001040699	54384	Mm.294871	NM_019433	ENSMUSG00000039431	Mtmr7	-	myotubularin related protein 7	protein-coding
mm_10926.1	chr2	25428718	25428730	+	1	NA	promoter-TSS (NM_007379)	promoter-TSS (NM_007379)	50	NM_007379	11305	Mm.2210	NM_007379	ENSMUSG00000026944	Abca2	AI413825|Abc2|D2H0S1474E|mKIAA1062	ATP-binding cassette, sub-family A (ABC1), member 2	protein-coding
mm_66996.1	chr7	64392197	64392205	-	1	NA	promoter-TSS (NM_026483)	promoter-TSS (NM_026483)	35	NM_026483	67973	Mm.26973	NM_026483	ENSMUSG00000030521	Mphosph10	2810453H10Rik|5730405D16Rik|AI326008	M-phase phosphoprotein 10 (U3 small nucleolar ribonucleoprotein)	protein-coding
mm_2645.1	chr1	125435987	125436011	+	1	NA	promoter-TSS (NM_023735)	promoter-TSS (NM_023735)	-272	NM_001205386	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding
mm_28787.1	chr3	95995792	95995802	-	1	NA	promoter-TSS (NM_023320)	promoter-TSS (NM_023320)	42	NM_023320	67220	Mm.458147	NM_023320	ENSMUSG00000015745	Plekho1	2810052M02Rik|CKIP-1|Ckip1|JZA-20|Jza2	pleckstrin homology domain containing, family O member 1	protein-coding
mm_127552.1	chr15	102150383	102150393	+	1	NA	promoter-TSS (NM_146064)	promoter-TSS (NM_146064)	-187	NM_146064	223920	Mm.358862	NM_146064	ENSMUSG00000023045	Soat2	ACAT2|D15Wsu97e	sterol O-acyltransferase 2	protein-coding
mm_18688.1	chr2	71511286	71511289	-	1	NA	intron (NM_025633, intron 3 of 9)	intron (NM_025633, intron 3 of 9)	-18158	NM_010053	13390	Mm.475101	NM_010053	ENSMUSG00000041911	Dlx1	Dlx|Dlx-1	distal-less homeobox 1	protein-coding
mm_16308.1	chr2	174294753	174294770	+	1	NA	intron (NR_002846, intron 1 of 4)	intron (NR_002846, intron 1 of 4)	675	NR_002846	56802	Mm.125770	NR_002846	ENSMUSG00000086537	Nespas	Gnas-as|Nespos	neuroendocrine secretory protein antisense	ncRNA
mm_10957.1	chr2	25676786	25676797	+	1	NA	promoter-TSS (NM_177840)	promoter-TSS (NM_177840)	5	NM_001276448	620709	Mm.99499	NM_177840	ENSMUSG00000045684	Lcn6	9230101D24Rik	lipocalin 6	protein-coding
mm_29442.1	chr3	110143563	110143579	-	1	NA	promoter-TSS (NM_001163350)	promoter-TSS (NM_001163350)	-99	NM_030699	80883	Mm.39262	NM_030699	ENSMUSG00000059857	Ntng1	A930010C08Rik|AI853992|Lmnt1	netrin G1	protein-coding
mm_128675.1	chr15	60187430	60187463	-	1	NA	Intergenic	Intergenic	-170828	NM_027668	71088	Mm.425950	NM_027668	ENSMUSG00000071749	4933412E24Rik	-	RIKEN cDNA 4933412E24 gene	protein-coding
mm_95331.1	chr11	46750597	46750605	+	1	NA	promoter-TSS (NM_001166631)	promoter-TSS (NM_001166631)	90	NM_001166631	171283	Mm.17771	NM_134248	ENSMUSG00000040405	Havcr1	AI503787|KIM-1|TIM-1|Tim1|Timd1	hepatitis A virus cellular receptor 1	protein-coding
mm_39423.1	chr5	15991097	15991097	+	1	NA	intron (NM_001110846, intron 1 of 37)	intron (NM_001110846, intron 1 of 37)	56406	NM_001110844	12293	Mm.159842	NM_009784	ENSMUSG00000040118	Cacna2d1	Ca(v)alpha2delta1|Cacna2|Cchl2a	calcium channel, voltage-dependent, alpha2/delta subunit 1	protein-coding
mm_92996.1	chr10	86705454	86705471	-	1	NA	promoter-TSS (NM_011631)	promoter-TSS (NM_011631)	-18	NM_011631	22027	Mm.87773	NM_011631	ENSMUSG00000020048	Hsp90b1	ERp99|GRP94|TA-3|Targ2|Tra-1|Tra1|endoplasmin|gp96	heat shock protein 90, beta (Grp94), member 1	protein-coding
mm_81047.1	chr9	105483156	105483159	+	1	NA	intron (NM_001253831, intron 1 of 26)	intron (NM_001253831, intron 1 of 26)	11976	NM_175025	235574	Mm.326247	NM_175025	ENSMUSG00000032570	Atp2c1	1700121J11Rik|ATP2C1A|AW061228|BCPM|D930003G21Rik|HHD|SPCA|pmr1	ATPase, Ca++-sequestering	protein-coding
mm_140977.1	chr17	24696570	24696585	-	1	NA	promoter-TSS (NM_023040)	promoter-TSS (NM_023040)	343	NM_027988	71893	Mm.390971	NM_027988	ENSMUSG00000019320	Noxo1	2310034C04Rik|P41NOX|P41NOXA|P41NOXB|P41NOXC|Snx28|hslt	NADPH oxidase organizer 1	protein-coding
mm_30021.1	chr3	135665399	135665407	-	1	NA	intron (NM_008689, intron 3 of 24)	intron (NM_008689, intron 3 of 24)	26144	NM_008689	18033	Mm.256765	NM_008689	ENSMUSG00000028163	Nfkb1	NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105	nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105	protein-coding
mm_22872.1	chr3	29109802	29109807	+	1	NA	intron (NM_029412, intron 1 of 14)	B1_Mur4|SINE|Alu	27227	NM_029412	75740	Mm.330948	NM_029412	ENSMUSG00000063600	Egfem1	6130401L20Rik|Efcab11	EGF-like and EMI domain containing 1	protein-coding
mm_58897.1	chr7	17150211	17150236	+	1	NA	promoter-TSS (NM_054059)	promoter-TSS (NM_054059)	-177	NM_054059	384557	Mm.486145	NM_054059	ENSMUSG00000053228	Ceacam3	EG384557|Psg24|cea12	carcinoembryonic antigen-related cell adhesion molecule 3	protein-coding
mm_8732.1	chr1	160153539	160153550	-	1	NA	promoter-TSS (NM_177839)	promoter-TSS (NM_177839)	31	NM_177839	329278	Mm.90140	NM_177839	ENSMUSG00000026725	Tnn	Tnw|tenascin-W	tenascin N	protein-coding
mm_153366.1	chr19	40271773	40271794	-	1	NA	promoter-TSS (NM_016861)	promoter-TSS (NM_016861)	-167	NM_016861	54132	Mm.5567	NM_016861	ENSMUSG00000055044	Pdlim1	CLP36|Clim1|mClim1	PDZ and LIM domain 1 (elfin)	protein-coding
mm_45608.1	chr5	75119745	75119747	-	1	NA	intron (NR_045792, intron 1 of 3)	intron (NR_045792, intron 1 of 3)	9425	NR_045792	100503184	Mm.386273	NR_045792	ENSMUSG00000107192	Gm19583	-	predicted gene, 19583	ncRNA
mm_97794.1	chr11	82911310	82911331	+	1	NA	promoter-TSS (NM_178680)	promoter-TSS (NM_178680)	67	NM_178680	217012	Mm.295205	NM_178680	ENSMUSG00000018845	Unc45b	AA445617|Cmya4|D230041A13Rik|Unc45	unc-45 myosin chaperone B	protein-coding
mm_107639.1	chr12	52503754	52503786	+	1	NA	Intergenic	GC_rich|Low_complexity|Low_complexity	-12307	NM_009706	11855	Mm.35059	NM_009706	ENSMUSG00000035133	Arhgap5	p190-B|p190B	Rho GTPase activating protein 5	protein-coding
mm_79488.1	chr9	57072025	57072048	+	1	NA	promoter-TSS (NM_001110351)	promoter-TSS (NM_001110351)	-4	NM_001110351	20466	Mm.15755	NM_011378	ENSMUSG00000042557	Sin3a	AW553200|Sin3|mKIAA4126|mSin3A	transcriptional regulator, SIN3A (yeast)	protein-coding
mm_11653.1	chr2	34963207	34963215	+	1	NA	Intergenic	Intergenic	-1439	NM_001326601	22029	Mm.239514	NM_009421	ENSMUSG00000026875	Traf1	4732496E14Rik	TNF receptor-associated factor 1	protein-coding
mm_42875.1	chr5	122241024	122241063	+	1	NA	non-coding (NR_104441, exon 13 of 13)	non-coding (NR_104441, exon 13 of 13)	23417	NR_104441	654470	Mm.28804	NM_001039153	ENSMUSG00000038593	Tctn1	G730031O11Rik|Tect1	tectonic family member 1	protein-coding
mm_105754.1	chr11	109473094	109473112	-	1	NA	promoter-TSS (NM_028710)	promoter-TSS (NM_028710)	126	NM_134038	104681	Mm.265874	NM_134038	ENSMUSG00000041920	Slc16a6	AW743111|ESTM12|MCT 6|MCT 7|MCT6	solute carrier family 16 (monocarboxylic acid transporters), member 6	protein-coding
mm_55173.1	chr6	51921334	51921353	-	1	NA	exon (NM_018773, exon 6 of 13)	exon (NM_018773, exon 6 of 13)	91206	NM_018773	54353	Mm.221479	NM_018773	ENSMUSG00000059182	Skap2	2610021A10Rik|AA960083|BB137539|RA70|SKAP-HOM|Saps|Scap2|mSKAP55R	src family associated phosphoprotein 2	protein-coding
mm_62675.1	chr7	109439228	109439241	+	1	NA	promoter-TSS (NM_054103)	promoter-TSS (NM_054103)	-181	NM_054103	117229	Mm.389950	NM_054103	ENSMUSG00000031027	Stk33	4921505G21Rik|AW061264	serine/threonine kinase 33	protein-coding
mm_90265.1	chr10	122678765	122678811	+	1	NA	promoter-TSS (NR_106182)	promoter-TSS (NR_106182)	26	NM_001110218	319468	Mm.489703	NM_176919	ENSMUSG00000034613	Ppm1h	A430075L18Rik|ARHCL1|C030002B11Rik	protein phosphatase 1H (PP2C domain containing)	protein-coding
mm_31552.1	chr4	56743407	56743438	+	1	NA	promoter-TSS (NM_009611)	promoter-TSS (NM_009611)	0	NM_009611	11470	Mm.30959	NM_009611	ENSMUSG00000070979	Actl7a	Tact2	actin-like 7a	protein-coding
mm_108495.1	chr12	83688124	83688249	+	1	NA	promoter-TSS (NM_008943)	promoter-TSS (NM_008943)	-377	NM_008943	19164	Mm.998	NM_008943	ENSMUSG00000019969	Psen1	Ad3h|PS-1|PS1|S182	presenilin 1	protein-coding
mm_54866.1	chr6	42597663	42597679	-	1	NA	promoter-TSS (NM_203396)	promoter-TSS (NM_203396)	-299	NM_203396	403088	Mm.354652	NM_203396	ENSMUSG00000018656	Tcaf3	Eapa2|Fam115e	TRPM8 channel-associated factor 3	protein-coding
mm_115191.1	chr13	108775135	108775166	+	1	NA	intron (NM_011056, intron 1 of 16)	intron (NM_011056, intron 1 of 16)	120973	NM_011056	238871	Mm.434429	NM_011056	ENSMUSG00000021699	Pde4d	9630011N22Rik|Dpde3	phosphodiesterase 4D, cAMP specific	protein-coding
mm_33675.1	chr4	133220912	133220927	+	1	NA	5' UTR (NM_027152, exon 1 of 6)	5' UTR (NM_027152, exon 1 of 6)	110	NM_027152	69655	Mm.285685	NM_027152	ENSMUSG00000028865	Cd164l2	2310047N01Rik	CD164 sialomucin-like 2	protein-coding
mm_42512.1	chr5	115542973	115543007	+	1	NA	intron (NM_133915, intron 1 of 11)	intron (NM_133915, intron 1 of 11)	-16477	NM_007475	11837	Mm.5286	NM_007475	ENSMUSG00000067274	Rplp0	36B4|Arbp|L10E	ribosomal protein, large, P0	protein-coding
mm_17727.1	chr2	32431116	32431178	-	1	NA	promoter-TSS (NM_001164358)	promoter-TSS (NM_001164358)	4	NM_001164358	227731	Mm.37395	NM_146118	ENSMUSG00000026819	Slc25a25	1110030N17Rik|MCSC|mKIAA1896	solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 25	protein-coding
mm_86814.1	chr10	20505771	20505780	+	1	NA	intron (NM_013875, intron 2 of 12)	intron (NM_013875, intron 2 of 12)	42553	NM_001347366	29863	Mm.425617	NM_013875	ENSMUSG00000019990	Pde7b	-	phosphodiesterase 7B	protein-coding
mm_38133.1	chr4	134703742	134703778	-	1	NA	5' UTR (NM_207237, exon 1 of 12)	5' UTR (NM_207237, exon 1 of 12)	530	NM_207237	230815	Mm.18905	NM_207237	ENSMUSG00000037306	Man1c1	AI593348	mannosidase, alpha, class 1C, member 1	protein-coding
mm_172908.1	chr9	61913369	61913383	+	1	NA	TTS (NM_018853)	TTS (NM_018853)	1134	NM_018853	56040	Mm.3158	NM_018853	ENSMUSG00000007892	Rplp1	2410042H16Rik|Arpp1|C430017H15Rik	ribosomal protein, large, P1	protein-coding
mm_108004.1	chr12	73584235	73584245	+	1	NA	promoter-TSS (NM_008856)	promoter-TSS (NM_008856)	-556	NM_001313977	18755	Mm.341677	NM_008856	ENSMUSG00000021108	Prkch	Pkch	protein kinase C, eta	protein-coding
mm_122441.1	chr14	45270198	45270205	-	1	NA	intron (NM_027518, intron 3 of 6)	L1_Mur2|LINE|L1	48371	NM_015774	50527	Mm.387108	NM_015774	ENSMUSG00000021831	Ero1l	ERO1-L|Ero1a	ERO1-like (S. cerevisiae)	protein-coding
mm_52355.1	chr6	112459673	112459703	+	1	NA	5' UTR (NM_007617, exon 1 of 2)	5' UTR (NM_007617, exon 1 of 2)	183	NM_007617	12391	Mm.3924	NM_007617	ENSMUSG00000062694	Cav3	AI385751|Cav-3|M-cav	caveolin 3	protein-coding
mm_13916.1	chr2	120567688	120567726	+	1	NA	promoter-TSS (NM_001177793)	promoter-TSS (NM_001177793)	36	NM_009222	20619	Mm.245715	NM_009222	ENSMUSG00000027287	Snap23	23kDa|AA408749|SNAP-23|Sndt|Syndet	synaptosomal-associated protein 23	protein-coding
mm_80757.1	chr9	95557228	95557236	+	1	NA	Intergenic	Intergenic	-2585	NM_198414	75552	Mm.151485	NM_198414	ENSMUSG00000064225	Paqr9	1700020G04Rik	progestin and adipoQ receptor family member IX	protein-coding
mm_28726.1	chr3	95702004	95702034	-	1	NA	Intergenic	Intergenic	-14102	NM_001301705	229595	Mm.490574	NM_144899	ENSMUSG00000015850	Adamtsl4	ADAMTSL-4|Tsrc1	ADAMTS-like 4	protein-coding
mm_144689.1	chr18	34840601	34840614	+	1	NA	promoter-TSS (NM_001204914)	promoter-TSS (NM_001204914)	18	NM_144865	225362	Mm.293588	NM_144865	ENSMUSG00000038555	Reep2	-	receptor accessory protein 2	protein-coding
mm_66614.1	chr7	45466794	45466854	-	1	NA	promoter-TSS (NM_007527)	promoter-TSS (NM_007527)	74	NM_007527	12028	Mm.19904	NM_007527	ENSMUSG00000003873	Bax	-	BCL2-associated X protein	protein-coding
mm_28317.1	chr3	89279603	89279627	-	1	NA	promoter-TSS (NM_010107)	promoter-TSS (NM_010107)	30	NM_010107	13636	Mm.15675	NM_010107	ENSMUSG00000027954	Efna1	AI325262|B61|Efl1|Epl1|Eplg1|Lerk1	ephrin A1	protein-coding
mm_67116.1	chr7	70361529	70361549	-	1	NA	promoter-TSS (NM_009697)	promoter-TSS (NM_009697)	-946	NM_009697	11819	Mm.158143	NM_009697	ENSMUSG00000030551	Nr2f2	2700033K02Rik|9430015G03Rik|ARP-1|Aporp1|COUP-TF2|COUP-TFII|COUPTFB|EAR3|SVP40|Tcfcoup2	nuclear receptor subfamily 2, group F, member 2	protein-coding
mm_144110.1	chr18	4353062	4353072	+	1	NA	promoter-TSS (NM_007746)	promoter-TSS (NM_007746)	-114	NM_007746	26410	Mm.3275	NM_007746	ENSMUSG00000024235	Map3k8	Cot|Cot/Tpl2|Est|Estf|Tpl-2|Tpl2|c-COT	mitogen-activated protein kinase kinase kinase 8	protein-coding
mm_42037.1	chr5	108397608	108397615	+	1	NA	intron (NM_008806, intron 1 of 21)	MER65-int|LTR|ERV1	9238	NM_008806	18587	Mm.1372	NM_008806	ENSMUSG00000029491	Pde6b	Pdeb|r|rd|rd-1|rd1|rd10	phosphodiesterase 6B, cGMP, rod receptor, beta polypeptide	protein-coding
mm_60321.1	chr7	44218558	44218561	+	1	NA	exon (NM_008456, exon 2 of 5)	exon (NM_008456, exon 2 of 5)	2085	NM_008456	16622	Mm.443373	NM_008456	ENSMUSG00000066512	Klk1b5	Klk5|kallikrein|mGK-5	kallikrein 1-related peptidase b5	protein-coding
mm_152869.1	chr19	24225081	24225116	-	1	NA	promoter-TSS (NM_011597)	promoter-TSS (NM_011597)	-72	NM_011597	21873	Mm.104744	NM_011597	ENSMUSG00000024812	Tjp2	ZO-2	tight junction protein 2	protein-coding
mm_94541.1	chr11	9191770	9191779	+	1	NA	promoter-TSS (NM_178259)	promoter-TSS (NM_178259)	-168	NM_178259	268379	Mm.39270	NM_178259	ENSMUSG00000004668	Abca13	9830132L24|A930002G16Rik|AI956815	ATP-binding cassette, sub-family A (ABC1), member 13	protein-coding
mm_132101.1	chr16	31422316	31422347	+	1	NA	promoter-TSS (NM_175177)	promoter-TSS (NM_175177)	34	NM_175177	71911	Mm.293470	NM_175177	ENSMUSG00000046598	Bdh1	2310032J20Rik|AI327223|Bdh	3-hydroxybutyrate dehydrogenase, type 1	protein-coding
mm_109834.1	chr12	4201520	4201520	-	1	NA	intron (NM_001159537, intron 11 of 21)	intron (NM_001159537, intron 11 of 21)	-32507	NM_001204912	69709	Mm.250552	NM_001204912	ENSMUSG00000096199	Ptrhd1	2410017P09Rik	peptidyl-tRNA hydrolase domain containing 1	protein-coding
mm_33311.1	chr4	129066119	129066121	+	1	NA	intron (NM_029219, intron 1 of 8)	intron (NM_029219, intron 1 of 8)	7849	NM_029219	75234	Mm.259672	NM_029219	ENSMUSG00000028793	Rnf19b	4930534K13Rik|4930555L03Rik|Ibrdc3	ring finger protein 19B	protein-coding
mm_127710.1	chr15	103009546	103009558	+	1	NA	promoter-TSS (NM_010465)	promoter-TSS (NM_010465)	-10	NM_010465	15425	Mm.4444	NM_010465	ENSMUSG00000001661	Hoxc6	Hox-3.3|Hox-6.1	homeobox C6	protein-coding
mm_87445.1	chr10	51481707	51481720	+	1	NA	exon (NM_008147, exon 4 of 9)	exon (NM_008147, exon 4 of 9)	1101	NM_001291892	14727	Mm.439661	NM_008147	ENSMUSG00000062593	Lilr4b	Gp49a|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4B	protein-coding
mm_38662.1	chr4	144438715	144438717	-	1	NA	promoter-TSS (NM_027056)	promoter-TSS (NM_027056)	56	NM_027056	69364	Mm.158267	NM_027056	ENSMUSG00000028589	1700012P22Rik	-	RIKEN cDNA 1700012P22 gene	protein-coding
mm_8572.1	chr1	155527173	155527186	-	1	NA	promoter-TSS (NR_132128)	promoter-TSS (NR_132128)	-68	NR_132128	433367	Mm.359304	NR_132128	ENSMUSG00000073535	Gm5532	EG433367	predicted gene 5532	ncRNA
mm_44598.1	chr5	25100190	25100212	-	1	NA	promoter-TSS (NR_027851)	promoter-TSS (NR_027851)	441	NM_145401	108099	Mm.33649	NM_145401	ENSMUSG00000028944	Prkag2	2410051C13Rik|AAKG|AAKG2|AI854673|H91620p|WPWS	protein kinase, AMP-activated, gamma 2 non-catalytic subunit	protein-coding
mm_41061.1	chr5	86833268	86833276	+	1	NA	intron (NM_001347376, intron 14 of 15)	AT_rich|Low_complexity|Low_complexity	28782	NM_177680	231386	Mm.196325	NM_177680	ENSMUSG00000035851	Ythdc1	A730098D12Rik|C80342|mKIAA1966	YTH domain containing 1	protein-coding
mm_92241.1	chr10	70096726	70096765	-	1	NA	promoter-TSS (NM_001111121)	promoter-TSS (NM_001111121)	-376	NM_001111121	76551	Mm.281741	NM_001111121	ENSMUSG00000048701	Ccdc6	2810012H18Rik|AA536681|AA960498|AW061011	coiled-coil domain containing 6	protein-coding
mm_97435.1	chr11	78165666	78165687	+	1	NA	promoter-TSS (NM_009423)	promoter-TSS (NM_009423)	-126	NM_009423	22032	Mm.390418	NM_009423	ENSMUSG00000017386	Traf4	A530032M13Rik|CART1|msp2	TNF receptor associated factor 4	protein-coding
mm_50435.1	chr6	48846035	48846052	+	1	NA	TTS (NM_025326)	TTS (NM_025326)	4387	NM_001098271	66058	Mm.27061	NM_025326	ENSMUSG00000023367	Tmem176a	0610011I04Rik|AU040201|AU041743|Keg2	transmembrane protein 176A	protein-coding
mm_115954.1	chr13	23757604	23757629	-	1	NA	TTS (NM_178193)	TTS (NM_178193)	679	NM_178193	326620	Mm.261642	NM_178193	ENSMUSG00000069266	Hist1h4b	-	histone cluster 1, H4b	protein-coding
mm_140063.1	chr17	74702725	74702727	+	1	NA	3' UTR (NM_007566, exon 73 of 73)	3' UTR (NM_007566, exon 73 of 73)	-15024	NM_152817	74196	Mm.209503	NM_152817	ENSMUSG00000024078	Ttc27	2610511O17Rik	tetratricopeptide repeat domain 27	protein-coding
mm_21645.1	chr2	164333489	164333491	-	1	NA	exon (NM_009301, exon 2 of 3)	exon (NM_009301, exon 2 of 3)	725	NM_009301	20944	Mm.140154	NM_009301	ENSMUSG00000017004	Svs5	BB115186|Semg1|Svp-1|Svp1|Svp5	seminal vesicle secretory protein 5	protein-coding
mm_85816.1	chr9	110408132	110408155	-	1	NA	promoter-TSS (NM_001081043)	promoter-TSS (NM_001081043)	67	NM_001081043	104831	Mm.335477	NM_001081043	ENSMUSG00000036057	Ptpn23	AI462446|PTP-TD14	protein tyrosine phosphatase, non-receptor type 23	protein-coding
mm_109225.1	chr12	108793286	108793375	+	1	NA	promoter-TSS (NM_009537)	promoter-TSS (NM_009537)	19	NM_009537	22632	Mm.3868	NM_009537	ENSMUSG00000021264	Yy1	AW488674|NF-E1	YY1 transcription factor	protein-coding
mm_51082.1	chr6	67017499	67017522	+	1	NA	exon (NM_001177559, exon 5 of 5)	exon (NM_001177559, exon 5 of 5)	-19089	NR_040278	320172	Mm.449039	NR_040278	ENSMUSG00000087231	E230016M11Rik	-	RIKEN cDNA E230016M11 gene	ncRNA
mm_100352.1	chr11	118428459	118428468	+	1	NA	promoter-TSS (NM_001204129)	promoter-TSS (NM_001204129)	6	NM_001204129	56745	Mm.23845	NM_019959	ENSMUSG00000017446	C1qtnf1	1600017K21Rik|CTRP1|Zsig37	C1q and tumor necrosis factor related protein 1	protein-coding
mm_172352.1	chr7	114705948	114705956	-	1	NA	Intergenic	Intergenic	-12691	NM_054084	116903	Mm.273838	NM_054084	ENSMUSG00000030666	Calcb	CGRP2|Calc2	calcitonin-related polypeptide, beta	protein-coding
mm_94134.1	chr10	128696258	128696273	-	1	NA	promoter-TSS (NM_177411)	promoter-TSS (NM_177411)	3	NM_177411	19344	Mm.12815	NM_011229	ENSMUSG00000000711	Rab5b	C030027M18Rik	RAB5B, member RAS oncogene family	protein-coding
mm_19277.1	chr2	85519019	85519033	-	1	NA	promoter-TSS (NM_001081664)	promoter-TSS (NM_001081664)	-91	NM_001081664	228151	Mm.17636	NM_001081664	ENSMUSG00000075217	4833423E24Rik	Fads2p1|Gm113	RIKEN cDNA 4833423E24 gene	protein-coding
mm_74636.1	chr8	13254033	13254043	-	1	NA	5' UTR (NM_172750, exon 1 of 7)	5' UTR (NM_172750, exon 1 of 7)	124	NM_172750	234072	Mm.132785	NM_172750	ENSMUSG00000031448	Adprhl1	Arh2|D330008N11Rik	ADP-ribosylhydrolase like 1	protein-coding
mm_121833.1	chr14	20501088	20501100	-	1	NA	3' UTR (NM_008914, exon 14 of 14)	3' UTR (NM_008914, exon 14 of 14)	-4193	NM_029104	74843	Mm.295241	NM_029104	ENSMUSG00000021815	Mss51	4833444M15Rik|Zmynd17	MSS51 mitochondrial translational activator	protein-coding
mm_103712.1	chr11	79519354	79519362	-	1	NA	intron (NM_146023, intron 3 of 3)	intron (NM_146023, intron 3 of 3)	4404	NM_001077496	216984	Mm.439665	NM_001077496	ENSMUSG00000093938	Evi2b	Evi-2|Evi2	ecotropic viral integration site 2b	protein-coding
mm_52817.1	chr6	121346679	121346708	+	1	NA	promoter-TSS (NM_133661)	promoter-TSS (NM_133661)	-4	NM_133661	14411	Mm.274506	NM_133661	ENSMUSG00000030109	Slc6a12	BGT1|GAT-2|GAT2|Gabt2	solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12	protein-coding
mm_122443.1	chr14	45285930	45285971	-	1	NA	3' UTR (NM_015774, exon 16 of 16)	3' UTR (NM_015774, exon 16 of 16)	32622	NM_015774	50527	Mm.387108	NM_015774	ENSMUSG00000021831	Ero1l	ERO1-L|Ero1a	ERO1-like (S. cerevisiae)	protein-coding
mm_17636.1	chr2	31141944	31142001	-	1	NA	promoter-TSS (NM_019406)	promoter-TSS (NM_019406)	36	NM_001177649	14269	Mm.52297	NM_019406	ENSMUSG00000075415	Fnbp1	1110057E06Rik|2210010H06Rik|FBP1|Fbp17	formin binding protein 1	protein-coding
mm_142484.1	chr17	45746787	45746793	-	1	NA	Intergenic	Intergenic	-12946	NM_028164	72240	Mm.482897	NM_028164	ENSMUSG00000094690	1600014C23Rik	-	RIKEN cDNA 1600014C23 gene	protein-coding
mm_159399.1	chr3	95870625	95870625	-	1	NA	promoter-TSS (NR_040446)	promoter-TSS (NR_040446)	-6	NM_078479	66292	Mm.24108	NM_078479	ENSMUSG00000054312	Mrps21	1810031B19Rik	mitochondrial ribosomal protein S21	protein-coding
mm_151073.1	chr19	47537213	47537221	+	1	NA	promoter-TSS (NM_175360)	promoter-TSS (NM_175360)	-197	NM_175360	108689	Mm.218048	NM_175360	ENSMUSG00000042694	Obfc1	0610009H20Rik|2310057J23Rik|AAF-44|AAF44|AI413458|RPA-32	oligonucleotide/oligosaccharide-binding fold containing 1	protein-coding
mm_170741.1	chr2	154892781	154892781	-	1	NA	5' UTR (NM_026030, exon 1 of 9)	5' UTR (NM_026030, exon 1 of 9)	125	NM_026030	67204	Mm.377134	NM_026030	ENSMUSG00000074656	Eif2s2	2810026E11Rik|38kDa|AA408636|AA571381|AA986487|AW822225|D2Ertd303e|EIF2|EIF2B	eukaryotic translation initiation factor 2, subunit 2 (beta)	protein-coding
mm_93542.1	chr10	115505647	115505661	-	1	NA	intron (NM_010195, intron 2 of 17)	B4A|SINE|B4	-64332	NM_029982	77798	Mm.446685	NM_029982	ENSMUSG00000092210	A930009A15Rik	-	RIKEN cDNA A930009A15 gene	protein-coding
mm_20145.1	chr2	121474042	121474048	-	1	NA	promoter-TSS (NM_001081975)	promoter-TSS (NM_001081975)	-22	NM_001081975	100034361	Mm.270393	NM_001081975	ENSMUSG00000048222	Mfap1b	-	microfibrillar-associated protein 1B	protein-coding
mm_85482.1	chr9	106080205	106080216	-	1	NA	exon (NM_026763, exon 3 of 38)	exon (NM_026763, exon 3 of 38)	16481	NM_026763	68553	Mm.28854	NM_026763	ENSMUSG00000032572	Col6a4	1110001D15Rik|AI413310|AU023415|Dvwa|EG235580|Vwa6	collagen, type VI, alpha 4	protein-coding
mm_27327.1	chr3	50368575	50368586	-	1	NA	3' UTR (NM_011990, exon 12 of 12)	3' UTR (NM_011990, exon 12 of 12)	75033	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_46738.1	chr5	110810081	110810113	-	1	NA	promoter-TSS (NM_009469)	promoter-TSS (NM_009469)	-16	NM_001347394	22241	Mm.271898	NM_009469	ENSMUSG00000029512	Ulk1	AU041434|Unc51.1|mKIAA0722	unc-51 like kinase 1	protein-coding
mm_31845.1	chr4	74252025	74252056	+	1	NA	5' UTR (NM_144787, exon 1 of 22)	5' UTR (NM_144787, exon 1 of 22)	161	NM_144787	76804	Mm.209059	NM_144787	ENSMUSG00000028397	Kdm4c	2410141F18Rik|AA517467|Gasc1|Jmjd2c	lysine (K)-specific demethylase 4C	protein-coding
mm_158828.1	chrX	168122913	168122954	-	1	NA	promoter-TSS (NM_001290427)	promoter-TSS (NM_001290427)	64	NM_001290427	333605	Mm.426168	NM_001033330	ENSMUSG00000049176	Frmpd4	Gm196|PKAP1|Pdzd10|Pdzk10|Preso1|preso	FERM and PDZ domain containing 4	protein-coding
mm_34856.1	chr4	155522593	155522622	+	1	NA	intron (NM_001160016, intron 2 of 11)	intron (NM_001160016, intron 2 of 11)	31246	NM_001160016	14688	Mm.2344	NM_008142	ENSMUSG00000029064	Gnb1	AA409223|C77571|Gnb-1	guanine nucleotide binding protein (G protein), beta 1	protein-coding
mm_49866.1	chr6	38552893	38552896	+	1	NA	intron (NM_138680, intron 1 of 9)	intron (NM_138680, intron 1 of 9)	1560	NM_001170848	192196	Mm.276133	NM_138680	ENSMUSG00000029823	Luc7l2	4930471C18Rik|AA522013|AU015269|CGI59|Cgi74	LUC7-like 2 (S. cerevisiae)	protein-coding
mm_146674.1	chr18	12819685	12819698	-	1	NA	non-coding (NR_045524, exon 1 of 12)	non-coding (NR_045524, exon 1 of 12)	216	NR_045524	64291	Mm.259470	NM_020573	ENSMUSG00000044252	Osbpl1a	G430090F17Rik|Gm753|ORP-1|Osbpl1b	oxysterol binding protein-like 1A	protein-coding
mm_14044.1	chr2	122264816	122264824	+	1	NA	3' UTR (NM_146126, exon 9 of 9)	3' UTR (NM_146126, exon 9 of 9)	29981	NM_146126	20322	Mm.371580	NM_146126	ENSMUSG00000027227	Sord	Sdh-1|Sdh1|Sodh-1	sorbitol dehydrogenase	protein-coding
mm_30596.1	chr4	6367963	6367966	+	1	NA	intron (NM_001098227, intron 1 of 8)	intron (NM_001098227, intron 1 of 8)	2284	NM_001098227	53378	Mm.247473	NM_016807	ENSMUSG00000028249	Sdcbp	MDA-9|Sycl|syntenin-1	syndecan binding protein	protein-coding
mm_157803.1	chrX	73928093	73928101	-	1	NA	intron (NM_023132, intron 7 of 10)	intron (NM_023132, intron 7 of 10)	2753	NM_023132	19703	Mm.236969	NM_023132	ENSMUSG00000031387	Renbp	Age|Rnbp	renin binding protein	protein-coding
mm_77206.1	chr8	113854918	113854924	-	1	NA	Intergenic	Intergenic	-6082	NM_172466	208936	Mm.167471	NM_172466	ENSMUSG00000053399	Adamts18	9630038L21|ADAMTS21|E130314N14Rik	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 18	protein-coding
mm_10016.1	chr1	192061824	192061844	-	1	NA	intron (NM_011633, intron 4 of 9)	intron (NM_011633, intron 4 of 9)	30765	NM_011633	22033	Mm.380491	NM_011633		Traf5	-	TNF receptor-associated factor 5	protein-coding
mm_137588.1	chr17	28022169	28022198	+	1	NA	intron (NM_001286040, intron 12 of 24)	intron (NM_001286040, intron 12 of 24)	58401	NM_013687	21463	Mm.29758	NM_013687	ENSMUSG00000062859	Tcp11	D17Ken1|Tcp-11	t-complex protein 11	protein-coding
mm_157886.1	chrX	75843242	75843264	-	1	NA	promoter-TSS (NM_001346520)	promoter-TSS (NM_001346520)	-190	NM_001346520	102866	Mm.28777	NM_145629	ENSMUSG00000016382	Pls3	AI115446|AL024105	plastin 3 (T-isoform)	protein-coding
mm_53669.1	chr6	141644911	141644917	+	1	NA	intron (NM_020495, intron 3 of 15)	ORR1D1|LTR|ERVL-MaLR	15396	NM_020495	28253	Mm.272223	NM_020495	ENSMUSG00000030236	Slco1b2	7330442B20Rik|OATP-C|OATP2|Oatp1b2|Oatp4|Slc21a10|Slc21a6|lst-1|mlst-1	solute carrier organic anion transporter family, member 1b2	protein-coding
mm_114275.1	chr13	58215691	58215719	+	1	NA	promoter-TSS (NM_152234)	promoter-TSS (NM_152234)	-52	NM_026842	56085	Mm.182053	NM_026842	ENSMUSG00000005312	Ubqln1	1110046H03Rik|1810030E05Rik|AU019746|C77538|D13Ertd372e|Da41|Dsk2|Plic-1|Plic1|Xdrp1	ubiquilin 1	protein-coding
mm_48308.1	chr5	138619688	138619701	-	1	NA	promoter-TSS (NM_001163797)	promoter-TSS (NM_001163797)	49	NM_001163797	24135	Mm.27575	NM_013844	ENSMUSG00000058291	Zfp68	KRAB3|KRAZ2|Zfp70|mszf22|mszf49	zinc finger protein 68	protein-coding
mm_152884.1	chr19	24556191	24556266	-	1	NA	promoter-TSS (NM_008846)	promoter-TSS (NM_008846)	-401	NM_008846	18719	Mm.217214	NM_008846	ENSMUSG00000024867	Pip5k1b	PI4P5K-I[b]|PIP5K1-beta|PIP5KIbeta|Pipk5b|STM7	phosphatidylinositol-4-phosphate 5-kinase, type 1 beta	protein-coding
mm_154735.1	chrX	9849708	9849710	+	1	NA	promoter-TSS (NM_029229)	promoter-TSS (NM_029229)	6	NM_029229	385317	Mm.108656	NM_029229	ENSMUSG00000048994	H2al3	4930557A04Rik	H2A histone family member L3	protein-coding
mm_72282.1	chr8	75100417	75100430	+	1	NA	3' UTR (NM_010442, exon 5 of 5)	3' UTR (NM_010442, exon 5 of 5)	6805	NM_010442	15368	Mm.276389	NM_010442	ENSMUSG00000005413	Hmox1	D8Wsu38e|HO-1|HO1|Hemox|Hmox|Hsp32	heme oxygenase 1	protein-coding
mm_132179.1	chr16	32400726	32400734	+	1	NA	5' UTR (NM_001160402, exon 1 of 5)	5' UTR (NM_001160402, exon 1 of 5)	224	NM_001160402	277203	Mm.484240	NM_001160402	ENSMUSG00000079625	Tm4sf19	EG277203	transmembrane 4 L six family member 19	protein-coding
mm_32210.1	chr4	101550300	101550327	+	1	NA	promoter-TSS (NM_001164583)	promoter-TSS (NM_001164583)	-281	NM_001164583	72685	Mm.76494	NM_198412	ENSMUSG00000028528	Dnajc6	2810027M23Rik|mKIAA0473	DnaJ heat shock protein family (Hsp40) member C6	protein-coding
mm_70585.1	chr8	13171200	13171212	+	1	NA	exon (NM_010684, exon 5 of 9)	exon (NM_010684, exon 5 of 9)	12045	NM_010684	16783	Mm.16716	NM_010684	ENSMUSG00000031447	Lamp1	CD107a|LGP-120|LGP-A|Lamp-1|P2B	lysosomal-associated membrane protein 1	protein-coding
mm_97790.1	chr11	82829122	82829168	+	1	NA	promoter-TSS (NM_026097)	promoter-TSS (NM_026097)	-102	NM_026097	67338	Mm.341608	NM_026097	ENSMUSG00000020696	Rffl	1700051E09Rik|4930516L10Rik|BG080975|Carp2	ring finger and FYVE like domain containing protein	protein-coding
mm_25657.1	chr3	121532656	121532667	+	1	NA	promoter-TSS (NM_145394)	promoter-TSS (NM_145394)	-317	NM_145394	213603	Mm.33062	NM_145394	ENSMUSG00000039865	Slc44a3	BC010552	solute carrier family 44, member 3	protein-coding
mm_29714.1	chr3	123690807	123690847	-	1	NA	promoter-TSS (NR_121616)	promoter-TSS (NR_121616)	25	NR_121616	83398	Mm.443908	NM_031186	ENSMUSG00000027977	Ndst3	4921531K01Rik|4930511P15Rik|N-HSST 3|NDST-3	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 3	protein-coding
mm_30736.1	chr4	13890080	13890082	+	1	NA	3' UTR (NM_009822, exon 11 of 11)	3' UTR (NM_009822, exon 11 of 11)	105299	NM_009822	12395	Mm.4909	NM_009822	ENSMUSG00000006586	Runx1t1	Cbfa2t1h|ETO|MTG8	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	protein-coding
mm_162713.1	chr10	28747514	28747558	+	1	NA	intron (NM_001305663, intron 3 of 5)	Lx3A|LINE|L1	79176	NM_178666	210757	Mm.123021	NM_178666	ENSMUSG00000049109	Themis	E430004N04Rik|Gasp|Spot|Tsepa|thylex	thymocyte selection associated	protein-coding
mm_96874.1	chr11	70214137	70214162	+	1	NA	5' UTR (NM_153081, exon 1 of 5)	5' UTR (NM_153081, exon 1 of 5)	239	NM_153081	216867	Mm.289238	NM_153081	ENSMUSG00000040938	Slc16a11	AB041591|MCT 11|MNCb-2717	solute carrier family 16 (monocarboxylic acid transporters), member 11	protein-coding
mm_26511.1	chr3	145891499	145891514	+	1	NA	exon (NM_026993, exon 6 of 6)	exon (NM_026993, exon 6 of 6)	-32756	NM_009740	12042	Mm.239141	NM_009740	ENSMUSG00000028191	Bcl10	AI132454|BCL-10|C81403|CARMEN|CIPER|CLAP|ME10|cE10	B cell leukemia/lymphoma 10	protein-coding
mm_65547.1	chr7	27131189	27131215	-	1	NA	exon (NM_007817, exon 8 of 10)	exon (NM_007817, exon 8 of 10)	11247	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_130038.1	chr15	88980425	88980441	-	1	NA	Intergenic	Intergenic	-1880	NM_133241	170790	Mm.32780	NM_133241	ENSMUSG00000035805	Mlc1	AW048630|BB074274|Kiaa0027-hp|LVM|MLC|VL|WKL1|mKIAA0027	megalencephalic leukoencephalopathy with subcortical cysts 1 homolog (human)	protein-coding
mm_40986.1	chr5	77266217	77266232	+	1	NA	intron (NM_011263, intron 1 of 3)	CpG	730	NM_011263	19712	Mm.28840	NM_011263	ENSMUSG00000029249	Rest	2610008J04Rik|AA407358|NRSF|REST4	RE1-silencing transcription factor	protein-coding
mm_69418.1	chr7	132599615	132599636	-	1	NA	promoter-TSS (NM_009123)	promoter-TSS (NM_009123)	12	NM_009123	20231	Mm.334281	NM_009123	ENSMUSG00000048528	Nkx1-2	Nkx-1.1|Nkx-1.2|Sax1	NK1 transcription factor related, locus 2 (Drosophila)	protein-coding
mm_21306.1	chr2	157079198	157079209	-	1	NA	promoter-TSS (NM_001164663)	promoter-TSS (NM_001164663)	62	NM_001164663	320706	Mm.79466	NM_001164663	ENSMUSG00000055485	Soga1	9830001H06Rik|AI426038|D430036N24Rik|Soga	suppressor of glucose, autophagy associated 1	protein-coding
mm_92326.1	chr10	75764266	75764359	-	1	NA	promoter-TSS (NM_172549)	promoter-TSS (NM_172549)	45	NM_172549	104248	Mm.257404	NM_172549	ENSMUSG00000020196	Cabin1	A330070M20Rik|Cain|Ppp3in	calcineurin binding protein 1	protein-coding
mm_157082.1	chrX	9436067	9436083	-	1	NA	3' UTR (NM_007807, exon 13 of 13)	3' UTR (NM_007807, exon 13 of 13)	33249	NM_007807	13058	Mm.200362	NM_007807	ENSMUSG00000015340	Cybb	C88302|CGD91-phox|Cgd|Cyd|Nox2|gp91-1|gp91phox	cytochrome b-245, beta polypeptide	protein-coding
mm_108089.1	chr12	74284319	74284330	+	1	NA	promoter-TSS (NR_030735)	promoter-TSS (NR_030735)	48	NR_030735	74284	Mm.287421	NR_030733	ENSMUSG00000071265	1700086L19Rik	1700006L05Rik|AU016007	RIKEN cDNA 1700086L19 gene	ncRNA
mm_168639.1	chr1	184848288	184848301	+	1	NA	Intergenic	BGLII|LTR|ERVK	-2447	NM_133684	67247	Mm.177724	NM_133684	ENSMUSG00000073481	Marc2	2810484M10Rik|Mosc2|mARC1	mitochondrial amidoxime reducing component 2	protein-coding
mm_124343.1	chr14	103844392	103844403	-	1	NA	promoter-TSS (NM_001136061)	promoter-TSS (NM_001136061)	79	NM_001136061	13618	Mm.229532	NM_007904	ENSMUSG00000022122	Ednrb	ET-B|ET-BR|ETR-b|ETb|Sox10m1	endothelin receptor type B	protein-coding
mm_99810.1	chr11	108395289	108395324	+	1	NA	promoter-TSS (NM_013475)	promoter-TSS (NM_013475)	9	NM_013475	11818	Mm.2266	NM_013475	ENSMUSG00000000049	Apoh	B2GPI|beta-2-GPI|beta2-GPI	apolipoprotein H	protein-coding
mm_53874.1	chr6	149409040	149409094	+	1	NA	promoter-TSS (NM_001112796)	promoter-TSS (NM_001112796)	83	NM_009753	12121	Mm.177181	NM_009753	ENSMUSG00000003452	Bicd1	B830009D06Rik|bic-D 1	bicaudal D homolog 1 (Drosophila)	protein-coding
mm_48921.1	chr6	4004300	4004302	+	1	NA	5' UTR (NM_025331, exon 1 of 2)	5' UTR (NM_025331, exon 1 of 2)	314	NM_025331	66066	Mm.25547	NM_025331	ENSMUSG00000032766	Gng11	0610037B21Rik	guanine nucleotide binding protein (G protein), gamma 11	protein-coding
mm_23197.1	chr3	41354142	41354163	+	1	NA	Intergenic	Intergenic	139047	NR_040385	78706	Mm.366094	NR_040385	ENSMUSG00000097639	Platr4	C430002E04Rik	pluripotency associated transcript 4	ncRNA
mm_90464.1	chr10	127759806	127759816	+	1	NA	promoter-TSS (NM_080436)	promoter-TSS (NM_080436)	48	NM_080436	107605	Mm.484271	NM_080436	ENSMUSG00000089789	Rdh1	-	retinol dehydrogenase 1 (all trans)	protein-coding
mm_2640.1	chr1	125174885	125174896	+	1	NA	Intergenic	Intergenic	260837	NM_023735	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding
mm_139265.1	chr17	47769192	47769201	+	1	NA	intron (NM_001161723, intron 1 of 8)	intron (NM_001161723, intron 1 of 8)	-16548	NM_011549	21425	Mm.2305	NM_011549	ENSMUSG00000023990	Tfeb	Tcfeb|bHLHe35	transcription factor EB	protein-coding
mm_152148.1	chr19	7215368	7215393	-	1	NA	3' UTR (NM_007750, exon 2 of 2)	3' UTR (NM_007750, exon 2 of 2)	2236	NM_007750	12868	Mm.14022	NM_007750	ENSMUSG00000035885	Cox8a	COX8L	cytochrome c oxidase subunit VIIIa	protein-coding
mm_5279.1	chr1	20565251	20565258	-	1	NA	intron (NM_153179, intron 16 of 66)	intron (NM_153179, intron 16 of 66)	52803	NM_153179	241035	Mm.249253	NM_153179	ENSMUSG00000043760	Pkhd1	AI118496|AI182499|FPC|Tigm1	polycystic kidney and hepatic disease 1	protein-coding
mm_1265.1	chr1	63178461	63178480	+	1	NA	promoter-TSS (NR_028558)	promoter-TSS (NR_028558)	-553	NR_028558	100217464	Mm.484706	NR_028558	ENSMUSG00000064602	Snora41	MBI-83	small nucleolar RNA, H/ACA box 41	snoRNA
mm_49882.1	chr6	38611112	38611121	+	1	NA	Intergenic	B1_Mus1|SINE|Alu	26123	NM_001033171	74253	Mm.121859	NM_001033171	ENSMUSG00000071537	Klrg2	2310020F24Rik	killer cell lectin-like receptor subfamily G, member 2	protein-coding
mm_16181.1	chr2	172646642	172646654	+	1	NA	Intergenic	Intergenic	95657	NM_001159696	21420	Mm.3629	NM_009335	ENSMUSG00000028640	Tfap2c	AA409384|AP2gamma|Ap-2.2|Stra2|Tcfap2c	transcription factor AP-2, gamma	protein-coding
mm_43181.1	chr5	127905704	127905718	+	1	NA	intron (NM_172885, intron 4 of 8)	intron (NM_172885, intron 4 of 8)	273449	NM_177005	319804	Mm.237888	NM_177005	ENSMUSG00000049971	Glt1d1	5730455A04Rik	glycosyltransferase 1 domain containing 1	protein-coding
mm_132655.1	chr16	41556854	41556858	+	1	NA	intron (NM_001347236, intron 1 of 6)	intron (NM_001347236, intron 1 of 6)	23514	NM_175548	268890	Mm.310524	NM_175548	ENSMUSG00000061080	Lsamp	5430428I19|AW046674|B130007O04Rik|D930023J12Rik|Lam|Lamp	limbic system-associated membrane protein	protein-coding
mm_13706.1	chr2	117157498	117157509	+	1	NA	intron (NM_033524, intron 2 of 6)	intron (NM_033524, intron 2 of 6)	-27624	NR_030440	732489		NR_030440	ENSMUSG00000076376	Mir674	Mirn674|mir-674|mmu-mir-674	microRNA 674	ncRNA
mm_77470.1	chr8	122426962	122426997	-	1	NA	exon (NM_007806, exon 4 of 6)	exon (NM_007806, exon 4 of 6)	4894	NM_145834	234836	Mm.222808	NM_145834	ENSMUSG00000046108	Il17c	IL-17C	interleukin 17C	protein-coding
mm_114816.1	chr13	91609278	91609303	+	1	NA	intron (NM_024186, intron 4 of 15)	L1M3|LINE|L1	-132231	NM_028790	74156	Mm.275963	NM_028790	ENSMUSG00000021620	Acot12	1300004O04Rik|4930449F15Rik|AV027244|Cach|mCACH-1	acyl-CoA thioesterase 12	protein-coding
mm_408.1	chr1	34212945	34212994	+	1	NA	exon (NM_134448, exon 49 of 98)	exon (NM_134448, exon 49 of 98)	52639	NM_010081	13518	Mm.336625	NM_010081	ENSMUSG00000026131	Dst	2310001O04Rik|A830042E19Rik|AW554249|BP230|BPAG1-n|Bpag|Bpag1|Macf2|ah|athetoid|dt|mKIAA0728|nmf203|nmf339	dystonin	protein-coding
mm_38761.1	chr4	147903008	147903027	-	1	NA	intron (NM_001285920, intron 2 of 19)	intron (NM_001285920, intron 2 of 19)	1681	NM_001285923	170731	Mm.154312	NM_133201	ENSMUSG00000029020	Mfn2	D630023P19Rik|Fzo	mitofusin 2	protein-coding
mm_69593.1	chr7	135716086	135716086	-	1	NA	exon (NM_001081117, exon 1 of 14)	exon (NM_001081117, exon 1 of 14)	293	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_95771.1	chr11	54909053	54909067	+	1	NA	exon (NM_008161, exon 4 of 5)	exon (NM_008161, exon 4 of 5)	6206	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_121189.1	chr14	103049698	103049703	+	1	NA	intron (NM_008392, intron 3 of 4)	intron (NM_008392, intron 3 of 4)	2688	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_82533.1	chr9	20746234	20746251	-	1	NA	Intergenic	Intergenic	-18028	NM_173777	244723	Mm.293552	NM_173777	ENSMUSG00000032172	Olfm2	A030009A06Rik	olfactomedin 2	protein-coding
mm_62717.1	chr7	110772763	110772767	+	1	NA	5' UTR (NM_009667, exon 1 of 15)	5' UTR (NM_009667, exon 1 of 15)	161	NM_009667	11717	Mm.3238	NM_009667	ENSMUSG00000005686	Ampd3	-	adenosine monophosphate deaminase 3	protein-coding
mm_141824.1	chr17	34617196	34617229	-	1	NA	3' UTR (NM_019441, exon 8 of 8)	3' UTR (NM_019441, exon 8 of 8)	-1241	NM_152922	81701	Mm.231343	NM_152922	ENSMUSG00000015467	Egfl8	Ng3	EGF-like domain 8	protein-coding
mm_688.1	chr1	40542958	40542970	+	1	NA	intron (NM_010553, intron 10 of 12)	intron (NM_010553, intron 10 of 12)	27602	NM_010553	16174	Mm.20466	NM_010553	ENSMUSG00000026068	Il18rap	AcPL|IL-18R-beta|IL-18RAcP|IL-18Rbeta|IL-1RAcPL	interleukin 18 receptor accessory protein	protein-coding
mm_22393.1	chr2	181227956	181227972	-	1	NA	3' UTR (NM_183162, exon 19 of 19)	3' UTR (NM_183162, exon 19 of 19)	7948	NM_199312	332713	Mm.23349	NM_199312	ENSMUSG00000047841	BC051628	1700026M20Rik|Fndc11	cDNA sequence BC051628	protein-coding
mm_157682.1	chrX	59585671	59585687	-	1	NA	promoter-TSS (NM_001290414)	promoter-TSS (NM_001290414)	-107	NM_001290414	14168	Mm.7995	NM_010200	ENSMUSG00000031137	Fgf13	Fhf2	fibroblast growth factor 13	protein-coding
mm_12069.1	chr2	59630067	59630075	+	1	NA	intron (NM_198294, intron 1 of 26)	intron (NM_198294, intron 1 of 26)	-16698	NM_001290659	66860	Mm.27917	NM_198294	ENSMUSG00000035168	Tanc1	1200003E16Rik|Tanc|mKIAA1728	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	protein-coding
mm_45880.1	chr5	88328375	88328405	-	1	NA	exon (NM_008644, exon 3 of 3)	exon (NM_008644, exon 3 of 3)	11078	NM_008644	17830	Mm.200411	NM_008644	ENSMUSG00000064156	Prol1	Muc10	proline rich, lacrimal 1	protein-coding
mm_50055.1	chr6	41178381	41178401	+	1	NA	Intergenic	Intergenic	-123881	NM_011646	22074	Mm.383263	NM_011646	ENSMUSG00000054106	Try4	0910001B19Rik|Td	trypsin 4	protein-coding
mm_128564.1	chr15	56429233	56429233	-	1	NA	Intergenic	Intergenic	-260711	NR_002874	594843	Mm.484850	NR_002874	ENSMUSG00000086541	Has2os	EG594843|Has2as|Hasnt	hyaluronan synthase 2, opposite strand	ncRNA
mm_11313.1	chr2	30312628	30312651	+	1	NA	exon (NM_198304, exon 12 of 44)	exon (NM_198304, exon 12 of 44)	26206	NM_198304	227699	Mm.330119	NM_198304	ENSMUSG00000052533	Nup188	BC025526|U89435|mKIAA0169	nucleoporin 188	protein-coding
mm_47896.1	chr5	134739506	134739509	-	1	NA	intron (NM_007925, intron 2 of 36)	intron (NM_007925, intron 2 of 36)	7816	NM_007925	13717	Mm.275320	NM_007925	ENSMUSG00000029675	Eln	AI385707|AI480567|E030024M20Rik	elastin	protein-coding
mm_4233.1	chr1	171370161	171370171	+	1	NA	promoter-TSS (NM_027893)	promoter-TSS (NM_027893)	-7	NM_027893	71740	Mm.263414	NM_027893	ENSMUSG00000006411	Nectin4	1200017F15Rik|Prr4|Pvrl4	nectin cell adhesion molecule 4	protein-coding
mm_115400.1	chr13	113870672	113870688	+	1	NA	intron (NM_172595, intron 1 of 4)	intron (NM_172595, intron 1 of 4)	76172	NM_172595	218639	Mm.79837	NM_172595	ENSMUSG00000042348	Arl15	A430036I03|Arfrp2|C230032K13Rik	ADP-ribosylation factor-like 15	protein-coding
mm_133583.1	chr16	91407499	91407519	+	1	NA	intron (NM_008349, intron 1 of 6)	T-rich|Low_complexity|Low_complexity	1274	NM_008349	16155	Mm.4154	NM_008349	ENSMUSG00000022969	Il10rb	6620401D04Rik|AI528744|CRF2-4|Crfb4|D16H21S58|D21S58h|IL-10R2|Il10r2	interleukin 10 receptor, beta	protein-coding
mm_161485.1	chr15	84325969	84325969	+	1	NA	promoter-TSS (NM_001162500)	promoter-TSS (NM_001162500)	-150	NM_001162500	64099	Mm.251356	NM_022321	ENSMUSG00000022439	Parvg	AI413459	parvin, gamma	protein-coding
mm_32783.1	chr4	116708688	116708696	+	1	NA	promoter-TSS (NM_026714)	promoter-TSS (NM_026714)	-238	NM_026714	68394	Mm.425201	NM_026714	ENSMUSG00000028689	Ccdc163	0610037D15Rik|4933430J04Rik	coiled-coil domain containing 163	protein-coding
mm_1962.1	chr1	86470758	86470771	+	1	NA	Intergenic	Intergenic	44435	NM_027966	71863	Mm.179627	NM_027966	ENSMUSG00000036574	1700019O17Rik	-	RIKEN cDNA 1700019O17 gene	protein-coding
mm_88939.1	chr10	81317876	81317892	+	1	NA	3' UTR (NM_001146687, exon 17 of 17)	3' UTR (NM_001146687, exon 17 of 17)	-3219	NM_027381	70312	Mm.87628	NM_027381	ENSMUSG00000034889	Cactin	2510012J08Rik	cactin, spliceosome C complex subunit	protein-coding
mm_26790.1	chr3	9761154	9761156	-	1	NA	intron (NM_053182, intron 1 of 7)	B1_Mur2|SINE|Alu	72524	NM_053182	94212	Mm.23897	NM_053182	ENSMUSG00000027508	Pag1	Cbp|F730007C19Rik|Pag	phosphoprotein associated with glycosphingolipid microdomains 1	protein-coding
mm_34044.1	chr4	138216625	138216650	+	1	NA	promoter-TSS (NM_001122896)	promoter-TSS (NM_001122896)	25	NM_001285478	15441	Mm.348429	NM_010470	ENSMUSG00000028759	Hp1bp3	Hp1bp74	heterochromatin protein 1, binding protein 3	protein-coding
mm_74257.1	chr8	124863192	124863227	+	1	NA	promoter-TSS (NM_025615)	promoter-TSS (NM_025615)	176	NM_010322	14712	Mm.29114	NM_010322	ENSMUSG00000031985	Gnpat	AU019525|D1Ertd819e|DHAPAT	glyceronephosphate O-acyltransferase	protein-coding
mm_33363.1	chr4	129491294	129491300	+	1	NA	promoter-TSS (NM_080442)	promoter-TSS (NM_080442)	107	NM_001085491	68233	Mm.424983	NM_001085491	ENSMUSG00000078554	Fam229a	1700125D06Rik	family with sequence similarity 229, member A	protein-coding
mm_88408.1	chr10	77011985	77012005	+	1	NA	promoter-TSS (NR_045882)	promoter-TSS (NR_045882)	0	NR_045882	100038479	Mm.387034	NR_045882	ENSMUSG00000074919	Gm10787	ENSMUSG00000074919	predicted gene 10787	ncRNA
mm_44634.1	chr5	27791651	27791694	-	1	NA	promoter-TSS (NM_018878)	promoter-TSS (NM_018878)	-122	NM_018878	55982	Mm.277190	NM_018878	ENSMUSG00000002221	Paxip1	D5Ertd149e|PTIP	PAX interacting (with transcription-activation domain) protein 1	protein-coding
mm_69488.1	chr7	134172875	134172888	-	1	NA	intron (NM_007400, intron 1 of 22)	intron (NM_007400, intron 1 of 22)	52216	NM_007400	11489	Mm.439714	NM_007400	ENSMUSG00000054555	Adam12	Mltna	a disintegrin and metallopeptidase domain 12 (meltrin alpha)	protein-coding
mm_43895.1	chr5	144186580	144186582	+	1	NA	3' UTR (NM_001081109, exon 14 of 14)	3' UTR (NM_001081109, exon 14 of 14)	-3705	NM_010800	17341	Mm.386767	NM_010800	ENSMUSG00000052271	Bhlha15	1810009C13Rik|Bhlhb8|MIST-1|Mist1	basic helix-loop-helix family, member a15	protein-coding
mm_35599.1	chr4	43031430	43031434	-	1	NA	promoter-TSS (NM_023231)	promoter-TSS (NM_023231)	-48	NM_023231	66592	Mm.331565	NM_023231	ENSMUSG00000028455	Stoml2	0610038F01Rik|MSLP2|SLP-2	stomatin (Epb7.2)-like 2	protein-coding
mm_50460.1	chr6	48907813	48907821	+	1	NA	exon (NM_001161622, exon 3 of 5)	exon (NM_001161622, exon 3 of 5)	2831	NM_001161621	76507	Mm.213898	NM_029638	ENSMUSG00000029811	Aoc1	1600012D06Rik|Abp1|DAO	amine oxidase, copper-containing 1	protein-coding
mm_26799.1	chr3	9879488	9879528	-	1	NA	Intergenic	Intergenic	-45829	NM_001195031	94212	Mm.23897	NM_053182	ENSMUSG00000027508	Pag1	Cbp|F730007C19Rik|Pag	phosphoprotein associated with glycosphingolipid microdomains 1	protein-coding
mm_124468.1	chr14	121303493	121303516	-	1	NA	intron (NM_145465, intron 3 of 10)	intron (NM_145465, intron 3 of 10)	75726	NM_145465	223255	Mm.390756	NM_145465	ENSMUSG00000063410	Stk24	1810013H02Rik|C76483|MST-3|Mst3|STE20	serine/threonine kinase 24	protein-coding
mm_95757.1	chr11	54906258	54906265	+	1	NA	intron (NM_001329860, intron 1 of 5)	intron (NM_001329860, intron 1 of 5)	3407	NM_008161	14778	Mm.200916	NM_008161	ENSMUSG00000018339	Gpx3	AA960521|EGPx|GPx|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding
mm_33518.1	chr4	130929409	130929485	+	1	NA	exon (NM_010686, exon 5 of 8)	exon (NM_010686, exon 5 of 8)	-14938	NM_010769	17180	Mm.271796	NM_010769	ENSMUSG00000040533	Matn1	CMP|Crtm|Mat1|matrilin-1	matrilin 1, cartilage matrix protein	protein-coding
mm_93835.1	chr10	121586842	121586852	-	1	NA	promoter-TSS (NM_019786)	promoter-TSS (NM_019786)	-53	NM_019786	56480	Mm.34580	NM_019786	ENSMUSG00000020115	Tbk1	1200008B05Rik|AI462036|AW048562	TANK-binding kinase 1	protein-coding
mm_138778.1	chr17	37246952	37246954	+	1	NA	Intergenic	Intergenic	-14585	NM_146512	258505	Mm.353371	NM_146512	ENSMUSG00000058802	Olfr97	MOR156-2	olfactory receptor 97	protein-coding
mm_109228.1	chr12	108829707	108829713	+	1	NA	intron (NM_181328, intron 2 of 3)	RMER17C|LTR|ERVK	6166	NM_181328	214663	Mm.266264	NM_181328	ENSMUSG00000021265	Slc25a29	C030003J19Rik|CACL|mCACL	solute carrier family 25 (mitochondrial carrier, palmitoylcarnitine transporter), member 29	protein-coding
mm_152639.1	chr19	12502083	12502152	-	1	NA	promoter-TSS (NM_172442)	promoter-TSS (NM_172442)	-121	NM_172442	207521	Mm.247695	NM_172442	ENSMUSG00000039982	Dtx4	AI449438|BC044798|D930042H13|RNF155	deltex 4, E3 ubiquitin ligase	protein-coding
mm_26810.1	chr3	10205338	10205354	-	1	NA	intron (NM_024406, intron 2 of 3)	intron (NM_024406, intron 2 of 3)	3230	NM_024406	11770	Mm.582	NM_024406	ENSMUSG00000062515	Fabp4	422/aP2|ALBP/Ap2|Ap2|Lbpl	fatty acid binding protein 4, adipocyte	protein-coding
mm_94455.1	chr11	6403869	6403881	+	1	NA	exon (NM_028601, exon 17 of 19)	exon (NM_028601, exon 17 of 19)	2245	NR_106109	102465759		NR_106109	ENSMUSG00000098516	Mir7651	Gm27664|mmu-mir-7651	microRNA 7651	ncRNA
mm_102595.1	chr11	62185065	62185067	-	1	NA	intron (NM_001029936, intron 10 of 12)	intron (NM_001029936, intron 10 of 12)	-63918	NM_007413	11541	Mm.40740	NM_007413	ENSMUSG00000018500	Adora2b	A2BAR|A2BR|A2b|AA2BR|AI480866|AI605384	adenosine A2b receptor	protein-coding
mm_84022.1	chr9	57682023	57682032	-	1	NA	exon (NM_009993, exon 2 of 7)	exon (NM_009993, exon 2 of 7)	1628	NM_009993	13077	Mm.15537	NM_009993	ENSMUSG00000032310	Cyp1a2	CP12|Cyp1a1|P450-3	cytochrome P450, family 1, subfamily a, polypeptide 2	protein-coding
mm_162924.1	chr10	121202750	121202752	+	1	NA	Intergenic	RLTR20A2B_MM|LTR|ERVK	108438	NM_029057	74694	Mm.233833	NM_029057	ENSMUSG00000052302	Tbc1d30	4930505D03Rik	TBC1 domain family, member 30	protein-coding
mm_133923.1	chr16	97995020	97995021	+	1	NA	Intergenic	Intergenic	-2327	NR_130962	245305	Mm.148033	NR_130962		B230307C23Rik	EG245305|OTTMUSG00000028475	RIKEN cDNA B230307C23 gene	ncRNA
mm_85771.1	chr9	109040904	109040915	-	1	NA	exon (NM_001284332, exon 2 of 6)	exon (NM_001284332, exon 2 of 6)	2342	NM_001284332	66940	Mm.196533	NM_025858	ENSMUSG00000025647	Shisa5	2310008D10Rik|6430628I05Rik|Scotin|mShisa5	shisa family member 5	protein-coding
mm_43318.1	chr5	134986017	134986033	+	1	NA	promoter-TSS (NM_009902)	promoter-TSS (NM_009902)	-189	NM_009902	12739	Mm.158662	NM_009902	ENSMUSG00000070473	Cldn3	AI182374|Cpetr2|mRVP1	claudin 3	protein-coding
mm_160888.1	chr11	69964873	69964873	+	1	NA	promoter-TSS (NM_001193619)	promoter-TSS (NM_001193619)	94	NM_001193619	53624	Mm.281896	NM_016887	ENSMUSG00000018569	Cldn7	-	claudin 7	protein-coding
mm_8030.1	chr1	135132561	135132601	-	1	NA	promoter-TSS (NM_177081)	promoter-TSS (NM_177081)	-6	NM_007955	13924	Mm.4450	NM_007955		Ptprv	Esp|OST|OST-PTP|mOST-PTP	protein tyrosine phosphatase, receptor type, V	protein-coding
mm_29889.1	chr3	131234158	131234182	-	1	NA	exon (NM_008212, exon 8 of 8)	exon (NM_008212, exon 8 of 8)	37931	NM_008212	15107	Mm.260164	NM_008212	ENSMUSG00000027984	Hadh	AA409008|AU019341|AW742602|HCDH|Hadhsc|Schad	hydroxyacyl-Coenzyme A dehydrogenase	protein-coding
mm_56329.1	chr6	92534903	92534913	-	1	NA	promoter-TSS (NM_001134459)	promoter-TSS (NM_001134459)	-47	NM_001134459	243548	Mm.248820	NM_001081146	ENSMUSG00000030020	Prickle2	6230400G14Rik|6720451F06Rik|mpk2	prickle planar cell polarity protein 2	protein-coding
mm_98951.1	chr11	98451834	98451839	+	1	NA	intron (NM_010346, intron 5 of 14)	intron (NM_010346, intron 5 of 14)	5002	NM_010346	14786	Mm.276702	NM_010346	ENSMUSG00000019312	Grb7	mKIAA4028	growth factor receptor bound protein 7	protein-coding
mm_51316.1	chr6	72314512	72314520	+	1	NA	TTS (NM_001282071)	TTS (NM_001282071)	9906	NM_147779	20388	Mm.46033	NM_147779	ENSMUSG00000056370	Sftpb	AI562151|SF-B|SP-B|Sftp-3|Sftp3	surfactant associated protein B	protein-coding
mm_12188.1	chr2	65334324	65334331	+	1	NA	intron (NM_177074, intron 9 of 11)	intron (NM_177074, intron 9 of 11)	29699	NM_177074	320106	Mm.227703	NM_177074	ENSMUSG00000061171	Slc38a11	9330158F14Rik	solute carrier family 38, member 11	protein-coding
mm_63132.1	chr7	123003644	123003650	+	1	NA	Intergenic	Intergenic	33083	NM_175023	19647	Mm.4480	NM_011247	ENSMUSG00000030779	Rbbp6	4933422O15Rik|AI316869|BB233631|C030034J04Rik|C77662|P2P-R|PACT	retinoblastoma binding protein 6	protein-coding
mm_70279.1	chr8	3600652	3600683	+	1	NA	intron (NM_001347112, intron 5 of 17)	intron (NM_001347112, intron 5 of 17)	13217	NM_001347111	69697	Mm.390010	NM_027171	ENSMUSG00000044433	Camsap3	2310057J16Rik|Kiaa1543|Nezha	calmodulin regulated spectrin-associated protein family, member 3	protein-coding
mm_84529.1	chr9	67048154	67048168	-	1	NA	exon (NM_001164249, exon 2 of 9)	exon (NM_001164249, exon 2 of 9)	1052	NM_001164255	22003	Mm.121878	NM_024427	ENSMUSG00000032366	Tpm1	AA986836|AI854628|TM2|Tm3|Tmpa|Tpm-1|alpha-TM	tropomyosin 1, alpha	protein-coding
mm_91119.1	chr10	19506070	19506080	-	1	NA	Intergenic	Intergenic	-85874	NM_010511	15979	Mm.549	NM_010511	ENSMUSG00000020009	Ifngr1	CD119|IFN-gammaR|Ifgr|Ifngr|Nktar	interferon gamma receptor 1	protein-coding
mm_56283.1	chr6	91411342	91411360	-	1	NA	promoter-TSS (NM_009527)	promoter-TSS (NM_009527)	18	NM_009527	22421	Mm.56964	NM_009527	ENSMUSG00000030093	Wnt7a	AI849442|Wnt-7a|px|tw	wingless-type MMTV integration site family, member 7A	protein-coding
mm_124759.1	chr15	6644890	6644933	+	1	NA	intron (NM_011815, intron 11 of 17)	intron (NM_011815, intron 11 of 17)	-63470	NM_030168	78757	Mm.275811	NM_030168	ENSMUSG00000050310	Rictor	4921505C17Rik|6030405M08Rik|AVO3|AW492497|D530039E11Rik	RPTOR independent companion of MTOR, complex 2	protein-coding
mm_86944.1	chr10	24639855	24639869	+	1	NA	3' UTR (NM_008813, exon 25 of 25)	3' UTR (NM_008813, exon 25 of 25)	44420	NM_010217	14219	Mm.390287	NM_010217	ENSMUSG00000019997	Ctgf	Ccn2|Fisp12|Hcs24|fisp-12	connective tissue growth factor	protein-coding
mm_42219.1	chr5	113330655	113330666	+	1	NA	Intergenic	ORR1B1-int|LTR|ERVL-MaLR	-6115	NR_106088	102465709		NR_106088	ENSMUSG00000105778	Mir7229	mmu-mir-7229	microRNA 7229	ncRNA
mm_159142.1	chr2	86020626	86020626	+	1	NA	promoter-TSS (NM_146578)	promoter-TSS (NM_146578)	-14	NM_146578	258571	Mm.223099	NM_146578	ENSMUSG00000045392	Olfr1033	MOR199-2	olfactory receptor 1033	protein-coding
mm_168718.1	chr12	10900283	10900287	-	1	NA	Intergenic	Intergenic	-147528	NR_045860	71457	Mm.95280	NR_045860		7420701I03Rik	-	RIKEN cDNA 7420701I03 gene	ncRNA
mm_37879.1	chr4	132422395	132422468	-	1	NA	promoter-TSS (NM_175306)	promoter-TSS (NM_175306)	15	NM_001161797	100169	Mm.158361	NM_175306	ENSMUSG00000066043	Phactr4	3110001B12Rik|AI527228|AW495572|C330013F19Rik|N28169|mKIAA4120	phosphatase and actin regulator 4	protein-coding
mm_7312.1	chr1	98057717	98057732	-	1	NA	intron (NM_013626, intron 1 of 25)	intron (NM_013626, intron 1 of 25)	-9931	NR_037993	78603	Mm.442597	NR_037993	ENSMUSG00000089706	B230216N24Rik	-	RIKEN cDNA B230216N24 gene	ncRNA
mm_20679.1	chr2	132455293	132455302	-	1	NA	Intergenic	Intergenic	30556	NR_045802	70845	Mm.158461	NR_045802	ENSMUSG00000027345	4921508D12Rik	-	RIKEN cDNA 4921508D12 gene	ncRNA
mm_50581.1	chr6	49056241	49056255	+	1	NA	exon (NM_053110, exon 11 of 11)	exon (NM_053110, exon 11 of 11)	-17547	NM_029353	75593	Mm.439947	NM_029353	ENSMUSG00000029815	Malsu1	2410003K15Rik|Matsu1	mitochondrial assembly of ribosomal large subunit 1	protein-coding
mm_7524.1	chr1	124110691	124110702	-	1	NA	Intergenic	L1_Mur2|LINE|L1	-65137	NM_199021	269109	Mm.417716	NM_199021	ENSMUSG00000036815	Dpp10	6430601K09Rik|DPP X|Dprp3	dipeptidylpeptidase 10	protein-coding
mm_3284.1	chr1	136627800	136627821	+	1	NA	exon (NM_001160251, exon 2 of 2)	exon (NM_001160251, exon 2 of 2)	2909	NM_001160251	226442	Mm.62521	NM_177643	ENSMUSG00000041483	Zfp281	Znf281	zinc finger protein 281	protein-coding
mm_51952.1	chr6	91754970	91754980	+	1	NA	exon (NM_009320, exon 15 of 15)	exon (NM_009320, exon 15 of 15)	52418	NM_001159507	243547	Mm.333264	NM_001033353	ENSMUSG00000030098	Grip2	-	glutamate receptor interacting protein 2	protein-coding
mm_17696.1	chr2	32349607	32349615	-	1	NA	intron (NM_001301737, intron 1 of 21)	intron (NM_001301737, intron 1 of 21)	3718	NM_001301737	13429	Mm.44736	NM_010065	ENSMUSG00000026825	Dnm1	AI838169|Dnm|Ftfl|mKIAA4093	dynamin 1	protein-coding
mm_41971.1	chr5	107359827	107359849	+	1	NA	exon (NM_054054, exon 13 of 19)	exon (NM_054054, exon 13 of 19)	28644	NM_054054	114642	Mm.182836	NM_054054	ENSMUSG00000029279	Brdt	7420412D09Rik|Brd6|Fsrg3	bromodomain, testis-specific	protein-coding
mm_64563.1	chr7	144857415	144857433	+	1	NA	Intergenic	L1MB3|LINE|L1	-3962	NM_010202	14175	Mm.4956	NM_010202	ENSMUSG00000050917	Fgf4	Fgf-4|Fgfk|HBGF-4|Hst1|Hstf-1|KS3|hst|hst-1|kFGF	fibroblast growth factor 4	protein-coding
mm_164485.1	chr16	75909324	75909335	-	1	NA	promoter-TSS (NM_023380)	promoter-TSS (NM_023380)	-63	NM_023380	67742	Mm.131406	NM_023380	ENSMUSG00000022876	Samsn1	4930571B16Rik|930571B16Rik|Hacs1|SLy2	SAM domain, SH3 domain and nuclear localization signals, 1	protein-coding
mm_37717.1	chr4	129542711	129542727	-	1	NA	promoter-TSS (NM_008228)	promoter-TSS (NM_008228)	-73	NM_008228	433759	Mm.202504	NM_008228	ENSMUSG00000028800	Hdac1	HD1|Hdac1-ps|MommeD5|RPD3	histone deacetylase 1	protein-coding
mm_31523.1	chr4	54947606	54947650	+	1	NA	promoter-TSS (NM_172867)	promoter-TSS (NM_172867)	-317	NM_172867	242466	Mm.102904	NM_172867	ENSMUSG00000060206	Zfp462	6030417H05|9430078C22Rik|Gt4-2|Zfpip	zinc finger protein 462	protein-coding
mm_169161.1	chr13	65415127	65415131	-	1	NA	Intergenic	Intergenic	136275	NM_178364	170936	Mm.151546	NM_178364	ENSMUSG00000021514	Zfp369	B930030B22Rik|D230020H11Rik|NRIF2	zinc finger protein 369	protein-coding
mm_9852.1	chr1	184732617	184732627	-	1	NA	promoter-TSS (NM_008250)	promoter-TSS (NM_008250)	-129	NM_008250	15284	Mm.1347	NM_008250	ENSMUSG00000039377	Hlx	Hlx1	H2.0-like homeobox	protein-coding
mm_10797.1	chr2	24349578	24349596	+	1	NA	exon (NM_031167, exon 5 of 5)	exon (NM_031167, exon 5 of 5)	4216	NM_001039701	16181	Mm.882	NM_031167	ENSMUSG00000026981	Il1rn	F630041P17Rik|IL-1ra	interleukin 1 receptor antagonist	protein-coding
mm_62770.1	chr7	112336594	112336606	+	1	NA	intron (NM_001193305, intron 20 of 25)	intron (NM_001193305, intron 20 of 25)	-31708	NM_027587	100504195	Mm.291129	NM_027587	ENSMUSG00000030771	Micalcl	4921517J23Rik	MICAL C-terminal like	protein-coding
mm_73801.1	chr8	117275138	117275174	+	1	NA	intron (NM_001163262, intron 1 of 20)	intron (NM_001163262, intron 1 of 20)	18137	NM_001163262	74440	Mm.233181	NM_028941	ENSMUSG00000034390	Cmip	4933407C03Rik|5830471E12Rik|AI314065|AI464126	c-Maf inducing protein	protein-coding
mm_121205.1	chr14	103053350	103053366	+	1	NA	intron (NM_008392, intron 4 of 4)	intron (NM_008392, intron 4 of 4)	6346	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_31169.1	chr4	43453786	43453798	+	1	NA	intron (NM_007654, intron 2 of 8)	intron (NM_007654, intron 2 of 8)	834	NM_001110320	12517	Mm.188157	NM_007654	ENSMUSG00000028459	Cd72	CD72c|Ly-19|Ly-32|Ly-m19|Lyb-2	CD72 antigen	protein-coding
mm_49390.1	chr6	24863924	24863928	+	1	NA	intron (NM_028957, intron 1 of 3)	intron (NM_028957, intron 1 of 3)	5929	NM_028957	74468	Mm.251601	NM_028957	ENSMUSG00000029678	Hyal5	4933439A12Rik	hyaluronoglucosaminidase 5	protein-coding
mm_31827.1	chr4	69925672	69925696	+	1	NA	Intergenic	Intergenic	484751	NM_001313762	214444	Mm.370777	NM_145990	ENSMUSG00000039298	Cdk5rap2	2900018K03Rik|an|mKIAA1633	CDK5 regulatory subunit associated protein 2	protein-coding
mm_84809.1	chr9	77347788	77347815	-	1	NA	promoter-TSS (NM_027150)	promoter-TSS (NM_027150)	69	NM_027150	69642	Mm.35008	NM_027150	ENSMUSG00000032355	Mlip	2310046A06Rik|AI931782|CIP	muscular LMNA-interacting protein	protein-coding
mm_153150.1	chr19	34251850	34251861	-	1	NA	exon (NM_007392, exon 3 of 9)	exon (NM_007392, exon 3 of 9)	3518	NM_007392	11475	Mm.213025	NM_007392	ENSMUSG00000035783	Acta2	0610041G09Rik|Actvs|SMalphaA|a-SMA|alphaSMA	actin, alpha 2, smooth muscle, aorta	protein-coding
mm_103184.1	chr11	70514626	70514634	-	1	NA	promoter-TSS (NM_001013607)	promoter-TSS (NM_001013607)	-14	NM_001013607	327956	Mm.244514	NM_001013607	ENSMUSG00000020830	Vmo1	Gm741	vitelline membrane outer layer 1 homolog (chicken)	protein-coding
mm_114503.1	chr13	70574478	70574495	+	1	NA	intron (NR_045934, intron 1 of 2)	intron (NR_045934, intron 1 of 2)	1245	NR_045934	73584	Mm.442491	NR_045934	ENSMUSG00000101051	1700100L14Rik	-	RIKEN cDNA 1700100L14 gene	ncRNA
mm_88536.1	chr10	78425732	78425747	+	1	NA	promoter-TSS (NM_007793)	promoter-TSS (NM_007793)	69	NM_007793	13014	Mm.6095	NM_007793	ENSMUSG00000005054	Cstb	AA960480|Stfb	cystatin B	protein-coding
mm_30940.1	chr4	33031725	33031740	+	1	NA	promoter-TSS (NR_036602)	promoter-TSS (NR_036602)	307	NM_019586	56228	Mm.259095	NM_019586	ENSMUSG00000028277	Ube2j1	0710008M05Rik|1110030I22Rik|NCUBE-1|Ncube|Ncube1|Ubc6p	ubiquitin-conjugating enzyme E2J 1	protein-coding
mm_86192.1	chr9	119564748	119564756	-	1	NA	intron (NM_021544, intron 1 of 27)	intron (NM_021544, intron 1 of 27)	-2074	NM_001253860	20271	Mm.103584	NM_021544	ENSMUSG00000032511	Scn5a	Nav1.5|Nav1.5c|SkM1|SkM2|mH1	sodium channel, voltage-gated, type V, alpha	protein-coding
mm_43552.1	chr5	137597006	137597015	+	1	NA	3' UTR (NM_030037, exon 6 of 6)	3' UTR (NM_030037, exon 6 of 6)	3698	NM_001254762	68929	Mm.41355	NM_030037	ENSMUSG00000037221	Mospd3	1190005J19Rik|5133401H10Rik|Gtig2|R124	motile sperm domain containing 3	protein-coding
mm_87006.1	chr10	26809729	26809734	+	1	NA	intron (NM_176837, intron 1 of 14)	intron (NM_176837, intron 1 of 14)	37219	NM_176837	73910	Mm.356496	NM_176837	ENSMUSG00000039031	Arhgap18	4833419J07Rik|AI314906|AI843501	Rho GTPase activating protein 18	protein-coding
mm_150780.1	chr19	44294967	44294980	+	1	NA	exon (NM_009128, exon 2 of 6)	exon (NM_009128, exon 2 of 6)	1297	NM_009128	20250	Mm.487021	NM_009128	ENSMUSG00000025203	Scd2	Mir5114|Scd-2|mir-5114|swty	stearoyl-Coenzyme A desaturase 2	protein-coding
mm_96101.1	chr11	60476287	60476301	+	1	NA	5' UTR (NM_010862, exon 2 of 65)	5' UTR (NM_010862, exon 2 of 65)	6955	NM_001103171	17910	Mm.89960	NM_010862	ENSMUSG00000042678	Myo15	Myo15a|sh-2|sh2	myosin XV	protein-coding
mm_103333.1	chr11	74590016	74590033	-	1	NA	5' UTR (NM_001015046, exon 1 of 25)	5' UTR (NM_001015046, exon 1 of 25)	134	NM_001015046	380711	Mm.425690	NM_001015046	ENSMUSG00000038807	Rap1gap2	AU067654|Garnl4|Gm1561|mKIAA1039	RAP1 GTPase activating protein 2	protein-coding
mm_146691.1	chr18	12879963	12879970	-	1	NA	promoter-TSS (NM_001252489)	promoter-TSS (NM_001252489)	13	NM_001252489	64291	Mm.259470	NM_020573	ENSMUSG00000044252	Osbpl1a	G430090F17Rik|Gm753|ORP-1|Osbpl1b	oxysterol binding protein-like 1A	protein-coding
mm_85526.1	chr9	106465288	106465302	-	1	NA	exon (NM_001159652, exon 1 of 1)	exon (NM_001159652, exon 1 of 1)	645	NM_001159652	436090	Mm.482905	NM_001159652	ENSMUSG00000091735	Gpr62	4933402E03Rik	G protein-coupled receptor 62	protein-coding
mm_1309.1	chr1	64994272	64994311	+	1	NA	Intergenic	Intergenic	-37467	NM_001039493	241075	Mm.239534	NM_175509	ENSMUSG00000051344	Plekhm3	9430067K14Rik|A230102O09Rik|AI449570|DAPR|Plekhm1l	pleckstrin homology domain containing, family M, member 3	protein-coding
mm_83383.1	chr9	44573436	44573447	-	1	NA	Intergenic	MIRb|SINE|MIR	-31451	NM_001110826	13209	Mm.267061	NM_007841	ENSMUSG00000032097	Ddx6	1110001P04Rik|E230023J21Rik|HLR2|mRCK/P54|p54|rck	DEAD (Asp-Glu-Ala-Asp) box polypeptide 6	protein-coding
mm_161221.1	chr13	67484214	67484214	-	1	NA	promoter-TSS (NM_001076791)	promoter-TSS (NM_001076791)	39	NM_001076791	408067	Mm.315879	NM_001076791	ENSMUSG00000059839	Zfp874b	9630025I21Rik|Rslcan16	zinc finger protein 874b	protein-coding
mm_165785.1	chr3	131368727	131368734	-	1	NA	Intergenic	B3|SINE|B2	-23807	NM_028943	74442	Mm.273360	NM_028943	ENSMUSG00000050931	Sgms2	4933405A16Rik|5133401H06Rik|AI854299	sphingomyelin synthase 2	protein-coding
mm_54578.1	chr6	38124450	38124456	-	1	NA	5' UTR (NM_080467, exon 1 of 21)	5' UTR (NM_080467, exon 1 of 21)	133	NM_080467	140494	Mm.462308	NM_080467	ENSMUSG00000038600	Atp6v0a4	Atp6n1b|a4	ATPase, H+ transporting, lysosomal V0 subunit A4	protein-coding
mm_86235.1	chr9	120743195	120743200	-	1	NA	Intergenic	B4|SINE|B4	165866	NR_073359	76100	Mm.48212	NR_073359	ENSMUSG00000052658	5830454E08Rik	-	RIKEN cDNA 5830454E08 gene	ncRNA
mm_52254.1	chr6	107529718	107529780	+	1	NA	promoter-TSS (NM_008516)	promoter-TSS (NM_008516)	23	NM_008516	16979	Mm.428543	NM_008516	ENSMUSG00000034648	Lrrn1	2810047E21Rik|NLRR-1	leucine rich repeat protein 1, neuronal	protein-coding
mm_91352.1	chr10	27616832	27616891	-	1	NA	promoter-TSS (NM_008481)	promoter-TSS (NM_008481)	81	NM_008481	16773	Mm.256087	NM_008481	ENSMUSG00000019899	Lama2	5830440B04|dy|mKIAA4087|mer|merosin	laminin, alpha 2	protein-coding
mm_120126.1	chr14	60177284	60177309	+	1	NA	Intergenic	CpG	51619	NR_030458	751526		NR_030458	ENSMUSG00000076270	Mir719	Mirn719|mmu-mir-719	microRNA 719	ncRNA
mm_45462.1	chr5	67815867	67815877	-	1	NA	intron (NM_001284345, intron 1 of 36)	intron (NM_001284345, intron 1 of 36)	31559	NM_009727	11980	Mm.153230	NM_009727	ENSMUSG00000037685	Atp8a1	AI481521|AI853962|APLT|AW743152|AW822227|Atp3a2|B230107D19Rik|ClassI	ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1	protein-coding
mm_172474.1	chr7	44986358	44986375	-	1	NA	promoter-TSS (NR_045266)	promoter-TSS (NR_045266)	54	NM_001252476	15469	Mm.27545	NM_019830	ENSMUSG00000109324	Prmt1	6720434D09Rik|AW214366|Hrmt1l2|Mrmt1	protein arginine N-methyltransferase 1	protein-coding
mm_164253.1	chr15	98145673	98145675	-	1	NA	promoter-TSS (NM_030121)	promoter-TSS (NM_030121)	28	NM_030121	78541	Mm.200766	NM_030121	ENSMUSG00000048175	Asb8	4930539L19Rik|AI788835|C430011H06Rik	ankyrin repeat and SOCS box-containing 8	protein-coding
mm_156315.1	chrX	136993254	136993272	+	1	NA	promoter-TSS (NM_001114179)	promoter-TSS (NM_001114179)	108	NM_001035509	66995	Mm.440155	NM_025893	ENSMUSG00000031428	Zcchc18	1500031H04Rik|Sizn2	zinc finger, CCHC domain containing 18	protein-coding
mm_94828.1	chr11	23306737	23306747	+	1	NA	promoter-TSS (NM_001190401)	promoter-TSS (NM_001190401)	-153	NM_001190401	17847	Mm.119155	NM_001190401	ENSMUSG00000056342	Usp34	A530081C03Rik|Murr2	ubiquitin specific peptidase 34	protein-coding
mm_26100.1	chr3	136935695	136935741	+	1	NA	3' UTR (NM_001293622, exon 13 of 13)	3' UTR (NM_001293622, exon 13 of 13)	265652	NM_001293622	19055	Mm.331389	NM_008913	ENSMUSG00000028161	Ppp3ca	2900074D19Rik|CN|Caln|Calna|CnA	protein phosphatase 3, catalytic subunit, alpha isoform	protein-coding
mm_34973.1	chr4	156012582	156012586	+	1	NA	3' UTR (NM_011341, exon 7 of 7)	3' UTR (NM_011341, exon 7 of 7)	-1111	NM_011659	22163	Mm.13885	NM_011659	ENSMUSG00000029075	Tnfrsf4	ACT35|CD134|Ly-70|Ox40|TXGP1L|Txgp1	tumor necrosis factor receptor superfamily, member 4	protein-coding
mm_91428.1	chr10	33206548	33206580	-	1	NA	intron (NM_029726, intron 9 of 37)	L1VL4|LINE|L1	49793	NR_040657	442820	Mm.490725	NR_040657		D830005E20Rik	-	RIKEN cDNA D830005E20 gene	ncRNA
mm_61459.1	chr7	75596370	75596380	+	1	NA	intron (NM_029332, intron 5 of 36)	intron (NM_029332, intron 5 of 36)	140841	NM_029332	75547	Mm.216107	NM_029332	ENSMUSG00000066406	Akap13	1700026G02Rik|5730522G15Rik|5830460E08Rik|AKAP-13|AKAP-Lbc|BRX|Ht31|LBC|PROTO-LB|PROTO-LBC	A kinase (PRKA) anchor protein 13	protein-coding
mm_25064.1	chr3	99240362	99240385	+	1	NA	Intergenic	Intergenic	-13387	NM_009323	21384	Mm.88761	NM_009323	ENSMUSG00000027868	Tbx15	Tbx14|Tbx8|de	T-box 15	protein-coding
mm_40977.1	chr5	77037046	77037072	+	1	NA	intron (NM_027970, intron 1 of 8)	intron (NM_027970, intron 1 of 8)	-18196	NR_077218	68246	Mm.319633	NR_077218	ENSMUSG00000086632	1700112J05Rik	1700110A09Rik	RIKEN cDNA 1700112J05 gene	ncRNA
mm_92775.1	chr10	81168881	81168884	-	1	NA	Intergenic	Intergenic	-1162	NM_021501	59004	Mm.34428	NM_021501	ENSMUSG00000004934	Pias4	PIASY|Pias-gamma|Piasg	protein inhibitor of activated STAT 4	protein-coding
mm_1001.1	chr1	58714317	58714323	+	1	NA	intron (NM_009805, intron 1 of 4)	intron (NM_009805, intron 1 of 4)	1034	NM_207653	12633	Mm.336848	NM_009805	ENSMUSG00000026031	Cflar	2310024N18Rik|A430105C05Rik|CLARP|Cash|Casper|ENSMUSG00000072980|FLAME|FLAME-1|Flip|Gm9845|I-FLICE|MRIT|c-Flip	CASP8 and FADD-like apoptosis regulator	protein-coding
mm_44556.1	chr5	24602086	24602099	-	1	NA	promoter-TSS (NM_025891)	promoter-TSS (NM_025891)	-90	NM_025891	66993	Mm.436539	NM_025891	ENSMUSG00000028949	Smarcd3	1500001J14Rik|2210409C08Rik|BAF60C	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3	protein-coding
mm_166921.1	chr7	30977041	30977045	+	1	NA	promoter-TSS (NM_175240)	promoter-TSS (NM_175240)	0	NM_175240	76415	Mm.259739	NM_175240	ENSMUSG00000046826	Fam187b	1700020B09Rik|Tmem162	family with sequence similarity 187, member B	protein-coding
mm_12319.1	chr2	69380534	69380542	+	1	NA	promoter-TSS (NM_175512)	promoter-TSS (NM_175512)	76	NM_175512	241452	Mm.211655	NM_175512	ENSMUSG00000027068	Dhrs9	C730025I08Rik|Rdh15	dehydrogenase/reductase (SDR family) member 9	protein-coding
mm_164226.1	chr15	85777096	85777103	+	1	NA	intron (NM_001113418, intron 2 of 7)	intron (NM_001113418, intron 2 of 7)	34598	NM_001164626	72355	Mm.33706	NM_197998	ENSMUSG00000064284	Cdpf1	2210021J22Rik	cysteine rich, DPF motif domain containing 1	protein-coding
mm_31107.1	chr4	42917111	42917136	+	1	NA	promoter-TSS (NM_172690)	promoter-TSS (NM_172690)	-120	NM_001346526	230085	Mm.240965	NM_172690	ENSMUSG00000036062	Phf24	GINIP|N28178	PHD finger protein 24	protein-coding
mm_111616.1	chr12	102404282	102404296	-	1	NA	exon (NM_011175, exon 5 of 14)	exon (NM_011175, exon 5 of 14)	35524	NM_011175	19141	Mm.17185	NM_011175	ENSMUSG00000021190	Lgmn	AEP|AI746452|AU022324|Prsc1	legumain	protein-coding
mm_149826.1	chr19	24476782	24476792	+	1	NA	exon (NM_026520, exon 1 of 1)	exon (NM_026520, exon 1 of 1)	687	NM_026520	68034	Mm.440181	NM_026520	ENSMUSG00000074922	Fam122a	2410124L17Rik|2900009I07Rik|ENSMUSG00000051082|Gm9849	family with sequence similarity 122, member A	protein-coding
mm_109293.1	chr12	109559534	109559548	+	1	NA	non-coding (NR_003633, exon 5 of 5)	non-coding (NR_003633, exon 5 of 5)	-4151	NR_030427	791079		NR_030427	ENSMUSG00000076451	Mir770	Mirn770|mir-770|mmu-mir-770	microRNA 770	ncRNA
mm_170708.1	chr2	142416163	142416164	-	1	NA	Intergenic	ORR1C1|LTR|ERVL-MaLR	485301	NM_001081133	16558	Mm.251934	NM_001081133	ENSMUSG00000038844	Kif16b	8430434E15Rik|AA623607|AI789011|C80253|C80902|mKIAA1590	kinesin family member 16B	protein-coding
mm_133172.1	chr16	72027628	72027644	+	1	NA	Intergenic	Intergenic	206691	NR_131116	319533	Mm.373754	NR_131115		8030451O07Rik	-	RIKEN cDNA 8030451O07 gene	ncRNA
mm_97675.1	chr11	79715900	79715903	+	1	NA	Intergenic	B2_Mm2|SINE|B2	3932	NR_029579	387188		NR_029579	ENSMUSG00000065395	Mir193a	Mir193|Mirn193|mir-193a|mmu-mir-193|mmu-mir-193a	microRNA 193a	ncRNA
mm_131783.1	chr16	22896423	22896432	+	1	NA	intron (NR_075099, intron 3 of 5)	C-rich|Low_complexity|Low_complexity	-2041	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_109401.1	chr12	110279229	110279231	+	1	NA	promoter-TSS (NM_172119)	promoter-TSS (NM_172119)	0	NM_172119	107585	Mm.154427	NM_172119	ENSMUSG00000075707	Dio3	-	deiodinase, iodothyronine type III	protein-coding
mm_94568.1	chr11	11686399	11686403	+	1	NA	5' UTR (NM_009578, exon 1 of 7)	5' UTR (NM_009578, exon 1 of 7)	476	NM_001025597	22778	Mm.103545	NM_009578	ENSMUSG00000018654	Ikzf1	5832432G11Rik|Ikaros|LyF-1|Zfpn1a1|Znfn1a1|hlk-1|mKIAA4227	IKAROS family zinc finger 1	protein-coding
mm_98847.1	chr11	97659707	97659781	+	1	NA	Intergenic	Intergenic	-3668	NM_139311	246198	Mm.23685	NM_139311	ENSMUSG00000038437	Mllt6	AI315037|Af17	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 6	protein-coding
mm_168998.1	chr13	100415489	100415499	+	1	NA	intron (NM_008670, intron 12 of 15)	intron (NM_008670, intron 12 of 15)	37370	NM_008670	17940	Mm.6898	NM_008670	ENSMUSG00000021640	Naip1	AV364616|Birc1a|D13Lsd1|Naip|Naip-rs1	NLR family, apoptosis inhibitory protein 1	protein-coding
mm_35833.1	chr4	48042494	48042499	-	1	NA	Intergenic	Intergenic	-2809	NM_015743	18124	Mm.247261	NM_015743	ENSMUSG00000028341	Nr4a3	AI573420|CHN|CSMF|MINOR|NOR-1|Nor1|TEC	nuclear receptor subfamily 4, group A, member 3	protein-coding
mm_124112.1	chr14	79480969	79480977	-	1	NA	promoter-TSS (NM_007920)	promoter-TSS (NM_007920)	-221	NM_007920	13709	Mm.20938	NM_007920	ENSMUSG00000036461	Elf1	Elf-1|Sts1|mElf-1|p70	E74-like factor 1	protein-coding
mm_38998.1	chr4	151569018	151569051	-	1	NA	intron (NM_001081557, intron 4 of 23)	intron (NM_001081557, intron 4 of 23)	292734	NM_001081557	100072	Mm.318846	NM_001081557	ENSMUSG00000014592	Camta1	1810059M14Rik|2310058O09Rik|AI316882|AW987475|mKIAA0833	calmodulin binding transcription activator 1	protein-coding
mm_65804.1	chr7	28962266	28962310	-	1	NA	promoter-TSS (NM_021895)	promoter-TSS (NM_021895)	-8	NM_021895	60595	Mm.81144	NM_021895	ENSMUSG00000054808	Actn4	C77391	actinin alpha 4	protein-coding
mm_143731.1	chr17	81388274	81388276	-	1	NA	non-coding (NR_104580, exon 9 of 9)	non-coding (NR_104580, exon 9 of 9)	-323190	NM_028138	72167	Mm.273257	NM_028138	ENSMUSG00000024246	Thumpd2	2810025A12Rik	THUMP domain containing 2	protein-coding
mm_9214.1	chr1	171231200	171231219	-	1	NA	exon (NM_010185, exon 2 of 5)	exon (NM_010185, exon 2 of 5)	3140	NM_010185	14127	Mm.22673	NM_010185	ENSMUSG00000058715	Fcer1g	AI573376|CD23|FcR-gamma|FcR[g]|FcRgamma|Fce1g|FcepsilonRI|Ly-50	Fc receptor, IgE, high affinity I, gamma polypeptide	protein-coding
mm_76245.1	chr8	83591789	83591796	-	1	NA	intron (NM_134118, intron 1 of 12)	intron (NM_134118, intron 1 of 12)	2699	NM_027179	106529	Mm.352239	NM_027179	ENSMUSG00000031708	Tecr	2410016D23Rik|A230102P12Rik|AI173355|D17Ertd178e|Gpsn2|SC2	trans-2,3-enoyl-CoA reductase	protein-coding
mm_123053.1	chr14	55643307	55643382	-	1	NA	intron (NM_028780, intron 1 of 5)	CpG	462	NM_028780	74140	Mm.132857	NM_028780	ENSMUSG00000002320	Tm9sf1	1200014D02Rik|AI893436|MP70	transmembrane 9 superfamily member 1	protein-coding
mm_142925.1	chr17	53846246	53846248	-	1	NA	promoter-TSS (NM_026935)	promoter-TSS (NM_026935)	-289	NM_026935	69083	Mm.19320	NM_026935	ENSMUSG00000023122	Sult1c2	1810008N17Rik|ST1C1|ST1C2|Sult1c1	sulfotransferase family, cytosolic, 1C, member 2	protein-coding
mm_172824.1	chr9	16833647	16833649	+	1	NA	Intergenic	Intergenic	-455417	NM_001080814	270120	Mm.195010	NM_001080814	ENSMUSG00000074505	Fat3	9430076A06Rik|D430038H04Rik|Gm1132|Gm510|MFAT3F	FAT atypical cadherin 3	protein-coding
mm_2654.1	chr1	125677021	125677075	+	1	NA	promoter-TSS (NM_027677)	promoter-TSS (NM_027677)	52	NM_027677	71111	Mm.32727	NM_027677	ENSMUSG00000026343	Gpr39	4933415E13Rik	G protein-coupled receptor 39	protein-coding
mm_151255.1	chr19	53944064	53944096	+	1	NA	promoter-TSS (NM_019658)	promoter-TSS (NM_019658)	-226	NM_001168505	56392	Mm.228669	NM_019658	ENSMUSG00000024976	Shoc2	AU017287|Sur8|mKIAA0862	soc-2 (suppressor of clear) homolog (C. elegans)	protein-coding
mm_20580.1	chr2	131146767	131146790	-	1	NA	TTS (NM_028306)	TTS (NM_028306)	13242	NM_026091	67326	Mm.27711	NM_026091	ENSMUSG00000027327	1700037H04Rik	-	RIKEN cDNA 1700037H04 gene	protein-coding
mm_86680.1	chr10	18318634	18318725	+	1	NA	Intergenic	CpG	-83698	NM_144820	215814	Mm.296565	NM_144820	ENSMUSG00000059554	Ccdc28a	1700009P13Rik|AI480677	coiled-coil domain containing 28A	protein-coding
mm_2113.1	chr1	87864185	87864198	+	1	NA	intron (NM_177646, intron 1 of 29)	intron (NM_177646, intron 1 of 29)	-9892	NR_136921	100503175	Mm.426422	NR_136921	ENSMUSG00000101942	Gm19582	-	predicted gene, 19582	ncRNA
mm_150183.1	chr19	32645144	32645160	+	1	NA	intron (NM_001201470, intron 7 of 11)	intron (NM_001201470, intron 7 of 11)	25147	NM_011864	23972	Mm.203916	NM_011864	ENSMUSG00000024899	Papss2	1810018P12Rik|AI159688|AtpsU2|Atpsk2|Sk2|bm	3'-phosphoadenosine 5'-phosphosulfate synthase 2	protein-coding
mm_166785.1	chr6	143992386	143992387	+	1	NA	intron (NM_001113559, intron 6 of 13)	intron (NM_001113559, intron 6 of 13)	-45280	NM_001347506	20678	Mm.1752	NM_011444	ENSMUSG00000041540	Sox5	A730017D01Rik|AI528773	SRY (sex determining region Y)-box 5	protein-coding
mm_140786.1	chr17	18231553	18231559	-	1	NA	Intergenic	Intergenic	46010	NM_001104543	665227		NM_001104543	ENSMUSG00000090417	Vmn2r94	EG665227	vomeronasal 2, receptor 94	protein-coding
mm_69005.1	chr7	126701173	126701191	-	1	NA	intron (NM_001301374, intron 6 of 10)	intron (NM_001301374, intron 6 of 10)	3038	NM_001301374	12721	Mm.290482	NM_009898	ENSMUSG00000030707	Coro1a	Clabp|Lmb3|TACO|p57	coronin, actin binding protein 1A	protein-coding
mm_124495.1	chr14	121797671	121797753	-	1	NA	promoter-TSS (NM_134074)	promoter-TSS (NM_134074)	22	NM_134074	105445	Mm.378591	NM_134074	ENSMUSG00000025558	Dock9	AA959601|AW538057|B230309H04Rik|D14Wsu89e|Zizimin1|mKIAA1058	dedicator of cytokinesis 9	protein-coding
mm_91517.1	chr10	37138603	37138636	-	1	NA	5' UTR (NM_008538, exon 1 of 2)	5' UTR (NM_008538, exon 1 of 2)	307	NM_008538	17118	Mm.30059	NM_008538	ENSMUSG00000069662	Marcks	Macs|PKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding
mm_155983.1	chrX	106127182	106127199	+	1	NA	3' UTR (NM_009726, exon 23 of 23)	3' UTR (NM_009726, exon 23 of 23)	-16085	NM_205820	279572	Mm.336203	NM_205820	ENSMUSG00000033777	Tlr13	AI666735|Gm713	toll-like receptor 13	protein-coding
mm_91092.1	chr10	19062112	19062114	-	1	NA	Intergenic	Intergenic	-46703	NM_009397	21929	Mm.116683	NM_009397	ENSMUSG00000019850	Tnfaip3	A20|Tnfip3	tumor necrosis factor, alpha-induced protein 3	protein-coding
mm_158877.1	chrY	2170394	2170396	-	1	NA	promoter-TSS (NM_009571)	promoter-TSS (NM_009571)	14	NM_009571	22768	Mm.411381	NM_009571	ENSMUSG00000000103	Zfy2	Zfy-2	zinc finger protein 2, Y-linked	protein-coding
mm_52090.1	chr6	97831332	97831343	+	1	NA	intron (NM_001113198, intron 1 of 9)	intron (NM_001113198, intron 1 of 9)	24279	NM_001113198	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_91589.1	chr10	40258083	40258092	-	1	NA	promoter-TSS (NM_026113)	promoter-TSS (NM_026113)	-422	NM_026113	67371	Mm.64104	NM_026113	ENSMUSG00000019837	Gtf3c6	2410016F19Rik|AU019813	general transcription factor IIIC, polypeptide 6, alpha	protein-coding
mm_149320.1	chr19	10842339	10842369	+	1	NA	promoter-TSS (NM_023044)	promoter-TSS (NM_023044)	-190	NM_023044	65221	Mm.27387	NM_023044	ENSMUSG00000024737	Slc15a3	Ci1|cI-1	solute carrier family 15, member 3	protein-coding
mm_23678.1	chr3	68584311	68584313	+	1	NA	intron (NM_013928, intron 1 of 6)	intron (NM_013928, intron 1 of 6)	11944	NM_013928	30953	Mm.331064	NM_013928	ENSMUSG00000027777	Schip1	Nf2ip|Schip-1	schwannomin interacting protein 1	protein-coding
mm_122944.1	chr14	54965464	54965473	-	1	NA	5' UTR (NM_010856, exon 3 of 39)	5' UTR (NM_010856, exon 3 of 39)	1139	NM_001164171	17888	Mm.290003	NM_010856	ENSMUSG00000040752	Myh6	A830009F23Rik|AA517445|Myhc-a|Myhca|alpha-MHC	myosin, heavy polypeptide 6, cardiac muscle, alpha	protein-coding
mm_127023.1	chr15	96286861	96286919	+	1	NA	promoter-TSS (NM_175251)	promoter-TSS (NM_175251)	-632	NM_175251	77044	Mm.17166	NM_175251	ENSMUSG00000033237	Arid2	1700124K17Rik|4432409D24Rik|zipzap/p200	AT rich interactive domain 2 (ARID, RFX-like)	protein-coding
mm_142275.1	chr17	39848227	39848242	-	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	5237	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_148516.1	chr19	4232436	4232479	+	1	NA	promoter-TSS (NR_132280)	promoter-TSS (NR_132280)	42	NR_132280	69745	Mm.32518	NM_027196	ENSMUSG00000024854	Pold4	2410012M21Rik|AI463381|AW060307|Polds|p12	polymerase (DNA-directed), delta 4	protein-coding
mm_155711.1	chrX	96096059	96096077	+	1	NA	promoter-TSS (NM_010833)	promoter-TSS (NM_010833)	23	NM_010833	17698	Mm.138876	NM_010833	ENSMUSG00000031207	Msn	C78546	moesin	protein-coding
mm_100986.1	chr11	7213851	7213859	-	1	NA	promoter-TSS (NM_008343)	promoter-TSS (NM_008343)	68	NM_008343	16009	Mm.29254	NM_008343	ENSMUSG00000020427	Igfbp3	AI649005|IGFBP-3|IGgfbp3	insulin-like growth factor binding protein 3	protein-coding
mm_67121.1	chr7	70361701	70361707	-	1	NA	intron (NM_183261, intron 1 of 2)	intron (NM_183261, intron 1 of 2)	-1111	NM_009697	11819	Mm.158143	NM_009697	ENSMUSG00000030551	Nr2f2	2700033K02Rik|9430015G03Rik|ARP-1|Aporp1|COUP-TF2|COUP-TFII|COUPTFB|EAR3|SVP40|Tcfcoup2	nuclear receptor subfamily 2, group F, member 2	protein-coding
mm_158477.1	chrX	141725182	141725195	-	1	NA	promoter-TSS (NM_010572)	promoter-TSS (NM_010572)	29	NM_010572	16370	Mm.261591	NM_010572	ENSMUSG00000054667	Irs4	IRS-4	insulin receptor substrate 4	protein-coding
mm_12259.1	chr2	68939529	68939540	+	1	NA	intron (NM_172856, intron 2 of 9)	L1_Mus3|LINE|L1	78093	NM_001347161	241447	Mm.222222	NM_172856	ENSMUSG00000027035	Cers6	4732462C07Rik|AW544719|Lass6|T1L	ceramide synthase 6	protein-coding
mm_61503.1	chr7	78019130	78019134	+	1	NA	Intergenic	Intergenic	558706	NM_008746	18213	Mm.33496	NM_008746	ENSMUSG00000059146	Ntrk3	AW125844|Ntrk3_tv3|TrkC	neurotrophic tyrosine kinase, receptor, type 3	protein-coding
mm_130563.1	chr15	99370350	99370381	-	1	NA	5' UTR (NM_011711, exon 1 of 27)	5' UTR (NM_011711, exon 1 of 27)	117	NM_001310623	22379	Mm.29043	NM_011711	ENSMUSG00000023008	Fmnl3	2700073B04Rik|FBP11|Wbp3|mKIAA2014	formin-like 3	protein-coding
mm_167453.1	chr8	123001198	123001202	-	1	NA	intron (NM_001081379, intron 1 of 12)	A-rich|Low_complexity|Low_complexity	41084	NR_037865	77087	Mm.31567	NM_001081379	ENSMUSG00000035569	Ankrd11	2410104C19Rik|3010027A04Rik|6330578C09Rik|9530048I21Rik|AA930108|Gm176|Yod	ankyrin repeat domain 11	protein-coding
mm_114048.1	chr13	54209631	54209650	+	1	NA	intron (NM_001010973, intron 1 of 2)	intron (NM_001010973, intron 1 of 2)	17511	NM_008286	15466	Mm.57243	NM_008286	ENSMUSG00000034987	Hrh2	-	histamine receptor H2	protein-coding
mm_22465.1	chr3	3634146	3634161	+	1	NA	intron (NM_013920, intron 1 of 9)	intron (NM_013920, intron 1 of 9)	126123	NM_013920	30942	Mm.330897	NM_013920	ENSMUSG00000017688	Hnf4g	NR2A2	hepatocyte nuclear factor 4, gamma	protein-coding
mm_99847.1	chr11	109362089	109362104	+	1	NA	promoter-TSS (NM_010303)	promoter-TSS (NM_010303)	-698	NM_010303	14674	Mm.193925	NM_010303	ENSMUSG00000020611	Gna13	AU024132|AU043124|Galpha13	guanine nucleotide binding protein, alpha 13	protein-coding
mm_17845.1	chr2	34372592	34372598	-	1	NA	promoter-TSS (NM_001290576)	promoter-TSS (NM_001290576)	-550	NM_016768	18516	Mm.239941	NM_016768	ENSMUSG00000038718	Pbx3	-	pre B cell leukemia homeobox 3	protein-coding
mm_166297.1	chr5	104113930	104113943	-	1	NA	5' UTR (NM_010097, exon 1 of 11)	5' UTR (NM_010097, exon 1 of 11)	152	NM_010097	13602	Mm.29027	NM_010097	ENSMUSG00000029309	Sparcl1	Ecm2|Sc1|hevin|mast9	SPARC-like 1	protein-coding
mm_170672.1	chr2	121413913	121413915	+	1	NA	promoter-TSS (NM_007952)	promoter-TSS (NM_007952)	12	NM_007952	14827	Mm.263177	NM_007952	ENSMUSG00000027248	Pdia3	58kDa|ERp57|ERp60|ERp61|Erp|Grp58|PDI|PDI-Q2|PI-PLC|PLC[a]|Plca	protein disulfide isomerase associated 3	protein-coding
mm_59188.1	chr7	24475241	24475261	+	1	NA	exon (NM_011113, exon 7 of 7)	exon (NM_011113, exon 7 of 7)	-6772	NM_153112	260299	Mm.178322	NM_153112	ENSMUSG00000054793	Cadm4	Igdf4c|Igsf4c|Tsll2	cell adhesion molecule 4	protein-coding
mm_149222.1	chr19	10018242	10018257	+	1	NA	promoter-TSS (NM_144538)	promoter-TSS (NM_144538)	21	NM_144538	74760	Mm.281969	NM_144538	ENSMUSG00000024663	Rab3il1	1200014K04Rik|AI115013|C76746|Rab3ail1	RAB3A interacting protein (rabin3)-like 1	protein-coding
mm_42456.1	chr5	115435446	115435452	+	1	NA	intron (NM_008629, intron 5 of 14)	intron (NM_008629, intron 5 of 14)	5764	NM_008629	17690	Mm.5077	NM_008629	ENSMUSG00000054256	Msi1	Msi1h|Musahi1|m-Msi-1	musashi RNA-binding protein 1	protein-coding
mm_86050.1	chr9	114563243	114563253	-	1	NA	5' UTR (NM_001042503, exon 1 of 4)	5' UTR (NM_001042503, exon 1 of 4)	1121	NM_001042503	636931	Mm.17857	NM_001042503	ENSMUSG00000079259	Trim71	2610206G21Rik|AL022943|Gm1127|Lin41|lin-41|mLin41|mlin-41	tripartite motif-containing 71	protein-coding
mm_43410.1	chr5	135889039	135889042	+	1	NA	intron (NM_013560, intron 1 of 2)	intron (NM_013560, intron 1 of 2)	1121	NM_013560	15507	Mm.13849	NM_013560	ENSMUSG00000004951	Hspb1	27kDa|Hsp25	heat shock protein 1	protein-coding
mm_23327.1	chr3	53703407	53703461	+	1	NA	Intergenic	Intergenic	-46079	NM_172862	242022	Mm.38378	NM_172862	ENSMUSG00000037016	Frem2	6030440P17Rik|8430406N05Rik|Gm409|b2b1562Clo|my|ne|nv1	Fras1 related extracellular matrix protein 2	protein-coding
mm_63714.1	chr7	130692890	130692898	+	1	NA	5' UTR (NM_021314, exon 1 of 18)	5' UTR (NM_021314, exon 1 of 18)	338	NM_021314	57752	Mm.86322	NM_021314	ENSMUSG00000030852	Tacc2	mKIAA4180	transforming, acidic coiled-coil containing protein 2	protein-coding
mm_74119.1	chr8	123102432	123102454	+	1	NA	promoter-TSS (NM_016738)	promoter-TSS (NM_016738)	93	NM_016738	270106	Mm.319719	NM_016738	ENSMUSG00000000740	Rpl13	A52|L13	ribosomal protein L13	protein-coding
mm_47031.1	chr5	115732212	115732256	-	1	NA	promoter-TSS (NM_001080808)	promoter-TSS (NM_001080808)	-675	NM_001080808	75665	Mm.233914	NM_001080808	ENSMUSG00000041609	Ccdc64	2210403N09Rik|BICDR-1|Bicdl1	coiled-coil domain containing 64	protein-coding
mm_85018.1	chr9	88380185	88380188	-	1	NA	exon (NM_172926, exon 26 of 28)	exon (NM_172926, exon 26 of 28)	52577	NM_011851	23959	Mm.244235	NM_011851	ENSMUSG00000032420	Nt5e	2210401F01Rik|5'-NT|AI447961|CD73|NT|Nt5|eNT	5' nucleotidase, ecto	protein-coding
mm_1174.1	chr1	60977941	60977957	+	1	NA	promoter-TSS (NM_017480)	promoter-TSS (NM_017480)	35	NM_017480	54167	Mm.42044	NM_017480	ENSMUSG00000026009	Icos	AILIM|CCLP|CRP-1|H4|Ly115	inducible T cell co-stimulator	protein-coding
mm_165384.1	chr2	130292305	130292305	+	1	NA	Intergenic	Intergenic	-3634	NM_001110513	228598	Mm.32582	NM_152993	ENSMUSG00000053552	Ebf4	Ebf3|O/E-4|Olf-1	early B cell factor 4	protein-coding
mm_85180.1	chr9	96630872	96630900	-	1	NA	intron (NM_053268, intron 1 of 23)	CpG	617	NM_053268	114713	Mm.124502	NM_053268	ENSMUSG00000032413	Rasa2	5430433H21Rik|AA517451|AU023900|GAP1m	RAS p21 protein activator 2	protein-coding
mm_51284.1	chr6	72304304	72304314	+	1	NA	promoter-TSS (NM_001282071)	promoter-TSS (NM_001282071)	-301	NM_001282071	20388	Mm.46033	NM_147779	ENSMUSG00000056370	Sftpb	AI562151|SF-B|SP-B|Sftp-3|Sftp3	surfactant associated protein B	protein-coding
mm_21539.1	chr2	163730362	163730372	-	1	NA	exon (NM_001272052, exon 8 of 12)	exon (NM_001272052, exon 8 of 12)	19872	NM_007398	11486	Mm.388	NM_007398	ENSMUSG00000017697	Ada	-	adenosine deaminase	protein-coding
mm_131182.1	chr16	7189469	7189471	+	1	NA	intron (NM_183188, intron 1 of 12)	intron (NM_183188, intron 1 of 12)	119635	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_100948.1	chr11	6561001	6561023	-	1	NA	intron (NM_001190344, intron 1 of 9)	intron (NM_001190344, intron 1 of 9)	829	NM_001190344	216527	Mm.221271	NM_146014	ENSMUSG00000000378	Ccm2	BC029157	cerebral cavernous malformation 2	protein-coding
mm_138413.1	chr17	35068860	35068885	+	1	NA	exon (NM_023463, exon 2 of 3)	exon (NM_023463, exon 2 of 3)	1547	NM_023463	68468	Mm.215096	NM_023463	ENSMUSG00000092586	Ly6g6c	1110003M04Rik|AU016360|G6c|NG24	lymphocyte antigen 6 complex, locus G6C	protein-coding
mm_124513.1	chr14	121929430	121929447	-	1	NA	intron (NM_026861, intron 4 of 8)	intron (NM_026861, intron 4 of 8)	-13664	NM_182806	110168	Mm.37405	NM_182806	ENSMUSG00000050350	Gpr18	-	G protein-coupled receptor 18	protein-coding
mm_7474.1	chr1	120494808	120494818	-	1	NA	exon (NM_010766, exon 2 of 17)	exon (NM_010766, exon 2 of 17)	10271	NM_010766	17167	Mm.1856	NM_010766	ENSMUSG00000026390	Marco	AI323439|Ly112|Scara2	macrophage receptor with collagenous structure	protein-coding
mm_101579.1	chr11	34393901	34393935	-	1	NA	intron (NM_001025382, intron 1 of 3)	intron (NM_001025382, intron 1 of 3)	79096	NM_001025382	574403	Mm.444796	NM_001025382	ENSMUSG00000069911	Fam196b	EG574403|Gm6041	family with sequence similarity 196, member B	protein-coding
mm_101525.1	chr11	33147409	33147448	-	1	NA	promoter-TSS (NM_008005)	promoter-TSS (NM_008005)	-28	NR_102395	14172	Mm.339812	NM_008005	ENSMUSG00000057967	Fgf18	D130055P09Rik|FGF-18	fibroblast growth factor 18	protein-coding
mm_103289.1	chr11	72361838	72361899	-	1	NA	promoter-TSS (NM_011569)	promoter-TSS (NM_011569)	14	NM_011569	21689	Mm.42257	NM_011569	ENSMUSG00000020799	Tekt1	MT14	tektin 1	protein-coding
mm_100511.1	chr11	120530509	120530518	+	1	NA	promoter-TSS (NM_008101)	promoter-TSS (NM_008101)	-214	NM_008101	14527	Mm.22329	NM_008101	ENSMUSG00000025127	Gcgr	GR	glucagon receptor	protein-coding
mm_39880.1	chr5	31077506	31077510	+	1	NA	intron (NM_023525, intron 41 of 43)	intron (NM_023525, intron 41 of 43)	16019	NM_011773	22784	Mm.1396	NM_011773	ENSMUSG00000029151	Slc30a3	Znt3	solute carrier family 30 (zinc transporter), member 3	protein-coding
mm_105345.1	chr11	102997587	102997597	-	1	NA	intron (NM_026551, intron 3 of 4)	intron (NM_026551, intron 3 of 4)	2329	NR_105896	102466988		NR_105896	ENSMUSG00000098613	Mir6931	Gm27303|mmu-mir-6931	microRNA 6931	ncRNA
mm_115661.1	chr13	12461433	12461520	-	1	NA	5' UTR (NM_001291060, exon 1 of 9)	5' UTR (NM_001291060, exon 1 of 9)	262	NM_001291060	56048	Mm.474138	NM_018886	ENSMUSG00000057554	Lgals8	1200015E08Rik|AI326142|D13Ertd524e|Lgals-8	lectin, galactose binding, soluble 8	protein-coding
mm_23735.1	chr3	69045077	69045087	+	1	NA	promoter-TSS (NM_025863)	promoter-TSS (NM_025863)	-340	NM_025863	66949	Mm.176695	NM_025863	ENSMUSG00000034317	Trim59	2310035M22Rik|2700022F13Rik|Mrf1|TSBF1	tripartite motif-containing 59	protein-coding
mm_125733.1	chr15	73182663	73182671	+	1	NA	intron (NM_153178, intron 1 of 18)	intron (NM_153178, intron 1 of 18)	2280	NM_153178	239528	Mm.23095	NM_153178	ENSMUSG00000036698	Ago2	1110029L17Rik|2310051F07Rik|AI225898|AL022874|AW546247|ENSMUSG00000072493|Eif2c2|Gerp95|Gm10365|mKIAA4215	argonaute RISC catalytic subunit 2	protein-coding
mm_125552.1	chr15	58802784	58802794	+	1	NA	intron (NM_175212, intron 1 of 6)	intron (NM_175212, intron 1 of 6)	20638	NM_175212	74868	Mm.293754	NM_175212	ENSMUSG00000062373	Tmem65	2610029O13Rik|4930438D12Rik	transmembrane protein 65	protein-coding
mm_8878.1	chr1	162860115	162860126	-	1	NA	promoter-TSS (NM_001330291)	promoter-TSS (NM_001330291)	-120	NM_001330318	14261	Mm.976	NM_010231	ENSMUSG00000040181	Fmo1	-	flavin containing monooxygenase 1	protein-coding
mm_102734.1	chr11	67250630	67250644	-	1	NA	exon (NM_010855, exon 21 of 40)	exon (NM_010855, exon 21 of 40)	12825	NM_010855	17884	Mm.297382	NM_010855	ENSMUSG00000057003	Myh4	AI506973|MHC2B|MM|MYH-2B|Minimsc|Minmus|MyHC-IIb|Myhsf	myosin, heavy polypeptide 4, skeletal muscle	protein-coding
mm_50030.1	chr6	41130114	41130143	+	1	NA	Intergenic	Intergenic	-94619	NM_023333	67373	Mm.153729	NM_023333	ENSMUSG00000029882	2210010C04Rik	AV072249	RIKEN cDNA 2210010C04 gene	protein-coding
mm_133367.1	chr16	84705877	84705885	+	1	NA	Intergenic	Intergenic	-7142	NR_132106	100653389	Mm.261808	NR_132106	ENSMUSG00000097418	Mir155hg	Bic|Gm26667	Mir155 host gene (non-protein coding)	ncRNA
mm_19717.1	chr2	104410582	104410589	-	1	NA	promoter-TSS (NM_001033347)	promoter-TSS (NM_001033347)	-251	NM_001033347	241589	Mm.358909	NM_001033347	ENSMUSG00000068373	D430041D05Rik	9630056G07Rik|G2	RIKEN cDNA D430041D05 gene	protein-coding
mm_122049.1	chr14	30094881	30094884	-	1	NA	intron (NM_001302637, intron 30 of 48)	intron (NM_001302637, intron 30 of 48)	72249	NM_175343	218865	Mm.259916	NM_172264	ENSMUSG00000015970	Chdh	AU041472|D630034H06Rik	choline dehydrogenase	protein-coding
mm_33703.1	chr4	133632239	133632264	+	1	NA	intron (NM_001017968, intron 1 of 7)	intron (NM_001017968, intron 1 of 7)	1178	NM_001017968	503610	Mm.331948	NM_001017968	ENSMUSG00000037553	Zdhhc18	-	zinc finger, DHHC domain containing 18	protein-coding
mm_19132.1	chr2	80257793	80257797	-	1	NA	Intergenic	Intergenic	-34675	NM_177256	320769	Mm.60992	NM_177256	ENSMUSG00000050114	Prdx6b	1-cysPrx-P1|4930414C22Rik|Aop2-rs1|Prdx5-rs1|Prdx6-ps1|Prdx6-rs1|Prdx6-rs1-ps	peroxiredoxin 6B	protein-coding
mm_39780.1	chr5	30156726	30156729	+	1	NA	intron (NM_001289798, intron 1 of 15)	intron (NM_001289798, intron 1 of 15)	1474	NM_001289798	231086	Mm.291463	NM_145558	ENSMUSG00000059447	Hadhb	4930479F15Rik|Mtpb|TP-beta	hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), beta subunit	protein-coding
mm_2519.1	chr1	106334540	106334580	+	1	NA	intron (NM_133821, intron 4 of 16)	(T)n|Simple_repeat|Simple_repeat	162691	NM_133821	98432	Mm.24115	NM_133821	ENSMUSG00000044340	Phlpp1	AI836256|Phlpp|Plekhe1|SCOP|mKIAA0606	PH domain and leucine rich repeat protein phosphatase 1	protein-coding
mm_63392.1	chr7	127278562	127278575	+	1	NA	Intergenic	B3|SINE|B2	-4509	NM_009266	20768	Mm.20294	NM_009266	ENSMUSG00000049091	Sephs2	Sps2|Ysg3	selenophosphate synthetase 2	protein-coding
mm_111436.1	chr12	92792889	92792890	-	1	NA	Intergenic	Intergenic	651934	NR_126436	75295	Mm.243878	NR_126436		4930559C10Rik	-	RIKEN cDNA 4930559C10 gene	ncRNA
mm_7827.1	chr1	132068014	132068025	-	1	NA	promoter-TSS (NM_001114662)	promoter-TSS (NM_001114662)	43	NM_172510	213006	Mm.208445	NM_172510	ENSMUSG00000059149	Mfsd4a	A230072B04|A930031D07Rik|AI850289|Mfsd4	major facilitator superfamily domain containing 4A	protein-coding
mm_90080.1	chr10	116509038	116509064	+	1	NA	TTS (NM_001037848)	TTS (NM_001037848)	-35528	NM_021452	58802	Mm.440652	NM_021452	ENSMUSG00000054934	Kcnmb4	1700058G18Rik|2900045G12Rik	potassium large conductance calcium-activated channel, subfamily M, beta member 4	protein-coding
mm_153258.1	chr19	36919053	36919064	-	1	NA	exon (NM_028263, exon 2 of 2)	exon (NM_028263, exon 2 of 2)	541	NM_028263	72514	Mm.41674	NM_028263	ENSMUSG00000047632	Fgfbp3	2610306H15Rik|Fgf-bp3	fibroblast growth factor binding protein 3	protein-coding
mm_126004.1	chr15	76538813	76538876	+	1	NA	promoter-TSS (NM_013909)	promoter-TSS (NM_013909)	-98	NM_013909	30840	Mm.275279	NM_013909	ENSMUSG00000022559	Fbxl6	AU021795|Fbl6	F-box and leucine-rich repeat protein 6	protein-coding
mm_90415.1	chr10	127452722	127452743	+	1	NA	exon (NM_001168293, exon 4 of 24)	exon (NM_001168293, exon 4 of 24)	31865	NM_001168293	71750	Mm.29342	NM_027900	ENSMUSG00000025404	R3hdm2	1300003K24Rik|AU041262|mKIAA1002	R3H domain containing 2	protein-coding
mm_101044.1	chr11	8624601	8624615	-	1	NA	intron (NM_001083587, intron 1 of 30)	CpG	39927	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
mm_77085.1	chr8	110755584	110755595	-	1	NA	5' UTR (NM_001135100, exon 2 of 7)	5' UTR (NM_001135100, exon 2 of 7)	29863	NM_001310591	244654	Mm.490385	NM_198625	ENSMUSG00000033763	Mtss1l	ABBA	metastasis suppressor 1-like	protein-coding
mm_52737.1	chr6	120439880	120439912	+	1	NA	3' UTR (NM_145997, exon 28 of 28)	3' UTR (NM_145997, exon 28 of 28)	-23301	NM_008359	16172	Mm.4481	NM_008359	ENSMUSG00000002897	Il17ra	AW538159|Cdw217|Il17r|VDw217	interleukin 17 receptor A	protein-coding
mm_118677.1	chr14	22079794	22079821	+	1	NA	intron (NM_028275, intron 2 of 6)	B3|SINE|B2	60095	NM_028275	76633	Mm.489898	NM_028275	ENSMUSG00000063458	1700112E06Rik	2700009F18Rik	RIKEN cDNA 1700112E06 gene	protein-coding
mm_148233.1	chr18	80469641	80469649	-	1	NA	promoter-TSS (NM_026295)	promoter-TSS (NM_026295)	22	NM_026295	67655	Mm.312893	NM_026295	ENSMUSG00000033323	Ctdp1	4930563P03Rik|AW553592	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) phosphatase, subunit 1	protein-coding
mm_34493.1	chr4	148591982	148591992	+	1	NA	intron (NM_009272, intron 1 of 6)	CpG	474	NM_009272	20810	Mm.10	NM_009272	ENSMUSG00000006442	Srm	AA407669|SpdST|SpdSy	spermidine synthase	protein-coding
mm_87451.1	chr10	51483368	51483420	+	1	NA	intron (NM_001291892, intron 5 of 8)	intron (NM_001291892, intron 5 of 8)	2782	NM_001291892	14727	Mm.439661	NM_008147	ENSMUSG00000062593	Lilr4b	Gp49a|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4B	protein-coding
mm_49651.1	chr6	30806544	30806583	+	1	NA	intron (NM_017478, intron 20 of 23)	PB1D10|SINE|Alu	65264	NR_029900	723930		NR_029900	ENSMUSG00000065501	Mir335	Mirn335|mir-335|mmu-mir-335	microRNA 335	ncRNA
mm_71167.1	chr8	40546531	40546549	+	1	NA	3' UTR (NM_033560, exon 12 of 12)	3' UTR (NM_033560, exon 12 of 12)	-30693	NM_001271542	18983	Mm.272551	NM_011135	ENSMUSG00000031601	Cnot7	AU022737|CAF-1|Caf1|Pop2	CCR4-NOT transcription complex, subunit 7	protein-coding
mm_78967.1	chr9	45299406	45299436	+	1	NA	Intergenic	Intergenic	-19679	NM_001013373	214531	Mm.394987	NM_001013373	ENSMUSG00000037129	Tmprss13	BC010843|Tpmrss13	transmembrane protease, serine 13	protein-coding
mm_170680.1	chr2	123880180	123880186	+	1	NA	Intergenic	L1Md_T|LINE|L1	-209786	NM_001290997	214968	Mm.330536	NM_172537	ENSMUSG00000027200	Sema6d	1110067B02Rik|AA409156|D330011G23|mKIAA1479	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	protein-coding
mm_78848.1	chr9	44334686	44334704	+	1	NA	promoter-TSS (NM_010436)	promoter-TSS (NM_010436)	-20	NM_010436	15270	Mm.245931	NM_010436	ENSMUSG00000049932	H2afx	AW228881|H2A.X|H2ax|Hist5-2ax|gammaH2ax	H2A histone family, member X	protein-coding
mm_72066.1	chr8	71474812	71474836	+	1	NA	non-coding (NR_122115, exon 5 of 5)	non-coding (NR_122115, exon 5 of 5)	5630	NR_122114	66498	Mm.260360	NM_025600	ENSMUSG00000074247	Dda1	1500034J01Rik|1700095J19Rik|R74921	DET1 and DDB1 associated 1	protein-coding
mm_166447.1	chr5	137268176	137268180	-	1	NA	Intergenic	Intergenic	-20076	NM_009599	11423	Mm.255464	NM_009599	ENSMUSG00000023328	Ache	-	acetylcholinesterase	protein-coding
mm_125828.1	chr15	74957470	74957474	+	1	NA	intron (NM_001164039, intron 2 of 4)	intron (NM_001164039, intron 2 of 4)	2366	NM_001164040	17069	Mm.788	NM_008529	ENSMUSG00000022587	Ly6e	Ly67|RIG-E|Sca-2|TSA-1|Tsa1	lymphocyte antigen 6 complex, locus E	protein-coding
mm_22483.1	chr3	5400598	5400624	+	1	NA	exon (NM_030708, exon 10 of 11)	exon (NM_030708, exon 10 of 11)	175637	NM_001163301	19302	Mm.132336	NM_008994	ENSMUSG00000040374	Pex2	D3Ertd138e|PAF-1|PMP35|Pxmp3	peroxisomal biogenesis factor 2	protein-coding
mm_85369.1	chr9	103221027	103221049	-	1	NA	exon (NM_133977, exon 9 of 17)	exon (NM_133977, exon 9 of 17)	9248	NM_133977	22041	Mm.37214	NM_133977	ENSMUSG00000032554	Trf	AI266983|Cd176|HP|Tf|Tfn|hpx	transferrin	protein-coding
mm_134498.1	chr16	18812004	18812025	-	1	NA	promoter-TSS (NM_001161623)	promoter-TSS (NM_001161623)	-42	NM_009862	12544	Mm.1248	NM_009862	ENSMUSG00000000028	Cdc45	Cdc45l	cell division cycle 45	protein-coding
mm_91421.1	chr10	32755625	32755628	-	1	NA	intron (NM_001013411, intron 1 of 6)	intron (NM_001013411, intron 1 of 6)	134289	NM_001013411	432450	Mm.49665	NM_001013411	ENSMUSG00000069670	Nkain2	6330571D19Rik|AW455467|Tcba1	Na+/K+ transporting ATPase interacting 2	protein-coding
mm_22625.1	chr3	14766413	14766419	+	1	NA	3' UTR (NM_001083957, exon 7 of 7)	3' UTR (NM_001083957, exon 7 of 7)	12044	NM_001083957	12346	Mm.273195	NM_009799	ENSMUSG00000027556	Car1	AW555628|Ca1|Car-1	carbonic anhydrase 1	protein-coding
mm_64782.1	chr7	5062055	5062104	-	1	NA	promoter-TSS (NM_001205231)	promoter-TSS (NM_001205231)	-64	NM_133671	22185	Mm.360389	NM_133671	ENSMUSG00000030435	U2af2	65kDa	U2 small nuclear ribonucleoprotein auxiliary factor (U2AF) 2	protein-coding
mm_60713.1	chr7	45277503	45277518	+	1	NA	Intergenic	CpG	-5363	NM_001033176	76713	Mm.425445	NM_001033176	ENSMUSG00000070568	Slc6a21	1700039E15Rik|Gm19188	solute carrier family 6 member 21	protein-coding
mm_122370.1	chr14	39472112	39472128	-	1	NA	promoter-TSS (NR_131973)	promoter-TSS (NR_131973)	-309	NR_131973	432842	Mm.352566	NR_131973		LOC432842	-	uncharacterized LOC432842	ncRNA
mm_22253.1	chr2	174853304	174853310	-	1	NA	Intergenic	Intergenic	92688	NM_007903	13616	Mm.9478	NM_007903	ENSMUSG00000027524	Edn3	ET-3|PPET3|ls|tmgc48	endothelin 3	protein-coding
mm_115867.1	chr13	21468475	21468508	-	1	NA	promoter-TSS (NM_025719)	promoter-TSS (NM_025719)	10	NM_025719	66707	Mm.116869	NM_025719	ENSMUSG00000059395	Nkapl	4921504I05Rik	NFKB activating protein-like	protein-coding
mm_31837.1	chr4	73790902	73790904	+	1	NA	promoter-TSS (NR_046042)	promoter-TSS (NR_046042)	-301	NM_001017427	242505	Mm.389582	NM_001017427	ENSMUSG00000043003	Rasef	BC030882|RAB45	RAS and EF hand domain containing	protein-coding
mm_27191.1	chr3	34757894	34757926	-	1	NA	Intergenic	Intergenic	-14165	NR_110488	102638436	Mm.261793	NR_110488	ENSMUSG00000106519	Gm38509	Peril	predicted gene, 38509	ncRNA
mm_168142.1	chr10	32499425	32499429	+	1	NA	intron (NM_001013411, intron 1 of 6)	L1Md_Gf|LINE|L1	390488	NM_001013411	432450	Mm.49665	NM_001013411	ENSMUSG00000069670	Nkain2	6330571D19Rik|AW455467|Tcba1	Na+/K+ transporting ATPase interacting 2	protein-coding
mm_158902.1	chr1	34439684	34439684	-	1	NA	promoter-TSS (NM_178601)	promoter-TSS (NM_178601)	-12	NM_027159	69668	Mm.379170	NM_027159	ENSMUSG00000042111	Ccdc115	2310061I09Rik|Ccp1	coiled-coil domain containing 115	protein-coding
mm_106063.1	chr11	116132521	116132540	-	1	NA	exon (NM_024177, exon 8 of 9)	exon (NM_024177, exon 8 of 9)	-1402	NM_178802	338364	Mm.439976	NM_178802	ENSMUSG00000054517	Trim65	4732463G12Rik	tripartite motif-containing 65	protein-coding
mm_11105.1	chr2	28192939	28192970	+	1	NA	promoter-TSS (NM_001038613)	promoter-TSS (NM_001038613)	-139	NM_001038613	56177	Mm.43278	NM_019498	ENSMUSG00000026833	Olfm1	AMY|AW742568|Noe1|OlfA|Pancortin|Pancortin3	olfactomedin 1	protein-coding
mm_171699.1	chr4	71371219	71371241	-	1	NA	Intergenic	Intergenic	829663	NM_011599	21885	Mm.278444	NM_011599	ENSMUSG00000008305	Tle1	C230057C06Rik|Estm14|Grg-1|Grg1|Tle4l	transducin-like enhancer of split 1	protein-coding
mm_172293.1	chr6	9656128	9656130	-	1	NA	Intergenic	RLTR9D|LTR|ERVK	706110	NM_008751	18231	Mm.46954	NM_008751	ENSMUSG00000046178	Nxph1	C130005L03Rik	neurexophilin 1	protein-coding
mm_22312.1	chr2	180439487	180439521	-	1	NA	Intergenic	B4|SINE|B4	-21474	NM_148933	108115	Mm.133687	NM_148933	ENSMUSG00000038963	Slco4a1	OATP-E|Slc21a12	solute carrier organic anion transporter family, member 4a1	protein-coding
mm_167969.1	chrX	152537502	152537547	+	1	NA	Intergenic	Intergenic	-25810	NM_001199311	635396	Mm.485766	NM_001199311	ENSMUSG00000091863	Cldn34a	Gm7157	claudin 34A	protein-coding
mm_150059.1	chr19	29383798	29383814	+	1	NA	intron (NM_021893, intron 5 of 6)	intron (NM_021893, intron 5 of 6)	16368	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_167194.1	chr7	142653047	142653057	+	1	NA	3' UTR (NM_010514, exon 4 of 4)	3' UTR (NM_010514, exon 4 of 4)	1944	NR_030251	723874		NR_030251	ENSMUSG00000070140	Mir483	Mirn483|mir-483|mmu-mir-483	microRNA 483	ncRNA
mm_5774.1	chr1	51477713	51477730	-	1	NA	intron (NM_001310549, intron 1 of 5)	intron (NM_001310549, intron 1 of 5)	678	NM_028696	109019	Mm.196290	NM_028696	ENSMUSG00000026107	Nabp1	4930434H03Rik|4930442A21Rik|4930488J04Rik|4933440J18Rik|5830411E10Rik|AI852561|Nbp1|Obfc2a|Ssb2	nucleic acid binding protein 1	protein-coding
mm_162870.1	chr10	95180324	95180347	+	1	NA	intron (NM_009950, intron 2 of 2)	intron (NM_009950, intron 2 of 2)	-34510	NR_131146	628062		NR_131146		Gm29684	-	predicted gene, 29684	ncRNA
mm_71222.1	chr8	40899218	40899237	+	1	NA	exon (NM_001044740, exon 2 of 12)	exon (NM_001044740, exon 2 of 12)	-27006	NM_026840	68797	Mm.284246	NM_026840	ENSMUSG00000031595	Pdgfrl	1110039P19Rik|AV013190	platelet-derived growth factor receptor-like	protein-coding
mm_166138.1	chr4	156238742	156238745	+	1	NA	intron (NM_021303, intron 4 of 18)	B1F|SINE|Alu	2733	NM_021303	57741	Mm.423051	NM_021303	ENSMUSG00000095567	Noc2l	AA410003|AF155546|NIR	NOC2 like nucleolar associated transcriptional repressor	protein-coding
mm_62704.1	chr7	110241606	110241609	+	1	NA	intron (NM_009302, intron 1 of 11)	intron (NM_009302, intron 1 of 11)	19904	NM_009302	20947	Mm.334144	NM_009302	ENSMUSG00000031015	Swap70	70kDa|AV235546	SWA-70 protein	protein-coding
mm_57929.1	chr6	134566818	134566845	-	1	NA	promoter-TSS (NM_008514)	promoter-TSS (NM_008514)	82	NM_008514	16974	Mm.321990	NM_008514	ENSMUSG00000030201	Lrp6	C030016K15Rik|Cd|Gw|ska26|ska<m26Jus>|skax26	low density lipoprotein receptor-related protein 6	protein-coding
mm_114370.1	chr13	62964939	62964951	+	1	NA	promoter-TSS (NM_001289924)	promoter-TSS (NM_001289924)	52	NM_001289924	72061	Mm.188105	NM_028079	ENSMUSG00000021458	2010111I01Rik	2300006M17Rik|AP-O|AW742919|Aopep|ApO|mir-23b|mir-24-1|mir-27b	RIKEN cDNA 2010111I01 gene	protein-coding
mm_142279.1	chr17	40208560	40208584	-	1	NA	promoter-TSS (NM_031190)	promoter-TSS (NM_031190)	37	NM_031190	18663	Mm.717	NM_031190	ENSMUSG00000031233	Pgk2	Pgk-2|Tcp-2	phosphoglycerate kinase 2	protein-coding
mm_58359.1	chr6	148212360	148212367	-	1	NA	promoter-TSS (NM_026168)	promoter-TSS (NM_026168)	11	NM_026168	67456	Mm.59812	NM_026168	ENSMUSG00000030304	Ergic2	1200009B18Rik|4930572C01Rik|AA408438|Ptx1	ERGIC and golgi 2	protein-coding
mm_149080.1	chr19	8892999	8893052	+	1	NA	promoter-TSS (NM_176843)	promoter-TSS (NM_176843)	38	NM_176843	109077	Mm.290474	NM_176843	ENSMUSG00000071652	Ints5	1110055N21Rik|mKIAA1698	integrator complex subunit 5	protein-coding
mm_114074.1	chr13	54382764	54382783	+	1	NA	3' UTR (NM_009946, exon 4 of 4)	3' UTR (NM_009946, exon 4 of 4)	11424	NM_009946	12890	Mm.268902	NM_009946	ENSMUSG00000025867	Cplx2	921-L|AI413745|AW492120	complexin 2	protein-coding
mm_88545.1	chr10	78576977	78576993	+	1	NA	exon (NM_173751, exon 4 of 16)	exon (NM_173751, exon 4 of 16)	2485	NM_173751	216136	Mm.2644	NM_173751	ENSMUSG00000032763	Ilvbl	5830463I21|AI415009	ilvB (bacterial acetolactate synthase)-like	protein-coding
mm_51211.1	chr6	71341466	71341499	+	1	NA	Intergenic	Intergenic	18670	NM_009858	12526	Mm.333148	NM_009858	ENSMUSG00000053044	Cd8b1	Cd8b|Ly-3|Ly-C|Lyt-3	CD8 antigen, beta chain 1	protein-coding
mm_84119.1	chr9	58555130	58555143	-	1	NA	Intergenic	CpG	-14196	NM_133983	102657	Mm.5356	NM_133983	ENSMUSG00000035914	Cd276	6030411F23Rik|AU016588|B7RP-2|B7h3	CD276 antigen	protein-coding
mm_29506.1	chr3	116252738	116252760	-	1	NA	intron (NM_022427, intron 1 of 1)	intron (NM_022427, intron 1 of 1)	735	NM_022427	64378	Mm.40025	NM_022427	ENSMUSG00000068696	Gpr88	AW061286|Strg	G-protein coupled receptor 88	protein-coding
mm_125532.1	chr15	57976157	57976172	+	1	NA	Intergenic	Intergenic	-9739	NM_173862	239463	Mm.221241	NM_173862	ENSMUSG00000051225	Fam83a	-	family with sequence similarity 83, member A	protein-coding
mm_18683.1	chr2	71367567	71367577	-	1	NA	promoter-TSS (NM_172436)	promoter-TSS (NM_172436)	-18	NM_172436	78830	Mm.30928	NM_172436	ENSMUSG00000027010	Slc25a12	2610002D09Rik|AI839531|B230107K20Rik|BB129864	solute carrier family 25 (mitochondrial carrier, Aralar), member 12	protein-coding
mm_3738.1	chr1	155158685	155158701	+	1	NA	promoter-TSS (NM_021433)	promoter-TSS (NM_021433)	-10	NM_021433	58244	Mm.66264	NM_021433	ENSMUSG00000026470	Stx6	2310039E05Rik|2410005I16Rik|AA437559|AI415714|AI845861	syntaxin 6	protein-coding
mm_64983.1	chr7	16915798	16915813	-	1	NA	3' UTR (NM_007590, exon 6 of 6)	3' UTR (NM_007590, exon 6 of 6)	8227	NM_007590	12315	Mm.288630	NM_007590	ENSMUSG00000019370	Calm3	CaMA|R75142	calmodulin 3	protein-coding
mm_66185.1	chr7	34189495	34189524	-	1	NA	intron (NM_026549, intron 4 of 6)	intron (NM_026549, intron 4 of 6)	7138	NM_026549	68079	Mm.38173	NM_026549	ENSMUSG00000002635	Pdcd2l	6030457N17Rik	programmed cell death 2-like	protein-coding
mm_143566.1	chr17	74294821	74294831	-	1	NA	promoter-TSS (NM_133771)	promoter-TSS (NM_133771)	37	NM_133771	76890	Mm.311874	NM_133771	ENSMUSG00000058704	Memo1	0610016J10Rik|D930048L02Rik	mediator of cell motility 1	protein-coding
mm_145301.1	chr18	53341638	53341671	+	1	NA	intron (NM_029394, intron 3 of 6)	intron (NM_029394, intron 3 of 6)	76353	NM_008908	19038	Mm.4587	NM_008908	ENSMUSG00000024538	Ppic	CyP-20c	peptidylprolyl isomerase C	protein-coding
mm_27965.1	chr3	80688338	80688365	-	1	NA	3' UTR (NM_013540, exon 16 of 16)	3' UTR (NM_013540, exon 16 of 16)	114440	NM_013540	14800	Mm.220224	NM_013540	ENSMUSG00000033981	Gria2	GluA2|GluR-B|Glur-2|Glur2	glutamate receptor, ionotropic, AMPA2 (alpha 2)	protein-coding
mm_85002.1	chr9	86880415	86880467	-	1	NA	promoter-TSS (NM_001277986)	promoter-TSS (NM_001277986)	8	NM_001277986	20616	Mm.281651	NM_013669	ENSMUSG00000033419	Snap91	91kDa|AP180|F1-20|mKIAA0656	synaptosomal-associated protein 91	protein-coding
mm_72256.1	chr8	75096881	75096903	+	1	NA	exon (NM_010442, exon 3 of 5)	exon (NM_010442, exon 3 of 5)	3274	NM_010442	15368	Mm.276389	NM_010442	ENSMUSG00000005413	Hmox1	D8Wsu38e|HO-1|HO1|Hemox|Hmox|Hsp32	heme oxygenase 1	protein-coding
mm_22886.1	chr3	30602618	30602653	+	1	NA	5' UTR (NM_030557, exon 1 of 8)	5' UTR (NM_030557, exon 1 of 8)	548	NM_001289621	80732	Mm.200378	NM_030557	ENSMUSG00000037730	Mynn	2810011C24Rik|AA415053|AI661031|AW049392|Mynr|SBBIZ1	myoneurin	protein-coding
mm_30373.1	chr3	152193834	152193842	-	1	NA	promoter-TSS (NM_025926)	promoter-TSS (NM_025926)	7	NM_025926	67035	Mm.46746	NM_025926	ENSMUSG00000028035	Dnajb4	1700029A20Rik|2010306G19Rik|5730460G06Rik	DnaJ heat shock protein family (Hsp40) member B4	protein-coding
mm_83737.1	chr9	51077111	51077121	-	1	NA	promoter-TSS (NM_001033534)	promoter-TSS (NM_001033534)	-22	NM_001033534	244864	Mm.335152	NM_001033534	ENSMUSG00000060594	Layn	E030012M19Rik|Gm511	layilin	protein-coding
mm_9413.1	chr1	172293667	172293677	-	1	NA	exon (NM_178405, exon 2 of 23)	exon (NM_178405, exon 2 of 23)	4392	NM_178405	98660	Mm.207432	NM_178405	ENSMUSG00000007097	Atp1a2	AW060654|Atpa-3|mKIAA0778	ATPase, Na+/K+ transporting, alpha 2 polypeptide	protein-coding
mm_118739.1	chr14	22310877	22310894	+	1	NA	intron (NM_028275, intron 2 of 6)	RSINE1|SINE|B4	231913	NR_046307	74896	Mm.444661	NR_046307		4930405A10Rik	4930456G20Rik	RIKEN cDNA 4930405A10 gene	ncRNA
mm_67106.1	chr7	70353985	70353999	-	1	NA	3' UTR (NM_183261, exon 3 of 3)	3' UTR (NM_183261, exon 3 of 3)	6601	NM_009697	11819	Mm.158143	NM_009697	ENSMUSG00000030551	Nr2f2	2700033K02Rik|9430015G03Rik|ARP-1|Aporp1|COUP-TF2|COUP-TFII|COUPTFB|EAR3|SVP40|Tcfcoup2	nuclear receptor subfamily 2, group F, member 2	protein-coding
mm_13870.1	chr2	119843919	119843957	+	1	NA	Intergenic	RLTR41|LTR|ERV1	44424	NM_019392	22174	Mm.2901	NM_019392	ENSMUSG00000027298	Tyro3	AI323366|Brt|Dtk|Etk-2|Rse|Sky|TK19-2|Tif|etk2/tyro3|tk19-1	TYRO3 protein tyrosine kinase 3	protein-coding
mm_168629.1	chr1	181842393	181842414	-	1	NA	promoter-TSS (NM_133815)	promoter-TSS (NM_133815)	-2	NM_133815	98386	Mm.4538	NM_133815	ENSMUSG00000004880	Lbr	AI505894|ic	lamin B receptor	protein-coding
mm_49815.1	chr6	36715702	36715736	+	1	NA	TTS (NM_008973)	TTS (NM_008973)	95642	NM_008973	19242	Mm.279690	NM_008973	ENSMUSG00000029838	Ptn	HARP|HB-GAM|HBBN|HBGF-8|HBNF|OSF|Osf-1|Osf1	pleiotrophin	protein-coding
mm_83654.1	chr9	49509809	49509839	-	1	NA	exon (NM_001311065, exon 16 of 18)	exon (NM_001311065, exon 16 of 18)	-8464	NR_029465	100036537	Mm.437541	NR_029465	ENSMUSG00000079564	Gm11149	ENSMUSG00000060603|ENSMUSG00000079564	predicted gene 11149	ncRNA
mm_85941.1	chr9	112099327	112099338	-	1	NA	intron (NM_001177618, intron 17 of 18)	B4|SINE|B4	19379	NR_029823	723815		NR_029823	ENSMUSG00000065441	Mir128-2	Mirn128-2|Mirn128b|mir-128-2|mir-128b	microRNA 128-2	ncRNA
mm_88043.1	chr10	67538300	67538309	+	1	NA	exon (NM_010118, exon 1 of 2)	exon (NM_010118, exon 1 of 2)	374	NM_001347458	13654	Mm.290421	NM_010118	ENSMUSG00000037868	Egr2	Egr-2|Krox-20|Krox20|NGF1-B|Zfp-25|Zfp-6	early growth response 2	protein-coding
mm_118234.1	chr13	111490056	111490100	-	1	NA	promoter-TSS (NM_028487)	promoter-TSS (NM_028487)	-37	NM_001122963	73274	Mm.57286	NM_028487	ENSMUSG00000032745	Gpbp1	1700034P14Rik|AU019836|D230035M11Rik|Gpbp|mGPBP	GC-rich promoter binding protein 1	protein-coding
mm_162437.1	chr1	105990818	105990831	+	1	NA	exon (NM_001122675, exon 1 of 13)	exon (NM_001122675, exon 1 of 13)	418	NM_001122675	227449	Mm.210188	NM_001122675	ENSMUSG00000038866	Zcchc2	9930114B20Rik|AW212015	zinc finger, CCHC domain containing 2	protein-coding
mm_103377.1	chr11	75348336	75348342	-	1	NA	promoter-TSS (NM_026653)	promoter-TSS (NM_026653)	44	NM_001164223	68275	Mm.102574	NM_026653	ENSMUSG00000000751	Rpa1	5031405K23Rik|70kDa|AA589576|AW557552|RF-A|RP-A|Rpa	replication protein A1	protein-coding
mm_34099.1	chr4	138967155	138967157	+	1	NA	promoter-TSS (NM_025786)	promoter-TSS (NM_025786)	44	NM_025786	66825	Mm.252312	NM_025786	ENSMUSG00000070661	Rnf186	9130020G10Rik	ring finger protein 186	protein-coding
mm_165385.1	chr2	130397594	130397598	-	1	NA	promoter-TSS (NM_019696)	promoter-TSS (NM_019696)	33	NM_019696	56264	Mm.112701	NM_019696	ENSMUSG00000027408	Cpxm1	AA986902|Cpx-1|Cpx1|Cpxm	carboxypeptidase X 1 (M14 family)	protein-coding
mm_60333.1	chr7	44319795	44319808	+	1	NA	intron (NM_001034115, intron 8 of 24)	intron (NM_001034115, intron 8 of 24)	9537	NM_001034115	243961	Mm.360368	NM_001034115	ENSMUSG00000038738	Shank1	-	SH3/ankyrin domain gene 1	protein-coding
mm_48122.1	chr5	137144013	137144022	-	1	NA	Intergenic	Intergenic	-27810	NM_201373	384309	Mm.100647	NM_201373	ENSMUSG00000043279	Trim56	A130009K11Rik|Gm452|RNF109	tripartite motif-containing 56	protein-coding
mm_94724.1	chr11	20647160	20647179	+	1	NA	intron (NM_001038625, intron 1 of 1)	intron (NM_001038625, intron 1 of 1)	15192	NM_001038625	58172	Mm.339676	NM_021372	ENSMUSG00000049800	Sertad2	AB041541|AU021878|Kiaa0127|MNCb-1504|SEI-2|Sei2|TRIP-Br2|mKIAA0127	SERTA domain containing 2	protein-coding
mm_146953.1	chr18	32559915	32560018	-	1	NA	promoter-TSS (NM_001048207)	promoter-TSS (NM_001048207)	68	NM_001347610	71683	Mm.292145	NM_027863	ENSMUSG00000090523	Gypc	0610037F22Rik|Cd236r	glycophorin C	protein-coding
mm_51007.1	chr6	64734512	64734518	+	1	NA	Intergenic	Intergenic	5369	NM_007500	11921	Mm.57229	NM_007500	ENSMUSG00000073043	Atoh1	Hath1|MATH-1|Math1|bHLHa14	atonal bHLH transcription factor 1	protein-coding
mm_135404.1	chr16	44746231	44746241	-	1	NA	exon (NM_025332, exon 1 of 6)	exon (NM_025332, exon 1 of 6)	127	NM_001159329	66067	Mm.34520	NM_025332	ENSMUSG00000022668	Gtpbp8	0610037H22Rik	GTP-binding protein 8 (putative)	protein-coding
mm_14956.1	chr2	152080864	152080874	+	1	NA	promoter-TSS (NM_001160410)	promoter-TSS (NM_001160410)	-660	NM_001160410	545474	Mm.214317	NM_001160410	ENSMUSG00000060257	Scrt2	AW060659	scratch family zinc finger 2	protein-coding
mm_153153.1	chr19	34252502	34252523	-	1	NA	exon (NM_007392, exon 2 of 9)	exon (NM_007392, exon 2 of 9)	2861	NM_007392	11475	Mm.213025	NM_007392	ENSMUSG00000035783	Acta2	0610041G09Rik|Actvs|SMalphaA|a-SMA|alphaSMA	actin, alpha 2, smooth muscle, aorta	protein-coding
mm_71578.1	chr8	54565868	54565886	+	1	NA	intron (NM_029569, intron 1 of 6)	intron (NM_029569, intron 1 of 6)	15546	NM_029569	76294	Mm.33171	NM_029569	ENSMUSG00000031519	Asb5	1110018D09Rik	ankyrin repeat and SOCs box-containing 5	protein-coding
mm_4192.1	chr1	171225078	171225100	+	1	NA	promoter-TSS (NM_013474)	promoter-TSS (NM_013474)	35	NM_013474	11807	Mm.389209	NM_013474	ENSMUSG00000005681	Apoa2	Alp-2|Apo-AII|ApoA-II|ApoAII|Apoa-2|Hdl-1	apolipoprotein A-II	protein-coding
mm_8456.1	chr1	153186012	153186056	-	1	NA	5' UTR (NM_008485, exon 2 of 24)	5' UTR (NM_008485, exon 2 of 24)	413	NM_008485	16782	Mm.329272	NM_008485	ENSMUSG00000026479	Lamc2	AA589349	laminin, gamma 2	protein-coding
mm_56779.1	chr6	116633410	116633415	-	1	NA	3' UTR (NM_178045, exon 11 of 11)	3' UTR (NM_178045, exon 11 of 11)	-4413	NM_026057	67255	Mm.18810	NM_026057	ENSMUSG00000059878	Zfp422	2900028O21Rik|AU041373|KOX15|Krox-25-2|Krox-26|Krox25|Krox26|Znf22	zinc finger protein 422	protein-coding
mm_26677.1	chr3	155093503	155093544	+	1	NA	promoter-TSS (NM_028938)	promoter-TSS (NM_028938)	89	NM_028938	74435	Mm.195711	NM_028938	ENSMUSG00000028182	Lrriq3	4930438B07Rik|4930511J15Rik|4933403H06Rik|BB020367|Lrrc44	leucine-rich repeats and IQ motif containing 3	protein-coding
mm_67508.1	chr7	80782326	80782335	-	1	NA	intron (NM_016721, intron 2 of 37)	intron (NM_016721, intron 2 of 37)	21001	NM_016721	29875	Mm.207619	NM_016721	ENSMUSG00000030536	Iqgap1	AA682088|D7Ertd237e|D7Ertd257e|mKIAA0051	IQ motif containing GTPase activating protein 1	protein-coding
mm_168152.1	chr10	39223199	39223207	-	1	NA	Intergenic	BGLII|LTR|ERVK	-59409	NM_001127376	327743	Mm.208111	NM_001127376	ENSMUSG00000062074	Wisp3	CCN6|ENSMUSG00000062074|Gm735|WISP-3	WNT1 inducible signaling pathway protein 3	protein-coding
mm_50345.1	chr6	48589451	48589468	+	1	NA	promoter-TSS (NM_183309)	promoter-TSS (NM_183309)	14	NM_183309	330305	Mm.123868	NM_183309	ENSMUSG00000052730	Gm5111	A630038D02|EG330305	predicted gene 5111	protein-coding
mm_143402.1	chr17	70755055	70755083	-	1	NA	intron (NM_001347411, intron 9 of 14)	intron (NM_001347411, intron 9 of 14)	91708	NM_001164077	21815	Mm.101034	NM_009372	ENSMUSG00000047407	Tgif1	AA959811|AI462167|Tgif	TGFB-induced factor homeobox 1	protein-coding
mm_167308.1	chr8	61130536	61130539	+	1	NA	3' UTR (NM_001293639, exon 32 of 32)	3' UTR (NM_001293639, exon 32 of 32)	-93634	NM_021506	59009	Mm.27949	NM_021506	ENSMUSG00000031642	Sh3rf1	2200003J05Rik|Posh|R75531|Sh3md2	SH3 domain containing ring finger 1	protein-coding
mm_128725.1	chr15	64060328	64060435	-	1	NA	promoter-TSS (NM_144846)	promoter-TSS (NM_144846)	67	NM_144846	223601	Mm.246108	NM_144846	ENSMUSG00000022378	Fam49b	0910001A06Rik|AW122079	family with sequence similarity 49, member B	protein-coding
mm_139742.1	chr17	62941049	62941056	+	1	NA	Intergenic	RMER17C|LTR|ERVK	-59735	NM_010109	13640	Mm.7978	NM_010109	ENSMUSG00000048915	Efna5	AL-1|AV158822|EFL-5|Ephrin-A5|Epl7|LERK-7|RAGS	ephrin A5	protein-coding
mm_125712.1	chr15	68928396	68928409	+	1	NA	promoter-TSS (NM_010158)	promoter-TSS (NM_010158)	-18	NM_010158	13992	Mm.17964	NM_010158	ENSMUSG00000022332	Khdrbs3	Etle|SLM-2|Salp|Slm2|T-STAR	KH domain containing, RNA binding, signal transduction associated 3	protein-coding
mm_82028.1	chr9	121898459	121898466	+	1	NA	5' UTR (NM_021609, exon 1 of 3)	5' UTR (NM_021609, exon 1 of 3)	107	NM_021609	59289	Mm.258105	NM_021609	ENSMUSG00000044534	Ackr2	AI464239|CCR10|CCR9|Ccbp2|Cmkbr9|D6	atypical chemokine receptor 2	protein-coding
mm_108174.1	chr12	76405553	76405563	+	1	NA	exon (NM_001002012, exon 2 of 2)	exon (NM_001002012, exon 2 of 2)	1188	NM_008301	15512	Mm.296181	NM_008301	ENSMUSG00000059970	Hspa2	70kDa|HSP70.2|HSP70A2|Hsp70-2	heat shock protein 2	protein-coding
mm_55291.1	chr6	54566461	54566483	-	1	NA	promoter-TSS (NM_027268)	promoter-TSS (NM_027268)	-90	NM_027268	69938	Mm.41557	NM_027268	ENSMUSG00000019124	Scrn1	2810019K23Rik|6330535A03Rik|AI852905|SES1|mKIAA0193	secernin 1	protein-coding
mm_2632.1	chr1	121462235	121462247	+	1	NA	exon (NM_029955, exon 10 of 24)	exon (NM_029955, exon 10 of 24)	31174	NM_001025156	70829	Mm.25788	NM_027567	ENSMUSG00000026339	Ccdc93	4633402D15Rik|9230102M16Rik	coiled-coil domain containing 93	protein-coding
mm_107305.1	chr12	31073899	31073905	+	1	NA	promoter-TSS (NM_027828)	promoter-TSS (NM_027828)	-66	NM_027828	104943	Mm.248938	NM_027828	ENSMUSG00000036136	Fam110c	9030611O19Rik|AU019489	family with sequence similarity 110, member C	protein-coding
mm_92315.1	chr10	75517249	75517265	-	1	NA	promoter-TSS (NM_026095)	promoter-TSS (NM_026095)	124	NM_175133	68778	Mm.29382	NM_175133	ENSMUSG00000033416	Gucd1	1110038D17Rik	guanylyl cyclase domain containing 1	protein-coding
mm_138170.1	chr17	34264781	34264796	+	1	NA	exon (NM_207105, exon 2 of 6)	exon (NM_207105, exon 2 of 6)	1561	NM_207105	14961	Mm.254067	NM_207105	ENSMUSG00000073421	H2-Ab1	AI845868|Abeta|H-2Ab|H2-Ab|I-Abeta|IAb|Ia-2|Ia2|Rmcs1	histocompatibility 2, class II antigen A, beta 1	protein-coding
mm_16316.1	chr2	174304335	174304348	+	1	NA	intron (NM_001310085, intron 2 of 12)	intron (NM_001310085, intron 2 of 12)	6482	NM_001310085	14683	Mm.125770	NM_010309	ENSMUSG00000027523	Gnas	5530400H20Rik|A930027G11Rik|C130027O20Rik|GPSA|GSP|Galphas|Gnas1|Gnasxl|Gs-alpha|Gsa|Nesp|Nesp55|Nespl|Oed-Sml|Oedsml|P1|P2|P3|PHP1A|PHP1B|POH|SCG6	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	protein-coding
mm_117235.1	chr13	64275032	64275042	-	1	NA	promoter-TSS (NM_172587)	promoter-TSS (NM_172587)	-49	NM_172587	218294	Mm.25335	NM_172587	ENSMUSG00000033102	Cdc14b	2810432N10Rik|A530086E13Rik|AA472821|CDC14B3|Cdc14B1	CDC14 cell division cycle 14B	protein-coding
mm_89773.1	chr10	100487574	100487633	+	1	NA	promoter-TSS (NM_001110013)	promoter-TSS (NM_001110013)	-256	NM_001110013	237500	Mm.296805	NM_001033332	ENSMUSG00000036676	Tmtc3	9130014E20Rik|B130008E12Rik|mSmile	transmembrane and tetratricopeptide repeat containing 3	protein-coding
mm_8788.1	chr1	161647125	161647135	-	1	NA	Intergenic	L1MB7|LINE|L1	141365	NM_001205243	14103	Mm.3355	NM_010177	ENSMUSG00000000817	Fasl	APT1LG1|CD178|CD95-L|CD95L|Fas-L|Faslg|Tnfsf6|Tnlg1a|gld	Fas ligand (TNF superfamily, member 6)	protein-coding
mm_173094.1	chrX	151414534	151414548	-	1	NA	intron (NM_198105, intron 4 of 15)	intron (NM_198105, intron 4 of 15)	70318	NM_198105	207375	Mm.391339	NM_198105	ENSMUSG00000025262	Fam120c	D930001I21Rik|ORF34	family with sequence similarity 120, member C	protein-coding
mm_101715.1	chr11	42179691	42179725	-	1	NA	intron (NM_010250, intron 1 of 9)	intron (NM_010250, intron 1 of 9)	3222	NM_010250	14394	Mm.439668	NM_010250	ENSMUSG00000010803	Gabra1	Gabra-1	gamma-aminobutyric acid (GABA) A receptor, subunit alpha 1	protein-coding
mm_91976.1	chr10	61476676	61476690	-	1	NA	intron (NM_153542, intron 1 of 4)	intron (NM_153542, intron 1 of 4)	850	NM_153542	216011	Mm.136116	NM_153542	ENSMUSG00000037151	Lrrc20	BC036304	leucine rich repeat containing 20	protein-coding
mm_15306.1	chr2	155387028	155387055	+	1	NA	3' UTR (NM_178111, exon 4 of 4)	3' UTR (NM_178111, exon 4 of 4)	5185	NM_178111	68728	Mm.293605	NM_178111	ENSMUSG00000038375	Trp53inp2	1110029F20Rik|Tp53inp2	transformation related protein 53 inducible nuclear protein 2	protein-coding
mm_30219.1	chr3	145024581	145024596	-	1	NA	exon (NM_017474, exon 4 of 14)	exon (NM_017474, exon 4 of 14)	8188	NM_017474	23844	Mm.33483	NM_017474	ENSMUSG00000028255	Clca1	Clca2|Clca3|gob-5|gob5	chloride channel accessory 1	protein-coding
mm_119582.1	chr14	50924972	50925004	+	1	NA	promoter-TSS (NM_009687)	promoter-TSS (NM_009687)	39	NM_009687	11792	Mm.203	NM_009687	ENSMUSG00000035960	Apex1	APE|Apex|HAP1|Ref-1	apurinic/apyrimidinic endonuclease 1	protein-coding
mm_22036.1	chr2	168206755	168206759	-	1	NA	5' UTR (NM_009628, exon 1 of 4)	5' UTR (NM_009628, exon 1 of 4)	355	NM_009628	11538	Mm.201322	NM_009628	ENSMUSG00000051149	Adnp	AA589558|mKIAA0784	activity-dependent neuroprotective protein	protein-coding
mm_143797.1	chr17	82956332	82956383	-	1	NA	Intergenic	Intergenic	121868	NR_045094	100503434	Mm.187281	NR_045094		Gm19689	-	predicted gene, 19689	ncRNA
mm_83027.1	chr9	37255358	37255364	-	1	NA	5' UTR (NM_001145960, exon 1 of 19)	5' UTR (NM_001145960, exon 1 of 19)	377	NM_020258	56857	Mm.440037	NM_020258	ENSMUSG00000032122	Slc37a2	G3PP|Slc37a1|cI-2|ci2	solute carrier family 37 (glycerol-3-phosphate transporter), member 2	protein-coding
mm_25198.1	chr3	103774187	103774197	+	1	NA	intron (NM_001301304, intron 2 of 15)	intron (NM_001301304, intron 2 of 15)	17083	NM_001301306	15257	Mm.20827	NM_010432	ENSMUSG00000008730	Hipk1	1110062K04Rik|Myak	homeodomain interacting protein kinase 1	protein-coding
mm_118421.1	chr14	7847897	7847930	+	1	NA	intron (NM_134080, intron 1 of 45)	intron (NM_134080, intron 1 of 45)	29956	NM_134080	286940	Mm.489652	NM_134080	ENSMUSG00000025278	Flnb	AL024016|Fln-b	filamin, beta	protein-coding
mm_139317.1	chr17	48409981	48410104	+	1	NA	promoter-TSS (NM_001289491)	promoter-TSS (NM_001289491)	42	NM_207219	106821	Mm.203943	NM_207219	ENSMUSG00000040771	Oard1	AI314976|AW558560	O-acyl-ADP-ribose deacylase 1	protein-coding
mm_129247.1	chr15	76660112	76660142	-	1	NA	promoter-TSS (NM_019396)	promoter-TSS (NM_019396)	81	NM_001276322	54151	Mm.247752	NM_019396	ENSMUSG00000053929	Cyhr1	1110031M01Rik|AU042374|Chrp	cysteine and histidine rich 1	protein-coding
mm_26355.1	chr3	142548994	142549005	+	1	NA	3' UTR (NM_001083312, exon 11 of 11)	3' UTR (NM_001083312, exon 11 of 11)	-11053	NM_018734	55932	Mm.439718	NM_018734	ENSMUSG00000028268	Gbp3	AW228655|GBP-3|GBP-4|Gbp4	guanylate binding protein 3	protein-coding
mm_14211.1	chr2	127270758	127270774	+	1	NA	exon (NM_139308, exon 1 of 8)	exon (NM_139308, exon 1 of 8)	537	NM_139308	99138	Mm.41271	NM_139308	ENSMUSG00000027367	Stard7	AI852671|AL022671|AW544915	START domain containing 7	protein-coding
mm_55186.1	chr6	52183829	52183855	-	1	NA	intron (NM_010452, intron 2 of 4)	intron (NM_010452, intron 2 of 4)	7861	NM_008265	15401	Mm.439647	NM_008265	ENSMUSG00000000942	Hoxa4	AV206827|Hox-1.4	homeobox A4	protein-coding
mm_50739.1	chr6	52721367	52721379	+	1	NA	exon (NM_025816, exon 2 of 18)	exon (NM_025816, exon 2 of 18)	7644	NM_025816	52440	Mm.389757	NM_025816	ENSMUSG00000004535	Tax1bp1	1200003J11Rik|1700069J21Rik|AA930106|D6Ertd404e|D6Ertd772e|T6bp|TXBP151	Tax1 (human T cell leukemia virus type I) binding protein 1	protein-coding
mm_105843.1	chr11	113684161	113684186	-	1	NA	promoter-TSS (NM_138598)	promoter-TSS (NM_138598)	-22	NM_138598	28081	Mm.351688	NM_138598	ENSMUSG00000041629	Fam104a	D11Wsu99e	family with sequence similarity 104, member A	protein-coding
mm_59308.1	chr7	25279620	25279649	+	1	NA	intron (NM_001302811, intron 2 of 20)	intron (NM_001302811, intron 2 of 20)	-2545	NM_027882	71722	Mm.28833	NM_027882	ENSMUSG00000005442	Cic	1200010B10Rik|mKIAA0306	capicua transcriptional repressor	protein-coding
mm_123129.1	chr14	56238733	56238747	-	1	NA	Intergenic	Intergenic	-4083	NM_010371	14940	Mm.14465	NM_010371	ENSMUSG00000079186	Gzmc	AI323531|B10|CCP2|Ctla-5|Ctla5	granzyme C	protein-coding
mm_69284.1	chr7	128203310	128203317	-	1	NA	promoter-TSS (NR_045183)	promoter-TSS (NR_045183)	15	NR_045183	70973	Mm.441564	NR_045183	ENSMUSG00000108354	4931431B13Rik	1700108I23Rik|AA536668	RIKEN cDNA 4931431B13 gene	ncRNA
mm_165313.1	chr2	103008383	103008392	+	1	NA	Intergenic	Intergenic	65126	NM_175094	27402	Mm.315011	NM_175094	ENSMUSG00000010914	Pdhx	AI481367|E3bp|Pdx1	pyruvate dehydrogenase complex, component X	protein-coding
mm_99000.1	chr11	98798607	98798613	+	1	NA	non-coding (NR_033551, exon 3 of 3)	non-coding (NR_033551, exon 3 of 3)	2841	NM_028722	74026	Mm.258352	NM_028722	ENSMUSG00000052915	Msl1	2810017F12Rik|4121402D02Rik|4930463F05Rik|AA682082|Msl-1	male-specific lethal 1 homolog (Drosophila)	protein-coding
mm_109041.1	chr12	104236127	104236150	+	1	NA	intron (NM_009251, intron 2 of 5)	intron (NM_009251, intron 2 of 5)	-11758	NR_033450	546546	Mm.390522	NM_001034870		Serpina3h	6C28|Spi2	serine (or cysteine) peptidase inhibitor, clade A, member 3H	pseudo
mm_95885.1	chr11	58104052	58104081	+	1	NA	promoter-TSS (NM_026949)	promoter-TSS (NM_026949)	-87	NM_026949	69125	Mm.28910	NM_026949	ENSMUSG00000020515	Cnot8	1500015I04Rik|1810022F04Rik|AA536816|AU015770|AU043059	CCR4-NOT transcription complex, subunit 8	protein-coding
mm_51265.1	chr6	72097796	72097806	+	1	NA	5' UTR (NM_011375, exon 1 of 7)	5' UTR (NM_011375, exon 1 of 7)	193	NM_011375	20454	Mm.38248	NM_011375	ENSMUSG00000056091	St3gal5	3S-T|Siat9|[a]2	ST3 beta-galactoside alpha-2,3-sialyltransferase 5	protein-coding
mm_172501.1	chr7	67295543	67295561	-	1	NA	exon (NM_001291195, exon 4 of 11)	exon (NM_001291195, exon 4 of 11)	72936	NM_001191051	75099	Mm.121691	NM_175215	ENSMUSG00000043831	Lysmd4	4930506D23Rik	LysM, putative peptidoglycan-binding, domain containing 4	protein-coding
mm_115200.1	chr13	109116208	109116218	+	1	NA	intron (NM_011056, intron 3 of 16)	intron (NM_011056, intron 3 of 16)	-208531	NR_030644	100124489		NR_030644	ENSMUSG00000076946	Mir582	Mirn582|mir-582|mmu-mir-582	microRNA 582	ncRNA
mm_3161.1	chr1	135232078	135232110	+	1	NA	Intergenic	Intergenic	26378	NM_001163131	13710	Mm.441439	NM_007921	ENSMUSG00000003051	Elf3	ESE-1|ESX|jen	E74-like factor 3	protein-coding
mm_80288.1	chr9	73064439	73064442	+	1	NA	intron (NM_001301232, intron 1 of 5)	intron (NM_001301232, intron 1 of 5)	292	NM_001301232	11891	Mm.34867	NM_023635	ENSMUSG00000032202	Rab27a	2210402C08Rik|2410003M20Rik|4933437C11Rik|ash	RAB27A, member RAS oncogene family	protein-coding
mm_132929.1	chr16	49853155	49853177	+	1	NA	Intergenic	Intergenic	-2488	NM_010581	16423	Mm.31752	NM_010581	ENSMUSG00000055447	Cd47	9130415E20Rik|AA407862|AI848868|AW108519|B430305P08Rik|IAP|Itgp	CD47 antigen (Rh-related antigen, integrin-associated signal transducer)	protein-coding
mm_108777.1	chr12	89813232	89813244	+	1	NA	5' UTR (NM_001252074, exon 1 of 7)	5' UTR (NM_001252074, exon 1 of 7)	755	NM_001252074	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding
mm_22601.1	chr3	14481383	14481392	+	1	NA	exon (NM_080852, exon 1 of 4)	exon (NM_080852, exon 1 of 4)	688	NM_080852	140918	Mm.215250	NM_080852	ENSMUSG00000039710	Slc7a12	Asc-2|XAT1	solute carrier family 7 (cationic amino acid transporter, y+ system), member 12	protein-coding
mm_66700.1	chr7	45920676	45920678	-	1	NA	5' UTR (NM_001146346, exon 1 of 5)	5' UTR (NM_001146346, exon 1 of 5)	172	NM_001146346	13732	Mm.20829	NM_010129	ENSMUSG00000040212	Emp3	H-4|H4|HNMP-1|MI-35|Ymp	epithelial membrane protein 3	protein-coding
mm_61468.1	chr7	75611828	75611838	+	1	NA	intron (NM_029332, intron 7 of 36)	intron (NM_029332, intron 7 of 36)	156299	NM_029332	75547	Mm.216107	NM_029332	ENSMUSG00000066406	Akap13	1700026G02Rik|5730522G15Rik|5830460E08Rik|AKAP-13|AKAP-Lbc|BRX|Ht31|LBC|PROTO-LB|PROTO-LBC	A kinase (PRKA) anchor protein 13	protein-coding
mm_13732.1	chr2	117990228	117990243	+	1	NA	intron (NR_126479, intron 8 of 9)	intron (NR_126479, intron 8 of 9)	120967	NR_126479	329496	Mm.235844	NR_126479	ENSMUSG00000087203	Gm13986	C230060E24|OTTMUSG00000015236	predicted gene 13986	ncRNA
mm_114158.1	chr13	55409029	55409045	+	1	NA	exon (NM_011392, exon 10 of 13)	exon (NM_011392, exon 10 of 13)	6195	NM_029303	75477	Mm.432537	NM_029303	ENSMUSG00000044444	Pfn3	1700012P12Rik	profilin 3	protein-coding
mm_25873.1	chr3	130180836	130180854	+	1	NA	promoter-TSS (NM_001244952)	promoter-TSS (NM_001244952)	0	NM_029838	77018	Mm.91728	NM_029838	ENSMUSG00000058897	Col25a1	2700062B08Rik|CLAC-P	collagen, type XXV, alpha 1	protein-coding
mm_141767.1	chr17	34282971	34283010	-	1	NA	3' UTR (NM_010378, exon 5 of 5)	3' UTR (NM_010378, exon 5 of 5)	4781	NM_010378	14960	Mm.235338	NM_010378	ENSMUSG00000036594	H2-Aa	Aalpha|H-2Aa|H2Aa|I-Aalpha|IAalpha|Ia-1|Ia1	histocompatibility 2, class II antigen A, alpha	protein-coding
mm_59448.1	chr7	27133476	27133486	+	1	NA	3' UTR (NM_007817, exon 10 of 10)	3' UTR (NM_007817, exon 10 of 10)	13526	NM_007817	13107	Mm.4515	NM_007817	ENSMUSG00000052974	Cyp2f2	Cyp2f	cytochrome P450, family 2, subfamily f, polypeptide 2	protein-coding
mm_25337.1	chr3	106684944	106685021	+	1	NA	promoter-TSS (NM_001039478)	promoter-TSS (NM_001039478)	-5	NM_001039478	321000	Mm.259638	NM_028081	ENSMUSG00000056260	Lrif1	2010012G17Rik|4933421E11Rik|AI450568	ligand dependent nuclear receptor interacting factor 1	protein-coding
mm_164014.1	chr14	70707979	70707986	-	1	NA	intron (NM_023045, intron 1 of 27)	intron (NM_023045, intron 1 of 27)	-54898	NM_181345	328440	Mm.347749	NM_181345	ENSMUSG00000047911	Npm2	-	nucleophosmin/nucleoplasmin 2	protein-coding
mm_81648.1	chr9	110953694	110953702	+	1	NA	intron (NM_028838, intron 1 of 8)	intron (NM_028838, intron 1 of 8)	2153	NM_028838	74249	Mm.307615	NM_028838	ENSMUSG00000032495	Lrrc2	2400002D05Rik|4933431K03Rik	leucine rich repeat containing 2	protein-coding
mm_61710.1	chr7	81226443	81226446	+	1	NA	intron (NM_008803, intron 1 of 21)	B2_Mm2|SINE|B2	12640	NM_008803	18584	Mm.371577	NM_008803	ENSMUSG00000025584	Pde8a	AI551852|Pde8	phosphodiesterase 8A	protein-coding
mm_62611.1	chr7	107187094	107187146	+	1	NA	intron (NM_001002894, intron 5 of 10)	intron (NM_001002894, intron 5 of 10)	20130	NM_001002894	76858	Mm.35644	NM_001002894	ENSMUSG00000016626	Nlrp14	4921520L01Rik|GC-LRR|Nalp-iota|Nalp14|Nalp14l	NLR family, pyrin domain containing 14	protein-coding
mm_170117.1	chr17	39846667	39846667	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	3670	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_98211.1	chr11	87797608	87797617	+	1	NA	exon (NM_010824, exon 8 of 14)	exon (NM_010824, exon 8 of 14)	3828	NM_010824	17523	Mm.4668	NM_010824	ENSMUSG00000009350	Mpo	mKIAA4033	myeloperoxidase	protein-coding
mm_151693.1	chr19	4377361	4377364	-	1	NA	intron (NM_001001984, intron 2 of 20)	B1_Mur1|SINE|Alu	19715	NM_001001984	225876	Mm.31941	NM_001001984	ENSMUSG00000054611	Kdm2a	100043628|5530401A10Rik|AA589516|AW536790|Cxxc8|Fbl11|Fbl7|Fbxl11|Gm4560|Jhdm1|Jhdm1a|lalina	lysine (K)-specific demethylase 2A	protein-coding
mm_86523.1	chr10	7780266	7780277	+	1	NA	intron (NM_001346750, intron 1 of 7)	intron (NM_001346750, intron 1 of 7)	646	NM_145418	215751	Mm.471825	NM_145418	ENSMUSG00000040006	Ginm1	AA589616	glycoprotein integral membrane 1	protein-coding
mm_116875.1	chr13	55021288	55021303	-	1	NA	promoter-TSS (NM_001206391)	promoter-TSS (NM_001206391)	90	NM_001206392	212032	Mm.267479	NM_001033245	ENSMUSG00000025877	Hk3	HK III|HK-III	hexokinase 3	protein-coding
mm_146867.1	chr18	24603792	24603843	-	1	NA	promoter-TSS (NM_021448)	promoter-TSS (NM_021448)	0	NM_139143	106957	Mm.21688	NM_139143	ENSMUSG00000024270	Slc39a6	Ermelin	solute carrier family 39 (metal ion transporter), member 6	protein-coding
mm_110738.1	chr12	69791230	69791293	-	1	NA	promoter-TSS (NM_183294)	promoter-TSS (NM_183294)	-554	NM_183294	71091	Mm.132325	NM_183294	ENSMUSG00000020990	Cdkl1	4933411O17Rik	cyclin-dependent kinase-like 1 (CDC2-related kinase)	protein-coding
mm_142966.1	chr17	56121952	56121958	-	1	NA	promoter-TSS (NM_029796)	promoter-TSS (NM_029796)	-9	NM_029796	76905	Mm.348025	NM_029796	ENSMUSG00000037095	Lrg1	1300008B03Rik|2310031E04Rik|Lrg|Lrhg	leucine-rich alpha-2-glycoprotein 1	protein-coding
mm_70105.1	chr7	142661844	142661857	-	1	NA	promoter-TSS (NM_001122736)	promoter-TSS (NM_001122736)	-579	NM_001122736	16002	Mm.3862	NM_010514	ENSMUSG00000048583	Igf2	AL033362|Igf-2|Igf-II|M6pr|Mpr|Peg2	insulin-like growth factor 2	protein-coding
mm_51594.1	chr6	83953874	83953876	+	1	NA	intron (NM_008717, intron 10 of 26)	B1_Mur3|SINE|Alu	39522	NM_008717	18139	Mm.132392	NM_008717	ENSMUSG00000030016	Zfp638	AI323587|Np220|Zfml|Znf638|mNP220	zinc finger protein 638	protein-coding
mm_163062.1	chr11	65096404	65096406	+	1	NA	intron (NM_175003, intron 1 of 20)	intron (NM_175003, intron 1 of 20)	66556	NM_001099288	216831	Mm.134338	NM_175003	ENSMUSG00000033389	Arhgap44	6330543G20|AI840762|AU040829|AW493732|Rich2	Rho GTPase activating protein 44	protein-coding
mm_83579.1	chr9	48340653	48340668	-	1	NA	5' UTR (NM_030069, exon 1 of 6)	5' UTR (NM_030069, exon 1 of 6)	238	NM_030069	78252	Mm.31626	NM_030069	ENSMUSG00000032028	Nxpe2	4432416J03Rik|AI323362|Fam55b	neurexophilin and PC-esterase domain family, member 2	protein-coding
mm_74265.1	chr8	124898455	124898472	+	1	NA	promoter-TSS (NM_198103)	promoter-TSS (NM_198103)	577	NM_001111141	244666	Mm.482915	NM_001111141	ENSMUSG00000031986	Sprtn	Gm505	SprT-like N-terminal domain	protein-coding
mm_5066.1	chr1	195017417	195017431	+	1	NA	promoter-TSS (NR_015566)	promoter-TSS (NR_015566)	25	NR_015566	320977	Mm.99905	NR_015566	ENSMUSG00000096929	A330023F24Rik	C030002C11Rik	RIKEN cDNA A330023F24 gene	ncRNA
mm_172279.1	chr6	88060035	88060036	-	1	NA	Intergenic	RLTR17|LTR|ERVK	-14765	NM_009005	19349	Mm.333233	NM_009005	ENSMUSG00000079477	Rab7	Rab7a	RAB7, member RAS oncogene family	protein-coding
mm_96980.1	chr11	70655157	70655172	+	1	NA	promoter-TSS (NM_011072)	promoter-TSS (NM_011072)	-514	NM_011072	18643	Mm.2647	NM_011072	ENSMUSG00000018293	Pfn1	Pfn	profilin 1	protein-coding
mm_74553.1	chr8	10865999	10866082	-	1	NA	Intergenic	Intergenic	16414	NR_040705	320014	Mm.403203	NR_040705	ENSMUSG00000109473	B930025P03Rik	-	RIKEN cDNA B930025P03 gene	ncRNA
mm_153244.1	chr19	36119714	36119723	-	1	NA	intron (NM_013468, intron 1 of 8)	intron (NM_013468, intron 1 of 8)	126	NM_013468	107765	Mm.10279	NM_013468	ENSMUSG00000024803	Ankrd1	Alrp|CARP|Crap|MARP1	ankyrin repeat domain 1 (cardiac muscle)	protein-coding
mm_160088.1	chr7	14623050	14623050	-	1	NA	promoter-TSS (NR_045120)	promoter-TSS (NR_045120)	16	NR_045119	100417675	Mm.372763	NR_045119	ENSMUSG00000041596	Nlrp5-ps	Gm18756	NLR family, pyrin domain containing 5, pseudogene	pseudo
mm_92718.1	chr10	80798221	80798299	-	1	NA	promoter-TSS (NM_013651)	promoter-TSS (NM_013651)	366	NM_023900	78670	Mm.41479	NM_023900	ENSMUSG00000035278	Plekhj1	9530063M10Rik	pleckstrin homology domain containing, family J member 1	protein-coding
mm_93838.1	chr10	121603563	121603586	-	1	NA	intron (NM_001081056, intron 17 of 24)	intron (NM_001081056, intron 17 of 24)	-16780	NM_019786	56480	Mm.34580	NM_019786	ENSMUSG00000020115	Tbk1	1200008B05Rik|AI462036|AW048562	TANK-binding kinase 1	protein-coding
mm_102302.1	chr11	55607901	55607912	-	1	NA	5' UTR (NM_020492, exon 1 of 9)	5' UTR (NM_020492, exon 1 of 9)	292	NM_001290821	14654	Mm.89320	NM_020492	ENSMUSG00000000263	Glra1	nmf11|oscillator|ot|spasmodic|spd	glycine receptor, alpha 1 subunit	protein-coding
mm_50619.1	chr6	50110838	50110888	+	1	NA	intron (NM_019939, intron 1 of 12)	intron (NM_019939, intron 1 of 12)	622	NM_001164733	56524	Mm.41288	NM_008016	ENSMUSG00000038388	Mpp6	P55t|Pals2	membrane protein, palmitoylated 6 (MAGUK p55 subfamily member 6)	protein-coding
mm_159645.1	chr4	144213015	144213015	-	1	NA	promoter-TSS (NM_001177542)	promoter-TSS (NM_001177542)	2	NM_001177542	97187	Mm.422698	NM_001177542	ENSMUSG00000046262	C87977	C85819	expressed sequence C87977	protein-coding
mm_162073.1	chrX	20617394	20617394	+	1	NA	promoter-TSS (NM_145627)	promoter-TSS (NM_145627)	-109	NM_001167775	236732	Mm.279194	NM_145627	ENSMUSG00000031060	Rbm10	E430039K10Rik	RNA binding motif protein 10	protein-coding
mm_77570.1	chr8	123432353	123432355	-	1	NA	Intergenic	MuLV-int|LTR|ERV1	-10602	NM_001253784	23854	Mm.275127	NM_054046	ENSMUSG00000001482	Def8	AI449518|D8Ertd713e|DEF-8	differentially expressed in FDCP 8	protein-coding
mm_5192.1	chr1	13225958	13225970	-	1	NA	intron (NM_001302702, intron 2 of 21)	(TC)n|Simple_repeat|Simple_repeat	-98801	NM_001081209	383491	Mm.309380	NM_001081209	ENSMUSG00000042414	Prdm14	-	PR domain containing 14	protein-coding
mm_73953.1	chr8	120276726	120276734	+	1	NA	Intergenic	Intergenic	-48500	NR_110496	434353	Mm.411793	NR_110496	ENSMUSG00000097960	A330074K22Rik	-	RIKEN cDNA A330074K22 gene	ncRNA
mm_134649.1	chr16	21984311	21984335	-	1	NA	intron (NM_001289582, intron 1 of 9)	intron (NM_001289582, intron 1 of 9)	11219	NM_001289582	239759	Mm.33192	NM_153404	ENSMUSG00000044626	Liph	C130037N08Rik|D16Wsu119e|H06|Lpdlr|P3|PLA1B|lpd1|lpd2|mPA-PLA1	lipase, member H	protein-coding
mm_54646.1	chr6	38875966	38875986	-	1	NA	5' UTR (NM_010433, exon 1 of 15)	5' UTR (NM_010433, exon 1 of 15)	214	NM_010433	15258	Mm.23790	NM_010433	ENSMUSG00000061436	Hipk2	1110014O20Rik|B230339E18Rik|Stank	homeodomain interacting protein kinase 2	protein-coding
mm_126125.1	chr15	78331719	78331739	+	1	NA	intron (NM_007780, intron 1 of 13)	intron (NM_007780, intron 1 of 13)	5739	NM_007780	12983	Mm.235324	NM_007780	ENSMUSG00000071713	Csf2rb	AI848964|AIC2B|Bc|CDw131|Csf2rb1|Csfgmrb|Il3r|Il3rb|Il3rb1|Il5rb	colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage)	protein-coding
mm_47473.1	chr5	123720934	123720960	-	1	NA	promoter-TSS (NM_027494)	promoter-TSS (NM_027494)	97	NM_027494	70650	Mm.279427	NM_027494	ENSMUSG00000029427	Zcchc8	5730565F05Rik	zinc finger, CCHC domain containing 8	protein-coding
mm_54697.1	chr6	39557776	39557793	-	1	NA	promoter-TSS (NM_172477)	promoter-TSS (NM_172477)	50	NM_172477	209773	Mm.440021	NM_172477	ENSMUSG00000038456	Dennd2a	B930096L08Rik|C130031G22|mKIAA1277	DENN/MADD domain containing 2A	protein-coding
mm_151105.1	chr19	47860764	47860771	+	1	NA	intron (NM_010362, intron 4 of 5)	intron (NM_010362, intron 4 of 5)	-4778	NM_030051	68214	Mm.63791	NM_026619	ENSMUSG00000025069	Gsto2	1700020F09Rik|4930425C18Rik|GSTO 2-2	glutathione S-transferase omega 2	protein-coding
mm_90926.1	chr10	12822171	12822178	-	1	NA	intron (NM_011682, intron 1 of 73)	B4|SINE|B4	39561	NM_011682	22288	Mm.331784	NM_011682	ENSMUSG00000019820	Utrn	AA589569|DRP|Dmdl	utrophin	protein-coding
mm_158161.1	chrX	103482781	103482794	-	1	NA	non-coding (NR_002844, exon 4 of 4)	non-coding (NR_002844, exon 4 of 4)	446	NR_001570	213742	Mm.274770	NR_001463	ENSMUSG00000086503	Xist	A430022B11|AI314753	inactive X specific transcripts	ncRNA
mm_113361.1	chr13	32965255	32965267	+	1	NA	promoter-TSS (NM_011454)	promoter-TSS (NM_011454)	-252	NM_011454	20708	Mm.36526	NM_011454	ENSMUSG00000042842	Serpinb6b	NK13|Spi12|ovalbumin	serine (or cysteine) peptidase inhibitor, clade B, member 6b	protein-coding
mm_109644.1	chr12	112809334	112809364	+	1	NA	5' UTR (NM_145450, exon 1 of 5)	5' UTR (NM_145450, exon 1 of 5)	374	NM_145450	217887	Mm.186678	NM_145450	ENSMUSG00000037594	BC022687	AW050009|C130001I08Rik|Flj20080	cDNA sequence BC022687	protein-coding
mm_150355.1	chr19	34648832	34648843	+	1	NA	exon (NM_008331, exon 2 of 2)	exon (NM_008331, exon 2 of 2)	7948	NM_008331	15957	Mm.439751	NM_008331	ENSMUSG00000034459	Ifit1	ISG56|Ifi56|P56	interferon-induced protein with tetratricopeptide repeats 1	protein-coding
mm_94466.1	chr11	6475103	6475116	+	1	NA	exon (NM_011221, exon 1 of 1)	exon (NM_011221, exon 1 of 1)	967	NM_011221	19291	Mm.296150	NM_011221	ENSMUSG00000094483	Purb	2310015K15Rik|AA114818|Cager-2|D11Bwg0414e	purine rich element binding protein B	protein-coding
mm_57109.1	chr6	122593325	122593337	-	1	NA	intron (NM_031159, intron 3 of 7)	B1_Mur2|SINE|Alu	9113	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_175.1	chr1	13668740	13668772	+	1	NA	promoter-TSS (NM_001011873)	promoter-TSS (NM_001011873)	-15	NM_001011873	381246	Mm.311142	NM_001011873	ENSMUSG00000067813	Xkr9	Gm1620|XRG9	X-linked Kx blood group related 9	protein-coding
mm_113483.1	chr13	37345385	37345407	+	1	NA	promoter-TSS (NM_010745)	promoter-TSS (NM_010745)	51	NM_010745	17084	Mm.2639	NM_010745	ENSMUSG00000021423	Ly86	MD-1|MD1|ly86_tv2	lymphocyte antigen 86	protein-coding
mm_131785.1	chr16	22898116	22898161	+	1	NA	exon (NM_001276450, exon 6 of 7)	exon (NM_001276450, exon 6 of 7)	-3752	NR_110508	102632430	Mm.474375	NR_110508		Gm30505	-	predicted gene, 30505	ncRNA
mm_125467.1	chr15	52959317	52959321	+	1	NA	Intergenic	Intergenic	246874	NM_027212	69790	Mm.195562	NM_027212	ENSMUSG00000038622	Med30	1810038N03Rik|2510044J04Rik|TRAP25|Thrap6	mediator complex subunit 30	protein-coding
mm_95004.1	chr11	31882547	31882561	+	1	NA	intron (NM_001290676, intron 1 of 8)	intron (NM_001290676, intron 1 of 8)	11614	NM_026252	67579	Mm.339792	NM_026252	ENSMUSG00000020300	Cpeb4	Cpe-bp4|Cpeb-4|mCPEB-4	cytoplasmic polyadenylation element binding protein 4	protein-coding
mm_81887.1	chr9	119392236	119392265	+	1	NA	3' UTR (NM_001199568, exon 20 of 20)	3' UTR (NM_001199568, exon 20 of 20)	-9928	NM_001313757	11481	Mm.8940	NM_007397	ENSMUSG00000061393	Acvr2b	4930516B21Rik|ActRIIB	activin receptor IIB	protein-coding
mm_14906.1	chr2	150311466	150311498	+	1	NA	intron (NM_027017, intron 3 of 3)	intron (NM_027017, intron 3 of 3)	51283	NM_027017	69277	Mm.272470	NM_027017	ENSMUSG00000063364	3300002I08Rik	2900016H11Rik	RIKEN cDNA 3300002I08 gene	protein-coding
mm_16130.1	chr2	170316479	170316486	+	1	NA	Intergenic	Intergenic	-39879	NR_040610	73303	Mm.443297	NR_040610	ENSMUSG00000086999	Bcas1os2	1700040N02Rik	breast carcinoma amplified sequence 1, opposite strand 2	ncRNA
mm_69203.1	chr7	127393605	127393663	-	1	NA	promoter-TSS (NM_198011)	promoter-TSS (NM_198011)	-13	NM_198011	101604	Mm.334241	NM_198011	ENSMUSG00000078580	E430018J23Rik	AI480612	RIKEN cDNA E430018J23 gene	protein-coding
mm_148621.1	chr19	5414975	5414978	+	1	NA	intron (NR_027938, intron 1 of 3)	AT_rich|Low_complexity|Low_complexity	8161	NR_027938	74931	Mm.388511	NR_015545	ENSMUSG00000086938	4930481A15Rik	-	RIKEN cDNA 4930481A15 gene	ncRNA
mm_151431.1	chr19	57119109	57119122	+	1	NA	promoter-TSS (NM_001103178)	promoter-TSS (NM_001103178)	-91	NM_001103178	226251	Mm.217161	NM_178688	ENSMUSG00000025085	Ablim1	2210411C18Rik|2610209L21Rik|4833406P10Rik|9330196J19Rik|AV079770|AW060987|AW215784|Limab1|mKIAA0059	actin-binding LIM protein 1	protein-coding
mm_79940.1	chr9	65909024	65909083	+	1	NA	promoter-TSS (NM_019797)	promoter-TSS (NM_019797)	43	NM_173185	214897	Mm.325816	NM_173185	ENSMUSG00000032384	Csnk1g1	9130020E21Rik	casein kinase 1, gamma 1	protein-coding
mm_147233.1	chr18	38250158	38250212	-	1	NA	promoter-TSS (NM_024179)	promoter-TSS (NM_024179)	13	NR_015475	73516	Mm.48776	NR_015475	ENSMUSG00000097080	1700086O06Rik	-	RIKEN cDNA 1700086O06 gene	ncRNA
mm_169565.1	chr15	16121742	16121745	-	1	NA	Intergenic	Intergenic	-656358	NM_009869	12565	Mm.439758	NM_009869	ENSMUSG00000025370	Cdh9	-	cadherin 9	protein-coding
mm_142851.1	chr17	51805237	51805249	-	1	NA	exon (NM_001163632, exon 3 of 11)	exon (NM_001163632, exon 3 of 11)	6811	NM_001163630	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_40899.1	chr5	75155948	75155956	+	1	NA	promoter-TSS (NM_001083316)	promoter-TSS (NM_001083316)	-214	NM_001083316	18595	Mm.221403	NM_011058	ENSMUSG00000029231	Pdgfra	AI115593|CD140a|Pdgfr-2	platelet derived growth factor receptor, alpha polypeptide	protein-coding
mm_92765.1	chr10	81105842	81105883	-	1	NA	promoter-TSS (NM_001347144)	promoter-TSS (NM_001347144)	-53	NM_023138	26396	Mm.275436	NM_023138	ENSMUSG00000035027	Map2k2	AA589381|MEK2|MK2|Prkmk2	mitogen-activated protein kinase kinase 2	protein-coding
mm_63327.1	chr7	126945113	126945139	+	1	NA	TTS (NM_001039645)	TTS (NM_001039645)	4455	NM_001347657	233879	Mm.444143	NM_001039645	ENSMUSG00000046378	Asphd1	A830007L07Rik|Gm168	aspartate beta-hydroxylase domain containing 1	protein-coding
mm_115745.1	chr13	17944138	17944142	-	1	NA	promoter-TSS (NM_019491)	promoter-TSS (NM_019491)	77	NM_019491	56044	Mm.27348	NM_019491	ENSMUSG00000008859	Rala	3010001O15Rik|AW322615|Ral|Rasl1	v-ral simian leukemia viral oncogene A (ras related)	protein-coding
mm_145659.1	chr18	61130711	61130724	+	1	NA	TTS (NM_178277)	TTS (NM_178277)	13249	NR_105949	102466212		NR_105949	ENSMUSG00000098389	Mir6983	Gm27496|mmu-mir-6983	microRNA 6983	ncRNA
mm_12387.1	chr2	69870405	69870424	+	1	NA	TTS (NR_110977)	TTS (NR_110977)	8852	NM_009278	20823	Mm.10508	NM_009278	ENSMUSG00000068882	Ssb	SS-B	Sjogren syndrome antigen B	protein-coding
mm_33104.1	chr4	124703738	124703740	+	1	NA	intron (NM_010213, intron 1 of 5)	intron (NM_010213, intron 1 of 5)	3040	NM_010213	14201	Mm.331856	NM_010213	ENSMUSG00000032643	Fhl3	SLIM2	four and a half LIM domains 3	protein-coding
mm_131443.1	chr16	16213326	16213364	+	1	NA	promoter-TSS (NM_026163)	promoter-TSS (NM_026163)	0	NM_026163	67451	Mm.2252	NM_026163	ENSMUSG00000041957	Pkp2	1200008D14Rik|1200012P04Rik|AA516617|Pkp2l	plakophilin 2	protein-coding
mm_23816.1	chr3	79908647	79908657	+	1	NA	exon (NM_133187, exon 2 of 4)	exon (NM_133187, exon 2 of 4)	22722	NM_133187	68659	Mm.427274	NM_133187	ENSMUSG00000027955	Fam198b	1110032E23Rik|2210419I08Rik|AV011458|Ened	family with sequence similarity 198, member B	protein-coding
mm_105348.1	chr11	102999829	102999840	-	1	NA	promoter-TSS (NR_105896)	promoter-TSS (NR_105896)	87	NR_105896	102466988		NR_105896	ENSMUSG00000098613	Mir6931	Gm27303|mmu-mir-6931	microRNA 6931	ncRNA
mm_16161.1	chr2	172442191	172442197	+	1	NA	intron (NM_025542, intron 1 of 8)	intron (NM_025542, intron 1 of 8)	1616	NM_025542	66404	Mm.25157	NM_025542	ENSMUSG00000027502	Rtfdc1	1700067C04Rik|2410001C21Rik|5730427M17Rik|AA589417	replication termination factor 2 domain containing 1	protein-coding
mm_160988.1	chr11	105181713	105181713	+	1	NA	promoter-TSS (NR_027956)	promoter-TSS (NR_027956)	186	NM_001294329	24086	Mm.126976	NM_011903	ENSMUSG00000020694	Tlk2	4933403M19Rik|PKU-alpha|PKUalpha|Tlk	tousled-like kinase 2 (Arabidopsis)	protein-coding
mm_73456.1	chr8	106510854	106510924	+	1	NA	promoter-TSS (NM_007665)	promoter-TSS (NM_007665)	37	NM_001037809	12560	Mm.4658	NM_007665	ENSMUSG00000061048	Cdh3	AI385538|Cadp|Cdhp|P-cadherin|Pcad	cadherin 3	protein-coding
mm_103128.1	chr11	70227290	70227297	-	1	NA	intron (NM_007528, intron 5 of 8)	intron (NM_007528, intron 5 of 8)	2505	NM_007528	12029	Mm.12930	NM_007528	ENSMUSG00000000317	Bcl6b	Bazf	B cell CLL/lymphoma 6, member B	protein-coding
mm_118867.1	chr14	25855594	25855602	+	1	NA	intron (NM_013469, intron 1 of 14)	intron (NM_013469, intron 1 of 14)	13443	NM_013469	11744	Mm.294083	NM_013469	ENSMUSG00000021866	Anxa11	A830099O17Rik|Anx11	annexin A11	protein-coding
mm_34830.1	chr4	155234537	155234547	+	1	NA	Intergenic	Intergenic	-12007	NM_011385	20481	Mm.28520	NM_011385	ENSMUSG00000029050	Ski	2310012I02Rik|2610001A11Rik|AA062172|AA589460|BC004088	ski sarcoma viral oncogene homolog (avian)	protein-coding
mm_138838.1	chr17	39848699	39848717	+	1	NA	non-coding (NR_046233, exon 1 of 1)	non-coding (NR_046233, exon 1 of 1)	5711	NR_046233	100861531		NR_046233		Rn45s	-	45S pre-ribosomal RNA	rRNA
mm_157020.1	chrX	7750890	7750916	-	1	NA	Intergenic	CpG	-2186	NR_030454	735274		NR_030454	ENSMUSG00000106252	Mir684-1	Mirn684-1	microRNA 684-1	ncRNA
mm_70980.1	chr8	27175335	27175343	+	1	NA	promoter-TSS (NM_001080813)	promoter-TSS (NM_001080813)	-693	NM_001080813	75767	Mm.205335	NM_029423	ENSMUSG00000031488	Rab11fip1	2010200K21Rik|4833414G05Rik|Rcp	RAB11 family interacting protein 1 (class I)	protein-coding
mm_147587.1	chr18	56562188	56562209	-	1	NA	promoter-TSS (NM_138600)	promoter-TSS (NM_138600)	100	NM_138600	110695	Mm.30250	NM_138600	ENSMUSG00000053644	Aldh7a1	Atq1|D18Wsu181e	aldehyde dehydrogenase family 7, member A1	protein-coding
mm_17836.1	chr2	34322868	34322872	-	1	NA	intron (NM_016768, intron 2 of 8)	intron (NM_016768, intron 2 of 8)	49175	NM_001290576	18516	Mm.239941	NM_016768	ENSMUSG00000038718	Pbx3	-	pre B cell leukemia homeobox 3	protein-coding
mm_2776.1	chr1	130800636	130800640	+	1	NA	promoter-TSS (NM_144960)	promoter-TSS (NM_144960)	-264	NM_001170632	64435	Mm.31821	NM_144960	ENSMUSG00000026415	Fcamr	-	Fc receptor, IgA, IgM, high affinity	protein-coding
mm_96517.1	chr11	68491958	68491969	+	1	NA	exon (NM_177320, exon 9 of 19)	exon (NM_177320, exon 9 of 19)	-11056	NM_001004435	104709	Mm.234573	NM_001004435	ENSMUSG00000046207	Pik3r6	BB220380|p84|p84 PIKAP|p87(PIKAP)|p87PIKAP	phosphoinositide-3-kinase, regulatory subunit 6	protein-coding
mm_57270.1	chr6	123288907	123289007	-	1	NA	exon (NM_019948, exon 2 of 6)	exon (NM_019948, exon 2 of 6)	914	NM_019948	56619	Mm.248327	NM_019948	ENSMUSG00000030142	Clec4e	C86253|Clecsf9|Mincle	C-type lectin domain family 4, member e	protein-coding
mm_61084.1	chr7	51622378	51622386	+	1	NA	5' UTR (NM_080853, exon 1 of 12)	5' UTR (NM_080853, exon 1 of 12)	552	NM_080853	140919	Mm.256618	NM_080853	ENSMUSG00000030500	Slc17a6	2900073D12Rik|DNPI|VGLUT2	solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 6	protein-coding
mm_144788.1	chr18	35888549	35888586	+	1	NA	Intergenic	CpG	58749	NM_133687	67393	Mm.94560	NM_133687	ENSMUSG00000046668	Cxxc5	4930415K17Rik	CXXC finger 5	protein-coding
mm_13981.1	chr2	121506703	121506709	+	1	NA	promoter-TSS (NM_030234)	promoter-TSS (NM_030234)	-17	NM_001290987	241627	Mm.293284	NM_030234	ENSMUSG00000027242	Wdr76	5830411K18Rik|6030457D09|AA517836	WD repeat domain 76	protein-coding
mm_28974.1	chr3	101029544	101029558	-	1	NA	promoter-TSS (NM_001167906)	promoter-TSS (NM_001167906)	-56	NM_001167906	630146	Mm.190915	NM_001099332	ENSMUSG00000086564	Cd101	EWI-101|Gm1016|Gm734|Igsf2	CD101 antigen	protein-coding
mm_163176.1	chr11	87799907	87799921	-	1	NA	exon (NM_010824, exon 9 of 14)	exon (NM_010824, exon 9 of 14)	6130	NM_010824	17523	Mm.4668	NM_010824	ENSMUSG00000009350	Mpo	mKIAA4033	myeloperoxidase	protein-coding
mm_15727.1	chr2	164084622	164084641	+	1	NA	intron (NM_021420, intron 3 of 10)	intron (NM_021420, intron 3 of 10)	10453	NM_021420	58231	Mm.234472	NM_021420	ENSMUSG00000018209	Stk4	AI447339|AU020804|Kas-2|Mst1|Ysk3	serine/threonine kinase 4	protein-coding
mm_162075.1	chrX	21089239	21089239	-	1	NA	promoter-TSS (NM_183185)	promoter-TSS (NM_183185)	-10	NM_183185	245368	Mm.220470	NM_183185	ENSMUSG00000031079	Zfp300	D930016N04Rik	zinc finger protein 300	protein-coding
mm_70029.1	chr7	142576493	142576531	-	1	NA	TTS (NR_030416)	TTS (NR_030416)	635	NR_030416	735280		NR_030416	ENSMUSG00000076275	Mir675	Mirn675|mir-675|mmu-mir-675	microRNA 675	ncRNA
mm_147203.1	chr18	37893374	37893411	-	1	NA	exon (NM_001305981, exon 15 of 29)	exon (NM_001305981, exon 15 of 29)	-38732	NR_105945	102465592		NR_105945	ENSMUSG00000098706	Mir6979	Gm27524|mmu-mir-6979	microRNA 6979	ncRNA
mm_95518.1	chr11	52117998	52118010	+	1	NA	exon (NM_019411, exon 3 of 7)	exon (NM_019411, exon 3 of 7)	-8742	NR_037221	100526467		NR_037221	ENSMUSG00000092870	Mir3061	mir-3061|mmu-mir-3061	microRNA 3061	ncRNA
mm_118473.1	chr14	11570101	11570115	+	1	NA	intron (NM_008981, intron 1 of 29)	intron (NM_008981, intron 1 of 29)	16555	NM_008981	19270	Mm.431266	NM_008981	ENSMUSG00000021745	Ptprg	5430405N12Rik|AW046354|AW549872|RPTPgamma	protein tyrosine phosphatase, receptor type, G	protein-coding
mm_10719.1	chr2	22816519	22816536	+	1	NA	intron (NM_019456, intron 1 of 13)	intron (NM_019456, intron 1 of 13)	42200	NM_019456	54519	Mm.14255	NM_019456	ENSMUSG00000026786	Apbb1ip	9930118P07Rik|Prp48	amyloid beta (A4) precursor protein-binding, family B, member 1 interacting protein	protein-coding
mm_69326.1	chr7	128697583	128697586	-	1	NA	3' UTR (NM_145955, exon 16 of 16)	3' UTR (NM_145955, exon 16 of 16)	8714	NM_001346517	101490	Mm.490344	NM_178641	ENSMUSG00000042105	Inpp5f	5830435P03Rik|AI115354|AW561896|SAC2|cI-27|hSAC2|mKIAA0966	inositol polyphosphate-5-phosphatase F	protein-coding
mm_21913.1	chr2	166659752	166659766	-	1	NA	intron (NM_177782, intron 1 of 39)	intron (NM_177782, intron 1 of 39)	-12959	NR_105783	102465188		NR_105783	ENSMUSG00000098675	Mir6364	Gm27327|mmu-mir-6364	microRNA 6364	ncRNA
mm_17237.1	chr2	25581693	25581758	-	1	NA	Intergenic	Intergenic	-1626	NM_001005424	381353	Mm.379511	NM_001005424	ENSMUSG00000029419	Gm996	-	predicted gene 996	protein-coding
mm_141814.1	chr17	34605718	34605731	-	1	NA	promoter-TSS (NM_001163379)	promoter-TSS (NM_001163379)	-137	NM_001163379	55979	Mm.8684	NM_018862	ENSMUSG00000034254	Agpat1	1-AGP|1-AGPAT|AW047140	1-acylglycerol-3-phosphate O-acyltransferase 1 (lysophosphatidic acid acyltransferase, alpha)	protein-coding
mm_65446.1	chr7	25395611	25395695	-	1	NA	non-coding (NR_073027, exon 2 of 6)	non-coding (NR_073027, exon 2 of 6)	334	NM_010719	16890	Mm.158548	NM_010719	ENSMUSG00000003123	Lipe	4933403G17Rik|HSL	lipase, hormone sensitive	protein-coding
mm_59297.1	chr7	25088392	25088403	+	1	NA	Intergenic	Intergenic	8778	NR_105855	102465968		NR_105855	ENSMUSG00000098441	Mir6537	Gm27808|mmu-mir-6537	microRNA 6537	ncRNA
mm_146829.1	chr18	21652092	21652120	-	1	NA	exon (NM_001081403, exon 1 of 8)	exon (NM_001081403, exon 1 of 8)	262	NM_001081403	225266	Mm.436836	NM_001081403	ENSMUSG00000042514	Klhl14	6330403N15Rik|AI785250|printor	kelch-like 14	protein-coding
mm_133674.1	chr16	92292331	92292341	+	1	NA	promoter-TSS (NM_134110)	promoter-TSS (NM_134110)	-53	NM_134110	246133	Mm.156736	NM_134110	ENSMUSG00000039672	Kcne2	2200002I16Rik|AW048273|MiRP1	potassium voltage-gated channel, Isk-related subfamily, gene 2	protein-coding
mm_102854.1	chr11	69398227	69398243	-	1	NA	promoter-TSS (NM_025915)	promoter-TSS (NM_025915)	-1	NM_025915	67020	Mm.390406	NM_025915	ENSMUSG00000045377	Tmem88	2600017H02Rik	transmembrane protein 88	protein-coding
mm_163762.1	chr13	120010386	120010420	+	1	NA	Intergenic	Intergenic	41801	NM_001302966	100861753	Mm.165042	NM_001302966	ENSMUSG00000095609	Gm21188	-	predicted gene, 21188	protein-coding
mm_106935.1	chr12	8674236	8674275	+	1	NA	promoter-TSS (NM_001160219)	promoter-TSS (NM_001160219)	-4	NR_027670	80913	Mm.341243	NM_030723	ENSMUSG00000020594	Pum2	5730503J23Rik|Pumm2	pumilio RNA-binding family member 2	protein-coding
mm_78248.1	chr9	21670101	21670140	+	1	NA	intron (NM_001174079, intron 21 of 33)	intron (NM_001174079, intron 21 of 33)	-53456	NM_001252658	16835	Mm.3213	NM_010700	ENSMUSG00000032193	Ldlr	Hlb301	low density lipoprotein receptor	protein-coding
mm_107844.1	chr12	69310522	69310526	+	1	NA	3' UTR (NM_027117, exon 13 of 13)	3' UTR (NM_027117, exon 13 of 13)	13843	NM_027117	69554	Mm.234368	NM_027117	ENSMUSG00000020978	Klhdc2	2310022K15Rik|D12Ertd522e|HCLP-1|LCP	kelch domain containing 2	protein-coding
mm_10065.1	chr1	193510081	193510089	-	1	NA	Intergenic	Intergenic	-2555	NR_029592	387201		NR_029592	ENSMUSG00000065533	Mir205	Mirn205|mir-205|mmu-mir-205	microRNA 205	ncRNA
mm_39231.1	chr4	156234778	156234873	-	1	NA	promoter-TSS (NM_198305)	promoter-TSS (NM_198305)	32	NM_198305	231003	Mm.423038	NM_198305	ENSMUSG00000078484	Klhl17	AL022703|BC058738	kelch-like 17	protein-coding
mm_1500.1	chr1	72236446	72236493	+	1	NA	Intergenic	CpG	-24162	NM_001005423	381269	Mm.422636	NM_001005423	ENSMUSG00000039395	Mreg	Gm974|Wdt2|dsu	melanoregulin	protein-coding
mm_53673.1	chr6	141866344	141866356	+	1	NA	Intergenic	Intergenic	-10179	NM_030687	28250	Mm.255586	NM_030687	ENSMUSG00000030237	Slco1a4	AI785519|Oatp1a4|Oatp2|Slc21a5	solute carrier organic anion transporter family, member 1a4	protein-coding
mm_143135.1	chr17	57218133	57218144	-	1	NA	promoter-TSS (NR_105944)	promoter-TSS (NR_105944)	-910	NR_105944	102465591		NR_105944	ENSMUSG00000099066	Mir6978	Gm27858|mmu-mir-6978	microRNA 6978	ncRNA
mm_68965.1	chr7	126584385	126584397	-	1	NA	promoter-TSS (NM_138310)	promoter-TSS (NM_138310)	-617	NM_138310	171504	Mm.170665	NM_138310	ENSMUSG00000042759	Apobr	Apob-48r|Apob48r	apolipoprotein B receptor	protein-coding
mm_136455.1	chr16	94997654	94997704	-	1	NA	promoter-TSS (NM_010606)	promoter-TSS (NM_010606)	17	NM_001025584	16522	Mm.328720	NM_010606	ENSMUSG00000043301	Kcnj6	BIR1|GIRK2|KATP2|KCNJ7|Kir3.2|weaver|wv	potassium inwardly-rectifying channel, subfamily J, member 6	protein-coding
mm_25293.1	chr3	105892033	105892052	+	1	NA	intron (NM_027025, intron 1 of 6)	intron (NM_027025, intron 1 of 6)	-12379	NM_009631	11542	Mm.235024	NM_009631	ENSMUSG00000000562	Adora3	A3AR|A3R|AA3R|ARA3|Gpcr2	adenosine A3 receptor	protein-coding
mm_28713.1	chr3	95658545	95658554	-	1	NA	promoter-TSS (NM_008562)	promoter-TSS (NM_008562)	-172	NM_008562	17210	Mm.1639	NM_008562	ENSMUSG00000038612	Mcl1	AW556805|Mcl-1	myeloid cell leukemia sequence 1	protein-coding
mm_39323.1	chr5	8422909	8422925	+	1	NA	promoter-TSS (NM_178766)	promoter-TSS (NM_178766)	79	NM_178766	319653	Mm.146262	NM_178766	ENSMUSG00000054099	Slc25a40	B230315F11Rik	solute carrier family 25, member 40	protein-coding
mm_81698.1	chr9	111205764	111205780	+	1	NA	exon (NM_001164838, exon 9 of 15)	exon (NM_001164838, exon 9 of 15)	65836	NM_026810	17350	Mm.486383	NM_026810	ENSMUSG00000032498	Mlh1	1110035C23Rik|AI317206|AI325952|AI561766	mutL homolog 1	protein-coding
mm_72134.1	chr8	71908596	71908654	+	1	NA	promoter-TSS (NM_001166645)	promoter-TSS (NM_001166645)	19	NM_001166645	382019	Mm.251482	NM_001166645	ENSMUSG00000089857	Zfp882	ENSMUSG00000052439|Gm15468|OTTMUSG00000022410	zinc finger protein 882	protein-coding
mm_148023.1	chr18	68589442	68589445	-	1	NA	Intergenic	Intergenic	-149957	NR_105774	102465183		NR_105774	ENSMUSG00000099300	Mir6356	Gm27461|mmu-mir-6356	microRNA 6356	ncRNA
mm_83480.1	chr9	45906838	45906894	-	1	NA	promoter-TSS (NM_178709)	promoter-TSS (NM_178709)	11	NM_178709	235315	Mm.3255	NM_178709	ENSMUSG00000042790	Rnf214	D130054N24Rik	ring finger protein 214	protein-coding
mm_157938.1	chrX	85700358	85700363	-	1	NA	Intergenic	Intergenic	76459	NM_001294140	14933	Mm.246682	NM_008194	ENSMUSG00000025059	Gk	D930012N15Rik|Gyk	glycerol kinase	protein-coding
mm_40697.1	chr5	65851136	65851146	+	1	NA	Intergenic	Intergenic	-12428	NM_001081105	74734	Mm.20323	NM_001081105	ENSMUSG00000029204	Rhoh	5830400A04Rik|AU019774|Arhh	ras homolog family member H	protein-coding
mm_109193.1	chr12	108605758	108605814	+	1	NA	promoter-TSS (NM_001163395)	promoter-TSS (NM_001163395)	20	NM_001163395	14026	Mm.238841	NM_007965	ENSMUSG00000021262	Evl	AI528774	Ena-vasodilator stimulated phosphoprotein	protein-coding
mm_34876.1	chr4	155563733	155563743	+	1	NA	promoter-TSS (NM_001159637)	promoter-TSS (NM_001159637)	-77	NM_001159637	192185	Mm.28347	NM_138671	ENSMUSG00000029063	Nadk	4432404C02Rik|BC004012	NAD kinase	protein-coding
mm_109103.1	chr12	105032639	105032705	+	1	NA	promoter-TSS (NR_003145)	promoter-TSS (NR_003145)	54	NM_028419	73046	Mm.29128	NM_028419	ENSMUSG00000021102	Glrx5	-	glutaredoxin 5	protein-coding
mm_115734.1	chr13	17783606	17783610	-	1	NA	intron (NM_027118, intron 1 of 13)	intron (NM_027118, intron 1 of 13)	21489	NM_001081058	69562	Mm.193924	NM_027118	ENSMUSG00000041297	Cdk13	2310015O17Rik|Cdc2l5	cyclin-dependent kinase 13	protein-coding
mm_97851.1	chr11	83069509	83069520	+	1	NA	exon (NM_011408, exon 2 of 2)	exon (NM_011408, exon 2 of 2)	4402	NM_011408	20556	Mm.278689	NM_011408	ENSMUSG00000072620	Slfn2	Shlf2	schlafen 2	protein-coding
mm_12846.1	chr2	83644478	83644490	+	1	NA	promoter-TSS (NM_026934)	promoter-TSS (NM_026934)	-94	NM_026934	69082	Mm.27804	NM_026934	ENSMUSG00000027091	Zc3h15	1700006A17Rik|1810012H02Rik|2610312B22Rik|FM22|Ierepo4	zinc finger CCCH-type containing 15	protein-coding
mm_124653.1	chr15	5237466	5237476	+	1	NA	intron (NM_008965, intron 2 of 2)	intron (NM_008965, intron 2 of 2)	6716	NM_001136079	19219	Mm.18509	NM_008965	ENSMUSG00000039942	Ptger4	EP4|Ptgerep4	prostaglandin E receptor 4 (subtype EP4)	protein-coding
mm_138497.1	chr17	35200752	35200758	+	1	NA	intron (NM_001278601, intron 2 of 2)	intron (NM_001278601, intron 2 of 2)	1252	NM_013693	21926	Mm.1293	NM_013693	ENSMUSG00000024401	Tnf	DIF|TNF-a|TNF-alpha|TNFSF2|TNFalpha|Tnfa|Tnfsf1a|Tnlg1f	tumor necrosis factor	protein-coding
mm_10141.1	chr2	4165965	4165969	+	1	NA	intron (NM_172475, intron 1 of 22)	intron (NM_172475, intron 1 of 22)	13104	NM_172475	209630	Mm.37932	NM_172475	ENSMUSG00000026657	Frmd4a	2700017I06Rik|5330420J21|AI594879|C230040M21Rik|Frmd4|Gm13190|OTTMUSG00000010806|mKIAA1294	FERM domain containing 4A	protein-coding
mm_92887.1	chr10	82764089	82764119	-	1	NA	promoter-TSS (NM_010914)	promoter-TSS (NM_010914)	37	NM_010914	18045	Mm.245998	NM_010914	ENSMUSG00000020248	Nfyb	AA985999|Cbf-A	nuclear transcription factor-Y beta	protein-coding
mm_139036.1	chr17	46163457	46163486	+	1	NA	intron (NM_019581, intron 1 of 11)	intron (NM_019581, intron 1 of 11)	2439	NM_001145979	56055	Mm.22147	NM_019581	ENSMUSG00000023952	Gtpbp2	nmf205	GTP binding protein 2	protein-coding
mm_149830.1	chr19	24529202	24529206	+	1	NA	intron (NM_008846, intron 1 of 14)	intron (NM_008846, intron 1 of 14)	26623	NM_008846	18719	Mm.217214	NM_008846	ENSMUSG00000024867	Pip5k1b	PI4P5K-I[b]|PIP5K1-beta|PIP5KIbeta|Pipk5b|STM7	phosphatidylinositol-4-phosphate 5-kinase, type 1 beta	protein-coding
mm_57087.1	chr6	122586450	122586474	-	1	NA	intron (NM_001134391, intron 5 of 7)	(CAAAA)n|Simple_repeat|Simple_repeat	15982	NM_031159	11810	Mm.3333	NM_031159	ENSMUSG00000040613	Apobec1	Cdar1	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	protein-coding
mm_107302.1	chr12	30912160	30912200	+	1	NA	promoter-TSS (NM_021330)	promoter-TSS (NM_021330)	511	NM_013709	24057	Mm.218624	NM_013709	ENSMUSG00000020669	Sh3yl1	AI314953|Ray|YSC84	Sh3 domain YSC-like 1	protein-coding
mm_87901.1	chr10	62072058	62072088	+	1	NA	Intergenic	Intergenic	38940	NM_027251	69894	Mm.294126	NM_027251	ENSMUSG00000020083	2010107G23Rik	AA545165	RIKEN cDNA 2010107G23 gene	protein-coding
mm_69485.1	chr7	133810641	133810673	-	1	NA	intron (NM_025850, intron 1 of 10)	L1MC4|LINE|L1	-27872	NM_001286031	101437	Mm.199223	NM_133941	ENSMUSG00000030986	Dhx32	3110079L04Rik|4732469F02Rik|AA408140|Ddx32	DEAH (Asp-Glu-Ala-His) box polypeptide 32	protein-coding
mm_104971.1	chr11	100206066	100206094	-	1	NA	promoter-TSS (NM_001313957)	promoter-TSS (NM_001313957)	-50	NM_001313957	16664	Mm.439898	NM_016958	ENSMUSG00000045545	Krt14	AI626930|CK-14|K14|Krt-1.14|Krt1-14	keratin 14	protein-coding
mm_115777.1	chr13	19311364	19311372	-	1	NA	Intergenic	Intergenic	84445	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_117198.1	chr13	63968697	63968736	-	1	NA	Intergenic	ORR1C2|LTR|ERVL-MaLR	120485	NM_008291	15487	Mm.5109	NM_008291	ENSMUSG00000033122	Hsd17b3	-	hydroxysteroid (17-beta) dehydrogenase 3	protein-coding
mm_101281.1	chr11	21571775	21571780	-	1	NA	promoter-TSS (NM_145425)	promoter-TSS (NM_145425)	157	NM_008618	17449	Mm.212703	NM_008618	ENSMUSG00000020321	Mdh1	B230377B03Rik|D17921|MDH-s|MDHA|Mor-2|Mor2	malate dehydrogenase 1, NAD (soluble)	protein-coding
mm_84509.1	chr9	67031078	67031102	-	1	NA	exon (NM_001164251, exon 8 of 10)	exon (NM_001164251, exon 8 of 10)	12781	NM_001164252	22003	Mm.121878	NM_024427	ENSMUSG00000032366	Tpm1	AA986836|AI854628|TM2|Tm3|Tmpa|Tpm-1|alpha-TM	tropomyosin 1, alpha	protein-coding
mm_128268.1	chr15	36793477	36793496	-	1	NA	5' UTR (NM_011740, exon 2 of 7)	5' UTR (NM_011740, exon 2 of 7)	1052	NM_011740	22631	Mm.3360	NM_011740	ENSMUSG00000022285	Ywhaz	1110013I11Rik|14-3-3zeta|AI596267|AL022924|AU020854	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide	protein-coding
mm_63240.1	chr7	126584969	126584988	+	1	NA	promoter-TSS (NM_138310)	promoter-TSS (NM_138310)	-30	NM_138310	171504	Mm.170665	NM_138310	ENSMUSG00000042759	Apobr	Apob-48r|Apob48r	apolipoprotein B receptor	protein-coding
mm_113308.1	chr13	30752729	30752740	+	1	NA	exon (NM_013674, exon 4 of 9)	exon (NM_013674, exon 4 of 9)	3501	NM_013674	16364	Mm.4677	NM_013674	ENSMUSG00000021356	Irf4	AI385587|IRF-4|LSIRF|NF-EM5|Spip	interferon regulatory factor 4	protein-coding
mm_32687.1	chr4	115847769	115847797	+	1	NA	intron (NM_001285487, intron 2 of 14)	intron (NM_001285487, intron 2 of 14)	8585	NM_001285487	17346	Mm.209327	NM_021461	ENSMUSG00000028708	Mknk1	2410048M24Rik|Mnk1	MAP kinase-interacting serine/threonine kinase 1	protein-coding
mm_64338.1	chr7	142376711	142376725	+	1	NA	exon (NM_009983, exon 9 of 9)	exon (NM_009983, exon 9 of 9)	-2972	NM_001347541	320802	Mm.154486	NM_177265	ENSMUSG00000045777	Ifitm10	6330512M04Rik|AI848576|DSPA3	interferon induced transmembrane protein 10	protein-coding
mm_51882.1	chr6	90597674	90597689	+	1	NA	intron (NM_027406, intron 21 of 22)	intron (NM_027406, intron 21 of 22)	-7199	NM_027868	71699	Mm.272633	NM_027868	ENSMUSG00000030089	Slc41a3	1010001P06Rik|AI480742|SLC41A1-L2	solute carrier family 41, member 3	protein-coding
mm_131710.1	chr16	20837153	20837168	+	1	NA	Intergenic	RLTR42-int|LTR|ERVK	-102649	NM_009379	21832	Mm.3943	NM_009379	ENSMUSG00000022847	Thpo	Mgdf|Ml|Mpllg|Tpo	thrombopoietin	protein-coding
mm_114385.1	chr13	63246876	63246880	+	1	NA	intron (NR_110520, intron 2 of 5)	intron (NR_110520, intron 2 of 5)	6849	NR_110521	72061	Mm.188105	NM_028079	ENSMUSG00000021458	2010111I01Rik	2300006M17Rik|AP-O|AW742919|Aopep|ApO|mir-23b|mir-24-1|mir-27b	RIKEN cDNA 2010111I01 gene	protein-coding
mm_171317.1	chr3	95929382	95929382	+	1	NA	5' UTR (NM_001253757, exon 1 of 7)	5' UTR (NM_001253757, exon 1 of 7)	125	NM_023210	66471	Mm.218657	NM_023210	ENSMUSG00000015749	Anp32e	2810018A15Rik|AI047746|AI326868|CPD1|LANP-L|LANPL|mLANP-L	acidic (leucine-rich) nuclear phosphoprotein 32 family, member E	protein-coding
mm_85831.1	chr9	110461056	110461087	-	1	NA	intron (NM_177771, intron 1 of 9)	L2c|LINE|L2	15623	NM_177771	270201	Mm.41744	NM_177771	ENSMUSG00000054792	Klhl18	A930041K15|AW545966	kelch-like 18	protein-coding
mm_55270.1	chr6	53820849	53820859	-	1	NA	promoter-TSS (NM_025817)	promoter-TSS (NM_025817)	-29	NM_025817	66873	Mm.422727	NM_025817	ENSMUSG00000043496	Tril	1200009O22Rik|AI316813|mKIAA0644	TLR4 interactor with leucine-rich repeats	protein-coding
mm_62982.1	chr7	120203935	120203943	+	1	NA	promoter-TSS (NM_026458)	promoter-TSS (NM_026458)	-25	NM_026458	67928	Mm.158178	NM_026458	ENSMUSG00000062017	Abca14	1700110B15Rik|4930539G24Rik	ATP-binding cassette, sub-family A (ABC1), member 14	protein-coding
mm_112630.1	chr13	15930232	15930236	+	1	NA	Intergenic	Intergenic	-81617	NM_008380	16323	Mm.8042	NM_008380	ENSMUSG00000041324	Inhba	-	inhibin beta-A	protein-coding
mm_99719.1	chr11	106276716	106276727	+	1	NA	promoter-TSS (NM_029467)	promoter-TSS (NM_029467)	49	NM_029467	75870	Mm.159608	NM_029467	ENSMUSG00000020712	Tcam1	4930570F09Rik|AI429105	testicular cell adhesion molecule 1	protein-coding
mm_19987.1	chr2	118549626	118549655	-	1	NA	promoter-TSS (NM_138313)	promoter-TSS (NM_138313)	46	NM_138313	171543	Mm.210125	NM_138313	ENSMUSG00000040093	Bmf	AW260063|AW411872	BCL2 modifying factor	protein-coding
mm_50884.1	chr6	56125084	56125088	+	1	NA	intron (NM_001025568, intron 15 of 16)	intron (NM_001025568, intron 15 of 16)	107571	NM_011153	19051	Mm.42096	NM_011153	ENSMUSG00000002930	Ppp1r17	G-substrate|Gsbs|Ppp1r2	protein phosphatase 1, regulatory subunit 17	protein-coding
mm_133637.1	chr16	91663959	91663970	+	1	NA	TTS (NM_019973)	TTS (NM_019973)	16140	NM_178880	20658	Mm.46401	NM_019973	ENSMUSG00000022961	Son	2900011L12Rik|AA409051|AU067731|C81487|mKIAA1019|nrebp	Son DNA binding protein	protein-coding
mm_57754.1	chr6	129225442	129225447	-	1	NA	Intergenic	Intergenic	12601	NR_040265	76432	Mm.261738	NR_040265	ENSMUSG00000097354	2310001H17Rik	AI646108	RIKEN cDNA 2310001H17 gene	ncRNA
mm_136745.1	chr17	8434266	8434283	+	1	NA	promoter-TSS (NM_009309)	promoter-TSS (NM_009309)	-149	NM_009309	20997	Mm.913	NM_009309	ENSMUSG00000062327	T	Bra|D17Mit170|Low|Lr|T1|Tl2|Tl3|cou|me75	brachyury	protein-coding
mm_146775.1	chr18	20059327	20059347	-	1	NA	5' UTR (NM_013505, exon 1 of 17)	5' UTR (NM_013505, exon 1 of 17)	217	NM_013505	13506	Mm.280547	NM_013505	ENSMUSG00000024331	Dsc2	AW228162	desmocollin 2	protein-coding
mm_136055.1	chr16	78577179	78577193	-	1	NA	promoter-TSS (NM_001252440)	promoter-TSS (NM_001252440)	-498	NM_025967	67102	Mm.37332	NM_025967	ENSMUSG00000022864	D16Ertd472e	1700010I10Rik|2310009O17Rik|E330003K22Rik|Eurl	DNA segment, Chr 16, ERATO Doi 472, expressed	protein-coding
mm_166585.1	chr6	54681787	54681793	+	1	NA	exon (NM_001289741, exon 1 of 5)	exon (NM_001289741, exon 1 of 5)	166	NM_001289740	68235	Mm.233860	NM_026629	ENSMUSG00000038065	Mturn	2410066E13Rik|AI448550|B230212L03Rik	maturin, neural progenitor differentiation regulator homolog (Xenopus)	protein-coding
mm_52153.1	chr6	98004757	98004781	+	1	NA	intron (NM_008601, intron 5 of 8)	intron (NM_008601, intron 5 of 8)	12986	NM_008601	17342	Mm.333284	NM_008601	ENSMUSG00000035158	Mitf	BCC2|Bhlhe32|Gsfbcc2|Vitiligo|Wh|bw|mi|vit	microphthalmia-associated transcription factor	protein-coding
mm_58140.1	chr6	141856193	141856234	-	1	NA	promoter-TSS (NM_030687)	promoter-TSS (NM_030687)	-42	NM_030687	28250	Mm.255586	NM_030687	ENSMUSG00000030237	Slco1a4	AI785519|Oatp1a4|Oatp2|Slc21a5	solute carrier organic anion transporter family, member 1a4	protein-coding
mm_142085.1	chr17	35744101	35744138	-	1	NA	Intergenic	Intergenic	-28331	NR_045459	74601	Mm.410840	NR_045459	ENSMUSG00000092171	4833427F10Rik	-	RIKEN cDNA 4833427F10 gene	ncRNA
mm_119093.1	chr14	30892605	30892615	+	1	NA	exon (NM_001289633, exon 11 of 22)	exon (NM_001289633, exon 11 of 22)	6134	NM_001289632	16427	Mm.34819	NM_018746	ENSMUSG00000021922	Itih4	ITI-HC4|Itih-4|PK-120	inter alpha-trypsin inhibitor, heavy chain 4	protein-coding
mm_37369.1	chr4	120924915	120924925	-	1	NA	promoter-TSS (NM_001160043)	promoter-TSS (NM_001160043)	85	NM_028457	73172	Mm.151436	NM_028457	ENSMUSG00000028629	Exo5	3110037I16Rik|AV297100|Dem1|Exo V|mExo5	exonuclease 5	protein-coding
mm_62353.1	chr7	100498855	100498876	+	1	NA	exon (NM_011671, exon 7 of 8)	exon (NM_011671, exon 7 of 8)	5507	NM_011671	22228	Mm.171378	NM_011671	ENSMUSG00000033685	Ucp2	Slc25a8	uncoupling protein 2 (mitochondrial, proton carrier)	protein-coding
mm_136679.1	chr17	6430168	6430204	+	1	NA	promoter-TSS (NM_009342)	promoter-TSS (NM_009342)	74	NM_009342	21648	Mm.1948	NM_009342	ENSMUSG00000096255	Dynlt1b	AGS2|Dynlt1|Tctex-1|Tctex1	dynein light chain Tctex-type 1B	protein-coding
mm_72826.1	chr8	88244684	88244687	+	1	NA	intron (NM_001164498, intron 3 of 12)	intron (NM_001164498, intron 3 of 12)	-27718	NM_007406	11513	Mm.288206	NM_007406	ENSMUSG00000031659	Adcy7	AA407758	adenylate cyclase 7	protein-coding
mm_69597.1	chr7	135716346	135716356	-	1	NA	promoter-TSS (NM_001081117)	promoter-TSS (NM_001081117)	28	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_1098.1	chr1	59710518	59710549	+	1	NA	exon (NM_018868, exon 14 of 15)	exon (NM_018868, exon 14 of 15)	5725	NR_028521	100217421		NR_028521		Snord11	MBII-95	small nucleolar RNA, C/D box 11	snoRNA
mm_151150.1	chr19	53140610	53140620	+	1	NA	5' UTR (NM_001164099, exon 1 of 15)	5' UTR (NM_001164099, exon 1 of 15)	172	NM_001164101	27360	Mm.426080	NM_013758	ENSMUSG00000025026	Add3	AI463285|R75380	adducin 3 (gamma)	protein-coding
mm_7010.1	chr1	86492220	86492251	-	1	NA	Intergenic	Intergenic	-34501	NM_008972	19231	Mm.19187	NM_008972	ENSMUSG00000026238	Ptma	Thym	prothymosin alpha	protein-coding
mm_95294.1	chr11	46055974	46056068	+	1	NA	promoter-TSS (NM_009616)	promoter-TSS (NM_009616)	37	NM_001291891	11492	Mm.89940	NM_009616	ENSMUSG00000011256	Adam19	AL024287|MADDAM|MTLNB|Mltnb	a disintegrin and metallopeptidase domain 19 (meltrin beta)	protein-coding
mm_128101.1	chr15	27923693	27923739	-	1	NA	intron (NM_001081302, intron 1 of 56)	intron (NM_001081302, intron 1 of 56)	102132	NM_001081302	223435	Mm.485422	NM_001081302	ENSMUSG00000022263	Trio	6720464I07Rik|AA408740|Solo	triple functional domain (PTPRF interacting)	protein-coding
mm_155695.1	chrX	94367113	94367134	+	1	NA	promoter-TSS (NM_026673)	promoter-TSS (NM_026673)	-1	NR_004438	621156	Mm.343319	NR_004438		Apoo-ps	Apoo|EG621156	apolipoprotein O, pseudogene	pseudo
mm_119821.1	chr14	54232244	54232249	+	1	NA	Intergenic	Intergenic	21683	NM_001113358	13135	Mm.319038	NM_010015	ENSMUSG00000022174	Dad1	AI323713	defender against cell death 1	protein-coding
mm_130290.1	chr15	97008898	97008908	-	1	NA	exon (NM_027052, exon 10 of 16)	exon (NM_027052, exon 10 of 16)	47053	NM_027052	69354	Mm.250980	NM_027052	ENSMUSG00000022464	Slc38a4	1110012E16Rik|1700012A18Rik|Ata3|mATA3|mNAT3	solute carrier family 38, member 4	protein-coding
mm_60266.1	chr7	43841908	43841918	+	1	NA	promoter-TSS (NM_026806)	promoter-TSS (NM_026806)	-356	NM_026806	68668	Mm.458122	NM_026806	ENSMUSG00000074155	Klk5	1110030O19Rik	kallikrein related-peptidase 5	protein-coding
mm_108078.1	chr12	73946031	73946048	+	1	NA	3' UTR (NM_010431, exon 15 of 15)	3' UTR (NM_010431, exon 15 of 15)	-18491	NM_178392	75627	Mm.25937	NM_178392	ENSMUSG00000021113	Snapc1	2700033G17Rik|AU015787	small nuclear RNA activating complex, polypeptide 1	protein-coding
mm_102834.1	chr11	69197835	69197838	-	1	NA	promoter-TSS (NM_009661)	promoter-TSS (NM_009661)	7	NM_009661	11688	Mm.289672	NM_009661	ENSMUSG00000020891	Alox8	15-LOX-2|15-LOX-B|8-LOX|8S-LOX|Alox15b	arachidonate 8-lipoxygenase	protein-coding
mm_50346.1	chr6	48589485	48589499	+	1	NA	promoter-TSS (NM_183309)	promoter-TSS (NM_183309)	47	NM_183309	330305	Mm.123868	NM_183309	ENSMUSG00000052730	Gm5111	A630038D02|EG330305	predicted gene 5111	protein-coding
mm_72184.1	chr8	72350077	72350099	+	1	NA	intron (NM_007944, intron 22 of 23)	intron (NM_007944, intron 22 of 23)	31026	NM_008452	16598	Mm.26938	NM_008452	ENSMUSG00000055148	Klf2	Lklf	Kruppel-like factor 2 (lung)	protein-coding
mm_158751.1	chrX	165327377	165327421	-	1	NA	promoter-TSS (NM_183427)	promoter-TSS (NM_183427)	-418	NM_183427	237213	Mm.113877	NM_183427	ENSMUSG00000018589	Glra2	-	glycine receptor, alpha 2 subunit	protein-coding
mm_173351.1	chrY	90813583	90813585	+	1	NA	intron (NM_133362, intron 2 of 3)	IMPB_01|Satellite|Satellite	25822	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_155630.1	chrX	84772702	84772719	+	1	NA	intron (NM_007868, intron 55 of 78)	intron (NM_007868, intron 55 of 78)	-275585	NM_001314038	13405	Mm.275608	NM_007868	ENSMUSG00000045103	Dmd	DXSmh7|DXSmh9|Dp427|Dp71|dys|mdx|pke	dystrophin, muscular dystrophy	protein-coding
mm_31613.1	chr4	59017667	59017713	+	1	NA	exon (NM_001033165, exon 2 of 4)	exon (NM_001033165, exon 2 of 4)	14497	NM_001033165	72429	Mm.317801	NM_001033165	ENSMUSG00000070972	Dnajc25	2010109C08Rik|2010203O07Rik	DnaJ heat shock protein family (Hsp40) member C25	protein-coding
mm_140811.1	chr17	22519381	22519382	-	1	NA	Intergenic	Intergenic	53892	NM_001104573	210876	Mm.390947	NM_001104573	ENSMUSG00000095093	Vmn2r111	EG210876|V2rp2	vomeronasal 2, receptor 111	protein-coding
mm_5691.1	chr1	43186151	43186159	-	1	NA	intron (NM_001289533, intron 1 of 5)	B4|SINE|B4	10606	NM_001289533	14200	Mm.6799	NM_010212	ENSMUSG00000008136	Fhl2	FHL-2|SLIM-3|SLIM3	four and a half LIM domains 2	protein-coding
mm_84279.1	chr9	62811670	62811676	-	1	NA	promoter-TSS (NM_010193)	promoter-TSS (NM_010193)	-25	NM_010193	14155	Mm.24069	NM_010193	ENSMUSG00000032244	Fem1b	mKIAA0396	feminization 1 homolog b (C. elegans)	protein-coding
mm_114186.1	chr13	55693083	55693151	+	1	NA	promoter-TSS (NM_181278)	promoter-TSS (NM_181278)	-7	NM_181278	78521	Mm.28449	NM_181278	ENSMUSG00000045767	B230219D22Rik	AA119856|D530037I19Rik	RIKEN cDNA B230219D22 gene	protein-coding
mm_41639.1	chr5	98030696	98030724	+	1	NA	5' UTR (NM_133738, exon 1 of 17)	5' UTR (NM_133738, exon 1 of 17)	252	NM_133738	71914	Mm.24842	NM_133738	ENSMUSG00000029338	Antxr2	2310046B19Rik|AW561899|CMG-2|CMG2|cI-35	anthrax toxin receptor 2	protein-coding
mm_82998.1	chr9	36693144	36693149	-	1	NA	promoter-TSS (NM_007391)	promoter-TSS (NM_007391)	43	NR_040741	75567	Mm.426883	NR_040741	ENSMUSG00000098304	1700027I24Rik	-	RIKEN cDNA 1700027I24 gene	ncRNA
mm_96925.1	chr11	70510181	70510199	+	1	NA	intron (NM_029360, intron 2 of 4)	intron (NM_029360, intron 2 of 4)	4426	NM_001013607	327956	Mm.244514	NM_001013607	ENSMUSG00000020830	Vmo1	Gm741	vitelline membrane outer layer 1 homolog (chicken)	protein-coding
mm_19237.1	chr2	84715129	84715151	-	1	NA	promoter-TSS (NM_144887)	promoter-TSS (NM_144887)	24	NM_144887	228136	Mm.288508	NM_144887	ENSMUSG00000034075	Zdhhc5	1110032A17Rik|AI451382|Zisp	zinc finger, DHHC domain containing 5	protein-coding
mm_151556.1	chr19	59459519	59459556	+	1	NA	promoter-TSS (NR_002863)	promoter-TSS (NR_002863)	847	NM_010132	13797	Mm.245394	NM_010132	ENSMUSG00000043969	Emx2	Pdo	empty spiracles homeobox 2	protein-coding
mm_45939.1	chr5	90243780	90243825	-	1	NA	exon (NM_030886, exon 29 of 34)	exon (NM_030886, exon 29 of 34)	-19806	NM_001163456	231430	Mm.319697	NM_001033310	ENSMUSG00000035505	Cox18	BC038311	cytochrome c oxidase assembly protein 18	protein-coding
mm_69771.1	chr7	141016792	141016802	-	1	NA	promoter-TSS (NM_001033632)	promoter-TSS (NM_001033632)	95	NM_001033632	213002	Mm.276440	NM_001033632	ENSMUSG00000059108	Ifitm6	A330075D07|Dspa2f|Fgls5|fragilis5	interferon induced transmembrane protein 6	protein-coding
mm_99568.1	chr11	103954127	103954141	+	1	NA	promoter-TSS (NM_008740)	promoter-TSS (NM_008740)	-78	NM_008740	18195	Mm.260117	NM_008740	ENSMUSG00000034187	Nsf	AI316878|AU020090|AU067812|SKD2	N-ethylmaleimide sensitive fusion protein	protein-coding
mm_151872.1	chr19	5798058	5798069	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	-2082	NR_144621	109146451		NR_144621		Mascrna	-	Malat1-associated small cytoplasmic RNA	scRNA
mm_37686.1	chr4	129227884	129227923	-	1	NA	promoter-TSS (NM_001285866)	promoter-TSS (NM_001285866)	8	NM_001285866	97130	Mm.331907	NM_001033189	ENSMUSG00000050390	C77080	Kiaa1522|mKIAA1522	expressed sequence C77080	protein-coding
mm_88106.1	chr10	69104942	69104946	+	1	NA	Intergenic	Intergenic	-103608	NM_001252636	69288	Mm.26659	NM_001081347	ENSMUSG00000019944	Rhobtb1	1700008H16Rik|3110048G13Rik|AI173445|AI573858|AV350930	Rho-related BTB domain containing 1	protein-coding
mm_158342.1	chrX	134162506	134162512	-	1	NA	promoter-TSS (NM_183319)	promoter-TSS (NM_183319)	-581	NM_183319	331524	Mm.235055	NM_183319	ENSMUSG00000031258	Xkrx	A630026F04	X-linked Kx blood group related, X-linked	protein-coding
mm_103592.1	chr11	78246169	78246251	-	1	NA	promoter-TSS (NM_009297)	promoter-TSS (NM_009297)	464	NM_009143	20316	Mm.20755	NM_009143	ENSMUSG00000002064	Sdf2	AI853825	stromal cell derived factor 2	protein-coding
mm_137007.1	chr17	17826948	17826964	+	1	NA	Intergenic	Intergenic	-3232	NR_029536	387230		NR_029536	ENSMUSG00000065396	Mir99b	Mirn99b|mmu-mir-99b	microRNA 99b	ncRNA
mm_70746.1	chr8	19194320	19194333	+	1	NA	promoter-TSS (NM_183026)	promoter-TSS (NM_183026)	-2	NM_183026	244332	Mm.358923	NM_183026	ENSMUSG00000046354	Defb14	BD-14	defensin beta 14	protein-coding
mm_91268.1	chr10	23787216	23787252	-	1	NA	promoter-TSS (NM_011295)	promoter-TSS (NM_011295)	-25	NM_011295	20042	Mm.371846	NM_011295	ENSMUSG00000061983	Rps12	-	ribosomal protein S12	protein-coding
mm_88913.1	chr10	81179924	81179962	+	1	NA	TTS (NR_028549)	TTS (NR_028549)	982	NR_028549	100217454		NR_028549	ENSMUSG00000064441	Snord37	MBII-376	small nucleolar RNA, C/D box 37	snoRNA
mm_158200.1	chrX	105307989	105308005	-	1	NA	Intergenic	L1_Mur3|LINE|L1	36372	NR_029910	723861		NR_029910	ENSMUSG00000065499	Mir384	Mirn384|mir-384|mmu-mir-384	microRNA 384	ncRNA
mm_70593.1	chr8	13200947	13200971	+	1	NA	promoter-TSS (NM_025768)	promoter-TSS (NM_025768)	-335	NM_025768	66790	Mm.34901	NM_025768	ENSMUSG00000038515	Grtp1	5430401C05Rik|C81211|Tbc1d6	GH regulated TBC protein 1	protein-coding
mm_143474.1	chr17	71256348	71256364	-	1	NA	exon (NM_145158, exon 5 of 8)	exon (NM_145158, exon 5 of 8)	51702	NM_001164885	64898	Mm.227924	NM_022882	ENSMUSG00000024052	Lpin2	2610511G02Rik|AI481352|AW742896	lipin 2	protein-coding
mm_5942.1	chr1	56637456	56637460	-	1	NA	promoter-TSS (NM_027661)	promoter-TSS (NM_027661)	-7	NM_027661	71066	Mm.152656	NM_027661	ENSMUSG00000045336	Hsfy2	4933413G11Rik|Hspy2l	heat shock transcription factor, Y-linked 2	protein-coding
mm_113595.1	chr13	41001232	41001248	+	1	NA	5' UTR (NM_026550, exon 1 of 10)	5' UTR (NM_026550, exon 1 of 10)	230	NM_026550	68083	Mm.24789	NM_026550	ENSMUSG00000038683	Pak1ip1	5830431I15Rik|5930415H02Rik|AA419825|AI314040|AW556169|Gdpd1|PIP1	PAK1 interacting protein 1	protein-coding
mm_109410.1	chr12	110460761	110460773	+	1	NA	intron (NM_001135001, intron 2 of 13)	intron (NM_001135001, intron 2 of 13)	13588	NM_001135001	26931	Mm.240396	NM_012023	ENSMUSG00000017843	Ppp2r5c	2610043M05Rik|2700063L20Rik|AI060890|AW545884|C85228|D12Bwg0916e|mKIAA0044	protein phosphatase 2, regulatory subunit B', gamma	protein-coding
mm_82021.1	chr9	121759733	121759767	+	1	NA	promoter-TSS (NM_001166644)	promoter-TSS (NM_001166644)	193	NR_033503	320301	Mm.373883	NR_033503		E530011L22Rik	-	RIKEN cDNA E530011L22 gene	ncRNA
mm_137733.1	chr17	29318851	29318886	+	1	NA	promoter-TSS (NM_023734)	promoter-TSS (NM_023734)	-14	NM_023734	74116	Mm.30950	NM_023734	ENSMUSG00000024011	Pi16	1200009H11Rik|Cripi|PI-16	peptidase inhibitor 16	protein-coding
mm_29429.1	chr3	109022324	109022339	-	1	NA	intron (NM_001163567, intron 1 of 10)	intron (NM_001163567, intron 1 of 10)	5276	NM_001163567	329739	Mm.69013	NM_001163567	ENSMUSG00000040339	Fam102b	1600010D10Rik|B430201A12Rik	family with sequence similarity 102, member B	protein-coding
mm_146556.1	chr18	6224071	6224083	-	1	NA	intron (NM_008448, intron 8 of 25)	intron (NM_008448, intron 8 of 25)	17447	NM_008448	16573	Mm.223744	NM_008448	ENSMUSG00000006740	Kif5b	AL022807|Khc|Khcs|Kns1|Ukhc	kinesin family member 5B	protein-coding
mm_94336.1	chr11	4637735	4637789	+	1	NA	promoter-TSS (NM_029291)	promoter-TSS (NM_029291)	-31	NM_029291	75452	Mm.439906	NM_029291	ENSMUSG00000020412	Ascc2	1700011I11Rik|2610034L15Rik|AI482016|ASC1p100|AW046480	activating signal cointegrator 1 complex subunit 2	protein-coding
mm_32928.1	chr4	119195445	119195455	+	1	NA	promoter-TSS (NM_001038998)	promoter-TSS (NM_001038998)	-75	NM_001038998	69216	Mm.36697	NM_024462	ENSMUSG00000028643	Svbp	2410005K17Rik|AI851162|Ccdc23	small vasohibin binding protein	protein-coding
mm_122703.1	chr14	52180173	52180189	-	1	NA	exon (NM_033618, exon 7 of 26)	exon (NM_033618, exon 7 of 26)	17058	NM_033618	114741	Mm.21662	NM_033618	ENSMUSG00000035726	Supt16	Cdc68|Fact140|Spt16|Supt16h	suppressor of Ty 16	protein-coding
mm_156980.1	chrX	7188714	7188743	-	1	NA	promoter-TSS (NM_016691)	promoter-TSS (NM_016691)	-14	NM_016691	12728	Mm.486257	NM_016691	ENSMUSG00000004317	Clcn5	5430408K11Rik|ClC-5|Clc4-1|Clc5|Clcn4-1|D930009B12Rik|DXImx42e|Sfc13|T25545	chloride channel, voltage-sensitive 5	protein-coding
mm_55024.1	chr6	48841431	48841435	-	1	NA	promoter-TSS (NM_001164209)	promoter-TSS (NM_001164209)	-50	NM_025326	66058	Mm.27061	NM_025326	ENSMUSG00000023367	Tmem176a	0610011I04Rik|AU040201|AU041743|Keg2	transmembrane protein 176A	protein-coding
mm_66898.1	chr7	59930829	59930840	-	1	NA	Intergenic	Intergenic	43597	NR_015456	52480	Mm.482346	NR_015456	ENSMUSG00000100826	Snhg14	AU018661|D7Ertd715e|Lncat	small nucleolar RNA host gene 14	ncRNA
mm_151933.1	chr19	5800306	5800319	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	2360	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_31008.1	chr4	40260504	40260519	+	1	NA	exon (NM_134097, exon 3 of 3)	exon (NM_134097, exon 3 of 3)	-9068	NR_045265	100504309	Mm.392019	NR_045265		Toporsos	2010003O02Rik	topoisomerase I binding, arginine/serine-rich, opposite strand	ncRNA
mm_138338.1	chr17	34898932	34898986	+	1	NA	promoter-TSS (NM_145830)	promoter-TSS (NM_145830)	-15	NM_001286573	110147	Mm.35345	NM_145830	ENSMUSG00000013787	Ehmt2	Bat8|D17Ertd710e|G9a|KMT1C|NG36	euchromatic histone lysine N-methyltransferase 2	protein-coding
mm_61311.1	chr7	67998218	67998220	+	1	NA	intron (NM_010513, intron 1 of 20)	intron (NM_010513, intron 1 of 20)	45962	NM_010513	16001	Mm.275742	NM_010513	ENSMUSG00000005533	Igf1r	A330103N21Rik|CD221|D930020L01|IGF-1R|hyft	insulin-like growth factor I receptor	protein-coding
mm_144488.1	chr18	24168637	24168643	+	1	NA	Intergenic	MTE2b|LTR|ERVL-MaLR	-36704	NM_013814	14423	Mm.30249	NM_013814	ENSMUSG00000000420	Galnt1	-	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 1	protein-coding
mm_60773.1	chr7	45559171	45559211	+	1	NA	intron (NM_025330, intron 4 of 8)	intron (NM_025330, intron 4 of 8)	4263	NM_025330	66065	Mm.285710	NM_025330	ENSMUSG00000030825	Hsd17b14	0610039E24Rik|Dhrs10|retSDR3	hydroxysteroid (17-beta) dehydrogenase 14	protein-coding
mm_89343.1	chr10	87936090	87936100	+	1	NA	3' UTR (NM_010512, exon 5 of 5)	3' UTR (NM_010512, exon 5 of 5)	-30576	NR_000040	22172	Mm.391420	NR_000040		Tyms-ps	-	thymidylate synthase, pseudogene	pseudo
mm_162823.1	chr10	81057524	81057527	+	1	NA	intron (NM_024499, intron 1 of 11)	PB1D7|SINE|Alu	2629	NM_024499	52551	Mm.30068	NM_024499	ENSMUSG00000004937	Sgta	5330427H01Rik|AI194281|D10Ertd190e|Sgt|Stg	small glutamine-rich tetratricopeptide repeat (TPR)-containing, alpha	protein-coding
mm_82921.1	chr9	35099081	35099087	-	1	NA	intron (NM_009178, intron 1 of 10)	intron (NM_009178, intron 1 of 10)	-17644	NR_029475	78934	Mm.391688	NR_029475	ENSMUSG00000070315	4930581F22Rik	-	RIKEN cDNA 4930581F22 gene	ncRNA
mm_99273.1	chr11	101259156	101259177	+	1	NA	3' UTR (NM_026776, exon 6 of 6)	3' UTR (NM_026776, exon 6 of 6)	-1401	NM_175638	69847	Mm.23656	NM_175638	ENSMUSG00000035112	Wnk4	2010002J11Rik|Pha2b|Prkwnk4	WNK lysine deficient protein kinase 4	protein-coding
mm_40326.1	chr5	43910459	43910472	+	1	NA	3' UTR (NM_007646, exon 8 of 8)	3' UTR (NM_007646, exon 8 of 8)	41656	NM_007646	12494	Mm.249873	NM_007646	ENSMUSG00000029084	Cd38	ADPRC 1|Cd38-rs1|I-19	CD38 antigen	protein-coding
mm_155290.1	chrX	61183678	61183800	+	1	NA	3' UTR (NM_001166658, exon 1 of 1)	3' UTR (NM_001166658, exon 1 of 1)	1819	NM_001166658	631990	Mm.401324	NM_001166658	ENSMUSG00000090546	Cdr1	100039759|Cdr|Cdr34|EG631990|Gm2409|Gm7077	cerebellar degeneration related antigen 1	protein-coding
mm_150455.1	chr19	38162220	38162232	+	1	NA	intron (NM_033614, intron 12 of 21)	intron (NM_033614, intron 12 of 21)	29445	NM_001170959	110855	Mm.450141	NM_033614	ENSMUSG00000024992	Pde6c	cpfl1	phosphodiesterase 6C, cGMP specific, cone, alpha prime	protein-coding
mm_73372.1	chr8	105617880	105617901	+	1	NA	exon (NM_001081241, exon 13 of 22)	exon (NM_001081241, exon 13 of 22)	2424	NR_035492	100316712		NR_035492	ENSMUSG00000089432	Mir1966	mir-1966|mmu-mir-1966	microRNA 1966	ncRNA
mm_77918.1	chr9	7351974	7351985	+	1	NA	intron (NM_001320077, intron 5 of 10)	intron (NM_001320077, intron 5 of 10)	4605	NM_008605	17381	Mm.2055	NM_008605	ENSMUSG00000049723	Mmp12	AV378681|MME|Mmel	matrix metallopeptidase 12	protein-coding
mm_63348.1	chr7	126976280	126976297	+	1	NA	5' UTR (NM_026638, exon 1 of 6)	5' UTR (NM_026638, exon 1 of 6)	374	NM_001347656	52858	Mm.28219	NM_026638	ENSMUSG00000030682	Cdipt	9530042F15Rik|D7Bwg0575e|Pis|Pis1	CDP-diacylglycerol--inositol 3-phosphatidyltransferase (phosphatidylinositol synthase)	protein-coding
mm_30946.1	chr4	33077389	33077417	+	1	NA	intron (NM_008076, intron 2 of 8)	intron (NM_008076, intron 2 of 8)	14291	NM_008076	14409	Mm.6227	NM_008076	ENSMUSG00000023267	Gabrr2	-	gamma-aminobutyric acid (GABA) C receptor, subunit rho 2	protein-coding
mm_109927.1	chr12	8674631	8674670	-	1	NA	promoter-TSS (NM_030723)	promoter-TSS (NM_030723)	-31	NM_030723	80913	Mm.341243	NM_030723	ENSMUSG00000020594	Pum2	5730503J23Rik|Pumm2	pumilio RNA-binding family member 2	protein-coding
mm_82568.1	chr9	21078479	21078510	-	1	NA	intron (NR_038081, intron 9 of 16)	B4|SINE|B4	-2906	NR_106050	102465656		NR_106050	ENSMUSG00000098907	Mir7082	Gm27933|mmu-mir-7082	microRNA 7082	ncRNA
mm_86282.1	chr9	121847019	121847022	-	1	NA	Intergenic	A-rich|Low_complexity|Low_complexity	-7559	NM_028384	100502861	Mm.335550	NM_028384	ENSMUSG00000079235	Ccdc13	2900041A11Rik|Gm188	coiled-coil domain containing 13	protein-coding
mm_34025.1	chr4	138045806	138045810	+	1	NA	intron (NM_172703, intron 3 of 34)	B1_Mur3|SINE|Alu	52352	NM_172703	230861	Mm.268903	NM_172703	ENSMUSG00000028760	Eif4g3	1500002J22Rik|4930523M17Rik|G1-419-52|eIF4GII|repro8	eukaryotic translation initiation factor 4 gamma, 3	protein-coding
mm_43642.1	chr5	138255856	138255866	+	1	NA	intron (NM_001081108, intron 1 of 3)	CpG	379	NM_001081108	66096	Mm.206901	NM_001081108	ENSMUSG00000050552	Lamtor4	0910001L09Rik|AV006840	late endosomal/lysosomal adaptor, MAPK and MTOR activator 4	protein-coding
mm_48624.1	chr5	145128108	145128156	-	1	NA	TTS (NM_001033313)	TTS (NM_001033313)	11957	NM_001033313	231887	Mm.188851	NM_001033313	ENSMUSG00000029623	Pdap1	HASPP28|PAP|PAP1	PDGFA associated protein 1	protein-coding
mm_110120.1	chr12	26444024	26444028	-	1	NA	3' UTR (NM_021384, exon 6 of 6)	3' UTR (NM_021384, exon 6 of 6)	12426	NM_021384	58185	Mm.24045	NM_021384	ENSMUSG00000020641	Rsad2	2510004L01Rik|Vig1|cig5	radical S-adenosyl methionine domain containing 2	protein-coding
mm_114155.1	chr13	55402914	55402923	+	1	NA	exon (NM_011392, exon 7 of 13)	exon (NM_011392, exon 7 of 13)	3270	NM_011392	20505	Mm.276355	NM_011392	ENSMUSG00000021490	Slc34a1	NaPi-IIa|Npt2|Npt2a|Slc17a2	solute carrier family 34 (sodium phosphate), member 1	protein-coding
mm_132642.1	chr16	40119974	40119977	+	1	NA	Intergenic	Intergenic	1217630	NM_170599	207683	Mm.245564	NM_170599	ENSMUSG00000022790	Igsf11	1700025L02Rik|BT-IgSF|Igsf13	immunoglobulin superfamily, member 11	protein-coding
mm_82308.1	chr9	7872776	7872788	-	1	NA	intron (NM_007464, intron 1 of 8)	CpG	388	NM_007464	11796	Mm.2026	NM_007464	ENSMUSG00000032000	Birc3	AW107670|Api1|Api2|Birc2|C-IAP2|HIAP2|IAP1|IAP2|MIAP1|MIAP2|MIHB|MIHC|RNF49|cIAP-1|cIAP-2|cIAP1|cIAP2	baculoviral IAP repeat-containing 3	protein-coding
mm_40447.1	chr5	53591918	53591965	+	1	NA	intron (NM_001080927, intron 1 of 10)	intron (NM_001080927, intron 1 of 10)	1455	NM_001080927	19664	Mm.209292	NM_009035	ENSMUSG00000039191	Rbpj	AI843960|CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBP-Jkappa|RBPjk|Rbpsuh	recombination signal binding protein for immunoglobulin kappa J region	protein-coding
mm_146300.1	chr18	80206888	80206900	+	1	NA	promoter-TSS (NM_025299)	promoter-TSS (NM_025299)	27	NM_001042408	27366	Mm.172411	NM_025299	ENSMUSG00000057130	Txnl4a	D18Wsu98e|Dim1|ENSMUSG00000057130|Txnl4|U5-15kD|U5-15kDa	thioredoxin-like 4A	protein-coding
mm_92852.1	chr10	81524301	81524317	-	1	NA	promoter-TSS (NM_010304)	promoter-TSS (NM_010304)	-84	NM_010304	14676	Mm.1546	NM_010304	ENSMUSG00000034792	Gna15	G[a]15|Galpha15	guanine nucleotide binding protein, alpha 15	protein-coding
mm_11740.1	chr2	38003484	38003484	+	1	NA	intron (NM_146122, intron 9 of 21)	intron (NM_146122, intron 9 of 21)	227235	NM_001163566	241324	Mm.392369	NM_001163566	ENSMUSG00000035403	Crb2	5930402A21|BC043114	crumbs family member 2	protein-coding
mm_3183.1	chr1	135766238	135766240	+	1	NA	5' UTR (NM_013750, exon 1 of 2)	5' UTR (NM_013750, exon 1 of 2)	154	NM_013750	27280	Mm.34346	NM_013750	ENSMUSG00000041801	Phlda3	Tih1	pleckstrin homology like domain, family A, member 3	protein-coding
mm_112721.1	chr13	19192191	19192197	+	1	NA	Intergenic	Intergenic	203619	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_67536.1	chr7	81372421	81372458	-	1	NA	intron (NM_001252525, intron 2 of 11)	intron (NM_001252525, intron 2 of 11)	-27205	NM_009092	20068	Mm.42767	NM_009092	ENSMUSG00000061787	Rps17	-	ribosomal protein S17	protein-coding
mm_13934.1	chr2	121016399	121016423	+	1	NA	exon (NM_010761, exon 11 of 11)	exon (NM_010761, exon 11 of 11)	8003	NM_010761	17151	Mm.7838	NM_010761	ENSMUSG00000023572	Ccndbp1	AU022347|DIP1|GCIP|Maid|SECC-8|SSEC-8	cyclin D-type binding-protein 1	protein-coding
mm_74985.1	chr8	27142315	27142325	-	1	NA	promoter-TSS (NR_045840)	promoter-TSS (NR_045840)	-590	NR_045840	71082	Mm.395259	NR_045840		4933416M07Rik	-	RIKEN cDNA 4933416M07 gene	ncRNA
mm_88224.1	chr10	70378697	70378710	+	1	NA	Intergenic	Intergenic	-61965	NM_001143777	71721	Mm.477813	NM_024244	ENSMUSG00000043259	Fam13c	1200015N20Rik|C030038O19Rik|mKIAA1796	family with sequence similarity 13, member C	protein-coding
mm_48511.1	chr5	142821807	142821823	-	1	NA	Intergenic	Intergenic	-4428	NM_001122730	231861	Mm.354649	NM_178242	ENSMUSG00000039477	Tnrc18	BC025631|EG381742|Zfp469	trinucleotide repeat containing 18	protein-coding
mm_29078.1	chr3	103968279	103968321	-	1	NA	promoter-TSS (NR_030676)	promoter-TSS (NR_030676)	16	NR_030676	100125931	Mm.400392	NR_030676	ENSMUSG00000089998	Phtf1os	A130049A11Rik	putative homeodomain transcription factor 1, opposite strand	ncRNA
mm_142879.1	chr17	51826536	51826551	-	1	NA	promoter-TSS (NM_001163631)	promoter-TSS (NM_001163631)	45	NM_001163631	20230	Mm.311655	NM_009122	ENSMUSG00000023927	Satb1	2610306G12Rik|AW413156	special AT-rich sequence binding protein 1	protein-coding
mm_167164.1	chr7	135716400	135716405	-	1	NA	promoter-TSS (NM_001081117)	promoter-TSS (NM_001081117)	-23	NM_001081117	17345	Mm.4078	NM_001081117	ENSMUSG00000031004	Mki67	D630048A14Rik|Ki-67|Ki67	antigen identified by monoclonal antibody Ki 67	protein-coding
mm_115262.1	chr13	110542063	110542066	+	1	NA	Intergenic	Intergenic	147020	NM_152804	20620	Mm.380	NM_152804	ENSMUSG00000021701	Plk2	Snk	polo-like kinase 2	protein-coding
mm_115592.1	chr13	11827138	11827155	-	1	NA	intron (NM_023868, intron 15 of 104)	intron (NM_023868, intron 15 of 104)	279799	NM_023868	20191	Mm.239871	NM_023868	ENSMUSG00000021313	Ryr2	9330127I20Rik|RYR-2	ryanodine receptor 2, cardiac	protein-coding
mm_75472.1	chr8	48070735	48070735	-	1	NA	Intergenic	Intergenic	-28357	NM_001161516	320685	Mm.121549	NM_178788	ENSMUSG00000031562	Dctd	6030466N05Rik	dCMP deaminase	protein-coding
mm_150578.1	chr19	40638852	40638854	+	1	NA	intron (NM_001304721, intron 1 of 9)	intron (NM_001304721, intron 1 of 9)	-20917	NM_009848	12495	Mm.2824	NM_009848	ENSMUSG00000048120	Entpd1	2610206B08Rik|AA408691|Cd39|NTPDase-1	ectonucleoside triphosphate diphosphohydrolase 1	protein-coding
mm_9168.1	chr1	170976024	170976038	-	1	NA	promoter-TSS (NM_001077189)	promoter-TSS (NM_001077189)	40	NM_001077189	14130	Mm.425062	NM_010187	ENSMUSG00000026656	Fcgr2b	AI528646|CD32|F630109E10Rik|Fc[g]RII|FcgRII|Fcgr2|Fcgr2a|Fcr-2|Fcr-3|Ly-17|Ly-m20|LyM-1|Lym-1|fcRII	Fc receptor, IgG, low affinity IIb	protein-coding
mm_151638.1	chr19	4012657	4012736	-	1	NA	promoter-TSS (NM_133666)	promoter-TSS (NM_133666)	59	NM_133666	17995	Mm.29842	NM_133666	ENSMUSG00000037916	Ndufv1	CI-51kD	NADH dehydrogenase (ubiquinone) flavoprotein 1	protein-coding
mm_11275.1	chr2	30061950	30061965	+	1	NA	promoter-TSS (NM_023871)	promoter-TSS (NM_023871)	-39	NM_023871	56086	Mm.326055	NM_023871	ENSMUSG00000054766	Set	2610030F17Rik|5730420M11Rik|AA407739|I-2PP2A|StF-IT-1|TAF-I	SET nuclear oncogene	protein-coding
mm_160691.1	chr10	24049390	24049390	+	1	NA	promoter-TSS (NM_001010839)	promoter-TSS (NM_001010839)	-120	NM_001010839	435207	Mm.377966	NM_001010839	ENSMUSG00000100950	Taar7f	taR-7f	trace amine-associated receptor 7F	protein-coding
mm_21223.1	chr2	155826648	155826710	-	1	NA	5' UTR (NM_010579, exon 1 of 6)	5' UTR (NM_010579, exon 1 of 6)	246	NM_010579	16418	Mm.271674	NM_010579	ENSMUSG00000027613	Eif6	1110004P11|AA408895|CAB|Itgb4bp|eIF-6|imc-415|p27(BBP)|p27BBP	eukaryotic translation initiation factor 6	protein-coding
mm_13419.1	chr2	104413966	104413969	+	1	NA	Intergenic	Intergenic	-3633	NM_001033347	241589	Mm.358909	NM_001033347	ENSMUSG00000068373	D430041D05Rik	9630056G07Rik|G2	RIKEN cDNA D430041D05 gene	protein-coding
mm_69988.1	chr7	142380983	142380996	-	1	NA	exon (NM_009983, exon 5 of 9)	exon (NM_009983, exon 5 of 9)	6881	NM_009983	13033	Mm.231395	NM_009983	ENSMUSG00000007891	Ctsd	CD|CatD	cathepsin D	protein-coding
mm_3569.1	chr1	150448846	150448851	+	1	NA	TTS (NM_021400)	TTS (NM_021400)	17317	NM_021400	96875	Mm.174256	NM_021400	ENSMUSG00000006014	Prg4	CACP|DOL54|JCAP|MSF|SZP|lubricin	proteoglycan 4 (megakaryocyte stimulating factor, articular superficial zone protein)	protein-coding
mm_135141.1	chr16	35854570	35854581	-	1	NA	intron (NM_001039530, intron 6 of 16)	intron (NM_001039530, intron 6 of 16)	16807	NM_001039530	547253	Mm.244406	NM_001039530	ENSMUSG00000034422	Parp14	1600029O10Rik|ARTD8|BC021340|CoaSt6|mKIAA1268	poly (ADP-ribose) polymerase family, member 14	protein-coding
mm_41355.1	chr5	90504967	90505036	+	1	NA	exon (NM_007423, exon 11 of 15)	exon (NM_007423, exon 11 of 15)	-13948	NM_145146	280662	Mm.348786	NM_145146	ENSMUSG00000029369	Afm	Alf|alpha-Alb	afamin	protein-coding
mm_33498.1	chr4	130823873	130823881	+	1	NA	3' UTR (NM_011520, exon 5 of 5)	3' UTR (NM_011520, exon 5 of 5)	31340	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_69235.1	chr7	127708739	127708791	-	1	NA	promoter-TSS (NM_009746)	promoter-TSS (NM_009746)	1	NM_009746	12055	Mm.89667	NM_009746	ENSMUSG00000030814	Bcl7c	C230096E12Rik	B cell CLL/lymphoma 7C	protein-coding
mm_153602.1	chr19	43890556	43890566	-	1	NA	intron (NM_028029, intron 4 of 15)	intron (NM_028029, intron 4 of 15)	-10793	NM_001306088	71972	Mm.159024	NM_028029	ENSMUSG00000025195	Dnmbp	2410003L07Rik|2410003M15Rik|TUBA	dynamin binding protein	protein-coding
mm_85625.1	chr9	107615091	107615101	-	1	NA	3' UTR (NM_008138, exon 9 of 9)	3' UTR (NM_008138, exon 9 of 9)	-5855	NM_001291539	20347	Mm.4083	NM_009153	ENSMUSG00000057969	Sema3b	SemA|Semaa|sema5|semaV	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B	protein-coding
mm_159473.1	chr4	21847578	21847578	+	1	NA	promoter-TSS (NM_025669)	promoter-TSS (NM_025669)	-5	NM_025669	66625	Mm.100117	NM_025669	ENSMUSG00000028248	Pnisr	5730406M06Rik|AA673174|Pinsr|Sfrs18|Srsf18	PNN interacting serine/arginine-rich	protein-coding
mm_81754.1	chr9	113956683	113956687	+	1	NA	intron (NM_013699, intron 5 of 15)	intron (NM_013699, intron 5 of 15)	25751	NM_013699	22221	Mm.28052	NM_013699	ENSMUSG00000009741	Ubp1	Cp2b|LBP-1a|LBP-1b|NF2d9	upstream binding protein 1	protein-coding
mm_69482.1	chr7	133776773	133776811	-	1	NA	promoter-TSS (NM_025850)	promoter-TSS (NM_025850)	11	NM_001286032	101437	Mm.199223	NM_133941	ENSMUSG00000030986	Dhx32	3110079L04Rik|4732469F02Rik|AA408140|Ddx32	DEAH (Asp-Glu-Ala-His) box polypeptide 32	protein-coding
mm_33373.1	chr4	129515497	129515508	+	1	NA	TTS (NM_008228)	TTS (NM_008228)	1921	NM_010807	17357	Mm.424974	NM_010807	ENSMUSG00000047945	Marcksl1	AL022768|AW215397|AW536807|D4Bc1|F52|MacMARCKS|Macs2|Macs3|Mlp|Mrp	MARCKS-like 1	protein-coding
mm_9385.1	chr1	172213165	172213178	-	1	NA	intron (NM_009813, intron 8 of 10)	intron (NM_009813, intron 8 of 10)	-6367	NM_011063	18611	Mm.544	NM_011063	ENSMUSG00000013698	Pea15a	Mat1|PEA-15|Pea15|Pkcs15	phosphoprotein enriched in astrocytes 15A	protein-coding
mm_150237.1	chr19	34067347	34067362	+	1	NA	promoter-TSS (NM_027340)	promoter-TSS (NM_027340)	-4	NM_027340	70166	Mm.75602	NM_027340	ENSMUSG00000024770	Lipn	2210418G03Rik|Lipl4	lipase, family member N	protein-coding
mm_13542.1	chr2	110731551	110731561	+	1	NA	exon (NM_001290786, exon 2 of 4)	exon (NM_001290786, exon 2 of 4)	10062	NM_172979	269328	Mm.32566	NM_172979	ENSMUSG00000050808	Muc15	4732460E09|D730046L02Rik|MUC-15	mucin 15	protein-coding
mm_144914.1	chr18	37477806	37477835	+	1	NA	promoter-TSS (NM_053141)	promoter-TSS (NM_053141)	52	NM_053141	93887	Mm.197441	NM_053141	ENSMUSG00000047910	Pcdhb16	Pcdhb8|PcdhbP	protocadherin beta 16	protein-coding
mm_16076.1	chr2	168231196	168231217	+	1	NA	promoter-TSS (NM_010072)	promoter-TSS (NM_010072)	584	NM_001160330	69372	Mm.482182	NM_001160330	ENSMUSG00000074576	Mocs3	1700020H17Rik|Uba4	molybdenum cofactor synthesis 3	protein-coding
mm_168487.1	chr1	149506412	149506418	-	1	NA	Intergenic	IAPLTR1_Mm|LTR|ERVK	416024	NM_001305632	18783	Mm.4186	NM_008869	ENSMUSG00000056220	Pla2g4a	Pla2g4|cPLA2|cPLA2-alpha|cPLA2alpha	phospholipase A2, group IVA (cytosolic, calcium-dependent)	protein-coding
mm_25173.1	chr3	103127391	103127406	+	1	NA	promoter-TSS (NM_177857)	promoter-TSS (NM_177857)	-158	NM_177857	329727	Mm.293641	NM_177857	ENSMUSG00000007379	Dennd2c	A930010I20Rik	DENN/MADD domain containing 2C	protein-coding
mm_22163.1	chr2	172940562	172940617	-	1	NA	promoter-TSS (NM_007557)	promoter-TSS (NM_007557)	-268	NM_007557	12162	Mm.595	NM_007557	ENSMUSG00000008999	Bmp7	OP1	bone morphogenetic protein 7	protein-coding
mm_26027.1	chr3	135439102	135439174	+	1	NA	promoter-TSS (NR_030689)	promoter-TSS (NR_030689)	379	NM_025356	66105	Mm.49884	NM_025356	ENSMUSG00000078578	Ube2d3	1100001F19Rik|9430029A22Rik|AA414951	ubiquitin-conjugating enzyme E2D 3	protein-coding
mm_57772.1	chr6	129237173	129237179	-	1	NA	intron (NR_040265, intron 1 of 2)	ORR1E|LTR|ERVL-MaLR	869	NR_040265	76432	Mm.261738	NR_040265	ENSMUSG00000097354	2310001H17Rik	AI646108	RIKEN cDNA 2310001H17 gene	ncRNA
mm_78682.1	chr9	40785070	40785108	+	1	NA	Intergenic	Intergenic	-16184	NM_031165	15481	Mm.290774	NM_031165	ENSMUSG00000015656	Hspa8	2410008N15Rik|Hsc70|Hsc71|Hsc73|Hsp73|Hspa10	heat shock protein 8	protein-coding
mm_69218.1	chr7	127588120	127588142	-	1	NA	promoter-TSS (NM_172281)	promoter-TSS (NM_172281)	464	NM_001033040	233899	Mm.25220	NM_001033040	ENSMUSG00000057176	Ccdc189	Gm166	coiled-coil domain containing 189	protein-coding
mm_24478.1	chr3	90725888	90725909	+	1	NA	Intergenic	Intergenic	-1008	NM_001165968	384997	Mm.316644	NM_207263	ENSMUSG00000042250	Pglyrp4	Gm1478|Gm413	peptidoglycan recognition protein 4	protein-coding
mm_95643.1	chr11	53720791	53720795	+	1	NA	promoter-TSS (NM_010558)	promoter-TSS (NM_010558)	-1	NM_010558	16191	Mm.4461	NM_010558	ENSMUSG00000036117	Il5	Il-5	interleukin 5	protein-coding
mm_143455.1	chr17	70987068	70987072	-	1	NA	intron (NM_023402, intron 1 of 3)	intron (NM_023402, intron 1 of 3)	3446	NM_023402	67938	Mm.261329	NM_023402	ENSMUSG00000034868	Myl12b	1500001M02Rik|C77744|Mylc2b|RLC-B	myosin, light chain 12B, regulatory	protein-coding
mm_102847.1	chr11	69369378	69369415	-	1	NA	promoter-TSS (NM_146019)	promoter-TSS (NM_146019)	30	NM_146019	216848	Mm.178246	NM_146019	ENSMUSG00000018474	Chd3	2600010P09Rik|AF020312|Chd7|Prp7|Prp9-1	chromodomain helicase DNA binding protein 3	protein-coding
mm_75449.1	chr8	47675131	47675165	-	1	NA	promoter-TSS (NM_023503)	promoter-TSS (NM_023503)	11	NM_023503	69260	Mm.430733	NM_023503	ENSMUSG00000063049	Ing2	2810011M06Rik|Ing1l|Ing2b|P33ING2	inhibitor of growth family, member 2	protein-coding
mm_78082.1	chr9	15730922	15730974	+	1	NA	intron (NM_172289, intron 8 of 10)	intron (NM_172289, intron 8 of 10)	21179	NM_172289	234967	Mm.138815	NM_172289	ENSMUSG00000043885	Slc36a4	6330573I15Rik|PAT4	solute carrier family 36 (proton/amino acid symporter), member 4	protein-coding
mm_116877.1	chr13	55021487	55021493	-	1	NA	promoter-TSS (NM_001206391)	promoter-TSS (NM_001206391)	-105	NM_001033245	212032	Mm.267479	NM_001033245	ENSMUSG00000025877	Hk3	HK III|HK-III	hexokinase 3	protein-coding
mm_58544.1	chr7	4526549	4526563	+	1	NA	intron (NM_001033548, intron 8 of 11)	intron (NM_001033548, intron 8 of 11)	-4113	NM_009406	21954	Mm.27674	NM_009406	ENSMUSG00000035458	Tnni3	Tn1|cTnI	troponin I, cardiac 3	protein-coding
mm_123457.1	chr14	65425454	65425466	-	1	NA	promoter-TSS (NM_010932)	promoter-TSS (NM_010932)	12	NM_001205075	18155	Mm.16347	NM_010932	ENSMUSG00000045731	Pnoc	N/OFQ|Npnc1|OFQ/N	prepronociceptin	protein-coding
mm_22790.1	chr3	22154669	22154682	+	1	NA	intron (NM_030732, intron 2 of 15)	intron (NM_030732, intron 2 of 15)	78023	NM_030732	81004	Mm.202966	NM_030732	ENSMUSG00000027630	Tbl1xr1	8030499H02Rik|A630076E03Rik|AW539987|C21|C230089I12Rik|DC42|Ira1|TBLR1	transducin (beta)-like 1X-linked receptor 1	protein-coding
mm_107718.1	chr12	56253251	56253261	+	1	NA	promoter-TSS (NR_045048)	promoter-TSS (NR_045048)	13	NR_045048	100503961	Mm.136732	NR_045048		Gm19990	-	predicted gene, 19990	ncRNA
mm_73741.1	chr8	114151679	114151694	+	1	NA	exon (NM_024446, exon 4 of 4)	exon (NM_024446, exon 4 of 4)	18112	NM_024437	67528	Mm.27889	NM_024437	ENSMUSG00000031767	Nudt7	1300007B24Rik|2210404C19Rik	nudix (nucleoside diphosphate linked moiety X)-type motif 7	protein-coding
mm_53794.1	chr6	146724958	146724998	+	1	NA	promoter-TSS (NM_172734)	promoter-TSS (NM_172734)	48	NM_172734	232533	Mm.322121	NM_172734	ENSMUSG00000001630	Stk38l	4930473A22Rik|Ndr2|Ndr54	serine/threonine kinase 38 like	protein-coding
mm_18100.1	chr2	44988000	44988004	-	1	NA	3' UTR (NM_015753, exon 10 of 10)	3' UTR (NM_015753, exon 10 of 10)	35175	NR_039591	100628598		NR_039591	ENSMUSG00000092679	Mir5129	mir-5129|mmu-mir-5129|mu-mir-5129	microRNA 5129	ncRNA
mm_56802.1	chr6	116657146	116657187	-	1	NA	intron (NM_178045, intron 3 of 10)	(TG)n|Simple_repeat|Simple_repeat	6482	NM_001166580	213393	Mm.38231	NM_145980	ENSMUSG00000048489	8430408G22Rik	Depp|Fseg	RIKEN cDNA 8430408G22 gene	protein-coding
mm_153082.1	chr19	32388006	32388019	-	1	NA	intron (NM_144792, intron 1 of 9)	CpG	442	NM_144792	208449	Mm.329810	NM_144792	ENSMUSG00000040451	Sgms1	9530058O11Rik|AI841905|C80702|Mob|Sms1|Sor1|Tmem23	sphingomyelin synthase 1	protein-coding
mm_48789.1	chr5	148652643	148652690	-	1	NA	Intergenic	Intergenic	-89174	NR_028285	70138	Mm.417834	NR_028285	ENSMUSG00000086494	2210417A02Rik	AV081004	RIKEN cDNA 2210417A02 gene	ncRNA
mm_63158.1	chr7	123422370	123422374	+	1	NA	intron (NM_025304, intron 8 of 10)	B1F|SINE|Alu	-39922	NM_007474	11833	Mm.273175	NM_007474	ENSMUSG00000030762	Aqp8	AI255744|AQP-8	aquaporin 8	protein-coding
mm_124569.1	chr14	124192530	124192560	-	1	NA	promoter-TSS (NM_010201)	promoter-TSS (NM_010201)	1	NM_010201	14169	Mm.206362	NM_010201	ENSMUSG00000025551	Fgf14	FHF-4|Fhf4|mFHF-4(1B)	fibroblast growth factor 14	protein-coding
mm_50247.1	chr6	42357322	42357336	+	1	NA	exon (NM_001289618, exon 8 of 10)	exon (NM_001289618, exon 8 of 10)	7501	NM_001289619	22793	Mm.282303	NM_011777	ENSMUSG00000029860	Zyx	9530098H06Rik|R75157	zyxin	protein-coding
mm_147487.1	chr18	47321614	47321618	-	1	NA	intron (NM_001311097, intron 1 of 17)	intron (NM_001311097, intron 1 of 17)	47252	NM_018744	20358	Mm.40909	NM_018744	ENSMUSG00000019647	Sema6a	A730020P05Rik|AI851735|Sema6A-1|Semaq|VIa	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A	protein-coding
mm_90619.1	chr10	128411731	128411757	+	1	NA	non-coding (NR_104290, exon 1 of 8)	non-coding (NR_104290, exon 1 of 8)	128	NM_026259	67588	Mm.294120	NM_026259	ENSMUSG00000025373	Rnf41	2210404G21Rik|4930511A05Rik|4933415P08Rik|D10Ertd722e|FLRF|Nrdp1	ring finger protein 41	protein-coding
mm_1176.1	chr1	61075638	61075639	+	1	NA	Intergenic	Intergenic	97724	NM_017480	54167	Mm.42044	NM_017480	ENSMUSG00000026009	Icos	AILIM|CCLP|CRP-1|H4|Ly115	inducible T cell co-stimulator	protein-coding
mm_81759.1	chr9	113976288	113976314	+	1	NA	TTS (NM_178624)	TTS (NM_178624)	17499	NR_039590	100628597		NR_039590	ENSMUSG00000092958	Mir5128	mir-5128|mmu-mir-5128|mu-mir-5128	microRNA 5128	ncRNA
mm_100357.1	chr11	118449839	118449847	+	1	NA	3' UTR (NM_019959, exon 4 of 4)	3' UTR (NM_019959, exon 4 of 4)	5152	NR_045902	100126224	Mm.441989	NR_045902	ENSMUSG00000086514	Gm11747	OTTMUSG00000003972	predicted gene 11747	ncRNA
mm_39829.1	chr5	30814723	30814776	+	1	NA	5' UTR (NM_133350, exon 1 of 7)	5' UTR (NM_133350, exon 1 of 7)	108	NM_133350	100732	Mm.332295	NM_133350	ENSMUSG00000029166	Mapre3	AI790651|EB2|EB3|EBF3|RP3	microtubule-associated protein, RP/EB family, member 3	protein-coding
mm_129536.1	chr15	79328202	79328261	-	1	NA	5' UTR (NM_001199024, exon 1 of 16)	5' UTR (NM_001199024, exon 1 of 16)	140	NM_016915	53357	Mm.155620	NM_016915	ENSMUSG00000042632	Pla2g6	BB112799|PNPLA9|iPLA(2)beta|iPLA2|iPLA2beta	phospholipase A2, group VI	protein-coding
mm_151548.1	chr19	59458122	59458133	+	1	NA	promoter-TSS (NM_010132)	promoter-TSS (NM_010132)	508	NR_002863	329078	Mm.80382	NR_002863	ENSMUSG00000087095	Emx2os	-	Emx2 opposite strand/antisense transcript (non-protein coding)	ncRNA
mm_101222.1	chr11	20200806	20200809	-	1	NA	promoter-TSS (NM_008996)	promoter-TSS (NM_008996)	-795	NM_008996	19324	Mm.271944	NM_008996	ENSMUSG00000020149	Rab1a	Gtbp|Rab-1|Rab1|Ypt1|mKIAA3012	RAB1A, member RAS oncogene family	protein-coding
mm_57492.1	chr6	125308769	125308782	-	1	NA	intron (NM_010736, intron 8 of 9)	B1F|SINE|Alu	5095	NM_010736	17000	Mm.3122	NM_010736	ENSMUSG00000030339	Ltbr	AI256028|CD18|LTbetaR|Ltar|TNF-R-III|TNFCR|TNFR-RP|TNFR2-RP|TNFRrp|Tnfbr|Tnfrsf3	lymphotoxin B receptor	protein-coding
mm_8890.1	chr1	162898318	162898328	-	1	NA	intron (NM_018881, intron 1 of 8)	intron (NM_018881, intron 1 of 8)	389	NM_018881	55990	Mm.10929	NM_018881	ENSMUSG00000040170	Fmo2	2310008D08Rik|2310042I22Rik|AW107733	flavin containing monooxygenase 2	protein-coding
mm_59111.1	chr7	19816614	19816631	+	1	NA	intron (NM_033601, intron 2 of 8)	intron (NM_033601, intron 2 of 8)	6133	NM_033601	12051	Mm.439658	NM_033601	ENSMUSG00000053175	Bcl3	AI528691|Bcl-3	B cell leukemia/lymphoma 3	protein-coding
mm_146315.1	chr18	80470119	80470134	+	1	NA	promoter-TSS (NM_026295)	promoter-TSS (NM_026295)	-459	NM_026295	67655	Mm.312893	NM_026295	ENSMUSG00000033323	Ctdp1	4930563P03Rik|AW553592	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) phosphatase, subunit 1	protein-coding
mm_64907.1	chr7	16048054	16048082	-	1	NA	Intergenic	GC_rich|Low_complexity|Low_complexity	-23777	NM_001347559	666528	Mm.290718	NM_001099277	ENSMUSG00000078796	Zfp541	EG666528|Znf541	zinc finger protein 541	protein-coding
mm_106051.1	chr11	116080664	116080675	-	1	NA	exon (NM_016852, exon 5 of 8)	exon (NM_016852, exon 5 of 8)	-2708	NM_001009573	70450	Mm.259460	NM_001009573	ENSMUSG00000057948	Unc13d	2610108D09Rik|Jinx|Munc13-4|mFLJ00067	unc-13 homolog D (C. elegans)	protein-coding
mm_16875.1	chr2	12419388	12419399	-	1	NA	promoter-TSS (NM_024185)	promoter-TSS (NM_024185)	67	NM_024185	66960	Mm.34059	NM_024185	ENSMUSG00000026767	Fam188a	1810041E18Rik|2310047O13Rik|5830410F13Rik|AI447827|AW111958	family with sequence similarity 188, member A	protein-coding
mm_114235.1	chr13	56609514	56609515	+	1	NA	promoter-TSS (NM_009369)	promoter-TSS (NM_009369)	-89	NM_009369	21810	Mm.14455	NM_009369	ENSMUSG00000035493	Tgfbi	68kDa|AI181842|AI747162|Beta-ig|big-h3	transforming growth factor, beta induced	protein-coding
mm_95135.1	chr11	34827207	34827215	+	1	NA	intron (NM_027411, intron 2 of 11)	intron (NM_027411, intron 2 of 11)	6430	NM_027411	70385	Mm.194368	NM_027411	ENSMUSG00000069910	Spdl1	1700018I02Rik|2600001J17Rik|2810049B11Rik|AA409762|Ccdc99	spindle apparatus coiled-coil protein 1	protein-coding
mm_16673.1	chr2	6783764	6783795	-	1	NA	intron (NM_001110229, intron 2 of 14)	intron (NM_001110229, intron 2 of 14)	-62117	NM_001310447	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding
mm_58679.1	chr7	12479155	12479159	+	1	NA	intron (NM_001039951, intron 1 of 3)	intron (NM_001039951, intron 1 of 3)	852	NM_026112	67370	Mm.98929	NM_026112	ENSMUSG00000030386	Zfp606	2410022M24Rik|AW494727	zinc finger protein 606	protein-coding
mm_59926.1	chr7	30423306	30423314	+	1	NA	promoter-TSS (NM_172142)	promoter-TSS (NM_172142)	6	NM_172142	243910	Mm.386878	NM_172142	ENSMUSG00000036931	Nfkbid	IkappaBNS	nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta	protein-coding
mm_112202.1	chr12	113426784	113426794	-	1	NA	Intergenic	Intergenic	-62776	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_61313.1	chr7	68081140	68081144	+	1	NA	intron (NM_010513, intron 2 of 20)	intron (NM_010513, intron 2 of 20)	128885	NM_010513	16001	Mm.275742	NM_010513	ENSMUSG00000005533	Igf1r	A330103N21Rik|CD221|D930020L01|IGF-1R|hyft	insulin-like growth factor I receptor	protein-coding
mm_78971.1	chr9	45328495	45328508	+	1	NA	exon (NM_001013373, exon 2 of 13)	exon (NM_001013373, exon 2 of 13)	-6422	NR_040720	72229	Mm.234192	NR_040720	ENSMUSG00000085831	1700003G13Rik	-	RIKEN cDNA 1700003G13 gene	ncRNA
mm_28640.1	chr3	95219902	95219917	-	1	NA	3' UTR (NM_019914, exon 2 of 2)	3' UTR (NM_019914, exon 2 of 2)	-1967	NM_029885	213054	Mm.224820	NM_029885	ENSMUSG00000038766	Gabpb2	1810015F01Rik|5830427M07|9430006E19Rik|A430024B14Rik|AV050852|Gabpb2-1	GA repeat binding protein, beta 2	protein-coding
mm_541.1	chr1	38017849	38017862	+	1	NA	exon (NM_198303, exon 2 of 24)	exon (NM_198303, exon 2 of 24)	19845	NM_198303	226982	Mm.260943	NM_198303	ENSMUSG00000026083	Eif5b	A030003E17Rik|BC018347|IF2	eukaryotic translation initiation factor 5B	protein-coding
mm_67102.1	chr7	69909596	69909596	-	1	NA	Intergenic	Intergenic	413502	NR_045940	73796	Mm.410832	NR_045940	ENSMUSG00000108885	4930402F11Rik	-	RIKEN cDNA 4930402F11 gene	ncRNA
mm_51958.1	chr6	91756984	91756994	+	1	NA	3' UTR (NM_009320, exon 15 of 15)	3' UTR (NM_009320, exon 15 of 15)	50404	NM_001159507	243547	Mm.333264	NM_001033353	ENSMUSG00000030098	Grip2	-	glutamate receptor interacting protein 2	protein-coding
mm_73330.1	chr8	105297664	105297742	+	1	NA	promoter-TSS (NM_148952)	promoter-TSS (NM_148952)	40	NM_148952	104394	Mm.34554	NM_148952	ENSMUSG00000014859	E2f4	2010111M04Rik|AI427446	E2F transcription factor 4	protein-coding
mm_9730.1	chr1	180199588	180199606	-	1	NA	Intergenic	L2a|LINE|L2	-3577	NM_023341	67426	Mm.38330	NM_023341	ENSMUSG00000026489	Coq8a	4632432J16Rik|AI462003|Adck3|Cabc1|mKIAA0451	coenzyme Q8A	protein-coding
mm_73752.1	chr8	114772957	114772958	+	1	NA	intron (NM_019573, intron 8 of 8)	intron (NM_019573, intron 8 of 8)	333305	NM_019573	80707	Mm.440420	NM_019573	ENSMUSG00000004637	Wwox	5330426P09Rik|9030416C10Rik|WOX1	WW domain-containing oxidoreductase	protein-coding
mm_89465.1	chr10	93453383	93453397	+	1	NA	promoter-TSS (NM_008517)	promoter-TSS (NM_008517)	-6	NM_001313897	16993	Mm.271071	NM_008517	ENSMUSG00000015889	Lta4h	-	leukotriene A4 hydrolase	protein-coding
mm_153507.1	chr19	41363842	41363852	-	1	NA	intron (NM_031376, intron 2 of 16)	intron (NM_031376, intron 2 of 16)	21223	NM_031376	83490	Mm.222266	NM_031376	ENSMUSG00000025017	Pik3ap1	1810044J04Rik|BCAP	phosphoinositide-3-kinase adaptor protein 1	protein-coding
mm_42540.1	chr5	115945309	115945341	+	1	NA	intron (NM_007708, intron 18 of 46)	intron (NM_007708, intron 18 of 46)	79103	NM_031869	19079	Mm.458152	NM_031869	ENSMUSG00000029513	Prkab1	1300015D22Rik|AU021155|E430008F22	protein kinase, AMP-activated, beta 1 non-catalytic subunit	protein-coding
mm_143661.1	chr17	79714982	79714990	-	1	NA	promoter-TSS (NM_009994)	promoter-TSS (NM_009994)	55	NM_009994	13078	Mm.214016	NM_009994	ENSMUSG00000024087	Cyp1b1	CP1B|P4501b1	cytochrome P450, family 1, subfamily b, polypeptide 1	protein-coding
mm_110506.1	chr12	54695277	54695283	-	1	NA	intron (NM_025456, intron 1 of 5)	intron (NM_025456, intron 1 of 5)	614	NM_001331162	66266	Mm.156440	NM_025456	ENSMUSG00000054302	Eapp	1810011O16Rik	E2F-associated phosphoprotein	protein-coding
mm_43875.1	chr5	143651223	143651246	+	1	NA	promoter-TSS (NM_001163548)	promoter-TSS (NM_001163548)	-7	NM_001163548	19159	Mm.281003	NM_011182	ENSMUSG00000018001	Cyth3	AI648983|ARNO3|CLM3|Grp1|Pscd3	cytohesin 3	protein-coding
mm_51922.1	chr6	91265931	91265937	+	1	NA	intron (NM_007992, intron 12 of 17)	intron (NM_007992, intron 12 of 17)	53170	NM_007992	14115	Mm.249146	NM_007992	ENSMUSG00000064080	Fbln2	5730577E14Rik|FIBL-2	fibulin 2	protein-coding
mm_169388.1	chr14	42478624	42478638	+	1	NA	Intergenic	BGLII|LTR|ERVK	-218583	NR_105055	101056136	Mm.489000	NR_105055	ENSMUSG00000092152	Gm17026	-	predicted gene 17026	ncRNA
mm_74314.1	chr8	126596217	126596221	+	1	NA	Intergenic	Intergenic	-2783	NM_001164598	270110	Mm.334918	NM_001164598	ENSMUSG00000051495	Irf2bp2	E130305N23Rik|IRF-2BP2	interferon regulatory factor 2 binding protein 2	protein-coding
mm_108270.1	chr12	78802889	78802911	+	1	NA	intron (NM_019579, intron 3 of 14)	intron (NM_019579, intron 3 of 14)	53953	NM_019579	56217	Mm.425777	NM_019579	ENSMUSG00000021112	Mpp5	3830420B02Rik|AI255216|AI644496|Pals1	membrane protein, palmitoylated 5 (MAGUK p55 subfamily member 5)	protein-coding
mm_48193.1	chr5	137529877	137529892	-	1	NA	promoter-TSS (NR_105846)	promoter-TSS (NR_105846)	-290	NR_105846	102465227		NR_105846	ENSMUSG00000098597	Mir6418	Gm27629|mir-6418|mmu-mir-6418	microRNA 6418	ncRNA
mm_67498.1	chr7	80769565	80769588	-	1	NA	intron (NM_016721, intron 2 of 37)	RSINE1|SINE|B4	33755	NM_016721	29875	Mm.207619	NM_016721	ENSMUSG00000030536	Iqgap1	AA682088|D7Ertd237e|D7Ertd257e|mKIAA0051	IQ motif containing GTPase activating protein 1	protein-coding
mm_20858.1	chr2	148436075	148436096	-	1	NA	TTS (NM_010740)	TTS (NM_010740)	7450	NM_010740	17064	Mm.681	NM_010740	ENSMUSG00000027435	Cd93	6030404G09Rik|AA145088|AA4.1|AW555904|C1qr1|C1qrp|Ly68	CD93 antigen	protein-coding
mm_171590.1	chr4	147642510	147642510	-	1	NA	promoter-TSS (NM_145078)	promoter-TSS (NM_145078)	-2	NM_145078	112422	Mm.327194	NM_145078	ENSMUSG00000066000	Zfp979	2610305D13Rik|Ssm1b	zinc finger protein 979	protein-coding
mm_145331.1	chr18	56360852	56360862	+	1	NA	Intergenic	ORR1D2|LTR|ERVL-MaLR	-71275	NM_026240	107022	Mm.24356	NM_026240	ENSMUSG00000001700	Gramd3	9030613F08Rik|9130427A09Rik|AW061306|NS3TP2	GRAM domain containing 3	protein-coding
mm_15054.1	chr2	152911312	152911366	+	1	NA	promoter-TSS (NM_001081044)	promoter-TSS (NM_001081044)	-13	NM_001081044	228785	Mm.250604	NM_001081044	ENSMUSG00000027470	Mylk2	9830004H17Rik|BB138278	myosin, light polypeptide kinase 2, skeletal muscle	protein-coding
mm_173316.1	chrY	90736212	90736221	+	1	NA	Intergenic	IMPB_01|Satellite|Satellite	18834	NR_137283	654820	Mm.34441	NM_001039559	ENSMUSG00000072844	G530011O06Rik	-	RIKEN cDNA G530011O06 gene	ncRNA
mm_23772.1	chr3	75557595	75557605	+	1	NA	promoter-TSS (NM_009250)	promoter-TSS (NM_009250)	67	NM_009250	20713	Mm.41560	NM_009250	ENSMUSG00000027834	Serpini1	AI837402|Ns|PI-12|PI12|Spi17	serine (or cysteine) peptidase inhibitor, clade I, member 1	protein-coding
mm_82124.1	chr9	123509181	123509205	+	1	NA	intron (NM_013860, intron 2 of 7)	intron (NM_013860, intron 2 of 7)	-20689	NM_030692	83493	Mm.273671	NM_030692	ENSMUSG00000025240	Sacm1l	SAC1|Sac1p|mKIAA0851	SAC1 suppressor of actin mutations 1-like (yeast)	protein-coding
mm_160574.1	chr9	58202702	58202702	-	1	NA	promoter-TSS (NM_177193)	promoter-TSS (NM_177193)	-168	NM_001161538	320563	Mm.186499	NM_177193	ENSMUSG00000051243	Islr2	B930052A04Rik|Linx|Mbu-3|mKIAA1465	immunoglobulin superfamily containing leucine-rich repeat 2	protein-coding
mm_98390.1	chr11	94213978	94213989	+	1	NA	exon (NM_009427, exon 2 of 2)	exon (NM_009427, exon 2 of 2)	2529	NM_009427	22057	Mm.259673	NM_009427	ENSMUSG00000037573	Tob1	Tob|Trob	transducer of ErbB-2.1	protein-coding
mm_149053.1	chr19	8838772	8838778	+	1	NA	promoter-TSS (NM_008144)	promoter-TSS (NM_008144)	471	NM_010316	14704	Mm.329700	NM_010316	ENSMUSG00000071658	Gng3	-	guanine nucleotide binding protein (G protein), gamma 3	protein-coding
mm_64898.1	chr7	15959553	15959566	-	1	NA	intron (NM_153068, intron 3 of 5)	intron (NM_153068, intron 3 of 5)	7976	NM_153068	259300	Mm.138215	NM_153068	ENSMUSG00000074364	Ehd2	BC027084|C130052H20Rik	EH-domain containing 2	protein-coding
mm_53072.1	chr6	124931427	124931451	+	1	NA	promoter-TSS (NM_001170341)	promoter-TSS (NM_001170341)	51	NM_001170341	30853	Mm.29737	NM_145385	ENSMUSG00000030120	Mlf2	AI256856|AU018944|C77284	myeloid leukemia factor 2	protein-coding
mm_9361.1	chr1	172198334	172198343	-	1	NA	3' UTR (NM_001329871, exon 4 of 4)	3' UTR (NM_001329871, exon 4 of 4)	8466	NM_001329871	18611	Mm.544	NM_011063	ENSMUSG00000013698	Pea15a	Mat1|PEA-15|Pea15|Pkcs15	phosphoprotein enriched in astrocytes 15A	protein-coding
mm_105901.1	chr11	114982982	114982994	-	1	NA	3' UTR (NM_145437, exon 4 of 4)	3' UTR (NM_145437, exon 4 of 4)	6898	NM_145437	217305	Mm.275986	NM_145437	ENSMUSG00000034641	Cd300ld	4732429D16Rik|CLM5|Cd300ld1|LMIR4|MAIR-IV|clm-5	CD300 molecule like family member d	protein-coding
mm_133961.1	chr16	4091878	4091900	-	1	NA	exon (NM_001025432, exon 28 of 31)	exon (NM_001025432, exon 28 of 31)	-14079	NM_026508	68015	Mm.123366	NM_026508	ENSMUSG00000005981	Trap1	2410002K23Rik|HSP75	TNF receptor-associated protein 1	protein-coding
mm_94462.1	chr11	6446175	6446195	+	1	NA	Intergenic	Intergenic	-1742	NM_001347064	77605	Mm.27624	NM_029938	ENSMUSG00000041126	H2afv	C530002L11Rik|H2a.z-2|H2av	H2A histone family, member V	protein-coding
mm_172942.1	chr9	80305804	80305805	+	1	NA	intron (NM_001039546, intron 31 of 32)	intron (NM_001039546, intron 31 of 32)	140770	NM_001039546	17920	Mm.4040	NM_008662	ENSMUSG00000033577	Myo6	BC029719|Tlc|sv	myosin VI	protein-coding
mm_161448.1	chr15	74574124	74574124	+	1	NA	exon (NM_174991, exon 23 of 31)	exon (NM_174991, exon 23 of 31)	57928	NM_174991	107831	Mm.43133	NM_174991	ENSMUSG00000034730	Adgrb1	B830018M07Rik|Bai1|R75078|mKIAA4089	adhesion G protein-coupled receptor B1	protein-coding
mm_18208.1	chr2	48912264	48912277	-	1	NA	intron (NM_011958, intron 10 of 13)	intron (NM_011958, intron 10 of 13)	36997	NM_001177313	26428	Mm.291059	NM_011958	ENSMUSG00000026761	Orc4	Orc4P|Orc4l|mMmORC4	origin recognition complex, subunit 4	protein-coding
mm_151387.1	chr19	56397101	56397157	+	1	NA	promoter-TSS (NM_007611)	promoter-TSS (NM_007611)	0	NM_007611	12369	Mm.35687	NM_007611	ENSMUSG00000025076	Casp7	AI314680|CMH-1|ICE-IAP3|Mch3|caspase-7|mCASP-7	caspase 7	protein-coding
mm_140302.1	chr17	85623920	85623963	+	1	NA	3' UTR (NM_011381, exon 2 of 2)	3' UTR (NM_011381, exon 2 of 2)	3107	NM_011381	20473	Mm.370208	NM_011381	ENSMUSG00000038805	Six3	E130112M24Rik|Six3a|Six3alpha|Six3b|Six3beta	sine oculis-related homeobox 3	protein-coding
mm_134694.1	chr16	22622297	22622310	-	1	NA	5' UTR (NM_138650, exon 2 of 25)	5' UTR (NM_138650, exon 2 of 25)	34928	NM_138650	110197	Mm.194986	NM_138650	ENSMUSG00000022861	Dgkg	2900055E17Rik|90kDa|AI854428|Dagk3|E430001K23Rik|mKIAA4131	diacylglycerol kinase, gamma	protein-coding
mm_38881.1	chr4	149698703	149698711	-	1	NA	promoter-TSS (NM_001164049)	promoter-TSS (NM_001164049)	1	NM_001164050	18707	Mm.229108	NM_008840	ENSMUSG00000039936	Pik3cd	2410099E07Rik|2610208K16Rik|AW545373|p110delta	phosphatidylinositol 3-kinase catalytic delta polypeptide	protein-coding
mm_72634.1	chr8	84676407	84676433	+	1	NA	exon (NM_025788, exon 2 of 6)	exon (NM_025788, exon 2 of 6)	11442	NM_025788	66830	Mm.289698	NM_025788	ENSMUSG00000001910	Nacc1	2010001H03Rik|4930511N13Rik|Btbd14b|Nac1	nucleus accumbens associated 1, BEN and BTB (POZ) domain containing	protein-coding
mm_56385.1	chr6	94665194	94665220	-	1	NA	intron (NM_008377, intron 1 of 18)	intron (NM_008377, intron 1 of 18)	34938	NM_008377	16206	Mm.245210	NM_008377	ENSMUSG00000030029	Lrig1	D6Bwg0781e|Img|LIG-1	leucine-rich repeats and immunoglobulin-like domains 1	protein-coding
mm_106764.1	chr12	4592651	4592673	+	1	NA	promoter-TSS (NM_001198969)	promoter-TSS (NM_001198969)	-346	NM_001198969	20403	Mm.341204	NM_011365	ENSMUSG00000020640	Itsn2	AI327390|Ese2|Sh3d1B|Sh3p18|mKIAA1256	intersectin 2	protein-coding
mm_109.1	chr1	9601312	9601325	+	1	NA	promoter-TSS (NM_178399)	promoter-TSS (NM_178399)	51	NM_178399	76982	Mm.491098	NM_178399	ENSMUSG00000067879	3110035E14Rik	AI415019|AV164974|R75066	RIKEN cDNA 3110035E14 gene	protein-coding
mm_150498.1	chr19	39018735	39018742	+	1	NA	exon (NM_028089, exon 4 of 9)	exon (NM_028089, exon 4 of 9)	11719	NM_028089	72082	Mm.142581	NM_028089	ENSMUSG00000025002	Cyp2c55	2010318C06Rik	cytochrome P450, family 2, subfamily c, polypeptide 55	protein-coding
mm_9424.1	chr1	172377982	172378000	-	1	NA	3' UTR (NM_026234, exon 1 of 1)	3' UTR (NM_026234, exon 1 of 1)	1460	NM_026234	67556	Mm.26612	NM_026234	ENSMUSG00000050229	Pigm	4933437L05Rik|AI644422|AV302080|C920011G20Rik	phosphatidylinositol glycan anchor biosynthesis, class M	protein-coding
mm_140556.1	chr17	7871956	7871961	-	1	NA	Intergenic	Intergenic	-54042	NM_145968	72536	Mm.119680	NM_145968	ENSMUSG00000033450	Tagap	2610315E15Rik	T cell activation Rho GTPase activating protein	protein-coding
mm_88095.1	chr10	68723859	68723865	+	1	NA	5' UTR (NM_177794, exon 1 of 6)	5' UTR (NM_177794, exon 1 of 6)	116	NM_177794	327766	Mm.2479	NM_177794	ENSMUSG00000060044	Tmem26	3230401A06|AI195372	transmembrane protein 26	protein-coding
mm_126124.1	chr15	78329710	78329754	+	1	NA	intron (NM_007780, intron 1 of 13)	intron (NM_007780, intron 1 of 13)	3742	NM_007780	12983	Mm.235324	NM_007780	ENSMUSG00000071713	Csf2rb	AI848964|AIC2B|Bc|CDw131|Csf2rb1|Csfgmrb|Il3r|Il3rb|Il3rb1|Il5rb	colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage)	protein-coding
mm_20771.1	chr2	142901507	142901576	-	1	NA	promoter-TSS (NM_001081133)	promoter-TSS (NM_001081133)	-77	NM_001081133	16558	Mm.251934	NM_001081133	ENSMUSG00000038844	Kif16b	8430434E15Rik|AA623607|AI789011|C80253|C80902|mKIAA1590	kinesin family member 16B	protein-coding
mm_164719.1	chr17	56613499	56613501	+	1	NA	TTS (NM_028782)	TTS (NM_028782)	105	NM_018730	54217	Mm.11376	NM_018730	ENSMUSG00000057863	Rpl36	-	ribosomal protein L36	protein-coding
mm_21609.1	chr2	164254694	164254709	-	1	NA	3' UTR (NM_173377, exon 3 of 3)	3' UTR (NM_173377, exon 3 of 3)	1942	NM_173377	329557	Mm.118769	NM_173377	ENSMUSG00000050383	Svs3b	9530004A22Rik	seminal vesicle secretory protein 3B	protein-coding
mm_118393.1	chr13	118715658	118715669	-	1	NA	exon (NM_008002, exon 1 of 3)	exon (NM_008002, exon 1 of 3)	964	NM_008002	14165	Mm.317323	NM_008002	ENSMUSG00000021732	Fgf10	AEY17|BB213776|Fgf-10|Gsfaey17	fibroblast growth factor 10	protein-coding
mm_20994.1	chr2	152332288	152332298	-	1	NA	5' UTR (NM_001083921, exon 1 of 12)	5' UTR (NM_001083921, exon 1 of 12)	132	NM_001083921	24105	Mm.182145	NM_019705	ENSMUSG00000027466	Rbck1	AL033326|HOIL-1|HOIL-1L|UIP28|Ubce7ip3	RanBP-type and C3HC4-type zinc finger containing 1	protein-coding
mm_33473.1	chr4	130818632	130818647	+	1	NA	exon (NM_011520, exon 3 of 5)	exon (NM_011520, exon 3 of 5)	26102	NM_011520	20970	Mm.206536	NM_011520	ENSMUSG00000025743	Sdc3	Synd3|mKIAA0468|syn-3	syndecan 3	protein-coding
mm_36008.1	chr4	56802266	56802322	-	1	NA	promoter-TSS (NM_026079)	promoter-TSS (NM_026079)	-35	NM_001081420	230234	Mm.268148	NM_001081420	ENSMUSG00000038827	Fam206a	simiate	family with sequence similarity 206, member A	protein-coding
mm_86357.1	chr9	123710588	123710622	-	1	NA	intron (NM_033322, intron 4 of 9)	intron (NM_033322, intron 4 of 9)	6952	NM_033322	93730	Mm.378263	NM_033322	ENSMUSG00000025245	Lztfl1	5530402H04Rik|6130400H19Rik|AI414725|AW048545	leucine zipper transcription factor-like 1	protein-coding
mm_31984.1	chr4	89137375	89137447	+	1	NA	promoter-TSS (NM_024433)	promoter-TSS (NM_024433)	41	NM_024433	66902	Mm.28500	NM_024433	ENSMUSG00000062937	Mtap	1300019I21Rik|MSAP	methylthioadenosine phosphorylase	protein-coding
mm_43717.1	chr5	139406678	139406689	+	1	NA	intron (NM_177000, intron 1 of 1)	intron (NM_177000, intron 1 of 1)	296	NM_177000	319772	Mm.440271	NM_177000	ENSMUSG00000044092	C130050O18Rik	-	RIKEN cDNA C130050O18 gene	protein-coding
mm_101692.1	chr11	40750347	40750398	-	1	NA	3' UTR (NM_009831, exon 6 of 6)	3' UTR (NM_009831, exon 6 of 6)	4914	NM_009831	12450	Mm.2103	NM_009831	ENSMUSG00000020326	Ccng1	AI314029	cyclin G1	protein-coding
mm_102397.1	chr11	59002356	59002366	-	1	NA	intron (NM_001171512, intron 89 of 103)	intron (NM_001171512, intron 89 of 103)	24268	NM_053168	94091	Mm.248049	NM_053168	ENSMUSG00000020455	Trim11	-	tripartite motif-containing 11	protein-coding
mm_150853.1	chr19	45002042	45002062	+	1	NA	3' UTR (NM_011976, exon 15 of 15)	3' UTR (NM_011976, exon 15 of 15)	4390	NM_053164	94067	Mm.44174	NM_053164	ENSMUSG00000025208	Mrpl43	4930442D21Rik|bMRP36a	mitochondrial ribosomal protein L43	protein-coding
mm_50239.1	chr6	42351543	42351557	+	1	NA	exon (NM_001289618, exon 4 of 10)	exon (NM_001289618, exon 4 of 10)	1722	NM_001289619	22793	Mm.282303	NM_011777	ENSMUSG00000029860	Zyx	9530098H06Rik|R75157	zyxin	protein-coding
mm_150335.1	chr19	34575305	34575334	+	1	NA	3' UTR (NM_008332, exon 3 of 3)	3' UTR (NM_008332, exon 3 of 3)	-8210	NM_010501	15959	Mm.426079	NM_010501	ENSMUSG00000074896	Ifit3	Ifi49|P49	interferon-induced protein with tetratricopeptide repeats 3	protein-coding
mm_17773.1	chr2	32829397	32829418	-	1	NA	intron (NM_009295, intron 1 of 18)	intron (NM_009295, intron 1 of 18)	17825	NM_009295	20910	Mm.278865	NM_009295	ENSMUSG00000026797	Stxbp1	AI317162|AI326233|MMS10-G|Ms10g|Munc-18a|Munc18-1|N-sec1|Rb-sec1|Sxtbp1|Unc18-1|Unc18h|nsec1	syntaxin binding protein 1	protein-coding
mm_122209.1	chr14	32085563	32085590	-	1	NA	promoter-TSS (NM_145460)	promoter-TSS (NM_145460)	116	NR_104303	105638	Mm.2519	NM_172254	ENSMUSG00000021905	Dph3	DELGIP1|DelgipP1|Desr1|KTI11|Zcsl2	diphthamine biosynthesis 3	protein-coding
mm_32411.1	chr4	107002714	107002726	+	1	NA	intron (NM_023672, intron 4 of 17)	intron (NM_023672, intron 4 of 17)	64146	NM_025500	56280	Mm.29517	NM_025500	ENSMUSG00000028622	Mrpl37	2300004O14Rik|AI132596|MRP-L2|Rpml2	mitochondrial ribosomal protein L37	protein-coding
mm_58696.1	chr7	12925517	12925530	+	1	NA	exon (NM_009095, exon 3 of 6)	exon (NM_009095, exon 3 of 6)	-1893	NM_029809	381845	Mm.439896	NM_029809	ENSMUSG00000033967	Rnf225	2310014L17Rik|AV237412|C77118	ring finger protein 225	protein-coding
mm_124999.1	chr15	23038849	23038852	+	1	NA	intron (NM_001081299, intron 1 of 11)	intron (NM_001081299, intron 1 of 11)	2387	NM_001081299	320865	Mm.241965	NM_001081299	ENSMUSG00000040420	Cdh18	B230220E17Rik|Cdh14l	cadherin 18	protein-coding
mm_122721.1	chr14	52296432	52296435	-	1	NA	TTS (NM_023434)	TTS (NM_023434)	8691	NM_019721	56335	Mm.271759	NM_019721	ENSMUSG00000022160	Mettl3	2310024F18Rik|M6A|Spo8	methyltransferase like 3	protein-coding
mm_136191.1	chr16	89403804	89403806	-	1	NA	promoter-TSS (NM_028621)	promoter-TSS (NM_028621)	-31	NM_028621	170656	Mm.46109	NM_028621	ENSMUSG00000058368	Krtap21-1	1110017B05Rik|AI506979|KAP21.1|Krtap16-7	keratin associated protein 21-1	protein-coding
mm_95922.1	chr11	58275023	58275037	+	1	NA	Intergenic	Intergenic	-32039	NM_182996	103836	Mm.41440	NM_182996	ENSMUSG00000037243	Zfp692	AI746306|AI839920|Zfp692-ps|Znf692	zinc finger protein 692	protein-coding
mm_160108.1	chr7	24587524	24587524	+	1	NA	promoter-TSS (NM_023154)	promoter-TSS (NM_023154)	-19	NM_023154	66071	Mm.29553	NM_023154	ENSMUSG00000064254	Ethe1	0610025L15Rik|Hsco	ethylmalonic encephalopathy 1	protein-coding
mm_129940.1	chr15	84856096	84856111	-	1	NA	promoter-TSS (NM_001081166)	promoter-TSS (NM_001081166)	26	NM_001081166	271305	Mm.101022	NM_001081166	ENSMUSG00000016624	Phf21b	A730032D07Rik	PHD finger protein 21B	protein-coding
mm_30395.1	chr3	152248352	152248374	-	1	NA	exon (NM_199465, exon 6 of 13)	exon (NM_199465, exon 6 of 13)	17957	NM_199465	68810	Mm.200188	NM_199465	ENSMUSG00000039103	Nexn	1110046H09Rik|AA553326|NELIN	nexilin	protein-coding
mm_109531.1	chr12	111538820	111538874	+	1	NA	intron (NM_178041, intron 2 of 11)	CpG-3539	746	NM_173363	217869	Mm.271222	NM_173363	ENSMUSG00000021282	Eif5	2810011H21Rik|D12Ertd549e	eukaryotic translation initiation factor 5	protein-coding
mm_10517.1	chr2	16356720	16356742	+	1	NA	5' UTR (NM_026162, exon 1 of 14)	5' UTR (NM_026162, exon 1 of 14)	427	NM_026162	67448	Mm.313938	NM_026162	ENSMUSG00000026748	Plxdc2	1200007L24Rik|5430431D22Rik|AI646728|AU022916|AV231634|Tem7r	plexin domain containing 2	protein-coding
mm_68938.1	chr7	126502357	126502376	-	1	NA	promoter-TSS (NM_001347658)	promoter-TSS (NM_001347658)	59	NM_001347658	233871	Mm.231450	NM_183020	ENSMUSG00000032637	Atxn2l	A2D|A2LG|A2RP|A2lp|Atxnl2	ataxin 2-like	protein-coding
mm_29361.1	chr3	108562350	108562417	-	1	NA	promoter-TSS (NM_026198)	promoter-TSS (NM_026198)	83	NM_026198	67495	Mm.32615	NM_026198	ENSMUSG00000068732	Tmem167b	2010200O16Rik	transmembrane protein 167B	protein-coding
mm_128254.1	chr15	36771057	36771087	-	1	NA	3' UTR (NM_001253807, exon 5 of 5)	3' UTR (NM_001253807, exon 5 of 5)	19860	NM_001253807	22631	Mm.3360	NM_011740	ENSMUSG00000022285	Ywhaz	1110013I11Rik|14-3-3zeta|AI596267|AL022924|AU020854	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide	protein-coding
mm_172336.1	chr7	109986130	109986137	-	1	NA	promoter-TSS (NM_153525)	promoter-TSS (NM_153525)	97	NM_153525	233724	Mm.43212	NM_153525	ENSMUSG00000047554	Tmem41b	1500015G02Rik|1500031M19Rik|AU018901|D7Ertd70e|D7Ertd743e	transmembrane protein 41B	protein-coding
mm_146692.1	chr18	12879974	12879981	-	1	NA	promoter-TSS (NM_001252489)	promoter-TSS (NM_001252489)	2	NM_001252489	64291	Mm.259470	NM_020573	ENSMUSG00000044252	Osbpl1a	G430090F17Rik|Gm753|ORP-1|Osbpl1b	oxysterol binding protein-like 1A	protein-coding
mm_53251.1	chr6	127790351	127790355	+	1	NA	Intergenic	Intergenic	-2210	NR_106092	102466996		NR_106092	ENSMUSG00000104804	Mir7233	mmu-mir-7233	microRNA 7233	ncRNA
mm_1192.1	chr1	62703443	62703457	+	1	NA	5' UTR (NM_001077407, exon 1 of 16)	5' UTR (NM_001077407, exon 1 of 16)	133	NM_001077405	18187	Mm.266341	NM_010939	ENSMUSG00000025969	Nrp2	1110048P06Rik|Np-2|Np2|Npn-2|Npn2	neuropilin 2	protein-coding
mm_80956.1	chr9	103008176	103008184	+	1	NA	promoter-TSS (NM_033314)	promoter-TSS (NM_033314)	-309	NM_033314	24059	Mm.207106	NM_033314	ENSMUSG00000032548	Slco2a1	2310021C19Rik|Pgt|Slc21a2|mPgt	solute carrier organic anion transporter family, member 2a1	protein-coding
mm_56060.1	chr6	86775105	86775120	-	1	NA	promoter-TSS (NM_001331120)	promoter-TSS (NM_001331120)	2	NM_001331120	11746	Mm.259702	NM_013471	ENSMUSG00000029994	Anxa4	AI265406|AIV|AW106930|Anx4|Xanx-4	annexin A4	protein-coding
mm_62125.1	chr7	96946875	96946902	+	1	NA	Intergenic	RLTR45|LTR|ERVK	-4639	NM_153591	244141	Mm.274864	NM_153591	ENSMUSG00000018995	Nars2	AI875199	asparaginyl-tRNA synthetase 2 (mitochondrial)(putative)	protein-coding
mm_158193.1	chrX	104671015	104671034	-	1	NA	promoter-TSS (NM_175358)	promoter-TSS (NM_175358)	40	NM_175358	108672	Mm.30574	NM_175358	ENSMUSG00000033906	Zdhhc15	6030457O13Rik	zinc finger, DHHC domain containing 15	protein-coding
mm_12040.1	chr2	58769979	58769994	+	1	NA	intron (NM_029692, intron 2 of 6)	intron (NM_029692, intron 2 of 6)	14802	NM_029692	76654	Mm.200370	NM_029692	ENSMUSG00000026839	Upp2	1700124F02Rik|AI266885|UDRPASE2|UP2|UPASE2	uridine phosphorylase 2	protein-coding
mm_104514.1	chr11	96005976	96005985	-	1	NA	promoter-TSS (NM_009951)	promoter-TSS (NM_009951)	-36	NM_009951	140486	Mm.294769	NM_009951	ENSMUSG00000013415	Igf2bp1	AL024068|AW549074|CRD-BP|Crdbp|D030026A21Rik|D11Moh40e|D11Moh45|IMP-1|IMP1|Neilsen|ZBP-1|Zbp1|mir-3063	insulin-like growth factor 2 mRNA binding protein 1	protein-coding
mm_22296.1	chr2	180273444	180273478	-	1	NA	promoter-TSS (NM_145851)	promoter-TSS (NM_145851)	4	NM_145851	252966	Mm.386884	NM_145851	ENSMUSG00000038990	Cables2	ik3-2	CDK5 and Abl enzyme substrate 2	protein-coding
mm_137724.1	chr17	29268819	29268829	+	1	NA	promoter-TSS (NM_030561)	promoter-TSS (NM_030561)	36	NM_030561	80748	Mm.290116	NM_030561	ENSMUSG00000052712	BC004004	2400006G15Rik	cDNA sequence BC004004	protein-coding
mm_116322.1	chr13	37979512	37979529	-	1	NA	3' UTR (NM_025965, exon 8 of 8)	3' UTR (NM_025965, exon 8 of 8)	14670	NM_025965	107513	Mm.426670	NM_025965	ENSMUSG00000021427	Ssr1	2510001K09Rik|6330400D04|AI159733|AI452176|SSR|TRAPA	signal sequence receptor, alpha	protein-coding
mm_44224.1	chr5	4804529	4804545	-	1	NA	3' UTR (NM_001310448, exon 14 of 14)	3' UTR (NM_001310448, exon 14 of 14)	-46321	NM_021457	14362	Mm.246003	NM_021457	ENSMUSG00000044674	Fzd1	AW227548|FZ-1|Fz1	frizzled class receptor 1	protein-coding
mm_44783.1	chr5	32134867	32134884	-	1	NA	Intergenic	(A)n|Simple_repeat|Simple_repeat	-1597	NM_008037	14284	Mm.24684	NM_008037	ENSMUSG00000029135	Fosl2	Fra-2	fos-like antigen 2	protein-coding
mm_34556.1	chr4	149629325	149629351	+	1	NA	exon (NM_023051, exon 5 of 19)	exon (NM_023051, exon 5 of 19)	26229	NR_105990	102465983		NR_105990	ENSMUSG00000098580	Mir7023	Gm27912|mmu-mir-7023	microRNA 7023	ncRNA
mm_125794.1	chr15	74819082	74819092	+	1	NA	promoter-TSS (NM_010416)	promoter-TSS (NM_010416)	11	NM_010416	15202	Mm.17336	NM_010416	ENSMUSG00000068600	Gml2	1700057K19Rik|HemT|Hemt1	glycosylphosphatidylinositol anchored molecule like 2	protein-coding
mm_108882.1	chr12	99965180	99965280	+	1	NA	5' UTR (NM_001164426, exon 2 of 3)	5' UTR (NM_001164426, exon 2 of 3)	731	NM_001164427	217826	Mm.312335	NM_146037	ENSMUSG00000045404	Kcnk13	BB085247|F730021E22Rik|Gm1570|Gm1685	potassium channel, subfamily K, member 13	protein-coding
mm_136818.1	chr17	12404080	12404090	+	1	NA	exon (NM_008877, exon 12 of 19)	exon (NM_008877, exon 12 of 19)	25476	NM_008877	18815	Mm.971	NM_008877	ENSMUSG00000059481	Plg	AI649309|Pg	plasminogen	protein-coding
mm_152692.1	chr19	16780980	16780990	-	1	NA	promoter-TSS (NM_173028)	promoter-TSS (NM_173028)	-52	NM_173028	271564	Mm.211963	NM_173028	ENSMUSG00000046230	Vps13a	4930425F11|4930516E05Rik|4930543C13Rik|9930023P20|Chac|Chorein|D330038K10Rik|mKIAA0986	vacuolar protein sorting 13A	protein-coding
mm_37028.1	chr4	114987126	114987203	-	1	NA	promoter-TSS (NM_025647)	promoter-TSS (NM_025647)	64	NM_025647	66588	Mm.294159	NM_025647	ENSMUSG00000028719	Cmpk1	0610011D08Rik|CK|Cmpk|UMP-CMPk	cytidine monophosphate (UMP-CMP) kinase 1	protein-coding
mm_164765.1	chr17	85621285	85621294	+	1	NA	exon (NM_011381, exon 1 of 2)	exon (NM_011381, exon 1 of 2)	455	NM_011381	20473	Mm.370208	NM_011381	ENSMUSG00000038805	Six3	E130112M24Rik|Six3a|Six3alpha|Six3b|Six3beta	sine oculis-related homeobox 3	protein-coding
mm_100434.1	chr11	119469165	119469210	+	1	NA	Intergenic	Intergenic	-22160	NM_001164636	338371	Mm.271946	NM_177394	ENSMUSG00000039850	Endov	A730011L01Rik	endonuclease V	protein-coding
mm_101799.1	chr11	46238804	46238807	-	1	NA	3' UTR (NM_177075, exon 2 of 2)	3' UTR (NM_177075, exon 2 of 2)	3248	NM_177075	320116	Mm.39600	NM_177075	ENSMUSG00000048721	Fndc9	C030019I05Rik	fibronectin type III domain containing 9	protein-coding
mm_66374.1	chr7	43656672	43656679	-	1	NA	intron (NM_031181, intron 4 of 6)	intron (NM_031181, intron 4 of 6)	3486	NM_031181	83382	Mm.157702	NM_031181	ENSMUSG00000030474	Siglece	Cd170|Siglec12|Siglec5|Siglec9|Siglecl1|mSiglec-E	sialic acid binding Ig-like lectin E	protein-coding
mm_88780.1	chr10	80589382	80589387	+	1	NA	intron (NM_145421, intron 1 of 4)	intron (NM_145421, intron 1 of 4)	957	NM_145421	216169	Mm.29802	NM_145421	ENSMUSG00000003346	Abhd17a	1700013O15Rik|BC005632|D10Bwg1364e|Fam108a	abhydrolase domain containing 17A	protein-coding
mm_29371.1	chr3	108711455	108711457	-	1	NA	5' UTR (NM_029522, exon 2 of 15)	5' UTR (NM_029522, exon 2 of 15)	10843	NM_029522	76123	Mm.226941	NM_029522	ENSMUSG00000027883	Gpsm2	6230410J09Rik|LGN|Pins	G-protein signalling modulator 2 (AGS3-like, C. elegans)	protein-coding
mm_120908.1	chr14	76110886	76110928	+	1	NA	promoter-TSS (NM_013745)	promoter-TSS (NM_013745)	16	NM_013745	27275	Mm.21138	NM_013745	ENSMUSG00000022009	Nufip1	Nufip	nuclear fragile X mental retardation protein interacting protein 1	protein-coding
mm_20295.1	chr2	126933230	126933241	-	1	NA	promoter-TSS (NM_023220)	promoter-TSS (NM_023220)	0	NM_023220	66552	Mm.269928	NM_023220	ENSMUSG00000027366	Sppl2a	2010106G01Rik|C130089K23Rik	signal peptide peptidase like 2A	protein-coding
mm_14582.1	chr2	135764881	135764908	+	1	NA	intron (NM_013829, intron 1 of 36)	intron (NM_013829, intron 1 of 36)	23064	NM_013829	18798	Mm.38009	NM_013829	ENSMUSG00000039943	Plcb4	A930039J07Rik|AI854601|C230058B11Rik	phospholipase C, beta 4	protein-coding
mm_94379.1	chr11	5146571	5146618	+	1	NA	intron (NM_080595, intron 1 of 14)	RSINE1|SINE|B4	5628	NM_080595	140703	Mm.840	NM_080595	ENSMUSG00000034164	Emid1	AW122071|CO-5|Emu1	EMI domain containing 1	protein-coding
mm_159765.1	chr5	95776024	95776024	+	1	NA	5' UTR (NM_001122668, exon 1 of 4)	5' UTR (NM_001122668, exon 1 of 4)	154	NM_001122668	665943	Mm.348795	NM_001122668	ENSMUSG00000072813	E330014E10Rik	-	RIKEN cDNA E330014E10 gene	protein-coding
mm_24096.1	chr3	88043099	88043128	+	1	NA	promoter-TSS (NM_001110809)	promoter-TSS (NM_001110809)	7	NM_025663	66614	Mm.46029	NM_025663	ENSMUSG00000028069	Gpatch4	2610029K21Rik|Gpatc4	G patch domain containing 4	protein-coding
mm_112265.1	chr12	114060316	114060322	-	1	NA	Intergenic	Intergenic	409147	NR_106062	102465663		NR_106062	ENSMUSG00000105438	Mir7094-1	mmu-mir-7094-1	microRNA 7094-1	ncRNA
mm_143605.1	chr17	78418049	78418066	-	1	NA	promoter-TSS (NM_199448)	promoter-TSS (NM_199448)	95	NM_001285949	225020	Mm.236835	NM_199448	ENSMUSG00000056121	Fez2	9030616F16|D17Ertd315e	fasciculation and elongation protein zeta 2 (zygin II)	protein-coding
mm_163437.1	chr12	85472325	85472345	+	1	NA	Intergenic	CpG	-1566	NM_010234	14281	Mm.246513	NM_010234	ENSMUSG00000021250	Fos	D12Rfj1|c-fos|cFos	FBJ osteosarcoma oncogene	protein-coding
mm_105626.1	chr11	106897141	106897144	-	1	NA	intron (NM_025481, intron 1 of 18)	RSINE1|SINE|B4	23573	NM_025481	66313	Mm.340955	NM_025481	ENSMUSG00000018363	Smurf2	2810411E22Rik|AI558114|AI649275	SMAD specific E3 ubiquitin protein ligase 2	protein-coding
mm_126168.1	chr15	78560874	78560885	+	1	NA	3' UTR (NM_009008, exon 7 of 7)	3' UTR (NM_009008, exon 7 of 7)	11904	NM_009008	19354	Mm.1972	NM_009008	ENSMUSG00000033220	Rac2	AI323801|AI452260	RAS-related C3 botulinum substrate 2	protein-coding
mm_86533.1	chr10	7836469	7836487	+	1	NA	promoter-TSS (NR_039563)	promoter-TSS (NR_039563)	97	NR_039563	100628581		NR_039563	ENSMUSG00000093060	Mir5104	mir-5104|mmu-mir-5104|mu-mir-5104	microRNA 5104	ncRNA
mm_70274.1	chr8	3598372	3598401	+	1	NA	intron (NM_001347112, intron 2 of 17)	intron (NM_001347112, intron 2 of 17)	10936	NM_001347111	69697	Mm.390010	NM_027171	ENSMUSG00000044433	Camsap3	2310057J16Rik|Kiaa1543|Nezha	calmodulin regulated spectrin-associated protein family, member 3	protein-coding
mm_123582.1	chr14	67055804	67055807	-	1	NA	intron (NM_001205188, intron 2 of 9)	intron (NM_001205188, intron 2 of 9)	16666	NM_028032	71978	Mm.273997	NM_028032	ENSMUSG00000022052	Ppp2r2a	2410004D02Rik|mKIAA1541	protein phosphatase 2, regulatory subunit B, alpha	protein-coding
mm_164532.1	chr17	6253790	6253802	+	1	NA	Intergenic	CpG	-16674	NM_001033178	77106	Mm.381893	NM_001033178	ENSMUSG00000038141	Tmem181a	5930418K15Rik|C76977|Gpr178|Tmem181|mKIAA1423	transmembrane protein 181A	protein-coding
mm_24527.1	chr3	93273520	93273524	+	1	NA	Intergenic	Intergenic	-46227	NM_133698	68723	Mm.208047	NM_133698	ENSMUSG00000041991	Hrnr	1110033K19Rik|A530063N20Rik|S100a18	hornerin	protein-coding
mm_82837.1	chr9	31158463	31158489	-	1	NA	intron (NM_001102455, intron 12 of 16)	intron (NM_001102455, intron 12 of 16)	-26677	NM_011176	19143	Mm.243926	NM_011176	ENSMUSG00000031995	St14	Epithin|MT-SP1|Prss14|Tmprss14|mCAP3|matriptase	suppression of tumorigenicity 14 (colon carcinoma)	protein-coding
mm_138930.1	chr17	43801892	43801899	+	1	NA	promoter-TSS (NM_207649)	promoter-TSS (NM_207649)	44	NM_207649	53901	Mm.251242	NM_030598	ENSMUSG00000039601	Rcan2	Csp2|Dscr1l1|MCIP2|ZAKI-4	regulator of calcineurin 2	protein-coding
mm_92615.1	chr10	80139348	80139370	-	1	NA	promoter-TSS (NR_036582)	promoter-TSS (NR_036582)	8	NR_036582	100503659	Mm.485395	NM_015761	ENSMUSG00000035640	Cbarp	9630008F14|Dos|R29144/1	calcium channel, voltage-dependent, beta subunit associated regulatory protein	protein-coding
mm_99571.1	chr11	103966717	103966790	+	1	NA	promoter-TSS (NM_007477)	promoter-TSS (NM_007477)	28	NM_001304574	11841	Mm.5061	NM_007477	ENSMUSG00000062421	Arf2	-	ADP-ribosylation factor 2	protein-coding
mm_12778.1	chr2	79328813	79328840	+	1	NA	3' UTR (NM_010576, exon 28 of 28)	3' UTR (NM_010576, exon 28 of 28)	73400	NM_010576	16401	Mm.31903	NM_010576	ENSMUSG00000027009	Itga4	CD49D|Itga4B	integrin alpha 4	protein-coding
mm_164012.1	chr14	70466611	70466621	+	1	NA	intron (NM_145981, intron 4 of 4)	intron (NM_145981, intron 4 of 4)	9099	NM_145981	105653	Mm.192598	NM_145981	ENSMUSG00000003469	Phyhip	AW049870|C630010D02Rik|Lnap1ip|PAHX-AP#1|PAHX-AP1	phytanoyl-CoA hydroxylase interacting protein	protein-coding
mm_74995.1	chr8	27202568	27202581	-	1	NA	promoter-TSS (NM_029674)	promoter-TSS (NM_029674)	-27	NM_029674	76615	Mm.272794	NM_029674	ENSMUSG00000039720	Got1l1	1700083M11Rik	glutamic-oxaloacetic transaminase 1-like 1	protein-coding
mm_133370.1	chr16	84709321	84709332	+	1	NA	Intergenic	Intergenic	-3697	NR_132106	100653389	Mm.261808	NR_132106	ENSMUSG00000097418	Mir155hg	Bic|Gm26667	Mir155 host gene (non-protein coding)	ncRNA
mm_127856.1	chr15	8350316	8350336	-	1	NA	exon (NM_027707, exon 10 of 47)	exon (NM_027707, exon 10 of 47)	94137	NM_027707	71175	Mm.240329	NM_027707	ENSMUSG00000022141	Nipbl	Idn3	Nipped-B homolog (Drosophila)	protein-coding
mm_30061.1	chr3	137864318	137864331	-	1	NA	promoter-TSS (NM_016750)	promoter-TSS (NM_016750)	-163	NM_001316995	51788	Mm.117541	NM_016750	ENSMUSG00000037894	H2afz	H2A.Z|H2a.z-1	H2A histone family, member Z	protein-coding
mm_143959.1	chr17	87023409	87023411	-	1	NA	intron (NM_008838, intron 2 of 5)	intron (NM_008838, intron 2 of 5)	1991	NM_008838	18701	Mm.219685	NM_008838	ENSMUSG00000024145	Pigf	-	phosphatidylinositol glycan anchor biosynthesis, class F	protein-coding
mm_53921.1	chr6	4086886	4086904	-	1	NA	promoter-TSS (NM_009748)	promoter-TSS (NM_009748)	32	NM_009748	12068	Mm.286457	NM_009748	ENSMUSG00000032757	Bet1	AW555236|Bet-1	Bet1 golgi vesicular membrane trafficking protein	protein-coding
mm_78976.1	chr9	45370213	45370282	+	1	NA	promoter-TSS (NM_022004)	promoter-TSS (NM_022004)	62	NM_022004	59095	Mm.208287	NM_022004	ENSMUSG00000066705	Fxyd6	0610030I18Rik|Php	FXYD domain-containing ion transport regulator 6	protein-coding
mm_155096.1	chrX	48270472	48270482	+	1	NA	intron (NM_028276, intron 6 of 14)	PB1D9|SINE|Alu	13543	NM_028276	72554	Mm.336045	NM_028276	ENSMUSG00000063785	Utp14a	2700066J21Rik|JsdX|NY-CO-16|SDCCAG16|T25628|mKIAA0266	UTP14A small subunit processome component	protein-coding
mm_83303.1	chr9	44022166	44022185	-	1	NA	Intergenic	Intergenic	-21209	NM_009382	21838	Mm.3951	NM_009382	ENSMUSG00000032011	Thy1	CD90|T25|Thy-1|Thy-1.2|Thy1.1|Thy1.2	thymus cell antigen 1, theta	protein-coding
mm_73449.1	chr8	106282250	106282258	+	1	NA	promoter-TSS (NR_126090)	promoter-TSS (NR_126090)	25	NR_126090	75044	Mm.445896	NR_126090		4930506A18Rik	-	RIKEN cDNA 4930506A18 gene	ncRNA
mm_91798.1	chr10	53519701	53519718	-	1	NA	promoter-TSS (NR_037973)	promoter-TSS (NR_037973)	-720	NR_037973	100502868	Mm.297722	NR_037973		Gm20597	B230314j19	predicted gene, 20597	ncRNA
mm_91906.1	chr10	60220028	60220038	-	1	NA	promoter-TSS (NM_016803)	promoter-TSS (NM_016803)	-773	NM_016803	53374	Mm.12866	NM_016803	ENSMUSG00000057337	Chst3	C6ST|C6ST-1|GST-0	carbohydrate (chondroitin 6/keratan) sulfotransferase 3	protein-coding
mm_132288.1	chr16	33185046	33185153	+	1	NA	promoter-TSS (NM_176840)	promoter-TSS (NM_176840)	28	NM_176840	106326	Mm.486405	NM_176840	ENSMUSG00000022807	Osbpl11	9430097N02Rik|AI132306|AU019795|ORP-11	oxysterol binding protein-like 11	protein-coding
mm_148654.1	chr19	5493896	5493937	+	1	NA	3' UTR (NM_007687, exon 4 of 4)	3' UTR (NM_007687, exon 4 of 4)	3461	NM_007687	12631	Mm.329655	NM_007687	ENSMUSG00000056201	Cfl1	AA959946|Cof	cofilin 1, non-muscle	protein-coding
mm_119360.1	chr14	41115887	41115918	+	1	NA	intron (NM_133653, intron 6 of 9)	Lx8|LINE|L1	10869	NM_133653	11720	Mm.14064	NM_133653	ENSMUSG00000037798	Mat1a	AI046368|AdoMet|Ams|MAT|MATA1|SAMS|SAMS1	methionine adenosyltransferase I, alpha	protein-coding
mm_100474.1	chr11	120098911	120098983	+	1	NA	promoter-TSS (NM_183137)	promoter-TSS (NM_183137)	13	NM_001110242	208501	Mm.46699	NM_001110242	ENSMUSG00000078572	Ndufaf8	1810043H04Rik	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex assembly factor 8	protein-coding
mm_135090.1	chr16	34573527	34573554	-	1	NA	Intergenic	Intergenic	-59513	NM_177357	545156	Mm.82274	NM_177357	ENSMUSG00000061751	Kalrn	2210407G14Rik|AV235988|DUET|E530005C20Rik|Gm539|Hapip|TRAD	kalirin, RhoGEF kinase	protein-coding
mm_133942.1	chr16	3908518	3908543	-	1	NA	promoter-TSS (NM_029738)	promoter-TSS (NM_029738)	159	NM_028484	73261	Mm.486226	NM_028484	ENSMUSG00000005983	1700037C18Rik	2810022L20Rik	RIKEN cDNA 1700037C18 gene	protein-coding
mm_25333.1	chr3	106573899	106573909	+	1	NA	3' UTR (NM_026013, exon 9 of 9)	3' UTR (NM_026013, exon 9 of 9)	-26102	NM_133869	99712	Mm.429443	NM_133869	ENSMUSG00000040774	Cept1	9930118K05Rik|mCEPT1	choline/ethanolaminephosphotransferase 1	protein-coding
mm_40196.1	chr5	36868468	36868560	+	1	NA	promoter-TSS (NM_172994)	promoter-TSS (NM_172994)	-56	NM_172994	269643	Mm.41694	NM_172994	ENSMUSG00000029120	Ppp2r2c	6330548O06Rik|IMYPNO|IMYPNO1|PR52	protein phosphatase 2, regulatory subunit B, gamma	protein-coding
mm_127385.1	chr15	101040860	101040871	+	1	NA	3' UTR (NM_011323, exon 26 of 26)	3' UTR (NM_011323, exon 26 of 26)	13534	NM_001214911	668225	Mm.385011	NM_001214911	ENSMUSG00000095440	Fignl2	EG668225	fidgetin-like 2	protein-coding
mm_106617.1	chr11	120819162	120819182	-	1	NA	exon (NM_007988, exon 9 of 43)	exon (NM_007988, exon 9 of 43)	5375	NM_007988	14104	Mm.236443	NM_007988	ENSMUSG00000025153	Fasn	A630082H08Rik|FAS	fatty acid synthase	protein-coding
mm_48328.1	chr5	138996092	138996112	-	1	NA	Intergenic	CpG-11694	-1149	NM_008808	18590	Mm.2675	NM_008808	ENSMUSG00000025856	Pdgfa	-	platelet derived growth factor, alpha	protein-coding
mm_52426.1	chr6	113483299	113483316	+	1	NA	promoter-TSS (NM_133930)	promoter-TSS (NM_133930)	-262	NM_133930	171508	Mm.41593	NM_133930	ENSMUSG00000030284	Creld1	AI843811	cysteine-rich with EGF-like domains 1	protein-coding
mm_77814.1	chr9	3199909	3199928	+	1	NA	promoter-TSS (NR_027988)	promoter-TSS (NR_027988)	-105	NR_027988	114673	Mm.422774	NM_053265	ENSMUSG00000042360	4930433N12Rik	-	RIKEN cDNA 4930433N12 gene	ncRNA
mm_10378.1	chr2	11778481	11778586	+	1	NA	5' UTR (NM_177268, exon 1 of 7)	5' UTR (NM_177268, exon 1 of 7)	780	NM_177268	320816	Mm.260201	NM_177268	ENSMUSG00000047909	Ankrd16	2810455F06Rik|AI646698|D430029B21Rik	ankyrin repeat domain 16	protein-coding
mm_62197.1	chr7	97788349	97788390	+	1	NA	Intergenic	CpG	-50122	NM_175105	66333	Mm.29756	NM_175105	ENSMUSG00000042797	Aqp11	1700015P13Rik|AI648923|sjds	aquaporin 11	protein-coding
mm_49144.1	chr6	11907752	11907793	+	1	NA	promoter-TSS (NM_010886)	promoter-TSS (NM_010886)	-326	NM_010886	17992	Mm.415865	NM_010886	ENSMUSG00000029632	Ndufa4	MLRQ	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 4	protein-coding
mm_146312.1	chr18	80362778	80362782	+	1	NA	intron (NM_001190373, intron 1 of 3)	CpG	1474	NM_001190373	240444	Mm.279568	NM_001190373	ENSMUSG00000059852	Kcng2	AA591524	potassium voltage-gated channel, subfamily G, member 2	protein-coding
mm_119928.1	chr14	54969227	54969260	+	1	NA	intron (NR_033497, intron 1 of 4)	intron (NR_033497, intron 1 of 4)	456	NR_033497	791403	Mm.319176	NR_033497	ENSMUSG00000097652	Mhrt	D830015G02Rik|ENSMUSG00000053118|Myheart	myosin heavy chain associated RNA transcript	ncRNA
mm_172798.1	chr9	114432100	114432104	+	1	NA	intron (NR_108101, intron 5 of 14)	B1_Mus2|SINE|Alu	31007	NM_001200002	100504715	Mm.290516	NM_001200002	ENSMUSG00000079260	Tmppe	-	transmembrane protein with metallophosphoesterase domain	protein-coding
mm_164188.1	chr15	77933619	77933642	-	1	NA	Intergenic	Intergenic	-4636	NM_019913	56551	Mm.291917	NM_019913	ENSMUSG00000005354	Txn2	2510006J11Rik|AI788873|Trx2	thioredoxin 2	protein-coding
mm_2976.1	chr1	133108130	133108137	+	1	NA	3' UTR (NM_001099276, exon 33 of 33)	3' UTR (NM_001099276, exon 33 of 33)	-23033	NM_133819	108954	Mm.293628	NM_133819	ENSMUSG00000046062	Ppp1r15b	1810033K10Rik|AI606441|C530022L24Rik|CReP	protein phosphatase 1, regulatory (inhibitor) subunit 15b	protein-coding
mm_96735.1	chr11	69765900	69765925	+	1	NA	promoter-TSS (NM_029348)	promoter-TSS (NM_029348)	0	NM_029348	75580	Mm.426361	NM_029348	ENSMUSG00000018750	Zbtb4	2310026P19Rik|9230111I22Rik|mKIAA1538	zinc finger and BTB domain containing 4	protein-coding
mm_165539.1	chr2	180621797	180621803	-	1	NA	TTS (NM_178254)	TTS (NM_178254)	20891	NM_178254	277353	Mm.473700	NM_178254	ENSMUSG00000038932	Tcfl5	AV260129|Figlb|Sosf1	transcription factor-like 5 (basic helix-loop-helix)	protein-coding
mm_121233.1	chr14	103055859	103055863	+	1	NA	3' UTR (NM_008392, exon 5 of 5)	3' UTR (NM_008392, exon 5 of 5)	8849	NM_008392	16365	Mm.4662	NM_008392	ENSMUSG00000022126	Acod1	AI323667|CAD|Irg1	aconitate decarboxylase 1	protein-coding
mm_163943.1	chr14	51145703	51145707	-	1	NA	exon (NM_011271, exon 2 of 2)	exon (NM_011271, exon 2 of 2)	1062	NM_011271	19752	Mm.235538	NM_011271	ENSMUSG00000035896	Rnase1	AI574248|Rib-1|Rib1	ribonuclease, RNase A family, 1 (pancreatic)	protein-coding
mm_137817.1	chr17	30088786	30088795	+	1	NA	intron (NM_148926, intron 2 of 4)	Lx5|LINE|L1	83703	NM_148926	21769	Mm.220972	NM_148926	ENSMUSG00000044477	Zfand3	AW539211|TEG-27|Tex27	zinc finger, AN1-type domain 3	protein-coding
mm_117965.1	chr13	99516667	99516677	-	1	NA	promoter-TSS (NM_008634)	promoter-TSS (NM_008634)	-70	NM_008634	17755	Mm.4173	NM_008634	ENSMUSG00000052727	Map1b	A230055D22|AI843217|LC1|MAP5|Mtap-5|Mtap1b|Mtap5	microtubule-associated protein 1B	protein-coding
mm_167807.1	chr9	123928874	123928881	-	1	NA	Intergenic	ORR1F|LTR|ERVL-MaLR	39815	NM_009912	12768	Mm.274927	NM_009912	ENSMUSG00000025804	Ccr1	Cmkbr1|Mip-1a-R	chemokine (C-C motif) receptor 1	protein-coding
mm_78230.1	chr9	21592886	21592898	+	1	NA	promoter-TSS (NM_138303)	promoter-TSS (NM_138303)	-61	NM_001205157	74766	Mm.475712	NM_138303	ENSMUSG00000032182	Yipf2	1300010K09Rik	Yip1 domain family, member 2	protein-coding
mm_165447.1	chr2	155869236	155869237	+	1	NA	intron (NR_024487, intron 7 of 9)	intron (NR_024487, intron 7 of 9)	-34382	NM_027788	71405	Mm.260918	NM_027788	ENSMUSG00000074647	Fam83c	5530400B04Rik	family with sequence similarity 83, member C	protein-coding
mm_41135.1	chr5	87808118	87808128	+	1	NA	promoter-TSS (NM_009973)	promoter-TSS (NM_009973)	2	NM_009973	12992	Mm.153308	NM_009973	ENSMUSG00000061388	Csn1s2b	AW987150|Csnd|Csne	casein alpha s2-like B	protein-coding
mm_60811.1	chr7	45675026	45675031	+	1	NA	Intergenic	L1MB5|LINE|L1	-8634	NM_001271993	14344	Mm.290046	NM_018876	ENSMUSG00000055978	Fut2	-	fucosyltransferase 2	protein-coding
mm_46874.1	chr5	113832604	113832663	-	1	NA	Intergenic	Intergenic	-2132	NM_009151	20345	Mm.332590	NM_009151	ENSMUSG00000048163	Selplg	CD162|Psgl-1|Psgl1|Selp1|Selpl	selectin, platelet (p-selectin) ligand	protein-coding
mm_101087.1	chr11	11836213	11836231	-	1	NA	intron (NM_001190448, intron 8 of 14)	intron (NM_001190448, intron 8 of 14)	-27260	NM_001163360	60530	Mm.236114	NM_021891	ENSMUSG00000035455	Fignl1	-	fidgetin-like 1	protein-coding
mm_129216.1	chr15	76523237	76523248	-	1	NA	Intergenic	CpG	-1113	NM_130893	170729	Mm.218747	NM_130893	ENSMUSG00000048385	Scrt1	-	scratch family zinc finger 1	protein-coding
mm_88880.1	chr10	81120934	81120986	+	1	NA	intron (NM_001347144, intron 7 of 10)	intron (NM_001347144, intron 7 of 10)	15045	NM_001347144	26396	Mm.275436	NM_023138	ENSMUSG00000035027	Map2k2	AA589381|MEK2|MK2|Prkmk2	mitogen-activated protein kinase kinase 2	protein-coding
mm_125045.1	chr15	25812824	25812827	+	1	NA	3' UTR (NM_019472, exon 41 of 41)	3' UTR (NM_019472, exon 41 of 41)	-30473	NM_001034851	66270	Mm.25311	NM_025459	ENSMUSG00000022270	Fam134b	1810015C04Rik|AU015349	family with sequence similarity 134, member B	protein-coding
mm_122491.1	chr14	46575850	46575855	-	1	NA	promoter-TSS (NR_046459)	promoter-TSS (NR_046459)	-1	NR_046459	100873094	Mm.318596	NR_046459		Rubie	-	RNA upstream of Bmp4 expressed in inner ear	ncRNA
mm_765.1	chr1	44101637	44101641	+	1	NA	intron (NM_029368, intron 2 of 7)	intron (NM_029368, intron 2 of 7)	749	NM_029368	75623	Mm.348017	NM_029368	ENSMUSG00000026049	Tex30	1700029F09Rik|3110030D08Rik	testis expressed 30	protein-coding
mm_116390.1	chr13	41185001	41185003	-	1	NA	3' UTR (NM_019423, exon 8 of 8)	3' UTR (NM_019423, exon 8 of 8)	35160	NM_001311121	54326	Mm.2567	NM_019423	ENSMUSG00000021364	Elovl2	AI317360|Ssc2	elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 2	protein-coding
mm_70697.1	chr8	15027959	15027983	+	1	NA	exon (NM_029116, exon 2 of 2)	exon (NM_029116, exon 2 of 2)	16946	NM_029116	74901	Mm.46675	NM_029116	ENSMUSG00000055675	Kbtbd11	2900016B01Rik|4930465M17Rik|mKIAA0711	kelch repeat and BTB (POZ) domain containing 11	protein-coding
mm_97509.1	chr11	78499067	78499080	+	1	NA	promoter-TSS (NM_011707)	promoter-TSS (NM_011707)	-47	NM_011707	22370	Mm.3667	NM_011707	ENSMUSG00000017344	Vtn	AI256434|Vn	vitronectin	protein-coding
mm_108780.1	chr12	89834836	89834836	+	1	NA	intron (NM_001252074, intron 1 of 6)	intron (NM_001252074, intron 1 of 6)	22353	NM_001252074	18191	Mm.425766	NM_172544	ENSMUSG00000066392	Nrxn3	-	neurexin III	protein-coding
mm_25749.1	chr3	123267209	123267221	+	1	NA	promoter-TSS (NM_027135)	promoter-TSS (NM_027135)	-281	NM_027135	69608	Mm.29293	NM_027135	ENSMUSG00000039234	Sec24d	2310020L09Rik|Gm1349	Sec24 related gene family, member D (S. cerevisiae)	protein-coding
mm_37019.1	chr4	113999521	113999531	-	1	NA	promoter-TSS (NM_001167878)	promoter-TSS (NM_001167878)	-23	NM_001167876	242627	Mm.484115	NM_001167876	ENSMUSG00000078598	Skint5	OTTMUSG00000008560|Skint-5	selection and upkeep of intraepithelial T cells 5	protein-coding
mm_113141.1	chr13	24651435	24651438	+	1	NA	intron (NM_029679, intron 1 of 22)	intron (NM_029679, intron 1 of 22)	12788	NM_029679	193385	Mm.217319	NM_029679	ENSMUSG00000036006	Fam65b	-	family with sequence similarity 65, member B	protein-coding
mm_172932.1	chr9	7751668	7751684	+	1	NA	Intergenic	Intergenic	-12401	NM_133739	71929	Mm.283293	NM_133739	ENSMUSG00000050912	Tmem123	2310075C12Rik	transmembrane protein 123	protein-coding
mm_71137.1	chr8	39045662	39045691	+	1	NA	intron (NM_030254, intron 1 of 7)	intron (NM_030254, intron 1 of 7)	39809	NM_030254	80286	Mm.272722	NM_030254	ENSMUSG00000039530	Tusc3	AU022242|BC003311|N33	tumor suppressor candidate 3	protein-coding
mm_162603.1	chr1	183221429	183221442	-	1	NA	promoter-TSS (NM_001278219)	promoter-TSS (NM_001278219)	94	NM_001278218	68897	Mm.327216	NM_026866	ENSMUSG00000030768	Disp1	1190008H24Rik|DispA	dispatched RND transporter family member 1	protein-coding
mm_63194.1	chr7	125603617	125603625	+	1	NA	5' UTR (NM_021887, exon 1 of 9)	5' UTR (NM_021887, exon 1 of 9)	192	NM_021887	60504	Mm.155643	NM_021887	ENSMUSG00000030745	Il21r	NILR	interleukin 21 receptor	protein-coding
mm_2137.1	chr1	88073750	88073796	+	1	NA	intron (NM_201644, intron 1 of 4)	intron (NM_201644, intron 1 of 4)	2994	NM_201644	394434	Mm.300095	NM_201644	ENSMUSG00000090175	Ugt1a9	UDPGT|UDPGT 1-9|UGT1-09|UGT1.9|UGTP4|Ugt1a12|mUGTBr/P	UDP glucuronosyltransferase 1 family, polypeptide A9	protein-coding
mm_71824.1	chr8	68895845	68895853	+	1	NA	exon (NM_008509, exon 5 of 10)	exon (NM_008509, exon 5 of 10)	15294	NM_008509	16956	Mm.1514	NM_008509	ENSMUSG00000015568	Lpl	-	lipoprotein lipase	protein-coding
mm_12168.1	chr2	62610475	62610514	+	1	NA	exon (NM_027835, exon 7 of 16)	exon (NM_027835, exon 7 of 16)	35761	NM_027835	71586	Mm.136224	NM_027835	ENSMUSG00000026896	Ifih1	9130009C22Rik|Helicard|Hlcd|MDA5|RLR-2	interferon induced with helicase C domain 1	protein-coding
mm_105982.1	chr11	115612508	115612547	-	1	NA	promoter-TSS (NM_027162)	promoter-TSS (NM_027162)	-24	NM_001243586	69674	Mm.390387	NM_027162	ENSMUSG00000020743	Mif4gd	1110014L05Rik|2310075G12Rik	MIF4G domain containing	protein-coding
mm_114182.1	chr13	55645422	55645432	+	1	NA	exon (NM_001282055, exon 4 of 23)	exon (NM_001282055, exon 4 of 23)	10428	NM_001282055	212880	Mm.202725	NM_145975	ENSMUSG00000021500	Ddx46	2200005K02Rik|8430438J23Rik|AI325430|AI957095|mKIAA0801	DEAD (Asp-Glu-Ala-Asp) box polypeptide 46	protein-coding
mm_39259.1	chr5	3544083	3544112	+	1	NA	intron (NM_001042501, intron 1 of 10)	CpG	264	NM_001042501	68152	Mm.240265	NM_026583	ENSMUSG00000058503	Fam133b	2900022K02Rik|5830415L20Rik	family with sequence similarity 133, member B	protein-coding
mm_58618.1	chr7	5068902	5069002	+	1	NA	intron (NM_133671, intron 5 of 11)	C-rich|Low_complexity|Low_complexity	6809	NM_001205231	22185	Mm.360389	NM_133671	ENSMUSG00000030435	U2af2	65kDa	U2 small nuclear ribonucleoprotein auxiliary factor (U2AF) 2	protein-coding
mm_64016.1	chr7	140247151	140247175	+	1	NA	promoter-TSS (NM_001128145)	promoter-TSS (NM_001128145)	-138	NM_175533	244234	Mm.85125	NM_175533	ENSMUSG00000054672	5830411N06Rik	Scart2	RIKEN cDNA 5830411N06 gene	protein-coding
mm_122439.1	chr14	45219436	45219446	-	1	NA	promoter-TSS (NM_027518)	promoter-TSS (NM_027518)	-16	NM_001310534	70561	Mm.28129	NM_172597	ENSMUSG00000021830	Txndc16	5730420B22Rik|C77647	thioredoxin domain containing 16	protein-coding
mm_79680.1	chr9	59751143	59751225	+	1	NA	promoter-TSS (NM_001172071)	promoter-TSS (NM_001172071)	10	NM_173018	270163	Mm.249545	NM_173018	ENSMUSG00000039585	Myo9a	4732465J09Rik|C130068I12Rik|C230003M11	myosin IXa	protein-coding
mm_149992.1	chr19	29252455	29252485	+	1	NA	5' UTR (NM_008413, exon 2 of 25)	5' UTR (NM_008413, exon 2 of 25)	667	NM_008413	16452	Mm.275839	NM_008413	ENSMUSG00000024789	Jak2	Fd17	Janus kinase 2	protein-coding
mm_163825.1	chr14	19416894	19416904	+	1	NA	Intergenic	GSAT_MM|Satellite|Satellite	185688	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
mm_113554.1	chr13	38151284	38151307	+	1	NA	promoter-TSS (NM_023842)	promoter-TSS (NM_023842)	1	NM_023842	109620	Mm.355327	NM_023842	ENSMUSG00000054889	Dsp	2300002E22Rik|5730453H04Rik|AA407887|AA407888|AW109828|DP|rul	desmoplakin	protein-coding
mm_99714.1	chr11	106256141	106256172	+	1	NA	promoter-TSS (NM_025310)	promoter-TSS (NM_025310)	-29	NM_008950	19184	Mm.272361	NM_008950	ENSMUSG00000020708	Psmc5	mSUG1	protease (prosome, macropain) 26S subunit, ATPase 5	protein-coding
mm_154301.1	chr19	61224988	61224998	-	1	NA	3' UTR (NM_009970, exon 12 of 12)	3' UTR (NM_009970, exon 12 of 12)	3425	NM_009970	12982	Mm.287228	NM_009970	ENSMUSG00000059326	Csf2ra	CD116|Csfgmra|GM-CSF-Ra|GM-CSFR	colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)	protein-coding
mm_130377.1	chr15	97831538	97831580	-	1	NA	5' UTR (NM_019572, exon 1 of 24)	5' UTR (NM_019572, exon 1 of 24)	208	NM_019572	56233	Mm.384027	NM_019572	ENSMUSG00000022475	Hdac7	5830434K02Rik|HD7|HD7a|Hdac7a|mFLJ00062	histone deacetylase 7	protein-coding
mm_96578.1	chr11	69060109	69060131	+	1	NA	exon (NM_028005, exon 1 of 1)	exon (NM_028005, exon 1 of 1)	345	NM_028005	71923	Mm.340257	NM_028005	ENSMUSG00000045176	Borcs6	2310047M10Rik	BLOC-1 related complex subunit 6	protein-coding
mm_115892.1	chr13	22009731	22009749	-	1	NA	promoter-TSS (NM_019429)	promoter-TSS (NM_019429)	1	NM_019429	54373	Mm.32043	NM_019429	ENSMUSG00000006179	Prss16	AI448615|TSSP	protease, serine 16 (thymus)	protein-coding
mm_110341.1	chr12	36042477	36042516	-	1	NA	promoter-TSS (NM_025359)	promoter-TSS (NM_025359)	-18	NM_025359	66109	Mm.254663	NM_025359	ENSMUSG00000020577	Tspan13	1100001I23Rik|NET-6|Tm4sf13	tetraspanin 13	protein-coding
mm_51478.1	chr6	83015279	83015317	+	1	NA	intron (NM_033079, intron 7 of 9)	intron (NM_033079, intron 7 of 9)	18173	NM_010070	13448	Mm.156	NM_010070	ENSMUSG00000068335	Dok1	AW557123|p62DOK	docking protein 1	protein-coding
mm_164497.1	chr16	91355338	91355369	-	1	NA	Intergenic	Intergenic	-17430	NM_010509	15976	Mm.6834	NM_010509	ENSMUSG00000022971	Ifnar2	AI747302|Ifnar-2	interferon (alpha and beta) receptor 2	protein-coding
mm_87515.1	chr10	52690497	52690554	+	1	NA	promoter-TSS (NM_178675)	promoter-TSS (NM_178675)	24	NM_178675	215085	Mm.338690	NM_178675	ENSMUSG00000038602	Slc35f1	Duf6|E130016L02	solute carrier family 35, member F1	protein-coding
mm_160998.1	chr11	115091435	115091435	+	1	NA	promoter-TSS (NM_001163753)	promoter-TSS (NM_001163753)	4	NM_001163753	58222	Mm.143789	NM_021411	ENSMUSG00000020732	Rab37	B230331O03Rik|B230354I04Rik	RAB37, member RAS oncogene family	protein-coding
mm_62936.1	chr7	118740725	118740754	+	1	NA	exon (NM_027815, exon 1 of 31)	exon (NM_027815, exon 1 of 31)	468	NM_027815	71517	Mm.213298	NM_027815	ENSMUSG00000030982	9030624J02Rik	2610029J22Rik	RIKEN cDNA 9030624J02 gene	protein-coding
mm_91770.1	chr10	51590440	51590464	-	1	NA	promoter-TSS (NM_029894)	promoter-TSS (NM_029894)	8	NM_029894	77296	Mm.30588	NM_029894	ENSMUSG00000019909	Fam162b	9430073N08Rik	family with sequence similarity 162, member B	protein-coding
mm_36709.1	chr4	97584613	97584643	-	1	NA	promoter-TSS (NR_015513)	promoter-TSS (NR_015513)	-37	NR_015513	319865	Mm.373807	NM_177023		E130114P18Rik	-	RIKEN cDNA E130114P18 gene	ncRNA
mm_130707.1	chr15	100720224	100720227	-	1	NA	5' UTR (NM_172451, exon 2 of 12)	5' UTR (NM_172451, exon 2 of 12)	252	NM_001161768	207839	Mm.22969	NM_172451	ENSMUSG00000037280	Galnt6	4632410F13|AW047994|GalNAc-T6	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 6	protein-coding
mm_11219.1	chr2	29699788	29699808	+	1	NA	exon (NM_054050, exon 7 of 24)	exon (NM_054050, exon 7 of 24)	-61730	NM_001177392	433416	Mm.330112	NM_001034887	ENSMUSG00000075425	Gm13547	OTTMUSG00000012686	predicted gene 13547	protein-coding
mm_64582.1	chr7	145300807	145300831	+	1	NA	promoter-TSS (NM_145379)	promoter-TSS (NM_145379)	-90	NM_145379	211577	Mm.215151	NM_145379	ENSMUSG00000031070	Mrgprf	BC019711|Mgrc|MrgF	MAS-related GPR, member F	protein-coding
mm_102136.1	chr11	53480011	53480024	-	1	NA	5' UTR (NM_183173, exon 1 of 1)	5' UTR (NM_183173, exon 1 of 1)	178	NM_183173	237761	Mm.145208	NM_183173	ENSMUSG00000044352	Sowaha	A830006N08Rik|Ankrd43	sosondowah ankyrin repeat domain family member A	protein-coding
mm_104381.1	chr11	94474053	94474069	-	1	NA	5' UTR (NM_001177890, exon 1 of 35)	5' UTR (NM_001177890, exon 1 of 35)	137	NM_001177888	12291	Mm.29585	NM_009783	ENSMUSG00000020866	Cacna1g	Cav3.1d|[a]1G|a1G|alpha-1G|mKIAA1123	calcium channel, voltage-dependent, T type, alpha 1G subunit	protein-coding
mm_104775.1	chr11	98545951	98545981	-	1	NA	promoter-TSS (NM_011771)	promoter-TSS (NM_011771)	65	NM_011771	22780	Mm.133367	NM_011771	ENSMUSG00000018168	Ikzf3	5830411O07Rik|Aiolos|Zfpn1a3|Znfn1a3	IKAROS family zinc finger 3	protein-coding
mm_69089.1	chr7	127017267	127017292	-	1	NA	promoter-TSS (NM_030240)	promoter-TSS (NM_030240)	73	NM_030240	67278	Mm.345385	NM_030240	ENSMUSG00000030680	Pagr1a	2900092E17Rik|C77040|PA1|PAGR1	PAXIP1 associated glutamate rich protein 1A	protein-coding
mm_106110.1	chr11	116329428	116329440	-	1	NA	Intergenic	Intergenic	5920	NM_008240	15223	Mm.378938	NM_008240	ENSMUSG00000034227	Foxj1	FKHL-13|HFH-4|Hfh4	forkhead box J1	protein-coding
mm_77335.1	chr8	119558682	119558692	-	1	NA	promoter-TSS (NM_001167910)	promoter-TSS (NM_001167910)	74	NM_001167910	56453	Mm.206934	NM_019709	ENSMUSG00000031835	Mbtps1	0610038M03Rik|AV003995|S1P|SKI-1|Ski1|mKIAA0091	membrane-bound transcription factor peptidase, site 1	protein-coding
mm_88616.1	chr10	79840887	79840904	+	1	NA	intron (NR_038088, intron 3 of 4)	ZP3AR|Satellite|Satellite	-13537	NM_001077363	19205	Mm.265610	NM_008956	ENSMUSG00000006498	Ptbp1	AA407203|AL033359|HNRPI|PTB-1|PTB2|PTB3|PTB4|Ptb|pPTB	polypyrimidine tract binding protein 1	protein-coding
mm_76940.1	chr8	105941667	105941680	-	1	NA	exon (NM_008490, exon 5 of 6)	exon (NM_008490, exon 5 of 6)	1729	NM_008490	16816	Mm.1593	NM_008490	ENSMUSG00000035237	Lcat	AI046659|D8Wsu61e	lecithin cholesterol acyltransferase	protein-coding
mm_121511.1	chr14	121963826	121963833	+	1	NA	intron (NM_183031, intron 1 of 1)	intron (NM_183031, intron 1 of 1)	1364	NM_183031	321019	Mm.265618	NM_183031	ENSMUSG00000051212	Gpr183	Ebi2	G protein-coupled receptor 183	protein-coding
mm_138123.1	chr17	34153153	34153164	+	1	NA	promoter-TSS (NM_010387)	promoter-TSS (NM_010387)	-33	NM_010387	14999	Mm.460938	NM_010387	ENSMUSG00000079547	H2-DMb1	AI385589|H-2Mb1|H2-Mb1	histocompatibility 2, class II, locus Mb1	protein-coding
mm_116580.1	chr13	47105791	47105875	-	1	NA	intron (NM_025900, intron 1 of 10)	CpG	388	NM_025900	110052	Mm.131150	NM_025900	ENSMUSG00000021377	Dek	1810019E15Rik|D13H6S231E	DEK oncogene (DNA binding)	protein-coding
mm_151450.1	chr19	57691367	57691372	+	1	NA	intron (NM_181415, intron 13 of 28)	MER57C2|LTR|ERV1	80335	NM_181415	226255	Mm.245340	NM_181415	ENSMUSG00000054843	Atrnl1	AI504415|AW555641|Alp|Atrnl|Atrnlp	attractin like 1	protein-coding
mm_38315.1	chr4	137249117	137249119	-	1	NA	Intergenic	Intergenic	-28517	NM_009523	22417	Mm.20355	NM_009523	ENSMUSG00000036856	Wnt4	Wnt-4	wingless-type MMTV integration site family, member 4	protein-coding
mm_127239.1	chr15	99582862	99582865	+	1	NA	intron (NM_009699, intron 2 of 3)	B1_Mur2|SINE|Alu	3807	NM_009699	11827	Mm.20206	NM_009699	ENSMUSG00000023013	Aqp2	AQP-CD|WCH-CD|cph|jpk	aquaporin 2	protein-coding
mm_163061.1	chr11	65032232	65032237	+	1	NA	intron (NM_175003, intron 10 of 20)	intron (NM_175003, intron 10 of 20)	53199	NM_023479	68626	Mm.157711	NM_023479	ENSMUSG00000020549	Elac2	1110017O07Rik|D11Wsu80e|Hpc2	elaC ribonuclease Z 2	protein-coding
mm_137327.1	chr17	25016507	25016579	+	1	NA	5' UTR (NM_134126, exon 1 of 30)	5' UTR (NM_134126, exon 1 of 30)	457	NM_134126	106633	Mm.32802	NM_134126	ENSMUSG00000024169	Ift140	AI661311|Tce5|Wdtc2|mKIAA0590	intraflagellar transport 140	protein-coding
mm_99936.1	chr11	111026899	111026909	+	1	NA	3' UTR (NM_001252208, exon 2 of 2)	3' UTR (NM_001252208, exon 2 of 2)	3044	NM_001252208	16517	Mm.30176	NM_010604	ENSMUSG00000051497	Kcnj16	6430410F18Rik|AI132396|Kir5.1	potassium inwardly-rectifying channel, subfamily J, member 16	protein-coding
mm_80419.1	chr9	77838893	77838894	+	1	NA	Intergenic	Intergenic	-78472	NM_134255	68801	Mm.430736	NM_134255	ENSMUSG00000032349	Elovl5	1110059L23Rik|AI747313|AU043003|HELO1	ELOVL family member 5, elongation of long chain fatty acids (yeast)	protein-coding
mm_58470.1	chr7	3390630	3390707	+	1	NA	Intergenic	C-rich|Low_complexity|Low_complexity	-3374	NM_133190	81905	Mm.357990	NM_133190	ENSMUSG00000053395	Cacng8	-	calcium channel, voltage-dependent, gamma subunit 8	protein-coding
mm_25986.1	chr3	133534403	133534413	+	1	NA	intron (NM_001040400, intron 1 of 10)	intron (NM_001040400, intron 1 of 10)	9982	NM_001346736	214133	Mm.347816	NM_145989	ENSMUSG00000040943	Tet2	Ayu17-449|E130014J05Rik|mKIAA1546	tet methylcytosine dioxygenase 2	protein-coding
mm_54783.1	chr6	41544357	41544369	-	1	NA	Intergenic	Intergenic	22587	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_128170.1	chr15	34269863	34269863	-	1	NA	intron (NM_033521, intron 2 of 6)	intron (NM_033521, intron 2 of 6)	31837	NM_033521	114128	Mm.197518	NM_033521	ENSMUSG00000022257	Laptm4b	C330023P13Rik|LAPTM4beta	lysosomal-associated protein transmembrane 4B	protein-coding
mm_148060.1	chr18	72166234	72166281	-	1	NA	intron (NM_007831, intron 1 of 28)	intron (NM_007831, intron 1 of 28)	184812	NM_007831	13176	Mm.167882	NM_007831	ENSMUSG00000060534	Dcc	C030036D22Rik|Igdcc1	deleted in colorectal carcinoma	protein-coding
mm_49322.1	chr6	18866343	18866355	+	1	NA	promoter-TSS (NM_029202)	promoter-TSS (NM_029202)	31	NM_001167757	75196	Mm.67665	NM_029202	ENSMUSG00000029517	Ankrd7	4930532L20Rik|AV278427	ankyrin repeat domain 7	protein-coding
mm_147022.1	chr18	34624823	34624844	-	1	NA	promoter-TSS (NM_009004)	promoter-TSS (NM_009004)	30	NM_030147	78656	Mm.45602	NM_030147	ENSMUSG00000003778	Brd8	2610007E11Rik|4432404P07Rik|SMAP	bromodomain containing 8	protein-coding
mm_147584.1	chr18	56504441	56504447	-	1	NA	TTS (NM_026240)	TTS (NM_026240)	-33695	NR_106160	102465790		NR_106160	ENSMUSG00000099196	Mir1258	Gm27371|mmu-mir-1258	microRNA 1258	ncRNA
mm_156411.1	chrX	140664532	140664554	+	1	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	-13485	NM_011845	23947	Mm.131097	NM_011845	ENSMUSG00000000266	Mid2	FXY2|Trim1	midline 2	protein-coding
mm_112042.1	chr12	111671323	111671332	-	1	NA	exon (NM_021273, exon 4 of 8)	exon (NM_021273, exon 4 of 8)	1011	NM_021273	12709	Mm.16831	NM_021273	ENSMUSG00000001270	Ckb	B-CK|Bck|Ck-3|Ck3|Ckbb	creatine kinase, brain	protein-coding
mm_157616.1	chrX	55895849	55895853	-	1	NA	Intergenic	Intergenic	-240721	NM_027510	70691	Mm.335676	NM_027510	ENSMUSG00000031125	3830403N18Rik	Xlrl	RIKEN cDNA 3830403N18 gene	protein-coding
mm_80802.1	chr9	96259271	96259277	+	1	NA	promoter-TSS (NM_001184710)	promoter-TSS (NM_001184710)	26	NM_001184710	211586	Mm.17977	NM_178667	ENSMUSG00000032411	Tfdp2	1110029I05Rik|A330080J22Rik|DP-3|DP3	transcription factor Dp 2	protein-coding
mm_135281.1	chr16	38447521	38447568	-	1	NA	exon (NM_007414, exon 3 of 4)	exon (NM_007414, exon 3 of 4)	5145	NM_007414	11544	Mm.20047	NM_007414	ENSMUSG00000002844	Adprh	Arh1	ADP-ribosylarginine hydrolase	protein-coding
mm_92249.1	chr10	70559414	70559430	-	1	NA	TTS (NM_001143777)	TTS (NM_001143777)	33390	NM_001162846	70911	Mm.19825	NM_178621	ENSMUSG00000037747	Phyhipl	4921522K17Rik|AI267048	phytanoyl-CoA hydroxylase interacting protein-like	protein-coding
mm_98209.1	chr11	87797558	87797568	+	1	NA	exon (NM_010824, exon 8 of 14)	exon (NM_010824, exon 8 of 14)	3779	NM_010824	17523	Mm.4668	NM_010824	ENSMUSG00000009350	Mpo	mKIAA4033	myeloperoxidase	protein-coding
mm_151148.1	chr19	53140509	53140525	+	1	NA	promoter-TSS (NM_001164099)	promoter-TSS (NM_001164099)	74	NM_001164101	27360	Mm.426080	NM_013758	ENSMUSG00000025026	Add3	AI463285|R75380	adducin 3 (gamma)	protein-coding
mm_59526.1	chr7	27619352	27619354	+	1	NA	intron (NM_007434, intron 4 of 13)	B2_Mm2|SINE|B2	12017	NM_001331109	11652	Mm.177194	NM_007434	ENSMUSG00000004056	Akt2	2410016A19Rik|AW554154|PKB|PKBbeta	thymoma viral proto-oncogene 2	protein-coding
mm_150599.1	chr19	40737267	40737281	+	1	NA	intron (NM_001304721, intron 9 of 9)	intron (NM_001304721, intron 9 of 9)	77504	NM_009848	12495	Mm.2824	NM_009848	ENSMUSG00000048120	Entpd1	2610206B08Rik|AA408691|Cd39|NTPDase-1	ectonucleoside triphosphate diphosphohydrolase 1	protein-coding
mm_70589.1	chr8	13173620	13173669	+	1	NA	exon (NM_010684, exon 7 of 9)	exon (NM_010684, exon 7 of 9)	14483	NM_010684	16783	Mm.16716	NM_010684	ENSMUSG00000031447	Lamp1	CD107a|LGP-120|LGP-A|Lamp-1|P2B	lysosomal-associated membrane protein 1	protein-coding
mm_40369.1	chr5	51040099	51040105	+	1	NA	Intergenic	Intergenic	513819	NR_027710	19017	Mm.259072	NM_008904	ENSMUSG00000029167	Ppargc1a	A830037N07Rik|ENSMUSG00000079510|Gm11133|PGC-1|PPARGC-1-alpha|Pgc-1alpha|Pgc1|Pgco1|Ppargc1	peroxisome proliferative activated receptor, gamma, coactivator 1 alpha	protein-coding
mm_63512.1	chr7	127875743	127875758	+	1	NA	intron (NM_146259, intron 1 of 2)	CpG	1073	NM_146259	244219	Mm.207872	NM_146259	ENSMUSG00000049728	Zfp668	BC030314|E130018B19Rik|Znf668	zinc finger protein 668	protein-coding
mm_120079.1	chr14	57571595	57571625	+	1	NA	promoter-TSS (NM_026526)	promoter-TSS (NM_026526)	-41	NM_026526	68043	Mm.45225	NM_026526	ENSMUSG00000021951	Eef1akmt1	2510005D08Rik|AW045965|Ayu21-96|Gt(pU21)96Imeg|GtAyu21-96|N6amt2	eukaryotic translation elongation factor 1 alpha lysine methyltransferase 1	protein-coding
mm_36535.1	chr4	86655504	86655519	-	1	NA	Intergenic	B1_Mus1|SINE|Alu	14548	NM_007408	11520	Mm.381	NM_007408	ENSMUSG00000028494	Plin2	AA407157|ADPH|Adfp|Adrp	perilipin 2	protein-coding
mm_72895.1	chr8	90828849	90828895	+	1	NA	promoter-TSS (NM_177224)	promoter-TSS (NM_177224)	37	NM_177224	109151	Mm.100615	NM_177224	ENSMUSG00000056608	Chd9	1810014J18Rik|9030205D12Rik|A330063D19Rik|AD013|PRIC320|mKIAA0308	chromodomain helicase DNA binding protein 9	protein-coding
mm_133895.1	chr16	97536080	97536085	+	1	NA	promoter-TSS (NR_003508)	promoter-TSS (NR_003508)	1	NR_003508	17858	Mm.14157	NM_013606	ENSMUSG00000023341	Mx2	AI528743|Mx-2	MX dynamin-like GTPase 2	protein-coding
mm_133784.1	chr16	95257575	95257579	+	1	NA	promoter-TSS (NM_001271695)	promoter-TSS (NM_001271695)	19	NM_001271690	16516	Mm.272239	NM_019664	ENSMUSG00000062609	Kcnj15	4930414N08Rik|AI182284|AI267127|IRKK|Kir4.2	potassium inwardly-rectifying channel, subfamily J, member 15	protein-coding
mm_131178.1	chr16	7080739	7080742	+	1	NA	intron (NM_183188, intron 1 of 12)	intron (NM_183188, intron 1 of 12)	10905	NM_183188	268859	Mm.370334	NM_021477	ENSMUSG00000008658	Rbfox1	A2bp|A2bp1|Hrnbp1|fox-1	RNA binding protein, fox-1 homolog (C. elegans) 1	protein-coding
mm_81979.1	chr9	121314281	121314317	+	1	NA	Intergenic	Intergenic	-37127	NM_177589	209012	Mm.371804	NM_177589	ENSMUSG00000040936	Ulk4	4932415A06Rik|A730098P15	unc-51-like kinase 4	protein-coding
mm_118740.1	chr14	22310942	22310974	+	1	NA	intron (NM_028275, intron 2 of 6)	B4A|SINE|B4	231840	NR_046307	74896	Mm.444661	NR_046307		4930405A10Rik	4930456G20Rik	RIKEN cDNA 4930405A10 gene	ncRNA
mm_169806.1	chr16	18533251	18533251	-	1	NA	intron (NR_104347, intron 2 of 8)	SSU-rRNA_Hsa|rRNA|rRNA	34380	NR_104347	13972	Mm.236139	NM_023120	ENSMUSG00000000884	Gnb1l	ESTM55|Gm16314|Me49f07|OTTMUSG00000033458|Wdr14|Wdvcf	guanine nucleotide binding protein (G protein), beta polypeptide 1-like	protein-coding
mm_110731.1	chr12	69769304	69769307	-	1	NA	intron (NM_183294, intron 3 of 9)	intron (NM_183294, intron 3 of 9)	-5361	NR_030450	751538		NR_030450	ENSMUSG00000076065	Mir681	Mirn681|mmu-mir-681	microRNA 681	ncRNA
mm_148973.1	chr19	7557474	7557497	+	1	NA	promoter-TSS (NM_139269)	promoter-TSS (NM_139269)	26	NM_139269	225845	Mm.274810	NM_139269	ENSMUSG00000060675	Pla2g16	C78643|HRSL3|Hrasls3|Hrev107|MLP-3	phospholipase A2, group XVI	protein-coding
mm_92503.1	chr10	78352324	78352459	-	1	NA	promoter-TSS (NM_053014)	promoter-TSS (NM_053014)	-691	NM_053014	28169	Mm.141230	NM_053014	ENSMUSG00000001211	Agpat3	AW061257|AW493985|D10Jhu12e|lpaat3	1-acylglycerol-3-phosphate O-acyltransferase 3	protein-coding
mm_23893.1	chr3	83031592	83031603	+	1	NA	exon (NM_010196, exon 5 of 5)	exon (NM_010196, exon 5 of 5)	5444	NM_001111048	14161	Mm.88793	NM_010196	ENSMUSG00000028001	Fga	ENSMUSG00000059807|Fib	fibrinogen alpha chain	protein-coding
mm_162581.1	chr1	178337588	178337591	-	1	NA	5' UTR (NM_016805, exon 1 of 14)	5' UTR (NM_016805, exon 1 of 14)	195	NM_016805	51810	Mm.86589	NM_016805	ENSMUSG00000039630	Hnrnpu	AA408410|AI256620|AL024194|AL024437|AW557595|C86794|Hnrpu|SAFA|Sp120|hnRNP U	heterogeneous nuclear ribonucleoprotein U	protein-coding
mm_145167.1	chr18	46742846	46742892	+	1	NA	intron (NM_001303015, intron 1 of 6)	intron (NM_001303015, intron 1 of 6)	993	NM_001303015	11777	Mm.312536	NM_009681	ENSMUSG00000024480	Ap3s1	-	adaptor-related protein complex 3, sigma 1 subunit	protein-coding
mm_8846.1	chr1	162705545	162705564	-	1	NA	exon (NM_001081290, exon 16 of 35)	exon (NM_001081290, exon 16 of 35)	35002	NM_001081290	226562	Mm.245446	NM_001081290	ENSMUSG00000040225	Prrc2c	1810043M20Rik|9630039I18Rik|A630006J20|Bat2d|Bat2d1|Bat2l2|E130112L15Rik|Prrc3|mKIAA1096	proline-rich coiled-coil 2C	protein-coding
mm_136938.1	chr17	14249810	14249830	+	1	NA	Intergenic	Intergenic	-29686	NM_022315	64074	Mm.30162	NM_022315	ENSMUSG00000023886	Smoc2	1700056C05Rik|5430426J21Rik|Smoc2l	SPARC related modular calcium binding 2	protein-coding
mm_158539.1	chrX	143933145	143933151	-	1	NA	promoter-TSS (NM_010025)	promoter-TSS (NM_010025)	-24	NM_001110222	13193	Mm.12871	NM_010025	ENSMUSG00000031285	Dcx	Dbct	doublecortin	protein-coding
mm_163598.1	chr13	43266423	43266434	-	1	NA	intron (NM_001033399, intron 1 of 1)	L1_Mur3|LINE|L1	37744	NM_001033399	328232	Mm.441399	NM_001033399	ENSMUSG00000051335	Gfod1	9630032O13|AI850995	glucose-fructose oxidoreductase domain containing 1	protein-coding
mm_75336.1	chr8	43305899	43305910	-	1	NA	intron (NM_009556, intron 1 of 3)	intron (NM_009556, intron 1 of 3)	1105	NM_009556	22702	Mm.285848	NM_009556	ENSMUSG00000051176	Zfp42	Rex-1|Rex1|Zfp-42	zinc finger protein 42	protein-coding
mm_8115.1	chr1	135919343	135919353	-	1	NA	promoter-TSS (NM_019645)	promoter-TSS (NM_019645)	-141	NM_019645	18772	Mm.4494	NM_019645	ENSMUSG00000026413	Pkp1	-	plakophilin 1	protein-coding
mm_85107.1	chr9	95404510	95404541	-	1	NA	3' UTR (NM_018763, exon 2 of 2)	3' UTR (NM_018763, exon 2 of 2)	2745	NM_018763	54371	Mm.212446	NM_018763	ENSMUSG00000033350	Chst2	AI428561|AW121776|C130041E03Rik|Chts2|GST-2|GlcNAc6ST|Gn6st	carbohydrate sulfotransferase 2	protein-coding
mm_6007.1	chr1	58973422	58973440	-	1	NA	promoter-TSS (NM_172406)	promoter-TSS (NM_172406)	51	NM_172406	70827	Mm.222887	NM_172406	ENSMUSG00000026028	Trak2	2900022D04Rik|4733401O11Rik|AI480836|AW046271|Als2cr3|CALS-C|GRIF-1|GRIF1|OIP98|mKIAA0549	trafficking protein, kinesin binding 2	protein-coding
mm_50821.1	chr6	54456201	54456209	+	1	NA	intron (NM_001167860, intron 1 of 7)	RSINE1|SINE|B4	3322	NM_001167861	330319	Mm.434326	NM_001167860	ENSMUSG00000086040	Wipf3	9030621G03|BQ952480	WAS/WASL interacting protein family, member 3	protein-coding
mm_91293.1	chr10	24915573	24915581	-	1	NA	3' UTR (NM_007482, exon 8 of 8)	3' UTR (NM_007482, exon 8 of 8)	4913	NR_105870	102465545		NR_105870	ENSMUSG00000099181	Mir6905	Gm27879|mmu-mir-6905	microRNA 6905	ncRNA
mm_38641.1	chr4	143162141	143162172	-	1	NA	exon (NM_001081355, exon 6 of 10)	exon (NM_001081355, exon 6 of 10)	-25994	NR_105988	102465618		NR_105988	ENSMUSG00000106597	Mir7021	mmu-mir-7021	microRNA 7021	ncRNA
mm_49818.1	chr6	37442502	37442524	+	1	NA	promoter-TSS (NM_178661)	promoter-TSS (NM_178661)	-365	NM_178661	208647	Mm.169929	NM_178661	ENSMUSG00000038648	Creb3l2	BBF2H7|C530025K05Rik|SCIRR69	cAMP responsive element binding protein 3-like 2	protein-coding
mm_63774.1	chr7	131548756	131548761	+	1	NA	Intergenic	Intergenic	-5304	NM_145998	15372	Mm.303357	NM_145998	ENSMUSG00000050100	Hmx2	Nkx-5.2|Nkx5-2	H6 homeobox 2	protein-coding
mm_1796.1	chr1	79855954	79855988	+	1	NA	intron (NM_009255, intron 1 of 8)	intron (NM_009255, intron 1 of 8)	2694	NM_009255	20720	Mm.3093	NM_009255	ENSMUSG00000026249	Serpine2	B230326M24Rik|PAI-1|PI-7|PI7|PN-1|Spi4	serine (or cysteine) peptidase inhibitor, clade E, member 2	protein-coding
mm_31009.1	chr4	40269564	40269595	+	1	NA	promoter-TSS (NR_045265)	promoter-TSS (NR_045265)	0	NR_045265	100504309	Mm.392019	NR_045265		Toporsos	2010003O02Rik	topoisomerase I binding, arginine/serine-rich, opposite strand	ncRNA
mm_71804.1	chr8	68368462	68368469	+	1	NA	promoter-TSS (NR_038189)	promoter-TSS (NR_038189)	6	NR_038181	73609	Mm.443247	NR_038181	ENSMUSG00000085197	1700125H03Rik	4930510D22Rik	RIKEN cDNA 1700125H03 gene	ncRNA
mm_68956.1	chr7	126566108	126566127	-	1	NA	exon (NM_146200, exon 2 of 21)	exon (NM_146200, exon 2 of 21)	249	NM_146200	56347	Mm.22776	NM_146200	ENSMUSG00000030738	Eif3c	110kDa|3230401O13Rik|Eif3s8|NIPIL(A3)|NipilA3|Xs|Xsl	eukaryotic translation initiation factor 3, subunit C	protein-coding
mm_27246.1	chr3	36613371	36613397	-	1	NA	promoter-TSS (NM_027810)	promoter-TSS (NM_027810)	5	NM_027810	71492	Mm.286187	NM_027810	ENSMUSG00000037325	Bbs7	8430406N16Rik	Bardet-Biedl syndrome 7 (human)	protein-coding
mm_4680.1	chr1	180568914	180568960	+	1	NA	promoter-TSS (NM_007415)	promoter-TSS (NM_007415)	-38	NM_007415	11545	Mm.277779	NM_007415	ENSMUSG00000026496	Parp1	5830444G22Rik|AI893648|ARTD1|Adprp|Adprt1|C80510|PARP|PPOL|parp-1|sPARP-1	poly (ADP-ribose) polymerase family, member 1	protein-coding
mm_97306.1	chr11	76679758	76679787	+	1	NA	promoter-TSS (NM_177709)	promoter-TSS (NM_177709)	-101	NM_177709	237858	Mm.127006	NM_177709	ENSMUSG00000046275	Tusc5	C130069F04Rik|DSPB1|Lost1	tumor suppressor candidate 5	protein-coding
mm_19982.1	chr2	118538991	118538995	-	1	NA	intron (NM_138313, intron 4 of 4)	intron (NM_138313, intron 4 of 4)	5594	NR_138603	171543	Mm.210125	NM_138313	ENSMUSG00000040093	Bmf	AW260063|AW411872	BCL2 modifying factor	protein-coding
mm_23891.1	chr3	83031428	83031461	+	1	NA	exon (NM_010196, exon 5 of 5)	exon (NM_010196, exon 5 of 5)	5291	NM_001111048	14161	Mm.88793	NM_010196	ENSMUSG00000028001	Fga	ENSMUSG00000059807|Fib	fibrinogen alpha chain	protein-coding
mm_45399.1	chr5	66151685	66151695	-	1	NA	promoter-TSS (NM_001291226)	promoter-TSS (NM_001291226)	264	NM_001127382	245945	Mm.36863	NM_139065	ENSMUSG00000070780	Rbm47	9530077J19Rik	RNA binding motif protein 47	protein-coding
mm_8406.1	chr1	151754991	151755031	-	1	NA	promoter-TSS (NM_001039644)	promoter-TSS (NM_001039644)	-363	NM_001311165	66967	Mm.337691	NM_001039644	ENSMUSG00000043019	Edem3	2310050N11Rik	ER degradation enhancer, mannosidase alpha-like 3	protein-coding
mm_8709.1	chr1	158968479	158968482	-	1	NA	Intergenic	Intergenic	-11042	NM_001085376	23850	Mm.458621	NM_001085376	ENSMUSG00000073530	Pappa2	PAPP-A2|PLAC3|Pappe	pappalysin 2	protein-coding
mm_150020.1	chr19	29370339	29370377	+	1	NA	intron (NM_021893, intron 1 of 6)	MER20|DNA|hAT-Charlie	2920	NM_021893	60533	Mm.245363	NM_021893	ENSMUSG00000016496	Cd274	A530045L16Rik|B7h1|Pdcd1l1|Pdcd1lg1|Pdl1	CD274 antigen	protein-coding
mm_154276.1	chr19	60790564	60790570	-	1	NA	5' UTR (NM_010123, exon 1 of 22)	5' UTR (NM_010123, exon 1 of 22)	126	NM_010123	13669	Mm.2238	NM_010123	ENSMUSG00000024991	Eif3a	A830012B05Rik|Csma|Eif3|Eif3s10|mKIAA0139	eukaryotic translation initiation factor 3, subunit A	protein-coding
mm_73725.1	chr8	112570044	112570060	+	1	NA	promoter-TSS (NM_130457)	promoter-TSS (NM_130457)	9	NM_130457	170571	Mm.209232	NM_130457	ENSMUSG00000031772	Cntnap4	Caspr4|E130114F09Rik	contactin associated protein-like 4	protein-coding
mm_98264.1	chr11	88970252	88970263	+	1	NA	Intergenic	RMER6BA|LTR|ERVK	-2381	NR_003492	72381	Mm.288885	NR_003492	ENSMUSG00000081766	2210409E12Rik	AU021711|C76890|OTTMUSG00000001303	transcription elongation factor B (SIII), polypeptide 2 pseudogene	pseudo
mm_141865.1	chr17	34804547	34804568	-	1	NA	promoter-TSS (NM_009995)	promoter-TSS (NM_009995)	-131	NM_009995	13079	Mm.440407	NM_009995	ENSMUSG00000024365	Cyp21a1	21-OH|21OH|21OHA|21OHB|CYP21OH-A|Cyp21|Cyp21-ps1|Cyp21B|Cyp21a2-ps|Cyp21a2ps|Oh21-1|Oh21-2	cytochrome P450, family 21, subfamily a, polypeptide 1	protein-coding
mm_42129.1	chr5	110978657	110978676	+	1	NA	intron (NM_001267622, intron 2 of 22)	intron (NM_001267622, intron 2 of 22)	-25478	NR_030482	735278		NR_030482	ENSMUSG00000076163	Mir701	Mirn701|mir-701|mmu-mir-701	microRNA 701	ncRNA
mm_10475.1	chr2	14388391	14388420	+	1	NA	promoter-TSS (NM_001012305)	promoter-TSS (NM_001012305)	7	NM_001012305	277468	Mm.44662	NM_001012305	ENSMUSG00000036949	Slc39a12	AW046938|Gm731	solute carrier family 39 (zinc transporter), member 12	protein-coding
mm_172052.1	chr6	128764220	128764227	-	1	NA	Intergenic	4.5SRNA|scRNA|scRNA	24418	NM_008527	17059	Mm.480764	NM_008527	ENSMUSG00000030325	Klrb1c	AI462337|CD161|Ly-59|Ly55c|Ly59|NK-RP1|NK1.1|NKR-P1.9|NKRP1|NKRP140|Nk-1|Nk-1.2|Nk1|Nk1.2|Nkrp1c|ly-55c	killer cell lectin-like receptor subfamily B member 1C	protein-coding
mm_128642.1	chr15	59374134	59374144	-	1	NA	promoter-TSS (NM_026746)	promoter-TSS (NM_026746)	13	NM_153548	223593	Mm.218665	NM_153548	ENSMUSG00000022350	Washc5	AL022848|C76463|E430025E21Rik|Kiaa0196|mKIAA0196|strumpellin	WASH complex subunit 5	protein-coding
mm_68256.1	chr7	105581599	105581614	-	1	NA	promoter-TSS (NM_001253886)	promoter-TSS (NM_001253886)	47	NM_009685	11785	Mm.38469	NM_009685	ENSMUSG00000037032	Apbb1	Fe65|Rir	amyloid beta (A4) precursor protein-binding, family B, member 1	protein-coding
mm_591.1	chr1	39551708	39551724	+	1	NA	3' UTR (NM_001033135, exon 7 of 7)	3' UTR (NM_001033135, exon 7 of 7)	-2876	NR_028555	100217461		NR_028555	ENSMUSG00000077704	Snord89	MBII-289	small nucleolar RNA, C/D box 89	snoRNA
mm_95530.1	chr11	52232307	52232315	+	1	NA	intron (NM_011543, intron 1 of 5)	CpG	316	NM_011543	21402	Mm.42944	NM_011543	ENSMUSG00000036309	Skp1a	15kDa|2610043E24Rik|2610206H23Rik|EMC19|OCP-II|OCP2|SKP1|Tceb1l|p19A|p19Skp1	S-phase kinase-associated protein 1A	protein-coding
mm_172477.1	chr7	4684671	4684671	-	1	NA	intron (NM_024172, intron 1 of 7)	intron (NM_024172, intron 1 of 7)	292	NM_024172	66245	Mm.6803	NM_024172	ENSMUSG00000063802	Hspbp1	1500019G21Rik	HSPA (heat shock 70kDa) binding protein, cytoplasmic cochaperone 1	protein-coding
mm_10059.1	chr1	193273100	193273117	-	1	NA	promoter-TSS (NM_008059)	promoter-TSS (NM_008059)	80	NM_008059	14373	Mm.439721	NM_008059	ENSMUSG00000009633	G0s2	AI255151|AV006465	G0/G1 switch gene 2	protein-coding
mm_84907.1	chr9	79977575	79977585	-	1	NA	5' UTR (NM_001081243, exon 1 of 6)	5' UTR (NM_001081243, exon 1 of 6)	302	NM_001081243	70598	Mm.23049	NM_001081243	ENSMUSG00000034898	Filip1	5730485H21Rik|AI843021	filamin A interacting protein 1	protein-coding
mm_119441.1	chr14	46760568	46760626	+	1	NA	promoter-TSS (NM_028222)	promoter-TSS (NM_028222)	56	NM_028222	72391	Mm.272394	NM_028222	ENSMUSG00000037628	Cdkn3	2410006H10Rik|KAP	cyclin-dependent kinase inhibitor 3	protein-coding
mm_126133.1	chr15	78337231	78337275	+	1	NA	intron (NM_007780, intron 3 of 13)	intron (NM_007780, intron 3 of 13)	11263	NM_007780	12983	Mm.235324	NM_007780	ENSMUSG00000071713	Csf2rb	AI848964|AIC2B|Bc|CDw131|Csf2rb1|Csfgmrb|Il3r|Il3rb|Il3rb1|Il5rb	colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage)	protein-coding
mm_164072.1	chr14	120279003	120279013	-	1	NA	intron (NM_175341, intron 1 of 8)	intron (NM_175341, intron 1 of 8)	3339	NM_175341	105559	Mm.238266	NM_175341	ENSMUSG00000022139	Mbnl2	1110002M11Rik|AI047808|AI837313|AI849185|AL118326|MBLL|R75232|mKIAA4072	muscleblind-like 2	protein-coding
mm_126007.1	chr15	76538968	76539002	+	1	NA	promoter-TSS (NM_013909)	promoter-TSS (NM_013909)	42	NM_029643	52710	Mm.28597	NM_029643	ENSMUSG00000022560	Slc52a2	2010003P03Rik|D15Ertd747e|GPCR42|Gpr172b|PAR2|mRFT1	solute carrier protein 52, member 2	protein-coding
mm_36353.1	chr4	74251742	74251758	-	1	NA	promoter-TSS (NM_144787)	promoter-TSS (NM_144787)	-129	NM_144787	76804	Mm.209059	NM_144787	ENSMUSG00000028397	Kdm4c	2410141F18Rik|AA517467|Gasc1|Jmjd2c	lysine (K)-specific demethylase 4C	protein-coding
mm_161517.1	chr15	99238064	99238064	+	1	NA	intron (NM_010601, intron 10 of 14)	intron (NM_010601, intron 10 of 14)	13088	NM_010601	16512	Mm.374793	NM_010601	ENSMUSG00000037579	Kcnh3	AU019351|C030044P22Rik|Elk2|Kv12.2|Melk2	potassium voltage-gated channel, subfamily H (eag-related), member 3	protein-coding
mm_50270.1	chr6	45105098	45105100	+	1	NA	intron (NM_001004357, intron 1 of 23)	Lx2|LINE|L1	45038	NM_001004357	66797	Mm.440084	NM_025771	ENSMUSG00000039419	Cntnap2	5430425M22Rik|Caspr2|mKIAA0868	contactin associated protein-like 2	protein-coding
mm_72239.1	chr8	75015101	75015102	+	1	NA	intron (NM_178017, intron 5 of 10)	L1MC1|LINE|L1	-1121	NM_001316754	70823	Mm.261739	NM_178017	ENSMUSG00000034518	Hmgxb4	4733401K04Rik|AI316803|Hmgb2l1	HMG box domain containing 4	protein-coding
mm_95812.1	chr11	55123800	55123810	+	1	NA	Intergenic	Intergenic	25820	NM_010299	14667	Mm.287807	NM_010299	ENSMUSG00000000594	Gm2a	AA408702|AW215435|GM2-AP|SAP-3	GM2 ganglioside activator protein	protein-coding
mm_1647.1	chr1	74626305	74626329	+	1	NA	intron (NM_175031, intron 16 of 26)	intron (NM_175031, intron 16 of 26)	24862	NM_175031	269209	Mm.310974	NM_175031	ENSMUSG00000033276	Stk36	1700112N14Rik|B930045J24|FU|Fused|mKIAA1278	serine/threonine kinase 36	protein-coding
mm_76882.1	chr8	105623146	105623166	-	1	NA	TTS (NM_001081241)	TTS (NM_001081241)	7690	NR_035492	100316712		NR_035492	ENSMUSG00000089432	Mir1966	mir-1966|mmu-mir-1966	microRNA 1966	ncRNA
mm_117210.1	chr13	64089180	64089192	-	1	NA	promoter-TSS (NM_008291)	promoter-TSS (NM_008291)	15	NM_008291	15487	Mm.5109	NM_008291	ENSMUSG00000033122	Hsd17b3	-	hydroxysteroid (17-beta) dehydrogenase 3	protein-coding
mm_160634.1	chr9	107705496	107705496	-	1	NA	promoter-TSS (NM_001311151)	promoter-TSS (NM_001311151)	95	NM_001311151	20350	Mm.12903	NM_011349	ENSMUSG00000034684	Sema3f	Sema4|Semak	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F	protein-coding
mm_84377.1	chr9	65175273	65175278	-	1	NA	intron (NM_008988, intron 2 of 13)	intron (NM_008988, intron 2 of 13)	34086	NM_008988	19289	Mm.41529	NM_008988	ENSMUSG00000032394	Igdcc3	2810401C09Rik|AI851425|Punc|WI-14920	immunoglobulin superfamily, DCC subclass, member 3	protein-coding
mm_41737.1	chr5	102724942	102724970	+	1	NA	intron (NM_146161, intron 2 of 8)	intron (NM_146161, intron 2 of 8)	-43854	NM_001286468	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding
mm_132391.1	chr16	35000515	35000540	+	1	NA	exon (NM_139300, exon 32 of 32)	exon (NM_139300, exon 32 of 32)	-21894	NM_023587	70757	Mm.27286	NM_023587	ENSMUSG00000035376	Hacd2	6330408J20Rik|AI255777|AI481689|Hcad2|Ptplb	3-hydroxyacyl-CoA dehydratase 2	protein-coding
mm_169272.1	chr1	38665742	38665750	-	1	NA	Intergenic	ORR1A4|LTR|ERVL-MaLR	-38502	NM_001290814	16764	Mm.336679	NM_010678	ENSMUSG00000037138	Aff3	3222402O04Rik|A730046J16|LAF-4|Laf4	AF4/FMR2 family, member 3	protein-coding
mm_139787.1	chr17	65800050	65800058	+	1	NA	intron (NM_001114131, intron 2 of 19)	intron (NM_001114131, intron 2 of 19)	16699	NR_104465	70351	Mm.48686	NM_146081	ENSMUSG00000061950	Ppp4r1	3110001J10Rik|Pp4r1	protein phosphatase 4, regulatory subunit 1	protein-coding
mm_143051.1	chr17	56935414	56935504	-	1	NA	promoter-TSS (NM_022328)	promoter-TSS (NM_022328)	-71	NM_022328	64144	Mm.148748	NM_022328	ENSMUSG00000024212	Mllt1	AA407901|BAM11|ENL|LTG19	myeloid/lymphoid or mixed-lineage leukemia; translocated to, 1	protein-coding
mm_67776.1	chr7	97210032	97210048	-	1	NA	intron (NM_001162477, intron 1 of 9)	intron (NM_001162477, intron 1 of 9)	115924	NM_001177412	244144	Mm.297541	NM_001177412	ENSMUSG00000035713	Usp35	Gm1088|Gm493	ubiquitin specific peptidase 35	protein-coding
mm_57732.1	chr6	128966922	128966932	-	1	NA	intron (NR_045009, intron 1 of 1)	BGLII_B|LTR|ERVK	-4233	NM_001168224	70809	Mm.439891	NM_027562	ENSMUSG00000000248	Clec2g	4632413B12Rik|Clr-c|Clr-d|Clrc|Clrd|Clrx|Ddv10|Ocilrp1	C-type lectin domain family 2, member g	protein-coding
mm_108013.1	chr12	73591863	73591868	+	1	NA	intron (NM_008856, intron 1 of 13)	intron (NM_008856, intron 1 of 13)	7069	NM_008856	18755	Mm.341677	NM_008856	ENSMUSG00000021108	Prkch	Pkch	protein kinase C, eta	protein-coding
mm_152820.1	chr19	23136262	23136271	-	1	NA	Intergenic	CpG	-4960	NM_010638	16601	Mm.291595	NM_010638	ENSMUSG00000033863	Klf9	2310051E17Rik|AA589643|BTEB-1|Bteb1|ENSMUSG00000055440|Gm9971	Kruppel-like factor 9	protein-coding
mm_136288.1	chr16	91373100	91373111	-	1	NA	intron (NM_001347258, intron 1 of 7)	CpG	322	NM_001110498	15976	Mm.6834	NM_010509	ENSMUSG00000022971	Ifnar2	AI747302|Ifnar-2	interferon (alpha and beta) receptor 2	protein-coding
mm_132900.1	chr16	48871995	48872009	+	1	NA	promoter-TSS (NM_181596)	promoter-TSS (NM_181596)	-606	NM_181596	245195	Mm.231288	NM_181596	ENSMUSG00000022651	Retnlg	Fizz3|Relmg|Xcp1	resistin like gamma	protein-coding
mm_96030.1	chr11	59549742	59549753	+	1	NA	intron (NM_145827, intron 4 of 9)	intron (NM_145827, intron 4 of 9)	7061	NM_145827	216799	Mm.54174	NM_145827	ENSMUSG00000032691	Nlrp3	AGTAVPRL|AII/AVP|Cias1|FCAS|FCU|MWS|Mmig1|NALP3|Pypaf1	NLR family, pyrin domain containing 3	protein-coding
mm_104289.1	chr11	90382724	90382731	-	1	NA	intron (NM_172563, intron 2 of 3)	intron (NM_172563, intron 2 of 3)	8190	NM_172563	217082	Mm.158903	NM_172563	ENSMUSG00000003949	Hlf	E230015K02Rik	hepatic leukemia factor	protein-coding
mm_79827.1	chr9	64736357	64736363	+	1	NA	intron (NM_017382, intron 1 of 4)	intron (NM_017382, intron 1 of 4)	1396	NM_017382	53869	Mm.1387	NM_017382	ENSMUSG00000004771	Rab11a	-	RAB11A, member RAS oncogene family	protein-coding
mm_173085.1	chrX	144228470	144228485	-	1	NA	Intergenic	RMER5|LTR|ERV1	74782	NR_040271	319764	Mm.208482	NR_040271	ENSMUSG00000085139	A730046J19Rik	-	RIKEN cDNA A730046J19 gene	ncRNA
mm_140199.1	chr17	83706138	83706169	+	1	NA	promoter-TSS (NM_001171052)	promoter-TSS (NM_001171052)	-10	NM_001171054	116871	Mm.277668	NM_054082	ENSMUSG00000055817	Mta3	1110002J22Rik|mKIAA1266	metastasis associated 3	protein-coding
mm_33155.1	chr4	125504077	125504078	+	1	NA	promoter-TSS (NR_109835)	promoter-TSS (NR_109835)	-672	NR_109835	735288		NR_109835	ENSMUSG00000094403	Mir692-2	Mir692-2a|Mir692-3|Mirn692-2|Mirn692-2a|mir-692-2|mmu-mir-692-2	microRNA 692-2	ncRNA
mm_9727.1	chr1	180195954	180195977	-	1	NA	promoter-TSS (NM_023341)	promoter-TSS (NM_023341)	55	NM_023341	67426	Mm.38330	NM_023341	ENSMUSG00000026489	Coq8a	4632432J16Rik|AI462003|Adck3|Cabc1|mKIAA0451	coenzyme Q8A	protein-coding
mm_54253.1	chr6	28262443	28262453	-	1	NA	promoter-TSS (NM_001081678)	promoter-TSS (NM_001081678)	-847	NM_001081678	627049	Mm.84441	NM_001081678	ENSMUSG00000039841	Zfp800	AA407452|Znf800	zinc finger protein 800	protein-coding
mm_131195.1	chr16	7828206	7828208	+	1	NA	Intergenic	Intergenic	596929	NM_029070	74720	Mm.159318	NM_029070	ENSMUSG00000022715	Tmem114	4930511J11Rik|Cldn26	transmembrane protein 114	protein-coding
mm_92021.1	chr10	62422365	62422375	-	1	NA	promoter-TSS (NM_145419)	promoter-TSS (NM_145419)	87	NM_145419	216019	Mm.213213	NM_145419	ENSMUSG00000020080	Hkdc1	BC016235	hexokinase domain containing 1	protein-coding
mm_153180.1	chr19	34494165	34494224	-	1	NA	exon (NM_021460, exon 10 of 10)	exon (NM_021460, exon 10 of 10)	-19059	NM_009890	12642	Mm.30824	NM_009890	ENSMUSG00000050370	Ch25h	AI462618|m25OH	cholesterol 25-hydroxylase	protein-coding
mm_83430.1	chr9	44987167	44987180	-	1	NA	TTS (NM_013487)	TTS (NM_013487)	5387	NM_013487	12500	Mm.4527	NM_013487	ENSMUSG00000032094	Cd3d	T3d	CD3 antigen, delta polypeptide	protein-coding
mm_62201.1	chr7	97789509	97789516	+	1	NA	Intergenic	Intergenic	-51265	NM_175105	66333	Mm.29756	NM_175105	ENSMUSG00000042797	Aqp11	1700015P13Rik|AI648923|sjds	aquaporin 11	protein-coding
mm_119073.1	chr14	30879317	30879327	+	1	NA	promoter-TSS (NM_181390)	promoter-TSS (NM_181390)	65	NM_181390	66175	Mm.220895	NM_181390	ENSMUSG00000042485	Mustn1	1110028G01Rik|Mustang	musculoskeletal, embryonic nuclear protein 1	protein-coding
mm_58527.1	chr7	4147868	4147879	+	1	NA	TTS (NM_175529)	TTS (NM_175529)	1999	NM_175529	243813	Mm.347643	NM_175529	ENSMUSG00000043432	Leng9	9530024C23Rik|F630035L11Rik	leukocyte receptor cluster (LRC) member 9	protein-coding
mm_6047.1	chr1	59990975	59990990	-	1	NA	3' UTR (NM_027407, exon 11 of 11)	3' UTR (NM_027407, exon 11 of 11)	52140	NM_001316694	70375	Mm.17834	NM_027407	ENSMUSG00000026018	Ica1l	1700030B17Rik|Als2cr15	islet cell autoantigen 1-like	protein-coding
mm_93150.1	chr10	93025158	93025166	-	1	NA	intron (NM_001347060, intron 18 of 67)	intron (NM_001347060, intron 18 of 67)	56434	NM_001347060	380654	Mm.34980	NM_001347060	ENSMUSG00000020014	Cfap54	4930485B16Rik|Gm872	cilia and flagella associated protein 54	protein-coding
mm_99076.1	chr11	99388741	99388753	+	1	NA	exon (NM_010660, exon 1 of 8)	exon (NM_010660, exon 1 of 8)	617	NM_010660	16661	Mm.22662	NM_010660	ENSMUSG00000019761	Krt10	D130054E02Rik|K10|K1C1|Krt-1.10|Krt1-10	keratin 10	protein-coding
mm_38463.1	chr4	140610572	140610602	-	1	NA	intron (NM_001290803, intron 3 of 28)	intron (NM_001290803, intron 3 of 28)	38169	NM_001112723	72754	Mm.29329	NM_172415	ENSMUSG00000040964	Arhgef10l	2810441C07Rik	Rho guanine nucleotide exchange factor (GEF) 10-like	protein-coding
mm_58356.1	chr6	148048104	148048116	-	1	NA	intron (NM_001347516, intron 1 of 11)	intron (NM_001347516, intron 1 of 11)	694	NM_178797	330450	Mm.447274	NM_178797	ENSMUSG00000030303	Far2	A230046P18|AW048109|BC055759|Mlstd1	fatty acyl CoA reductase 2	protein-coding
mm_35643.1	chr4	43520046	43520059	-	1	NA	intron (NM_001277875, intron 2 of 8)	intron (NM_001277875, intron 2 of 8)	3502	NM_009416	22004	Mm.646	NM_009416	ENSMUSG00000028464	Tpm2	Tpm-2|Trop-2	tropomyosin 2, beta	protein-coding
mm_159200.1	chr2	120555319	120555319	-	1	NA	intron (NM_011743, intron 1 of 21)	intron (NM_011743, intron 1 of 21)	8512	NM_011743	20402	Mm.485295	NM_011743	ENSMUSG00000027288	Zfp106	Cd-1|D2Dcr28|H3a|Sh3bp3|Znf106|sirm	zinc finger protein 106	protein-coding
mm_63807.1	chr7	133637668	133637676	+	1	NA	promoter-TSS (NM_178115)	promoter-TSS (NM_178115)	-3	NM_178115	214764	Mm.174044	NM_145995	ENSMUSG00000039990	Edrf1	2700050L05Rik|AU022667|AW558805	erythroid differentiation regulatory factor 1	protein-coding
mm_52877.1	chr6	122456864	122456865	+	1	NA	intron (NM_027664, intron 5 of 5)	intron (NM_027664, intron 5 of 5)	29441	NM_027664	108653	Mm.277939	NM_027664	ENSMUSG00000040649	Rimklb	4931417E21Rik|4933426K21Rik|AA097693|AI325948|AU015629|Naags	ribosomal modification protein rimK-like family member B	protein-coding
mm_9433.1	chr1	172506946	172506986	-	1	NA	3' UTR (NM_178598, exon 5 of 5)	3' UTR (NM_178598, exon 5 of 5)	6720	NM_178598	21346	Mm.271711	NM_178598	ENSMUSG00000026547	Tagln2	2700094C18Rik|SM22beta|Sm22B|Sm22a	transgelin 2	protein-coding
mm_98341.1	chr11	93098406	93098437	+	1	NA	promoter-TSS (NM_028296)	promoter-TSS (NM_028296)	-869	NM_028296	72605	Mm.342160	NM_028296	ENSMUSG00000056158	Car10	2700029L05Rik|BB085816|Ca10	carbonic anhydrase 10	protein-coding
mm_29296.1	chr3	107895744	107895750	-	1	NA	promoter-TSS (NM_010360)	promoter-TSS (NM_010360)	-107	NM_010360	14866	Mm.282351	NM_010360	ENSMUSG00000004032	Gstm5	-	glutathione S-transferase, mu 5	protein-coding
mm_109164.1	chr12	108202244	108202259	+	1	NA	exon (NM_009832, exon 12 of 12)	exon (NM_009832, exon 12 of 12)	22513	NM_009832	12454	Mm.474441	NM_009832	ENSMUSG00000021258	Ccnk	AW123198|AW413594|CPR4|CycK	cyclin K	protein-coding
mm_83993.1	chr9	57443334	57443364	-	1	NA	3' UTR (NM_020270, exon 7 of 7)	3' UTR (NM_020270, exon 7 of 7)	-3235	NM_176831	66812	Mm.250508	NM_176831	ENSMUSG00000063849	Ppcdc	1810057I13Rik|8430432M10Rik	phosphopantothenoylcysteine decarboxylase	protein-coding
mm_111467.1	chr12	98574575	98574586	-	1	NA	5' UTR (NM_001316665, exon 1 of 7)	5' UTR (NM_001316665, exon 1 of 7)	132	NM_001316666	72258	Mm.196158	NM_029911	ENSMUSG00000033854	Kcnk10	1700024D23Rik|3010005K24Rik|Trek2	potassium channel, subfamily K, member 10	protein-coding
mm_156853.1	chrX	164401263	164401285	+	1	NA	TTS (NM_001308489)	TTS (NM_001308489)	-18513	NM_011081	18700	Mm.3781	NM_011081	ENSMUSG00000031381	Piga	AI194334|Pig-a	phosphatidylinositol glycan anchor biosynthesis, class A	protein-coding
mm_29845.1	chr3	129847015	129847063	-	1	NA	intron (NM_001329552, intron 1 of 13)	RMER15|LTR|ERVL	10300	NM_007686	12630	Mm.117180	NM_007686	ENSMUSG00000058952	Cfi	-	complement component factor i	protein-coding
mm_151905.1	chr19	5799427	5799442	-	1	NA	non-coding (NR_002847, exon 1 of 1)	non-coding (NR_002847, exon 1 of 1)	3238	NR_002847	72289	Mm.298256	NR_002847	ENSMUSG00000092341	Malat1	2210401K01Rik|9430072K23Rik|AI647968|Neat2	metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)	ncRNA
mm_49041.1	chr6	4760102	4760110	+	1	NA	3' UTR (NM_130877, exon 2 of 2)	3' UTR (NM_130877, exon 2 of 2)	12800	NM_130877	170676	Mm.320575	NM_130877	ENSMUSG00000092035	Peg10	AA407948|Edr|HB-1|MEF3L|Mar2|Mart2|MyEF-3	paternally expressed 10	protein-coding
mm_151116.1	chr19	47864564	47864586	+	1	NA	promoter-TSS (NM_030051)	promoter-TSS (NM_030051)	-970	NM_030051	68214	Mm.63791	NM_026619	ENSMUSG00000025069	Gsto2	1700020F09Rik|4930425C18Rik|GSTO 2-2	glutathione S-transferase omega 2	protein-coding
mm_76568.1	chr8	88654199	88654201	-	1	NA	intron (NM_145857, intron 2 of 12)	intron (NM_145857, intron 2 of 12)	6853	NM_145857	257632	Mm.222633	NM_145857	ENSMUSG00000055994	Nod2	ACUG|BLAU|CD|Card15|F830032C23Rik|IBD1|Nlrc2	nucleotide-binding oligomerization domain containing 2	protein-coding
mm_68139.1	chr7	102239835	102239867	-	1	NA	exon (NM_019566, exon 2 of 2)	exon (NM_019566, exon 2 of 2)	10267	NM_019566	56212	Mm.259795	NM_019566	ENSMUSG00000073982	Rhog	2810426G09Rik|Arhg|Sid10750	ras homolog family member G	protein-coding
mm_89655.1	chr10	97482362	97482372	+	1	NA	promoter-TSS (NM_007833)	promoter-TSS (NM_007833)	36	NM_007833	13179	Mm.56769	NM_007833	ENSMUSG00000019929	Dcn	DC|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding
mm_101932.1	chr11	50206088	50206092	-	1	NA	exon (NM_011018, exon 5 of 8)	exon (NM_011018, exon 5 of 8)	4730	NM_001290769	18412	Mm.40828	NM_011018	ENSMUSG00000015837	Sqstm1	A170|OSF-6|Osi|STAP|STONE14|p62	sequestosome 1	protein-coding
mm_52533.1	chr6	115853549	115853598	+	1	NA	promoter-TSS (NM_031177)	promoter-TSS (NM_031177)	45	NM_031177	81896	Mm.333335	NM_031177	ENSMUSG00000030323	Ift122	C86139|Wdr10|sopb	intraflagellar transport 122	protein-coding
mm_38128.1	chr4	134563478	134563489	-	1	NA	3' UTR (NM_207237, exon 12 of 12)	3' UTR (NM_207237, exon 12 of 12)	4368	NR_105829	102465216		NR_105829	ENSMUSG00000099289	Mir6403	Gm27992|mmu-mir-6403	microRNA 6403	ncRNA
mm_80760.1	chr9	95559120	95559148	+	1	NA	promoter-TSS (NM_198414)	promoter-TSS (NM_198414)	-683	NM_198414	75552	Mm.151485	NM_198414	ENSMUSG00000064225	Paqr9	1700020G04Rik	progestin and adipoQ receptor family member IX	protein-coding
mm_108798.1	chr12	91588551	91588563	+	1	NA	intron (NM_175335, intron 1 of 8)	CpG	1092	NM_031391	83602	Mm.275728	NM_031391	ENSMUSG00000020962	Gtf2a1	6330549H03Rik|AA536742|AA959775|AW060250|TfIIAa/b|Tfiia1	general transcription factor II A, 1	protein-coding
mm_149254.1	chr19	10403982	10403996	+	1	NA	intron (NM_173067, intron 1 of 9)	intron (NM_173067, intron 1 of 9)	14899	NM_173068	54525	Mm.182654	NM_018801	ENSMUSG00000024743	Syt7	AI851541|B230112P13Rik	synaptotagmin VII	protein-coding
mm_9675.1	chr1	178331197	178331207	-	1	NA	exon (NM_016805, exon 10 of 14)	exon (NM_016805, exon 10 of 14)	6582	NM_016805	51810	Mm.86589	NM_016805	ENSMUSG00000039630	Hnrnpu	AA408410|AI256620|AL024194|AL024437|AW557595|C86794|Hnrpu|SAFA|Sp120|hnRNP U	heterogeneous nuclear ribonucleoprotein U	protein-coding
mm_31153.1	chr4	43414722	43414733	+	1	NA	exon (NM_001037709, exon 2 of 12)	exon (NM_001037709, exon 2 of 12)	8225	NM_199057	100213	Mm.235730	NM_199057	ENSMUSG00000035969	Rusc2	AI840675|mKIAA0375	RUN and SH3 domain containing 2	protein-coding
mm_171879.1	chr5	32617404	32617406	+	1	NA	intron (NM_009535, intron 1 of 11)	BGLII|LTR|ERVK	6234	NM_009535	22612	Mm.4558	NM_009535	ENSMUSG00000014932	Yes1	Yes|p61-Yes	YES proto-oncogene 1, Src family tyrosine kinase	protein-coding
mm_171887.1	chr5	36695935	36695945	-	1	NA	promoter-TSS (NM_001081232)	promoter-TSS (NM_001081232)	81	NM_001081232	320661	Mm.26480	NM_177221	ENSMUSG00000029190	D5Ertd579e	9030221A05Rik|A930018H20Rik|Kiaa0232	DNA segment, Chr 5, ERATO Doi 579, expressed	protein-coding
mm_8504.1	chr1	154116177	154116187	-	1	NA	Intergenic	Intergenic	-85005	NM_001204908	100503355	Mm.484410	NM_001204908	ENSMUSG00000066797	Zfp648	ENSMUSG00000066797|Gm10178|Gm203	zinc finger protein 648	protein-coding
mm_68298.1	chr7	105743926	105743947	-	1	NA	TTS (NM_009906)	TTS (NM_009906)	402	NM_020024	24075	Mm.274846	NM_020024	ENSMUSG00000043866	Taf10	30kDa|AU041226|TAFII30|Taf2h	TATA-box binding protein associated factor 10	protein-coding
mm_6834.1	chr1	84225679	84225691	-	1	NA	intron (NM_001003948, intron 1 of 2)	intron (NM_001003948, intron 1 of 2)	-6724	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
mm_75172.1	chr8	36732790	36732863	-	1	NA	5' UTR (NM_001194941, exon 1 of 14)	5' UTR (NM_001194941, exon 1 of 14)	228	NM_001194941	50768	Mm.125155	NM_015802	ENSMUSG00000031523	Dlc1	A730069N07Rik|Arhgap7|HP|STARD12|dlc-1	deleted in liver cancer 1	protein-coding
mm_57169.1	chr6	122820607	122820625	-	1	NA	5' UTR (NM_021899, exon 1 of 11)	5' UTR (NM_021899, exon 1 of 11)	432	NM_021899	60611	Mm.87142	NM_021899	ENSMUSG00000003154	Foxj2	Fhx	forkhead box J2	protein-coding
mm_155571.1	chrX	77510910	77510926	+	1	NA	promoter-TSS (NM_020601)	promoter-TSS (NM_020601)	-309	NM_020601	21372	Mm.258476	NM_020601	ENSMUSG00000025246	Tbl1x	5330429M20|Tbl1	transducin (beta)-like 1 X-linked	protein-coding
mm_163097.1	chr11	69735220	69735226	-	1	NA	exon (NM_001291068, exon 29 of 29)	exon (NM_001291068, exon 29 of 29)	23410	NM_001291068	20020	Mm.16533	NM_009089	ENSMUSG00000005198	Polr2a	220kDa|Rpb1|Rpo2-1	polymerase (RNA) II (DNA directed) polypeptide A	protein-coding
mm_12365.1	chr2	69789648	69789749	+	1	NA	promoter-TSS (NM_028521)	promoter-TSS (NM_028521)	-39	NM_028521	73373	Mm.9621	NM_028521	ENSMUSG00000027088	Phospho2	1700048E23Rik|AI661517|AU021728|AV006103|Phos2	phosphatase, orphan 2	protein-coding
mm_157312.1	chrX	20961969	20961987	-	1	NA	promoter-TSS (NM_013840)	promoter-TSS (NM_013840)	0	NM_013840	22294	Mm.34779	NM_013840	ENSMUSG00000001134	Uxt	0910002B17Rik	ubiquitously expressed transcript	protein-coding
mm_100222.1	chr11	117109910	117109923	+	1	NA	Intergenic	Intergenic	-5256	NR_029459	74136	Mm.272312	NM_028777	ENSMUSG00000020823	Sec14l1	1200017E04Rik|2810012L19Rik|Naa-35	SEC14-like lipid binding 1	protein-coding
mm_165242.1	chr2	64191543	64191544	+	1	NA	Intergenic	Intergenic	-93505	NM_001267847	60344	Mm.130769	NM_021716	ENSMUSG00000075324	Fign	fi|fidget	fidgetin	protein-coding
mm_37671.1	chr4	129121582	129121600	-	1	NA	promoter-TSS (NM_010471)	promoter-TSS (NM_010471)	156	NM_001130419	15444	Mm.384452	NM_010471	ENSMUSG00000028785	Hpca	-	hippocalcin	protein-coding
mm_20576.1	chr2	131086739	131086819	-	1	NA	promoter-TSS (NM_011426)	promoter-TSS (NM_011426)	-14	NM_011426	20612	Mm.1374	NM_011426	ENSMUSG00000027322	Siglec1	Cd169|Siglec-1|Sn	sialic acid binding Ig-like lectin 1, sialoadhesin	protein-coding
mm_95848.1	chr11	57708977	57708997	+	1	NA	intron (NM_134189, intron 1 of 11)	intron (NM_134189, intron 1 of 11)	63545	NM_134189	171212	Mm.271670	NM_134189	ENSMUSG00000020520	Galnt10	AU018154|C330012K04Rik|GalNAc-T10|GalNAc-T9|Galnt9|ppGaNTase	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 10	protein-coding
mm_153568.1	chr19	42600052	42600058	-	1	NA	exon (NM_053083, exon 11 of 15)	exon (NM_053083, exon 11 of 15)	12751	NM_001164311	67573	Mm.178767	NM_053083	ENSMUSG00000025185	Loxl4	4833426I20Rik|Loxc	lysyl oxidase-like 4	protein-coding
mm_59101.1	chr7	19697562	19697577	+	1	NA	exon (NM_009696, exon 3 of 4)	exon (NM_009696, exon 3 of 4)	829	NM_001305819	11816	Mm.305152	NM_009696	ENSMUSG00000002985	Apoe	AI255918|Apo-E	apolipoprotein E	protein-coding
mm_18803.1	chr2	73892620	73892635	-	1	NA	promoter-TSS (NM_009715)	promoter-TSS (NM_009715)	12	NM_001284371	11909	Mm.209903	NM_009715	ENSMUSG00000027104	Atf2	Atf-2|CRE-BP|Creb2|D130078H02Rik|D18875|Tg(Gzma-Klra1)7Wum|mXBP	activating transcription factor 2	protein-coding
mm_107988.1	chr12	73123710	73123761	+	1	NA	promoter-TSS (NM_008612)	promoter-TSS (NM_008612)	18	NM_008612	17420	Mm.246750	NM_008612	ENSMUSG00000021103	Mnat1	E130115E11Rik|MAT1|P36	menage a trois 1	protein-coding
mm_61416.1	chr7	73595573	73595584	+	1	NA	Intergenic	Intergenic	-37183	NR_037569	69170	Mm.34539	NR_037569	ENSMUSG00000101970	1810026B05Rik	-	RIKEN cDNA 1810026B05 gene	ncRNA
mm_9322.1	chr1	171652924	171652932	-	1	NA	5' UTR (NM_144539, exon 1 of 8)	5' UTR (NM_144539, exon 1 of 8)	109	NM_144539	75345	Mm.164642	NM_144539	ENSMUSG00000038179	Slamf7	19A|19A24|4930560D03Rik|CRACC|CS1	SLAM family member 7	protein-coding
mm_18932.1	chr2	76748945	76748957	-	1	NA	exon (NM_011652, exon 275 of 313)	exon (NM_011652, exon 275 of 313)	73636	NM_031256	83435	Mm.41636	NM_031256	ENSMUSG00000002733	Plekha3	FAPP1	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3	protein-coding
mm_67369.1	chr7	79840980	79840996	-	1	NA	exon (NM_008486, exon 3 of 20)	exon (NM_008486, exon 3 of 20)	1364	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_20729.1	chr2	136891132	136891186	-	1	NA	promoter-TSS (NM_028201)	promoter-TSS (NM_028201)	-59	NM_028201	74243	Mm.330612	NM_028201	ENSMUSG00000027281	Slx4ip	2210009G21Rik|2410004I22Rik|C85661|Slxip	SLX4 interacting protein	protein-coding
mm_92079.1	chr10	62753354	62753369	-	1	NA	exon (NM_026201, exon 18 of 25)	exon (NM_026201, exon 18 of 25)	12245	NR_028557	100217463		NR_028557		Snord98	MBII-419	small nucleolar RNA, C/D box 98	snoRNA
mm_156593.1	chrX	152221674	152221685	+	1	NA	exon (NM_001005475, exon 13 of 14)	exon (NM_001005475, exon 13 of 14)	-11548	NM_013668	20591	Mm.142655	NM_013668	ENSMUSG00000025332	Kdm5c	D930009K15Rik|Jarid1c|Smcx|mKIAA0234	lysine (K)-specific demethylase 5C	protein-coding
mm_170528.1	chr1	93421663	93421682	+	1	NA	intron (NM_001301364, intron 14 of 27)	intron (NM_001301364, intron 14 of 27)	24029	NM_001301364	110611	Mm.30012	NM_133808	ENSMUSG00000034088	Hdlbp	1110005P14Rik|AA960365|AI118566|D1Ertd101e	high density lipoprotein (HDL) binding protein	protein-coding
mm_87553.1	chr10	54118057	54118071	+	1	NA	Intergenic	Intergenic	42142	NR_038016	100502920	Mm.403982	NR_038016	ENSMUSG00000097069	Gm16998	-	predicted gene, 16998	ncRNA
mm_133102.1	chr16	65198870	65198874	+	1	NA	Intergenic	RMER19C|LTR|ERVK	-93088	NM_008310	15557	Mm.5040	NM_008310	ENSMUSG00000050783	Htr1f	Htr1eb	5-hydroxytryptamine (serotonin) receptor 1F	protein-coding
mm_83754.1	chr9	51318361	51318379	-	1	NA	5' UTR (NM_027217, exon 2 of 5)	5' UTR (NM_027217, exon 2 of 5)	10547	NM_027217	69809	Mm.75315	NM_027217	ENSMUSG00000036027	1810046K07Rik	-	RIKEN cDNA 1810046K07 gene	protein-coding
mm_61256.1	chr7	65879724	65879726	+	1	NA	intron (NM_011048, intron 1 of 21)	intron (NM_011048, intron 1 of 21)	17589	NM_011048	18553	Mm.294007	NM_011048	ENSMUSG00000030513	Pcsk6	C86343|Pace4|SPC4	proprotein convertase subtilisin/kexin type 6	protein-coding
mm_67040.1	chr7	67234586	67234596	-	1	NA	3' UTR (NM_001291196, exon 12 of 12)	3' UTR (NM_001291196, exon 12 of 12)	11975	NM_001191051	75099	Mm.121691	NM_175215	ENSMUSG00000043831	Lysmd4	4930506D23Rik	LysM, putative peptidoglycan-binding, domain containing 4	protein-coding
mm_16773.1	chr2	9881121	9881155	-	1	NA	promoter-TSS (NR_024257)	promoter-TSS (NR_024257)	-108	NR_024257	381347	Mm.441450	NR_024257		4930412O13Rik	ENSMUSG00000075535|Gm10853	RIKEN cDNA 4930412O13 gene	ncRNA
mm_115787.1	chr13	19337127	19337133	-	1	NA	Intergenic	Intergenic	58683	NM_024270	76205	Mm.41940	NM_024270	ENSMUSG00000003062	Stard3nl	0610035N01Rik|6530409L22Rik|AW124774|MENTHO	STARD3 N-terminal like	protein-coding
mm_38029.1	chr4	133872998	133873044	-	1	NA	intron (NM_001285505, intron 2 of 21)	intron (NM_001285505, intron 2 of 21)	1710	NM_001285506	20111	Mm.301827	NM_009097	ENSMUSG00000003644	Rps6ka1	Mapkapk-1a|Rsk|Rsk-1|Rsk1|S6K-alpha-1|p90-Rsk1|p90Rsk1|p90S6K|p90rsk	ribosomal protein S6 kinase polypeptide 1	protein-coding
mm_20409.1	chr2	129300055	129300072	-	1	NA	3' UTR (NM_010554, exon 7 of 7)	3' UTR (NM_010554, exon 7 of 7)	2693	NR_040371	100503468	Mm.446943	NR_040371	ENSMUSG00000085498	Gm14023	OTTMUSG00000015408	predicted gene 14023	ncRNA
mm_34907.1	chr4	155694456	155694523	+	1	NA	5' UTR (NM_178699, exon 1 of 1)	5' UTR (NM_178699, exon 1 of 1)	147	NM_178699	230991	Mm.29083	NM_178699	ENSMUSG00000074738	Fndc10	B930041F14Rik|MNCb-3966	fibronectin type III domain containing 10	protein-coding
mm_147621.1	chr18	58009136	58009144	-	1	NA	3' UTR (NM_010181, exon 65 of 65)	3' UTR (NM_010181, exon 65 of 65)	130462	NM_009194	20496	Mm.399997	NM_009194	ENSMUSG00000024597	Slc12a2	9330166H04Rik|Nkcc1|mBSC2|sy-ns	solute carrier family 12, member 2	protein-coding
mm_52978.1	chr6	123262162	123262185	+	1	NA	promoter-TSS (NM_010819)	promoter-TSS (NM_010819)	66	NM_010819	17474	Mm.441101	NM_010819	ENSMUSG00000030144	Clec4d	Clecsf8|Mpcl|mcl	C-type lectin domain family 4, member d	protein-coding
mm_157284.1	chrX	20861061	20861121	-	1	NA	TTS (NM_009703)	TTS (NM_009703)	2091	NR_049190	100885829		NR_049190	ENSMUSG00000093408	Mir5617	Gm25192|mir-5617|mmu-mir-5617	microRNA 5617	ncRNA
mm_70045.1	chr7	142577999	142578012	-	1	NA	promoter-TSS (NR_030416)	promoter-TSS (NR_030416)	141	NR_130974	14955	Mm.14802	NR_001592	ENSMUSG00000000031	H19	AI747191	H19, imprinted maternally expressed transcript	ncRNA
mm_43676.1	chr5	138799577	138799592	+	1	NA	intron (NM_030565, intron 5 of 9)	intron (NM_030565, intron 5 of 9)	-20496	NM_001195128	384244	Mm.485002	NM_001195128	ENSMUSG00000094504	Gm5294	EG384244	predicted gene 5294	protein-coding
mm_40675.1	chr5	65536905	65536931	+	1	NA	promoter-TSS (NM_016786)	promoter-TSS (NM_016786)	-327	NM_016786	53323	Mm.319512	NM_016786	ENSMUSG00000029203	Ube2k	AW492011|D5Ertd601e|E2-25k|HIP-2|Hip2|Hypg|Lig	ubiquitin-conjugating enzyme E2K	protein-coding
mm_119122.1	chr14	31131080	31131111	+	1	NA	Intergenic	CpG	-2165	NM_001308464	66487	Mm.379116	NM_001308091	ENSMUSG00000058351	Smim4	2010107H07Rik|Gm41122	small integral membrane protein 4	protein-coding
mm_37840.1	chr4	132075300	132075338	-	1	NA	promoter-TSS (NM_001128607)	promoter-TSS (NM_001128607)	-6	NM_001128607	269587	Mm.30038	NM_183428	ENSMUSG00000028906	Epb41	4.1R|AI415518|D4Ertd442e|Elp-1|Elp1|Epb4.1|mKIAA4056	erythrocyte membrane protein band 4.1	protein-coding
mm_85651.1	chr9	107657896	107657906	-	1	NA	exon (NM_001199218, exon 6 of 16)	exon (NM_001199218, exon 6 of 16)	9498	NM_023805	76257	Mm.296560	NM_023805	ENSMUSG00000010064	Slc38a3	0610012J02Rik|D9Ucla2|Nat1|Slc38-3|Sn1|Snat3|mNAT	solute carrier family 38, member 3	protein-coding
mm_42240.1	chr5	113819545	113819630	+	1	NA	exon (NM_009151, exon 2 of 2)	exon (NM_009151, exon 2 of 2)	10914	NM_009151	20345	Mm.332590	NM_009151	ENSMUSG00000048163	Selplg	CD162|Psgl-1|Psgl1|Selp1|Selpl	selectin, platelet (p-selectin) ligand	protein-coding
mm_121286.1	chr14	105258613	105258629	+	1	NA	promoter-TSS (NM_029561)	promoter-TSS (NM_029561)	-52	NM_029561	76273	Mm.290669	NM_029561	ENSMUSG00000053253	Ndfip2	0710001O20Rik|2810436B12Rik|9130207N19Rik|N4wbp5a|mKIAA1165	Nedd4 family interacting protein 2	protein-coding
mm_66916.1	chr7	60046941	60046943	-	1	NA	intron (NM_001082962, intron 2 of 10)	intron (NM_001082962, intron 2 of 10)	-41786	NM_033174	84704	Mm.274995	NM_033174	ENSMUSG00000000948	Snurf	2410045I01Rik|Snrpn	SNRPN upstream reading frame	protein-coding
mm_126794.1	chr15	86334977	86335013	+	1	NA	intron (NM_145476, intron 8 of 12)	intron (NM_145476, intron 8 of 12)	120536	NM_145476	223754	Mm.28904	NM_145476	ENSMUSG00000051864	Tbc1d22a	BC023106|D15Ertd781e	TBC1 domain family, member 22a	protein-coding
mm_85362.1	chr9	103217476	103217528	-	1	NA	exon (NM_133977, exon 12 of 17)	exon (NM_133977, exon 12 of 17)	12784	NM_133977	22041	Mm.37214	NM_133977	ENSMUSG00000032554	Trf	AI266983|Cd176|HP|Tf|Tfn|hpx	transferrin	protein-coding
mm_65408.1	chr7	25237850	25237856	-	1	NA	promoter-TSS (NM_001031667)	promoter-TSS (NM_001031667)	-2	NM_001031667	606496	Mm.491101	NM_001031667	ENSMUSG00000057177	Gsk3a	2700086H06Rik	glycogen synthase kinase 3 alpha	protein-coding
mm_129147.1	chr15	76206298	76206302	-	1	NA	promoter-TSS (NM_201389)	promoter-TSS (NM_201389)	21	NM_201389	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
mm_30706.1	chr4	11966628	11966674	+	1	NA	promoter-TSS (NM_001290387)	promoter-TSS (NM_001290387)	77	NR_040577	100503636	Mm.209078	NR_040577		1700123M08Rik	1600025K15Rik	RIKEN cDNA 1700123M08 gene	ncRNA
mm_84178.1	chr9	59950041	59950051	-	1	NA	promoter-TSS (NM_013708)	promoter-TSS (NM_013708)	33	NM_013708	23958	Mm.103641	NM_013708	ENSMUSG00000032292	Nr2e3	A930035N01Rik|PNR|RNR|rd7	nuclear receptor subfamily 2, group E, member 3	protein-coding
mm_32617.1	chr4	114388435	114388440	+	1	NA	Intergenic	Intergenic	-18287	NM_001085549	666048	Mm.331779	NM_001085549	ENSMUSG00000070867	Trabd2b	Gm12824|Hkat|OTTMUSG00000008561	TraB domain containing 2B	protein-coding
mm_69638.1	chr7	138846111	138846131	-	1	NA	promoter-TSS (NM_026391)	promoter-TSS (NM_026391)	146	NM_001045483	69546	Mm.31598	NM_027115	ENSMUSG00000041775	Mapk1ip1	2310009E07Rik|AU043776|MISS	mitogen-activated protein kinase 1 interacting protein 1	protein-coding
mm_79127.1	chr9	47530344	47530362	+	1	NA	promoter-TSS (NM_018770)	promoter-TSS (NM_018770)	1	NM_018770	54725	Mm.234832	NM_018770	ENSMUSG00000032076	Cadm1	2900073G06Rik|3100001I08Rik|AI987920|Bl2|Igsf4|Igsf4a|Necl2|RA175|RA175A|RA175B|RA175C|RA175N|ST17|SgIGSF|SynCam|Tslc1	cell adhesion molecule 1	protein-coding
mm_18217.1	chr2	49743712	49743725	-	1	NA	intron (NM_008449, intron 19 of 25)	MTD|LTR|ERVL-MaLR	-43968	NM_027990	71897	Mm.41381	NM_027990	ENSMUSG00000026765	Lypd6b	2310010M24Rik|AW049525	LY6/PLAUR domain containing 6B	protein-coding
mm_121918.1	chr14	22801229	22801266	-	1	NA	intron (NM_028275, intron 5 of 6)	intron (NM_028275, intron 5 of 6)	-258449	NR_046307	74896	Mm.444661	NR_046307		4930405A10Rik	4930456G20Rik	RIKEN cDNA 4930405A10 gene	ncRNA
mm_145668.1	chr18	61275003	61275041	+	1	NA	intron (NM_146086, intron 17 of 21)	intron (NM_146086, intron 17 of 21)	54523	NM_146086	225600	Mm.391106	NM_146086	ENSMUSG00000024575	Pde6a	Pdea|nmf282	phosphodiesterase 6A, cGMP-specific, rod, alpha	protein-coding
mm_136859.1	chr17	12807167	12807204	+	1	NA	intron (NR_027784, intron 2 of 2)	B1_Mus2|SINE|Alu	-37479	NM_010515	16004	Mm.26553	NM_010515	ENSMUSG00000023830	Igf2r	AI661837|CD222|CI-MPR|M6P/IGF2R|Mpr300	insulin-like growth factor 2 receptor	protein-coding
mm_63444.1	chr7	127485110	127485161	+	1	NA	promoter-TSS (NM_010183)	promoter-TSS (NM_010183)	-86	NM_010183	14123	Mm.323505	NM_010183	ENSMUSG00000042423	Fbrs	Fbs|Fbs1	fibrosin	protein-coding
mm_150943.1	chr19	46306259	46306263	+	1	NA	intron (NM_001177369, intron 2 of 22)	intron (NM_001177369, intron 2 of 22)	331	NM_001177370	18034	Mm.102365	NM_019408	ENSMUSG00000025225	Nfkb2	NF-kappaB2|lyt|p49|p49/p100|p50B|p52	nuclear factor of kappa light polypeptide gene enhancer in B cells 2, p49/p100	protein-coding
mm_95715.1	chr11	54516778	54516789	+	1	NA	3' UTR (NM_173753, exon 18 of 18)	3' UTR (NM_173753, exon 18 of 18)	-6062	NM_001252494	192786	Mm.254404	NM_175258	ENSMUSG00000037533	Rapgef6	A530068K01|AI844632|BB085664|C030018K18Rik|PDZ-GEF2|Pdzgef2|RA-GEF-2|Ragef2|mKIAA4052	Rap guanine nucleotide exchange factor (GEF) 6	protein-coding
mm_140403.1	chr17	87640372	87640390	+	1	NA	exon (NM_008532, exon 4 of 10)	exon (NM_008532, exon 4 of 10)	4402	NM_008532	17075	Mm.4259	NM_008532	ENSMUSG00000045394	Epcam	CD326|EGP|EGP-2|Egp314|Ep-CAM|EpCAM1|GA733-2|Ly74|TROP1|Tacsd1|Tacstd1|gp40	epithelial cell adhesion molecule	protein-coding
mm_76732.1	chr8	95024499	95024522	-	1	NA	intron (NM_173036, intron 2 of 11)	intron (NM_173036, intron 2 of 11)	6818	NM_173036	54672	Mm.27995	NM_173036	ENSMUSG00000060470	Adgrg3	A030001G24Rik|AW214383|Gpr97|Pb1|Pb99	adhesion G protein-coupled receptor G3	protein-coding
mm_152713.1	chr19	17394470	17394485	-	1	NA	intron (NM_019437, intron 1 of 3)	CpG	434	NM_019437	54391	Mm.7013	NM_019437	ENSMUSG00000024712	Rfk	0610038L10Rik|AF031381|KOI-4	riboflavin kinase	protein-coding
mm_30718.1	chr4	13517177	13517184	+	1	NA	Intergenic	MT2B1|LTR|ERVL	-226122	NM_001111026	12395	Mm.4909	NM_009822	ENSMUSG00000006586	Runx1t1	Cbfa2t1h|ETO|MTG8	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	protein-coding
mm_167201.1	chr7	143106359	143106364	+	1	NA	promoter-TSS (NM_008434)	promoter-TSS (NM_008434)	-893	NM_008434	16535	Mm.439769	NM_008434	ENSMUSG00000009545	Kcnq1	AW559127|KVLQT1|Kcna9	potassium voltage-gated channel, subfamily Q, member 1	protein-coding
mm_148891.1	chr19	6894285	6894300	+	1	NA	Intergenic	RLTR44B|LTR|ERVK	15353	NM_012021	54683	Mm.279782	NM_012021	ENSMUSG00000024953	Prdx5	AOEB166|AOPP|Pmp20|Prdx6|PrxV	peroxiredoxin 5	protein-coding
mm_158839.1	chrX	168674350	168674361	-	1	NA	promoter-TSS (NM_010832)	promoter-TSS (NM_010832)	-453	NM_010832	17692	Mm.24248	NM_010832	ENSMUSG00000031358	Msl3	AU018931|Msl31|Msl3l1	male-specific lethal 3 homolog (Drosophila)	protein-coding
mm_73104.1	chr8	94602086	94602111	+	1	NA	promoter-TSS (NM_028221)	promoter-TSS (NM_028221)	157	NM_026274	67610	Mm.109074	NM_026274	ENSMUSG00000050079	Rspry1	4930470D19Rik|AI608258	ring finger and SPRY domain containing 1	protein-coding
mm_63423.1	chr7	127471600	127471628	+	1	NA	promoter-TSS (NM_145589)	promoter-TSS (NM_145589)	0	NM_145589	233895	Mm.44183	NM_145589	ENSMUSG00000030822	Prr14	BC006909	proline rich 14	protein-coding
mm_168640.1	chr11	84870976	84870990	+	1	NA	promoter-TSS (NM_153144)	promoter-TSS (NM_153144)	60	NR_131197	102635561	Mm.341797	NR_131197		Ggnbp2os	-	gametogenetin binding protein 2, opposite strand	ncRNA
mm_140215.1	chr17	83810910	83810930	+	1	NA	intron (NM_054082, intron 16 of 16)	B4|SINE|B4	35870	NM_025325	107766	Mm.30100	NM_025325	ENSMUSG00000000673	Haao	0610007K21Rik|0610012J07Rik|3-HAO|3-HAOxase|3HAO	3-hydroxyanthranilate 3,4-dioxygenase	protein-coding
mm_30805.1	chr4	20029355	20029390	+	1	NA	3' UTR (NM_015767, exon 5 of 5)	3' UTR (NM_015767, exon 5 of 5)	-12680	NM_010281	14590	Mm.20461	NM_010281	ENSMUSG00000073987	Ggh	gamma-GH	gamma-glutamyl hydrolase	protein-coding
mm_152625.1	chr19	12473325	12473348	-	1	NA	intron (NM_172442, intron 7 of 8)	intron (NM_172442, intron 7 of 8)	12557	NM_010821	17476	Mm.3999	NM_010821	ENSMUSG00000046805	Mpeg1	MPS1|Mpg-1	macrophage expressed gene 1	protein-coding
mm_83140.1	chr9	40455343	40455384	-	1	NA	exon (NM_172768, exon 1 of 20)	exon (NM_172768, exon 1 of 20)	401	NM_172768	235283	Mm.138434	NM_172768	ENSMUSG00000040111	Gramd1b	3222402H23|A930008A22Rik|AI593249|mKIAA1201	GRAM domain containing 1B	protein-coding
mm_103250.1	chr11	70970723	70970729	-	1	NA	promoter-TSS (NM_001276406)	promoter-TSS (NM_001276406)	526	NM_001252415	69723	Mm.275691	NM_027186	ENSMUSG00000018449	Rpain	2400006N03Rik|Rip	RPA interacting protein	protein-coding
mm_100249.1	chr11	117308789	117308826	+	1	NA	intron (NM_001113487, intron 2 of 10)	intron (NM_001113487, intron 2 of 10)	-22908	NM_017380	53860	Mm.38450	NM_017380	ENSMUSG00000059248	Sept9	MSF1|Msf|PNUTL4|Sint1	septin 9	protein-coding
mm_19090.1	chr2	79368859	79368868	-	1	NA	intron (NM_001048176, intron 2 of 12)	intron (NM_001048176, intron 2 of 12)	60125	NM_001048176	228094	Mm.440704	NM_001033295	ENSMUSG00000075256	Cerkl	Gm1958|Rp26	ceramide kinase-like	protein-coding
mm_95418.1	chr11	50119593	50119608	+	1	NA	3' UTR (NM_001290750, exon 8 of 8)	3' UTR (NM_001290750, exon 8 of 8)	-11760	NM_001290759	76795	Mm.290975	NM_029745	ENSMUSG00000036644	Tbc1d9b	-	TBC1 domain family, member 9B	protein-coding
mm_17925.1	chr2	35461273	35461291	-	1	NA	5' UTR (NM_001145821, exon 1 of 8)	5' UTR (NM_001145821, exon 1 of 8)	167	NM_001308299	14594	Mm.281124	NM_010283	ENSMUSG00000035778	Ggta1	AW108479|GALT|Gal|Ggta|Ggta-1|alpha Gal|alpha3GalT	glycoprotein galactosyltransferase alpha 1, 3	protein-coding
mm_35187.1	chr4	16013767	16013775	-	1	NA	5' UTR (NM_145950, exon 1 of 6)	5' UTR (NM_145950, exon 1 of 6)	106	NM_145950	209212	Mm.46455	NM_145950	ENSMUSG00000041153	Osgin2	BC010311|C230027H09Rik	oxidative stress induced growth inhibitor family member 2	protein-coding
mm_65691.1	chr7	28372564	28372583	-	1	NA	promoter-TSS (NM_001083912)	promoter-TSS (NM_001083912)	89	NM_138752	101497	Mm.235700	NM_138752	ENSMUSG00000037552	Plekhg2	AI194308|Clg|Cslg	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	protein-coding
mm_148308.1	chr18	83525292	83525305	-	1	NA	Intergenic	Intergenic	-199414	NR_045361	70960	Mm.410834	NR_045361		4921531P14Rik	1700108N05Rik	RIKEN cDNA 4921531P14 gene	ncRNA
mm_50139.1	chr6	41543217	41543234	+	1	NA	Intergenic	Intergenic	21449	NM_009430	22072	Mm.276926	NM_009430	ENSMUSG00000057163	Prss2	TRY8|TRYP|Ta|Tesp4|Try2	protease, serine 2	protein-coding
mm_5765.1	chr1	48462293	48462293	-	1	NA	Intergenic	L1_Mm|LINE|L1	-995168	NR_105768	102466969		NR_105768	ENSMUSG00000098876	Mir6350	Gm27958|mmu-mir-6350	microRNA 6350	ncRNA
mm_113892.1	chr13	49191072	49191084	+	1	NA	intron (NM_013610, intron 1 of 3)	intron (NM_013610, intron 1 of 3)	3531	NM_013610	18081	Mm.18503	NM_013610	ENSMUSG00000037966	Ninj1	AU024536	ninjurin 1	protein-coding
mm_31323.1	chr4	46371152	46371161	+	1	NA	Intergenic	Intergenic	18267	NM_029086	74753	Mm.45973	NM_029086	ENSMUSG00000028331	Trmo	5830415F09Rik|AV014846|Nap1	tRNA methyltransferase O	protein-coding
mm_17817.1	chr2	33733420	33733423	-	1	NA	3' UTR (NM_175184, exon 10 of 10)	3' UTR (NM_175184, exon 10 of 10)	-72395	NR_045729	320482	Mm.442057	NR_045729	ENSMUSG00000086484	Nron	A630071L07Rik|Gm24353	non-protein coding RNA, repressor of NFAT	ncRNA
mm_62816.1	chr7	113295321	113295333	+	1	NA	intron (NM_001243048, intron 8 of 16)	intron (NM_001243048, intron 8 of 16)	74012	NM_133700	68815	Mm.238034	NM_133700	ENSMUSG00000038187	Btbd10	1110056N09Rik|Gmrp1	BTB (POZ) domain containing 10	protein-coding
mm_5838.1	chr1	52952682	52952709	-	1	NA	5' UTR (NM_144953, exon 1 of 2)	5' UTR (NM_144953, exon 1 of 2)	145	NM_144953	67080	Mm.236287	NM_144953	ENSMUSG00000043629	1700019D03Rik	2410136C24Rik|AA410151|smAKAP	RIKEN cDNA 1700019D03 gene	protein-coding
mm_170489.1	chr19	17926900	17926913	-	1	NA	Intergenic	Intergenic	-89274	NM_001190483	18552	Mm.3401	NM_001163144	ENSMUSG00000024713	Pcsk5	PC5|PC6|SPC6|b2b1549Clo|b2b585Clo	proprotein convertase subtilisin/kexin type 5	protein-coding
mm_15216.1	chr2	154273097	154273099	+	1	NA	Intergenic	Intergenic	15219	NM_175167	71425	Mm.389341	NM_175167	ENSMUSG00000067998	Bpifb9a	4833413D08Rik|AI413838	BPI fold containing family B, member 9A	protein-coding
mm_3256.1	chr1	136172704	136172710	+	1	NA	intron (NM_001039472, intron 33 of 34)	intron (NM_001039472, intron 33 of 34)	40121	NM_001329610	76422	Mm.159735	NM_001329610		Mroh3	2310006M14Rik	maestro heat-like repeat family member 3	protein-coding
mm_38039.1	chr4	133910664	133910674	-	1	NA	Intergenic	CpG	-22872	NM_009097	20111	Mm.301827	NM_009097	ENSMUSG00000003644	Rps6ka1	Mapkapk-1a|Rsk|Rsk-1|Rsk1|S6K-alpha-1|p90-Rsk1|p90Rsk1|p90S6K|p90rsk	ribosomal protein S6 kinase polypeptide 1	protein-coding
mm_155970.1	chrX	106091210	106091218	+	1	NA	intron (NM_001109757, intron 5 of 22)	intron (NM_001109757, intron 5 of 22)	-52061	NM_205820	279572	Mm.336203	NM_205820	ENSMUSG00000033777	Tlr13	AI666735|Gm713	toll-like receptor 13	protein-coding
mm_112168.1	chr12	113414584	113414594	-	1	NA	Intergenic	Intergenic	-74976	NM_001009545	238405	Mm.442216	NM_001009545	ENSMUSG00000051804	Adam6b	4930523C11Rik	a disintegrin and metallopeptidase domain 6B	protein-coding
mm_67624.1	chr7	84109493	84109496	-	1	NA	3' UTR (NM_133722, exon 3 of 3)	3' UTR (NM_133722, exon 3 of 3)	-22989	NM_030728	80982	Mm.160389	NM_030728	ENSMUSG00000052353	Cemip	12H19.01.T7|6330404C01Rik|9930013L23Rik|AY007814|Kiaa1199	cell migration inducing protein, hyaluronan binding	protein-coding
mm_136132.1	chr16	86805522	86805538	-	1	NA	Intergenic	Intergenic	-548655	NM_001159331	67768	Mm.296532	NM_026366	ENSMUSG00000044442	N6amt1	5830445C04Rik|Hemk2|Pred28	N-6 adenine-specific DNA methyltransferase 1 (putative)	protein-coding
mm_100347.1	chr11	118428151	118428191	+	1	NA	promoter-TSS (NM_001204129)	promoter-TSS (NM_001204129)	-286	NM_001204129	56745	Mm.23845	NM_019959	ENSMUSG00000017446	C1qtnf1	1600017K21Rik|CTRP1|Zsig37	C1q and tumor necrosis factor related protein 1	protein-coding
mm_62712.1	chr7	110768170	110768193	+	1	NA	promoter-TSS (NM_001276301)	promoter-TSS (NM_001276301)	-25	NM_001276301	11717	Mm.3238	NM_009667	ENSMUSG00000005686	Ampd3	-	adenosine monophosphate deaminase 3	protein-coding
mm_17308.1	chr2	26360874	26360914	-	1	NA	Intergenic	Intergenic	-1347	NM_001037747	332579	Mm.330064	NM_001037747	ENSMUSG00000026928	Card9	Gm782	caspase recruitment domain family, member 9	protein-coding
mm_122903.1	chr14	54953122	54953132	-	1	NA	exon (NM_010856, exon 23 of 39)	exon (NM_010856, exon 23 of 39)	-3985	NR_029724	387204		NR_029724	ENSMUSG00000065432	Mir208a	Mirn208|Mirn208a|mir-208|mir-208a|mmu-mir-208	microRNA 208a	ncRNA
mm_168980.1	chr12	91891336	91891349	-	1	NA	Intergenic	Intergenic	-42185	NM_011344	20338	Mm.250605	NM_011344	ENSMUSG00000020964	Sel1l	AW493766|Sel1h|mKIAA4137	sel-1 suppressor of lin-12-like (C. elegans)	protein-coding
mm_142061.1	chr17	35670518	35670538	-	1	NA	intron (NM_010364, intron 6 of 13)	intron (NM_010364, intron 6 of 13)	-2936	NM_175137	68915	Mm.32002	NM_175137	ENSMUSG00000038838	Vars2	1190004I24Rik|Vars2l|mKIAA1885	valyl-tRNA synthetase 2, mitochondrial	protein-coding
mm_27321.1	chr3	50367044	50367060	-	1	NA	3' UTR (NM_011990, exon 12 of 12)	3' UTR (NM_011990, exon 12 of 12)	76561	NM_011990	26570	Mm.260988	NM_011990	ENSMUSG00000027737	Slc7a11	9930009M05Rik|AI451155|sut|xCT	solute carrier family 7 (cationic amino acid transporter, y+ system), member 11	protein-coding
mm_86305.1	chr9	122351517	122351532	-	1	NA	promoter-TSS (NM_026179)	promoter-TSS (NM_026179)	-92	NM_026179	67469	Mm.280254	NM_026179	ENSMUSG00000032540	Abhd5	1300003D03Rik|2010002J10Rik|CDS|CGI-58|IECN5|NCIE2	abhydrolase domain containing 5	protein-coding
mm_39565.1	chr5	23387262	23387269	+	1	NA	Intergenic	Intergenic	47088	NR_040469	269630	Mm.425231	NR_040469	ENSMUSG00000073147	5031425E22Rik	-	RIKEN cDNA 5031425E22 gene	ncRNA
mm_78440.1	chr9	32115980	32115996	+	1	NA	promoter-TSS (NM_001195632)	promoter-TSS (NM_001195632)	-148	NM_001195632	330914	Mm.46683	NM_177379	ENSMUSG00000041444	Arhgap32	3426406O18Rik|Gc-gap|Grit|Px-rics|Rics|mKIAA0712|p200Rhogap|p250Gap	Rho GTPase activating protein 32	protein-coding
mm_77268.1	chr8	116435721	116435732	-	1	NA	Intergenic	Intergenic	-69289	NM_029297	75465	Mm.23114	NM_029297	ENSMUSG00000034467	Dynlrb2	1700009A04Rik|DNLC2B|Dncl2b	dynein light chain roadblock-type 2	protein-coding
mm_130504.1	chr15	98832104	98832107	-	1	NA	promoter-TSS (NM_016781)	promoter-TSS (NM_016781)	-597	NM_016781	19082	Mm.6670	NM_016781	ENSMUSG00000067713	Prkag1	AA571379|BB036179|Prkaac	protein kinase, AMP-activated, gamma 1 non-catalytic subunit	protein-coding
mm_171401.1	chr4	123664577	123664578	-	1	NA	intron (NM_001199136, intron 1 of 97)	CpG	-1304	NR_136925	102633214	Mm.399387	NR_136925		Gm12925	OTTMUSG00000009214	predicted gene 12925	ncRNA
mm_113589.1	chr13	40918148	40918157	+	1	NA	exon (NM_133219, exon 1 of 3)	exon (NM_133219, exon 1 of 3)	518	NM_133219	14538	Mm.314757	NM_008105	ENSMUSG00000021360	Gcnt2	5330430K10Rik|IGnT|IGnTA|IGnTB|IGnTC	glucosaminyl (N-acetyl) transferase 2, I-branching enzyme	protein-coding
mm_109615.1	chr12	112760684	112760717	+	1	NA	promoter-TSS (NM_178911)	promoter-TSS (NM_178911)	45	NM_178911	104759	Mm.203915	NM_178911	ENSMUSG00000052160	Pld4	AI132321|thss	phospholipase D family, member 4	protein-coding
mm_123365.1	chr14	63164926	63164941	-	1	NA	intron (NM_010191, intron 3 of 9)	intron (NM_010191, intron 3 of 9)	14645	NM_010191	14137	Mm.474432	NM_010191	ENSMUSG00000021273	Fdft1	SQS|SS	farnesyl diphosphate farnesyl transferase 1	protein-coding
mm_137480.1	chr17	26917112	26917159	+	1	NA	promoter-TSS (NM_053173)	promoter-TSS (NM_053173)	44	NM_053173	16580	Mm.491138	NM_016761	ENSMUSG00000024301	Kifc5b	Hset|KNSL2|Kifc5a	kinesin family member C5B	protein-coding
mm_104374.1	chr11	94365435	94365448	-	1	NA	intron (NM_029600, intron 11 of 30)	intron (NM_029600, intron 11 of 30)	27535	NM_029600	76408	Mm.23942	NM_029600	ENSMUSG00000020865	Abcc3	1700019L09Rik|ABC31|MLP2|MOAT-D|MRP3	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	protein-coding
mm_66214.1	chr7	34385244	34385252	-	1	NA	intron (NM_025948, intron 1 of 10)	intron (NM_025948, intron 1 of 10)	4292	NM_025948	67070	Mm.276503	NM_025948	ENSMUSG00000066568	Lsm14a	2700023B17Rik|AA407828|AU017544|Tral	LSM14A mRNA processing body assembly factor	protein-coding
mm_138804.1	chr17	39036695	39036696	+	1	NA	promoter-TSS (NM_001256050)	promoter-TSS (NM_001256050)	0	NM_001256050	100126776	Mm.471588	NM_001256050	ENSMUSG00000095625	Esp24	Gm21947	exocrine gland secreted peptide 24	protein-coding
mm_39102.1	chr4	154921500	154921511	-	1	NA	TTS (NM_178931)	TTS (NM_178931)	6572	NM_178931	230979	Mm.215147	NM_178931	ENSMUSG00000042333	Tnfrsf14	Atar|HveA|Hvem|Tnfrs14	tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)	protein-coding
mm_129074.1	chr15	75748208	75748239	-	1	NA	promoter-TSS (NM_194350)	promoter-TSS (NM_194350)	-301	NM_194350	378435	Mm.309589	NM_194350	ENSMUSG00000047591	Mafa	RIPE3b1	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein A (avian)	protein-coding
mm_69055.1	chr7	126884639	126884670	-	1	NA	5' UTR (NM_001163775, exon 1 of 16)	5' UTR (NM_001163775, exon 1 of 16)	313	NM_001163775	381921	Mm.259634	NM_001163774	ENSMUSG00000059981	Taok2	1110033K02Rik|B230344N16|MAP3K17|PSK|PSK1|TAO1|TAO2|mKIAA0881	TAO kinase 2	protein-coding
mm_28288.1	chr3	89089749	89089759	-	1	NA	exon (NM_001083807, exon 3 of 10)	exon (NM_001083807, exon 3 of 10)	277	NM_001083808	72296	Mm.27687	NM_028188	ENSMUSG00000041263	Rusc1	2210403N08Rik|AA408288|NESCA	RUN and SH3 domain containing 1	protein-coding
mm_140570.1	chr17	8734742	8734742	-	1	NA	intron (NM_001290707, intron 1 of 22)	intron (NM_001290707, intron 1 of 22)	-67003	NM_011866	23984	Mm.87161	NM_011866	ENSMUSG00000023868	Pde10a	-	phosphodiesterase 10A	protein-coding
mm_12200.1	chr2	65845834	65845850	+	1	NA	promoter-TSS (NM_153409)	promoter-TSS (NM_153409)	75	NM_178634	77771	Mm.102025	NM_153409	ENSMUSG00000044647	Csrnp3	A330102K23Rik|CSRNP-3|Csnrp3|Mbu1|taip-2	cysteine-serine-rich nuclear protein 3	protein-coding
mm_67367.1	chr7	79840904	79840917	-	1	NA	exon (NM_008486, exon 3 of 20)	exon (NM_008486, exon 3 of 20)	1442	NM_008486	16790	Mm.4487	NM_008486	ENSMUSG00000039062	Anpep	AP-M|AP-N|Apn|Cd13|P150	alanyl (membrane) aminopeptidase	protein-coding
mm_20727.1	chr2	136781229	136781274	-	1	NA	3' UTR (NM_001291056, exon 8 of 8)	3' UTR (NM_001291056, exon 8 of 8)	67801	NM_001291056	20614	Mm.45953	NM_011428	ENSMUSG00000027273	Snap25	Bdr|GENA70|SNAP-25|SUP|sp	synaptosomal-associated protein 25	protein-coding
mm_41324.1	chr5	90472544	90472575	+	1	NA	exon (NM_009654, exon 12 of 15)	exon (NM_009654, exon 12 of 15)	11689	NM_009654	11657	Mm.16773	NM_009654	ENSMUSG00000029368	Alb	Alb-1|Alb1|BCL002	albumin	protein-coding
mm_23900.1	chr3	83031798	83031821	+	1	NA	exon (NM_010196, exon 5 of 5)	exon (NM_010196, exon 5 of 5)	5656	NM_001111048	14161	Mm.88793	NM_010196	ENSMUSG00000028001	Fga	ENSMUSG00000059807|Fib	fibrinogen alpha chain	protein-coding
mm_25668.1	chr3	121890771	121890777	+	1	NA	Intergenic	Intergenic	-62552	NM_172525	214137	Mm.229287	NM_172525	ENSMUSG00000039831	Arhgap29	6720461J18Rik|A830014I19|AU040217|B130017I01Rik|C76601|Parg1	Rho GTPase activating protein 29	protein-coding
mm_56312.1	chr6	92214844	92214877	-	1	NA	promoter-TSS (NM_030081)	promoter-TSS (NM_030081)	-49	NM_030081	78287	Mm.290734	NM_030081	ENSMUSG00000014550	Rbsn	5330426D11Rik|Zfyve20	rabenosyn, RAB effector	protein-coding
mm_158140.1	chrX	103311778	103311802	-	1	NA	Intergenic	Intergenic	-9608	NM_007674	12592	Mm.4353	NM_007674	ENSMUSG00000031326	Cdx4	Cdx-3|Cdx-4|Cdx3	caudal type homeobox 4	protein-coding
mm_168415.1	chr11	3203980	3203982	+	1	NA	intron (NM_023743, intron 2 of 18)	intron (NM_023743, intron 2 of 18)	962	NM_001166549	74203	Mm.255649	NM_023743	ENSMUSG00000020454	Eif4enif1	2610509L04Rik|A930019J01Rik|AA410001|AU021239|Clast4|D11Ertd166e	eukaryotic translation initiation factor 4E nuclear import factor 1	protein-coding
mm_9255.1	chr1	171562034	171562075	-	1	NA	intron (NM_018729, intron 1 of 8)	intron (NM_018729, intron 1 of 8)	2861	NM_018729	18106	Mm.2299	NM_018729	ENSMUSG00000004709	Cd244	2B4|C9.1|F730046O15Rik|Ly90|NAIL|NKR2B4|Nmrk|SLAMF4	CD244 natural killer cell receptor 2B4	protein-coding
mm_156901.1	chrX	168869023	168869027	+	1	NA	intron (NM_009707, intron 1 of 12)	intron (NM_009707, intron 1 of 12)	73926	NM_009707	11856	Mm.441810	NM_009707	ENSMUSG00000031355	Arhgap6	AI504284|RhoGAPX-1	Rho GTPase activating protein 6	protein-coding
mm_56478.1	chr6	99095582	99095593	-	1	NA	intron (NM_001347345, intron 5 of 19)	intron (NM_001347345, intron 5 of 19)	-67289	NM_001197322	108655	Mm.234965	NM_053202	ENSMUSG00000030067	Foxp1	3110052D19Rik|4932443N09Rik|AI461938|AW494214	forkhead box P1	protein-coding
mm_11423.1	chr2	31759994	31760023	+	1	NA	promoter-TSS (NM_009594)	promoter-TSS (NM_009594)	69	NM_009594	11350	Mm.1318	NM_009594	ENSMUSG00000026842	Abl1	AI325092|Abl|E430008G22Rik|c-Abl	c-abl oncogene 1, non-receptor tyrosine kinase	protein-coding
mm_40958.1	chr5	76951384	76951394	+	1	NA	promoter-TSS (NM_025939)	promoter-TSS (NM_025939)	-22	NM_025939	67054	Mm.182931	NM_025939	ENSMUSG00000029247	Paics	2610511I09Rik|ADE2H1|AIRC|PAIS	phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoribosylaminoimidazole, succinocarboxamide synthetase	protein-coding
mm_91946.1	chr10	60834966	60834992	-	1	NA	Intergenic	MIRb|SINE|MIR	-3398	NM_029770	107449	Mm.290433	NM_029770	ENSMUSG00000020099	Unc5b	6330415E02Rik|A630020F16|D10Bwg0792e|Unc5h2	unc-5 netrin receptor B	protein-coding
mm_85614.1	chr9	107609216	107609246	-	1	NA	promoter-TSS (NM_001291539)	promoter-TSS (NM_001291539)	10	NM_001042779	20347	Mm.4083	NM_009153	ENSMUSG00000057969	Sema3b	SemA|Semaa|sema5|semaV	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B	protein-coding
mm_73867.1	chr8	118561438	118561440	+	1	NA	intron (NM_019707, intron 2 of 13)	intron (NM_019707, intron 2 of 13)	277828	NM_019707	12554	Mm.334841	NM_019707	ENSMUSG00000031841	Cdh13	4932416G01Rik|Cdht|Tcad	cadherin 13	protein-coding
mm_53760.1	chr6	145746740	145746767	+	1	NA	Intergenic	(CCCCG)n|Simple_repeat|Simple_repeat	-61630	NM_027760	71323	Mm.158669	NM_027760	ENSMUSG00000030259	Rassf8	5133400D11Rik|AA815821|AW123240|Hoj1|mHoj-1	Ras association (RalGDS/AF-6) domain family (N-terminal) member 8	protein-coding
mm_89057.1	chr10	82881840	82881854	+	1	NA	exon (NM_001042523, exon 8 of 15)	exon (NM_001042523, exon 8 of 15)	15221	NM_025499	66341	Mm.443284	NM_025499	ENSMUSG00000109864	Eid3	1700027M21Rik|NS4EB	EP300 interacting inhibitor of differentiation 3	protein-coding
mm_62007.1	chr7	91262341	91262358	+	1	NA	intron (NM_011807, intron 1 of 22)	intron (NM_011807, intron 1 of 22)	171563	NM_011807	23859	Mm.147213	NM_011807	ENSMUSG00000052572	Dlg2	A330103J02Rik|B230218P12Rik|B330007M19Rik|Dlgh2|Gm1197|Gm21505|PSD93	discs, large homolog 2 (Drosophila)	protein-coding
mm_158325.1	chrX	133901210	133901219	-	1	NA	Intergenic	Intergenic	-2785	NM_019656	56496	Mm.46701	NM_019656	ENSMUSG00000067377	Tspan6	6720473L21Rik|AI316786|T245|TSPAN-6|Tm4sf|Tm4sf6	tetraspanin 6	protein-coding
mm_108540.1	chr12	84296220	84296222	+	1	NA	intron (NM_029880, intron 3 of 9)	MLT2B3|LTR|ERVL	10925	NM_001252626	77219	Mm.246127	NM_029880	ENSMUSG00000072946	Ptgr2	1810016I24Rik|9130222H03Rik|9630002F03Rik|AI838763|B830026H24Rik|PGR-2|PRG-2|Zadh1	prostaglandin reductase 2	protein-coding
mm_79088.1	chr9	46242633	46242642	+	1	NA	exon (NM_007468, exon 3 of 3)	exon (NM_007468, exon 3 of 3)	1793	NM_007468	11808	Mm.4533	NM_007468	ENSMUSG00000032080	Apoa4	Apoa-4	apolipoprotein A-IV	protein-coding
mm_24491.1	chr3	92365149	92365156	+	1	NA	promoter-TSS (NM_011472)	promoter-TSS (NM_011472)	-35	NM_011472	20760	Mm.10692	NM_011472	ENSMUSG00000050635	Sprr2f	-	small proline-rich protein 2F	protein-coding
mm_48284.1	chr5	138171823	138171833	-	1	NA	promoter-TSS (NM_008568)	promoter-TSS (NM_008568)	34	NM_008568	17220	Mm.378965	NM_008568	ENSMUSG00000029730	Mcm7	AI747533|Mcmd7|mCDC47	minichromosome maintenance complex component 7	protein-coding
mm_57353.1	chr6	124756963	124756975	-	1	NA	promoter-TSS (NM_007881)	promoter-TSS (NM_007881)	-482	NM_007881	13498	Mm.333380	NM_007881	ENSMUSG00000004263	Atn1	Atr1|Drpla|atrophin-1	atrophin 1	protein-coding
mm_164573.1	chr17	23857312	23857322	+	1	NA	exon (NM_027220, exon 4 of 5)	exon (NM_027220, exon 4 of 5)	3545	NM_027220	69814	Mm.244143	NM_027220	ENSMUSG00000048992	Prss32	2010001P08Rik|mT5|tryptase-5	protease, serine 32	protein-coding
mm_47014.1	chr5	115488923	115488932	-	1	NA	Intergenic	Intergenic	-4443	NM_133760	75387	Mm.332616	NM_133760	ENSMUSG00000029524	Sirt4	4930596O17Rik	sirtuin 4	protein-coding
mm_149427.1	chr19	11469354	11469381	+	1	NA	promoter-TSS (NM_028595)	promoter-TSS (NM_028595)	-1	NM_001166376	73656	Mm.440719	NM_028595	ENSMUSG00000079419	Ms4a6c	2200009H22Rik|2210417N07Rik	membrane-spanning 4-domains, subfamily A, member 6C	protein-coding
mm_37561.1	chr4	126198729	126198737	-	1	NA	intron (NM_146153, intron 1 of 10)	intron (NM_146153, intron 1 of 10)	3977	NM_146153	230753	Mm.29813	NM_146153	ENSMUSG00000043962	Thrap3	9330151F09Rik|B230333E16Rik|Trap150	thyroid hormone receptor associated protein 3	protein-coding
mm_71445.1	chr8	46519222	46519232	+	1	NA	intron (NM_001302163, intron 10 of 20)	intron (NM_001302163, intron 10 of 20)	28261	NM_001302163	14081	Mm.210323	NM_007981	ENSMUSG00000018796	Acsl1	Acas|Acas1|Acs|FACS|Facl2|LACS 1|LACS1	acyl-CoA synthetase long-chain family member 1	protein-coding
mm_113938.1	chr13	49682119	49682169	+	1	NA	promoter-TSS (NM_172015)	promoter-TSS (NM_172015)	14	NM_172015	105148	Mm.21118	NM_172015	ENSMUSG00000037851	Iars	2510016L12Rik|AI327140|AU044614|E430001P04Rik|ILRS	isoleucine-tRNA synthetase	protein-coding
mm_92332.1	chr10	75797529	75797536	-	1	NA	intron (NM_008185, intron 1 of 4)	intron (NM_008185, intron 1 of 4)	1052	NM_008185	14871	Mm.2746	NM_008185	ENSMUSG00000001663	Gstt1	AI255817|Gstt1-1	glutathione S-transferase, theta 1	protein-coding
mm_170977.1	chr2	6871869	6871869	-	1	NA	5' UTR (NM_001347094, exon 1 of 13)	5' UTR (NM_001347094, exon 1 of 13)	166	NM_001347094	14007	Mm.398543	NM_010160	ENSMUSG00000002107	Celf2	B230218O03|B230345P09Rik|C88023|CELF-2|CUG-BP2|Cugbp2|D230046B21Rik|Etr-3|Napor|Napor-2|mETR-3	CUGBP, Elav-like family member 2	protein-coding